PARADIGM pathway analysis of mRNASeq expression and copy number data
Prostate Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1KK99VJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1KK99VJ
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 50 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
Ephrin A reverse signaling 96
Angiopoietin receptor Tie2-mediated signaling 90
Signaling mediated by p38-alpha and p38-beta 89
Glypican 2 network 87
Endothelins 76
Glucocorticoid receptor regulatory network 66
IL23-mediated signaling events 58
Nephrin/Neph1 signaling in the kidney podocyte 57
Reelin signaling pathway 53
EPHB forward signaling 52
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 497 . 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 ( 497 ).

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
Ephrin A reverse signaling 0.1932 96 677 7 -0.049 0 1000 -1000 -0.013 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1811 90 8003 88 -0.29 0.075 1000 -1000 -0.047 -1000
Signaling mediated by p38-alpha and p38-beta 0.1791 89 3940 44 -0.15 0.027 1000 -1000 -0.009 -1000
Glypican 2 network 0.1751 87 349 4 0.031 0.061 1000 -1000 0.02 -1000
Endothelins 0.1529 76 7347 96 -0.19 0.028 1000 -1000 -0.042 -1000
Glucocorticoid receptor regulatory network 0.1328 66 7545 114 -0.41 0.21 1000 -1000 -0.04 -1000
IL23-mediated signaling events 0.1167 58 3507 60 -0.3 0.046 1000 -1000 -0.074 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1147 57 1967 34 -0.05 0.03 1000 -1000 -0.03 -1000
Reelin signaling pathway 0.1066 53 3005 56 -0.095 0.07 1000 -1000 -0.022 -1000
EPHB forward signaling 0.1046 52 4501 85 -0.075 0.094 1000 -1000 -0.042 -1000
Thromboxane A2 receptor signaling 0.1006 50 5256 105 -0.12 0.037 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.0946 47 3977 84 -0.099 0.083 1000 -1000 -0.024 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0885 44 3461 78 -0.12 0.059 1000 -1000 -0.047 -1000
Aurora B signaling 0.0885 44 3011 67 -0.091 0.12 1000 -1000 -0.026 -1000
LPA receptor mediated events 0.0865 43 4392 102 -0.057 0.1 1000 -1000 -0.044 -1000
Syndecan-1-mediated signaling events 0.0845 42 1439 34 -0.019 0.1 1000 -1000 -0.018 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0845 42 2879 68 -0.16 0.062 1000 -1000 -0.054 -1000
HIF-1-alpha transcription factor network 0.0805 40 3068 76 -0.073 0.07 1000 -1000 -0.045 -1000
Ephrin B reverse signaling 0.0805 40 1926 48 -0.068 0.034 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 0.0805 40 683 17 -0.081 0.041 1000 -1000 -0.014 -1000
Noncanonical Wnt signaling pathway 0.0785 39 1016 26 -0.04 0.027 1000 -1000 -0.026 -1000
S1P1 pathway 0.0765 38 1376 36 -0.19 0.026 1000 -1000 -0.02 -1000
Signaling events mediated by the Hedgehog family 0.0744 37 1962 52 -0.041 0.037 1000 -1000 -0.023 -1000
p75(NTR)-mediated signaling 0.0724 36 4582 125 -0.073 0.072 1000 -1000 -0.048 -1000
IL6-mediated signaling events 0.0724 36 2745 75 -0.16 0.032 1000 -1000 -0.041 -1000
EPO signaling pathway 0.0704 35 1938 55 -0.019 0.048 1000 -1000 -0.023 -1000
amb2 Integrin signaling 0.0704 35 2876 82 -0.11 0.1 1000 -1000 -0.021 -1000
S1P5 pathway 0.0704 35 602 17 -0.045 0.042 1000 -1000 -0.002 -1000
Calcium signaling in the CD4+ TCR pathway 0.0704 35 1103 31 -0.088 0.032 1000 -1000 -0.031 -1000
EGFR-dependent Endothelin signaling events 0.0704 35 753 21 -0.029 0.045 1000 -1000 -0.028 -1000
Nongenotropic Androgen signaling 0.0684 34 1800 52 -0.12 0.06 1000 -1000 -0.018 -1000
Osteopontin-mediated events 0.0664 33 1278 38 -0.054 0.051 1000 -1000 -0.037 -1000
Wnt signaling 0.0664 33 235 7 -0.03 0.027 1000 -1000 0 -1000
Signaling events regulated by Ret tyrosine kinase 0.0644 32 2628 82 -0.03 0.044 1000 -1000 -0.03 -1000
JNK signaling in the CD4+ TCR pathway 0.0624 31 542 17 -0.12 0.065 1000 -1000 -0.027 -1000
BMP receptor signaling 0.0624 31 2574 81 -0.079 0.067 1000 -1000 -0.02 -1000
Effects of Botulinum toxin 0.0624 31 815 26 -0.027 0.05 1000 -1000 -0.013 -1000
S1P4 pathway 0.0624 31 796 25 -0.045 0.048 1000 -1000 -0.014 -1000
Glypican 1 network 0.0604 30 1455 48 -0.034 0.063 1000 -1000 -0.027 -1000
TCR signaling in naïve CD8+ T cells 0.0604 30 2818 93 -0.056 0.073 1000 -1000 -0.027 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0604 30 3655 120 -0.073 0.089 1000 -1000 -0.041 -1000
FOXM1 transcription factor network 0.0604 30 1560 51 -0.095 0.067 1000 -1000 -0.077 -1000
Fc-epsilon receptor I signaling in mast cells 0.0563 28 2737 97 -0.067 0.04 1000 -1000 -0.04 -1000
IL4-mediated signaling events 0.0543 27 2468 91 -0.24 0.12 1000 -1000 -0.11 -1000
PLK1 signaling events 0.0543 27 2349 85 -0.026 0.081 1000 -1000 -0.032 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0543 27 1446 52 -0.046 0.068 1000 -1000 -0.03 -1000
Arf6 signaling events 0.0523 26 1672 62 -0.037 0.043 1000 -1000 -0.023 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0523 26 2294 85 -0.12 0.034 1000 -1000 -0.028 -1000
IL12-mediated signaling events 0.0503 25 2212 87 -0.17 0.065 1000 -1000 -0.049 -1000
FAS signaling pathway (CD95) 0.0503 25 1188 47 -0.22 0.042 1000 -1000 -0.026 -1000
Visual signal transduction: Cones 0.0483 24 922 38 -0.041 0.042 1000 -1000 -0.02 -1000
Aurora C signaling 0.0483 24 172 7 0 0.067 1000 -1000 -0.009 -1000
Rapid glucocorticoid signaling 0.0483 24 493 20 -0.054 0.033 1000 -1000 -0.011 -1000
ErbB2/ErbB3 signaling events 0.0463 23 1546 65 -0.08 0.037 1000 -1000 -0.047 -1000
PDGFR-alpha signaling pathway 0.0463 23 1013 44 -0.13 0.051 1000 -1000 -0.024 -1000
Plasma membrane estrogen receptor signaling 0.0463 23 1989 86 -0.13 0.055 1000 -1000 -0.043 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0443 22 1228 54 -0.095 0.07 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 0.0443 22 1537 69 -0.008 0.044 1000 -1000 -0.033 -1000
Signaling events mediated by PTP1B 0.0443 22 1684 76 -0.14 0.096 1000 -1000 -0.042 -1000
Presenilin action in Notch and Wnt signaling 0.0443 22 1401 61 -0.12 0.073 1000 -1000 -0.039 -1000
Canonical Wnt signaling pathway 0.0443 22 1170 51 -0.12 0.12 1000 -1000 -0.031 -1000
Regulation of p38-alpha and p38-beta 0.0443 22 1200 54 -0.098 0.06 1000 -1000 -0.036 -1000
BARD1 signaling events 0.0423 21 1205 57 -0.03 0.045 1000 -1000 -0.039 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0423 21 2721 125 -0.06 0.051 1000 -1000 -0.026 -1000
BCR signaling pathway 0.0423 21 2135 99 -0.11 0.064 1000 -1000 -0.042 -1000
Visual signal transduction: Rods 0.0423 21 1126 52 -0.041 0.058 1000 -1000 -0.019 -1000
S1P3 pathway 0.0402 20 843 42 -0.028 0.04 1000 -1000 -0.032 -1000
Syndecan-4-mediated signaling events 0.0382 19 1330 67 -0.049 0.098 1000 -1000 -0.029 -1000
IGF1 pathway 0.0382 19 1093 57 -0.017 0.059 1000 -1000 -0.024 -1000
ErbB4 signaling events 0.0362 18 1263 69 -0.08 0.059 1000 -1000 -0.024 -1000
IL1-mediated signaling events 0.0362 18 1138 62 -0.037 0.067 1000 -1000 -0.023 -1000
IL27-mediated signaling events 0.0362 18 946 51 -0.35 0.077 1000 -1000 -0.04 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0362 18 1355 74 -0.14 0.052 1000 -1000 -0.044 -1000
Insulin Pathway 0.0362 18 1348 74 -0.12 0.076 1000 -1000 -0.037 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0362 18 601 33 -0.066 0.061 1000 -1000 -0.01 -1000
Caspase cascade in apoptosis 0.0342 17 1273 74 -0.038 0.063 1000 -1000 -0.025 -1000
Regulation of nuclear SMAD2/3 signaling 0.0342 17 2341 136 -0.07 0.15 1000 -1000 -0.04 -1000
a4b1 and a4b7 Integrin signaling 0.0342 17 88 5 0.015 0.034 1000 -1000 0.021 -1000
Ceramide signaling pathway 0.0342 17 1358 76 -0.022 0.072 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 0.0322 16 1259 76 -0.015 0.068 1000 -1000 -0.022 -1000
Nectin adhesion pathway 0.0322 16 1030 63 -0.037 0.061 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0322 16 798 49 0 0.038 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 0.0322 16 690 43 -0.048 0.049 1000 -1000 -0.034 -1000
TCGA08_p53 0.0322 16 118 7 -0.013 0.026 1000 -1000 -0.011 -1000
VEGFR1 specific signals 0.0322 16 948 56 -0.055 0.042 1000 -1000 -0.029 -1000
Cellular roles of Anthrax toxin 0.0302 15 598 39 -0.023 0.026 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0302 15 999 65 -0.22 0.065 1000 -1000 -0.02 -1000
Aurora A signaling 0.0302 15 908 60 -0.061 0.074 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0302 15 582 37 -0.02 0.063 1000 -1000 -0.022 -1000
TCGA08_rtk_signaling 0.0302 15 392 26 -0.013 0.048 1000 -1000 -0.003 -1000
Class I PI3K signaling events 0.0302 15 1103 73 -0.042 0.063 1000 -1000 -0.026 -1000
TCGA08_retinoblastoma 0.0302 15 127 8 -0.01 0.058 1000 -1000 -0.003 -1000
Signaling events mediated by PRL 0.0302 15 531 34 -0.037 0.046 1000 -1000 -0.034 -1000
Regulation of Androgen receptor activity 0.0302 15 1068 70 -0.078 0.042 1000 -1000 -0.036 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0282 14 406 28 -0.026 0.052 1000 -1000 -0.02 -1000
mTOR signaling pathway 0.0282 14 754 53 -0.14 0.05 1000 -1000 -0.028 -1000
Retinoic acid receptors-mediated signaling 0.0282 14 842 58 -0.042 0.049 1000 -1000 -0.022 -1000
IL2 signaling events mediated by PI3K 0.0282 14 840 58 -0.037 0.07 1000 -1000 -0.027 -1000
FOXA2 and FOXA3 transcription factor networks 0.0262 13 636 46 -0.056 0.044 1000 -1000 -0.079 -1000
IL2 signaling events mediated by STAT5 0.0262 13 294 22 -0.014 0.048 1000 -1000 -0.029 -1000
LPA4-mediated signaling events 0.0221 11 134 12 -0.03 0.021 1000 -1000 -0.018 -1000
IFN-gamma pathway 0.0221 11 797 68 -0.023 0.073 1000 -1000 -0.039 -1000
PDGFR-beta signaling pathway 0.0221 11 1075 97 -0.1 0.07 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 0.0201 10 420 40 -0.068 0.05 1000 -1000 -0.039 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0201 10 904 83 -0.047 0.049 1000 -1000 -0.017 -1000
Syndecan-3-mediated signaling events 0.0201 10 350 35 -0.022 0.072 1000 -1000 -0.014 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0201 10 492 45 0 0.063 1000 -1000 -0.028 -1000
E-cadherin signaling in keratinocytes 0.0201 10 458 43 -0.016 0.046 1000 -1000 -0.014 -1000
Paxillin-dependent events mediated by a4b1 0.0181 9 324 36 -0.046 0.048 1000 -1000 -0.028 -1000
E-cadherin signaling in the nascent adherens junction 0.0181 9 721 76 -0.019 0.056 1000 -1000 -0.041 -1000
Class I PI3K signaling events mediated by Akt 0.0161 8 552 68 -0.033 0.05 1000 -1000 -0.02 -1000
FoxO family signaling 0.0161 8 536 64 -0.021 0.06 1000 -1000 -0.049 -1000
p38 MAPK signaling pathway 0.0161 8 369 44 -0.03 0.069 1000 -1000 -0.012 -1000
Canonical NF-kappaB pathway 0.0141 7 290 39 -0.004 0.056 1000 -1000 -0.019 -1000
Atypical NF-kappaB pathway 0.0141 7 232 31 -0.01 0.031 1000 -1000 -0.021 -1000
Regulation of Telomerase 0.0141 7 813 102 -0.025 0.058 1000 -1000 -0.038 -1000
Signaling mediated by p38-gamma and p38-delta 0.0101 5 85 15 -0.017 0.029 1000 -1000 -0.024 -1000
Class IB PI3K non-lipid kinase events 0.0101 5 15 3 -0.028 0.028 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 0.0080 4 318 75 -0.028 0.065 1000 -1000 -0.023 -1000
PLK2 and PLK4 events 0.0080 4 13 3 -0.013 0.027 1000 -1000 -0.021 -1000
Circadian rhythm pathway 0.0080 4 99 22 -0.007 0.04 1000 -1000 -0.034 -1000
TRAIL signaling pathway 0.0080 4 219 48 -0.011 0.049 1000 -1000 -0.021 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0060 3 86 23 0.008 0.053 1000 -1000 -0.021 -1000
Insulin-mediated glucose transport 0.0060 3 127 32 -0.013 0.046 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class I 0.0060 3 329 104 -0.052 0.064 1000 -1000 -0.035 -1000
Arf6 trafficking events 0.0040 2 179 71 -0.046 0.05 1000 -1000 -0.035 -1000
Arf1 pathway 0.0040 2 127 54 -0.006 0.048 1000 -1000 -0.011 -1000
Arf6 downstream pathway 0.0020 1 67 43 -0.053 0.054 1000 -1000 -0.032 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 11 27 -0.011 0.059 1000 -1000 -0.026 -1000
E-cadherin signaling events 0.0000 0 0 5 0.024 0.046 1000 -1000 0.021 -1000
Alternative NF-kappaB pathway 0.0000 0 9 13 0 0.07 1000 -1000 0 -1000
Total NA 3194 188001 7203 -9 7.6 131000 -131000 -3.6 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.028 0.1 0.13 1 -0.19 136 137
EFNA5 -0.003 0.094 0.17 1 -0.31 42 43
FYN -0.045 0.074 0.18 3 -0.18 107 110
neuron projection morphogenesis -0.028 0.1 0.13 1 -0.19 136 137
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.028 0.1 0.13 1 -0.19 136 137
EPHA5 -0.049 0.14 0.17 2 -0.31 111 113
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 -0.21 0.39 -10000 0 -0.79 143 143
NCK1/PAK1/Dok-R -0.11 0.17 -10000 0 -0.38 136 136
NCK1/Dok-R -0.23 0.44 -10000 0 -0.9 141 141
PIK3CA 0.024 0.027 -10000 0 -0.31 3 3
mol:beta2-estradiol 0.067 0.11 0.24 143 -10000 0 143
RELA 0.026 0.006 -10000 0 -10000 0 0
SHC1 0.025 0.006 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -10000 0 -10000 0 0
F2 0.075 0.13 0.26 147 -10000 0 147
TNIP2 0.027 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.21 0.43 -10000 0 -0.86 143 143
FN1 0.02 0.052 0.17 4 -0.31 11 15
PLD2 -0.26 0.45 -10000 0 -0.94 143 143
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
GRB14 0.048 0.062 0.17 82 -0.31 3 85
ELK1 -0.23 0.41 -10000 0 -0.86 142 142
GRB7 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.022 0.037 -10000 0 -0.31 6 6
Tie2/Ang1/alpha5/beta1 Integrin -0.22 0.46 -10000 0 -0.91 142 142
CDKN1A -0.14 0.28 -10000 0 -0.57 129 129
ITGA5 0.018 0.054 0.17 1 -0.31 13 14
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.23 0.45 -10000 0 -0.9 142 142
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO -0.14 0.29 0.43 1 -0.6 138 139
PLG -0.26 0.46 -10000 0 -0.95 143 143
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.19 0.37 -10000 0 -0.75 141 141
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.031 -10000 0 -0.31 4 4
ANGPT2 -0.14 0.26 -10000 0 -0.57 102 102
BMX -0.26 0.46 -10000 0 -0.95 143 143
ANGPT1 -0.29 0.49 -10000 0 -1.1 136 136
tube development -0.17 0.3 -10000 0 -0.62 141 141
ANGPT4 0.022 0.016 0.18 1 -10000 0 1
response to hypoxia -0.018 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.25 0.49 -10000 0 -0.97 143 143
alpha5/beta1 Integrin 0.032 0.042 0.14 1 -0.21 13 14
FGF2 0.005 0.081 0.18 1 -0.31 31 32
STAT5A (dimer) -0.18 0.35 -10000 0 -0.71 139 139
mol:L-citrulline -0.14 0.29 0.43 1 -0.6 138 139
AGTR1 0.036 0.09 0.18 80 -0.31 20 100
MAPK14 -0.25 0.46 -10000 0 -0.95 143 143
Tie2/SHP2 -0.15 0.34 -10000 0 -0.94 70 70
TEK -0.16 0.38 -10000 0 -1 70 70
RPS6KB1 -0.2 0.37 0.4 1 -0.77 142 143
Angiotensin II/AT1 0.028 0.062 0.12 80 -0.21 20 100
Tie2/Ang1/GRB2 -0.25 0.48 -10000 0 -0.96 143 143
MAPK3 -0.24 0.42 -10000 0 -0.88 142 142
MAPK1 -0.24 0.42 -10000 0 -0.88 142 142
Tie2/Ang1/GRB7 -0.25 0.48 -10000 0 -0.97 143 143
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.26 0.46 -10000 0 -0.95 143 143
PI3K -0.24 0.44 -10000 0 -0.9 143 143
FES -0.25 0.47 -10000 0 -0.95 144 144
Crk/Dok-R -0.23 0.45 -10000 0 -0.9 143 143
Tie2/Ang1/ABIN2 -0.26 0.48 -10000 0 -0.97 143 143
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.18 0.35 -10000 0 -0.71 143 143
STAT5A 0.026 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.18 0.38 0.39 3 -0.75 139 142
Tie2/Ang2 -0.22 0.4 -10000 0 -0.83 140 140
Tie2/Ang1 -0.27 0.49 -10000 0 -1 143 143
FOXO1 -0.18 0.35 -10000 0 -0.71 143 143
ELF1 0.009 0.045 -10000 0 -0.18 15 15
ELF2 -0.25 0.45 -10000 0 -0.92 143 143
mol:Choline -0.25 0.43 -10000 0 -0.9 143 143
cell migration -0.059 0.1 -10000 0 -0.22 139 139
FYN -0.19 0.34 -10000 0 -0.7 139 139
DOK2 0.019 0.023 0.17 3 -0.31 1 4
negative regulation of cell cycle -0.13 0.25 -10000 0 -0.52 131 131
ETS1 -0.046 0.13 0.18 1 -0.26 131 132
PXN -0.14 0.32 0.42 7 -0.63 136 143
ITGB1 0.026 0.004 -10000 0 -10000 0 0
NOS3 -0.17 0.33 0.44 1 -0.68 138 139
RAC1 0.025 0.008 -10000 0 -10000 0 0
TNF -0.063 0.15 0.18 11 -0.28 156 167
MAPKKK cascade -0.25 0.43 -10000 0 -0.9 143 143
RASA1 0.025 0.016 -10000 0 -0.31 1 1
Tie2/Ang1/Shc -0.25 0.47 -10000 0 -0.96 143 143
NCK1 0.025 0.007 -10000 0 -10000 0 0
vasculogenesis -0.13 0.27 0.43 1 -0.54 139 140
mol:Phosphatidic acid -0.25 0.43 -10000 0 -0.9 143 143
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.14 0.29 0.43 1 -0.6 138 139
Rac1/GTP -0.18 0.35 -10000 0 -0.71 141 141
MMP2 -0.26 0.46 -10000 0 -0.95 143 143
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.37 -10000 0 -0.82 108 108
MKNK1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.033 0.14 -10000 0 -0.3 106 106
ATF2/c-Jun -0.052 0.15 -10000 0 -0.3 102 102
MAPK11 -0.031 0.14 0.2 5 -0.3 104 109
MITF -0.052 0.17 -10000 0 -0.37 101 101
MAPKAPK5 -0.049 0.16 -10000 0 -0.35 101 101
KRT8 -0.047 0.16 -10000 0 -0.35 100 100
MAPKAPK3 0.026 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.046 0.21 -10000 0 -0.43 106 106
CEBPB -0.046 0.16 -10000 0 -0.35 99 99
SLC9A1 -0.051 0.16 -10000 0 -0.35 105 105
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.068 0.19 -10000 0 -0.37 122 122
p38alpha-beta/MNK1 -0.02 0.18 -10000 0 -0.35 103 103
JUN -0.053 0.14 -10000 0 -0.29 102 102
PPARGC1A -0.13 0.24 -10000 0 -0.4 184 184
USF1 -0.051 0.16 -10000 0 -0.36 102 102
RAB5/GDP/GDI1 -0.026 0.12 -10000 0 -0.26 98 98
NOS2 -0.079 0.25 -10000 0 -0.49 105 105
DDIT3 -0.05 0.16 -10000 0 -0.35 104 104
RAB5A 0.026 0.005 -10000 0 -10000 0 0
HSPB1 -0.038 0.14 0.28 21 -0.3 87 108
p38alpha-beta/HBP1 -0.018 0.17 -10000 0 -0.34 96 96
CREB1 -0.054 0.17 0.21 1 -0.38 101 102
RAB5/GDP 0.019 0.004 -10000 0 -10000 0 0
EIF4E -0.049 0.14 0.22 1 -0.32 101 102
RPS6KA4 -0.048 0.16 0.26 1 -0.35 103 104
PLA2G4A -0.057 0.15 0.22 1 -0.33 106 107
GDI1 -0.05 0.16 -10000 0 -0.35 105 105
TP53 -0.071 0.18 0.18 1 -0.44 97 98
RPS6KA5 -0.055 0.17 -10000 0 -0.36 105 105
ESR1 -0.06 0.18 -10000 0 -0.37 112 112
HBP1 0.025 0.008 -10000 0 -10000 0 0
MEF2C -0.058 0.18 -10000 0 -0.38 107 107
MEF2A -0.053 0.16 -10000 0 -0.36 105 105
EIF4EBP1 -0.064 0.19 0.21 1 -0.43 99 100
KRT19 -0.073 0.2 -10000 0 -0.38 123 123
ELK4 -0.05 0.16 -10000 0 -0.35 101 101
ATF6 -0.051 0.16 -10000 0 -0.36 103 103
ATF1 -0.053 0.17 0.21 1 -0.38 100 101
p38alpha-beta/MAPKAPK2 -0.02 0.17 -10000 0 -0.34 103 103
p38alpha-beta/MAPKAPK3 -0.019 0.17 -10000 0 -0.35 101 101
Glypican 2 network

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
MDK 0.031 0.027 0.17 16 -10000 0 16
GPC2 0.055 0.064 0.17 104 -0.31 1 105
GPC2/Midkine 0.061 0.056 0.15 112 -0.16 2 114
neuron projection morphogenesis 0.061 0.056 0.15 112 -0.16 2 114
Endothelins

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
AKT1 -0.04 0.14 0.26 23 -0.28 93 116
PTK2B 0.019 0.012 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.39 -10000 0 -0.93 93 93
EDN1 -0.007 0.11 0.2 31 -0.27 46 77
EDN3 -0.091 0.16 0.17 2 -0.31 172 174
EDN2 0.015 0.073 0.17 11 -0.31 22 33
HRAS/GDP -0.076 0.2 0.28 5 -0.44 83 88
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.042 0.16 0.2 3 -0.37 68 71
ADCY4 -0.064 0.16 0.2 30 -0.34 85 115
ADCY5 -0.075 0.18 0.2 31 -0.38 98 129
ADCY6 -0.062 0.16 0.2 33 -0.34 86 119
ADCY7 -0.062 0.15 0.19 26 -0.34 85 111
ADCY1 -0.056 0.16 0.19 26 -0.34 82 108
ADCY2 -0.063 0.16 0.2 29 -0.35 86 115
ADCY3 -0.062 0.16 0.2 29 -0.34 84 113
ADCY8 -0.06 0.14 0.18 10 -0.33 76 86
ADCY9 -0.061 0.16 0.2 31 -0.34 84 115
arachidonic acid secretion -0.13 0.29 0.32 6 -0.55 124 130
ETB receptor/Endothelin-1/Gq/GTP -0.041 0.14 -10000 0 -0.3 82 82
GNAO1 -0.024 0.12 -10000 0 -0.31 71 71
HRAS 0.028 0.017 0.17 6 -10000 0 6
ETA receptor/Endothelin-1/G12/GTP 0.001 0.15 0.33 20 -0.25 93 113
ETA receptor/Endothelin-1/Gs/GTP -0.038 0.18 0.31 19 -0.29 123 142
mol:GTP -0.002 0.007 -10000 0 -10000 0 0
COL3A1 -0.038 0.15 0.26 25 -0.36 50 75
EDNRB -0.01 0.1 0.18 1 -0.31 51 52
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.06 0.18 0.25 17 -0.44 77 94
CYSLTR1 -0.052 0.17 0.25 24 -0.35 92 116
SLC9A1 -0.019 0.091 0.18 23 -0.2 61 84
mol:GDP -0.087 0.21 0.28 8 -0.46 88 96
SLC9A3 -0.16 0.4 -10000 0 -0.89 93 93
RAF1 -0.095 0.22 0.28 10 -0.45 107 117
JUN -0.11 0.29 -10000 0 -0.7 74 74
JAK2 -0.041 0.15 0.25 23 -0.28 99 122
mol:IP3 -0.044 0.15 0.22 1 -0.38 59 60
ETA receptor/Endothelin-1 -0.024 0.19 0.38 23 -0.31 109 132
PLCB1 0.022 0.031 -10000 0 -0.31 4 4
PLCB2 0.021 0.02 0.17 2 -10000 0 2
ETA receptor/Endothelin-3 -0.078 0.16 0.17 16 -0.25 194 210
FOS -0.16 0.35 0.37 4 -0.84 92 96
Gai/GDP -0.17 0.37 -10000 0 -0.78 123 123
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.071 0.2 0.23 18 -0.45 75 93
BCAR1 0.022 0.011 -10000 0 -10000 0 0
PRKCB1 -0.048 0.15 0.2 2 -0.37 62 64
GNAQ 0.015 0.023 -10000 0 -10000 0 0
GNAZ -0.002 0.094 -10000 0 -0.31 42 42
GNAL -0.054 0.14 -10000 0 -0.31 117 117
Gs family/GDP -0.1 0.22 0.27 6 -0.46 106 112
ETA receptor/Endothelin-1/Gq/GTP -0.047 0.16 0.18 18 -0.37 75 93
MAPK14 -0.045 0.13 0.21 1 -0.31 71 72
TRPC6 -0.18 0.42 -10000 0 -1 93 93
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.04 0.14 -10000 0 -0.31 75 75
ETB receptor/Endothelin-2 0.002 0.092 0.15 8 -0.22 71 79
ETB receptor/Endothelin-3 -0.067 0.14 0.14 2 -0.24 185 187
ETB receptor/Endothelin-1 -0.009 0.12 0.2 2 -0.26 69 71
MAPK3 -0.15 0.32 0.35 5 -0.75 96 101
MAPK1 -0.15 0.33 0.37 4 -0.76 96 100
Rac1/GDP -0.074 0.2 0.29 5 -0.43 83 88
cAMP biosynthetic process -0.053 0.18 0.28 21 -0.37 85 106
MAPK8 -0.14 0.36 -10000 0 -0.8 91 91
SRC 0.026 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.059 0.16 0.16 2 -0.36 89 91
p130Cas/CRK/Src/PYK2 -0.14 0.28 0.3 7 -0.63 101 108
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.074 0.2 0.29 5 -0.43 83 88
COL1A2 -0.05 0.17 0.25 15 -0.47 49 64
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.007 0.12 0.22 3 -0.24 73 76
mol:DAG -0.044 0.15 0.22 1 -0.38 59 60
MAP2K2 -0.12 0.26 0.3 8 -0.57 103 111
MAP2K1 -0.12 0.26 0.32 7 -0.56 105 112
EDNRA -0.028 0.14 0.21 24 -0.26 101 125
positive regulation of muscle contraction -0.028 0.13 0.22 39 -0.31 51 90
Gq family/GDP -0.065 0.2 0.25 1 -0.44 87 88
HRAS/GTP -0.078 0.2 0.27 6 -0.42 85 91
PRKCH -0.048 0.15 0.21 3 -0.37 60 63
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.054 0.16 0.21 3 -0.39 64 67
PRKCB -0.072 0.18 0.21 6 -0.42 81 87
PRKCE -0.045 0.14 0.25 3 -0.36 58 61
PRKCD -0.049 0.15 0.21 5 -0.37 59 64
PRKCG -0.051 0.15 0.21 6 -0.37 64 70
regulation of vascular smooth muscle contraction -0.19 0.41 0.39 4 -1 91 95
PRKCQ -0.055 0.16 0.21 1 -0.4 60 61
PLA2G4A -0.15 0.33 0.33 6 -0.61 124 130
GNA14 0.014 0.028 -10000 0 -0.31 1 1
GNA15 0.005 0.07 -10000 0 -0.31 21 21
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA11 0.009 0.06 -10000 0 -0.31 15 15
Rac1/GTP 0.001 0.15 0.33 20 -0.25 94 114
MMP1 -0.008 0.18 0.28 21 -0.67 28 49
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.075 0.1 0.28 25 -10000 0 25
SMARCC2 0.01 0.044 -10000 0 -0.11 42 42
SMARCC1 0.009 0.045 -10000 0 -0.11 45 45
TBX21 -0.079 0.16 0.43 2 -0.43 52 54
SUMO2 0.029 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.034 0.021 0.19 8 -10000 0 8
FKBP4 0.025 0.007 -10000 0 -10000 0 0
FKBP5 0.026 0.016 -10000 0 -0.31 1 1
GR alpha/HSP90/FKBP51/HSP90 0.1 0.12 0.28 92 -0.15 1 93
PRL -0.066 0.12 -10000 0 -0.49 2 2
cortisol/GR alpha (dimer)/TIF2 0.12 0.24 0.52 100 -10000 0 100
RELA -0.028 0.1 -10000 0 -0.2 118 118
FGG 0.16 0.23 0.45 147 -0.3 1 148
GR beta/TIF2 0.049 0.14 0.28 82 -0.24 30 112
IFNG -0.21 0.29 0.37 1 -0.63 124 125
apoptosis 0.1 0.2 0.52 66 -0.46 1 67
CREB1 0.002 0.1 -10000 0 -0.29 49 49
histone acetylation -0.053 0.17 0.32 16 -0.38 70 86
BGLAP -0.09 0.15 -10000 0 -0.39 53 53
GR/PKAc 0.11 0.11 0.29 78 -10000 0 78
NF kappa B1 p50/RelA -0.046 0.18 -10000 0 -0.34 125 125
SMARCD1 0.01 0.045 -10000 0 -0.11 45 45
MDM2 0.084 0.11 0.22 148 -10000 0 148
GATA3 -0.065 0.15 -10000 0 -0.31 139 139
AKT1 0.023 0.004 -10000 0 -10000 0 0
CSF2 -0.07 0.13 -10000 0 -0.45 21 21
GSK3B 0.028 0.019 -10000 0 -10000 0 0
NR1I3 0.1 0.2 0.52 54 -0.68 3 57
CSN2 0.13 0.19 0.38 143 -0.26 1 144
BRG1/BAF155/BAF170/BAF60A 0.017 0.13 -10000 0 -0.3 67 67
NFATC1 0.025 0.009 -10000 0 -10000 0 0
POU2F1 0.026 0.007 -10000 0 -10000 0 0
CDKN1A -0.028 0.14 -10000 0 -1.4 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.005 0.014 -10000 0 -10000 0 0
SFN -0.006 0.1 -10000 0 -0.31 49 49
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.11 0.29 70 -0.16 4 74
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.064 0.26 0.49 56 -0.66 33 89
JUN -0.12 0.18 0.29 1 -0.38 130 131
IL4 -0.088 0.15 -10000 0 -0.45 32 32
CDK5R1 0.036 0.033 0.18 23 -10000 0 23
PRKACA 0.027 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.071 0.11 0.18 24 -0.25 95 119
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.29 83 -10000 0 83
cortisol/GR alpha (monomer) 0.21 0.31 0.61 146 -0.34 1 147
NCOA2 -0.015 0.1 -10000 0 -0.31 53 53
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.068 0.14 0.2 4 -0.3 103 107
AP-1/NFAT1-c-4 -0.21 0.29 -10000 0 -0.55 173 173
AFP -0.087 0.14 -10000 0 -0.48 9 9
SUV420H1 0.026 0.006 -10000 0 -10000 0 0
IRF1 0.13 0.16 0.38 103 -10000 0 103
TP53 0.032 0.014 -10000 0 -10000 0 0
PPP5C 0.027 0.003 -10000 0 -10000 0 0
KRT17 -0.32 0.44 -10000 0 -0.94 143 143
KRT14 -0.35 0.53 0.36 2 -1.1 147 149
TBP 0.031 0.013 -10000 0 -0.21 1 1
CREBBP 0.054 0.14 0.26 107 -0.26 38 145
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.023 0.009 -10000 0 -10000 0 0
AP-1 -0.21 0.29 -10000 0 -0.55 173 173
MAPK14 0.029 0.017 -10000 0 -10000 0 0
MAPK10 0.026 0.035 -10000 0 -0.3 4 4
MAPK11 0.032 0.027 0.17 8 -10000 0 8
KRT5 -0.41 0.5 -10000 0 -1 187 187
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.034 0.021 0.19 8 -10000 0 8
CGA -0.15 0.3 -10000 0 -0.83 68 68
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.069 0.17 0.36 93 -0.33 21 114
MAPK3 0.029 0.019 -10000 0 -10000 0 0
MAPK1 0.029 0.017 -10000 0 -10000 0 0
ICAM1 -0.15 0.24 -10000 0 -0.53 105 105
NFKB1 -0.03 0.11 -10000 0 -0.2 111 111
MAPK8 -0.11 0.18 0.34 2 -0.34 149 151
MAPK9 0.028 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.1 0.2 0.52 66 -0.48 1 67
BAX -0.02 0.076 -10000 0 -10000 0 0
POMC -0.24 0.45 0.42 1 -1.4 58 59
EP300 0.053 0.14 0.26 110 -0.27 41 151
cortisol/GR alpha (dimer)/p53 0.16 0.25 0.52 129 -10000 0 129
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.088 0.2 86 -10000 0 86
SGK1 -0.063 0.45 0.48 2 -1.1 71 73
IL13 -0.28 0.36 -10000 0 -0.78 143 143
IL6 -0.24 0.39 0.31 1 -0.82 131 132
PRKACG 0.019 0.005 -10000 0 -10000 0 0
IL5 -0.24 0.3 -10000 0 -0.65 150 150
IL2 -0.22 0.29 -10000 0 -0.63 134 134
CDK5 0.027 0.011 -10000 0 -10000 0 0
PRKACB 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.31 -10000 0 -0.66 112 112
CDK5R1/CDK5 0.045 0.032 0.16 22 -10000 0 22
NF kappa B1 p50/RelA/PKAc -0.007 0.16 -10000 0 -0.29 83 83
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.17 0.24 0.5 138 -10000 0 138
SMARCA4 0.011 0.045 -10000 0 -0.11 48 48
chromatin remodeling 0.068 0.2 0.36 94 -0.34 33 127
NF kappa B1 p50/RelA/Cbp -0.008 0.22 0.34 41 -0.39 78 119
JUN (dimer) -0.12 0.18 0.29 1 -0.38 129 130
YWHAH 0.027 0.004 -10000 0 -10000 0 0
VIPR1 -0.074 0.15 0.33 3 -0.38 53 56
NR3C1 0.14 0.2 0.41 127 -10000 0 127
NR4A1 -0.024 0.16 -10000 0 -0.43 60 60
TIF2/SUV420H1 0.004 0.078 -10000 0 -0.21 53 53
MAPKKK cascade 0.1 0.2 0.52 66 -0.46 1 67
cortisol/GR alpha (dimer)/Src-1 0.19 0.26 0.51 158 -10000 0 158
PBX1 0.026 0.016 -10000 0 -0.31 1 1
POU1F1 0.021 0.014 0.18 3 -10000 0 3
SELE -0.25 0.39 -10000 0 -0.83 136 136
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.068 0.2 0.36 94 -0.34 33 127
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.17 0.24 0.5 138 -10000 0 138
mol:cortisol 0.13 0.19 0.35 158 -0.19 1 159
MMP1 -0.1 0.28 -10000 0 -0.98 42 42
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.22 0.51 -10000 0 -1.2 85 85
IL23A -0.23 0.52 -10000 0 -1.2 83 83
NF kappa B1 p50/RelA/I kappa B alpha -0.2 0.52 -10000 0 -1.1 102 102
positive regulation of T cell mediated cytotoxicity -0.24 0.58 0.56 1 -1.2 104 105
ITGA3 -0.22 0.5 -10000 0 -1.2 82 82
IL17F -0.14 0.32 0.42 2 -0.67 101 103
IL12B 0.014 0.07 0.21 26 -0.14 3 29
STAT1 (dimer) -0.23 0.56 0.59 1 -1.2 103 104
CD4 -0.2 0.48 -10000 0 -1.1 75 75
IL23 -0.22 0.51 0.62 1 -1.2 85 86
IL23R -0.022 0.16 -10000 0 -0.77 13 13
IL1B -0.25 0.56 -10000 0 -1.3 85 85
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.2 0.48 -10000 0 -1.1 74 74
TYK2 0.006 0.043 -10000 0 -10000 0 0
STAT4 0.028 0.039 0.17 13 -0.31 4 17
STAT3 0.026 0.005 -10000 0 -10000 0 0
IL18RAP 0.022 0.064 0.17 16 -0.3 15 31
IL12RB1 0.008 0.067 0.2 18 -0.34 6 24
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
IL12Rbeta1/TYK2 0.011 0.067 0.18 13 -0.26 6 19
IL23R/JAK2 -0.014 0.17 -10000 0 -0.84 8 8
positive regulation of chronic inflammatory response -0.24 0.58 0.56 1 -1.2 104 105
natural killer cell activation 0.002 0.008 -10000 0 -10000 0 0
JAK2 0.008 0.054 0.15 1 -0.32 1 2
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
NFKB1 0.023 0.013 -10000 0 -10000 0 0
RELA 0.023 0.014 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.2 0.48 0.58 2 -1.1 85 87
ALOX12B -0.21 0.5 -10000 0 -1.1 83 83
CXCL1 -0.3 0.6 0.66 1 -1.2 128 129
T cell proliferation -0.24 0.58 0.56 1 -1.2 104 105
NFKBIA 0.023 0.014 -10000 0 -10000 0 0
IL17A -0.088 0.26 0.42 3 -0.54 84 87
PI3K -0.21 0.52 -10000 0 -1.1 100 100
IFNG 0 0.028 0.088 1 -0.099 9 10
STAT3 (dimer) -0.2 0.5 0.54 1 -1 100 101
IL18R1 0.024 0.037 -10000 0 -0.3 6 6
IL23/IL23R/JAK2/TYK2/SOCS3 -0.12 0.33 0.42 2 -0.7 90 92
IL18/IL18R 0.046 0.063 0.16 4 -0.19 27 31
macrophage activation -0.011 0.021 0.034 4 -0.044 81 85
TNF -0.24 0.54 0.57 1 -1.3 81 82
STAT3/STAT4 -0.21 0.53 0.57 1 -1.1 103 104
STAT4 (dimer) -0.23 0.56 0.57 2 -1.2 103 105
IL18 0.018 0.052 -10000 0 -0.3 12 12
IL19 -0.2 0.48 -10000 0 -1.1 76 76
STAT5A (dimer) -0.23 0.55 -10000 0 -1.2 103 103
STAT1 0.029 0.019 0.17 8 -10000 0 8
SOCS3 -0.012 0.11 0.17 6 -0.31 58 64
CXCL9 -0.2 0.49 0.66 1 -1.1 77 78
MPO -0.24 0.54 -10000 0 -1.2 99 99
positive regulation of humoral immune response -0.24 0.58 0.56 1 -1.2 104 105
IL23/IL23R/JAK2/TYK2 -0.27 0.66 0.56 1 -1.3 103 104
IL6 -0.29 0.61 -10000 0 -1.2 129 129
STAT5A 0.026 0.005 -10000 0 -10000 0 0
IL2 0.015 0.024 0.17 2 -10000 0 2
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -10000 0 -10000 0 0
CD3E -0.2 0.49 -10000 0 -1.1 86 86
keratinocyte proliferation -0.24 0.58 0.56 1 -1.2 104 105
NOS2 -0.23 0.52 -10000 0 -1.2 90 90
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.009 0.1 0.22 91 -0.16 10 101
KIRREL -0.036 0.13 -10000 0 -0.32 91 91
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.009 0.11 0.16 10 -0.22 91 101
PLCG1 0.026 0.005 -10000 0 -10000 0 0
ARRB2 0.025 0.008 -10000 0 -10000 0 0
WASL 0.025 0.008 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.021 0.095 0.23 1 -0.17 90 91
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.015 0.078 -10000 0 -0.19 80 80
FYN -0.028 0.068 0.22 12 -0.16 72 84
mol:Ca2+ 0.019 0.092 0.22 1 -0.17 89 90
mol:DAG 0.02 0.093 0.22 1 -0.17 89 90
NPHS2 -0.003 0.033 0.18 3 -10000 0 3
mol:IP3 0.02 0.093 0.22 1 -0.17 89 90
regulation of endocytosis 0.006 0.08 -10000 0 -0.15 92 92
Nephrin/NEPH1/podocin/Cholesterol 0.01 0.087 0.21 1 -0.16 91 92
establishment of cell polarity -0.009 0.1 0.16 10 -0.22 91 101
Nephrin/NEPH1/podocin/NCK1-2 0.03 0.092 0.23 1 -0.16 86 87
Nephrin/NEPH1/beta Arrestin2 0.008 0.081 -10000 0 -0.15 92 92
NPHS1 0.004 0.042 0.19 11 -10000 0 11
Nephrin/NEPH1/podocin 0.007 0.083 0.17 1 -0.16 92 93
TJP1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.021 0.094 0.23 1 -0.17 89 90
CD2AP 0.027 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.022 0.094 0.23 1 -0.17 88 89
GRB2 0.026 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.05 0.095 0.22 12 -0.2 116 128
cytoskeleton organization -0.028 0.075 0.2 3 -0.2 77 80
Nephrin/NEPH1 0 0.074 0.13 10 -0.15 91 101
Nephrin/NEPH1/ZO-1 0.01 0.091 0.18 1 -0.18 89 90
Reelin signaling pathway

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
CDK5R1/CDK5 0.041 0.025 0.14 21 -10000 0 21
VLDLR 0.026 0.016 -10000 0 -0.31 1 1
CRKL 0.026 0.005 -10000 0 -10000 0 0
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
FYN 0.023 0.018 -10000 0 -0.31 1 1
ITGA3 0.02 0.047 -10000 0 -0.31 10 10
RELN/VLDLR/Fyn 0.049 0.047 -10000 0 -0.16 7 7
MAPK8IP1/MKK7/MAP3K11/JNK1 0.064 0.046 -10000 0 -0.16 12 12
AKT1 -0.053 0.094 0.14 2 -0.18 152 154
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
DAB1 -0.095 0.16 0.17 2 -0.31 178 180
RELN/LRP8/DAB1 -0.02 0.11 0.23 2 -0.17 160 162
LRPAP1/LRP8 0.04 0.015 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.011 0.11 0.23 2 -0.16 158 160
DAB1/alpha3/beta1 Integrin -0.016 0.1 -10000 0 -0.16 144 144
long-term memory -0.039 0.13 0.33 1 -0.18 184 185
DAB1/LIS1 -0.006 0.11 0.22 1 -0.16 154 155
DAB1/CRLK/C3G -0.014 0.1 -10000 0 -0.16 141 141
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
DAB1/NCK2 -0.004 0.11 0.23 1 -0.16 149 150
ARHGEF2 0.026 0.006 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.041 0.13 0.17 1 -0.31 99 100
CDK5R1 0.034 0.031 0.17 23 -10000 0 23
RELN 0.04 0.059 0.17 60 -0.31 4 64
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
RELN/LRP8/Fyn 0.051 0.048 0.24 3 -0.16 6 9
GRIN2A/RELN/LRP8/DAB1/Fyn -0.036 0.14 -10000 0 -0.19 195 195
MAPK8 0.018 0.052 -10000 0 -0.31 12 12
RELN/VLDLR/DAB1 -0.022 0.11 -10000 0 -0.17 161 161
ITGB1 0.026 0.004 -10000 0 -10000 0 0
MAP1B -0.061 0.092 0.17 13 -0.19 151 164
RELN/LRP8 0.057 0.046 0.24 3 -0.17 4 7
GRIN2B/RELN/LRP8/DAB1/Fyn -0.008 0.11 0.24 2 -0.16 150 152
PI3K 0.031 0.034 -10000 0 -0.24 6 6
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.035 -10000 0 -0.21 9 9
RAP1A -0.045 0.1 0.34 13 -0.25 1 14
PAFAH1B1 0.025 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.009 0.17 1 -10000 0 1
CRLK/C3G 0.037 0.011 -10000 0 -10000 0 0
GRIN2B 0.018 0.01 0.17 1 -10000 0 1
NCK2 0.027 0.003 -10000 0 -10000 0 0
neuron differentiation -0.044 0.1 0.19 1 -0.26 43 44
neuron adhesion -0.048 0.11 0.34 16 -0.28 6 22
LRP8 0.028 0.018 0.17 7 -10000 0 7
GSK3B -0.052 0.089 0.15 3 -0.18 126 129
RELN/VLDLR/DAB1/Fyn -0.013 0.11 -10000 0 -0.16 159 159
MAP3K11 0.026 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.049 0.1 0.15 2 -0.19 156 158
CDK5 0.025 0.008 -10000 0 -10000 0 0
MAPT 0.004 0.059 0.75 3 -10000 0 3
neuron migration -0.06 0.11 0.28 9 -0.25 15 24
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.044 0.1 0.19 1 -0.26 42 43
RELN/VLDLR 0.07 0.051 0.25 3 -0.16 5 8
EPHB forward signaling

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
Ephrin A5/EPHB2 0.015 0.065 0.13 3 -0.19 42 45
cell-cell adhesion 0.059 0.071 0.17 102 -10000 0 102
Ephrin B/EPHB2/RasGAP 0.035 0.088 -10000 0 -0.17 59 59
ITSN1 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
SHC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.022 0.13 3 -0.18 4 7
Ephrin B1/EPHB1 -0.027 0.097 -10000 0 -0.18 137 137
HRAS/GDP -0.033 0.1 -10000 0 -0.23 57 57
Ephrin B/EPHB1/GRB7 -0.016 0.12 -10000 0 -0.17 163 163
Endophilin/SYNJ1 -0.026 0.064 0.19 9 -0.31 7 16
KRAS 0.025 0.007 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.015 0.12 -10000 0 -0.17 163 163
endothelial cell migration 0.044 0.036 -10000 0 -0.19 4 4
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.027 0.004 -10000 0 -10000 0 0
PAK1 -0.02 0.08 0.22 23 -0.39 5 28
HRAS 0.028 0.017 0.17 6 -10000 0 6
RRAS -0.028 0.065 0.17 8 -0.32 8 16
DNM1 0.025 0.018 0.17 1 -0.31 1 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.052 0.097 0.2 21 -0.27 29 50
lamellipodium assembly -0.059 0.071 -10000 0 -0.17 102 102
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.056 0.12 0.19 1 -0.22 149 150
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
EPHB2 0.025 0.032 0.17 3 -0.31 4 7
EPHB3 0.026 0.013 0.17 3 -10000 0 3
EPHB1 -0.069 0.15 -10000 0 -0.31 138 138
EPHB4 0.024 0.008 -10000 0 -10000 0 0
mol:GDP -0.046 0.091 0.2 10 -0.24 59 69
Ephrin B/EPHB2 0.026 0.082 -10000 0 -0.17 58 58
Ephrin B/EPHB3 0.028 0.075 -10000 0 -0.16 53 53
JNK cascade -0.045 0.098 0.31 18 -0.16 133 151
Ephrin B/EPHB1 -0.023 0.11 -10000 0 -0.17 164 164
RAP1/GDP -0.024 0.11 0.25 13 -0.26 34 47
EFNB2 0.03 0.027 0.17 16 -10000 0 16
EFNB3 -0.016 0.11 -10000 0 -0.31 58 58
EFNB1 0.024 0.034 -10000 0 -0.31 5 5
Ephrin B2/EPHB1-2 -0.011 0.098 -10000 0 -0.16 137 137
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.029 0.12 -10000 0 -0.23 76 76
Rap1/GTP -0.036 0.092 -10000 0 -0.18 111 111
axon guidance 0.014 0.065 0.13 3 -0.19 42 45
MAPK3 -0.062 0.11 0.18 3 -0.28 60 63
MAPK1 -0.063 0.11 0.18 2 -0.28 62 64
Rac1/GDP -0.037 0.096 0.26 5 -0.26 34 39
actin cytoskeleton reorganization -0.057 0.063 -10000 0 -0.2 47 47
CDC42/GDP -0.032 0.1 0.24 14 -0.26 36 50
PI3K 0.049 0.038 0.17 1 -0.19 4 5
EFNA5 -0.003 0.094 0.17 1 -0.31 42 43
Ephrin B2/EPHB4 0.034 0.02 0.13 13 -10000 0 13
Ephrin B/EPHB2/Intersectin/N-WASP -0.004 0.081 -10000 0 -0.22 51 51
CDC42 0.027 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.066 0.071 -10000 0 -0.17 107 107
PTK2 0.094 0.22 0.59 77 -10000 0 77
MAP4K4 -0.046 0.098 0.31 18 -0.16 133 151
SRC 0.026 0.006 -10000 0 -10000 0 0
KALRN 0.026 0.012 0.17 2 -10000 0 2
Intersectin/N-WASP 0.036 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis -0.044 0.11 0.32 20 -0.29 22 42
MAP2K1 -0.06 0.11 0.17 1 -0.22 129 130
WASL 0.025 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.003 0.11 -10000 0 -0.17 136 136
cell migration -0.075 0.14 0.27 12 -0.32 71 83
NRAS 0.026 0.016 -10000 0 -0.31 1 1
SYNJ1 -0.026 0.064 0.2 9 -0.31 7 16
PXN 0.026 0.006 -10000 0 -10000 0 0
TF -0.047 0.081 0.17 3 -0.28 35 38
HRAS/GTP -0.023 0.1 -10000 0 -0.16 152 152
Ephrin B1/EPHB1-2 -0.013 0.1 -10000 0 -0.17 137 137
cell adhesion mediated by integrin 0.018 0.061 0.17 49 -0.22 4 53
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.024 0.11 -10000 0 -0.17 155 155
RAC1-CDC42/GTP -0.065 0.072 -10000 0 -0.18 105 105
RASA1 0.025 0.016 -10000 0 -0.31 1 1
RAC1-CDC42/GDP -0.031 0.097 0.27 3 -0.26 33 36
ruffle organization -0.031 0.13 0.33 33 -0.29 20 53
NCK1 0.025 0.007 -10000 0 -10000 0 0
receptor internalization -0.03 0.058 0.16 6 -0.3 8 14
Ephrin B/EPHB2/KALRN 0.038 0.084 -10000 0 -0.18 51 51
ROCK1 -0.004 0.044 0.18 24 -0.16 3 27
RAS family/GDP -0.055 0.063 -10000 0 -0.21 44 44
Rac1/GTP -0.062 0.075 -10000 0 -0.18 102 102
Ephrin B/EPHB1/Src/Paxillin -0.062 0.13 -10000 0 -0.23 161 161
Thromboxane A2 receptor signaling

