PARADIGM pathway analysis of mRNASeq expression data
Lung Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C11N7ZM7
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C11N7ZM7
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 39 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
Glypican 2 network 186
Angiopoietin receptor Tie2-mediated signaling 141
FOXM1 transcription factor network 133
Aurora B signaling 121
Signaling events mediated by the Hedgehog family 100
Aurora C signaling 74
Endothelins 71
PLK1 signaling events 69
HIF-1-alpha transcription factor network 66
Visual signal transduction: Cones 60
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 488 . 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 ( 488 ).

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
Glypican 2 network 0.3811 186 746 4 -0.21 -0.13 1000 -1000 -0.028 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2889 141 12424 88 -0.6 0.057 1000 -1000 -0.095 -1000
FOXM1 transcription factor network 0.2725 133 6794 51 -0.56 0.01 1000 -1000 -0.19 -1000
Aurora B signaling 0.2480 121 8142 67 -0.41 0.01 1000 -1000 -0.062 -1000
Signaling events mediated by the Hedgehog family 0.2049 100 5203 52 -0.37 0.18 1000 -1000 -0.066 -1000
Aurora C signaling 0.1516 74 519 7 -0.27 0.005 1000 -1000 -0.035 -1000
Endothelins 0.1455 71 6826 96 -0.3 0.022 1000 -1000 -0.071 -1000
PLK1 signaling events 0.1414 69 5895 85 -0.3 0.06 1000 -1000 -0.041 -1000
HIF-1-alpha transcription factor network 0.1352 66 5090 76 -0.49 0.016 1000 -1000 -0.16 -1000
Visual signal transduction: Cones 0.1230 60 2284 38 -0.17 0.01 1000 -1000 -0.053 -1000
Signaling mediated by p38-alpha and p38-beta 0.1209 59 2631 44 -0.12 0.01 1000 -1000 -0.046 -1000
Osteopontin-mediated events 0.1189 58 2205 38 -0.36 0.011 1000 -1000 -0.084 -1000
Signaling events regulated by Ret tyrosine kinase 0.1127 55 4542 82 -0.16 0.01 1000 -1000 -0.072 -1000
IL4-mediated signaling events 0.1086 53 4836 91 -0.79 0.52 1000 -1000 -0.18 -1000
amb2 Integrin signaling 0.1045 51 4245 82 -0.46 0.01 1000 -1000 -0.067 -1000
BMP receptor signaling 0.1004 49 4021 81 -0.35 0.027 1000 -1000 -0.078 -1000
Fc-epsilon receptor I signaling in mast cells 0.0984 48 4679 97 -0.15 0.028 1000 -1000 -0.076 -1000
FOXA2 and FOXA3 transcription factor networks 0.0963 47 2165 46 -0.49 0.016 1000 -1000 -0.085 -1000
TCGA08_retinoblastoma 0.0922 45 366 8 -0.15 0.05 1000 -1000 -0.016 -1000
Glucocorticoid receptor regulatory network 0.0861 42 4849 114 -0.42 0.25 1000 -1000 -0.059 -1000
TCGA08_p53 0.0861 42 294 7 -0.1 0.054 1000 -1000 -0.01 -1000
Syndecan-1-mediated signaling events 0.0820 40 1365 34 -0.34 0.01 1000 -1000 -0.049 -1000
Visual signal transduction: Rods 0.0779 38 1992 52 -0.15 0.01 1000 -1000 -0.072 -1000
Arf6 signaling events 0.0758 37 2350 62 -0.19 0.012 1000 -1000 -0.059 -1000
p75(NTR)-mediated signaling 0.0758 37 4711 125 -0.29 0.019 1000 -1000 -0.089 -1000
LPA4-mediated signaling events 0.0738 36 436 12 -0.12 0.013 1000 -1000 -0.019 -1000
Canonical Wnt signaling pathway 0.0717 35 1817 51 -0.34 0.15 1000 -1000 -0.058 -1000
Thromboxane A2 receptor signaling 0.0697 34 3664 105 -0.089 0.029 1000 -1000 -0.061 -1000
Glypican 1 network 0.0676 33 1584 48 -0.12 0.019 1000 -1000 -0.039 -1000
Effects of Botulinum toxin 0.0656 32 833 26 -0.09 0.01 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 0.0635 31 1515 48 -0.093 0.054 1000 -1000 -0.051 -1000
Integrins in angiogenesis 0.0635 31 2670 84 -0.36 0.025 1000 -1000 -0.071 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0635 31 3761 120 -0.25 0.2 1000 -1000 -0.066 -1000
EGFR-dependent Endothelin signaling events 0.0615 30 633 21 -0.089 0.01 1000 -1000 -0.061 -1000
ErbB4 signaling events 0.0574 28 2000 69 -0.19 0.21 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.0574 28 1699 60 -0.28 0.015 1000 -1000 -0.16 -1000
Presenilin action in Notch and Wnt signaling 0.0533 26 1597 61 -0.34 0.021 1000 -1000 -0.066 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0533 26 1815 68 -0.14 0.028 1000 -1000 -0.12 -1000
IL6-mediated signaling events 0.0512 25 1898 75 -0.33 0.042 1000 -1000 -0.089 -1000
Aurora A signaling 0.0492 24 1451 60 -0.29 0.015 1000 -1000 -0.059 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0492 24 808 33 -0.15 0.025 1000 -1000 -0.048 -1000
PDGFR-alpha signaling pathway 0.0471 23 1012 44 -0.32 0.027 1000 -1000 -0.047 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0430 21 1143 52 -0.26 0.044 1000 -1000 -0.051 -1000
Nongenotropic Androgen signaling 0.0430 21 1141 52 -0.057 0.01 1000 -1000 -0.052 -1000
Wnt signaling 0.0430 21 147 7 -0.059 0.009 1000 -1000 -0.029 -1000
Class IB PI3K non-lipid kinase events 0.0430 21 63 3 -0.012 -1000 1000 -1000 -0.015 -1000
HIF-2-alpha transcription factor network 0.0410 20 866 43 -0.13 0.064 1000 -1000 -0.087 -1000
Reelin signaling pathway 0.0389 19 1082 56 -0.095 0.01 1000 -1000 -0.066 -1000
Regulation of Androgen receptor activity 0.0389 19 1357 70 -0.26 0.027 1000 -1000 -0.062 -1000
PLK2 and PLK4 events 0.0369 18 54 3 -0.018 -0.003 1000 -1000 -0.017 -1000
Syndecan-4-mediated signaling events 0.0369 18 1224 67 -0.17 0.016 1000 -1000 -0.074 -1000
Coregulation of Androgen receptor activity 0.0328 16 1252 76 -0.15 0.018 1000 -1000 -0.047 -1000
Syndecan-2-mediated signaling events 0.0328 16 1123 69 -0.096 0.032 1000 -1000 -0.049 -1000
Nectin adhesion pathway 0.0328 16 1015 63 -0.041 0.013 1000 -1000 -0.063 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0307 15 541 34 -0.04 0.01 1000 -1000 -0.053 -1000
Noncanonical Wnt signaling pathway 0.0307 15 405 26 -0.059 0.01 1000 -1000 -0.076 -1000
IL12-mediated signaling events 0.0287 14 1256 87 -0.097 0.038 1000 -1000 -0.12 -1000
Syndecan-3-mediated signaling events 0.0287 14 517 35 -0.2 0.01 1000 -1000 -0.057 -1000
Caspase cascade in apoptosis 0.0266 13 962 74 -0.041 0.032 1000 -1000 -0.043 -1000
Signaling events mediated by PTP1B 0.0266 13 1034 76 -0.092 0.017 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class III 0.0266 13 526 40 -0.11 0.018 1000 -1000 -0.039 -1000
FAS signaling pathway (CD95) 0.0266 13 612 47 -0.24 0.012 1000 -1000 -0.042 -1000
EPHB forward signaling 0.0266 13 1122 85 -0.066 0.049 1000 -1000 -0.08 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0266 13 1682 125 -0.32 0.034 1000 -1000 -0.084 -1000
LPA receptor mediated events 0.0266 13 1378 102 -0.12 0.03 1000 -1000 -0.074 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0266 13 1060 78 -0.039 0.038 1000 -1000 -0.072 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0246 12 659 54 -0.14 0.021 1000 -1000 -0.085 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0246 12 1053 85 -0.041 0.03 1000 -1000 -0.068 -1000
IL1-mediated signaling events 0.0246 12 759 62 -0.15 0.049 1000 -1000 -0.083 -1000
S1P1 pathway 0.0246 12 462 36 -0.063 0.011 1000 -1000 -0.05 -1000
TCR signaling in naïve CD8+ T cells 0.0246 12 1136 93 -0.075 0.043 1000 -1000 -0.069 -1000
BCR signaling pathway 0.0246 12 1256 99 -0.13 0.026 1000 -1000 -0.078 -1000
Signaling events mediated by PRL 0.0246 12 429 34 -0.18 0.021 1000 -1000 -0.034 -1000
BARD1 signaling events 0.0225 11 656 57 -0.18 0.03 1000 -1000 -0.053 -1000
Ephrin A reverse signaling 0.0225 11 77 7 -0.01 0.008 1000 -1000 -0.024 -1000
S1P5 pathway 0.0225 11 199 17 -0.033 0.03 1000 -1000 -0.048 -1000
S1P4 pathway 0.0225 11 280 25 -0.033 0.011 1000 -1000 -0.046 -1000
Calcium signaling in the CD4+ TCR pathway 0.0205 10 339 31 -0.073 0.012 1000 -1000 -0.085 -1000
ErbB2/ErbB3 signaling events 0.0184 9 631 65 -0.095 0.019 1000 -1000 -0.063 -1000
Regulation of p38-alpha and p38-beta 0.0184 9 523 54 -0.075 0.018 1000 -1000 -0.053 -1000
IL2 signaling events mediated by STAT5 0.0184 9 203 22 -0.12 0.055 1000 -1000 -0.061 -1000
Regulation of nuclear SMAD2/3 signaling 0.0164 8 1142 136 -0.11 0.051 1000 -1000 -0.06 -1000
Plasma membrane estrogen receptor signaling 0.0164 8 763 86 -0.035 0.03 1000 -1000 -0.074 -1000
Signaling mediated by p38-gamma and p38-delta 0.0143 7 119 15 0 0.022 1000 -1000 -0.025 -1000
IL27-mediated signaling events 0.0143 7 378 51 -0.11 0.011 1000 -1000 -0.064 -1000
Ras signaling in the CD4+ TCR pathway 0.0143 7 133 17 -0.014 0.021 1000 -1000 -0.043 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0123 6 192 28 -0.033 0.021 1000 -1000 -0.048 -1000
Cellular roles of Anthrax toxin 0.0123 6 238 39 -0.045 0.015 1000 -1000 -0.022 -1000
Retinoic acid receptors-mediated signaling 0.0123 6 362 58 -0.17 0.032 1000 -1000 -0.063 -1000
Arf6 trafficking events 0.0123 6 465 71 -0.081 0.034 1000 -1000 -0.064 -1000
Regulation of Telomerase 0.0123 6 712 102 -0.092 0.03 1000 -1000 -0.094 -1000
Insulin Pathway 0.0123 6 469 74 -0.15 0.03 1000 -1000 -0.079 -1000
VEGFR1 specific signals 0.0123 6 375 56 -0.32 0.042 1000 -1000 -0.069 -1000
p38 MAPK signaling pathway 0.0123 6 287 44 -0.082 0.025 1000 -1000 -0.058 -1000
Signaling events mediated by HDAC Class II 0.0102 5 400 75 -0.046 0.027 1000 -1000 -0.054 -1000
JNK signaling in the CD4+ TCR pathway 0.0102 5 89 17 -0.013 0.031 1000 -1000 -0.055 -1000
Hedgehog signaling events mediated by Gli proteins 0.0102 5 382 65 -0.17 0.054 1000 -1000 -0.056 -1000
Ceramide signaling pathway 0.0102 5 417 76 -0.089 0.036 1000 -1000 -0.052 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0102 5 433 83 -0.067 0.04 1000 -1000 -0.072 -1000
FoxO family signaling 0.0102 5 330 64 -0.13 0.055 1000 -1000 -0.081 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0102 5 373 74 -0.11 0.06 1000 -1000 -0.076 -1000
IFN-gamma pathway 0.0082 4 310 68 -0.082 0.047 1000 -1000 -0.084 -1000
Signaling events mediated by HDAC Class I 0.0082 4 484 104 -0.046 0.043 1000 -1000 -0.059 -1000
IL2 signaling events mediated by PI3K 0.0082 4 272 58 -0.15 0.066 1000 -1000 -0.079 -1000
Class I PI3K signaling events 0.0082 4 362 73 -0.075 0.023 1000 -1000 -0.067 -1000
Circadian rhythm pathway 0.0061 3 79 22 -0.029 0.034 1000 -1000 -0.064 -1000
Arf6 downstream pathway 0.0061 3 164 43 -0.039 0.026 1000 -1000 -0.037 -1000
TCGA08_rtk_signaling 0.0061 3 96 26 -0.023 0.037 1000 -1000 -0.02 -1000
S1P3 pathway 0.0061 3 154 42 -0.032 0.023 1000 -1000 -0.053 -1000
TRAIL signaling pathway 0.0041 2 128 48 -0.008 0.04 1000 -1000 -0.055 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0041 2 117 45 -0.012 0.062 1000 -1000 -0.083 -1000
E-cadherin signaling in the nascent adherens junction 0.0041 2 187 76 -0.041 0.05 1000 -1000 -0.069 -1000
IGF1 pathway 0.0041 2 168 57 -0.037 0.04 1000 -1000 -0.083 -1000
Rapid glucocorticoid signaling 0.0041 2 59 20 -0.007 0.01 1000 -1000 -0.029 -1000
PDGFR-beta signaling pathway 0.0041 2 226 97 -0.036 0.048 1000 -1000 -0.07 -1000
Canonical NF-kappaB pathway 0.0020 1 44 39 -0.014 0.066 1000 -1000 -0.069 -1000
a4b1 and a4b7 Integrin signaling 0.0020 1 8 5 -0.002 0.009 1000 -1000 -0.032 -1000
EPO signaling pathway 0.0020 1 83 55 -0.006 0.058 1000 -1000 -0.085 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0020 1 59 37 -0.005 0.037 1000 -1000 -0.048 -1000
ceramide signaling pathway 0.0020 1 55 49 -0.012 0.04 1000 -1000 -0.043 -1000
E-cadherin signaling events 0.0020 1 8 5 -0.002 0.01 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 11 23 -0.003 0.036 1000 -1000 -0.06 -1000
Insulin-mediated glucose transport 0.0000 0 24 32 -0.003 0.035 1000 -1000 -0.059 -1000
mTOR signaling pathway 0.0000 0 13 53 -0.001 0.026 1000 -1000 -0.05 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 25 68 -0.034 0.046 1000 -1000 -0.055 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 21 36 -0.003 0.018 1000 -1000 -0.059 -1000
Atypical NF-kappaB pathway 0.0000 0 17 31 -0.002 0.038 1000 -1000 -0.045 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 11 27 -0.001 0.024 1000 -1000 -0.049 -1000
E-cadherin signaling in keratinocytes 0.0000 0 28 43 -0.007 0.037 1000 -1000 -0.055 -1000
Arf1 pathway 0.0000 0 30 54 -0.006 0.024 1000 -1000 -0.035 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.01 1000 -1000 -0.053 -1000
Total NA 2938 169893 7203 -19 -1000 131000 -131000 -8.2 -131000
Glypican 2 network

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
MDK -0.15 0.24 -9999 0 -0.52 151 151
GPC2 -0.13 0.23 -9999 0 -0.52 131 131
GPC2/Midkine -0.21 0.23 -9999 0 -0.43 232 232
neuron projection morphogenesis -0.21 0.23 -9999 0 -0.43 232 232
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.42 0.52 -10000 0 -0.95 229 229
NCK1/PAK1/Dok-R -0.21 0.22 -10000 0 -0.43 229 229
NCK1/Dok-R -0.54 0.61 -10000 0 -1.1 229 229
PIK3CA 0.011 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.057 0.1 0.24 113 -10000 0 113
RELA 0.01 0 -10000 0 -10000 0 0
SHC1 0.006 0.024 -10000 0 -0.52 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.003 0.21 0.25 110 -0.52 53 163
TNIP2 0.01 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.49 0.54 -10000 0 -1 229 229
FN1 0.005 0.052 -10000 0 -0.5 5 5
PLD2 -0.52 0.66 -10000 0 -1.2 229 229
PTPN11 0.01 0 -10000 0 -10000 0 0
GRB14 -0.026 0.13 -10000 0 -0.51 33 33
ELK1 -0.45 0.57 -10000 0 -1 229 229
GRB7 0.004 0.057 -10000 0 -0.51 6 6
PAK1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.52 0.58 -10000 0 -1.1 229 229
CDKN1A -0.28 0.35 -10000 0 -0.65 227 227
ITGA5 0.008 0.033 -10000 0 -0.51 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.54 0.61 -10000 0 -1.1 229 229
CRK 0.01 0 -10000 0 -10000 0 0
mol:NO -0.29 0.37 -10000 0 -0.68 229 229
PLG -0.53 0.66 -10000 0 -1.2 229 229
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.39 0.48 -10000 0 -0.89 229 229
GRB2 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.005 0.024 -10000 0 -0.5 1 1
ANGPT2 -0.21 0.29 -10000 0 -0.64 127 127
BMX -0.6 0.7 -10000 0 -1.3 229 229
ANGPT1 -0.3 0.53 -10000 0 -1.3 113 113
tube development -0.32 0.4 -10000 0 -0.73 228 228
ANGPT4 -0.25 0.25 -10000 0 -0.5 248 248
response to hypoxia -0.029 0.035 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.56 0.69 -10000 0 -1.2 229 229
alpha5/beta1 Integrin -0.001 0.023 -10000 0 -0.36 2 2
FGF2 -0.059 0.17 -10000 0 -0.5 66 66
STAT5A (dimer) -0.37 0.46 -10000 0 -0.85 227 227
mol:L-citrulline -0.29 0.37 -10000 0 -0.68 229 229
AGTR1 -0.15 0.24 -10000 0 -0.5 153 153
MAPK14 -0.55 0.67 -10000 0 -1.2 229 229
Tie2/SHP2 -0.47 0.55 -10000 0 -1.1 203 203
TEK -0.51 0.62 -10000 0 -1.2 203 203
RPS6KB1 -0.39 0.49 -10000 0 -0.91 229 229
Angiotensin II/AT1 -0.11 0.17 -10000 0 -0.36 153 153
Tie2/Ang1/GRB2 -0.54 0.69 -10000 0 -1.2 229 229
MAPK3 -0.46 0.59 -10000 0 -1.1 229 229
MAPK1 -0.46 0.59 -10000 0 -1.1 229 229
Tie2/Ang1/GRB7 -0.55 0.69 -10000 0 -1.2 229 229
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.52 0.66 -10000 0 -1.2 229 229
PI3K -0.5 0.61 -10000 0 -1.1 229 229
FES -0.55 0.67 -10000 0 -1.2 229 229
Crk/Dok-R -0.54 0.61 -10000 0 -1.1 229 229
Tie2/Ang1/ABIN2 -0.54 0.69 -10000 0 -1.2 229 229
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.36 0.45 -10000 0 -0.83 229 229
STAT5A 0.009 0.023 -10000 0 -0.5 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.39 0.49 -10000 0 -0.91 229 229
Tie2/Ang2 -0.47 0.57 -10000 0 -1.1 228 228
Tie2/Ang1 -0.59 0.75 -10000 0 -1.3 229 229
FOXO1 -0.36 0.46 -10000 0 -0.84 229 229
ELF1 -0.028 0.051 -10000 0 -10000 0 0
ELF2 -0.53 0.67 -10000 0 -1.2 229 229
mol:Choline -0.49 0.62 -10000 0 -1.1 229 229
cell migration -0.11 0.12 -10000 0 -0.24 229 229
FYN -0.38 0.46 -10000 0 -0.85 228 228
DOK2 -0.031 0.14 -10000 0 -0.5 39 39
negative regulation of cell cycle -0.25 0.32 -10000 0 -0.58 227 227
ETS1 -0.045 0.1 -10000 0 -0.26 19 19
PXN -0.31 0.4 -10000 0 -0.73 229 229
ITGB1 0.01 0 -10000 0 -10000 0 0
NOS3 -0.34 0.43 -10000 0 -0.78 229 229
RAC1 0.01 0 -10000 0 -10000 0 0
TNF -0.064 0.14 -10000 0 -0.54 19 19
MAPKKK cascade -0.49 0.62 -10000 0 -1.1 229 229
RASA1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.56 0.68 -10000 0 -1.2 229 229
NCK1 0.01 0 -10000 0 -10000 0 0
vasculogenesis -0.25 0.33 -10000 0 -0.6 229 229
mol:Phosphatidic acid -0.49 0.62 -10000 0 -1.1 229 229
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP -0.29 0.37 -10000 0 -0.68 229 229
Rac1/GTP -0.4 0.42 -10000 0 -0.84 229 229
MMP2 -0.52 0.66 -10000 0 -1.2 229 229
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.43 0.55 -9999 0 -1 163 163
PLK1 -0.15 0.2 -9999 0 -0.37 216 216
BIRC5 -0.19 0.2 -9999 0 -10000 0 0
HSPA1B -0.44 0.55 -9999 0 -1 173 173
MAP2K1 -0.001 0.034 -9999 0 -10000 0 0
BRCA2 -0.44 0.55 -9999 0 -1 163 163
FOXM1 -0.56 0.7 -9999 0 -1.3 192 192
XRCC1 -0.43 0.55 -9999 0 -1 161 161
FOXM1B/p19 -0.51 0.49 -9999 0 -1.1 181 181
Cyclin D1/CDK4 -0.43 0.51 -9999 0 -0.97 173 173
CDC2 -0.46 0.58 -9999 0 -1.1 191 191
TGFA -0.42 0.5 -9999 0 -0.95 167 167
SKP2 -0.44 0.55 -9999 0 -1 167 167
CCNE1 -0.19 0.26 -9999 0 -0.53 178 178
CKS1B -0.44 0.55 -9999 0 -1 168 168
RB1 -0.22 0.18 -9999 0 -0.44 138 138
FOXM1C/SP1 -0.5 0.61 -9999 0 -1.2 180 180
AURKB -0.17 0.2 -9999 0 -10000 0 0
CENPF -0.49 0.59 -9999 0 -1.1 195 195
CDK4 0.002 0.05 -9999 0 -0.54 4 4
MYC -0.38 0.48 -9999 0 -0.9 167 167
CHEK2 -0.008 0.071 -9999 0 -0.57 6 6
ONECUT1 -0.47 0.55 -9999 0 -1 182 182
CDKN2A -0.14 0.24 -9999 0 -0.51 145 145
LAMA4 -0.44 0.55 -9999 0 -1 172 172
FOXM1B/HNF6 -0.56 0.65 -9999 0 -1.2 182 182
FOS -0.46 0.57 -9999 0 -1.1 172 172
SP1 0.01 0.001 -9999 0 -10000 0 0
CDC25B -0.43 0.55 -9999 0 -1 167 167
response to radiation -0.012 0.032 -9999 0 -10000 0 0
CENPB -0.43 0.55 -9999 0 -1 163 163
CENPA -0.51 0.6 -9999 0 -1.1 191 191
NEK2 -0.51 0.6 -9999 0 -1.1 202 202
HIST1H2BA -0.44 0.55 -9999 0 -1 163 163
CCNA2 -0.12 0.23 -9999 0 -0.53 119 119
EP300 0.01 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.52 0.64 -9999 0 -1.2 175 175
CCNB2 -0.5 0.6 -9999 0 -1.1 192 192
CCNB1 -0.48 0.6 -9999 0 -1.1 174 174
ETV5 -0.44 0.55 -9999 0 -1.1 162 162
ESR1 -0.45 0.56 -9999 0 -1.1 166 166
CCND1 -0.44 0.52 -9999 0 -0.99 175 175
GSK3A 0.002 0.028 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.18 0.26 -9999 0 -0.45 210 210
CDK2 0.006 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.016 0.038 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.55 0.5 -9999 0 -1.1 197 197
GAS1 -0.45 0.56 -9999 0 -1.1 160 160
MMP2 -0.44 0.55 -9999 0 -1 161 161
RB1/FOXM1C -0.47 0.56 -9999 0 -1.1 181 181
CREBBP 0.01 0 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.15 0.17 -9999 0 -0.33 202 202
STMN1 -0.18 0.19 -9999 0 -0.36 255 255
Aurora B/RasGAP/Survivin -0.31 0.27 -9999 0 -0.51 304 304
Chromosomal passenger complex/Cul3 protein complex -0.13 0.14 -9999 0 -0.3 155 155
BIRC5 -0.3 0.26 -9999 0 -0.53 281 281
DES -0.41 0.37 -9999 0 -0.74 262 262
Aurora C/Aurora B/INCENP -0.14 0.15 -9999 0 -0.28 259 259
Aurora B/TACC1 -0.16 0.17 -9999 0 -0.32 261 261
Aurora B/PP2A -0.18 0.19 -9999 0 -0.36 255 255
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.033 0.045 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.004 -9999 0 -10000 0 0
NDC80 -0.34 0.32 -9999 0 -0.59 284 284
Cul3 protein complex -0.013 0.063 -9999 0 -0.31 21 21
KIF2C -0.12 0.11 -9999 0 -0.22 264 264
PEBP1 0.004 0.005 -9999 0 -10000 0 0
KIF20A -0.28 0.26 -9999 0 -0.52 267 267
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.18 0.19 -9999 0 -0.36 255 255
SEPT1 0.009 0.023 -9999 0 -0.5 1 1
SMC2 0.01 0 -9999 0 -10000 0 0
SMC4 0.01 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.064 0.076 -9999 0 -10000 0 0
PSMA3 0.01 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.004 -9999 0 -10000 0 0
H3F3B -0.09 0.1 -9999 0 -0.18 255 255
AURKB -0.26 0.27 -9999 0 -0.52 255 255
AURKC 0.005 0.052 -9999 0 -0.51 5 5
CDCA8 -0.17 0.25 -9999 0 -0.53 162 162
cytokinesis -0.23 0.21 -9999 0 -0.45 207 207
Aurora B/Septin1 -0.21 0.2 -9999 0 -0.44 183 183
AURKA -0.094 0.21 -9999 0 -0.52 96 96
INCENP 0.003 0.007 -9999 0 -10000 0 0
KLHL13 -0.01 0.099 -9999 0 -0.5 19 19
BUB1 -0.13 0.24 -9999 0 -0.52 131 131
hSgo1/Aurora B/Survivin -0.41 0.36 -9999 0 -0.65 311 311
EVI5 0.009 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.22 0.22 -9999 0 -0.48 177 177
SGOL1 -0.24 0.26 -9999 0 -0.52 228 228
CENPA -0.16 0.16 -9999 0 -0.31 241 241
NCAPG -0.23 0.26 -9999 0 -0.52 220 220
Aurora B/HC8 Proteasome -0.18 0.19 -9999 0 -0.36 255 255
NCAPD2 0.009 0.024 -9999 0 -0.52 1 1
Aurora B/PP1-gamma -0.18 0.19 -9999 0 -0.36 255 255
RHOA 0.01 0 -9999 0 -10000 0 0
NCAPH -0.22 0.26 -9999 0 -0.52 211 211
NPM1 -0.085 0.083 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
KLHL9 0.007 0.04 -9999 0 -0.5 3 3
mitotic prometaphase -0.009 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.18 0.19 -9999 0 -0.36 255 255
PPP1CC 0.01 0 -9999 0 -10000 0 0
Centraspindlin -0.24 0.24 -9999 0 -0.47 215 215
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.085 0.083 -9999 0 -10000 0 0
MYLK -0.1 0.12 -9999 0 -0.2 258 258
KIF23 -0.11 0.22 -9999 0 -0.53 104 104
VIM -0.18 0.19 -9999 0 -0.36 255 255
RACGAP1 0 0.054 -9999 0 -0.53 5 5
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.085 0.083 -9999 0 -10000 0 0
Chromosomal passenger complex -0.2 0.2 -9999 0 -0.38 245 245
Chromosomal passenger complex/EVI5 -0.33 0.32 -9999 0 -0.63 244 244
TACC1 -0.011 0.1 -9999 0 -0.5 20 20
PPP2R5D 0.01 0 -9999 0 -10000 0 0
CUL3 0.01 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.21 0.25 -10000 0 -0.65 85 85
IHH -0.31 0.27 -10000 0 -0.54 276 276
SHH Np/Cholesterol/GAS1 -0.04 0.1 -10000 0 -0.28 71 71
LRPAP1 0.01 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.04 0.1 0.28 71 -10000 0 71
SMO/beta Arrestin2 -0.21 0.21 -10000 0 -0.5 97 97
SMO -0.22 0.23 -10000 0 -0.51 110 110
AKT1 -0.092 0.11 -10000 0 -0.34 10 10
ARRB2 0.01 0 -10000 0 -10000 0 0
BOC 0.008 0.033 -10000 0 -0.51 2 2
ADRBK1 0.01 0 -10000 0 -10000 0 0
heart looping -0.22 0.22 -10000 0 -0.5 110 110
STIL -0.19 0.22 -10000 0 -0.48 134 134
DHH N/PTCH2 -0.029 0.097 -10000 0 -0.35 40 40
DHH N/PTCH1 -0.19 0.19 -10000 0 -0.49 93 93
PIK3CA 0.01 0 -10000 0 -10000 0 0
DHH -0.031 0.14 -10000 0 -0.5 39 39
PTHLH -0.27 0.29 -10000 0 -0.77 85 85
determination of left/right symmetry -0.22 0.22 -10000 0 -0.5 110 110
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
skeletal system development -0.27 0.28 -10000 0 -0.76 85 85
IHH N/Hhip -0.37 0.26 -10000 0 -0.49 368 368
DHH N/Hhip -0.22 0.2 -10000 0 -0.38 280 280
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.22 0.22 -10000 0 -0.5 110 110
pancreas development -0.27 0.25 -10000 0 -0.5 268 268
HHAT 0.008 0.032 -10000 0 -0.5 2 2
PI3K -0.001 0.016 -10000 0 -0.35 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.004 0.082 -10000 0 -0.5 13 13
somite specification -0.22 0.22 -10000 0 -0.5 110 110
SHH Np/Cholesterol/PTCH1 -0.17 0.19 -10000 0 -0.46 108 108
SHH Np/Cholesterol/PTCH2 -0.034 0.088 -10000 0 -0.26 63 63
SHH Np/Cholesterol/Megalin -0.1 0.15 -10000 0 -0.29 173 173
SHH -0.029 0.12 -10000 0 -0.35 62 62
catabolic process -0.2 0.2 -10000 0 -0.49 86 86
SMO/Vitamin D3 -0.2 0.21 -10000 0 -0.51 105 105
SHH Np/Cholesterol/Hhip -0.18 0.16 -10000 0 -0.3 288 288
LRP2 -0.13 0.22 -10000 0 -0.5 130 130
receptor-mediated endocytosis -0.25 0.22 -10000 0 -0.52 166 166
SHH Np/Cholesterol/BOC -0.035 0.089 -10000 0 -0.26 64 64
SHH Np/Cholesterol/CDO -0.039 0.097 -10000 0 -0.27 71 71
mesenchymal cell differentiation 0.18 0.16 0.3 288 -10000 0 288
mol:Vitamin D3 -0.18 0.2 -10000 0 -0.46 108 108
IHH N/PTCH2 -0.18 0.16 -10000 0 -0.32 276 276
CDON -0.002 0.075 -10000 0 -0.5 11 11
IHH N/PTCH1 -0.2 0.2 -10000 0 -0.49 86 86
Megalin/LRPAP1 -0.094 0.16 -10000 0 -0.35 130 130
PTCH2 0.009 0.023 -10000 0 -0.5 1 1
SHH Np/Cholesterol -0.034 0.09 -10000 0 -0.27 62 62
PTCH1 -0.2 0.2 -10000 0 -0.49 86 86
HHIP -0.27 0.25 -10000 0 -0.5 268 268
Aurora C signaling

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
INCENP 0.01 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.15 0.14 -9999 0 -0.28 259 259
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.042 0.04 -9999 0 -10000 0 0
AURKB -0.27 0.26 -9999 0 -0.52 255 255
AURKC 0.005 0.052 -9999 0 -0.51 5 5
Endothelins

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
AKT1 -0.052 0.2 -10000 0 -0.53 37 37
PTK2B 0.008 0.033 -10000 0 -0.5 2 2
mol:Ca2+ -0.051 0.28 -10000 0 -0.94 37 37
EDN1 -0.07 0.23 -10000 0 -0.54 79 79
EDN3 -0.13 0.22 -10000 0 -0.5 134 134
EDN2 -0.14 0.24 -10000 0 -0.52 139 139
HRAS/GDP -0.083 0.2 -10000 0 -0.46 68 68
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.006 0.13 -10000 0 -0.39 26 26
ADCY4 -0.069 0.17 -10000 0 -0.48 46 46
ADCY5 -0.089 0.2 -10000 0 -0.52 59 59
ADCY6 -0.056 0.16 -10000 0 -0.47 39 39
ADCY7 -0.057 0.16 -10000 0 -0.47 40 40
ADCY1 -0.062 0.16 -10000 0 -0.47 43 43
ADCY2 -0.082 0.18 -10000 0 -0.5 53 53
ADCY3 -0.056 0.16 -10000 0 -0.47 38 38
ADCY8 -0.17 0.19 -10000 0 -0.45 97 97
ADCY9 -0.061 0.16 -10000 0 -0.48 41 41
arachidonic acid secretion -0.071 0.2 -10000 0 -0.49 63 63
ETB receptor/Endothelin-1/Gq/GTP -0.16 0.2 -10000 0 -0.36 172 172
GNAO1 0.004 0.057 -10000 0 -0.51 6 6
HRAS 0.01 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.022 0.22 0.23 154 -0.5 37 191
ETA receptor/Endothelin-1/Gs/GTP 0.013 0.22 0.22 152 -0.48 42 194
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.11 0.26 -10000 0 -0.49 123 123
EDNRB -0.29 0.25 -10000 0 -0.5 287 287
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.061 0.22 -10000 0 -0.63 38 38
CYSLTR1 -0.065 0.23 -10000 0 -0.66 40 40
SLC9A1 -0.024 0.11 0.18 1 -0.29 33 34
mol:GDP -0.095 0.22 -10000 0 -0.5 70 70
SLC9A3 -0.3 0.36 -10000 0 -0.54 292 292
RAF1 -0.094 0.21 -10000 0 -0.51 63 63
JUN -0.02 0.19 -10000 0 -0.67 25 25
JAK2 -0.053 0.2 0.26 1 -0.52 41 42
mol:IP3 -0.093 0.18 -10000 0 -0.39 82 82
ETA receptor/Endothelin-1 -0.028 0.28 0.26 163 -0.52 62 225
PLCB1 0.008 0.024 -10000 0 -0.52 1 1
PLCB2 -0.001 0.072 -10000 0 -0.5 10 10
ETA receptor/Endothelin-3 -0.096 0.18 -10000 0 -0.37 136 136
FOS -0.09 0.26 -10000 0 -0.83 42 42
Gai/GDP -0.009 0.083 -10000 0 -0.58 3 3
CRK 0.01 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.15 0.25 -10000 0 -0.56 101 101
BCAR1 0.009 0.023 -10000 0 -0.5 1 1
PRKCB1 -0.089 0.17 -10000 0 -0.37 85 85
GNAQ 0.01 0.024 -10000 0 -0.5 1 1
GNAZ -0.033 0.14 -10000 0 -0.5 41 41
GNAL -0.002 0.076 -10000 0 -0.5 11 11
Gs family/GDP -0.12 0.17 -10000 0 -0.45 74 74
ETA receptor/Endothelin-1/Gq/GTP -0.011 0.14 -10000 0 -0.36 42 42
MAPK14 -0.12 0.18 -10000 0 -0.4 89 89
TRPC6 -0.057 0.3 -10000 0 -1 37 37
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.19 -10000 0 -0.38 127 127
ETB receptor/Endothelin-2 -0.3 0.23 -10000 0 -0.44 337 337
ETB receptor/Endothelin-3 -0.3 0.23 -10000 0 -0.43 337 337
ETB receptor/Endothelin-1 -0.26 0.26 -10000 0 -0.44 293 293
MAPK3 -0.096 0.26 -10000 0 -0.74 49 49
MAPK1 -0.096 0.26 -10000 0 -0.74 49 49
Rac1/GDP -0.083 0.2 -10000 0 -0.46 68 68
cAMP biosynthetic process -0.1 0.18 -10000 0 -0.48 66 66
MAPK8 -0.03 0.2 -10000 0 -0.59 40 40
SRC 0.01 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.15 0.18 -10000 0 -0.38 129 129
p130Cas/CRK/Src/PYK2 -0.092 0.23 -10000 0 -0.58 62 62
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.083 0.2 -10000 0 -0.46 68 68
COL1A2 -0.2 0.28 -10000 0 -0.64 105 105
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.1 0.19 -10000 0 -0.38 141 141
mol:DAG -0.093 0.18 -10000 0 -0.39 82 82
MAP2K2 -0.09 0.22 -10000 0 -0.6 54 54
MAP2K1 -0.09 0.22 -10000 0 -0.61 53 53
EDNRA 0.008 0.1 -10000 0 -0.42 6 6
positive regulation of muscle contraction -0.037 0.17 -10000 0 -0.48 33 33
Gq family/GDP -0.076 0.17 -10000 0 -0.49 45 45
HRAS/GTP -0.099 0.2 -10000 0 -0.45 74 74
PRKCH -0.083 0.17 -10000 0 -0.45 49 49
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.084 0.18 -10000 0 -0.46 50 50
PRKCB -0.089 0.19 -10000 0 -0.49 54 54
PRKCE -0.085 0.18 -10000 0 -0.46 51 51
PRKCD -0.083 0.17 -10000 0 -0.46 49 49
PRKCG -0.11 0.19 -10000 0 -0.46 73 73
regulation of vascular smooth muscle contraction -0.11 0.3 -10000 0 -0.98 42 42
PRKCQ -0.12 0.21 -10000 0 -0.44 102 102
PLA2G4A -0.078 0.22 -10000 0 -0.54 63 63
GNA14 -0.004 0.086 -10000 0 -0.51 14 14
GNA15 0.01 0.004 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
GNA11 0.008 0.033 -10000 0 -0.5 2 2
Rac1/GTP 0.022 0.22 0.23 154 -0.5 37 191
MMP1 -0.22 0.2 -10000 0 -0.38 267 267
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.06 0.072 0.14 228 -10000 0 228
BUB1B -0.12 0.12 -10000 0 -0.2 296 296
PLK1 -0.025 0.049 -10000 0 -0.11 87 87
PLK1S1 -0.009 0.026 -10000 0 -0.11 1 1
KIF2A -0.016 0.045 -10000 0 -0.18 1 1
regulation of mitotic centrosome separation -0.025 0.049 -10000 0 -0.11 87 87
GOLGA2 0.01 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.22 0.26 -10000 0 -0.44 248 248
WEE1 -0.022 0.054 -10000 0 -0.19 1 1
cytokinesis -0.11 0.13 -10000 0 -0.24 209 209
PP2A-alpha B56 -0.014 0.035 -10000 0 -10000 0 0
AURKA -0.019 0.044 -10000 0 -0.11 86 86
PICH/PLK1 -0.14 0.22 -10000 0 -0.4 185 185
CENPE -0.076 0.15 -10000 0 -0.35 103 103
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.016 0.044 -10000 0 -0.18 1 1
PPP2CA 0.01 0 -10000 0 -10000 0 0
FZR1 0.01 0 -10000 0 -10000 0 0
TPX2 -0.045 0.053 -10000 0 -0.098 211 211
PAK1 0.008 0.004 -10000 0 -10000 0 0
SPC24 -0.14 0.24 -10000 0 -0.52 143 143
FBXW11 0.01 0 -10000 0 -10000 0 0
CLSPN -0.038 0.059 -10000 0 -0.13 102 102
GORASP1 0.01 0 -10000 0 -10000 0 0
metaphase -0.002 0.004 -10000 0 -0.011 85 85
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.013 0.026 -10000 0 -0.058 86 86
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.011 2 2
STAG2 0.01 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0.011 -10000 0 -10000 0 0
spindle elongation -0.025 0.049 -10000 0 -0.11 87 87
ODF2 0.008 0.004 -10000 0 -10000 0 0
BUB1 -0.023 0.042 -10000 0 -10000 0 0
TPT1 -0.009 0.026 -10000 0 -0.11 1 1
CDC25C -0.065 0.061 -10000 0 -0.14 86 86
CDC25B 0.008 0.003 -10000 0 -10000 0 0
SGOL1 -0.06 0.072 -10000 0 -0.14 228 228
RHOA 0.01 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.066 0.11 -10000 0 -0.24 128 128
CDC14B 0.008 0.004 -10000 0 -10000 0 0
CDC20 -0.3 0.26 -10000 0 -0.52 286 286
PLK1/PBIP1 -0.045 0.087 -10000 0 -0.34 34 34
mitosis -0.003 0.008 0.02 19 -0.018 77 96
FBXO5 -0.016 0.043 -10000 0 -0.17 1 1
CDC2 -0.003 0.005 -10000 0 -0.011 128 128
NDC80 -0.25 0.26 -10000 0 -0.52 237 237
metaphase plate congression -0.014 0.032 -10000 0 -0.11 1 1
ERCC6L -0.14 0.19 -10000 0 -0.39 166 166
NLP/gamma Tubulin -0.011 0.027 -10000 0 -0.11 2 2
microtubule cytoskeleton organization -0.009 0.026 -10000 0 -0.11 1 1
G2/M transition DNA damage checkpoint -0.001 0.002 -10000 0 -0.011 1 1
PPP1R12A 0.009 0.001 -10000 0 -10000 0 0
interphase -0.001 0.002 -10000 0 -0.011 1 1
PLK1/PRC1-2 -0.19 0.22 -10000 0 -0.37 267 267
GRASP65/GM130/RAB1/GTP/PLK1 -0.017 0.027 -10000 0 -10000 0 0
RAB1A 0.01 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.015 0.046 -10000 0 -0.37 1 1
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.04 0.036 -10000 0 -10000 0 0
microtubule-based process -0.17 0.17 -10000 0 -0.32 267 267
Golgi organization -0.025 0.049 -10000 0 -0.11 87 87
Cohesin/SA2 -0.028 0.036 -10000 0 -0.17 1 1
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.28 0.26 -10000 0 -0.52 267 267
APC/C/CDC20 -0.18 0.17 -10000 0 -0.32 286 286
PPP2R1A 0.01 0 -10000 0 -10000 0 0
chromosome segregation -0.045 0.086 -10000 0 -0.33 34 34
PRC1 -0.066 0.18 -10000 0 -0.52 70 70
ECT2 -0.032 0.091 -10000 0 -0.36 29 29
C13orf34 -0.015 0.044 -10000 0 -0.36 1 1
NUDC -0.014 0.032 -10000 0 -0.11 1 1
regulation of attachment of spindle microtubules to kinetochore -0.12 0.12 -10000 0 -0.2 296 296
spindle assembly -0.017 0.04 -10000 0 -0.09 77 77
spindle stabilization -0.009 0.026 -10000 0 -0.11 1 1
APC/C/HCDH1 0.012 0.005 -10000 0 -10000 0 0
MKLP2/PLK1 -0.17 0.17 -10000 0 -0.33 267 267
CCNB1 -0.13 0.23 -10000 0 -0.52 134 134
PPP1CB 0.009 0.001 -10000 0 -10000 0 0
BTRC 0.01 0 -10000 0 -10000 0 0
ROCK2 -0.008 0.038 -10000 0 -0.4 1 1
TUBG1 -0.009 0.026 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.066 0.1 -10000 0 -0.23 128 128
MLF1IP -0.022 0.1 -10000 0 -0.39 34 34
INCENP 0.01 0.001 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.34 0.47 -9999 0 -1.1 91 91
HDAC7 0.008 0.007 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.36 -9999 0 -0.84 90 90
SMAD4 0.011 0.003 -9999 0 -10000 0 0
ID2 -0.34 0.47 -9999 0 -1.1 91 91
AP1 -0.028 0.094 -9999 0 -0.36 36 36
ABCG2 -0.36 0.5 -9999 0 -1.1 97 97
HIF1A -0.041 0.071 -9999 0 -10000 0 0
TFF3 -0.39 0.51 -9999 0 -1.1 115 115
GATA2 -0.035 0.14 -9999 0 -0.5 41 41
AKT1 -0.046 0.08 -9999 0 -10000 0 0
response to hypoxia -0.064 0.083 -9999 0 -0.24 8 8
MCL1 -0.34 0.47 -9999 0 -1.1 91 91
NDRG1 -0.34 0.47 -9999 0 -1.1 92 92
SERPINE1 -0.34 0.47 -9999 0 -1.1 92 92
FECH -0.34 0.47 -9999 0 -1.1 91 91
FURIN -0.34 0.48 -9999 0 -1.1 93 93
NCOA2 0.007 0.046 -9999 0 -0.5 4 4
EP300 -0.048 0.11 -9999 0 -0.33 14 14
HMOX1 -0.34 0.47 -9999 0 -1.1 90 90
BHLHE40 -0.34 0.47 -9999 0 -1.1 91 91
BHLHE41 -0.34 0.48 -9999 0 -1.1 95 95
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.039 0.071 -9999 0 -0.4 4 4
ENG -0.012 0.11 -9999 0 -0.58 6 6
JUN 0.004 0.046 -9999 0 -0.5 4 4
RORA -0.34 0.47 -9999 0 -1.1 92 92
ABCB1 -0.12 0.25 -9999 0 -1.2 21 21
TFRC -0.34 0.47 -9999 0 -1.1 96 96
CXCR4 -0.34 0.47 -9999 0 -1.1 91 91
TF -0.39 0.52 -9999 0 -1.1 117 117
CITED2 -0.34 0.47 -9999 0 -1.1 91 91
HIF1A/ARNT -0.38 0.55 -9999 0 -1.2 104 104
LDHA -0.046 0.059 -9999 0 -0.46 1 1
ETS1 -0.34 0.47 -9999 0 -1.1 91 91
PGK1 -0.34 0.47 -9999 0 -1.1 92 92
NOS2 -0.36 0.49 -9999 0 -1.1 107 107
ITGB2 -0.34 0.48 -9999 0 -1.1 94 94
ALDOA -0.34 0.47 -9999 0 -1.1 92 92
Cbp/p300/CITED2 -0.33 0.48 -9999 0 -1.1 89 89
FOS -0.025 0.13 -9999 0 -0.5 32 32
HK2 -0.34 0.47 -9999 0 -1.1 95 95
SP1 0.015 0.014 -9999 0 -10000 0 0
GCK -0.11 0.27 -9999 0 -1.2 17 17
HK1 -0.34 0.47 -9999 0 -1.1 91 91
NPM1 -0.34 0.47 -9999 0 -1.1 91 91
EGLN1 -0.34 0.47 -9999 0 -1.1 91 91
CREB1 0.016 0.001 -9999 0 -10000 0 0
PGM1 -0.34 0.47 -9999 0 -1.1 92 92
SMAD3 0.011 0.003 -9999 0 -10000 0 0
EDN1 -0.21 0.45 -9999 0 -1.2 82 82
IGFBP1 -0.37 0.49 -9999 0 -1.1 104 104
VEGFA -0.25 0.36 -9999 0 -0.78 80 80
HIF1A/JAB1 -0.025 0.032 -9999 0 -10000 0 0
CP -0.45 0.53 -9999 0 -1.1 138 138
CXCL12 -0.35 0.48 -9999 0 -1.1 97 97
COPS5 0.011 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 -0.34 0.47 -9999 0 -1.1 92 92
EGLN3 -0.39 0.52 -9999 0 -1.1 118 118
CA9 -0.49 0.51 -9999 0 -1.1 143 143
TERT -0.4 0.52 -9999 0 -1.1 114 114
ENO1 -0.34 0.47 -9999 0 -1.1 91 91
PFKL -0.34 0.47 -9999 0 -1.1 90 90
NCOA1 0.01 0 -9999 0 -10000 0 0
ADM -0.34 0.47 -9999 0 -1.1 92 92
ARNT -0.042 0.071 -9999 0 -10000 0 0
HNF4A -0.11 0.22 -9999 0 -0.52 107 107
ADFP -0.34 0.47 -9999 0 -1 103 103
SLC2A1 -0.34 0.42 -9999 0 -0.88 119 119
LEP -0.36 0.48 -9999 0 -1.1 101 101
HIF1A/ARNT/Cbp/p300 -0.29 0.38 -9999 0 -0.86 96 96
EPO -0.15 0.27 -9999 0 -0.78 7 7
CREBBP -0.048 0.11 -9999 0 -0.35 12 12
HIF1A/ARNT/Cbp/p300/HDAC7 -0.31 0.39 -9999 0 -0.91 92 92
PFKFB3 -0.34 0.47 -9999 0 -1.1 91 91
NT5E -0.35 0.48 -9999 0 -1.1 98 98
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.022 0.072 -9999 0 -0.26 42 42
RGS9BP -0.066 0.18 -9999 0 -0.5 73 73
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.028 0.13 -9999 0 -0.52 31 31
mol:Na + -0.16 0.18 -9999 0 -0.35 228 228
mol:ADP -0.014 0.094 -9999 0 -0.37 32 32
GNAT2 0.007 0.024 -9999 0 -0.52 1 1
RGS9-1/Gbeta5/R9AP -0.13 0.17 -9999 0 -0.32 201 201
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.02 -9999 0 -0.31 2 2
GRK7 0.005 0.024 -9999 0 -0.52 1 1
CNGB3 -0.093 0.2 -9999 0 -0.52 91 91
Cone Metarhodopsin II/X-Arrestin -0.002 0.024 -9999 0 -0.38 2 2
mol:Ca2+ -0.16 0.19 -9999 0 -0.33 251 251
Cone PDE6 -0.11 0.15 -9999 0 -0.49 26 26
Cone Metarhodopsin II -0.019 0.07 -9999 0 -0.28 32 32
Na + (4 Units) -0.17 0.18 -9999 0 -0.33 251 251
GNAT2/GDP -0.11 0.14 -9999 0 -0.49 26 26
GNB5 0.01 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.019 -9999 0 -0.28 2 2
Cone Transducin -0.024 0.077 -9999 0 -0.27 42 42
SLC24A2 -0.036 0.14 -9999 0 -0.52 40 40
GNB3/GNGT2 -0.031 0.1 -9999 0 -0.36 41 41
GNB3 -0.025 0.13 -9999 0 -0.52 32 32
GNAT2/GTP -0.001 0.017 -9999 0 -0.38 1 1
CNGA3 -0.17 0.25 -9999 0 -0.52 166 166
ARR3 0 0.033 -9999 0 -0.52 2 2
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.16 0.19 -9999 0 -0.35 228 228
mol:Pi -0.13 0.17 -9999 0 -0.32 201 201
Cone CNG Channel -0.13 0.15 -9999 0 -0.47 36 36
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.036 0.14 -9999 0 -0.52 40 40
RGS9 -0.15 0.24 -9999 0 -0.5 153 153
PDE6C 0.003 0.004 -9999 0 -10000 0 0
GNGT2 0.001 0.068 -9999 0 -0.5 9 9
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.001 0.024 -9999 0 -0.52 1 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.098 0.33 -9999 0 -0.98 52 52
MKNK1 0.01 0 -9999 0 -10000 0 0
MAPK14 -0.031 0.12 -9999 0 -0.42 9 9
ATF2/c-Jun -0.016 0.12 -9999 0 -0.49 13 13
MAPK11 -0.035 0.13 -9999 0 -0.47 12 12
MITF -0.037 0.16 -9999 0 -0.36 90 90
MAPKAPK5 -0.031 0.15 -9999 0 -0.34 86 86
KRT8 -0.033 0.15 -9999 0 -0.35 86 86
MAPKAPK3 0.01 0 -9999 0 -10000 0 0
MAPKAPK2 0.01 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.049 0.18 -9999 0 -0.43 86 86
CEBPB -0.031 0.15 -9999 0 -0.34 86 86
SLC9A1 -0.031 0.15 -9999 0 -0.34 86 86
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.027 0.15 -9999 0 -0.34 86 86
p38alpha-beta/MNK1 -0.03 0.15 -9999 0 -0.34 86 86
JUN -0.015 0.12 -9999 0 -0.5 12 12
PPARGC1A -0.12 0.22 -9999 0 -0.37 181 181
USF1 -0.031 0.15 -9999 0 -0.34 86 86
RAB5/GDP/GDI1 -0.045 0.096 -9999 0 -0.37 12 12
NOS2 -0.091 0.31 -9999 0 -1 44 44
DDIT3 -0.032 0.15 -9999 0 -0.34 86 86
RAB5A 0.01 0 -9999 0 -10000 0 0
HSPB1 -0.019 0.13 -9999 0 -0.44 13 13
p38alpha-beta/HBP1 -0.03 0.15 -9999 0 -0.34 86 86
CREB1 -0.032 0.16 -9999 0 -0.37 86 86
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.021 0.13 -9999 0 -0.45 12 12
RPS6KA4 -0.031 0.15 -9999 0 -0.34 86 86
PLA2G4A -0.061 0.16 -9999 0 -0.5 22 22
GDI1 -0.031 0.15 -9999 0 -0.34 86 86
TP53 -0.042 0.18 -9999 0 -0.42 86 86
RPS6KA5 -0.033 0.15 -9999 0 -0.35 87 87
ESR1 -0.047 0.18 -9999 0 -0.38 92 92
HBP1 0.01 0 -9999 0 -10000 0 0
MEF2C -0.031 0.15 -9999 0 -0.34 86 86
MEF2A -0.031 0.15 -9999 0 -0.34 86 86
EIF4EBP1 -0.034 0.16 -9999 0 -0.37 86 86
KRT19 -0.034 0.15 -9999 0 -0.34 88 88
ELK4 -0.031 0.15 -9999 0 -0.34 86 86
ATF6 -0.031 0.15 -9999 0 -0.34 86 86
ATF1 -0.032 0.16 -9999 0 -0.37 86 86
p38alpha-beta/MAPKAPK2 -0.03 0.15 -9999 0 -0.34 86 86
p38alpha-beta/MAPKAPK3 -0.03 0.15 -9999 0 -0.34 86 86
Osteopontin-mediated 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
IKK alpha homodimer -0.18 0.15 -9999 0 -0.35 85 85
NF kappa B1 p50/RelA/I kappa B alpha -0.15 0.12 -9999 0 -0.46 21 21
alphaV/beta3 Integrin/Osteopontin/Src -0.26 0.16 -9999 0 -0.36 345 345
AP1 -0.17 0.13 -9999 0 -0.45 47 47
ILK -0.19 0.15 -9999 0 -0.36 86 86
bone resorption -0.16 0.11 -9999 0 -0.44 27 27
PTK2B 0.008 0.032 -9999 0 -0.5 2 2
PYK2/p130Cas -0.18 0.12 -9999 0 -0.49 24 24
ITGAV 0.011 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.006 0.047 -9999 0 -0.35 9 9
alphaV/beta3 Integrin/Osteopontin -0.23 0.16 -9999 0 -0.32 351 351
MAP3K1 -0.19 0.15 -9999 0 -0.36 86 86
JUN 0.006 0.046 -9999 0 -0.5 4 4
MAPK3 -0.18 0.15 -9999 0 -0.38 85 85
MAPK1 -0.18 0.15 -9999 0 -0.38 85 85
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 -0.17 0.15 -9999 0 -0.34 86 86
ITGB3 -0.018 0.12 -9999 0 -0.51 27 27
NFKBIA -0.16 0.15 -9999 0 -0.37 85 85
FOS -0.023 0.13 -9999 0 -0.5 32 32
CD44 0.002 0.065 -9999 0 -0.5 8 8
CHUK 0.01 0 -9999 0 -10000 0 0
PLAU -0.17 0.18 -9999 0 -0.51 75 75
NF kappa B1 p50/RelA -0.16 0.12 -9999 0 -0.48 21 21
BCAR1 0.009 0.023 -9999 0 -0.5 1 1
RELA 0.01 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.02 0.083 -9999 0 -0.36 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.19 0.15 -9999 0 -0.36 86 86
VAV3 -0.18 0.15 -9999 0 -0.52 25 25
MAP3K14 -0.19 0.16 -9999 0 -0.38 86 86
ROCK2 0.009 0.023 -9999 0 -0.5 1 1
SPP1 -0.36 0.24 -9999 0 -0.51 345 345
RAC1 0.01 0 -9999 0 -10000 0 0
Rac1/GTP -0.17 0.12 -9999 0 -0.47 25 25
MMP2 -0.12 0.13 -9999 0 -0.43 18 18
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.033 0.042 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.085 0.12 -9999 0 -0.36 31 31
JUN -0.052 0.12 -9999 0 -0.35 25 25
HRAS 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.12 0.16 -9999 0 -0.3 194 194
RAP1A 0.01 0 -9999 0 -10000 0 0
FRS2 0.008 0.034 -9999 0 -0.52 2 2
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.12 0.16 -9999 0 -0.3 194 194
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.083 0.13 -9999 0 -0.27 149 149
RHOA 0.01 0 -9999 0 -10000 0 0
RAP1A/GTP -0.1 0.14 -9999 0 -0.48 25 25
GRB7 0.004 0.057 -9999 0 -0.51 6 6
RET51/GFRalpha1/GDNF -0.12 0.16 -9999 0 -0.3 194 194
MAPKKK cascade -0.095 0.13 -9999 0 -0.44 29 29
BCAR1 0.009 0.023 -9999 0 -0.5 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.084 0.13 -9999 0 -0.27 149 149
lamellipodium assembly -0.081 0.11 -9999 0 -0.34 31 31
RET51/GFRalpha1/GDNF/SHC -0.12 0.16 -9999 0 -0.32 136 136
PIK3CA 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.084 0.13 -9999 0 -0.27 149 149
RET9/GFRalpha1/GDNF/Shank3 -0.087 0.14 -9999 0 -0.28 150 150
MAPK3 -0.077 0.14 -9999 0 -0.45 25 25
DOK1 0.01 0 -9999 0 -10000 0 0
DOK6 -0.039 0.15 -9999 0 -0.5 47 47
PXN 0.01 0 -9999 0 -10000 0 0
neurite development -0.074 0.15 -9999 0 -0.37 55 55
DOK5 -0.068 0.19 -9999 0 -0.52 72 72
GFRA1 -0.14 0.23 -9999 0 -0.5 143 143
MAPK8 -0.059 0.12 -9999 0 -0.35 24 24
HRAS/GTP -0.1 0.14 -9999 0 -0.47 25 25
tube development -0.08 0.13 -9999 0 -0.26 150 150
MAPK1 -0.077 0.14 -9999 0 -0.45 25 25
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.054 0.12 -9999 0 -0.23 142 142
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
PDLIM7 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.18 -9999 0 -0.52 55 55
SHC1 0.009 0.024 -9999 0 -0.52 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.12 0.16 -9999 0 -0.3 194 194
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.18 -9999 0 -0.32 245 245
PRKCA 0.008 0.032 -9999 0 -0.5 2 2
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.07 0.14 -9999 0 -0.28 142 142
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.056 0.12 -9999 0 -0.24 142 142
RET51/GFRalpha1/GDNF/Grb7 -0.12 0.16 -9999 0 -0.32 139 139
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.062 0.18 -9999 0 -0.52 67 67
DOK4 0.01 0 -9999 0 -10000 0 0
JNK cascade -0.051 0.12 -9999 0 -0.34 25 25
RET9/GFRalpha1/GDNF/FRS2 -0.084 0.13 -9999 0 -0.27 151 151
SHANK3 0.002 0.065 -9999 0 -0.5 8 8
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.054 0.12 -9999 0 -0.23 142 142
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.07 0.13 -9999 0 -0.37 24 24
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.069 0.13 -9999 0 -0.27 84 84
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.072 0.14 -9999 0 -0.42 25 25
PI3K -0.089 0.19 -9999 0 -0.52 31 31
SOS1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.08 0.13 -9999 0 -0.26 150 150
GRB10 0.01 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.064 0.12 -9999 0 -0.35 23 23
RET51/GFRalpha1/GDNF/FRS2 -0.12 0.16 -9999 0 -0.32 137 137
GAB1 0.007 0.04 -9999 0 -0.5 3 3
IRS1 0.009 0.023 -9999 0 -0.5 1 1
IRS2 0.009 0.023 -9999 0 -0.5 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.074 0.14 -9999 0 -0.44 27 27
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.16 -9999 0 -0.32 136 136
GRB2 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GDNF -0.004 0.071 -9999 0 -0.52 9 9
RAC1 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.16 -9999 0 -0.36 75 75
Rac1/GTP -0.095 0.13 -9999 0 -0.4 31 31
RET9/GFRalpha1/GDNF -0.094 0.14 -9999 0 -0.31 149 149
GFRalpha1/GDNF -0.11 0.17 -9999 0 -0.36 149 149
IL4-mediated signaling events

