PARADIGM pathway analysis of mRNASeq expression data
Prostate Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C11R6PZ2
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C11R6PZ2
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 56 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 117
Glypican 2 network 108
FOXM1 transcription factor network 91
Angiopoietin receptor Tie2-mediated signaling 88
Aurora B signaling 81
Signaling mediated by p38-alpha and p38-beta 67
Endothelins 64
Syndecan-1-mediated signaling events 60
IL23-mediated signaling events 60
IL4-mediated signaling events 58
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 497 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 497 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Ephrin A reverse signaling 0.2354 117 822 7 -0.11 0 1000 -1000 -0.019 -1000
Glypican 2 network 0.2173 108 434 4 -0.14 -0.11 1000 -1000 -0.023 -1000
FOXM1 transcription factor network 0.1831 91 4674 51 -0.42 0.013 1000 -1000 -0.18 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1771 88 7769 88 -0.32 0.06 1000 -1000 -0.088 -1000
Aurora B signaling 0.1630 81 5489 67 -0.26 0.013 1000 -1000 -0.053 -1000
Signaling mediated by p38-alpha and p38-beta 0.1348 67 2990 44 -0.18 0.013 1000 -1000 -0.041 -1000
Endothelins 0.1288 64 6220 96 -0.17 0.013 1000 -1000 -0.071 -1000
Syndecan-1-mediated signaling events 0.1207 60 2042 34 -0.31 0.013 1000 -1000 -0.043 -1000
IL23-mediated signaling events 0.1207 60 3605 60 -0.41 0.013 1000 -1000 -0.17 -1000
IL4-mediated signaling events 0.1167 58 5279 91 -0.61 0.51 1000 -1000 -0.15 -1000
Glucocorticoid receptor regulatory network 0.1167 58 6707 114 -0.52 0.28 1000 -1000 -0.069 -1000
TCGA08_retinoblastoma 0.1147 57 458 8 -0.12 0.029 1000 -1000 -0.012 -1000
Signaling events mediated by the Hedgehog family 0.0986 49 2559 52 -0.09 0.088 1000 -1000 -0.045 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0986 49 3824 78 -0.17 0.17 1000 -1000 -0.05 -1000
Aurora C signaling 0.0966 48 340 7 -0.18 0.008 1000 -1000 -0.024 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0946 47 3212 68 -0.26 0.077 1000 -1000 -0.11 -1000
Thromboxane A2 receptor signaling 0.0926 46 4882 105 -0.12 0.033 1000 -1000 -0.06 -1000
Glypican 1 network 0.0905 45 2177 48 -0.2 0.023 1000 -1000 -0.033 -1000
Ras signaling in the CD4+ TCR pathway 0.0905 45 781 17 -0.098 0.018 1000 -1000 -0.032 -1000
Integrins in angiogenesis 0.0865 43 3633 84 -0.22 0.026 1000 -1000 -0.083 -1000
IL6-mediated signaling events 0.0865 43 3236 75 -0.2 0.05 1000 -1000 -0.064 -1000
FOXA2 and FOXA3 transcription factor networks 0.0825 41 1887 46 -0.22 0.02 1000 -1000 -0.084 -1000
PLK1 signaling events 0.0825 41 3516 85 -0.21 0.03 1000 -1000 -0.037 -1000
amb2 Integrin signaling 0.0805 40 3320 82 -0.31 0.018 1000 -1000 -0.065 -1000
Reelin signaling pathway 0.0785 39 2211 56 -0.18 0.032 1000 -1000 -0.074 -1000
LPA receptor mediated events 0.0785 39 4014 102 -0.31 0.026 1000 -1000 -0.073 -1000
HIF-1-alpha transcription factor network 0.0724 36 2746 76 -0.22 0.049 1000 -1000 -0.16 -1000
S1P1 pathway 0.0724 36 1306 36 -0.19 0.013 1000 -1000 -0.051 -1000
BMP receptor signaling 0.0664 33 2711 81 -0.16 0.046 1000 -1000 -0.077 -1000
Signaling events mediated by PRL 0.0664 33 1130 34 -0.11 0.051 1000 -1000 -0.033 -1000
JNK signaling in the CD4+ TCR pathway 0.0644 32 560 17 -0.12 0.019 1000 -1000 -0.032 -1000
Signaling events regulated by Ret tyrosine kinase 0.0644 32 2640 82 -0.1 0.013 1000 -1000 -0.071 -1000
S1P5 pathway 0.0644 32 552 17 -0.082 0.067 1000 -1000 -0.029 -1000
TCGA08_p53 0.0644 32 230 7 -0.082 0.045 1000 -1000 -0.013 -1000
Nongenotropic Androgen signaling 0.0644 32 1705 52 -0.1 0.04 1000 -1000 -0.046 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0644 32 3890 120 -0.25 0.075 1000 -1000 -0.069 -1000
Osteopontin-mediated events 0.0624 31 1190 38 -0.081 0.013 1000 -1000 -0.09 -1000
Calcium signaling in the CD4+ TCR pathway 0.0624 31 979 31 -0.16 0.013 1000 -1000 -0.056 -1000
IL12-mediated signaling events 0.0604 30 2645 87 -0.21 0.015 1000 -1000 -0.12 -1000
Wnt signaling 0.0584 29 208 7 -0.084 0.013 1000 -1000 -0.028 -1000
EPHB forward signaling 0.0563 28 2418 85 -0.14 0.089 1000 -1000 -0.078 -1000
S1P4 pathway 0.0563 28 710 25 -0.082 0.02 1000 -1000 -0.031 -1000
Noncanonical Wnt signaling pathway 0.0543 27 715 26 -0.084 0.013 1000 -1000 -0.043 -1000
Aurora A signaling 0.0543 27 1660 60 -0.2 0.026 1000 -1000 -0.031 -1000
IL27-mediated signaling events 0.0543 27 1397 51 -0.34 0.028 1000 -1000 -0.068 -1000
EGFR-dependent Endothelin signaling events 0.0543 27 575 21 -0.091 0.02 1000 -1000 -0.067 -1000
Rapid glucocorticoid signaling 0.0543 27 554 20 -0.11 0.018 1000 -1000 -0.016 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0523 26 898 34 -0.087 0.013 1000 -1000 -0.035 -1000
p75(NTR)-mediated signaling 0.0523 26 3318 125 -0.15 0.04 1000 -1000 -0.085 -1000
Effects of Botulinum toxin 0.0523 26 694 26 -0.095 0.014 1000 -1000 -0.061 -1000
BCR signaling pathway 0.0523 26 2580 99 -0.15 0.042 1000 -1000 -0.076 -1000
Syndecan-4-mediated signaling events 0.0523 26 1792 67 -0.31 0.02 1000 -1000 -0.062 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0503 25 1385 54 -0.18 0.026 1000 -1000 -0.09 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0503 25 2153 85 -0.12 0.016 1000 -1000 -0.061 -1000
Signaling events mediated by PTP1B 0.0503 25 1939 76 -0.27 0.048 1000 -1000 -0.067 -1000
PDGFR-alpha signaling pathway 0.0503 25 1141 44 -0.16 0.023 1000 -1000 -0.057 -1000
Visual signal transduction: Cones 0.0483 24 935 38 -0.091 0.012 1000 -1000 -0.048 -1000
TCR signaling in naïve CD8+ T cells 0.0483 24 2296 93 -0.068 0.025 1000 -1000 -0.068 -1000
ErbB4 signaling events 0.0463 23 1613 69 -0.16 0.042 1000 -1000 -0.075 -1000
Regulation of nuclear SMAD2/3 signaling 0.0443 22 3081 136 -0.51 0.06 1000 -1000 -0.061 -1000
a4b1 and a4b7 Integrin signaling 0.0443 22 110 5 -0.014 0.001 1000 -1000 -0.013 -1000
Presenilin action in Notch and Wnt signaling 0.0443 22 1365 61 -0.22 0.04 1000 -1000 -0.052 -1000
FAS signaling pathway (CD95) 0.0443 22 1034 47 -0.26 0.02 1000 -1000 -0.038 -1000
Canonical Wnt signaling pathway 0.0443 22 1162 51 -0.22 0.11 1000 -1000 -0.048 -1000
S1P3 pathway 0.0443 22 924 42 -0.078 0.02 1000 -1000 -0.028 -1000
Visual signal transduction: Rods 0.0443 22 1160 52 -0.11 0.013 1000 -1000 -0.07 -1000
Arf6 signaling events 0.0402 20 1299 62 -0.12 0.017 1000 -1000 -0.042 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0402 20 764 37 -0.1 0.029 1000 -1000 -0.04 -1000
Plasma membrane estrogen receptor signaling 0.0402 20 1798 86 -0.19 0.021 1000 -1000 -0.076 -1000
Fc-epsilon receptor I signaling in mast cells 0.0382 19 1931 97 -0.1 0.026 1000 -1000 -0.075 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0382 19 2426 125 -0.084 0.036 1000 -1000 -0.084 -1000
Syndecan-2-mediated signaling events 0.0362 18 1261 69 -0.072 0.031 1000 -1000 -0.033 -1000
IL2 signaling events mediated by STAT5 0.0362 18 411 22 -0.081 0.033 1000 -1000 -0.05 -1000
ErbB2/ErbB3 signaling events 0.0342 17 1114 65 -0.16 0.02 1000 -1000 -0.06 -1000
Ephrin B reverse signaling 0.0342 17 826 48 -0.14 0.05 1000 -1000 -0.053 -1000
Regulation of p38-alpha and p38-beta 0.0342 17 961 54 -0.17 0.034 1000 -1000 -0.051 -1000
Coregulation of Androgen receptor activity 0.0322 16 1223 76 -0.16 0.025 1000 -1000 -0.031 -1000
Cellular roles of Anthrax toxin 0.0322 16 661 39 -0.037 0.014 1000 -1000 -0.018 -1000
EPO signaling pathway 0.0322 16 895 55 -0.065 0.019 1000 -1000 -0.086 -1000
Insulin Pathway 0.0322 16 1223 74 -0.22 0.027 1000 -1000 -0.074 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0322 16 552 33 -0.13 0.034 1000 -1000 -0.035 -1000
BARD1 signaling events 0.0302 15 891 57 -0.038 0.033 1000 -1000 -0.05 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0302 15 423 28 -0.08 0.034 1000 -1000 -0.029 -1000
HIF-2-alpha transcription factor network 0.0302 15 651 43 -0.089 0.022 1000 -1000 -0.062 -1000
Signaling mediated by p38-gamma and p38-delta 0.0302 15 227 15 -0.011 0.015 1000 -1000 -0.03 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0282 14 731 52 -0.1 0.027 1000 -1000 -0.048 -1000
Retinoic acid receptors-mediated signaling 0.0282 14 833 58 -0.075 0.027 1000 -1000 -0.057 -1000
IL2 signaling events mediated by PI3K 0.0282 14 844 58 -0.18 0.028 1000 -1000 -0.073 -1000
LPA4-mediated signaling events 0.0262 13 165 12 -0.029 0.018 1000 -1000 -0.022 -1000
Caspase cascade in apoptosis 0.0262 13 1002 74 -0.06 0.03 1000 -1000 -0.03 -1000
Nectin adhesion pathway 0.0262 13 854 63 -0.084 0.027 1000 -1000 -0.063 -1000
Syndecan-3-mediated signaling events 0.0262 13 464 35 -0.073 0.04 1000 -1000 -0.042 -1000
IGF1 pathway 0.0262 13 797 57 -0.047 0.027 1000 -1000 -0.074 -1000
Signaling events mediated by HDAC Class III 0.0241 12 501 40 -0.13 0.025 1000 -1000 -0.024 -1000
IL1-mediated signaling events 0.0241 12 801 62 -0.087 0.059 1000 -1000 -0.079 -1000
Class I PI3K signaling events 0.0241 12 920 73 -0.1 0.034 1000 -1000 -0.052 -1000
Regulation of Telomerase 0.0241 12 1315 102 -0.21 0.039 1000 -1000 -0.087 -1000
VEGFR1 specific signals 0.0241 12 686 56 -0.056 0.029 1000 -1000 -0.049 -1000
Hedgehog signaling events mediated by Gli proteins 0.0201 10 675 65 -0.29 0.052 1000 -1000 -0.056 -1000
TCGA08_rtk_signaling 0.0201 10 281 26 -0.036 0.043 1000 -1000 -0.018 -1000
TRAIL signaling pathway 0.0181 9 454 48 -0.037 0.04 1000 -1000 -0.057 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0181 9 821 83 -0.097 0.055 1000 -1000 -0.063 -1000
