PARADIGM pathway analysis of mRNASeq expression data
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1Q81CDN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1Q81CDN
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 46 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
Signaling events regulated by Ret tyrosine kinase 113
Aurora B signaling 87
FOXM1 transcription factor network 64
Angiopoietin receptor Tie2-mediated signaling 63
HIF-1-alpha transcription factor network 61
Signaling events mediated by VEGFR1 and VEGFR2 60
p75(NTR)-mediated signaling 53
Plasma membrane estrogen receptor signaling 52
E-cadherin signaling events 52
Endothelins 47
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 304 . 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 ( 304 ).

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
Signaling events regulated by Ret tyrosine kinase 0.3717 113 9273 82 -0.32 0.007 1000 -1000 -0.041 -1000
Aurora B signaling 0.2862 87 5842 67 -0.53 0.03 1000 -1000 -0.03 -1000
FOXM1 transcription factor network 0.2105 64 3270 51 -0.68 0.007 1000 -1000 -0.16 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2072 63 5545 88 -0.38 0.024 1000 -1000 -0.063 -1000
HIF-1-alpha transcription factor network 0.2007 61 4692 76 -0.43 0.012 1000 -1000 -0.081 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1974 60 7520 125 -0.19 0.008 1000 -1000 -0.048 -1000
p75(NTR)-mediated signaling 0.1743 53 6730 125 -0.2 0.009 1000 -1000 -0.046 -1000
Plasma membrane estrogen receptor signaling 0.1711 52 4545 86 -0.24 0.22 1000 -1000 -0.043 -1000
E-cadherin signaling events 0.1711 52 264 5 -0.22 0.007 1000 -1000 -0.026 -1000
Endothelins 0.1546 47 4520 96 -0.16 0.011 1000 -1000 -0.043 -1000
PDGFR-alpha signaling pathway 0.1414 43 1913 44 -0.097 0.015 1000 -1000 -0.03 -1000
Nongenotropic Androgen signaling 0.1382 42 2207 52 -0.18 0.054 1000 -1000 -0.028 -1000
Signaling events mediated by the Hedgehog family 0.1349 41 2168 52 -0.18 0.096 1000 -1000 -0.034 -1000
Aurora C signaling 0.1349 41 289 7 -0.23 0.006 1000 -1000 -0.019 -1000
Integrins in angiogenesis 0.1349 41 3469 84 -0.23 0.022 1000 -1000 -0.042 -1000
LPA4-mediated signaling events 0.1316 40 490 12 -0.13 0.012 1000 -1000 -0.013 -1000
TCGA08_p53 0.1316 40 286 7 -0.16 0.072 1000 -1000 -0.009 -1000
IGF1 pathway 0.1250 38 2200 57 -0.12 0.022 1000 -1000 -0.041 -1000
Reelin signaling pathway 0.1217 37 2109 56 -0.13 0.007 1000 -1000 -0.037 -1000
TCGA08_retinoblastoma 0.1184 36 288 8 -0.24 0.036 1000 -1000 -0.009 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.1118 34 4108 120 -0.23 0.1 1000 -1000 -0.038 -1000
Syndecan-2-mediated signaling events 0.1053 32 2213 69 -0.14 0.007 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 0.1020 31 1242 39 -0.18 0.013 1000 -1000 -0.015 -1000
HIF-2-alpha transcription factor network 0.0921 28 1214 43 -0.35 0.17 1000 -1000 -0.049 -1000
Glypican 1 network 0.0888 27 1299 48 -0.16 0.017 1000 -1000 -0.022 -1000
Thromboxane A2 receptor signaling 0.0855 26 2811 105 -0.11 0.026 1000 -1000 -0.034 -1000
amb2 Integrin signaling 0.0855 26 2193 82 -0.19 0.038 1000 -1000 -0.04 -1000
Coregulation of Androgen receptor activity 0.0822 25 1949 76 -0.23 0.013 1000 -1000 -0.036 -1000
S1P1 pathway 0.0789 24 875 36 -0.12 0.008 1000 -1000 -0.027 -1000
IL4-mediated signaling events 0.0757 23 2145 91 -0.64 0.35 1000 -1000 -0.14 -1000
Arf6 signaling events 0.0724 22 1390 62 -0.18 0.012 1000 -1000 -0.03 -1000
PLK1 signaling events 0.0724 22 1904 85 -0.25 0.046 1000 -1000 -0.025 -1000
S1P5 pathway 0.0724 22 374 17 -0.084 0.044 1000 -1000 -0.025 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0691 21 1713 78 -0.09 0.023 1000 -1000 -0.051 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0658 20 1123 54 -0.13 0.015 1000 -1000 -0.042 -1000
BCR signaling pathway 0.0658 20 2009 99 -0.068 0.032 1000 -1000 -0.039 -1000
Aurora A signaling 0.0625 19 1145 60 -0.24 0.027 1000 -1000 -0.031 -1000
Fc-epsilon receptor I signaling in mast cells 0.0625 19 1917 97 -0.06 0.018 1000 -1000 -0.039 -1000
Syndecan-1-mediated signaling events 0.0592 18 620 34 -0.065 0.007 1000 -1000 -0.03 -1000
BMP receptor signaling 0.0592 18 1487 81 -0.32 0.026 1000 -1000 -0.048 -1000
Nectin adhesion pathway 0.0592 18 1166 63 -0.22 0.007 1000 -1000 -0.041 -1000
Effects of Botulinum toxin 0.0592 18 492 26 -0.17 0.01 1000 -1000 -0.029 -1000
S1P3 pathway 0.0592 18 795 42 -0.11 0.012 1000 -1000 -0.03 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0559 17 495 28 -0.11 0.013 1000 -1000 -0.026 -1000
EPHB forward signaling 0.0559 17 1529 85 -0.064 0.033 1000 -1000 -0.044 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0526 16 543 33 -0.23 0.022 1000 -1000 -0.032 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0493 15 522 34 -0.026 0.007 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 0.0461 14 1091 76 -0.2 0.02 1000 -1000 -0.043 -1000
EGFR-dependent Endothelin signaling events 0.0461 14 297 21 -0.054 0.009 1000 -1000 -0.03 -1000
ErbB4 signaling events 0.0428 13 901 69 -0.2 0.027 1000 -1000 -0.039 -1000
Canonical Wnt signaling pathway 0.0428 13 710 51 -0.41 0.14 1000 -1000 -0.036 -1000
S1P4 pathway 0.0428 13 338 25 -0.084 0.019 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 0.0395 12 797 65 -0.13 0.027 1000 -1000 -0.045 -1000
FOXA2 and FOXA3 transcription factor networks 0.0395 12 567 46 -0.21 0.017 1000 -1000 -0.088 -1000
Signaling mediated by p38-alpha and p38-beta 0.0395 12 538 44 -0.084 0.017 1000 -1000 -0.026 -1000
LPA receptor mediated events 0.0395 12 1244 102 -0.12 0.012 1000 -1000 -0.046 -1000
Insulin Pathway 0.0395 12 906 74 -0.15 0.02 1000 -1000 -0.036 -1000
Glucocorticoid receptor regulatory network 0.0362 11 1357 114 -0.29 0.15 1000 -1000 -0.048 -1000
IL1-mediated signaling events 0.0362 11 691 62 -0.19 0.038 1000 -1000 -0.044 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0362 11 859 74 -0.22 0.084 1000 -1000 -0.046 -1000
Osteopontin-mediated events 0.0296 9 359 38 -0.04 0.019 1000 -1000 -0.042 -1000
Insulin-mediated glucose transport 0.0296 9 292 32 -0.24 0.018 1000 -1000 -0.032 -1000
Syndecan-3-mediated signaling events 0.0296 9 332 35 -0.16 0.007 1000 -1000 -0.032 -1000
Wnt signaling 0.0296 9 65 7 -0.007 0.007 1000 -1000 -0.014 -1000
Syndecan-4-mediated signaling events 0.0296 9 653 67 -0.25 0.014 1000 -1000 -0.04 -1000
PDGFR-beta signaling pathway 0.0296 9 876 97 -0.024 0.024 1000 -1000 -0.037 -1000
Regulation of Telomerase 0.0263 8 851 102 -0.34 0.031 1000 -1000 -0.057 -1000
Regulation of Androgen receptor activity 0.0263 8 617 70 -0.11 0.017 1000 -1000 -0.038 -1000
IL12-mediated signaling events 0.0230 7 651 87 -0.055 0.039 1000 -1000 -0.085 -1000
Noncanonical Wnt signaling pathway 0.0230 7 183 26 -0.041 0.011 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 0.0230 7 450 61 -0.14 0.023 1000 -1000 -0.035 -1000
EPO signaling pathway 0.0230 7 419 55 -0.021 0.028 1000 -1000 -0.041 -1000
Class I PI3K signaling events mediated by Akt 0.0230 7 513 68 -0.24 0.029 1000 -1000 -0.029 -1000
Regulation of nuclear SMAD2/3 signaling 0.0197 6 858 136 -0.18 0.04 1000 -1000 -0.034 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0197 6 574 85 -0.054 0.016 1000 -1000 -0.039 -1000
FoxO family signaling 0.0197 6 400 64 -0.24 0.065 1000 -1000 -0.052 -1000
E-cadherin signaling in keratinocytes 0.0197 6 274 43 -0.22 0.012 1000 -1000 -0.034 -1000
Ephrin B reverse signaling 0.0164 5 259 48 -0.038 0.014 1000 -1000 -0.032 -1000
Visual signal transduction: Rods 0.0164 5 297 52 -0.055 0.01 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class II 0.0132 4 305 75 -0.14 0.017 1000 -1000 -0.031 -1000
Visual signal transduction: Cones 0.0132 4 186 38 -0.04 0.008 1000 -1000 -0.028 -1000
IFN-gamma pathway 0.0132 4 323 68 -0.12 0.037 1000 -1000 -0.048 -1000
Ceramide signaling pathway 0.0132 4 344 76 -0.12 0.033 1000 -1000 -0.031 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0132 4 378 83 -0.24 0.035 1000 -1000 -0.036 -1000
TCR signaling in naïve CD8+ T cells 0.0132 4 438 93 -0.049 0.052 1000 -1000 -0.041 -1000
Regulation of p38-alpha and p38-beta 0.0132 4 223 54 -0.092 0.04 1000 -1000 -0.035 -1000
TCGA08_rtk_signaling 0.0132 4 124 26 -0.085 0.023 1000 -1000 -0.011 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0132 4 296 68 -0.068 0.04 1000 -1000 -0.074 -1000
Ras signaling in the CD4+ TCR pathway 0.0132 4 82 17 -0.012 0.012 1000 -1000 -0.021 -1000
ErbB2/ErbB3 signaling events 0.0099 3 231 65 -0.04 0.035 1000 -1000 -0.036 -1000
mTOR signaling pathway 0.0099 3 177 53 -0.01 0.016 1000 -1000 -0.031 -1000
FAS signaling pathway (CD95) 0.0099 3 187 47 -0.049 0.038 1000 -1000 -0.028 -1000
Calcium signaling in the CD4+ TCR pathway 0.0099 3 113 31 -0.021 0.017 1000 -1000 -0.039 -1000
IL6-mediated signaling events 0.0099 3 256 75 -0.081 0.069 1000 -1000 -0.07 -1000
E-cadherin signaling in the nascent adherens junction 0.0099 3 268 76 -0.22 0.074 1000 -1000 -0.046 -1000
Signaling events mediated by PRL 0.0099 3 131 34 -0.072 0.024 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0066 2 99 37 -0.023 0.025 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0066 2 135 52 -0.022 0.042 1000 -1000 -0.032 -1000
Retinoic acid receptors-mediated signaling 0.0066 2 172 58 -0.014 0.026 1000 -1000 -0.035 -1000
IL27-mediated signaling events 0.0066 2 106 51 -0.031 0.013 1000 -1000 -0.056 -1000
VEGFR1 specific signals 0.0066 2 113 56 -0.033 0.033 1000 -1000 -0.035 -1000
Rapid glucocorticoid signaling 0.0066 2 54 20 -0.01 0.007 1000 -1000 -0.02 -1000
p38 MAPK signaling pathway 0.0066 2 102 44 -0.03 0.025 1000 -1000 -0.035 -1000
Caspase cascade in apoptosis 0.0033 1 86 74 -0.009 0.049 1000 -1000 -0.029 -1000
BARD1 signaling events 0.0033 1 60 57 -0.011 0.039 1000 -1000 -0.033 -1000
Ephrin A reverse signaling 0.0033 1 9 7 0 0.009 1000 -1000 -0.013 -1000
Signaling events mediated by HDAC Class III 0.0033 1 58 40 -0.025 0.013 1000 -1000 -0.016 -1000
Signaling mediated by p38-gamma and p38-delta 0.0033 1 23 15 0 0.02 1000 -1000 -0.011 -1000
IL2 signaling events mediated by PI3K 0.0033 1 83 58 -0.01 0.046 1000 -1000 -0.047 -1000
Glypican 2 network 0.0033 1 6 4 -0.001 -1000 1000 -1000 -0.018 -1000
IL2 signaling events mediated by STAT5 0.0033 1 41 22 -0.006 0.047 1000 -1000 -0.026 -1000
Class I PI3K signaling events 0.0033 1 102 73 -0.04 0.043 1000 -1000 -0.029 -1000
Arf6 trafficking events 0.0033 1 121 71 -0.13 0.025 1000 -1000 -0.033 -1000
Class IB PI3K non-lipid kinase events 0.0033 1 3 3 -0.006 0.006 1000 -1000 -0.007 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 -0.004 0.027 1000 -1000 -0.029 -1000
Canonical NF-kappaB pathway 0.0000 0 27 39 -0.003 0.046 1000 -1000 -0.038 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.007 0.013 1000 -1000 -0.01 -1000
Circadian rhythm pathway 0.0000 0 4 22 -0.008 0.03 1000 -1000 -0.038 -1000
JNK signaling in the CD4+ TCR pathway 0.0000 0 10 17 0 0.032 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0 0.007 1000 -1000 -0.021 -1000
Arf6 downstream pathway 0.0000 0 25 43 -0.017 0.018 1000 -1000 -0.018 -1000
TRAIL signaling pathway 0.0000 0 16 48 -0.002 0.03 1000 -1000 -0.031 -1000
ceramide signaling pathway 0.0000 0 29 49 -0.002 0.035 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class I 0.0000 0 59 104 -0.018 0.033 1000 -1000 -0.03 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 16 36 -0.005 0.013 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 0.0000 0 2 31 -0.001 0.03 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0000 0 16 45 -0.003 0.048 1000 -1000 -0.045 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.017 1000 -1000 -0.025 -1000
IL23-mediated signaling events 0.0000 0 30 60 -0.028 0.036 1000 -1000 -0.13 -1000
Arf1 pathway 0.0000 0 0 54 0 0.021 1000 -1000 -0.022 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.007 1000 -1000 -0.026 -1000
Total NA 2032 131791 7203 -17 -1000 131000 -131000 -4.9 -131000
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.051 0.028 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.17 0.091 -9999 0 -0.21 242 242
JUN -0.14 0.093 -9999 0 -0.37 15 15
HRAS 0.007 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.095 -9999 0 -0.21 242 242
RAP1A 0.007 0 -9999 0 -10000 0 0
FRS2 0.007 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.094 -9999 0 -0.21 242 242
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.007 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.16 0.082 -9999 0 -0.2 242 242
RHOA 0.007 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.083 -9999 0 -0.18 242 242
GRB7 0.001 0.041 -9999 0 -0.25 8 8
RET51/GFRalpha1/GDNF -0.17 0.094 -9999 0 -0.21 242 242
MAPKKK cascade -0.15 0.086 -9999 0 -0.19 242 242
BCAR1 0.007 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.17 0.097 -9999 0 -0.22 242 242
lamellipodium assembly -0.17 0.089 -9999 0 -0.21 242 242
RET51/GFRalpha1/GDNF/SHC -0.17 0.094 -9999 0 -0.21 242 242
PIK3CA 0.007 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.16 0.082 -9999 0 -0.2 242 242
RET9/GFRalpha1/GDNF/Shank3 -0.16 0.082 -9999 0 -0.2 242 242
MAPK3 -0.13 0.086 -9999 0 -0.18 169 169
DOK1 0.007 0 -9999 0 -10000 0 0
DOK6 -0.006 0.073 -9999 0 -0.4 10 10
PXN 0.007 0 -9999 0 -10000 0 0
neurite development -0.12 0.088 -9999 0 -0.3 21 21
DOK5 -0.002 0.058 -9999 0 -0.38 7 7
GFRA1 -0.32 0.16 -9999 0 -0.4 242 242
MAPK8 -0.15 0.096 -9999 0 -0.38 15 15
HRAS/GTP -0.17 0.098 -9999 0 -0.22 242 242
tube development -0.15 0.075 -9999 0 -0.19 242 242
MAPK1 -0.13 0.086 -9999 0 -0.34 13 13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.086 -9999 0 -0.2 242 242
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.007 0 -9999 0 -10000 0 0
PDLIM7 0.007 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.16 0.098 -9999 0 -0.2 242 242
SHC1 0.007 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.094 -9999 0 -0.21 242 242
RET51/GFRalpha1/GDNF/Dok5 -0.17 0.1 -9999 0 -0.22 242 242
PRKCA -0.002 0.061 -9999 0 -0.4 7 7
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.19 0.11 -9999 0 -0.24 242 242
PIK3R1 0.007 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.15 0.086 -9999 0 -0.2 242 242
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.095 -9999 0 -0.21 242 242
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.01 0.082 -9999 0 -0.4 13 13
DOK4 0.007 0 -9999 0 -10000 0 0
JNK cascade -0.14 0.092 -9999 0 -0.36 15 15
RET9/GFRalpha1/GDNF/FRS2 -0.16 0.082 -9999 0 -0.2 242 242
SHANK3 0.007 0 -9999 0 -10000 0 0
RASA1 0.006 0.023 -9999 0 -0.4 1 1
NCK1 0.007 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.16 0.086 -9999 0 -0.2 242 242
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.16 0.099 -9999 0 -0.2 242 242
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.16 0.1 -9999 0 -0.21 242 242
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.16 0.11 -9999 0 -0.21 242 242
PI3K -0.23 0.14 -9999 0 -0.3 242 242
SOS1 0.007 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.075 -9999 0 -0.19 242 242
GRB10 0.006 0.023 -9999 0 -0.4 1 1
activation of MAPKK activity -0.15 0.089 -9999 0 -0.19 242 242
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.094 -9999 0 -0.21 242 242
GAB1 0.007 0 -9999 0 -10000 0 0
IRS1 -0.011 0.085 -9999 0 -0.4 14 14
IRS2 -0.005 0.069 -9999 0 -0.4 9 9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.16 0.11 -9999 0 -0.21 242 242
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.099 -9999 0 -0.22 243 243
GRB2 0.007 0 -9999 0 -10000 0 0
PRKACA 0.007 0 -9999 0 -10000 0 0
GDNF 0.002 0.003 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.18 0.11 -9999 0 -0.22 242 242
Rac1/GTP -0.2 0.1 -9999 0 -0.24 242 242
RET9/GFRalpha1/GDNF -0.18 0.094 -9999 0 -0.23 242 242
GFRalpha1/GDNF -0.22 0.11 -9999 0 -0.28 242 242
Aurora B signaling

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
Condensin I complex -0.067 0.027 -10000 0 -10000 0 0
STMN1 -0.14 0.038 -10000 0 -0.15 287 287
Aurora B/RasGAP/Survivin -0.23 0.038 -10000 0 -0.24 282 282
Chromosomal passenger complex/Cul3 protein complex -0.07 0.068 -10000 0 -0.22 48 48
BIRC5 -0.24 0.038 -10000 0 -0.25 297 297
DES -0.53 0.11 -10000 0 -0.56 293 293
Aurora C/Aurora B/INCENP -0.098 0.031 -10000 0 -0.32 1 1
Aurora B/TACC1 -0.12 0.034 -10000 0 -0.12 286 286
Aurora B/PP2A -0.14 0.038 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.011 0.005 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.001 -10000 0 -10000 0 0
NDC80 -0.14 0.038 -10000 0 -0.15 287 287
Cul3 protein complex -0.035 0.081 -10000 0 -0.22 48 48
KIF2C -0.023 0.011 -10000 0 -10000 0 0
PEBP1 0 0.001 -10000 0 -10000 0 0
KIF20A -0.25 0.039 -10000 0 -0.25 297 297
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.14 0.041 -10000 0 -0.15 287 287
SEPT1 0.007 0 -10000 0 -10000 0 0
SMC2 0.007 0 -10000 0 -10000 0 0
SMC4 0.007 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.03 0.009 -10000 0 -10000 0 0
PSMA3 0.007 0 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.001 -10000 0 -10000 0 0
H3F3B -0.044 0.014 -10000 0 -10000 0 0
AURKB -0.23 0.06 -10000 0 -0.24 287 287
AURKC 0.006 0.023 -10000 0 -0.4 1 1
CDCA8 -0.16 0.12 -10000 0 -0.25 201 201
cytokinesis -0.09 0.021 -10000 0 -10000 0 0
Aurora B/Septin1 -0.062 0.051 -10000 0 -10000 0 0
AURKA -0.012 0.065 -10000 0 -0.25 21 21
INCENP 0.004 0.001 -10000 0 -10000 0 0
KLHL13 -0.057 0.15 -10000 0 -0.4 48 48
BUB1 -0.15 0.13 -10000 0 -0.25 183 183
hSgo1/Aurora B/Survivin -0.31 0.05 -10000 0 -0.32 299 299
EVI5 0.009 0 -10000 0 -10000 0 0
RhoA/GTP -0.042 0.019 -10000 0 -10000 0 0
SGOL1 -0.23 0.073 -10000 0 -0.25 277 277
CENPA -0.033 0.013 -10000 0 -10000 0 0
NCAPG -0.22 0.076 -10000 0 -0.25 274 274
Aurora B/HC8 Proteasome -0.14 0.038 -10000 0 -0.15 287 287
NCAPD2 0.007 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.14 0.038 -10000 0 -0.15 287 287
RHOA 0.007 0 -10000 0 -10000 0 0
NCAPH -0.18 0.12 -10000 0 -0.25 217 217
NPM1 -0.004 0.003 -10000 0 -10000 0 0
RASA1 0.006 0.023 -10000 0 -0.4 1 1
KLHL9 0.007 0 -10000 0 -10000 0 0
mitotic prometaphase -0.007 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.038 -10000 0 -0.15 287 287
PPP1CC 0.007 0 -10000 0 -10000 0 0
Centraspindlin -0.05 0.021 -10000 0 -10000 0 0
RhoA/GDP 0 0 -10000 0 -10000 0 0
NSUN2 -0.004 0.003 -10000 0 -10000 0 0
MYLK -0.2 0.14 -10000 0 -0.33 170 170
KIF23 0.007 0.001 -10000 0 -10000 0 0
VIM -0.15 0.051 -10000 0 -0.16 288 288
RACGAP1 0.007 0.001 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.004 0.003 -10000 0 -10000 0 0
Chromosomal passenger complex -0.06 0.02 -10000 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.012 0.25 0.22 157 -0.27 143 300
TACC1 0.006 0.023 -10000 0 -0.4 1 1
PPP2R5D 0.007 0 -10000 0 -10000 0 0
CUL3 0.007 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.43 0.34 -9999 0 -0.86 87 87
PLK1 -0.054 0.053 -9999 0 -10000 0 0
BIRC5 -0.11 0.03 -9999 0 -10000 0 0
HSPA1B -0.43 0.34 -9999 0 -0.88 78 78
MAP2K1 -0.018 0.017 -9999 0 -10000 0 0
BRCA2 -0.43 0.34 -9999 0 -0.87 87 87
FOXM1 -0.5 0.42 -9999 0 -1 90 90
XRCC1 -0.43 0.34 -9999 0 -0.88 78 78
FOXM1B/p19 -0.48 0.42 -9999 0 -0.97 92 92
Cyclin D1/CDK4 -0.4 0.32 -9999 0 -0.81 78 78
CDC2 -0.45 0.36 -9999 0 -0.9 90 90
TGFA -0.39 0.31 -9999 0 -0.79 78 78
SKP2 -0.43 0.34 -9999 0 -0.86 87 87
CCNE1 -0.003 0.033 -9999 0 -0.26 5 5
CKS1B -0.43 0.34 -9999 0 -0.86 88 88
RB1 -0.18 0.13 -9999 0 -10000 0 0
FOXM1C/SP1 -0.46 0.39 -9999 0 -0.96 89 89
AURKB -0.11 0.034 -9999 0 -10000 0 0
CENPF -0.44 0.34 -9999 0 -0.89 78 78
CDK4 -0.001 0.006 -9999 0 -10000 0 0
MYC -0.39 0.31 -9999 0 -0.78 89 89
CHEK2 -0.018 0.017 -9999 0 -10000 0 0
ONECUT1 -0.42 0.33 -9999 0 -0.84 89 89
CDKN2A -0.23 0.06 -9999 0 -0.24 286 286
LAMA4 -0.47 0.41 -9999 0 -1 91 91
FOXM1B/HNF6 -0.46 0.38 -9999 0 -0.95 89 89
FOS -0.46 0.39 -9999 0 -0.96 93 93
SP1 0.007 0.001 -9999 0 -10000 0 0
CDC25B -0.43 0.34 -9999 0 -0.86 88 88
response to radiation -0.024 0.015 -9999 0 -10000 0 0
CENPB -0.43 0.34 -9999 0 -0.86 87 87
CENPA -0.46 0.35 -9999 0 -0.9 89 89
NEK2 -0.47 0.34 -9999 0 -0.91 88 88
HIST1H2BA -0.43 0.34 -9999 0 -0.87 88 88
CCNA2 0 0.021 -9999 0 -0.26 2 2
EP300 0.007 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.48 0.39 -9999 0 -0.98 88 88
CCNB2 -0.46 0.34 -9999 0 -0.9 89 89
CCNB1 -0.45 0.36 -9999 0 -0.91 88 88
ETV5 -0.43 0.34 -9999 0 -0.86 87 87
ESR1 -0.62 0.52 -9999 0 -1.2 129 129
CCND1 -0.4 0.32 -9999 0 -0.82 85 85
GSK3A -0.013 0.013 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.008 0.024 -9999 0 -0.16 4 4
CDK2 0.001 0.004 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.029 0.019 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.45 0.36 -9999 0 -0.91 90 90
GAS1 -0.68 0.54 -9999 0 -1.2 154 154
MMP2 -0.45 0.38 -9999 0 -0.95 85 85
RB1/FOXM1C -0.41 0.34 -9999 0 -0.84 87 87
CREBBP 0.007 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.25 0.44 -10000 0 -0.87 100 100
NCK1/PAK1/Dok-R -0.13 0.19 -10000 0 -0.41 100 100
NCK1/Dok-R -0.32 0.48 -10000 0 -0.96 100 100
PIK3CA 0.008 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.024 0.069 0.23 29 -10000 0 29
RELA 0.007 0 -10000 0 -10000 0 0
SHC1 0.005 0.004 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.023 0.07 0.23 29 -10000 0 29
TNIP2 0.007 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.29 0.44 -10000 0 -0.9 100 100
FN1 -0.003 0.065 -10000 0 -0.4 8 8
PLD2 -0.3 0.52 -10000 0 -1 100 100
PTPN11 0.007 0 -10000 0 -10000 0 0
GRB14 -0.041 0.1 -10000 0 -0.25 57 57
ELK1 -0.26 0.47 -10000 0 -0.91 100 100
GRB7 0.001 0.041 -10000 0 -0.25 8 8
PAK1 0.007 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.31 0.47 -10000 0 -0.95 100 100
CDKN1A -0.18 0.3 -10000 0 -0.61 99 99
ITGA5 0.005 0.033 -10000 0 -0.4 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.32 0.48 -10000 0 -0.96 100 100
CRK 0.007 0 -10000 0 -10000 0 0
mol:NO -0.18 0.33 -10000 0 -0.64 100 100
PLG -0.3 0.52 -10000 0 -1 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.24 0.41 -10000 0 -0.82 100 100
GRB2 0.007 0 -10000 0 -10000 0 0
PIK3R1 0.005 0.004 -10000 0 -10000 0 0
ANGPT2 -0.13 0.2 -10000 0 -0.47 57 57
BMX -0.38 0.54 -10000 0 -1.1 100 100
ANGPT1 -0.12 0.35 -10000 0 -1.2 29 29
tube development -0.2 0.34 -10000 0 -0.68 100 100
ANGPT4 0.003 0.004 -10000 0 -10000 0 0
response to hypoxia -0.019 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.3 0.55 -10000 0 -1 100 100
alpha5/beta1 Integrin -0.002 0.022 -10000 0 -0.27 2 2
FGF2 -0.12 0.19 -10000 0 -0.4 95 95
STAT5A (dimer) -0.23 0.39 -10000 0 -0.77 100 100
mol:L-citrulline -0.18 0.33 -10000 0 -0.64 100 100
AGTR1 -0.18 0.2 -10000 0 -0.4 141 141
MAPK14 -0.33 0.55 -10000 0 -1.1 100 100
Tie2/SHP2 -0.31 0.46 -10000 0 -0.98 93 93
TEK -0.31 0.52 -10000 0 -1.1 93 93
RPS6KB1 -0.24 0.42 -10000 0 -0.83 100 100
Angiotensin II/AT1 -0.13 0.14 -10000 0 -0.28 141 141
Tie2/Ang1/GRB2 -0.31 0.54 -10000 0 -1 100 100
MAPK3 -0.27 0.47 -10000 0 -0.92 100 100
MAPK1 -0.27 0.47 -10000 0 -0.92 100 100
Tie2/Ang1/GRB7 -0.31 0.54 -10000 0 -1 100 100
NFKB1 0.007 0 -10000 0 -10000 0 0
MAPK8 -0.3 0.52 -10000 0 -1 100 100
PI3K -0.3 0.51 -10000 0 -1 100 100
FES -0.33 0.55 -10000 0 -1.1 100 100
Crk/Dok-R -0.32 0.48 -10000 0 -0.96 100 100
Tie2/Ang1/ABIN2 -0.31 0.54 -10000 0 -1 100 100
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.22 0.39 -10000 0 -0.77 100 100
STAT5A 0.007 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.24 0.42 -10000 0 -0.83 100 100
Tie2/Ang2 -0.29 0.47 -10000 0 -0.93 100 100
Tie2/Ang1 -0.33 0.57 -10000 0 -1.1 100 100
FOXO1 -0.22 0.4 -10000 0 -0.77 100 100
ELF1 -0.019 0.047 -10000 0 -10000 0 0
ELF2 -0.3 0.52 -10000 0 -1 100 100
mol:Choline -0.28 0.49 -10000 0 -0.96 100 100
cell migration -0.075 0.11 -10000 0 -0.23 100 100
FYN -0.24 0.39 -10000 0 -0.78 100 100
DOK2 0.007 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.16 0.28 -10000 0 -0.55 99 99
ETS1 -0.015 0.067 -10000 0 -0.22 29 29
PXN -0.19 0.35 -10000 0 -0.69 100 100
ITGB1 0.007 0 -10000 0 -10000 0 0
NOS3 -0.21 0.38 -10000 0 -0.74 100 100
RAC1 0.007 0 -10000 0 -10000 0 0
TNF -0.02 0.082 -10000 0 -0.24 33 33
MAPKKK cascade -0.28 0.49 -10000 0 -0.96 100 100
RASA1 0.006 0.023 -10000 0 -0.4 1 1
Tie2/Ang1/Shc -0.31 0.54 -10000 0 -1 100 100
NCK1 0.007 0 -10000 0 -10000 0 0
vasculogenesis -0.16 0.3 -10000 0 -0.57 100 100
mol:Phosphatidic acid -0.28 0.49 -10000 0 -0.96 100 100
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.18 0.33 -10000 0 -0.64 100 100
Rac1/GTP -0.25 0.37 -10000 0 -0.78 100 100
MMP2 -0.31 0.53 -10000 0 -1 100 100
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 -0.31 0.38 -9999 0 -0.78 86 86
HDAC7 0.008 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.29 0.31 -9999 0 -0.71 80 80
SMAD4 0.007 0.023 -9999 0 -0.4 1 1
ID2 -0.31 0.38 -9999 0 -0.78 87 87
AP1 -0.021 0.072 -9999 0 -0.27 23 23
ABCG2 -0.41 0.44 -9999 0 -0.84 129 129
HIF1A -0.046 0.061 -9999 0 -10000 0 0
TFF3 -0.36 0.42 -9999 0 -0.85 97 97
GATA2 -0.006 0.076 -9999 0 -0.4 11 11
AKT1 -0.055 0.077 -9999 0 -0.21 21 21
response to hypoxia -0.068 0.079 -9999 0 -0.2 38 38
MCL1 -0.31 0.38 -9999 0 -0.78 86 86
NDRG1 -0.31 0.38 -9999 0 -0.78 87 87
SERPINE1 -0.31 0.38 -9999 0 -0.79 86 86
FECH -0.31 0.38 -9999 0 -0.78 87 87
FURIN -0.31 0.38 -9999 0 -0.78 86 86
NCOA2 0.002 0.047 -9999 0 -0.4 4 4
EP300 -0.063 0.12 -9999 0 -0.32 34 34
HMOX1 -0.31 0.38 -9999 0 -0.78 86 86
BHLHE40 -0.31 0.38 -9999 0 -0.78 86 86
BHLHE41 -0.31 0.38 -9999 0 -0.78 87 87
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.055 0.069 -9999 0 -0.31 1 1
ENG -0.031 0.084 -9999 0 -0.28 1 1
JUN 0.006 0.023 -9999 0 -0.4 1 1
RORA -0.31 0.38 -9999 0 -0.78 87 87
ABCB1 -0.37 0.48 -9999 0 -1.1 93 93
TFRC -0.31 0.38 -9999 0 -0.78 88 88
CXCR4 -0.31 0.38 -9999 0 -0.78 87 87
TF -0.32 0.38 -9999 0 -0.8 87 87
CITED2 -0.33 0.39 -9999 0 -0.81 92 92
HIF1A/ARNT -0.36 0.4 -9999 0 -0.84 95 95
LDHA -0.054 0.048 -9999 0 -10000 0 0
ETS1 -0.31 0.38 -9999 0 -0.78 86 86
PGK1 -0.31 0.38 -9999 0 -0.78 86 86
NOS2 -0.32 0.38 -9999 0 -0.79 90 90
ITGB2 -0.31 0.38 -9999 0 -0.78 86 86
ALDOA -0.31 0.38 -9999 0 -0.78 86 86
Cbp/p300/CITED2 -0.35 0.42 -9999 0 -0.88 91 91
FOS -0.022 0.1 -9999 0 -0.4 22 22
HK2 -0.34 0.4 -9999 0 -0.81 95 95
SP1 -0.003 0.033 -9999 0 -10000 0 0
GCK -0.18 0.4 -9999 0 -1.3 33 33
HK1 -0.31 0.38 -9999 0 -0.78 88 88
NPM1 -0.31 0.38 -9999 0 -0.78 86 86
EGLN1 -0.31 0.38 -9999 0 -0.78 87 87
CREB1 0.012 0 -9999 0 -10000 0 0
PGM1 -0.31 0.38 -9999 0 -0.78 86 86
SMAD3 0.008 0 -9999 0 -10000 0 0
EDN1 -0.076 0.17 -9999 0 -0.47 30 30
IGFBP1 -0.33 0.39 -9999 0 -0.8 92 92
VEGFA -0.23 0.3 -9999 0 -0.63 72 72
HIF1A/JAB1 -0.03 0.028 -9999 0 -10000 0 0
CP -0.33 0.4 -9999 0 -0.82 94 94
CXCL12 -0.43 0.44 -9999 0 -0.85 132 132
COPS5 0.007 0.004 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.016 -9999 0 -0.27 1 1
BNIP3 -0.31 0.38 -9999 0 -0.78 86 86
EGLN3 -0.31 0.38 -9999 0 -0.78 86 86
CA9 -0.36 0.4 -9999 0 -0.83 98 98
TERT -0.32 0.38 -9999 0 -0.78 89 89
ENO1 -0.31 0.38 -9999 0 -0.78 86 86
PFKL -0.31 0.38 -9999 0 -0.78 86 86
NCOA1 0.007 0.002 -9999 0 -10000 0 0
ADM -0.31 0.38 -9999 0 -0.79 86 86
ARNT -0.046 0.06 -9999 0 -10000 0 0
HNF4A -0.012 0.064 -9999 0 -0.31 11 11
ADFP -0.32 0.38 -9999 0 -0.76 95 95
SLC2A1 -0.23 0.31 -9999 0 -0.65 72 72
LEP -0.32 0.38 -9999 0 -0.79 90 90
HIF1A/ARNT/Cbp/p300 -0.3 0.32 -9999 0 -0.73 80 80
EPO -0.23 0.32 -9999 0 -0.73 52 52
CREBBP -0.063 0.12 -9999 0 -0.32 34 34
HIF1A/ARNT/Cbp/p300/HDAC7 -0.29 0.31 -9999 0 -0.71 80 80
PFKFB3 -0.31 0.38 -9999 0 -0.78 87 87
NT5E -0.34 0.4 -9999 0 -0.82 97 97
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.031 0.086 -9999 0 -0.27 34 34
AKT1 -0.11 0.23 -9999 0 -0.44 99 99
PTK2B -0.14 0.25 -9999 0 -0.49 99 99
VEGFR2 homodimer/Frs2 -0.16 0.26 -9999 0 -0.55 99 99
CAV1 -0.033 0.12 -9999 0 -0.4 30 30
CALM1 0.007 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.16 0.23 -9999 0 -0.5 99 99
endothelial cell proliferation -0.098 0.22 -9999 0 -0.41 99 99
mol:Ca2+ -0.12 0.23 -9999 0 -0.45 99 99
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.15 0.22 -9999 0 -0.47 99 99
RP11-342D11.1 -0.13 0.23 -9999 0 -0.46 99 99
CDH5 -0.002 0.061 -9999 0 -0.4 7 7
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0.007 0 -9999 0 -10000 0 0
SHC2 -0.009 0.079 -9999 0 -0.4 12 12
HRAS/GDP -0.13 0.18 -9999 0 -0.39 99 99
SH2D2A 0 0.043 -9999 0 -0.25 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.2 -9999 0 -0.42 99 99
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.16 0.24 -9999 0 -0.5 99 99
VEGFR1 homodimer 0.006 0.023 -9999 0 -0.4 1 1
SHC/GRB2/SOS1 -0.14 0.2 -9999 0 -0.42 99 99
GRB10 -0.12 0.23 -9999 0 -0.45 99 99
PTPN11 0.007 0 -9999 0 -10000 0 0
GRB2 0.007 0 -9999 0 -10000 0 0
PAK1 0.007 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.15 0.22 -9999 0 -0.46 99 99
HRAS 0.007 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.096 0.18 -9999 0 -0.34 99 99
HIF1A 0.007 0 -9999 0 -10000 0 0
FRS2 0.007 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.15 0.22 -9999 0 -0.46 99 99
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.014 0.091 -9999 0 -0.4 16 16
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.16 0.24 -9999 0 -0.5 99 99
mol:GDP -0.14 0.19 -9999 0 -0.41 99 99
mol:NADP -0.088 0.2 -9999 0 -0.37 99 99
eNOS/Hsp90 -0.08 0.19 -9999 0 -0.34 99 99
PIK3R1 0.007 0 -9999 0 -10000 0 0
mol:IP3 -0.13 0.23 -9999 0 -0.46 99 99
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.007 0 -9999 0 -10000 0 0
VEGFA 0.008 0.001 -9999 0 -10000 0 0
VEGFC -0.006 0.073 -9999 0 -0.4 10 10
FAK1/Vinculin -0.15 0.28 -9999 0 -0.55 99 99
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.007 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.17 0.25 -9999 0 -0.52 99 99
PTPN6 0.007 0 -9999 0 -10000 0 0
EPAS1 -0.089 0.15 -9999 0 -0.3 99 99
mol:L-citrulline -0.088 0.2 -9999 0 -0.37 99 99
ITGAV 0.007 0 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.15 0.22 -9999 0 -0.47 99 99
VEGFR2 homodimer/VEGFA homodimer -0.16 0.23 -9999 0 -0.5 99 99
VEGFR2/3 heterodimer -0.17 0.28 -9999 0 -0.57 100 100
VEGFB 0.007 0 -9999 0 -10000 0 0
MAPK11 -0.13 0.24 -9999 0 -0.48 99 99
VEGFR2 homodimer -0.19 0.3 -9999 0 -0.63 99 99
FLT1 0.006 0.023 -9999 0 -0.4 1 1
NEDD4 0.008 0.001 -9999 0 -10000 0 0
MAPK3 -0.11 0.21 -9999 0 -0.42 99 99
MAPK1 -0.11 0.21 -9999 0 -0.42 99 99
VEGFA145/NRP2 -0.007 0.044 -9999 0 -0.27 8 8
VEGFR1/2 heterodimer -0.16 0.26 -9999 0 -0.55 99 99
KDR -0.19 0.3 -9999 0 -0.63 99 99
VEGFA165/NRP1/VEGFR2 homodimer -0.15 0.22 -9999 0 -0.46 99 99
SRC 0.007 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.12 0.22 -9999 0 -0.43 99 99
PI3K -0.16 0.22 -9999 0 -0.48 99 99
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.16 0.23 -9999 0 -0.5 99 99
FES -0.13 0.23 -9999 0 -0.46 99 99
GAB1 -0.16 0.23 -9999 0 -0.5 99 99
VEGFR2 homodimer/VEGFA homodimer/Src -0.16 0.23 -9999 0 -0.5 99 99
CTNNB1 0.007 0 -9999 0 -10000 0 0
SOS1 0.007 0 -9999 0 -10000 0 0
ARNT 0.007 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.095 0.2 -9999 0 -0.37 99 99
VEGFR2 homodimer/VEGFA homodimer/Yes -0.16 0.23 -9999 0 -0.5 99 99
PI3K/GAB1 -0.11 0.24 -9999 0 -0.46 99 99
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.15 0.21 -9999 0 -0.45 99 99
PRKACA 0.007 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.18 0.26 -9999 0 -0.54 99 99
HSP90AA1 0.007 0 -9999 0 -10000 0 0
CDC42 -0.13 0.23 -9999 0 -0.46 99 99
actin cytoskeleton reorganization -0.16 0.24 -9999 0 -0.5 99 99
PTK2 -0.17 0.3 -9999 0 -0.59 99 99
EDG1 -0.13 0.23 -9999 0 -0.46 99 99
mol:DAG -0.13 0.23 -9999 0 -0.46 99 99
CaM/Ca2+ -0.14 0.2 -9999 0 -0.42 99 99
MAP2K3 -0.12 0.22 -9999 0 -0.44 99 99
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.15 0.22 -9999 0 -0.47 99 99
PLCG1 -0.13 0.23 -9999 0 -0.46 99 99
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.15 0.22 -9999 0 -0.47 99 99
IQGAP1 0.007 0 -9999 0 -10000 0 0
YES1 0.007 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.16 0.23 -9999 0 -0.5 99 99
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.16 0.23 -9999 0 -0.5 99 99
cell migration -0.12 0.25 -9999 0 -0.48 99 99
mol:PI-3-4-5-P3 -0.15 0.21 -9999 0 -0.45 99 99
FYN 0.001 0.052 -9999 0 -0.4 5 5
VEGFB/NRP1 -0.12 0.22 -9999 0 -0.43 99 99
mol:NO -0.088 0.2 -9999 0 -0.37 99 99
PXN 0.007 0 -9999 0 -10000 0 0
HRAS/GTP -0.13 0.18 -9999 0 -0.39 99 99
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.13 0.24 -9999 0 -0.47 99 99
VHL 0.007 0 -9999 0 -10000 0 0
ITGB3 -0.038 0.13 -9999 0 -0.4 34 34
NOS3 -0.1 0.22 -9999 0 -0.41 99 99
VEGFR2 homodimer/VEGFA homodimer/Sck -0.17 0.24 -9999 0 -0.52 99 99
RAC1 0.007 0 -9999 0 -10000 0 0
PRKCA -0.12 0.22 -9999 0 -0.43 99 99
PRKCB -0.12 0.22 -9999 0 -0.43 99 99
VCL 0.007 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.13 0.23 -9999 0 -0.46 99 99
VEGFR1/2 heterodimer/VEGFA homodimer -0.16 0.23 -9999 0 -0.5 99 99
VEGFA165/NRP2 -0.007 0.044 -9999 0 -0.27 8 8
MAPKKK cascade -0.13 0.18 -9999 0 -0.39 99 99
NRP2 -0.003 0.065 -9999 0 -0.4 8 8
VEGFC homodimer -0.006 0.073 -9999 0 -0.4 10 10
NCK1 0.007 0 -9999 0 -10000 0 0
ROCK1 0.007 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.15 0.28 -9999 0 -0.55 99 99
MAP3K13 -0.13 0.23 -9999 0 -0.46 99 99
PDPK1 -0.099 0.21 -9999 0 -0.4 99 99
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.12 0.13 -10000 0 -0.27 139 139
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.095 0.12 -10000 0 -0.21 137 137
NGF (dimer)/p75(NTR)/BEX1 -0.2 0.17 -10000 0 -0.31 199 199
NT-4/5 (dimer)/p75(NTR) -0.1 0.092 -10000 0 -0.17 178 178
IKBKB 0.007 0 -10000 0 -10000 0 0
AKT1 -0.074 0.12 -10000 0 -0.2 134 134
IKBKG 0.007 0 -10000 0 -10000 0 0
BDNF -0.006 0.057 -10000 0 -0.25 16 16
MGDIs/NGR/p75(NTR)/LINGO1 -0.017 0.059 -10000 0 -0.22 23 23
FURIN 0.007 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.021 0.062 -10000 0 -0.24 19 19
LINGO1 0.002 0.046 -10000 0 -0.4 4 4
Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.006 0.057 -10000 0 -0.25 16 16
NTRK1 0.007 0.002 -10000 0 -10000 0 0
RTN4R 0.007 0 -10000 0 -10000 0 0
neuron apoptosis -0.046 0.098 -10000 0 -0.35 14 14
IRAK1 0.007 0 -10000 0 -10000 0 0
SHC1 -0.099 0.14 -10000 0 -0.24 134 134
ARHGDIA 0.007 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.1 0.13 -10000 0 -0.23 136 136
MAGEH1 -0.009 0.079 -10000 0 -0.4 12 12
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.18 0.17 -10000 0 -0.29 190 190
Mammalian IAPs/DIABLO -0.002 0.016 -10000 0 -10000 0 0
proNGF (dimer) -0.17 0.2 -10000 0 -0.4 129 129
MAGED1 0.005 0.033 -10000 0 -0.4 2 2
APP 0.007 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.13 0.13 -10000 0 -0.25 162 162
ZNF274 0.007 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.088 0.11 -10000 0 -0.2 134 134
NGF -0.17 0.2 -10000 0 -0.4 129 129
cell cycle arrest -0.047 0.13 0.13 65 -0.17 134 199
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.082 0.12 -10000 0 -0.21 134 134
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.08 0.074 -10000 0 -0.24 19 19
NCSTN 0.007 0 -10000 0 -10000 0 0
mol:GTP -0.11 0.13 -10000 0 -0.24 134 134
PSENEN 0.007 0 -10000 0 -10000 0 0
mol:ceramide -0.084 0.12 -10000 0 -0.22 134 134
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.067 0.11 -10000 0 -0.34 15 15
p75(NTR)/beta APP -0.017 0.066 -10000 0 -0.27 19 19
BEX1 -0.17 0.2 -10000 0 -0.4 129 129
mol:GDP -0.1 0.14 -10000 0 -0.25 134 134
NGF (dimer) -0.1 0.12 -10000 0 -0.22 144 144
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.015 0.052 -10000 0 -0.2 23 23
PIK3R1 0.007 0 -10000 0 -10000 0 0
RAC1/GTP -0.092 0.11 -10000 0 -0.21 134 134
MYD88 0.007 0 -10000 0 -10000 0 0
CHUK 0.007 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.11 0.13 -10000 0 -0.25 134 134
RHOB 0.006 0.023 -10000 0 -0.4 1 1
RHOA 0.007 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.006 0.031 -10000 0 -0.16 12 12
NT3 (dimer) -0.048 0.14 -10000 0 -0.4 41 41
TP53 0.009 0.054 -10000 0 -0.18 19 19
PRDM4 -0.085 0.12 -10000 0 -0.22 134 134
BDNF (dimer) -0.056 0.081 -10000 0 -0.24 34 34
PIK3CA 0.007 0 -10000 0 -10000 0 0
SORT1 0.007 0 -10000 0 -10000 0 0
activation of caspase activity -0.094 0.12 -10000 0 -0.21 137 137
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.096 0.12 -10000 0 -0.22 134 134
RHOC 0.007 0 -10000 0 -10000 0 0
XIAP 0.007 0 -10000 0 -10000 0 0
MAPK10 -0.12 0.16 -10000 0 -0.37 61 61
DIABLO 0.007 0 -10000 0 -10000 0 0
SMPD2 -0.085 0.12 -10000 0 -0.22 134 134
APH1B 0.007 0 -10000 0 -10000 0 0
APH1A 0.007 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.11 0.13 -10000 0 -0.25 134 134
PSEN1 0.007 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.054 0.12 -10000 0 -0.29 56 56
MAPK8 -0.066 0.12 -10000 0 -0.31 25 25
MAPK9 -0.065 0.12 -10000 0 -0.31 24 24
APAF1 0.007 0 -10000 0 -10000 0 0
NTF3 -0.048 0.14 -10000 0 -0.4 41 41
NTF4 -0.13 0.13 -10000 0 -0.25 162 162
NDN -0.16 0.2 -10000 0 -0.4 128 128
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.08 0.097 -10000 0 -0.18 135 135
p75 CTF/Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.13 -10000 0 -0.24 134 134
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.016 0.05 -10000 0 -0.19 19 19
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.018 0.055 -10000 0 -0.21 19 19
PRKACB 0.007 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.008 0.035 -10000 0 -0.16 16 16
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.002 0.036 -10000 0 -0.25 6 6
BIRC2 0.006 0.015 -10000 0 -0.25 1 1
neuron projection morphogenesis -0.11 0.17 0.14 44 -0.29 111 155
BAD -0.086 0.13 -10000 0 -0.3 55 55
RIPK2 0.007 0 -10000 0 -10000 0 0
NGFR -0.018 0.099 -10000 0 -0.4 19 19
CYCS -0.076 0.12 -10000 0 -0.2 135 135
ADAM17 0.007 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.096 0.12 -10000 0 -0.22 134 134
BCL2L11 -0.086 0.13 -10000 0 -0.3 55 55
BDNF (dimer)/p75(NTR) -0.025 0.076 -10000 0 -0.23 33 33
PI3K -0.096 0.12 -10000 0 -0.22 134 134
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.096 0.12 -10000 0 -0.22 134 134
NDNL2 0.007 0 -10000 0 -10000 0 0
YWHAE 0.007 0 -10000 0 -10000 0 0
PRKCI 0.007 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.13 0.16 -10000 0 -0.3 134 134
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.097 0.12 -10000 0 -0.22 135 135
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 0.007 0 -10000 0 -10000 0 0
PRKCZ 0.007 0 -10000 0 -10000 0 0
PLG -0.001 0.025 -10000 0 -0.25 3 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.085 0.12 -10000 0 -0.21 134 134
SQSTM1 0.006 0.023 -10000 0 -0.4 1 1
NGFRAP1 -0.009 0.079 -10000 0 -0.4 12 12
CASP3 -0.08 0.13 -10000 0 -0.28 55 55
E2F1 -0.003 0.05 -10000 0 -0.25 12 12
CASP9 0.007 0 -10000 0 -10000 0 0
IKK complex -0.1 0.12 -10000 0 -0.24 129 129
NGF (dimer)/TRKA -0.12 0.14 -10000 0 -0.27 129 129
MMP7 -0.029 0.12 -10000 0 -0.39 28 28
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.088 0.11 -10000 0 -0.2 134 134
MMP3 -0.064 0.12 -10000 0 -0.25 85 85
APAF-1/Caspase 9 -0.064 0.078 -10000 0 -0.26 19 19
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.064 0.087 -10000 0 -0.18 106 106
ER alpha/Gai/GDP/Gbeta gamma -0.13 0.18 -10000 0 -0.35 106 106
AKT1 -0.23 0.34 -10000 0 -0.69 106 106
PIK3CA 0.007 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.24 0.34 -10000 0 -0.7 106 106
mol:Ca2+ -0.11 0.18 -10000 0 -0.37 90 90
IGF1R 0.005 0.033 -10000 0 -0.4 2 2
E2/ER alpha (dimer)/Striatin -0.08 0.11 -10000 0 -0.23 106 106
SHC1 0.007 0 -10000 0 -10000 0 0
apoptosis 0.22 0.32 0.66 106 -10000 0 106
RhoA/GTP -0.054 0.074 -10000 0 -0.16 106 106
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.14 0.17 -10000 0 -0.36 106 106
regulation of stress fiber formation 0.024 0.076 0.27 2 -10000 0 2
E2/ERA-ERB (dimer) -0.08 0.11 -10000 0 -0.23 106 106
KRAS 0.007 0 -10000 0 -10000 0 0
G13/GTP -0.072 0.098 -10000 0 -0.2 106 106
pseudopodium formation -0.024 0.076 -10000 0 -0.27 2 2
E2/ER alpha (dimer)/PELP1 -0.08 0.11 -10000 0 -0.23 106 106
GRB2 0.007 0 -10000 0 -10000 0 0
GNG2 0.007 0 -10000 0 -10000 0 0
GNAO1 0.002 0.046 -10000 0 -0.4 4 4
HRAS 0.007 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.15 0.23 -10000 0 -0.44 108 108
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.14 -10000 0 -0.3 106 106
mol:NADP -0.15 0.23 -10000 0 -0.44 108 108
PIK3R1 0.007 0 -10000 0 -10000 0 0
mol:IP3 -0.12 0.18 -10000 0 -0.38 90 90
IGF-1R heterotetramer 0.005 0.033 -10000 0 -0.4 2 2
PLCB1 -0.12 0.19 -10000 0 -0.4 90 90
PLCB2 -0.12 0.19 -10000 0 -0.39 88 88
IGF1 -0.12 0.19 -10000 0 -0.4 95 95
mol:L-citrulline -0.15 0.23 -10000 0 -0.44 108 108
RHOA 0.007 0 -10000 0 -10000 0 0
Gai/GDP -0.061 0.12 -10000 0 -0.82 4 4
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.007 0 -10000 0 -10000 0 0
ESR2 0.007 0 -10000 0 -10000 0 0
GNAQ 0.007 0 -10000 0 -10000 0 0
ESR1 -0.14 0.19 -10000 0 -0.4 106 106
Gq family/GDP/Gbeta gamma -0.047 0.096 -10000 0 -0.34 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.067 0.11 -10000 0 -0.24 31 31
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.14 0.17 -10000 0 -0.36 106 106
GNAZ -0.084 0.17 -10000 0 -0.4 68 68
E2/ER alpha (dimer) -0.098 0.13 -10000 0 -0.28 106 106
STRN 0.007 0 -10000 0 -10000 0 0
GNAL -0.01 0.082 -10000 0 -0.4 13 13
PELP1 0.007 0 -10000 0 -10000 0 0
MAPK11 0.011 0 -10000 0 -10000 0 0
GNAI2 0.007 0 -10000 0 -10000 0 0
GNAI3 0.007 0 -10000 0 -10000 0 0
GNAI1 0.006 0.023 -10000 0 -0.4 1 1
HBEGF -0.12 0.17 -10000 0 -0.32 109 109
cAMP biosynthetic process -0.069 0.094 -10000 0 -0.19 113 113
SRC -0.12 0.18 -10000 0 -0.33 106 106
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.007 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.09 0.12 -10000 0 -0.26 106 106
SOS1 0.007 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.16 0.17 -10000 0 -0.34 123 123
Gs family/GTP -0.07 0.095 -10000 0 -0.19 113 113
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation -0.15 0.22 -10000 0 -0.43 108 108
mol:DAG -0.12 0.18 -10000 0 -0.38 90 90
Gs family/GDP/Gbeta gamma -0.093 0.12 -10000 0 -0.26 106 106
MSN -0.026 0.08 -10000 0 -0.29 2 2
Gq family/GTP -0.14 0.19 -10000 0 -0.41 90 90
mol:PI-3-4-5-P3 -0.23 0.33 -10000 0 -0.68 106 106
NRAS 0.007 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.15 0.22 0.43 108 -10000 0 108
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.099 0.14 -10000 0 -0.28 106 106
NOS3 -0.16 0.24 -10000 0 -0.47 108 108
GNA11 0.005 0.033 -10000 0 -0.4 2 2
MAPKKK cascade -0.17 0.26 -10000 0 -0.51 106 106
E2/ER alpha (dimer)/PELP1/Src -0.15 0.18 -10000 0 -0.38 106 106
ruffle organization -0.024 0.076 -10000 0 -0.27 2 2
ROCK2 -0.033 0.083 -10000 0 -0.32 1 1
GNA14 -0.11 0.18 -10000 0 -0.4 88 88
GNA15 -0.011 0.066 -10000 0 -0.25 22 22
GNA13 0.007 0 -10000 0 -10000 0 0
MMP9 -0.12 0.18 -10000 0 -0.32 117 117
MMP2 -0.12 0.17 -10000 0 -0.32 109 109
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.11 0.042 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.14 0.054 -9999 0 -10000 0 0
CTNNB1 0.007 0 -9999 0 -10000 0 0
JUP 0.007 0 -9999 0 -10000 0 0
CDH1 -0.22 0.086 -9999 0 -0.25 264 264
Endothelins