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
BCL2L1 -0.46 0.53 -10000 0 -1.2 116 116
STAT6 (cleaved dimer) -0.49 0.5 -10000 0 -1.2 143 143
IGHG1 -0.15 0.17 -10000 0 -0.38 1 1
IGHG3 -0.45 0.51 -10000 0 -1.2 124 124
AKT1 -0.18 0.24 -10000 0 -0.75 13 13
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.13 0.2 -10000 0 -0.83 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.19 0.25 -10000 0 -0.88 10 10
THY1 -0.46 0.53 -10000 0 -1.2 117 117
MYB 0.003 0.061 -10000 0 -0.51 7 7
HMGA1 -0.04 0.15 -10000 0 -0.52 46 46
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.28 -10000 0 -0.63 88 88
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.19 0.25 -10000 0 -0.84 12 12
SP1 0.016 0.004 -10000 0 -10000 0 0
INPP5D 0.007 0.04 -10000 0 -0.5 3 3
SOCS5 0.021 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.47 0.49 -10000 0 -1.2 124 124
SOCS1 -0.27 0.33 -10000 0 -0.77 89 89
SOCS3 -0.2 0.26 -10000 0 -0.89 15 15
FCER2 -0.35 0.43 -10000 0 -0.99 97 97
PARP14 0.01 0.003 -10000 0 -10000 0 0
CCL17 -0.51 0.6 -10000 0 -1.4 128 128
GRB2 0.01 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.15 0.2 -10000 0 -0.73 8 8
T cell proliferation -0.44 0.54 -10000 0 -1.2 117 117
IL4R/JAK1 -0.46 0.53 -10000 0 -1.2 117 117
EGR2 -0.48 0.57 -10000 0 -1.3 113 113
JAK2 -0.013 0.045 -10000 0 -0.54 2 2
JAK3 0.015 0.004 -10000 0 -10000 0 0
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
JAK1 0.006 0.011 -10000 0 -10000 0 0
COL1A2 -0.14 0.19 -10000 0 -0.74 13 13
CCL26 -0.48 0.54 -10000 0 -1.3 115 115
IL4R -0.49 0.56 -10000 0 -1.3 116 116
PTPN6 0.021 0.013 -10000 0 -10000 0 0
IL13RA2 -0.5 0.58 -10000 0 -1.3 129 129
IL13RA1 -0.011 0.03 -10000 0 -10000 0 0
IRF4 -0.11 0.25 -10000 0 -0.96 26 26
ARG1 -0.12 0.19 -10000 0 -0.71 21 21
CBL -0.22 0.27 -10000 0 -0.61 74 74
GTF3A 0.005 0.031 -10000 0 -0.51 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.015 0.05 -10000 0 -0.4 2 2
IRF4/BCL6 -0.094 0.23 -10000 0 -0.96 22 22
CD40LG -0.008 0.11 -10000 0 -0.5 22 22
MAPK14 -0.22 0.27 -10000 0 -0.63 60 60
mitosis -0.17 0.23 -10000 0 -0.7 13 13
STAT6 -0.54 0.63 -10000 0 -1.4 122 122
SPI1 -0.013 0.11 -10000 0 -0.5 25 25
RPS6KB1 -0.16 0.23 -10000 0 -0.72 10 10
STAT6 (dimer) -0.54 0.63 -10000 0 -1.4 122 122
STAT6 (dimer)/PARP14 -0.49 0.58 -10000 0 -1.3 121 121
mast cell activation 0.01 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.26 -10000 0 -0.76 29 29
FRAP1 -0.18 0.24 -10000 0 -0.75 13 13
LTA -0.46 0.53 -10000 0 -1.2 112 112
FES 0.009 0.023 -10000 0 -0.5 1 1
T-helper 1 cell differentiation 0.52 0.6 1.4 122 -10000 0 122
CCL11 -0.47 0.54 -10000 0 -1.2 124 124
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.18 0.24 -10000 0 -0.79 13 13
IL2RG 0.009 0.051 -10000 0 -0.49 5 5
IL10 -0.46 0.54 -10000 0 -1.3 117 117
IRS1 0.009 0.023 -10000 0 -0.5 1 1
IRS2 0.009 0.023 -10000 0 -0.5 1 1
IL4 -0.099 0.12 -10000 0 -10000 0 0
IL5 -0.46 0.53 -10000 0 -1.2 117 117
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.4 -10000 0 -0.92 117 117
COL1A1 -0.23 0.24 -10000 0 -0.65 45 45
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.55 -10000 0 -1.3 107 107
IL2R gamma/JAK3 0.014 0.037 -10000 0 -0.34 5 5
TFF3 -0.51 0.56 -10000 0 -1.3 126 126
ALOX15 -0.79 0.73 -10000 0 -1.4 260 260
MYBL1 -0.002 0.078 -10000 0 -0.52 11 11
T-helper 2 cell differentiation -0.36 0.41 -10000 0 -0.93 119 119
SHC1 0.009 0.024 -10000 0 -0.52 1 1
CEBPB 0.013 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.18 0.24 -10000 0 -0.82 11 11
mol:PI-3-4-5-P3 -0.18 0.24 -10000 0 -0.75 13 13
PI3K -0.18 0.25 -10000 0 -0.81 13 13
DOK2 -0.031 0.14 -10000 0 -0.5 39 39
ETS1 0.019 0.025 -10000 0 -0.46 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.19 -10000 0 -0.69 8 8
ITGB3 -0.47 0.54 -10000 0 -1.2 120 120
PIGR -0.6 0.69 -10000 0 -1.5 155 155
IGHE 0.034 0.042 -10000 0 -10000 0 0
MAPKKK cascade -0.14 0.19 -10000 0 -0.68 8 8
BCL6 0.01 0.003 -10000 0 -10000 0 0
OPRM1 -0.46 0.53 -10000 0 -1.2 117 117
RETNLB -0.46 0.53 -10000 0 -1.2 113 113
SELP -0.58 0.68 -10000 0 -1.5 153 153
AICDA -0.47 0.54 -10000 0 -1.2 125 125
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.022 0.092 -9999 0 -0.42 22 22
alphaM/beta2 Integrin/GPIbA -0.027 0.1 -9999 0 -0.4 29 29
alphaM/beta2 Integrin/proMMP-9 -0.083 0.15 -9999 0 -0.33 119 119
PLAUR 0.01 0 -9999 0 -10000 0 0
HMGB1 0.006 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.022 0.095 -9999 0 -0.44 21 21
AGER -0.46 0.15 -9999 0 -0.51 445 445
RAP1A 0.01 0 -9999 0 -10000 0 0
SELPLG -0.009 0.096 -9999 0 -0.5 18 18
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.29 0.16 -9999 0 -0.5 125 125
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.097 0.21 -9999 0 -0.52 99 99
CYR61 -0.017 0.11 -9999 0 -0.5 26 26
TLN1 0.009 0.023 -9999 0 -0.5 1 1
Rap1/GTP -0.083 0.14 -9999 0 -0.43 45 45
RHOA 0.01 0 -9999 0 -10000 0 0
P-selectin oligomer -0.1 0.21 -9999 0 -0.5 109 109
MYH2 -0.15 0.2 -9999 0 -0.48 95 95
MST1R 0.008 0.032 -9999 0 -0.5 2 2
leukocyte activation during inflammatory response -0.045 0.11 -9999 0 -0.3 69 69
APOB -0.043 0.16 -9999 0 -0.51 49 49
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.009 0.024 -9999 0 -0.52 1 1
JAM3 0.005 0.051 -9999 0 -0.5 5 5
GP1BA 0 0.069 -9999 0 -0.5 9 9
alphaM/beta2 Integrin/CTGF -0.038 0.12 -9999 0 -0.4 43 43
alphaM/beta2 Integrin -0.085 0.18 -9999 0 -0.44 62 62
JAM3 homodimer 0.005 0.051 -9999 0 -0.5 5 5
ICAM2 0.005 0.051 -9999 0 -0.5 5 5
ICAM1 0.003 0.06 -9999 0 -0.5 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.084 0.18 -9999 0 -0.44 62 62
cell adhesion -0.027 0.1 -9999 0 -0.4 29 29
NFKB1 -0.3 0.22 -9999 0 -0.62 125 125
THY1 -0.005 0.088 -9999 0 -0.52 14 14
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.033 0.096 -9999 0 -0.31 52 52
alphaM/beta2 Integrin/LRP/tPA -0.051 0.14 -9999 0 -0.34 67 67
IL6 -0.35 0.33 -9999 0 -0.85 132 132
ITGB2 -0.005 0.074 -9999 0 -0.51 10 10
elevation of cytosolic calcium ion concentration -0.066 0.13 -9999 0 -0.3 103 103
alphaM/beta2 Integrin/JAM2/JAM3 -0.048 0.14 -9999 0 -0.36 65 65
JAM2 -0.046 0.16 -9999 0 -0.5 54 54
alphaM/beta2 Integrin/ICAM1 -0.026 0.1 -9999 0 -0.5 16 16
alphaM/beta2 Integrin/uPA/Plg -0.075 0.14 -9999 0 -0.3 116 116
RhoA/GTP -0.1 0.19 -9999 0 -0.49 60 60
positive regulation of phagocytosis -0.077 0.16 -9999 0 -0.64 27 27
Ron/MSP -0.013 0.067 -9999 0 -0.36 17 17
alphaM/beta2 Integrin/uPAR/uPA -0.067 0.13 -9999 0 -0.3 103 103
alphaM/beta2 Integrin/uPAR -0.021 0.091 -9999 0 -0.43 21 21
PLAU -0.087 0.2 -9999 0 -0.52 90 90
PLAT -0.052 0.17 -9999 0 -0.52 57 57
actin filament polymerization -0.14 0.19 -9999 0 -0.46 95 95
MST1 -0.006 0.091 -9999 0 -0.52 15 15
alphaM/beta2 Integrin/lipoprotein(a) -0.045 0.11 -9999 0 -0.31 69 69
TNF -0.28 0.23 -9999 0 -0.6 125 125
RAP1B 0.01 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.077 0.14 -9999 0 -0.33 110 110
fibrinolysis -0.074 0.14 -9999 0 -0.3 116 116
HCK -0.012 0.1 -9999 0 -0.5 21 21
dendritic cell antigen processing and presentation -0.084 0.18 -9999 0 -0.44 62 62
VTN -0.084 0.2 -9999 0 -0.5 90 90
alphaM/beta2 Integrin/CYR61 -0.037 0.12 -9999 0 -0.39 43 43
LPA 0 0.04 -9999 0 -0.51 3 3
LRP1 0.006 0.046 -9999 0 -0.5 4 4
cell migration -0.073 0.13 -9999 0 -0.3 112 112
FN1 0.005 0.052 -9999 0 -0.5 5 5
alphaM/beta2 Integrin/Thy1 -0.03 0.1 -9999 0 -0.38 35 35
MPO -0.003 0.079 -9999 0 -0.5 12 12
KNG1 -0.03 0.13 -9999 0 -0.52 32 32
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.09 0.18 -9999 0 -0.47 55 55
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.007 0.07 -9999 0 -0.52 9 9
CTGF -0.019 0.12 -9999 0 -0.5 28 28
alphaM/beta2 Integrin/Hck -0.033 0.13 -9999 0 -0.53 28 28
ITGAM -0.016 0.1 -9999 0 -0.51 20 20
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.084 0.18 -9999 0 -0.35 116 116
HP -0.13 0.23 -9999 0 -0.5 136 136
leukocyte adhesion -0.27 0.18 -9999 0 -0.47 164 164
SELP -0.1 0.21 -9999 0 -0.5 109 109
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.078 0.13 -9999 0 -0.51 18 18
SMAD6-7/SMURF1 -0.043 0.1 -9999 0 -0.29 72 72
NOG -0.028 0.13 -9999 0 -0.5 36 36
SMAD9 -0.12 0.2 -9999 0 -0.48 108 108
SMAD4 0.01 0 -9999 0 -10000 0 0
SMAD5 -0.029 0.12 -9999 0 -0.37 26 26
BMP7/USAG1 -0.27 0.19 -9999 0 -0.39 346 346
SMAD5/SKI -0.022 0.11 -9999 0 -0.43 12 12
SMAD1 0.023 0.029 -9999 0 -10000 0 0
BMP2 -0.063 0.18 -9999 0 -0.5 70 70
SMAD1/SMAD1/SMAD4 -0.028 0.068 -9999 0 -0.41 1 1
BMPR1A 0.01 0 -9999 0 -10000 0 0
BMPR1B -0.045 0.16 -9999 0 -0.5 53 53
BMPR1A-1B/BAMBI -0.044 0.11 -9999 0 -0.31 70 70
AHSG -0.036 0.14 -9999 0 -0.52 38 38
CER1 -0.004 0.057 -9999 0 -0.52 6 6
BMP2-4/CER1 -0.055 0.13 -9999 0 -0.32 83 83
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.021 0.12 -9999 0 -0.41 23 23
BMP2-4 (homodimer) -0.061 0.14 -9999 0 -0.38 79 79
RGMB 0.01 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.067 0.13 -9999 0 -0.52 18 18
RGMA -0.001 0.074 -9999 0 -0.51 10 10
SMURF1 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.028 0.12 -9999 0 -0.38 23 23
BMP2-4/USAG1 -0.24 0.18 -9999 0 -0.34 342 342
SMAD6/SMURF1/SMAD5 -0.022 0.11 -9999 0 -0.42 13 13
SOSTDC1 -0.33 0.24 -9999 0 -0.5 324 324
BMP7/BMPR2/BMPR1A-1B -0.061 0.12 -9999 0 -0.34 28 28
SKI 0.01 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.067 0.18 -9999 0 -0.5 74 74
HFE2 -0.007 0.081 -9999 0 -0.52 12 12
ZFYVE16 0.01 0 -9999 0 -10000 0 0
MAP3K7 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.065 0.14 -9999 0 -0.32 97 97
SMAD5/SMAD5/SMAD4 -0.022 0.11 -9999 0 -0.43 12 12
MAPK1 0.01 0 -9999 0 -10000 0 0
TAK1/TAB family -0.043 0.085 -9999 0 -0.37 15 15
BMP7 (homodimer) -0.054 0.17 -9999 0 -0.5 61 61
NUP214 0.01 0 -9999 0 -10000 0 0
BMP6/FETUA -0.082 0.16 -9999 0 -0.37 107 107
SMAD1/SKI 0.027 0.028 -9999 0 -10000 0 0
SMAD6 -0.065 0.18 -9999 0 -0.5 72 72
CTDSP2 0.01 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.074 0.14 -9999 0 -0.33 111 111
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.35 0.24 -9999 0 -0.52 335 335
BMPR2 (homodimer) 0.01 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.019 -9999 0 -0.29 2 2
BMPR1A-1B (homodimer) -0.038 0.11 -9999 0 -0.35 53 53
CHRDL1 -0.17 0.24 -9999 0 -0.5 171 171
ENDOFIN/SMAD1 0.027 0.028 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.033 0.077 -9999 0 -0.46 1 1
SMAD6/SMURF1 0.01 0 -9999 0 -10000 0 0
BAMBI -0.013 0.11 -9999 0 -0.51 21 21
SMURF2 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.15 0.2 -9999 0 -0.37 200 200
BMP2-4/GREM1 -0.26 0.18 -9999 0 -0.35 357 357
SMAD7 0.009 0.023 -9999 0 -0.5 1 1
SMAD8A/SMAD8A/SMAD4 -0.093 0.2 -9999 0 -0.45 108 108
SMAD1/SMAD6 0.027 0.028 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.054 0.17 -9999 0 -0.5 61 61
BMP6 -0.067 0.18 -9999 0 -0.5 74 74
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.022 0.11 -9999 0 -0.36 23 23
PPM1A 0.01 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.027 0.028 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.001 0.016 -9999 0 -0.35 1 1
CTDSPL 0.01 0 -9999 0 -10000 0 0
PPP1CA 0.01 0 -9999 0 -10000 0 0
XIAP 0.01 0 -9999 0 -10000 0 0
CTDSP1 0.01 0 -9999 0 -10000 0 0
PPP1R15A 0.008 0.032 -9999 0 -0.5 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.043 0.13 -9999 0 -0.39 36 36
CHRD -0.015 0.11 -9999 0 -0.52 23 23
BMPR2 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.034 0.12 -9999 0 -0.41 23 23
BMP4 -0.006 0.088 -9999 0 -0.5 15 15
FST -0.038 0.15 -9999 0 -0.51 45 45
BMP2-4/NOG -0.072 0.15 -9999 0 -0.35 101 101
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.056 0.11 -9999 0 -0.49 8 8
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.009 0.024 -9999 0 -0.52 1 1
LAT2 -0.089 0.2 -9999 0 -0.48 76 76
AP1 -0.13 0.21 -9999 0 -0.5 96 96
mol:PIP3 -0.094 0.22 -9999 0 -0.5 85 85
IKBKB -0.04 0.12 -9999 0 -0.27 79 79
AKT1 -0.061 0.16 -9999 0 -0.38 73 73
IKBKG -0.04 0.12 -9999 0 -0.27 79 79
MS4A2 -0.11 0.21 -9999 0 -0.5 111 111
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.002 -9999 0 -10000 0 0
MAP3K1 -0.063 0.18 -9999 0 -0.4 85 85
mol:Ca2+ -0.066 0.17 -9999 0 -0.37 85 85
LYN 0.008 0.005 -9999 0 -10000 0 0
CBLB -0.084 0.18 -9999 0 -0.45 74 74
SHC1 0.009 0.024 -9999 0 -0.52 1 1
RasGAP/p62DOK -0.027 0.08 -9999 0 -0.26 50 50
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.007 0.04 -9999 0 -0.5 3 3
PLD2 -0.093 0.18 -9999 0 -0.46 71 71
PTPN13 -0.11 0.22 -9999 0 -0.5 93 93
PTPN11 0.007 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.041 0.15 -9999 0 -0.32 73 73
SYK 0.005 0.042 -9999 0 -0.53 3 3
GRB2 0.01 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.13 0.2 -9999 0 -0.52 85 85
LAT -0.085 0.19 -9999 0 -0.45 76 76
PAK2 -0.077 0.2 -9999 0 -0.46 85 85
NFATC2 -0.069 0.16 -9999 0 -0.74 20 20
HRAS -0.092 0.22 -9999 0 -0.51 85 85
GAB2 0.006 0.046 -9999 0 -0.5 4 4
PLA2G1B -0.002 0.031 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.21 -9999 0 -0.4 177 177
Antigen/IgE/Fc epsilon R1 -0.13 0.2 -9999 0 -0.36 177 177
mol:GDP -0.1 0.24 -9999 0 -0.55 87 87
JUN 0.006 0.046 -9999 0 -0.5 4 4
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.023 -9999 0 -0.5 1 1
FOS -0.023 0.13 -9999 0 -0.5 32 32
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.18 -9999 0 -0.39 116 116
CHUK -0.04 0.12 -9999 0 -0.27 79 79
KLRG1 -0.08 0.18 -9999 0 -0.42 74 74
VAV1 -0.087 0.19 -9999 0 -0.46 76 76
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.084 0.18 -9999 0 -0.45 76 76
negative regulation of mast cell degranulation -0.071 0.17 -9999 0 -0.4 74 74
BTK -0.12 0.26 -9999 0 -0.6 88 88
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.22 -9999 0 -0.41 132 132
GAB2/PI3K/SHP2 -0.1 0.15 -9999 0 -0.42 73 73
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.095 0.19 -9999 0 -0.5 71 71
RAF1 0.02 0.023 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.18 -9999 0 -0.5 71 71
FCER1G -0.002 0.087 -9999 0 -0.51 14 14
FCER1A -0.13 0.23 -9999 0 -0.51 128 128
Antigen/IgE/Fc epsilon R1/Fyn -0.12 0.18 -9999 0 -0.49 73 73
MAPK3 0.028 0.019 -9999 0 -10000 0 0
MAPK1 0.028 0.019 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 -0.01 0.061 -9999 0 -10000 0 0
DUSP1 -0.042 0.15 -9999 0 -0.5 50 50
NF-kappa-B/RelA -0.042 0.061 -9999 0 -0.23 7 7
actin cytoskeleton reorganization -0.092 0.2 -9999 0 -0.49 73 73
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.11 0.18 -9999 0 -0.45 83 83
FER -0.084 0.18 -9999 0 -0.45 75 75
RELA 0.01 0 -9999 0 -10000 0 0
ITK -0.037 0.087 -9999 0 -0.53 12 12
SOS1 0.01 0 -9999 0 -10000 0 0
PLCG1 -0.1 0.24 -9999 0 -0.55 85 85
cytokine secretion -0.031 0.044 -9999 0 -10000 0 0
SPHK1 -0.086 0.19 -9999 0 -0.46 75 75
PTK2 -0.096 0.21 -9999 0 -0.51 73 73
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.21 -9999 0 -0.54 86 86
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.09 0.22 -9999 0 -0.49 86 86
MAP2K2 0.025 0.02 -9999 0 -10000 0 0
MAP2K1 0.025 0.02 -9999 0 -10000 0 0
MAP2K7 0.01 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.091 0.15 -9999 0 -0.38 74 74
MAP2K4 0.011 0.011 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.13 0.19 -9999 0 -0.4 135 135
mol:Choline -0.092 0.18 -9999 0 -0.46 71 71
SHC/Grb2/SOS1 -0.098 0.16 -9999 0 -0.42 73 73
FYN 0.009 0.023 -9999 0 -0.5 1 1
DOK1 0.01 0 -9999 0 -10000 0 0
PXN -0.084 0.19 -9999 0 -0.47 73 73
HCLS1 -0.086 0.19 -9999 0 -0.46 76 76
PRKCB -0.067 0.17 -9999 0 -0.38 86 86
FCGR2B 0.009 0.023 -9999 0 -0.5 1 1
IGHE -0.002 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.072 0.17 -9999 0 -0.41 74 74
LCP2 0.006 0.04 -9999 0 -0.5 3 3
PLA2G4A -0.12 0.21 -9999 0 -0.48 96 96
RASA1 0.01 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.092 0.18 -9999 0 -0.46 71 71
IKK complex -0.018 0.098 -9999 0 -0.23 24 24
WIPF1 0.01 0 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.21 0.32 -10000 0 -0.83 51 51
PCK1 -0.18 0.24 -10000 0 -0.66 45 45
HNF4A -0.39 0.5 -10000 0 -1 146 146
KCNJ11 -0.18 0.33 -10000 0 -0.87 53 53
AKT1 -0.073 0.14 -10000 0 -0.42 6 6
response to starvation -0.028 0.046 -10000 0 -10000 0 0
DLK1 -0.2 0.32 -10000 0 -0.88 46 46
NKX2-1 -0.11 0.38 -10000 0 -1.3 35 35
ACADM -0.21 0.32 -10000 0 -0.81 55 55
TAT -0.17 0.22 -10000 0 -0.59 56 56
CEBPB 0.009 0.005 -10000 0 -10000 0 0
CEBPA -0.016 0.11 -10000 0 -0.5 25 25
TTR -0.2 0.25 -10000 0 -0.75 48 48
PKLR -0.22 0.32 -10000 0 -0.86 51 51
APOA1 -0.49 0.63 -10000 0 -1.3 167 167
CPT1C -0.22 0.32 -10000 0 -0.87 51 51
ALAS1 -0.073 0.16 -10000 0 -10000 0 0
TFRC -0.16 0.26 -10000 0 -0.76 30 30
FOXF1 -0.085 0.2 0.22 2 -0.48 93 95
NF1 0.016 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.12 0.24 -10000 0 -0.57 100 100
CPT1A -0.21 0.32 -10000 0 -0.81 55 55
HMGCS1 -0.21 0.32 -10000 0 -0.83 51 51
NR3C1 0.004 0.033 -10000 0 -10000 0 0
CPT1B -0.22 0.32 -10000 0 -0.84 51 51
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.001 0.026 -10000 0 -10000 0 0
GCK -0.23 0.34 -10000 0 -0.86 63 63
CREB1 0.005 0.021 -10000 0 -10000 0 0
IGFBP1 -0.13 0.2 -10000 0 -0.57 32 32
PDX1 -0.16 0.26 -10000 0 -0.68 56 56
UCP2 -0.21 0.32 -10000 0 -0.83 50 50
ALDOB -0.2 0.34 -10000 0 -0.86 59 59
AFP -0.073 0.14 -10000 0 -0.44 31 31
BDH1 -0.21 0.32 -10000 0 -0.84 50 50
HADH -0.17 0.31 -10000 0 -0.82 48 48
F2 -0.32 0.43 -10000 0 -1 78 78
HNF1A -0.12 0.24 -10000 0 -0.58 100 100
G6PC -0.083 0.16 -10000 0 -0.63 12 12
SLC2A2 -0.15 0.24 -10000 0 -0.66 32 32
INS 0.001 0.028 -10000 0 -10000 0 0
FOXA1 -0.015 0.11 0.25 6 -0.54 13 19
FOXA3 -0.17 0.27 -10000 0 -0.58 138 138
FOXA2 -0.21 0.36 -10000 0 -0.9 57 57
ABCC8 -0.24 0.4 -10000 0 -0.94 86 86
ALB -0.085 0.16 -10000 0 -0.47 37 37
TCGA08_retinoblastoma

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
CDKN2B -0.023 0.12 -10000 0 -0.47 35 35
CDKN2C 0.022 0.032 -10000 0 -0.46 1 1
CDKN2A -0.15 0.25 -10000 0 -0.53 145 145
CCND2 0.042 0.066 0.2 36 -0.12 5 41
RB1 -0.046 0.069 -10000 0 -0.2 36 36
CDK4 0.05 0.072 0.21 37 -10000 0 37
CDK6 0.047 0.071 0.22 35 -10000 0 35
G1/S progression 0.038 0.074 0.2 36 -10000 0 36
Glucocorticoid receptor regulatory network

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
PCK2 0.031 0.086 0.32 6 -10000 0 6
SMARCC2 0.011 0.007 -10000 0 -10000 0 0
SMARCC1 0.011 0.007 -10000 0 -10000 0 0
TBX21 -0.11 0.22 -10000 0 -0.52 75 75
SUMO2 0.009 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0 -10000 0 -10000 0 0
FKBP4 0.009 0.024 -10000 0 -0.52 1 1
FKBP5 0.007 0.04 -10000 0 -0.5 3 3
GR alpha/HSP90/FKBP51/HSP90 0.091 0.11 0.29 57 -10000 0 57
PRL -0.07 0.13 -10000 0 -0.51 9 9
cortisol/GR alpha (dimer)/TIF2 0.21 0.26 0.53 150 -10000 0 150
RELA -0.033 0.089 -10000 0 -0.3 2 2
FGG 0.004 0.33 0.47 62 -0.46 111 173
GR beta/TIF2 0.096 0.12 0.3 72 -0.25 3 75
IFNG -0.24 0.28 -10000 0 -0.7 84 84
apoptosis -0.013 0.15 0.48 9 -0.56 14 23
CREB1 -0.005 0.048 -10000 0 -10000 0 0
histone acetylation -0.033 0.15 0.27 6 -0.36 38 44
BGLAP -0.066 0.14 -10000 0 -0.47 13 13
GR/PKAc 0.09 0.1 0.28 54 -10000 0 54
NF kappa B1 p50/RelA -0.057 0.16 -10000 0 -0.44 29 29
SMARCD1 0.011 0.007 -10000 0 -10000 0 0
MDM2 0.077 0.097 0.25 72 -0.24 1 73
GATA3 0.012 0.041 -10000 0 -0.5 3 3
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.12 0.31 -10000 0 -0.98 46 46
GSK3B 0.009 0.005 -10000 0 -10000 0 0
NR1I3 0.011 0.14 0.48 6 -0.56 4 10
CSN2 0.12 0.17 0.39 62 -10000 0 62
BRG1/BAF155/BAF170/BAF60A 0.021 0.029 -10000 0 -0.31 2 2
NFATC1 0.008 0.046 -10000 0 -0.5 4 4
POU2F1 0.01 0.015 -10000 0 -10000 0 0
CDKN1A 0.025 0.061 -10000 0 -1.3 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.005 -10000 0 -10000 0 0
SFN 0 0.071 -10000 0 -0.52 9 9
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.087 0.11 0.28 54 -10000 0 54
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.021 0.22 0.45 8 -0.8 31 39
JUN -0.18 0.18 -10000 0 -0.45 100 100
IL4 -0.079 0.15 -10000 0 -0.62 11 11
CDK5R1 -0.007 0.091 -10000 0 -0.52 15 15
PRKACA 0.01 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.22 0.2 2 -0.46 101 103
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.092 0.1 0.28 53 -10000 0 53
cortisol/GR alpha (monomer) 0.25 0.32 0.63 152 -10000 0 152
NCOA2 0.006 0.046 -10000 0 -0.5 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.076 0.14 -10000 0 -0.57 32 32
AP-1/NFAT1-c-4 -0.29 0.28 -10000 0 -0.64 149 149
AFP -0.14 0.17 -10000 0 -0.52 37 37
SUV420H1 0.01 0 -10000 0 -10000 0 0
IRF1 0.13 0.15 0.42 51 -10000 0 51
TP53 0.027 0.023 -10000 0 -0.48 1 1
PPP5C 0.01 0 -10000 0 -10000 0 0
KRT17 -0.27 0.34 -10000 0 -0.76 114 114
KRT14 -0.18 0.2 -10000 0 -0.51 79 79
TBP 0.017 0 -10000 0 -10000 0 0
CREBBP 0.051 0.064 -10000 0 -0.26 2 2
HDAC1 0.008 0.004 -10000 0 -10000 0 0
HDAC2 0.015 0.023 -10000 0 -10000 0 0
AP-1 -0.29 0.28 -10000 0 -0.65 149 149
MAPK14 0.009 0.005 -10000 0 -10000 0 0
MAPK10 -0.047 0.16 -10000 0 -0.5 54 54
MAPK11 0.006 0.04 -10000 0 -0.5 3 3
KRT5 -0.42 0.51 -10000 0 -1.1 162 162
interleukin-1 receptor activity 0.005 0.023 -10000 0 -10000 0 0
NCOA1 0.012 0.001 -10000 0 -10000 0 0
STAT1 0.017 0 -10000 0 -10000 0 0
CGA -0.11 0.19 -10000 0 -0.55 46 46
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.19 0.43 88 -10000 0 88
MAPK3 0.009 0.005 -10000 0 -10000 0 0
MAPK1 0.009 0.005 -10000 0 -10000 0 0
ICAM1 -0.14 0.24 -10000 0 -0.64 53 53
NFKB1 -0.033 0.089 -10000 0 -0.27 7 7
MAPK8 -0.15 0.17 -10000 0 -0.42 97 97
MAPK9 0.009 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.017 0.16 0.48 9 -0.59 14 23
BAX 0.027 0.021 -10000 0 -10000 0 0
POMC -0.19 0.32 -10000 0 -1.1 33 33
EP300 0.052 0.064 0.22 5 -0.26 2 7
cortisol/GR alpha (dimer)/p53 0.23 0.26 0.55 147 -10000 0 147
proteasomal ubiquitin-dependent protein catabolic process 0.054 0.075 0.22 26 -0.2 1 27
SGK1 0.094 0.11 -10000 0 -1.1 2 2
IL13 -0.16 0.2 -10000 0 -0.6 36 36
IL6 -0.3 0.44 -10000 0 -0.97 132 132
PRKACG 0.002 0.004 -10000 0 -10000 0 0
IL5 -0.15 0.17 -10000 0 -0.55 24 24
IL2 -0.21 0.24 -10000 0 -0.62 72 72
CDK5 0.009 0.003 -10000 0 -10000 0 0
PRKACB 0.009 0.024 -10000 0 -0.52 1 1
HSP90AA1 0.01 0 -10000 0 -10000 0 0
IL8 -0.14 0.23 -10000 0 -0.6 60 60
CDK5R1/CDK5 -0.01 0.064 -10000 0 -0.37 15 15
NF kappa B1 p50/RelA/PKAc -0.025 0.12 -10000 0 -0.37 16 16
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.24 0.51 142 -10000 0 142
SMARCA4 0.01 0.024 -10000 0 -0.5 1 1
chromatin remodeling 0.14 0.15 0.37 83 -10000 0 83
NF kappa B1 p50/RelA/Cbp 0.009 0.15 0.32 14 -0.39 17 31
JUN (dimer) -0.18 0.18 -10000 0 -0.45 101 101
YWHAH 0.01 0 -10000 0 -10000 0 0
VIPR1 -0.36 0.43 -10000 0 -0.85 207 207
NR3C1 0.14 0.19 0.43 98 -10000 0 98
NR4A1 -0.1 0.22 -10000 0 -0.5 109 109
TIF2/SUV420H1 -0.003 0.032 -10000 0 -0.35 4 4
MAPKKK cascade -0.013 0.15 0.48 9 -0.56 14 23
cortisol/GR alpha (dimer)/Src-1 0.22 0.26 0.55 144 -10000 0 144
PBX1 -0.006 0.089 -10000 0 -0.5 15 15
POU1F1 0.001 0.033 -10000 0 -0.62 1 1
SELE -0.25 0.43 -10000 0 -1 103 103
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.38 81 -10000 0 81
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.24 0.51 142 -10000 0 142
mol:cortisol 0.13 0.19 0.37 142 -0.21 13 155
MMP1 -0.27 0.2 -10000 0 -0.47 151 151
TCGA08_p53

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
CDKN2A -0.1 0.18 -10000 0 -0.38 145 145
TP53 -0.028 0.046 0.18 1 -10000 0 1
Senescence -0.028 0.045 0.18 1 -10000 0 1
Apoptosis -0.028 0.045 0.18 1 -10000 0 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.054 0.089 0.19 144 -0.33 2 146
MDM4 0.01 0 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0 -9999 0 -10000 0 0
CCL5 0.005 0.051 -9999 0 -0.5 5 5
SDCBP 0.01 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.11 -9999 0 -0.27 72 72
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.1 0.11 -9999 0 -0.33 31 31
Syndecan-1/Syntenin -0.1 0.1 -9999 0 -0.32 27 27
MAPK3 -0.081 0.097 -9999 0 -0.5 2 2
HGF/MET -0.042 0.12 -9999 0 -0.37 55 55
TGFB1/TGF beta receptor Type II 0.01 0 -9999 0 -10000 0 0
BSG 0.01 0 -9999 0 -10000 0 0
keratinocyte migration -0.1 0.11 -9999 0 -0.33 31 31
Syndecan-1/RANTES -0.1 0.11 -9999 0 -0.33 31 31
Syndecan-1/CD147 -0.091 0.1 -9999 0 -0.31 28 28
Syndecan-1/Syntenin/PIP2 -0.11 0.088 -9999 0 -0.31 27 27
LAMA5 0.006 0.046 -9999 0 -0.5 4 4
positive regulation of cell-cell adhesion -0.1 0.086 -9999 0 -0.3 27 27
MMP7 -0.084 0.2 -9999 0 -0.52 87 87
HGF -0.018 0.12 -9999 0 -0.5 27 27
Syndecan-1/CASK -0.11 0.1 -9999 0 -0.26 72 72
Syndecan-1/HGF/MET -0.12 0.14 -9999 0 -0.38 65 65
regulation of cell adhesion -0.073 0.095 -9999 0 -0.48 2 2
HPSE 0.008 0.034 -9999 0 -0.52 2 2
positive regulation of cell migration -0.11 0.11 -9999 0 -0.27 72 72
SDC1 -0.11 0.11 -9999 0 -0.28 72 72
Syndecan-1/Collagen -0.11 0.11 -9999 0 -0.27 72 72
PPIB 0.009 0.024 -9999 0 -0.52 1 1
MET -0.023 0.13 -9999 0 -0.51 31 31
PRKACA 0.01 0 -9999 0 -10000 0 0
MMP9 -0.097 0.21 -9999 0 -0.52 99 99
MAPK1 -0.081 0.097 -9999 0 -0.29 28 28
homophilic cell adhesion -0.11 0.11 -9999 0 -0.27 72 72
MMP1 -0.34 0.25 -9999 0 -0.52 323 323
Visual signal transduction: Rods

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
mol:K + 0.01 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.05 -9999 0 -0.38 9 9
Metarhodopsin II/Arrestin -0.001 0.014 -9999 0 -0.32 1 1
PDE6G/GNAT1/GTP -0.009 0.059 -9999 0 -0.35 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.007 0.07 -9999 0 -0.52 9 9
GRK1 -0.028 0.13 -9999 0 -0.52 31 31
CNG Channel -0.1 0.15 -9999 0 -0.49 38 38
mol:Na + -0.12 0.16 -9999 0 -0.5 40 40
mol:ADP -0.028 0.13 -9999 0 -0.52 31 31
RGS9-1/Gbeta5/R9AP -0.13 0.17 -9999 0 -0.32 201 201
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.16 -9999 0 -0.51 40 40
CNGB1 -0.087 0.2 -9999 0 -0.52 90 90
RDH5 -0.001 0.075 -9999 0 -0.52 10 10
SAG 0.001 0.024 -9999 0 -0.52 1 1
mol:Ca2+ -0.093 0.16 -9999 0 -0.48 40 40
Na + (4 Units) -0.11 0.14 -9999 0 -0.46 40 40
RGS9 -0.15 0.24 -9999 0 -0.5 153 153
GNB1/GNGT1 -0.073 0.15 -9999 0 -0.37 97 97
GNAT1/GDP -0.12 0.15 -9999 0 -0.49 30 30
GUCY2D 0 0.07 -9999 0 -0.51 9 9
GNGT1 -0.098 0.21 -9999 0 -0.52 97 97
GUCY2F 0.001 0.024 -9999 0 -0.52 1 1
GNB5 0.01 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.013 0.094 -9999 0 -0.42 6 6
mol:11-cis-retinal -0.001 0.075 -9999 0 -0.52 10 10
mol:cGMP -0.051 0.11 -9999 0 -0.52 5 5
GNB1 0.01 0 -9999 0 -10000 0 0
Rhodopsin -0.008 0.053 -9999 0 -0.37 10 10
SLC24A1 0.01 0 -9999 0 -10000 0 0
CNGA1 -0.063 0.18 -9999 0 -0.52 67 67
Metarhodopsin II -0.018 0.07 -9999 0 -0.29 31 31
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.055 0.12 -9999 0 -0.29 92 92
RGS9BP -0.066 0.18 -9999 0 -0.5 73 73
Metarhodopsin II/Transducin -0.021 0.062 -9999 0 -0.23 3 3
GCAP Family/Ca ++ -0.051 0.11 -9999 0 -0.3 84 84
PDE6A/B -0.033 0.1 -9999 0 -0.35 46 46
mol:Pi -0.13 0.17 -9999 0 -0.32 201 201
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.061 0.12 -9999 0 -0.29 103 103
PDE6B 0.003 0.06 -9999 0 -0.5 7 7
PDE6A -0.031 0.14 -9999 0 -0.5 39 39
PDE6G 0.004 0.057 -9999 0 -0.5 6 6
RHO 0.004 0.005 -9999 0 -10000 0 0
PDE6 -0.13 0.16 -9999 0 -0.48 55 55
GUCA1A -0.078 0.19 -9999 0 -0.52 80 80
GC2/GCAP Family -0.051 0.11 -9999 0 -0.29 85 85
GUCA1C 0 0.002 -9999 0 -10000 0 0
GUCA1B 0.001 0.066 -9999 0 -0.51 8 8
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.002 0.023 -9999 0 -0.3 3 3
ARNO/beta Arrestin1-2 -0.094 0.11 -9999 0 -0.35 21 21
EGFR -0.005 0.086 -9999 0 -0.51 14 14
EPHA2 -0.001 0.072 -9999 0 -0.5 10 10
USP6 0.01 0 -9999 0 -10000 0 0
IQSEC1 0.009 0.023 -9999 0 -0.5 1 1
EGFR/EGFR/EGF/EGF -0.079 0.16 -9999 0 -0.38 103 103
ARRB2 -0.007 0.057 -9999 0 -0.19 43 43
mol:GTP 0.012 0.021 -9999 0 -0.13 2 2
ARRB1 0.005 0.051 -9999 0 -0.5 5 5
FBXO8 0.01 0 -9999 0 -10000 0 0
TSHR -0.043 0.16 -9999 0 -0.52 48 48
EGF -0.089 0.21 -9999 0 -0.52 92 92
somatostatin receptor activity 0 0 -9999 0 -0.001 121 121
ARAP2 -0.008 0.093 -9999 0 -0.5 17 17
mol:GDP -0.086 0.12 -9999 0 -0.26 113 113
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 79 79
ITGA2B -0.043 0.16 -9999 0 -0.5 50 50
ARF6 0.01 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.038 -9999 0 -10000 0 0
ADAP1 0.009 0.023 -9999 0 -0.5 1 1
KIF13B 0.008 0.032 -9999 0 -0.5 2 2
HGF/MET -0.042 0.12 -9999 0 -0.37 55 55
PXN 0.01 0 -9999 0 -10000 0 0
ARF6/GTP -0.082 0.11 -9999 0 -0.24 111 111
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.066 0.13 -9999 0 -0.31 103 103
ADRB2 -0.19 0.25 -9999 0 -0.5 189 189
receptor agonist activity 0 0 -9999 0 0 125 125
actin filament binding 0 0 -9999 0 0 121 121
SRC 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.019 0.12 -9999 0 -0.51 27 27
GNAQ 0.009 0.023 -9999 0 -0.5 1 1
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 81 81
ARF6/GDP -0.009 0.074 -9999 0 -0.37 8 8
ARF6/GDP/GULP/ACAP1 -0.079 0.097 -9999 0 -0.32 27 27
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.041 0.097 -9999 0 -0.26 76 76
ACAP1 0.008 0.032 -9999 0 -0.5 2 2
ACAP2 0.009 0.024 -9999 0 -0.52 1 1
LHCGR/beta Arrestin2 -0.021 0.079 -9999 0 -0.28 43 43
EFNA1 0.009 0.023 -9999 0 -0.5 1 1
HGF -0.018 0.12 -9999 0 -0.5 27 27
CYTH3 0.007 0.025 -9999 0 -0.38 2 2
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 79 79
endosomal lumen acidification 0 0 -9999 0 0 35 35
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.006 0.046 -9999 0 -0.5 4 4
GNAQ/ARNO 0.007 0.013 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 35 35
MET -0.023 0.13 -9999 0 -0.51 31 31
GNA14 -0.005 0.085 -9999 0 -0.5 14 14
GNA15 0.01 0 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 107 107
GNA11 0.008 0.033 -9999 0 -0.5 2 2
LHCGR -0.041 0.15 -9999 0 -0.52 43 43
AGTR1 -0.15 0.24 -9999 0 -0.5 153 153
desensitization of G-protein coupled receptor protein signaling pathway -0.021 0.079 -9999 0 -0.28 43 43
IPCEF1/ARNO -0.044 0.1 -9999 0 -0.46 3 3
alphaIIb/beta3 Integrin -0.056 0.13 -9999 0 -0.36 76 76
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.001 0.022 -10000 0 -0.35 2 2
Necdin/E2F1 -0.01 0.058 -10000 0 -0.36 13 13
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.029 0.079 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.17 -10000 0 -0.33 176 176
NT-4/5 (dimer)/p75(NTR) -0.03 0.1 -10000 0 -0.37 39 39
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 0.002 0.084 -10000 0 -10000 0 0
IKBKG 0.01 0 -10000 0 -10000 0 0
BDNF -0.25 0.25 -10000 0 -0.5 252 252
MGDIs/NGR/p75(NTR)/LINGO1 -0.049 0.12 -10000 0 -0.31 76 76
FURIN -0.004 0.085 -10000 0 -0.52 13 13
proBDNF (dimer)/p75(NTR)/Sortilin -0.16 0.15 -10000 0 -0.3 261 261
LINGO1 -0.057 0.18 -10000 0 -0.52 62 62
Sortilin/TRAF6/NRIF -0.002 0.02 -10000 0 -10000 0 0
proBDNF (dimer) -0.25 0.25 -10000 0 -0.5 252 252
NTRK1 -0.011 0.1 -10000 0 -0.5 20 20
RTN4R 0.009 0.023 -10000 0 -0.5 1 1
neuron apoptosis -0.11 0.14 -10000 0 -0.41 29 29
IRAK1 0.009 0.024 -10000 0 -0.52 1 1
SHC1 -0.013 0.099 -10000 0 -0.3 53 53
ARHGDIA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.019 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.029 0.083 -10000 0 -0.26 54 54
MAGEH1 0.01 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.032 0.09 -10000 0 -0.27 58 58
Mammalian IAPs/DIABLO -0.003 0.029 -10000 0 -0.27 4 4
proNGF (dimer) -0.028 0.14 -10000 0 -0.51 36 36
MAGED1 0.009 0.024 -10000 0 -0.52 1 1
APP 0.01 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.11 -10000 0 -0.5 25 25
ZNF274 0.01 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.026 0.076 -10000 0 -0.25 52 52
NGF -0.029 0.14 -10000 0 -0.51 36 36
cell cycle arrest 0.012 0.11 -10000 0 -0.29 22 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.063 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.025 0.085 -10000 0 -0.31 39 39
NCSTN 0.01 0 -10000 0 -10000 0 0
mol:GTP -0.032 0.093 -10000 0 -0.3 53 53
PSENEN 0.009 0.024 -10000 0 -0.52 1 1
mol:ceramide -0.005 0.09 -10000 0 -0.26 54 54
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.015 0.057 -10000 0 -0.39 1 1
p75(NTR)/beta APP -0.012 0.064 -10000 0 -0.36 16 16
BEX1 -0.14 0.23 -10000 0 -0.5 144 144
mol:GDP -0.02 0.098 -10000 0 -0.3 52 52
NGF (dimer) -0.081 0.13 -10000 0 -0.29 138 138
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.043 0.1 -10000 0 -0.28 76 76
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
RAC1/GTP -0.027 0.078 -10000 0 -0.25 52 52
MYD88 0.01 0 -10000 0 -10000 0 0
CHUK 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.032 0.093 -10000 0 -0.3 53 53
RHOB 0.01 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.005 0.044 -10000 0 -0.37 7 7
NT3 (dimer) -0.018 0.12 -10000 0 -0.5 27 27
TP53 -0.1 0.14 -10000 0 -0.46 9 9
PRDM4 -0.005 0.091 -10000 0 -0.26 54 54
BDNF (dimer) -0.29 0.22 -10000 0 -0.39 368 368
PIK3CA 0.01 0 -10000 0 -10000 0 0
SORT1 0.008 0.032 -10000 0 -0.5 2 2
activation of caspase activity -0.029 0.078 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.029 0.083 -10000 0 -0.26 54 54
RHOC 0.01 0 -10000 0 -10000 0 0
XIAP 0.01 0 -10000 0 -10000 0 0
MAPK10 -0.096 0.15 -10000 0 -0.41 50 50
DIABLO 0.01 0 -10000 0 -10000 0 0
SMPD2 -0.005 0.091 -10000 0 -0.26 54 54
APH1B 0.008 0.032 -10000 0 -0.5 2 2
APH1A 0.01 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.033 0.093 -10000 0 -0.3 54 54
PSEN1 0.01 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.031 0.11 -10000 0 -0.39 39 39
MAPK8 -0.073 0.12 -10000 0 -0.37 27 27
MAPK9 -0.073 0.12 -10000 0 -0.37 27 27
APAF1 0.01 0 -10000 0 -10000 0 0
NTF3 -0.018 0.12 -10000 0 -0.5 27 27
NTF4 -0.016 0.11 -10000 0 -0.5 25 25
NDN 0.004 0.056 -10000 0 -0.5 6 6
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.024 0.068 -10000 0 -10000 0 0
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.016 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.032 0.092 -10000 0 -0.3 53 53
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.13 0.13 -10000 0 -0.49 9 9
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.14 0.14 -10000 0 -0.27 261 261
PRKACB 0.009 0.024 -10000 0 -0.52 1 1
proBDNF (dimer)/p75 ECD -0.18 0.18 -10000 0 -0.35 252 252
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.004 0.057 -10000 0 -0.51 6 6
BIRC2 0.01 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.019 0.11 0.17 104 -0.27 14 118
BAD -0.076 0.13 -10000 0 -0.41 23 23
RIPK2 0.01 0 -10000 0 -10000 0 0
NGFR -0.007 0.092 -10000 0 -0.51 16 16
CYCS 0.001 0.087 -10000 0 -0.5 1 1
ADAM17 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.028 0.081 -10000 0 -0.26 52 52
BCL2L11 -0.076 0.13 -10000 0 -0.41 23 23
BDNF (dimer)/p75(NTR) -0.19 0.18 -10000 0 -0.36 261 261
PI3K -0.029 0.082 -10000 0 -0.27 31 31
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.029 0.083 -10000 0 -0.26 54 54
NDNL2 0.01 0 -10000 0 -10000 0 0
YWHAE 0.01 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.038 0.11 -10000 0 -0.36 52 52
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.03 0.085 -10000 0 -0.28 31 31
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.007 0.04 -10000 0 -0.5 3 3
PLG -0.007 0.07 -10000 0 -0.52 9 9
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.13 0.16 -10000 0 -0.47 33 33
SQSTM1 0.009 0.024 -10000 0 -0.52 1 1
NGFRAP1 0.005 0.051 -10000 0 -0.5 5 5
CASP3 -0.07 0.12 -10000 0 -0.38 23 23
E2F1 0.002 0.063 -10000 0 -0.52 7 7
CASP9 0.01 0 -10000 0 -10000 0 0
IKK complex -0.026 0.068 -10000 0 -0.39 3 3
NGF (dimer)/TRKA -0.041 0.12 -10000 0 -0.36 55 55
MMP7 -0.084 0.2 -10000 0 -0.52 87 87
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.027 0.076 -10000 0 -10000 0 0
MMP3 -0.2 0.26 -10000 0 -0.52 189 189
APAF-1/Caspase 9 -0.021 0.058 -10000 0 -0.37 2 2
LPA4-mediated signaling events