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
TGM2 0.026 0.028 0.17 7 -0.31 2 9
GNB1/GNG2 -0.045 0.078 -10000 0 -0.18 111 111
AKT1 -0.023 0.11 0.27 5 -0.23 26 31
EGF 0.023 0.084 0.17 40 -0.31 23 63
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.01 0.075 0.23 24 -0.24 5 29
mol:Ca2+ -0.049 0.15 0.3 6 -0.29 115 121
LYN -0.012 0.058 0.26 10 -0.23 4 14
RhoA/GTP -0.022 0.061 -10000 0 -0.13 99 99
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.057 0.17 0.31 13 -0.34 110 123
GNG2 0.023 0.037 -10000 0 -0.31 6 6
ARRB2 0.025 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.016 0.13 0.27 1 -0.37 45 46
G beta5/gamma2 -0.054 0.11 -10000 0 -0.24 110 110
PRKCH -0.059 0.17 0.32 7 -0.34 111 118
DNM1 0.025 0.018 0.17 1 -0.31 1 2
TXA2/TP beta/beta Arrestin3 0.011 0.017 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.005 0.083 0.17 1 -0.31 32 33
G12 family/GTP -0.058 0.13 -10000 0 -0.3 104 104
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
ADRBK2 0.026 0.016 -10000 0 -0.31 1 1
RhoA/GTP/ROCK1 0.033 0.014 -10000 0 -0.18 1 1
mol:GDP 0.028 0.11 0.32 29 -0.25 4 33
mol:NADP 0.026 0.018 0.17 6 -10000 0 6
RAB11A 0.027 0.003 -10000 0 -10000 0 0
PRKG1 -0.062 0.15 -10000 0 -0.31 129 129
mol:IP3 -0.065 0.18 0.34 5 -0.37 115 120
cell morphogenesis 0.033 0.013 -10000 0 -0.18 1 1
PLCB2 -0.094 0.24 0.38 4 -0.5 115 119
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.071 0.26 13 -0.23 8 21
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.013 0.07 0.22 19 -0.25 6 25
RHOA 0.026 0.005 -10000 0 -10000 0 0
PTGIR 0.037 0.053 0.17 44 -0.31 4 48
PRKCB1 -0.065 0.18 0.32 5 -0.36 113 118
GNAQ 0.026 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.018 0.17 6 -10000 0 6
TXA2/TXA2-R family -0.099 0.24 0.38 4 -0.51 114 118
LCK -0.011 0.067 0.24 15 -0.23 4 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.016 0.059 0.18 3 -0.17 37 40
TXA2-R family/G12 family/GDP/G beta/gamma 0.016 0.056 -10000 0 -0.4 7 7
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.016 0.057 -10000 0 -0.17 29 29
MAPK14 -0.035 0.12 0.26 16 -0.23 108 124
TGM2/GTP -0.077 0.2 0.39 1 -0.41 113 114
MAPK11 -0.036 0.12 0.26 14 -0.23 109 123
ARHGEF1 -0.033 0.082 0.2 1 -0.18 103 104
GNAI2 0.026 0.005 -10000 0 -10000 0 0
JNK cascade -0.068 0.18 0.32 6 -0.38 115 121
RAB11/GDP 0.027 0.004 -10000 0 -10000 0 0
ICAM1 -0.046 0.14 0.27 6 -0.28 112 118
cAMP biosynthetic process -0.064 0.17 0.32 6 -0.34 114 120
Gq family/GTP/EBP50 0.006 0.063 0.24 11 -0.18 35 46
actin cytoskeleton reorganization 0.033 0.013 -10000 0 -0.18 1 1
SRC -0.011 0.066 0.24 16 -0.23 4 20
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.027 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.016 0.099 0.29 22 -0.22 22 44
VCAM1 -0.05 0.14 0.27 6 -0.29 114 120
TP beta/Gq family/GDP/G beta5/gamma2 -0.016 0.13 0.27 1 -0.37 45 46
platelet activation -0.047 0.15 0.33 14 -0.29 112 126
PGI2/IP 0.027 0.037 0.12 44 -0.21 4 48
PRKACA 0.004 0.052 0.11 1 -0.18 36 37
Gq family/GDP/G beta5/gamma2 -0.01 0.11 0.23 2 -0.32 44 46
TXA2/TP beta/beta Arrestin2 0.004 0.043 -10000 0 -0.4 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.008 0.053 0.15 2 -0.18 38 40
mol:DAG -0.073 0.2 0.34 5 -0.41 113 118
EGFR -0.002 0.09 -10000 0 -0.31 39 39
TXA2/TP alpha -0.09 0.22 0.38 5 -0.47 114 119
Gq family/GTP -0.007 0.052 0.14 1 -0.16 47 48
YES1 -0.01 0.068 0.26 15 -0.23 4 19
GNAI2/GTP 0.003 0.053 -10000 0 -0.16 30 30
PGD2/DP 0.005 0.057 0.12 1 -0.21 32 33
SLC9A3R1 0.026 0.005 -10000 0 -10000 0 0
FYN -0.01 0.065 0.23 16 -0.23 5 21
mol:NO 0.026 0.018 0.17 6 -10000 0 6
GNA15 0.012 0.068 -10000 0 -0.31 21 21
PGK/cGMP -0.018 0.091 0.13 6 -0.18 117 123
RhoA/GDP 0.026 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.031 0.07 0.2 1 -0.2 27 28
NOS3 0.027 0.018 0.17 6 -10000 0 6
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.062 0.17 0.3 7 -0.35 114 121
PRKCB -0.077 0.18 0.27 6 -0.38 115 121
PRKCE -0.058 0.16 0.29 6 -0.34 110 116
PRKCD -0.067 0.18 0.32 4 -0.37 110 114
PRKCG -0.067 0.18 0.34 5 -0.37 114 119
muscle contraction -0.092 0.22 0.38 5 -0.48 114 119
PRKCZ -0.06 0.16 0.33 6 -0.34 114 120
ARR3 0.021 0.008 0.17 1 -10000 0 1
TXA2/TP beta 0.017 0.059 -10000 0 -0.17 32 32
PRKCQ -0.064 0.17 0.31 6 -0.35 115 121
MAPKKK cascade -0.086 0.21 0.35 5 -0.45 114 119
SELE -0.067 0.17 0.27 6 -0.36 114 120
TP beta/GNAI2/GDP/G beta/gamma 0.03 0.068 -10000 0 -0.19 29 29
ROCK1 0.025 0.016 -10000 0 -0.31 1 1
GNA14 0.025 0.016 -10000 0 -0.31 1 1
chemotaxis -0.12 0.27 0.39 3 -0.59 113 116
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.016 0.058 -10000 0 -0.31 15 15
Rac1/GTP 0.018 0.006 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.016 0.078 0.14 5 -0.23 44 49
alphaV beta3 Integrin -0.002 0.11 -10000 0 -0.22 92 92
PTK2 -0.082 0.18 0.3 10 -0.4 92 102
IGF1R 0.026 0.017 0.17 1 -0.31 1 2
PI4KB 0.026 0.006 -10000 0 -10000 0 0
MFGE8 0.025 0.026 -10000 0 -0.31 3 3
SRC 0.026 0.006 -10000 0 -10000 0 0
CDKN1B -0.042 0.15 -10000 0 -0.4 62 62
VEGFA 0.01 0.077 0.17 5 -0.31 26 31
ILK -0.032 0.14 -10000 0 -0.42 47 47
ROCK1 0.025 0.016 -10000 0 -0.31 1 1
AKT1 -0.036 0.12 -10000 0 -0.39 47 47
PTK2B -0.038 0.072 0.17 4 -0.28 22 26
alphaV/beta3 Integrin/JAM-A -0.006 0.12 0.25 1 -0.2 122 123
CBL 0.025 0.016 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.029 0.12 -10000 0 -0.19 94 94
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.047 0.078 0.25 1 -0.2 40 41
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.042 0.12 -10000 0 -0.31 51 51
alphaV/beta3 Integrin/Syndecan-1 0 0.1 -10000 0 -0.19 102 102
PI4KA 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.007 0.13 -10000 0 -0.25 95 95
PI4 Kinase 0.037 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
alphaV/beta3 Integrin/Osteopontin 0.017 0.1 -10000 0 -0.18 90 90
RPS6KB1 -0.055 0.12 0.4 5 -0.34 43 48
TLN1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.09 0.2 -10000 0 -0.44 101 101
GPR124 0.014 0.048 -10000 0 -0.31 10 10
MAPK1 -0.091 0.2 -10000 0 -0.44 103 103
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
alphaV/beta3 Integrin/Tumstatin -0.003 0.11 -10000 0 -0.21 101 101
cell adhesion 0.004 0.1 -10000 0 -0.21 87 87
ANGPTL3 0.083 0.073 0.17 193 -10000 0 193
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.073 -10000 0 -0.19 44 44
IGF-1R heterotetramer 0.026 0.017 0.17 1 -0.31 1 2
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
TGFBR2 0.019 0.05 -10000 0 -0.31 11 11
ITGB3 -0.037 0.13 -10000 0 -0.31 92 92
IGF1 0.008 0.089 0.17 17 -0.31 33 50
RAC1 0.025 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.001 0.09 -10000 0 -0.18 86 86
apoptosis 0.026 0.005 -10000 0 -10000 0 0
CD47 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.008 0.089 -10000 0 -0.18 89 89
VCL 0.01 0.072 -10000 0 -0.31 24 24
alphaV/beta3 Integrin/Del1 -0.028 0.14 -10000 0 -0.25 126 126
CSF1 0.019 0.05 -10000 0 -0.31 11 11
PIK3C2A -0.03 0.13 -10000 0 -0.41 45 45
PI4 Kinase/Pyk2 -0.032 0.11 -10000 0 -0.27 54 54
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.006 0.11 -10000 0 -0.19 110 110
FAK1/Vinculin -0.06 0.16 0.29 13 -0.34 94 107
alphaV beta3/Integrin/ppsTEM5 0.001 0.09 -10000 0 -0.18 86 86
RHOA 0.026 0.005 -10000 0 -10000 0 0
VTN 0.007 0.12 0.17 51 -0.31 51 102
BCAR1 0.022 0.011 -10000 0 -10000 0 0
FGF2 0.005 0.082 0.17 1 -0.31 31 32
F11R -0.023 0.046 -10000 0 -0.21 27 27
alphaV/beta3 Integrin/Lactadherin 0.008 0.092 -10000 0 -0.18 89 89
alphaV/beta3 Integrin/TGFBR2 0.006 0.097 -10000 0 -0.2 87 87
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.044 -10000 0 -0.17 11 11
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.009 0.081 -10000 0 -0.16 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.02 0.052 0.17 4 -0.31 11 15
alphaV/beta3 Integrin/Pyk2 -0.013 0.093 0.18 2 -0.18 106 108
SDC1 0.013 0.066 -10000 0 -0.31 20 20
VAV3 -0.027 0.058 0.2 7 -0.3 8 15
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
IRS1 0.017 0.058 -10000 0 -0.31 15 15
FAK1/Paxillin -0.059 0.16 0.3 10 -0.33 91 101
cell migration -0.062 0.14 0.26 10 -0.32 87 97
ITGAV 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.001 0.12 0.23 1 -0.2 102 103
SPP1 0.045 0.058 0.17 69 -0.31 3 72
KDR 0.012 0.069 -10000 0 -0.31 22 22
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.005 -10000 0 -10000 0 0
COL4A3 0.007 0.079 0.17 1 -0.31 29 30
angiogenesis -0.099 0.21 0.25 2 -0.47 99 101
Rac1/GTP 0.005 0.061 0.17 7 -0.28 7 14
EDIL3 -0.037 0.13 0.17 1 -0.31 92 93
cell proliferation 0.005 0.096 -10000 0 -0.19 87 87
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.046 0.15 0.26 3 -0.43 56 59
CRKL -0.048 0.15 0.2 2 -0.45 56 58
HRAS -0.025 0.15 -10000 0 -0.41 56 56
mol:PIP3 -0.016 0.15 0.23 7 -0.4 52 59
SPRED1 0.023 0.034 -10000 0 -0.31 5 5
SPRED2 0.023 0.034 -10000 0 -0.31 5 5
GAB1 -0.047 0.16 -10000 0 -0.45 63 63
FOXO3 -0.018 0.15 0.26 6 -0.4 52 58
AKT1 -0.017 0.16 0.27 4 -0.43 52 56
BAD -0.013 0.16 0.32 12 -0.4 52 64
megakaryocyte differentiation -0.048 0.16 -10000 0 -0.44 64 64
GSK3B -0.01 0.16 0.32 9 -0.4 51 60
RAF1 -0.021 0.12 0.24 5 -0.33 56 61
SHC1 0.026 0.006 -10000 0 -10000 0 0
STAT3 -0.048 0.16 -10000 0 -0.44 63 63
STAT1 -0.11 0.36 -10000 0 -1 65 65
HRAS/SPRED1 -0.007 0.13 -10000 0 -0.34 55 55
cell proliferation -0.05 0.16 -10000 0 -0.44 63 63
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
TEC 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.03 0.17 -10000 0 -0.46 57 57
HRAS/SPRED2 -0.007 0.13 -10000 0 -0.34 56 56
LYN/TEC/p62DOK -0.007 0.16 -10000 0 -0.43 50 50
MAPK3 -0.006 0.1 0.26 16 -0.24 51 67
STAP1 -0.06 0.17 0.24 2 -0.47 64 66
GRAP2 0.016 0.06 0.17 2 -0.31 16 18
JAK2 -0.094 0.31 -10000 0 -0.86 64 64
STAT1 (dimer) -0.11 0.35 -10000 0 -0.97 65 65
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.011 0.18 -10000 0 -0.46 56 56
actin filament polymerization -0.044 0.15 0.22 3 -0.42 62 65
LYN 0.023 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.082 0.24 -10000 0 -0.67 63 63
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
CBL/CRKL/GRB2 -0.019 0.15 -10000 0 -0.41 55 55
PI3K -0.012 0.18 -10000 0 -0.46 55 55
PTEN 0.021 0.011 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.41 -10000 0 -1.2 57 57
MAPK8 -0.051 0.16 -10000 0 -0.45 64 64
STAT3 (dimer) -0.047 0.16 -10000 0 -0.44 63 63
positive regulation of transcription -0.002 0.088 0.24 16 -0.2 50 66
mol:GDP -0.022 0.16 -10000 0 -0.43 57 57
PIK3C2B -0.046 0.16 -10000 0 -0.45 61 61
CBL/CRKL -0.03 0.15 -10000 0 -0.42 56 56
FER -0.05 0.16 -10000 0 -0.45 65 65
SH2B3 -0.046 0.16 -10000 0 -0.45 60 60
PDPK1 -0.012 0.15 0.26 15 -0.37 51 66
SNAI2 -0.067 0.18 -10000 0 -0.49 64 64
positive regulation of cell proliferation -0.08 0.28 -10000 0 -0.77 64 64
KITLG 0.001 0.081 -10000 0 -0.33 25 25
cell motility -0.08 0.28 -10000 0 -0.77 64 64
PTPN6 0.026 0.012 -10000 0 -10000 0 0
EPOR -0.005 0.12 -10000 0 -1.1 1 1
STAT5A (dimer) -0.066 0.24 -10000 0 -0.65 63 63
SOCS1 0.026 0.02 0.17 3 -0.31 1 4
cell migration 0.059 0.16 0.46 63 -0.19 1 64
SOS1 0.026 0.005 -10000 0 -10000 0 0
EPO -0.002 0.1 0.18 25 -0.32 42 67
VAV1 0.013 0.068 0.17 1 -0.31 21 22
GRB10 -0.047 0.15 -10000 0 -0.43 62 62
PTPN11 0.026 0.018 -10000 0 -0.3 1 1
SCF/KIT -0.045 0.17 -10000 0 -0.47 63 63
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.012 0.11 0.26 14 -0.27 53 67
CBL 0.025 0.016 -10000 0 -0.31 1 1
KIT -0.12 0.4 -10000 0 -1.2 57 57
MAP2K2 -0.012 0.11 0.26 14 -0.27 53 67
SHC/Grb2/SOS1 -0.006 0.16 -10000 0 -0.44 55 55
STAT5A -0.068 0.24 -10000 0 -0.67 63 63
GRB2 0.026 0.005 -10000 0 -10000 0 0
response to radiation -0.066 0.17 -10000 0 -0.48 64 64
SHC/GRAP2 0.03 0.045 0.14 2 -0.21 15 17
PTPRO -0.048 0.16 -10000 0 -0.44 63 63
SH2B2 -0.045 0.16 0.22 3 -0.42 62 65
DOK1 0.026 0.016 -10000 0 -0.31 1 1
MATK -0.06 0.17 0.19 1 -0.46 63 64
CREBBP 0.018 0.053 -10000 0 -0.18 8 8
BCL2 -0.1 0.36 -10000 0 -1.3 32 32
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.026 0.051 0.17 9 -0.18 8 17
STMN1 -0.02 0.028 0.24 1 -0.15 1 2
Aurora B/RasGAP/Survivin 0.091 0.099 0.24 121 -0.14 19 140
Chromosomal passenger complex/Cul3 protein complex 0.013 0.055 0.15 5 -0.19 14 19
BIRC5 0.076 0.074 0.18 165 -0.32 1 166
DES -0.091 0.28 -10000 0 -0.58 114 114
Aurora C/Aurora B/INCENP 0.067 0.057 0.16 34 -0.1 16 50
Aurora B/TACC1 0.039 0.055 0.13 94 -0.13 14 108
Aurora B/PP2A 0.062 0.06 0.15 45 -0.11 16 61
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.012 0.017 0.11 11 -10000 0 11
mitotic metaphase/anaphase transition -0.001 0.004 -10000 0 -10000 0 0
NDC80 -0.017 0.044 0.27 7 -0.22 3 10
Cul3 protein complex 0.041 0.052 -10000 0 -0.18 25 25
KIF2C 0.026 0.042 0.16 11 -0.29 2 13
PEBP1 0.025 0.006 -10000 0 -10000 0 0
KIF20A 0.078 0.072 0.18 171 -10000 0 171
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.06 0.06 0.15 131 -0.13 12 143
SEPT1 0.03 0.023 0.17 12 -10000 0 12
SMC2 0.026 0.006 -10000 0 -10000 0 0
SMC4 0.026 0.009 0.17 1 -10000 0 1
NSUN2/NPM1/Nucleolin -0.005 0.17 0.29 11 -0.46 53 64
PSMA3 0.027 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.022 0.025 0.14 5 -0.14 3 8
AURKB 0.07 0.072 0.18 145 -10000 0 145
AURKC 0.026 0.025 0.17 3 -0.31 2 5
CDCA8 0.044 0.047 0.18 53 -10000 0 53
cytokinesis 0.032 0.066 0.21 16 -0.25 12 28
Aurora B/Septin1 0.06 0.11 0.26 27 -0.24 18 45
AURKA 0.034 0.033 0.17 26 -10000 0 26
INCENP 0.027 0.006 -10000 0 -10000 0 0
KLHL13 0.009 0.075 -10000 0 -0.31 26 26
BUB1 0.058 0.061 0.18 104 -10000 0 104
hSgo1/Aurora B/Survivin 0.1 0.12 0.27 136 -0.15 16 152
EVI5 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.059 0.067 0.21 25 -0.23 4 29
SGOL1 0.053 0.058 0.17 91 -10000 0 91
CENPA 0.03 0.069 0.19 16 -0.16 24 40
NCAPG 0.074 0.069 0.17 159 -10000 0 159
Aurora B/HC8 Proteasome 0.063 0.06 0.15 98 -0.11 15 113
NCAPD2 0.025 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.061 0.058 0.15 132 -0.11 12 144
RHOA 0.026 0.005 -10000 0 -10000 0 0
NCAPH 0.064 0.064 0.17 126 -10000 0 126
NPM1 0.002 0.1 -10000 0 -0.3 47 47
RASA1 0.025 0.016 -10000 0 -0.31 1 1
KLHL9 0.026 0.005 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.062 0.06 0.15 83 -0.11 15 98
PPP1CC 0.026 0.006 -10000 0 -10000 0 0
Centraspindlin 0.057 0.074 0.23 31 -0.23 5 36
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
NSUN2 0.003 0.1 0.2 1 -0.28 47 48
MYLK -0.034 0.11 0.14 7 -0.24 100 107
KIF23 0.038 0.037 0.18 32 -10000 0 32
VIM -0.019 0.03 0.26 2 -10000 0 2
RACGAP1 0.03 0.016 0.18 5 -10000 0 5
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0.1 -10000 0 -0.3 49 49
Chromosomal passenger complex 0.026 0.06 0.18 18 -0.2 8 26
Chromosomal passenger complex/EVI5 0.12 0.11 0.28 122 -0.16 12 134
TACC1 0.017 0.035 -10000 0 -0.31 5 5
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
CUL3 0.027 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.03 0.073 -10000 0 -0.19 44 44
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.099 0.26 5 -0.25 32 37
AP1 -0.02 0.11 0.16 1 -0.19 131 132
mol:PIP3 -0.044 0.073 -10000 0 -0.19 78 78
AKT1 0.006 0.092 0.31 20 -0.24 9 29
PTK2B -0.053 0.12 0.24 2 -0.23 125 127
RHOA 0.006 0.043 0.2 7 -0.26 4 11
PIK3CB 0.025 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.085 0.21 24 -0.23 22 46
MAGI3 0.027 0.004 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
apoptosis -0.024 0.091 -10000 0 -0.21 88 88
HRAS/GDP 0.021 0.012 0.12 6 -10000 0 6
positive regulation of microtubule depolymerization -0.044 0.11 0.26 11 -0.27 55 66
NF kappa B1 p50/RelA -0.012 0.094 -10000 0 -0.22 63 63
endothelial cell migration -0.004 0.075 -10000 0 -0.25 34 34
ADCY4 -0.036 0.15 0.23 3 -0.42 53 56
ADCY5 -0.057 0.19 0.23 2 -0.5 65 67
ADCY6 -0.034 0.15 0.23 4 -0.41 52 56
ADCY7 -0.034 0.15 0.23 4 -0.41 53 57
ADCY1 -0.035 0.14 0.23 2 -0.42 49 51
ADCY2 -0.041 0.16 0.23 4 -0.43 57 61
ADCY3 -0.035 0.15 0.23 4 -0.41 53 57
ADCY8 -0.033 0.13 -10000 0 -0.4 47 47
ADCY9 -0.035 0.15 0.18 7 -0.41 53 60
GSK3B -0.046 0.12 0.25 11 -0.28 64 75
arachidonic acid secretion -0.042 0.15 -10000 0 -0.39 59 59
GNG2 0.022 0.037 -10000 0 -0.31 6 6
TRIP6 0.014 0.034 0.19 1 -0.26 6 7
GNAO1 -0.026 0.1 -10000 0 -0.25 72 72
HRAS 0.028 0.017 0.17 6 -10000 0 6
NFKBIA -0.02 0.11 0.3 13 -0.24 53 66
GAB1 0.026 0.016 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.001 0.19 -10000 0 -0.81 25 25
JUN 0.024 0.031 0.17 1 -0.31 4 5
LPA/LPA2/NHERF2 0.035 0.022 0.13 5 -0.12 4 9
TIAM1 -0.017 0.22 -10000 0 -0.95 25 25
PIK3R1 0.021 0.031 -10000 0 -0.31 4 4
mol:IP3 -0.017 0.079 0.19 22 -0.23 23 45
PLCB3 0.015 0.037 0.18 20 -10000 0 20
FOS -0.026 0.12 0.17 4 -0.31 78 82
positive regulation of mitosis -0.042 0.15 -10000 0 -0.39 59 59
LPA/LPA1-2-3 0.008 0.098 -10000 0 -0.19 90 90
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.011 -10000 0 -10000 0 0
stress fiber formation -0.028 0.11 0.29 9 -0.3 43 52
GNAZ -0.017 0.091 -10000 0 -0.24 62 62
EGFR/PI3K-beta/Gab1 -0.016 0.089 -10000 0 -0.2 78 78
positive regulation of dendritic cell cytokine production 0.007 0.097 -10000 0 -0.18 90 90
LPA/LPA2/MAGI-3 0.035 0.019 -10000 0 -0.12 4 4
ARHGEF1 0.013 0.079 0.2 47 -0.17 32 79
GNAI2 -0.003 0.061 -10000 0 -0.2 40 40
GNAI3 -0.004 0.063 -10000 0 -0.2 42 42
GNAI1 -0.002 0.061 0.19 1 -0.21 35 36
LPA/LPA3 -0.01 0.08 0.12 6 -0.2 69 75
LPA/LPA2 0.019 0.018 -10000 0 -0.14 4 4
LPA/LPA1 0.001 0.077 -10000 0 -0.23 44 44
HB-EGF/EGFR -0.028 0.068 0.2 6 -0.2 45 51
HBEGF -0.032 0.052 0.26 10 -0.22 7 17
mol:DAG -0.017 0.079 0.19 22 -0.23 23 45
cAMP biosynthetic process -0.035 0.17 0.26 20 -0.39 63 83
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
LYN -0.008 0.12 0.31 21 -0.25 47 68
GNAQ -0.01 0.065 -10000 0 -0.18 59 59
LPAR2 0.026 0.015 -10000 0 -0.31 1 1
LPAR3 -0.016 0.12 0.17 7 -0.31 65 72
LPAR1 -0.003 0.099 -10000 0 -0.32 43 43
IL8 -0.054 0.18 0.41 8 -0.41 77 85
PTK2 -0.017 0.068 0.18 6 -0.17 65 71
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
CASP3 -0.024 0.091 -10000 0 -0.21 88 88
EGFR -0.002 0.09 -10000 0 -0.31 39 39
PLCG1 -0.019 0.074 0.16 1 -0.21 58 59
PLD2 -0.019 0.082 0.19 13 -0.18 80 93
G12/G13 0.032 0.063 -10000 0 -0.18 35 35
PI3K-beta 0.005 0.054 -10000 0 -0.24 13 13
cell migration -0.005 0.066 -10000 0 -0.24 24 24
SLC9A3R2 0.027 0.016 0.17 5 -10000 0 5
PXN -0.029 0.12 0.29 9 -0.3 43 52
HRAS/GTP -0.045 0.15 -10000 0 -0.4 59 59
RAC1 0.025 0.008 -10000 0 -10000 0 0
MMP9 0.1 0.085 0.17 258 -0.31 5 263
PRKCE 0.026 0.006 -10000 0 -10000 0 0
PRKCD -0.016 0.089 0.23 26 -0.26 16 42
Gi(beta/gamma) -0.035 0.14 0.15 6 -0.38 56 62
mol:LPA 0 0.016 -10000 0 -0.11 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.012 0.094 -10000 0 -0.28 25 25
MAPKKK cascade -0.042 0.15 -10000 0 -0.39 59 59
contractile ring contraction involved in cytokinesis 0.007 0.045 0.2 8 -0.25 4 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.011 0.066 -10000 0 -0.18 61 61
GNA15 -0.016 0.076 -10000 0 -0.2 71 71
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
MAPT -0.045 0.12 0.26 11 -0.28 55 66
GNA11 -0.015 0.076 -10000 0 -0.2 67 67
Rac1/GTP 0.001 0.2 -10000 0 -0.86 25 25
MMP2 -0.004 0.076 -10000 0 -0.25 34 34
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.016 -10000 0 -0.31 1 1
CCL5 0.021 0.055 0.17 7 -0.31 12 19
SDCBP 0.022 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.013 0.1 0.25 9 -0.23 54 63
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.002 0.1 0.22 12 -0.25 43 55
Syndecan-1/Syntenin 0 0.095 0.24 8 -0.3 20 28
MAPK3 -0.005 0.099 0.22 14 -0.31 21 35
HGF/MET 0.007 0.095 -10000 0 -0.26 50 50
TGFB1/TGF beta receptor Type II 0.026 0.016 -10000 0 -0.31 1 1
BSG 0.027 0.007 0.17 1 -10000 0 1
keratinocyte migration -0.002 0.1 0.22 12 -0.24 43 55
Syndecan-1/RANTES -0.001 0.11 0.22 16 -0.25 48 64
Syndecan-1/CD147 0.013 0.11 0.25 12 -0.31 22 34
Syndecan-1/Syntenin/PIP2 -0.002 0.09 0.21 6 -0.3 19 25
LAMA5 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.003 0.089 0.21 6 -0.29 19 25
MMP7 0.017 0.1 0.17 50 -0.31 35 85
HGF 0.011 0.075 0.17 9 -0.31 24 33
Syndecan-1/CASK -0.019 0.093 0.18 5 -0.22 57 62
Syndecan-1/HGF/MET -0.011 0.13 0.2 4 -0.33 44 48
regulation of cell adhesion -0.013 0.096 0.23 15 -0.32 19 34
HPSE 0.017 0.066 0.17 8 -0.31 18 26
positive regulation of cell migration -0.013 0.1 0.25 9 -0.23 54 63
SDC1 -0.013 0.098 0.23 7 -0.21 73 80
Syndecan-1/Collagen -0.013 0.1 0.25 9 -0.23 54 63
PPIB 0.028 0.012 0.17 3 -10000 0 3
MET -0.004 0.093 -10000 0 -0.31 42 42
PRKACA 0.027 0.003 -10000 0 -10000 0 0
MMP9 0.1 0.085 0.17 258 -0.31 5 263
MAPK1 -0.005 0.1 0.22 15 -0.3 22 37
homophilic cell adhesion -0.011 0.1 0.25 13 -0.25 42 55
MMP1 0.024 0.096 0.17 60 -0.31 29 89
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.033 0.047 0.2 17 -0.27 5 22
NFATC2 0.016 0.16 -10000 0 -0.44 32 32
NFATC3 0.025 0.061 -10000 0 -0.2 17 17
CD40LG -0.092 0.26 -10000 0 -0.74 48 48
ITCH -0.018 0.082 -10000 0 -0.18 94 94
CBLB -0.019 0.082 -10000 0 -0.18 95 95
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.074 0.26 -10000 0 -0.69 47 47
JUNB 0.024 0.053 0.17 12 -0.31 10 22
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.018 0.1 -10000 0 -0.22 100 100
T cell anergy -0.058 0.15 0.29 3 -0.33 98 101
TLE4 -0.003 0.12 0.3 2 -0.36 24 26
Jun/NFAT1-c-4/p21SNFT -0.011 0.24 -10000 0 -0.73 31 31
AP-1/NFAT1-c-4 -0.046 0.32 0.5 1 -0.81 46 47
IKZF1 0 0.11 0.29 1 -0.39 17 18
T-helper 2 cell differentiation -0.15 0.26 -10000 0 -0.64 65 65
AP-1/NFAT1 -0.014 0.17 0.39 1 -0.34 59 60
CALM1 -0.003 0.07 -10000 0 -0.14 100 100
EGR2 -0.059 0.27 -10000 0 -0.95 30 30
EGR3 -0.067 0.29 -10000 0 -1 33 33
NFAT1/FOXP3 0.02 0.15 0.32 9 -0.37 23 32
EGR1 0.007 0.095 0.17 24 -0.31 36 60
JUN 0.013 0.042 0.18 1 -0.32 4 5
EGR4 0.062 0.067 0.17 128 -10000 0 128
mol:Ca2+ -0.022 0.056 -10000 0 -0.13 106 106
GBP3 -0.041 0.2 -10000 0 -0.55 56 56
FOSL1 -0.012 0.13 0.17 33 -0.31 70 103
NFAT1-c-4/MAF/IRF4 -0.006 0.23 -10000 0 -0.73 29 29
DGKA -0.002 0.11 0.29 1 -0.34 20 21
CREM 0.026 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.019 0.23 -10000 0 -0.75 30 30
CTLA4 -0.002 0.12 0.33 5 -0.34 22 27
NFAT1-c-4 (dimer)/EGR1 -0.017 0.25 -10000 0 -0.77 33 33
NFAT1-c-4 (dimer)/EGR4 0.003 0.24 -10000 0 -0.72 30 30
FOS -0.035 0.13 0.18 4 -0.32 78 82
IFNG -0.049 0.19 -10000 0 -0.62 22 22
T cell activation -0.032 0.16 0.4 1 -0.61 13 14
MAF 0.021 0.024 -10000 0 -0.31 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.019 0.16 0.6 28 -10000 0 28
TNF -0.06 0.24 -10000 0 -0.67 44 44
FASLG -0.12 0.39 -10000 0 -1.2 44 44
TBX21 0.03 0.051 0.19 18 -0.31 7 25
BATF3 0.032 0.031 0.17 22 -10000 0 22
PRKCQ 0.008 0.087 0.18 10 -0.28 36 46
PTPN1 -0.004 0.11 -10000 0 -0.34 21 21
NFAT1-c-4/ICER1 -0.013 0.22 -10000 0 -0.72 30 30
GATA3 -0.068 0.15 -10000 0 -0.31 139 139
T-helper 1 cell differentiation -0.048 0.19 -10000 0 -0.62 22 22
IL2RA -0.062 0.26 0.34 1 -0.64 54 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.003 0.11 -10000 0 -0.35 20 20
E2F1 0.034 0.028 0.18 18 -10000 0 18
PPARG 0.01 0.075 0.17 3 -0.31 25 28
SLC3A2 -0.003 0.11 0.32 1 -0.35 20 21
IRF4 0.022 0.07 0.17 24 -0.31 17 41
PTGS2 -0.11 0.28 -10000 0 -0.73 60 60
CSF2 -0.091 0.25 -10000 0 -0.71 47 47
JunB/Fra1/NFAT1-c-4 -0.022 0.24 -10000 0 -0.75 32 32
IL4 -0.16 0.27 -10000 0 -0.67 64 64
IL5 -0.091 0.24 -10000 0 -0.71 48 48
IL2 -0.033 0.16 0.4 1 -0.62 13 14
IL3 -0.018 0.12 -10000 0 -0.6 13 13
RNF128 -0.066 0.18 0.28 1 -0.41 103 104
NFATC1 -0.019 0.16 -10000 0 -0.6 28 28
CDK4 0.039 0.14 0.5 22 -10000 0 22
PTPRK -0.004 0.11 -10000 0 -0.34 21 21
IL8 -0.095 0.26 -10000 0 -0.71 54 54
POU2F1 0.026 0.006 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.03 0.24 0.3 8 -0.57 54 62
HDAC7 0.025 0.013 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.024 0.3 -10000 0 -0.71 43 43
SMAD4 0.025 0.008 -10000 0 -10000 0 0
ID2 -0.02 0.26 0.34 5 -0.62 47 52
AP1 -0.003 0.1 0.18 4 -0.22 78 82
ABCG2 -0.031 0.27 0.34 5 -0.63 54 59
HIF1A 0.011 0.065 -10000 0 -0.25 3 3
TFF3 -0.002 0.27 0.36 7 -0.6 49 56
GATA2 0.023 0.018 0.18 1 -0.11 1 2
AKT1 0.008 0.078 -10000 0 -0.21 23 23
response to hypoxia -0.01 0.073 -10000 0 -0.17 51 51
MCL1 -0.023 0.24 0.35 4 -0.59 48 52
NDRG1 -0.021 0.23 0.33 1 -0.61 37 38
SERPINE1 -0.016 0.25 0.33 2 -0.59 49 51
FECH -0.019 0.25 0.34 6 -0.6 47 53
FURIN -0.017 0.25 0.34 5 -0.59 48 53
NCOA2 -0.019 0.1 -10000 0 -0.31 53 53
EP300 -0.002 0.11 -10000 0 -0.31 37 37
HMOX1 -0.017 0.25 0.34 6 -0.6 48 54
BHLHE40 -0.019 0.25 0.35 5 -0.63 43 48
BHLHE41 -0.02 0.25 0.36 6 -0.6 47 53
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.061 0.096 -10000 0 -0.21 1 1
ENG 0.014 0.076 0.26 14 -10000 0 14
JUN 0.022 0.034 0.18 1 -0.27 5 6
RORA -0.017 0.25 0.35 5 -0.6 47 52
ABCB1 0.004 0.16 -10000 0 -0.94 10 10
TFRC -0.017 0.25 0.34 6 -0.6 46 52
CXCR4 -0.018 0.25 0.34 6 -0.61 45 51
TF -0.041 0.28 0.34 6 -0.61 61 67
CITED2 -0.017 0.25 0.34 6 -0.6 46 52
HIF1A/ARNT 0.07 0.35 0.55 4 -0.75 32 36
LDHA 0.028 0.082 -10000 0 -0.79 2 2
ETS1 -0.02 0.25 0.35 4 -0.62 44 48
PGK1 -0.017 0.25 0.34 6 -0.6 48 54
NOS2 -0.021 0.27 0.34 6 -0.61 52 58
ITGB2 -0.016 0.25 0.34 5 -0.6 48 53
ALDOA -0.018 0.25 0.35 5 -0.6 48 53
Cbp/p300/CITED2 -0.024 0.31 -10000 0 -0.75 50 50
FOS -0.027 0.12 0.18 4 -0.31 78 82
HK2 -0.018 0.25 0.34 5 -0.59 49 54
SP1 0.029 0.016 -10000 0 -10000 0 0
GCK -0.035 0.3 -10000 0 -1.3 25 25
HK1 -0.018 0.25 0.34 5 -0.6 46 51
NPM1 -0.018 0.25 0.33 4 -0.59 48 52
EGLN1 -0.022 0.25 0.35 4 -0.6 46 50
CREB1 0.031 0.004 -10000 0 -10000 0 0
PGM1 -0.019 0.25 0.35 5 -0.6 47 52
SMAD3 0.027 0.002 -10000 0 -10000 0 0
EDN1 -0.052 0.29 -10000 0 -0.97 37 37
IGFBP1 -0.018 0.25 0.36 6 -0.6 45 51
VEGFA -0.019 0.25 0.37 5 -0.6 50 55
HIF1A/JAB1 0.021 0.051 -10000 0 -0.19 2 2
CP -0.03 0.28 0.35 7 -0.62 58 65
CXCL12 -0.02 0.26 0.34 6 -0.62 49 55
COPS5 0.018 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4 0.037 0.013 -10000 0 -10000 0 0
BNIP3 -0.018 0.25 0.34 5 -0.59 48 53
EGLN3 -0.02 0.26 0.33 4 -0.61 48 52
CA9 -0.022 0.25 0.34 5 -0.59 48 53
TERT -0.005 0.26 0.38 5 -0.59 50 55
ENO1 -0.018 0.25 0.34 6 -0.6 48 54
PFKL -0.016 0.25 0.34 5 -0.61 45 50
NCOA1 0.024 0.012 -10000 0 -10000 0 0
ADM -0.015 0.25 0.36 7 -0.6 47 54
ARNT 0.011 0.061 -10000 0 -0.19 3 3
HNF4A 0.024 0.045 0.18 26 -0.11 16 42
ADFP -0.03 0.24 0.3 8 -0.57 54 62
SLC2A1 -0.013 0.24 0.37 5 -0.62 42 47
LEP -0.018 0.24 0.33 3 -0.6 46 49
HIF1A/ARNT/Cbp/p300 0.016 0.31 -10000 0 -0.73 42 42
EPO -0.073 0.32 0.44 1 -0.8 63 64
CREBBP 0.001 0.1 -10000 0 -0.32 31 31
HIF1A/ARNT/Cbp/p300/HDAC7 0.024 0.31 -10000 0 -0.75 38 38
PFKFB3 -0.021 0.26 0.34 5 -0.62 46 51
NT5E -0.03 0.26 0.33 2 -0.62 51 53
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.03 0.027 0.17 16 -10000 0 16
EPHB2 0.025 0.033 0.17 3 -0.31 4 7
EFNB1 -0.011 0.026 -10000 0 -0.21 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.003 0.099 -10000 0 -0.16 112 112
Ephrin B2/EPHB1-2 -0.011 0.096 -10000 0 -0.16 137 137
neuron projection morphogenesis -0.01 0.086 -10000 0 -0.16 112 112
Ephrin B1/EPHB1-2/Tiam1 -0.007 0.1 -10000 0 -0.17 125 125
DNM1 0.025 0.018 0.17 1 -0.31 1 2
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.006 0.054 0.2 1 -0.44 7 8
YES1 0.003 0.083 -10000 0 -0.68 7 7
Ephrin B1/EPHB1-2/NCK2 -0.006 0.096 -10000 0 -0.16 125 125
PI3K 0.028 0.069 -10000 0 -0.49 7 7
mol:GDP -0.008 0.099 -10000 0 -0.17 125 125
ITGA2B 0.02 0.048 0.17 5 -0.31 9 14
endothelial cell proliferation 0.033 0.02 0.13 13 -10000 0 13
FYN 0 0.085 -10000 0 -0.68 7 7
MAP3K7 -0.004 0.053 -10000 0 -0.48 6 6
FGR 0.005 0.086 -10000 0 -0.65 8 8
TIAM1 0.023 0.03 -10000 0 -0.31 4 4
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
RGS3 0.025 0.007 -10000 0 -10000 0 0
cell adhesion -0.013 0.09 -10000 0 -0.42 11 11
LYN 0.004 0.081 -10000 0 -0.66 7 7
Ephrin B1/EPHB1-2/Src Family Kinases -0.004 0.083 -10000 0 -0.65 8 8
Ephrin B1/EPHB1-2 -0.003 0.062 -10000 0 -0.51 7 7
SRC 0.005 0.085 -10000 0 -0.65 8 8
ITGB3 -0.037 0.13 -10000 0 -0.31 92 92
EPHB1 -0.068 0.15 -10000 0 -0.31 137 137
EPHB4 0.024 0.008 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.02 0.13 13 -10000 0 13
alphaIIb/beta3 Integrin -0.014 0.1 0.14 2 -0.21 101 103
BLK -0.015 0.1 -10000 0 -0.68 8 8
HCK 0.003 0.087 -10000 0 -0.66 8 8
regulation of stress fiber formation 0.007 0.095 0.16 125 -10000 0 125
MAPK8 -0.007 0.062 0.21 4 -0.44 7 11
Ephrin B1/EPHB1-2/RGS3 -0.006 0.097 -10000 0 -0.16 127 127
endothelial cell migration 0.002 0.065 0.2 25 -0.38 7 32
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTPN13 0.026 0.03 -10000 0 -0.42 2 2
regulation of focal adhesion formation 0.007 0.095 0.16 125 -10000 0 125
chemotaxis 0.007 0.095 0.16 127 -10000 0 127
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
Rac1/GTP -0.004 0.092 -10000 0 -0.16 112 112
angiogenesis -0.002 0.062 -10000 0 -0.51 7 7
LCK 0.006 0.086 -10000 0 -0.65 8 8
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.048 0.18 0.26 1 -0.45 58 59
MAP3K8 0.017 0.055 0.17 1 -0.31 13 14
FOS -0.039 0.15 0.26 1 -0.37 54 55
PRKCA 0.005 0.07 -10000 0 -0.31 22 22
PTPN7 0.024 0.039 0.17 22 -10000 0 22
HRAS 0.028 0.017 0.17 6 -10000 0 6
PRKCB -0.051 0.14 -10000 0 -0.31 107 107
NRAS 0.026 0.016 -10000 0 -0.32 1 1
RAS family/GTP 0.041 0.028 -10000 0 -10000 0 0
MAPK3 -0.01 0.093 -10000 0 -0.37 8 8
MAP2K1 -0.081 0.21 -10000 0 -0.43 105 105
ELK1 0.017 0.023 -10000 0 -10000 0 0
BRAF -0.065 0.18 -10000 0 -0.41 90 90
mol:GTP -0.001 0.002 -10000 0 -0.004 84 84
MAPK1 -0.015 0.11 -10000 0 -0.54 9 9
RAF1 -0.071 0.18 -10000 0 -0.4 101 101
KRAS 0.025 0.007 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.029 0.12 -10000 0 -0.31 81 81
GNB1/GNG2 -0.008 0.12 -10000 0 -0.3 36 36
mol:DAG -0.019 0.1 0.19 15 -0.28 36 51
PLCG1 -0.02 0.11 0.19 14 -0.28 36 50
YES1 -0.028 0.093 -10000 0 -0.23 67 67
FZD3 0.02 0.012 -10000 0 -10000 0 0
FZD6 0.021 0.011 -10000 0 -10000 0 0
G protein -0.004 0.12 0.28 3 -0.29 36 39
MAP3K7 -0.04 0.1 0.19 17 -0.27 48 65
mol:Ca2+ -0.018 0.1 0.18 15 -0.27 36 51
mol:IP3 -0.019 0.1 0.19 15 -0.28 36 51
NLK 0.003 0.08 -10000 0 -0.78 5 5
GNB1 0.027 0.004 -10000 0 -10000 0 0
CAMK2A -0.038 0.12 0.21 20 -0.27 57 77
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.019 0.1 -10000 0 -0.24 71 71
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
GNAS -0.03 0.094 -10000 0 -0.23 71 71
GO:0007205 -0.023 0.1 0.21 18 -0.27 37 55
WNT6 -0.03 0.13 0.17 7 -0.31 87 94
WNT4 0.023 0.034 -10000 0 -0.31 5 5
NFAT1/CK1 alpha -0.033 0.12 -10000 0 -0.29 44 44
GNG2 0.023 0.037 -10000 0 -0.31 6 6
WNT5A 0.015 0.074 0.17 12 -0.31 22 34
WNT11 0.027 0.054 0.17 23 -0.31 8 31
CDC42 -0.027 0.092 0.17 1 -0.29 31 32
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.08 0.14 3 -0.23 44 47
PDGFRB 0.025 0.014 0.17 2 -10000 0 2
SPHK1 -0.007 0.084 -10000 0 -0.63 7 7
mol:S1P -0.01 0.08 0.29 1 -0.52 7 8
S1P1/S1P/Gi -0.1 0.2 0.22 1 -0.42 117 118
GNAO1 -0.03 0.12 -10000 0 -0.31 71 71
PDGFB-D/PDGFRB/PLCgamma1 -0.077 0.19 0.24 4 -0.38 111 115
PLCG1 -0.096 0.19 0.21 1 -0.4 112 113
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.014 0.17 2 -10000 0 2
GNAI2 0.018 0.021 -10000 0 -10000 0 0
GNAI3 0.018 0.02 -10000 0 -10000 0 0
GNAI1 0.015 0.033 0.17 1 -0.32 3 4
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.027 0.054 -10000 0 -0.19 44 44
S1P1/S1P -0.027 0.091 0.18 8 -0.3 23 31
negative regulation of cAMP metabolic process -0.098 0.2 0.21 1 -0.41 117 118
MAPK3 -0.13 0.25 0.28 1 -0.55 115 116
calcium-dependent phospholipase C activity -0.002 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
KDR 0.007 0.07 -10000 0 -0.31 22 22
PLCB2 -0.019 0.09 0.25 7 -0.29 20 27
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.079 -10000 0 -0.26 25 25
receptor internalization -0.027 0.084 0.16 5 -0.27 25 30
PTGS2 -0.19 0.39 0.37 1 -0.94 96 97
Rac1/GTP -0.021 0.077 -10000 0 -0.26 23 23
RHOA 0.026 0.005 -10000 0 -10000 0 0
VEGFA 0.006 0.078 0.17 5 -0.31 26 31
negative regulation of T cell proliferation -0.098 0.2 0.21 1 -0.41 117 118
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.01 0.095 -10000 0 -0.32 42 42
MAPK1 -0.13 0.26 -10000 0 -0.56 115 115
S1P1/S1P/PDGFB-D/PDGFRB -0.022 0.1 0.22 8 -0.25 42 50
ABCC1 0.019 0.018 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.006 0.12 -10000 0 -0.51 21 21
IHH 0.036 0.075 0.21 30 -0.2 22 52
SHH Np/Cholesterol/GAS1 -0.023 0.083 0.16 3 -0.18 98 101
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.024 0.081 0.18 98 -0.12 1 99
SMO/beta Arrestin2 0.014 0.098 -10000 0 -0.33 22 22
SMO -0.002 0.089 -10000 0 -0.34 23 23
AKT1 0 0.094 -10000 0 -0.39 13 13
ARRB2 0.025 0.008 -10000 0 -10000 0 0
BOC 0.018 0.052 -10000 0 -0.31 12 12
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
heart looping -0.001 0.088 -10000 0 -0.34 23 23
STIL -0.011 0.096 0.19 28 -0.28 23 51
DHH N/PTCH2 0.037 0.035 -10000 0 -0.21 8 8
DHH N/PTCH1 0.02 0.079 -10000 0 -0.24 35 35
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
DHH 0.024 0.039 0.17 3 -0.31 6 9
PTHLH -0.007 0.15 -10000 0 -0.65 21 21
determination of left/right symmetry -0.001 0.088 -10000 0 -0.34 23 23
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
skeletal system development -0.006 0.15 -10000 0 -0.65 21 21
IHH N/Hhip 0.015 0.11 0.15 30 -0.28 53 83
DHH N/Hhip 0.014 0.079 -10000 0 -0.21 51 51
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.001 0.088 -10000 0 -0.34 23 23
pancreas development -0.003 0.097 0.17 3 -0.31 45 48
HHAT 0.021 0.04 -10000 0 -0.31 7 7
PI3K 0.031 0.034 -10000 0 -0.24 6 6
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.007 0.1 0.17 1 -0.31 48 49
somite specification -0.001 0.088 -10000 0 -0.34 23 23
SHH Np/Cholesterol/PTCH1 -0.009 0.089 0.18 3 -0.26 31 34
SHH Np/Cholesterol/PTCH2 -0.009 0.071 0.15 9 -0.16 71 80
SHH Np/Cholesterol/Megalin -0.02 0.082 0.14 11 -0.17 99 110
SHH -0.041 0.078 0.26 5 -0.22 69 74
catabolic process 0.007 0.081 -10000 0 -0.27 35 35
SMO/Vitamin D3 -0.012 0.096 0.22 4 -0.3 27 31
SHH Np/Cholesterol/Hhip -0.022 0.089 0.16 6 -0.19 92 98
LRP2 0.001 0.093 0.17 9 -0.31 39 48
receptor-mediated endocytosis -0.027 0.1 -10000 0 -0.32 32 32
SHH Np/Cholesterol/BOC -0.013 0.072 0.18 4 -0.16 78 82
SHH Np/Cholesterol/CDO -0.009 0.067 0.16 5 -0.16 70 75
mesenchymal cell differentiation 0.023 0.087 0.19 92 -0.14 3 95
mol:Vitamin D3 -0.004 0.1 0.19 30 -0.26 31 61
IHH N/PTCH2 0.037 0.066 0.2 3 -0.21 23 26
CDON 0.026 0.02 0.17 3 -0.31 1 4
IHH N/PTCH1 0.022 0.09 0.25 1 -0.27 35 36
Megalin/LRPAP1 0.019 0.071 0.14 9 -0.21 40 49
PTCH2 0.027 0.025 0.17 4 -0.31 2 6
SHH Np/Cholesterol -0.017 0.061 -10000 0 -0.16 72 72
PTCH1 0.007 0.082 -10000 0 -0.27 35 35
HHIP -0.003 0.097 0.17 3 -0.31 45 48
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.038 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.039 0.03 0.14 15 -0.24 3 18
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.043 0.08 -10000 0 -0.16 59 59
NGF (dimer)/p75(NTR)/BEX1 -0.038 0.13 -10000 0 -0.21 170 170
NT-4/5 (dimer)/p75(NTR) -0.032 0.13 -10000 0 -0.26 116 116
IKBKB 0.021 0.011 -10000 0 -10000 0 0
AKT1 -0.024 0.069 0.17 27 -0.29 5 32
IKBKG 0.027 0.002 -10000 0 -10000 0 0
BDNF -0.039 0.13 -10000 0 -0.31 96 96
MGDIs/NGR/p75(NTR)/LINGO1 0.041 0.073 -10000 0 -0.18 40 40
FURIN 0.027 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.008 0.11 -10000 0 -0.21 110 110
LINGO1 0.042 0.045 0.17 51 -10000 0 51
Sortilin/TRAF6/NRIF 0.033 0.014 -10000 0 -10000 0 0
proBDNF (dimer) -0.039 0.13 -10000 0 -0.31 96 96
NTRK1 0.01 0.078 0.17 8 -0.31 26 34
RTN4R 0.026 0.005 -10000 0 -10000 0 0
neuron apoptosis -0.042 0.13 0.35 6 -0.33 47 53
IRAK1 0.027 0.002 -10000 0 -10000 0 0
SHC1 -0.032 0.055 -10000 0 -0.19 54 54
ARHGDIA 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.072 0.025 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.037 0.082 -10000 0 -0.17 60 60
MAGEH1 0.028 0.023 0.17 7 -0.31 1 8
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.036 0.081 -10000 0 -0.18 59 59
Mammalian IAPs/DIABLO 0.063 0.026 -10000 0 -0.17 2 2
proNGF (dimer) 0.013 0.068 0.17 2 -0.31 21 23
MAGED1 0.027 0.007 0.17 1 -10000 0 1
APP 0.025 0.022 -10000 0 -0.31 2 2
NT-4/5 (dimer) -0.048 0.14 -10000 0 -0.31 109 109
ZNF274 0.027 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.011 0.064 -10000 0 -0.16 59 59
NGF 0.013 0.069 0.17 2 -0.31 21 23
cell cycle arrest 0 0.084 0.24 25 -0.26 2 27
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.003 0.065 -10000 0 -0.19 46 46
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.01 0.12 -10000 0 -0.22 113 113
NCSTN 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0.022 0.079 -10000 0 -0.18 60 60
PSENEN 0.027 0.003 -10000 0 -10000 0 0
mol:ceramide -0.024 0.054 0.18 10 -0.17 42 52
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.003 0.055 -10000 0 -0.29 3 3
p75(NTR)/beta APP 0.017 0.071 -10000 0 -0.22 40 40
BEX1 -0.073 0.16 0.17 5 -0.31 149 154
mol:GDP -0.03 0.057 -10000 0 -0.18 60 60
NGF (dimer) 0.05 0.088 0.24 2 -0.17 51 53
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.055 0.074 -10000 0 -0.17 40 40
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
RAC1/GTP 0.019 0.065 -10000 0 -0.16 56 56
MYD88 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.025 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.022 0.08 -10000 0 -0.19 60 60
RHOB 0.021 0.042 -10000 0 -0.31 8 8
RHOA 0.026 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.041 0.021 0.14 16 -10000 0 16
NT3 (dimer) -0.005 0.095 -10000 0 -0.31 44 44
TP53 -0.039 0.086 0.22 18 -0.27 20 38
PRDM4 -0.031 0.056 0.18 7 -0.17 56 63
BDNF (dimer) -0.001 0.14 0.25 7 -0.19 146 153
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
SORT1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.038 0.077 -10000 0 -0.16 59 59
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.037 0.078 -10000 0 -0.17 57 57
RHOC 0.027 0.004 -10000 0 -10000 0 0
XIAP 0.027 0.001 -10000 0 -10000 0 0
MAPK10 -0.037 0.12 0.41 7 -0.3 46 53
DIABLO 0.026 0.006 -10000 0 -10000 0 0
SMPD2 -0.024 0.055 0.18 10 -0.17 42 52
APH1B 0.027 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.023 0.08 -10000 0 -0.19 60 60
PSEN1 0.026 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.004 0.1 -10000 0 -0.24 70 70
MAPK8 -0.041 0.12 0.44 6 -0.3 51 57
MAPK9 -0.037 0.11 0.4 7 -0.29 46 53
APAF1 0.026 0.006 -10000 0 -10000 0 0
NTF3 -0.005 0.095 -10000 0 -0.31 44 44
NTF4 -0.048 0.14 -10000 0 -0.31 109 109
NDN 0.024 0.026 -10000 0 -0.31 3 3
RAC1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.035 0.079 -10000 0 -0.16 58 58
p75 CTF/Sortilin/TRAF6/NRIF 0.062 0.032 -10000 0 -0.17 6 6
RhoA-B-C/GTP 0.021 0.079 -10000 0 -0.18 60 60
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.016 0.11 -10000 0 -0.18 110 110
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.006 0.11 -10000 0 -0.19 110 110
PRKACB 0.026 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.012 0.1 -10000 0 -0.22 95 95
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.025 0.025 0.17 3 -0.31 2 5
BIRC2 0.026 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.003 0.08 0.28 6 -0.2 29 35
BAD -0.035 0.13 0.32 19 -0.3 48 67
RIPK2 0.021 0.011 -10000 0 -10000 0 0
NGFR -0.001 0.093 -10000 0 -0.31 41 41
CYCS -0.03 0.056 0.2 8 -0.26 3 11
ADAM17 0.022 0.037 -10000 0 -0.31 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.032 0.076 -10000 0 -0.17 48 48
BCL2L11 -0.037 0.13 0.31 18 -0.3 48 66
BDNF (dimer)/p75(NTR) -0.027 0.12 -10000 0 -0.25 111 111
PI3K 0.029 0.08 -10000 0 -0.17 59 59
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.036 0.079 -10000 0 -0.17 58 58
NDNL2 0.026 0.005 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.025 0.01 0.17 1 -10000 0 1
NGF (dimer)/p75(NTR) 0.007 0.086 -10000 0 -0.22 60 60
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.037 0.08 -10000 0 -0.17 60 60
TRAF6 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
PLG 0.029 0.033 0.17 23 -10000 0 23
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.039 0.11 0.15 3 -0.21 119 122
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
NGFRAP1 0.027 0.001 -10000 0 -10000 0 0
CASP3 -0.032 0.12 0.31 18 -0.29 48 66
E2F1 0.032 0.028 0.17 18 -10000 0 18
CASP9 0.027 0.003 -10000 0 -10000 0 0
IKK complex 0.026 0.088 -10000 0 -0.24 23 23
NGF (dimer)/TRKA 0.016 0.078 0.14 10 -0.22 46 56
MMP7 0.017 0.1 0.17 50 -0.31 35 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.046 0.079 -10000 0 -0.16 56 56
MMP3 0.003 0.1 0.17 31 -0.31 45 76
APAF-1/Caspase 9 -0.04 0.043 -10000 0 -0.23 5 5
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0.15 0.43 2 -0.53 6 8
CRP 0.001 0.15 0.53 3 -0.61 3 6
cell cycle arrest -0.005 0.16 -10000 0 -0.57 10 10
TIMP1 0.003 0.17 -10000 0 -0.82 9 9
IL6ST -0.033 0.12 -10000 0 -0.3 82 82
Rac1/GDP -0.053 0.17 -10000 0 -0.36 90 90
AP1 0.017 0.13 -10000 0 -0.52 13 13
GAB2 0.026 0.006 -10000 0 -10000 0 0
TNFSF11 -0.005 0.16 0.47 1 -0.66 10 11
HSP90B1 0.027 0.079 -10000 0 -0.63 3 3
GAB1 0.026 0.016 -10000 0 -0.31 1 1
MAPK14 -0.11 0.24 0.23 2 -0.57 87 89
AKT1 0.024 0.065 0.25 2 -0.48 4 6
FOXO1 0.018 0.062 0.24 2 -0.45 4 6
MAP2K6 -0.086 0.2 -10000 0 -0.45 95 95
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.043 0.16 0.3 3 -0.36 69 72
MITF -0.064 0.16 -10000 0 -0.37 91 91
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.003 -10000 0 -10000 0 0
A2M -0.058 0.3 -10000 0 -1.1 35 35
CEBPB 0.03 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.002 0.1 -10000 0 -0.45 13 13
STAT3 -0.01 0.16 -10000 0 -0.6 10 10
STAT1 0.015 0.075 -10000 0 -0.87 3 3
CEBPD 0.016 0.16 -10000 0 -0.6 3 3
PIK3CA 0.024 0.027 -10000 0 -0.31 3 3
PI3K 0.032 0.035 -10000 0 -0.24 6 6
JUN 0.024 0.031 0.17 1 -0.31 4 5
PIAS3/MITF -0.055 0.17 0.22 3 -0.36 90 93
MAPK11 -0.11 0.24 0.23 2 -0.58 88 90
STAT3 (dimer)/FOXO1 0.004 0.13 0.37 1 -0.47 6 7
GRB2/SOS1/GAB family -0.032 0.16 -10000 0 -0.32 85 85
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.06 0.16 0.16 4 -0.34 95 99
GRB2 0.026 0.005 -10000 0 -10000 0 0
JAK2 0.026 0.016 -10000 0 -0.31 1 1
LBP 0.01 0.14 0.46 1 -0.55 4 5
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
JAK1 0.021 0.021 -10000 0 -10000 0 0
MYC 0.03 0.16 0.48 6 -0.61 2 8
FGG -0.006 0.14 -10000 0 -0.58 4 4
macrophage differentiation -0.005 0.16 -10000 0 -0.57 10 10
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.009 0.15 -10000 0 -0.23 127 127
JUNB -0.015 0.19 0.51 1 -0.91 12 13
FOS -0.026 0.12 0.17 4 -0.31 78 82
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.061 0.17 -10000 0 -0.38 93 93
STAT1/PIAS1 -0.025 0.15 0.28 2 -0.31 70 72
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.068 -10000 0 -0.45 5 5
STAT3 (dimer) -0.006 0.16 -10000 0 -0.61 9 9
PRKCD -0.022 0.17 0.31 18 -0.47 25 43
IL6R -0.004 0.089 -10000 0 -0.31 37 37
SOCS3 -0.16 0.38 0.42 1 -1.1 60 61
gp130 (dimer)/JAK1/JAK1/LMO4 0.005 0.095 -10000 0 -0.18 85 85
Rac1/GTP -0.049 0.17 -10000 0 -0.36 84 84
HCK 0.024 0.031 0.17 1 -0.31 4 5
MAPKKK cascade 0.011 0.11 -10000 0 -0.54 12 12
bone resorption -0.003 0.15 0.47 1 -0.62 10 11
IRF1 -0.002 0.15 0.43 2 -0.54 7 9
mol:GDP -0.066 0.17 -10000 0 -0.37 94 94
SOS1 0.026 0.005 -10000 0 -10000 0 0
VAV1 -0.067 0.17 -10000 0 -0.37 95 95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.27 0.32 1 -0.58 99 100
PTPN11 0.008 0.086 -10000 0 -0.68 7 7
IL6/IL6RA -0.016 0.13 0.15 43 -0.23 114 157
gp130 (dimer)/TYK2/TYK2/LMO4 0.006 0.091 -10000 0 -0.18 82 82
gp130 (dimer)/JAK2/JAK2/LMO4 0.006 0.091 -10000 0 -0.18 82 82
IL6 -0.022 0.15 0.18 46 -0.32 90 136
PIAS3 0.026 0.005 -10000 0 -10000 0 0
PTPRE 0.016 0.035 0.16 1 -0.31 4 5
PIAS1 0.026 0.015 -10000 0 -0.31 1 1
RAC1 0.025 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.058 0.15 0.16 5 -0.28 138 143
LMO4 0.022 0.03 -10000 0 -0.38 1 1
STAT3 (dimer)/PIAS3 -0.01 0.16 -10000 0 -0.56 12 12
MCL1 0.03 0.079 0.38 5 -0.79 1 6
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.026 0.12 0.39 6 -0.46 5 11
CRKL -0.004 0.079 0.18 50 -0.2 5 55
mol:DAG 0.005 0.077 0.17 2 -0.23 37 39
HRAS -0.005 0.088 0.28 21 -0.21 3 24
MAPK8 -0.002 0.084 0.18 67 -0.16 43 110
RAP1A -0.004 0.08 0.18 51 -0.21 5 56
GAB1 -0.004 0.08 0.18 52 -0.21 6 58
MAPK14 0.002 0.083 0.18 70 -0.16 36 106
EPO 0.005 0.1 0.19 25 -0.31 40 65
PLCG1 0.005 0.079 0.17 2 -0.24 37 39
EPOR/TRPC2/IP3 Receptors 0.027 0.032 0.19 10 -10000 0 10
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.012 0.099 0.21 2 -0.19 85 87
GAB1/SHC/GRB2/SOS1 0.034 0.071 0.27 2 -0.2 6 8
EPO/EPOR (dimer) 0.024 0.082 0.16 32 -0.22 41 73
IRS2 -0.009 0.073 0.17 40 -0.2 6 46
STAT1 0.007 0.088 0.21 4 -0.24 41 45
STAT5B 0.005 0.082 -10000 0 -0.24 37 37
cell proliferation 0.006 0.1 0.21 79 -0.17 12 91
GAB1/SHIP/PIK3R1/SHP2/SHC 0.01 0.077 -10000 0 -0.25 17 17
TEC -0.004 0.079 0.18 49 -0.21 5 54
SOCS3 -0.012 0.11 0.17 6 -0.31 58 64
STAT1 (dimer) 0.008 0.087 0.21 4 -0.24 41 45
JAK2 0.023 0.025 -10000 0 -0.31 1 1
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
EPO/EPOR (dimer)/JAK2 0.048 0.079 0.24 2 -0.16 40 42
EPO/EPOR 0.024 0.082 0.16 32 -0.22 41 73
LYN 0.022 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.016 0.068 0.21 9 -0.21 5 14
elevation of cytosolic calcium ion concentration 0.027 0.032 0.19 10 -10000 0 10
SHC1 0.026 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.032 0.072 0.2 1 -0.18 38 39
mol:IP3 0.005 0.077 0.17 2 -0.23 37 39
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.016 0.086 0.29 4 -0.24 17 21
SH2B3 0.022 0.02 -10000 0 -10000 0 0
NFKB1 0.002 0.083 0.18 71 -0.16 34 105
EPO/EPOR (dimer)/JAK2/SOCS3 -0.019 0.08 -10000 0 -0.19 79 79
PTPN6 0.009 0.073 0.17 51 -0.2 7 58
TEC/VAV2/GRB2 0.029 0.069 0.25 4 -0.2 5 9
EPOR 0.027 0.032 0.19 10 -10000 0 10
INPP5D 0.01 0.074 -10000 0 -0.31 25 25
mol:GDP 0.033 0.071 0.27 2 -0.2 6 8
SOS1 0.026 0.005 -10000 0 -10000 0 0
PLCG2 0.021 0.026 0.17 2 -0.31 2 4
CRKL/CBL/C3G 0.027 0.069 0.27 3 -0.22 5 8
VAV2 -0.008 0.072 0.17 43 -0.21 5 48
CBL -0.008 0.075 0.18 41 -0.22 6 47
SHC/Grb2/SOS1 0.021 0.062 -10000 0 -0.2 5 5
STAT5A 0.005 0.082 -10000 0 -0.24 36 36
GRB2 0.026 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.018 0.092 -10000 0 -0.3 17 17
LYN/PLCgamma2 0.028 0.026 0.14 2 -0.22 2 4
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
BTK -0.003 0.083 0.18 53 -0.21 8 61
BCL2 0.002 0.18 0.4 6 -0.67 24 30
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.02 0.069 0.3 2 -0.17 23 25
alphaM/beta2 Integrin/GPIbA 0.021 0.067 0.28 3 -0.16 22 25
alphaM/beta2 Integrin/proMMP-9 0.073 0.093 0.23 10 -0.15 24 34
PLAUR 0.029 0.019 0.17 8 -10000 0 8
HMGB1 0.008 0.036 -10000 0 -0.13 2 2
alphaM/beta2 Integrin/Talin 0.024 0.061 0.25 2 -0.14 16 18
AGER 0.013 0.053 0.17 19 -0.28 3 22
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.027 0.023 0.17 6 -0.31 1 7
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.012 0.12 0.28 3 -0.2 114 117
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.1 0.085 0.17 258 -0.31 5 263
CYR61 0.022 0.051 0.17 7 -0.31 10 17
TLN1 0.026 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.013 0.098 -10000 0 -0.25 38 38
RHOA 0.026 0.005 -10000 0 -10000 0 0
P-selectin oligomer 0.02 0.045 -10000 0 -0.31 9 9
MYH2 -0.05 0.11 0.16 1 -0.32 46 47
MST1R 0.02 0.052 0.17 4 -0.31 11 15
leukocyte activation during inflammatory response -0.03 0.11 -10000 0 -0.19 141 141
APOB -0.047 0.14 0.17 2 -0.31 108 110
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.048 0.17 1 -0.31 10 11
JAM3 0.016 0.058 -10000 0 -0.31 15 15
GP1BA 0.021 0.042 0.17 3 -0.31 7 10
alphaM/beta2 Integrin/CTGF 0.016 0.076 0.25 2 -0.21 25 27
alphaM/beta2 Integrin -0.028 0.1 -10000 0 -0.28 41 41
JAM3 homodimer 0.016 0.058 -10000 0 -0.31 15 15
ICAM2 0.026 0.017 0.17 1 -0.31 1 2
ICAM1 0.03 0.022 0.17 11 -10000 0 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.027 0.1 0.19 1 -0.28 41 42
cell adhesion 0.02 0.066 0.28 3 -0.16 22 25
NFKB1 -0.055 0.17 0.36 5 -0.33 115 120
THY1 0.028 0.025 0.17 8 -0.31 1 9
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.033 0.11 0.13 8 -0.2 146 154
alphaM/beta2 Integrin/LRP/tPA 0.029 0.07 0.23 3 -0.21 11 14
IL6 -0.11 0.25 0.48 4 -0.55 109 113
ITGB2 0.009 0.042 0.17 5 -0.098 15 20
elevation of cytosolic calcium ion concentration 0.029 0.075 0.34 2 -0.19 17 19
alphaM/beta2 Integrin/JAM2/JAM3 0.028 0.08 0.25 2 -0.21 23 25
JAM2 0.023 0.034 -10000 0 -0.31 5 5
alphaM/beta2 Integrin/ICAM1 0.053 0.082 0.26 4 -0.18 17 21
alphaM/beta2 Integrin/uPA/Plg 0.032 0.077 0.3 2 -0.2 17 19
RhoA/GTP -0.036 0.11 0.17 1 -0.32 40 41
positive regulation of phagocytosis -0.015 0.093 0.2 3 -0.27 24 27
Ron/MSP 0.046 0.053 0.15 58 -0.22 11 69
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.077 0.27 4 -0.2 17 21
alphaM/beta2 Integrin/uPAR 0.025 0.064 0.23 4 -0.13 22 26
PLAU 0.019 0.05 0.17 1 -0.31 11 12
PLAT 0.021 0.042 0.17 12 -0.31 5 17
actin filament polymerization -0.048 0.11 -10000 0 -0.3 46 46
MST1 0.043 0.047 0.17 56 -10000 0 56
alphaM/beta2 Integrin/lipoprotein(a) -0.027 0.12 0.18 2 -0.19 141 143
TNF -0.081 0.18 0.39 6 -0.37 113 119
RAP1B 0.026 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.019 0.071 0.3 2 -0.21 18 20
fibrinolysis 0.03 0.075 0.29 2 -0.2 17 19
HCK 0.024 0.031 0.17 1 -0.31 4 5
dendritic cell antigen processing and presentation -0.027 0.1 0.19 1 -0.28 41 42
VTN 0.007 0.12 0.17 51 -0.31 51 102
alphaM/beta2 Integrin/CYR61 0.022 0.07 0.3 2 -0.17 24 26
LPA -0.013 0.11 0.17 7 -0.31 60 67
LRP1 0.026 0.017 0.17 1 -0.31 1 2
cell migration 0.016 0.075 0.19 10 -0.2 22 32
FN1 0.02 0.052 0.17 4 -0.31 11 15
alphaM/beta2 Integrin/Thy1 0.025 0.065 0.3 2 -0.15 17 19
MPO 0 0.089 -10000 0 -0.31 38 38
KNG1 0.037 0.05 0.17 58 -10000 0 58
RAP1/GDP 0.034 0.01 -10000 0 -10000 0 0
ROCK1 -0.035 0.11 0.16 1 -0.31 37 38
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.029 0.033 0.17 23 -10000 0 23
CTGF 0.014 0.065 0.17 1 -0.31 19 20
alphaM/beta2 Integrin/Hck 0.023 0.066 0.3 2 -0.2 11 13
ITGAM 0.005 0.048 0.18 2 -0.24 7 9
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.032 0.074 0.26 5 -0.22 12 17
HP 0.026 0.079 0.17 51 -0.31 17 68
leukocyte adhesion -0.003 0.11 0.25 3 -0.25 38 41
SELP 0.02 0.045 -10000 0 -0.31 9 9
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.042 0.14 0.34 63 -10000 0 63
GNAI2 0.026 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0.072 -10000 0 -0.18 67 67
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.024 0.12 -10000 0 -0.31 71 71
RhoA/GTP -0.043 0.14 -10000 0 -0.34 63 63
negative regulation of cAMP metabolic process -0.044 0.14 -10000 0 -0.28 107 107
GNAZ -0.002 0.094 -10000 0 -0.31 42 42
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.024 0.008 -10000 0 -10000 0 0
S1PR5 -0.026 0.12 -10000 0 -0.31 78 78
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.045 0.14 -10000 0 -0.28 107 107
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.001 0.021 -10000 0 -0.085 1 1
NFATC2 -0.028 0.071 -10000 0 -0.18 77 77
NFATC3 0.001 0.02 -10000 0 -10000 0 0
CD40LG -0.074 0.15 0.33 1 -0.36 73 74
PTGS2 -0.088 0.17 0.33 1 -0.39 96 97
JUNB 0.024 0.053 0.17 12 -0.31 10 22
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.02 -10000 0 -10000 0 0
CALM1 0.02 0.018 -10000 0 -10000 0 0
JUN 0.018 0.036 0.17 1 -0.32 4 5
mol:Ca2+ -0.003 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.006 -10000 0 -10000 0 0
FOSL1 -0.012 0.13 0.17 33 -0.31 70 103
CREM 0.026 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.008 0.1 -10000 0 -0.24 34 34
FOS -0.031 0.13 0.17 4 -0.32 78 82
IFNG -0.067 0.13 0.27 2 -0.33 64 66
AP-1/NFAT1-c-4 -0.031 0.18 0.36 1 -0.37 71 72
FASLG -0.071 0.14 0.33 1 -0.35 68 69
NFAT1-c-4/ICER1 -0.019 0.077 -10000 0 -0.17 73 73
IL2RA -0.064 0.14 0.27 2 -0.34 69 71
FKBP12/FK506 0.02 0.003 -10000 0 -10000 0 0
CSF2 -0.071 0.13 -10000 0 -0.33 67 67
JunB/Fra1/NFAT1-c-4 -0.023 0.11 0.22 4 -0.22 65 69
IL4 -0.072 0.13 -10000 0 -0.34 66 66
IL2 -0.005 0.15 -10000 0 -0.94 12 12
IL3 -0.012 0.14 -10000 0 -0.65 21 21
FKBP1A 0.027 0.004 -10000 0 -10000 0 0
BATF3 0.032 0.031 0.17 22 -10000 0 22
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.006 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.017 0.17 6 -10000 0 6
EGFR -0.002 0.09 -10000 0 -0.31 39 39
EGF/EGFR 0.005 0.11 0.2 2 -0.19 95 97
EGF/EGFR dimer/SHC/GRB2/SOS1 0.045 0.083 -10000 0 -0.17 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.007 0.1 -10000 0 -0.31 50 50
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.023 0.084 0.17 40 -0.31 23 63
EGF/EGFR dimer/SHC 0.027 0.083 -10000 0 -0.19 52 52
mol:GDP 0.04 0.079 -10000 0 -0.17 49 49
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.013 0.076 0.17 10 -0.31 24 34
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.024 0.067 -10000 0 -0.16 49 49
SHC1 0.026 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.038 0.077 -10000 0 -0.16 49 49
FRAP1 -0.029 0.049 0.13 7 -0.16 49 56
EGF/EGFR dimer 0.013 0.092 0.14 34 -0.23 56 90
SOS1 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.005 0.1 0.14 9 -0.25 61 70
Nongenotropic Androgen 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
PTK2 -0.005 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.065 -10000 0 -0.16 49 49
regulation of S phase of mitotic cell cycle -0.004 0.072 -10000 0 -0.21 45 45
GNAO1 -0.024 0.12 -10000 0 -0.31 71 71
HRAS 0.028 0.017 0.17 6 -10000 0 6
SHBG/T-DHT 0.015 0.019 0.11 5 -0.15 4 9
PELP1 0.024 0.01 -10000 0 -10000 0 0
AKT1 -0.005 0.004 -10000 0 -10000 0 0
MAP2K1 -0.039 0.065 0.21 7 -0.21 14 21
T-DHT/AR -0.002 0.065 -10000 0 -0.21 43 43
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 84 84
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
mol:GDP -0.033 0.097 -10000 0 -0.34 43 43
cell proliferation -0.07 0.17 0.32 9 -0.41 80 89
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
FOS -0.12 0.28 0.3 5 -0.73 84 89
mol:Ca2+ -0.011 0.027 -10000 0 -0.067 79 79
MAPK3 -0.049 0.12 0.31 11 -0.29 71 82
MAPK1 -0.03 0.097 0.24 3 -0.31 19 22
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
mol:IP3 -0.001 0.002 -10000 0 -0.005 84 84
cAMP biosynthetic process 0.002 0.024 0.083 6 -0.17 3 9
GNG2 0.023 0.037 -10000 0 -0.31 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 84 84
HRAS/GTP 0.014 0.068 -10000 0 -0.16 46 46
actin cytoskeleton reorganization 0.032 0.026 -10000 0 -0.18 4 4
SRC 0.025 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 84 84
PI3K 0.028 0.029 -10000 0 -0.2 6 6
apoptosis 0.06 0.17 0.41 83 -0.28 7 90
T-DHT/AR/PELP1 0.013 0.06 -10000 0 -0.18 43 43
HRAS/GDP -0.018 0.1 -10000 0 -0.33 43 43
CREB1 -0.065 0.18 0.29 7 -0.44 83 90
RAC1-CDC42/GTP 0.04 0.03 -10000 0 -0.18 4 4
AR -0.004 0.095 -10000 0 -0.31 43 43
GNB1 0.027 0.004 -10000 0 -10000 0 0
RAF1 -0.032 0.06 0.22 8 -0.2 11 19
RAC1-CDC42/GDP 0.005 0.1 -10000 0 -0.31 43 43
T-DHT/AR/PELP1/Src 0.019 0.063 -10000 0 -0.16 44 44
MAP2K2 -0.039 0.065 0.21 7 -0.21 15 22
T-DHT/AR/PELP1/Src/PI3K -0.004 0.072 -10000 0 -0.21 45 45
GNAZ -0.002 0.094 -10000 0 -0.31 42 42
SHBG 0.022 0.032 0.17 5 -0.31 3 8
Gi family/GNB1/GNG2/GDP -0.05 0.14 -10000 0 -0.35 74 74
mol:T-DHT 0 0.002 -10000 0 -0.003 64 64
RAC1 0.025 0.008 -10000 0 -10000 0 0
GNRH1 -0.005 0.008 -10000 0 -10000 0 0
Gi family/GTP -0.035 0.094 -10000 0 -0.26 60 60
CDC42 0.027 0.003 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.01 0.08 0.2 9 -0.2 20 29
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.09 0.35 1 -0.28 17 18
alphaV/beta3 Integrin/Osteopontin/Src 0.051 0.046 0.15 56 -0.19 4 60
AP1 -0.019 0.13 0.23 1 -0.32 39 40
ILK -0.021 0.078 0.2 9 -0.2 21 30
bone resorption -0.028 0.094 0.16 9 -0.28 41 50
PTK2B 0.019 0.012 -10000 0 -10000 0 0
PYK2/p130Cas 0.021 0.094 0.26 2 -0.21 16 18
ITGAV 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.013 0.079 -10000 0 -0.23 45 45
alphaV/beta3 Integrin/Osteopontin 0.021 0.1 -10000 0 -0.18 88 88
MAP3K1 -0.019 0.072 0.18 6 -0.17 73 79
JUN 0.024 0.031 0.17 1 -0.31 4 5
MAPK3 -0.037 0.075 0.22 11 -0.26 14 25
MAPK1 -0.038 0.075 0.22 10 -0.26 14 24
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.037 0.07 0.18 8 -0.23 25 33
ITGB3 -0.036 0.13 -10000 0 -0.31 92 92
NFKBIA -0.03 0.082 0.2 7 -0.3 17 24
FOS -0.026 0.12 0.17 4 -0.31 78 82
CD44 0.02 0.045 -10000 0 -0.31 9 9
CHUK 0.025 0.007 -10000 0 -10000 0 0
PLAU -0.047 0.18 0.52 1 -1.1 12 13
NF kappa B1 p50/RelA 0.008 0.095 0.31 1 -0.36 12 13
BCAR1 0.022 0.011 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.008 0.099 -10000 0 -0.21 92 92
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.022 0.08 0.2 8 -0.18 83 91
VAV3 -0.051 0.093 0.22 10 -0.28 36 46
MAP3K14 -0.02 0.078 0.2 9 -0.17 79 88
ROCK2 -0.001 0.093 -10000 0 -0.31 41 41
SPP1 0.045 0.06 0.18 69 -0.31 3 72
RAC1 0.025 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.031 0.089 0.19 7 -0.26 31 38
MMP2 -0.054 0.096 -10000 0 -0.32 33 33
Wnt 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
Noncanonical Wnts/FZD -0.019 0.1 -10000 0 -0.24 71 71
FZD6 0.021 0.011 -10000 0 -10000 0 0
WNT6 -0.03 0.13 0.17 7 -0.31 87 94
WNT4 0.023 0.034 -10000 0 -0.31 5 5
FZD3 0.02 0.012 -10000 0 -10000 0 0
WNT5A 0.015 0.074 0.17 12 -0.31 22 34
WNT11 0.027 0.054 0.17 23 -0.31 8 31
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.044 -10000 0 -0.34 6 6
Crk/p130 Cas/Paxillin -0.022 0.086 -10000 0 -0.24 51 51
JUN -0.023 0.082 -10000 0 -0.3 24 24
HRAS 0.028 0.017 0.17 6 -10000 0 6
RET51/GFRalpha1/GDNF/GRB10 0.042 0.093 -10000 0 -0.19 54 54
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.044 0.099 -10000 0 -0.19 60 60
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.019 0.083 -10000 0 -0.19 60 60
RHOA 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.034 0.09 -10000 0 -0.18 60 60
GRB7 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.044 0.098 -10000 0 -0.19 61 61
MAPKKK cascade 0.011 0.082 -10000 0 -0.2 52 52
BCAR1 0.022 0.011 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.017 0.082 -10000 0 -0.18 65 65
lamellipodium assembly -0.012 0.085 -10000 0 -0.23 54 54
RET51/GFRalpha1/GDNF/SHC 0.042 0.097 -10000 0 -0.19 60 60
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
RET9/GFRalpha1/GDNF/SHC 0.021 0.072 -10000 0 -0.17 55 55
RET9/GFRalpha1/GDNF/Shank3 0.022 0.072 -10000 0 -0.17 57 57
MAPK3 -0.03 0.076 0.22 19 -0.25 16 35
DOK1 0.026 0.016 -10000 0 -0.31 1 1
DOK6 0.017 0.065 0.17 14 -0.31 16 30
PXN 0.026 0.006 -10000 0 -10000 0 0
neurite development -0.028 0.069 0.21 12 -0.26 14 26
DOK5 0.014 0.073 0.17 9 -0.31 22 31
GFRA1 -0.001 0.093 0.17 1 -0.31 41 42
MAPK8 -0.017 0.082 -10000 0 -0.22 54 54
HRAS/GTP 0.034 0.1 0.21 2 -0.22 53 55
tube development 0.022 0.072 0.21 9 -0.16 55 64
MAPK1 -0.029 0.079 0.22 19 -0.25 16 35
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.003 0.067 -10000 0 -0.19 53 53
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
PDLIM7 0.019 0.053 0.17 2 -0.31 12 14
RET51/GFRalpha1/GDNF/Dok6 0.042 0.1 -10000 0 -0.19 67 67
SHC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.039 0.1 -10000 0 -0.19 61 61
RET51/GFRalpha1/GDNF/Dok5 0.038 0.11 0.25 5 -0.21 68 73
PRKCA 0.011 0.069 -10000 0 -0.31 22 22
HRAS/GDP 0.021 0.012 0.12 6 -10000 0 6
CREB1 -0.007 0.088 -10000 0 -0.23 54 54
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.004 0.071 -10000 0 -0.2 53 53
RET51/GFRalpha1/GDNF/Grb7 0.043 0.098 -10000 0 -0.19 62 62
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.044 0.075 0.17 81 -0.31 10 91
DOK4 0.022 0.031 -10000 0 -0.31 4 4
JNK cascade -0.021 0.083 0.24 2 -0.3 24 26
RET9/GFRalpha1/GDNF/FRS2 0.022 0.071 -10000 0 -0.17 55 55
SHANK3 0.027 0.004 -10000 0 -10000 0 0
RASA1 0.025 0.016 -10000 0 -0.31 1 1
NCK1 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.004 0.07 -10000 0 -0.2 53 53
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0 0.078 0.15 1 -0.2 60 61
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.001 0.086 0.15 1 -0.22 55 56
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.001 0.082 0.15 1 -0.21 59 60
PI3K -0.021 0.12 0.24 3 -0.31 61 64
SOS1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.032 0.073 -10000 0 -0.16 55 55
GRB10 0.025 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.006 0.081 -10000 0 -0.21 59 59
RET51/GFRalpha1/GDNF/FRS2 0.044 0.096 -10000 0 -0.18 60 60
GAB1 0.026 0.016 -10000 0 -0.31 1 1
IRS1 0.017 0.058 -10000 0 -0.31 15 15
IRS2 0.026 0.02 0.17 3 -0.31 1 4
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.002 0.087 0.15 1 -0.22 61 62
RET51/GFRalpha1/GDNF/PKC alpha 0.035 0.11 0.18 1 -0.21 69 70
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GDNF 0.009 0.07 -10000 0 -0.31 23 23
RAC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.039 0.11 -10000 0 -0.2 69 69
Rac1/GTP -0.012 0.1 -10000 0 -0.27 52 52
RET9/GFRalpha1/GDNF 0.008 0.073 0.13 1 -0.19 57 58
GFRalpha1/GDNF 0.006 0.086 0.14 1 -0.23 57 58
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.06 0.07 0.28 10 -0.19 21 31
MAP4K1 0.031 0.048 0.17 26 -0.31 5 31
MAP3K8 0.018 0.054 0.17 1 -0.31 13 14
PRKCB -0.047 0.14 -10000 0 -0.31 107 107
DBNL 0.025 0.008 -10000 0 -10000 0 0
CRKL 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.058 0.17 1 -0.36 6 7
JUN -0.12 0.25 0.35 1 -0.54 122 123
MAP3K7 0.009 0.049 0.17 1 -0.34 4 5
GRAP2 0.016 0.06 0.17 2 -0.31 16 18
CRK 0.025 0.007 -10000 0 -10000 0 0
MAP2K4 0.002 0.073 0.27 5 -0.35 10 15
LAT 0.029 0.032 0.17 13 -0.31 2 15
LCP2 0.025 0.03 0.17 4 -0.31 3 7
MAPK8 -0.12 0.26 -10000 0 -0.56 122 122
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.017 0.064 0.18 1 -0.24 18 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.065 0.069 0.29 9 -0.18 19 28
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.017 0.11 -10000 0 -0.18 101 101
SMAD6-7/SMURF1 0.04 0.037 -10000 0 -0.18 9 9
NOG -0.011 0.11 0.17 1 -0.31 55 56
SMAD9 -0.073 0.19 -10000 0 -0.43 102 102
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD5 -0.007 0.072 0.25 1 -0.29 14 15
BMP7/USAG1 -0.073 0.15 -10000 0 -0.26 175 175
SMAD5/SKI 0.006 0.081 0.23 3 -0.3 11 14
SMAD1 0.02 0.032 -10000 0 -0.23 1 1
BMP2 0.006 0.08 0.17 1 -0.31 30 31
SMAD1/SMAD1/SMAD4 0.03 0.036 -10000 0 -10000 0 0
BMPR1A 0.024 0.017 -10000 0 -0.31 1 1
BMPR1B 0.025 0.029 0.17 3 -0.31 3 6
BMPR1A-1B/BAMBI 0.05 0.033 -10000 0 -0.17 4 4
AHSG 0.03 0.04 0.17 35 -10000 0 35
CER1 0.022 0.021 0.17 9 -10000 0 9
BMP2-4/CER1 0.026 0.08 -10000 0 -0.22 41 41
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.007 0.1 0.19 1 -0.32 33 34
BMP2-4 (homodimer) 0.014 0.087 0.14 1 -0.26 41 42
RGMB 0.024 0.009 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.067 0.043 -10000 0 -0.17 3 3
RGMA 0.012 0.069 -10000 0 -0.31 22 22
SMURF1 0.024 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.011 0.095 -10000 0 -0.32 32 32
BMP2-4/USAG1 -0.038 0.13 -10000 0 -0.22 155 155
SMAD6/SMURF1/SMAD5 0.004 0.073 0.26 1 -0.3 9 10
SOSTDC1 -0.079 0.15 -10000 0 -0.31 151 151
BMP7/BMPR2/BMPR1A-1B 0.019 0.09 -10000 0 -0.16 90 90
SKI 0.027 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.043 0.047 0.17 57 -10000 0 57
HFE2 0.037 0.046 0.17 50 -10000 0 50
ZFYVE16 0.025 0.007 -10000 0 -10000 0 0
MAP3K7 0.022 0.01 -10000 0 -10000 0 0
BMP2-4/CHRD 0.035 0.087 -10000 0 -0.22 41 41
SMAD5/SMAD5/SMAD4 0.007 0.079 0.3 2 -0.3 11 13
MAPK1 0.027 0.004 -10000 0 -10000 0 0
TAK1/TAB family 0.003 0.086 -10000 0 -0.29 24 24
BMP7 (homodimer) -0.034 0.13 0.17 1 -0.31 89 90
NUP214 0.026 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.051 0.046 0.16 53 -10000 0 53
SMAD1/SKI 0.037 0.043 0.29 3 -10000 0 3
SMAD6 0.021 0.045 -10000 0 -0.31 9 9
CTDSP2 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.031 0.083 -10000 0 -0.23 39 39
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.008 0.1 0.17 31 -0.31 41 72
BMPR2 (homodimer) 0.027 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.048 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.034 0.026 0.14 2 -0.2 4 6
CHRDL1 -0.058 0.15 -10000 0 -0.31 125 125
ENDOFIN/SMAD1 0.035 0.045 0.32 4 -10000 0 4
SMAD6-7/SMURF1/SMAD1 0.044 0.048 0.28 2 -10000 0 2
SMAD6/SMURF1 0.024 0.008 -10000 0 -10000 0 0
BAMBI 0.033 0.029 0.17 20 -10000 0 20
SMURF2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.022 0.14 -10000 0 -0.23 128 128
BMP2-4/GREM1 0.018 0.11 -10000 0 -0.22 71 71
SMAD7 0.025 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.065 0.19 -10000 0 -0.41 108 108
SMAD1/SMAD6 0.031 0.038 0.28 2 -10000 0 2
TAK1/SMAD6 0.031 0.017 -10000 0 -10000 0 0
BMP7 -0.034 0.13 0.17 1 -0.31 89 90
BMP6 0.043 0.048 0.17 57 -10000 0 57
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.009 0.096 -10000 0 -0.32 31 31
PPM1A 0.027 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.036 0.046 0.35 3 -10000 0 3
SMAD7/SMURF1 0.033 0.016 -10000 0 -10000 0 0
CTDSPL 0.026 0.005 -10000 0 -10000 0 0
PPP1CA 0.026 0.006 -10000 0 -10000 0 0
XIAP 0.027 0.001 -10000 0 -10000 0 0
CTDSP1 0.027 0.003 -10000 0 -10000 0 0
PPP1R15A 0.028 0.014 0.17 4 -10000 0 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.034 0.14 -10000 0 -0.41 44 44
CHRD 0.036 0.049 0.17 41 -0.31 3 44
BMPR2 0.027 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.011 0.1 -10000 0 -0.35 32 32
BMP4 0.01 0.074 -10000 0 -0.31 25 25
FST 0.003 0.086 0.17 3 -0.31 34 37
BMP2-4/NOG 0.007 0.11 -10000 0 -0.24 76 76
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.03 0.085 -10000 0 -0.16 75 75
Effects of Botulinum toxin