Regulation of Androgen receptor activity 0.0181 9 679 70 -0.1 0.064 1000 -1000 -0.052 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0161 8 362 45 -0.026 0.058 1000 -1000 -0.081 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0161 8 645 74 -0.18 0.054 1000 -1000 -0.073 -1000
p38 MAPK signaling pathway 0.0161 8 378 44 -0.054 0.026 1000 -1000 -0.056 -1000
IFN-gamma pathway 0.0141 7 496 68 -0.085 0.052 1000 -1000 -0.082 -1000
Ceramide signaling pathway 0.0141 7 578 76 -0.058 0.04 1000 -1000 -0.035 -1000
Paxillin-dependent events mediated by a4b1 0.0141 7 265 36 -0.024 0.026 1000 -1000 -0.06 -1000
Atypical NF-kappaB pathway 0.0141 7 220 31 -0.033 0.043 1000 -1000 -0.033 -1000
PLK2 and PLK4 events 0.0121 6 20 3 0.007 0.013 1000 -1000 -0.019 -1000
mTOR signaling pathway 0.0121 6 368 53 -0.016 0.027 1000 -1000 -0.055 -1000
ceramide signaling pathway 0.0121 6 296 49 -0.026 0.04 1000 -1000 -0.037 -1000
Class IB PI3K non-lipid kinase events 0.0121 6 18 3 -0.006 0.006 1000 -1000 -0.017 -1000
Canonical NF-kappaB pathway 0.0101 5 213 39 -0.026 0.062 1000 -1000 -0.069 -1000
Signaling events mediated by HDAC Class II 0.0101 5 446 75 -0.045 0.036 1000 -1000 -0.041 -1000
FoxO family signaling 0.0101 5 353 64 -0.076 0.082 1000 -1000 -0.067 -1000
Arf6 trafficking events 0.0080 4 289 71 -0.091 0.041 1000 -1000 -0.065 -1000
Circadian rhythm pathway 0.0060 3 72 22 -0.022 0.04 1000 -1000 -0.042 -1000
Arf6 downstream pathway 0.0060 3 144 43 -0.022 0.025 1000 -1000 -0.033 -1000
Insulin-mediated glucose transport 0.0060 3 119 32 -0.035 0.029 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 0.0060 3 346 97 -0.084 0.044 1000 -1000 -0.075 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 65 23 -0.014 0.042 1000 -1000 -0.043 -1000
E-cadherin signaling in keratinocytes 0.0040 2 102 43 -0.038 0.041 1000 -1000 -0.04 -1000
Class I PI3K signaling events mediated by Akt 0.0020 1 75 68 -0.035 0.046 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class I 0.0020 1 160 104 -0.027 0.052 1000 -1000 -0.058 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 129 76 -0.009 0.056 1000 -1000 -0.073 -1000
E-cadherin signaling events 0.0020 1 6 5 0.011 0.026 1000 -1000 -0.02 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 10 27 -0.001 0.034 1000 -1000 -0.047 -1000
Arf1 pathway 0.0000 0 29 54 -0.001 0.031 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0.0000 0 9 13 0 0.038 1000 -1000 -0.027 -1000
Total NA 3275 184755 7203 -17 5 131000 -131000 -7.4 -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 -0.088 0.16 -9999 0 -0.31 160 160
EFNA5 -0.04 0.15 -9999 0 -0.47 55 55
FYN -0.073 0.15 -9999 0 -0.28 160 160
neuron projection morphogenesis -0.088 0.16 -9999 0 -0.31 160 160
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.088 0.16 -9999 0 -0.31 160 160
EPHA5 -0.11 0.21 -9999 0 -0.47 127 127
Glypican 2 network

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
MDK -0.011 0.12 -9999 0 -0.56 21 21
GPC2 -0.14 0.26 -9999 0 -0.57 131 131
GPC2/Midkine -0.11 0.21 -9999 0 -0.44 141 141
neuron projection morphogenesis -0.11 0.21 -9999 0 -0.44 141 141
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.28 0.57 -9999 0 -1.1 101 101
PLK1 -0.12 0.23 -9999 0 -0.45 151 151
BIRC5 -0.14 0.24 -9999 0 -0.46 141 141
HSPA1B -0.29 0.57 -9999 0 -1.1 109 109
MAP2K1 0.011 0.04 -9999 0 -10000 0 0
BRCA2 -0.3 0.59 -9999 0 -1.2 115 115
FOXM1 -0.42 0.83 -9999 0 -1.6 126 126
XRCC1 -0.28 0.57 -9999 0 -1.1 110 110
FOXM1B/p19 -0.4 0.5 -9999 0 -1.1 128 128
Cyclin D1/CDK4 -0.25 0.52 -9999 0 -1 104 104
CDC2 -0.3 0.6 -9999 0 -1.2 124 124
TGFA -0.25 0.52 -9999 0 -1 107 107
SKP2 -0.29 0.58 -9999 0 -1.1 117 117
CCNE1 0.005 0.066 -9999 0 -0.59 6 6
CKS1B -0.28 0.57 -9999 0 -1.1 110 110
RB1 -0.16 0.18 -9999 0 -0.5 37 37
FOXM1C/SP1 -0.35 0.66 -9999 0 -1.3 125 125
AURKB -0.12 0.23 -9999 0 -0.45 156 156
CENPF -0.33 0.62 -9999 0 -1.2 147 147
CDK4 0.012 0.015 -9999 0 -10000 0 0
MYC -0.25 0.52 -9999 0 -0.99 118 118
CHEK2 0.01 0.049 -9999 0 -0.63 1 1
ONECUT1 -0.28 0.55 -9999 0 -1.1 114 114
CDKN2A -0.11 0.24 -9999 0 -0.57 106 106
LAMA4 -0.29 0.58 -9999 0 -1.1 112 112
FOXM1B/HNF6 -0.35 0.67 -9999 0 -1.3 117 117
FOS -0.36 0.64 -9999 0 -1.2 145 145
SP1 0.013 0.005 -9999 0 -10000 0 0
CDC25B -0.28 0.57 -9999 0 -1.1 103 103
response to radiation -0.003 0.036 -9999 0 -10000 0 0
CENPB -0.28 0.57 -9999 0 -1.1 110 110
CENPA -0.36 0.63 -9999 0 -1.2 149 149
NEK2 -0.36 0.63 -9999 0 -1.2 149 149
HIST1H2BA -0.29 0.57 -9999 0 -1.1 110 110
CCNA2 -0.083 0.22 -9999 0 -0.59 80 80
EP300 0.01 0.037 -9999 0 -0.47 3 3
CCNB1/CDK1 -0.35 0.67 -9999 0 -1.4 114 114
CCNB2 -0.3 0.6 -9999 0 -1.2 112 112
CCNB1 -0.31 0.61 -9999 0 -1.2 114 114
ETV5 -0.3 0.6 -9999 0 -1.2 122 122
ESR1 -0.29 0.58 -9999 0 -1.1 115 115
CCND1 -0.26 0.53 -9999 0 -1 107 107
GSK3A 0.012 0.04 -9999 0 -0.5 1 1
Cyclin A-E1/CDK1-2 -0.038 0.16 -9999 0 -0.4 81 81
CDK2 0.012 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.043 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.52 -9999 0 -1.2 129 129
GAS1 -0.32 0.61 -9999 0 -1.2 124 124
MMP2 -0.29 0.58 -9999 0 -1.1 111 111
RB1/FOXM1C -0.28 0.57 -9999 0 -1.1 113 113
CREBBP 0.013 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.18 0.41 -10000 0 -0.79 148 148
NCK1/PAK1/Dok-R -0.12 0.18 -10000 0 -0.39 148 148
NCK1/Dok-R -0.24 0.48 -10000 0 -0.95 148 148
PIK3CA 0.011 0.037 -10000 0 -0.47 3 3
mol:beta2-estradiol 0.06 0.11 0.23 146 -10000 0 146
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0.002 -10000 0 -10000 0 0
Rac/GDP 0.01 0 -10000 0 -10000 0 0
F2 0.033 0.17 0.24 126 -0.5 29 155
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.22 0.45 -10000 0 -0.89 148 148
FN1 -0.003 0.09 -10000 0 -0.49 16 16
PLD2 -0.25 0.49 -10000 0 -0.98 148 148
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
GRB14 -0.096 0.23 -10000 0 -0.57 93 93
ELK1 -0.21 0.44 -10000 0 -0.88 148 148
GRB7 0.012 0.026 -10000 0 -0.57 1 1
PAK1 0.006 0.06 -10000 0 -0.47 8 8
Tie2/Ang1/alpha5/beta1 Integrin -0.24 0.48 -10000 0 -0.96 148 148
CDKN1A -0.1 0.28 -10000 0 -0.59 67 67
ITGA5 -0.002 0.086 -10000 0 -0.47 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.24 0.48 -10000 0 -0.95 148 148
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO -0.12 0.31 -10000 0 -0.6 148 148
PLG -0.27 0.49 -10000 0 -1 148 148
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.17 0.39 -10000 0 -0.77 148 148
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.053 -10000 0 -0.47 6 6
ANGPT2 -0.11 0.23 -10000 0 -0.56 56 56
BMX -0.27 0.51 -10000 0 -1 148 148
ANGPT1 -0.32 0.55 -10000 0 -1.2 147 147
tube development -0.12 0.3 -10000 0 -0.58 136 136
ANGPT4 0.01 0.027 -10000 0 -0.57 1 1
response to hypoxia -0.016 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.31 0.52 -10000 0 -1.1 148 148
alpha5/beta1 Integrin 0.008 0.062 -10000 0 -0.33 16 16
FGF2 -0.024 0.13 -10000 0 -0.47 38 38
STAT5A (dimer) -0.13 0.34 -10000 0 -0.65 134 134
mol:L-citrulline -0.12 0.31 -10000 0 -0.6 148 148
AGTR1 -0.11 0.24 -10000 0 -0.55 113 113
MAPK14 -0.24 0.48 -10000 0 -0.94 148 148
Tie2/SHP2 -0.07 0.26 -10000 0 -1.2 19 19
TEK -0.083 0.29 -10000 0 -1.4 19 19
RPS6KB1 -0.17 0.39 -10000 0 -0.76 148 148
Angiotensin II/AT1 -0.081 0.17 -10000 0 -0.4 113 113
Tie2/Ang1/GRB2 -0.26 0.51 -10000 0 -1 148 148
MAPK3 -0.22 0.46 -10000 0 -0.91 148 148
MAPK1 -0.22 0.46 -10000 0 -0.91 148 148
Tie2/Ang1/GRB7 -0.26 0.51 -10000 0 -1 148 148
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.25 0.5 -10000 0 -0.99 148 148
PI3K -0.21 0.46 -10000 0 -0.9 148 148
FES -0.24 0.48 -10000 0 -0.95 148 148
Crk/Dok-R -0.24 0.48 -10000 0 -0.95 148 148
Tie2/Ang1/ABIN2 -0.26 0.51 -10000 0 -1 148 148
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.16 0.37 -10000 0 -0.71 148 148
STAT5A 0.013 0.022 -10000 0 -0.47 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.17 0.39 -10000 0 -0.76 148 148
Tie2/Ang2 -0.17 0.39 -10000 0 -0.76 134 134
Tie2/Ang1 -0.27 0.54 -10000 0 -1.1 148 148
FOXO1 -0.15 0.37 -10000 0 -0.71 148 148
ELF1 0.008 0.067 -10000 0 -0.5 8 8
ELF2 -0.25 0.49 -10000 0 -0.97 148 148
mol:Choline -0.24 0.47 -10000 0 -0.94 148 148
cell migration -0.068 0.1 -10000 0 -0.22 144 144
FYN -0.14 0.34 -10000 0 -0.65 135 135
DOK2 0.009 0.05 -10000 0 -0.55 4 4
negative regulation of cell cycle -0.09 0.26 -10000 0 -0.53 74 74
ETS1 -0.05 0.12 -10000 0 -0.6 5 5
PXN -0.13 0.33 -10000 0 -0.63 148 148
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 -0.14 0.35 -10000 0 -0.67 148 148
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.084 0.17 -10000 0 -0.55 37 37
MAPKKK cascade -0.24 0.47 -10000 0 -0.94 148 148
RASA1 0.011 0.03 -10000 0 -0.47 2 2
Tie2/Ang1/Shc -0.26 0.51 -10000 0 -1 148 148
NCK1 0.012 0.026 -10000 0 -0.57 1 1
vasculogenesis -0.1 0.28 -10000 0 -0.54 148 148
mol:Phosphatidic acid -0.24 0.47 -10000 0 -0.94 148 148
mol:Angiotensin II 0.001 0.003 -10000 0 -10000 0 0
mol:NADP -0.12 0.31 -10000 0 -0.6 148 148
Rac1/GTP -0.21 0.33 -10000 0 -0.71 148 148
MMP2 -0.25 0.5 -10000 0 -1 148 148
Aurora B 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
Condensin I complex -0.11 0.19 -9999 0 -0.38 153 153
STMN1 -0.13 0.21 -9999 0 -0.42 166 166
Aurora B/RasGAP/Survivin -0.21 0.31 -9999 0 -0.57 203 203
Chromosomal passenger complex/Cul3 protein complex -0.09 0.17 -9999 0 -0.31 154 154
BIRC5 -0.21 0.29 -9999 0 -0.58 184 184
DES -0.17 0.29 -9999 0 -0.75 91 91
Aurora C/Aurora B/INCENP -0.09 0.16 -9999 0 -0.32 169 169
Aurora B/TACC1 -0.11 0.18 -9999 0 -0.36 169 169
Aurora B/PP2A -0.12 0.2 -9999 0 -0.41 166 166
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.021 0.052 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.004 -9999 0 -10000 0 0
NDC80 -0.12 0.2 -9999 0 -0.41 170 170
Cul3 protein complex 0.01 0.069 -9999 0 -0.27 29 29
KIF2C -0.075 0.12 -9999 0 -0.26 123 123
PEBP1 0.008 0.006 -9999 0 -10000 0 0
KIF20A -0.21 0.29 -9999 0 -0.58 188 188