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.003 0.077 -9999 0 -0.31 29 29
ADCY5 -0.029 0.11 -9999 0 -0.31 68 68
ADCY6 0.012 0.034 -9999 0 -0.3 6 6
ADCY7 0.011 0.037 -9999 0 -0.3 7 7
ADCY1 0.005 0.057 -9999 0 -0.3 16 16
ADCY2 -0.02 0.1 -9999 0 -0.31 54 54
ADCY3 0.013 0.032 -9999 0 -0.3 5 5
ADCY8 -0.12 0.15 -9999 0 -0.3 204 204
PRKCE 0.005 0.037 -9999 0 -0.36 5 5
ADCY9 0.006 0.054 -9999 0 -0.3 15 15
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.062 0.098 -9999 0 -0.34 27 27
Canonical Wnt signaling 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
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.003 0.015 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.01 0 -10000 0 -10000 0 0
DKK2 -0.094 0.2 -10000 0 -0.5 100 100
TLE1 0.003 0.015 -10000 0 -10000 0 0
MACF1 0.006 0.046 -10000 0 -0.5 4 4
CTNNB1 0.088 0.079 0.23 18 -10000 0 18
WIF1 -0.34 0.23 -10000 0 -0.5 339 339
beta catenin/RanBP3 0.011 0.085 0.39 21 -10000 0 21
KREMEN2 -0.13 0.23 -10000 0 -0.52 126 126
DKK1 -0.13 0.23 -10000 0 -0.51 129 129
beta catenin/beta TrCP1 0.089 0.074 0.23 18 -10000 0 18
FZD1 0.01 0.001 -10000 0 -10000 0 0
AXIN2 -0.023 0.23 -10000 0 -1.3 16 16
AXIN1 0.011 0.001 -10000 0 -10000 0 0
RAN 0.009 0.024 -10000 0 -0.52 1 1
Axin1/APC/GSK3/beta catenin 0.008 0.024 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.072 0.061 0.27 1 -10000 0 1
Axin1/APC/GSK3 0.021 0.061 0.2 43 -10000 0 43
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.045 -10000 0 -10000 0 0
HNF1A -0.1 0.21 -10000 0 -0.52 100 100
CTBP1 0.003 0.017 -10000 0 -10000 0 0
MYC 0.007 0.1 -10000 0 -1.4 2 2
RANBP3 0.01 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.14 0.19 -10000 0 -0.36 186 186
NKD1 -0.051 0.16 -10000 0 -0.5 58 58
TCF4 0.001 0.036 -10000 0 -0.5 2 2
TCF3 0.003 0.016 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.005 0.038 -10000 0 -0.27 4 4
Ran/GTP 0 0.017 -10000 0 -0.38 1 1
CtBP/CBP/TCF/TLE1/AES 0 0.1 0.44 22 -10000 0 22
LEF1 0.001 0.037 -10000 0 -0.52 2 2
DVL1 0.074 0.052 0.19 1 -0.27 1 2
CSNK2A1 0.01 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.076 0.067 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.16 0.19 -10000 0 -0.35 216 216
LRP6 0.011 0.001 -10000 0 -10000 0 0
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.01 0.002 -10000 0 -10000 0 0
CCND1 -0.002 0.16 -10000 0 -1.3 6 6
WNT1 -0.001 0.075 -10000 0 -0.52 10 10
GSK3A 0.011 0.001 -10000 0 -10000 0 0
GSK3B 0.01 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.001 -10000 0 -10000 0 0
PPP2R5D 0.073 0.086 0.3 58 -10000 0 58
APC 0.025 0.04 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.15 0.1 0.22 332 -10000 0 332
CREBBP 0.003 0.016 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.004 0.046 -10000 0 -0.5 4 4
GNB1/GNG2 -0.039 0.071 -10000 0 -0.18 94 94
AKT1 -0.003 0.1 -10000 0 -0.19 94 94
EGF -0.089 0.21 -10000 0 -0.52 92 92
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.012 0.083 -10000 0 -0.41 9 9
mol:Ca2+ -0.022 0.14 -10000 0 -0.3 95 95
LYN 0.029 0.048 -10000 0 -0.37 4 4
RhoA/GTP -0.026 0.048 -10000 0 -0.13 42 42
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.025 0.16 -10000 0 -0.34 95 95
GNG2 0.008 0.033 -10000 0 -0.5 2 2
ARRB2 0.01 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.024 0.042 -10000 0 -0.33 3 3
G beta5/gamma2 -0.05 0.093 -10000 0 -0.23 94 94
PRKCH -0.028 0.16 -10000 0 -0.34 95 95
DNM1 0.003 0.058 -10000 0 -0.52 6 6
TXA2/TP beta/beta Arrestin3 -0.003 0.017 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.002 0.076 -10000 0 -0.5 11 11
G12 family/GTP -0.064 0.12 -10000 0 -0.3 95 95
ADRBK1 0.01 0 -10000 0 -10000 0 0
ADRBK2 0.009 0.023 -10000 0 -0.5 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.095 0.34 10 -10000 0 10
mol:NADP -0.003 0.08 -10000 0 -0.51 12 12
RAB11A 0.01 0 -10000 0 -10000 0 0
PRKG1 -0.047 0.16 -10000 0 -0.5 55 55
mol:IP3 -0.034 0.18 -10000 0 -0.37 95 95
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.057 0.23 -10000 0 -0.5 95 95
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.095 -10000 0 -0.37 5 5
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.019 0.072 -10000 0 -0.39 8 8
RHOA 0.01 0 -10000 0 -10000 0 0
PTGIR 0.001 0.069 -10000 0 -0.5 9 9
PRKCB1 -0.034 0.17 -10000 0 -0.37 95 95
GNAQ 0.009 0.023 -10000 0 -0.5 1 1
mol:L-citrulline -0.003 0.08 -10000 0 -0.51 12 12
TXA2/TXA2-R family -0.058 0.23 -10000 0 -0.52 95 95
LCK 0.027 0.054 -10000 0 -0.37 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.009 0.051 -10000 0 -0.5 3 3
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.021 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.008 0.049 -10000 0 -0.49 3 3
MAPK14 -0.007 0.11 -10000 0 -0.22 93 93
TGM2/GTP -0.041 0.19 -10000 0 -0.41 95 95
MAPK11 -0.008 0.11 -10000 0 -0.22 93 93
ARHGEF1 -0.006 0.086 -10000 0 -0.17 93 93
GNAI2 0.01 0 -10000 0 -10000 0 0
JNK cascade -0.035 0.18 -10000 0 -0.38 95 95
RAB11/GDP 0.01 0.001 -10000 0 -10000 0 0
ICAM1 -0.02 0.14 -10000 0 -0.28 93 93
cAMP biosynthetic process -0.034 0.16 -10000 0 -0.34 95 95
Gq family/GTP/EBP50 0.015 0.047 -10000 0 -0.34 4 4
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.029 0.048 -10000 0 -0.37 4 4
GNB5 0.01 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
EGF/EGFR 0.008 0.078 -10000 0 -0.32 13 13
VCAM1 -0.022 0.14 -10000 0 -0.29 93 93
TP beta/Gq family/GDP/G beta5/gamma2 0.024 0.042 -10000 0 -0.33 3 3
platelet activation -0.01 0.15 -10000 0 -0.29 95 95
PGI2/IP -0.007 0.048 -10000 0 -0.36 9 9
PRKACA 0.005 0.065 -10000 0 -0.31 17 17
Gq family/GDP/G beta5/gamma2 0.022 0.044 -10000 0 -0.28 6 6
TXA2/TP beta/beta Arrestin2 -0.002 0.014 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.012 0.061 -10000 0 -0.37 7 7
mol:DAG -0.04 0.19 -10000 0 -0.41 95 95
EGFR -0.005 0.086 -10000 0 -0.51 14 14
TXA2/TP alpha -0.051 0.22 -10000 0 -0.47 95 95
Gq family/GTP -0.007 0.049 -10000 0 -0.24 16 16
YES1 0.029 0.048 -10000 0 -0.37 4 4
GNAI2/GTP -0.008 0.048 -10000 0 -0.43 4 4
PGD2/DP -0.008 0.053 -10000 0 -0.36 11 11
SLC9A3R1 0.008 0.034 -10000 0 -0.52 2 2
FYN 0.028 0.049 -10000 0 -0.37 4 4
mol:NO -0.003 0.08 -10000 0 -0.51 12 12
GNA15 0.01 0 -10000 0 -10000 0 0
PGK/cGMP -0.041 0.11 -10000 0 -0.31 65 65
RhoA/GDP 0.01 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.011 0.056 -10000 0 -0.46 5 5
NOS3 -0.003 0.08 -10000 0 -0.51 12 12
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.028 0.16 -10000 0 -0.34 96 96
PRKCB -0.03 0.17 -10000 0 -0.35 97 97
PRKCE -0.027 0.16 -10000 0 -0.34 96 96
PRKCD -0.033 0.17 -10000 0 -0.37 95 95
PRKCG -0.044 0.18 -10000 0 -0.39 95 95
muscle contraction -0.051 0.22 -10000 0 -0.48 95 95
PRKCZ -0.026 0.16 -10000 0 -0.34 95 95
ARR3 0 0.033 -10000 0 -0.52 2 2
TXA2/TP beta -0.009 0.053 -10000 0 -0.48 4 4
PRKCQ -0.05 0.18 -10000 0 -0.38 97 97
MAPKKK cascade -0.049 0.21 -10000 0 -0.45 95 95
SELE -0.042 0.18 -10000 0 -0.39 95 95
TP beta/GNAI2/GDP/G beta/gamma -0.009 0.052 -10000 0 -0.47 4 4
ROCK1 0.01 0 -10000 0 -10000 0 0
GNA14 -0.005 0.085 -10000 0 -0.5 14 14
chemotaxis -0.072 0.26 -10000 0 -0.59 95 95
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
GNA11 0.008 0.032 -10000 0 -0.5 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.043 0.11 -10000 0 -0.31 68 68
fibroblast growth factor receptor signaling pathway -0.043 0.11 -10000 0 -0.31 68 68
LAMA1 -0.018 0.12 -10000 0 -0.51 26 26
PRNP 0.007 0.04 -10000 0 -0.5 3 3
GPC1/SLIT2 -0.089 0.15 -10000 0 -0.35 123 123
SMAD2 0.019 0.046 -10000 0 -0.27 1 1
GPC1/PrPc/Cu2+ -0.004 0.033 -10000 0 -0.3 6 6
GPC1/Laminin alpha1 -0.021 0.088 -10000 0 -0.37 28 28
TDGF1 -0.02 0.12 -10000 0 -0.51 27 27
CRIPTO/GPC1 -0.022 0.087 -10000 0 -0.36 30 30
APP/GPC1 -0.002 0.027 -10000 0 -0.35 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.002 0.077 -10000 0 -0.3 30 30
FLT1 0.01 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.008 0.047 -10000 0 -0.29 13 13
SERPINC1 -0.002 0.071 -10000 0 -0.52 9 9
FYN 0.001 0.08 -10000 0 -0.31 30 30
FGR -0.022 0.12 -10000 0 -0.32 62 62
positive regulation of MAPKKK cascade -0.017 0.12 -10000 0 -0.37 33 33
SLIT2 -0.12 0.22 -10000 0 -0.5 121 121
GPC1/NRG -0.075 0.15 -10000 0 -0.36 102 102
NRG1 -0.095 0.21 -10000 0 -0.5 101 101
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.002 0.023 -10000 0 -0.29 3 3
LYN 0.002 0.077 -10000 0 -0.3 30 30
mol:Spermine 0.007 0.029 -10000 0 -0.36 3 3
cell growth -0.043 0.11 -10000 0 -0.31 68 68
BMP signaling pathway -0.007 0.04 0.5 3 -10000 0 3
SRC 0.002 0.077 -10000 0 -0.3 30 30
TGFBR1 0.009 0.024 -10000 0 -0.52 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.075 0.19 -10000 0 -0.5 81 81
GPC1 0.007 0.04 -10000 0 -0.5 3 3
TGFBR1 (dimer) 0.009 0.024 -10000 0 -0.52 1 1
VEGFA 0.01 0 -10000 0 -10000 0 0
BLK -0.051 0.14 -10000 0 -0.31 106 106
HCK -0.012 0.1 -10000 0 -0.31 48 48
FGF2 -0.059 0.17 -10000 0 -0.5 66 66
FGFR1 0.007 0.04 -10000 0 -0.5 3 3
VEGFR1 homodimer 0.01 0 -10000 0 -10000 0 0
TGFBR2 0.001 0.068 -10000 0 -0.5 9 9
cell death -0.002 0.027 -10000 0 -0.35 3 3
ATIII/GPC1 -0.009 0.056 -10000 0 -0.36 12 12
PLA2G2A/GPC1 -0.061 0.14 -10000 0 -0.36 83 83
LCK 0 0.08 -10000 0 -0.3 33 33
neuron differentiation -0.075 0.15 -10000 0 -0.36 102 102
PrPc/Cu2+ -0.002 0.028 -10000 0 -0.36 3 3
APP 0.01 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.001 0.068 -10000 0 -0.5 9 9
Effects of Botulinum toxin

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
STX1A -0.09 0.17 -9999 0 -0.38 126 126
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.039 0.11 -9999 0 -0.36 54 54
STXBP1 0.007 0.04 -9999 0 -0.5 3 3
ACh/CHRNA1 -0.034 0.099 -9999 0 -0.34 42 42
RAB3GAP2/RIMS1/UNC13B -0.033 0.093 -9999 0 -0.3 54 54
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.048 0.16 -9999 0 -0.5 54 54
mol:ACh -0.016 0.04 -9999 0 -0.079 129 129
RAB3GAP2 0.01 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.081 0.11 -9999 0 -0.36 24 24
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.033 0.099 -9999 0 -0.34 42 42
UNC13B 0.01 0 -9999 0 -10000 0 0
CHRNA1 -0.034 0.14 -9999 0 -0.51 41 41
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.036 0.11 -9999 0 -0.36 45 45
SNAP25 -0.002 0.039 -9999 0 -0.18 21 21
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.038 0.15 -9999 0 -0.51 45 45
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.072 0.14 -9999 0 -0.31 129 129
STX1A/SNAP25 fragment 1/VAMP2 -0.081 0.11 -9999 0 -0.36 24 24
Ephrin B reverse signaling

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
EFNB2 0.002 0.065 -10000 0 -0.5 8 8
EPHB2 -0.047 0.16 -10000 0 -0.52 53 53
EFNB1 0.011 0.051 -10000 0 -0.36 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.058 0.12 -10000 0 -0.5 15 15
Ephrin B2/EPHB1-2 -0.06 0.13 -10000 0 -0.3 107 107
neuron projection morphogenesis -0.055 0.11 -10000 0 -0.47 15 15
Ephrin B1/EPHB1-2/Tiam1 -0.058 0.13 -10000 0 -0.49 18 18
DNM1 0.003 0.058 -10000 0 -0.52 6 6
cell-cell signaling 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.045 0.18 -10000 0 -0.58 50 50
YES1 -0.081 0.24 -10000 0 -0.81 50 50
Ephrin B1/EPHB1-2/NCK2 -0.054 0.12 -10000 0 -0.4 22 22
PI3K -0.046 0.18 -10000 0 -0.59 50 50
mol:GDP -0.058 0.13 -10000 0 -0.42 24 24
ITGA2B -0.043 0.16 -10000 0 -0.5 50 50
endothelial cell proliferation -0.005 0.038 -10000 0 -0.3 8 8
FYN -0.082 0.24 -10000 0 -0.81 50 50
MAP3K7 -0.063 0.19 -10000 0 -0.62 50 50
FGR -0.093 0.25 -10000 0 -0.82 50 50
TIAM1 0.002 0.065 -10000 0 -0.5 8 8
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
RGS3 0.01 0 -10000 0 -10000 0 0
cell adhesion -0.07 0.2 -10000 0 -0.58 50 50
LYN -0.081 0.24 -10000 0 -0.81 50 50
Ephrin B1/EPHB1-2/Src Family Kinases -0.076 0.23 -10000 0 -0.74 50 50
Ephrin B1/EPHB1-2 -0.071 0.2 -10000 0 -0.67 50 50
SRC -0.081 0.24 -10000 0 -0.8 50 50
ITGB3 -0.019 0.12 -10000 0 -0.51 27 27
EPHB1 -0.051 0.17 -10000 0 -0.52 56 56
EPHB4 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.038 -10000 0 -0.3 8 8
alphaIIb/beta3 Integrin -0.056 0.13 -10000 0 -0.36 76 76
BLK -0.087 0.24 -10000 0 -0.81 50 50
HCK -0.087 0.25 -10000 0 -0.82 50 50
regulation of stress fiber formation 0.054 0.12 0.4 22 -10000 0 22
MAPK8 -0.037 0.17 -10000 0 -0.55 50 50
Ephrin B1/EPHB1-2/RGS3 -0.054 0.12 -10000 0 -0.4 22 22
endothelial cell migration -0.055 0.17 -10000 0 -0.53 51 51
NCK2 0.01 0 -10000 0 -10000 0 0
PTPN13 -0.057 0.19 -10000 0 -0.61 50 50
regulation of focal adhesion formation 0.054 0.12 0.4 22 -10000 0 22
chemotaxis 0.054 0.12 0.4 22 -10000 0 22
PIK3CA 0.01 0 -10000 0 -10000 0 0
Rac1/GTP -0.057 0.12 -10000 0 -0.49 15 15
angiogenesis -0.071 0.2 -10000 0 -0.67 50 50
LCK -0.082 0.24 -10000 0 -0.8 50 50
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.054 -9999 0 -0.35 12 12
alphaV beta3 Integrin -0.056 0.12 -9999 0 -0.31 89 89
PTK2 -0.056 0.15 -9999 0 -0.44 36 36
IGF1R 0.008 0.032 -9999 0 -0.5 2 2
PI4KB 0.01 0 -9999 0 -10000 0 0
MFGE8 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
CDKN1B -0.1 0.2 -9999 0 -0.5 84 84
VEGFA 0.01 0 -9999 0 -10000 0 0
ILK -0.1 0.2 -9999 0 -0.5 84 84
ROCK1 0.01 0 -9999 0 -10000 0 0
AKT1 -0.094 0.18 -9999 0 -0.46 84 84
PTK2B 0.009 0.079 -9999 0 -0.48 2 2
alphaV/beta3 Integrin/JAM-A -0.09 0.15 -9999 0 -0.51 29 29
CBL 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.032 0.094 -9999 0 -0.3 52 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.046 -9999 0 -0.52 1 1
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.017 0.097 -9999 0 -0.37 9 9
alphaV/beta3 Integrin/Syndecan-1 -0.017 0.069 -9999 0 -0.3 27 27
PI4KA 0.01 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.049 0.11 -9999 0 -0.53 11 11
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.23 0.16 -9999 0 -0.32 351 351
RPS6KB1 -0.009 0.12 -9999 0 -0.49 11 11
TLN1 0.009 0.023 -9999 0 -0.5 1 1
MAPK3 -0.093 0.19 -9999 0 -0.51 69 69
GPR124 0.007 0.04 -9999 0 -0.5 3 3
MAPK1 -0.093 0.19 -9999 0 -0.51 69 69
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
alphaV/beta3 Integrin/Tumstatin -0.097 0.14 -9999 0 -0.3 156 156
cell adhesion -0.025 0.07 -9999 0 -0.28 5 5
ANGPTL3 -0.021 0.12 -9999 0 -0.52 25 25
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.045 -9999 0 -0.29 12 12
IGF-1R heterotetramer 0.008 0.032 -9999 0 -0.5 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.001 0.068 -9999 0 -0.5 9 9
ITGB3 -0.019 0.12 -9999 0 -0.51 27 27
IGF1 -0.002 0.076 -9999 0 -0.5 11 11
RAC1 0.01 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.076 -9999 0 -0.32 28 28
apoptosis 0.01 0 -9999 0 -10000 0 0
CD47 0.008 0.032 -9999 0 -0.5 2 2
alphaV/beta3 Integrin/CD47 -0.018 0.071 -9999 0 -0.3 29 29
VCL 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.041 0.11 -9999 0 -0.32 63 63
CSF1 0.005 0.051 -9999 0 -0.5 5 5
PIK3C2A -0.1 0.2 -9999 0 -0.5 84 84
PI4 Kinase/Pyk2 -0.078 0.13 -9999 0 -0.44 32 32
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.021 0.074 -9999 0 -0.27 38 38
FAK1/Vinculin -0.04 0.12 -9999 0 -0.34 36 36
alphaV beta3/Integrin/ppsTEM5 -0.018 0.076 -9999 0 -0.32 28 28
RHOA 0.01 0 -9999 0 -10000 0 0
VTN -0.084 0.2 -9999 0 -0.5 90 90
BCAR1 0.009 0.023 -9999 0 -0.5 1 1
FGF2 -0.059 0.17 -9999 0 -0.5 66 66
F11R -0.033 0.13 -9999 0 -0.35 67 67
alphaV/beta3 Integrin/Lactadherin -0.017 0.069 -9999 0 -0.3 27 27
alphaV/beta3 Integrin/TGFBR2 -0.022 0.078 -9999 0 -0.3 36 36
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.028 -9999 0 -0.26 6 6
HSP90AA1 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.016 0.066 -9999 0 -0.28 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.005 0.052 -9999 0 -0.5 5 5
alphaV/beta3 Integrin/Pyk2 -0.02 0.071 -9999 0 -0.48 2 2
SDC1 0.01 0 -9999 0 -10000 0 0
VAV3 0.025 0.045 -9999 0 -0.49 1 1
PTPN11 0.01 0 -9999 0 -10000 0 0
IRS1 0.009 0.023 -9999 0 -0.5 1 1
FAK1/Paxillin -0.04 0.12 -9999 0 -0.34 36 36
cell migration -0.03 0.12 -9999 0 -0.36 16 16
ITGAV 0.01 0 -9999 0 -10000 0 0
PI3K -0.08 0.13 -9999 0 -0.46 29 29
SPP1 -0.36 0.24 -9999 0 -0.52 345 345
KDR -0.003 0.079 -9999 0 -0.5 12 12
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0 -9999 0 -10000 0 0
COL4A3 -0.13 0.23 -9999 0 -0.5 135 135
angiogenesis -0.072 0.21 -9999 0 -0.51 71 71
Rac1/GTP -0.005 0.036 -9999 0 -0.44 1 1
EDIL3 -0.033 0.14 -9999 0 -0.5 41 41
cell proliferation -0.022 0.078 -9999 0 -0.3 36 36
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.01 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.038 0.075 -10000 0 -0.28 18 18
NT3 (dimer)/TRKC -0.087 0.17 -10000 0 -0.39 110 110
NT3 (dimer)/TRKB -0.13 0.17 -10000 0 -0.32 200 200
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.024 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
BDNF -0.25 0.25 -10000 0 -0.5 252 252
PIK3CA 0.01 0 -10000 0 -10000 0 0
DYNLT1 0.01 0 -10000 0 -10000 0 0
NTRK1 -0.011 0.1 -10000 0 -0.5 20 20
NTRK2 -0.18 0.24 -10000 0 -0.5 179 179
NTRK3 -0.09 0.2 -10000 0 -0.5 96 96
NT-4/5 (dimer)/TRKB -0.13 0.17 -10000 0 -0.32 196 196
neuron apoptosis 0.2 0.19 0.52 104 -10000 0 104
SHC 2-3/Grb2 -0.21 0.22 -10000 0 -0.57 104 104
SHC1 0.009 0.024 -10000 0 -0.52 1 1
SHC2 -0.14 0.14 -10000 0 -0.47 44 44
SHC3 -0.22 0.26 -10000 0 -0.64 112 112
STAT3 (dimer) 0.012 0.038 -10000 0 -0.32 6 6
NT3 (dimer)/TRKA -0.038 0.11 -10000 0 -0.32 58 58
RIN/GDP -0.024 0.075 -10000 0 -0.27 5 5
GIPC1 0.01 0 -10000 0 -10000 0 0
KRAS 0.009 0.024 -10000 0 -0.52 1 1
DNAJA3 -0.027 0.07 -10000 0 -0.31 10 10
RIN/GTP -0.002 0.029 -10000 0 -0.38 3 3
CCND1 0.015 0.083 -10000 0 -0.73 6 6
MAGED1 0.009 0.024 -10000 0 -0.52 1 1
PTPN11 0.01 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.11 -10000 0 -0.5 25 25
SHC/GRB2/SOS1 -0.001 0.014 -10000 0 -0.3 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.046 0.12 -10000 0 -0.33 68 68
TRKA/NEDD4-2 -0.014 0.07 -10000 0 -0.35 20 20
ELMO1 0.005 0.052 -10000 0 -0.5 5 5
RhoG/GTP/ELMO1/DOCK1 -0.003 0.03 -10000 0 -0.3 5 5
NGF -0.029 0.14 -10000 0 -0.51 36 36
HRAS 0.01 0 -10000 0 -10000 0 0
DOCK1 0.01 0 -10000 0 -10000 0 0
GAB2 0.006 0.046 -10000 0 -0.5 4 4
RIT2 -0.002 0.041 -10000 0 -0.52 3 3
RIT1 0.01 0 -10000 0 -10000 0 0
FRS2 0.008 0.034 -10000 0 -0.52 2 2
DNM1 0.003 0.058 -10000 0 -0.52 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.028 0.075 -10000 0 -0.32 14 14
mol:GDP -0.034 0.1 -10000 0 -0.32 11 11
NGF (dimer) -0.028 0.14 -10000 0 -0.51 36 36
RhoG/GDP -0.004 0.036 -10000 0 -0.36 5 5
RIT1/GDP -0.019 0.074 -10000 0 -0.24 3 3
TIAM1 0.002 0.065 -10000 0 -0.5 8 8
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
BDNF (dimer)/TRKB -0.25 0.21 -10000 0 -0.38 328 328
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.001 0.017 -10000 0 -0.37 1 1
FRS2 family/SHP2 -0.001 0.019 -10000 0 -0.3 2 2
SHC/GRB2/SOS1/GAB1 -0.002 0.023 -10000 0 -0.27 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.12 -10000 0 -0.5 27 27
RAP1/GDP -0.031 0.051 -10000 0 -0.24 1 1
KIDINS220/CRKL 0.01 0 -10000 0 -10000 0 0
BDNF (dimer) -0.25 0.25 -10000 0 -0.5 252 252
ubiquitin-dependent protein catabolic process -0.034 0.096 -10000 0 -0.3 55 55
Schwann cell development -0.047 0.034 -10000 0 -10000 0 0
EHD4 0.01 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.017 -10000 0 -0.27 2 2
FRS2 family/SHP2/CRK family/C3G/GAB2 0.03 0.021 -10000 0 -10000 0 0
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.24 0.21 -10000 0 -0.5 166 166
ABL1 0.01 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.091 0.074 -10000 0 -0.28 1 1
STAT3 0.012 0.038 -10000 0 -0.32 6 6
axon guidance -0.23 0.2 -10000 0 -0.48 166 166
MAPK3 -0.018 0.12 -10000 0 -0.3 68 68
MAPK1 -0.018 0.12 -10000 0 -0.3 68 68
CDC42/GDP -0.019 0.074 -10000 0 -0.24 3 3
NTF3 -0.018 0.12 -10000 0 -0.5 27 27
NTF4 -0.016 0.11 -10000 0 -0.5 25 25
NGF (dimer)/TRKA/FAIM -0.034 0.096 -10000 0 -0.3 55 55
PI3K -0.001 0.016 -10000 0 -0.35 1 1
FRS3 0.01 0 -10000 0 -10000 0 0
FAIM 0.01 0 -10000 0 -10000 0 0
GAB1 0.007 0.04 -10000 0 -0.5 3 3
RASGRF1 -0.12 0.14 -10000 0 -0.27 209 209
SOS1 0.01 0 -10000 0 -10000 0 0
MCF2L -0.058 0.15 -10000 0 -0.32 113 113
RGS19 0.01 0 -10000 0 -10000 0 0
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP -0.009 0.064 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.074 -10000 0 -0.24 3 3
NGF (dimer)/TRKA/GRIT -0.035 0.098 -10000 0 -0.31 55 55
neuron projection morphogenesis -0.001 0.08 -10000 0 -0.45 2 2
NGF (dimer)/TRKA/NEDD4-2 -0.034 0.096 -10000 0 -0.3 55 55
MAP2K1 0.029 0.024 -10000 0 -10000 0 0
NGFR -0.007 0.092 -10000 0 -0.51 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.004 0.071 -10000 0 -0.36 1 1
RAS family/GTP/PI3K 0.024 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.016 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.007 0.04 -10000 0 -0.5 3 3
MAPKKK cascade -0.085 0.16 -10000 0 -0.65 33 33
RASA1 0.01 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.014 0.07 -10000 0 -0.35 20 20
SQSTM1 0.009 0.024 -10000 0 -0.52 1 1
BDNF (dimer)/TRKB/GIPC -0.23 0.19 -10000 0 -0.52 103 103
NGF (dimer)/TRKA/p62/Atypical PKCs -0.03 0.082 -10000 0 -0.49 2 2
MATK -0.012 0.1 -10000 0 -0.5 21 21
NEDD4L 0.01 0 -10000 0 -10000 0 0
RAS family/GDP -0.026 0.048 -10000 0 -0.22 1 1
NGF (dimer)/TRKA -0.029 0.076 -10000 0 -0.25 40 40
Rac1/GTP -0.086 0.097 -10000 0 -0.29 46 46
FRS2 family/SHP2/CRK family -0.001 0.016 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.01 0 -9999 0 -10000 0 0
EGFR -0.005 0.086 -9999 0 -0.51 14 14
EGF/EGFR -0.088 0.14 -9999 0 -0.28 156 156
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.054 0.11 -9999 0 -0.5 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.008 0.032 -9999 0 -0.5 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.089 0.21 -9999 0 -0.52 92 92
EGF/EGFR dimer/SHC -0.066 0.13 -9999 0 -0.31 104 104
mol:GDP -0.054 0.1 -9999 0 -0.49 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.065 0.18 -9999 0 -0.5 72 72
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.048 0.095 -9999 0 -0.46 3 3
SHC1 0.009 0.024 -9999 0 -0.52 1 1
HRAS/GDP -0.05 0.097 -9999 0 -0.46 3 3
FRAP1 -0.028 0.11 -9999 0 -0.48 3 3
EGF/EGFR dimer -0.079 0.16 -9999 0 -0.38 103 103
SOS1 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.053 0.13 -9999 0 -0.35 74 74
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.074 0.14 -10000 0 -0.41 42 42
epithelial cell differentiation -0.077 0.12 -10000 0 -0.43 24 24
ITCH 0.023 0.018 -10000 0 -10000 0 0
WWP1 -0.02 0.068 -10000 0 -10000 0 0
FYN 0.009 0.023 -10000 0 -0.5 1 1
EGFR -0.005 0.086 -10000 0 -0.51 14 14
PRL -0.01 0.084 -10000 0 -0.52 13 13
neuron projection morphogenesis -0.027 0.11 -10000 0 -0.44 2 2
PTPRZ1 -0.11 0.22 -10000 0 -0.51 114 114
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.067 0.1 -10000 0 -0.49 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.068 0.14 -10000 0 -0.36 51 51
ADAM17 0.023 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.034 0.089 -10000 0 -0.38 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.14 0.17 -10000 0 -0.41 85 85
NCOR1 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.077 0.12 -10000 0 -0.34 51 51
GRIN2B -0.059 0.13 -10000 0 -0.5 5 5
ErbB4/ErbB2/betacellulin -0.033 0.061 -10000 0 -0.34 11 11
STAT1 0.01 0 -10000 0 -10000 0 0
HBEGF -0.077 0.19 -10000 0 -0.5 83 83
PRLR -0.054 0.17 -10000 0 -0.51 60 60
E4ICDs/ETO2 -0.043 0.11 -10000 0 -0.42 18 18
axon guidance 0.002 0.076 -10000 0 -10000 0 0
NEDD4 0.022 0.029 -10000 0 -0.47 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.055 0.13 -10000 0 -0.38 71 71
CBFA2T3 -0.023 0.13 -10000 0 -0.5 32 32
ErbB4/ErbB2/HBEGF -0.069 0.11 -10000 0 -0.34 44 44
MAPK3 -0.034 0.12 -10000 0 -0.46 2 2
STAT1 (dimer) -0.025 0.074 -10000 0 -0.32 1 1
MAPK1 -0.034 0.12 -10000 0 -0.46 2 2
JAK2 0.008 0.032 -10000 0 -0.5 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.078 0.12 -10000 0 -0.34 54 54
NRG1 -0.052 0.15 -10000 0 -0.35 101 101
NRG3 -0.19 0.25 -10000 0 -0.5 192 192
NRG2 -0.048 0.16 -10000 0 -0.5 55 55
NRG4 -0.036 0.15 -10000 0 -0.51 42 42
heart development 0.002 0.076 -10000 0 -10000 0 0
neural crest cell migration -0.059 0.13 -10000 0 -0.34 54 54
ERBB2 0.024 0.032 -10000 0 -0.36 3 3
WWOX/E4ICDs -0.025 0.074 -10000 0 -0.32 1 1
SHC1 0.009 0.024 -10000 0 -0.52 1 1
ErbB4/EGFR/neuregulin 4 -0.068 0.11 -10000 0 -0.4 27 27
apoptosis 0.21 0.23 0.45 191 -10000 0 191
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.058 0.12 -10000 0 -0.4 31 31
ErbB4/ErbB2/epiregulin -0.11 0.13 -10000 0 -0.34 70 70
ErbB4/ErbB4/betacellulin/betacellulin -0.032 0.091 -10000 0 -0.4 10 10
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.11 0.15 -10000 0 -0.4 76 76
MDM2 -0.023 0.078 -10000 0 -0.32 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.07 0.11 -10000 0 -0.32 51 51
STAT5A 0.007 0.072 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.084 0.12 -10000 0 -0.36 55 55
DLG4 0.01 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.017 -10000 0 -0.37 1 1
E4ICDs/TAB2/NCoR1 -0.04 0.055 -10000 0 -0.3 1 1
STAT5A (dimer) -0.082 0.13 -10000 0 -0.47 24 24
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.069 -10000 0 -10000 0 0
LRIG1 0.008 0.032 -10000 0 -0.5 2 2
EREG -0.15 0.24 -10000 0 -0.51 154 154
BTC -0.003 0.079 -10000 0 -0.5 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.074 -10000 0 -10000 0 0
ERBB4 -0.034 0.089 -10000 0 -0.38 1 1
STAT5B 0.01 0 -10000 0 -10000 0 0
YAP1 -0.001 0.024 -10000 0 -0.53 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.049 0.086 -10000 0 -0.34 22 22
glial cell differentiation 0.04 0.055 0.3 1 -10000 0 1
WWOX 0.01 0 -10000 0 -10000 0 0
cell proliferation -0.067 0.15 -10000 0 -0.44 34 34
IL23-mediated signaling events

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
CCL2 -0.12 0.4 -10000 0 -1.1 45 45
IL23A -0.15 0.42 -10000 0 -1.2 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.2 0.34 -10000 0 -1.1 45 45
positive regulation of T cell mediated cytotoxicity -0.15 0.44 -10000 0 -1.2 46 46
ITGA3 -0.13 0.4 -10000 0 -1.2 38 38
IL17F -0.068 0.28 -10000 0 -0.72 34 34
IL12B 0.011 0.06 -10000 0 -0.53 5 5
STAT1 (dimer) -0.14 0.42 -10000 0 -1.2 45 45
CD4 -0.12 0.4 -10000 0 -1.1 41 41
IL23 -0.15 0.4 -10000 0 -1.2 40 40
IL23R 0 0.083 -10000 0 -10000 0 0
IL1B -0.16 0.46 -10000 0 -1.3 47 47
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.12 0.38 -10000 0 -1.1 37 37
TYK2 0.01 0.019 -10000 0 -10000 0 0
STAT4 0.01 0 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
IL18RAP -0.009 0.096 -10000 0 -0.5 18 18
IL12RB1 -0.005 0.095 -10000 0 -0.53 15 15
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.001 0.073 -10000 0 -0.39 15 15
IL23R/JAK2 0.003 0.1 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.15 0.44 -10000 0 -1.2 46 46
natural killer cell activation 0.001 0.007 0.035 2 -10000 0 2
JAK2 0.015 0.042 -10000 0 -0.52 2 2
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
NFKB1 0.009 0.003 -10000 0 -10000 0 0
RELA 0.009 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.14 0.38 -10000 0 -1.1 40 40
ALOX12B -0.14 0.4 -10000 0 -1.1 46 46
CXCL1 -0.14 0.43 -10000 0 -1.2 48 48
T cell proliferation -0.15 0.44 -10000 0 -1.2 46 46
NFKBIA 0.009 0.003 -10000 0 -10000 0 0
IL17A -0.047 0.23 -10000 0 -0.58 25 25
PI3K -0.2 0.35 -10000 0 -1.1 45 45
IFNG -0.006 0.032 -10000 0 -0.12 11 11
STAT3 (dimer) -0.19 0.33 -10000 0 -1.1 45 45
IL18R1 -0.012 0.1 -10000 0 -0.5 21 21
IL23/IL23R/JAK2/TYK2/SOCS3 -0.058 0.25 -10000 0 -0.69 28 28
IL18/IL18R -0.016 0.11 -10000 0 -0.35 39 39
macrophage activation -0.013 0.016 -10000 0 -0.044 36 36
TNF -0.15 0.44 -10000 0 -1.2 44 44
STAT3/STAT4 -0.2 0.35 -10000 0 -1.1 46 46
STAT4 (dimer) -0.14 0.42 -10000 0 -1.2 45 45
IL18 0 0.068 -10000 0 -0.5 9 9
IL19 -0.13 0.39 -10000 0 -1.1 42 42
STAT5A (dimer) -0.14 0.42 -10000 0 -1.2 45 45
STAT1 0.01 0 -10000 0 -10000 0 0
SOCS3 0.006 0.046 -10000 0 -0.5 4 4
CXCL9 -0.14 0.41 -10000 0 -1.1 48 48
MPO -0.13 0.41 -10000 0 -1.1 47 47
positive regulation of humoral immune response -0.15 0.44 -10000 0 -1.2 46 46
IL23/IL23R/JAK2/TYK2 -0.16 0.48 -10000 0 -1.3 46 46
IL6 -0.28 0.58 -10000 0 -1.2 121 121
STAT5A 0.009 0.023 -10000 0 -0.5 1 1
IL2 0.007 0.009 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.007 0.035 2 -10000 0 2
CD3E -0.12 0.39 -10000 0 -1.1 44 44
keratinocyte proliferation -0.15 0.44 -10000 0 -1.2 46 46
NOS2 -0.18 0.47 -10000 0 -1.1 72 72
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.01 0.061 -10000 0 -0.54 5 5
HDAC1 0.002 0.007 -10000 0 -10000 0 0
AES 0.009 0.002 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
DTX1 0.007 0.041 -10000 0 -0.52 3 3
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.009 0.002 -10000 0 -10000 0 0
AP1 -0.031 0.12 -10000 0 -0.29 79 79
NCSTN 0.01 0 -10000 0 -10000 0 0
ADAM10 0.01 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.01 0.057 -10000 0 -0.33 2 2
NICD/RBPSUH -0.006 0.054 -10000 0 -0.54 5 5
WIF1 -0.34 0.23 -10000 0 -0.5 339 339
NOTCH1 -0.006 0.058 -10000 0 -0.57 5 5
PSENEN 0.009 0.024 -10000 0 -0.52 1 1
KREMEN2 -0.13 0.23 -10000 0 -0.52 126 126
DKK1 -0.13 0.23 -10000 0 -0.51 129 129
beta catenin/beta TrCP1 0.018 0.052 -10000 0 -10000 0 0
APH1B 0.008 0.032 -10000 0 -0.5 2 2
APH1A 0.01 0 -10000 0 -10000 0 0
AXIN1 -0.005 0.026 -10000 0 -0.19 3 3
CtBP/CBP/TCF1/TLE1/AES -0.013 0.065 0.28 1 -10000 0 1
PSEN1 0.01 0 -10000 0 -10000 0 0
FOS -0.023 0.13 -10000 0 -0.5 32 32
JUN 0.006 0.046 -10000 0 -0.5 4 4
MAP3K7 0.009 0.002 -10000 0 -10000 0 0
CTNNB1 0.013 0.055 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.14 0.19 -10000 0 -0.36 186 186
HNF1A -0.099 0.21 -10000 0 -0.52 100 100
CTBP1 0.009 0.002 -10000 0 -10000 0 0
MYC 0.016 0.086 -10000 0 -1.3 2 2
NKD1 -0.051 0.16 -10000 0 -0.5 58 58
FZD1 0.01 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.007 0.057 -10000 0 -0.54 5 5
apoptosis -0.031 0.12 -10000 0 -0.28 79 79
Delta 1/NOTCHprecursor -0.01 0.061 -10000 0 -0.54 5 5
DLL1 0.002 0.065 -10000 0 -0.5 8 8
PPARD 0.021 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.019 -10000 0 -10000 0 0
APC -0.005 0.026 -10000 0 -0.19 3 3
DVL1 -0.031 0.033 -10000 0 -0.43 2 2
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.16 0.19 -10000 0 -0.35 216 216
LRP6 0.01 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.011 0.005 -10000 0 -10000 0 0
CCND1 0.006 0.14 -10000 0 -1.3 6 6
WNT1 -0.002 0.075 -10000 0 -0.52 10 10
Axin1/APC/beta catenin 0.012 0.041 -10000 0 -0.28 1 1
DKK2 -0.094 0.2 -10000 0 -0.5 100 100
NOTCH1 precursor/DVL1 -0.016 0.055 -10000 0 -0.49 6 6
GSK3B 0.01 0 -10000 0 -10000 0 0
FRAT1 0.009 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.007 0.057 -10000 0 -0.54 5 5
PPP2R5D 0.015 0.084 0.24 58 -10000 0 58
MAPK1 0.01 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.18 0.12 -10000 0 -0.41 11 11
RBPJ 0.01 0 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.068 0.19 -10000 0 -0.52 74 74
NFATC2 0.004 0.17 -10000 0 -0.73 15 15
NFATC3 -0.009 0.08 -10000 0 -0.3 7 7
CD40LG -0.071 0.36 -10000 0 -0.95 51 51
ITCH -0.01 0.099 -10000 0 -10000 0 0
CBLB -0.01 0.099 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.23 -10000 0 -0.94 22 22
JUNB 0.007 0.04 -10000 0 -0.5 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.051 0.1 -10000 0 -10000 0 0
T cell anergy -0.06 0.16 -10000 0 -0.38 92 92
TLE4 0.02 0.16 -10000 0 -0.9 9 9
Jun/NFAT1-c-4/p21SNFT -0.12 0.3 -10000 0 -0.93 48 48
AP-1/NFAT1-c-4 -0.082 0.4 -10000 0 -1.1 49 49
IKZF1 0.021 0.16 -10000 0 -0.85 10 10
T-helper 2 cell differentiation 0.007 0.19 -10000 0 -0.84 12 12
AP-1/NFAT1 -0.051 0.13 -10000 0 -0.51 23 23
CALM1 -0.011 0.066 -10000 0 -10000 0 0
EGR2 -0.047 0.39 -10000 0 -1.5 26 26
EGR3 -0.088 0.46 -10000 0 -1.4 53 53
NFAT1/FOXP3 -0.046 0.18 -10000 0 -0.53 27 27
EGR1 -0.022 0.12 -10000 0 -0.5 31 31
JUN 0.004 0.049 -10000 0 -0.5 4 4
EGR4 -0.044 0.16 -10000 0 -0.52 49 49
mol:Ca2+ -0.022 0.07 -10000 0 -10000 0 0
GBP3 0.005 0.19 -10000 0 -0.74 25 25
FOSL1 -0.015 0.11 -10000 0 -0.52 23 23
NFAT1-c-4/MAF/IRF4 -0.11 0.29 -10000 0 -0.9 46 46
DGKA 0.025 0.13 -10000 0 -0.7 8 8
CREM 0.009 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.32 -10000 0 -0.98 50 50
CTLA4 -0.03 0.17 -10000 0 -0.62 16 16
NFAT1-c-4 (dimer)/EGR1 -0.12 0.33 -10000 0 -0.98 52 52
NFAT1-c-4 (dimer)/EGR4 -0.13 0.31 -10000 0 -0.94 50 50
FOS -0.026 0.13 -10000 0 -0.52 32 32
IFNG -0.092 0.23 -10000 0 -0.91 26 26
T cell activation 0.012 0.2 -10000 0 -0.77 13 13
MAF 0.009 0.023 -10000 0 -0.5 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.028 0.28 0.92 25 -10000 0 25
TNF -0.071 0.33 -10000 0 -0.92 51 51
FASLG -0.11 0.48 -10000 0 -1.3 61 61
TBX21 -0.015 0.11 -10000 0 -0.5 23 23
BATF3 0.009 0.024 -10000 0 -0.52 1 1
PRKCQ -0.065 0.18 -10000 0 -0.5 74 74
PTPN1 0.026 0.13 -10000 0 -0.74 7 7
NFAT1-c-4/ICER1 -0.11 0.3 -10000 0 -0.92 49 49
GATA3 0.008 0.04 -10000 0 -0.5 3 3
T-helper 1 cell differentiation -0.053 0.24 -10000 0 -0.89 26 26
IL2RA -0.12 0.22 -10000 0 -0.78 29 29
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.026 0.13 -10000 0 -0.74 7 7
E2F1 0.007 0.063 -10000 0 -0.51 7 7
PPARG -0.053 0.17 -10000 0 -0.5 61 61
SLC3A2 0.026 0.13 -10000 0 -0.74 7 7
IRF4 -0.007 0.093 -10000 0 -0.51 16 16
PTGS2 -0.087 0.37 -10000 0 -0.98 54 54
CSF2 -0.08 0.36 -10000 0 -0.95 53 53
JunB/Fra1/NFAT1-c-4 -0.11 0.3 -10000 0 -0.91 47 47
IL4 0.006 0.19 -10000 0 -0.89 12 12
IL5 -0.065 0.34 -10000 0 -0.91 49 49
IL2 0.011 0.2 -10000 0 -0.78 13 13
IL3 -0.026 0.046 -10000 0 -10000 0 0
RNF128 -0.08 0.24 -10000 0 -0.57 93 93
NFATC1 -0.029 0.28 -10000 0 -0.93 25 25
CDK4 0.007 0.17 0.57 18 -10000 0 18
PTPRK 0.026 0.13 -10000 0 -0.74 7 7
IL8 -0.071 0.35 -10000 0 -0.91 50 50
POU2F1 0.01 0.001 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.22 -10000 0 -0.64 19 19
CRP -0.15 0.23 -10000 0 -0.68 16 16
cell cycle arrest -0.17 0.25 -10000 0 -0.57 83 83
TIMP1 -0.11 0.19 -10000 0 -0.66 9 9
IL6ST -0.011 0.093 -10000 0 -0.5 17 17
Rac1/GDP -0.067 0.14 -10000 0 -0.42 24 24
AP1 0.001 0.09 -10000 0 -0.59 3 3
GAB2 0.008 0.046 -10000 0 -0.5 4 4
TNFSF11 -0.19 0.25 -10000 0 -0.64 45 45
HSP90B1 -0.004 0.044 -10000 0 -10000 0 0
GAB1 0.008 0.04 -10000 0 -0.5 3 3
MAPK14 -0.045 0.14 -10000 0 -0.52 17 17
AKT1 0.036 0.033 -10000 0 -10000 0 0
FOXO1 0.041 0.031 -10000 0 -10000 0 0
MAP2K6 -0.063 0.14 -10000 0 -0.47 20 20
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
MAP2K4 -0.08 0.16 -10000 0 -0.48 19 19
MITF -0.069 0.14 -10000 0 -0.35 55 55
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.01 0 -10000 0 -10000 0 0
A2M -0.081 0.34 -10000 0 -1.3 37 37
CEBPB 0.015 0.003 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.009 0.082 0.22 1 -0.5 4 5
STAT3 -0.17 0.26 -10000 0 -0.59 83 83
STAT1 -0.002 0.012 -10000 0 -10000 0 0
CEBPD -0.14 0.23 -10000 0 -0.69 19 19
PIK3CA 0.011 0 -10000 0 -10000 0 0
PI3K 0.015 0.017 -10000 0 -0.35 1 1
JUN 0.006 0.046 -10000 0 -0.5 4 4
PIAS3/MITF -0.059 0.14 -10000 0 -0.42 23 23
MAPK11 -0.047 0.14 -10000 0 -0.52 18 18
STAT3 (dimer)/FOXO1 -0.12 0.23 -10000 0 -0.65 29 29
GRB2/SOS1/GAB family -0.058 0.12 -10000 0 -0.44 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.064 0.15 -10000 0 -0.34 75 75
GRB2 0.011 0.004 -10000 0 -10000 0 0
JAK2 0.008 0.032 -10000 0 -0.5 2 2
LBP -0.13 0.2 -10000 0 -0.6 14 14
PIK3R1 0.01 0.023 -10000 0 -0.5 1 1
JAK1 0.009 0.005 -10000 0 -10000 0 0
MYC -0.14 0.23 -10000 0 -0.65 21 21
FGG -0.33 0.46 -10000 0 -0.99 148 148
macrophage differentiation -0.17 0.25 -10000 0 -0.57 83 83
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.071 0.12 -10000 0 -0.43 15 15
JUNB -0.14 0.22 -10000 0 -0.73 14 14
FOS -0.023 0.13 -10000 0 -0.5 32 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.076 0.14 -10000 0 -0.35 68 68
STAT1/PIAS1 -0.079 0.14 -10000 0 -0.34 61 61
GRB2/SOS1/GAB family/SHP2/PI3K 0.018 0.038 -10000 0 -0.26 2 2
STAT3 (dimer) -0.17 0.26 -10000 0 -0.59 83 83
PRKCD -0.095 0.18 -10000 0 -0.55 16 16
IL6R -0.002 0.076 -10000 0 -0.5 11 11
SOCS3 -0.035 0.16 -10000 0 -0.73 11 11
gp130 (dimer)/JAK1/JAK1/LMO4 0.001 0.061 -10000 0 -0.29 18 18
Rac1/GTP -0.078 0.15 -10000 0 -0.39 40 40
HCK -0.012 0.1 -10000 0 -0.5 21 21
MAPKKK cascade 0.009 0.08 -10000 0 -0.59 4 4
bone resorption -0.18 0.24 -10000 0 -0.61 45 45
IRF1 -0.14 0.22 -10000 0 -0.67 15 15
mol:GDP -0.07 0.14 -10000 0 -0.38 40 40
SOS1 0.012 0.006 -10000 0 -10000 0 0
VAV1 -0.071 0.15 -10000 0 -0.39 40 40
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.04 0.14 -10000 0 -0.5 20 20
PTPN11 -0.001 0.01 -10000 0 -10000 0 0
IL6/IL6RA -0.082 0.16 -10000 0 -0.36 120 120
gp130 (dimer)/TYK2/TYK2/LMO4 -0.001 0.059 -10000 0 -0.29 18 18
gp130 (dimer)/JAK2/JAK2/LMO4 -0.002 0.062 -10000 0 -0.29 20 20
IL6 -0.11 0.21 -10000 0 -0.5 111 111
PIAS3 0.01 0 -10000 0 -10000 0 0
PTPRE 0.012 0.034 -10000 0 -0.49 2 2
PIAS1 0.01 0 -10000 0 -10000 0 0
RAC1 0.009 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.066 0.13 -10000 0 -0.3 89 89
LMO4 0.006 0.024 -10000 0 -0.5 1 1
STAT3 (dimer)/PIAS3 -0.19 0.21 -10000 0 -0.58 64 64
MCL1 0.042 0.03 -10000 0 -10000 0 0
Aurora A signaling