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
AKT1 -0.022 0.14 -10000 0 -0.43 23 23
PTK2B 0.007 0 -10000 0 -10000 0 0
mol:Ca2+ -0.069 0.19 -10000 0 -0.54 26 26
EDN1 0.011 0.043 -10000 0 -0.3 2 2
EDN3 -0.11 0.18 -10000 0 -0.4 84 84
EDN2 -0.16 0.12 -10000 0 -0.25 193 193
HRAS/GDP -0.082 0.17 -10000 0 -0.35 71 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.068 0.15 -10000 0 -0.34 49 49
ADCY4 -0.044 0.14 -10000 0 -0.35 43 43
ADCY5 -0.13 0.15 -10000 0 -0.29 93 93
ADCY6 -0.027 0.12 -10000 0 -0.34 28 28
ADCY7 -0.027 0.12 -10000 0 -0.35 26 26
ADCY1 -0.034 0.13 -10000 0 -0.34 33 33
ADCY2 -0.14 0.15 -10000 0 -0.3 94 94
ADCY3 -0.027 0.12 -10000 0 -0.35 26 26
ADCY8 -0.035 0.12 -10000 0 -0.35 28 28
ADCY9 -0.027 0.12 -10000 0 -0.34 28 28
arachidonic acid secretion -0.081 0.18 -10000 0 -0.36 73 73
ETB receptor/Endothelin-1/Gq/GTP -0.098 0.18 -10000 0 -0.29 118 118
GNAO1 0.002 0.046 -10000 0 -0.4 4 4
HRAS 0.007 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.018 0.14 -10000 0 -0.41 22 22
ETA receptor/Endothelin-1/Gs/GTP -0.027 0.14 -10000 0 -0.36 28 28
mol:GTP 0 0.003 -10000 0 -10000 0 0
COL3A1 -0.032 0.17 -10000 0 -0.58 22 22
EDNRB -0.082 0.17 -10000 0 -0.4 66 66
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.023 0.14 -10000 0 -0.44 22 22
CYSLTR1 -0.023 0.14 -10000 0 -0.45 22 22
SLC9A1 -0.025 0.08 -10000 0 -0.26 22 22
mol:GDP -0.091 0.18 -10000 0 -0.37 74 74
SLC9A3 -0.11 0.25 -10000 0 -0.54 70 70
RAF1 -0.091 0.18 -10000 0 -0.37 73 73
JUN -0.068 0.18 -10000 0 -0.52 27 27
JAK2 -0.022 0.14 -10000 0 -0.43 23 23
mol:IP3 -0.097 0.18 -10000 0 -0.32 102 102
ETA receptor/Endothelin-1 -0.029 0.17 -10000 0 -0.37 48 48
PLCB1 0 0.052 -10000 0 -0.4 5 5
PLCB2 0.007 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.12 0.17 -10000 0 -0.32 117 117
FOS -0.1 0.25 -10000 0 -0.73 31 31
Gai/GDP -0.045 0.12 -10000 0 -0.73 4 4
CRK 0.007 0 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.21 -10000 0 -0.45 70 70
BCAR1 0.008 0 -10000 0 -10000 0 0
PRKCB1 -0.093 0.17 -10000 0 -0.3 102 102
GNAQ 0.008 0.003 -10000 0 -10000 0 0
GNAZ -0.084 0.17 -10000 0 -0.4 68 68
GNAL -0.01 0.082 -10000 0 -0.4 13 13
Gs family/GDP -0.11 0.15 -10000 0 -0.35 73 73
ETA receptor/Endothelin-1/Gq/GTP -0.078 0.17 -10000 0 -0.37 52 52
MAPK14 -0.076 0.15 -10000 0 -0.34 57 57
TRPC6 -0.072 0.2 -10000 0 -0.6 21 21
GNAI2 0.007 0 -10000 0 -10000 0 0
GNAI3 0.007 0 -10000 0 -10000 0 0
GNAI1 0.006 0.023 -10000 0 -0.4 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.085 0.16 -10000 0 -0.33 70 70
ETB receptor/Endothelin-2 -0.16 0.14 -10000 0 -0.22 214 214
ETB receptor/Endothelin-3 -0.14 0.15 -10000 0 -0.3 139 139
ETB receptor/Endothelin-1 -0.059 0.13 -10000 0 -0.28 70 70
MAPK3 -0.1 0.24 -10000 0 -0.59 42 42
MAPK1 -0.1 0.24 -10000 0 -0.59 42 42
Rac1/GDP -0.081 0.17 -10000 0 -0.35 71 71
cAMP biosynthetic process -0.15 0.16 -10000 0 -0.36 75 75
MAPK8 -0.083 0.2 -10000 0 -0.6 27 27
SRC 0.007 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.065 0.12 -10000 0 -0.29 39 39
p130Cas/CRK/Src/PYK2 -0.074 0.18 -10000 0 -0.38 58 58
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.081 0.17 -10000 0 -0.35 71 71
COL1A2 -0.088 0.25 -10000 0 -0.75 29 29
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.14 0.14 -10000 0 -0.28 103 103
mol:DAG -0.097 0.18 -10000 0 -0.32 102 102
MAP2K2 -0.093 0.2 -10000 0 -0.41 69 69
MAP2K1 -0.093 0.2 -10000 0 -0.41 69 69
EDNRA -0.051 0.18 -10000 0 -0.45 47 47
positive regulation of muscle contraction -0.015 0.12 -10000 0 -0.38 22 22
Gq family/GDP -0.11 0.16 -10000 0 -0.35 76 76
HRAS/GTP -0.092 0.18 -10000 0 -0.36 74 74
PRKCH -0.088 0.17 -10000 0 -0.36 68 68
RAC1 0.007 0 -10000 0 -10000 0 0
PRKCA -0.093 0.17 -10000 0 -0.36 73 73
PRKCB -0.09 0.17 -10000 0 -0.36 67 67
PRKCE -0.088 0.17 -10000 0 -0.36 67 67
PRKCD -0.088 0.17 -10000 0 -0.36 68 68
PRKCG -0.098 0.17 -10000 0 -0.36 72 72
regulation of vascular smooth muscle contraction -0.12 0.29 -10000 0 -0.87 30 30
PRKCQ -0.088 0.17 -10000 0 -0.35 68 68
PLA2G4A -0.088 0.2 -10000 0 -0.39 73 73
GNA14 -0.11 0.18 -10000 0 -0.4 88 88
GNA15 -0.011 0.066 -10000 0 -0.25 22 22
GNA12 0.007 0 -10000 0 -10000 0 0
GNA11 0.005 0.033 -10000 0 -0.4 2 2
Rac1/GTP -0.018 0.14 -10000 0 -0.4 23 23
MMP1 -0.01 0.1 0.23 13 -10000 0 13
PDGFR-alpha signaling pathway

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
PDGFRA -0.087 0.17 -9999 0 -0.4 69 69
PDGF/PDGFRA/CRKL -0.061 0.11 -9999 0 -0.27 69 69
positive regulation of JUN kinase activity -0.042 0.078 -9999 0 -0.18 69 69
CRKL 0.007 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.063 0.11 -9999 0 -0.27 69 69
AP1 -0.097 0.21 -9999 0 -0.8 22 22
mol:IP3 -0.055 0.12 -9999 0 -0.28 69 69
PLCG1 -0.055 0.12 -9999 0 -0.28 69 69
PDGF/PDGFRA/alphaV Integrin -0.061 0.11 -9999 0 -0.27 69 69
RAPGEF1 0.007 0 -9999 0 -10000 0 0
CRK 0.007 0 -9999 0 -10000 0 0
mol:Ca2+ -0.054 0.12 -9999 0 -0.28 69 69
CAV3 0.001 0.003 -9999 0 -10000 0 0
CAV1 -0.033 0.12 -9999 0 -0.4 30 30
SHC/Grb2/SOS1 -0.042 0.078 -9999 0 -0.19 69 69
PDGF/PDGFRA/Shf -0.076 0.14 -9999 0 -0.31 73 73
FOS -0.077 0.22 -9999 0 -0.79 22 22
JUN -0.01 0.022 -9999 0 -0.28 1 1
oligodendrocyte development -0.061 0.11 -9999 0 -0.26 69 69
GRB2 0.007 0 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
mol:DAG -0.055 0.12 -9999 0 -0.28 69 69
PDGF/PDGFRA -0.087 0.17 -9999 0 -0.4 69 69
actin cytoskeleton reorganization -0.061 0.11 -9999 0 -0.26 69 69
SRF 0.015 0.007 -9999 0 -10000 0 0
SHC1 0.007 0 -9999 0 -10000 0 0
PI3K -0.048 0.089 -9999 0 -0.21 69 69
PDGF/PDGFRA/Crk/C3G -0.049 0.09 -9999 0 -0.21 69 69
JAK1 -0.051 0.12 -9999 0 -0.26 69 69
ELK1/SRF -0.03 0.093 -9999 0 -0.2 69 69
SHB 0.007 0 -9999 0 -10000 0 0
SHF -0.017 0.096 -9999 0 -0.4 18 18
CSNK2A1 0.009 0.015 -9999 0 -10000 0 0
GO:0007205 -0.061 0.13 -9999 0 -0.3 69 69
SOS1 0.007 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.042 0.078 -9999 0 -0.18 69 69
PDGF/PDGFRA/SHB -0.061 0.11 -9999 0 -0.27 69 69
PDGF/PDGFRA/Caveolin-1 -0.087 0.14 -9999 0 -0.3 87 87
ITGAV 0.007 0 -9999 0 -10000 0 0
ELK1 -0.049 0.12 -9999 0 -0.26 69 69
PIK3CA 0.007 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.061 0.11 -9999 0 -0.27 69 69
JAK-STAT cascade -0.051 0.12 -9999 0 -0.26 69 69
cell proliferation -0.076 0.14 -9999 0 -0.31 73 73
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.007 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.092 0.1 -10000 0 -0.2 140 140
regulation of S phase of mitotic cell cycle -0.081 0.11 -10000 0 -0.2 140 140
GNAO1 0.002 0.046 -10000 0 -0.4 4 4
HRAS 0.007 0.001 -10000 0 -10000 0 0
SHBG/T-DHT 0 0.001 -10000 0 -10000 0 0
PELP1 0.007 0.001 -10000 0 -10000 0 0
AKT1 0.007 0 -10000 0 -10000 0 0
MAP2K1 -0.061 0.094 -10000 0 -0.27 11 11
T-DHT/AR -0.13 0.14 -10000 0 -0.28 140 140
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 22 22
GNAI2 0.007 0 -10000 0 -10000 0 0
GNAI3 0.007 0 -10000 0 -10000 0 0
GNAI1 0.006 0.023 -10000 0 -0.4 1 1
mol:GDP -0.15 0.17 -10000 0 -0.34 140 140
cell proliferation -0.072 0.13 -10000 0 -0.43 22 22
PIK3CA 0.007 0 -10000 0 -10000 0 0
FOS -0.069 0.2 -10000 0 -0.76 22 22
mol:Ca2+ -0.026 0.026 -10000 0 -0.062 83 83
MAPK3 -0.068 0.11 -10000 0 -0.32 22 22
MAPK1 -0.032 0.067 -10000 0 -0.22 22 22
PIK3R1 0.007 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 22 22
cAMP biosynthetic process 0.023 0.023 0.091 1 -10000 0 1
GNG2 0.007 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 22 22
HRAS/GTP -0.083 0.088 -10000 0 -0.18 140 140
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.007 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 22 22
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.054 0.12 0.43 22 -10000 0 22
T-DHT/AR/PELP1 -0.11 0.11 -10000 0 -0.23 140 140
HRAS/GDP -0.14 0.16 -10000 0 -0.31 140 140
CREB1 -0.058 0.13 -10000 0 -0.46 22 22
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.18 0.2 -10000 0 -0.4 140 140
GNB1 0.007 0 -10000 0 -10000 0 0
RAF1 -0.067 0.095 -10000 0 -0.17 140 140
RAC1-CDC42/GDP -0.14 0.15 -10000 0 -0.3 140 140
T-DHT/AR/PELP1/Src -0.093 0.1 -10000 0 -0.2 140 140
MAP2K2 -0.061 0.094 -10000 0 -0.27 11 11
T-DHT/AR/PELP1/Src/PI3K -0.081 0.11 -10000 0 -0.2 140 140
GNAZ -0.084 0.17 -10000 0 -0.4 68 68
SHBG 0.007 0.002 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.054 0.098 -10000 0 -0.24 45 45
mol:T-DHT 0 0 -10000 0 -0.003 11 11
RAC1 0.007 0 -10000 0 -10000 0 0
GNRH1 0.007 0 -10000 0 -10000 0 0
Gi family/GTP -0.09 0.1 -10000 0 -0.24 72 72
CDC42 0.007 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.043 0.12 -10000 0 -0.41 9 9
IHH -0.12 0.2 -10000 0 -0.42 94 94
SHH Np/Cholesterol/GAS1 -0.096 0.1 -10000 0 -0.21 139 139
LRPAP1 0.007 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.096 0.1 0.21 139 -10000 0 139
SMO/beta Arrestin2 -0.08 0.17 -10000 0 -0.31 94 94
SMO -0.088 0.18 -10000 0 -0.32 94 94
AKT1 -0.032 0.087 -10000 0 -0.25 9 9
ARRB2 0.007 0 -10000 0 -10000 0 0
BOC -0.085 0.17 -10000 0 -0.4 69 69
ADRBK1 0.007 0 -10000 0 -10000 0 0
heart looping -0.086 0.17 -10000 0 -0.32 94 94
STIL -0.038 0.095 -10000 0 -0.26 12 12
DHH N/PTCH2 -0.02 0.071 -10000 0 -0.28 22 22
DHH N/PTCH1 -0.045 0.11 -10000 0 -0.2 96 96
PIK3CA 0.007 0 -10000 0 -10000 0 0
DHH 0.007 0.002 -10000 0 -10000 0 0
PTHLH -0.071 0.17 -10000 0 -0.54 9 9
determination of left/right symmetry -0.086 0.17 -10000 0 -0.32 94 94
PIK3R1 0.007 0 -10000 0 -10000 0 0
skeletal system development -0.071 0.17 -10000 0 -0.54 9 9
IHH N/Hhip -0.069 0.13 -10000 0 -0.25 94 94
DHH N/Hhip -0.008 0.045 -10000 0 -0.26 9 9
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.086 0.17 -10000 0 -0.32 94 94
pancreas development -0.006 0.066 -10000 0 -0.38 9 9
HHAT 0.006 0.023 -10000 0 -0.4 1 1
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.18 0.2 -10000 0 -0.4 138 138
somite specification -0.086 0.17 -10000 0 -0.32 94 94
SHH Np/Cholesterol/PTCH1 -0.039 0.099 -10000 0 -0.27 10 10
SHH Np/Cholesterol/PTCH2 -0.019 0.056 -10000 0 -0.2 23 23
SHH Np/Cholesterol/Megalin -0.006 0.028 -10000 0 -0.22 2 2
SHH 0.004 0.033 -10000 0 -0.17 10 10
catabolic process -0.056 0.12 -10000 0 -0.24 96 96
SMO/Vitamin D3 -0.059 0.13 -10000 0 -0.24 95 95
SHH Np/Cholesterol/Hhip -0.01 0.039 -10000 0 -0.2 9 9
LRP2 0.001 0.035 -10000 0 -0.25 6 6
receptor-mediated endocytosis -0.074 0.11 -10000 0 -0.33 17 17
SHH Np/Cholesterol/BOC -0.05 0.089 -10000 0 -0.21 69 69
SHH Np/Cholesterol/CDO -0.022 0.061 -10000 0 -0.2 28 28
mesenchymal cell differentiation 0.01 0.039 0.2 9 -10000 0 9
mol:Vitamin D3 -0.038 0.1 -10000 0 -0.27 10 10
IHH N/PTCH2 -0.081 0.14 -10000 0 -0.26 105 105
CDON -0.029 0.12 -10000 0 -0.4 27 27
IHH N/PTCH1 -0.055 0.13 -10000 0 -0.24 96 96
Megalin/LRPAP1 -0.003 0.022 -10000 0 -0.16 6 6
PTCH2 -0.022 0.1 -10000 0 -0.4 22 22
SHH Np/Cholesterol -0.004 0.023 -10000 0 -0.21 1 1
PTCH1 -0.056 0.12 -10000 0 -0.24 96 96
HHIP -0.006 0.066 -10000 0 -0.38 9 9
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.007 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.1 0.028 -9999 0 -0.32 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.029 0.008 -9999 0 -10000 0 0
AURKB -0.23 0.059 -9999 0 -0.25 287 287
AURKC 0.006 0.023 -9999 0 -0.4 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.089 0.13 -9999 0 -0.27 99 99
alphaV beta3 Integrin -0.094 0.14 -9999 0 -0.26 110 110
PTK2 -0.14 0.22 -9999 0 -0.46 87 87
IGF1R 0.005 0.033 -9999 0 -0.4 2 2
PI4KB 0.007 0 -9999 0 -10000 0 0
MFGE8 0.006 0.023 -9999 0 -0.4 1 1
SRC 0.007 0 -9999 0 -10000 0 0
CDKN1B -0.082 0.15 -9999 0 -0.48 31 31
VEGFA 0.007 0 -9999 0 -10000 0 0
ILK -0.082 0.15 -9999 0 -0.48 31 31
ROCK1 0.007 0 -9999 0 -10000 0 0
AKT1 -0.075 0.14 -9999 0 -0.44 31 31
PTK2B -0.064 0.13 -9999 0 -0.23 106 106
alphaV/beta3 Integrin/JAM-A -0.098 0.13 -9999 0 -0.23 126 126
CBL 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.025 0.071 -9999 0 -0.23 34 34
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.072 0.1 -9999 0 -0.21 104 104
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.08 0.15 -9999 0 -0.35 49 49
alphaV/beta3 Integrin/Syndecan-1 -0.14 0.08 -9999 0 -0.34 34 34
PI4KA 0.007 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.16 -9999 0 -0.4 66 66
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.03 0.073 -9999 0 -0.22 34 34
RPS6KB1 -0.11 0.16 -9999 0 -0.37 66 66
TLN1 0.007 0 -9999 0 -10000 0 0
MAPK3 -0.2 0.25 -9999 0 -0.5 111 111
GPR124 -0.086 0.17 -9999 0 -0.4 70 70
MAPK1 -0.2 0.25 -9999 0 -0.5 111 111
PXN 0.007 0 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.028 0.072 -9999 0 -0.22 34 34
cell adhesion -0.025 0.072 -9999 0 -0.22 34 34
ANGPTL3 0.005 0.003 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.073 0.1 -9999 0 -0.22 99 99
IGF-1R heterotetramer 0.005 0.033 -9999 0 -0.4 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.002 0.046 -9999 0 -0.4 4 4
ITGB3 -0.038 0.13 -9999 0 -0.4 34 34
IGF1 -0.12 0.19 -9999 0 -0.4 95 95
RAC1 0.007 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.076 0.13 -9999 0 -0.27 85 85
apoptosis 0.007 0 -9999 0 -10000 0 0
CD47 0.007 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.025 0.07 -9999 0 -0.22 34 34
VCL 0.007 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.071 0.13 -9999 0 -0.28 77 77
CSF1 0.005 0.033 -9999 0 -0.4 2 2
PIK3C2A -0.082 0.15 -9999 0 -0.48 31 31
PI4 Kinase/Pyk2 -0.13 0.16 -9999 0 -0.37 76 76
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.086 0.13 -9999 0 -0.25 106 106
FAK1/Vinculin -0.11 0.18 -9999 0 -0.36 87 87
alphaV beta3/Integrin/ppsTEM5 -0.076 0.13 -9999 0 -0.27 85 85
RHOA 0.007 0 -9999 0 -10000 0 0
VTN -0.04 0.13 -9999 0 -0.38 37 37
BCAR1 0.007 0 -9999 0 -10000 0 0
FGF2 -0.12 0.19 -9999 0 -0.4 95 95
F11R -0.076 0.13 -9999 0 -0.27 95 95
alphaV/beta3 Integrin/Lactadherin -0.026 0.073 -9999 0 -0.23 34 34
alphaV/beta3 Integrin/TGFBR2 -0.028 0.078 -9999 0 -0.24 36 36
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.001 0.016 -9999 0 -0.2 2 2
HSP90AA1 0.007 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.022 0.063 -9999 0 -0.2 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.003 0.065 -9999 0 -0.4 8 8
alphaV/beta3 Integrin/Pyk2 -0.079 0.12 -9999 0 -0.23 106 106
SDC1 -0.23 0.066 -9999 0 -0.25 282 282
VAV3 0.022 0.016 -9999 0 -0.18 2 2
PTPN11 0.007 0 -9999 0 -10000 0 0
IRS1 -0.011 0.085 -9999 0 -0.4 14 14
FAK1/Paxillin -0.11 0.18 -9999 0 -0.36 86 86
cell migration -0.097 0.16 -9999 0 -0.32 86 86
ITGAV 0.007 0 -9999 0 -10000 0 0
PI3K -0.086 0.12 -9999 0 -0.35 32 32
SPP1 -0.003 0.05 -9999 0 -0.25 12 12
KDR -0.12 0.19 -9999 0 -0.4 99 99
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.007 0 -9999 0 -10000 0 0
COL4A3 0.002 0.036 -9999 0 -0.25 6 6
angiogenesis -0.18 0.26 -9999 0 -0.49 116 116
Rac1/GTP -0.001 0.013 -9999 0 -10000 0 0
EDIL3 -0.077 0.16 -9999 0 -0.4 63 63
cell proliferation -0.028 0.078 -9999 0 -0.24 36 36
LPA4-mediated signaling events

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
ADCY4 -0.011 0.07 -9999 0 -0.23 28 28
ADCY5 -0.11 0.12 -9999 0 -0.23 155 155
ADCY6 0.012 0 -9999 0 -10000 0 0
ADCY7 0.012 0 -9999 0 -10000 0 0
ADCY1 0.003 0.045 -9999 0 -0.23 11 11
ADCY2 -0.13 0.12 -9999 0 -0.23 175 175
ADCY3 0.012 0 -9999 0 -10000 0 0
ADCY8 0.006 0.008 -9999 0 -0.13 1 1
PRKCE 0.007 0 -9999 0 -10000 0 0
ADCY9 0.012 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.081 0.072 -9999 0 -0.15 120 120
TCGA08_p53

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
CDKN2A -0.16 0.041 -9999 0 -0.16 286 286
TP53 -0.033 0.008 -9999 0 -10000 0 0
Senescence -0.033 0.008 -9999 0 -10000 0 0
Apoptosis -0.033 0.008 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.072 0.018 -9999 0 -10000 0 0
MDM4 0.007 0 -9999 0 -10000 0 0
IGF1 pathway

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
NCK2 0.007 0 -10000 0 -10000 0 0
PTK2 0.007 0 -10000 0 -10000 0 0
CRKL -0.056 0.1 -10000 0 -0.2 96 96
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.007 0 -10000 0 -10000 0 0
IRS1/Crk -0.056 0.1 -10000 0 -0.2 96 96
IGF-1R heterotetramer/IGF1/PTP1B -0.069 0.1 -10000 0 -0.22 96 96
AKT1 -0.035 0.09 -10000 0 -0.32 6 6
BAD -0.029 0.086 -10000 0 -0.3 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.056 0.1 -10000 0 -0.2 96 96
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.056 0.1 -10000 0 -0.2 96 96
RAF1 -0.026 0.084 -10000 0 -0.28 6 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.061 0.09 -10000 0 -0.19 96 96
YWHAZ 0.007 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.067 0.11 -10000 0 -0.22 97 97
PIK3CA 0.007 0 -10000 0 -10000 0 0
RPS6KB1 -0.035 0.09 -10000 0 -0.32 6 6
GNB2L1 0.007 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.024 0.075 -10000 0 -0.25 6 6
PXN 0.007 0 -10000 0 -10000 0 0
PIK3R1 0.007 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.053 0.079 -10000 0 -0.32 6 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.05 0.076 -10000 0 -0.16 96 96
IGF-1R heterotetramer -0.014 0.045 -10000 0 -0.45 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.066 0.097 -10000 0 -0.2 96 96
Crk/p130 Cas/Paxillin -0.057 0.085 -10000 0 -0.34 6 6
IGF1R -0.014 0.045 -10000 0 -0.45 2 2
IGF1 -0.12 0.2 -10000 0 -0.42 95 95
IRS2/Crk -0.054 0.11 -10000 0 -0.19 101 101
PI3K -0.061 0.09 -10000 0 -0.18 96 96
apoptosis 0.022 0.077 0.26 6 -10000 0 6
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD -0.079 0.15 -10000 0 -0.3 96 96
RAF1/14-3-3 E -0.019 0.076 -10000 0 -0.25 6 6
BAD/14-3-3 -0.023 0.081 -10000 0 -0.28 6 6
PRKCZ -0.035 0.09 -10000 0 -0.32 6 6
Crk/p130 Cas/Paxillin/FAK1 -0.043 0.064 -10000 0 -0.27 6 6
PTPN1 0.007 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.087 0.16 -10000 0 -0.32 96 96
BCAR1 0.007 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.057 0.087 -10000 0 -0.18 96 96
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.007 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.056 0.1 -10000 0 -0.2 96 96
GRB10 0.006 0.023 -10000 0 -0.4 1 1
PTPN11 -0.056 0.1 -10000 0 -0.2 96 96
IRS1 -0.063 0.11 -10000 0 -0.22 96 96
IRS2 -0.062 0.11 -10000 0 -0.21 101 101
IGF-1R heterotetramer/IGF1 -0.095 0.14 -10000 0 -0.3 96 96
GRB2 0.007 0 -10000 0 -10000 0 0
PDPK1 -0.041 0.094 -10000 0 -0.17 96 96
YWHAE 0.007 0 -10000 0 -10000 0 0
PRKD1 -0.1 0.18 -10000 0 -0.34 97 97
SHC1 0.007 0 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0 0 -9999 0 -10000 0 0
VLDLR 0.007 0 -9999 0 -10000 0 0
CRKL 0.007 0 -9999 0 -10000 0 0
LRPAP1 0.007 0 -9999 0 -10000 0 0
FYN 0.001 0.052 -9999 0 -0.4 5 5
ITGA3 0.007 0 -9999 0 -10000 0 0
RELN/VLDLR/Fyn -0.079 0.11 -9999 0 -0.23 105 105
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.03 -9999 0 -0.18 9 9
AKT1 -0.048 0.095 -9999 0 -0.18 102 102
MAP2K7 0.007 0 -9999 0 -10000 0 0
RAPGEF1 0.007 0 -9999 0 -10000 0 0
DAB1 0.002 0.021 -9999 0 -0.25 2 2
RELN/LRP8/DAB1 -0.069 0.096 -9999 0 -0.2 102 102
LRPAP1/LRP8 -0.001 0.009 -9999 0 -0.16 1 1
RELN/LRP8/DAB1/Fyn -0.066 0.091 -9999 0 -0.19 105 105
DAB1/alpha3/beta1 Integrin -0.054 0.075 -9999 0 -10000 0 0
long-term memory -0.098 0.12 -9999 0 -0.21 139 139
DAB1/LIS1 -0.057 0.079 -9999 0 -0.17 102 102
DAB1/CRLK/C3G -0.054 0.075 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.057 0.08 -9999 0 -0.17 48 48
ARHGEF2 0.007 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.071 0.16 -9999 0 -0.4 58 58
CDK5R1 0.007 0 -9999 0 -10000 0 0
RELN -0.13 0.19 -9999 0 -0.4 102 102
PIK3R1 0.007 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.079 0.11 -9999 0 -0.23 105 105
GRIN2A/RELN/LRP8/DAB1/Fyn -0.1 0.12 -9999 0 -0.22 138 138
MAPK8 0.005 0.033 -9999 0 -0.4 2 2
RELN/VLDLR/DAB1 -0.069 0.096 -9999 0 -0.2 102 102
ITGB1 0.007 0 -9999 0 -10000 0 0
MAP1B -0.076 0.12 -9999 0 -0.21 124 124
RELN/LRP8 -0.075 0.1 -9999 0 -0.22 102 102
GRIN2B/RELN/LRP8/DAB1/Fyn -0.068 0.091 -9999 0 -0.19 106 106
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0 0 -9999 0 -10000 0 0
RAP1A -0.03 0.084 -9999 0 -10000 0 0
PAFAH1B1 0.007 0 -9999 0 -10000 0 0
MAPK8IP1 -0.002 0.061 -9999 0 -0.4 7 7
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.003 0.032 -9999 0 -0.25 5 5
NCK2 0.007 0 -9999 0 -10000 0 0
neuron differentiation -0.04 0.089 -9999 0 -0.29 8 8
neuron adhesion -0.021 0.081 -9999 0 -10000 0 0
LRP8 0.006 0.015 -9999 0 -0.25 1 1
GSK3B -0.041 0.091 -9999 0 -0.17 102 102
RELN/VLDLR/DAB1/Fyn -0.066 0.091 -9999 0 -0.19 105 105
MAP3K11 0.007 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.056 0.1 -9999 0 -0.2 102 102
CDK5 0.007 0 -9999 0 -10000 0 0
MAPT 0.004 0.063 -9999 0 -0.36 8 8
neuron migration -0.053 0.12 -9999 0 -0.23 102 102
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.04 0.09 -9999 0 -0.3 8 8
RELN/VLDLR -0.066 0.093 -9999 0 -0.2 102 102
TCGA08_retinoblastoma

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
CDKN2B 0.01 0.023 -9999 0 -0.26 2 2
CDKN2C 0.036 0.008 -9999 0 -10000 0 0
CDKN2A -0.24 0.063 -9999 0 -0.26 286 286
CCND2 0.023 0.021 -9999 0 -10000 0 0
RB1 -0.027 0.014 -9999 0 -10000 0 0
CDK4 0.032 0.013 -9999 0 -10000 0 0
CDK6 0.027 0.014 -9999 0 -10000 0 0
G1/S progression 0.027 0.016 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.007 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.082 0.076 -10000 0 -0.22 33 33
NT3 (dimer)/TRKC -0.19 0.17 -10000 0 -0.31 186 186
NT3 (dimer)/TRKB -0.079 0.13 -10000 0 -0.27 89 89
SHC/Grb2/SOS1/GAB1/PI3K 0.022 0 -10000 0 -10000 0 0
RAPGEF1 0.007 0 -10000 0 -10000 0 0
BDNF -0.006 0.057 -10000 0 -0.25 16 16
PIK3CA 0.007 0 -10000 0 -10000 0 0
DYNLT1 0.007 0 -10000 0 -10000 0 0
NTRK1 0.007 0.002 -10000 0 -10000 0 0
NTRK2 -0.057 0.15 -10000 0 -0.39 49 49
NTRK3 -0.23 0.2 -10000 0 -0.4 176 176
NT-4/5 (dimer)/TRKB -0.12 0.11 -10000 0 -0.29 63 63
neuron apoptosis 0.1 0.13 0.35 48 -10000 0 48
SHC 2-3/Grb2 -0.11 0.14 -10000 0 -0.38 48 48
SHC1 0.007 0 -10000 0 -10000 0 0
SHC2 -0.11 0.15 -10000 0 -0.4 48 48
SHC3 -0.1 0.13 -10000 0 -0.38 39 39
STAT3 (dimer) 0.012 0 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.044 0.096 -10000 0 -0.24 56 56
RIN/GDP -0.061 0.069 -10000 0 -0.17 33 33
GIPC1 0.007 0 -10000 0 -10000 0 0
KRAS 0.007 0 -10000 0 -10000 0 0
DNAJA3 -0.09 0.12 0.2 1 -0.21 133 134
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.018 0 -10000 0 -10000 0 0
MAGED1 0.005 0.033 -10000 0 -0.4 2 2
PTPN11 0.007 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.13 0.13 -10000 0 -0.25 162 162
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.007 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.095 0.11 -10000 0 -0.22 129 129
TRKA/NEDD4-2 0 0 -10000 0 -10000 0 0
ELMO1 0.006 0.023 -10000 0 -0.4 1 1
RhoG/GTP/ELMO1/DOCK1 -0.001 0.013 -10000 0 -0.23 1 1
NGF -0.17 0.2 -10000 0 -0.4 129 129
HRAS 0.007 0 -10000 0 -10000 0 0
DOCK1 0.007 0 -10000 0 -10000 0 0
GAB2 0.005 0.033 -10000 0 -0.4 2 2
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.007 0 -10000 0 -10000 0 0
FRS2 0.007 0 -10000 0 -10000 0 0
DNM1 0.007 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.007 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.088 0.11 0.18 1 -0.2 133 134
mol:GDP -0.086 0.097 -10000 0 -0.24 34 34
NGF (dimer) -0.17 0.2 -10000 0 -0.4 129 129
RhoG/GDP -0.001 0.016 -10000 0 -0.28 1 1
RIT1/GDP -0.058 0.069 -10000 0 -0.17 28 28
TIAM1 0.005 0.033 -10000 0 -0.4 2 2
PIK3R1 0.007 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.042 0.089 -10000 0 -0.24 48 48
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.001 0.016 -10000 0 -0.27 1 1
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.048 0.14 -10000 0 -0.4 41 41
RAP1/GDP -0.057 0.049 -10000 0 -0.15 22 22
KIDINS220/CRKL 0.007 0 -10000 0 -10000 0 0
BDNF (dimer) -0.006 0.057 -10000 0 -0.25 16 16
ubiquitin-dependent protein catabolic process -0.095 0.11 -10000 0 -0.22 129 129
Schwann cell development -0.036 0.026 -10000 0 -10000 0 0
EHD4 0.007 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.022 0.015 -10000 0 -10000 0 0
RAP1B 0.007 0 -10000 0 -10000 0 0
RAP1A 0.007 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.13 -10000 0 -0.35 65 65
ABL1 0.007 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.015 0.033 -10000 0 -10000 0 0
STAT3 0.012 0 -10000 0 -10000 0 0
axon guidance -0.14 0.13 -10000 0 -0.33 65 65
MAPK3 -0.072 0.11 -10000 0 -0.2 129 129
MAPK1 -0.072 0.11 -10000 0 -0.2 129 129
CDC42/GDP -0.058 0.069 -10000 0 -0.17 27 27
NTF3 -0.048 0.14 -10000 0 -0.4 41 41
NTF4 -0.13 0.13 -10000 0 -0.25 162 162
NGF (dimer)/TRKA/FAIM -0.095 0.11 -10000 0 -0.22 129 129
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.007 0 -10000 0 -10000 0 0
FAIM 0.007 0 -10000 0 -10000 0 0
GAB1 0.007 0 -10000 0 -10000 0 0
RASGRF1 -0.091 0.12 0.2 1 -0.21 133 134
SOS1 0.007 0 -10000 0 -10000 0 0
MCF2L -0.16 0.15 -10000 0 -0.26 188 188
RGS19 0.007 0 -10000 0 -10000 0 0
CDC42 0.007 0 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.051 -10000 0 -10000 0 0
Rac1/GDP -0.058 0.069 -10000 0 -0.17 27 27
NGF (dimer)/TRKA/GRIT -0.097 0.11 -10000 0 -0.23 129 129
neuron projection morphogenesis -0.075 0.12 -10000 0 -0.42 14 14
NGF (dimer)/TRKA/NEDD4-2 -0.095 0.11 -10000 0 -0.22 129 129
MAP2K1 0.023 0 -10000 0 -10000 0 0
NGFR -0.018 0.099 -10000 0 -0.4 19 19
NGF (dimer)/TRKA/GIPC/GAIP -0.069 0.1 -10000 0 -0.19 129 129
RAS family/GTP/PI3K 0.018 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.007 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.007 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.007 0 -10000 0 -10000 0 0
PRKCZ 0.007 0 -10000 0 -10000 0 0
MAPKKK cascade -0.21 0.25 -10000 0 -0.49 129 129
RASA1 0.006 0.023 -10000 0 -0.4 1 1
TRKA/c-Abl 0 0 -10000 0 -10000 0 0
SQSTM1 0.006 0.023 -10000 0 -0.4 1 1
BDNF (dimer)/TRKB/GIPC -0.037 0.078 -10000 0 -0.21 48 48
NGF (dimer)/TRKA/p62/Atypical PKCs -0.077 0.09 -10000 0 -0.18 129 129
MATK 0.007 0 -10000 0 -10000 0 0
NEDD4L 0.007 0 -10000 0 -10000 0 0
RAS family/GDP -0.054 0.047 -10000 0 -0.15 20 20
NGF (dimer)/TRKA -0.096 0.12 0.2 1 -0.22 133 134
Rac1/GTP -0.09 0.082 -10000 0 -0.19 101 101
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.033 0.1 -9999 0 -0.23 58 58
EPHB2 0.007 0 -9999 0 -10000 0 0
Syndecan-2/TACI -0.029 0.09 -9999 0 -0.22 53 53
LAMA1 -0.011 0.069 -9999 0 -0.26 21 21
Syndecan-2/alpha2 ITGB1 -0.032 0.068 -9999 0 -0.18 54 54
HRAS 0.007 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.04 0.087 -9999 0 -0.23 53 53
ITGA5 0.005 0.033 -9999 0 -0.4 2 2
BAX -0.015 0.082 -9999 0 -10000 0 0
EPB41 0.007 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.035 0.076 -9999 0 -0.2 53 53
LAMA3 0.005 0.027 -9999 0 -0.32 2 2
EZR 0.007 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.006 0.023 -9999 0 -0.4 1 1
Syndecan-2/MMP2 -0.04 0.12 -9999 0 -0.27 57 57
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.001 0.009 -9999 0 -0.16 1 1
dendrite morphogenesis -0.027 0.09 -9999 0 -0.22 53 53
Syndecan-2/GM-CSF -0.031 0.091 -9999 0 -0.22 53 53
determination of left/right symmetry -0.038 0.11 -9999 0 -0.27 53 53
Syndecan-2/PKC delta -0.027 0.09 -9999 0 -0.22 53 53
GNB2L1 0.007 0 -9999 0 -10000 0 0
MAPK3 -0.022 0.082 -9999 0 -0.2 53 53
MAPK1 -0.022 0.082 -9999 0 -0.2 53 53
Syndecan-2/RACK1 -0.032 0.07 -9999 0 -0.18 53 53
NF1 0.007 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.038 0.11 -9999 0 -0.27 53 53
ITGA2 0.006 0.015 -9999 0 -0.25 1 1
MAPK8 -0.023 0.092 -9999 0 -0.22 55 55
Syndecan-2/alpha2/beta1 Integrin -0.039 0.075 -9999 0 -0.19 53 53
Syndecan-2/Kininogen -0.04 0.087 -9999 0 -0.23 53 53
ITGB1 0.007 0 -9999 0 -10000 0 0
SRC -0.012 0.072 -9999 0 -0.17 53 53
Syndecan-2/CASK/Protein 4.1 -0.035 0.076 -9999 0 -0.2 53 53
extracellular matrix organization -0.027 0.09 -9999 0 -0.22 53 53
actin cytoskeleton reorganization -0.033 0.1 -9999 0 -0.23 58 58
Syndecan-2/Caveolin-2/Ras -0.035 0.077 -9999 0 -0.2 53 53
Syndecan-2/Laminin alpha3 -0.028 0.091 -9999 0 -0.22 54 54
Syndecan-2/RasGAP -0.03 0.067 -9999 0 -0.17 53 53
alpha5/beta1 Integrin -0.002 0.022 -9999 0 -0.27 2 2
PRKCD 0.007 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.027 0.09 -9999 0 -0.22 53 53
GO:0007205 0.002 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.008 0.073 -9999 0 -0.16 53 53
RHOA 0.007 0 -9999 0 -10000 0 0
SDCBP 0.007 0 -9999 0 -10000 0 0
TNFRSF13B 0.006 0.015 -9999 0 -0.25 1 1
RASA1 0.006 0.023 -9999 0 -0.4 1 1
alpha2/beta1 Integrin -0.001 0.009 -9999 0 -0.16 1 1
Syndecan-2/Synbindin -0.027 0.09 -9999 0 -0.22 53 53
TGFB1 0.007 0 -9999 0 -10000 0 0
CASP3 -0.018 0.081 -9999 0 -0.2 53 53
FN1 -0.003 0.065 -9999 0 -0.4 8 8
Syndecan-2/IL8 -0.1 0.11 -9999 0 -0.3 53 53
SDC2 -0.038 0.11 -9999 0 -0.27 53 53
KNG1 0 0 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin -0.027 0.09 -9999 0 -0.22 53 53
TRAPPC4 0.007 0 -9999 0 -10000 0 0
CSF2 0.001 0.038 -9999 0 -0.25 7 7
Syndecan-2/TGFB1 -0.027 0.09 -9999 0 -0.22 53 53
Syndecan-2/Syntenin/PI-4-5-P2 -0.035 0.076 -9999 0 -0.2 53 53
Syndecan-2/Ezrin -0.034 0.074 -9999 0 -0.2 53 53
PRKACA -0.018 0.081 -9999 0 -0.2 53 53
angiogenesis -0.1 0.11 -9999 0 -0.3 53 53
MMP2 -0.015 0.094 -9999 0 -0.4 17 17
IL8 -0.14 0.13 -9999 0 -0.25 169 169
calcineurin-NFAT signaling pathway -0.029 0.09 -9999 0 -0.22 53 53
Cellular roles of Anthrax toxin

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
ANTXR1 0.006 0.023 -10000 0 -0.4 1 1
ANTXR2 -0.093 0.18 -10000 0 -0.4 75 75
negative regulation of myeloid dendritic cell antigen processing and presentation -0.013 0.023 -10000 0 -0.054 75 75
monocyte activation -0.007 0.064 -10000 0 -0.39 8 8
MAP2K2 -0.006 0.01 -10000 0 -10000 0 0
MAP2K1 -0.011 0.019 -10000 0 -10000 0 0
MAP2K7 -0.011 0.019 -10000 0 -10000 0 0
MAP2K6 -0.011 0.02 -10000 0 -0.094 2 2
CYAA -0.041 0.088 -10000 0 -0.19 75 75
MAP2K4 -0.011 0.019 -10000 0 -10000 0 0
IL1B -0.022 0.048 -10000 0 -0.11 53 53
Channel -0.051 0.091 -10000 0 -0.21 75 75
NLRP1 -0.012 0.024 -10000 0 -0.24 1 1
CALM1 0.007 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.015 0.026 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.013 0.023 0.054 75 -10000 0 75
MAPK3 -0.011 0.019 -10000 0 -0.077 1 1
MAPK1 -0.011 0.019 -10000 0 -10000 0 0
PGR -0.18 0.077 -10000 0 -0.21 255 255
PA/Cellular Receptors -0.057 0.1 -10000 0 -0.23 75 75
apoptosis -0.013 0.023 -10000 0 -0.054 75 75
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.042 0.09 -10000 0 -0.2 75 75
macrophage activation -0.001 0.022 -10000 0 -10000 0 0
TNF 0.002 0.036 -10000 0 -0.25 6 6
VCAM1 -0.007 0.064 -10000 0 -0.39 8 8
platelet activation -0.015 0.026 -10000 0 -10000 0 0
MAPKKK cascade 0.004 0.024 0.079 1 -10000 0 1
IL18 -0.003 0.025 -10000 0 -0.11 4 4
negative regulation of macrophage activation -0.013 0.023 -10000 0 -0.054 75 75
LEF -0.013 0.023 -10000 0 -0.054 75 75
CASP1 -0.012 0.021 -10000 0 -0.12 2 2
mol:cAMP -0.015 0.026 -10000 0 -10000 0 0
necrosis -0.013 0.023 -10000 0 -0.054 75 75
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.048 0.085 -10000 0 -0.2 75 75
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.022 0.026 -10000 0 -10000 0 0
oxygen homeostasis -0.011 0.014 -10000 0 -10000 0 0
TCEB2 0.007 0 -10000 0 -10000 0 0
TCEB1 0.007 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.047 0.048 -10000 0 -10000 0 0
EPO -0.17 0.23 -10000 0 -0.5 64 64
FIH (dimer) 0 0.011 -10000 0 -10000 0 0
APEX1 -0.004 0.015 -10000 0 -10000 0 0
SERPINE1 -0.15 0.22 -10000 0 -0.49 57 57
FLT1 -0.066 0.1 -10000 0 -1.1 1 1
ADORA2A -0.15 0.22 -10000 0 -0.47 60 60
germ cell development -0.16 0.23 -10000 0 -0.5 60 60
SLC11A2 -0.15 0.22 -10000 0 -0.49 57 57
BHLHE40 -0.15 0.22 -10000 0 -0.49 57 57
HIF1AN 0 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.1 0.099 -10000 0 -0.28 36 36
ETS1 0.007 0.02 -10000 0 -10000 0 0
CITED2 -0.11 0.29 -10000 0 -1 29 29
KDR -0.35 0.49 -10000 0 -1.1 99 99
PGK1 -0.15 0.22 -10000 0 -0.49 57 57
SIRT1 0.007 0.002 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT -0.17 0.26 -10000 0 -0.54 62 62
EPAS1 -0.046 0.083 -10000 0 -10000 0 0
SP1 0.012 0 -10000 0 -10000 0 0
ABCG2 -0.27 0.3 -10000 0 -0.58 122 122
EFNA1 -0.15 0.22 -10000 0 -0.49 57 57
FXN -0.15 0.22 -10000 0 -0.47 60 60
POU5F1 -0.16 0.24 -10000 0 -0.52 60 60
neuron apoptosis 0.17 0.25 0.53 62 -10000 0 62
EP300 0.007 0 -10000 0 -10000 0 0
EGLN3 -0.001 0.018 -10000 0 -0.25 1 1
EGLN2 0 0.011 -10000 0 -10000 0 0
EGLN1 0 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.007 0 -10000 0 -10000 0 0
ARNT -0.004 0.015 -10000 0 -10000 0 0
SLC2A1 -0.16 0.22 -10000 0 -0.48 60 60
TWIST1 -0.19 0.27 -10000 0 -0.56 80 80
ELK1 0.009 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.094 0.095 -10000 0 -0.29 16 16
VEGFA -0.15 0.22 -10000 0 -0.49 57 57
CREBBP 0.007 0 -10000 0 -10000 0 0
Glypican 1 network