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.12 0.2 -9999 0 -0.41 166 166
SEPT1 -0.001 0.09 -9999 0 -0.57 12 12
SMC2 0.012 0.026 -9999 0 -0.57 1 1
SMC4 0.012 0.026 -9999 0 -0.57 1 1
NSUN2/NPM1/Nucleolin -0.047 0.1 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 -9999 0 -10000 0 0
H3F3B -0.063 0.11 -9999 0 -0.22 166 166
AURKB -0.18 0.28 -9999 0 -0.58 166 166
AURKC 0.008 0.055 -9999 0 -0.53 5 5
CDCA8 -0.057 0.19 -9999 0 -0.59 55 55
cytokinesis -0.14 0.24 -9999 0 -0.46 153 153
Aurora B/Septin1 -0.16 0.22 -9999 0 -0.48 144 144
AURKA -0.028 0.15 -9999 0 -0.58 36 36
INCENP 0.007 0.008 -9999 0 -10000 0 0
KLHL13 -0.014 0.11 -9999 0 -0.47 28 28
BUB1 -0.12 0.25 -9999 0 -0.58 115 115
hSgo1/Aurora B/Survivin -0.26 0.37 -9999 0 -0.66 210 210
EVI5 0.012 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.15 0.22 -9999 0 -0.49 120 120
SGOL1 -0.11 0.24 -9999 0 -0.57 107 107
CENPA -0.14 0.19 -9999 0 -0.36 181 181
NCAPG -0.18 0.28 -9999 0 -0.57 168 168
Aurora B/HC8 Proteasome -0.12 0.2 -9999 0 -0.41 166 166
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.12 0.2 -9999 0 -0.41 166 166
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.15 0.26 -9999 0 -0.57 135 135
NPM1 -0.062 0.11 -9999 0 -0.23 91 91
RASA1 0.011 0.03 -9999 0 -0.47 2 2
KLHL9 0.012 0.022 -9999 0 -0.47 1 1
mitotic prometaphase -0.006 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.12 0.2 -9999 0 -0.41 166 166
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.15 0.26 -9999 0 -0.49 147 147
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
NSUN2 -0.062 0.11 -9999 0 -0.24 29 29
MYLK -0.15 0.21 -9999 0 -0.35 226 226
KIF23 -0.029 0.15 -9999 0 -0.58 33 33
VIM -0.12 0.2 -9999 0 -0.41 166 166
RACGAP1 0.003 0.065 -9999 0 -0.59 6 6
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.062 0.11 -9999 0 -10000 0 0
Chromosomal passenger complex -0.15 0.22 -9999 0 -0.41 186 186
Chromosomal passenger complex/EVI5 -0.22 0.32 -9999 0 -0.64 157 157
TACC1 0.001 0.077 -9999 0 -0.47 13 13
PPP2R5D 0.013 0.001 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.18 0.41 -9999 0 -1 95 95
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.053 0.14 -9999 0 -0.38 23 23
ATF2/c-Jun -0.051 0.17 -9999 0 -0.56 30 30
MAPK11 -0.063 0.16 -9999 0 -0.46 31 31
MITF -0.064 0.18 -9999 0 -0.37 113 113
MAPKAPK5 -0.06 0.17 -9999 0 -0.35 112 112
KRT8 -0.06 0.17 -9999 0 -0.35 113 113
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.084 0.22 -9999 0 -0.44 117 117
CEBPB -0.06 0.17 -9999 0 -0.35 112 112
SLC9A1 -0.06 0.17 -9999 0 -0.35 112 112
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.076 0.21 -9999 0 -0.64 30 30
p38alpha-beta/MNK1 -0.056 0.18 -9999 0 -0.51 26 26
JUN -0.05 0.17 -9999 0 -0.55 30 30
PPARGC1A -0.17 0.28 -9999 0 -0.58 126 126
USF1 -0.06 0.17 -9999 0 -0.35 112 112
RAB5/GDP/GDI1 -0.04 0.12 -9999 0 -0.39 20 20
NOS2 -0.11 0.3 -9999 0 -1 34 34
DDIT3 -0.06 0.17 -9999 0 -0.35 112 112
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.056 0.16 -9999 0 -0.44 32 32
p38alpha-beta/HBP1 -0.056 0.18 -9999 0 -0.51 26 26
CREB1 -0.065 0.19 -9999 0 -0.38 113 113
RAB5/GDP 0.01 0 -9999 0 -10000 0 0
EIF4E -0.046 0.16 -9999 0 -0.52 19 19
RPS6KA4 -0.061 0.17 -9999 0 -0.36 113 113
PLA2G4A -0.061 0.18 -9999 0 -0.54 39 39
GDI1 -0.06 0.17 -9999 0 -0.35 112 112
TP53 -0.081 0.21 -9999 0 -0.44 113 113
RPS6KA5 -0.068 0.19 -9999 0 -0.37 115 115
ESR1 -0.072 0.2 -9999 0 -0.39 113 113
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.064 0.18 -9999 0 -0.36 114 114
MEF2A -0.062 0.18 -9999 0 -0.36 113 113
EIF4EBP1 -0.071 0.19 -9999 0 -0.39 114 114
KRT19 -0.091 0.22 -9999 0 -0.43 115 115
ELK4 -0.061 0.17 -9999 0 -0.35 113 113
ATF6 -0.06 0.17 -9999 0 -0.35 112 112
ATF1 -0.065 0.19 -9999 0 -0.38 114 114
p38alpha-beta/MAPKAPK2 -0.056 0.18 -9999 0 -0.51 26 26
p38alpha-beta/MAPKAPK3 -0.056 0.18 -9999 0 -0.51 26 26
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.041 0.22 -10000 0 -0.59 43 43
PTK2B 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.41 -10000 0 -0.97 92 92
EDN1 -0.027 0.17 -10000 0 -0.48 46 46
EDN3 -0.17 0.23 -10000 0 -0.47 191 191
EDN2 -0.022 0.13 -10000 0 -0.5 34 34
HRAS/GDP -0.061 0.24 -10000 0 -0.55 73 73
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.027 0.18 -10000 0 -0.44 56 56
ADCY4 -0.092 0.24 -10000 0 -0.55 87 87
ADCY5 -0.13 0.3 -10000 0 -0.63 107 107
ADCY6 -0.09 0.24 -10000 0 -0.54 87 87
ADCY7 -0.091 0.24 -10000 0 -0.54 88 88
ADCY1 -0.12 0.25 -10000 0 -0.56 92 92
ADCY2 -0.1 0.26 -10000 0 -0.57 90 90
ADCY3 -0.091 0.24 -10000 0 -0.54 87 87
ADCY8 -0.1 0.24 -10000 0 -0.55 88 88
ADCY9 -0.091 0.24 -10000 0 -0.55 87 87
arachidonic acid secretion -0.098 0.31 -10000 0 -0.66 88 88
ETB receptor/Endothelin-1/Gq/GTP -0.039 0.17 -10000 0 -0.4 67 67
GNAO1 -0.08 0.19 -10000 0 -0.47 96 96
HRAS 0.006 0.064 -10000 0 -0.57 6 6
ETA receptor/Endothelin-1/G12/GTP -0.025 0.22 0.3 56 -0.56 43 99
ETA receptor/Endothelin-1/Gs/GTP -0.1 0.26 0.28 53 -0.57 87 140
mol:GTP -0.001 0.007 -10000 0 -10000 0 0
COL3A1 -0.047 0.23 -10000 0 -0.59 51 51
EDNRB -0.049 0.17 -10000 0 -0.47 67 67
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.083 0.28 -10000 0 -0.63 87 87
CYSLTR1 -0.061 0.26 -10000 0 -0.71 53 53
SLC9A1 -0.034 0.11 0.19 23 -0.3 43 66
mol:GDP -0.07 0.25 -10000 0 -0.56 77 77
SLC9A3 -0.15 0.38 -10000 0 -0.89 85 85
RAF1 -0.077 0.26 -10000 0 -0.57 75 75
JUN -0.069 0.29 -10000 0 -0.73 58 58
JAK2 -0.041 0.22 -10000 0 -0.59 44 44
mol:IP3 -0.031 0.18 -10000 0 -0.44 51 51
ETA receptor/Endothelin-1 -0.067 0.26 0.35 59 -0.64 50 109
PLCB1 0.008 0.043 -10000 0 -0.47 4 4
PLCB2 0.009 0.037 -10000 0 -0.57 2 2
ETA receptor/Endothelin-3 -0.15 0.23 -10000 0 -0.4 196 196
FOS -0.14 0.38 -10000 0 -0.92 88 88
Gai/GDP -0.14 0.36 -10000 0 -0.86 96 96
CRK 0.013 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.065 0.27 -10000 0 -0.66 61 61
BCAR1 0.013 0.001 -10000 0 -10000 0 0
PRKCB1 -0.034 0.17 -10000 0 -0.43 51 51
GNAQ 0.012 0.007 -10000 0 -10000 0 0
GNAZ -0.034 0.14 -10000 0 -0.47 49 49
GNAL -0.11 0.21 -10000 0 -0.47 129 129
Gs family/GDP -0.16 0.25 -10000 0 -0.56 115 115
ETA receptor/Endothelin-1/Gq/GTP -0.04 0.2 -10000 0 -0.48 65 65
MAPK14 -0.021 0.15 -10000 0 -0.41 39 39
TRPC6 -0.15 0.45 -10000 0 -1.1 92 92
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.006 0.064 -10000 0 -0.53 7 7
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.03 0.16 -10000 0 -0.39 54 54
ETB receptor/Endothelin-2 -0.05 0.15 -10000 0 -0.34 98 98
ETB receptor/Endothelin-3 -0.15 0.22 -10000 0 -0.39 208 208
ETB receptor/Endothelin-1 -0.05 0.18 -10000 0 -0.4 91 91
MAPK3 -0.12 0.36 -10000 0 -0.81 94 94
MAPK1 -0.12 0.36 -10000 0 -0.81 93 93
Rac1/GDP -0.057 0.24 -10000 0 -0.53 71 71
cAMP biosynthetic process -0.099 0.26 -10000 0 -0.57 93 93
MAPK8 -0.098 0.36 -10000 0 -0.71 100 100
SRC 0.013 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.075 0.22 -10000 0 -0.52 76 76
p130Cas/CRK/Src/PYK2 -0.084 0.3 -10000 0 -0.63 96 96
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.057 0.24 -10000 0 -0.53 71 71
COL1A2 -0.065 0.26 -10000 0 -0.68 53 53
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.046 0.16 -10000 0 -0.38 80 80
mol:DAG -0.031 0.18 -10000 0 -0.44 51 51
MAP2K2 -0.095 0.3 -10000 0 -0.63 96 96
MAP2K1 -0.095 0.3 -10000 0 -0.63 95 95
EDNRA -0.042 0.19 -10000 0 -0.52 53 53
positive regulation of muscle contraction -0.029 0.19 -10000 0 -0.52 43 43
Gq family/GDP -0.11 0.21 -10000 0 -0.56 71 71
HRAS/GTP -0.065 0.23 -10000 0 -0.5 76 76
PRKCH -0.027 0.17 -10000 0 -0.45 44 44
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.037 0.19 -10000 0 -0.49 54 54
PRKCB -0.081 0.24 -10000 0 -0.5 90 90
PRKCE -0.025 0.17 -10000 0 -0.44 44 44
PRKCD -0.027 0.17 -10000 0 -0.44 47 47
PRKCG -0.04 0.18 -10000 0 -0.44 57 57
regulation of vascular smooth muscle contraction -0.16 0.44 -10000 0 -1.1 87 87
PRKCQ -0.049 0.2 -10000 0 -0.49 59 59
PLA2G4A -0.12 0.35 -10000 0 -0.75 88 88
GNA14 0.01 0.032 -10000 0 -0.47 2 2
GNA15 -0.012 0.11 -10000 0 -0.47 25 25
GNA12 0.013 0 -10000 0 -10000 0 0
GNA11 -0.004 0.088 -10000 0 -0.47 17 17
Rac1/GTP -0.025 0.22 0.3 57 -0.56 43 100
MMP1 -0.066 0.26 -10000 0 -0.59 82 82
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.012 0.022 -9999 0 -0.47 1 1
CCL5 -0.009 0.1 -9999 0 -0.5 21 21
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.15 0.15 -9999 0 -0.36 119 119
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 -0.14 0.15 -9999 0 -0.43 55 55
Syndecan-1/Syntenin -0.14 0.15 -9999 0 -0.43 55 55
MAPK3 -0.12 0.14 -9999 0 -0.41 51 51
HGF/MET -0.042 0.16 -9999 0 -0.4 72 72
TGFB1/TGF beta receptor Type II 0.012 0.022 -9999 0 -0.47 1 1
BSG 0.012 0.026 -9999 0 -0.57 1 1
keratinocyte migration -0.14 0.14 -9999 0 -0.42 55 55
Syndecan-1/RANTES -0.15 0.16 -9999 0 -0.45 66 66
Syndecan-1/CD147 -0.13 0.15 -9999 0 -0.42 59 59
Syndecan-1/Syntenin/PIP2 -0.13 0.14 -9999 0 -0.42 55 55
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.13 0.14 -9999 0 -0.41 55 55
MMP7 -0.09 0.21 -9999 0 -0.53 95 95
HGF -0.026 0.14 -9999 0 -0.5 38 38
Syndecan-1/CASK -0.15 0.15 -9999 0 -0.35 119 119
Syndecan-1/HGF/MET -0.17 0.19 -9999 0 -0.47 98 98
regulation of cell adhesion -0.11 0.14 -9999 0 -0.39 51 51
HPSE -0.015 0.12 -9999 0 -0.5 27 27
positive regulation of cell migration -0.15 0.15 -9999 0 -0.36 119 119
SDC1 -0.15 0.16 -9999 0 -0.37 119 119
Syndecan-1/Collagen -0.15 0.15 -9999 0 -0.36 119 119
PPIB 0.007 0.059 -9999 0 -0.57 5 5
MET -0.036 0.15 -9999 0 -0.47 51 51
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.31 0.29 -9999 0 -0.57 272 272
MAPK1 -0.12 0.14 -9999 0 -0.41 51 51
homophilic cell adhesion -0.15 0.15 -9999 0 -0.36 119 119
MMP1 -0.09 0.22 -9999 0 -0.54 93 93
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.3 0.53 -10000 0 -1.3 83 83