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.011 0.069 -9999 0 -0.3 2 2
BIRC5 -0.29 0.26 -9999 0 -0.52 281 281
NFKBIA -0.009 0.067 -9999 0 -10000 0 0
CPEB1 -0.064 0.18 -9999 0 -0.5 70 70
AKT1 -0.009 0.067 -9999 0 -10000 0 0
NDEL1 0.01 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.017 0.063 -9999 0 -0.36 3 3
NDEL1/TACC3 -0.012 0.058 -9999 0 -0.38 2 2
GADD45A 0.008 0.033 -9999 0 -0.51 2 2
GSK3B 0.012 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.01 0.067 -9999 0 -10000 0 0
MDM2 0.008 0.034 -9999 0 -0.52 2 2
JUB 0.008 0.032 -9999 0 -0.5 2 2
TPX2 -0.19 0.19 -9999 0 -0.37 268 268
TP53 0.002 0.045 -9999 0 -10000 0 0
DLG7 -0.017 0.067 -9999 0 -10000 0 0
AURKAIP1 0.009 0.023 -9999 0 -0.5 1 1
ARHGEF7 0.01 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.013 0.061 -9999 0 -0.41 2 2
G2/M transition of mitotic cell cycle -0.017 0.063 -9999 0 -0.36 3 3
AURKA -0.019 0.083 -9999 0 -10000 0 0
AURKB -0.058 0.055 -9999 0 -10000 0 0
CDC25B -0.012 0.054 -9999 0 -0.22 1 1
G2/M transition checkpoint -0.017 0.06 -9999 0 -0.33 2 2
mRNA polyadenylation -0.056 0.12 -9999 0 -0.3 70 70
Aurora A/CPEB -0.056 0.12 -9999 0 -0.3 70 70
Aurora A/TACC1/TRAP/chTOG -0.017 0.075 -9999 0 -0.37 6 6
BRCA1 0.007 0.041 -9999 0 -0.52 3 3
centrosome duplication -0.01 0.067 -9999 0 -10000 0 0
regulation of centrosome cycle -0.013 0.057 -9999 0 -0.38 2 2
spindle assembly -0.018 0.073 -9999 0 -0.36 6 6
TDRD7 0.01 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.16 0.15 -9999 0 -0.37 91 91
CENPA -0.054 0.054 -9999 0 -10000 0 0
Aurora A/PP2A -0.01 0.067 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.004 0.051 -9999 0 -10000 0 0
negative regulation of DNA binding 0.002 0.045 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.017 0.06 -9999 0 -0.33 2 2
mitotic prometaphase 0.015 0.015 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.018 0.083 -9999 0 -10000 0 0
TACC1 -0.011 0.1 -9999 0 -0.5 20 20
TACC3 0.008 0.034 -9999 0 -0.52 2 2
Aurora A/Antizyme1 -0.012 0.058 -9999 0 -0.26 1 1
Aurora A/RasGAP -0.01 0.067 -9999 0 -10000 0 0
OAZ1 0.01 0 -9999 0 -10000 0 0
RAN 0.009 0.024 -9999 0 -0.52 1 1
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.003 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.19 0.19 -9999 0 -0.37 268 268
PPP2R5D 0.01 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.16 0.18 -9999 0 -0.32 268 268
PAK1 0.01 0 -9999 0 -10000 0 0
CKAP5 0.01 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.13 0.23 -9999 0 -0.5 132 132
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0 -9999 0 -10000 0 0
TCEB1 0.008 0.034 -9999 0 -0.52 2 2
HIF1A/p53 0.005 0.035 -9999 0 -10000 0 0
HIF1A -0.001 0.037 -9999 0 -10000 0 0
COPS5 0.01 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.016 -9999 0 -10000 0 0
FIH (dimer) 0.01 0 -9999 0 -10000 0 0
CDKN2A -0.15 0.24 -9999 0 -0.52 145 145
ARNT/IPAS -0.095 0.16 -9999 0 -0.35 132 132
HIF1AN 0.01 0 -9999 0 -10000 0 0
GNB2L1 0.01 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.005 0.035 -9999 0 -10000 0 0
CUL2 0.01 0 -9999 0 -10000 0 0
OS9 0.01 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.019 -9999 0 -0.3 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.005 0.035 -9999 0 -10000 0 0
PHD1-3/OS9 -0.069 0.12 -9999 0 -0.27 124 124
HIF1A/RACK1/Elongin B/Elongin C -0.011 0.023 -9999 0 -0.28 1 1
VHL 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.005 0.035 -9999 0 -10000 0 0
EGLN3 -0.12 0.23 -9999 0 -0.52 125 125
EGLN2 0.01 0 -9999 0 -10000 0 0
EGLN1 0.01 0 -9999 0 -10000 0 0
TP53 0.01 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.025 0.01 -9999 0 -10000 0 0
ARNT 0.01 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.01 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.071 0.13 -9999 0 -0.26 145 145
PDGFR-alpha signaling pathway

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
PDGFRA 0.005 0.047 -9999 0 -0.5 4 4
PDGF/PDGFRA/CRKL -0.003 0.031 -9999 0 -0.34 4 4
positive regulation of JUN kinase activity -0.003 0.025 -9999 0 -0.27 1 1
CRKL 0.01 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.084 0.15 -9999 0 -0.36 113 113
AP1 -0.06 0.22 -9999 0 -0.87 32 32
mol:IP3 0.014 0.037 -9999 0 -0.35 4 4
PLCG1 0.014 0.037 -9999 0 -0.35 4 4
PDGF/PDGFRA/alphaV Integrin -0.003 0.031 -9999 0 -0.34 4 4
RAPGEF1 0.01 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0.014 0.037 -9999 0 -0.35 4 4
CAV3 -0.11 0.21 -9999 0 -0.5 109 109
CAV1 -0.32 0.24 -9999 0 -0.5 313 313
SHC/Grb2/SOS1 -0.003 0.025 -9999 0 -0.27 1 1
PDGF/PDGFRA/Shf -0.005 0.039 -9999 0 -0.35 6 6
FOS -0.025 0.22 -9999 0 -0.86 32 32
JUN -0.007 0.035 -9999 0 -0.36 4 4
oligodendrocyte development -0.003 0.031 -9999 0 -0.34 4 4
GRB2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
mol:DAG 0.014 0.037 -9999 0 -0.35 4 4
PDGF/PDGFRA 0.005 0.047 -9999 0 -0.5 4 4
actin cytoskeleton reorganization -0.004 0.035 -9999 0 -0.35 5 5
SRF 0.018 0.006 -9999 0 -10000 0 0
SHC1 0.009 0.024 -9999 0 -0.52 1 1
PI3K -0.003 0.028 -9999 0 -0.28 5 5
PDGF/PDGFRA/Crk/C3G -0.002 0.025 -9999 0 -0.28 4 4
JAK1 0.015 0.033 -9999 0 -0.34 4 4
ELK1/SRF 0.027 0.028 -9999 0 -10000 0 0
SHB 0.009 0.023 -9999 0 -0.5 1 1
SHF 0.008 0.034 -9999 0 -0.52 2 2
CSNK2A1 0.004 0.014 -9999 0 -10000 0 0
GO:0007205 0.014 0.039 -9999 0 -0.37 4 4
SOS1 0.01 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.003 0.025 -9999 0 -0.27 1 1
PDGF/PDGFRA/SHB -0.004 0.035 -9999 0 -0.35 5 5
PDGF/PDGFRA/Caveolin-1 -0.23 0.18 -9999 0 -0.36 314 314
ITGAV 0.01 0 -9999 0 -10000 0 0
ELK1 0.018 0.04 -9999 0 -0.31 4 4
PIK3CA 0.01 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.003 0.031 -9999 0 -0.34 4 4
JAK-STAT cascade 0.015 0.033 -9999 0 -0.34 4 4
cell proliferation -0.005 0.039 -9999 0 -0.35 6 6
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.027 0.024 -9999 0 -10000 0 0
VDR 0.008 0.033 -9999 0 -0.51 2 2
FAM120B 0.01 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.094 0.14 -9999 0 -0.46 11 11
RXRs/LXRs/DNA/Oxysterols -0.075 0.14 -9999 0 -0.48 20 20
MED1 0.01 0 -9999 0 -10000 0 0
mol:9cRA 0.003 0.009 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.003 0.078 -9999 0 -0.46 1 1
RXRs/NUR77 -0.17 0.18 -9999 0 -0.48 63 63
RXRs/PPAR -0.13 0.16 -9999 0 -0.43 50 50
NCOR2 0.01 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.023 -9999 0 -0.37 2 2
RARs/VDR/DNA/Vit D3 -0.002 0.022 -9999 0 -0.24 4 4
RARA 0.01 0 -9999 0 -10000 0 0
NCOA1 0.01 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.008 0.033 -9999 0 -0.51 2 2
RARs/RARs/DNA/9cRA -0.001 0.016 -9999 0 -0.25 2 2
RARG 0.01 0 -9999 0 -10000 0 0
RPS6KB1 0.044 0.04 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.003 0.078 -9999 0 -0.46 1 1
THRA 0.01 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.023 -9999 0 -0.37 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.14 -9999 0 -0.37 11 11
NR1H4 -0.032 0.14 -9999 0 -0.52 35 35
RXRs/LXRs/DNA -0.097 0.14 -9999 0 -0.39 11 11
NR1H2 0.014 0.007 -9999 0 -10000 0 0
NR1H3 0.013 0.008 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.14 -9999 0 -0.32 13 13
NR4A1 -0.091 0.2 -9999 0 -0.5 97 97
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.1 0.12 -9999 0 -0.31 31 31
RXRG -0.26 0.25 -9999 0 -0.5 259 259
RXR alpha/CCPG 0.018 0.004 -9999 0 -10000 0 0
RXRA 0.013 0.007 -9999 0 -10000 0 0
RXRB 0.013 0.008 -9999 0 -10000 0 0
THRB -0.041 0.15 -9999 0 -0.5 49 49
PPARG -0.054 0.17 -9999 0 -0.5 61 61
PPARD 0.01 0 -9999 0 -10000 0 0
TNF -0.086 0.22 -9999 0 -1 19 19
mol:Oxysterols 0.003 0.009 -9999 0 -10000 0 0
cholesterol transport -0.075 0.14 -9999 0 -0.48 20 20
PPARA 0.01 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.008 0.032 -9999 0 -0.5 2 2
RXRs/NUR77/BCL2 -0.16 0.16 -9999 0 -0.26 306 306
SREBF1 -0.062 0.13 -9999 0 -0.53 11 11
RXRs/RXRs/DNA/9cRA -0.12 0.14 -9999 0 -0.37 11 11
ABCA1 -0.065 0.14 -9999 0 -0.61 12 12
RARs/THRs -0.025 0.074 -9999 0 -0.49 1 1
RXRs/FXR -0.14 0.16 -9999 0 -0.46 31 31
BCL2 0.007 0.041 -9999 0 -0.51 3 3
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.009 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.035 0.092 -10000 0 -0.27 65 65
regulation of S phase of mitotic cell cycle -0.009 0.085 -10000 0 -0.23 62 62
GNAO1 0.004 0.057 -10000 0 -0.51 6 6
HRAS 0.01 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.001 0.02 -10000 0 -0.32 2 2
PELP1 0.01 0.001 -10000 0 -10000 0 0
AKT1 0.009 0 -10000 0 -10000 0 0
MAP2K1 0.001 0.09 -10000 0 -0.31 12 12
T-DHT/AR -0.047 0.12 -10000 0 -0.36 64 64
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 32 32
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
mol:GDP -0.051 0.13 -10000 0 -0.4 62 62
cell proliferation 0 0.14 -10000 0 -0.42 32 32
PIK3CA 0.01 0 -10000 0 -10000 0 0
FOS -0.02 0.21 -10000 0 -0.79 32 32
mol:Ca2+ -0.01 0.022 -10000 0 -0.064 49 49
MAPK3 0.001 0.11 -10000 0 -0.45 12 12
MAPK1 0.005 0.067 -10000 0 -0.26 12 12
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
mol:IP3 0 0.001 -10000 0 -0.004 32 32
cAMP biosynthetic process 0.008 0.028 -10000 0 -0.31 2 2
GNG2 0.008 0.032 -10000 0 -0.5 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 32 32
HRAS/GTP -0.033 0.081 -10000 0 -0.28 13 13
actin cytoskeleton reorganization 0 0.01 -10000 0 -10000 0 0
SRC 0.01 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 32 32
PI3K -0.001 0.013 -10000 0 -0.3 1 1
apoptosis 0.001 0.12 0.43 32 -10000 0 32
T-DHT/AR/PELP1 -0.039 0.1 -10000 0 -0.3 64 64
HRAS/GDP -0.048 0.12 -10000 0 -0.37 62 62
CREB1 -0.003 0.13 -10000 0 -0.46 32 32
RAC1-CDC42/GTP 0 0.01 -10000 0 -10000 0 0
AR -0.057 0.17 -10000 0 -0.5 64 64
GNB1 0.01 0 -10000 0 -10000 0 0
RAF1 -0.004 0.089 -10000 0 -0.3 12 12
RAC1-CDC42/GDP -0.045 0.12 -10000 0 -0.35 62 62
T-DHT/AR/PELP1/Src -0.035 0.09 -10000 0 -0.27 64 64
MAP2K2 0.001 0.09 -10000 0 -0.31 12 12
T-DHT/AR/PELP1/Src/PI3K -0.009 0.086 -10000 0 -0.23 62 62
GNAZ -0.033 0.14 -10000 0 -0.5 41 41
SHBG 0.007 0.034 -10000 0 -0.52 2 2
Gi family/GNB1/GNG2/GDP 0.005 0.079 -10000 0 -0.39 4 4
mol:T-DHT 0 0.001 0.001 1 -0.003 20 21
RAC1 0.01 0 -10000 0 -10000 0 0
GNRH1 0.006 0.033 -10000 0 -0.36 4 4
Gi family/GTP -0.035 0.082 -10000 0 -0.25 44 44
CDC42 0.01 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.031 0.12 -9999 0 -0.47 16 16
FZD6 0.009 0.023 -9999 0 -0.5 1 1
WNT6 -0.021 0.12 -9999 0 -0.52 28 28
WNT4 -0.022 0.12 -9999 0 -0.5 30 30
FZD3 0.009 0.024 -9999 0 -0.52 1 1
WNT5A 0.005 0.051 -9999 0 -0.5 5 5
WNT11 -0.059 0.17 -9999 0 -0.5 66 66
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.012 0.1 0.5 21 -10000 0 21
PI3K Class IB/PDE3B -0.012 0.1 -10000 0 -0.5 21 21
PDE3B -0.012 0.1 -10000 0 -0.5 21 21
HIF-2-alpha transcription factor network

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
MMP14 -0.009 0.037 -10000 0 -10000 0 0
oxygen homeostasis 0 0.014 -10000 0 -10000 0 0
TCEB2 0.01 0 -10000 0 -10000 0 0
TCEB1 0.008 0.034 -10000 0 -0.52 2 2
VHL/Elongin B/Elongin C/HIF2A -0.069 0.12 -10000 0 -0.38 39 39
EPO -0.032 0.23 -10000 0 -0.66 15 15
FIH (dimer) 0.01 0.012 -10000 0 -10000 0 0
APEX1 0.012 0.012 -10000 0 -10000 0 0
SERPINE1 -0.054 0.26 -10000 0 -0.7 27 27
FLT1 -0.009 0.053 -10000 0 -0.89 1 1
ADORA2A -0.049 0.25 -10000 0 -0.65 26 26
germ cell development -0.066 0.26 -10000 0 -0.65 32 32
SLC11A2 -0.052 0.26 -10000 0 -0.67 26 26
BHLHE40 -0.052 0.26 -10000 0 -0.67 26 26
HIF1AN 0.01 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.091 0.15 -10000 0 -0.44 45 45
ETS1 0.021 0.025 -10000 0 -0.52 1 1
CITED2 -0.009 0.048 -10000 0 -0.96 1 1
KDR -0.033 0.18 -10000 0 -1.2 12 12
PGK1 -0.052 0.26 -10000 0 -0.66 27 27
SIRT1 0.01 0 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.066 0.29 -10000 0 -0.77 30 30
EPAS1 -0.047 0.17 -10000 0 -0.39 57 57
SP1 0.016 0.001 -10000 0 -10000 0 0
ABCG2 -0.078 0.3 -10000 0 -0.76 44 44
EFNA1 -0.052 0.26 -10000 0 -0.67 27 27
FXN -0.049 0.25 -10000 0 -0.65 26 26
POU5F1 -0.07 0.27 -10000 0 -0.68 32 32
neuron apoptosis 0.064 0.28 0.74 30 -10000 0 30
EP300 0.01 0 -10000 0 -10000 0 0
EGLN3 -0.13 0.24 -10000 0 -0.53 125 125
EGLN2 0.01 0.012 -10000 0 -10000 0 0
EGLN1 0.01 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.001 0.019 -10000 0 -0.3 2 2
VHL 0.01 0 -10000 0 -10000 0 0
ARNT 0.012 0.012 -10000 0 -10000 0 0
SLC2A1 -0.13 0.32 -10000 0 -0.65 84 84
TWIST1 -0.09 0.3 -10000 0 -0.67 59 59
ELK1 0.016 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.089 0.14 -10000 0 -0.44 43 43
VEGFA -0.052 0.26 -10000 0 -0.66 27 27
CREBBP 0.01 0 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 -0.011 0.063 -9999 0 -0.37 15 15
VLDLR -0.002 0.075 -9999 0 -0.5 11 11
CRKL 0.01 0 -9999 0 -10000 0 0
LRPAP1 0.01 0 -9999 0 -10000 0 0
FYN 0.009 0.023 -9999 0 -0.5 1 1
ITGA3 0.006 0.046 -9999 0 -0.5 4 4
RELN/VLDLR/Fyn -0.052 0.12 -9999 0 -0.31 81 81
MAPK8IP1/MKK7/MAP3K11/JNK1 0 0.011 -9999 0 -10000 0 0
AKT1 -0.015 0.097 -9999 0 -0.39 8 8
MAP2K7 0.01 0 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
DAB1 -0.003 0.067 -9999 0 -0.52 8 8
RELN/LRP8/DAB1 -0.052 0.11 -9999 0 -0.28 90 90
LRPAP1/LRP8 -0.008 0.054 -9999 0 -0.37 11 11
RELN/LRP8/DAB1/Fyn -0.048 0.1 -9999 0 -0.3 25 25
DAB1/alpha3/beta1 Integrin -0.048 0.1 -9999 0 -0.45 10 10
long-term memory -0.095 0.14 -9999 0 -0.51 25 25
DAB1/LIS1 -0.048 0.1 -9999 0 -0.47 9 9
DAB1/CRLK/C3G -0.046 0.098 -9999 0 -0.45 9 9
PIK3CA 0.01 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.049 0.1 -9999 0 -0.47 9 9
ARHGEF2 0.01 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.089 0.2 -9999 0 -0.51 93 93
CDK5R1 -0.006 0.091 -9999 0 -0.52 15 15
RELN -0.069 0.18 -9999 0 -0.5 75 75
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
RELN/LRP8/Fyn -0.052 0.11 -9999 0 -0.3 86 86
GRIN2A/RELN/LRP8/DAB1/Fyn -0.094 0.14 -9999 0 -0.52 21 21
MAPK8 0.01 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.052 0.12 -9999 0 -0.29 86 86
ITGB1 0.01 0 -9999 0 -10000 0 0
MAP1B -0.033 0.12 -9999 0 -0.48 12 12
RELN/LRP8 -0.052 0.11 -9999 0 -0.29 86 86
GRIN2B/RELN/LRP8/DAB1/Fyn -0.053 0.11 -9999 0 -0.51 10 10
PI3K -0.001 0.016 -9999 0 -0.35 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.032 -9999 0 -0.35 4 4
RAP1A -0.008 0.11 -9999 0 -0.42 9 9
PAFAH1B1 0.01 0 -9999 0 -10000 0 0
MAPK8IP1 0.01 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.009 0.074 -9999 0 -0.52 10 10
NCK2 0.01 0 -9999 0 -10000 0 0
neuron differentiation 0.001 0.072 -9999 0 -0.31 3 3
neuron adhesion 0.002 0.11 -9999 0 -0.4 10 10
LRP8 -0.002 0.078 -9999 0 -0.52 11 11
GSK3B -0.008 0.093 -9999 0 -0.38 7 7
RELN/VLDLR/DAB1/Fyn -0.048 0.11 -9999 0 -0.27 86 86
MAP3K11 0.009 0.023 -9999 0 -0.5 1 1
RELN/VLDLR/DAB1/P13K -0.023 0.1 -9999 0 -0.25 76 76
CDK5 0.01 0 -9999 0 -10000 0 0
MAPT -0.018 0.11 -9999 0 -0.46 27 27
neuron migration -0.01 0.13 -9999 0 -0.43 10 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.001 0.073 -9999 0 -0.31 3 3
RELN/VLDLR -0.052 0.11 -9999 0 -0.32 23 23
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.001 -9999 0 -10000 0 0
SMARCC1 0.003 0.006 -9999 0 -10000 0 0
REL 0.01 0.001 -9999 0 -10000 0 0
HDAC7 0.023 0.091 -9999 0 -0.41 5 5
JUN 0.006 0.046 -9999 0 -0.5 4 4
EP300 0.01 0 -9999 0 -10000 0 0
KAT2B 0.01 0 -9999 0 -10000 0 0
KAT5 0.01 0 -9999 0 -10000 0 0
MAPK14 0.004 0.075 -9999 0 -0.37 19 19
FOXO1 0.01 0 -9999 0 -10000 0 0
T-DHT/AR 0.02 0.096 -9999 0 -0.42 6 6
MAP2K6 -0.01 0.1 -9999 0 -0.52 19 19
BRM/BAF57 -0.003 0.032 -9999 0 -0.35 4 4
MAP2K4 0.01 0.004 -9999 0 -10000 0 0
SMARCA2 0.006 0.046 -9999 0 -0.5 4 4
PDE9A -0.045 0.17 -9999 0 -1.2 8 8
NCOA2 0.006 0.046 -9999 0 -0.5 4 4
CEBPA -0.016 0.11 -9999 0 -0.5 25 25
EHMT2 0.01 0.001 -9999 0 -10000 0 0
cell proliferation 0.019 0.13 -9999 0 -0.45 19 19
NR0B1 -0.1 0.21 -9999 0 -0.52 97 97
EGR1 -0.022 0.12 -9999 0 -0.5 31 31
RXRs/9cRA -0.14 0.13 -9999 0 -0.26 259 259
AR/RACK1/Src -0.002 0.067 -9999 0 -0.36 3 3
AR/GR -0.006 0.096 -9999 0 -0.3 24 24
GNB2L1 0.01 0.001 -9999 0 -10000 0 0
PKN1 0.01 0 -9999 0 -10000 0 0
RCHY1 0.01 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.019 0.009 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.003 0.07 -9999 0 -0.38 3 3
SRC 0.022 0.059 -9999 0 -0.29 5 5
NR3C1 0.01 0 -9999 0 -10000 0 0
KLK3 -0.066 0.1 -9999 0 -0.52 2 2
APPBP2 0.01 0.004 -9999 0 -10000 0 0
TRIM24 0.01 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.013 0.072 -9999 0 -0.4 3 3
TMPRSS2 -0.1 0.3 -9999 0 -1.1 40 40
RXRG -0.26 0.25 -9999 0 -0.5 259 259
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.01 0 -9999 0 -10000 0 0
RXRB 0.01 0 -9999 0 -10000 0 0
CARM1 0.01 0.002 -9999 0 -10000 0 0
NR2C2 0.01 0 -9999 0 -10000 0 0
KLK2 0.013 0.098 -9999 0 -0.4 8 8
AR -0.011 0.11 -9999 0 -0.33 27 27
SENP1 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
MDM2 0.008 0.034 -9999 0 -0.52 2 2
SRY 0.001 0.004 -9999 0 -10000 0 0
GATA2 -0.033 0.14 -9999 0 -0.5 41 41
MYST2 0.01 0 -9999 0 -10000 0 0
HOXB13 -0.19 0.25 -9999 0 -0.52 179 179
T-DHT/AR/RACK1/Src 0.018 0.071 -9999 0 -0.38 3 3
positive regulation of transcription -0.033 0.14 -9999 0 -0.5 41 41
DNAJA1 0.01 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.009 -9999 0 -10000 0 0
NCOA1 0.013 0.003 -9999 0 -10000 0 0
SPDEF -0.17 0.25 -9999 0 -0.52 167 167
T-DHT/AR/TIF2 0.027 0.052 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.013 0.072 -9999 0 -0.37 4 4
GSK3B 0.01 0.003 -9999 0 -10000 0 0
NR2C1 0.01 0 -9999 0 -10000 0 0
mol:T-DHT 0.017 0.063 -9999 0 -0.29 9 9
SIRT1 0.01 0 -9999 0 -10000 0 0
ZMIZ2 0.01 0.002 -9999 0 -10000 0 0
POU2F1 0.016 0.023 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.06 0.13 -9999 0 -0.38 33 33
CREBBP 0.01 0 -9999 0 -10000 0 0
SMARCE1 0.01 0.001 -9999 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.009 0.023 -9999 0 -0.5 1 1
PLK4 -0.018 0.12 -9999 0 -0.52 26 26
regulation of centriole replication -0.003 0.088 -9999 0 -0.37 27 27
Syndecan-4-mediated 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
PTK2 0.01 0.048 -9999 0 -0.48 4 4
Syndecan-4/Syndesmos -0.024 0.087 -9999 0 -0.53 2 2
positive regulation of JNK cascade -0.054 0.085 -9999 0 -0.35 15 15
Syndecan-4/ADAM12 -0.11 0.16 -9999 0 -0.38 88 88
CCL5 0.005 0.051 -9999 0 -0.5 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.01 0 -9999 0 -10000 0 0
ITGA5 0.008 0.033 -9999 0 -0.51 2 2
SDCBP 0.01 0 -9999 0 -10000 0 0
PLG -0.006 0.072 -9999 0 -0.52 9 9
ADAM12 -0.17 0.25 -9999 0 -0.52 166 166
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.036 0.05 -9999 0 -0.16 1 1
Syndecan-4/Laminin alpha1 -0.037 0.11 -9999 0 -0.41 14 14
Syndecan-4/CXCL12/CXCR4 -0.033 0.1 -9999 0 -0.37 14 14
Syndecan-4/Laminin alpha3 -0.073 0.13 -9999 0 -0.37 37 37
MDK -0.15 0.24 -9999 0 -0.52 151 151
Syndecan-4/FZD7 -0.024 0.089 -9999 0 -0.47 3 3
Syndecan-4/Midkine -0.1 0.15 -9999 0 -0.38 57 57
FZD7 0.009 0.023 -9999 0 -0.5 1 1
Syndecan-4/FGFR1/FGF -0.07 0.11 -9999 0 -0.48 10 10
THBS1 0.007 0.04 -9999 0 -0.5 3 3
integrin-mediated signaling pathway -0.04 0.11 -9999 0 -0.41 11 11
positive regulation of MAPKKK cascade -0.054 0.085 -9999 0 -0.35 15 15
Syndecan-4/TACI -0.044 0.12 -9999 0 -0.39 23 23
CXCR4 0.01 0 -9999 0 -10000 0 0
cell adhesion 0.007 0.039 -9999 0 -0.33 4 4
Syndecan-4/Dynamin -0.024 0.087 -9999 0 -0.53 2 2
Syndecan-4/TSP1 -0.025 0.092 -9999 0 -0.63 2 2
Syndecan-4/GIPC -0.024 0.087 -9999 0 -0.53 2 2
Syndecan-4/RANTES -0.026 0.089 -9999 0 -0.53 2 2
ITGB1 0.01 0 -9999 0 -10000 0 0
LAMA1 -0.018 0.12 -9999 0 -0.51 26 26
LAMA3 -0.093 0.2 -9999 0 -0.5 99 99
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA 0.016 0.04 -9999 0 -0.46 2 2
Syndecan-4/alpha-Actinin -0.024 0.087 -9999 0 -0.53 2 2
TFPI -0.012 0.1 -9999 0 -0.5 21 21
F2 -0.073 0.18 -9999 0 -0.52 71 71
alpha5/beta1 Integrin -0.001 0.023 -9999 0 -0.36 2 2
positive regulation of cell adhesion -0.078 0.14 -9999 0 -0.39 32 32
ACTN1 0.01 0 -9999 0 -10000 0 0
TNC -0.028 0.14 -9999 0 -0.51 35 35
Syndecan-4/CXCL12 -0.039 0.11 -9999 0 -0.39 15 15
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
CXCL12 -0.022 0.12 -9999 0 -0.5 31 31
TNFRSF13B -0.033 0.14 -9999 0 -0.51 40 40
FGF2 -0.059 0.17 -9999 0 -0.5 66 66
FGFR1 0.007 0.04 -9999 0 -0.5 3 3
Syndecan-4/PI-4-5-P2 -0.03 0.087 -9999 0 -0.53 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.007 0.051 -9999 0 -0.49 5 5
cell migration -0.015 0.021 -9999 0 -10000 0 0
PRKCD 0.012 0.006 -9999 0 -10000 0 0
vasculogenesis -0.024 0.089 -9999 0 -0.6 2 2
SDC4 -0.031 0.091 -9999 0 -0.56 2 2
Syndecan-4/Tenascin C -0.042 0.11 -9999 0 -0.42 11 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.04 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.024 0.087 -9999 0 -0.53 2 2
MMP9 -0.098 0.21 -9999 0 -0.52 99 99
Rac1/GTP 0.005 0.039 -9999 0 -0.34 4 4
cytoskeleton organization -0.023 0.085 -9999 0 -0.51 2 2
GIPC1 0.01 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.034 0.1 -9999 0 -0.43 7 7
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.001 -9999 0 -10000 0 0
SVIL 0.01 0.001 -9999 0 -10000 0 0
ZNF318 0.009 0.007 -9999 0 -10000 0 0
JMJD2C -0.001 0.018 -9999 0 -0.079 24 24
T-DHT/AR/Ubc9 -0.036 0.12 -9999 0 -0.33 64 64
CARM1 0.01 0 -9999 0 -10000 0 0
PRDX1 0.009 0.024 -9999 0 -0.52 1 1
PELP1 0.01 0.001 -9999 0 -10000 0 0
CTNNB1 0.01 0.001 -9999 0 -10000 0 0
AKT1 0.01 0.002 -9999 0 -10000 0 0
PTK2B 0.008 0.033 -9999 0 -0.5 2 2
MED1 0.01 0.002 -9999 0 -10000 0 0
MAK -0.007 0.088 -9999 0 -0.5 15 15
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.005 0.051 -9999 0 -0.5 5 5
GSN 0.01 0.001 -9999 0 -10000 0 0
NCOA2 0.006 0.046 -9999 0 -0.5 4 4
NCOA6 0.01 0.001 -9999 0 -10000 0 0
DNA-PK 0.001 0.009 -9999 0 -10000 0 0
NCOA4 0.01 0 -9999 0 -10000 0 0
PIAS3 0.01 0.001 -9999 0 -10000 0 0
cell proliferation -0.034 0.13 -9999 0 -0.73 15 15
XRCC5 0.01 0.001 -9999 0 -10000 0 0
UBE3A 0.01 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.048 0.13 -9999 0 -0.33 81 81
FHL2 -0.053 0.14 -9999 0 -0.44 22 22
RANBP9 0.01 0.001 -9999 0 -10000 0 0
JMJD1A 0 0.04 -9999 0 -0.12 45 45
CDK6 0.007 0.04 -9999 0 -0.5 3 3
TGFB1I1 0.007 0.04 -9999 0 -0.5 3 3
T-DHT/AR/CyclinD1 -0.039 0.12 -9999 0 -0.33 69 69
XRCC6 0.01 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.038 0.14 -9999 0 -0.34 73 73
CTDSP1 0.01 0.001 -9999 0 -10000 0 0
CTDSP2 0.01 0.004 -9999 0 -10000 0 0
BRCA1 0.007 0.041 -9999 0 -0.52 3 3
TCF4 0.008 0.033 -9999 0 -0.5 2 2
CDKN2A -0.15 0.24 -9999 0 -0.52 145 145
SRF 0.005 0.027 -9999 0 -10000 0 0
NKX3-1 -0.045 0.13 -9999 0 -0.94 6 6
KLK3 0.016 0.047 -9999 0 -10000 0 0
TMF1 0.01 0.001 -9999 0 -10000 0 0
HNRNPA1 0.01 0.002 -9999 0 -10000 0 0
AOF2 0 0.003 -9999 0 -10000 0 0
APPL1 0.018 0.004 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.039 0.12 -9999 0 -0.33 65 65
AR -0.064 0.18 -9999 0 -0.52 64 64
UBA3 0.01 0.001 -9999 0 -10000 0 0
PATZ1 0.01 0.002 -9999 0 -10000 0 0
PAWR 0.01 0.001 -9999 0 -10000 0 0
PRKDC 0.01 0.001 -9999 0 -10000 0 0
PA2G4 0.01 0.003 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.031 0.11 -9999 0 -0.3 64 64
RPS6KA3 0.01 0.001 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.035 0.12 -9999 0 -0.33 64 64
LATS2 0.01 0.002 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.033 0.11 -9999 0 -0.3 64 64
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0.004 0.057 -9999 0 -0.5 6 6
KLK2 -0.042 0.091 -9999 0 -0.44 10 10
CASP8 0.009 0.023 -9999 0 -0.5 1 1
T-DHT/AR/TIF2/CARM1 -0.027 0.11 -9999 0 -0.29 68 68
TMPRSS2 -0.096 0.27 -9999 0 -0.98 40 40
CCND1 0.004 0.056 -9999 0 -0.5 6 6
PIAS1 0.01 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.007 0.026 -9999 0 -0.079 34 34
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.01 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.038 0.12 -9999 0 -0.33 67 67
CMTM2 -0.091 0.2 -9999 0 -0.5 97 97
SNURF -0.01 0.098 -9999 0 -0.5 19 19
ZMIZ1 0.004 0.023 -9999 0 -10000 0 0
CCND3 0.01 0 -9999 0 -10000 0 0
TGIF1 0.01 0.002 -9999 0 -10000 0 0
FKBP4 0.009 0.024 -9999 0 -0.52 1 1
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.014 0.045 -9999 0 -0.33 8 8
EPHB2 -0.047 0.16 -9999 0 -0.52 53 53
Syndecan-2/TACI -0.01 0.092 -9999 0 -0.3 44 44
LAMA1 -0.018 0.12 -9999 0 -0.51 26 26
Syndecan-2/alpha2 ITGB1 -0.058 0.11 -9999 0 -0.33 16 16
HRAS 0.01 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.002 0.027 -9999 0 -0.3 4 4
ITGA5 0.008 0.033 -9999 0 -0.51 2 2
BAX 0.03 0.025 -9999 0 -10000 0 0
EPB41 0.01 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.024 -9999 0 -0.26 4 4
LAMA3 -0.093 0.2 -9999 0 -0.5 99 99
EZR 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.096 0.21 -9999 0 -0.5 102 102
Syndecan-2/MMP2 0.016 0.031 -9999 0 -0.29 5 5
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.011 0.063 -9999 0 -0.36 15 15
dendrite morphogenesis -0.019 0.1 -9999 0 -0.3 57 57
Syndecan-2/GM-CSF -0.01 0.092 -9999 0 -0.3 44 44
determination of left/right symmetry 0.013 0.033 -9999 0 -0.35 4 4
Syndecan-2/PKC delta 0.017 0.028 -9999 0 -0.29 4 4
GNB2L1 0.01 0 -9999 0 -10000 0 0
MAPK3 -0.001 0.084 -9999 0 -0.26 44 44
MAPK1 -0.001 0.084 -9999 0 -0.26 44 44
Syndecan-2/RACK1 -0.002 0.022 -9999 0 -10000 0 0
NF1 0.01 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.013 0.033 -9999 0 -0.35 4 4
ITGA2 -0.006 0.091 -9999 0 -0.52 15 15
MAPK8 0.025 0.028 -9999 0 -0.28 4 4
Syndecan-2/alpha2/beta1 Integrin -0.023 0.08 -9999 0 -0.29 30 30
Syndecan-2/Kininogen -0.014 0.082 -9999 0 -0.3 36 36
ITGB1 0.01 0 -9999 0 -10000 0 0
SRC 0.027 0.023 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 -0.002 0.024 -9999 0 -0.26 4 4
extracellular matrix organization 0.017 0.028 -9999 0 -0.29 4 4
actin cytoskeleton reorganization 0.014 0.045 -9999 0 -0.33 8 8
Syndecan-2/Caveolin-2/Ras -0.056 0.11 -9999 0 -10000 0 0
Syndecan-2/Laminin alpha3 -0.046 0.13 -9999 0 -0.29 103 103
Syndecan-2/RasGAP -0.002 0.02 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.001 0.023 -9999 0 -0.36 2 2
PRKCD 0.01 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.019 0.1 -9999 0 -0.3 57 57
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.032 0.022 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
SDCBP 0.01 0 -9999 0 -10000 0 0
TNFRSF13B -0.033 0.14 -9999 0 -0.51 40 40
RASA1 0.01 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.011 0.063 -9999 0 -0.36 15 15
Syndecan-2/Synbindin 0.017 0.028 -9999 0 -0.29 4 4
TGFB1 0.01 0 -9999 0 -10000 0 0
CASP3 0.023 0.025 -9999 0 -0.26 4 4
FN1 0.005 0.052 -9999 0 -0.5 5 5
Syndecan-2/IL8 0.003 0.071 -9999 0 -0.3 25 25
SDC2 0.013 0.033 -9999 0 -0.35 4 4
KNG1 -0.03 0.13 -9999 0 -0.52 32 32
Syndecan-2/Neurofibromin 0.017 0.028 -9999 0 -0.29 4 4
TRAPPC4 0.01 0 -9999 0 -10000 0 0
CSF2 -0.033 0.14 -9999 0 -0.5 41 41
Syndecan-2/TGFB1 0.017 0.028 -9999 0 -0.29 4 4
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.024 -9999 0 -0.26 4 4
Syndecan-2/Ezrin -0.002 0.023 -9999 0 -0.26 4 4
PRKACA 0.023 0.025 -9999 0 -0.26 4 4
angiogenesis 0.003 0.07 -9999 0 -0.3 25 25
MMP2 0.009 0.024 -9999 0 -0.52 1 1
IL8 -0.013 0.11 -9999 0 -0.51 21 21
calcineurin-NFAT signaling pathway -0.01 0.092 -9999 0 -0.3 44 44
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.023 -9999 0 -0.5 1 1
alphaV beta3 Integrin -0.02 0.083 -9999 0 -0.36 27 27
PTK2 -0.037 0.11 -9999 0 -0.39 35 35
positive regulation of JNK cascade -0.021 0.074 -9999 0 -0.29 35 35
CDC42/GDP 0.012 0.11 -9999 0 -0.38 35 35
Rac1/GDP 0.013 0.11 -9999 0 -0.38 35 35
RAP1B 0.01 0 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP -0.026 0.091 -9999 0 -0.35 35 35
nectin-3/I-afadin -0.026 0.092 -9999 0 -0.35 36 36
RAPGEF1 0.006 0.12 -9999 0 -0.42 35 35
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.002 0.14 -9999 0 -0.48 35 35
PDGFB-D/PDGFRB 0.009 0.023 -9999 0 -0.5 1 1
TLN1 0.002 0.09 -9999 0 -0.42 15 15
Rap1/GTP -0.022 0.078 -9999 0 -0.3 35 35
IQGAP1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.026 0.092 -9999 0 -0.35 36 36
PVR 0.01 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.01 0 -9999 0 -10000 0 0
mol:GDP 0.006 0.13 -9999 0 -0.46 35 35
MLLT4 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.018 0.067 -9999 0 -0.49 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.008 0.054 -9999 0 -0.37 11 11
positive regulation of lamellipodium assembly -0.023 0.079 -9999 0 -0.3 36 36
PVRL1 -0.002 0.078 -9999 0 -0.52 11 11
PVRL3 -0.028 0.13 -9999 0 -0.5 36 36
PVRL2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
CDH1 0.008 0.032 -9999 0 -0.5 2 2
CLDN1 -0.009 0.098 -9999 0 -0.51 18 18
JAM-A/CLDN1 -0.029 0.089 -9999 0 -0.52 4 4
SRC -0.041 0.14 -9999 0 -0.54 35 35
ITGB3 -0.019 0.12 -9999 0 -0.51 27 27
nectin-1(dimer)/I-afadin/I-afadin -0.008 0.054 -9999 0 -0.37 11 11
FARP2 0.002 0.13 -9999 0 -0.46 35 35
RAC1 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.021 0.076 -9999 0 -0.29 36 36
nectin-1/I-afadin -0.008 0.054 -9999 0 -0.37 11 11
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.028 0.089 -9999 0 -0.3 46 46
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.009 0.023 -9999 0 -0.5 1 1
positive regulation of filopodium formation -0.021 0.074 -9999 0 -0.29 35 35
alphaV/beta3 Integrin/Talin -0.001 0.1 -9999 0 -0.39 17 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C -0.004 0.093 -9999 0 -0.44 15 15
VAV2 0 0.13 -9999 0 -0.47 36 36
RAP1/GDP -0.026 0.091 -9999 0 -0.35 35 35
ITGAV 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.021 0.076 -9999 0 -0.29 36 36
nectin-3(dimer)/I-afadin/I-afadin -0.026 0.092 -9999 0 -0.35 36 36
Rac1/GTP -0.028 0.095 -9999 0 -0.36 36 36
PTPRM -0.026 0.097 -9999 0 -0.48 15 15
E-cadherin/beta catenin/alpha catenin -0.006 0.037 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.04 0.11 0.36 54 -10000 0 54
KIRREL -0.008 0.085 -10000 0 -0.5 14 14
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.04 0.11 -10000 0 -0.36 54 54
PLCG1 0.01 0 -10000 0 -10000 0 0
ARRB2 0.01 0 -10000 0 -10000 0 0
WASL 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.028 0.079 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.006 0.057 -10000 0 -10000 0 0
FYN -0.011 0.076 -10000 0 -0.24 14 14
mol:Ca2+ -0.028 0.078 -10000 0 -0.25 13 13
mol:DAG -0.028 0.079 -10000 0 -0.25 13 13
NPHS2 -0.002 0.015 -10000 0 -10000 0 0
mol:IP3 -0.028 0.079 -10000 0 -0.25 13 13
regulation of endocytosis -0.023 0.065 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol -0.029 0.081 -10000 0 -0.26 54 54
establishment of cell polarity -0.04 0.11 -10000 0 -0.36 54 54
Nephrin/NEPH1/podocin/NCK1-2 -0.025 0.07 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 -0.01 0.071 -10000 0 -10000 0 0
NPHS1 -0.035 0.14 -10000 0 -0.51 40 40
Nephrin/NEPH1/podocin -0.025 0.071 -10000 0 -0.24 14 14
TJP1 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
NCK2 0.01 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.028 0.079 -10000 0 -0.26 13 13
CD2AP 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.028 0.079 -10000 0 -0.26 4 4
GRB2 0.01 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.028 0.1 -10000 0 -0.26 79 79
cytoskeleton organization 0.008 0.066 -10000 0 -10000 0 0
Nephrin/NEPH1 -0.028 0.078 -10000 0 -0.25 54 54
Nephrin/NEPH1/ZO-1 -0.031 0.087 -10000 0 -0.28 54 54
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.011 0.1 -9999 0 -0.5 20 20
GNB1/GNG2 -0.047 0.1 -9999 0 -0.43 16 16
mol:DAG -0.009 0.11 -9999 0 -0.39 16 16
PLCG1 -0.01 0.11 -9999 0 -0.4 16 16
YES1 -0.022 0.12 -9999 0 -0.44 16 16
FZD3 0.009 0.024 -9999 0 -0.52 1 1
FZD6 0.009 0.023 -9999 0 -0.5 1 1
G protein -0.041 0.096 -9999 0 -0.41 16 16
MAP3K7 -0.017 0.12 -9999 0 -0.38 29 29
mol:Ca2+ -0.009 0.1 -9999 0 -0.38 16 16
mol:IP3 -0.009 0.11 -9999 0 -0.39 16 16
NLK -0.002 0.006 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
CAMK2A -0.025 0.13 -9999 0 -0.42 30 30
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.031 0.12 -9999 0 -0.47 16 16
CSNK1A1 0.01 0 -9999 0 -10000 0 0
GNAS -0.022 0.12 -9999 0 -0.44 16 16
GO:0007205 -0.009 0.1 -9999 0 -0.39 16 16
WNT6 -0.021 0.12 -9999 0 -0.52 28 28
WNT4 -0.022 0.12 -9999 0 -0.5 30 30
NFAT1/CK1 alpha -0.049 0.099 -9999 0 -0.42 17 17
GNG2 0.008 0.032 -9999 0 -0.5 2 2
WNT5A 0.005 0.051 -9999 0 -0.5 5 5
WNT11 -0.059 0.17 -9999 0 -0.5 66 66
CDC42 -0.015 0.11 -9999 0 -0.41 16 16
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.024 0.093 -10000 0 -0.35 12 12
TBX21 -0.008 0.34 -10000 0 -1.2 30 30
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.001 0.094 -10000 0 -0.52 15 15
GADD45B 0.013 0.28 -10000 0 -1 20 20
IL12RB2 -0.026 0.15 -10000 0 -0.51 41 41
GADD45G 0.014 0.27 -10000 0 -1 21 21
natural killer cell activation 0.008 0.016 -10000 0 -10000 0 0
RELB 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL18 0.005 0.07 -10000 0 -0.5 9 9
IL2RA -0.028 0.14 -10000 0 -0.52 35 35
IFNG -0.034 0.14 -10000 0 -0.51 40 40
STAT3 (dimer) 0.025 0.23 -10000 0 -0.79 21 21
HLA-DRB5 -0.044 0.16 -10000 0 -0.5 52 52
FASLG 0.012 0.29 -10000 0 -1 22 22
NF kappa B2 p52/RelB -0.083 0.22 -10000 0 -0.88 25 25
CD4 0 0.072 -10000 0 -0.5 10 10
SOCS1 0.009 0.024 -10000 0 -0.52 1 1
EntrezGene:6955 0 0.008 -10000 0 -10000 0 0
CD3D 0.008 0.041 -10000 0 -0.5 3 3
CD3E 0.006 0.052 -10000 0 -0.5 5 5
CD3G 0 0.076 -10000 0 -0.5 11 11
IL12Rbeta2/JAK2 -0.004 0.11 -10000 0 -0.36 43 43
CCL3 0.016 0.27 -10000 0 -0.96 22 22
CCL4 0.015 0.28 -10000 0 -1 22 22
HLA-A 0.011 0.004 -10000 0 -10000 0 0
IL18/IL18R 0.018 0.12 -10000 0 -0.36 39 39
NOS2 -0.044 0.41 -10000 0 -1.2 50 50
IL12/IL12R/TYK2/JAK2/SPHK2 0.024 0.094 -10000 0 -0.35 12 12
IL1R1 0.016 0.28 -10000 0 -1 21 21
IL4 -0.004 0.017 -10000 0 -10000 0 0
JAK2 0.015 0.036 -10000 0 -0.5 2 2
EntrezGene:6957 0 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.013 0.16 -10000 0 -0.87 11 11
RAB7A 0.035 0.23 -10000 0 -0.82 15 15
lysosomal transport 0.037 0.22 -10000 0 -0.76 16 16
FOS -0.048 0.35 -10000 0 -1.1 42 42
STAT4 (dimer) 0.034 0.26 -10000 0 -0.87 22 22
STAT5A (dimer) -0.097 0.23 -10000 0 -0.84 31 31
GZMA 0.013 0.28 -10000 0 -1.1 21 21
GZMB -0.001 0.32 -10000 0 -1.2 26 26
HLX 0.005 0.052 -10000 0 -0.5 5 5
LCK 0.014 0.29 -10000 0 -1 23 23
TCR/CD3/MHC II/CD4 -0.023 0.17 -10000 0 -0.55 30 30
IL2/IL2R -0.023 0.081 -10000 0 -0.28 40 40
MAPK14 0.021 0.27 -10000 0 -0.93 22 22
CCR5 0.016 0.26 -10000 0 -1 18 18
IL1B -0.012 0.12 -10000 0 -0.5 28 28
STAT6 0.028 0.085 -10000 0 -0.26 4 4
STAT4 0.01 0 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
STAT1 0.01 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
NFKB2 0.01 0 -10000 0 -10000 0 0
IL12B 0.013 0.057 -10000 0 -0.53 5 5
CD8A 0.004 0.061 -10000 0 -0.5 7 7
CD8B 0.003 0.066 -10000 0 -0.5 8 8
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.024 0.093 0.34 12 -10000 0 12
IL2RB 0.008 0.032 -10000 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.24 -10000 0 -0.78 22 22
IL2RG 0.005 0.051 -10000 0 -0.5 5 5
IL12 0.021 0.064 -10000 0 -0.37 11 11
STAT5A 0.009 0.023 -10000 0 -0.5 1 1
CD247 0.005 0.057 -10000 0 -0.5 6 6
IL2 0.006 0.005 -10000 0 -10000 0 0
SPHK2 0.009 0.023 -10000 0 -0.5 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.011 0.06 -10000 0 -0.51 6 6
IL12/IL12R/TYK2/JAK2 0.009 0.32 -10000 0 -1 26 26
MAP2K3 0.018 0.28 -10000 0 -0.96 21 21
RIPK2 0.01 0 -10000 0 -10000 0 0
MAP2K6 0.016 0.28 -10000 0 -0.93 23 23
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.011 0.1 -10000 0 -0.5 20 20
IL18RAP -0.005 0.098 -10000 0 -0.5 18 18
IL12Rbeta1/TYK2 0.014 0.072 -10000 0 -0.37 15 15
EOMES -0.007 0.14 -10000 0 -1.2 6 6
STAT1 (dimer) 0.018 0.24 -10000 0 -0.78 22 22
T cell proliferation 0.03 0.21 -10000 0 -0.68 19 19
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.008 0.1 -10000 0 -0.5 21 21
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.077 0.18 -10000 0 -0.73 21 21
ATF2 0.029 0.25 -10000 0 -0.87 20 20
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.01 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.029 0.073 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.008 0.044 -9999 0 -0.25 15 15
POMC -0.014 0.11 -9999 0 -0.5 23 23
EGFR -0.005 0.086 -9999 0 -0.51 14 14
Syndecan-3/EGFR -0.007 0.041 -9999 0 -0.25 7 7
AGRP -0.2 0.25 -9999 0 -0.5 203 203
NCSTN 0.01 0 -9999 0 -10000 0 0
PSENEN 0.009 0.024 -9999 0 -0.52 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.008 0.032 -9999 0 -0.5 2 2
APH1A 0.01 0 -9999 0 -10000 0 0
NCAN -0.01 0.091 -9999 0 -0.52 15 15
long-term memory -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.011 0.05 -9999 0 -0.25 17 17
PSEN1 0.01 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.009 0.023 -9999 0 -0.5 1 1
limb bud formation 0 0.004 -9999 0 -10000 0 0
MC4R -0.032 0.14 -9999 0 -0.52 36 36
SRC 0.01 0 -9999 0 -10000 0 0
PTN -0.059 0.17 -9999 0 -0.5 66 66
FGFR/FGF/Syndecan-3 0 0.004 -9999 0 -10000 0 0
neuron projection morphogenesis -0.034 0.082 -9999 0 -0.44 4 4
Syndecan-3/AgRP -0.099 0.12 -9999 0 -0.3 2 2
Syndecan-3/AgRP/MC4R -0.11 0.13 -9999 0 -0.45 16 16
Fyn/Cortactin -0.001 0.016 -9999 0 -0.35 1 1
SDC3 0 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.011 0.05 -9999 0 -0.25 17 17
IL8 -0.013 0.11 -9999 0 -0.51 21 21
Syndecan-3/Fyn/Cortactin -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.044 0.12 -9999 0 -0.38 56 56
Gamma Secretase -0.001 0.019 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.004 0.084 -10000 0 -0.29 33 33
ACTA1 -0.008 0.1 -10000 0 -0.36 34 34
NUMA1 0.004 0.084 -10000 0 -0.33 16 16
SPTAN1 -0.004 0.1 -10000 0 -0.36 34 34
LIMK1 -0.004 0.1 -10000 0 -0.36 34 34
BIRC3 0.004 0.057 -10000 0 -0.51 6 6
BIRC2 0.01 0 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
CASP10 -0.002 0.096 -10000 0 -0.33 36 36
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0 -10000 0 -10000 0 0
PTK2 0.004 0.084 -10000 0 -0.29 33 33
DIABLO 0.01 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.1 -10000 0 -0.35 34 34
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.009 0.024 -10000 0 -0.52 1 1
GSN -0.004 0.1 -10000 0 -0.36 34 34
MADD 0.01 0 -10000 0 -10000 0 0
TFAP2A -0.041 0.12 -10000 0 -0.64 18 18
BID 0.004 0.057 -10000 0 -0.2 35 35
MAP3K1 0.004 0.038 -10000 0 -0.2 5 5
TRADD 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.002 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.004 0.1 -10000 0 -0.36 34 34
CASP9 0.01 0 -10000 0 -10000 0 0
DNA repair -0.002 0.028 -10000 0 -10000 0 0
neuron apoptosis 0.017 0.021 -10000 0 -0.35 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.1 -10000 0 -0.34 33 33
APAF1 0.01 0 -10000 0 -10000 0 0
CASP6 0.016 0.052 -10000 0 -0.32 1 1
TRAF2 0.01 0 -10000 0 -10000 0 0
ICAD/CAD 0.002 0.1 -10000 0 -0.34 33 33
CASP7 -0.005 0.028 0.22 6 -10000 0 6
KRT18 0.012 0.017 -10000 0 -10000 0 0
apoptosis 0.006 0.091 -10000 0 -0.52 6 6
DFFA -0.004 0.1 -10000 0 -0.36 34 34
DFFB -0.004 0.1 -10000 0 -0.36 34 34
PARP1 0.002 0.028 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.097 0.33 32 -10000 0 32
TNF -0.01 0.099 -10000 0 -0.5 19 19
CYCS 0.008 0.041 -10000 0 -0.22 5 5
SATB1 0.016 0.066 -10000 0 -0.4 3 3
SLK -0.004 0.1 -10000 0 -0.36 34 34
p15 BID/BAX 0.009 0.051 -10000 0 -0.28 5 5
CASP2 0.03 0.043 -10000 0 -10000 0 0
JNK cascade -0.004 0.037 0.2 5 -10000 0 5
CASP3 -0.011 0.11 -10000 0 -0.38 34 34
LMNB2 0.029 0.037 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
CASP4 0.01 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.003 0.029 -10000 0 -0.27 4 4
negative regulation of DNA binding -0.041 0.12 -10000 0 -0.63 18 18
stress fiber formation -0.004 0.1 -10000 0 -0.35 34 34
GZMB -0.011 0.11 -10000 0 -0.4 34 34
CASP1 0.01 0.033 -10000 0 -0.31 5 5
LMNB1 0.029 0.038 -10000 0 -0.22 1 1
APP 0.017 0.021 -10000 0 -0.35 1 1
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.017 -10000 0 -0.36 1 1
VIM 0.002 0.089 -10000 0 -0.3 33 33
LMNA 0.029 0.037 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.025 0.045 -10000 0 -10000 0 0
LRDD 0.008 0.032 -10000 0 -0.5 2 2
SREBF1 -0.004 0.1 -10000 0 -0.36 34 34
APAF-1/Caspase 9 -0.003 0.016 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.004 0.083 -10000 0 -0.28 33 33
CFL2 0.002 0.099 -10000 0 -0.34 32 32
GAS2 -0.018 0.12 -10000 0 -0.37 35 35
positive regulation of apoptosis 0.032 0.037 -10000 0 -10000 0 0
PRF1 -0.014 0.11 -10000 0 -0.5 23 23
Signaling events mediated by PTP1B