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
STX1A -0.005 0.012 0.25 1 -10000 0 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.031 0.14 8 -0.21 5 13
STXBP1 0.024 0.022 -10000 0 -0.31 2 2
ACh/CHRNA1 0.026 0.065 0.14 82 -0.093 55 137
RAB3GAP2/RIMS1/UNC13B 0.047 0.031 -10000 0 -0.18 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.038 0.17 6 -0.31 5 11
mol:ACh -0.01 0.049 0.09 36 -0.11 62 98
RAB3GAP2 0.026 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.015 0.068 0.16 1 -0.16 43 44
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.026 0.065 0.14 82 -0.093 55 137
UNC13B 0.027 0.01 0.17 2 -10000 0 2
CHRNA1 0.05 0.056 0.17 84 -10000 0 84
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.009 0.08 0.12 7 -0.18 72 79
SNAP25 -0.027 0.077 -10000 0 -0.22 68 68
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.026 0.13 0.17 9 -0.31 80 89
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.021 0.015 0.2 1 -0.18 1 2
STX1A/SNAP25 fragment 1/VAMP2 0.015 0.068 0.16 1 -0.16 43 44
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.024 0.12 -10000 0 -0.31 71 71
CDC42/GTP -0.013 0.11 0.2 1 -0.29 42 43
PLCG1 -0.023 0.1 0.21 1 -0.25 67 68
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.035 0.013 -10000 0 -10000 0 0
cell migration -0.014 0.1 0.2 1 -0.29 42 43
S1PR5 -0.026 0.12 -10000 0 -0.31 78 78
S1PR4 0.031 0.033 0.17 20 -0.31 1 21
MAPK3 -0.023 0.1 0.21 1 -0.25 67 68
MAPK1 -0.021 0.098 0.21 1 -0.25 65 66
S1P/S1P5/Gi -0.045 0.14 -10000 0 -0.28 107 107
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
CDC42/GDP 0.02 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0.072 -10000 0 -0.18 67 67
RHOA 0.003 0.062 0.19 44 -10000 0 44
S1P/S1P4/Gi -0.018 0.11 -10000 0 -0.25 74 74
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.002 0.094 -10000 0 -0.31 42 42
S1P/S1P4/G12/G13 0.048 0.026 -10000 0 -10000 0 0
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.003 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.055 -10000 0 -0.17 29 29
fibroblast growth factor receptor signaling pathway 0.028 0.055 -10000 0 -0.17 29 29
LAMA1 0.02 0.07 0.17 22 -0.31 17 39
PRNP 0.026 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 0.008 0.083 -10000 0 -0.22 58 58
SMAD2 -0.011 0.042 0.18 18 -0.17 9 27
GPC1/PrPc/Cu2+ 0.035 0.012 -10000 0 -0.18 1 1
GPC1/Laminin alpha1 0.033 0.053 -10000 0 -0.21 18 18
TDGF1 -0.009 0.1 0.17 6 -0.31 53 59
CRIPTO/GPC1 0.012 0.08 -10000 0 -0.21 53 53
APP/GPC1 0.037 0.019 -10000 0 -0.21 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.03 0.052 0.17 1 -0.18 50 51
FLT1 0.025 0.028 0.17 2 -0.31 3 5
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.035 -10000 0 -0.18 9 9
SERPINC1 0.034 0.037 0.17 31 -10000 0 31
FYN -0.028 0.05 0.17 1 -0.18 46 47
FGR -0.032 0.053 0.17 1 -0.18 54 55
positive regulation of MAPKKK cascade -0.034 0.11 0.28 10 -0.28 50 60
SLIT2 -0.013 0.11 -10000 0 -0.31 58 58
GPC1/NRG 0 0.079 -10000 0 -0.21 57 57
NRG1 -0.019 0.1 -10000 0 -0.31 57 57
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.04 0.058 0.24 1 -0.18 28 29
LYN -0.026 0.047 -10000 0 -0.18 40 40
mol:Spermine -0.007 0.009 -10000 0 -0.21 1 1
cell growth 0.028 0.055 -10000 0 -0.17 29 29
BMP signaling pathway -0.026 0.015 0.31 1 -10000 0 1
SRC -0.031 0.052 0.17 1 -0.18 52 53
TGFBR1 0.026 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.063 0.1 0.17 161 -0.31 18 179
GPC1 0.026 0.015 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.026 0.006 -10000 0 -10000 0 0
VEGFA 0.01 0.077 0.17 5 -0.31 26 31
BLK -0.032 0.074 0.076 28 -0.2 69 97
HCK -0.032 0.054 0.17 1 -0.18 55 56
FGF2 0.005 0.082 0.17 1 -0.31 31 32
FGFR1 0.02 0.019 -10000 0 -0.31 1 1
VEGFR1 homodimer 0.024 0.028 0.17 2 -0.31 3 5
TGFBR2 0.019 0.05 -10000 0 -0.31 11 11
cell death 0.037 0.019 -10000 0 -0.21 2 2
ATIII/GPC1 0.043 0.029 -10000 0 -0.21 1 1
PLA2G2A/GPC1 0.063 0.073 -10000 0 -0.21 19 19
LCK -0.03 0.053 0.17 1 -0.18 51 52
neuron differentiation -0.001 0.079 -10000 0 -0.21 57 57
PrPc/Cu2+ 0.02 0.003 -10000 0 -10000 0 0
APP 0.025 0.022 -10000 0 -0.31 2 2
TGFBR2 (dimer) 0.019 0.05 -10000 0 -0.31 11 11
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.025 0.13 0.3 21 -0.38 27 48
FYN 0.006 0.16 0.3 28 -0.48 29 57
LAT/GRAP2/SLP76 0.013 0.13 0.26 11 -0.4 27 38
IKBKB 0.021 0.011 -10000 0 -10000 0 0
AKT1 0.013 0.13 0.32 30 -0.35 27 57
B2M 0.027 0.008 -10000 0 -10000 0 0
IKBKG 0.006 0.042 0.12 22 -0.13 15 37
MAP3K8 0.018 0.054 0.17 1 -0.31 13 14
mol:Ca2+ -0.013 0.012 0.086 2 -0.052 8 10
integrin-mediated signaling pathway 0.025 0.043 -10000 0 -0.17 21 21
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.004 0.17 0.36 22 -0.49 30 52
TRPV6 0.073 0.3 1.1 37 -10000 0 37
CD28 0.032 0.061 0.18 37 -0.31 9 46
SHC1 0.003 0.15 0.27 27 -0.44 32 59
receptor internalization -0.009 0.15 0.26 2 -0.38 50 52
PRF1 -0.014 0.22 -10000 0 -0.86 23 23
KRAS 0.025 0.007 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
COT/AKT1 0.02 0.12 0.31 26 -0.3 27 53
LAT -0.002 0.14 0.26 15 -0.43 32 47
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.026 0.059 0.18 23 -0.32 10 33
CD3E 0.022 0.054 0.18 9 -0.32 10 19
CD3G 0.009 0.089 0.18 17 -0.31 32 49
RASGRP2 0 0.037 0.085 4 -0.17 20 24
RASGRP1 0.008 0.13 0.33 26 -0.35 30 56
HLA-A 0.001 0.004 -10000 0 -10000 0 0
RASSF5 0.012 0.068 -10000 0 -0.31 21 21
RAP1A/GTP/RAPL 0.026 0.043 -10000 0 -0.17 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.079 0.23 37 -0.12 19 56
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.048 -10000 0 -0.19 21 21
PRKCA -0.005 0.072 0.17 15 -0.23 28 43
GRAP2 0.016 0.06 0.17 2 -0.31 16 18
mol:IP3 -0.005 0.093 0.17 2 -0.32 28 30
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.13 -10000 0 -0.49 24 24
ORAI1 -0.056 0.25 0.35 16 -0.94 33 49
CSK 0 0.14 0.23 17 -0.44 30 47
B7 family/CD28 0.038 0.15 0.3 17 -0.44 27 44
CHUK 0.025 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.007 0.16 0.2 8 -0.45 37 45
PTPN6 -0.007 0.14 0.22 10 -0.44 31 41
VAV1 -0.007 0.15 0.24 12 -0.45 35 47
Monovalent TCR/CD3 -0.002 0.094 0.13 3 -0.26 43 46
CBL 0.025 0.016 -10000 0 -0.31 1 1
LCK 0.008 0.15 0.29 25 -0.48 26 51
PAG1 0.013 0.14 0.2 64 -0.5 22 86
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.008 0.15 0.2 8 -0.45 36 44
CD80 0.035 0.038 0.18 32 -10000 0 32
CD86 0.027 0.029 0.18 7 -0.31 2 9
PDK1/CARD11/BCL10/MALT1 0 0.061 -10000 0 -0.23 21 21
HRAS 0.028 0.017 0.17 6 -10000 0 6
GO:0035030 -0.003 0.11 0.22 9 -0.35 30 39
CD8A 0.022 0.052 0.18 6 -0.32 10 16
CD8B 0.024 0.049 0.18 9 -0.32 8 17
PTPRC 0.016 0.066 0.18 7 -0.31 18 25
PDK1/PKC theta 0.006 0.16 0.41 27 -0.44 26 53
CSK/PAG1 0.016 0.14 0.2 70 -0.47 23 93
SOS1 0.026 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.021 0.009 -10000 0 -10000 0 0
GRAP2/SLP76 0.014 0.14 0.24 5 -0.43 32 37
STIM1 -0.013 0.17 1.1 7 -0.94 5 12
RAS family/GTP 0.022 0.086 0.25 29 -0.15 37 66
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.012 0.16 0.17 1 -0.4 50 51
mol:DAG -0.017 0.079 -10000 0 -0.27 32 32
RAP1A/GDP 0.014 0.036 0.12 27 -0.058 14 41
PLCG1 0.026 0.005 -10000 0 -10000 0 0
CD247 0.028 0.045 0.18 17 -0.32 5 22
cytotoxic T cell degranulation -0.012 0.2 -10000 0 -0.82 23 23
RAP1A/GTP 0 0.014 -10000 0 -0.061 21 21
mol:PI-3-4-5-P3 0.008 0.14 0.33 24 -0.4 30 54
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.001 0.12 0.2 1 -0.41 27 28
NRAS 0.026 0.016 -10000 0 -0.31 1 1
ZAP70 0.041 0.053 0.17 52 -0.31 3 55
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.002 0.12 0.2 6 -0.41 27 33
MALT1 0.023 0.019 0.17 1 -0.31 1 2
TRAF6 0.026 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.035 0.059 0.17 12 -0.26 15 27
CARD11 0.021 0.046 0.17 6 -0.31 8 14
PRKCB -0.016 0.079 0.16 7 -0.23 46 53
PRKCE -0.001 0.067 0.17 15 -0.22 22 37
PRKCQ -0.001 0.17 0.37 22 -0.49 29 51
LCP2 0.025 0.03 0.17 4 -0.31 3 7
BCL10 0.026 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.015 0.12 0.3 31 -0.3 26 57
IKK complex 0.005 0.084 0.25 32 -0.11 30 62
RAS family/GDP 0 0.01 -10000 0 -0.037 9 9
MAP3K14 0.012 0.092 0.26 26 -0.22 27 53
PDPK1 0.014 0.13 0.35 30 -0.33 26 56
TCR/CD3/MHC I/CD8/Fyn -0.012 0.18 0.29 1 -0.55 35 36
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.012 0.072 -10000 0 -0.21 38 38
NT3 (dimer)/TRKC -0.025 0.13 -10000 0 -0.26 102 102
NT3 (dimer)/TRKB -0.012 0.12 -10000 0 -0.23 106 106
SHC/Grb2/SOS1/GAB1/PI3K 0.018 0.03 -10000 0 -0.2 7 7
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
BDNF -0.039 0.13 -10000 0 -0.31 96 96
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.01 0.078 0.17 8 -0.31 26 34
NTRK2 -0.016 0.11 0.17 1 -0.31 62 63
NTRK3 -0.035 0.13 -10000 0 -0.31 91 91
NT-4/5 (dimer)/TRKB -0.036 0.14 -10000 0 -0.24 147 147
neuron apoptosis 0.051 0.16 0.39 68 -0.23 1 69
SHC 2-3/Grb2 -0.056 0.18 0.24 1 -0.42 68 69
SHC1 0.026 0.006 -10000 0 -10000 0 0
SHC2 -0.051 0.15 -10000 0 -0.42 52 52
SHC3 -0.073 0.19 0.25 1 -0.48 69 70
STAT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.006 0.11 -10000 0 -0.22 81 81
RIN/GDP 0.006 0.094 0.27 16 -0.22 21 37
GIPC1 0.027 0.003 -10000 0 -10000 0 0
KRAS 0.025 0.007 -10000 0 -10000 0 0
DNAJA3 -0.029 0.095 -10000 0 -0.25 63 63
RIN/GTP 0.022 0.028 0.12 31 -0.11 2 33
CCND1 0.014 0.006 -10000 0 -10000 0 0
MAGED1 0.027 0.007 0.17 1 -10000 0 1
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.048 0.14 -10000 0 -0.31 109 109
SHC/GRB2/SOS1 0.049 0.018 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.062 0.1 0.24 1 -0.2 48 49
TRKA/NEDD4-2 0.024 0.06 -10000 0 -0.21 25 25
ELMO1 0.023 0.023 -10000 0 -0.31 2 2
RhoG/GTP/ELMO1/DOCK1 0.029 0.025 -10000 0 -0.18 5 5
NGF 0.013 0.069 0.17 2 -0.31 21 23
HRAS 0.028 0.017 0.17 6 -10000 0 6
DOCK1 0.023 0.03 -10000 0 -0.31 4 4
GAB2 0.026 0.006 -10000 0 -10000 0 0
RIT2 0.031 0.038 0.17 31 -10000 0 31
RIT1 0.026 0.006 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
DNM1 0.025 0.018 0.17 1 -0.31 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.012 0.1 -10000 0 -0.24 65 65
mol:GDP -0.009 0.12 0.31 17 -0.32 26 43
NGF (dimer) 0.013 0.068 0.17 2 -0.31 21 23
RhoG/GDP 0.017 0.016 -10000 0 -0.21 2 2
RIT1/GDP 0.001 0.089 0.26 13 -0.22 21 34
TIAM1 0.023 0.03 -10000 0 -0.31 4 4
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
BDNF (dimer)/TRKB -0.015 0.13 -10000 0 -0.24 111 111
KIDINS220/CRKL/C3G 0.037 0.011 -10000 0 -10000 0 0
SHC/RasGAP 0.035 0.017 -10000 0 -0.21 1 1
FRS2 family/SHP2 0.05 0.018 -10000 0 -0.18 1 1
SHC/GRB2/SOS1/GAB1 0.061 0.025 -10000 0 -0.17 1 1
RIT1/GTP 0.019 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.005 0.095 -10000 0 -0.31 44 44
RAP1/GDP -0.005 0.068 0.14 3 -0.2 20 23
KIDINS220/CRKL 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.039 0.13 -10000 0 -0.31 96 96
ubiquitin-dependent protein catabolic process 0.026 0.073 -10000 0 -0.18 43 43
Schwann cell development -0.022 0.026 -10000 0 -0.1 4 4
EHD4 0.026 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.062 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.023 0.029 -10000 0 -10000 0 0
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.044 0.14 -10000 0 -0.24 138 138
ABL1 0.026 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.005 0.084 -10000 0 -0.32 18 18
STAT3 0.031 0.007 -10000 0 -10000 0 0
axon guidance -0.05 0.13 -10000 0 -0.24 140 140
MAPK3 -0.038 0.06 0.18 11 -0.2 37 48
MAPK1 -0.039 0.061 0.18 12 -0.19 40 52
CDC42/GDP 0.003 0.092 0.25 17 -0.23 19 36
NTF3 -0.005 0.095 -10000 0 -0.31 44 44
NTF4 -0.048 0.14 -10000 0 -0.31 109 109
NGF (dimer)/TRKA/FAIM 0.028 0.071 -10000 0 -0.18 43 43
PI3K 0.031 0.034 -10000 0 -0.24 6 6
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.025 0.007 -10000 0 -10000 0 0
GAB1 0.026 0.016 -10000 0 -0.31 1 1
RASGRF1 -0.049 0.12 -10000 0 -0.3 69 69
SOS1 0.026 0.005 -10000 0 -10000 0 0
MCF2L -0.053 0.089 -10000 0 -0.22 93 93
RGS19 0.026 0.009 0.17 1 -10000 0 1
CDC42 0.027 0.003 -10000 0 -10000 0 0
RAS family/GTP 0 0.11 0.28 6 -0.44 13 19
Rac1/GDP 0.001 0.083 0.26 9 -0.23 18 27
NGF (dimer)/TRKA/GRIT 0.016 0.066 0.13 10 -0.18 46 56
neuron projection morphogenesis -0.033 0.18 -10000 0 -0.77 17 17
NGF (dimer)/TRKA/NEDD4-2 0.027 0.073 -10000 0 -0.19 43 43
MAP2K1 -0.001 0.07 0.22 36 -0.16 1 37
NGFR -0.001 0.093 -10000 0 -0.31 41 41
NGF (dimer)/TRKA/GIPC/GAIP 0.006 0.06 -10000 0 -0.19 40 40
RAS family/GTP/PI3K 0.016 0.027 -10000 0 -0.2 6 6
FRS2 family/SHP2/GRB2/SOS1 0.07 0.03 -10000 0 -0.16 1 1
NRAS 0.026 0.016 -10000 0 -0.31 1 1
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
PRKCI 0.025 0.01 0.17 1 -10000 0 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.06 0.21 -10000 0 -0.55 70 70
RASA1 0.025 0.016 -10000 0 -0.31 1 1
TRKA/c-Abl 0.026 0.057 0.14 8 -0.21 24 32
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.001 0.12 -10000 0 -0.22 112 112
NGF (dimer)/TRKA/p62/Atypical PKCs 0.048 0.073 -10000 0 -0.16 41 41
MATK 0.089 0.076 0.17 213 -0.31 1 214
NEDD4L 0.027 0.026 0.17 13 -10000 0 13
RAS family/GDP -0.02 0.051 -10000 0 -0.16 35 35
NGF (dimer)/TRKA -0.027 0.1 -10000 0 -0.26 68 68
Rac1/GTP -0.04 0.092 -10000 0 -0.24 63 63
FRS2 family/SHP2/CRK family 0.069 0.03 -10000 0 -0.16 1 1
FOXM1 transcription factor network

