PARADIGM pathway analysis of mRNASeq expression data
Liver Hepatocellular Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1TM795B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1TM795B
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 68 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
Plasma membrane estrogen receptor signaling 103
PDGFR-alpha signaling pathway 97
FOXM1 transcription factor network 94
Signaling events regulated by Ret tyrosine kinase 92
Nongenotropic Androgen signaling 83
Glypican 2 network 81
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 77
EPO signaling pathway 75
IL4-mediated signaling events 74
IGF1 pathway 74
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 371 . 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 ( 371 ).

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
Plasma membrane estrogen receptor signaling 0.2776 103 8889 86 -0.55 0.5 1000 -1000 -0.065 -1000
PDGFR-alpha signaling pathway 0.2615 97 4289 44 -0.74 0.033 1000 -1000 -0.062 -1000
FOXM1 transcription factor network 0.2534 94 4816 51 -0.25 0.46 1000 -1000 -0.098 -1000
Signaling events regulated by Ret tyrosine kinase 0.2480 92 7581 82 -0.48 0.014 1000 -1000 -0.076 -1000
Nongenotropic Androgen signaling 0.2237 83 4333 52 -0.43 0.24 1000 -1000 -0.043 -1000
Glypican 2 network 0.2183 81 324 4 0.043 0.15 1000 -1000 -0.015 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2075 77 5303 68 -0.77 0.25 1000 -1000 -0.079 -1000
EPO signaling pathway 0.2022 75 4149 55 -0.3 0 1000 -1000 -0.079 -1000
IL4-mediated signaling events 0.1995 74 6757 91 -0.99 0.5 1000 -1000 -0.11 -1000
IGF1 pathway 0.1995 74 4255 57 -0.34 0.13 1000 -1000 -0.068 -1000
HIF-1-alpha transcription factor network 0.1968 73 5562 76 -0.53 0.014 1000 -1000 -0.048 -1000
IL6-mediated signaling events 0.1887 70 5292 75 -0.52 0.04 1000 -1000 -0.057 -1000
p75(NTR)-mediated signaling 0.1860 69 8734 125 -0.55 0.2 1000 -1000 -0.082 -1000
Signaling mediated by p38-alpha and p38-beta 0.1860 69 3071 44 -0.4 0 1000 -1000 -0.042 -1000
FOXA2 and FOXA3 transcription factor networks 0.1833 68 3158 46 -0.72 0.035 1000 -1000 -0.014 -1000
Reelin signaling pathway 0.1833 68 3817 56 -0.29 0.065 1000 -1000 -0.069 -1000
TCGA08_retinoblastoma 0.1833 68 550 8 -0.085 0.21 1000 -1000 -0.011 -1000
Aurora B signaling 0.1833 68 4614 67 -0.019 0.29 1000 -1000 -0.048 -1000
Ephrin A reverse signaling 0.1752 65 455 7 -0.17 0.011 1000 -1000 -0.023 -1000
Ephrin B reverse signaling 0.1725 64 3114 48 -0.3 0.084 1000 -1000 -0.048 -1000
Wnt signaling 0.1725 64 453 7 -0.24 0.019 1000 -1000 -0.03 -1000
LPA receptor mediated events 0.1644 61 6282 102 -0.42 0.032 1000 -1000 -0.069 -1000
EPHB forward signaling 0.1617 60 5122 85 -0.25 0.2 1000 -1000 -0.08 -1000
Endothelins 0.1456 54 5266 96 -0.55 0.15 1000 -1000 -0.059 -1000
IL23-mediated signaling events 0.1456 54 3281 60 -0.33 0.031 1000 -1000 -0.097 -1000
S1P5 pathway 0.1402 52 900 17 -0.41 0.15 1000 -1000 -0.031 -1000
Calcium signaling in the CD4+ TCR pathway 0.1402 52 1625 31 -0.46 0.002 1000 -1000 -0.043 -1000
PLK1 signaling events 0.1375 51 4374 85 -0.05 0.27 1000 -1000 -0.033 -1000
ErbB2/ErbB3 signaling events 0.1348 50 3257 65 -0.36 0.066 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 0.1348 50 1303 26 -0.24 0.019 1000 -1000 -0.051 -1000
Syndecan-1-mediated signaling events 0.1321 49 1682 34 -0.46 0.072 1000 -1000 -0.052 -1000
Glypican 1 network 0.1321 49 2366 48 -0.36 0.059 1000 -1000 -0.039 -1000
S1P4 pathway 0.1213 45 1142 25 -0.41 0.15 1000 -1000 -0.036 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1186 44 3798 85 -0.46 0.016 1000 -1000 -0.058 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1159 43 3827 88 -0.27 0.008 1000 -1000 -0.089 -1000
Signaling events mediated by the Hedgehog family 0.1132 42 2204 52 -0.4 0.27 1000 -1000 -0.056 -1000
Thromboxane A2 receptor signaling 0.1132 42 4413 105 -0.15 0.075 1000 -1000 -0.054 -1000
S1P3 pathway 0.1132 42 1801 42 -0.41 0.15 1000 -1000 -0.03 -1000
S1P1 pathway 0.1105 41 1487 36 -0.43 0.15 1000 -1000 -0.047 -1000
BCR signaling pathway 0.1051 39 3868 99 -0.42 0.016 1000 -1000 -0.069 -1000
amb2 Integrin signaling 0.0997 37 3047 82 -0.42 0.08 1000 -1000 -0.05 -1000
IL12-mediated signaling events 0.0943 35 3121 87 -0.66 0.018 1000 -1000 -0.092 -1000
Glucocorticoid receptor regulatory network 0.0943 35 3991 114 -0.76 0.21 1000 -1000 -0.067 -1000
Signaling events mediated by PRL 0.0943 35 1214 34 -0.34 0.052 1000 -1000 -0.044 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0916 34 1858 54 -0.31 0.03 1000 -1000 -0.081 -1000
Syndecan-4-mediated signaling events 0.0916 34 2339 67 -0.36 0.18 1000 -1000 -0.067 -1000
Osteopontin-mediated events 0.0889 33 1288 38 -0.42 0.055 1000 -1000 -0.071 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0889 33 4075 120 -0.6 0.18 1000 -1000 -0.061 -1000
Ras signaling in the CD4+ TCR pathway 0.0889 33 577 17 -0.21 0.002 1000 -1000 -0.051 -1000
ErbB4 signaling events 0.0863 32 2276 69 -0.28 0.066 1000 -1000 -0.062 -1000
Arf6 signaling events 0.0836 31 1956 62 -0.46 0.075 1000 -1000 -0.037 -1000
Aurora C signaling 0.0755 28 201 7 0 0.17 1000 -1000 -0.021 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0728 27 771 28 -0.41 0.15 1000 -1000 -0.038 -1000
Fc-epsilon receptor I signaling in mast cells 0.0701 26 2536 97 -0.42 0.05 1000 -1000 -0.07 -1000
Integrins in angiogenesis 0.0701 26 2206 84 -0.34 0.069 1000 -1000 -0.07 -1000
TCR signaling in naïve CD8+ T cells 0.0674 25 2358 93 -0.26 0.12 1000 -1000 -0.055 -1000
Coregulation of Androgen receptor activity 0.0647 24 1844 76 -0.25 0.22 1000 -1000 -0.029 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0647 24 1790 74 -0.46 0.075 1000 -1000 -0.082 -1000
p38 MAPK signaling pathway 0.0647 24 1070 44 -0.42 0.012 1000 -1000 -0.049 -1000
Nectin adhesion pathway 0.0620 23 1500 63 -0.11 0.007 1000 -1000 -0.055 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0566 21 726 34 -0.074 0.017 1000 -1000 -0.044 -1000
PLK2 and PLK4 events 0.0566 21 64 3 -0.002 0.053 1000 -1000 -0.009 -1000
Presenilin action in Notch and Wnt signaling 0.0566 21 1315 61 -0.42 0.11 1000 -1000 -0.05 -1000
BMP receptor signaling 0.0566 21 1765 81 -0.18 0.065 1000 -1000 -0.069 -1000
Visual signal transduction: Rods 0.0539 20 1069 52 -0.21 0.043 1000 -1000 -0.058 -1000
LPA4-mediated signaling events 0.0512 19 238 12 -0.21 0.02 1000 -1000 -0.014 -1000
IL1-mediated signaling events 0.0512 19 1239 62 -0.16 0.004 1000 -1000 -0.077 -1000
FAS signaling pathway (CD95) 0.0512 19 917 47 -0.46 0.04 1000 -1000 -0.031 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0485 18 678 37 -0.3 0.007 1000 -1000 -0.039 -1000
FoxO family signaling 0.0485 18 1169 64 -0.2 0.27 1000 -1000 -0.054 -1000
IL27-mediated signaling events 0.0485 18 928 51 -0.21 0.13 1000 -1000 -0.056 -1000
Regulation of Androgen receptor activity 0.0458 17 1195 70 -0.3 0.064 1000 -1000 -0.055 -1000
JNK signaling in the CD4+ TCR pathway 0.0431 16 272 17 -0.074 0.024 1000 -1000 -0.03 -1000
IL2 signaling events mediated by PI3K 0.0431 16 942 58 -0.075 0.14 1000 -1000 -0.059 -1000
Canonical Wnt signaling pathway 0.0431 16 824 51 -0.19 0.13 1000 -1000 -0.051 -1000
Regulation of Telomerase 0.0431 16 1708 102 -0.47 0.2 1000 -1000 -0.061 -1000
Regulation of nuclear SMAD2/3 signaling 0.0404 15 2155 136 -0.48 0.4 1000 -1000 -0.055 -1000
HIF-2-alpha transcription factor network 0.0404 15 650 43 -0.24 0.078 1000 -1000 -0.052 -1000
IL2 signaling events mediated by STAT5 0.0404 15 348 22 -0.067 0.17 1000 -1000 -0.038 -1000
Syndecan-3-mediated signaling events 0.0377 14 493 35 -0.19 0.012 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class III 0.0350 13 542 40 -0.35 0.013 1000 -1000 -0.031 -1000
E-cadherin signaling events 0.0350 13 66 5 -0.051 0 1000 -1000 -0.022 -1000
Syndecan-2-mediated signaling events 0.0323 12 833 69 -0.19 0.062 1000 -1000 -0.039 -1000
Signaling events mediated by PTP1B 0.0323 12 954 76 -0.19 0.12 1000 -1000 -0.056 -1000
Aurora A signaling 0.0323 12 724 60 -0.02 0.21 1000 -1000 -0.043 -1000
Hedgehog signaling events mediated by Gli proteins 0.0296 11 742 65 -0.41 0.15 1000 -1000 -0.069 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0296 11 575 52 -0.13 0.04 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0296 11 512 45 -0.1 0.027 1000 -1000 -0.06 -1000
Class IB PI3K non-lipid kinase events 0.0296 11 33 3 -0.025 -1000 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0296 11 883 78 -0.31 0.025 1000 -1000 -0.078 -1000
Ceramide signaling pathway 0.0270 10 823 76 -0.34 0.075 1000 -1000 -0.04 -1000
Retinoic acid receptors-mediated signaling 0.0270 10 581 58 -0.17 0.038 1000 -1000 -0.051 -1000
Effects of Botulinum toxin 0.0270 10 279 26 -0.12 0.013 1000 -1000 -0.045 -1000
E-cadherin signaling in the nascent adherens junction 0.0270 10 777 76 -0.051 0.026 1000 -1000 -0.078 -1000
EGFR-dependent Endothelin signaling events 0.0270 10 218 21 -0.023 0.075 1000 -1000 -0.049 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0270 10 343 33 -0.02 0.22 1000 -1000 -0.041 -1000
E-cadherin signaling in keratinocytes 0.0270 10 453 43 -0.095 0.02 1000 -1000 -0.059 -1000
Cellular roles of Anthrax toxin 0.0243 9 370 39 -0.089 0.014 1000 -1000 -0.019 -1000
Insulin-mediated glucose transport 0.0243 9 291 32 -0.039 0.18 1000 -1000 -0.046 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0243 9 748 83 -0.15 0.18 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 0.0243 9 238 26 -0.34 0.022 1000 -1000 -0.019 -1000
Caspase cascade in apoptosis 0.0216 8 609 74 -0.033 0.031 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class II 0.0189 7 525 75 -0.48 0.008 1000 -1000 -0.041 -1000
a4b1 and a4b7 Integrin signaling 0.0189 7 38 5 -0.025 -0.012 1000 -1000 -0.014 -1000
Regulation of p38-alpha and p38-beta 0.0189 7 406 54 -0.15 0.032 1000 -1000 -0.059 -1000
Rapid glucocorticoid signaling 0.0189 7 153 20 -0.026 0.051 1000 -1000 -0.021 -1000
IFN-gamma pathway 0.0162 6 457 68 -0.42 0.067 1000 -1000 -0.07 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0162 6 864 125 -0.07 0.049 1000 -1000 -0.088 -1000
BARD1 signaling events 0.0135 5 328 57 -0.012 0.11 1000 -1000 -0.047 -1000
Arf6 downstream pathway 0.0135 5 230 43 -0.046 0.029 1000 -1000 -0.027 -1000
Class I PI3K signaling events mediated by Akt 0.0135 5 405 68 -0.1 0.18 1000 -1000 -0.045 -1000
Paxillin-dependent events mediated by a4b1 0.0135 5 205 36 -0.041 0.018 1000 -1000 -0.043 -1000
Class I PI3K signaling events 0.0135 5 369 73 -0.15 0.025 1000 -1000 -0.059 -1000
Visual signal transduction: Cones 0.0108 4 185 38 -0.012 0.031 1000 -1000 -0.035 -1000
TRAIL signaling pathway 0.0108 4 209 48 -0.018 0.009 1000 -1000 -0.056 -1000
Signaling mediated by p38-gamma and p38-delta 0.0108 4 61 15 -0.009 0.061 1000 -1000 -0.035 -1000
PDGFR-beta signaling pathway 0.0108 4 471 97 -0.12 0.046 1000 -1000 -0.06 -1000
mTOR signaling pathway 0.0081 3 199 53 -0.072 0.027 1000 -1000 -0.043 -1000
Atypical NF-kappaB pathway 0.0081 3 110 31 -0.03 0.018 1000 -1000 -0.053 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0054 2 53 23 -0.051 0.034 1000 -1000 -0.044 -1000
ceramide signaling pathway 0.0054 2 113 49 -0.04 0.039 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class I 0.0054 2 208 104 -0.031 0.006 1000 -1000 -0.042 -1000
Insulin Pathway 0.0054 2 201 74 -0.081 0.04 1000 -1000 -0.074 -1000
VEGFR1 specific signals 0.0054 2 117 56 -0.019 0.05 1000 -1000 -0.052 -1000
Canonical NF-kappaB pathway 0.0027 1 54 39 -0.031 0.065 1000 -1000 -0.063 -1000
Arf6 trafficking events 0.0027 1 112 71 -0.033 0.029 1000 -1000 -0.063 -1000
Arf1 pathway 0.0027 1 90 54 -0.07 0.016 1000 -1000 -0.026 -1000
Circadian rhythm pathway 0.0000 0 17 22 -0.011 0.036 1000 -1000 -0.051 -1000
TCGA08_p53 0.0000 0 0 7 -0.057 0.027 1000 -1000 -0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 0 0.001 1000 -1000 -0.043 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.002 1000 -1000 -0.032 -1000
Total NA 3801 224005 7203 -33 -990 131000 -131000 -6.6 -131000
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.28 0.26 -10000 0 -0.51 206 206
ER alpha/Gai/GDP/Gbeta gamma -0.5 0.46 -10000 0 -0.77 237 237
AKT1 -0.54 0.48 -10000 0 -0.96 206 206
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.55 0.5 -10000 0 -0.99 206 206
mol:Ca2+ -0.19 0.3 -10000 0 -0.77 70 70
IGF1R -0.015 0.13 0.32 4 -0.86 8 12
E2/ER alpha (dimer)/Striatin -0.34 0.3 -10000 0 -0.6 214 214
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.5 0.46 0.9 206 -10000 0 206
RhoA/GTP -0.24 0.22 -10000 0 -0.44 205 205
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.44 0.36 -10000 0 -0.74 205 205
regulation of stress fiber formation 0.18 0.2 0.53 15 -10000 0 15
E2/ERA-ERB (dimer) -0.32 0.29 -10000 0 -0.59 205 205
KRAS 0 0 -10000 0 -10000 0 0
G13/GTP -0.3 0.27 -10000 0 -0.54 205 205
pseudopodium formation -0.18 0.2 -10000 0 -0.53 15 15
E2/ER alpha (dimer)/PELP1 -0.32 0.29 -10000 0 -0.59 205 205
GRB2 0 0 -10000 0 -10000 0 0
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
HRAS 0.002 0.023 0.32 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.42 0.4 -10000 0 -0.75 206 206
E2/ER beta (dimer) 0.001 0.016 0.21 2 -10000 0 2
mol:GDP -0.32 0.29 -10000 0 -0.59 205 205
mol:NADP -0.42 0.4 -10000 0 -0.75 206 206
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
mol:IP3 -0.22 0.32 -10000 0 -0.83 70 70
IGF-1R heterotetramer -0.015 0.13 0.32 4 -0.86 8 12
PLCB1 -0.22 0.32 -10000 0 -0.86 66 66
PLCB2 -0.23 0.33 -10000 0 -0.86 70 70
IGF1 -0.34 0.42 -10000 0 -0.86 145 145
mol:L-citrulline -0.42 0.4 -10000 0 -0.75 206 206
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.44 0.49 -10000 0 -0.93 178 178
JNK cascade 0.001 0.016 0.21 2 -10000 0 2
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.002 0.023 0.32 2 -10000 0 2
GNAQ -0.002 0.045 -10000 0 -0.86 1 1
ESR1 -0.48 0.43 -10000 0 -0.86 205 205
Gq family/GDP/Gbeta gamma -0.093 0.2 -10000 0 -0.47 62 62
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.2 0.19 -10000 0 -0.36 204 204
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.44 0.36 -10000 0 -0.74 205 205
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
E2/ER alpha (dimer) -0.37 0.34 -10000 0 -0.67 205 205
STRN -0.028 0.15 -10000 0 -0.86 12 12
GNAL 0.051 0.12 0.32 60 -10000 0 60
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.007 0.034 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
HBEGF -0.4 0.38 -10000 0 -0.68 213 213
cAMP biosynthetic process -0.25 0.25 -10000 0 -0.48 205 205
SRC -0.45 0.43 -10000 0 -0.77 205 205
PI3K -0.005 0.071 -10000 0 -0.94 2 2
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.29 0.26 -10000 0 -0.52 206 206
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.42 0.32 -10000 0 -0.65 227 227
Gs family/GTP -0.26 0.26 -10000 0 -0.48 205 205
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.014 -10000 0 -10000 0 0
vasodilation -0.39 0.37 -10000 0 -0.7 206 206
mol:DAG -0.22 0.32 -10000 0 -0.83 70 70
Gs family/GDP/Gbeta gamma -0.26 0.24 -10000 0 -0.47 206 206
MSN -0.2 0.22 -10000 0 -0.59 15 15
Gq family/GTP -0.24 0.34 -10000 0 -0.89 71 71
mol:PI-3-4-5-P3 -0.52 0.47 -10000 0 -0.93 206 206
NRAS 0 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.39 0.37 0.7 206 -10000 0 206
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.3 0.27 -10000 0 -0.55 205 205
NOS3 -0.46 0.44 -10000 0 -0.82 206 206
GNA11 -0.028 0.15 -10000 0 -0.86 12 12
MAPKKK cascade -0.43 0.39 -10000 0 -0.76 214 214
E2/ER alpha (dimer)/PELP1/Src -0.47 0.39 -10000 0 -0.8 205 205
ruffle organization -0.18 0.2 -10000 0 -0.53 15 15
ROCK2 -0.24 0.22 -10000 0 -0.42 211 211
GNA14 -0.15 0.32 -10000 0 -0.86 63 63
GNA15 -0.001 0.05 0.32 2 -0.86 1 3
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.41 0.39 -10000 0 -0.72 201 201
MMP2 -0.42 0.4 -10000 0 -0.72 210 210
PDGFR-alpha signaling pathway

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
PDGFRA -0.36 0.43 -10000 0 -0.89 149 149
PDGF/PDGFRA/CRKL -0.27 0.33 -10000 0 -0.68 149 149
positive regulation of JUN kinase activity -0.21 0.26 -10000 0 -0.53 149 149
CRKL 0 0 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.28 0.33 -10000 0 -0.68 149 149
AP1 -0.74 0.68 -10000 0 -1.4 179 179
mol:IP3 -0.29 0.35 -10000 0 -0.71 149 149
PLCG1 -0.29 0.35 -10000 0 -0.71 149 149
PDGF/PDGFRA/alphaV Integrin -0.27 0.33 -10000 0 -0.68 149 149
RAPGEF1 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.28 0.35 -10000 0 -0.71 149 149
CAV3 0 0 -10000 0 -10000 0 0
CAV1 0 0 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.21 0.26 -10000 0 -0.53 149 149
PDGF/PDGFRA/Shf -0.31 0.36 -10000 0 -0.7 161 161
FOS -0.71 0.67 -10000 0 -1.4 179 179
JUN -0.048 0.095 -10000 0 -0.75 6 6
oligodendrocyte development -0.27 0.33 -10000 0 -0.68 149 149
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
mol:DAG -0.29 0.35 -10000 0 -0.71 149 149
PDGF/PDGFRA -0.36 0.43 -10000 0 -0.89 149 149
actin cytoskeleton reorganization -0.27 0.33 -10000 0 -0.68 150 150
SRF 0.025 0.02 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
PI3K -0.24 0.3 -10000 0 -0.59 150 150
PDGF/PDGFRA/Crk/C3G -0.24 0.29 -10000 0 -0.59 149 149
JAK1 -0.26 0.34 -10000 0 -0.68 149 149
ELK1/SRF -0.22 0.26 -10000 0 -0.55 149 149
SHB -0.002 0.045 -10000 0 -0.86 1 1
SHF -0.044 0.19 -10000 0 -0.86 19 19
CSNK2A1 0.033 0.026 -10000 0 -10000 0 0
GO:0007205 -0.29 0.35 -10000 0 -0.72 149 149
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction -0.21 0.26 -10000 0 -0.53 149 149
PDGF/PDGFRA/SHB -0.28 0.33 -10000 0 -0.68 150 150
PDGF/PDGFRA/Caveolin-1 -0.27 0.33 -10000 0 -0.68 149 149
ITGAV 0.001 0.016 0.32 1 -10000 0 1
ELK1 -0.27 0.32 -10000 0 -0.66 149 149
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
PDGF/PDGFRA/Crk -0.27 0.33 -10000 0 -0.68 149 149
JAK-STAT cascade -0.26 0.34 -10000 0 -0.68 149 149
cell proliferation -0.3 0.35 -10000 0 -0.7 161 161
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 0.38 0.52 1 87 -0.85 15 102
PLK1 0.28 0.23 0.59 97 -10000 0 97
BIRC5 0.3 0.23 0.62 78 -10000 0 78
HSPA1B 0.39 0.53 1.1 86 -0.85 15 101
MAP2K1 0.12 0.12 0.37 24 -10000 0 24
BRCA2 0.38 0.55 1.1 83 -0.99 16 99
FOXM1 0.44 0.63 1.2 97 -1 16 113
XRCC1 0.39 0.53 1.1 83 -0.86 14 97
FOXM1B/p19 0.21 0.48 0.7 145 -0.84 24 169
Cyclin D1/CDK4 0.23 0.53 0.9 75 -0.93 24 99
CDC2 0.41 0.57 1.1 94 -0.88 16 110
TGFA 0.17 0.67 0.95 79 -1 58 137
SKP2 0.38 0.52 1 87 -0.85 15 102
CCNE1 0.14 0.16 0.35 134 -10000 0 134
CKS1B 0.39 0.53 1.1 84 -0.86 14 98
RB1 0.15 0.33 0.65 96 -10000 0 96
FOXM1C/SP1 0.24 0.52 0.8 140 -0.93 18 158
AURKB 0.27 0.23 0.6 81 -10000 0 81
CENPF 0.45 0.57 1.1 102 -0.85 15 117
CDK4 0.044 0.046 -10000 0 -10000 0 0
MYC 0.26 0.55 0.92 82 -0.84 35 117
CHEK2 0.12 0.13 0.38 44 -10000 0 44
ONECUT1 0.27 0.55 0.97 79 -0.94 24 103
CDKN2A 0.1 0.18 0.3 103 -10000 0 103
LAMA4 0.39 0.53 1.1 87 -0.85 15 102
FOXM1B/HNF6 0.26 0.58 0.98 78 -1.1 24 102
FOS -0.13 0.86 1.1 74 -1.1 127 201
SP1 -0.009 0.035 -10000 0 -0.28 1 1
CDC25B 0.39 0.53 1.1 85 -0.85 15 100
response to radiation 0.074 0.089 0.26 22 -10000 0 22
CENPB 0.38 0.52 1.1 83 -0.88 13 96
CENPA 0.44 0.57 1.2 97 -0.86 14 111
NEK2 0.46 0.56 1.1 101 -0.84 14 115
HIST1H2BA 0.38 0.52 1 87 -0.86 15 102
CCNA2 0.19 0.17 0.35 197 -10000 0 197
EP300 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.4 0.57 1.1 87 -0.95 16 103
CCNB2 0.46 0.57 1.2 97 -0.86 14 111
CCNB1 0.43 0.59 1.2 93 -0.9 15 108
ETV5 0.38 0.52 1.1 83 -0.88 13 96
ESR1 -0.25 0.74 1.1 42 -1 118 160
CCND1 0.28 0.56 0.99 79 -0.95 25 104
GSK3A 0.084 0.086 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.25 0.21 0.48 143 -10000 0 143
CDK2 0.031 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.11 0.12 0.3 85 -10000 0 85
FOXM1B/Cbp/p300 -0.082 0.21 -10000 0 -0.85 18 18
GAS1 0.2 0.76 1.1 82 -1.1 66 148
MMP2 0.35 0.6 1.1 85 -1.1 26 111
RB1/FOXM1C 0.32 0.52 0.95 80 -0.89 21 101
CREBBP 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.1 0.077 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -10000 0 -0.48 108 108
JUN -0.29 0.26 -10000 0 -0.67 84 84
HRAS 0.002 0.023 0.32 2 -10000 0 2
RET51/GFRalpha1/GDNF/GRB10 -0.43 0.37 -10000 0 -0.67 244 244
RAP1A 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
RAP1A/GDP 0 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.43 0.37 -10000 0 -0.67 244 244
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.15 0.25 -10000 0 -0.54 109 109
RHOA 0 0 -10000 0 -10000 0 0
RAP1A/GTP -0.39 0.34 -10000 0 -0.6 244 244
GRB7 -0.004 0.098 0.32 6 -0.86 4 10
RET51/GFRalpha1/GDNF -0.43 0.37 -10000 0 -0.67 244 244
MAPKKK cascade -0.35 0.29 -10000 0 -0.54 235 235
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.15 0.25 -10000 0 -0.54 109 109
lamellipodium assembly -0.22 0.18 -10000 0 -0.43 111 111
RET51/GFRalpha1/GDNF/SHC -0.43 0.37 -10000 0 -0.67 244 244
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
RET9/GFRalpha1/GDNF/SHC -0.15 0.25 -10000 0 -0.54 109 109
RET9/GFRalpha1/GDNF/Shank3 -0.15 0.25 -10000 0 -0.54 109 109
MAPK3 -0.37 0.31 -10000 0 -0.56 244 244
DOK1 0 0 -10000 0 -10000 0 0
DOK6 -0.12 0.31 0.32 4 -0.86 55 59
PXN 0 0 -10000 0 -10000 0 0
neurite development -0.36 0.3 -10000 0 -0.76 93 93
DOK5 -0.005 0.11 0.32 8 -0.86 5 13
GFRA1 -0.25 0.39 -10000 0 -0.86 109 109
MAPK8 -0.3 0.27 -10000 0 -0.71 80 80
HRAS/GTP -0.41 0.35 -10000 0 -0.62 244 244
tube development -0.14 0.24 -10000 0 -0.51 109 109
MAPK1 -0.37 0.31 -10000 0 -0.57 236 236
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.17 -10000 0 -0.36 109 109
Rac1/GDP 0 0 -10000 0 -10000 0 0
SRC 0.004 0.036 0.32 5 -10000 0 5
PDLIM7 0.003 0.028 0.32 3 -10000 0 3
RET51/GFRalpha1/GDNF/Dok6 -0.48 0.41 -10000 0 -0.71 255 255
SHC1 0 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.43 0.37 -10000 0 -0.67 244 244
RET51/GFRalpha1/GDNF/Dok5 -0.44 0.38 -10000 0 -0.67 246 246
PRKCA 0 0 -10000 0 -10000 0 0
HRAS/GDP 0.001 0.016 0.21 2 -10000 0 2
CREB1 -0.22 0.24 -10000 0 -0.55 109 109
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.17 -10000 0 -0.36 105 105
RET51/GFRalpha1/GDNF/Grb7 -0.44 0.37 -10000 0 -0.67 246 246
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.46 0.43 0.32 2 -0.86 200 202
DOK4 0 0 -10000 0 -10000 0 0
JNK cascade -0.27 0.27 -10000 0 -0.65 84 84
RET9/GFRalpha1/GDNF/FRS2 -0.15 0.25 -10000 0 -0.54 109 109
SHANK3 0.001 0.016 0.32 1 -10000 0 1
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
NCK1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.17 -10000 0 -0.36 109 109
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.29 0.25 -10000 0 -0.45 236 236
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.29 0.26 -10000 0 -0.46 236 236
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.34 0.35 -10000 0 -0.54 236 236
PI3K -0.36 0.32 -10000 0 -0.74 111 111
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.14 0.24 -10000 0 -0.51 109 109
GRB10 0 0 -10000 0 -10000 0 0
activation of MAPKK activity -0.23 0.21 -10000 0 -0.49 106 106
RET51/GFRalpha1/GDNF/FRS2 -0.43 0.37 -10000 0 -0.67 244 244
GAB1 0 0 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.016 0.12 -10000 0 -0.86 7 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.34 0.35 -10000 0 -0.54 236 236
RET51/GFRalpha1/GDNF/PKC alpha -0.43 0.37 -10000 0 -0.67 244 244
GRB2 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GDNF 0.014 0.064 0.32 16 -10000 0 16
RAC1 0 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.43 0.37 -10000 0 -0.67 244 244
Rac1/GTP -0.27 0.22 -10000 0 -0.54 111 111
RET9/GFRalpha1/GDNF -0.17 0.28 -10000 0 -0.59 109 109
GFRalpha1/GDNF -0.19 0.31 -10000 0 -0.67 109 109
Nongenotropic Androgen signaling

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
PTK2 0.009 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.15 0.25 -10000 0 -0.55 103 103
regulation of S phase of mitotic cell cycle -0.099 0.16 -10000 0 -0.36 101 101
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
HRAS 0.002 0.023 0.31 2 -10000 0 2
SHBG/T-DHT -0.23 0.29 -10000 0 -0.6 143 143
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.008 0.003 -10000 0 -10000 0 0
MAP2K1 -0.14 0.22 -10000 0 -0.48 101 101
T-DHT/AR -0.18 0.3 -10000 0 -0.68 101 101
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.004 -10000 0 -0.008 123 123
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
mol:GDP -0.18 0.29 -10000 0 -0.66 102 102
cell proliferation -0.26 0.28 -10000 0 -0.53 145 145
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
FOS -0.43 0.44 -10000 0 -0.88 179 179
mol:Ca2+ -0.051 0.056 -10000 0 -0.1 189 189
MAPK3 -0.21 0.25 -10000 0 -0.55 101 101
MAPK1 -0.12 0.13 -10000 0 -0.32 56 56
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
mol:IP3 -0.002 0.002 -10000 0 -0.004 179 179
cAMP biosynthetic process -0.18 0.29 -10000 0 -0.54 143 143
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
potassium channel inhibitor activity -0.002 0.002 -10000 0 -0.004 179 179
HRAS/GTP -0.15 0.22 -10000 0 -0.51 101 101
actin cytoskeleton reorganization -0.004 0.054 -10000 0 -0.7 2 2
SRC 0.004 0.036 0.32 5 -10000 0 5
voltage-gated calcium channel activity -0.002 0.002 -10000 0 -0.004 179 179
PI3K -0.005 0.065 -10000 0 -0.85 2 2
apoptosis 0.24 0.26 0.48 179 -10000 0 179
T-DHT/AR/PELP1 -0.16 0.26 -10000 0 -0.6 101 101
HRAS/GDP -0.17 0.28 -10000 0 -0.62 102 102
CREB1 -0.26 0.28 -10000 0 -0.52 179 179
RAC1-CDC42/GTP -0.004 0.055 -10000 0 -0.72 2 2
AR -0.24 0.38 -10000 0 -0.86 101 101
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.15 0.21 -10000 0 -0.5 101 101
RAC1-CDC42/GDP -0.16 0.27 -10000 0 -0.59 102 102
T-DHT/AR/PELP1/Src -0.15 0.25 -10000 0 -0.55 101 101
MAP2K2 -0.14 0.22 -10000 0 -0.48 101 101
T-DHT/AR/PELP1/Src/PI3K -0.099 0.17 -10000 0 -0.37 101 101
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
SHBG -0.33 0.42 -10000 0 -0.86 143 143
Gi family/GNB1/GNG2/GDP -0.24 0.29 -10000 0 -0.51 178 178
mol:T-DHT -0.001 0.002 -10000 0 -0.003 87 87
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.01 0.01 -10000 0 -10000 0 0
Gi family/GTP -0.21 0.27 -10000 0 -0.46 156 156
CDC42 0 0 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.18 0.16 0.32 208 -9999 0 208
GPC2 0.043 0.11 0.32 50 -9999 0 50
GPC2/Midkine 0.15 0.14 0.44 33 -9999 0 33
neuron projection morphogenesis 0.15 0.14 0.44 33 -9999 0 33
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.005 0.15 0.32 18 -0.86 8 26
NFATC2 -0.18 0.38 0.64 1 -0.81 85 86
NFATC3 -0.058 0.12 -10000 0 -0.3 30 30
CD40LG -0.57 0.61 0.76 1 -1.2 161 162
ITCH -0.004 0.033 -10000 0 -10000 0 0
CBLB -0.004 0.033 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.34 0.5 0.62 7 -1.2 74 81
JUNB -0.044 0.19 -10000 0 -0.86 19 19
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.041 -10000 0 -0.35 5 5
T cell anergy 0.002 0.084 -10000 0 -0.5 5 5
TLE4 -0.11 0.3 -10000 0 -0.63 81 81
Jun/NFAT1-c-4/p21SNFT -0.41 0.56 0.67 1 -1.1 130 131
AP-1/NFAT1-c-4 -0.77 0.85 0.72 4 -1.6 159 163
IKZF1 -0.12 0.33 0.58 1 -0.7 73 74
T-helper 2 cell differentiation -0.26 0.4 0.48 1 -0.88 94 95
AP-1/NFAT1 -0.41 0.42 0.55 1 -0.75 201 202
CALM1 -0.003 0.022 -10000 0 -10000 0 0
EGR2 -0.54 0.85 -10000 0 -1.7 118 118
EGR3 -0.45 0.78 -10000 0 -1.6 96 96
NFAT1/FOXP3 -0.13 0.32 0.44 7 -0.68 76 83
EGR1 -0.3 0.41 -10000 0 -0.86 128 128
JUN -0.015 0.11 -10000 0 -0.86 6 6
EGR4 0.002 0.029 0.31 3 -10000 0 3
mol:Ca2+ -0.003 0.024 -10000 0 -10000 0 0
GBP3 -0.15 0.37 -10000 0 -0.76 86 86
FOSL1 -0.035 0.18 0.32 3 -0.86 16 19
NFAT1-c-4/MAF/IRF4 -0.47 0.6 0.63 2 -1.2 143 145
DGKA -0.1 0.3 0.58 1 -0.65 71 72
CREM 0 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.4 0.55 0.55 1 -1.1 132 133
CTLA4 -0.077 0.31 0.46 7 -0.68 55 62
NFAT1-c-4 (dimer)/EGR1 -0.56 0.68 0.55 1 -1.3 143 144
NFAT1-c-4 (dimer)/EGR4 -0.4 0.56 0.55 1 -1.1 133 134
FOS -0.42 0.43 -10000 0 -0.87 179 179
IFNG -0.2 0.34 0.47 3 -0.81 66 69
T cell activation -0.34 0.44 -10000 0 -0.93 117 117
MAF -0.002 0.045 -10000 0 -0.86 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.25 0.43 0.77 130 -10000 0 130
TNF -0.44 0.58 -10000 0 -1.1 138 138
FASLG -0.53 0.8 -10000 0 -1.5 133 133
TBX21 -0.009 0.14 -10000 0 -0.86 9 9
BATF3 -0.008 0.09 0.32 1 -0.86 4 5
PRKCQ -0.027 0.17 0.35 2 -0.86 15 17
PTPN1 -0.1 0.29 -10000 0 -0.64 71 71
NFAT1-c-4/ICER1 -0.41 0.55 0.54 1 -1.1 131 132
GATA3 -0.062 0.22 0.32 1 -0.86 27 28
T-helper 1 cell differentiation -0.2 0.33 0.46 4 -0.77 71 75
IL2RA -0.34 0.46 0.6 7 -1.1 77 84
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.11 0.29 -10000 0 -0.65 71 71
E2F1 0.2 0.15 0.32 230 -10000 0 230
PPARG 0.001 0.016 0.32 1 -10000 0 1
SLC3A2 -0.1 0.29 -10000 0 -0.64 70 70
IRF4 -0.16 0.35 0.32 9 -0.86 74 83
PTGS2 -0.65 0.69 -10000 0 -1.4 166 166
CSF2 -0.55 0.61 -10000 0 -1.2 158 158
JunB/Fra1/NFAT1-c-4 -0.42 0.58 0.54 2 -1.1 132 134
IL4 -0.28 0.43 -10000 0 -0.99 83 83
IL5 -0.55 0.61 -10000 0 -1.2 156 156
IL2 -0.35 0.45 -10000 0 -0.95 117 117
IL3 -0.084 0.066 -10000 0 -10000 0 0
RNF128 -0.012 0.11 -10000 0 -0.92 5 5
NFATC1 -0.25 0.44 -10000 0 -0.78 130 130
CDK4 0.21 0.29 0.67 67 -10000 0 67
PTPRK -0.1 0.29 -10000 0 -0.63 75 75
IL8 -0.63 0.65 -10000 0 -1.2 180 180
POU2F1 0.002 0.005 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 -0.11 0.24 -10000 0 -10000 0 0
CRKL -0.16 0.21 -10000 0 -0.43 137 137
mol:DAG -0.17 0.24 -10000 0 -0.48 136 136
HRAS -0.13 0.17 -10000 0 -10000 0 0
MAPK8 -0.2 0.28 -10000 0 -0.53 147 147
RAP1A -0.16 0.21 -10000 0 -0.43 137 137
GAB1 -0.16 0.21 -10000 0 -0.43 137 137
MAPK14 -0.18 0.24 -10000 0 -0.5 136 136
EPO -0.3 0.42 0.32 12 -0.86 136 148
PLCG1 -0.18 0.24 -10000 0 -0.49 136 136
EPOR/TRPC2/IP3 Receptors -0.011 0.016 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.28 0.34 -10000 0 -0.62 168 168
GAB1/SHC/GRB2/SOS1 -0.14 0.18 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.24 0.33 -10000 0 -0.66 136 136
IRS2 -0.17 0.22 -10000 0 -0.44 141 141
STAT1 -0.14 0.26 -10000 0 -0.49 136 136
STAT5B -0.18 0.24 -10000 0 -0.49 136 136
cell proliferation -0.17 0.27 -10000 0 -0.5 147 147
GAB1/SHIP/PIK3R1/SHP2/SHC -0.13 0.17 -10000 0 -0.74 1 1
TEC -0.16 0.22 -10000 0 -0.44 141 141
SOCS3 -0.12 0.29 -10000 0 -0.86 50 50
STAT1 (dimer) -0.14 0.26 -10000 0 -0.47 136 136
JAK2 -0.014 0.047 -10000 0 -0.86 1 1
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
EPO/EPOR (dimer)/JAK2 -0.14 0.25 -10000 0 -0.46 137 137
EPO/EPOR -0.24 0.33 -10000 0 -0.66 136 136
LYN 0 0 -10000 0 -10000 0 0
TEC/VAV2 -0.16 0.21 -10000 0 -0.42 141 141
elevation of cytosolic calcium ion concentration -0.011 0.016 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.2 0.28 -10000 0 -0.56 136 136
mol:IP3 -0.17 0.24 -10000 0 -0.48 136 136
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.15 0.2 -10000 0 -0.81 4 4
SH2B3 -0.011 0.016 -10000 0 -10000 0 0
NFKB1 -0.18 0.24 -10000 0 -0.5 136 136
EPO/EPOR (dimer)/JAK2/SOCS3 -0.18 0.21 -10000 0 -0.4 168 168
PTPN6 -0.17 0.22 -10000 0 -0.46 137 137
TEC/VAV2/GRB2 -0.15 0.2 -10000 0 -0.57 6 6
EPOR -0.011 0.016 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.14 0.18 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 -0.016 0.12 -10000 0 -0.86 7 7
CRKL/CBL/C3G -0.14 0.2 -10000 0 -10000 0 0
VAV2 -0.16 0.21 -10000 0 -0.43 137 137
CBL -0.16 0.21 -10000 0 -0.43 137 137
SHC/Grb2/SOS1 -0.14 0.2 -10000 0 -10000 0 0
STAT5A -0.18 0.24 -10000 0 -0.49 136 136
GRB2 0 0 -10000 0 -10000 0 0
STAT5 (dimer) -0.16 0.22 -10000 0 -0.44 136 136
LYN/PLCgamma2 -0.013 0.091 -10000 0 -0.67 7 7
PTPN11 0 0 -10000 0 -10000 0 0
BTK -0.17 0.22 -10000 0 -0.44 142 142
BCL2 -0.12 0.24 -10000 0 -0.99 1 1
IL4-mediated 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
BCL2L1 -0.44 0.6 -10000 0 -1.1 121 121
STAT6 (cleaved dimer) -0.55 0.56 -10000 0 -1.1 172 172
IGHG1 -0.14 0.24 0.52 2 -0.42 64 66
IGHG3 -0.43 0.57 -10000 0 -0.99 164 164
AKT1 -0.21 0.35 0.6 1 -0.66 97 98
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.3 0.58 1 -0.56 82 83
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.33 0.57 1 -0.59 91 92
THY1 -0.42 0.62 0.88 1 -1.1 125 126
MYB 0.032 0.096 0.32 38 -10000 0 38
HMGA1 0.017 0.071 0.32 20 -10000 0 20
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.46 0.65 2 -0.79 137 139
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.2 0.33 0.57 1 -0.59 89 90
SP1 0.019 0.022 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.021 0.025 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.54 0.55 -10000 0 -1.2 141 141
SOCS1 -0.29 0.39 -10000 0 -0.73 124 124
SOCS3 -0.33 0.55 -10000 0 -1.2 84 84
FCER2 -0.41 0.58 0.78 1 -1 141 142
PARP14 -0.001 0.045 -10000 0 -0.86 1 1
CCL17 -0.44 0.6 -10000 0 -1.1 126 126
GRB2 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.15 0.27 0.53 1 -0.5 57 58
T cell proliferation -0.46 0.62 -10000 0 -1.2 134 134
IL4R/JAK1 -0.45 0.6 -10000 0 -1.1 128 128
EGR2 -0.64 0.82 -10000 0 -1.6 145 145
JAK2 -0.004 0.064 -10000 0 -0.89 1 1
JAK3 0.009 0.057 0.34 4 -0.84 1 5
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
JAK1 0.01 0.02 -10000 0 -10000 0 0
COL1A2 -0.11 0.26 -10000 0 -1.7 4 4
CCL26 -0.43 0.61 0.81 1 -1.1 129 130
IL4R -0.47 0.65 -10000 0 -1.2 128 128
PTPN6 0.016 0.014 -10000 0 -10000 0 0
IL13RA2 -0.99 0.76 -10000 0 -1.4 256 256
IL13RA1 -0.002 0.044 -10000 0 -10000 0 0
IRF4 -0.35 0.67 0.72 1 -1.6 79 80
ARG1 -0.33 0.61 -10000 0 -1.6 68 68
CBL -0.28 0.43 0.6 1 -0.74 134 135
GTF3A 0.025 0.032 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
IL13RA1/JAK2 -0.001 0.076 -10000 0 -0.7 1 1
IRF4/BCL6 -0.36 0.58 -10000 0 -1.5 79 79
CD40LG -0.02 0.17 0.39 2 -0.87 14 16
MAPK14 -0.31 0.48 0.6 1 -0.84 129 130
mitosis -0.2 0.34 0.59 1 -0.62 97 98
STAT6 -0.52 0.73 0.91 2 -1.3 139 141
SPI1 -0.018 0.096 -10000 0 -0.58 6 6
RPS6KB1 -0.19 0.32 0.58 1 -0.62 83 84
STAT6 (dimer) -0.52 0.73 0.91 2 -1.3 139 141
STAT6 (dimer)/PARP14 -0.49 0.64 -10000 0 -1.2 134 134
mast cell activation 0.008 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.35 0.6 1 -0.62 100 101
FRAP1 -0.21 0.35 0.6 1 -0.66 97 98
LTA -0.44 0.6 -10000 0 -1.1 124 124
FES -0.012 0.099 -10000 0 -0.86 5 5
T-helper 1 cell differentiation 0.5 0.7 1.2 139 -0.91 2 141
CCL11 -0.42 0.58 -10000 0 -1.1 119 119
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.35 0.6 1 -0.62 99 100
IL2RG 0.002 0.11 0.31 7 -0.85 5 12
IL10 -0.52 0.69 -10000 0 -1.3 137 137
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.016 0.12 -10000 0 -0.86 7 7
IL4 -0.08 0.18 0.57 1 -10000 0 1
IL5 -0.44 0.6 -10000 0 -1.2 115 115
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.33 0.48 0.83 1 -0.85 128 129
COL1A1 -0.13 0.36 0.65 6 -1.8 10 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.61 -10000 0 -1.2 117 117
IL2R gamma/JAK3 -0.003 0.1 0.4 2 -0.77 5 7
TFF3 -0.45 0.62 -10000 0 -1.2 125 125
ALOX15 -0.44 0.6 -10000 0 -1.2 120 120
MYBL1 0.005 0.04 0.32 6 -10000 0 6
T-helper 2 cell differentiation -0.36 0.5 -10000 0 -0.91 134 134
SHC1 0 0 -10000 0 -10000 0 0
CEBPB -0.011 0.056 -10000 0 -0.29 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.32 0.55 1 -0.58 94 95
mol:PI-3-4-5-P3 -0.21 0.35 0.6 1 -0.66 97 98
PI3K -0.23 0.37 0.6 1 -0.7 97 98
DOK2 -0.012 0.099 -10000 0 -0.86 5 5
ETS1 0.012 0.048 -10000 0 -0.82 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.26 0.5 1 -0.48 49 50
ITGB3 -0.5 0.68 -10000 0 -1.3 129 129
PIGR -0.6 0.74 -10000 0 -1.4 151 151
IGHE 0.021 0.059 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.25 0.5 1 -0.47 49 50
BCL6 0 0.002 -10000 0 -10000 0 0
OPRM1 -0.45 0.6 -10000 0 -1.1 126 126
RETNLB -0.45 0.6 -10000 0 -1.1 128 128
SELP -0.66 0.81 -10000 0 -1.5 155 155
AICDA -0.43 0.57 -10000 0 -1.1 122 122
IGF1 pathway