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 0.009 0.023 -10000 0 -0.5 1 1
Jak2/Leptin Receptor -0.038 0.094 0.18 1 -0.36 19 20
PTP1B/AKT1 0.011 0.037 -10000 0 -0.22 1 1
FYN 0.009 0.023 -10000 0 -0.5 1 1
p210 bcr-abl/PTP1B 0.006 0.041 -10000 0 -0.23 2 2
EGFR -0.006 0.087 -10000 0 -0.51 14 14
EGF/EGFR -0.049 0.09 -10000 0 -0.29 20 20
CSF1 0.005 0.051 -10000 0 -0.5 5 5
AKT1 0.01 0.001 -10000 0 -10000 0 0
INSR 0.01 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.019 0.094 -10000 0 -0.26 56 56
Insulin Receptor/Insulin -0.006 0.021 -10000 0 -10000 0 0
HCK -0.012 0.1 -10000 0 -0.5 21 21
CRK 0.01 0 -10000 0 -10000 0 0
TYK2 0.012 0.039 -10000 0 -0.23 1 1
EGF -0.088 0.2 -10000 0 -0.51 92 92
YES1 0.01 0 -10000 0 -10000 0 0
CAV1 -0.092 0.096 -10000 0 -0.25 72 72
TXN 0.006 0.033 -10000 0 -0.51 2 2
PTP1B/IRS1/GRB2 0.016 0.039 -10000 0 -0.3 1 1
cell migration -0.006 0.041 0.23 2 -10000 0 2
STAT3 0.01 0.001 -10000 0 -10000 0 0
PRLR -0.054 0.17 -10000 0 -0.51 60 60
ITGA2B -0.043 0.16 -10000 0 -0.5 50 50
CSF1R 0.003 0.06 -10000 0 -0.5 7 7
Prolactin Receptor/Prolactin -0.054 0.13 -10000 0 -0.38 71 71
FGR -0.029 0.14 -10000 0 -0.5 37 37
PTP1B/p130 Cas 0.011 0.04 -10000 0 -0.25 2 2
Crk/p130 Cas 0.016 0.039 -10000 0 -0.26 1 1
DOK1 0.017 0.038 -10000 0 -0.25 1 1
JAK2 -0.005 0.066 -10000 0 -0.3 13 13
Jak2/Leptin Receptor/Leptin -0.027 0.067 -10000 0 -0.41 5 5
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
PTPN1 0.006 0.041 -10000 0 -0.23 2 2
LYN 0.01 0 -10000 0 -10000 0 0
CDH2 -0.049 0.17 -10000 0 -0.52 55 55
SRC 0.015 0.018 -10000 0 -10000 0 0
ITGB3 -0.02 0.12 -10000 0 -0.51 27 27
CAT1/PTP1B -0.03 0.13 -10000 0 -0.48 22 22
CAPN1 0.01 0.001 -10000 0 -10000 0 0
CSK 0.01 0 -10000 0 -10000 0 0
PI3K -0.003 0.02 -10000 0 -10000 0 0
mol:H2O2 -0.001 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.023 0.065 -10000 0 -0.42 5 5
negative regulation of transcription -0.005 0.065 -10000 0 -0.29 13 13
FCGR2A 0.001 0.068 -10000 0 -0.5 9 9
FER 0.008 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.056 0.13 -10000 0 -0.36 76 76
BLK -0.075 0.19 -10000 0 -0.52 79 79
Insulin Receptor/Insulin/Shc -0.001 0.014 -10000 0 -0.31 1 1
RHOA 0.01 0.001 -10000 0 -10000 0 0
LEPR -0.042 0.15 -10000 0 -0.5 50 50
BCAR1 0.009 0.023 -10000 0 -0.5 1 1
p210 bcr-abl/Grb2 0.01 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.039 0.14 -10000 0 -0.54 22 22
PRL -0.011 0.084 -10000 0 -0.52 13 13
SOCS3 0 0.11 -10000 0 -1.2 4 4
SPRY2 0.007 0.023 -10000 0 -0.5 1 1
Insulin Receptor/Insulin/IRS1 -0.001 0.014 -10000 0 -0.3 1 1
CSF1/CSF1R 0.011 0.061 -10000 0 -0.36 6 6
Ras protein signal transduction 0.01 0.014 -10000 0 -10000 0 0
IRS1 0.009 0.023 -10000 0 -0.5 1 1
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.045 0.16 -10000 0 -0.52 50 50
STAT5B 0.004 0.044 -10000 0 -0.23 2 2
STAT5A 0.004 0.045 -10000 0 -0.23 3 3
GRB2 0.01 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.041 -10000 0 -0.26 2 2
CSN2 -0.015 0.045 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
LAT 0.006 0.066 -10000 0 -0.45 9 9
YBX1 0.016 0.001 -10000 0 -10000 0 0
LCK 0.007 0.04 -10000 0 -0.5 3 3
SHC1 0.009 0.024 -10000 0 -0.52 1 1
NOX4 -0.01 0.096 -10000 0 -0.51 17 17
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.01 0 -10000 0 -10000 0 0
HDAC4 0.009 0.024 -10000 0 -0.52 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.088 0.37 27 -10000 0 27
CDKN1A -0.001 0.031 -10000 0 -0.68 1 1
KAT2B 0.01 0 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.01 0 -10000 0 -10000 0 0
FOXO4 0.018 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
TAT -0.038 0.15 -10000 0 -0.52 44 44
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.007 0.03 -10000 0 -0.37 3 3
PPARGC1A -0.11 0.22 -10000 0 -0.5 119 119
FHL2 -0.061 0.18 -10000 0 -0.52 66 66
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.006 -10000 0 -10000 0 0
HIST2H4A -0.005 0.088 -10000 0 -0.37 27 27
SIRT1/FOXO3a 0 0.006 -10000 0 -10000 0 0
SIRT1 0 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.015 -10000 0 -0.3 1 1
SIRT1/Histone H1b -0.01 0.034 -10000 0 -10000 0 0
apoptosis 0 0.006 -10000 0 -10000 0 0
SIRT1/PGC1A -0.072 0.13 -10000 0 -0.3 119 119
p53/SIRT1 0.001 0.017 0.38 1 -10000 0 1
SIRT1/FOXO4 0 0.007 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.037 0.095 -10000 0 -0.28 66 66
HIST1H1E 0.003 0.047 -10000 0 -10000 0 0
SIRT1/p300 0 0.006 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.025 0.3 3 -10000 0 3
TP53 0 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.006 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
MEF2D 0.01 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.033 0.11 -10000 0 -0.37 44 44
ACSS2 0.015 0.018 -10000 0 -0.35 1 1
SIRT1/PCAF/MYOD -0.002 0.025 -10000 0 -0.3 3 3
FAS signaling pathway (CD95)

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
SPTAN1 0.001 0.019 0.2 2 -10000 0 2
RFC1 0.001 0.019 0.2 2 -10000 0 2
PRKDC 0.001 0.019 0.2 2 -10000 0 2
RIPK1 0.012 0.004 -10000 0 -10000 0 0
CASP7 -0.016 0.04 0.23 1 -0.5 1 2
FASLG/FAS/FADD/FAF1 0.006 0.073 0.21 34 -0.26 8 42
MAP2K4 -0.024 0.13 -10000 0 -0.46 7 7
mol:ceramide -0.008 0.091 -10000 0 -0.37 10 10
GSN 0.001 0.019 0.21 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 8 0.012 0.076 0.29 1 -0.33 8 9
FAS 0.004 0.047 -10000 0 -0.51 4 4
BID 0.001 0.02 0.28 1 -0.3 1 2
MAP3K1 -0.006 0.081 0.19 1 -0.32 4 5
MAP3K7 0.008 0.004 -10000 0 -10000 0 0
RB1 0.001 0.019 0.2 2 -10000 0 2
CFLAR 0.012 0.004 -10000 0 -10000 0 0
HGF/MET -0.064 0.14 -10000 0 -0.34 91 91
ARHGDIB 0.001 0.019 0.2 2 -10000 0 2
FADD 0.008 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.001 0.019 -10000 0 -0.21 1 1
NFKB1 -0.046 0.084 -10000 0 -0.26 6 6
MAPK8 -0.055 0.2 -10000 0 -0.42 112 112
DFFA 0.001 0.019 0.2 2 -10000 0 2
DNA fragmentation during apoptosis 0.001 0.019 0.2 2 -10000 0 2
FAS/FADD/MET -0.021 0.077 -10000 0 -0.3 35 35
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.007 0.047 -10000 0 -0.51 4 4
FAF1 0.009 0.005 -10000 0 -10000 0 0
PARP1 0.001 0.019 0.2 2 -10000 0 2
DFFB 0.001 0.019 0.2 2 -10000 0 2
CHUK -0.041 0.074 -10000 0 -10000 0 0
FASLG 0.001 0.062 -10000 0 -0.51 7 7
FAS/FADD -0.005 0.033 -10000 0 -0.36 4 4
HGF -0.018 0.12 -10000 0 -0.5 27 27
LMNA 0.001 0.018 0.2 1 -10000 0 1
CASP6 0.001 0.019 0.2 2 -10000 0 2
CASP10 0.006 0.033 -10000 0 -0.51 2 2
CASP3 0.002 0.023 0.21 4 -0.23 1 5
PTPN13 -0.042 0.15 -10000 0 -0.5 50 50
CASP8 0.001 0.028 0.24 4 -0.36 1 5
IL6 -0.24 0.51 -10000 0 -1.2 111 111
MET -0.023 0.13 -10000 0 -0.51 31 31
ICAD/CAD 0.001 0.018 0.2 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.008 0.092 -10000 0 -0.38 10 10
activation of caspase activity by cytochrome c 0.001 0.02 0.28 1 -0.3 1 2
PAK2 0.001 0.019 0.2 2 -10000 0 2
BCL2 0.007 0.041 -10000 0 -0.51 3 3
EPHB forward 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
Ephrin A5/EPHB2 -0.038 0.11 -10000 0 -0.32 57 57
cell-cell adhesion 0.049 0.097 0.42 12 -10000 0 12
Ephrin B/EPHB2/RasGAP -0.034 0.088 -10000 0 -0.49 2 2
ITSN1 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
SHC1 0.009 0.024 -10000 0 -0.52 1 1
Ephrin B1/EPHB3 -0.009 0.051 -10000 0 -0.31 14 14
Ephrin B1/EPHB1 -0.037 0.1 -10000 0 -0.32 58 58
HRAS/GDP -0.035 0.085 -10000 0 -0.52 4 4
Ephrin B/EPHB1/GRB7 -0.039 0.1 -10000 0 -0.54 6 6
Endophilin/SYNJ1 -0.006 0.092 -10000 0 -0.46 2 2
KRAS 0.009 0.024 -10000 0 -0.52 1 1
Ephrin B/EPHB1/Src -0.036 0.095 -10000 0 -0.55 4 4
endothelial cell migration -0.004 0.032 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
GRB7 0.004 0.057 -10000 0 -0.51 6 6
PAK1 -0.002 0.096 -10000 0 -0.46 3 3
HRAS 0.01 0 -10000 0 -10000 0 0
RRAS -0.008 0.098 -10000 0 -0.47 4 4
DNM1 0.003 0.058 -10000 0 -0.52 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.008 0.1 -10000 0 -0.53 4 4
lamellipodium assembly -0.049 0.097 -10000 0 -0.42 12 12
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.071 -10000 0 -0.46 4 4
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
EPHB2 -0.047 0.16 -10000 0 -0.52 53 53
EPHB3 -0.002 0.078 -10000 0 -0.52 11 11
EPHB1 -0.05 0.17 -10000 0 -0.52 56 56
EPHB4 0.01 0 -10000 0 -10000 0 0
mol:GDP -0.032 0.085 -10000 0 -0.4 9 9
Ephrin B/EPHB2 -0.035 0.09 -10000 0 -0.26 57 57
Ephrin B/EPHB3 -0.013 0.06 -10000 0 -0.27 24 24
JNK cascade -0.031 0.12 -10000 0 -0.5 9 9
Ephrin B/EPHB1 -0.037 0.097 -10000 0 -0.27 58 58
RAP1/GDP -0.026 0.074 -10000 0 -0.47 4 4
EFNB2 0.002 0.065 -10000 0 -0.5 8 8
EFNB3 0.006 0.047 -10000 0 -0.51 4 4
EFNB1 0.007 0.04 -10000 0 -0.5 3 3
Ephrin B2/EPHB1-2 -0.066 0.13 -10000 0 -0.3 107 107
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.048 0.098 -10000 0 -0.44 12 12
Rap1/GTP -0.049 0.097 -10000 0 -0.43 12 12
axon guidance -0.038 0.11 -10000 0 -0.32 57 57
MAPK3 0.019 0.064 -10000 0 -0.41 4 4
MAPK1 0.019 0.064 -10000 0 -0.41 4 4
Rac1/GDP 0.002 0.09 -10000 0 -0.49 4 4
actin cytoskeleton reorganization -0.04 0.079 -10000 0 -0.35 12 12
CDC42/GDP 0.002 0.09 -10000 0 -0.49 4 4
PI3K -0.004 0.032 -10000 0 -10000 0 0
EFNA5 0.002 0.062 -10000 0 -0.51 7 7
Ephrin B2/EPHB4 -0.005 0.038 -10000 0 -0.3 8 8
Ephrin B/EPHB2/Intersectin/N-WASP 0.006 0.064 -10000 0 -0.46 2 2
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP -0.048 0.095 -10000 0 -0.42 12 12
PTK2 0.015 0.028 -10000 0 -10000 0 0
MAP4K4 -0.032 0.13 -10000 0 -0.5 9 9
SRC 0.01 0 -10000 0 -10000 0 0
KALRN 0.007 0.04 -10000 0 -0.5 3 3
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.009 0.095 -10000 0 -0.32 13 13
MAP2K1 0.013 0.067 -10000 0 -0.43 4 4
WASL 0.01 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.062 0.12 -10000 0 -0.29 103 103
cell migration 0.019 0.07 -10000 0 -0.47 4 4
NRAS 0.01 0 -10000 0 -10000 0 0
SYNJ1 -0.006 0.094 -10000 0 -0.46 2 2
PXN 0.01 0 -10000 0 -10000 0 0
TF -0.065 0.14 -10000 0 -0.48 19 19
HRAS/GTP -0.053 0.1 -10000 0 -0.45 12 12
Ephrin B1/EPHB1-2 -0.063 0.13 -10000 0 -0.3 103 103
cell adhesion mediated by integrin 0.003 0.054 0.3 11 -10000 0 11
RAC1 0.01 0 -10000 0 -10000 0 0
mol:GTP -0.057 0.11 -10000 0 -0.49 12 12
RAC1-CDC42/GTP -0.053 0.1 -10000 0 -0.44 14 14
RASA1 0.01 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.074 -10000 0 -0.47 4 4
ruffle organization -0.01 0.12 -10000 0 -0.43 12 12
NCK1 0.01 0 -10000 0 -10000 0 0
receptor internalization -0.003 0.094 -10000 0 -0.44 3 3
Ephrin B/EPHB2/KALRN -0.036 0.091 -10000 0 -0.49 3 3
ROCK1 0.012 0.049 -10000 0 -0.27 14 14
RAS family/GDP -0.037 0.075 -10000 0 -0.34 11 11
Rac1/GTP -0.052 0.1 -10000 0 -0.45 12 12
Ephrin B/EPHB1/Src/Paxillin 0.004 0.072 -10000 0 -0.31 12 12
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.02 0.083 -9999 0 -0.36 27 27
AKT1 0.028 0.12 -9999 0 -0.52 13 13
PTK2B -0.011 0.13 -9999 0 -0.57 14 14
VEGFR2 homodimer/Frs2 -0.023 0.14 -9999 0 -0.7 12 12
CAV1 -0.32 0.24 -9999 0 -0.5 313 313
CALM1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.042 0.12 -9999 0 -0.64 12 12
endothelial cell proliferation 0.034 0.12 -9999 0 -0.5 13 13
mol:Ca2+ 0.002 0.12 -9999 0 -0.56 13 13
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.038 0.11 -9999 0 -0.59 12 12
RP11-342D11.1 -0.004 0.12 -9999 0 -0.56 13 13
CDH5 -0.058 0.17 -9999 0 -0.5 65 65
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0.009 0.024 -9999 0 -0.52 1 1
SHC2 0.001 0.069 -9999 0 -0.5 9 9
HRAS/GDP -0.031 0.091 -9999 0 -0.48 13 13
SH2D2A 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.033 0.098 -9999 0 -0.49 15 15
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.041 0.12 -9999 0 -0.62 12 12
VEGFR1 homodimer 0.01 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.034 0.1 -9999 0 -0.52 13 13
GRB10 0.003 0.12 -9999 0 -0.56 13 13
PTPN11 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
PAK1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.066 0.16 -9999 0 -0.55 36 36
HRAS 0.01 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.005 0.085 -9999 0 -0.35 13 13
HIF1A 0.01 0 -9999 0 -10000 0 0
FRS2 0.008 0.034 -9999 0 -0.52 2 2
oxygen and reactive oxygen species metabolic process -0.038 0.11 -9999 0 -0.58 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.004 0.082 -9999 0 -0.5 13 13
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.042 0.12 -9999 0 -0.62 12 12
mol:GDP -0.033 0.097 -9999 0 -0.51 13 13
mol:NADP 0.023 0.11 -9999 0 -0.42 17 17
eNOS/Hsp90 0.027 0.1 -9999 0 -0.41 14 14
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
mol:IP3 0.002 0.12 -9999 0 -0.56 13 13
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.009 0.023 -9999 0 -0.5 1 1
VEGFA 0.012 0 -9999 0 -10000 0 0
VEGFC 0.007 0.04 -9999 0 -0.5 3 3
FAK1/Vinculin 0.004 0.14 -9999 0 -0.6 14 14
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.051 0.12 -9999 0 -0.6 13 13
PTPN6 0.01 0 -9999 0 -10000 0 0
EPAS1 -0.049 0.17 -9999 0 -0.48 65 65
mol:L-citrulline 0.023 0.11 -9999 0 -0.42 17 17
ITGAV 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.039 0.11 -9999 0 -0.61 12 12
VEGFR2 homodimer/VEGFA homodimer -0.041 0.12 -9999 0 -0.61 13 13
VEGFR2/3 heterodimer -0.029 0.16 -9999 0 -0.69 17 17
VEGFB 0.01 0 -9999 0 -10000 0 0
MAPK11 0.003 0.13 -9999 0 -0.56 14 14
VEGFR2 homodimer -0.03 0.16 -9999 0 -0.42 65 65
FLT1 0.01 0 -9999 0 -10000 0 0
NEDD4 0.011 0.023 -9999 0 -0.5 1 1
MAPK3 0.007 0.12 -9999 0 -0.53 13 13
MAPK1 0.007 0.12 -9999 0 -0.53 13 13
VEGFA145/NRP2 -0.002 0.027 -9999 0 -0.35 3 3
VEGFR1/2 heterodimer -0.022 0.14 -9999 0 -0.68 12 12
KDR -0.03 0.16 -9999 0 -0.42 65 65
VEGFA165/NRP1/VEGFR2 homodimer -0.038 0.11 -9999 0 -0.56 14 14
SRC 0.01 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.008 0.12 -9999 0 -0.54 13 13
PI3K -0.037 0.11 -9999 0 -0.57 14 14
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.041 0.12 -9999 0 -0.62 12 12
FES 0.002 0.12 -9999 0 -0.57 13 13
GAB1 -0.04 0.11 -9999 0 -0.58 14 14
VEGFR2 homodimer/VEGFA homodimer/Src -0.041 0.12 -9999 0 -0.62 12 12
CTNNB1 0.01 0 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
ARNT 0.01 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.11 0.14 -9999 0 -0.4 53 53
VEGFR2 homodimer/VEGFA homodimer/Yes -0.041 0.12 -9999 0 -0.62 12 12
PI3K/GAB1 0.026 0.12 -9999 0 -0.52 14 14
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.037 0.11 -9999 0 -0.58 12 12
PRKACA 0.01 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.05 0.14 -9999 0 -0.63 18 18
HSP90AA1 0.01 0 -9999 0 -10000 0 0
CDC42 0.002 0.12 -9999 0 -0.57 13 13
actin cytoskeleton reorganization -0.041 0.12 -9999 0 -0.62 12 12
PTK2 -0.002 0.14 -9999 0 -0.65 14 14
EDG1 -0.004 0.12 -9999 0 -0.56 13 13
mol:DAG 0.002 0.12 -9999 0 -0.56 13 13
CaM/Ca2+ -0.034 0.099 -9999 0 -0.52 13 13
MAP2K3 0.009 0.12 -9999 0 -0.54 13 13
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.038 0.11 -9999 0 -0.58 13 13
PLCG1 0.002 0.12 -9999 0 -0.57 13 13
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.039 0.11 -9999 0 -0.58 13 13
IQGAP1 0.01 0 -9999 0 -10000 0 0
YES1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.041 0.12 -9999 0 -0.62 12 12
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.041 0.12 -9999 0 -0.62 12 12
cell migration 0.01 0.14 -9999 0 -0.58 13 13
mol:PI-3-4-5-P3 -0.035 0.1 -9999 0 -0.52 14 14
FYN 0.009 0.023 -9999 0 -0.5 1 1
VEGFB/NRP1 0.002 0.12 -9999 0 -0.53 13 13
mol:NO 0.023 0.11 -9999 0 -0.42 17 17
PXN 0.01 0 -9999 0 -10000 0 0
HRAS/GTP -0.031 0.09 -9999 0 -0.48 13 13
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.001 0.12 -9999 0 -0.58 13 13
VHL 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.019 0.12 -9999 0 -0.51 27 27
NOS3 0.022 0.12 -9999 0 -0.47 17 17
VEGFR2 homodimer/VEGFA homodimer/Sck -0.046 0.13 -9999 0 -0.63 15 15
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA 0.008 0.12 -9999 0 -0.52 13 13
PRKCB 0.003 0.13 -9999 0 -0.56 15 15
VCL 0.01 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.004 0.12 -9999 0 -0.56 13 13
VEGFR1/2 heterodimer/VEGFA homodimer -0.041 0.12 -9999 0 -0.62 12 12
VEGFA165/NRP2 -0.002 0.027 -9999 0 -0.35 3 3
MAPKKK cascade -0.03 0.089 -9999 0 -0.48 12 12
NRP2 0.007 0.04 -9999 0 -0.5 3 3
VEGFC homodimer 0.007 0.04 -9999 0 -0.5 3 3
NCK1 0.01 0 -9999 0 -10000 0 0
ROCK1 0.01 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.004 0.14 -9999 0 -0.6 14 14
MAP3K13 0.002 0.12 -9999 0 -0.57 13 13
PDPK1 0.025 0.11 -9999 0 -0.48 13 13
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.001 0.018 -9999 0 -0.25 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.025 0.068 -9999 0 -0.36 3 3
AP1 -0.039 0.087 -9999 0 -0.45 4 4
mol:PIP3 -0.028 0.073 -9999 0 -0.48 3 3
AKT1 -0.002 0.014 -9999 0 -10000 0 0
PTK2B 0.018 0.032 -9999 0 -0.27 2 2
RHOA 0.025 0.024 -9999 0 -10000 0 0
PIK3CB 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0.005 0.085 -9999 0 -0.37 4 4
MAGI3 0.004 0.056 -9999 0 -0.5 6 6
RELA 0.01 0 -9999 0 -10000 0 0
apoptosis -0.005 0.083 -9999 0 -0.25 46 46
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.015 0.064 -9999 0 -0.26 8 8
NF kappa B1 p50/RelA -0.025 0.07 -9999 0 -0.38 2 2
endothelial cell migration 0.022 0.021 -9999 0 -0.44 1 1
ADCY4 0.011 0.069 -9999 0 -0.36 5 5
ADCY5 -0.002 0.084 -9999 0 -0.29 18 18
ADCY6 0.02 0.052 -9999 0 -0.35 1 1
ADCY7 0.019 0.052 -9999 0 -0.35 1 1
ADCY1 0.018 0.058 -9999 0 -0.3 4 4
ADCY2 0.004 0.075 -9999 0 -0.3 11 11
ADCY3 0.02 0.051 -9999 0 -0.35 1 1
ADCY8 -0.055 0.1 -9999 0 -0.3 21 21
ADCY9 0.016 0.061 -9999 0 -0.33 5 5
GSK3B 0.024 0.03 -9999 0 -0.25 2 2
arachidonic acid secretion 0.024 0.049 -9999 0 -0.31 1 1
GNG2 0.008 0.032 -9999 0 -0.5 2 2
TRIP6 0.017 0.03 -9999 0 -0.36 3 3
GNAO1 0.018 0.037 -9999 0 -0.3 6 6
HRAS 0.01 0 -9999 0 -10000 0 0
NFKBIA 0.012 0.095 -9999 0 -0.41 3 3
GAB1 0.007 0.04 -9999 0 -0.5 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.021 0.14 -9999 0 -0.87 12 12
JUN 0.006 0.046 -9999 0 -0.5 4 4
LPA/LPA2/NHERF2 -0.004 0.035 -9999 0 -0.3 7 7
TIAM1 -0.025 0.16 -9999 0 -1 12 12
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
mol:IP3 0.004 0.086 -9999 0 -0.38 4 4
PLCB3 0.019 0.034 -9999 0 -0.26 7 7
FOS -0.023 0.13 -9999 0 -0.5 32 32
positive regulation of mitosis 0.024 0.049 -9999 0 -0.31 1 1
LPA/LPA1-2-3 -0.028 0.08 -9999 0 -0.26 52 52
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.009 0.023 -9999 0 -0.5 1 1
stress fiber formation 0.017 0.051 -9999 0 -10000 0 0
GNAZ -0.004 0.087 -9999 0 -0.29 41 41
EGFR/PI3K-beta/Gab1 -0.029 0.076 -9999 0 -0.5 3 3
positive regulation of dendritic cell cytokine production -0.028 0.079 -9999 0 -0.26 52 52
LPA/LPA2/MAGI-3 -0.004 0.035 -9999 0 -0.3 7 7
ARHGEF1 0.03 0.014 -9999 0 -10000 0 0
GNAI2 0.022 0.01 -9999 0 -10000 0 0
GNAI3 0.022 0.01 -9999 0 -10000 0 0
GNAI1 0.021 0.022 -9999 0 -0.29 2 2
LPA/LPA3 -0.037 0.11 -9999 0 -0.36 51 51
LPA/LPA2 -0.001 0.017 -9999 0 -0.37 1 1
LPA/LPA1 0 0.011 -9999 0 -0.24 1 1
HB-EGF/EGFR -0.11 0.18 -9999 0 -0.33 177 177
HBEGF -0.12 0.19 -9999 0 -0.38 172 172
mol:DAG 0.004 0.086 -9999 0 -0.38 4 4
cAMP biosynthetic process 0.006 0.061 -9999 0 -0.37 1 1
NFKB1 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
LYN 0.012 0.095 -9999 0 -0.41 3 3
GNAQ -0.01 0.087 -9999 0 -0.26 52 52
LPAR2 0.009 0.024 -9999 0 -0.52 1 1
LPAR3 -0.044 0.16 -9999 0 -0.5 51 51
LPAR1 0.013 0.007 -9999 0 -10000 0 0
IL8 -0.043 0.14 -9999 0 -0.38 32 32
PTK2 0.003 0.082 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.005 0.083 -9999 0 -0.25 46 46
EGFR -0.005 0.086 -9999 0 -0.51 14 14
PLCG1 -0.007 0.096 -9999 0 -0.28 47 47
PLD2 0.003 0.082 -9999 0 -10000 0 0
G12/G13 0 0.007 -9999 0 -10000 0 0
PI3K-beta -0.002 0.016 -9999 0 -10000 0 0
cell migration -0.014 0.046 -9999 0 -0.25 12 12
SLC9A3R2 0.004 0.056 -9999 0 -0.5 6 6
PXN 0.017 0.051 -9999 0 -10000 0 0
HRAS/GTP 0.024 0.05 -9999 0 -0.32 1 1
RAC1 0.01 0 -9999 0 -10000 0 0
MMP9 -0.097 0.21 -9999 0 -0.52 99 99
PRKCE 0.005 0.051 -9999 0 -0.5 5 5
PRKCD 0.01 0.083 -9999 0 -0.35 4 4
Gi(beta/gamma) 0.022 0.052 -9999 0 -0.34 1 1
mol:LPA 0.003 0.007 -9999 0 -0.15 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.022 0.063 -9999 0 -10000 0 0
MAPKKK cascade 0.024 0.049 -9999 0 -0.31 1 1
contractile ring contraction involved in cytokinesis 0.024 0.024 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.017 0.098 -9999 0 -0.26 64 64
GNA15 -0.009 0.084 -9999 0 -0.25 52 52
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
MAPT 0.015 0.066 -9999 0 -0.27 8 8
GNA11 -0.01 0.089 -9999 0 -0.26 52 52
Rac1/GTP -0.022 0.14 -9999 0 -0.93 12 12
MMP2 0.022 0.021 -9999 0 -0.45 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.019 0.097 -10000 0 -0.4 21 21
CRKL 0.016 0.097 -10000 0 -0.42 21 21
HRAS 0.028 0.1 -10000 0 -0.47 10 10
mol:PIP3 0.005 0.092 0.22 2 -0.41 20 22
SPRED1 0.01 0 -10000 0 -10000 0 0
SPRED2 0.01 0 -10000 0 -10000 0 0
GAB1 0.01 0.1 -10000 0 -0.44 21 21
FOXO3 0.021 0.087 -10000 0 -0.38 20 20
AKT1 0.015 0.094 -10000 0 -0.42 20 20
BAD 0.021 0.087 -10000 0 -0.38 20 20
megakaryocyte differentiation -0.012 0.13 -10000 0 -0.46 26 26
GSK3B 0.021 0.087 -10000 0 -0.38 20 20
RAF1 0.034 0.085 -10000 0 -0.38 10 10
SHC1 0.009 0.024 -10000 0 -0.52 1 1
STAT3 0.011 0.099 -10000 0 -0.45 20 20
STAT1 0.008 0.21 -10000 0 -0.95 21 21
HRAS/SPRED1 -0.019 0.071 -10000 0 -0.38 10 10
cell proliferation 0.012 0.098 -10000 0 -0.44 20 20
PIK3CA 0.01 0 -10000 0 -10000 0 0
TEC 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.011 0.1 -10000 0 -0.45 20 20
HRAS/SPRED2 -0.019 0.071 -10000 0 -0.38 10 10
LYN/TEC/p62DOK -0.019 0.085 -10000 0 -0.41 20 20
MAPK3 0.038 0.064 -10000 0 -0.27 8 8
STAP1 0.004 0.11 -10000 0 -0.45 23 23
GRAP2 -0.006 0.088 -10000 0 -0.5 15 15
JAK2 -0.039 0.17 -10000 0 -0.8 22 22
STAT1 (dimer) 0.009 0.2 -10000 0 -0.93 21 21
mol:Gleevec -0.002 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.022 0.088 -10000 0 -0.41 21 21
actin filament polymerization 0.011 0.098 -10000 0 -0.44 20 20
LYN 0.01 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) 0.011 0.14 -10000 0 -0.59 23 23
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
CBL/CRKL/GRB2 -0.018 0.079 -10000 0 -0.38 20 20
PI3K 0.02 0.096 -10000 0 -0.42 20 20
PTEN 0.01 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.005 0.25 -10000 0 -1.2 20 20
MAPK8 0.011 0.099 -10000 0 -0.45 20 20
STAT3 (dimer) 0.012 0.098 -10000 0 -0.44 20 20
positive regulation of transcription 0.036 0.054 -10000 0 -0.22 8 8
mol:GDP -0.025 0.092 -10000 0 -0.4 23 23
PIK3C2B 0.01 0.1 -10000 0 -0.46 20 20
CBL/CRKL 0.021 0.092 -10000 0 -0.39 21 21
FER 0.011 0.099 -10000 0 -0.45 20 20
SH2B3 0.01 0.1 -10000 0 -0.45 21 21
PDPK1 0.011 0.085 -10000 0 -0.38 20 20
SNAI2 0.009 0.11 -10000 0 -0.47 21 21
positive regulation of cell proliferation 0.013 0.16 -10000 0 -0.72 21 21
KITLG 0.009 0.049 -10000 0 -0.52 4 4
cell motility 0.013 0.16 -10000 0 -0.72 21 21
PTPN6 0.002 0.007 -10000 0 -10000 0 0
EPOR 0.031 0.064 -10000 0 -10000 0 0
STAT5A (dimer) 0.015 0.14 -10000 0 -0.61 20 20
SOCS1 0.009 0.024 -10000 0 -0.52 1 1
cell migration -0.001 0.11 0.45 21 -10000 0 21
SOS1 0.01 0 -10000 0 -10000 0 0
EPO 0.004 0.048 -10000 0 -0.52 4 4
VAV1 0.005 0.051 -10000 0 -0.5 5 5
GRB10 0.011 0.099 -10000 0 -0.45 20 20
PTPN11 0.009 0.004 -10000 0 -10000 0 0
SCF/KIT 0.005 0.1 -10000 0 -0.46 21 21
GO:0007205 -0.002 0.005 -10000 0 -10000 0 0
MAP2K1 0.037 0.069 -10000 0 -0.3 8 8
CBL 0.01 0 -10000 0 -10000 0 0
KIT -0.01 0.25 -10000 0 -1.2 20 20
MAP2K2 0.037 0.069 -10000 0 -0.3 8 8
SHC/Grb2/SOS1 -0.02 0.088 -10000 0 -0.42 20 20
STAT5A 0.014 0.14 -10000 0 -0.63 20 20
GRB2 0.01 0 -10000 0 -10000 0 0
response to radiation 0.009 0.1 -10000 0 -0.46 21 21
SHC/GRAP2 -0.012 0.063 -10000 0 -0.35 16 16
PTPRO -0.012 0.13 -10000 0 -0.47 26 26
SH2B2 0.011 0.1 -10000 0 -0.45 20 20
DOK1 0.01 0 -10000 0 -10000 0 0
MATK 0 0.11 -10000 0 -0.46 21 21
CREBBP 0.029 0.007 -10000 0 -10000 0 0
BCL2 0.028 0.085 -10000 0 -1.2 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.01 0 -9999 0 -10000 0 0
VLDLR -0.002 0.075 -9999 0 -0.5 11 11
LRPAP1 0.01 0 -9999 0 -10000 0 0
NUDC 0.01 0 -9999 0 -10000 0 0
RELN/LRP8 -0.052 0.11 -9999 0 -0.29 86 86
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.01 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.024 0.11 -9999 0 -0.27 18 18
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.003 0.067 -9999 0 -0.52 8 8
IQGAP1 0.01 0 -9999 0 -10000 0 0
PLA2G7 -0.001 0.074 -9999 0 -0.51 10 10
CALM1 0.01 0 -9999 0 -10000 0 0
DYNLT1 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.008 0.054 -9999 0 -0.37 11 11
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.01 0 -9999 0 -10000 0 0
CDK5R1 -0.006 0.091 -9999 0 -0.52 15 15
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.14 0.23 -9999 0 -0.52 133 133
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.057 0.13 -9999 0 -0.32 86 86
YWHAE 0.01 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.038 0.11 -9999 0 -0.33 28 28
MAP1B -0.002 0.02 -9999 0 -0.28 1 1
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.017 0.1 -9999 0 -0.47 1 1
RELN -0.069 0.18 -9999 0 -0.5 75 75
PAFAH/LIS1 0.014 0.046 -9999 0 -0.3 10 10
LIS1/CLIP170 0.021 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.048 0.072 -9999 0 -0.33 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.019 0.11 -9999 0 -0.37 15 15
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.046 0.12 -9999 0 -0.35 28 28
LIS1/IQGAP1 0.021 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 -0.015 0.11 -9999 0 -0.52 23 23
PAFAH1B2 0.01 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.014 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.061 0.088 -9999 0 -0.4 1 1
LRP8 -0.002 0.078 -9999 0 -0.52 11 11
NDEL1/Katanin 60 -0.038 0.11 -9999 0 -0.33 28 28
P39/CDK5 -0.082 0.16 -9999 0 -0.47 28 28
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0 -9999 0 -10000 0 0
CDK5 -0.015 0.1 -9999 0 -10000 0 0
PPP2R5D 0.01 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.01 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.046 0.1 -9999 0 -0.49 8 8
RELN/VLDLR -0.052 0.11 -9999 0 -0.32 23 23
CDC42 0 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.023 0.088 -9999 0 -0.36 31 31
CRKL 0.006 0.081 -9999 0 -0.4 7 7
mol:PIP3 -0.016 0.006 -9999 0 -10000 0 0
AKT1 0.001 0.004 -9999 0 -10000 0 0
PTK2B 0.008 0.032 -9999 0 -0.5 2 2
RAPGEF1 0.012 0.078 -9999 0 -0.4 6 6
RANBP10 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.035 0.1 -9999 0 -0.31 55 55
MAP3K5 0.017 0.08 -9999 0 -0.4 7 7
HGF/MET/CIN85/CBL/ENDOPHILINS -0.031 0.089 -9999 0 -0.28 55 55
AP1 -0.028 0.085 -9999 0 -0.32 36 36
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.009 0.024 -9999 0 -0.52 1 1
apoptosis -0.041 0.19 -9999 0 -0.7 36 36
STAT3 (dimer) 0.008 0.077 -9999 0 -0.39 4 4
GAB1/CRKL/SHP2/PI3K -0.019 0.064 -9999 0 -0.42 5 5
INPP5D 0.007 0.04 -9999 0 -0.5 3 3
CBL/CRK 0.011 0.078 -9999 0 -0.4 6 6
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.01 0 -9999 0 -10000 0 0
PTEN 0.01 0 -9999 0 -10000 0 0
ELK1 -0.011 0.047 -9999 0 -0.19 31 31
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.014 0.043 -9999 0 -0.25 4 4
PAK1 0.007 0.004 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.035 0.1 -9999 0 -0.31 55 55
HRAS -0.007 0.12 -9999 0 -0.56 18 18
DOCK1 0.012 0.078 -9999 0 -0.4 6 6
GAB1 0 0.085 -9999 0 -0.31 21 21
CRK 0.006 0.081 -9999 0 -0.29 21 21
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.041 0.13 -9999 0 -0.49 38 38
JUN 0.006 0.046 -9999 0 -0.5 4 4
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.022 0.065 -9999 0 -0.22 38 38
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
cell morphogenesis 0.028 0.085 -9999 0 -0.43 4 4
GRB2/SHC 0.002 0.062 -9999 0 -0.3 4 4
FOS -0.023 0.13 -9999 0 -0.5 32 32
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.011 0.047 -9999 0 -0.19 31 31
HGF/MET/MUC20 -0.036 0.1 -9999 0 -0.32 55 55
cell migration 0.002 0.061 -9999 0 -0.29 4 4
GRB2 0.01 0 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
MET/RANBP10 -0.023 0.088 -9999 0 -0.36 31 31
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.003 0.079 -9999 0 -0.41 4 4
MET/MUC20 -0.023 0.089 -9999 0 -0.37 31 31
RAP1B 0.017 0.074 -9999 0 -0.43 4 4
RAP1A 0.017 0.074 -9999 0 -0.43 4 4
HGF/MET/RANBP9 -0.035 0.1 -9999 0 -0.31 55 55
RAF1 0 0.12 -9999 0 -0.52 18 18
STAT3 0.008 0.078 -9999 0 -0.4 4 4
cell proliferation 0.01 0.1 -9999 0 -0.33 38 38
RPS6KB1 0.002 0.027 -9999 0 -10000 0 0
MAPK3 -0.014 0.042 -9999 0 -10000 0 0
MAPK1 -0.014 0.042 -9999 0 -10000 0 0
RANBP9 0.01 0 -9999 0 -10000 0 0
MAPK8 0.03 0.068 -9999 0 -0.38 3 3
SRC 0.009 0.074 -9999 0 -0.38 4 4
PI3K 0.002 0.064 -9999 0 -0.34 4 4
MET/Glomulin -0.011 0.08 -9999 0 -0.32 31 31
SOS1 0.01 0 -9999 0 -10000 0 0
MAP2K1 0.007 0.11 -9999 0 -0.5 16 16
MET -0.023 0.13 -9999 0 -0.51 31 31
MAP4K1 0.011 0.085 -9999 0 -0.4 9 9
PTK2 0.01 0 -9999 0 -10000 0 0
MAP2K2 0.007 0.11 -9999 0 -0.5 16 16
BAD 0.007 0.004 -9999 0 -10000 0 0
MAP2K4 0.022 0.074 -9999 0 -0.38 6 6
SHP2/GRB2/SOS1/GAB1 -0.024 0.078 -9999 0 -0.34 20 20
INPPL1 0.01 0 -9999 0 -10000 0 0
PXN 0.01 0 -9999 0 -10000 0 0
SH3KBP1 0.01 0 -9999 0 -10000 0 0
HGS -0.004 0.064 -9999 0 -0.24 18 18
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.018 0.12 -9999 0 -0.5 27 27
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
PTPRJ 0.01 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.003 0.064 -9999 0 -0.33 3 3
PDPK1 -0.006 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.037 0.11 -9999 0 -0.32 55 55
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.001 0.017 -10000 0 -0.37 1 1
PRKCZ 0.007 0.04 -10000 0 -0.5 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.039 -10000 0 -0.26 2 2
IRAK/TOLLIP 0.021 0.019 -10000 0 -0.27 2 2
IKBKB 0.01 0 -10000 0 -10000 0 0
IKBKG 0.01 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.17 -10000 0 -0.36 168 168
IL1A -0.15 0.24 -10000 0 -0.5 151 151
IL1B -0.007 0.093 -10000 0 -0.35 33 33
IRAK/TRAF6/p62/Atypical PKCs -0.003 0.024 -10000 0 -10000 0 0
IL1R2 -0.012 0.1 -10000 0 -0.51 20 20
IL1R1 0.007 0.04 -10000 0 -0.5 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.023 0.051 0.19 9 -0.38 2 11
TOLLIP 0.01 0 -10000 0 -10000 0 0
TICAM2 0.006 0.046 -10000 0 -0.5 4 4
MAP3K3 0.009 0.023 -10000 0 -0.5 1 1
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.049 0.017 -10000 0 -10000 0 0
JUN 0.024 0.053 -10000 0 -0.43 1 1
MAP3K7 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.017 0.062 -10000 0 -0.46 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.081 0.12 -10000 0 -0.39 4 4
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.074 0.11 -10000 0 -0.49 2 2
IL1 beta fragment/IL1R1/IL1RAP -0.019 0.071 -10000 0 -0.27 34 34
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.021 0.049 -10000 0 -10000 0 0
IRAK1 0.016 0.021 -10000 0 -0.31 2 2
IL1RN/IL1R1 -0.007 0.05 -10000 0 -0.35 10 10
IRAK4 0.01 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
PI3K -0.001 0.016 -10000 0 -0.35 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.018 0.054 -10000 0 -0.39 2 2
CHUK 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.019 0.071 -10000 0 -0.27 34 34
IL1 beta/IL1R2 -0.032 0.097 -10000 0 -0.31 50 50
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.015 0.055 -10000 0 -0.42 2 2
IRAK3 -0.003 0.079 -10000 0 -0.5 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.018 0.064 -10000 0 -0.46 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.049 0.12 -10000 0 -0.46 2 2
IL1 alpha/IL1R1/IL1RAP -0.092 0.14 -10000 0 -0.29 152 152
RELA 0.01 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.009 0.024 -10000 0 -0.52 1 1
MYD88 0.01 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.014 0.024 -10000 0 -10000 0 0
IL1RAP 0.01 0 -10000 0 -10000 0 0
UBE2N 0.01 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.053 -10000 0 -0.38 2 2
CASP1 0.005 0.051 -10000 0 -0.5 5 5
IL1RN/IL1R2 -0.02 0.085 -10000 0 -0.37 26 26
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.017 0.065 -10000 0 -0.49 2 2
TMEM189-UBE2V1 0.003 0.024 -10000 0 -0.52 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.031 0.099 -10000 0 -0.42 3 3
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL1RN 0.003 0.06 -10000 0 -0.5 7 7
TRAF6/TAK1/TAB1/TAB2 0 0.011 -10000 0 -10000 0 0
MAP2K6 0.015 0.051 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.009 0.055 -9999 0 -0.36 12 12
PDGFRB 0.008 0.023 -9999 0 -0.5 1 1
SPHK1 -0.009 0.021 -9999 0 -10000 0 0
mol:S1P -0.011 0.027 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.013 0.14 -9999 0 -0.36 49 49
GNAO1 0.003 0.058 -9999 0 -0.52 6 6
PDGFB-D/PDGFRB/PLCgamma1 -0.005 0.12 -9999 0 -0.45 11 11
PLCG1 -0.008 0.13 -9999 0 -0.34 47 47
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.023 -9999 0 -0.5 1 1
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.01 0.003 -9999 0 -10000 0 0
GNAI1 0.008 0.033 -9999 0 -0.51 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.005 0.05 -9999 0 -0.3 12 12
S1P1/S1P -0.02 0.053 -9999 0 -0.35 4 4
negative regulation of cAMP metabolic process -0.012 0.13 -9999 0 -0.35 49 49
MAPK3 -0.023 0.18 -9999 0 -0.53 47 47
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.003 0.079 -9999 0 -0.5 12 12
PLCB2 0.01 0.071 -9999 0 -0.34 7 7
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.017 0.045 -9999 0 -0.3 4 4
receptor internalization -0.019 0.05 -9999 0 -0.3 6 6
PTGS2 -0.063 0.31 -9999 0 -0.98 47 47
Rac1/GTP -0.017 0.045 -9999 0 -0.3 4 4
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFA 0.009 0.003 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.012 0.13 -9999 0 -0.35 49 49
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.033 0.14 -9999 0 -0.5 41 41
MAPK1 -0.023 0.18 -9999 0 -0.53 47 47
S1P1/S1P/PDGFB-D/PDGFRB 0.011 0.074 -9999 0 -0.37 4 4
ABCC1 0.01 0.002 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.02 0.085 -10000 0 -0.49 12 12
FYN 0.03 0.13 -10000 0 -0.61 15 15
LAT/GRAP2/SLP76 -0.016 0.11 -10000 0 -0.5 18 18
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 0.037 0.095 -10000 0 -0.41 15 15
B2M 0.011 0.003 -10000 0 -10000 0 0
IKBKG -0.009 0.024 -10000 0 -0.14 6 6
MAP3K8 0.008 0.032 -10000 0 -0.5 2 2
mol:Ca2+ -0.01 0.025 -10000 0 -0.11 13 13
integrin-mediated signaling pathway -0.001 0.019 -10000 0 -0.3 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.034 0.14 -10000 0 -0.6 16 16
TRPV6 -0.075 0.18 -10000 0 -0.51 72 72
CD28 0.009 0.023 -10000 0 -0.5 1 1
SHC1 0.029 0.12 -10000 0 -0.57 15 15
receptor internalization 0.022 0.13 -10000 0 -0.53 17 17
PRF1 -0.017 0.26 -10000 0 -1.1 25 25
KRAS 0.009 0.024 -10000 0 -0.52 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
COT/AKT1 0.038 0.08 -10000 0 -0.35 14 14
LAT 0.029 0.12 -10000 0 -0.58 14 14
EntrezGene:6955 0 0.005 -10000 0 -10000 0 0
CD3D 0.008 0.041 -10000 0 -0.51 3 3
CD3E 0.006 0.053 -10000 0 -0.52 5 5
CD3G -0.001 0.076 -10000 0 -0.5 11 11
RASGRP2 0.002 0.041 -10000 0 -0.16 26 26
RASGRP1 0.035 0.1 -10000 0 -0.4 18 18
HLA-A 0.011 0.003 -10000 0 -10000 0 0
RASSF5 0.008 0.032 -10000 0 -0.5 2 2
RAP1A/GTP/RAPL -0.001 0.019 -10000 0 -0.3 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.029 0.037 -10000 0 -0.12 11 11
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.043 -10000 0 -0.23 9 9
PRKCA -0.005 0.053 -10000 0 -0.26 12 12
GRAP2 -0.006 0.088 -10000 0 -0.5 15 15
mol:IP3 0.01 0.11 0.21 62 -0.42 12 74
EntrezGene:6957 0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.014 0.11 -10000 0 -0.57 12 12
ORAI1 0.043 0.1 0.28 72 -10000 0 72
CSK 0.029 0.12 -10000 0 -0.64 12 12
B7 family/CD28 -0.034 0.14 -10000 0 -0.65 18 18
CHUK 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.023 0.14 -10000 0 -0.63 16 16
PTPN6 0.026 0.12 -10000 0 -0.59 14 14
VAV1 0.028 0.13 -10000 0 -0.58 16 16
Monovalent TCR/CD3 0.007 0.088 -10000 0 -0.37 18 18
CBL 0.01 0 -10000 0 -10000 0 0
LCK 0.027 0.13 -10000 0 -0.64 14 14
PAG1 0.028 0.12 -10000 0 -0.64 12 12
RAP1A 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.022 0.14 -10000 0 -0.68 14 14
CD80 -0.001 0.076 -10000 0 -0.5 11 11
CD86 0.001 0.069 -10000 0 -0.5 9 9
PDK1/CARD11/BCL10/MALT1 -0.018 0.052 -10000 0 -0.26 11 11
HRAS 0.01 0 -10000 0 -10000 0 0
GO:0035030 0.024 0.13 -10000 0 -0.55 17 17
CD8A 0.004 0.062 -10000 0 -0.51 7 7
CD8B 0.003 0.066 -10000 0 -0.51 8 8
PTPRC -0.005 0.089 -10000 0 -0.5 15 15
PDK1/PKC theta 0.032 0.12 -10000 0 -0.47 20 20
CSK/PAG1 0.032 0.12 -10000 0 -0.64 11 11
SOS1 0.01 0 -10000 0 -10000 0 0
peptide-MHC class I 0.016 0.007 -10000 0 -10000 0 0
GRAP2/SLP76 -0.02 0.13 -10000 0 -0.58 18 18
STIM1 0.021 0.05 -10000 0 -10000 0 0
RAS family/GTP 0.038 0.042 -10000 0 -0.18 6 6
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.021 0.14 -10000 0 -0.57 17 17
mol:DAG -0.006 0.077 -10000 0 -0.35 15 15
RAP1A/GDP 0.013 0.016 -10000 0 -10000 0 0
PLCG1 0.01 0 -10000 0 -10000 0 0
CD247 0.004 0.057 -10000 0 -0.5 6 6
cytotoxic T cell degranulation -0.013 0.24 -10000 0 -1.1 25 25
RAP1A/GTP -0.004 0.013 -10000 0 -0.066 5 5
mol:PI-3-4-5-P3 0.036 0.11 -10000 0 -0.48 16 16
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.007 0.13 0.23 62 -0.52 14 76
NRAS 0.01 0 -10000 0 -10000 0 0
ZAP70 0.004 0.056 -10000 0 -0.5 6 6
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.016 0.1 -10000 0 -0.52 15 15
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
CD8 heterodimer 0.005 0.076 -10000 0 -0.48 11 11
CARD11 -0.022 0.13 -10000 0 -0.52 30 30
PRKCB -0.008 0.067 -10000 0 -0.3 18 18
PRKCE -0.006 0.055 -10000 0 -0.27 12 12
PRKCQ 0.024 0.14 -10000 0 -0.52 22 22
LCP2 0.007 0.04 -10000 0 -0.5 3 3
BCL10 0.01 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.037 0.082 -10000 0 -0.35 15 15
IKK complex 0.037 0.034 -10000 0 -0.11 11 11
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.039 0.062 -10000 0 -0.29 10 10
PDPK1 0.039 0.091 -10000 0 -0.4 14 14
TCR/CD3/MHC I/CD8/Fyn 0.02 0.14 -10000 0 -0.72 12 12
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.016 0.086 -10000 0 -0.41 5 5
IKBKB -0.002 0.048 -10000 0 -0.25 3 3
AKT1 -0.03 0.08 -10000 0 -0.26 4 4
IKBKG 0 0.05 -10000 0 -0.26 4 4
CALM1 -0.014 0.079 0.23 1 -0.59 5 6
PIK3CA 0.01 0 -10000 0 -10000 0 0
MAP3K1 -0.035 0.11 -10000 0 -0.56 4 4
MAP3K7 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.084 0.2 5 -0.63 5 10
DOK1 0.01 0 -10000 0 -10000 0 0
AP-1 -0.005 0.058 0.16 3 -0.25 6 9
LYN 0.01 0 -10000 0 -10000 0 0
BLNK 0.008 0.032 -10000 0 -0.5 2 2
SHC1 0.009 0.024 -10000 0 -0.52 1 1
BCR complex -0.075 0.16 -10000 0 -0.39 93 93
CD22 -0.05 0.11 -10000 0 -0.44 16 16
CAMK2G -0.007 0.074 0.22 1 -0.54 5 6
CSNK2A1 0.01 0 -10000 0 -10000 0 0
INPP5D 0.007 0.04 -10000 0 -0.5 3 3
SHC/GRB2/SOS1 -0.045 0.098 -10000 0 -0.44 11 11
GO:0007205 -0.021 0.086 0.2 5 -0.65 5 10
SYK 0.007 0.04 -10000 0 -0.5 3 3
ELK1 -0.014 0.081 0.23 1 -0.6 5 6
NFATC1 -0.055 0.12 -10000 0 -0.41 14 14
B-cell antigen/BCR complex -0.075 0.16 -10000 0 -0.39 93 93
PAG1/CSK -0.001 0.016 -10000 0 -0.35 1 1
NFKBIB 0.006 0.019 -10000 0 -10000 0 0
HRAS -0.012 0.079 0.21 1 -0.54 5 6
NFKBIA 0.007 0.019 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.011 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.052 0.11 -10000 0 -0.5 9 9
mol:GDP -0.021 0.083 0.24 1 -0.63 5 6
PTEN 0.01 0 -10000 0 -10000 0 0
CD79B 0 0.071 -10000 0 -0.52 9 9
NF-kappa-B/RelA/I kappa B alpha 0.011 0.016 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.065 0.13 -10000 0 -0.43 12 12
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
mol:IP3 -0.026 0.085 0.2 5 -0.66 5 10
CSK 0.01 0 -10000 0 -10000 0 0
FOS -0.022 0.096 0.22 1 -0.44 11 12
CHUK 0 0.05 -10000 0 -0.26 4 4
IBTK 0.01 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.033 0.077 -10000 0 -0.42 9 9
PTPN6 -0.046 0.098 -10000 0 -0.54 9 9
RELA 0.01 0 -10000 0 -10000 0 0
BCL2A1 0.01 0.02 -10000 0 -0.089 13 13
VAV2 -0.11 0.15 -10000 0 -0.37 91 91
ubiquitin-dependent protein catabolic process 0.01 0.018 -10000 0 -10000 0 0
BTK -0.069 0.25 0.32 1 -1 32 33
CD19 -0.13 0.17 -10000 0 -0.42 91 91
MAP4K1 0.005 0.051 -10000 0 -0.5 5 5
CD72 0.008 0.032 -10000 0 -0.5 2 2
PAG1 0.009 0.023 -10000 0 -0.5 1 1
MAPK14 -0.024 0.1 -10000 0 -0.46 4 4
SH3BP5 0.004 0.056 -10000 0 -0.5 6 6
PIK3AP1 -0.015 0.1 0.21 4 -0.55 11 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.011 0.11 -10000 0 -0.84 6 6
RAF1 -0.006 0.075 0.21 1 -0.5 5 6
RasGAP/p62DOK/SHIP -0.05 0.11 -10000 0 -0.48 10 10
CD79A -0.089 0.21 -10000 0 -0.52 92 92
re-entry into mitotic cell cycle -0.005 0.058 0.16 3 -0.25 6 9
RASA1 0.01 0 -10000 0 -10000 0 0
MAPK3 0.007 0.064 0.2 1 -0.4 5 6
MAPK1 0.007 0.064 -10000 0 -0.4 5 5
CD72/SHP1 -0.015 0.11 -10000 0 -0.52 9 9
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.024 0.1 -10000 0 -0.46 4 4
actin cytoskeleton organization -0.074 0.15 -10000 0 -0.32 91 91
NF-kappa-B/RelA 0.026 0.029 0.14 1 -10000 0 1
Calcineurin -0.02 0.058 -10000 0 -0.48 5 5
PI3K -0.097 0.12 -10000 0 -0.44 12 12
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.026 0.084 0.22 4 -0.67 5 9
SOS1 0.01 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.009 0.1 -10000 0 -0.69 6 6
DAPP1 -0.028 0.094 -10000 0 -0.85 4 4
cytokine secretion -0.051 0.12 -10000 0 -0.38 14 14
mol:DAG -0.026 0.085 0.2 5 -0.66 5 10
PLCG2 0.007 0.04 -10000 0 -0.5 3 3
MAP2K1 0.001 0.07 0.2 1 -0.46 5 6
B-cell antigen/BCR complex/FcgammaRIIB -0.063 0.14 -10000 0 -0.33 93 93
mol:PI-3-4-5-P3 -0.074 0.091 -10000 0 -0.31 12 12
ETS1 -0.001 0.07 0.22 1 -0.46 6 7
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.054 0.12 -10000 0 -0.5 11 11
B-cell antigen/BCR complex/LYN -0.039 0.091 -10000 0 -0.43 10 10
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 -0.078 0.16 -10000 0 -0.34 88 88
B-cell antigen/BCR complex/LYN/SYK -0.054 0.11 -10000 0 -0.42 17 17
CARD11 -0.03 0.1 0.23 1 -0.31 34 35
FCGR2B 0.009 0.023 -10000 0 -0.5 1 1
PPP3CA 0.01 0 -10000 0 -10000 0 0
BCL10 0.01 0 -10000 0 -10000 0 0
IKK complex 0.004 0.025 -10000 0 -0.092 2 2
PTPRC -0.006 0.088 -10000 0 -0.5 15 15
PDPK1 -0.032 0.079 -10000 0 -0.25 4 4
PPP3CB 0.01 0 -10000 0 -10000 0 0
PPP3CC 0.01 0 -10000 0 -10000 0 0
POU2F2 0.012 0.012 -10000 0 -0.1 1 1
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 -0.18 0.25 -10000 0 -0.52 178 178
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.006 0.046 -10000 0 -0.5 4 4
CDKN1A 0.017 0.042 -10000 0 -0.61 1 1
PRL-3/alpha Tubulin -0.001 0.017 -10000 0 -0.37 1 1
mol:Ca2+ -0.064 0.14 0.2 1 -0.38 83 84
AGT -0.079 0.2 -10000 0 -0.52 83 83
CCNA2 -0.051 0.14 -10000 0 -0.49 15 15
TUBA1B 0.01 0 -10000 0 -10000 0 0
EGR1 -0.004 0.09 -10000 0 -0.35 31 31
CDK2/Cyclin E1 -0.072 0.14 -10000 0 -0.37 20 20
MAPK3 0.017 0.017 -10000 0 -0.37 1 1
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.017 -10000 0 -0.37 1 1
PTP4A1 0.012 0.068 -10000 0 -10000 0 0
PTP4A3 0.009 0.024 -10000 0 -0.52 1 1
PTP4A2 0.01 0 -10000 0 -10000 0 0
ITGB1 0.017 0.017 -10000 0 -0.37 1 1
SRC 0.01 0 -10000 0 -10000 0 0
RAC1 0.018 0.032 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.015 0.065 -10000 0 -10000 0 0
RABGGTA 0.01 0 -10000 0 -10000 0 0
BCAR1 0 0.019 0.2 1 -0.36 1 2
RHOC 0.018 0.032 -10000 0 -10000 0 0
RHOA 0.018 0.032 -10000 0 -10000 0 0
cell motility 0.021 0.035 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.016 0.063 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.004 0.036 -10000 0 -0.36 5 5
ROCK1 0.021 0.035 -10000 0 -10000 0 0
RABGGTB 0.01 0 -10000 0 -10000 0 0
CDK2 0.01 0 -10000 0 -10000 0 0
mitosis 0.012 0.068 -10000 0 -10000 0 0
ATF5 0.009 0.024 -10000 0 -0.52 1 1
BARD1 signaling events