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
NFATC3 0.01 0.36 0.66 1 -1.1 32 33
PLK1 0.05 0.05 -10000 0 -10000 0 0
BIRC5 0.039 0.12 -10000 0 -0.72 9 9
HSPA1B 0.01 0.36 0.63 1 -1.1 32 33
MAP2K1 0.029 0.046 -10000 0 -10000 0 0
BRCA2 -0.009 0.4 -10000 0 -1.1 43 43
FOXM1 -0.01 0.46 -10000 0 -1.4 35 35
XRCC1 0.007 0.36 -10000 0 -1.1 32 32
FOXM1B/p19 -0.033 0.41 -10000 0 -1.2 38 38
Cyclin D1/CDK4 0.014 0.34 -10000 0 -0.98 33 33
CDC2 0.007 0.38 -10000 0 -1.1 35 35
TGFA -0.004 0.36 -10000 0 -0.98 39 39
SKP2 0.005 0.38 0.62 6 -1.1 35 41
CCNE1 0.027 0.024 0.18 5 -10000 0 5
CKS1B 0.009 0.36 -10000 0 -1 35 35
RB1 -0.005 0.27 -10000 0 -0.8 35 35
FOXM1C/SP1 0 0.41 -10000 0 -1.2 35 35
AURKB -0.038 0.28 -10000 0 -0.82 51 51
CENPF 0.016 0.37 0.61 3 -1.1 33 36
CDK4 0.023 0.026 -10000 0 -10000 0 0
MYC 0 0.31 0.57 1 -0.9 32 33
CHEK2 0.029 0.045 -10000 0 -0.14 1 1
ONECUT1 0.006 0.36 -10000 0 -1 34 34
CDKN2A 0.046 0.064 0.17 100 -10000 0 100
LAMA4 0.004 0.38 -10000 0 -1.1 34 34
FOXM1B/HNF6 -0.011 0.42 -10000 0 -1.3 34 34
FOS -0.095 0.51 0.61 1 -1.1 90 91
SP1 0.028 0.006 -10000 0 -10000 0 0
CDC25B 0.008 0.36 -10000 0 -1.1 32 32
response to radiation 0.011 0.025 -10000 0 -10000 0 0
CENPB 0.008 0.36 -10000 0 -1.1 32 32
CENPA 0.014 0.36 -10000 0 -1.1 32 32
NEK2 0.017 0.37 0.6 1 -1.1 30 31
HIST1H2BA 0.005 0.36 -10000 0 -1.1 33 33
CCNA2 0.048 0.058 0.18 74 -10000 0 74
EP300 0.025 0.026 -10000 0 -0.31 3 3
CCNB1/CDK1 -0.006 0.42 -10000 0 -1.3 33 33
CCNB2 0.01 0.36 0.63 2 -1.1 33 35
CCNB1 0.007 0.38 -10000 0 -1.1 34 34
ETV5 -0.011 0.43 0.67 1 -1.2 45 46
ESR1 -0.005 0.39 0.66 1 -1.1 37 38
CCND1 0.002 0.34 -10000 0 -1 33 33
GSK3A 0.028 0.04 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.067 0.065 0.21 42 -10000 0 42
CDK2 0.024 0.019 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.012 0.03 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.006 0.39 -10000 0 -1.1 35 35
GAS1 -0.039 0.47 0.65 3 -1.2 58 61
MMP2 0.002 0.38 0.66 1 -1.1 34 35
RB1/FOXM1C -0.023 0.36 -10000 0 -1 36 36
CREBBP 0.026 0.005 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.016 0.17 4 -10000 0 4
LAT2 -0.009 0.083 0.21 3 -0.29 28 31
AP1 0 0.14 0.27 3 -0.4 34 37
mol:PIP3 0.011 0.15 0.33 41 -0.36 25 66
IKBKB 0.009 0.12 0.28 52 -0.21 35 87
AKT1 -0.004 0.12 0.32 38 -0.25 17 55
IKBKG -0.003 0.11 0.25 39 -0.22 36 75
MS4A2 0.014 0.068 0.18 4 -0.31 19 23
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
MAP3K1 0.009 0.12 0.28 31 -0.34 20 51
mol:Ca2+ 0.014 0.12 0.29 44 -0.28 24 68
LYN 0.022 0.012 -10000 0 -10000 0 0
CBLB -0.008 0.083 0.16 2 -0.28 29 31
SHC1 0.026 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.04 0.041 -10000 0 -0.16 18 18
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.01 0.074 -10000 0 -0.31 25 25
PLD2 -0.015 0.085 0.27 21 -0.22 24 45
PTPN13 0 0.13 0.39 1 -0.55 12 13
PTPN11 0.023 0.023 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.014 0.13 0.39 33 -0.29 15 48
SYK 0.023 0.037 0.17 1 -0.32 5 6
GRB2 0.026 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.004 0.1 0.17 1 -0.34 28 29
LAT -0.01 0.083 0.15 1 -0.29 28 29
PAK2 0.009 0.12 0.28 31 -0.34 26 57
NFATC2 -0.067 0.16 -10000 0 -0.43 78 78
HRAS 0.002 0.12 0.26 18 -0.34 32 50
GAB2 0.026 0.006 -10000 0 -10000 0 0
PLA2G1B 0.017 0.089 -10000 0 -0.81 5 5
Fc epsilon R1 0.019 0.092 -10000 0 -0.22 58 58
Antigen/IgE/Fc epsilon R1 0.02 0.082 0.15 1 -0.19 58 59
mol:GDP -0.003 0.11 0.26 3 -0.37 29 32
JUN 0.024 0.031 0.17 1 -0.31 4 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
FOS -0.026 0.12 0.17 4 -0.31 78 82
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.003 0.089 0.16 2 -0.3 29 31
CHUK 0 0.11 0.26 42 -0.21 36 78
KLRG1 -0.004 0.075 0.15 4 -0.27 25 29
VAV1 -0.012 0.095 0.17 3 -0.31 33 36
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.009 0.085 0.16 3 -0.28 31 34
negative regulation of mast cell degranulation 0.001 0.099 0.18 7 -0.32 29 36
BTK 0.002 0.11 0.23 2 -0.41 19 21
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.024 0.13 -10000 0 -0.31 65 65
GAB2/PI3K/SHP2 -0.037 0.055 -10000 0 -0.21 36 36
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.088 -10000 0 -0.27 39 39
RAF1 0.017 0.094 -10000 0 -0.88 5 5
Fc epsilon R1/FcgammaRIIB/SHIP 0.034 0.12 0.25 3 -0.24 65 68
FCER1G 0.026 0.016 0.18 3 -10000 0 3
FCER1A -0.011 0.11 -10000 0 -0.32 53 53
Antigen/IgE/Fc epsilon R1/Fyn 0.026 0.081 -10000 0 -0.18 57 57
MAPK3 0.014 0.087 -10000 0 -0.8 5 5
MAPK1 0.014 0.09 -10000 0 -0.83 5 5
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.019 0.19 -10000 0 -0.59 37 37
DUSP1 0.015 0.061 -10000 0 -0.31 17 17
NF-kappa-B/RelA -0.001 0.054 0.12 11 -0.14 32 43
actin cytoskeleton reorganization 0 0.13 -10000 0 -0.55 13 13
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.008 0.11 0.24 4 -0.35 29 33
FER -0.009 0.085 0.16 3 -0.31 26 29
RELA 0.026 0.006 -10000 0 -10000 0 0
ITK 0 0.061 0.17 1 -0.32 14 15
SOS1 0.026 0.005 -10000 0 -10000 0 0
PLCG1 0.005 0.13 0.27 20 -0.37 29 49
cytokine secretion -0.005 0.035 -10000 0 -0.11 19 19
SPHK1 -0.009 0.084 0.19 3 -0.28 29 32
PTK2 -0.001 0.13 -10000 0 -0.59 12 12
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.001 0.11 0.18 1 -0.35 30 31
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.005 0.14 0.32 33 -0.34 31 64
MAP2K2 0.01 0.088 -10000 0 -0.83 5 5
MAP2K1 0.011 0.089 -10000 0 -0.82 5 5
MAP2K7 0.027 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 0.005 0.078 0.19 5 -0.25 25 30
MAP2K4 -0.035 0.25 -10000 0 -0.86 41 41
Fc epsilon R1/FcgammaRIIB 0.032 0.099 0.25 3 -0.21 60 63
mol:Choline -0.015 0.084 0.27 21 -0.22 24 45
SHC/Grb2/SOS1 0.032 0.097 0.24 2 -0.3 21 23
FYN 0.023 0.018 -10000 0 -0.31 1 1
DOK1 0.026 0.016 -10000 0 -0.31 1 1
PXN 0.004 0.13 0.38 8 -0.55 12 20
HCLS1 -0.007 0.081 0.16 2 -0.28 28 30
PRKCB -0.007 0.13 0.29 39 -0.28 42 81
FCGR2B 0.023 0.051 0.17 12 -0.31 9 21
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP 0.001 0.1 0.18 7 -0.32 29 36
LCP2 0.026 0.03 0.17 4 -0.31 3 7
PLA2G4A -0.015 0.1 0.16 3 -0.32 36 39
RASA1 0.025 0.016 -10000 0 -0.31 1 1
mol:Phosphatidic acid -0.015 0.084 0.27 21 -0.22 24 45
IKK complex 0.012 0.11 0.27 50 -0.18 19 69
WIPF1 0.023 0.031 -10000 0 -0.31 4 4
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.11 0.42 -10000 0 -1.2 35 35
STAT6 (cleaved dimer) -0.14 0.44 -10000 0 -1.2 48 48
IGHG1 -0.009 0.17 -10000 0 -0.51 5 5
IGHG3 -0.11 0.4 -10000 0 -1.1 43 43
AKT1 -0.055 0.27 -10000 0 -0.71 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.035 0.24 -10000 0 -0.71 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.048 0.28 -10000 0 -0.77 28 28
THY1 -0.11 0.42 -10000 0 -1.2 33 33
MYB 0.033 0.031 0.17 23 -10000 0 23
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.077 0.34 -10000 0 -0.85 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.054 0.29 -10000 0 -0.84 28 28
SP1 0.03 0.01 -10000 0 -10000 0 0
INPP5D 0.01 0.074 -10000 0 -0.31 25 25
SOCS5 0.01 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.13 0.44 -10000 0 -1.2 46 46
SOCS1 -0.073 0.3 -10000 0 -0.74 42 42
SOCS3 -0.14 0.45 -10000 0 -1.2 70 70
FCER2 -0.087 0.38 -10000 0 -1 44 44
PARP14 0.026 0.011 -10000 0 -10000 0 0
CCL17 -0.11 0.42 -10000 0 -1.2 35 35
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.035 0.24 0.38 1 -0.69 27 28
T cell proliferation -0.12 0.43 -10000 0 -1.2 38 38
IL4R/JAK1 -0.12 0.42 -10000 0 -1.2 36 36
EGR2 -0.12 0.46 -10000 0 -1.4 38 38
JAK2 0.011 0.056 -10000 0 -0.34 1 1
JAK3 0.021 0.041 0.18 11 -0.29 3 14
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
JAK1 0.015 0.032 -10000 0 -10000 0 0
COL1A2 -0.001 0.18 -10000 0 -1.2 3 3
CCL26 -0.096 0.42 -10000 0 -1.2 33 33
IL4R -0.12 0.44 -10000 0 -1.3 36 36
PTPN6 0.012 0.028 -10000 0 -10000 0 0
IL13RA2 -0.19 0.55 -10000 0 -1.3 76 76
IL13RA1 0.012 0.054 -10000 0 -10000 0 0
IRF4 -0.054 0.34 -10000 0 -1.2 32 32
ARG1 0.002 0.15 -10000 0 -0.58 3 3
CBL -0.073 0.31 -10000 0 -0.79 49 49
GTF3A 0.031 0.009 -10000 0 -0.092 1 1
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
IL13RA1/JAK2 0.025 0.078 -10000 0 -0.24 1 1
IRF4/BCL6 -0.048 0.31 -10000 0 -1.1 31 31
CD40LG 0.018 0.085 0.19 22 -0.24 37 59
MAPK14 -0.098 0.36 -10000 0 -0.88 61 61
mitosis -0.05 0.26 0.4 1 -0.66 38 39
STAT6 -0.13 0.49 -10000 0 -1.4 39 39
SPI1 0.03 0.022 0.18 4 -0.31 1 5
RPS6KB1 -0.049 0.25 0.39 1 -0.64 38 39
STAT6 (dimer) -0.13 0.49 -10000 0 -1.4 40 40
STAT6 (dimer)/PARP14 -0.12 0.44 -10000 0 -1.3 37 37
mast cell activation 0 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.076 0.29 -10000 0 -0.75 41 41
FRAP1 -0.055 0.27 -10000 0 -0.71 38 38
LTA -0.11 0.42 -10000 0 -1.2 36 36
FES 0.024 0.034 -10000 0 -0.31 5 5
T-helper 1 cell differentiation 0.12 0.47 1.3 42 -10000 0 42
CCL11 -0.11 0.4 -10000 0 -1.2 34 34
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.041 0.27 -10000 0 -0.69 38 38
IL2RG 0.021 0.048 0.18 15 -0.3 5 20
IL10 -0.13 0.46 -10000 0 -1.3 45 45
IRS1 0.017 0.058 -10000 0 -0.31 15 15
IRS2 0.026 0.02 0.17 3 -0.31 1 4
IL4 -0.01 0.17 -10000 0 -0.9 8 8
IL5 -0.11 0.42 -10000 0 -1.2 36 36
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.072 0.35 -10000 0 -0.92 33 33
COL1A1 0 0.18 -10000 0 -1.2 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.12 0.43 -10000 0 -1.3 32 32
IL2R gamma/JAK3 0.033 0.059 0.22 15 -0.24 7 22
TFF3 -0.1 0.42 -10000 0 -1.2 34 34
ALOX15 -0.13 0.48 -10000 0 -1.3 52 52
MYBL1 0.021 0.018 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.1 0.37 -10000 0 -1 40 40
SHC1 0.026 0.006 -10000 0 -10000 0 0
CEBPB 0.03 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.043 0.26 -10000 0 -0.75 24 24
mol:PI-3-4-5-P3 -0.055 0.28 -10000 0 -0.71 38 38
PI3K -0.061 0.29 -10000 0 -0.76 38 38
DOK2 0.019 0.023 0.17 3 -0.31 1 4
ETS1 0.002 0.043 0.15 1 -0.27 4 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.028 0.22 0.37 1 -0.61 24 25
ITGB3 -0.24 0.6 -10000 0 -1.3 103 103
PIGR -0.24 0.61 -10000 0 -1.3 108 108
IGHE -0.006 0.061 0.18 15 -0.14 4 19
MAPKKK cascade -0.027 0.21 0.37 1 -0.6 24 25
BCL6 0.025 0.007 -10000 0 -10000 0 0
OPRM1 -0.12 0.41 -10000 0 -1.2 33 33
RETNLB -0.11 0.42 -10000 0 -1.2 33 33
SELP -0.12 0.44 -10000 0 -1.3 38 38
AICDA -0.11 0.4 -10000 0 -1.2 35 35
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.012 0.031 0.12 5 -0.16 13 18
BUB1B 0.015 0.035 0.16 14 -0.11 1 15
PLK1 0.015 0.029 0.1 30 -0.086 5 35
PLK1S1 0.012 0.026 0.13 7 -0.16 5 12
KIF2A 0.009 0.032 0.16 12 -0.11 1 13
regulation of mitotic centrosome separation 0.015 0.029 0.1 30 -0.086 5 35
GOLGA2 0.026 0.007 -10000 0 -10000 0 0
Hec1/SPC24 0.063 0.056 0.15 118 -0.15 4 122
WEE1 0.018 0.038 0.17 6 -0.33 3 9
cytokinesis 0.018 0.071 0.22 18 -0.2 4 22
PP2A-alpha B56 0.061 0.092 -10000 0 -0.51 10 10
AURKA 0.018 0.027 0.14 13 -0.14 1 14
PICH/PLK1 0.02 0.041 0.22 12 -0.14 2 14
CENPE 0.007 0.036 0.17 14 -0.11 1 15
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.01 0.033 0.16 12 -0.11 1 13
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.026 0.005 -10000 0 -10000 0 0
TPX2 0.027 0.035 0.15 18 -0.18 1 19
PAK1 0.021 0.038 -10000 0 -0.32 6 6
SPC24 0.067 0.066 0.17 136 -10000 0 136
FBXW11 0.026 0.005 -10000 0 -10000 0 0
CLSPN 0.016 0.043 0.13 5 -0.24 9 14
GORASP1 0.026 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 8 -0.013 1 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.017 0.057 31 -0.046 6 37
G2 phase of mitotic cell cycle -0.001 0.002 0.012 2 -10000 0 2
STAG2 0.027 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.017 0.037 -10000 0 -0.43 3 3
spindle elongation 0.015 0.029 0.1 30 -0.086 5 35
ODF2 0.026 0.007 -10000 0 -10000 0 0
BUB1 0.036 0.096 -10000 0 -0.55 11 11
TPT1 -0.026 0.077 0.12 5 -0.17 100 105
CDC25C 0.038 0.052 0.17 13 -0.25 8 21
CDC25B 0.023 0.022 0.18 1 -0.32 1 2
SGOL1 0.012 0.031 0.16 13 -0.12 5 18
RHOA 0.026 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.041 0.033 0.2 4 -0.17 3 7
CDC14B -0.008 0.021 -10000 0 -0.21 5 5
CDC20 0.076 0.069 0.17 163 -10000 0 163
PLK1/PBIP1 0.008 0.019 0.087 14 -0.079 3 17
mitosis -0.003 0.003 0.025 1 -0.015 2 3
FBXO5 0.009 0.03 0.16 11 -10000 0 11
CDC2 0.001 0.002 0.013 3 -0.012 2 5
NDC80 0.023 0.027 -10000 0 -0.31 3 3
metaphase plate congression 0.015 0.025 0.13 1 -0.22 3 4
ERCC6L 0.019 0.043 0.23 7 -0.16 4 11
NLP/gamma Tubulin 0.007 0.022 0.086 13 -0.069 11 24
microtubule cytoskeleton organization -0.026 0.077 0.12 5 -0.17 100 105
G2/M transition DNA damage checkpoint -0.001 0.002 0.015 3 -10000 0 3
PPP1R12A 0.026 0.006 -10000 0 -10000 0 0
interphase -0.001 0.002 0.015 3 -10000 0 3
PLK1/PRC1-2 0.081 0.069 0.17 143 -10000 0 143
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.025 0.18 1 -10000 0 1
RAB1A 0.027 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.011 0.026 0.095 29 -0.079 1 30
mitotic prometaphase -0.001 0.002 0.018 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.05 0.18 17 -0.22 8 25
microtubule-based process 0.063 0.061 0.14 171 -0.1 3 174
Golgi organization 0.015 0.029 0.1 30 -0.086 5 35
Cohesin/SA2 0.027 0.022 0.11 13 -0.097 1 14
PPP1CB/MYPT1 0.038 0.009 -10000 0 -10000 0 0
KIF20A 0.077 0.071 0.17 171 -10000 0 171
APC/C/CDC20 0.063 0.061 0.14 165 -0.093 6 171
PPP2R1A 0.027 0.003 -10000 0 -10000 0 0
chromosome segregation 0.008 0.019 0.086 14 -0.078 3 17
PRC1 0.034 0.032 0.17 24 -10000 0 24
ECT2 0.024 0.066 0.22 42 -0.11 1 43
C13orf34 0.012 0.025 0.096 26 -0.072 5 31
NUDC 0.015 0.025 0.13 1 -0.22 3 4
regulation of attachment of spindle microtubules to kinetochore 0.015 0.035 0.16 14 -0.11 1 15
spindle assembly 0.01 0.024 0.093 23 -0.074 5 28
spindle stabilization 0.012 0.026 0.13 7 -0.16 5 12
APC/C/HCDH1 0.02 0.02 -10000 0 -0.17 5 5
MKLP2/PLK1 0.063 0.061 0.14 171 -0.1 3 174
CCNB1 0.031 0.031 0.18 19 -10000 0 19
PPP1CB 0.027 0.003 -10000 0 -10000 0 0
BTRC 0.026 0.007 -10000 0 -10000 0 0
ROCK2 -0.009 0.11 0.18 4 -0.35 43 47
TUBG1 0.006 0.039 0.11 4 -0.16 19 23
G2/M transition of mitotic cell cycle 0.004 0.026 0.23 1 -0.17 3 4
MLF1IP -0.005 0.034 0.26 7 -10000 0 7
INCENP 0.026 0.004 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0 0.059 0.35 1 -1 1 2
VDR 0.024 0.035 0.17 2 -0.31 5 7
FAM120B 0.026 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.017 0.099 -10000 0 -0.28 26 26
RXRs/LXRs/DNA/Oxysterols -0.015 0.12 -10000 0 -0.41 24 24
MED1 0.027 0.004 -10000 0 -10000 0 0
mol:9cRA 0.001 0.011 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.032 -10000 0 -0.18 12 12
RXRs/NUR77 0.016 0.1 0.26 1 -0.18 92 93
RXRs/PPAR -0.023 0.097 -10000 0 -0.2 101 101
NCOR2 0.026 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.024 0.12 2 -0.21 5 7
RARs/VDR/DNA/Vit D3 0.052 0.045 -10000 0 -0.17 15 15
RARA 0.027 0.004 -10000 0 -10000 0 0
NCOA1 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.035 0.17 2 -0.31 5 7
RARs/RARs/DNA/9cRA 0.038 0.037 -10000 0 -0.15 13 13
RARG 0.02 0.045 -10000 0 -0.31 9 9
RPS6KB1 0.009 0.059 0.53 5 -0.41 1 6
RARs/THRs/DNA/SMRT 0.019 0.034 -10000 0 -0.18 13 13
THRA 0.027 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.024 0.12 2 -0.21 5 7
RXRs/PPAR/9cRA/PGJ2/DNA 0.008 0.093 0.27 1 -0.16 109 110
NR1H4 -0.029 0.13 0.17 18 -0.31 85 103
RXRs/LXRs/DNA 0.027 0.11 -10000 0 -0.22 23 23
NR1H2 0.026 0.018 -10000 0 -10000 0 0
NR1H3 0.025 0.02 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.015 0.092 -10000 0 -0.16 94 94
NR4A1 0.02 0.058 0.17 9 -0.31 13 22
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.046 0.1 0.15 2 -0.19 153 155
RXRG -0.043 0.14 0.18 6 -0.31 102 108
RXR alpha/CCPG 0.035 0.02 -10000 0 -10000 0 0
RXRA 0.024 0.019 -10000 0 -10000 0 0
RXRB 0.026 0.019 -10000 0 -10000 0 0
THRB 0.028 0.018 0.17 7 -10000 0 7
PPARG 0.01 0.075 0.17 3 -0.31 25 28
PPARD 0.027 0.004 -10000 0 -10000 0 0
TNF -0.044 0.21 0.34 1 -0.94 24 25
mol:Oxysterols 0.001 0.01 -10000 0 -10000 0 0
cholesterol transport -0.015 0.12 -10000 0 -0.4 24 24
PPARA 0.026 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.03 -10000 0 -0.31 4 4
RXRs/NUR77/BCL2 -0.028 0.099 -10000 0 -0.21 99 99
SREBF1 -0.018 0.1 -10000 0 -0.52 6 6
RXRs/RXRs/DNA/9cRA 0.008 0.093 0.27 1 -0.16 109 110
ABCA1 -0.021 0.11 -10000 0 -0.59 6 6
RARs/THRs 0.068 0.045 -10000 0 -0.16 13 13
RXRs/FXR -0.017 0.12 0.26 1 -0.18 154 155
BCL2 0.016 0.052 -10000 0 -0.31 12 12
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.024 0.02 -10000 0 -0.18 1 1
ARNO/beta Arrestin1-2 0.028 0.097 -10000 0 -0.75 7 7
EGFR -0.002 0.09 -10000 0 -0.31 39 39
EPHA2 -0.002 0.096 0.17 3 -0.31 43 46
USP6 0.025 0.008 -10000 0 -10000 0 0
IQSEC1 0.026 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.013 0.092 0.14 34 -0.23 56 90
ARRB2 0.009 0.005 -10000 0 -10000 0 0
mol:GTP 0.007 0.04 0.12 16 -0.14 7 23
ARRB1 0.025 0.016 -10000 0 -0.31 1 1
FBXO8 0.026 0.005 -10000 0 -10000 0 0
TSHR 0.019 0.057 0.17 6 -0.31 13 19
EGF 0.023 0.084 0.17 40 -0.31 23 63
somatostatin receptor activity 0 0 0.001 36 -0.001 19 55
ARAP2 0.026 0.016 -10000 0 -0.31 1 1
mol:GDP 0.009 0.089 0.22 27 -0.23 25 52
mol:PI-3-4-5-P3 0 0 0.001 30 -0.001 4 34
ITGA2B 0.02 0.048 0.17 5 -0.31 9 14
ARF6 0.027 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.066 0.19 1 -0.17 39 40
ADAP1 0.024 0.018 0.17 1 -0.31 1 2
KIF13B 0.02 0.012 -10000 0 -10000 0 0
HGF/MET 0.007 0.095 -10000 0 -0.26 50 50
PXN 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.11 0.27 37 -0.23 18 55
EGFR/EGFR/EGF/EGF/ARFGEP100 0.027 0.084 -10000 0 -0.19 54 54
ADRB2 0.028 0.016 0.17 5 -10000 0 5
receptor agonist activity 0 0 0 25 0 16 41
actin filament binding 0 0 0.001 37 0 18 55
SRC 0.026 0.006 -10000 0 -10000 0 0
ITGB3 -0.037 0.13 -10000 0 -0.31 92 92
GNAQ 0.026 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 48 -0.001 13 61
ARF6/GDP 0 0.12 0.28 15 -0.32 26 41
ARF6/GDP/GULP/ACAP1 0.032 0.094 0.24 19 -0.25 13 32
alphaIIb/beta3 Integrin/paxillin/GIT1 0.014 0.093 -10000 0 -0.16 99 99
ACAP1 0.03 0.033 0.17 22 -10000 0 22
ACAP2 0.025 0.016 -10000 0 -0.31 1 1
LHCGR/beta Arrestin2 0.015 0.022 0.15 4 -10000 0 4
EFNA1 0.026 0.006 -10000 0 -10000 0 0
HGF 0.011 0.075 0.17 9 -0.31 24 33
CYTH3 -0.005 0.017 0.25 2 -10000 0 2
CYTH2 0.005 0.12 -10000 0 -0.98 7 7
NCK1 0.025 0.007 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 42 0 14 56
endosomal lumen acidification 0 0 0.001 34 0 25 59
microtubule-based process 0 0 -10000 0 0 5 5
GULP1 0.026 0.018 0.17 2 -0.31 1 3
GNAQ/ARNO 0.022 0.11 -10000 0 -0.87 7 7
mol:Phosphatidic acid 0 0 0 13 -10000 0 13
PIP3-E 0 0 0 29 0 4 33
MET -0.004 0.093 -10000 0 -0.31 42 42
GNA14 0.025 0.016 -10000 0 -0.31 1 1
GNA15 0.012 0.068 -10000 0 -0.31 21 21
GIT1 0.027 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 44 -0.001 14 58
GNA11 0.016 0.058 -10000 0 -0.31 15 15
LHCGR 0.019 0.018 0.17 4 -10000 0 4
AGTR1 0.036 0.09 0.17 80 -0.31 20 100
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.022 0.15 4 -10000 0 4
IPCEF1/ARNO 0.017 0.12 -10000 0 -0.82 7 7
alphaIIb/beta3 Integrin -0.014 0.1 0.14 2 -0.21 101 103
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.016 0.068 -10000 0 -0.21 39 39
CRKL -0.006 0.12 0.26 9 -0.45 20 29
mol:PIP3 -0.005 0.068 -10000 0 -0.73 4 4
AKT1 -0.001 0.077 0.36 3 -0.6 4 7
PTK2B 0.019 0.012 -10000 0 -10000 0 0
RAPGEF1 0.001 0.13 0.32 17 -0.42 20 37
RANBP10 0.024 0.009 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
HGF/MET/SHIP2 0.023 0.086 -10000 0 -0.22 49 49
MAP3K5 0.004 0.13 0.31 14 -0.42 21 35
HGF/MET/CIN85/CBL/ENDOPHILINS 0.034 0.085 -10000 0 -0.2 48 48
AP1 -0.006 0.091 0.18 3 -0.2 69 72
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis -0.12 0.32 -10000 0 -0.75 96 96
STAT3 (dimer) -0.023 0.1 -10000 0 -0.33 38 38
GAB1/CRKL/SHP2/PI3K 0.019 0.12 0.27 3 -0.42 21 24
INPP5D 0.01 0.074 -10000 0 -0.31 25 25
CBL/CRK 0.008 0.13 0.32 7 -0.43 20 27
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.011 -10000 0 -10000 0 0
ELK1 0.003 0.1 0.33 37 -10000 0 37
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.066 -10000 0 -0.26 21 21
PAK1 0.001 0.085 0.41 7 -0.58 3 10
HGF/MET/RANBP10 0.019 0.085 -10000 0 -0.22 49 49
HRAS -0.036 0.18 -10000 0 -0.55 48 48
DOCK1 -0.008 0.12 0.27 7 -0.43 21 28
GAB1 -0.007 0.12 0.26 5 -0.45 22 27
CRK -0.006 0.12 0.28 11 -0.45 20 31
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.033 0.17 -10000 0 -0.52 50 50
JUN 0.024 0.031 0.17 1 -0.31 4 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.013 0.073 -10000 0 -0.22 51 51
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
cell morphogenesis -0.011 0.15 0.33 23 -0.39 36 59
GRB2/SHC 0.018 0.081 0.19 1 -0.2 47 48
FOS -0.026 0.12 0.17 4 -0.31 78 82
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.003 0.1 0.32 37 -10000 0 37
HGF/MET/MUC20 0.009 0.081 0.13 9 -0.22 50 59
cell migration 0.017 0.08 0.19 1 -0.2 47 48
GRB2 0.026 0.005 -10000 0 -10000 0 0
CBL 0.025 0.016 -10000 0 -0.31 1 1
MET/RANBP10 0.012 0.069 -10000 0 -0.21 42 42
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.007 0.085 -10000 0 -0.27 40 40
MET/MUC20 -0.001 0.064 -10000 0 -0.21 42 42
RAP1B 0.007 0.14 0.35 23 -0.4 20 43
RAP1A 0.003 0.13 0.32 20 -0.4 19 39
HGF/MET/RANBP9 0.023 0.087 -10000 0 -0.22 49 49
RAF1 -0.027 0.17 0.3 2 -0.52 47 49
STAT3 -0.024 0.1 -10000 0 -0.33 38 38
cell proliferation -0.016 0.15 0.31 21 -0.39 46 67
RPS6KB1 -0.001 0.045 -10000 0 -0.24 10 10
MAPK3 -0.007 0.099 0.39 15 -10000 0 15
MAPK1 -0.001 0.12 0.5 15 -10000 0 15
RANBP9 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.002 0.14 0.32 11 -0.42 31 42
SRC -0.021 0.081 -10000 0 -0.26 38 38
PI3K 0.016 0.086 0.17 14 -0.22 46 60
MET/Glomulin 0.015 0.029 -10000 0 -0.13 13 13
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K1 -0.02 0.17 0.32 8 -0.49 47 55
MET -0.004 0.093 -10000 0 -0.31 42 42
MAP4K1 0.005 0.13 0.31 9 -0.45 20 29
PTK2 0.022 0.011 -10000 0 -10000 0 0
MAP2K2 -0.02 0.17 0.36 8 -0.48 47 55
BAD 0.001 0.082 0.42 5 -0.64 3 8
MAP2K4 0.002 0.12 0.29 14 -0.38 21 35
SHP2/GRB2/SOS1/GAB1 0.005 0.12 -10000 0 -0.36 34 34
INPPL1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.026 0.006 -10000 0 -10000 0 0
SH3KBP1 0.027 0.003 -10000 0 -10000 0 0
HGS -0.016 0.067 -10000 0 -0.21 48 48
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF 0.011 0.075 0.17 9 -0.31 24 33
RASA1 0.025 0.016 -10000 0 -0.31 1 1
NCK1 0.025 0.007 -10000 0 -10000 0 0
PTPRJ 0.026 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.019 0.085 0.17 17 -0.21 46 63
PDPK1 -0.001 0.075 -10000 0 -0.63 4 4
HGF/MET/SHIP 0.015 0.11 -10000 0 -0.25 56 56
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.017 0.083 0.2 6 -0.27 15 21
TBX21 -0.033 0.3 -10000 0 -1 29 29
B2M 0.026 0.014 -10000 0 -10000 0 0
TYK2 0.02 0.032 -10000 0 -10000 0 0
IL12RB1 0.022 0.061 0.2 18 -0.34 6 24
GADD45B -0.011 0.26 -10000 0 -0.87 25 25
IL12RB2 0.011 0.069 0.2 5 -0.31 16 21
GADD45G -0.003 0.25 -10000 0 -0.88 22 22
natural killer cell activation 0.003 0.016 0.041 9 -0.039 19 28
RELB 0.027 0.004 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
IL18 0.018 0.055 -10000 0 -0.31 12 12
IL2RA 0.045 0.064 0.17 76 -0.31 5 81
IFNG 0.033 0.037 0.17 31 -10000 0 31
STAT3 (dimer) -0.014 0.24 -10000 0 -0.69 36 36
HLA-DRB5 -0.003 0.008 -10000 0 -0.023 64 64
FASLG -0.037 0.31 -10000 0 -1 30 30
NF kappa B2 p52/RelB -0.02 0.28 -10000 0 -0.85 34 34
CD4 0.018 0.034 0.18 5 -0.31 2 7
SOCS1 0.026 0.02 0.17 3 -0.31 1 4
EntrezGene:6955 -0.003 0.012 -10000 0 -0.027 85 85
CD3D 0.017 0.064 0.18 23 -0.28 12 35
CD3E 0.013 0.057 0.18 9 -0.28 12 21
CD3G 0.001 0.092 0.18 17 -0.31 33 50
IL12Rbeta2/JAK2 0.026 0.066 0.19 4 -0.22 17 21
CCL3 -0.038 0.31 -10000 0 -0.96 36 36
CCL4 -0.031 0.29 -10000 0 -0.94 29 29
HLA-A 0 0.007 -10000 0 -0.043 13 13
IL18/IL18R 0.057 0.08 0.2 11 -0.21 27 38
NOS2 -0.052 0.36 -10000 0 -1.1 41 41
IL12/IL12R/TYK2/JAK2/SPHK2 0.018 0.082 0.2 5 -0.25 16 21
IL1R1 -0.031 0.28 -10000 0 -0.88 33 33
IL4 -0.008 0.031 -10000 0 -10000 0 0
JAK2 0.02 0.035 -10000 0 -0.32 1 1
EntrezGene:6957 -0.003 0.011 -10000 0 -0.026 75 75
TCR/CD3/MHC I/CD8 -0.032 0.2 -10000 0 -0.65 35 35
RAB7A 0.019 0.22 0.52 2 -0.73 20 22
lysosomal transport 0.021 0.22 0.52 2 -0.69 20 22
FOS -0.17 0.48 -10000 0 -1.1 93 93
STAT4 (dimer) 0.012 0.25 -10000 0 -0.76 28 28
STAT5A (dimer) -0.015 0.28 0.4 1 -0.81 37 38
GZMA -0.034 0.29 0.52 1 -0.94 32 33
GZMB -0.05 0.33 -10000 0 -1.1 36 36
HLX 0.031 0.027 0.17 16 -10000 0 16
LCK -0.036 0.3 0.48 1 -0.87 38 39
TCR/CD3/MHC II/CD4 -0.038 0.13 -10000 0 -0.26 99 99
IL2/IL2R 0.065 0.084 0.3 14 -0.21 24 38
MAPK14 0.001 0.26 -10000 0 -0.86 25 25
CCR5 -0.014 0.27 -10000 0 -0.97 22 22
IL1B -0.004 0.12 0.19 22 -0.33 49 71
STAT6 0.015 0.092 -10000 0 -0.41 3 3
STAT4 0.028 0.039 0.17 13 -0.31 4 17
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.019 0.17 8 -10000 0 8
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.026 0.013 0.17 3 -10000 0 3
IL12B 0.029 0.051 0.19 30 -10000 0 30
CD8A 0.021 0.053 0.18 6 -0.31 10 16
CD8B 0.023 0.049 0.18 9 -0.31 8 17
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.017 0.083 0.27 15 -0.2 6 21
IL2RB 0.014 0.072 0.17 7 -0.31 22 29
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.23 0.38 1 -0.69 28 29
IL2RG 0.028 0.042 0.17 15 -0.31 5 20
IL12 0.035 0.067 0.19 27 -0.22 8 35
STAT5A 0.026 0.005 -10000 0 -10000 0 0
CD247 0.019 0.051 0.18 17 -0.32 5 22
IL2 0.022 0.012 0.17 2 -10000 0 2
SPHK2 0.027 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.056 0.19 5 -0.31 8 13
IL12/IL12R/TYK2/JAK2 -0.034 0.32 -10000 0 -0.93 38 38
MAP2K3 -0.005 0.26 -10000 0 -0.88 25 25
RIPK2 0.021 0.011 -10000 0 -10000 0 0
MAP2K6 -0.003 0.26 -10000 0 -0.89 25 25
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.003 0.009 -10000 0 -0.025 75 75
IL18RAP 0.021 0.067 0.18 16 -0.31 15 31
IL12Rbeta1/TYK2 0.033 0.059 0.18 16 -0.26 6 22
EOMES -0.025 0.21 -10000 0 -1.1 18 18
STAT1 (dimer) 0.006 0.24 0.42 3 -0.68 35 38
T cell proliferation 0.012 0.2 0.34 1 -0.56 32 33
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.023 0.041 -10000 0 -0.31 6 6
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.004 0.21 -10000 0 -0.63 25 25
ATF2 -0.004 0.24 0.42 1 -0.8 25 26
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.049 0.2 26 -0.18 3 29
RFC1 -0.004 0.033 0.16 14 -0.18 3 17
PRKDC 0.016 0.069 0.2 57 -0.18 2 59
RIPK1 0.028 0.007 -10000 0 -10000 0 0
CASP7 -0.014 0.097 -10000 0 -0.55 13 13
FASLG/FAS/FADD/FAF1 -0.01 0.06 0.16 1 -0.19 33 34
MAP2K4 -0.062 0.16 0.25 3 -0.32 107 110
mol:ceramide -0.023 0.099 0.22 1 -0.2 86 87
GSN 0 0.044 0.19 22 -0.18 3 25
FASLG/FAS/FADD/FAF1/Caspase 8 -0.017 0.076 0.18 2 -0.23 29 31
FAS 0.01 0.042 -10000 0 -0.31 6 6
BID -0.024 0.013 -10000 0 -10000 0 0
MAP3K1 -0.021 0.098 0.26 5 -0.28 24 29
MAP3K7 0.017 0.017 -10000 0 -10000 0 0
RB1 -0.004 0.025 0.15 10 -0.16 1 11
CFLAR 0.029 0.005 -10000 0 -10000 0 0
HGF/MET 0.023 0.087 -10000 0 -0.22 47 47
ARHGDIB -0.002 0.038 0.18 16 -0.18 3 19
FADD 0.015 0.023 -10000 0 -10000 0 0
actin filament polymerization 0 0.045 0.18 4 -0.19 22 26
NFKB1 -0.02 0.1 -10000 0 -0.53 5 5
MAPK8 -0.098 0.21 0.36 3 -0.47 110 113
DFFA -0.005 0.031 0.16 13 -0.18 3 16
DNA fragmentation during apoptosis -0.004 0.037 0.17 16 -0.18 5 21
FAS/FADD/MET 0.014 0.07 -10000 0 -0.19 39 39
CFLAR/RIP1 0.042 0.011 -10000 0 -10000 0 0
FAIM3 0.03 0.023 0.18 11 -10000 0 11
FAF1 0.015 0.026 -10000 0 -10000 0 0
PARP1 -0.005 0.028 0.15 11 -0.18 3 14
DFFB -0.003 0.035 0.17 16 -0.18 3 19
CHUK -0.021 0.091 -10000 0 -0.5 5 5
FASLG 0.012 0.064 0.17 17 -0.32 12 29
FAS/FADD 0.018 0.041 -10000 0 -0.23 6 6
HGF 0.011 0.075 0.17 9 -0.31 24 33
LMNA -0.006 0.032 0.19 4 -0.17 1 5
CASP6 -0.005 0.028 0.15 12 -0.18 2 14
CASP10 0.011 0.046 0.17 1 -0.31 7 8
CASP3 0 0.031 0.19 12 -10000 0 12
PTPN13 0.025 0.022 -10000 0 -0.31 2 2
CASP8 -0.025 0.016 -10000 0 -0.12 2 2
IL6 -0.22 0.48 -10000 0 -1.1 106 106
MET -0.004 0.093 -10000 0 -0.31 42 42
ICAD/CAD -0.005 0.034 0.16 15 -0.18 1 16
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.099 0.22 1 -0.2 86 87
activation of caspase activity by cytochrome c -0.024 0.013 -10000 0 -10000 0 0
PAK2 0.001 0.046 0.19 26 -0.19 2 28
BCL2 0.016 0.052 -10000 0 -0.31 12 12
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.028 0.054 -10000 0 -0.15 38 38
RGS9BP 0.026 0.022 0.17 1 -0.31 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.02 0.015 0.17 4 -10000 0 4
mol:Na + 0.026 0.025 0.15 7 -10000 0 7
mol:ADP -0.016 0.007 -10000 0 -10000 0 0
GNAT2 0.026 0.014 0.17 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.005 0.095 -10000 0 -0.18 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.029 0.018 0.14 7 -10000 0 7
GRK7 0.021 0.007 -10000 0 -10000 0 0
CNGB3 0.019 0.024 0.17 10 -10000 0 10
Cone Metarhodopsin II/X-Arrestin 0.016 0.006 0.12 1 -10000 0 1
mol:Ca2+ 0.03 0.086 0.19 98 -10000 0 98
Cone PDE6 0.018 0.09 -10000 0 -0.16 94 94
Cone Metarhodopsin II 0.025 0.013 0.12 4 -10000 0 4
Na + (4 Units) 0.042 0.039 0.24 3 -10000 0 3
GNAT2/GDP 0.017 0.088 -10000 0 -0.15 99 99
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.011 0.029 0.18 11 -10000 0 11
Cone Transducin 0.03 0.058 -10000 0 -0.16 38 38
SLC24A2 0.036 0.043 0.17 44 -10000 0 44
GNB3/GNGT2 0.017 0.068 0.14 1 -0.21 38 39
GNB3 0.003 0.084 -10000 0 -0.31 33 33
GNAT2/GTP 0.019 0.01 0.12 4 -10000 0 4
CNGA3 0.027 0.027 0.17 15 -10000 0 15
ARR3 0.021 0.008 0.17 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.027 0.026 0.15 7 -10000 0 7
mol:Pi 0.005 0.095 -10000 0 -0.18 100 100
Cone CNG Channel 0.039 0.033 0.23 1 -10000 0 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.036 0.043 0.17 44 -10000 0 44
RGS9 -0.041 0.14 0.17 3 -0.31 100 103
PDE6C 0.018 0.007 -10000 0 -10000 0 0
GNGT2 0.023 0.034 0.17 1 -0.31 5 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.016 0.17 4 -10000 0 4
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.026 0.004 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.066 0.056 0.18 1 -0.096 17 18
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.005 0.031 -10000 0 -0.32 4 4
AURKB 0.067 0.069 0.17 145 -10000 0 145
AURKC 0.026 0.025 0.17 3 -0.31 2 5
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.003 0.087 -10000 0 -0.16 115 115
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.013 0.25 1 -10000 0 1
GNB1/GNG2 0.033 0.024 -10000 0 -0.18 6 6
GNB1 0.027 0.004 -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 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.024 0.073 -10000 0 -0.15 117 117
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 0.012 0.019 0.045 117 -10000 0 117
GNAL -0.054 0.14 -10000 0 -0.31 117 117
GNG2 0.023 0.037 -10000 0 -0.31 6 6
CRH 0.015 0.013 0.17 2 -10000 0 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.038 -10000 0 -0.24 12 12
MAPK11 0.007 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.01 0.008 0.058 2 -10000 0 2
RAS family/GTP 0.001 0.092 0.19 1 -0.19 50 51
NFATC4 -0.035 0.063 0.28 6 -0.24 4 10
ERBB2IP 0.025 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.014 0.069 0.16 1 -0.19 51 52
JUN -0.009 0.071 0.22 8 -0.3 1 9
HRAS 0.028 0.017 0.17 6 -10000 0 6
DOCK7 -0.04 0.058 0.22 2 -0.2 16 18
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.01 0.067 -10000 0 -0.17 51 51
AKT1 -0.005 0.007 -10000 0 -10000 0 0
BAD -0.01 0.005 -10000 0 -10000 0 0
MAPK10 -0.017 0.061 0.19 20 -0.18 3 23
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.013 0.074 0.17 1 -0.2 51 52
RAF1 -0.014 0.092 0.3 9 -0.24 23 32
ErbB2/ErbB3/neuregulin 2 -0.028 0.092 -10000 0 -0.18 129 129
STAT3 -0.01 0.19 -10000 0 -0.9 22 22
cell migration -0.005 0.088 0.26 30 -0.19 3 33
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.034 0.18 0.4 5 -0.49 29 34
FOS -0.053 0.19 0.31 9 -0.45 85 94
NRAS 0.026 0.016 -10000 0 -0.31 1 1
mol:Ca2+ -0.014 0.069 0.16 1 -0.19 51 52
MAPK3 -0.017 0.14 0.37 7 -0.44 14 21
MAPK1 -0.021 0.15 0.37 7 -0.46 18 25
JAK2 -0.039 0.058 0.18 4 -0.2 16 20
NF2 0.003 0.055 -10000 0 -0.69 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.011 0.066 -10000 0 -0.2 48 48
NRG1 -0.019 0.1 -10000 0 -0.31 56 56
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
MAPK8 -0.042 0.096 0.2 1 -0.24 57 58
MAPK9 -0.016 0.058 0.18 20 -0.16 1 21
ERBB2 -0.021 0.02 0.24 1 -0.23 2 3
ERBB3 0.025 0.016 -10000 0 -0.31 1 1
SHC1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.01 0.01 -10000 0 -10000 0 0
STAT3 (dimer) -0.01 0.19 -10000 0 -0.86 23 23
RNF41 -0.014 0.007 -10000 0 -10000 0 0
FRAP1 -0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.037 0.04 -10000 0 -0.15 47 47
ErbB2/ErbB2/HSP90 (dimer) -0.019 0.019 0.18 1 -0.19 2 3
CHRNA1 -0.008 0.12 0.35 7 -0.36 12 19
myelination -0.017 0.099 0.32 24 -0.24 3 27
PPP3CB -0.038 0.054 0.18 3 -0.19 16 19
KRAS 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.004 0.083 -10000 0 -0.19 46 46
NRG2 -0.08 0.16 -10000 0 -0.31 155 155
mol:GDP -0.011 0.066 -10000 0 -0.2 48 48
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.022 0.089 0.26 11 -0.25 22 33
SRC 0.026 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.04 0.057 0.18 4 -0.19 17 21
MAP2K1 -0.041 0.15 -10000 0 -0.49 18 18
heart morphogenesis -0.014 0.069 0.16 1 -0.19 51 52
RAS family/GDP 0.006 0.092 -10000 0 -0.19 48 48
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.007 0.058 -10000 0 -0.72 3 3
CHRNE 0.003 0.02 0.12 4 -0.15 1 5
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.005 0.007 -10000 0 -10000 0 0
nervous system development -0.014 0.069 0.16 1 -0.19 51 52
CDC42 0.027 0.003 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.001 0.077 0.15 1 -0.33 22 23
PDGF/PDGFRA/CRKL 0.019 0.057 -10000 0 -0.22 21 21
positive regulation of JUN kinase activity 0.05 0.047 -10000 0 -0.17 17 17
CRKL 0.026 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.024 0.11 0.15 1 -0.23 105 106
AP1 -0.13 0.28 -10000 0 -0.74 80 80
mol:IP3 -0.029 0.052 -10000 0 -0.24 22 22
PLCG1 -0.029 0.052 -10000 0 -0.24 22 22
PDGF/PDGFRA/alphaV Integrin 0.018 0.057 -10000 0 -0.22 22 22
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.052 -10000 0 -0.24 22 22
CAV3 -0.031 0.13 0.17 17 -0.31 90 107
CAV1 -0.013 0.1 -10000 0 -0.31 55 55
SHC/Grb2/SOS1 0.051 0.048 -10000 0 -0.17 17 17
PDGF/PDGFRA/Shf 0.019 0.058 0.14 1 -0.23 20 21
FOS -0.13 0.27 0.3 1 -0.72 82 83
JUN -0.031 0.03 -10000 0 -0.28 3 3
oligodendrocyte development 0.018 0.057 -10000 0 -0.22 22 22
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
mol:DAG -0.029 0.052 -10000 0 -0.24 22 22
PDGF/PDGFRA 0.001 0.077 0.15 1 -0.33 22 23
actin cytoskeleton reorganization 0.018 0.058 -10000 0 -0.23 20 20
SRF -0.005 0.017 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.033 0.057 -10000 0 -0.21 22 22
PDGF/PDGFRA/Crk/C3G 0.037 0.048 -10000 0 -0.18 19 19
JAK1 -0.023 0.043 -10000 0 -0.22 20 20
ELK1/SRF -0.026 0.048 0.15 11 -0.21 20 31
SHB 0.024 0.026 -10000 0 -0.31 3 3
SHF 0.026 0.017 0.17 1 -0.31 1 2
CSNK2A1 0.032 0.018 -10000 0 -10000 0 0
GO:0007205 -0.026 0.059 -10000 0 -0.28 21 21
SOS1 0.026 0.005 -10000 0 -10000 0 0
Ras protein signal transduction 0.05 0.047 -10000 0 -0.17 17 17
PDGF/PDGFRA/SHB 0.018 0.058 -10000 0 -0.23 20 20
PDGF/PDGFRA/Caveolin-1 -0.007 0.1 -10000 0 -0.27 57 57
ITGAV 0.026 0.005 -10000 0 -10000 0 0
ELK1 -0.032 0.06 0.22 1 -0.26 22 23
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
PDGF/PDGFRA/Crk 0.017 0.057 -10000 0 -0.22 22 22
JAK-STAT cascade -0.023 0.043 -10000 0 -0.22 20 20
cell proliferation 0.019 0.058 0.14 1 -0.23 20 21
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.055 0.051 -10000 0 -0.17 19 19
ER alpha/Gai/GDP/Gbeta gamma -0.049 0.16 -10000 0 -0.4 58 58
AKT1 -0.023 0.18 -10000 0 -0.72 28 28
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.018 0.18 -10000 0 -0.72 28 28
mol:Ca2+ -0.005 0.054 0.17 1 -0.33 6 7
IGF1R 0.026 0.017 0.17 1 -0.31 1 2
E2/ER alpha (dimer)/Striatin 0.013 0.068 0.13 1 -0.19 47 48
SHC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.022 0.17 0.68 28 -10000 0 28
RhoA/GTP 0.019 0.03 -10000 0 -0.15 14 14
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.017 0.13 0.24 1 -0.35 43 44
regulation of stress fiber formation 0.023 0.065 0.25 7 -0.27 7 14
E2/ERA-ERB (dimer) 0.032 0.042 0.13 20 -0.18 15 35
KRAS 0.025 0.007 -10000 0 -10000 0 0
G13/GTP 0.027 0.034 0.12 1 -0.16 15 16
pseudopodium formation -0.023 0.065 0.27 7 -0.25 7 14
E2/ER alpha (dimer)/PELP1 0.027 0.038 0.13 1 -0.17 16 17
GRB2 0.026 0.005 -10000 0 -10000 0 0
GNG2 0.023 0.037 -10000 0 -0.31 6 6
GNAO1 -0.024 0.12 -10000 0 -0.31 71 71
HRAS 0.028 0.017 0.17 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.022 0.14 0.33 2 -0.47 24 26
E2/ER beta (dimer) 0.024 0.02 0.12 19 -10000 0 19
mol:GDP 0.009 0.058 0.16 1 -0.3 14 15
mol:NADP -0.022 0.14 0.33 2 -0.47 24 26
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
mol:IP3 -0.006 0.055 -10000 0 -0.34 6 6
IGF-1R heterotetramer 0.026 0.017 0.17 1 -0.31 1 2
PLCB1 0 0.058 -10000 0 -0.35 6 6
PLCB2 0.001 0.057 -10000 0 -0.33 6 6
IGF1 0.008 0.089 0.17 17 -0.31 33 50
mol:L-citrulline -0.022 0.14 0.33 2 -0.47 24 26
RHOA 0.026 0.005 -10000 0 -10000 0 0
Gai/GDP -0.13 0.29 -10000 0 -0.62 124 124
JNK cascade 0.023 0.02 0.12 19 -10000 0 19
BCAR1 0.022 0.011 -10000 0 -10000 0 0
ESR2 0.032 0.029 0.17 19 -10000 0 19
GNAQ 0.026 0.006 -10000 0 -10000 0 0
ESR1 0.016 0.06 0.17 1 -0.31 16 17
Gq family/GDP/Gbeta gamma -0.018 0.15 -10000 0 -0.43 49 49
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.073 -10000 0 -0.46 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.018 0.14 0.24 1 -0.36 44 45
GNAZ -0.002 0.094 -10000 0 -0.31 42 42
E2/ER alpha (dimer) 0.012 0.041 0.12 1 -0.21 16 17
STRN 0.002 0.087 -10000 0 -0.31 36 36
GNAL -0.054 0.14 -10000 0 -0.31 117 117
PELP1 0.025 0.008 -10000 0 -10000 0 0
MAPK11 0.01 0.014 -10000 0 -10000 0 0
GNAI2 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
HBEGF -0.048 0.16 0.38 6 -0.39 53 59
cAMP biosynthetic process -0.012 0.081 -10000 0 -0.15 119 119
SRC -0.05 0.15 -10000 0 -0.39 56 56
PI3K 0.031 0.034 -10000 0 -0.24 6 6
GNB1 0.027 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.037 0.066 -10000 0 -0.28 14 14
SOS1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.037 0.12 -10000 0 -0.32 50 50
Gs family/GTP -0.007 0.085 -10000 0 -0.15 119 119
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.019 -10000 0 -10000 0 0
vasodilation -0.021 0.13 0.33 2 -0.44 25 27
mol:DAG -0.006 0.055 -10000 0 -0.34 6 6
Gs family/GDP/Gbeta gamma -0.017 0.089 -10000 0 -0.29 23 23
MSN -0.024 0.068 0.27 7 -0.26 7 14
Gq family/GTP 0.007 0.062 -10000 0 -0.34 6 6
mol:PI-3-4-5-P3 -0.017 0.18 -10000 0 -0.7 28 28
NRAS 0.026 0.016 -10000 0 -0.31 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.021 0.13 0.44 25 -0.33 2 27
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.063 -10000 0 -0.29 14 14
NOS3 -0.024 0.14 0.33 2 -0.5 24 26
GNA11 0.016 0.058 -10000 0 -0.31 15 15
MAPKKK cascade -0.035 0.16 0.36 2 -0.49 34 36
E2/ER alpha (dimer)/PELP1/Src -0.021 0.14 0.27 3 -0.37 45 48
ruffle organization -0.023 0.065 0.27 7 -0.25 7 14
ROCK2 -0.019 0.069 0.29 7 -0.26 4 11
GNA14 0.025 0.016 -10000 0 -0.31 1 1
GNA15 0.012 0.068 -10000 0 -0.31 21 21
GNA13 0.026 0.005 -10000 0 -10000 0 0
MMP9 -0.058 0.15 0.38 4 -0.38 53 57
MMP2 -0.041 0.15 0.26 3 -0.41 48 51
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.005 -10000 0 -10000 0 0
VLDLR 0.026 0.016 -10000 0 -0.31 1 1
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
NUDC 0.027 0.002 -10000 0 -10000 0 0
RELN/LRP8 0.057 0.046 0.24 3 -0.17 4 7
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.005 0.056 0.18 38 -0.17 3 41
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 -0.095 0.16 0.17 2 -0.31 178 180
IQGAP1 0.027 0.003 -10000 0 -10000 0 0
PLA2G7 0.061 0.065 0.17 119 -0.31 1 120
CALM1 0.026 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.04 0.015 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.006 -10000 0 -10000 0 0
CDK5R1 0.034 0.031 0.17 23 -10000 0 23
LIS1/Poliovirus Protein 3A -0.009 0.003 -10000 0 -10000 0 0
CDK5R2 0.041 0.045 0.17 50 -10000 0 50
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.026 0.12 -10000 0 -0.19 161 161
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.031 0.077 0.27 33 -0.21 1 34
MAP1B -0.009 0.054 -10000 0 -0.22 30 30
RAC1 0.01 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.009 0.053 0.2 20 -10000 0 20
RELN 0.04 0.059 0.17 60 -0.31 4 64
PAFAH/LIS1 0.046 0.046 0.13 106 -0.18 1 107
LIS1/CLIP170 0.024 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.018 0.042 -10000 0 -0.19 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.048 0.1 -10000 0 -0.33 19 19
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.012 0.078 0.25 40 -0.2 1 41
LIS1/IQGAP1 0.025 0.008 -10000 0 -10000 0 0
RHOA 0.011 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.011 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.028 0.17 17 -10000 0 17
PAFAH1B2 0.016 0.056 -10000 0 -0.31 14 14
MAP1B/LIS1/Dynein heavy chain 0.006 0.048 -10000 0 -0.15 27 27
NDEL1/Katanin 60/Dynein heavy chain 0.034 0.074 0.31 17 -0.2 2 19
LRP8 0.028 0.018 0.17 7 -10000 0 7
NDEL1/Katanin 60 0.027 0.078 0.27 32 -0.2 2 34
P39/CDK5 0 0.069 0.23 24 -0.18 1 25
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0.009 -10000 0 -10000 0 0
CDK5 -0.015 0.036 0.17 14 -0.16 3 17
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.008 -10000 0 -10000 0 0
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.016 0.11 0.18 4 -0.16 157 161
RELN/VLDLR 0.07 0.051 0.25 3 -0.16 5 8
CDC42 0.011 0.004 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin 0.017 0.039 0.16 4 -0.2 11 15
EPHB2 0.025 0.032 0.17 3 -0.31 4 7
Syndecan-2/TACI 0.029 0.051 0.16 42 -0.17 7 49
LAMA1 0.02 0.07 0.17 22 -0.31 17 39
Syndecan-2/alpha2 ITGB1 0.017 0.074 -10000 0 -0.18 49 49
HRAS 0.028 0.017 0.17 6 -10000 0 6
Syndecan-2/CASK 0.004 0.016 -10000 0 -0.17 4 4
ITGA5 0.018 0.054 0.17 1 -0.31 13 14
BAX -0.008 0.025 -10000 0 -10000 0 0
EPB41 0.027 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.019 -10000 0 -0.15 4 4
LAMA3 0 0.09 0.17 1 -0.31 38 39
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.003 0.092 -10000 0 -0.31 41 41
Syndecan-2/MMP2 0.017 0.03 0.13 1 -0.19 8 9
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.013 0.073 -10000 0 -0.21 45 45
dendrite morphogenesis 0.02 0.027 0.13 3 -0.2 5 8
Syndecan-2/GM-CSF 0.018 0.027 0.17 6 -0.18 4 10
determination of left/right symmetry 0.006 0.019 -10000 0 -0.2 4 4
Syndecan-2/PKC delta 0.02 0.021 -10000 0 -0.17 4 4
GNB2L1 0.028 0.014 0.17 4 -10000 0 4
MAPK3 0.027 0.074 0.19 84 -0.16 4 88
MAPK1 0.03 0.077 0.19 91 -0.16 4 95
Syndecan-2/RACK1 0.032 0.029 0.22 2 -0.15 4 6
NF1 0.027 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.019 -10000 0 -0.2 4 4
ITGA2 -0.007 0.098 -10000 0 -0.31 47 47
MAPK8 -0.001 0.029 -10000 0 -0.17 14 14
Syndecan-2/alpha2/beta1 Integrin 0.027 0.071 0.25 5 -0.17 40 45
Syndecan-2/Kininogen 0.032 0.054 0.16 58 -0.18 4 62
ITGB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.026 0.083 0.19 95 -0.14 4 99
Syndecan-2/CASK/Protein 4.1 0.018 0.019 -10000 0 -0.16 4 4
extracellular matrix organization 0.019 0.025 -10000 0 -0.21 4 4
actin cytoskeleton reorganization 0.017 0.038 0.16 4 -0.2 11 15
Syndecan-2/Caveolin-2/Ras 0.02 0.055 -10000 0 -0.18 28 28
Syndecan-2/Laminin alpha3 0.008 0.05 0.13 1 -0.18 31 32
Syndecan-2/RasGAP 0.04 0.033 0.23 2 -0.14 4 6
alpha5/beta1 Integrin 0.032 0.042 0.14 1 -0.21 13 14
PRKCD 0.026 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.02 0.027 0.13 3 -0.2 5 8
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.027 0.18 4 -0.14 3 7
RHOA 0.026 0.005 -10000 0 -10000 0 0
SDCBP 0.022 0.01 -10000 0 -10000 0 0
TNFRSF13B 0.034 0.055 0.17 42 -0.31 5 47
RASA1 0.025 0.016 -10000 0 -0.31 1 1
alpha2/beta1 Integrin 0.013 0.073 -10000 0 -0.21 45 45
Syndecan-2/Synbindin 0.019 0.021 -10000 0 -0.17 4 4
TGFB1 0.026 0.016 -10000 0 -0.31 1 1
CASP3 0.04 0.071 0.19 87 -0.16 4 91
FN1 0.02 0.052 0.17 4 -0.31 11 15
Syndecan-2/IL8 0.018 0.057 0.16 24 -0.18 25 49
SDC2 0.006 0.02 -10000 0 -0.2 4 4
KNG1 0.037 0.05 0.17 58 -10000 0 58
Syndecan-2/Neurofibromin 0.02 0.021 -10000 0 -0.17 4 4
TRAPPC4 0.026 0.006 -10000 0 -10000 0 0
CSF2 0.022 0.018 0.17 6 -10000 0 6
Syndecan-2/TGFB1 0.019 0.025 -10000 0 -0.21 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.019 -10000 0 -0.16 4 4
Syndecan-2/Ezrin 0.031 0.025 -10000 0 -0.16 4 4
PRKACA 0.044 0.074 0.19 99 -0.16 4 103
angiogenesis 0.017 0.057 0.16 24 -0.18 25 49
MMP2 0.018 0.048 0.17 1 -0.31 10 11
IL8 0.01 0.094 0.17 24 -0.31 35 59
calcineurin-NFAT signaling pathway 0.029 0.051 0.16 42 -0.17 7 49
Signaling events mediated by PTP1B