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
NCK2 -0.001 0.048 0.32 1 -0.86 1 2
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.19 0.24 -10000 0 -0.48 150 150
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.002 0.023 0.32 2 -10000 0 2
IRS1/Crk -0.2 0.24 -10000 0 -0.48 150 150
IGF-1R heterotetramer/IGF1/PTP1B -0.22 0.28 -10000 0 -0.56 150 150
AKT1 -0.16 0.21 -10000 0 -0.41 150 150
BAD -0.13 0.21 -10000 0 -0.38 147 147
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.19 0.24 -10000 0 -0.48 150 150
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.2 0.24 -10000 0 -0.48 150 150
RAF1 -0.12 0.2 -10000 0 -0.71 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.18 0.23 -10000 0 -0.46 150 150
YWHAZ 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.21 0.26 -10000 0 -0.52 150 150
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
RPS6KB1 -0.16 0.21 -10000 0 -0.41 147 147
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.1 0.18 -10000 0 -0.57 5 5
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.16 0.2 -10000 0 -0.41 146 146
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.18 0.23 -10000 0 -0.45 150 150
IGF-1R heterotetramer -0.053 0.14 0.33 1 -0.91 8 9
IGF-1R heterotetramer/IGF1/IRS/Nck -0.2 0.25 -10000 0 -0.49 150 150
Crk/p130 Cas/Paxillin -0.17 0.22 -10000 0 -0.43 150 150
IGF1R -0.053 0.14 0.33 1 -0.91 8 9
IGF1 -0.34 0.42 -10000 0 -0.87 145 145
IRS2/Crk -0.19 0.24 -10000 0 -0.46 154 154
PI3K -0.19 0.24 -10000 0 -0.46 150 150
apoptosis 0.13 0.16 0.63 5 -10000 0 5
HRAS/GDP 0.001 0.016 0.21 2 -10000 0 2
PRKCD -0.22 0.27 -10000 0 -0.54 150 150
RAF1/14-3-3 E -0.12 0.16 -10000 0 -0.58 5 5
BAD/14-3-3 -0.14 0.18 -10000 0 -0.69 5 5
PRKCZ -0.18 0.24 -10000 0 -0.44 153 153
Crk/p130 Cas/Paxillin/FAK1 -0.14 0.17 -10000 0 -0.7 5 5
PTPN1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.23 0.28 -10000 0 -0.57 150 150
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.2 0.25 -10000 0 -0.49 150 150
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.19 0.24 -10000 0 -0.48 150 150
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.19 0.24 -10000 0 -0.48 150 150
IRS1 -0.21 0.26 -10000 0 -0.52 150 150
IRS2 -0.2 0.25 -10000 0 -0.49 154 154
IGF-1R heterotetramer/IGF1 -0.28 0.34 -10000 0 -0.69 150 150
GRB2 0 0 -10000 0 -10000 0 0
PDPK1 -0.18 0.22 -10000 0 -0.44 150 150
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.22 0.27 -10000 0 -0.54 152 152
SHC1 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.24 0.5 -10000 0 -0.99 82 82
HDAC7 0.001 0.017 0.32 1 -10000 0 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.43 0.67 9 -0.84 122 131
SMAD4 -0.002 0.044 -10000 0 -0.86 1 1
ID2 -0.25 0.5 -10000 0 -1 81 81
AP1 -0.33 0.35 -10000 0 -0.68 179 179
ABCG2 -0.31 0.55 -10000 0 -1.1 97 97
HIF1A -0.025 0.068 -10000 0 -10000 0 0
TFF3 -0.25 0.51 -10000 0 -1 85 85
GATA2 -0.003 0.067 0.32 2 -0.86 2 4
AKT1 -0.038 0.12 -10000 0 -0.24 3 3
response to hypoxia -0.053 0.12 -10000 0 -0.24 34 34
MCL1 -0.24 0.49 -10000 0 -1 81 81
NDRG1 -0.24 0.5 -10000 0 -1 81 81
SERPINE1 -0.36 0.59 -10000 0 -1.1 129 129
FECH -0.24 0.5 -10000 0 -1 82 82
FURIN -0.25 0.51 -10000 0 -1 82 82
NCOA2 -0.11 0.29 -10000 0 -0.86 48 48
EP300 -0.074 0.21 0.42 5 -0.32 123 128
HMOX1 -0.26 0.51 -10000 0 -1 86 86
BHLHE40 -0.25 0.5 -10000 0 -1 82 82
BHLHE41 -0.25 0.51 0.8 1 -0.99 90 91
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.025 0.067 0.35 1 -0.42 1 2
ENG -0.017 0.066 -10000 0 -10000 0 0
JUN -0.014 0.11 -10000 0 -0.86 6 6
RORA -0.25 0.5 -10000 0 -1 84 84
ABCB1 -0.22 0.45 -10000 0 -1.4 45 45
TFRC -0.24 0.49 -10000 0 -1 80 80
CXCR4 -0.25 0.5 -10000 0 -1 81 81
TF -0.28 0.53 -10000 0 -1.1 90 90
CITED2 -0.25 0.5 -10000 0 -1 82 82
HIF1A/ARNT -0.32 0.56 0.89 6 -1.2 79 85
LDHA -0.056 0.054 -10000 0 -10000 0 0
ETS1 -0.24 0.5 -10000 0 -1 80 80
PGK1 -0.24 0.49 -10000 0 -1 82 82
NOS2 -0.23 0.51 0.8 1 -1 82 83
ITGB2 -0.25 0.5 -10000 0 -0.99 87 87
ALDOA -0.24 0.49 -10000 0 -1 82 82
Cbp/p300/CITED2 -0.39 0.54 -10000 0 -1.1 114 114
FOS -0.42 0.43 -10000 0 -0.86 179 179
HK2 -0.24 0.51 -10000 0 -1 83 83
SP1 0.008 0.029 -10000 0 -10000 0 0
GCK -0.52 0.8 0.65 2 -1.5 145 147
HK1 -0.24 0.49 -10000 0 -1 80 80
NPM1 -0.24 0.49 -10000 0 -1 82 82
EGLN1 -0.24 0.49 -10000 0 -1 82 82
CREB1 0.014 0 -10000 0 -10000 0 0
PGM1 -0.25 0.5 -10000 0 -1 81 81
SMAD3 0 0 -10000 0 -10000 0 0
EDN1 -0.25 0.34 -10000 0 -0.66 106 106
IGFBP1 -0.36 0.58 -10000 0 -1.1 113 113
VEGFA -0.24 0.39 -10000 0 -0.74 96 96
HIF1A/JAB1 -0.015 0.041 -10000 0 -10000 0 0
CP -0.3 0.56 -10000 0 -1.1 92 92
CXCL12 -0.44 0.58 -10000 0 -1.1 145 145
COPS5 -0.001 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.002 0.034 -10000 0 -0.66 1 1
BNIP3 -0.25 0.49 -10000 0 -1 82 82
EGLN3 -0.24 0.52 0.84 2 -1.1 78 80
CA9 -0.35 0.58 0.82 1 -1 126 127
TERT -0.19 0.53 0.83 4 -0.99 81 85
ENO1 -0.24 0.49 -10000 0 -1 81 81
PFKL -0.24 0.49 -10000 0 -1 80 80
NCOA1 0 0.005 -10000 0 -10000 0 0
ADM -0.24 0.49 -10000 0 -1 82 82
ARNT -0.024 0.065 -10000 0 -10000 0 0
HNF4A -0.032 0.12 -10000 0 -0.9 6 6
ADFP -0.25 0.5 -10000 0 -0.96 91 91
SLC2A1 -0.24 0.4 0.77 2 -0.75 100 102
LEP -0.24 0.5 0.83 2 -1 82 84
HIF1A/ARNT/Cbp/p300 -0.34 0.44 0.71 7 -0.85 125 132
EPO -0.53 0.63 0.75 1 -1.2 160 161
CREBBP -0.074 0.21 0.41 6 -0.32 126 132
HIF1A/ARNT/Cbp/p300/HDAC7 -0.32 0.42 0.73 6 -0.86 107 113
PFKFB3 -0.26 0.52 -10000 0 -1.1 82 82
NT5E -0.26 0.51 -10000 0 -1 84 84
IL6-mediated signaling events

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
BCL2L1 -0.31 0.37 -10000 0 -0.74 128 128
CRP -0.52 0.56 -10000 0 -1.1 175 175
cell cycle arrest -0.38 0.46 -10000 0 -0.89 136 136
TIMP1 -0.28 0.34 -10000 0 -0.68 120 120
IL6ST -0.21 0.38 -10000 0 -0.87 91 91
Rac1/GDP -0.23 0.28 -10000 0 -0.59 111 111
AP1 -0.22 0.26 -10000 0 -0.49 155 155
GAB2 0.004 0.011 -10000 0 -10000 0 0
TNFSF11 -0.44 0.51 -10000 0 -0.98 153 153
HSP90B1 -0.023 0.06 -10000 0 -10000 0 0
GAB1 0.003 0.008 -10000 0 -10000 0 0
MAPK14 -0.23 0.34 -10000 0 -0.84 65 65
AKT1 0.022 0.043 -10000 0 -0.53 1 1
FOXO1 0.035 0.064 -10000 0 -0.47 5 5
MAP2K6 -0.23 0.31 -10000 0 -0.59 119 119
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.23 0.32 -10000 0 -0.62 115 115
MITF -0.19 0.28 -10000 0 -0.47 150 150
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0 0 -10000 0 -10000 0 0
A2M -0.2 0.54 -10000 0 -1.5 52 52
CEBPB 0.014 0.003 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.046 0.091 -10000 0 -0.29 3 3
STAT3 -0.41 0.51 -10000 0 -0.97 136 136
STAT1 -0.019 0.033 -10000 0 -10000 0 0
CEBPD -0.32 0.38 -10000 0 -0.76 128 128
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
PI3K -0.005 0.071 -10000 0 -0.93 2 2
JUN -0.014 0.11 -10000 0 -0.86 6 6
PIAS3/MITF -0.2 0.24 -10000 0 -0.52 105 105
MAPK11 -0.22 0.34 -10000 0 -0.85 64 64
STAT3 (dimer)/FOXO1 -0.28 0.37 -10000 0 -0.67 144 144
GRB2/SOS1/GAB family -0.14 0.22 -10000 0 -0.65 34 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.19 0.27 -10000 0 -0.49 135 135
GRB2 0.003 0.008 -10000 0 -10000 0 0
JAK2 -0.002 0.045 -10000 0 -0.86 1 1
LBP -0.28 0.36 -10000 0 -0.77 92 92
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
JAK1 -0.001 0.007 -10000 0 -10000 0 0
MYC -0.37 0.45 -10000 0 -0.86 140 140
FGG -0.36 0.44 -10000 0 -0.85 135 135
macrophage differentiation -0.38 0.46 -10000 0 -0.89 136 136
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.23 0.3 -10000 0 -0.59 139 139
JUNB -0.32 0.39 -10000 0 -0.77 129 129
FOS -0.42 0.43 -10000 0 -0.86 179 179
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.21 0.29 -10000 0 -0.5 154 154
STAT1/PIAS1 -0.22 0.25 -10000 0 -0.55 103 103
GRB2/SOS1/GAB family/SHP2/PI3K 0.007 0.04 -10000 0 -0.43 2 2
STAT3 (dimer) -0.41 0.5 -10000 0 -0.96 136 136
PRKCD -0.26 0.34 -10000 0 -0.65 127 127
IL6R -0.022 0.13 -10000 0 -0.87 9 9
SOCS3 -0.25 0.47 -10000 0 -1.2 61 61
gp130 (dimer)/JAK1/JAK1/LMO4 -0.15 0.26 -10000 0 -0.6 92 92
Rac1/GTP -0.25 0.29 -10000 0 -0.61 116 116
HCK -0.027 0.15 -10000 0 -0.86 12 12
MAPKKK cascade -0.003 0.082 -10000 0 -10000 0 0
bone resorption -0.4 0.46 -10000 0 -0.89 153 153
IRF1 -0.31 0.37 -10000 0 -0.74 128 128
mol:GDP -0.22 0.31 -10000 0 -0.58 124 124
SOS1 0.004 0.011 -10000 0 -10000 0 0
VAV1 -0.22 0.32 -10000 0 -0.59 124 124
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.2 0.29 -10000 0 -0.63 81 81
PTPN11 -0.018 0.027 -10000 0 -10000 0 0
IL6/IL6RA -0.11 0.26 -10000 0 -0.69 61 61
gp130 (dimer)/TYK2/TYK2/LMO4 -0.15 0.26 -10000 0 -0.6 92 92
gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.26 -10000 0 -0.6 92 92
IL6 -0.11 0.31 0.32 8 -0.88 52 60
PIAS3 0 0 -10000 0 -10000 0 0
PTPRE 0.014 0.07 0.32 2 -0.86 2 4
PIAS1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.18 0.24 -10000 0 -0.46 135 135
LMO4 0 0.067 -10000 0 -0.89 2 2
STAT3 (dimer)/PIAS3 -0.41 0.4 -10000 0 -0.87 136 136
MCL1 0.04 0.035 -10000 0 -0.47 1 1
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.006 0.054 -10000 0 -0.67 1 1
Necdin/E2F1 0.12 0.17 0.44 9 -0.64 9 18
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.23 0.32 -10000 0 -0.58 150 150
NGF (dimer)/p75(NTR)/BEX1 -0.4 0.43 -10000 0 -0.74 209 209
NT-4/5 (dimer)/p75(NTR) -0.26 0.33 -10000 0 -0.67 143 143
IKBKB 0 0 -10000 0 -10000 0 0
AKT1 -0.22 0.29 -10000 0 -0.55 146 146
IKBKG 0 0 -10000 0 -10000 0 0
BDNF 0.01 0.056 0.32 12 -10000 0 12
MGDIs/NGR/p75(NTR)/LINGO1 -0.2 0.32 -10000 0 -0.59 144 144
FURIN -0.016 0.12 -10000 0 -0.86 7 7
proBDNF (dimer)/p75(NTR)/Sortilin -0.21 0.29 0.39 2 -0.58 143 145
LINGO1 0.049 0.13 0.32 60 -0.86 1 61
Sortilin/TRAF6/NRIF -0.001 0.023 -10000 0 -10000 0 0
proBDNF (dimer) 0.01 0.056 0.32 12 -10000 0 12
NTRK1 0.002 0.023 0.32 2 -10000 0 2
RTN4R -0.009 0.089 -10000 0 -0.86 4 4
neuron apoptosis -0.11 0.27 -10000 0 -0.55 44 44
IRAK1 0.001 0.016 0.32 1 -10000 0 1
SHC1 -0.25 0.32 -10000 0 -0.63 146 146
ARHGDIA 0 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 -0.23 0.32 -10000 0 -0.59 147 147
MAGEH1 -0.011 0.1 0.32 1 -0.86 5 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.23 0.33 0.38 1 -0.6 148 149
Mammalian IAPs/DIABLO 0.005 0.054 -10000 0 -0.53 2 2
proNGF (dimer) -0.038 0.18 0.32 1 -0.86 17 18
MAGED1 -0.007 0.077 -10000 0 -0.86 3 3
APP -0.009 0.089 -10000 0 -0.86 4 4
NT-4/5 (dimer) 0.003 0.028 0.32 3 -10000 0 3
ZNF274 0 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.21 0.28 -10000 0 -0.55 146 146
NGF -0.039 0.18 0.32 1 -0.86 17 18
cell cycle arrest -0.17 0.31 -10000 0 -0.53 146 146
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.15 0.2 -10000 0 -0.39 146 146
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.23 0.29 -10000 0 -0.59 144 144
NCSTN 0 0 -10000 0 -10000 0 0
mol:GTP -0.25 0.32 -10000 0 -0.63 147 147
PSENEN 0 0 -10000 0 -10000 0 0
mol:ceramide -0.22 0.29 -10000 0 -0.57 146 146
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.14 0.19 -10000 0 -0.68 24 24
p75(NTR)/beta APP -0.26 0.33 -10000 0 -0.67 145 145
BEX1 -0.24 0.42 0.32 32 -0.86 113 145
mol:GDP -0.25 0.32 -10000 0 -0.63 146 146
NGF (dimer) -0.23 0.32 -10000 0 -0.6 150 150
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.18 0.3 -10000 0 -0.54 144 144
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
RAC1/GTP -0.22 0.29 -10000 0 -0.56 146 146
MYD88 0 0 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.25 0.32 -10000 0 -0.63 147 147
RHOB -0.044 0.19 -10000 0 -0.86 19 19
RHOA 0 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.14 0.11 -10000 0 -10000 0 0
NT3 (dimer) -0.42 0.43 -10000 0 -0.86 183 183
TP53 -0.18 0.23 -10000 0 -0.47 144 144
PRDM4 -0.22 0.3 -10000 0 -0.57 146 146
BDNF (dimer) -0.19 0.29 0.42 4 -0.54 142 146
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
SORT1 0.012 0.06 0.32 14 -10000 0 14
activation of caspase activity -0.23 0.31 -10000 0 -0.57 150 150
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.22 0.31 -10000 0 -0.58 146 146
RHOC 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.17 0.29 -10000 0 -0.51 136 136
DIABLO 0 0 -10000 0 -10000 0 0
SMPD2 -0.22 0.3 -10000 0 -0.57 146 146
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.24 0.33 -10000 0 -0.63 146 146
PSEN1 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.55 0.5 -10000 0 -0.93 218 218
MAPK8 -0.17 0.27 -10000 0 -0.49 136 136
MAPK9 -0.15 0.26 -10000 0 -0.47 136 136
APAF1 0 0 -10000 0 -10000 0 0
NTF3 -0.42 0.43 -10000 0 -0.86 183 183
NTF4 0.003 0.028 0.32 3 -10000 0 3
NDN -0.012 0.14 0.32 10 -0.86 9 19
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.22 0.29 -10000 0 -0.55 152 152
p75 CTF/Sortilin/TRAF6/NRIF 0.006 0.047 -10000 0 -0.53 1 1
RhoA-B-C/GTP -0.25 0.32 -10000 0 -0.62 147 147
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.18 0.25 0.36 2 -0.5 144 146
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.2 0.27 0.38 2 -0.53 144 146
PRKACB -0.002 0.045 -10000 0 -0.86 1 1
proBDNF (dimer)/p75 ECD 0.007 0.039 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.007 0.088 0.32 14 -0.86 2 16
BIRC2 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.17 0.33 0.28 1 -0.54 145 146
BAD -0.16 0.27 -10000 0 -0.48 135 135
RIPK2 0 0 -10000 0 -10000 0 0
NGFR -0.33 0.42 -10000 0 -0.86 143 143
CYCS -0.21 0.28 -10000 0 -0.54 148 148
ADAM17 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.23 0.3 -10000 0 -0.58 146 146
BCL2L11 -0.16 0.27 -10000 0 -0.48 135 135
BDNF (dimer)/p75(NTR) -0.25 0.33 -10000 0 -0.67 143 143
PI3K -0.23 0.31 -10000 0 -0.59 146 146
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.22 0.3 -10000 0 -0.58 146 146
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.28 0.36 -10000 0 -0.72 146 146
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.23 0.31 -10000 0 -0.58 148 148
TRAF6 -0.002 0.045 -10000 0 -0.86 1 1
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.039 0.18 -10000 0 -0.86 17 17
PLG -0.13 0.31 -10000 0 -0.86 58 58
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.22 0.3 -10000 0 -0.58 146 146
SQSTM1 0.004 0.036 0.32 5 -10000 0 5
NGFRAP1 -0.036 0.18 0.32 1 -0.86 16 17
CASP3 -0.14 0.25 -10000 0 -0.44 135 135
E2F1 0.2 0.15 0.32 230 -10000 0 230
CASP9 0 0 -10000 0 -10000 0 0
IKK complex -0.12 0.19 -10000 0 -0.7 26 26
NGF (dimer)/TRKA -0.029 0.14 -10000 0 -0.67 17 17
MMP7 -0.18 0.39 0.32 30 -0.86 88 118
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.21 0.29 -10000 0 -0.55 146 146
MMP3 0.018 0.073 0.32 21 -10000 0 21
APAF-1/Caspase 9 -0.16 0.21 -10000 0 -0.7 15 15
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.4 0.65 -10000 0 -1.3 125 125
MKNK1 0 0 -10000 0 -10000 0 0
MAPK14 -0.078 0.16 -10000 0 -0.38 7 7
ATF2/c-Jun -0.086 0.2 -10000 0 -1.2 8 8
MAPK11 -0.067 0.18 0.35 12 -0.38 6 18
MITF -0.081 0.2 -10000 0 -0.36 114 114
MAPKAPK5 -0.082 0.2 -10000 0 -0.36 113 113
KRT8 -0.084 0.2 -10000 0 -0.36 115 115
MAPKAPK3 0 0 -10000 0 -10000 0 0
MAPKAPK2 0 0 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.11 0.25 0.37 1 -0.46 114 115
CEBPB -0.082 0.2 -10000 0 -0.36 113 113
SLC9A1 -0.081 0.2 -10000 0 -0.36 114 114
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.083 0.22 -10000 0 -0.37 115 115
p38alpha-beta/MNK1 -0.1 0.19 -10000 0 -0.48 6 6
JUN -0.065 0.2 -10000 0 -1.1 8 8
PPARGC1A -0.15 0.29 -10000 0 -0.47 141 141
USF1 -0.082 0.2 -10000 0 -0.36 113 113
RAB5/GDP/GDI1 -0.082 0.12 -10000 0 -0.35 6 6
NOS2 -0.065 0.21 -10000 0 -0.48 5 5
DDIT3 -0.081 0.2 -10000 0 -0.36 111 111
RAB5A 0 0 -10000 0 -10000 0 0
HSPB1 -0.059 0.16 -10000 0 -0.39 4 4
p38alpha-beta/HBP1 -0.1 0.19 -10000 0 -0.48 6 6
CREB1 -0.092 0.22 -10000 0 -0.39 113 113
RAB5/GDP 0 0 -10000 0 -10000 0 0
EIF4E -0.069 0.17 -10000 0 -0.43 5 5
RPS6KA4 -0.082 0.2 -10000 0 -0.36 112 112
PLA2G4A -0.12 0.26 -10000 0 -0.74 39 39
GDI1 -0.082 0.2 -10000 0 -0.36 113 113
TP53 -0.11 0.24 -10000 0 -0.45 114 114
RPS6KA5 -0.096 0.23 -10000 0 -0.4 116 116
ESR1 -0.38 0.38 -10000 0 -0.6 237 237
HBP1 0 0 -10000 0 -10000 0 0
MEF2C -0.082 0.2 -10000 0 -0.36 113 113
MEF2A -0.082 0.2 -10000 0 -0.36 113 113
EIF4EBP1 -0.092 0.22 -10000 0 -0.39 113 113
KRT19 -0.26 0.4 -10000 0 -0.61 175 175
ELK4 -0.082 0.2 -10000 0 -0.36 113 113
ATF6 -0.082 0.2 -10000 0 -0.36 113 113
ATF1 -0.092 0.22 -10000 0 -0.39 113 113
p38alpha-beta/MAPKAPK2 -0.1 0.19 -10000 0 -0.48 6 6
p38alpha-beta/MAPKAPK3 -0.1 0.19 -10000 0 -0.48 6 6
FOXA2 and FOXA3 transcription factor networks

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.34 0.58 -10000 0 -1.1 101 101
PCK1 -0.72 0.85 -10000 0 -1.6 167 167
HNF4A -0.4 0.69 -10000 0 -1.4 101 101
KCNJ11 -0.34 0.61 -10000 0 -1.2 101 101
AKT1 -0.13 0.22 -10000 0 -0.42 90 90
response to starvation -0.005 0.025 -10000 0 -10000 0 0
DLK1 -0.32 0.61 0.74 1 -1.2 92 93
NKX2-1 -0.087 0.23 0.61 2 -0.52 6 8
ACADM -0.35 0.6 -10000 0 -1.2 104 104
TAT -0.72 0.86 -10000 0 -1.7 158 158
CEBPB -0.001 0.024 -10000 0 -10000 0 0
CEBPA -0.005 0.085 0.32 1 -0.89 3 4
TTR -0.42 0.66 -10000 0 -1.4 107 107
PKLR -0.37 0.64 -10000 0 -1.2 106 106
APOA1 -0.48 0.78 -10000 0 -1.6 107 107
CPT1C -0.34 0.58 -10000 0 -1.1 102 102
ALAS1 -0.14 0.31 -10000 0 -1.9 5 5
TFRC -0.29 0.48 -10000 0 -0.9 98 98
FOXF1 -0.091 0.26 -10000 0 -0.86 39 39
NF1 0.01 0.046 -10000 0 -0.86 1 1
HNF1A (dimer) -0.005 0.12 -10000 0 -0.91 4 4
CPT1A -0.34 0.58 -10000 0 -1.1 102 102
HMGCS1 -0.34 0.58 -10000 0 -1.1 103 103
NR3C1 -0.068 0.1 -10000 0 -0.32 11 11
CPT1B -0.34 0.58 -10000 0 -1.1 104 104
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.01 0.058 -10000 0 -10000 0 0
GCK -0.59 0.76 -10000 0 -1.3 172 172
CREB1 -0.048 0.086 -10000 0 -0.31 1 1
IGFBP1 -0.47 0.7 -10000 0 -1.6 97 97
PDX1 -0.18 0.48 0.63 1 -1.5 34 35
UCP2 -0.34 0.58 -10000 0 -1.2 97 97
ALDOB -0.49 0.78 -10000 0 -1.5 119 119
AFP -0.092 0.33 -10000 0 -1.1 27 27
BDH1 -0.36 0.63 -10000 0 -1.2 101 101
HADH -0.33 0.59 -10000 0 -1.2 97 97
F2 -0.4 0.69 -10000 0 -1.3 104 104
HNF1A -0.005 0.12 -10000 0 -0.91 4 4
G6PC -0.3 0.6 -10000 0 -1.6 64 64
SLC2A2 -0.28 0.6 -10000 0 -1.6 52 52
INS 0.035 0.082 0.3 8 -10000 0 8
FOXA1 -0.006 0.16 -10000 0 -0.74 10 10
FOXA3 -0.16 0.29 -10000 0 -0.59 76 76
FOXA2 -0.4 0.72 0.84 1 -1.3 117 118
ABCC8 -0.32 0.6 0.74 1 -1.2 95 96
ALB -0.22 0.51 -10000 0 -1.3 64 64
Reelin signaling pathway

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.002 0.023 -10000 0 -10000 0 0
VLDLR -0.034 0.26 0.32 42 -0.86 30 72
CRKL 0 0 -10000 0 -10000 0 0
LRPAP1 0 0 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
ITGA3 0.02 0.093 0.32 26 -0.86 1 27
RELN/VLDLR/Fyn -0.22 0.34 -10000 0 -0.64 138 138
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.03 0.13 -10000 0 -0.52 23 23
AKT1 -0.18 0.23 -10000 0 -0.41 161 161
MAP2K7 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
DAB1 -0.13 0.31 0.32 1 -0.86 56 57
RELN/LRP8/DAB1 -0.25 0.31 -10000 0 -0.57 167 167
LRPAP1/LRP8 0.021 0.064 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.24 0.29 -10000 0 -0.54 167 167
DAB1/alpha3/beta1 Integrin -0.24 0.31 0.36 3 -0.54 162 165
long-term memory -0.21 0.28 -10000 0 -0.51 167 167
DAB1/LIS1 -0.25 0.32 -10000 0 -0.55 178 178
DAB1/CRLK/C3G -0.24 0.31 -10000 0 -0.54 174 174
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
DAB1/NCK2 -0.25 0.33 -10000 0 -0.56 178 178
ARHGEF2 0.003 0.033 0.32 4 -10000 0 4
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.053 0.12 0.32 62 -10000 0 62
CDK5R1 0.003 0.033 0.32 4 -10000 0 4
RELN -0.29 0.41 0.32 3 -0.86 125 128
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
RELN/LRP8/Fyn -0.18 0.29 -10000 0 -0.58 125 125
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.3 0.36 5 -0.53 167 172
MAPK8 -0.046 0.19 -10000 0 -0.86 20 20
RELN/VLDLR/DAB1 -0.29 0.36 -10000 0 -0.63 178 178
ITGB1 0 0 -10000 0 -10000 0 0
MAP1B -0.26 0.32 -10000 0 -0.57 178 178
RELN/LRP8 -0.18 0.29 -10000 0 -0.58 125 125
GRIN2B/RELN/LRP8/DAB1/Fyn -0.24 0.29 -10000 0 -0.54 167 167
PI3K -0.005 0.071 -10000 0 -0.94 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.066 -10000 0 -0.67 1 1
RAP1A -0.24 0.27 -10000 0 -0.52 147 147
PAFAH1B1 0 0 -10000 0 -10000 0 0
MAPK8IP1 -0.009 0.089 -10000 0 -0.86 4 4
CRLK/C3G 0 0 -10000 0 -10000 0 0
GRIN2B 0 0 -10000 0 -10000 0 0
NCK2 -0.001 0.048 0.32 1 -0.86 1 2
neuron differentiation -0.13 0.17 -10000 0 -0.55 26 26
neuron adhesion -0.21 0.26 -10000 0 -0.79 32 32
LRP8 0.03 0.092 0.32 35 -10000 0 35
GSK3B -0.17 0.22 -10000 0 -0.66 34 34
RELN/VLDLR/DAB1/Fyn -0.27 0.34 -10000 0 -0.59 178 178
MAP3K11 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.2 0.25 -10000 0 -0.43 174 174
CDK5 0 0 -10000 0 -10000 0 0
MAPT 0.065 0.06 -10000 0 -10000 0 0
neuron migration -0.18 0.27 -10000 0 -0.46 171 171
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.17 -10000 0 -0.55 26 26
RELN/VLDLR -0.19 0.33 0.38 7 -0.59 138 145
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.064 0.32 16 -10000 0 16
CDKN2C 0.03 0.084 0.31 30 -10000 0 30
CDKN2A 0.21 0.14 0.31 254 -10000 0 254
CCND2 -0.07 0.057 -10000 0 -0.17 52 52
RB1 0.078 0.064 0.19 52 -10000 0 52
CDK4 -0.075 0.058 -10000 0 -0.18 40 40
CDK6 -0.085 0.077 -10000 0 -0.23 54 54
G1/S progression -0.078 0.064 -10000 0 -0.19 52 52
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.14 0.11 0.25 145 -10000 0 145
STMN1 0.096 0.085 0.27 26 -10000 0 26
Aurora B/RasGAP/Survivin 0.22 0.18 0.38 187 -0.52 2 189
Chromosomal passenger complex/Cul3 protein complex 0.12 0.1 0.22 143 -0.28 5 148
BIRC5 0.22 0.15 0.32 245 -10000 0 245
DES 0.021 0.25 0.42 2 -0.5 46 48
Aurora C/Aurora B/INCENP 0.1 0.094 0.36 2 -10000 0 2
Aurora B/TACC1 0.1 0.094 -10000 0 -10000 0 0
Aurora B/PP2A 0.12 0.1 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.036 0.031 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.008 0.005 -10000 0 -10000 0 0
NDC80 0.17 0.11 0.28 57 -10000 0 57
Cul3 protein complex -0.018 0.1 -10000 0 -0.58 12 12
KIF2C 0.18 0.12 0.26 243 -10000 0 243
PEBP1 -0.01 0.1 -10000 0 -0.86 5 5
KIF20A 0.22 0.14 0.31 260 -10000 0 260
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.12 -10000 0 -0.64 2 2
SEPT1 0.001 0.016 0.32 1 -10000 0 1
SMC2 0.001 0.016 0.32 1 -10000 0 1
SMC4 0.003 0.028 0.32 3 -10000 0 3
NSUN2/NPM1/Nucleolin 0.16 0.12 0.28 120 -10000 0 120
PSMA3 0 0 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.005 -10000 0 -10000 0 0
H3F3B 0.073 0.066 -10000 0 -10000 0 0
AURKB 0.17 0.16 0.31 196 -10000 0 196
AURKC 0.001 0.016 0.32 1 -10000 0 1
CDCA8 0.16 0.16 0.33 176 -10000 0 176
cytokinesis 0.2 0.18 0.37 183 -10000 0 183
Aurora B/Septin1 0.22 0.2 0.4 190 -10000 0 190
AURKA 0.089 0.14 0.31 106 -10000 0 106
INCENP 0.012 0.025 0.33 2 -10000 0 2
KLHL13 -0.019 0.14 0.32 2 -0.86 9 11
BUB1 0.21 0.14 0.31 256 -10000 0 256
hSgo1/Aurora B/Survivin 0.29 0.22 0.47 206 -10000 0 206
EVI5 0.008 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.19 0.22 0.42 166 -10000 0 166
SGOL1 0.12 0.15 0.32 146 -10000 0 146
CENPA 0.2 0.13 0.31 192 -10000 0 192
NCAPG 0.21 0.15 0.32 246 -10000 0 246
Aurora B/HC8 Proteasome 0.12 0.1 -10000 0 -10000 0 0
NCAPD2 0.004 0.036 0.32 5 -10000 0 5
Aurora B/PP1-gamma 0.12 0.1 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
NCAPH 0.15 0.16 0.32 177 -10000 0 177
NPM1 0.1 0.093 -10000 0 -10000 0 0
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
KLHL9 -0.007 0.077 -10000 0 -0.86 3 3
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 -10000 0 -10000 0 0
PPP1CC 0 0 -10000 0 -10000 0 0
Centraspindlin 0.22 0.25 0.48 168 -10000 0 168
RhoA/GDP 0 0 -10000 0 -10000 0 0
NSUN2 0.1 0.093 -10000 0 -10000 0 0
MYLK 0.063 0.088 -10000 0 -0.34 8 8
KIF23 0.15 0.16 0.33 170 -10000 0 170
VIM 0.088 0.073 -10000 0 -10000 0 0
RACGAP1 0.055 0.11 0.34 49 -10000 0 49
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.1 0.093 -10000 0 -10000 0 0
Chromosomal passenger complex 0.21 0.14 0.3 233 -10000 0 233
Chromosomal passenger complex/EVI5 0.28 0.21 0.45 215 -10000 0 215
TACC1 0 0 -10000 0 -10000 0 0
PPP2R5D 0 0 -10000 0 -10000 0 0
CUL3 0 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.11 0.26 0.38 4 -0.59 81 85
EFNA5 -0.17 0.38 0.32 25 -0.86 81 106
FYN -0.11 0.23 -10000 0 -0.54 81 81
neuron projection morphogenesis -0.11 0.26 0.38 4 -0.59 81 85
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.11 0.26 0.39 4 -0.59 81 85
EPHA5 0.011 0.058 0.32 13 -10000 0 13
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 0.062 0.14 0.32 76 -0.87 1 77
EFNB1 0.011 0.1 -10000 0 -0.67 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.1 0.26 -10000 0 -0.5 99 99
Ephrin B2/EPHB1-2 -0.089 0.24 -10000 0 -0.53 83 83
neuron projection morphogenesis -0.11 0.24 -10000 0 -0.48 99 99
Ephrin B1/EPHB1-2/Tiam1 -0.11 0.28 -10000 0 -0.54 99 99
DNM1 0.004 0.13 0.32 21 -0.86 6 27
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.2 0.36 -10000 0 -0.8 99 99
YES1 -0.27 0.46 -10000 0 -1 99 99
Ephrin B1/EPHB1-2/NCK2 -0.084 0.25 0.47 1 -0.51 87 88
PI3K -0.22 0.37 -10000 0 -0.82 100 100
mol:GDP -0.11 0.28 -10000 0 -0.54 99 99
ITGA2B 0.007 0.046 0.32 8 -10000 0 8
endothelial cell proliferation 0.001 0.01 -10000 0 -10000 0 0
FYN -0.27 0.46 -10000 0 -1 99 99
MAP3K7 -0.23 0.38 -10000 0 -0.85 99 99
FGR -0.28 0.46 -10000 0 -1 99 99
TIAM1 -0.046 0.19 -10000 0 -0.86 20 20
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.23 0.38 -10000 0 -0.77 113 113
LYN -0.27 0.46 -10000 0 -1 99 99
Ephrin B1/EPHB1-2/Src Family Kinases -0.26 0.43 -10000 0 -0.97 99 99
Ephrin B1/EPHB1-2 -0.25 0.41 -10000 0 -0.92 99 99
SRC -0.27 0.46 -10000 0 -1 99 99
ITGB3 -0.07 0.23 -10000 0 -0.86 30 30
EPHB1 -0.19 0.36 -10000 0 -0.86 82 82
EPHB4 0.001 0.016 0.32 1 -10000 0 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.001 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.049 0.19 -10000 0 -0.67 30 30
BLK -0.3 0.47 -10000 0 -1.1 99 99
HCK -0.28 0.46 -10000 0 -1 99 99
regulation of stress fiber formation 0.084 0.25 0.5 87 -0.46 1 88
MAPK8 -0.21 0.37 -10000 0 -0.76 111 111
Ephrin B1/EPHB1-2/RGS3 -0.083 0.25 -10000 0 -0.51 87 87
endothelial cell migration -0.2 0.34 -10000 0 -0.75 99 99
NCK2 -0.001 0.048 0.32 1 -0.86 1 2
PTPN13 -0.25 0.44 0.32 2 -0.97 99 101
regulation of focal adhesion formation 0.084 0.25 0.5 87 -0.46 1 88
chemotaxis 0.083 0.25 0.5 87 -10000 0 87
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
Rac1/GTP -0.1 0.26 -10000 0 -0.5 99 99
angiogenesis -0.24 0.4 -10000 0 -0.91 99 99
LCK -0.28 0.46 -10000 0 -1 99 99
Wnt 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
Noncanonical Wnts/FZD -0.2 0.3 -10000 0 -0.48 169 169
FZD6 -0.001 0.048 0.32 1 -0.86 1 2
WNT6 0.019 0.075 0.32 22 -10000 0 22
WNT4 -0.12 0.35 0.32 36 -0.86 65 101
FZD3 -0.021 0.13 -10000 0 -0.86 9 9
WNT5A -0.088 0.27 0.32 5 -0.86 40 45
WNT11 -0.24 0.39 -10000 0 -0.86 105 105
LPA receptor mediated 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
GNB1/GNG2 -0.14 0.26 0.32 2 -0.57 92 94
NF kappa B1 p50/RelA/I kappa B alpha -0.049 0.084 -10000 0 -0.44 4 4
AP1 -0.35 0.38 -10000 0 -0.64 206 206
mol:PIP3 -0.13 0.22 -10000 0 -0.47 95 95
AKT1 -0.095 0.16 -10000 0 -0.55 15 15
PTK2B -0.056 0.15 -10000 0 -0.3 93 93
RHOA -0.014 0.069 -10000 0 -0.53 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.006 0.09 -10000 0 -0.4 9 9
MAGI3 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
apoptosis -0.11 0.21 0.26 1 -0.45 98 99
HRAS/GDP 0.001 0.016 0.21 2 -10000 0 2
positive regulation of microtubule depolymerization -0.026 0.13 -10000 0 -0.37 13 13
NF kappa B1 p50/RelA -0.11 0.22 -10000 0 -0.46 90 90
endothelial cell migration -0.17 0.33 0.32 5 -0.68 98 103
ADCY4 -0.26 0.34 -10000 0 -0.58 153 153
ADCY5 -0.34 0.42 -10000 0 -0.71 166 166
ADCY6 -0.26 0.34 -10000 0 -0.58 153 153
ADCY7 -0.26 0.34 -10000 0 -0.58 153 153
ADCY1 -0.41 0.45 -10000 0 -0.77 188 188
ADCY2 -0.26 0.34 -10000 0 -0.59 152 152
ADCY3 -0.26 0.34 -10000 0 -0.74 101 101
ADCY8 -0.26 0.34 -10000 0 -0.6 145 145
ADCY9 -0.26 0.34 -10000 0 -0.58 153 153
GSK3B -0.047 0.14 -10000 0 -0.35 30 30
arachidonic acid secretion -0.28 0.32 -10000 0 -0.5 216 216
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
TRIP6 -0.002 0.062 -10000 0 -0.48 5 5
GNAO1 -0.42 0.39 -10000 0 -0.71 223 223
HRAS 0.002 0.023 0.32 2 -10000 0 2
NFKBIA -0.023 0.12 -10000 0 -0.42 10 10
GAB1 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.053 0.23 -10000 0 -0.99 21 21
JUN -0.014 0.11 -10000 0 -0.86 6 6
LPA/LPA2/NHERF2 0.001 0.075 -10000 0 -0.58 4 4
TIAM1 -0.065 0.28 -10000 0 -1.2 21 21
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
mol:IP3 0.005 0.092 -10000 0 -0.4 9 9
PLCB3 -0.003 0.059 -10000 0 -0.53 4 4
FOS -0.42 0.43 -10000 0 -0.86 179 179
positive regulation of mitosis -0.28 0.32 -10000 0 -0.5 216 216
LPA/LPA1-2-3 -0.12 0.28 0.37 7 -0.57 94 101
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation -0.072 0.19 -10000 0 -0.38 92 92
GNAZ -0.088 0.32 0.28 4 -0.59 95 99
EGFR/PI3K-beta/Gab1 -0.13 0.23 -10000 0 -0.49 95 95
positive regulation of dendritic cell cytokine production -0.12 0.28 0.36 7 -0.56 95 102
LPA/LPA2/MAGI-3 0.006 0.053 -10000 0 -0.58 1 1
ARHGEF1 -0.13 0.23 -10000 0 -0.53 91 91
GNAI2 -0.15 0.27 -10000 0 -0.59 98 98
GNAI3 -0.15 0.27 -10000 0 -0.59 98 98
GNAI1 -0.16 0.28 -10000 0 -0.6 99 99
LPA/LPA3 0.015 0.064 0.22 30 -10000 0 30
LPA/LPA2 0.005 0.06 0.22 16 -0.67 1 17
LPA/LPA1 -0.18 0.31 0.3 4 -0.68 98 102
HB-EGF/EGFR -0.015 0.15 -10000 0 -0.57 24 24
HBEGF 0.016 0.15 -10000 0 -0.67 14 14
mol:DAG 0.005 0.092 -10000 0 -0.4 9 9
cAMP biosynthetic process -0.35 0.39 -10000 0 -0.62 222 222
NFKB1 0 0 -10000 0 -10000 0 0
SRC 0.004 0.036 0.32 5 -10000 0 5
GNB1 0 0 -10000 0 -10000 0 0
LYN -0.023 0.12 -10000 0 -0.42 10 10
GNAQ 0.008 0.05 -10000 0 -0.46 2 2
LPAR2 0.011 0.079 0.32 16 -0.86 1 17
LPAR3 0.026 0.087 0.32 31 -10000 0 31
LPAR1 -0.21 0.38 0.36 4 -0.88 91 95
IL8 -0.21 0.28 0.33 7 -0.52 149 156
PTK2 -0.13 0.24 -10000 0 -0.54 91 91
Rac1/GDP 0 0 -10000 0 -10000 0 0
CASP3 -0.11 0.21 0.26 1 -0.45 98 99
EGFR -0.023 0.14 -10000 0 -0.86 10 10
PLCG1 -0.021 0.083 -10000 0 -0.33 10 10
PLD2 -0.13 0.24 -10000 0 -0.54 91 91
G12/G13 -0.14 0.25 0.32 2 -0.56 91 93
PI3K-beta -0.11 0.19 -10000 0 -0.46 77 77
cell migration -0.046 0.1 -10000 0 -0.28 31 31
SLC9A3R2 -0.007 0.077 -10000 0 -0.86 3 3
PXN -0.073 0.19 -10000 0 -0.39 92 92
HRAS/GTP -0.29 0.34 -10000 0 -0.52 216 216
RAC1 0 0 -10000 0 -10000 0 0
MMP9 0.032 0.2 0.32 70 -0.86 12 82
PRKCE -0.001 0.047 0.32 1 -0.86 1 2
PRKCD 0.012 0.088 -10000 0 -0.46 5 5
Gi(beta/gamma) -0.26 0.32 -10000 0 -0.73 99 99
mol:LPA -0.003 0.033 -10000 0 -0.22 7 7
TRIP6/p130 Cas/FAK1/Paxillin -0.11 0.23 -10000 0 -0.49 90 90
MAPKKK cascade -0.28 0.32 -10000 0 -0.5 216 216
contractile ring contraction involved in cytokinesis -0.007 0.071 -10000 0 -0.52 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.068 0.18 -10000 0 -0.44 64 64
GNA15 0.009 0.05 0.19 2 -0.41 2 4
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
MAPT -0.027 0.14 -10000 0 -0.38 13 13
GNA11 -0.006 0.094 -10000 0 -0.46 13 13
Rac1/GTP -0.057 0.25 -10000 0 -1.1 21 21
MMP2 -0.17 0.34 0.32 5 -0.68 98 103
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.084 0.28 0.39 5 -0.58 82 87
cell-cell adhesion 0.2 0.26 0.52 120 -10000 0 120
Ephrin B/EPHB2/RasGAP -0.12 0.25 0.36 1 -0.5 107 108
ITSN1 0 0 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.055 0.18 -10000 0 -0.59 38 38
Ephrin B1/EPHB1 -0.13 0.25 -10000 0 -0.59 82 82
HRAS/GDP -0.2 0.27 -10000 0 -0.55 118 118
Ephrin B/EPHB1/GRB7 -0.25 0.34 -10000 0 -0.63 151 151
Endophilin/SYNJ1 -0.12 0.22 -10000 0 -0.46 106 106
KRAS 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.25 0.34 -10000 0 -0.63 148 148
endothelial cell migration -0.004 0.057 -10000 0 -0.73 2 2
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.004 0.098 0.32 6 -0.86 4 10
PAK1 -0.12 0.23 -10000 0 -0.47 106 106
HRAS 0.002 0.023 0.32 2 -10000 0 2
RRAS -0.12 0.22 -10000 0 -0.47 106 106
DNM1 0.004 0.13 0.32 21 -0.86 6 27
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.24 0.32 -10000 0 -0.6 148 148
lamellipodium assembly -0.2 0.26 -10000 0 -0.52 120 120
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.16 0.22 -10000 0 -0.49 81 81
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
EPHB2 0.062 0.14 0.32 76 -0.86 1 77
EPHB3 -0.078 0.26 0.32 9 -0.86 37 46
EPHB1 -0.19 0.36 -10000 0 -0.86 82 82
EPHB4 0.001 0.016 0.32 1 -10000 0 1
mol:GDP -0.18 0.27 -10000 0 -0.58 92 92
Ephrin B/EPHB2 -0.12 0.25 0.35 1 -0.5 106 107
Ephrin B/EPHB3 -0.19 0.31 0.35 1 -0.6 119 120
JNK cascade -0.097 0.21 -10000 0 -0.49 83 83
Ephrin B/EPHB1 -0.25 0.34 -10000 0 -0.64 148 148
RAP1/GDP -0.16 0.22 -10000 0 -0.49 91 91
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.24 0.39 0.32 1 -0.86 105 106
EFNB1 -0.002 0.045 -10000 0 -0.86 1 1
Ephrin B2/EPHB1-2 -0.09 0.24 -10000 0 -0.53 83 83
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.2 0.3 -10000 0 -0.64 88 88
Rap1/GTP -0.2 0.27 -10000 0 -0.78 42 42
axon guidance -0.084 0.28 0.38 5 -0.58 82 87
MAPK3 -0.11 0.21 -10000 0 -0.56 40 40
MAPK1 -0.11 0.21 -10000 0 -0.56 40 40
Rac1/GDP -0.16 0.24 -10000 0 -0.52 91 91
actin cytoskeleton reorganization -0.15 0.2 -10000 0 -0.56 42 42
CDC42/GDP -0.16 0.24 -10000 0 -0.52 91 91
PI3K -0.004 0.059 -10000 0 -0.75 2 2
EFNA5 -0.17 0.38 0.32 25 -0.86 81 106
Ephrin B2/EPHB4 0.001 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.082 0.17 -10000 0 -0.36 79 79
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.2 0.26 -10000 0 -0.75 42 42
PTK2 0.024 0.044 -10000 0 -10000 0 0
MAP4K4 -0.098 0.22 -10000 0 -0.49 83 83
SRC 0.004 0.036 0.32 5 -10000 0 5
KALRN -0.005 0.063 -10000 0 -0.86 2 2
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.14 0.22 -10000 0 -0.57 42 42
MAP2K1 -0.15 0.2 -10000 0 -0.59 40 40
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.089 0.25 -10000 0 -0.53 83 83
cell migration -0.14 0.25 -10000 0 -0.51 80 80
NRAS 0 0 -10000 0 -10000 0 0
SYNJ1 -0.12 0.22 -10000 0 -0.47 106 106
PXN 0 0 -10000 0 -10000 0 0
TF -0.15 0.23 -10000 0 -0.46 129 129
HRAS/GTP -0.21 0.3 -10000 0 -0.57 119 119
Ephrin B1/EPHB1-2 -0.091 0.25 -10000 0 -0.54 83 83
cell adhesion mediated by integrin 0.15 0.24 0.52 106 -10000 0 106
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.22 0.33 -10000 0 -0.58 149 149
RAC1-CDC42/GTP -0.24 0.31 -10000 0 -0.82 59 59
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
RAC1-CDC42/GDP -0.16 0.22 -10000 0 -0.51 79 79
ruffle organization -0.2 0.27 -10000 0 -0.78 42 42
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization -0.12 0.22 -10000 0 -0.45 109 109
Ephrin B/EPHB2/KALRN -0.12 0.26 0.36 1 -0.5 106 107
ROCK1 -0.053 0.16 -10000 0 -0.54 38 38
RAS family/GDP -0.15 0.19 -10000 0 -0.54 42 42
Rac1/GTP -0.22 0.29 -10000 0 -0.57 120 120
Ephrin B/EPHB1/Src/Paxillin -0.18 0.24 -10000 0 -0.44 147 147
Endothelins

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
AKT1 -0.046 0.16 0.34 1 -0.57 25 26
PTK2B 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.25 0.46 3 -0.63 34 37
EDN1 -0.039 0.16 0.27 1 -0.66 16 17
EDN3 0.008 0.049 0.32 9 -10000 0 9
EDN2 -0.069 0.25 0.32 6 -0.86 32 38
HRAS/GDP -0.15 0.26 0.33 1 -0.62 64 65
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.084 0.21 0.3 1 -0.47 62 63
ADCY4 -0.03 0.14 -10000 0 -0.54 18 18
ADCY5 -0.12 0.25 -10000 0 -0.56 77 77
ADCY6 -0.03 0.14 -10000 0 -0.54 18 18
ADCY7 -0.03 0.14 -10000 0 -0.54 18 18
ADCY1 -0.21 0.29 -10000 0 -0.54 149 149
ADCY2 -0.027 0.14 0.33 2 -0.54 18 20
ADCY3 -0.029 0.14 -10000 0 -0.54 18 18
ADCY8 -0.01 0.16 0.29 4 -0.54 18 22
ADCY9 -0.03 0.14 -10000 0 -0.49 23 23
arachidonic acid secretion -0.22 0.34 0.36 3 -0.52 174 177
ETB receptor/Endothelin-1/Gq/GTP -0.1 0.28 -10000 0 -0.54 83 83
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
HRAS 0.002 0.023 0.32 2 -10000 0 2
ETA receptor/Endothelin-1/G12/GTP -0.041 0.16 0.4 3 -0.53 25 28
ETA receptor/Endothelin-1/Gs/GTP -0.016 0.16 0.37 3 -0.52 23 26
mol:GTP -0.001 0.007 -10000 0 -10000 0 0
COL3A1 -0.073 0.27 0.44 4 -0.94 28 32
EDNRB -0.057 0.22 -10000 0 -0.86 26 26
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.056 0.2 0.34 1 -0.69 28 29
CYSLTR1 -0.061 0.22 0.34 1 -0.72 30 31
SLC9A1 -0.026 0.085 0.25 1 -0.32 18 19
mol:GDP -0.14 0.3 0.35 1 -0.62 78 79
SLC9A3 -0.033 0.27 0.38 5 -0.76 34 39
RAF1 -0.21 0.34 -10000 0 -0.7 84 84
JUN -0.066 0.28 -10000 0 -0.84 26 26
JAK2 -0.047 0.17 0.34 1 -0.57 26 27
mol:IP3 -0.12 0.28 0.28 1 -0.58 76 77
ETA receptor/Endothelin-1 -0.059 0.19 0.41 5 -0.66 25 30
PLCB1 0.01 0.055 0.32 10 -10000 0 10
PLCB2 -0.018 0.13 -10000 0 -0.86 8 8
ETA receptor/Endothelin-3 -0.011 0.083 0.31 1 -0.76 2 3
FOS -0.47 0.54 -10000 0 -1 182 182
Gai/GDP -0.35 0.42 -10000 0 -0.76 178 178
CRK 0 0 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.32 0.38 1 -0.79 49 50
BCAR1 0 0.001 -10000 0 -10000 0 0
PRKCB1 -0.11 0.27 -10000 0 -0.55 78 78
GNAQ 0 0.046 -10000 0 -0.86 1 1
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
GNAL 0.051 0.12 0.32 60 -10000 0 60
Gs family/GDP -0.13 0.25 0.25 21 -0.57 68 89
ETA receptor/Endothelin-1/Gq/GTP -0.077 0.23 0.3 3 -0.47 77 80
MAPK14 -0.08 0.24 -10000 0 -0.59 46 46
TRPC6 -0.052 0.26 0.46 3 -0.67 33 36
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.1 0.25 -10000 0 -0.51 72 72
ETB receptor/Endothelin-2 -0.098 0.25 0.27 1 -0.69 56 57
ETB receptor/Endothelin-3 -0.04 0.18 -10000 0 -0.67 26 26
ETB receptor/Endothelin-1 -0.067 0.23 -10000 0 -0.77 31 31
MAPK3 -0.39 0.47 -10000 0 -0.84 186 186
MAPK1 -0.39 0.47 -10000 0 -0.84 186 186
Rac1/GDP -0.15 0.25 0.29 3 -0.61 65 68
cAMP biosynthetic process -0.09 0.21 -10000 0 -0.5 58 58
MAPK8 -0.085 0.31 0.41 3 -0.73 47 50
SRC 0.004 0.036 0.32 5 -10000 0 5
ETB receptor/Endothelin-1/Gi/GTP -0.14 0.23 0.21 1 -0.4 108 109
p130Cas/CRK/Src/PYK2 -0.098 0.29 0.38 3 -0.62 64 67
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.15 0.25 0.29 3 -0.61 66 69
COL1A2 -0.073 0.26 0.43 5 -0.84 27 32
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.067 0.2 0.34 3 -0.68 34 37
mol:DAG -0.12 0.28 0.28 1 -0.58 76 77
MAP2K2 -0.29 0.38 -10000 0 -0.62 185 185
MAP2K1 -0.29 0.38 -10000 0 -0.62 185 185
EDNRA -0.022 0.11 0.41 3 -0.54 6 9
positive regulation of muscle contraction -0.037 0.14 0.3 1 -0.57 18 19
Gq family/GDP -0.2 0.3 -10000 0 -0.7 82 82
HRAS/GTP -0.16 0.31 -10000 0 -0.62 83 83
PRKCH -0.11 0.27 -10000 0 -0.6 65 65
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.11 0.27 -10000 0 -0.59 65 65
PRKCB -0.15 0.33 -10000 0 -0.66 85 85
PRKCE -0.11 0.27 -10000 0 -0.6 65 65
PRKCD -0.11 0.27 -10000 0 -0.59 66 66
PRKCG -0.11 0.27 -10000 0 -0.58 71 71
regulation of vascular smooth muscle contraction -0.55 0.62 -10000 0 -1.2 182 182
PRKCQ -0.13 0.3 -10000 0 -0.62 75 75
PLA2G4A -0.25 0.38 0.45 1 -0.58 174 175
GNA14 -0.14 0.33 -10000 0 -0.86 63 63
GNA15 0.001 0.051 0.32 2 -0.86 1 3
GNA12 0 0 -10000 0 -10000 0 0
GNA11 -0.026 0.15 -10000 0 -0.86 12 12
Rac1/GTP -0.041 0.16 0.4 3 -0.55 23 26
MMP1 0.077 0.13 0.45 9 -10000 0 9
IL23-mediated signaling events