IL23A -0.3 0.54 -10000 0 -1.3 90 90
NF kappa B1 p50/RelA/I kappa B alpha -0.35 0.47 -10000 0 -1.1 104 104
positive regulation of T cell mediated cytotoxicity -0.33 0.6 -10000 0 -1.3 104 104
ITGA3 -0.29 0.52 -10000 0 -1.2 92 92
IL17F -0.18 0.34 -10000 0 -0.75 77 77
IL12B -0.029 0.15 -10000 0 -0.6 30 30
STAT1 (dimer) -0.32 0.57 -10000 0 -1.2 104 104
CD4 -0.28 0.5 -10000 0 -1.2 75 75
IL23 -0.3 0.53 -10000 0 -1.2 91 91
IL23R -0.031 0.11 -10000 0 -0.54 5 5
IL1B -0.33 0.58 -10000 0 -1.4 92 92
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.28 0.5 -10000 0 -1.1 92 92
TYK2 0.006 0.023 -10000 0 -10000 0 0
STAT4 -0.007 0.1 -10000 0 -0.54 18 18
STAT3 0.013 0.001 -10000 0 -10000 0 0
IL18RAP -0.021 0.13 -10000 0 -0.52 32 32
IL12RB1 -0.021 0.13 -10000 0 -0.58 24 24
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
IL12Rbeta1/TYK2 -0.012 0.1 -10000 0 -0.44 24 24
IL23R/JAK2 -0.033 0.13 -10000 0 -0.53 5 5
positive regulation of chronic inflammatory response -0.33 0.6 -10000 0 -1.3 104 104
natural killer cell activation 0.003 0.009 0.046 6 -10000 0 6
JAK2 0.009 0.038 -10000 0 -0.47 1 1
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
NFKB1 0.012 0.004 -10000 0 -10000 0 0
RELA 0.012 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.28 0.5 -10000 0 -1.1 91 91
ALOX12B -0.29 0.51 -10000 0 -1.2 87 87
CXCL1 -0.4 0.62 -10000 0 -1.3 146 146
T cell proliferation -0.33 0.6 -10000 0 -1.3 104 104
NFKBIA 0.012 0.004 -10000 0 -10000 0 0
IL17A -0.13 0.28 -10000 0 -0.6 64 64
PI3K -0.36 0.48 -10000 0 -1.2 107 107
IFNG -0.008 0.031 0.1 1 -0.1 7 8
STAT3 (dimer) -0.35 0.45 -10000 0 -1.1 106 106
IL18R1 0.006 0.06 -10000 0 -0.46 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.35 -10000 0 -0.8 75 75
IL18/IL18R -0.004 0.11 -10000 0 -0.32 45 45
macrophage activation -0.018 0.018 -10000 0 -0.045 62 62
TNF -0.32 0.56 -10000 0 -1.3 97 97
STAT3/STAT4 -0.37 0.49 -10000 0 -1.2 107 107
STAT4 (dimer) -0.32 0.57 -10000 0 -1.2 107 107
IL18 0 0.079 -10000 0 -0.46 14 14
IL19 -0.28 0.5 -10000 0 -1.1 91 91
STAT5A (dimer) -0.32 0.56 -10000 0 -1.2 104 104
STAT1 0.003 0.078 -10000 0 -0.57 9 9
SOCS3 -0.053 0.17 -10000 0 -0.48 67 67
CXCL9 -0.31 0.52 -10000 0 -1.2 86 86
MPO -0.32 0.55 -10000 0 -1.2 118 118
positive regulation of humoral immune response -0.33 0.6 -10000 0 -1.3 104 104
IL23/IL23R/JAK2/TYK2 -0.36 0.68 -10000 0 -1.5 104 104
IL6 -0.41 0.62 -10000 0 -1.3 142 142
STAT5A 0.012 0.022 -10000 0 -0.47 1 1
IL2 0.006 0.039 -10000 0 -0.58 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.009 0.046 6 -10000 0 6
CD3E -0.28 0.51 -10000 0 -1.2 82 82
keratinocyte proliferation -0.33 0.6 -10000 0 -1.3 104 104
NOS2 -0.31 0.54 -10000 0 -1.2 95 95
IL4-mediated 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
BCL2L1 -0.45 0.45 -10000 0 -1.2 98 98
STAT6 (cleaved dimer) -0.49 0.47 -10000 0 -1.1 151 151
IGHG1 -0.16 0.15 -10000 0 -0.41 9 9
IGHG3 -0.44 0.43 -10000 0 -1 138 138
AKT1 -0.22 0.26 -10000 0 -0.71 61 61
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.23 -10000 0 -0.75 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.26 -10000 0 -0.7 55 55
THY1 -0.45 0.46 -10000 0 -1.2 98 98
MYB -0.015 0.13 -10000 0 -0.57 24 24
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.34 -10000 0 -0.84 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.27 -10000 0 -0.74 60 60
SP1 0.021 0.002 -10000 0 -10000 0 0
INPP5D -0.014 0.11 -10000 0 -0.47 28 28
SOCS5 0.028 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.49 -10000 0 -1.2 113 113
SOCS1 -0.29 0.3 -10000 0 -0.75 94 94
SOCS3 -0.33 0.43 -10000 0 -1.1 89 89
FCER2 -0.4 0.41 -10000 0 -1.1 85 85
PARP14 0.013 0.005 -10000 0 -10000 0 0
CCL17 -0.49 0.48 -10000 0 -1.2 113 113
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.23 -10000 0 -0.7 42 42
T cell proliferation -0.45 0.48 -10000 0 -1.2 105 105
IL4R/JAK1 -0.45 0.46 -10000 0 -1.2 101 101
EGR2 -0.49 0.49 -10000 0 -1.3 104 104
JAK2 -0.015 0.033 -10000 0 -0.51 1 1
JAK3 -0.001 0.096 -10000 0 -0.54 15 15
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
JAK1 0.004 0.009 -10000 0 -10000 0 0
COL1A2 -0.14 0.16 -10000 0 -1 5 5
CCL26 -0.46 0.45 -10000 0 -1.2 98 98
IL4R -0.48 0.48 -10000 0 -1.3 98 98
PTPN6 0.025 0.009 -10000 0 -10000 0 0
IL13RA2 -0.53 0.55 -10000 0 -1.4 123 123
IL13RA1 -0.014 0.024 -10000 0 -10000 0 0
IRF4 -0.18 0.34 -10000 0 -1 54 54
ARG1 -0.14 0.16 -10000 0 -0.6 26 26
CBL -0.28 0.31 -10000 0 -0.8 85 85
GTF3A 0.018 0.012 -10000 0 -10000 0 0
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
IL13RA1/JAK2 -0.019 0.037 -10000 0 -0.37 1 1
IRF4/BCL6 -0.16 0.32 -10000 0 -0.97 53 53
CD40LG -0.037 0.17 -10000 0 -0.54 49 49
MAPK14 -0.3 0.35 -10000 0 -0.91 87 87
mitosis -0.21 0.25 -10000 0 -0.66 61 61
STAT6 -0.52 0.55 -10000 0 -1.3 131 131
SPI1 0.006 0.06 -10000 0 -0.55 5 5
RPS6KB1 -0.2 0.24 -10000 0 -0.64 60 60
STAT6 (dimer) -0.52 0.55 -10000 0 -1.3 132 132
STAT6 (dimer)/PARP14 -0.48 0.5 -10000 0 -1.2 118 118
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.26 -10000 0 -0.72 57 57
FRAP1 -0.22 0.26 -10000 0 -0.71 61 61
LTA -0.47 0.47 -10000 0 -1.2 108 108
FES 0.007 0.057 -10000 0 -0.47 7 7
T-helper 1 cell differentiation 0.51 0.52 1.2 132 -10000 0 132
CCL11 -0.47 0.46 -10000 0 -1.1 124 124
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.27 -10000 0 -0.71 61 61
IL2RG -0.009 0.12 -10000 0 -0.54 22 22
IL10 -0.48 0.49 -10000 0 -1.2 108 108
IRS1 -0.003 0.087 -10000 0 -0.47 17 17
IRS2 0.006 0.062 -10000 0 -0.56 6 6
IL4 -0.11 0.1 -10000 0 -10000 0 0
IL5 -0.46 0.45 -10000 0 -1.2 101 101
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.34 -10000 0 -0.87 99 99
COL1A1 -0.18 0.19 -10000 0 -0.67 26 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.45 0.47 -10000 0 -1.2 97 97
IL2R gamma/JAK3 -0.009 0.13 -10000 0 -0.54 26 26
TFF3 -0.53 0.48 -10000 0 -1.2 131 131
ALOX15 -0.58 0.49 -10000 0 -1.2 137 137
MYBL1 0.012 0.022 -10000 0 -0.47 1 1
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.95 107 107
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.012 0.021 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.25 -10000 0 -0.69 49 49
mol:PI-3-4-5-P3 -0.22 0.26 -10000 0 -0.71 61 61
PI3K -0.23 0.28 -10000 0 -0.76 62 62
DOK2 0.009 0.05 -10000 0 -0.55 4 4
ETS1 0.021 0.049 -10000 0 -0.45 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.21 -10000 0 -0.66 39 39
ITGB3 -0.57 0.6 -10000 0 -1.4 142 142
PIGR -0.61 0.6 -10000 0 -1.4 158 158
IGHE 0.038 0.035 0.26 1 -10000 0 1
MAPKKK cascade -0.17 0.21 -10000 0 -0.64 39 39
BCL6 0.014 0.003 -10000 0 -10000 0 0
OPRM1 -0.46 0.45 -10000 0 -1.2 98 98
RETNLB -0.46 0.45 -10000 0 -1.2 98 98
SELP -0.46 0.47 -10000 0 -1.2 97 97
AICDA -0.44 0.44 -10000 0 -1.1 98 98
Glucocorticoid receptor regulatory network

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.02 0.081 0.33 8 -10000 0 8
SMARCC2 0.002 0.032 -10000 0 -10000 0 0
SMARCC1 0.002 0.032 -10000 0 -10000 0 0
TBX21 -0.098 0.21 -10000 0 -0.5 81 81
SUMO2 0.016 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.007 0.089 -10000 0 -0.62 9 9
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.011 0.03 -10000 0 -0.47 2 2
GR alpha/HSP90/FKBP51/HSP90 0.11 0.12 0.3 74 -0.32 2 76
PRL -0.077 0.14 -10000 0 -0.64 4 4
cortisol/GR alpha (dimer)/TIF2 0.2 0.29 0.56 142 -0.48 9 151
RELA -0.053 0.1 -10000 0 -0.29 10 10
FGG 0.19 0.24 0.51 110 -0.55 14 124
GR beta/TIF2 0.071 0.19 0.32 85 -0.36 37 122
IFNG -0.29 0.34 -10000 0 -0.72 147 147
apoptosis 0.062 0.23 0.52 61 -0.55 8 69
CREB1 -0.039 0.11 -10000 0 -0.32 33 33
histone acetylation -0.056 0.18 0.36 10 -0.41 70 80
BGLAP -0.083 0.18 -10000 0 -0.56 22 22
GR/PKAc 0.11 0.11 0.3 62 -0.32 1 63
NF kappa B1 p50/RelA -0.092 0.19 -10000 0 -0.44 71 71
SMARCD1 0.002 0.032 -10000 0 -10000 0 0
MDM2 0.1 0.1 0.26 107 -10000 0 107
GATA3 -0.13 0.22 -10000 0 -0.47 148 148
AKT1 0.004 0.003 -10000 0 -10000 0 0
CSF2 -0.079 0.14 -10000 0 -0.46 21 21
GSK3B 0.016 0.014 -10000 0 -10000 0 0
NR1I3 0.081 0.22 0.51 57 -0.61 8 65
CSN2 0.17 0.19 0.42 108 -0.5 3 111
BRG1/BAF155/BAF170/BAF60A -0.003 0.11 -10000 0 -0.34 31 31
NFATC1 0.015 0.003 -10000 0 -10000 0 0
POU2F1 0.012 0.028 -10000 0 -0.56 1 1
CDKN1A 0.006 0.13 -10000 0 -1.3 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.003 0.014 -10000 0 -10000 0 0
SFN -0.035 0.14 -10000 0 -0.47 50 50
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.082 0.12 0.3 49 -0.32 1 50
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.032 0.29 0.48 56 -0.72 40 96
JUN -0.17 0.22 -10000 0 -0.5 100 100
IL4 -0.09 0.16 -10000 0 -0.47 25 25
CDK5R1 -0.014 0.13 -10000 0 -0.57 24 24
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.22 0.22 3 -0.53 70 73
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.11 0.3 71 -0.32 1 72
cortisol/GR alpha (monomer) 0.28 0.32 0.67 155 -0.52 1 156
NCOA2 -0.045 0.16 -10000 0 -0.47 60 60
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.12 0.2 -10000 0 -0.52 91 91
AP-1/NFAT1-c-4 -0.31 0.36 -10000 0 -0.78 148 148
AFP -0.14 0.19 -10000 0 -0.62 33 33
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.15 0.18 0.44 77 -0.57 3 80
TP53 0.022 0.07 -10000 0 -0.44 10 10
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.4 0.53 -10000 0 -1.1 146 146
KRT14 -0.39 0.58 0.47 1 -1.2 155 156
TBP 0.017 0.032 -10000 0 -10000 0 0
CREBBP 0.049 0.13 0.28 74 -0.25 6 80
HDAC1 0.013 0.009 -10000 0 -10000 0 0
HDAC2 0.012 0.022 -10000 0 -0.47 1 1
AP-1 -0.32 0.36 -10000 0 -0.78 148 148
MAPK14 0.016 0.012 -10000 0 -10000 0 0
MAPK10 0.01 0.055 -10000 0 -0.47 6 6
MAPK11 0.007 0.076 -10000 0 -0.58 8 8
KRT5 -0.52 0.59 -10000 0 -1.2 194 194
interleukin-1 receptor activity 0 0.005 -10000 0 -10000 0 0
NCOA1 0.016 0.001 -10000 0 -10000 0 0
STAT1 0.007 0.089 -10000 0 -0.62 9 9
CGA -0.23 0.37 -10000 0 -0.77 132 132
