PARADIGM pathway analysis of mRNASeq expression data
Colorectal Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1154FWN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1154FWN
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 48 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 99
IL23-mediated signaling events 98
Signaling mediated by p38-alpha and p38-beta 95
IL4-mediated signaling events 93
Wnt signaling 89
amb2 Integrin signaling 70
Syndecan-4-mediated signaling events 68
Noncanonical Wnt signaling pathway 65
Glypican 1 network 64
EGFR-dependent Endothelin signaling events 60
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 606 . 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 ( 606 ).

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 0.1634 99 694 7 -0.1 0 1000 -1000 -0.016 -1000
IL23-mediated signaling events 0.1617 98 5927 60 -0.54 0.011 1000 -1000 -0.17 -1000
Signaling mediated by p38-alpha and p38-beta 0.1568 95 4212 44 -0.19 0.011 1000 -1000 -0.04 -1000
IL4-mediated signaling events 0.1535 93 8509 91 -0.68 0.61 1000 -1000 -0.17 -1000
Wnt signaling 0.1469 89 625 7 -0.14 0.005 1000 -1000 -0.026 -1000
amb2 Integrin signaling 0.1155 70 5781 82 -0.17 0.015 1000 -1000 -0.065 -1000
Syndecan-4-mediated signaling events 0.1122 68 4611 67 -0.18 0.038 1000 -1000 -0.074 -1000
Noncanonical Wnt signaling pathway 0.1073 65 1697 26 -0.14 0.011 1000 -1000 -0.05 -1000
Glypican 1 network 0.1056 64 3077 48 -0.21 0.015 1000 -1000 -0.039 -1000
EGFR-dependent Endothelin signaling events 0.0990 60 1263 21 -0.18 0.016 1000 -1000 -0.06 -1000
TCR signaling in naïve CD8+ T cells 0.0974 59 5506 93 -0.12 0.055 1000 -1000 -0.076 -1000
BCR signaling pathway 0.0974 59 5902 99 -0.17 0.014 1000 -1000 -0.078 -1000
Syndecan-1-mediated signaling events 0.0957 58 1972 34 -0.14 0.011 1000 -1000 -0.048 -1000
IL12-mediated signaling events 0.0941 57 5030 87 -0.3 0.067 1000 -1000 -0.14 -1000
FOXA2 and FOXA3 transcription factor networks 0.0941 57 2623 46 -0.43 0.016 1000 -1000 -0.12 -1000
Ephrin B reverse signaling 0.0875 53 2550 48 -0.14 0.044 1000 -1000 -0.063 -1000
Signaling events mediated by the Hedgehog family 0.0858 52 2742 52 -0.13 0.081 1000 -1000 -0.055 -1000
TCGA08_retinoblastoma 0.0858 52 418 8 -0.07 0.027 1000 -1000 -0.012 -1000
HIF-1-alpha transcription factor network 0.0842 51 3887 76 -0.31 0.016 1000 -1000 -0.18 -1000
Endothelins 0.0842 51 4970 96 -0.16 0.011 1000 -1000 -0.076 -1000
BMP receptor signaling 0.0809 49 4029 81 -0.17 0.027 1000 -1000 -0.084 -1000
Fc-epsilon receptor I signaling in mast cells 0.0809 49 4794 97 -0.15 0.03 1000 -1000 -0.074 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0809 49 3357 68 -0.31 0.12 1000 -1000 -0.12 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0792 48 1663 34 -0.06 0.011 1000 -1000 -0.039 -1000
Reelin signaling pathway 0.0792 48 2721 56 -0.12 0.021 1000 -1000 -0.069 -1000
Calcium signaling in the CD4+ TCR pathway 0.0776 47 1470 31 -0.21 0.011 1000 -1000 -0.062 -1000
p75(NTR)-mediated signaling 0.0759 46 5778 125 -0.18 0.03 1000 -1000 -0.086 -1000
TCGA08_p53 0.0726 44 314 7 -0.051 0.031 1000 -1000 -0.009 -1000
Thromboxane A2 receptor signaling 0.0677 41 4395 105 -0.18 0.046 1000 -1000 -0.055 -1000
Osteopontin-mediated events 0.0660 40 1533 38 -0.16 0.011 1000 -1000 -0.094 -1000
Syndecan-2-mediated signaling events 0.0660 40 2822 69 -0.11 0.022 1000 -1000 -0.032 -1000
Glucocorticoid receptor regulatory network 0.0660 40 4589 114 -0.34 0.21 1000 -1000 -0.068 -1000
Signaling events regulated by Ret tyrosine kinase 0.0627 38 3191 82 -0.11 0.011 1000 -1000 -0.073 -1000
Visual signal transduction: Cones 0.0594 36 1399 38 -0.054 0.007 1000 -1000 -0.049 -1000
LPA receptor mediated events 0.0594 36 3709 102 -0.11 0.012 1000 -1000 -0.079 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0578 35 4212 120 -0.18 0.14 1000 -1000 -0.068 -1000
Caspase cascade in apoptosis 0.0561 34 2519 74 -0.084 0.044 1000 -1000 -0.04 -1000
JNK signaling in the CD4+ TCR pathway 0.0561 34 592 17 -0.047 0.011 1000 -1000 -0.038 -1000
Canonical Wnt signaling pathway 0.0561 34 1753 51 -0.18 0.089 1000 -1000 -0.058 -1000
Presenilin action in Notch and Wnt signaling 0.0528 32 1970 61 -0.18 0.061 1000 -1000 -0.059 -1000
Glypican 2 network 0.0528 32 130 4 -0.012 -0.007 1000 -1000 -0.016 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0528 32 2888 88 -0.12 0.044 1000 -1000 -0.091 -1000
Visual signal transduction: Rods 0.0528 32 1708 52 -0.12 0.011 1000 -1000 -0.067 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0528 32 2551 78 -0.084 0.057 1000 -1000 -0.087 -1000
Cellular roles of Anthrax toxin 0.0512 31 1214 39 -0.045 0.011 1000 -1000 -0.018 -1000
Arf6 signaling events 0.0512 31 1948 62 -0.18 0.024 1000 -1000 -0.045 -1000
IL1-mediated signaling events 0.0512 31 1973 62 -0.1 0.021 1000 -1000 -0.086 -1000
Effects of Botulinum toxin 0.0512 31 806 26 -0.12 0.01 1000 -1000 -0.059 -1000
Integrins in angiogenesis 0.0495 30 2592 84 -0.16 0.019 1000 -1000 -0.081 -1000
a4b1 and a4b7 Integrin signaling 0.0479 29 149 5 -0.024 -0.006 1000 -1000 -0.022 -1000
Retinoic acid receptors-mediated signaling 0.0479 29 1710 58 -0.15 0.019 1000 -1000 -0.065 -1000
Signaling events mediated by PTP1B 0.0462 28 2194 76 -0.18 0.029 1000 -1000 -0.073 -1000
FAS signaling pathway (CD95) 0.0462 28 1327 47 -0.17 0.014 1000 -1000 -0.041 -1000
IL27-mediated signaling events 0.0462 28 1442 51 -0.2 0.024 1000 -1000 -0.073 -1000
Ras signaling in the CD4+ TCR pathway 0.0446 27 468 17 -0.048 0.011 1000 -1000 -0.044 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0429 26 1455 54 -0.13 0.022 1000 -1000 -0.085 -1000
Plasma membrane estrogen receptor signaling 0.0413 25 2163 86 -0.075 0.019 1000 -1000 -0.074 -1000
LPA4-mediated signaling events 0.0396 24 293 12 -0.058 0.016 1000 -1000 -0.027 -1000
ErbB4 signaling events 0.0380 23 1625 69 -0.17 0.036 1000 -1000 -0.066 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0380 23 880 37 -0.13 0.026 1000 -1000 -0.045 -1000
S1P1 pathway 0.0380 23 847 36 -0.1 0.011 1000 -1000 -0.053 -1000
Nongenotropic Androgen signaling 0.0380 23 1247 52 -0.05 0.012 1000 -1000 -0.047 -1000
IL6-mediated signaling events 0.0380 23 1798 75 -0.11 0.043 1000 -1000 -0.068 -1000
Coregulation of Androgen receptor activity 0.0363 22 1732 76 -0.17 0.041 1000 -1000 -0.026 -1000
IGF1 pathway 0.0363 22 1307 57 -0.076 0.023 1000 -1000 -0.08 -1000
EPHB forward signaling 0.0347 21 1847 85 -0.1 0.06 1000 -1000 -0.084 -1000
Class I PI3K signaling events 0.0347 21 1539 73 -0.11 0.024 1000 -1000 -0.056 -1000
PDGFR-alpha signaling pathway 0.0330 20 915 44 -0.062 0.017 1000 -1000 -0.059 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0314 19 1007 52 -0.12 0.034 1000 -1000 -0.044 -1000
IL2 signaling events mediated by STAT5 0.0314 19 419 22 -0.052 0.015 1000 -1000 -0.055 -1000
Nectin adhesion pathway 0.0281 17 1072 63 -0.033 0.02 1000 -1000 -0.064 -1000
Regulation of Telomerase 0.0281 17 1750 102 -0.18 0.036 1000 -1000 -0.1 -1000
FOXM1 transcription factor network 0.0281 17 906 51 -0.12 0.076 1000 -1000 -0.2 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0264 16 461 28 -0.045 0.018 1000 -1000 -0.031 -1000
IFN-gamma pathway 0.0264 16 1118 68 -0.067 0.02 1000 -1000 -0.09 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0264 16 551 33 -0.08 0.029 1000 -1000 -0.046 -1000
ErbB2/ErbB3 signaling events 0.0248 15 1033 65 -0.07 0.016 1000 -1000 -0.06 -1000
Signaling events mediated by PRL 0.0248 15 536 34 -0.024 0.028 1000 -1000 -0.034 -1000
S1P4 pathway 0.0248 15 396 25 -0.045 0.016 1000 -1000 -0.033 -1000
Regulation of nuclear SMAD2/3 signaling 0.0231 14 1953 136 -0.078 0.04 1000 -1000 -0.065 -1000
Ceramide signaling pathway 0.0231 14 1100 76 -0.18 0.059 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class III 0.0231 14 598 40 -0.047 0.018 1000 -1000 -0.024 -1000
Syndecan-3-mediated signaling events 0.0231 14 500 35 -0.11 0.03 1000 -1000 -0.039 -1000
PDGFR-beta signaling pathway 0.0231 14 1419 97 -0.096 0.031 1000 -1000 -0.074 -1000
PLK2 and PLK4 events 0.0215 13 39 3 -0.003 0.009 1000 -1000 -0.015 -1000
Regulation of p38-alpha and p38-beta 0.0215 13 709 54 -0.11 0.027 1000 -1000 -0.059 -1000
S1P3 pathway 0.0215 13 574 42 -0.045 0.018 1000 -1000 -0.035 -1000
Regulation of Androgen receptor activity 0.0215 13 959 70 -0.2 0.028 1000 -1000 -0.057 -1000
S1P5 pathway 0.0198 12 207 17 -0.045 0.011 1000 -1000 -0.025 -1000
Class IB PI3K non-lipid kinase events 0.0198 12 36 3 0 -1000 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0182 11 747 65 -0.045 0.035 1000 -1000 -0.053 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0182 11 948 83 -0.16 0.052 1000 -1000 -0.064 -1000
Signaling mediated by p38-gamma and p38-delta 0.0182 11 179 15 -0.024 0.017 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 0.0182 11 658 58 -0.047 0.027 1000 -1000 -0.079 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0182 11 495 45 -0.06 0.039 1000 -1000 -0.085 -1000
Signaling events mediated by HDAC Class II 0.0165 10 777 75 -0.038 0.025 1000 -1000 -0.044 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0165 10 893 85 -0.039 0.028 1000 -1000 -0.065 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0165 10 282 27 -0.017 0.016 1000 -1000 -0.051 -1000
Insulin Pathway 0.0165 10 743 74 -0.12 0.027 1000 -1000 -0.081 -1000
Aurora B signaling 0.0165 10 716 67 -0.12 0.029 1000 -1000 -0.06 -1000
BARD1 signaling events 0.0149 9 561 57 -0.045 0.049 1000 -1000 -0.054 -1000
Paxillin-dependent events mediated by a4b1 0.0149 9 326 36 -0.024 0.02 1000 -1000 -0.062 -1000
TCGA08_rtk_signaling 0.0149 9 245 26 -0.044 0.036 1000 -1000 -0.018 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0149 9 730 74 -0.18 0.052 1000 -1000 -0.078 -1000
p38 MAPK signaling pathway 0.0149 9 410 44 -0.056 0.02 1000 -1000 -0.064 -1000
VEGFR1 specific signals 0.0132 8 484 56 -0.016 0.031 1000 -1000 -0.049 -1000
Rapid glucocorticoid signaling 0.0132 8 160 20 -0.018 0.011 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0116 7 905 125 -0.041 0.056 1000 -1000 -0.082 -1000
Canonical NF-kappaB pathway 0.0099 6 235 39 -0.017 0.055 1000 -1000 -0.075 -1000
Aurora A signaling 0.0099 6 400 60 -0.054 0.029 1000 -1000 -0.03 -1000
Arf6 downstream pathway 0.0099 6 292 43 -0.042 0.025 1000 -1000 -0.03 -1000
Aurora C signaling 0.0099 6 46 7 -0.01 0.011 1000 -1000 -0.02 -1000
EPO signaling pathway 0.0099 6 377 55 -0.026 0.041 1000 -1000 -0.088 -1000
Signaling events mediated by HDAC Class I 0.0099 6 710 104 -0.022 0.041 1000 -1000 -0.058 -1000
TRAIL signaling pathway 0.0083 5 269 48 -0.014 0.037 1000 -1000 -0.061 -1000
ceramide signaling pathway 0.0083 5 269 49 -0.017 0.029 1000 -1000 -0.043 -1000
HIF-2-alpha transcription factor network 0.0083 5 243 43 -0.083 0.085 1000 -1000 -0.085 -1000
Atypical NF-kappaB pathway 0.0083 5 159 31 -0.031 0.029 1000 -1000 -0.039 -1000
E-cadherin signaling in the nascent adherens junction 0.0083 5 400 76 -0.044 0.044 1000 -1000 -0.074 -1000
mTOR signaling pathway 0.0066 4 244 53 -0.006 0.025 1000 -1000 -0.058 -1000
Class I PI3K signaling events mediated by Akt 0.0066 4 302 68 -0.032 0.042 1000 -1000 -0.046 -1000
FoxO family signaling 0.0066 4 283 64 -0.081 0.1 1000 -1000 -0.069 -1000
Arf6 trafficking events 0.0066 4 343 71 -0.037 0.027 1000 -1000 -0.065 -1000
PLK1 signaling events 0.0050 3 283 85 -0.007 0.029 1000 -1000 -0.038 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0033 2 50 23 0.004 0.034 1000 -1000 -0.055 -1000
Circadian rhythm pathway 0.0033 2 59 22 -0.011 0.037 1000 -1000 -0.044 -1000
Insulin-mediated glucose transport 0.0033 2 91 32 0 0.033 1000 -1000 -0.053 -1000
E-cadherin signaling in keratinocytes 0.0033 2 116 43 -0.033 0.038 1000 -1000 -0.057 -1000
Arf1 pathway 0.0033 2 118 54 -0.013 0.021 1000 -1000 -0.032 -1000
Alternative NF-kappaB pathway 0.0033 2 32 13 0 0.029 1000 -1000 -0.033 -1000
E-cadherin signaling events 0.0017 1 5 5 0.01 0.022 1000 -1000 -0.025 -1000
Total NA 3511 202482 7203 -14 -1000 131000 -131000 -7.9 -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 -0.063 0.14 -9999 0 -0.32 138 138
EFNA5 -0.1 0.22 -9999 0 -0.52 127 127
FYN -0.054 0.14 -9999 0 -0.29 140 140
neuron projection morphogenesis -0.063 0.14 -9999 0 -0.32 138 138
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.063 0.14 -9999 0 -0.32 138 138
EPHA5 -0.004 0.067 -9999 0 -0.46 13 13
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.43 0.54 -10000 0 -1.2 159 159
IL23A -0.44 0.55 -10000 0 -1.3 140 140
NF kappa B1 p50/RelA/I kappa B alpha -0.47 0.51 -10000 0 -1.2 167 167
positive regulation of T cell mediated cytotoxicity -0.48 0.63 -10000 0 -1.4 161 161
ITGA3 -0.41 0.52 -10000 0 -1.2 143 143
IL17F -0.29 0.34 -10000 0 -0.74 145 145
IL12B -0.017 0.078 -10000 0 -0.48 14 14
STAT1 (dimer) -0.46 0.59 -10000 0 -1.3 162 162
CD4 -0.42 0.52 -10000 0 -1.2 151 151
IL23 -0.42 0.52 -10000 0 -1.2 139 139
IL23R -0.1 0.3 -10000 0 -1.4 27 27
IL1B -0.46 0.58 -10000 0 -1.3 155 155
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.53 0.61 -10000 0 -1.3 205 205
TYK2 -0.002 0.033 -10000 0 -0.62 1 1
STAT4 -0.029 0.15 -10000 0 -0.56 43 43
STAT3 0.011 0.002 -10000 0 -10000 0 0
IL18RAP -0.034 0.15 -10000 0 -0.55 48 48
IL12RB1 -0.047 0.16 -10000 0 -0.57 50 50
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
IL12Rbeta1/TYK2 -0.036 0.12 -10000 0 -0.43 51 51
IL23R/JAK2 -0.12 0.3 -10000 0 -1.3 29 29
positive regulation of chronic inflammatory response -0.48 0.63 -10000 0 -1.4 161 161
natural killer cell activation 0.007 0.017 0.069 32 -10000 0 32
JAK2 -0.02 0.11 -10000 0 -0.57 21 21
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
NFKB1 0.008 0.025 -10000 0 -0.59 1 1
RELA 0.009 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.4 0.49 -10000 0 -1.1 141 141
ALOX12B -0.46 0.56 -10000 0 -1.2 168 168
CXCL1 -0.42 0.54 -10000 0 -1.2 159 159
T cell proliferation -0.48 0.63 -10000 0 -1.4 161 161
NFKBIA 0.009 0.004 -10000 0 -10000 0 0
IL17A -0.25 0.3 -10000 0 -0.61 156 156
PI3K -0.48 0.52 -10000 0 -1.2 167 167
IFNG -0.019 0.051 0.13 20 -0.12 55 75
STAT3 (dimer) -0.47 0.48 -10000 0 -1.1 177 177
IL18R1 -0.013 0.11 -10000 0 -0.56 25 25
IL23/IL23R/JAK2/TYK2/SOCS3 -0.24 0.32 -10000 0 -0.73 109 109
IL18/IL18R -0.025 0.14 -10000 0 -0.37 69 69
macrophage activation -0.022 0.018 -10000 0 -0.045 134 134
TNF -0.44 0.56 -10000 0 -1.3 150 150
STAT3/STAT4 -0.49 0.52 -10000 0 -1.2 166 166
STAT4 (dimer) -0.47 0.6 -10000 0 -1.3 164 164
IL18 0.002 0.067 -10000 0 -0.54 9 9
IL19 -0.41 0.51 -10000 0 -1.1 147 147
STAT5A (dimer) -0.46 0.59 -10000 0 -1.3 161 161
STAT1 0.006 0.054 -10000 0 -0.49 7 7
SOCS3 -0.002 0.082 -10000 0 -0.5 16 16
CXCL9 -0.47 0.58 -10000 0 -1.3 173 173
MPO -0.44 0.54 -10000 0 -1.2 168 168
positive regulation of humoral immune response -0.48 0.63 -10000 0 -1.4 161 161
IL23/IL23R/JAK2/TYK2 -0.54 0.75 -10000 0 -1.5 161 161
IL6 -0.48 0.58 -10000 0 -1.3 169 169
STAT5A 0.011 0 -10000 0 -10000 0 0
IL2 0.004 0.029 -10000 0 -0.46 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.017 0.069 32 -10000 0 32
CD3E -0.42 0.53 -10000 0 -1.2 143 143
keratinocyte proliferation -0.48 0.63 -10000 0 -1.4 161 161
NOS2 -0.48 0.58 -10000 0 -1.2 186 186
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 -0.16 0.36 -9999 0 -0.96 81 81
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.063 0.14 -9999 0 -0.31 117 117
ATF2/c-Jun -0.045 0.15 -9999 0 -0.5 26 26
MAPK11 -0.078 0.17 -9999 0 -0.36 130 130
MITF -0.094 0.2 -9999 0 -0.41 147 147
MAPKAPK5 -0.074 0.18 -9999 0 -0.39 126 126
KRT8 -0.075 0.18 -9999 0 -0.39 127 127
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.11 0.23 -9999 0 -0.5 128 128
CEBPB -0.075 0.18 -9999 0 -0.39 128 128
SLC9A1 -0.075 0.18 -9999 0 -0.39 127 127
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.071 0.18 -9999 0 -0.38 128 128
p38alpha-beta/MNK1 -0.075 0.19 -9999 0 -0.41 114 114
JUN -0.044 0.14 -9999 0 -0.5 26 26
PPARGC1A -0.11 0.22 -9999 0 -0.42 165 165
USF1 -0.074 0.18 -9999 0 -0.39 126 126
RAB5/GDP/GDI1 -0.073 0.12 -9999 0 -0.42 37 37
NOS2 -0.19 0.41 -9999 0 -1.1 89 89
DDIT3 -0.075 0.18 -9999 0 -0.39 127 127
RAB5A 0.007 0.054 -9999 0 -0.58 5 5
HSPB1 -0.06 0.16 -9999 0 -0.46 41 41
p38alpha-beta/HBP1 -0.075 0.19 -9999 0 -0.4 126 126
CREB1 -0.074 0.18 -9999 0 -0.4 127 127
RAB5/GDP 0.005 0.04 -9999 0 -0.43 5 5
EIF4E -0.064 0.17 -9999 0 -0.56 34 34
RPS6KA4 -0.074 0.18 -9999 0 -0.39 127 127
PLA2G4A -0.15 0.22 -9999 0 -0.47 145 145
GDI1 -0.074 0.18 -9999 0 -0.38 126 126
TP53 -0.12 0.24 -9999 0 -0.52 128 128
RPS6KA5 -0.076 0.18 -9999 0 -0.39 128 128
ESR1 -0.1 0.2 -9999 0 -0.42 150 150
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.08 0.18 -9999 0 -0.39 134 134
MEF2A -0.075 0.18 -9999 0 -0.4 114 114
EIF4EBP1 -0.074 0.18 -9999 0 -0.4 127 127
KRT19 -0.076 0.18 -9999 0 -0.39 127 127
ELK4 -0.076 0.18 -9999 0 -0.4 126 126
ATF6 -0.074 0.18 -9999 0 -0.38 126 126
ATF1 -0.074 0.18 -9999 0 -0.41 115 115
p38alpha-beta/MAPKAPK2 -0.075 0.19 -9999 0 -0.4 126 126
p38alpha-beta/MAPKAPK3 -0.075 0.19 -9999 0 -0.4 126 126
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.53 0.57 -10000 0 -1.3 178 178
STAT6 (cleaved dimer) -0.58 0.56 -10000 0 -1.2 219 219
IGHG1 -0.16 0.18 -10000 0 -0.56 4 4
IGHG3 -0.52 0.55 -10000 0 -1.2 208 208
AKT1 -0.24 0.29 -10000 0 -0.72 85 85
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.19 0.26 -10000 0 -0.67 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.28 -10000 0 -0.7 79 79
THY1 -0.53 0.58 -10000 0 -1.3 179 179
MYB 0.003 0.072 -10000 0 -0.58 9 9
HMGA1 0.006 0.055 -10000 0 -0.54 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.35 -10000 0 -0.78 146 146
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.29 -10000 0 -0.68 96 96
SP1 0.015 0.025 -10000 0 -0.58 1 1
INPP5D -0.018 0.13 -10000 0 -0.58 30 30
SOCS5 0.027 0.016 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.6 -10000 0 -1.3 190 190
SOCS1 -0.35 0.36 -10000 0 -0.81 153 153
SOCS3 -0.26 0.31 -10000 0 -0.85 68 68
FCER2 -0.52 0.56 -10000 0 -1.2 176 176
PARP14 0.009 0.021 -10000 0 -0.46 1 1
CCL17 -0.57 0.61 -10000 0 -1.3 190 190
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.23 -10000 0 -0.63 54 54
T cell proliferation -0.54 0.59 -10000 0 -1.3 185 185
IL4R/JAK1 -0.54 0.57 -10000 0 -1.3 179 179
EGR2 -0.57 0.61 -10000 0 -1.4 178 178
JAK2 -0.033 0.11 -10000 0 -0.58 21 21
JAK3 0.002 0.077 -10000 0 -0.53 12 12
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
JAK1 0.003 0.043 -10000 0 -0.58 3 3
COL1A2 -0.21 0.34 -10000 0 -1.2 46 46
CCL26 -0.58 0.62 -10000 0 -1.3 201 201
IL4R -0.57 0.62 -10000 0 -1.4 178 178
PTPN6 0.023 0.012 -10000 0 -10000 0 0
IL13RA2 -0.59 0.63 -10000 0 -1.4 197 197
IL13RA1 -0.016 0.052 -10000 0 -0.6 3 3
IRF4 -0.27 0.5 -10000 0 -1.4 81 81
ARG1 -0.14 0.18 -10000 0 -0.79 16 16
CBL -0.3 0.33 -10000 0 -0.74 136 136
GTF3A 0.012 0.04 -10000 0 -0.51 3 3
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
IL13RA1/JAK2 -0.032 0.096 -10000 0 -0.45 22 22
IRF4/BCL6 -0.24 0.46 -10000 0 -1.3 81 81
CD40LG -0.037 0.16 -10000 0 -0.58 49 49
MAPK14 -0.29 0.34 -10000 0 -0.78 121 121
mitosis -0.23 0.27 -10000 0 -0.68 84 84
STAT6 -0.65 0.76 -10000 0 -1.5 201 201
SPI1 -0.014 0.12 -10000 0 -0.52 30 30
RPS6KB1 -0.22 0.27 -10000 0 -0.68 74 74
STAT6 (dimer) -0.65 0.78 -10000 0 -1.5 201 201
STAT6 (dimer)/PARP14 -0.59 0.64 -10000 0 -1.4 190 190
mast cell activation 0.012 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.3 -10000 0 -0.74 88 88
FRAP1 -0.24 0.29 -10000 0 -0.72 85 85
LTA -0.56 0.61 -10000 0 -1.3 181 181
FES 0 0.08 -10000 0 -0.56 12 12
T-helper 1 cell differentiation 0.61 0.68 1.4 202 -10000 0 202
CCL11 -0.57 0.62 -10000 0 -1.4 192 192
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.3 -10000 0 -0.74 83 83
IL2RG 0.001 0.083 -10000 0 -0.56 13 13
IL10 -0.57 0.62 -10000 0 -1.4 179 179
IRS1 0.002 0.076 -10000 0 -0.58 10 10
IRS2 0.003 0.067 -10000 0 -0.54 9 9
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.53 0.57 -10000 0 -1.3 171 171
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.41 0.42 -10000 0 -0.92 188 188
COL1A1 -0.25 0.4 -10000 0 -1.2 65 65
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.55 0.6 -10000 0 -1.4 166 166
IL2R gamma/JAK3 -0.001 0.083 -10000 0 -0.39 25 25
TFF3 -0.57 0.61 -10000 0 -1.3 191 191
ALOX15 -0.62 0.64 -10000 0 -1.4 218 218
MYBL1 0 0.079 -10000 0 -0.55 12 12
T-helper 2 cell differentiation -0.43 0.44 -10000 0 -0.98 186 186
SHC1 0.011 0 -10000 0 -10000 0 0
CEBPB 0.009 0.042 -10000 0 -0.49 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.28 -10000 0 -0.68 82 82
mol:PI-3-4-5-P3 -0.24 0.29 -10000 0 -0.72 85 85
PI3K -0.26 0.31 -10000 0 -0.78 85 85
DOK2 -0.012 0.11 -10000 0 -0.55 25 25
ETS1 0.015 0.063 -10000 0 -0.46 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.22 -10000 0 -0.62 43 43
ITGB3 -0.54 0.58 -10000 0 -1.3 175 175
PIGR -0.68 0.7 -10000 0 -1.5 237 237
IGHE 0.041 0.051 0.26 10 -0.31 1 11
MAPKKK cascade -0.18 0.22 -10000 0 -0.61 43 43
BCL6 0.01 0.038 -10000 0 -0.45 4 4
OPRM1 -0.53 0.57 -10000 0 -1.3 175 175
RETNLB -0.68 0.67 -10000 0 -1.4 244 244
SELP -0.6 0.66 -10000 0 -1.4 193 193
AICDA -0.52 0.55 -10000 0 -1.2 179 179
Wnt signaling

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.38 200 200
FZD6 0.005 0.064 -9999 0 -0.58 7 7
WNT6 -0.1 0.21 -9999 0 -0.5 131 131
WNT4 -0.054 0.18 -9999 0 -0.54 72 72
FZD3 -0.008 0.11 -9999 0 -0.58 20 20
WNT5A -0.01 0.11 -9999 0 -0.55 23 23
WNT11 -0.14 0.25 -9999 0 -0.53 172 172
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.084 0.22 -9999 0 -0.48 120 120
alphaM/beta2 Integrin/GPIbA -0.075 0.19 -9999 0 -0.44 117 117
alphaM/beta2 Integrin/proMMP-9 -0.1 0.24 -9999 0 -0.49 137 137
PLAUR 0.009 0.039 -9999 0 -0.54 3 3
HMGB1 -0.012 0.097 -9999 0 -0.59 16 16
alphaM/beta2 Integrin/Talin -0.059 0.18 -9999 0 -0.44 97 97
AGER -0.012 0.096 -9999 0 -0.58 16 16
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
SELPLG -0.006 0.099 -9999 0 -0.55 19 19
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.09 0.21 -9999 0 -0.47 106 106
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.062 0.18 -9999 0 -0.52 83 83
CYR61 -0.022 0.12 -9999 0 -0.48 41 41
TLN1 0.01 0.024 -9999 0 -0.58 1 1
Rap1/GTP -0.12 0.17 -9999 0 -0.45 91 91
RHOA 0.01 0.024 -9999 0 -0.58 1 1
P-selectin oligomer -0.087 0.22 -9999 0 -0.55 105 105
MYH2 -0.13 0.2 -9999 0 -0.46 117 117
MST1R 0.007 0.054 -9999 0 -0.58 5 5
leukocyte activation during inflammatory response -0.14 0.19 -9999 0 -0.4 158 158
APOB -0.12 0.22 -9999 0 -0.5 147 147
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.033 0.15 -9999 0 -0.53 50 50
JAM3 0.007 0.046 -9999 0 -0.46 6 6
GP1BA -0.015 0.11 -9999 0 -0.52 28 28
alphaM/beta2 Integrin/CTGF -0.069 0.19 -9999 0 -0.44 108 108
alphaM/beta2 Integrin -0.14 0.21 -9999 0 -0.46 128 128
JAM3 homodimer 0.007 0.046 -9999 0 -0.46 6 6
ICAM2 0.002 0.069 -9999 0 -0.5 11 11
ICAM1 0.005 0.056 -9999 0 -0.51 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.14 0.2 -9999 0 -0.45 128 128
cell adhesion -0.074 0.19 -9999 0 -0.44 117 117
NFKB1 -0.11 0.25 -9999 0 -0.62 70 70
THY1 -0.001 0.081 -9999 0 -0.55 13 13
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
Lipoprotein(a) -0.086 0.15 -9999 0 -0.31 181 181
alphaM/beta2 Integrin/LRP/tPA -0.055 0.18 -9999 0 -0.45 87 87
IL6 -0.17 0.33 -9999 0 -0.78 105 105
ITGB2 -0.038 0.15 -9999 0 -0.54 47 47
elevation of cytosolic calcium ion concentration -0.055 0.18 -9999 0 -0.45 84 84
alphaM/beta2 Integrin/JAM2/JAM3 -0.082 0.22 -9999 0 -0.5 108 108
JAM2 -0.05 0.18 -9999 0 -0.55 67 67
alphaM/beta2 Integrin/ICAM1 -0.065 0.19 -9999 0 -0.45 94 94
alphaM/beta2 Integrin/uPA/Plg -0.082 0.2 -9999 0 -0.45 115 115
RhoA/GTP -0.14 0.21 -9999 0 -0.48 116 116
positive regulation of phagocytosis -0.13 0.21 -9999 0 -0.55 95 95
Ron/MSP -0.018 0.12 -9999 0 -0.38 55 55
alphaM/beta2 Integrin/uPAR/uPA -0.055 0.18 -9999 0 -0.45 84 84
alphaM/beta2 Integrin/uPAR -0.061 0.18 -9999 0 -0.44 99 99
PLAU -0.001 0.081 -9999 0 -0.51 15 15
PLAT 0 0.078 -9999 0 -0.54 12 12
actin filament polymerization -0.13 0.19 -9999 0 -0.44 117 117
MST1 -0.033 0.15 -9999 0 -0.51 51 51
alphaM/beta2 Integrin/lipoprotein(a) -0.13 0.2 -9999 0 -0.41 159 159
TNF -0.11 0.26 -9999 0 -0.72 62 62
RAP1B 0.011 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.066 0.19 -9999 0 -0.44 105 105
fibrinolysis -0.082 0.2 -9999 0 -0.45 115 115
HCK -0.017 0.12 -9999 0 -0.54 31 31
dendritic cell antigen processing and presentation -0.14 0.2 -9999 0 -0.45 128 128
VTN -0.054 0.17 -9999 0 -0.5 76 76
alphaM/beta2 Integrin/CYR61 -0.078 0.2 -9999 0 -0.43 123 123
LPA -0.027 0.12 -9999 0 -0.46 43 43
LRP1 0.006 0.057 -9999 0 -0.56 6 6
cell migration -0.11 0.26 -9999 0 -0.55 125 125
FN1 -0.088 0.21 -9999 0 -0.52 112 112
alphaM/beta2 Integrin/Thy1 -0.065 0.2 -9999 0 -0.46 101 101
MPO -0.039 0.16 -9999 0 -0.53 55 55
KNG1 -0.11 0.22 -9999 0 -0.52 138 138
RAP1/GDP 0.015 0.015 -9999 0 -0.36 1 1
ROCK1 -0.13 0.2 -9999 0 -0.46 117 117
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.04 0.16 -9999 0 -0.58 46 46
CTGF -0.006 0.09 -9999 0 -0.47 22 22
alphaM/beta2 Integrin/Hck -0.074 0.22 -9999 0 -0.5 104 104
ITGAM -0.072 0.19 -9999 0 -0.53 86 86
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.11 0.24 -9999 0 -0.48 145 145
HP -0.077 0.19 -9999 0 -0.5 102 102
leukocyte adhesion -0.13 0.22 -9999 0 -0.59 88 88
SELP -0.087 0.22 -9999 0 -0.55 105 105
Syndecan-4-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
PTK2 -0.069 0.18 -9999 0 -0.52 69 69
Syndecan-4/Syndesmos -0.14 0.24 -9999 0 -0.55 120 120
positive regulation of JNK cascade -0.14 0.23 -9999 0 -0.53 127 127
Syndecan-4/ADAM12 -0.18 0.28 -9999 0 -0.6 150 150
CCL5 -0.038 0.15 -9999 0 -0.51 57 57
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.01 0.024 -9999 0 -0.58 1 1
ITGA5 -0.006 0.093 -9999 0 -0.49 21 21
SDCBP 0.003 0.072 -9999 0 -0.58 9 9
PLG -0.036 0.15 -9999 0 -0.56 46 46
ADAM12 -0.078 0.2 -9999 0 -0.51 103 103
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0.027 -9999 0 -0.46 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.031 0.04 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.17 0.26 -9999 0 -0.59 138 138
Syndecan-4/CXCL12/CXCR4 -0.15 0.25 -9999 0 -0.57 127 127
Syndecan-4/Laminin alpha3 -0.15 0.24 -9999 0 -0.56 126 126
MDK -0.009 0.1 -9999 0 -0.51 24 24
Syndecan-4/FZD7 -0.14 0.24 -9999 0 -0.56 122 122
Syndecan-4/Midkine -0.15 0.24 -9999 0 -0.57 124 124
FZD7 0 0.078 -9999 0 -0.5 14 14
Syndecan-4/FGFR1/FGF -0.18 0.23 -9999 0 -0.56 130 130
THBS1 -0.002 0.084 -9999 0 -0.52 15 15
integrin-mediated signaling pathway -0.17 0.26 -9999 0 -0.57 139 139
positive regulation of MAPKKK cascade -0.14 0.23 -9999 0 -0.53 127 127
Syndecan-4/TACI -0.18 0.26 -9999 0 -0.58 141 141
CXCR4 -0.016 0.12 -9999 0 -0.5 33 33
cell adhesion -0.027 0.12 -9999 0 -0.33 59 59
Syndecan-4/Dynamin -0.14 0.24 -9999 0 -0.56 118 118
Syndecan-4/TSP1 -0.14 0.24 -9999 0 -0.56 124 124
Syndecan-4/GIPC -0.14 0.24 -9999 0 -0.56 119 119
Syndecan-4/RANTES -0.16 0.25 -9999 0 -0.57 131 131
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.059 0.18 -9999 0 -0.54 77 77
LAMA3 -0.014 0.11 -9999 0 -0.51 30 30
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA 0.038 0.056 -9999 0 -0.47 2 2
Syndecan-4/alpha-Actinin -0.14 0.24 -9999 0 -0.56 118 118
TFPI -0.009 0.1 -9999 0 -0.54 22 22
F2 -0.12 0.22 -9999 0 -0.5 150 150
alpha5/beta1 Integrin 0.004 0.067 -9999 0 -0.35 21 21
positive regulation of cell adhesion -0.17 0.26 -9999 0 -0.58 141 141
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC -0.063 0.19 -9999 0 -0.52 85 85
Syndecan-4/CXCL12 -0.15 0.25 -9999 0 -0.57 127 127
FGF6 -0.001 0.026 -9999 0 -0.46 2 2
RHOA 0.01 0.024 -9999 0 -0.58 1 1
CXCL12 -0.013 0.11 -9999 0 -0.49 29 29
TNFRSF13B -0.064 0.18 -9999 0 -0.52 84 84
FGF2 -0.039 0.16 -9999 0 -0.52 57 57
FGFR1 -0.01 0.1 -9999 0 -0.52 24 24
Syndecan-4/PI-4-5-P2 -0.14 0.24 -9999 0 -0.56 118 118
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.083 0.21 -9999 0 -0.51 112 112
cell migration -0.006 0.017 -9999 0 -10000 0 0
PRKCD 0.016 0.009 -9999 0 -10000 0 0
vasculogenesis -0.14 0.23 -9999 0 -0.54 124 124
SDC4 -0.15 0.25 -9999 0 -0.6 118 118
Syndecan-4/Tenascin C -0.17 0.27 -9999 0 -0.59 139 139
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.032 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.24 -9999 0 -0.55 124 124
MMP9 -0.062 0.18 -9999 0 -0.52 83 83
Rac1/GTP -0.028 0.12 -9999 0 -0.34 59 59
cytoskeleton organization -0.13 0.23 -9999 0 -0.53 120 120
GIPC1 0.007 0.048 -9999 0 -0.58 4 4
Syndecan-4/TFPI -0.15 0.25 -9999 0 -0.57 124 124
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.039 0.16 -9999 0 -0.57 52 52
GNB1/GNG2 -0.11 0.2 -9999 0 -0.5 82 82
mol:DAG -0.095 0.18 -9999 0 -0.46 81 81
PLCG1 -0.099 0.19 -9999 0 -0.47 81 81
YES1 -0.12 0.2 -9999 0 -0.52 84 84
FZD3 -0.008 0.11 -9999 0 -0.58 20 20
FZD6 0.005 0.064 -9999 0 -0.58 7 7
G protein -0.099 0.19 -9999 0 -0.51 64 64
MAP3K7 -0.084 0.16 -9999 0 -0.43 67 67
mol:Ca2+ -0.092 0.17 -9999 0 -0.44 81 81
mol:IP3 -0.095 0.18 -9999 0 -0.46 81 81
NLK -0.005 0.009 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.096 0.17 -9999 0 -0.46 74 74
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.38 200 200
CSNK1A1 0.009 0.034 -9999 0 -0.58 2 2
GNAS -0.12 0.2 -9999 0 -0.52 80 80
GO:0007205 -0.094 0.18 -9999 0 -0.48 64 64
WNT6 -0.1 0.21 -9999 0 -0.5 131 131
WNT4 -0.054 0.18 -9999 0 -0.54 72 72
NFAT1/CK1 alpha -0.12 0.22 -9999 0 -0.55 87 87
GNG2 0.003 0.067 -9999 0 -0.54 9 9
WNT5A -0.01 0.11 -9999 0 -0.55 23 23
WNT11 -0.14 0.25 -9999 0 -0.53 172 172
CDC42 -0.11 0.2 -9999 0 -0.51 83 83
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.028 0.14 -10000 0 -0.43 48 48
fibroblast growth factor receptor signaling pathway -0.028 0.14 -10000 0 -0.43 48 48
LAMA1 -0.059 0.18 -10000 0 -0.54 77 77
PRNP -0.003 0.091 -10000 0 -0.58 15 15
GPC1/SLIT2 -0.089 0.18 -10000 0 -0.39 159 159
SMAD2 0.015 0.065 -10000 0 -0.34 17 17
GPC1/PrPc/Cu2+ -0.002 0.078 -10000 0 -0.35 29 29
GPC1/Laminin alpha1 -0.043 0.15 -10000 0 -0.4 87 87
TDGF1 -0.073 0.21 -10000 0 -0.58 86 86
CRIPTO/GPC1 -0.055 0.16 -10000 0 -0.42 100 100
APP/GPC1 0.007 0.065 -10000 0 -0.4 15 15
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.043 0.14 -10000 0 -0.35 106 106
FLT1 0.007 0.052 -10000 0 -0.56 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.012 0.062 -10000 0 -0.33 19 19
SERPINC1 -0.014 0.096 -10000 0 -0.46 27 27
FYN -0.043 0.14 -10000 0 -0.36 105 105
FGR -0.062 0.16 -10000 0 -0.37 131 131
positive regulation of MAPKKK cascade -0.096 0.21 -10000 0 -0.46 125 125
SLIT2 -0.12 0.24 -10000 0 -0.53 150 150
GPC1/NRG -0.052 0.16 -10000 0 -0.39 103 103
NRG1 -0.07 0.2 -10000 0 -0.53 91 91
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.012 0.066 -10000 0 -0.34 19 19
LYN -0.039 0.14 -10000 0 -0.35 100 100
mol:Spermine 0 0.062 -10000 0 -0.4 14 14
cell growth -0.028 0.14 -10000 0 -0.43 48 48
BMP signaling pathway 0.001 0.084 0.55 14 -10000 0 14
SRC -0.039 0.14 -10000 0 -0.35 100 100
TGFBR1 0.007 0.048 -10000 0 -0.58 4 4
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.21 0.27 -10000 0 -0.53 244 244
GPC1 -0.001 0.085 -10000 0 -0.55 14 14
TGFBR1 (dimer) 0.007 0.048 -10000 0 -0.58 4 4
VEGFA 0.011 0.019 -10000 0 -0.46 1 1
BLK -0.11 0.2 -10000 0 -0.38 206 206
HCK -0.056 0.16 -10000 0 -0.36 123 123
FGF2 -0.039 0.16 -10000 0 -0.52 57 57
FGFR1 -0.01 0.1 -10000 0 -0.52 24 24
VEGFR1 homodimer 0.007 0.052 -10000 0 -0.56 5 5
TGFBR2 0.011 0.019 -10000 0 -0.46 1 1
cell death 0.007 0.064 -10000 0 -0.4 15 15
ATIII/GPC1 -0.01 0.091 -10000 0 -0.34 41 41
PLA2G2A/GPC1 -0.15 0.21 -10000 0 -0.39 250 250
LCK -0.064 0.17 -10000 0 -0.38 130 130
neuron differentiation -0.052 0.16 -10000 0 -0.39 103 103
PrPc/Cu2+ -0.002 0.067 -10000 0 -0.42 15 15
APP 0.01 0.024 -10000 0 -0.58 1 1
TGFBR2 (dimer) 0.011 0.019 -10000 0 -0.46 1 1
EGFR-dependent Endothelin signaling events

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.008 0.041 -9999 0 -0.49 4 4
EGFR 0.005 0.058 -9999 0 -0.53 7 7
EGF/EGFR -0.12 0.15 -9999 0 -0.34 132 132
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.072 0.14 -9999 0 -0.3 95 95
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.021 0.13 -9999 0 -0.52 37 37
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.18 0.25 -9999 0 -0.51 222 222
EGF/EGFR dimer/SHC -0.099 0.16 -9999 0 -0.3 228 228
mol:GDP -0.073 0.14 -9999 0 -0.29 95 95
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.023 0.13 -9999 0 -0.52 39 39
GRB2/SOS1 0.016 0.018 -9999 0 -0.42 1 1
HRAS/GTP -0.085 0.11 -9999 0 -0.45 3 3
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP -0.087 0.11 -9999 0 -0.46 3 3
FRAP1 -0.071 0.13 -9999 0 -0.28 95 95
EGF/EGFR dimer -0.13 0.19 -9999 0 -0.36 228 228
SOS1 0.01 0.024 -9999 0 -0.58 1 1
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.031 0.13 -9999 0 -0.38 73 73
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.094 0.19 -10000 0 -0.54 79 79
FYN -0.09 0.29 -10000 0 -0.7 88 88
LAT/GRAP2/SLP76 -0.11 0.23 -10000 0 -0.58 97 97
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
AKT1 -0.052 0.19 -10000 0 -0.45 92 92
B2M 0.007 0.044 -10000 0 -0.52 4 4
IKBKG -0.036 0.054 -10000 0 -0.16 70 70
MAP3K8 0.01 0.031 -10000 0 -0.52 2 2
mol:Ca2+ -0.024 0.04 -10000 0 -0.1 110 110
integrin-mediated signaling pathway 0.008 0.05 -10000 0 -0.32 13 13
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.091 0.28 -10000 0 -0.68 92 92
TRPV6 -0.094 0.19 -10000 0 -0.48 120 120
CD28 -0.031 0.15 -10000 0 -0.56 45 45
SHC1 -0.086 0.27 -10000 0 -0.67 87 87
receptor internalization -0.095 0.3 -10000 0 -0.74 84 84
PRF1 -0.1 0.33 -10000 0 -1 55 55
KRAS 0.006 0.057 -10000 0 -0.56 6 6
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 -0.034 0.15 -10000 0 -0.36 83 83
LAT -0.094 0.28 -10000 0 -0.68 90 90
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.033 0.15 -10000 0 -0.57 46 46
CD3E -0.026 0.14 -10000 0 -0.57 39 39
CD3G -0.055 0.18 -10000 0 -0.57 69 69
RASGRP2 -0.01 0.043 -10000 0 -0.17 31 31
RASGRP1 -0.057 0.2 -10000 0 -0.48 92 92
HLA-A 0.002 0.069 -10000 0 -0.53 10 10
RASSF5 0.001 0.076 -10000 0 -0.53 12 12
RAP1A/GTP/RAPL 0.008 0.05 -10000 0 -0.33 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.06 -10000 0 -0.12 77 77
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.065 0.096 -10000 0 -0.27 88 88
PRKCA -0.049 0.1 -10000 0 -0.28 78 78
GRAP2 -0.023 0.14 -10000 0 -0.55 37 37
mol:IP3 -0.058 0.19 0.2 77 -0.45 82 159
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.089 0.29 -10000 0 -0.75 75 75
ORAI1 0.055 0.11 0.27 117 -0.33 1 118
CSK -0.09 0.28 -10000 0 -0.71 82 82
B7 family/CD28 -0.12 0.32 -10000 0 -0.73 106 106
CHUK 0.007 0.048 -10000 0 -0.58 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.33 -10000 0 -0.8 89 89
PTPN6 -0.09 0.28 -10000 0 -0.71 83 83
VAV1 -0.1 0.29 -10000 0 -0.71 93 93
Monovalent TCR/CD3 -0.067 0.26 -10000 0 -0.59 86 86
CBL 0.011 0 -10000 0 -10000 0 0
LCK -0.099 0.3 -10000 0 -0.73 89 89
PAG1 -0.091 0.28 -10000 0 -0.7 87 87
RAP1A 0.01 0.024 -10000 0 -0.58 1 1
TCR/CD3/MHC I/CD8/LCK -0.11 0.33 -10000 0 -0.8 88 88
CD80 -0.04 0.16 -10000 0 -0.57 53 53
CD86 -0.036 0.16 -10000 0 -0.54 52 52
PDK1/CARD11/BCL10/MALT1 -0.079 0.12 -10000 0 -0.32 93 93
HRAS 0.008 0.041 -10000 0 -0.49 4 4
GO:0035030 -0.09 0.25 -10000 0 -0.59 103 103
CD8A -0.06 0.19 -10000 0 -0.54 79 79
CD8B -0.047 0.17 -10000 0 -0.56 61 61
PTPRC -0.044 0.17 -10000 0 -0.55 59 59
PDK1/PKC theta -0.07 0.23 -10000 0 -0.56 93 93
CSK/PAG1 -0.084 0.27 -10000 0 -0.7 81 81
SOS1 0.01 0.024 -10000 0 -0.58 1 1
peptide-MHC class I 0.006 0.06 -10000 0 -0.38 14 14
GRAP2/SLP76 -0.12 0.27 -10000 0 -0.68 94 94
STIM1 0.03 0.053 0.2 3 -10000 0 3
RAS family/GTP -0.003 0.083 -10000 0 -0.18 68 68
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.11 0.33 -10000 0 -0.82 84 84
mol:DAG -0.069 0.15 0.13 1 -0.39 92 93
RAP1A/GDP 0.001 0.027 -10000 0 -0.15 1 1
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
CD247 -0.017 0.12 -10000 0 -0.55 30 30
cytotoxic T cell degranulation -0.097 0.31 -10000 0 -0.96 55 55
RAP1A/GTP -0.006 0.015 -10000 0 -0.071 19 19
mol:PI-3-4-5-P3 -0.068 0.22 -10000 0 -0.54 92 92
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.084 0.24 0.22 67 -0.58 88 155
NRAS 0.002 0.076 -10000 0 -0.58 10 10
ZAP70 -0.036 0.15 -10000 0 -0.53 52 52
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
LAT/GRAP2/SLP76/VAV1 -0.11 0.22 -10000 0 -0.56 99 99
MALT1 0.007 0.054 -10000 0 -0.58 5 5
TRAF6 0.01 0.024 -10000 0 -0.58 1 1
CD8 heterodimer -0.075 0.2 -10000 0 -0.46 118 118
CARD11 -0.12 0.22 -10000 0 -0.49 156 156
PRKCB -0.064 0.13 -10000 0 -0.34 88 88
PRKCE -0.049 0.1 -10000 0 -0.28 78 78
PRKCQ -0.089 0.27 -10000 0 -0.64 96 96
LCP2 -0.015 0.12 -10000 0 -0.55 29 29
BCL10 0.007 0.048 -10000 0 -0.58 4 4
regulation of survival gene product expression -0.041 0.16 -10000 0 -0.38 92 92
IKK complex 0.005 0.057 -10000 0 -0.12 59 59
RAS family/GDP -0.007 0.016 -10000 0 -0.096 9 9
MAP3K14 -0.019 0.12 -10000 0 -0.29 65 65
PDPK1 -0.046 0.18 -10000 0 -0.42 92 92
TCR/CD3/MHC I/CD8/Fyn -0.11 0.34 -10000 0 -0.78 94 94
BCR signaling pathway

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
JUN -0.063 0.16 -10000 0 -0.4 86 86
IKBKB -0.029 0.092 -10000 0 -0.25 34 34
AKT1 -0.051 0.11 0.21 1 -0.25 93 94
IKBKG -0.03 0.098 -10000 0 -0.27 42 42
CALM1 -0.041 0.16 0.25 24 -0.47 51 75
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
MAP3K1 -0.11 0.24 -10000 0 -0.56 106 106
MAP3K7 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ -0.05 0.17 0.25 24 -0.48 55 79
DOK1 0.011 0 -10000 0 -10000 0 0
AP-1 -0.023 0.1 0.2 19 -0.25 53 72
LYN 0.011 0 -10000 0 -10000 0 0
BLNK -0.01 0.11 -10000 0 -0.58 22 22
SHC1 0.011 0 -10000 0 -10000 0 0
BCR complex -0.1 0.22 -10000 0 -0.47 145 145
CD22 -0.16 0.28 -10000 0 -0.57 146 146
CAMK2G -0.033 0.15 0.24 23 -0.44 49 72
CSNK2A1 0.011 0 -10000 0 -10000 0 0
INPP5D -0.018 0.13 -10000 0 -0.58 30 30
SHC/GRB2/SOS1 -0.078 0.14 -10000 0 -0.46 45 45
GO:0007205 -0.051 0.17 0.25 24 -0.49 55 79
SYK 0.011 0.019 -10000 0 -0.46 1 1
ELK1 -0.043 0.16 0.24 23 -0.48 51 74
NFATC1 -0.1 0.22 -10000 0 -0.49 105 105
B-cell antigen/BCR complex -0.1 0.22 -10000 0 -0.47 145 145
PAG1/CSK 0.012 0.048 -10000 0 -0.4 8 8
NFKBIB -0.001 0.033 0.084 15 -0.12 2 17
HRAS -0.039 0.16 0.23 23 -0.43 55 78
NFKBIA -0.001 0.033 0.084 15 -0.12 2 17
NF-kappa-B/RelA/I kappa B beta 0.005 0.028 -10000 0 -0.17 1 1
RasGAP/Csk -0.11 0.22 -10000 0 -0.44 145 145
mol:GDP -0.046 0.16 0.26 24 -0.46 55 79
PTEN 0.006 0.059 -10000 0 -0.58 6 6
CD79B -0.029 0.14 -10000 0 -0.51 47 47
NF-kappa-B/RelA/I kappa B alpha 0.005 0.028 -10000 0 -0.17 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.11 0.22 -10000 0 -0.49 126 126
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
mol:IP3 -0.052 0.18 0.26 24 -0.5 55 79
CSK 0.01 0.024 -10000 0 -0.58 1 1
FOS -0.051 0.16 0.24 20 -0.42 71 91
CHUK -0.032 0.1 -10000 0 -0.28 40 40
IBTK 0.002 0.076 -10000 0 -0.58 10 10
CARD11/BCL10/MALT1/TAK1 -0.1 0.17 -10000 0 -0.45 86 86
PTPN6 -0.13 0.27 -10000 0 -0.64 103 103
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 -0.002 0.036 -10000 0 -0.11 28 28
VAV2 -0.16 0.29 -10000 0 -0.61 135 135
ubiquitin-dependent protein catabolic process 0.002 0.032 0.087 15 -0.11 2 17
BTK -0.055 0.27 0.36 27 -1.1 36 63
CD19 -0.17 0.28 -10000 0 -0.53 171 171
MAP4K1 -0.045 0.17 -10000 0 -0.56 60 60
CD72 -0.005 0.089 -10000 0 -0.5 19 19
PAG1 0.005 0.06 -10000 0 -0.55 7 7
MAPK14 -0.089 0.2 -10000 0 -0.46 103 103
SH3BP5 0.003 0.072 -10000 0 -0.58 9 9
PIK3AP1 -0.055 0.18 0.3 2 -0.51 58 60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.076 0.23 -10000 0 -0.52 98 98
RAF1 -0.031 0.15 0.23 23 -0.44 42 65
RasGAP/p62DOK/SHIP -0.14 0.21 -10000 0 -0.6 72 72
CD79A -0.11 0.23 -10000 0 -0.54 138 138
re-entry into mitotic cell cycle -0.023 0.1 0.2 20 -0.25 54 74
RASA1 0.009 0.034 -10000 0 -0.58 2 2
MAPK3 -0.016 0.12 0.22 22 -0.41 28 50
MAPK1 -0.016 0.12 0.22 2 -0.41 28 30
CD72/SHP1 -0.12 0.26 -10000 0 -0.63 99 99
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.089 0.2 -10000 0 -0.47 101 101
actin cytoskeleton organization -0.12 0.24 -10000 0 -0.54 116 116
NF-kappa-B/RelA 0.014 0.054 0.17 15 -0.22 2 17
Calcineurin -0.054 0.12 -10000 0 -0.41 48 48
PI3K -0.15 0.21 -10000 0 -0.53 115 115
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.056 0.17 0.31 2 -0.5 56 58
SOS1 0.01 0.024 -10000 0 -0.58 1 1
Bam32/HPK1 -0.15 0.34 -10000 0 -0.82 103 103
DAPP1 -0.17 0.36 -10000 0 -0.96 88 88
cytokine secretion -0.093 0.2 -10000 0 -0.44 106 106
mol:DAG -0.052 0.18 0.26 24 -0.5 55 79
PLCG2 -0.01 0.11 -10000 0 -0.55 23 23
MAP2K1 -0.024 0.14 0.22 22 -0.43 35 57
B-cell antigen/BCR complex/FcgammaRIIB -0.14 0.25 -10000 0 -0.44 210 210
mol:PI-3-4-5-P3 -0.1 0.14 0.28 1 -0.36 112 113
ETS1 -0.027 0.14 0.24 23 -0.41 50 73
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.066 0.18 -10000 0 -0.38 128 128
B-cell antigen/BCR complex/LYN -0.12 0.25 -10000 0 -0.53 121 121
MALT1 0.007 0.054 -10000 0 -0.58 5 5
TRAF6 0.011 0.024 -10000 0 -0.58 1 1
RAC1 -0.14 0.26 -10000 0 -0.59 115 115
B-cell antigen/BCR complex/LYN/SYK -0.15 0.26 -10000 0 -0.66 98 98
CARD11 -0.1 0.22 0.25 20 -0.5 99 119
FCGR2B -0.087 0.21 -10000 0 -0.54 109 109
PPP3CA 0.011 0 -10000 0 -10000 0 0
BCL10 0.008 0.048 -10000 0 -0.58 4 4
IKK complex -0.006 0.041 0.092 15 -0.11 11 26
PTPRC -0.043 0.17 -10000 0 -0.55 59 59
PDPK1 -0.053 0.11 0.19 1 -0.25 97 98
PPP3CB 0.011 0 -10000 0 -10000 0 0
PPP3CC 0.006 0.059 -10000 0 -0.58 6 6
POU2F2 0.004 0.029 -10000 0 -0.11 12 12
Syndecan-1-mediated signaling events