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
PDGFRB 0.027 0.01 0.17 2 -10000 0 2
Jak2/Leptin Receptor 0.023 0.11 0.28 5 -0.37 16 21
PTP1B/AKT1 0.011 0.073 0.25 5 -0.2 13 18
FYN 0.023 0.018 -10000 0 -0.31 1 1
p210 bcr-abl/PTP1B 0.002 0.074 0.23 7 -0.22 15 22
EGFR -0.004 0.092 -10000 0 -0.32 39 39
EGF/EGFR 0.003 0.099 0.19 1 -0.24 43 44
CSF1 0.019 0.05 -10000 0 -0.31 11 11
AKT1 0.027 0.005 -10000 0 -10000 0 0
INSR 0.027 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.007 0.095 0.25 4 -0.23 51 55
Insulin Receptor/Insulin 0.026 0.072 0.21 1 -0.21 5 6
HCK 0.024 0.031 0.17 1 -0.31 4 5
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 -0.001 0.073 0.28 6 -0.21 14 20
EGF 0.02 0.087 0.18 40 -0.31 23 63
YES1 0.025 0.007 -10000 0 -10000 0 0
CAV1 -0.007 0.11 0.25 16 -0.29 32 48
TXN 0.026 0.01 0.17 1 -10000 0 1
PTP1B/IRS1/GRB2 0.014 0.085 0.24 1 -0.26 15 16
cell migration -0.002 0.074 0.22 15 -0.23 7 22
STAT3 0.026 0.005 -10000 0 -10000 0 0
PRLR 0.019 0.077 0.18 22 -0.31 22 44
ITGA2B 0.02 0.048 0.17 5 -0.31 9 14
CSF1R 0.025 0.023 0.17 1 -0.31 2 3
Prolactin Receptor/Prolactin 0.031 0.059 0.18 3 -0.22 20 23
FGR 0.026 0.022 0.17 1 -0.31 2 3
PTP1B/p130 Cas 0.01 0.067 0.22 4 -0.21 12 16
Crk/p130 Cas 0.017 0.073 0.24 3 -0.22 8 11
DOK1 0.008 0.074 0.25 12 -0.22 8 20
JAK2 0.012 0.097 0.26 4 -0.36 15 19
Jak2/Leptin Receptor/Leptin -0.008 0.11 -10000 0 -0.3 27 27
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
PTPN1 0.002 0.074 0.23 7 -0.22 15 22
LYN 0.023 0.01 -10000 0 -10000 0 0
CDH2 -0.047 0.14 0.17 9 -0.31 110 119
SRC 0.016 0.073 -10000 0 -0.38 12 12
ITGB3 -0.037 0.13 -10000 0 -0.31 92 92
CAT1/PTP1B -0.003 0.11 0.3 16 -0.28 25 41
CAPN1 0.026 0.006 -10000 0 -10000 0 0
CSK 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.029 0.076 -10000 0 -0.29 5 5
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.01 0.11 -10000 0 -0.28 47 47
negative regulation of transcription 0.013 0.097 0.26 4 -0.36 15 19
FCGR2A 0.025 0.024 0.17 2 -0.31 2 4
FER 0.017 0.053 -10000 0 -0.31 12 12
alphaIIb/beta3 Integrin -0.014 0.1 0.15 1 -0.21 101 102
BLK 0 0.1 0.17 32 -0.31 43 75
Insulin Receptor/Insulin/Shc 0.048 0.022 -10000 0 -0.092 1 1
RHOA 0.027 0.006 -10000 0 -10000 0 0
LEPR 0.012 0.07 -10000 0 -0.3 23 23
BCAR1 0.022 0.011 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.03 0.13 0.25 8 -0.32 45 53
PRL 0.006 0.026 0.17 4 -10000 0 4
SOCS3 -0.14 0.4 -10000 0 -1.1 69 69
SPRY2 0.021 0.031 -10000 0 -0.31 4 4
Insulin Receptor/Insulin/IRS1 0.043 0.044 -10000 0 -0.18 15 15
CSF1/CSF1R 0.016 0.088 0.27 2 -0.26 18 20
Ras protein signal transduction 0.004 0.084 0.48 13 -10000 0 13
IRS1 0.017 0.058 -10000 0 -0.31 15 15
INS 0.015 0.03 0.18 12 -10000 0 12
LEP 0.017 0.028 0.17 10 -10000 0 10
STAT5B 0.009 0.079 0.24 8 -0.26 10 18
STAT5A 0.009 0.079 0.24 8 -0.26 10 18
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.076 0.24 5 -0.21 14 19
CSN2 0 0.051 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
LAT 0.012 0.092 -10000 0 -0.39 20 20
YBX1 0.033 0.005 -10000 0 -10000 0 0
LCK 0.03 0.02 0.17 9 -10000 0 9
SHC1 0.026 0.006 -10000 0 -10000 0 0
NOX4 0.096 0.076 0.18 230 -10000 0 230
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.01 0.14 -10000 0 -0.5 31 31
HDAC1 0.024 0.004 -10000 0 -10000 0 0
AES 0.026 0.005 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
DTX1 0.031 0.032 0.17 18 -0.31 1 19
LRP6/FZD1 0.032 0.02 -10000 0 -0.21 1 1
TLE1 0.025 0.006 -10000 0 -10000 0 0
AP1 -0.026 0.1 -10000 0 -0.24 76 76
NCSTN 0.026 0.006 -10000 0 -10000 0 0
ADAM10 0.012 0.068 -10000 0 -0.31 21 21
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.039 -10000 0 -0.49 1 1
NICD/RBPSUH 0.009 0.13 -10000 0 -0.48 31 31
WIF1 -0.12 0.17 0.17 7 -0.31 220 227
NOTCH1 -0.009 0.13 -10000 0 -0.51 31 31
PSENEN 0.027 0.003 -10000 0 -10000 0 0
KREMEN2 0.023 0.062 0.17 21 -0.31 13 34
DKK1 -0.029 0.13 0.17 12 -0.31 87 99
beta catenin/beta TrCP1 0.037 0.058 0.26 5 -0.24 2 7
APH1B 0.027 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.006 -10000 0 -10000 0 0
AXIN1 0.002 0.069 0.25 1 -0.31 5 6
CtBP/CBP/TCF1/TLE1/AES 0.018 0.024 -10000 0 -10000 0 0
PSEN1 0.027 0.004 -10000 0 -10000 0 0
FOS -0.026 0.12 0.17 4 -0.31 78 82
JUN 0.024 0.031 0.17 1 -0.31 4 5
MAP3K7 0.022 0.01 -10000 0 -10000 0 0
CTNNB1 0.027 0.059 0.25 6 -0.25 2 8
MAPK3 0.026 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.067 0.24 2 -0.19 32 34
HNF1A 0.04 0.046 0.17 51 -10000 0 51
CTBP1 0.026 0.004 -10000 0 -10000 0 0
MYC 0.025 0.021 -10000 0 -10000 0 0
NKD1 0.005 0.083 0.17 6 -0.31 31 37
FZD1 0.024 0.017 -10000 0 -0.31 1 1
NOTCH1 precursor/Deltex homolog 1 0.012 0.13 -10000 0 -0.49 30 30
apoptosis -0.026 0.1 -10000 0 -0.24 76 76
Delta 1/NOTCHprecursor 0.008 0.13 -10000 0 -0.49 31 31
DLL1 0.022 0.04 -10000 0 -0.31 7 7
PPARD 0.025 0.052 -10000 0 -0.76 2 2
Gamma Secretase 0.073 0.025 -10000 0 -10000 0 0
APC -0.018 0.11 0.24 2 -0.36 31 33
DVL1 -0.001 0.032 -10000 0 -0.23 5 5
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.007 0.096 -10000 0 -0.18 91 91
LRP6 0.024 0.009 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
NLK 0.009 0.004 -10000 0 -10000 0 0
CCND1 0.027 0.014 -10000 0 -10000 0 0
WNT1 0.029 0.023 0.17 12 -10000 0 12
Axin1/APC/beta catenin 0.018 0.09 0.32 9 -0.37 7 16
DKK2 0.016 0.072 0.17 12 -0.31 21 33
NOTCH1 precursor/DVL1 -0.005 0.12 -10000 0 -0.45 31 31
GSK3B 0.025 0.007 -10000 0 -10000 0 0
FRAT1 0.025 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.014 0.14 -10000 0 -0.5 30 30
PPP2R5D 0.022 0.052 -10000 0 -0.37 3 3
MAPK1 0.027 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.034 0.11 -10000 0 -0.16 199 199
RBPJ 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.024 0.009 -10000 0 -10000 0 0
AES 0.024 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.02 -10000 0 -0.21 1 1
SMAD4 0.025 0.008 -10000 0 -10000 0 0
DKK2 0.016 0.072 0.17 12 -0.31 21 33
TLE1 0.024 0.007 -10000 0 -10000 0 0
MACF1 0.028 0.002 -10000 0 -10000 0 0
CTNNB1 0.071 0.099 0.3 37 -0.42 1 38
WIF1 -0.12 0.17 0.17 7 -0.31 220 227
beta catenin/RanBP3 0.029 0.068 0.44 5 -0.34 1 6
KREMEN2 0.023 0.062 0.17 21 -0.31 13 34
DKK1 -0.029 0.13 0.17 12 -0.31 87 99
beta catenin/beta TrCP1 0.075 0.091 0.3 26 -0.38 1 27
FZD1 0.024 0.017 -10000 0 -0.31 1 1
AXIN2 -0.005 0.15 0.54 6 -1.3 5 11
AXIN1 0.027 0.006 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.028 0.083 -10000 0 -0.49 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.11 0.28 12 -0.43 10 22
Axin1/APC/GSK3 0.042 0.056 0.24 11 -0.43 1 12
Axin1/APC/GSK3/beta catenin/Macf1 0.038 0.091 0.31 18 -0.36 6 24
HNF1A 0.039 0.046 0.17 51 -10000 0 51
CTBP1 0.024 0.007 -10000 0 -10000 0 0
MYC 0.12 0.22 0.55 99 -10000 0 99
RANBP3 0.026 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.067 0.24 2 -0.18 32 34
NKD1 0.005 0.083 0.17 6 -0.31 31 37
TCF4 0.02 0.028 -10000 0 -0.31 3 3
TCF3 0.024 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.056 0.035 -10000 0 -0.16 1 1
Ran/GTP 0.019 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.004 0.068 0.39 3 -0.35 2 5
LEF1 0.026 0.048 0.17 21 -0.31 6 27
DVL1 0.034 0.035 0.18 1 -10000 0 1
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.059 0.086 0.29 11 -0.37 3 14
DKK1/LRP6/Kremen 2 0.008 0.096 -10000 0 -0.18 91 91
LRP6 0.025 0.009 -10000 0 -10000 0 0
CSNK1A1 0.025 0.009 -10000 0 -10000 0 0
NLK 0.027 0.006 -10000 0 -10000 0 0
CCND1 0.024 0.12 0.53 21 -10000 0 21
WNT1 0.029 0.024 0.18 12 -10000 0 12
GSK3A 0.027 0.006 -10000 0 -10000 0 0
GSK3B 0.026 0.007 -10000 0 -10000 0 0
FRAT1 0.025 0.007 -10000 0 -10000 0 0
PPP2R5D 0.042 0.063 0.24 22 -0.34 3 25
APC 0.009 0.077 0.21 51 -0.15 1 52
WNT1/LRP6/FZD1 0.059 0.078 0.17 152 -10000 0 152
CREBBP 0.024 0.007 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.034 0.17 10 -0.31 3 13
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.045 0.084 -10000 0 -0.16 161 161
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
FYN 0.023 0.018 -10000 0 -0.31 1 1
MAP3K12 0.022 0.037 -10000 0 -0.31 6 6
FGR 0.026 0.022 0.17 1 -0.31 2 3
p38 alpha/TAB1 -0.043 0.078 -10000 0 -0.25 42 42
PRKG1 -0.062 0.15 -10000 0 -0.31 129 129
DUSP8 0.028 0.015 0.17 5 -10000 0 5
PGK/cGMP/p38 alpha -0.045 0.12 0.17 2 -0.27 72 74
apoptosis -0.042 0.075 -10000 0 -0.24 42 42
RAL/GTP 0.032 0.013 -10000 0 -10000 0 0
LYN 0.023 0.01 -10000 0 -10000 0 0
DUSP1 0.015 0.061 -10000 0 -0.31 17 17
PAK1 0.022 0.037 -10000 0 -0.31 6 6
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.06 0.025 -10000 0 -10000 0 0
TRAF6 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.011 -10000 0 -10000 0 0
MAPK11 -0.023 0.12 0.27 16 -0.3 38 54
BLK 0 0.1 0.17 32 -0.31 43 75
HCK 0.024 0.031 0.17 1 -0.31 4 5
MAP2K3 0.026 0.005 -10000 0 -10000 0 0
DUSP16 0.024 0.009 -10000 0 -10000 0 0
DUSP10 0.026 0.006 -10000 0 -10000 0 0
TRAF6/MEKK3 0.033 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.013 0.11 0.25 17 -0.29 36 53
positive regulation of innate immune response -0.023 0.14 0.31 15 -0.34 40 55
LCK 0.03 0.02 0.17 9 -10000 0 9
p38alpha-beta/MKP7 -0.012 0.14 0.32 13 -0.34 32 45
p38alpha-beta/MKP5 -0.015 0.14 0.33 11 -0.34 34 45
PGK/cGMP -0.041 0.1 -10000 0 -0.21 129 129
PAK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.02 0.14 0.33 11 -0.34 37 48
CDC42 0.027 0.003 -10000 0 -10000 0 0
RALB 0.026 0.006 -10000 0 -10000 0 0
RALA 0.024 0.008 -10000 0 -10000 0 0
PAK3 -0.098 0.16 -10000 0 -0.31 183 183
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.012 0.077 -10000 0 -0.21 51 51
ATM 0.025 0.016 -10000 0 -0.31 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.023 0.012 0.17 1 -10000 0 1
ATR 0.025 0.007 -10000 0 -10000 0 0
UBE2L3 0.026 0.005 -10000 0 -10000 0 0
FANCD2 0.017 0.011 0.2 1 -10000 0 1
protein ubiquitination 0.04 0.071 -10000 0 -0.16 49 49
XRCC5 0.027 0.004 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.024 -10000 0 -10000 0 0
MRE11A 0.026 0.006 -10000 0 -10000 0 0
DNA-PK 0.045 0.023 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.011 0.05 -10000 0 -0.3 1 1
FANCF 0.027 0.004 -10000 0 -10000 0 0
BRCA1 0.026 0.009 0.17 1 -10000 0 1
CCNE1 0.028 0.015 0.17 5 -10000 0 5
CDK2/Cyclin E1 0.04 0.013 0.14 5 -10000 0 5
FANCG 0.026 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.012 0.077 0.14 1 -0.21 51 52
FANCE 0.027 0.004 -10000 0 -10000 0 0
FANCC 0.026 0.006 -10000 0 -10000 0 0
NBN 0.021 0.011 -10000 0 -10000 0 0
FANCA 0.03 0.042 0.17 28 -0.31 2 30
DNA repair -0.01 0.067 0.62 1 -0.25 1 2
BRCA1/BARD1/ubiquitin 0.012 0.077 0.14 1 -0.21 51 52
BARD1/DNA-PK 0.033 0.072 -10000 0 -0.16 50 50
FANCL 0.026 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.012 0.077 0.21 51 -10000 0 51
BRCA1/BARD1/CTIP/M/R/N Complex 0.005 0.066 -10000 0 -0.18 47 47
BRCA1/BACH1/BARD1/TopBP1 0.025 0.071 -10000 0 -0.18 49 49
BRCA1/BARD1/P53 0.031 0.071 -10000 0 -0.16 49 49
BARD1/CSTF1/BRCA1 0.027 0.071 -10000 0 -0.18 49 49
BRCA1/BACH1 0.026 0.009 0.17 1 -10000 0 1
BARD1 -0.009 0.1 -10000 0 -0.31 53 53
PCNA 0.026 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.027 0.072 -10000 0 -0.18 51 51
BRCA1/BARD1/UbcH7 0.027 0.072 -10000 0 -0.18 51 51
BRCA1/BARD1/RAD51/PCNA 0.045 0.078 0.26 2 -0.17 49 51
BARD1/DNA-PK/P53 0.036 0.073 -10000 0 -0.15 50 50
BRCA1/BARD1/Ubiquitin 0.012 0.077 0.14 1 -0.21 51 52
BRCA1/BARD1/CTIP 0.016 0.064 -10000 0 -0.17 50 50
FA complex 0.023 0.035 0.19 3 -0.17 3 6
BARD1/EWS 0.012 0.078 -10000 0 -0.21 53 53
RBBP8 -0.011 0.01 -10000 0 -0.21 1 1
TP53 0.023 0.01 -10000 0 -10000 0 0
TOPBP1 0.025 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.03 0.069 0.16 49 -10000 0 49
BRCA1/BARD1 0.045 0.074 -10000 0 -0.16 49 49
CSTF1 0.026 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.005 0.071 -10000 0 -0.21 53 53
CDK2 0.026 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.037 0.039 0.17 37 -10000 0 37
RAD50 0.026 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.012 0.077 0.14 1 -0.21 51 52
EWSR1 0.026 0.005 -10000 0 -10000 0 0
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 -0.009 0.098 -10000 0 -0.21 92 92
AKT1 -0.013 0.15 0.35 8 -0.42 41 49
PTK2B -0.046 0.11 0.18 2 -0.48 24 26
VEGFR2 homodimer/Frs2 0.008 0.11 -10000 0 -0.49 21 21
CAV1 -0.013 0.1 -10000 0 -0.31 55 55
CALM1 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.015 0.11 -10000 0 -0.47 21 21
endothelial cell proliferation -0.02 0.16 0.33 16 -0.47 30 46
mol:Ca2+ -0.014 0.11 0.18 6 -0.47 21 27
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.026 0.11 -10000 0 -0.46 20 20
RP11-342D11.1 -0.032 0.1 0.17 7 -0.46 22 29
CDH5 0.024 0.009 -10000 0 -10000 0 0
VEGFA homodimer 0.051 0.056 -10000 0 -0.16 27 27
SHC1 0.026 0.006 -10000 0 -10000 0 0
SHC2 0.029 0.031 0.17 11 -0.31 2 13
HRAS/GDP 0.016 0.1 -10000 0 -0.41 22 22
SH2D2A 0.03 0.041 0.17 22 -0.31 3 25
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.019 0.12 0.31 1 -0.43 22 23
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.017 0.12 -10000 0 -0.32 43 43
VEGFR1 homodimer 0.024 0.028 0.17 2 -0.31 3 5
SHC/GRB2/SOS1 0.037 0.12 -10000 0 -0.44 22 22
GRB10 -0.014 0.1 0.18 3 -0.47 20 23
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
PAK1 0.022 0.037 -10000 0 -0.31 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.035 0.11 -10000 0 -0.44 21 21
HRAS 0.028 0.017 0.17 6 -10000 0 6
VEGF/Rho/ROCK1/Integrin Complex -0.039 0.13 -10000 0 -0.38 39 39
HIF1A 0.026 0.016 -10000 0 -0.31 1 1
FRS2 0.026 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.025 0.11 -10000 0 -0.45 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.025 0.023 0.17 1 -0.31 2 3
Nck/Pak 0.033 0.03 -10000 0 -0.21 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.01 0.11 -10000 0 -0.34 38 38
mol:GDP 0.025 0.11 -10000 0 -0.43 22 22
mol:NADP 0.006 0.11 0.35 12 -0.37 22 34
eNOS/Hsp90 0.013 0.1 0.3 6 -0.35 22 28
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
mol:IP3 -0.014 0.11 0.18 6 -0.48 21 27
HIF1A/ARNT 0.037 0.016 -10000 0 -0.21 1 1
SHB 0.024 0.026 -10000 0 -0.31 3 3
VEGFA 0.011 0.077 0.18 5 -0.31 26 31
VEGFC 0.026 0.017 0.17 1 -0.31 1 2
FAK1/Vinculin -0.05 0.18 0.27 3 -0.49 49 52
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.007 0.14 -10000 0 -0.49 26 26
PTPN6 0.025 0.007 -10000 0 -10000 0 0
EPAS1 0.017 0.071 0.18 1 -0.31 21 22
mol:L-citrulline 0.006 0.11 0.35 12 -0.37 22 34
ITGAV 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.028 0.11 -10000 0 -0.44 21 21
VEGFR2 homodimer/VEGFA homodimer 0.016 0.12 -10000 0 -0.5 22 22
VEGFR2/3 heterodimer 0.007 0.11 -10000 0 -0.49 22 22
VEGFB 0.026 0.005 -10000 0 -10000 0 0
MAPK11 -0.029 0.11 0.24 3 -0.46 24 27
VEGFR2 homodimer -0.009 0.12 -10000 0 -0.57 21 21
FLT1 0.025 0.028 0.17 2 -0.31 3 5
NEDD4 0.022 0.045 -10000 0 -0.31 9 9
MAPK3 -0.045 0.11 0.25 5 -0.46 25 30
MAPK1 -0.044 0.12 0.26 6 -0.48 23 29
VEGFA145/NRP2 0.011 0.084 0.14 4 -0.22 56 60
VEGFR1/2 heterodimer 0.007 0.11 -10000 0 -0.52 21 21
KDR -0.009 0.12 -10000 0 -0.57 21 21
VEGFA165/NRP1/VEGFR2 homodimer 0.007 0.13 -10000 0 -0.49 25 25
SRC 0.026 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.04 0.12 0.25 10 -0.47 25 35
PI3K -0.011 0.14 -10000 0 -0.43 41 41
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.013 0.11 -10000 0 -0.47 21 21
FES -0.015 0.11 0.18 7 -0.49 22 29
GAB1 -0.01 0.14 -10000 0 -0.41 43 43
VEGFR2 homodimer/VEGFA homodimer/Src 0.014 0.12 -10000 0 -0.32 42 42
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
ARNT 0.026 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.002 0.11 0.37 3 -0.42 22 25
VEGFR2 homodimer/VEGFA homodimer/Yes 0.014 0.11 -10000 0 -0.49 20 20
PI3K/GAB1 -0.011 0.15 -10000 0 -0.44 42 42
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.034 0.12 -10000 0 -0.47 19 19
PRKACA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.022 0.11 -10000 0 -0.46 22 22
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
CDC42 -0.015 0.11 0.18 7 -0.47 22 29
actin cytoskeleton reorganization 0.016 0.12 -10000 0 -0.31 43 43
PTK2 -0.056 0.17 -10000 0 -0.53 41 41
EDG1 -0.032 0.1 0.17 7 -0.46 22 29
mol:DAG -0.014 0.11 0.18 6 -0.48 21 27
CaM/Ca2+ 0 0.1 -10000 0 -0.44 21 21
MAP2K3 -0.039 0.1 0.17 6 -0.45 23 29
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.026 0.12 -10000 0 -0.48 20 20
PLCG1 -0.015 0.11 0.18 6 -0.48 21 27
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.11 -10000 0 -0.44 21 21
IQGAP1 0.027 0.003 -10000 0 -10000 0 0
YES1 0.025 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.014 0.12 -10000 0 -0.32 42 42
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.013 0.11 -10000 0 -0.47 21 21
cell migration -0.045 0.17 0.24 4 -0.47 46 50
mol:PI-3-4-5-P3 -0.009 0.13 -10000 0 -0.4 41 41
FYN 0.023 0.018 -10000 0 -0.31 1 1
VEGFB/NRP1 -0.007 0.1 0.18 6 -0.45 21 27
mol:NO 0.006 0.11 0.35 12 -0.37 22 34
PXN 0.026 0.006 -10000 0 -10000 0 0
HRAS/GTP 0 0.098 -10000 0 -0.41 22 22
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.007 0.11 -10000 0 -0.48 20 20
VHL 0.025 0.016 -10000 0 -0.31 1 1
ITGB3 -0.037 0.13 -10000 0 -0.31 92 92
NOS3 0.005 0.12 0.36 12 -0.42 22 34
VEGFR2 homodimer/VEGFA homodimer/Sck 0.015 0.12 -10000 0 -0.48 22 22
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.039 0.11 0.22 7 -0.49 20 27
PRKCB -0.06 0.12 0.17 5 -0.51 24 29
VCL 0.01 0.072 -10000 0 -0.31 24 24
VEGFA165/NRP1 -0.002 0.11 0.18 3 -0.46 22 25
VEGFR1/2 heterodimer/VEGFA homodimer 0.014 0.12 0.24 1 -0.49 21 22
VEGFA165/NRP2 0.011 0.084 0.14 4 -0.22 56 60
MAPKKK cascade 0.004 0.1 0.34 3 -0.42 20 23
NRP2 0.005 0.083 -10000 0 -0.31 32 32
VEGFC homodimer 0.026 0.017 0.17 1 -0.31 1 2
NCK1 0.025 0.007 -10000 0 -10000 0 0
ROCK1 0.025 0.016 -10000 0 -0.31 1 1
FAK1/Paxillin -0.046 0.17 0.3 3 -0.51 41 44
MAP3K13 -0.019 0.11 0.18 4 -0.47 24 28
PDPK1 -0.02 0.11 0.25 1 -0.37 38 39
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.028 0.13 0.28 12 -0.35 37 49
IKBKB -0.008 0.11 0.3 14 -0.26 39 53
AKT1 0.02 0.1 0.28 39 -0.23 5 44
IKBKG 0.028 0.074 0.29 13 -0.24 6 19
CALM1 0.01 0.084 0.28 8 -0.32 10 18
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
MAP3K1 -0.055 0.18 0.33 8 -0.47 52 60
MAP3K7 0.022 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.01 0.082 0.27 5 -0.34 10 15
DOK1 0.026 0.016 -10000 0 -0.31 1 1
AP-1 -0.01 0.082 0.28 9 -0.23 22 31
LYN 0.023 0.01 -10000 0 -10000 0 0
BLNK 0.024 0.017 -10000 0 -0.31 1 1
SHC1 0.026 0.006 -10000 0 -10000 0 0
BCR complex 0.039 0.08 0.18 52 -0.23 26 78
CD22 -0.015 0.1 0.18 1 -0.33 32 33
CAMK2G 0.008 0.078 0.28 7 -0.34 6 13
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
INPP5D 0.01 0.074 -10000 0 -0.31 25 25
SHC/GRB2/SOS1 0.021 0.046 -10000 0 -0.17 18 18
GO:0007205 0.011 0.085 0.27 5 -0.34 11 16
SYK 0.023 0.035 0.17 1 -0.31 5 6
ELK1 0.008 0.085 0.26 6 -0.32 12 18
NFATC1 0 0.1 0.29 15 -0.31 18 33
B-cell antigen/BCR complex 0.039 0.08 0.18 52 -0.23 26 78
PAG1/CSK 0.032 0.017 -10000 0 -10000 0 0
NFKBIB 0.015 0.046 0.15 13 -0.12 7 20
HRAS 0.019 0.078 0.26 14 -0.27 5 19
NFKBIA 0.016 0.045 0.15 14 -0.12 7 21
NF-kappa-B/RelA/I kappa B beta 0.019 0.04 0.15 16 -10000 0 16
RasGAP/Csk 0.064 0.085 0.27 19 -0.18 33 52
mol:GDP 0.013 0.086 0.26 6 -0.31 13 19
PTEN 0.022 0.011 -10000 0 -10000 0 0
CD79B 0.024 0.057 0.17 16 -0.31 11 27
NF-kappa-B/RelA/I kappa B alpha 0.02 0.04 0.15 16 -10000 0 16
GRB2 0.026 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.022 0.14 0.35 8 -0.43 24 32
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
mol:IP3 0.011 0.079 0.28 4 -0.35 10 14
CSK 0.027 0.003 -10000 0 -10000 0 0
FOS -0.012 0.094 0.3 5 -0.31 19 24
CHUK 0.014 0.1 0.3 12 -0.28 29 41
IBTK 0.023 0.01 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.025 0.077 0.25 6 -0.32 5 11
PTPN6 -0.021 0.095 -10000 0 -0.41 20 20
RELA 0.026 0.006 -10000 0 -10000 0 0
BCL2A1 0.015 0.03 0.12 9 -10000 0 9
VAV2 -0.019 0.1 0.33 1 -0.45 16 17
ubiquitin-dependent protein catabolic process 0.017 0.045 0.16 13 -0.12 7 20
BTK 0.024 0.097 -10000 0 -0.92 4 4
CD19 -0.025 0.1 0.19 2 -0.35 29 31
MAP4K1 0.031 0.048 0.17 26 -0.31 5 31
CD72 0.03 0.04 0.17 20 -0.31 3 23
PAG1 0.021 0.011 -10000 0 -10000 0 0
MAPK14 -0.046 0.16 0.32 10 -0.4 51 61
SH3BP5 0.026 0.005 -10000 0 -10000 0 0
PIK3AP1 0.009 0.082 0.3 3 -0.37 11 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.014 0.096 0.29 1 -0.43 13 14
RAF1 0.019 0.079 0.28 15 -0.26 5 20
RasGAP/p62DOK/SHIP 0.053 0.098 0.24 19 -0.2 46 65
CD79A 0.029 0.083 0.17 53 -0.31 20 73
re-entry into mitotic cell cycle -0.01 0.081 0.28 9 -0.22 22 31
RASA1 0.025 0.016 -10000 0 -0.31 1 1
MAPK3 0.017 0.08 0.28 18 -0.25 3 21
MAPK1 0.014 0.076 0.29 15 -0.25 3 18
CD72/SHP1 0 0.11 0.24 5 -0.39 21 26
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.048 0.16 0.33 10 -0.4 54 64
actin cytoskeleton organization -0.01 0.098 0.3 7 -0.39 14 21
NF-kappa-B/RelA 0.041 0.077 0.28 13 -0.19 1 14
Calcineurin 0.022 0.07 0.25 4 -0.32 5 9
PI3K -0.017 0.086 -10000 0 -0.32 20 20
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.007 0.081 0.22 1 -0.38 14 15
SOS1 0.026 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.081 0.3 -10000 0 -0.74 77 77
DAPP1 -0.11 0.32 -10000 0 -0.83 77 77
cytokine secretion 0.001 0.097 0.28 15 -0.29 18 33
mol:DAG 0.011 0.079 0.28 4 -0.35 10 14
PLCG2 0.021 0.026 0.17 2 -0.31 2 4
MAP2K1 0.017 0.076 0.28 14 -0.26 4 18
B-cell antigen/BCR complex/FcgammaRIIB 0.048 0.086 0.26 20 -0.2 32 52
mol:PI-3-4-5-P3 -0.024 0.061 0.18 6 -0.25 14 20
ETS1 0.01 0.082 0.28 14 -0.33 5 19
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.059 0.073 0.26 13 -0.17 21 34
B-cell antigen/BCR complex/LYN 0.001 0.098 0.23 1 -0.33 27 28
MALT1 0.023 0.019 0.17 1 -0.31 1 2
TRAF6 0.026 0.005 -10000 0 -10000 0 0
RAC1 -0.015 0.097 0.28 3 -0.42 14 17
B-cell antigen/BCR complex/LYN/SYK 0.023 0.11 0.28 1 -0.37 18 19
CARD11 0.021 0.098 0.28 27 -0.33 8 35
FCGR2B 0.023 0.051 0.17 12 -0.31 9 21
PPP3CA 0.027 0.013 0.17 3 -10000 0 3
BCL10 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.012 0.056 0.19 27 -0.11 6 33
PTPRC 0.016 0.066 0.17 7 -0.31 18 25
PDPK1 -0.013 0.061 0.22 14 -0.18 12 26
PPP3CB 0.026 0.005 -10000 0 -10000 0 0
PPP3CC 0.019 0.013 -10000 0 -10000 0 0
POU2F2 0.014 0.03 0.12 7 -0.099 1 8
Visual signal transduction: Rods

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
mol:K + 0.027 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.015 0.008 0.12 2 -10000 0 2
Metarhodopsin II/Arrestin 0.026 0.012 0.13 3 -10000 0 3
PDE6G/GNAT1/GTP 0.039 0.03 0.12 48 -10000 0 48
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.02 0.011 0.17 2 -10000 0 2
GRK1 0.02 0.015 0.17 4 -10000 0 4
CNG Channel 0.021 0.076 0.16 1 -0.16 60 61
mol:Na + 0.03 0.042 -10000 0 -0.15 8 8
mol:ADP 0.02 0.015 0.17 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.005 0.095 -10000 0 -0.18 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.044 0.044 -10000 0 -0.16 7 7
CNGB1 0.024 0.022 0.17 9 -10000 0 9
RDH5 0.016 0.061 0.17 3 -0.31 16 19
SAG 0.02 0.008 0.17 1 -10000 0 1
mol:Ca2+ -0.021 0.069 0.31 14 -10000 0 14
Na + (4 Units) 0.019 0.042 -10000 0 -0.15 7 7
RGS9 -0.041 0.14 0.17 3 -0.31 100 103
GNB1/GNGT1 0.031 0.013 -10000 0 -10000 0 0
GNAT1/GDP 0.014 0.087 -10000 0 -0.16 97 97
GUCY2D 0.036 0.06 0.17 55 -0.31 5 60
GNGT1 0.017 0.012 0.17 2 -10000 0 2
GUCY2F 0.019 0.007 0.17 1 -10000 0 1
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.067 0.16 3 -0.17 58 61
mol:11-cis-retinal 0.016 0.061 0.17 3 -0.31 16 19
mol:cGMP 0.039 0.034 -10000 0 -0.16 6 6
GNB1 0.027 0.004 -10000 0 -10000 0 0
Rhodopsin 0.026 0.044 0.14 5 -0.22 14 19
SLC24A1 0.027 0.003 -10000 0 -10000 0 0
CNGA1 0.025 0.032 0.17 3 -0.31 4 7
Metarhodopsin II 0.024 0.014 0.12 6 -10000 0 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.058 0.05 0.24 4 -0.17 6 10
RGS9BP 0.026 0.022 0.17 1 -0.31 2 3
Metarhodopsin II/Transducin 0.009 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.044 0.021 -10000 0 -0.16 1 1
PDE6A/B 0.002 0.096 0.14 1 -0.24 65 66
mol:Pi 0.005 0.095 -10000 0 -0.18 100 100
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.017 -10000 0 -10000 0 0
PDE6B -0.01 0.1 0.17 1 -0.31 54 55
PDE6A 0.013 0.069 0.17 3 -0.31 21 24
PDE6G 0.041 0.044 0.17 48 -10000 0 48
RHO 0.02 0.012 0.17 2 -10000 0 2
PDE6 0.009 0.13 0.23 1 -0.2 126 127
GUCA1A 0.023 0.011 0.17 2 -10000 0 2
GC2/GCAP Family 0.055 0.023 -10000 0 -0.17 1 1
GUCA1C 0.018 0.008 0.17 1 -10000 0 1
GUCA1B 0.031 0.03 0.17 15 -0.31 1 16
S1P3 pathway

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
PDGFRB 0.027 0.01 0.17 2 -10000 0 2
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.026 0.1 0.15 1 -0.25 74 75
GNAO1 -0.024 0.12 -10000 0 -0.31 71 71
S1P/S1P3/G12/G13 0.04 0.04 -10000 0 -0.16 14 14
AKT1 0.007 0.07 -10000 0 -0.46 6 6
AKT3 -0.016 0.12 -10000 0 -0.75 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.01 0.17 2 -10000 0 2
GNAI2 0.027 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.016 0.06 0.18 1 -0.31 16 17
S1PR2 0.027 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.12 -10000 0 -0.36 44 44
MAPK3 -0.027 0.12 -10000 0 -0.35 43 43
MAPK1 -0.024 0.11 -10000 0 -0.35 40 40
JAK2 -0.028 0.12 0.18 2 -0.36 48 50
CXCR4 -0.022 0.11 0.16 1 -0.36 39 40
FLT1 0.026 0.029 0.18 2 -0.31 3 5
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC -0.025 0.11 -10000 0 -0.35 41 41
S1P/S1P3/Gi -0.022 0.12 -10000 0 -0.36 44 44
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.12 -10000 0 -0.33 46 46
VEGFA 0.012 0.077 0.18 5 -0.31 26 31
S1P/S1P2/Gi -0.016 0.11 -10000 0 -0.26 69 69
VEGFR1 homodimer/VEGFA homodimer 0.029 0.062 0.16 6 -0.22 27 33
RHOA 0.026 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.001 0.074 -10000 0 -0.22 42 42
GNAQ 0.026 0.006 -10000 0 -10000 0 0
GNAZ -0.002 0.094 -10000 0 -0.31 42 42
G12/G13 0.035 0.013 -10000 0 -10000 0 0
GNA14 0.025 0.016 -10000 0 -0.31 1 1
GNA15 0.012 0.068 -10000 0 -0.31 21 21
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.016 0.058 -10000 0 -0.31 15 15
Rac1/GTP -0.015 0.12 -10000 0 -0.34 41 41
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.026 0.08 0.22 3 -0.35 14 17
Syndecan-4/Syndesmos 0.037 0.12 0.32 6 -0.55 12 18
positive regulation of JNK cascade 0.039 0.12 0.29 4 -0.5 14 18
Syndecan-4/ADAM12 0.039 0.12 0.28 7 -0.53 14 21
CCL5 0.021 0.055 0.17 7 -0.31 12 19
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
ITGA5 0.018 0.054 0.17 1 -0.31 13 14
SDCBP 0.022 0.01 -10000 0 -10000 0 0
PLG 0.025 0.038 0.17 23 -0.12 2 25
ADAM12 0.029 0.043 0.17 20 -0.31 4 24
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.049 0.025 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.033 0.12 0.32 5 -0.52 15 20
Syndecan-4/CXCL12/CXCR4 0.041 0.13 0.3 4 -0.54 14 18
Syndecan-4/Laminin alpha3 0.028 0.13 0.27 3 -0.49 18 21
MDK 0.031 0.027 0.17 16 -10000 0 16
Syndecan-4/FZD7 0.035 0.13 0.31 7 -0.47 20 27
Syndecan-4/Midkine 0.041 0.12 0.3 7 -0.58 11 18
FZD7 0.015 0.061 -10000 0 -0.31 17 17
Syndecan-4/FGFR1/FGF 0.029 0.12 -10000 0 -0.46 18 18
THBS1 0.016 0.063 0.17 5 -0.31 17 22
integrin-mediated signaling pathway 0.032 0.12 0.31 6 -0.42 20 26
positive regulation of MAPKKK cascade 0.039 0.12 0.29 4 -0.5 14 18
Syndecan-4/TACI 0.042 0.13 0.3 10 -0.53 14 24
CXCR4 0.025 0.032 0.17 6 -0.31 3 9
cell adhesion 0.004 0.062 0.19 7 -0.28 16 23
Syndecan-4/Dynamin 0.038 0.12 0.31 7 -0.52 14 21
Syndecan-4/TSP1 0.035 0.12 0.31 5 -0.47 17 22
Syndecan-4/GIPC 0.037 0.12 0.31 7 -0.52 14 21
Syndecan-4/RANTES 0.037 0.13 0.3 7 -0.49 18 25
ITGB1 0.026 0.004 -10000 0 -10000 0 0
LAMA1 0.02 0.07 0.17 22 -0.31 17 39
LAMA3 0 0.09 0.17 1 -0.31 38 39
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.011 0.12 0.73 9 -0.29 15 24
Syndecan-4/alpha-Actinin 0.036 0.12 0.31 7 -0.51 15 22
TFPI 0.023 0.056 0.17 15 -0.31 11 26
F2 0.032 0.038 0.17 26 -0.14 1 27
alpha5/beta1 Integrin 0.032 0.042 0.14 1 -0.21 13 14
positive regulation of cell adhesion 0.016 0.12 0.27 3 -0.49 18 21
ACTN1 0.022 0.037 -10000 0 -0.31 6 6
TNC 0.009 0.074 -10000 0 -0.31 25 25
Syndecan-4/CXCL12 0.034 0.12 0.31 3 -0.5 16 19
FGF6 0.018 0.011 0.17 2 -10000 0 2
RHOA 0.026 0.005 -10000 0 -10000 0 0
CXCL12 0.015 0.062 0.17 1 -0.31 17 18
TNFRSF13B 0.034 0.055 0.17 42 -0.31 5 47
FGF2 0.005 0.082 0.17 1 -0.31 31 32
FGFR1 0.02 0.019 -10000 0 -0.31 1 1
Syndecan-4/PI-4-5-P2 0.019 0.12 0.29 4 -0.52 14 18
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.05 0.17 4 -0.27 12 16
cell migration -0.027 0.015 -10000 0 -10000 0 0
PRKCD 0.024 0.019 -10000 0 -0.13 2 2
vasculogenesis 0.035 0.12 0.31 5 -0.45 17 22
SDC4 0.023 0.12 0.32 4 -0.56 14 18
Syndecan-4/Tenascin C 0.032 0.12 0.32 6 -0.44 20 26
Syndecan-4/PI-4-5-P2/PKC alpha -0.039 0.02 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.031 0.11 0.29 3 -0.54 11 14
MMP9 0.098 0.084 0.17 259 -0.31 5 264
Rac1/GTP 0.004 0.063 0.2 7 -0.28 16 23
cytoskeleton organization 0.037 0.12 0.31 6 -0.52 12 18
GIPC1 0.027 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.038 0.13 0.33 6 -0.46 19 25
IGF1 pathway