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.15 -9999 0 -0.28 111 111
fibroblast growth factor receptor signaling pathway -0.1 0.15 -9999 0 -0.28 111 111
LAMA1 -0.011 0.069 -9999 0 -0.26 21 21
PRNP 0.001 0.052 -9999 0 -0.4 5 5
GPC1/SLIT2 -0.11 0.13 -9999 0 -0.27 123 123
SMAD2 0.017 0.024 -9999 0 -0.2 4 4
GPC1/PrPc/Cu2+ -0.004 0.029 -9999 0 -0.23 5 5
GPC1/Laminin alpha1 -0.012 0.044 -9999 0 -0.17 21 21
TDGF1 -0.027 0.11 -9999 0 -0.39 24 24
CRIPTO/GPC1 -0.021 0.073 -9999 0 -0.27 24 24
APP/GPC1 0 0 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.004 0.063 -9999 0 -0.22 23 23
FLT1 0.006 0.023 -9999 0 -0.4 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.003 0.025 -9999 0 -0.22 4 4
SERPINC1 0.002 0.032 -9999 0 -0.25 5 5
FYN -0.008 0.069 -9999 0 -0.22 28 28
FGR -0.004 0.063 -9999 0 -0.22 23 23
positive regulation of MAPKKK cascade -0.003 0.079 -9999 0 -0.27 23 23
SLIT2 -0.16 0.2 -9999 0 -0.4 123 123
GPC1/NRG -0.029 0.061 -9999 0 -0.16 56 56
NRG1 -0.04 0.099 -9999 0 -0.25 56 56
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.001 0.013 -9999 0 -0.22 1 1
LYN -0.004 0.063 -9999 0 -0.22 23 23
mol:Spermine 0.007 0 -9999 0 -10000 0 0
cell growth -0.1 0.15 -9999 0 -0.28 111 111
BMP signaling pathway -0.007 0 -9999 0 -10000 0 0
SRC -0.004 0.063 -9999 0 -0.22 23 23
TGFBR1 0.007 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.032 0.11 -9999 0 -0.35 32 32
GPC1 0.007 0 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.007 0 -9999 0 -10000 0 0
VEGFA 0.007 0 -9999 0 -10000 0 0
BLK -0.03 0.079 -9999 0 -0.23 23 23
HCK -0.004 0.063 -9999 0 -0.22 23 23
FGF2 -0.12 0.19 -9999 0 -0.4 95 95
FGFR1 -0.056 0.15 -9999 0 -0.4 47 47
VEGFR1 homodimer 0.006 0.023 -9999 0 -0.4 1 1
TGFBR2 0.002 0.046 -9999 0 -0.4 4 4
cell death 0 0 -9999 0 -10000 0 0
ATIII/GPC1 -0.003 0.02 -9999 0 -0.16 5 5
PLA2G2A/GPC1 -0.025 0.075 -9999 0 -0.24 32 32
LCK -0.004 0.063 -9999 0 -0.22 23 23
neuron differentiation -0.029 0.061 -9999 0 -0.16 56 56
PrPc/Cu2+ -0.005 0.036 -9999 0 -0.28 5 5
APP 0.007 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.002 0.046 -9999 0 -0.4 4 4
Thromboxane A2 receptor signaling

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
TGM2 -0.046 0.14 -10000 0 -0.4 39 39
GNB1/GNG2 -0.039 0.071 -10000 0 -0.18 57 57
AKT1 -0.022 0.096 -10000 0 -0.2 56 56
EGF -0.013 0.088 -10000 0 -0.4 15 15
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.022 0.026 -10000 0 -10000 0 0
mol:Ca2+ -0.05 0.14 -10000 0 -0.28 81 81
LYN 0.022 0.026 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.051 -10000 0 -0.12 57 57
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.051 0.15 -10000 0 -0.33 59 59
GNG2 0.007 0 -10000 0 -10000 0 0
ARRB2 0.007 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.017 0.062 -10000 0 -0.29 2 2
G beta5/gamma2 -0.051 0.094 -10000 0 -0.24 56 56
PRKCH -0.058 0.16 -10000 0 -0.34 65 65
DNM1 0.007 0 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 -0.001 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.002 0.046 -10000 0 -0.4 4 4
G12 family/GTP -0.072 0.12 -10000 0 -0.29 62 62
ADRBK1 0.007 0 -10000 0 -10000 0 0
ADRBK2 0.007 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.088 0.22 20 -10000 0 20
mol:NADP -0.005 0.069 -10000 0 -0.4 9 9
RAB11A 0.007 0 -10000 0 -10000 0 0
PRKG1 -0.092 0.18 -10000 0 -0.4 74 74
mol:IP3 -0.067 0.18 -10000 0 -0.35 81 81
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.095 0.24 -10000 0 -0.47 81 81
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.026 0.038 -10000 0 -10000 0 0
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.022 0.026 -10000 0 -10000 0 0
RHOA 0.007 0 -10000 0 -10000 0 0
PTGIR 0.006 0.023 -10000 0 -0.4 1 1
PRKCB1 -0.065 0.17 -10000 0 -0.34 81 81
GNAQ 0.007 0 -10000 0 -10000 0 0
mol:L-citrulline -0.005 0.069 -10000 0 -0.4 9 9
TXA2/TXA2-R family -0.09 0.23 -10000 0 -0.52 59 59
LCK 0.022 0.026 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.004 0.025 -10000 0 -0.16 8 8
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.008 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.004 0.025 -10000 0 -0.16 8 8
MAPK14 -0.027 0.11 -10000 0 -0.22 59 59
TGM2/GTP -0.081 0.21 -10000 0 -0.41 81 81
MAPK11 -0.027 0.11 -10000 0 -0.22 57 57
ARHGEF1 -0.023 0.084 -10000 0 -0.17 58 58
GNAI2 0.007 0 -10000 0 -10000 0 0
JNK cascade -0.061 0.17 -10000 0 -0.38 59 59
RAB11/GDP 0.008 0.001 -10000 0 -10000 0 0
ICAM1 -0.04 0.13 -10000 0 -0.28 57 57
cAMP biosynthetic process -0.066 0.17 -10000 0 -0.33 81 81
Gq family/GTP/EBP50 -0.039 0.081 -10000 0 -0.16 90 90
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.022 0.026 -10000 0 -10000 0 0
GNB5 0.007 0 -10000 0 -10000 0 0
GNB1 0.007 0 -10000 0 -10000 0 0
EGF/EGFR 0.024 0.036 -10000 0 -0.17 2 2
VCAM1 -0.044 0.14 -10000 0 -0.3 57 57
TP beta/Gq family/GDP/G beta5/gamma2 -0.017 0.062 -10000 0 -0.29 2 2
platelet activation -0.038 0.14 -10000 0 -0.28 65 65
PGI2/IP -0.001 0.016 -10000 0 -0.28 1 1
PRKACA 0.008 0.028 -10000 0 -0.2 5 5
Gq family/GDP/G beta5/gamma2 -0.018 0.062 -10000 0 -0.26 2 2
TXA2/TP beta/beta Arrestin2 0 0.003 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.011 0.033 -10000 0 -0.19 8 8
mol:DAG -0.073 0.19 -10000 0 -0.41 65 65
EGFR 0.002 0.041 -10000 0 -0.31 5 5
TXA2/TP alpha -0.092 0.22 -10000 0 -0.45 81 81
Gq family/GTP -0.059 0.089 -10000 0 -0.2 90 90
YES1 0.022 0.026 -10000 0 -10000 0 0
GNAI2/GTP -0.004 0.024 -10000 0 -10000 0 0
PGD2/DP -0.004 0.032 -10000 0 -0.28 4 4
SLC9A3R1 -0.009 0.062 -10000 0 -0.25 19 19
FYN 0.019 0.035 -10000 0 -10000 0 0
mol:NO -0.005 0.069 -10000 0 -0.4 9 9
GNA15 -0.011 0.066 -10000 0 -0.25 22 22
PGK/cGMP -0.062 0.11 -10000 0 -0.24 80 80
RhoA/GDP 0.008 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.024 0.06 -10000 0 -0.33 3 3
NOS3 -0.005 0.069 -10000 0 -0.4 9 9
RAC1 0.007 0 -10000 0 -10000 0 0
PRKCA -0.06 0.16 -10000 0 -0.35 65 65
PRKCB -0.059 0.16 -10000 0 -0.36 59 59
PRKCE -0.057 0.16 -10000 0 -0.36 59 59
PRKCD -0.062 0.17 -10000 0 -0.38 58 58
PRKCG -0.069 0.18 -10000 0 -0.38 65 65
muscle contraction -0.081 0.21 -10000 0 -0.48 59 59
PRKCZ -0.051 0.15 -10000 0 -0.33 59 59
ARR3 0.002 0.003 -10000 0 -10000 0 0
TXA2/TP beta -0.004 0.027 -10000 0 -0.17 5 5
PRKCQ -0.058 0.16 -10000 0 -0.36 59 59
MAPKKK cascade -0.08 0.2 -10000 0 -0.44 65 65
SELE -0.059 0.16 -10000 0 -0.38 56 56
TP beta/GNAI2/GDP/G beta/gamma -0.004 0.024 -10000 0 -10000 0 0
ROCK1 0.007 0 -10000 0 -10000 0 0
GNA14 -0.11 0.18 -10000 0 -0.4 88 88
chemotaxis -0.1 0.25 -10000 0 -0.59 57 57
GNA12 0.007 0 -10000 0 -10000 0 0
GNA13 0.007 0 -10000 0 -10000 0 0
GNA11 0.005 0.033 -10000 0 -0.4 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.012 0.051 -9999 0 -0.22 17 17
alphaM/beta2 Integrin/GPIbA -0.001 0.01 -9999 0 -10000 0 0
alphaM/beta2 Integrin/proMMP-9 -0.02 0.045 -9999 0 -10000 0 0
PLAUR 0.007 0 -9999 0 -10000 0 0
HMGB1 0.009 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0 0.001 -9999 0 -10000 0 0
AGER 0.009 0.003 -9999 0 -10000 0 0
RAP1A 0.007 0 -9999 0 -10000 0 0
SELPLG 0.007 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.001 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.034 0.094 -9999 0 -0.25 49 49
CYR61 -0.04 0.13 -9999 0 -0.4 35 35
TLN1 0.007 0 -9999 0 -10000 0 0
Rap1/GTP -0.074 0.09 -9999 0 -0.3 26 26
RHOA 0.007 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.2 -9999 0 -0.4 145 145
MYH2 -0.11 0.15 -9999 0 -0.25 123 123
MST1R -0.068 0.12 -9999 0 -0.25 89 89
leukocyte activation during inflammatory response -0.003 0.017 -9999 0 -10000 0 0
APOB 0.001 0.029 -9999 0 -0.25 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.015 0.094 -9999 0 -0.4 17 17
JAM3 -0.064 0.15 -9999 0 -0.4 53 53
GP1BA 0.005 0.021 -9999 0 -0.25 2 2
alphaM/beta2 Integrin/CTGF -0.062 0.099 -9999 0 -0.22 86 86
alphaM/beta2 Integrin -0.08 0.12 -9999 0 -0.34 27 27
JAM3 homodimer -0.064 0.15 -9999 0 -0.4 53 53
ICAM2 -0.007 0.076 -9999 0 -0.4 11 11
ICAM1 0.007 0 -9999 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.079 0.12 -9999 0 -0.34 27 27
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
NFKB1 0.035 0.02 -9999 0 -10000 0 0
THY1 0.006 0.023 -9999 0 -0.4 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.004 0.023 -9999 0 -0.13 10 10
alphaM/beta2 Integrin/LRP/tPA -0.007 0.038 -9999 0 -0.19 12 12
IL6 0.037 0.027 -9999 0 -10000 0 0
ITGB2 0.009 0.003 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0 0.007 -9999 0 -10000 0 0
alphaM/beta2 Integrin/JAM2/JAM3 -0.13 0.15 -9999 0 -0.26 150 150
JAM2 -0.19 0.2 -9999 0 -0.4 148 148
alphaM/beta2 Integrin/ICAM1 -0.026 0.042 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg -0.001 0.012 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.16 -9999 0 -0.25 143 143
positive regulation of phagocytosis -0.053 0.067 -9999 0 -0.28 10 10
Ron/MSP -0.046 0.072 -9999 0 -0.16 89 89
alphaM/beta2 Integrin/uPAR/uPA 0 0.007 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR 0 0.001 -9999 0 -10000 0 0
PLAU 0.006 0.015 -9999 0 -0.25 1 1
PLAT -0.009 0.079 -9999 0 -0.4 12 12
actin filament polymerization -0.1 0.14 -9999 0 -0.24 123 123
MST1 0.007 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.003 0.017 -9999 0 -10000 0 0
TNF 0.038 0.026 -9999 0 -10000 0 0
RAP1B 0.007 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0 0.008 -9999 0 -10000 0 0
fibrinolysis -0.001 0.012 -9999 0 -10000 0 0
HCK 0.007 0 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.079 0.12 -9999 0 -0.34 27 27
VTN -0.04 0.13 -9999 0 -0.38 37 37
alphaM/beta2 Integrin/CYR61 -0.025 0.07 -9999 0 -0.22 35 35
LPA -0.001 0.035 -9999 0 -0.25 6 6
LRP1 0.007 0 -9999 0 -10000 0 0
cell migration -0.027 0.057 -9999 0 -0.2 17 17
FN1 -0.003 0.065 -9999 0 -0.4 8 8
alphaM/beta2 Integrin/Thy1 -0.001 0.013 -9999 0 -0.22 1 1
MPO 0.005 0.015 -9999 0 -0.25 1 1
KNG1 0 0 -9999 0 -10000 0 0
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.1 0.15 -9999 0 -0.39 34 34
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.025 -9999 0 -0.25 3 3
CTGF -0.11 0.18 -9999 0 -0.4 86 86
alphaM/beta2 Integrin/Hck 0 0.001 -9999 0 -10000 0 0
ITGAM 0.009 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.092 0.097 -9999 0 -0.19 145 145
HP -0.17 0.2 -9999 0 -0.4 132 132
leukocyte adhesion -0.1 0.12 -9999 0 -0.32 53 53
SELP -0.19 0.2 -9999 0 -0.4 145 145
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.007 0.002 -9999 0 -10000 0 0
SVIL 0.002 0.047 -9999 0 -0.4 4 4
ZNF318 0.005 0.004 -9999 0 -10000 0 0
JMJD2C 0.001 0.006 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.1 0.12 -9999 0 -0.23 140 140
CARM1 0.007 0 -9999 0 -10000 0 0
PRDX1 0.007 0 -9999 0 -10000 0 0
PELP1 0.007 0 -9999 0 -10000 0 0
CTNNB1 0.007 0.001 -9999 0 -10000 0 0
AKT1 0.007 0.001 -9999 0 -10000 0 0
PTK2B 0.007 0.001 -9999 0 -10000 0 0
MED1 0.007 0.001 -9999 0 -10000 0 0
MAK -0.008 0.057 -9999 0 -0.25 16 16
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.003 0.04 -9999 0 -0.4 3 3
GSN 0.007 0.002 -9999 0 -10000 0 0
NCOA2 0.002 0.046 -9999 0 -0.4 4 4
NCOA6 0.007 0.002 -9999 0 -10000 0 0
DNA-PK 0.001 0.005 -9999 0 -10000 0 0
NCOA4 0.007 0 -9999 0 -10000 0 0
PIAS3 0.007 0.001 -9999 0 -10000 0 0
cell proliferation -0.019 0.025 -9999 0 -10000 0 0
XRCC5 0.007 0.001 -9999 0 -10000 0 0
UBE3A 0.008 0.002 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.13 0.14 -9999 0 -0.26 153 153
FHL2 -0.043 0.087 -9999 0 -0.9 2 2
RANBP9 0.007 0.002 -9999 0 -10000 0 0
JMJD1A -0.005 0.021 -9999 0 -0.13 2 2
CDK6 0.007 0 -9999 0 -10000 0 0
TGFB1I1 -0.041 0.13 -9999 0 -0.4 36 36
T-DHT/AR/CyclinD1 -0.1 0.12 -9999 0 -0.23 140 140
XRCC6 0.007 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.13 -9999 0 -0.24 141 141
CTDSP1 0.007 0 -9999 0 -10000 0 0
CTDSP2 0.007 0.002 -9999 0 -10000 0 0
BRCA1 0.007 0.001 -9999 0 -10000 0 0
TCF4 0.003 0.04 -9999 0 -0.4 3 3
CDKN2A -0.23 0.06 -9999 0 -0.25 286 286
SRF 0.011 0.01 -9999 0 -10000 0 0
NKX3-1 -0.059 0.094 -9999 0 -1 2 2
KLK3 0.008 0.024 -9999 0 -10000 0 0
TMF1 0.007 0 -9999 0 -10000 0 0
HNRNPA1 0.007 0.001 -9999 0 -10000 0 0
AOF2 0 0.001 -9999 0 -10000 0 0
APPL1 0.013 0.002 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.11 0.12 -9999 0 -0.23 140 140
AR -0.18 0.2 -9999 0 -0.4 140 140
UBA3 0.007 0 -9999 0 -10000 0 0
PATZ1 0.007 0.001 -9999 0 -10000 0 0
PAWR 0.007 0 -9999 0 -10000 0 0
PRKDC 0.007 0.001 -9999 0 -10000 0 0
PA2G4 0.007 0.001 -9999 0 -10000 0 0
UBE2I 0.007 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.094 0.11 -9999 0 -0.21 140 140
RPS6KA3 0.007 0.002 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.1 0.12 -9999 0 -0.23 140 140
LATS2 0.007 0.001 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.094 0.11 -9999 0 -0.21 140 140
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0.007 0.001 -9999 0 -10000 0 0
KLK2 -0.052 0.057 -9999 0 -10000 0 0
CASP8 0.007 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.091 0.11 -9999 0 -0.21 142 142
TMPRSS2 -0.081 0.077 -9999 0 -0.41 2 2
CCND1 0.007 0 -9999 0 -10000 0 0
PIAS1 0.008 0.002 -9999 0 -10000 0 0
mol:T-DHT -0.004 0.012 -9999 0 -0.055 4 4
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.008 0.002 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.1 0.12 -9999 0 -0.23 140 140
CMTM2 0.007 0.001 -9999 0 -10000 0 0
SNURF -0.032 0.12 -9999 0 -0.4 29 29
ZMIZ1 0.005 0.009 -9999 0 -10000 0 0
CCND3 0.007 0 -9999 0 -10000 0 0
TGIF1 0.007 0.001 -9999 0 -10000 0 0
FKBP4 0.007 0.002 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.089 0.13 -9999 0 -0.27 99 99
PDGFRB -0.016 0.091 -9999 0 -0.4 16 16
SPHK1 -0.007 0.013 -9999 0 -10000 0 0
mol:S1P -0.008 0.016 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.054 0.11 -9999 0 -0.28 34 34
GNAO1 0.002 0.047 -9999 0 -0.4 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.046 0.11 -9999 0 -0.26 38 38
PLCG1 -0.047 0.1 -9999 0 -0.27 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.016 0.091 -9999 0 -0.4 16 16
GNAI2 0.008 0.002 -9999 0 -10000 0 0
GNAI3 0.007 0.002 -9999 0 -10000 0 0
GNAI1 0.006 0.024 -9999 0 -0.4 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.067 0.11 -9999 0 -0.23 99 99
S1P1/S1P -0.062 0.081 -9999 0 -0.21 42 42
negative regulation of cAMP metabolic process -0.053 0.11 -9999 0 -0.28 34 34
MAPK3 -0.046 0.11 -9999 0 -0.27 29 29
calcium-dependent phospholipase C activity -0.001 0.001 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.12 0.19 -9999 0 -0.4 99 99
PLCB2 -0.041 0.085 -9999 0 -0.19 35 35
RAC1 0.007 0 -9999 0 -10000 0 0
RhoA/GTP -0.054 0.07 -9999 0 -0.18 40 40
receptor internalization -0.06 0.077 -9999 0 -0.2 42 42
PTGS2 -0.041 0.1 -9999 0 -0.41 3 3
Rac1/GTP -0.054 0.07 -9999 0 -0.19 35 35
RHOA 0.007 0 -9999 0 -10000 0 0
VEGFA 0.007 0 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.053 0.11 -9999 0 -0.28 34 34
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.084 0.17 -9999 0 -0.4 68 68
MAPK1 -0.046 0.11 -9999 0 -0.27 29 29
S1P1/S1P/PDGFB-D/PDGFRB -0.057 0.11 -9999 0 -0.24 48 48
ABCC1 0.007 0.001 -9999 0 -10000 0 0
IL4-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
BCL2L1 -0.32 0.42 -10000 0 -1.1 44 44
STAT6 (cleaved dimer) -0.35 0.38 -10000 0 -0.98 58 58
IGHG1 -0.11 0.16 -10000 0 -0.34 44 44
IGHG3 -0.31 0.41 -10000 0 -0.95 59 59
AKT1 -0.13 0.2 -10000 0 -0.51 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.091 0.15 -10000 0 -0.51 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.15 0.21 -10000 0 -0.54 14 14
THY1 -0.32 0.43 -10000 0 -1.1 44 44
MYB -0.021 0.081 -10000 0 -0.25 34 34
HMGA1 0.003 0.033 -10000 0 -0.25 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.17 0.24 -10000 0 -0.55 44 44
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.2 -10000 0 -0.51 9 9
SP1 0.009 0.015 -10000 0 -10000 0 0
INPP5D 0.007 0 -10000 0 -10000 0 0
SOCS5 0.016 0.012 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.32 0.39 -10000 0 -1 51 51
SOCS1 -0.2 0.29 -10000 0 -0.68 44 44
SOCS3 -0.14 0.21 -10000 0 -0.73 1 1
FCER2 -0.23 0.31 -10000 0 -0.75 44 44
PARP14 0.008 0.001 -10000 0 -10000 0 0
CCL17 -0.32 0.42 -10000 0 -1.1 47 47
GRB2 0.007 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.17 -10000 0 -0.42 4 4
T cell proliferation -0.3 0.42 -10000 0 -1.1 46 46
IL4R/JAK1 -0.32 0.42 -10000 0 -1.1 45 45
EGR2 -0.32 0.43 -10000 0 -1.1 46 46
JAK2 -0.01 0.029 -10000 0 -10000 0 0
JAK3 0.012 0.003 -10000 0 -10000 0 0
PIK3R1 0.007 0 -10000 0 -10000 0 0
JAK1 0.006 0.009 -10000 0 -10000 0 0
COL1A2 -0.16 0.32 -10000 0 -1.3 18 18
CCL26 -0.32 0.42 -10000 0 -1.1 45 45
IL4R -0.34 0.45 -10000 0 -1.1 45 45
PTPN6 0.016 0.012 -10000 0 -10000 0 0
IL13RA2 -0.32 0.42 -10000 0 -1.1 44 44
IL13RA1 -0.01 0.029 -10000 0 -10000 0 0
IRF4 -0.05 0.12 -10000 0 -1.3 1 1
ARG1 -0.076 0.13 -10000 0 -10000 0 0
CBL -0.16 0.23 -10000 0 -0.52 44 44
GTF3A 0.012 0.001 -10000 0 -10000 0 0
PIK3CA 0.007 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.011 0.042 -10000 0 -10000 0 0
IRF4/BCL6 -0.045 0.11 -10000 0 -1.2 1 1
CD40LG 0.012 0.001 -10000 0 -10000 0 0
MAPK14 -0.16 0.23 -10000 0 -0.52 40 40
mitosis -0.13 0.2 -10000 0 -0.49 10 10
STAT6 -0.36 0.48 -10000 0 -1.1 55 55
SPI1 0.01 0.002 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.19 -10000 0 -0.49 6 6
STAT6 (dimer) -0.36 0.48 -10000 0 -1.1 55 55
STAT6 (dimer)/PARP14 -0.33 0.44 -10000 0 -1.1 52 52
mast cell activation 0.008 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.13 0.2 -10000 0 -0.48 9 9
FRAP1 -0.13 0.2 -10000 0 -0.51 9 9
LTA -0.32 0.42 -10000 0 -1.1 44 44
FES 0.007 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.35 0.47 1.1 55 -10000 0 55
CCL11 -0.33 0.44 -10000 0 -1.1 50 50
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.13 0.2 -10000 0 -0.48 9 9
IL2RG 0.008 0.03 -10000 0 -0.25 4 4
IL10 -0.32 0.42 -10000 0 -1.1 44 44
IRS1 -0.011 0.085 -10000 0 -0.4 14 14
IRS2 -0.005 0.069 -10000 0 -0.4 9 9
IL4 -0.08 0.11 -10000 0 -10000 0 0
IL5 -0.32 0.42 -10000 0 -1.1 44 44
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.35 -10000 0 -0.82 49 49
COL1A1 -0.11 0.18 -10000 0 -1.5 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.32 0.43 -10000 0 -1.1 44 44
IL2R gamma/JAK3 0.01 0.02 -10000 0 -0.16 4 4
TFF3 -0.45 0.6 -10000 0 -1.4 79 79
ALOX15 -0.33 0.42 -10000 0 -1.1 47 47
MYBL1 0.007 0 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.26 0.34 -10000 0 -0.83 50 50
SHC1 0.007 0 -10000 0 -10000 0 0
CEBPB 0.01 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.2 -10000 0 -0.49 13 13
mol:PI-3-4-5-P3 -0.13 0.2 -10000 0 -0.51 9 9
PI3K -0.14 0.21 -10000 0 -0.54 9 9
DOK2 0.007 0 -10000 0 -10000 0 0
ETS1 0.016 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.1 0.16 -10000 0 -0.4 2 2
ITGB3 -0.38 0.52 -10000 0 -1.2 62 62
PIGR -0.49 0.62 -10000 0 -1.3 95 95
IGHE 0.027 0.035 -10000 0 -10000 0 0
MAPKKK cascade -0.1 0.16 -10000 0 -0.39 2 2
BCL6 0.007 0 -10000 0 -10000 0 0
OPRM1 -0.32 0.42 -10000 0 -1.1 45 45
RETNLB -0.32 0.42 -10000 0 -1.1 44 44
SELP -0.64 0.68 -10000 0 -1.3 146 146
AICDA -0.31 0.41 -10000 0 -1 44 44
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.001 0.01 -9999 0 -0.13 2 2
ARNO/beta Arrestin1-2 -0.003 0.021 -9999 0 -10000 0 0
EGFR 0.002 0.041 -9999 0 -0.31 5 5
EPHA2 0.007 0 -9999 0 -10000 0 0
USP6 0.007 0 -9999 0 -10000 0 0
IQSEC1 0.007 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.017 0.065 -9999 0 -0.26 20 20
ARRB2 0.005 0.001 -9999 0 -10000 0 0
mol:GTP 0.012 0.002 -9999 0 -10000 0 0
ARRB1 0.007 0 -9999 0 -10000 0 0
FBXO8 0.007 0 -9999 0 -10000 0 0
TSHR 0.005 0.015 -9999 0 -0.25 1 1
EGF -0.013 0.088 -9999 0 -0.4 15 15
somatostatin receptor activity 0 0 -9999 0 0 73 73
ARAP2 0.007 0 -9999 0 -10000 0 0
mol:GDP -0.065 0.08 -9999 0 -0.18 66 66
mol:PI-3-4-5-P3 0 0 -9999 0 0 61 61
ITGA2B 0.004 0.036 -9999 0 -0.35 3 3
ARF6 0.007 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0 0 -9999 0 -10000 0 0
ADAP1 0.006 0.021 -9999 0 -0.25 2 2
KIF13B 0.007 0 -9999 0 -10000 0 0
HGF/MET -0.037 0.094 -9999 0 -0.27 41 41
PXN 0.007 0 -9999 0 -10000 0 0
ARF6/GTP -0.074 0.095 -9999 0 -0.21 73 73
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.014 0.053 -9999 0 -0.22 17 17
ADRB2 0 0.052 -9999 0 -0.4 5 5
receptor agonist activity 0 0 -9999 0 0 92 92
actin filament binding 0 0 -9999 0 0 77 77
SRC 0.007 0 -9999 0 -10000 0 0
ITGB3 -0.038 0.13 -9999 0 -0.4 34 34
GNAQ 0.007 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 72 72
ARF6/GDP 0.002 0.037 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.094 0.093 -9999 0 -0.23 71 71
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.024 0.066 -9999 0 -0.2 35 35
ACAP1 0.007 0 -9999 0 -10000 0 0
ACAP2 0.007 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0 0.002 -9999 0 -10000 0 0
EFNA1 0.007 0 -9999 0 -10000 0 0
HGF -0.049 0.14 -9999 0 -0.4 42 42
CYTH3 0.006 0 -9999 0 -10000 0 0
CYTH2 0.004 0.002 -9999 0 -10000 0 0
NCK1 0.007 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 68 68
endosomal lumen acidification 0 0 -9999 0 0 77 77
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.08 0.17 -9999 0 -0.4 65 65
GNAQ/ARNO 0.006 0.005 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 0 2 2
PIP3-E 0 0 -9999 0 0 11 11
MET 0.007 0 -9999 0 -10000 0 0
GNA14 -0.11 0.18 -9999 0 -0.4 88 88
GNA15 -0.011 0.066 -9999 0 -0.25 22 22
GIT1 0.007 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 71 71
GNA11 0.004 0.033 -9999 0 -0.4 2 2
LHCGR 0 0.002 -9999 0 -10000 0 0
AGTR1 -0.18 0.2 -9999 0 -0.4 141 141
desensitization of G-protein coupled receptor protein signaling pathway 0 0.002 -9999 0 -10000 0 0
IPCEF1/ARNO -0.003 0.042 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin -0.033 0.091 -9999 0 -0.28 36 36
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.019 0.009 -9999 0 -10000 0 0
BUB1B -0.031 0.01 -9999 0 -10000 0 0
PLK1 0.007 0.008 -9999 0 -10000 0 0
PLK1S1 0.007 0.005 -9999 0 -10000 0 0
KIF2A 0.011 0.007 -9999 0 -10000 0 0
regulation of mitotic centrosome separation 0.007 0.008 -9999 0 -10000 0 0
GOLGA2 0.007 0 -9999 0 -10000 0 0
Hec1/SPC24 0.004 0.036 -9999 0 -0.12 5 5
WEE1 0.009 0.007 -9999 0 -10000 0 0
cytokinesis -0.029 0.014 -9999 0 -0.16 2 2
PP2A-alpha B56 0.046 0.021 -9999 0 -10000 0 0
AURKA 0.008 0.004 -9999 0 -10000 0 0
PICH/PLK1 -0.006 0.041 -9999 0 -10000 0 0
CENPE 0.011 0.013 -9999 0 -0.12 2 2
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.011 0.007 -9999 0 -10000 0 0
PPP2CA 0.007 0 -9999 0 -10000 0 0
FZR1 0.007 0 -9999 0 -10000 0 0
TPX2 0.013 0.004 -9999 0 -10000 0 0
PAK1 0.007 0 -9999 0 -10000 0 0
SPC24 -0.017 0.075 -9999 0 -0.25 29 29
FBXW11 0.007 0 -9999 0 -10000 0 0
CLSPN 0.014 0.005 -9999 0 -10000 0 0
GORASP1 0.007 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.004 0.005 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0.001 -9999 0 -10000 0 0
STAG2 0.007 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.005 -9999 0 -10000 0 0
spindle elongation 0.007 0.008 -9999 0 -10000 0 0
ODF2 0.007 0 -9999 0 -10000 0 0
BUB1 0.038 0.031 -9999 0 -10000 0 0
TPT1 0.007 0.005 -9999 0 -10000 0 0
CDC25C 0.019 0.005 -9999 0 -10000 0 0
CDC25B 0.007 0 -9999 0 -10000 0 0
SGOL1 -0.019 0.009 -9999 0 -10000 0 0
RHOA 0.007 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.005 0.006 -9999 0 -10000 0 0
CDC14B 0.007 0 -9999 0 -10000 0 0
CDC20 -0.25 0.021 -9999 0 -0.25 302 302
PLK1/PBIP1 -0.039 0.049 -9999 0 -0.1 116 116
mitosis -0.001 0.003 -9999 0 -0.014 16 16
FBXO5 0.009 0.006 -9999 0 -10000 0 0
CDC2 0 0.001 -9999 0 -10000 0 0
NDC80 0.007 0 -9999 0 -10000 0 0
metaphase plate congression 0.006 0.006 -9999 0 -10000 0 0
ERCC6L -0.011 0.038 -9999 0 -10000 0 0
NLP/gamma Tubulin 0.006 0.005 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.007 0.005 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0 -9999 0 -10000 0 0
PPP1R12A 0.007 0 -9999 0 -10000 0 0
interphase 0 0 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.097 0.019 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.001 0.003 -9999 0 -10000 0 0
RAB1A 0.007 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.01 0.007 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.004 -9999 0 -10000 0 0
microtubule-based process -0.11 0.02 -9999 0 -0.11 297 297
Golgi organization 0.007 0.008 -9999 0 -10000 0 0
Cohesin/SA2 -0.001 0.002 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0.001 -9999 0 -10000 0 0
KIF20A -0.24 0.038 -9999 0 -0.25 297 297
APC/C/CDC20 -0.11 0.012 -9999 0 -0.11 302 302
PPP2R1A 0.007 0 -9999 0 -10000 0 0
chromosome segregation -0.039 0.049 -9999 0 -0.1 116 116
PRC1 0.007 0 -9999 0 -10000 0 0
ECT2 0.009 0.017 -9999 0 -0.11 5 5
C13orf34 0.01 0.006 -9999 0 -10000 0 0
NUDC 0.006 0.006 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.03 0.01 -9999 0 -10000 0 0
spindle assembly 0.007 0.007 -9999 0 -10000 0 0
spindle stabilization 0.007 0.005 -9999 0 -10000 0 0
APC/C/HCDH1 0.01 0 -9999 0 -10000 0 0
MKLP2/PLK1 -0.11 0.02 -9999 0 -0.11 297 297
CCNB1 0.007 0 -9999 0 -10000 0 0
PPP1CB 0.007 0 -9999 0 -10000 0 0
BTRC 0.007 0 -9999 0 -10000 0 0
ROCK2 0.009 0.031 -9999 0 -0.36 2 2
TUBG1 0.007 0.005 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
MLF1IP -0.062 0.084 -9999 0 -0.17 116 116
INCENP 0.007 0 -9999 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.044 0.07 0.19 28 -10000 0 28
GNAI2 0.007 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.043 0.061 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.002 0.046 -10000 0 -0.4 4 4
RhoA/GTP -0.044 0.071 -10000 0 -0.2 28 28
negative regulation of cAMP metabolic process -0.041 0.086 -10000 0 -0.19 72 72
GNAZ -0.084 0.17 -10000 0 -0.4 68 68
GNAI3 0.007 0 -10000 0 -10000 0 0
GNA12 0.007 0 -10000 0 -10000 0 0
S1PR5 -0.078 0.12 -10000 0 -0.25 101 101
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.041 0.087 -10000 0 -0.19 72 72
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.007 0 -10000 0 -10000 0 0
GNAI1 0.006 0.023 -10000 0 -0.4 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.012 0.12 -10000 0 -0.36 30 30
CRKL -0.018 0.12 -10000 0 -0.38 30 30
HRAS 0.001 0.11 -10000 0 -0.32 30 30
mol:PIP3 -0.024 0.12 -10000 0 -0.37 30 30
SPRED1 0.007 0 -10000 0 -10000 0 0
SPRED2 0.007 0 -10000 0 -10000 0 0
GAB1 -0.023 0.13 -10000 0 -0.38 34 34
FOXO3 -0.013 0.12 -10000 0 -0.35 30 30
AKT1 -0.019 0.12 -10000 0 -0.38 30 30
BAD -0.013 0.12 -10000 0 -0.35 30 30
megakaryocyte differentiation -0.026 0.13 -10000 0 -0.38 34 34
GSK3B -0.013 0.12 -10000 0 -0.35 30 30
RAF1 0.008 0.091 -10000 0 -0.26 30 30
SHC1 0.007 0 -10000 0 -10000 0 0
STAT3 -0.023 0.13 -10000 0 -0.38 34 34
STAT1 -0.068 0.29 -10000 0 -0.86 34 34
HRAS/SPRED1 -0.027 0.079 -10000 0 -0.26 30 30
cell proliferation -0.024 0.13 -10000 0 -0.39 31 31
PIK3CA 0.007 0 -10000 0 -10000 0 0
TEC 0.007 0 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.13 -10000 0 -0.41 30 30
HRAS/SPRED2 -0.027 0.079 -10000 0 -0.26 30 30
LYN/TEC/p62DOK -0.04 0.11 -10000 0 -0.38 30 30
MAPK3 0.015 0.069 -10000 0 -0.19 30 30
STAP1 -0.023 0.13 -10000 0 -0.39 34 34
GRAP2 0.007 0 -10000 0 -10000 0 0
JAK2 -0.088 0.24 -10000 0 -0.74 34 34
STAT1 (dimer) -0.066 0.28 -10000 0 -0.85 34 34
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.04 0.11 -10000 0 -0.38 30 30
actin filament polymerization -0.023 0.13 -10000 0 -0.38 34 34
LYN 0.007 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.031 0.18 -10000 0 -0.53 34 34
PIK3R1 0.007 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.036 0.1 -10000 0 -0.35 30 30
PI3K -0.015 0.12 -10000 0 -0.38 30 30
PTEN 0.006 0.023 -10000 0 -0.4 1 1
SCF/KIT/EPO/EPOR -0.087 0.34 -10000 0 -1.1 30 30
MAPK8 -0.025 0.13 -10000 0 -0.41 30 30
STAT3 (dimer) -0.023 0.13 -10000 0 -0.38 34 34
positive regulation of transcription 0.015 0.058 -10000 0 -0.16 30 30
mol:GDP -0.035 0.099 -10000 0 -0.33 30 30
PIK3C2B -0.023 0.13 -10000 0 -0.38 34 34
CBL/CRKL -0.012 0.12 -10000 0 -0.36 30 30
FER -0.024 0.13 -10000 0 -0.38 34 34
SH2B3 -0.023 0.13 -10000 0 -0.38 34 34
PDPK1 -0.018 0.11 -10000 0 -0.34 30 30
SNAI2 -0.035 0.14 -10000 0 -0.44 31 31
positive regulation of cell proliferation -0.045 0.22 -10000 0 -0.65 34 34
KITLG 0.007 0.009 -10000 0 -10000 0 0
cell motility -0.045 0.22 -10000 0 -0.65 34 34
PTPN6 0.004 0.009 -10000 0 -10000 0 0
EPOR -0.002 0.093 -10000 0 -10000 0 0
STAT5A (dimer) -0.035 0.18 -10000 0 -0.54 34 34
SOCS1 0.007 0 -10000 0 -10000 0 0
cell migration 0.023 0.13 0.38 34 -10000 0 34
SOS1 0.007 0 -10000 0 -10000 0 0
EPO -0.023 0.11 -10000 0 -0.41 22 22
VAV1 0.007 0 -10000 0 -10000 0 0
GRB10 -0.024 0.13 -10000 0 -0.39 34 34
PTPN11 0.008 0.005 -10000 0 -10000 0 0
SCF/KIT -0.029 0.14 -10000 0 -0.41 34 34
GO:0007205 0.001 0.007 -10000 0 -10000 0 0
MAP2K1 0.013 0.075 -10000 0 -0.2 30 30
CBL 0.007 0 -10000 0 -10000 0 0
KIT -0.09 0.35 -10000 0 -1.1 30 30
MAP2K2 0.013 0.075 -10000 0 -0.2 30 30
SHC/Grb2/SOS1 -0.04 0.11 -10000 0 -0.38 30 30
STAT5A -0.037 0.19 -10000 0 -0.56 34 34
GRB2 0.007 0 -10000 0 -10000 0 0
response to radiation -0.034 0.14 -10000 0 -0.43 31 31
SHC/GRAP2 0 0 -10000 0 -10000 0 0
PTPRO -0.026 0.13 -10000 0 -0.39 34 34
SH2B2 -0.023 0.13 -10000 0 -0.38 34 34
DOK1 0.007 0 -10000 0 -10000 0 0
MATK -0.023 0.13 -10000 0 -0.38 34 34
CREBBP 0.01 0.033 -10000 0 -10000 0 0
BCL2 -0.016 0.17 -10000 0 -1.2 5 5
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.007 0 -9999 0 -10000 0 0
VLDLR 0.007 0 -9999 0 -10000 0 0
LRPAP1 0.007 0 -9999 0 -10000 0 0
NUDC 0.007 0 -9999 0 -10000 0 0
RELN/LRP8 -0.075 0.1 -9999 0 -0.22 102 102
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.007 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.054 0.1 -9999 0 -0.2 102 102
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.002 0.021 -9999 0 -0.25 2 2
IQGAP1 0.007 0 -9999 0 -10000 0 0
PLA2G7 -0.006 0.057 -9999 0 -0.25 16 16
CALM1 0.007 0 -9999 0 -10000 0 0
DYNLT1 0.007 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.009 -9999 0 -0.16 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.007 0 -9999 0 -10000 0 0
CDK5R1 0.007 0 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.002 0.038 -9999 0 -0.25 7 7
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.077 0.11 -9999 0 -0.23 102 102
YWHAE 0.007 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.028 0.083 -9999 0 -0.19 1 1
MAP1B -0.03 0.08 -9999 0 -0.25 37 37
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.038 0.089 -9999 0 -0.16 102 102
RELN -0.13 0.19 -9999 0 -0.4 102 102
PAFAH/LIS1 0.008 0.031 -9999 0 -10000 0 0
LIS1/CLIP170 0.015 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.037 0.052 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.049 0.098 -9999 0 -0.19 102 102
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.034 0.087 -9999 0 -0.2 1 1
LIS1/IQGAP1 0.015 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
PAFAH1B3 0.007 0 -9999 0 -10000 0 0
PAFAH1B2 0.007 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.005 0.053 -9999 0 -0.15 37 37
NDEL1/Katanin 60/Dynein heavy chain -0.045 0.064 -9999 0 -10000 0 0
LRP8 0.006 0.015 -9999 0 -0.25 1 1
NDEL1/Katanin 60 -0.028 0.083 -9999 0 -10000 0 0
P39/CDK5 -0.039 0.092 -9999 0 -0.17 102 102
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.015 0 -9999 0 -10000 0 0
CDK5 -0.045 0.094 -9999 0 -0.18 102 102
PPP2R5D 0.007 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.007 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.061 0.085 -9999 0 -0.18 102 102
RELN/VLDLR -0.066 0.093 -9999 0 -0.2 102 102
CDC42 0 0 -9999 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.004 0.1 -10000 0 -0.28 37 37
IKBKB 0.013 0.05 -10000 0 -10000 0 0
AKT1 0.004 0.069 0.17 1 -0.18 36 37
IKBKG 0.014 0.052 -10000 0 -10000 0 0
CALM1 -0.005 0.085 0.16 20 -0.23 31 51
PIK3CA 0.007 0 -10000 0 -10000 0 0
MAP3K1 -0.02 0.15 -10000 0 -0.42 36 36
MAP3K7 0.007 0 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.089 0.17 20 -0.24 31 51
DOK1 0.007 0 -10000 0 -10000 0 0
AP-1 0.004 0.068 0.13 16 -0.16 32 48
LYN 0.007 0 -10000 0 -10000 0 0
BLNK 0.006 0.015 -10000 0 -0.25 1 1
SHC1 0.007 0 -10000 0 -10000 0 0
BCR complex -0.034 0.089 -10000 0 -0.26 39 39
CD22 -0.055 0.15 -10000 0 -0.44 37 37
CAMK2G 0 0.081 0.16 20 -0.21 31 51
CSNK2A1 0.007 0 -10000 0 -10000 0 0
INPP5D 0.007 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.018 0.048 -10000 0 -10000 0 0
GO:0007205 -0.01 0.09 0.17 20 -0.25 31 51
SYK 0.007 0 -10000 0 -10000 0 0
ELK1 -0.005 0.086 0.16 20 -0.23 31 51
NFATC1 -0.014 0.11 -10000 0 -0.32 36 36
B-cell antigen/BCR complex -0.034 0.089 -10000 0 -0.26 39 39
PAG1/CSK 0 0 -10000 0 -10000 0 0
NFKBIB 0.012 0.019 -10000 0 -10000 0 0
HRAS -0.002 0.078 -10000 0 -0.21 31 31
NFKBIA 0.012 0.019 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.014 0.017 -10000 0 -10000 0 0
RasGAP/Csk -0.024 0.064 -10000 0 -0.19 38 38
mol:GDP -0.01 0.085 0.16 20 -0.23 31 51
PTEN 0.006 0.023 -10000 0 -0.4 1 1
CD79B -0.041 0.13 -10000 0 -0.4 36 36
NF-kappa-B/RelA/I kappa B alpha 0.015 0.017 -10000 0 -10000 0 0
GRB2 0.007 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.018 0.16 -10000 0 -0.44 36 36
PIK3R1 0.007 0 -10000 0 -10000 0 0
mol:IP3 -0.016 0.09 0.17 20 -0.25 31 51
CSK 0.007 0 -10000 0 -10000 0 0
FOS -0.013 0.09 0.16 18 -0.22 31 49
CHUK 0.014 0.052 -10000 0 -10000 0 0
IBTK 0.007 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.021 0.059 -10000 0 -0.2 31 31
PTPN6 -0.052 0.14 -10000 0 -0.42 37 37
RELA 0.007 0 -10000 0 -10000 0 0
BCL2A1 0.013 0.013 -10000 0 -10000 0 0
VAV2 -0.054 0.15 -10000 0 -0.45 36 36
ubiquitin-dependent protein catabolic process 0.014 0.019 -10000 0 -10000 0 0
BTK -0.001 0.003 -10000 0 -10000 0 0
CD19 -0.054 0.15 -10000 0 -0.44 36 36
MAP4K1 0.007 0 -10000 0 -10000 0 0
CD72 0.007 0 -10000 0 -10000 0 0
PAG1 0.007 0 -10000 0 -10000 0 0
MAPK14 -0.011 0.13 -10000 0 -0.36 36 36
SH3BP5 -0.026 0.11 -10000 0 -0.4 25 25
PIK3AP1 -0.006 0.1 0.19 20 -0.28 31 51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.001 0.057 -10000 0 -10000 0 0
RAF1 0.003 0.075 -10000 0 -0.2 31 31
RasGAP/p62DOK/SHIP -0.023 0.06 -10000 0 -0.18 38 38
CD79A 0.005 0.025 -10000 0 -0.25 3 3
re-entry into mitotic cell cycle 0.004 0.068 0.13 16 -0.16 32 48
RASA1 0.006 0.023 -10000 0 -0.4 1 1
MAPK3 0.012 0.066 -10000 0 -10000 0 0
MAPK1 0.012 0.066 -10000 0 -10000 0 0
CD72/SHP1 -0.025 0.14 -10000 0 -0.39 37 37
NFKB1 0.007 0 -10000 0 -10000 0 0
MAPK8 -0.012 0.13 -10000 0 -0.36 36 36
actin cytoskeleton organization -0.022 0.14 -10000 0 -0.39 36 36
NF-kappa-B/RelA 0.032 0.033 -10000 0 -10000 0 0
Calcineurin -0.02 0.058 -10000 0 -0.19 31 31
PI3K -0.04 0.11 -10000 0 -0.33 36 36
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.019 0.1 0.19 20 -0.29 31 51
SOS1 0.007 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.042 0.18 -10000 0 -0.52 36 36
DAPP1 -0.068 0.19 -10000 0 -0.57 36 36
cytokine secretion -0.012 0.11 -10000 0 -0.3 36 36
mol:DAG -0.016 0.09 0.17 20 -0.25 31 51
PLCG2 0.007 0 -10000 0 -10000 0 0
MAP2K1 0.007 0.071 -10000 0 -0.18 30 30
B-cell antigen/BCR complex/FcgammaRIIB -0.03 0.079 -10000 0 -0.24 37 37
mol:PI-3-4-5-P3 -0.029 0.081 0.21 1 -0.24 36 37
ETS1 0.005 0.076 0.16 20 -0.19 31 51
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.022 0.058 -10000 0 -0.18 36 36
B-cell antigen/BCR complex/LYN -0.054 0.14 -10000 0 -0.45 36 36
MALT1 0.007 0 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 -0.024 0.14 -10000 0 -0.41 36 36
B-cell antigen/BCR complex/LYN/SYK -0.047 0.13 -10000 0 -0.39 37 37
CARD11 -0.005 0.086 0.16 20 -0.23 31 51
FCGR2B 0.003 0.04 -10000 0 -0.4 3 3
PPP3CA 0.007 0 -10000 0 -10000 0 0
BCL10 0.007 0 -10000 0 -10000 0 0
IKK complex 0.013 0.024 -10000 0 -10000 0 0
PTPRC 0.006 0.023 -10000 0 -0.4 1 1
PDPK1 0.002 0.064 0.16 1 -0.17 36 37
PPP3CB 0.007 0 -10000 0 -10000 0 0
PPP3CC 0.007 0 -10000 0 -10000 0 0
POU2F2 0.013 0.012 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.002 0.016 -9999 0 -10000 0 0
BIRC5 -0.24 0.038 -9999 0 -0.25 297 297
NFKBIA -0.002 0.016 -9999 0 -10000 0 0
CPEB1 -0.1 0.18 -9999 0 -0.4 80 80
AKT1 -0.002 0.016 -9999 0 -10000 0 0
NDEL1 0.007 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.002 0.014 -9999 0 -10000 0 0
NDEL1/TACC3 0 0.015 -9999 0 -10000 0 0
GADD45A 0.007 0 -9999 0 -10000 0 0
GSK3B 0.001 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.002 0.016 -9999 0 -10000 0 0
MDM2 0.007 0 -9999 0 -10000 0 0
JUB 0.007 0 -9999 0 -10000 0 0
TPX2 -0.16 0.02 -9999 0 -0.16 300 300
TP53 0.004 0.01 -9999 0 -10000 0 0
DLG7 -0.008 0.016 -9999 0 -10000 0 0
AURKAIP1 0.007 0 -9999 0 -10000 0 0
ARHGEF7 0.007 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.004 0.017 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.012 -9999 0 -10000 0 0
AURKA -0.01 0.02 -9999 0 -10000 0 0
AURKB 0.019 0.009 -9999 0 -10000 0 0
CDC25B 0.001 0.012 -9999 0 -10000 0 0
G2/M transition checkpoint -0.005 0.012 -9999 0 -10000 0 0
mRNA polyadenylation -0.061 0.092 -9999 0 -0.21 80 80
Aurora A/CPEB -0.06 0.093 -9999 0 -0.21 80 80
Aurora A/TACC1/TRAP/chTOG 0.009 0.017 -9999 0 -0.19 1 1
BRCA1 0.007 0 -9999 0 -10000 0 0
centrosome duplication -0.002 0.016 -9999 0 -10000 0 0
regulation of centrosome cycle 0 0.015 -9999 0 -10000 0 0
spindle assembly 0.004 0.016 -9999 0 -0.19 1 1
TDRD7 0.007 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.023 -9999 0 -0.29 1 1
CENPA 0.027 0.016 -9999 0 -10000 0 0
Aurora A/PP2A -0.002 0.016 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.01 -9999 0 -10000 0 0
negative regulation of DNA binding 0.004 0.01 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.006 0.023 -9999 0 -0.4 1 1
Ajuba/Aurora A -0.002 0.014 -9999 0 -10000 0 0
mitotic prometaphase -0.024 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.02 -9999 0 -10000 0 0
TACC1 0.006 0.023 -9999 0 -0.4 1 1
TACC3 0.006 0.021 -9999 0 -0.25 2 2
Aurora A/Antizyme1 0.005 0.014 -9999 0 -10000 0 0
Aurora A/RasGAP -0.003 0.021 -9999 0 -0.24 1 1
OAZ1 0.007 0 -9999 0 -10000 0 0
RAN 0.007 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.001 0.003 -9999 0 -10000 0 0
GIT1 0.007 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.16 0.02 -9999 0 -0.16 300 300
PPP2R5D 0.007 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.12 0.021 -9999 0 -10000 0 0
PAK1 0.007 0 -9999 0 -10000 0 0
CKAP5 0.007 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.007 0 -9999 0 -10000 0 0
LAT2 -0.029 0.1 -9999 0 -0.24 44 44
AP1 -0.055 0.097 -9999 0 -0.35 16 16
mol:PIP3 -0.025 0.12 -9999 0 -0.27 44 44
IKBKB -0.006 0.075 -9999 0 -0.21 12 12
AKT1 -0.01 0.086 -9999 0 -0.28 13 13
IKBKG -0.006 0.075 -9999 0 -0.21 12 12
MS4A2 -0.05 0.14 -9999 0 -0.4 43 43
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.007 0.001 -9999 0 -10000 0 0
MAP3K1 -0.011 0.094 -9999 0 -0.32 10 10
mol:Ca2+ -0.017 0.098 -9999 0 -0.21 44 44
LYN 0.007 0.003 -9999 0 -10000 0 0
CBLB -0.029 0.1 -9999 0 -0.24 44 44
SHC1 0.007 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.005 0.03 -9999 0 -0.2 7 7
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.007 0 -9999 0 -10000 0 0
PLD2 -0.03 0.097 -9999 0 -0.22 46 46
PTPN13 -0.03 0.11 -9999 0 -0.38 11 11
PTPN11 0.007 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.005 0.09 -9999 0 -0.26 13 13
SYK 0.007 0.003 -9999 0 -10000 0 0
GRB2 0.007 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.056 0.11 -9999 0 -0.27 44 44
LAT -0.029 0.1 -9999 0 -0.24 44 44
PAK2 -0.017 0.1 -9999 0 -0.34 11 11
NFATC2 -0.033 0.089 -9999 0 -0.3 19 19
HRAS -0.023 0.11 -9999 0 -0.25 44 44
GAB2 0.005 0.033 -9999 0 -0.4 2 2
PLA2G1B 0.018 0.013 -9999 0 -10000 0 0
Fc epsilon R1 -0.06 0.11 -9999 0 -0.25 74 74
Antigen/IgE/Fc epsilon R1 -0.053 0.1 -9999 0 -0.22 74 74
mol:GDP -0.028 0.11 -9999 0 -0.26 44 44
JUN 0.006 0.023 -9999 0 -0.4 1 1
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.001 -9999 0 -10000 0 0
FOS -0.022 0.11 -9999 0 -0.4 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.052 0.099 -9999 0 -0.25 44 44
CHUK -0.006 0.075 -9999 0 -0.21 12 12
KLRG1 -0.027 0.094 -9999 0 -0.2 44 44
VAV1 -0.029 0.1 -9999 0 -0.24 44 44
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.029 0.1 -9999 0 -0.24 44 44
negative regulation of mast cell degranulation -0.021 0.088 -9999 0 -0.31 11 11
BTK -0.033 0.11 -9999 0 -0.27 44 44
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.039 0.12 -9999 0 -0.23 75 75
GAB2/PI3K/SHP2 -0.041 0.078 -9999 0 -0.29 14 14
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.031 0.1 -9999 0 -0.23 41 41
RAF1 0.012 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.049 0.095 -9999 0 -0.23 47 47
FCER1G 0.01 0.007 -9999 0 -10000 0 0
FCER1A -0.049 0.14 -9999 0 -0.41 41 41
Antigen/IgE/Fc epsilon R1/Fyn -0.051 0.095 -9999 0 -0.2 77 77
MAPK3 0.018 0.013 -9999 0 -10000 0 0
MAPK1 0.018 0.013 -9999 0 -10000 0 0
NFKB1 0.007 0 -9999 0 -10000 0 0
MAPK8 0 0.055 -9999 0 -0.51 2 2
DUSP1 -0.001 0.057 -9999 0 -0.4 6 6
NF-kappa-B/RelA -0.02 0.037 -9999 0 -0.14 10 10
actin cytoskeleton reorganization -0.034 0.11 -9999 0 -0.41 10 10
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.044 0.086 -9999 0 -0.34 11 11
FER -0.029 0.1 -9999 0 -0.24 45 45
RELA 0.007 0 -9999 0 -10000 0 0
ITK -0.014 0.025 -9999 0 -10000 0 0
SOS1 0.007 0 -9999 0 -10000 0 0
PLCG1 -0.025 0.11 -9999 0 -0.26 44 44
cytokine secretion -0.015 0.027 -9999 0 -10000 0 0
SPHK1 -0.029 0.1 -9999 0 -0.24 44 44
PTK2 -0.036 0.12 -9999 0 -0.42 10 10
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.058 0.11 -9999 0 -0.28 44 44
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.022 0.12 -9999 0 -0.26 44 44
MAP2K2 0.015 0.013 -9999 0 -10000 0 0
MAP2K1 0.015 0.013 -9999 0 -10000 0 0
MAP2K7 0.007 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.038 0.074 -9999 0 -0.3 11 11
MAP2K4 0.01 0.007 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.054 0.1 -9999 0 -0.22 74 74
mol:Choline -0.029 0.096 -9999 0 -0.21 46 46
SHC/Grb2/SOS1 -0.044 0.084 -9999 0 -0.28 17 17
FYN 0.001 0.052 -9999 0 -0.4 5 5
DOK1 0.007 0 -9999 0 -10000 0 0
PXN -0.029 0.11 -9999 0 -0.39 10 10
HCLS1 -0.029 0.1 -9999 0 -0.24 44 44
PRKCB -0.017 0.098 -9999 0 -0.21 45 45
FCGR2B 0.003 0.04 -9999 0 -0.4 3 3
IGHE 0 0.003 -9999 0 -10000 0 0
KLRG1/SHIP -0.021 0.09 -9999 0 -0.32 11 11
LCP2 0.007 0 -9999 0 -10000 0 0
PLA2G4A -0.034 0.11 -9999 0 -0.25 47 47
RASA1 0.006 0.023 -9999 0 -0.4 1 1
mol:Phosphatidic acid -0.029 0.096 -9999 0 -0.21 46 46
IKK complex 0.004 0.06 -9999 0 -0.16 11 11
WIPF1 0.007 0 -9999 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.007 0 -9999 0 -10000 0 0
CCL5 0.007 0 -9999 0 -10000 0 0
SDCBP 0.007 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.044 0.053 -9999 0 -0.21 26 26
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 -0.037 0.05 -9999 0 -0.2 24 24
Syndecan-1/Syntenin -0.037 0.05 -9999 0 -0.2 24 24
MAPK3 -0.025 0.046 -9999 0 -0.19 4 4
HGF/MET -0.037 0.094 -9999 0 -0.27 41 41
TGFB1/TGF beta receptor Type II 0.007 0 -9999 0 -10000 0 0
BSG 0.007 0 -9999 0 -10000 0 0
keratinocyte migration -0.036 0.05 -9999 0 -0.2 24 24
Syndecan-1/RANTES -0.037 0.05 -9999 0 -0.2 24 24
Syndecan-1/CD147 -0.031 0.049 -9999 0 -0.19 24 24
Syndecan-1/Syntenin/PIP2 -0.037 0.047 -9999 0 -0.19 24 24
LAMA5 0.007 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.036 0.046 -9999 0 -0.19 24 24
MMP7 -0.029 0.12 -9999 0 -0.39 28 28
HGF -0.049 0.14 -9999 0 -0.4 42 42
Syndecan-1/CASK -0.041 0.05 -9999 0 -0.2 26 26
Syndecan-1/HGF/MET -0.057 0.082 -9999 0 -0.23 42 42
regulation of cell adhesion -0.02 0.045 -9999 0 -10000 0 0
HPSE 0.007 0 -9999 0 -10000 0 0
positive regulation of cell migration -0.044 0.053 -9999 0 -0.21 26 26
SDC1 -0.044 0.053 -9999 0 -0.21 26 26
Syndecan-1/Collagen -0.044 0.053 -9999 0 -0.21 26 26
PPIB 0.007 0 -9999 0 -10000 0 0
MET 0.007 0 -9999 0 -10000 0 0
PRKACA 0.007 0 -9999 0 -10000 0 0
MMP9 -0.034 0.094 -9999 0 -0.25 49 49
MAPK1 -0.025 0.046 -9999 0 -0.19 4 4
homophilic cell adhesion -0.044 0.053 -9999 0 -0.21 26 26
MMP1 -0.065 0.12 -9999 0 -0.25 86 86
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.051 0.075 -9999 0 -0.21 38 38
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG 0.005 0.021 -9999 0 -0.25 2 2
SMAD9 -0.062 0.15 -9999 0 -0.46 34 34
SMAD4 0.006 0.023 -9999 0 -0.4 1 1
SMAD5 -0.006 0.075 -9999 0 -0.27 5 5
BMP7/USAG1 -0.056 0.082 -9999 0 -0.17 102 102
SMAD5/SKI -0.001 0.071 -9999 0 -0.3 3 3
SMAD1 0.022 0.015 -9999 0 -10000 0 0
BMP2 0.006 0.023 -9999 0 -0.4 1 1
SMAD1/SMAD1/SMAD4 0 0.009 -9999 0 -10000 0 0
BMPR1A 0.005 0.033 -9999 0 -0.4 2 2
BMPR1B -0.031 0.12 -9999 0 -0.4 29 29
BMPR1A-1B/BAMBI -0.031 0.083 -9999 0 -0.24 39 39
AHSG 0 0 -9999 0 -10000 0 0
CER1 0.001 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.01 0.046 -9999 0 -0.23 13 13
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.007 0.079 -9999 0 -0.33 5 5
BMP2-4 (homodimer) -0.012 0.055 -9999 0 -0.27 13 13
RGMB 0.007 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.022 0.061 -9999 0 -0.2 33 33
RGMA -0.019 0.1 -9999 0 -0.4 20 20
SMURF1 0.007 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.014 0.081 -9999 0 -0.34 5 5
BMP2-4/USAG1 -0.021 0.058 -9999 0 -0.24 13 13
SMAD6/SMURF1/SMAD5 -0.001 0.071 -9999 0 -0.3 3 3
SOSTDC1 -0.018 0.074 -9999 0 -0.25 28 28
BMP7/BMPR2/BMPR1A-1B -0.048 0.079 -9999 0 -0.24 31 31
SKI 0.007 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.003 0.04 -9999 0 -0.4 3 3
HFE2 0.002 0.003 -9999 0 -10000 0 0
ZFYVE16 0.007 0 -9999 0 -10000 0 0
MAP3K7 0.007 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.081 0.12 -9999 0 -0.24 102 102
SMAD5/SMAD5/SMAD4 -0.002 0.074 -9999 0 -0.36 3 3
MAPK1 0.007 0 -9999 0 -10000 0 0
TAK1/TAB family -0.027 0.059 -9999 0 -0.29 5 5
BMP7 (homodimer) -0.06 0.11 -9999 0 -0.25 79 79
NUP214 0.007 0 -9999 0 -10000 0 0
BMP6/FETUA -0.003 0.028 -9999 0 -0.28 3 3
SMAD1/SKI 0.026 0.015 -9999 0 -10000 0 0
SMAD6 0.007 0 -9999 0 -10000 0 0
CTDSP2 0.007 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.01 0.046 -9999 0 -0.23 13 13
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.001 0.052 -9999 0 -0.4 5 5
BMPR2 (homodimer) 0.007 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.028 0.082 -9999 0 -0.27 31 31
CHRDL1 -0.32 0.16 -9999 0 -0.4 240 240
ENDOFIN/SMAD1 0.026 0.015 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.001 0.002 -9999 0 -10000 0 0
SMAD6/SMURF1 0.007 0 -9999 0 -10000 0 0
BAMBI -0.009 0.079 -9999 0 -0.4 12 12
SMURF2 0.007 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.19 0.099 -9999 0 -0.23 244 244
BMP2-4/GREM1 -0.013 0.056 -9999 0 -0.24 17 17
SMAD7 0.007 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.042 0.14 -9999 0 -0.43 35 35
SMAD1/SMAD6 0.026 0.015 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.06 0.11 -9999 0 -0.25 79 79
BMP6 0.003 0.04 -9999 0 -0.4 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.009 0.075 -9999 0 -0.32 5 5
PPM1A 0.007 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.015 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.007 0 -9999 0 -10000 0 0
PPP1CA 0.007 0 -9999 0 -10000 0 0
XIAP 0.007 0 -9999 0 -10000 0 0
CTDSP1 0.007 0 -9999 0 -10000 0 0
PPP1R15A 0.007 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.022 0.096 -9999 0 -0.36 10 10
CHRD -0.12 0.19 -9999 0 -0.4 98 98
BMPR2 0.007 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.016 0.085 -9999 0 -0.36 5 5
BMP4 -0.009 0.079 -9999 0 -0.4 12 12
FST -0.012 0.078 -9999 0 -0.3 19 19
BMP2-4/NOG -0.01 0.046 -9999 0 -0.22 13 13
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.043 0.072 -9999 0 -0.22 31 31
Nectin adhesion 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
PDGFRB -0.014 0.091 -9999 0 -0.4 16 16
alphaV beta3 Integrin -0.031 0.086 -9999 0 -0.27 34 34
PTK2 -0.037 0.1 -9999 0 -0.38 20 20
positive regulation of JNK cascade -0.021 0.07 -9999 0 -0.28 20 20
CDC42/GDP 0 0.1 -9999 0 -0.38 20 20
Rac1/GDP 0.001 0.1 -9999 0 -0.37 20 20
RAP1B 0.007 0 -9999 0 -10000 0 0
RAP1A 0.007 0 -9999 0 -10000 0 0
CTNNB1 0.007 0 -9999 0 -10000 0 0
CDC42/GTP -0.025 0.086 -9999 0 -0.34 20 20
nectin-3/I-afadin -0.018 0.068 -9999 0 -0.27 20 20
RAPGEF1 -0.005 0.11 -9999 0 -0.41 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.012 0.12 -9999 0 -0.47 20 20
PDGFB-D/PDGFRB -0.014 0.091 -9999 0 -0.4 16 16
TLN1 -0.009 0.084 -9999 0 -0.29 20 20
Rap1/GTP -0.022 0.074 -9999 0 -0.3 20 20
IQGAP1 0.007 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.018 0.068 -9999 0 -0.27 20 20
PVR 0.007 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.007 0 -9999 0 -10000 0 0
mol:GDP -0.006 0.12 -9999 0 -0.46 20 20
MLLT4 0.007 0 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
PI3K -0.021 0.062 -9999 0 -0.19 34 34
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.017 0.049 -9999 0 -0.16 32 32
positive regulation of lamellipodium assembly -0.022 0.074 -9999 0 -0.3 20 20
PVRL1 -0.02 0.078 -9999 0 -0.25 32 32
PVRL3 -0.02 0.1 -9999 0 -0.4 20 20
PVRL2 0.007 0 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
CDH1 -0.22 0.086 -9999 0 -0.25 264 264
CLDN1 -0.014 0.091 -9999 0 -0.4 16 16
JAM-A/CLDN1 -0.023 0.065 -9999 0 -0.2 35 35
SRC -0.038 0.13 -9999 0 -0.52 20 20
ITGB3 -0.038 0.13 -9999 0 -0.4 34 34
nectin-1(dimer)/I-afadin/I-afadin -0.017 0.049 -9999 0 -0.16 32 32
FARP2 -0.009 0.12 -9999 0 -0.45 20 20
RAC1 0.007 0 -9999 0 -10000 0 0
CTNNA1 0.007 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.015 0.055 -9999 0 -0.22 20 20
nectin-1/I-afadin -0.017 0.049 -9999 0 -0.16 32 32
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 -0.028 0.064 -9999 0 -0.22 20 20
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.007 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.021 0.07 -9999 0 -0.28 20 20
alphaV/beta3 Integrin/Talin -0.02 0.11 -9999 0 -0.32 23 23
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 -0.014 0.089 -9999 0 -0.31 20 20
VAV2 -0.009 0.12 -9999 0 -0.46 20 20
RAP1/GDP -0.025 0.087 -9999 0 -0.35 20 20
ITGAV 0.007 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.015 0.055 -9999 0 -0.22 20 20
nectin-3(dimer)/I-afadin/I-afadin -0.018 0.068 -9999 0 -0.27 20 20
Rac1/GTP -0.026 0.089 -9999 0 -0.36 20 20
PTPRM -0.032 0.094 -9999 0 -0.26 37 37
E-cadherin/beta catenin/alpha catenin -0.085 0.045 -9999 0 -0.19 29 29
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.007 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.007 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.003 0.02 -9999 0 -0.16 5 5
STXBP1 0.006 0.023 -9999 0 -0.4 1 1
ACh/CHRNA1 -0.021 0.043 -9999 0 -0.17 6 6
RAB3GAP2/RIMS1/UNC13B -0.002 0.016 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.001 0.032 -9999 0 -0.25 5 5
mol:ACh -0.03 0.051 -9999 0 -0.1 100 100
RAB3GAP2 0.007 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.055 -9999 0 -0.24 2 2
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.021 0.043 -9999 0 -0.16 6 6
UNC13B 0.007 0 -9999 0 -10000 0 0
CHRNA1 0.001 0.036 -9999 0 -0.25 6 6
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.12 0.14 -9999 0 -0.28 129 129
SNAP25 -0.078 0.12 -9999 0 -0.25 100 100
VAMP2 0.004 0 -9999 0 -10000 0 0
SYT1 -0.17 0.2 -9999 0 -0.4 129 129
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.01 0.014 -9999 0 -0.23 1 1
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.055 -9999 0 -0.24 2 2
S1P3 pathway