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
TGFB1 -0.002 0.088 -9999 0 -0.55 15 15
CCL5 -0.038 0.15 -9999 0 -0.51 57 57
SDCBP 0.003 0.072 -9999 0 -0.58 9 9
FGFR/FGF2/Syndecan-1 -0.12 0.2 -9999 0 -0.54 70 70
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.13 0.21 -9999 0 -0.5 102 102
Syndecan-1/Syntenin -0.11 0.19 -9999 0 -0.51 77 77
MAPK3 -0.088 0.18 -9999 0 -0.52 54 54
HGF/MET -0.021 0.12 -9999 0 -0.39 57 57
TGFB1/TGF beta receptor Type II -0.002 0.088 -9999 0 -0.55 15 15
BSG 0.01 0.024 -9999 0 -0.58 1 1
keratinocyte migration -0.13 0.21 -9999 0 -0.49 102 102
Syndecan-1/RANTES -0.13 0.21 -9999 0 -0.51 103 103
Syndecan-1/CD147 -0.098 0.19 -9999 0 -0.5 70 70
Syndecan-1/Syntenin/PIP2 -0.11 0.19 -9999 0 -0.49 77 77
LAMA5 -0.031 0.15 -9999 0 -0.57 44 44
positive regulation of cell-cell adhesion -0.11 0.18 -9999 0 -0.48 77 77
MMP7 -0.14 0.24 -9999 0 -0.52 170 170
HGF -0.039 0.16 -9999 0 -0.55 55 55
Syndecan-1/CASK -0.11 0.19 -9999 0 -0.52 70 70
Syndecan-1/HGF/MET -0.12 0.22 -9999 0 -0.53 95 95
regulation of cell adhesion -0.081 0.17 -9999 0 -0.5 54 54
HPSE -0.005 0.092 -9999 0 -0.51 19 19
positive regulation of cell migration -0.12 0.2 -9999 0 -0.54 70 70
SDC1 -0.12 0.2 -9999 0 -0.55 70 70
Syndecan-1/Collagen -0.12 0.2 -9999 0 -0.54 70 70
PPIB 0.011 0 -9999 0 -10000 0 0
MET 0.01 0.031 -9999 0 -0.52 2 2
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.062 0.18 -9999 0 -0.52 83 83
MAPK1 -0.088 0.18 -9999 0 -0.52 53 53
homophilic cell adhesion -0.12 0.2 -9999 0 -0.54 70 70
MMP1 -0.13 0.24 -9999 0 -0.53 161 161
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.068 0.19 -10000 0 -0.45 77 77
TBX21 -0.24 0.51 -10000 0 -1.1 120 120
B2M 0.005 0.045 -10000 0 -0.52 4 4
TYK2 0.007 0.034 -10000 0 -0.61 1 1
IL12RB1 -0.038 0.16 -10000 0 -0.57 50 50
GADD45B -0.15 0.37 -10000 0 -0.92 73 73
IL12RB2 -0.039 0.16 -10000 0 -0.53 55 55
GADD45G -0.16 0.38 -10000 0 -0.94 74 74
natural killer cell activation -0.003 0.023 -10000 0 -10000 0 0
RELB 0.009 0.036 -10000 0 -0.5 3 3
RELA 0.011 0 -10000 0 -10000 0 0
IL18 0.003 0.069 -10000 0 -0.55 9 9
IL2RA -0.047 0.17 -10000 0 -0.55 63 63
IFNG -0.068 0.19 -10000 0 -0.52 89 89
STAT3 (dimer) -0.15 0.37 -10000 0 -0.79 113 113
HLA-DRB5 -0.083 0.21 -10000 0 -0.52 107 107
FASLG -0.24 0.52 -10000 0 -1.1 123 123
NF kappa B2 p52/RelB -0.27 0.4 -10000 0 -0.96 124 124
CD4 -0.013 0.12 -10000 0 -0.56 26 26
SOCS1 -0.028 0.14 -10000 0 -0.5 47 47
EntrezGene:6955 -0.004 0.015 -10000 0 -10000 0 0
CD3D -0.035 0.15 -10000 0 -0.57 46 46
CD3E -0.028 0.14 -10000 0 -0.56 39 39
CD3G -0.058 0.19 -10000 0 -0.57 69 69
IL12Rbeta2/JAK2 -0.035 0.15 -10000 0 -0.41 74 74
CCL3 -0.24 0.51 -10000 0 -1.1 120 120
CCL4 -0.22 0.49 -10000 0 -1.1 108 108
HLA-A -0.001 0.069 -10000 0 -0.52 10 10
IL18/IL18R -0.011 0.15 -10000 0 -0.38 72 72
NOS2 -0.28 0.56 -10000 0 -1.2 134 134
IL12/IL12R/TYK2/JAK2/SPHK2 -0.053 0.16 -10000 0 -0.41 71 71
IL1R1 -0.21 0.46 -10000 0 -1 111 111
IL4 0.005 0.024 -10000 0 -10000 0 0
JAK2 -0.012 0.11 -10000 0 -0.57 21 21
EntrezGene:6957 -0.004 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.18 0.45 -10000 0 -0.97 116 116
RAB7A -0.11 0.32 -10000 0 -0.78 62 62
lysosomal transport -0.1 0.3 -10000 0 -0.73 65 65
FOS -0.17 0.41 -10000 0 -1.1 84 84
STAT4 (dimer) -0.17 0.42 -10000 0 -0.92 109 109
STAT5A (dimer) -0.3 0.42 -10000 0 -0.96 144 144
GZMA -0.24 0.5 -10000 0 -1.1 112 112
GZMB -0.25 0.51 -10000 0 -1.1 127 127
HLX 0.006 0.055 -10000 0 -0.54 6 6
LCK -0.24 0.52 -10000 0 -1.1 129 129
TCR/CD3/MHC II/CD4 -0.12 0.33 -10000 0 -0.74 97 97
IL2/IL2R -0.034 0.15 -10000 0 -0.42 68 68
MAPK14 -0.15 0.39 -10000 0 -0.89 92 92
CCR5 -0.17 0.42 -10000 0 -1.1 77 77
IL1B -0.062 0.19 -10000 0 -0.54 79 79
STAT6 -0.036 0.12 0.2 10 -0.25 48 58
STAT4 -0.029 0.15 -10000 0 -0.56 43 43
STAT3 0.011 0 -10000 0 -10000 0 0
STAT1 0.006 0.054 -10000 0 -0.49 7 7
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
NFKB2 0.01 0.031 -10000 0 -0.52 2 2
IL12B -0.005 0.075 -10000 0 -0.47 14 14
CD8A -0.063 0.19 -10000 0 -0.54 79 79
CD8B -0.049 0.17 -10000 0 -0.56 61 61
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.067 0.18 0.45 77 -10000 0 77
IL2RB -0.018 0.13 -10000 0 -0.55 32 32
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.38 -10000 0 -0.82 109 109
IL2RG -0.001 0.084 -10000 0 -0.56 13 13
IL12 -0.029 0.13 -10000 0 -0.4 61 61
STAT5A 0.011 0 -10000 0 -10000 0 0
CD247 -0.02 0.12 -10000 0 -0.55 30 30
IL2 0.001 0.027 -10000 0 -0.46 2 2
SPHK2 0.009 0.036 -10000 0 -0.5 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.039 0.16 -10000 0 -0.57 48 48
IL12/IL12R/TYK2/JAK2 -0.26 0.59 -10000 0 -1.2 127 127
MAP2K3 -0.16 0.39 -10000 0 -0.89 94 94
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 -0.16 0.4 -10000 0 -0.9 95 95
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.045 0.17 -10000 0 -0.52 64 64
IL18RAP -0.033 0.16 -10000 0 -0.56 48 48
IL12Rbeta1/TYK2 -0.023 0.13 -10000 0 -0.43 51 51
EOMES -0.14 0.41 -10000 0 -1.3 63 63
STAT1 (dimer) -0.18 0.38 -10000 0 -0.82 125 125
T cell proliferation -0.11 0.3 0.4 1 -0.65 107 108
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.012 0.12 -10000 0 -0.57 25 25
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.2 0.28 -10000 0 -0.71 109 109
ATF2 -0.13 0.36 -10000 0 -0.84 81 81
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.28 0.36 -10000 0 -0.94 86 86
PCK1 -0.27 0.45 -10000 0 -1.3 81 81
HNF4A -0.36 0.45 -10000 0 -1.1 111 111
KCNJ11 -0.27 0.38 -10000 0 -1 76 76
AKT1 -0.14 0.16 -10000 0 -0.46 20 20
response to starvation -0.019 0.035 -10000 0 -10000 0 0
DLK1 -0.28 0.37 -10000 0 -1 75 75
NKX2-1 -0.18 0.35 -10000 0 -1.1 48 48
ACADM -0.29 0.38 -10000 0 -0.98 89 89
TAT -0.18 0.22 -10000 0 -0.68 44 44
CEBPB 0.004 0.042 -10000 0 -0.49 4 4
CEBPA -0.007 0.098 -10000 0 -0.58 17 17
TTR -0.3 0.41 -10000 0 -1.1 103 103
PKLR -0.43 0.48 -10000 0 -1 185 185
APOA1 -0.38 0.49 -10000 0 -1.2 103 103
CPT1C -0.3 0.4 -10000 0 -1 97 97
ALAS1 -0.12 0.18 -10000 0 -0.81 3 3
TFRC -0.18 0.27 -10000 0 -0.96 27 27
FOXF1 0.012 0.11 0.28 8 -0.56 17 25
NF1 0.014 0.042 -10000 0 -0.58 3 3
HNF1A (dimer) 0.002 0.072 -10000 0 -0.58 6 6
CPT1A -0.28 0.36 -10000 0 -0.98 75 75
HMGCS1 -0.29 0.37 -10000 0 -1 77 77
NR3C1 -0.037 0.13 -10000 0 -0.56 28 28
CPT1B -0.3 0.39 -10000 0 -1 88 88
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.008 0.044 -10000 0 -0.58 1 1
GCK -0.3 0.39 -10000 0 -1 96 96
CREB1 -0.008 0.061 -10000 0 -0.61 2 2
IGFBP1 -0.27 0.4 -10000 0 -0.94 117 117
PDX1 -0.18 0.36 -10000 0 -1.4 38 38
UCP2 -0.29 0.38 -10000 0 -0.96 96 96
ALDOB -0.38 0.49 -10000 0 -1.1 140 140
AFP -0.069 0.17 -10000 0 -0.53 42 42
BDH1 -0.28 0.37 -10000 0 -1 74 74
HADH -0.26 0.36 -10000 0 -1 69 69
F2 -0.42 0.53 -10000 0 -1.3 124 124
HNF1A 0.002 0.072 -10000 0 -0.58 6 6
G6PC -0.032 0.14 -10000 0 -0.71 9 9
SLC2A2 -0.17 0.24 -10000 0 -0.88 18 18
INS 0.016 0.065 0.22 9 -0.47 3 12
FOXA1 -0.071 0.21 0.29 1 -0.57 81 82
FOXA3 -0.033 0.12 -10000 0 -0.53 20 20
FOXA2 -0.31 0.42 -10000 0 -1.1 89 89
ABCC8 -0.29 0.39 -10000 0 -1 80 80
ALB -0.077 0.18 -10000 0 -0.54 37 37
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.01 0.031 -10000 0 -0.52 2 2
EPHB2 0 0.079 -10000 0 -0.56 12 12
EFNB1 0.004 0.072 -10000 0 -0.36 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.063 0.16 -10000 0 -0.49 35 35
Ephrin B2/EPHB1-2 -0.049 0.13 -10000 0 -0.27 136 136
neuron projection morphogenesis -0.084 0.14 -10000 0 -0.47 35 35
Ephrin B1/EPHB1-2/Tiam1 -0.072 0.17 -10000 0 -0.42 63 63
DNM1 -0.007 0.096 -10000 0 -0.5 22 22
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.079 0.23 -10000 0 -0.66 80 80
YES1 -0.12 0.3 -10000 0 -0.89 79 79
Ephrin B1/EPHB1-2/NCK2 -0.043 0.14 -10000 0 -0.34 56 56
PI3K -0.079 0.24 -10000 0 -0.66 83 83
mol:GDP -0.072 0.16 -10000 0 -0.42 63 63
ITGA2B -0.043 0.16 -10000 0 -0.5 63 63
endothelial cell proliferation 0.014 0.019 -10000 0 -0.32 2 2
FYN -0.12 0.3 -10000 0 -0.89 79 79
MAP3K7 -0.088 0.24 -10000 0 -0.7 79 79
FGR -0.13 0.3 -10000 0 -0.88 81 81
TIAM1 -0.044 0.16 -10000 0 -0.52 63 63
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
RGS3 0.011 0 -10000 0 -10000 0 0
cell adhesion -0.097 0.24 -10000 0 -0.63 86 86
LYN -0.12 0.3 -10000 0 -0.89 79 79
Ephrin B1/EPHB1-2/Src Family Kinases -0.11 0.28 -10000 0 -0.83 79 79
Ephrin B1/EPHB1-2 -0.11 0.26 -10000 0 -0.76 79 79
SRC -0.12 0.3 -10000 0 -0.88 79 79
ITGB3 -0.008 0.1 -10000 0 -0.55 21 21
EPHB1 -0.1 0.21 -10000 0 -0.49 139 139
EPHB4 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.014 0.019 -10000 0 -0.32 2 2
alphaIIb/beta3 Integrin -0.037 0.14 -10000 0 -0.37 83 83
BLK -0.14 0.31 -10000 0 -0.9 82 82
HCK -0.12 0.3 -10000 0 -0.88 81 81
regulation of stress fiber formation 0.044 0.13 0.33 56 -10000 0 56
MAPK8 -0.07 0.22 -10000 0 -0.62 81 81
Ephrin B1/EPHB1-2/RGS3 -0.043 0.13 -10000 0 -0.33 57 57
endothelial cell migration -0.072 0.21 -10000 0 -0.6 80 80
NCK2 0.01 0.024 -10000 0 -0.58 1 1
PTPN13 -0.093 0.25 -10000 0 -0.65 97 97
regulation of focal adhesion formation 0.044 0.13 0.33 56 -10000 0 56
chemotaxis 0.043 0.13 0.33 57 -10000 0 57
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
Rac1/GTP -0.085 0.14 -10000 0 -0.48 35 35
angiogenesis -0.11 0.25 -10000 0 -0.75 79 79
LCK -0.13 0.31 -10000 0 -0.9 80 80
Signaling events mediated by the Hedgehog family

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.052 0.22 -10000 0 -0.63 55 55
IHH -0.039 0.17 -10000 0 -0.63 43 43
SHH Np/Cholesterol/GAS1 -0.082 0.16 -10000 0 -0.31 190 190
LRPAP1 0.01 0.024 -10000 0 -0.58 1 1
dorsoventral neural tube patterning 0.081 0.16 0.3 190 -10000 0 190
SMO/beta Arrestin2 -0.038 0.19 -10000 0 -0.64 35 35
SMO -0.046 0.2 -10000 0 -0.67 37 37
AKT1 -0.005 0.11 -10000 0 -0.5 11 11
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.032 0.14 -10000 0 -0.48 54 54
ADRBK1 0.01 0.031 -10000 0 -0.52 2 2
heart looping -0.044 0.2 -10000 0 -0.64 39 39
STIL -0.027 0.16 -10000 0 -0.58 30 30
DHH N/PTCH2 -0.041 0.16 -10000 0 -0.43 78 78
DHH N/PTCH1 -0.047 0.17 -10000 0 -0.44 54 54
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
DHH -0.03 0.14 -10000 0 -0.54 44 44
PTHLH -0.078 0.3 -10000 0 -0.92 54 54
determination of left/right symmetry -0.044 0.2 -10000 0 -0.64 39 39
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
skeletal system development -0.077 0.29 -10000 0 -0.91 54 54
IHH N/Hhip -0.085 0.2 -10000 0 -0.46 128 128
DHH N/Hhip -0.079 0.19 -10000 0 -0.42 132 132
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.044 0.2 -10000 0 -0.64 39 39
pancreas development -0.081 0.21 -10000 0 -0.55 100 100
HHAT 0.004 0.068 -10000 0 -0.58 8 8
PI3K 0.013 0.04 -10000 0 -0.43 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.13 0.24 -10000 0 -0.52 163 163
somite specification -0.044 0.2 -10000 0 -0.64 39 39
SHH Np/Cholesterol/PTCH1 -0.033 0.17 -10000 0 -0.6 32 32
SHH Np/Cholesterol/PTCH2 -0.025 0.12 -10000 0 -0.32 80 80
SHH Np/Cholesterol/Megalin -0.023 0.11 -10000 0 -0.36 36 36
SHH -0.01 0.11 -10000 0 -0.41 40 40
catabolic process -0.033 0.16 -10000 0 -0.43 60 60
SMO/Vitamin D3 -0.041 0.19 -10000 0 -0.63 40 40
SHH Np/Cholesterol/Hhip -0.054 0.15 -10000 0 -0.36 95 95
LRP2 -0.027 0.12 -10000 0 -0.46 43 43
receptor-mediated endocytosis -0.044 0.19 -10000 0 -0.63 37 37
SHH Np/Cholesterol/BOC -0.026 0.12 -10000 0 -0.36 45 45
SHH Np/Cholesterol/CDO -0.008 0.1 -10000 0 -0.36 41 41
mesenchymal cell differentiation 0.054 0.15 0.36 95 -10000 0 95
mol:Vitamin D3 -0.031 0.17 -10000 0 -0.6 32 32
IHH N/PTCH2 -0.044 0.16 -10000 0 -0.44 81 81
CDON -0.001 0.081 -10000 0 -0.52 14 14
IHH N/PTCH1 -0.032 0.17 -10000 0 -0.43 60 60
Megalin/LRPAP1 -0.011 0.087 -10000 0 -0.32 44 44
PTCH2 -0.029 0.14 -10000 0 -0.54 44 44
SHH Np/Cholesterol -0.009 0.083 -10000 0 -0.32 40 40
PTCH1 -0.033 0.16 -10000 0 -0.44 54 54
HHIP -0.081 0.21 -10000 0 -0.55 100 100
TCGA08_retinoblastoma

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
CDKN2B -0.012 0.1 -10000 0 -0.51 25 25
CDKN2C 0.019 0.017 -10000 0 -10000 0 0
CDKN2A -0.07 0.19 -10000 0 -0.5 96 96
CCND2 0.019 0.074 0.2 56 -0.14 28 84
RB1 -0.016 0.079 -10000 0 -0.22 54 54
CDK4 0.027 0.077 0.24 49 -10000 0 49
CDK6 0.026 0.078 0.22 56 -10000 0 56
G1/S progression 0.016 0.079 0.22 54 -10000 0 54
HIF-1-alpha transcription factor network

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
PKM2 -0.23 0.46 -9999 0 -1.1 68 68
HDAC7 0.011 0.025 -9999 0 -0.58 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.33 -9999 0 -0.92 50 50
SMAD4 0.005 0.068 -9999 0 -0.58 8 8
ID2 -0.23 0.46 -9999 0 -1.1 67 67
AP1 -0.013 0.11 -9999 0 -0.39 45 45
ABCG2 -0.26 0.49 -9999 0 -1.2 81 81
HIF1A -0.029 0.11 -9999 0 -0.68 9 9
TFF3 -0.25 0.49 -9999 0 -1.2 86 86
GATA2 -0.021 0.13 -9999 0 -0.56 34 34
AKT1 -0.023 0.088 -9999 0 -0.72 1 1
response to hypoxia -0.037 0.086 -9999 0 -0.25 7 7
MCL1 -0.23 0.46 -9999 0 -1.1 69 69
NDRG1 -0.23 0.46 -9999 0 -1.1 68 68
SERPINE1 -0.24 0.48 -9999 0 -1.2 77 77
FECH -0.23 0.46 -9999 0 -1.1 72 72
FURIN -0.23 0.46 -9999 0 -1.1 70 70
NCOA2 0.004 0.066 -9999 0 -0.57 8 8
EP300 -0.015 0.12 -9999 0 -0.37 20 20
HMOX1 -0.23 0.47 -9999 0 -1.1 72 72
BHLHE40 -0.23 0.46 -9999 0 -1.1 69 69
BHLHE41 -0.24 0.48 -9999 0 -1.2 73 73
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.037 0.11 -9999 0 -0.49 17 17
ENG -0.004 0.13 -9999 0 -0.5 13 13
JUN 0.006 0.052 -9999 0 -0.56 5 5
RORA -0.24 0.48 -9999 0 -1.2 75 75
ABCB1 -0.22 0.39 -9999 0 -1.1 94 94
TFRC -0.23 0.47 -9999 0 -1.1 69 69
CXCR4 -0.24 0.48 -9999 0 -1.2 78 78
TF -0.28 0.5 -9999 0 -1.1 92 92
CITED2 -0.23 0.46 -9999 0 -1.2 66 66
HIF1A/ARNT -0.3 0.51 -9999 0 -1.3 80 80
LDHA -0.036 0.077 -9999 0 -1.1 2 2
ETS1 -0.23 0.47 -9999 0 -1.2 67 67
PGK1 -0.23 0.46 -9999 0 -1.2 66 66
NOS2 -0.28 0.51 -9999 0 -1.2 93 93
ITGB2 -0.24 0.49 -9999 0 -1.2 81 81
ALDOA -0.23 0.46 -9999 0 -1.1 67 67
Cbp/p300/CITED2 -0.22 0.48 -9999 0 -1.2 63 63
FOS -0.026 0.14 -9999 0 -0.54 41 41
HK2 -0.23 0.46 -9999 0 -1.1 73 73
SP1 0.005 0.043 -9999 0 -0.58 1 1
GCK -0.054 0.3 -9999 0 -1.4 21 21
HK1 -0.23 0.46 -9999 0 -1.1 67 67
NPM1 -0.23 0.47 -9999 0 -1.2 68 68
EGLN1 -0.23 0.46 -9999 0 -1.1 67 67
CREB1 0.016 0.035 -9999 0 -0.58 2 2
PGM1 -0.23 0.46 -9999 0 -1.1 73 73
SMAD3 0.005 0.066 -9999 0 -0.57 8 8
EDN1 -0.064 0.28 -9999 0 -1.1 27 27
IGFBP1 -0.28 0.5 -9999 0 -1.1 103 103
VEGFA -0.11 0.34 -9999 0 -0.85 31 31
HIF1A/JAB1 -0.024 0.069 -9999 0 -0.49 10 10
CP -0.29 0.51 -9999 0 -1.2 100 100
CXCL12 -0.24 0.48 -9999 0 -1.2 73 73
COPS5 0.011 0.019 -9999 0 -0.46 1 1
SMAD3/SMAD4 0.007 0.07 -9999 0 -0.42 16 16
BNIP3 -0.26 0.49 -9999 0 -1.2 84 84
EGLN3 -0.24 0.47 -9999 0 -1.2 73 73
CA9 -0.31 0.52 -9999 0 -1.1 118 118
TERT -0.25 0.48 -9999 0 -1.1 83 83
ENO1 -0.23 0.46 -9999 0 -1.1 67 67
PFKL -0.23 0.47 -9999 0 -1.2 67 67
NCOA1 0.011 0.024 -9999 0 -0.58 1 1
ADM -0.23 0.47 -9999 0 -1.1 77 77
ARNT -0.021 0.078 -9999 0 -0.64 1 1
HNF4A 0.004 0.065 -9999 0 -0.58 7 7
ADFP -0.23 0.46 -9999 0 -1.1 76 76
SLC2A1 -0.12 0.34 -9999 0 -0.88 34 34
LEP -0.24 0.47 -9999 0 -1.2 73 73
HIF1A/ARNT/Cbp/p300 -0.2 0.34 -9999 0 -0.95 49 49
EPO -0.094 0.3 -9999 0 -1 12 12
CREBBP -0.013 0.12 -9999 0 -0.36 17 17
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.34 -9999 0 -0.95 45 45
PFKFB3 -0.23 0.46 -9999 0 -1.1 67 67
NT5E -0.24 0.48 -9999 0 -1.2 71 71
Endothelins

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
AKT1 -0.037 0.23 -10000 0 -0.62 54 54
PTK2B 0.01 0.034 -10000 0 -0.59 2 2
mol:Ca2+ -0.027 0.25 -10000 0 -0.94 35 35
EDN1 -0.023 0.17 -10000 0 -0.44 56 56
EDN3 -0.097 0.22 -10000 0 -0.56 116 116
EDN2 -0.065 0.19 -10000 0 -0.53 86 86
HRAS/GDP -0.046 0.19 -10000 0 -0.5 60 60
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.022 0.17 -10000 0 -0.45 50 50
ADCY4 -0.05 0.2 -10000 0 -0.54 59 59
ADCY5 -0.11 0.24 -10000 0 -0.54 95 95
ADCY6 -0.046 0.2 -10000 0 -0.54 55 55
ADCY7 -0.047 0.2 -10000 0 -0.54 57 57
ADCY1 -0.074 0.22 -10000 0 -0.54 74 74
ADCY2 -0.072 0.24 -10000 0 -0.6 72 72
ADCY3 -0.046 0.2 -10000 0 -0.54 55 55
ADCY8 -0.058 0.2 -10000 0 -0.54 58 58
ADCY9 -0.047 0.2 -10000 0 -0.54 56 56
arachidonic acid secretion -0.068 0.2 -10000 0 -0.54 58 58
ETB receptor/Endothelin-1/Gq/GTP -0.011 0.14 -10000 0 -0.47 30 30
GNAO1 -0.045 0.16 -10000 0 -0.49 68 68
HRAS 0.008 0.041 -10000 0 -0.49 4 4
ETA receptor/Endothelin-1/G12/GTP -0.032 0.24 0.35 55 -0.6 49 104
ETA receptor/Endothelin-1/Gs/GTP -0.046 0.24 0.33 55 -0.56 58 113
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.059 0.29 -10000 0 -0.75 67 67
EDNRB -0.009 0.11 -10000 0 -0.57 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.072 0.29 -10000 0 -0.68 86 86
CYSLTR1 -0.066 0.29 -10000 0 -0.72 77 77
SLC9A1 -0.026 0.12 0.19 48 -0.31 49 97
mol:GDP -0.054 0.2 -10000 0 -0.51 65 65
SLC9A3 -0.16 0.32 -10000 0 -0.62 160 160
RAF1 -0.049 0.18 -10000 0 -0.49 52 52
JUN -0.01 0.2 -10000 0 -0.74 28 28
JAK2 -0.048 0.24 -10000 0 -0.6 66 66
mol:IP3 -0.023 0.17 -10000 0 -0.46 45 45
ETA receptor/Endothelin-1 -0.047 0.29 0.42 55 -0.65 64 119
PLCB1 -0.032 0.15 -10000 0 -0.57 45 45
PLCB2 0.004 0.061 -10000 0 -0.52 8 8
ETA receptor/Endothelin-3 -0.099 0.21 -10000 0 -0.45 139 139
FOS -0.052 0.23 -10000 0 -0.82 35 35
Gai/GDP -0.026 0.16 -10000 0 -0.82 20 20
CRK 0.011 0.019 -10000 0 -0.46 1 1
mol:Ca ++ -0.054 0.26 -10000 0 -0.66 68 68
BCAR1 0.008 0.043 -10000 0 -0.52 4 4
PRKCB1 -0.023 0.16 -10000 0 -0.44 45 45
GNAQ 0.006 0.059 -10000 0 -0.58 6 6
GNAZ -0.013 0.11 -10000 0 -0.55 26 26
GNAL -0.018 0.12 -10000 0 -0.51 34 34
Gs family/GDP -0.091 0.17 -10000 0 -0.47 73 73
ETA receptor/Endothelin-1/Gq/GTP -0.016 0.18 -10000 0 -0.49 46 46
MAPK14 -0.012 0.13 -10000 0 -0.46 28 28
TRPC6 -0.032 0.27 -10000 0 -1 35 35
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.019 0.14 -10000 0 -0.44 36 36
ETB receptor/Endothelin-2 -0.053 0.16 -10000 0 -0.39 105 105
ETB receptor/Endothelin-3 -0.077 0.18 -10000 0 -0.41 133 133
ETB receptor/Endothelin-1 -0.02 0.16 -10000 0 -0.41 58 58
MAPK3 -0.051 0.22 -10000 0 -0.68 43 43
MAPK1 -0.051 0.22 -10000 0 -0.69 41 41
Rac1/GDP -0.044 0.19 -10000 0 -0.5 53 53
cAMP biosynthetic process -0.074 0.21 -10000 0 -0.53 74 74
MAPK8 -0.021 0.23 -10000 0 -0.72 39 39
SRC 0.01 0.024 -10000 0 -0.59 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.02 0.12 -10000 0 -0.41 31 31
p130Cas/CRK/Src/PYK2 -0.056 0.22 -10000 0 -0.62 52 52
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.044 0.19 -10000 0 -0.49 59 59
COL1A2 -0.064 0.32 -10000 0 -0.83 66 66
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.076 0.19 -10000 0 -0.41 118 118
mol:DAG -0.024 0.17 -10000 0 -0.46 45 45
MAP2K2 -0.047 0.19 -10000 0 -0.54 47 47
MAP2K1 -0.047 0.19 -10000 0 -0.54 48 48
EDNRA -0.024 0.19 0.22 29 -0.52 55 84
positive regulation of muscle contraction -0.026 0.21 -10000 0 -0.57 48 48
Gq family/GDP -0.082 0.17 -10000 0 -0.56 49 49
HRAS/GTP -0.053 0.18 -10000 0 -0.46 65 65
PRKCH -0.02 0.16 -10000 0 -0.47 44 44
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.018 0.16 -10000 0 -0.49 34 34
PRKCB -0.044 0.2 -10000 0 -0.5 69 69
PRKCE -0.016 0.16 -10000 0 -0.48 36 36
PRKCD -0.017 0.16 -10000 0 -0.47 37 37
PRKCG -0.099 0.2 -10000 0 -0.47 81 81
regulation of vascular smooth muscle contraction -0.062 0.26 -10000 0 -0.94 36 36
PRKCQ -0.048 0.19 -10000 0 -0.5 57 57
PLA2G4A -0.075 0.22 -10000 0 -0.59 58 58
GNA14 -0.006 0.1 -10000 0 -0.56 19 19
GNA15 -0.008 0.1 -10000 0 -0.55 22 22
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 0.007 0.05 -10000 0 -0.54 5 5
Rac1/GTP -0.032 0.24 0.35 55 -0.6 49 104
MMP1 -0.16 0.37 -10000 0 -0.74 146 146
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.2 -9999 0 -0.38 189 189
SMAD6-7/SMURF1 0.019 0.045 -9999 0 -0.38 7 7
NOG -0.024 0.12 -9999 0 -0.47 41 41
SMAD9 -0.064 0.17 -9999 0 -0.53 57 57
SMAD4 0.004 0.068 -9999 0 -0.58 8 8
SMAD5 -0.044 0.14 -9999 0 -0.46 27 27
BMP7/USAG1 -0.17 0.24 -9999 0 -0.44 245 245
SMAD5/SKI -0.036 0.13 -9999 0 -0.45 24 24
SMAD1 0.022 0.045 -9999 0 -0.47 3 3
BMP2 -0.003 0.09 -9999 0 -0.55 16 16
SMAD1/SMAD1/SMAD4 -0.007 0.048 -9999 0 -0.48 3 3
BMPR1A 0.01 0.024 -9999 0 -0.58 1 1
BMPR1B -0.092 0.21 -9999 0 -0.51 119 119
BMPR1A-1B/BAMBI -0.078 0.17 -9999 0 -0.33 175 175
AHSG -0.044 0.15 -9999 0 -0.46 66 66
CER1 -0.006 0.067 -9999 0 -0.46 13 13
BMP2-4/CER1 -0.011 0.1 -9999 0 -0.32 53 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.05 0.14 -9999 0 -0.42 46 46
BMP2-4 (homodimer) -0.011 0.1 -9999 0 -0.38 42 42
RGMB -0.013 0.1 -9999 0 -0.46 31 31
BMP6/BMPR2/BMPR1A-1B -0.044 0.14 -9999 0 -0.34 68 68
RGMA -0.074 0.2 -9999 0 -0.54 93 93
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.05 0.13 -9999 0 -0.39 44 44
BMP2-4/USAG1 -0.073 0.17 -9999 0 -0.35 155 155
SMAD6/SMURF1/SMAD5 -0.036 0.13 -9999 0 -0.45 25 25
SOSTDC1 -0.1 0.23 -9999 0 -0.56 124 124
BMP7/BMPR2/BMPR1A-1B -0.11 0.19 -9999 0 -0.38 151 151
SKI 0.011 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.009 0.1 -9999 0 -0.52 23 23
HFE2 -0.001 0.042 -9999 0 -0.46 5 5
ZFYVE16 -0.004 0.096 -9999 0 -0.58 16 16
MAP3K7 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.02 0.13 -9999 0 -0.34 71 71
SMAD5/SMAD5/SMAD4 -0.04 0.13 -9999 0 -0.45 26 26
MAPK1 0.01 0.024 -9999 0 -0.58 1 1
TAK1/TAB family -0.057 0.098 -9999 0 -0.38 29 29
BMP7 (homodimer) -0.13 0.24 -9999 0 -0.54 155 155
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA -0.037 0.13 -9999 0 -0.34 88 88
SMAD1/SKI 0.027 0.043 -9999 0 -0.44 3 3
SMAD6 0.006 0.055 -9999 0 -0.54 6 6
CTDSP2 0.011 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.034 0.13 -9999 0 -0.3 103 103
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.086 0.21 -9999 0 -0.54 106 106
BMPR2 (homodimer) 0.007 0.054 -9999 0 -0.58 5 5
GADD34/PP1CA 0.013 0.062 -9999 0 -0.35 17 17
BMPR1A-1B (homodimer) -0.059 0.15 -9999 0 -0.36 120 120
CHRDL1 -0.16 0.25 -9999 0 -0.52 199 199
ENDOFIN/SMAD1 0.019 0.071 -9999 0 -0.51 5 5
SMAD6-7/SMURF1/SMAD1 -0.001 0.05 -9999 0 -0.54 3 3
SMAD6/SMURF1 0.011 0 -9999 0 -10000 0 0
BAMBI -0.049 0.17 -9999 0 -0.53 68 68
SMURF2 0.007 0.05 -9999 0 -0.53 5 5
BMP2-4/CHRDL1 -0.11 0.18 -9999 0 -0.33 227 227
BMP2-4/GREM1 -0.061 0.16 -9999 0 -0.34 140 140
SMAD7 0.009 0.034 -9999 0 -0.58 2 2
SMAD8A/SMAD8A/SMAD4 -0.059 0.16 -9999 0 -0.49 62 62
SMAD1/SMAD6 0.027 0.043 -9999 0 -0.44 3 3
TAK1/SMAD6 0.017 0 -9999 0 -10000 0 0
BMP7 -0.13 0.24 -9999 0 -0.54 155 155
BMP6 -0.009 0.1 -9999 0 -0.52 23 23
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.04 0.12 -9999 0 -0.36 45 45
PPM1A 0.011 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.025 0.054 -9999 0 -0.48 4 4
SMAD7/SMURF1 0.016 0.025 -9999 0 -0.42 2 2
CTDSPL 0.011 0 -9999 0 -10000 0 0
PPP1CA 0.011 0 -9999 0 -10000 0 0
XIAP 0.01 0.024 -9999 0 -0.58 1 1
CTDSP1 0.01 0.024 -9999 0 -0.58 1 1
PPP1R15A 0.011 0.019 -9999 0 -0.46 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.082 0.18 -9999 0 -0.49 71 71
CHRD -0.02 0.13 -9999 0 -0.55 34 34
BMPR2 0.007 0.054 -9999 0 -0.58 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.057 0.14 -9999 0 -0.43 44 44
BMP4 -0.012 0.11 -9999 0 -0.5 28 28
FST -0.052 0.18 -9999 0 -0.53 71 71
BMP2-4/NOG -0.022 0.12 -9999 0 -0.31 79 79
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.1 0.18 -9999 0 -0.35 151 151
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0.031 -10000 0 -0.52 2 2
LAT2 -0.066 0.17 -10000 0 -0.49 59 59
AP1 -0.11 0.2 -10000 0 -0.6 73 73
mol:PIP3 -0.085 0.22 -10000 0 -0.57 74 74
IKBKB -0.036 0.13 0.15 14 -0.31 79 93
AKT1 -0.054 0.16 -10000 0 -0.47 45 45
IKBKG -0.036 0.13 0.15 14 -0.31 80 94
MS4A2 -0.082 0.21 -10000 0 -0.54 102 102
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.034 -10000 0 -0.59 2 2
MAP3K1 -0.055 0.19 -10000 0 -0.51 65 65
mol:Ca2+ -0.059 0.16 -10000 0 -0.41 74 74
LYN 0.009 0.006 -10000 0 -10000 0 0
CBLB -0.063 0.17 -10000 0 -0.42 83 83
SHC1 0.011 0 -10000 0 -10000 0 0
RasGAP/p62DOK 0.011 0.054 -10000 0 -0.32 5 5
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.018 0.13 -10000 0 -0.58 30 30
PLD2 -0.079 0.18 -10000 0 -0.4 102 102
PTPN13 -0.098 0.2 -10000 0 -0.58 58 58
PTPN11 0.003 0.056 -10000 0 -0.6 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.028 0.13 -10000 0 -0.36 44 44
SYK 0.008 0.02 -10000 0 -0.46 1 1
GRB2 0.011 0.001 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.21 -10000 0 -0.59 75 75
LAT -0.072 0.18 -10000 0 -0.48 66 66
PAK2 -0.067 0.21 -10000 0 -0.56 70 70
NFATC2 -0.084 0.18 -10000 0 -0.65 49 49
HRAS -0.08 0.23 -10000 0 -0.61 72 72
GAB2 0.009 0.034 -10000 0 -0.58 2 2
PLA2G1B 0.03 0.026 -10000 0 -10000 0 0
Fc epsilon R1 -0.12 0.2 -10000 0 -0.4 189 189
Antigen/IgE/Fc epsilon R1 -0.11 0.19 -10000 0 -0.36 189 189
mol:GDP -0.091 0.25 -10000 0 -0.67 72 72
JUN 0.007 0.052 -10000 0 -0.56 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.042 -10000 0 -0.59 3 3
FOS -0.026 0.14 -10000 0 -0.54 41 41
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.071 0.18 -10000 0 -0.43 84 84
CHUK -0.037 0.13 0.15 14 -0.31 78 92
KLRG1 -0.067 0.17 -10000 0 -0.42 73 73
VAV1 -0.081 0.2 -10000 0 -0.53 73 73
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.061 0.17 -10000 0 -0.47 59 59
negative regulation of mast cell degranulation -0.071 0.17 -10000 0 -0.43 77 77
BTK -0.095 0.26 -10000 0 -0.71 71 71
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.25 -10000 0 -0.55 112 112
GAB2/PI3K/SHP2 -0.093 0.16 -10000 0 -0.5 49 49
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.062 0.16 -10000 0 -0.45 58 58
RAF1 0.024 0.025 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.15 0.26 -10000 0 -0.47 189 189
FCER1G -0.023 0.14 -10000 0 -0.54 39 39
FCER1A -0.08 0.21 -10000 0 -0.56 95 95
Antigen/IgE/Fc epsilon R1/Fyn -0.09 0.19 -10000 0 -0.38 138 138
MAPK3 0.03 0.026 -10000 0 -10000 0 0
MAPK1 0.03 0.026 -10000 0 -10000 0 0
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.006 0.073 -10000 0 -0.5 5 5
DUSP1 -0.006 0.091 -10000 0 -0.47 22 22
NF-kappa-B/RelA -0.039 0.064 -10000 0 -0.22 22 22
actin cytoskeleton reorganization -0.063 0.18 -10000 0 -0.59 41 41
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.1 0.19 -10000 0 -0.56 69 69
FER -0.066 0.17 -10000 0 -0.48 60 60
RELA 0.011 0 -10000 0 -10000 0 0
ITK -0.051 0.13 -10000 0 -0.45 46 46
SOS1 0.01 0.024 -10000 0 -0.58 1 1
PLCG1 -0.088 0.25 -10000 0 -0.67 71 71
cytokine secretion -0.029 0.046 -10000 0 -10000 0 0
SPHK1 -0.082 0.19 -10000 0 -0.46 88 88
PTK2 -0.066 0.19 -10000 0 -0.64 40 40
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.12 0.21 -10000 0 -0.61 73 73
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.077 0.21 -10000 0 -0.55 74 74
MAP2K2 0.027 0.026 -10000 0 -10000 0 0
MAP2K1 0.026 0.03 -10000 0 -10000 0 0
MAP2K7 0.01 0.024 -10000 0 -0.58 1 1
KLRG1/SHP2 -0.063 0.16 -10000 0 -0.46 54 54
MAP2K4 0.008 0.078 -10000 0 -0.94 4 4
Fc epsilon R1/FcgammaRIIB -0.14 0.26 -10000 0 -0.5 169 169
mol:Choline -0.078 0.18 -10000 0 -0.39 102 102
SHC/Grb2/SOS1 -0.049 0.16 -10000 0 -0.51 41 41
FYN 0.005 0.06 -10000 0 -0.55 7 7
DOK1 0.011 0 -10000 0 -10000 0 0
PXN -0.055 0.17 -10000 0 -0.58 40 40
HCLS1 -0.068 0.18 -10000 0 -0.46 74 74
PRKCB -0.062 0.18 -10000 0 -0.44 84 84
FCGR2B -0.087 0.21 -10000 0 -0.54 109 109
IGHE -0.003 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.073 0.18 -10000 0 -0.44 77 77
LCP2 -0.016 0.12 -10000 0 -0.55 29 29
PLA2G4A -0.14 0.22 -10000 0 -0.46 147 147
RASA1 0.009 0.034 -10000 0 -0.58 2 2
mol:Phosphatidic acid -0.078 0.18 -10000 0 -0.39 102 102
IKK complex -0.015 0.1 0.15 14 -0.24 59 73
WIPF1 -0.001 0.081 -10000 0 -0.55 13 13
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.039 0.17 -10000 0 -0.62 48 48
NFATC2 -0.092 0.26 -10000 0 -0.67 67 67
NFATC3 -0.019 0.077 -10000 0 -0.29 3 3
CD40LG -0.28 0.42 -10000 0 -1 111 111
ITCH 0.028 0.084 -10000 0 -0.81 5 5
CBLB 0.029 0.08 -10000 0 -0.85 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.28 0.46 -10000 0 -1.2 98 98
JUNB 0.007 0.05 -10000 0 -0.53 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.059 -10000 0 -0.37 14 14
T cell anergy 0.005 0.1 -10000 0 -0.55 14 14
TLE4 -0.057 0.21 -10000 0 -0.68 39 39
Jun/NFAT1-c-4/p21SNFT -0.18 0.37 -10000 0 -1 69 69
AP-1/NFAT1-c-4 -0.3 0.48 -10000 0 -1.1 110 110
IKZF1 -0.076 0.26 -10000 0 -0.78 54 54
T-helper 2 cell differentiation -0.13 0.26 -10000 0 -0.79 55 55
AP-1/NFAT1 -0.094 0.21 -10000 0 -0.55 67 67
CALM1 0.019 0.033 -10000 0 -0.3 3 3
EGR2 -0.14 0.36 -10000 0 -1.2 43 43
EGR3 -0.15 0.38 -10000 0 -1.2 51 51
NFAT1/FOXP3 -0.095 0.27 -10000 0 -0.74 69 69
EGR1 -0.01 0.1 -10000 0 -0.5 25 25
JUN -0.009 0.059 -10000 0 -0.58 5 5
EGR4 -0.055 0.17 -10000 0 -0.51 75 75
mol:Ca2+ 0.007 0.035 -10000 0 -0.32 3 3
GBP3 -0.11 0.31 -10000 0 -0.8 86 86
FOSL1 -0.024 0.13 -10000 0 -0.51 41 41
NFAT1-c-4/MAF/IRF4 -0.18 0.38 -10000 0 -1 77 77
DGKA -0.053 0.2 -10000 0 -0.65 36 36
CREM 0.011 0.019 -10000 0 -0.46 1 1
NFAT1-c-4/PPARG -0.15 0.35 -10000 0 -0.97 64 64
CTLA4 -0.097 0.29 -10000 0 -0.77 76 76
NFAT1-c-4 (dimer)/EGR1 -0.16 0.36 -10000 0 -0.98 68 68
NFAT1-c-4 (dimer)/EGR4 -0.19 0.37 -10000 0 -1 70 70
FOS -0.042 0.14 -10000 0 -0.55 41 41
IFNG -0.24 0.4 -10000 0 -0.98 110 110
T cell activation -0.11 0.2 -10000 0 -0.72 20 20
MAF 0.001 0.074 -10000 0 -0.54 11 11
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.12 0.3 0.91 48 -10000 0 48
TNF -0.18 0.35 -10000 0 -0.93 75 75
FASLG -0.24 0.51 -10000 0 -1.4 77 77
TBX21 -0.062 0.19 -10000 0 -0.56 73 73
BATF3 -0.006 0.093 -10000 0 -0.51 20 20
PRKCQ -0.052 0.18 -10000 0 -0.59 62 62
PTPN1 -0.049 0.19 -10000 0 -0.62 34 34
NFAT1-c-4/ICER1 -0.15 0.35 -10000 0 -1 59 59
GATA3 -0.017 0.12 -10000 0 -0.52 32 32
T-helper 1 cell differentiation -0.22 0.4 -10000 0 -0.94 112 112
IL2RA -0.27 0.42 -10000 0 -1.1 100 100
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.051 0.19 -10000 0 -0.63 34 34
E2F1 0.014 0.036 -10000 0 -0.49 3 3
PPARG 0.004 0.068 -10000 0 -0.58 8 8
SLC3A2 -0.049 0.19 -10000 0 -0.64 28 28
IRF4 -0.075 0.2 -10000 0 -0.54 95 95
PTGS2 -0.3 0.44 -10000 0 -0.98 133 133
CSF2 -0.31 0.44 -10000 0 -0.98 134 134
JunB/Fra1/NFAT1-c-4 -0.16 0.34 -10000 0 -0.97 62 62
IL4 -0.13 0.27 -10000 0 -0.84 54 54
IL5 -0.27 0.4 -10000 0 -0.98 95 95
IL2 -0.11 0.2 -10000 0 -0.75 18 18
IL3 -0.064 0.099 -10000 0 -0.79 7 7
RNF128 0.025 0.091 -10000 0 -0.63 11 11
NFATC1 -0.12 0.3 -10000 0 -0.93 47 47
CDK4 0.082 0.18 0.59 26 -10000 0 26
PTPRK -0.049 0.19 -10000 0 -0.63 32 32
IL8 -0.31 0.45 -10000 0 -1 130 130
POU2F1 0.002 0.071 -10000 0 -0.55 10 10
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.06 0.16 0.4 107 -10000 0 107
KIRREL -0.032 0.15 -10000 0 -0.58 39 39
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.06 0.17 -10000 0 -0.4 107 107
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
ARRB2 0.011 0 -10000 0 -10000 0 0
WASL 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.057 0.16 -10000 0 -0.38 89 89
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.023 0.11 -10000 0 -0.35 37 37
FYN -0.042 0.13 -10000 0 -0.34 67 67
mol:Ca2+ -0.041 0.14 -10000 0 -0.37 63 63
mol:DAG -0.041 0.14 -10000 0 -0.37 63 63
NPHS2 -0.02 0.09 -10000 0 -0.47 22 22
mol:IP3 -0.041 0.14 -10000 0 -0.37 63 63
regulation of endocytosis -0.032 0.12 -10000 0 -0.32 63 63
Nephrin/NEPH1/podocin/Cholesterol -0.047 0.13 -10000 0 -0.3 121 121
establishment of cell polarity -0.06 0.16 -10000 0 -0.4 107 107
Nephrin/NEPH1/podocin/NCK1-2 -0.031 0.13 -10000 0 -0.48 18 18
Nephrin/NEPH1/beta Arrestin2 -0.032 0.12 -10000 0 -0.33 63 63
NPHS1 -0.058 0.17 -10000 0 -0.51 75 75
Nephrin/NEPH1/podocin -0.042 0.13 -10000 0 -0.35 67 67
TJP1 0.01 0.024 -10000 0 -0.58 1 1
NCK1 0.009 0.034 -10000 0 -0.58 2 2
NCK2 0.01 0.024 -10000 0 -0.58 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.041 0.14 -10000 0 -0.37 63 63
CD2AP -0.016 0.12 -10000 0 -0.58 28 28
Nephrin/NEPH1/podocin/GRB2 -0.04 0.14 -10000 0 -0.36 63 63
GRB2 0.011 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.053 0.15 -10000 0 -0.38 78 78
cytoskeleton organization -0.027 0.13 -10000 0 -0.41 41 41
Nephrin/NEPH1 -0.041 0.12 -10000 0 -0.28 107 107
Nephrin/NEPH1/ZO-1 -0.04 0.14 -10000 0 -0.32 107 107
Reelin signaling pathway

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
CDK5R1/CDK5 0.015 0.023 -9999 0 -0.32 3 3
VLDLR -0.041 0.16 -9999 0 -0.55 57 57
CRKL 0.011 0 -9999 0 -10000 0 0
LRPAP1 0.01 0.024 -9999 0 -0.58 1 1
FYN 0.005 0.06 -9999 0 -0.55 7 7
ITGA3 0.008 0.043 -9999 0 -0.52 4 4
RELN/VLDLR/Fyn -0.079 0.17 -9999 0 -0.4 101 101
MAPK8IP1/MKK7/MAP3K11/JNK1 0.021 0.068 -9999 0 -0.89 1 1
AKT1 -0.071 0.15 -9999 0 -0.47 34 34
MAP2K7 0.01 0.024 -9999 0 -0.58 1 1
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
DAB1 -0.081 0.2 -9999 0 -0.52 104 104
RELN/LRP8/DAB1 -0.091 0.17 -9999 0 -0.32 200 200
LRPAP1/LRP8 0.014 0.036 -9999 0 -0.42 4 4
RELN/LRP8/DAB1/Fyn -0.083 0.16 -9999 0 -0.36 115 115
DAB1/alpha3/beta1 Integrin -0.11 0.16 -9999 0 -0.5 49 49
long-term memory -0.11 0.2 -9999 0 -0.53 60 60
DAB1/LIS1 -0.11 0.16 -9999 0 -0.52 47 47
DAB1/CRLK/C3G -0.11 0.16 -9999 0 -0.5 48 48
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
DAB1/NCK2 -0.12 0.16 -9999 0 -0.52 48 48
ARHGEF2 0.011 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.02 0.11 -9999 0 -0.48 35 35
CDK5R1 0.009 0.033 -9999 0 -0.46 3 3
RELN -0.096 0.22 -9999 0 -0.52 121 121
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
RELN/LRP8/Fyn -0.049 0.14 -9999 0 -0.36 70 70
GRIN2A/RELN/LRP8/DAB1/Fyn -0.093 0.18 -9999 0 -0.38 131 131
MAPK8 0.01 0.024 -9999 0 -0.58 1 1
RELN/VLDLR/DAB1 -0.12 0.19 -9999 0 -0.34 235 235
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.11 0.19 -9999 0 -0.38 158 158
RELN/LRP8 -0.046 0.14 -9999 0 -0.31 125 125
GRIN2B/RELN/LRP8/DAB1/Fyn -0.1 0.19 -9999 0 -0.38 150 150
PI3K 0.013 0.04 -9999 0 -0.43 5 5
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.032 -9999 0 -0.37 4 4
RAP1A -0.076 0.16 -9999 0 -0.47 48 48
PAFAH1B1 0.011 0 -9999 0 -10000 0 0
MAPK8IP1 -0.01 0.11 -9999 0 -0.53 24 24
CRLK/C3G 0.016 0.018 -9999 0 -0.42 1 1
GRIN2B -0.038 0.16 -9999 0 -0.56 52 52
NCK2 0.01 0.024 -9999 0 -0.58 1 1
neuron differentiation -0.036 0.12 -9999 0 -0.38 28 28
neuron adhesion -0.064 0.16 -9999 0 -0.48 37 37
LRP8 0.008 0.042 -9999 0 -0.58 3 3
GSK3B -0.062 0.14 -9999 0 -0.45 36 36
RELN/VLDLR/DAB1/Fyn -0.11 0.19 -9999 0 -0.38 147 147
MAP3K11 0.01 0.024 -9999 0 -0.58 1 1
RELN/VLDLR/DAB1/P13K -0.081 0.15 -9999 0 -0.32 146 146
CDK5 0.011 0 -9999 0 -10000 0 0
MAPT -0.063 0.18 -9999 0 -0.46 103 103
neuron migration -0.065 0.16 -9999 0 -0.46 39 39
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.037 0.12 -9999 0 -0.38 28 28
RELN/VLDLR -0.063 0.16 -9999 0 -0.35 99 99
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.02 0.085 -9999 0 -0.34 33 33
NFATC2 -0.035 0.11 -9999 0 -0.39 52 52
NFATC3 -0.002 0.033 -9999 0 -10000 0 0
CD40LG -0.18 0.32 -9999 0 -0.72 111 111
PTGS2 -0.2 0.33 -9999 0 -0.69 145 145
JUNB 0.007 0.05 -9999 0 -0.53 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.01 0.015 -9999 0 -10000 0 0
CALM1 0.006 0.011 -9999 0 -10000 0 0
JUN 0.001 0.053 -9999 0 -0.57 5 5
mol:Ca2+ -0.009 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.007 -9999 0 -10000 0 0
FOSL1 -0.024 0.13 -9999 0 -0.51 41 41
CREM 0.011 0.019 -9999 0 -0.46 1 1
Jun/NFAT1-c-4/p21SNFT -0.1 0.2 -9999 0 -0.52 74 74
FOS -0.032 0.14 -9999 0 -0.54 41 41
IFNG -0.19 0.33 -9999 0 -0.67 152 152
AP-1/NFAT1-c-4 -0.2 0.35 -9999 0 -0.74 132 132
FASLG -0.19 0.32 -9999 0 -0.7 130 130
NFAT1-c-4/ICER1 -0.064 0.14 -9999 0 -0.4 58 58
IL2RA -0.18 0.33 -9999 0 -0.76 107 107
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.21 0.34 -9999 0 -0.69 154 154
JunB/Fra1/NFAT1-c-4 -0.077 0.15 -9999 0 -0.4 75 75
IL4 -0.16 0.28 -9999 0 -0.63 117 117
IL2 -0.007 0.024 -9999 0 -10000 0 0
IL3 -0.031 0.092 -9999 0 -0.84 7 7
FKBP1A 0.011 0 -9999 0 -10000 0 0
BATF3 -0.006 0.093 -9999 0 -0.51 20 20
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.002 0.071 -9999 0 -0.55 10 10
p75(NTR)-mediated 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
Sortilin/TRAF6 0.016 0.025 -10000 0 -0.42 2 2
Necdin/E2F1 0.006 0.065 -10000 0 -0.37 17 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.056 0.16 -10000 0 -0.36 107 107
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.2 -10000 0 -0.38 181 181
NT-4/5 (dimer)/p75(NTR) -0.066 0.16 -10000 0 -0.37 124 124
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
AKT1 -0.042 0.14 -10000 0 -0.34 88 88
IKBKG 0.01 0.024 -10000 0 -0.58 1 1
BDNF -0.021 0.13 -10000 0 -0.53 36 36
MGDIs/NGR/p75(NTR)/LINGO1 -0.062 0.16 -10000 0 -0.42 62 62
FURIN 0.01 0.031 -10000 0 -0.52 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.053 0.15 -10000 0 -0.33 131 131
LINGO1 -0.023 0.12 -10000 0 -0.47 44 44
Sortilin/TRAF6/NRIF -0.008 0.051 -10000 0 -0.8 1 1
proBDNF (dimer) -0.021 0.13 -10000 0 -0.53 36 36
NTRK1 -0.037 0.15 -10000 0 -0.53 53 53
RTN4R -0.003 0.085 -10000 0 -0.48 18 18
neuron apoptosis -0.06 0.17 -10000 0 -0.59 26 26
IRAK1 0.01 0.031 -10000 0 -0.52 2 2
SHC1 -0.059 0.16 -10000 0 -0.35 132 132
ARHGDIA 0.008 0.042 -10000 0 -0.58 3 3
RhoA/GTP 0.008 0.018 -10000 0 -0.43 1 1
Gamma Secretase 0.03 0.035 -10000 0 -0.3 7 7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.053 0.16 -10000 0 -0.38 89 89
MAGEH1 0.001 0.078 -10000 0 -0.57 11 11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.053 0.16 -10000 0 -0.39 89 89
Mammalian IAPs/DIABLO 0.006 0.1 -10000 0 -0.45 22 22
proNGF (dimer) -0.032 0.15 -10000 0 -0.52 48 48
MAGED1 0.011 0 -10000 0 -10000 0 0
APP 0.01 0.024 -10000 0 -0.58 1 1
NT-4/5 (dimer) -0.013 0.089 -10000 0 -0.46 23 23
ZNF274 0.002 0.076 -10000 0 -0.58 10 10
RhoA/GDP/RHOGDI -0.046 0.14 -10000 0 -0.34 86 86
NGF -0.032 0.15 -10000 0 -0.53 48 48
cell cycle arrest -0.051 0.14 -10000 0 -0.34 82 82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.024 0.11 -10000 0 -0.31 24 24
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.049 0.14 -10000 0 -0.38 49 49
NCSTN 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.078 0.18 -10000 0 -0.37 154 154
PSENEN 0.01 0.024 -10000 0 -0.58 1 1
mol:ceramide -0.048 0.15 -10000 0 -0.37 82 82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.098 -10000 0 -0.44 8 8
p75(NTR)/beta APP -0.05 0.15 -10000 0 -0.36 107 107
BEX1 -0.058 0.17 -10000 0 -0.5 79 79
mol:GDP -0.067 0.16 -10000 0 -0.36 132 132
NGF (dimer) -0.11 0.18 -10000 0 -0.38 144 144
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.05 0.15 -10000 0 -0.39 63 63
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
RAC1/GTP -0.05 0.14 -10000 0 -0.35 82 82
MYD88 0.011 0 -10000 0 -10000 0 0
CHUK 0.007 0.048 -10000 0 -0.58 4 4
NGF (dimer)/p75(NTR)/PKA -0.078 0.18 -10000 0 -0.38 154 154
RHOB 0.009 0.039 -10000 0 -0.54 3 3
RHOA 0.01 0.024 -10000 0 -0.58 1 1
MAGE-G1/E2F1 0.015 0.026 -10000 0 -0.36 3 3
NT3 (dimer) -0.018 0.12 -10000 0 -0.53 33 33
TP53 -0.061 0.16 -10000 0 -0.55 20 20
PRDM4 -0.048 0.15 -10000 0 -0.37 82 82
BDNF (dimer) -0.18 0.22 -10000 0 -0.43 212 212
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
SORT1 0.01 0.024 -10000 0 -0.58 1 1
activation of caspase activity -0.058 0.16 -10000 0 -0.36 107 107
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.047 0.15 -10000 0 -0.37 83 83
RHOC 0.011 0 -10000 0 -10000 0 0
XIAP 0.01 0.024 -10000 0 -0.58 1 1
MAPK10 -0.042 0.16 -10000 0 -0.5 31 31
DIABLO 0.011 0 -10000 0 -10000 0 0
SMPD2 -0.048 0.15 -10000 0 -0.37 82 82
APH1B 0.006 0.059 -10000 0 -0.58 6 6
APH1A 0.011 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.06 0.16 -10000 0 -0.36 132 132
PSEN1 0.011 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.014 0.036 -10000 0 -0.42 4 4
NT3 (dimer)/p75(NTR) -0.07 0.17 -10000 0 -0.39 128 128
MAPK8 -0.026 0.14 -10000 0 -0.52 17 17
MAPK9 -0.025 0.14 -10000 0 -0.52 17 17
APAF1 0.008 0.042 -10000 0 -0.58 3 3
NTF3 -0.018 0.12 -10000 0 -0.53 33 33
NTF4 -0.013 0.09 -10000 0 -0.46 23 23
NDN -0.001 0.082 -10000 0 -0.53 14 14
RAC1/GDP 0.009 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.074 0.14 -10000 0 -0.47 33 33
p75 CTF/Sortilin/TRAF6/NRIF 0.022 0.061 -10000 0 -0.37 12 12
RhoA-B-C/GTP -0.078 0.18 -10000 0 -0.37 154 154
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.14 -10000 0 -0.58 15 15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.14 -10000 0 -0.37 61 61
PRKACB -0.02 0.13 -10000 0 -0.57 33 33
proBDNF (dimer)/p75 ECD -0.008 0.097 -10000 0 -0.38 38 38
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.53 31 31
BIRC2 -0.001 0.086 -10000 0 -0.58 13 13
neuron projection morphogenesis -0.065 0.16 0.19 18 -0.39 84 102
BAD -0.027 0.15 -10000 0 -0.49 22 22
RIPK2 0.011 0 -10000 0 -10000 0 0
NGFR -0.08 0.2 -10000 0 -0.51 106 106
CYCS -0.047 0.15 -10000 0 -0.36 95 95
ADAM17 0.009 0.034 -10000 0 -0.58 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.047 0.15 -10000 0 -0.37 83 83
BCL2L11 -0.026 0.15 -10000 0 -0.49 22 22
BDNF (dimer)/p75(NTR) -0.071 0.18 -10000 0 -0.39 131 131
PI3K -0.049 0.15 -10000 0 -0.36 87 87
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.047 0.15 -10000 0 -0.37 82 82
NDNL2 0.011 0 -10000 0 -10000 0 0
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKCI 0.008 0.042 -10000 0 -0.58 3 3
NGF (dimer)/p75(NTR) -0.079 0.19 -10000 0 -0.42 132 132
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.047 0.15 -10000 0 -0.37 82 82
TRAF6 0.01 0.024 -10000 0 -0.58 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
PLG -0.04 0.16 -10000 0 -0.58 46 46
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.057 0.16 -10000 0 -0.42 65 65
SQSTM1 0.011 0 -10000 0 -10000 0 0
NGFRAP1 -0.023 0.14 -10000 0 -0.58 35 35
CASP3 -0.023 0.14 -10000 0 -0.45 22 22
E2F1 0.009 0.036 -10000 0 -0.5 3 3
CASP9 0.01 0.024 -10000 0 -0.58 1 1
IKK complex -0.06 0.12 -10000 0 -0.52 20 20
NGF (dimer)/TRKA -0.049 0.16 -10000 0 -0.41 91 91
MMP7 -0.14 0.24 -10000 0 -0.52 170 170
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.044 0.15 -10000 0 -0.36 89 89
MMP3 -0.13 0.24 -10000 0 -0.54 161 161
APAF-1/Caspase 9 -0.067 0.14 -10000 0 -0.57 25 25
TCGA08_p53