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
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTK2 0.022 0.011 -10000 0 -10000 0 0
CRKL -0.001 0.052 0.13 2 -0.19 29 31
GRB2/SOS1/SHC 0.049 0.018 -10000 0 -10000 0 0
HRAS 0.028 0.017 0.17 6 -10000 0 6
IRS1/Crk 0.009 0.056 -10000 0 -0.19 32 32
IGF-1R heterotetramer/IGF1/PTP1B 0.038 0.061 0.25 1 -0.18 29 30
AKT1 -0.013 0.069 0.18 28 -0.28 8 36
BAD -0.017 0.064 0.17 26 -0.27 7 33
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.002 0.05 -10000 0 -0.19 28 28
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.016 0.063 0.22 1 -0.2 32 33
RAF1 0.004 0.073 0.28 3 -0.4 6 9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.043 0.069 0.24 1 -0.18 32 33
YWHAZ 0.021 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.066 0.14 15 -0.2 32 47
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
RPS6KB1 -0.014 0.07 0.18 29 -0.28 8 37
GNB2L1 0.028 0.014 0.17 4 -10000 0 4
positive regulation of MAPKKK cascade 0.009 0.081 0.29 13 -0.34 4 17
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.018 0.053 -10000 0 -0.17 28 28
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.059 0.063 0.26 1 -0.15 29 30
IGF-1R heterotetramer 0.022 0.027 0.2 1 -0.068 31 32
IGF-1R heterotetramer/IGF1/IRS/Nck 0.034 0.066 0.24 1 -0.19 31 32
Crk/p130 Cas/Paxillin 0.033 0.063 0.23 1 -0.19 22 23
IGF1R 0.022 0.027 0.2 1 -0.068 31 32
IGF1 0.026 0.057 0.2 17 -0.36 7 24
IRS2/Crk 0.008 0.056 0.16 3 -0.19 30 33
PI3K 0.037 0.072 0.24 1 -0.19 32 33
apoptosis 0.016 0.048 0.22 5 -0.15 13 18
HRAS/GDP 0.021 0.012 0.12 6 -10000 0 6
PRKCD -0.006 0.08 0.19 2 -0.3 30 32
RAF1/14-3-3 E 0.023 0.074 0.28 7 -0.34 6 13
BAD/14-3-3 -0.017 0.05 0.16 13 -0.23 5 18
PRKCZ -0.014 0.069 0.18 27 -0.28 8 35
Crk/p130 Cas/Paxillin/FAK1 0.016 0.052 0.15 2 -0.27 4 6
PTPN1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.004 0.084 -10000 0 -0.3 32 32
BCAR1 0.022 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.047 0.058 0.25 1 -0.16 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.06 0.15 2 -0.19 31 33
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 -0.002 0.054 -10000 0 -0.2 31 31
IRS1 0.003 0.06 0.12 19 -0.21 31 50
IRS2 -0.002 0.054 0.13 2 -0.2 30 32
IGF-1R heterotetramer/IGF1 0.023 0.075 0.21 3 -0.24 32 35
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDPK1 -0.016 0.064 0.18 17 -0.2 24 41
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKD1 -0.006 0.081 0.19 2 -0.29 32 34
SHC1 0.026 0.006 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.031 0.063 -10000 0 -0.34 3 3
epithelial cell differentiation 0.042 0.065 -10000 0 -0.32 1 1
ITCH 0.031 0.016 -10000 0 -10000 0 0
WWP1 0.028 0.079 -10000 0 -0.44 1 1
FYN 0.023 0.018 -10000 0 -0.31 1 1
EGFR -0.002 0.09 -10000 0 -0.31 39 39
PRL 0.02 0.015 0.17 4 -10000 0 4
neuron projection morphogenesis 0 0.094 0.26 27 -0.32 5 32
PTPRZ1 -0.072 0.16 0.17 12 -0.31 146 158
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.014 0.079 -10000 0 -0.27 12 12
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.007 0.068 -10000 0 -0.28 12 12
ADAM17 0.028 0.033 -10000 0 -0.3 4 4
ErbB4/ErbB4 0.019 0.063 -10000 0 -0.38 3 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.025 0.066 -10000 0 -0.32 5 5
NCOR1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.002 0.068 -10000 0 -0.27 10 10
GRIN2B -0.007 0.063 0.22 4 -0.26 9 13
ErbB4/ErbB2/betacellulin 0.02 0.078 0.25 1 -0.31 15 16
STAT1 0.029 0.019 0.17 8 -10000 0 8
HBEGF 0.027 0.027 0.17 6 -0.31 2 8
PRLR 0.018 0.077 0.17 22 -0.31 22 44
E4ICDs/ETO2 0.027 0.054 -10000 0 -0.32 3 3
axon guidance 0.024 0.062 -10000 0 -0.34 2 2
NEDD4 0.025 0.038 -10000 0 -0.29 6 6
Prolactin receptor/Prolactin receptor/Prolactin 0.027 0.056 0.14 7 -0.22 20 27
CBFA2T3 0.02 0.028 -10000 0 -0.31 3 3
ErbB4/ErbB2/HBEGF 0.029 0.058 0.25 1 -0.28 7 8
MAPK3 0.005 0.083 0.25 17 -0.33 5 22
STAT1 (dimer) 0.033 0.065 -10000 0 -0.29 5 5
MAPK1 0.006 0.082 0.24 16 -0.33 5 21
JAK2 0.026 0.016 -10000 0 -0.31 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.01 0.068 -10000 0 -0.27 12 12
NRG1 -0.032 0.07 -10000 0 -0.22 60 60
NRG3 0.009 0.083 0.17 18 -0.31 28 46
NRG2 -0.08 0.16 -10000 0 -0.31 155 155
NRG4 -0.076 0.16 0.17 8 -0.31 154 162
heart development 0.024 0.062 -10000 0 -0.34 2 2
neural crest cell migration -0.009 0.067 -10000 0 -0.27 12 12
ERBB2 -0.007 0.033 0.27 1 -0.2 9 10
WWOX/E4ICDs 0.025 0.054 -10000 0 -0.33 3 3
SHC1 0.026 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.025 0.12 -10000 0 -0.32 33 33
apoptosis -0.002 0.1 0.33 31 -10000 0 31
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.006 0.084 -10000 0 -0.28 31 31
ErbB4/ErbB2/epiregulin 0.024 0.069 0.24 1 -0.27 8 9
ErbB4/ErbB4/betacellulin/betacellulin 0.024 0.079 -10000 0 -0.31 15 15
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.052 0.082 -10000 0 -0.28 8 8
MDM2 0.017 0.07 0.34 11 -0.34 3 14
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.066 -10000 0 -0.24 12 12
STAT5A 0.03 0.07 0.31 3 -0.32 2 5
ErbB4/EGFR/neuregulin 1 beta -0.012 0.088 -10000 0 -0.3 23 23
DLG4 0.017 0.045 -10000 0 -0.31 9 9
GRB2/SHC 0.037 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.026 0.055 -10000 0 -0.32 3 3
STAT5A (dimer) 0.059 0.078 0.3 2 -0.34 1 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.057 0.079 0.33 4 -0.32 2 6
LRIG1 0.026 0.005 -10000 0 -10000 0 0
EREG 0.013 0.08 0.17 19 -0.31 25 44
BTC 0.005 0.081 -10000 0 -0.31 31 31
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.016 0.055 -10000 0 -0.34 2 2
ERBB4 0.003 0.048 -10000 0 -0.38 3 3
STAT5B 0.026 0.005 -10000 0 -10000 0 0
YAP1 0.015 0.067 -10000 0 -0.48 7 7
GRB2 0.026 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.014 0.097 0.25 1 -0.28 20 21
glial cell differentiation -0.025 0.054 0.32 3 -10000 0 3
WWOX 0.022 0.011 -10000 0 -10000 0 0
cell proliferation -0.025 0.11 0.24 4 -0.5 12 16
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.019 0.004 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.004 0.055 -10000 0 -0.21 15 15
IRAK/TOLLIP 0.028 0.008 -10000 0 -10000 0 0
IKBKB 0.021 0.011 -10000 0 -10000 0 0
IKBKG 0.027 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.012 0.1 0.14 3 -0.22 96 99
IL1A 0.022 0.029 0.17 3 -0.31 3 6
IL1B -0.037 0.075 0.26 1 -0.24 52 53
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.032 -10000 0 -10000 0 0
IL1R2 -0.036 0.13 -10000 0 -0.31 93 93
IL1R1 0.026 0.021 -10000 0 -0.31 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.047 -10000 0 -0.2 4 4
TOLLIP 0.027 0.004 -10000 0 -10000 0 0
TICAM2 0.02 0.04 -10000 0 -0.31 7 7
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.003 0.085 0.26 3 -0.31 12 15
JUN -0.008 0.054 0.18 27 -0.18 3 30
MAP3K7 0.022 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.033 0.083 -10000 0 -0.17 58 58
IL1 alpha/IL1R1/IL1RAP/MYD88 0.058 0.036 -10000 0 -0.19 6 6
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.067 0.039 -10000 0 -0.18 6 6
IL1 beta fragment/IL1R1/IL1RAP 0.014 0.074 0.2 1 -0.18 56 57
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.001 0.055 0.19 29 -0.14 9 38
IRAK1 0.012 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.03 0.053 0.14 7 -0.21 21 28
IRAK4 0.027 0.004 -10000 0 -10000 0 0
PRKCI 0.025 0.01 0.17 1 -10000 0 1
TRAF6 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.034 -10000 0 -0.24 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.06 -10000 0 -0.22 14 14
CHUK 0.025 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.014 0.074 0.2 1 -0.18 56 57
IL1 beta/IL1R2 -0.031 0.11 -10000 0 -0.21 121 121
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.02 0.074 -10000 0 -0.17 48 48
IRAK3 0.012 0.066 -10000 0 -0.31 20 20
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.034 0.083 0.21 1 -0.17 60 61
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.028 -10000 0 -0.21 6 6
IL1 alpha/IL1R1/IL1RAP 0.046 0.034 -10000 0 -0.21 6 6
RELA 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.004 -10000 0 -10000 0 0
MYD88 0.026 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.049 0.029 0.18 21 -10000 0 21
IL1RAP 0.023 0.031 -10000 0 -0.31 4 4
UBE2N 0.026 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 0.004 0.065 -10000 0 -0.26 7 7
CASP1 0.016 0.056 -10000 0 -0.31 14 14
IL1RN/IL1R2 -0.016 0.11 0.14 6 -0.22 106 112
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.076 0.2 1 -0.17 55 56
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.023 0.042 -10000 0 -0.27 4 4
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
IL1RN 0.016 0.067 0.17 7 -0.31 19 26
TRAF6/TAK1/TAB1/TAB2 0.031 0.017 -10000 0 -10000 0 0
MAP2K6 0.007 0.055 0.2 29 -0.14 1 30
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.028 0.016 -10000 0 -0.31 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.006 0.15 0.74 11 -0.7 1 12
IL27/IL27R/JAK1 0.046 0.19 0.4 6 -0.93 9 15
TBX21 0.022 0.16 0.4 12 -0.53 11 23
IL12B 0.034 0.036 0.18 30 -10000 0 30
IL12A -0.002 0.03 0.25 1 -0.21 8 9
IL6ST -0.029 0.13 0.19 1 -0.31 81 82
IL27RA/JAK1 0.009 0.15 0.45 1 -1.1 9 10
IL27 0.03 0.033 0.19 16 -10000 0 16
TYK2 0.029 0.011 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.016 0.11 0.46 1 -10000 0 1
T-helper 2 cell differentiation 0.006 0.15 0.74 11 -0.7 1 12
T cell proliferation during immune response 0.006 0.15 0.74 11 -0.7 1 12
MAPKKK cascade -0.006 0.15 0.7 1 -0.74 11 12
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT2 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.032 0.02 0.17 9 -10000 0 9
IL12RB1 0.029 0.047 0.18 18 -0.31 6 24
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.02 0.17 0.46 12 -0.51 13 25
IL27/IL27R/JAK2/TYK2 -0.007 0.15 0.7 1 -0.76 11 12
positive regulation of T cell mediated cytotoxicity -0.006 0.15 0.7 1 -0.74 11 12
STAT1 (dimer) 0.077 0.24 0.5 81 -0.75 9 90
JAK2 0.026 0.017 -10000 0 -0.31 1 1
JAK1 0.029 0.009 0.14 1 -10000 0 1
STAT2 (dimer) -0.001 0.15 0.59 1 -0.67 12 13
T cell proliferation -0.024 0.15 0.37 7 -0.7 12 19
IL12/IL12R/TYK2/JAK2 0.039 0.088 -10000 0 -0.57 6 6
IL17A -0.016 0.11 0.47 1 -10000 0 1
mast cell activation 0.006 0.15 0.74 11 -0.7 1 12
IFNG 0.007 0.029 0.18 2 -0.094 9 11
T cell differentiation -0.001 0.005 0.012 8 -0.02 12 20
STAT3 (dimer) -0.002 0.15 0.59 1 -0.68 12 13
STAT5A (dimer) -0.002 0.15 0.59 1 -0.72 11 12
STAT4 (dimer) 0 0.15 0.59 1 -0.69 12 13
STAT4 0.028 0.039 0.17 13 -0.31 4 17
T cell activation -0.005 0.013 0.12 5 -10000 0 5
IL27R/JAK2/TYK2 0.004 0.16 -10000 0 -0.97 9 9
GATA3 -0.35 0.54 0.65 3 -1.2 145 148
IL18 -0.01 0.032 -10000 0 -0.21 12 12
positive regulation of mast cell cytokine production -0.002 0.14 0.44 2 -0.66 12 14
IL27/EBI3 0.045 0.039 0.17 6 -0.22 4 10
IL27RA -0.011 0.16 -10000 0 -1.1 9 9
IL6 -0.021 0.14 0.2 6 -0.31 90 96
STAT5A 0.026 0.005 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.004 0.069 0.45 9 -10000 0 9
IL1B -0.028 0.061 -10000 0 -0.21 49 49
EBI3 0.029 0.041 0.18 9 -0.31 5 14
TNF -0.016 0.046 0.25 1 -0.21 24 25
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.019 0.01 -10000 0 -10000 0 0
epithelial cell differentiation 0.047 0.023 -10000 0 -10000 0 0
CYFIP2 0.026 0.005 -10000 0 -10000 0 0
ENAH -0.009 0.088 0.38 15 -10000 0 15
EGFR -0.002 0.09 -10000 0 -0.31 39 39
EPHA2 -0.002 0.096 0.17 3 -0.31 43 46
MYO6 0.007 0.055 0.19 24 -10000 0 24
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.051 0.015 -10000 0 -10000 0 0
AQP5 -0.14 0.19 -10000 0 -0.39 186 186
CTNND1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.052 0.19 29 -10000 0 29
regulation of calcium-dependent cell-cell adhesion -0.004 0.058 0.2 29 -10000 0 29
EGF 0.023 0.084 0.17 40 -0.31 23 63
NCKAP1 0.026 0.005 -10000 0 -10000 0 0
AQP3 0.002 0.071 0.34 2 -0.37 14 16
cortical microtubule organization 0.047 0.023 -10000 0 -10000 0 0
GO:0000145 -0.002 0.049 0.18 29 -10000 0 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.052 0.026 -10000 0 -10000 0 0
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.032 0.034 -10000 0 -0.15 28 28
ARF6 0.027 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.066 0.19 1 -0.17 39 40
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.035 0.17 11 -10000 0 11
PVRL2 0.027 0.004 -10000 0 -10000 0 0
ZYX -0.005 0.043 0.2 18 -10000 0 18
ARF6/GTP 0.048 0.067 -10000 0 -0.16 39 39
CDH1 0.024 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.022 0.068 -10000 0 -0.15 54 54
RhoA/GDP 0.048 0.024 -10000 0 -10000 0 0
actin cytoskeleton organization -0.013 0.041 0.16 19 -0.16 1 20
IGF-1R heterotetramer 0.026 0.017 0.17 1 -0.31 1 2
GIT1 0.027 0.002 -10000 0 -10000 0 0
IGF1R 0.026 0.017 0.17 1 -0.31 1 2
IGF1 0.008 0.089 0.17 17 -0.31 33 50
DIAPH1 0.025 0.12 -10000 0 -0.48 19 19
Wnt receptor signaling pathway -0.047 0.023 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.034 -10000 0 -0.15 28 28
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL -0.013 0.042 0.16 19 -0.16 1 20
EFNA1 0.026 0.006 -10000 0 -10000 0 0
LPP -0.014 0.047 0.18 16 -10000 0 16
Ephrin A1/EPHA2 0.027 0.056 -10000 0 -0.14 40 40
SEC6/SEC8 -0.02 0.012 -10000 0 -10000 0 0
MGAT3 -0.004 0.059 0.2 29 -10000 0 29
HGF/MET 0.02 0.07 -10000 0 -0.18 45 45
HGF 0.011 0.075 0.17 9 -0.31 24 33
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.019 0.01 -10000 0 -10000 0 0
actin cable formation 0.016 0.11 0.31 42 -0.24 5 47
KIAA1543 -0.005 0.044 0.18 22 -10000 0 22
KIFC3 -0.006 0.044 0.19 21 -10000 0 21
NCK1 0.025 0.007 -10000 0 -10000 0 0
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ACTN1 -0.004 0.048 0.19 23 -10000 0 23
NCK1/GIT1 0.037 0.011 -10000 0 -10000 0 0
mol:GDP 0.047 0.023 -10000 0 -10000 0 0
EXOC4 0.024 0.008 -10000 0 -10000 0 0
STX4 -0.002 0.051 0.2 26 -10000 0 26
PIP5K1C -0.001 0.053 0.2 29 -10000 0 29
LIMA1 0.027 0.003 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 -0.006 0.096 0.4 15 -10000 0 15
adherens junction assembly -0.009 0.098 0.27 18 -0.47 9 27
IGF-1R heterotetramer/IGF1 0.032 0.048 0.16 1 -0.15 24 25
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.009 -10000 0 -10000 0 0
MET -0.004 0.093 -10000 0 -0.31 42 42
PLEKHA7 -0.004 0.047 0.2 22 -10000 0 22
mol:GTP 0.041 0.065 -10000 0 -0.16 39 39
establishment of epithelial cell apical/basal polarity 0.005 0.091 0.32 27 -10000 0 27
cortical actin cytoskeleton stabilization 0.019 0.01 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.013 0.041 0.16 19 -0.16 1 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.019 0.01 -10000 0 -10000 0 0
Insulin Pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.018 0.078 -10000 0 -0.17 63 63
TC10/GTP 0.018 0.064 -10000 0 -0.15 48 48
Insulin Receptor/Insulin/IRS1/Shp2 0.056 0.048 -10000 0 -0.18 14 14
HRAS 0.028 0.017 0.17 6 -10000 0 6
APS homodimer 0.028 0.03 0.17 14 -0.31 1 15
GRB14 0.048 0.062 0.17 82 -0.31 3 85
FOXO3 -0.12 0.26 -10000 0 -0.56 126 126
AKT1 -0.011 0.079 0.24 20 -0.28 5 25
INSR 0.029 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.056 0.028 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.008 -10000 0 -10000 0 0
SORBS1 -0.022 0.12 -10000 0 -0.31 70 70
CRK 0.025 0.007 -10000 0 -10000 0 0
PTPN1 -0.007 0.021 0.15 8 -10000 0 8
CAV1 -0.031 0.057 0.2 4 -0.18 51 55
CBL/APS/CAP/Crk-II/C3G 0.038 0.08 -10000 0 -0.16 54 54
Insulin Receptor/Insulin/IRS1/NCK2 0.059 0.044 -10000 0 -0.17 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.049 -10000 0 -0.19 15 15
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.051 -10000 0 -0.27 8 8
RPS6KB1 -0.015 0.073 0.18 38 -0.27 5 43
PARD6A 0.025 0.018 0.17 5 -10000 0 5
CBL 0.025 0.016 -10000 0 -0.31 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.068 -10000 0 -0.59 6 6
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.022 0.061 0.16 9 -0.26 6 15
HRAS/GTP -0.033 0.038 -10000 0 -0.17 29 29
Insulin Receptor 0.029 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.065 0.049 -10000 0 -0.16 14 14
PRKCI 0.021 0.051 -10000 0 -0.33 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.024 0.049 -10000 0 -0.2 16 16
SHC1 0.026 0.006 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.034 0.061 -10000 0 -0.45 6 6
PI3K 0.049 0.053 -10000 0 -0.19 15 15
NCK2 0.027 0.003 -10000 0 -10000 0 0
RHOQ 0.026 0.005 -10000 0 -10000 0 0
mol:H2O2 -0.001 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.012 0.12 6 -10000 0 6
AKT2 -0.012 0.076 0.2 29 -0.28 5 34
PRKCZ 0.022 0.049 -10000 0 -0.33 4 4
SH2B2 0.028 0.03 0.17 14 -0.31 1 15
SHC/SHIP 0.011 0.054 0.17 6 -0.18 30 36
F2RL2 0.076 0.074 0.17 173 -0.31 1 174
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.047 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.035 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.07 0.032 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
RASA1 0.025 0.016 -10000 0 -0.31 1 1
NCK1 0.025 0.007 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.03 0.081 -10000 0 -0.17 59 59
TC10/GDP 0.02 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.058 0.03 -10000 0 -10000 0 0
INPP5D -0.023 0.05 0.18 8 -0.18 29 37
SOS1 0.026 0.005 -10000 0 -10000 0 0
SGK1 -0.11 0.28 -10000 0 -0.77 76 76
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
IRS1 0.017 0.058 -10000 0 -0.31 15 15
p62DOK/RasGAP 0.035 0.061 -10000 0 -0.45 6 6
INS 0.024 0.026 0.19 12 -10000 0 12
mol:PI-3-4-P2 -0.023 0.05 0.18 8 -0.18 29 37
GRB2 0.026 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.059 0.18 21 -0.28 5 26
PTPRA 0.029 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
TC10/GTP/CIP4 0.035 0.008 -10000 0 -10000 0 0
PDPK1 0.026 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.017 0.037 -10000 0 -0.18 13 13
Insulin Receptor/Insulin/IRS1 0.043 0.04 -10000 0 -0.16 14 14
Insulin Receptor/Insulin/IRS3 0.038 0.021 0.15 12 -10000 0 12
Par3/Par6 0.073 0.061 0.23 2 -0.13 2 4
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.066 0.15 0.17 1 -0.31 137 138
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.028 0.018 0.17 7 -10000 0 7
TCEB1 0.021 0.011 -10000 0 -10000 0 0
HIF1A/p53 0.01 0.067 0.23 4 -0.25 26 30
HIF1A -0.007 0.062 -10000 0 -0.26 25 25
COPS5 0.022 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.061 0.039 -10000 0 -0.19 1 1
FIH (dimer) 0.025 0.007 -10000 0 -10000 0 0
CDKN2A 0.056 0.06 0.17 100 -10000 0 100
ARNT/IPAS -0.028 0.11 0.14 1 -0.21 128 129
HIF1AN 0.025 0.007 -10000 0 -10000 0 0
GNB2L1 0.028 0.014 0.17 4 -10000 0 4
HIF1A/ARNT 0.009 0.065 0.2 3 -0.26 24 27
CUL2 0.026 0.004 -10000 0 -10000 0 0
OS9 0.027 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.044 0.028 0.24 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.009 0.067 -10000 0 -0.26 26 26
PHD1-3/OS9 0.06 0.035 -10000 0 -0.16 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.026 0.066 -10000 0 -0.24 21 21
VHL 0.025 0.016 -10000 0 -0.31 1 1
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.005 0.061 -10000 0 -0.25 23 23
EGLN3 0.02 0.045 -10000 0 -0.31 9 9
EGLN2 0.027 0.004 -10000 0 -10000 0 0
EGLN1 0.026 0.006 -10000 0 -10000 0 0
TP53 0.023 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.021 0.082 -10000 0 -0.46 13 13
ARNT 0.026 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.003 -10000 0 -10000 0 0
HIF1A/p19ARF 0.028 0.084 0.2 12 -0.26 25 37
Caspase cascade in apoptosis

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
TOP1 0.005 0.076 0.22 4 -0.33 14 18
ACTA1 -0.038 0.094 0.19 8 -0.35 23 31
NUMA1 0.007 0.073 0.22 4 -0.32 14 18
SPTAN1 -0.005 0.09 0.21 25 -0.34 17 42
LIMK1 0.001 0.097 0.21 41 -0.32 19 60
BIRC3 0.025 0.025 0.17 3 -0.31 2 5
BIRC2 0.026 0.006 -10000 0 -10000 0 0
BAX 0.027 0.01 0.17 2 -10000 0 2
CASP10 -0.025 0.053 0.22 3 -0.24 23 26
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.001 -10000 0 -10000 0 0
PTK2 0.001 0.077 0.21 4 -0.3 19 23
DIABLO 0.026 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.089 0.21 25 -0.34 17 42
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.006 -10000 0 -10000 0 0
GSN -0.007 0.09 0.21 22 -0.35 17 39
MADD 0.026 0.006 -10000 0 -10000 0 0
TFAP2A -0.003 0.16 -10000 0 -0.57 32 32
BID -0.003 0.034 0.14 2 -0.17 17 19
MAP3K1 -0.034 0.12 -10000 0 -0.36 54 54
TRADD 0.024 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.012 0.088 0.24 11 -0.35 19 30
CASP9 0.027 0.003 -10000 0 -10000 0 0
DNA repair 0.003 0.047 0.21 14 -10000 0 14
neuron apoptosis 0.004 0.12 -10000 0 -0.63 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.001 0.084 0.24 9 -0.4 12 21
APAF1 0.026 0.006 -10000 0 -10000 0 0
CASP6 0.012 0.098 -10000 0 -0.85 4 4
TRAF2 0.026 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.015 0.085 0.26 9 -0.34 18 27
CASP7 -0.006 0.056 0.23 2 -0.23 8 10
KRT18 0.02 0.034 -10000 0 -0.48 1 1
apoptosis -0.004 0.083 0.32 6 -0.35 14 20
DFFA -0.015 0.083 0.23 6 -0.34 19 25
DFFB -0.013 0.085 0.24 9 -0.35 18 27
PARP1 -0.003 0.048 -10000 0 -0.21 14 14
actin filament polymerization -0.001 0.1 0.32 18 -0.22 39 57
TNF 0.014 0.076 0.17 12 -0.31 24 36
CYCS 0.004 0.039 0.16 8 -0.16 8 16
SATB1 0.01 0.1 0.36 5 -0.83 4 9
SLK -0.013 0.084 0.26 8 -0.33 19 27
p15 BID/BAX 0.013 0.044 -10000 0 -0.2 11 11
CASP2 0.005 0.059 0.2 14 -0.27 6 20
JNK cascade 0.033 0.12 0.36 54 -10000 0 54
CASP3 -0.013 0.085 0.2 7 -0.36 19 26
LMNB2 0.019 0.097 0.27 13 -0.35 12 25
RIPK1 0.026 0.005 -10000 0 -10000 0 0
CASP4 0.025 0.016 -10000 0 -0.31 1 1
Mammalian IAPs/DIABLO 0.063 0.026 -10000 0 -0.17 2 2
negative regulation of DNA binding -0.002 0.16 -10000 0 -0.56 32 32
stress fiber formation -0.012 0.083 0.26 8 -0.33 19 27
GZMB -0.023 0.055 0.26 2 -0.26 20 22
CASP1 0.004 0.047 -10000 0 -0.26 14 14
LMNB1 0.019 0.1 0.28 13 -0.4 9 22
APP 0.004 0.12 -10000 0 -0.63 16 16
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.002 -10000 0 -10000 0 0
VIM -0.003 0.08 0.26 4 -0.35 15 19
LMNA 0.022 0.083 0.28 11 -0.36 5 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.05 -10000 0 -0.16 30 30
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.013 0.084 0.2 11 -0.34 19 30
APAF-1/Caspase 9 0.012 0.074 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis 0.007 0.072 0.22 4 -0.32 14 18
CFL2 0.001 0.1 0.22 39 -0.32 18 57
GAS2 -0.015 0.08 0.19 7 -0.33 19 26
positive regulation of apoptosis 0.024 0.096 0.27 16 -0.4 6 22
PRF1 0.022 0.045 0.17 4 -0.31 8 12
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.022 0.029 -10000 0 -0.31 3 3
HSPA8 0.026 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.033 0.062 -10000 0 -0.2 16 16
AKT1 0.027 0.008 -10000 0 -10000 0 0
GSC 0.034 0.11 0.9 1 -1.2 2 3
NKX2-5 0.001 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.026 0.069 0.27 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.074 0.054 -10000 0 -0.26 3 3
SMAD4 0.022 0.035 -10000 0 -0.13 7 7
CBFB 0.024 0.009 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.008 0.093 -10000 0 -0.18 89 89
SMAD3/SMAD4/VDR 0.063 0.057 -10000 0 -0.19 3 3
MYC 0.027 0.034 0.17 24 -10000 0 24
CDKN2B -0.023 0.13 -10000 0 -0.93 5 5
AP1 0.009 0.084 0.21 1 -0.18 55 56
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.075 -10000 0 -0.25 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.052 -10000 0 -0.24 3 3
SP3 0.027 0.006 -10000 0 -10000 0 0
CREB1 0.027 0.003 -10000 0 -10000 0 0
FOXH1 0.041 0.052 0.18 57 -0.19 1 58
SMAD3/SMAD4/GR 0.038 0.061 -10000 0 -0.21 12 12
GATA3 -0.07 0.15 -10000 0 -0.3 148 148
SKI/SIN3/HDAC complex/NCoR1 0.013 0.043 -10000 0 -10000 0 0
MEF2C/TIF2 0.006 0.068 0.23 7 -0.27 4 11
endothelial cell migration 0.014 0.21 0.99 20 -10000 0 20
MAX 0.026 0.01 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.015 -10000 0 -0.31 1 1
RUNX2 0.026 0.023 0.17 1 -0.31 2 3
RUNX3 0.028 0.029 0.17 8 -0.31 2 10
RUNX1 0.025 0.018 0.17 1 -0.31 1 2
CTBP1 0.026 0.004 -10000 0 -10000 0 0
NR3C1 0.018 0.051 -10000 0 -0.31 11 11
VDR 0.024 0.035 0.17 2 -0.31 5 7
CDKN1A 0.01 0.11 -10000 0 -1 5 5
KAT2B 0.024 0.011 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.06 0.055 -10000 0 -0.3 1 1
DCP1A 0.026 0.005 -10000 0 -10000 0 0
SKI 0.027 0.004 -10000 0 -10000 0 0
SERPINE1 -0.015 0.22 -10000 0 -1 20 20
SMAD3/SMAD4/ATF2 0.028 0.071 -10000 0 -0.19 28 28
SMAD3/SMAD4/ATF3 0.025 0.093 0.2 2 -0.21 48 50
SAP30 0.026 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.045 0.032 0.18 1 -0.18 3 4
JUN -0.005 0.075 0.17 1 -0.29 12 13
SMAD3/SMAD4/IRF7 0.047 0.052 -10000 0 -0.17 1 1
TFE3 0.028 0.017 -10000 0 -10000 0 0
COL1A2 0.019 0.055 -10000 0 -0.79 2 2
mesenchymal cell differentiation -0.043 0.049 0.2 2 -10000 0 2
DLX1 0.15 0.054 0.17 423 -10000 0 423
TCF3 0.026 0.005 -10000 0 -10000 0 0
FOS -0.016 0.12 0.19 4 -0.32 63 67
SMAD3/SMAD4/Max 0.043 0.049 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.048 0.027 -10000 0 -0.18 3 3
ZBTB17 0.026 0.004 -10000 0 -10000 0 0
LAMC1 0.012 0.033 0.2 3 -10000 0 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.043 0.047 -10000 0 -10000 0 0
IRF7 0.034 0.031 0.17 23 -10000 0 23
ESR1 0.015 0.058 0.17 1 -0.31 15 16
HNF4A 0.029 0.035 0.17 27 -10000 0 27
MEF2C 0.032 0.075 0.2 61 -0.29 4 65
SMAD2-3/SMAD4 0.053 0.046 -10000 0 -0.26 1 1
Cbp/p300/Src-1 0.046 0.029 -10000 0 -0.18 3 3
IGHV3OR16-13 0.01 0.017 -10000 0 -0.33 1 1
TGIF2/HDAC complex 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.012 -10000 0 -10000 0 0
SKIL 0.021 0.042 0.17 3 -0.31 7 10
HDAC1 0.027 0.003 -10000 0 -10000 0 0
HDAC2 0.023 0.01 -10000 0 -10000 0 0
SNIP1 0.027 0.003 -10000 0 -10000 0 0
GCN5L2 -0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.053 0.047 -10000 0 -0.17 2 2
MSG1/HSC70 -0.004 0.1 0.14 11 -0.21 89 100
SMAD2 0.028 0.018 -10000 0 -0.15 2 2
SMAD3 0.02 0.035 -10000 0 -0.12 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 0.012 0.049 0.17 6 -0.16 22 28
SMAD2/SMAD2/SMAD4 -0.003 0.055 0.22 2 -0.18 16 18
NCOR1 0.026 0.007 -10000 0 -10000 0 0
NCOA2 -0.015 0.1 -10000 0 -0.31 53 53
NCOA1 0.027 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.033 0.029 0.14 11 -0.21 4 15
SMAD2-3/SMAD4/SP1/MIZ-1 0.084 0.057 -10000 0 -0.27 2 2
IFNB1 0.003 0.035 0.2 3 -10000 0 3
SMAD3/SMAD4/MEF2C 0.06 0.074 0.24 9 -0.32 3 12
CITED1 -0.033 0.14 0.17 12 -0.31 94 106
SMAD2-3/SMAD4/ARC105 0.067 0.046 -10000 0 -0.23 1 1
RBL1 0.008 0.076 -10000 0 -0.31 27 27
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.008 0.053 0.22 1 -0.32 4 5
RUNX1-3/PEBPB2 0.046 0.029 -10000 0 -0.17 3 3
SMAD7 0.014 0.087 -10000 0 -0.43 5 5
MYC/MIZ-1 0.034 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.011 0.093 0.31 2 -0.39 18 20
IL10 -0.042 0.11 0.19 3 -0.26 50 53
PIASy/HDAC complex 0.027 0.008 -10000 0 -10000 0 0
PIAS3 0.025 0.01 -10000 0 -10000 0 0
CDK2 0.024 0.011 -10000 0 -10000 0 0
IL5 -0.039 0.092 0.18 4 -0.21 54 58
CDK4 0.024 0.012 -10000 0 -10000 0 0
PIAS4 0.027 0.008 -10000 0 -10000 0 0
ATF3 -0.003 0.11 0.17 24 -0.31 53 77
SMAD3/SMAD4/SP1 0.055 0.05 -10000 0 -0.23 4 4
FOXG1 0.004 0.048 0.17 32 -10000 0 32
FOXO3 0.01 0.006 -10000 0 -10000 0 0
FOXO1 0.01 0.007 -10000 0 -10000 0 0
FOXO4 0.012 0.006 -10000 0 -10000 0 0
heart looping 0.032 0.074 0.2 62 -0.28 4 66
CEBPB 0.027 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.11 0.085 0.2 7 -0.17 5 12
MYOD1 0.019 0.038 0.17 11 -0.31 4 15
SMAD3/SMAD4/HNF4 0.044 0.053 -10000 0 -0.17 1 1
SMAD3/SMAD4/GATA3 -0.017 0.12 -10000 0 -0.2 142 142
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.042 0.17 3 -0.31 7 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.064 0.054 -10000 0 -0.17 2 2
SMAD3/SMAD4/SP1-3 0.068 0.053 -10000 0 -0.25 2 2
MED15 0.026 0.005 -10000 0 -10000 0 0
SP1 0.029 0.017 -10000 0 -0.16 2 2
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.06 0.054 0.22 1 -0.23 3 4
ITGB5 0.015 0.043 0.2 10 -0.28 1 11
TGIF/SIN3/HDAC complex/CtBP 0.014 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/AR 0.023 0.079 -10000 0 -0.19 42 42
AR -0.003 0.095 -10000 0 -0.31 43 43
negative regulation of cell growth -0.001 0.069 0.18 1 -0.25 12 13
SMAD3/SMAD4/MYOD 0.039 0.054 -10000 0 -0.18 5 5
E2F5 0.022 0.013 0.17 1 -10000 0 1
E2F4 0.024 0.009 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.086 0.067 0.24 1 -0.19 3 4
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.038 -10000 0 -0.32 4 4
TFDP1 0.025 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.028 0.093 0.22 1 -0.29 12 13
SMAD3/SMAD4/RUNX2 0.043 0.049 -10000 0 -0.2 2 2
TGIF2 0.026 0.005 -10000 0 -10000 0 0
TGIF1 0.025 0.007 -10000 0 -10000 0 0
ATF2 0.007 0.078 -10000 0 -0.31 28 28
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.026 0.004 -10000 0 -10000 0 0
ITGB7 0.015 0.064 0.17 3 -0.31 18 21
ITGA4 0.021 0.059 0.17 11 -0.31 13 24
alpha4/beta7 Integrin 0.026 0.067 0.25 3 -0.23 27 30
alpha4/beta1 Integrin 0.034 0.045 -10000 0 -0.21 13 13
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0 0.051 -10000 0 -0.29 4 4
BAG4 0.008 0.063 -10000 0 -0.31 18 18
PKC zeta/ceramide 0.003 0.07 -10000 0 -0.2 41 41
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.025 0.025 0.17 3 -0.31 2 5
BAX -0.001 0.059 -10000 0 -0.34 12 12
RIPK1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.005 0.1 0.73 10 -10000 0 10
BAD -0.011 0.071 0.2 10 -0.2 36 46
SMPD1 0.016 0.062 0.2 22 -0.15 5 27
RB1 -0.016 0.062 -10000 0 -0.19 41 41
FADD/Caspase 8 0.006 0.055 0.21 5 -0.28 5 10
MAP2K4 -0.017 0.061 0.17 2 -0.2 35 37
NSMAF 0.022 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.019 0.071 0.17 9 -0.2 44 53
EGF 0.023 0.084 0.17 40 -0.31 23 63
mol:ceramide -0.014 0.069 -10000 0 -0.2 42 42
MADD 0.026 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.008 0.006 -10000 0 -10000 0 0
ASAH1 0.019 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle -0.016 0.062 -10000 0 -0.19 41 41
cell proliferation -0.001 0.079 0.22 3 -0.2 35 38
BID 0.005 0.11 -10000 0 -0.63 11 11
MAP3K1 -0.016 0.064 0.19 1 -0.19 40 41
EIF2A -0.008 0.071 0.18 26 -0.19 30 56
TRADD 0.024 0.009 -10000 0 -10000 0 0
CRADD 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.017 0.07 0.19 9 -0.21 31 40
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.072 0.19 9 -0.21 31 40
Cathepsin D/ceramide 0.004 0.069 -10000 0 -0.2 38 38
FADD 0.002 0.054 0.2 5 -0.29 4 9
KSR1 -0.022 0.073 0.19 1 -0.2 54 55
MAPK8 -0.012 0.075 -10000 0 -0.26 20 20
PRKRA -0.015 0.062 0.19 2 -0.19 40 42
PDGFA 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.026 0.006 -10000 0 -10000 0 0
IGF1 0.008 0.089 0.17 17 -0.31 33 50
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.069 -10000 0 -0.2 42 42
CTSD 0.027 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0 0.085 0.24 3 -0.22 35 38
PRKCD 0.026 0.005 -10000 0 -10000 0 0
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.008 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.008 0.047 -10000 0 -0.3 4 4
TNFR1A/BAG4/TNF-alpha 0.022 0.068 -10000 0 -0.18 41 41
mol:Sphingosine-1-phosphate -0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.021 0.069 0.17 9 -0.21 30 39
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
CYCS 0.015 0.055 0.14 16 -0.21 10 26
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.02 0.049 -10000 0 -0.21 18 18
EIF2AK2 -0.017 0.059 0.18 3 -0.19 36 39
TNF-alpha/TNFR1A/FAN 0.033 0.055 -10000 0 -0.18 24 24
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.037 -10000 0 -10000 0 0
MAP2K2 -0.021 0.071 0.21 8 -0.21 34 42
SMPD3 -0.002 0.083 0.19 5 -0.29 26 31
TNF 0.014 0.076 0.17 12 -0.31 24 36
PKC zeta/PAR4 0.038 0.009 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.005 0.062 0.17 21 -0.16 30 51
NF kappa B1/RelA/I kappa B alpha 0.072 0.026 -10000 0 -10000 0 0
AIFM1 0.008 0.06 0.14 13 -0.2 12 25
BCL2 0.016 0.052 -10000 0 -0.31 12 12
Coregulation of Androgen receptor activity

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
NRIP1 0.025 0.017 -10000 0 -0.12 5 5
SVIL 0.014 0.064 -10000 0 -0.31 18 18
ZNF318 0.027 0.018 0.18 6 -10000 0 6
JMJD2C 0.003 0.009 -10000 0 -0.099 3 3
T-DHT/AR/Ubc9 0.015 0.065 -10000 0 -0.17 44 44
CARM1 0.026 0.008 -10000 0 -10000 0 0
PRDX1 0.027 0.003 -10000 0 -10000 0 0
PELP1 0.025 0.008 -10000 0 -10000 0 0
CTNNB1 0.026 0.012 -10000 0 -0.084 1 1
AKT1 0.027 0.008 -10000 0 -10000 0 0
PTK2B 0.019 0.015 -10000 0 -10000 0 0
MED1 0.027 0.007 -10000 0 -10000 0 0
MAK 0.068 0.07 0.18 142 -10000 0 142
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.015 0.055 -10000 0 -0.31 13 13
GSN 0.023 0.029 -10000 0 -0.26 4 4
NCOA2 -0.015 0.1 -10000 0 -0.31 53 53
NCOA6 0.025 0.013 -10000 0 -0.09 1 1
DNA-PK 0.045 0.028 0.21 5 -10000 0 5
NCOA4 0.026 0.007 -10000 0 -10000 0 0
PIAS3 0.025 0.012 -10000 0 -10000 0 0
cell proliferation 0.036 0.07 0.26 2 -0.4 6 8
XRCC5 0.027 0.006 -10000 0 -10000 0 0
UBE3A 0.026 0.016 -10000 0 -0.11 6 6
T-DHT/AR/SNURF 0.01 0.075 -10000 0 -0.16 71 71
FHL2 -0.014 0.16 -10000 0 -0.75 21 21
RANBP9 0.026 0.013 -10000 0 -0.11 1 1
JMJD1A 0.003 0.011 -10000 0 -0.082 6 6
CDK6 0.016 0.054 -10000 0 -0.31 13 13
TGFB1I1 0.001 0.088 -10000 0 -0.31 36 36
T-DHT/AR/CyclinD1 0.017 0.065 0.14 1 -0.17 43 44
XRCC6 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR 0.018 0.076 -10000 0 -0.16 70 70
CTDSP1 0.026 0.008 -10000 0 -10000 0 0
CTDSP2 0.027 0.013 0.13 6 -10000 0 6
BRCA1 0.025 0.015 0.17 1 -0.095 2 3
TCF4 0.022 0.029 0.13 2 -0.31 3 5
CDKN2A 0.056 0.061 0.18 100 -10000 0 100
SRF 0.023 0.037 -10000 0 -0.15 21 21
NKX3-1 -0.007 0.034 -10000 0 -0.095 48 48
KLK3 -0.013 0.16 -10000 0 -1.3 7 7
TMF1 0.026 0.008 -10000 0 -10000 0 0
HNRNPA1 0.027 0.009 0.13 1 -10000 0 1
AOF2 0 0.009 -10000 0 -0.076 7 7
APPL1 -0.011 0.014 0.11 6 -10000 0 6
T-DHT/AR/Caspase 8 0.016 0.065 -10000 0 -0.17 44 44
AR -0.005 0.096 -10000 0 -0.3 43 43
UBA3 0.025 0.009 -10000 0 -10000 0 0
PATZ1 0.026 0.007 -10000 0 -10000 0 0
PAWR 0.026 0.008 -10000 0 -10000 0 0
PRKDC 0.023 0.014 0.21 1 -10000 0 1
PA2G4 0.027 0.01 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.016 0.059 -10000 0 -0.16 43 43
RPS6KA3 0.025 0.021 -10000 0 -0.16 4 4
T-DHT/AR/ARA70 0.016 0.065 -10000 0 -0.17 45 45
LATS2 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.016 0.06 0.15 2 -0.16 44 46
Cyclin D3/CDK11 p58 0.02 0.003 -10000 0 -10000 0 0
VAV3 -0.01 0.1 -10000 0 -0.3 54 54
KLK2 0.003 0.053 -10000 0 -0.67 2 2
CASP8 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.007 0.099 -10000 0 -0.25 55 55
TMPRSS2 -0.011 0.09 -10000 0 -0.42 19 19
CCND1 0.025 0.012 0.17 1 -10000 0 1
PIAS1 0.025 0.022 -10000 0 -0.14 7 7
mol:T-DHT -0.001 0.018 -10000 0 -0.064 31 31
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.025 0.023 -10000 0 -0.16 7 7
T-DHT/AR/CDK6 0.01 0.071 -10000 0 -0.18 52 52
CMTM2 0.023 0.02 0.17 2 -0.31 1 3
SNURF 0.015 0.058 -10000 0 -0.31 15 15
ZMIZ1 0.021 0.031 -10000 0 -0.2 4 4
CCND3 0.027 0.004 -10000 0 -10000 0 0
TGIF1 0.025 0.009 0.13 1 -10000 0 1
FKBP4 0.024 0.015 -10000 0 -0.087 7 7
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.027 0.01 0.17 2 -10000 0 2
alphaV beta3 Integrin -0.009 0.098 -10000 0 -0.21 92 92
PTK2 -0.008 0.096 0.23 1 -0.38 22 23
positive regulation of JNK cascade 0.007 0.086 -10000 0 -0.29 26 26
CDC42/GDP 0.03 0.12 0.32 6 -0.37 29 35
Rac1/GDP 0.026 0.12 0.35 3 -0.38 23 26
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.017 0.11 -10000 0 -0.35 26 26
nectin-3/I-afadin 0.034 0.049 0.14 21 -0.21 14 35
RAPGEF1 0.002 0.12 0.31 7 -0.4 29 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.007 0.12 -10000 0 -0.44 30 30
PDGFB-D/PDGFRB 0.027 0.01 0.17 2 -10000 0 2
TLN1 -0.008 0.023 0.11 1 -0.12 16 17
Rap1/GTP 0.001 0.084 -10000 0 -0.3 29 29
IQGAP1 0.027 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.016 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.034 0.049 0.14 21 -0.21 14 35
PVR 0.027 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.003 -10000 0 -10000 0 0
mol:GDP 0.018 0.14 0.36 5 -0.44 29 34
MLLT4 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
PI3K 0.059 0.062 -10000 0 -0.19 16 16
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.037 0.011 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.01 0.086 -10000 0 -0.3 23 23
PVRL1 0.026 0.006 -10000 0 -10000 0 0
PVRL3 0.023 0.065 0.17 23 -0.31 14 37
PVRL2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
CDH1 0.024 0.009 -10000 0 -10000 0 0
CLDN1 -0.011 0.1 0.17 1 -0.31 53 54
JAM-A/CLDN1 0.032 0.083 0.19 1 -0.17 61 62
SRC -0.003 0.13 -10000 0 -0.48 30 30
ITGB3 -0.037 0.13 -10000 0 -0.31 92 92
nectin-1(dimer)/I-afadin/I-afadin 0.037 0.011 -10000 0 -10000 0 0
FARP2 0.013 0.14 0.33 1 -0.47 25 26
RAC1 0.025 0.008 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.048 0.046 -10000 0 -0.18 14 14
nectin-1/I-afadin 0.037 0.011 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.045 0.046 -10000 0 -0.18 14 14
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.006 -10000 0 -10000 0 0
F11R 0.026 0.006 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.007 0.086 -10000 0 -0.29 26 26
alphaV/beta3 Integrin/Talin -0.002 0.084 0.21 12 -0.23 18 30
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.009 -10000 0 -10000 0 0
PIP5K1C 0.001 0.022 0.12 1 -0.12 14 15
VAV2 0.015 0.14 -10000 0 -0.48 21 21
RAP1/GDP 0.028 0.11 0.31 2 -0.35 27 29
ITGAV 0.026 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.048 0.046 -10000 0 -0.18 14 14
nectin-3(dimer)/I-afadin/I-afadin 0.034 0.049 0.14 21 -0.21 14 35
Rac1/GTP 0.016 0.11 -10000 0 -0.37 22 22
PTPRM 0.008 0.026 0.13 1 -0.14 14 15
E-cadherin/beta catenin/alpha catenin 0.061 0.035 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.003 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.004 0.068 0.22 5 -0.29 7 12
BAG4 0.008 0.063 -10000 0 -0.31 18 18
BAD 0.011 0.059 0.23 22 -0.13 4 26
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.025 0.025 0.17 3 -0.31 2 5
BAX 0.007 0.044 0.16 20 -0.13 4 24
EnzymeConsortium:3.1.4.12 0.003 0.025 0.083 13 -0.079 7 20
IKBKB 0.013 0.078 0.24 20 -0.28 7 27
MAP2K2 0.001 0.063 0.23 18 -0.19 8 26
MAP2K1 0 0.061 0.21 20 -0.18 9 29
SMPD1 0.006 0.032 0.14 12 -0.095 2 14
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.014 0.078 0.27 11 -0.3 6 17
MAP2K4 0.005 0.042 0.18 13 -0.14 2 15
protein ubiquitination 0.01 0.082 0.28 11 -0.29 7 18
EnzymeConsortium:2.7.1.37 0 0.066 0.23 19 -0.19 8 27
response to UV 0 0.001 0.003 17 -0.002 6 23
RAF1 0.002 0.06 0.22 17 -0.19 9 26
CRADD 0.026 0.006 -10000 0 -10000 0 0
mol:ceramide 0.009 0.042 0.15 18 -0.11 7 25
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.009 -10000 0 -10000 0 0
MADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K1 0.007 0.042 0.17 16 -0.14 3 19
TRADD 0.024 0.009 -10000 0 -10000 0 0
RELA/p50 0.026 0.006 -10000 0 -10000 0 0
MAPK3 0.003 0.062 0.23 18 -0.18 7 25
MAPK1 0.003 0.063 0.22 20 -0.18 8 28
p50/RELA/I-kappa-B-alpha 0.038 0.01 -10000 0 -10000 0 0
FADD 0.006 0.073 0.25 10 -0.29 7 17
KSR1 0.002 0.051 0.16 15 -0.15 19 34
MAPK8 0.002 0.052 0.2 14 -0.18 4 18
TRAF2 0.026 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.002 13 -0.002 1 14
CHUK 0.007 0.071 0.27 9 -0.28 6 15
TNF R/SODD 0.02 0.049 -10000 0 -0.21 18 18
TNF 0.013 0.077 0.17 12 -0.31 24 36
CYCS 0.023 0.061 0.19 33 -0.13 2 35
IKBKG 0.004 0.072 0.25 7 -0.28 7 14
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.007 0.066 0.27 1 -0.27 9 10
RELA 0.026 0.006 -10000 0 -10000 0 0
RIPK1 0.026 0.005 -10000 0 -10000 0 0
AIFM1 0.017 0.055 0.18 28 -0.13 2 30
TNF/TNF R/SODD 0.022 0.068 -10000 0 -0.18 41 41
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
response to heat 0 0.001 0.002 13 -0.002 1 14
CASP8 0.026 0.037 -10000 0 -0.45 2 2
NSMAF 0.016 0.08 0.21 34 -0.29 7 41
response to hydrogen peroxide 0 0.001 0.003 17 -0.002 6 23
BCL2 0.016 0.052 -10000 0 -0.31 12 12
HIF-2-alpha transcription factor network

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
MMP14 0.014 0.15 -10000 0 -0.83 13 13
oxygen homeostasis 0 0.01 -10000 0 -0.098 1 1
TCEB2 0.028 0.018 0.17 7 -10000 0 7
TCEB1 0.021 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.026 0.078 0.28 1 -0.3 3 4
EPO -0.015 0.2 0.31 1 -0.47 53 54
FIH (dimer) 0.018 0.024 -10000 0 -0.11 1 1
APEX1 0.02 0.028 -10000 0 -10000 0 0
SERPINE1 0.006 0.17 0.34 6 -0.45 31 37
FLT1 -0.006 0.19 -10000 0 -0.78 22 22
ADORA2A -0.006 0.15 0.31 7 -0.45 23 30
germ cell development 0.002 0.17 0.35 5 -0.43 38 43
SLC11A2 0.004 0.15 -10000 0 -0.45 23 23
BHLHE40 0.004 0.16 0.37 3 -0.49 24 27
HIF1AN 0.018 0.024 -10000 0 -0.11 1 1
HIF2A/ARNT/SIRT1 0.02 0.12 0.29 1 -0.31 18 19
ETS1 0.026 0.042 0.18 1 -0.25 7 8
CITED2 0.022 0.079 -10000 0 -0.51 9 9
KDR -0.023 0.25 -10000 0 -0.99 28 28
PGK1 0.007 0.16 0.34 5 -0.44 25 30
SIRT1 0.024 0.01 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.049 0.2 -10000 0 -0.51 23 23
EPAS1 0.002 0.068 -10000 0 -0.24 11 11
SP1 0.028 0.016 -10000 0 -10000 0 0
ABCG2 -0.01 0.19 0.37 3 -0.52 38 41
EFNA1 0.002 0.15 0.29 1 -0.45 23 24
FXN -0.008 0.15 0.32 7 -0.45 23 30
POU5F1 0.001 0.17 0.39 3 -0.44 40 43
neuron apoptosis -0.048 0.19 0.5 23 -10000 0 23
EP300 0.025 0.026 -10000 0 -0.31 3 3
EGLN3 0.013 0.05 -10000 0 -0.31 9 9
EGLN2 0.019 0.025 -10000 0 -0.11 1 1
EGLN1 0.018 0.025 -10000 0 -0.11 1 1
VHL/Elongin B/Elongin C 0.042 0.028 -10000 0 -0.21 1 1
VHL 0.025 0.016 -10000 0 -0.31 1 1
ARNT 0.018 0.028 -10000 0 -10000 0 0
SLC2A1 -0.006 0.15 0.32 8 -0.45 23 31
TWIST1 0 0.16 0.32 9 -0.46 23 32
ELK1 0.031 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.032 0.12 0.3 1 -0.34 9 10
VEGFA -0.003 0.17 0.34 5 -0.43 44 49
CREBBP 0.026 0.005 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.013 0.027 0.25 3 -10000 0 3
TP53 -0.003 0.045 -10000 0 -0.17 31 31
Senescence -0.003 0.045 -10000 0 -0.17 31 31
Apoptosis -0.003 0.045 -10000 0 -0.17 31 31
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.063 0.3 20 -0.17 2 22
MDM4 0.026 0.005 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0.046 -10000 0 -0.39 5 5
VEGFR1 homodimer/NRP1 0.007 0.043 -10000 0 -0.38 5 5
mol:DAG -0.03 0.063 0.19 6 -0.4 4 10
VEGFR1 homodimer/NRP1/VEGFR 121 0.015 0.061 0.17 1 -0.21 24 25
CaM/Ca2+ 0.003 0.07 0.18 6 -0.38 4 10
HIF1A 0.028 0.032 -10000 0 -0.28 5 5
GAB1 0.026 0.016 -10000 0 -0.31 1 1
AKT1 -0.025 0.076 0.29 2 -0.36 7 9
PLCG1 -0.03 0.064 0.19 6 -0.41 4 10
NOS3 -0.004 0.08 0.28 9 -0.45 3 12
CBL 0.025 0.016 -10000 0 -0.31 1 1
mol:NO 0 0.09 0.32 13 -0.44 4 17
FLT1 0.011 0.048 -10000 0 -0.49 4 4
PGF -0.011 0.11 0.17 2 -0.31 56 58
VEGFR1 homodimer/NRP2/VEGFR121 0.018 0.082 -10000 0 -0.2 51 51
CALM1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
eNOS/Hsp90 0.011 0.084 0.28 7 -0.42 4 11
endothelial cell proliferation -0.053 0.13 0.34 3 -0.39 45 48
mol:Ca2+ -0.029 0.063 0.19 6 -0.4 4 10
MAPK3 -0.034 0.072 0.22 7 -0.34 11 18
MAPK1 -0.033 0.073 0.23 8 -0.34 11 19
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
PLGF homodimer -0.011 0.11 0.17 2 -0.31 56 58
PRKACA 0.027 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.013 0.1 -10000 0 -0.31 55 55
VEGFA homodimer 0.01 0.077 0.17 5 -0.31 26 31
VEGFR1 homodimer/VEGFA homodimer 0.016 0.067 0.19 1 -0.23 24 25
platelet activating factor biosynthetic process -0.036 0.067 0.18 6 -0.34 11 17
PI3K 0.023 0.081 -10000 0 -0.34 7 7
PRKCA -0.034 0.073 0.21 6 -0.36 11 17
PRKCB -0.055 0.091 0.18 4 -0.3 38 42
VEGFR1 homodimer/PLGF homodimer 0.002 0.078 -10000 0 -0.2 58 58
VEGFA 0.01 0.077 0.17 5 -0.31 26 31
VEGFB 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.03 0.063 0.19 6 -0.4 4 10
RASA1 -0.012 0.047 0.19 10 -0.4 4 14
NRP2 0.005 0.083 -10000 0 -0.31 32 32
VEGFR1 homodimer 0.011 0.048 -10000 0 -0.49 4 4
VEGFB homodimer 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.001 0.099 0.38 5 -0.32 21 26
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
mol:PI-3-4-5-P3 0.022 0.079 -10000 0 -0.34 7 7
mol:L-citrulline 0 0.09 0.32 13 -0.44 4 17
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.042 0.068 -10000 0 -0.22 21 21
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.066 -10000 0 -0.22 24 24
CD2AP 0.027 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.032 0.084 -10000 0 -0.33 7 7
PDPK1 -0.023 0.073 0.23 9 -0.35 6 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.067 -10000 0 -0.22 23 23
mol:NADP 0 0.09 0.32 13 -0.44 4 17
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.067 -10000 0 -0.22 21 21
VEGFR1 homodimer/NRP2 0.012 0.067 -10000 0 -0.22 32 32
Cellular roles of Anthrax toxin