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
CCL2 -0.19 0.62 0.8 4 -1.2 86 90
IL23A -0.18 0.6 0.81 4 -1.2 74 78
NF kappa B1 p50/RelA/I kappa B alpha -0.29 0.45 -10000 0 -1 81 81
positive regulation of T cell mediated cytotoxicity -0.18 0.64 0.81 10 -1.2 82 92
ITGA3 -0.14 0.56 0.81 7 -1.1 66 73
IL17F -0.068 0.38 0.63 3 -0.66 81 84
IL12B 0.024 0.066 0.46 3 -10000 0 3
STAT1 (dimer) -0.28 0.53 0.57 22 -1.1 81 103
CD4 -0.18 0.6 0.8 3 -1.1 83 86
IL23 -0.2 0.56 0.77 3 -1.1 74 77
IL23R 0.022 0.13 0.52 1 -10000 0 1
IL1B -0.24 0.7 0.79 6 -1.3 99 105
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.14 0.54 0.84 3 -1 81 84
TYK2 0.018 0.034 -10000 0 -10000 0 0
STAT4 -0.034 0.17 0.32 1 -0.86 15 16
STAT3 0 0 -10000 0 -10000 0 0
IL18RAP -0.052 0.21 -10000 0 -0.86 23 23
IL12RB1 -0.013 0.17 -10000 0 -0.9 13 13
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
IL12Rbeta1/TYK2 -0.008 0.14 -10000 0 -0.71 13 13
IL23R/JAK2 0.027 0.16 0.55 1 -0.69 1 2
positive regulation of chronic inflammatory response -0.18 0.64 0.81 10 -1.2 82 92
natural killer cell activation -0.001 0.012 -10000 0 -0.048 3 3
JAK2 0.031 0.066 -10000 0 -0.89 1 1
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
NFKB1 0.001 0.005 -10000 0 -10000 0 0
RELA 0.001 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.17 0.54 0.76 3 -1.1 74 77
ALOX12B -0.14 0.54 0.82 4 -1 81 85
CXCL1 -0.33 0.74 0.82 7 -1.3 126 133
T cell proliferation -0.18 0.64 0.81 10 -1.2 82 92
NFKBIA 0.001 0.005 -10000 0 -10000 0 0
IL17A -0.026 0.31 0.59 5 -0.55 55 60
PI3K -0.3 0.47 -10000 0 -1.1 81 81
IFNG -0.003 0.052 0.16 11 -0.1 29 40
STAT3 (dimer) -0.28 0.44 -10000 0 -1 81 81
IL18R1 -0.13 0.31 -10000 0 -0.86 58 58
IL23/IL23R/JAK2/TYK2/SOCS3 -0.092 0.43 0.63 10 -0.79 70 80
IL18/IL18R -0.13 0.3 -10000 0 -0.7 73 73
macrophage activation -0.012 0.023 0.061 15 -0.044 72 87
TNF -0.18 0.61 0.82 3 -1.3 62 65
STAT3/STAT4 -0.31 0.48 0.5 1 -1.1 81 82
STAT4 (dimer) -0.29 0.54 0.57 21 -1.2 81 102
IL18 -0.02 0.14 0.31 3 -0.86 10 13
IL19 -0.15 0.54 0.81 2 -1.1 64 66
STAT5A (dimer) -0.28 0.53 0.57 21 -1.1 81 102
STAT1 0.002 0.023 0.32 2 -10000 0 2
SOCS3 -0.12 0.29 -10000 0 -0.86 50 50
CXCL9 -0.14 0.55 0.84 5 -1 82 87
MPO -0.16 0.56 0.8 3 -1 87 90
positive regulation of humoral immune response -0.18 0.64 0.81 10 -1.2 82 92
IL23/IL23R/JAK2/TYK2 -0.21 0.71 0.82 10 -1.3 81 91
IL6 -0.24 0.66 0.81 3 -1.2 101 104
STAT5A 0.001 0.016 0.32 1 -10000 0 1
IL2 0.005 0.013 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.012 -10000 0 -0.048 3 3
CD3E -0.15 0.56 0.84 3 -1 81 84
keratinocyte proliferation -0.18 0.64 0.81 10 -1.2 82 92
NOS2 -0.13 0.54 0.79 4 -0.99 81 85
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.14 0.15 0.33 84 -10000 0 84
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.007 0.069 -10000 0 -0.59 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
RhoA/GTP -0.14 0.16 -10000 0 -0.33 84 84
negative regulation of cAMP metabolic process -0.14 0.19 -10000 0 -0.33 182 182
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.011 0.1 0.32 1 -0.86 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.14 0.2 -10000 0 -0.33 182 182
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.006 0.065 -10000 0 -0.6 4 4
NFATC2 -0.11 0.23 -10000 0 -0.6 67 67
NFATC3 0 0.018 -10000 0 -10000 0 0
CD40LG -0.35 0.36 0.47 4 -0.78 130 134
PTGS2 -0.46 0.47 0.43 3 -1 142 145
JUNB -0.044 0.19 -10000 0 -0.86 19 19
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.011 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.011 -10000 0 -10000 0 0
CALM1 0 0.005 -10000 0 -10000 0 0
JUN -0.013 0.11 -10000 0 -0.86 6 6
mol:Ca2+ -0.003 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.001 -10000 0 -10000 0 0
FOSL1 -0.035 0.18 0.32 3 -0.86 16 19
CREM 0 0 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.11 0.23 0.42 3 -0.52 76 79
FOS -0.42 0.43 -10000 0 -0.87 179 179
IFNG -0.33 0.35 0.53 5 -0.75 129 134
AP-1/NFAT1-c-4 -0.42 0.46 0.59 6 -0.97 129 135
FASLG -0.35 0.36 0.58 3 -0.78 130 133
NFAT1-c-4/ICER1 -0.099 0.21 0.31 1 -0.52 69 70
IL2RA -0.34 0.36 0.52 6 -0.76 131 137
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSF2 -0.33 0.35 0.43 3 -0.75 129 132
JunB/Fra1/NFAT1-c-4 -0.14 0.26 0.35 2 -0.54 93 95
IL4 -0.33 0.36 0.42 3 -0.75 129 132
IL2 -0.017 0.023 -10000 0 -10000 0 0
IL3 -0.033 0.028 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
BATF3 -0.008 0.09 0.32 1 -0.86 4 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.002 0.005 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.05 0.049 -10000 0 -0.11 146 146
BUB1B 0.1 0.063 0.16 157 -10000 0 157
PLK1 0.055 0.029 0.11 2 -10000 0 2
PLK1S1 0.032 0.016 0.14 3 -10000 0 3
KIF2A 0.056 0.025 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.055 0.029 0.11 2 -10000 0 2
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 0.26 0.18 0.37 252 -10000 0 252
WEE1 0.057 0.046 -10000 0 -0.6 1 1
cytokinesis 0.14 0.099 0.24 83 -10000 0 83
PP2A-alpha B56 0 0.001 -10000 0 -10000 0 0
AURKA 0.06 0.05 0.14 106 -10000 0 106
PICH/PLK1 0.1 0.12 0.26 105 -0.3 1 106
CENPE 0.075 0.043 0.15 1 -10000 0 1
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.056 0.025 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 0.045 0.041 0.14 51 -10000 0 51
PAK1 0 0 -10000 0 -10000 0 0
SPC24 0.15 0.16 0.32 179 -10000 0 179
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN 0.069 0.061 0.16 117 -10000 0 117
GORASP1 0 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.027 0.013 0.053 1 -10000 0 1
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -10000 0 0
STAG2 0 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0.002 -10000 0 -10000 0 0
spindle elongation 0.055 0.029 0.11 2 -10000 0 2
ODF2 0.003 0.005 -10000 0 -10000 0 0
BUB1 0.14 0.097 0.41 1 -10000 0 1
TPT1 0.031 0.013 -10000 0 -10000 0 0
CDC25C 0.13 0.067 0.17 281 -10000 0 281
CDC25B 0.009 0.019 0.33 1 -10000 0 1
SGOL1 0.05 0.049 0.11 146 -10000 0 146
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.092 0.1 0.38 1 -0.37 1 2
CDC14B -0.014 0.12 -10000 0 -0.68 11 11
CDC20 0.23 0.14 0.32 265 -10000 0 265
PLK1/PBIP1 0.018 0.048 0.15 41 -10000 0 41
mitosis -0.004 0.006 -10000 0 -10000 0 0
FBXO5 0.048 0.021 -10000 0 -10000 0 0
CDC2 0.006 0.005 0.011 172 -0.011 1 173
NDC80 0.22 0.15 0.32 254 -10000 0 254
metaphase plate congression 0.038 0.019 -10000 0 -10000 0 0
ERCC6L 0.1 0.11 0.25 104 -0.34 1 105
NLP/gamma Tubulin 0.032 0.014 0.089 1 -10000 0 1
microtubule cytoskeleton organization 0.031 0.013 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0 0 -10000 0 -10000 0 0
interphase -0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 0.27 0.19 0.39 246 -10000 0 246
GRASP65/GM130/RAB1/GTP/PLK1 0 0 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.048 0.025 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.068 0.061 -10000 0 -10000 0 0
microtubule-based process 0.18 0.12 0.26 260 -10000 0 260
Golgi organization 0.055 0.029 0.11 2 -10000 0 2
Cohesin/SA2 0 0 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A 0.22 0.14 0.32 260 -10000 0 260
APC/C/CDC20 0.19 0.12 0.26 265 -10000 0 265
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation 0.017 0.048 0.15 41 -10000 0 41
PRC1 0.16 0.16 0.32 186 -10000 0 186
ECT2 0.066 0.037 -10000 0 -10000 0 0
C13orf34 0.049 0.023 -10000 0 -10000 0 0
NUDC 0.038 0.019 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.1 0.063 0.16 157 -10000 0 157
spindle assembly 0.045 0.021 0.094 2 -10000 0 2
spindle stabilization 0.032 0.016 0.14 3 -10000 0 3
APC/C/HCDH1 -0.018 0.1 -10000 0 -0.59 11 11
MKLP2/PLK1 0.18 0.12 0.26 260 -10000 0 260
CCNB1 0.15 0.16 0.32 172 -10000 0 172
PPP1CB 0 0 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 0.026 0.1 -10000 0 -0.5 14 14
TUBG1 0.032 0.014 0.14 1 -10000 0 1
G2/M transition of mitotic cell cycle 0.055 0.064 0.21 1 -0.36 1 2
MLF1IP 0.02 0.047 -10000 0 -10000 0 0
INCENP 0.003 0.023 0.32 2 -10000 0 2
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.01 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.13 0.16 0.28 1 -0.49 6 7
NFATC4 -0.12 0.17 -10000 0 -0.32 155 155
ERBB2IP 0.006 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.19 0.22 -10000 0 -0.43 161 161
JUN -0.056 0.092 -10000 0 -0.5 7 7
HRAS 0.002 0.023 0.32 2 -10000 0 2
DOCK7 -0.18 0.21 -10000 0 -0.41 161 161
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.23 0.26 -10000 0 -0.52 161 161
AKT1 0.005 0.005 -10000 0 -10000 0 0
BAD 0.01 0.009 -10000 0 -10000 0 0
MAPK10 -0.1 0.12 0.16 2 -0.37 28 30
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.2 0.24 -10000 0 -0.47 161 161
RAF1 -0.11 0.17 -10000 0 -0.46 7 7
ErbB2/ErbB3/neuregulin 2 0.025 0.12 -10000 0 -0.53 9 9
STAT3 0 0.025 -10000 0 -10000 0 0
cell migration -0.082 0.12 -10000 0 -0.31 23 23
mol:PI-3-4-5-P3 -0.003 0.004 -10000 0 -10000 0 0
cell proliferation -0.2 0.22 -10000 0 -0.52 73 73
FOS -0.27 0.28 -10000 0 -0.54 179 179
NRAS 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.19 0.22 -10000 0 -0.43 161 161
MAPK3 -0.16 0.18 -10000 0 -0.43 73 73
MAPK1 -0.16 0.18 -10000 0 -0.43 73 73
JAK2 -0.18 0.21 -10000 0 -0.41 161 161
NF2 -0.01 0.012 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.17 0.19 -10000 0 -0.39 158 158
NRG1 -0.36 0.42 -10000 0 -0.86 156 156
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 -0.17 0.18 -10000 0 -0.36 173 173
MAPK9 -0.088 0.1 -10000 0 -0.3 4 4
ERBB2 -0.011 0.086 -10000 0 -0.68 6 6
ERBB3 -0.007 0.077 -10000 0 -0.86 3 3
SHC1 0 0.001 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
apoptosis -0.003 0.011 -10000 0 -10000 0 0
STAT3 (dimer) 0 0.025 -10000 0 -10000 0 0
RNF41 0.013 0.012 -10000 0 -10000 0 0
FRAP1 0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.12 0.14 -10000 0 -0.45 4 4
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.075 -10000 0 -0.59 6 6
CHRNA1 -0.11 0.14 0.35 1 -0.39 8 9
myelination -0.12 0.18 -10000 0 -0.32 159 159
PPP3CB -0.16 0.19 -10000 0 -0.38 161 161
KRAS 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.14 0.16 -10000 0 -0.58 4 4
NRG2 0.066 0.13 0.32 78 -10000 0 78
mol:GDP -0.16 0.19 -10000 0 -0.38 158 158
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.099 0.16 -10000 0 -0.47 5 5
SRC 0.004 0.036 0.32 5 -10000 0 5
mol:cAMP -0.002 0.003 -10000 0 -10000 0 0
PTPN11 -0.18 0.2 -10000 0 -0.41 161 161
MAP2K1 -0.19 0.2 -10000 0 -0.5 70 70
heart morphogenesis -0.19 0.22 -10000 0 -0.43 161 161
RAS family/GDP -0.14 0.16 -10000 0 -0.56 4 4
GRB2 0 0 -10000 0 -10000 0 0
PRKACA -0.014 0.016 -10000 0 -10000 0 0
CHRNE -0.007 0.037 -10000 0 -0.25 7 7
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity -0.005 0.005 -10000 0 -10000 0 0
nervous system development -0.19 0.22 -10000 0 -0.43 161 161
CDC42 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.16 0.33 -10000 0 -0.86 67 67
GNB1/GNG2 -0.18 0.28 -10000 0 -0.76 48 48
mol:DAG -0.16 0.25 -10000 0 -0.67 48 48
PLCG1 -0.17 0.26 -10000 0 -0.7 48 48
YES1 -0.19 0.28 -10000 0 -0.46 160 160
FZD3 -0.021 0.13 -10000 0 -0.86 9 9
FZD6 -0.001 0.048 0.32 1 -0.86 1 2
G protein -0.17 0.26 -10000 0 -0.71 48 48
MAP3K7 -0.11 0.22 -10000 0 -0.53 47 47
mol:Ca2+ -0.16 0.24 -10000 0 -0.64 48 48
mol:IP3 -0.16 0.25 -10000 0 -0.67 48 48
NLK -0.009 0.013 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
CAMK2A -0.12 0.23 -10000 0 -0.59 48 48
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.2 0.3 -10000 0 -0.48 169 169
CSNK1A1 0 0 -10000 0 -10000 0 0
GNAS -0.19 0.28 -10000 0 -0.78 47 47
GO:0007205 -0.14 0.25 -10000 0 -0.65 48 48
WNT6 0.019 0.075 0.32 22 -10000 0 22
WNT4 -0.12 0.35 0.32 36 -0.86 65 101
NFAT1/CK1 alpha -0.24 0.31 -10000 0 -0.68 95 95
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
WNT5A -0.088 0.27 0.32 5 -0.86 40 45
WNT11 -0.24 0.39 -10000 0 -0.86 105 105
CDC42 -0.18 0.27 -10000 0 -0.73 47 47
Syndecan-1-mediated 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
TGFB1 0.004 0.036 0.32 5 -10000 0 5
CCL5 -0.019 0.14 0.32 2 -0.86 9 11
SDCBP 0 0 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.047 0.21 0.3 1 -0.36 87 88
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.071 0.19 0.32 4 -0.57 23 27
Syndecan-1/Syntenin -0.074 0.18 0.26 1 -0.57 23 24
MAPK3 -0.062 0.17 0.25 1 -0.65 14 15
HGF/MET -0.36 0.34 -10000 0 -0.67 201 201
TGFB1/TGF beta receptor Type II 0.004 0.036 0.32 5 -10000 0 5
BSG 0.002 0.023 0.32 2 -10000 0 2
keratinocyte migration -0.07 0.19 0.29 6 -0.56 23 29
Syndecan-1/RANTES -0.085 0.22 0.37 2 -0.67 27 29
Syndecan-1/CD147 -0.086 0.16 -10000 0 -0.7 14 14
Syndecan-1/Syntenin/PIP2 -0.089 0.16 -10000 0 -0.55 23 23
LAMA5 0.004 0.036 0.32 5 -10000 0 5
positive regulation of cell-cell adhesion -0.087 0.16 -10000 0 -0.54 23 23
MMP7 -0.18 0.39 0.32 30 -0.86 88 118
HGF -0.46 0.43 0.32 1 -0.86 201 202
Syndecan-1/CASK -0.049 0.2 0.25 1 -0.35 87 88
Syndecan-1/HGF/MET -0.34 0.32 0.3 2 -0.59 199 201
regulation of cell adhesion -0.017 0.18 -10000 0 -0.63 14 14
HPSE -0.048 0.2 0.32 1 -0.86 21 22
positive regulation of cell migration -0.047 0.21 0.3 1 -0.36 87 88
SDC1 -0.047 0.21 0.3 1 -0.37 87 88
Syndecan-1/Collagen -0.047 0.21 0.3 1 -0.36 87 88
PPIB 0 0 -10000 0 -10000 0 0
MET -0.001 0.048 0.32 1 -0.86 1 2
PRKACA 0 0 -10000 0 -10000 0 0
MMP9 0.032 0.2 0.32 70 -0.86 12 82
MAPK1 -0.062 0.17 0.25 1 -0.65 14 15
homophilic cell adhesion -0.046 0.21 0.3 1 -0.36 87 88
MMP1 0.072 0.13 0.32 85 -10000 0 85
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.078 0.24 0.39 1 -0.67 46 47
fibroblast growth factor receptor signaling pathway -0.077 0.24 0.39 1 -0.66 46 47
LAMA1 -0.087 0.3 0.32 20 -0.86 45 65
PRNP -0.053 0.21 -10000 0 -0.86 23 23
GPC1/SLIT2 -0.1 0.27 0.44 1 -0.71 58 59
SMAD2 -0.037 0.14 -10000 0 -0.53 26 26
GPC1/PrPc/Cu2+ -0.076 0.22 -10000 0 -0.67 42 42
GPC1/Laminin alpha1 -0.12 0.28 0.44 1 -0.7 67 68
TDGF1 0.021 0.26 0.32 87 -0.86 23 110
CRIPTO/GPC1 -0.04 0.26 -10000 0 -0.68 47 47
APP/GPC1 -0.053 0.18 -10000 0 -0.67 30 30
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.053 0.21 -10000 0 -0.59 47 47
FLT1 0 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.04 0.15 -10000 0 -0.58 26 26
SERPINC1 -0.12 0.29 -10000 0 -0.86 50 50
FYN -0.053 0.21 -10000 0 -0.59 47 47
FGR -0.056 0.22 -10000 0 -0.59 49 49
positive regulation of MAPKKK cascade -0.078 0.26 -10000 0 -0.63 56 56
SLIT2 -0.075 0.27 0.32 13 -0.86 37 50
GPC1/NRG -0.32 0.36 -10000 0 -0.7 170 170
NRG1 -0.36 0.42 -10000 0 -0.86 156 156
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.04 0.15 -10000 0 -0.58 26 26
LYN -0.053 0.21 -10000 0 -0.59 47 47
mol:Spermine -0.039 0.18 -10000 0 -0.67 26 26
cell growth -0.077 0.24 0.39 1 -0.66 46 47
BMP signaling pathway 0.059 0.22 0.86 26 -0.32 1 27
SRC -0.051 0.22 -10000 0 -0.59 47 47
TGFBR1 0 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.32 0.46 0.32 35 -0.86 152 187
GPC1 -0.059 0.22 0.32 1 -0.86 26 27
TGFBR1 (dimer) 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.16 0.31 -10000 0 -0.63 102 102
HCK -0.072 0.24 -10000 0 -0.61 57 57
FGF2 -0.047 0.21 0.32 5 -0.86 22 27
FGFR1 -0.011 0.11 0.32 3 -0.86 6 9
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
TGFBR2 0 0 -10000 0 -10000 0 0
cell death -0.053 0.18 -10000 0 -0.66 30 30
ATIII/GPC1 -0.14 0.27 -10000 0 -0.67 75 75
PLA2G2A/GPC1 -0.3 0.39 -10000 0 -0.71 164 164
LCK -0.07 0.24 -10000 0 -0.61 56 56
neuron differentiation -0.32 0.36 -10000 0 -0.7 170 170
PrPc/Cu2+ -0.042 0.16 -10000 0 -0.67 23 23
APP -0.009 0.089 -10000 0 -0.86 4 4
TGFBR2 (dimer) 0 0 -10000 0 -10000 0 0
S1P4 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
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
CDC42/GTP -0.14 0.15 -10000 0 -0.33 82 82
PLCG1 -0.12 0.18 -10000 0 -0.34 82 82
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
G12/G13 0 0 -10000 0 -10000 0 0
cell migration -0.14 0.15 -10000 0 -0.32 82 82
S1PR5 -0.011 0.1 0.32 1 -0.86 5 6
S1PR4 -0.001 0.048 0.32 1 -0.86 1 2
MAPK3 -0.12 0.18 -10000 0 -0.34 82 82
MAPK1 -0.12 0.18 -10000 0 -0.34 82 82
S1P/S1P5/Gi -0.14 0.2 -10000 0 -0.33 182 182
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
CDC42/GDP 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.007 0.069 -10000 0 -0.59 5 5
RHOA -0.001 0.026 -10000 0 -0.5 1 1
S1P/S1P4/Gi -0.14 0.19 -10000 0 -0.33 178 178
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
S1P/S1P4/G12/G13 -0.001 0.03 -10000 0 -0.54 1 1
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.001 0.036 -10000 0 -0.67 1 1
CRKL -0.13 0.15 -10000 0 -0.49 2 2
mol:PIP3 -0.006 0.057 0.76 2 -10000 0 2
AKT1 0.009 0.035 0.48 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.12 0.15 -10000 0 -0.46 2 2
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
HGF/MET/SHIP2 -0.32 0.29 -10000 0 -0.58 201 201
MAP3K5 -0.16 0.23 -10000 0 -0.65 50 50
HGF/MET/CIN85/CBL/ENDOPHILINS -0.29 0.27 -10000 0 -0.54 201 201
AP1 -0.3 0.32 -10000 0 -0.62 179 179
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.42 0.44 -10000 0 -0.88 179 179
STAT3 (dimer) -0.18 0.17 -10000 0 -0.33 199 199
GAB1/CRKL/SHP2/PI3K -0.13 0.12 -10000 0 -0.62 3 3
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.14 0.13 -10000 0 -0.46 2 2
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.005 0.063 -10000 0 -0.86 2 2
ELK1 -0.014 0.022 -10000 0 -0.29 1 1
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.11 0.1 -10000 0 -0.34 2 2
PAK1 0.016 0.032 0.44 2 -10000 0 2
HGF/MET/RANBP10 -0.32 0.29 -10000 0 -0.58 201 201
HRAS -0.23 0.22 -10000 0 -1.1 1 1
DOCK1 -0.13 0.17 -10000 0 -0.63 10 10
GAB1 -0.15 0.16 -10000 0 -0.29 201 201
CRK -0.13 0.15 -10000 0 -0.49 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.32 0.3 -10000 0 -0.6 201 201
JUN -0.014 0.11 -10000 0 -0.86 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.15 0.14 -10000 0 -0.27 201 201
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
cell morphogenesis -0.15 0.19 -10000 0 -0.68 3 3
GRB2/SHC -0.12 0.12 -10000 0 -0.56 1 1
FOS -0.42 0.43 -10000 0 -0.86 179 179
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.014 0.022 -10000 0 -0.29 1 1
HGF/MET/MUC20 -0.32 0.3 -10000 0 -0.59 201 201
cell migration -0.12 0.11 -10000 0 -0.55 1 1
GRB2 0 0 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.001 0.036 -10000 0 -0.67 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.19 0.18 -10000 0 -0.35 202 202
MET/MUC20 -0.001 0.037 0.21 1 -0.67 1 2
RAP1B -0.11 0.14 -10000 0 -0.53 1 1
RAP1A -0.11 0.14 -10000 0 -0.53 1 1
HGF/MET/RANBP9 -0.32 0.29 -10000 0 -0.58 201 201
RAF1 -0.2 0.22 -10000 0 -1 1 1
STAT3 -0.18 0.17 -10000 0 -0.34 199 199
cell proliferation -0.22 0.25 -10000 0 -0.45 201 201
RPS6KB1 -0.051 0.047 -10000 0 -0.19 1 1
MAPK3 -0.014 0.018 -10000 0 -0.26 1 1
MAPK1 -0.014 0.018 -10000 0 -0.26 1 1
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.14 0.22 -10000 0 -0.54 61 61
SRC -0.18 0.17 -10000 0 -0.66 2 2
PI3K -0.13 0.12 -10000 0 -0.67 3 3
MET/Glomulin -0.001 0.034 0.23 1 -0.61 1 2
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.18 0.2 -10000 0 -0.87 1 1
MET -0.001 0.048 0.32 1 -0.86 1 2
MAP4K1 -0.12 0.16 -10000 0 -0.51 9 9
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.18 0.2 -10000 0 -0.87 1 1
BAD 0.016 0.032 0.44 2 -10000 0 2
MAP2K4 -0.14 0.21 -10000 0 -0.57 50 50
SHP2/GRB2/SOS1/GAB1 -0.13 0.12 -10000 0 -0.76 1 1
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 -0.002 0.045 -10000 0 -0.86 1 1
HGS -0.13 0.12 -10000 0 -0.24 201 201
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.46 0.43 0.32 1 -0.86 201 202
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.14 0.13 -10000 0 -0.59 1 1
PDPK1 0.002 0.041 0.55 2 -10000 0 2
HGF/MET/SHIP -0.32 0.29 -10000 0 -0.58 201 201
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.12 0.44 -10000 0 -0.99 74 74
NCK1/PAK1/Dok-R -0.092 0.18 -10000 0 -0.44 74 74
NCK1/Dok-R -0.24 0.47 -10000 0 -1.2 74 74
PIK3CA 0 0.045 -10000 0 -0.86 1 1
mol:beta2-estradiol -0.001 0.029 0.25 3 -10000 0 3
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.001 0.003 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.048 0.22 0.26 3 -0.86 24 27
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.22 0.43 -10000 0 -1.1 74 74
FN1 -0.002 0.045 -10000 0 -0.86 1 1
PLD2 -0.19 0.51 -10000 0 -1.2 74 74
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.014 0.11 -10000 0 -0.86 6 6
ELK1 -0.16 0.46 -10000 0 -1.1 74 74
GRB7 -0.004 0.098 0.32 6 -0.86 4 10
PAK1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.23 0.45 -10000 0 -1.1 74 74
CDKN1A -0.072 0.33 -10000 0 -0.7 77 77
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.24 0.47 -10000 0 -1.2 74 74
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.067 0.32 -10000 0 -0.7 74 74
PLG -0.26 0.54 -10000 0 -1.3 75 75
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.18 0.38 -10000 0 -0.92 74 74
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 -0.004 0.063 -10000 0 -0.86 2 2
ANGPT2 0 0.16 0.39 1 -0.59 11 12
BMX -0.23 0.56 -10000 0 -1.3 74 74
ANGPT1 -0.004 0.18 0.42 1 -0.9 7 8
tube development -0.083 0.35 -10000 0 -0.76 74 74
ANGPT4 0.007 0.043 0.32 7 -10000 0 7
response to hypoxia -0.01 0.029 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.26 0.5 -10000 0 -1.2 74 74
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.047 0.21 0.32 5 -0.86 22 27
STAT5A (dimer) -0.11 0.41 -10000 0 -0.89 77 77
mol:L-citrulline -0.067 0.32 -10000 0 -0.7 74 74
AGTR1 -0.075 0.24 -10000 0 -0.86 33 33
MAPK14 -0.2 0.54 -10000 0 -1.3 74 74
Tie2/SHP2 -0.25 0.49 -10000 0 -1.2 73 73
TEK -0.27 0.55 -10000 0 -1.4 73 73
RPS6KB1 -0.12 0.42 -10000 0 -0.94 74 74
Angiotensin II/AT1 -0.056 0.19 -10000 0 -0.67 33 33
Tie2/Ang1/GRB2 -0.25 0.5 -10000 0 -1.2 74 74
MAPK3 -0.16 0.47 -10000 0 -1.1 74 74
MAPK1 -0.16 0.47 -10000 0 -1.1 74 74
Tie2/Ang1/GRB7 -0.25 0.5 -10000 0 -1.2 74 74
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.21 0.53 -10000 0 -1.2 74 74
PI3K -0.16 0.5 -10000 0 -1.2 74 74
FES -0.2 0.54 -10000 0 -1.3 74 74
Crk/Dok-R -0.24 0.47 -10000 0 -1.2 74 74
Tie2/Ang1/ABIN2 -0.25 0.5 -10000 0 -1.2 74 74
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.1 0.39 -10000 0 -0.86 74 74
STAT5A 0.001 0.016 0.32 1 -10000 0 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.12 0.42 -10000 0 -0.94 74 74
Tie2/Ang2 -0.15 0.49 -10000 0 -1.1 74 74
Tie2/Ang1 -0.21 0.56 -10000 0 -1.3 74 74
FOXO1 -0.099 0.4 -10000 0 -0.88 74 74
ELF1 -0.009 0.078 -10000 0 -0.9 2 2
ELF2 -0.2 0.52 -10000 0 -1.2 74 74
mol:Choline -0.18 0.49 -10000 0 -1.1 74 74
cell migration -0.05 0.096 -10000 0 -0.24 70 70
FYN -0.11 0.4 -10000 0 -0.89 74 74
DOK2 -0.012 0.099 -10000 0 -0.86 5 5
negative regulation of cell cycle -0.058 0.3 -10000 0 -0.62 77 77
ETS1 0.008 0.053 -10000 0 -0.89 1 1
PXN -0.078 0.34 -10000 0 -0.76 74 74
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.087 0.37 -10000 0 -0.82 74 74
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.019 0.17 0.33 2 -0.87 14 16
MAPKKK cascade -0.18 0.49 -10000 0 -1.1 74 74
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
Tie2/Ang1/Shc -0.23 0.51 -10000 0 -1.2 74 74
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.052 0.29 -10000 0 -0.62 74 74
mol:Phosphatidic acid -0.18 0.49 -10000 0 -1.1 74 74
mol:Angiotensin II 0.002 0.005 -10000 0 -10000 0 0
mol:NADP -0.067 0.32 -10000 0 -0.7 74 74
Rac1/GTP -0.18 0.35 -10000 0 -0.87 74 74
MMP2 -0.2 0.55 -10000 0 -1.3 74 74
Signaling events mediated by the Hedgehog family

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
TGFB2 0.038 0.28 0.54 13 -0.89 23 36
IHH 0.013 0.18 0.37 17 -0.88 11 28
SHH Np/Cholesterol/GAS1 -0.12 0.24 -10000 0 -0.57 79 79
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.12 0.24 0.56 79 -10000 0 79
SMO/beta Arrestin2 -0.023 0.25 -10000 0 -0.8 28 28
SMO -0.024 0.27 0.38 1 -0.86 28 29
AKT1 0.001 0.14 0.25 1 -0.42 19 20
ARRB2 0 0 -10000 0 -10000 0 0
BOC 0.009 0.054 0.32 11 -10000 0 11
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.022 0.26 0.38 1 -0.83 28 29
STIL -0.004 0.24 0.35 7 -0.69 28 35
DHH N/PTCH2 -0.002 0.053 -10000 0 -0.67 2 2
DHH N/PTCH1 -0.016 0.23 0.36 2 -0.76 26 28
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
DHH 0.001 0.016 0.32 1 -10000 0 1
PTHLH 0.045 0.29 0.62 1 -0.88 23 24
determination of left/right symmetry -0.022 0.26 0.38 1 -0.83 28 29
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
skeletal system development 0.046 0.28 0.62 1 -0.87 23 24
IHH N/Hhip -0.34 0.38 0.27 1 -0.72 179 180
DHH N/Hhip -0.31 0.34 -10000 0 -0.67 173 173
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.022 0.26 0.38 1 -0.83 28 29
pancreas development -0.4 0.43 0.32 1 -0.86 173 174
HHAT -0.001 0.05 0.32 2 -0.86 1 3
PI3K -0.005 0.071 -10000 0 -0.94 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.16 0.34 0.32 1 -0.86 70 71
somite specification -0.022 0.26 0.38 1 -0.83 28 29
SHH Np/Cholesterol/PTCH1 -0.029 0.24 0.33 1 -0.69 34 35
SHH Np/Cholesterol/PTCH2 -0.021 0.12 -10000 0 -0.57 15 15
SHH Np/Cholesterol/Megalin -0.081 0.22 -10000 0 -0.55 64 64
SHH -0.007 0.14 -10000 0 -0.71 13 13
catabolic process 0.012 0.26 0.46 1 -0.8 28 29
SMO/Vitamin D3 -0.025 0.26 0.42 1 -0.72 36 37
SHH Np/Cholesterol/Hhip -0.27 0.28 -10000 0 -0.55 182 182
LRP2 -0.099 0.32 0.32 25 -0.86 52 77
receptor-mediated endocytosis -0.07 0.27 -10000 0 -0.76 33 33
SHH Np/Cholesterol/BOC -0.014 0.11 -10000 0 -0.57 13 13
SHH Np/Cholesterol/CDO -0.02 0.11 -10000 0 -0.57 13 13
mesenchymal cell differentiation 0.27 0.28 0.55 182 -10000 0 182
mol:Vitamin D3 0.007 0.25 0.42 1 -0.69 34 35
IHH N/PTCH2 0 0.13 -10000 0 -0.61 13 13
CDON 0 0 -10000 0 -10000 0 0
IHH N/PTCH1 -0.002 0.27 0.41 17 -0.8 28 45
Megalin/LRPAP1 -0.079 0.24 -10000 0 -0.67 52 52
PTCH2 -0.003 0.067 0.32 2 -0.86 2 4
SHH Np/Cholesterol -0.019 0.11 -10000 0 -0.58 13 13
PTCH1 0.012 0.26 0.46 1 -0.8 28 29
HHIP -0.4 0.43 0.32 1 -0.86 173 174
Thromboxane A2 receptor 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
TGM2 -0.009 0.089 -10000 0 -0.86 4 4
GNB1/GNG2 -0.066 0.088 -10000 0 -0.21 56 56
AKT1 -0.026 0.13 0.23 1 -0.22 53 54
EGF 0.075 0.13 0.32 88 -10000 0 88
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.058 0.14 -10000 0 -0.5 18 18
mol:Ca2+ -0.051 0.17 0.27 1 -0.31 108 109
LYN -0.056 0.14 -10000 0 -0.45 22 22
RhoA/GTP -0.038 0.057 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.058 0.2 -10000 0 -0.35 108 108
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.039 0.15 -10000 0 -0.53 19 19
G beta5/gamma2 -0.087 0.12 -10000 0 -0.29 57 57
PRKCH -0.063 0.2 -10000 0 -0.36 107 107
DNM1 0.004 0.13 0.32 21 -0.86 6 27
TXA2/TP beta/beta Arrestin3 -0.009 0.054 -10000 0 -0.32 6 6
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.049 0.2 -10000 0 -0.86 21 21
G12 family/GTP -0.095 0.14 -10000 0 -0.31 107 107
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 0.008 0.072 0.32 12 -0.86 1 13
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.048 0.16 0.39 41 -10000 0 41
mol:NADP -0.005 0.063 -10000 0 -0.86 2 2
RAB11A 0 0 -10000 0 -10000 0 0
PRKG1 -0.041 0.19 0.32 1 -0.86 18 19
mol:IP3 -0.072 0.21 -10000 0 -0.39 108 108
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.11 0.28 -10000 0 -0.53 108 108
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.12 0.21 -10000 0 -0.47 81 81
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.068 0.16 -10000 0 -0.48 31 31
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.083 0.26 -10000 0 -0.86 36 36
PRKCB1 -0.071 0.21 -10000 0 -0.38 107 107
GNAQ -0.002 0.045 -10000 0 -0.86 1 1
mol:L-citrulline -0.005 0.063 -10000 0 -0.86 2 2
TXA2/TXA2-R family -0.11 0.29 -10000 0 -0.55 107 107
LCK -0.067 0.16 -10000 0 -0.48 30 30
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.075 0.18 -10000 0 -0.6 23 23
TXA2-R family/G12 family/GDP/G beta/gamma -0.02 0.048 -10000 0 -0.37 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.075 0.18 -10000 0 -0.58 24 24
MAPK14 -0.027 0.14 0.24 1 -0.24 54 55
TGM2/GTP -0.085 0.24 -10000 0 -0.44 108 108
MAPK11 -0.026 0.14 0.26 2 -0.24 45 47
ARHGEF1 -0.025 0.1 0.18 7 -0.2 19 26
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade -0.072 0.22 -10000 0 -0.4 107 107
RAB11/GDP 0 0 -10000 0 -10000 0 0
ICAM1 -0.043 0.16 -10000 0 -0.28 107 107
cAMP biosynthetic process -0.067 0.2 -10000 0 -0.36 108 108
Gq family/GTP/EBP50 -0.055 0.13 -10000 0 -0.29 71 71
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.054 0.14 -10000 0 -0.45 22 22
GNB5 0.001 0.016 0.32 1 -10000 0 1
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.021 0.14 -10000 0 -0.35 30 30
VCAM1 -0.053 0.18 0.27 5 -0.32 106 111
TP beta/Gq family/GDP/G beta5/gamma2 -0.039 0.15 -10000 0 -0.53 19 19
platelet activation -0.038 0.18 0.3 2 -0.31 107 109
PGI2/IP -0.065 0.2 -10000 0 -0.68 36 36
PRKACA -0.064 0.17 -10000 0 -0.45 53 53
Gq family/GDP/G beta5/gamma2 -0.039 0.14 -10000 0 -0.43 29 29
TXA2/TP beta/beta Arrestin2 -0.006 0.1 0.24 1 -0.69 6 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.087 0.21 -10000 0 -0.48 67 67
mol:DAG -0.083 0.23 -10000 0 -0.44 107 107
EGFR -0.023 0.14 -10000 0 -0.86 10 10
TXA2/TP alpha -0.099 0.27 -10000 0 -0.5 108 108
Gq family/GTP -0.058 0.14 -10000 0 -0.32 71 71
YES1 -0.056 0.14 -10000 0 -0.45 22 22
GNAI2/GTP -0.065 0.16 -10000 0 -0.53 23 23
PGD2/DP -0.038 0.16 -10000 0 -0.68 21 21
SLC9A3R1 -0.002 0.045 -10000 0 -0.86 1 1
FYN -0.056 0.14 -10000 0 -0.45 22 22
mol:NO -0.005 0.063 -10000 0 -0.86 2 2
GNA15 -0.001 0.05 0.32 2 -0.86 1 3
PGK/cGMP -0.031 0.13 -10000 0 -0.59 20 20
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.082 0.2 -10000 0 -0.63 26 26
NOS3 -0.005 0.063 -10000 0 -0.86 2 2
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.062 0.2 -10000 0 -0.36 107 107
PRKCB -0.085 0.23 -10000 0 -0.4 119 119
PRKCE -0.062 0.2 -10000 0 -0.36 107 107
PRKCD -0.071 0.21 -10000 0 -0.39 107 107
PRKCG -0.073 0.21 -10000 0 -0.39 107 107
muscle contraction -0.097 0.27 -10000 0 -0.5 107 107
PRKCZ -0.068 0.2 -10000 0 -0.36 108 108
ARR3 0.001 0.016 0.32 1 -10000 0 1
TXA2/TP beta -0.072 0.19 -10000 0 -0.62 23 23
PRKCQ -0.072 0.21 -10000 0 -0.38 113 113
MAPKKK cascade -0.095 0.25 -10000 0 -0.47 107 107
SELE -0.082 0.22 0.27 2 -0.42 107 109
TP beta/GNAI2/GDP/G beta/gamma -0.077 0.18 -10000 0 -0.61 24 24
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.15 0.32 -10000 0 -0.86 63 63
chemotaxis -0.13 0.32 -10000 0 -0.63 107 107
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.028 0.15 -10000 0 -0.86 12 12
Rac1/GTP 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.007 0.046 0.32 8 -10000 0 8
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.1 0.16 -10000 0 -0.3 86 86
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
S1P/S1P3/G12/G13 -0.015 0.092 -10000 0 -0.54 11 11
AKT1 -0.041 0.08 -10000 0 -10000 0 0
AKT3 -0.059 0.18 -10000 0 -1.5 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.046 0.32 8 -10000 0 8
GNAI2 0 0.002 -10000 0 -10000 0 0
GNAI3 0 0.001 -10000 0 -10000 0 0
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.025 0.15 0.32 1 -0.86 11 12
S1PR2 -0.007 0.077 -10000 0 -0.86 3 3
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.23 -10000 0 -0.35 179 179
MAPK3 -0.12 0.22 -10000 0 -0.39 88 88
MAPK1 -0.12 0.22 -10000 0 -0.39 88 88
JAK2 -0.12 0.22 -10000 0 -0.39 89 89
CXCR4 -0.13 0.23 -10000 0 -0.4 90 90
FLT1 0 0.003 -10000 0 -10000 0 0
RhoA/GDP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0 0 -10000 0 -10000 0 0
SRC -0.12 0.22 -10000 0 -0.39 87 87
S1P/S1P3/Gi -0.15 0.23 -10000 0 -0.35 179 179
RAC1 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.15 0.19 -10000 0 -0.38 88 88
VEGFA 0 0.003 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.14 0.2 -10000 0 -0.33 178 178
VEGFR1 homodimer/VEGFA homodimer 0 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.086 0.18 -10000 0 -0.4 80 80
GNAQ -0.002 0.045 -10000 0 -0.86 1 1
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
G12/G13 0 0 -10000 0 -10000 0 0
GNA14 -0.15 0.32 -10000 0 -0.86 63 63
GNA15 -0.001 0.05 0.32 2 -0.86 1 3
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.028 0.15 -10000 0 -0.86 12 12
Rac1/GTP -0.15 0.19 -10000 0 -0.38 88 88
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.016 0.1 -10000 0 -0.67 9 9
PDGFRB 0.007 0.046 0.32 8 -10000 0 8
SPHK1 -0.012 0.14 -10000 0 -1 5 5
mol:S1P -0.02 0.14 0.23 1 -0.94 5 6
S1P1/S1P/Gi -0.25 0.3 -10000 0 -0.53 150 150
GNAO1 -0.42 0.43 -10000 0 -0.87 178 178
PDGFB-D/PDGFRB/PLCgamma1 -0.21 0.25 0.29 3 -0.6 75 78
PLCG1 -0.22 0.28 -10000 0 -0.65 76 76
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.046 0.31 8 -10000 0 8
GNAI2 0 0.001 -10000 0 -10000 0 0
GNAI3 0 0.001 -10000 0 -10000 0 0
GNAI1 -0.005 0.064 -10000 0 -0.87 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.003 0.093 -10000 0 -0.59 9 9
S1P1/S1P -0.037 0.14 -10000 0 -0.62 13 13
negative regulation of cAMP metabolic process -0.24 0.29 -10000 0 -0.51 150 150
MAPK3 -0.3 0.36 -10000 0 -0.72 128 128
calcium-dependent phospholipase C activity -0.004 0.004 -10000 0 -10000 0 0
Rac1/GDP 0 0 -10000 0 -10000 0 0
RhoA/GDP 0 0 -10000 0 -10000 0 0
KDR -0.021 0.13 -10000 0 -0.86 9 9
PLCB2 -0.026 0.15 -10000 0 -0.56 19 19
RAC1 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.044 0.1 -10000 0 -0.52 12 12
receptor internalization -0.035 0.13 -10000 0 -0.57 13 13
PTGS2 -0.43 0.54 -10000 0 -1.1 127 127
Rac1/GTP -0.044 0.1 -10000 0 -0.52 12 12
RHOA 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.24 0.29 -10000 0 -0.51 150 150
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.15 0.16 0.31 176 -0.87 1 177
MAPK1 -0.3 0.36 -10000 0 -0.72 128 128
S1P1/S1P/PDGFB-D/PDGFRB -0.036 0.15 -10000 0 -0.66 12 12
ABCC1 0.007 0.046 0.32 8 -10000 0 8
BCR signaling pathway