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
PDGFRB -0.014 0.091 -9999 0 -0.4 16 16
mol:S1P 0 0.006 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.035 0.095 -9999 0 -0.2 72 72
GNAO1 0.002 0.047 -9999 0 -0.41 4 4
S1P/S1P3/G12/G13 -0.023 0.064 -9999 0 -0.2 33 33
AKT1 -0.051 0.12 -9999 0 -0.51 16 16
AKT3 -0.061 0.25 -9999 0 -1.1 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.014 0.091 -9999 0 -0.4 16 16
GNAI2 0.007 0.005 -9999 0 -10000 0 0
GNAI3 0.007 0.004 -9999 0 -10000 0 0
GNAI1 0.006 0.024 -9999 0 -0.4 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.037 0.13 -9999 0 -0.4 33 33
S1PR2 0.007 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.054 0.13 -9999 0 -0.3 44 44
MAPK3 -0.047 0.12 -9999 0 -0.35 28 28
MAPK1 -0.047 0.12 -9999 0 -0.35 28 28
JAK2 -0.046 0.13 -9999 0 -0.35 28 28
CXCR4 -0.047 0.12 -9999 0 -0.35 28 28
FLT1 0.007 0.025 -9999 0 -0.42 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC -0.047 0.12 -9999 0 -0.35 28 28
S1P/S1P3/Gi -0.054 0.13 -9999 0 -0.3 44 44
RAC1 0.007 0 -9999 0 -10000 0 0
RhoA/GTP -0.065 0.11 -9999 0 -0.34 28 28
VEGFA 0.008 0.005 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.028 0.09 -9999 0 -0.22 19 19
VEGFR1 homodimer/VEGFA homodimer 0.012 0.022 -9999 0 -0.3 1 1
RHOA 0.007 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.072 0.13 -9999 0 -0.24 104 104
GNAQ 0.007 0 -9999 0 -10000 0 0
GNAZ -0.084 0.17 -9999 0 -0.4 68 68
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.11 0.18 -9999 0 -0.4 88 88
GNA15 -0.011 0.066 -9999 0 -0.25 22 22
GNA12 0.007 0 -9999 0 -10000 0 0
GNA13 0.007 0 -9999 0 -10000 0 0
GNA11 0.005 0.033 -9999 0 -0.4 2 2
Rac1/GTP -0.065 0.11 -9999 0 -0.34 28 28
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.007 0 -9999 0 -10000 0 0
SPHK1 0.007 0 -9999 0 -10000 0 0
GNAI2 0.007 0 -9999 0 -10000 0 0
mol:S1P 0.013 0 -9999 0 -10000 0 0
GNAO1 0.002 0.046 -9999 0 -0.4 4 4
mol:Sphinganine-1-P 0.013 0 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0 -9999 0 -10000 0 0
GNAI3 0.007 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.037 0.13 -9999 0 -0.4 33 33
S1PR2 0.007 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0 -9999 0 -10000 0 0
S1PR5 -0.078 0.12 -9999 0 -0.25 101 101
S1PR4 0.007 0 -9999 0 -10000 0 0
GNAI1 0.006 0.023 -9999 0 -0.4 1 1
S1P/S1P5/G12 -0.034 0.049 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.073 0.14 -9999 0 -0.25 104 104
S1P/S1P4/Gi -0.022 0.085 -9999 0 -0.17 72 72
GNAQ 0.007 0 -9999 0 -10000 0 0
GNAZ -0.084 0.17 -9999 0 -0.4 68 68
GNA14 -0.11 0.18 -9999 0 -0.4 88 88
GNA15 -0.011 0.066 -9999 0 -0.25 22 22
GNA12 0.007 0 -9999 0 -10000 0 0
GNA13 0.007 0 -9999 0 -10000 0 0
GNA11 0.005 0.033 -9999 0 -0.4 2 2
ABCC1 0.007 0 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0 0 -10000 0 -10000 0 0
cell-cell adhesion 0.033 0.066 0.3 6 -10000 0 6
Ephrin B/EPHB2/RasGAP -0.032 0.068 -10000 0 -0.18 54 54
ITSN1 0.007 0 -10000 0 -10000 0 0
PIK3CA 0.007 0 -10000 0 -10000 0 0
SHC1 0.007 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.001 0.013 -10000 0 -0.23 1 1
Ephrin B1/EPHB1 -0.012 0.051 -10000 0 -0.22 17 17
HRAS/GDP -0.039 0.079 -10000 0 -0.2 52 52
Ephrin B/EPHB1/GRB7 -0.044 0.085 -10000 0 -0.2 63 63
Endophilin/SYNJ1 -0.011 0.072 -10000 0 -0.17 53 53
KRAS 0.007 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.041 0.084 -10000 0 -0.2 63 63
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.007 0 -10000 0 -10000 0 0
GRB7 0.001 0.041 -10000 0 -0.25 8 8
PAK1 -0.019 0.091 -10000 0 -0.35 7 7
HRAS 0.007 0 -10000 0 -10000 0 0
RRAS -0.011 0.073 -10000 0 -0.17 53 53
DNM1 0.007 0 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.022 0.088 -10000 0 -0.19 63 63
lamellipodium assembly -0.033 0.066 -10000 0 -0.3 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.021 0.09 -10000 0 -0.19 63 63
PIK3R1 0.007 0 -10000 0 -10000 0 0
EPHB2 0.007 0 -10000 0 -10000 0 0
EPHB3 0.006 0.023 -10000 0 -0.4 1 1
EPHB1 -0.015 0.092 -10000 0 -0.39 17 17
EPHB4 0.007 0 -10000 0 -10000 0 0
mol:GDP -0.041 0.084 -10000 0 -0.21 52 52
Ephrin B/EPHB2 -0.032 0.07 -10000 0 -0.18 53 53
Ephrin B/EPHB3 -0.033 0.072 -10000 0 -0.19 53 53
JNK cascade 0.012 0.045 -10000 0 -0.18 16 16
Ephrin B/EPHB1 -0.042 0.086 -10000 0 -0.2 63 63
RAP1/GDP -0.036 0.073 -10000 0 -0.29 6 6
EFNB2 0.007 0 -10000 0 -10000 0 0
EFNB3 -0.064 0.15 -10000 0 -0.4 53 53
EFNB1 0.007 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.011 0.045 -10000 0 -0.2 16 16
RAP1B 0.007 0 -10000 0 -10000 0 0
RAP1A 0.007 0 -10000 0 -10000 0 0
CDC42/GTP -0.04 0.081 -10000 0 -0.35 6 6
Rap1/GTP -0.032 0.066 -10000 0 -0.3 6 6
axon guidance 0 0 -10000 0 -10000 0 0
MAPK3 -0.009 0.081 -10000 0 -0.32 6 6
MAPK1 -0.009 0.081 -10000 0 -0.32 6 6
Rac1/GDP -0.015 0.088 -10000 0 -0.2 52 52
actin cytoskeleton reorganization -0.029 0.059 -10000 0 -0.25 6 6
CDC42/GDP -0.015 0.088 -10000 0 -0.2 52 52
PI3K 0 0 -10000 0 -10000 0 0
EFNA5 0.007 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.016 0.081 -10000 0 -0.19 53 53
CDC42 0.007 0 -10000 0 -10000 0 0
RAS family/GTP -0.032 0.065 -10000 0 -0.3 6 6
PTK2 0.003 0.013 -10000 0 -10000 0 0
MAP4K4 0.012 0.045 -10000 0 -0.18 16 16
SRC 0.007 0 -10000 0 -10000 0 0
KALRN -0.018 0.099 -10000 0 -0.4 19 19
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.007 0.091 -10000 0 -0.28 13 13
MAP2K1 -0.015 0.085 -10000 0 -0.24 16 16
WASL 0.007 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.011 0.044 -10000 0 -0.2 16 16
cell migration -0.02 0.1 -10000 0 -0.22 62 62
NRAS 0.007 0 -10000 0 -10000 0 0
SYNJ1 -0.011 0.073 -10000 0 -0.17 53 53
PXN 0.007 0 -10000 0 -10000 0 0
TF -0.012 0.076 -10000 0 -0.23 7 7
HRAS/GTP -0.035 0.071 -10000 0 -0.32 6 6
Ephrin B1/EPHB1-2 -0.011 0.045 -10000 0 -0.2 16 16
cell adhesion mediated by integrin 0.031 0.072 0.18 53 -10000 0 53
RAC1 0.007 0 -10000 0 -10000 0 0
mol:GTP -0.038 0.077 -10000 0 -0.34 6 6
RAC1-CDC42/GTP -0.032 0.067 -10000 0 -0.3 7 7
RASA1 0.006 0.023 -10000 0 -0.4 1 1
RAC1-CDC42/GDP -0.036 0.073 -10000 0 -0.29 6 6
ruffle organization -0.004 0.08 -10000 0 -0.3 6 6
NCK1 0.007 0 -10000 0 -10000 0 0
receptor internalization -0.006 0.07 -10000 0 -0.16 53 53
Ephrin B/EPHB2/KALRN -0.043 0.086 -10000 0 -0.2 65 65
ROCK1 0.014 0.012 -10000 0 -0.2 1 1
RAS family/GDP -0.03 0.061 -10000 0 -0.25 6 6
Rac1/GTP -0.034 0.07 -10000 0 -0.32 6 6
Ephrin B/EPHB1/Src/Paxillin -0.027 0.098 -10000 0 -0.21 63 63
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.16 0.2 -9999 0 -0.4 128 128
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.007 0 -9999 0 -10000 0 0
TCEB1 0.007 0 -9999 0 -10000 0 0
HIF1A/p53 0.019 0.002 -9999 0 -10000 0 0
HIF1A 0.015 0.002 -9999 0 -10000 0 0
COPS5 0.007 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.007 0 -9999 0 -10000 0 0
CDKN2A -0.23 0.06 -9999 0 -0.25 286 286
ARNT/IPAS -0.12 0.14 -9999 0 -0.27 128 128
HIF1AN 0.007 0 -9999 0 -10000 0 0
GNB2L1 0.007 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.019 0.002 -9999 0 -10000 0 0
CUL2 0.007 0 -9999 0 -10000 0 0
OS9 0.007 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.019 0.002 -9999 0 -10000 0 0
PHD1-3/OS9 0 0.006 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
VHL 0.007 0 -9999 0 -10000 0 0
HSP90AA1 0.007 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.019 0.002 -9999 0 -10000 0 0
EGLN3 0.006 0.015 -9999 0 -0.25 1 1
EGLN2 0.007 0 -9999 0 -10000 0 0
EGLN1 0.007 0 -9999 0 -10000 0 0
TP53 0.007 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.022 0.001 -9999 0 -10000 0 0
ARNT 0.007 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.007 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.082 0.025 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.026 0.081 0.26 29 -10000 0 29
KIRREL -0.025 0.11 -10000 0 -0.41 23 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.026 0.081 -10000 0 -0.27 29 29
PLCG1 0.007 0 -10000 0 -10000 0 0
ARRB2 0.007 0 -10000 0 -10000 0 0
WASL 0.007 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.017 0.057 -10000 0 -0.21 23 23
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.001 0.059 -10000 0 -0.2 23 23
FYN -0.01 0.06 -10000 0 -0.19 28 28
mol:Ca2+ -0.017 0.056 -10000 0 -0.2 23 23
mol:DAG -0.017 0.056 -10000 0 -0.21 23 23
NPHS2 -0.002 0.012 -10000 0 -10000 0 0
mol:IP3 -0.017 0.056 -10000 0 -0.21 23 23
regulation of endocytosis -0.014 0.054 -10000 0 -0.18 23 23
Nephrin/NEPH1/podocin/Cholesterol -0.019 0.058 -10000 0 -0.21 23 23
establishment of cell polarity -0.026 0.081 -10000 0 -0.26 29 29
Nephrin/NEPH1/podocin/NCK1-2 -0.012 0.051 -10000 0 -0.18 23 23
Nephrin/NEPH1/beta Arrestin2 -0.003 0.057 -10000 0 -0.18 23 23
NPHS1 -0.006 0.042 -10000 0 -0.25 8 8
Nephrin/NEPH1/podocin -0.016 0.058 -10000 0 -0.19 28 28
TJP1 0.007 0 -10000 0 -10000 0 0
NCK1 0.007 0 -10000 0 -10000 0 0
NCK2 0.007 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.017 0.057 -10000 0 -0.21 23 23
CD2AP 0.007 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.017 0.057 -10000 0 -0.21 23 23
GRB2 0.007 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.007 0.058 -10000 0 -0.19 26 26
cytoskeleton organization 0.002 0.062 -10000 0 -0.21 23 23
Nephrin/NEPH1 -0.018 0.055 -10000 0 -0.2 23 23
Nephrin/NEPH1/ZO-1 -0.019 0.061 -10000 0 -0.22 23 23
Signaling events mediated by PTP1B

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
PDGFRB -0.014 0.091 -10000 0 -0.4 16 16
Jak2/Leptin Receptor -0.13 0.1 -10000 0 -0.26 61 61
PTP1B/AKT1 0.005 0.044 -10000 0 -0.2 6 6
FYN 0.001 0.052 -10000 0 -0.4 5 5
p210 bcr-abl/PTP1B 0.002 0.048 -10000 0 -0.23 6 6
EGFR 0.002 0.041 -10000 0 -0.31 5 5
EGF/EGFR -0.02 0.059 -10000 0 -0.22 21 21
CSF1 0.005 0.033 -10000 0 -0.4 2 2
AKT1 0.007 0 -10000 0 -10000 0 0
INSR 0.007 0 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.014 0.087 -10000 0 -0.24 33 33
Insulin Receptor/Insulin -0.01 0.028 -10000 0 -10000 0 0
HCK 0.007 0 -10000 0 -10000 0 0
CRK 0.007 0 -10000 0 -10000 0 0
TYK2 0.006 0.046 -10000 0 -0.21 6 6
EGF -0.013 0.089 -10000 0 -0.41 15 15
YES1 0.007 0 -10000 0 -10000 0 0
CAV1 -0.007 0.069 -10000 0 -0.25 11 11
TXN 0.006 0.014 -10000 0 -0.24 1 1
PTP1B/IRS1/GRB2 0.001 0.06 -10000 0 -0.2 18 18
cell migration -0.002 0.048 0.23 6 -10000 0 6
STAT3 0.007 0 -10000 0 -10000 0 0
PRLR -0.2 0.2 -10000 0 -0.4 156 156
ITGA2B 0.003 0.036 -10000 0 -0.35 3 3
CSF1R 0.005 0.033 -10000 0 -0.4 2 2
Prolactin Receptor/Prolactin -0.2 0.17 -10000 0 -0.32 191 191
FGR 0.007 0 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.006 0.046 -10000 0 -0.22 6 6
Crk/p130 Cas 0.01 0.044 -10000 0 -0.2 6 6
DOK1 0.001 0.069 -10000 0 -0.28 12 12
JAK2 -0.13 0.11 -10000 0 -0.26 71 71
Jak2/Leptin Receptor/Leptin -0.035 0.044 -10000 0 -0.23 3 3
PIK3R1 0.007 0 -10000 0 -10000 0 0
PTPN1 0.002 0.048 -10000 0 -0.23 6 6
LYN 0.007 0 -10000 0 -10000 0 0
CDH2 -0.035 0.12 -10000 0 -0.4 32 32
SRC 0.01 0.02 -10000 0 -10000 0 0
ITGB3 -0.039 0.13 -10000 0 -0.4 34 34
CAT1/PTP1B 0.013 0.049 -10000 0 -0.27 3 3
CAPN1 0.007 0.001 -10000 0 -10000 0 0
CSK 0.007 0 -10000 0 -10000 0 0
PI3K -0.008 0.024 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.031 0.04 -10000 0 -0.22 1 1
negative regulation of transcription -0.13 0.11 -10000 0 -0.25 73 73
FCGR2A 0.007 0 -10000 0 -10000 0 0
FER 0.006 0.024 -10000 0 -0.41 1 1
alphaIIb/beta3 Integrin -0.033 0.092 -10000 0 -0.28 36 36
BLK -0.04 0.098 -10000 0 -0.25 55 55
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.007 0.001 -10000 0 -10000 0 0
LEPR -0.005 0.069 -10000 0 -0.4 9 9
BCAR1 0.007 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.007 0 -10000 0 -10000 0 0
mol:NADPH 0 0.001 -10000 0 -10000 0 0
TRPV6 0.015 0.033 -10000 0 -0.23 3 3
PRL -0.09 0.17 -10000 0 -0.4 69 69
SOCS3 0.02 0.013 -10000 0 -10000 0 0
SPRY2 0.003 0.041 -10000 0 -0.4 3 3
Insulin Receptor/Insulin/IRS1 -0.011 0.048 -10000 0 -0.23 14 14
CSF1/CSF1R 0.007 0.051 -10000 0 -0.22 7 7
Ras protein signal transduction 0.008 0.015 -10000 0 -10000 0 0
IRS1 -0.011 0.085 -10000 0 -0.4 14 14
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.016 0.07 -10000 0 -0.25 25 25
STAT5B -0.048 0.058 -10000 0 -0.24 8 8
STAT5A -0.048 0.058 -10000 0 -0.24 8 8
GRB2 0.007 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.074 -10000 0 -0.26 18 18
CSN2 -0.091 0.076 -10000 0 -10000 0 0
PIK3CA 0.007 0 -10000 0 -10000 0 0
LAT 0.01 0.02 -10000 0 -10000 0 0
YBX1 0.012 0.001 -10000 0 -10000 0 0
LCK 0.007 0 -10000 0 -10000 0 0
SHC1 0.007 0 -10000 0 -10000 0 0
NOX4 -0.007 0.073 -10000 0 -0.4 10 10
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.007 0 -9999 0 -10000 0 0
EGFR 0.002 0.041 -9999 0 -0.31 5 5
EGF/EGFR -0.038 0.078 -9999 0 -0.19 61 61
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.011 0.042 -9999 0 -0.18 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.054 0.15 -9999 0 -0.4 46 46
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.013 0.088 -9999 0 -0.4 15 15
EGF/EGFR dimer/SHC -0.014 0.052 -9999 0 -0.22 17 17
mol:GDP -0.011 0.042 -9999 0 -0.18 17 17
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.006 0.023 -9999 0 -0.4 1 1
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.01 0.037 -9999 0 -0.16 17 17
SHC1 0.007 0 -9999 0 -10000 0 0
HRAS/GDP -0.01 0.038 -9999 0 -0.16 17 17
FRAP1 0.009 0.045 -9999 0 -0.17 17 17
EGF/EGFR dimer -0.017 0.064 -9999 0 -0.26 20 20
SOS1 0.007 0 -9999 0 -10000 0 0
GRB2 0.007 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.042 0.099 -9999 0 -0.27 47 47
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.021 0.003 -9999 0 -10000 0 0
epithelial cell differentiation -0.1 0.092 -9999 0 -0.29 34 34
ITCH 0.008 0.001 -9999 0 -10000 0 0
WWP1 0.021 0.004 -9999 0 -10000 0 0
FYN 0.001 0.052 -9999 0 -0.4 5 5
EGFR 0.002 0.041 -9999 0 -0.31 5 5
PRL -0.09 0.17 -9999 0 -0.4 69 69
neuron projection morphogenesis 0.016 0.048 -9999 0 -0.23 1 1
PTPRZ1 -0.12 0.13 -9999 0 -0.25 146 146
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.017 0.04 -9999 0 -0.26 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.001 0.049 -9999 0 -10000 0 0
ADAM17 0.008 0.001 -9999 0 -10000 0 0
ErbB4/ErbB4 0.021 0.004 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.007 0.015 -9999 0 -10000 0 0
NCOR1 0.007 0 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.016 0.045 -9999 0 -0.29 1 1
GRIN2B 0 0.051 -9999 0 -0.27 1 1
ErbB4/ErbB2/betacellulin 0.002 0.017 -9999 0 -10000 0 0
STAT1 0.007 0 -9999 0 -10000 0 0
HBEGF 0.007 0 -9999 0 -10000 0 0
PRLR -0.2 0.2 -9999 0 -0.4 156 156
E4ICDs/ETO2 0.016 0.032 -9999 0 -0.22 2 2
axon guidance 0.024 0.021 -9999 0 -10000 0 0
NEDD4 0.008 0.001 -9999 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.2 0.17 -9999 0 -0.32 191 191
CBFA2T3 -0.001 0.057 -9999 0 -0.4 6 6
ErbB4/ErbB2/HBEGF 0.003 0.017 -9999 0 -10000 0 0
MAPK3 0.011 0.049 -9999 0 -0.24 1 1
STAT1 (dimer) 0.021 0.003 -9999 0 -10000 0 0
MAPK1 0.011 0.049 -9999 0 -0.24 1 1
JAK2 0.007 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.015 0.04 -9999 0 -10000 0 0
NRG1 -0.019 0.068 -9999 0 -0.16 56 56
NRG3 0 0.025 -9999 0 -0.25 3 3
NRG2 -0.04 0.13 -9999 0 -0.4 35 35
NRG4 -0.015 0.072 -9999 0 -0.25 26 26
heart development 0.024 0.021 -9999 0 -10000 0 0
neural crest cell migration 0.001 0.047 -9999 0 -10000 0 0
ERBB2 0.01 0.026 -9999 0 -0.16 7 7
WWOX/E4ICDs 0.021 0.003 -9999 0 -10000 0 0
SHC1 0.007 0 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.01 0.033 -9999 0 -10000 0 0
apoptosis -0.01 0.018 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.007 0.072 -9999 0 -0.22 3 3
ErbB4/ErbB2/epiregulin 0.02 0.046 -9999 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.005 -9999 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.12 0.11 -9999 0 -0.34 34 34
MDM2 0.023 0.004 -9999 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.017 0.038 -9999 0 -10000 0 0
STAT5A 0.027 0.019 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.014 0.042 -9999 0 -10000 0 0
DLG4 -0.005 0.069 -9999 0 -0.4 9 9
GRB2/SHC 0 0 -9999 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0 0.002 -9999 0 -10000 0 0
STAT5A (dimer) -0.11 0.098 -9999 0 -0.31 34 34
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.026 0.019 -9999 0 -10000 0 0
LRIG1 0.006 0.023 -9999 0 -0.4 1 1
EREG -0.054 0.11 -9999 0 -0.25 73 73
BTC 0.007 0.002 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.024 0.021 -9999 0 -10000 0 0
ERBB4 0.021 0.004 -9999 0 -10000 0 0
STAT5B 0.007 0 -9999 0 -10000 0 0
YAP1 0 0.001 -9999 0 -10000 0 0
GRB2 0.007 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.01 0.032 -9999 0 -10000 0 0
glial cell differentiation 0 0.002 -9999 0 -10000 0 0
WWOX 0.007 0 -9999 0 -10000 0 0
cell proliferation 0.017 0.034 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.037 -10000 0 -10000 0 0
AES 0.023 0.031 -10000 0 -10000 0 0
FBXW11 0.007 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.006 0.023 -10000 0 -0.4 1 1
DKK2 -0.003 0.063 -10000 0 -0.38 8 8
TLE1 0.023 0.031 -10000 0 -10000 0 0
MACF1 0.008 0 -10000 0 -10000 0 0
CTNNB1 0.036 0.059 0.2 9 -10000 0 9
WIF1 -0.072 0.16 -10000 0 -0.39 59 59
beta catenin/RanBP3 0.11 0.16 0.33 106 -10000 0 106
KREMEN2 -0.14 0.12 -10000 0 -0.25 181 181
DKK1 -0.018 0.096 -10000 0 -0.38 20 20
beta catenin/beta TrCP1 0.045 0.053 0.19 9 -10000 0 9
FZD1 0.007 0.002 -10000 0 -10000 0 0
AXIN2 -0.41 0.58 -10000 0 -1.2 102 102
AXIN1 0.008 0.001 -10000 0 -10000 0 0
RAN 0.008 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.022 0.029 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.037 0.045 -10000 0 -0.26 1 1
Axin1/APC/GSK3 0.017 0.028 0.16 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.04 0.023 -10000 0 -10000 0 0
HNF1A 0.024 0.038 0.18 1 -0.25 1 2
CTBP1 0.025 0.034 -10000 0 -10000 0 0
MYC -0.074 0.16 -10000 0 -1.2 4 4
RANBP3 0.008 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.079 0.072 -10000 0 -0.33 7 7
NKD1 -0.004 0.062 -10000 0 -0.35 9 9
TCF4 0.02 0.05 -10000 0 -0.35 3 3
TCF3 0.024 0.033 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0.004 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.14 0.2 0.42 103 -10000 0 103
LEF1 0.024 0.033 -10000 0 -10000 0 0
DVL1 0.026 0.034 -10000 0 -10000 0 0
CSNK2A1 0.008 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.008 0.093 -10000 0 -0.3 3 3
DKK1/LRP6/Kremen 2 -0.087 0.078 -10000 0 -0.28 19 19
LRP6 0.007 0.001 -10000 0 -10000 0 0
CSNK1A1 0.027 0.037 -10000 0 -10000 0 0
NLK 0.005 0.004 -10000 0 -10000 0 0
CCND1 -0.06 0.098 -10000 0 -10000 0 0
WNT1 0.005 0.015 -10000 0 -0.25 1 1
GSK3A 0.007 0.001 -10000 0 -10000 0 0
GSK3B 0.007 0.002 -10000 0 -10000 0 0
FRAT1 0.007 0.001 -10000 0 -10000 0 0
PPP2R5D 0.029 0.037 0.24 6 -10000 0 6
APC 0.022 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.045 0.07 0.19 55 -10000 0 55
CREBBP 0.024 0.033 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.002 0.046 -9999 0 -0.4 4 4
CDC42/GTP -0.036 0.066 -9999 0 -0.21 4 4
PLCG1 -0.019 0.079 -9999 0 -0.22 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.007 0 -9999 0 -10000 0 0
GNAI3 0.007 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.036 0.065 -9999 0 -0.21 4 4
S1PR5 -0.078 0.12 -9999 0 -0.25 101 101
S1PR4 0.007 0 -9999 0 -10000 0 0
MAPK3 -0.019 0.079 -9999 0 -0.22 4 4
MAPK1 -0.019 0.079 -9999 0 -0.22 4 4
S1P/S1P5/Gi -0.041 0.087 -9999 0 -0.19 72 72
GNAI1 0.006 0.023 -9999 0 -0.4 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.043 0.061 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.026 0.083 -9999 0 -0.17 72 72
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.084 0.17 -9999 0 -0.4 68 68
S1P/S1P4/G12/G13 0 0 -9999 0 -10000 0 0
GNA12 0.007 0 -9999 0 -10000 0 0
GNA13 0.007 0 -9999 0 -10000 0 0
CDC42 0.007 0 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.007 0.001 -10000 0 -10000 0 0
HDAC2 0.007 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.014 0.054 -10000 0 -0.22 19 19
forebrain development -0.086 0.19 -10000 0 -0.45 50 50
GNAO1 0.001 0.046 -10000 0 -0.4 4 4
SMO/beta Arrestin2 -0.007 0.069 -10000 0 -0.27 19 19
SMO -0.018 0.099 -10000 0 -0.4 19 19
ARRB2 0.007 0.003 -10000 0 -10000 0 0
GLI3/SPOP 0.013 0.071 -10000 0 -0.2 25 25
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.007 0 -10000 0 -10000 0 0
GNAI2 0.007 0.003 -10000 0 -10000 0 0
SIN3/HDAC complex 0.003 0.009 -10000 0 -10000 0 0
GNAI1 0.005 0.023 -10000 0 -0.4 1 1
XPO1 0.008 0.003 -10000 0 -10000 0 0
GLI1/Su(fu) -0.086 0.15 -10000 0 -0.49 23 23
SAP30 0.007 0.001 -10000 0 -10000 0 0
mol:GDP -0.018 0.098 -10000 0 -0.4 19 19
MIM/GLI2A 0.001 0.027 -10000 0 -10000 0 0
IFT88 0.007 0 -10000 0 -10000 0 0
GNAI3 0.007 0.003 -10000 0 -10000 0 0
GLI2 -0.001 0.063 -10000 0 -10000 0 0
GLI3 0.009 0.075 0.16 13 -0.22 25 38
CSNK1D 0.007 0 -10000 0 -10000 0 0
CSNK1E 0.007 0 -10000 0 -10000 0 0
SAP18 0.007 0.001 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.007 0 -10000 0 -10000 0 0
GNG2 0.007 0 -10000 0 -10000 0 0
Gi family/GTP -0.042 0.1 -10000 0 -0.2 85 85
SIN3B 0.007 0.001 -10000 0 -10000 0 0
SIN3A 0.007 0.001 -10000 0 -10000 0 0
GLI3/Su(fu) 0.016 0.054 -10000 0 -10000 0 0
GLI2/Su(fu) 0 0.064 -10000 0 -0.24 4 4
FOXA2 -0.13 0.32 -10000 0 -0.98 38 38
neural tube patterning -0.086 0.19 -10000 0 -0.45 50 50
SPOP 0.007 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.008 0.037 -10000 0 -10000 0 0
GNB1 0.007 0 -10000 0 -10000 0 0
CSNK1G2 0.007 0 -10000 0 -10000 0 0
CSNK1G3 0.007 0 -10000 0 -10000 0 0
MTSS1 0.001 0.027 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.086 0.19 -10000 0 -0.45 50 50
SUFU 0.005 0.042 -10000 0 -0.15 19 19
LGALS3 0.007 0 -10000 0 -10000 0 0
catabolic process 0.008 0.074 -10000 0 -0.28 2 2
GLI3A/CBP -0.037 0.11 -10000 0 -0.3 47 47
KIF3A 0.007 0 -10000 0 -10000 0 0
GLI1 -0.088 0.19 -10000 0 -0.46 50 50
RAB23 0.007 0 -10000 0 -10000 0 0
CSNK1A1 0.007 0 -10000 0 -10000 0 0
IFT172 0.007 0 -10000 0 -10000 0 0
RBBP7 0.007 0.001 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.008 0.037 -10000 0 -10000 0 0
GNAZ -0.084 0.17 -10000 0 -0.4 68 68
RBBP4 0.007 0.001 -10000 0 -10000 0 0
CSNK1G1 0.007 0 -10000 0 -10000 0 0
PIAS1 0.007 0 -10000 0 -10000 0 0
PRKACA 0.007 0 -10000 0 -10000 0 0
GLI2/SPOP 0.002 0.059 -10000 0 -10000 0 0
STK36 0.008 0.003 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.034 0.097 -10000 0 -0.25 18 18
PTCH1 -0.077 0.19 -10000 0 -0.56 24 24
MIM/GLI1 -0.11 0.23 -10000 0 -0.46 78 78
CREBBP -0.037 0.11 -10000 0 -0.3 47 47
Su(fu)/SIN3/HDAC complex 0.027 0.013 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.034 0.18 -10000 0 -0.63 4 4
PCK1 -0.011 0.1 -10000 0 -10000 0 0
HNF4A -0.04 0.2 -10000 0 -0.75 6 6
KCNJ11 -0.038 0.2 -10000 0 -0.68 4 4
AKT1 -0.021 0.11 -10000 0 -0.34 3 3
response to starvation 0.001 0.001 -10000 0 -10000 0 0
DLK1 -0.1 0.31 -10000 0 -0.82 38 38
NKX2-1 0.001 0.12 -10000 0 -10000 0 0
ACADM -0.034 0.18 -10000 0 -0.63 4 4
TAT -0.016 0.11 -10000 0 -10000 0 0
CEBPB 0.007 0.002 -10000 0 -10000 0 0
CEBPA 0.008 0.002 -10000 0 -10000 0 0
TTR 0.017 0.069 -10000 0 -10000 0 0
PKLR -0.04 0.18 -10000 0 -0.63 4 4
APOA1 -0.065 0.22 -10000 0 -0.81 3 3
CPT1C -0.037 0.19 -10000 0 -0.67 7 7
ALAS1 -0.017 0.13 -10000 0 -10000 0 0
TFRC -0.015 0.14 -10000 0 -10000 0 0
FOXF1 -0.001 0.057 -10000 0 -0.4 6 6
NF1 0.012 0 -10000 0 -10000 0 0
HNF1A (dimer) 0.006 0.021 -10000 0 -0.25 2 2
CPT1A -0.034 0.18 -10000 0 -0.63 4 4
HMGCS1 -0.034 0.18 -10000 0 -0.63 4 4
NR3C1 0 0.045 -10000 0 -0.18 11 11
CPT1B -0.035 0.18 -10000 0 -0.63 4 4
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.007 0 -10000 0 -10000 0 0
GCK -0.088 0.28 -10000 0 -0.74 35 35
CREB1 0.009 0.005 -10000 0 -10000 0 0
IGFBP1 -0.081 0.3 -10000 0 -1.1 22 22
PDX1 -0.016 0.12 -10000 0 -10000 0 0
UCP2 -0.034 0.18 -10000 0 -0.63 4 4
ALDOB -0.04 0.2 -10000 0 -0.69 4 4
AFP -0.034 0.024 -10000 0 -10000 0 0
BDH1 -0.035 0.18 -10000 0 -0.63 4 4
HADH -0.038 0.2 -10000 0 -0.65 5 5
F2 -0.068 0.22 -10000 0 -0.82 3 3
HNF1A 0.006 0.021 -10000 0 -0.25 2 2
G6PC 0.017 0.018 -10000 0 -10000 0 0
SLC2A2 -0.025 0.14 -10000 0 -10000 0 0
INS 0.006 0.047 0.18 19 -10000 0 19
FOXA1 -0.21 0.084 -10000 0 -0.24 267 267
FOXA3 -0.017 0.09 -10000 0 -0.24 43 43
FOXA2 -0.052 0.23 -10000 0 -0.72 6 6
ABCC8 -0.12 0.33 -10000 0 -0.79 49 49
ALB -0.034 0.029 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.011 0.063 -9999 0 -10000 0 0
MKNK1 0.007 0 -9999 0 -10000 0 0
MAPK14 0.005 0.049 -9999 0 -0.26 9 9
ATF2/c-Jun 0.016 0.049 -9999 0 -0.52 1 1
MAPK11 0.005 0.049 -9999 0 -0.26 9 9
MITF -0.055 0.14 -9999 0 -0.27 81 81
MAPKAPK5 0.014 0.059 -9999 0 -0.31 9 9
KRT8 -0.003 0.068 -9999 0 -0.34 9 9
MAPKAPK3 0.007 0 -9999 0 -10000 0 0
MAPKAPK2 0.007 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.008 0.071 -9999 0 -0.38 9 9
CEBPB 0.014 0.059 -9999 0 -0.31 9 9
SLC9A1 0.014 0.059 -9999 0 -0.31 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.016 0.059 -9999 0 -0.3 9 9
p38alpha-beta/MNK1 0.013 0.057 -9999 0 -0.3 9 9
JUN 0.016 0.049 -9999 0 -0.52 1 1
PPARGC1A -0.009 0.11 -9999 0 -0.31 29 29
USF1 0.014 0.059 -9999 0 -0.31 9 9
RAB5/GDP/GDI1 -0.007 0.038 -9999 0 -0.22 9 9
NOS2 -0.006 0.16 -9999 0 -0.91 9 9
DDIT3 0.014 0.059 -9999 0 -0.31 9 9
RAB5A 0.007 0 -9999 0 -10000 0 0
HSPB1 0.017 0.048 -9999 0 -0.25 9 9
p38alpha-beta/HBP1 0.013 0.057 -9999 0 -0.3 9 9
CREB1 0.016 0.063 -9999 0 -0.34 9 9
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.016 0.049 -9999 0 -0.25 9 9
RPS6KA4 0.014 0.059 -9999 0 -0.31 9 9
PLA2G4A 0.01 0.062 -9999 0 -0.23 18 18
GDI1 0.014 0.059 -9999 0 -0.31 9 9
TP53 0.013 0.071 -9999 0 -0.38 9 9
RPS6KA5 0.014 0.059 -9999 0 -0.31 9 9
ESR1 -0.084 0.15 -9999 0 -0.27 111 111
HBP1 0.007 0 -9999 0 -10000 0 0
MEF2C -0.011 0.1 -9999 0 -0.29 35 35
MEF2A 0.014 0.059 -9999 0 -0.31 9 9
EIF4EBP1 0.016 0.063 -9999 0 -0.34 9 9
KRT19 0.006 0.064 -9999 0 -0.31 10 10
ELK4 0.014 0.059 -9999 0 -0.31 9 9
ATF6 0.014 0.059 -9999 0 -0.31 9 9
ATF1 0.016 0.063 -9999 0 -0.34 9 9
p38alpha-beta/MAPKAPK2 0.013 0.057 -9999 0 -0.3 9 9
p38alpha-beta/MAPKAPK3 0.013 0.057 -9999 0 -0.3 9 9
LPA receptor mediated events