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
CDKN2A -0.051 0.14 -10000 0 -0.37 96 96
TP53 -0.048 0.11 0.25 1 -0.36 56 57
Senescence -0.048 0.11 0.25 1 -0.36 56 57
Apoptosis -0.048 0.11 0.25 1 -0.36 56 57
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.031 0.084 0.26 41 -0.34 4 45
MDM4 0.01 0.031 -10000 0 -0.52 2 2
Thromboxane A2 receptor signaling

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
TGM2 -0.005 0.093 -10000 0 -0.55 17 17
GNB1/GNG2 -0.054 0.07 -10000 0 -0.2 84 84
AKT1 -0.024 0.093 -10000 0 -0.21 60 60
EGF -0.18 0.25 -10000 0 -0.51 222 222
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.034 0.12 -10000 0 -0.41 27 27
mol:Ca2+ -0.049 0.13 -10000 0 -0.3 86 86
LYN -0.018 0.095 -10000 0 -0.42 10 10
RhoA/GTP -0.031 0.046 -10000 0 -0.14 46 46
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.054 0.14 -10000 0 -0.35 81 81
GNG2 0.003 0.067 -10000 0 -0.54 9 9
ARRB2 0.011 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.006 0.11 -10000 0 -0.47 24 24
G beta5/gamma2 -0.069 0.093 -10000 0 -0.26 88 88
PRKCH -0.055 0.15 -10000 0 -0.35 83 83
DNM1 -0.007 0.096 -10000 0 -0.5 22 22
TXA2/TP beta/beta Arrestin3 -0.016 0.037 -10000 0 -0.25 7 7
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.12 0.23 -10000 0 -0.51 155 155
G12 family/GTP -0.075 0.11 -10000 0 -0.31 84 84
ADRBK1 0.01 0.031 -10000 0 -0.52 2 2
ADRBK2 -0.002 0.088 -10000 0 -0.58 14 14
RhoA/GTP/ROCK1 0.006 0.056 -10000 0 -0.39 11 11
mol:GDP 0.046 0.11 0.32 47 -10000 0 47
mol:NADP -0.008 0.1 -10000 0 -0.54 21 21
RAB11A 0.011 0 -10000 0 -10000 0 0
PRKG1 -0.025 0.14 -10000 0 -0.56 38 38
mol:IP3 -0.064 0.16 -10000 0 -0.38 86 86
cell morphogenesis 0.006 0.056 -10000 0 -0.39 11 11
PLCB2 -0.09 0.21 -10000 0 -0.52 85 85
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.073 0.14 -10000 0 -0.4 52 52
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.03 0.12 -10000 0 -0.44 21 21
RHOA 0.01 0.024 -10000 0 -0.58 1 1
PTGIR -0.007 0.095 -10000 0 -0.51 21 21
PRKCB1 -0.061 0.15 -10000 0 -0.37 84 84
GNAQ 0.006 0.059 -10000 0 -0.58 6 6
mol:L-citrulline -0.008 0.1 -10000 0 -0.54 21 21
TXA2/TXA2-R family -0.093 0.21 -10000 0 -0.53 87 87
LCK -0.036 0.12 -10000 0 -0.42 24 24
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.05 0.097 -10000 0 -0.5 9 9
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.041 -10000 0 -0.3 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.047 0.095 -10000 0 -0.49 9 9
MAPK14 -0.03 0.1 -10000 0 -0.23 74 74
TGM2/GTP -0.078 0.18 -10000 0 -0.45 84 84
MAPK11 -0.034 0.1 -10000 0 -0.24 78 78
ARHGEF1 -0.024 0.08 -10000 0 -0.18 63 63
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.066 0.16 -10000 0 -0.39 87 87
RAB11/GDP 0.012 0.001 -10000 0 -10000 0 0
ICAM1 -0.043 0.12 -10000 0 -0.29 75 75
cAMP biosynthetic process -0.067 0.15 -10000 0 -0.37 85 85
Gq family/GTP/EBP50 0.004 0.079 -10000 0 -0.34 20 20
actin cytoskeleton reorganization 0.006 0.056 -10000 0 -0.39 11 11
SRC -0.019 0.096 -10000 0 -0.42 11 11
GNB5 0.007 0.048 -10000 0 -0.58 4 4
GNB1 0.011 0 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.12 -10000 0 -0.33 58 58
VCAM1 -0.052 0.14 -10000 0 -0.33 88 88
TP beta/Gq family/GDP/G beta5/gamma2 -0.006 0.11 -10000 0 -0.47 24 24
platelet activation -0.043 0.14 -10000 0 -0.3 85 85
PGI2/IP -0.005 0.069 -10000 0 -0.37 21 21
PRKACA -0.048 0.12 -10000 0 -0.31 69 69
Gq family/GDP/G beta5/gamma2 -0.01 0.1 -10000 0 -0.44 25 25
TXA2/TP beta/beta Arrestin2 -0.017 0.066 -10000 0 -0.49 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.042 0.12 -10000 0 -0.3 72 72
mol:DAG -0.068 0.17 -10000 0 -0.42 84 84
EGFR 0.005 0.058 -10000 0 -0.53 7 7
TXA2/TP alpha -0.092 0.2 -10000 0 -0.51 85 85
Gq family/GTP -0.011 0.079 -10000 0 -0.28 35 35
YES1 -0.021 0.1 -10000 0 -0.44 12 12
GNAI2/GTP -0.05 0.093 -10000 0 -0.46 12 12
PGD2/DP -0.088 0.17 -10000 0 -0.37 155 155
SLC9A3R1 0.011 0 -10000 0 -10000 0 0
FYN -0.021 0.098 -10000 0 -0.42 11 11
mol:NO -0.008 0.1 -10000 0 -0.54 21 21
GNA15 -0.009 0.1 -10000 0 -0.54 22 22
PGK/cGMP -0.019 0.11 -10000 0 -0.34 58 58
RhoA/GDP 0.011 0.024 -10000 0 -0.57 1 1
TP alpha/TGM2/GDP/G beta/gamma -0.031 0.12 -10000 0 -0.49 16 16
NOS3 -0.008 0.1 -10000 0 -0.54 21 21
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.054 0.14 -10000 0 -0.35 82 82
PRKCB -0.068 0.17 -10000 0 -0.39 100 100
PRKCE -0.051 0.14 -10000 0 -0.35 78 78
PRKCD -0.057 0.15 -10000 0 -0.38 82 82
PRKCG -0.092 0.18 -10000 0 -0.41 108 108
muscle contraction -0.086 0.2 -10000 0 -0.5 87 87
PRKCZ -0.054 0.14 -10000 0 -0.35 82 82
ARR3 -0.001 0.042 -10000 0 -0.46 5 5
TXA2/TP beta -0.038 0.12 -10000 0 -0.52 12 12
PRKCQ -0.07 0.16 -10000 0 -0.37 99 99
MAPKKK cascade -0.081 0.19 -10000 0 -0.47 88 88
SELE -0.065 0.16 -10000 0 -0.37 100 100
TP beta/GNAI2/GDP/G beta/gamma -0.023 0.11 -10000 0 -0.5 12 12
ROCK1 0.001 0.08 -10000 0 -0.58 11 11
GNA14 -0.007 0.1 -10000 0 -0.56 19 19
chemotaxis -0.1 0.23 -10000 0 -0.6 84 84
GNA12 0.011 0 -10000 0 -10000 0 0
GNA13 0.009 0.034 -10000 0 -0.58 2 2
GNA11 0.007 0.05 -10000 0 -0.53 5 5
Rac1/GTP 0.007 0.004 -10000 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer -0.065 0.16 -9999 0 -0.46 31 31
NF kappa B1 p50/RelA/I kappa B alpha -0.039 0.15 -9999 0 -0.52 18 18
alphaV/beta3 Integrin/Osteopontin/Src -0.11 0.19 -9999 0 -0.37 206 206
AP1 -0.074 0.2 -9999 0 -0.6 43 43
ILK -0.075 0.16 -9999 0 -0.46 30 30
bone resorption -0.051 0.16 -9999 0 -0.55 20 20
PTK2B 0.009 0.034 -9999 0 -0.58 2 2
PYK2/p130Cas -0.059 0.16 -9999 0 -0.51 20 20
ITGAV 0.004 0.076 -9999 0 -0.58 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.006 0.071 -9999 0 -0.45 14 14
alphaV/beta3 Integrin/Osteopontin -0.09 0.18 -9999 0 -0.37 129 129
MAP3K1 -0.079 0.18 -9999 0 -0.36 119 119
JUN 0.007 0.052 -9999 0 -0.56 5 5
MAPK3 -0.062 0.16 -9999 0 -0.43 36 36
MAPK1 -0.062 0.16 -9999 0 -0.5 25 25
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
MAPK8 -0.069 0.17 -9999 0 -0.46 39 39
ITGB3 -0.005 0.1 -9999 0 -0.55 21 21
NFKBIA -0.054 0.16 -9999 0 -0.5 26 26
FOS -0.026 0.14 -9999 0 -0.54 41 41
CD44 0.007 0.048 -9999 0 -0.58 4 4
CHUK 0.007 0.048 -9999 0 -0.58 4 4
PLAU -0.051 0.19 -9999 0 -0.74 22 22
NF kappa B1 p50/RelA -0.078 0.13 -9999 0 -0.53 20 20
BCAR1 0.008 0.043 -9999 0 -0.52 4 4
RELA 0.011 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.097 -9999 0 -0.42 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.076 0.16 -9999 0 -0.34 118 118
VAV3 -0.1 0.19 -9999 0 -0.48 64 64
MAP3K14 -0.074 0.17 -9999 0 -0.34 121 121
ROCK2 0.001 0.08 -9999 0 -0.58 11 11
SPP1 -0.16 0.25 -9999 0 -0.51 197 197
RAC1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.092 0.18 -9999 0 -0.5 46 46
MMP2 -0.074 0.21 -9999 0 -0.6 56 56
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.053 0.16 -9999 0 -0.35 120 120
EPHB2 0 0.079 -9999 0 -0.55 12 12
Syndecan-2/TACI -0.039 0.13 -9999 0 -0.32 103 103
LAMA1 -0.059 0.18 -9999 0 -0.54 77 77
Syndecan-2/alpha2 ITGB1 0.005 0.091 -9999 0 -0.31 34 34
HRAS 0.008 0.041 -9999 0 -0.49 4 4
Syndecan-2/CASK 0 0.066 -9999 0 -0.34 21 21
ITGA5 -0.006 0.093 -9999 0 -0.49 21 21
BAX 0.018 0.077 -9999 0 -1.1 1 1
EPB41 0.007 0.048 -9999 0 -0.58 4 4
positive regulation of cell-cell adhesion 0.002 0.074 -9999 0 -0.32 29 29
LAMA3 -0.014 0.11 -9999 0 -0.51 30 30
EZR 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.003 0.087 -9999 0 -0.51 17 17
Syndecan-2/MMP2 -0.019 0.13 -9999 0 -0.4 56 56
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.013 0.044 -9999 0 -0.42 6 6
dendrite morphogenesis 0.001 0.083 -9999 0 -0.34 33 33
Syndecan-2/GM-CSF -0.06 0.15 -9999 0 -0.32 142 142
determination of left/right symmetry 0.001 0.078 -9999 0 -0.4 22 22
Syndecan-2/PKC delta 0.008 0.066 -9999 0 -0.34 21 21
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
MAPK3 -0.047 0.13 -9999 0 -0.32 81 81
MAPK1 -0.047 0.13 -9999 0 -0.32 81 81
Syndecan-2/RACK1 0.012 0.064 -9999 0 -0.32 19 19
NF1 0.008 0.042 -9999 0 -0.58 3 3
FGFR/FGF/Syndecan-2 0.001 0.078 -9999 0 -0.4 22 22
ITGA2 0.006 0.059 -9999 0 -0.58 6 6
MAPK8 0.014 0.07 -9999 0 -0.35 19 19
Syndecan-2/alpha2/beta1 Integrin -0.019 0.12 -9999 0 -0.31 71 71
Syndecan-2/Kininogen -0.068 0.15 -9999 0 -0.32 156 156
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.017 0.065 -9999 0 -0.31 19 19
Syndecan-2/CASK/Protein 4.1 0.005 0.066 -9999 0 -0.31 25 25
extracellular matrix organization 0 0.095 -9999 0 -0.39 31 31
actin cytoskeleton reorganization -0.052 0.16 -9999 0 -0.35 120 120
Syndecan-2/Caveolin-2/Ras 0.005 0.087 -9999 0 -0.37 22 22
Syndecan-2/Laminin alpha3 -0.008 0.095 -9999 0 -0.32 51 51
Syndecan-2/RasGAP 0.017 0.066 -9999 0 -0.31 21 21
alpha5/beta1 Integrin 0.004 0.067 -9999 0 -0.35 21 21
PRKCD 0.011 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.001 0.083 -9999 0 -0.34 33 33
GO:0007205 0.003 0.006 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.022 0.068 -9999 0 -0.52 3 3
RHOA 0.01 0.024 -9999 0 -0.58 1 1
SDCBP 0.003 0.072 -9999 0 -0.58 9 9
TNFRSF13B -0.064 0.18 -9999 0 -0.52 84 84
RASA1 0.009 0.034 -9999 0 -0.58 2 2
alpha2/beta1 Integrin 0.013 0.044 -9999 0 -0.42 6 6
Syndecan-2/Synbindin 0.008 0.066 -9999 0 -0.34 21 21
TGFB1 -0.002 0.088 -9999 0 -0.55 15 15
CASP3 0.014 0.063 -9999 0 -0.32 19 19
FN1 -0.088 0.21 -9999 0 -0.52 112 112
Syndecan-2/IL8 -0.066 0.16 -9999 0 -0.33 150 150
SDC2 0.001 0.078 -9999 0 -0.4 22 22
KNG1 -0.11 0.22 -9999 0 -0.52 138 138
Syndecan-2/Neurofibromin 0.006 0.071 -9999 0 -0.34 24 24
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 -0.098 0.22 -9999 0 -0.52 123 123
Syndecan-2/TGFB1 0 0.096 -9999 0 -0.39 31 31
Syndecan-2/Syntenin/PI-4-5-P2 0.002 0.075 -9999 0 -0.32 29 29
Syndecan-2/Ezrin 0.015 0.062 -9999 0 -0.32 18 18
PRKACA 0.013 0.065 -9999 0 -0.32 20 20
angiogenesis -0.066 0.16 -9999 0 -0.33 150 150
MMP2 -0.033 0.15 -9999 0 -0.53 50 50
IL8 -0.11 0.22 -9999 0 -0.52 137 137
calcineurin-NFAT signaling pathway -0.039 0.13 -9999 0 -0.32 103 103
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.022 0.075 0.32 14 -10000 0 14
SMARCC2 0.012 0.006 -10000 0 -10000 0 0
SMARCC1 0.012 0.006 -10000 0 -10000 0 0
TBX21 -0.11 0.27 -10000 0 -0.71 84 84
SUMO2 0.01 0.025 -10000 0 -0.58 1 1
STAT1 (dimer) 0.012 0.057 -10000 0 -0.51 7 7
FKBP4 0.009 0.033 -10000 0 -0.46 3 3
FKBP5 0.01 0.031 -10000 0 -0.52 2 2
GR alpha/HSP90/FKBP51/HSP90 0.076 0.11 0.3 48 -0.39 6 54
PRL -0.064 0.14 -10000 0 -0.58 15 15
cortisol/GR alpha (dimer)/TIF2 0.18 0.24 0.53 125 -0.48 6 131
RELA -0.036 0.093 -10000 0 -0.33 11 11
FGG 0.12 0.21 0.48 66 -0.43 16 82
GR beta/TIF2 0.075 0.13 0.32 55 -0.46 12 67
IFNG -0.27 0.38 -10000 0 -0.95 106 106
apoptosis 0.008 0.16 0.47 21 -0.63 5 26
CREB1 0.009 0.041 -10000 0 -0.58 2 2
histone acetylation -0.033 0.12 0.33 1 -0.37 39 40
BGLAP -0.054 0.15 -10000 0 -0.61 17 17
GR/PKAc 0.056 0.13 0.29 36 -0.36 18 54
NF kappa B1 p50/RelA -0.068 0.18 -10000 0 -0.53 37 37
SMARCD1 0.011 0.025 -10000 0 -0.58 1 1
MDM2 0.073 0.088 0.27 52 -0.28 3 55
GATA3 -0.016 0.12 -10000 0 -0.52 32 32
AKT1 0.003 0.024 -10000 0 -0.59 1 1
CSF2 -0.19 0.38 -10000 0 -1.2 71 71
GSK3B 0.009 0.035 -10000 0 -0.59 2 2
NR1I3 0.023 0.18 0.46 18 -0.82 13 31
CSN2 0.12 0.15 0.41 54 -0.38 3 57
BRG1/BAF155/BAF170/BAF60A 0.032 0.029 -10000 0 -0.32 2 2
NFATC1 -0.016 0.12 -10000 0 -0.51 33 33
POU2F1 0.001 0.075 -10000 0 -0.55 10 10
CDKN1A -0.018 0.16 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.007 -10000 0 -10000 0 0
SFN 0.005 0.055 -10000 0 -0.47 8 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.077 0.11 0.3 36 -0.41 5 41
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.02 0.17 0.45 18 -0.79 11 29
JUN -0.16 0.19 -10000 0 -0.5 83 83
IL4 -0.078 0.14 -10000 0 -0.5 25 25
CDK5R1 0.009 0.033 -10000 0 -0.46 3 3
PRKACA 0.011 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.2 0.22 30 -0.48 92 122
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.08 0.1 0.3 39 -0.39 4 43
cortisol/GR alpha (monomer) 0.21 0.28 0.64 127 -0.46 4 131
NCOA2 0.004 0.066 -10000 0 -0.57 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.078 0.15 -10000 0 -0.58 41 41
AP-1/NFAT1-c-4 -0.27 0.31 -10000 0 -0.71 139 139
AFP -0.12 0.17 -10000 0 -0.77 11 11
SUV420H1 0.01 0.024 -10000 0 -0.58 1 1
IRF1 0.12 0.14 0.48 27 -0.59 1 28
TP53 -0.031 0.18 -10000 0 -0.57 60 60
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.34 0.45 -10000 0 -1 156 156
KRT14 -0.12 0.2 -10000 0 -0.65 36 36
TBP 0.017 0.029 -10000 0 -0.36 3 3
CREBBP 0.034 0.054 0.29 2 -10000 0 2
HDAC1 0.011 0.009 -10000 0 -10000 0 0
HDAC2 0.022 0.027 -10000 0 -10000 0 0
AP-1 -0.28 0.31 -10000 0 -0.72 140 140
MAPK14 0.011 0.006 -10000 0 -10000 0 0
MAPK10 -0.032 0.15 -10000 0 -0.55 47 47
MAPK11 -0.002 0.079 -10000 0 -0.48 16 16
KRT5 -0.32 0.41 -10000 0 -0.96 133 133
interleukin-1 receptor activity 0.011 0.028 -10000 0 -10000 0 0
NCOA1 0.013 0.024 -10000 0 -0.58 1 1
STAT1 0.012 0.057 -10000 0 -0.51 7 7
CGA -0.064 0.13 -10000 0 -0.49 21 21
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.2 0.48 97 -0.53 5 102
MAPK3 0.01 0.025 -10000 0 -0.58 1 1
MAPK1 0.01 0.025 -10000 0 -0.58 1 1
ICAM1 -0.14 0.24 -10000 0 -0.74 46 46
NFKB1 -0.037 0.098 -10000 0 -0.41 8 8
MAPK8 -0.13 0.17 -10000 0 -0.43 82 82
MAPK9 0.011 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.001 0.16 0.48 21 -0.67 5 26
BAX -0.013 0.13 -10000 0 -1.4 1 1
POMC -0.15 0.33 -10000 0 -1.1 47 47
EP300 0.032 0.073 0.28 3 -0.55 4 7
cortisol/GR alpha (dimer)/p53 0.15 0.26 0.56 106 -0.42 18 124
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.069 0.24 18 -0.24 3 21
SGK1 0.065 0.13 0.42 1 -1.4 3 4
IL13 -0.18 0.22 -10000 0 -0.67 56 56
IL6 -0.25 0.42 -10000 0 -0.93 128 128
PRKACG 0 0.038 -10000 0 -0.46 4 4
IL5 -0.15 0.18 -10000 0 -0.68 24 24
IL2 -0.2 0.24 -10000 0 -0.64 79 79
CDK5 0.012 0.003 -10000 0 -10000 0 0
PRKACB -0.02 0.13 -10000 0 -0.57 33 33
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
IL8 -0.25 0.41 -10000 0 -0.99 117 117
CDK5R1/CDK5 0.015 0.025 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA/PKAc -0.049 0.16 -10000 0 -0.52 32 32
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.22 0.5 126 -0.38 2 128
SMARCA4 0.011 0.025 -10000 0 -0.58 1 1
chromatin remodeling 0.12 0.14 0.39 67 -0.41 4 71
NF kappa B1 p50/RelA/Cbp -0.016 0.17 0.31 2 -0.62 16 18
JUN (dimer) -0.16 0.19 -10000 0 -0.5 83 83
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 -0.079 0.21 -10000 0 -0.66 53 53
NR3C1 0.12 0.18 0.45 81 -0.46 12 93
NR4A1 -0.033 0.15 -10000 0 -0.48 56 56
TIF2/SUV420H1 0.011 0.052 -10000 0 -0.41 9 9
MAPKKK cascade 0.008 0.16 0.47 21 -0.63 5 26
cortisol/GR alpha (dimer)/Src-1 0.19 0.23 0.54 128 -0.43 4 132
PBX1 -0.003 0.089 -10000 0 -0.57 14 14
POU1F1 -0.001 0.036 -10000 0 -0.51 2 2
SELE -0.23 0.4 -10000 0 -0.96 110 110
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.12 0.14 0.39 67 -0.42 4 71
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.22 0.5 126 -0.38 2 128
mol:cortisol 0.12 0.17 0.37 132 -10000 0 132
MMP1 -0.27 0.46 -10000 0 -1.1 129 129
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.026 0.051 -9999 0 -0.56 2 2
Crk/p130 Cas/Paxillin -0.061 0.11 -9999 0 -0.39 28 28
JUN -0.031 0.12 -9999 0 -0.44 24 24
HRAS 0.008 0.041 -9999 0 -0.49 4 4
RET51/GFRalpha1/GDNF/GRB10 -0.076 0.17 -9999 0 -0.41 90 90
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
FRS2 0.009 0.034 -9999 0 -0.58 2 2
RAP1A/GDP 0.008 0.018 -9999 0 -0.43 1 1
RET51/GFRalpha1/GDNF/DOK1 -0.074 0.17 -9999 0 -0.4 89 89
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.019 -9999 0 -0.46 1 1
RET9/GFRalpha1/GDNF/Enigma -0.031 0.12 -9999 0 -0.29 100 100
RHOA 0.01 0.024 -9999 0 -0.58 1 1
RAP1A/GTP -0.083 0.14 -9999 0 -0.36 90 90
GRB7 0.002 0.065 -9999 0 -0.46 12 12
RET51/GFRalpha1/GDNF -0.074 0.17 -9999 0 -0.4 89 89
MAPKKK cascade -0.075 0.13 -9999 0 -0.48 33 33
BCAR1 0.008 0.043 -9999 0 -0.52 4 4
RET9/GFRalpha1/GDNF/IRS1 -0.034 0.12 -9999 0 -0.3 103 103
lamellipodium assembly -0.056 0.098 -9999 0 -0.32 44 44
RET51/GFRalpha1/GDNF/SHC -0.074 0.17 -9999 0 -0.4 89 89
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
RET9/GFRalpha1/GDNF/SHC -0.028 0.12 -9999 0 -0.29 95 95
RET9/GFRalpha1/GDNF/Shank3 -0.031 0.12 -9999 0 -0.3 97 97
MAPK3 -0.055 0.15 -9999 0 -0.49 28 28
DOK1 0.011 0 -9999 0 -10000 0 0
DOK6 -0.029 0.14 -9999 0 -0.55 43 43
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.05 0.15 -9999 0 -0.47 35 35
DOK5 -0.053 0.18 -9999 0 -0.55 70 70
GFRA1 -0.071 0.2 -9999 0 -0.53 92 92
MAPK8 -0.036 0.12 -9999 0 -0.45 21 21
HRAS/GTP -0.084 0.14 -9999 0 -0.38 91 91
tube development -0.024 0.12 -9999 0 -0.32 59 59
MAPK1 -0.055 0.15 -9999 0 -0.49 28 28
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.015 0.095 -9999 0 -0.27 62 62
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.01 0.024 -9999 0 -0.58 1 1
PDLIM7 0.006 0.052 -9999 0 -0.48 7 7
RET51/GFRalpha1/GDNF/Dok6 -0.085 0.19 -9999 0 -0.41 114 114
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.074 0.17 -9999 0 -0.4 89 89
RET51/GFRalpha1/GDNF/Dok5 -0.11 0.2 -9999 0 -0.43 129 129
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
HRAS/GDP 0.006 0.029 -9999 0 -0.35 4 4
CREB1 -0.029 0.12 -9999 0 -0.35 56 56
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.011 0.087 -9999 0 -0.26 56 56
RET51/GFRalpha1/GDNF/Grb7 -0.079 0.17 -9999 0 -0.4 90 90
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.084 0.2 -9999 0 -0.5 113 113
DOK4 0.01 0.024 -9999 0 -0.58 1 1
JNK cascade -0.03 0.12 -9999 0 -0.44 24 24
RET9/GFRalpha1/GDNF/FRS2 -0.03 0.12 -9999 0 -0.29 97 97
SHANK3 0.006 0.055 -9999 0 -0.54 6 6
RASA1 0.009 0.034 -9999 0 -0.58 2 2
NCK1 0.009 0.034 -9999 0 -0.58 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.088 -9999 0 -0.26 57 57
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.046 0.13 -9999 0 -0.41 33 33
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.044 0.13 -9999 0 -0.4 31 31
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.046 0.14 -9999 0 -0.54 23 23
PI3K -0.047 0.17 -9999 0 -0.45 62 62
SOS1 0.01 0.024 -9999 0 -0.58 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.023 0.12 -9999 0 -0.32 59 59
GRB10 0.007 0.048 -9999 0 -0.58 4 4
activation of MAPKK activity -0.036 0.12 -9999 0 -0.42 23 23
RET51/GFRalpha1/GDNF/FRS2 -0.075 0.17 -9999 0 -0.4 91 91
GAB1 0.011 0 -9999 0 -10000 0 0
IRS1 0.002 0.076 -9999 0 -0.58 10 10
IRS2 0.003 0.067 -9999 0 -0.54 9 9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.046 0.14 -9999 0 -0.38 51 51
RET51/GFRalpha1/GDNF/PKC alpha -0.075 0.17 -9999 0 -0.4 89 89
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF 0.005 0.043 -9999 0 -0.52 4 4
RAC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.079 0.18 -9999 0 -0.41 95 95
Rac1/GTP -0.066 0.12 -9999 0 -0.43 28 28
RET9/GFRalpha1/GDNF -0.04 0.13 -9999 0 -0.33 95 95
GFRalpha1/GDNF -0.048 0.15 -9999 0 -0.38 95 95
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.016 0.099 -9999 0 -0.28 73 73
RGS9BP -0.01 0.1 -9999 0 -0.54 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.046 -9999 0 -0.46 6 6
mol:Na + -0.048 0.12 -9999 0 -0.3 110 110
mol:ADP -0.002 0.057 -9999 0 -0.34 16 16
GNAT2 -0.007 0.096 -9999 0 -0.52 20 20
RGS9-1/Gbeta5/R9AP -0.021 0.12 -9999 0 -0.33 75 75
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.004 0.06 -9999 0 -0.32 21 21
GRK7 -0.001 0.062 -9999 0 -0.46 11 11
CNGB3 -0.03 0.12 -9999 0 -0.46 44 44
Cone Metarhodopsin II/X-Arrestin 0 0.03 -9999 0 -0.32 5 5
mol:Ca2+ -0.049 0.12 -9999 0 -0.28 126 126
Cone PDE6 -0.017 0.1 -9999 0 -0.32 44 44
Cone Metarhodopsin II -0.001 0.044 -9999 0 -0.26 16 16
Na + (4 Units) -0.048 0.12 -9999 0 -0.28 126 126
GNAT2/GDP -0.021 0.11 -9999 0 -0.32 55 55
GNB5 0.007 0.048 -9999 0 -0.58 4 4
mol:GMP (4 units) -0.004 0.058 -9999 0 -0.28 25 25
Cone Transducin -0.017 0.11 -9999 0 -0.3 73 73
SLC24A2 -0.011 0.092 -9999 0 -0.48 22 22
GNB3/GNGT2 -0.019 0.12 -9999 0 -0.4 53 53
GNB3 -0.018 0.12 -9999 0 -0.54 32 32
GNAT2/GTP -0.005 0.07 -9999 0 -0.38 20 20
CNGA3 -0.05 0.17 -9999 0 -0.52 67 67
ARR3 -0.001 0.042 -9999 0 -0.46 5 5
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.048 0.12 -9999 0 -0.3 110 110
mol:Pi -0.021 0.12 -9999 0 -0.32 75 75
Cone CNG Channel -0.054 0.11 -9999 0 -0.32 43 43
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.011 0.092 -9999 0 -0.48 22 22
RGS9 -0.034 0.15 -9999 0 -0.52 51 51
PDE6C 0 0.038 -9999 0 -0.46 4 4
GNGT2 -0.009 0.11 -9999 0 -0.56 22 22
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0.019 -9999 0 -0.46 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.015 0.12 -9999 0 -0.41 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.014 0.11 -9999 0 -0.4 13 13
AP1 -0.086 0.14 -9999 0 -0.49 38 38
mol:PIP3 -0.065 0.12 -9999 0 -0.49 23 23
AKT1 0.01 0.094 -9999 0 -0.43 13 13
PTK2B -0.014 0.094 -9999 0 -0.32 25 25
RHOA 0.011 0.051 -9999 0 -0.35 3 3
PIK3CB 0.008 0.046 -9999 0 -0.55 4 4
mol:Ca2+ -0.017 0.11 -9999 0 -0.31 42 42
MAGI3 0.009 0.042 -9999 0 -0.58 3 3
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.052 0.14 -9999 0 -0.33 95 95
HRAS/GDP 0.006 0.029 -9999 0 -0.35 4 4
positive regulation of microtubule depolymerization -0.043 0.13 -9999 0 -0.37 33 33
NF kappa B1 p50/RelA -0.064 0.12 -9999 0 -0.47 28 28
endothelial cell migration -0.046 0.19 -9999 0 -0.52 78 78
ADCY4 -0.039 0.16 -9999 0 -0.5 51 51
ADCY5 -0.072 0.2 -9999 0 -0.55 64 64
ADCY6 -0.037 0.16 -9999 0 -0.53 44 44
ADCY7 -0.038 0.16 -9999 0 -0.5 49 49
ADCY1 -0.05 0.17 -9999 0 -0.51 55 55
ADCY2 -0.055 0.19 -9999 0 -0.52 67 67
ADCY3 -0.038 0.16 -9999 0 -0.52 45 45
ADCY8 -0.042 0.16 -9999 0 -0.5 49 49
ADCY9 -0.038 0.16 -9999 0 -0.5 49 49
GSK3B -0.008 0.092 -9999 0 -0.35 19 19
arachidonic acid secretion -0.034 0.16 -9999 0 -0.5 45 45
GNG2 0.003 0.067 -9999 0 -0.54 9 9
TRIP6 -0.015 0.12 -9999 0 -0.42 42 42
GNAO1 -0.054 0.16 -9999 0 -0.35 118 118
HRAS 0.008 0.041 -9999 0 -0.49 4 4
NFKBIA -0.02 0.12 -9999 0 -0.41 21 21
GAB1 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.032 0.2 -9999 0 -0.91 31 31
JUN 0.007 0.052 -9999 0 -0.56 5 5
LPA/LPA2/NHERF2 0.007 0.046 -9999 0 -0.33 7 7
TIAM1 -0.059 0.24 -9999 0 -1.1 31 31
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:IP3 -0.018 0.11 -9999 0 -0.32 42 42
PLCB3 0.012 0.055 -9999 0 -0.36 8 8
FOS -0.026 0.14 -9999 0 -0.54 41 41
positive regulation of mitosis -0.034 0.16 -9999 0 -0.5 45 45
LPA/LPA1-2-3 -0.063 0.15 -9999 0 -0.38 77 77
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.008 0.043 -9999 0 -0.52 4 4
stress fiber formation -0.023 0.11 -9999 0 -0.36 26 26
GNAZ -0.035 0.14 -9999 0 -0.37 79 79
EGFR/PI3K-beta/Gab1 -0.067 0.13 -9999 0 -0.52 23 23
positive regulation of dendritic cell cytokine production -0.063 0.15 -9999 0 -0.38 77 77
LPA/LPA2/MAGI-3 0.006 0.049 -9999 0 -0.33 9 9
ARHGEF1 -0.007 0.11 -9999 0 -0.35 40 40
GNAI2 -0.02 0.12 -9999 0 -0.36 58 58
GNAI3 -0.02 0.12 -9999 0 -0.36 58 58
GNAI1 -0.029 0.14 -9999 0 -0.39 66 66
LPA/LPA3 -0.056 0.14 -9999 0 -0.37 92 92
LPA/LPA2 -0.001 0.046 -9999 0 -0.34 7 7
LPA/LPA1 -0.034 0.14 -9999 0 -0.38 78 78
HB-EGF/EGFR -0.036 0.13 -9999 0 -0.32 99 99
HBEGF -0.042 0.14 -9999 0 -0.37 94 94
mol:DAG -0.018 0.11 -9999 0 -0.32 42 42
cAMP biosynthetic process -0.051 0.18 -9999 0 -0.48 65 65
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
SRC 0.01 0.024 -9999 0 -0.58 1 1
GNB1 0.011 0.001 -9999 0 -10000 0 0
LYN -0.02 0.12 -9999 0 -0.4 22 22
GNAQ -0.031 0.1 -9999 0 -0.32 47 47
LPAR2 0.006 0.052 -9999 0 -0.48 7 7
LPAR3 -0.07 0.19 -9999 0 -0.51 92 92
LPAR1 -0.034 0.15 -9999 0 -0.61 37 37
IL8 -0.11 0.21 -9999 0 -0.48 107 107
PTK2 -0.051 0.15 -9999 0 -0.36 76 76
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.053 0.14 -9999 0 -0.33 95 95
EGFR 0.005 0.058 -9999 0 -0.53 7 7
PLCG1 -0.031 0.12 -9999 0 -0.34 50 50
PLD2 -0.051 0.15 -9999 0 -0.36 75 75
G12/G13 -0.012 0.11 -9999 0 -0.38 38 38
PI3K-beta -0.031 0.09 -9999 0 -0.44 17 17
cell migration -0.018 0.089 -9999 0 -0.26 40 40
SLC9A3R2 0.01 0.024 -9999 0 -0.58 1 1
PXN -0.023 0.11 -9999 0 -0.37 26 26
HRAS/GTP -0.035 0.16 -9999 0 -0.51 45 45
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.062 0.18 -9999 0 -0.52 83 83
PRKCE 0.011 0 -9999 0 -10000 0 0
PRKCD -0.011 0.11 -9999 0 -0.42 13 13
Gi(beta/gamma) -0.034 0.16 -9999 0 -0.5 45 45
mol:LPA -0.009 0.044 -9999 0 -0.19 21 21
TRIP6/p130 Cas/FAK1/Paxillin -0.075 0.14 -9999 0 -0.5 31 31
MAPKKK cascade -0.034 0.16 -9999 0 -0.5 45 45
contractile ring contraction involved in cytokinesis 0.011 0.051 -9999 0 -0.34 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.037 0.12 -9999 0 -0.34 59 59
GNA15 -0.038 0.11 -9999 0 -0.33 57 57
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
MAPT -0.044 0.13 -9999 0 -0.39 33 33
GNA11 -0.03 0.1 -9999 0 -0.32 45 45
Rac1/GTP -0.035 0.22 -9999 0 -0.97 31 31
MMP2 -0.046 0.19 -9999 0 -0.52 78 78
Neurotrophic factor-mediated Trk 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
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.027 0.11 -10000 0 -0.32 50 50
NT3 (dimer)/TRKC -0.044 0.15 -10000 0 -0.39 90 90
NT3 (dimer)/TRKB -0.16 0.21 -10000 0 -0.45 145 145
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.032 -10000 0 -0.52 1 1
RAPGEF1 0.01 0.024 -10000 0 -0.58 1 1
BDNF -0.021 0.13 -10000 0 -0.53 36 36
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
DYNLT1 0.011 0 -10000 0 -10000 0 0
NTRK1 -0.037 0.15 -10000 0 -0.53 53 53
NTRK2 -0.18 0.25 -10000 0 -0.5 219 219
NTRK3 -0.044 0.16 -10000 0 -0.51 62 62
NT-4/5 (dimer)/TRKB -0.16 0.2 -10000 0 -0.37 225 225
neuron apoptosis 0.14 0.19 0.45 118 -10000 0 118
SHC 2-3/Grb2 -0.15 0.21 -10000 0 -0.5 118 118
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.13 0.2 -10000 0 -0.56 81 81
SHC3 -0.14 0.21 -10000 0 -0.56 90 90
STAT3 (dimer) 0.017 0.021 -10000 0 -0.35 2 2
NT3 (dimer)/TRKA -0.08 0.18 -10000 0 -0.44 93 93
RIN/GDP -0.003 0.07 -10000 0 -0.27 10 10
GIPC1 0.007 0.048 -10000 0 -0.58 4 4
KRAS 0.006 0.057 -10000 0 -0.56 6 6
DNAJA3 -0.058 0.14 -10000 0 -0.36 69 69
RIN/GTP -0.001 0.019 -10000 0 -0.32 2 2
CCND1 0.023 0.048 -10000 0 -0.82 2 2
MAGED1 0.011 0 -10000 0 -10000 0 0
PTPN11 0.007 0.054 -10000 0 -0.58 5 5
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.013 0.089 -10000 0 -0.46 23 23
SHC/GRB2/SOS1 0.023 0.015 -10000 0 -0.36 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.082 0.19 -10000 0 -0.38 158 158
TRKA/NEDD4-2 -0.019 0.11 -10000 0 -0.38 54 54
ELMO1 0.001 0.075 -10000 0 -0.52 12 12
RhoG/GTP/ELMO1/DOCK1 0.008 0.049 -10000 0 -0.32 13 13
NGF -0.032 0.15 -10000 0 -0.53 48 48
HRAS 0.008 0.041 -10000 0 -0.49 4 4
DOCK1 0.01 0.024 -10000 0 -0.58 1 1
GAB2 0.009 0.034 -10000 0 -0.58 2 2
RIT2 -0.001 0.026 -10000 0 -0.46 2 2
RIT1 0.011 0 -10000 0 -10000 0 0
FRS2 0.009 0.034 -10000 0 -0.58 2 2
DNM1 -0.007 0.096 -10000 0 -0.5 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.019 -10000 0 -0.46 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.074 0.14 -10000 0 -0.38 61 61
mol:GDP -0.006 0.099 -10000 0 -0.38 14 14
NGF (dimer) -0.032 0.15 -10000 0 -0.52 48 48
RhoG/GDP 0.001 0.054 -10000 0 -0.38 12 12
RIT1/GDP 0.002 0.07 -10000 0 -0.27 8 8
TIAM1 -0.044 0.16 -10000 0 -0.52 63 63
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
BDNF (dimer)/TRKB -0.11 0.18 -10000 0 -0.32 239 239
KIDINS220/CRKL/C3G 0.016 0.018 -10000 0 -0.42 1 1
SHC/RasGAP 0.016 0.025 -10000 0 -0.42 2 2
FRS2 family/SHP2 0.018 0.051 -10000 0 -0.44 7 7
SHC/GRB2/SOS1/GAB1 0.029 0.014 -10000 0 -0.32 1 1
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.12 -10000 0 -0.53 33 33
RAP1/GDP -0.021 0.046 -10000 0 -0.27 5 5
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.021 0.13 -10000 0 -0.53 36 36
ubiquitin-dependent protein catabolic process -0.034 0.14 -10000 0 -0.35 92 92
Schwann cell development -0.032 0.032 -10000 0 -10000 0 0
EHD4 0.011 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.027 0.03 -10000 0 -0.32 4 4
FRS2 family/SHP2/CRK family/C3G/GAB2 0.028 0.049 -10000 0 -0.42 6 6
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.01 0.024 -10000 0 -0.58 1 1
CDC42/GTP -0.13 0.16 -10000 0 -0.48 65 65
ABL1 0.01 0.024 -10000 0 -0.58 1 1
SH2B family/GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
Rap1/GTP -0.017 0.08 -10000 0 -0.39 3 3
STAT3 0.017 0.021 -10000 0 -0.35 2 2
axon guidance -0.12 0.15 -10000 0 -0.46 65 65
MAPK3 -0.069 0.17 -10000 0 -0.39 109 109
MAPK1 -0.069 0.17 -10000 0 -0.39 109 109
CDC42/GDP 0.001 0.074 -10000 0 -0.31 9 9
NTF3 -0.018 0.12 -10000 0 -0.53 33 33
NTF4 -0.013 0.09 -10000 0 -0.46 23 23
NGF (dimer)/TRKA/FAIM -0.037 0.14 -10000 0 -0.35 96 96
PI3K 0.013 0.04 -10000 0 -0.43 5 5
FRS3 0.01 0.031 -10000 0 -0.52 2 2
FAIM 0.006 0.057 -10000 0 -0.56 6 6
GAB1 0.011 0 -10000 0 -10000 0 0
RASGRF1 -0.092 0.17 -10000 0 -0.38 107 107
SOS1 0.01 0.024 -10000 0 -0.58 1 1
MCF2L -0.033 0.13 -10000 0 -0.32 95 95
RGS19 -0.001 0.081 -10000 0 -0.55 13 13
CDC42 0.007 0.054 -10000 0 -0.58 5 5
RAS family/GTP -0.002 0.095 -10000 0 -0.54 9 9
Rac1/GDP 0.002 0.07 -10000 0 -0.27 8 8
NGF (dimer)/TRKA/GRIT -0.041 0.14 -10000 0 -0.35 91 91
neuron projection morphogenesis -0.041 0.14 -10000 0 -0.6 10 10
NGF (dimer)/TRKA/NEDD4-2 -0.034 0.14 -10000 0 -0.35 92 92
MAP2K1 0.03 0.023 -10000 0 -0.29 3 3
NGFR -0.08 0.2 -10000 0 -0.51 106 106
NGF (dimer)/TRKA/GIPC/GAIP -0.022 0.12 -10000 0 -0.28 81 81
RAS family/GTP/PI3K 0.014 0.08 -10000 0 -0.42 15 15
FRS2 family/SHP2/GRB2/SOS1 0.029 0.047 -10000 0 -0.36 8 8
NRAS 0.002 0.076 -10000 0 -0.58 10 10
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
PRKCI 0.008 0.042 -10000 0 -0.58 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
MAPKKK cascade -0.09 0.19 -10000 0 -0.63 59 59
RASA1 0.009 0.034 -10000 0 -0.58 2 2
TRKA/c-Abl -0.019 0.11 -10000 0 -0.38 54 54
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.096 0.16 -10000 0 -0.36 102 102
NGF (dimer)/TRKA/p62/Atypical PKCs -0.018 0.12 -10000 0 -0.33 65 65
MATK -0.069 0.19 -10000 0 -0.52 91 91
NEDD4L 0.01 0.024 -10000 0 -0.58 1 1
RAS family/GDP -0.02 0.048 -10000 0 -0.27 8 8
NGF (dimer)/TRKA -0.076 0.14 -10000 0 -0.33 114 114
Rac1/GTP -0.079 0.11 -10000 0 -0.34 57 57
FRS2 family/SHP2/CRK family 0.029 0.049 -10000 0 -0.4 7 7
Caspase cascade in apoptosis

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
TOP1 -0.029 0.13 0.19 2 -0.34 65 67
ACTA1 -0.052 0.16 0.22 3 -0.42 70 73
NUMA1 -0.029 0.13 0.19 2 -0.33 65 67
SPTAN1 -0.043 0.15 0.23 2 -0.42 65 67
LIMK1 -0.043 0.15 0.23 2 -0.42 65 67
BIRC3 -0.016 0.12 -10000 0 -0.53 31 31
BIRC2 -0.001 0.086 -10000 0 -0.59 13 13
BAX 0.01 0.024 -10000 0 -0.58 1 1
CASP10 -0.058 0.16 -10000 0 -0.34 136 136
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0.024 -10000 0 -0.58 1 1
PTK2 -0.029 0.13 0.19 2 -0.34 64 66
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.042 0.15 0.23 2 -0.41 65 67
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0.024 -10000 0 -0.58 1 1
GSN -0.049 0.16 0.23 2 -0.43 66 68
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A -0.084 0.2 -10000 0 -0.56 83 83
BID -0.024 0.087 -10000 0 -0.23 68 68
MAP3K1 -0.014 0.07 -10000 0 -0.31 14 14
TRADD 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.014 0.036 -10000 0 -0.42 4 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.045 0.16 0.23 2 -0.42 66 68
CASP9 0.011 0.024 -10000 0 -0.58 1 1
DNA repair 0.004 0.049 -10000 0 -0.2 7 7
neuron apoptosis 0.012 0.036 -10000 0 -0.5 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.035 0.15 0.22 2 -0.4 62 64
APAF1 0.009 0.042 -10000 0 -0.58 3 3
CASP6 -0.006 0.086 -10000 0 -0.52 5 5
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
ICAD/CAD -0.036 0.15 0.22 2 -0.4 62 64
CASP7 0.009 0.059 0.28 18 -10000 0 18
KRT18 0.006 0.033 -10000 0 -0.55 1 1
apoptosis -0.04 0.15 0.25 2 -0.37 71 73
DFFA -0.043 0.15 0.23 2 -0.42 63 65
DFFB -0.043 0.15 0.23 2 -0.42 64 66
PARP1 -0.005 0.05 0.2 7 -10000 0 7
actin filament polymerization 0.044 0.15 0.38 71 -0.22 2 73
TNF -0.017 0.12 -10000 0 -0.54 31 31
CYCS -0.023 0.086 -10000 0 -0.27 36 36
SATB1 -0.02 0.11 -10000 0 -0.41 20 20
SLK -0.054 0.16 0.23 2 -0.42 79 81
p15 BID/BAX -0.016 0.079 -10000 0 -0.29 14 14
CASP2 0.022 0.061 -10000 0 -0.4 2 2
JNK cascade 0.014 0.07 0.31 14 -10000 0 14
CASP3 -0.051 0.16 0.23 3 -0.44 66 69
LMNB2 0.016 0.061 -10000 0 -0.36 6 6
RIPK1 0.011 0 -10000 0 -10000 0 0
CASP4 0.008 0.046 -10000 0 -0.55 4 4
Mammalian IAPs/DIABLO 0.006 0.1 -10000 0 -0.45 22 22
negative regulation of DNA binding -0.083 0.2 -10000 0 -0.56 83 83
stress fiber formation -0.053 0.16 0.23 2 -0.41 79 81
GZMB -0.076 0.19 -10000 0 -0.41 135 135
CASP1 -0.007 0.086 -10000 0 -0.31 40 40
LMNB1 0.017 0.054 -10000 0 -0.27 5 5
APP 0.012 0.037 -10000 0 -0.5 2 2
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.018 -10000 0 -0.43 1 1
VIM -0.034 0.14 0.22 6 -0.36 65 71
LMNA 0.016 0.059 -10000 0 -0.35 5 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.017 0.064 -10000 0 -0.43 2 2
LRDD 0.008 0.042 -10000 0 -0.58 3 3
SREBF1 -0.044 0.16 0.23 2 -0.42 65 67
APAF-1/Caspase 9 -0.003 0.065 0.4 7 -0.76 1 8
nuclear fragmentation during apoptosis -0.028 0.12 0.19 2 -0.33 65 67
CFL2 -0.045 0.15 0.22 2 -0.39 71 73
GAS2 -0.074 0.18 0.23 1 -0.41 98 99
positive regulation of apoptosis 0.019 0.059 -10000 0 -0.33 5 5
PRF1 -0.041 0.16 -10000 0 -0.51 61 61
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.047 0.19 -9999 0 -0.49 75 75
MAP4K1 -0.045 0.17 -9999 0 -0.56 60 60
MAP3K8 0.01 0.031 -9999 0 -0.52 2 2
PRKCB -0.044 0.17 -9999 0 -0.55 60 60
DBNL 0.01 0.024 -9999 0 -0.58 1 1
CRKL 0.011 0 -9999 0 -10000 0 0
MAP3K1 -0.02 0.15 -9999 0 -0.52 39 39
JUN -0.034 0.2 -9999 0 -0.72 44 44
MAP3K7 -0.017 0.15 -9999 0 -0.54 33 33
GRAP2 -0.023 0.14 -9999 0 -0.55 37 37
CRK 0.011 0.019 -9999 0 -0.46 1 1
MAP2K4 -0.013 0.15 -9999 0 -0.52 36 36
LAT -0.009 0.1 -9999 0 -0.51 24 24
LCP2 -0.015 0.12 -9999 0 -0.55 29 29
MAPK8 -0.04 0.21 -9999 0 -0.76 43 43
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.024 0.16 -9999 0 -0.58 33 33
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.039 0.18 -9999 0 -0.47 75 75
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0.026 -10000 0 -10000 0 0
AES 0.013 0.033 -10000 0 -0.58 1 1
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.014 0.039 -10000 0 -0.4 5 5
SMAD4 0.004 0.068 -10000 0 -0.58 8 8
DKK2 -0.087 0.21 -10000 0 -0.54 108 108
TLE1 0.01 0.053 -10000 0 -0.59 4 4
MACF1 0.012 0 -10000 0 -10000 0 0
CTNNB1 0.05 0.098 0.25 13 -0.95 2 15
WIF1 -0.18 0.25 -10000 0 -0.5 221 221
beta catenin/RanBP3 0.025 0.13 0.39 58 -0.7 2 60
KREMEN2 -0.038 0.15 -10000 0 -0.48 61 61
DKK1 -0.16 0.24 -10000 0 -0.51 192 192
beta catenin/beta TrCP1 0.054 0.09 0.25 10 -0.8 2 12
FZD1 0.009 0.039 -10000 0 -0.54 3 3
AXIN2 -0.11 0.42 -10000 0 -1.4 55 55
AXIN1 0.011 0.024 -10000 0 -0.59 1 1
RAN 0.012 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.014 0.081 -10000 0 -0.95 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.049 0.1 -10000 0 -0.62 7 7
Axin1/APC/GSK3 0.046 0.078 0.22 15 -0.78 2 17
Axin1/APC/GSK3/beta catenin/Macf1 0.037 0.093 -10000 0 -0.71 4 4
HNF1A 0.009 0.059 -10000 0 -0.53 6 6
CTBP1 0.013 0.034 -10000 0 -0.59 1 1
MYC -0.013 0.16 -10000 0 -1.6 5 5
RANBP3 0.011 0.024 -10000 0 -0.58 1 1
DKK2/LRP6/Kremen 2 -0.07 0.16 -10000 0 -0.32 162 162
NKD1 -0.13 0.24 -10000 0 -0.53 162 162
TCF4 0.001 0.088 -10000 0 -0.52 15 15
TCF3 0.013 0.033 -10000 0 -0.59 1 1
WNT1/LRP6/FZD1/Axin1 0.017 0.059 -10000 0 -0.37 5 5
Ran/GTP 0.009 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.028 0.16 0.46 51 -0.62 6 57
LEF1 -0.01 0.11 -10000 0 -0.52 27 27
DVL1 0.046 0.06 0.21 1 -0.5 4 5
CSNK2A1 0.012 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.042 0.11 -10000 0 -0.51 12 12
DKK1/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.32 234 234
LRP6 0.01 0.034 -10000 0 -0.59 2 2
CSNK1A1 0.013 0.043 -10000 0 -0.59 2 2
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 -0.007 0.11 -10000 0 -0.88 5 5
WNT1 -0.007 0.083 -10000 0 -0.46 20 20
GSK3A 0.012 0.001 -10000 0 -10000 0 0
GSK3B 0.01 0.034 -10000 0 -0.59 2 2
FRAT1 0.01 0.024 -10000 0 -0.58 1 1
PPP2R5D 0.089 0.11 0.27 158 -10000 0 158
APC 0.011 0.082 -10000 0 -0.38 12 12
WNT1/LRP6/FZD1 0.07 0.1 0.23 78 -0.69 3 81
CREBBP 0.014 0.023 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.017 0.091 -10000 0 -0.64 10 10
HDAC1 0.008 0.004 -10000 0 -10000 0 0
AES 0.01 0.024 -10000 0 -0.58 1 1
FBXW11 0.011 0 -10000 0 -10000 0 0
DTX1 -0.011 0.11 -10000 0 -0.54 25 25
LRP6/FZD1 0.014 0.038 -10000 0 -0.4 5 5
TLE1 0.007 0.048 -10000 0 -0.59 4 4
AP1 -0.061 0.13 -10000 0 -0.3 115 115
NCSTN 0.011 0 -10000 0 -10000 0 0
ADAM10 0.006 0.054 -10000 0 -0.58 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.036 0.068 -10000 0 -1.3 1 1
NICD/RBPSUH 0.016 0.085 -10000 0 -0.65 9 9
WIF1 -0.18 0.25 -10000 0 -0.5 221 221
NOTCH1 -0.011 0.078 -10000 0 -0.63 9 9
PSENEN 0.01 0.024 -10000 0 -0.58 1 1
KREMEN2 -0.038 0.15 -10000 0 -0.48 61 61
DKK1 -0.16 0.24 -10000 0 -0.51 192 192
beta catenin/beta TrCP1 0.051 0.068 0.25 3 -10000 0 3
APH1B 0.006 0.059 -10000 0 -0.58 6 6
APH1A 0.011 0 -10000 0 -10000 0 0
AXIN1 -0.013 0.047 -10000 0 -0.3 8 8
CtBP/CBP/TCF1/TLE1/AES 0.013 0.053 -10000 0 -0.34 9 9
PSEN1 0.011 0 -10000 0 -10000 0 0
FOS -0.026 0.14 -10000 0 -0.54 41 41
JUN 0.007 0.052 -10000 0 -0.56 5 5
MAP3K7 0.01 0.002 -10000 0 -10000 0 0
CTNNB1 0.048 0.073 0.2 62 -10000 0 62
MAPK3 0.01 0.024 -10000 0 -0.58 1 1
DKK2/LRP6/Kremen 2 -0.069 0.16 -10000 0 -0.32 162 162
HNF1A 0.005 0.057 -10000 0 -0.56 6 6
CTBP1 0.01 0.024 -10000 0 -0.58 1 1
MYC 0.01 0.13 -10000 0 -1.4 5 5
NKD1 -0.13 0.24 -10000 0 -0.53 162 162
FZD1 0.009 0.039 -10000 0 -0.54 3 3
NOTCH1 precursor/Deltex homolog 1 0.005 0.098 -10000 0 -0.59 10 10
apoptosis -0.061 0.13 -10000 0 -0.3 115 115
Delta 1/NOTCHprecursor 0.01 0.095 -10000 0 -0.63 10 10
DLL1 -0.003 0.086 -10000 0 -0.52 16 16
PPARD 0.019 0.057 -10000 0 -1.4 1 1
Gamma Secretase 0.031 0.035 -10000 0 -0.3 7 7
APC -0.028 0.1 -10000 0 -0.49 22 22
DVL1 -0.009 0.051 -10000 0 -0.5 4 4
CSNK2A1 0.012 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.32 234 234
LRP6 0.01 0.034 -10000 0 -0.58 2 2
CSNK1A1 0.01 0.034 -10000 0 -0.58 2 2
NLK 0.011 0.005 -10000 0 -10000 0 0
CCND1 0.017 0.081 -10000 0 -1.4 2 2
WNT1 -0.008 0.083 -10000 0 -0.46 20 20
Axin1/APC/beta catenin 0.026 0.077 -10000 0 -0.36 12 12
DKK2 -0.087 0.21 -10000 0 -0.54 108 108
NOTCH1 precursor/DVL1 -0.016 0.088 -10000 0 -0.66 10 10
GSK3B 0.009 0.034 -10000 0 -0.58 2 2
FRAT1 0.01 0.024 -10000 0 -0.58 1 1
NOTCH/Deltex homolog 1 -0.022 0.093 -10000 0 -0.6 10 10
PPP2R5D 0.061 0.12 0.25 158 -10000 0 158
MAPK1 0.01 0.024 -10000 0 -0.58 1 1
WNT1/LRP6/FZD1 -0.092 0.15 -10000 0 -0.34 88 88
RBPJ 0.01 0.031 -10000 0 -0.52 2 2
CREBBP 0.014 0.002 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.009 0.1 -9999 0 -0.51 24 24
GPC2 -0.007 0.1 -9999 0 -0.55 20 20
GPC2/Midkine -0.012 0.1 -9999 0 -0.39 43 43
neuron projection morphogenesis -0.012 0.1 -9999 0 -0.38 43 43
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.024 0.26 -10000 0 -0.88 39 39
NCK1/PAK1/Dok-R -0.039 0.11 -10000 0 -0.42 42 42
NCK1/Dok-R -0.028 0.3 -10000 0 -1.1 39 39
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
mol:beta2-estradiol 0.006 0.057 0.24 31 -10000 0 31
RELA 0.011 0 -10000 0 -10000 0 0
SHC1 0.012 0.001 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 -0.11 0.23 0.24 26 -0.5 147 173
TNIP2 0.01 0.024 -10000 0 -0.58 1 1
NF kappa B/RelA -0.043 0.26 -10000 0 -1 39 39
FN1 -0.088 0.21 -10000 0 -0.52 112 112
PLD2 -0.008 0.31 -10000 0 -1.1 39 39
PTPN11 0.007 0.054 -10000 0 -0.58 5 5
GRB14 -0.12 0.24 -10000 0 -0.54 144 144
ELK1 0.004 0.27 -10000 0 -0.99 39 39
GRB7 0.002 0.065 -10000 0 -0.46 12 12
PAK1 0.011 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.087 0.3 -10000 0 -1.1 43 43
CDKN1A 0.041 0.2 -10000 0 -0.6 39 39
ITGA5 -0.006 0.093 -10000 0 -0.49 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.028 0.3 -10000 0 -1.1 39 39
CRK 0.011 0.019 -10000 0 -0.46 1 1
mol:NO 0.033 0.21 -10000 0 -0.64 43 43
PLG -0.035 0.31 -10000 0 -1.1 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.02 0.25 -10000 0 -0.84 39 39
GRB2 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.042 -10000 0 -0.58 3 3
ANGPT2 0.018 0.2 -10000 0 -0.64 22 22
BMX -0.054 0.33 -10000 0 -1.2 41 41
ANGPT1 -0.019 0.31 -10000 0 -1.2 33 33
tube development 0.035 0.22 -10000 0 -0.65 41 41
ANGPT4 0.001 0.042 -10000 0 -0.46 5 5
response to hypoxia -0.001 0.019 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.079 0.33 -10000 0 -1.2 40 40
alpha5/beta1 Integrin 0.004 0.067 -10000 0 -0.35 21 21
FGF2 -0.04 0.16 -10000 0 -0.52 57 57
STAT5A (dimer) 0.036 0.24 -10000 0 -0.74 39 39
mol:L-citrulline 0.033 0.21 -10000 0 -0.64 43 43
AGTR1 -0.096 0.21 -10000 0 -0.51 123 123
MAPK14 0 0.3 -10000 0 -1.1 39 39
Tie2/SHP2 -0.042 0.19 -10000 0 -0.99 20 20
TEK -0.018 0.22 -10000 0 -1.2 16 16
RPS6KB1 0.024 0.25 -10000 0 -0.86 39 39
Angiotensin II/AT1 -0.068 0.16 -10000 0 -0.37 123 123
Tie2/Ang1/GRB2 -0.012 0.32 -10000 0 -1.2 39 39
MAPK3 0.001 0.28 -10000 0 -1 39 39
MAPK1 0.001 0.28 -10000 0 -1 39 39
Tie2/Ang1/GRB7 -0.016 0.32 -10000 0 -1.2 39 39
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.008 0.31 -10000 0 -1.1 39 39
PI3K 0.012 0.29 -10000 0 -1 39 39
FES -0.006 0.32 -10000 0 -1.1 40 40
Crk/Dok-R -0.027 0.3 -10000 0 -1.1 39 39
Tie2/Ang1/ABIN2 -0.013 0.32 -10000 0 -1.2 39 39
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.03 0.24 -10000 0 -0.78 39 39
STAT5A 0.012 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.026 0.25 -10000 0 -0.84 39 39
Tie2/Ang2 0.02 0.28 -10000 0 -0.89 40 40
Tie2/Ang1 -0.017 0.34 -10000 0 -1.2 39 39
FOXO1 0.032 0.24 -10000 0 -0.77 42 42
ELF1 0.013 0.046 -10000 0 -0.59 3 3
ELF2 -0.009 0.31 -10000 0 -1.1 39 39
mol:Choline -0.004 0.29 -10000 0 -1.1 39 39
cell migration -0.03 0.068 -10000 0 -0.23 45 45
FYN 0.03 0.24 -10000 0 -0.76 40 40
DOK2 -0.012 0.11 -10000 0 -0.55 25 25
negative regulation of cell cycle 0.044 0.19 -10000 0 -0.55 39 39
ETS1 -0.003 0.088 -10000 0 -0.46 14 14
PXN 0.037 0.21 -10000 0 -0.69 39 39
ITGB1 0.011 0 -10000 0 -10000 0 0
NOS3 0.027 0.23 -10000 0 -0.74 43 43
RAC1 0.011 0 -10000 0 -10000 0 0
TNF -0.023 0.14 -10000 0 -0.53 35 35
MAPKKK cascade -0.004 0.29 -10000 0 -1.1 39 39
RASA1 0.009 0.034 -10000 0 -0.58 2 2
Tie2/Ang1/Shc -0.011 0.32 -10000 0 -1.2 39 39
NCK1 0.009 0.034 -10000 0 -0.58 2 2
vasculogenesis 0.036 0.19 -10000 0 -0.57 43 43
mol:Phosphatidic acid -0.004 0.29 -10000 0 -1.1 39 39
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP 0.033 0.21 -10000 0 -0.64 43 43
Rac1/GTP -0.061 0.2 -10000 0 -0.78 40 40
MMP2 -0.028 0.33 -10000 0 -1.2 40 40
Visual signal transduction: Rods