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
BARD1/CSTF1 -0.002 0.028 -10000 0 -0.36 3 3
ATM 0.01 0 -10000 0 -10000 0 0
UBE2D3 0.01 0 -10000 0 -10000 0 0
PRKDC 0.01 0 -10000 0 -10000 0 0
ATR 0.01 0 -10000 0 -10000 0 0
UBE2L3 0.01 0 -10000 0 -10000 0 0
FANCD2 0.02 0.013 -10000 0 -10000 0 0
protein ubiquitination -0.092 0.12 -10000 0 -0.5 4 4
XRCC5 0.01 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.01 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.006 0.02 -10000 0 -10000 0 0
FANCF 0.01 0 -10000 0 -10000 0 0
BRCA1 0.007 0.041 -10000 0 -0.52 3 3
CCNE1 -0.18 0.25 -10000 0 -0.52 178 178
CDK2/Cyclin E1 -0.13 0.18 -10000 0 -0.37 178 178
FANCG 0.01 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.04 -10000 0 -0.36 6 6
FANCE 0.01 0 -10000 0 -10000 0 0
FANCC 0.01 0 -10000 0 -10000 0 0
NBN 0.01 0 -10000 0 -10000 0 0
FANCA -0.01 0.099 -10000 0 -0.52 18 18
DNA repair -0.017 0.12 -10000 0 -0.4 13 13
BRCA1/BARD1/ubiquitin -0.004 0.04 -10000 0 -0.36 6 6
BARD1/DNA-PK -0.002 0.02 -10000 0 -0.27 1 1
FANCL 0.01 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.002 0.028 0.36 3 -10000 0 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.03 0.019 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.004 0.033 -10000 0 -0.3 6 6
BRCA1/BARD1/P53 -0.003 0.029 -10000 0 -0.26 6 6
BARD1/CSTF1/BRCA1 -0.004 0.033 -10000 0 -0.3 6 6
BRCA1/BACH1 0.007 0.041 -10000 0 -0.52 3 3
BARD1 0.007 0.04 -10000 0 -0.5 3 3
PCNA 0.008 0.034 -10000 0 -0.52 2 2
BRCA1/BARD1/UbcH5C -0.004 0.033 -10000 0 -0.3 6 6
BRCA1/BARD1/UbcH7 -0.004 0.033 -10000 0 -0.3 6 6
BRCA1/BARD1/RAD51/PCNA -0.052 0.11 -10000 0 -0.28 87 87
BARD1/DNA-PK/P53 -0.001 0.019 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.04 -10000 0 -0.36 6 6
BRCA1/BARD1/CTIP -0.003 0.029 -10000 0 -0.27 4 4
FA complex 0.026 0.029 -10000 0 -10000 0 0
BARD1/EWS -0.002 0.028 -10000 0 -0.36 3 3
RBBP8 0.018 0 -10000 0 -10000 0 0
TP53 0.01 0 -10000 0 -10000 0 0
TOPBP1 0.01 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.003 0.029 0.26 6 -10000 0 6
BRCA1/BARD1 -0.093 0.12 -10000 0 -0.51 4 4
CSTF1 0.01 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.002 0.028 -10000 0 -0.36 3 3
CDK2 0.01 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.083 0.2 -10000 0 -0.52 86 86
RAD50 0.01 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.04 -10000 0 -0.36 6 6
EWSR1 0.01 0 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.01 0.058 -9999 0 -0.33 15 15
EFNA5 0.002 0.062 -9999 0 -0.51 7 7
FYN 0.008 0.056 -9999 0 -0.29 16 16
neuron projection morphogenesis -0.01 0.058 -9999 0 -0.33 15 15
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.01 0.058 -9999 0 -0.33 15 15
EPHA5 -0.003 0.071 -9999 0 -0.52 9 9
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.03 0.073 0.4 5 -10000 0 5
GNAI2 0.01 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.021 0.076 -10000 0 -0.3 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.057 -10000 0 -0.51 6 6
RhoA/GTP -0.03 0.075 -10000 0 -0.41 5 5
negative regulation of cAMP metabolic process -0.011 0.093 -10000 0 -0.25 36 36
GNAZ -0.033 0.14 -10000 0 -0.5 41 41
GNAI3 0.01 0 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
S1PR5 -0.026 0.13 -10000 0 -0.5 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.011 0.094 -10000 0 -0.25 36 36
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.004 0.057 -9999 0 -0.51 6 6
CDC42/GTP -0.027 0.069 -9999 0 -0.4 4 4
PLCG1 0 0.083 -9999 0 -0.41 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.01 0 -9999 0 -10000 0 0
GNAI3 0.01 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.027 0.068 -9999 0 -0.39 4 4
S1PR5 -0.026 0.13 -9999 0 -0.5 34 34
S1PR4 -0.017 0.11 -9999 0 -0.5 26 26
MAPK3 0 0.083 -9999 0 -0.41 4 4
MAPK1 0 0.083 -9999 0 -0.41 4 4
S1P/S1P5/Gi -0.011 0.094 -9999 0 -0.25 36 36
GNAI1 0.008 0.032 -9999 0 -0.5 2 2
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.021 0.076 -9999 0 -0.3 34 34
RHOA 0.011 0.059 -9999 0 -0.24 26 26
S1P/S1P4/Gi -0.007 0.088 -9999 0 -0.25 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.033 0.14 -9999 0 -0.5 41 41
S1P/S1P4/G12/G13 -0.014 0.059 -9999 0 -0.26 26 26
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.009 0.039 -9999 0 -0.32 4 4
NFATC2 -0.001 0.068 -9999 0 -0.31 20 20
NFATC3 0.012 0.025 -9999 0 -10000 0 0
CD40LG -0.031 0.22 -9999 0 -0.71 23 23
PTGS2 -0.047 0.24 -9999 0 -0.66 34 34
JUNB 0.007 0.04 -9999 0 -0.5 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.009 -9999 0 -10000 0 0
CALM1 0.009 0.007 -9999 0 -10000 0 0
JUN 0.005 0.046 -9999 0 -0.5 4 4
mol:Ca2+ -0.005 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.015 0.11 -9999 0 -0.52 23 23
CREM 0.01 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.048 0.095 -9999 0 -0.48 11 11
FOS -0.024 0.13 -9999 0 -0.51 32 32
IFNG -0.04 0.23 -9999 0 -0.65 37 37
AP-1/NFAT1-c-4 -0.073 0.21 -9999 0 -0.7 25 25
FASLG -0.024 0.2 -9999 0 -0.66 21 21
NFAT1-c-4/ICER1 -0.031 0.069 -9999 0 -0.4 9 9
IL2RA -0.037 0.22 -9999 0 -0.62 33 33
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.041 0.23 -9999 0 -0.69 29 29
JunB/Fra1/NFAT1-c-4 -0.04 0.086 -9999 0 -0.43 10 10
IL4 -0.026 0.2 -9999 0 -0.62 20 20
IL2 -0.002 0.01 -9999 0 -10000 0 0
IL3 -0.01 0.016 -9999 0 -10000 0 0
FKBP1A 0.01 0 -9999 0 -10000 0 0
BATF3 0.009 0.024 -9999 0 -0.52 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.01 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.015 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.04 0.077 -9999 0 -0.34 1 1
NFATC4 -0.007 0.087 -9999 0 -0.35 2 2
ERBB2IP 0.01 0.002 -9999 0 -10000 0 0
HSP90 (dimer) 0.01 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.048 0.091 -9999 0 -0.42 1 1
JUN 0.019 0.064 -9999 0 -0.21 4 4
HRAS 0.01 0.001 -9999 0 -10000 0 0
DOCK7 -0.017 0.1 -9999 0 -0.4 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.054 0.1 -9999 0 -0.51 2 2
AKT1 0.008 0.003 -9999 0 -10000 0 0
BAD 0.015 0.002 -9999 0 -10000 0 0
MAPK10 -0.04 0.071 -9999 0 -0.26 23 23
mol:GTP 0 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.025 0.11 -9999 0 -0.46 1 1
RAF1 0.002 0.095 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.033 0.089 -9999 0 -0.27 60 60
STAT3 0.001 0.002 -9999 0 -10000 0 0
cell migration -0.003 0.079 -9999 0 -0.22 23 23
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.007 0.17 -9999 0 -0.53 23 23
FOS -0.006 0.16 -9999 0 -0.44 44 44
NRAS 0.01 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.048 0.091 -9999 0 -0.42 1 1
MAPK3 -0.001 0.14 -9999 0 -0.49 12 12
MAPK1 -0.001 0.14 -9999 0 -0.49 12 12
JAK2 -0.018 0.1 -9999 0 -0.41 2 2
NF2 -0.002 0.004 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.032 0.11 -9999 0 -0.24 102 102
NRG1 -0.095 0.21 -9999 0 -0.5 101 101
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.019 0.11 -9999 0 -0.34 1 1
MAPK9 -0.023 0.045 -9999 0 -0.2 1 1
ERBB2 -0.002 0.03 -9999 0 -0.38 3 3
ERBB3 0.006 0.033 -9999 0 -0.5 2 2
SHC1 0.009 0.024 -9999 0 -0.52 1 1
RAC1 0.01 0 -9999 0 -10000 0 0
apoptosis 0 0.007 -9999 0 -10000 0 0
STAT3 (dimer) 0.002 0.004 -9999 0 -10000 0 0
RNF41 0.019 0.007 -9999 0 -10000 0 0
FRAP1 0.007 0.002 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.032 0.062 -9999 0 -0.28 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.025 -9999 0 -0.31 3 3
CHRNA1 -0.001 0.14 -9999 0 -0.46 22 22
myelination -0.005 0.087 -9999 0 -0.33 2 2
PPP3CB -0.016 0.096 -9999 0 -0.37 1 1
KRAS 0.009 0.024 -9999 0 -0.52 1 1
RAC1-CDC42/GDP -0.039 0.084 -9999 0 -0.32 2 2
NRG2 -0.048 0.16 -9999 0 -0.5 55 55
mol:GDP -0.032 0.11 -9999 0 -0.24 102 102
SOS1 0.01 0.001 -9999 0 -10000 0 0
MAP2K2 0.009 0.094 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.001 -9999 0 -10000 0 0
PTPN11 -0.018 0.1 -9999 0 -0.4 1 1
MAP2K1 -0.014 0.14 -9999 0 -0.48 11 11
heart morphogenesis -0.048 0.091 -9999 0 -0.42 1 1
RAS family/GDP -0.04 0.078 -9999 0 -0.35 1 1
GRB2 0.01 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.007 -9999 0 -10000 0 0
CHRNE 0.012 0.022 -9999 0 -0.16 4 4
HSP90AA1 0.01 0 -9999 0 -10000 0 0
activation of caspase activity -0.008 0.003 -9999 0 -10000 0 0
nervous system development -0.048 0.091 -9999 0 -0.42 1 1
CDC42 0.01 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 -0.001 0.013 -9999 0 -0.3 1 1
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.01 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.011 0.1 -9999 0 -0.52 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.005 0.043 -9999 0 -0.2 4 4
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.01 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.009 0.023 -9999 0 -0.5 1 1
FYN 0.009 0.023 -9999 0 -0.5 1 1
MAP3K12 0.01 0 -9999 0 -10000 0 0
FGR -0.029 0.14 -9999 0 -0.5 37 37
p38 alpha/TAB1 -0.016 0.051 -9999 0 -0.28 10 10
PRKG1 -0.047 0.16 -9999 0 -0.5 55 55
DUSP8 -0.002 0.075 -9999 0 -0.5 11 11
PGK/cGMP/p38 alpha -0.036 0.094 -9999 0 -0.37 24 24
apoptosis -0.015 0.049 -9999 0 -0.33 6 6
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.01 0 -9999 0 -10000 0 0
DUSP1 -0.042 0.15 -9999 0 -0.5 50 50
PAK1 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.012 -9999 0 -0.26 1 1
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.01 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.008 0.094 -9999 0 -0.37 18 18
BLK -0.075 0.19 -9999 0 -0.52 79 79
HCK -0.012 0.1 -9999 0 -0.5 21 21
MAP2K3 0.01 0 -9999 0 -10000 0 0
DUSP16 0.01 0 -9999 0 -10000 0 0
DUSP10 0.008 0.032 -9999 0 -0.5 2 2
TRAF6/MEKK3 -0.001 0.012 -9999 0 -0.27 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.016 0.068 -9999 0 -0.37 6 6
positive regulation of innate immune response 0.013 0.099 -9999 0 -0.39 17 17
LCK 0.007 0.04 -9999 0 -0.5 3 3
p38alpha-beta/MKP7 0.018 0.095 -9999 0 -0.42 11 11
p38alpha-beta/MKP5 0.017 0.099 -9999 0 -0.44 12 12
PGK/cGMP -0.04 0.11 -9999 0 -0.36 55 55
PAK2 0.01 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.004 0.12 -9999 0 -0.45 16 16
CDC42 0.01 0 -9999 0 -10000 0 0
RALB 0.01 0 -9999 0 -10000 0 0
RALA 0.01 0 -9999 0 -10000 0 0
PAK3 -0.058 0.18 -9999 0 -0.52 62 62
IL2 signaling events mediated by STAT5

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
GAB2 0.006 0.046 -9999 0 -0.5 4 4
ELF1 0 0.059 -9999 0 -0.32 1 1
CCNA2 -0.12 0.23 -9999 0 -0.52 119 119
PIK3CA 0.011 0 -9999 0 -10000 0 0
JAK3 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
JAK1 0.011 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.051 0.047 -9999 0 -0.5 1 1
SHC1 0.009 0.024 -9999 0 -0.52 1 1
SP1 0.01 0.046 -9999 0 -0.32 9 9
IL2RA -0.005 0.11 -9999 0 -0.4 35 35
IL2RB 0.008 0.033 -9999 0 -0.5 2 2
SOS1 0.011 0 -9999 0 -10000 0 0
IL2RG 0.005 0.051 -9999 0 -0.5 5 5
G1/S transition of mitotic cell cycle -0.017 0.13 -9999 0 -0.72 10 10
PTPN11 0.011 0 -9999 0 -10000 0 0
CCND2 0.01 0.1 -9999 0 -0.73 9 9
LCK 0.007 0.04 -9999 0 -0.5 3 3
GRB2 0.011 0 -9999 0 -10000 0 0
IL2 0.007 0.005 -9999 0 -10000 0 0
CDK6 0.007 0.04 -9999 0 -0.5 3 3
CCND3 0.055 0.043 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.013 0.008 -10000 0 -10000 0 0
HSPA8 0.009 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.012 0.078 0.2 1 -0.32 24 25
AKT1 0.007 0.02 -10000 0 -10000 0 0
GSC -0.026 0.1 -10000 0 -0.43 1 1
NKX2-5 -0.028 0.13 -10000 0 -0.51 31 31
muscle cell differentiation 0.021 0.054 0.33 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.044 0.056 -10000 0 -10000 0 0
SMAD4 0.018 0.024 -10000 0 -10000 0 0
CBFB 0.01 0 -10000 0 -10000 0 0
SAP18 0.01 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.012 0.078 -10000 0 -0.29 34 34
SMAD3/SMAD4/VDR 0.01 0.032 -10000 0 -0.31 1 1
MYC 0.011 0.038 -10000 0 -0.5 2 2
CDKN2B -0.062 0.34 -10000 0 -1.3 35 35
AP1 0.027 0.084 -10000 0 -0.49 4 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.045 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.095 -10000 0 -0.32 23 23
SP3 0.012 0 -10000 0 -10000 0 0
CREB1 0.01 0 -10000 0 -10000 0 0
FOXH1 -0.057 0.17 -10000 0 -0.52 61 61
SMAD3/SMAD4/GR 0.002 0.022 -10000 0 -10000 0 0
GATA3 0.009 0.044 -10000 0 -0.5 3 3
SKI/SIN3/HDAC complex/NCoR1 0.032 0.015 -10000 0 -10000 0 0
MEF2C/TIF2 -0.036 0.1 -10000 0 -0.46 7 7
endothelial cell migration -0.005 0.068 1.3 1 -10000 0 1
MAX 0.009 0.003 -10000 0 -10000 0 0
RBBP7 0.01 0.001 -10000 0 -10000 0 0
RBBP4 0.01 0.001 -10000 0 -10000 0 0
RUNX2 0.002 0.063 -10000 0 -0.52 7 7
RUNX3 0.007 0.04 -10000 0 -0.5 3 3
RUNX1 0.01 0 -10000 0 -10000 0 0
CTBP1 0.01 0 -10000 0 -10000 0 0
NR3C1 0.009 0.003 -10000 0 -10000 0 0
VDR 0.008 0.033 -10000 0 -0.51 2 2
CDKN1A 0.049 0.068 -10000 0 -1.2 1 1
KAT2B 0.011 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.043 0.1 -10000 0 -0.31 60 60
DCP1A 0.01 0 -10000 0 -10000 0 0
SKI 0.01 0.001 -10000 0 -10000 0 0
SERPINE1 0.005 0.069 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.003 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.013 0.069 -10000 0 -0.3 23 23
SAP30 0.01 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.012 0.027 -10000 0 -10000 0 0
JUN 0.027 0.083 -10000 0 -0.49 4 4
SMAD3/SMAD4/IRF7 0.001 0.037 -10000 0 -0.43 2 2
TFE3 0.015 0.003 -10000 0 -10000 0 0
COL1A2 -0.01 0.093 -10000 0 -0.41 20 20
mesenchymal cell differentiation 0.002 0.044 0.32 7 -10000 0 7
DLX1 -0.026 0.13 -10000 0 -0.52 31 31
TCF3 0.01 0 -10000 0 -10000 0 0
FOS -0.019 0.13 -10000 0 -0.5 32 32
SMAD3/SMAD4/Max 0.002 0.022 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.013 -10000 0 -10000 0 0
ZBTB17 0.012 0.015 -10000 0 -10000 0 0
LAMC1 0.044 0.026 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.003 0.022 -10000 0 -10000 0 0
IRF7 0.008 0.038 -10000 0 -0.58 2 2
ESR1 -0.017 0.11 -10000 0 -0.51 25 25
HNF4A -0.11 0.22 -10000 0 -0.52 107 107
MEF2C -0.016 0.12 -10000 0 -0.46 6 6
SMAD2-3/SMAD4 -0.006 0.027 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.008 0.019 -10000 0 -10000 0 0
IGHV3OR16-13 -0.001 0.006 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0 -10000 0 -10000 0 0
CREBBP 0.012 0.005 -10000 0 -10000 0 0
SKIL 0.01 0 -10000 0 -10000 0 0
HDAC1 0.01 0.001 -10000 0 -10000 0 0
HDAC2 0.01 0.001 -10000 0 -10000 0 0
SNIP1 0.009 0.003 -10000 0 -10000 0 0
GCN5L2 0.002 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.005 0.025 -10000 0 -10000 0 0
MSG1/HSC70 -0.025 0.091 -10000 0 -0.36 34 34
SMAD2 0.007 0.022 -10000 0 -10000 0 0
SMAD3 0.019 0.022 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.036 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.016 0.012 -10000 0 -10000 0 0
NCOR1 0.01 0.001 -10000 0 -10000 0 0
NCOA2 0.006 0.046 -10000 0 -0.5 4 4
NCOA1 0.01 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.029 -10000 0 -0.37 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.049 0.055 -10000 0 -10000 0 0
IFNB1 0.032 0.049 -10000 0 -0.58 2 2
SMAD3/SMAD4/MEF2C -0.003 0.12 -10000 0 -0.47 5 5
CITED1 -0.027 0.13 -10000 0 -0.5 34 34
SMAD2-3/SMAD4/ARC105 -0.003 0.023 -10000 0 -10000 0 0
RBL1 0.01 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.017 0.13 -10000 0 -0.46 35 35
RUNX1-3/PEBPB2 -0.002 0.023 -10000 0 -0.29 3 3
SMAD7 0.051 0.091 -10000 0 -0.57 3 3
MYC/MIZ-1 0.009 0.045 -10000 0 -0.36 2 2
SMAD3/SMAD4 0.025 0.065 0.28 2 -0.44 1 3
IL10 0.033 0.078 -10000 0 -0.49 9 9
PIASy/HDAC complex 0.008 0.004 -10000 0 -10000 0 0
PIAS3 0.011 0.003 -10000 0 -10000 0 0
CDK2 0.012 0.005 -10000 0 -10000 0 0
IL5 0.033 0.045 -10000 0 -10000 0 0
CDK4 0.008 0.048 -10000 0 -0.52 4 4
PIAS4 0.008 0.005 -10000 0 -10000 0 0
ATF3 -0.015 0.11 -10000 0 -0.5 24 24
SMAD3/SMAD4/SP1 0.003 0.037 -10000 0 -10000 0 0
FOXG1 -0.054 0.16 -10000 0 -0.52 53 53
FOXO3 0.015 0.026 -10000 0 -10000 0 0
FOXO1 0.015 0.026 -10000 0 -10000 0 0
FOXO4 0.015 0.026 -10000 0 -10000 0 0
heart looping -0.016 0.12 -10000 0 -0.46 6 6
CEBPB 0.009 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.019 0.083 -10000 0 -0.33 31 31
MYOD1 -0.002 0.041 -10000 0 -0.52 3 3
SMAD3/SMAD4/HNF4 -0.067 0.13 -10000 0 -0.31 107 107
SMAD3/SMAD4/GATA3 -0.001 0.044 -10000 0 -0.35 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.01 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.003 0.032 -10000 0 -0.31 3 3
SMAD3/SMAD4/SP1-3 0.023 0.042 -10000 0 -10000 0 0
MED15 0.01 0 -10000 0 -10000 0 0
SP1 0.013 0.022 -10000 0 -10000 0 0
SIN3B 0.01 0.001 -10000 0 -10000 0 0
SIN3A 0.01 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.035 0.13 -10000 0 -0.38 23 23
ITGB5 0.05 0.035 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.037 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.037 0.11 -10000 0 -0.31 63 63
AR -0.057 0.17 -10000 0 -0.5 64 64
negative regulation of cell growth 0.035 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.001 0.033 -10000 0 -0.32 3 3
E2F5 0.006 0.048 -10000 0 -0.52 4 4
E2F4 0.01 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.031 0.083 -10000 0 -0.33 6 6
SMAD2-3/SMAD4/FOXO1-3a-4 0.024 0.095 -10000 0 -0.31 35 35
TFDP1 0.009 0.024 -10000 0 -0.52 1 1
SMAD3/SMAD4/AP1 0.03 0.085 -10000 0 -0.5 4 4
SMAD3/SMAD4/RUNX2 -0.002 0.045 -10000 0 -0.32 7 7
TGIF2 0.01 0 -10000 0 -10000 0 0
TGIF1 0.01 0 -10000 0 -10000 0 0
ATF2 0.01 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.015 0.061 -10000 0 -0.26 27 27
ER alpha/Gai/GDP/Gbeta gamma 0.005 0.09 -10000 0 -0.37 14 14
AKT1 0.008 0.12 -10000 0 -0.72 12 12
PIK3CA 0.01 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.005 0.12 -10000 0 -0.73 12 12
mol:Ca2+ 0.014 0.089 -10000 0 -0.41 15 15
IGF1R 0.008 0.032 -10000 0 -0.5 2 2
E2/ER alpha (dimer)/Striatin -0.016 0.068 -10000 0 -0.3 26 26
SHC1 0.009 0.024 -10000 0 -0.52 1 1
apoptosis -0.008 0.11 0.69 12 -10000 0 12
RhoA/GTP -0.011 0.047 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.025 0.074 -10000 0 -0.38 14 14
regulation of stress fiber formation -0.029 0.051 0.36 1 -10000 0 1
E2/ERA-ERB (dimer) -0.017 0.07 -10000 0 -0.3 27 27
KRAS 0.009 0.024 -10000 0 -0.52 1 1
G13/GTP -0.014 0.061 -10000 0 -0.28 25 25
pseudopodium formation 0.029 0.051 -10000 0 -0.36 1 1
E2/ER alpha (dimer)/PELP1 -0.016 0.067 -10000 0 -0.3 25 25
GRB2 0.01 0 -10000 0 -10000 0 0
GNG2 0.008 0.032 -10000 0 -0.5 2 2
GNAO1 0.004 0.057 -10000 0 -0.51 6 6
HRAS 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.012 0.091 -10000 0 -0.43 14 14
E2/ER beta (dimer) -0.002 0.023 -10000 0 -0.37 2 2
mol:GDP -0.014 0.061 -10000 0 -0.34 13 13
mol:NADP 0.012 0.091 -10000 0 -0.43 14 14
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
mol:IP3 0.014 0.093 -10000 0 -0.43 15 15
IGF-1R heterotetramer 0.008 0.032 -10000 0 -0.5 2 2
PLCB1 0.013 0.083 -10000 0 -0.42 14 14
PLCB2 0.008 0.095 -10000 0 -0.45 15 15
IGF1 -0.002 0.076 -10000 0 -0.5 11 11
mol:L-citrulline 0.012 0.091 -10000 0 -0.43 14 14
RHOA 0.01 0 -10000 0 -10000 0 0
Gai/GDP -0.021 0.074 -10000 0 -0.65 3 3
JNK cascade -0.002 0.023 -10000 0 -0.37 2 2
BCAR1 0.009 0.023 -10000 0 -0.5 1 1
ESR2 0.008 0.033 -10000 0 -0.51 2 2
GNAQ 0.009 0.023 -10000 0 -0.5 1 1
ESR1 -0.017 0.11 -10000 0 -0.51 25 25
Gq family/GDP/Gbeta gamma 0.023 0.055 -10000 0 -0.43 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.019 0.047 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.025 0.073 -10000 0 -0.39 13 13
GNAZ -0.033 0.14 -10000 0 -0.5 41 41
E2/ER alpha (dimer) -0.019 0.081 -10000 0 -0.37 25 25
STRN 0.009 0.023 -10000 0 -0.5 1 1
GNAL -0.002 0.076 -10000 0 -0.5 11 11
PELP1 0.01 0 -10000 0 -10000 0 0
MAPK11 0.012 0.032 -10000 0 -0.3 5 5
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.032 -10000 0 -0.5 2 2
HBEGF -0.031 0.11 -10000 0 -0.39 19 19
cAMP biosynthetic process -0.019 0.067 -10000 0 -0.25 36 36
SRC 0.011 0.086 -10000 0 -0.36 13 13
PI3K -0.001 0.016 -10000 0 -0.35 1 1
GNB1 0.01 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.013 0.056 -10000 0 -0.32 12 12
SOS1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.024 0.07 -10000 0 -0.45 5 5
Gs family/GTP -0.019 0.068 -10000 0 -0.26 36 36
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.012 -10000 0 -0.28 1 1
vasodilation 0.013 0.088 -10000 0 -0.41 14 14
mol:DAG 0.014 0.093 -10000 0 -0.43 15 15
Gs family/GDP/Gbeta gamma -0.016 0.062 -10000 0 -0.34 12 12
MSN 0.03 0.054 -10000 0 -0.39 1 1
Gq family/GTP -0.018 0.08 -10000 0 -0.45 14 14
mol:PI-3-4-5-P3 0.005 0.12 -10000 0 -0.7 12 12
NRAS 0.01 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.013 0.088 0.41 14 -10000 0 14
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.013 0.057 -10000 0 -0.32 13 13
NOS3 0.012 0.095 -10000 0 -0.45 14 14
GNA11 0.008 0.032 -10000 0 -0.5 2 2
MAPKKK cascade 0.02 0.097 -10000 0 -0.53 12 12
E2/ER alpha (dimer)/PELP1/Src -0.026 0.077 -10000 0 -0.41 13 13
ruffle organization 0.029 0.051 -10000 0 -0.36 1 1
ROCK2 0.026 0.053 -10000 0 -10000 0 0
GNA14 -0.005 0.085 -10000 0 -0.5 14 14
GNA15 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
MMP9 -0.035 0.13 -10000 0 -0.45 13 13
MMP2 0.016 0.083 -10000 0 -0.5 3 3
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.024 0 -9999 0 -10000 0 0
SNTA1 0.006 0.048 -9999 0 -0.52 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.022 0.026 -9999 0 -0.3 3 3
MAPK12 0.012 0.057 -9999 0 -0.26 20 20
CCND1 0.007 0.056 -9999 0 -0.43 6 6
p38 gamma/SNTA1 0.015 0.059 -9999 0 -0.25 21 21
MAP2K3 0.01 0 -9999 0 -10000 0 0
PKN1 0.01 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.012 0.057 -9999 0 -0.26 20 20
MAP2K6 0.006 0.063 -9999 0 -0.3 20 20
MAPT 0.006 0.072 -9999 0 -0.29 24 24
MAPK13 0.018 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.013 0.015 -9999 0 -0.31 1 1
IL27-mediated signaling events