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
GNB1/GNG2 -0.013 0.05 -9999 0 -0.2 20 20
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.031 -9999 0 -0.2 1 1
AP1 -0.026 0.06 -9999 0 -0.17 37 37
mol:PIP3 -0.014 0.042 -9999 0 -0.27 2 2
AKT1 -0.008 0.032 -9999 0 -0.27 1 1
PTK2B -0.001 0.049 -9999 0 -0.17 20 20
RHOA 0.012 0.028 -9999 0 -10000 0 0
PIK3CB 0.007 0 -9999 0 -10000 0 0
mol:Ca2+ -0.008 0.047 -9999 0 -10000 0 0
MAGI3 0.007 0 -9999 0 -10000 0 0
RELA 0.007 0 -9999 0 -10000 0 0
apoptosis -0.001 0.057 -9999 0 -0.2 20 20
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.054 -9999 0 -0.18 15 15
NF kappa B1 p50/RelA -0.023 0.048 -9999 0 -0.23 8 8
endothelial cell migration -0.015 0.12 -9999 0 -0.46 20 20
ADCY4 -0.039 0.12 -9999 0 -0.33 29 29
ADCY5 -0.11 0.13 -9999 0 -0.3 65 65
ADCY6 -0.023 0.093 -9999 0 -0.28 21 21
ADCY7 -0.023 0.093 -9999 0 -0.28 21 21
ADCY1 -0.029 0.1 -9999 0 -0.3 26 26
ADCY2 -0.12 0.13 -9999 0 -0.3 71 71
ADCY3 -0.023 0.093 -9999 0 -0.28 21 21
ADCY8 -0.025 0.093 -9999 0 -0.28 21 21
ADCY9 -0.023 0.093 -9999 0 -0.28 21 21
GSK3B 0.003 0.046 -9999 0 -0.19 8 8
arachidonic acid secretion -0.018 0.088 -9999 0 -0.26 21 21
GNG2 0.007 0 -9999 0 -10000 0 0
TRIP6 0.012 0.012 -9999 0 -10000 0 0
GNAO1 -0.003 0.068 -9999 0 -0.23 23 23
HRAS 0.007 0 -9999 0 -10000 0 0
NFKBIA 0 0.049 -9999 0 -0.23 1 1
GAB1 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.005 0.067 -9999 0 -0.82 2 2
JUN 0.006 0.023 -9999 0 -0.4 1 1
LPA/LPA2/NHERF2 -0.004 0.016 -9999 0 -10000 0 0
TIAM1 -0.006 0.077 -9999 0 -0.96 2 2
PIK3R1 0.007 0 -9999 0 -10000 0 0
mol:IP3 -0.009 0.047 -9999 0 -10000 0 0
PLCB3 0.012 0.017 -9999 0 -10000 0 0
FOS -0.022 0.1 -9999 0 -0.4 22 22
positive regulation of mitosis -0.018 0.088 -9999 0 -0.26 21 21
LPA/LPA1-2-3 -0.017 0.055 -9999 0 -0.2 20 20
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.007 0 -9999 0 -10000 0 0
stress fiber formation 0.005 0.051 -9999 0 -0.23 5 5
GNAZ -0.053 0.12 -9999 0 -0.24 82 82
EGFR/PI3K-beta/Gab1 -0.014 0.043 -9999 0 -0.28 2 2
positive regulation of dendritic cell cytokine production -0.017 0.054 -9999 0 -0.2 20 20
LPA/LPA2/MAGI-3 -0.004 0.016 -9999 0 -10000 0 0
ARHGEF1 0.009 0.051 -9999 0 -0.18 20 20
GNAI2 0 0.061 -9999 0 -0.22 20 20
GNAI3 0 0.061 -9999 0 -0.22 20 20
GNAI1 0 0.062 -9999 0 -0.22 21 21
LPA/LPA3 -0.012 0.039 -9999 0 -0.17 12 12
LPA/LPA2 -0.005 0.021 -9999 0 -10000 0 0
LPA/LPA1 -0.018 0.069 -9999 0 -0.27 20 20
HB-EGF/EGFR -0.017 0.053 -9999 0 -0.22 2 2
HBEGF -0.015 0.063 -9999 0 -0.16 49 49
mol:DAG -0.009 0.047 -9999 0 -10000 0 0
cAMP biosynthetic process -0.048 0.1 -9999 0 -0.3 24 24
NFKB1 0.007 0 -9999 0 -10000 0 0
SRC 0.007 0 -9999 0 -10000 0 0
GNB1 0.007 0 -9999 0 -10000 0 0
LYN 0 0.049 -9999 0 -0.23 1 1
GNAQ 0.007 0.025 -9999 0 -0.15 1 1
LPAR2 0.007 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.05 -9999 0 -0.25 12 12
LPAR1 -0.004 0.061 -9999 0 -0.43 4 4
IL8 -0.036 0.068 -9999 0 -0.3 4 4
PTK2 0.005 0.056 -9999 0 -0.18 20 20
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.001 0.057 -9999 0 -0.2 20 20
EGFR 0.002 0.041 -9999 0 -0.31 5 5
PLCG1 -0.021 0.055 -9999 0 -0.16 9 9
PLD2 0.005 0.056 -9999 0 -0.18 20 20
G12/G13 -0.013 0.05 -9999 0 -0.2 20 20
PI3K-beta -0.009 0.036 -9999 0 -0.31 1 1
cell migration -0.002 0.031 -9999 0 -0.22 3 3
SLC9A3R2 0.007 0 -9999 0 -10000 0 0
PXN 0.005 0.052 -9999 0 -0.23 5 5
HRAS/GTP -0.019 0.09 -9999 0 -0.27 21 21
RAC1 0.007 0 -9999 0 -10000 0 0
MMP9 -0.034 0.094 -9999 0 -0.25 49 49
PRKCE 0.007 0.001 -9999 0 -10000 0 0
PRKCD -0.004 0.045 -9999 0 -10000 0 0
Gi(beta/gamma) -0.021 0.09 -9999 0 -0.26 21 21
mol:LPA -0.007 0.036 -9999 0 -0.16 16 16
TRIP6/p130 Cas/FAK1/Paxillin -0.007 0.05 -9999 0 -0.31 2 2
MAPKKK cascade -0.018 0.088 -9999 0 -0.26 21 21
contractile ring contraction involved in cytokinesis 0.012 0.028 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.059 0.11 -9999 0 -0.22 89 89
GNA15 0.001 0.032 -9999 0 -0.14 2 2
GNA12 0.007 0 -9999 0 -10000 0 0
GNA13 0.007 0 -9999 0 -10000 0 0
MAPT 0.003 0.055 -9999 0 -0.19 15 15
GNA11 0.005 0.031 -9999 0 -0.19 3 3
Rac1/GTP -0.005 0.07 -9999 0 -0.87 2 2
MMP2 -0.015 0.12 -9999 0 -0.46 20 20
Insulin Pathway

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
CBL/APS/CAP -0.073 0.092 -9999 0 -0.18 126 126
TC10/GTP -0.063 0.078 -9999 0 -0.16 120 120
Insulin Receptor/Insulin/IRS1/Shp2 -0.009 0.043 -9999 0 -0.2 14 14
HRAS 0.007 0 -9999 0 -10000 0 0
APS homodimer 0.007 0 -9999 0 -10000 0 0
GRB14 -0.041 0.1 -9999 0 -0.25 57 57
FOXO3 -0.003 0.007 -9999 0 -10000 0 0
AKT1 0.003 0.053 -9999 0 -0.24 2 2
INSR 0.008 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.006 0.023 -9999 0 -0.4 1 1
SORBS1 -0.15 0.2 -9999 0 -0.4 120 120
CRK 0.007 0 -9999 0 -10000 0 0
PTPN1 0.02 0 -9999 0 -10000 0 0
CAV1 -0.014 0.082 -9999 0 -0.22 38 38
CBL/APS/CAP/Crk-II/C3G -0.071 0.087 -9999 0 -0.18 120 120
Insulin Receptor/Insulin/IRS1/NCK2 -0.009 0.043 -9999 0 -0.2 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.036 -9999 0 -0.17 14 14
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.014 0.037 -9999 0 -10000 0 0
RPS6KB1 0.008 0.05 -9999 0 -0.22 2 2
PARD6A 0.007 0 -9999 0 -10000 0 0
CBL 0.007 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.004 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.017 0.037 -9999 0 -0.22 2 2
HRAS/GTP -0.007 0.03 -9999 0 -10000 0 0
Insulin Receptor 0.008 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.009 0.039 -9999 0 -0.18 14 14
PRKCI -0.005 0.011 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.022 0.045 -9999 0 -0.26 2 2
SHC1 0.007 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.011 -9999 0 -10000 0 0
PI3K -0.008 0.037 -9999 0 -0.18 14 14
NCK2 0.007 0 -9999 0 -10000 0 0
RHOQ 0.007 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 0.003 0.053 -9999 0 -0.24 2 2
PRKCZ -0.005 0.011 -9999 0 -10000 0 0
SH2B2 0.007 0 -9999 0 -10000 0 0
SHC/SHIP 0.011 0.041 -9999 0 -0.17 14 14
F2RL2 -0.017 0.096 -9999 0 -0.4 18 18
TRIP10 0.007 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.007 0 -9999 0 -10000 0 0
RASA1 0.006 0.023 -9999 0 -0.4 1 1
NCK1 0.007 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.077 0.096 -9999 0 -0.2 120 120
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.012 -9999 0 -0.2 1 1
INPP5D 0.006 0.043 -9999 0 -0.19 14 14
SOS1 0.007 0 -9999 0 -10000 0 0
SGK1 -0.001 0.003 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.007 0 -9999 0 -10000 0 0
IRS1 -0.011 0.085 -9999 0 -0.4 14 14
p62DOK/RasGAP 0 0.011 -9999 0 -10000 0 0
INS 0.002 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.006 0.043 -9999 0 -0.19 14 14
GRB2 0.007 0 -9999 0 -10000 0 0
EIF4EBP1 0.008 0.05 -9999 0 -0.22 2 2
PTPRA 0.008 0 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.007 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.01 0.044 -9999 0 -0.19 14 14
Insulin Receptor/Insulin/IRS1 -0.01 0.044 -9999 0 -0.21 14 14
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.011 0.043 -9999 0 -0.18 18 18
Glucocorticoid receptor regulatory network