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
mol:K + 0.009 0.034 -9999 0 -0.58 2 2
GNAT1/GTP 0 0.023 -9999 0 -0.32 3 3
Metarhodopsin II/Arrestin 0 0.022 -9999 0 -0.27 4 4
PDE6G/GNAT1/GTP -0.016 0.091 -9999 0 -0.33 45 45
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0 0.033 -9999 0 -0.46 3 3
GRK1 -0.003 0.046 -9999 0 -0.46 6 6
CNG Channel -0.12 0.18 -9999 0 -0.37 162 162
mol:Na + -0.066 0.13 -9999 0 -0.5 23 23
mol:ADP -0.003 0.046 -9999 0 -0.46 6 6
RGS9-1/Gbeta5/R9AP -0.021 0.12 -9999 0 -0.33 75 75
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.068 0.13 -9999 0 -0.51 23 23
CNGB1 -0.004 0.067 -9999 0 -0.46 13 13
RDH5 0 0.078 -9999 0 -0.53 13 13
SAG 0.002 0.019 -9999 0 -0.46 1 1
mol:Ca2+ -0.043 0.14 -9999 0 -0.48 23 23
Na + (4 Units) -0.063 0.12 -9999 0 -0.46 23 23
RGS9 -0.034 0.15 -9999 0 -0.52 51 51
GNB1/GNGT1 -0.023 0.12 -9999 0 -0.38 58 58
GNAT1/GDP -0.017 0.1 -9999 0 -0.32 45 45
GUCY2D -0.015 0.1 -9999 0 -0.46 30 30
GNGT1 -0.043 0.16 -9999 0 -0.52 58 58
GUCY2F 0 0.019 -9999 0 -0.46 1 1
GNB5 0.007 0.048 -9999 0 -0.58 4 4
mol:GMP (4 units) -0.087 0.18 -9999 0 -0.37 130 130
mol:11-cis-retinal 0 0.078 -9999 0 -0.52 13 13
mol:cGMP -0.025 0.11 -9999 0 -0.34 33 33
GNB1 0.011 0 -9999 0 -10000 0 0
Rhodopsin -0.001 0.061 -9999 0 -0.37 16 16
SLC24A1 0.009 0.034 -9999 0 -0.58 2 2
CNGA1 -0.05 0.17 -9999 0 -0.53 69 69
Metarhodopsin II -0.002 0.033 -9999 0 -0.28 8 8
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.027 0.11 -9999 0 -0.36 35 35
RGS9BP -0.01 0.1 -9999 0 -0.54 22 22
Metarhodopsin II/Transducin -0.012 0.071 -9999 0 -0.28 33 33
GCAP Family/Ca ++ -0.019 0.094 -9999 0 -0.34 30 30
PDE6A/B -0.1 0.2 -9999 0 -0.42 164 164
mol:Pi -0.021 0.12 -9999 0 -0.32 75 75
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.016 0.092 -9999 0 -0.33 32 32
PDE6B -0.033 0.15 -9999 0 -0.53 49 49
PDE6A -0.11 0.23 -9999 0 -0.54 130 130
PDE6G -0.027 0.14 -9999 0 -0.55 42 42
RHO -0.001 0.032 -9999 0 -0.46 3 3
PDE6 -0.12 0.18 -9999 0 -0.56 53 53
GUCA1A -0.02 0.12 -9999 0 -0.49 34 34
GC2/GCAP Family -0.019 0.095 -9999 0 -0.34 31 31
GUCA1C -0.001 0.026 -9999 0 -0.46 2 2
GUCA1B -0.016 0.12 -9999 0 -0.54 30 30
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.032 0.14 -10000 0 -0.41 47 47
CRKL -0.011 0.12 -10000 0 -0.42 38 38
HRAS -0.025 0.15 -10000 0 -0.49 31 31
mol:PIP3 -0.021 0.12 -10000 0 -0.41 39 39
SPRED1 0.006 0.059 -10000 0 -0.58 6 6
SPRED2 0.008 0.042 -10000 0 -0.58 3 3
GAB1 -0.018 0.13 -10000 0 -0.44 39 39
FOXO3 -0.006 0.12 -10000 0 -0.38 40 40
AKT1 -0.014 0.13 -10000 0 -0.42 40 40
BAD -0.007 0.12 -10000 0 -0.39 40 40
megakaryocyte differentiation -0.082 0.18 -10000 0 -0.36 137 137
GSK3B -0.007 0.12 -10000 0 -0.39 41 41
RAF1 -0.012 0.13 -10000 0 -0.4 28 28
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.018 0.13 -10000 0 -0.44 39 39
STAT1 -0.062 0.32 -10000 0 -1.1 41 41
HRAS/SPRED1 -0.015 0.13 -10000 0 -0.41 33 33
cell proliferation -0.018 0.13 -10000 0 -0.44 39 39
PIK3CA 0.009 0.034 -10000 0 -0.59 2 2
TEC 0.011 0.019 -10000 0 -0.46 1 1
RPS6KB1 -0.02 0.14 -10000 0 -0.46 40 40
HRAS/SPRED2 -0.015 0.13 -10000 0 -0.4 32 32
LYN/TEC/p62DOK -0.006 0.12 -10000 0 -0.41 38 38
MAPK3 0.002 0.095 -10000 0 -0.29 20 20
STAP1 -0.05 0.17 -10000 0 -0.5 54 54
GRAP2 -0.023 0.14 -10000 0 -0.55 37 37
JAK2 -0.054 0.28 -10000 0 -0.97 42 42
STAT1 (dimer) -0.059 0.31 -10000 0 -1.1 41 41
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.043 0.17 -10000 0 -0.48 53 53
actin filament polymerization -0.03 0.14 -10000 0 -0.46 41 41
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.057 0.22 -10000 0 -0.65 55 55
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
CBL/CRKL/GRB2 0.002 0.12 -10000 0 -0.38 37 37
PI3K -0.01 0.14 -10000 0 -0.45 40 40
PTEN 0.006 0.059 -10000 0 -0.58 6 6
SCF/KIT/EPO/EPOR -0.064 0.34 -10000 0 -1.3 37 37
MAPK8 -0.018 0.13 -10000 0 -0.44 39 39
STAT3 (dimer) -0.017 0.13 -10000 0 -0.44 39 39
positive regulation of transcription 0.005 0.08 -10000 0 -0.24 15 15
mol:GDP -0.035 0.16 -10000 0 -0.49 41 41
PIK3C2B -0.018 0.13 -10000 0 -0.44 39 39
CBL/CRKL -0.004 0.12 -10000 0 -0.39 38 38
FER -0.022 0.14 -10000 0 -0.46 40 40
SH2B3 -0.018 0.13 -10000 0 -0.44 39 39
PDPK1 -0.014 0.11 -10000 0 -0.38 38 38
SNAI2 -0.027 0.14 -10000 0 -0.45 45 45
positive regulation of cell proliferation -0.039 0.23 -10000 0 -0.78 42 42
KITLG -0.003 0.099 -10000 0 -0.6 16 16
cell motility -0.039 0.23 -10000 0 -0.78 42 42
PTPN6 0.011 0.007 -10000 0 -10000 0 0
EPOR -0.001 0.14 -10000 0 -1.2 4 4
STAT5A (dimer) -0.03 0.19 -10000 0 -0.64 43 43
SOCS1 -0.028 0.14 -10000 0 -0.5 47 47
cell migration 0.057 0.16 0.42 70 -10000 0 70
SOS1 0.01 0.024 -10000 0 -0.58 1 1
EPO 0.001 0.054 -10000 0 -0.46 8 8
VAV1 -0.028 0.15 -10000 0 -0.58 40 40
GRB10 -0.02 0.13 -10000 0 -0.45 41 41
PTPN11 0.007 0.053 -10000 0 -0.58 5 5
SCF/KIT -0.025 0.14 -10000 0 -0.45 44 44
GO:0007205 0 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.1 -10000 0 -0.31 29 29
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.065 0.33 -10000 0 -1.4 33 33
MAP2K2 -0.002 0.1 -10000 0 -0.31 26 26
SHC/Grb2/SOS1 -0.006 0.12 -10000 0 -0.42 38 38
STAT5A -0.032 0.2 -10000 0 -0.66 43 43
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.026 0.14 -10000 0 -0.44 45 45
SHC/GRAP2 -0.008 0.1 -10000 0 -0.4 37 37
PTPRO -0.084 0.18 -10000 0 -0.36 137 137
SH2B2 -0.031 0.14 -10000 0 -0.47 41 41
DOK1 0.011 0 -10000 0 -10000 0 0
MATK -0.058 0.17 -10000 0 -0.43 70 70
CREBBP 0.022 0.031 -10000 0 -10000 0 0
BCL2 -0.019 0.23 -10000 0 -1.3 16 16
Cellular roles of Anthrax toxin

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
ANTXR1 -0.045 0.17 -10000 0 -0.54 63 63
ANTXR2 0.005 0.058 -10000 0 -0.53 7 7
negative regulation of myeloid dendritic cell antigen processing and presentation -0.008 0.022 -10000 0 -0.069 69 69
monocyte activation -0.026 0.14 -10000 0 -0.49 40 40
MAP2K2 -0.004 0.032 -10000 0 -0.77 1 1
MAP2K1 -0.008 0.027 -10000 0 -0.35 2 2
MAP2K7 -0.007 0.022 -10000 0 -0.32 1 1
MAP2K6 -0.012 0.046 -10000 0 -0.32 11 11
CYAA -0.021 0.094 -10000 0 -0.28 69 69
MAP2K4 -0.008 0.029 -10000 0 -0.32 3 3
IL1B -0.039 0.11 -10000 0 -0.28 89 89
Channel -0.021 0.1 -10000 0 -0.3 69 69
NLRP1 -0.02 0.065 -10000 0 -0.28 31 31
CALM1 0.011 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.009 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.008 0.022 0.069 69 -10000 0 69
MAPK3 -0.007 0.022 -10000 0 -0.32 1 1
MAPK1 -0.007 0.024 -10000 0 -0.38 1 1
PGR -0.041 0.099 -10000 0 -0.29 78 78
PA/Cellular Receptors -0.024 0.11 -10000 0 -0.33 69 69
apoptosis -0.008 0.022 -10000 0 -0.069 69 69
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.019 0.094 -10000 0 -0.28 69 69
macrophage activation 0.007 0.028 -10000 0 -0.33 2 2
TNF -0.017 0.12 -10000 0 -0.54 31 31
VCAM1 -0.026 0.14 -10000 0 -0.5 40 40
platelet activation -0.009 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.002 0.027 0.14 4 -10000 0 4
IL18 -0.007 0.055 -10000 0 -0.26 17 17
negative regulation of macrophage activation -0.008 0.022 -10000 0 -0.069 69 69
LEF -0.008 0.022 -10000 0 -0.069 69 69
CASP1 -0.017 0.041 -10000 0 -0.16 33 33
mol:cAMP -0.009 0.025 -10000 0 -10000 0 0
necrosis -0.008 0.022 -10000 0 -0.069 69 69
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.019 0.096 -10000 0 -0.28 69 69
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.013 0.034 -9999 0 -0.44 3 3
ARNO/beta Arrestin1-2 -0.004 0.07 -9999 0 -10000 0 0
EGFR 0.005 0.058 -9999 0 -0.53 7 7
EPHA2 0.006 0.055 -9999 0 -0.54 6 6
USP6 0.008 0.041 -9999 0 -0.49 4 4
IQSEC1 0.011 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.13 0.19 -9999 0 -0.36 228 228
ARRB2 0.007 0.008 -9999 0 -0.19 1 1
mol:GTP 0.004 0.046 -9999 0 -0.26 12 12
ARRB1 0.009 0.034 -9999 0 -0.58 2 2
FBXO8 0.009 0.034 -9999 0 -0.58 2 2
TSHR -0.011 0.093 -9999 0 -0.46 25 25
EGF -0.18 0.25 -9999 0 -0.51 222 222
somatostatin receptor activity 0 0 -9999 0 -0.001 47 47
ARAP2 -0.005 0.098 -9999 0 -0.58 17 17
mol:GDP -0.033 0.085 -9999 0 -0.26 44 44
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 19 19
ITGA2B -0.043 0.16 -9999 0 -0.5 63 63
ARF6 0.01 0.024 -9999 0 -0.58 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.024 0.045 -9999 0 -0.37 6 6
ADAP1 0.01 0.031 -9999 0 -0.52 2 2
KIF13B 0.009 0.034 -9999 0 -0.58 2 2
HGF/MET -0.021 0.12 -9999 0 -0.39 57 57
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.038 0.092 -9999 0 -0.26 44 44
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.099 0.16 -9999 0 -0.3 228 228
ADRB2 -0.029 0.15 -9999 0 -0.55 44 44
receptor agonist activity 0 0 -9999 0 0 44 44
actin filament binding 0 0 -9999 0 0 45 45
SRC 0.01 0.024 -9999 0 -0.58 1 1
ITGB3 -0.008 0.1 -9999 0 -0.55 21 21
GNAQ 0.005 0.059 -9999 0 -0.59 6 6
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 35 35
ARF6/GDP -0.002 0.1 -9999 0 -0.36 33 33
ARF6/GDP/GULP/ACAP1 -0.06 0.14 -9999 0 -0.38 68 68
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.013 0.11 -9999 0 -0.32 40 40
ACAP1 -0.026 0.14 -9999 0 -0.54 41 41
ACAP2 0.002 0.076 -9999 0 -0.58 10 10
LHCGR/beta Arrestin2 0.001 0.011 -9999 0 -0.26 1 1
EFNA1 0.011 0.019 -9999 0 -0.46 1 1
HGF -0.039 0.16 -9999 0 -0.55 55 55
CYTH3 0.007 0.029 -9999 0 -0.4 3 3
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.009 0.034 -9999 0 -0.58 2 2
fibronectin binding 0 0 -9999 0 0 31 31
endosomal lumen acidification 0 0 -9999 0 0 35 35
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.051 0.18 -9999 0 -0.54 69 69
GNAQ/ARNO 0.011 0.031 -9999 0 -0.3 6 6
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 21 21
MET 0.01 0.031 -9999 0 -0.52 2 2
GNA14 -0.007 0.1 -9999 0 -0.56 19 19
GNA15 -0.009 0.1 -9999 0 -0.54 22 22
GIT1 0.01 0.024 -9999 0 -0.58 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 36 36
GNA11 0.007 0.05 -9999 0 -0.53 5 5
LHCGR 0 0.019 -9999 0 -0.46 1 1
AGTR1 -0.097 0.21 -9999 0 -0.51 123 123
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.011 -9999 0 -0.26 1 1
IPCEF1/ARNO -0.074 0.12 -9999 0 -0.48 1 1
alphaIIb/beta3 Integrin -0.037 0.14 -9999 0 -0.37 83 83
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.035 0.12 -10000 0 -0.33 84 84
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.009 0.033 -10000 0 -0.46 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.033 0.072 -10000 0 -0.32 12 12
IRAK/TOLLIP -0.014 0.096 -10000 0 -0.42 7 7
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
IKBKG 0.01 0.024 -10000 0 -0.58 1 1
IL1 alpha/IL1R2 -0.1 0.2 -10000 0 -0.41 171 171
IL1A -0.09 0.21 -10000 0 -0.52 116 116
IL1B -0.056 0.17 -10000 0 -0.4 108 108
IRAK/TRAF6/p62/Atypical PKCs 0.003 0.095 -10000 0 -0.58 5 5
IL1R2 -0.055 0.18 -10000 0 -0.52 76 76
IL1R1 -0.006 0.095 -10000 0 -0.51 20 20
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.008 0.09 0.2 9 -0.36 11 20
TOLLIP 0.01 0.024 -10000 0 -0.58 1 1
TICAM2 -0.009 0.11 -10000 0 -0.58 20 20
MAP3K3 0.009 0.034 -10000 0 -0.58 2 2
TAK1/TAB1/TAB2 0.008 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.021 0.086 -10000 0 -0.62 4 4
JUN -0.001 0.089 -10000 0 -0.55 4 4
MAP3K7 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.031 0.14 -10000 0 -0.55 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.043 0.14 -10000 0 -0.35 71 71
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.035 0.13 -10000 0 -0.32 71 71
IL1 beta fragment/IL1R1/IL1RAP -0.045 0.15 -10000 0 -0.37 74 74
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.005 0.089 -10000 0 -0.53 4 4
IRAK1 -0.022 0.1 -10000 0 -0.41 7 7
IL1RN/IL1R1 -0.04 0.15 -10000 0 -0.39 84 84
IRAK4 0.011 0 -10000 0 -10000 0 0
PRKCI 0.008 0.042 -10000 0 -0.58 3 3
TRAF6 0.01 0.024 -10000 0 -0.58 1 1
PI3K 0.013 0.04 -10000 0 -0.43 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.013 0.096 -10000 0 -0.33 22 22
CHUK 0.007 0.048 -10000 0 -0.58 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.045 0.15 -10000 0 -0.37 74 74
IL1 beta/IL1R2 -0.081 0.19 -10000 0 -0.37 159 159
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.017 0.081 -10000 0 -0.58 2 2
NF kappa B1 p50/RelA -0.055 0.11 -10000 0 -0.5 18 18
IRAK3 -0.026 0.14 -10000 0 -0.54 41 41
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.039 0.15 -10000 0 -0.55 18 18
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.11 -10000 0 -0.4 12 12
IL1 alpha/IL1R1/IL1RAP -0.056 0.15 -10000 0 -0.33 138 138
RELA 0.011 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.011 0 -10000 0 -10000 0 0
MYD88 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.006 0.093 -10000 0 -0.46 4 4
IL1RAP 0.002 0.076 -10000 0 -0.58 10 10
UBE2N 0.01 0.024 -10000 0 -0.58 1 1
IRAK/TRAF6 -0.08 0.14 -10000 0 -0.45 45 45
CASP1 -0.022 0.13 -10000 0 -0.54 37 37
IL1RN/IL1R2 -0.074 0.19 -10000 0 -0.43 123 123
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.035 0.14 -10000 0 -0.34 74 74
TMEM189-UBE2V1 -0.06 0.16 -10000 0 -0.46 84 84
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.025 0.11 -10000 0 -0.41 22 22
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
IL1RN -0.05 0.17 -10000 0 -0.52 70 70
TRAF6/TAK1/TAB1/TAB2 -0.03 0.078 -10000 0 -0.39 5 5
MAP2K6 -0.011 0.092 -10000 0 -0.37 10 10
Effects of Botulinum toxin

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
STX1A 0.002 0.051 -9999 0 -0.34 13 13
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.032 0.12 -9999 0 -0.36 73 73
STXBP1 -0.006 0.1 -9999 0 -0.56 19 19
ACh/CHRNA1 -0.026 0.1 -9999 0 -0.36 49 49
RAB3GAP2/RIMS1/UNC13B -0.021 0.11 -9999 0 -0.36 34 34
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.054 0.17 -9999 0 -0.51 72 72
mol:ACh -0.007 0.036 -9999 0 -0.13 32 32
RAB3GAP2 0.008 0.042 -9999 0 -0.58 3 3
STX1A/SNAP25/VAMP2 -0.051 0.1 -9999 0 -0.46 13 13
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.026 0.1 -9999 0 -0.36 49 49
UNC13B 0.01 0.031 -9999 0 -0.52 2 2
CHRNA1 -0.032 0.15 -9999 0 -0.53 49 49
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.083 0.16 -9999 0 -0.38 134 134
SNAP25 -0.024 0.076 -9999 0 -0.2 85 85
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.12 0.24 -9999 0 -0.57 134 134
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.002 0.075 -9999 0 -0.32 32 32
STX1A/SNAP25 fragment 1/VAMP2 -0.051 0.1 -9999 0 -0.46 13 13
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.012 0.045 -9999 0 -0.37 8 8
alphaV beta3 Integrin -0.026 0.14 -9999 0 -0.37 76 76
PTK2 -0.027 0.15 -9999 0 -0.54 29 29
IGF1R 0.01 0.024 -9999 0 -0.58 1 1
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0.001 0.074 -9999 0 -0.5 13 13
SRC 0.01 0.024 -9999 0 -0.58 1 1
CDKN1B -0.038 0.14 -9999 0 -0.51 32 32
VEGFA 0.011 0.019 -9999 0 -0.46 1 1
ILK -0.037 0.13 -9999 0 -0.5 31 31
ROCK1 0.001 0.08 -9999 0 -0.58 11 11
AKT1 -0.026 0.13 -9999 0 -0.46 32 32
PTK2B 0.011 0.081 -9999 0 -0.59 2 2
alphaV/beta3 Integrin/JAM-A -0.043 0.15 -9999 0 -0.37 78 78
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.001 0.084 -9999 0 -0.34 33 33
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.029 0.13 -9999 0 -0.33 65 65
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.006 0.11 -9999 0 -0.6 12 12
alphaV/beta3 Integrin/Syndecan-1 0.004 0.084 -9999 0 -0.35 31 31
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.2 -9999 0 -0.59 71 71
PI4 Kinase 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Osteopontin -0.1 0.18 -9999 0 -0.33 215 215
RPS6KB1 -0.085 0.21 -9999 0 -0.55 74 74
TLN1 0.01 0.024 -9999 0 -0.58 1 1
MAPK3 -0.068 0.21 -9999 0 -0.68 50 50
GPR124 0.003 0.069 -9999 0 -0.56 9 9
MAPK1 -0.068 0.21 -9999 0 -0.68 50 50
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
alphaV/beta3 Integrin/Tumstatin -0.048 0.14 -9999 0 -0.32 124 124
cell adhesion 0.002 0.093 -9999 0 -0.37 29 29
ANGPTL3 0.002 0.033 -9999 0 -0.46 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.018 0.041 -9999 0 -0.31 9 9
IGF-1R heterotetramer 0.01 0.024 -9999 0 -0.58 1 1
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.019 -9999 0 -0.46 1 1
ITGB3 -0.008 0.1 -9999 0 -0.55 21 21
IGF1 -0.075 0.2 -9999 0 -0.52 97 97
RAC1 0.011 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0 0.096 -9999 0 -0.37 36 36
apoptosis 0.002 0.076 -9999 0 -0.58 10 10
CD47 0.009 0.034 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/CD47 0.004 0.087 -9999 0 -0.36 31 31
VCL 0.009 0.034 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Del1 -0.025 0.15 -9999 0 -0.43 64 64
CSF1 0.006 0.055 -9999 0 -0.54 6 6
PIK3C2A -0.055 0.18 -9999 0 -0.59 48 48
PI4 Kinase/Pyk2 -0.059 0.12 -9999 0 -0.47 25 25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.009 0.084 -9999 0 -0.34 27 27
FAK1/Vinculin -0.014 0.13 -9999 0 -0.43 28 28
alphaV beta3/Integrin/ppsTEM5 0 0.097 -9999 0 -0.37 36 36
RHOA 0.01 0.024 -9999 0 -0.58 1 1
VTN -0.054 0.17 -9999 0 -0.5 76 76
BCAR1 0.008 0.043 -9999 0 -0.52 4 4
FGF2 -0.039 0.16 -9999 0 -0.52 57 57
F11R -0.018 0.12 -9999 0 -0.37 57 57
alphaV/beta3 Integrin/Lactadherin -0.002 0.097 -9999 0 -0.35 40 40
alphaV/beta3 Integrin/TGFBR2 0.005 0.083 -9999 0 -0.34 31 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.019 0.061 -9999 0 -0.33 16 16
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
alphaV/beta3 Integrin/Talin 0.005 0.076 -9999 0 -0.34 25 25
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.088 0.21 -9999 0 -0.52 112 112
alphaV/beta3 Integrin/Pyk2 0.013 0.081 -9999 0 -0.6 2 2
SDC1 0.01 0.024 -9999 0 -0.58 1 1
VAV3 -0.02 0.12 -9999 0 -0.31 90 90
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
IRS1 0.002 0.076 -9999 0 -0.58 10 10
FAK1/Paxillin -0.014 0.12 -9999 0 -0.42 28 28
cell migration -0.006 0.12 -9999 0 -0.4 23 23
ITGAV 0.002 0.076 -9999 0 -0.58 10 10
PI3K -0.063 0.13 -9999 0 -0.52 26 26
SPP1 -0.16 0.25 -9999 0 -0.52 197 197
KDR 0.005 0.058 -9999 0 -0.53 7 7
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.002 0.076 -9999 0 -0.58 10 10
COL4A3 -0.074 0.19 -9999 0 -0.51 98 98
angiogenesis -0.067 0.21 -9999 0 -0.68 50 50
Rac1/GTP -0.013 0.11 -9999 0 -0.59 3 3
EDIL3 -0.037 0.16 -9999 0 -0.58 50 50
cell proliferation 0.004 0.083 -9999 0 -0.34 31 31
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 -0.016 0.12 -9999 0 -0.53 30 30
ITGA4 -0.019 0.13 -9999 0 -0.57 32 32
alpha4/beta7 Integrin -0.024 0.14 -9999 0 -0.44 55 55
alpha4/beta1 Integrin -0.006 0.096 -9999 0 -0.41 32 32
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.011 0 -10000 0 -10000 0 0
VDR 0.01 0.024 -10000 0 -0.58 1 1
Cbp/p300/PCAF 0.01 0.072 -10000 0 -0.37 20 20
EP300 0.007 0.048 -10000 0 -0.58 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.003 0.079 -10000 0 -0.35 16 16
KAT2B -0.005 0.098 -10000 0 -0.58 17 17
MAPK14 0.011 0 -10000 0 -10000 0 0
AKT1 0.003 0.085 0.21 12 -0.3 16 28
RAR alpha/9cRA/Cyclin H -0.049 0.085 -10000 0 -0.46 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.007 0.086 -10000 0 -0.38 17 17
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0.001 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.033 0.083 -10000 0 -0.48 1 1
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
VDR/VDR/Vit D3 0.008 0.018 -10000 0 -0.43 1 1
RXRs/RARs/NRIP1/9cRA -0.055 0.18 -10000 0 -0.42 98 98
NCOA2 0.004 0.066 -10000 0 -0.57 8 8
NCOA3 0.01 0.024 -10000 0 -0.58 1 1
NCOA1 0.01 0.024 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.01 0.024 -10000 0 -0.58 1 1
RARG 0.006 0.059 -10000 0 -0.58 6 6
RAR gamma1/9cRA 0.012 0.038 -10000 0 -0.36 6 6
MAPK3 0.011 0.024 -10000 0 -0.58 1 1
MAPK1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 0.011 0.024 -10000 0 -0.58 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.063 0.17 -10000 0 -0.43 92 92
RARA -0.042 0.1 -10000 0 -0.25 94 94
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.01 0.094 -10000 0 -0.4 19 19
PRKCA 0.012 0.031 -10000 0 -0.52 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.063 0.18 -10000 0 -0.43 97 97
RXRG -0.076 0.14 -10000 0 -0.35 93 93
RXRA -0.031 0.094 -10000 0 -0.26 5 5
RXRB -0.065 0.14 -10000 0 -0.34 91 91
VDR/Vit D3/DNA 0.008 0.018 -10000 0 -0.43 1 1
RBP1 -0.083 0.2 -10000 0 -0.49 115 115
CRBP1/9-cic-RA -0.059 0.14 -10000 0 -0.35 115 115
RARB -0.004 0.098 -10000 0 -0.54 19 19
PRKCG -0.15 0.25 -10000 0 -0.52 190 190
MNAT1 0.008 0.046 -10000 0 -0.55 4 4
RAR alpha/RXRs -0.049 0.18 -10000 0 -0.43 95 95
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.045 0.16 -10000 0 -0.37 93 93
proteasomal ubiquitin-dependent protein catabolic process -0.02 0.097 -10000 0 -0.36 18 18
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.063 0.18 -10000 0 -0.43 97 97
positive regulation of DNA binding -0.046 0.081 -10000 0 -0.43 5 5
NRIP1 -0.064 0.2 -10000 0 -0.91 15 15
RXRs/RARs -0.066 0.17 -10000 0 -0.42 99 99
RXRs/RXRs/DNA/9cRA -0.072 0.17 -10000 0 -0.44 97 97
PRKACA 0.011 0 -10000 0 -10000 0 0
CDK7 0.008 0.042 -10000 0 -0.58 3 3
TFIIH 0.019 0.044 -10000 0 -0.4 6 6
RAR alpha/9cRA -0.035 0.062 -10000 0 -0.37 5 5
CCNH 0.011 0 -10000 0 -10000 0 0
CREBBP 0.011 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.006 0.042 -10000 0 -0.42 2 2
Signaling events mediated by PTP1B

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
PDGFRB -0.006 0.097 -10000 0 -0.54 19 19
Jak2/Leptin Receptor -0.054 0.13 0.19 2 -0.41 50 52
PTP1B/AKT1 -0.021 0.079 -10000 0 -0.32 16 16
FYN 0.005 0.06 -10000 0 -0.55 7 7
p210 bcr-abl/PTP1B -0.029 0.084 0.17 1 -0.3 25 26
EGFR 0.002 0.059 -10000 0 -0.54 7 7
EGF/EGFR -0.11 0.14 -10000 0 -0.34 113 113
CSF1 0.006 0.055 -10000 0 -0.54 6 6
AKT1 0.01 0.025 -10000 0 -0.59 1 1
INSR 0.009 0.034 -10000 0 -0.59 2 2
PTP1B/N-cadherin -0.071 0.15 -10000 0 -0.35 109 109
Insulin Receptor/Insulin -0.026 0.061 -10000 0 -0.34 10 10
HCK -0.017 0.12 -10000 0 -0.54 31 31
CRK 0.011 0.019 -10000 0 -0.46 1 1
TYK2 -0.022 0.083 -10000 0 -0.33 18 18
EGF -0.18 0.25 -10000 0 -0.51 222 222
YES1 0.005 0.064 -10000 0 -0.58 7 7
CAV1 -0.042 0.1 -10000 0 -0.37 21 21
TXN 0.009 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.02 0.088 -10000 0 -0.35 19 19
cell migration 0.029 0.084 0.3 25 -0.17 1 26
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.042 0.17 -10000 0 -0.58 54 54
ITGA2B -0.044 0.16 -10000 0 -0.5 63 63
CSF1R -0.03 0.15 -10000 0 -0.54 46 46
Prolactin Receptor/Prolactin -0.043 0.14 -10000 0 -0.42 71 71
FGR -0.026 0.14 -10000 0 -0.54 41 41
PTP1B/p130 Cas -0.024 0.085 -10000 0 -0.32 22 22
Crk/p130 Cas -0.017 0.084 -10000 0 -0.34 18 18
DOK1 -0.019 0.092 -10000 0 -0.37 22 22
JAK2 -0.046 0.13 -10000 0 -0.42 48 48
Jak2/Leptin Receptor/Leptin -0.054 0.12 -10000 0 -0.47 26 26
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
PTPN1 -0.029 0.085 0.17 1 -0.3 25 26
LYN 0.011 0 -10000 0 -10000 0 0
CDH2 -0.084 0.21 -10000 0 -0.53 106 106
SRC 0 0.059 -10000 0 -1.2 1 1
ITGB3 -0.009 0.1 -10000 0 -0.55 21 21
CAT1/PTP1B -0.08 0.16 -10000 0 -0.47 57 57
CAPN1 0.01 0.025 -10000 0 -0.6 1 1
CSK 0.01 0.024 -10000 0 -0.58 1 1
PI3K -0.022 0.066 -10000 0 -0.44 7 7
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.049 0.11 -10000 0 -0.46 24 24
negative regulation of transcription -0.045 0.13 -10000 0 -0.41 48 48
FCGR2A -0.022 0.13 -10000 0 -0.54 37 37
FER 0 0.07 -10000 0 -0.54 10 10
alphaIIb/beta3 Integrin -0.039 0.13 -10000 0 -0.37 83 83
BLK -0.11 0.23 -10000 0 -0.53 138 138
Insulin Receptor/Insulin/Shc 0.013 0.031 -10000 0 -0.32 5 5
RHOA 0.01 0.025 -10000 0 -0.59 1 1
LEPR 0 0.079 -10000 0 -0.55 12 12
BCAR1 0.008 0.043 -10000 0 -0.52 4 4
p210 bcr-abl/Grb2 0.011 0 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.082 0.18 -10000 0 -0.51 62 62
PRL -0.013 0.088 -10000 0 -0.46 23 23
SOCS3 -0.003 0.13 -10000 0 -1.3 5 5
SPRY2 0.008 0.042 -10000 0 -0.59 3 3
Insulin Receptor/Insulin/IRS1 0.007 0.06 -10000 0 -0.37 14 14
CSF1/CSF1R -0.038 0.13 -10000 0 -0.39 47 47
Ras protein signal transduction 0.021 0.025 -10000 0 -10000 0 0
IRS1 0.002 0.076 -10000 0 -0.58 10 10
INS -0.002 0.035 -10000 0 -0.5 3 3
LEP -0.025 0.12 -10000 0 -0.46 40 40
STAT5B -0.032 0.09 -10000 0 -0.29 35 35
STAT5A -0.032 0.09 -10000 0 -0.29 35 35
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.031 0.11 -10000 0 -0.41 30 30
CSN2 -0.008 0.06 -10000 0 -10000 0 0
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
LAT -0.033 0.14 -10000 0 -0.57 33 33
YBX1 0.016 0.016 -10000 0 -0.36 1 1
LCK -0.031 0.14 -10000 0 -0.51 49 49
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 -0.073 0.2 -10000 0 -0.53 93 93
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.057 0.26 15 -0.3 4 19
RFC1 0.01 0.061 0.24 21 -0.38 4 25
PRKDC 0.01 0.06 0.23 25 -0.3 6 31
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 -0.01 0.051 0.24 5 -0.43 1 6
FASLG/FAS/FADD/FAF1 0.002 0.12 0.22 65 -0.3 34 99
MAP2K4 -0.029 0.13 -10000 0 -0.43 25 25
mol:ceramide -0.028 0.12 -10000 0 -0.39 46 46
GSN 0.005 0.069 0.26 15 -0.3 13 28
FASLG/FAS/FADD/FAF1/Caspase 8 -0.001 0.12 -10000 0 -0.36 36 36
FAS -0.003 0.085 -10000 0 -0.57 13 13
BID 0.008 0.05 0.29 13 -0.32 2 15
MAP3K1 -0.006 0.089 0.22 5 -0.3 15 20
MAP3K7 0.01 0.004 -10000 0 -10000 0 0
RB1 0 0.084 0.26 14 -0.35 21 35
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.066 0.17 -10000 0 -0.37 138 138
ARHGDIB 0.009 0.059 0.24 23 -0.31 5 28
FADD 0.009 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.005 0.069 0.3 13 -0.26 15 28
NFKB1 -0.044 0.086 -10000 0 -1.2 1 1
MAPK8 -0.047 0.18 -10000 0 -0.46 72 72
DFFA 0.012 0.055 0.24 21 -0.29 3 24
DNA fragmentation during apoptosis 0.012 0.055 0.24 21 -0.28 3 24
FAS/FADD/MET 0.01 0.058 -10000 0 -0.35 15 15
CFLAR/RIP1 0.013 0.007 -10000 0 -10000 0 0
FAIM3 -0.011 0.11 -10000 0 -0.52 27 27
FAF1 0.009 0.008 -10000 0 -10000 0 0
PARP1 0.012 0.055 0.26 15 -0.29 3 18
DFFB 0.012 0.055 0.24 21 -0.29 3 24
CHUK -0.04 0.081 -10000 0 -0.77 2 2
FASLG -0.054 0.18 -10000 0 -0.54 70 70
FAS/FADD 0.004 0.064 -10000 0 -0.42 13 13
HGF -0.039 0.16 -10000 0 -0.55 55 55
LMNA 0.009 0.051 0.23 14 -0.3 3 17
CASP6 0.011 0.053 0.23 21 -0.29 3 24
CASP10 0.008 0.025 -10000 0 -0.58 1 1
CASP3 0.014 0.066 0.28 26 -0.33 3 29
PTPN13 -0.08 0.21 -10000 0 -0.56 97 97
CASP8 0.012 0.066 0.3 27 -0.44 1 28
IL6 -0.17 0.41 -10000 0 -1.2 70 70
MET 0.01 0.031 -10000 0 -0.52 2 2
ICAD/CAD 0.011 0.051 0.24 15 -0.29 2 17
FASLG/FAS/FADD/FAF1/Caspase 10 -0.029 0.13 -10000 0 -0.39 46 46
activation of caspase activity by cytochrome c 0.008 0.05 0.29 13 -0.32 2 15
PAK2 0.011 0.059 0.24 21 -0.4 3 24
BCL2 -0.007 0.1 -10000 0 -0.55 20 20
IL27-mediated 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
TGFB1 -0.044 0.14 -10000 0 -0.42 63 63
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.024 0.12 0.49 15 -10000 0 15
IL27/IL27R/JAK1 -0.025 0.16 -10000 0 -0.62 17 17
TBX21 -0.047 0.23 -10000 0 -0.55 75 75
IL12B -0.004 0.07 -10000 0 -0.46 14 14
IL12A -0.026 0.12 -10000 0 -0.42 48 48
IL6ST -0.004 0.093 -10000 0 -0.59 15 15
IL27RA/JAK1 0.006 0.095 -10000 0 -1.2 3 3
IL27 -0.007 0.082 -10000 0 -0.46 19 19
TYK2 0.01 0.025 -10000 0 -0.59 1 1
T-helper cell lineage commitment -0.19 0.41 -10000 0 -1.3 64 64
T-helper 2 cell differentiation 0.024 0.12 0.49 15 -10000 0 15
T cell proliferation during immune response 0.024 0.12 0.49 15 -10000 0 15
MAPKKK cascade -0.024 0.12 -10000 0 -0.49 15 15
STAT3 0.011 0 -10000 0 -10000 0 0
STAT2 0.011 0.019 -10000 0 -0.46 1 1
STAT1 0.006 0.055 -10000 0 -0.5 7 7
IL12RB1 -0.036 0.15 -10000 0 -0.55 50 50
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.043 0.22 -10000 0 -0.59 52 52
IL27/IL27R/JAK2/TYK2 -0.024 0.13 -10000 0 -0.49 15 15
positive regulation of T cell mediated cytotoxicity -0.024 0.12 -10000 0 -0.49 15 15
STAT1 (dimer) -0.058 0.24 0.4 21 -0.74 33 54
JAK2 -0.008 0.1 -10000 0 -0.55 21 21
JAK1 0.009 0.042 -10000 0 -0.59 3 3
STAT2 (dimer) -0.018 0.12 -10000 0 -0.49 13 13
T cell proliferation -0.1 0.18 -10000 0 -0.5 60 60
IL12/IL12R/TYK2/JAK2 -0.044 0.14 -10000 0 -0.55 15 15
IL17A -0.2 0.41 -10000 0 -1.3 64 64
mast cell activation 0.024 0.12 0.49 15 -10000 0 15
IFNG -0.011 0.043 -10000 0 -0.11 61 61
T cell differentiation -0.004 0.007 0.014 2 -0.022 65 67
STAT3 (dimer) -0.018 0.12 -10000 0 -0.5 12 12
STAT5A (dimer) -0.018 0.12 -10000 0 -0.5 12 12
STAT4 (dimer) -0.039 0.16 -10000 0 -0.52 37 37
STAT4 -0.029 0.15 -10000 0 -0.56 43 43
T cell activation -0.006 0.01 0.12 3 -10000 0 3
IL27R/JAK2/TYK2 -0.013 0.12 -10000 0 -0.85 6 6
GATA3 -0.028 0.23 -10000 0 -1.3 17 17
IL18 0.003 0.049 -10000 0 -0.4 9 9
positive regulation of mast cell cytokine production -0.018 0.12 -10000 0 -0.49 12 12
IL27/EBI3 -0.028 0.13 -10000 0 -0.4 63 63
IL27RA -0.002 0.096 -10000 0 -1.3 3 3
IL6 -0.16 0.26 -10000 0 -0.54 174 174
STAT5A 0.011 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.005 0.039 0.47 3 -10000 0 3
IL1B -0.041 0.13 -10000 0 -0.38 79 79
EBI3 -0.032 0.15 -10000 0 -0.56 46 46
TNF -0.012 0.09 -10000 0 -0.4 31 31
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.022 0.17 -9999 0 -0.51 45 45
MAP3K8 0.009 0.031 -9999 0 -0.52 2 2
FOS -0.023 0.15 -9999 0 -0.58 30 30
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
PTPN7 -0.048 0.16 -9999 0 -0.5 72 72
HRAS 0.008 0.041 -9999 0 -0.49 4 4
PRKCB -0.044 0.17 -9999 0 -0.55 60 60
NRAS 0.002 0.076 -9999 0 -0.58 10 10
RAS family/GTP 0.011 0.069 -9999 0 -0.38 16 16
MAPK3 -0.019 0.14 -9999 0 -0.58 26 26
MAP2K1 -0.009 0.12 -9999 0 -0.42 45 45
ELK1 0.01 0.025 -9999 0 -0.58 1 1
BRAF -0.015 0.12 -9999 0 -0.43 44 44
mol:GTP 0 0.001 -9999 0 -0.005 40 40
MAPK1 -0.019 0.14 -9999 0 -0.63 22 22
RAF1 -0.014 0.12 -9999 0 -0.42 43 43
KRAS 0.006 0.057 -9999 0 -0.56 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR -0.041 0.16 -9999 0 -0.55 57 57
LRPAP1 0.01 0.024 -9999 0 -0.58 1 1
NUDC 0.011 0.019 -9999 0 -0.46 1 1
RELN/LRP8 -0.046 0.14 -9999 0 -0.31 125 125
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.01 0.024 -9999 0 -0.58 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.036 0.12 -9999 0 -0.32 65 65
IQGAP1/CaM 0.015 0.029 -9999 0 -0.39 3 3
DAB1 -0.081 0.2 -9999 0 -0.52 104 104
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
PLA2G7 -0.023 0.14 -9999 0 -0.56 36 36
CALM1 0.011 0 -9999 0 -10000 0 0
DYNLT1 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.014 0.036 -9999 0 -0.42 4 4
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.009 0.034 -9999 0 -0.58 2 2
CDK5R1 0.009 0.033 -9999 0 -0.46 3 3
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.052 0.17 -9999 0 -0.5 73 73
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.13 0.21 -9999 0 -0.37 235 235
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.026 0.12 -9999 0 -0.43 16 16
MAP1B -0.012 0.05 -9999 0 -0.31 10 10
RAC1 0.017 0.012 -9999 0 -10000 0 0
p35/CDK5 -0.021 0.11 -9999 0 -0.49 3 3
RELN -0.096 0.22 -9999 0 -0.52 121 121
PAFAH/LIS1 0.001 0.086 -9999 0 -0.34 36 36
LIS1/CLIP170 0.021 0.022 -9999 0 -0.36 2 2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.046 0.082 -9999 0 -0.37 9 9
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.073 0.16 -9999 0 -0.32 133 133
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.034 0.13 -9999 0 -0.41 25 25
LIS1/IQGAP1 0.021 0.025 -9999 0 -0.32 3 3
RHOA 0.016 0.035 -9999 0 -0.81 1 1
PAFAH1B1 0.019 0 -9999 0 -10000 0 0
PAFAH1B3 0.008 0.043 -9999 0 -0.52 4 4
PAFAH1B2 0.007 0.048 -9999 0 -0.58 4 4
MAP1B/LIS1/Dynein heavy chain 0.013 0.035 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.021 0.12 -9999 0 -0.41 17 17
LRP8 0.008 0.042 -9999 0 -0.58 3 3
NDEL1/Katanin 60 -0.027 0.12 -9999 0 -0.43 17 17
P39/CDK5 -0.051 0.15 -9999 0 -0.48 25 25
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.011 -9999 0 -0.26 1 1
CDK5 -0.027 0.12 -9999 0 -0.3 65 65
PPP2R5D 0.011 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.019 -9999 0 -0.31 2 2
CSNK2A1 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.1 0.18 -9999 0 -0.37 141 141
RELN/VLDLR -0.063 0.16 -9999 0 -0.35 99 99
CDC42 0.013 0.057 -9999 0 -0.58 5 5
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.012 0.11 -10000 0 -0.33 50 50
ER alpha/Gai/GDP/Gbeta gamma -0.023 0.14 -10000 0 -0.47 36 36
AKT1 -0.021 0.18 -10000 0 -0.74 33 33
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.023 0.18 -10000 0 -0.78 31 31
mol:Ca2+ -0.023 0.13 -10000 0 -0.43 31 31
IGF1R 0.01 0.024 -10000 0 -0.58 1 1
E2/ER alpha (dimer)/Striatin -0.017 0.1 -10000 0 -0.32 58 58
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis 0.019 0.17 0.71 33 -10000 0 33
RhoA/GTP -0.029 0.088 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.048 0.12 -10000 0 -0.47 35 35
regulation of stress fiber formation -0.009 0.095 0.48 10 -10000 0 10
E2/ERA-ERB (dimer) -0.025 0.11 -10000 0 -0.34 69 69
KRAS 0.006 0.057 -10000 0 -0.56 6 6
G13/GTP -0.013 0.088 -10000 0 -0.29 54 54
pseudopodium formation 0.009 0.095 -10000 0 -0.48 10 10
E2/ER alpha (dimer)/PELP1 -0.014 0.096 -10000 0 -0.32 53 53
GRB2 0.011 0 -10000 0 -10000 0 0
GNG2 0.003 0.067 -10000 0 -0.54 9 9
GNAO1 -0.045 0.16 -10000 0 -0.49 68 68
HRAS 0.008 0.041 -10000 0 -0.49 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.02 0.14 -10000 0 -0.52 34 34
E2/ER beta (dimer) -0.005 0.073 -10000 0 -0.4 20 20
mol:GDP -0.04 0.11 -10000 0 -0.38 48 48
mol:NADP -0.02 0.14 -10000 0 -0.52 34 34
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
mol:IP3 -0.025 0.13 -10000 0 -0.45 31 31
IGF-1R heterotetramer 0.01 0.024 -10000 0 -0.58 1 1
PLCB1 -0.028 0.13 -10000 0 -0.46 31 31
PLCB2 -0.01 0.11 -10000 0 -0.45 26 26
IGF1 -0.075 0.2 -10000 0 -0.52 97 97
mol:L-citrulline -0.02 0.14 -10000 0 -0.52 34 34
RHOA 0.01 0.024 -10000 0 -0.58 1 1
Gai/GDP -0.022 0.15 -10000 0 -0.77 19 19
JNK cascade -0.005 0.073 -10000 0 -0.4 20 20
BCAR1 0.008 0.043 -10000 0 -0.52 4 4
ESR2 -0.007 0.1 -10000 0 -0.55 20 20
GNAQ 0.006 0.059 -10000 0 -0.58 6 6
ESR1 -0.035 0.15 -10000 0 -0.53 52 52
Gq family/GDP/Gbeta gamma 0.002 0.11 -10000 0 -0.51 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.008 0.071 -10000 0 -0.32 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.047 0.12 -10000 0 -0.47 34 34
GNAZ -0.013 0.11 -10000 0 -0.55 26 26
E2/ER alpha (dimer) -0.026 0.11 -10000 0 -0.38 52 52
STRN 0.006 0.059 -10000 0 -0.58 6 6
GNAL -0.018 0.12 -10000 0 -0.51 34 34
PELP1 0.01 0.024 -10000 0 -0.58 1 1
MAPK11 -0.004 0.081 -10000 0 -0.33 34 34
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
HBEGF -0.038 0.16 -10000 0 -0.51 36 36
cAMP biosynthetic process -0.044 0.11 -10000 0 -0.27 97 97
SRC -0.016 0.14 -10000 0 -0.45 33 33
PI3K 0.013 0.04 -10000 0 -0.43 5 5
GNB1 0.011 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.038 0.1 -10000 0 -0.38 35 35
SOS1 0.01 0.024 -10000 0 -0.58 1 1
IGF-1R heterotetramer/IGF1 -0.067 0.13 -10000 0 -0.43 54 54
Gs family/GTP -0.045 0.11 -10000 0 -0.28 97 97
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.012 0.069 -10000 0 -0.38 16 16
vasodilation -0.019 0.14 -10000 0 -0.5 34 34
mol:DAG -0.025 0.13 -10000 0 -0.45 31 31
Gs family/GDP/Gbeta gamma -0.046 0.11 -10000 0 -0.38 38 38
MSN 0.008 0.1 -10000 0 -0.53 10 10
Gq family/GTP -0.013 0.11 -10000 0 -0.49 24 24
mol:PI-3-4-5-P3 -0.022 0.18 -10000 0 -0.75 31 31
NRAS 0.002 0.076 -10000 0 -0.58 10 10
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.019 0.14 0.5 34 -10000 0 34
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
RhoA/GDP -0.038 0.1 -10000 0 -0.37 46 46
NOS3 -0.022 0.15 -10000 0 -0.55 34 34
GNA11 0.007 0.05 -10000 0 -0.53 5 5
MAPKKK cascade -0.007 0.15 -10000 0 -0.57 35 35
E2/ER alpha (dimer)/PELP1/Src -0.05 0.13 -10000 0 -0.5 34 34
ruffle organization 0.009 0.095 -10000 0 -0.48 10 10
ROCK2 0.002 0.11 -10000 0 -0.62 9 9
GNA14 -0.007 0.1 -10000 0 -0.56 19 19
GNA15 -0.009 0.1 -10000 0 -0.54 22 22
GNA13 0.009 0.034 -10000 0 -0.58 2 2
MMP9 -0.044 0.16 -10000 0 -0.56 30 30
MMP2 -0.03 0.16 -10000 0 -0.58 26 26
LPA4-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
ADCY4 0.011 0.04 -9999 0 -0.31 9 9
ADCY5 -0.058 0.14 -9999 0 -0.32 134 134
ADCY6 0.016 0 -9999 0 -10000 0 0
ADCY7 0.014 0.022 -9999 0 -0.3 3 3
ADCY1 -0.019 0.097 -9999 0 -0.29 69 69
ADCY2 -0.017 0.1 -9999 0 -0.34 55 55
ADCY3 0.015 0.015 -9999 0 -0.36 1 1
ADCY8 0.003 0.042 -9999 0 -0.27 14 14
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 0.014 0.025 -9999 0 -0.33 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.014 0.068 -9999 0 -0.34 5 5
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.014 0.1 -10000 0 -0.98 4 4
epithelial cell differentiation -0.048 0.12 -10000 0 -0.46 26 26
ITCH 0.008 0.056 -10000 0 -0.6 5 5
WWP1 0.017 0.11 -10000 0 -1.1 5 5
FYN 0.005 0.06 -10000 0 -0.55 7 7
EGFR 0.005 0.058 -10000 0 -0.53 7 7
PRL -0.013 0.088 -10000 0 -0.46 23 23
neuron projection morphogenesis 0.006 0.12 -10000 0 -0.79 4 4
PTPRZ1 -0.078 0.19 -10000 0 -0.51 102 102
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.005 0.13 -10000 0 -1.1 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.025 0.14 -10000 0 -0.36 58 58
ADAM17 0.011 0.038 -10000 0 -0.63 2 2
ErbB4/ErbB4 0.018 0.1 -10000 0 -0.9 5 5
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.001 0.1 -10000 0 -1 4 4
NCOR1 0.01 0.024 -10000 0 -0.58 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.021 0.14 -10000 0 -1 4 4
GRIN2B -0.038 0.16 -10000 0 -0.66 17 17
ErbB4/ErbB2/betacellulin 0.013 0.11 -10000 0 -0.44 18 18
STAT1 0.006 0.054 -10000 0 -0.49 7 7
HBEGF 0.001 0.068 -10000 0 -0.46 13 13
PRLR -0.041 0.17 -10000 0 -0.58 54 54
E4ICDs/ETO2 -0.036 0.15 -10000 0 -0.38 55 55
axon guidance 0.015 0.13 -10000 0 -0.67 9 9
NEDD4 0.008 0.048 -10000 0 -0.58 4 4
Prolactin receptor/Prolactin receptor/Prolactin -0.039 0.14 -10000 0 -0.42 71 71
CBFA2T3 -0.084 0.2 -10000 0 -0.51 112 112
ErbB4/ErbB2/HBEGF 0.016 0.1 -10000 0 -0.78 5 5
MAPK3 0 0.12 -10000 0 -0.84 4 4
STAT1 (dimer) 0.016 0.11 -10000 0 -1.1 4 4
MAPK1 0 0.12 -10000 0 -0.94 3 3
JAK2 -0.008 0.1 -10000 0 -0.55 21 21
ErbB4/ErbB2/neuregulin 1 beta -0.023 0.14 -10000 0 -0.34 57 57
NRG1 -0.043 0.15 -10000 0 -0.39 92 92
NRG3 -0.003 0.065 -10000 0 -0.46 12 12
NRG2 -0.016 0.1 -10000 0 -0.46 32 32
NRG4 -0.022 0.12 -10000 0 -0.47 39 39
heart development 0.015 0.13 -10000 0 -0.67 9 9
neural crest cell migration -0.023 0.14 -10000 0 -0.34 57 57
ERBB2 0.01 0.059 -10000 0 -0.35 16 16
WWOX/E4ICDs 0.018 0.095 -10000 0 -0.76 6 6
SHC1 0.011 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.004 0.12 -10000 0 -0.56 13 13
apoptosis 0.036 0.096 0.85 5 -10000 0 5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.002 0.12 -10000 0 -0.79 7 7
ErbB4/ErbB2/epiregulin -0.075 0.17 -10000 0 -0.32 147 147
ErbB4/ErbB4/betacellulin/betacellulin 0.011 0.11 -10000 0 -0.48 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.018 0.16 -10000 0 -0.57 23 23
MDM2 0.02 0.1 -10000 0 -0.9 5 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.023 0.14 -10000 0 -0.35 59 59
STAT5A 0.019 0.12 -10000 0 -0.82 6 6
ErbB4/EGFR/neuregulin 1 beta -0.02 0.14 -10000 0 -0.35 58 58
DLG4 0.007 0.047 -10000 0 -0.51 5 5
GRB2/SHC 0.017 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.017 0.089 -10000 0 -0.81 5 5
STAT5A (dimer) -0.052 0.13 -10000 0 -0.52 25 25
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.018 0.12 -10000 0 -0.82 6 6
LRIG1 -0.001 0.086 -10000 0 -0.58 13 13
EREG -0.17 0.26 -10000 0 -0.55 191 191
BTC -0.002 0.09 -10000 0 -0.58 14 14
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.014 0.13 -10000 0 -0.7 9 9
ERBB4 0.018 0.1 -10000 0 -0.91 5 5
STAT5B 0.011 0 -10000 0 -10000 0 0
YAP1 -0.006 0.085 -10000 0 -1.1 3 3
GRB2 0.011 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.002 0.11 -10000 0 -0.51 12 12
glial cell differentiation -0.007 0.086 0.79 5 -10000 0 5
WWOX 0.009 0.034 -10000 0 -0.58 2 2
cell proliferation -0.017 0.15 -10000 0 -0.61 12 12
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.01 0.12 -9999 0 -0.42 41 41
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DOCK1 0.01 0.024 -9999 0 -0.58 1 1
ITGA4 -0.019 0.13 -9999 0 -0.57 32 32
alpha4/beta7 Integrin/MAdCAM1 -0.081 0.17 -9999 0 -0.37 117 117
EPO 0 0.053 -9999 0 -0.46 8 8
alpha4/beta7 Integrin -0.024 0.14 -9999 0 -0.44 55 55
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.019 -9999 0 -0.46 1 1
alpha4/beta1 Integrin -0.006 0.096 -9999 0 -0.41 32 32
EPO/EPOR (dimer) 0.002 0.063 -9999 0 -0.35 18 18
lamellipodium assembly 0.026 0.049 -9999 0 -0.44 5 5
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
PI3K 0.013 0.04 -9999 0 -0.43 5 5
ARF6 0.01 0.024 -9999 0 -0.58 1 1
JAK2 -0.007 0.11 -9999 0 -0.49 18 18
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
MADCAM1 -0.13 0.23 -9999 0 -0.52 156 156
cell adhesion -0.081 0.17 -9999 0 -0.36 117 117
CRKL/CBL 0.017 0 -9999 0 -10000 0 0
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC -0.009 0.13 -9999 0 -0.44 41 41
ITGB7 -0.016 0.12 -9999 0 -0.53 30 30
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.016 0.14 -9999 0 -0.44 51 51
p130Cas/Crk/Dock1 0.008 0.12 -9999 0 -0.52 20 20
VCAM1 -0.022 0.13 -9999 0 -0.53 37 37
RHOA 0.01 0.024 -9999 0 -0.58 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.011 0.077 -9999 0 -0.32 29 29
BCAR1 -0.004 0.12 -9999 0 -0.41 42 42
EPOR 0.002 0.068 -9999 0 -0.49 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
GIT1 0.01 0.024 -9999 0 -0.58 1 1
Rac1/GTP -0.002 0.051 -9999 0 -0.46 5 5
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.045 -9999 0 -0.37 8 8
PDGFRB -0.007 0.098 -9999 0 -0.55 19 19
SPHK1 -0.046 0.15 -9999 0 -0.8 22 22
mol:S1P -0.045 0.14 -9999 0 -0.69 23 23
S1P1/S1P/Gi -0.047 0.16 -9999 0 -0.4 64 64
GNAO1 -0.047 0.16 -9999 0 -0.49 68 68
PDGFB-D/PDGFRB/PLCgamma1 -0.043 0.15 -9999 0 -0.48 27 27
PLCG1 -0.042 0.15 -9999 0 -0.38 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.098 -9999 0 -0.55 19 19
GNAI2 0.01 0.005 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GNAI1 -0.004 0.089 -9999 0 -0.56 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.008 0.039 -9999 0 -0.32 8 8
S1P1/S1P -0.021 0.12 -9999 0 -0.49 27 27
negative regulation of cAMP metabolic process -0.046 0.15 -9999 0 -0.38 64 64
MAPK3 -0.061 0.2 -9999 0 -0.56 59 59
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
KDR 0.004 0.058 -9999 0 -0.53 7 7
PLCB2 -0.015 0.11 -9999 0 -0.42 30 30
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.038 0.092 -9999 0 -0.41 27 27
receptor internalization -0.041 0.1 -9999 0 -0.45 27 27
PTGS2 -0.1 0.31 -9999 0 -0.98 57 57
Rac1/GTP -0.037 0.092 -9999 0 -0.41 27 27
RHOA 0.01 0.024 -9999 0 -0.58 1 1
VEGFA 0.01 0.019 -9999 0 -0.46 1 1
negative regulation of T cell proliferation -0.046 0.15 -9999 0 -0.38 64 64
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.014 0.12 -9999 0 -0.55 26 26
MAPK1 -0.061 0.2 -9999 0 -0.56 59 59
S1P1/S1P/PDGFB-D/PDGFRB -0.022 0.13 -9999 0 -0.45 31 31
ABCC1 0.01 0.024 -9999 0 -0.59 1 1
Nongenotropic Androgen signaling