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
TGFB1 0.009 0.023 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.002 0.078 0.52 2 -10000 0 2
IL27/IL27R/JAK1 -0.027 0.085 -10000 0 -0.76 2 2
TBX21 -0.001 0.14 -10000 0 -0.49 24 24
IL12B 0.004 0.053 -10000 0 -0.52 5 5
IL12A 0.004 0.041 -10000 0 -0.36 6 6
IL6ST -0.008 0.094 -10000 0 -0.5 17 17
IL27RA/JAK1 0.011 0.056 -10000 0 -1.2 1 1
IL27 -0.005 0.083 -10000 0 -0.5 13 13
TYK2 0.011 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.064 0.12 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.002 0.078 0.52 2 -10000 0 2
T cell proliferation during immune response -0.002 0.078 0.52 2 -10000 0 2
MAPKKK cascade 0.002 0.078 -10000 0 -0.52 2 2
STAT3 0.01 0 -10000 0 -10000 0 0
STAT2 0.01 0 -10000 0 -10000 0 0
STAT1 0.01 0.002 -10000 0 -10000 0 0
IL12RB1 -0.006 0.088 -10000 0 -0.5 15 15
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.009 0.16 -10000 0 -0.51 20 20
IL27/IL27R/JAK2/TYK2 0.002 0.079 -10000 0 -0.53 2 2
positive regulation of T cell mediated cytotoxicity 0.002 0.078 -10000 0 -0.52 2 2
STAT1 (dimer) -0.046 0.13 0.48 1 -0.63 9 10
JAK2 0.008 0.033 -10000 0 -0.5 2 2
JAK1 0.01 0.002 -10000 0 -10000 0 0
STAT2 (dimer) 0.007 0.075 -10000 0 -0.5 2 2
T cell proliferation -0.05 0.13 -10000 0 -0.45 16 16
IL12/IL12R/TYK2/JAK2 0.008 0.079 -10000 0 -0.6 2 2
IL17A -0.064 0.12 -10000 0 -10000 0 0
mast cell activation -0.002 0.078 0.52 2 -10000 0 2
IFNG 0.001 0.027 -10000 0 -0.12 9 9
T cell differentiation -0.003 0.005 -10000 0 -0.021 20 20
STAT3 (dimer) 0.007 0.075 -10000 0 -0.5 2 2
STAT5A (dimer) 0.007 0.079 -10000 0 -0.61 2 2
STAT4 (dimer) 0.007 0.075 -10000 0 -0.5 2 2
STAT4 0.01 0 -10000 0 -10000 0 0
T cell activation -0.006 0.006 0.12 1 -10000 0 1
IL27R/JAK2/TYK2 -0.011 0.074 -10000 0 -0.74 2 2
GATA3 0.003 0.082 -10000 0 -1.2 2 2
IL18 0.002 0.05 -10000 0 -0.36 9 9
positive regulation of mast cell cytokine production 0.007 0.074 -10000 0 -0.49 2 2
IL27/EBI3 -0.005 0.064 -10000 0 -0.36 15 15
IL27RA 0.001 0.058 -10000 0 -1.2 1 1
IL6 -0.11 0.21 -10000 0 -0.5 111 111
STAT5A 0.009 0.023 -10000 0 -0.5 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.003 0.022 0.46 1 -10000 0 1
IL1B -0.012 0.086 -10000 0 -0.36 28 28
EBI3 0.007 0.033 -10000 0 -0.51 2 2
TNF -0.005 0.071 -10000 0 -0.36 19 19
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.019 0.1 -9999 0 -0.33 32 32
MAP3K8 0.008 0.033 -9999 0 -0.5 2 2
FOS 0.021 0.07 -9999 0 -0.37 5 5
PRKCA 0.008 0.033 -9999 0 -0.5 2 2
PTPN7 0.011 0.003 -9999 0 -10000 0 0
HRAS 0.01 0.001 -9999 0 -10000 0 0
PRKCB -0.003 0.082 -9999 0 -0.5 13 13
NRAS 0.01 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.013 -9999 0 -0.3 1 1
MAPK3 0.02 0.041 -9999 0 -10000 0 0
MAP2K1 0.017 0.08 -9999 0 -0.41 15 15
ELK1 0.009 0.005 -9999 0 -10000 0 0
BRAF -0.014 0.067 -9999 0 -0.39 15 15
mol:GTP 0 0.001 -9999 0 -0.005 32 32
MAPK1 0.02 0.041 -9999 0 -10000 0 0
RAF1 -0.014 0.067 -9999 0 -0.39 15 15
KRAS 0.009 0.024 -9999 0 -0.52 1 1
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.009 0.023 -9999 0 -0.5 1 1
SPHK1 0.006 0.048 -9999 0 -0.52 4 4
GNAI2 0.01 0 -9999 0 -10000 0 0
mol:S1P 0.016 0.019 -9999 0 -0.27 1 1
GNAO1 0.004 0.057 -9999 0 -0.51 6 6
mol:Sphinganine-1-P 0.014 0.038 -9999 0 -0.36 5 5
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.011 -9999 0 -10000 0 0
GNAI3 0.01 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.009 0.024 -9999 0 -0.52 1 1
S1PR2 0.01 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.015 -9999 0 -0.23 1 1
S1PR5 -0.026 0.13 -9999 0 -0.5 34 34
S1PR4 -0.017 0.11 -9999 0 -0.5 26 26
GNAI1 0.008 0.032 -9999 0 -0.5 2 2
S1P/S1P5/G12 -0.019 0.065 -9999 0 -0.25 34 34
S1P/S1P3/Gq 0.021 0.056 -9999 0 -0.27 14 14
S1P/S1P4/Gi -0.001 0.089 -9999 0 -0.42 5 5
GNAQ 0.009 0.023 -9999 0 -0.5 1 1
GNAZ -0.033 0.14 -9999 0 -0.5 41 41
GNA14 -0.005 0.085 -9999 0 -0.5 14 14
GNA15 0.01 0 -9999 0 -10000 0 0
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
GNA11 0.008 0.032 -9999 0 -0.5 2 2
ABCC1 0.01 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.008 0.032 -10000 0 -0.5 2 2
ANTXR2 0.009 0.023 -10000 0 -0.5 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.005 -10000 0 -0.066 3 3
monocyte activation -0.005 0.092 -10000 0 -0.44 19 19
MAP2K2 0 0.002 -10000 0 -10000 0 0
MAP2K1 0 0.004 -10000 0 -10000 0 0
MAP2K7 0 0.004 -10000 0 -10000 0 0
MAP2K6 -0.011 0.052 -10000 0 -0.27 19 19
CYAA 0.011 0.021 -10000 0 -0.25 3 3
MAP2K4 0 0.004 -10000 0 -10000 0 0
IL1B -0.002 0.064 -10000 0 -0.26 29 29
Channel -0.002 0.021 -10000 0 -0.27 3 3
NLRP1 -0.001 0.017 -10000 0 -0.26 2 2
CALM1 0.01 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.005 0.066 3 -10000 0 3
MAPK3 0 0.004 -10000 0 -10000 0 0
MAPK1 0 0.004 -10000 0 -10000 0 0
PGR -0.045 0.098 -10000 0 -0.26 84 84
PA/Cellular Receptors -0.002 0.023 -10000 0 -0.3 3 3
apoptosis 0 0.005 -10000 0 -0.066 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.011 0.021 -10000 0 -0.25 3 3
macrophage activation 0.015 0.005 -10000 0 -10000 0 0
TNF -0.01 0.099 -10000 0 -0.5 19 19
VCAM1 -0.005 0.093 -10000 0 -0.44 19 19
platelet activation 0 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.015 -10000 0 -10000 0 0
IL18 0.008 0.045 -10000 0 -0.31 9 9
negative regulation of macrophage activation 0 0.005 -10000 0 -0.066 3 3
LEF 0 0.005 -10000 0 -0.066 3 3
CASP1 -0.002 0.017 -10000 0 -0.22 2 2
mol:cAMP 0 0.006 -10000 0 -10000 0 0
necrosis 0 0.005 -10000 0 -0.066 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.002 0.02 -10000 0 -0.25 3 3
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.01 0 -10000 0 -10000 0 0
HDAC3 0.01 0 -10000 0 -10000 0 0
VDR 0.008 0.033 -10000 0 -0.51 2 2
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.01 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.032 0.02 -10000 0 -10000 0 0
KAT2B 0.01 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
AKT1 0.016 0.027 0.2 1 -0.23 2 3
RAR alpha/9cRA/Cyclin H -0.007 0.024 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.029 0.021 -10000 0 -10000 0 0
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.006 0.03 -10000 0 -10000 0 0
NCOR2 0.01 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.023 -10000 0 -0.37 2 2
RXRs/RARs/NRIP1/9cRA -0.013 0.068 -10000 0 -0.55 2 2
NCOA2 0.006 0.046 -10000 0 -0.5 4 4
NCOA3 0.01 0 -10000 0 -10000 0 0
NCOA1 0.01 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.008 0.033 -10000 0 -0.51 2 2
RARG 0.011 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.011 0 -10000 0 -10000 0 0
MAPK1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.011 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.045 0.058 -10000 0 -0.5 3 3
RARA 0.01 0.041 -10000 0 -0.23 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.028 0.028 -10000 0 -10000 0 0
PRKCA 0.011 0.033 -10000 0 -0.5 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.027 0.076 -10000 0 -0.59 2 2
RXRG -0.17 0.18 -10000 0 -0.33 259 259
RXRA 0.017 0.038 -10000 0 -0.22 2 2
RXRB 0.002 0.062 -10000 0 -0.31 2 2
VDR/Vit D3/DNA -0.002 0.023 -10000 0 -0.37 2 2
RBP1 0.003 0.058 -10000 0 -0.51 6 6
CRBP1/9-cic-RA -0.005 0.041 -10000 0 -0.37 6 6
RARB 0.01 0.033 -10000 0 -0.5 2 2
PRKCG -0.039 0.15 -10000 0 -0.51 46 46
MNAT1 0.01 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.067 -10000 0 -0.59 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.005 0.06 -10000 0 -0.45 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.03 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.027 0.076 -10000 0 -0.59 2 2
positive regulation of DNA binding -0.007 0.023 -10000 0 -10000 0 0
NRIP1 -0.025 0.072 -10000 0 -0.54 2 2
RXRs/RARs -0.034 0.078 -10000 0 -0.49 3 3
RXRs/RXRs/DNA/9cRA -0.048 0.06 -10000 0 -0.61 2 2
PRKACA 0.01 0 -10000 0 -10000 0 0
CDK7 0.01 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.016 -10000 0 -10000 0 0
CCNH 0.01 0 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.004 0.056 -9999 0 -0.5 6 6
CLTC 0.01 0.047 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.02 0.003 -9999 0 -10000 0 0
Dynamin 2/GTP -0.027 0.081 -9999 0 -0.28 47 47
EXOC4 0.01 0 -9999 0 -10000 0 0
CD59 0.013 0.031 -9999 0 -10000 0 0
CPE 0.003 0.06 -9999 0 -0.31 17 17
CTNNB1 0.01 0 -9999 0 -10000 0 0
membrane fusion 0.021 0 -9999 0 -10000 0 0
CTNND1 -0.001 0.082 -9999 0 -0.25 47 47
DNM2 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.022 -9999 0 -10000 0 0
TSHR -0.018 0.097 -9999 0 -0.31 48 48
INS 0.007 0.008 -9999 0 -10000 0 0
BIN1 0.01 0 -9999 0 -10000 0 0
mol:Choline 0.021 0 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP -0.017 0.096 -9999 0 -0.31 47 47
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ -0.026 0.081 -9999 0 -0.27 47 47
JUP 0.013 0.032 -9999 0 -10000 0 0
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 0.012 0.033 -9999 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 0.008 0.034 -9999 0 -0.52 2 2
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.01 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.034 0 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.01 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.019 0.056 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.015 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 -0.001 0.02 -9999 0 -0.31 2 2
ACAP1 0.02 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 -0.027 0.088 -9999 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.015 0.044 -9999 0 -10000 0 0
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.01 0 -9999 0 -10000 0 0
exocyst 0.034 0 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 -0.001 0.082 -9999 0 -10000 0 0
NME1 -0.017 0.096 -9999 0 -0.31 47 47
clathrin coat assembly 0.01 0.047 -9999 0 -10000 0 0
IL2RA 0.003 0.047 -9999 0 -10000 0 0
VAMP3 0.015 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.013 0.043 -9999 0 -0.34 3 3
EXOC6 0.01 0 -9999 0 -10000 0 0
PLD1 0 0 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.01 0 -9999 0 -10000 0 0
PIP5K1C 0.019 0.022 -9999 0 -10000 0 0
SDC1 0.013 0.031 -9999 0 -10000 0 0
ARF6/GDP -0.017 0.096 -9999 0 -0.31 47 47
EXOC7 0.01 0 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.019 0.058 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.021 0 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.01 0 -9999 0 -10000 0 0
ADRB2 -0.081 0.14 -9999 0 -0.37 32 32
EXOC3 0.01 0 -9999 0 -10000 0 0
ASAP2 0.01 0 -9999 0 -10000 0 0
Dynamin 2/GDP -0.009 0.087 -9999 0 -0.27 47 47
KLC1 0.01 0 -9999 0 -10000 0 0
AVPR2 -0.039 0.12 -9999 0 -0.37 16 16
RALA 0.01 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.051 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.063 0.18 -9999 0 -0.57 13 13
RAD9A 0.01 0 -9999 0 -10000 0 0
AP1 -0.016 0.096 -9999 0 -0.36 36 36
IFNAR2 0.008 0.005 -9999 0 -10000 0 0
AKT1 0.002 0.044 -9999 0 -0.22 6 6
ER alpha/Oestrogen -0.015 0.082 -9999 0 -0.37 25 25
NFX1/SIN3/HDAC complex 0.028 0.018 -9999 0 -10000 0 0
EGF -0.092 0.21 -9999 0 -0.52 92 92
SMG5 0.01 0 -9999 0 -10000 0 0
SMG6 0.01 0 -9999 0 -10000 0 0
SP3/HDAC2 0.012 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.086 0.14 -9999 0 -0.56 11 11
SAP18 0.008 0.004 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.034 0.14 -9999 0 -0.51 39 39
WRN 0.01 0 -9999 0 -10000 0 0
SP1 0.009 0.006 -9999 0 -10000 0 0
SP3 0.008 0.005 -9999 0 -10000 0 0
TERF2IP 0.01 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.079 0.12 -9999 0 -0.66 5 5
Mad/Max 0.011 0.008 -9999 0 -10000 0 0
TERT -0.065 0.18 -9999 0 -0.6 12 12
CCND1 -0.058 0.19 -9999 0 -1.2 6 6
MAX 0.008 0.005 -9999 0 -10000 0 0
RBBP7 0.008 0.004 -9999 0 -10000 0 0
RBBP4 0.008 0.004 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.01 0 -9999 0 -10000 0 0
SIN3A 0.008 0.004 -9999 0 -10000 0 0
Telomerase/911 0.022 0.029 -9999 0 -10000 0 0
CDKN1B -0.004 0.087 -9999 0 -10000 0 0
RAD1 0.01 0 -9999 0 -10000 0 0
XRCC5 0.01 0 -9999 0 -10000 0 0
XRCC6 0.01 0 -9999 0 -10000 0 0
SAP30 0.008 0.004 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.007 0.005 -9999 0 -10000 0 0
JUN 0.004 0.046 -9999 0 -0.5 4 4
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.005 -9999 0 -10000 0 0
FOS -0.026 0.13 -9999 0 -0.5 32 32
IFN-gamma/IRF1 -0.029 0.097 -9999 0 -0.36 40 40
PARP2 0.01 0 -9999 0 -10000 0 0
BLM -0.042 0.16 -9999 0 -0.52 48 48
Telomerase -0.021 0.058 -9999 0 -10000 0 0
IRF1 0.01 0.007 -9999 0 -10000 0 0
ESR1 -0.018 0.11 -9999 0 -0.51 25 25
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.03 0.02 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.03 0.02 -9999 0 -10000 0 0
HDAC1 0.008 0.004 -9999 0 -10000 0 0
HDAC2 0.009 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.02 0.004 -9999 0 -10000 0 0
ABL1 0.01 0 -9999 0 -10000 0 0
MXD1 0.008 0.005 -9999 0 -10000 0 0
MRE11A 0.01 0 -9999 0 -10000 0 0
HUS1 0.01 0 -9999 0 -10000 0 0
RPS6KB1 0.01 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.08 0.14 -9999 0 -0.61 7 7
NR2F2 0.013 0.007 -9999 0 -10000 0 0
MAPK3 0.011 0.008 -9999 0 -10000 0 0
MAPK1 0.011 0.008 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.011 0.002 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
HNRNPC 0.01 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.01 0 -9999 0 -10000 0 0
EGFR -0.007 0.087 -9999 0 -0.51 14 14
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.08 0.16 -9999 0 -0.38 103 103
MYC 0.006 0.033 -9999 0 -0.5 2 2
IL2 0.004 0.011 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
TGFB1 0.011 0.002 -9999 0 -10000 0 0
TRF2/BLM -0.033 0.1 -9999 0 -0.34 48 48
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.081 0.14 -9999 0 -0.64 7 7
SP1/HDAC2 0.013 0.011 -9999 0 -10000 0 0
PINX1 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.079 0.12 -9999 0 -0.66 5 5
Smad3/Myc 0.021 0.02 -9999 0 -0.29 2 2
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.033 0.14 -9999 0 -0.51 40 40
Telomerase/PinX1 -0.079 0.12 -9999 0 -0.66 5 5
Telomerase/AKT1/mTOR/p70S6K 0.006 0.054 -9999 0 -10000 0 0
SIN3B 0.008 0.004 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.079 0.12 -9999 0 -0.66 5 5
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.079 0.12 -9999 0 -0.66 5 5
E2F1 0.001 0.064 -9999 0 -0.52 7 7
ZNFX1 0.008 0.004 -9999 0 -10000 0 0
PIF1 -0.064 0.18 -9999 0 -0.52 68 68
NCL 0.01 0 -9999 0 -10000 0 0
DKC1 0.01 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.013 0.054 -9999 0 -0.46 1 1
TC10/GTP -0.012 0.051 -9999 0 -0.44 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.012 -9999 0 -10000 0 0
HRAS 0.01 0 -9999 0 -10000 0 0
APS homodimer 0.009 0.023 -9999 0 -0.5 1 1
GRB14 -0.026 0.13 -9999 0 -0.51 33 33
FOXO3 -0.005 0.04 -9999 0 -0.6 2 2
AKT1 0.024 0.062 -9999 0 -10000 0 0
INSR 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0 -9999 0 -10000 0 0
SORBS1 -0.018 0.12 -9999 0 -0.5 27 27
CRK 0.01 0 -9999 0 -10000 0 0
PTPN1 0.028 0 -9999 0 -10000 0 0
CAV1 -0.15 0.13 -9999 0 -0.25 313 313
CBL/APS/CAP/Crk-II/C3G -0.014 0.057 -9999 0 -0.49 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.001 0.012 -9999 0 -0.27 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.015 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.03 0.012 -9999 0 -10000 0 0
RPS6KB1 0.029 0.058 -9999 0 -10000 0 0
PARD6A 0.009 0.023 -9999 0 -0.5 1 1
CBL 0.01 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.001 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.045 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.019 -9999 0 -10000 0 0
Insulin Receptor 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.001 0.016 -9999 0 -10000 0 0
PRKCI -0.004 0.013 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.015 0.056 -9999 0 -10000 0 0
SHC1 0.009 0.024 -9999 0 -0.52 1 1
negative regulation of MAPKKK cascade 0 0.002 -9999 0 -10000 0 0
PI3K -0.001 0.015 -9999 0 -10000 0 0
NCK2 0.01 0 -9999 0 -10000 0 0
RHOQ 0.01 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 0.024 0.062 -9999 0 -10000 0 0
PRKCZ -0.007 0.037 -9999 0 -0.45 3 3
SH2B2 0.009 0.023 -9999 0 -0.5 1 1
SHC/SHIP 0.024 0.026 -9999 0 -10000 0 0
F2RL2 -0.031 0.14 -9999 0 -0.52 38 38
TRIP10 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.013 -9999 0 -0.29 1 1
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.012 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.015 0.062 -9999 0 -0.27 27 27
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.013 -9999 0 -0.28 1 1
INPP5D 0.019 0.024 -9999 0 -0.25 4 4
SOS1 0.01 0 -9999 0 -10000 0 0
SGK1 -0.005 0.054 -9999 0 -0.85 2 2
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
IRS1 0.009 0.023 -9999 0 -0.5 1 1
p62DOK/RasGAP 0 0.002 -9999 0 -10000 0 0
INS 0.002 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.019 0.024 -9999 0 -0.25 4 4
GRB2 0.01 0 -9999 0 -10000 0 0
EIF4EBP1 0.021 0.075 -9999 0 -0.42 3 3
PTPRA 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.026 0.013 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.001 0.012 -9999 0 -0.28 1 1
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.02 0.068 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG 0.021 0.054 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -9999 0 -10000 0 0
CaM/Ca2+ 0.026 0.051 -9999 0 -10000 0 0
HIF1A 0.016 0 -9999 0 -10000 0 0
GAB1 0.007 0.04 -9999 0 -0.5 3 3
AKT1 0.038 0.045 -9999 0 -10000 0 0
PLCG1 0.022 0.054 -9999 0 -10000 0 0
NOS3 0.038 0.053 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
mol:NO 0.038 0.052 -9999 0 -10000 0 0
FLT1 0.024 0 -9999 0 -10000 0 0
PGF -0.008 0.097 -9999 0 -0.52 17 17
VEGFR1 homodimer/NRP2/VEGFR121 -0.002 0.02 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.042 0.051 -9999 0 -10000 0 0
endothelial cell proliferation 0.029 0.06 -9999 0 -0.38 3 3
mol:Ca2+ 0.021 0.054 -9999 0 -10000 0 0
MAPK3 0.031 0.053 -9999 0 -0.46 1 1
MAPK1 0.031 0.053 -9999 0 -0.46 1 1
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
PLGF homodimer -0.008 0.097 -9999 0 -0.52 17 17
PRKACA 0.01 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.32 0.24 -9999 0 -0.5 313 313
VEGFA homodimer 0.01 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.025 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.036 0.051 -9999 0 -0.44 1 1
PI3K -0.009 0.045 -9999 0 -10000 0 0
PRKCA 0.026 0.055 -9999 0 -0.49 1 1
PRKCB 0.02 0.069 -9999 0 -0.49 2 2
VEGFR1 homodimer/PLGF homodimer 0.014 0.06 -9999 0 -10000 0 0
VEGFA 0.01 0 -9999 0 -10000 0 0
VEGFB 0.01 0 -9999 0 -10000 0 0
mol:IP3 0.021 0.054 -9999 0 -10000 0 0
RASA1 0.032 0 -9999 0 -10000 0 0
NRP2 0.007 0.04 -9999 0 -0.5 3 3
VEGFR1 homodimer 0.024 0 -9999 0 -10000 0 0
VEGFB homodimer 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.11 0.12 -9999 0 -0.4 12 12
PTPN11 0.01 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.045 -9999 0 -10000 0 0
mol:L-citrulline 0.038 0.052 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -9999 0 -10000 0 0
CD2AP 0.01 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.01 0.045 -9999 0 -10000 0 0
PDPK1 0.03 0.049 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -9999 0 -10000 0 0
mol:NADP 0.038 0.052 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.024 0.024 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -10000 0 -10000 0 0
TRAF2/ASK1 0 0 -10000 0 -10000 0 0
ATM 0.01 0 -10000 0 -10000 0 0
MAP2K3 0.021 0.026 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.031 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.004 0.057 -10000 0 -0.5 6 6
TXN 0.006 0.013 -10000 0 -0.2 2 2
CALM1 0.01 0 -10000 0 -10000 0 0
GADD45A 0.008 0.033 -10000 0 -0.51 2 2
GADD45B 0.005 0.051 -10000 0 -0.5 5 5
MAP3K1 0.01 0 -10000 0 -10000 0 0
MAP3K6 0.01 0 -10000 0 -10000 0 0
MAP3K7 0.01 0 -10000 0 -10000 0 0
MAP3K4 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0 0 -10000 0 -10000 0 0
TAK1/TAB family 0.001 0.013 0.17 3 -10000 0 3
RAC1/OSM/MEKK3 -0.001 0.012 -10000 0 -0.26 1 1
TRAF2 0.01 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.003 0.009 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.082 0.2 -10000 0 -0.52 85 85
CCM2 0.01 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.054 0.12 -10000 0 -0.31 85 85
MAPK11 0.007 0.04 -10000 0 -0.5 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.048 0.1 -10000 0 -0.28 85 85
OSM/MEKK3 -0.001 0.016 -10000 0 -0.35 1 1
TAOK1 0.013 0.015 -10000 0 -0.31 1 1
TAOK2 0.014 0 -10000 0 -10000 0 0
TAOK3 0.014 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.01 0 -10000 0 -10000 0 0
MAP3K10 0.007 0.04 -10000 0 -0.5 3 3
MAP3K3 0.009 0.023 -10000 0 -0.5 1 1
TRX/ASK1 0.012 0.011 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 -0.007 0.046 -10000 0 -0.38 4 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.016 -9999 0 -0.26 2 2
HDAC3 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.014 -9999 0 -10000 0 0
GATA1/HDAC4 -0.038 0.11 -9999 0 -0.35 53 53
GATA1/HDAC5 -0.037 0.11 -9999 0 -0.35 52 52
GATA2/HDAC5 -0.03 0.098 -9999 0 -0.35 41 41
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.003 0.08 -9999 0 -0.51 12 12
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.014 -9999 0 -0.3 1 1
HDAC4/ANKRA2 -0.001 0.017 -9999 0 -0.37 1 1
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
GATA2 -0.033 0.14 -9999 0 -0.5 41 41
HDAC4/RFXANK -0.001 0.017 -9999 0 -0.37 1 1
BCOR 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.009 0.023 -9999 0 -0.5 1 1
HDAC5 0.01 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.022 -9999 0 -0.35 2 2
Histones 0.027 0.031 -9999 0 -10000 0 0
ADRBK1 0.01 0 -9999 0 -10000 0 0
HDAC4 0.009 0.024 -9999 0 -0.52 1 1
XPO1 0.01 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.017 -9999 0 -0.37 1 1
HDAC7 0.01 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.01 0 -9999 0 -10000 0 0
HDAC6 0.009 0.024 -9999 0 -0.52 1 1
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 0 0.069 -9999 0 -0.5 9 9
Tubulin/HDAC6 -0.009 0.053 -9999 0 -0.3 15 15
SUMO1 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.01 0 -9999 0 -10000 0 0
GATA1 -0.046 0.16 -9999 0 -0.5 52 52
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
NR3C1 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.023 0.012 -9999 0 -0.24 1 1
SRF 0.01 0 -9999 0 -10000 0 0
HDAC4/YWHAB -0.001 0.017 -9999 0 -0.37 1 1
Tubulin -0.011 0.061 -9999 0 -0.37 14 14
HDAC4/14-3-3 E -0.001 0.017 -9999 0 -0.37 1 1
GNB1 0.01 0 -9999 0 -10000 0 0
RANGAP1 0.01 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.014 -9999 0 -0.3 1 1
HDAC4/SRF -0.006 0.042 -9999 0 -0.29 10 10
HDAC4/ER alpha -0.019 0.081 -9999 0 -0.36 26 26
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.027 0.031 -9999 0 -10000 0 0
cell motility -0.009 0.052 -9999 0 -0.3 15 15
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.01 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.009 0.024 -9999 0 -0.52 1 1
Hsp90/HDAC6 -0.001 0.017 -9999 0 -0.37 1 1
ESR1 -0.017 0.11 -9999 0 -0.51 25 25
HDAC6/HDAC11 -0.001 0.017 -9999 0 -0.37 1 1
Ran/GTP/Exportin 1 0 0.01 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.01 0 -9999 0 -10000 0 0
RAN 0.009 0.024 -9999 0 -0.52 1 1
HDAC4/MEF2C -0.001 0.011 -9999 0 -10000 0 0
GNG2 0.008 0.032 -9999 0 -0.5 2 2
NCOR2 0.01 0 -9999 0 -10000 0 0
TUBB2A -0.005 0.088 -9999 0 -0.52 14 14
HDAC11 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
ANKRA2 0.01 0 -9999 0 -10000 0 0
RFXANK 0.01 0 -9999 0 -10000 0 0
nuclear import 0 0.009 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.013 0.073 -9999 0 -0.64 4 4
MAP4K1 0.005 0.051 -9999 0 -0.5 5 5
MAP3K8 0.008 0.032 -9999 0 -0.5 2 2
PRKCB -0.004 0.082 -9999 0 -0.5 13 13
DBNL 0.01 0 -9999 0 -10000 0 0
CRKL 0.01 0 -9999 0 -10000 0 0
MAP3K1 0.025 0.069 -9999 0 -0.6 4 4
JUN 0.011 0.11 -9999 0 -0.62 13 13
MAP3K7 0.025 0.069 -9999 0 -0.6 4 4
GRAP2 -0.006 0.088 -9999 0 -0.5 15 15
CRK 0.01 0 -9999 0 -10000 0 0
MAP2K4 0.031 0.075 -9999 0 -0.67 4 4
LAT 0.009 0.024 -9999 0 -0.52 1 1
LCP2 0.007 0.04 -9999 0 -0.5 3 3
MAPK8 0.007 0.11 -9999 0 -0.64 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.073 -9999 0 -0.64 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.012 0.068 -9999 0 -0.61 4 4
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.01 0.001 -9999 0 -10000 0 0
HDAC2 0.01 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.004 0.033 -9999 0 -0.3 6 6
forebrain development -0.013 0.14 -9999 0 -0.53 18 18
GNAO1 0.003 0.057 -9999 0 -0.51 6 6
SMO/beta Arrestin2 0.012 0.035 -9999 0 -0.37 4 4
SMO 0.005 0.048 -9999 0 -0.52 4 4
ARRB2 0.009 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.034 0.036 -9999 0 -10000 0 0
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
GSK3B 0.01 0 -9999 0 -10000 0 0
GNAI2 0.009 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0.006 0.013 -9999 0 -10000 0 0
GNAI1 0.007 0.033 -9999 0 -0.5 2 2
XPO1 0.011 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.045 0.11 -9999 0 -0.53 12 12
SAP30 0.01 0.001 -9999 0 -10000 0 0
mol:GDP 0.005 0.047 -9999 0 -0.51 4 4
MIM/GLI2A 0.003 0.04 -9999 0 -0.53 1 1
IFT88 0.01 0 -9999 0 -10000 0 0
GNAI3 0.009 0.004 -9999 0 -10000 0 0
GLI2 0.036 0.012 -9999 0 -10000 0 0
GLI3 0.03 0.038 -9999 0 -10000 0 0
CSNK1D 0.01 0 -9999 0 -10000 0 0
CSNK1E 0.01 0 -9999 0 -10000 0 0
SAP18 0.01 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.01 0 -9999 0 -10000 0 0
GNG2 0.008 0.032 -9999 0 -0.5 2 2
Gi family/GTP 0.001 0.079 -9999 0 -0.27 20 20
SIN3B 0.01 0.001 -9999 0 -10000 0 0
SIN3A 0.01 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.038 0.033 -9999 0 -10000 0 0
GLI2/Su(fu) 0.04 0.027 -9999 0 -10000 0 0
FOXA2 -0.17 0.39 -9999 0 -1 82 82
neural tube patterning -0.013 0.14 -9999 0 -0.53 18 18
SPOP 0.01 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.017 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
CSNK1G2 0.01 0 -9999 0 -10000 0 0
CSNK1G3 0.01 0 -9999 0 -10000 0 0
MTSS1 0.003 0.04 -9999 0 -0.53 1 1
embryonic limb morphogenesis -0.013 0.14 -9999 0 -0.53 18 18
SUFU 0.019 0.018 -9999 0 -10000 0 0
LGALS3 0.01 0 -9999 0 -10000 0 0
catabolic process 0.054 0.034 -9999 0 -10000 0 0
GLI3A/CBP 0.005 0.055 -9999 0 -0.33 12 12
KIF3A 0.01 0 -9999 0 -10000 0 0
GLI1 -0.014 0.14 -9999 0 -0.55 18 18
RAB23 0.01 0 -9999 0 -10000 0 0
CSNK1A1 0.01 0 -9999 0 -10000 0 0
IFT172 0.01 0 -9999 0 -10000 0 0
RBBP7 0.01 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.017 -9999 0 -10000 0 0
GNAZ -0.034 0.14 -9999 0 -0.5 41 41
RBBP4 0.01 0.001 -9999 0 -10000 0 0
CSNK1G1 0.01 0 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.011 -9999 0 -10000 0 0
STK36 0.01 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.008 0.074 -9999 0 -0.5 2 2
PTCH1 -0.012 0.17 -9999 0 -0.86 12 12
MIM/GLI1 -0.044 0.22 -9999 0 -0.49 87 87
CREBBP 0.005 0.055 -9999 0 -0.33 12 12
Su(fu)/SIN3/HDAC complex 0.041 0.007 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0.055 -10000 0 -0.35 11 11
MAP4K4 0.029 0.042 -10000 0 -10000 0 0
BAG4 0.009 0.024 -10000 0 -0.52 1 1
PKC zeta/ceramide -0.011 0.034 0.13 5 -0.24 2 7
NFKBIA 0.01 0 -10000 0 -10000 0 0
BIRC3 0.004 0.057 -10000 0 -0.51 6 6
BAX -0.002 0.016 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AKT1 0.017 0.007 -10000 0 -10000 0 0
BAD -0.009 0.032 0.14 6 -10000 0 6
SMPD1 0.017 0.036 -10000 0 -0.16 18 18
RB1 -0.009 0.032 0.14 6 -10000 0 6
FADD/Caspase 8 0.036 0.045 -10000 0 -0.45 1 1
MAP2K4 -0.003 0.03 -10000 0 -10000 0 0
NSMAF 0.01 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.03 -10000 0 -10000 0 0
EGF -0.089 0.21 -10000 0 -0.52 92 92
mol:ceramide -0.017 0.034 0.14 6 -10000 0 6
MADD 0.01 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.055 -10000 0 -0.35 11 11
ASAH1 0.009 0.023 -10000 0 -0.5 1 1
negative regulation of cell cycle -0.009 0.031 0.14 6 -10000 0 6
cell proliferation -0.01 0.03 -10000 0 -10000 0 0
BID 0.02 0.033 -10000 0 -10000 0 0
MAP3K1 -0.009 0.032 0.14 6 -10000 0 6
EIF2A 0.003 0.029 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
CRADD 0.009 0.024 -10000 0 -0.52 1 1
MAPK3 0.006 0.028 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.028 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.01 0.031 0.13 6 -10000 0 6
FADD 0.029 0.042 -10000 0 -10000 0 0
KSR1 -0.009 0.032 0.14 6 -10000 0 6
MAPK8 -0.001 0.032 0.14 5 -0.2 2 7
PRKRA -0.009 0.032 0.14 6 -10000 0 6
PDGFA 0 0.072 -10000 0 -0.5 10 10
TRAF2 0.01 0 -10000 0 -10000 0 0
IGF1 -0.002 0.076 -10000 0 -0.5 11 11
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.017 0.034 0.14 6 -10000 0 6
CTSD 0.01 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 0.008 0.039 -10000 0 -10000 0 0
PRKCD 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.007 0.04 -10000 0 -0.5 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.055 -10000 0 -0.35 11 11
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.024 0.045 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.012 0.058 -10000 0 -0.29 20 20
mol:Sphingosine-1-phosphate 0.01 0.055 -10000 0 -0.35 11 11
MAP2K1 0.003 0.029 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
CYCS -0.004 0.024 0.15 1 -10000 0 1
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.017 -10000 0 -0.37 1 1
EIF2AK2 -0.003 0.03 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.011 0.056 -10000 0 -0.29 19 19
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.038 -10000 0 -0.58 1 1
MAP2K2 0.003 0.029 -10000 0 -10000 0 0
SMPD3 0.016 0.042 -10000 0 -0.29 1 1
TNF -0.01 0.099 -10000 0 -0.5 19 19
PKC zeta/PAR4 -0.002 0.027 -10000 0 -0.35 3 3
mol:PHOSPHOCHOLINE 0.022 0.067 0.15 92 -10000 0 92
NF kappa B1/RelA/I kappa B alpha -0.001 0.018 -10000 0 -10000 0 0
AIFM1 -0.004 0.024 0.15 1 -10000 0 1
BCL2 0.007 0.041 -10000 0 -0.51 3 3
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.01 0 -10000 0 -10000 0 0
NFATC1 0.036 0.04 -10000 0 -0.4 1 1
NFATC2 0.013 0.044 -10000 0 -0.26 2 2
NFATC3 0.013 0.031 -10000 0 -0.37 3 3
YWHAE 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.016 0.097 -10000 0 -0.36 18 18
Exportin 1/Ran/NUP214 -0.001 0.014 -10000 0 -0.3 1 1
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.035 0.082 -10000 0 -0.39 15 15
BCL2/BAX -0.002 0.028 -10000 0 -0.36 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.005 0.007 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
MAPK14 0.008 0.004 -10000 0 -10000 0 0
BAD 0.01 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.011 0.092 -10000 0 -0.34 18 18
Calcineurin A alpha-beta B1/BCL2 0.007 0.041 -10000 0 -0.51 3 3
FKBP8 0.009 0.023 -10000 0 -0.5 1 1
activation-induced cell death of T cells 0.011 0.091 0.34 18 -10000 0 18
KPNB1 0.01 0 -10000 0 -10000 0 0
KPNA2 0.002 0.063 -10000 0 -0.52 7 7
XPO1 0.01 0.001 -10000 0 -10000 0 0
SFN 0 0.071 -10000 0 -0.52 9 9
MAP3K8 0.006 0.033 -10000 0 -0.5 2 2
NFAT4/CK1 alpha -0.001 0.016 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.052 0.099 -10000 0 -0.39 5 5
CABIN1 -0.016 0.098 -10000 0 -0.37 18 18
CALM1 0.008 0.004 -10000 0 -10000 0 0
RAN 0.009 0.024 -10000 0 -0.52 1 1
MAP3K1 0.01 0 -10000 0 -10000 0 0
CAMK4 0 0.069 -10000 0 -0.5 9 9
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.028 -10000 0 -0.35 3 3
YWHAB 0.01 0 -10000 0 -10000 0 0
MAPK8 0.008 0.004 -10000 0 -10000 0 0
MAPK9 0.01 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.003 0.035 -10000 0 -0.34 3 3
PRKCH 0.01 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.008 0.004 -10000 0 -10000 0 0
PIM1 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0.014 0.21 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.016 -10000 0 -10000 0 0
PRKCB -0.004 0.082 -10000 0 -0.5 13 13
PRKCE 0.005 0.051 -10000 0 -0.5 5 5
JNK2/NFAT4 0.016 0.029 -10000 0 -0.33 3 3
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.01 0 -10000 0 -10000 0 0
NUP214 0.01 0.001 -10000 0 -10000 0 0
PRKCZ 0.005 0.04 -10000 0 -0.5 3 3
PRKCA 0.008 0.032 -10000 0 -0.5 2 2
PRKCG -0.042 0.15 -10000 0 -0.52 46 46
PRKCQ -0.067 0.18 -10000 0 -0.5 74 74
FKBP38/BCL2 -0.003 0.032 -10000 0 -0.36 4 4
EP300 0.008 0.005 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
NFATc/JNK1 0.035 0.041 -10000 0 -0.38 1 1
CaM/Ca2+/FKBP38 -0.001 0.014 -10000 0 -0.31 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.012 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.005 0.04 -10000 0 -0.3 9 9
NFATc/ERK1 0.04 0.038 -10000 0 -0.38 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.034 0.081 -10000 0 -0.39 15 15
NR4A1 -0.053 0.21 -10000 0 -0.47 97 97
GSK3B 0.008 0.004 -10000 0 -10000 0 0
positive T cell selection 0.013 0.031 -10000 0 -0.37 3 3
NFAT1/CK1 alpha -0.011 0.025 -10000 0 -0.26 1 1
RCH1/ KPNB1 -0.005 0.044 -10000 0 -0.37 7 7
YWHAQ 0.01 0 -10000 0 -10000 0 0
PRKACA 0.008 0.004 -10000 0 -10000 0 0
AKAP5 0.007 0.04 -10000 0 -0.5 3 3
MEF2D 0.008 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.01 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.035 0.041 -10000 0 -0.38 1 1
CREBBP 0.008 0.005 -10000 0 -10000 0 0
BCL2 0.007 0.041 -10000 0 -0.51 3 3
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.016 0.048 -9999 0 -10000 0 0
PLK1 -0.13 0.26 -9999 0 -0.6 47 47
CDKN1B 0.014 0.11 -9999 0 -10000 0 0
FOXO3 -0.073 0.21 -9999 0 -0.52 44 44
KAT2B 0.004 0.019 -9999 0 -10000 0 0
FOXO1/SIRT1 0.014 0.029 -9999 0 -10000 0 0
CAT -0.071 0.24 -9999 0 -1.3 7 7
CTNNB1 0.01 0 -9999 0 -10000 0 0
AKT1 0.005 0.02 -9999 0 -10000 0 0
FOXO1 0.021 0.029 -9999 0 -10000 0 0
MAPK10 -0.005 0.088 -9999 0 -0.25 54 54
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.052 0.064 -9999 0 -10000 0 0
response to oxidative stress -0.008 0.024 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.12 0.16 -9999 0 -0.49 42 42
XPO1 0.011 0 -9999 0 -10000 0 0
EP300 0.01 0.004 -9999 0 -10000 0 0
BCL2L11 0.008 0.032 -9999 0 -10000 0 0
FOXO1/SKP2 0.021 0.037 -9999 0 -0.28 2 2
mol:GDP -0.008 0.024 -9999 0 -10000 0 0
RAN 0.01 0.024 -9999 0 -0.52 1 1
GADD45A 0.008 0.12 -9999 0 -0.71 2 2
YWHAQ 0.01 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.055 0.016 -9999 0 -10000 0 0
MST1 -0.013 0.094 -9999 0 -0.53 15 15
CSNK1D 0.01 0 -9999 0 -10000 0 0
CSNK1E 0.01 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.042 0.021 -9999 0 -10000 0 0
YWHAB 0.01 0 -9999 0 -10000 0 0
MAPK8 0.025 0.01 -9999 0 -10000 0 0
MAPK9 0.025 0.01 -9999 0 -10000 0 0
YWHAG 0.01 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
YWHAZ 0.01 0 -9999 0 -10000 0 0
SIRT1 0.007 0.009 -9999 0 -10000 0 0
SOD2 0.012 0.14 -9999 0 -10000 0 0
RBL2 -0.023 0.15 -9999 0 -0.49 4 4
RAL/GDP 0.013 0.015 -9999 0 -10000 0 0
CHUK 0.004 0.019 -9999 0 -10000 0 0
Ran/GTP 0.01 0.017 -9999 0 -0.37 1 1
CSNK1G2 0.01 0 -9999 0 -10000 0 0
RAL/GTP 0.019 0.015 -9999 0 -10000 0 0
CSNK1G1 0.01 0 -9999 0 -10000 0 0
FASLG -0.008 0.15 -9999 0 -1.3 6 6
SKP2 0.006 0.048 -9999 0 -0.52 4 4
USP7 0.011 0.001 -9999 0 -10000 0 0
IKBKB 0.004 0.019 -9999 0 -10000 0 0
CCNB1 -0.1 0.25 -9999 0 -0.6 45 45
FOXO1-3a-4/beta catenin -0.035 0.074 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.037 -9999 0 -0.28 2 2
CSNK1A1 0.01 0 -9999 0 -10000 0 0
SGK1 0.002 0.039 -9999 0 -0.52 2 2
CSNK1G3 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.018 0.015 -9999 0 -0.31 1 1
ZFAND5 0.055 0.057 -9999 0 -10000 0 0
SFN 0 0.071 -9999 0 -0.52 9 9
CDK2 0.01 0.006 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.022 0.047 -9999 0 -0.37 1 1
CREBBP 0.01 0.006 -9999 0 -10000 0 0
FBXO32 -0.081 0.22 -9999 0 -0.6 37 37
BCL6 -0.023 0.15 -9999 0 -0.49 4 4
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
YWHAH 0.01 0 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.024 0.016 -10000 0 -0.22 2 2
epithelial cell differentiation -0.001 0.015 -10000 0 -0.24 2 2
CYFIP2 0.003 0.06 -10000 0 -0.5 7 7
ENAH 0.048 0.031 -10000 0 -10000 0 0
EGFR -0.005 0.086 -10000 0 -0.51 14 14
EPHA2 0 0.072 -10000 0 -0.5 10 10
MYO6 0.029 0.016 -10000 0 -10000 0 0
CTNNB1 0.01 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.004 0.035 -10000 0 -0.29 7 7
AQP5 -0.1 0.17 -10000 0 -0.42 108 108
CTNND1 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.016 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.11 0.13 -10000 0 -0.46 1 1
EGF -0.089 0.21 -10000 0 -0.52 92 92
NCKAP1 0.01 0 -10000 0 -10000 0 0
AQP3 -0.017 0.084 -10000 0 -0.44 18 18
cortical microtubule organization -0.001 0.015 -10000 0 -0.24 2 2
GO:0000145 0.028 0.015 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.001 0.015 -10000 0 -0.24 2 2
MLLT4 0.01 0 -10000 0 -10000 0 0
ARF6/GDP -0.005 0.032 -10000 0 -0.39 1 1
ARF6 0.01 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.038 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.037 0.02 -10000 0 -10000 0 0
PVRL2 0.01 0 -10000 0 -10000 0 0
ZYX 0.029 0.02 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.034 -10000 0 -10000 0 0
CDH1 0.008 0.032 -10000 0 -0.5 2 2
EGFR/EGFR/EGF/EGF -0.049 0.096 -10000 0 -0.46 3 3
RhoA/GDP -0.001 0.014 -10000 0 -10000 0 0
actin cytoskeleton organization 0.034 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.008 0.032 -10000 0 -0.5 2 2
GIT1 0.01 0 -10000 0 -10000 0 0
IGF1R 0.008 0.032 -10000 0 -0.5 2 2
IGF1 -0.002 0.076 -10000 0 -0.5 11 11
DIAPH1 -0.008 0.067 -10000 0 -0.56 7 7
Wnt receptor signaling pathway 0.001 0.015 0.24 2 -10000 0 2
RHOA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.032 -10000 0 -0.39 1 1
CTNNA1 0.01 0 -10000 0 -10000 0 0
VCL 0.034 0.016 -10000 0 -10000 0 0
EFNA1 0.009 0.023 -10000 0 -0.5 1 1
LPP 0.034 0.019 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.006 0.037 -10000 0 -0.45 1 1
SEC6/SEC8 -0.001 0.012 -10000 0 -10000 0 0
MGAT3 -0.11 0.13 -10000 0 -0.47 1 1
HGF/MET -0.027 0.077 -10000 0 -0.46 4 4
HGF -0.018 0.12 -10000 0 -0.5 27 27
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.024 0.016 -10000 0 -0.22 2 2
actin cable formation 0.06 0.031 -10000 0 -10000 0 0
KIAA1543 0.034 0.027 -10000 0 -0.45 1 1
KIFC3 0.029 0.02 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
EXOC3 0.01 0 -10000 0 -10000 0 0
ACTN1 0.029 0.016 -10000 0 -10000 0 0
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.001 0.015 -10000 0 -0.24 2 2
EXOC4 0.01 0 -10000 0 -10000 0 0
STX4 0.029 0.016 -10000 0 -10000 0 0
PIP5K1C 0.029 0.016 -10000 0 -10000 0 0
LIMA1 0.01 0 -10000 0 -10000 0 0
ABI1 0.01 0 -10000 0 -10000 0 0
ROCK1 -0.004 0.028 -10000 0 -0.34 1 1
adherens junction assembly 0.045 0.038 -10000 0 -0.52 2 2
IGF-1R heterotetramer/IGF1 -0.007 0.037 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.023 0.13 -10000 0 -0.51 31 31
PLEKHA7 0.029 0.016 -10000 0 -10000 0 0
mol:GTP -0.006 0.038 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.049 0.015 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.024 0.016 -10000 0 -0.22 2 2
regulation of cell-cell adhesion 0.034 0.016 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.024 0.016 -10000 0 -0.22 2 2
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.069 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.013 0.045 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.004 0.021 -9999 0 -0.29 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.014 0.043 -9999 0 -0.33 3 3
CaM/Ca2+ -0.017 0.054 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.017 0.065 -9999 0 -10000 0 0
AKT1 0.026 0.06 -9999 0 -10000 0 0
MAP2K1 0.024 0.063 -9999 0 -10000 0 0
MAP3K11 0.016 0.066 -9999 0 -10000 0 0
IFNGR1 0.009 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.054 0.11 -9999 0 -0.37 46 46
Rap1/GTP -0.012 0.04 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.02 0.065 -9999 0 -10000 0 0
CEBPB 0.044 0.085 -9999 0 -0.42 9 9
STAT3 0.01 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.018 0.057 -9999 0 -10000 0 0
STAT1 0.017 0.065 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.032 0.14 -9999 0 -0.51 40 40
PIK3CA 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.022 0.062 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.011 0.04 -9999 0 -0.35 2 2
mol:Ca2+ -0.018 0.059 -9999 0 -10000 0 0
MAPK3 0.033 0.062 -9999 0 -10000 0 0
STAT1 (dimer) -0.017 0.058 -9999 0 -0.47 3 3
MAPK1 0.033 0.062 -9999 0 -10000 0 0
JAK2 0.007 0.033 -9999 0 -0.5 2 2
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
JAK1 0.009 0.007 -9999 0 -10000 0 0
CAMK2D 0.01 0 -9999 0 -10000 0 0
DAPK1 0.04 0.096 -9999 0 -0.6 9 9
SMAD7 0.028 0.041 -9999 0 -0.26 1 1
CBL/CRKL/C3G -0.015 0.048 -9999 0 -10000 0 0
PI3K -0.016 0.052 -9999 0 -10000 0 0
IFNG -0.032 0.14 -9999 0 -0.51 40 40
apoptosis 0.029 0.073 -9999 0 -0.44 9 9
CAMK2G 0.01 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.01 0 -9999 0 -10000 0 0
CAMK2A -0.039 0.15 -9999 0 -0.5 47 47
CAMK2B -0.082 0.2 -9999 0 -0.52 85 85
FRAP1 0.026 0.057 -9999 0 -10000 0 0
PRKCD 0.027 0.061 -9999 0 -10000 0 0
RAP1B 0.01 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.014 0.043 -9999 0 -0.33 3 3
PTPN2 0.01 0 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
IRF1 0.047 0.052 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.015 0.052 -9999 0 -10000 0 0
SOCS1 0.002 0.016 -9999 0 -10000 0 0
mol:GDP -0.014 0.047 -9999 0 -10000 0 0
CASP1 0.026 0.048 -9999 0 -0.3 5 5
PTGES2 0.01 0 -9999 0 -10000 0 0
IRF9 0.041 0.029 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.051 -9999 0 -10000 0 0
RAP1/GDP -0.012 0.04 -9999 0 -10000 0 0
CBL 0.016 0.065 -9999 0 -10000 0 0
MAP3K1 0.017 0.066 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
PIAS4 0.01 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.014 0.043 -9999 0 -0.33 3 3
PTPN11 0.01 0.068 -9999 0 -10000 0 0
CREBBP 0.01 0 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.011 0.055 -9999 0 -0.29 18 18
Ran/GTP/Exportin 1/HDAC1 0 0.01 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.059 -9999 0 -0.27 18 18
SUMO1 0.01 0 -9999 0 -10000 0 0
ZFPM1 0.009 0.024 -9999 0 -0.52 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
FKBP3 0.009 0.024 -9999 0 -0.52 1 1
Histones -0.005 0.025 -9999 0 -10000 0 0
YY1/LSF 0.024 0 -9999 0 -10000 0 0
SMG5 0.01 0 -9999 0 -10000 0 0
RAN 0.009 0.024 -9999 0 -0.52 1 1
I kappa B alpha/HDAC3 0.017 0.049 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.019 0.035 -9999 0 -10000 0 0
SAP18 0.01 0 -9999 0 -10000 0 0
RELA 0.021 0.047 -9999 0 -0.22 18 18
HDAC1/Smad7 -0.001 0.013 -9999 0 -0.29 1 1
RANGAP1 0.01 0 -9999 0 -10000 0 0
HDAC3/TR2 0.019 0.035 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.012 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.024 0.043 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.033 0.14 -9999 0 -0.5 41 41
GATA1 -0.046 0.16 -9999 0 -0.5 52 52
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.024 0.063 -9999 0 -0.28 1 1
RBBP7 0.01 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.01 0 -9999 0 -10000 0 0
MAX 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.01 0 -9999 0 -10000 0 0
NFKBIA 0.015 0.039 -9999 0 -10000 0 0
KAT2B 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.035 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0.01 0 -9999 0 -10000 0 0
CHD3 0.01 0 -9999 0 -10000 0 0
SAP30 0.01 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.01 0 -9999 0 -10000 0 0
YY1/HDAC3 0.028 0.033 -9999 0 -10000 0 0
YY1/HDAC2 0.024 0 -9999 0 -10000 0 0
YY1/HDAC1 0.024 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.038 0 -9999 0 -10000 0 0
PPARG -0.046 0.12 -9999 0 -0.3 73 73
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -10000 0 0
TNFRSF1A 0.01 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.019 0.035 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.013 -9999 0 -0.29 1 1
CREBBP 0.01 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.04 0.013 -9999 0 -10000 0 0
HDAC1 0.01 0 -9999 0 -10000 0 0
HDAC3 0.015 0.039 -9999 0 -10000 0 0
HDAC2 0.01 0 -9999 0 -10000 0 0
YY1 0.024 0 -9999 0 -10000 0 0
HDAC8 0.01 0 -9999 0 -10000 0 0
SMAD7 0.009 0.023 -9999 0 -0.5 1 1
NCOR2 0.01 0 -9999 0 -10000 0 0
MXD1 0.01 0 -9999 0 -10000 0 0
STAT3 0.02 0 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0 0 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.039 -9999 0 -10000 0 0
histone deacetylation 0.038 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.026 0.033 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GATAD2B 0.01 0 -9999 0 -10000 0 0
GATAD2A 0.01 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.005 0.088 -9999 0 -0.27 41 41
GATA1/HDAC1 -0.037 0.11 -9999 0 -0.35 52 52
GATA1/HDAC3 -0.014 0.092 -9999 0 -0.26 52 52
CHD4 0.01 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.014 0.068 -9999 0 -0.35 19 19
SIN3/HDAC complex/Mad/Max 0.038 0 -9999 0 -10000 0 0
NuRD Complex 0.043 0.013 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.005 0.024 -9999 0 -10000 0 0
SIN3B 0.01 0 -9999 0 -10000 0 0
MTA2 0.01 0 -9999 0 -10000 0 0
SIN3A 0.01 0 -9999 0 -10000 0 0
XPO1 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.024 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.038 0.11 -9999 0 -0.36 52 52
FKBP25/HDAC1/HDAC2 -0.001 0.014 -9999 0 -0.3 1 1
TNF -0.01 0.099 -9999 0 -0.5 19 19
negative regulation of cell growth 0.038 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.038 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0.01 -9999 0 -0.23 1 1
NF kappa B/RelA/I kappa B alpha -0.011 0.055 -9999 0 -0.29 18 18
SIN3/HDAC complex/NCoR1 0.036 0 -9999 0 -10000 0 0
TFCP2 0.01 0 -9999 0 -10000 0 0
NR2C1 0.01 0 -9999 0 -10000 0 0
MBD3 0.008 0.032 -9999 0 -0.5 2 2
MBD2 0.01 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.047 0.037 -10000 0 -0.43 1 1
UGCG -0.002 0.029 -10000 0 -0.62 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.04 0.056 -10000 0 -0.31 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.021 0.031 -10000 0 -0.61 1 1
mol:DAG 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.038 -10000 0 -0.34 5 5
FRAP1 0.064 0.059 -10000 0 -0.39 5 5
FOXO3 0.066 0.052 -10000 0 -0.35 4 4
AKT1 0.062 0.055 -10000 0 -0.38 4 4
GAB2 0.007 0.046 -10000 0 -0.5 4 4
SMPD1 -0.001 0.007 -10000 0 -10000 0 0
SGMS1 -0.001 0.007 -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 0.018 0.014 -10000 0 -0.29 1 1
CALM1 0.01 0 -10000 0 -10000 0 0
cell proliferation 0.039 0.033 -10000 0 -0.27 3 3
EIF3A 0.01 0 -10000 0 -10000 0 0
PI3K 0.019 0.017 -10000 0 -0.35 1 1
RPS6KB1 0.021 0.022 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.001 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -0.011 2 2
JAK3 0.012 0.001 -10000 0 -10000 0 0
PIK3R1 0.012 0.023 -10000 0 -0.5 1 1
JAK1 0.012 0.001 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
MYC 0.062 0.076 -10000 0 -0.92 2 2
MYB 0.016 0.11 -10000 0 -1.2 4 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.055 0.05 -10000 0 -0.38 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.02 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.055 0.049 -10000 0 -0.37 2 2
Rac1/GDP 0.022 0.013 -10000 0 -0.26 1 1
T cell proliferation 0.057 0.052 -10000 0 -0.37 2 2
SHC1 0.01 0.024 -10000 0 -0.52 1 1
RAC1 0.01 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.007 -10000 0 -0.051 7 7
PRKCZ 0.057 0.053 -10000 0 -0.38 2 2
NF kappa B1 p50/RelA -0.004 0.038 -10000 0 -0.37 3 3
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.043 0.04 -10000 0 -0.43 2 2
HSP90AA1 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL2RA -0.027 0.14 -10000 0 -0.52 35 35
IL2RB 0.01 0.033 -10000 0 -0.5 2 2
TERT -0.15 0.24 -10000 0 -0.52 146 146
E2F1 0.019 0.044 -10000 0 -0.42 4 4
SOS1 0.011 0.001 -10000 0 -10000 0 0
RPS6 0.01 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.003 0.025 7 -10000 0 7
PTPN11 0.011 0.001 -10000 0 -10000 0 0
IL2RG 0.007 0.051 -10000 0 -0.5 5 5
actin cytoskeleton organization 0.057 0.052 -10000 0 -0.37 2 2
GRB2 0.011 0.001 -10000 0 -10000 0 0
IL2 0.009 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.013 -10000 0 -0.24 1 1
LCK 0.009 0.04 -10000 0 -0.5 3 3
BCL2 0.065 0.065 -10000 0 -0.65 2 2
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.002 0.021 -9999 0 -10000 0 0
DAPP1 -0.003 0.11 -9999 0 -0.48 17 17
Src family/SYK family/BLNK-LAT/BTK-ITK -0.002 0.15 -9999 0 -0.61 22 22
mol:DAG 0.023 0.068 -9999 0 -0.31 8 8
HRAS 0.011 0.001 -9999 0 -10000 0 0
RAP1A 0.01 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.022 0.07 -9999 0 -0.44 8 8
PLCG2 0.007 0.04 -9999 0 -0.5 3 3
PLCG1 0.01 0 -9999 0 -10000 0 0
ARF5 0.01 0 -9999 0 -10000 0 0
mol:GTP -0.002 0.018 -9999 0 -10000 0 0
ARF1/GTP -0.002 0.019 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
YES1 0.01 0 -9999 0 -10000 0 0
RAP1A/GTP -0.002 0.018 -9999 0 -10000 0 0
ADAP1 -0.002 0.024 -9999 0 -0.42 1 1
ARAP3 -0.002 0.018 -9999 0 -10000 0 0
INPPL1 0.01 0 -9999 0 -10000 0 0
PREX1 0.004 0.056 -9999 0 -0.5 6 6
ARHGEF6 -0.008 0.093 -9999 0 -0.5 17 17
ARHGEF7 0.01 0 -9999 0 -10000 0 0
ARF1 0.01 0 -9999 0 -10000 0 0
NRAS 0.011 0.001 -9999 0 -10000 0 0
FYN 0.009 0.023 -9999 0 -0.5 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
FGR -0.029 0.14 -9999 0 -0.5 37 37
mol:Ca2+ 0.02 0.037 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.002 0.065 -9999 0 -0.5 8 8
ZAP70 0.004 0.056 -9999 0 -0.5 6 6
mol:IP3 0.023 0.05 -9999 0 -0.21 6 6
LYN 0.01 0 -9999 0 -10000 0 0
ARF1/GDP 0.022 0.07 -9999 0 -0.44 8 8
RhoA/GDP -0.006 0.035 -9999 0 -0.36 2 2
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK 0.008 0.032 -9999 0 -0.5 2 2
actin cytoskeleton reorganization 0.04 0.062 -9999 0 -0.46 4 4
SRC 0.01 0 -9999 0 -10000 0 0
PLEKHA2 0.021 0.028 -9999 0 -0.29 4 4
RAC1 0.01 0 -9999 0 -10000 0 0
PTEN 0 0.003 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.016 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.017 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.002 0.12 -9999 0 -0.49 17 17
BLK -0.075 0.19 -9999 0 -0.52 79 79
PDPK1 0.01 0 -9999 0 -10000 0 0
CYTH1 -0.002 0.017 -9999 0 -10000 0 0
HCK -0.012 0.1 -9999 0 -0.5 21 21
CYTH3 -0.002 0.022 -9999 0 -10000 0 0
CYTH2 -0.002 0.017 -9999 0 -10000 0 0
KRAS 0.01 0.024 -9999 0 -0.51 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.003 0.033 -9999 0 -0.49 2 2
SGK1 -0.003 0.036 -9999 0 -0.54 2 2
INPP5D 0.007 0.04 -9999 0 -0.5 3 3
mol:GDP 0.016 0.074 -9999 0 -0.44 9 9
SOS1 0.01 0 -9999 0 -10000 0 0
SYK 0.007 0.04 -9999 0 -0.5 3 3
ARF6/GDP -0.006 0.035 -9999 0 -0.36 2 2
mol:PI-3-4-5-P3 -0.002 0.018 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.002 0.018 -9999 0 -10000 0 0
VAV1 0.005 0.051 -9999 0 -0.5 5 5
mol:PI-3-4-P2 0.016 0.029 -9999 0 -0.35 3 3
RAS family/GTP/PI3K Class I -0.002 0.018 -9999 0 -10000 0 0
PLEKHA1 0.022 0.024 -9999 0 -0.29 3 3
Rac1/GDP 0.022 0.07 -9999 0 -0.42 9 9
LAT 0.009 0.024 -9999 0 -0.52 1 1
Rac1/GTP 0.013 0.11 -9999 0 -0.46 19 19
ITK -0.007 0.038 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.023 0.092 -9999 0 -0.35 18 18
LCK 0.007 0.04 -9999 0 -0.5 3 3
BTK -0.016 0.06 -9999 0 -0.42 2 2
Circadian rhythm pathway