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.11 0.18 0.38 110 -0.54 5 115
MAPK3 0.016 0.014 -10000 0 -10000 0 0
MAPK1 0.016 0.012 -10000 0 -10000 0 0
ICAM1 -0.19 0.28 -10000 0 -0.66 94 94
NFKB1 -0.053 0.1 -10000 0 -0.28 13 13
MAPK8 -0.15 0.2 -10000 0 -0.43 122 122
MAPK9 0.016 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.054 0.23 0.53 61 -0.57 8 69
BAX 0.014 0.062 -10000 0 -10000 0 0
POMC -0.26 0.47 -10000 0 -1.4 66 66
EP300 0.046 0.14 0.28 61 -0.52 3 64
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.57 148 -0.52 1 149
proteasomal ubiquitin-dependent protein catabolic process 0.072 0.081 0.22 59 -10000 0 59
SGK1 -0.05 0.46 0.39 6 -1.1 72 78
IL13 -0.36 0.42 -10000 0 -0.89 161 161
IL6 -0.35 0.47 -10000 0 -0.96 163 163
PRKACG 0.003 0.006 -10000 0 -10000 0 0
IL5 -0.3 0.34 -10000 0 -0.76 146 146
IL2 -0.28 0.32 -10000 0 -0.73 132 132
CDK5 0.015 0.006 -10000 0 -10000 0 0
PRKACB 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.25 0.38 -10000 0 -0.81 120 120
CDK5R1/CDK5 0.001 0.094 -10000 0 -0.41 24 24
NF kappa B1 p50/RelA/PKAc -0.046 0.14 -10000 0 -0.39 17 17
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.24 0.53 152 -0.4 1 153
SMARCA4 0.002 0.032 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.21 0.39 94 -0.41 19 113
NF kappa B1 p50/RelA/Cbp -0.038 0.21 0.34 22 -0.52 32 54
JUN (dimer) -0.17 0.21 -10000 0 -0.5 98 98
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.076 0.17 -10000 0 -0.42 69 69
NR3C1 0.17 0.2 0.47 108 -0.44 4 112
NR4A1 -0.051 0.18 -10000 0 -0.46 72 72
TIF2/SUV420H1 -0.022 0.11 -10000 0 -0.32 60 60
MAPKKK cascade 0.062 0.23 0.52 61 -0.55 8 69
cortisol/GR alpha (dimer)/Src-1 0.24 0.26 0.56 153 -0.44 1 154
PBX1 0.011 0.032 -10000 0 -0.47 2 2
POU1F1 0 0.05 -10000 0 -0.62 3 3
SELE -0.34 0.48 -10000 0 -1 151 151
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.21 0.39 94 -0.41 19 113
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.24 0.53 152 -0.4 1 153
mol:cortisol 0.16 0.2 0.4 160 -0.21 8 168
MMP1 -0.18 0.31 -10000 0 -0.87 63 63
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.033 -10000 0 -0.48 2 2
CDKN2C 0.019 0.056 -10000 0 -0.55 4 4
CDKN2A -0.12 0.25 -10000 0 -0.59 106 106
CCND2 0.018 0.059 0.21 3 -0.12 22 25
RB1 -0.011 0.066 0.14 5 -0.14 98 103
CDK4 0.029 0.064 0.15 103 -10000 0 103
CDK6 0.02 0.066 0.23 4 -0.2 8 12
G1/S progression 0.011 0.066 0.14 98 -0.14 5 103
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 0.003 0.16 -10000 0 -0.66 23 23
IHH -0.038 0.17 -10000 0 -0.53 53 53
SHH Np/Cholesterol/GAS1 -0.088 0.16 -10000 0 -0.3 172 172
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.088 0.16 0.3 172 -10000 0 172
SMO/beta Arrestin2 0.002 0.12 -10000 0 -0.46 16 16
SMO -0.005 0.12 -10000 0 -0.48 18 18
AKT1 0.014 0.081 -10000 0 -0.51 5 5
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC 0.002 0.074 -10000 0 -0.47 12 12
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.005 0.12 -10000 0 -0.47 18 18
STIL -0.063 0.17 -10000 0 -0.46 38 38
DHH N/PTCH2 0.007 0.068 -10000 0 -0.36 16 16
DHH N/PTCH1 0.005 0.11 -10000 0 -0.45 14 14
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
DHH 0.003 0.072 -10000 0 -0.5 10 10
PTHLH -0.003 0.2 -10000 0 -0.83 23 23
determination of left/right symmetry -0.005 0.12 -10000 0 -0.47 18 18
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
skeletal system development -0.003 0.2 -10000 0 -0.82 23 23
IHH N/Hhip -0.049 0.16 -10000 0 -0.38 92 92
DHH N/Hhip -0.024 0.12 -10000 0 -0.33 62 62
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.005 0.12 -10000 0 -0.47 18 18
pancreas development -0.038 0.15 -10000 0 -0.47 52 52
HHAT 0.004 0.067 -10000 0 -0.47 10 10
PI3K 0.014 0.049 -10000 0 -0.36 8 8
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.042 0.15 -10000 0 -0.47 57 57
somite specification -0.005 0.12 -10000 0 -0.47 18 18
SHH Np/Cholesterol/PTCH1 -0.059 0.16 -10000 0 -0.45 31 31
SHH Np/Cholesterol/PTCH2 -0.063 0.14 -10000 0 -0.28 142 142
SHH Np/Cholesterol/Megalin -0.09 0.16 -10000 0 -0.3 175 175
SHH -0.086 0.18 -10000 0 -0.36 138 138
catabolic process 0.004 0.12 -10000 0 -0.49 12 12
SMO/Vitamin D3 -0.049 0.16 -10000 0 -0.47 27 27
SHH Np/Cholesterol/Hhip -0.086 0.17 -10000 0 -0.31 161 161
LRP2 -0.045 0.16 -10000 0 -0.49 57 57
receptor-mediated endocytosis -0.065 0.17 -10000 0 -0.48 39 39
SHH Np/Cholesterol/BOC -0.065 0.14 -10000 0 -0.28 145 145
SHH Np/Cholesterol/CDO -0.063 0.14 -10000 0 -0.28 142 142
mesenchymal cell differentiation 0.085 0.17 0.31 161 -10000 0 161
mol:Vitamin D3 -0.056 0.16 -10000 0 -0.45 31 31
IHH N/PTCH2 -0.016 0.12 -10000 0 -0.32 58 58
CDON 0.006 0.062 -10000 0 -0.56 6 6
IHH N/PTCH1 0.005 0.12 -10000 0 -0.49 12 12
Megalin/LRPAP1 -0.022 0.12 -10000 0 -0.34 57 57
PTCH2 0.007 0.06 -10000 0 -0.54 6 6
SHH Np/Cholesterol -0.067 0.13 -10000 0 -0.28 138 138
PTCH1 0.004 0.12 -10000 0 -0.49 12 12
HHIP -0.038 0.15 -10000 0 -0.47 52 52
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.041 0.17 -10000 0 -0.44 63 63
CRKL -0.032 0.17 -10000 0 -0.46 59 59
HRAS -0.018 0.18 -10000 0 -0.44 63 63
mol:PIP3 -0.038 0.15 -10000 0 -0.42 58 58
SPRED1 0.007 0.052 -10000 0 -0.47 6 6
SPRED2 0.008 0.048 -10000 0 -0.47 5 5
GAB1 -0.04 0.18 -10000 0 -0.49 59 59
FOXO3 -0.021 0.15 -10000 0 -0.41 59 59
AKT1 -0.031 0.16 -10000 0 -0.44 59 59
BAD -0.022 0.15 -10000 0 -0.41 60 60
megakaryocyte differentiation -0.049 0.18 -10000 0 -0.47 71 71
GSK3B -0.021 0.15 -10000 0 -0.41 59 59
RAF1 -0.004 0.14 -10000 0 -0.41 36 36
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.04 0.18 -10000 0 -0.48 60 60
STAT1 -0.11 0.38 -10000 0 -1 67 67
HRAS/SPRED1 -0.007 0.15 -10000 0 -0.42 37 37
cell proliferation -0.044 0.18 -10000 0 -0.49 61 61
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.039 0.18 -10000 0 -0.48 61 61
HRAS/SPRED2 -0.007 0.15 -10000 0 -0.42 38 38
LYN/TEC/p62DOK -0.024 0.17 -10000 0 -0.45 59 59
MAPK3 0.011 0.1 -10000 0 -0.3 28 28
STAP1 -0.11 0.22 -10000 0 -0.42 134 134
GRAP2 -0.007 0.099 -10000 0 -0.48 21 21
JAK2 -0.091 0.32 -10000 0 -0.87 67 67
STAT1 (dimer) -0.11 0.37 -10000 0 -1 67 67
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.037 0.19 -10000 0 -0.49 62 62
actin filament polymerization -0.05 0.18 -10000 0 -0.45 74 74
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.12 0.28 -10000 0 -0.67 82 82
PIK3R1 0.007 0.053 -10000 0 -0.47 6 6
CBL/CRKL/GRB2 -0.015 0.16 -10000 0 -0.41 58 58
PI3K -0.028 0.18 -10000 0 -0.47 61 61
PTEN 0.001 0.077 -10000 0 -0.47 13 13
SCF/KIT/EPO/EPOR -0.14 0.44 -10000 0 -1.3 61 61
MAPK8 -0.045 0.18 -10000 0 -0.5 61 61
STAT3 (dimer) -0.038 0.17 -10000 0 -0.47 60 60
positive regulation of transcription 0.013 0.088 -10000 0 -0.25 25 25
mol:GDP -0.023 0.18 -10000 0 -0.45 64 64
PIK3C2B -0.04 0.18 -10000 0 -0.49 59 59
CBL/CRKL -0.022 0.16 -10000 0 -0.43 59 59
FER -0.049 0.19 -10000 0 -0.5 68 68
SH2B3 -0.04 0.18 -10000 0 -0.48 59 59
PDPK1 -0.029 0.14 -10000 0 -0.4 56 56
SNAI2 -0.096 0.23 -10000 0 -0.6 73 73
positive regulation of cell proliferation -0.075 0.29 -10000 0 -0.77 67 67
KITLG -0.014 0.12 -10000 0 -0.49 27 27
cell motility -0.075 0.29 -10000 0 -0.77 67 67
PTPN6 0.014 0.009 -10000 0 -10000 0 0
EPOR -0.008 0.13 -10000 0 -0.45 1 1
STAT5A (dimer) -0.062 0.25 -10000 0 -0.63 71 71
SOCS1 0.008 0.055 -10000 0 -0.53 5 5
cell migration 0.17 0.24 0.37 244 -10000 0 244
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.067 0.19 -10000 0 -0.51 76 76
VAV1 -0.011 0.11 -10000 0 -0.47 25 25
GRB10 -0.04 0.18 -10000 0 -0.49 59 59
PTPN11 0.013 0.022 -10000 0 -0.46 1 1
SCF/KIT -0.049 0.18 -10000 0 -0.48 68 68
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 0.007 0.11 -10000 0 -0.34 28 28
CBL 0.012 0.022 -10000 0 -0.47 1 1
KIT -0.12 0.42 -10000 0 -1.3 58 58
MAP2K2 0.007 0.12 -10000 0 -0.34 28 28
SHC/Grb2/SOS1 -0.023 0.17 -10000 0 -0.45 59 59
STAT5A -0.065 0.25 -10000 0 -0.65 71 71
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.093 0.23 -10000 0 -0.58 73 73
SHC/GRAP2 0.005 0.071 -10000 0 -0.33 21 21
PTPRO -0.051 0.19 -10000 0 -0.48 71 71
SH2B2 -0.052 0.19 -10000 0 -0.46 74 74
DOK1 0.012 0.022 -10000 0 -0.47 1 1
MATK -0.17 0.24 -10000 0 -0.38 244 244
CREBBP 0.028 0.026 -10000 0 -10000 0 0
BCL2 -0.047 0.3 -10000 0 -1.3 23 23
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.091 0.16 -9999 0 -0.32 169 169
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.03 0.042 -9999 0 -10000 0 0
AURKB -0.18 0.28 -9999 0 -0.57 166 166
AURKC 0.008 0.055 -9999 0 -0.53 5 5
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.031 0.15 -10000 0 -0.68 21 21
NFATC2 -0.095 0.25 -10000 0 -0.64 47 47
NFATC3 -0.008 0.085 -10000 0 -10000 0 0
CD40LG -0.22 0.4 -10000 0 -0.98 75 75
ITCH -0.012 0.1 -10000 0 -10000 0 0
CBLB -0.012 0.1 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.4 -10000 0 -0.9 106 106
JUNB -0.014 0.12 -10000 0 -0.52 25 25
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.029 0.12 -10000 0 -10000 0 0
T cell anergy -0.075 0.18 -10000 0 -0.41 93 93
TLE4 -0.048 0.18 -10000 0 -0.59 24 24
Jun/NFAT1-c-4/p21SNFT -0.14 0.33 -10000 0 -0.88 51 51
AP-1/NFAT1-c-4 -0.23 0.45 -10000 0 -1.1 69 69
IKZF1 -0.061 0.21 -10000 0 -0.67 30 30
T-helper 2 cell differentiation -0.21 0.31 -10000 0 -0.76 78 78
AP-1/NFAT1 -0.1 0.23 -10000 0 -0.57 64 64
CALM1 -0.011 0.07 -10000 0 -10000 0 0
EGR2 -0.13 0.36 -10000 0 -0.95 54 54
EGR3 -0.14 0.4 -10000 0 -1 58 58
NFAT1/FOXP3 -0.094 0.24 -10000 0 -0.66 48 48
EGR1 -0.056 0.18 -10000 0 -0.51 66 66
JUN 0 0.064 -10000 0 -0.51 7 7
EGR4 -0.14 0.26 -10000 0 -0.57 132 132
mol:Ca2+ -0.025 0.073 -10000 0 -10000 0 0
GBP3 -0.1 0.27 -10000 0 -0.72 65 65
FOSL1 -0.1 0.22 -10000 0 -0.5 113 113
NFAT1-c-4/MAF/IRF4 -0.13 0.34 -10000 0 -0.89 54 54
DGKA -0.047 0.18 -10000 0 -0.63 18 18