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
PTK2 0.009 0.018 -10000 0 -0.43 1 1
GNB1/GNG2 -0.017 0.1 -10000 0 -0.35 29 29
regulation of S phase of mitotic cell cycle -0.001 0.073 -10000 0 -0.27 28 28
GNAO1 -0.045 0.16 -10000 0 -0.49 68 68
HRAS 0.008 0.041 -10000 0 -0.49 4 4
SHBG/T-DHT -0.008 0.061 -10000 0 -0.27 30 30
PELP1 0.01 0.024 -10000 0 -0.58 1 1
AKT1 0.009 0.018 -10000 0 -0.43 1 1
MAP2K1 0.001 0.089 -10000 0 -0.42 5 5
T-DHT/AR -0.036 0.12 -10000 0 -0.36 71 71
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 40 40
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
mol:GDP -0.033 0.098 -10000 0 -0.44 24 24
cell proliferation 0.001 0.12 -10000 0 -0.38 30 30
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
FOS -0.014 0.18 -10000 0 -0.76 29 29
mol:Ca2+ -0.011 0.021 -10000 0 -0.062 67 67
MAPK3 0.002 0.1 -10000 0 -0.48 5 5
MAPK1 0.005 0.062 -10000 0 -0.31 4 4
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
mol:IP3 0 0.001 -10000 0 -0.004 41 41
cAMP biosynthetic process -0.003 0.061 -10000 0 -0.26 30 30
GNG2 0.003 0.067 -10000 0 -0.54 9 9
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 41 41
HRAS/GTP -0.031 0.083 -10000 0 -0.3 27 27
actin cytoskeleton reorganization -0.005 0.046 -10000 0 -0.41 7 7
SRC 0.01 0.024 -10000 0 -0.58 1 1
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 41 41
PI3K 0.012 0.034 -10000 0 -0.36 5 5
apoptosis -0.001 0.11 0.39 31 -10000 0 31
T-DHT/AR/PELP1 -0.023 0.1 -10000 0 -0.3 72 72
HRAS/GDP -0.032 0.094 -10000 0 -0.42 25 25
CREB1 0 0.11 -10000 0 -0.42 31 31
RAC1-CDC42/GTP -0.004 0.047 -10000 0 -0.42 7 7
AR -0.05 0.16 -10000 0 -0.5 71 71
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.003 0.089 -10000 0 -0.29 25 25
RAC1-CDC42/GDP -0.03 0.093 -10000 0 -0.4 27 27
T-DHT/AR/PELP1/Src -0.014 0.096 -10000 0 -0.27 72 72
MAP2K2 0.001 0.091 -10000 0 -0.47 4 4
T-DHT/AR/PELP1/Src/PI3K -0.001 0.074 -10000 0 -0.27 28 28
GNAZ -0.013 0.11 -10000 0 -0.55 26 26
SHBG -0.014 0.1 -10000 0 -0.46 30 30
Gi family/GNB1/GNG2/GDP -0.008 0.1 -10000 0 -0.39 20 20
mol:T-DHT 0 0.001 -10000 0 -0.002 34 34
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0 0.062 -10000 0 -0.42 13 13
Gi family/GTP -0.022 0.089 -10000 0 -0.23 67 67
CDC42 0.007 0.054 -10000 0 -0.58 5 5
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.021 0.2 -10000 0 -0.72 12 12
CRP -0.029 0.2 -10000 0 -0.7 17 17
cell cycle arrest -0.036 0.22 -10000 0 -0.7 26 26
TIMP1 -0.01 0.18 -10000 0 -0.62 12 12
IL6ST -0.001 0.093 -10000 0 -0.58 15 15
Rac1/GDP -0.041 0.18 -10000 0 -0.54 40 40
AP1 0.002 0.12 -10000 0 -0.55 10 10
GAB2 0.01 0.034 -10000 0 -0.58 2 2
TNFSF11 -0.076 0.33 -10000 0 -1 54 54
HSP90B1 0.009 0.14 -10000 0 -1.3 6 6
GAB1 0.012 0.001 -10000 0 -10000 0 0
MAPK14 -0.03 0.16 -10000 0 -0.55 30 30
AKT1 0.038 0.071 -10000 0 -0.73 4 4
FOXO1 0.041 0.069 -10000 0 -0.68 4 4
MAP2K6 -0.037 0.16 -10000 0 -0.53 34 34
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.031 0.18 -10000 0 -0.57 35 35
MITF -0.049 0.17 -10000 0 -0.5 47 47
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.01 0.024 -10000 0 -0.58 1 1
A2M 0.009 0.09 -10000 0 -1.4 2 2
CEBPB 0.013 0.041 -10000 0 -0.49 4 4
GRB2/SOS1/GAB family/SHP2 0.001 0.089 0.22 1 -0.6 5 6
STAT3 -0.04 0.23 -10000 0 -0.73 28 28
STAT1 -0.009 0.066 -10000 0 -1.1 2 2
CEBPD -0.023 0.2 -10000 0 -0.8 12 12
PIK3CA 0.011 0.034 -10000 0 -0.58 2 2
PI3K 0.016 0.04 -10000 0 -0.42 5 5
JUN 0.007 0.052 -10000 0 -0.56 5 5
PIAS3/MITF -0.042 0.17 -10000 0 -0.53 35 35
MAPK11 -0.037 0.17 -10000 0 -0.6 32 32
STAT3 (dimer)/FOXO1 0.01 0.19 -10000 0 -0.62 14 14
GRB2/SOS1/GAB family -0.058 0.13 -10000 0 -0.54 29 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.047 0.17 -10000 0 -0.47 54 54
GRB2 0.012 0.001 -10000 0 -10000 0 0
JAK2 -0.008 0.1 -10000 0 -0.55 21 21
LBP -0.094 0.32 -10000 0 -0.86 67 67
PIK3R1 0.009 0.042 -10000 0 -0.58 3 3
JAK1 0.01 0.042 -10000 0 -0.58 3 3
MYC -0.026 0.21 -10000 0 -0.84 15 15
FGG -0.038 0.22 -10000 0 -0.72 20 20
macrophage differentiation -0.036 0.22 -10000 0 -0.7 26 26
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.069 0.17 -10000 0 -0.44 59 59
JUNB -0.024 0.2 -10000 0 -0.77 14 14
FOS -0.026 0.14 -10000 0 -0.54 41 41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.039 0.16 -10000 0 -0.45 49 49
STAT1/PIAS1 -0.029 0.16 -10000 0 -0.47 36 36
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.074 -10000 0 -0.56 7 7
STAT3 (dimer) -0.038 0.23 -10000 0 -0.73 26 26
PRKCD -0.022 0.2 -10000 0 -0.61 28 28
IL6R -0.005 0.1 -10000 0 -0.56 19 19
SOCS3 -0.034 0.18 -10000 0 -0.82 16 16
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.078 -10000 0 -0.33 27 27
Rac1/GTP -0.04 0.18 -10000 0 -0.53 44 44
HCK -0.017 0.12 -10000 0 -0.54 31 31
MAPKKK cascade 0.013 0.093 -10000 0 -0.8 5 5
bone resorption -0.067 0.31 -10000 0 -0.93 54 54
IRF1 -0.022 0.2 -10000 0 -0.72 12 12
mol:GDP -0.05 0.18 -10000 0 -0.52 50 50
SOS1 0.011 0.024 -10000 0 -0.58 1 1
VAV1 -0.051 0.19 -10000 0 -0.53 50 50
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.04 0.17 -10000 0 -0.56 37 37
PTPN11 -0.011 0.084 -10000 0 -0.9 5 5
IL6/IL6RA -0.082 0.18 -10000 0 -0.38 156 156
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.073 -10000 0 -0.34 22 22
gp130 (dimer)/JAK2/JAK2/LMO4 0 0.1 -10000 0 -0.35 42 42
IL6 -0.11 0.23 -10000 0 -0.52 142 142
PIAS3 0.01 0.031 -10000 0 -0.52 2 2
PTPRE 0.007 0.026 -10000 0 -0.57 1 1
PIAS1 0.011 0 -10000 0 -10000 0 0
RAC1 0.012 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.043 0.14 -10000 0 -0.41 48 48
LMO4 0.006 0.062 -10000 0 -0.49 9 9
STAT3 (dimer)/PIAS3 -0.035 0.22 -10000 0 -0.7 28 28
MCL1 0.043 0.062 -10000 0 -0.7 3 3
Coregulation of Androgen receptor activity

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
NRIP1 -0.006 0.071 -10000 0 -0.59 8 8
SVIL 0 0.045 -10000 0 -0.49 4 4
ZNF318 0.033 0.05 -10000 0 -10000 0 0
JMJD2C 0.003 0.02 -10000 0 -0.077 29 29
T-DHT/AR/Ubc9 -0.023 0.11 -10000 0 -0.3 71 71
CARM1 0.009 0.024 -10000 0 -0.58 1 1
PRDX1 0.012 0.025 -10000 0 -0.58 1 1
PELP1 0.014 0.026 -10000 0 -0.58 1 1
CTNNB1 0.005 0.016 -10000 0 -10000 0 0
AKT1 0.016 0.028 -10000 0 -0.59 1 1
PTK2B 0.004 0.037 -10000 0 -0.58 2 2
MED1 0.015 0.046 -10000 0 -0.51 4 4
MAK 0.007 0.12 -10000 0 -0.47 31 31
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.003 0.063 -10000 0 -0.6 6 6
GSN -0.009 0.08 -10000 0 -0.52 13 13
NCOA2 0.003 0.067 -10000 0 -0.57 8 8
NCOA6 0.004 0.031 -10000 0 -0.58 1 1
DNA-PK 0.041 0.058 -10000 0 -0.48 2 2
NCOA4 0.008 0.034 -10000 0 -0.58 2 2
PIAS3 0.004 0.034 -10000 0 -0.52 2 2
cell proliferation -0.004 0.11 -10000 0 -0.5 16 16
XRCC5 0.015 0.027 -10000 0 -0.58 1 1
UBE3A -0.006 0.057 -10000 0 -0.58 4 4
T-DHT/AR/SNURF -0.077 0.16 -10000 0 -0.34 154 154
FHL2 0.022 0.098 -10000 0 -1.1 3 3
RANBP9 0.004 0.031 -10000 0 -0.58 1 1
JMJD1A -0.006 0.044 -10000 0 -0.11 80 80
CDK6 0.012 0.002 -10000 0 -10000 0 0
TGFB1I1 -0.002 0.056 -10000 0 -0.52 6 6
T-DHT/AR/CyclinD1 -0.031 0.11 -10000 0 -0.31 73 73
XRCC6 0.016 0.011 -10000 0 -10000 0 0
T-DHT/AR -0.019 0.12 -10000 0 -0.3 77 77
CTDSP1 0.007 0.025 -10000 0 -0.58 1 1
CTDSP2 0.026 0.033 -10000 0 -10000 0 0
BRCA1 0.002 0.031 -10000 0 -0.58 1 1
TCF4 0.008 0.09 -10000 0 -0.53 15 15
CDKN2A -0.064 0.19 -10000 0 -0.5 96 96
SRF 0.022 0.033 -10000 0 -0.45 2 2
NKX3-1 -0.076 0.25 -10000 0 -0.63 81 81
KLK3 -0.17 0.43 -10000 0 -1.4 59 59
TMF1 0.003 0.059 -10000 0 -0.58 6 6
HNRNPA1 0.019 0.018 -10000 0 -10000 0 0
AOF2 -0.009 0.022 -10000 0 -0.069 59 59
APPL1 0.023 0.07 -10000 0 -0.42 12 12
T-DHT/AR/Caspase 8 -0.015 0.11 -10000 0 -0.3 71 71
AR -0.053 0.17 -10000 0 -0.5 71 71
UBA3 0.007 0.025 -10000 0 -0.58 1 1
PATZ1 0.019 0.018 -10000 0 -10000 0 0
PAWR 0.008 0.025 -10000 0 -0.58 1 1
PRKDC 0.013 0.04 -10000 0 -0.52 3 3
PA2G4 0.021 0.022 -10000 0 -10000 0 0
UBE2I 0.011 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.016 0.1 -10000 0 -0.27 75 75
RPS6KA3 -0.002 0.054 -10000 0 -0.6 4 4
T-DHT/AR/ARA70 -0.029 0.11 -10000 0 -0.31 72 72
LATS2 0.018 0.024 -10000 0 -0.4 1 1
T-DHT/AR/PRX1 -0.01 0.11 0.17 1 -0.27 71 72
Cyclin D3/CDK11 p58 0.007 0.031 -10000 0 -0.32 5 5
VAV3 -0.071 0.2 -10000 0 -0.59 78 78
KLK2 -0.027 0.095 -10000 0 -0.4 29 29
CASP8 0.013 0.025 -10000 0 -0.58 1 1
T-DHT/AR/TIF2/CARM1 -0.025 0.11 -10000 0 -0.32 48 48
TMPRSS2 -0.019 0.11 -10000 0 -0.95 4 4
CCND1 0.006 0.036 -10000 0 -0.59 2 2
PIAS1 -0.002 0.032 -10000 0 -10000 0 0
mol:T-DHT -0.003 0.024 -10000 0 -0.072 39 39
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.01 0.054 -10000 0 -0.58 1 1
T-DHT/AR/CDK6 -0.02 0.11 -10000 0 -0.3 71 71
CMTM2 -0.028 0.14 -10000 0 -0.52 47 47
SNURF -0.077 0.2 -10000 0 -0.54 93 93
ZMIZ1 0.008 0.028 -10000 0 -0.45 1 1
CCND3 0.008 0.042 -10000 0 -0.46 5 5
TGIF1 0.019 0.018 -10000 0 -10000 0 0
FKBP4 0.002 0.038 -10000 0 -0.46 3 3
IGF1 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
NCK2 0.01 0.024 -10000 0 -0.58 1 1
PTK2 0.01 0.024 -10000 0 -0.58 1 1
CRKL -0.023 0.1 -10000 0 -0.3 52 52
GRB2/SOS1/SHC 0.023 0.015 -10000 0 -0.36 1 1
HRAS 0.008 0.041 -10000 0 -0.49 4 4
IRS1/Crk -0.023 0.1 -10000 0 -0.3 53 53
IGF-1R heterotetramer/IGF1/PTP1B -0.029 0.12 -10000 0 -0.34 53 53
AKT1 -0.006 0.094 -10000 0 -0.48 3 3
BAD -0.001 0.092 -10000 0 -0.46 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.023 0.1 -10000 0 -0.3 53 53
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.026 0.11 -10000 0 -0.31 57 57
RAF1 0.005 0.087 -10000 0 -0.42 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.014 0.1 -10000 0 -0.29 53 53
YWHAZ 0.008 0.042 -10000 0 -0.58 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.032 0.11 -10000 0 -0.32 60 60
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
RPS6KB1 -0.008 0.1 -10000 0 -0.51 6 6
GNB2L1 0.011 0.019 -10000 0 -0.46 1 1
positive regulation of MAPKKK cascade 0.003 0.077 -10000 0 -0.36 3 3
PXN 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
HRAS/GTP -0.035 0.08 -10000 0 -0.48 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.008 0.096 -10000 0 -0.38 4 4
IGF-1R heterotetramer -0.001 0.038 -10000 0 -0.67 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.022 0.11 -10000 0 -0.31 53 53
Crk/p130 Cas/Paxillin -0.01 0.098 -10000 0 -0.42 5 5
IGF1R -0.001 0.038 -10000 0 -0.67 1 1
IGF1 -0.076 0.2 -10000 0 -0.53 97 97
IRS2/Crk -0.02 0.1 -10000 0 -0.29 57 57
PI3K -0.016 0.1 -10000 0 -0.28 57 57
apoptosis -0.005 0.088 0.42 8 -10000 0 8
HRAS/GDP 0.006 0.029 -10000 0 -0.35 4 4
PRKCD -0.015 0.12 -10000 0 -0.39 52 52
RAF1/14-3-3 E 0.012 0.078 -10000 0 -0.36 3 3
BAD/14-3-3 0.005 0.093 -10000 0 -0.45 8 8
PRKCZ -0.006 0.095 -10000 0 -0.47 4 4
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.077 -10000 0 -0.44 8 8
PTPN1 0.01 0.024 -10000 0 -0.58 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.022 0.13 -10000 0 -0.41 52 52
BCAR1 0.008 0.043 -10000 0 -0.52 4 4
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.018 0.11 -10000 0 -0.3 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.01 0.024 -10000 0 -0.58 1 1
IRS1/NCK2 -0.023 0.1 -10000 0 -0.3 53 53
GRB10 0.007 0.048 -10000 0 -0.58 4 4
PTPN11 -0.026 0.11 -10000 0 -0.31 57 57
IRS1 -0.032 0.11 -10000 0 -0.32 60 60
IRS2 -0.027 0.11 -10000 0 -0.31 60 60
IGF-1R heterotetramer/IGF1 -0.049 0.15 -10000 0 -0.39 97 97
GRB2 0.011 0 -10000 0 -10000 0 0
PDPK1 -0.012 0.097 -10000 0 -0.42 5 5
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKD1 -0.037 0.16 -10000 0 -0.43 75 75
SHC1 0.011 0 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.06 0.15 -10000 0 -0.33 133 133
cell-cell adhesion 0.06 0.1 0.43 15 -10000 0 15
Ephrin B/EPHB2/RasGAP 0.008 0.09 -10000 0 -0.57 3 3
ITSN1 0.01 0.024 -10000 0 -0.58 1 1
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
SHC1 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.004 0.083 -10000 0 -0.34 33 33
Ephrin B1/EPHB1 -0.056 0.13 -10000 0 -0.29 140 140
HRAS/GDP -0.058 0.1 -10000 0 -0.43 13 13
Ephrin B/EPHB1/GRB7 -0.05 0.14 -10000 0 -0.49 17 17
Endophilin/SYNJ1 0.006 0.083 -10000 0 -0.53 3 3
KRAS 0.006 0.057 -10000 0 -0.56 6 6
Ephrin B/EPHB1/Src -0.046 0.14 -10000 0 -0.53 11 11
endothelial cell migration -0.003 0.035 -10000 0 -0.36 5 5
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 0.002 0.065 -10000 0 -0.46 12 12
PAK1 0.01 0.093 -10000 0 -0.6 5 5
HRAS 0.008 0.041 -10000 0 -0.49 4 4
RRAS 0.006 0.087 -10000 0 -0.64 3 3
DNM1 -0.007 0.096 -10000 0 -0.5 22 22
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.045 0.13 -10000 0 -0.48 11 11
lamellipodium assembly -0.06 0.1 -10000 0 -0.43 15 15
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.022 0.1 -10000 0 -0.42 8 8
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
EPHB2 0 0.079 -10000 0 -0.55 12 12
EPHB3 -0.019 0.13 -10000 0 -0.55 33 33
EPHB1 -0.1 0.21 -10000 0 -0.49 139 139
EPHB4 0.011 0 -10000 0 -10000 0 0
mol:GDP -0.023 0.11 -10000 0 -0.42 12 12
Ephrin B/EPHB2 0.002 0.088 -10000 0 -0.33 28 28
Ephrin B/EPHB3 -0.008 0.1 -10000 0 -0.34 40 40
JNK cascade -0.036 0.12 -10000 0 -0.3 51 51
Ephrin B/EPHB1 -0.052 0.14 -10000 0 -0.34 60 60
RAP1/GDP -0.01 0.1 -10000 0 -0.41 8 8
EFNB2 0.01 0.031 -10000 0 -0.52 2 2
EFNB3 -0.021 0.13 -10000 0 -0.52 37 37
EFNB1 0.01 0.024 -10000 0 -0.58 1 1
Ephrin B2/EPHB1-2 -0.05 0.13 -10000 0 -0.27 150 150
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.01 0.024 -10000 0 -0.58 1 1
CDC42/GTP -0.065 0.12 -10000 0 -0.48 19 19
Rap1/GTP -0.06 0.1 -10000 0 -0.43 17 17
axon guidance -0.06 0.15 -10000 0 -0.33 133 133
MAPK3 -0.01 0.093 -10000 0 -0.39 9 9
MAPK1 -0.01 0.094 -10000 0 -0.46 6 6
Rac1/GDP -0.015 0.11 -10000 0 -0.44 7 7
actin cytoskeleton reorganization -0.052 0.091 -10000 0 -0.4 16 16
CDC42/GDP -0.017 0.11 -10000 0 -0.42 11 11
PI3K 0.024 0.038 -10000 0 -0.36 5 5
EFNA5 -0.1 0.22 -10000 0 -0.52 127 127
Ephrin B2/EPHB4 0.014 0.019 -10000 0 -0.32 2 2
Ephrin B/EPHB2/Intersectin/N-WASP 0.011 0.073 -10000 0 -0.49 4 4
CDC42 0.007 0.054 -10000 0 -0.58 5 5
RAS family/GTP -0.066 0.12 -10000 0 -0.46 23 23
PTK2 0.016 0.038 -10000 0 -0.58 1 1
MAP4K4 -0.037 0.12 -10000 0 -0.31 51 51
SRC 0.01 0.024 -10000 0 -0.58 1 1
KALRN 0.007 0.054 -10000 0 -0.58 5 5
Intersectin/N-WASP 0.016 0.018 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.008 0.11 -10000 0 -0.41 14 14
MAP2K1 -0.016 0.097 -10000 0 -0.4 10 10
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.044 0.13 -10000 0 -0.33 50 50
cell migration -0.013 0.11 -10000 0 -0.44 10 10
NRAS 0.002 0.076 -10000 0 -0.58 10 10
SYNJ1 0.006 0.085 -10000 0 -0.55 3 3
PXN 0.011 0 -10000 0 -10000 0 0
TF -0.047 0.13 -10000 0 -0.45 19 19
HRAS/GTP -0.066 0.11 -10000 0 -0.47 17 17
Ephrin B1/EPHB1-2 -0.049 0.13 -10000 0 -0.34 48 48
cell adhesion mediated by integrin 0.011 0.081 0.32 23 -10000 0 23
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.044 0.13 -10000 0 -0.49 15 15
RAC1-CDC42/GTP -0.073 0.12 -10000 0 -0.47 29 29
RASA1 0.009 0.034 -10000 0 -0.58 2 2
RAC1-CDC42/GDP -0.012 0.11 -10000 0 -0.42 9 9
ruffle organization -0.025 0.12 -10000 0 -0.46 12 12
NCK1 0.009 0.034 -10000 0 -0.58 2 2
receptor internalization 0.003 0.097 -10000 0 -0.49 8 8
Ephrin B/EPHB2/KALRN 0.007 0.098 -10000 0 -0.64 5 5
ROCK1 -0.003 0.094 -10000 0 -0.34 40 40
RAS family/GDP -0.048 0.088 -10000 0 -0.4 16 16
Rac1/GTP -0.063 0.11 -10000 0 -0.45 15 15
Ephrin B/EPHB1/Src/Paxillin -0.027 0.1 -10000 0 -0.46 8 8
Class I PI3K signaling events

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.01 0.07 0.25 6 -0.56 4 10
DAPP1 -0.065 0.19 -10000 0 -0.51 68 68
Src family/SYK family/BLNK-LAT/BTK-ITK -0.068 0.22 -10000 0 -0.61 63 63
mol:DAG -0.015 0.1 0.18 2 -0.28 53 55
HRAS 0.008 0.041 -10000 0 -0.49 4 4
RAP1A 0.01 0.026 -10000 0 -0.62 1 1
ARF5/GDP 0 0.11 -10000 0 -0.44 25 25
PLCG2 -0.01 0.11 -10000 0 -0.55 23 23
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
ARF5 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.01 0.072 0.23 6 -0.32 22 28
ARF1/GTP -0.01 0.069 0.24 6 -0.57 4 10
RHOA 0.01 0.024 -10000 0 -0.58 1 1
YES1 0.005 0.064 -10000 0 -0.58 7 7
RAP1A/GTP 0.011 0.074 0.22 6 -0.32 22 28
ADAP1 -0.01 0.07 0.22 6 -0.56 5 11
ARAP3 -0.01 0.07 0.23 6 -0.32 22 28
INPPL1 0.01 0.024 -10000 0 -0.58 1 1
PREX1 0.005 0.06 -10000 0 -0.55 7 7
ARHGEF6 -0.006 0.097 -10000 0 -0.54 19 19
ARHGEF7 0.011 0 -10000 0 -10000 0 0
ARF1 0.011 0.019 -10000 0 -0.46 1 1
NRAS 0.002 0.077 -10000 0 -0.6 10 10
FYN 0.005 0.06 -10000 0 -0.55 7 7
ARF6 0.01 0.024 -10000 0 -0.58 1 1
FGR -0.026 0.14 -10000 0 -0.54 41 41
mol:Ca2+ 0 0.055 -10000 0 -0.21 1 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.044 0.16 -10000 0 -0.52 63 63
ZAP70 -0.035 0.15 -10000 0 -0.53 52 52
mol:IP3 -0.005 0.076 -10000 0 -0.23 18 18
LYN 0.011 0 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.11 -10000 0 -0.45 24 24
RhoA/GDP -0.021 0.082 0.24 3 -0.41 15 18
PDK1/Src/Hsp90 0.022 0.022 -10000 0 -0.36 2 2
BLNK -0.01 0.11 -10000 0 -0.58 22 22
actin cytoskeleton reorganization 0.013 0.11 0.23 3 -0.47 17 20
SRC 0.01 0.024 -10000 0 -0.58 1 1
PLEKHA2 0.002 0.09 -10000 0 -0.36 34 34
RAC1 0.011 0 -10000 0 -10000 0 0
PTEN 0.004 0.057 -10000 0 -0.56 6 6
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
ARF6/GTP -0.01 0.072 0.25 6 -0.63 4 10
RhoA/GTP 0.016 0.075 0.22 6 -0.37 13 19
Src family/SYK family/BLNK-LAT -0.064 0.2 -10000 0 -0.56 62 62
BLK -0.11 0.23 -10000 0 -0.53 138 138
PDPK1 0.011 0 -10000 0 -10000 0 0
CYTH1 -0.01 0.067 0.22 6 -0.56 4 10
HCK -0.017 0.12 -10000 0 -0.54 31 31
CYTH3 -0.011 0.069 0.22 6 -0.47 6 12
CYTH2 -0.01 0.067 0.22 6 -0.56 4 10
KRAS 0.006 0.059 -10000 0 -0.58 6 6
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.024 0.068 -10000 0 -0.54 5 5
SGK1 -0.01 0.071 0.19 6 -0.6 5 11
INPP5D -0.018 0.13 -10000 0 -0.58 30 30
mol:GDP -0.007 0.11 -10000 0 -0.46 26 26
SOS1 0.01 0.024 -10000 0 -0.58 1 1
SYK 0.011 0.019 -10000 0 -0.46 1 1
ARF6/GDP -0.021 0.081 0.24 3 -0.41 15 18
mol:PI-3-4-5-P3 -0.01 0.074 0.29 6 -0.37 13 19
ARAP3/RAP1A/GTP 0.011 0.075 0.22 6 -0.32 22 28
VAV1 -0.028 0.15 -10000 0 -0.58 40 40
mol:PI-3-4-P2 -0.004 0.1 -10000 0 -0.44 30 30
RAS family/GTP/PI3K Class I 0.012 0.073 -10000 0 -0.33 22 22
PLEKHA1 0.002 0.089 -10000 0 -0.36 33 33
Rac1/GDP 0 0.11 -10000 0 -0.44 24 24
LAT -0.009 0.1 -10000 0 -0.51 24 24
Rac1/GTP -0.015 0.14 -10000 0 -0.57 27 27
ITK -0.031 0.097 0.22 5 -0.32 40 45
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.14 0.21 2 -0.4 54 56
LCK -0.031 0.14 -10000 0 -0.51 49 49
BTK -0.03 0.094 0.22 3 -0.32 37 40
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.012 0.11 -9999 0 -0.58 23 23
PDGF/PDGFRA/CRKL 0.001 0.081 -9999 0 -0.41 23 23
positive regulation of JUN kinase activity 0.015 0.064 -9999 0 -0.3 22 22
CRKL 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.01 0.088 -9999 0 -0.41 28 28
AP1 -0.062 0.21 -9999 0 -0.9 30 30
mol:IP3 0 0.087 -9999 0 -0.42 24 24
PLCG1 0 0.088 -9999 0 -0.42 24 24
PDGF/PDGFRA/alphaV Integrin -0.007 0.1 -9999 0 -0.42 32 32
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
CRK 0.011 0.019 -9999 0 -0.46 1 1
mol:Ca2+ 0 0.087 -9999 0 -0.42 24 24
CAV3 -0.003 0.046 -9999 0 -0.46 6 6
CAV1 -0.002 0.082 -9999 0 -0.5 16 16
SHC/Grb2/SOS1 0.016 0.064 -9999 0 -0.31 22 22
PDGF/PDGFRA/Shf -0.033 0.14 -9999 0 -0.38 75 75
FOS -0.029 0.22 -9999 0 -0.89 30 30
JUN -0.008 0.042 -9999 0 -0.44 5 5
oligodendrocyte development -0.007 0.1 -9999 0 -0.42 32 32
GRB2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:DAG 0 0.087 -9999 0 -0.42 24 24
PDGF/PDGFRA -0.012 0.11 -9999 0 -0.58 23 23
actin cytoskeleton reorganization 0 0.082 -9999 0 -0.4 24 24
SRF 0.017 0.02 -9999 0 -0.31 2 2
SHC1 0.011 0 -9999 0 -10000 0 0
PI3K 0.006 0.077 -9999 0 -0.35 26 26
PDGF/PDGFRA/Crk/C3G 0.008 0.072 -9999 0 -0.34 23 23
JAK1 0 0.087 -9999 0 -0.41 26 26
ELK1/SRF 0.015 0.07 -9999 0 -0.32 23 23
SHB 0.011 0.019 -9999 0 -0.46 1 1
SHF -0.034 0.14 -9999 0 -0.48 56 56
CSNK2A1 0.005 0.014 -9999 0 -10000 0 0
GO:0007205 0 0.091 -9999 0 -0.44 24 24
SOS1 0.01 0.024 -9999 0 -0.58 1 1
Ras protein signal transduction 0.015 0.064 -9999 0 -0.3 22 22
PDGF/PDGFRA/SHB 0 0.082 -9999 0 -0.4 24 24
PDGF/PDGFRA/Caveolin-1 -0.009 0.11 -9999 0 -0.42 35 35
ITGAV 0.002 0.076 -9999 0 -0.58 10 10
ELK1 0.005 0.083 -9999 0 -0.39 23 23
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
PDGF/PDGFRA/Crk 0 0.082 -9999 0 -0.4 24 24
JAK-STAT cascade 0 0.087 -9999 0 -0.41 26 26
cell proliferation -0.033 0.13 -9999 0 -0.38 75 75
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.024 0.17 -10000 0 -1.2 11 11
VDR 0.01 0.024 -10000 0 -0.58 1 1
FAM120B 0.01 0.024 -10000 0 -0.58 1 1
RXRs/LXRs/DNA/9cRA 0.026 0.083 -10000 0 -0.66 2 2
RXRs/LXRs/DNA/Oxysterols 0.026 0.11 -10000 0 -0.41 29 29
MED1 0.008 0.043 -10000 0 -0.52 4 4
mol:9cRA 0.003 0.013 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.021 0.12 -10000 0 -0.28 92 92
RXRs/NUR77 0.009 0.089 -10000 0 -0.42 6 6
RXRs/PPAR 0.021 0.059 -10000 0 -0.52 2 2
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
VDR/VDR/Vit D3 0.008 0.018 -10000 0 -0.43 1 1
RARs/VDR/DNA/Vit D3 0.012 0.071 -10000 0 -0.33 19 19
RARA 0.007 0.045 -10000 0 -0.48 5 5
NCOA1 0.01 0.024 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.01 0.024 -10000 0 -0.58 1 1
RARs/RARs/DNA/9cRA 0.008 0.068 -10000 0 -0.29 29 29
RARG 0.006 0.059 -10000 0 -0.58 6 6
RPS6KB1 -0.008 0.081 -10000 0 -0.46 17 17
RARs/THRs/DNA/SMRT -0.022 0.12 -10000 0 -0.28 93 93
THRA 0.008 0.041 -10000 0 -0.49 4 4
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.008 0.018 -10000 0 -0.43 1 1
RXRs/PPAR/9cRA/PGJ2/DNA 0.021 0.072 0.28 7 -0.32 4 11
NR1H4 -0.12 0.23 -10000 0 -0.5 156 156
RXRs/LXRs/DNA 0.034 0.077 -10000 0 -0.73 1 1
NR1H2 0.013 0.027 -10000 0 -0.61 1 1
NR1H3 0.014 0.024 -10000 0 -0.49 1 1
RXRs/VDR/DNA/Vit D3 0.022 0.058 -10000 0 -0.3 3 3
NR4A1 -0.017 0.11 -10000 0 -0.46 36 36
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.032 0.1 -10000 0 -0.26 62 62
RXRG -0.01 0.096 -10000 0 -0.46 26 26
RXR alpha/CCPG 0.018 0.027 -10000 0 -0.43 2 2
RXRA 0.013 0.027 -10000 0 -0.6 1 1
RXRB 0.014 0.012 -10000 0 -10000 0 0
THRB -0.072 0.2 -10000 0 -0.56 88 88
PPARG 0.004 0.068 -10000 0 -0.58 8 8
PPARD 0.01 0.024 -10000 0 -0.58 1 1
TNF 0.004 0.22 -10000 0 -1.1 22 22
mol:Oxysterols 0.003 0.011 -10000 0 -10000 0 0
cholesterol transport 0.026 0.11 -10000 0 -0.41 29 29
PPARA 0.009 0.034 -10000 0 -0.58 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.006 0.097 -10000 0 -0.54 19 19
RXRs/NUR77/BCL2 0.002 0.069 -10000 0 -0.31 9 9
SREBF1 0.03 0.11 -10000 0 -1.1 2 2
RXRs/RXRs/DNA/9cRA 0.021 0.072 0.28 7 -0.32 4 11
ABCA1 0.022 0.16 -10000 0 -1.1 9 9
RARs/THRs -0.028 0.13 -10000 0 -0.32 91 91
RXRs/FXR -0.053 0.14 -10000 0 -0.34 67 67
BCL2 -0.007 0.1 -10000 0 -0.55 20 20
IL2 signaling events mediated by STAT5

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
GAB2 0.01 0.034 -9999 0 -0.58 2 2
ELF1 -0.019 0.11 -9999 0 -0.36 50 50
CCNA2 0.01 0.024 -9999 0 -0.58 1 1
PIK3CA 0.01 0.034 -9999 0 -0.58 2 2
JAK3 0.001 0.076 -9999 0 -0.53 12 12
PIK3R1 0.009 0.042 -9999 0 -0.58 3 3
JAK1 0.009 0.042 -9999 0 -0.58 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.14 -9999 0 -0.46 33 33
SHC1 0.012 0.001 -9999 0 -10000 0 0
SP1 -0.009 0.097 -9999 0 -0.35 43 43
IL2RA -0.052 0.23 -9999 0 -0.7 66 66
IL2RB -0.018 0.13 -9999 0 -0.55 32 32
SOS1 0.011 0.024 -9999 0 -0.58 1 1
IL2RG 0 0.084 -9999 0 -0.56 13 13
G1/S transition of mitotic cell cycle -0.019 0.19 -9999 0 -0.69 44 44
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
CCND2 -0.036 0.22 -9999 0 -0.78 46 46
LCK -0.03 0.14 -9999 0 -0.51 49 49
GRB2 0.012 0.001 -9999 0 -10000 0 0
IL2 0.002 0.027 -9999 0 -0.46 2 2
CDK6 0.011 0 -9999 0 -10000 0 0
CCND3 0.015 0.13 -9999 0 -0.56 12 12
Nectin adhesion pathway

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
PDGFRB -0.006 0.097 -9999 0 -0.54 19 19
alphaV beta3 Integrin -0.004 0.095 -9999 0 -0.42 30 30
PTK2 -0.029 0.1 -9999 0 -0.43 31 31
positive regulation of JNK cascade -0.018 0.069 -9999 0 -0.3 31 31
CDC42/GDP 0.017 0.11 -9999 0 -0.42 32 32
Rac1/GDP 0.02 0.11 -9999 0 -0.42 29 29
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.022 0.085 -9999 0 -0.38 30 30
nectin-3/I-afadin -0.004 0.094 -9999 0 -0.42 29 29
RAPGEF1 0.018 0.11 -9999 0 -0.46 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0.12 -9999 0 -0.52 29 29
PDGFB-D/PDGFRB -0.006 0.097 -9999 0 -0.54 19 19
TLN1 0.012 0.062 -9999 0 -0.49 4 4
Rap1/GTP -0.017 0.07 -9999 0 -0.32 29 29
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
Rap1/GTP/I-afadin 0.02 0.024 -9999 0 -0.32 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.004 0.094 -9999 0 -0.42 29 29
PVR 0.011 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.012 0.13 -9999 0 -0.53 29 29
MLLT4 0.009 0.034 -9999 0 -0.58 2 2
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
PI3K 0.006 0.093 -9999 0 -0.31 44 44
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
positive regulation of lamellipodium assembly -0.027 0.086 -9999 0 -0.3 51 51
PVRL1 0.009 0.034 -9999 0 -0.58 2 2
PVRL3 -0.015 0.12 -9999 0 -0.58 27 27
PVRL2 0.01 0.031 -9999 0 -0.52 2 2
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
CDH1 0.01 0.024 -9999 0 -0.58 1 1
CLDN1 -0.014 0.12 -9999 0 -0.57 27 27
JAM-A/CLDN1 -0.002 0.099 -9999 0 -0.32 51 51
SRC 0.005 0.13 -9999 0 -0.57 29 29
ITGB3 -0.008 0.1 -9999 0 -0.55 21 21
nectin-1(dimer)/I-afadin/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
FARP2 0.015 0.12 -9999 0 -0.5 29 29
RAC1 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.009 0.034 -9999 0 -0.58 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.005 0.08 -9999 0 -0.35 29 29
nectin-1/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
nectin-2/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
RAC1/GTP/IQGAP1/filamentous actin 0.014 0.025 -9999 0 -0.33 3 3
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.004 0.083 -9999 0 -0.35 31 31
CDC42/GTP/IQGAP1/filamentous actin 0.011 0.05 -9999 0 -0.46 6 6
F11R 0.011 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.018 0.069 -9999 0 -0.3 31 31
alphaV/beta3 Integrin/Talin 0.01 0.094 -9999 0 -0.54 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
nectin-2(dimer)/I-afadin/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
PIP5K1C 0.007 0.061 -9999 0 -0.44 4 4
VAV2 -0.006 0.16 -9999 0 -0.51 51 51
RAP1/GDP -0.023 0.085 -9999 0 -0.39 29 29
ITGAV 0.002 0.076 -9999 0 -0.58 10 10
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.004 0.082 -9999 0 -0.35 31 31
nectin-3(dimer)/I-afadin/I-afadin -0.004 0.094 -9999 0 -0.42 29 29
Rac1/GTP -0.033 0.1 -9999 0 -0.36 51 51
PTPRM 0.001 0.066 -9999 0 -0.25 30 30
E-cadherin/beta catenin/alpha catenin -0.004 0.037 -9999 0 -0.57 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.007 0.054 -9999 0 -0.58 5 5
Regulation of Telomerase

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
Telomerase catalytic core complex -0.096 0.28 -9999 0 -1.1 39 39
RAD9A 0.01 0.024 -9999 0 -0.58 1 1
AP1 -0.013 0.11 -9999 0 -0.39 45 45
IFNAR2 0.011 0.025 -9999 0 -0.58 1 1
AKT1 -0.005 0.061 -9999 0 -0.31 3 3
ER alpha/Oestrogen -0.026 0.11 -9999 0 -0.38 52 52
NFX1/SIN3/HDAC complex 0.033 0.029 -9999 0 -10000 0 0
EGF -0.18 0.25 -9999 0 -0.51 222 222
SMG5 0.01 0.024 -9999 0 -0.58 1 1
SMG6 0.011 0 -9999 0 -10000 0 0
SP3/HDAC2 0.017 0.02 -9999 0 -0.42 1 1
TERT/c-Abl -0.085 0.26 -9999 0 -0.97 41 41
SAP18 0.011 0.019 -9999 0 -0.46 1 1
MRN complex 0.008 0.09 -9999 0 -0.46 19 19
WT1 -0.18 0.26 -9999 0 -0.53 208 208
WRN 0.005 0.062 -9999 0 -0.57 7 7
SP1 0.011 0.025 -9999 0 -0.58 1 1
SP3 0.01 0.024 -9999 0 -0.58 1 1
TERF2IP 0.01 0.024 -9999 0 -0.58 1 1
Telomerase/Nucleolin -0.093 0.22 -9999 0 -0.88 39 39
Mad/Max 0.015 0.027 -9999 0 -0.35 3 3
TERT -0.1 0.3 -9999 0 -1.1 39 39
CCND1 -0.079 0.25 -9999 0 -0.99 35 35
MAX 0.011 0.004 -9999 0 -10000 0 0
RBBP7 0.009 0.034 -9999 0 -0.58 2 2
RBBP4 0.01 0.024 -9999 0 -0.58 1 1
TERF2 0.012 0.009 -9999 0 -10000 0 0
PTGES3 0.009 0.034 -9999 0 -0.58 2 2
SIN3A 0.01 0.024 -9999 0 -0.58 1 1
Telomerase/911 0.019 0.047 -9999 0 -0.7 1 1
CDKN1B -0.021 0.12 -9999 0 -0.48 6 6
RAD1 0.011 0.019 -9999 0 -0.46 1 1
XRCC5 0.01 0.024 -9999 0 -0.58 1 1
XRCC6 0.011 0 -9999 0 -10000 0 0
SAP30 0.009 0.034 -9999 0 -0.58 2 2
TRF2/PARP2 0.017 0.018 -9999 0 -0.38 1 1
UBE3A 0.007 0.048 -9999 0 -0.59 4 4
JUN 0.006 0.052 -9999 0 -0.56 5 5
E6 0 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.036 -9999 0 -0.43 4 4
FOS -0.026 0.14 -9999 0 -0.54 41 41
IFN-gamma/IRF1 -0.035 0.14 -9999 0 -0.36 90 90
PARP2 0.01 0.024 -9999 0 -0.58 1 1
BLM 0.006 0.057 -9999 0 -0.56 6 6
Telomerase 0.003 0.063 -9999 0 -0.45 6 6
IRF1 0.012 0.034 -9999 0 -0.45 3 3
ESR1 -0.036 0.15 -9999 0 -0.53 52 52
KU/TER 0.016 0.018 -9999 0 -0.42 1 1
ATM/TRF2 0.012 0.048 -9999 0 -0.38 9 9
ubiquitin-dependent protein catabolic process 0.035 0.037 -9999 0 -0.38 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.036 0.038 -9999 0 -0.39 2 2
HDAC1 0.011 0.001 -9999 0 -10000 0 0
HDAC2 0.011 0.008 -9999 0 -10000 0 0
ATM -0.007 0.053 -9999 0 -0.44 9 9
SMAD3 0.003 0.081 -9999 0 -0.4 23 23
ABL1 0.01 0.024 -9999 0 -0.58 1 1
MXD1 0.009 0.036 -9999 0 -0.5 3 3
MRE11A 0.004 0.068 -9999 0 -0.58 8 8
HUS1 0.011 0 -9999 0 -10000 0 0
RPS6KB1 0.006 0.057 -9999 0 -0.56 6 6
TERT/NF kappa B1/14-3-3 -0.089 0.25 -9999 0 -1 34 34
NR2F2 0.012 0.007 -9999 0 -10000 0 0
MAPK3 0.01 0.027 -9999 0 -0.35 3 3
MAPK1 0.01 0.027 -9999 0 -0.35 3 3
TGFB1/TGF beta receptor Type II -0.002 0.088 -9999 0 -0.55 15 15
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
HNRNPC 0.011 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.007 0.053 -9999 0 -0.44 9 9
NBN -0.004 0.096 -9999 0 -0.58 16 16
EGFR 0.005 0.058 -9999 0 -0.53 7 7
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.13 0.19 -9999 0 -0.36 228 228
MYC 0.005 0.057 -9999 0 -0.56 6 6
IL2 0.001 0.028 -9999 0 -0.45 2 2
KU 0.016 0.018 -9999 0 -0.42 1 1
RAD50 0.01 0.024 -9999 0 -0.58 1 1
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
TGFB1 -0.002 0.088 -9999 0 -0.55 15 15
TRF2/BLM 0.014 0.04 -9999 0 -0.37 6 6
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.079 0.26 -9999 0 -0.99 39 39
SP1/HDAC2 0.017 0.022 -9999 0 -0.42 1 1
PINX1 0.005 0.064 -9999 0 -0.58 7 7
Telomerase/EST1A -0.093 0.22 -9999 0 -0.88 39 39
Smad3/Myc 0.006 0.077 -9999 0 -0.34 28 28
911 complex 0.022 0.019 -9999 0 -0.36 1 1
IFNG -0.064 0.19 -9999 0 -0.51 89 89
Telomerase/PinX1 -0.095 0.22 -9999 0 -0.87 41 41
Telomerase/AKT1/mTOR/p70S6K -0.001 0.076 -9999 0 -0.74 2 2
SIN3B 0.01 0.024 -9999 0 -0.58 1 1
YWHAE 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.093 0.22 -9999 0 -0.87 40 40
response to DNA damage stimulus 0.001 0.017 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.02 0.08 -9999 0 -0.63 6 6
TRF2/WRN 0.013 0.042 -9999 0 -0.37 7 7
Telomerase/hnRNP C1/C2 -0.093 0.22 -9999 0 -0.88 39 39
E2F1 0.009 0.036 -9999 0 -0.5 3 3
ZNFX1 0.011 0.001 -9999 0 -10000 0 0
PIF1 0.007 0.052 -9999 0 -0.56 5 5
NCL 0.011 0 -9999 0 -10000 0 0
DKC1 0.011 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.075 0.32 -9999 0 -0.99 18 18
PLK1 0.043 0.073 -9999 0 -1.4 1 1
BIRC5 0.045 0.047 -9999 0 -10000 0 0
HSPA1B 0.061 0.34 -9999 0 -1 19 19
MAP2K1 0.028 0.049 -9999 0 -0.63 2 2
BRCA2 0.058 0.37 -9999 0 -1.1 30 30
FOXM1 0.063 0.38 -9999 0 -1.3 19 19
XRCC1 0.074 0.33 -9999 0 -1 19 19
FOXM1B/p19 -0.12 0.28 -9999 0 -1.1 26 26
Cyclin D1/CDK4 0.072 0.31 -9999 0 -0.93 17 17
CDC2 0.07 0.34 -9999 0 -1 19 19
TGFA 0.073 0.31 -9999 0 -1 11 11
SKP2 0.074 0.33 -9999 0 -1 18 18
CCNE1 0.013 0.034 -9999 0 -0.46 3 3
CKS1B 0.074 0.32 -9999 0 -0.98 19 19
RB1 -0.063 0.18 -9999 0 -0.96 18 18
FOXM1C/SP1 0.063 0.34 -9999 0 -1.1 19 19
AURKB 0.045 0.043 -9999 0 -10000 0 0
CENPF 0.063 0.36 -9999 0 -1.1 26 26
CDK4 0.019 0.012 -9999 0 -10000 0 0
MYC 0.076 0.3 -9999 0 -0.9 20 20
CHEK2 0.029 0.041 -9999 0 -0.63 1 1
ONECUT1 0.069 0.32 -9999 0 -0.98 18 18
CDKN2A -0.075 0.19 -9999 0 -0.52 96 96
LAMA4 0.072 0.33 -9999 0 -1.1 17 17
FOXM1B/HNF6 0.063 0.35 -9999 0 -1.2 18 18
FOS 0.036 0.39 -9999 0 -1 41 41
SP1 0.011 0.024 -9999 0 -0.58 1 1
CDC25B 0.074 0.32 -9999 0 -0.99 17 17
response to radiation 0.016 0.028 -9999 0 -10000 0 0
CENPB 0.073 0.33 -9999 0 -1 20 20
CENPA 0.074 0.33 -9999 0 -1 18 18
NEK2 0.074 0.32 -9999 0 -1 18 18
HIST1H2BA 0.068 0.32 -9999 0 -1 17 17
CCNA2 0.014 0.026 -9999 0 -0.6 1 1
EP300 0.007 0.048 -9999 0 -0.58 4 4
CCNB1/CDK1 0.064 0.35 -9999 0 -1.2 18 18
CCNB2 0.072 0.33 -9999 0 -1 20 20
CCNB1 0.072 0.34 -9999 0 -1 18 18
ETV5 0.057 0.36 -9999 0 -1.1 28 28
ESR1 0.034 0.41 -9999 0 -1.2 40 40
CCND1 0.075 0.32 -9999 0 -0.94 18 18
GSK3A 0.029 0.026 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.038 0.049 -9999 0 -0.42 3 3
CDK2 0.014 0.026 -9999 0 -0.6 1 1
G2/M transition of mitotic cell cycle 0.018 0.033 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.09 0.25 -9999 0 -1.1 19 19
GAS1 -0.05 0.51 -9999 0 -1.1 90 90
MMP2 0.038 0.41 -9999 0 -1.2 36 36
RB1/FOXM1C 0.07 0.33 -9999 0 -0.99 24 24
CREBBP 0.011 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.009 0.036 -9999 0 -0.5 3 3
SPHK1 -0.03 0.14 -9999 0 -0.52 48 48
GNAI2 0.011 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.069 -9999 0 -0.3 24 24
GNAO1 -0.045 0.16 -9999 0 -0.49 68 68
mol:Sphinganine-1-P -0.014 0.11 -9999 0 -0.37 51 51
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.018 0.054 -9999 0 -0.29 2 2
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.016 0.025 -9999 0 -0.42 2 2
S1PR3 0.004 0.063 -9999 0 -0.54 8 8
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.004 0.058 -9999 0 -0.26 24 24
S1PR5 0.001 0.076 -9999 0 -0.53 12 12
S1PR4 -0.025 0.14 -9999 0 -0.53 40 40
GNAI1 -0.003 0.089 -9999 0 -0.56 15 15
S1P/S1P5/G12 0.006 0.069 -9999 0 -0.32 9 9
S1P/S1P3/Gq -0.002 0.11 -9999 0 -0.4 25 25
S1P/S1P4/Gi -0.022 0.12 -9999 0 -0.34 49 49
GNAQ 0.006 0.059 -9999 0 -0.58 6 6
GNAZ -0.013 0.11 -9999 0 -0.55 26 26
GNA14 -0.007 0.1 -9999 0 -0.56 19 19
GNA15 -0.009 0.1 -9999 0 -0.54 22 22
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
GNA11 0.007 0.05 -9999 0 -0.53 5 5
ABCC1 0.01 0.024 -9999 0 -0.58 1 1
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.02 0.12 -9999 0 -0.31 57 57
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.011 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.002 0.12 -9999 0 -0.55 13 13
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.078 -9999 0 -0.37 23 23
antigen processing and presentation of peptide antigen via MHC class I -0.039 0.075 -9999 0 -0.29 20 20
CaM/Ca2+ -0.018 0.11 -9999 0 -0.42 11 11
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
STAT1 (dimer)/SHP2 -0.013 0.12 -9999 0 -0.51 13 13
AKT1 -0.004 0.11 -9999 0 -0.46 12 12
MAP2K1 -0.01 0.12 -9999 0 -0.5 14 14
MAP3K11 -0.014 0.11 -9999 0 -0.38 16 16
IFNGR1 0.008 0.012 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.052 0.12 -9999 0 -0.47 32 32
Rap1/GTP -0.031 0.074 -9999 0 -0.41 6 6
CRKL/C3G 0.016 0.018 -9999 0 -0.42 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.022 0.12 -9999 0 -0.38 22 22
CEBPB -0.01 0.16 -9999 0 -0.47 37 37
STAT3 0.011 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.053 0.22 -9999 0 -1 19 19
STAT1 -0.014 0.12 -9999 0 -0.5 13 13
CALM1 0.011 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.067 0.19 -9999 0 -0.51 89 89
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
STAT1 (dimer)/PIAS1 -0.006 0.12 -9999 0 -0.49 12 12
CEBPB/PTGES2/Cbp/p300 -0.04 0.086 -9999 0 -0.41 14 14
mol:Ca2+ -0.021 0.11 -9999 0 -0.31 57 57
MAPK3 -0.006 0.13 -9999 0 -0.68 8 8
STAT1 (dimer) -0.052 0.1 -9999 0 -0.4 19 19
MAPK1 -0.006 0.12 -9999 0 -0.66 8 8
JAK2 -0.011 0.1 -9999 0 -0.56 21 21
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
JAK1 0.005 0.044 -9999 0 -0.6 3 3
CAMK2D 0.008 0.048 -9999 0 -0.58 4 4
DAPK1 -0.014 0.16 -9999 0 -0.54 39 39
SMAD7 0.011 0.06 -9999 0 -0.29 2 2
CBL/CRKL/C3G -0.002 0.1 -9999 0 -0.43 8 8
PI3K -0.042 0.1 -9999 0 -0.5 12 12
IFNG -0.067 0.19 -9999 0 -0.51 89 89
apoptosis -0.013 0.12 -9999 0 -0.4 37 37
CAMK2G 0.011 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.02 0.12 -9999 0 -0.53 34 34
CAMK2B -0.056 0.17 -9999 0 -0.5 79 79
FRAP1 -0.003 0.1 -9999 0 -0.42 12 12
PRKCD -0.003 0.11 -9999 0 -0.47 12 12
RAP1B 0.011 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.039 0.075 -9999 0 -0.29 20 20
PTPN2 0.008 0.042 -9999 0 -0.58 3 3
EP300 0.008 0.048 -9999 0 -0.58 4 4
IRF1 0 0.13 -9999 0 -0.51 15 15
STAT1 (dimer)/PIASy -0.006 0.12 -9999 0 -0.48 12 12
SOCS1 -0.046 0.22 -9999 0 -1.4 14 14
mol:GDP -0.031 0.087 -9999 0 -0.42 8 8
CASP1 0.002 0.087 -9999 0 -0.28 37 37
PTGES2 0.007 0.045 -9999 0 -0.48 5 5
IRF9 0.02 0.054 -9999 0 -0.23 4 4
mol:PI-3-4-5-P3 -0.041 0.1 -9999 0 -0.49 12 12
RAP1/GDP -0.032 0.074 -9999 0 -0.41 6 6
CBL -0.013 0.11 -9999 0 -0.43 11 11
MAP3K1 -0.017 0.12 -9999 0 -0.49 14 14
PIAS1 0.011 0 -9999 0 -10000 0 0
PIAS4 0.011 0.024 -9999 0 -0.57 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.039 0.075 -9999 0 -0.29 20 20
PTPN11 -0.02 0.12 -9999 0 -0.31 57 57
CREBBP 0.012 0.001 -9999 0 -10000 0 0
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.08 0.2 -9999 0 -0.51 106 106
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.005 0.055 -9999 0 -0.47 8 8
TCEB1 0.011 0.019 -9999 0 -0.46 1 1
HIF1A/p53 -0.009 0.096 -9999 0 -0.28 57 57
HIF1A 0.013 0.037 -9999 0 -0.25 9 9
COPS5 0.011 0.019 -9999 0 -0.46 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 0.029 0.042 -9999 0 -0.39 4 4
FIH (dimer) 0.011 0 -9999 0 -10000 0 0
CDKN2A -0.071 0.19 -9999 0 -0.51 96 96
ARNT/IPAS -0.05 0.15 -9999 0 -0.36 107 107
HIF1AN 0.011 0 -9999 0 -10000 0 0
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
HIF1A/ARNT 0.019 0.04 -9999 0 -0.4 2 2
CUL2 0.011 0 -9999 0 -10000 0 0
OS9 0.011 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.019 0.04 -9999 0 -0.43 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.019 0.04 -9999 0 -0.4 2 2
PHD1-3/OS9 0.018 0.06 -9999 0 -0.32 13 13
HIF1A/RACK1/Elongin B/Elongin C 0.025 0.055 -9999 0 -0.4 8 8
VHL 0.01 0.024 -9999 0 -0.58 1 1
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
HIF1A/JAB1 0.019 0.036 -9999 0 -0.29 1 1
EGLN3 -0.007 0.098 -9999 0 -0.53 20 20
EGLN2 0.009 0.036 -9999 0 -0.5 3 3
EGLN1 0.011 0 -9999 0 -10000 0 0
TP53 -0.045 0.17 -9999 0 -0.58 57 57
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.045 -9999 0 -0.86 1 1
ARNT 0.01 0.024 -9999 0 -0.58 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.01 0.031 -9999 0 -0.52 2 2
HIF1A/p19ARF -0.021 0.1 -9999 0 -0.29 47 47
ErbB2/ErbB3 signaling events