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
JUN -0.077 0.16 0.36 1 -0.42 28 29
IKBKB -0.02 0.079 -10000 0 -0.28 6 6
AKT1 -0.053 0.12 0.23 3 -0.25 70 73
IKBKG -0.018 0.083 -10000 0 -0.28 9 9
CALM1 -0.05 0.12 -10000 0 -0.48 11 11
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
MAP3K1 -0.11 0.21 0.44 1 -0.47 69 70
MAP3K7 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.065 0.13 0.24 1 -0.52 11 12
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.11 0.13 0.26 1 -0.27 89 90
LYN 0 0 -10000 0 -10000 0 0
BLNK -0.021 0.13 -10000 0 -0.86 9 9
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.15 0.29 0.44 2 -0.67 85 87
CD22 -0.21 0.3 0.32 2 -0.62 108 110
CAMK2G -0.041 0.12 -10000 0 -0.44 11 11
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.11 0.2 -10000 0 -0.45 92 92
GO:0007205 -0.06 0.13 0.24 1 -0.52 11 12
SYK -0.007 0.077 -10000 0 -0.86 3 3
ELK1 -0.051 0.12 -10000 0 -0.49 11 11
NFATC1 -0.099 0.19 -10000 0 -0.4 78 78
B-cell antigen/BCR complex -0.15 0.29 0.44 2 -0.67 85 87
PAG1/CSK -0.002 0.051 -10000 0 -0.67 2 2
NFKBIB 0.001 0.028 -10000 0 -0.1 1 1
HRAS -0.042 0.14 -10000 0 -0.5 11 11
NFKBIA 0.001 0.027 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.006 0.022 -10000 0 -10000 0 0
RasGAP/Csk -0.35 0.36 0.35 2 -0.62 214 216
mol:GDP -0.047 0.12 0.26 1 -0.49 11 12
PTEN -0.005 0.063 -10000 0 -0.86 2 2
CD79B 0.003 0.028 0.32 3 -10000 0 3
NF-kappa-B/RelA/I kappa B alpha 0.006 0.022 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.12 0.22 0.34 2 -0.49 88 90
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
mol:IP3 -0.066 0.13 0.24 1 -0.53 11 12
CSK 0 0 -10000 0 -10000 0 0
FOS -0.27 0.28 -10000 0 -0.53 181 181
CHUK -0.018 0.083 -10000 0 -0.28 10 10
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.062 0.12 -10000 0 -0.52 17 17
PTPN6 -0.2 0.28 0.32 1 -0.58 108 109
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.001 0.041 -10000 0 -0.14 24 24
VAV2 -0.16 0.24 0.32 1 -0.52 97 98
ubiquitin-dependent protein catabolic process 0.004 0.027 -10000 0 -10000 0 0
BTK -0.029 0.16 -10000 0 -1.2 7 7
CD19 -0.17 0.25 0.32 2 -0.53 101 103
MAP4K1 -0.014 0.12 0.32 3 -0.86 7 10
CD72 -0.007 0.093 0.32 3 -0.86 4 7
PAG1 -0.003 0.067 0.32 2 -0.86 2 4
MAPK14 -0.09 0.18 0.43 1 -0.4 65 66
SH3BP5 -0.005 0.063 -10000 0 -0.86 2 2
PIK3AP1 -0.054 0.14 -10000 0 -0.52 14 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.12 0.22 -10000 0 -0.5 86 86
RAF1 -0.033 0.13 -10000 0 -0.46 11 11
RasGAP/p62DOK/SHIP -0.34 0.34 -10000 0 -0.6 214 214
CD79A -0.19 0.37 0.32 9 -0.86 85 94
re-entry into mitotic cell cycle -0.11 0.13 0.26 1 -0.26 89 90
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
MAPK3 -0.015 0.11 -10000 0 -0.41 8 8
MAPK1 -0.015 0.11 -10000 0 -0.41 8 8
CD72/SHP1 -0.18 0.27 0.49 1 -0.59 89 90
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.11 0.21 0.43 1 -0.49 49 50
actin cytoskeleton organization -0.12 0.21 -10000 0 -0.46 86 86
NF-kappa-B/RelA 0.016 0.044 -10000 0 -10000 0 0
Calcineurin -0.051 0.093 -10000 0 -0.44 8 8
PI3K -0.16 0.21 -10000 0 -0.52 81 81
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.067 0.13 0.28 1 -0.54 11 12
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.16 0.27 0.66 1 -0.6 69 70
DAPP1 -0.18 0.29 0.5 1 -0.63 77 78
cytokine secretion -0.092 0.17 -10000 0 -0.37 81 81
mol:DAG -0.066 0.13 0.24 1 -0.53 11 12
PLCG2 -0.016 0.12 -10000 0 -0.86 7 7
MAP2K1 -0.024 0.12 -10000 0 -0.46 8 8
B-cell antigen/BCR complex/FcgammaRIIB -0.4 0.4 0.39 2 -0.72 213 215
mol:PI-3-4-5-P3 -0.11 0.14 0.35 1 -0.36 73 74
ETS1 -0.032 0.11 -10000 0 -0.44 9 9
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.24 0.36 2 -0.52 92 94
B-cell antigen/BCR complex/LYN -0.19 0.26 0.31 2 -0.56 102 104
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 -0.002 0.045 -10000 0 -0.86 1 1
RAC1 -0.13 0.23 -10000 0 -0.49 85 85
B-cell antigen/BCR complex/LYN/SYK -0.22 0.31 0.39 2 -0.69 95 97
CARD11 -0.063 0.16 -10000 0 -0.61 18 18
FCGR2B -0.42 0.43 0.32 2 -0.86 184 186
PPP3CA 0 0 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
IKK complex -0.002 0.038 0.12 1 -0.14 1 2
PTPRC -0.066 0.23 0.32 1 -0.86 29 30
PDPK1 -0.067 0.1 0.21 3 -0.27 35 38
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.004 0.034 0.12 1 -0.15 14 15
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.043 0.17 -10000 0 -0.69 22 22
alphaM/beta2 Integrin/GPIbA -0.026 0.12 0.34 1 -0.64 13 14
alphaM/beta2 Integrin/proMMP-9 0 0.18 0.4 1 -0.69 18 19
PLAUR -0.002 0.069 0.32 3 -0.86 2 5
HMGB1 -0.006 0.016 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.02 0.1 -10000 0 -0.67 8 8
AGER -0.003 0.038 0.32 4 -10000 0 4
RAP1A 0 0 -10000 0 -10000 0 0
SELPLG -0.005 0.063 -10000 0 -0.86 2 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.04 0.13 0.32 1 -0.67 8 9
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.032 0.2 0.32 70 -0.86 12 82
CYR61 -0.1 0.28 -10000 0 -0.86 43 43
TLN1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.099 0.17 -10000 0 -0.54 34 34
RHOA 0 0 -10000 0 -10000 0 0
P-selectin oligomer -0.26 0.39 -10000 0 -0.86 112 112
MYH2 -0.14 0.29 -10000 0 -0.48 121 121
MST1R 0.027 0.16 0.32 51 -0.86 7 58
leukocyte activation during inflammatory response -0.28 0.28 -10000 0 -0.53 192 192
APOB -0.037 0.18 -10000 0 -0.86 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.034 0.18 0.32 6 -0.86 17 23
JAM3 0.001 0.016 0.32 1 -10000 0 1
GP1BA -0.007 0.11 0.32 5 -0.86 5 10
alphaM/beta2 Integrin/CTGF -0.034 0.15 -10000 0 -0.7 15 15
alphaM/beta2 Integrin -0.12 0.2 -10000 0 -0.5 53 53
JAM3 homodimer 0.001 0.016 0.32 1 -10000 0 1
ICAM2 0.001 0.016 0.32 1 -10000 0 1
ICAM1 0 0 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.2 -10000 0 -0.5 53 53
cell adhesion -0.025 0.12 0.34 1 -0.64 13 14
NFKB1 -0.07 0.19 -10000 0 -0.74 14 14
THY1 0.08 0.14 0.32 94 -10000 0 94
RhoA/GDP 0 0 -10000 0 -10000 0 0
Lipoprotein(a) -0.31 0.32 -10000 0 -0.61 186 186
alphaM/beta2 Integrin/LRP/tPA -0.025 0.13 -10000 0 -0.62 14 14
IL6 -0.1 0.39 -10000 0 -0.99 57 57
ITGB2 -0.015 0.092 0.32 1 -0.87 4 5
elevation of cytosolic calcium ion concentration -0.015 0.11 0.37 2 -0.6 10 12
alphaM/beta2 Integrin/JAM2/JAM3 -0.035 0.14 0.38 1 -0.6 20 21
JAM2 -0.029 0.16 0.32 1 -0.86 13 14
alphaM/beta2 Integrin/ICAM1 -0.039 0.17 -10000 0 -0.5 40 40
alphaM/beta2 Integrin/uPA/Plg -0.099 0.21 -10000 0 -0.55 65 65
RhoA/GTP -0.17 0.29 -10000 0 -0.49 125 125
positive regulation of phagocytosis -0.094 0.18 -10000 0 -0.63 30 30
Ron/MSP -0.034 0.2 -10000 0 -0.65 32 32
alphaM/beta2 Integrin/uPAR/uPA -0.015 0.11 0.38 2 -0.6 10 12
alphaM/beta2 Integrin/uPAR -0.022 0.11 -10000 0 -0.66 10 10
PLAU 0.005 0.04 0.32 6 -10000 0 6
PLAT -0.01 0.11 0.32 4 -0.86 6 10
actin filament polymerization -0.13 0.26 -10000 0 -0.45 121 121
MST1 -0.058 0.22 -10000 0 -0.86 25 25
alphaM/beta2 Integrin/lipoprotein(a) -0.28 0.28 -10000 0 -0.54 192 192
TNF -0.039 0.27 -10000 0 -1 18 18
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.017 0.11 -10000 0 -0.67 8 8
fibrinolysis -0.098 0.21 -10000 0 -0.54 65 65
HCK -0.028 0.15 -10000 0 -0.86 12 12
dendritic cell antigen processing and presentation -0.12 0.2 -10000 0 -0.5 53 53
VTN -0.03 0.16 -10000 0 -0.86 13 13
alphaM/beta2 Integrin/CYR61 -0.087 0.23 -10000 0 -0.66 46 46
LPA -0.42 0.43 -10000 0 -0.86 179 179
LRP1 -0.002 0.045 -10000 0 -0.86 1 1
cell migration -0.035 0.21 0.3 1 -0.65 31 32
FN1 -0.002 0.045 -10000 0 -0.86 1 1
alphaM/beta2 Integrin/Thy1 0.032 0.14 0.4 2 -0.67 8 10
MPO -0.02 0.13 0.32 1 -0.86 9 10
KNG1 -0.067 0.23 -10000 0 -0.86 29 29
RAP1/GDP 0 0 -10000 0 -10000 0 0
ROCK1 -0.13 0.27 -10000 0 -0.45 119 119
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.13 0.31 -10000 0 -0.86 58 58
CTGF -0.021 0.13 -10000 0 -0.86 9 9
alphaM/beta2 Integrin/Hck -0.038 0.18 -10000 0 -0.88 14 14
ITGAM -0.017 0.1 0.3 2 -0.88 5 7
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.18 0.28 -10000 0 -0.58 115 115
HP -0.27 0.4 -10000 0 -0.86 117 117
leukocyte adhesion -0.01 0.17 0.34 2 -0.53 20 22
SELP -0.26 0.4 -10000 0 -0.86 112 112
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.005 0.14 0.31 1 -0.43 24 25
TBX21 -0.16 0.42 0.64 1 -0.96 57 58
B2M -0.002 0.009 -10000 0 -10000 0 0
TYK2 0.009 0.019 -10000 0 -10000 0 0
IL12RB1 -0.022 0.17 -10000 0 -0.9 13 13
GADD45B -0.28 0.57 -10000 0 -1.2 92 92
IL12RB2 -0.009 0.17 0.31 12 -0.87 12 24
GADD45G -0.26 0.54 0.57 1 -1.2 86 87
natural killer cell activation -0.003 0.023 -10000 0 -10000 0 0
RELB 0.002 0.023 0.32 2 -10000 0 2
RELA 0 0 -10000 0 -10000 0 0
IL18 -0.012 0.15 0.32 3 -0.87 10 13
IL2RA -0.007 0.13 0.32 11 -0.86 7 18
IFNG 0.014 0.064 0.32 16 -10000 0 16
STAT3 (dimer) -0.15 0.35 0.55 1 -0.75 67 68
HLA-DRB5 -0.021 0.15 0.31 5 -0.86 11 16
FASLG -0.17 0.44 0.74 1 -1.1 45 46
NF kappa B2 p52/RelB -0.21 0.34 0.3 1 -0.85 64 65
CD4 -0.07 0.24 -10000 0 -0.87 30 30
SOCS1 -0.001 0.071 0.32 4 -0.86 2 6
EntrezGene:6955 -0.014 0.019 -10000 0 -10000 0 0
CD3D -0.018 0.17 0.31 16 -0.87 12 28
CD3E -0.038 0.17 0.32 1 -0.88 15 16
CD3G -0.026 0.16 0.31 7 -0.88 12 19
IL12Rbeta2/JAK2 -0.004 0.14 -10000 0 -0.68 13 13
CCL3 -0.21 0.52 0.64 1 -1.3 53 54
CCL4 -0.18 0.48 0.64 1 -1.3 43 44
HLA-A -0.002 0.008 -10000 0 -10000 0 0
IL18/IL18R -0.11 0.33 -10000 0 -0.72 73 73
NOS2 -0.13 0.39 0.63 1 -0.86 57 58
IL12/IL12R/TYK2/JAK2/SPHK2 -0.004 0.13 -10000 0 -0.42 23 23
IL1R1 -0.15 0.41 0.64 1 -1.1 41 42
IL4 0.003 0.023 -10000 0 -10000 0 0
JAK2 0.007 0.051 -10000 0 -0.89 1 1
EntrezGene:6957 -0.012 0.018 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.16 0.49 0.4 1 -1.3 50 51
RAB7A -0.18 0.39 -10000 0 -0.77 87 87
lysosomal transport -0.17 0.37 -10000 0 -0.72 89 89
FOS -0.66 0.75 -10000 0 -1.4 181 181
STAT4 (dimer) -0.18 0.41 0.56 1 -0.78 91 92
STAT5A (dimer) -0.2 0.36 0.38 9 -0.84 66 75
GZMA -0.16 0.42 0.7 1 -1.1 41 42
GZMB -0.16 0.43 0.7 1 -1 54 55
HLX 0 0 -10000 0 -10000 0 0
LCK -0.16 0.46 0.64 1 -0.97 66 67
TCR/CD3/MHC II/CD4 -0.15 0.31 0.27 2 -0.71 53 55
IL2/IL2R -0.049 0.21 0.38 2 -0.66 33 35
MAPK14 -0.25 0.5 0.57 1 -0.9 115 116
CCR5 -0.15 0.4 -10000 0 -0.93 54 54
IL1B -0.14 0.34 -10000 0 -0.88 64 64
STAT6 -0.027 0.14 0.4 1 -0.29 29 30
STAT4 -0.034 0.17 0.32 1 -0.86 15 16
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0.002 0.023 0.32 2 -10000 0 2
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B 0.006 0.037 0.34 3 -10000 0 3
CD8A -0.053 0.21 0.32 4 -0.87 23 27
CD8B -0.039 0.21 0.32 12 -0.87 20 32
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.005 0.14 0.43 24 -0.31 1 25
IL2RB -0.067 0.23 -10000 0 -0.86 29 29
proteasomal ubiquitin-dependent protein catabolic process -0.16 0.37 0.56 1 -0.71 91 92
IL2RG -0.006 0.11 0.32 7 -0.86 5 12
IL12 0.018 0.054 -10000 0 -10000 0 0
STAT5A 0.001 0.016 0.32 1 -10000 0 1
CD247 -0.007 0.067 0.32 1 -0.87 2 3
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.018 0.058 0.32 11 -10000 0 11
IL12/IL12R/TYK2/JAK2 -0.18 0.52 0.72 1 -1.1 66 67
MAP2K3 -0.25 0.5 0.57 1 -0.88 119 120
RIPK2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.25 0.5 0.57 1 -0.89 119 120
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.013 0.11 0.32 1 -0.86 6 7
IL18RAP -0.045 0.21 -10000 0 -0.87 23 23
IL12Rbeta1/TYK2 -0.014 0.14 -10000 0 -0.71 13 13
EOMES -0.16 0.48 -10000 0 -1.5 44 44
STAT1 (dimer) -0.13 0.34 0.69 1 -0.75 60 61
T cell proliferation -0.15 0.32 0.5 1 -0.6 95 96
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.13 0.32 -10000 0 -0.87 58 58
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.25 0.32 -10000 0 -0.72 98 98
ATF2 -0.22 0.45 0.54 1 -0.81 117 118
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.068 0.38 -10000 0 -1.2 33 33
SMARCC2 -0.002 0.009 -10000 0 -10000 0 0
SMARCC1 -0.002 0.009 -10000 0 -10000 0 0
TBX21 -0.091 0.23 -10000 0 -0.57 37 37
SUMO2 0.003 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.016 0.023 0.32 2 -10000 0 2
FKBP4 0 0 -10000 0 -10000 0 0
FKBP5 -0.002 0.045 -10000 0 -0.86 1 1
GR alpha/HSP90/FKBP51/HSP90 0.07 0.11 0.31 10 -0.47 1 11
PRL -0.066 0.16 -10000 0 -0.59 12 12
cortisol/GR alpha (dimer)/TIF2 0.088 0.37 0.52 91 -0.58 46 137
RELA -0.067 0.11 -10000 0 -0.32 2 2
FGG 0.031 0.37 0.47 34 -0.92 37 71
GR beta/TIF2 -0.019 0.27 0.32 17 -0.65 48 65
IFNG -0.14 0.26 0.5 4 -0.62 32 36
apoptosis -0.17 0.31 0.63 6 -0.76 42 48
CREB1 0.017 0.033 -10000 0 -10000 0 0
histone acetylation -0.068 0.13 -10000 0 -0.32 47 47
BGLAP -0.041 0.13 -10000 0 -0.5 2 2
GR/PKAc 0.069 0.1 0.36 2 -0.52 1 3
NF kappa B1 p50/RelA -0.12 0.2 -10000 0 -0.45 48 48
SMARCD1 -0.002 0.009 -10000 0 -10000 0 0
MDM2 0.056 0.093 0.24 27 -10000 0 27
GATA3 -0.051 0.23 0.33 1 -0.85 27 28
AKT1 0.014 0.045 -10000 0 -10000 0 0
CSF2 -0.054 0.11 -10000 0 -0.49 2 2
GSK3B 0.003 0.01 -10000 0 -10000 0 0
NR1I3 -0.24 0.44 0.6 6 -0.98 80 86
CSN2 0.067 0.18 0.37 27 -0.43 7 34
BRG1/BAF155/BAF170/BAF60A -0.006 0.032 -10000 0 -10000 0 0
NFATC1 -0.009 0.089 -10000 0 -0.86 4 4
POU2F1 0.002 0.009 -10000 0 -10000 0 0
CDKN1A -0.006 0.26 -10000 0 -1.6 10 10
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.004 0.011 -10000 0 -10000 0 0
SFN 0.18 0.17 0.32 214 -0.86 2 216
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.17 0.15 0.36 79 -0.42 3 82
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.33 0.48 0.57 6 -0.93 131 137
JUN -0.023 0.24 0.43 10 -0.62 29 39
IL4 -0.061 0.14 -10000 0 -0.61 7 7
CDK5R1 0.004 0.032 0.31 4 -10000 0 4
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.28 0.28 -10000 0 -0.55 166 166
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.072 0.1 0.36 2 -0.42 1 3
cortisol/GR alpha (monomer) 0.21 0.34 0.57 124 -0.49 14 138
NCOA2 -0.11 0.29 -10000 0 -0.86 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.38 0.45 -10000 0 -0.84 179 179
AP-1/NFAT1-c-4 -0.25 0.41 0.51 5 -0.68 138 143
AFP -0.017 0.34 -10000 0 -1.2 18 18
SUV420H1 0.001 0.016 0.32 1 -10000 0 1
IRF1 0.099 0.15 0.44 10 -10000 0 10
TP53 0.012 0.083 -10000 0 -0.48 10 10
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.15 0.37 0.51 10 -0.86 42 52
KRT14 -0.038 0.15 -10000 0 -10000 0 0
TBP 0.016 0.009 -10000 0 -10000 0 0
CREBBP -0.007 0.05 -10000 0 -0.25 8 8
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
AP-1 -0.25 0.41 0.51 5 -0.68 136 141
MAPK14 0.003 0.008 -10000 0 -10000 0 0
MAPK10 -0.048 0.22 0.3 7 -0.86 24 31
MAPK11 0.015 0.059 0.31 14 -10000 0 14
KRT5 -0.13 0.28 0.55 3 -0.71 22 25
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 -0.005 0.019 -10000 0 -10000 0 0
STAT1 0.016 0.023 0.32 2 -10000 0 2
CGA -0.034 0.14 -10000 0 -0.5 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.031 0.13 0.33 8 -0.36 6 14
MAPK3 0.003 0.009 -10000 0 -10000 0 0
MAPK1 0.003 0.008 -10000 0 -10000 0 0
ICAM1 -0.15 0.24 -10000 0 -0.64 40 40
NFKB1 -0.067 0.11 -10000 0 -0.31 3 3
MAPK8 -0.074 0.24 0.39 7 -0.61 37 44
MAPK9 0.003 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.18 0.33 0.64 6 -0.82 42 48
BAX 0.027 0.069 -10000 0 -10000 0 0
POMC -0.12 0.26 -10000 0 -0.66 36 36
EP300 -0.007 0.05 -10000 0 -0.25 4 4
cortisol/GR alpha (dimer)/p53 0.18 0.29 0.53 99 -0.54 5 104
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.072 0.24 3 -10000 0 3
SGK1 0 0.28 -10000 0 -1.5 12 12
IL13 -0.15 0.29 0.54 1 -0.92 26 27
IL6 -0.29 0.54 0.42 1 -1.3 70 71
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.14 0.24 -10000 0 -0.84 19 19
IL2 -0.15 0.26 -10000 0 -0.63 31 31
CDK5 0.001 0.004 -10000 0 -10000 0 0
PRKACB -0.002 0.045 -10000 0 -0.86 1 1
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.38 0.62 0.42 4 -1.3 98 102
CDK5R1/CDK5 0.004 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.093 0.13 -10000 0 -0.54 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.26 0.49 103 -0.46 4 107
SMARCA4 -0.002 0.009 -10000 0 -10000 0 0
chromatin remodeling 0.094 0.17 0.37 39 -0.41 8 47
NF kappa B1 p50/RelA/Cbp -0.11 0.15 -10000 0 -0.48 16 16
JUN (dimer) -0.022 0.24 0.43 10 -0.61 29 39
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.76 0.58 -10000 0 -1.2 243 243
NR3C1 0.11 0.18 0.39 67 -10000 0 67
NR4A1 -0.13 0.32 -10000 0 -0.83 61 61
TIF2/SUV420H1 -0.086 0.22 -10000 0 -0.67 48 48
MAPKKK cascade -0.17 0.31 0.63 6 -0.76 42 48
cortisol/GR alpha (dimer)/Src-1 0.17 0.29 0.52 102 -0.51 11 113
PBX1 -0.074 0.25 0.32 1 -0.86 33 34
POU1F1 0.002 0.018 0.32 1 -10000 0 1
SELE -0.41 0.64 -10000 0 -1.4 98 98
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.094 0.17 0.37 39 -0.41 8 47
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.26 0.49 103 -0.46 4 107
mol:cortisol 0.094 0.19 0.33 104 -0.27 15 119
MMP1 0.012 0.16 0.43 10 -10000 0 10
Signaling events mediated by PRL

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
CCNE1 0.11 0.15 0.32 134 -10000 0 134
mol:Halofuginone 0 0.003 -10000 0 -10000 0 0
ITGA1 -0.005 0.063 -10000 0 -0.86 2 2
CDKN1A -0.083 0.14 -10000 0 -0.65 11 11
PRL-3/alpha Tubulin 0.036 0.081 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.1 -10000 0 -0.68 4 4
AGT -0.009 0.089 -10000 0 -0.86 4 4
CCNA2 -0.12 0.26 -10000 0 -0.47 127 127
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.22 0.33 -10000 0 -0.67 128 128
CDK2/Cyclin E1 -0.018 0.16 -10000 0 -0.59 10 10
MAPK3 0.041 0.052 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.041 0.052 -10000 0 -10000 0 0
PTP4A1 -0.16 0.27 -10000 0 -0.53 128 128
PTP4A3 0.052 0.12 0.32 61 -10000 0 61
PTP4A2 0 0 -10000 0 -10000 0 0
ITGB1 0.041 0.052 -10000 0 -10000 0 0
SRC 0.004 0.036 0.32 5 -10000 0 5
RAC1 -0.04 0.12 -10000 0 -0.32 1 1
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.34 0.34 -10000 0 -0.6 209 209
RABGGTA 0 0 -10000 0 -10000 0 0
BCAR1 -0.034 0.076 -10000 0 -10000 0 0
RHOC -0.04 0.12 -10000 0 -0.32 1 1
RHOA -0.04 0.12 -10000 0 -0.32 1 1
cell motility -0.03 0.13 -10000 0 -0.35 1 1
PRL-1/alpha Tubulin -0.17 0.24 -10000 0 -0.49 128 128
PRL-3/alpha1 Integrin 0.032 0.096 -10000 0 -0.67 2 2
ROCK1 -0.03 0.13 -10000 0 -0.36 1 1
RABGGTB 0 0 -10000 0 -10000 0 0
CDK2 0 0 -10000 0 -10000 0 0
mitosis -0.16 0.27 -10000 0 -0.52 128 128
ATF5 -0.3 0.41 -10000 0 -0.86 128 128
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -10000 0 -10000 0 0
VLDLR -0.034 0.26 0.32 42 -0.86 30 72
LRPAP1 0 0 -10000 0 -10000 0 0
NUDC 0 0 -10000 0 -10000 0 0
RELN/LRP8 -0.18 0.29 -10000 0 -0.58 125 125
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
KATNA1 0 0 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.17 0.25 -10000 0 -0.52 125 125
IQGAP1/CaM 0 0 -10000 0 -10000 0 0
DAB1 -0.13 0.31 0.32 1 -0.86 56 57
IQGAP1 0 0 -10000 0 -10000 0 0
PLA2G7 0.007 0.088 0.32 14 -0.86 2 16
CALM1 0 0 -10000 0 -10000 0 0
DYNLT1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.021 0.064 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.003 0.033 0.32 4 -10000 0 4
LIS1/Poliovirus Protein 3A 0 0 -10000 0 -10000 0 0
CDK5R2 0.009 0.051 0.32 10 -10000 0 10
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.31 0.38 -10000 0 -0.67 178 178
YWHAE 0 0 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.19 -10000 0 -10000 0 0
MAP1B 0.002 0.013 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
p35/CDK5 -0.15 0.22 -10000 0 -0.46 125 125
RELN -0.29 0.41 0.32 3 -0.86 125 128
PAFAH/LIS1 0.005 0.061 -10000 0 -0.58 2 2
LIS1/CLIP170 0 0 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.15 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.19 0.27 -10000 0 -0.45 145 145
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.14 0.21 -10000 0 -0.44 113 113
LIS1/IQGAP1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PAFAH1B1 0.018 0 -10000 0 -10000 0 0
PAFAH1B3 0.03 0.11 0.32 38 -0.86 1 39
PAFAH1B2 -0.005 0.063 -10000 0 -0.86 2 2
MAP1B/LIS1/Dynein heavy chain 0 0 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.18 -10000 0 -10000 0 0
LRP8 0.03 0.092 0.32 35 -10000 0 35
NDEL1/Katanin 60 -0.13 0.19 -10000 0 -0.41 109 109
P39/CDK5 -0.15 0.23 -10000 0 -0.46 125 125
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -10000 0 -10000 0 0
CDK5 -0.16 0.24 -10000 0 -0.49 125 125
PPP2R5D 0 0 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.27 0.34 -10000 0 -0.59 178 178
RELN/VLDLR -0.19 0.33 0.38 7 -0.59 138 145
CDC42 0 0 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.057 -10000 0 -0.84 1 1
Syndecan-4/Syndesmos -0.09 0.27 -10000 0 -0.82 37 37
positive regulation of JNK cascade -0.27 0.29 -10000 0 -0.78 59 59
Syndecan-4/ADAM12 -0.079 0.28 0.34 10 -0.81 38 48
CCL5 -0.019 0.14 0.32 2 -0.86 9 11
Rac1/GDP 0 0 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
ITGA5 0 0 -10000 0 -10000 0 0
SDCBP 0 0 -10000 0 -10000 0 0
PLG -0.13 0.31 -10000 0 -0.84 58 58
ADAM12 0.03 0.11 0.32 38 -0.86 1 39
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.022 0.041 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.14 0.3 0.34 1 -0.64 80 81
Syndecan-4/CXCL12/CXCR4 -0.29 0.32 -10000 0 -0.86 59 59
Syndecan-4/Laminin alpha3 -0.068 0.3 -10000 0 -0.83 37 37
MDK 0.18 0.16 0.32 208 -10000 0 208
Syndecan-4/FZD7 -0.1 0.28 -10000 0 -0.76 45 45
Syndecan-4/Midkine 0.008 0.32 0.34 38 -0.81 37 75
FZD7 -0.015 0.13 0.32 4 -0.86 8 12
Syndecan-4/FGFR1/FGF -0.13 0.27 -10000 0 -0.78 45 45
THBS1 -0.12 0.3 -10000 0 -0.86 54 54
integrin-mediated signaling pathway -0.12 0.28 0.33 2 -0.68 61 63
positive regulation of MAPKKK cascade -0.27 0.29 -10000 0 -0.78 59 59
Syndecan-4/TACI -0.084 0.28 0.34 3 -0.81 39 42
CXCR4 -0.007 0.077 -10000 0 -0.86 3 3
cell adhesion -0.001 0.021 -10000 0 -0.4 1 1
Syndecan-4/Dynamin -0.09 0.27 -10000 0 -0.82 37 37
Syndecan-4/TSP1 -0.16 0.32 -10000 0 -0.66 85 85
Syndecan-4/GIPC -0.09 0.27 -10000 0 -0.82 37 37
Syndecan-4/RANTES -0.1 0.29 -10000 0 -0.8 43 43
ITGB1 0 0 -10000 0 -10000 0 0
LAMA1 -0.087 0.3 0.32 20 -0.86 45 65
LAMA3 0.038 0.15 0.32 55 -0.86 4 59
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.021 0.052 -10000 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.09 0.27 -10000 0 -0.82 37 37
TFPI -0.035 0.17 -10000 0 -0.86 15 15
F2 -0.051 0.21 -10000 0 -0.84 24 24
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.12 0.3 -10000 0 -0.65 66 66
ACTN1 0 0 -10000 0 -10000 0 0
TNC -0.068 0.24 0.32 5 -0.86 31 36
Syndecan-4/CXCL12 -0.28 0.35 -10000 0 -0.6 172 172
FGF6 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
CXCL12 -0.36 0.42 -10000 0 -0.86 157 157
TNFRSF13B 0 0.073 0.32 5 -0.86 2 7
FGF2 -0.047 0.21 0.32 5 -0.86 22 27
FGFR1 -0.011 0.11 0.32 3 -0.86 6 9
Syndecan-4/PI-4-5-P2 -0.069 0.28 -10000 0 -0.83 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0 0.043 -10000 0 -0.81 1 1
cell migration -0.006 0.013 -10000 0 -10000 0 0
PRKCD 0.002 0.008 -10000 0 -10000 0 0
vasculogenesis -0.15 0.3 -10000 0 -0.63 85 85
SDC4 -0.075 0.31 -10000 0 -0.9 37 37
Syndecan-4/Tenascin C -0.13 0.3 0.34 2 -0.72 61 63
Syndecan-4/PI-4-5-P2/PKC alpha -0.017 0.032 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.09 0.27 -10000 0 -0.82 37 37
MMP9 0.032 0.2 0.32 70 -0.86 12 82
Rac1/GTP -0.001 0.022 -10000 0 -0.41 1 1
cytoskeleton organization -0.085 0.26 -10000 0 -0.77 37 37
GIPC1 0.001 0.016 0.32 1 -10000 0 1
Syndecan-4/TFPI -0.11 0.3 -10000 0 -0.83 45 45
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.035 0.2 -10000 0 -0.5 51 51
NF kappa B1 p50/RelA/I kappa B alpha -0.059 0.15 -10000 0 -0.66 5 5
alphaV/beta3 Integrin/Osteopontin/Src 0.036 0.21 0.3 5 -0.66 24 29
AP1 -0.27 0.37 0.42 1 -0.94 57 58
ILK -0.04 0.2 -10000 0 -0.53 51 51
bone resorption -0.044 0.22 -10000 0 -0.88 11 11
PTK2B 0 0 -10000 0 -10000 0 0
PYK2/p130Cas -0.005 0.23 0.37 1 -0.5 52 53
ITGAV 0.001 0.017 0.32 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.024 0.14 -10000 0 -0.67 16 16
alphaV/beta3 Integrin/Osteopontin -0.012 0.25 0.35 2 -0.59 51 53
MAP3K1 -0.041 0.21 -10000 0 -0.54 51 51
JUN -0.014 0.11 -10000 0 -0.86 6 6
MAPK3 -0.006 0.2 -10000 0 -0.5 51 51
MAPK1 -0.006 0.2 -10000 0 -0.5 51 51
Rac1/GDP 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.04 0.26 -10000 0 -0.58 60 60
ITGB3 -0.069 0.23 -10000 0 -0.85 30 30
NFKBIA 0.003 0.2 -10000 0 -0.48 51 51
FOS -0.42 0.43 -10000 0 -0.86 179 179
CD44 0.002 0.078 0.32 8 -0.86 2 10
CHUK 0 0 -10000 0 -10000 0 0
PLAU -0.006 0.19 -10000 0 -0.82 3 3
NF kappa B1 p50/RelA -0.054 0.15 -10000 0 -0.8 3 3
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.053 0.18 -10000 0 -0.66 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.046 0.22 -10000 0 -0.56 52 52
VAV3 -0.017 0.22 -10000 0 -0.53 52 52
MAP3K14 -0.015 0.21 -10000 0 -0.53 51 51
ROCK2 -0.032 0.16 -10000 0 -0.86 14 14
SPP1 0.055 0.28 0.32 127 -0.85 24 151
RAC1 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.04 0.19 -10000 0 -0.48 52 52
MMP2 -0.22 0.3 0.39 4 -0.75 59 63
Neurotrophic factor-mediated Trk receptor signaling

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.15 0.16 -10000 0 -0.52 26 26
NT3 (dimer)/TRKC -0.36 0.35 -10000 0 -0.69 194 194
NT3 (dimer)/TRKB -0.6 0.57 -10000 0 -1 224 224
SHC/Grb2/SOS1/GAB1/PI3K -0.003 0.041 -10000 0 -0.53 2 2
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF 0.01 0.056 0.32 12 -10000 0 12
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 0.002 0.023 0.32 2 -10000 0 2
NTRK2 -0.18 0.36 0.32 9 -0.86 82 91
NTRK3 -0.038 0.19 0.32 4 -0.86 18 22
NT-4/5 (dimer)/TRKB -0.34 0.42 -10000 0 -0.78 165 165
neuron apoptosis 0.18 0.24 0.57 76 -0.29 1 77
SHC 2-3/Grb2 -0.19 0.26 0.3 1 -0.64 76 77
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.2 0.28 -10000 0 -0.63 86 86
SHC3 -0.18 0.26 0.29 2 -0.64 68 70
STAT3 (dimer) -0.014 0.075 -10000 0 -0.39 14 14
NT3 (dimer)/TRKA -0.49 0.46 -10000 0 -0.84 218 218
RIN/GDP -0.088 0.12 -10000 0 -0.25 63 63
GIPC1 0.001 0.016 0.32 1 -10000 0 1
KRAS 0 0 -10000 0 -10000 0 0
DNAJA3 -0.19 0.25 0.27 2 -0.48 143 145
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.017 0.21 -10000 0 -1.1 14 14
MAGED1 -0.007 0.077 -10000 0 -0.86 3 3
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.028 0.32 3 -10000 0 3
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.028 0.14 -10000 0 -0.58 20 20
TRKA/NEDD4-2 0.001 0.016 -10000 0 -10000 0 0
ELMO1 -0.002 0.045 -10000 0 -0.86 1 1
RhoG/GTP/ELMO1/DOCK1 -0.014 0.098 -10000 0 -0.65 8 8
NGF -0.039 0.18 0.32 1 -0.86 17 18
HRAS 0.002 0.023 0.32 2 -10000 0 2
DOCK1 -0.019 0.12 -10000 0 -0.86 8 8
GAB2 0 0 -10000 0 -10000 0 0
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
DNM1 0.004 0.13 0.32 21 -0.86 6 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.18 0.24 -10000 0 -0.47 143 143
mol:GDP -0.13 0.18 -10000 0 -0.36 114 114
NGF (dimer) -0.038 0.18 0.32 1 -0.86 17 18
RhoG/GDP -0.002 0.035 -10000 0 -0.67 1 1
RIT1/GDP -0.085 0.12 -10000 0 -0.25 65 65
TIAM1 -0.046 0.19 -10000 0 -0.86 20 20
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
BDNF (dimer)/TRKB -0.12 0.25 0.39 2 -0.58 82 84
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.004 0.049 -10000 0 -0.67 2 2
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) -0.42 0.43 -10000 0 -0.86 183 183
RAP1/GDP -0.09 0.086 -10000 0 -0.26 1 1
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) 0.01 0.056 0.32 12 -10000 0 12
ubiquitin-dependent protein catabolic process -0.025 0.12 -10000 0 -0.58 17 17
Schwann cell development -0.055 0.045 -10000 0 -10000 0 0
EHD4 0 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 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.33 0.34 -10000 0 -0.59 211 211
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.042 0.089 -10000 0 -10000 0 0
STAT3 -0.014 0.075 -10000 0 -0.39 14 14
axon guidance -0.31 0.32 -10000 0 -0.56 211 211
MAPK3 -0.027 0.12 -10000 0 -0.53 20 20
MAPK1 -0.027 0.12 -10000 0 -0.53 20 20
CDC42/GDP -0.085 0.12 -10000 0 -0.25 56 56
NTF3 -0.42 0.43 -10000 0 -0.86 183 183
NTF4 0.003 0.028 0.32 3 -10000 0 3
NGF (dimer)/TRKA/FAIM -0.025 0.12 -10000 0 -0.58 17 17
PI3K -0.005 0.071 -10000 0 -0.94 2 2
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0.001 0.016 0.32 1 -10000 0 1
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.18 0.25 0.27 2 -0.48 143 145
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.31 0.31 -10000 0 -0.6 194 194
RGS19 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.019 0.092 -10000 0 -10000 0 0
Rac1/GDP -0.085 0.12 -10000 0 -0.26 30 30
NGF (dimer)/TRKA/GRIT -0.025 0.12 -10000 0 -0.59 17 17
neuron projection morphogenesis -0.16 0.25 -10000 0 -0.51 74 74
NGF (dimer)/TRKA/NEDD4-2 -0.025 0.12 -10000 0 -0.58 17 17
MAP2K1 0 0 -10000 0 -10000 0 0
NGFR -0.33 0.42 -10000 0 -0.86 143 143
NGF (dimer)/TRKA/GIPC/GAIP -0.015 0.089 -10000 0 -0.35 20 20
RAS family/GTP/PI3K -0.002 0.037 -10000 0 -0.48 2 2
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.039 0.18 -10000 0 -0.86 17 17
MAPKKK cascade -0.071 0.16 -10000 0 -0.78 17 17
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
TRKA/c-Abl 0.001 0.016 -10000 0 -10000 0 0
SQSTM1 0.004 0.036 0.32 5 -10000 0 5
BDNF (dimer)/TRKB/GIPC -0.11 0.23 0.38 2 -0.53 82 84
NGF (dimer)/TRKA/p62/Atypical PKCs -0.043 0.15 -10000 0 -0.51 33 33
MATK -0.004 0.082 0.32 3 -0.86 3 6
NEDD4L 0 0 -10000 0 -10000 0 0
RAS family/GDP -0.085 0.081 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.2 0.26 0.3 2 -0.51 145 147
Rac1/GTP -0.16 0.16 -10000 0 -0.37 128 128
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.21 0.23 -10000 0 -0.42 180 180
MAP3K8 -0.005 0.063 -10000 0 -0.86 2 2
FOS -0.1 0.18 -10000 0 -0.55 27 27
PRKCA 0 0 -10000 0 -10000 0 0
PTPN7 -0.001 0.071 0.32 4 -0.86 2 6
HRAS 0.002 0.023 0.31 2 -10000 0 2
PRKCB -0.075 0.24 -10000 0 -0.87 32 32
NRAS 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.013 -10000 0 -10000 0 0
MAPK3 -0.047 0.11 -10000 0 -0.32 27 27
MAP2K1 -0.064 0.18 -10000 0 -0.63 32 32
ELK1 -0.006 0.007 -10000 0 -10000 0 0
BRAF -0.065 0.16 -10000 0 -0.59 32 32
mol:GTP -0.003 0.003 -10000 0 -0.006 178 178
MAPK1 -0.047 0.11 -10000 0 -0.32 27 27
RAF1 -0.065 0.16 -10000 0 -0.59 32 32
KRAS 0 0 -10000 0 -10000 0 0
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 -0.002 0.044 -10000 0 -0.55 2 2
epithelial cell differentiation -0.057 0.093 -10000 0 -0.46 13 13
ITCH 0 0.004 -10000 0 -10000 0 0
WWP1 0.017 0.02 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
EGFR -0.023 0.14 -10000 0 -0.86 10 10
PRL 0.003 0.028 0.32 3 -10000 0 3
neuron projection morphogenesis -0.14 0.22 -10000 0 -0.52 1 1
PTPRZ1 0.01 0.056 0.32 12 -10000 0 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.19 0.22 -10000 0 -0.46 150 150
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.22 0.26 -10000 0 -0.53 156 156
ADAM17 0 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4 0.001 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.083 0.21 0.29 1 -0.55 59 60
NCOR1 -0.005 0.063 -10000 0 -0.86 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.21 0.25 -10000 0 -0.5 156 156
GRIN2B -0.2 0.23 -10000 0 -0.47 156 156
ErbB4/ErbB2/betacellulin -0.007 0.067 -10000 0 -0.5 6 6
STAT1 0.002 0.023 0.32 2 -10000 0 2
HBEGF -0.005 0.063 -10000 0 -0.86 2 2
PRLR -0.025 0.15 -10000 0 -0.86 11 11
E4ICDs/ETO2 -0.081 0.2 -10000 0 -0.55 55 55
axon guidance -0.055 0.094 -10000 0 -10000 0 0
NEDD4 -0.005 0.063 -10000 0 -0.86 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.019 0.12 -10000 0 -0.67 11 11
CBFA2T3 -0.13 0.31 -10000 0 -0.86 55 55
ErbB4/ErbB2/HBEGF -0.011 0.073 -10000 0 -0.5 8 8
MAPK3 -0.18 0.21 -10000 0 -0.54 1 1
STAT1 (dimer) 0.002 0.023 -10000 0 -10000 0 0
MAPK1 -0.18 0.21 -10000 0 -0.54 1 1
JAK2 -0.002 0.045 -10000 0 -0.86 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.22 0.26 -10000 0 -0.51 159 159
NRG1 -0.28 0.34 -10000 0 -0.68 156 156
NRG3 -0.13 0.32 0.32 6 -0.86 59 65
NRG2 0.066 0.13 0.32 78 -10000 0 78
NRG4 -0.12 0.3 0.32 1 -0.86 53 54
heart development -0.055 0.094 -10000 0 -10000 0 0
neural crest cell migration -0.22 0.25 -10000 0 -0.5 159 159
ERBB2 0.007 0.088 -10000 0 -0.68 6 6
WWOX/E4ICDs 0.001 0.016 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.087 0.2 -10000 0 -0.53 61 61
apoptosis 0.056 0.16 0.42 55 -10000 0 55
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.051 0.099 0.29 3 -10000 0 3
ErbB4/ErbB2/epiregulin 0.011 0.092 -10000 0 -0.5 6 6
ErbB4/ErbB4/betacellulin/betacellulin 0.003 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.017 0.092 -10000 0 -0.47 14 14
MDM2 0.033 0.016 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.22 0.25 -10000 0 -0.51 156 156
STAT5A -0.045 0.089 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.22 0.26 -10000 0 -0.51 162 162
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.004 0.039 -10000 0 -0.52 2 2
STAT5A (dimer) -0.06 0.1 -10000 0 -0.51 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.063 0.073 -10000 0 -10000 0 0
LRIG1 0 0 -10000 0 -10000 0 0
EREG 0.027 0.089 0.32 32 -10000 0 32
BTC 0.003 0.028 0.32 3 -10000 0 3
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.06 0.091 -10000 0 -10000 0 0
ERBB4 0.001 0.02 -10000 0 -10000 0 0
STAT5B 0 0 -10000 0 -10000 0 0
YAP1 0.001 0.006 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.079 0.18 -10000 0 -0.5 59 59
glial cell differentiation 0.003 0.039 0.51 2 -10000 0 2
WWOX 0 0 -10000 0 -10000 0 0
cell proliferation -0.19 0.26 -10000 0 -0.49 157 157
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.006 0.094 -10000 0 -0.59 8 8
ARNO/beta Arrestin1-2 -0.059 0.15 -10000 0 -0.44 49 49
EGFR -0.023 0.14 -10000 0 -0.86 10 10
EPHA2 -0.053 0.21 -10000 0 -0.86 23 23
USP6 -0.002 0.045 -10000 0 -0.86 1 1
IQSEC1 0 0 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.032 0.15 -10000 0 -0.66 10 10
ARRB2 0 0 -10000 0 -10000 0 0
mol:GTP 0.005 0.047 -10000 0 -0.21 10 10
ARRB1 -0.012 0.099 -10000 0 -0.86 5 5
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0 0 -10000 0 -10000 0 0
EGF 0.075 0.13 0.32 88 -10000 0 88
somatostatin receptor activity 0 0 -10000 0 -0.001 89 89
ARAP2 -0.028 0.15 -10000 0 -0.86 12 12
mol:GDP -0.074 0.13 -10000 0 -0.33 53 53
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 59 59
ITGA2B 0.007 0.046 0.32 8 -10000 0 8
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.037 0.14 -10000 0 -0.53 26 26
ADAP1 -0.007 0.14 0.32 13 -0.86 8 21
KIF13B 0 0 -10000 0 -10000 0 0
HGF/MET -0.36 0.34 -10000 0 -0.67 201 201
PXN 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.076 0.14 -10000 0 -0.29 88 88
EGFR/EGFR/EGF/EGF/ARFGEP100 0.031 0.13 -10000 0 -0.57 10 10
ADRB2 -0.1 0.28 -10000 0 -0.86 44 44
receptor agonist activity 0 0 -10000 0 0 92 92
actin filament binding 0 0 -10000 0 -0.001 90 90
SRC 0.004 0.036 0.32 5 -10000 0 5
ITGB3 -0.07 0.23 -10000 0 -0.86 30 30
GNAQ -0.002 0.045 -10000 0 -0.86 1 1
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 79 79
ARF6/GDP -0.023 0.12 -10000 0 -0.39 21 21
ARF6/GDP/GULP/ACAP1 -0.1 0.2 0.23 1 -0.51 59 60
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.039 0.15 -10000 0 -0.53 30 30
ACAP1 -0.021 0.14 0.32 3 -0.86 10 13
ACAP2 0 0 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0 0 -10000 0 -10000 0 0
EFNA1 -0.007 0.077 -10000 0 -0.86 3 3
HGF -0.46 0.43 0.32 1 -0.86 201 202
CYTH3 0.009 0.011 -10000 0 -10000 0 0
CYTH2 0.005 0.002 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 86 86
endosomal lumen acidification 0 0 -10000 0 0 82 82
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.035 0.28 0.32 51 -0.86 34 85
GNAQ/ARNO -0.001 0.026 -10000 0 -0.5 1 1
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 24 24
MET -0.001 0.048 0.32 1 -0.86 1 2
GNA14 -0.15 0.32 -10000 0 -0.86 63 63
GNA15 -0.001 0.05 0.32 2 -0.86 1 3
GIT1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 84 84
GNA11 -0.028 0.15 -10000 0 -0.86 12 12
LHCGR 0 0 -10000 0 -10000 0 0
AGTR1 -0.077 0.24 -10000 0 -0.86 33 33
desensitization of G-protein coupled receptor protein signaling pathway 0 0 -10000 0 -10000 0 0
IPCEF1/ARNO 0.028 0.11 -10000 0 -0.46 10 10
alphaIIb/beta3 Integrin -0.049 0.19 -10000 0 -0.67 30 30
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.002 0.023 0.32 2 -9999 0 2
Aurora C/Aurora B/INCENP 0.1 0.097 0.37 2 -9999 0 2
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0 0 -10000 0 -9999 0 0
AURKB 0.17 0.16 0.32 196 -9999 0 196
AURKC 0.001 0.016 0.32 1 -9999 0 1
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -10000 0 -10000 0 0
SPHK1 0.044 0.16 0.32 65 -0.86 5 70
GNAI2 0 0 -10000 0 -10000 0 0
mol:S1P 0.018 0.069 0.22 7 -0.38 5 12
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
mol:Sphinganine-1-P 0.033 0.098 -10000 0 -0.67 5 5
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 -0.008 0.06 -10000 0 -0.59 3 3
GNAI3 0 0 -10000 0 -10000 0 0
G12/G13 0 0 -10000 0 -10000 0 0
S1PR3 -0.025 0.15 0.32 1 -0.86 11 12
S1PR2 -0.007 0.077 -10000 0 -0.86 3 3
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.011 0.052 -10000 0 -0.33 5 5
S1PR5 -0.011 0.1 0.32 1 -0.86 5 6
S1PR4 -0.001 0.048 0.32 1 -0.86 1 2
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
S1P/S1P5/G12 -0.01 0.075 -10000 0 -0.58 5 5
S1P/S1P3/Gq -0.065 0.16 -10000 0 -0.37 65 65
S1P/S1P4/Gi -0.12 0.18 -10000 0 -0.32 139 139
GNAQ -0.002 0.045 -10000 0 -0.86 1 1
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
GNA14 -0.15 0.32 -10000 0 -0.86 63 63
GNA15 -0.001 0.05 0.32 2 -0.86 1 3
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.028 0.15 -10000 0 -0.86 12 12
ABCC1 0.007 0.046 0.32 8 -10000 0 8
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0 0 -10000 0 -10000 0 0
LAT2 -0.037 0.1 -10000 0 -0.49 6 6
AP1 -0.24 0.24 -10000 0 -0.46 179 179
mol:PIP3 -0.019 0.19 -10000 0 -0.45 51 51
IKBKB -0.004 0.12 -10000 0 -0.34 23 23
AKT1 -0.053 0.14 -10000 0 -0.5 5 5
IKBKG -0.004 0.12 -10000 0 -0.34 23 23
MS4A2 0.005 0.044 0.32 7 -10000 0 7
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
MAP3K1 0.003 0.14 -10000 0 -0.62 9 9
mol:Ca2+ -0.007 0.14 -10000 0 -0.34 51 51
LYN 0 0 -10000 0 -10000 0 0
CBLB -0.035 0.099 -10000 0 -0.44 6 6
SHC1 0 0 -10000 0 -10000 0 0
RasGAP/p62DOK -0.054 0.16 -10000 0 -0.55 36 36
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.059 0.16 -10000 0 -0.48 47 47
PTPN13 -0.13 0.25 -10000 0 -0.51 98 98
PTPN11 0 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.017 0.12 -10000 0 -0.36 5 5
SYK -0.007 0.078 -10000 0 -0.87 3 3
GRB2 0 0 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.072 0.17 -10000 0 -0.47 52 52
LAT -0.034 0.099 -10000 0 -0.47 5 5
PAK2 -0.006 0.15 -10000 0 -0.54 17 17
NFATC2 -0.16 0.3 -10000 0 -0.77 67 67
HRAS -0.016 0.17 -10000 0 -0.59 18 18
GAB2 0 0 -10000 0 -10000 0 0
PLA2G1B 0.05 0.032 -10000 0 -10000 0 0
Fc epsilon R1 -0.07 0.2 -10000 0 -0.59 47 47
Antigen/IgE/Fc epsilon R1 -0.065 0.18 -10000 0 -0.55 47 47
mol:GDP -0.025 0.18 -10000 0 -0.65 19 19
JUN -0.014 0.11 -10000 0 -0.86 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
FOS -0.42 0.43 -10000 0 -0.86 179 179
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.037 0.11 -10000 0 -0.33 21 21
CHUK -0.004 0.12 -10000 0 -0.34 23 23
KLRG1 -0.039 0.11 -10000 0 -0.47 9 9
VAV1 -0.057 0.16 -10000 0 -0.62 18 18
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.035 0.099 -10000 0 -0.47 5 5
negative regulation of mast cell degranulation -0.035 0.1 -10000 0 -0.53 5 5
BTK -0.05 0.16 -10000 0 -0.83 10 10
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.24 0.3 -10000 0 -0.47 192 192
GAB2/PI3K/SHP2 -0.058 0.15 -10000 0 -0.44 46 46
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.039 0.11 -10000 0 -0.31 48 48
RAF1 0.04 0.037 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.31 0.33 -10000 0 -0.6 195 195
FCER1G -0.006 0.078 0.31 1 -0.86 3 4
FCER1A -0.1 0.28 0.32 1 -0.87 44 45
Antigen/IgE/Fc epsilon R1/Fyn -0.06 0.17 -10000 0 -0.51 47 47
MAPK3 0.045 0.031 -10000 0 -10000 0 0
MAPK1 0.045 0.031 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.02 0.14 -10000 0 -0.57 20 20
DUSP1 -0.081 0.25 -10000 0 -0.86 35 35
NF-kappa-B/RelA -0.027 0.059 -10000 0 -0.24 1 1
actin cytoskeleton reorganization -0.007 0.11 -10000 0 -0.48 4 4
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.054 0.15 -10000 0 -0.61 19 19
FER -0.035 0.099 -10000 0 -0.44 6 6
RELA 0 0 -10000 0 -10000 0 0
ITK -0.037 0.13 -10000 0 -0.58 20 20
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.021 0.18 -10000 0 -0.64 18 18
cytokine secretion -0.019 0.042 -10000 0 -10000 0 0
SPHK1 -0.027 0.13 -10000 0 -0.56 9 9
PTK2 -0.008 0.11 -10000 0 -0.51 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.075 0.18 -10000 0 -0.49 52 52
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.016 0.18 -10000 0 -0.44 52 52
MAP2K2 0.043 0.032 -10000 0 -10000 0 0
MAP2K1 0.043 0.032 -10000 0 -10000 0 0
MAP2K7 0 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.038 0.11 -10000 0 -0.52 6 6
MAP2K4 0.013 0.009 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.33 0.35 -10000 0 -0.63 195 195
mol:Choline -0.058 0.16 -10000 0 -0.47 47 47
SHC/Grb2/SOS1 -0.031 0.091 -10000 0 -0.58 2 2
FYN 0 0 -10000 0 -10000 0 0
DOK1 0 0 -10000 0 -10000 0 0
PXN -0.001 0.1 -10000 0 -0.5 3 3
HCLS1 -0.037 0.11 -10000 0 -0.52 7 7
PRKCB -0.022 0.17 -10000 0 -0.38 59 59
FCGR2B -0.42 0.43 0.32 2 -0.86 184 186
IGHE 0 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.036 0.1 -10000 0 -0.54 5 5
LCP2 -0.014 0.11 -10000 0 -0.86 6 6
PLA2G4A -0.079 0.19 -10000 0 -0.57 37 37
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
mol:Phosphatidic acid -0.058 0.16 -10000 0 -0.47 47 47
IKK complex 0.013 0.094 -10000 0 -0.26 17 17
WIPF1 0 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.016 0.1 -10000 0 -0.67 9 9
alphaV beta3 Integrin -0.077 0.22 -10000 0 -0.65 46 46
PTK2 -0.015 0.2 -10000 0 -0.57 34 34
IGF1R -0.015 0.13 0.32 4 -0.86 8 12
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.004 0.036 0.32 5 -10000 0 5
SRC 0.004 0.036 0.32 5 -10000 0 5
CDKN1B -0.048 0.14 -10000 0 -0.66 13 13
VEGFA 0 0 -10000 0 -10000 0 0
ILK -0.048 0.14 -10000 0 -0.66 13 13
ROCK1 0 0 -10000 0 -10000 0 0
AKT1 -0.044 0.13 -10000 0 -0.62 13 13
PTK2B -0.052 0.17 -10000 0 -0.56 34 34
alphaV/beta3 Integrin/JAM-A -0.085 0.21 -10000 0 -0.56 58 58
CBL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.11 0.24 -10000 0 -0.62 64 64
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.22 0.27 -10000 0 -0.54 150 150
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.039 0.11 -10000 0 -0.57 5 5
alphaV/beta3 Integrin/Syndecan-1 -0.053 0.17 -10000 0 -0.58 34 34
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.25 0.31 -10000 0 -0.55 168 168
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
alphaV/beta3 Integrin/Osteopontin -0.019 0.26 0.39 1 -0.6 51 52
RPS6KB1 -0.23 0.28 -10000 0 -0.52 161 161
TLN1 0 0 -10000 0 -10000 0 0
MAPK3 -0.16 0.28 -10000 0 -0.86 46 46
GPR124 -0.007 0.077 -10000 0 -0.86 3 3
MAPK1 -0.16 0.28 -10000 0 -0.86 46 46
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
alphaV/beta3 Integrin/Tumstatin -0.063 0.22 -10000 0 -0.66 42 42
cell adhesion -0.091 0.21 -10000 0 -0.52 65 65
ANGPTL3 -0.09 0.26 -10000 0 -0.86 39 39
VEGFR2 homodimer/VEGFA homodimer/Src -0.011 0.093 -10000 0 -0.58 9 9
IGF-1R heterotetramer -0.015 0.13 0.32 4 -0.86 8 12
Rac1/GDP 0 0 -10000 0 -10000 0 0
TGFBR2 0 0 -10000 0 -10000 0 0
ITGB3 -0.07 0.23 -10000 0 -0.86 30 30
IGF1 -0.34 0.42 -10000 0 -0.86 145 145
RAC1 0 0 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.051 0.16 -10000 0 -0.58 33 33
apoptosis 0.001 0.016 0.32 1 -10000 0 1
CD47 -0.002 0.045 -10000 0 -0.86 1 1
alphaV/beta3 Integrin/CD47 -0.048 0.16 -10000 0 -0.58 31 31
VCL 0.001 0.016 0.32 1 -10000 0 1
alphaV/beta3 Integrin/Del1 -0.003 0.19 0.39 1 -0.58 30 31
CSF1 -0.008 0.092 0.32 2 -0.86 4 6
PIK3C2A -0.048 0.14 -10000 0 -0.66 13 13
PI4 Kinase/Pyk2 -0.081 0.2 -10000 0 -0.94 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.055 0.18 -10000 0 -0.6 34 34
FAK1/Vinculin -0.002 0.16 -10000 0 -0.45 30 30
alphaV beta3/Integrin/ppsTEM5 -0.051 0.17 -10000 0 -0.58 33 33
RHOA 0 0 -10000 0 -10000 0 0
VTN -0.03 0.16 -10000 0 -0.86 13 13
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 -0.047 0.21 0.32 5 -0.86 22 27
F11R -0.021 0.16 -10000 0 -0.67 22 22
alphaV/beta3 Integrin/Lactadherin -0.044 0.16 -10000 0 -0.58 30 30
alphaV/beta3 Integrin/TGFBR2 -0.046 0.16 -10000 0 -0.58 30 30
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.004 0.058 -10000 0 -0.53 4 4
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.043 0.15 -10000 0 -0.54 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.002 0.045 -10000 0 -0.86 1 1
alphaV/beta3 Integrin/Pyk2 -0.052 0.17 -10000 0 -0.57 34 34
SDC1 -0.009 0.089 -10000 0 -0.86 4 4
VAV3 -0.003 0.064 -10000 0 -0.5 5 5
PTPN11 0 0 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
FAK1/Paxillin -0.002 0.16 -10000 0 -0.45 30 30
cell migration 0.009 0.15 -10000 0 -0.49 11 11
ITGAV 0.001 0.016 0.32 1 -10000 0 1
PI3K -0.081 0.21 -10000 0 -0.52 58 58
SPP1 0.053 0.28 0.32 127 -0.86 24 151
KDR -0.021 0.13 -10000 0 -0.86 9 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.001 0.016 0.32 1 -10000 0 1
COL4A3 -0.026 0.2 0.32 19 -0.86 18 37
angiogenesis -0.13 0.3 -10000 0 -0.79 53 53
Rac1/GTP -0.002 0.058 -10000 0 -0.45 5 5
EDIL3 0.069 0.13 0.32 81 -10000 0 81
cell proliferation -0.046 0.16 -10000 0 -0.58 30 30
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.055 0.16 -10000 0 -0.6 27 27
FYN -0.026 0.26 0.34 4 -0.77 34 38
LAT/GRAP2/SLP76 -0.044 0.2 0.36 3 -0.63 31 34
IKBKB 0 0 -10000 0 -10000 0 0
AKT1 0.009 0.16 0.35 4 -0.48 30 34
B2M 0 0.002 -10000 0 -10000 0 0
IKBKG -0.014 0.04 -10000 0 -0.17 11 11
MAP3K8 -0.005 0.063 -10000 0 -0.86 2 2
mol:Ca2+ -0.041 0.06 -10000 0 -0.13 112 112
integrin-mediated signaling pathway -0.006 0.06 -10000 0 -0.58 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.01 0.24 0.39 4 -0.68 35 39
TRPV6 -0.26 0.4 -10000 0 -0.87 113 113
CD28 -0.001 0.048 0.32 1 -0.86 1 2
SHC1 -0.017 0.24 0.36 4 -0.75 31 35
receptor internalization -0.022 0.24 0.37 4 -0.66 37 41
PRF1 -0.022 0.26 -10000 0 -0.98 20 20
KRAS 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
COT/AKT1 0.014 0.13 0.32 4 -0.38 31 35
LAT -0.016 0.24 0.38 4 -0.75 31 35
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.014 0.17 0.32 16 -0.87 12 28
CD3E -0.034 0.17 0.33 1 -0.87 15 16
CD3G -0.022 0.16 0.32 7 -0.86 12 19
RASGRP2 -0.002 0.029 0.13 5 -0.19 3 8
RASGRP1 0.016 0.17 0.41 4 -0.48 31 35
HLA-A 0.001 0.003 -10000 0 -10000 0 0
RASSF5 -0.009 0.089 -10000 0 -0.86 4 4
RAP1A/GTP/RAPL -0.006 0.061 -10000 0 -0.59 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.029 0.057 0.22 6 -0.12 22 28
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.072 -10000 0 -0.27 25 25
PRKCA -0.013 0.093 0.28 2 -0.28 28 30
GRAP2 -0.016 0.14 0.32 6 -0.86 9 15
mol:IP3 0.027 0.2 0.28 95 -0.46 29 124
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.028 0.24 0.31 4 -0.55 45 49
ORAI1 0.12 0.18 0.39 113 -10000 0 113
CSK -0.02 0.25 0.36 4 -0.77 31 35
B7 family/CD28 -0.087 0.24 0.5 1 -0.71 40 41
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.036 0.29 0.38 4 -0.91 31 35
PTPN6 -0.024 0.25 0.33 4 -0.78 31 35
VAV1 -0.029 0.28 0.36 4 -0.8 35 39
Monovalent TCR/CD3 -0.037 0.18 0.22 6 -0.56 29 35
CBL 0 0 -10000 0 -10000 0 0
LCK -0.034 0.29 0.33 4 -0.84 34 38
PAG1 -0.02 0.25 0.36 4 -0.78 31 35
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.078 0.28 0.36 4 -0.91 31 35
CD80 -0.032 0.16 0.32 1 -0.86 14 15
CD86 -0.023 0.14 -10000 0 -0.86 10 10
PDK1/CARD11/BCL10/MALT1 -0.03 0.089 -10000 0 -0.32 27 27
HRAS 0.002 0.023 0.32 2 -10000 0 2
GO:0035030 -0.068 0.19 0.42 1 -0.57 40 41
CD8A -0.05 0.21 0.32 4 -0.87 23 27
CD8B -0.036 0.21 0.32 12 -0.87 20 32
PTPRC -0.067 0.23 0.32 1 -0.86 29 30
PDK1/PKC theta 0.007 0.2 0.39 4 -0.6 31 35
CSK/PAG1 -0.015 0.24 0.35 4 -0.75 31 35
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0 0 -10000 0 -10000 0 0
GRAP2/SLP76 -0.057 0.23 0.64 1 -0.7 35 36
STIM1 0.063 0.094 -10000 0 -10000 0 0
RAS family/GTP 0.032 0.072 0.29 4 -0.18 21 25
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.028 0.27 0.37 4 -0.72 37 41
mol:DAG -0.015 0.14 0.16 5 -0.41 30 35
RAP1A/GDP 0.013 0.026 0.13 4 -10000 0 4
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.004 0.066 0.32 1 -0.87 2 3
cytotoxic T cell degranulation -0.018 0.24 -10000 0 -0.87 22 22
RAP1A/GTP -0.002 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.001 0.19 0.38 4 -0.54 35 39
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.015 0.24 0.3 89 -0.63 29 118
NRAS 0 0 -10000 0 -10000 0 0
ZAP70 -0.005 0.097 0.32 5 -0.86 4 9
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.045 0.2 0.35 3 -0.61 33 36
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 -0.002 0.045 -10000 0 -0.86 1 1
CD8 heterodimer -0.065 0.26 0.45 4 -0.82 34 38
CARD11 -0.019 0.14 0.32 5 -0.86 10 15
PRKCB -0.034 0.14 0.28 2 -0.41 40 42
PRKCE -0.014 0.095 0.25 3 -0.29 29 32
PRKCQ -0.006 0.23 0.4 4 -0.68 33 37
LCP2 -0.014 0.11 -10000 0 -0.86 6 6
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.014 0.14 0.34 4 -0.4 30 34
IKK complex 0.032 0.058 0.21 5 -0.13 21 26
RAS family/GDP -0.003 0.007 -10000 0 -10000 0 0
MAP3K14 0.022 0.1 0.28 4 -0.3 24 28
PDPK1 0.013 0.16 0.35 4 -0.45 30 34
TCR/CD3/MHC I/CD8/Fyn -0.046 0.32 0.39 4 -1 31 35
Coregulation of Androgen receptor activity