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.13 0.32 -10000 0 -0.84 55 55
CTLA4 -0.11 0.28 -10000 0 -0.67 81 81
NFAT1-c-4 (dimer)/EGR1 -0.15 0.37 -10000 0 -0.93 67 67
NFAT1-c-4 (dimer)/EGR4 -0.2 0.36 -10000 0 -0.86 84 84
FOS -0.084 0.2 -10000 0 -0.49 91 91
IFNG -0.13 0.27 -10000 0 -0.73 53 53
T cell activation -0.082 0.22 -10000 0 -0.7 27 27
MAF 0.007 0.057 -10000 0 -0.47 7 7
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.077 0.23 0.62 45 -10000 0 45
TNF -0.21 0.38 -10000 0 -0.91 81 81
FASLG -0.19 0.45 -10000 0 -1.2 57 57
TBX21 -0.018 0.13 -10000 0 -0.56 28 28
BATF3 -0.016 0.13 -10000 0 -0.57 25 25
PRKCQ -0.031 0.15 -10000 0 -0.5 44 44
PTPN1 -0.046 0.18 -10000 0 -0.6 19 19
NFAT1-c-4/ICER1 -0.12 0.31 -10000 0 -0.84 50 50
GATA3 -0.13 0.22 -10000 0 -0.47 148 148
T-helper 1 cell differentiation -0.12 0.27 -10000 0 -0.71 55 55
IL2RA -0.26 0.33 -10000 0 -0.8 103 103
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.046 0.18 -10000 0 -0.61 18 18
E2F1 -0.008 0.12 -10000 0 -0.57 23 23
PPARG -0.017 0.12 -10000 0 -0.48 31 31
SLC3A2 -0.046 0.18 -10000 0 -0.61 18 18
IRF4 -0.037 0.16 -10000 0 -0.53 46 46
PTGS2 -0.24 0.42 -10000 0 -0.98 84 84
CSF2 -0.2 0.38 -10000 0 -0.95 67 67
JunB/Fra1/NFAT1-c-4 -0.17 0.35 -10000 0 -0.94 62 62
IL4 -0.22 0.32 -10000 0 -0.81 74 74
IL5 -0.2 0.38 -10000 0 -0.94 69 69
IL2 -0.084 0.22 -10000 0 -0.71 27 27
IL3 -0.045 0.052 -10000 0 -10000 0 0
RNF128 -0.089 0.24 -10000 0 -0.54 113 113
NFATC1 -0.077 0.23 -10000 0 -0.63 45 45
CDK4 0.072 0.18 0.6 8 -10000 0 8
PTPRK -0.046 0.18 -10000 0 -0.55 26 26
IL8 -0.22 0.41 -10000 0 -0.98 82 82
POU2F1 0.012 0.026 -10000 0 -0.57 1 1
Thromboxane A2 receptor signaling

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
TGM2 0.001 0.081 -10000 0 -0.54 11 11
GNB1/GNG2 -0.057 0.078 -10000 0 -0.19 86 86
AKT1 -0.021 0.11 -10000 0 -0.21 26 26
EGF -0.058 0.19 -10000 0 -0.53 65 65
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.007 0.076 -10000 0 -0.32 8 8
mol:Ca2+ -0.052 0.15 -10000 0 -0.3 119 119
LYN 0.008 0.073 -10000 0 -0.3 6 6
RhoA/GTP -0.035 0.052 -10000 0 -0.13 29 29
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.059 0.18 -10000 0 -0.34 120 120
GNG2 0.007 0.053 -10000 0 -0.47 6 6
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.004 0.11 -10000 0 -0.36 43 43
G beta5/gamma2 -0.074 0.1 -10000 0 -0.26 87 87
PRKCH -0.06 0.17 -10000 0 -0.34 118 118
DNM1 0.011 0.034 -10000 0 -0.52 2 2
TXA2/TP beta/beta Arrestin3 -0.007 0.018 -10000 0 -0.19 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.023 0.13 -10000 0 -0.47 37 37
G12 family/GTP -0.087 0.12 -10000 0 -0.3 119 119
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.022 -10000 0 -0.47 1 1
RhoA/GTP/ROCK1 0.017 0.013 -10000 0 -0.28 1 1
mol:GDP 0.033 0.11 0.3 34 -10000 0 34
mol:NADP 0.006 0.064 -10000 0 -0.57 6 6
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.12 0.22 -10000 0 -0.47 143 143
mol:IP3 -0.069 0.18 -10000 0 -0.37 119 119
cell morphogenesis 0.017 0.013 -10000 0 -0.27 1 1
PLCB2 -0.1 0.24 -10000 0 -0.5 118 118
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.045 0.12 -10000 0 -0.35 38 38
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.006 0.08 -10000 0 -0.34 9 9
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR -0.043 0.17 -10000 0 -0.56 48 48
PRKCB1 -0.068 0.18 -10000 0 -0.36 119 119
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.006 0.064 -10000 0 -0.57 6 6
TXA2/TXA2-R family -0.1 0.25 -10000 0 -0.52 119 119
LCK 0.004 0.085 -10000 0 -0.34 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.024 0.079 -10000 0 -0.34 8 8
TXA2-R family/G12 family/GDP/G beta/gamma 0.017 0.035 -10000 0 -0.22 3 3
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.003 0.084 -10000 0 -0.38 6 6
MAPK14 -0.03 0.12 -10000 0 -0.23 85 85
TGM2/GTP -0.083 0.21 -10000 0 -0.42 117 117
MAPK11 -0.033 0.12 -10000 0 -0.23 119 119
ARHGEF1 -0.023 0.094 -10000 0 -0.18 67 67
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.071 0.19 -10000 0 -0.38 119 119
RAB11/GDP 0.014 0.002 -10000 0 -10000 0 0
ICAM1 -0.046 0.14 -10000 0 -0.28 120 120
cAMP biosynthetic process -0.069 0.18 -10000 0 -0.35 118 118
Gq family/GTP/EBP50 0.007 0.068 -10000 0 -0.22 42 42
actin cytoskeleton reorganization 0.017 0.013 -10000 0 -0.27 1 1
SRC 0.008 0.073 -10000 0 -0.3 6 6
GNB5 0.012 0.022 -10000 0 -0.47 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.011 0.092 -10000 0 -0.28 17 17
VCAM1 -0.051 0.15 -10000 0 -0.29 118 118
TP beta/Gq family/GDP/G beta5/gamma2 -0.004 0.11 -10000 0 -0.36 43 43
platelet activation -0.042 0.16 -10000 0 -0.3 116 116
PGI2/IP -0.031 0.13 -10000 0 -0.42 48 48
PRKACA -0.02 0.089 -10000 0 -0.21 84 84
Gq family/GDP/G beta5/gamma2 -0.004 0.1 -10000 0 -0.33 43 43
TXA2/TP beta/beta Arrestin2 -0.004 0.023 -10000 0 -0.45 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.017 0.095 -10000 0 -0.27 24 24
mol:DAG -0.078 0.2 -10000 0 -0.41 119 119
EGFR -0.025 0.13 -10000 0 -0.47 40 40
TXA2/TP alpha -0.098 0.24 -10000 0 -0.48 117 117
Gq family/GTP -0.011 0.054 -10000 0 -0.18 42 42
YES1 0.008 0.073 -10000 0 -0.3 6 6
GNAI2/GTP -0.029 0.066 -10000 0 -0.35 6 6
PGD2/DP -0.016 0.092 -10000 0 -0.34 37 37
SLC9A3R1 0.013 0 -10000 0 -10000 0 0
FYN 0.007 0.076 -10000 0 -0.34 7 7
mol:NO 0.006 0.064 -10000 0 -0.57 6 6
GNA15 -0.011 0.1 -10000 0 -0.47 25 25
PGK/cGMP -0.071 0.14 -10000 0 -0.28 149 149
RhoA/GDP 0.014 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.003 0.1 -10000 0 -0.45 8 8
NOS3 0.006 0.064 -10000 0 -0.57 6 6
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.066 0.18 -10000 0 -0.35 118 118
PRKCB -0.091 0.2 -10000 0 -0.4 123 123
PRKCE -0.057 0.17 -10000 0 -0.34 118 118
PRKCD -0.067 0.18 -10000 0 -0.37 119 119
PRKCG -0.073 0.19 -10000 0 -0.38 120 120
muscle contraction -0.096 0.24 -10000 0 -0.48 119 119
PRKCZ -0.057 0.17 -10000 0 -0.34 117 117
ARR3 0.002 0.037 -10000 0 -0.57 2 2
TXA2/TP beta -0.008 0.086 -10000 0 -0.39 6 6
PRKCQ -0.071 0.18 -10000 0 -0.36 122 122
MAPKKK cascade -0.093 0.22 -10000 0 -0.46 119 119
SELE -0.076 0.19 -10000 0 -0.39 120 120
TP beta/GNAI2/GDP/G beta/gamma 0.003 0.091 -10000 0 -0.4 8 8
ROCK1 0.012 0.022 -10000 0 -0.47 1 1
GNA14 0.011 0.03 -10000 0 -0.47 2 2
chemotaxis -0.12 0.28 -10000 0 -0.6 119 119
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.003 0.087 -10000 0 -0.47 17 17
Rac1/GTP 0.008 0.004 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.003 0.086 -10000 0 -0.29 38 38
fibroblast growth factor receptor signaling pathway 0.003 0.086 -10000 0 -0.29 38 38
LAMA1 -0.038 0.16 -10000 0 -0.53 47 47
PRNP 0.012 0.022 -10000 0 -0.47 1 1
GPC1/SLIT2 -0.024 0.12 -10000 0 -0.33 62 62
SMAD2 0.023 0.048 -10000 0 -0.48 1 1
GPC1/PrPc/Cu2+ 0.017 0.018 -10000 0 -0.27 2 2
GPC1/Laminin alpha1 -0.018 0.12 -10000 0 -0.38 47 47
TDGF1 -0.051 0.16 -10000 0 -0.48 64 64
CRIPTO/GPC1 -0.027 0.12 -10000 0 -0.33 65 65
APP/GPC1 0.017 0.036 -10000 0 -0.42 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.014 0.1 -10000 0 -0.27 65 65
FLT1 0.007 0.057 -10000 0 -0.5 6 6
GPC1/TGFB/TGFBR1/TGFBR2 0.018 0.053 -10000 0 -0.52 1 1
SERPINC1 -0.027 0.14 -10000 0 -0.57 32 32
FYN -0.015 0.1 -10000 0 -0.27 67 67
FGR -0.016 0.1 -10000 0 -0.27 68 68
positive regulation of MAPKKK cascade -0.036 0.14 -10000 0 -0.34 64 64
SLIT2 -0.047 0.16 -10000 0 -0.47 62 62
GPC1/NRG -0.079 0.16 -10000 0 -0.32 142 142
NRG1 -0.12 0.22 -10000 0 -0.47 141 141
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.004 0.088 -10000 0 -0.3 35 35
LYN -0.014 0.1 -10000 0 -0.27 65 65
mol:Spermine 0.01 0.015 -10000 0 -0.33 1 1
cell growth 0.003 0.086 -10000 0 -0.29 38 38
BMP signaling pathway -0.012 0.022 0.47 1 -10000 0 1
SRC -0.014 0.1 -10000 0 -0.27 65 65
TGFBR1 0.013 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.2 0.28 -10000 0 -0.56 183 183
GPC1 0.012 0.022 -10000 0 -0.47 1 1
TGFBR1 (dimer) 0.013 0 -10000 0 -10000 0 0
VEGFA -0.018 0.12 -10000 0 -0.48 31 31
BLK -0.086 0.17 -10000 0 -0.32 159 159
HCK -0.017 0.1 -10000 0 -0.27 70 70
FGF2 -0.024 0.13 -10000 0 -0.47 38 38
FGFR1 0.011 0.03 -10000 0 -0.47 2 2
VEGFR1 homodimer 0.007 0.057 -10000 0 -0.5 6 6
TGFBR2 0 0.08 -10000 0 -0.47 14 14
cell death 0.017 0.035 -10000 0 -0.42 3 3
ATIII/GPC1 -0.011 0.11 -10000 0 -0.41 33 33
PLA2G2A/GPC1 -0.14 0.2 -10000 0 -0.4 184 184
LCK -0.021 0.11 -10000 0 -0.29 72 72
neuron differentiation -0.079 0.16 -10000 0 -0.32 142 142
PrPc/Cu2+ 0.009 0.015 -10000 0 -0.33 1 1
APP 0.01 0.037 -10000 0 -0.47 3 3
TGFBR2 (dimer) 0 0.079 -10000 0 -0.47 14 14
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.071 0.2 -9999 0 -0.5 58 58
MAP3K8 -0.002 0.084 -9999 0 -0.48 15 15
FOS -0.057 0.16 -9999 0 -0.4 60 60
PRKCA -0.01 0.1 -9999 0 -0.47 23 23
PTPN7 -0.015 0.12 -9999 0 -0.57 23 23
HRAS 0.006 0.064 -9999 0 -0.57 6 6
PRKCB -0.098 0.2 -9999 0 -0.47 114 114
NRAS 0.012 0.022 -9999 0 -0.47 1 1
RAS family/GTP 0.018 0.04 -9999 0 -0.31 7 7
MAPK3 -0.027 0.093 -9999 0 -0.25 25 25
MAP2K1 -0.094 0.25 -9999 0 -0.5 116 116
ELK1 0.011 0.008 -9999 0 -10000 0 0
BRAF -0.09 0.23 -9999 0 -0.47 116 116
mol:GTP -0.001 0.002 -9999 0 -0.005 87 87
MAPK1 -0.027 0.093 -9999 0 -0.28 14 14
RAF1 -0.089 0.23 -9999 0 -0.46 116 116
KRAS 0.013 0.001 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.018 0.12 -9999 0 -0.35 51 51
alphaV beta3 Integrin -0.054 0.17 -9999 0 -0.54 35 35
PTK2 -0.1 0.24 -9999 0 -0.53 96 96
IGF1R 0.011 0.034 -9999 0 -0.52 2 2
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 0.01 0.037 -9999 0 -0.47 3 3
SRC 0.013 0 -9999 0 -10000 0 0
CDKN1B -0.083 0.19 -9999 0 -0.48 70 70
VEGFA -0.018 0.12 -9999 0 -0.48 31 31
ILK -0.083 0.19 -9999 0 -0.48 70 70
ROCK1 0.012 0.022 -9999 0 -0.47 1 1
AKT1 -0.07 0.18 -9999 0 -0.46 61 61
PTK2B -0.043 0.14 -9999 0 -0.45 31 31
alphaV/beta3 Integrin/JAM-A -0.092 0.2 -9999 0 -0.54 53 53