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.007 0.014 -10000 0 -10000 0 0
SMARCC2 0.008 0 -10000 0 -10000 0 0
SMARCC1 0.008 0 -10000 0 -10000 0 0
TBX21 -0.035 0.077 -10000 0 -0.74 2 2
SUMO2 0.007 0.002 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0 -10000 0 -10000 0 0
FKBP4 0.007 0 -10000 0 -10000 0 0
FKBP5 0.006 0.023 -10000 0 -0.4 1 1
GR alpha/HSP90/FKBP51/HSP90 0.057 0.047 0.18 12 -0.17 1 13
PRL -0.29 0.5 -10000 0 -1.2 69 69
cortisol/GR alpha (dimer)/TIF2 0.14 0.12 0.42 19 -10000 0 19
RELA -0.028 0.06 -10000 0 -10000 0 0
FGG 0.09 0.096 0.34 13 -10000 0 13
GR beta/TIF2 0.055 0.061 0.2 11 -0.25 4 15
IFNG -0.12 0.091 -10000 0 -0.43 2 2
apoptosis -0.033 0.12 -10000 0 -0.48 7 7
CREB1 0.008 0.009 -10000 0 -10000 0 0
histone acetylation -0.005 0.061 -10000 0 -0.22 1 1
BGLAP -0.024 0.054 -10000 0 -10000 0 0
GR/PKAc 0.055 0.043 0.19 5 -10000 0 5
NF kappa B1 p50/RelA -0.047 0.1 -10000 0 -0.28 36 36
SMARCD1 0.008 0 -10000 0 -10000 0 0
MDM2 0.042 0.042 0.16 13 -10000 0 13
GATA3 -0.013 0.076 -10000 0 -0.24 30 30
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.016 0.048 -10000 0 -10000 0 0
GSK3B 0.007 0.002 -10000 0 -10000 0 0
NR1I3 -0.021 0.1 -10000 0 -0.47 4 4
CSN2 0.073 0.082 0.29 13 -10000 0 13
BRG1/BAF155/BAF170/BAF60A 0.023 0.005 -10000 0 -10000 0 0
NFATC1 0.006 0.023 -10000 0 -0.4 1 1
POU2F1 -0.046 0.099 -10000 0 -0.23 69 69
CDKN1A 0.023 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.002 -10000 0 -10000 0 0
SFN -0.24 0.05 -10000 0 -0.25 292 292
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.043 0.13 0.19 63 -0.27 1 64
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.031 0.15 -10000 0 -0.8 8 8
JUN -0.089 0.067 -10000 0 -0.4 3 3
IL4 -0.043 0.057 -10000 0 -10000 0 0
CDK5R1 0.007 0.001 -10000 0 -10000 0 0
PRKACA 0.007 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.15 0.11 -10000 0 -0.29 77 77
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.059 0.045 0.18 11 -10000 0 11
cortisol/GR alpha (monomer) 0.15 0.14 0.48 19 -10000 0 19
NCOA2 0.002 0.046 -10000 0 -0.4 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.058 0.11 -10000 0 -0.44 22 22
AP-1/NFAT1-c-4 -0.14 0.095 -10000 0 -0.42 8 8
AFP -0.054 0.056 -10000 0 -0.46 1 1
SUV420H1 0.007 0 -10000 0 -10000 0 0
IRF1 0.077 0.067 0.29 3 -10000 0 3
TP53 0.02 0 -10000 0 -10000 0 0
PPP5C 0.007 0 -10000 0 -10000 0 0
KRT17 -0.16 0.09 -10000 0 -0.41 6 6
KRT14 -0.12 0.069 -10000 0 -10000 0 0
TBP 0.013 0 -10000 0 -10000 0 0
CREBBP 0.04 0.017 -10000 0 -10000 0 0
HDAC1 0.005 0.004 -10000 0 -10000 0 0
HDAC2 0.006 0.001 -10000 0 -10000 0 0
AP-1 -0.14 0.096 -10000 0 -0.43 8 8
MAPK14 0.007 0.002 -10000 0 -10000 0 0
MAPK10 -0.11 0.18 -10000 0 -0.4 86 86
MAPK11 0.007 0.002 -10000 0 -10000 0 0
KRT5 -0.16 0.096 -10000 0 -0.43 2 2
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.009 0 -10000 0 -10000 0 0
STAT1 0.012 0 -10000 0 -10000 0 0
CGA -0.039 0.061 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.062 0.05 -10000 0 -10000 0 0
MAPK3 0.007 0.002 -10000 0 -10000 0 0
MAPK1 0.007 0.002 -10000 0 -10000 0 0
ICAM1 -0.073 0.11 -10000 0 -0.39 10 10
NFKB1 -0.028 0.06 -10000 0 -10000 0 0
MAPK8 -0.08 0.068 -10000 0 -0.28 11 11
MAPK9 0.007 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.04 0.12 -10000 0 -0.5 7 7
BAX 0.023 0.012 -10000 0 -10000 0 0
POMC -0.051 0.1 -10000 0 -1.2 1 1
EP300 0.04 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.15 0.12 0.43 19 -10000 0 19
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.034 0.14 1 -10000 0 1
SGK1 0.066 0.024 -10000 0 -10000 0 0
IL13 -0.079 0.069 -10000 0 -10000 0 0
IL6 -0.074 0.11 -10000 0 -0.39 9 9
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.074 0.062 -10000 0 -10000 0 0
IL2 -0.11 0.084 -10000 0 -0.38 2 2
CDK5 0.007 0.001 -10000 0 -10000 0 0
PRKACB 0.007 0 -10000 0 -10000 0 0
HSP90AA1 0.007 0 -10000 0 -10000 0 0
IL8 -0.11 0.13 -10000 0 -0.4 21 21
CDK5R1/CDK5 0 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.014 0.076 -10000 0 -0.2 7 7
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.11 0.4 19 -10000 0 19
SMARCA4 0.008 0 -10000 0 -10000 0 0
chromatin remodeling 0.086 0.068 0.27 13 -10000 0 13
NF kappa B1 p50/RelA/Cbp 0.015 0.091 -10000 0 -10000 0 0
JUN (dimer) -0.089 0.066 -10000 0 -0.4 3 3
YWHAH 0.007 0 -10000 0 -10000 0 0
VIPR1 -0.034 0.069 -10000 0 -0.42 3 3
NR3C1 0.075 0.073 0.28 14 -10000 0 14
NR4A1 0.001 0.063 -10000 0 -0.41 7 7
TIF2/SUV420H1 -0.004 0.031 -10000 0 -0.27 4 4
MAPKKK cascade -0.033 0.12 -10000 0 -0.48 7 7
cortisol/GR alpha (dimer)/Src-1 0.14 0.12 0.42 19 -10000 0 19
PBX1 -0.06 0.12 -10000 0 -0.26 79 79
POU1F1 -0.052 0.1 -10000 0 -0.24 69 69
SELE -0.19 0.35 -10000 0 -0.94 54 54
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.086 0.068 0.27 13 -10000 0 13
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.11 0.4 19 -10000 0 19
mol:cortisol 0.067 0.075 0.26 19 -10000 0 19
MMP1 -0.059 0.056 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ 0.007 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.007 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.015 -10000 0 -10000 0 0
IRAK/TOLLIP 0.017 0.002 -10000 0 -10000 0 0
IKBKB 0.007 0 -10000 0 -10000 0 0
IKBKG 0.007 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.087 0.083 -10000 0 -0.16 164 164
IL1A -0.12 0.13 -10000 0 -0.25 154 154
IL1B -0.017 0.065 -10000 0 -0.16 53 53
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.009 -10000 0 -10000 0 0
IL1R2 -0.004 0.054 -10000 0 -0.25 14 14
IL1R1 0.003 0.04 -10000 0 -0.4 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.038 0.17 9 -0.21 3 12
TOLLIP 0.007 0 -10000 0 -10000 0 0
TICAM2 0.007 0.001 -10000 0 -10000 0 0
MAP3K3 0.007 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.038 0.004 -10000 0 -10000 0 0
JUN 0.025 0.023 -10000 0 -0.32 1 1
MAP3K7 0.007 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.016 0.036 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.056 0.054 -10000 0 -0.2 3 3
PIK3R1 0.007 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.049 0.048 -10000 0 -0.18 3 3
IL1 beta fragment/IL1R1/IL1RAP -0.021 0.044 -10000 0 -0.2 3 3
NFKB1 0.007 0 -10000 0 -10000 0 0
MAPK8 0.022 0.016 -10000 0 -0.16 2 2
IRAK1 0.014 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.13 0.07 -10000 0 -0.37 3 3
IRAK4 0.007 0 -10000 0 -10000 0 0
PRKCI 0.007 0 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.03 -10000 0 -0.18 3 3
CHUK 0.007 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.021 0.044 -10000 0 -0.2 3 3
IL1 beta/IL1R2 -0.027 0.052 -10000 0 -0.26 1 1
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.014 0.03 -10000 0 -10000 0 0
IRAK3 -0.005 0.069 -10000 0 -0.4 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.016 0.036 -10000 0 -0.17 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.03 -10000 0 -0.19 3 3
IL1 alpha/IL1R1/IL1RAP -0.065 0.064 -10000 0 -0.22 3 3
RELA 0.007 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.006 0.023 -10000 0 -0.4 1 1
MYD88 0.007 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.008 0.009 -10000 0 -10000 0 0
IL1RAP 0.006 0.015 -10000 0 -0.25 1 1
UBE2N 0.007 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.012 0.026 -10000 0 -10000 0 0
CASP1 0.007 0 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.13 0.069 -10000 0 -0.31 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.018 0.039 -10000 0 -0.18 3 3
TMEM189-UBE2V1 0.004 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.031 -10000 0 -0.27 3 3
PIK3CA 0.007 0 -10000 0 -10000 0 0
IL1RN -0.19 0.11 -10000 0 -0.25 236 236
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 0.019 0.007 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.022 0.016 -9999 0 -10000 0 0
epithelial cell differentiation -0.084 0.033 -9999 0 -10000 0 0
CYFIP2 0.007 0 -9999 0 -10000 0 0
ENAH -0.033 0.028 -9999 0 -10000 0 0
EGFR 0.002 0.041 -9999 0 -0.31 5 5
EPHA2 0.007 0 -9999 0 -10000 0 0
MYO6 -0.074 0.037 -9999 0 -10000 0 0
CTNNB1 0.007 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.1 0.13 -9999 0 -0.46 35 35
CTNND1 0.007 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.073 0.037 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.079 0.048 -9999 0 -0.24 10 10
EGF -0.013 0.088 -9999 0 -0.4 15 15
NCKAP1 0.007 0 -9999 0 -10000 0 0
AQP3 -0.058 0.029 -9999 0 -10000 0 0
cortical microtubule organization -0.084 0.033 -9999 0 -10000 0 0
GO:0000145 -0.069 0.035 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.085 0.033 -9999 0 -10000 0 0
MLLT4 0.007 0 -9999 0 -10000 0 0
ARF6/GDP -0.054 0.021 -9999 0 -10000 0 0
ARF6 0.007 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP -0.059 0.034 -9999 0 -10000 0 0
PVRL2 0.007 0 -9999 0 -10000 0 0
ZYX -0.074 0.037 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 -0.22 0.086 -9999 0 -0.25 264 264
EGFR/EGFR/EGF/EGF -0.081 0.049 -9999 0 -0.26 15 15
RhoA/GDP -0.076 0.03 -9999 0 -10000 0 0
actin cytoskeleton organization -0.062 0.034 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.005 0.033 -9999 0 -0.4 2 2
GIT1 0.007 0 -9999 0 -10000 0 0
IGF1R 0.005 0.033 -9999 0 -0.4 2 2
IGF1 -0.12 0.19 -9999 0 -0.4 95 95
DIAPH1 0.01 0.004 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0.084 0.033 -9999 0 -10000 0 0
RHOA 0.007 0 -9999 0 -10000 0 0
RhoA/GTP -0.054 0.021 -9999 0 -10000 0 0
CTNNA1 0.007 0 -9999 0 -10000 0 0
VCL -0.063 0.034 -9999 0 -10000 0 0
EFNA1 0.007 0 -9999 0 -10000 0 0
LPP -0.066 0.036 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.07 0.027 -9999 0 -10000 0 0
SEC6/SEC8 -0.059 0.023 -9999 0 -10000 0 0
MGAT3 -0.08 0.048 -9999 0 -0.25 10 10
HGF/MET -0.095 0.07 -9999 0 -0.26 38 38
HGF -0.049 0.14 -9999 0 -0.4 42 42
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.022 0.016 -9999 0 -10000 0 0
actin cable formation -0.022 0.027 -9999 0 -10000 0 0
KIAA1543 -0.16 0.05 -9999 0 -0.19 241 241
KIFC3 -0.074 0.037 -9999 0 -10000 0 0
NCK1 0.007 0 -9999 0 -10000 0 0
EXOC3 0.007 0 -9999 0 -10000 0 0
ACTN1 -0.074 0.037 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP -0.084 0.033 -9999 0 -10000 0 0
EXOC4 0.007 0 -9999 0 -10000 0 0
STX4 -0.074 0.037 -9999 0 -10000 0 0
PIP5K1C -0.074 0.037 -9999 0 -10000 0 0
LIMA1 0.007 0 -9999 0 -10000 0 0
ABI1 0.007 0 -9999 0 -10000 0 0
ROCK1 -0.046 0.018 -9999 0 -10000 0 0
adherens junction assembly -0.1 0.038 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.13 0.092 -9999 0 -0.27 85 85
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.007 0 -9999 0 -10000 0 0
PLEKHA7 -0.074 0.037 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.05 0.034 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.022 0.016 -9999 0 -10000 0 0
regulation of cell-cell adhesion -0.062 0.034 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.022 0.016 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.006 0.066 -9999 0 -0.19 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.047 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src -0.006 0.029 -9999 0 -0.15 12 12
AP1 -0.04 0.082 -9999 0 -0.34 11 11
ILK -0.001 0.071 -9999 0 -0.22 5 5
bone resorption -0.018 0.049 -9999 0 -0.31 1 1
PTK2B 0.007 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.014 0.055 -9999 0 -0.18 5 5
ITGAV 0.01 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.002 0.022 -9999 0 -0.27 2 2
alphaV/beta3 Integrin/Osteopontin -0.028 0.07 -9999 0 -0.22 34 34
MAP3K1 -0.001 0.072 -9999 0 -0.19 34 34
JUN 0.006 0.023 -9999 0 -0.4 1 1
MAPK3 0.009 0.067 -9999 0 -0.19 5 5
MAPK1 0.009 0.067 -9999 0 -0.19 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.007 0 -9999 0 -10000 0 0
MAPK8 0.003 0.07 -9999 0 -0.23 5 5
ITGB3 -0.036 0.13 -9999 0 -0.4 34 34
NFKBIA 0.015 0.067 -9999 0 -10000 0 0
FOS -0.022 0.1 -9999 0 -0.4 22 22
CD44 0.007 0 -9999 0 -10000 0 0
CHUK 0.007 0 -9999 0 -10000 0 0
PLAU 0.019 0.065 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.016 0.041 -9999 0 -10000 0 0
BCAR1 0.007 0 -9999 0 -10000 0 0
RELA 0.007 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.03 0.085 -9999 0 -0.27 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.001 0.071 -9999 0 -0.19 34 34
VAV3 0.005 0.066 -9999 0 -0.17 34 34
MAP3K14 0.001 0.071 -9999 0 -0.19 34 34
ROCK2 0.005 0.033 -9999 0 -0.4 2 2
SPP1 0 0.049 -9999 0 -0.24 12 12
RAC1 0.007 0 -9999 0 -10000 0 0
Rac1/GTP -0.019 0.049 -9999 0 -0.17 5 5
MMP2 -0.006 0.12 -9999 0 -0.37 23 23
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.053 0.075 -9999 0 -10000 0 0
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0.007 0 -9999 0 -10000 0 0
AKT2 0.007 0 -9999 0 -10000 0 0
STXBP4 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.048 0.09 -9999 0 -10000 0 0
YWHAZ 0.007 0 -9999 0 -10000 0 0
CALM1 0.007 0 -9999 0 -10000 0 0
YWHAQ 0.007 0 -9999 0 -10000 0 0
TBC1D4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.007 0 -9999 0 -10000 0 0
YWHAB 0.007 0 -9999 0 -10000 0 0
SNARE/Synip 0 0 -9999 0 -10000 0 0
YWHAG 0.007 0 -9999 0 -10000 0 0
ASIP 0.004 0.004 -9999 0 -10000 0 0
PRKCI 0.007 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0.007 0 -9999 0 -10000 0 0
GYS1 0.018 0 -9999 0 -10000 0 0
PRKCZ 0.007 0 -9999 0 -10000 0 0
TRIP10 0.007 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.004 0.006 -9999 0 -10000 0 0
VAMP2 0.007 0 -9999 0 -10000 0 0
SLC2A4 -0.052 0.097 -9999 0 -10000 0 0
STX4 0.007 0 -9999 0 -10000 0 0
GSK3B 0.015 0 -9999 0 -10000 0 0
SFN -0.24 0.05 -9999 0 -0.25 292 292
LNPEP 0.007 0 -9999 0 -10000 0 0
YWHAE 0.007 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.007 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.068 0.079 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0 0.006 -9999 0 -10000 0 0
POMC 0 0.045 -9999 0 -0.27 8 8
EGFR 0.002 0.041 -9999 0 -0.31 5 5
Syndecan-3/EGFR -0.002 0.017 -9999 0 -10000 0 0
AGRP 0 0 -9999 0 -10000 0 0
NCSTN 0.007 0 -9999 0 -10000 0 0
PSENEN 0.007 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.007 0 -9999 0 -10000 0 0
APH1A 0.007 0 -9999 0 -10000 0 0
NCAN 0.005 0.015 -9999 0 -0.25 1 1
long-term memory -0.003 0.021 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.054 0.048 -9999 0 -10000 0 0
PSEN1 0.007 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.001 0.052 -9999 0 -0.4 5 5
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R 0.001 0.015 -9999 0 -0.25 1 1
SRC 0.007 0 -9999 0 -10000 0 0
PTN -0.16 0.2 -9999 0 -0.4 129 129
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.065 0.075 -9999 0 -10000 0 0
Syndecan-3/AgRP 0 0 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0 0.005 -9999 0 -10000 0 0
Fyn/Cortactin -0.005 0.035 -9999 0 -0.27 5 5
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.054 0.048 -9999 0 -10000 0 0
IL8 -0.14 0.13 -9999 0 -0.25 169 169
Syndecan-3/Fyn/Cortactin -0.003 0.022 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.005 0.03 -9999 0 -0.18 9 9
Gamma Secretase 0 0 -9999 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.002 0.074 -9999 0 -0.21 31 31
FZD6 0.007 0 -9999 0 -10000 0 0
WNT6 -0.006 0.073 -9999 0 -0.4 10 10
WNT4 0.002 0.046 -9999 0 -0.4 4 4
FZD3 -0.007 0.076 -9999 0 -0.4 11 11
WNT5A 0.007 0 -9999 0 -10000 0 0
WNT11 -0.004 0.067 -9999 0 -0.38 9 9
Syndecan-4-mediated 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
PTK2 0.006 0.068 -9999 0 -0.4 8 8
Syndecan-4/Syndesmos 0.014 0.034 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.099 0.084 -9999 0 -0.34 8 8
Syndecan-4/ADAM12 0.014 0.034 -9999 0 -10000 0 0
CCL5 0.007 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.007 0 -9999 0 -10000 0 0
ITGA5 0.005 0.033 -9999 0 -0.4 2 2
SDCBP 0.007 0 -9999 0 -10000 0 0
PLG -0.001 0.026 -9999 0 -0.26 3 3
ADAM12 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.007 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.012 0.025 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.014 0.045 -9999 0 -0.36 1 1
Syndecan-4/CXCL12/CXCR4 -0.094 0.097 -9999 0 -0.35 8 8
Syndecan-4/Laminin alpha3 0.013 0.036 -9999 0 -10000 0 0
MDK 0.007 0 -9999 0 -10000 0 0
Syndecan-4/FZD7 0.008 0.045 -9999 0 -10000 0 0
Syndecan-4/Midkine 0.014 0.034 -9999 0 -10000 0 0
FZD7 -0.005 0.069 -9999 0 -0.4 9 9
Syndecan-4/FGFR1/FGF -0.077 0.11 -9999 0 -0.33 36 36
THBS1 -0.064 0.15 -9999 0 -0.4 53 53
integrin-mediated signaling pathway 0.008 0.047 -9999 0 -0.35 1 1
positive regulation of MAPKKK cascade -0.099 0.084 -9999 0 -0.34 8 8
Syndecan-4/TACI 0.013 0.034 -9999 0 -10000 0 0
CXCR4 0.007 0 -9999 0 -10000 0 0
cell adhesion 0.007 0.047 -9999 0 -0.19 15 15
Syndecan-4/Dynamin 0.014 0.034 -9999 0 -10000 0 0
Syndecan-4/TSP1 -0.018 0.084 -9999 0 -0.36 6 6
Syndecan-4/GIPC 0.014 0.034 -9999 0 -10000 0 0
Syndecan-4/RANTES 0.014 0.034 -9999 0 -10000 0 0
ITGB1 0.007 0 -9999 0 -10000 0 0
LAMA1 -0.011 0.069 -9999 0 -0.26 21 21
LAMA3 0.005 0.027 -9999 0 -0.32 2 2
RAC1 0.007 0 -9999 0 -10000 0 0
PRKCA -0.004 0.058 -9999 0 -0.37 7 7
Syndecan-4/alpha-Actinin 0.014 0.034 -9999 0 -10000 0 0
TFPI -0.034 0.12 -9999 0 -0.4 31 31
F2 0.001 0.001 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.002 0.022 -9999 0 -0.27 2 2
positive regulation of cell adhesion 0.009 0.047 -9999 0 -0.35 1 1
ACTN1 0.007 0 -9999 0 -10000 0 0
TNC -0.006 0.073 -9999 0 -0.4 10 10
Syndecan-4/CXCL12 -0.1 0.099 -9999 0 -0.36 8 8
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.007 0 -9999 0 -10000 0 0
CXCL12 -0.25 0.2 -9999 0 -0.4 189 189
TNFRSF13B 0.006 0.015 -9999 0 -0.25 1 1
FGF2 -0.12 0.19 -9999 0 -0.4 95 95
FGFR1 -0.056 0.15 -9999 0 -0.4 47 47
Syndecan-4/PI-4-5-P2 0.009 0.033 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.003 0.063 -9999 0 -0.38 8 8
cell migration -0.006 0.013 -9999 0 -10000 0 0
PRKCD 0.008 0.004 -9999 0 -10000 0 0
vasculogenesis -0.018 0.082 -9999 0 -0.35 6 6
SDC4 0.01 0.035 -9999 0 -10000 0 0
Syndecan-4/Tenascin C 0.008 0.049 -9999 0 -0.36 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.009 0.02 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.014 0.034 -9999 0 -10000 0 0
MMP9 -0.033 0.094 -9999 0 -0.25 49 49
Rac1/GTP -0.007 0.045 -9999 0 -0.19 15 15
cytoskeleton organization 0.014 0.033 -9999 0 -10000 0 0
GIPC1 0.007 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.005 0.067 -9999 0 -0.36 2 2
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.02 0.084 -9999 0 -0.37 16 16
PDGFB-D/PDGFRB/SLAP -0.014 0.061 -9999 0 -0.27 16 16
PDGFB-D/PDGFRB/APS/CBL -0.012 0.049 -9999 0 -0.22 16 16
AKT1 0.02 0.044 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.003 0.097 -9999 0 -0.4 16 16
PIK3CA 0.007 0 -9999 0 -10000 0 0
FGR -0.014 0.057 -9999 0 -0.26 16 16
mol:Ca2+ -0.001 0.1 -9999 0 -0.43 16 16
MYC 0.012 0.11 -9999 0 -0.57 7 7
SHC1 0.007 0 -9999 0 -10000 0 0
HRAS/GDP -0.01 0.04 -9999 0 -0.17 17 17
LRP1/PDGFRB/PDGFB -0.012 0.049 -9999 0 -0.22 16 16
GRB10 0.006 0.023 -9999 0 -0.4 1 1
PTPN11 0.007 0 -9999 0 -10000 0 0
GO:0007205 -0.001 0.1 -9999 0 -0.44 16 16
PTEN 0.006 0.023 -9999 0 -0.4 1 1
GRB2 0.007 0 -9999 0 -10000 0 0
GRB7 0.001 0.041 -9999 0 -0.25 8 8
PDGFB-D/PDGFRB/SHP2 -0.014 0.061 -9999 0 -0.27 16 16
PDGFB-D/PDGFRB/GRB10 -0.015 0.066 -9999 0 -0.29 16 16
cell cycle arrest -0.014 0.061 -9999 0 -0.27 16 16
HRAS 0.007 0 -9999 0 -10000 0 0
HIF1A 0.024 0.041 -9999 0 -10000 0 0
GAB1 0.003 0.098 -9999 0 -0.4 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.007 0.09 -9999 0 -0.36 16 16
PDGFB-D/PDGFRB -0.009 0.053 -9999 0 -0.23 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.014 0.061 -9999 0 -0.27 16 16
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.015 0.078 -9999 0 -0.33 16 16
positive regulation of MAPKKK cascade -0.014 0.061 -9999 0 -0.27 16 16
PIK3R1 0.007 0 -9999 0 -10000 0 0
mol:IP3 -0.001 0.1 -9999 0 -0.44 16 16
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.007 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.019 0.065 -9999 0 -0.24 24 24
SHB 0.007 0 -9999 0 -10000 0 0
BLK -0.007 0.061 -9999 0 -0.26 16 16
PTPN2 0.007 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.014 0.061 -9999 0 -0.27 16 16
BCAR1 0.007 0 -9999 0 -10000 0 0
VAV2 0.005 0.1 -9999 0 -0.4 16 16
CBL 0.007 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.014 0.061 -9999 0 -0.27 16 16
LCK -0.014 0.057 -9999 0 -0.26 16 16
PDGFRB -0.014 0.092 -9999 0 -0.4 16 16
ACP1 0.007 0 -9999 0 -10000 0 0
HCK -0.014 0.057 -9999 0 -0.26 16 16
ABL1 0.005 0.084 -9999 0 -0.34 16 16
PDGFB-D/PDGFRB/CBL -0.001 0.12 -9999 0 -0.48 16 16
PTPN1 0.007 0.002 -9999 0 -10000 0 0
SNX15 0.007 0 -9999 0 -10000 0 0
STAT3 0.007 0 -9999 0 -10000 0 0
STAT1 0.007 0 -9999 0 -10000 0 0
cell proliferation 0.013 0.1 -9999 0 -0.51 7 7
SLA 0.007 0 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.021 0.042 -9999 0 -10000 0 0
SRC -0.014 0.057 -9999 0 -0.26 16 16
PI3K -0.013 0.037 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.015 0.053 -9999 0 -0.22 16 16
SH2B2 0.007 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.003 0.099 -9999 0 -0.41 16 16
LYN -0.014 0.057 -9999 0 -0.26 16 16
LRP1 0.007 0 -9999 0 -10000 0 0
SOS1 0.007 0 -9999 0 -10000 0 0
STAT5B 0.007 0 -9999 0 -10000 0 0
STAT5A 0.007 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.009 0.038 -9999 0 -0.18 1 1
SPHK1 0.007 0.002 -9999 0 -10000 0 0
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG -0.001 0.1 -9999 0 -0.44 16 16
PLCG1 -0.001 0.11 -9999 0 -0.45 16 16
NHERF/PDGFRB -0.019 0.056 -9999 0 -0.22 16 16
YES1 -0.014 0.057 -9999 0 -0.26 16 16
cell migration -0.019 0.056 -9999 0 -0.22 16 16
SHC/Grb2/SOS1 -0.009 0.038 -9999 0 -0.17 16 16
SLC9A3R2 0.007 0 -9999 0 -10000 0 0
SLC9A3R1 -0.009 0.062 -9999 0 -0.25 19 19
NHERF1-2/PDGFRB/PTEN -0.017 0.05 -9999 0 -0.19 17 17
FYN -0.024 0.12 -9999 0 -0.42 17 17
DOK1 0.008 0.049 -9999 0 -0.2 16 16
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.007 0 -9999 0 -10000 0 0
RAC1 0.011 0.1 -9999 0 -0.38 19 19
PRKCD 0.009 0.049 -9999 0 -0.2 16 16
FER 0.008 0.051 -9999 0 -0.2 17 17
MAPKKK cascade -0.008 0.037 -9999 0 -0.16 16 16
RASA1 0.008 0.051 -9999 0 -0.2 17 17
NCK1 0.007 0 -9999 0 -10000 0 0
NCK2 0.007 0 -9999 0 -10000 0 0
p62DOK/Csk -0.005 0.042 -9999 0 -0.18 16 16
PDGFB-D/PDGFRB/SHB -0.014 0.061 -9999 0 -0.27 16 16
chemotaxis 0.006 0.082 -9999 0 -0.33 16 16
STAT1-3-5/STAT1-3-5 -0.008 0.035 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.015 0.063 -9999 0 -0.28 16 16
PTPRJ 0.007 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.09 0.067 -9999 0 -10000 0 0
RAD9A 0.007 0 -9999 0 -10000 0 0
AP1 -0.021 0.072 -9999 0 -0.27 23 23
IFNAR2 0.008 0 -9999 0 -10000 0 0
AKT1 -0.048 0.082 -9999 0 -0.16 106 106
ER alpha/Oestrogen -0.097 0.13 -9999 0 -0.28 106 106
NFX1/SIN3/HDAC complex 0.027 0 -9999 0 -10000 0 0
EGF -0.013 0.088 -9999 0 -0.4 15 15
SMG5 0.007 0 -9999 0 -10000 0 0
SMG6 0.007 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.085 0.051 -9999 0 -10000 0 0
SAP18 0.007 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.34 0.14 -9999 0 -0.4 259 259
WRN 0.007 0 -9999 0 -10000 0 0
SP1 0.008 0 -9999 0 -10000 0 0
SP3 0.008 0 -9999 0 -10000 0 0
TERF2IP 0.007 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.072 0.044 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.091 0.068 -9999 0 -10000 0 0
CCND1 -0.079 0.062 -9999 0 -10000 0 0
MAX 0.008 0 -9999 0 -10000 0 0
RBBP7 0.007 0 -9999 0 -10000 0 0
RBBP4 0.007 0 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.007 0 -9999 0 -10000 0 0
SIN3A 0.007 0 -9999 0 -10000 0 0
Telomerase/911 0.004 0.013 -9999 0 -10000 0 0
CDKN1B -0.002 0.053 -9999 0 -10000 0 0
RAD1 0.007 0 -9999 0 -10000 0 0
XRCC5 0.007 0 -9999 0 -10000 0 0
XRCC6 0.007 0 -9999 0 -10000 0 0
SAP30 0.007 0 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.008 0 -9999 0 -10000 0 0
JUN 0.006 0.023 -9999 0 -0.4 1 1
E6 0 0 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0.001 -9999 0 -10000 0 0
FOS -0.022 0.11 -9999 0 -0.4 22 22
IFN-gamma/IRF1 -0.027 0.057 -9999 0 -10000 0 0
PARP2 0.007 0 -9999 0 -10000 0 0
BLM -0.061 0.11 -9999 0 -0.25 81 81
Telomerase -0.003 0.017 -9999 0 -10000 0 0
IRF1 0.01 0 -9999 0 -10000 0 0
ESR1 -0.14 0.19 -9999 0 -0.4 106 106
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.03 0 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.031 0 -9999 0 -10000 0 0
HDAC1 0.007 0 -9999 0 -10000 0 0
HDAC2 0.008 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.013 0 -9999 0 -10000 0 0
ABL1 0.007 0 -9999 0 -10000 0 0
MXD1 0.008 0 -9999 0 -10000 0 0
MRE11A 0.007 0 -9999 0 -10000 0 0
HUS1 0.007 0 -9999 0 -10000 0 0
RPS6KB1 0.007 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.082 0.06 -9999 0 -10000 0 0
NR2F2 -0.029 0.12 -9999 0 -0.4 27 27
MAPK3 0.01 0.003 -9999 0 -10000 0 0
MAPK1 0.01 0.003 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.007 0 -9999 0 -10000 0 0
NFKB1 0.007 0 -9999 0 -10000 0 0
HNRNPC 0.007 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.007 0 -9999 0 -10000 0 0
EGFR 0.002 0.041 -9999 0 -0.31 5 5
mol:Oestrogen 0 0 -9999 0 -10000 0 0
EGF/EGFR -0.017 0.064 -9999 0 -0.26 20 20
MYC 0.002 0.046 -9999 0 -0.4 4 4
IL2 0.004 0.004 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.007 0 -9999 0 -10000 0 0
HSP90AA1 0.007 0 -9999 0 -10000 0 0
TGFB1 0.007 0 -9999 0 -10000 0 0
TRF2/BLM -0.038 0.063 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.08 0.055 -9999 0 -10000 0 0
SP1/HDAC2 0.012 0.001 -9999 0 -10000 0 0
PINX1 0.007 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.072 0.044 -9999 0 -10000 0 0
Smad3/Myc 0.012 0.027 -9999 0 -0.22 4 4
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.035 0.097 -9999 0 -0.24 54 54
Telomerase/PinX1 -0.072 0.044 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.022 0.037 -9999 0 -10000 0 0
SIN3B 0.007 0 -9999 0 -10000 0 0
YWHAE 0.007 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.072 0.044 -9999 0 -10000 0 0
response to DNA damage stimulus 0.002 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.072 0.044 -9999 0 -10000 0 0
E2F1 -0.002 0.05 -9999 0 -0.25 12 12
ZNFX1 0.007 0 -9999 0 -10000 0 0
PIF1 0.002 0.036 -9999 0 -0.25 6 6
NCL 0.007 0 -9999 0 -10000 0 0
DKC1 0.007 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.013 0 -9999 0 -10000 0 0
SMARCC1 0.009 0.007 -9999 0 -10000 0 0
REL 0.007 0.001 -9999 0 -10000 0 0
HDAC7 -0.021 0.065 -9999 0 -0.23 12 12
JUN 0.006 0.023 -9999 0 -0.4 1 1
EP300 0.007 0 -9999 0 -10000 0 0
KAT2B 0.007 0 -9999 0 -10000 0 0
KAT5 0.007 0 -9999 0 -10000 0 0
MAPK14 0.01 0.012 -9999 0 -0.15 1 1
FOXO1 0.005 0.033 -9999 0 -0.4 2 2
T-DHT/AR -0.026 0.069 -9999 0 -0.24 12 12
MAP2K6 0.005 0.015 -9999 0 -0.24 1 1
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.006 0.004 -9999 0 -10000 0 0
SMARCA2 0.007 0.001 -9999 0 -10000 0 0
PDE9A -0.07 0.25 -9999 0 -0.98 21 21
NCOA2 0.002 0.046 -9999 0 -0.4 4 4
CEBPA 0.007 0 -9999 0 -10000 0 0
EHMT2 0.007 0.001 -9999 0 -10000 0 0
cell proliferation -0.009 0.083 -9999 0 -0.29 12 12
NR0B1 -0.004 0.045 -9999 0 -0.25 10 10
EGR1 -0.004 0.065 -9999 0 -0.4 8 8
RXRs/9cRA -0.001 0.013 -9999 0 -0.2 1 1
AR/RACK1/Src -0.017 0.044 -9999 0 -0.28 1 1
AR/GR -0.08 0.11 -9999 0 -0.19 140 140
GNB2L1 0.007 0 -9999 0 -10000 0 0
PKN1 0.007 0 -9999 0 -10000 0 0
RCHY1 0.007 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 0.008 0.025 -9999 0 -0.28 2 2
T-DHT/AR/TIF2/CARM1 -0.02 0.054 -9999 0 -0.36 3 3
SRC 0.014 0.024 -9999 0 -0.18 2 2
NR3C1 0.007 0 -9999 0 -10000 0 0
KLK3 -0.01 0.053 -9999 0 -0.34 1 1
APPBP2 0.006 0.004 -9999 0 -10000 0 0
TRIM24 0.007 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.019 0.048 -9999 0 -0.25 2 2
TMPRSS2 -0.038 0.068 -9999 0 -10000 0 0
RXRG 0.003 0.028 -9999 0 -0.32 2 2
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.007 0 -9999 0 -10000 0 0
RXRB 0.007 0 -9999 0 -10000 0 0
CARM1 0.007 0 -9999 0 -10000 0 0
NR2C2 0.005 0.033 -9999 0 -0.4 2 2
KLK2 -0.007 0.054 -9999 0 -0.34 2 2
AR -0.093 0.12 -9999 0 -0.22 140 140
SENP1 0.007 0 -9999 0 -10000 0 0
HSP90AA1 0.007 0 -9999 0 -10000 0 0
MDM2 0.007 0.001 -9999 0 -10000 0 0
SRY 0 0.001 -9999 0 -10000 0 0
GATA2 -0.007 0.076 -9999 0 -0.4 11 11
MYST2 0.007 0 -9999 0 -10000 0 0
HOXB13 -0.11 0.13 -9999 0 -0.25 143 143
T-DHT/AR/RACK1/Src -0.014 0.047 -9999 0 -0.29 1 1
positive regulation of transcription -0.007 0.076 -9999 0 -0.4 11 11
DNAJA1 0.006 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0 -9999 0 -10000 0 0
NCOA1 0.011 0.002 -9999 0 -10000 0 0
SPDEF -0.043 0.11 -9999 0 -0.27 55 55
T-DHT/AR/TIF2 -0.007 0.048 -9999 0 -0.31 3 3
T-DHT/AR/Hsp90 -0.019 0.048 -9999 0 -0.25 2 2
GSK3B 0.007 0.002 -9999 0 -10000 0 0
NR2C1 0.007 0 -9999 0 -10000 0 0
mol:T-DHT 0.01 0.026 -9999 0 -0.2 2 2
SIRT1 0.007 0 -9999 0 -10000 0 0
ZMIZ2 0.007 0.001 -9999 0 -10000 0 0
POU2F1 0.004 0.024 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.029 0.051 -9999 0 -0.2 7 7
CREBBP 0.007 0 -9999 0 -10000 0 0
SMARCE1 0.007 0.001 -9999 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.026 0.041 -9999 0 -10000 0 0
TBX21 0.031 0.17 -9999 0 -0.83 5 5
B2M 0.008 0.001 -9999 0 -10000 0 0
TYK2 0.012 0.01 -9999 0 -10000 0 0
IL12RB1 0.012 0.01 -9999 0 -10000 0 0
GADD45B 0.037 0.14 -9999 0 -0.55 4 4
IL12RB2 -0.043 0.11 -9999 0 -0.25 66 66
GADD45G -0.037 0.33 -9999 0 -1 29 29
natural killer cell activation 0.005 0.012 -9999 0 -10000 0 0
RELB 0.007 0 -9999 0 -10000 0 0
RELA 0.007 0 -9999 0 -10000 0 0
IL18 0.006 0.026 -9999 0 -0.24 3 3
IL2RA 0.001 0.038 -9999 0 -0.25 7 7
IFNG -0.038 0.098 -9999 0 -0.25 54 54
STAT3 (dimer) 0.031 0.15 -9999 0 -0.55 6 6
HLA-DRB5 -0.004 0.065 -9999 0 -0.4 8 8
FASLG 0.034 0.14 -9999 0 -0.67 4 4
NF kappa B2 p52/RelB -0.039 0.11 -9999 0 -0.59 6 6
CD4 0.007 0.004 -9999 0 -10000 0 0
SOCS1 0.007 0 -9999 0 -10000 0 0
EntrezGene:6955 0 0.007 -9999 0 -10000 0 0
CD3D 0.005 0.028 -9999 0 -0.33 2 2
CD3E 0.008 0.005 -9999 0 -10000 0 0
CD3G 0.007 0.016 -9999 0 -0.26 1 1
IL12Rbeta2/JAK2 -0.017 0.075 -9999 0 -0.16 39 39
CCL3 0.034 0.14 -9999 0 -0.67 4 4
CCL4 0.034 0.14 -9999 0 -0.67 4 4
HLA-A 0.008 0.001 -9999 0 -10000 0 0
IL18/IL18R 0.032 0.032 -9999 0 -0.22 1 1
NOS2 0.011 0.22 -9999 0 -1 11 11
IL12/IL12R/TYK2/JAK2/SPHK2 0.026 0.041 -9999 0 -10000 0 0
IL1R1 0.028 0.18 -9999 0 -0.84 7 7
IL4 -0.005 0.012 -9999 0 -10000 0 0
JAK2 0.012 0.01 -9999 0 -10000 0 0
EntrezGene:6957 0 0.006 -9999 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.025 0.024 -9999 0 -10000 0 0
RAB7A 0.02 0.19 -9999 0 -0.5 29 29
lysosomal transport 0.022 0.18 -9999 0 -0.48 29 29
FOS -0.035 0.3 -9999 0 -1.1 23 23
STAT4 (dimer) 0.032 0.17 -9999 0 -0.63 5 5
STAT5A (dimer) -0.026 0.13 -9999 0 -0.58 7 7
GZMA 0.029 0.16 -9999 0 -0.92 4 4
GZMB 0.028 0.15 -9999 0 -0.71 5 5
HLX 0.007 0 -9999 0 -10000 0 0
LCK 0.033 0.15 -9999 0 -0.63 6 6
TCR/CD3/MHC II/CD4 0.008 0.059 -9999 0 -0.18 23 23
IL2/IL2R -0.004 0.02 -9999 0 -10000 0 0
MAPK14 0.011 0.22 -9999 0 -0.59 29 29
CCR5 0.034 0.13 -9999 0 -0.56 4 4
IL1B -0.032 0.097 -9999 0 -0.24 53 53
STAT6 0.023 0.056 -9999 0 -0.24 1 1
STAT4 0.007 0 -9999 0 -10000 0 0
STAT3 0.007 0 -9999 0 -10000 0 0
STAT1 0.007 0 -9999 0 -10000 0 0
NFKB1 0.007 0 -9999 0 -10000 0 0
NFKB2 0.007 0 -9999 0 -10000 0 0
IL12B 0.009 0.03 -9999 0 -0.24 4 4
CD8A 0.008 0.015 -9999 0 -0.26 1 1
CD8B 0.001 0.046 -9999 0 -0.29 7 7
T-helper 1 cell differentiation 0 0 -9999 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.026 0.041 -9999 0 -10000 0 0
IL2RB 0.007 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.16 -9999 0 -0.59 5 5
IL2RG 0.004 0.029 -9999 0 -0.25 4 4
IL12 0.009 0.043 -9999 0 -0.15 7 7
STAT5A 0.007 0 -9999 0 -10000 0 0
CD247 0.008 0.005 -9999 0 -10000 0 0
IL2 0.003 0.004 -9999 0 -10000 0 0
SPHK2 0.007 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
IL12A -0.001 0.056 -9999 0 -0.23 16 16
IL12/IL12R/TYK2/JAK2 0.031 0.16 -9999 0 -0.67 6 6
MAP2K3 0.011 0.21 -9999 0 -0.55 29 29
RIPK2 0.007 0 -9999 0 -10000 0 0
MAP2K6 0.011 0.21 -9999 0 -0.55 29 29
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -10000 0 0
HLA-DRA 0.007 0.005 -9999 0 -10000 0 0
IL18RAP 0.009 0.007 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 0.018 0.015 -9999 0 -10000 0 0
EOMES 0.007 0.02 -9999 0 -10000 0 0
STAT1 (dimer) 0.039 0.14 -9999 0 -0.6 4 4
T cell proliferation 0.022 0.16 -9999 0 -0.47 8 8
T-helper 1 cell lineage commitment 0 0 -9999 0 -10000 0 0
IL18R1 0.008 0.025 -9999 0 -0.4 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.055 0.14 -9999 0 -0.45 22 22
ATF2 0.016 0.2 -9999 0 -0.55 29 29
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.005 0.069 -9999 0 -0.4 9 9
GNB1/GNG2 -0.019 0.059 -9999 0 -0.44 2 2
mol:DAG 0.011 0.063 -9999 0 -0.4 2 2
PLCG1 0.011 0.064 -9999 0 -0.41 2 2
YES1 0.003 0.07 -9999 0 -0.19 31 31
FZD3 -0.007 0.076 -9999 0 -0.4 11 11
FZD6 0.007 0 -9999 0 -10000 0 0
G protein 0.011 0.065 -9999 0 -0.41 2 2
MAP3K7 -0.034 0.1 -9999 0 -0.31 14 14
mol:Ca2+ 0.011 0.062 -9999 0 -0.39 2 2
mol:IP3 0.011 0.063 -9999 0 -0.4 2 2
NLK -0.001 0.005 -9999 0 -10000 0 0
GNB1 0.007 0 -9999 0 -10000 0 0
CAMK2A -0.041 0.11 -9999 0 -0.33 14 14
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.002 0.074 -9999 0 -0.21 31 31
CSNK1A1 0.007 0 -9999 0 -10000 0 0
GNAS 0.003 0.07 -9999 0 -0.19 31 31
GO:0007205 0.011 0.062 -9999 0 -0.4 2 2
WNT6 -0.006 0.073 -9999 0 -0.4 10 10
WNT4 0.002 0.046 -9999 0 -0.4 4 4
NFAT1/CK1 alpha -0.021 0.058 -9999 0 -0.33 3 3
GNG2 0.007 0 -9999 0 -10000 0 0
WNT5A 0.007 0 -9999 0 -10000 0 0
WNT11 -0.004 0.067 -9999 0 -0.38 9 9
CDC42 0.008 0.067 -9999 0 -0.43 2 2
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0 0 -10000 0 -10000 0 0
HDAC1 0.001 0.005 -10000 0 -10000 0 0
AES 0.007 0.001 -10000 0 -10000 0 0
FBXW11 0.007 0 -10000 0 -10000 0 0
DTX1 0.007 0 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.007 0.001 -10000 0 -10000 0 0
AP1 -0.008 0.073 -10000 0 -0.23 28 28
NCSTN 0.007 0 -10000 0 -10000 0 0
ADAM10 0.007 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.023 0.029 -10000 0 -10000 0 0
NICD/RBPSUH 0 0.002 -10000 0 -10000 0 0
WIF1 -0.072 0.16 -10000 0 -0.39 59 59
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0.007 0 -10000 0 -10000 0 0
KREMEN2 -0.14 0.13 -10000 0 -0.25 181 181
DKK1 -0.018 0.096 -10000 0 -0.38 20 20
beta catenin/beta TrCP1 0.016 0.02 -10000 0 -10000 0 0
APH1B 0.007 0 -10000 0 -10000 0 0
APH1A 0.007 0 -10000 0 -10000 0 0
AXIN1 0.003 0.007 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.013 0.015 -10000 0 -10000 0 0
PSEN1 0.007 0 -10000 0 -10000 0 0
FOS -0.022 0.11 -10000 0 -0.4 22 22
JUN 0.006 0.023 -10000 0 -0.4 1 1
MAP3K7 0.006 0.002 -10000 0 -10000 0 0
CTNNB1 0.012 0.021 -10000 0 -10000 0 0
MAPK3 0.007 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.08 0.072 -10000 0 -0.33 7 7
HNF1A 0.005 0.021 -10000 0 -0.25 2 2
CTBP1 0.007 0.001 -10000 0 -10000 0 0
MYC -0.001 0.14 -10000 0 -1.2 4 4
NKD1 -0.004 0.061 -10000 0 -0.35 9 9
FZD1 0.007 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0 0.002 -10000 0 -10000 0 0
apoptosis -0.008 0.072 -10000 0 -0.23 28 28
Delta 1/NOTCHprecursor 0 0.002 -10000 0 -10000 0 0
DLL1 0.007 0 -10000 0 -10000 0 0
PPARD 0.013 0.01 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC 0.003 0.007 -10000 0 -10000 0 0
DVL1 -0.006 0.014 -10000 0 -10000 0 0
CSNK2A1 0.008 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.088 0.078 -10000 0 -0.28 19 19
LRP6 0.007 0 -10000 0 -10000 0 0
CSNK1A1 0.008 0.001 -10000 0 -10000 0 0
NLK 0.008 0.005 -10000 0 -10000 0 0
CCND1 0.013 0.01 -10000 0 -10000 0 0
WNT1 0.006 0.015 -10000 0 -0.25 1 1
Axin1/APC/beta catenin 0.022 0.017 -10000 0 -10000 0 0
DKK2 -0.003 0.063 -10000 0 -0.38 8 8
NOTCH1 precursor/DVL1 -0.002 0.006 -10000 0 -10000 0 0
GSK3B 0.007 0 -10000 0 -10000 0 0
FRAT1 0.007 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.002 0.033 0.22 6 -10000 0 6
MAPK1 0.007 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.037 0.076 -10000 0 -0.2 55 55
RBPJ 0.007 0 -10000 0 -10000 0 0
CREBBP 0.009 0.001 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.023 0.079 -9999 0 -10000 0 0
CRKL 0.015 0.048 -9999 0 -10000 0 0
mol:DAG 0.012 0.067 -9999 0 -0.22 22 22
HRAS 0.028 0.043 -9999 0 -10000 0 0
MAPK8 0.006 0.055 -9999 0 -0.18 24 24
RAP1A 0.015 0.048 -9999 0 -10000 0 0
GAB1 0.015 0.048 -9999 0 -10000 0 0
MAPK14 0.007 0.052 -9999 0 -0.18 22 22
EPO -0.021 0.1 -9999 0 -0.4 22 22
PLCG1 0.012 0.068 -9999 0 -0.22 22 22
EPOR/TRPC2/IP3 Receptors 0.008 0.006 -9999 0 -10000 0 0
RAPGEF1 0.007 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.015 0.055 -9999 0 -0.21 22 22
GAB1/SHC/GRB2/SOS1 -0.01 0.033 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.007 0.074 -9999 0 -0.27 22 22
IRS2 0.009 0.057 -9999 0 -0.16 9 9
STAT1 0.017 0.072 -9999 0 -0.22 22 22
STAT5B 0.014 0.07 -9999 0 -0.22 22 22
cell proliferation 0.011 0.051 -9999 0 -0.18 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.009 0.031 -9999 0 -10000 0 0
TEC 0.015 0.048 -9999 0 -10000 0 0
SOCS3 0.007 0 -9999 0 -10000 0 0
STAT1 (dimer) 0.017 0.071 -9999 0 -0.21 22 22
JAK2 0.007 0.005 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.017 0.053 -9999 0 -0.16 22 22
EPO/EPOR -0.007 0.074 -9999 0 -0.27 22 22
LYN 0.008 0.002 -9999 0 -10000 0 0
TEC/VAV2 0.019 0.047 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.008 0.006 -9999 0 -10000 0 0
SHC1 0.007 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.005 0.06 -9999 0 -0.21 22 22
mol:IP3 0.012 0.067 -9999 0 -0.22 22 22
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.042 -9999 0 -10000 0 0
SH2B3 0.007 0.005 -9999 0 -10000 0 0
NFKB1 0.007 0.052 -9999 0 -0.18 22 22
EPO/EPOR (dimer)/JAK2/SOCS3 -0.016 0.057 -9999 0 -0.22 22 22
PTPN6 0.01 0.05 -9999 0 -0.16 22 22
TEC/VAV2/GRB2 0.022 0.045 -9999 0 -10000 0 0
EPOR 0.008 0.006 -9999 0 -10000 0 0
INPP5D 0.007 0 -9999 0 -10000 0 0
mol:GDP -0.01 0.033 -9999 0 -10000 0 0
SOS1 0.007 0 -9999 0 -10000 0 0
PLCG2 0.007 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.022 0.045 -9999 0 -10000 0 0
VAV2 0.015 0.048 -9999 0 -10000 0 0
CBL 0.015 0.048 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.011 0.036 -9999 0 -10000 0 0
STAT5A 0.014 0.07 -9999 0 -0.22 22 22
GRB2 0.007 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.026 0.069 -9999 0 -0.26 5 5
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.007 0 -9999 0 -10000 0 0
BTK 0.015 0.048 -9999 0 -10000 0 0
BCL2 0.016 0.12 -9999 0 -0.76 5 5
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.022 0 -9999 0 -10000 0 0
CDKN1A 0.022 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.007 0 -9999 0 -10000 0 0
FOXO3 0.022 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.007 0 -9999 0 -10000 0 0
AKT3 -0.004 0.061 -9999 0 -0.27 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.022 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.007 0 -9999 0 -10000 0 0
RAF1 0.007 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.022 0 -9999 0 -10000 0 0
YWHAZ 0.007 0 -9999 0 -10000 0 0
AKT1/RAF1 0.021 0 -9999 0 -10000 0 0
EP300 0.007 0 -9999 0 -10000 0 0
mol:GDP 0.018 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.022 0 -9999 0 -10000 0 0
YWHAQ 0.007 0 -9999 0 -10000 0 0
TBC1D4 0.014 0 -9999 0 -10000 0 0
MAP3K5 0.007 0 -9999 0 -10000 0 0
MAPKAP1 0.007 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.01 0.003 -9999 0 -10000 0 0
YWHAH 0.007 0 -9999 0 -10000 0 0
AKT1S1 0.022 0 -9999 0 -10000 0 0
CASP9 0.022 0 -9999 0 -10000 0 0
YWHAB 0.007 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.025 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 0.007 0 -9999 0 -10000 0 0
SRC 0.007 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 0.011 0 -9999 0 -10000 0 0
CHUK 0.022 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.029 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.01 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.019 0.006 -9999 0 -10000 0 0
PDPK1 0.007 0 -9999 0 -10000 0 0
MDM2 0.022 0 -9999 0 -10000 0 0
MAPKKK cascade -0.021 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.029 0 -9999 0 -10000 0 0
TSC1/TSC2 0.026 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
glucose import -0.054 0.1 -9999 0 -0.2 103 103
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.019 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.055 0.1 -9999 0 -0.2 103 103
GSK3A 0.022 0 -9999 0 -10000 0 0
FOXO1 0.021 0.015 -9999 0 -10000 0 0
GSK3B 0.022 0 -9999 0 -10000 0 0
SFN -0.24 0.05 -9999 0 -0.25 292 292
G1/S transition of mitotic cell cycle 0.026 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.007 0.004 -9999 0 -10000 0 0
PRKACA 0.007 0 -9999 0 -10000 0 0
KPNA1 0.007 0 -9999 0 -10000 0 0
HSP90AA1 0.007 0 -9999 0 -10000 0 0
YWHAG 0.007 0 -9999 0 -10000 0 0
RHEB 0.007 0 -9999 0 -10000 0 0
CREBBP 0.007 0 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.007 0.002 -10000 0 -10000 0 0
HSPA8 0.007 0 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.072 0.12 0.17 14 -0.23 102 116
AKT1 0.009 0.001 -10000 0 -10000 0 0
GSC 0.01 0.019 -10000 0 -10000 0 0
NKX2-5 -0.004 0.019 -10000 0 -10000 0 0
muscle cell differentiation 0.02 0.06 0.27 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.036 0.046 -10000 0 -10000 0 0
SMAD4 0.013 0.028 -10000 0 -0.38 1 1
CBFB 0.007 0 -10000 0 -10000 0 0
SAP18 0.007 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.001 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0 0.008 -10000 0 -10000 0 0
MYC 0 0.047 -10000 0 -0.4 4 4
CDKN2B 0.023 0.017 -10000 0 -10000 0 0
AP1 0.022 0.059 -10000 0 -0.39 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.037 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.029 0.022 -10000 0 -10000 0 0
SP3 0.009 0 -10000 0 -10000 0 0
CREB1 0.007 0 -10000 0 -10000 0 0
FOXH1 -0.012 0.066 -10000 0 -0.25 20 20
SMAD3/SMAD4/GR -0.001 0.012 -10000 0 -0.19 1 1
GATA3 -0.015 0.075 -10000 0 -0.24 30 30
SKI/SIN3/HDAC complex/NCoR1 0.028 0.001 -10000 0 -10000 0 0
MEF2C/TIF2 -0.012 0.12 -10000 0 -0.37 29 29
endothelial cell migration 0.001 0.067 1.2 1 -10000 0 1
MAX 0.006 0.003 -10000 0 -10000 0 0
RBBP7 0.007 0 -10000 0 -10000 0 0
RBBP4 0.007 0 -10000 0 -10000 0 0
RUNX2 0.007 0 -10000 0 -10000 0 0
RUNX3 0.006 0.015 -10000 0 -0.25 1 1
RUNX1 0.007 0 -10000 0 -10000 0 0
CTBP1 0.007 0 -10000 0 -10000 0 0
NR3C1 0.006 0.003 -10000 0 -10000 0 0
VDR 0.007 0 -10000 0 -10000 0 0
CDKN1A 0.035 0.036 -10000 0 -10000 0 0
KAT2B 0.007 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.011 0.051 -10000 0 -0.28 2 2
DCP1A 0.007 0 -10000 0 -10000 0 0
SKI 0.007 0 -10000 0 -10000 0 0
SERPINE1 -0.002 0.068 -10000 0 -1.2 1 1
SMAD3/SMAD4/ATF2 0 0.013 -10000 0 -0.19 1 1
SMAD3/SMAD4/ATF3 0 0.013 -10000 0 -0.19 1 1
SAP30 0.007 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0 0.003 -10000 0 -10000 0 0
JUN 0.022 0.058 -10000 0 -0.4 1 1
SMAD3/SMAD4/IRF7 -0.001 0.012 -10000 0 -10000 0 0
TFE3 0.011 0.003 -10000 0 -10000 0 0
COL1A2 -0.007 0.2 -10000 0 -0.76 18 18
mesenchymal cell differentiation 0 0.013 0.19 1 -10000 0 1
DLX1 -0.032 0.091 -10000 0 -0.25 46 46
TCF3 0.007 0 -10000 0 -10000 0 0
FOS -0.018 0.11 -10000 0 -0.4 22 22
SMAD3/SMAD4/Max -0.001 0.012 -10000 0 -0.19 1 1
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 0.006 0.001 -10000 0 -10000 0 0
LAMC1 0.035 0.018 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0 0.013 -10000 0 -0.19 1 1
IRF7 0.008 0.001 -10000 0 -10000 0 0
ESR1 -0.13 0.2 -10000 0 -0.4 106 106
HNF4A -0.006 0.059 -10000 0 -0.3 11 11
MEF2C -0.012 0.13 -10000 0 -0.41 27 27
SMAD2-3/SMAD4 -0.004 0.016 -10000 0 -0.18 1 1
Cbp/p300/Src-1 0 0.003 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.003 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.007 0 -10000 0 -10000 0 0
CREBBP 0.007 0.001 -10000 0 -10000 0 0
SKIL 0.007 0 -10000 0 -10000 0 0
HDAC1 0.007 0 -10000 0 -10000 0 0
HDAC2 0.007 0 -10000 0 -10000 0 0
SNIP1 0.007 0 -10000 0 -10000 0 0
GCN5L2 0 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.006 0.019 -10000 0 -10000 0 0
MSG1/HSC70 -0.001 0.013 -10000 0 -0.16 2 2
SMAD2 0.007 0.017 -10000 0 -10000 0 0
SMAD3 0.016 0.01 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.029 0.02 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.009 0.02 -10000 0 -0.26 1 1
NCOR1 0.007 0 -10000 0 -10000 0 0
NCOA2 0.002 0.046 -10000 0 -0.4 4 4
NCOA1 0.007 0 -10000 0 -10000 0 0
MYOD/E2A 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.04 0.043 -10000 0 -10000 0 0
IFNB1 0.029 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0 0.12 -10000 0 -0.38 27 27
CITED1 0.006 0.021 -10000 0 -0.25 2 2
SMAD2-3/SMAD4/ARC105 0.001 0.018 -10000 0 -10000 0 0
RBL1 0.007 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.037 0.02 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0 0.007 -10000 0 -10000 0 0
SMAD7 0.038 0.063 -10000 0 -10000 0 0
MYC/MIZ-1 -0.003 0.032 -10000 0 -0.28 4 4
SMAD3/SMAD4 -0.002 0.027 -10000 0 -0.41 1 1
IL10 0.021 0.043 -10000 0 -10000 0 0
PIASy/HDAC complex 0.007 0.002 -10000 0 -10000 0 0
PIAS3 0.007 0.001 -10000 0 -10000 0 0
CDK2 0.007 0.001 -10000 0 -10000 0 0
IL5 0.018 0.042 -10000 0 -10000 0 0
CDK4 0.007 0.001 -10000 0 -10000 0 0
PIAS4 0.007 0.002 -10000 0 -10000 0 0
ATF3 0.007 0 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.006 0.042 -10000 0 -10000 0 0
FOXG1 -0.014 0.059 -10000 0 -0.25 18 18
FOXO3 0.016 0.001 -10000 0 -10000 0 0
FOXO1 0.014 0.023 -10000 0 -0.27 2 2
FOXO4 0.016 0.001 -10000 0 -10000 0 0
heart looping -0.012 0.13 -10000 0 -0.4 27 27
CEBPB 0.008 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.02 0.047 -10000 0 -0.19 2 2
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.006 0.036 -10000 0 -0.25 5 5
SMAD3/SMAD4/GATA3 -0.005 0.038 -10000 0 -10000 0 0
SnoN/SIN3/HDAC complex/NCoR1 0.007 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.021 0.041 -10000 0 -10000 0 0
MED15 0.007 0 -10000 0 -10000 0 0
SP1 0.006 0.03 -10000 0 -10000 0 0
SIN3B 0.007 0 -10000 0 -10000 0 0
SIN3A 0.007 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.005 0.077 -10000 0 -0.22 27 27
ITGB5 0.037 0.034 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.028 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.11 0.12 -10000 0 -0.23 140 140
AR -0.18 0.2 -10000 0 -0.4 140 140
negative regulation of cell growth 0.034 0.023 -10000 0 -0.25 1 1
SMAD3/SMAD4/MYOD -0.001 0.013 -10000 0 -0.19 1 1
E2F5 0.006 0.023 -10000 0 -0.4 1 1
E2F4 0.007 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.006 0.039 -10000 0 -0.23 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.034 0.022 -10000 0 -10000 0 0
TFDP1 0.007 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.024 0.059 -10000 0 -0.4 1 1
SMAD3/SMAD4/RUNX2 0 0.013 -10000 0 -0.19 1 1
TGIF2 0.007 0 -10000 0 -10000 0 0
TGIF1 0.007 0 -10000 0 -10000 0 0
ATF2 0.007 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0 0 -10000 0 -10000 0 0
CRKL -0.002 0.064 -10000 0 -10000 0 0
mol:PIP3 -0.01 0.022 0.36 1 -10000 0 1
AKT1 0.002 0.016 0.27 1 -10000 0 1
PTK2B 0.007 0 -10000 0 -10000 0 0
RAPGEF1 0.003 0.061 -10000 0 -10000 0 0
RANBP10 0.007 0 -10000 0 -10000 0 0
PIK3CA 0.007 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.031 0.076 -10000 0 -0.22 41 41
MAP3K5 0.009 0.058 -10000 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.027 0.067 -10000 0 -0.2 41 41
AP1 -0.008 0.064 -10000 0 -0.23 23 23
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.007 0 -10000 0 -10000 0 0
apoptosis -0.041 0.18 -10000 0 -0.67 23 23
STAT3 (dimer) -0.005 0.075 -10000 0 -0.2 1 1
GAB1/CRKL/SHP2/PI3K -0.019 0.047 -10000 0 -10000 0 0
INPP5D 0.007 0 -10000 0 -10000 0 0
CBL/CRK 0.002 0.061 -10000 0 -10000 0 0
PTPN11 0.007 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.007 0 -10000 0 -10000 0 0
PTEN 0.006 0.023 -10000 0 -0.4 1 1
ELK1 0 0.004 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.016 0.04 -10000 0 -10000 0 0
PAK1 0.006 0.014 0.25 1 -10000 0 1
HGF/MET/RANBP10 -0.031 0.076 -10000 0 -0.22 41 41
HRAS -0.01 0.084 -10000 0 -10000 0 0
DOCK1 0.003 0.061 -10000 0 -10000 0 0
GAB1 -0.007 0.067 -10000 0 -10000 0 0
CRK -0.002 0.064 -10000 0 -10000 0 0
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.054 0.14 -10000 0 -0.4 41 41
JUN 0.006 0.023 -10000 0 -0.4 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.022 0.054 -10000 0 -0.16 41 41
PIK3R1 0.007 0 -10000 0 -10000 0 0
cell morphogenesis 0.01 0.08 -10000 0 -10000 0 0
GRB2/SHC -0.003 0.051 -10000 0 -10000 0 0
FOS -0.022 0.11 -10000 0 -0.4 22 22
GLMN 0 0 -10000 0 -10000 0 0
cell motility 0 0.004 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.031 0.078 -10000 0 -0.23 41 41
cell migration -0.003 0.05 -10000 0 -10000 0 0
GRB2 0.007 0 -10000 0 -10000 0 0
CBL 0.007 0 -10000 0 -10000 0 0
MET/RANBP10 0 0 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.008 0.074 -10000 0 -0.19 42 42
MET/MUC20 0 0 -10000 0 -10000 0 0
RAP1B 0.007 0.058 -10000 0 -10000 0 0
RAP1A 0.007 0.058 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.031 0.076 -10000 0 -0.22 41 41
RAF1 -0.005 0.08 -10000 0 -10000 0 0
STAT3 -0.005 0.075 -10000 0 -0.2 1 1
cell proliferation -0.008 0.1 -10000 0 -0.27 41 41
RPS6KB1 -0.001 0.022 -10000 0 -10000 0 0
MAPK3 -0.003 0.003 -10000 0 -10000 0 0
MAPK1 -0.003 0.003 -10000 0 -10000 0 0
RANBP9 0.007 0 -10000 0 -10000 0 0
MAPK8 0.016 0.062 -10000 0 -0.43 2 2
SRC -0.002 0.07 -10000 0 -10000 0 0
PI3K -0.003 0.051 -10000 0 -10000 0 0
MET/Glomulin 0.007 0 -10000 0 -10000 0 0
SOS1 0.007 0 -10000 0 -10000 0 0
MAP2K1 0 0.076 -10000 0 -10000 0 0
MET 0.007 0 -10000 0 -10000 0 0
MAP4K1 0.004 0.061 -10000 0 -10000 0 0
PTK2 0.007 0 -10000 0 -10000 0 0
MAP2K2 0 0.076 -10000 0 -10000 0 0
BAD 0.006 0.014 0.25 1 -10000 0 1
MAP2K4 0.013 0.055 -10000 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.019 0.048 -10000 0 -10000 0 0
INPPL1 0.007 0 -10000 0 -10000 0 0
PXN 0.007 0 -10000 0 -10000 0 0
SH3KBP1 0.007 0 -10000 0 -10000 0 0
HGS -0.008 0.053 -10000 0 -0.14 41 41
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.049 0.14 -10000 0 -0.4 42 42
RASA1 0.006 0.023 -10000 0 -0.4 1 1
NCK1 0.007 0 -10000 0 -10000 0 0
PTPRJ 0.007 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.004 0.057 -10000 0 -10000 0 0
PDPK1 -0.003 0.018 0.3 1 -10000 0 1
HGF/MET/SHIP -0.031 0.076 -10000 0 -0.22 41 41
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.017 0.017 -9999 0 -10000 0 0
PLK1 0.04 0.069 -9999 0 -10000 0 0
CDKN1B 0.064 0.037 -9999 0 -10000 0 0
FOXO3 0.052 0.063 -9999 0 -0.42 2 2
KAT2B 0.012 0.007 -9999 0 -10000 0 0
FOXO1/SIRT1 0.006 0.019 -9999 0 -0.19 2 2
CAT 0.053 0.058 -9999 0 -10000 0 0
CTNNB1 0.007 0 -9999 0 -10000 0 0
AKT1 0.013 0.007 -9999 0 -10000 0 0
FOXO1 0.019 0.019 -9999 0 -0.22 2 2
MAPK10 -0.035 0.092 -9999 0 -0.18 86 86
mol:GTP 0.001 0 -9999 0 -10000 0 0
FOXO4 0.02 0.067 -9999 0 -10000 0 0
response to oxidative stress 0.006 0.007 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.004 0.047 -9999 0 -0.36 5 5
XPO1 0.008 0 -9999 0 -10000 0 0
EP300 0.008 0 -9999 0 -10000 0 0
BCL2L11 0.022 0.01 -9999 0 -10000 0 0
FOXO1/SKP2 0.021 0.018 -9999 0 -0.19 2 2
mol:GDP 0.006 0.007 -9999 0 -10000 0 0
RAN 0.008 0 -9999 0 -10000 0 0
GADD45A 0.046 0.04 -9999 0 -10000 0 0
YWHAQ 0.007 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.026 0.005 -9999 0 -10000 0 0
MST1 0.012 0.007 -9999 0 -10000 0 0
CSNK1D 0.007 0 -9999 0 -10000 0 0
CSNK1E 0.007 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.021 0.006 -9999 0 -10000 0 0
YWHAB 0.007 0 -9999 0 -10000 0 0
MAPK8 0.021 0.017 -9999 0 -0.18 2 2
MAPK9 0.023 0.003 -9999 0 -10000 0 0
YWHAG 0.007 0 -9999 0 -10000 0 0
YWHAE 0.007 0 -9999 0 -10000 0 0
YWHAZ 0.007 0 -9999 0 -10000 0 0
SIRT1 0.002 0.003 -9999 0 -10000 0 0
SOD2 0.065 0.045 -9999 0 -10000 0 0
RBL2 0.053 0.047 -9999 0 -10000 0 0
RAL/GDP 0.017 0.004 -9999 0 -10000 0 0
CHUK 0.012 0.007 -9999 0 -10000 0 0
Ran/GTP 0.008 0 -9999 0 -10000 0 0
CSNK1G2 0.007 0 -9999 0 -10000 0 0
RAL/GTP 0.021 0.004 -9999 0 -10000 0 0
CSNK1G1 0.007 0 -9999 0 -10000 0 0
FASLG 0.021 0.014 -9999 0 -10000 0 0
SKP2 0.007 0 -9999 0 -10000 0 0
USP7 0.008 0 -9999 0 -10000 0 0
IKBKB 0.012 0.007 -9999 0 -10000 0 0
CCNB1 0.053 0.058 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin 0.02 0.038 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.017 -9999 0 -0.19 2 2
CSNK1A1 0.007 0 -9999 0 -10000 0 0
SGK1 0.012 0.007 -9999 0 -10000 0 0
CSNK1G3 0.007 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.014 0 -9999 0 -10000 0 0
ZFAND5 0.025 0.059 -9999 0 -10000 0 0
SFN -0.24 0.05 -9999 0 -0.25 292 292
CDK2 0.007 0 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.027 0.012 -9999 0 -10000 0 0
CREBBP 0.007 0 -9999 0 -10000 0 0
FBXO32 0.041 0.15 -9999 0 -1.1 5 5
BCL6 0.053 0.047 -9999 0 -10000 0 0
RALB 0.008 0 -9999 0 -10000 0 0
RALA 0.008 0 -9999 0 -10000 0 0
YWHAH 0.007 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.007 0.009 -9999 0 -10000 0 0
adherens junction organization 0.01 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.012 0.019 -9999 0 -10000 0 0
FMN1 0.008 0.007 -9999 0 -10000 0 0
mol:IP3 -0.004 0.001 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.007 0.006 -9999 0 -10000 0 0
CTNNB1 0.009 0.001 -9999 0 -10000 0 0
AKT1 0.007 0.009 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.011 0.007 -9999 0 -10000 0 0
CTNND1 0.007 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.007 -9999 0 -10000 0 0
VASP 0.008 0.007 -9999 0 -10000 0 0
ZYX 0.008 0.007 -9999 0 -10000 0 0
JUB 0.008 0.007 -9999 0 -10000 0 0
EGFR(dimer) 0.009 0.02 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin -0.11 0.044 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.003 0.001 -9999 0 -10000 0 0
PIK3CA 0.007 0.001 -9999 0 -10000 0 0
PI3K 0.003 0.001 -9999 0 -10000 0 0
FYN 0.005 0.037 -9999 0 -0.27 5 5
mol:Ca2+ 0 0.01 -9999 0 -10000 0 0
JUP 0.009 0.001 -9999 0 -10000 0 0
PIK3R1 0.007 0.001 -9999 0 -10000 0 0
mol:DAG -0.004 0.001 -9999 0 -10000 0 0
CDH1 -0.22 0.086 -9999 0 -0.25 264 264
RhoA/GDP 0.012 0.019 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.008 0.007 -9999 0 -10000 0 0
SRC 0.007 0 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
RHOA 0.007 0 -9999 0 -10000 0 0
EGFR 0.002 0.041 -9999 0 -0.31 5 5
CASR 0.004 0.009 -9999 0 -10000 0 0
RhoA/GTP 0.005 0.002 -9999 0 -10000 0 0
AKT2 0.007 0.009 -9999 0 -10000 0 0
actin cable formation 0.011 0.007 -9999 0 -10000 0 0
apoptosis 0 0 -9999 0 -10000 0 0
CTNNA1 0.007 0.001 -9999 0 -10000 0 0
mol:GDP 0.008 0.02 -9999 0 -10000 0 0
PIP5K1A 0.008 0.007 -9999 0 -10000 0 0
PLCG1 -0.004 0.001 -9999 0 -10000 0 0
Rac1/GTP 0.009 0.018 -9999 0 -10000 0 0
homophilic cell adhesion -0.001 0.001 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.007 0 -10000 0 -10000 0 0
EPHB2 0.008 0.001 -10000 0 -10000 0 0
EFNB1 0.013 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.01 0.038 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.011 0.045 -10000 0 -0.2 16 16
neuron projection morphogenesis -0.009 0.037 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 -0.007 0.044 -10000 0 -0.18 17 17
DNM1 0.007 0 -10000 0 -10000 0 0
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.011 0.042 -10000 0 -0.5 2 2
YES1 -0.004 0.059 -10000 0 -0.73 2 2
Ephrin B1/EPHB1-2/NCK2 -0.006 0.042 -10000 0 -0.18 16 16
PI3K 0.011 0.042 -10000 0 -0.51 2 2
mol:GDP -0.011 0.042 -10000 0 -0.18 17 17
ITGA2B 0.004 0.036 -10000 0 -0.35 3 3
endothelial cell proliferation 0 0.001 -10000 0 -10000 0 0
FYN -0.007 0.062 -10000 0 -0.73 2 2
MAP3K7 -0.002 0.043 -10000 0 -0.54 2 2
FGR -0.004 0.058 -10000 0 -0.72 2 2
TIAM1 0.005 0.033 -10000 0 -0.4 2 2
PIK3R1 0.007 0 -10000 0 -10000 0 0
RGS3 0.007 0 -10000 0 -10000 0 0
cell adhesion -0.003 0.073 -10000 0 -0.42 3 3
LYN -0.004 0.059 -10000 0 -0.73 2 2
Ephrin B1/EPHB1-2/Src Family Kinases -0.004 0.054 -10000 0 -0.67 2 2
Ephrin B1/EPHB1-2 -0.004 0.047 -10000 0 -0.58 2 2
SRC -0.004 0.058 -10000 0 -0.72 2 2
ITGB3 -0.038 0.13 -10000 0 -0.4 34 34
EPHB1 -0.015 0.092 -10000 0 -0.39 17 17
EPHB4 0.007 0 -10000 0 -10000 0 0
RAC1 0.007 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.001 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.033 0.091 -10000 0 -0.28 36 36
BLK 0 0.06 -10000 0 -0.73 2 2
HCK -0.004 0.058 -10000 0 -0.72 2 2
regulation of stress fiber formation 0.009 0.039 0.18 16 -10000 0 16
MAPK8 0.014 0.049 -10000 0 -0.56 2 2
Ephrin B1/EPHB1-2/RGS3 -0.006 0.042 -10000 0 -0.18 16 16
endothelial cell migration -0.001 0.036 -10000 0 -0.44 2 2
NCK2 0.007 0 -10000 0 -10000 0 0
PTPN13 -0.001 0.042 -10000 0 -0.51 2 2
regulation of focal adhesion formation 0.009 0.039 0.18 16 -10000 0 16
chemotaxis 0.009 0.039 0.18 16 -10000 0 16
PIK3CA 0.007 0 -10000 0 -10000 0 0
Rac1/GTP -0.01 0.037 -10000 0 -10000 0 0
angiogenesis -0.004 0.047 -10000 0 -0.58 2 2
LCK -0.004 0.058 -10000 0 -0.72 2 2
Visual signal transduction: Rods