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
ANTXR1 0.018 0.054 0.17 1 -0.31 13 14
ANTXR2 0.02 0.047 -10000 0 -0.31 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.009 -10000 0 -0.045 21 21
monocyte activation -0.012 0.11 -10000 0 -0.34 46 46
MAP2K2 0.006 0.074 -10000 0 -0.56 8 8
MAP2K1 -0.007 0.008 -10000 0 -0.07 1 1
MAP2K7 -0.007 0.008 -10000 0 -0.07 1 1
MAP2K6 -0.007 0.014 0.14 1 -0.12 3 4
CYAA -0.014 0.03 -10000 0 -0.15 21 21
MAP2K4 -0.006 0.008 -10000 0 -0.07 1 1
IL1B -0.021 0.055 0.15 3 -0.17 47 50
Channel 0.025 0.041 0.12 1 -0.16 21 22
NLRP1 -0.009 0.023 -10000 0 -0.15 11 11
CALM1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.003 0.055 -10000 0 -0.41 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.009 0.045 21 -10000 0 21
MAPK3 -0.007 0.008 -10000 0 -0.07 1 1
MAPK1 -0.007 0.008 -10000 0 -0.07 1 1
PGR -0.023 0.048 -10000 0 -0.16 57 57
PA/Cellular Receptors 0.026 0.046 0.13 1 -0.18 21 22
apoptosis -0.003 0.009 -10000 0 -0.045 21 21
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.04 0.12 1 -0.16 21 22
macrophage activation -0.009 0.012 0.14 2 -10000 0 2
TNF 0.014 0.076 0.17 12 -0.31 24 36
VCAM1 -0.011 0.11 -10000 0 -0.35 45 45
platelet activation 0.003 0.055 -10000 0 -0.41 8 8
MAPKKK cascade 0.003 0.02 0.082 2 -0.083 14 16
IL18 -0.012 0.043 0.11 2 -0.2 18 20
negative regulation of macrophage activation -0.003 0.009 -10000 0 -0.045 21 21
LEF -0.003 0.009 -10000 0 -0.045 21 21
CASP1 -0.005 0.027 -10000 0 -0.14 15 15
mol:cAMP 0.002 0.056 -10000 0 -0.42 8 8
necrosis -0.003 0.009 -10000 0 -0.045 21 21
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.039 0.12 1 -0.15 21 22
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.003 -10000 0 -10000 0 0
HDAC2 0.024 0.01 -10000 0 -10000 0 0
GNB1/GNG2 0.044 0.031 -10000 0 -0.18 6 6
forebrain development -0.041 0.13 0.3 2 -0.42 21 23
GNAO1 -0.026 0.12 -10000 0 -0.31 71 71
SMO/beta Arrestin2 0.022 0.027 -10000 0 -10000 0 0
SMO 0.015 0.02 -10000 0 -10000 0 0
ARRB2 0.023 0.01 -10000 0 -10000 0 0
GLI3/SPOP 0.031 0.085 0.28 9 -0.34 9 18
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
GSK3B 0.025 0.007 -10000 0 -10000 0 0
GNAI2 0.024 0.008 -10000 0 -10000 0 0
SIN3/HDAC complex 0.065 0.021 -10000 0 -10000 0 0
GNAI1 0.022 0.028 0.17 1 -0.31 3 4
XPO1 0.014 0.024 -10000 0 -10000 0 0
GLI1/Su(fu) -0.044 0.13 -10000 0 -0.43 21 21
SAP30 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0.015 0.02 -10000 0 -10000 0 0
MIM/GLI2A -0.007 0.06 -10000 0 -0.12 105 105
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.006 -10000 0 -10000 0 0
GLI2 0.012 0.054 0.22 6 -0.23 4 10
GLI3 0.017 0.086 0.28 9 -0.31 14 23
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.027 0.003 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.023 0.037 -10000 0 -0.31 6 6
Gi family/GTP -0.029 0.11 -10000 0 -0.27 70 70
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.016 0.072 0.28 4 -0.32 11 15
GLI2/Su(fu) 0.015 0.046 -10000 0 -0.25 4 4
FOXA2 -0.22 0.41 -10000 0 -0.87 139 139
neural tube patterning -0.041 0.13 0.3 2 -0.42 21 23
SPOP 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.047 -10000 0 -0.15 12 12
GNB1 0.027 0.004 -10000 0 -10000 0 0
CSNK1G2 0.026 0.005 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 -0.007 0.06 -10000 0 -0.12 105 105
embryonic limb morphogenesis -0.041 0.13 0.3 2 -0.42 21 23
SUFU 0.012 0.014 -10000 0 -10000 0 0
LGALS3 0.003 0.086 -10000 0 -0.31 35 35
catabolic process 0.034 0.096 0.32 7 -0.33 14 21
GLI3A/CBP 0.024 0.036 -10000 0 -0.33 4 4
KIF3A 0.026 0.005 -10000 0 -10000 0 0
GLI1 -0.042 0.14 0.3 2 -0.43 21 23
RAB23 0.025 0.022 -10000 0 -0.31 2 2
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
IFT172 0.027 0.003 -10000 0 -10000 0 0
RBBP7 0.027 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.01 0.063 -10000 0 -0.17 21 21
GNAZ -0.004 0.094 -10000 0 -0.31 42 42
RBBP4 0.027 0.015 -10000 0 -0.31 1 1
CSNK1G1 0.027 0.003 -10000 0 -10000 0 0
PIAS1 0.026 0.015 -10000 0 -0.31 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.024 0.055 0.25 2 -0.22 4 6
STK36 0.014 0.024 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.026 0.1 -10000 0 -0.32 41 41
PTCH1 -0.031 0.13 0.45 2 -0.46 10 12
MIM/GLI1 -0.069 0.19 -10000 0 -0.41 106 106
CREBBP 0.024 0.036 -10000 0 -0.33 4 4
Su(fu)/SIN3/HDAC complex 0.021 0.038 -10000 0 -0.26 2 2
Aurora A signaling

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
Aurora A/GADD45A 0.01 0.041 -10000 0 -0.22 2 2
BIRC5 0.074 0.072 0.17 165 -0.31 1 166
NFKBIA -0.004 0.038 0.2 12 -10000 0 12
CPEB1 -0.061 0.15 0.17 2 -0.31 129 131
AKT1 -0.004 0.034 0.23 6 -10000 0 6
NDEL1 0.024 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.007 0.031 -10000 0 -10000 0 0
NDEL1/TACC3 0.039 0.04 0.22 6 -0.13 1 7
GADD45A 0.025 0.022 -10000 0 -0.31 2 2
GSK3B 0.003 0.025 -10000 0 -10000 0 0
PAK1/Aurora A 0.008 0.042 -10000 0 -0.18 6 6
MDM2 0.026 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.018 0.045 0.26 10 -10000 0 10
TP53 -0.008 0.066 -10000 0 -0.21 47 47
DLG7 -0.003 0.022 0.13 5 -0.13 2 7
AURKAIP1 0.029 0.02 0.17 9 -10000 0 9
ARHGEF7 0.025 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.041 0.042 0.23 6 -0.14 1 7
G2/M transition of mitotic cell cycle 0.007 0.031 -10000 0 -10000 0 0
AURKA 0.001 0.029 0.16 5 -0.16 2 7
AURKB 0.028 0.049 0.11 19 -0.11 33 52
CDC25B 0.005 0.027 0.29 1 -0.25 2 3
G2/M transition checkpoint -0.003 0.02 -10000 0 -0.12 2 2
mRNA polyadenylation -0.034 0.077 -10000 0 -0.16 117 117
Aurora A/CPEB -0.034 0.078 -10000 0 -0.16 117 117
Aurora A/TACC1/TRAP/chTOG 0.038 0.039 -10000 0 -0.16 5 5
BRCA1 0.026 0.009 0.17 1 -10000 0 1
centrosome duplication 0.008 0.042 -10000 0 -0.18 6 6
regulation of centrosome cycle 0.037 0.038 0.22 6 -0.13 1 7
spindle assembly 0.036 0.038 -10000 0 -0.16 5 5
TDRD7 0.026 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.065 0.059 0.22 7 -0.16 4 11
CENPA 0.043 0.042 0.15 22 -0.22 1 23
Aurora A/PP2A 0.011 0.038 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.004 0.028 0.23 4 -10000 0 4
negative regulation of DNA binding -0.01 0.068 -10000 0 -0.2 53 53
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.011 -10000 0 -10000 0 0
RASA1 0.025 0.016 -10000 0 -0.31 1 1
Ajuba/Aurora A -0.003 0.02 -10000 0 -0.12 2 2
mitotic prometaphase -0.002 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.029 0.16 5 -0.16 2 7
TACC1 0.017 0.035 -10000 0 -0.31 5 5
TACC3 0.037 0.038 0.17 35 -10000 0 35
Aurora A/Antizyme1 0.039 0.032 -10000 0 -10000 0 0
Aurora A/RasGAP 0.011 0.038 -10000 0 -0.19 1 1
OAZ1 0.027 0.004 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.002 0.026 -10000 0 -10000 0 0
GIT1 0.027 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.046 0.031 -10000 0 -0.18 6 6
Importin alpha/Importin beta/TPX2 -0.018 0.045 0.26 10 -10000 0 10
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.004 0.049 0.22 9 -0.15 1 10
PAK1 0.022 0.037 -10000 0 -0.31 6 6
CKAP5 0.026 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.053 -10000 0 -0.24 20 20
CRKL 0.026 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DOCK1 0.023 0.03 -10000 0 -0.31 4 4
ITGA4 0.021 0.059 0.17 11 -0.31 13 24
alpha4/beta7 Integrin/MAdCAM1 0.063 0.076 0.23 4 -0.19 27 31
EPO 0.003 0.1 0.17 25 -0.31 42 67
alpha4/beta7 Integrin 0.026 0.067 0.25 3 -0.23 27 30
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.045 -10000 0 -0.21 13 13
EPO/EPOR (dimer) 0.022 0.078 0.15 33 -0.21 41 74
lamellipodium assembly 0.013 0.042 -10000 0 -0.42 1 1
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
PI3K 0.031 0.034 -10000 0 -0.24 6 6
ARF6 0.027 0.004 -10000 0 -10000 0 0
JAK2 0 0.067 0.16 2 -0.18 53 55
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
MADCAM1 0.053 0.06 0.17 92 -0.31 1 93
cell adhesion 0.06 0.074 0.24 3 -0.19 27 30
CRKL/CBL 0.037 0.015 -10000 0 -0.21 1 1
ITGB1 0.026 0.004 -10000 0 -10000 0 0
SRC -0.02 0.038 0.18 6 -0.17 17 23
ITGB7 0.015 0.064 0.17 3 -0.31 18 21
RAC1 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.053 0.24 4 -0.18 18 22
p130Cas/Crk/Dock1 0.016 0.046 0.19 2 -0.28 3 5
VCAM1 0.025 0.039 0.17 8 -0.31 5 13
RHOA 0.026 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.045 -10000 0 -0.17 13 13
BCAR1 -0.019 0.032 0.18 3 -0.17 14 17
EPOR 0.03 0.021 0.17 10 -10000 0 10
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.016 -10000 0 -0.31 1 1
GIT1 0.027 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.042 -10000 0 -0.44 1 1
TCGA08_rtk_signaling

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
PDGFRA 0.012 0.07 0.17 1 -0.31 22 23
HRAS 0.028 0.017 0.17 6 -10000 0 6
EGFR -0.002 0.09 -10000 0 -0.31 39 39
AKT 0.03 0.098 0.24 29 -0.25 21 50
FOXO3 0.023 0.01 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.022 0.011 -10000 0 -10000 0 0
AKT3 0.025 0.016 -10000 0 -0.31 1 1
FOXO4 0.026 0.015 -10000 0 -0.31 1 1
MET -0.004 0.093 -10000 0 -0.31 42 42
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
PIK3CB 0.025 0.007 -10000 0 -10000 0 0
NRAS 0.026 0.016 -10000 0 -0.31 1 1
PIK3CG 0.003 0.086 0.17 5 -0.31 34 39
PIK3R3 0.027 0.004 -10000 0 -10000 0 0
PIK3R2 0.027 0.002 -10000 0 -10000 0 0
NF1 0.027 0.003 -10000 0 -10000 0 0
RAS -0.004 0.065 0.18 1 -0.16 56 57
ERBB2 0.025 0.026 -10000 0 -0.31 3 3
proliferation/survival/translation -0.013 0.092 0.26 29 -0.2 5 34
PI3K 0.012 0.095 0.22 28 -0.2 48 76
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
KRAS 0.025 0.007 -10000 0 -10000 0 0
FOXO 0.048 0.054 0.22 13 -10000 0 13
AKT2 0.027 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.011 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.014 0.039 0.23 4 -10000 0 4
DAPP1 -0.042 0.14 0.24 9 -0.33 59 68
Src family/SYK family/BLNK-LAT/BTK-ITK -0.02 0.13 0.33 4 -0.42 19 23
mol:DAG 0.004 0.082 0.26 18 -0.19 13 31
HRAS 0.031 0.019 0.18 6 -10000 0 6
RAP1A 0.029 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.025 0.072 0.23 7 -0.31 8 15
PLCG2 0.021 0.026 0.17 2 -0.31 2 4
PLCG1 0.026 0.005 -10000 0 -10000 0 0
ARF5 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.014 0.033 0.16 14 -10000 0 14
ARF1/GTP -0.003 0.047 0.24 9 -10000 0 9
RHOA 0.026 0.005 -10000 0 -10000 0 0
YES1 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP -0.014 0.03 0.16 11 -10000 0 11
ADAP1 -0.014 0.042 0.18 15 -0.26 1 16
ARAP3 -0.014 0.033 0.15 14 -10000 0 14
INPPL1 0.026 0.005 -10000 0 -10000 0 0
PREX1 0.025 0.016 -10000 0 -0.31 1 1
ARHGEF6 0.026 0.015 -10000 0 -0.31 1 1
ARHGEF7 0.025 0.007 -10000 0 -10000 0 0
ARF1 0.026 0.006 -10000 0 -10000 0 0
NRAS 0.029 0.009 -10000 0 -10000 0 0
FYN 0.023 0.018 -10000 0 -0.31 1 1
ARF6 0.027 0.004 -10000 0 -10000 0 0
FGR 0.026 0.022 0.17 1 -0.31 2 3
mol:Ca2+ 0.011 0.067 0.17 52 -0.12 5 57
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.023 0.03 -10000 0 -0.31 4 4
ZAP70 0.04 0.053 0.17 52 -0.31 3 55
mol:IP3 0.006 0.076 0.2 44 -0.16 7 51
LYN 0.023 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.027 0.074 0.23 7 -0.27 11 18
RhoA/GDP 0.022 0.046 0.21 7 -0.22 2 9
PDK1/Src/Hsp90 0.05 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.017 -10000 0 -0.31 1 1
actin cytoskeleton reorganization 0.032 0.09 0.3 25 -0.27 4 29
SRC 0.026 0.006 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.039 -10000 0 -0.24 13 13
RAC1 0.025 0.008 -10000 0 -10000 0 0
PTEN 0.021 0.015 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.018 0.034 0.2 3 -10000 0 3
RhoA/GTP -0.017 0.029 0.17 8 -10000 0 8
Src family/SYK family/BLNK-LAT -0.013 0.093 0.19 1 -0.28 28 29
BLK 0 0.1 0.17 32 -0.31 43 75
PDPK1 0.026 0.006 -10000 0 -10000 0 0
CYTH1 -0.014 0.035 0.14 19 -10000 0 19
HCK 0.024 0.031 0.17 1 -0.31 4 5
CYTH3 -0.014 0.036 0.16 14 -10000 0 14
CYTH2 -0.013 0.042 0.16 22 -10000 0 22
KRAS 0.028 0.011 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.035 0.13 -10000 0 -0.38 56 56
SGK1 -0.031 0.14 -10000 0 -0.42 54 54
INPP5D 0.01 0.074 -10000 0 -0.31 25 25
mol:GDP 0.015 0.075 0.22 9 -0.28 12 21
SOS1 0.026 0.005 -10000 0 -10000 0 0
SYK 0.023 0.035 0.17 1 -0.31 5 6
ARF6/GDP -0.008 0.044 0.25 5 -0.26 1 6
mol:PI-3-4-5-P3 -0.012 0.041 0.16 20 -10000 0 20
ARAP3/RAP1A/GTP -0.014 0.03 0.16 11 -10000 0 11
VAV1 0.013 0.068 0.17 1 -0.31 21 22
mol:PI-3-4-P2 -0.021 0.043 -10000 0 -0.21 23 23
RAS family/GTP/PI3K Class I 0.063 0.066 0.19 92 -0.14 2 94
PLEKHA1 -0.021 0.035 -10000 0 -0.18 22 22
Rac1/GDP 0.023 0.071 0.23 5 -0.28 10 15
LAT 0.029 0.032 0.17 13 -0.31 2 15
Rac1/GTP 0.016 0.062 0.18 1 -0.31 9 10
ITK -0.018 0.044 0.15 19 -0.27 2 21
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.005 0.091 0.29 11 -0.26 16 27
LCK 0.03 0.02 0.17 9 -10000 0 9
BTK -0.015 0.038 0.15 13 -10000 0 13
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.022 -10000 0 -10000 0 0
CDKN2C 0.031 0.018 0.16 3 -0.095 1 4
CDKN2A 0.058 0.06 0.18 99 -0.14 1 100
CCND2 -0.009 0.02 -10000 0 -0.14 4 4
RB1 0.005 0.019 0.18 2 -10000 0 2
CDK4 -0.007 0.014 -10000 0 -0.18 2 2
CDK6 -0.01 0.029 -10000 0 -0.17 12 12
G1/S progression -0.005 0.019 -10000 0 -0.16 3 3
Signaling events mediated by PRL

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
CCNE1 0.028 0.015 0.17 5 -10000 0 5
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.004 0.081 -10000 0 -0.31 31 31
CDKN1A 0.009 0.047 -10000 0 -0.41 5 5
PRL-3/alpha Tubulin 0.046 0.042 0.14 66 -10000 0 66
mol:Ca2+ -0.037 0.053 0.21 4 -0.21 17 21
AGT 0.027 0.082 0.17 49 -0.31 20 69
CCNA2 -0.021 0.038 -10000 0 -10000 0 0
TUBA1B 0.027 0.003 -10000 0 -10000 0 0
EGR1 -0.006 0.058 0.26 1 -0.2 36 37
CDK2/Cyclin E1 0.042 0.057 0.26 2 -0.35 6 8
MAPK3 0.001 0.069 0.26 31 -10000 0 31
PRL-2 /Rab GGTase beta 0.038 0.009 -10000 0 -10000 0 0
MAPK1 0.001 0.07 0.26 32 -10000 0 32
PTP4A1 -0.017 0.036 -10000 0 -10000 0 0
PTP4A3 0.042 0.053 0.17 66 -10000 0 66
PTP4A2 0.027 0.003 -10000 0 -10000 0 0
ITGB1 0.003 0.072 0.26 34 -10000 0 34
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.02 0.053 -10000 0 -0.32 7 7
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 0.009 0.052 -10000 0 -10000 0 0
RABGGTA 0.027 0.003 -10000 0 -10000 0 0
BCAR1 -0.027 0.035 -10000 0 -10000 0 0
RHOC 0.021 0.057 -10000 0 -0.31 8 8
RHOA 0.023 0.051 -10000 0 -0.32 5 5
cell motility 0.032 0.079 0.4 6 -0.3 6 12
PRL-1/alpha Tubulin 0.008 0.051 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.028 0.072 0.14 54 -0.22 26 80
ROCK1 0.031 0.069 0.35 3 -0.3 6 9
RABGGTB 0.026 0.005 -10000 0 -10000 0 0
CDK2 0.026 0.005 -10000 0 -10000 0 0
mitosis -0.017 0.036 -10000 0 -10000 0 0
ATF5 0.028 0.015 0.17 5 -10000 0 5
Regulation of Androgen receptor activity

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
HDAC1 -0.012 0.003 -10000 0 -10000 0 0
SMARCC1 0.012 0.006 -10000 0 -10000 0 0
REL -0.005 0.098 -10000 0 -0.31 46 46
HDAC7 -0.018 0.056 0.2 9 -0.23 13 22
JUN 0.024 0.031 0.17 1 -0.31 4 5
EP300 0.025 0.026 -10000 0 -0.31 3 3
KAT2B 0.026 0.005 -10000 0 -10000 0 0
KAT5 0.026 0.006 -10000 0 -10000 0 0
MAPK14 0.005 0.024 0.23 1 -0.21 3 4
FOXO1 0.022 0.011 -10000 0 -10000 0 0
T-DHT/AR 0.026 0.065 0.26 3 -0.23 14 17
MAP2K6 0.027 0.035 0.18 10 -0.31 3 13
BRM/BAF57 0.038 0.013 -10000 0 -10000 0 0
MAP2K4 0.025 0.01 -10000 0 -10000 0 0
SMARCA2 0.026 0.008 -10000 0 -10000 0 0
PDE9A 0.006 0.11 -10000 0 -0.5 19 19
NCOA2 -0.015 0.1 -10000 0 -0.31 53 53
CEBPA 0.027 0.003 -10000 0 -10000 0 0
EHMT2 0.027 0.006 -10000 0 -10000 0 0
cell proliferation 0.042 0.12 0.36 35 -0.26 8 43
NR0B1 0.023 0.018 0.17 6 -10000 0 6
EGR1 0.008 0.095 0.17 24 -0.31 36 60
RXRs/9cRA 0.007 0.083 -10000 0 -0.16 91 91
AR/RACK1/Src 0.009 0.064 0.19 22 -0.24 12 34
AR/GR 0.002 0.088 0.2 8 -0.24 43 51
GNB2L1 0.028 0.014 0.17 4 -10000 0 4
PKN1 0.029 0.019 0.17 8 -10000 0 8
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.018 2 2
MAPK8 0.002 0.036 -10000 0 -0.22 12 12
T-DHT/AR/TIF2/CARM1 -0.001 0.083 0.21 3 -0.24 38 41
SRC -0.013 0.043 0.18 15 -0.16 13 28
NR3C1 0.019 0.05 -10000 0 -0.31 11 11
KLK3 0.008 0.14 0.36 1 -1.1 7 8
APPBP2 0.026 0.008 -10000 0 -10000 0 0
TRIM24 0.024 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.004 0.058 0.19 12 -0.23 14 26
TMPRSS2 -0.078 0.22 -10000 0 -0.51 96 96
RXRG -0.042 0.14 0.17 6 -0.31 102 108
mol:9cRA 0 0.001 -10000 0 -0.01 1 1
RXRA 0.026 0.006 -10000 0 -10000 0 0
RXRB 0.027 0.003 -10000 0 -10000 0 0
CARM1 0.027 0.005 -10000 0 -10000 0 0
NR2C2 0.016 0.058 -10000 0 -0.31 15 15
KLK2 -0.012 0.08 0.22 1 -0.34 10 11
AR -0.012 0.075 0.15 10 -0.25 39 49
SENP1 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
MDM2 0.026 0.007 -10000 0 -10000 0 0
SRY 0 0.004 0.031 7 -10000 0 7
GATA2 0.025 0.01 0.17 1 -10000 0 1
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.008 0.069 0.21 23 -0.24 12 35
positive regulation of transcription 0.025 0.01 0.17 1 -10000 0 1
DNAJA1 0.026 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.004 -10000 0 -10000 0 0
NCOA1 0.03 0.014 -10000 0 -10000 0 0
SPDEF 0.027 0.01 0.18 1 -10000 0 1
T-DHT/AR/TIF2 0.006 0.11 0.25 23 -0.26 38 61
T-DHT/AR/Hsp90 0.006 0.062 0.21 15 -0.23 15 30
GSK3B 0.026 0.007 -10000 0 -10000 0 0
NR2C1 0.026 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.029 0.18 1 -0.17 13 14
SIRT1 0.026 0.005 -10000 0 -10000 0 0
ZMIZ2 0.024 0.009 -10000 0 -10000 0 0
POU2F1 0.031 0.013 -10000 0 -0.11 1 1
T-DHT/AR/DAX-1 -0.005 0.063 0.2 15 -0.23 15 30
CREBBP 0.026 0.005 -10000 0 -10000 0 0
SMARCE1 0.026 0.008 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.027 0.004 -10000 0 -10000 0 0
SPHK1 0.03 0.025 0.17 14 -10000 0 14
GNAI2 0.026 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.011 0.16 2 -10000 0 2
GNAO1 -0.024 0.12 -10000 0 -0.31 71 71
mol:Sphinganine-1-P -0.012 0.015 0.26 1 -10000 0 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.052 0.03 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.035 0.013 -10000 0 -10000 0 0
S1PR3 0.015 0.06 0.17 1 -0.31 16 17
S1PR2 0.027 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.007 0.016 0.096 1 -10000 0 1
S1PR5 -0.026 0.12 -10000 0 -0.31 78 78
S1PR4 0.031 0.033 0.17 20 -0.31 1 21
GNAI1 0.023 0.028 0.17 1 -0.31 3 4
S1P/S1P5/G12 0.014 0.069 0.17 2 -0.15 63 65
S1P/S1P3/Gq 0.009 0.075 -10000 0 -0.39 9 9
S1P/S1P4/Gi -0.014 0.11 0.2 3 -0.32 41 44
GNAQ 0.026 0.006 -10000 0 -10000 0 0
GNAZ -0.002 0.094 -10000 0 -0.31 42 42
GNA14 0.025 0.016 -10000 0 -0.31 1 1
GNA15 0.012 0.068 -10000 0 -0.31 21 21
GNA12 0.024 0.008 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.016 0.058 -10000 0 -0.31 15 15
ABCC1 0.026 0.005 -10000 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.011 0.043 -10000 0 -0.27 10 10
FRAP1 0.024 0.055 0.27 1 -0.34 3 4
AKT1 0.013 0.068 0.15 74 -0.26 8 82
INSR 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.032 0.018 0.13 12 -0.092 1 13
mol:GTP 0.045 0.069 0.23 15 -0.24 7 22
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.007 0.024 -10000 0 -0.16 3 3
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.012 0.033 -10000 0 -0.21 7 7
TSC1 0.026 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.016 0.054 -10000 0 -0.26 17 17
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.023 0.037 -10000 0 -0.18 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 0.033 0.069 0.23 16 -0.26 3 19
MAP3K5 0.002 0.032 0.18 4 -0.19 10 14
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
apoptosis 0.002 0.032 0.18 4 -0.19 10 14
mol:LY294002 0 0 -10000 0 -0.001 17 17
EIF4B 0.033 0.073 0.24 22 -0.24 3 25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.049 0.061 0.23 11 -0.23 3 14
eIF4E/eIF4G1/eIF4A1 0.016 0.029 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.061 -10000 0 -0.26 17 17
mTOR/RHEB/GTP/Raptor/GBL 0.03 0.062 0.2 34 -0.18 1 35
FKBP1A 0.027 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.044 0.06 0.24 9 -0.28 3 12
mol:Amino Acids 0 0 -10000 0 -0.001 17 17
FKBP12/Rapamycin 0.021 0.004 -10000 0 -10000 0 0
PDPK1 -0.011 0.046 0.15 10 -0.28 8 18
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.031 0.1 -10000 0 -0.54 11 11
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.011 0.038 -10000 0 -0.23 1 1
TSC1/TSC2 0.05 0.074 0.24 17 -0.25 7 24
tumor necrosis factor receptor activity 0 0 0.001 17 -10000 0 17
RPS6 0.027 0.01 0.17 2 -10000 0 2
PPP5C 0.027 0.003 -10000 0 -10000 0 0
EIF4G1 0.026 0.006 -10000 0 -10000 0 0
IRS1 -0.001 0.055 -10000 0 -0.28 18 18
INS 0.022 0.024 0.17 12 -10000 0 12
PTEN 0.021 0.011 -10000 0 -10000 0 0
PDK2 -0.01 0.047 0.16 11 -0.28 8 19
EIF4EBP1 -0.14 0.4 -10000 0 -1 79 79
PIK3CA 0.024 0.027 -10000 0 -0.31 3 3
PPP2R5D 0.024 0.058 0.26 5 -0.32 3 8
peptide biosynthetic process -0.012 0.03 0.18 11 -10000 0 11
RHEB 0.025 0.008 -10000 0 -10000 0 0
EIF4A1 0.023 0.01 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 89 -0.002 1 90
EEF2 -0.012 0.03 0.18 11 -10000 0 11
eIF4E/4E-BP1 -0.12 0.38 -10000 0 -0.97 79 79
Retinoic acid receptors-mediated signaling

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 0.027 0.003 -10000 0 -10000 0 0
HDAC3 0.026 0.005 -10000 0 -10000 0 0
VDR 0.024 0.035 0.17 2 -0.31 5 7
Cbp/p300/PCAF 0.049 0.024 -10000 0 -0.18 3 3
EP300 0.025 0.026 -10000 0 -0.31 3 3
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.013 0.048 0.2 1 -0.23 8 9
KAT2B 0.026 0.005 -10000 0 -10000 0 0
MAPK14 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.014 0.068 0.19 28 -0.21 13 41
RAR alpha/9cRA/Cyclin H 0.032 0.077 0.21 4 -0.26 19 23
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.014 0.05 0.2 1 -0.22 8 9
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.012 0.07 0.15 2 -0.23 31 33
NCOR2 0.026 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.024 0.12 2 -0.21 5 7
RXRs/RARs/NRIP1/9cRA 0.002 0.11 0.36 4 -0.4 22 26
NCOA2 -0.015 0.1 -10000 0 -0.31 53 53
NCOA3 0.026 0.006 -10000 0 -10000 0 0
NCOA1 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.035 0.17 2 -0.31 5 7
RARG 0.021 0.045 -10000 0 -0.31 9 9
RAR gamma1/9cRA 0.032 0.029 -10000 0 -0.18 9 9
MAPK3 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.019 0.052 -10000 0 -0.31 12 12
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.007 0.1 0.23 1 -0.4 23 24
RARA 0.002 0.056 -10000 0 -0.21 29 29
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.007 0.073 -10000 0 -0.28 18 18
PRKCA 0.013 0.069 -10000 0 -0.31 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.001 0.11 0.32 2 -0.41 22 24
RXRG -0.042 0.12 0.2 1 -0.26 108 109
RXRA 0.005 0.056 0.13 2 -0.19 30 32
RXRB 0.009 0.054 0.17 2 -0.24 21 23
VDR/Vit D3/DNA 0.018 0.024 0.12 2 -0.21 5 7
RBP1 0.002 0.088 0.17 3 -0.31 36 39
CRBP1/9-cic-RA 0.003 0.06 0.12 3 -0.21 36 39
RARB 0.024 0.031 -10000 0 -0.31 4 4
PRKCG 0.028 0.025 0.18 13 -10000 0 13
MNAT1 0.026 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs 0.004 0.11 0.23 3 -0.41 23 26
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.006 0.097 0.28 6 -0.35 23 29
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.074 0.25 10 -0.26 13 23
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.001 0.11 0.34 2 -0.41 22 24
positive regulation of DNA binding 0.021 0.068 -10000 0 -0.23 25 25
NRIP1 -0.001 0.1 -10000 0 -0.46 11 11
RXRs/RARs -0.004 0.11 0.28 3 -0.39 28 31
RXRs/RXRs/DNA/9cRA -0.008 0.095 -10000 0 -0.4 22 22
PRKACA 0.027 0.003 -10000 0 -10000 0 0
CDK7 0.025 0.008 -10000 0 -10000 0 0
TFIIH 0.048 0.021 -10000 0 -10000 0 0
RAR alpha/9cRA 0.041 0.062 -10000 0 -0.28 6 6
CCNH 0.027 0.015 0.17 4 -10000 0 4
CREBBP 0.026 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.042 0.032 -10000 0 -0.15 7 7
IL2 signaling events mediated by PI3K

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
BCL2L1 0.007 0.072 -10000 0 -0.42 5 5
UGCG -0.037 0.19 -10000 0 -0.63 44 44
AKT1/mTOR/p70S6K/Hsp90/TERT 0.046 0.1 0.3 11 -0.34 14 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.035 0.19 -10000 0 -0.62 44 44
mol:DAG -0.006 0.11 -10000 0 -0.82 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.12 0.29 5 -0.41 27 32
FRAP1 0.025 0.14 0.33 7 -0.46 27 34
FOXO3 0.026 0.1 0.35 7 -0.37 15 22
AKT1 0.028 0.11 0.31 4 -0.39 16 20
GAB2 0.026 0.006 -10000 0 -10000 0 0
SMPD1 0.018 0.041 -10000 0 -0.54 2 2
SGMS1 0.009 0.085 -10000 0 -0.59 9 9
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 -0.008 0.023 -10000 0 -0.2 6 6
CALM1 0.026 0.005 -10000 0 -10000 0 0
cell proliferation 0.016 0.14 0.3 11 -0.39 29 40
EIF3A 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.033 0.035 -10000 0 -0.24 6 6
RPS6KB1 0.017 0.087 -10000 0 -0.7 7 7
mol:sphingomyelin -0.006 0.11 -10000 0 -0.82 9 9
natural killer cell activation 0 0.001 -10000 0 -0.01 1 1
JAK3 0.03 0.034 0.18 11 -0.31 3 14
PIK3R1 0.023 0.031 -10000 0 -0.31 4 4
JAK1 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC 0.066 0.13 0.4 19 -0.42 5 24
MYB 0.025 0.04 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.021 0.09 0.23 1 -0.32 19 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.045 0.086 -10000 0 -0.64 7 7
mol:PI-3-4-5-P3 0.022 0.089 0.23 1 -0.32 18 19
Rac1/GDP 0.015 0.024 -10000 0 -0.2 4 4
T cell proliferation 0.021 0.088 0.24 6 -0.31 16 22
SHC1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.002 -10000 0 -10000 0 0
PRKCZ 0.02 0.089 0.23 4 -0.32 16 20
NF kappa B1 p50/RelA 0.035 0.12 -10000 0 -0.42 26 26
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.012 0.069 -10000 0 -0.35 13 13
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
IL2RA 0.046 0.065 0.17 76 -0.31 5 81
IL2RB 0.015 0.072 0.18 7 -0.31 22 29
TERT 0.07 0.069 0.17 149 -10000 0 149
E2F1 0.029 0.042 -10000 0 -0.38 3 3
SOS1 0.026 0.006 -10000 0 -10000 0 0
RPS6 0.027 0.01 0.17 2 -10000 0 2
mol:cAMP -0.002 0.001 -10000 0 -10000 0 0
PTPN11 0.026 0.016 -10000 0 -0.31 1 1
IL2RG 0.03 0.043 0.18 15 -0.31 5 20
actin cytoskeleton organization 0.021 0.088 0.24 6 -0.31 16 22
GRB2 0.026 0.006 -10000 0 -10000 0 0
IL2 0.022 0.014 0.18 2 -10000 0 2
PIK3CA 0.025 0.027 -10000 0 -0.31 3 3
Rac1/GTP 0.039 0.034 -10000 0 -0.18 4 4
LCK 0.031 0.02 0.18 9 -10000 0 9
BCL2 0.008 0.19 0.34 4 -0.8 23 27
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.015 0.17 0.41 1 -0.64 10 11
PCK1 -0.006 0.15 -10000 0 -0.6 10 10
HNF4A -0.025 0.22 0.54 1 -0.79 19 20
KCNJ11 -0.006 0.19 -10000 0 -0.66 8 8
AKT1 0.036 0.11 0.34 1 -10000 0 1
response to starvation -0.001 0.021 -10000 0 -0.13 9 9
DLK1 -0.034 0.25 0.61 3 -0.76 32 35
NKX2-1 -0.001 0.11 0.27 4 -0.33 6 10
ACADM -0.021 0.18 -10000 0 -0.64 12 12
TAT -0.024 0.17 -10000 0 -0.65 15 15
CEBPB 0.026 0.017 -10000 0 -10000 0 0
CEBPA 0.028 0.016 -10000 0 -10000 0 0
TTR -0.011 0.25 0.42 2 -1.1 19 21
PKLR -0.01 0.19 0.4 1 -0.66 10 11
APOA1 -0.056 0.3 0.51 1 -1.1 23 24
CPT1C -0.022 0.2 0.47 1 -0.74 14 15
ALAS1 0.005 0.12 -10000 0 -0.53 2 2
TFRC -0.01 0.19 -10000 0 -0.66 15 15
FOXF1 0.006 0.07 -10000 0 -0.31 23 23
NF1 0.03 0.003 -10000 0 -10000 0 0
HNF1A (dimer) 0.044 0.049 0.18 51 -0.16 2 53
CPT1A -0.01 0.18 0.4 2 -0.64 10 12
HMGCS1 -0.013 0.18 -10000 0 -0.64 10 10
NR3C1 0.024 0.051 -10000 0 -0.3 11 11
CPT1B -0.015 0.18 -10000 0 -0.63 11 11
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.028 0.014 -10000 0 -0.16 2 2
GCK -0.024 0.23 0.44 2 -0.73 28 30
CREB1 0.032 0.012 -10000 0 -0.18 1 1
IGFBP1 0.001 0.11 -10000 0 -0.61 2 2
PDX1 0.01 0.15 0.46 2 -1.3 2 4
UCP2 -0.014 0.19 -10000 0 -0.66 12 12
ALDOB 0.003 0.2 0.47 6 -0.66 8 14
AFP 0.01 0.066 -10000 0 -0.26 3 3
BDH1 -0.012 0.18 0.42 1 -0.63 11 12
HADH -0.007 0.19 -10000 0 -0.71 6 6
F2 -0.036 0.23 -10000 0 -0.86 10 10
HNF1A 0.044 0.049 0.18 51 -0.16 2 53
G6PC 0.015 0.071 0.4 1 -10000 0 1
SLC2A2 0.015 0.13 0.44 1 -0.52 2 3
INS -0.016 0.031 0.17 12 -10000 0 12
FOXA1 0.044 0.036 0.27 1 -0.25 2 3
FOXA3 0.023 0.12 0.22 7 -0.3 53 60
FOXA2 0.006 0.23 -10000 0 -0.7 12 12
ABCC8 -0.056 0.29 -10000 0 -0.76 55 55
ALB 0.015 0.086 -10000 0 -0.81 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.006 -10000 0 -10000 0 0
ELF1 0.027 0.048 -10000 0 -0.3 8 8
CCNA2 0.048 0.053 0.17 74 -10000 0 74
PIK3CA 0.024 0.027 -10000 0 -0.31 3 3
JAK3 0.029 0.034 0.17 11 -0.31 3 14
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
JAK1 0.026 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.018 0.081 -10000 0 -0.36 10 10
SHC1 0.026 0.006 -10000 0 -10000 0 0
SP1 0.014 0.072 -10000 0 -0.28 27 27
IL2RA 0.015 0.065 0.31 1 -0.4 8 9
IL2RB 0.014 0.072 0.17 7 -0.31 22 29
SOS1 0.026 0.005 -10000 0 -10000 0 0
IL2RG 0.028 0.042 0.17 15 -0.31 5 20
G1/S transition of mitotic cell cycle -0.013 0.2 0.35 12 -0.69 30 42
PTPN11 0.026 0.016 -10000 0 -0.31 1 1
CCND2 -0.014 0.13 -10000 0 -0.58 23 23
LCK 0.03 0.02 0.17 9 -10000 0 9
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.022 0.012 0.17 2 -10000 0 2
CDK6 0.016 0.054 -10000 0 -0.31 13 13
CCND3 0.021 0.084 0.42 3 -0.4 3 6
LPA4-mediated signaling events

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
ADCY4 -0.01 0.013 -10000 0 -0.18 3 3
ADCY5 -0.03 0.055 -10000 0 -0.18 61 61
ADCY6 -0.009 0.002 -10000 0 -10000 0 0
ADCY7 -0.009 0.004 -10000 0 -10000 0 0
ADCY1 -0.01 0.031 0.22 6 -0.18 3 9
ADCY2 -0.014 0.028 -10000 0 -0.18 14 14
ADCY3 -0.009 0.002 -10000 0 -10000 0 0
ADCY8 -0.009 0.006 -10000 0 -10000 0 0
PRKCE -0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.01 0.011 -10000 0 -0.18 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.021 0.093 0.25 44 -0.18 1 45
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 0.064 0.037 0.2 3 -0.27 1 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.052 0.053 0.29 15 -0.25 1 16
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.053 0.025 -10000 0 -0.22 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.002 0.05 -10000 0 -0.21 11 11
CaM/Ca2+ 0.063 0.037 -10000 0 -0.26 1 1
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.023 0.031 0.16 8 -0.26 1 9
AKT1 0.001 0.075 0.21 40 -0.47 1 41
MAP2K1 -0.009 0.049 0.22 17 -0.38 1 18
MAP3K11 -0.007 0.052 0.24 18 -0.26 1 19
IFNGR1 0.028 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.017 0.13 -10000 0 -0.3 73 73
Rap1/GTP -0.023 0.018 -10000 0 -0.32 1 1
CRKL/C3G 0.037 0.011 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.073 0.041 0.26 1 -0.2 1 2
CEBPB 0.025 0.07 0.31 12 -0.42 1 13
STAT3 0.026 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.072 0.072 -10000 0 -0.88 2 2
STAT1 -0.005 0.057 0.23 23 -0.26 1 24
CALM1 0.026 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.027 0.045 0.18 31 -10000 0 31
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
STAT1 (dimer)/PIAS1 0.029 0.057 0.27 17 -0.26 1 18
CEBPB/PTGES2/Cbp/p300 0.031 0.038 -10000 0 -0.28 1 1
mol:Ca2+ 0.061 0.036 0.19 3 -0.27 1 4
MAPK3 0.011 0.069 -10000 0 -0.51 4 4
STAT1 (dimer) 0.009 0.07 -10000 0 -0.28 11 11
MAPK1 0.005 0.097 -10000 0 -0.63 8 8
JAK2 0.027 0.018 -10000 0 -0.33 1 1
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
JAK1 0.028 0.009 -10000 0 -10000 0 0
CAMK2D 0.026 0.005 -10000 0 -10000 0 0
DAPK1 0.026 0.07 0.28 16 -0.48 1 17
SMAD7 0.009 0.051 0.18 19 -0.13 4 23
CBL/CRKL/C3G 0.035 0.046 0.28 9 -0.37 1 10
PI3K 0.051 0.048 -10000 0 -0.21 6 6
IFNG 0.027 0.045 0.18 31 -10000 0 31
apoptosis 0.026 0.067 0.28 11 -0.35 3 14
CAMK2G 0.026 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.005 -10000 0 -10000 0 0
CAMK2A -0.022 0.13 0.17 14 -0.31 77 91
CAMK2B 0.031 0.041 0.17 26 -0.31 2 28
FRAP1 0 0.071 0.19 44 -0.44 1 45
PRKCD -0.001 0.072 0.22 33 -0.48 1 34
RAP1B 0.026 0.006 -10000 0 -10000 0 0
negative regulation of cell growth 0.002 0.05 -10000 0 -0.21 11 11
PTPN2 0.026 0.006 -10000 0 -10000 0 0
EP300 0.025 0.026 -10000 0 -0.31 3 3
IRF1 -0.001 0.059 0.25 15 -0.31 1 16
STAT1 (dimer)/PIASy 0.02 0.058 0.26 18 -0.26 1 19
SOCS1 0.02 0.075 -10000 0 -1.1 2 2
mol:GDP 0.032 0.043 0.26 9 -0.36 1 10
CASP1 0.005 0.061 0.19 19 -0.2 15 34
PTGES2 0.025 0.007 -10000 0 -10000 0 0
IRF9 0.023 0.037 0.16 18 -10000 0 18
mol:PI-3-4-5-P3 0.037 0.04 -10000 0 -0.2 6 6
RAP1/GDP 0.03 0.029 -10000 0 -0.33 1 1
CBL -0.008 0.052 0.24 17 -0.39 1 18
MAP3K1 -0.008 0.048 0.22 16 -0.39 1 17
PIAS1 0.026 0.015 -10000 0 -0.31 1 1
PIAS4 0.026 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.002 0.05 -10000 0 -0.21 11 11
PTPN11 -0.01 0.03 0.16 10 -0.27 1 11
CREBBP 0.026 0.005 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.049 0.2 4 -0.29 3 7
PDGFB-D/PDGFRB/SLAP 0.034 0.027 0.16 11 -10000 0 11
PDGFB-D/PDGFRB/APS/CBL 0.049 0.03 -10000 0 -0.18 2 2
AKT1 0.014 0.096 0.26 44 -0.26 1 45
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.03 0.064 0.25 11 -0.32 4 15
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
FGR 0.014 0.048 -10000 0 -0.4 4 4
mol:Ca2+ 0.016 0.066 0.24 10 -0.38 4 14
MYC 0.069 0.13 0.4 40 -10000 0 40
SHC1 0.026 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.031 0.032 0.16 20 -0.15 1 21
LRP1/PDGFRB/PDGFB 0.053 0.018 -10000 0 -0.18 1 1
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 0.025 0.016 -10000 0 -0.31 1 1
GO:0007205 0.016 0.066 0.25 8 -0.38 4 12
PTEN 0.021 0.011 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.038 0.017 0.14 2 -0.22 1 3
PDGFB-D/PDGFRB/GRB10 0.037 0.015 0.14 2 -10000 0 2
cell cycle arrest 0.034 0.027 0.16 11 -10000 0 11
HRAS 0.028 0.017 0.17 6 -10000 0 6
HIF1A 0.006 0.089 0.24 43 -0.25 2 45
GAB1 0.017 0.074 0.26 9 -0.27 13 22
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.017 0.069 0.26 15 -0.26 4 19
PDGFB-D/PDGFRB 0.051 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.04 0.01 0.14 2 -10000 0 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.033 0.037 0.2 1 -0.2 1 2
positive regulation of MAPKKK cascade 0.038 0.017 0.14 2 -0.22 1 3
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
mol:IP3 0.016 0.067 0.25 8 -0.39 4 12
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.04 0.011 0.14 2 -10000 0 2
SHB 0.024 0.026 -10000 0 -0.31 3 3
BLK -0.1 0.2 0.33 2 -0.4 142 144
PTPN2 0.027 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.039 0.012 0.14 2 -10000 0 2
BCAR1 0.022 0.011 -10000 0 -10000 0 0
VAV2 0.024 0.081 0.28 14 -0.28 12 26
CBL 0.025 0.016 -10000 0 -0.31 1 1
PDGFB-D/PDGFRB/DEP1 0.039 0.012 0.14 2 -10000 0 2
LCK 0.017 0.035 0.21 1 -0.36 1 2
PDGFRB 0.028 0.011 0.18 2 -10000 0 2
ACP1 0.027 0.004 -10000 0 -10000 0 0
HCK 0.014 0.059 -10000 0 -0.45 6 6
ABL1 0.007 0.076 0.24 9 -0.25 16 25
PDGFB-D/PDGFRB/CBL 0.012 0.078 0.35 3 -0.31 14 17
PTPN1 0.027 0.006 -10000 0 -10000 0 0
SNX15 0.026 0.006 -10000 0 -10000 0 0
STAT3 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.019 0.17 8 -10000 0 8
cell proliferation 0.068 0.13 0.38 44 -0.27 1 45
SLA 0.025 0.025 0.17 11 -10000 0 11
actin cytoskeleton reorganization 0.01 0.071 0.2 48 -10000 0 48
SRC 0.009 0.068 0.36 1 -0.45 8 9
PI3K -0.02 0.022 -10000 0 -0.18 5 5
PDGFB-D/PDGFRB/GRB7/SHC 0.051 0.017 -10000 0 -10000 0 0
SH2B2 0.028 0.03 0.17 14 -0.31 1 15
PLCgamma1/SPHK1 0.03 0.065 0.25 11 -0.33 4 15
LYN 0.007 0.055 -10000 0 -0.37 8 8
LRP1 0.026 0.017 0.17 1 -0.31 1 2
SOS1 0.026 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.005 -10000 0 -10000 0 0
STAT5A 0.026 0.005 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.061 0.039 -10000 0 -10000 0 0
SPHK1 0.031 0.025 0.18 14 -10000 0 14
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.016 0.067 0.25 8 -0.39 4 12
PLCG1 0.016 0.067 0.25 8 -0.4 4 12
NHERF/PDGFRB 0.052 0.02 -10000 0 -10000 0 0
YES1 -0.007 0.12 -10000 0 -0.5 24 24
cell migration 0.051 0.02 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.07 0.033 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.016 0.17 5 -10000 0 5
SLC9A3R1 0.026 0.005 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.052 0.034 -10000 0 -10000 0 0
FYN -0.033 0.13 -10000 0 -0.36 65 65
DOK1 -0.005 0.042 0.17 25 -0.17 1 26
HRAS/GTP 0.021 0.012 0.12 6 -10000 0 6
PDGFB 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.037 0.099 0.35 20 -0.3 5 25
PRKCD -0.004 0.041 0.17 24 -10000 0 24
FER -0.009 0.044 0.17 18 -0.17 11 29
MAPKKK cascade 0.003 0.083 0.23 44 -10000 0 44
RASA1 -0.004 0.043 0.17 25 -0.17 1 26
NCK1 0.025 0.007 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.033 0.033 0.17 24 -0.16 1 25
PDGFB-D/PDGFRB/SHB 0.038 0.023 0.14 2 -0.22 3 5
chemotaxis 0.007 0.075 0.23 10 -0.24 16 26
STAT1-3-5/STAT1-3-5 0.06 0.027 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.021 0.008 0.12 2 -10000 0 2
PTPRJ 0.026 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.025 0.026 -10000 0 -0.31 3 3
HDAC4 0.027 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.012 0.021 -10000 0 -0.15 6 6
CDKN1A -0.009 0.005 -10000 0 -10000 0 0
KAT2B 0.026 0.005 -10000 0 -10000 0 0
BAX 0.027 0.01 0.17 2 -10000 0 2
FOXO3 -0.002 0.024 0.3 3 -10000 0 3
FOXO1 0.022 0.011 -10000 0 -10000 0 0
FOXO4 0.011 0.02 -10000 0 -0.21 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
TAT 0.028 0.035 0.17 25 -10000 0 25
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.023 0.26 1 -0.21 4 5
PPARGC1A -0.068 0.15 -10000 0 -0.31 139 139
FHL2 0.013 0.066 -10000 0 -0.31 20 20
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.013 -10000 0 -10000 0 0
HIST2H4A -0.012 0.021 0.15 6 -10000 0 6
SIRT1/FOXO3a 0.014 0.027 0.23 3 -0.19 1 4
SIRT1 0.024 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.049 0.017 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.03 0.037 0.21 1 -0.18 6 7
apoptosis -0.05 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A -0.025 0.093 -10000 0 -0.17 135 135
p53/SIRT1 0.027 0.016 -10000 0 -10000 0 0
SIRT1/FOXO4 0.027 0.029 -10000 0 -0.18 4 4
FOXO1/FHL2/SIRT1 0.033 0.043 -10000 0 -0.15 20 20
HIST1H1E 0.018 0.034 0.15 9 -0.21 6 15
SIRT1/p300 0.035 0.023 -10000 0 -0.22 3 3
muscle cell differentiation -0.027 0.03 0.18 4 -0.21 4 8
TP53 0.02 0.011 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.05 0.016 -10000 0 -10000 0 0
CREBBP 0.026 0.005 -10000 0 -10000 0 0
MEF2D 0.026 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.035 0.029 -10000 0 -10000 0 0
ACSS2 -0.012 0.01 0.1 3 -10000 0 3
SIRT1/PCAF/MYOD 0.027 0.03 0.22 4 -0.18 4 8
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.026 0.005 -10000 0 -10000 0 0
NFATC1 0.017 0.083 0.28 10 -0.32 6 16
NFATC2 -0.002 0.066 0.18 10 -0.2 20 30
NFATC3 0.017 0.008 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.031 0.11 0.2 4 -0.3 51 55
Exportin 1/Ran/NUP214 0.049 0.017 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.01 0.12 0.21 1 -0.29 51 52
BCL2/BAX 0.029 0.042 0.14 2 -0.21 12 14
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.027 0.01 0.17 2 -10000 0 2
MAPK14 0.027 0.004 -10000 0 -10000 0 0
BAD 0.027 0.008 0.17 1 -10000 0 1
CABIN1/MEF2D -0.018 0.11 0.25 4 -0.29 51 55
Calcineurin A alpha-beta B1/BCL2 0.016 0.052 -10000 0 -0.31 12 12
FKBP8 0.027 0.002 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.017 0.11 0.28 51 -0.24 4 55
KPNB1 0.026 0.005 -10000 0 -10000 0 0
KPNA2 0.028 0.015 0.17 5 -10000 0 5
XPO1 0.027 0.004 -10000 0 -10000 0 0
SFN -0.006 0.1 -10000 0 -0.31 49 49
MAP3K8 0.018 0.054 0.17 1 -0.31 13 14
NFAT4/CK1 alpha 0.023 0.02 -10000 0 -0.15 1 1
MEF2D/NFAT1/Cbp/p300 0.029 0.087 0.22 4 -0.23 21 25
CABIN1 -0.031 0.11 0.2 4 -0.3 50 54
CALM1 0.026 0.006 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
MAP3K1 0.023 0.017 -10000 0 -0.31 1 1
CAMK4 0.006 0.078 0.17 1 -0.31 28 29
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.005 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.039 0.021 0.14 6 -0.21 2 8
YWHAB 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.052 -10000 0 -0.31 12 12
MAPK9 0.026 0.005 -10000 0 -10000 0 0
YWHAG 0.025 0.008 -10000 0 -10000 0 0
FKBP1A 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.016 0.079 0.29 4 -0.33 5 9
PRKCH 0.026 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.036 0.024 -10000 0 -0.21 3 3
CASP3 0.027 0.004 -10000 0 -10000 0 0
PIM1 0.028 0.021 0.17 5 -0.31 1 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.005 -10000 0 -10000 0 0
apoptosis 0.015 0.018 -10000 0 -0.22 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.049 -10000 0 -0.24 5 5
PRKCB -0.047 0.14 -10000 0 -0.31 107 107
PRKCE 0.026 0.005 -10000 0 -10000 0 0
JNK2/NFAT4 0.016 0.053 -10000 0 -0.14 4 4
BAD/BCL-XL 0.038 0.011 0.14 1 -10000 0 1
PRKCD 0.026 0.005 -10000 0 -10000 0 0
NUP214 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
PRKCA 0.011 0.069 -10000 0 -0.31 22 22
PRKCG 0.027 0.025 0.17 13 -10000 0 13
PRKCQ 0.008 0.085 0.17 10 -0.31 31 41
FKBP38/BCL2 0.029 0.041 -10000 0 -0.21 12 12
EP300 0.024 0.027 -10000 0 -0.31 3 3
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.004 -10000 0 -10000 0 0
NFATc/JNK1 0.028 0.082 0.28 10 -0.32 5 15
CaM/Ca2+/FKBP38 0.035 0.011 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.003 -10000 0 -10000 0 0
CSNK1A1 0.011 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.021 0.049 0.13 1 -0.17 27 28
NFATc/ERK1 0.028 0.081 0.28 9 -0.3 6 15
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.01 0.12 -10000 0 -0.29 51 51
NR4A1 0.004 0.086 0.21 8 -0.34 14 22
GSK3B 0.025 0.007 -10000 0 -10000 0 0
positive T cell selection 0.017 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.002 0.049 0.15 2 -0.17 15 17
RCH1/ KPNB1 0.04 0.014 0.14 5 -10000 0 5
YWHAQ 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.004 -10000 0 -10000 0 0
AKAP5 0.027 0.028 0.17 7 -0.31 2 9
MEF2D 0.025 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.021 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.028 0.08 0.27 7 -0.3 6 13
CREBBP 0.025 0.009 -10000 0 -10000 0 0
BCL2 0.016 0.052 -10000 0 -0.31 12 12
Syndecan-3-mediated signaling events