CBL 0.012 0.022 -9999 0 -0.47 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.18 0.22 -9999 0 -0.38 251 251
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.12 -9999 0 -0.4 29 29
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.065 0.16 -9999 0 -0.4 59 59
alphaV/beta3 Integrin/Syndecan-1 -0.046 0.14 -9999 0 -0.29 114 114
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.096 0.2 -9999 0 -0.59 55 55
PI4 Kinase 0.02 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
alphaV/beta3 Integrin/Osteopontin -0.09 0.17 -9999 0 -0.32 165 165
RPS6KB1 -0.052 0.2 -9999 0 -0.55 55 55
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.11 0.28 -9999 0 -0.74 65 65
GPR124 -0.01 0.1 -9999 0 -0.47 24 24
MAPK1 -0.11 0.28 -9999 0 -0.74 65 65
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
alphaV/beta3 Integrin/Tumstatin -0.051 0.16 -9999 0 -0.32 111 111
cell adhesion -0.14 0.19 -9999 0 -0.56 51 51
ANGPTL3 -0.22 0.29 -9999 0 -0.57 198 198
VEGFR2 homodimer/VEGFA homodimer/Src -0.005 0.098 -9999 0 -0.29 51 51
IGF-1R heterotetramer 0.011 0.034 -9999 0 -0.52 2 2
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
TGFBR2 0 0.08 -9999 0 -0.47 14 14
ITGB3 -0.084 0.19 -9999 0 -0.47 101 101
IGF1 -0.045 0.16 -9999 0 -0.5 56 56
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.047 0.16 -9999 0 -0.54 24 24
apoptosis 0.01 0.037 -9999 0 -0.47 3 3
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.034 0.12 -9999 0 -0.27 101 101
VCL -0.017 0.12 -9999 0 -0.47 31 31
alphaV/beta3 Integrin/Del1 -0.09 0.2 -9999 0 -0.5 77 77
CSF1 0.002 0.074 -9999 0 -0.47 12 12
PIK3C2A -0.083 0.19 -9999 0 -0.48 70 70
PI4 Kinase/Pyk2 -0.12 0.18 -9999 0 -0.49 68 68
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.05 0.16 -9999 0 -0.48 31 31
FAK1/Vinculin -0.08 0.21 -9999 0 -0.49 74 74
alphaV beta3/Integrin/ppsTEM5 -0.047 0.16 -9999 0 -0.55 24 24
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.1 0.22 -9999 0 -0.52 107 107
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 -0.024 0.13 -9999 0 -0.47 38 38
F11R -0.006 0.093 -9999 0 -0.33 38 38
alphaV/beta3 Integrin/Lactadherin -0.036 0.13 -9999 0 -0.28 101 101
alphaV/beta3 Integrin/TGFBR2 -0.041 0.14 -9999 0 -0.31 102 102
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.026 0.05 -9999 0 -0.48 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.03 0.11 -9999 0 -0.48 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.003 0.09 -9999 0 -0.49 16 16
alphaV/beta3 Integrin/Pyk2 -0.041 0.15 -9999 0 -0.45 31 31
SDC1 -0.007 0.097 -9999 0 -0.47 21 21
VAV3 0 0.1 -9999 0 -0.47 10 10
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
IRS1 -0.003 0.087 -9999 0 -0.47 17 17
FAK1/Paxillin -0.072 0.19 -9999 0 -0.45 68 68
cell migration -0.064 0.19 -9999 0 -0.44 74 74
ITGAV 0.01 0.037 -9999 0 -0.47 3 3
PI3K -0.11 0.17 -9999 0 -0.51 55 55
SPP1 -0.076 0.21 -9999 0 -0.57 76 76
KDR -0.009 0.1 -9999 0 -0.47 23 23
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.037 -9999 0 -0.47 3 3
COL4A3 -0.017 0.12 -9999 0 -0.47 31 31
angiogenesis -0.12 0.28 -9999 0 -0.6 105 105
Rac1/GTP 0.007 0.094 -9999 0 -0.43 10 10
EDIL3 -0.086 0.19 -9999 0 -0.47 102 102
cell proliferation -0.041 0.14 -9999 0 -0.31 102 102
IL6-mediated signaling events

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
BCL2L1 -0.057 0.22 -10000 0 -0.65 20 20
CRP -0.077 0.24 -10000 0 -0.71 27 27
cell cycle arrest -0.072 0.24 -10000 0 -0.65 41 41
TIMP1 -0.054 0.22 -10000 0 -0.7 23 23
IL6ST -0.084 0.2 -10000 0 -0.47 102 102
Rac1/GDP -0.11 0.23 -10000 0 -0.48 105 105
AP1 -0.017 0.14 -10000 0 -0.5 10 10
GAB2 0.014 0.002 -10000 0 -10000 0 0
TNFSF11 -0.065 0.23 -10000 0 -0.73 21 21
HSP90B1 0.018 0.044 -10000 0 -10000 0 0
GAB1 0.013 0.022 -10000 0 -0.47 1 1
MAPK14 -0.15 0.3 -10000 0 -0.64 109 109
AKT1 0.044 0.057 -10000 0 -1 1 1
FOXO1 0.049 0.053 -10000 0 -0.94 1 1
MAP2K6 -0.14 0.27 -10000 0 -0.57 110 110
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.087 0.23 -10000 0 -0.52 78 78
MITF -0.11 0.23 -10000 0 -0.47 114 114
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.013 0 -10000 0 -10000 0 0
A2M 0.016 0.049 -10000 0 -10000 0 0
CEBPB 0.02 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.016 0.086 -10000 0 -0.4 2 2
STAT3 -0.074 0.26 -10000 0 -0.68 42 42
STAT1 -0.009 0.025 -10000 0 -10000 0 0
CEBPD -0.062 0.23 -10000 0 -0.71 23 23
PIK3CA 0.012 0.037 -10000 0 -0.47 3 3
PI3K 0.016 0.05 -10000 0 -0.36 8 8
JUN 0.006 0.06 -10000 0 -0.5 7 7
PIAS3/MITF -0.1 0.22 -10000 0 -0.45 109 109
MAPK11 -0.15 0.31 -10000 0 -0.65 112 112
STAT3 (dimer)/FOXO1 -0.013 0.2 -10000 0 -0.58 11 11
GRB2/SOS1/GAB family -0.11 0.16 -10000 0 -0.45 69 69
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.22 -10000 0 -0.45 115 115
GRB2 0.014 0.001 -10000 0 -10000 0 0
JAK2 0.012 0.022 -10000 0 -0.47 1 1
LBP -0.054 0.21 -10000 0 -0.59 27 27
PIK3R1 0.009 0.053 -10000 0 -0.47 6 6
JAK1 0.013 0.007 -10000 0 -10000 0 0
MYC -0.071 0.24 -10000 0 -0.69 22 22
FGG -0.072 0.23 -10000 0 -0.68 29 29
macrophage differentiation -0.072 0.24 -10000 0 -0.65 41 41
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.12 0.21 -10000 0 -0.44 104 104
JUNB -0.072 0.25 -10000 0 -0.78 32 32
FOS -0.076 0.19 -10000 0 -0.47 91 91
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.24 -10000 0 -0.49 119 119
STAT1/PIAS1 -0.091 0.2 -10000 0 -0.45 81 81
GRB2/SOS1/GAB family/SHP2/PI3K 0.034 0.06 -10000 0 -1.1 1 1
STAT3 (dimer) -0.072 0.25 -10000 0 -0.68 41 41
PRKCD -0.07 0.24 -10000 0 -0.55 58 58
IL6R -0.024 0.13 -10000 0 -0.47 39 39
SOCS3 -0.2 0.42 -10000 0 -1 83 83
gp130 (dimer)/JAK1/JAK1/LMO4 -0.031 0.12 -10000 0 -0.28 72 72
Rac1/GTP -0.1 0.23 -10000 0 -0.51 89 89
HCK 0.008 0.05 -10000 0 -0.49 5 5
MAPKKK cascade 0.009 0.074 -10000 0 -0.85 1 1
bone resorption -0.06 0.22 -10000 0 -0.69 21 21
IRF1 -0.062 0.23 -10000 0 -0.7 22 22
mol:GDP -0.12 0.24 -10000 0 -0.48 122 122
SOS1 0.014 0.002 -10000 0 -10000 0 0
VAV1 -0.12 0.24 -10000 0 -0.48 122 122
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.31 -10000 0 -0.68 112 112
PTPN11 -0.008 0.047 -10000 0 -1 1 1
IL6/IL6RA -0.12 0.2 -10000 0 -0.38 186 186
gp130 (dimer)/TYK2/TYK2/LMO4 -0.033 0.12 -10000 0 -0.28 70 70
gp130 (dimer)/JAK2/JAK2/LMO4 -0.034 0.12 -10000 0 -0.29 50 50
IL6 -0.15 0.25 -10000 0 -0.51 159 159
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE 0.004 0.055 -10000 0 -0.48 6 6
PIAS1 0.012 0.022 -10000 0 -0.47 1 1
RAC1 0.014 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.21 0.2 1 -0.43 117 118
LMO4 0.014 0.025 -10000 0 -0.51 1 1
STAT3 (dimer)/PIAS3 -0.076 0.24 -10000 0 -0.66 38 38
MCL1 0.05 0.049 -10000 0 -0.85 1 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.15 0.34 -10000 0 -0.91 49 49
PCK1 -0.14 0.25 -10000 0 -0.69 46 46
HNF4A -0.2 0.41 -10000 0 -1.1 57 57
KCNJ11 -0.16 0.36 -10000 0 -0.94 50 50
AKT1 -0.032 0.13 -10000 0 -0.43 10 10
response to starvation -0.006 0.02 -10000 0 -10000 0 0
DLK1 -0.2 0.4 -10000 0 -0.95 74 74
NKX2-1 -0.14 0.26 0.48 1 -0.58 74 75
ACADM -0.16 0.34 -10000 0 -0.93 48 48
TAT -0.14 0.27 -10000 0 -0.74 56 56
CEBPB 0.007 0.015 -10000 0 -10000 0 0
CEBPA 0.01 0.013 -10000 0 -10000 0 0
TTR -0.22 0.35 -10000 0 -0.87 74 74
PKLR -0.18 0.37 -10000 0 -0.94 61 61
APOA1 -0.22 0.45 -10000 0 -1.2 63 63
CPT1C -0.16 0.36 -10000 0 -0.96 52 52
ALAS1 -0.045 0.16 -10000 0 -10000 0 0
TFRC -0.15 0.29 -10000 0 -0.78 50 50
FOXF1 0 0.15 -10000 0 -0.44 44 44
NF1 0.02 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.06 0.19 -10000 0 -0.58 59 59
CPT1A -0.15 0.34 -10000 0 -0.91 49 49
HMGCS1 -0.15 0.34 -10000 0 -0.93 46 46
NR3C1 -0.001 0.082 -10000 0 -0.47 13 13
CPT1B -0.19 0.37 -10000 0 -0.95 62 62
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.012 0.018 -10000 0 -10000 0 0
GCK -0.18 0.38 -10000 0 -0.96 63 63
CREB1 0.009 0.03 -10000 0 -10000 0 0
IGFBP1 -0.081 0.21 -10000 0 -0.72 26 26
PDX1 -0.093 0.22 -10000 0 -0.65 29 29
UCP2 -0.16 0.34 -10000 0 -0.94 49 49
ALDOB -0.17 0.38 -10000 0 -1 48 48
AFP -0.089 0.19 -10000 0 -0.54 55 55
BDH1 -0.15 0.34 -10000 0 -0.93 46 46
HADH -0.15 0.35 -10000 0 -0.95 45 45
F2 -0.2 0.41 -10000 0 -1.1 49 49
HNF1A -0.06 0.19 -10000 0 -0.58 59 59
G6PC -0.073 0.17 -10000 0 -0.56 24 24
SLC2A2 -0.12 0.24 -10000 0 -0.74 25 25
INS -0.02 0.097 -10000 0 -0.58 14 14
FOXA1 -0.014 0.12 -10000 0 -0.34 13 13
FOXA3 -0.11 0.21 -10000 0 -0.52 76 76
FOXA2 -0.19 0.4 -10000 0 -1 55 55
ABCC8 -0.22 0.44 -10000 0 -0.98 92 92
ALB -0.14 0.24 -10000 0 -0.56 81 81
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.03 0.073 0.17 107 -10000 0 107
BUB1B -0.056 0.12 -10000 0 -0.25 133 133
PLK1 -0.012 0.048 -10000 0 -0.13 42 42
PLK1S1 0 0.025 -10000 0 -0.13 2 2
KIF2A -0.004 0.045 -10000 0 -0.25 3 3
regulation of mitotic centrosome separation -0.012 0.048 -10000 0 -0.13 42 42
GOLGA2 0.013 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.085 0.17 -10000 0 -0.34 146 146
WEE1 -0.003 0.05 -10000 0 -0.26 5 5
cytokinesis -0.1 0.15 -10000 0 -0.27 194 194
PP2A-alpha B56 0.001 0.068 -10000 0 -0.6 1 1
AURKA -0.007 0.043 -10000 0 -0.14 36 36
PICH/PLK1 -0.025 0.14 -10000 0 -0.45 44 44
CENPE -0.045 0.14 -10000 0 -0.4 64 64
RhoA/GTP 0.01 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.045 -10000 0 -0.25 3 3
PPP2CA 0.013 0 -10000 0 -10000 0 0
FZR1 0.013 0 -10000 0 -10000 0 0
TPX2 -0.031 0.066 -10000 0 -0.13 156 156
PAK1 0.005 0.062 -10000 0 -0.48 8 8
SPC24 -0.16 0.26 -10000 0 -0.57 142 142
FBXW11 0.013 0 -10000 0 -10000 0 0
CLSPN -0.018 0.064 -10000 0 -0.17 63 63
GORASP1 0.013 0 -10000 0 -10000 0 0
metaphase -0.002 0.005 -10000 0 -0.011 108 108
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.006 0.025 -10000 0 -0.064 44 44
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.009 20 20