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
NRIP1 -0.002 0.046 -10000 0 -0.86 1 1
SVIL -0.004 0.063 -10000 0 -0.85 2 2
ZNF318 0.002 0.024 -10000 0 -10000 0 0
JMJD2C 0.012 0.033 0.12 31 -10000 0 31
T-DHT/AR/Ubc9 -0.18 0.28 -10000 0 -0.62 101 101
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0 0.002 -10000 0 -10000 0 0
PELP1 0.001 0.004 -10000 0 -10000 0 0
CTNNB1 0 0.007 -10000 0 -10000 0 0
AKT1 0.001 0.006 -10000 0 -10000 0 0
PTK2B 0.001 0.005 -10000 0 -10000 0 0
MED1 0.001 0.006 -10000 0 -10000 0 0
MAK 0.002 0.024 -10000 0 -10000 0 0
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 -0.018 0.12 -10000 0 -0.86 8 8
GSN 0.001 0.02 0.34 1 -10000 0 1
NCOA2 -0.11 0.29 -10000 0 -0.86 48 48
NCOA6 0.001 0.009 -10000 0 -10000 0 0
DNA-PK 0.003 0.023 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 0 0.007 -10000 0 -10000 0 0
cell proliferation -0.032 0.05 -10000 0 -10000 0 0
XRCC5 0.001 0.006 -10000 0 -10000 0 0
UBE3A 0 0.014 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.19 0.29 -10000 0 -0.63 107 107
FHL2 -0.19 0.4 -10000 0 -1.3 38 38
RANBP9 0.001 0.009 -10000 0 -10000 0 0
JMJD1A -0.013 0.055 -10000 0 -0.13 66 66
CDK6 -0.058 0.22 -10000 0 -0.86 25 25
TGFB1I1 0 0.009 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.2 0.3 -10000 0 -0.64 111 111
XRCC6 0.001 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.18 0.31 -10000 0 -0.63 108 108
CTDSP1 0.001 0.003 -10000 0 -10000 0 0
CTDSP2 0.002 0.015 -10000 0 -10000 0 0
BRCA1 0.001 0.019 0.32 1 -10000 0 1
TCF4 0.001 0.011 -10000 0 -10000 0 0
CDKN2A 0.22 0.15 0.32 254 -10000 0 254
SRF 0.003 0.037 -10000 0 -10000 0 0
NKX3-1 -0.24 0.45 -10000 0 -1.3 54 54
KLK3 -0.017 0.21 -10000 0 -1.6 6 6
TMF1 0 0.002 -10000 0 -10000 0 0
HNRNPA1 0.001 0.008 -10000 0 -10000 0 0
AOF2 0 0.01 -10000 0 -0.072 6 6
APPL1 0.017 0.014 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.18 0.28 -10000 0 -0.62 101 101
AR -0.25 0.39 -10000 0 -0.88 101 101
UBA3 0.001 0.003 -10000 0 -10000 0 0
PATZ1 0.001 0.008 -10000 0 -10000 0 0
PAWR 0 0.002 -10000 0 -10000 0 0
PRKDC 0.001 0.006 -10000 0 -10000 0 0
PA2G4 0.001 0.011 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.16 0.26 -10000 0 -0.58 101 101
RPS6KA3 -0.006 0.078 -10000 0 -0.86 3 3
T-DHT/AR/ARA70 -0.18 0.28 -10000 0 -0.62 101 101
LATS2 0.001 0.009 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.16 0.26 -10000 0 -0.58 101 101
Cyclin D3/CDK11 p58 0 0 -10000 0 -10000 0 0
VAV3 0.003 0.06 0.32 6 -0.86 1 7
KLK2 -0.048 0.13 -10000 0 -10000 0 0
CASP8 0 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.23 0.34 -10000 0 -0.69 120 120
TMPRSS2 -0.15 0.31 -10000 0 -0.92 35 35
CCND1 -0.032 0.16 0.32 1 -0.86 14 15
PIAS1 0 0.014 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.034 -10000 0 -0.083 54 54
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0 0.023 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.22 0.31 -10000 0 -0.65 118 118
CMTM2 0.002 0.023 0.32 2 -10000 0 2
SNURF -0.012 0.13 0.32 8 -0.86 8 16
ZMIZ1 -0.006 0.031 0.3 1 -10000 0 1
CCND3 0 0 -10000 0 -10000 0 0
TGIF1 0.001 0.008 -10000 0 -10000 0 0
FKBP4 0.001 0.009 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.021 0.083 -10000 0 -0.35 22 22
epithelial cell differentiation -0.03 0.12 -10000 0 -0.5 22 22
CYFIP2 -0.051 0.2 -10000 0 -0.86 22 22
ENAH 0.016 0.12 -10000 0 -0.51 7 7
EGFR -0.023 0.14 -10000 0 -0.86 10 10
EPHA2 -0.053 0.21 -10000 0 -0.86 23 23
MYO6 -0.031 0.13 -10000 0 -0.52 22 22
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.034 0.14 -10000 0 -0.58 22 22
AQP5 -0.016 0.1 -10000 0 -10000 0 0
CTNND1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.028 0.11 -10000 0 -0.47 22 22
regulation of calcium-dependent cell-cell adhesion -0.017 0.13 -10000 0 -0.46 24 24
EGF 0.075 0.13 0.32 88 -10000 0 88
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.074 0.2 -10000 0 -0.68 30 30
cortical microtubule organization -0.03 0.12 -10000 0 -0.5 22 22
GO:0000145 0.003 0.11 -10000 0 -0.44 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.03 0.12 -10000 0 -0.5 22 22
MLLT4 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.051 0.15 -10000 0 -0.78 7 7
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.037 0.14 -10000 0 -0.53 26 26
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.027 0.1 -10000 0 -0.44 22 22
PVRL2 0 0 -10000 0 -10000 0 0
ZYX -0.028 0.11 -10000 0 -0.48 22 22
ARF6/GTP -0.034 0.12 -10000 0 -0.49 26 26
CDH1 -0.051 0.2 -10000 0 -0.86 22 22
EGFR/EGFR/EGF/EGF -0.013 0.16 -10000 0 -0.52 28 28
RhoA/GDP -0.028 0.11 -10000 0 -0.47 22 22
actin cytoskeleton organization -0.029 0.12 -10000 0 -0.48 22 22
IGF-1R heterotetramer -0.015 0.13 0.32 4 -0.86 8 12
GIT1 0 0 -10000 0 -10000 0 0
IGF1R -0.015 0.13 0.32 4 -0.86 8 12
IGF1 -0.34 0.42 -10000 0 -0.86 145 145
DIAPH1 -0.05 0.18 -10000 0 -0.74 23 23
Wnt receptor signaling pathway 0.03 0.12 0.5 22 -10000 0 22
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.051 0.15 -10000 0 -0.78 7 7
CTNNA1 0 0 -10000 0 -10000 0 0
VCL -0.03 0.12 -10000 0 -0.5 22 22
EFNA1 -0.007 0.077 -10000 0 -0.86 3 3
LPP -0.028 0.11 -10000 0 -0.45 23 23
Ephrin A1/EPHA2 -0.059 0.18 -10000 0 -0.54 41 41
SEC6/SEC8 -0.025 0.099 -10000 0 -10000 0 0
MGAT3 -0.018 0.13 -10000 0 -0.47 24 24
HGF/MET -0.28 0.27 -10000 0 -0.5 206 206
HGF -0.46 0.43 0.32 1 -0.86 201 202
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.021 0.084 -10000 0 -0.36 22 22
actin cable formation 0.026 0.11 -10000 0 -0.4 12 12
KIAA1543 -0.035 0.13 -10000 0 -0.5 26 26
KIFC3 -0.028 0.11 -10000 0 -0.48 22 22
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.028 0.11 -10000 0 -0.48 22 22
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.03 0.12 -10000 0 -0.5 22 22
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.028 0.11 -10000 0 -0.48 22 22
PIP5K1C -0.028 0.11 -10000 0 -0.48 22 22
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.044 0.13 -10000 0 -0.64 7 7
adherens junction assembly 0.012 0.14 -10000 0 -0.6 8 8
IGF-1R heterotetramer/IGF1 -0.22 0.25 -10000 0 -0.48 167 167
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.001 0.048 0.32 1 -0.86 1 2
PLEKHA7 -0.032 0.12 -10000 0 -0.48 25 25
mol:GTP -0.037 0.13 -10000 0 -0.53 26 26
establishment of epithelial cell apical/basal polarity -0.024 0.094 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.021 0.083 -10000 0 -0.35 22 22
regulation of cell-cell adhesion -0.029 0.12 -10000 0 -0.48 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.021 0.084 -10000 0 -0.36 22 22
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.061 0.17 -10000 0 -0.51 44 44
TRAF2/ASK1 -0.068 0.19 -10000 0 -0.59 43 43
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 -0.054 0.099 -10000 0 -0.3 25 25
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.083 0.18 -10000 0 -0.55 45 45
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.11 0.29 -10000 0 -0.86 48 48
TXN 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A -0.014 0.11 -10000 0 -0.86 6 6
GADD45B -0.13 0.31 -10000 0 -0.86 56 56
MAP3K1 0 0 -10000 0 -10000 0 0
MAP3K6 0.001 0.016 0.32 1 -10000 0 1
MAP3K7 0 0 -10000 0 -10000 0 0
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.077 0.21 -10000 0 -0.67 43 43
TAK1/TAB family -0.003 0.017 -10000 0 -0.22 1 1
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.048 0.066 -10000 0 -10000 0 0
TRAF6 -0.001 0.025 -10000 0 -0.47 1 1
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.42 0.43 -10000 0 -0.86 181 181
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.29 0.29 -10000 0 -0.59 181 181
MAPK11 0.012 0.06 0.32 14 -10000 0 14
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.32 0.32 -10000 0 -0.6 200 200
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 -0.003 0.034 -10000 0 -0.47 2 2
TAOK2 0 0 -10000 0 -10000 0 0
TAOK3 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.1 0.28 -10000 0 -0.86 43 43
MAP3K10 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.067 0.18 -10000 0 -0.58 43 43
GADD45/MTK1/MTK1 -0.15 0.27 -10000 0 -0.59 93 93
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.007 0.046 0.32 8 -10000 0 8
alphaV beta3 Integrin -0.053 0.18 -10000 0 -0.67 30 30
PTK2 -0.094 0.24 -10000 0 -0.66 49 49
positive regulation of JNK cascade -0.051 0.12 -10000 0 -0.36 51 51
CDC42/GDP -0.067 0.17 -10000 0 -0.5 49 49
Rac1/GDP -0.028 0.18 -10000 0 -0.49 49 49
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CTNNB1 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.064 0.16 -10000 0 -0.45 51 51
nectin-3/I-afadin -0.088 0.23 -10000 0 -0.67 49 49
RAPGEF1 -0.038 0.21 -10000 0 -0.56 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.055 0.24 -10000 0 -0.66 49 49
PDGFB-D/PDGFRB 0.007 0.046 0.32 8 -10000 0 8
TLN1 -0.035 0.099 -10000 0 -0.73 2 2
Rap1/GTP -0.052 0.13 -10000 0 -0.38 49 49
IQGAP1 0 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.088 0.23 -10000 0 -0.67 49 49
PVR 0 0 -10000 0 -10000 0 0
Necl-5(dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.047 0.23 -10000 0 -0.63 49 49
MLLT4 0 0 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
PI3K -0.066 0.18 -10000 0 -0.52 50 50
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.001 0.011 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.052 0.13 -10000 0 -0.38 49 49
PVRL1 0.001 0.016 0.32 1 -10000 0 1
PVRL3 -0.11 0.29 -10000 0 -0.86 49 49
PVRL2 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
CDH1 -0.051 0.2 -10000 0 -0.86 22 22
CLDN1 -0.012 0.099 -10000 0 -0.86 5 5
JAM-A/CLDN1 -0.077 0.19 -10000 0 -0.54 53 53
SRC -0.1 0.26 -10000 0 -0.76 49 49
ITGB3 -0.07 0.23 -10000 0 -0.86 30 30
nectin-1(dimer)/I-afadin/I-afadin 0.001 0.011 -10000 0 -10000 0 0
FARP2 -0.053 0.23 -10000 0 -0.62 51 51
RAC1 0 0 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.077 0.2 -10000 0 -0.58 49 49
nectin-1/I-afadin 0.001 0.011 -10000 0 -10000 0 0
nectin-2/I-afadin 0 0 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.076 0.2 -10000 0 -0.58 49 49
CDC42/GTP/IQGAP1/filamentous actin 0 0 -10000 0 -10000 0 0
F11R 0 0 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.051 0.12 -10000 0 -0.36 51 51
alphaV/beta3 Integrin/Talin -0.069 0.18 -10000 0 -0.63 30 30
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
PIP5K1C -0.039 0.11 -10000 0 -0.29 50 50
VAV2 -0.05 0.23 -10000 0 -0.62 49 49
RAP1/GDP -0.063 0.16 -10000 0 -0.46 49 49
ITGAV 0.001 0.016 0.32 1 -10000 0 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.077 0.2 -10000 0 -0.58 49 49
nectin-3(dimer)/I-afadin/I-afadin -0.088 0.23 -10000 0 -0.67 49 49
Rac1/GTP -0.064 0.16 -10000 0 -0.46 49 49
PTPRM -0.044 0.12 -10000 0 -0.33 50 50
E-cadherin/beta catenin/alpha catenin -0.028 0.11 -10000 0 -0.48 22 22
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.045 0.2 0.67 33 -10000 0 33
KIRREL -0.074 0.25 0.32 2 -0.86 33 35
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.045 0.2 -10000 0 -0.67 33 33
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.032 0.16 -10000 0 -0.52 33 33
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.026 0.12 -10000 0 -0.4 32 32
FYN -0.039 0.14 -10000 0 -0.49 33 33
mol:Ca2+ -0.032 0.16 -10000 0 -0.51 33 33
mol:DAG -0.032 0.16 -10000 0 -0.52 33 33
NPHS2 0 0.043 0.31 5 -10000 0 5
mol:IP3 -0.032 0.16 -10000 0 -0.52 33 33
regulation of endocytosis -0.028 0.14 -10000 0 -0.46 33 33
Nephrin/NEPH1/podocin/Cholesterol -0.033 0.16 -10000 0 -0.52 33 33
establishment of cell polarity -0.045 0.2 -10000 0 -0.67 33 33
Nephrin/NEPH1/podocin/NCK1-2 -0.029 0.15 -10000 0 -0.49 33 33
Nephrin/NEPH1/beta Arrestin2 -0.028 0.14 -10000 0 -0.46 33 33
NPHS1 0.017 0.083 0.32 25 -10000 0 25
Nephrin/NEPH1/podocin -0.03 0.15 -10000 0 -0.49 33 33
TJP1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
NCK2 -0.001 0.048 0.32 1 -0.86 1 2
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.032 0.16 -10000 0 -0.52 33 33
CD2AP 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.032 0.16 -10000 0 -0.52 33 33
GRB2 0 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.018 0.16 -10000 0 -0.48 33 33
cytoskeleton organization -0.035 0.15 -10000 0 -0.5 33 33
Nephrin/NEPH1 -0.033 0.16 -10000 0 -0.51 33 33
Nephrin/NEPH1/ZO-1 -0.037 0.17 -10000 0 -0.56 33 33
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.002 0.045 -10000 0 -0.86 1 1
PLK4 0.053 0.12 0.32 62 -10000 0 62
regulation of centriole replication 0.039 0.064 -10000 0 -0.67 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.011 0.094 -10000 0 -0.58 8 8
HDAC1 0.007 0.017 -10000 0 -10000 0 0
AES 0.003 0.008 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.24 0.39 -10000 0 -0.86 104 104
LRP6/FZD1 -0.014 0.098 -10000 0 -0.67 8 8
TLE1 -0.001 0.045 -10000 0 -0.86 1 1
AP1 -0.19 0.24 -10000 0 -0.43 141 141
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.002 0.045 -10000 0 -0.86 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.035 0.1 -10000 0 -0.39 9 9
NICD/RBPSUH -0.002 0.039 -10000 0 -0.75 1 1
WIF1 0.031 0.095 0.32 37 -10000 0 37
NOTCH1 -0.002 0.041 -10000 0 -0.8 1 1
PSENEN 0 0 -10000 0 -10000 0 0
KREMEN2 0.034 0.098 0.32 40 -10000 0 40
DKK1 0.11 0.15 0.32 126 -10000 0 126
beta catenin/beta TrCP1 -0.007 0.046 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.004 0.029 0.35 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.018 0.078 0.28 8 -0.48 3 11
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.42 0.43 -10000 0 -0.86 179 179
JUN -0.014 0.11 -10000 0 -0.86 6 6
MAP3K7 0.003 0.009 -10000 0 -10000 0 0
CTNNB1 0.006 0.058 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.047 0.09 0.39 4 -10000 0 4
HNF1A -0.006 0.089 -10000 0 -0.86 4 4
CTBP1 0.003 0.008 -10000 0 -10000 0 0
MYC -0.18 0.5 -10000 0 -1.6 43 43
NKD1 0.029 0.23 0.32 80 -0.86 17 97
FZD1 -0.018 0.13 0.32 1 -0.86 8 9
NOTCH1 precursor/Deltex homolog 1 -0.14 0.22 -10000 0 -0.5 105 105
apoptosis -0.19 0.24 -10000 0 -0.43 141 141
Delta 1/NOTCHprecursor -0.011 0.093 -10000 0 -0.58 8 8
DLL1 -0.017 0.13 0.32 2 -0.86 8 10
PPARD -0.011 0.03 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC 0.004 0.029 0.35 1 -10000 0 1
DVL1 -0.002 0.012 -10000 0 -10000 0 0
CSNK2A1 0 0.001 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.007 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.089 0.12 0.39 21 -10000 0 21
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0 0.001 -10000 0 -10000 0 0
NLK 0.007 0.019 -10000 0 -10000 0 0
CCND1 -0.066 0.3 -10000 0 -1.6 14 14
WNT1 0.003 0.033 0.32 4 -10000 0 4
Axin1/APC/beta catenin 0.024 0.04 0.33 1 -10000 0 1
DKK2 0.04 0.1 0.32 47 -10000 0 47
NOTCH1 precursor/DVL1 -0.003 0.036 -10000 0 -0.68 1 1
GSK3B 0.002 0.004 -10000 0 -10000 0 0
FRAT1 0 0.045 -10000 0 -0.86 1 1
NOTCH/Deltex homolog 1 -0.14 0.22 -10000 0 -0.5 105 105
PPP2R5D 0.002 0.084 0.36 17 -10000 0 17
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.01 0.1 -10000 0 -0.54 8 8
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.01 0.004 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.26 0.36 1 -0.52 103 104
SMAD6-7/SMURF1 -0.023 0.11 -10000 0 -0.58 15 15
NOG 0.004 0.036 0.32 5 -10000 0 5
SMAD9 -0.051 0.15 -10000 0 -0.65 18 18
SMAD4 -0.002 0.045 -10000 0 -0.86 1 1
SMAD5 -0.06 0.17 -10000 0 -0.38 70 70
BMP7/USAG1 0.065 0.12 0.44 13 -10000 0 13
SMAD5/SKI -0.086 0.14 -10000 0 -0.54 8 8
SMAD1 0.013 0.06 -10000 0 -0.59 2 2
BMP2 -0.008 0.092 0.32 2 -0.86 4 6
SMAD1/SMAD1/SMAD4 -0.023 0.088 -10000 0 -0.57 3 3
BMPR1A 0 0 -10000 0 -10000 0 0
BMPR1B -0.18 0.35 0.32 4 -0.86 77 81
BMPR1A-1B/BAMBI -0.16 0.29 -10000 0 -0.64 92 92
AHSG -0.13 0.31 -10000 0 -0.86 58 58
CER1 0.004 0.036 0.32 5 -10000 0 5
BMP2-4/CER1 0.013 0.085 -10000 0 -0.58 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.071 0.15 -10000 0 -0.59 8 8
BMP2-4 (homodimer) 0.011 0.092 -10000 0 -0.66 4 4
RGMB -0.004 0.065 0.32 1 -0.86 2 3
BMP6/BMPR2/BMPR1A-1B -0.11 0.23 -10000 0 -0.54 81 81
RGMA 0.028 0.09 0.32 33 -10000 0 33
SMURF1 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.077 0.16 -10000 0 -0.54 11 11
BMP2-4/USAG1 0.046 0.12 0.39 6 -0.57 4 10
SMAD6/SMURF1/SMAD5 -0.086 0.14 -10000 0 -0.57 7 7
SOSTDC1 0.055 0.12 0.32 65 -10000 0 65
BMP7/BMPR2/BMPR1A-1B -0.086 0.24 0.38 1 -0.53 77 78
SKI 0 0 -10000 0 -10000 0 0
BMP6 (homodimer) -0.009 0.1 0.32 3 -0.86 5 8
HFE2 -0.095 0.27 -10000 0 -0.86 41 41
ZFYVE16 0 0 -10000 0 -10000 0 0
MAP3K7 0 0 -10000 0 -10000 0 0
BMP2-4/CHRD 0 0.12 -10000 0 -0.57 11 11
SMAD5/SMAD5/SMAD4 -0.087 0.14 -10000 0 -0.55 8 8
MAPK1 0 0 -10000 0 -10000 0 0
TAK1/TAB family -0.074 0.12 -10000 0 -0.54 8 8
BMP7 (homodimer) 0.039 0.1 0.32 46 -10000 0 46
NUP214 0 0 -10000 0 -10000 0 0
BMP6/FETUA -0.11 0.25 -10000 0 -0.67 63 63
SMAD1/SKI -0.014 0.045 -10000 0 -0.55 2 2
SMAD6 -0.03 0.16 -10000 0 -0.86 13 13
CTDSP2 0 0 -10000 0 -10000 0 0
BMP2-4/FETUA -0.082 0.23 -10000 0 -0.58 62 62
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.06 0.28 0.32 30 -0.86 37 67
BMPR2 (homodimer) 0 0 -10000 0 -10000 0 0
GADD34/PP1CA 0.001 0.01 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.14 0.27 -10000 0 -0.67 77 77
CHRDL1 -0.14 0.33 0.32 10 -0.86 64 74
ENDOFIN/SMAD1 -0.014 0.045 -10000 0 -0.55 2 2
SMAD6-7/SMURF1/SMAD1 -0.028 0.098 -10000 0 -0.46 16 16
SMAD6/SMURF1 0 0 -10000 0 -10000 0 0
BAMBI -0.057 0.22 0.32 1 -0.86 25 26
SMURF2 0 0 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.087 0.24 -10000 0 -0.58 67 67
BMP2-4/GREM1 -0.033 0.2 0.39 1 -0.58 41 42
SMAD7 -0.005 0.063 -10000 0 -0.86 2 2
SMAD8A/SMAD8A/SMAD4 -0.053 0.14 -10000 0 -0.6 19 19
SMAD1/SMAD6 -0.014 0.045 -10000 0 -0.55 2 2
TAK1/SMAD6 0 0 -10000 0 -10000 0 0
BMP7 0.039 0.1 0.32 46 -10000 0 46
BMP6 -0.009 0.1 0.32 3 -0.86 5 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.061 0.13 -10000 0 -0.5 9 9
PPM1A 0 0 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.014 0.045 -10000 0 -0.55 2 2
SMAD7/SMURF1 -0.004 0.049 -10000 0 -0.67 2 2
CTDSPL 0 0 -10000 0 -10000 0 0
PPP1CA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0 0 -10000 0 -10000 0 0
PPP1R15A 0.001 0.016 0.32 1 -10000 0 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.095 0.18 -10000 0 -0.35 94 94
CHRD -0.015 0.12 0.32 1 -0.86 7 8
BMPR2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.078 0.16 -10000 0 -0.58 10 10
BMP4 0.026 0.086 0.32 30 -10000 0 30
FST -0.071 0.24 0.32 1 -0.86 31 32
BMP2-4/NOG 0.013 0.085 -10000 0 -0.58 4 4
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.081 0.22 0.36 1 -0.5 77 78
Visual signal transduction: Rods

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
mol:K + 0 0 -10000 0 -10000 0 0
GNAT1/GTP 0.003 0.024 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.01 0.042 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP -0.02 0.12 -10000 0 -0.59 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.004 0.036 0.32 5 -10000 0 5
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.12 0.23 -10000 0 -0.48 97 97
mol:Na + -0.11 0.21 -10000 0 -0.47 95 95
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.001 0.12 0.39 2 -0.58 11 13
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.11 0.22 -10000 0 -0.48 95 95
CNGB1 0.01 0.056 0.32 12 -10000 0 12
RDH5 -0.12 0.3 -10000 0 -0.86 51 51
SAG 0.001 0.016 0.32 1 -10000 0 1
mol:Ca2+ -0.11 0.2 -10000 0 -0.45 93 93
Na + (4 Units) -0.11 0.19 -10000 0 -0.44 93 93
RGS9 -0.012 0.16 0.32 16 -0.86 11 27
GNB1/GNGT1 0.03 0.075 -10000 0 -10000 0 0
GNAT1/GDP 0.002 0.1 0.35 3 -0.5 11 14
GUCY2D 0.039 0.1 0.32 46 -10000 0 46
GNGT1 0.043 0.11 0.32 51 -10000 0 51
GUCY2F 0 0 -10000 0 -10000 0 0
GNB5 0.001 0.016 0.32 1 -10000 0 1
mol:GMP (4 units) -0.008 0.12 -10000 0 -0.54 15 15
mol:11-cis-retinal -0.12 0.3 -10000 0 -0.86 51 51
mol:cGMP 0.003 0.08 -10000 0 -0.52 7 7
GNB1 0 0 -10000 0 -10000 0 0
Rhodopsin -0.084 0.23 -10000 0 -0.66 51 51
SLC24A1 0 0 -10000 0 -10000 0 0
CNGA1 -0.21 0.37 -10000 0 -0.86 90 90
Metarhodopsin II 0.009 0.039 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.014 0.1 0.37 1 -0.54 7 8
RGS9BP 0.011 0.058 0.32 13 -10000 0 13
Metarhodopsin II/Transducin 0.02 0.042 -10000 0 -10000 0 0
GCAP Family/Ca ++ -0.009 0.076 -10000 0 -0.55 7 7
PDE6A/B 0.013 0.077 -10000 0 -0.67 2 2
mol:Pi -0.001 0.12 0.39 2 -0.58 11 13
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.029 0.069 0.37 1 -10000 0 1
PDE6B 0.01 0.092 0.32 17 -0.86 2 19
PDE6A 0.01 0.056 0.32 12 -10000 0 12
PDE6G -0.032 0.16 -10000 0 -0.86 14 14
RHO 0.015 0.068 0.32 18 -10000 0 18
PDE6 -0.01 0.15 -10000 0 -0.52 24 24
GUCA1A 0.002 0.023 0.32 2 -10000 0 2
GC2/GCAP Family -0.009 0.076 -10000 0 -0.55 7 7
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B -0.016 0.12 -10000 0 -0.86 7 7
LPA4-mediated signaling events

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
ADCY4 0.015 0.032 -9999 0 -0.59 1 1
ADCY5 -0.091 0.23 -9999 0 -0.59 66 66
ADCY6 0.015 0.032 -9999 0 -0.59 1 1
ADCY7 0.015 0.032 -9999 0 -0.59 1 1
ADCY1 -0.21 0.3 -9999 0 -0.59 140 140
ADCY2 0.012 0.034 -9999 0 -0.59 1 1
ADCY3 0.016 0.032 -9999 0 -0.59 1 1
ADCY8 0.02 0.042 -9999 0 -0.59 1 1
PRKCE 0.007 0.036 -9999 0 -0.68 1 1
ADCY9 0.015 0.032 -9999 0 -0.59 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.035 0.089 -9999 0 -0.27 24 24
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ -0.039 0.18 -10000 0 -0.86 17 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.088 0.17 -10000 0 -0.42 45 45
IRAK/TOLLIP 0 0.008 -10000 0 -10000 0 0
IKBKB 0 0 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0 0.04 -10000 0 -0.67 1 1
IL1A 0.002 0.023 0.32 2 -10000 0 2
IL1B -0.1 0.27 -10000 0 -0.68 64 64
IRAK/TRAF6/p62/Atypical PKCs -0.02 0.1 -10000 0 -0.46 18 18
IL1R2 -0.001 0.048 0.32 1 -0.86 1 2
IL1R1 -0.007 0.077 -10000 0 -0.86 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.07 0.14 -10000 0 -0.68 9 9
TOLLIP 0 0 -10000 0 -10000 0 0
TICAM2 -0.002 0.045 -10000 0 -0.86 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS -0.005 0.029 -10000 0 -10000 0 0
JUN -0.003 0.14 -10000 0 -0.46 31 31
MAP3K7 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.15 0.27 -10000 0 -0.54 100 100
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.066 0.19 -10000 0 -0.57 44 44
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.062 0.18 -10000 0 -0.54 44 44
IL1 beta fragment/IL1R1/IL1RAP -0.16 0.28 -10000 0 -0.6 100 100
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.032 0.12 -10000 0 -0.47 27 27
IRAK1 0 0.01 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.083 0.22 -10000 0 -0.67 46 46
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
TRAF6 -0.002 0.045 -10000 0 -0.86 1 1
PI3K -0.005 0.071 -10000 0 -0.94 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.096 0.19 -10000 0 -0.45 45 45
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.16 0.28 -10000 0 -0.6 100 100
IL1 beta/IL1R2 -0.1 0.23 -10000 0 -0.6 64 64
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.025 -10000 0 -0.47 1 1
NF kappa B1 p50/RelA -0.13 0.24 -10000 0 -0.96 11 11
IRAK3 -0.02 0.13 0.32 1 -0.86 9 10
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.14 0.26 -10000 0 -0.53 101 101
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.044 0.13 -10000 0 -0.38 44 44
IL1 alpha/IL1R1/IL1RAP -0.072 0.21 -10000 0 -0.62 44 44
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.004 0.036 0.32 5 -10000 0 5
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.027 -10000 0 -0.5 1 1
IL1RAP -0.1 0.28 -10000 0 -0.86 44 44
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.12 0.21 -10000 0 -0.85 10 10
CASP1 -0.005 0.063 -10000 0 -0.86 2 2
IL1RN/IL1R2 -0.078 0.22 -10000 0 -0.68 43 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.15 0.27 -10000 0 -0.56 100 100
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.034 0.1 -10000 0 -0.68 3 3
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
IL1RN -0.1 0.28 -10000 0 -0.86 43 43
TRAF6/TAK1/TAB1/TAB2 -0.001 0.026 -10000 0 -0.49 1 1
MAP2K6 -0.007 0.081 -10000 0 -0.54 7 7
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.037 0.48 1 -0.39 1 2
RFC1 0.002 0.037 0.48 1 -0.39 1 2
PRKDC 0.002 0.037 0.48 1 -0.39 1 2
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.011 0.044 0.27 2 -10000 0 2
FASLG/FAS/FADD/FAF1 0.04 0.15 0.27 70 -0.39 14 84
MAP2K4 -0.012 0.14 -10000 0 -0.44 15 15
mol:ceramide -0.043 0.13 -10000 0 -0.52 16 16
GSN 0.002 0.037 0.48 1 -0.39 1 2
FASLG/FAS/FADD/FAF1/Caspase 8 0.019 0.14 0.32 3 -0.43 11 14
FAS -0.027 0.15 -10000 0 -0.86 12 12
BID 0.003 0.035 0.32 4 -10000 0 4
MAP3K1 0.003 0.085 -10000 0 -0.3 7 7
MAP3K7 0 0.002 -10000 0 -10000 0 0
RB1 0.002 0.037 0.48 1 -0.39 1 2
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.46 0.44 -10000 0 -0.79 215 215
ARHGDIB 0.002 0.037 0.48 1 -0.39 1 2
FADD 0.001 0.017 0.32 1 -10000 0 1
actin filament polymerization -0.002 0.037 0.38 1 -0.48 1 2
NFKB1 -0.032 0.082 -10000 0 -0.3 5 5
MAPK8 -0.053 0.21 -10000 0 -0.46 71 71
DFFA 0.002 0.037 0.48 1 -0.39 1 2
DNA fragmentation during apoptosis 0 0.047 0.3 3 -0.47 2 5
FAS/FADD/MET -0.02 0.11 -10000 0 -0.58 13 13
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.007 0.091 0.32 1 -0.86 4 5
FAF1 0.001 0.005 -10000 0 -10000 0 0
PARP1 0.002 0.037 0.48 1 -0.39 1 2
DFFB 0 0.047 0.3 3 -0.47 2 5
CHUK -0.027 0.072 -10000 0 -10000 0 0
FASLG -0.029 0.17 0.32 3 -0.87 14 17
FAS/FADD -0.021 0.12 -10000 0 -0.67 12 12
HGF -0.46 0.43 0.32 1 -0.86 201 202
LMNA 0.002 0.033 0.42 1 -0.35 1 2
CASP6 0.002 0.037 0.48 1 -0.39 1 2
CASP10 0.001 0.004 -10000 0 -10000 0 0
CASP3 0.002 0.047 0.35 4 -0.44 1 5
PTPN13 -0.23 0.38 0.32 2 -0.86 99 101
CASP8 0.004 0.05 0.47 4 -10000 0 4
IL6 -0.17 0.49 -10000 0 -1.4 52 52
MET -0.001 0.048 0.32 1 -0.86 1 2
ICAD/CAD 0 0.044 0.43 1 -0.44 2 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.043 0.13 -10000 0 -0.52 16 16
activation of caspase activity by cytochrome c 0.003 0.034 0.32 4 -10000 0 4
PAK2 0.002 0.037 0.48 1 -0.39 1 2
BCL2 -0.002 0.045 -10000 0 -0.86 1 1
Paxillin-independent events mediated by a4b1 and a4b7

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.02 0.11 -10000 0 -0.55 14 14
CRKL 0 0 -10000 0 -10000 0 0
Rac1/GDP 0 0 -10000 0 -10000 0 0
DOCK1 -0.019 0.12 -10000 0 -0.86 8 8
ITGA4 -0.02 0.13 0.32 1 -0.86 9 10
alpha4/beta7 Integrin/MAdCAM1 -0.015 0.11 0.38 1 -0.53 14 15
EPO -0.3 0.43 0.32 12 -0.86 136 148
alpha4/beta7 Integrin -0.025 0.13 -10000 0 -0.67 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.016 0.1 -10000 0 -0.67 9 9
EPO/EPOR (dimer) -0.24 0.33 -10000 0 -0.67 136 136
lamellipodium assembly -0.003 0.053 -10000 0 -0.7 2 2
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
PI3K -0.005 0.071 -10000 0 -0.94 2 2
ARF6 0 0 -10000 0 -10000 0 0
JAK2 -0.15 0.21 -10000 0 -0.41 140 140
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
MADCAM1 0.007 0.046 0.32 8 -10000 0 8
cell adhesion -0.015 0.11 0.37 1 -0.53 14 15
CRKL/CBL 0 0 -10000 0 -10000 0 0
ITGB1 0 0 -10000 0 -10000 0 0
SRC -0.038 0.15 -10000 0 -0.56 27 27
ITGB7 -0.012 0.099 -10000 0 -0.86 5 5
RAC1 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.041 0.17 -10000 0 -0.62 27 27
p130Cas/Crk/Dock1 -0.043 0.16 -10000 0 -0.53 31 31
VCAM1 -0.041 0.2 0.32 6 -0.86 20 26
RHOA 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.012 0.082 -10000 0 -0.53 9 9
BCAR1 -0.036 0.14 -10000 0 -0.52 27 27
EPOR 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.056 -10000 0 -0.73 2 2
FoxO family signaling