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
USP8 0.011 0.037 -10000 0 -0.36 6 6
RAS family/GTP -0.001 0.097 -10000 0 -0.36 12 12
NFATC4 0.003 0.088 -10000 0 -0.42 4 4
ERBB2IP -0.008 0.11 -10000 0 -0.58 20 20
HSP90 (dimer) 0.01 0.024 -10000 0 -0.58 1 1
mammary gland morphogenesis -0.011 0.1 0.22 6 -0.32 12 18
JUN 0.005 0.1 0.16 3 -0.28 49 52
HRAS 0.008 0.041 -10000 0 -0.49 4 4
DOCK7 -0.004 0.1 -10000 0 -0.41 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.02 0.12 0.23 13 -0.32 54 67
AKT1 0.008 0.018 -10000 0 -0.44 1 1
BAD 0.014 0.031 -10000 0 -0.48 2 2
MAPK10 -0.007 0.082 -10000 0 -0.29 19 19
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.01 0.11 0.24 6 -0.35 12 18
RAF1 0.009 0.098 -10000 0 -0.36 11 11
ErbB2/ErbB3/neuregulin 2 0 0.073 0.23 12 -0.25 39 51
STAT3 0 0.044 -10000 0 -1.1 1 1
cell migration 0.008 0.075 0.16 7 -0.25 15 22
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.002 0.19 -10000 0 -0.59 38 38
FOS 0.003 0.16 -10000 0 -0.42 55 55
NRAS 0.002 0.076 -10000 0 -0.58 10 10
mol:Ca2+ -0.011 0.1 0.22 6 -0.32 12 18
MAPK3 0.003 0.16 -10000 0 -0.5 32 32
MAPK1 0.003 0.15 -10000 0 -0.49 31 31
JAK2 -0.011 0.11 -10000 0 -0.43 10 10
NF2 -0.002 0.009 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.01 0.094 -10000 0 -0.28 53 53
NRG1 -0.07 0.2 -10000 0 -0.53 91 91
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
MAPK8 0 0.098 0.2 5 -0.3 13 18
MAPK9 0.008 0.059 -10000 0 -0.25 4 4
ERBB2 0.005 0.085 0.39 19 -0.34 13 32
ERBB3 0.01 0.024 -10000 0 -0.58 1 1
SHC1 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.003 0.035 0.82 1 -10000 0 1
STAT3 (dimer) 0.014 0.043 -10000 0 -1 1 1
RNF41 0.016 0.034 -10000 0 -0.32 6 6
FRAP1 0.007 0.016 -10000 0 -0.37 1 1
RAC1-CDC42/GTP -0.028 0.066 -10000 0 -0.33 7 7
ErbB2/ErbB2/HSP90 (dimer) 0.008 0.061 0.26 18 -0.28 13 31
CHRNA1 -0.002 0.18 -10000 0 -0.6 36 36
myelination 0.005 0.087 -10000 0 -0.4 4 4
PPP3CB -0.003 0.095 -10000 0 -0.4 3 3
KRAS 0.006 0.057 -10000 0 -0.56 6 6
RAC1-CDC42/GDP -0.001 0.085 -10000 0 -0.31 6 6
NRG2 -0.016 0.1 -10000 0 -0.46 32 32
mol:GDP -0.01 0.094 -10000 0 -0.28 53 53
SOS1 0.01 0.024 -10000 0 -0.58 1 1
MAP2K2 0.013 0.1 -10000 0 -0.38 12 12
SRC 0.01 0.024 -10000 0 -0.58 1 1
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.006 0.1 -10000 0 -0.42 5 5
MAP2K1 -0.001 0.15 -10000 0 -0.52 18 18
heart morphogenesis -0.011 0.1 0.22 6 -0.32 12 18
RAS family/GDP -0.001 0.097 -10000 0 -0.39 9 9
GRB2 0.011 0.001 -10000 0 -10000 0 0
PRKACA -0.003 0.006 -10000 0 -10000 0 0
CHRNE 0 0.056 -10000 0 -0.18 50 50
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
activation of caspase activity -0.008 0.018 0.44 1 -10000 0 1
nervous system development -0.011 0.1 0.22 6 -0.32 12 18
CDC42 0.007 0.054 -10000 0 -0.58 5 5
Signaling events mediated by PRL

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
CCNE1 0.009 0.033 -10000 0 -0.46 3 3
mol:Halofuginone 0.004 0.009 -10000 0 -0.23 1 1
ITGA1 0.006 0.059 -10000 0 -0.58 6 6
CDKN1A 0.019 0.047 -10000 0 -0.44 4 4
PRL-3/alpha Tubulin -0.006 0.093 -10000 0 -0.37 36 36
mol:Ca2+ -0.008 0.12 0.3 35 -0.39 38 73
AGT -0.024 0.13 -10000 0 -0.53 39 39
CCNA2 0.02 0.067 -10000 0 -0.89 1 1
TUBA1B 0.011 0 -10000 0 -10000 0 0
EGR1 0.004 0.076 -10000 0 -0.35 26 26
CDK2/Cyclin E1 0.028 0.047 -10000 0 -0.39 4 4
MAPK3 -0.005 0.095 -10000 0 -0.37 37 37
PRL-2 /Rab GGTase beta 0.015 0.031 -10000 0 -0.42 3 3
MAPK1 -0.005 0.095 -10000 0 -0.37 37 37
PTP4A1 0.016 0.071 -10000 0 -0.95 1 1
PTP4A3 -0.02 0.13 -10000 0 -0.52 36 36
PTP4A2 0.011 0 -10000 0 -10000 0 0
ITGB1 -0.005 0.093 -10000 0 -0.37 36 36
SRC 0.01 0.024 -10000 0 -0.58 1 1
RAC1 0.005 0.085 -10000 0 -0.43 18 18
Rab GGTase beta/Rab GGTase alpha 0.014 0.036 -10000 0 -0.42 4 4
PRL-1/ATF-5 0.02 0.067 -10000 0 -0.89 1 1
RABGGTA 0.01 0.024 -10000 0 -0.58 1 1
BCAR1 0.015 0.075 0.3 34 -0.27 4 38
RHOC 0.005 0.085 -10000 0 -0.42 19 19
RHOA 0.004 0.087 -10000 0 -0.41 21 21
cell motility 0.005 0.092 -10000 0 -0.42 21 21
PRL-1/alpha Tubulin 0.021 0.066 -10000 0 -0.89 1 1
PRL-3/alpha1 Integrin -0.01 0.1 -10000 0 -0.39 41 41
ROCK1 0.005 0.092 -10000 0 -0.43 21 21
RABGGTB 0.008 0.042 -10000 0 -0.58 3 3
CDK2 0.01 0.024 -10000 0 -0.58 1 1
mitosis 0.016 0.07 -10000 0 -0.93 1 1
ATF5 0.011 0.019 -10000 0 -0.46 1 1
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.045 0.16 -9999 0 -0.49 68 68
CDC42/GTP -0.017 0.11 -9999 0 -0.42 18 18
PLCG1 -0.015 0.11 -9999 0 -0.46 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.011 0 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.016 0.025 -9999 0 -0.42 2 2
cell migration -0.017 0.1 -9999 0 -0.4 18 18
S1PR5 0.001 0.076 -9999 0 -0.53 12 12
S1PR4 -0.025 0.14 -9999 0 -0.53 40 40
MAPK3 -0.015 0.11 -9999 0 -0.48 14 14
MAPK1 -0.015 0.11 -9999 0 -0.48 14 14
S1P/S1P5/Gi -0.011 0.096 -9999 0 -0.31 29 29
GNAI1 -0.003 0.089 -9999 0 -0.56 15 15
CDC42/GDP 0.005 0.04 -9999 0 -0.43 5 5
S1P/S1P5/G12 0.009 0.048 -9999 0 -0.32 12 12
RHOA 0.005 0.076 -9999 0 -0.3 27 27
S1P/S1P4/Gi -0.022 0.11 -9999 0 -0.32 49 49
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.013 0.11 -9999 0 -0.55 26 26
S1P/S1P4/G12/G13 0.001 0.08 -9999 0 -0.32 26 26
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
CDC42 0.007 0.054 -9999 0 -0.58 5 5
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.007 0.048 -10000 0 -0.58 4 4
HSPA8 0.01 0.034 -10000 0 -0.58 2 2
SMAD3/SMAD4/ER alpha -0.037 0.12 0.2 7 -0.36 49 56
AKT1 0.011 0.027 -10000 0 -0.58 1 1
GSC -0.016 0.14 -10000 0 -1.4 4 4
NKX2-5 -0.014 0.085 -10000 0 -0.46 21 21
muscle cell differentiation 0.04 0.096 0.47 16 -10000 0 16
SMAD2-3/SMAD4/SP1 0.023 0.1 -10000 0 -0.41 10 10
SMAD4 -0.002 0.081 -10000 0 -0.58 8 8
CBFB 0.007 0.048 -10000 0 -0.58 4 4
SAP18 0.011 0.019 -10000 0 -0.46 1 1
Cbp/p300/MSG1 -0.034 0.12 -10000 0 -0.34 39 39
SMAD3/SMAD4/VDR -0.009 0.061 -10000 0 -0.39 5 5
MYC 0.006 0.058 -10000 0 -0.56 6 6
CDKN2B -0.011 0.22 -10000 0 -1.4 14 14
AP1 0.009 0.11 -10000 0 -0.47 15 15
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.038 0.056 -10000 0 -0.44 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.005 0.088 -10000 0 -0.32 20 20
SP3 0.013 0.024 -10000 0 -0.58 1 1
CREB1 0.009 0.034 -10000 0 -0.58 2 2
FOXH1 -0.053 0.17 -10000 0 -0.5 75 75
SMAD3/SMAD4/GR -0.015 0.11 -10000 0 -0.38 32 32
GATA3 -0.027 0.13 -10000 0 -0.54 32 32
SKI/SIN3/HDAC complex/NCoR1 0.036 0.025 -10000 0 -10000 0 0
MEF2C/TIF2 -0.019 0.14 -10000 0 -0.54 16 16
endothelial cell migration 0.033 0.19 1.3 10 -10000 0 10
MAX 0.013 0.01 -10000 0 -10000 0 0
RBBP7 0.01 0.034 -10000 0 -0.58 2 2
RBBP4 0.011 0.024 -10000 0 -0.58 1 1
RUNX2 -0.006 0.096 -10000 0 -0.54 19 19
RUNX3 -0.022 0.13 -10000 0 -0.51 39 39
RUNX1 0.011 0 -10000 0 -10000 0 0
CTBP1 0.01 0.024 -10000 0 -0.58 1 1
NR3C1 -0.013 0.12 -10000 0 -0.53 28 28
VDR 0.01 0.024 -10000 0 -0.58 1 1
CDKN1A 0.027 0.13 -10000 0 -1 5 5
KAT2B -0.006 0.099 -10000 0 -0.59 17 17
SMAD2/SMAD2/SMAD4/FOXH1 -0.022 0.13 -10000 0 -0.38 36 36
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.011 0.001 -10000 0 -10000 0 0
SERPINE1 -0.033 0.2 -10000 0 -1.4 10 10
SMAD3/SMAD4/ATF2 0.01 0.08 -10000 0 -0.35 16 16
SMAD3/SMAD4/ATF3 0.002 0.095 -10000 0 -0.36 20 20
SAP30 0.01 0.034 -10000 0 -0.58 2 2
Cbp/p300/PIAS3 0.02 0.04 -10000 0 -0.34 6 6
JUN 0.008 0.11 -10000 0 -0.47 14 14
SMAD3/SMAD4/IRF7 0.005 0.09 -10000 0 -0.42 12 12
TFE3 0.014 0.012 -10000 0 -10000 0 0
COL1A2 -0.049 0.22 -10000 0 -0.72 48 48
mesenchymal cell differentiation 0.001 0.099 0.36 28 -10000 0 28
DLX1 -0.044 0.15 -10000 0 -0.46 68 68
TCF3 0.01 0.024 -10000 0 -0.58 1 1
FOS -0.024 0.14 -10000 0 -0.54 41 41
SMAD3/SMAD4/Max 0.002 0.074 -10000 0 -0.34 12 12
Cbp/p300/SNIP1 0.02 0.031 -10000 0 -0.35 4 4
ZBTB17 0.011 0.026 -10000 0 -0.59 1 1
LAMC1 0.022 0.071 -10000 0 -0.44 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.008 0.084 -10000 0 -0.35 19 19
IRF7 0.005 0.06 -10000 0 -0.55 7 7
ESR1 -0.033 0.15 -10000 0 -0.52 52 52
HNF4A 0.005 0.064 -10000 0 -0.58 7 7
MEF2C -0.023 0.14 -10000 0 -0.51 21 21
SMAD2-3/SMAD4 0.012 0.089 -10000 0 -0.37 15 15
Cbp/p300/Src-1 0.02 0.04 -10000 0 -0.43 4 4
IGHV3OR16-13 -0.01 0.05 -10000 0 -0.8 2 2
TGIF2/HDAC complex 0.007 0.054 -10000 0 -0.58 5 5
CREBBP 0.011 0.005 -10000 0 -10000 0 0
SKIL 0.001 0.08 -10000 0 -0.58 11 11
HDAC1 0.011 0.001 -10000 0 -10000 0 0
HDAC2 0.011 0.001 -10000 0 -10000 0 0
SNIP1 0.012 0.002 -10000 0 -10000 0 0
GCN5L2 0 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.021 0.08 -10000 0 -0.41 4 4
MSG1/HSC70 -0.049 0.14 -10000 0 -0.34 110 110
SMAD2 0.007 0.052 -10000 0 -0.58 4 4
SMAD3 0 0.079 -10000 0 -0.57 8 8
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.071 -10000 0 -0.34 5 5
SMAD2/SMAD2/SMAD4 -0.005 0.077 -10000 0 -0.35 25 25
NCOR1 0.011 0.024 -10000 0 -0.58 1 1
NCOA2 0.004 0.066 -10000 0 -0.57 8 8
NCOA1 0.01 0.024 -10000 0 -0.58 1 1
MYOD/E2A 0.007 0.026 -10000 0 -0.36 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.031 0.1 -10000 0 -0.44 6 6
IFNB1 0.008 0.087 -10000 0 -0.48 8 8
SMAD3/SMAD4/MEF2C -0.019 0.14 -10000 0 -0.56 16 16
CITED1 -0.078 0.19 -10000 0 -0.49 108 108
SMAD2-3/SMAD4/ARC105 0.02 0.082 -10000 0 -0.38 9 9
RBL1 0.009 0.039 -10000 0 -0.54 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.024 0.1 -10000 0 -0.48 17 17
RUNX1-3/PEBPB2 0 0.086 -10000 0 -0.31 43 43
SMAD7 0.026 0.12 -10000 0 -0.66 6 6
MYC/MIZ-1 0.012 0.05 -10000 0 -0.4 7 7
SMAD3/SMAD4 -0.016 0.098 0.31 4 -0.43 14 18
IL10 -0.039 0.21 -10000 0 -0.62 53 53
PIASy/HDAC complex 0.011 0.025 -10000 0 -0.58 1 1
PIAS3 0.009 0.031 -10000 0 -0.52 2 2
CDK2 0.01 0.025 -10000 0 -0.58 1 1
IL5 -0.015 0.14 -10000 0 -0.58 12 12
CDK4 0.011 0.006 -10000 0 -10000 0 0
PIAS4 0.011 0.025 -10000 0 -0.58 1 1
ATF3 -0.003 0.083 -10000 0 -0.46 19 19
SMAD3/SMAD4/SP1 0.013 0.1 -10000 0 -0.4 11 11
FOXG1 -0.066 0.17 -10000 0 -0.49 83 83
FOXO3 0.019 0.024 -10000 0 -0.42 1 1
FOXO1 0.017 0.035 -10000 0 -0.42 3 3
FOXO4 0.018 0.03 -10000 0 -0.42 2 2
heart looping -0.023 0.14 -10000 0 -0.51 21 21
CEBPB 0.008 0.041 -10000 0 -0.49 4 4
SMAD3/SMAD4/DLX1 -0.024 0.12 -10000 0 -0.37 20 20
MYOD1 -0.001 0.026 -10000 0 -0.46 2 2
SMAD3/SMAD4/HNF4 0.007 0.091 -10000 0 -0.39 18 18
SMAD3/SMAD4/GATA3 -0.03 0.14 -10000 0 -0.48 25 25
SnoN/SIN3/HDAC complex/NCoR1 0.001 0.079 -10000 0 -0.58 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.006 0.1 -10000 0 -0.4 13 13
SMAD3/SMAD4/SP1-3 0.025 0.092 -10000 0 -0.42 4 4
MED15 0.01 0.024 -10000 0 -0.58 1 1
SP1 0.008 0.044 -10000 0 -0.57 1 1
SIN3B 0.011 0.024 -10000 0 -0.58 1 1
SIN3A 0.011 0.024 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.024 0.13 -10000 0 -0.42 19 19
ITGB5 0.027 0.081 -10000 0 -0.44 2 2
TGIF/SIN3/HDAC complex/CtBP 0.036 0.029 -10000 0 -0.46 1 1
SMAD3/SMAD4/AR -0.028 0.13 -10000 0 -0.37 52 52
AR -0.05 0.16 -10000 0 -0.5 71 71
negative regulation of cell growth 0.019 0.084 -10000 0 -0.4 8 8
SMAD3/SMAD4/MYOD 0.003 0.078 -10000 0 -0.34 14 14
E2F5 -0.001 0.086 -10000 0 -0.58 13 13
E2F4 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.006 0.11 -10000 0 -0.42 12 12
SMAD2-3/SMAD4/FOXO1-3a-4 0.025 0.082 -10000 0 -0.34 18 18
TFDP1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.011 0.12 -10000 0 -0.48 14 14
SMAD3/SMAD4/RUNX2 0 0.099 -10000 0 -0.36 28 28
TGIF2 0.007 0.054 -10000 0 -0.58 5 5
TGIF1 0.011 0 -10000 0 -10000 0 0
ATF2 0.009 0.034 -10000 0 -0.58 2 2
Ceramide signaling 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
SPHK2 0.013 0.046 -10000 0 -0.34 10 10
MAP4K4 0.019 0.066 -10000 0 -0.51 2 2
BAG4 0.008 0.042 -10000 0 -0.58 3 3
PKC zeta/ceramide -0.024 0.041 0.15 1 -0.2 2 3
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.53 31 31
BAX -0.009 0.023 -10000 0 -0.31 1 1
RIPK1 0.011 0 -10000 0 -10000 0 0
AKT1 0.018 0.023 -10000 0 -0.52 1 1
BAD -0.025 0.041 0.16 1 -0.2 2 3
SMPD1 0.012 0.047 -10000 0 -0.2 22 22
RB1 -0.034 0.067 0.16 2 -0.32 20 22
FADD/Caspase 8 0.028 0.062 -10000 0 -0.4 2 2
MAP2K4 -0.021 0.052 -10000 0 -0.31 9 9
NSMAF 0.011 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.018 0.041 -10000 0 -0.31 2 2
EGF -0.18 0.25 -10000 0 -0.51 222 222
mol:ceramide -0.032 0.043 0.14 7 -10000 0 7
MADD 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.038 -10000 0 -0.33 7 7
ASAH1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.034 0.066 0.16 2 -0.32 20 22
cell proliferation -0.037 0.091 -10000 0 -0.26 58 58
BID 0.009 0.047 -10000 0 -0.33 2 2
MAP3K1 -0.027 0.05 0.16 2 -0.33 6 8
EIF2A -0.021 0.063 -10000 0 -0.32 17 17
TRADD 0.011 0 -10000 0 -10000 0 0
CRADD 0.01 0.024 -10000 0 -0.58 1 1
MAPK3 -0.009 0.039 -10000 0 -0.29 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.039 -10000 0 -0.29 2 2
Cathepsin D/ceramide -0.024 0.041 0.15 1 -0.23 2 3
FADD 0.02 0.063 -10000 0 -0.53 1 1
KSR1 -0.025 0.044 0.14 7 -0.34 2 9
MAPK8 -0.016 0.045 0.16 1 -0.26 5 6
PRKRA -0.024 0.04 0.16 2 -0.2 1 3
PDGFA 0.006 0.052 -10000 0 -0.48 7 7
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
IGF1 -0.075 0.2 -10000 0 -0.52 97 97
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.032 0.042 0.14 7 -10000 0 7
CTSD 0.009 0.036 -10000 0 -0.5 3 3
regulation of nitric oxide biosynthetic process 0.016 0.018 -10000 0 -0.42 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.097 -10000 0 -0.28 58 58
PRKCD 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.038 -10000 0 -0.33 7 7
RelA/NF kappa B1 0.016 0.018 -10000 0 -0.42 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0.024 -10000 0 -0.58 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.066 -10000 0 -0.56 1 1
TNFR1A/BAG4/TNF-alpha 0.004 0.082 -10000 0 -0.33 34 34
mol:Sphingosine-1-phosphate 0.013 0.046 -10000 0 -0.34 10 10
MAP2K1 -0.012 0.041 -10000 0 -0.29 3 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
CYCS -0.016 0.047 0.16 7 -0.23 12 19
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
TNFR1A/BAG4 0.015 0.031 -10000 0 -0.42 3 3
EIF2AK2 -0.027 0.061 -10000 0 -0.32 16 16
TNF-alpha/TNFR1A/FAN 0.005 0.077 -10000 0 -0.32 31 31
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.024 0.047 -10000 0 -0.38 3 3
MAP2K2 -0.012 0.04 -10000 0 -0.29 2 2
SMPD3 0.007 0.071 -10000 0 -0.26 34 34
TNF -0.017 0.12 -10000 0 -0.54 31 31
PKC zeta/PAR4 0.015 0.029 -10000 0 -0.39 3 3
mol:PHOSPHOCHOLINE 0.059 0.095 0.18 214 -10000 0 214
NF kappa B1/RelA/I kappa B alpha 0.032 0.029 -10000 0 -0.52 1 1
AIFM1 -0.01 0.038 0.16 7 -0.26 1 8
BCL2 -0.007 0.1 -10000 0 -0.55 20 20
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.007 0.048 -10000 0 -0.58 4 4
HDAC4 0.011 0.019 -10000 0 -0.46 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.006 0.091 0.36 37 -10000 0 37
CDKN1A 0.007 0.068 -10000 0 -0.58 5 5
KAT2B -0.005 0.098 -10000 0 -0.58 17 17
BAX 0.01 0.024 -10000 0 -0.58 1 1
FOXO3 0.004 0.041 0.49 4 -10000 0 4
FOXO1 0.009 0.034 -10000 0 -0.58 2 2
FOXO4 0.016 0.028 -10000 0 -0.3 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
TAT -0.018 0.11 -10000 0 -0.46 34 34
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.004 0.075 -10000 0 -0.42 19 19
PPARGC1A -0.044 0.17 -10000 0 -0.57 58 58
FHL2 0.008 0.042 -10000 0 -0.58 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.011 0.041 -10000 0 -0.42 5 5
HIST2H4A -0.006 0.091 -10000 0 -0.36 37 37
SIRT1/FOXO3a 0 0.031 0.29 2 -0.36 3 5
SIRT1 0.004 0.055 0.2 2 -0.59 5 7
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.017 0.04 -10000 0 -0.34 7 7
SIRT1/Histone H1b 0.003 0.067 -10000 0 -0.3 20 20
apoptosis -0.017 0.038 0.36 6 -10000 0 6
SIRT1/PGC1A -0.035 0.11 -10000 0 -0.35 63 63
p53/SIRT1 -0.041 0.13 0.32 4 -0.43 61 65
SIRT1/FOXO4 0.014 0.048 -10000 0 -0.37 8 8
FOXO1/FHL2/SIRT1 0.015 0.045 -10000 0 -0.33 10 10
HIST1H1E 0.003 0.062 -10000 0 -0.31 17 17
SIRT1/p300 0.009 0.061 -10000 0 -0.53 7 7
muscle cell differentiation 0 0.079 0.4 21 -10000 0 21
TP53 -0.047 0.17 -10000 0 -0.58 57 57
KU70/SIRT1/BAX 0.018 0.038 -10000 0 -0.36 6 6
CREBBP 0.011 0 -10000 0 -10000 0 0
MEF2D 0.01 0.024 -10000 0 -0.58 1 1
HIV-1 Tat/SIRT1 -0.011 0.085 -10000 0 -0.33 39 39
ACSS2 0.013 0.044 -10000 0 -0.42 6 6
SIRT1/PCAF/MYOD 0 0.08 -10000 0 -0.4 21 21
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.013 0.073 -9999 0 -0.45 2 2
Syndecan-3/Neurocan 0.004 0.041 -9999 0 -0.6 1 1
POMC -0.029 0.14 -9999 0 -0.52 45 45
EGFR 0.005 0.058 -9999 0 -0.53 7 7
Syndecan-3/EGFR 0.016 0.04 -9999 0 -0.36 5 5
AGRP -0.001 0.05 -9999 0 -0.46 7 7
NCSTN 0.011 0 -9999 0 -10000 0 0
PSENEN 0.01 0.024 -9999 0 -0.58 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.006 0.059 -9999 0 -0.58 6 6
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.004 0.065 -9999 0 -0.46 12 12
long-term memory 0.022 0.041 -9999 0 -0.42 3 3
Syndecan-3/IL8 -0.042 0.12 -9999 0 -0.31 69 69
PSEN1 0.011 0 -9999 0 -10000 0 0
Src/Cortactin 0.016 0.018 -9999 0 -0.42 1 1
FYN 0.005 0.06 -9999 0 -0.55 7 7
limb bud formation -0.002 0.026 -9999 0 -0.62 1 1
MC4R -0.004 0.056 -9999 0 -0.46 9 9
SRC 0.01 0.024 -9999 0 -0.58 1 1
PTN -0.025 0.14 -9999 0 -0.54 40 40
FGFR/FGF/Syndecan-3 -0.002 0.026 -9999 0 -0.63 1 1
neuron projection morphogenesis -0.005 0.073 -9999 0 -0.43 2 2
Syndecan-3/AgRP 0.003 0.036 -9999 0 -0.6 1 1
Syndecan-3/AgRP/MC4R -0.004 0.044 -9999 0 -0.42 3 3
Fyn/Cortactin 0.012 0.044 -9999 0 -0.39 7 7
SDC3 -0.002 0.027 -9999 0 -0.64 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.042 0.12 -9999 0 -0.3 69 69
IL8 -0.11 0.22 -9999 0 -0.52 137 137
Syndecan-3/Fyn/Cortactin 0.023 0.042 -9999 0 -0.43 3 3
Syndecan-3/CASK -0.002 0.025 -9999 0 -0.61 1 1
alpha-MSH/MC4R -0.023 0.11 -9999 0 -0.39 51 51
Gamma Secretase 0.03 0.035 -9999 0 -0.3 7 7
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.015 0.13 -9999 0 -0.47 30 30
PDGFB-D/PDGFRB/SLAP -0.015 0.12 -9999 0 -0.43 43 43
PDGFB-D/PDGFRB/APS/CBL -0.004 0.093 -9999 0 -0.32 44 44
AKT1 0.031 0.068 -9999 0 -0.48 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.016 0.13 -9999 0 -0.49 30 30
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
FGR -0.043 0.17 -9999 0 -0.6 40 40
mol:Ca2+ -0.006 0.11 -9999 0 -0.58 18 18
MYC 0 0.12 -9999 0 -0.61 15 15
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP 0.016 0.068 -9999 0 -0.33 12 12
LRP1/PDGFRB/PDGFB 0.006 0.083 -9999 0 -0.41 20 20
GRB10 0.007 0.048 -9999 0 -0.58 4 4
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
GO:0007205 -0.007 0.12 -9999 0 -0.6 18 18
PTEN 0.006 0.059 -9999 0 -0.58 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
GRB7 0.002 0.065 -9999 0 -0.46 12 12
PDGFB-D/PDGFRB/SHP2 0 0.082 -9999 0 -0.4 24 24
PDGFB-D/PDGFRB/GRB10 0.001 0.08 -9999 0 -0.4 23 23
cell cycle arrest -0.015 0.12 -9999 0 -0.42 43 43
HRAS 0.008 0.041 -9999 0 -0.49 4 4
HIF1A 0.031 0.079 -9999 0 -0.5 7 7
GAB1 -0.017 0.13 -9999 0 -0.6 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.012 0.12 -9999 0 -0.55 20 20
PDGFB-D/PDGFRB 0.011 0.071 -9999 0 -0.35 22 22
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.004 0.072 -9999 0 -0.39 19 19
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.04 0.12 -9999 0 -0.48 31 31
positive regulation of MAPKKK cascade 0 0.082 -9999 0 -0.4 24 24
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:IP3 -0.007 0.12 -9999 0 -0.6 18 18
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.01 0.024 -9999 0 -0.58 1 1
PDGFB-D/PDGFRB/GRB7 -0.003 0.087 -9999 0 -0.37 30 30
SHB 0.011 0.019 -9999 0 -0.46 1 1
BLK -0.096 0.21 -9999 0 -0.56 89 89
PTPN2 0.008 0.042 -9999 0 -0.59 3 3
PDGFB-D/PDGFRB/SNX15 0.004 0.072 -9999 0 -0.39 19 19
BCAR1 0.008 0.043 -9999 0 -0.52 4 4
VAV2 -0.02 0.15 -9999 0 -0.61 25 25
CBL 0.011 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.003 0.074 -9999 0 -0.39 20 20
LCK -0.038 0.13 -9999 0 -0.5 38 38
PDGFRB -0.006 0.099 -9999 0 -0.55 19 19
ACP1 0.011 0 -9999 0 -10000 0 0
HCK -0.033 0.15 -9999 0 -0.58 35 35
ABL1 -0.017 0.12 -9999 0 -0.55 21 21
PDGFB-D/PDGFRB/CBL -0.019 0.14 -9999 0 -0.64 21 21
PTPN1 0.01 0.025 -9999 0 -0.59 1 1
SNX15 0.011 0 -9999 0 -10000 0 0
STAT3 0.011 0 -9999 0 -10000 0 0
STAT1 0.006 0.054 -9999 0 -0.49 7 7
cell proliferation 0.002 0.11 -9999 0 -0.51 18 18
SLA -0.015 0.12 -9999 0 -0.53 29 29
actin cytoskeleton reorganization 0.026 0.069 -9999 0 -0.5 3 3
SRC -0.013 0.071 -9999 0 -0.39 18 18
PI3K -0.014 0.06 -9999 0 -0.53 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.006 0.074 -9999 0 -0.37 14 14
SH2B2 -0.015 0.12 -9999 0 -0.52 30 30
PLCgamma1/SPHK1 -0.017 0.14 -9999 0 -0.51 30 30
LYN -0.011 0.068 -9999 0 -0.38 17 17
LRP1 0.006 0.057 -9999 0 -0.56 6 6
SOS1 0.01 0.024 -9999 0 -0.58 1 1
STAT5B 0.011 0 -9999 0 -10000 0 0
STAT5A 0.011 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.002 0.066 -9999 0 -0.55 2 2
SPHK1 -0.03 0.14 -9999 0 -0.52 48 48
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.007 0.12 -9999 0 -0.6 18 18
PLCG1 -0.008 0.12 -9999 0 -0.62 18 18
NHERF/PDGFRB 0.011 0.063 -9999 0 -0.33 19 19
YES1 -0.018 0.1 -9999 0 -0.5 21 21
cell migration 0.011 0.063 -9999 0 -0.33 19 19
SHC/Grb2/SOS1 0.001 0.057 -9999 0 -10000 0 0
SLC9A3R2 0.01 0.024 -9999 0 -0.58 1 1
SLC9A3R1 0.011 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.016 0.067 -9999 0 -0.32 20 20
FYN -0.016 0.089 -9999 0 -0.44 21 21
DOK1 0.014 0.063 -9999 0 -0.32 17 17
HRAS/GTP 0.006 0.029 -9999 0 -0.35 4 4
PDGFB 0.007 0.047 -9999 0 -0.51 5 5
RAC1 -0.01 0.14 -9999 0 -0.6 23 23
PRKCD 0.014 0.064 -9999 0 -0.33 17 17
FER 0.009 0.079 -9999 0 -0.36 21 21
MAPKKK cascade -0.009 0.051 -9999 0 -10000 0 0
RASA1 0.013 0.069 -9999 0 -0.35 18 18
NCK1 0.009 0.034 -9999 0 -0.58 2 2
NCK2 0.01 0.024 -9999 0 -0.58 1 1
p62DOK/Csk 0.02 0.059 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.003 0.073 -9999 0 -0.39 20 20
chemotaxis -0.016 0.12 -9999 0 -0.53 21 21
STAT1-3-5/STAT1-3-5 -0.011 0.055 -9999 0 -0.56 1 1
Bovine Papilomavirus E5/PDGFRB -0.005 0.072 -9999 0 -0.4 19 19
PTPRJ 0.01 0.024 -9999 0 -0.58 1 1
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.003 0.084 -9999 0 -0.48 18 18
PLK4 0.009 0.034 -9999 0 -0.58 2 2
regulation of centriole replication 0.007 0.068 -9999 0 -0.36 19 19
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.014 0.022 -9999 0 -0.36 2 2
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.011 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.001 0.08 -9999 0 -0.58 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.008 0.042 -9999 0 -0.58 3 3
RAC1-CDC42/GTP/PAK family 0.016 0.034 -9999 0 -0.29 5 5
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.005 0.064 -9999 0 -0.58 7 7
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.009 0.034 -9999 0 -0.58 2 2
FYN 0.005 0.06 -9999 0 -0.55 7 7
MAP3K12 0.003 0.067 -9999 0 -0.54 9 9
FGR -0.026 0.14 -9999 0 -0.54 41 41
p38 alpha/TAB1 -0.037 0.084 -9999 0 -0.35 26 26
PRKG1 -0.025 0.14 -9999 0 -0.56 38 38
DUSP8 0.007 0.048 -9999 0 -0.58 4 4
PGK/cGMP/p38 alpha -0.049 0.11 -9999 0 -0.36 47 47
apoptosis -0.035 0.08 -9999 0 -0.34 25 25
RAL/GTP 0.016 0 -9999 0 -10000 0 0
LYN 0.011 0 -9999 0 -10000 0 0
DUSP1 -0.006 0.091 -9999 0 -0.47 22 22
PAK1 0.011 0 -9999 0 -10000 0 0
SRC 0.01 0.024 -9999 0 -0.58 1 1
RAC1/OSM/MEKK3/MKK3 0.027 0.034 -9999 0 -0.38 4 4
TRAF6 0.01 0.024 -9999 0 -0.58 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.01 0.031 -9999 0 -0.52 2 2
RAC1-CDC42/GTP 0.012 0.034 -9999 0 -0.36 5 5
MAPK11 -0.023 0.14 -9999 0 -0.44 36 36
BLK -0.11 0.23 -9999 0 -0.53 138 138
HCK -0.017 0.12 -9999 0 -0.54 31 31
MAP2K3 0.01 0.024 -9999 0 -0.58 1 1
DUSP16 0.011 0 -9999 0 -10000 0 0
DUSP10 0.009 0.039 -9999 0 -0.54 3 3
TRAF6/MEKK3 0.013 0.024 -9999 0 -0.33 3 3
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.007 0.11 -9999 0 -0.38 25 25
positive regulation of innate immune response -0.019 0.15 -9999 0 -0.48 33 33
LCK -0.031 0.14 -9999 0 -0.51 49 49
p38alpha-beta/MKP7 -0.012 0.14 -9999 0 -0.51 23 23
p38alpha-beta/MKP5 -0.014 0.14 -9999 0 -0.52 24 24
PGK/cGMP -0.018 0.1 -9999 0 -0.41 38 38
PAK2 0.01 0.024 -9999 0 -0.58 1 1
p38alpha-beta/MKP1 -0.02 0.15 -9999 0 -0.49 28 28
CDC42 0.007 0.054 -9999 0 -0.58 5 5
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
PAK3 0 0.056 -9999 0 -0.46 9 9
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.006 0.097 -9999 0 -0.54 19 19
mol:S1P 0 0.005 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.009 0.09 -9999 0 -0.27 50 50
GNAO1 -0.045 0.16 -9999 0 -0.5 68 68
S1P/S1P3/G12/G13 0.018 0.044 -9999 0 -0.32 9 9
AKT1 -0.003 0.11 -9999 0 -0.62 14 14
AKT3 -0.015 0.21 -9999 0 -0.95 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.097 -9999 0 -0.54 19 19
GNAI2 0.012 0.004 -9999 0 -10000 0 0
GNAI3 0.012 0.004 -9999 0 -10000 0 0
GNAI1 -0.002 0.089 -9999 0 -0.56 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.005 0.065 -9999 0 -0.55 8 8
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.12 -9999 0 -0.36 32 32
MAPK3 -0.004 0.11 -9999 0 -0.49 15 15
MAPK1 -0.004 0.11 -9999 0 -0.49 15 15
JAK2 -0.012 0.13 -9999 0 -0.46 28 28
CXCR4 -0.017 0.14 -9999 0 -0.49 28 28
FLT1 0.008 0.053 -9999 0 -0.57 5 5
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC -0.004 0.11 -9999 0 -0.48 15 15
S1P/S1P3/Gi -0.01 0.12 -9999 0 -0.37 32 32
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.11 -9999 0 -0.46 15 15
VEGFA 0.012 0.02 -9999 0 -0.46 1 1
S1P/S1P2/Gi -0.006 0.092 -9999 0 -0.32 21 21
VEGFR1 homodimer/VEGFA homodimer 0.018 0.043 -9999 0 -0.4 6 6
RHOA 0.01 0.024 -9999 0 -0.58 1 1
S1P/S1P3/Gq 0 0.098 -9999 0 -0.33 38 38
GNAQ 0.006 0.059 -9999 0 -0.58 6 6
GNAZ -0.012 0.11 -9999 0 -0.55 26 26
G12/G13 0.016 0.025 -9999 0 -0.42 2 2
GNA14 -0.007 0.1 -9999 0 -0.56 19 19
GNA15 -0.009 0.1 -9999 0 -0.54 22 22
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
GNA11 0.007 0.05 -9999 0 -0.53 5 5
Rac1/GTP -0.004 0.11 -9999 0 -0.48 14 14
Regulation of Androgen receptor activity