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
CTTN 0.026 0.006 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.028 0.07 -10000 0 -0.42 2 2
Syndecan-3/Neurocan 0.032 0.04 -10000 0 -0.45 2 2
POMC -0.006 0.1 0.17 5 -0.31 50 55
EGFR -0.002 0.09 -10000 0 -0.31 39 39
Syndecan-3/EGFR 0.012 0.053 -10000 0 -0.45 2 2
AGRP 0.02 0.013 0.17 2 -10000 0 2
NCSTN 0.026 0.006 -10000 0 -10000 0 0
PSENEN 0.027 0.003 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.027 0.003 -10000 0 -10000 0 0
APH1A 0.026 0.006 -10000 0 -10000 0 0
NCAN 0.034 0.037 0.17 31 -10000 0 31
long-term memory 0.036 0.036 -10000 0 -0.4 2 2
Syndecan-3/IL8 0.022 0.056 -10000 0 -0.45 2 2
PSEN1 0.026 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.037 0.011 -10000 0 -10000 0 0
FYN 0.023 0.018 -10000 0 -0.31 1 1
limb bud formation 0.01 0.03 -10000 0 -0.46 2 2
MC4R 0.018 0.013 0.17 2 -10000 0 2
SRC 0.026 0.006 -10000 0 -10000 0 0
PTN -0.022 0.12 0.17 3 -0.31 70 73
FGFR/FGF/Syndecan-3 0.01 0.031 -10000 0 -0.46 2 2
neuron projection morphogenesis 0.012 0.074 0.27 4 -0.41 2 6
Syndecan-3/AgRP 0.023 0.033 -10000 0 -0.44 2 2
Syndecan-3/AgRP/MC4R 0.032 0.036 -10000 0 -0.4 2 2
Fyn/Cortactin 0.032 0.019 -10000 0 -0.21 1 1
SDC3 0.01 0.031 -10000 0 -0.47 2 2
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.021 0.055 -10000 0 -0.44 2 2
IL8 0.01 0.094 0.17 24 -0.31 35 59
Syndecan-3/Fyn/Cortactin 0.037 0.037 -10000 0 -0.41 2 2
Syndecan-3/CASK 0.009 0.029 -10000 0 -0.44 2 2
alpha-MSH/MC4R 0.008 0.076 0.14 5 -0.21 50 55
Gamma Secretase 0.072 0.025 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.008 0.063 -10000 0 -0.31 18 18
Caspase 8 (4 units) 0.029 0.06 -10000 0 -0.2 15 15
NEF 0 0.02 -10000 0 -0.13 10 10
NFKBIA 0.027 0.009 -10000 0 -10000 0 0
BIRC3 0.017 0.037 0.18 13 -0.37 2 15
CYCS 0.01 0.063 0.18 34 -0.22 15 49
RIPK1 0.026 0.005 -10000 0 -10000 0 0
CD247 0.026 0.054 0.18 17 -0.21 15 32
MAP2K7 0.013 0.1 0.28 1 -0.58 9 10
protein ubiquitination 0.014 0.085 0.3 20 -0.27 6 26
CRADD 0.026 0.006 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.02 0.037 -10000 0 -0.31 6 6
BID 0.006 0.049 0.18 5 -0.22 16 21
NF-kappa-B/RelA/I kappa B alpha 0.055 0.025 -10000 0 -0.21 2 2
TRADD 0.024 0.009 -10000 0 -10000 0 0
MAP3K5 0.026 0.017 0.17 1 -0.31 1 2
CFLAR 0.027 0.003 -10000 0 -10000 0 0
FADD 0.026 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.055 0.026 -10000 0 -0.21 2 2
MAPK8 0.011 0.1 0.34 4 -0.58 8 12
APAF1 0.026 0.006 -10000 0 -10000 0 0
TRAF1 0.026 0.009 0.17 1 -10000 0 1
TRAF2 0.026 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.012 0.053 0.19 5 -0.23 17 22
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.008 0.067 -10000 0 -0.33 7 7
CHUK 0.01 0.076 0.29 14 -0.29 6 20
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.063 0.041 -10000 0 -0.19 5 5
TCRz/NEF 0.021 0.054 0.15 17 -0.24 15 32
TNF 0.014 0.076 0.17 12 -0.31 24 36
FASLG 0.004 0.072 -10000 0 -0.38 15 15
NFKB1 0.027 0.013 -10000 0 -0.16 1 1
TNFR1A/BAG4/TNF-alpha 0.022 0.068 -10000 0 -0.18 41 41
CASP6 0.033 0.064 -10000 0 -0.45 4 4
CASP7 0.019 0.088 0.33 14 -0.45 3 17
RELA 0.026 0.01 -10000 0 -0.086 2 2
CASP2 0.021 0.034 -10000 0 -0.31 5 5
CASP3 0.021 0.08 0.3 15 -0.45 3 18
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.02 0.049 -10000 0 -0.21 18 18
CASP8 0.027 0.002 -10000 0 -10000 0 0
CASP9 0.027 0.003 -10000 0 -10000 0 0
MAP3K14 0.006 0.066 0.24 3 -0.31 7 10
APAF-1/Caspase 9 0.016 0.059 -10000 0 -0.32 4 4
BCL2 0.007 0.098 0.34 6 -0.52 8 14
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.005 0.051 0.22 2 -0.22 8 10
adherens junction organization -0.004 0.06 0.19 5 -0.2 18 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.065 0.23 2 -0.26 6 8
FMN1 -0.013 0.066 0.15 2 -0.23 19 21
mol:IP3 0.006 0.034 -10000 0 -0.18 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.004 0.058 0.16 2 -0.24 11 13
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.006 0.043 0.17 2 -0.17 10 12
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.004 0.099 -10000 0 -0.42 11 11
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.052 0.15 1 -0.22 12 13
VASP -0.001 0.055 0.15 3 -0.23 11 14
ZYX -0.001 0.051 -10000 0 -0.24 9 9
JUB 0.001 0.055 0.15 3 -0.22 12 15
EGFR(dimer) 0.003 0.076 -10000 0 -0.24 23 23
E-cadherin/beta catenin-gamma catenin 0.046 0.02 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.024 0.051 0.21 1 -0.18 8 9
PIK3CA 0.024 0.027 -10000 0 -0.31 3 3
PI3K 0.025 0.052 0.21 1 -0.18 8 9
FYN 0 0.05 0.15 10 -0.22 14 24
mol:Ca2+ 0.006 0.034 -10000 0 -0.17 6 6
JUP 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.31 4 4
mol:DAG 0.006 0.034 -10000 0 -0.18 6 6
CDH1 0.024 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.072 0.24 3 -0.21 14 17
establishment of polarity of embryonic epithelium -0.001 0.054 0.15 3 -0.23 11 14
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
EGFR -0.002 0.09 -10000 0 -0.31 39 39
CASR -0.001 0.038 0.16 11 -0.2 3 14
RhoA/GTP 0.02 0.044 -10000 0 -0.2 3 3
AKT2 0.007 0.043 0.17 3 -0.17 9 12
actin cable formation -0.016 0.066 0.18 4 -0.22 19 23
apoptosis -0.01 0.054 0.19 8 -0.17 19 27
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
mol:GDP -0.005 0.059 0.16 14 -0.22 14 28
PIP5K1A -0.002 0.053 0.15 1 -0.22 12 13
PLCG1 0.006 0.035 -10000 0 -0.18 6 6
Rac1/GTP 0.012 0.077 -10000 0 -0.22 23 23
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.013 -10000 0 -10000 0 0
DOCK1 0.023 0.03 -10000 0 -0.31 4 4
ITGA4 0.021 0.059 0.17 11 -0.31 13 24
RAC1 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.026 0.067 0.25 3 -0.23 27 30
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.047 0.043 -10000 0 -0.18 13 13
alpha4/beta7 Integrin/Paxillin 0.03 0.056 0.23 3 -0.18 26 29
lamellipodium assembly -0.017 0.11 -10000 0 -0.41 31 31
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
PI3K 0.031 0.034 -10000 0 -0.24 6 6
ARF6 0.027 0.004 -10000 0 -10000 0 0
TLN1 0.026 0.005 -10000 0 -10000 0 0
PXN -0.012 0.003 -10000 0 -10000 0 0
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
ARF6/GTP 0.046 0.039 -10000 0 -0.15 13 13
cell adhesion 0.046 0.04 -10000 0 -0.16 12 12
CRKL/CBL 0.037 0.015 -10000 0 -0.21 1 1
alpha4/beta1 Integrin/Paxillin 0.035 0.039 -10000 0 -0.17 13 13
ITGB1 0.026 0.004 -10000 0 -10000 0 0
ITGB7 0.015 0.064 0.17 3 -0.31 18 21
ARF6/GDP 0.026 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.046 0.051 0.24 4 -0.17 17 21
p130Cas/Crk/Dock1 0.04 0.031 -10000 0 -0.18 4 4
VCAM1 0.025 0.039 0.17 8 -0.31 5 13
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.041 -10000 0 -0.16 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.042 -10000 0 -0.16 13 13
BCAR1 0.022 0.011 -10000 0 -10000 0 0
mol:GDP -0.046 0.041 0.16 13 -10000 0 13
CBL 0.025 0.016 -10000 0 -0.31 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GIT1 0.027 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.041 -10000 0 -0.16 12 12
Rac1/GTP -0.021 0.13 -10000 0 -0.46 31 31
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.01 0.086 -10000 0 -0.26 52 52
KLHL20 0.014 0.043 0.16 3 -0.19 1 4
CYFIP2 0.026 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.062 0.34 6 -10000 0 6
ENAH -0.01 0.085 -10000 0 -0.26 50 50
AP1M1 0.027 0.003 -10000 0 -10000 0 0
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.018 0.026 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.021 -10000 0 -0.13 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.048 0.049 -10000 0 -0.16 17 17
RAPGEF1 -0.008 0.079 0.29 4 -0.23 33 37
CTNND1 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.003 0.092 -10000 0 -0.26 55 55
CRK -0.008 0.076 -10000 0 -0.25 41 41
E-cadherin/gamma catenin/alpha catenin 0.046 0.021 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.028 0.048 -10000 0 -0.21 18 18
IQGAP1 0.027 0.003 -10000 0 -10000 0 0
NCKAP1 0.026 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.016 -10000 0 -10000 0 0
DLG1 -0.009 0.084 -10000 0 -0.26 49 49
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.015 0.015 -10000 0 -0.16 1 1
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.049 0.026 -10000 0 -0.16 3 3
PI3K -0.019 0.019 -10000 0 -0.2 1 1
ARF6 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.035 0.014 -10000 0 -10000 0 0
TIAM1 0.023 0.03 -10000 0 -0.31 4 4
E-cadherin(dimer)/Ca2+ 0.052 0.026 -10000 0 -10000 0 0
AKT1 -0.008 0.027 0.11 4 -0.12 1 5
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
CDH1 0.024 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.069 0.31 11 -10000 0 11
actin cytoskeleton organization 0.015 0.043 0.2 11 -0.14 1 12
CDC42/GDP 0.02 0.072 0.29 16 -10000 0 16
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.015 0.007 -10000 0 -10000 0 0
ITGB7 0.015 0.064 0.17 3 -0.31 18 21
RAC1 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.056 0.028 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.039 0.019 -10000 0 -10000 0 0
mol:GDP 0.007 0.076 0.3 16 -10000 0 16
CDC42/GTP/IQGAP1 0.036 0.006 -10000 0 -10000 0 0
JUP 0.027 0.004 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.021 0.062 0.38 3 -10000 0 3
RAC1/GTP/IQGAP1 0.033 0.011 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.039 0.008 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.003 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.037 0.18 11 -10000 0 11
NME1 0.03 0.022 0.17 11 -10000 0 11
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.008 0.084 -10000 0 -0.26 48 48
regulation of cell-cell adhesion 0.011 0.02 -10000 0 -10000 0 0
WASF2 0.006 0.02 -10000 0 -10000 0 0
Rap1/GTP 0.021 0.036 0.19 11 -10000 0 11
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.051 -10000 0 -0.15 15 15
CCND1 0.016 0.042 0.24 8 -0.11 1 9
VAV2 0.006 0.088 0.33 1 -0.55 1 2
RAP1/GDP 0.026 0.051 0.27 8 -10000 0 8
adherens junction assembly -0.008 0.082 -10000 0 -0.25 48 48
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.026 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.041 0.046 0.18 6 -0.15 14 20
E-cadherin/beta catenin 0.011 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.01 0.087 -10000 0 -0.26 52 52
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
Rac1/GTP 0.002 0.045 -10000 0 -0.3 1 1
E-cadherin/beta catenin/alpha catenin 0.045 0.022 -10000 0 -10000 0 0
ITGAE 0.025 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.094 -10000 0 -0.26 55 55
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.012 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.034 0.019 -10000 0 -10000 0 0
CDKN1B 0.005 0.048 -10000 0 -0.29 10 10
CDKN1A 0.005 0.055 -10000 0 -0.28 13 13
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.023 0.012 0.17 1 -10000 0 1
FOXO3 0.006 0.041 -10000 0 -0.26 10 10
AKT1 0.006 0.053 -10000 0 -0.29 13 13
BAD 0.027 0.008 0.17 1 -10000 0 1
AKT3 0.011 0.012 -10000 0 -0.24 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.052 -10000 0 -0.28 13 13
AKT1/ASK1 0.031 0.066 0.3 1 -0.28 12 13
BAD/YWHAZ 0.042 0.024 -10000 0 -10000 0 0
RICTOR 0.026 0.005 -10000 0 -10000 0 0
RAF1 0.026 0.005 -10000 0 -10000 0 0
JNK cascade -0.027 0.061 0.27 12 -10000 0 12
TSC1 0.005 0.043 -10000 0 -0.26 12 12
YWHAZ 0.021 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.033 0.069 0.32 1 -0.28 13 14
EP300 0.025 0.026 -10000 0 -0.31 3 3
mol:GDP 0.008 0.053 -10000 0 -0.29 13 13
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.004 0.051 -10000 0 -0.28 13 13
YWHAQ 0.027 0.004 -10000 0 -10000 0 0
TBC1D4 0.003 0.003 -10000 0 -10000 0 0
MAP3K5 0.026 0.017 0.17 1 -0.31 1 2
MAPKAP1 0.026 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.028 0.074 0.27 9 -0.23 19 28
YWHAH 0.027 0.004 -10000 0 -10000 0 0
AKT1S1 0.005 0.053 0.19 1 -0.28 13 14
CASP9 0.004 0.052 -10000 0 -0.28 13 13
YWHAB 0.026 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.034 0.071 0.32 8 -0.29 9 17
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.017 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0.01 0.053 -10000 0 -0.32 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.043 -10000 0 -0.33 6 6
CHUK 0.008 0.039 -10000 0 -0.26 8 8
BAD/BCL-XL 0.037 0.066 0.26 2 -0.28 12 14
mTORC2 0.032 0.01 -10000 0 -10000 0 0
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.034 0.09 0.28 17 -0.32 9 26
PDPK1 0.026 0.006 -10000 0 -10000 0 0
MDM2 0.006 0.056 -10000 0 -0.28 13 13
MAPKKK cascade -0.033 0.068 0.28 13 -0.32 1 14
MDM2/Cbp/p300 0.047 0.082 0.32 14 -0.35 4 18
TSC1/TSC2 0.009 0.071 0.28 16 -0.28 13 29
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.079 0.31 14 -0.26 12 26
glucose import -0.016 0.041 -10000 0 -0.15 41 41
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.009 0.041 0.18 1 -0.36 2 3
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.016 0.041 -10000 0 -0.15 41 41
GSK3A 0.005 0.051 -10000 0 -0.29 12 12
FOXO1 0.009 0.028 0.19 2 -0.24 4 6
GSK3B 0.009 0.054 -10000 0 -0.29 10 10
SFN -0.006 0.1 -10000 0 -0.31 49 49
G1/S transition of mitotic cell cycle 0.012 0.063 0.28 5 -0.3 9 14
p27Kip1/14-3-3 family 0.016 0.048 -10000 0 -0.43 2 2
PRKACA 0.027 0.003 -10000 0 -10000 0 0
KPNA1 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
YWHAG 0.025 0.008 -10000 0 -10000 0 0
RHEB 0.025 0.008 -10000 0 -10000 0 0
CREBBP 0.026 0.005 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.004 0.051 -10000 0 -10000 0 0
PLK1 0.027 0.13 0.47 3 -1.1 1 4
CDKN1B 0.051 0.092 0.39 6 -0.34 3 9
FOXO3 0.023 0.12 0.4 1 -0.54 6 7
KAT2B 0.031 0.015 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.052 0.27 1 -10000 0 1
CAT 0.021 0.12 0.44 4 -1 1 5
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.015 -10000 0 -10000 0 0
FOXO1 0.008 0.056 0.25 3 -10000 0 3
MAPK10 0.029 0.046 0.19 35 -0.17 1 36
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.05 0.082 0.31 22 -0.36 3 25
response to oxidative stress 0.009 0.007 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.026 0.11 0.37 1 -0.75 2 3
XPO1 0.027 0.004 -10000 0 -10000 0 0
EP300 0.026 0.026 -10000 0 -0.31 3 3
BCL2L11 0.013 0.12 -10000 0 -0.8 9 9
FOXO1/SKP2 0.016 0.054 -10000 0 -0.26 2 2
mol:GDP 0.009 0.007 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
GADD45A 0.042 0.14 0.35 1 -0.6 13 14
YWHAQ 0.027 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.025 0.069 0.24 1 -0.41 2 3
MST1 0.048 0.049 0.18 55 -0.14 1 56
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.027 0.003 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.006 0.1 -10000 0 -0.41 14 14
YWHAB 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.028 0.048 0.19 35 -0.19 3 38
MAPK9 0.03 0.047 0.19 38 -10000 0 38
YWHAG 0.025 0.008 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
YWHAZ 0.021 0.011 -10000 0 -10000 0 0
SIRT1 0.025 0.012 -10000 0 -10000 0 0
SOD2 0.049 0.1 0.39 8 -0.53 1 9
RBL2 -0.021 0.23 -10000 0 -0.68 43 43
RAL/GDP 0.038 0.018 -10000 0 -10000 0 0
CHUK 0.03 0.015 -10000 0 -10000 0 0
Ran/GTP 0.021 0.006 -10000 0 -10000 0 0
CSNK1G2 0.026 0.005 -10000 0 -10000 0 0
RAL/GTP 0.04 0.018 -10000 0 -10000 0 0
CSNK1G1 0.027 0.003 -10000 0 -10000 0 0
FASLG -0.011 0.22 -10000 0 -1 19 19
SKP2 0.021 0.04 -10000 0 -0.31 7 7
USP7 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.025 0.018 -10000 0 -10000 0 0
CCNB1 0.02 0.12 0.42 2 -1 1 3
FOXO1-3a-4/beta catenin 0.06 0.1 0.36 13 -0.4 5 18
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.054 -10000 0 -0.26 2 2
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
SGK1 -0.012 0.12 0.18 6 -0.3 68 74
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.012 -10000 0 -10000 0 0
ZFAND5 0.051 0.086 0.4 11 -10000 0 11
SFN -0.006 0.1 -10000 0 -0.31 49 49
CDK2 0.027 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.01 0.099 -10000 0 -0.39 13 13
CREBBP 0.027 0.006 -10000 0 -10000 0 0
FBXO32 0.056 0.16 0.54 6 -1.1 2 8
BCL6 0.032 0.13 -10000 0 -0.64 10 10
RALB 0.026 0.006 -10000 0 -10000 0 0
RALA 0.025 0.008 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0.019 0.014 0.11 1 -0.087 6 7
TRAF2/ASK1 0.034 0.014 0.13 1 -0.18 1 2
ATM 0.025 0.016 -10000 0 -0.31 1 1
MAP2K3 -0.021 0.11 0.28 8 -0.3 46 54
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.012 0.092 0.3 5 -0.29 23 28
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.041 0.048 0.17 52 -0.31 1 53
TXN 0.006 0.002 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
GADD45A 0.025 0.022 -10000 0 -0.31 2 2
GADD45B 0.031 0.033 0.17 19 -0.31 1 20
MAP3K1 0.023 0.017 -10000 0 -0.31 1 1
MAP3K6 0.027 0.002 -10000 0 -10000 0 0
MAP3K7 0.022 0.01 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.039 0.014 0.14 1 -0.21 1 2
TAK1/TAB family -0.002 0.011 -10000 0 -0.13 2 2
RAC1/OSM/MEKK3 0.046 0.018 -10000 0 -10000 0 0
TRAF2 0.026 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.003 0.088 -10000 0 -0.27 29 29
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.031 0.041 0.17 26 -0.31 2 28
CCM2 0.025 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.036 0.028 0.13 25 -0.18 2 27
MAPK11 0.029 0.019 0.17 8 -10000 0 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.049 0.032 -10000 0 -0.16 3 3
OSM/MEKK3 0.036 0.013 -10000 0 -10000 0 0
TAOK1 -0.03 0.094 -10000 0 -0.24 81 81
TAOK2 0.011 0.012 -10000 0 -0.24 1 1
TAOK3 0.011 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.017 0.17 1 -0.31 1 2
MAP3K10 0.027 0.004 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.023 0.012 0.13 1 -0.17 1 2
GADD45/MTK1/MTK1 0.069 0.045 0.23 13 -0.15 3 16
Canonical NF-kappaB pathway

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
FBXW11 0.028 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.083 0.29 5 -0.24 9 14
ERC1 0.025 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.024 0.042 -10000 0 -0.21 12 12
NFKBIA -0.004 0.043 0.22 17 -10000 0 17
BIRC2 0.026 0.006 -10000 0 -10000 0 0
IKBKB 0.021 0.011 -10000 0 -10000 0 0
RIPK2 0.021 0.011 -10000 0 -10000 0 0
IKBKG 0.024 0.042 -10000 0 -0.3 1 1
IKK complex/A20 0.023 0.1 0.25 2 -0.29 25 27
NEMO/A20/RIP2 0.021 0.011 -10000 0 -10000 0 0
XPO1 0.027 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.018 0.094 0.26 2 -0.29 24 26
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.018 0.083 -10000 0 -0.27 22 22
BCL10/MALT1/TRAF6 0.046 0.023 -10000 0 -0.18 1 1
NOD2 0.014 0.06 0.17 2 -0.31 16 18
NFKB1 0.028 0.004 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
MALT1 0.023 0.019 0.17 1 -0.31 1 2
cIAP1/UbcH5C 0.038 0.01 -10000 0 -10000 0 0
ATM 0.025 0.016 -10000 0 -0.31 1 1
TNF/TNFR1A 0.027 0.058 -10000 0 -0.21 24 24
TRAF6 0.026 0.005 -10000 0 -10000 0 0
PRKCA 0.011 0.069 -10000 0 -0.31 22 22
CHUK 0.025 0.007 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF 0.014 0.076 0.17 12 -0.31 24 36
NF kappa B1 p50/RelA 0.056 0.017 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.043 0.22 17 -10000 0 17
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
IKK complex 0.021 0.089 0.25 2 -0.29 22 24
CYLD 0.024 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.023 0.098 0.25 2 -0.3 24 26
Atypical NF-kappaB 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
BCL3/RelA 0.041 0.02 0.14 13 -10000 0 13
FBXW11 0.026 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.003 0.058 -10000 0 -0.18 46 46
NF kappa B1 p50/RelA/I kappa B alpha 0.023 0.029 -10000 0 -10000 0 0
NFKBIA 0.012 0.024 0.21 1 -0.16 4 5
MAPK14 0.027 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.012 -10000 0 -10000 0 0
ARRB2 0.012 0.004 -10000 0 -10000 0 0
REL -0.005 0.097 -10000 0 -0.31 46 46
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.024 0.023 0.14 12 -10000 0 12
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.012 -10000 0 -10000 0 0
PIK3CA 0.023 0.027 -10000 0 -0.31 3 3
NF kappa B1 p50 dimer 0.016 0.02 0.25 3 -10000 0 3
PIK3R1 0.022 0.031 -10000 0 -0.31 4 4
NFKB1 -0.01 0.005 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.015 0.03 -10000 0 -0.16 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.029 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.031 0.034 -10000 0 -0.24 6 6
NF kappa B1 p50/RelA 0.015 0.03 -10000 0 -0.16 4 4
IKBKB 0.021 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.005 -10000 0 -10000 0 0
SYK 0.023 0.035 0.17 1 -0.31 5 6
I kappa B alpha/PIK3R1 0.028 0.037 0.21 7 -0.15 5 12
cell death 0.023 0.028 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.003 0.058 -10000 0 -0.18 46 46
LCK 0.03 0.02 0.17 9 -10000 0 9
BCL3 0.031 0.024 0.17 13 -10000 0 13
Regulation of Telomerase

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
Telomerase catalytic core complex 0.041 0.094 0.43 7 -10000 0 7
RAD9A 0.026 0.009 0.17 1 -10000 0 1
AP1 0 0.098 0.17 4 -0.22 78 82
IFNAR2 0.028 0.006 -10000 0 -10000 0 0
AKT1 0.015 0.029 -10000 0 -0.31 1 1
ER alpha/Oestrogen 0.014 0.041 0.12 1 -0.21 16 17
NFX1/SIN3/HDAC complex 0.022 0.027 -10000 0 -0.24 1 1
EGF 0.024 0.084 0.18 40 -0.31 23 63
SMG5 0.026 0.005 -10000 0 -10000 0 0
SMG6 0.025 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.037 0.017 -10000 0 -10000 0 0
TERT/c-Abl 0.046 0.089 0.41 6 -10000 0 6
SAP18 0.026 0.006 -10000 0 -10000 0 0
MRN complex 0.041 0.024 -10000 0 -10000 0 0
WT1 0.05 0.12 0.18 152 -0.31 34 186
WRN 0.02 0.012 -10000 0 -10000 0 0
SP1 0.029 0.006 -10000 0 -10000 0 0
SP3 0.027 0.006 -10000 0 -10000 0 0
TERF2IP 0.022 0.011 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.053 0.081 -10000 0 -10000 0 0
Mad/Max 0.041 0.009 -10000 0 -10000 0 0
TERT 0.041 0.095 0.44 7 -10000 0 7
CCND1 0.047 0.11 0.58 7 -10000 0 7
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.027 0.015 -10000 0 -0.31 1 1
TERF2 0.02 0.011 -10000 0 -10000 0 0
PTGES3 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.003 -10000 0 -10000 0 0
Telomerase/911 0.037 0.042 0.23 1 -10000 0 1
CDKN1B 0.01 0.018 -10000 0 -10000 0 0
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.004 -10000 0 -10000 0 0
XRCC6 0.027 0.004 -10000 0 -10000 0 0
SAP30 0.027 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.033 0.015 -10000 0 -10000 0 0
UBE3A 0.027 0.005 -10000 0 -10000 0 0
JUN 0.025 0.031 0.17 1 -0.31 4 5
E6 0.001 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.004 -10000 0 -10000 0 0
FOS -0.025 0.12 0.17 4 -0.31 78 82
IFN-gamma/IRF1 0.053 0.037 0.27 4 -10000 0 4
PARP2 0.027 0.004 -10000 0 -10000 0 0
BLM 0.033 0.031 0.17 22 -10000 0 22
Telomerase 0.022 0.035 0.22 2 -0.25 1 3
IRF1 0.033 0.025 0.18 13 -10000 0 13
ESR1 0.016 0.06 0.17 1 -0.31 16 17
KU/TER 0.039 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.033 0.019 -10000 0 -0.22 1 1
ubiquitin-dependent protein catabolic process 0.026 0.033 -10000 0 -0.29 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.026 0.033 -10000 0 -0.29 1 1
HDAC1 0.027 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.011 -10000 0 -10000 0 0
ATM 0.016 0.023 -10000 0 -0.29 1 1
SMAD3 -0.014 0.009 -10000 0 -0.21 1 1
ABL1 0.026 0.006 -10000 0 -10000 0 0
MXD1 0.028 0.004 -10000 0 -10000 0 0
MRE11A 0.026 0.006 -10000 0 -10000 0 0
HUS1 0.024 0.008 -10000 0 -10000 0 0
RPS6KB1 0.026 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.054 0.087 0.4 2 -0.48 1 3
NR2F2 0.025 0.004 -10000 0 -10000 0 0
MAPK3 -0.004 0.013 -10000 0 -10000 0 0
MAPK1 -0.005 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.025 0.016 -10000 0 -0.31 1 1
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.016 0.023 -10000 0 -0.29 1 1
NBN 0.021 0.011 -10000 0 -10000 0 0
EGFR -0.001 0.09 -10000 0 -0.31 39 39
mol:Oestrogen 0.001 0 -10000 0 -10000 0 0
EGF/EGFR 0.014 0.092 0.14 34 -0.22 56 90
MYC 0.029 0.035 0.18 24 -10000 0 24
IL2 0.025 0.012 0.18 2 -10000 0 2
KU 0.039 0.008 -10000 0 -10000 0 0
RAD50 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
TGFB1 0.025 0.016 -10000 0 -0.31 1 1
TRF2/BLM 0.036 0.022 0.14 10 -10000 0 10
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.058 0.095 0.42 5 -10000 0 5
SP1/HDAC2 0.038 0.018 -10000 0 -10000 0 0
PINX1 0.02 0.012 -10000 0 -10000 0 0
Telomerase/EST1A 0.05 0.08 -10000 0 -10000 0 0
Smad3/Myc 0.025 0.028 0.13 24 -0.18 1 25
911 complex 0.047 0.02 -10000 0 -10000 0 0
IFNG 0.036 0.037 0.18 31 -10000 0 31
Telomerase/PinX1 0.038 0.076 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.028 0.057 0.28 4 -0.26 5 9
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.052 0.08 -10000 0 -10000 0 0
response to DNA damage stimulus 0.006 0.023 0.13 4 -0.1 11 15
MRN complex/TRF2/Rap1 0.051 0.037 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.018 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.053 0.081 -10000 0 -10000 0 0
E2F1 0.034 0.029 0.18 18 -10000 0 18
ZNFX1 0.026 0.006 -10000 0 -10000 0 0
PIF1 0.028 0.023 0.17 7 -0.31 1 8
NCL 0.027 0.003 -10000 0 -10000 0 0
DKC1 0.027 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.023 -10000 0 -0.18 9 9
SNTA1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.026 0.2 2 -0.18 8 10
MAPK12 -0.009 0.019 0.17 2 -0.15 4 6
CCND1 0.009 0.017 -10000 0 -10000 0 0
p38 gamma/SNTA1 0.014 0.033 0.19 11 -0.16 3 14
MAP2K3 0.026 0.005 -10000 0 -10000 0 0
PKN1 0.029 0.019 0.17 8 -10000 0 8
G2/M transition checkpoint -0.009 0.019 0.17 2 -0.15 4 6
MAP2K6 -0.004 0.018 0.23 1 -0.16 4 5
MAPT -0.003 0.049 0.21 6 -0.17 12 18
MAPK13 -0.015 0.027 -10000 0 -0.21 9 9
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.004 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.028 0.015 -10000 0 -0.17 5 5
PI3K Class IB/PDE3B 0.028 0.015 0.17 5 -10000 0 5
PDE3B 0.028 0.015 0.17 5 -10000 0 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.058 0.034 -10000 0 -0.16 6 6
HDAC3 0.026 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.013 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 0.038 0.014 -10000 0 -0.21 1 1
GATA1/HDAC5 0.036 0.015 -10000 0 -0.18 1 1
GATA2/HDAC5 0.034 0.015 0.14 1 -10000 0 1
HDAC5/BCL6/BCoR 0.048 0.019 -10000 0 -10000 0 0
HDAC9 0.008 0.084 0.17 13 -0.31 30 43
Glucocorticoid receptor/Hsp90/HDAC6 0.047 0.036 -10000 0 -0.18 10 10
HDAC4/ANKRA2 0.036 0.012 -10000 0 -10000 0 0
HDAC5/YWHAB 0.036 0.012 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.006 0.1 1 -10000 0 1
GATA2 0.025 0.01 0.17 1 -10000 0 1
HDAC4/RFXANK 0.041 0.014 0.14 7 -10000 0 7
BCOR 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.028 0.014 0.17 4 -10000 0 4
HDAC5 0.025 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.029 -10000 0 -0.21 6 6
Histones 0.015 0.055 0.21 1 -0.22 5 6
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
HDAC4 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.004 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.015 -10000 0 -10000 0 0
HDAC4/Ubc9 0.038 0.01 -10000 0 -10000 0 0
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.035 0.014 -10000 0 -10000 0 0
TUBA1B 0.027 0.003 -10000 0 -10000 0 0
HDAC6 0.027 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.039 0.017 0.14 7 -10000 0 7
CAMK4 0.006 0.078 0.17 1 -0.31 28 29
Tubulin/HDAC6 0.061 0.031 -10000 0 -10000 0 0
SUMO1 0.027 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.026 0.005 -10000 0 -10000 0 0
GATA1 0.025 0.017 0.17 1 -0.31 1 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NR3C1 0.019 0.05 -10000 0 -0.31 11 11
SUMO1/HDAC4 0.041 0.024 -10000 0 -10000 0 0
SRF 0.027 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.038 0.009 -10000 0 -10000 0 0
Tubulin 0.048 0.032 0.14 46 -10000 0 46
HDAC4/14-3-3 E 0.037 0.012 -10000 0 -10000 0 0
GNB1 0.027 0.004 -10000 0 -10000 0 0
RANGAP1 0.028 0.012 0.17 3 -10000 0 3
BCL6/BCoR 0.037 0.011 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.049 0.017 -10000 0 -10000 0 0
HDAC4/SRF 0.036 0.056 -10000 0 -0.18 28 28
HDAC4/ER alpha 0.031 0.046 -10000 0 -0.21 16 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.015 0.055 0.21 1 -0.21 5 6
cell motility 0.06 0.031 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.038 0.009 -10000 0 -10000 0 0
BCL6 0.025 0.007 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.039 0.008 -10000 0 -10000 0 0
ESR1 0.016 0.06 0.17 1 -0.31 16 17
HDAC6/HDAC11 0.039 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.027 -10000 0 -10000 0 0
NPC 0.016 0.004 -10000 0 -10000 0 0
MEF2C 0.024 0.024 0.17 2 -0.31 2 4
RAN 0.026 0.006 -10000 0 -10000 0 0
HDAC4/MEF2C 0.065 0.035 -10000 0 -0.15 2 2
GNG2 0.023 0.037 -10000 0 -0.31 6 6
NCOR2 0.026 0.006 -10000 0 -10000 0 0
TUBB2A 0.04 0.043 0.17 46 -10000 0 46
HDAC11 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
RANBP2 0.027 0.008 0.17 1 -10000 0 1
ANKRA2 0.025 0.008 -10000 0 -10000 0 0
RFXANK 0.029 0.018 0.17 7 -10000 0 7
nuclear import -0.028 0.013 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.021 0.034 -10000 0 -0.31 5 5
PLK4 0.027 0.013 0.17 3 -10000 0 3
regulation of centriole replication -0.013 0.021 -10000 0 -0.21 5 5
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.037 0.031 -10000 0 -10000 0 0
CLOCK 0.001 0.091 -10000 0 -0.31 40 40
TIMELESS/CRY2 0.028 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.032 0.019 0.14 1 -0.22 2 3
ATR 0.025 0.007 -10000 0 -10000 0 0
NR1D1 0.012 0.017 -10000 0 -10000 0 0
ARNTL 0.027 0.022 -10000 0 -0.31 2 2
TIMELESS 0.012 0.018 -10000 0 -10000 0 0
NPAS2 0.028 0.017 0.18 1 -0.31 1 2
CRY2 0.026 0.005 -10000 0 -10000 0 0
mol:CO -0.007 0.001 -10000 0 -10000 0 0
CHEK1 0.026 0.006 -10000 0 -10000 0 0
mol:HEME 0.007 0.001 -10000 0 -10000 0 0
PER1 0.019 0.043 -10000 0 -0.31 8 8
BMAL/CLOCK/NPAS2 0.04 0.068 -10000 0 -0.18 42 42
BMAL1/CLOCK -0.006 0.093 -10000 0 -0.48 1 1
S phase of mitotic cell cycle 0.037 0.031 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.037 0.032 -10000 0 -10000 0 0
mol:NADPH 0.007 0.001 -10000 0 -10000 0 0
PER1/TIMELESS 0.026 0.028 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.009 0.17 1 -10000 0 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.024 0.023 0.17 1 -0.31 2 3
positive regulation of NF-kappaB transcription factor activity 0.022 0.039 0.14 1 -0.21 10 11
MAP2K4 0.012 0.031 -10000 0 -0.22 3 3
IKBKB 0.021 0.011 -10000 0 -10000 0 0
TNFRSF10B 0.019 0.013 -10000 0 -10000 0 0
TNFRSF10A 0.017 0.028 -10000 0 -0.31 3 3
SMPD1 0.008 0.009 -10000 0 -0.13 1 1
IKBKG 0.027 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.012 0.048 -10000 0 -0.31 10 10
TRAIL/TRAILR2 0.026 0.024 0.14 1 -0.18 2 3
TRAIL/TRAILR3 0.016 0.053 0.14 2 -0.21 22 24
TRAIL/TRAILR1 0.024 0.03 0.14 1 -0.2 5 6
TRAIL/TRAILR4 0.022 0.039 0.14 1 -0.21 10 11
TRAIL/TRAILR1/DAP3/GTP 0.032 0.031 -10000 0 -0.16 4 4
IKK complex 0.002 0.057 -10000 0 -0.26 1 1
RIPK1 0.026 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.004 -10000 0 -10000 0 0
MAPK3 -0.011 0.022 0.26 2 -0.21 2 4
MAP3K1 0.015 0.024 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.012 0.048 -10000 0 -0.31 10 10
TRADD 0.024 0.009 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.017 0.028 -10000 0 -0.31 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.016 0.02 -10000 0 -0.18 3 3
CFLAR 0.027 0.003 -10000 0 -10000 0 0
MAPK1 -0.011 0.02 0.26 2 -0.21 1 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.047 0.044 -10000 0 -0.15 4 4
mol:ceramide 0.008 0.009 -10000 0 -0.12 1 1
FADD 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.007 0.037 -10000 0 -0.21 5 5
TRAF2 0.026 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.005 0.066 0.17 1 -0.31 20 21
CHUK 0.025 0.007 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.033 0.034 -10000 0 -0.17 5 5
DAP3 0.026 0.006 -10000 0 -10000 0 0
CASP10 0.005 0.053 0.17 33 -0.22 4 37
JNK cascade 0.022 0.039 0.14 1 -0.21 10 11
TRAIL (trimer) 0.024 0.023 0.17 1 -0.31 2 3
TNFRSF10C 0.005 0.066 0.17 1 -0.31 20 21
TRAIL/TRAILR1/DAP3/GTP/FADD 0.038 0.036 -10000 0 -0.15 4 4
TRAIL/TRAILR2/FADD 0.035 0.03 -10000 0 -0.15 2 2
cell death 0.008 0.009 -10000 0 -0.12 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.017 0.014 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.019 0.013 -10000 0 -10000 0 0
CASP8 0.015 0.012 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.049 0.041 -10000 0 -0.13 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD2 0.013 0.043 0.19 10 -0.2 2 12
SMAD3 0.02 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.033 0.038 -10000 0 -0.32 4 4
SMAD4/Ubc9/PIASy 0.047 0.02 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.053 0.042 0.28 1 -10000 0 1
PPM1A 0.027 0.004 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.022 0.036 0.18 6 -0.18 2 8
MAP3K1 0.023 0.017 -10000 0 -0.31 1 1
TRAP-1/SMAD4 0.022 0.058 -10000 0 -0.21 27 27
MAPK3 0.026 0.005 -10000 0 -10000 0 0
MAPK1 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.026 0.006 -10000 0 -10000 0 0
CTDSP1 0.027 0.003 -10000 0 -10000 0 0
CTDSP2 0.027 0.004 -10000 0 -10000 0 0
CTDSPL 0.026 0.005 -10000 0 -10000 0 0
KPNB1 0.026 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.008 0.076 -10000 0 -0.31 27 27
UBE2I 0.026 0.006 -10000 0 -10000 0 0
NUP153 0.026 0.016 -10000 0 -0.31 1 1
KPNA2 0.028 0.015 0.17 5 -10000 0 5
PIAS4 0.027 0.004 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.002 0.1 -10000 0 -0.39 8 8
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.027 0.004 -10000 0 -10000 0 0
STXBP4 0.026 0.016 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.01 0.1 -10000 0 -0.38 11 11
YWHAZ 0.021 0.011 -10000 0 -10000 0 0
CALM1 0.026 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.004 -10000 0 -10000 0 0
TBC1D4 -0.011 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
YWHAB 0.026 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.046 0.022 -10000 0 -0.18 1 1
YWHAG 0.025 0.008 -10000 0 -10000 0 0
ASIP 0.022 0.033 0.17 4 -0.31 4 8
PRKCI 0.025 0.01 0.17 1 -10000 0 1
AS160/CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
RHOQ 0.026 0.005 -10000 0 -10000 0 0
GYS1 0.008 0.018 0.24 3 -10000 0 3
PRKCZ 0.027 0.004 -10000 0 -10000 0 0
TRIP10 0.027 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.035 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.008 0.053 -10000 0 -0.23 7 7
VAMP2 0.024 0.009 -10000 0 -10000 0 0
SLC2A4 -0.013 0.11 -10000 0 -0.43 11 11
STX4 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.017 0.006 -10000 0 -10000 0 0
SFN -0.006 0.1 -10000 0 -0.31 49 49
LNPEP 0.006 0.076 -10000 0 -0.31 27 27
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.046 0.071 -10000 0 -0.22 21 21
Ran/GTP/Exportin 1/HDAC1 -0.013 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.072 0.22 1 -0.22 24 25
SUMO1 0.027 0.003 -10000 0 -10000 0 0
ZFPM1 0.022 0.011 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.006 0.1 1 -10000 0 1
FKBP3 0.027 0.003 -10000 0 -10000 0 0
Histones 0.043 0.051 -10000 0 -10000 0 0
YY1/LSF 0.029 0.033 -10000 0 -0.18 4 4
SMG5 0.026 0.005 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.013 0.043 0.16 1 -0.18 23 24
I kappa B alpha/HDAC1 0.024 0.041 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
RELA 0.008 0.044 -10000 0 -0.16 24 24
HDAC1/Smad7 0.044 0.022 -10000 0 -10000 0 0
RANGAP1 0.028 0.012 0.17 3 -10000 0 3
HDAC3/TR2 0.023 0.042 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.004 0.05 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.063 0.22 10 -0.2 3 13
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.025 0.01 0.17 1 -10000 0 1
GATA1 0.025 0.017 0.17 1 -0.31 1 2
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.004 0.068 -10000 0 -0.24 9 9
RBBP7 0.026 0.004 -10000 0 -10000 0 0
NPC 0.016 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.015 -10000 0 -0.31 1 1
MAX 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
NFKBIA 0.012 0.033 0.14 1 -10000 0 1
KAT2B 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.021 -10000 0 -10000 0 0
SIN3 complex 0.064 0.02 -10000 0 -10000 0 0
SMURF1 0.024 0.008 -10000 0 -10000 0 0
CHD3 0.023 0.01 -10000 0 -10000 0 0
SAP30 0.026 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.025 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.018 0.038 -10000 0 -10000 0 0
YY1/HDAC2 0.026 0.033 -10000 0 -0.18 4 4
YY1/HDAC1 0.03 0.034 -10000 0 -0.18 4 4
NuRD/MBD2 Complex (MeCP1) 0.005 0.049 -10000 0 -10000 0 0
PPARG -0.006 0.084 0.18 2 -0.26 42 44
HDAC8/hEST1B 0.052 0.013 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.024 0.041 -10000 0 -10000 0 0
MBD3L2 0.018 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.022 -10000 0 -10000 0 0
CREBBP 0.026 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.008 0.053 -10000 0 -0.21 6 6
HDAC1 0.027 0.003 -10000 0 -10000 0 0
HDAC3 0.012 0.033 0.14 1 -10000 0 1
HDAC2 0.023 0.01 -10000 0 -10000 0 0
YY1 0.014 0.018 -10000 0 -0.21 3 3
HDAC8 0.027 0.002 -10000 0 -10000 0 0
SMAD7 0.025 0.008 -10000 0 -10000 0 0
NCOR2 0.026 0.006 -10000 0 -10000 0 0
MXD1 0.027 0.003 -10000 0 -10000 0 0
STAT3 0.016 0.021 -10000 0 -0.24 3 3
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.008 0.17 1 -10000 0 1
YY1/LSF/HDAC1 0.044 0.036 -10000 0 -0.17 4 4
YY1/SAP30/HDAC1 0.044 0.036 -10000 0 -0.17 4 4
EP300 0.025 0.026 -10000 0 -0.31 3 3
STAT3 (dimer non-phopshorylated) 0.016 0.021 -10000 0 -0.24 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.033 0.14 1 -10000 0 1
histone deacetylation 0.001 0.057 -10000 0 -0.24 8 8
STAT3 (dimer non-phopshorylated)/HDAC3 0.015 0.039 -10000 0 -0.17 4 4
nuclear export -0.052 0.012 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GATAD2B 0.026 0.006 -10000 0 -10000 0 0
GATAD2A 0.027 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.022 0.042 -10000 0 -10000 0 0
GATA1/HDAC1 0.038 0.014 -10000 0 -0.21 1 1
GATA1/HDAC3 0.023 0.044 -10000 0 -10000 0 0
CHD4 0.025 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.027 0.058 -10000 0 -0.21 24 24
SIN3/HDAC complex/Mad/Max 0.015 0.04 -10000 0 -0.33 1 1
NuRD Complex 0.003 0.064 -10000 0 -0.22 12 12
positive regulation of chromatin silencing 0.041 0.05 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
MTA2 0.026 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.003 -10000 0 -10000 0 0
XPO1 0.027 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.041 0.024 -10000 0 -10000 0 0
HDAC complex 0.058 0.028 -10000 0 -0.17 1 1
GATA1/Fog1 0.031 0.018 -10000 0 -0.18 1 1
FKBP25/HDAC1/HDAC2 0.046 0.02 -10000 0 -10000 0 0
TNF 0.014 0.076 0.17 12 -0.31 24 36
negative regulation of cell growth 0.014 0.043 -10000 0 -0.27 3 3
NuRD/MBD2/PRMT5 Complex 0.005 0.049 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.027 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.006 0.066 0.22 1 -0.23 23 24
SIN3/HDAC complex/NCoR1 0.015 0.038 -10000 0 -0.24 1 1
TFCP2 0.026 0.005 -10000 0 -10000 0 0
NR2C1 0.026 0.006 -10000 0 -10000 0 0
MBD3 0.027 0.01 0.17 2 -10000 0 2
MBD2 0.025 0.01 0.17 1 -10000 0 1
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.023 0.12 0.17 1 -0.31 68 69
CLTC 0.022 0.029 0.28 1 -10000 0 1
calcium ion-dependent exocytosis 0.012 0.034 0.2 2 -0.15 3 5
Dynamin 2/GTP 0.023 0.012 -10000 0 -10000 0 0
EXOC4 0.024 0.008 -10000 0 -10000 0 0
CD59 0.013 0.017 -10000 0 -10000 0 0
CPE 0.01 0.017 -10000 0 -0.18 4 4
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
membrane fusion 0.011 0.03 -10000 0 -10000 0 0
CTNND1 -0.01 0.036 0.19 14 -10000 0 14
DNM2 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.035 0.22 6 -10000 0 6
TSHR 0.006 0.032 -10000 0 -0.18 13 13
INS 0.013 0.046 -10000 0 -0.44 4 4
BIN1 0.026 0.011 0.17 2 -10000 0 2
mol:Choline 0.011 0.03 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.009 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.012 -10000 0 -10000 0 0
JUP 0.013 0.017 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.048 0.016 -10000 0 -10000 0 0
ARF6/GTP 0.02 0.003 -10000 0 -10000 0 0
CDH1 0.012 0.017 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.011 0.17 2 -10000 0 2
positive regulation of endocytosis 0.02 0.003 -10000 0 -10000 0 0
EXOC2 0.026 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.013 0.041 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.04 0.029 -10000 0 -0.25 1 1
positive regulation of phagocytosis 0.012 0.002 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.011 0.13 2 -10000 0 2
ACAP1 0.018 0.034 0.17 8 -0.14 1 9
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.014 0.058 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.02 0.037 0.26 3 -10000 0 3
JIP4/KLC1 0.05 0.012 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.017 0.027 -10000 0 -10000 0 0
RALA/GTP 0.018 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.007 -10000 0 -10000 0 0
receptor recycling 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 -0.01 0.033 0.18 14 -10000 0 14
NME1 0.013 0.009 -10000 0 -10000 0 0
clathrin coat assembly 0.023 0.032 0.28 1 -10000 0 1
IL2RA 0.013 0.024 -10000 0 -10000 0 0
VAMP3 0.012 0.002 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.011 0.055 -10000 0 -10000 0 0
EXOC6 0.025 0.008 -10000 0 -10000 0 0
PLD1 0.003 0.041 -10000 0 -0.22 16 16
PLD2 0.011 0.005 -10000 0 -10000 0 0
EXOC5 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.023 0.19 2 -10000 0 2
SDC1 0.008 0.035 -10000 0 -10000 0 0
ARF6/GDP 0.024 0.006 -10000 0 -10000 0 0
EXOC7 0.026 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.043 0.03 0.26 1 -10000 0 1
mol:Phosphatidic acid 0.011 0.03 -10000 0 -10000 0 0
endocytosis -0.046 0.016 -10000 0 -10000 0 0
SCAMP2 0.027 0.003 -10000 0 -10000 0 0
ADRB2 0.023 0.047 0.32 6 -10000 0 6
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ASAP2 0.027 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.029 0.01 -10000 0 -10000 0 0
KLC1 0.026 0.005 -10000 0 -10000 0 0
AVPR2 0.018 0.038 0.24 2 -0.26 1 3
RALA 0.024 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.036 0.24 1 -10000 0 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0.029 0.15 16 -0.17 1 17
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.004 0.042 0.15 5 -0.16 15 20
AP2 0.037 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.033 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.008 0.17 1 -10000 0 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.016 0.007 -10000 0 -10000 0 0
CD4 0.025 0.027 0.17 5 -0.31 2 7
CLTA 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.006 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.032 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.005 0.016 -10000 0 -10000 0 0
mol:Choline 0.003 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.027 0.009 -10000 0 -10000 0 0
DDEF1 0.002 0.006 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.015 -10000 0 -0.11 5 5
AP2M1 0.025 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.018 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.035 0.014 -10000 0 -10000 0 0
ARFIP2 0.021 0.017 -10000 0 -10000 0 0
COPA 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.026 0.13 4 -10000 0 4
ARF1/GTP/ARHGAP10 0.017 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.046 -10000 0 -0.23 16 16
AP2A1 0.027 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.013 0.006 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.013 0.052 -10000 0 -0.26 16 16
Arfaptin 2/Rac/GDP 0.032 0.013 -10000 0 -10000 0 0
CYTH2 0.027 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.034 0.012 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.013 0.027 -10000 0 -0.16 4 4
PLD2 0.003 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.006 0.003 -10000 0 -10000 0 0
PIP5K1A 0.004 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.024 -10000 0 -0.095 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.003 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.006 0.003 -10000 0 -10000 0 0
GOSR2 0.001 0.054 -10000 0 -0.31 14 14
USO1 0.01 0.016 -10000 0 -0.33 1 1
GBF1 -0.002 0.063 -10000 0 -0.32 19 19
ARF1/GTP/Arfaptin 2 0.035 0.013 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.048 0.026 -10000 0 -0.18 2 2
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.021 0.012 -10000 0 -10000 0 0
regulation of axonogenesis -0.006 0.019 -10000 0 -10000 0 0
myoblast fusion -0.026 0.024 -10000 0 -10000 0 0
mol:GTP 0.024 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.053 0.029 0.16 3 -10000 0 3
ARF1/GTP 0.037 0.012 -10000 0 -10000 0 0
mol:GM1 0.011 0.006 -10000 0 -10000 0 0
mol:Choline 0.002 0.029 -10000 0 -0.16 14 14
lamellipodium assembly 0.016 0.017 -10000 0 -10000 0 0
MAPK3 0.023 0.009 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.054 0.029 -10000 0 -0.16 3 3
ARF1 0.026 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.024 -10000 0 -10000 0 0
ARF1/GDP 0.032 0.022 -10000 0 -10000 0 0
ARF6 0.035 0.008 -10000 0 -10000 0 0
RAB11A 0.027 0.003 -10000 0 -10000 0 0
TIAM1 0.024 0.03 -10000 0 -0.3 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.009 -10000 0 -10000 0 0
actin filament bundle formation -0.035 0.018 -10000 0 -10000 0 0
KALRN 0.013 0.013 0.19 1 -10000 0 1
RAB11FIP3/RAB11A 0.038 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.036 0.018 -10000 0 -10000 0 0
NME1 0.03 0.022 0.17 11 -10000 0 11
Rac1/GDP 0.034 0.019 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.024 0.008 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.016 0.017 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
liver development 0.024 0.008 -10000 0 -10000 0 0
ARF6/GTP 0.024 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.038 0.011 -10000 0 -10000 0 0
mol:GDP 0.014 0.008 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.052 0.015 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
PLD1 0.011 0.038 -10000 0 -0.19 17 17
RAB11FIP3 0.026 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.016 0.017 -10000 0 -10000 0 0
ruffle organization 0.006 0.019 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.024 0.008 -10000 0 -10000 0 0
PLD2 0.019 0.008 -10000 0 -10000 0 0
PIP5K1A 0.006 0.019 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.002 0.029 -10000 0 -0.16 14 14
Rac1/GTP 0.016 0.018 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.027 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.011 0.006 -10000 0 -10000 0 0
MDM2/SUMO1 0.04 0.024 -10000 0 -10000 0 0
HDAC4 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.011 0.006 -10000 0 -10000 0 0
SUMO1 0.027 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.013 0.099 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.007 0.004 0.091 1 -10000 0 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.008 0.17 1 -10000 0 1
SUMO1/HDAC4 0.041 0.024 -10000 0 -10000 0 0
SUMO1/HDAC1 0.041 0.024 -10000 0 -10000 0 0
RANGAP1 0.028 0.012 0.17 3 -10000 0 3
MDM2/SUMO1/SUMO1 0.059 0.027 -10000 0 -0.17 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.012 0.006 0.1 1 -10000 0 1
Ran/GTP 0.027 0.024 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.006 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.025 0.25 1 -10000 0 1
NPC 0.016 0.004 0.098 1 -10000 0 1
PIAS2 0.025 0.008 -10000 0 -10000 0 0
PIAS1 0.026 0.015 -10000 0 -0.31 1 1
EntrezGene:9972 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.046 0.02 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.034 0.015 -9999 0 -9999 0 0
CTNNB1 0.026 0.005 -9999 0 -9999 0 0
JUP 0.027 0.004 -9999 0 -9999 0 0
CDH1 0.024 0.009 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.036 0.013 -10000 0 -9999 0 0
FBXW11 0.026 0.005 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.005 -10000 0 -9999 0 0
CHUK 0.025 0.007 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.07 0.029 -10000 0 -9999 0 0
NFKB1 0.027 0.004 -10000 0 -9999 0 0
MAP3K14 0.026 0.006 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.039 0.008 -10000 0 -9999 0 0
RELB 0.027 0.004 -10000 0 -9999 0 0
NFKB2 0.026 0.013 0.17 3 -9999 0 3
NF kappa B2 p52/RelB 0.035 0.012 0.13 3 -9999 0 3
regulation of B cell activation 0.034 0.012 0.13 3 -9999 0 3
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 491 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZG.A9NI TCGA.ZG.A9ND TCGA.ZG.A9N3 TCGA.ZG.A9MC
109_MAP3K5 0.2 -0.21 -0.053 0.12
47_PPARGC1A 0.027 0 0.027 0.027
105_BMP4 0.027 0.027 -0.31 0.027
105_BMP6 0 0.027 0 0.027
105_BMP7 0.027 -0.31 0 0.027
105_BMP2 0.027 0.027 0 0.027
131_RELN/VLDLR 0 0.16 0 0.07
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.026 0.027
84_STAT5B -0.034 -0.015 0.099 0.044
84_STAT5A -0.034 -0.015 0.099 0.044
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/PRAD-TP/14527481/PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/PRAD-TP/15087323/GDAC_Gistic2Report_15093611/all_data_by_genes.txt

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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