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
G6PC -0.2 0.56 -10000 0 -1.4 63 63
PLK1 0.28 0.25 0.55 102 -0.76 3 105
CDKN1B 0.18 0.16 0.46 10 -0.34 4 14
FOXO3 0.24 0.24 0.49 126 -0.74 5 131
KAT2B 0.045 0.089 -10000 0 -0.86 3 3
FOXO1/SIRT1 -0.066 0.16 -10000 0 -0.4 65 65
CAT 0.19 0.36 0.6 6 -1.3 15 21
CTNNB1 0 0 -10000 0 -10000 0 0
AKT1 0.047 0.038 -10000 0 -10000 0 0
FOXO1 -0.029 0.18 -10000 0 -0.42 65 65
MAPK10 0.011 0.14 -10000 0 -0.5 24 24
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
FOXO4 0.07 0.13 -10000 0 -0.51 9 9
response to oxidative stress 0.04 0.041 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.029 0.18 0.42 33 -0.79 6 39
XPO1 0 0 -10000 0 -10000 0 0
EP300 -0.001 0.019 -10000 0 -10000 0 0
BCL2L11 0.075 0.057 -10000 0 -10000 0 0
FOXO1/SKP2 -0.067 0.15 -10000 0 -0.38 65 65
mol:GDP 0.04 0.04 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
GADD45A 0.16 0.2 0.41 9 -0.85 9 18
YWHAQ 0 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.075 0.051 -10000 0 -10000 0 0
MST1 -0.006 0.22 -10000 0 -0.82 25 25
CSNK1D 0 0 -10000 0 -10000 0 0
CSNK1E 0.001 0.016 0.32 1 -10000 0 1
FOXO4/14-3-3 family 0.074 0.072 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.013 0.13 -10000 0 -0.52 20 20
MAPK9 0.042 0.019 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
SIRT1 0 0.066 -10000 0 -0.86 2 2
SOD2 0.18 0.2 0.49 6 -0.76 6 12
RBL2 0.18 0.28 0.5 8 -1.3 9 17
RAL/GDP 0.033 0.033 -10000 0 -10000 0 0
CHUK 0.053 0.036 -10000 0 -10000 0 0
Ran/GTP 0 0 -10000 0 -10000 0 0
CSNK1G2 0 0 -10000 0 -10000 0 0
RAL/GTP 0.046 0.027 -10000 0 -10000 0 0
CSNK1G1 0 0 -10000 0 -10000 0 0
FASLG 0.022 0.31 -10000 0 -1.5 14 14
SKP2 0 0 -10000 0 -10000 0 0
USP7 0 0 -10000 0 -10000 0 0
IKBKB 0.053 0.036 -10000 0 -10000 0 0
CCNB1 0.27 0.24 0.54 122 -0.76 3 125
FOXO1-3a-4/beta catenin -0.022 0.087 -10000 0 -0.41 11 11
proteasomal ubiquitin-dependent protein catabolic process -0.066 0.15 -10000 0 -0.38 65 65
CSNK1A1 0 0 -10000 0 -10000 0 0
SGK1 0.024 0.16 -10000 0 -0.84 12 12
CSNK1G3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
ZFAND5 0.073 0.12 -10000 0 -0.63 3 3
SFN 0.18 0.17 0.32 214 -0.86 2 216
CDK2 -0.013 0.03 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.14 0.076 -10000 0 -10000 0 0
CREBBP -0.013 0.03 -10000 0 -10000 0 0
FBXO32 0.23 0.24 0.69 8 -0.92 4 12
BCL6 0.2 0.18 0.5 8 -0.65 4 12
RALB 0 0 -10000 0 -10000 0 0
RALA 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.007 0.037 0.32 5 -10000 0 5
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.13 0.24 0.89 18 -10000 0 18
IL27/IL27R/JAK1 -0.2 0.29 -10000 0 -0.88 24 24
TBX21 -0.12 0.25 -10000 0 -0.67 28 28
IL12B 0.004 0.03 0.33 3 -10000 0 3
IL12A 0.013 0.025 -10000 0 -10000 0 0
IL6ST -0.21 0.37 -10000 0 -0.86 91 91
IL27RA/JAK1 -0.005 0.019 -10000 0 -10000 0 0
IL27 -0.13 0.32 -10000 0 -0.86 58 58
TYK2 0.007 0.009 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.036 0.14 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.13 0.24 0.89 18 -10000 0 18
T cell proliferation during immune response 0.13 0.24 0.89 18 -10000 0 18
MAPKKK cascade -0.13 0.24 -10000 0 -0.89 18 18
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 0.002 0.023 0.32 2 -10000 0 2
IL12RB1 -0.029 0.16 -10000 0 -0.86 13 13
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.12 0.26 -10000 0 -0.69 29 29
IL27/IL27R/JAK2/TYK2 -0.14 0.24 -10000 0 -0.91 18 18
positive regulation of T cell mediated cytotoxicity -0.13 0.24 -10000 0 -0.89 18 18
STAT1 (dimer) -0.19 0.32 0.53 13 -0.96 24 37
JAK2 0 0.046 -10000 0 -0.87 1 1
JAK1 0.001 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.14 0.22 -10000 0 -0.85 18 18
T cell proliferation -0.19 0.28 -10000 0 -0.65 67 67
IL12/IL12R/TYK2/JAK2 0.014 0.079 -10000 0 -10000 0 0
IL17A -0.036 0.14 -10000 0 -10000 0 0
mast cell activation 0.13 0.24 0.89 18 -10000 0 18
IFNG -0.01 0.034 0.11 4 -0.092 14 18
T cell differentiation -0.005 0.007 -10000 0 -0.023 16 16
STAT3 (dimer) -0.14 0.22 -10000 0 -0.85 18 18
STAT5A (dimer) -0.14 0.22 -10000 0 -0.85 18 18
STAT4 (dimer) -0.16 0.24 -10000 0 -0.81 30 30
STAT4 -0.034 0.17 0.32 1 -0.86 15 16
T cell activation -0.012 0.01 -10000 0 -0.13 1 1
IL27R/JAK2/TYK2 -0.12 0.23 -10000 0 -0.6 21 21
GATA3 -0.071 0.4 -10000 0 -1.5 27 27
IL18 -0.008 0.11 -10000 0 -0.68 10 10
positive regulation of mast cell cytokine production -0.14 0.21 -10000 0 -0.82 18 18
IL27/EBI3 -0.13 0.27 -10000 0 -0.67 76 76
IL27RA -0.01 0.022 -10000 0 -10000 0 0
IL6 -0.11 0.3 0.32 8 -0.86 52 60
STAT5A 0.001 0.016 0.32 1 -10000 0 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.009 0.018 -10000 0 -10000 0 0
IL1B -0.11 0.26 -10000 0 -0.68 64 64
EBI3 -0.04 0.18 -10000 0 -0.86 18 18
TNF -0.016 0.13 -10000 0 -0.68 14 14
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.003 -10000 0 -10000 0 0
SMARCC1 0.005 0.009 -10000 0 -10000 0 0
REL -0.03 0.16 -10000 0 -0.86 13 13
HDAC7 -0.034 0.17 -10000 0 -0.54 25 25
JUN -0.013 0.11 -10000 0 -0.86 6 6
EP300 0 0 -10000 0 -10000 0 0
KAT2B -0.007 0.077 -10000 0 -0.86 3 3
KAT5 0 0.001 -10000 0 -10000 0 0
MAPK14 0.007 0.096 -10000 0 -0.67 7 7
FOXO1 -0.009 0.089 -10000 0 -0.86 4 4
T-DHT/AR -0.044 0.18 -10000 0 -0.56 28 28
MAP2K6 -0.011 0.12 0.32 6 -0.86 7 13
BRM/BAF57 -0.016 0.11 -10000 0 -0.67 10 10
MAP2K4 0.001 0.004 -10000 0 -10000 0 0
SMARCA2 -0.022 0.14 -10000 0 -0.86 10 10
PDE9A -0.13 0.37 -10000 0 -1.2 37 37
NCOA2 -0.11 0.29 -10000 0 -0.86 48 48
CEBPA -0.006 0.079 0.32 1 -0.86 3 4
EHMT2 0.001 0.004 -10000 0 -10000 0 0
cell proliferation -0.016 0.17 -10000 0 -0.51 23 23
NR0B1 0.054 0.12 0.32 63 -10000 0 63
EGR1 -0.3 0.41 -10000 0 -0.86 128 128
RXRs/9cRA 0.015 0.094 -10000 0 -0.54 6 6
AR/RACK1/Src -0.048 0.15 -10000 0 -0.53 27 27
AR/GR -0.11 0.18 -10000 0 -0.37 94 94
GNB2L1 0.001 0.004 -10000 0 -10000 0 0
PKN1 0.001 0.016 0.32 1 -10000 0 1
RCHY1 0 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.002 -10000 0 -10000 0 0
MAPK8 -0.019 0.16 -10000 0 -0.67 20 20
T-DHT/AR/TIF2/CARM1 -0.12 0.27 -10000 0 -0.71 55 55
SRC -0.002 0.14 -10000 0 -0.5 27 27
NR3C1 0 0 -10000 0 -10000 0 0
KLK3 -0.014 0.2 -10000 0 -1.2 7 7
APPBP2 0 0.001 -10000 0 -10000 0 0
TRIM24 0.001 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.069 0.15 -10000 0 -0.58 27 27
TMPRSS2 -0.078 0.29 -10000 0 -1.3 19 19
RXRG 0.026 0.14 0.32 44 -0.86 5 49
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA -0.002 0.045 -10000 0 -0.86 1 1
RXRB 0 0 -10000 0 -10000 0 0
CARM1 0.001 0.004 -10000 0 -10000 0 0
NR2C2 -0.014 0.11 -10000 0 -0.86 6 6
KLK2 -0.031 0.2 -10000 0 -0.56 26 26
AR -0.12 0.2 -10000 0 -0.39 115 115
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.001 0.005 -10000 0 -10000 0 0
SRY 0.002 0.029 0.32 3 -10000 0 3
GATA2 -0.003 0.067 0.32 2 -0.86 2 4
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.064 0.13 0.32 74 -10000 0 74
T-DHT/AR/RACK1/Src -0.057 0.15 -10000 0 -0.55 27 27
positive regulation of transcription -0.003 0.067 0.32 2 -0.86 2 4
DNAJA1 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.008 0.011 -10000 0 -10000 0 0
SPDEF 0.05 0.12 0.32 57 -10000 0 57
T-DHT/AR/TIF2 -0.051 0.2 -10000 0 -0.55 41 41
T-DHT/AR/Hsp90 -0.069 0.15 -10000 0 -0.58 27 27
GSK3B 0.003 0.005 -10000 0 -10000 0 0
NR2C1 0 0.001 -10000 0 -10000 0 0
mol:T-DHT -0.01 0.15 -10000 0 -0.54 27 27
SIRT1 -0.005 0.063 -10000 0 -0.86 2 2
ZMIZ2 0.001 0.005 -10000 0 -10000 0 0
POU2F1 0.01 0.031 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.035 0.18 -10000 0 -0.58 27 27
CREBBP 0 0 -10000 0 -10000 0 0
SMARCE1 0.001 0.005 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.025 0.16 0.56 1 -0.64 18 19
MAP4K1 -0.014 0.12 0.32 3 -0.86 7 10
MAP3K8 -0.005 0.063 -10000 0 -0.86 2 2
PRKCB -0.074 0.24 -10000 0 -0.86 32 32
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0 0 -10000 0 -10000 0 0
MAP3K1 -0.017 0.1 -10000 0 -0.46 13 13
JUN -0.071 0.25 -10000 0 -0.64 56 56
MAP3K7 -0.017 0.1 -10000 0 -0.46 13 13
GRAP2 -0.016 0.14 0.32 6 -0.86 9 15
CRK 0 0 -10000 0 -10000 0 0
MAP2K4 0.024 0.11 -10000 0 -0.44 14 14
LAT 0.002 0.023 0.32 2 -10000 0 2
LCP2 -0.014 0.11 -10000 0 -0.86 6 6
MAPK8 -0.073 0.25 -10000 0 -0.67 52 52
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.018 0.11 0.25 1 -0.43 18 19
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.024 0.15 0.53 1 -0.6 18 19
IL2 signaling events mediated by PI3K

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
BCL2L1 0.005 0.16 -10000 0 -0.8 11 11
UGCG -0.071 0.22 -10000 0 -0.75 32 32
AKT1/mTOR/p70S6K/Hsp90/TERT 0.055 0.13 0.32 1 -0.33 12 13
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.053 0.22 -10000 0 -0.74 32 32
mol:DAG -0.001 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.059 0.14 -10000 0 -0.38 44 44
FRAP1 0.002 0.2 0.34 1 -0.43 49 50
FOXO3 0.001 0.19 0.32 1 -0.42 55 56
AKT1 -0.008 0.21 0.33 1 -0.45 56 57
GAB2 0 0.001 -10000 0 -10000 0 0
SMPD1 -0.007 0.029 -10000 0 -10000 0 0
SGMS1 -0.007 0.029 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.066 -10000 0 -0.84 2 2
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation -0.04 0.2 -10000 0 -0.37 73 73
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.005 0.071 -10000 0 -0.93 2 2
RPS6KB1 0.026 0.038 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.005 -10000 0 -10000 0 0
natural killer cell activation 0 0.004 -10000 0 -10000 0 0
JAK3 0.002 0.056 0.32 4 -0.86 1 5
PIK3R1 -0.004 0.063 -10000 0 -0.86 2 2
JAK1 0.001 0.003 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC -0.075 0.37 -10000 0 -1 47 47
MYB 0.13 0.1 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.003 0.18 0.33 1 -0.61 18 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.004 0.17 0.33 1 -0.59 18 19
Rac1/GDP -0.004 0.059 -10000 0 -0.77 2 2
T cell proliferation -0.009 0.19 0.31 1 -0.51 33 34
SHC1 0 0.001 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.015 0.03 0.1 38 -10000 0 38
PRKCZ -0.012 0.2 0.32 1 -0.54 33 34
NF kappa B1 p50/RelA -0.058 0.14 -10000 0 -0.61 9 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.036 0.17 0.26 1 -0.87 12 13
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.007 0.13 0.32 11 -0.86 7 18
IL2RB -0.066 0.23 -10000 0 -0.86 29 29
TERT 0.13 0.16 0.32 157 -10000 0 157
E2F1 0.14 0.1 0.36 36 -10000 0 36
SOS1 0 0.001 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.006 0.012 -10000 0 -0.043 38 38
PTPN11 0 0.001 -10000 0 -10000 0 0
IL2RG -0.005 0.11 0.32 7 -0.86 5 12
actin cytoskeleton organization -0.009 0.19 0.31 1 -0.51 33 34
GRB2 0 0.001 -10000 0 -10000 0 0
IL2 0.001 0.004 -10000 0 -10000 0 0
PIK3CA -0.001 0.045 -10000 0 -0.86 1 1
Rac1/GTP 0.018 0.06 -10000 0 -0.75 2 2
LCK -0.024 0.15 0.32 1 -0.86 11 12
BCL2 0.016 0.16 -10000 0 -0.56 9 9
Canonical Wnt signaling pathway

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.017 0.044 0.27 1 -10000 0 1
AES 0.015 0.038 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 -0.014 0.098 -10000 0 -0.67 8 8
SMAD4 -0.002 0.045 -10000 0 -0.86 1 1
DKK2 0.04 0.1 0.32 47 -10000 0 47
TLE1 0.013 0.059 -10000 0 -0.86 1 1
MACF1 0 0 -10000 0 -10000 0 0
CTNNB1 0.038 0.073 -10000 0 -0.37 6 6
WIF1 0.032 0.095 0.32 37 -10000 0 37
beta catenin/RanBP3 0.05 0.17 0.42 58 -0.4 1 59
KREMEN2 0.034 0.098 0.32 40 -10000 0 40
DKK1 0.11 0.15 0.32 126 -10000 0 126
beta catenin/beta TrCP1 0.001 0.06 -10000 0 -0.35 3 3
FZD1 -0.018 0.13 0.32 1 -0.86 8 9
AXIN2 -0.073 0.39 -10000 0 -1.4 24 24
AXIN1 0 0 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.011 0.032 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.059 0.072 0.31 2 -0.51 2 4
Axin1/APC/GSK3 -0.001 0.047 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.031 0.079 -10000 0 -0.46 8 8
HNF1A 0.006 0.098 -10000 0 -0.85 4 4
CTBP1 0.016 0.04 0.25 1 -10000 0 1
MYC -0.19 0.54 -10000 0 -1.6 44 44
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.047 0.09 0.39 4 -10000 0 4
NKD1 0.029 0.23 0.32 80 -0.86 17 97
TCF4 0.016 0.04 0.25 1 -10000 0 1
TCF3 0.016 0.04 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.009 0.081 -10000 0 -0.54 8 8
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.089 0.23 0.56 59 -0.65 1 60
LEF1 0.13 0.15 0.31 147 -0.73 1 148
DVL1 0.009 0.036 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.049 0.12 -10000 0 -0.5 4 4
DKK1/LRP6/Kremen 2 0.089 0.12 0.39 21 -10000 0 21
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0.017 0.044 -10000 0 -10000 0 0
NLK 0.002 0.004 -10000 0 -10000 0 0
CCND1 -0.082 0.34 -10000 0 -1.4 19 19
WNT1 0.003 0.033 0.32 4 -10000 0 4
GSK3A 0 0 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
FRAT1 -0.002 0.045 -10000 0 -0.86 1 1
PPP2R5D 0.005 0.09 0.37 17 -10000 0 17
APC -0.01 0.073 -10000 0 -0.5 8 8
WNT1/LRP6/FZD1 -0.012 0.059 -10000 0 -0.36 8 8
CREBBP 0.016 0.04 0.24 1 -10000 0 1
Regulation of Telomerase

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
Telomerase catalytic core complex 0.097 0.16 0.4 2 -0.53 4 6
RAD9A 0 0 -10000 0 -10000 0 0
AP1 -0.32 0.35 -10000 0 -0.68 179 179
IFNAR2 0.012 0.015 -10000 0 -10000 0 0
AKT1 -0.15 0.16 -10000 0 -0.29 179 179
ER alpha/Oestrogen -0.37 0.34 -10000 0 -0.67 205 205
NFX1/SIN3/HDAC complex 0.028 0.035 -10000 0 -10000 0 0
EGF 0.08 0.13 0.32 88 -10000 0 88
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.02 0.024 -10000 0 -10000 0 0
TERT/c-Abl -0.023 0.067 -10000 0 -0.54 3 3
SAP18 0.004 0.006 -10000 0 -10000 0 0
MRN complex 0 0 -10000 0 -10000 0 0
WT1 0.036 0.086 0.33 29 -10000 0 29
WRN 0 0 -10000 0 -10000 0 0
SP1 0.019 0.019 -10000 0 -10000 0 0
SP3 0.007 0.009 -10000 0 -10000 0 0
TERF2IP 0 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.017 0.059 -10000 0 -0.48 3 3
Mad/Max 0.017 0.024 -10000 0 -10000 0 0
TERT 0.097 0.17 -10000 0 -0.54 4 4
CCND1 0.065 0.28 -10000 0 -1.2 14 14
MAX 0.008 0.01 -10000 0 -10000 0 0
RBBP7 0.004 0.006 -10000 0 -10000 0 0
RBBP4 0.004 0.006 -10000 0 -10000 0 0
TERF2 0 0 -10000 0 -10000 0 0
PTGES3 0 0 -10000 0 -10000 0 0
SIN3A 0.004 0.006 -10000 0 -10000 0 0
Telomerase/911 0.034 0.049 -10000 0 -10000 0 0
CDKN1B 0.023 0.03 -10000 0 -10000 0 0
RAD1 0 0 -10000 0 -10000 0 0
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
SAP30 0.004 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0 0 -10000 0 -10000 0 0
UBE3A 0.007 0.009 -10000 0 -10000 0 0
JUN -0.01 0.11 -10000 0 -0.86 6 6
E6 0.004 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.015 -10000 0 -10000 0 0
FOS -0.41 0.43 -10000 0 -0.86 179 179
IFN-gamma/IRF1 0.028 0.051 -10000 0 -10000 0 0
PARP2 0 0 -10000 0 -10000 0 0
BLM 0.11 0.15 0.32 124 -10000 0 124
Telomerase 0.044 0.064 -10000 0 -10000 0 0
IRF1 0.01 0.012 -10000 0 -10000 0 0
ESR1 -0.47 0.43 -10000 0 -0.86 205 205
KU/TER 0 0 -10000 0 -10000 0 0
ATM/TRF2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.029 0.036 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.029 0.036 -10000 0 -10000 0 0
HDAC1 0.004 0.006 -10000 0 -10000 0 0
HDAC2 0.014 0.017 -10000 0 -10000 0 0
ATM 0 0 -10000 0 -10000 0 0
SMAD3 0.013 0.019 -10000 0 -10000 0 0
ABL1 0 0 -10000 0 -10000 0 0
MXD1 0.009 0.019 0.33 1 -10000 0 1
MRE11A 0 0 -10000 0 -10000 0 0
HUS1 0 0 -10000 0 -10000 0 0
RPS6KB1 0 0 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.035 0.11 -10000 0 -0.57 3 3
NR2F2 0.001 0.003 -10000 0 -10000 0 0
MAPK3 0.02 0.011 -10000 0 -10000 0 0
MAPK1 0.02 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.004 0.036 0.32 5 -10000 0 5
NFKB1 0 0 -10000 0 -10000 0 0
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -10000 0 -10000 0 0
NBN 0 0 -10000 0 -10000 0 0
EGFR -0.017 0.14 -10000 0 -0.85 10 10
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.041 0.15 -10000 0 -0.65 10 10
MYC -0.092 0.28 -10000 0 -0.86 43 43
IL2 0.016 0.017 -10000 0 -10000 0 0
KU 0 0 -10000 0 -10000 0 0
RAD50 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.004 0.036 0.32 5 -10000 0 5
TRF2/BLM 0.07 0.099 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.021 0.066 -10000 0 -0.53 3 3
SP1/HDAC2 0.03 0.037 -10000 0 -10000 0 0
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.017 0.059 -10000 0 -0.48 3 3
Smad3/Myc -0.066 0.19 -10000 0 -0.58 43 43
911 complex 0 0 -10000 0 -10000 0 0
IFNG 0.023 0.066 0.33 16 -10000 0 16
Telomerase/PinX1 -0.017 0.059 -10000 0 -0.48 3 3
Telomerase/AKT1/mTOR/p70S6K 0.013 0.082 -10000 0 -10000 0 0
SIN3B 0.004 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Telomerase/EST1B -0.017 0.059 -10000 0 -0.48 3 3
response to DNA damage stimulus 0.002 0 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -10000 0 -10000 0 0
TRF2/WRN 0 0 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.017 0.059 -10000 0 -0.48 3 3
E2F1 0.2 0.16 0.33 230 -10000 0 230
ZNFX1 0.004 0.006 -10000 0 -10000 0 0
PIF1 0.088 0.14 0.32 103 -10000 0 103
NCL 0 0 -10000 0 -10000 0 0
DKC1 0 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 -0.005 0.008 -10000 0 -10000 0 0
HSPA8 0.002 0.045 -10000 0 -0.86 1 1
SMAD3/SMAD4/ER alpha -0.36 0.31 -10000 0 -0.63 205 205
AKT1 0.002 0.009 -10000 0 -10000 0 0
GSC 0.038 0.065 -10000 0 -10000 0 0
NKX2-5 0.015 0.068 0.32 18 -10000 0 18
muscle cell differentiation 0.013 0.05 0.64 1 -10000 0 1
SMAD2-3/SMAD4/SP1 -0.004 0.072 -10000 0 -0.48 2 2
SMAD4 -0.011 0.069 -10000 0 -0.92 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0.003 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.002 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR -0.019 0.093 -10000 0 -0.53 9 9
MYC -0.1 0.28 -10000 0 -0.87 43 43
CDKN2B 0.069 0.085 0.5 2 -10000 0 2
AP1 -0.24 0.27 -10000 0 -0.52 122 122
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.023 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.005 0.048 -10000 0 -10000 0 0
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 0.029 0.091 0.33 32 -10000 0 32
SMAD3/SMAD4/GR -0.017 0.057 -10000 0 -0.63 1 1
GATA3 -0.079 0.24 0.32 1 -0.92 27 28
SKI/SIN3/HDAC complex/NCoR1 0.017 0.032 -10000 0 -10000 0 0
MEF2C/TIF2 -0.054 0.16 -10000 0 -0.48 33 33
endothelial cell migration 0.4 0.67 1.5 101 -10000 0 101
MAX 0.015 0.025 -10000 0 -10000 0 0
RBBP7 0.003 0.005 -10000 0 -10000 0 0
RBBP4 0.003 0.005 -10000 0 -10000 0 0
RUNX2 -0.02 0.14 0.32 4 -0.86 10 14
RUNX3 -0.019 0.12 -10000 0 -0.86 8 8
RUNX1 -0.002 0.045 -10000 0 -0.86 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 0.015 0.025 -10000 0 -10000 0 0
VDR -0.009 0.14 0.32 11 -0.86 8 19
CDKN1A -0.011 0.24 -10000 0 -1.4 10 10
KAT2B -0.007 0.078 -10000 0 -0.87 3 3
SMAD2/SMAD2/SMAD4/FOXH1 0.02 0.078 0.34 5 -0.57 1 6
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0.003 0.005 -10000 0 -10000 0 0
SERPINE1 -0.41 0.68 -10000 0 -1.5 101 101
SMAD3/SMAD4/ATF2 -0.028 0.089 -10000 0 -0.61 6 6
SMAD3/SMAD4/ATF3 -0.043 0.14 -10000 0 -0.66 15 15
SAP30 0.003 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 -0.008 0.013 -10000 0 -10000 0 0
JUN -0.21 0.28 -10000 0 -0.51 123 123
SMAD3/SMAD4/IRF7 -0.029 0.094 -10000 0 -0.66 6 6
TFE3 -0.009 0.017 -10000 0 -10000 0 0
COL1A2 0.1 0.18 0.46 10 -1.2 4 14
mesenchymal cell differentiation 0.034 0.12 0.67 11 -0.34 1 12
DLX1 0.026 0.086 0.32 30 -10000 0 30
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.41 0.43 -10000 0 -0.86 179 179
SMAD3/SMAD4/Max -0.017 0.057 -10000 0 -0.63 1 1
Cbp/p300/SNIP1 -0.001 0.002 -10000 0 -10000 0 0
ZBTB17 -0.001 0.005 -10000 0 -10000 0 0
LAMC1 0.009 0.069 -10000 0 -0.54 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.02 0.059 -10000 0 -0.62 1 1
IRF7 -0.012 0.099 -10000 0 -0.86 5 5
ESR1 -0.48 0.43 -10000 0 -0.86 205 205
HNF4A -0.014 0.11 -10000 0 -0.86 6 6
MEF2C 0.014 0.048 -10000 0 -0.47 1 1
SMAD2-3/SMAD4 -0.016 0.061 -10000 0 -0.62 1 1
Cbp/p300/Src-1 -0.003 0.005 -10000 0 -10000 0 0
IGHV3OR16-13 -0.005 0.021 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP -0.001 0.004 -10000 0 -10000 0 0
SKIL 0 0 -10000 0 -10000 0 0
HDAC1 0.003 0.005 -10000 0 -10000 0 0
HDAC2 0.003 0.005 -10000 0 -10000 0 0
SNIP1 0.004 0.007 -10000 0 -10000 0 0
GCN5L2 -0.008 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.022 0.064 -10000 0 -0.62 1 1
MSG1/HSC70 0.013 0.052 -10000 0 -0.62 1 1
SMAD2 0.005 0.013 -10000 0 -10000 0 0
SMAD3 -0.013 0.052 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0 0.048 -10000 0 -0.39 2 2
SMAD2/SMAD2/SMAD4 -0.009 0.057 -10000 0 -0.48 4 4
NCOR1 -0.002 0.063 -10000 0 -0.86 2 2
NCOA2 -0.11 0.29 -10000 0 -0.86 48 48
NCOA1 0 0 -10000 0 -10000 0 0
MYOD/E2A 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.001 0.07 -10000 0 -0.51 1 1
IFNB1 -0.008 0.091 -10000 0 -0.59 6 6
SMAD3/SMAD4/MEF2C 0.005 0.058 -10000 0 -0.49 1 1
CITED1 0.013 0.058 0.32 13 -10000 0 13
SMAD2-3/SMAD4/ARC105 -0.009 0.053 -10000 0 -0.56 1 1
RBL1 0.011 0.058 0.32 13 -10000 0 13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.005 0.051 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.014 0.097 -10000 0 -0.64 8 8
SMAD7 -0.16 0.21 -10000 0 -0.69 15 15
MYC/MIZ-1 -0.081 0.22 -10000 0 -0.68 43 43
SMAD3/SMAD4 -0.14 0.21 -10000 0 -0.47 102 102
IL10 -0.13 0.34 -10000 0 -0.86 61 61
PIASy/HDAC complex 0.011 0.016 -10000 0 -10000 0 0
PIAS3 0 0 -10000 0 -10000 0 0
CDK2 0 0.001 -10000 0 -10000 0 0
IL5 -0.062 0.21 -10000 0 -0.68 28 28
CDK4 0 0.001 -10000 0 -10000 0 0
PIAS4 0.011 0.016 -10000 0 -10000 0 0
ATF3 -0.032 0.16 -10000 0 -0.86 14 14
SMAD3/SMAD4/SP1 -0.015 0.076 -10000 0 -0.54 2 2
FOXG1 0.008 0.052 0.32 10 -10000 0 10
FOXO3 0.023 0.01 -10000 0 -10000 0 0
FOXO1 0.016 0.071 -10000 0 -0.66 4 4
FOXO4 0.023 0.01 -10000 0 -10000 0 0
heart looping 0.014 0.048 -10000 0 -0.47 1 1
CEBPB 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.007 0.082 0.34 1 -0.63 1 2
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.03 0.096 -10000 0 -0.62 7 7
SMAD3/SMAD4/GATA3 -0.091 0.22 -10000 0 -0.76 28 28
SnoN/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.023 0.1 -10000 0 -0.62 9 9
SMAD3/SMAD4/SP1-3 -0.008 0.066 -10000 0 -0.48 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 0 0.023 -10000 0 -10000 0 0
SIN3B 0.003 0.005 -10000 0 -10000 0 0
SIN3A 0.003 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.03 0.092 0.38 10 -0.52 1 11
ITGB5 -0.007 0.056 -10000 0 -0.49 1 1
TGIF/SIN3/HDAC complex/CtBP 0.012 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.18 0.28 -10000 0 -0.63 102 102
AR -0.23 0.38 -10000 0 -0.86 101 101
negative regulation of cell growth -0.01 0.067 -10000 0 -0.41 2 2
SMAD3/SMAD4/MYOD -0.023 0.061 -10000 0 -0.63 1 1
E2F5 0.006 0.068 0.32 10 -0.86 1 11
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.017 0.066 0.32 1 -0.48 1 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.05 -10000 0 -10000 0 0
TFDP1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.23 0.28 -10000 0 -0.53 111 111
SMAD3/SMAD4/RUNX2 -0.034 0.12 0.34 1 -0.67 11 12
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.012 0.099 -10000 0 -0.86 5 5
HIF-2-alpha transcription factor network

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
MMP14 -0.003 0.052 0.49 1 -10000 0 1
oxygen homeostasis 0.001 0.019 -10000 0 -10000 0 0
TCEB2 0.001 0.016 0.32 1 -10000 0 1
TCEB1 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.03 0.07 -10000 0 -0.41 7 7
EPO -0.24 0.47 0.67 3 -0.8 139 142
FIH (dimer) 0.011 0.015 -10000 0 -10000 0 0
APEX1 0.002 0.017 -10000 0 -10000 0 0
SERPINE1 -0.14 0.44 0.72 1 -0.81 101 102
FLT1 -0.014 0.066 -10000 0 -1.2 1 1
ADORA2A -0.025 0.27 0.67 1 -0.65 18 19
germ cell development 0.009 0.27 0.66 5 -0.61 18 23
SLC11A2 -0.009 0.26 0.72 1 -0.7 12 13
BHLHE40 -0.017 0.28 0.72 1 -0.85 14 15
HIF1AN 0.011 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.076 0.17 0.46 6 -0.54 11 17
ETS1 0.016 0.047 -10000 0 -0.86 1 1
CITED2 -0.018 0.1 -10000 0 -1.4 2 2
KDR -0.042 0.2 -10000 0 -1.3 10 10
PGK1 -0.009 0.26 0.72 1 -0.64 18 19
SIRT1 -0.004 0.063 -10000 0 -0.86 2 2
response to hypoxia -0.005 0.008 -10000 0 -10000 0 0
HIF2A/ARNT -0.08 0.26 0.67 5 -0.76 18 23
EPAS1 0.015 0.14 0.49 1 -0.46 9 10
SP1 0.017 0.017 -10000 0 -10000 0 0
ABCG2 -0.082 0.36 0.72 1 -0.75 59 60
EFNA1 -0.013 0.27 0.72 1 -0.68 21 22
FXN -0.025 0.27 0.67 1 -0.65 18 19
POU5F1 0.007 0.27 0.66 5 -0.64 18 23
neuron apoptosis 0.078 0.25 0.73 18 -0.66 5 23
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0.012 0.18 0.35 18 -0.87 11 29
EGLN2 0.011 0.015 -10000 0 -10000 0 0
EGLN1 0.011 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.001 0.01 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.002 0.017 -10000 0 -10000 0 0
SLC2A1 -0.026 0.28 0.75 1 -0.69 21 22
TWIST1 -0.023 0.27 0.75 1 -0.65 18 19
ELK1 0.014 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.037 0.13 0.41 5 -0.49 7 12
VEGFA -0.009 0.26 0.72 1 -0.7 12 13
CREBBP 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0 0 -10000 0 -10000 0 0
ELF1 -0.007 0.086 -10000 0 -0.49 9 9
CCNA2 0.17 0.16 0.32 197 -10000 0 197
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
JAK3 0.001 0.055 0.32 4 -0.86 1 5
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
JAK1 0 0 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.029 0.14 0.3 1 -0.63 15 16
SHC1 0 0 -10000 0 -10000 0 0
SP1 0.002 0.018 -10000 0 -10000 0 0
IL2RA 0.008 0.16 -10000 0 -0.98 9 9
IL2RB -0.067 0.23 -10000 0 -0.86 29 29
SOS1 0 0 -10000 0 -10000 0 0
IL2RG -0.006 0.11 0.32 7 -0.86 5 12
G1/S transition of mitotic cell cycle 0.054 0.15 -10000 0 -0.46 25 25
PTPN11 0 0 -10000 0 -10000 0 0
CCND2 0.027 0.031 -10000 0 -10000 0 0
LCK -0.025 0.15 0.32 1 -0.86 11 12
GRB2 0 0 -10000 0 -10000 0 0
IL2 0 0 -10000 0 -10000 0 0
CDK6 -0.058 0.22 -10000 0 -0.86 25 25
CCND3 0.033 0.13 -10000 0 -0.72 6 6
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0 0 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.064 0.17 -10000 0 -0.47 53 53
Syndecan-3/Neurocan 0.001 0.048 -10000 0 -0.77 1 1
POMC -0.004 0.084 0.32 4 -0.86 3 7
EGFR -0.023 0.14 -10000 0 -0.86 10 10
Syndecan-3/EGFR -0.015 0.09 -10000 0 -0.52 11 11
AGRP 0.012 0.06 0.32 14 -10000 0 14
NCSTN 0 0 -10000 0 -10000 0 0
PSENEN 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
NCAN 0.005 0.04 0.32 6 -10000 0 6
long-term memory -0.002 0.037 -10000 0 -0.71 1 1
Syndecan-3/IL8 -0.11 0.22 -10000 0 -0.51 85 85
PSEN1 0 0 -10000 0 -10000 0 0
Src/Cortactin 0.003 0.025 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
limb bud formation -0.002 0.041 -10000 0 -0.78 1 1
MC4R 0.001 0.016 0.32 1 -10000 0 1
SRC 0.004 0.036 0.32 5 -10000 0 5
PTN -0.12 0.3 0.32 3 -0.86 53 56
FGFR/FGF/Syndecan-3 -0.002 0.041 -10000 0 -0.79 1 1
neuron projection morphogenesis -0.06 0.16 -10000 0 -0.45 53 53
Syndecan-3/AgRP 0.006 0.056 -10000 0 -0.77 1 1
Syndecan-3/AgRP/MC4R 0.006 0.055 -10000 0 -0.74 1 1
Fyn/Cortactin 0 0 -10000 0 -10000 0 0
SDC3 -0.002 0.042 -10000 0 -0.81 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.11 0.22 -10000 0 -0.5 85 85
IL8 -0.19 0.37 0.32 10 -0.86 85 95
Syndecan-3/Fyn/Cortactin -0.002 0.038 -10000 0 -0.73 1 1
Syndecan-3/CASK -0.002 0.04 -10000 0 -0.77 1 1
alpha-MSH/MC4R -0.003 0.066 -10000 0 -0.67 3 3
Gamma Secretase 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 0.001 0.016 0.32 1 -10000 0 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.066 0.61 2 -10000 0 2
CDKN1A -0.027 0.16 -10000 0 -1 10 10
KAT2B -0.007 0.077 -10000 0 -0.86 3 3
BAX 0 0 -10000 0 -10000 0 0
FOXO3 0.001 0.012 -10000 0 -10000 0 0
FOXO1 -0.009 0.089 -10000 0 -0.86 4 4
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.35 0.42 -10000 0 -0.86 152 152
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.003 0.061 -10000 0 -0.67 3 3
PPARGC1A -0.11 0.28 -10000 0 -0.86 46 46
FHL2 -0.088 0.26 -10000 0 -0.86 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.052 -10000 0 -0.63 2 2
HIST2H4A 0.013 0.066 -10000 0 -0.61 2 2
SIRT1/FOXO3a 0.001 0.047 -10000 0 -0.55 2 2
SIRT1 0.001 0.068 -10000 0 -0.82 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.047 -10000 0 -0.55 2 2
SIRT1/Histone H1b 0.005 0.048 -10000 0 -0.51 2 2
apoptosis 0 0.046 0.55 2 -10000 0 2
SIRT1/PGC1A -0.073 0.2 -10000 0 -0.59 47 47
p53/SIRT1 0.007 0.081 0.43 9 -0.61 2 11
SIRT1/FOXO4 0.001 0.047 -10000 0 -0.54 2 2
FOXO1/FHL2/SIRT1 -0.061 0.18 -10000 0 -0.54 43 43
HIST1H1E 0.005 0.024 -10000 0 -10000 0 0
SIRT1/p300 0 0.052 -10000 0 -0.63 2 2
muscle cell differentiation 0.004 0.079 0.7 4 -10000 0 4
TP53 0.005 0.032 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.046 -10000 0 -0.55 2 2
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.28 0.33 -10000 0 -0.67 152 152
ACSS2 0 0.051 -10000 0 -0.63 2 2
SIRT1/PCAF/MYOD -0.004 0.08 -10000 0 -0.7 4 4
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.034 0.14 -9999 0 -0.58 22 22
E-cadherin/beta catenin -0.04 0.16 -9999 0 -0.67 22 22
CTNNB1 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
CDH1 -0.051 0.2 -9999 0 -0.86 22 22
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.002 0.03 -10000 0 -0.58 1 1
EPHB2 0.062 0.14 0.32 76 -0.86 1 77
Syndecan-2/TACI 0 0.05 -10000 0 -0.58 2 2
LAMA1 -0.087 0.3 0.32 20 -0.86 45 65
Syndecan-2/alpha2 ITGB1 0.058 0.13 0.38 29 -0.5 4 33
HRAS 0.002 0.023 0.32 2 -10000 0 2
Syndecan-2/CASK 0 0 -10000 0 -10000 0 0
ITGA5 0 0 -10000 0 -10000 0 0
BAX 0.003 0.12 -10000 0 -0.52 20 20
EPB41 0 0 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -10000 0 -10000 0 0
LAMA3 0.038 0.15 0.32 55 -0.86 4 59
EZR -0.002 0.045 -10000 0 -0.86 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.023 0.14 -10000 0 -0.86 10 10
Syndecan-2/MMP2 -0.023 0.13 -10000 0 -0.58 17 17
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.038 0.083 -10000 0 -10000 0 0
dendrite morphogenesis 0.044 0.096 -10000 0 -0.58 1 1
Syndecan-2/GM-CSF 0 0 -10000 0 -10000 0 0
determination of left/right symmetry 0.015 0.001 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0 0 -10000 0 -10000 0 0
GNB2L1 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
Syndecan-2/RACK1 0.001 0.014 -10000 0 -10000 0 0
NF1 -0.002 0.045 -10000 0 -0.86 1 1
FGFR/FGF/Syndecan-2 0.015 0.001 -10000 0 -10000 0 0
ITGA2 0.055 0.12 0.32 65 -10000 0 65
MAPK8 -0.004 0.14 -10000 0 -0.58 20 20
Syndecan-2/alpha2/beta1 Integrin -0.02 0.2 0.38 7 -0.49 45 52
Syndecan-2/Kininogen -0.046 0.16 -10000 0 -0.58 29 29
ITGB1 0 0 -10000 0 -10000 0 0
SRC 0.003 0.023 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0 0 -10000 0 -10000 0 0
extracellular matrix organization 0.003 0.026 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.002 0.03 -10000 0 -0.58 1 1
Syndecan-2/Caveolin-2/Ras -0.013 0.088 -10000 0 -0.53 10 10
Syndecan-2/Laminin alpha3 0.027 0.1 -10000 0 -0.58 4 4
Syndecan-2/RasGAP -0.002 0.036 -10000 0 -0.47 2 2
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
Syndecan-2 dimer 0.044 0.096 -10000 0 -0.58 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0 0.039 -10000 0 -0.45 2 2
RHOA 0 0 -10000 0 -10000 0 0
SDCBP 0 0 -10000 0 -10000 0 0
TNFRSF13B 0 0.073 0.32 5 -0.86 2 7
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
alpha2/beta1 Integrin 0.038 0.083 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0 0 -10000 0 -10000 0 0
TGFB1 0.004 0.036 0.32 5 -10000 0 5
CASP3 -0.001 0.028 -10000 0 -0.54 1 1
FN1 -0.002 0.045 -10000 0 -0.86 1 1
Syndecan-2/IL8 -0.13 0.25 0.22 10 -0.58 85 95
SDC2 0.016 0.001 -10000 0 -10000 0 0
KNG1 -0.067 0.23 -10000 0 -0.86 29 29
Syndecan-2/Neurofibromin -0.002 0.03 -10000 0 -0.58 1 1
TRAPPC4 0 0 -10000 0 -10000 0 0
CSF2 0 0 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.003 0.026 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-2/Ezrin -0.001 0.028 -10000 0 -0.53 1 1
PRKACA -0.001 0.027 -10000 0 -0.53 1 1
angiogenesis -0.13 0.25 0.22 10 -0.58 85 95
MMP2 -0.034 0.18 0.32 6 -0.86 17 23
IL8 -0.19 0.37 0.32 10 -0.86 85 95
calcineurin-NFAT signaling pathway 0 0.05 -10000 0 -0.58 2 2
Signaling events mediated by PTP1B

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
PDGFRB 0.007 0.046 0.32 8 -10000 0 8
Jak2/Leptin Receptor -0.06 0.19 -10000 0 -0.46 62 62
PTP1B/AKT1 -0.007 0.032 -10000 0 -0.26 2 2
FYN 0 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.05 0.059 -10000 0 -0.29 2 2
EGFR -0.019 0.14 -10000 0 -0.86 10 10
EGF/EGFR 0.034 0.13 0.24 40 -0.5 10 50
CSF1 -0.008 0.092 0.32 2 -0.86 4 6
AKT1 0 0.001 -10000 0 -10000 0 0
INSR 0 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.021 0.086 -10000 0 -0.46 12 12
Insulin Receptor/Insulin -0.003 0.036 0.24 1 -10000 0 1
HCK -0.028 0.15 -10000 0 -0.86 12 12
CRK 0 0 -10000 0 -10000 0 0
TYK2 0.054 0.056 -10000 0 -0.28 1 1
EGF 0.076 0.14 0.32 88 -10000 0 88
YES1 0 0 -10000 0 -10000 0 0
CAV1 0.058 0.065 -10000 0 -0.28 2 2
TXN 0.002 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.007 0.029 -10000 0 -10000 0 0
cell migration -0.05 0.059 0.29 2 -10000 0 2
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.023 0.15 -10000 0 -0.86 11 11
ITGA2B 0.007 0.046 0.32 8 -10000 0 8
CSF1R -0.021 0.13 -10000 0 -0.86 9 9
Prolactin Receptor/Prolactin -0.012 0.12 -10000 0 -0.67 11 11
FGR -0.005 0.063 -10000 0 -0.86 2 2
PTP1B/p130 Cas -0.008 0.031 -10000 0 -0.27 2 2
Crk/p130 Cas -0.007 0.029 -10000 0 -10000 0 0
DOK1 0.057 0.053 -10000 0 -10000 0 0
JAK2 0.038 0.072 -10000 0 -0.44 2 2
Jak2/Leptin Receptor/Leptin -0.11 0.22 -10000 0 -0.63 51 51
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
PTPN1 0.05 0.059 -10000 0 -0.3 2 2
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.025 0.15 -10000 0 -0.86 11 11
SRC 0.036 0.031 -10000 0 -10000 0 0
ITGB3 -0.07 0.24 -10000 0 -0.86 30 30
CAT1/PTP1B -0.061 0.19 -10000 0 -0.49 32 32
CAPN1 0.002 0.005 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.006 0.063 -10000 0 -0.75 2 2
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.11 0.24 -10000 0 -0.67 51 51
negative regulation of transcription 0.038 0.071 -10000 0 -0.43 2 2
FCGR2A 0.002 0.023 0.32 2 -10000 0 2
FER 0.002 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.049 0.19 -10000 0 -0.67 30 30
BLK -0.15 0.33 0.32 2 -0.86 65 67
Insulin Receptor/Insulin/Shc 0.003 0.023 -10000 0 -10000 0 0
RHOA 0.002 0.005 -10000 0 -10000 0 0
LEPR -0.14 0.32 -10000 0 -0.86 62 62
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0 -10000 0 -10000 0 0
mol:NADPH 0.002 0.002 -10000 0 -10000 0 0
TRPV6 -0.13 0.23 -10000 0 -0.55 46 46
PRL 0.004 0.029 0.32 3 -10000 0 3
SOCS3 -0.19 0.52 -10000 0 -1.5 50 50
SPRY2 -0.01 0.1 -10000 0 -0.87 5 5
Insulin Receptor/Insulin/IRS1 0.003 0.023 -10000 0 -10000 0 0
CSF1/CSF1R -0.021 0.089 0.27 2 -0.45 13 15
Ras protein signal transduction -0.004 0.02 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
INS 0.005 0.037 0.32 5 -10000 0 5
LEP 0.01 0.056 0.32 12 -10000 0 12
STAT5B 0.048 0.057 -10000 0 -0.24 3 3
STAT5A 0.049 0.057 -10000 0 -0.24 3 3
GRB2 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.052 0.27 8 -0.28 1 9
CSN2 -0.014 0.041 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
LAT 0.036 0.032 0.32 1 -10000 0 1
YBX1 0 0 -10000 0 -10000 0 0
LCK -0.025 0.15 0.32 1 -0.86 11 12
SHC1 0 0 -10000 0 -10000 0 0
NOX4 0.12 0.15 0.32 142 -10000 0 142
Aurora A signaling