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
HDAC1 0.016 0.018 -9999 0 -0.42 1 1
SMARCC1 0.002 0.018 -9999 0 -10000 0 0
REL 0.011 0.043 -9999 0 -0.58 3 3
HDAC7 0.028 0.093 -9999 0 -0.52 8 8
JUN 0.004 0.052 -9999 0 -0.56 5 5
EP300 0.007 0.048 -9999 0 -0.58 4 4
KAT2B -0.006 0.098 -9999 0 -0.58 17 17
KAT5 0.011 0.024 -9999 0 -0.58 1 1
MAPK14 0.011 0.062 -9999 0 -0.44 11 11
FOXO1 0.009 0.034 -9999 0 -0.59 2 2
T-DHT/AR 0.024 0.098 -9999 0 -0.53 9 9
MAP2K6 0.001 0.081 -9999 0 -0.6 11 11
BRM/BAF57 0.009 0.041 -9999 0 -0.43 5 5
MAP2K4 0.009 0.042 -9999 0 -0.58 3 3
SMARCA2 0.005 0.049 -9999 0 -0.59 4 4
PDE9A -0.082 0.28 -9999 0 -1.1 44 44
NCOA2 0.004 0.066 -9999 0 -0.57 8 8
CEBPA -0.005 0.097 -9999 0 -0.58 17 17
EHMT2 0.007 0.031 -9999 0 -0.52 2 2
cell proliferation 0.021 0.13 -9999 0 -0.48 18 18
NR0B1 -0.001 0.05 -9999 0 -0.46 7 7
EGR1 -0.012 0.1 -9999 0 -0.5 25 25
RXRs/9cRA 0.004 0.055 -9999 0 -0.33 2 2
AR/RACK1/Src 0.016 0.076 -9999 0 -0.41 9 9
AR/GR -0.01 0.1 -9999 0 -0.35 33 33
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
PKN1 0.008 0.042 -9999 0 -0.58 3 3
RCHY1 0.01 0.024 -9999 0 -0.58 1 1
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.016 0.037 -9999 0 -0.42 4 4
T-DHT/AR/TIF2/CARM1 0.02 0.086 -9999 0 -0.43 11 11
SRC 0.023 0.062 -9999 0 -0.34 15 15
NR3C1 -0.014 0.12 -9999 0 -0.54 28 28
KLK3 -0.2 0.38 -9999 0 -1 82 82
APPBP2 0.008 0.048 -9999 0 -0.58 4 4
TRIM24 0.009 0.005 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.018 0.078 -9999 0 -0.4 14 14
TMPRSS2 -0.026 0.14 -9999 0 -0.88 9 9
RXRG -0.013 0.095 -9999 0 -0.46 26 26
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0.01 0.024 -9999 0 -0.58 1 1
RXRB 0.011 0.001 -9999 0 -10000 0 0
CARM1 0.011 0.024 -9999 0 -0.59 1 1
NR2C2 0.01 0.024 -9999 0 -0.58 1 1
KLK2 0.015 0.11 -9999 0 -0.44 13 13
AR 0 0.084 -9999 0 -0.29 31 31
SENP1 0.01 0.024 -9999 0 -0.58 1 1
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
MDM2 0.012 0.045 -9999 0 -0.52 4 4
SRY 0.002 0.038 -9999 0 -0.45 4 4
GATA2 -0.021 0.13 -9999 0 -0.56 34 34
MYST2 0.011 0.024 -9999 0 -0.58 1 1
HOXB13 -0.097 0.21 -9999 0 -0.5 125 125
T-DHT/AR/RACK1/Src 0.022 0.074 -9999 0 -0.43 8 8
positive regulation of transcription -0.021 0.13 -9999 0 -0.56 34 34
DNAJA1 0.012 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.041 -9999 0 -0.48 3 3
NCOA1 0.011 0.026 -9999 0 -0.61 1 1
SPDEF -0.15 0.25 -9999 0 -0.54 181 181
T-DHT/AR/TIF2 0.014 0.11 -9999 0 -0.63 8 8
T-DHT/AR/Hsp90 0.017 0.075 -9999 0 -0.41 12 12
GSK3B 0.009 0.034 -9999 0 -0.59 2 2
NR2C1 0.011 0.024 -9999 0 -0.58 1 1
mol:T-DHT 0.02 0.064 -9999 0 -0.37 14 14
SIRT1 0.006 0.054 -9999 0 -0.58 5 5
ZMIZ2 0.015 0.027 -9999 0 -0.59 1 1
POU2F1 0.011 0.076 -9999 0 -0.55 10 10
T-DHT/AR/DAX-1 0.009 0.076 -9999 0 -0.39 14 14
CREBBP 0.011 0.001 -9999 0 -10000 0 0
SMARCE1 0.008 0.025 -9999 0 -0.58 1 1
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.005 0.087 0.46 7 -10000 0 7
GNAI2 0.011 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.009 0.048 -10000 0 -0.32 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.045 0.16 -10000 0 -0.49 68 68
RhoA/GTP -0.005 0.089 -10000 0 -0.47 7 7
negative regulation of cAMP metabolic process -0.011 0.096 -10000 0 -0.31 29 29
GNAZ -0.013 0.11 -10000 0 -0.55 26 26
GNAI3 0.011 0 -10000 0 -10000 0 0
GNA12 0.011 0 -10000 0 -10000 0 0
S1PR5 0.001 0.076 -10000 0 -0.53 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.011 0.096 -10000 0 -0.31 29 29
RhoA/GDP 0.008 0.018 -10000 0 -0.43 1 1
RHOA 0.01 0.024 -10000 0 -0.58 1 1
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0 0.083 0.58 12 -10000 0 12
PI3K Class IB/PDE3B 0 0.083 -10000 0 -0.58 12 12
PDE3B 0 0.083 -10000 0 -0.58 12 12
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC2 0.011 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0 0.093 -9999 0 -0.38 30 30
forebrain development -0.003 0.15 -9999 0 -0.51 36 36
GNAO1 -0.045 0.16 -9999 0 -0.49 68 68
SMO/beta Arrestin2 -0.002 0.094 -9999 0 -0.4 31 31
SMO -0.017 0.13 -9999 0 -0.56 31 31
ARRB2 0.012 0.002 -9999 0 -10000 0 0
GLI3/SPOP 0.014 0.099 -9999 0 -0.67 5 5
mol:GTP 0 0.001 -9999 0 -10000 0 0
GSK3B 0.009 0.034 -9999 0 -0.58 2 2
GNAI2 0.012 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.026 0.03 -9999 0 -0.32 4 4
GNAI1 -0.002 0.089 -9999 0 -0.56 15 15
XPO1 0.003 0.08 -9999 0 -0.58 11 11
GLI1/Su(fu) -0.039 0.13 -9999 0 -0.57 21 21
SAP30 0.009 0.034 -9999 0 -0.58 2 2
mol:GDP -0.017 0.13 -9999 0 -0.56 31 31
MIM/GLI2A 0.002 0.092 -9999 0 -0.55 16 16
IFT88 0.007 0.048 -9999 0 -0.58 4 4
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GLI2 0.022 0.06 -9999 0 -0.57 2 2
GLI3 0.008 0.1 -9999 0 -0.32 37 37
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
SAP18 0.011 0.019 -9999 0 -0.46 1 1
embryonic digit morphogenesis 0.007 0.048 -9999 0 -0.58 4 4
GNG2 0.003 0.067 -9999 0 -0.54 9 9
Gi family/GTP -0.017 0.12 -9999 0 -0.34 44 44
SIN3B 0.01 0.024 -9999 0 -0.58 1 1
SIN3A 0.01 0.024 -9999 0 -0.58 1 1
GLI3/Su(fu) 0.024 0.082 -9999 0 -0.55 5 5
GLI2/Su(fu) 0.029 0.07 -9999 0 -0.35 9 9
FOXA2 -0.036 0.18 -9999 0 -0.94 22 22
neural tube patterning -0.003 0.15 -9999 0 -0.51 36 36
SPOP 0.011 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.044 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CSNK1G2 0.009 0.034 -9999 0 -0.58 2 2
CSNK1G3 0.01 0.024 -9999 0 -0.58 1 1
MTSS1 0.002 0.092 -9999 0 -0.55 16 16
embryonic limb morphogenesis -0.003 0.15 -9999 0 -0.51 36 36
SUFU 0.014 0.049 -9999 0 -10000 0 0
LGALS3 0.008 0.043 -9999 0 -0.52 4 4
catabolic process 0.026 0.11 -9999 0 -0.41 20 20
GLI3A/CBP 0.006 0.067 -9999 0 -0.35 19 19
KIF3A 0.001 0.08 -9999 0 -0.58 11 11
GLI1 -0.004 0.16 -9999 0 -0.53 36 36
RAB23 0.006 0.055 -9999 0 -0.54 6 6
CSNK1A1 0.009 0.034 -9999 0 -0.58 2 2
IFT172 0.011 0 -9999 0 -10000 0 0
RBBP7 0.009 0.034 -9999 0 -0.58 2 2
Su(fu)/Galectin3 0.016 0.052 -9999 0 -0.35 3 3
GNAZ -0.012 0.12 -9999 0 -0.55 26 26
RBBP4 0.01 0.024 -9999 0 -0.58 1 1
CSNK1G1 0.01 0.024 -9999 0 -0.58 1 1
PIAS1 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GLI2/SPOP 0.027 0.057 -9999 0 -0.54 2 2
STK36 0.014 0.003 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.009 0.11 -9999 0 -0.46 15 15
PTCH1 -0.003 0.17 -9999 0 -0.83 16 16
MIM/GLI1 -0.002 0.17 -9999 0 -0.59 31 31
CREBBP 0.006 0.067 -9999 0 -0.35 19 19
Su(fu)/SIN3/HDAC complex 0.035 0.028 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.011 0 -10000 0 -10000 0 0
NFATC1 0.031 0.06 -10000 0 -0.32 3 3
NFATC2 0.016 0.056 -10000 0 -0.24 12 12
NFATC3 0.018 0.02 -10000 0 -0.41 1 1
YWHAE 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.061 0.14 -10000 0 -0.47 42 42
Exportin 1/Ran/NUP214 0.016 0.051 -10000 0 -0.36 11 11
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.074 0.14 -10000 0 -0.48 45 45
BCL2/BAX 0.003 0.076 -10000 0 -0.39 21 21
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.009 0.004 -10000 0 -10000 0 0
BAX 0.01 0.024 -10000 0 -0.58 1 1
MAPK14 0.011 0.003 -10000 0 -10000 0 0
BAD 0.01 0.031 -10000 0 -0.52 2 2
CABIN1/MEF2D -0.053 0.14 -10000 0 -0.45 43 43
Calcineurin A alpha-beta B1/BCL2 -0.007 0.1 -10000 0 -0.55 20 20
FKBP8 0.009 0.034 -10000 0 -0.58 2 2
activation-induced cell death of T cells 0.052 0.14 0.44 43 -10000 0 43
KPNB1 0.011 0 -10000 0 -10000 0 0
KPNA2 0.011 0 -10000 0 -10000 0 0
XPO1 0.001 0.08 -10000 0 -0.58 11 11
SFN 0.005 0.055 -10000 0 -0.47 8 8
MAP3K8 0.009 0.031 -10000 0 -0.52 2 2
NFAT4/CK1 alpha 0.023 0.046 -10000 0 -0.39 6 6
MEF2D/NFAT1/Cbp/p300 0.027 0.093 -10000 0 -0.42 12 12
CABIN1 -0.062 0.15 -10000 0 -0.48 42 42
CALM1 0.011 0.002 -10000 0 -10000 0 0
RAN 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.006 0.059 -10000 0 -0.58 6 6
CAMK4 -0.014 0.12 -10000 0 -0.55 27 27
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.01 0.024 -10000 0 -0.58 1 1
YWHAH 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.006 0.092 -10000 0 -0.38 35 35
YWHAB 0.011 0 -10000 0 -10000 0 0
MAPK8 0.01 0.024 -10000 0 -0.58 1 1
MAPK9 0.011 0 -10000 0 -10000 0 0
YWHAG 0.011 0 -10000 0 -10000 0 0
FKBP1A 0.011 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.042 0.059 -10000 0 -0.36 3 3
PRKCH 0.006 0.059 -10000 0 -0.58 6 6
CABIN1/Cbp/p300 0.014 0.036 -10000 0 -0.42 4 4
CASP3 0.009 0.034 -10000 0 -0.58 2 2
PIM1 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.002 -10000 0 -10000 0 0
apoptosis -0.005 0.037 0.23 1 -0.66 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.03 -10000 0 -0.38 2 2
PRKCB -0.044 0.17 -10000 0 -0.55 60 60
PRKCE 0.011 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.023 0.018 -10000 0 -0.37 1 1
BAD/BCL-XL 0.016 0.022 -10000 0 -0.37 2 2
PRKCD 0.011 0 -10000 0 -10000 0 0
NUP214 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.031 -10000 0 -0.52 2 2
PRKCA 0.01 0.031 -10000 0 -0.52 2 2
PRKCG -0.16 0.25 -10000 0 -0.52 190 190
PRKCQ -0.049 0.18 -10000 0 -0.58 62 62
FKBP38/BCL2 0.002 0.078 -10000 0 -0.4 22 22
EP300 0.008 0.048 -10000 0 -0.58 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
NFATc/JNK1 0.035 0.06 -10000 0 -0.32 3 3
CaM/Ca2+/FKBP38 0.015 0.022 -10000 0 -0.36 2 2
FKBP12/FK506 0.009 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.022 -10000 0 -0.36 2 2
CaM/Ca2+/CAMK IV 0 0.074 -10000 0 -0.34 27 27
NFATc/ERK1 0.036 0.059 -10000 0 -0.31 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.073 0.14 -10000 0 -0.48 44 44
NR4A1 0.018 0.12 -10000 0 -0.42 39 39
GSK3B 0.009 0.034 -10000 0 -0.58 2 2
positive T cell selection 0.018 0.02 -10000 0 -0.41 1 1
NFAT1/CK1 alpha -0.011 0.044 -10000 0 -0.42 4 4
RCH1/ KPNB1 0.017 0 -10000 0 -10000 0 0
YWHAQ 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0.003 -10000 0 -10000 0 0
AKAP5 -0.02 0.13 -10000 0 -0.53 35 35
MEF2D 0.01 0.025 -10000 0 -0.6 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.008 0.042 -10000 0 -0.58 3 3
NFATc/p38 alpha 0.035 0.058 -10000 0 -0.31 2 2
CREBBP 0.011 0.002 -10000 0 -10000 0 0
BCL2 -0.007 0.1 -10000 0 -0.55 20 20
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.022 0.022 -9999 0 -0.36 2 2
SNTA1 0.006 0.055 -9999 0 -0.54 6 6
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.013 0.066 -9999 0 -0.38 16 16
MAPK12 -0.004 0.096 -9999 0 -0.38 24 24
CCND1 0.005 0.046 -9999 0 -0.25 8 8
p38 gamma/SNTA1 0 0.096 -9999 0 -0.38 23 23
MAP2K3 0.01 0.024 -9999 0 -0.58 1 1
PKN1 0.008 0.042 -9999 0 -0.58 3 3
G2/M transition checkpoint -0.004 0.095 -9999 0 -0.37 24 24
MAP2K6 0.009 0.061 -9999 0 -0.33 19 19
MAPT -0.024 0.11 -9999 0 -0.35 43 43
MAPK13 0.017 0.025 -9999 0 -0.42 2 2
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.009 0.042 -9999 0 -0.35 8 8
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.015 0.1 -10000 0 -0.52 12 12
UGCG 0.01 0.068 -10000 0 -0.84 3 3
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.13 -10000 0 -0.42 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.01 0.067 -10000 0 -0.82 3 3
mol:DAG -0.001 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.038 0.11 -10000 0 -0.46 27 27
FRAP1 0.018 0.15 -10000 0 -0.53 27 27
FOXO3 0.024 0.13 -10000 0 -0.48 21 21
AKT1 0.018 0.14 -10000 0 -0.49 26 26
GAB2 0.01 0.034 -10000 0 -0.58 2 2
SMPD1 0.013 0.038 -10000 0 -0.6 1 1
SGMS1 0.014 0.028 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.035 -10000 0 -0.36 5 5
CALM1 0.011 0 -10000 0 -10000 0 0
cell proliferation 0.019 0.08 -10000 0 -0.64 3 3
EIF3A 0.01 0.024 -10000 0 -0.58 1 1
PI3K 0.018 0.041 -10000 0 -0.43 5 5
RPS6KB1 0.008 0.095 -10000 0 -0.96 5 5
mol:sphingomyelin -0.001 0.009 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -0.012 4 4
JAK3 0.003 0.076 -10000 0 -0.53 12 12
PIK3R1 0.011 0.042 -10000 0 -0.59 3 3
JAK1 0.011 0.042 -10000 0 -0.58 3 3
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MYC 0.022 0.15 -10000 0 -0.69 12 12
MYB 0.007 0.16 -10000 0 -1.2 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.012 0.14 -10000 0 -0.47 26 26
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.091 -10000 0 -0.87 5 5
mol:PI-3-4-5-P3 0.012 0.13 -10000 0 -0.46 26 26
Rac1/GDP 0.021 0.032 -10000 0 -0.32 5 5
T cell proliferation 0.017 0.13 -10000 0 -0.49 18 18
SHC1 0.012 0.002 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.008 -10000 0 -0.065 9 9
PRKCZ 0.017 0.13 -10000 0 -0.51 18 18
NF kappa B1 p50/RelA -0.037 0.11 -10000 0 -0.49 22 22
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.008 0.11 -10000 0 -0.5 18 18
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
RELA 0.011 0 -10000 0 -10000 0 0
IL2RA -0.047 0.17 -10000 0 -0.55 63 63
IL2RB -0.016 0.13 -10000 0 -0.55 32 32
TERT -0.047 0.17 -10000 0 -0.52 67 67
E2F1 0.015 0.065 -10000 0 -0.44 11 11
SOS1 0.011 0.024 -10000 0 -0.58 1 1
RPS6 0.007 0.045 -10000 0 -0.48 5 5
mol:cAMP -0.002 0.004 0.031 9 -10000 0 9
PTPN11 0.007 0.054 -10000 0 -0.58 5 5
IL2RG 0.001 0.084 -10000 0 -0.56 13 13
actin cytoskeleton organization 0.017 0.13 -10000 0 -0.49 18 18
GRB2 0.012 0.002 -10000 0 -10000 0 0
IL2 0.004 0.027 -10000 0 -0.45 2 2
PIK3CA 0.012 0.034 -10000 0 -0.58 2 2
Rac1/GTP 0.027 0.031 -10000 0 -0.31 5 5
LCK -0.028 0.14 -10000 0 -0.51 49 49
BCL2 0.015 0.18 -10000 0 -0.84 17 17
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.008 0.042 -9999 0 -0.58 3 3
Caspase 8 (4 units) 0.006 0.087 -9999 0 -0.52 5 5
NEF -0.013 0.05 -9999 0 -10000 0 0
NFKBIA 0.009 0.023 -9999 0 -10000 0 0
BIRC3 0.007 0.12 -9999 0 -0.52 31 31
CYCS 0 0.11 -9999 0 -0.54 8 8
RIPK1 0.011 0 -9999 0 -10000 0 0
CD247 -0.031 0.15 -9999 0 -0.65 30 30
MAP2K7 0.013 0.083 -9999 0 -0.46 6 6
protein ubiquitination 0.039 0.057 -9999 0 -0.4 3 3
CRADD 0.01 0.024 -9999 0 -0.58 1 1
DAXX 0.011 0 -9999 0 -10000 0 0
FAS -0.001 0.084 -9999 0 -0.56 13 13
BID 0.001 0.097 -9999 0 -0.53 5 5
NF-kappa-B/RelA/I kappa B alpha 0.017 0.066 -9999 0 -0.34 1 1
TRADD 0.011 0 -9999 0 -10000 0 0
MAP3K5 0.009 0.034 -9999 0 -0.58 2 2
CFLAR 0.011 0 -9999 0 -10000 0 0
FADD 0.011 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.017 0.066 -9999 0 -0.34 1 1
MAPK8 0.018 0.082 -9999 0 -0.51 5 5
APAF1 0.008 0.042 -9999 0 -0.58 3 3
TRAF1 0.008 0.038 -9999 0 -0.46 4 4
TRAF2 0.01 0.024 -9999 0 -0.58 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.005 0.1 -9999 0 -0.3 50 50
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.033 0.057 -9999 0 -0.32 1 1
CHUK 0.039 0.061 -9999 0 -0.44 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.026 0.054 -9999 0 -0.32 13 13
TCRz/NEF -0.037 0.15 -9999 0 -0.39 80 80
TNF -0.017 0.12 -9999 0 -0.54 31 31
FASLG -0.06 0.23 -9999 0 -0.62 78 78
NFKB1 0.008 0.033 -9999 0 -0.58 1 1
TNFR1A/BAG4/TNF-alpha 0.004 0.082 -9999 0 -0.33 34 34
CASP6 -0.018 0.058 -9999 0 -0.51 4 4
CASP7 0.022 0.13 -9999 0 -0.56 19 19
RELA 0.009 0.023 -9999 0 -10000 0 0
CASP2 0.011 0 -9999 0 -10000 0 0
CASP3 0.021 0.13 -9999 0 -0.56 20 20
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.015 0.031 -9999 0 -0.42 3 3
CASP8 0.01 0.024 -9999 0 -0.58 1 1
CASP9 0.01 0.024 -9999 0 -0.58 1 1
MAP3K14 0.037 0.057 -9999 0 -0.42 1 1
APAF-1/Caspase 9 -0.038 0.1 -9999 0 -0.46 24 24
BCL2 0.015 0.094 -9999 0 -0.46 9 9
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.023 0.048 -10000 0 -0.36 7 7
HDAC3 0.011 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.013 0.075 -10000 0 -0.4 19 19
GATA1/HDAC4 0.005 0.053 -10000 0 -0.32 16 16
GATA1/HDAC5 0.005 0.055 -10000 0 -0.32 16 16
GATA2/HDAC5 -0.007 0.1 -10000 0 -0.41 34 34
HDAC5/BCL6/BCoR 0.021 0.028 -10000 0 -0.28 5 5
HDAC9 -0.038 0.16 -10000 0 -0.55 54 54
Glucocorticoid receptor/Hsp90/HDAC6 0.007 0.075 -10000 0 -0.32 29 29
HDAC4/ANKRA2 0.016 0.022 -10000 0 -0.37 2 2
HDAC5/YWHAB 0.016 0.018 -10000 0 -0.42 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0.095 -10000 0 -0.43 24 24
GATA2 -0.021 0.13 -10000 0 -0.56 34 34
HDAC4/RFXANK 0.014 0.032 -10000 0 -0.37 4 4
BCOR 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.008 0.046 -10000 0 -0.55 4 4
HDAC5 0.01 0.024 -10000 0 -0.58 1 1
GNB1/GNG2 0.011 0.049 -10000 0 -0.39 9 9
Histones 0.011 0.081 -10000 0 -0.73 2 2
ADRBK1 0.01 0.031 -10000 0 -0.52 2 2
HDAC4 0.011 0.019 -10000 0 -0.46 1 1
XPO1 0.001 0.08 -10000 0 -0.58 11 11
HDAC5/ANKRA2 0.016 0.025 -10000 0 -0.42 2 2
HDAC4/Ubc9 0.016 0.014 -10000 0 -0.32 1 1
HDAC7 0.01 0.024 -10000 0 -0.58 1 1
HDAC5/14-3-3 E 0.016 0.018 -10000 0 -0.42 1 1
TUBA1B 0.011 0 -10000 0 -10000 0 0
HDAC6 0.011 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.014 0.039 -10000 0 -0.51 3 3
CAMK4 -0.014 0.12 -10000 0 -0.55 27 27
Tubulin/HDAC6 0.004 0.076 -10000 0 -0.29 37 37
SUMO1 -0.007 0.1 -10000 0 -0.58 19 19
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.011 0 -10000 0 -10000 0 0
GATA1 -0.004 0.072 -10000 0 -0.46 15 15
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.011 0 -10000 0 -10000 0 0
NR3C1 -0.014 0.12 -10000 0 -0.54 28 28
SUMO1/HDAC4 0.005 0.1 -10000 0 -0.55 19 19
SRF 0.01 0.027 -10000 0 -0.46 2 2
HDAC4/YWHAB 0.016 0.014 -10000 0 -0.32 1 1
Tubulin -0.006 0.089 -10000 0 -0.35 37 37
HDAC4/14-3-3 E 0.016 0.014 -10000 0 -0.32 1 1
GNB1 0.011 0 -10000 0 -10000 0 0
RANGAP1 0.01 0.031 -10000 0 -0.52 2 2
BCL6/BCoR 0.015 0.027 -10000 0 -0.32 4 4
HDAC4/HDAC3/SMRT (N-CoR2) 0.021 0.031 -10000 0 -0.32 5 5
HDAC4/SRF 0.006 0.078 -10000 0 -0.37 20 20
HDAC4/ER alpha -0.018 0.11 -10000 0 -0.38 53 53
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.011 0.08 -10000 0 -0.72 2 2
cell motility 0.004 0.076 -10000 0 -0.29 37 37
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.011 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.016 0.018 -10000 0 -0.42 1 1
BCL6 0.008 0.038 -10000 0 -0.46 4 4
HDAC4/CaMK II delta B 0.011 0.019 -10000 0 -0.46 1 1
Hsp90/HDAC6 0.016 0.018 -10000 0 -0.42 1 1
ESR1 -0.035 0.15 -10000 0 -0.53 52 52
HDAC6/HDAC11 0.016 0.025 -10000 0 -0.42 2 2
Ran/GTP/Exportin 1 0.007 0.12 -10000 0 -0.69 15 15
NPC -0.003 0.056 -10000 0 -0.31 19 19
MEF2C 0 0.08 -10000 0 -0.54 13 13
RAN 0.011 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.025 0.051 -10000 0 -10000 0 0
GNG2 0.003 0.067 -10000 0 -0.54 9 9
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
TUBB2A -0.02 0.12 -10000 0 -0.5 37 37
HDAC11 0.009 0.034 -10000 0 -0.58 2 2
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
RANBP2 -0.007 0.1 -10000 0 -0.58 19 19
ANKRA2 0.01 0.024 -10000 0 -0.58 1 1
RFXANK 0.009 0.039 -10000 0 -0.54 3 3
nuclear import -0.024 0.016 0.32 1 -10000 0 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.015 0.035 -10000 0 -0.55 2 2
CRKL 0.013 0.062 -10000 0 -0.26 2 2
mol:PIP3 -0.011 0.054 0.52 6 -10000 0 6
AKT1 0.004 0.038 0.36 6 -0.31 1 7
PTK2B 0.009 0.034 -10000 0 -0.58 2 2
RAPGEF1 0.018 0.061 -10000 0 -0.37 1 1
RANBP10 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
HGF/MET/SHIP2 -0.01 0.1 -10000 0 -0.33 58 58
MAP3K5 0.003 0.1 -10000 0 -0.41 16 16
HGF/MET/CIN85/CBL/ENDOPHILINS -0.001 0.095 -10000 0 -0.32 40 40
AP1 -0.011 0.095 -10000 0 -0.34 45 45
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.023 0.16 -10000 0 -0.74 29 29
STAT3 (dimer) 0.011 0.076 -10000 0 -0.41 1 1
GAB1/CRKL/SHP2/PI3K -0.017 0.066 -10000 0 -0.69 3 3
INPP5D -0.018 0.13 -10000 0 -0.58 30 30
CBL/CRK 0.019 0.062 -10000 0 -0.45 1 1
PTPN11 0.007 0.054 -10000 0 -0.58 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
PTEN 0.006 0.059 -10000 0 -0.58 6 6
ELK1 -0.001 0.025 0.23 2 -0.32 2 4
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.014 0.046 -10000 0 -0.36 3 3
PAK1 0.009 0.035 0.34 6 -0.28 1 7
HGF/MET/RANBP10 -0.01 0.1 -10000 0 -0.33 57 57
HRAS 0.004 0.097 -10000 0 -1.1 1 1
DOCK1 0.018 0.063 -10000 0 -0.53 1 1
GAB1 0.008 0.065 -10000 0 -0.28 2 2
CRK 0.013 0.064 -10000 0 -0.37 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.13 -10000 0 -0.49 39 39
JUN 0.007 0.052 -10000 0 -0.56 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.005 0.058 -10000 0 -0.21 40 40
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
cell morphogenesis 0.028 0.092 -10000 0 -0.59 4 4
GRB2/SHC 0.009 0.052 -10000 0 -0.24 2 2
FOS -0.026 0.14 -10000 0 -0.54 41 41
GLMN -0.008 0.046 -10000 0 -0.27 18 18
cell motility -0.001 0.025 0.23 2 -0.32 2 4
HGF/MET/MUC20 -0.017 0.1 -10000 0 -0.33 57 57
cell migration 0.009 0.051 -10000 0 -0.24 2 2
GRB2 0.011 0 -10000 0 -10000 0 0
CBL 0.011 0 -10000 0 -10000 0 0
MET/RANBP10 0.016 0.022 -10000 0 -0.37 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.006 0.077 -10000 0 -10000 0 0
MET/MUC20 0.007 0.022 -10000 0 -0.38 2 2
RAP1B 0.023 0.059 -10000 0 -0.34 1 1
RAP1A 0.023 0.06 -10000 0 -0.34 1 1
HGF/MET/RANBP9 -0.01 0.11 -10000 0 -0.36 39 39
RAF1 0.01 0.091 -10000 0 -1 1 1
STAT3 0.01 0.077 -10000 0 -0.42 1 1
cell proliferation 0.014 0.098 -10000 0 -0.34 40 40
RPS6KB1 -0.001 0.043 -10000 0 -0.33 5 5
MAPK3 -0.004 0.03 0.67 1 -0.24 1 2
MAPK1 -0.004 0.03 0.67 1 -0.24 1 2
RANBP9 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 0.019 0.09 -10000 0 -0.36 15 15
SRC 0.011 0.075 -10000 0 -0.54 1 1
PI3K 0.007 0.063 -10000 0 -0.39 5 5
MET/Glomulin 0.003 0.042 -10000 0 -0.22 20 20
SOS1 0.01 0.024 -10000 0 -0.58 1 1
MAP2K1 0.014 0.09 -10000 0 -1.1 1 1
MET 0.01 0.031 -10000 0 -0.52 2 2
MAP4K1 -0.002 0.1 -10000 0 -0.43 15 15
PTK2 0.01 0.024 -10000 0 -0.58 1 1
MAP2K2 0.015 0.087 -10000 0 -0.7 2 2
BAD 0.008 0.042 0.34 6 -0.58 1 7
MAP2K4 0.008 0.096 -10000 0 -0.38 14 14
SHP2/GRB2/SOS1/GAB1 -0.017 0.057 -10000 0 -0.47 3 3
INPPL1 0.01 0.024 -10000 0 -0.58 1 1
PXN 0.011 0 -10000 0 -10000 0 0
SH3KBP1 0.01 0.024 -10000 0 -0.58 1 1
HGS 0.001 0.055 -10000 0 -0.25 3 3
PLCgamma1/PKC 0.008 0.018 -10000 0 -0.43 1 1
HGF -0.039 0.16 -10000 0 -0.55 55 55
RASA1 0.009 0.034 -10000 0 -0.58 2 2
NCK1 0.009 0.034 -10000 0 -0.58 2 2
PTPRJ 0.01 0.024 -10000 0 -0.58 1 1
NCK/PLCgamma1 0.008 0.063 -10000 0 -0.36 3 3
PDPK1 -0.003 0.042 0.41 6 -10000 0 6
HGF/MET/SHIP -0.028 0.13 -10000 0 -0.34 85 85
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.017 0.093 -9999 0 -0.5 19 19
MDM2/SUMO1 0.004 0.11 -9999 0 -0.58 19 19
HDAC4 0.011 0.019 -9999 0 -0.46 1 1
Ran/GTP/Exportin 1/HDAC1 -0.017 0.092 -9999 0 -0.5 19 19
SUMO1 -0.007 0.1 -9999 0 -0.58 19 19
NPC/RanGAP1/SUMO1 -0.004 0.095 -9999 0 -0.44 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0 0.12 -9999 0 -0.74 15 15
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 -0.007 0.1 -9999 0 -0.58 19 19
SUMO1/HDAC4 0.005 0.1 -9999 0 -0.55 19 19
SUMO1/HDAC1 0.006 0.1 -9999 0 -0.55 19 19
RANGAP1 0.01 0.031 -9999 0 -0.52 2 2
MDM2/SUMO1/SUMO1 0.016 0.072 -9999 0 -0.35 19 19
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0.095 -9999 0 -0.43 24 24
Ran/GTP 0.006 0.087 -9999 0 -0.39 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.008 0.043 -9999 0 -0.52 4 4
UBE2I 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.12 -9999 0 -0.69 15 15
NPC -0.003 0.056 -9999 0 -0.31 19 19
PIAS2 0.01 0.027 -9999 0 -0.46 2 2
PIAS1 0.011 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.029 0.084 -9999 0 -0.48 5 5
TC10/GTP -0.022 0.071 -9999 0 -0.48 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.014 0.063 -9999 0 -0.34 18 18
HRAS 0.008 0.041 -9999 0 -0.49 4 4
APS homodimer -0.015 0.12 -9999 0 -0.52 30 30
GRB14 -0.12 0.24 -9999 0 -0.54 144 144
FOXO3 0.002 0.057 -9999 0 -0.67 3 3
AKT1 -0.031 0.12 -9999 0 -0.42 3 3
INSR 0.011 0.034 -9999 0 -0.58 2 2
Insulin Receptor/Insulin 0.027 0.035 -9999 0 -0.6 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.007 0.048 -9999 0 -0.58 4 4
SORBS1 -0.013 0.11 -9999 0 -0.52 28 28
CRK 0.011 0.019 -9999 0 -0.46 1 1
PTPN1 0.024 0.035 -9999 0 -0.59 1 1
CAV1 0.007 0.068 -9999 0 -0.33 18 18
CBL/APS/CAP/Crk-II/C3G 0.006 0.088 -9999 0 -0.31 28 28
Insulin Receptor/Insulin/IRS1/NCK2 0.016 0.056 -9999 0 -0.34 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.051 -9999 0 -0.3 15 15
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.025 0.048 -9999 0 -0.46 3 3
RPS6KB1 -0.025 0.12 -9999 0 -0.47 4 4
PARD6A 0.006 0.051 -9999 0 -0.5 6 6
CBL 0.011 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.008 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.055 0.094 -9999 0 -0.46 4 4
HRAS/GTP -0.019 0.069 -9999 0 -0.47 3 3
Insulin Receptor 0.011 0.034 -9999 0 -0.58 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.022 0.051 -9999 0 -0.32 10 10
PRKCI -0.019 0.054 -9999 0 -0.59 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.064 0.11 -9999 0 -0.45 3 3
SHC1 0.011 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.02 0.027 -9999 0 -10000 0 0
PI3K -0.009 0.052 -9999 0 -0.3 15 15
NCK2 0.01 0.024 -9999 0 -0.58 1 1
RHOQ 0.011 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.006 0.029 -9999 0 -0.35 4 4
AKT2 -0.031 0.12 -9999 0 -0.41 5 5
PRKCZ -0.017 0.041 -9999 0 -0.78 1 1
SH2B2 -0.015 0.12 -9999 0 -0.52 30 30
SHC/SHIP 0.005 0.084 -9999 0 -0.3 39 39
F2RL2 -0.036 0.16 -9999 0 -0.56 50 50
TRIP10 0.01 0.024 -9999 0 -0.58 1 1
Insulin Receptor/Insulin/Shc 0.015 0.026 -9999 0 -0.31 3 3
TC10/GTP/CIP4/Exocyst 0.015 0.015 -9999 0 -0.36 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.027 0.028 -9999 0 -0.3 1 1
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
RASA1 0.009 0.034 -9999 0 -0.58 2 2
NCK1 0.009 0.034 -9999 0 -0.58 2 2
CBL/APS/CAP/Crk-II 0 0.093 -9999 0 -0.34 27 27
TC10/GDP 0.009 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.02 0.039 -9999 0 -0.32 7 7
INPP5D -0.002 0.088 -9999 0 -0.32 42 42
SOS1 0.01 0.024 -9999 0 -0.58 1 1
SGK1 -0.012 0.068 -9999 0 -0.93 3 3
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
IRS1 0.002 0.076 -9999 0 -0.58 10 10
p62DOK/RasGAP 0.02 0.028 -9999 0 -10000 0 0
INS 0 0.035 -9999 0 -0.5 3 3
mol:PI-3-4-P2 -0.002 0.088 -9999 0 -0.32 42 42
GRB2 0.011 0 -9999 0 -10000 0 0
EIF4EBP1 -0.024 0.12 -9999 0 -0.45 5 5
PTPRA 0.012 0.003 -9999 0 -10000 0 0
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
TC10/GTP/CIP4 0.015 0.015 -9999 0 -0.36 1 1
PDPK1 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.021 0.045 -9999 0 -0.26 14 14
Insulin Receptor/Insulin/IRS1 0.009 0.054 -9999 0 -0.35 13 13
Insulin Receptor/Insulin/IRS3 0.008 0.036 -9999 0 -0.38 5 5
Par3/Par6 -0.002 0.094 -9999 0 -0.31 44 44
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.017 0.087 -9999 0 -0.47 15 15
STMN1 0.009 0.07 -9999 0 -0.43 15 15
Aurora B/RasGAP/Survivin 0.025 0.031 -9999 0 -0.48 2 2
Chromosomal passenger complex/Cul3 protein complex -0.012 0.079 -9999 0 -0.22 34 34
BIRC5 0.012 0.019 -9999 0 -0.46 1 1
DES -0.11 0.2 -9999 0 -0.55 98 98
Aurora C/Aurora B/INCENP 0.013 0.063 -9999 0 -0.3 23 23
Aurora B/TACC1 0.012 0.047 -9999 0 -0.35 10 10
Aurora B/PP2A 0.019 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.013 0.012 -9999 0 -0.28 1 1
mitotic metaphase/anaphase transition 0 0.001 -9999 0 -10000 0 0
NDC80 0.01 0.068 -9999 0 -0.43 14 14
Cul3 protein complex -0.057 0.14 -9999 0 -0.3 152 152
KIF2C 0.02 0.02 -9999 0 -0.42 1 1
PEBP1 0.012 0 -9999 0 -10000 0 0
KIF20A 0.009 0.034 -9999 0 -0.59 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.018 0.026 -9999 0 -0.43 2 2
SEPT1 -0.008 0.1 -9999 0 -0.53 22 22
SMC2 0.003 0.072 -9999 0 -0.58 9 9
SMC4 -0.003 0.093 -9999 0 -0.58 15 15
NSUN2/NPM1/Nucleolin 0.024 0.03 -9999 0 -0.28 3 3
PSMA3 0.011 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.001 -9999 0 -10000 0 0
H3F3B 0.016 0.002 -9999 0 -10000 0 0
AURKB 0.015 0.006 -9999 0 -10000 0 0
AURKC -0.01 0.11 -9999 0 -0.55 23 23
CDCA8 0.012 0.001 -9999 0 -10000 0 0
cytokinesis 0.014 0.038 -9999 0 -10000 0 0
Aurora B/Septin1 0.006 0.057 -9999 0 -0.36 2 2
AURKA 0.011 0.001 -9999 0 -10000 0 0
INCENP 0.012 0.001 -9999 0 -10000 0 0
KLHL13 -0.12 0.22 -9999 0 -0.5 151 151
BUB1 0.01 0.024 -9999 0 -0.59 1 1
hSgo1/Aurora B/Survivin 0.022 0.035 -9999 0 -0.32 6 6
EVI5 0.005 0.064 -9999 0 -0.59 7 7
RhoA/GTP -0.001 0.018 -9999 0 -0.34 1 1
SGOL1 0.006 0.054 -9999 0 -0.58 5 5
CENPA 0.023 0.02 -9999 0 -0.25 3 3
NCAPG 0.008 0.042 -9999 0 -0.58 3 3
Aurora B/HC8 Proteasome 0.019 0.004 -9999 0 -10000 0 0
NCAPD2 0.011 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.019 0.019 -9999 0 -0.43 1 1
RHOA 0.01 0.024 -9999 0 -0.58 1 1
NCAPH 0.01 0.024 -9999 0 -0.58 1 1
NPM1 0.012 0.053 -9999 0 -0.48 7 7
RASA1 0.009 0.034 -9999 0 -0.58 2 2
KLHL9 0.01 0.024 -9999 0 -0.58 1 1
mitotic prometaphase 0.001 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.004 -9999 0 -10000 0 0
PPP1CC 0.01 0.024 -9999 0 -0.58 1 1
Centraspindlin 0.028 0.02 -9999 0 -10000 0 0
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
NSUN2 0.017 0.003 -9999 0 -10000 0 0
MYLK -0.005 0.073 -9999 0 -0.24 49 49
KIF23 0.012 0.001 -9999 0 -10000 0 0
VIM 0.014 0.051 -9999 0 -0.38 10 10
RACGAP1 0.012 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.017 0.003 -9999 0 -10000 0 0
Chromosomal passenger complex 0.029 0.016 -9999 0 -0.21 2 2
Chromosomal passenger complex/EVI5 0.022 0.051 -9999 0 -0.3 7 7
TACC1 0.002 0.073 -9999 0 -0.56 10 10
PPP2R5D 0.011 0 -9999 0 -10000 0 0
CUL3 0.009 0.034 -9999 0 -0.58 2 2
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
BARD1 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
BARD1/CSTF1 0.012 0.047 -10000 0 -0.42 7 7
ATM 0.003 0.072 -10000 0 -0.58 9 9
UBE2D3 0.011 0 -10000 0 -10000 0 0
PRKDC 0.009 0.039 -10000 0 -0.54 3 3
ATR 0.009 0.034 -10000 0 -0.58 2 2
UBE2L3 0.011 0 -10000 0 -10000 0 0
FANCD2 0.014 0.064 -10000 0 -0.44 10 10
protein ubiquitination 0.02 0.062 -10000 0 -0.33 16 16
XRCC5 0.01 0.024 -10000 0 -0.58 1 1
XRCC6 0.011 0 -10000 0 -10000 0 0
M/R/N Complex 0.008 0.09 -10000 0 -0.46 19 19
MRE11A 0.004 0.068 -10000 0 -0.58 8 8
DNA-PK 0.021 0.035 -10000 0 -0.43 3 3
FA complex/FANCD2/Ubiquitin 0.035 0.058 -10000 0 -0.62 3 3
FANCF 0.006 0.059 -10000 0 -0.58 6 6
BRCA1 0.01 0.024 -10000 0 -0.58 1 1
CCNE1 0.009 0.033 -10000 0 -0.46 3 3
CDK2/Cyclin E1 0.015 0.03 -10000 0 -0.34 4 4
FANCG 0.011 0.019 -10000 0 -0.46 1 1
BRCA1/BACH1/BARD1 0.011 0.05 -10000 0 -0.42 8 8
FANCE 0.011 0 -10000 0 -10000 0 0
FANCC 0.011 0 -10000 0 -10000 0 0
NBN -0.004 0.096 -10000 0 -0.58 16 16
FANCA 0.011 0 -10000 0 -10000 0 0
DNA repair 0.049 0.066 -10000 0 -0.58 4 4
BRCA1/BARD1/ubiquitin 0.011 0.05 -10000 0 -0.42 8 8
BARD1/DNA-PK 0.023 0.049 -10000 0 -0.35 9 9
FANCL 0.008 0.042 -10000 0 -0.58 3 3
mRNA polyadenylation -0.012 0.047 0.42 7 -10000 0 7
BRCA1/BARD1/CTIP/M/R/N Complex 0.006 0.15 -10000 0 -0.74 18 18
BRCA1/BACH1/BARD1/TopBP1 0.018 0.046 -10000 0 -0.36 9 9
BRCA1/BARD1/P53 -0.009 0.12 -10000 0 -0.33 64 64
BARD1/CSTF1/BRCA1 0.018 0.043 -10000 0 -0.36 8 8
BRCA1/BACH1 0.01 0.024 -10000 0 -0.58 1 1
BARD1 0.005 0.064 -10000 0 -0.58 7 7
PCNA 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.018 0.043 -10000 0 -0.36 8 8
BRCA1/BARD1/UbcH7 0.018 0.043 -10000 0 -0.36 8 8
BRCA1/BARD1/RAD51/PCNA 0.025 0.04 -10000 0 -0.32 8 8
BARD1/DNA-PK/P53 -0.002 0.11 -10000 0 -0.31 64 64
BRCA1/BARD1/Ubiquitin 0.011 0.05 -10000 0 -0.42 8 8
BRCA1/BARD1/CTIP 0.01 0.097 -10000 0 -0.42 25 25
FA complex 0.028 0.052 -10000 0 -1 1 1
BARD1/EWS 0.012 0.047 -10000 0 -0.42 7 7
RBBP8 0.001 0.1 -10000 0 -0.54 19 19
TP53 -0.045 0.17 -10000 0 -0.58 57 57
TOPBP1 0.01 0.024 -10000 0 -0.58 1 1
G1/S transition of mitotic cell cycle 0.009 0.11 0.33 64 -10000 0 64
BRCA1/BARD1 0.023 0.063 -10000 0 -0.33 16 16
CSTF1 0.011 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.003 0.047 -10000 0 -0.43 7 7
CDK2 0.01 0.024 -10000 0 -0.58 1 1
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.011 0 -10000 0 -10000 0 0
RAD50 0.01 0.024 -10000 0 -0.58 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.05 -10000 0 -0.42 8 8
EWSR1 0.011 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.003 0.012 -9999 0 -10000 0 0
DOCK1 0.01 0.024 -9999 0 -0.58 1 1
ITGA4 -0.019 0.13 -9999 0 -0.57 32 32
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.024 0.14 -9999 0 -0.44 55 55
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.019 -9999 0 -0.46 1 1
alpha4/beta1 Integrin 0.004 0.083 -9999 0 -0.36 28 28
alpha4/beta7 Integrin/Paxillin -0.005 0.11 -9999 0 -0.37 41 41
lamellipodium assembly -0.003 0.051 -9999 0 -0.5 5 5
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
PI3K 0.013 0.04 -9999 0 -0.43 5 5
ARF6 0.01 0.024 -9999 0 -0.58 1 1
TLN1 0.01 0.024 -9999 0 -0.58 1 1
PXN 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
ARF6/GTP -0.014 0.059 -9999 0 -10000 0 0
cell adhesion 0.016 0.072 -9999 0 -10000 0 0
CRKL/CBL 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.011 0.075 -9999 0 -0.32 28 28
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 -0.016 0.12 -9999 0 -0.53 30 30
ARF6/GDP 0.002 0.026 -9999 0 -0.58 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0 0.12 -9999 0 -0.42 40 40
p130Cas/Crk/Dock1 0.02 0.037 -9999 0 -0.37 5 5
VCAM1 -0.022 0.13 -9999 0 -0.53 37 37
alpha4/beta1 Integrin/Paxillin/Talin 0.017 0.072 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.017 0.072 -9999 0 -10000 0 0
BCAR1 0.008 0.043 -9999 0 -0.52 4 4
mol:GDP -0.016 0.072 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GIT1 0.01 0.024 -9999 0 -0.58 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.017 0.072 -9999 0 -10000 0 0
Rac1/GTP -0.003 0.058 -9999 0 -0.57 5 5
TCGA08_rtk_signaling

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
PDGFRA -0.011 0.11 -10000 0 -0.57 23 23
HRAS 0.008 0.041 -10000 0 -0.49 4 4
EGFR 0.005 0.058 -10000 0 -0.53 7 7
AKT 0.017 0.079 -10000 0 -0.34 21 21
FOXO3 0.011 0 -10000 0 -10000 0 0
AKT1 0.01 0.024 -10000 0 -0.58 1 1
FOXO1 0.009 0.034 -10000 0 -0.58 2 2
AKT3 -0.013 0.11 -10000 0 -0.52 28 28
FOXO4 0.01 0.024 -10000 0 -0.58 1 1
MET 0.01 0.031 -10000 0 -0.52 2 2
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
PIK3CB 0.008 0.046 -10000 0 -0.55 4 4
NRAS 0.002 0.076 -10000 0 -0.58 10 10
PIK3CG -0.044 0.17 -10000 0 -0.56 59 59
PIK3R3 0.008 0.042 -10000 0 -0.58 3 3
PIK3R2 0.01 0.024 -10000 0 -0.58 1 1
NF1 0.008 0.042 -10000 0 -0.58 3 3
RAS 0.008 0.054 0.21 1 -0.32 7 8
ERBB2 0 0.072 -10000 0 -0.47 14 14
proliferation/survival/translation -0.019 0.046 0.25 8 -0.14 3 11
PI3K 0.01 0.062 0.18 2 -0.25 19 21
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
KRAS 0.006 0.057 -10000 0 -0.56 6 6
FOXO 0.036 0.026 0.16 2 -10000 0 2
AKT2 0.009 0.036 -10000 0 -0.5 3 3
PTEN 0.006 0.059 -10000 0 -0.58 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.021 0.036 -10000 0 -0.26 10 10
epithelial cell differentiation 0.023 0.023 -10000 0 -0.3 3 3
CYFIP2 0.001 0.08 -10000 0 -0.58 11 11
ENAH 0.037 0.067 -10000 0 -0.43 6 6
EGFR 0.005 0.058 -10000 0 -0.53 7 7
EPHA2 0.006 0.055 -10000 0 -0.54 6 6
MYO6 0.029 0.022 -10000 0 -0.28 3 3
CTNNB1 0.011 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.015 0.06 -10000 0 -0.38 13 13
AQP5 -0.038 0.1 -10000 0 -0.47 26 26
CTNND1 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.025 -10000 0 -0.28 4 4
regulation of calcium-dependent cell-cell adhesion -0.003 0.093 -10000 0 -0.28 47 47
EGF -0.18 0.25 -10000 0 -0.51 222 222
NCKAP1 0.009 0.034 -10000 0 -0.58 2 2
AQP3 -0.022 0.066 -10000 0 -0.47 8 8
cortical microtubule organization 0.023 0.023 -10000 0 -0.3 3 3
GO:0000145 0.026 0.024 -10000 0 -0.26 4 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.023 -10000 0 -0.3 3 3
MLLT4 0.009 0.034 -10000 0 -0.58 2 2
ARF6/GDP -0.005 0.039 -10000 0 -0.49 2 2
ARF6 0.01 0.024 -10000 0 -0.58 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.024 0.045 -10000 0 -0.37 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.025 -10000 0 -10000 0 0
PVRL2 0.01 0.031 -10000 0 -0.52 2 2
ZYX 0.028 0.025 -10000 0 -0.28 4 4
ARF6/GTP 0.027 0.047 -10000 0 -0.39 6 6
CDH1 0.01 0.024 -10000 0 -0.58 1 1
EGFR/EGFR/EGF/EGF -0.085 0.11 -10000 0 -0.48 1 1
RhoA/GDP -0.002 0.023 -10000 0 -0.28 4 4
actin cytoskeleton organization 0.032 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.01 0.024 -10000 0 -0.58 1 1
GIT1 0.01 0.024 -10000 0 -0.58 1 1
IGF1R 0.01 0.024 -10000 0 -0.58 1 1
IGF1 -0.075 0.2 -10000 0 -0.52 97 97
DIAPH1 -0.013 0.091 -10000 0 -0.62 13 13
Wnt receptor signaling pathway -0.023 0.023 0.3 3 -10000 0 3
RHOA 0.01 0.024 -10000 0 -0.58 1 1
RhoA/GTP -0.005 0.038 -10000 0 -0.49 2 2
CTNNA1 0.009 0.034 -10000 0 -0.58 2 2
VCL 0.032 0.027 -10000 0 -10000 0 0
EFNA1 0.011 0.019 -10000 0 -0.46 1 1
LPP 0.033 0.026 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.004 0.031 -10000 0 -10000 0 0
SEC6/SEC8 -0.003 0.025 -10000 0 -10000 0 0
MGAT3 -0.003 0.095 -10000 0 -0.29 47 47
HGF/MET -0.024 0.074 -10000 0 -10000 0 0
HGF -0.039 0.16 -10000 0 -0.55 55 55
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.021 0.036 -10000 0 -0.26 10 10
actin cable formation 0.052 0.057 -10000 0 -0.35 5 5
KIAA1543 0.031 0.034 -10000 0 -10000 0 0
KIFC3 0.024 0.043 -10000 0 -0.28 10 10
NCK1 0.009 0.034 -10000 0 -0.58 2 2
EXOC3 0.011 0 -10000 0 -10000 0 0
ACTN1 0.029 0.022 -10000 0 -0.28 3 3
NCK1/GIT1 0.015 0.031 -10000 0 -0.42 3 3
mol:GDP 0.023 0.023 -10000 0 -0.3 3 3
EXOC4 0.011 0 -10000 0 -10000 0 0
STX4 0.029 0.022 -10000 0 -0.28 3 3
PIP5K1C 0.028 0.025 -10000 0 -0.28 4 4
LIMA1 0.005 0.064 -10000 0 -0.58 7 7
ABI1 0.01 0.024 -10000 0 -0.58 1 1
ROCK1 0.039 0.059 -10000 0 -0.48 4 4
adherens junction assembly 0.037 0.068 -10000 0 -0.44 7 7
IGF-1R heterotetramer/IGF1 -0.039 0.09 -10000 0 -0.56 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.034 -10000 0 -0.4 4 4
MET 0.01 0.031 -10000 0 -0.52 2 2
PLEKHA7 0.028 0.025 -10000 0 -0.28 4 4
mol:GTP 0.023 0.045 -10000 0 -0.37 6 6
establishment of epithelial cell apical/basal polarity 0.046 0.029 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.021 0.036 -10000 0 -0.26 10 10
regulation of cell-cell adhesion 0.032 0.027 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.021 0.036 -10000 0 -0.26 10 10
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.01 0.027 -10000 0 -0.44 2 2
TRAF2/ASK1 0.014 0.027 -10000 0 -0.36 3 3
ATM 0.003 0.072 -10000 0 -0.58 9 9
MAP2K3 0.013 0.095 -10000 0 -0.59 12 12
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.016 0.092 -10000 0 -0.54 12 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.003 0.083 -10000 0 -0.46 19 19
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
GADD45A 0.009 0.034 -10000 0 -0.58 2 2
GADD45B 0.008 0.038 -10000 0 -0.46 4 4
MAP3K1 0.006 0.059 -10000 0 -0.58 6 6
MAP3K6 0.005 0.064 -10000 0 -0.58 7 7
MAP3K7 0.011 0 -10000 0 -10000 0 0
MAP3K4 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.01 0.053 -10000 0 -0.42 9 9
TAK1/TAB family 0.003 0.021 0.18 3 -10000 0 3
RAC1/OSM/MEKK3 0.02 0.031 -10000 0 -0.4 3 3
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
RAC1/OSM/MEKK3/MKK3 -0.012 0.068 -10000 0 -0.48 11 11
TRAF6 0.007 0.015 -10000 0 -0.36 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.056 0.17 -10000 0 -0.5 79 79
CCM2 0.01 0.031 -10000 0 -0.52 2 2
CaM/Ca2+/CAMKIIB -0.026 0.11 -10000 0 -0.3 79 79
MAPK11 -0.002 0.079 -10000 0 -0.48 16 16
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.017 0.099 -10000 0 -0.27 80 80
OSM/MEKK3 0.014 0.038 -10000 0 -0.51 3 3
TAOK1 0.003 0.077 -10000 0 -0.46 14 14
TAOK2 0.008 0.047 -10000 0 -0.35 10 10
TAOK3 0.009 0.044 -10000 0 -0.35 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.034 -10000 0 -0.58 2 2
MAP3K10 0.007 0.05 -10000 0 -0.53 5 5
MAP3K3 0.009 0.034 -10000 0 -0.58 2 2
TRX/ASK1 0.013 0.021 -10000 0 -0.36 2 2
GADD45/MTK1/MTK1 0.017 0.053 -10000 0 -0.38 3 3
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.017 0.079 -9999 0 -0.48 13 13
VEGFR1 homodimer/NRP1 0.008 0.078 -9999 0 -0.48 13 13
mol:DAG 0.015 0.089 -9999 0 -0.64 7 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.015 0.074 -9999 0 -0.44 13 13
CaM/Ca2+ 0.02 0.084 -9999 0 -0.61 7 7
HIF1A 0.007 0.081 -9999 0 -0.54 12 12
GAB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.03 0.094 -9999 0 -0.62 10 10
PLCG1 0.015 0.089 -9999 0 -0.65 7 7
NOS3 0.026 0.11 -9999 0 -0.59 11 11
CBL 0.011 0 -9999 0 -10000 0 0
mol:NO 0.026 0.1 -9999 0 -0.56 11 11
FLT1 0.013 0.09 -9999 0 -0.55 13 13
PGF -0.001 0.078 -9999 0 -0.47 16 16
VEGFR1 homodimer/NRP2/VEGFR121 0.009 0.098 -9999 0 -0.79 4 4
CALM1 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
eNOS/Hsp90 0.031 0.1 -9999 0 -0.59 10 10
endothelial cell proliferation 0.003 0.12 -9999 0 -0.73 7 7
mol:Ca2+ 0.015 0.088 -9999 0 -0.64 7 7
MAPK3 0.024 0.081 -9999 0 -0.56 7 7
MAPK1 0.024 0.081 -9999 0 -0.56 7 7
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
PLGF homodimer -0.001 0.078 -9999 0 -0.47 16 16
PRKACA 0.011 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.002 0.082 -9999 0 -0.5 16 16
VEGFA homodimer 0.011 0.019 -9999 0 -0.46 1 1
VEGFR1 homodimer/VEGFA homodimer 0.016 0.079 -9999 0 -0.48 13 13
platelet activating factor biosynthetic process 0.028 0.08 -9999 0 -0.54 7 7
PI3K 0.02 0.098 -9999 0 -0.68 9 9
PRKCA 0.019 0.084 -9999 0 -0.6 7 7
PRKCB -0.009 0.13 -9999 0 -0.6 10 10
VEGFR1 homodimer/PLGF homodimer 0.009 0.094 -9999 0 -0.49 15 15
VEGFA 0.011 0.019 -9999 0 -0.46 1 1
VEGFB 0.011 0 -9999 0 -10000 0 0
mol:IP3 0.015 0.089 -9999 0 -0.64 7 7
RASA1 0.021 0.077 -9999 0 -0.63 6 6
NRP2 -0.012 0.11 -9999 0 -0.5 28 28
VEGFR1 homodimer 0.013 0.089 -9999 0 -0.55 13 13
VEGFB homodimer 0.011 0 -9999 0 -10000 0 0
NCK1 0.009 0.034 -9999 0 -0.58 2 2
eNOS/Caveolin-1 0.026 0.11 -9999 0 -0.57 11 11
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
mol:PI-3-4-5-P3 0.019 0.096 -9999 0 -0.66 9 9
mol:L-citrulline 0.026 0.1 -9999 0 -0.56 11 11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.014 0.12 -9999 0 -0.68 12 12
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.021 0.081 -9999 0 -0.69 6 6
CD2AP -0.016 0.12 -9999 0 -0.58 28 28
PI3K/GAB1 0.025 0.093 -9999 0 -0.64 9 9
PDPK1 0.023 0.091 -9999 0 -0.63 9 9
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.02 0.09 -9999 0 -0.72 7 7
mol:NADP 0.026 0.1 -9999 0 -0.56 11 11
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
ubiquitin-dependent protein catabolic process 0.013 0.12 -9999 0 -0.67 12 12
VEGFR1 homodimer/NRP2 0.002 0.1 -9999 0 -0.44 22 22
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.001 0.076 -10000 0 -0.33 19 19
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.019 -10000 0 -0.32 2 2
GNB1/GNG2 0.01 0.042 -10000 0 -0.33 9 9
GNB1 0.011 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.009 0.067 -10000 0 -0.28 34 34
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 0.004 0.017 0.075 34 -10000 0 34
GNAL -0.018 0.12 -10000 0 -0.51 34 34
GNG2 0.003 0.067 -10000 0 -0.54 9 9
CRH -0.001 0.026 -10000 0 -0.46 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.015 -10000 0 -0.36 1 1
MAPK11 0.001 0.039 -10000 0 -0.22 16 16
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.004 0.095 -9999 0 -0.42 30 30
AKT1 0.054 0.088 -9999 0 -0.54 9 9
PTK2B 0.023 0.096 -9999 0 -0.65 6 6
VEGFR2 homodimer/Frs2 0.022 0.078 -9999 0 -0.66 6 6
CAV1 -0.002 0.082 -9999 0 -0.5 16 16
CALM1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.029 0.076 -9999 0 -0.78 4 4
endothelial cell proliferation 0.045 0.098 -9999 0 -0.51 8 8
mol:Ca2+ 0.035 0.073 -9999 0 -0.67 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.035 0.073 -9999 0 -0.74 4 4
RP11-342D11.1 0.028 0.072 -9999 0 -0.67 4 4
CDH5 0.006 0.054 -9999 0 -0.49 7 7
VEGFA homodimer 0.024 0.054 -9999 0 -0.39 9 9
SHC1 0.011 0 -9999 0 -10000 0 0
SHC2 -0.041 0.16 -9999 0 -0.54 58 58
HRAS/GDP -0.01 0.061 -9999 0 -0.53 6 6
SH2D2A 0.011 0.019 -9999 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.017 0.078 -9999 0 -0.59 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.03 0.068 -9999 0 -0.7 4 4
VEGFR1 homodimer 0.007 0.052 -9999 0 -0.56 5 5
SHC/GRB2/SOS1 -0.009 0.064 -9999 0 -0.62 5 5
GRB10 0.033 0.088 -9999 0 -0.68 7 7
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
GRB2 0.011 0 -9999 0 -10000 0 0
PAK1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.036 0.083 -9999 0 -0.64 7 7
HRAS 0.008 0.041 -9999 0 -0.49 4 4
VEGF/Rho/ROCK1/Integrin Complex 0.018 0.12 -9999 0 -0.78 10 10
HIF1A 0.003 0.072 -9999 0 -0.58 9 9
FRS2 0.009 0.034 -9999 0 -0.58 2 2
oxygen and reactive oxygen species metabolic process 0.033 0.072 -9999 0 -0.72 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.006 0.095 -9999 0 -0.53 19 19
Nck/Pak 0.016 0.025 -9999 0 -0.42 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.027 0.077 -9999 0 -0.66 5 5
mol:GDP -0.009 0.062 -9999 0 -0.6 5 5
mol:NADP 0.042 0.087 -9999 0 -0.4 17 17
eNOS/Hsp90 0.045 0.084 -9999 0 -0.48 5 5
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:IP3 0.035 0.074 -9999 0 -0.68 4 4
HIF1A/ARNT 0.01 0.06 -9999 0 -0.46 9 9
SHB 0.011 0.019 -9999 0 -0.46 1 1
VEGFA 0.012 0.02 -9999 0 -0.45 1 1
VEGFC -0.013 0.12 -9999 0 -0.55 27 27
FAK1/Vinculin 0.036 0.11 -9999 0 -0.68 10 10
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.01 0.024 -9999 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.02 0.1 -9999 0 -0.69 6 6
PTPN6 0.011 0 -9999 0 -10000 0 0
EPAS1 0.015 0.042 -9999 0 -0.4 5 5
mol:L-citrulline 0.042 0.087 -9999 0 -0.4 17 17
ITGAV 0.002 0.076 -9999 0 -0.58 10 10
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.035 0.072 -9999 0 -0.74 4 4
VEGFR2 homodimer/VEGFA homodimer 0.032 0.078 -9999 0 -0.74 4 4
VEGFR2/3 heterodimer 0.013 0.1 -9999 0 -0.52 17 17
VEGFB 0.011 0 -9999 0 -10000 0 0
MAPK11 0.034 0.084 -9999 0 -0.61 7 7
VEGFR2 homodimer 0.021 0.078 -9999 0 -0.61 8 8
FLT1 0.007 0.052 -9999 0 -0.56 5 5
NEDD4 0.009 0.048 -9999 0 -0.58 4 4
MAPK3 0.027 0.076 -9999 0 -0.52 6 6
MAPK1 0.027 0.076 -9999 0 -0.52 6 6
VEGFA145/NRP2 0 0.08 -9999 0 -0.35 29 29
VEGFR1/2 heterodimer 0.02 0.079 -9999 0 -0.54 10 10
KDR 0.021 0.079 -9999 0 -0.62 8 8
VEGFA165/NRP1/VEGFR2 homodimer 0.024 0.096 -9999 0 -0.64 7 7
SRC 0.01 0.024 -9999 0 -0.58 1 1
platelet activating factor biosynthetic process 0.029 0.078 -9999 0 -0.63 4 4
PI3K 0.045 0.097 -9999 0 -0.64 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.029 0.07 -9999 0 -0.7 4 4
FES 0.029 0.087 -9999 0 -0.67 5 5
GAB1 -0.011 0.07 -9999 0 -0.66 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.069 -9999 0 -0.7 4 4
CTNNB1 0.011 0 -9999 0 -10000 0 0
SOS1 0.01 0.024 -9999 0 -0.58 1 1
ARNT 0.01 0.024 -9999 0 -0.58 1 1
eNOS/Caveolin-1 0.04 0.093 -9999 0 -0.39 18 18
VEGFR2 homodimer/VEGFA homodimer/Yes 0.026 0.082 -9999 0 -0.78 4 4
PI3K/GAB1 0.056 0.086 -9999 0 -0.58 7 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.038 0.074 -9999 0 -0.68 5 5
PRKACA 0.011 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.005 0.13 -9999 0 -0.68 13 13
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
CDC42 0.033 0.086 -9999 0 -0.72 5 5
actin cytoskeleton reorganization 0.029 0.068 -9999 0 -0.7 4 4
PTK2 0.031 0.12 -9999 0 -0.71 10 10
EDG1 0.028 0.072 -9999 0 -0.67 4 4
mol:DAG 0.035 0.074 -9999 0 -0.68 4 4
CaM/Ca2+ 0.037 0.068 -9999 0 -0.62 4 4
MAP2K3 0.039 0.074 -9999 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.035 0.091 -9999 0 -0.7 7 7
PLCG1 0.035 0.075 -9999 0 -0.69 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.035 0.067 -9999 0 -0.67 4 4
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
YES1 0.005 0.064 -9999 0 -0.58 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.079 -9999 0 -0.78 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.03 0.068 -9999 0 -0.7 4 4
cell migration 0.053 0.098 -9999 0 -0.64 7 7
mol:PI-3-4-5-P3 0.044 0.09 -9999 0 -0.58 8 8
FYN 0.005 0.06 -9999 0 -0.55 7 7
VEGFB/NRP1 0.033 0.068 -9999 0 -0.63 4 4
mol:NO 0.042 0.087 -9999 0 -0.4 17 17
PXN 0.011 0 -9999 0 -10000 0 0
HRAS/GTP -0.01 0.061 -9999 0 -0.53 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.035 0.091 -9999 0 -0.7 7 7
VHL 0.01 0.024 -9999 0 -0.58 1 1
ITGB3 -0.008 0.1 -9999 0 -0.55 21 21
NOS3 0.042 0.097 -9999 0 -0.46 17 17
VEGFR2 homodimer/VEGFA homodimer/Sck 0 0.11 -9999 0 -0.67 5 5
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA 0.038 0.071 -9999 0 -0.63 4 4
PRKCB 0.011 0.11 -9999 0 -0.59 7 7
VCL 0.009 0.034 -9999 0 -0.58 2 2
VEGFA165/NRP1 0.029 0.072 -9999 0 -0.67 4 4
VEGFR1/2 heterodimer/VEGFA homodimer 0.028 0.076 -9999 0 -0.63 6 6
VEGFA165/NRP2 0 0.08 -9999 0 -0.35 29 29
MAPKKK cascade 0.05 0.081 -9999 0 -0.54 9 9
NRP2 -0.012 0.11 -9999 0 -0.5 28 28
VEGFC homodimer -0.013 0.12 -9999 0 -0.55 27 27
NCK1 0.009 0.034 -9999 0 -0.58 2 2
ROCK1 0.001 0.08 -9999 0 -0.58 11 11
FAK1/Paxillin 0.037 0.11 -9999 0 -0.64 10 10
MAP3K13 0.035 0.077 -9999 0 -0.67 5 5
PDPK1 0.048 0.081 -9999 0 -0.51 8 8
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.055 0.057 -9999 0 -0.38 3 3
ERC1 0.009 0.033 -9999 0 -0.46 3 3
RIP2/NOD2 0 0.082 -9999 0 -0.4 24 24
NFKBIA 0.036 0.014 -9999 0 -10000 0 0
BIRC2 -0.001 0.086 -9999 0 -0.58 13 13
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
RIPK2 0.011 0 -9999 0 -10000 0 0
IKBKG 0.021 0.071 -9999 0 -0.46 5 5
IKK complex/A20 0.021 0.088 -9999 0 -0.48 5 5
NEMO/A20/RIP2 0.011 0 -9999 0 -10000 0 0
XPO1 0.001 0.08 -9999 0 -0.58 11 11
NEMO/ATM 0.022 0.09 -9999 0 -0.53 11 11
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.009 0.051 -9999 0 -0.36 11 11
IKK complex/ELKS -0.015 0.064 -9999 0 -0.52 5 5
BCL10/MALT1/TRAF6 0.017 0.061 -9999 0 -0.5 7 7
NOD2 -0.011 0.11 -9999 0 -0.56 24 24
NFKB1 0.013 0.024 -9999 0 -0.58 1 1
RELA 0.014 0 -9999 0 -10000 0 0
MALT1 0.007 0.054 -9999 0 -0.58 5 5
cIAP1/UbcH5C 0.008 0.064 -9999 0 -0.42 13 13
ATM 0.003 0.072 -9999 0 -0.58 9 9
TNF/TNFR1A -0.004 0.09 -9999 0 -0.39 31 31
TRAF6 0.01 0.024 -9999 0 -0.58 1 1
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
CHUK 0.007 0.048 -9999 0 -0.58 4 4
UBE2D3 0.011 0 -9999 0 -10000 0 0
TNF -0.017 0.12 -9999 0 -0.54 31 31
NF kappa B1 p50/RelA 0.032 0.015 -9999 0 -0.34 1 1
BCL10 0.007 0.048 -9999 0 -0.58 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.014 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
IKK complex 0.029 0.078 -9999 0 -0.56 5 5
CYLD 0.01 0.024 -9999 0 -0.58 1 1
IKK complex/PKC alpha 0.032 0.076 -9999 0 -0.59 4 4
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.02 0.025 -9999 0 -0.36 2 2
BIRC5 0.011 0.019 -9999 0 -0.46 1 1
NFKBIA 0.023 0.013 -9999 0 -10000 0 0
CPEB1 -0.054 0.18 -9999 0 -0.54 70 70
AKT1 0.022 0.02 -9999 0 -0.36 1 1
NDEL1 0.011 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.019 0.023 -9999 0 -0.5 1 1
NDEL1/TACC3 0.025 0.014 -9999 0 -10000 0 0
GADD45A 0.009 0.034 -9999 0 -0.58 2 2
GSK3B 0.009 0.033 -9999 0 -0.56 2 2
PAK1/Aurora A 0.021 0.013 -9999 0 -10000 0 0
MDM2 0.008 0.043 -9999 0 -0.52 4 4
JUB 0.011 0 -9999 0 -10000 0 0
TPX2 0.017 0.025 -9999 0 -0.42 2 2
TP53 -0.01 0.11 -9999 0 -0.33 58 58
DLG7 0.015 0.013 -9999 0 -0.2 2 2
AURKAIP1 0.01 0.031 -9999 0 -0.52 2 2
ARHGEF7 0.011 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.027 0.015 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.022 -9999 0 -0.49 1 1
AURKA 0.019 0.016 -9999 0 -0.24 2 2
AURKB 0.012 0.018 -9999 0 -0.24 3 3
CDC25B 0.023 0.015 -9999 0 -10000 0 0
G2/M transition checkpoint 0.019 0.011 -9999 0 -10000 0 0
mRNA polyadenylation -0.02 0.1 -9999 0 -0.29 70 70
Aurora A/CPEB -0.021 0.1 -9999 0 -0.29 70 70
Aurora A/TACC1/TRAP/chTOG 0.028 0.043 -9999 0 -0.32 8 8
BRCA1 0.01 0.024 -9999 0 -0.58 1 1
centrosome duplication 0.021 0.013 -9999 0 -10000 0 0
regulation of centrosome cycle 0.024 0.014 -9999 0 -10000 0 0
spindle assembly 0.027 0.043 -9999 0 -0.31 8 8
TDRD7 0.011 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.029 0.032 -9999 0 -0.41 3 3
CENPA 0.014 0.032 -9999 0 -0.42 3 3
Aurora A/PP2A 0.021 0.013 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.013 0.049 -9999 0 -0.57 1 1
negative regulation of DNA binding -0.01 0.11 -9999 0 -0.33 58 58
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.016 0.018 -9999 0 -0.42 1 1
RASA1 0.009 0.034 -9999 0 -0.58 2 2
Ajuba/Aurora A 0.019 0.011 -9999 0 -10000 0 0
mitotic prometaphase 0 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.016 -9999 0 -0.24 2 2
TACC1 0.002 0.073 -9999 0 -0.56 10 10
TACC3 0.011 0.019 -9999 0 -0.46 1 1
Aurora A/Antizyme1 0.026 0.021 -9999 0 -0.32 1 1
Aurora A/RasGAP 0.02 0.025 -9999 0 -0.36 2 2
OAZ1 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.011 0.004 -9999 0 -10000 0 0
GIT1 0.01 0.024 -9999 0 -0.58 1 1
GIT1/beta-PIX/PAK1 0.023 0.015 -9999 0 -0.36 1 1
Importin alpha/Importin beta/TPX2 0.017 0.025 -9999 0 -0.42 2 2
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.026 0.021 -9999 0 -0.29 2 2
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.025 0.071 -10000 0 -1.1 2 2
regulation of axonogenesis -0.02 0.045 0.6 2 -10000 0 2
myoblast fusion -0.016 0.036 0.4 3 -10000 0 3
mol:GTP 0.007 0.024 -10000 0 -0.3 3 3
regulation of calcium-dependent cell-cell adhesion 0.005 0.1 0.29 65 -10000 0 65
ARF1/GTP -0.002 0.021 -10000 0 -0.32 2 2
mol:GM1 0.007 0.019 -10000 0 -0.23 3 3
mol:Choline 0.02 0.035 -10000 0 -0.43 3 3
lamellipodium assembly 0.006 0.045 -10000 0 -0.45 3 3
MAPK3 0.019 0.032 -10000 0 -0.34 4 4
ARF6/GTP/NME1/Tiam1 -0.005 0.1 -10000 0 -0.29 65 65
ARF1 0.011 0.019 -10000 0 -0.46 1 1
ARF6/GDP 0.016 0.037 -10000 0 -0.41 3 3
ARF1/GDP 0.025 0.036 -10000 0 -0.37 3 3
ARF6 0.01 0.029 -10000 0 -0.68 1 1
RAB11A 0.011 0 -10000 0 -10000 0 0
TIAM1 -0.042 0.16 -10000 0 -0.52 63 63
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.019 0.032 -10000 0 -0.34 4 4
actin filament bundle formation -0.016 0.039 0.47 3 -10000 0 3
KALRN 0.002 0.044 -10000 0 -0.33 8 8
RAB11FIP3/RAB11A 0.016 0.022 -10000 0 -0.37 2 2
RhoA/GDP 0.017 0.039 -10000 0 -0.47 3 3
NME1 0.012 0.019 -10000 0 -0.45 1 1
Rac1/GDP 0.017 0.031 -10000 0 -0.37 3 3
substrate adhesion-dependent cell spreading 0.007 0.024 -10000 0 -0.3 3 3
cortical actin cytoskeleton organization 0.006 0.045 -10000 0 -0.46 3 3
RAC1 0.011 0 -10000 0 -10000 0 0
liver development 0.007 0.024 -10000 0 -0.3 3 3
ARF6/GTP 0.007 0.024 -10000 0 -0.3 3 3
RhoA/GTP -0.002 0.03 -10000 0 -0.69 1 1
mol:GDP 0.005 0.041 -10000 0 -0.41 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.018 0.025 -10000 0 -0.29 3 3
RHOA 0.01 0.024 -10000 0 -0.58 1 1
PLD1 0.014 0.039 -10000 0 -0.49 3 3
RAB11FIP3 0.01 0.031 -10000 0 -0.52 2 2
tube morphogenesis 0.006 0.045 -10000 0 -0.45 3 3
ruffle organization 0.02 0.045 -10000 0 -0.6 2 2
regulation of epithelial cell migration 0.007 0.024 -10000 0 -0.3 3 3
PLD2 0.016 0.019 -10000 0 -0.34 1 1
PIP5K1A 0.02 0.046 -10000 0 -0.61 2 2
mol:Phosphatidic acid 0.02 0.035 -10000 0 -0.43 3 3
Rac1/GTP 0.006 0.045 -10000 0 -0.46 3 3
Aurora C 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
INCENP 0.011 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.01 0.062 -9999 0 -0.3 23 23
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.003 0.017 -9999 0 -10000 0 0
AURKB 0.011 0 -9999 0 -10000 0 0
AURKC -0.01 0.11 -9999 0 -0.55 23 23
EPO 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
BCL2L1 0.041 0.082 -9999 0 -0.45 2 2
CRKL 0.02 0.068 -9999 0 -0.45 3 3
mol:DAG 0.026 0.062 -9999 0 -0.39 2 2
HRAS 0.036 0.065 -9999 0 -0.42 4 4
MAPK8 0.019 0.049 -9999 0 -0.34 5 5
RAP1A 0.02 0.071 -9999 0 -0.48 4 4
GAB1 0.02 0.068 -9999 0 -0.45 3 3
MAPK14 0.019 0.047 -9999 0 -0.34 4 4
EPO 0.001 0.054 -9999 0 -0.46 8 8
PLCG1 0.026 0.063 -9999 0 -0.4 2 2
EPOR/TRPC2/IP3 Receptors 0.003 0.068 -9999 0 -0.49 11 11
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
EPO/EPOR (dimer)/SOCS3 0.005 0.077 -9999 0 -0.37 16 16
GAB1/SHC/GRB2/SOS1 -0.013 0.052 -9999 0 -0.45 3 3
EPO/EPOR (dimer) 0.006 0.065 -9999 0 -0.35 18 18
IRS2 0.016 0.076 -9999 0 -0.43 4 4
STAT1 0.029 0.08 -9999 0 -0.49 4 4
STAT5B 0.029 0.066 -9999 0 -0.39 3 3
cell proliferation 0.024 0.046 -9999 0 -0.36 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.082 -9999 0 -0.51 8 8
TEC 0.02 0.068 -9999 0 -0.45 3 3
SOCS3 -0.002 0.082 -9999 0 -0.5 16 16
STAT1 (dimer) 0.029 0.078 -9999 0 -0.47 4 4
JAK2 -0.007 0.1 -9999 0 -0.55 21 21
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
EPO/EPOR (dimer)/JAK2 0.026 0.074 -9999 0 -0.48 3 3
EPO/EPOR 0.006 0.065 -9999 0 -0.35 18 18
LYN 0.013 0.003 -9999 0 -10000 0 0
TEC/VAV2 0.013 0.092 -9999 0 -0.49 4 4
elevation of cytosolic calcium ion concentration 0.003 0.068 -9999 0 -0.49 11 11
SHC1 0.011 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.019 0.054 -9999 0 -0.37 5 5
mol:IP3 0.026 0.062 -9999 0 -0.39 2 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.01 0.099 -9999 0 -0.52 5 5
SH2B3 0.011 0.007 -9999 0 -10000 0 0
NFKB1 0.019 0.049 -9999 0 -0.34 5 5
EPO/EPOR (dimer)/JAK2/SOCS3 -0.016 0.061 -9999 0 -0.29 21 21
PTPN6 0.014 0.07 -9999 0 -0.48 3 3
TEC/VAV2/GRB2 0.018 0.089 -9999 0 -0.47 4 4
EPOR 0.003 0.068 -9999 0 -0.5 11 11
INPP5D -0.018 0.13 -9999 0 -0.58 30 30
mol:GDP -0.013 0.053 -9999 0 -0.46 3 3
SOS1 0.01 0.024 -9999 0 -0.58 1 1
PLCG2 -0.01 0.11 -9999 0 -0.55 23 23
CRKL/CBL/C3G 0.031 0.066 -9999 0 -0.47 2 2
VAV2 0.006 0.094 -9999 0 -0.45 6 6
CBL 0.02 0.068 -9999 0 -0.45 3 3
SHC/Grb2/SOS1 -0.014 0.055 -9999 0 -0.48 3 3
STAT5A 0.029 0.066 -9999 0 -0.39 3 3
GRB2 0.011 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.041 0.08 -9999 0 -0.47 2 2
LYN/PLCgamma2 0.002 0.079 -9999 0 -0.39 23 23
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
BTK -0.003 0.11 -9999 0 -0.44 13 13
BCL2 0.026 0.16 -9999 0 -0.88 14 14
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.016 0.069 -10000 0 -0.35 22 22
Ran/GTP/Exportin 1/HDAC1 -0.013 0.075 -10000 0 -0.4 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.023 0.071 -10000 0 -0.32 22 22
SUMO1 -0.007 0.1 -10000 0 -0.58 19 19
ZFPM1 -0.003 0.084 -10000 0 -0.5 17 17
NPC/RanGAP1/SUMO1/Ubc9 0 0.095 -10000 0 -0.43 24 24
FKBP3 -0.002 0.09 -10000 0 -0.58 14 14
Histones 0.03 0.038 -10000 0 -10000 0 0
YY1/LSF 0.016 0.059 -10000 0 -0.28 21 21
SMG5 0.01 0.024 -10000 0 -0.58 1 1
RAN 0.011 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.058 -10000 0 -0.27 21 21
I kappa B alpha/HDAC1 0.018 0.042 -10000 0 -10000 0 0
SAP18 0.011 0.019 -10000 0 -0.46 1 1
RELA 0.018 0.057 -10000 0 -0.24 25 25
HDAC1/Smad7 0.022 0.022 -10000 0 -0.36 2 2
RANGAP1 0.01 0.031 -10000 0 -0.52 2 2
HDAC3/TR2 0.017 0.044 -10000 0 -0.32 1 1
NuRD/MBD3 Complex 0.036 0.032 -10000 0 -0.38 2 2
NF kappa B1 p50/RelA 0.021 0.056 -10000 0 -0.52 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.021 0.13 -10000 0 -0.56 34 34
GATA1 -0.004 0.072 -10000 0 -0.46 15 15
Mad/Max 0.015 0.026 -10000 0 -0.35 3 3
NuRD/MBD3 Complex/GATA1/Fog1 0.037 0.05 -10000 0 -0.41 4 4
RBBP7 0.009 0.034 -10000 0 -0.58 2 2
NPC -0.003 0.056 -10000 0 -0.31 19 19
RBBP4 0.01 0.024 -10000 0 -0.58 1 1
MAX 0.011 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
NFKBIA 0.013 0.047 -10000 0 -10000 0 0
KAT2B -0.005 0.098 -10000 0 -0.58 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.033 0.026 -10000 0 -10000 0 0
SIN3 complex 0.027 0.03 -10000 0 -0.32 4 4
SMURF1 0.011 0 -10000 0 -10000 0 0
CHD3 0.009 0.034 -10000 0 -0.58 2 2
SAP30 0.009 0.034 -10000 0 -0.58 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.01 0.024 -10000 0 -0.58 1 1
YY1/HDAC3 0.019 0.059 -10000 0 -0.54 1 1
YY1/HDAC2 0.017 0.053 -10000 0 -0.26 20 20
YY1/HDAC1 0.017 0.053 -10000 0 -0.26 20 20
NuRD/MBD2 Complex (MeCP1) 0.036 0.03 -10000 0 -0.37 1 1
PPARG 0.011 0.081 -10000 0 -0.32 30 30
HDAC8/hEST1B 0.023 0.015 -10000 0 -0.36 1 1
UBE2I 0.011 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -10000 0 -10000 0 0
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.016 0.049 -10000 0 -0.32 3 3
MBD3L2 -0.001 0.019 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.022 0.022 -10000 0 -0.36 2 2
CREBBP 0.011 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.038 0.033 -10000 0 -0.37 2 2
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.013 0.047 -10000 0 -10000 0 0
HDAC2 0.011 0 -10000 0 -10000 0 0
YY1 0.014 0.062 -10000 0 -0.31 20 20
HDAC8 0.011 0 -10000 0 -10000 0 0
SMAD7 0.009 0.034 -10000 0 -0.58 2 2
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
MXD1 0.009 0.036 -10000 0 -0.5 3 3
STAT3 0.019 0.03 -10000 0 -0.34 4 4
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 -0.007 0.1 -10000 0 -0.58 19 19
YY1/LSF/HDAC1 0.022 0.055 -10000 0 -0.47 3 3
YY1/SAP30/HDAC1 0.022 0.053 -10000 0 -0.4 3 3
EP300 0.007 0.048 -10000 0 -0.58 4 4
STAT3 (dimer non-phopshorylated) 0.019 0.03 -10000 0 -0.34 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.046 -10000 0 -10000 0 0
histone deacetylation 0.035 0.03 -10000 0 -0.36 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.024 0.044 -10000 0 -10000 0 0
nuclear export -0.022 0.015 0.36 1 -10000 0 1
PRKACA 0.011 0 -10000 0 -10000 0 0
GATAD2B 0.011 0 -10000 0 -10000 0 0
GATAD2A 0.01 0.024 -10000 0 -0.58 1 1
GATA2/HDAC3 0 0.087 -10000 0 -0.33 28 28
GATA1/HDAC1 0.006 0.052 -10000 0 -0.32 15 15
GATA1/HDAC3 0.003 0.057 -10000 0 -0.35 2 2
CHD4 0.011 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.004 0.09 -10000 0 -0.39 31 31
SIN3/HDAC complex/Mad/Max 0.036 0.027 -10000 0 -0.37 1 1
NuRD Complex 0.041 0.039 -10000 0 -0.36 3 3
positive regulation of chromatin silencing 0.029 0.037 -10000 0 -10000 0 0
SIN3B 0.01 0.024 -10000 0 -0.58 1 1
MTA2 0.011 0 -10000 0 -10000 0 0
SIN3A 0.01 0.024 -10000 0 -0.58 1 1
XPO1 0.001 0.08 -10000 0 -0.58 11 11
SUMO1/HDAC1 0.006 0.1 -10000 0 -0.55 19 19
HDAC complex 0.028 0.024 -10000 0 -0.32 3 3
GATA1/Fog1 -0.004 0.08 -10000 0 -0.35 31 31
FKBP25/HDAC1/HDAC2 0.015 0.057 -10000 0 -0.36 14 14
TNF -0.017 0.12 -10000 0 -0.54 31 31
negative regulation of cell growth 0.036 0.027 -10000 0 -0.36 1 1
NuRD/MBD2/PRMT5 Complex 0.036 0.03 -10000 0 -0.37 1 1
Ran/GTP/Exportin 1 0.007 0.12 -10000 0 -0.69 15 15
NF kappa B/RelA/I kappa B alpha 0.018 0.071 -10000 0 -0.33 21 21
SIN3/HDAC complex/NCoR1 0.034 0.025 -10000 0 -10000 0 0
TFCP2 0.009 0.034 -10000 0 -0.58 2 2
NR2C1 0.01 0.024 -10000 0 -0.58 1 1
MBD3 0.008 0.046 -10000 0 -0.55 4 4
MBD2 0.007 0.054 -10000 0 -0.58 5 5
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.007 0.054 -9999 0 -0.58 5 5
positive regulation of NF-kappaB transcription factor activity 0.011 0.05 -9999 0 -0.37 10 10
MAP2K4 0.033 0.038 -9999 0 -0.28 3 3
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
TNFRSF10B 0.01 0.024 -9999 0 -0.58 1 1
TNFRSF10A 0.011 0 -9999 0 -10000 0 0
SMPD1 0.013 0.03 -9999 0 -0.25 7 7
IKBKG 0.01 0.024 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.008 0.042 -9999 0 -0.46 5 5
TRAIL/TRAILR2 0.013 0.044 -9999 0 -0.42 6 6
TRAIL/TRAILR3 -0.005 0.09 -9999 0 -0.36 36 36
TRAIL/TRAILR1 0.013 0.04 -9999 0 -0.42 5 5
TRAIL/TRAILR4 0.011 0.05 -9999 0 -0.37 10 10
TRAIL/TRAILR1/DAP3/GTP 0.019 0.031 -9999 0 -0.32 5 5
IKK complex -0.005 0.038 -9999 0 -0.4 5 5
RIPK1 0.011 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.009 0 -9999 0 -10000 0 0
MAPK3 0.014 0.044 -9999 0 -0.42 6 6
MAP3K1 0.03 0.032 -9999 0 -0.25 6 6
TRAILR4 (trimer) 0.008 0.042 -9999 0 -0.46 5 5
TRADD 0.011 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.011 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.028 -9999 0 -0.25 6 6
CFLAR 0.011 0 -9999 0 -10000 0 0
MAPK1 0.014 0.044 -9999 0 -0.42 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.031 0.03 -9999 0 -0.29 5 5
mol:ceramide 0.013 0.03 -9999 0 -0.24 8 8
FADD 0.011 0 -9999 0 -10000 0 0
MAPK8 0.037 0.04 -9999 0 -0.39 1 1
TRAF2 0.01 0.024 -9999 0 -0.58 1 1
TRAILR3 (trimer) -0.014 0.11 -9999 0 -0.49 31 31
CHUK 0.007 0.048 -9999 0 -0.58 4 4
TRAIL/TRAILR1/FADD 0.02 0.034 -9999 0 -0.36 5 5
DAP3 0.011 0 -9999 0 -10000 0 0
CASP10 -0.002 0.039 -9999 0 -0.35 6 6
JNK cascade 0.011 0.05 -9999 0 -0.37 10 10
TRAIL (trimer) 0.007 0.054 -9999 0 -0.58 5 5
TNFRSF10C -0.014 0.11 -9999 0 -0.49 31 31
TRAIL/TRAILR1/DAP3/GTP/FADD 0.025 0.03 -9999 0 -0.3 5 5
TRAIL/TRAILR2/FADD 0.02 0.038 -9999 0 -0.36 6 6
cell death 0.013 0.03 -9999 0 -0.24 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.028 0.03 -9999 0 -0.25 7 7
TRAILR2 (trimer) 0.01 0.024 -9999 0 -0.58 1 1
CASP8 0 0.035 -9999 0 -0.8 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.031 0.033 -9999 0 -0.29 6 6
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.022 0.073 -10000 0 -0.41 4 4
BAG4 0.008 0.042 -10000 0 -0.58 3 3
BAD 0.018 0.036 -10000 0 -0.4 2 2
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.53 31 31
BAX 0.019 0.034 -10000 0 -0.52 1 1
EnzymeConsortium:3.1.4.12 0.008 0.019 -10000 0 -0.079 7 7
IKBKB 0.027 0.07 -10000 0 -0.48 2 2
MAP2K2 0.027 0.036 -10000 0 -0.3 3 3
MAP2K1 0.026 0.037 -10000 0 -0.27 4 4
SMPD1 0.012 0.025 -10000 0 -0.24 2 2
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.028 0.068 -10000 0 -0.37 2 2
MAP2K4 0.02 0.048 -10000 0 -0.29 10 10
protein ubiquitination 0.027 0.072 -10000 0 -0.44 4 4
EnzymeConsortium:2.7.1.37 0.029 0.041 -10000 0 -0.26 5 5
response to UV 0 0 -10000 0 -0.002 1 1
RAF1 0.023 0.033 -10000 0 -0.24 3 3
CRADD 0.011 0.024 -10000 0 -0.59 1 1
mol:ceramide 0.014 0.029 -10000 0 -0.17 3 3
I-kappa-B-alpha/RELA/p50/ubiquitin 0.016 0 -10000 0 -10000 0 0
MADD 0.012 0 -10000 0 -10000 0 0
MAP3K1 0.016 0.045 -10000 0 -0.32 7 7
TRADD 0.012 0 -10000 0 -10000 0 0
RELA/p50 0.011 0 -10000 0 -10000 0 0
MAPK3 0.029 0.036 -10000 0 -0.25 4 4
MAPK1 0.029 0.036 -10000 0 -0.25 4 4
p50/RELA/I-kappa-B-alpha 0.017 0 -10000 0 -10000 0 0
FADD 0.022 0.07 -10000 0 -0.36 3 3
KSR1 0.018 0.033 -10000 0 -0.26 3 3
MAPK8 0.024 0.047 -10000 0 -0.28 10 10
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.025 0.075 -10000 0 -0.51 3 3
TNF R/SODD 0.015 0.031 -10000 0 -0.42 3 3
TNF -0.017 0.12 -10000 0 -0.54 31 31
CYCS 0.019 0.046 0.13 11 -0.25 8 19
IKBKG 0.026 0.072 -10000 0 -0.51 3 3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.073 -10000 0 -0.3 18 18
RELA 0.011 0 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AIFM1 0.022 0.038 0.13 11 -0.36 2 13
TNF/TNF R/SODD 0.004 0.082 -10000 0 -0.33 34 34
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.031 -10000 0 -0.58 1 1
NSMAF 0.022 0.069 -10000 0 -0.36 3 3
response to hydrogen peroxide 0 0 -10000 0 -0.002 1 1
BCL2 -0.007 0.1 -10000 0 -0.55 20 20
HIF-2-alpha transcription factor network