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
mol:K + 0.007 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.002 0.018 -9999 0 -0.23 2 2
PDE6G/GNAT1/GTP 0 0.008 -9999 0 -0.14 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.023 0.04 -9999 0 -0.19 2 2
mol:Na + -0.023 0.04 -9999 0 -0.18 3 3
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.027 0.072 -9999 0 -0.22 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.024 0.041 -9999 0 -0.19 3 3
CNGB1 -0.055 0.11 -9999 0 -0.25 74 74
RDH5 0.006 0.023 -9999 0 -0.4 1 1
SAG -0.002 0.032 -9999 0 -0.4 2 2
mol:Ca2+ -0.004 0.048 -9999 0 -10000 0 0
Na + (4 Units) -0.021 0.037 -9999 0 -10000 0 0
RGS9 -0.04 0.13 -9999 0 -0.4 35 35
GNB1/GNGT1 0 0 -9999 0 -10000 0 0
GNAT1/GDP -0.023 0.06 -9999 0 -0.19 35 35
GUCY2D 0.006 0.015 -9999 0 -0.25 1 1
GNGT1 0 0 -9999 0 -10000 0 0
GUCY2F 0.001 0.002 -9999 0 -10000 0 0
GNB5 0.007 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.01 0.019 -9999 0 -10000 0 0
mol:11-cis-retinal 0.006 0.023 -9999 0 -0.4 1 1
mol:cGMP -0.002 0.02 -9999 0 -0.19 1 1
GNB1 0.007 0 -9999 0 -10000 0 0
Rhodopsin -0.001 0.016 -9999 0 -0.28 1 1
SLC24A1 0.007 0 -9999 0 -10000 0 0
CNGA1 0.007 0 -9999 0 -10000 0 0
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.004 0.021 -9999 0 -0.2 1 1
RGS9BP 0.004 0.029 -9999 0 -0.25 4 4
Metarhodopsin II/Transducin 0.005 0.002 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.003 0.02 -9999 0 -0.21 1 1
PDE6A/B -0.004 0.024 -9999 0 -0.16 7 7
mol:Pi -0.027 0.072 -9999 0 -0.22 35 35
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0 0 -9999 0 -10000 0 0
PDE6B 0.007 0 -9999 0 -10000 0 0
PDE6A 0 0.038 -9999 0 -0.25 7 7
PDE6G 0.006 0.015 -9999 0 -0.25 1 1
RHO 0.003 0.004 -9999 0 -10000 0 0
PDE6 -0.023 0.057 -9999 0 -0.17 35 35
GUCA1A 0.001 0.032 -9999 0 -0.25 5 5
GC2/GCAP Family -0.003 0.02 -9999 0 -0.21 1 1
GUCA1C 0 0.02 -9999 0 -0.25 2 2
GUCA1B 0.006 0.023 -9999 0 -0.4 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0 0 -9999 0 -10000 0 0
HDAC3 0.007 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.001 0.009 -9999 0 -0.16 1 1
GATA1/HDAC5 -0.001 0.009 -9999 0 -0.16 1 1
GATA2/HDAC5 -0.01 0.051 -9999 0 -0.27 11 11
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.011 0.085 -9999 0 -0.4 14 14
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 0.013 0 -9999 0 -10000 0 0
GATA2 -0.007 0.076 -9999 0 -0.4 11 11
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.007 0 -9999 0 -10000 0 0
HDAC5 0.007 0 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones 0.015 0.04 -9999 0 -10000 0 0
ADRBK1 0.007 0 -9999 0 -10000 0 0
HDAC4 0.007 0 -9999 0 -10000 0 0
XPO1 0.007 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 0.007 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.007 0 -9999 0 -10000 0 0
HDAC6 0.007 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 0.007 0.001 -9999 0 -10000 0 0
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0.007 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.007 0 -9999 0 -10000 0 0
GATA1 0.005 0.015 -9999 0 -0.25 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.007 0 -9999 0 -10000 0 0
NR3C1 0.007 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.017 0 -9999 0 -10000 0 0
SRF 0.007 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 0.007 0 -9999 0 -10000 0 0
RANGAP1 0.007 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 0 -9999 0 -10000 0 0
HDAC4/ER alpha -0.095 0.13 -9999 0 -0.27 106 106
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.015 0.04 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.007 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.007 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.007 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.14 0.19 -9999 0 -0.4 106 106
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.029 0.12 -9999 0 -0.4 27 27
RAN 0.007 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.016 0.051 -9999 0 -0.18 27 27
GNG2 0.007 0 -9999 0 -10000 0 0
NCOR2 0.007 0 -9999 0 -10000 0 0
TUBB2A 0.007 0 -9999 0 -10000 0 0
HDAC11 0.007 0 -9999 0 -10000 0 0
HSP90AA1 0.007 0 -9999 0 -10000 0 0
RANBP2 0.007 0 -9999 0 -10000 0 0
ANKRA2 0.007 0 -9999 0 -10000 0 0
RFXANK 0.007 0 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.001 0.011 -9999 0 -0.19 1 1
RGS9BP 0.004 0.029 -9999 0 -0.25 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0 0 -9999 0 -10000 0 0
mol:ADP 0.005 0.01 -9999 0 -0.16 1 1
GNAT2 0.006 0.003 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.027 0.072 -9999 0 -0.22 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 0.006 0.015 -9999 0 -0.25 1 1
CNGB3 0.005 0.004 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.004 -9999 0 -10000 0 0
Cone PDE6 -0.023 0.06 -9999 0 -0.19 35 35
Cone Metarhodopsin II 0 0.007 -9999 0 -0.12 1 1
Na + (4 Units) 0 0 -9999 0 -10000 0 0
GNAT2/GDP -0.022 0.059 -9999 0 -0.18 35 35
GNB5 0.007 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.004 0.002 -9999 0 -10000 0 0
Cone Transducin -0.001 0.012 -9999 0 -0.21 1 1
SLC24A2 0.003 0.004 -9999 0 -10000 0 0
GNB3/GNGT2 -0.001 0.016 -9999 0 -0.27 1 1
GNB3 0.006 0.023 -9999 0 -0.4 1 1
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0.004 0.004 -9999 0 -10000 0 0
ARR3 0.002 0.003 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0 0 -9999 0 -10000 0 0
mol:Pi -0.027 0.072 -9999 0 -0.22 35 35
Cone CNG Channel 0 0 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.003 0.004 -9999 0 -10000 0 0
RGS9 -0.04 0.13 -9999 0 -0.4 35 35
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 0.007 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.037 0.028 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.007 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.008 0.017 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.001 0.003 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.016 0.032 -9999 0 -10000 0 0
CaM/Ca2+ 0.015 0.032 -9999 0 -10000 0 0
RAP1A 0.007 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.011 0.035 -9999 0 -10000 0 0
AKT1 0.019 0.031 -9999 0 -10000 0 0
MAP2K1 0.017 0.034 -9999 0 -10000 0 0
MAP3K11 0.011 0.035 -9999 0 -10000 0 0
IFNGR1 0.007 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.099 0.15 -9999 0 -0.32 94 94
Rap1/GTP -0.007 0.015 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.017 0.037 -9999 0 -10000 0 0
CEBPB 0.036 0.037 -9999 0 -0.39 1 1
STAT3 0.007 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.038 -9999 0 -10000 0 0
STAT1 0.011 0.035 -9999 0 -10000 0 0
CALM1 0.007 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.037 0.096 -9999 0 -0.24 54 54
PIK3CA 0.007 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.015 0.033 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0 0.014 -9999 0 -0.25 1 1
mol:Ca2+ 0.016 0.035 -9999 0 -10000 0 0
MAPK3 0.025 0.03 -9999 0 -10000 0 0
STAT1 (dimer) -0.019 0.043 -9999 0 -10000 0 0
MAPK1 0.025 0.03 -9999 0 -10000 0 0
JAK2 0.007 0.002 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
JAK1 0.007 0.002 -9999 0 -10000 0 0
CAMK2D 0.007 0 -9999 0 -10000 0 0
DAPK1 0.034 0.041 -9999 0 -0.56 1 1
SMAD7 0.013 0.031 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.009 0.02 -9999 0 -10000 0 0
PI3K 0.013 0.027 -9999 0 -10000 0 0
IFNG -0.037 0.096 -9999 0 -0.24 54 54
apoptosis 0.022 0.033 -9999 0 -0.43 1 1
CAMK2G 0.007 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.007 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.19 -9999 0 -0.4 94 94
CAMK2B -0.012 0.068 -9999 0 -0.25 23 23
FRAP1 0.018 0.03 -9999 0 -10000 0 0
PRKCD 0.019 0.032 -9999 0 -10000 0 0
RAP1B 0.007 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.016 0.032 -9999 0 -10000 0 0
PTPN2 0.007 0 -9999 0 -10000 0 0
EP300 0.008 0 -9999 0 -10000 0 0
IRF1 0.033 0.028 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.022 -9999 0 -10000 0 0
SOCS1 0.003 0.006 -9999 0 -10000 0 0
mol:GDP -0.009 0.019 -9999 0 -10000 0 0
CASP1 0.013 0.031 -9999 0 -10000 0 0
PTGES2 0.007 0 -9999 0 -10000 0 0
IRF9 0.03 0.014 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.01 0.022 -9999 0 -10000 0 0
RAP1/GDP -0.007 0.015 -9999 0 -10000 0 0
CBL 0.01 0.035 -9999 0 -10000 0 0
MAP3K1 0.011 0.035 -9999 0 -10000 0 0
PIAS1 0.007 0 -9999 0 -10000 0 0
PIAS4 0.007 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.016 0.032 -9999 0 -10000 0 0
PTPN11 0.006 0.036 -9999 0 -10000 0 0
CREBBP 0.008 0 -9999 0 -10000 0 0
RAPGEF1 0.007 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -10000 0 -10000 0 0
MAP4K4 0.028 0.006 -10000 0 -10000 0 0
BAG4 0.007 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.004 0.013 -10000 0 -10000 0 0
NFKBIA 0.007 0 -10000 0 -10000 0 0
BIRC3 0.002 0.036 -10000 0 -0.25 6 6
BAX 0 0.007 -10000 0 -10000 0 0
RIPK1 0.007 0 -10000 0 -10000 0 0
AKT1 0.012 0.003 -10000 0 -10000 0 0
BAD -0.003 0.013 -10000 0 -10000 0 0
SMPD1 0.017 0.006 -10000 0 -10000 0 0
RB1 -0.003 0.013 -10000 0 -10000 0 0
FADD/Caspase 8 0.033 0.005 -10000 0 -10000 0 0
MAP2K4 0.001 0.013 -10000 0 -10000 0 0
NSMAF 0.007 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.001 0.013 -10000 0 -10000 0 0
EGF -0.013 0.088 -10000 0 -0.4 15 15
mol:ceramide -0.009 0.014 -10000 0 -10000 0 0
MADD 0.007 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0 -10000 0 -10000 0 0
ASAH1 0.007 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.003 0.013 -10000 0 -10000 0 0
cell proliferation -0.048 0.07 -10000 0 -0.15 95 95
BID 0.02 0.006 -10000 0 -10000 0 0
MAP3K1 -0.003 0.013 -10000 0 -10000 0 0
EIF2A 0.005 0.012 -10000 0 -10000 0 0
TRADD 0.007 0 -10000 0 -10000 0 0
CRADD 0.007 0 -10000 0 -10000 0 0
MAPK3 0.008 0.012 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.012 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.004 0.013 -10000 0 -10000 0 0
FADD 0.028 0.006 -10000 0 -10000 0 0
KSR1 -0.003 0.013 -10000 0 -10000 0 0
MAPK8 0.003 0.021 -10000 0 -0.2 2 2
PRKRA -0.003 0.013 -10000 0 -10000 0 0
PDGFA 0.007 0 -10000 0 -10000 0 0
TRAF2 0.007 0 -10000 0 -10000 0 0
IGF1 -0.12 0.19 -10000 0 -0.4 95 95
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.009 0.014 -10000 0 -10000 0 0
CTSD 0.007 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 -0.039 0.083 -10000 0 -0.16 95 95
PRKCD 0.007 0 -10000 0 -10000 0 0
PRKCZ 0.007 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0 -10000 0 -10000 0 0
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.007 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.024 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.002 0.017 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.013 0 -10000 0 -10000 0 0
MAP2K1 0.005 0.012 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.007 0 -10000 0 -10000 0 0
CYCS 0.001 0.02 0.14 5 -10000 0 5
TNFRSF1A 0.007 0 -10000 0 -10000 0 0
NFKB1 0.007 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 0.001 0.013 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.002 0.017 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.025 0.004 -10000 0 -10000 0 0
MAP2K2 0.005 0.012 -10000 0 -10000 0 0
SMPD3 0.019 0.006 -10000 0 -10000 0 0
TNF 0.002 0.036 -10000 0 -0.25 6 6
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.004 0.042 0.19 15 -10000 0 15
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.001 0.02 0.14 5 -10000 0 5
BCL2 0.001 0.052 -10000 0 -0.4 5 5
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.007 0 -9999 0 -10000 0 0
NFATC1 0.033 0.016 -9999 0 -0.24 1 1
NFATC2 0.019 0.024 -9999 0 -10000 0 0
NFATC3 0.014 0.002 -9999 0 -10000 0 0
YWHAE 0.007 0 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.016 0.032 -9999 0 -0.17 7 7
Exportin 1/Ran/NUP214 0 0 -9999 0 -10000 0 0
mol:DAG 0 0.001 -9999 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.004 0.021 -9999 0 -10000 0 0
BCL2/BAX -0.005 0.035 -9999 0 -0.27 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.002 -9999 0 -10000 0 0
CaM/Ca2+ 0.006 0.002 -9999 0 -10000 0 0
BAX 0.007 0 -9999 0 -10000 0 0
MAPK14 0.007 0.001 -9999 0 -10000 0 0
BAD 0.007 0 -9999 0 -10000 0 0
CABIN1/MEF2D 0.018 0.03 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/BCL2 0.001 0.052 -9999 0 -0.4 5 5
FKBP8 0.007 0 -9999 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.03 -9999 0 -10000 0 0
KPNB1 0.007 0 -9999 0 -10000 0 0
KPNA2 0.007 0 -9999 0 -10000 0 0
XPO1 0.007 0 -9999 0 -10000 0 0
SFN -0.24 0.05 -9999 0 -0.25 292 292
MAP3K8 0.007 0.001 -9999 0 -10000 0 0
NFAT4/CK1 alpha 0 0 -9999 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.007 0.032 -9999 0 -0.21 6 6
CABIN1 0.016 0.032 -9999 0 -0.17 7 7
CALM1 0.007 0.001 -9999 0 -10000 0 0
RAN 0.007 0 -9999 0 -10000 0 0
MAP3K1 0.007 0 -9999 0 -10000 0 0
CAMK4 0.007 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0 0.002 -9999 0 -10000 0 0
MAPK3 0.007 0 -9999 0 -10000 0 0
YWHAH 0.007 0 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -9999 0 -10000 0 0
YWHAB 0.007 0 -9999 0 -10000 0 0
MAPK8 0.005 0.033 -9999 0 -0.4 2 2
MAPK9 0.007 0 -9999 0 -10000 0 0
YWHAG 0.007 0 -9999 0 -10000 0 0
FKBP1A 0.007 0 -9999 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.001 0.011 -9999 0 -10000 0 0
PRKCH 0.007 0 -9999 0 -10000 0 0
CABIN1/Cbp/p300 0 0.002 -9999 0 -10000 0 0
CASP3 0.007 0.001 -9999 0 -10000 0 0
PIM1 0.007 0 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -9999 0 -10000 0 0
apoptosis -0.001 0.01 -9999 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.004 -9999 0 -10000 0 0
PRKCB 0.005 0.033 -9999 0 -0.4 2 2
PRKCE 0.007 0 -9999 0 -10000 0 0
JNK2/NFAT4 0.016 0.002 -9999 0 -10000 0 0
BAD/BCL-XL 0 0 -9999 0 -10000 0 0
PRKCD 0.007 0 -9999 0 -10000 0 0
NUP214 0.007 0 -9999 0 -10000 0 0
PRKCZ 0.008 0.001 -9999 0 -10000 0 0
PRKCA -0.002 0.061 -9999 0 -0.4 7 7
PRKCG -0.016 0.07 -9999 0 -0.25 25 25
PRKCQ 0.007 0 -9999 0 -10000 0 0
FKBP38/BCL2 -0.005 0.035 -9999 0 -0.27 5 5
EP300 0.007 0.002 -9999 0 -10000 0 0
PRKCB1 0 0 -9999 0 -10000 0 0
CSNK2A1 0.007 0 -9999 0 -10000 0 0
NFATc/JNK1 0.034 0.022 -9999 0 -0.23 1 1
CaM/Ca2+/FKBP38 0 0 -9999 0 -10000 0 0
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSNK1A1 0.012 0.003 -9999 0 -10000 0 0
CaM/Ca2+/CAMK IV 0 0 -9999 0 -10000 0 0
NFATc/ERK1 0.035 0.015 -9999 0 -0.23 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.004 0.022 -9999 0 -10000 0 0
NR4A1 0.03 0.062 -9999 0 -0.39 6 6
GSK3B 0.008 0.001 -9999 0 -10000 0 0
positive T cell selection 0.014 0.002 -9999 0 -10000 0 0
NFAT1/CK1 alpha -0.003 0.014 -9999 0 -10000 0 0
RCH1/ KPNB1 0 0 -9999 0 -10000 0 0
YWHAQ 0.007 0 -9999 0 -10000 0 0
PRKACA 0.007 0.001 -9999 0 -10000 0 0
AKAP5 0.007 0 -9999 0 -10000 0 0
MEF2D 0.007 0.002 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
YWHAZ 0.007 0 -9999 0 -10000 0 0
NFATc/p38 alpha 0.035 0.016 -9999 0 -0.23 1 1
CREBBP 0.007 0.002 -9999 0 -10000 0 0
BCL2 0.001 0.052 -9999 0 -0.4 5 5
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.002 0.023 -10000 0 -0.33 1 1
FYN 0.039 0.042 -10000 0 -0.41 2 2
LAT/GRAP2/SLP76 0.007 0.03 -10000 0 -0.33 1 1
IKBKB 0.007 0 -10000 0 -10000 0 0
AKT1 0.043 0.025 -10000 0 -0.28 1 1
B2M 0.009 0.001 -10000 0 -10000 0 0
IKBKG -0.001 0.006 -10000 0 -0.081 1 1
MAP3K8 0.007 0 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.026 -10000 0 -0.067 59 59
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.047 0.031 -10000 0 -0.38 1 1
TRPV6 -0.049 0.1 -10000 0 -0.26 59 59
CD28 0.006 0.023 -10000 0 -0.4 1 1
SHC1 0.04 0.032 -10000 0 -0.4 1 1
receptor internalization 0.035 0.026 -10000 0 -0.31 1 1
PRF1 0.03 0.068 -10000 0 -1.1 1 1
KRAS 0.007 0 -10000 0 -10000 0 0
GRB2 0.007 0 -10000 0 -10000 0 0
COT/AKT1 0.041 0.021 -10000 0 -0.23 1 1
LAT 0.04 0.032 -10000 0 -0.4 1 1
EntrezGene:6955 0.001 0.001 -10000 0 -10000 0 0
CD3D 0.006 0.028 -10000 0 -0.32 2 2
CD3E 0.009 0.001 -10000 0 -10000 0 0
CD3G 0.007 0.015 -10000 0 -0.25 1 1
RASGRP2 -0.013 0.053 -10000 0 -0.16 35 35
RASGRP1 0.048 0.024 -10000 0 -0.27 1 1
HLA-A 0.009 0.001 -10000 0 -10000 0 0
RASSF5 0.007 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.02 -10000 0 -0.091 2 2
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.001 0.01 -10000 0 -0.14 1 1
PRKCA 0.005 0.021 -10000 0 -0.17 1 1
GRAP2 0.007 0 -10000 0 -10000 0 0
mol:IP3 0.023 0.055 0.13 59 -0.26 1 60
EntrezGene:6957 0.001 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.026 0.026 -10000 0 -0.33 1 1
ORAI1 0.032 0.065 0.16 59 -10000 0 59
CSK 0.039 0.032 -10000 0 -0.4 1 1
B7 family/CD28 -0.002 0.027 -10000 0 -0.39 1 1
CHUK 0.007 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.037 0.034 -10000 0 -0.33 2 2
PTPN6 0.038 0.033 -10000 0 -0.4 1 1
VAV1 0.04 0.032 -10000 0 -0.4 1 1
Monovalent TCR/CD3 0.017 0.014 -10000 0 -0.21 1 1
CBL 0.007 0 -10000 0 -10000 0 0
LCK 0.039 0.034 -10000 0 -0.33 2 2
PAG1 0.039 0.032 -10000 0 -0.4 1 1
RAP1A 0.007 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.036 0.034 -10000 0 -0.33 2 2
CD80 0.007 0.015 -10000 0 -0.25 1 1
CD86 0.008 0.001 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.001 0.012 -10000 0 -0.17 1 1
HRAS 0.007 0 -10000 0 -10000 0 0
GO:0035030 0.038 0.029 -10000 0 -0.34 1 1
CD8A 0.008 0.015 -10000 0 -0.25 1 1
CD8B 0.002 0.047 -10000 0 -0.29 7 7
PTPRC 0.006 0.024 -10000 0 -0.4 1 1
PDK1/PKC theta 0.052 0.029 -10000 0 -0.33 1 1
CSK/PAG1 0.041 0.032 -10000 0 -0.39 1 1
SOS1 0.007 0 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.002 -10000 0 -10000 0 0
GRAP2/SLP76 0.006 0.032 -10000 0 -0.38 1 1
STIM1 0.015 0.03 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.035 0.026 -10000 0 -0.32 1 1
mol:DAG 0.009 0.027 -10000 0 -0.24 1 1
RAP1A/GDP 0.01 0.009 -10000 0 -0.047 1 1
PLCG1 0.007 0 -10000 0 -10000 0 0
CD247 0.008 0.001 -10000 0 -10000 0 0
cytotoxic T cell degranulation 0.03 0.064 -10000 0 -1.1 1 1
RAP1A/GTP -0.007 0.018 -10000 0 -0.057 35 35
mol:PI-3-4-5-P3 0.045 0.028 -10000 0 -0.33 1 1
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.025 0.06 0.14 58 -0.32 1 59
NRAS 0.007 0 -10000 0 -10000 0 0
ZAP70 0.007 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.007 0.029 -10000 0 -0.32 1 1
MALT1 0.007 0 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
CD8 heterodimer 0.008 0.034 -10000 0 -0.19 8 8
CARD11 0.007 0 -10000 0 -10000 0 0
PRKCB 0.006 0.019 -10000 0 -0.17 1 1
PRKCE 0.006 0.019 -10000 0 -0.17 1 1
PRKCQ 0.05 0.031 -10000 0 -0.37 1 1
LCP2 0.007 0 -10000 0 -10000 0 0
BCL10 0.007 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.041 0.022 -10000 0 -0.25 1 1
IKK complex 0.031 0.015 -10000 0 -0.066 1 1
RAS family/GDP -0.001 0.002 -10000 0 -10000 0 0
MAP3K14 0.039 0.017 -10000 0 -0.18 1 1
PDPK1 0.044 0.024 -10000 0 -0.27 1 1
TCR/CD3/MHC I/CD8/Fyn 0.032 0.039 -10000 0 -0.4 2 2
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.007 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.006 0.015 -9999 0 -0.25 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.007 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.014 0.002 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.007 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 0.007 0 -9999 0 -10000 0 0
FYN 0.001 0.052 -9999 0 -0.4 5 5
MAP3K12 0.006 0.023 -9999 0 -0.4 1 1
FGR 0.007 0 -9999 0 -10000 0 0
p38 alpha/TAB1 -0.002 0.014 -9999 0 -10000 0 0
PRKG1 -0.092 0.17 -9999 0 -0.4 74 74
DUSP8 0.006 0.023 -9999 0 -0.4 1 1
PGK/cGMP/p38 alpha -0.037 0.065 -9999 0 -0.27 4 4
apoptosis -0.002 0.014 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.007 0 -9999 0 -10000 0 0
DUSP1 -0.001 0.057 -9999 0 -0.4 6 6
PAK1 0.007 0 -9999 0 -10000 0 0
SRC 0.007 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.007 0 -9999 0 -10000 0 0
RAC1 0.007 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 0.007 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.031 0.028 -9999 0 -10000 0 0
BLK -0.04 0.098 -9999 0 -0.25 55 55
HCK 0.007 0 -9999 0 -10000 0 0
MAP2K3 0.007 0 -9999 0 -10000 0 0
DUSP16 0.007 0 -9999 0 -10000 0 0
DUSP10 0.007 0 -9999 0 -10000 0 0
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.031 0.021 -9999 0 -10000 0 0
positive regulation of innate immune response 0.037 0.03 -9999 0 -10000 0 0
LCK 0.007 0 -9999 0 -10000 0 0
p38alpha-beta/MKP7 0.04 0.029 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.04 0.029 -9999 0 -10000 0 0
PGK/cGMP -0.068 0.12 -9999 0 -0.28 74 74
PAK2 0.007 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.038 0.035 -9999 0 -0.32 1 1
CDC42 0.007 0 -9999 0 -10000 0 0
RALB 0.007 0 -9999 0 -10000 0 0
RALA 0.007 0 -9999 0 -10000 0 0
PAK3 0.003 0.015 -9999 0 -0.25 1 1
TCGA08_rtk_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
PDGFRA -0.085 0.17 -10000 0 -0.4 69 69
HRAS 0.007 0 -10000 0 -10000 0 0
EGFR 0.002 0.041 -10000 0 -0.31 5 5
AKT 0.006 0.063 -10000 0 -0.26 15 15
FOXO3 0.007 0 -10000 0 -10000 0 0
AKT1 0.007 0 -10000 0 -10000 0 0
FOXO1 0.005 0.033 -10000 0 -0.4 2 2
AKT3 -0.013 0.088 -10000 0 -0.4 15 15
FOXO4 0.007 0 -10000 0 -10000 0 0
MET 0.007 0 -10000 0 -10000 0 0
PIK3CA 0.007 0 -10000 0 -10000 0 0
PIK3CB 0.007 0 -10000 0 -10000 0 0
NRAS 0.007 0 -10000 0 -10000 0 0
PIK3CG 0.006 0.023 -10000 0 -0.4 1 1
PIK3R3 0.007 0 -10000 0 -10000 0 0
PIK3R2 0.007 0 -10000 0 -10000 0 0
NF1 0.007 0 -10000 0 -10000 0 0
RAS -0.017 0.059 -10000 0 -0.15 4 4
ERBB2 0.001 0.038 -10000 0 -0.25 7 7
proliferation/survival/translation -0.015 0.022 0.26 1 -10000 0 1
PI3K -0.008 0.055 -10000 0 -0.14 4 4
PIK3R1 0.007 0 -10000 0 -10000 0 0
KRAS 0.007 0 -10000 0 -10000 0 0
FOXO 0.023 0.013 -10000 0 -10000 0 0
AKT2 0.007 0 -10000 0 -10000 0 0
PTEN 0.006 0.023 -10000 0 -0.4 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.003 0.05 -10000 0 -0.29 8 8
NFATC2 0.033 0.066 -10000 0 -0.34 1 1
NFATC3 0.006 0.022 -10000 0 -0.22 1 1
CD40LG -0.01 0.11 -10000 0 -0.68 2 2
ITCH -0.001 0.046 -10000 0 -10000 0 0
CBLB -0.001 0.046 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.012 0.069 -10000 0 -10000 0 0
JUNB 0.007 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.029 0.045 -10000 0 -10000 0 0
T cell anergy -0.001 0.052 -10000 0 -10000 0 0
TLE4 0.039 0.056 -10000 0 -0.61 1 1
Jun/NFAT1-c-4/p21SNFT 0.005 0.077 -10000 0 -0.74 2 2
AP-1/NFAT1-c-4 0.024 0.13 -10000 0 -0.76 2 2
IKZF1 0.04 0.044 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.022 0.075 -10000 0 -0.41 1 1
AP-1/NFAT1 -0.007 0.072 -10000 0 -0.27 9 9
CALM1 -0.005 0.032 -10000 0 -10000 0 0
EGR2 0.039 0.086 -10000 0 -0.82 2 2
EGR3 0.04 0.066 -10000 0 -0.54 2 2
NFAT1/FOXP3 0.027 0.06 -10000 0 -0.27 2 2
EGR1 -0.003 0.065 -10000 0 -0.4 8 8
JUN -0.003 0.026 -10000 0 -0.4 1 1
EGR4 0.001 0.041 -10000 0 -0.25 8 8
mol:Ca2+ -0.014 0.035 -10000 0 -10000 0 0
GBP3 0.04 0.044 -10000 0 -10000 0 0
FOSL1 -0.013 0.069 -10000 0 -0.25 24 24
NFAT1-c-4/MAF/IRF4 0.01 0.073 -10000 0 -0.65 2 2
DGKA 0.04 0.044 -10000 0 -10000 0 0
CREM 0.007 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.003 0.085 -10000 0 -0.68 2 2
CTLA4 0.032 0.06 -10000 0 -0.29 4 4
NFAT1-c-4 (dimer)/EGR1 0.009 0.075 -10000 0 -0.68 2 2
NFAT1-c-4 (dimer)/EGR4 0.015 0.072 -10000 0 -0.68 2 2
FOS -0.031 0.1 -10000 0 -0.4 22 22
IFNG -0.008 0.078 -10000 0 -0.75 1 1
T cell activation 0.016 0.072 -10000 0 -0.53 1 1
MAF -0.001 0.057 -10000 0 -0.4 6 6
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.03 0.073 0.75 2 -10000 0 2
TNF 0.035 0.083 -10000 0 -0.62 2 2
FASLG 0.036 0.082 -10000 0 -0.74 2 2
TBX21 0.005 0.034 -10000 0 -0.4 2 2
BATF3 0.007 0 -10000 0 -10000 0 0
PRKCQ 0.01 0.001 -10000 0 -10000 0 0
PTPN1 0.04 0.044 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 0.011 0.068 -10000 0 -0.68 2 2
GATA3 -0.018 0.076 -10000 0 -0.25 30 30
T-helper 1 cell differentiation 0.006 0.083 -10000 0 -0.74 1 1
IL2RA -0.012 0.07 -10000 0 -10000 0 0
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.04 0.044 -10000 0 -10000 0 0
E2F1 0.001 0.05 -10000 0 -0.24 12 12
PPARG -0.022 0.1 -10000 0 -0.4 22 22
SLC3A2 0.04 0.044 -10000 0 -10000 0 0
IRF4 0.005 0.027 -10000 0 -0.32 2 2
PTGS2 -0.016 0.12 -10000 0 -0.68 2 2
CSF2 -0.013 0.12 -10000 0 -0.68 2 2
JunB/Fra1/NFAT1-c-4 0.015 0.073 -10000 0 -0.65 2 2
IL4 0.022 0.077 -10000 0 -0.42 1 1
IL5 -0.013 0.11 -10000 0 -0.68 2 2
IL2 0.016 0.072 -10000 0 -0.54 1 1
IL3 -0.009 0.019 -10000 0 -10000 0 0
RNF128 -0.033 0.094 -10000 0 -0.18 89 89
NFATC1 0.03 0.073 -10000 0 -0.76 2 2
CDK4 -0.025 0.051 -10000 0 -10000 0 0
PTPRK 0.04 0.044 -10000 0 -10000 0 0
IL8 -0.068 0.14 -10000 0 -0.73 2 2
POU2F1 0.007 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.007 0.091 -9999 0 -0.3 22 22
MAP3K8 0.007 0.002 -9999 0 -10000 0 0
FOS 0.011 0.061 -9999 0 -0.37 1 1
PRKCA -0.002 0.061 -9999 0 -0.4 7 7
PTPN7 0.008 0.002 -9999 0 -10000 0 0
HRAS 0.007 0.001 -9999 0 -10000 0 0
PRKCB 0.005 0.033 -9999 0 -0.4 2 2
NRAS 0.007 0.001 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.012 0.036 -9999 0 -0.2 1 1
MAP2K1 0.01 0.066 -9999 0 -0.35 9 9
ELK1 0.006 0.006 -9999 0 -10000 0 0
BRAF -0.012 0.058 -9999 0 -0.34 9 9
mol:GTP 0 0.001 -9999 0 -0.005 22 22
MAPK1 0.012 0.036 -9999 0 -10000 0 0
RAF1 -0.012 0.058 -9999 0 -0.34 9 9
KRAS 0.007 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.012 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.002 0.011 -9999 0 -10000 0 0
NFATC4 -0.003 0.057 -9999 0 -0.19 9 9
ERBB2IP 0.007 0.001 -9999 0 -10000 0 0
HSP90 (dimer) 0.007 0 -9999 0 -10000 0 0
mammary gland morphogenesis 0.013 0.037 -9999 0 -10000 0 0
JUN 0.035 0.036 -9999 0 -10000 0 0
HRAS 0.007 0 -9999 0 -10000 0 0
DOCK7 0.01 0.033 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.024 0.043 -9999 0 -0.21 1 1
AKT1 0.007 0.001 -9999 0 -10000 0 0
BAD 0.012 0.001 -9999 0 -10000 0 0
MAPK10 -0.038 0.055 -9999 0 -0.15 29 29
mol:GTP 0 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.032 0.036 -9999 0 -10000 0 0
RAF1 0.029 0.025 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.031 0.07 -9999 0 -0.21 36 36
STAT3 0.002 0.004 -9999 0 -10000 0 0
cell migration -0.011 0.057 -9999 0 -0.17 5 5
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation 0.031 0.098 -9999 0 -0.55 1 1
FOS 0.016 0.14 -9999 0 -0.45 23 23
NRAS 0.007 0 -9999 0 -10000 0 0
mol:Ca2+ 0.013 0.037 -9999 0 -10000 0 0
MAPK3 0.033 0.068 -9999 0 -0.42 1 1
MAPK1 0.033 0.068 -9999 0 -0.42 1 1
JAK2 0.01 0.033 -9999 0 -10000 0 0
NF2 0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.007 0.021 -9999 0 -10000 0 0
NRG1 -0.04 0.099 -9999 0 -0.25 56 56
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 0.026 0.025 -9999 0 -0.22 2 2
MAPK9 -0.005 0.01 -9999 0 -10000 0 0
ERBB2 -0.004 0.025 -9999 0 -0.17 7 7
ERBB3 -0.003 0.05 -9999 0 -0.25 12 12
SHC1 0.007 0.001 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
apoptosis 0.002 0.005 -9999 0 -10000 0 0
STAT3 (dimer) 0.003 0.004 -9999 0 -10000 0 0
RNF41 0.015 0.002 -9999 0 -10000 0 0
FRAP1 0.006 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.007 0.014 -9999 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.003 0.02 -9999 0 -0.13 2 2
CHRNA1 0.033 0.06 -9999 0 -0.32 1 1
myelination -0.001 0.053 -9999 0 -0.17 9 9
PPP3CB 0.009 0.032 -9999 0 -10000 0 0
KRAS 0.007 0 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.003 0.01 -9999 0 -10000 0 0
NRG2 -0.04 0.13 -9999 0 -0.4 35 35
mol:GDP 0.007 0.021 -9999 0 -10000 0 0
SOS1 0.007 0 -9999 0 -10000 0 0
MAP2K2 0.032 0.03 -9999 0 -10000 0 0
SRC 0.007 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.009 0.033 -9999 0 -10000 0 0
MAP2K1 0.031 0.067 -9999 0 -0.32 1 1
heart morphogenesis 0.013 0.037 -9999 0 -10000 0 0
RAS family/GDP 0.002 0.009 -9999 0 -10000 0 0
GRB2 0.007 0 -9999 0 -10000 0 0
PRKACA 0 0.001 -9999 0 -10000 0 0
CHRNE 0.015 0.009 -9999 0 -10000 0 0
HSP90AA1 0.007 0 -9999 0 -10000 0 0
activation of caspase activity -0.007 0.001 -9999 0 -10000 0 0
nervous system development 0.013 0.037 -9999 0 -10000 0 0
CDC42 0.007 0 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.007 0 -10000 0 -10000 0 0
mol:PIP3 -0.01 0.052 0.22 1 -0.24 14 15
FRAP1 0.007 0.01 -10000 0 -10000 0 0
AKT1 0.008 0.046 0.19 1 -0.2 14 15
INSR 0.007 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.007 0.032 -10000 0 -0.15 14 14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.002 0.01 -10000 0 -10000 0 0
TSC2 0.007 0 -10000 0 -10000 0 0
RHEB/GDP -0.006 0.027 -10000 0 -10000 0 0
TSC1 0.007 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.004 0.063 -10000 0 -0.29 14 14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.007 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0.025 0.15 1 -10000 0 1
MAP3K5 0.006 0.001 -10000 0 -10000 0 0
PIK3R1 0.007 0 -10000 0 -10000 0 0
apoptosis 0.006 0.001 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 14 14
EIF4B 0.015 0.023 0.15 1 -10000 0 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.016 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.002 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.001 0.058 -10000 0 -0.26 14 14
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.016 0.14 1 -10000 0 1
FKBP1A 0.007 0 -10000 0 -10000 0 0
RHEB/GTP -0.006 0.026 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 14 14
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.009 0.047 0.2 1 -0.22 14 15
EIF4E 0.007 0 -10000 0 -10000 0 0
ASK1/PP5C 0.011 0.007 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.01 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.007 0.034 -10000 0 -0.16 14 14
tumor necrosis factor receptor activity 0 0 0.001 14 -10000 0 14
RPS6 0.007 0 -10000 0 -10000 0 0
PPP5C 0.007 0 -10000 0 -10000 0 0
EIF4G1 0.007 0 -10000 0 -10000 0 0
IRS1 -0.01 0.068 -10000 0 -0.32 14 14
INS 0 0 -10000 0 -10000 0 0
PTEN 0.006 0.023 -10000 0 -0.4 1 1
PDK2 -0.009 0.047 0.2 1 -0.22 14 15
EIF4EBP1 0.007 0.001 -10000 0 -10000 0 0
PIK3CA 0.007 0 -10000 0 -10000 0 0
PPP2R5D 0.011 0.01 -10000 0 -10000 0 0
peptide biosynthetic process 0.01 0 -10000 0 -10000 0 0
RHEB 0.007 0 -10000 0 -10000 0 0
EIF4A1 0.007 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 1 -10000 0 1
EEF2 0.01 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.011 0 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.003 0.025 0.19 5 -10000 0 5
RFC1 0.003 0.025 0.19 5 -10000 0 5
PRKDC 0.003 0.025 0.19 5 -10000 0 5
RIPK1 0.007 0 -10000 0 -10000 0 0
CASP7 0 0.004 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.001 0.023 0.18 2 -0.21 2 4
MAP2K4 0.034 0.016 -10000 0 -10000 0 0
mol:ceramide 0.027 0.017 -10000 0 -10000 0 0
GSN 0.003 0.025 0.19 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 8 0.019 0.02 0.16 2 -10000 0 2
FAS 0.005 0.033 -10000 0 -0.4 2 2
BID 0 0 -10000 0 -10000 0 0
MAP3K1 0.026 0.013 -10000 0 -10000 0 0
MAP3K7 0.008 0 -10000 0 -10000 0 0
RB1 0.003 0.025 0.19 5 -10000 0 5
CFLAR 0.007 0 -10000 0 -10000 0 0
HGF/MET -0.032 0.08 -10000 0 -0.23 42 42
ARHGDIB 0.003 0.025 0.19 5 -10000 0 5
FADD 0.008 0.001 -10000 0 -10000 0 0
actin filament polymerization -0.003 0.025 -10000 0 -0.19 5 5
NFKB1 0 0.004 -10000 0 -10000 0 0
MAPK8 0.038 0.022 -10000 0 -10000 0 0
DFFA 0.003 0.025 0.19 5 -10000 0 5
DNA fragmentation during apoptosis 0.003 0.025 0.19 5 -10000 0 5
FAS/FADD/MET -0.001 0.018 -10000 0 -0.22 2 2
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.007 0 -10000 0 -10000 0 0
FAF1 0.008 0.001 -10000 0 -10000 0 0
PARP1 0.003 0.025 0.19 5 -10000 0 5
DFFB 0.003 0.025 0.19 5 -10000 0 5
CHUK 0 0.003 -10000 0 -10000 0 0
FASLG 0.005 0.029 -10000 0 -0.25 4 4
FAS/FADD -0.002 0.022 -10000 0 -0.27 2 2
HGF -0.049 0.14 -10000 0 -0.4 42 42
LMNA 0.003 0.023 0.18 5 -10000 0 5
CASP6 0.003 0.025 0.19 5 -10000 0 5
CASP10 0.008 0.001 -10000 0 -10000 0 0
CASP3 0.004 0.029 0.23 5 -10000 0 5
PTPN13 0.005 0.033 -10000 0 -0.4 2 2
CASP8 0 0 -10000 0 -10000 0 0
IL6 0.023 0.016 -10000 0 -10000 0 0
MET 0.007 0 -10000 0 -10000 0 0
ICAD/CAD 0.003 0.023 0.18 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 10 0.027 0.017 -10000 0 -10000 0 0
activation of caspase activity by cytochrome c 0 0 -10000 0 -10000 0 0
PAK2 0.003 0.025 0.19 5 -10000 0 5
BCL2 0.001 0.052 -10000 0 -0.4 5 5
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.012 0.019 -10000 0 -0.22 1 1
NFATC2 0.005 0.043 -10000 0 -0.23 9 9
NFATC3 0.012 0.014 -10000 0 -10000 0 0
CD40LG 0.017 0.092 -10000 0 -0.31 2 2
PTGS2 0.011 0.1 -10000 0 -0.31 6 6
JUNB 0.007 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.005 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.005 -10000 0 -10000 0 0
CALM1 0.008 0.004 -10000 0 -10000 0 0
JUN 0.007 0.023 -10000 0 -0.4 1 1
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.001 -10000 0 -10000 0 0
FOSL1 -0.013 0.069 -10000 0 -0.25 24 24
CREM 0.007 0 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.017 0.039 -10000 0 -0.22 2 2
FOS -0.021 0.1 -10000 0 -0.4 22 22
IFNG 0 0.12 -10000 0 -0.33 10 10
AP-1/NFAT1-c-4 -0.016 0.089 -10000 0 -0.32 4 4
FASLG 0.016 0.095 -10000 0 -0.31 5 5
NFAT1-c-4/ICER1 -0.012 0.033 -10000 0 -0.21 2 2
IL2RA 0.015 0.097 -10000 0 -0.3 7 7
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSF2 0.015 0.096 -10000 0 -0.33 3 3
JunB/Fra1/NFAT1-c-4 -0.007 0.045 0.1 10 -0.19 3 13
IL4 0.012 0.091 -10000 0 -0.31 2 2
IL2 -0.001 0.006 -10000 0 -10000 0 0
IL3 -0.004 0.008 -10000 0 -10000 0 0
FKBP1A 0.007 0 -10000 0 -10000 0 0
BATF3 0.007 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.007 0 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 0.066 0.065 -10000 0 -10000 0 0
CRP 0.063 0.065 -10000 0 -10000 0 0
cell cycle arrest 0.064 0.07 -10000 0 -0.43 1 1
TIMP1 0.067 0.059 -10000 0 -10000 0 0
IL6ST -0.008 0.088 -10000 0 -0.4 15 15
Rac1/GDP 0.039 0.054 -10000 0 -0.3 2 2
AP1 0.025 0.065 -10000 0 -0.43 2 2
GAB2 0.007 0.034 -10000 0 -0.4 2 2
TNFSF11 0.063 0.068 -10000 0 -10000 0 0
HSP90B1 0.034 0.015 -10000 0 -10000 0 0
GAB1 0.009 0.004 -10000 0 -10000 0 0
MAPK14 0.028 0.051 -10000 0 -0.33 1 1
AKT1 0.037 0.021 -10000 0 -10000 0 0
FOXO1 0.039 0.025 -10000 0 -10000 0 0
MAP2K6 0.028 0.055 -10000 0 -0.29 2 2
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.055 0.056 -10000 0 -0.3 2 2
MITF -0.015 0.1 -10000 0 -0.34 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.007 0 -10000 0 -10000 0 0
A2M -0.081 0.32 -10000 0 -1.2 23 23
CEBPB 0.012 0.001 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.038 0.06 0.2 21 -0.38 2 23
STAT3 0.065 0.072 -10000 0 -0.45 1 1
STAT1 0 0.004 -10000 0 -10000 0 0
CEBPD 0.066 0.065 -10000 0 -10000 0 0
PIK3CA 0.008 0 -10000 0 -10000 0 0
PI3K 0.012 0.003 -10000 0 -10000 0 0
JUN 0.006 0.023 -10000 0 -0.4 1 1
PIAS3/MITF -0.013 0.098 -10000 0 -0.32 10 10
MAPK11 0.028 0.051 -10000 0 -0.33 1 1
STAT3 (dimer)/FOXO1 0.068 0.094 -10000 0 -0.56 2 2
GRB2/SOS1/GAB family 0.002 0.058 0.16 21 -0.31 2 23
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.024 0.058 -10000 0 -0.29 2 2
GRB2 0.009 0.004 -10000 0 -10000 0 0
JAK2 0.007 0 -10000 0 -10000 0 0
LBP 0.067 0.059 -10000 0 -10000 0 0
PIK3R1 0.008 0 -10000 0 -10000 0 0
JAK1 0.01 0.002 -10000 0 -10000 0 0
MYC 0.058 0.12 -10000 0 -0.93 4 4
FGG 0.062 0.065 -10000 0 -10000 0 0
macrophage differentiation 0.064 0.07 -10000 0 -0.43 1 1
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.01 0.047 -10000 0 -0.28 2 2
JUNB 0.064 0.063 -10000 0 -10000 0 0
FOS -0.022 0.11 -10000 0 -0.4 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.059 -10000 0 -0.33 2 2
STAT1/PIAS1 0.034 0.053 -10000 0 -0.27 2 2
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.024 -10000 0 -0.22 2 2
STAT3 (dimer) 0.065 0.071 -10000 0 -0.44 1 1
PRKCD 0.069 0.06 -10000 0 -0.38 1 1
IL6R 0.003 0.052 -10000 0 -0.4 5 5
SOCS3 0.025 0.049 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.015 0.053 -10000 0 -0.21 15 15
Rac1/GTP 0.035 0.056 -10000 0 -0.3 2 2
HCK 0.008 0.002 -10000 0 -10000 0 0
MAPKKK cascade 0.043 0.061 -10000 0 -0.49 2 2
bone resorption 0.063 0.067 -10000 0 -10000 0 0
IRF1 0.066 0.065 -10000 0 -10000 0 0
mol:GDP 0.034 0.056 -10000 0 -0.31 2 2
SOS1 0.009 0.006 -10000 0 -10000 0 0
VAV1 0.034 0.056 -10000 0 -0.31 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.017 0.063 -10000 0 -0.34 5 5
PTPN11 0 0.004 -10000 0 -10000 0 0
IL6/IL6RA 0.01 0.045 -10000 0 -0.24 7 7
gp130 (dimer)/TYK2/TYK2/LMO4 0.009 0.052 -10000 0 -0.22 15 15
gp130 (dimer)/JAK2/JAK2/LMO4 0.009 0.052 -10000 0 -0.22 15 15
IL6 0.007 0.038 -10000 0 -0.24 7 7
PIAS3 0.007 0 -10000 0 -10000 0 0
PTPRE 0.001 0.003 -10000 0 -10000 0 0
PIAS1 0.007 0 -10000 0 -10000 0 0
RAC1 0.008 0 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.012 0.057 -10000 0 -0.2 19 19
LMO4 0.012 0.002 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.01 0.051 -10000 0 -10000 0 0
MCL1 0.04 0.02 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.029 0.002 -9999 0 -10000 0 0
KLHL20 0 0.005 -9999 0 -10000 0 0
CYFIP2 0.007 0 -9999 0 -10000 0 0
Rac1/GDP 0.01 0.01 -9999 0 -10000 0 0
ENAH 0.029 0.002 -9999 0 -10000 0 0
AP1M1 0.007 0 -9999 0 -10000 0 0
RAP1B 0.007 0 -9999 0 -10000 0 0
RAP1A 0.007 0 -9999 0 -10000 0 0
CTNNB1 0.007 0 -9999 0 -10000 0 0
CDC42/GTP -0.021 0.008 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0.003 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.091 0.036 -9999 0 -10000 0 0
RAPGEF1 0.026 0.002 -9999 0 -10000 0 0
CTNND1 0.007 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.038 0.015 -9999 0 -10000 0 0
CRK 0.026 0.001 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin -0.11 0.042 -9999 0 -10000 0 0
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.007 0 -9999 0 -10000 0 0
NCKAP1 0.007 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.029 0.002 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.012 0.005 -9999 0 -10000 0 0
MLLT4 0.007 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.016 -9999 0 -0.2 2 2
PI3K -0.015 0.006 -9999 0 -10000 0 0
ARF6 0.007 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.14 0.054 -9999 0 -10000 0 0
TIAM1 0.005 0.033 -9999 0 -0.4 2 2
E-cadherin(dimer)/Ca2+ -0.085 0.033 -9999 0 -10000 0 0
AKT1 -0.007 0.003 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
CDH1 -0.22 0.086 -9999 0 -0.25 264 264
RhoA/GDP 0.01 0.01 -9999 0 -10000 0 0
actin cytoskeleton organization 0.016 0.008 -9999 0 -10000 0 0
CDC42/GDP 0.01 0.01 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.026 0.016 -9999 0 -10000 0 0
ITGB7 0.007 0 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.091 0.036 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.089 0.035 -9999 0 -10000 0 0
mol:GDP 0.006 0.011 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.007 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0.006 0.003 -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 0.007 0 -9999 0 -10000 0 0
CDC42 0.007 0 -9999 0 -10000 0 0
CTNNA1 0.007 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.016 0.004 -9999 0 -10000 0 0
NME1 0.007 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.029 0.002 -9999 0 -10000 0 0
regulation of cell-cell adhesion -0.02 0.008 -9999 0 -10000 0 0
WASF2 0 0.002 -9999 0 -10000 0 0
Rap1/GTP -0.027 0.011 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.081 0.032 -9999 0 -10000 0 0
CCND1 0.018 0.005 -9999 0 -10000 0 0
VAV2 0.03 0 -9999 0 -10000 0 0
RAP1/GDP -0.015 0.006 -9999 0 -10000 0 0
adherens junction assembly 0.029 0.002 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.007 0 -9999 0 -10000 0 0
PIP5K1C 0.007 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.074 0.029 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.035 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.029 0.002 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.008 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.11 0.042 -9999 0 -10000 0 0
ITGAE 0.007 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.038 0.015 -9999 0 -10000 0 0
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.003 0.033 -9999 0 -0.25 5 5
mol:Halofuginone 0.003 0 -9999 0 -10000 0 0
ITGA1 0.007 0 -9999 0 -10000 0 0
CDKN1A 0.017 0.017 -9999 0 -10000 0 0
PRL-3/alpha Tubulin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.055 0.11 -9999 0 -0.28 59 59
AGT -0.072 0.16 -9999 0 -0.4 59 59
CCNA2 0.019 0.033 -9999 0 -10000 0 0
TUBA1B 0.007 0 -9999 0 -10000 0 0
EGR1 0.007 0.046 -9999 0 -0.27 8 8
CDK2/Cyclin E1 0.024 0.017 -9999 0 -10000 0 0
MAPK3 0.013 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
PTP4A1 0.016 0.034 -9999 0 -10000 0 0
PTP4A3 0.007 0 -9999 0 -10000 0 0
PTP4A2 0.007 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.007 0 -9999 0 -10000 0 0
RAC1 0.017 0.017 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 0.019 0.032 -9999 0 -10000 0 0
RABGGTA 0.007 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC 0.017 0.017 -9999 0 -10000 0 0
RHOA 0.017 0.017 -9999 0 -10000 0 0
cell motility 0.019 0.018 -9999 0 -10000 0 0
PRL-1/alpha Tubulin 0.019 0.032 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0 0 -9999 0 -10000 0 0
ROCK1 0.019 0.018 -9999 0 -10000 0 0
RABGGTB 0.007 0 -9999 0 -10000 0 0
CDK2 0.007 0 -9999 0 -10000 0 0
mitosis 0.016 0.034 -9999 0 -10000 0 0
ATF5 0.007 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.018 0 -9999 0 -10000 0 0
CRKL 0.007 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.007 0 -9999 0 -10000 0 0
ITGA4 0.007 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0 0.006 -9999 0 -10000 0 0
EPO -0.023 0.1 -9999 0 -0.4 22 22
alpha4/beta7 Integrin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.007 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.02 0.071 -9999 0 -0.27 22 22
lamellipodium assembly 0 0.001 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.007 0 -9999 0 -10000 0 0
JAK2 0.004 0.055 -9999 0 -0.2 22 22
PXN 0.007 0 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
MADCAM1 0.005 0.015 -9999 0 -0.25 1 1
cell adhesion 0 0.006 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.007 0 -9999 0 -10000 0 0
SRC 0.014 0.034 -9999 0 -0.2 8 8
ITGB7 0.007 0 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.006 0.036 -9999 0 -0.22 8 8
p130Cas/Crk/Dock1 0.025 0.029 -9999 0 -10000 0 0
VCAM1 -0.003 0.065 -9999 0 -0.4 8 8
RHOA 0.007 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0 0 -9999 0 -10000 0 0
BCAR1 0.018 0.032 -9999 0 -0.18 8 8
EPOR 0.007 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.007 0 -9999 0 -10000 0 0
GIT1 0.007 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.001 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.001 0.004 -9999 0 -10000 0 0
VDR 0.007 0 -9999 0 -10000 0 0
FAM120B 0.007 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.034 0.014 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.039 0.015 -9999 0 -10000 0 0
MED1 0.007 0 -9999 0 -10000 0 0
mol:9cRA 0.004 0.002 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.011 0.046 -9999 0 -0.19 15 15
RXRs/NUR77 0.021 0.034 -9999 0 -0.19 7 7
RXRs/PPAR 0.009 0.058 -9999 0 -0.19 24 24
NCOR2 0.007 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.001 0.015 -9999 0 -0.18 2 2
RARA 0.007 0 -9999 0 -10000 0 0
NCOA1 0.007 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.007 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.001 0.015 -9999 0 -0.19 2 2
RARG 0.007 0 -9999 0 -10000 0 0
RPS6KB1 0.001 0.005 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.011 0.046 -9999 0 -10000 0 0
THRA 0.007 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.024 0.015 -9999 0 -0.19 1 1
NR1H4 0 0.02 -9999 0 -0.25 2 2
RXRs/LXRs/DNA 0.037 0.014 -9999 0 -10000 0 0
NR1H2 0.011 0.002 -9999 0 -10000 0 0
NR1H3 0.011 0.001 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.023 0.014 -9999 0 -0.18 1 1
NR4A1 -0.001 0.057 -9999 0 -0.4 6 6
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.019 0.012 -9999 0 -0.17 1 1
RXRG 0.006 0.028 -9999 0 -0.32 2 2
RXR alpha/CCPG 0.013 0.002 -9999 0 -10000 0 0
RXRA 0.011 0.002 -9999 0 -10000 0 0
RXRB 0.011 0.001 -9999 0 -10000 0 0
THRB -0.01 0.082 -9999 0 -0.4 13 13
PPARG -0.022 0.11 -9999 0 -0.4 22 22
PPARD 0.007 0 -9999 0 -10000 0 0
TNF 0.041 0.018 -9999 0 -10000 0 0
mol:Oxysterols 0.004 0.001 -9999 0 -10000 0 0
cholesterol transport 0.039 0.015 -9999 0 -10000 0 0
PPARA 0.006 0.023 -9999 0 -0.4 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.005 0.033 -9999 0 -0.4 2 2
RXRs/NUR77/BCL2 0.011 0.042 -9999 0 -0.2 12 12
SREBF1 0.042 0.014 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.024 0.015 -9999 0 -0.19 1 1
ABCA1 0.042 0.014 -9999 0 -10000 0 0
RARs/THRs -0.009 0.039 -9999 0 -0.18 15 15
RXRs/FXR 0.021 0.018 -9999 0 -0.2 1 1
BCL2 0.001 0.052 -9999 0 -0.4 5 5
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0 -10000 0 -10000 0 0
HDAC3 0.007 0 -10000 0 -10000 0 0
VDR 0.007 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.007 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.023 0.02 -10000 0 -10000 0 0
KAT2B 0.007 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
AKT1 0.014 0.033 0.17 6 -0.2 2 8
RAR alpha/9cRA/Cyclin H -0.005 0.036 -10000 0 -0.22 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.021 -10000 0 -10000 0 0
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.004 0.039 -10000 0 -0.3 3 3
NCOR2 0.007 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.026 0.058 -10000 0 -0.33 7 7
NCOA2 0.002 0.046 -10000 0 -0.4 4 4
NCOA3 0.007 0 -10000 0 -10000 0 0
NCOA1 0.007 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.007 0 -10000 0 -10000 0 0
RARG 0.008 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.008 0 -10000 0 -10000 0 0
MAPK1 0.007 0 -10000 0 -10000 0 0
MAPK8 0.005 0.033 -10000 0 -0.4 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.006 0.053 -10000 0 -0.34 7 7
RARA 0.008 0.039 -10000 0 -0.21 9 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.019 0.033 -10000 0 -0.21 4 4
PRKCA 0 0.061 -10000 0 -0.4 7 7
RXRs/RARs/NRIP1/9cRA/HDAC1 0.021 0.059 -10000 0 -0.34 7 7
RXRG 0.002 0.048 -10000 0 -0.27 8 8
RXRA 0.013 0.037 -10000 0 -0.19 9 9
RXRB 0.005 0.045 -10000 0 -0.26 7 7
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.002 0.061 -10000 0 -0.4 7 7
CRBP1/9-cic-RA -0.006 0.042 -10000 0 -0.28 7 7
RARB 0.006 0.033 -10000 0 -0.4 2 2
PRKCG -0.014 0.07 -10000 0 -0.25 25 25
MNAT1 0.007 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.024 0.066 -10000 0 -0.36 7 7
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.025 0.052 -10000 0 -0.28 7 7
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.031 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.021 0.059 -10000 0 -0.34 7 7
positive regulation of DNA binding -0.006 0.035 -10000 0 -0.21 7 7
NRIP1 0.021 0.055 -10000 0 -10000 0 0
RXRs/RARs 0.017 0.06 -10000 0 -0.35 7 7
RXRs/RXRs/DNA/9cRA -0.006 0.055 -10000 0 -0.36 7 7
PRKACA 0.007 0 -10000 0 -10000 0 0
CDK7 0.007 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.003 0.021 -10000 0 -10000 0 0
CCNH 0.007 0 -10000 0 -10000 0 0
CREBBP 0.007 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.01 0.004 -9999 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -10000 0 0
cytokine production during immune response -0.002 0.048 -9999 0 -10000 0 0
IL27/IL27R/JAK1 -0.018 0.044 -9999 0 -10000 0 0
TBX21 -0.006 0.074 -9999 0 -10000 0 0
IL12B 0.003 0.029 -9999 0 -0.25 4 4
IL12A -0.003 0.038 -9999 0 -0.16 16 16
IL6ST -0.014 0.089 -9999 0 -0.4 15 15
IL27RA/JAK1 0.008 0.013 -9999 0 -10000 0 0
IL27 0.005 0.004 -9999 0 -10000 0 0
TYK2 0.007 0.003 -9999 0 -10000 0 0
T-helper cell lineage commitment 0.008 0.016 -9999 0 -10000 0 0
T-helper 2 cell differentiation -0.002 0.048 -9999 0 -10000 0 0
T cell proliferation during immune response -0.002 0.048 -9999 0 -10000 0 0
MAPKKK cascade 0.002 0.048 -9999 0 -10000 0 0
STAT3 0.007 0 -9999 0 -10000 0 0
STAT2 0.007 0 -9999 0 -10000 0 0
STAT1 0.007 0.001 -9999 0 -10000 0 0
IL12RB1 0.007 0.001 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -10000 0 0
IL12RB2 -0.026 0.1 -9999 0 -0.39 1 1
IL27/IL27R/JAK2/TYK2 0.002 0.048 -9999 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.002 0.048 -9999 0 -10000 0 0
STAT1 (dimer) -0.031 0.073 -9999 0 -10000 0 0
JAK2 0.006 0.003 -9999 0 -10000 0 0
JAK1 0.007 0.001 -9999 0 -10000 0 0
STAT2 (dimer) 0.006 0.046 -9999 0 -10000 0 0
T cell proliferation 0.005 0.049 -9999 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.013 0.023 -9999 0 -10000 0 0
IL17A 0.007 0.016 -9999 0 -10000 0 0
mast cell activation -0.002 0.048 -9999 0 -10000 0 0
IFNG 0.001 0.013 -9999 0 -10000 0 0
T cell differentiation -0.002 0.003 -9999 0 -0.015 1 1
STAT3 (dimer) 0.006 0.046 -9999 0 -10000 0 0
STAT5A (dimer) 0.006 0.046 -9999 0 -10000 0 0
STAT4 (dimer) 0.006 0.046 -9999 0 -10000 0 0
STAT4 0.007 0 -9999 0 -10000 0 0
T cell activation -0.005 0.002 -9999 0 -10000 0 0
IL27R/JAK2/TYK2 -0.005 0.046 -9999 0 -10000 0 0
GATA3 -0.003 0.021 -9999 0 -10000 0 0
IL18 0.005 0.017 -9999 0 -0.17 3 3
positive regulation of mast cell cytokine production 0.006 0.045 -9999 0 -10000 0 0
IL27/EBI3 0.005 0.006 -9999 0 -10000 0 0
IL27RA 0.003 0.011 -9999 0 -10000 0 0
IL6 0.004 0.038 -9999 0 -0.24 7 7
STAT5A 0.007 0 -9999 0 -10000 0 0
monocyte differentiation 0 0.001 -9999 0 -10000 0 0
IL2 0 0.003 -9999 0 -10000 0 0
IL1B -0.023 0.065 -9999 0 -0.16 53 53
EBI3 0.005 0.004 -9999 0 -10000 0 0
TNF 0.003 0.024 -9999 0 -0.16 6 6
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.017 0.032 -9999 0 -0.55 1 1
VEGFR1 homodimer/NRP1 -0.002 0.032 -9999 0 -0.55 1 1
mol:DAG 0.021 0.031 -9999 0 -0.5 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.029 -9999 0 -0.51 1 1
CaM/Ca2+ 0.024 0.029 -9999 0 -0.47 1 1
HIF1A 0.011 0.018 -9999 0 -0.3 1 1
GAB1 0.007 0 -9999 0 -10000 0 0
AKT1 0.033 0.028 -9999 0 -0.44 1 1
PLCG1 0.021 0.031 -9999 0 -0.5 1 1
NOS3 0.027 0.056 -9999 0 -0.27 10 10
CBL 0.007 0 -9999 0 -10000 0 0
mol:NO 0.027 0.055 -9999 0 -0.26 10 10
FLT1 0.016 0.037 -9999 0 -0.63 1 1
PGF 0.006 0.015 -9999 0 -0.25 1 1
VEGFR1 homodimer/NRP2/VEGFR121 -0.007 0.042 -9999 0 -0.5 1 1
CALM1 0.007 0 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.03 0.053 -9999 0 -0.41 1 1
endothelial cell proliferation 0.025 0.043 -9999 0 -0.49 1 1
mol:Ca2+ 0.021 0.03 -9999 0 -0.49 1 1
MAPK3 0.024 0.04 -9999 0 -0.43 1 1
MAPK1 0.024 0.04 -9999 0 -0.43 1 1
PIK3R1 0.007 0 -9999 0 -10000 0 0
PLGF homodimer 0.006 0.015 -9999 0 -0.25 1 1
PRKACA 0.007 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.033 0.12 -9999 0 -0.4 30 30
VEGFA homodimer 0.007 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.017 0.032 -9999 0 -0.55 1 1
platelet activating factor biosynthetic process 0.027 0.038 -9999 0 -0.42 1 1
PI3K -0.002 0.027 -9999 0 -0.47 1 1
PRKCA 0.02 0.042 -9999 0 -0.46 1 1
PRKCB 0.024 0.033 -9999 0 -0.46 1 1
VEGFR1 homodimer/PLGF homodimer 0.016 0.033 -9999 0 -0.55 1 1
VEGFA 0.007 0 -9999 0 -10000 0 0
VEGFB 0.007 0 -9999 0 -10000 0 0
mol:IP3 0.021 0.031 -9999 0 -0.5 1 1
RASA1 0.021 0.032 -9999 0 -0.5 1 1
NRP2 -0.003 0.065 -9999 0 -0.4 8 8
VEGFR1 homodimer 0.016 0.037 -9999 0 -0.63 1 1
VEGFB homodimer 0.007 0 -9999 0 -10000 0 0
NCK1 0.007 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.012 0.077 -9999 0 -0.57 1 1
PTPN11 0.007 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.027 -9999 0 -0.46 1 1
mol:L-citrulline 0.027 0.055 -9999 0 -0.26 10 10
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.027 -9999 0 -0.47 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.029 -9999 0 -0.5 1 1
CD2AP 0.007 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.001 0.026 -9999 0 -0.44 1 1
PDPK1 0.028 0.027 -9999 0 -0.44 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.029 -9999 0 -0.5 1 1
mol:NADP 0.027 0.055 -9999 0 -0.26 10 10
HSP90AA1 0.007 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.027 -9999 0 -0.47 1 1
VEGFR1 homodimer/NRP2 0.011 0.05 -9999 0 -0.55 1 1
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.008 0.038 -10000 0 -0.19 13 13
MAPK9 0.005 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0 0 -10000 0 -10000 0 0
GNB1 0.007 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 0.005 0 -10000 0 -10000 0 0
Gs family/GTP -0.009 0.043 -10000 0 -0.21 13 13
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 0.003 0.012 0.059 13 -10000 0 13
GNAL -0.01 0.082 -10000 0 -0.4 13 13
GNG2 0.007 0 -10000 0 -10000 0 0
CRH 0 0 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.023 -10000 0 -0.28 2 2
MAPK11 0.005 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0.007 0 -9999 0 -10000 0 0
MAP2K3 0.022 0.007 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.025 0.009 -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 -0.03 0.12 -9999 0 -0.4 28 28
TXN 0.005 0.004 -9999 0 -10000 0 0
CALM1 0.007 0 -9999 0 -10000 0 0
GADD45A 0.007 0 -9999 0 -10000 0 0
GADD45B 0.007 0 -9999 0 -10000 0 0
MAP3K1 0.007 0 -9999 0 -10000 0 0
MAP3K6 0.007 0 -9999 0 -10000 0 0
MAP3K7 0.007 0 -9999 0 -10000 0 0
MAP3K4 0.007 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.007 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.005 0 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.012 0.068 -9999 0 -0.25 23 23
CCM2 0.007 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.01 0.034 -9999 0 -0.13 23 23
MAPK11 0.007 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.008 0.029 -9999 0 -10000 0 0
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.01 0 -9999 0 -10000 0 0
TAOK2 0.01 0 -9999 0 -10000 0 0
TAOK3 0.01 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.007 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.007 0 -9999 0 -10000 0 0
MAP3K10 0.007 0 -9999 0 -10000 0 0
MAP3K3 0.007 0 -9999 0 -10000 0 0
TRX/ASK1 0.009 0.003 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.017 0.053 -9999 0 -0.18 28 28
Caspase cascade in apoptosis