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
Aurora A/GADD45A 0.001 0.084 -10000 0 -0.59 6 6
BIRC5 0.21 0.15 0.32 245 -10000 0 245
NFKBIA 0.02 0.033 -10000 0 -10000 0 0
CPEB1 0.01 0.056 0.32 12 -10000 0 12
AKT1 0.02 0.033 -10000 0 -10000 0 0
NDEL1 0 0 -10000 0 -10000 0 0
Aurora A/BRCA1 0.011 0.034 0.24 1 -10000 0 1
NDEL1/TACC3 0.035 0.073 -10000 0 -10000 0 0
GADD45A -0.014 0.11 -10000 0 -0.86 6 6
GSK3B 0 0.001 -10000 0 -10000 0 0
PAK1/Aurora A 0.011 0.036 -10000 0 -10000 0 0
MDM2 0 0 -10000 0 -10000 0 0
JUB -0.002 0.045 -10000 0 -0.86 1 1
TPX2 0.037 0.048 -10000 0 -10000 0 0
TP53 0.017 0.027 -10000 0 -10000 0 0
DLG7 0.007 0.037 -10000 0 -10000 0 0
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0 0 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.037 0.077 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.01 0.034 0.24 1 -10000 0 1
AURKA 0.012 0.053 -10000 0 -10000 0 0
AURKB 0.1 0.084 0.19 175 -10000 0 175
CDC25B 0.019 0.034 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.043 -10000 0 -0.53 1 1
mRNA polyadenylation 0.014 0.047 0.24 5 -10000 0 5
Aurora A/CPEB 0.014 0.048 0.24 5 -10000 0 5
Aurora A/TACC1/TRAP/chTOG 0.017 0.031 -10000 0 -10000 0 0
BRCA1 0.001 0.016 0.32 1 -10000 0 1
centrosome duplication 0.011 0.036 -10000 0 -10000 0 0
regulation of centrosome cycle 0.034 0.071 -10000 0 -10000 0 0
spindle assembly 0.017 0.03 -10000 0 -10000 0 0
TDRD7 0 0 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.1 0.4 1 -0.46 2 3
CENPA 0.11 0.092 0.19 211 -10000 0 211
Aurora A/PP2A 0.011 0.036 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.032 0.029 -10000 0 -10000 0 0
negative regulation of DNA binding 0.016 0.027 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0 0 -10000 0 -10000 0 0
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
Ajuba/Aurora A 0.009 0.043 -10000 0 -0.54 1 1
mitotic prometaphase -0.02 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.052 -10000 0 -10000 0 0
TACC1 0 0 -10000 0 -10000 0 0
TACC3 0.039 0.1 0.32 46 -10000 0 46
Aurora A/Antizyme1 0.014 0.032 -10000 0 -10000 0 0
Aurora A/RasGAP 0.008 0.057 -10000 0 -0.59 2 2
OAZ1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0 0.001 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.037 0.048 -10000 0 -10000 0 0
PPP2R5D 0 0 -10000 0 -10000 0 0
Aurora A/TPX2 0.031 0.059 -10000 0 -10000 0 0
PAK1 0 0 -10000 0 -10000 0 0
CKAP5 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0 0.001 -10000 0 -10000 0 0
HDAC2 0 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.011 0.079 -10000 0 -0.58 7 7
forebrain development -0.025 0.14 -10000 0 -0.52 19 19
GNAO1 -0.41 0.43 -10000 0 -0.86 178 178
SMO/beta Arrestin2 -0.007 0.069 -10000 0 -0.67 4 4
SMO -0.009 0.089 -10000 0 -0.86 4 4
ARRB2 0 0 -10000 0 -10000 0 0
GLI3/SPOP -0.003 0.029 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0 0 -10000 0 -10000 0 0
GNAI1 -0.005 0.063 -10000 0 -0.86 2 2
XPO1 0.01 0.003 -10000 0 -10000 0 0
GLI1/Su(fu) -0.045 0.11 -10000 0 -0.5 18 18
SAP30 0 0.001 -10000 0 -10000 0 0
mol:GDP -0.009 0.089 -10000 0 -0.86 4 4
MIM/GLI2A 0.014 0.007 -10000 0 -10000 0 0
IFT88 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GLI2 0.017 0.07 -10000 0 -10000 0 0
GLI3 0.032 0.04 0.3 1 -0.32 3 4
CSNK1D 0 0 -10000 0 -10000 0 0
CSNK1E 0.001 0.016 0.32 1 -10000 0 1
SAP18 0 0.001 -10000 0 -10000 0 0
embryonic digit morphogenesis 0 0 -10000 0 -10000 0 0
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
Gi family/GTP -0.14 0.2 -10000 0 -0.34 180 180
SIN3B 0 0.001 -10000 0 -10000 0 0
SIN3A 0 0.001 -10000 0 -10000 0 0
GLI3/Su(fu) -0.003 0.027 -10000 0 -10000 0 0
GLI2/Su(fu) -0.015 0.056 -10000 0 -0.44 1 1
FOXA2 -0.007 0.096 -10000 0 -1.3 2 2
neural tube patterning -0.025 0.14 -10000 0 -0.52 19 19
SPOP 0 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 -0.003 0.028 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
CSNK1G2 0 0 -10000 0 -10000 0 0
CSNK1G3 0 0 -10000 0 -10000 0 0
MTSS1 0.014 0.007 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.025 0.14 -10000 0 -0.52 19 19
SUFU -0.003 0.032 -10000 0 -0.31 4 4
LGALS3 0.024 0.084 0.32 28 -10000 0 28
catabolic process -0.013 0.047 -10000 0 -0.42 1 1
GLI3A/CBP 0.006 0.039 -10000 0 -0.39 1 1
KIF3A 0 0 -10000 0 -10000 0 0
GLI1 -0.025 0.14 -10000 0 -0.53 19 19
RAB23 0 0 -10000 0 -10000 0 0
CSNK1A1 0 0 -10000 0 -10000 0 0
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0 0.001 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.014 0.066 -10000 0 -10000 0 0
GNAZ 0.15 0.17 0.32 176 -0.86 1 177
RBBP4 0 0.001 -10000 0 -10000 0 0
CSNK1G1 0 0 -10000 0 -10000 0 0
PIAS1 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GLI2/SPOP -0.016 0.054 -10000 0 -10000 0 0
STK36 0.01 0.003 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.11 0.17 -10000 0 -0.54 9 9
PTCH1 -0.056 0.29 -10000 0 -1.2 19 19
MIM/GLI1 -0.015 0.14 -10000 0 -0.52 18 18
CREBBP 0.006 0.039 -10000 0 -0.39 1 1
Su(fu)/SIN3/HDAC complex 0.002 0.013 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.007 0.035 -10000 0 -10000 0 0
VDR -0.009 0.14 0.32 11 -0.86 8 19
FAM120B -0.002 0.045 -10000 0 -0.86 1 1
RXRs/LXRs/DNA/9cRA -0.001 0.084 -10000 0 -0.33 6 6
RXRs/LXRs/DNA/Oxysterols -0.008 0.1 -10000 0 -0.4 16 16
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0.003 0.013 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.019 0.079 -10000 0 -0.35 20 20
RXRs/NUR77 -0.072 0.22 -10000 0 -0.53 63 63
RXRs/PPAR 0.008 0.061 -10000 0 -0.34 6 6
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.008 0.1 0.21 11 -0.67 8 19
RARs/VDR/DNA/Vit D3 -0.029 0.14 -10000 0 -0.52 24 24
RARA 0 0 -10000 0 -10000 0 0
NCOA1 0 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.009 0.14 0.32 11 -0.86 8 19
RARs/RARs/DNA/9cRA -0.023 0.11 -10000 0 -0.51 17 17
RARG 0 0 -10000 0 -10000 0 0
RPS6KB1 0.007 0.029 -10000 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.019 0.079 -10000 0 -0.35 20 20
THRA 0 0 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.008 0.1 0.21 11 -0.67 8 19
RXRs/PPAR/9cRA/PGJ2/DNA 0.01 0.1 -10000 0 -0.52 6 6
NR1H4 -0.023 0.14 -10000 0 -0.86 10 10
RXRs/LXRs/DNA 0.01 0.1 -10000 0 -0.48 6 6
NR1H2 0.011 0.009 -10000 0 -10000 0 0
NR1H3 0.011 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.006 0.12 0.36 4 -0.5 14 18
NR4A1 -0.13 0.31 -10000 0 -0.86 58 58
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.006 0.083 -10000 0 -0.35 15 15
RXRG 0.034 0.14 0.32 44 -0.86 5 49
RXR alpha/CCPG -0.004 0.049 -10000 0 -0.66 2 2
RXRA 0.008 0.046 -10000 0 -0.86 1 1
RXRB 0.01 0.011 -10000 0 -10000 0 0
THRB -0.007 0.077 -10000 0 -0.86 3 3
PPARG 0.001 0.016 0.32 1 -10000 0 1
PPARD 0 0 -10000 0 -10000 0 0
TNF 0.01 0.25 -10000 0 -1.2 14 14
mol:Oxysterols 0.003 0.011 -10000 0 -10000 0 0
cholesterol transport -0.008 0.1 -10000 0 -0.4 16 16
PPARA 0 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.039 0.18 -10000 0 -0.86 17 17
RXRs/NUR77/BCL2 -0.05 0.14 -10000 0 -0.35 64 64
SREBF1 0.04 0.12 -10000 0 -1.2 1 1
RXRs/RXRs/DNA/9cRA 0.01 0.1 -10000 0 -0.52 6 6
ABCA1 0.035 0.15 -10000 0 -1.2 3 3
RARs/THRs -0.027 0.11 -10000 0 -0.5 20 20
RXRs/FXR -0.001 0.14 -10000 0 -0.56 15 15
BCL2 -0.002 0.045 -10000 0 -0.86 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.028 0.15 -10000 0 -0.86 12 12
Caspase 8 (4 units) -0.06 0.16 -10000 0 -0.8 10 10
NEF -0.007 0.042 -10000 0 -0.22 13 13
NFKBIA 0.001 0.012 -10000 0 -10000 0 0
BIRC3 0.007 0.086 -10000 0 -0.86 2 2
CYCS -0.02 0.17 -10000 0 -0.77 10 10
RIPK1 0 0 -10000 0 -10000 0 0
CD247 -0.011 0.082 0.39 1 -0.96 2 3
MAP2K7 -0.018 0.16 -10000 0 -0.53 17 17
protein ubiquitination 0.023 0.1 -10000 0 -0.49 5 5
CRADD -0.002 0.045 -10000 0 -0.86 1 1
DAXX 0 0 -10000 0 -10000 0 0
FAS -0.028 0.15 -10000 0 -0.86 12 12
BID -0.061 0.17 -10000 0 -0.4 57 57
NF-kappa-B/RelA/I kappa B alpha 0.005 0.044 -10000 0 -10000 0 0
TRADD -0.002 0.045 -10000 0 -0.86 1 1
MAP3K5 -0.1 0.28 -10000 0 -0.86 43 43
CFLAR 0 0 -10000 0 -10000 0 0
FADD 0.001 0.016 0.32 1 -10000 0 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.005 0.045 -10000 0 -10000 0 0
MAPK8 -0.035 0.19 -10000 0 -0.55 33 33
APAF1 0 0 -10000 0 -10000 0 0
TRAF1 0.001 0.016 0.32 1 -10000 0 1
TRAF2 0 0 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.065 0.18 -10000 0 -0.42 58 58
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.035 0.11 -10000 0 -0.64 6 6
CHUK 0.022 0.11 -10000 0 -0.55 5 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.073 0.2 -10000 0 -0.56 49 49
TCRz/NEF -0.016 0.097 0.38 1 -0.44 15 16
TNF -0.031 0.17 0.32 2 -0.86 14 16
FASLG -0.036 0.19 0.37 1 -0.94 15 16
NFKB1 0.001 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.04 0.15 -10000 0 -0.58 26 26
CASP6 -0.044 0.12 -10000 0 -0.55 10 10
CASP7 0.027 0.14 -10000 0 -0.52 12 12
RELA 0.001 0.012 -10000 0 -10000 0 0
CASP2 0 0 -10000 0 -10000 0 0
CASP3 0.027 0.14 -10000 0 -0.52 13 13
TNFRSF1A 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.022 0.12 -10000 0 -0.67 12 12
CASP8 0 0 -10000 0 -10000 0 0
CASP9 0 0 -10000 0 -10000 0 0
MAP3K14 0.015 0.12 -10000 0 -0.63 5 5
APAF-1/Caspase 9 -0.031 0.11 0.26 1 -0.48 12 13
BCL2 -0.026 0.18 -10000 0 -0.5 34 34
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.025 0.14 0.86 11 -10000 0 11
PI3K Class IB/PDE3B -0.025 0.15 -10000 0 -0.86 11 11
PDE3B -0.025 0.15 -10000 0 -0.86 11 11
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.004 0.1 -10000 0 -0.44 17 17
CRKL 0.006 0.082 -10000 0 -0.42 11 11
HRAS -0.025 0.12 -10000 0 -0.58 9 9
mol:PIP3 -0.006 0.081 -10000 0 -0.4 12 12
SPRED1 -0.002 0.045 -10000 0 -0.86 1 1
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.02 0.08 -10000 0 -0.44 11 11
FOXO3 0.011 0.076 -10000 0 -0.38 11 11
AKT1 0.004 0.081 -10000 0 -0.42 11 11
BAD 0.011 0.076 -10000 0 -0.38 11 11
megakaryocyte differentiation -0.028 0.15 -10000 0 -0.49 31 31
GSK3B 0.011 0.076 -10000 0 -0.38 11 11
RAF1 0.013 0.1 -10000 0 -0.48 7 7
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.02 0.08 -10000 0 -0.44 11 11
STAT1 -0.041 0.21 -10000 0 -1.1 11 11
HRAS/SPRED1 -0.023 0.092 0.24 1 -0.47 8 9
cell proliferation -0.027 0.14 -10000 0 -0.5 29 29
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
TEC -0.014 0.11 -10000 0 -0.86 6 6
RPS6KB1 0 0.086 -10000 0 -0.44 11 11
HRAS/SPRED2 -0.022 0.09 0.24 1 -0.48 7 8
LYN/TEC/p62DOK -0.025 0.089 -10000 0 -0.43 17 17
MAPK3 0.024 0.076 -10000 0 -0.32 7 7
STAP1 -0.02 0.081 -10000 0 -0.45 11 11
GRAP2 -0.016 0.14 0.32 6 -0.86 9 15
JAK2 -0.066 0.16 -10000 0 -0.91 11 11
STAT1 (dimer) -0.039 0.21 -10000 0 -1.1 11 11
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.039 0.13 -10000 0 -0.47 28 28
actin filament polymerization 0 0.085 -10000 0 -0.43 11 11
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.027 0.11 -10000 0 -0.62 11 11
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
CBL/CRKL/GRB2 -0.015 0.063 -10000 0 -0.37 11 11
PI3K -0.022 0.092 -10000 0 -0.49 12 12
PTEN -0.005 0.063 -10000 0 -0.86 2 2
SCF/KIT/EPO/EPOR -0.21 0.33 -10000 0 -1.5 11 11
MAPK8 -0.047 0.14 -10000 0 -0.51 29 29
STAT3 (dimer) 0 0.085 -10000 0 -0.44 11 11
positive regulation of transcription 0.024 0.064 -10000 0 -0.26 7 7
mol:GDP -0.033 0.13 0.29 1 -0.6 11 12
PIK3C2B -0.02 0.08 -10000 0 -0.44 11 11
CBL/CRKL -0.015 0.069 -10000 0 -0.39 11 11
FER -0.02 0.08 -10000 0 -0.44 11 11
SH2B3 -0.02 0.08 -10000 0 -0.44 11 11
PDPK1 0.001 0.076 -10000 0 -0.38 11 11
SNAI2 -0.021 0.089 -10000 0 -0.46 13 13
positive regulation of cell proliferation -0.018 0.15 -10000 0 -0.77 11 11
KITLG 0.012 0.032 0.31 4 -10000 0 4
cell motility -0.018 0.15 -10000 0 -0.77 11 11
PTPN6 0.005 0.007 -10000 0 -10000 0 0
EPOR 0.013 0.065 -10000 0 -10000 0 0
STAT5A (dimer) -0.013 0.13 -10000 0 -0.63 11 11
SOCS1 -0.001 0.071 0.32 4 -0.86 2 6
cell migration 0.004 0.1 0.48 13 -10000 0 13
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.31 0.43 0.32 11 -0.86 136 147
VAV1 -0.039 0.18 -10000 0 -0.86 17 17
GRB10 -0.02 0.08 -10000 0 -0.44 11 11
PTPN11 0.001 0.004 -10000 0 -10000 0 0
SCF/KIT -0.024 0.085 -10000 0 -0.47 11 11
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.022 0.083 -10000 0 -0.36 7 7
CBL 0 0 -10000 0 -10000 0 0
KIT -0.021 0.26 -10000 0 -1.5 11 11
MAP2K2 0.022 0.083 -10000 0 -0.36 7 7
SHC/Grb2/SOS1 -0.018 0.07 -10000 0 -0.41 11 11
STAT5A -0.013 0.13 -10000 0 -0.65 11 11
GRB2 0 0 -10000 0 -10000 0 0
response to radiation -0.002 0.093 -10000 0 -0.45 13 13
SHC/GRAP2 -0.013 0.11 -10000 0 -0.67 9 9
PTPRO -0.048 0.14 -10000 0 -0.5 31 31
SH2B2 -0.019 0.08 -10000 0 -0.44 11 11
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.023 0.096 -10000 0 -0.49 13 13
CREBBP 0.025 0.014 -10000 0 -10000 0 0
BCL2 0.012 0.1 -10000 0 -1.6 1 1
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.034 -10000 0 -10000 0 0
MAP4K4 -0.008 0.06 -10000 0 -10000 0 0
BAG4 -0.028 0.15 -10000 0 -0.86 12 12
PKC zeta/ceramide -0.027 0.11 -10000 0 -0.52 17 17
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 0.007 0.088 0.32 14 -0.86 2 16
BAX 0.003 0.007 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.016 0.02 -10000 0 -10000 0 0
BAD 0.003 0.014 -10000 0 -10000 0 0
SMPD1 0.014 0.056 -10000 0 -0.26 14 14
RB1 0.003 0.014 -10000 0 -10000 0 0
FADD/Caspase 8 -0.007 0.056 -10000 0 -10000 0 0
MAP2K4 0.01 0.014 -10000 0 -10000 0 0
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.01 0.014 -10000 0 -10000 0 0
EGF 0.075 0.13 0.32 88 -10000 0 88
mol:ceramide -0.004 0.015 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.027 0.036 0.27 1 -10000 0 1
ASAH1 0.001 0.016 0.32 1 -10000 0 1
negative regulation of cell cycle 0.003 0.014 -10000 0 -10000 0 0
cell proliferation -0.16 0.2 -10000 0 -0.4 145 145
BID 0.022 0.046 -10000 0 -10000 0 0
MAP3K1 0.003 0.014 -10000 0 -10000 0 0
EIF2A 0.016 0.013 -10000 0 -10000 0 0
TRADD -0.002 0.045 -10000 0 -0.86 1 1
CRADD -0.002 0.045 -10000 0 -0.86 1 1
MAPK3 0.019 0.013 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.019 0.013 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.003 0.007 -10000 0 -10000 0 0
FADD -0.008 0.06 -10000 0 -10000 0 0
KSR1 0.004 0.014 -10000 0 -10000 0 0
MAPK8 -0.019 0.12 -10000 0 -0.34 34 34
PRKRA 0.003 0.014 -10000 0 -10000 0 0
PDGFA 0.02 0.078 0.32 24 -10000 0 24
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.34 0.42 -10000 0 -0.86 145 145
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.004 0.015 -10000 0 -10000 0 0
CTSD 0 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 -0.17 0.21 -10000 0 -0.43 145 145
PRKCD 0 0 -10000 0 -10000 0 0
PRKCZ -0.039 0.18 -10000 0 -0.86 17 17
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.027 0.036 0.27 1 -10000 0 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.009 0.064 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.04 0.15 -10000 0 -0.58 26 26
mol:Sphingosine-1-phosphate 0.027 0.034 -10000 0 -10000 0 0
MAP2K1 0.016 0.013 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS 0.004 0.014 0.2 1 -10000 0 1
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.022 0.12 -10000 0 -0.67 12 12
EIF2AK2 0.01 0.014 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.021 0.11 -10000 0 -0.58 14 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.004 0.036 -10000 0 -10000 0 0
MAP2K2 0.016 0.013 -10000 0 -10000 0 0
SMPD3 -0.026 0.15 -10000 0 -0.38 48 48
TNF -0.031 0.17 0.32 2 -0.86 14 16
PKC zeta/PAR4 -0.031 0.14 -10000 0 -0.67 17 17
mol:PHOSPHOCHOLINE -0.038 0.045 -10000 0 -0.17 8 8
NF kappa B1/RelA/I kappa B alpha -0.023 0.1 -10000 0 -0.5 17 17
AIFM1 0.004 0.014 0.2 1 -10000 0 1
BCL2 -0.002 0.045 -10000 0 -0.86 1 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR -0.009 0.14 0.32 11 -0.86 8 19
Cbp/p300/PCAF -0.005 0.052 -10000 0 -0.58 3 3
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.066 -10000 0 -0.34 2 2
KAT2B -0.007 0.077 -10000 0 -0.86 3 3
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.038 0.12 0.24 64 -0.37 11 75
RAR alpha/9cRA/Cyclin H -0.016 0.064 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.01 0.078 -10000 0 -0.29 20 20
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.038 0.16 -10000 0 -0.7 20 20
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.008 0.1 0.21 11 -0.67 8 19
RXRs/RARs/NRIP1/9cRA 0.033 0.09 -10000 0 -0.51 2 2
NCOA2 -0.11 0.29 -10000 0 -0.86 48 48
NCOA3 0 0 -10000 0 -10000 0 0
NCOA1 0 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.009 0.14 0.32 11 -0.86 8 19
RARG 0 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 -0.046 0.19 -10000 0 -0.86 20 20
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.015 0.093 -10000 0 -0.47 8 8
RARA -0.016 0.073 -10000 0 -0.32 20 20
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.03 0.15 -10000 0 -0.34 63 63
PRKCA 0.01 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.02 0.082 -10000 0 -0.54 2 2
RXRG 0.027 0.071 -10000 0 -0.46 5 5
RXRA 0.01 0.075 -10000 0 -0.29 21 21
RXRB 0.02 0.014 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.008 0.1 0.21 11 -0.67 8 19
RBP1 -0.17 0.35 0.32 7 -0.86 74 81
CRBP1/9-cic-RA -0.13 0.27 0.21 7 -0.67 74 81
RARB -0.038 0.18 -10000 0 -0.86 17 17
PRKCG 0.008 0.033 0.32 4 -10000 0 4
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.023 0.12 0.35 1 -0.52 1 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.035 0.085 -10000 0 -0.44 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.081 -10000 0 -0.44 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 0.02 0.082 -10000 0 -0.54 2 2
positive regulation of DNA binding -0.015 0.061 -10000 0 -10000 0 0
NRIP1 0.02 0.096 -10000 0 -1.3 1 1
RXRs/RARs 0.017 0.074 -10000 0 -0.44 2 2
RXRs/RXRs/DNA/9cRA -0.006 0.058 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.011 0.044 -10000 0 -10000 0 0
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.014 0.025 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.002 0.022 -10000 0 -10000 0 0
STXBP1 -0.005 0.063 -10000 0 -0.86 2 2
ACh/CHRNA1 0.003 0.061 0.26 15 -10000 0 15
RAB3GAP2/RIMS1/UNC13B 0.002 0.021 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.003 0.028 0.32 3 -10000 0 3
mol:ACh 0 0.048 -10000 0 -0.16 30 30
RAB3GAP2 0 0 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.015 0.068 -10000 0 -0.53 2 2
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.003 0.061 0.26 15 -10000 0 15
UNC13B 0.001 0.016 0.32 1 -10000 0 1
CHRNA1 0.013 0.062 0.32 15 -10000 0 15
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.094 0.24 0.24 20 -0.63 60 80
SNAP25 -0.021 0.12 -10000 0 -0.39 30 30
VAMP2 0 0 -10000 0 -10000 0 0
SYT1 -0.12 0.33 0.32 22 -0.86 60 82
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.048 -10000 0 -0.59 2 2
STX1A/SNAP25 fragment 1/VAMP2 -0.015 0.068 -10000 0 -0.53 2 2
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.036 0.14 -10000 0 -0.61 22 22
KLHL20 -0.026 0.069 -10000 0 -0.33 5 5
CYFIP2 -0.051 0.2 -10000 0 -0.86 22 22
Rac1/GDP 0.026 0.099 -10000 0 -0.37 21 21
ENAH -0.035 0.14 -10000 0 -0.61 22 22
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CTNNB1 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.018 0.073 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.027 0.061 -10000 0 -0.2 26 26
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.035 0.14 -10000 0 -0.53 27 27
RAPGEF1 0.012 0.13 -10000 0 -0.51 22 22
CTNND1 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.15 -10000 0 -0.63 22 22
CRK 0.003 0.14 -10000 0 -0.56 22 22
E-cadherin/gamma catenin/alpha catenin -0.034 0.14 -10000 0 -0.58 22 22
alphaE/beta7 Integrin -0.005 0.083 -10000 0 -0.67 5 5
IQGAP1 0 0 -10000 0 -10000 0 0
NCKAP1 0 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -10000 0 -10000 0 0
DLG1 -0.036 0.14 -10000 0 -0.61 22 22
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.015 0.056 -10000 0 -0.37 1 1
MLLT4 0 0 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.028 0.12 -10000 0 -0.54 20 20
PI3K -0.019 0.074 -10000 0 -0.51 1 1
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.04 0.16 -10000 0 -0.67 22 22
TIAM1 -0.046 0.19 -10000 0 -0.86 20 20
E-cadherin(dimer)/Ca2+ -0.03 0.12 -10000 0 -0.5 22 22
AKT1 -0.011 0.041 -10000 0 -0.26 1 1
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
CDH1 -0.051 0.2 -10000 0 -0.86 22 22
RhoA/GDP 0.026 0.099 -10000 0 -0.37 21 21
actin cytoskeleton organization -0.019 0.051 0.11 1 -0.24 5 6
CDC42/GDP 0.026 0.099 -10000 0 -0.37 21 21
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.021 0.085 -10000 0 -0.36 22 22
ITGB7 -0.012 0.099 -10000 0 -0.86 5 5
RAC1 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.031 0.12 -10000 0 -0.53 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin -0.03 0.12 -10000 0 -0.51 22 22
mol:GDP 0.022 0.12 -10000 0 -0.44 22 22
CDC42/GTP/IQGAP1 0 0 -10000 0 -10000 0 0
JUP 0 0 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.022 0.088 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.018 0.058 0.2 1 -0.28 14 15
NME1 0.002 0.023 0.32 2 -10000 0 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.036 0.14 -10000 0 -0.61 22 22
regulation of cell-cell adhesion -0.016 0.064 -10000 0 -10000 0 0
WASF2 -0.014 0.031 -10000 0 -0.14 1 1
Rap1/GTP -0.021 0.084 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.033 0.13 -10000 0 -0.5 27 27
CCND1 -0.022 0.074 0.23 1 -0.36 14 15
VAV2 0.007 0.14 -10000 0 -0.54 22 22
RAP1/GDP -0.021 0.084 -10000 0 -10000 0 0
adherens junction assembly -0.035 0.14 -10000 0 -0.58 22 22
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0 0 -10000 0 -10000 0 0
PIP5K1C 0 0 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.031 0.13 -10000 0 -0.48 27 27
E-cadherin/beta catenin -0.031 0.12 -10000 0 -0.53 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.035 0.14 -10000 0 -0.61 22 22
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
Rac1/GTP -0.043 0.12 0.21 1 -0.43 15 16
E-cadherin/beta catenin/alpha catenin -0.034 0.14 -10000 0 -0.58 22 22
ITGAE 0.006 0.043 0.32 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.039 0.15 -10000 0 -0.65 22 22
EGFR-dependent Endothelin signaling events

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
HRAS 0.002 0.023 0.32 2 -10000 0 2
EGFR -0.023 0.14 -10000 0 -0.86 10 10
EGF/EGFR 0.009 0.14 0.3 1 -0.48 21 22
EGF/EGFR dimer/SHC/GRB2/SOS1 0.03 0.12 -10000 0 -0.49 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.002 0.069 0.32 3 -0.86 2 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.075 0.13 0.32 88 -10000 0 88
EGF/EGFR dimer/SHC 0.031 0.13 -10000 0 -0.57 10 10
mol:GDP 0.026 0.11 -10000 0 -0.48 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.02 0.13 0.32 1 -0.86 9 10
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.013 0.089 -10000 0 -0.45 10 10
SHC1 0 0 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.1 -10000 0 -0.46 10 10
FRAP1 0.004 0.084 -10000 0 -0.47 10 10
EGF/EGFR dimer 0.032 0.15 -10000 0 -0.66 10 10
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.017 0.12 -10000 0 -0.67 11 11
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.02 0.16 0.32 9 -0.86 12 21
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.001 0.016 0.32 1 -10000 0 1
TCEB1 0 0 -10000 0 -10000 0 0
HIF1A/p53 -0.003 0.019 -10000 0 -10000 0 0
HIF1A 0 0.024 -10000 0 -10000 0 0
COPS5 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.001 0.01 -10000 0 -10000 0 0
FIH (dimer) 0 0 -10000 0 -10000 0 0
CDKN2A 0.22 0.15 0.32 254 -10000 0 254
ARNT/IPAS -0.016 0.12 -10000 0 -0.67 12 12
HIF1AN 0 0 -10000 0 -10000 0 0
GNB2L1 0 0 -10000 0 -10000 0 0
HIF1A/ARNT -0.003 0.019 -10000 0 -10000 0 0
CUL2 0 0 -10000 0 -10000 0 0
OS9 0 0 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.001 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.003 0.019 -10000 0 -10000 0 0
PHD1-3/OS9 0.002 0.11 -10000 0 -0.53 11 11
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.019 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
HIF1A/JAB1 -0.003 0.019 -10000 0 -10000 0 0
EGLN3 0.003 0.18 0.32 33 -0.86 11 44
EGLN2 0 0 -10000 0 -10000 0 0
EGLN1 0 0 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0.006 -10000 0 -10000 0 0
ARNT 0 0 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0 0 -10000 0 -10000 0 0
HIF1A/p19ARF 0.13 0.1 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.014 0.065 -10000 0 -0.67 2 2
adherens junction organization 0.015 0.086 -10000 0 -0.32 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.024 0.1 -10000 0 -0.54 11 11
FMN1 -0.017 0.078 -10000 0 -0.32 21 21
mol:IP3 -0.014 0.064 -10000 0 -0.64 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.021 0.081 -10000 0 -0.34 22 22
CTNNB1 0.001 0.005 -10000 0 -10000 0 0
AKT1 -0.016 0.068 -10000 0 -0.63 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.033 0.13 -10000 0 -0.56 22 22
CTNND1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.083 -10000 0 -0.31 22 22
VASP -0.02 0.076 -10000 0 -10000 0 0
ZYX -0.02 0.076 -10000 0 -0.32 22 22
JUB -0.021 0.079 -10000 0 -0.32 23 23
EGFR(dimer) -0.033 0.12 -10000 0 -0.42 28 28
E-cadherin/beta catenin-gamma catenin -0.033 0.13 -10000 0 -0.56 22 22
mol:PI-3-4-5-P3 -0.017 0.074 -10000 0 -0.68 2 2
PIK3CA -0.002 0.046 -10000 0 -0.88 1 1
PI3K -0.017 0.076 -10000 0 -0.71 2 2
FYN -0.047 0.17 -10000 0 -0.38 72 72
mol:Ca2+ -0.014 0.063 -10000 0 -0.62 2 2
JUP 0.001 0.005 -10000 0 -10000 0 0
PIK3R1 -0.005 0.064 -10000 0 -0.87 2 2
mol:DAG -0.014 0.064 -10000 0 -0.64 2 2
CDH1 -0.051 0.2 -10000 0 -0.86 22 22
RhoA/GDP -0.024 0.1 -10000 0 -0.54 11 11
establishment of polarity of embryonic epithelium 0.014 0.083 -10000 0 -10000 0 0
SRC 0.004 0.036 0.32 5 -10000 0 5
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.023 0.14 -10000 0 -0.86 10 10
CASR -0.095 0.19 -10000 0 -0.46 72 72
RhoA/GTP -0.012 0.056 -10000 0 -0.55 2 2
AKT2 -0.016 0.068 -10000 0 -0.63 2 2
actin cable formation 0.02 0.083 -10000 0 -10000 0 0
apoptosis 0.015 0.067 0.63 2 -10000 0 2
CTNNA1 0 0 -10000 0 -10000 0 0
mol:GDP -0.026 0.11 -10000 0 -0.6 11 11
PIP5K1A -0.02 0.076 -10000 0 -10000 0 0
PLCG1 -0.014 0.066 -10000 0 -0.66 2 2
Rac1/GTP -0.03 0.11 -10000 0 -0.56 10 10
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.015 0.12 0.32 1 -0.86 7 8
ANTXR2 -0.012 0.099 -10000 0 -0.86 5 5
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.019 -10000 0 -0.11 12 12
monocyte activation -0.044 0.17 -10000 0 -0.57 30 30
MAP2K2 -0.001 0.014 -10000 0 -10000 0 0
MAP2K1 -0.003 0.016 -10000 0 -10000 0 0
MAP2K7 -0.003 0.016 -10000 0 -10000 0 0
MAP2K6 -0.012 0.073 -10000 0 -0.52 7 7
CYAA -0.016 0.091 -10000 0 -0.51 12 12
MAP2K4 -0.003 0.016 -10000 0 -10000 0 0
IL1B -0.078 0.2 -10000 0 -0.52 64 64
Channel -0.017 0.097 -10000 0 -0.54 12 12
NLRP1 -0.003 0.016 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.023 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.019 0.11 12 -10000 0 12
MAPK3 -0.003 0.016 -10000 0 -10000 0 0
MAPK1 -0.003 0.016 -10000 0 -10000 0 0
PGR -0.089 0.2 -10000 0 -0.53 61 61
PA/Cellular Receptors -0.018 0.1 -10000 0 -0.59 12 12
apoptosis -0.003 0.019 -10000 0 -0.11 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.016 0.091 -10000 0 -0.51 12 12
macrophage activation 0.014 0.017 -10000 0 -10000 0 0
TNF -0.031 0.17 0.32 2 -0.86 14 16
VCAM1 -0.044 0.18 -10000 0 -0.58 30 30
platelet activation -0.004 0.023 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.025 0.1 7 -10000 0 7
IL18 -0.001 0.089 -10000 0 -0.53 10 10
negative regulation of macrophage activation -0.003 0.019 -10000 0 -0.11 12 12
LEF -0.003 0.019 -10000 0 -0.11 12 12
CASP1 -0.003 0.017 -10000 0 -10000 0 0
mol:cAMP -0.004 0.023 -10000 0 -10000 0 0
necrosis -0.003 0.019 -10000 0 -0.11 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.016 0.092 -10000 0 -0.52 12 12
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.021 0.085 -10000 0 -0.38 17 17
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
STXBP4 0.003 0.028 0.32 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.026 0.11 -10000 0 -0.42 17 17
YWHAZ 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.012 0.061 -10000 0 -0.67 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
SNARE/Synip 0.002 0.018 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.001 0.016 0.32 1 -10000 0 1
PRKCI 0 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0 0 -10000 0 -10000 0 0
GYS1 0 0.004 -10000 0 -10000 0 0
PRKCZ -0.039 0.18 -10000 0 -0.86 17 17
TRIP10 0 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.057 0.061 -10000 0 -10000 0 0
VAMP2 0 0 -10000 0 -10000 0 0
SLC2A4 0.025 0.12 -10000 0 -0.47 17 17
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
SFN 0.18 0.17 0.32 214 -0.86 2 216
LNPEP 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.021 0.093 -10000 0 -0.44 6 6
NFATC2 -0.035 0.11 -10000 0 -0.33 25 25
NFATC3 -0.025 0.12 -10000 0 -0.55 17 17
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.006 0.12 -10000 0 -0.6 8 8
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.062 0.15 -10000 0 -0.49 35 35
BCL2/BAX -0.002 0.035 -10000 0 -0.67 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.004 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.004 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.032 0.1 -10000 0 -0.62 7 7
Calcineurin A alpha-beta B1/BCL2 -0.002 0.044 -10000 0 -0.86 1 1
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.031 0.1 0.61 7 -10000 0 7
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 0.003 0.028 0.32 3 -10000 0 3
XPO1 0 0 -10000 0 -10000 0 0
SFN 0.18 0.17 0.32 214 -0.86 2 216
MAP3K8 -0.005 0.063 -10000 0 -0.86 2 2
NFAT4/CK1 alpha -0.017 0.078 -10000 0 -0.37 17 17
MEF2D/NFAT1/Cbp/p300 -0.088 0.15 -10000 0 -0.39 59 59
CABIN1 -0.006 0.12 -10000 0 -0.61 8 8
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.066 0.23 0.32 1 -0.86 29 30
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.001 0.016 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 -0.046 0.19 -10000 0 -0.86 20 20
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.033 0.1 -10000 0 -0.46 18 18
PRKCH -0.002 0.045 -10000 0 -0.86 1 1
CABIN1/Cbp/p300 -0.002 0.005 -10000 0 -10000 0 0
CASP3 -0.002 0.045 -10000 0 -0.86 1 1
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.001 0.011 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.053 0.051 -10000 0 -10000 0 0
PRKCB -0.074 0.24 -10000 0 -0.86 32 32
PRKCE -0.001 0.048 0.32 1 -0.86 1 2
JNK2/NFAT4 -0.023 0.1 -10000 0 -0.5 17 17
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ -0.039 0.18 -10000 0 -0.86 17 17
PRKCA 0 0 -10000 0 -10000 0 0
PRKCG 0.003 0.033 0.32 4 -10000 0 4
PRKCQ -0.033 0.17 0.32 2 -0.86 15 17
FKBP38/BCL2 -0.002 0.035 -10000 0 -0.67 1 1
EP300 -0.001 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 -0.041 0.13 -10000 0 -0.49 22 22
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.046 0.16 -10000 0 -0.59 29 29
NFATc/ERK1 -0.018 0.078 -10000 0 -0.48 3 3
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.062 0.15 -10000 0 -0.49 35 35
NR4A1 -0.15 0.28 -10000 0 -0.78 59 59
GSK3B 0 0 -10000 0 -10000 0 0
positive T cell selection -0.025 0.12 -10000 0 -0.55 17 17
NFAT1/CK1 alpha -0.045 0.076 -10000 0 -0.4 4 4
RCH1/ KPNB1 0.002 0.02 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 0.002 0.023 0.32 2 -10000 0 2
MEF2D -0.001 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
NFATc/p38 alpha -0.018 0.078 -10000 0 -0.45 4 4
CREBBP -0.001 0.002 -10000 0 -10000 0 0
BCL2 -0.002 0.045 -10000 0 -0.86 1 1
TCGA08_rtk_signaling

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
PDGFRA -0.34 0.42 -10000 0 -0.86 149 149
HRAS 0.002 0.023 0.32 2 -10000 0 2
EGFR -0.023 0.14 -10000 0 -0.86 10 10
AKT 0.016 0.052 -10000 0 -0.5 3 3
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.009 0.089 -10000 0 -0.86 4 4
AKT3 -0.006 0.079 0.32 1 -0.86 3 4
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.001 0.048 0.32 1 -0.86 1 2
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
PIK3CG -0.028 0.16 0.32 3 -0.86 13 16
PIK3R3 0.001 0.016 0.32 1 -10000 0 1
PIK3R2 0.001 0.016 0.32 1 -10000 0 1
NF1 -0.002 0.045 -10000 0 -0.86 1 1
RAS -0.068 0.11 -10000 0 -0.41 9 9
ERBB2 -0.014 0.11 -10000 0 -0.86 6 6
proliferation/survival/translation -0.017 0.035 0.23 2 -10000 0 2
PI3K -0.057 0.11 -10000 0 -0.29 23 23
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
KRAS 0 0 -10000 0 -10000 0 0
FOXO 0.022 0.023 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.005 0.063 -10000 0 -0.86 2 2
Caspase cascade in apoptosis

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
TOP1 0.003 0.097 -10000 0 -0.44 16 16
ACTA1 -0.003 0.12 -10000 0 -0.56 16 16
NUMA1 0.003 0.097 -10000 0 -0.44 16 16
SPTAN1 -0.004 0.12 -10000 0 -0.58 15 15
LIMK1 -0.003 0.12 -10000 0 -0.58 15 15
BIRC3 0.007 0.088 0.32 14 -0.86 2 16
BIRC2 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.002 0.13 -10000 0 -0.61 16 16
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.003 0.097 -10000 0 -0.44 16 16
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.003 0.12 -10000 0 -0.57 15 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD -0.002 0.045 -10000 0 -0.86 1 1
GSN -0.004 0.12 -10000 0 -0.58 15 15
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.02 0.15 0.37 2 -0.64 14 16
BID -0.012 0.06 -10000 0 -0.29 16 16
MAP3K1 0.004 0.04 -10000 0 -0.25 1 1
TRADD -0.002 0.045 -10000 0 -0.86 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.004 0.12 -10000 0 -0.58 15 15
CASP9 0 0 -10000 0 -10000 0 0
DNA repair 0 0.033 0.18 1 -0.22 1 2
neuron apoptosis 0.009 0.077 -10000 0 -0.72 4 4
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.12 -10000 0 -0.55 16 16
APAF1 0 0 -10000 0 -10000 0 0
CASP6 0.016 0.06 -10000 0 -0.4 1 1
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD 0.002 0.12 -10000 0 -0.55 16 16
CASP7 -0.012 0.037 0.37 2 -10000 0 2
KRT18 0.011 0.017 -10000 0 -10000 0 0
apoptosis 0.007 0.11 -10000 0 -0.5 15 15
DFFA -0.004 0.12 -10000 0 -0.58 15 15
DFFB -0.005 0.13 -10000 0 -0.57 16 16
PARP1 0 0.033 0.22 1 -0.18 1 2
actin filament polymerization -0.002 0.12 0.52 17 -10000 0 17
TNF -0.031 0.17 0.32 2 -0.86 14 16
CYCS 0.01 0.048 -10000 0 -0.21 16 16
SATB1 -0.033 0.17 -10000 0 -0.48 41 41
SLK -0.004 0.12 -10000 0 -0.58 15 15
p15 BID/BAX -0.011 0.052 -10000 0 -0.26 16 16
CASP2 -0.006 0.059 -10000 0 -10000 0 0
JNK cascade -0.004 0.04 0.24 1 -10000 0 1
CASP3 -0.011 0.13 -10000 0 -0.6 16 16
LMNB2 0.03 0.051 -10000 0 -0.3 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.002 0.045 -10000 0 -0.86 1 1
Mammalian IAPs/DIABLO 0.005 0.054 -10000 0 -0.53 2 2
negative regulation of DNA binding 0.021 0.15 0.37 2 -0.64 14 16
stress fiber formation -0.003 0.12 -10000 0 -0.57 15 15
GZMB -0.012 0.15 -10000 0 -0.7 16 16
CASP1 -0.004 0.042 -10000 0 -0.47 3 3
LMNB1 0.028 0.051 -10000 0 -0.3 1 1
APP 0.009 0.078 -10000 0 -0.72 4 4
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0 -10000 0 -10000 0 0
VIM 0.002 0.1 -10000 0 -0.48 15 15
LMNA 0.028 0.051 -10000 0 -0.3 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.063 -10000 0 -0.28 16 16
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.005 0.13 -10000 0 -0.57 16 16
APAF-1/Caspase 9 -0.005 0.022 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.003 0.095 -10000 0 -0.43 16 16
CFL2 0.001 0.12 -10000 0 -0.54 17 17
GAS2 -0.022 0.15 -10000 0 -0.54 28 28
positive regulation of apoptosis 0.031 0.051 -10000 0 -0.3 1 1
PRF1 -0.016 0.12 -10000 0 -0.86 7 7
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.004 0.048 -10000 0 -0.53 3 3
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 0.002 0.023 -10000 0 -10000 0 0
GATA1/HDAC5 0.002 0.02 -10000 0 -10000 0 0
GATA2/HDAC5 -0.002 0.051 -10000 0 -0.67 2 2
HDAC5/BCL6/BCoR -0.002 0.03 -10000 0 -0.58 1 1
HDAC9 -0.042 0.18 -10000 0 -0.86 18 18
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
HDAC4/ANKRA2 -0.001 0.036 -10000 0 -0.67 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.003 0.067 0.32 2 -0.86 2 4
HDAC4/RFXANK 0.002 0.02 -10000 0 -10000 0 0
BCOR -0.002 0.045 -10000 0 -0.86 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.005 0.06 -10000 0 -0.67 3 3
Histones -0.01 0.064 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 0.001 0.016 0.32 1 -10000 0 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.002 0.035 -10000 0 -0.67 1 1
HDAC4/Ubc9 0.001 0.011 -10000 0 -10000 0 0
HDAC7 0.001 0.016 0.32 1 -10000 0 1
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.001 0.016 -10000 0 -10000 0 0
CAMK4 -0.066 0.23 0.32 1 -0.86 29 30
Tubulin/HDAC6 0 0 -10000 0 -10000 0 0
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 0.003 0.028 0.32 3 -10000 0 3
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 0 0 -10000 0 -10000 0 0
SUMO1/HDAC4 0.001 0.011 -10000 0 -10000 0 0
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.001 0.011 -10000 0 -10000 0 0
Tubulin 0 0 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.001 0.011 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR -0.002 0.035 -10000 0 -0.67 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.001 0.01 -10000 0 -10000 0 0
HDAC4/SRF -0.044 0.16 -10000 0 -0.58 29 29
HDAC4/ER alpha -0.37 0.33 -10000 0 -0.67 205 205
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.01 0.064 -10000 0 -10000 0 0
cell motility 0 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.001 0.011 -10000 0 -10000 0 0
BCL6 0 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.001 0.016 0.32 1 -10000 0 1
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 -0.48 0.43 -10000 0 -0.86 205 205
HDAC6/HDAC11 0.005 0.034 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.001 0.01 -10000 0 -10000 0 0
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A 0 0 -10000 0 -10000 0 0
HDAC11 0.008 0.049 0.32 9 -10000 0 9
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 -0.002 0.045 -10000 0 -0.86 1 1
RFXANK 0.002 0.023 0.32 2 -10000 0 2
nuclear import 0 0.007 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -10000 0 -10000 0 0
ITGB7 -0.012 0.099 -10000 0 -0.86 5 5
ITGA4 -0.02 0.13 0.32 1 -0.86 9 10
alpha4/beta7 Integrin -0.025 0.13 -10000 0 -0.67 14 14
alpha4/beta1 Integrin -0.016 0.1 -10000 0 -0.67 9 9
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.011 0.12 0.32 6 -0.86 7 13
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.009 0.028 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
MAP3K12 0.002 0.023 0.32 2 -10000 0 2
FGR -0.005 0.063 -10000 0 -0.86 2 2
p38 alpha/TAB1 -0.034 0.075 -10000 0 -0.34 12 12
PRKG1 -0.041 0.19 0.32 1 -0.86 18 19
DUSP8 -0.004 0.065 0.32 1 -0.86 2 3
PGK/cGMP/p38 alpha -0.052 0.12 0.24 1 -0.41 28 29
apoptosis -0.033 0.072 -10000 0 -0.33 11 11
RAL/GTP 0 0 -10000 0 -10000 0 0
LYN 0 0 -10000 0 -10000 0 0
DUSP1 -0.081 0.25 -10000 0 -0.86 35 35
PAK1 0 0 -10000 0 -10000 0 0
SRC 0.004 0.036 0.32 5 -10000 0 5
RAC1/OSM/MEKK3/MKK3 0 0 -10000 0 -10000 0 0
TRAF6 -0.002 0.045 -10000 0 -0.86 1 1
RAC1 0 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
MAPK11 -0.006 0.13 -10000 0 -0.44 14 14
BLK -0.15 0.33 0.32 2 -0.86 65 67
HCK -0.028 0.15 -10000 0 -0.86 12 12
MAP2K3 0 0 -10000 0 -10000 0 0
DUSP16 -0.002 0.045 -10000 0 -0.86 1 1
DUSP10 -0.009 0.089 -10000 0 -0.86 4 4
TRAF6/MEKK3 -0.001 0.028 -10000 0 -0.54 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.003 0.1 -10000 0 -0.35 13 13
positive regulation of innate immune response -0.003 0.14 -10000 0 -0.47 14 14
LCK -0.025 0.15 0.32 1 -0.86 11 12
p38alpha-beta/MKP7 -0.052 0.11 -10000 0 -0.44 15 15
p38alpha-beta/MKP5 -0.055 0.12 -10000 0 -0.45 18 18
PGK/cGMP -0.032 0.14 0.21 1 -0.67 18 19
PAK2 0 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.087 0.16 -10000 0 -0.46 46 46
CDC42 0 0 -10000 0 -10000 0 0
RALB 0 0 -10000 0 -10000 0 0
RALA 0 0 -10000 0 -10000 0 0
PAK3 0.032 0.096 0.32 38 -10000 0 38
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0.025 0.081 -10000 0 -0.51 3 3
MAPK9 0 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.003 0.015 -10000 0 -10000 0 0
GNB1/GNG2 -0.005 0.053 -10000 0 -0.59 3 3
GNB1 0 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 0 -10000 0 -10000 0 0
Gs family/GTP 0.029 0.066 0.18 60 -10000 0 60
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 0 -10000 0 -10000 0 0
GNAL 0.051 0.12 0.32 60 -10000 0 60
GNG2 -0.007 0.077 -10000 0 -0.86 3 3
CRH 0.003 0.033 0.32 4 -10000 0 4
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.026 0.11 -10000 0 -0.47 20 20
MAPK11 0.005 0.025 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.047 -10000 0 -0.46 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0 0.026 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.031 -10000 0 -0.58 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.065 -10000 0 -0.42 4 4
CaM/Ca2+ 0.006 0.041 -10000 0 -0.43 1 1
RAP1A 0 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.004 0.034 -10000 0 -0.44 1 1
AKT1 -0.001 0.061 -10000 0 -0.72 2 2
MAP2K1 0.046 0.025 -10000 0 -0.41 1 1
MAP3K11 0.002 0.028 -10000 0 -0.44 1 1
IFNGR1 0.001 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.17 0.2 -10000 0 -0.38 158 158
Rap1/GTP -0.001 0.017 -10000 0 -10000 0 0
CRKL/C3G 0 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.007 0.047 -10000 0 -0.49 1 1
CEBPB 0.065 0.042 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0 0.1 -10000 0 -1.3 2 2
STAT1 0.004 0.033 -10000 0 -0.44 1 1
CALM1 0 0 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.014 0.065 0.32 16 -10000 0 16
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
STAT1 (dimer)/PIAS1 0.004 0.032 -10000 0 -0.41 1 1
CEBPB/PTGES2/Cbp/p300 -0.002 0.021 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.045 -10000 0 -0.46 1 1
MAPK3 0.051 0.028 -10000 0 -10000 0 0
STAT1 (dimer) -0.069 0.093 -10000 0 -0.65 4 4
MAPK1 0.051 0.028 -10000 0 -10000 0 0
JAK2 -0.002 0.045 -10000 0 -0.86 1 1
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
JAK1 0.001 0.003 -10000 0 -10000 0 0
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.059 0.056 -10000 0 -0.66 2 2
SMAD7 0.002 0.063 -10000 0 -0.4 2 2
CBL/CRKL/C3G -0.001 0.02 -10000 0 -10000 0 0
PI3K 0.001 0.075 -10000 0 -0.85 2 2
IFNG 0.014 0.066 0.32 16 -10000 0 16
apoptosis 0.037 0.042 -10000 0 -0.46 2 2
CAMK2G 0 0 -10000 0 -10000 0 0
STAT3 (dimer) 0 0 -10000 0 -10000 0 0
CAMK2A 0.024 0.084 0.32 28 -10000 0 28
CAMK2B -0.42 0.43 -10000 0 -0.86 181 181
FRAP1 0.044 0.055 -10000 0 -0.64 2 2
PRKCD -0.001 0.063 -10000 0 -0.75 2 2
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.053 0.065 -10000 0 -0.42 4 4
PTPN2 0 0 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
IRF1 0.067 0.034 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy 0.004 0.034 -10000 0 -0.41 1 1
SOCS1 -0.005 0.12 -10000 0 -1.5 2 2
mol:GDP -0.001 0.02 -10000 0 -10000 0 0
CASP1 0.002 0.063 -10000 0 -0.34 3 3
PTGES2 0.001 0.016 0.32 1 -10000 0 1
IRF9 0.049 0.014 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.067 -10000 0 -0.78 2 2
RAP1/GDP -0.001 0.017 -10000 0 -10000 0 0
CBL 0.002 0.028 -10000 0 -0.44 1 1
MAP3K1 0.003 0.029 -10000 0 -0.44 1 1
PIAS1 0 0 -10000 0 -10000 0 0
PIAS4 0 0.001 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.065 -10000 0 -0.42 4 4
PTPN11 0.002 0.028 -10000 0 -0.46 1 1
CREBBP 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.053 0.18 -10000 0 -0.67 30 30
AKT1 0.049 0.12 -10000 0 -0.67 9 9
PTK2B -0.056 0.19 -10000 0 -1 9 9
VEGFR2 homodimer/Frs2 -0.023 0.15 -10000 0 -0.96 9 9
CAV1 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.022 0.14 -10000 0 -0.89 9 9
endothelial cell proliferation 0.039 0.14 -10000 0 -0.64 9 9
mol:Ca2+ -0.022 0.13 -10000 0 -0.84 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.021 0.13 -10000 0 -0.85 9 9
RP11-342D11.1 -0.022 0.13 -10000 0 -0.81 10 10
CDH5 -0.002 0.045 -10000 0 -0.86 1 1
VEGFA homodimer 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.019 0.12 -10000 0 -0.86 8 8
HRAS/GDP -0.018 0.11 -10000 0 -0.71 9 9
SH2D2A -0.016 0.14 0.32 6 -0.86 9 15
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.019 0.11 -10000 0 -0.69 9 9
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.031 0.17 -10000 0 -0.74 17 17
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.021 0.13 -10000 0 -0.82 9 9
GRB10 -0.022 0.13 -10000 0 -0.84 9 9
PTPN11 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PAK1 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.021 0.14 -10000 0 -0.87 9 9
HRAS 0.002 0.023 0.32 2 -10000 0 2
VEGF/Rho/ROCK1/Integrin Complex -0.031 0.11 -10000 0 -0.55 9 9
HIF1A 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.02 0.13 -10000 0 -0.83 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.002 0.045 -10000 0 -0.86 1 1
Nck/Pak 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.022 0.14 -10000 0 -0.89 9 9
mol:GDP -0.02 0.12 -10000 0 -0.78 9 9
mol:NADP 0.046 0.1 -10000 0 -0.56 10 10
eNOS/Hsp90 0.047 0.097 -10000 0 -0.52 10 10
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
mol:IP3 -0.022 0.14 -10000 0 -0.86 9 9
HIF1A/ARNT 0 0 -10000 0 -10000 0 0
SHB -0.002 0.045 -10000 0 -0.86 1 1
VEGFA 0 0 -10000 0 -10000 0 0
VEGFC 0.001 0.016 0.32 1 -10000 0 1
FAK1/Vinculin -0.041 0.16 -10000 0 -0.93 9 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.059 0.21 -10000 0 -0.65 34 34
PTPN6 0 0 -10000 0 -10000 0 0
EPAS1 -0.01 0.06 -10000 0 -0.39 9 9
mol:L-citrulline 0.046 0.1 -10000 0 -0.56 10 10
ITGAV 0.001 0.016 0.32 1 -10000 0 1
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.021 0.13 -10000 0 -0.85 9 9
VEGFR2 homodimer/VEGFA homodimer -0.024 0.15 -10000 0 -0.9 10 10
VEGFR2/3 heterodimer -0.024 0.16 -10000 0 -1 9 9
VEGFB -0.019 0.14 0.32 2 -0.86 9 11
MAPK11 0.029 0.15 -10000 0 -0.84 10 10
VEGFR2 homodimer 0.002 0.17 -10000 0 -1.1 9 9
FLT1 0 0 -10000 0 -10000 0 0
NEDD4 -0.005 0.063 -10000 0 -0.86 2 2
MAPK3 0.019 0.14 -10000 0 -0.78 9 9
MAPK1 0.019 0.14 -10000 0 -0.78 9 9
VEGFA145/NRP2 -0.005 0.061 -10000 0 -0.67 3 3
VEGFR1/2 heterodimer -0.023 0.15 -10000 0 -0.96 9 9
KDR 0.002 0.17 -10000 0 -1.1 9 9
VEGFA165/NRP1/VEGFR2 homodimer -0.025 0.15 -10000 0 -0.92 9 9
SRC 0.004 0.036 0.32 5 -10000 0 5
platelet activating factor biosynthetic process 0.021 0.14 -10000 0 -0.8 9 9
PI3K -0.026 0.14 -10000 0 -0.87 9 9
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.022 0.14 -10000 0 -0.89 9 9
FES -0.029 0.15 -10000 0 -0.74 14 14
GAB1 -0.021 0.13 -10000 0 -0.84 9 9
VEGFR2 homodimer/VEGFA homodimer/Src -0.019 0.14 -10000 0 -0.89 9 9
CTNNB1 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.047 0.097 -10000 0 -0.52 10 10
VEGFR2 homodimer/VEGFA homodimer/Yes -0.022 0.14 -10000 0 -0.89 9 9
PI3K/GAB1 -0.02 0.11 -10000 0 -0.7 9 9
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.02 0.13 -10000 0 -0.82 9 9
PRKACA 0 0 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.022 0.15 -10000 0 -0.95 9 9
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 -0.023 0.14 -10000 0 -0.88 9 9
actin cytoskeleton reorganization -0.03 0.16 -10000 0 -0.74 17 17
PTK2 0.007 0.19 -10000 0 -1 9 9
EDG1 -0.022 0.13 -10000 0 -0.81 10 10
mol:DAG -0.022 0.14 -10000 0 -0.86 9 9
CaM/Ca2+ -0.02 0.12 -10000 0 -0.79 9 9
MAP2K3 0.025 0.15 -10000 0 -0.83 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.023 0.14 -10000 0 -0.9 9 9
PLCG1 -0.023 0.14 -10000 0 -0.88 9 9
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.019 0.14 -10000 0 -0.81 10 10
IQGAP1 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.022 0.14 -10000 0 -0.89 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.022 0.14 -10000 0 -0.89 9 9
cell migration 0.037 0.15 -10000 0 -0.74 9 9
mol:PI-3-4-5-P3 -0.023 0.13 -10000 0 -0.77 9 9
FYN 0 0 -10000 0 -10000 0 0
VEGFB/NRP1 -0.031 0.14 -10000 0 -0.63 18 18
mol:NO 0.046 0.1 -10000 0 -0.56 10 10
PXN 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.018 0.11 -10000 0 -0.72 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.023 0.14 -10000 0 -0.9 9 9
VHL 0 0 -10000 0 -10000 0 0
ITGB3 -0.07 0.23 -10000 0 -0.86 30 30
NOS3 0.045 0.12 -10000 0 -0.65 10 10
VEGFR2 homodimer/VEGFA homodimer/Sck -0.033 0.16 -10000 0 -0.72 17 17
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.13 -10000 0 -0.79 9 9
PRKCB -0.013 0.2 -10000 0 -0.84 9 9
VCL 0.001 0.016 0.32 1 -10000 0 1
VEGFA165/NRP1 -0.022 0.14 -10000 0 -0.82 10 10
VEGFR1/2 heterodimer/VEGFA homodimer -0.022 0.14 -10000 0 -0.89 9 9
VEGFA165/NRP2 -0.005 0.061 -10000 0 -0.67 3 3
MAPKKK cascade -0.018 0.11 -10000 0 -0.72 9 9
NRP2 -0.006 0.079 0.32 1 -0.86 3 4
VEGFC homodimer 0.001 0.016 0.32 1 -10000 0 1
NCK1 0 0 -10000 0 -10000 0 0
ROCK1 0 0 -10000 0 -10000 0 0
FAK1/Paxillin -0.042 0.16 -10000 0 -0.93 9 9
MAP3K13 -0.028 0.15 -10000 0 -0.88 9 9
PDPK1 -0.02 0.11 -10000 0 -0.66 9 9
BARD1 signaling events