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
MMP14 -0.009 0.064 -10000 0 -0.58 3 3
oxygen homeostasis 0.006 0.014 -10000 0 -10000 0 0
TCEB2 0.005 0.055 -10000 0 -0.47 8 8
TCEB1 0.011 0.019 -10000 0 -0.46 1 1
VHL/Elongin B/Elongin C/HIF2A -0.015 0.056 -10000 0 -0.46 4 4
EPO 0.078 0.18 -10000 0 -0.6 8 8
FIH (dimer) 0.018 0.012 -10000 0 -10000 0 0
APEX1 0.017 0.014 -10000 0 -10000 0 0
SERPINE1 0.059 0.23 -10000 0 -0.74 15 15
FLT1 -0.014 0.11 -10000 0 -0.89 8 8
ADORA2A 0.072 0.2 -10000 0 -0.73 7 7
germ cell development 0.068 0.21 -10000 0 -0.7 11 11
SLC11A2 0.078 0.19 -10000 0 -0.71 5 5
BHLHE40 0.078 0.19 -10000 0 -0.72 6 6
HIF1AN 0.018 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.022 0.12 -10000 0 -0.44 6 6
ETS1 0.015 0.067 -10000 0 -0.5 10 10
CITED2 -0.006 0.066 -10000 0 -1.1 2 2
KDR -0.014 0.11 -10000 0 -0.9 8 8
PGK1 0.078 0.19 -10000 0 -0.71 5 5
SIRT1 0.007 0.054 -10000 0 -0.58 5 5
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.085 0.22 -10000 0 -0.77 8 8
EPAS1 0.05 0.094 -10000 0 -0.37 5 5
SP1 0.017 0.025 -10000 0 -0.58 1 1
ABCG2 0.047 0.24 -10000 0 -0.79 13 13
EFNA1 0.078 0.19 -10000 0 -0.69 6 6
FXN 0.075 0.19 -10000 0 -0.69 6 6
POU5F1 0.068 0.22 -10000 0 -0.74 11 11
neuron apoptosis -0.083 0.21 0.74 8 -10000 0 8
EP300 0.007 0.048 -10000 0 -0.58 4 4
EGLN3 0 0.099 -10000 0 -0.53 20 20
EGLN2 0.015 0.038 -10000 0 -0.49 3 3
EGLN1 0.018 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.018 0.042 -10000 0 -0.31 9 9
VHL 0.01 0.024 -10000 0 -0.58 1 1
ARNT 0.016 0.029 -10000 0 -0.6 1 1
SLC2A1 0.07 0.2 -10000 0 -0.78 6 6
TWIST1 0.049 0.24 -10000 0 -0.72 19 19
ELK1 0.017 0.025 -10000 0 -0.58 1 1
HIF2A/ARNT/Cbp/p300 0.068 0.12 -10000 0 -0.43 4 4
VEGFA 0.078 0.19 -10000 0 -0.71 5 5
CREBBP 0.011 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.015 0.029 -9999 0 -0.39 3 3
FBXW11 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.033 -9999 0 -0.34 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.048 -9999 0 -10000 0 0
NFKBIA 0.009 0.051 -9999 0 -0.22 21 21
MAPK14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.019 -9999 0 -0.36 1 1
ARRB2 0.014 0 -9999 0 -10000 0 0
REL 0.008 0.042 -9999 0 -0.58 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.031 -9999 0 -0.32 5 5
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.019 -9999 0 -0.36 1 1
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
NF kappa B1 p50 dimer 0.016 0.022 -9999 0 -0.37 2 2
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
NFKB1 0.017 0.023 -9999 0 -0.37 2 2
RELA 0.011 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.014 0.052 -9999 0 -0.22 21 21
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.029 0.046 -9999 0 -10000 0 0
SRC 0.01 0.024 -9999 0 -0.58 1 1
PI3K 0.013 0.04 -9999 0 -0.43 5 5
NF kappa B1 p50/RelA 0.014 0.052 -9999 0 -0.22 21 21
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
SYK 0.011 0.019 -9999 0 -0.46 1 1
I kappa B alpha/PIK3R1 0.014 0.053 -9999 0 -0.28 4 4
cell death 0.028 0.045 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.019 0.033 -9999 0 -0.34 5 5
LCK -0.031 0.14 -9999 0 -0.51 49 49
BCL3 0.009 0.039 -9999 0 -0.54 3 3
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.033 0.026 -9999 0 -0.46 1 1
KLHL20 -0.019 0.054 -9999 0 -0.23 29 29
CYFIP2 0.001 0.08 -9999 0 -0.58 11 11
Rac1/GDP 0.044 0.04 -9999 0 -0.49 1 1
ENAH 0.026 0.052 -9999 0 -0.48 2 2
AP1M1 0.01 0.024 -9999 0 -0.58 1 1
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.004 0.032 -9999 0 -0.41 2 2
ABI1/Sra1/Nap1 -0.015 0.041 -9999 0 -0.21 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.013 0.072 -9999 0 -0.33 20 20
RAPGEF1 0.04 0.033 -9999 0 -0.45 2 2
CTNND1 0.011 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.027 0.026 -9999 0 -0.48 1 1
CRK 0.037 0.028 -9999 0 -0.43 1 1
E-cadherin/gamma catenin/alpha catenin 0.021 0.031 -9999 0 -0.36 4 4
alphaE/beta7 Integrin -0.003 0.09 -9999 0 -0.39 30 30
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
NCKAP1 0.009 0.034 -9999 0 -0.58 2 2
Rap1/GTP/I-afadin 0.021 0.024 -9999 0 -0.32 3 3
DLG1 0.031 0.033 -9999 0 -0.46 1 1
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.026 -9999 0 -0.26 5 5
MLLT4 0.009 0.034 -9999 0 -0.58 2 2
ARF6/GTP/NME1/Tiam1 -0.01 0.094 -9999 0 -0.32 32 32
PI3K -0.004 0.034 -9999 0 -0.34 5 5
ARF6 0.01 0.024 -9999 0 -0.58 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.016 0.025 -9999 0 -0.42 2 2
TIAM1 -0.044 0.16 -9999 0 -0.52 63 63
E-cadherin(dimer)/Ca2+ 0.026 0.023 -9999 0 -0.3 3 3
AKT1 -0.003 0.023 -9999 0 -0.23 4 4
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
CDH1 0.01 0.024 -9999 0 -0.58 1 1
RhoA/GDP 0.043 0.041 -9999 0 -0.49 1 1
actin cytoskeleton organization 0.017 0.051 -9999 0 -0.2 7 7
CDC42/GDP 0.041 0.047 -9999 0 -0.43 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.019 0.023 -9999 0 -0.26 4 4
ITGB7 -0.016 0.12 -9999 0 -0.53 30 30
RAC1 0.011 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.028 0.024 -9999 0 -0.32 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin 0.019 0.023 -9999 0 -0.31 3 3
mol:GDP 0.041 0.045 -9999 0 -0.46 2 2
CDC42/GTP/IQGAP1 0.011 0.05 -9999 0 -0.46 6 6
JUP 0.01 0.024 -9999 0 -0.58 1 1
p120 catenin/RhoA/GDP 0.035 0.041 -9999 0 -0.5 1 1
RAC1/GTP/IQGAP1 0.014 0.025 -9999 0 -0.33 3 3
PIP5K1C/AP1M1 0.016 0.032 -9999 0 -0.78 1 1
RHOA 0.01 0.024 -9999 0 -0.58 1 1
CDC42 0.007 0.054 -9999 0 -0.58 5 5
CTNNA1 0.009 0.034 -9999 0 -0.58 2 2
positive regulation of S phase of mitotic cell cycle 0.016 0.036 -9999 0 -0.26 2 2
NME1 0.011 0.019 -9999 0 -0.46 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.032 0.028 -9999 0 -0.46 1 1
regulation of cell-cell adhesion -0.004 0.028 -9999 0 -0.35 2 2
WASF2 -0.007 0.021 -9999 0 -10000 0 0
Rap1/GTP -0.003 0.026 -9999 0 -0.45 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.017 0.071 -9999 0 -0.44 1 1
CCND1 0.018 0.044 -9999 0 -0.33 2 2
VAV2 0.009 0.15 -9999 0 -0.69 28 28
RAP1/GDP 0.036 0.036 -9999 0 -0.49 1 1
adherens junction assembly 0.032 0.028 -9999 0 -0.45 1 1
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.01 0.024 -9999 0 -0.58 1 1
PIP5K1C 0.01 0.024 -9999 0 -0.58 1 1
regulation of heterotypic cell-cell adhesion 0.022 0.068 -9999 0 -0.42 1 1
E-cadherin/beta catenin 0 0.022 -9999 0 -0.36 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.032 0.028 -9999 0 -0.46 1 1
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
Rac1/GTP -0.03 0.087 -9999 0 -0.38 28 28
E-cadherin/beta catenin/alpha catenin 0.022 0.027 -9999 0 -0.36 3 3
ITGAE 0.011 0.019 -9999 0 -0.46 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.027 -9999 0 -0.49 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.011 0 -10000 0 -10000 0 0
mol:PIP3 -0.005 0.051 0.28 5 -0.29 14 19
FRAP1 0.012 0.017 -10000 0 -10000 0 0
AKT1 0.017 0.049 0.22 5 -0.26 15 20
INSR 0.009 0.034 -10000 0 -0.58 2 2
Insulin Receptor/Insulin 0.005 0.031 -10000 0 -0.33 5 5
mol:GTP -0.006 0.038 -10000 0 -0.55 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.026 -10000 0 -0.3 3 3
TSC2 0.01 0.031 -10000 0 -0.52 2 2
RHEB/GDP -0.005 0.034 -10000 0 -0.49 1 1
TSC1 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.007 0.05 -10000 0 -0.34 12 12
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.004 0.03 -10000 0 -0.35 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.01 0.024 -10000 0 -0.58 1 1
RPS6KB1 0.017 0.048 -10000 0 -0.4 5 5
MAP3K5 0.007 0.022 -10000 0 -0.38 2 2
PIK3R1 0.009 0.042 -10000 0 -0.58 3 3
apoptosis 0.007 0.022 -10000 0 -0.38 2 2
mol:LY294002 0 0 0.001 1 -0.002 10 11
EIF4B 0.022 0.042 -10000 0 -0.34 5 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.043 -10000 0 -0.34 4 4
eIF4E/eIF4G1/eIF4A1 -0.001 0.016 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.013 0.051 -10000 0 -0.31 15 15
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.024 0.16 5 -0.2 1 6
FKBP1A 0.012 0 -10000 0 -10000 0 0
RHEB/GTP -0.005 0.033 -10000 0 -0.48 1 1
mol:Amino Acids 0 0 0.001 1 -0.002 10 11
FKBP12/Rapamycin 0.009 0.001 -10000 0 -10000 0 0
PDPK1 -0.004 0.045 0.23 5 -0.26 14 19
EIF4E 0.009 0.039 -10000 0 -0.54 3 3
ASK1/PP5C 0.017 0.039 -10000 0 -0.62 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.012 0.031 -10000 0 -0.51 2 2
TSC1/TSC2 0.025 0.046 -10000 0 -0.6 1 1
tumor necrosis factor receptor activity 0 0 0.002 10 -0.001 1 11
RPS6 0.007 0.045 -10000 0 -0.48 5 5
PPP5C 0.011 0 -10000 0 -10000 0 0
EIF4G1 0.011 0 -10000 0 -10000 0 0
IRS1 0.001 0.049 -10000 0 -0.38 10 10
INS -0.002 0.035 -10000 0 -0.5 3 3
PTEN 0.005 0.059 -10000 0 -0.58 6 6
PDK2 -0.005 0.048 0.23 5 -0.27 16 21
EIF4EBP1 0.009 0.044 -10000 0 -1 1 1
PIK3CA 0.01 0.034 -10000 0 -0.58 2 2
PPP2R5D 0.017 0.016 -10000 0 -10000 0 0
peptide biosynthetic process 0.01 0.036 -10000 0 -0.29 7 7
RHEB 0.011 0 -10000 0 -10000 0 0
EIF4A1 0.011 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 6 -0.003 1 7
EEF2 0.01 0.036 -10000 0 -0.29 7 7
eIF4E/4E-BP1 0.013 0.046 -10000 0 -0.96 1 1
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.019 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.026 0.03 -10000 0 -0.32 4 4
CDKN1B 0.024 0.048 -10000 0 -0.53 4 4
CDKN1A 0.022 0.05 -10000 0 -0.41 6 6
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.009 0.039 -10000 0 -0.54 3 3
FOXO3 0.024 0.044 -10000 0 -0.54 3 3
AKT1 -0.005 0.043 -10000 0 -0.57 3 3
BAD 0.01 0.031 -10000 0 -0.52 2 2
AKT3 0.001 0.062 -10000 0 -0.27 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.024 0.045 -10000 0 -0.47 4 4
AKT1/ASK1 0.023 0.053 -10000 0 -0.58 4 4
BAD/YWHAZ 0.02 0.033 -10000 0 -0.36 4 4
RICTOR -0.008 0.11 -10000 0 -0.58 20 20
RAF1 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.022 0.05 0.56 4 -10000 0 4
TSC1 0.024 0.044 -10000 0 -0.54 3 3
YWHAZ 0.008 0.042 -10000 0 -0.58 3 3
AKT1/RAF1 0.025 0.044 -10000 0 -0.54 3 3
EP300 0.007 0.048 -10000 0 -0.58 4 4
mol:GDP 0.019 0.045 -10000 0 -0.56 3 3
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.024 0.053 -10000 0 -0.54 4 4
YWHAQ 0.011 0 -10000 0 -10000 0 0
TBC1D4 0.015 0.04 -10000 0 -0.34 7 7
MAP3K5 0.009 0.034 -10000 0 -0.58 2 2
MAPKAP1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.03 0.32 3 -10000 0 3
YWHAH 0.011 0 -10000 0 -10000 0 0
AKT1S1 0.024 0.051 -10000 0 -0.63 3 3
CASP9 0.024 0.045 -10000 0 -0.47 4 4
YWHAB 0.011 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.057 -10000 0 -0.63 4 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.022 0.022 -10000 0 -0.36 2 2
YWHAE 0.011 0 -10000 0 -10000 0 0
SRC 0.01 0.024 -10000 0 -0.58 1 1
AKT2/p21CIP1 0.026 0.051 -10000 0 -0.47 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.013 0.014 -10000 0 -10000 0 0
CHUK 0.023 0.058 -10000 0 -0.5 6 6
BAD/BCL-XL 0.035 0.049 -10000 0 -0.58 3 3
mTORC2 0.003 0.062 -10000 0 -0.33 20 20
AKT2 0.013 0.019 -10000 0 -0.24 3 3
FOXO1-3a-4/14-3-3 family 0.042 0.046 -10000 0 -0.52 3 3
PDPK1 0.011 0 -10000 0 -10000 0 0
MDM2 0.023 0.051 -10000 0 -0.49 5 5
MAPKKK cascade -0.025 0.043 0.52 3 -10000 0 3
MDM2/Cbp/p300 0.032 0.057 -10000 0 -0.5 5 5
TSC1/TSC2 0.029 0.051 -10000 0 -0.61 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.054 -10000 0 -0.47 5 5
glucose import 0.005 0.072 -10000 0 -0.27 38 38
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.021 0.031 -10000 0 -0.34 3 3
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.005 0.073 -10000 0 -0.27 38 38
GSK3A 0.024 0.044 -10000 0 -0.54 3 3
FOXO1 0.023 0.047 -10000 0 -0.43 5 5
GSK3B 0.024 0.054 -10000 0 -0.6 4 4
SFN 0.005 0.055 -10000 0 -0.47 8 8
G1/S transition of mitotic cell cycle 0.029 0.053 -10000 0 -0.57 4 4
p27Kip1/14-3-3 family 0.036 0.029 -10000 0 -0.39 1 1
PRKACA 0.011 0 -10000 0 -10000 0 0
KPNA1 0.009 0.034 -10000 0 -0.58 2 2
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
YWHAG 0.011 0 -10000 0 -10000 0 0
RHEB 0.011 0 -10000 0 -10000 0 0
CREBBP 0.011 0 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.015 0.072 -9999 0 -10000 0 0
PLK1 0.056 0.12 -9999 0 -0.89 3 3
CDKN1B 0.096 0.073 -9999 0 -0.41 5 5
FOXO3 0.054 0.12 -9999 0 -0.65 4 4
KAT2B 0.003 0.1 -9999 0 -0.58 17 17
FOXO1/SIRT1 0.001 0.054 -9999 0 -0.35 5 5
CAT 0.057 0.12 -9999 0 -0.74 2 2
CTNNB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.02 0.027 -9999 0 -0.58 1 1
FOXO1 0.022 0.048 -9999 0 -0.28 3 3
MAPK10 0.009 0.083 -9999 0 -0.29 38 38
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.068 0.065 -9999 0 -0.58 2 2
response to oxidative stress 0.009 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.001 0.088 -9999 0 -0.6 5 5
XPO1 0.001 0.08 -9999 0 -0.58 11 11
EP300 0.008 0.049 -9999 0 -0.59 4 4
BCL2L11 0.026 0.027 -9999 0 -10000 0 0
FOXO1/SKP2 0.024 0.053 -9999 0 -0.43 3 3
mol:GDP 0.009 0.013 -9999 0 -10000 0 0
RAN 0.013 0.001 -9999 0 -10000 0 0
GADD45A 0.081 0.088 -9999 0 -0.89 3 3
YWHAQ 0.011 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.054 0.052 -9999 0 -0.59 3 3
MST1 -0.025 0.15 -9999 0 -0.5 51 51
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.043 0.043 -9999 0 -0.46 3 3
YWHAB 0.011 0 -9999 0 -10000 0 0
MAPK8 0.032 0.017 -9999 0 -0.34 1 1
MAPK9 0.032 0.007 -9999 0 -10000 0 0
YWHAG 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
YWHAZ 0.008 0.042 -9999 0 -0.58 3 3
SIRT1 0.009 0.056 -9999 0 -0.58 5 5
SOD2 0.096 0.086 -9999 0 -0.64 2 2
RBL2 0.066 0.12 -9999 0 -1.4 2 2
RAL/GDP 0.026 0.01 -9999 0 -10000 0 0
CHUK 0.016 0.049 -9999 0 -0.58 4 4
Ran/GTP 0.012 0.002 -9999 0 -10000 0 0
CSNK1G2 0.009 0.034 -9999 0 -0.58 2 2
RAL/GTP 0.032 0.01 -9999 0 -10000 0 0
CSNK1G1 0.01 0.024 -9999 0 -0.58 1 1
FASLG -0.081 0.36 -9999 0 -1.4 42 42
SKP2 0.008 0.042 -9999 0 -0.58 3 3
USP7 0.013 0.001 -9999 0 -10000 0 0
IKBKB 0.019 0.021 -9999 0 -0.44 1 1
CCNB1 0.057 0.12 -9999 0 -0.74 2 2
FOXO1-3a-4/beta catenin 0.1 0.089 -9999 0 -0.44 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.053 -9999 0 -0.43 3 3
CSNK1A1 0.009 0.034 -9999 0 -0.58 2 2
SGK1 0.008 0.076 -9999 0 -0.48 14 14
CSNK1G3 0.01 0.024 -9999 0 -0.58 1 1
Ran/GTP/Exportin 1 0.014 0.051 -9999 0 -0.36 11 11
ZFAND5 0.069 0.067 -9999 0 -0.72 2 2
SFN 0.005 0.055 -9999 0 -0.47 8 8
CDK2 0.009 0.026 -9999 0 -0.58 1 1
FOXO3A/14-3-3 0.049 0.051 -9999 0 -0.42 4 4
CREBBP 0.01 0.009 -9999 0 -10000 0 0
FBXO32 0.055 0.12 -9999 0 -0.74 2 2
BCL6 0.066 0.099 -9999 0 -0.65 2 2
RALB 0.013 0.001 -9999 0 -10000 0 0
RALA 0.013 0.001 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.015 0.12 -10000 0 -0.51 31 31
CLTC 0.025 0.032 -10000 0 -0.71 1 1
calcium ion-dependent exocytosis 0.021 0.022 -10000 0 -0.46 1 1
Dynamin 2/GTP 0.019 0.022 -10000 0 -0.29 3 3
EXOC4 0.011 0 -10000 0 -10000 0 0
CD59 0.022 0.031 -10000 0 -0.7 1 1
CPE -0.037 0.12 -10000 0 -0.32 94 94
CTNNB1 0.011 0 -10000 0 -10000 0 0
membrane fusion 0.02 0.022 -10000 0 -0.45 1 1
CTNND1 0.024 0.021 -10000 0 -0.3 2 2
DNM2 0.01 0.024 -10000 0 -0.58 1 1
mol:PI-4-5-P2 0.024 0.031 -10000 0 -0.51 2 2
TSHR 0.001 0.06 -10000 0 -0.28 25 25
INS 0.008 0.024 -10000 0 -0.52 1 1
BIN1 0.007 0.054 -10000 0 -0.58 5 5
mol:Choline 0.02 0.022 -10000 0 -0.45 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.019 -10000 0 -0.31 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.01 0.024 -10000 0 -0.58 1 1
mol:Ca2+ 0.019 0.022 -10000 0 -0.29 3 3
JUP 0.022 0.031 -10000 0 -0.7 1 1
ASAP2/amphiphysin II 0.017 0.042 -10000 0 -0.32 9 9
ARF6/GTP 0.008 0.018 -10000 0 -0.43 1 1
CDH1 0.022 0.031 -10000 0 -0.7 1 1
clathrin-independent pinocytosis 0.008 0.018 -10000 0 -0.43 1 1
MAPK8IP3 0.005 0.056 -10000 0 -0.51 7 7
positive regulation of endocytosis 0.008 0.018 -10000 0 -0.43 1 1
EXOC2 0.01 0.024 -10000 0 -0.58 1 1
substrate adhesion-dependent cell spreading 0.026 0.064 -10000 0 -0.61 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.01 0.024 -10000 0 -0.58 1 1
regulation of calcium-dependent cell-cell adhesion 0.002 0.029 0.62 1 -10000 0 1
positive regulation of phagocytosis 0.015 0.015 -10000 0 -0.36 1 1
ARF6/GTP/JIP3 0.011 0.038 -10000 0 -0.32 8 8
ACAP1 0.014 0.032 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.009 0.072 -10000 0 -0.71 1 1
clathrin heavy chain/ACAP1 0.027 0.032 -10000 0 -0.46 2 2
JIP4/KLC1 0.021 0.02 -10000 0 -0.32 2 2
EXOC1 0.01 0.024 -10000 0 -0.58 1 1
exocyst 0.026 0.066 -10000 0 -0.62 4 4
RALA/GTP 0.009 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.014 0.022 -10000 0 -0.36 2 2
receptor recycling 0.008 0.018 -10000 0 -0.43 1 1
CTNNA1 0.023 0.028 -10000 0 -0.3 4 4
NME1 0.014 0.019 -10000 0 -0.32 2 2
clathrin coat assembly 0.024 0.031 -10000 0 -0.69 1 1
IL2RA 0.001 0.071 -10000 0 -0.5 2 2
VAMP3 0.015 0.015 -10000 0 -0.36 1 1
GLUT4/clathrin heavy chain/ACAP1 -0.013 0.054 -10000 0 -0.45 2 2
EXOC6 0.008 0.042 -10000 0 -0.58 3 3
PLD1 0.016 0.029 -10000 0 -0.38 3 3
PLD2 0.018 0.008 -10000 0 -0.17 1 1
EXOC5 -0.005 0.098 -10000 0 -0.58 17 17
PIP5K1C 0.024 0.032 -10000 0 -0.52 2 2
SDC1 0.022 0.031 -10000 0 -0.7 1 1
ARF6/GDP 0.014 0.019 -10000 0 -0.32 2 2
EXOC7 0.011 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.002 0.03 -10000 0 -0.65 1 1
mol:Phosphatidic acid 0.02 0.022 -10000 0 -0.45 1 1
endocytosis -0.016 0.042 0.32 9 -10000 0 9
SCAMP2 0.011 0 -10000 0 -10000 0 0
ADRB2 0.009 0.079 -10000 0 -0.29 32 32
EXOC3 0.011 0 -10000 0 -10000 0 0
ASAP2 0.008 0.042 -10000 0 -0.58 3 3
Dynamin 2/GDP 0.02 0.022 -10000 0 -0.29 3 3
KLC1 0.011 0 -10000 0 -10000 0 0
AVPR2 0.002 0.084 -10000 0 -0.29 26 26
RALA 0.011 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.03 -10000 0 -0.6 1 1
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.007 0.025 0.26 5 -10000 0 5
BUB1B 0.017 0.033 -10000 0 -0.34 5 5
PLK1 0.016 0.006 -10000 0 -10000 0 0
PLK1S1 0.011 0.019 -10000 0 -0.27 2 2
KIF2A 0.02 0.015 -10000 0 -0.32 1 1
regulation of mitotic centrosome separation 0.015 0.006 -10000 0 -10000 0 0
GOLGA2 0.009 0.034 -10000 0 -0.58 2 2
Hec1/SPC24 0.012 0.068 -10000 0 -0.29 29 29
WEE1 0.018 0.044 -10000 0 -0.51 4 4
cytokinesis 0.022 0.048 -10000 0 -0.34 7 7
PP2A-alpha B56 0.029 0.036 -10000 0 -0.78 1 1
AURKA 0.014 0.004 -10000 0 -10000 0 0
PICH/PLK1 0.022 0.058 -10000 0 -0.3 16 16
CENPE 0.01 0.059 -10000 0 -0.32 18 18
RhoA/GTP 0.008 0.018 -10000 0 -0.43 1 1
positive regulation of microtubule depolymerization 0.02 0.015 -10000 0 -0.32 1 1
PPP2CA 0.011 0 -10000 0 -10000 0 0
FZR1 0.01 0.024 -10000 0 -0.58 1 1
TPX2 0.012 0.016 -10000 0 -0.26 2 2
PAK1 0.011 0 -10000 0 -10000 0 0
SPC24 -0.003 0.089 -10000 0 -0.56 15 15
FBXW11 0.011 0 -10000 0 -10000 0 0
CLSPN 0.013 0.018 -10000 0 -0.3 2 2
GORASP1 0.011 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.016 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.009 0.003 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0.001 0.011 1 -10000 0 1
STAG2 0.007 0.048 -10000 0 -0.58 4 4
GRASP65/GM130/RAB1/GTP -0.001 0.018 -10000 0 -0.25 3 3
spindle elongation 0.015 0.006 -10000 0 -10000 0 0
ODF2 0.011 0.001 -10000 0 -10000 0 0
BUB1 -0.001 0.035 -10000 0 -0.86 1 1
TPT1 0.013 0.005 -10000 0 -10000 0 0
CDC25C 0.015 0.004 -10000 0 -10000 0 0
CDC25B 0.01 0.027 -10000 0 -0.45 2 2
SGOL1 0.007 0.025 -10000 0 -0.26 5 5
RHOA 0.01 0.024 -10000 0 -0.58 1 1
CCNB1/CDK1 -0.003 0.025 -10000 0 -0.28 4 4
CDC14B 0.007 0.031 -10000 0 -0.44 3 3
CDC20 0.011 0 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.046 -10000 0 -0.3 13 13
mitosis 0 0 -10000 0 -10000 0 0
FBXO5 0.016 0.027 -10000 0 -0.31 4 4
CDC2 0.001 0.001 -10000 0 -10000 0 0
NDC80 -0.002 0.09 -10000 0 -0.58 14 14
metaphase plate congression 0.014 0.006 -10000 0 -10000 0 0
ERCC6L 0.019 0.061 -10000 0 -0.32 17 17
NLP/gamma Tubulin 0.012 0.004 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.013 0.005 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0 -10000 0 -10000 0 0
PPP1R12A 0.007 0.049 -10000 0 -0.59 4 4
interphase 0 0 -10000 0 -10000 0 0
PLK1/PRC1-2 0.026 0.02 -10000 0 -0.3 2 2
GRASP65/GM130/RAB1/GTP/PLK1 0.028 0.023 -10000 0 -0.29 3 3
RAB1A 0.01 0.024 -10000 0 -0.58 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.017 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0 0.001 0.012 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.025 -10000 0 -0.4 1 1
microtubule-based process 0.019 0.021 -10000 0 -0.32 2 2
Golgi organization 0.015 0.006 -10000 0 -10000 0 0
Cohesin/SA2 0.016 0.027 -10000 0 -0.31 4 4
PPP1CB/MYPT1 0.012 0.051 -10000 0 -0.49 6 6
KIF20A 0.009 0.034 -10000 0 -0.58 2 2
APC/C/CDC20 0.021 0.006 -10000 0 -10000 0 0
PPP2R1A 0.01 0.024 -10000 0 -0.58 1 1
chromosome segregation 0.01 0.046 -10000 0 -0.3 13 13
PRC1 0.011 0 -10000 0 -10000 0 0
ECT2 0.013 0.051 -10000 0 -0.33 13 13
C13orf34 0.018 0.005 -10000 0 -10000 0 0
NUDC 0.014 0.006 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.033 -10000 0 -0.33 5 5
spindle assembly 0.015 0.005 -10000 0 -10000 0 0
spindle stabilization 0.011 0.019 -10000 0 -0.27 2 2
APC/C/HCDH1 0.013 0.031 -10000 0 -0.36 4 4
MKLP2/PLK1 0.02 0.021 -10000 0 -0.33 2 2
CCNB1 0.012 0.001 -10000 0 -10000 0 0
PPP1CB 0.008 0.042 -10000 0 -0.59 3 3
BTRC 0.01 0.024 -10000 0 -0.58 1 1
ROCK2 0.012 0.069 -10000 0 -0.48 11 11
TUBG1 0.013 0.003 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.025 -10000 0 -0.27 4 4
MLF1IP 0 0.065 -10000 0 -0.44 13 13
INCENP 0.011 0.001 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.004 0.068 -10000 0 -0.58 8 8
SMAD2 0.013 0.023 0.24 1 -0.25 2 3
SMAD3 0.029 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4 0.034 0.032 -10000 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.018 0.046 -10000 0 -0.36 9 9
SMAD2/SMAD2/SMAD4 0.028 0.037 -10000 0 -10000 0 0
PPM1A 0.011 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD4 0.014 0.043 -10000 0 -0.32 8 8
MAP3K1 0.006 0.059 -10000 0 -0.58 6 6
TRAP-1/SMAD4 0.01 0.056 -10000 0 -0.42 10 10
MAPK3 0.01 0.024 -10000 0 -0.58 1 1
MAPK1 0.01 0.024 -10000 0 -0.58 1 1
NUP214 0.011 0 -10000 0 -10000 0 0
CTDSP1 0.01 0.024 -10000 0 -0.58 1 1
CTDSP2 0.011 0 -10000 0 -10000 0 0
CTDSPL 0.011 0 -10000 0 -10000 0 0
KPNB1 0.011 0 -10000 0 -10000 0 0
TGFBRAP1 0.009 0.034 -10000 0 -0.58 2 2
UBE2I 0.011 0 -10000 0 -10000 0 0
NUP153 0.011 0 -10000 0 -10000 0 0
KPNA2 0.011 0 -10000 0 -10000 0 0
PIAS4 0.01 0.024 -10000 0 -0.58 1 1
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.036 0.056 -10000 0 -1.1 1 1
CLOCK 0.013 0.024 -10000 0 -0.58 1 1
TIMELESS/CRY2 0.033 0.054 -10000 0 -1.2 1 1
DEC1/BMAL1 0.007 0.046 -10000 0 -0.33 11 11
ATR 0.009 0.034 -10000 0 -0.58 2 2
NR1D1 0.031 0.059 -10000 0 -1.3 1 1
ARNTL 0.013 0.024 -10000 0 -0.58 1 1
TIMELESS 0.032 0.058 -10000 0 -1.3 1 1
NPAS2 0.012 0.031 -10000 0 -0.52 2 2
CRY2 0.011 0 -10000 0 -10000 0 0
mol:CO -0.011 0.009 0.12 3 -10000 0 3
CHEK1 0.01 0.024 -10000 0 -0.58 1 1
mol:HEME 0.011 0.009 -10000 0 -0.12 3 3
PER1 0.005 0.059 -10000 0 -0.5 8 8
BMAL/CLOCK/NPAS2 0.034 0.031 -10000 0 -0.32 4 4
BMAL1/CLOCK 0.036 0.064 -10000 0 -0.88 2 2
S phase of mitotic cell cycle 0.036 0.056 -10000 0 -1.1 1 1
TIMELESS/CHEK1/ATR 0.037 0.057 -10000 0 -1.2 1 1
mol:NADPH 0.011 0.009 -10000 0 -0.12 3 3
PER1/TIMELESS 0.03 0.066 -10000 0 -0.93 2 2
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.004 0.059 -10000 0 -0.46 10 10
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.01 0.059 -10000 0 -0.37 5 5
CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
AKT1 0.01 0.024 -10000 0 -0.58 1 1
AKT2 0.009 0.036 -10000 0 -0.5 3 3
STXBP4 0.006 0.059 -10000 0 -0.58 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.029 0.056 0.2 6 -0.36 4 10
YWHAZ 0.008 0.042 -10000 0 -0.58 3 3
CALM1 0.011 0 -10000 0 -10000 0 0
YWHAQ 0.011 0 -10000 0 -10000 0 0
TBC1D4 0.013 0.047 -10000 0 -0.42 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.011 0 -10000 0 -10000 0 0
YWHAB 0.011 0 -10000 0 -10000 0 0
SNARE/Synip 0.02 0.038 -10000 0 -0.36 6 6
YWHAG 0.011 0 -10000 0 -10000 0 0
ASIP 0 0.053 -10000 0 -0.46 8 8
PRKCI 0.008 0.042 -10000 0 -0.58 3 3
AS160/CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
RHOQ 0.011 0 -10000 0 -10000 0 0
GYS1 0.022 0.043 -10000 0 -0.47 4 4
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
TRIP10 0.01 0.024 -10000 0 -0.58 1 1
TC10/GTP/CIP4/Exocyst 0.015 0.015 -10000 0 -0.36 1 1
AS160/14-3-3 0.033 0.034 -10000 0 -0.35 2 2
VAMP2 0.011 0 -10000 0 -10000 0 0
SLC2A4 0.029 0.061 0.2 6 -0.4 4 10
STX4 0.011 0 -10000 0 -10000 0 0
GSK3B 0.018 0.045 -10000 0 -0.58 3 3
SFN 0.005 0.055 -10000 0 -0.47 8 8
LNPEP 0.004 0.068 -10000 0 -0.58 8 8
YWHAE 0.011 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.035 0.051 -10000 0 -0.41 6 6
adherens junction organization 0.033 0.033 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.049 -10000 0 -0.48 3 3
FMN1 0.028 0.049 -10000 0 -0.42 2 2
mol:IP3 0.03 0.038 -10000 0 -0.3 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.03 -10000 0 -0.37 2 2
CTNNB1 0.011 0.001 -10000 0 -10000 0 0
AKT1 0.035 0.043 -10000 0 -0.7 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.039 -10000 0 -0.56 2 2
CTNND1 0.012 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.032 0.036 -10000 0 -0.39 3 3
VASP 0.033 0.029 -10000 0 -0.46 1 1
ZYX 0.032 0.038 -10000 0 -0.74 1 1
JUB 0.033 0.029 -10000 0 -0.46 1 1
EGFR(dimer) 0.03 0.043 -10000 0 -0.4 3 3
E-cadherin/beta catenin-gamma catenin 0.021 0.021 -10000 0 -0.34 2 2
mol:PI-3-4-5-P3 0.03 0.038 -10000 0 -0.3 6 6
PIK3CA 0.01 0.034 -10000 0 -0.58 2 2
PI3K 0.031 0.038 -10000 0 -0.31 6 6
FYN 0.032 0.053 -10000 0 -0.33 7 7
mol:Ca2+ 0.03 0.037 -10000 0 -0.3 6 6
JUP 0.01 0.024 -10000 0 -0.59 1 1
PIK3R1 0.009 0.042 -10000 0 -0.58 3 3
mol:DAG 0.03 0.038 -10000 0 -0.3 6 6
CDH1 0.01 0.024 -10000 0 -0.58 1 1
RhoA/GDP 0.038 0.053 -10000 0 -0.49 4 4
establishment of polarity of embryonic epithelium 0.033 0.028 -10000 0 -0.45 1 1
SRC 0.01 0.024 -10000 0 -0.58 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
RHOA 0.01 0.024 -10000 0 -0.58 1 1
EGFR 0.005 0.058 -10000 0 -0.53 7 7
CASR 0.029 0.044 -10000 0 -0.45 1 1
RhoA/GTP -0.004 0.035 -10000 0 -0.48 2 2
AKT2 0.034 0.047 -10000 0 -0.58 2 2
actin cable formation 0.033 0.048 -10000 0 -0.4 2 2
apoptosis -0.033 0.047 0.37 6 -10000 0 6
CTNNA1 0.01 0.034 -10000 0 -0.59 2 2
mol:GDP 0.033 0.052 -10000 0 -0.52 3 3
PIP5K1A 0.032 0.037 -10000 0 -0.4 3 3
PLCG1 0.03 0.038 -10000 0 -0.31 6 6
Rac1/GTP -0.005 0.035 -10000 0 -0.37 3 3
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex -0.002 0.029 -9999 0 -0.34 3 3
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.021 -9999 0 -0.26 2 2
AP2 0.015 0.03 -9999 0 -0.34 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.016 0.002 -9999 0 -10000 0 0
CLTB 0.01 0.031 -9999 0 -0.52 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.014 -9999 0 -0.26 1 1
CD4 -0.013 0.12 -9999 0 -0.56 26 26
CLTA 0.011 0 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
ARFGAP1 0.007 0.026 -9999 0 -0.36 3 3
mol:PI-4-5-P2 -0.001 0.019 -9999 0 -0.33 2 2
ARF1/GTP -0.001 0.012 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.02 0.025 -9999 0 -0.3 3 3
mol:Choline -0.001 0.019 -9999 0 -0.32 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.011 0.019 -9999 0 -0.45 1 1
DDEF1 -0.001 0.019 -9999 0 -0.33 2 2
ARF1/GDP 0.005 0.02 -9999 0 -0.27 3 3
AP2M1 0.011 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.014 0.01 -9999 0 -0.22 1 1
Rac/GTP 0.01 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.02 0.021 -9999 0 -0.25 3 3
ARFIP2 0.01 0.003 -9999 0 -10000 0 0
COPA 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0.01 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.008 0.011 -9999 0 -0.26 1 1
GGA3 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.011 -9999 0 -10000 0 0
AP2A1 0.008 0.041 -9999 0 -0.49 4 4
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.021 0.028 -9999 0 -0.61 1 1
ARF1/GDP/Membrin 0.015 0.011 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.015 0.002 -9999 0 -10000 0 0
CYTH2 0.012 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.016 0.011 -9999 0 -0.25 1 1
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.009 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.018 0.049 -9999 0 -0.4 1 1
PLD2 -0.001 0.019 -9999 0 -0.32 2 2
ARF-GAP1/v-SNARE 0.007 0.026 -9999 0 -0.36 3 3
PIP5K1A -0.001 0.019 -9999 0 -0.33 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.002 0.019 -9999 0 -0.28 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.019 -9999 0 -0.32 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.026 -9999 0 -0.36 3 3
GOSR2 -0.001 0.008 -9999 0 -10000 0 0
USO1 -0.005 0.049 -9999 0 -0.48 6 6
GBF1 -0.001 0.019 -9999 0 -0.42 1 1
ARF1/GTP/Arfaptin 2 0.016 0.011 -9999 0 -0.25 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.006 0.077 -9999 0 -0.33 30 30
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.013 0.04 -9999 0 -0.42 5 5
FBXW11 0.011 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
CHUK 0.007 0.048 -9999 0 -0.58 4 4
NF kappa B2 p100/RelB 0.029 0.051 -9999 0 -0.42 6 6
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
MAP3K14 0.01 0.024 -9999 0 -0.58 1 1
NF kappa B1 p50/RelB 0.014 0.032 -9999 0 -0.37 4 4
RELB 0.009 0.036 -9999 0 -0.5 3 3
NFKB2 0.01 0.031 -9999 0 -0.52 2 2
NF kappa B2 p52/RelB 0.013 0.038 -9999 0 -0.49 3 3
regulation of B cell activation 0.013 0.038 -9999 0 -0.49 3 3
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.022 0.022 -9999 0 -0.36 2 2
E-cadherin/beta catenin 0.016 0.018 -9999 0 -0.42 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
JUP 0.01 0.024 -9999 0 -0.58 1 1
CDH1 0.01 0.024 -9999 0 -0.58 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 606 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.T9.A92H TCGA.SS.A7HO TCGA.RU.A8FL TCGA.QG.A5Z2
109_MAP3K5 0.044 0.044 -0.42 0.044
47_PPARGC1A 0.011 0.011 0.011 0.011
105_BMP4 0.011 0.011 0.011 0.011
105_BMP6 0.011 0.011 0.011 0.011
105_BMP7 -0.58 0.011 -0.46 0.011
105_BMP2 0.011 0.011 -0.58 0.011
131_RELN/VLDLR 0.03 0.022 0.03 0.03
30_TGFB1/TGF beta receptor Type II 0.011 0.011 -0.58 0.011
84_STAT5B -0.0062 0.039 -0.28 -0.14
84_STAT5A -0.0062 0.039 -0.28 -0.14
Methods & Data
Input

  • Expression Data Normalization = Tumor samples 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/COADREAD-TP/11493425/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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