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
chromatin modification -0.021 0.076 -9999 0 -0.5 5 5
CLOCK 0.012 0.003 -9999 0 -10000 0 0
TIMELESS/CRY2 0.03 0.036 -9999 0 -10000 0 0
DEC1/BMAL1 0 0.001 -9999 0 -10000 0 0
ATR 0.01 0 -9999 0 -10000 0 0
NR1D1 0.032 0.021 -9999 0 -10000 0 0
ARNTL 0.012 0.003 -9999 0 -10000 0 0
TIMELESS 0.029 0.04 -9999 0 -10000 0 0
NPAS2 0.009 0.041 -9999 0 -0.51 3 3
CRY2 0.01 0 -9999 0 -10000 0 0
mol:CO -0.01 0.009 -9999 0 -10000 0 0
CHEK1 -0.029 0.14 -9999 0 -0.52 36 36
mol:HEME 0.01 0.009 -9999 0 -10000 0 0
PER1 -0.012 0.1 -9999 0 -0.5 21 21
BMAL/CLOCK/NPAS2 0.031 0.027 -9999 0 -0.3 3 3
BMAL1/CLOCK 0.034 0.035 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.021 0.076 -9999 0 -0.5 5 5
TIMELESS/CHEK1/ATR -0.021 0.077 -9999 0 -0.51 5 5
mol:NADPH 0.01 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.018 0.068 -9999 0 -0.52 1 1
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.002 0.004 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.031 0.011 -10000 0 -10000 0 0
regulation of axonogenesis -0.023 0.003 -10000 0 -10000 0 0
myoblast fusion -0.015 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.007 0.1 0.29 53 -10000 0 53
ARF1/GTP 0 0.001 -10000 0 -10000 0 0
mol:GM1 0.009 0.003 -10000 0 -10000 0 0
mol:Choline 0.023 0.002 -10000 0 -10000 0 0
lamellipodium assembly 0.009 0.029 -10000 0 -10000 0 0
MAPK3 0.021 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.007 0.1 -10000 0 -0.29 53 53
ARF1 0.01 0 -10000 0 -10000 0 0
ARF6/GDP 0.015 0.011 -10000 0 -10000 0 0
ARF1/GDP 0.026 0.016 -10000 0 -10000 0 0
ARF6 0.01 0.002 -10000 0 -10000 0 0
RAB11A 0.01 0 -10000 0 -10000 0 0
TIAM1 0.003 0.065 -10000 0 -0.5 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.007 -10000 0 -10000 0 0
actin filament bundle formation 0 0.005 -10000 0 -10000 0 0
KALRN 0.005 0.029 -10000 0 -0.26 3 3
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP 0 0.005 -10000 0 -10000 0 0
NME1 -0.039 0.16 -10000 0 -0.51 47 47
Rac1/GDP 0 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.003 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.009 0.029 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
liver development 0 0.003 -10000 0 -10000 0 0
ARF6/GTP 0 0.003 -10000 0 -10000 0 0
RhoA/GTP 0 0.001 -10000 0 -10000 0 0
mol:GDP 0.008 0.024 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.001 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
PLD1 0.017 0.003 -10000 0 -10000 0 0
RAB11FIP3 0.01 0 -10000 0 -10000 0 0
tube morphogenesis 0.009 0.029 -10000 0 -10000 0 0
ruffle organization 0.023 0.003 -10000 0 -10000 0 0
regulation of epithelial cell migration 0 0.003 -10000 0 -10000 0 0
PLD2 0.017 0.003 -10000 0 -10000 0 0
PIP5K1A 0.023 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.023 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.029 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA 0.006 0.046 -10000 0 -0.5 4 4
HRAS 0.01 0 -10000 0 -10000 0 0
EGFR -0.005 0.086 -10000 0 -0.51 14 14
AKT 0.029 0.031 -10000 0 -0.34 3 3
FOXO3 0.01 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
FOXO1 0.01 0 -10000 0 -10000 0 0
AKT3 0.007 0.04 -10000 0 -0.5 3 3
FOXO4 0.01 0 -10000 0 -10000 0 0
MET -0.023 0.13 -10000 0 -0.51 31 31
PIK3CA 0.01 0 -10000 0 -10000 0 0
PIK3CB 0.01 0 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
PIK3CG -0.007 0.091 -10000 0 -0.5 16 16
PIK3R3 0.009 0.023 -10000 0 -0.5 1 1
PIK3R2 0.01 0 -10000 0 -10000 0 0
NF1 0.01 0 -10000 0 -10000 0 0
RAS 0.009 0.044 -10000 0 -0.24 4 4
ERBB2 0.007 0.041 -10000 0 -0.52 3 3
proliferation/survival/translation -0.02 0.03 0.18 5 -10000 0 5
PI3K 0.014 0.05 -10000 0 -0.22 10 10
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
KRAS 0.009 0.024 -10000 0 -0.52 1 1
FOXO 0.037 0.014 -10000 0 -10000 0 0
AKT2 0.01 0 -10000 0 -10000 0 0
PTEN 0.01 0 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.009 0.023 -9999 0 -0.5 1 1
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.003 0.076 -9999 0 -0.23 43 43
GNAO1 0.005 0.058 -9999 0 -0.51 6 6
S1P/S1P3/G12/G13 -0.001 0.012 -9999 0 -0.27 1 1
AKT1 -0.008 0.035 -9999 0 -0.62 1 1
AKT3 0.023 0.1 -9999 0 -1.1 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.023 -9999 0 -0.5 1 1
GNAI2 0.011 0.002 -9999 0 -10000 0 0
GNAI3 0.011 0.002 -9999 0 -10000 0 0
GNAI1 0.009 0.033 -9999 0 -0.5 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.024 -9999 0 -0.52 1 1
S1PR2 0.01 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.013 0.072 -9999 0 -0.47 2 2
MAPK3 0.019 0.068 -9999 0 -0.45 2 2
MAPK1 0.019 0.068 -9999 0 -0.45 2 2
JAK2 0.021 0.069 -9999 0 -0.4 3 3
CXCR4 0.019 0.068 -9999 0 -0.45 2 2
FLT1 0.012 0.003 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.019 0.068 -9999 0 -0.45 2 2
S1P/S1P3/Gi 0.013 0.072 -9999 0 -0.48 2 2
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.017 0.054 -9999 0 -0.43 2 2
VEGFA 0.012 0.003 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.011 0.069 -9999 0 -0.41 2 2
VEGFR1 homodimer/VEGFA homodimer 0.021 0.005 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.016 0.052 -9999 0 -0.25 16 16
GNAQ 0.009 0.023 -9999 0 -0.5 1 1
GNAZ -0.032 0.14 -9999 0 -0.5 41 41
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.005 0.085 -9999 0 -0.5 14 14
GNA15 0.01 0 -9999 0 -10000 0 0
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
GNA11 0.008 0.032 -9999 0 -0.5 2 2
Rac1/GTP -0.017 0.054 -9999 0 -0.43 2 2
TRAIL signaling 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
TNFSF10 0.005 0.052 -10000 0 -0.5 5 5
positive regulation of NF-kappaB transcription factor activity -0.005 0.046 -10000 0 -0.4 6 6
MAP2K4 0.035 0.027 -10000 0 -0.33 1 1
IKBKB 0.01 0 -10000 0 -10000 0 0
TNFRSF10B 0.01 0 -10000 0 -10000 0 0
TNFRSF10A 0.008 0.032 -10000 0 -0.5 2 2
SMPD1 -0.002 0.018 -10000 0 -0.19 4 4
IKBKG 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.008 0.032 -10000 0 -0.5 2 2
TRAIL/TRAILR2 -0.004 0.036 -10000 0 -0.36 5 5
TRAIL/TRAILR3 -0.008 0.061 -10000 0 -0.41 10 10
TRAIL/TRAILR1 -0.005 0.046 -10000 0 -0.4 6 6
TRAIL/TRAILR4 -0.005 0.046 -10000 0 -0.4 6 6
TRAIL/TRAILR1/DAP3/GTP -0.004 0.036 -10000 0 -0.31 6 6
IKK complex -0.001 0.013 -10000 0 -10000 0 0
RIPK1 0.01 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 0.014 0.037 -10000 0 -0.35 5 5
MAP3K1 -0.003 0.025 -10000 0 -0.36 1 1
TRAILR4 (trimer) 0.008 0.032 -10000 0 -0.5 2 2
TRADD 0.01 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.032 -10000 0 -0.5 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.026 0.032 -10000 0 -0.46 1 1
CFLAR 0.01 0 -10000 0 -10000 0 0
MAPK1 0.014 0.037 -10000 0 -0.35 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP -0.003 0.032 -10000 0 -0.49 1 1
mol:ceramide -0.002 0.018 -10000 0 -0.19 4 4
FADD 0.01 0 -10000 0 -10000 0 0
MAPK8 0.04 0.025 -10000 0 -0.31 1 1
TRAF2 0.01 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.003 0.06 -10000 0 -0.5 7 7
CHUK 0.01 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.004 0.039 -10000 0 -0.34 6 6
DAP3 0.01 0 -10000 0 -10000 0 0
CASP10 -0.004 0.043 0.24 1 -0.36 5 6
JNK cascade -0.005 0.046 -10000 0 -0.4 6 6
TRAIL (trimer) 0.005 0.052 -10000 0 -0.5 5 5
TNFRSF10C 0.003 0.06 -10000 0 -0.5 7 7
TRAIL/TRAILR1/DAP3/GTP/FADD -0.004 0.033 -10000 0 -0.28 6 6
TRAIL/TRAILR2/FADD -0.003 0.03 -10000 0 -0.29 5 5
cell death 0.014 0.02 -10000 0 -0.19 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.027 0.024 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.01 0 -10000 0 -10000 0 0
CASP8 -0.001 0.04 -10000 0 -0.86 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.024 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.009 0.024 -9999 0 -0.52 1 1
Caspase 8 (4 units) -0.006 0.038 -9999 0 -0.34 4 4
NEF 0.002 0.02 -9999 0 -10000 0 0
NFKBIA 0.011 0.011 -9999 0 -10000 0 0
BIRC3 0.029 0.057 -9999 0 -0.48 6 6
CYCS 0.036 0.043 -9999 0 -0.3 4 4
RIPK1 0.01 0 -9999 0 -10000 0 0
CD247 0.005 0.062 -9999 0 -0.52 6 6
MAP2K7 0.037 0.036 -9999 0 -0.33 1 1
protein ubiquitination 0.051 0.033 -9999 0 -10000 0 0
CRADD 0.009 0.024 -9999 0 -0.52 1 1
DAXX 0.01 0 -9999 0 -10000 0 0
FAS 0.006 0.046 -9999 0 -0.5 4 4
BID 0.031 0.045 -9999 0 -0.32 4 4
NF-kappa-B/RelA/I kappa B alpha -0.003 0.027 -9999 0 -10000 0 0
TRADD 0.01 0 -9999 0 -10000 0 0
MAP3K5 0.01 0 -9999 0 -10000 0 0
CFLAR 0.01 0 -9999 0 -10000 0 0
FADD 0.01 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.003 0.027 -9999 0 -10000 0 0
MAPK8 0.042 0.035 -9999 0 -0.31 1 1
APAF1 0.01 0 -9999 0 -10000 0 0
TRAF1 0.01 0 -9999 0 -10000 0 0
TRAF2 0.01 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.026 0.047 -9999 0 -0.29 10 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.044 0.038 -9999 0 -10000 0 0
CHUK 0.052 0.034 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.002 0.029 -9999 0 -0.49 1 1
TCRz/NEF -0.008 0.055 -9999 0 -0.34 12 12
TNF -0.01 0.099 -9999 0 -0.5 19 19
FASLG 0.011 0.081 -9999 0 -0.47 12 12
NFKB1 0.011 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.012 0.058 -9999 0 -0.29 20 20
CASP6 -0.004 0.034 -9999 0 -0.59 1 1
CASP7 0.062 0.056 -9999 0 -0.47 3 3
RELA 0.011 0.011 -9999 0 -10000 0 0
CASP2 0.01 0 -9999 0 -10000 0 0
CASP3 0.062 0.056 -9999 0 -0.47 3 3
TNFRSF1A 0.01 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.017 -9999 0 -0.37 1 1
CASP8 0.009 0.023 -9999 0 -0.5 1 1
CASP9 0.01 0 -9999 0 -10000 0 0
MAP3K14 0.048 0.036 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.007 0.041 -9999 0 -0.48 1 1
BCL2 0.044 0.041 -9999 0 -0.37 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.031 0.029 -9999 0 -0.42 2 2
KLHL20 -0.011 0.033 -9999 0 -0.25 2 2
CYFIP2 0.003 0.06 -9999 0 -0.5 7 7
Rac1/GDP 0.05 0.02 -9999 0 -10000 0 0
ENAH 0.031 0.029 -9999 0 -0.42 2 2
AP1M1 0.01 0 -9999 0 -10000 0 0
RAP1B 0.01 0 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.01 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.009 0.024 -9999 0 -0.17 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.002 0.02 -9999 0 -0.26 3 3
RAPGEF1 0.041 0.025 -9999 0 -0.35 2 2
CTNND1 0.01 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.002 0.028 -9999 0 -0.43 2 2
CRK 0.037 0.027 -9999 0 -0.39 2 2
E-cadherin/gamma catenin/alpha catenin -0.002 0.023 -9999 0 -0.3 3 3
alphaE/beta7 Integrin -0.001 0.016 -9999 0 -0.35 1 1
IQGAP1 0.01 0 -9999 0 -10000 0 0
NCKAP1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.032 0.029 -9999 0 -0.42 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.009 -9999 0 -10000 0 0
MLLT4 0.01 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.031 0.09 -9999 0 -0.28 53 53
PI3K -0.001 0.011 -9999 0 -10000 0 0
ARF6 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.002 0.028 -9999 0 -0.36 3 3
TIAM1 0.002 0.065 -9999 0 -0.5 8 8
E-cadherin(dimer)/Ca2+ -0.001 0.015 -9999 0 -0.24 2 2
AKT1 -0.001 0.006 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
CDH1 0.008 0.032 -9999 0 -0.5 2 2
RhoA/GDP 0.05 0.02 -9999 0 -10000 0 0
actin cytoskeleton organization -0.009 0.025 -9999 0 -0.18 2 2
CDC42/GDP 0.05 0.02 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.018 0.017 -9999 0 -0.23 2 2
ITGB7 0.009 0.023 -9999 0 -0.5 1 1
RAC1 0.01 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.001 0.016 -9999 0 -0.26 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin -0.001 0.016 -9999 0 -0.25 2 2
mol:GDP 0.048 0.023 -9999 0 -0.28 2 2
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.009 0.024 -9999 0 -0.52 1 1
p120 catenin/RhoA/GDP -0.001 0.015 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.019 0.034 -9999 0 -0.21 6 6
NME1 -0.041 0.16 -9999 0 -0.52 47 47
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.031 0.029 -9999 0 -0.42 2 2
regulation of cell-cell adhesion -0.001 0.009 -9999 0 -10000 0 0
WASF2 -0.004 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.012 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.002 0.021 -9999 0 -10000 0 0
CCND1 0.021 0.041 -9999 0 -0.26 6 6
VAV2 0.039 0.041 -9999 0 -0.46 3 3
RAP1/GDP 0 0.013 -9999 0 -10000 0 0
adherens junction assembly 0.032 0.028 -9999 0 -0.4 2 2
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.01 0 -9999 0 -10000 0 0
PIP5K1C 0.01 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.002 0.02 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.001 0.022 -9999 0 -0.34 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.032 0.029 -9999 0 -0.42 2 2
PIK3CA 0.01 0 -9999 0 -10000 0 0
Rac1/GTP -0.018 0.053 -9999 0 -0.42 2 2
E-cadherin/beta catenin/alpha catenin -0.001 0.019 -9999 0 -0.29 2 2
ITGAE 0.01 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.028 -9999 0 -0.44 2 2
IGF1 pathway

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
NCK2 0.01 0 -10000 0 -10000 0 0
PTK2 0.01 0 -10000 0 -10000 0 0
CRKL 0.014 0.045 -10000 0 -0.46 1 1
GRB2/SOS1/SHC -0.001 0.014 -10000 0 -0.3 1 1
HRAS 0.01 0 -10000 0 -10000 0 0
IRS1/Crk 0.014 0.045 -10000 0 -0.26 12 12
IGF-1R heterotetramer/IGF1/PTP1B -0.007 0.045 -10000 0 -0.28 13 13
AKT1 0.03 0.04 -10000 0 -0.38 1 1
BAD 0.035 0.038 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0.045 -10000 0 -0.26 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.014 0.045 -10000 0 -0.46 1 1
RAF1 0.038 0.037 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.006 0.039 -10000 0 -0.43 1 1
YWHAZ 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.007 0.046 -10000 0 -0.28 12 12
PIK3CA 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.03 0.04 -10000 0 -0.38 1 1
GNB2L1 0.01 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.032 0.033 -10000 0 -10000 0 0
PXN 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.006 0.035 -10000 0 -0.39 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.035 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.007 0.035 -10000 0 -0.51 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.042 -10000 0 -0.26 12 12
Crk/p130 Cas/Paxillin -0.006 0.037 -10000 0 -0.41 1 1
IGF1R 0.007 0.035 -10000 0 -0.51 2 2
IGF1 -0.002 0.078 -10000 0 -0.51 11 11
IRS2/Crk 0.019 0.044 -10000 0 -0.43 1 1
PI3K -0.007 0.04 -10000 0 -0.43 1 1
apoptosis -0.037 0.035 0.31 1 -10000 0 1
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD 0.024 0.057 -10000 0 -0.34 10 10
RAF1/14-3-3 E 0.04 0.034 -10000 0 -10000 0 0
BAD/14-3-3 0.039 0.036 -10000 0 -0.32 1 1
PRKCZ 0.028 0.044 -10000 0 -0.38 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.005 0.029 -10000 0 -0.32 1 1
PTPN1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.019 0.06 -10000 0 -0.37 10 10
BCAR1 0.009 0.023 -10000 0 -0.5 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.007 0.04 -10000 0 -0.29 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.01 0 -10000 0 -10000 0 0
IRS1/NCK2 0.014 0.045 -10000 0 -0.26 12 12
GRB10 0.01 0 -10000 0 -10000 0 0
PTPN11 0.014 0.045 -10000 0 -0.46 1 1
IRS1 0.008 0.048 -10000 0 -0.28 12 12
IRS2 0.014 0.046 -10000 0 -0.36 2 2
IGF-1R heterotetramer/IGF1 -0.01 0.06 -10000 0 -0.37 13 13
GRB2 0.01 0 -10000 0 -10000 0 0
PDPK1 0.024 0.042 -10000 0 -0.4 1 1
YWHAE 0.01 0 -10000 0 -10000 0 0
PRKD1 0.014 0.079 -10000 0 -0.38 11 11
SHC1 0.009 0.024 -10000 0 -0.52 1 1
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.007 0.04 -10000 0 -0.25 13 13
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.03 -10000 0 -0.38 3 3
GNB1/GNG2 -0.001 0.019 -10000 0 -0.3 2 2
GNB1 0.01 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 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.006 0.042 -10000 0 -0.28 11 11
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 0.002 0.011 0.075 11 -10000 0 11
GNAL -0.002 0.076 -10000 0 -0.5 11 11
GNG2 0.008 0.032 -10000 0 -0.5 2 2
CRH 0 0.041 -10000 0 -0.52 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0 -10000 0 -10000 0 0
MAPK11 0.005 0.026 -10000 0 -0.32 3 3
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.003 0.034 -9999 0 -0.55 1 1
PDGFB-D/PDGFRB/SLAP -0.009 0.061 -9999 0 -0.38 12 12
PDGFB-D/PDGFRB/APS/CBL -0.001 0.019 -9999 0 -0.29 2 2
AKT1 0.044 0.032 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.024 0.042 -9999 0 -0.59 1 1
PIK3CA 0.01 0 -9999 0 -10000 0 0
FGR -0.036 0.14 -9999 0 -0.51 37 37
mol:Ca2+ 0.022 0.039 -9999 0 -0.63 1 1
MYC 0.032 0.071 -9999 0 -0.68 3 3
SHC1 0.009 0.024 -9999 0 -0.52 1 1
HRAS/GDP 0.002 0.013 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.006 0.055 -9999 0 -0.39 8 8
GRB10 0.01 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0.022 0.039 -9999 0 -0.64 1 1
PTEN 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
GRB7 0.004 0.057 -9999 0 -0.51 6 6
PDGFB-D/PDGFRB/SHP2 0 0.016 -9999 0 -0.36 1 1
PDGFB-D/PDGFRB/GRB10 0 0.016 -9999 0 -0.36 1 1
cell cycle arrest -0.009 0.06 -9999 0 -0.38 12 12
HRAS 0.01 0 -9999 0 -10000 0 0
HIF1A 0.048 0.029 -9999 0 -10000 0 0
GAB1 0.02 0.05 -9999 0 -0.64 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.024 0.046 -9999 0 -0.57 1 1
PDGFB-D/PDGFRB 0.006 0.018 -9999 0 -0.31 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0.016 -9999 0 -0.36 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.004 0.035 -9999 0 -0.51 1 1
positive regulation of MAPKKK cascade 0 0.016 -9999 0 -0.35 1 1
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
mol:IP3 0.022 0.039 -9999 0 -0.65 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.009 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.005 0.043 -9999 0 -0.36 7 7
SHB 0.009 0.023 -9999 0 -0.5 1 1
BLK -0.016 0.054 -9999 0 -0.47 5 5
PTPN2 0.01 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0.016 -9999 0 -0.36 1 1
BCAR1 0.009 0.023 -9999 0 -0.5 1 1
VAV2 0.02 0.066 -9999 0 -0.55 2 2
CBL 0.01 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0 0.016 -9999 0 -0.36 1 1
LCK 0 0.037 -9999 0 -0.45 3 3
PDGFRB 0.01 0.023 -9999 0 -0.51 1 1
ACP1 0.01 0 -9999 0 -10000 0 0
HCK -0.019 0.11 -9999 0 -0.53 21 21
ABL1 0.017 0.051 -9999 0 -0.6 1 1
PDGFB-D/PDGFRB/CBL 0.018 0.055 -9999 0 -0.73 1 1
PTPN1 0.01 0.001 -9999 0 -10000 0 0
SNX15 0.01 0 -9999 0 -10000 0 0
STAT3 0.01 0 -9999 0 -10000 0 0
STAT1 0.01 0 -9999 0 -10000 0 0
cell proliferation 0.032 0.064 -9999 0 -0.6 3 3
SLA -0.003 0.079 -9999 0 -0.5 12 12
actin cytoskeleton reorganization 0.039 0.02 -9999 0 -10000 0 0
SRC 0.002 0.017 -9999 0 -0.34 1 1
PI3K -0.004 0.028 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.005 0.038 -9999 0 -0.3 8 8
SH2B2 0.009 0.023 -9999 0 -0.5 1 1
PLCgamma1/SPHK1 0.025 0.043 -9999 0 -0.62 1 1
LYN 0.003 0.017 -9999 0 -0.33 1 1
LRP1 0.006 0.046 -9999 0 -0.5 4 4
SOS1 0.01 0 -9999 0 -10000 0 0
STAT5B 0.01 0 -9999 0 -10000 0 0
STAT5A 0.009 0.023 -9999 0 -0.5 1 1
NCK1-2/p130 Cas 0.002 0.017 -9999 0 -10000 0 0
SPHK1 0.006 0.047 -9999 0 -0.51 4 4
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.022 0.039 -9999 0 -0.65 1 1
PLCG1 0.022 0.04 -9999 0 -0.67 1 1
NHERF/PDGFRB -0.005 0.04 -9999 0 -0.3 9 9
YES1 0.002 0.017 -9999 0 -0.34 1 1
cell migration -0.005 0.04 -9999 0 -0.29 9 9
SHC/Grb2/SOS1 0.002 0.018 -9999 0 -10000 0 0
SLC9A3R2 0.004 0.056 -9999 0 -0.5 6 6
SLC9A3R1 0.008 0.034 -9999 0 -0.52 2 2
NHERF1-2/PDGFRB/PTEN -0.005 0.035 -9999 0 -0.27 2 2
FYN 0.002 0.029 -9999 0 -0.42 2 2
DOK1 0.026 0.013 -9999 0 -0.26 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.004 0.056 -9999 0 -0.5 6 6
RAC1 0.029 0.066 -9999 0 -0.53 3 3
PRKCD 0.027 0.014 -9999 0 -0.27 1 1
FER 0.027 0.014 -9999 0 -0.27 1 1
MAPKKK cascade -0.001 0.014 -9999 0 -10000 0 0
RASA1 0.027 0.014 -9999 0 -0.27 1 1
NCK1 0.01 0 -9999 0 -10000 0 0
NCK2 0.01 0 -9999 0 -10000 0 0
p62DOK/Csk 0.007 0.017 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.001 0.023 -9999 0 -0.36 2 2
chemotaxis 0.017 0.05 -9999 0 -0.58 1 1
STAT1-3-5/STAT1-3-5 -0.001 0.014 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.001 0.017 -9999 0 -0.37 1 1
PTPRJ 0.01 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.066 0.012 -9999 0 -10000 0 0
ERC1 0.01 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.001 0.016 -9999 0 -0.35 1 1
NFKBIA 0.037 0 -9999 0 -10000 0 0
BIRC2 0.01 0 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
RIPK2 0.01 0 -9999 0 -10000 0 0
IKBKG 0 0.008 -9999 0 -10000 0 0
IKK complex/A20 -0.008 0.037 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.01 0 -9999 0 -10000 0 0
XPO1 0.01 0 -9999 0 -10000 0 0
NEMO/ATM 0.04 0.009 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.009 0.024 -9999 0 -0.52 1 1
Exportin 1/RanGTP -0.001 0.014 -9999 0 -0.31 1 1
IKK complex/ELKS 0 0.006 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 0.009 0.023 -9999 0 -0.5 1 1
NFKB1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
MALT1 0.01 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.01 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.014 0.068 -9999 0 -0.35 19 19
TRAF6 0.01 0 -9999 0 -10000 0 0
PRKCA 0.008 0.032 -9999 0 -0.5 2 2
CHUK 0.01 0 -9999 0 -10000 0 0
UBE2D3 0.01 0 -9999 0 -10000 0 0
TNF -0.01 0.099 -9999 0 -0.5 19 19
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.01 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.01 0 -9999 0 -10000 0 0
IKK complex 0 0.007 -9999 0 -10000 0 0
CYLD 0.01 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.001 0.014 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.01 0 -9999 0 -10000 0 0
ITGB7 0.009 0.023 -9999 0 -0.5 1 1
ITGA4 0.008 0.032 -9999 0 -0.5 2 2
alpha4/beta7 Integrin -0.002 0.027 -9999 0 -0.35 3 3
alpha4/beta1 Integrin -0.001 0.022 -9999 0 -0.35 2 2
EPO 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
BCL2L1 0.06 0.032 -10000 0 -10000 0 0
CRKL 0.035 0.034 -10000 0 -0.43 1 1
mol:DAG 0.04 0.027 -10000 0 -0.31 1 1
HRAS 0.05 0.039 -10000 0 -0.54 1 1
MAPK8 0.027 0.026 -10000 0 -0.28 1 1
RAP1A 0.035 0.034 -10000 0 -0.43 1 1
GAB1 0.033 0.044 -10000 0 -0.67 1 1
MAPK14 0.027 0.026 -10000 0 -0.28 1 1
EPO 0.005 0.048 -10000 0 -0.52 4 4
PLCG1 0.04 0.027 -10000 0 -0.32 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.004 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.005 0.038 -10000 0 -0.3 8 8
GAB1/SHC/GRB2/SOS1 -0.004 0.035 -10000 0 -0.58 1 1
EPO/EPOR (dimer) 0.014 0.035 -10000 0 -0.37 4 4
IRS2 0.034 0.039 -10000 0 -0.43 2 2
STAT1 0.048 0.03 -10000 0 -10000 0 0
STAT5B 0.044 0.029 -10000 0 -10000 0 0
cell proliferation 0.032 0.024 -10000 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.038 -10000 0 -0.46 2 2
TEC 0.035 0.034 -10000 0 -0.43 1 1
SOCS3 0.006 0.046 -10000 0 -0.5 4 4
STAT1 (dimer) 0.047 0.029 -10000 0 -10000 0 0
JAK2 0.009 0.034 -10000 0 -0.51 2 2
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
EPO/EPOR (dimer)/JAK2 0.039 0.037 -10000 0 -0.46 1 1
EPO/EPOR 0.014 0.035 -10000 0 -0.37 4 4
LYN 0.011 0.001 -10000 0 -10000 0 0
TEC/VAV2 0.04 0.035 -10000 0 -0.42 1 1
elevation of cytosolic calcium ion concentration 0.012 0.004 -10000 0 -10000 0 0
SHC1 0.009 0.024 -10000 0 -0.52 1 1
EPO/EPOR (dimer)/LYN 0.025 0.029 -10000 0 -0.29 4 4
mol:IP3 0.04 0.027 -10000 0 -0.31 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.005 0.037 -10000 0 -0.4 3 3
SH2B3 0.009 0.033 -10000 0 -0.5 2 2
NFKB1 0.027 0.026 -10000 0 -0.28 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.035 0.24 2 -0.35 2 4
PTPN6 0.029 0.035 -10000 0 -0.46 1 1
TEC/VAV2/GRB2 0.043 0.034 -10000 0 -0.4 1 1
EPOR 0.012 0.004 -10000 0 -10000 0 0
INPP5D 0.007 0.04 -10000 0 -0.5 3 3
mol:GDP -0.004 0.035 -10000 0 -0.59 1 1
SOS1 0.01 0 -10000 0 -10000 0 0
PLCG2 0.007 0.04 -10000 0 -0.5 3 3
CRKL/CBL/C3G 0.044 0.032 -10000 0 -0.4 1 1
VAV2 0.034 0.036 -10000 0 -0.43 1 1
CBL 0.035 0.034 -10000 0 -0.43 1 1
SHC/Grb2/SOS1 -0.003 0.028 -10000 0 -0.4 1 1
STAT5A 0.043 0.037 -10000 0 -0.49 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.057 0.04 -10000 0 -0.44 1 1
LYN/PLCgamma2 -0.002 0.027 -10000 0 -0.35 3 3
PTPN11 0.01 0 -10000 0 -10000 0 0
BTK 0.018 0.079 -10000 0 -0.46 5 5
BCL2 0.058 0.052 -10000 0 -0.81 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.026 -9999 0 -0.31 3 3
CRKL 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.01 0 -9999 0 -10000 0 0
ITGA4 0.008 0.032 -9999 0 -0.5 2 2
alpha4/beta7 Integrin/MAdCAM1 -0.005 0.036 -9999 0 -0.27 6 6
EPO 0.002 0.047 -9999 0 -0.52 4 4
alpha4/beta7 Integrin -0.002 0.027 -9999 0 -0.35 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.022 -9999 0 -0.35 2 2
EPO/EPOR (dimer) -0.003 0.033 -9999 0 -0.37 4 4
lamellipodium assembly 0 0.012 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.001 0.016 -9999 0 -0.35 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
JAK2 0.021 0.037 -9999 0 -0.44 2 2
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
MADCAM1 0.002 0.058 -9999 0 -0.52 6 6
cell adhesion -0.005 0.036 -9999 0 -0.27 6 6
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.01 0 -9999 0 -10000 0 0
SRC 0.023 0.031 -9999 0 -0.26 6 6
ITGB7 0.009 0.023 -9999 0 -0.5 1 1
RAC1 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.004 0.032 -9999 0 -0.29 6 6
p130Cas/Crk/Dock1 0.037 0.029 -9999 0 -10000 0 0
VCAM1 0.006 0.046 -9999 0 -0.5 4 4
RHOA 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.016 -9999 0 -0.26 2 2
BCAR1 0.028 0.032 -9999 0 -10000 0 0
EPOR 0.01 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.012 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.034 0.041 -10000 0 -10000 0 0
BAG4 0.009 0.024 -10000 0 -0.52 1 1
BAD 0.024 0.018 -10000 0 -10000 0 0
NFKBIA 0.01 0 -10000 0 -10000 0 0
BIRC3 0.003 0.057 -10000 0 -0.51 6 6
BAX 0.024 0.018 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.011 0.013 -10000 0 -10000 0 0
IKBKB 0.038 0.04 -10000 0 -10000 0 0
MAP2K2 0.033 0.02 -10000 0 -10000 0 0
MAP2K1 0.033 0.02 -10000 0 -10000 0 0
SMPD1 0.015 0.013 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.038 0.043 -10000 0 -0.29 1 1
MAP2K4 0.029 0.018 -10000 0 -10000 0 0
protein ubiquitination 0.04 0.04 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.037 0.023 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.029 0.02 -10000 0 -10000 0 0
CRADD 0.009 0.024 -10000 0 -0.52 1 1
mol:ceramide 0.019 0.018 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.01 0 -10000 0 -10000 0 0
MAP3K1 0.024 0.018 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
RELA/p50 0.01 0 -10000 0 -10000 0 0
MAPK3 0.035 0.02 -10000 0 -10000 0 0
MAPK1 0.035 0.02 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.034 0.041 -10000 0 -10000 0 0
KSR1 0.024 0.019 -10000 0 -10000 0 0
MAPK8 0.033 0.017 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.038 0.04 -10000 0 -10000 0 0
TNF R/SODD -0.001 0.017 -10000 0 -0.37 1 1
TNF -0.01 0.099 -10000 0 -0.5 19 19
CYCS 0.025 0.018 0.13 1 -10000 0 1
IKBKG 0.038 0.04 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.029 0.043 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AIFM1 0.025 0.018 0.13 1 -10000 0 1
TNF/TNF R/SODD -0.012 0.058 -10000 0 -0.29 20 20
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.021 0.034 -10000 0 -0.68 1 1
NSMAF 0.033 0.041 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 0.007 0.041 -10000 0 -0.51 3 3
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.002 0.023 -9999 0 -0.3 3 3
E-cadherin/beta catenin -0.001 0.022 -9999 0 -0.35 2 2
CTNNB1 0.01 0 -9999 0 -10000 0 0
JUP 0.009 0.024 -9999 0 -0.52 1 1
CDH1 0.008 0.032 -9999 0 -0.5 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.01 0 -9999 0 -10000 0 0
SMAD2 0.011 0 -9999 0 -10000 0 0
SMAD3 0.033 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.036 0.008 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.003 0.027 -9999 0 -10000 0 0
PPM1A 0.01 0 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.016 0 -9999 0 -10000 0 0
MAP3K1 0.01 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.001 0.022 -9999 0 -0.35 2 2
MAPK3 0.01 0 -9999 0 -10000 0 0
MAPK1 0.01 0 -9999 0 -10000 0 0
NUP214 0.01 0 -9999 0 -10000 0 0
CTDSP1 0.01 0 -9999 0 -10000 0 0
CTDSP2 0.01 0 -9999 0 -10000 0 0
CTDSPL 0.01 0 -9999 0 -10000 0 0
KPNB1 0.01 0 -9999 0 -10000 0 0
TGFBRAP1 0.008 0.032 -9999 0 -0.5 2 2
UBE2I 0.01 0 -9999 0 -10000 0 0
NUP153 0.01 0 -9999 0 -10000 0 0
KPNA2 0.002 0.063 -9999 0 -0.52 7 7
PIAS4 0.01 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.003 0.028 -10000 0 -0.29 3 3
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
AKT2 0.01 0 -10000 0 -10000 0 0
STXBP4 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.032 0.037 0.21 1 -0.32 3 4
YWHAZ 0.01 0 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
TBC1D4 0.018 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
YWHAB 0.01 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
ASIP 0.005 0.024 -10000 0 -0.52 1 1
PRKCI 0.01 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.01 0 -10000 0 -10000 0 0
GYS1 0.025 0 -10000 0 -10000 0 0
PRKCZ 0.007 0.04 -10000 0 -0.5 3 3
TRIP10 0.01 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.035 0.018 -10000 0 -10000 0 0
VAMP2 0.01 0 -10000 0 -10000 0 0
SLC2A4 0.032 0.04 0.21 1 -0.36 3 4
STX4 0.01 0 -10000 0 -10000 0 0
GSK3B 0.02 0 -10000 0 -10000 0 0
SFN 0 0.071 -10000 0 -0.52 9 9
LNPEP 0.01 0 -10000 0 -10000 0 0
YWHAE 0.01 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.01 0 -10000 0 -10000 0 0
mol:PIP3 -0.001 0.016 -10000 0 -0.25 2 2
FRAP1 0.012 0.005 -10000 0 -10000 0 0
AKT1 0.022 0.015 -10000 0 -10000 0 0
INSR 0.01 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.004 -10000 0 -10000 0 0
TSC2 0.01 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.013 -10000 0 -10000 0 0
TSC1 0.01 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.012 0.015 -10000 0 -0.32 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.01 -10000 0 -10000 0 0
MAP3K5 0.008 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.023 -10000 0 -0.5 1 1
apoptosis 0.008 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 1 1
EIF4B 0.026 0.009 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0.006 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.002 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.018 0.018 -10000 0 -0.26 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.009 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.013 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 1 1
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.001 0.015 -10000 0 -0.24 1 1
EIF4E 0.01 0 -10000 0 -10000 0 0
ASK1/PP5C 0.017 0.003 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.013 0.006 -10000 0 -10000 0 0
TSC1/TSC2 -0.001 0.012 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 1 -10000 0 1
RPS6 0.01 0 -10000 0 -10000 0 0
PPP5C 0.01 0 -10000 0 -10000 0 0
EIF4G1 0.01 0 -10000 0 -10000 0 0
IRS1 0.006 0.016 -10000 0 -0.35 1 1
INS 0 0 -10000 0 -10000 0 0
PTEN 0.01 0 -10000 0 -10000 0 0
PDK2 -0.001 0.015 -10000 0 -0.24 1 1
EIF4EBP1 0.007 0.012 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
PPP2R5D 0.017 0.005 -10000 0 -10000 0 0
peptide biosynthetic process 0.014 0 -10000 0 -10000 0 0
RHEB 0.009 0.024 -10000 0 -0.52 1 1
EIF4A1 0.01 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.014 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.012 0.011 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.03 0 -9999 0 -10000 0 0
CDKN1A 0.029 0.011 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.01 0 -9999 0 -10000 0 0
FOXO3 0.03 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.01 0 -9999 0 -10000 0 0
AKT3 0.012 0.026 -9999 0 -0.31 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.03 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.01 0 -9999 0 -10000 0 0
RAF1 0.01 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.03 0 -9999 0 -10000 0 0
YWHAZ 0.01 0 -9999 0 -10000 0 0
AKT1/RAF1 0.029 0 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
mol:GDP 0.024 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.03 0 -9999 0 -10000 0 0
YWHAQ 0.01 0 -9999 0 -10000 0 0
TBC1D4 0.019 0 -9999 0 -10000 0 0
MAP3K5 0.01 0 -9999 0 -10000 0 0
MAPKAP1 0.01 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.034 0.012 -9999 0 -10000 0 0
YWHAH 0.01 0 -9999 0 -10000 0 0
AKT1S1 0.03 0 -9999 0 -10000 0 0
CASP9 0.03 0 -9999 0 -10000 0 0
YWHAB 0.01 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.034 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0.01 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.003 -9999 0 -10000 0 0
CHUK 0.03 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.039 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.014 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.046 0.012 -9999 0 -10000 0 0
PDPK1 0.01 0 -9999 0 -10000 0 0
MDM2 0.029 0.017 -9999 0 -10000 0 0
MAPKKK cascade -0.029 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.038 0.016 -9999 0 -10000 0 0
TSC1/TSC2 0.035 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.013 -9999 0 -10000 0 0
glucose import 0.021 0.031 -9999 0 -0.26 6 6
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.003 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.021 0.031 -9999 0 -0.26 6 6
GSK3A 0.03 0 -9999 0 -10000 0 0
FOXO1 0.03 0 -9999 0 -10000 0 0
GSK3B 0.03 0 -9999 0 -10000 0 0
SFN 0 0.071 -9999 0 -0.52 9 9
G1/S transition of mitotic cell cycle 0.035 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.036 0.017 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
KPNA1 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
YWHAG 0.01 0 -9999 0 -10000 0 0
RHEB 0.009 0.024 -9999 0 -0.52 1 1
CREBBP 0.01 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0.01 0 -9999 0 -10000 0 0
ITGA4 0.008 0.032 -9999 0 -0.5 2 2
RAC1 0.01 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.002 0.027 -9999 0 -0.35 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.019 -9999 0 -0.29 2 2
alpha4/beta7 Integrin/Paxillin -0.002 0.02 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.019 -9999 0 -0.34 1 1
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.001 0.016 -9999 0 -0.35 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
TLN1 0.009 0.023 -9999 0 -0.5 1 1
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
ARF6/GTP -0.001 0.013 -9999 0 -10000 0 0
cell adhesion -0.001 0.018 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.016 -9999 0 -0.26 2 2
ITGB1 0.01 0 -9999 0 -10000 0 0
ITGB7 0.009 0.023 -9999 0 -0.5 1 1
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.003 0.026 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 -0.001 0.013 -9999 0 -0.29 1 1
VCAM1 0.006 0.046 -9999 0 -0.5 4 4
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.015 -9999 0 -10000 0 0
BCAR1 0.009 0.023 -9999 0 -0.5 1 1
mol:GDP 0.001 0.015 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.018 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.021 -9999 0 -0.38 1 1
Atypical NF-kappaB 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
BCL3/RelA -0.001 0.016 -9999 0 -0.35 1 1
FBXW11 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.02 -9999 0 -10000 0 0
NFKBIA 0.021 0.023 -9999 0 -0.2 5 5
MAPK14 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0 -9999 0 -10000 0 0
ARRB2 0.014 0 -9999 0 -10000 0 0
REL 0.01 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.014 -9999 0 -0.29 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.023 -9999 0 -0.5 1 1
NFKB1 0.018 0 -9999 0 -10000 0 0
RELA 0.01 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.026 0.022 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.038 0.02 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
PI3K -0.001 0.016 -9999 0 -0.35 1 1
NF kappa B1 p50/RelA 0.026 0.023 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -10000 0 0
SYK 0.007 0.04 -9999 0 -0.5 3 3
I kappa B alpha/PIK3R1 0.025 0.024 -9999 0 -0.23 1 1
cell death -0.002 0.015 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.021 0 -9999 0 -10000 0 0
LCK 0.007 0.04 -9999 0 -0.5 3 3
BCL3 0.009 0.023 -9999 0 -0.5 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.013 -9999 0 -10000 0 0
MDM2/SUMO1 0.022 0.017 -9999 0 -0.24 2 2
HDAC4 0.009 0.024 -9999 0 -0.52 1 1
Ran/GTP/Exportin 1/HDAC1 0 0.009 -9999 0 -10000 0 0
SUMO1 0.01 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.023 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.009 0.024 -9999 0 -0.52 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.023 0.012 -9999 0 -0.24 1 1
SUMO1/HDAC1 0.024 0 -9999 0 -10000 0 0
RANGAP1 0.01 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.017 -9999 0 -0.27 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0 -9999 0 -10000 0 0
Ran/GTP 0 0.011 -9999 0 -0.24 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.008 0.034 -9999 0 -0.52 2 2
UBE2I 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0.01 -9999 0 -0.23 1 1
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.01 0 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.039 0.017 -9999 0 -10000 0 0
adherens junction organization 0.032 0.025 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.036 0.043 -9999 0 -10000 0 0
FMN1 0.025 0.049 -9999 0 -10000 0 0
mol:IP3 -0.001 0.012 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.018 -9999 0 -0.23 2 2
CTNNB1 0.01 0.001 -9999 0 -10000 0 0
AKT1 0.037 0.016 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.028 -9999 0 -0.36 2 2
CTNND1 0.011 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.034 0.017 -9999 0 -10000 0 0
VASP 0.034 0.017 -9999 0 -10000 0 0
ZYX 0.033 0.021 -9999 0 -10000 0 0
JUB 0.033 0.024 -9999 0 -10000 0 0
EGFR(dimer) 0.026 0.047 -9999 0 -0.32 1 1
E-cadherin/beta catenin-gamma catenin -0.002 0.022 -9999 0 -0.29 3 3
mol:PI-3-4-5-P3 -0.001 0.014 -9999 0 -10000 0 0
PIK3CA 0.011 0.001 -9999 0 -10000 0 0
PI3K -0.001 0.014 -9999 0 -10000 0 0
FYN 0.02 0.064 -9999 0 -10000 0 0
mol:Ca2+ 0.032 0.015 -9999 0 -10000 0 0
JUP 0.009 0.024 -9999 0 -0.52 1 1
PIK3R1 0.01 0.023 -9999 0 -0.5 1 1
mol:DAG -0.001 0.012 -9999 0 -10000 0 0
CDH1 0.008 0.032 -9999 0 -0.5 2 2
RhoA/GDP 0.036 0.043 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.034 0.017 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
EGFR -0.005 0.086 -9999 0 -0.51 14 14
CASR 0.01 0.078 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.011 -9999 0 -10000 0 0
AKT2 0.037 0.016 -9999 0 -10000 0 0
actin cable formation 0.03 0.048 -9999 0 -10000 0 0
apoptosis 0.001 0.013 -9999 0 -10000 0 0
CTNNA1 0.011 0.001 -9999 0 -10000 0 0
mol:GDP 0.032 0.045 -9999 0 -0.29 1 1
PIP5K1A 0.034 0.017 -9999 0 -10000 0 0
PLCG1 -0.001 0.013 -9999 0 -10000 0 0
Rac1/GTP -0.007 0.037 -9999 0 -0.3 1 1
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -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 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0 -9999 0 -10000 0 0
CD4 0 0.072 -9999 0 -0.5 10 10
CLTA 0.01 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 0.022 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 0.01 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.01 0 -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 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.022 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 0.01 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 0.024 0.031 -9999 0 -0.19 10 10
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 -0.006 0.041 -9999 0 -0.29 10 10
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -9999 0 0
FBXW11 0.01 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -9999 0 0
CHUK 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -9999 0 0
NFKB1 0.01 0 -9999 0 -9999 0 0
MAP3K14 0.01 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0 0 -9999 0 -9999 0 0
RELB 0.01 0 -9999 0 -9999 0 0
NFKB2 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -9999 0 0
regulation of B cell activation 0 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 488 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.O1.A52J TCGA.NJ.A55R TCGA.NJ.A55O TCGA.NJ.A55A
109_MAP3K5 0.043 0.043 0.043 0.043
47_PPARGC1A 0.0099 0.0099 0.0099 0.0099
105_BMP4 0.0099 0.0099 0.0099 0.0099
105_BMP6 -0.5 0.0099 0.0099 0.0099
105_BMP7 0.0099 0.0099 0.0099 0.0099
105_BMP2 0.0099 0.0099 0.0099 0.0099
131_RELN/VLDLR -0.26 0 0 0
30_TGFB1/TGF beta receptor Type II 0.0094 0.014 0.0094 0.0094
84_STAT5B 0.035 0.037 0.022 -0.056
84_STAT5A 0.035 0.037 0.022 -0.056
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/LUAD-TP/6044650/LUAD-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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