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
TOP1 0.013 0.033 -10000 0 -0.48 1 1
ACTA1 0.008 0.041 -10000 0 -0.63 1 1
NUMA1 0.013 0.033 -10000 0 -0.48 1 1
SPTAN1 0.009 0.041 -10000 0 -0.62 1 1
LIMK1 0.009 0.041 -10000 0 -0.62 1 1
BIRC3 0.002 0.036 -10000 0 -0.25 6 6
BIRC2 0.007 0.015 -10000 0 -0.25 1 1
BAX 0.007 0 -10000 0 -10000 0 0
CASP10 0.005 0.046 -10000 0 -0.44 1 1
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.007 0 -10000 0 -10000 0 0
PTK2 0.013 0.033 -10000 0 -0.48 1 1
DIABLO 0.007 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.009 0.04 -10000 0 -0.61 1 1
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.007 0 -10000 0 -10000 0 0
GSN 0.009 0.041 -10000 0 -0.63 1 1
MADD 0.007 0 -10000 0 -10000 0 0
TFAP2A 0.049 0.019 -10000 0 -10000 0 0
BID 0.009 0.023 -10000 0 -0.29 1 1
MAP3K1 0.007 0.015 -10000 0 -0.19 1 1
TRADD 0.007 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.041 -10000 0 -0.62 1 1
CASP9 0.007 0 -10000 0 -10000 0 0
DNA repair -0.004 0.012 0.13 1 -10000 0 1
neuron apoptosis 0.015 0.005 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.014 0.039 -10000 0 -0.6 1 1
APAF1 0.007 0 -10000 0 -10000 0 0
CASP6 0.02 0.019 -10000 0 -0.25 1 1
TRAF2 0.007 0 -10000 0 -10000 0 0
ICAD/CAD 0.013 0.04 -10000 0 -0.6 1 1
CASP7 -0.006 0.011 -10000 0 -10000 0 0
KRT18 0.019 0.017 -10000 0 -10000 0 0
apoptosis 0.013 0.04 -10000 0 -0.5 1 1
DFFA 0.009 0.041 -10000 0 -0.62 1 1
DFFB 0.009 0.041 -10000 0 -0.62 1 1
PARP1 0.004 0.012 -10000 0 -0.14 1 1
actin filament polymerization -0.009 0.047 0.22 8 -10000 0 8
TNF 0.002 0.036 -10000 0 -0.25 6 6
CYCS 0.009 0.019 -10000 0 -0.18 1 1
SATB1 0.024 0.018 -10000 0 -0.24 1 1
SLK 0.009 0.041 -10000 0 -0.62 1 1
p15 BID/BAX 0.012 0.02 -10000 0 -0.26 1 1
CASP2 0.029 0.005 -10000 0 -10000 0 0
JNK cascade -0.007 0.014 0.19 1 -10000 0 1
CASP3 0.005 0.043 -10000 0 -0.66 1 1
LMNB2 0.028 0.007 -10000 0 -10000 0 0
RIPK1 0.007 0 -10000 0 -10000 0 0
CASP4 0.007 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.002 0.016 -10000 0 -10000 0 0
negative regulation of DNA binding 0.049 0.018 -10000 0 -10000 0 0
stress fiber formation 0.009 0.04 -10000 0 -0.61 1 1
GZMB -0.002 0.055 -10000 0 -0.17 25 25
CASP1 0.01 0 -10000 0 -10000 0 0
LMNB1 0.028 0.007 -10000 0 -10000 0 0
APP 0.015 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.007 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0 -10000 0 -10000 0 0
VIM 0.009 0.04 -10000 0 -0.49 1 1
LMNA 0.028 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.026 0.006 -10000 0 -10000 0 0
LRDD 0.007 0 -10000 0 -10000 0 0
SREBF1 0.009 0.041 -10000 0 -0.62 1 1
APAF-1/Caspase 9 -0.001 0.01 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.013 0.032 -10000 0 -0.47 1 1
CFL2 0.009 0.048 -10000 0 -0.22 8 8
GAS2 0.009 0.041 -10000 0 -0.63 1 1
positive regulation of apoptosis 0.03 0.007 -10000 0 -10000 0 0
PRF1 0.006 0.023 -10000 0 -0.4 1 1
BARD1 signaling events

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
BARD1/CSTF1 -0.001 0.016 -10000 0 -0.27 1 1
ATM 0.007 0 -10000 0 -10000 0 0
UBE2D3 0.007 0 -10000 0 -10000 0 0
PRKDC 0.007 0 -10000 0 -10000 0 0
ATR 0.007 0 -10000 0 -10000 0 0
UBE2L3 0.007 0 -10000 0 -10000 0 0
FANCD2 0.015 0 -10000 0 -10000 0 0
protein ubiquitination -0.002 0.015 -10000 0 -0.18 1 1
XRCC5 0.007 0 -10000 0 -10000 0 0
XRCC6 0.007 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.007 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0 0.009 -10000 0 -10000 0 0
FANCF 0.006 0.023 -10000 0 -0.4 1 1
BRCA1 0.007 0 -10000 0 -10000 0 0
CCNE1 0.003 0.033 -10000 0 -0.25 5 5
CDK2/Cyclin E1 -0.003 0.02 -10000 0 -0.16 5 5
FANCG 0.007 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.001 0.016 -10000 0 -0.27 1 1
FANCE 0.007 0 -10000 0 -10000 0 0
FANCC 0.007 0 -10000 0 -10000 0 0
NBN 0.007 0 -10000 0 -10000 0 0
FANCA -0.011 0.066 -10000 0 -0.25 22 22
DNA repair 0.039 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/ubiquitin -0.001 0.016 -10000 0 -0.27 1 1
BARD1/DNA-PK -0.001 0.011 -10000 0 -0.2 1 1
FANCL 0.007 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.001 0.016 0.27 1 -10000 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.023 0.012 -10000 0 -0.19 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.001 0.013 -10000 0 -0.22 1 1
BRCA1/BARD1/P53 -0.001 0.011 -10000 0 -0.2 1 1
BARD1/CSTF1/BRCA1 -0.001 0.013 -10000 0 -0.22 1 1
BRCA1/BACH1 0.007 0 -10000 0 -10000 0 0
BARD1 0.006 0.023 -10000 0 -0.4 1 1
PCNA 0.007 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.001 0.013 -10000 0 -0.22 1 1
BRCA1/BARD1/UbcH7 -0.001 0.013 -10000 0 -0.22 1 1
BRCA1/BARD1/RAD51/PCNA -0.002 0.017 -10000 0 -0.2 1 1
BARD1/DNA-PK/P53 -0.001 0.01 -10000 0 -0.18 1 1
BRCA1/BARD1/Ubiquitin -0.001 0.016 -10000 0 -0.27 1 1
BRCA1/BARD1/CTIP -0.001 0.011 -10000 0 -0.2 1 1
FA complex 0.02 0.016 -10000 0 -10000 0 0
BARD1/EWS -0.001 0.016 -10000 0 -0.27 1 1
RBBP8 0.013 0 -10000 0 -10000 0 0
TP53 0.007 0 -10000 0 -10000 0 0
TOPBP1 0.007 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.001 0.011 0.2 1 -10000 0 1
BRCA1/BARD1 -0.002 0.016 -10000 0 -0.18 1 1
CSTF1 0.007 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.001 0.016 -10000 0 -0.28 1 1
CDK2 0.007 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.003 0.033 -10000 0 -0.25 5 5
RAD50 0.007 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.001 0.016 -10000 0 -0.27 1 1
EWSR1 0.007 0 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0 0.007 -9999 0 -0.13 1 1
EFNA5 0.007 0 -9999 0 -10000 0 0
FYN 0.009 0.029 -9999 0 -0.2 5 5
neuron projection morphogenesis 0 0.007 -9999 0 -0.13 1 1
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0 0.007 -9999 0 -0.13 1 1
EPHA5 0.003 0.015 -9999 0 -0.25 1 1
Signaling events mediated by HDAC Class III

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
EP300 0.007 0 -9999 0 -10000 0 0
HDAC4 0.007 0 -9999 0 -10000 0 0
induction of apoptosis 0 0 -9999 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.012 0 -9999 0 -10000 0 0
CDKN1A 0 0 -9999 0 -10000 0 0
KAT2B 0.007 0 -9999 0 -10000 0 0
BAX 0.007 0 -9999 0 -10000 0 0
FOXO3 0 0 -9999 0 -10000 0 0
FOXO1 0.005 0.033 -9999 0 -0.4 2 2
FOXO4 0.013 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
XRCC6 0.007 0 -9999 0 -10000 0 0
TAT 0.003 0.015 -9999 0 -0.25 1 1
mol:Lysophosphatidic acid 0 0 -9999 0 -10000 0 0
MYOD1 0.007 0 -9999 0 -10000 0 0
PPARGC1A -0.025 0.11 -9999 0 -0.39 24 24
FHL2 0.005 0.033 -9999 0 -0.4 2 2
response to nutrient levels 0 0 -9999 0 -10000 0 0
KU70/SIRT1 0 0 -9999 0 -10000 0 0
HIST2H4A 0.012 0 -9999 0 -10000 0 0
SIRT1/FOXO3a 0 0 -9999 0 -10000 0 0
SIRT1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0 -9999 0 -10000 0 0
SIRT1/Histone H1b -0.001 0.004 -9999 0 -10000 0 0
apoptosis 0 0 -9999 0 -10000 0 0
SIRT1/PGC1A -0.018 0.061 -9999 0 -0.22 24 24
p53/SIRT1 0 0 -9999 0 -10000 0 0
SIRT1/FOXO4 0 0 -9999 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.003 0.023 -9999 0 -0.2 4 4
HIST1H1E 0.012 0.008 -9999 0 -10000 0 0
SIRT1/p300 0 0 -9999 0 -10000 0 0
muscle cell differentiation 0 0 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
KU70/SIRT1/BAX 0 0 -9999 0 -10000 0 0
CREBBP 0.007 0 -9999 0 -10000 0 0
MEF2D 0.007 0 -9999 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.001 0.009 -9999 0 -0.16 1 1
ACSS2 0.012 0 -9999 0 -10000 0 0
SIRT1/PCAF/MYOD 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.011 0.03 -9999 0 -10000 0 0
SNTA1 0.007 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.011 0.03 -9999 0 -10000 0 0
MAPK12 0.017 0.007 -9999 0 -10000 0 0
CCND1 0.013 0.003 -9999 0 -10000 0 0
p38 gamma/SNTA1 0.02 0.007 -9999 0 -10000 0 0
MAP2K3 0.007 0 -9999 0 -10000 0 0
PKN1 0.007 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.017 0.007 -9999 0 -10000 0 0
MAP2K6 0.014 0.008 -9999 0 -0.12 1 1
MAPT 0.009 0.045 -9999 0 -0.25 8 8
MAPK13 0.005 0.036 -9999 0 -0.16 14 14
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.01 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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 0.036 0.007 -9999 0 -10000 0 0
UGCG -0.003 0.033 -9999 0 -0.57 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.039 0.052 -9999 0 -0.25 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucosylceramide 0.015 0.035 -9999 0 -0.56 1 1
mol:DAG 0 0.001 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.056 -9999 0 -0.33 9 9
FRAP1 0.042 0.073 -9999 0 -0.37 9 9
FOXO3 0.046 0.057 -9999 0 -0.36 4 4
AKT1 0.043 0.06 -9999 0 -0.39 4 4
GAB2 0.005 0.033 -9999 0 -0.4 2 2
SMPD1 -0.001 0.008 -9999 0 -10000 0 0
SGMS1 -0.001 0.008 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
mol:GDP 0.013 0.003 -9999 0 -10000 0 0
CALM1 0.007 0 -9999 0 -10000 0 0
cell proliferation 0.027 0.038 -9999 0 -0.25 5 5
EIF3A 0.007 0 -9999 0 -10000 0 0
PI3K 0.014 0.003 -9999 0 -10000 0 0
RPS6KB1 0.013 0.014 -9999 0 -10000 0 0
mol:sphingomyelin 0 0.001 -9999 0 -10000 0 0
natural killer cell activation 0 0.002 -9999 0 -0.011 4 4
JAK3 0.009 0.002 -9999 0 -10000 0 0
PIK3R1 0.009 0.002 -9999 0 -10000 0 0
JAK1 0.009 0.002 -9999 0 -10000 0 0
NFKB1 0.007 0 -9999 0 -10000 0 0
MYC 0.039 0.11 -9999 0 -0.88 4 4
MYB 0.012 0.028 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.042 0.036 -9999 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.013 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.036 -9999 0 -0.2 3 3
Rac1/GDP 0.016 0.003 -9999 0 -10000 0 0
T cell proliferation 0.045 0.034 -9999 0 -10000 0 0
SHC1 0.008 0.001 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.004 -9999 0 -10000 0 0
PRKCZ 0.045 0.035 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.01 0.055 -9999 0 -0.32 9 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.034 0.007 -9999 0 -10000 0 0
HSP90AA1 0.007 0 -9999 0 -10000 0 0
RELA 0.007 0 -9999 0 -10000 0 0
IL2RA 0.002 0.038 -9999 0 -0.25 7 7
IL2RB 0.009 0.002 -9999 0 -10000 0 0
TERT 0 0 -9999 0 -10000 0 0
E2F1 0.013 0.02 -9999 0 -10000 0 0
SOS1 0.008 0.001 -9999 0 -10000 0 0
RPS6 0.007 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 0.008 0.001 -9999 0 -10000 0 0
IL2RG 0.006 0.029 -9999 0 -0.25 4 4
actin cytoskeleton organization 0.045 0.034 -9999 0 -10000 0 0
GRB2 0.008 0.001 -9999 0 -10000 0 0
IL2 0.005 0.004 -9999 0 -10000 0 0
PIK3CA 0.009 0.002 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.004 -9999 0 -10000 0 0
LCK 0.009 0.002 -9999 0 -10000 0 0
BCL2 0.036 0.12 -9999 0 -0.6 8 8
Glypican 2 network

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
MDK 0.007 0 -9999 0 -10000 0 0
GPC2 0.006 0.021 -9999 0 -0.25 2 2
GPC2/Midkine -0.001 0.013 -9999 0 -0.16 2 2
neuron projection morphogenesis -0.001 0.013 -9999 0 -0.16 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.005 0.033 -9999 0 -0.4 2 2
ELF1 0.01 0.014 -9999 0 -10000 0 0
CCNA2 0.006 0.021 -9999 0 -0.25 2 2
PIK3CA 0.008 0 -9999 0 -10000 0 0
JAK3 0.008 0 -9999 0 -10000 0 0
PIK3R1 0.008 0 -9999 0 -10000 0 0
JAK1 0.008 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.045 0.014 -9999 0 -10000 0 0
SHC1 0.008 0 -9999 0 -10000 0 0
SP1 0.001 0.059 -9999 0 -0.3 11 11
IL2RA 0.015 0.025 -9999 0 -10000 0 0
IL2RB 0.008 0 -9999 0 -10000 0 0
SOS1 0.008 0 -9999 0 -10000 0 0
IL2RG 0.004 0.029 -9999 0 -0.25 4 4
G1/S transition of mitotic cell cycle 0.006 0.11 -9999 0 -0.57 11 11
PTPN11 0.008 0 -9999 0 -10000 0 0
CCND2 -0.006 0.12 -9999 0 -0.63 11 11
LCK 0.008 0 -9999 0 -10000 0 0
GRB2 0.008 0 -9999 0 -10000 0 0
IL2 0.004 0.004 -9999 0 -10000 0 0
CDK6 0.007 0 -9999 0 -10000 0 0
CCND3 0.047 0.013 -9999 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.001 0.011 0.2 1 -10000 0 1
DAPP1 0.022 0.024 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK 0.037 0.019 -10000 0 -10000 0 0
mol:DAG 0.037 0.015 0.16 1 -10000 0 1
HRAS 0.008 0.001 -10000 0 -10000 0 0
RAP1A 0.008 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.024 0.023 -10000 0 -0.17 2 2
PLCG2 0.007 0 -10000 0 -10000 0 0
PLCG1 0.007 0 -10000 0 -10000 0 0
ARF5 0.007 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.011 0.2 1 -10000 0 1
ARF1/GTP 0.001 0.011 0.2 1 -10000 0 1
RHOA 0.007 0 -10000 0 -10000 0 0
YES1 0.007 0 -10000 0 -10000 0 0
RAP1A/GTP 0.001 0.011 0.19 1 -10000 0 1
ADAP1 0 0.013 0.19 1 -10000 0 1
ARAP3 0.001 0.011 0.19 1 -10000 0 1
INPPL1 0.007 0 -10000 0 -10000 0 0
PREX1 0.007 0 -10000 0 -10000 0 0
ARHGEF6 0.003 0.04 -10000 0 -0.4 3 3
ARHGEF7 0.007 0 -10000 0 -10000 0 0
ARF1 0.007 0 -10000 0 -10000 0 0
NRAS 0.008 0.001 -10000 0 -10000 0 0
FYN 0.001 0.052 -10000 0 -0.4 5 5
ARF6 0.007 0 -10000 0 -10000 0 0
FGR 0.007 0 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.008 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.005 0.033 -10000 0 -0.4 2 2
ZAP70 0.007 0 -10000 0 -10000 0 0
mol:IP3 0.031 0.01 -10000 0 -10000 0 0
LYN 0.007 0 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.023 -10000 0 -0.17 2 2
RhoA/GDP 0 0.012 0.19 1 -10000 0 1
PDK1/Src/Hsp90 0 0 -10000 0 -10000 0 0
BLNK 0.006 0.015 -10000 0 -0.25 1 1
actin cytoskeleton reorganization 0.037 0.017 0.19 1 -10000 0 1
SRC 0.007 0 -10000 0 -10000 0 0
PLEKHA2 0.017 0 -10000 0 -10000 0 0
RAC1 0.007 0 -10000 0 -10000 0 0
PTEN -0.001 0.022 -10000 0 -0.38 1 1
HSP90AA1 0.007 0 -10000 0 -10000 0 0
ARF6/GTP 0.001 0.011 0.2 1 -10000 0 1
RhoA/GTP 0.001 0.011 0.19 1 -10000 0 1
Src family/SYK family/BLNK-LAT 0.027 0.023 -10000 0 -10000 0 0
BLK -0.04 0.098 -10000 0 -0.25 55 55
PDPK1 0.007 0 -10000 0 -10000 0 0
CYTH1 0.001 0.011 0.19 1 -10000 0 1
HCK 0.007 0 -10000 0 -10000 0 0
CYTH3 0.001 0.011 0.19 1 -10000 0 1
CYTH2 0.001 0.011 0.19 1 -10000 0 1
KRAS 0.008 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.009 0.15 1 -10000 0 1
SGK1 0 0.009 0.15 1 -10000 0 1
INPP5D 0.007 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.024 -10000 0 -0.18 2 2
SOS1 0.007 0 -10000 0 -10000 0 0
SYK 0.007 0 -10000 0 -10000 0 0
ARF6/GDP 0 0.013 0.2 1 -10000 0 1
mol:PI-3-4-5-P3 0.001 0.013 0.22 1 -10000 0 1
ARAP3/RAP1A/GTP 0.001 0.011 0.19 1 -10000 0 1
VAV1 0.007 0 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.018 0.001 -10000 0 -10000 0 0
PLEKHA1 0.017 0 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.023 -10000 0 -0.17 2 2
LAT 0.007 0 -10000 0 -10000 0 0
Rac1/GTP 0.021 0.033 -10000 0 -0.24 5 5
ITK 0 0.012 0.19 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.043 0.019 0.18 1 -10000 0 1
LCK 0.007 0 -10000 0 -10000 0 0
BTK 0.001 0.011 0.19 1 -10000 0 1
Arf6 trafficking events

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
SLC2A4 -0.13 0.19 -9999 0 -0.4 103 103
CLTC 0.019 0 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.016 0 -9999 0 -10000 0 0
Dynamin 2/GTP 0 0 -9999 0 -10000 0 0
EXOC4 0.007 0 -9999 0 -10000 0 0
CD59 0.017 0 -9999 0 -10000 0 0
CPE -0.002 0.055 -9999 0 -0.23 17 17
CTNNB1 0.007 0 -9999 0 -10000 0 0
membrane fusion 0.015 0 -9999 0 -10000 0 0
CTNND1 0.019 0 -9999 0 -10000 0 0
DNM2 0.007 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.019 0 -9999 0 -10000 0 0
TSHR 0.01 0.008 -9999 0 -0.13 1 1
INS 0.007 0 -9999 0 -10000 0 0
BIN1 0.007 0 -9999 0 -10000 0 0
mol:Choline 0.015 0 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.011 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.007 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0.017 0 -9999 0 -10000 0 0
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 -0.022 0.015 -9999 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 0.007 0 -9999 0 -10000 0 0
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.007 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.025 0 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.007 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.015 0.006 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.011 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -9999 0 -10000 0 0
ACAP1 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 0.014 0.001 -9999 0 -10000 0 0
clathrin heavy chain/ACAP1 0.022 0 -9999 0 -10000 0 0
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.007 0 -9999 0 -10000 0 0
exocyst 0.025 0 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 0.019 0 -9999 0 -10000 0 0
NME1 0.011 0 -9999 0 -10000 0 0
clathrin coat assembly 0.019 0 -9999 0 -10000 0 0
IL2RA 0.016 0.007 -9999 0 -10000 0 0
VAMP3 0.011 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.052 0.073 -9999 0 -10000 0 0
EXOC6 0.007 0 -9999 0 -10000 0 0
PLD1 0 0 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.007 0 -9999 0 -10000 0 0
PIP5K1C 0.019 0 -9999 0 -10000 0 0
SDC1 -0.024 0.012 -9999 0 -10000 0 0
ARF6/GDP 0.01 0 -9999 0 -10000 0 0
EXOC7 0.007 0 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.015 0.006 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.015 0 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.007 0 -9999 0 -10000 0 0
ADRB2 0.019 0.024 -9999 0 -10000 0 0
EXOC3 0.007 0 -9999 0 -10000 0 0
ASAP2 0.007 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0.015 0 -9999 0 -10000 0 0
KLC1 0.007 0 -9999 0 -10000 0 0
AVPR2 -0.023 0.081 -9999 0 -10000 0 0
RALA 0.007 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.008 0.003 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.006 0.015 0.25 1 -10000 0 1
PI3K Class IB/PDE3B 0.006 0.015 -10000 0 -0.25 1 1
PDE3B 0.006 0.015 -10000 0 -0.25 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.006 0.023 -9999 0 -0.4 1 1
SMAD2 0.008 0 -9999 0 -10000 0 0
SMAD3 0.024 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.027 0.011 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.013 -9999 0 -0.22 1 1
SMAD2/SMAD2/SMAD4 -0.001 0.009 -9999 0 -10000 0 0
PPM1A 0.007 0 -9999 0 -10000 0 0
CALM1 0.007 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.011 0.012 -9999 0 -0.2 1 1
MAP3K1 0.007 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.004 0.031 -9999 0 -0.27 4 4
MAPK3 0.007 0 -9999 0 -10000 0 0
MAPK1 0.007 0 -9999 0 -10000 0 0
NUP214 0.007 0 -9999 0 -10000 0 0
CTDSP1 0.007 0 -9999 0 -10000 0 0
CTDSP2 0.007 0 -9999 0 -10000 0 0
CTDSPL 0.007 0 -9999 0 -10000 0 0
KPNB1 0.007 0 -9999 0 -10000 0 0
TGFBRAP1 0.003 0.04 -9999 0 -0.4 3 3
UBE2I 0.007 0 -9999 0 -10000 0 0
NUP153 0.007 0 -9999 0 -10000 0 0
KPNA2 0.007 0 -9999 0 -10000 0 0
PIAS4 0.007 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.009 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.019 -9999 0 -10000 0 0
ERC1 0.007 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.002 0.016 -9999 0 -0.16 3 3
NFKBIA 0.027 0 -9999 0 -10000 0 0
BIRC2 0.006 0.015 -9999 0 -0.25 1 1
IKBKB 0.007 0 -9999 0 -10000 0 0
RIPK2 0.007 0 -9999 0 -10000 0 0
IKBKG 0 0.001 -9999 0 -10000 0 0
IKK complex/A20 0.002 0.013 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.007 0 -9999 0 -10000 0 0
XPO1 0.007 0 -9999 0 -10000 0 0
NEMO/ATM 0.029 0.003 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.007 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.001 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 0.005 0.025 -9999 0 -0.25 3 3
NFKB1 0.009 0 -9999 0 -10000 0 0
RELA 0.009 0 -9999 0 -10000 0 0
MALT1 0.007 0 -9999 0 -10000 0 0
cIAP1/UbcH5C -0.001 0.009 -9999 0 -0.16 1 1
ATM 0.007 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.003 0.022 -9999 0 -0.16 6 6
TRAF6 0.007 0 -9999 0 -10000 0 0
PRKCA -0.002 0.061 -9999 0 -0.4 7 7
CHUK 0.007 0 -9999 0 -10000 0 0
UBE2D3 0.007 0 -9999 0 -10000 0 0
TNF 0.002 0.036 -9999 0 -0.25 6 6
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.007 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.009 0 -9999 0 -10000 0 0
TNFRSF1A 0.007 0 -9999 0 -10000 0 0
IKK complex 0 0.001 -9999 0 -10000 0 0
CYLD 0.007 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.003 0.022 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.007 0 -9999 0 -9999 0 0
PLK4 0.007 0 -9999 0 -9999 0 0
regulation of centriole replication 0.013 0 -9999 0 -9999 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0 0.002 -9999 0 -10000 0 0
CLOCK 0.009 0 -9999 0 -10000 0 0
TIMELESS/CRY2 0.025 0.005 -9999 0 -10000 0 0
DEC1/BMAL1 0 0 -9999 0 -10000 0 0
ATR 0.007 0 -9999 0 -10000 0 0
NR1D1 0.025 0.006 -9999 0 -10000 0 0
ARNTL 0.009 0 -9999 0 -10000 0 0
TIMELESS 0.025 0.006 -9999 0 -10000 0 0
NPAS2 0.007 0.033 -9999 0 -0.4 2 2
CRY2 0.007 0 -9999 0 -10000 0 0
mol:CO -0.008 0 -9999 0 -10000 0 0
CHEK1 0.007 0 -9999 0 -10000 0 0
mol:HEME 0.008 0 -9999 0 -10000 0 0
PER1 0.007 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.023 0.02 -9999 0 -0.22 2 2
BMAL1/CLOCK 0.03 0.008 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0 0.002 -9999 0 -10000 0 0
mol:NADPH 0.008 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.025 0.005 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.002 0.003 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0 0 -9999 0 -10000 0 0
MAP4K1 0.007 0 -9999 0 -10000 0 0
MAP3K8 0.007 0 -9999 0 -10000 0 0
PRKCB 0.005 0.033 -9999 0 -0.4 2 2
DBNL 0.007 0 -9999 0 -10000 0 0
CRKL 0.007 0 -9999 0 -10000 0 0
MAP3K1 0.027 0 -9999 0 -10000 0 0
JUN 0.016 0.062 -9999 0 -0.52 4 4
MAP3K7 0.027 0 -9999 0 -10000 0 0
GRAP2 0.007 0 -9999 0 -10000 0 0
CRK 0.007 0 -9999 0 -10000 0 0
MAP2K4 0.032 0 -9999 0 -10000 0 0
LAT 0.007 0 -9999 0 -10000 0 0
LCP2 0.007 0 -9999 0 -10000 0 0
MAPK8 0.013 0.059 -9999 0 -0.5 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.024 0 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 0 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.007 0 -9999 0 -9999 0 0
ITGB7 0.007 0 -9999 0 -9999 0 0
ITGA4 0.007 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -9999 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.025 0.003 -10000 0 -10000 0 0
regulation of axonogenesis -0.016 0.005 -10000 0 -10000 0 0
myoblast fusion -0.006 0.023 -10000 0 -10000 0 0
mol:GTP -0.002 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.019 0.21 2 -10000 0 2
ARF1/GTP -0.001 0.004 -10000 0 -10000 0 0
mol:GM1 0.005 0.007 -10000 0 -10000 0 0
mol:Choline 0.016 0.006 -10000 0 -10000 0 0
lamellipodium assembly 0 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.003 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.018 0.019 -10000 0 -0.21 2 2
ARF1 0.007 0 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.023 -10000 0 -10000 0 0
ARF1/GDP 0.011 0.021 -10000 0 -10000 0 0
ARF6 0.006 0.004 -10000 0 -10000 0 0
RAB11A 0.007 0 -10000 0 -10000 0 0
TIAM1 0.006 0.033 -10000 0 -0.4 2 2
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.003 -10000 0 -10000 0 0
actin filament bundle formation 0.004 0.016 -10000 0 -10000 0 0
KALRN -0.013 0.051 -10000 0 -0.21 19 19
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.004 0.016 -10000 0 -10000 0 0
NME1 0.008 0.001 -10000 0 -10000 0 0
Rac1/GDP -0.004 0.016 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.002 0.007 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0 0.005 -10000 0 -10000 0 0
RAC1 0.007 0 -10000 0 -10000 0 0
liver development -0.002 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.002 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.004 -10000 0 -10000 0 0
mol:GDP 0 0.006 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.002 -10000 0 -10000 0 0
RHOA 0.007 0 -10000 0 -10000 0 0
PLD1 0.011 0.007 -10000 0 -10000 0 0
RAB11FIP3 0.007 0 -10000 0 -10000 0 0
tube morphogenesis 0 0.005 -10000 0 -10000 0 0
ruffle organization 0.016 0.005 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.002 0.007 -10000 0 -10000 0 0
PLD2 0.011 0.007 -10000 0 -10000 0 0
PIP5K1A 0.016 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.016 0.006 -10000 0 -10000 0 0
Rac1/GTP 0 0.005 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.006 0.015 -9999 0 -0.25 1 1
positive regulation of NF-kappaB transcription factor activity -0.001 0.009 -9999 0 -0.16 1 1
MAP2K4 0.028 0.002 -9999 0 -10000 0 0
IKBKB 0.007 0 -9999 0 -10000 0 0
TNFRSF10B 0.007 0 -9999 0 -10000 0 0
TNFRSF10A 0.007 0 -9999 0 -10000 0 0
SMPD1 0 0.003 -9999 0 -10000 0 0
IKBKG 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.007 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.001 0.009 -9999 0 -0.16 1 1
TRAIL/TRAILR3 -0.002 0.024 -9999 0 -0.24 3 3
TRAIL/TRAILR1 -0.001 0.009 -9999 0 -0.16 1 1
TRAIL/TRAILR4 -0.001 0.009 -9999 0 -0.16 1 1
TRAIL/TRAILR1/DAP3/GTP 0 0.006 -9999 0 -10000 0 0
IKK complex 0 0.002 -9999 0 -10000 0 0
RIPK1 0.007 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.013 0.01 -9999 0 -0.16 1 1
MAP3K1 0 0.001 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.007 0 -9999 0 -10000 0 0
TRADD 0.007 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.007 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.022 0.003 -9999 0 -10000 0 0
CFLAR 0.007 0 -9999 0 -10000 0 0
MAPK1 0.013 0.01 -9999 0 -0.16 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0 0.005 -9999 0 -10000 0 0
mol:ceramide 0 0.003 -9999 0 -10000 0 0
FADD 0.007 0 -9999 0 -10000 0 0
MAPK8 0.03 0.015 -9999 0 -10000 0 0
TRAF2 0.007 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.005 0.033 -9999 0 -0.4 2 2
CHUK 0.007 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0 0.007 -9999 0 -10000 0 0
DAP3 0.007 0 -9999 0 -10000 0 0
CASP10 0 0.004 -9999 0 -10000 0 0
JNK cascade -0.001 0.009 -9999 0 -0.16 1 1
TRAIL (trimer) 0.006 0.015 -9999 0 -0.25 1 1
TNFRSF10C 0.005 0.033 -9999 0 -0.4 2 2
TRAIL/TRAILR1/DAP3/GTP/FADD 0 0.006 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD 0 0.007 -9999 0 -10000 0 0
cell death 0.011 0.003 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.022 0.003 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.007 0 -9999 0 -10000 0 0
CASP8 0 0.002 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0 0.005 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.031 0.004 -10000 0 -10000 0 0
BAG4 0.007 0 -10000 0 -10000 0 0
BAD 0.02 0.002 -10000 0 -10000 0 0
NFKBIA 0.007 0 -10000 0 -10000 0 0
BIRC3 0.002 0.036 -10000 0 -0.25 6 6
BAX 0.02 0.002 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.01 0.002 -10000 0 -10000 0 0
IKBKB 0.034 0.004 -10000 0 -10000 0 0
MAP2K2 0.027 0.003 -10000 0 -10000 0 0
MAP2K1 0.027 0.003 -10000 0 -10000 0 0
SMPD1 0.013 0.002 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.035 0.004 -10000 0 -10000 0 0
MAP2K4 0.024 0.002 -10000 0 -10000 0 0
protein ubiquitination 0.035 0.004 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.03 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.024 0.002 -10000 0 -10000 0 0
CRADD 0.008 0 -10000 0 -10000 0 0
mol:ceramide 0.016 0.002 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.008 0 -10000 0 -10000 0 0
MAP3K1 0.02 0.002 -10000 0 -10000 0 0
TRADD 0.008 0 -10000 0 -10000 0 0
RELA/p50 0.007 0 -10000 0 -10000 0 0
MAPK3 0.028 0.002 -10000 0 -10000 0 0
MAPK1 0.028 0.002 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.031 0.004 -10000 0 -10000 0 0
KSR1 0.02 0.002 -10000 0 -10000 0 0
MAPK8 0.026 0.015 -10000 0 -0.15 2 2
TRAF2 0.007 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.034 0.004 -10000 0 -10000 0 0
TNF R/SODD 0 0 -10000 0 -10000 0 0
TNF 0.003 0.035 -10000 0 -0.25 6 6
CYCS 0.022 0.012 0.11 5 -10000 0 5
IKBKG 0.034 0.004 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.004 -10000 0 -10000 0 0
RELA 0.007 0 -10000 0 -10000 0 0
RIPK1 0.007 0 -10000 0 -10000 0 0
AIFM1 0.022 0.012 0.11 5 -10000 0 5
TNF/TNF R/SODD -0.002 0.017 -10000 0 -10000 0 0
TNFRSF1A 0.007 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.001 -10000 0 -10000 0 0
NSMAF 0.031 0.004 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 0.001 0.052 -10000 0 -0.4 5 5
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.002 0.012 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.006 -9999 0 -10000 0 0
SUMO1 0.007 0 -9999 0 -10000 0 0
ZFPM1 0.007 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0 -9999 0 -10000 0 0
FKBP3 0.007 0 -9999 0 -10000 0 0
Histones 0 0.003 -9999 0 -10000 0 0
YY1/LSF 0.018 0 -9999 0 -10000 0 0
SMG5 0.007 0 -9999 0 -10000 0 0
RAN 0.007 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.019 0.009 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.018 0.007 -9999 0 -10000 0 0
SAP18 0.007 0 -9999 0 -10000 0 0
RELA 0.021 0.007 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.007 0 -9999 0 -10000 0 0
HDAC3/TR2 0.018 0.007 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.028 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.023 0.006 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.007 0.076 -9999 0 -0.4 11 11
GATA1 0.005 0.015 -9999 0 -0.25 1 1
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.033 0.002 -9999 0 -10000 0 0
RBBP7 0.007 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.007 0 -9999 0 -10000 0 0
MAX 0.007 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.007 0 -9999 0 -10000 0 0
NFKBIA 0.015 0.008 -9999 0 -10000 0 0
KAT2B 0.007 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.025 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0.007 0 -9999 0 -10000 0 0
CHD3 0.007 0 -9999 0 -10000 0 0
SAP30 0.007 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.007 0 -9999 0 -10000 0 0
YY1/HDAC3 0.025 0.007 -9999 0 -10000 0 0
YY1/HDAC2 0.018 0 -9999 0 -10000 0 0
YY1/HDAC1 0.018 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.028 0 -9999 0 -10000 0 0
PPARG -0.018 0.063 -9999 0 -0.24 22 22
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.007 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.007 0 -9999 0 -10000 0 0
TNFRSF1A 0.007 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.018 0.007 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.007 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.03 0 -9999 0 -10000 0 0
HDAC1 0.007 0 -9999 0 -10000 0 0
HDAC3 0.015 0.008 -9999 0 -10000 0 0
HDAC2 0.007 0 -9999 0 -10000 0 0
YY1 0.018 0 -9999 0 -10000 0 0
HDAC8 0.007 0 -9999 0 -10000 0 0
SMAD7 0.007 0 -9999 0 -10000 0 0
NCOR2 0.007 0 -9999 0 -10000 0 0
MXD1 0.007 0 -9999 0 -10000 0 0
STAT3 0.015 0 -9999 0 -10000 0 0
NFKB1 0.007 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.007 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0 0 -9999 0 -10000 0 0
EP300 0.007 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.015 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.008 -9999 0 -10000 0 0
histone deacetylation 0.028 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.007 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.007 0 -9999 0 -10000 0 0
GATAD2B 0.007 0 -9999 0 -10000 0 0
GATAD2A 0.007 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.01 0.04 -9999 0 -0.19 11 11
GATA1/HDAC1 -0.001 0.009 -9999 0 -0.16 1 1
GATA1/HDAC3 0.013 0.013 -9999 0 -10000 0 0
CHD4 0.007 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.003 0.022 -9999 0 -0.16 6 6
SIN3/HDAC complex/Mad/Max 0.028 0 -9999 0 -10000 0 0
NuRD Complex 0.033 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0 0.003 -9999 0 -10000 0 0
SIN3B 0.007 0 -9999 0 -10000 0 0
MTA2 0.007 0 -9999 0 -10000 0 0
SIN3A 0.007 0 -9999 0 -10000 0 0
XPO1 0.007 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.017 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.001 0.009 -9999 0 -0.16 1 1
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF 0.002 0.036 -9999 0 -0.25 6 6
negative regulation of cell growth 0.028 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.028 0 -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 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.027 0 -9999 0 -10000 0 0
TFCP2 0.007 0 -9999 0 -10000 0 0
NR2C1 0.007 0 -9999 0 -10000 0 0
MBD3 0.007 0 -9999 0 -10000 0 0
MBD2 0.007 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.007 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.007 0 -9999 0 -10000 0 0
ITGA4 0.007 0 -9999 0 -10000 0 0
RAC1 0.007 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.007 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0 0 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.007 0 -9999 0 -10000 0 0
TLN1 0.007 0 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0 0 -9999 0 -10000 0 0
ITGB1 0.007 0 -9999 0 -10000 0 0
ITGB7 0.007 0 -9999 0 -10000 0 0
ARF6/GDP 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.005 0.029 -9999 0 -0.18 8 8
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.003 0.065 -9999 0 -0.4 8 8
alpha4/beta1 Integrin/Paxillin/Talin 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0 0 -9999 0 -10000 0 0
BCAR1 0.007 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.007 0 -9999 0 -10000 0 0
PRKACA 0.007 0 -9999 0 -10000 0 0
GIT1 0.007 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0 0 -9999 0 -10000 0 0
Rac1/GTP 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.009 -9999 0 -0.16 1 1
FBXW11 0.007 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.015 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.028 0 -9999 0 -10000 0 0
NFKBIA 0.017 0 -9999 0 -10000 0 0
MAPK14 0.007 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.015 0 -9999 0 -10000 0 0
ARRB2 0.01 0 -9999 0 -10000 0 0
REL 0.007 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.015 0.008 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.007 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.007 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
RELA 0.007 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.021 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.03 0 -9999 0 -10000 0 0
SRC 0.007 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.021 0 -9999 0 -10000 0 0
IKBKB 0.007 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.007 0 -9999 0 -10000 0 0
SYK 0.007 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.02 0 -9999 0 -10000 0 0
cell death 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.015 0 -9999 0 -10000 0 0
LCK 0.007 0 -9999 0 -10000 0 0
BCL3 0.006 0.015 -9999 0 -0.25 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.007 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.002 0.014 -9999 0 -10000 0 0
NEF 0.002 0.009 -9999 0 -10000 0 0
NFKBIA 0.008 0.007 -9999 0 -10000 0 0
BIRC3 0.022 0.032 -9999 0 -10000 0 0
CYCS 0.029 0.017 -9999 0 -10000 0 0
RIPK1 0.007 0 -9999 0 -10000 0 0
CD247 0.009 0.009 -9999 0 -10000 0 0
MAP2K7 0.031 0.014 -9999 0 -10000 0 0
protein ubiquitination 0.042 0.007 -9999 0 -10000 0 0
CRADD 0.007 0 -9999 0 -10000 0 0
DAXX 0.007 0 -9999 0 -10000 0 0
FAS 0.005 0.033 -9999 0 -0.4 2 2
BID 0.026 0.018 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.002 0.016 -9999 0 -10000 0 0
TRADD 0.007 0 -9999 0 -10000 0 0
MAP3K5 0.007 0 -9999 0 -10000 0 0
CFLAR 0.007 0 -9999 0 -10000 0 0
FADD 0.007 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.002 0.016 -9999 0 -10000 0 0
MAPK8 0.033 0.02 -9999 0 -10000 0 0
APAF1 0.007 0 -9999 0 -10000 0 0
TRAF1 0.007 0 -9999 0 -10000 0 0
TRAF2 0.007 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.022 0.018 -9999 0 -0.18 2 2
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.038 0.008 -9999 0 -10000 0 0
CHUK 0.043 0.007 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.014 -9999 0 -0.18 2 2
TCRz/NEF -0.002 0.013 -9999 0 -10000 0 0
TNF 0.002 0.036 -9999 0 -0.25 6 6
FASLG 0.014 0.024 -9999 0 -0.19 4 4
NFKB1 0.008 0.007 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.002 0.017 -9999 0 -10000 0 0
CASP6 -0.001 0.012 -9999 0 -10000 0 0
CASP7 0.048 0.02 -9999 0 -10000 0 0
RELA 0.008 0.007 -9999 0 -10000 0 0
CASP2 0.007 0 -9999 0 -10000 0 0
CASP3 0.048 0.02 -9999 0 -10000 0 0
TNFRSF1A 0.007 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0 0 -9999 0 -10000 0 0
CASP8 0.007 0 -9999 0 -10000 0 0
CASP9 0.007 0 -9999 0 -10000 0 0
MAP3K14 0.04 0.008 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.003 0.017 -9999 0 -10000 0 0
BCL2 0.033 0.029 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.007 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.017 0 -9999 0 -9999 0 0
HDAC4 0.007 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.007 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.01 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.017 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.007 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.007 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.017 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.017 0 -9999 0 -9999 0 0
RANGAP1 0.007 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 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 0.007 0 -9999 0 -9999 0 0
UBE2I 0.007 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 0.007 0 -9999 0 -9999 0 0
PIAS1 0.007 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
IL23-mediated signaling events

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
CCL2 0.019 0.12 -9999 0 -10000 0 0
IL23A 0.016 0.13 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.028 0.094 -9999 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.015 0.13 -9999 0 -10000 0 0
ITGA3 0.018 0.12 -9999 0 -10000 0 0
IL17F 0.029 0.1 -9999 0 -10000 0 0
IL12B 0.009 0.03 -9999 0 -0.23 4 4
STAT1 (dimer) 0.016 0.12 -9999 0 -10000 0 0
CD4 0.019 0.12 -9999 0 -10000 0 0
IL23 0.014 0.12 -9999 0 -10000 0 0
IL23R 0.008 0.037 -9999 0 -10000 0 0
IL1B 0.013 0.13 -9999 0 -10000 0 0
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 0.01 0.13 -9999 0 -10000 0 0
TYK2 0.009 0.009 -9999 0 -10000 0 0
STAT4 0.007 0 -9999 0 -10000 0 0
STAT3 0.008 0 -9999 0 -10000 0 0
IL18RAP 0.006 0.003 -9999 0 -10000 0 0
IL12RB1 0.009 0.009 -9999 0 -10000 0 0
PIK3CA 0.008 0 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 0.01 0.013 -9999 0 -10000 0 0
IL23R/JAK2 0.016 0.046 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response 0.015 0.13 -9999 0 -10000 0 0
natural killer cell activation 0 0.003 -9999 0 -10000 0 0
JAK2 0.013 0.011 -9999 0 -10000 0 0
PIK3R1 0.008 0 -9999 0 -10000 0 0
NFKB1 0.008 0.002 -9999 0 -10000 0 0
RELA 0.008 0.002 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.014 0.12 -9999 0 -10000 0 0
ALOX12B 0.007 0.13 -9999 0 -10000 0 0
CXCL1 0 0.13 -9999 0 -10000 0 0
T cell proliferation 0.015 0.13 -9999 0 -10000 0 0
NFKBIA 0.008 0.002 -9999 0 -10000 0 0
IL17A 0.036 0.09 -9999 0 -10000 0 0
PI3K -0.025 0.097 -9999 0 -10000 0 0
IFNG 0.004 0.012 -9999 0 -10000 0 0
STAT3 (dimer) -0.025 0.092 -9999 0 -10000 0 0
IL18R1 0.005 0.023 -9999 0 -0.4 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.022 0.091 -9999 0 -10000 0 0
IL18/IL18R 0.012 0.022 -9999 0 -0.22 1 1
macrophage activation -0.001 0.008 -9999 0 -10000 0 0
TNF 0.016 0.13 -9999 0 -10000 0 0
STAT3/STAT4 -0.028 0.095 -9999 0 -10000 0 0
STAT4 (dimer) 0.016 0.12 -9999 0 -10000 0 0
IL18 0.004 0.026 -9999 0 -0.25 3 3
IL19 -0.01 0.23 -9999 0 -1 12 12
STAT5A (dimer) 0.016 0.12 -9999 0 -10000 0 0
STAT1 0.007 0 -9999 0 -10000 0 0
SOCS3 0.007 0 -9999 0 -10000 0 0
CXCL9 0.01 0.13 -9999 0 -10000 0 0
MPO 0.018 0.12 -9999 0 -10000 0 0
positive regulation of humoral immune response 0.015 0.13 -9999 0 -10000 0 0
IL23/IL23R/JAK2/TYK2 0.015 0.13 -9999 0 -10000 0 0
IL6 0.018 0.12 -9999 0 -10000 0 0
STAT5A 0.007 0 -9999 0 -10000 0 0
IL2 0.003 0.005 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.003 -9999 0 -10000 0 0
CD3E 0.019 0.12 -9999 0 -10000 0 0
keratinocyte proliferation 0.015 0.13 -9999 0 -10000 0 0
NOS2 -0.004 0.21 -9999 0 -1.1 9 9
Arf1 pathway

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
coatomer protein complex 0 0 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.012 0 -9999 0 -9999 0 0
AP2 0 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -9999 0 0
CLTB 0.007 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.015 0 -9999 0 -9999 0 0
CD4 0.007 0 -9999 0 -9999 0 0
CLTA 0.007 0 -9999 0 -9999 0 0
mol:GTP 0.001 0 -9999 0 -9999 0 0
ARFGAP1 0.007 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
ARF1/GTP 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0 -9999 0 -9999 0 0
mol:Choline 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.007 0 -9999 0 -9999 0 0
DDEF1 0 0 -9999 0 -9999 0 0
ARF1/GDP 0 0 -9999 0 -9999 0 0
AP2M1 0.007 0 -9999 0 -9999 0 0
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0 0 -9999 0 -9999 0 0
Rac/GTP 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -9999 0 0
ARFIP2 0 0 -9999 0 -9999 0 0
COPA 0.007 0 -9999 0 -9999 0 0
RAC1 0.007 0 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.015 0 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -9999 0 0
GGA3 0.007 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -9999 0 0
AP2A1 0.007 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.016 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -9999 0 0
CYTH2 0.007 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0 0 -9999 0 -9999 0 0
mol:Brefeldin A 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.021 0 -9999 0 -9999 0 0
PLD2 0 0 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.007 0 -9999 0 -9999 0 0
PIP5K1A 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0 0 -9999 0 -9999 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0 -9999 0 -9999 0 0
GOSR2 0 0 -9999 0 -9999 0 0
USO1 0 0 -9999 0 -9999 0 0
GBF1 0 0 -9999 0 -9999 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

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

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 304 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZX.AA5X TCGA.ZJ.AB0I TCGA.ZJ.AB0H TCGA.ZJ.AAXU
109_MAP3K5 0.032 -0.14 0.032 0.032
47_PPARGC1A 0.0073 0.0073 0.0073 0.0073
105_BMP4 0.0073 0.0073 0.0073 0.0073
105_BMP6 0.0073 0.0073 0.0073 0.0073
105_BMP7 0.0073 0.0073 0.0073 0.0073
105_BMP2 0.0073 0.0073 0.0073 0.0073
131_RELN/VLDLR 0 -0.2 -0.2 0
30_TGFB1/TGF beta receptor Type II 0.0072 0.0072 0.0072 0.0072
84_STAT5B -0.058 -0.059 -0.064 -0.15
84_STAT5A -0.058 -0.059 -0.064 -0.15
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/CESC-TP/22312681/CESC-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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