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
BARD1/CSTF1 0.012 0.051 -10000 0 -10000 0 0
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC 0 0 -10000 0 -10000 0 0
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 0.038 0.063 -10000 0 -10000 0 0
protein ubiquitination 0.072 0.098 0.33 17 -10000 0 17
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.023 0.054 -10000 0 -0.5 1 1
FANCF 0 0 -10000 0 -10000 0 0
BRCA1 0.001 0.016 0.32 1 -10000 0 1
CCNE1 0.11 0.15 0.32 134 -10000 0 134
CDK2/Cyclin E1 0.079 0.1 -10000 0 -10000 0 0
FANCG 0.002 0.023 0.32 2 -10000 0 2
BRCA1/BACH1/BARD1 0.013 0.052 -10000 0 -10000 0 0
FANCE 0.01 0.056 0.32 12 -10000 0 12
FANCC -0.002 0.045 -10000 0 -0.86 1 1
NBN 0 0 -10000 0 -10000 0 0
FANCA 0 0 -10000 0 -10000 0 0
DNA repair 0.089 0.048 -10000 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0.013 0.052 -10000 0 -10000 0 0
BARD1/DNA-PK 0.011 0.045 -10000 0 -10000 0 0
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.012 0.05 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.007 0.027 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.012 0.048 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.012 0.046 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.012 0.048 -10000 0 -10000 0 0
BRCA1/BACH1 0.001 0.016 0.32 1 -10000 0 1
BARD1 0.018 0.073 0.32 21 -10000 0 21
PCNA 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.012 0.048 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.012 0.048 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.066 0.11 0.38 16 -10000 0 16
BARD1/DNA-PK/P53 0.011 0.043 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.013 0.052 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.012 0.049 -10000 0 -10000 0 0
FA complex 0.004 0.027 -10000 0 -10000 0 0
BARD1/EWS 0.012 0.051 -10000 0 -10000 0 0
RBBP8 0.018 0 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
TOPBP1 0 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.011 0.045 -10000 0 -10000 0 0
BRCA1/BARD1 0.078 0.11 0.36 17 -10000 0 17
CSTF1 0 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.012 0.049 -10000 0 -10000 0 0
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.089 0.14 0.32 105 -10000 0 105
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.013 0.052 -10000 0 -10000 0 0
EWSR1 0 0 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.026 0.1 -10000 0 -1.3 2 2
regulation of axonogenesis 0.019 0.081 0.34 21 -10000 0 21
myoblast fusion 0.002 0.036 0.43 2 -10000 0 2
mol:GTP -0.001 0.02 -10000 0 -0.24 2 2
regulation of calcium-dependent cell-cell adhesion 0.029 0.13 0.56 20 -10000 0 20
ARF1/GTP 0 0.015 -10000 0 -10000 0 0
mol:GM1 0.007 0.016 -10000 0 -10000 0 0
mol:Choline -0.011 0.14 -10000 0 -0.57 21 21
lamellipodium assembly 0.004 0.048 -10000 0 -0.46 2 2
MAPK3 0.02 0.032 -10000 0 -0.35 2 2
ARF6/GTP/NME1/Tiam1 -0.029 0.13 -10000 0 -0.56 20 20
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.002 0.036 -10000 0 -0.43 2 2
ARF1/GDP 0.003 0.04 -10000 0 -0.39 2 2
ARF6 0 0.011 -10000 0 -10000 0 0
RAB11A 0 0 -10000 0 -10000 0 0
TIAM1 -0.046 0.19 -10000 0 -0.86 20 20
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.032 -10000 0 -0.35 2 2
actin filament bundle formation 0.003 0.03 0.39 2 -10000 0 2
KALRN 0 0.051 -10000 0 -0.43 4 4
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.003 0.031 -10000 0 -0.39 2 2
NME1 0.002 0.023 0.32 2 -10000 0 2
Rac1/GDP -0.003 0.031 -10000 0 -0.39 2 2
substrate adhesion-dependent cell spreading -0.001 0.02 -10000 0 -0.24 2 2
cortical actin cytoskeleton organization 0.004 0.048 -10000 0 -0.47 2 2
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.001 0.02 -10000 0 -0.24 2 2
ARF6/GTP -0.001 0.02 -10000 0 -0.24 2 2
RhoA/GTP 0 0.015 -10000 0 -10000 0 0
mol:GDP 0.004 0.046 -10000 0 -0.43 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0 0.013 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 -0.036 0.15 -10000 0 -0.64 21 21
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis 0.004 0.048 -10000 0 -0.46 2 2
ruffle organization -0.019 0.081 -10000 0 -0.34 21 21
regulation of epithelial cell migration -0.001 0.02 -10000 0 -0.24 2 2
PLD2 0 0.015 -10000 0 -10000 0 0
PIP5K1A -0.019 0.081 -10000 0 -0.34 21 21
mol:Phosphatidic acid -0.011 0.14 -10000 0 -0.57 21 21
Rac1/GTP 0.004 0.049 -10000 0 -0.47 2 2
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.031 0.003 -10000 0 -10000 0 0
CDKN1A 0.017 0.083 -10000 0 -0.48 10 10
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0 0 -10000 0 -10000 0 0
FOXO3 0.031 0.003 -10000 0 -10000 0 0
AKT1 0.001 0.007 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
AKT3 -0.003 0.042 -10000 0 -0.47 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.031 0.003 -10000 0 -10000 0 0
AKT1/ASK1 -0.054 0.15 -10000 0 -0.46 43 43
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.052 0.14 0.45 43 -10000 0 43
TSC1 0.031 0.003 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
AKT1/RAF1 0 0 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.028 0.038 -10000 0 -0.48 2 2
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 -0.005 0.051 -10000 0 -0.57 3 3
MAP3K5 -0.1 0.28 -10000 0 -0.86 43 43
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.059 0.031 0.24 1 -10000 0 1
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.031 0.003 -10000 0 -10000 0 0
CASP9 0.031 0.003 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0 0 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.003 0.023 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0.004 0.036 0.32 5 -10000 0 5
AKT2/p21CIP1 -0.012 0.075 -10000 0 -0.46 10 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.001 -10000 0 -10000 0 0
CHUK 0.031 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.075 0.035 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.031 0.003 -10000 0 -10000 0 0
MAPKKK cascade 0 0 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0 -10000 0 -10000 0 0
TSC1/TSC2 0.033 0.036 -10000 0 -0.46 2 2
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
glucose import 0.013 0.09 -10000 0 -0.52 10 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.013 0.091 -10000 0 -0.53 10 10
GSK3A 0.031 0.003 -10000 0 -10000 0 0
FOXO1 0.025 0.053 -10000 0 -0.48 4 4
GSK3B 0.031 0.003 -10000 0 -10000 0 0
SFN 0.18 0.17 0.32 214 -0.86 2 216
G1/S transition of mitotic cell cycle 0.036 0.003 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.057 0.054 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.01 -10000 0 -10000 0 0
DOCK1 -0.019 0.12 -10000 0 -0.86 8 8
ITGA4 -0.02 0.13 0.32 1 -0.86 9 10
RAC1 0 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.025 0.13 -10000 0 -0.67 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.014 0.09 -10000 0 -0.58 9 9
alpha4/beta7 Integrin/Paxillin -0.019 0.1 -10000 0 -0.53 14 14
lamellipodium assembly -0.01 0.077 -10000 0 -0.5 8 8
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
PI3K -0.005 0.071 -10000 0 -0.94 2 2
ARF6 0 0 -10000 0 -10000 0 0
TLN1 0 0 -10000 0 -10000 0 0
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
ARF6/GTP -0.011 0.071 -10000 0 -0.46 9 9
cell adhesion -0.011 0.077 -10000 0 -0.49 9 9
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.012 0.083 -10000 0 -0.53 9 9
ITGB1 0 0 -10000 0 -10000 0 0
ITGB7 -0.012 0.099 -10000 0 -0.86 5 5
ARF6/GDP 0.002 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.035 0.15 -10000 0 -0.54 27 27
p130Cas/Crk/Dock1 -0.013 0.084 -10000 0 -0.58 8 8
VCAM1 -0.041 0.2 0.32 6 -0.86 20 26
alpha4/beta1 Integrin/Paxillin/Talin -0.012 0.077 -10000 0 -0.5 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 -0.012 0.077 -10000 0 -0.5 9 9
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.077 0.49 9 -10000 0 9
CBL 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.012 0.077 -10000 0 -0.5 9 9
Rac1/GTP -0.011 0.091 -10000 0 -0.58 8 8
Class I PI3K signaling 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
ARF5/GTP 0.002 0.023 0.3 2 -10000 0 2
DAPP1 -0.032 0.16 -10000 0 -0.61 15 15
Src family/SYK family/BLNK-LAT/BTK-ITK -0.039 0.21 0.33 1 -0.73 20 21
mol:DAG 0.01 0.092 0.26 1 -0.31 11 12
HRAS 0.002 0.023 0.32 2 -10000 0 2
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.02 0.067 -10000 0 -0.48 3 3
PLCG2 -0.016 0.12 -10000 0 -0.86 7 7
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.019 -10000 0 -10000 0 0
ARF1/GTP 0.002 0.022 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
RAP1A/GTP 0.001 0.018 -10000 0 -10000 0 0
ADAP1 -0.004 0.074 -10000 0 -0.47 8 8
ARAP3 0.001 0.019 0.26 2 -10000 0 2
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0 0 -10000 0 -10000 0 0
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.005 0.063 -10000 0 -0.86 2 2
mol:Ca2+ 0.014 0.05 -10000 0 -0.2 1 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.046 0.19 -10000 0 -0.86 20 20
ZAP70 -0.005 0.096 0.32 5 -0.86 4 9
mol:IP3 0.015 0.068 0.22 1 -0.23 8 9
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.02 0.067 -10000 0 -0.48 3 3
RhoA/GDP -0.006 0.033 0.27 2 -10000 0 2
PDK1/Src/Hsp90 0.003 0.023 -10000 0 -10000 0 0
BLNK -0.021 0.13 -10000 0 -0.86 9 9
actin cytoskeleton reorganization 0.036 0.068 -10000 0 -10000 0 0
SRC 0.004 0.036 0.32 5 -10000 0 5
PLEKHA2 0.023 0.031 -10000 0 -0.58 1 1
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.005 0.061 -10000 0 -0.84 2 2
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.022 -10000 0 -10000 0 0
RhoA/GTP 0.001 0.018 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.069 0.17 0.28 1 -0.74 13 14
BLK -0.15 0.33 0.32 2 -0.86 65 67
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 0.002 0.019 -10000 0 -10000 0 0
HCK -0.028 0.15 -10000 0 -0.86 12 12
CYTH3 0.002 0.021 -10000 0 -10000 0 0
CYTH2 0.002 0.019 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.016 0.1 -10000 0 -0.57 12 12
SGK1 -0.018 0.11 -10000 0 -0.63 12 12
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.081 -10000 0 -0.26 17 17
SOS1 0 0 -10000 0 -10000 0 0
SYK -0.007 0.077 -10000 0 -0.86 3 3
ARF6/GDP -0.006 0.034 0.28 2 -10000 0 2
mol:PI-3-4-5-P3 0.002 0.027 0.37 2 -10000 0 2
ARAP3/RAP1A/GTP 0.001 0.018 -10000 0 -10000 0 0
VAV1 -0.039 0.18 -10000 0 -0.86 17 17
mol:PI-3-4-P2 0.018 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.001 0.014 -10000 0 -10000 0 0
PLEKHA1 0.025 0 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.067 -10000 0 -0.48 3 3
LAT 0.002 0.023 0.32 2 -10000 0 2
Rac1/GTP -0.031 0.1 -10000 0 -0.4 20 20
ITK -0.023 0.11 -10000 0 -0.47 20 20
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.005 0.12 0.29 1 -0.46 11 12
LCK -0.025 0.15 0.32 1 -0.86 11 12
BTK -0.007 0.067 -10000 0 -0.47 7 7
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.001 0.061 -10000 0 -0.51 4 4
RGS9BP 0.011 0.058 0.32 13 -10000 0 13
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.019 0.059 0.38 1 -10000 0 1
mol:ADP 0.003 0.004 -10000 0 -10000 0 0
GNAT2 0.001 0.016 0.32 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.001 0.12 0.39 2 -0.58 11 13
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.001 0.01 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.031 0.094 0.32 36 -10000 0 36
Cone Metarhodopsin II/X-Arrestin 0.001 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.021 -10000 0 -10000 0 0
Cone PDE6 0.009 0.11 0.35 4 -0.5 11 15
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.018 0.056 0.36 1 -10000 0 1
GNAT2/GDP 0 0.1 0.35 2 -0.5 11 13
GNB5 0.001 0.016 0.32 1 -10000 0 1
mol:GMP (4 units) 0.01 0.041 -10000 0 -10000 0 0
Cone Transducin -0.001 0.064 -10000 0 -0.54 4 4
SLC24A2 0 0 -10000 0 -10000 0 0
GNB3/GNGT2 -0.002 0.077 -10000 0 -0.67 4 4
GNB3 0.008 0.049 0.32 9 -10000 0 9
GNAT2/GTP 0.001 0.011 -10000 0 -10000 0 0
CNGA3 0.002 0.023 0.32 2 -10000 0 2
ARR3 0.001 0.016 0.32 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.02 0.06 0.39 1 -10000 0 1
mol:Pi -0.001 0.12 0.39 2 -0.58 11 13
Cone CNG Channel 0.023 0.057 0.3 3 -10000 0 3
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0 0 -10000 0 -10000 0 0
RGS9 -0.012 0.16 0.32 16 -0.86 11 27
PDE6C 0.016 0.07 0.32 19 -10000 0 19
GNGT2 -0.009 0.089 -10000 0 -0.86 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.012 0.099 -10000 0 -0.86 5 5
positive regulation of NF-kappaB transcription factor activity -0.011 0.084 -10000 0 -0.66 6 6
MAP2K4 -0.007 0.045 -10000 0 -0.33 6 6
IKBKB 0 0 -10000 0 -10000 0 0
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.012 0.099 -10000 0 -0.86 5 5
SMPD1 -0.004 0.035 -10000 0 -0.3 5 5
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.002 0.045 -10000 0 -0.86 1 1
TRAIL/TRAILR2 -0.009 0.077 -10000 0 -0.67 5 5
TRAIL/TRAILR3 -0.007 0.089 -10000 0 -0.67 6 6
TRAIL/TRAILR1 -0.018 0.11 -10000 0 -0.67 10 10
TRAIL/TRAILR4 -0.011 0.084 -10000 0 -0.67 6 6
TRAIL/TRAILR1/DAP3/GTP -0.014 0.087 -10000 0 -0.54 10 10
IKK complex -0.005 0.03 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.009 0.079 -10000 0 -0.66 5 5
MAP3K1 -0.008 0.048 -10000 0 -0.35 6 6
TRAILR4 (trimer) -0.002 0.044 -10000 0 -0.86 1 1
TRADD -0.002 0.045 -10000 0 -0.86 1 1
TRAILR1 (trimer) -0.012 0.099 -10000 0 -0.86 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.01 0.06 -10000 0 -0.35 11 11
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.079 -10000 0 -0.66 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP -0.014 0.085 -10000 0 -0.5 11 11
mol:ceramide -0.004 0.035 -10000 0 -0.3 5 5
FADD 0.001 0.016 0.32 1 -10000 0 1
MAPK8 0.008 0.13 -10000 0 -0.49 20 20
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.003 0.06 0.32 6 -0.86 1 7
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.015 0.095 -10000 0 -0.58 10 10
DAP3 0 0 -10000 0 -10000 0 0
CASP10 -0.01 0.073 0.31 1 -0.55 5 6
JNK cascade -0.011 0.084 -10000 0 -0.66 6 6
TRAIL (trimer) -0.012 0.099 -10000 0 -0.86 5 5
TNFRSF10C 0.003 0.06 0.32 6 -0.86 1 7
TRAIL/TRAILR1/DAP3/GTP/FADD -0.013 0.082 -10000 0 -0.5 10 10
TRAIL/TRAILR2/FADD -0.007 0.068 -10000 0 -0.58 5 5
cell death -0.004 0.035 -10000 0 -0.3 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.005 0.045 -10000 0 -0.35 6 6
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.019 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.008 0.064 -10000 0 -0.5 6 6
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0.07 -10000 0 -0.58 4 4
SNTA1 0.002 0.023 0.32 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.037 0.074 -10000 0 -0.58 4 4
MAPK12 0.023 0.077 -10000 0 -0.52 7 7
CCND1 -0.001 0.1 -10000 0 -0.49 14 14
p38 gamma/SNTA1 0.003 0.073 -10000 0 -0.48 7 7
MAP2K3 0 0 -10000 0 -10000 0 0
PKN1 0.001 0.016 0.32 1 -10000 0 1
G2/M transition checkpoint 0.023 0.076 -10000 0 -0.51 7 7
MAP2K6 -0.009 0.079 -10000 0 -0.57 7 7
MAPT 0.061 0.063 -10000 0 -0.29 4 4
MAPK13 0.034 0.09 -10000 0 -0.67 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0 0.007 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.017 0.11 0.31 2 -0.52 5 7
PDGFB-D/PDGFRB/SLAP -0.015 0.12 -10000 0 -0.67 11 11
PDGFB-D/PDGFRB/APS/CBL 0.006 0.038 0.39 1 -10000 0 1
AKT1 -0.009 0.065 -10000 0 -0.43 8 8
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.11 0.31 2 -0.53 5 7
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
FGR -0.008 0.066 -10000 0 -0.82 2 2
mol:Ca2+ 0.014 0.051 -10000 0 -10000 0 0
MYC -0.064 0.3 -10000 0 -0.88 43 43
SHC1 0 0 -10000 0 -10000 0 0
HRAS/GDP 0 0.037 -10000 0 -0.46 2 2
LRP1/PDGFRB/PDGFB 0.003 0.043 -10000 0 -0.58 1 1
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0.014 0.051 -10000 0 -10000 0 0
PTEN -0.005 0.063 -10000 0 -0.86 2 2
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.004 0.098 0.32 6 -0.86 4 10
PDGFB-D/PDGFRB/SHP2 0.005 0.032 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.005 0.032 -10000 0 -10000 0 0
cell cycle arrest -0.015 0.12 -10000 0 -0.67 11 11
HRAS 0.002 0.023 0.32 2 -10000 0 2
HIF1A 0.046 0.064 -10000 0 -0.4 5 5
GAB1 0.002 0.087 -10000 0 -0.5 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.009 0.087 -10000 0 -0.39 3 3
PDGFB-D/PDGFRB 0.008 0.03 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.005 0.032 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.008 0.13 0.36 2 -0.59 5 7
positive regulation of MAPKKK cascade 0.005 0.031 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
mol:IP3 0.014 0.052 -10000 0 -10000 0 0
E5 0 0.001 -10000 0 -10000 0 0
CSK 0 0.001 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.001 0.08 -10000 0 -0.66 4 4
SHB -0.002 0.045 -10000 0 -0.86 1 1
BLK -0.12 0.25 -10000 0 -0.65 65 65
PTPN2 0 0.001 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.005 0.032 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.004 0.11 -10000 0 -0.43 5 5
CBL 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.005 0.032 -10000 0 -10000 0 0
LCK -0.023 0.12 -10000 0 -0.7 11 11
PDGFRB 0.009 0.046 0.32 8 -10000 0 8
ACP1 0 0 -10000 0 -10000 0 0
HCK -0.021 0.12 -10000 0 -0.64 12 12
ABL1 0.002 0.076 -10000 0 -0.35 3 3
PDGFB-D/PDGFRB/CBL 0 0.088 -10000 0 -0.57 1 1
PTPN1 0 0.001 -10000 0 -10000 0 0
SNX15 0 0 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0.002 0.023 0.32 2 -10000 0 2
cell proliferation -0.051 0.26 -10000 0 -0.76 43 43
SLA -0.025 0.15 -10000 0 -0.86 11 11
actin cytoskeleton reorganization 0.004 0.045 -10000 0 -0.44 2 2
SRC 0 0.031 -10000 0 -10000 0 0
PI3K -0.01 0.073 -10000 0 -0.48 8 8
PDGFB-D/PDGFRB/GRB7/SHC 0.001 0.071 -10000 0 -0.57 4 4
SH2B2 0.003 0.033 0.32 4 -10000 0 4
PLCgamma1/SPHK1 0.019 0.12 0.32 2 -0.55 5 7
LYN -0.003 0.024 -10000 0 -10000 0 0
LRP1 -0.002 0.045 -10000 0 -0.86 1 1
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0 0 -10000 0 -10000 0 0
STAT5A 0.001 0.016 0.32 1 -10000 0 1
NCK1-2/p130 Cas 0.003 0.038 0.32 1 -0.48 1 2
SPHK1 0.044 0.16 0.32 65 -0.86 5 70
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.014 0.052 -10000 0 -10000 0 0
PLCG1 0.014 0.052 -10000 0 -10000 0 0
NHERF/PDGFRB -0.002 0.067 -10000 0 -0.58 4 4
YES1 -0.003 0.024 -10000 0 -10000 0 0
cell migration -0.002 0.067 -10000 0 -0.58 4 4
SHC/Grb2/SOS1 0.004 0.025 -10000 0 -10000 0 0
SLC9A3R2 -0.007 0.077 -10000 0 -0.86 3 3
SLC9A3R1 -0.002 0.045 -10000 0 -0.86 1 1
NHERF1-2/PDGFRB/PTEN -0.004 0.074 -10000 0 -0.53 6 6
FYN -0.002 0.023 -10000 0 -10000 0 0
DOK1 0.006 0.015 -10000 0 -10000 0 0
HRAS/GTP 0.001 0.016 0.21 2 -10000 0 2
PDGFB 0.001 0.016 0.32 1 -10000 0 1
RAC1 -0.019 0.17 -10000 0 -0.46 43 43
PRKCD 0.006 0.015 -10000 0 -10000 0 0
FER 0.006 0.015 -10000 0 -10000 0 0
MAPKKK cascade 0.001 0.011 -10000 0 -10000 0 0
RASA1 0.003 0.042 -10000 0 -0.54 2 2
NCK1 0 0 -10000 0 -10000 0 0
NCK2 -0.001 0.048 0.32 1 -0.86 1 2
p62DOK/Csk 0.004 0.014 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.002 0.044 -10000 0 -0.63 1 1
chemotaxis 0.002 0.074 -10000 0 -0.34 3 3
STAT1-3-5/STAT1-3-5 0.004 0.02 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.007 0.031 0.21 8 -10000 0 8
PTPRJ 0 0 -10000 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.002 0.059 0.34 2 -0.7 2 4
FRAP1 0.013 0.024 0.23 2 -10000 0 2
AKT1 -0.003 0.053 0.24 2 -0.64 2 4
INSR 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.003 0.023 -10000 0 -10000 0 0
mol:GTP -0.005 0.047 -10000 0 -0.43 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.014 -10000 0 -10000 0 0
TSC2 -0.005 0.063 -10000 0 -0.86 2 2
RHEB/GDP -0.005 0.043 -10000 0 -0.39 4 4
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.034 -10000 0 -0.35 2 2
MAP3K5 -0.046 0.15 -10000 0 -0.46 43 43
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
apoptosis -0.046 0.15 -10000 0 -0.46 43 43
mol:LY294002 0 0 0.001 2 -10000 0 2
EIF4B 0.027 0.031 -10000 0 -0.37 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.022 -10000 0 -0.34 1 1
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.056 -10000 0 -0.73 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.026 0.17 2 -0.26 2 4
FKBP1A 0 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.005 0.042 -10000 0 -0.38 4 4
mol:Amino Acids 0 0 0.001 2 -10000 0 2
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.002 0.053 0.26 2 -0.65 2 4
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.072 0.2 0.24 2 -0.63 43 45
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0 0.002 -10000 0 -10000 0 0
TSC1/TSC2 -0.006 0.052 -10000 0 -0.47 4 4
tumor necrosis factor receptor activity 0 0 -10000 0 -0.001 2 2
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 0.007 0.002 -10000 0 -10000 0 0
INS 0.004 0.036 0.32 5 -10000 0 5
PTEN -0.005 0.063 -10000 0 -0.86 2 2
PDK2 -0.003 0.058 0.26 2 -0.59 3 5
EIF4EBP1 0.008 0.016 0.31 1 -10000 0 1
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
PPP2R5D 0.018 0.023 -10000 0 -10000 0 0
peptide biosynthetic process 0.001 0.009 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 2 -0.004 2 4
EEF2 0.001 0.009 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.02 0.11 -10000 0 -0.58 13 13
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.064 -10000 0 -0.7 2 2
NFKBIA 0.012 0.079 -10000 0 -0.38 12 12
MAPK14 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
REL -0.03 0.16 -10000 0 -0.86 13 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0 0 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
NF kappa B1 p50 dimer 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
NFKB1 0.018 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.009 0.063 -10000 0 -0.33 12 12
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.01 0.062 -10000 0 -0.68 2 2
SRC 0.004 0.036 0.32 5 -10000 0 5
PI3K -0.005 0.071 -10000 0 -0.94 2 2
NF kappa B1 p50/RelA -0.009 0.064 -10000 0 -0.34 12 12
IKBKB 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -10000 0 -10000 0 0
SYK -0.007 0.077 -10000 0 -0.86 3 3
I kappa B alpha/PIK3R1 -0.014 0.078 -10000 0 -0.62 4 4
cell death -0.009 0.059 -10000 0 -0.64 2 2
NF kappa B1 p105/c-Rel -0.02 0.11 -10000 0 -0.58 13 13
LCK -0.025 0.15 0.32 1 -0.86 11 12
BCL3 0 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 -0.002 0.045 -10000 0 -0.86 1 1
SMAD2 0.012 0 -10000 0 -10000 0 0
SMAD3 0.034 0 -10000 0 -10000 0 0
SMAD3/SMAD4 0 0.022 -10000 0 -0.32 1 1
SMAD4/Ubc9/PIASy -0.002 0.03 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4 0 0.029 -10000 0 -0.46 1 1
PPM1A 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.001 0.027 -10000 0 -0.53 1 1
MAP3K1 0 0 -10000 0 -10000 0 0
TRAP-1/SMAD4 -0.041 0.16 -10000 0 -0.67 23 23
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
CTDSP1 0 0 -10000 0 -10000 0 0
CTDSP2 0 0 -10000 0 -10000 0 0
CTDSPL 0 0 -10000 0 -10000 0 0
KPNB1 0 0 -10000 0 -10000 0 0
TGFBRAP1 -0.051 0.2 -10000 0 -0.86 22 22
UBE2I 0 0 -10000 0 -10000 0 0
NUP153 0 0 -10000 0 -10000 0 0
KPNA2 0.003 0.028 0.32 3 -10000 0 3
PIAS4 0 0 -10000 0 -10000 0 0
ceramide signaling 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
MAP4K4 0.032 0.065 -10000 0 -0.33 2 2
BAG4 -0.028 0.15 -10000 0 -0.86 12 12
BAD 0.025 0.026 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 0.007 0.088 0.32 14 -0.86 2 16
BAX 0.025 0.026 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.011 0.019 -10000 0 -0.074 2 2
IKBKB 0.038 0.062 -10000 0 -10000 0 0
MAP2K2 0.034 0.03 -10000 0 -10000 0 0
MAP2K1 0.034 0.029 -10000 0 -10000 0 0
SMPD1 0.015 0.019 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.038 0.064 -10000 0 -10000 0 0
MAP2K4 0.03 0.027 -10000 0 -10000 0 0
protein ubiquitination 0.039 0.063 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.038 0.033 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.03 0.029 -10000 0 -10000 0 0
CRADD -0.002 0.045 -10000 0 -0.86 1 1
mol:ceramide 0.019 0.027 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.025 0.027 -10000 0 -10000 0 0
TRADD -0.002 0.045 -10000 0 -0.86 1 1
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.036 0.029 -10000 0 -10000 0 0
MAPK1 0.036 0.029 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.032 0.065 -10000 0 -0.33 2 2
KSR1 0.025 0.028 -10000 0 -10000 0 0
MAPK8 0.01 0.11 -10000 0 -0.44 20 20
TRAF2 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.038 0.062 -10000 0 -10000 0 0
TNF R/SODD -0.022 0.12 -10000 0 -0.67 12 12
TNF -0.031 0.17 0.32 2 -0.86 14 16
CYCS 0.026 0.025 -10000 0 -10000 0 0
IKBKG 0.038 0.062 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.006 0.064 -10000 0 -0.36 2 2
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AIFM1 0.026 0.025 -10000 0 -10000 0 0
TNF/TNF R/SODD -0.04 0.15 -10000 0 -0.58 26 26
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 -0.001 0.014 -10000 0 -10000 0 0
NSMAF 0.032 0.065 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.002 0.045 -10000 0 -0.86 1 1
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.019 0.1 -10000 0 -0.54 14 14
Ran/GTP/Exportin 1/HDAC1 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.085 -10000 0 -0.44 14 14
SUMO1 0 0 -10000 0 -10000 0 0
ZFPM1 -0.005 0.063 -10000 0 -0.86 2 2
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
FKBP3 0 0 -10000 0 -10000 0 0
Histones -0.009 0.043 -10000 0 -10000 0 0
YY1/LSF -0.006 0.05 -10000 0 -0.42 5 5
SMG5 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.014 0.075 -10000 0 -0.39 14 14
I kappa B alpha/HDAC1 -0.01 0.051 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
RELA -0.012 0.065 -10000 0 -0.34 14 14
HDAC1/Smad7 -0.003 0.043 -10000 0 -0.58 2 2
RANGAP1 0 0 -10000 0 -10000 0 0
HDAC3/TR2 -0.01 0.051 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.002 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.012 0.059 -10000 0 -0.31 14 14
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.003 0.067 0.32 2 -0.86 2 4
GATA1 0.003 0.028 0.32 3 -10000 0 3
Mad/Max 0.001 0.011 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.002 0.025 -10000 0 -10000 0 0
RBBP7 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
MAX 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
NFKBIA -0.011 0.057 -10000 0 -0.3 14 14
KAT2B -0.007 0.077 -10000 0 -0.86 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0 0 -10000 0 -10000 0 0
SIN3 complex 0 0 -10000 0 -10000 0 0
SMURF1 0 0 -10000 0 -10000 0 0
CHD3 0.006 0.043 0.32 7 -10000 0 7
SAP30 0 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 -0.005 0.063 -10000 0 -0.86 2 2
YY1/HDAC3 -0.011 0.055 -10000 0 -0.52 1 1
YY1/HDAC2 -0.003 0.028 -10000 0 -0.32 3 3
YY1/HDAC1 -0.003 0.028 -10000 0 -0.32 3 3
NuRD/MBD2 Complex (MeCP1) 0.002 0.013 -10000 0 -10000 0 0
PPARG -0.019 0.1 -10000 0 -0.51 15 15
HDAC8/hEST1B 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.01 0.051 -10000 0 -10000 0 0
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.003 0.042 -10000 0 -0.58 2 2
CREBBP 0 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.002 0.014 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 -0.011 0.057 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
YY1 -0.003 0.033 -10000 0 -0.37 3 3
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 -0.005 0.063 -10000 0 -0.86 2 2
NCOR2 0 0 -10000 0 -10000 0 0
MXD1 0.001 0.016 0.32 1 -10000 0 1
STAT3 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 -0.005 0.046 -10000 0 -0.52 2 2
YY1/SAP30/HDAC1 -0.002 0.026 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.057 -10000 0 -0.3 14 14
histone deacetylation 0.002 0.013 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.009 0.046 -10000 0 -10000 0 0
nuclear export 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0 0 -10000 0 -10000 0 0
GATA2/HDAC3 -0.011 0.066 -10000 0 -0.53 2 2
GATA1/HDAC1 0.002 0.02 -10000 0 -10000 0 0
GATA1/HDAC3 -0.008 0.056 -10000 0 -10000 0 0
CHD4 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.024 0.13 -10000 0 -0.67 14 14
SIN3/HDAC complex/Mad/Max 0 0.005 -10000 0 -10000 0 0
NuRD Complex 0.002 0.014 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.008 0.042 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
MTA2 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0 0 -10000 0 -10000 0 0
HDAC complex 0 0 -10000 0 -10000 0 0
GATA1/Fog1 -0.002 0.053 -10000 0 -0.67 2 2
FKBP25/HDAC1/HDAC2 0 0 -10000 0 -10000 0 0
TNF -0.031 0.17 0.32 2 -0.86 14 16
negative regulation of cell growth 0 0.005 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.002 0.013 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.017 0.09 -10000 0 -0.47 14 14
SIN3/HDAC complex/NCoR1 -0.001 0.016 -10000 0 -10000 0 0
TFCP2 -0.005 0.063 -10000 0 -0.86 2 2
NR2C1 0 0 -10000 0 -10000 0 0
MBD3 0 0 -10000 0 -10000 0 0
MBD2 0 0 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0 0.038 -10000 0 -0.45 2 2
TC10/GTP -0.002 0.034 -10000 0 -0.44 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.003 0.022 -10000 0 -10000 0 0
HRAS 0.002 0.023 0.32 2 -10000 0 2
APS homodimer 0.003 0.033 0.32 4 -10000 0 4
GRB14 -0.014 0.11 -10000 0 -0.86 6 6
FOXO3 -0.025 0.13 -10000 0 -0.74 12 12
AKT1 -0.01 0.069 -10000 0 -0.46 8 8
INSR 0 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.003 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0 0 -10000 0 -10000 0 0
SORBS1 -0.005 0.063 -10000 0 -0.86 2 2
CRK 0 0 -10000 0 -10000 0 0
PTPN1 0.031 0.005 -10000 0 -10000 0 0
CAV1 0.001 0.008 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G -0.001 0.039 -10000 0 -0.48 2 2
Insulin Receptor/Insulin/IRS1/NCK2 0.002 0.038 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.057 -10000 0 -0.71 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.002 0.014 -10000 0 -10000 0 0
RPS6KB1 0.04 0.069 -10000 0 -0.69 1 1
PARD6A 0.001 0.016 0.32 1 -10000 0 1
CBL 0 0 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.007 0.063 -10000 0 -0.68 1 1
HRAS/GTP 0 0 -10000 0 -10000 0 0
Insulin Receptor 0 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.003 0.022 -10000 0 -10000 0 0
PRKCI -0.003 0.017 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.011 0.076 -10000 0 -0.5 8 8
SHC1 0 0 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade -0.003 0.037 -10000 0 -0.51 2 2
PI3K -0.002 0.059 -10000 0 -0.73 2 2
NCK2 -0.001 0.048 0.32 1 -0.86 1 2
RHOQ 0 0 -10000 0 -10000 0 0
mol:H2O2 0 0 -10000 0 -10000 0 0
HRAS/GDP 0.001 0.016 0.21 2 -10000 0 2
AKT2 -0.01 0.069 -10000 0 -0.47 7 7
PRKCZ -0.033 0.14 -10000 0 -0.68 17 17
SH2B2 0.003 0.033 0.32 4 -10000 0 4
SHC/SHIP 0.001 0.008 -10000 0 -10000 0 0
F2RL2 -0.081 0.27 0.32 8 -0.86 38 46
TRIP10 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.003 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.003 0.022 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
RASA1 -0.005 0.063 -10000 0 -0.86 2 2
NCK1 0 0 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.001 0.042 -10000 0 -0.51 2 2
TC10/GDP 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.003 0.022 -10000 0 -10000 0 0
INPP5D 0.001 0.008 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.035 0.19 -10000 0 -1.1 12 12
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
p62DOK/RasGAP -0.003 0.038 -10000 0 -0.52 2 2
INS 0.007 0.037 0.32 5 -10000 0 5
mol:PI-3-4-P2 0.001 0.008 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
EIF4EBP1 0.04 0.07 -10000 0 -0.69 1 1
PTPRA 0 0.002 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
TC10/GTP/CIP4 0 0 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.002 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.003 0.022 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.003 0.025 -10000 0 -10000 0 0
Par3/Par6 -0.047 0.16 -10000 0 -0.5 38 38
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.013 0.091 -10000 0 -0.58 9 9
VEGFR1 homodimer/NRP1 0 0 -10000 0 -10000 0 0
mol:DAG 0.002 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -10000 0 -10000 0 0
CaM/Ca2+ 0.002 0.014 -10000 0 -10000 0 0
HIF1A 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
AKT1 -0.002 0.054 -10000 0 -0.68 2 2
PLCG1 0.002 0.016 -10000 0 -10000 0 0
NOS3 0.05 0.036 -10000 0 -0.4 2 2
CBL 0 0 -10000 0 -10000 0 0
mol:NO 0.05 0.035 -10000 0 -0.38 2 2
FLT1 0.024 0 -10000 0 -10000 0 0
PGF 0.005 0.04 0.32 6 -10000 0 6
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.049 -10000 0 -0.53 3 3
CALM1 0 0 -10000 0 -10000 0 0
PIK3CA -0.002 0.045 -10000 0 -0.86 1 1
eNOS/Hsp90 -0.003 0.028 -10000 0 -10000 0 0
endothelial cell proliferation 0.014 0.11 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.016 -10000 0 -10000 0 0
MAPK3 0.045 0.006 -10000 0 -10000 0 0
MAPK1 0.045 0.006 -10000 0 -10000 0 0
PIK3R1 -0.005 0.063 -10000 0 -0.86 2 2
PLGF homodimer 0.005 0.04 0.32 6 -10000 0 6
PRKACA 0 0 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0 0 -10000 0 -10000 0 0
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0 0 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.05 0.005 -10000 0 -10000 0 0
PI3K -0.001 0.063 -10000 0 -0.74 2 2
PRKCA 0.04 0.007 -10000 0 -10000 0 0
PRKCB -0.007 0.15 -10000 0 -0.5 32 32
VEGFR1 homodimer/PLGF homodimer 0.004 0.029 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB -0.019 0.14 0.32 2 -0.86 9 11
mol:IP3 0.002 0.016 -10000 0 -10000 0 0
RASA1 -0.015 0.09 -10000 0 -0.52 11 11
NRP2 -0.006 0.079 0.32 1 -0.86 3 4
VEGFR1 homodimer 0.023 0 -10000 0 -10000 0 0
VEGFB homodimer -0.019 0.13 0.32 2 -0.86 9 11
NCK1 0 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.003 0.028 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.061 -10000 0 -0.72 2 2
mol:L-citrulline 0.05 0.035 -10000 0 -0.38 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -10000 0 -10000 0 0
CD2AP 0 0 -10000 0 -10000 0 0
PI3K/GAB1 -0.001 0.06 -10000 0 -0.71 2 2
PDPK1 -0.002 0.054 -10000 0 -0.68 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -10000 0 -10000 0 0
mol:NADP 0.05 0.035 -10000 0 -0.38 2 2
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.004 0.053 -10000 0 -0.58 3 3
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.065 0.021 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 -0.007 0.069 -10000 0 -0.67 4 4
NFKBIA 0.039 0 -10000 0 -10000 0 0
BIRC2 0 0 -10000 0 -10000 0 0
IKBKB 0 0 -10000 0 -10000 0 0
RIPK2 0 0 -10000 0 -10000 0 0
IKBKG -0.003 0.03 -10000 0 -10000 0 0
IKK complex/A20 -0.018 0.09 -10000 0 -0.45 14 14
NEMO/A20/RIP2 0 0 -10000 0 -10000 0 0
XPO1 0 0 -10000 0 -10000 0 0
NEMO/ATM -0.003 0.028 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
Exportin 1/RanGTP 0 0 -10000 0 -10000 0 0
IKK complex/ELKS -0.003 0.024 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.03 -10000 0 -0.58 1 1
NOD2 -0.009 0.089 -10000 0 -0.86 4 4
NFKB1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
MALT1 0 0 -10000 0 -10000 0 0
cIAP1/UbcH5C 0 0 -10000 0 -10000 0 0
ATM 0 0 -10000 0 -10000 0 0
TNF/TNFR1A -0.024 0.13 -10000 0 -0.67 14 14
TRAF6 -0.002 0.045 -10000 0 -0.86 1 1
PRKCA 0 0 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
TNF -0.031 0.17 0.32 2 -0.86 14 16
NF kappa B1 p50/RelA 0 0 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.039 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
IKK complex -0.003 0.026 -10000 0 -10000 0 0
CYLD 0 0 -10000 0 -10000 0 0
IKK complex/PKC alpha -0.003 0.025 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.004 0.13 0.32 14 -0.86 7 21
CLTC 0.021 0.017 -10000 0 -10000 0 0
calcium ion-dependent exocytosis -0.011 0.046 -10000 0 -10000 0 0
Dynamin 2/GTP 0.001 0.008 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.018 0.023 -10000 0 -10000 0 0
CPE 0.003 0.042 -10000 0 -0.59 1 1
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.012 0.05 -10000 0 -10000 0 0
CTNND1 0 0.005 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.029 -10000 0 -10000 0 0
TSHR 0 0 -10000 0 -10000 0 0
INS 0.01 0.02 -10000 0 -10000 0 0
BIN1 -0.002 0.045 -10000 0 -0.86 1 1
mol:Choline -0.012 0.05 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.013 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.008 -10000 0 -10000 0 0
JUP 0.018 0.023 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0 0.033 -10000 0 -0.54 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 -0.001 0.086 -10000 0 -0.4 8 8
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.016 0.057 -10000 0 -10000 0 0
positive regulation of phagocytosis 0 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.012 0.046 -10000 0 -0.34 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.003 0.04 -10000 0 -0.4 1 1
clathrin heavy chain/ACAP1 0.021 0.035 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0 0.005 -10000 0 -10000 0 0
NME1 0.001 0.013 -10000 0 -10000 0 0
clathrin coat assembly 0.021 0.017 -10000 0 -10000 0 0
IL2RA 0.012 0.051 -10000 0 -0.4 1 1
VAMP3 0 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.007 0.074 -10000 0 -0.44 7 7
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.02 0.083 -10000 0 -0.36 21 21
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.02 0.029 -10000 0 -10000 0 0
SDC1 0.014 0.039 -10000 0 -10000 0 0
ARF6/GDP 0.001 0.008 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.016 0.059 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.012 0.05 -10000 0 -10000 0 0
endocytosis 0 0.032 0.53 1 -10000 0 1
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.033 0.16 -10000 0 -0.47 44 44
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 0.003 0.028 0.32 3 -10000 0 3
Dynamin 2/GDP 0.001 0.011 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.029 0.019 -10000 0 -10000 0 0
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.053 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.016 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0 -9999 0 -10000 0 0
CD4 -0.07 0.23 -9999 0 -0.86 30 30
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.009 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.023 0.079 -9999 0 -0.29 30 30
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.009 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.009 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.047 0.16 -9999 0 -0.58 30 30
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.003 0.033 -10000 0 -10000 0 0
CLOCK -0.002 0.044 -10000 0 -0.86 1 1
TIMELESS/CRY2 -0.001 0.019 -10000 0 -10000 0 0
DEC1/BMAL1 0 0.001 -10000 0 -10000 0 0
ATR 0 0 -10000 0 -10000 0 0
NR1D1 0.03 0.078 -10000 0 -1.5 1 1
ARNTL 0 0.002 -10000 0 -10000 0 0
TIMELESS 0.033 0.023 -10000 0 -10000 0 0
NPAS2 -0.002 0.044 -10000 0 -0.86 1 1
CRY2 0 0 -10000 0 -10000 0 0
mol:CO -0.011 0.008 0.14 1 -10000 0 1
CHEK1 0.006 0.043 0.32 7 -10000 0 7
mol:HEME 0.011 0.008 -10000 0 -0.14 1 1
PER1 0 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.003 0.042 -10000 0 -0.57 2 2
BMAL1/CLOCK 0.036 0.056 -10000 0 -0.67 2 2
S phase of mitotic cell cycle 0.003 0.033 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.003 0.033 -10000 0 -10000 0 0
mol:NADPH 0.011 0.008 -10000 0 -0.14 1 1
PER1/TIMELESS -0.001 0.019 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.1 0.064 -9999 0 -9999 0 0
TP53 0.027 0.019 -9999 0 -9999 0 0
Senescence 0.027 0.019 -9999 0 -9999 0 0
Apoptosis 0.027 0.019 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 -0.057 0.039 -9999 0 -9999 0 0
MDM4 0 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -9999 0 0
MDM2/SUMO1 0 0 -10000 0 -9999 0 0
HDAC4 0.001 0.016 0.32 1 -9999 0 1
Ran/GTP/Exportin 1/HDAC1 0 0 -10000 0 -9999 0 0
SUMO1 0 0 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0 0 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0 0 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0 0 -10000 0 -9999 0 0
SUMO1/HDAC4 0.001 0.011 -10000 0 -9999 0 0
SUMO1/HDAC1 0 0 -10000 0 -9999 0 0
RANGAP1 0 0 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -10000 0 -9999 0 0
Ran/GTP 0 0 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0 0 -10000 0 -9999 0 0
UBE2I 0 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -9999 0 0
NPC 0 0 -10000 0 -9999 0 0
PIAS2 0 0 -10000 0 -9999 0 0
PIAS1 0 0 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 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 0.001 0.011 -10000 0 -9999 0 0
FBXW11 0 0 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -10000 0 -9999 0 0
CHUK 0 0 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.002 0.017 -10000 0 -9999 0 0
NFKB1 0 0 -10000 0 -9999 0 0
MAP3K14 0.001 0.016 0.32 1 -9999 0 1
NF kappa B1 p50/RelB 0.001 0.016 -10000 0 -9999 0 0
RELB 0.002 0.023 0.32 2 -9999 0 2
NFKB2 0 0 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.001 0.014 -10000 0 -9999 0 0
regulation of B cell activation 0.001 0.014 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 371 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZS.A9CG TCGA.ZS.A9CF TCGA.ZS.A9CE TCGA.ZS.A9CD
109_MAP3K5 -0.23 -0.23 -0.23 0.044
47_PPARGC1A 0 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 0 0 0 0
131_RELN/VLDLR 0.2 -1 0 0
30_TGFB1/TGF beta receptor Type II 0 0 0 0
84_STAT5B 0.085 0.1 0.034 0.033
84_STAT5A 0.085 0.1 0.034 0.033
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/LIHC-TP/14527201/LIHC-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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