STAG2 0.013 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.004 0.009 -10000 0 -10000 0 0
spindle elongation -0.012 0.048 -10000 0 -0.13 42 42
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 -0.03 0.066 -10000 0 -0.66 1 1
TPT1 0 0.025 -10000 0 -0.13 2 2
CDC25C -0.061 0.084 -10000 0 -0.16 162 162
CDC25B 0.01 0.044 -10000 0 -0.55 3 3
SGOL1 -0.03 0.073 -10000 0 -0.17 107 107
RHOA 0.013 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.023 0.074 -10000 0 -0.33 24 24
CDC14B 0.007 0.035 -10000 0 -0.34 5 5
CDC20 -0.19 0.28 -10000 0 -0.57 169 169
PLK1/PBIP1 -0.038 0.12 -10000 0 -0.38 52 52
mitosis 0.001 0.006 0.021 32 -0.02 4 36
FBXO5 -0.001 0.037 -10000 0 -0.17 4 4
CDC2 0 0.004 -10000 0 -0.014 25 25
NDC80 0.009 0.043 -10000 0 -0.47 4 4
metaphase plate congression -0.004 0.032 -10000 0 -0.14 2 2
ERCC6L -0.02 0.13 -10000 0 -0.42 44 44
NLP/gamma Tubulin -0.003 0.027 -10000 0 -0.079 21 21
microtubule cytoskeleton organization 0 0.025 -10000 0 -0.13 2 2
G2/M transition DNA damage checkpoint 0 0.002 0.01 6 -10000 0 6
PPP1R12A 0.013 0.001 -10000 0 -10000 0 0
interphase 0 0.002 0.01 6 -10000 0 6
PLK1/PRC1-2 -0.13 0.21 -10000 0 -0.38 188 188
GRASP65/GM130/RAB1/GTP/PLK1 0.011 0.039 -10000 0 -10000 0 0
RAB1A 0.013 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.002 0.04 -10000 0 -0.18 5 5
mitotic prometaphase -0.002 0.003 -10000 0 -0.009 36 36
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.061 -10000 0 -0.3 4 4
microtubule-based process -0.12 0.19 -10000 0 -0.36 188 188
Golgi organization -0.012 0.048 -10000 0 -0.13 42 42
Cohesin/SA2 -0.007 0.044 -10000 0 -0.23 2 2
PPP1CB/MYPT1 0.019 0.002 -10000 0 -10000 0 0
KIF20A -0.21 0.28 -10000 0 -0.57 188 188
APC/C/CDC20 -0.11 0.19 -10000 0 -0.37 169 169
PPP2R1A 0.013 0 -10000 0 -10000 0 0
chromosome segregation -0.038 0.12 -10000 0 -0.38 52 52
PRC1 -0.017 0.13 -10000 0 -0.57 26 26
ECT2 -0.014 0.083 -10000 0 -0.39 18 18
C13orf34 -0.003 0.04 -10000 0 -0.18 5 5
NUDC -0.004 0.032 -10000 0 -0.14 2 2
regulation of attachment of spindle microtubules to kinetochore -0.055 0.12 -10000 0 -0.24 133 133
spindle assembly -0.006 0.039 -10000 0 -0.1 37 37
spindle stabilization 0 0.025 -10000 0 -0.13 2 2
APC/C/HCDH1 0.015 0.03 -10000 0 -0.28 5 5
MKLP2/PLK1 -0.13 0.19 -10000 0 -0.36 188 188
CCNB1 -0.014 0.12 -10000 0 -0.57 23 23
PPP1CB 0.013 0.001 -10000 0 -10000 0 0
BTRC 0.013 0 -10000 0 -10000 0 0
ROCK2 -0.031 0.12 -10000 0 -0.39 45 45
TUBG1 0 0.025 -10000 0 -0.13 2 2
G2/M transition of mitotic cell cycle -0.024 0.071 -10000 0 -0.32 24 24
MLF1IP -0.038 0.14 -10000 0 -0.43 52 52
INCENP 0.013 0.002 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.01 0.1 -9999 0 -0.4 24 24
alphaM/beta2 Integrin/GPIbA -0.008 0.097 -9999 0 -0.44 16 16
alphaM/beta2 Integrin/proMMP-9 -0.2 0.2 -9999 0 -0.37 276 276
PLAUR 0.004 0.074 -9999 0 -0.57 8 8
HMGB1 0 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.001 0.076 -9999 0 -0.43 11 11
AGER -0.027 0.12 -9999 0 -0.58 23 23
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG 0.005 0.067 -9999 0 -0.56 7 7
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.049 0.14 -9999 0 -0.39 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.31 0.29 -9999 0 -0.57 272 272
CYR61 -0.005 0.096 -9999 0 -0.51 17 17
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.066 0.1 -9999 0 -0.34 35 35
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer 0.005 0.064 -9999 0 -0.47 9 9
MYH2 -0.13 0.18 -9999 0 -0.42 89 89
MST1R -0.005 0.095 -9999 0 -0.49 18 18
leukocyte activation during inflammatory response -0.1 0.15 -9999 0 -0.34 95 95
APOB -0.1 0.2 -9999 0 -0.47 117 117
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.002 0.086 -9999 0 -0.47 16 16
JAM3 -0.004 0.09 -9999 0 -0.47 18 18
GP1BA 0 0.078 -9999 0 -0.49 12 12
alphaM/beta2 Integrin/CTGF -0.012 0.099 -9999 0 -0.36 29 29
alphaM/beta2 Integrin -0.07 0.13 -9999 0 -0.37 48 48
JAM3 homodimer -0.004 0.09 -9999 0 -0.47 18 18
ICAM2 0.01 0.04 -9999 0 -0.5 3 3
ICAM1 0 0.086 -9999 0 -0.57 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.069 0.13 -9999 0 -0.36 48 48
cell adhesion -0.009 0.096 -9999 0 -0.44 16 16
NFKB1 -0.088 0.21 -9999 0 -0.6 32 32
THY1 0.003 0.077 -9999 0 -0.56 9 9
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.092 0.16 -9999 0 -0.31 164 164
alphaM/beta2 Integrin/LRP/tPA -0.011 0.11 -9999 0 -0.36 37 37
IL6 -0.18 0.33 -9999 0 -0.62 162 162
ITGB2 -0.01 0.076 -9999 0 -0.58 8 8
elevation of cytosolic calcium ion concentration -0.005 0.1 -9999 0 -0.39 23 23
alphaM/beta2 Integrin/JAM2/JAM3 -0.005 0.1 -9999 0 -0.44 16 16
JAM2 0.006 0.06 -9999 0 -0.47 8 8
alphaM/beta2 Integrin/ICAM1 -0.041 0.15 -9999 0 -0.37 46 46
alphaM/beta2 Integrin/uPA/Plg -0.02 0.11 -9999 0 -0.36 40 40
RhoA/GTP -0.081 0.15 -9999 0 -0.43 45 45
positive regulation of phagocytosis -0.057 0.1 -9999 0 -0.44 17 17
Ron/MSP -0.049 0.16 -9999 0 -0.41 79 79
alphaM/beta2 Integrin/uPAR/uPA -0.005 0.11 -9999 0 -0.4 23 23
alphaM/beta2 Integrin/uPAR -0.007 0.095 -9999 0 -0.43 18 18
PLAU -0.001 0.084 -9999 0 -0.47 15 15
PLAT -0.019 0.13 -9999 0 -0.54 29 29
actin filament polymerization -0.13 0.17 -9999 0 -0.4 89 89
MST1 -0.062 0.2 -9999 0 -0.57 64 64
alphaM/beta2 Integrin/lipoprotein(a) -0.086 0.16 -9999 0 -0.34 95 95
TNF -0.097 0.24 -9999 0 -0.7 45 45
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.009 0.098 -9999 0 -0.38 24 24
fibrinolysis -0.021 0.11 -9999 0 -0.36 40 40
HCK 0.008 0.05 -9999 0 -0.49 5 5
dendritic cell antigen processing and presentation -0.069 0.13 -9999 0 -0.36 48 48
VTN -0.1 0.22 -9999 0 -0.52 107 107
alphaM/beta2 Integrin/CYR61 -0.012 0.1 -9999 0 -0.4 26 26
LPA -0.056 0.17 -9999 0 -0.48 69 69
LRP1 0.01 0.04 -9999 0 -0.5 3 3
cell migration -0.18 0.18 -9999 0 -0.33 282 282
FN1 -0.003 0.09 -9999 0 -0.49 16 16
alphaM/beta2 Integrin/Thy1 -0.007 0.095 -9999 0 -0.44 17 17
MPO -0.025 0.13 -9999 0 -0.47 39 39
KNG1 -0.072 0.2 -9999 0 -0.57 66 66
RAP1/GDP 0.018 0 -9999 0 -10000 0 0
ROCK1 -0.071 0.14 -9999 0 -0.42 40 40
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.022 0.12 -9999 0 -0.57 24 24
CTGF -0.006 0.096 -9999 0 -0.47 20 20
alphaM/beta2 Integrin/Hck -0.004 0.089 -9999 0 -0.44 14 14
ITGAM -0.006 0.061 -9999 0 -0.52 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 0 0.1 -9999 0 -0.45 16 16
HP -0.08 0.21 -9999 0 -0.54 83 83
leukocyte adhesion -0.071 0.12 -9999 0 -0.46 26 26
SELP 0.005 0.064 -9999 0 -0.47 9 9
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 -0.001 0.093 -9999 0 -0.41 24 24
VLDLR 0.012 0.022 -9999 0 -0.47 1 1
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.011 0.03 -9999 0 -0.47 2 2
ITGA3 0.003 0.071 -9999 0 -0.47 11 11
RELN/VLDLR/Fyn -0.035 0.14 -9999 0 -0.34 85 85
MAPK8IP1/MKK7/MAP3K11/JNK1 0.032 0.043 -9999 0 -0.28 1 1
AKT1 -0.087 0.14 -9999 0 -0.37 48 48
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 -0.18 0.23 -9999 0 -0.47 193 193
RELN/LRP8/DAB1 -0.14 0.19 -9999 0 -0.45 84 84
LRPAP1/LRP8 0.014 0.051 -9999 0 -0.41 7 7
RELN/LRP8/DAB1/Fyn -0.12 0.18 -9999 0 -0.43 83 83
DAB1/alpha3/beta1 Integrin -0.12 0.16 -9999 0 -0.51 48 48
long-term memory -0.16 0.22 -9999 0 -0.54 91 91
DAB1/LIS1 -0.13 0.16 -9999 0 -0.5 47 47
DAB1/CRLK/C3G -0.12 0.15 -9999 0 -0.48 47 47
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
DAB1/NCK2 -0.13 0.16 -9999 0 -0.5 47 47
ARHGEF2 0.012 0.022 -9999 0 -0.47 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.094 0.2 -9999 0 -0.47 110 110
CDK5R1 -0.015 0.13 -9999 0 -0.57 24 24
RELN -0.082 0.22 -9999 0 -0.57 82 82
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
RELN/LRP8/Fyn -0.04 0.15 -9999 0 -0.35 88 88
GRIN2A/RELN/LRP8/DAB1/Fyn -0.17 0.23 -9999 0 -0.56 90 90
MAPK8 0.002 0.074 -9999 0 -0.47 12 12
RELN/VLDLR/DAB1 -0.13 0.19 -9999 0 -0.31 232 232
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.14 0.2 -9999 0 -0.54 64 64
RELN/LRP8 -0.039 0.15 -9999 0 -0.35 86 86
GRIN2B/RELN/LRP8/DAB1/Fyn -0.12 0.18 -9999 0 -0.53 48 48
PI3K 0.014 0.049 -9999 0 -0.36 8 8
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.012 0.051 -9999 0 -0.32 11 11
RAP1A -0.085 0.16 -9999 0 -0.45 47 47
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0.026 -9999 0 -0.57 1 1
CRLK/C3G 0.02 0 -9999 0 -10000 0 0
GRIN2B 0.002 0.026 -9999 0 -0.57 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.066 0.12 -9999 0 -0.3 51 51
neuron adhesion -0.074 0.16 -9999 0 -0.45 46 46
LRP8 0.005 0.069 -9999 0 -0.57 7 7
GSK3B -0.077 0.13 -9999 0 -0.35 48 48
RELN/VLDLR/DAB1/Fyn -0.12 0.18 -9999 0 -0.42 80 80
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.1 0.15 -9999 0 -0.38 54 54
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.021 0.042 -9999 0 -0.41 3 3
neuron migration -0.089 0.17 -9999 0 -0.4 57 57
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.067 0.12 -9999 0 -0.3 51 51
RELN/VLDLR -0.027 0.14 -9999 0 -0.32 81 81
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.003 0.11 -9999 0 -0.49 13 13
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.12 -9999 0 -0.37 14 14
AP1 -0.098 0.16 -9999 0 -0.51 51 51
mol:PIP3 -0.069 0.14 -9999 0 -0.44 44 44
AKT1 0.026 0.086 -9999 0 -0.34 15 15
PTK2B -0.006 0.092 -9999 0 -0.3 30 30
RHOA 0.018 0.034 -9999 0 -0.29 1 1
PIK3CB 0.012 0.026 -9999 0 -0.57 1 1
mol:Ca2+ -0.011 0.11 -9999 0 -0.33 24 24
MAGI3 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.047 0.15 -9999 0 -0.53 24 24
HRAS/GDP 0.005 0.047 -9999 0 -0.42 6 6
positive regulation of microtubule depolymerization 0.006 0.083 -9999 0 -0.32 14 14
NF kappa B1 p50/RelA -0.059 0.12 -9999 0 -0.45 26 26
endothelial cell migration -0.018 0.14 -9999 0 -0.69 16 16
ADCY4 -0.058 0.23 -9999 0 -0.56 70 70
ADCY5 -0.098 0.3 -9999 0 -0.69 87 87
ADCY6 -0.056 0.22 -9999 0 -0.55 70 70
ADCY7 -0.056 0.22 -9999 0 -0.55 70 70
ADCY1 -0.068 0.23 -9999 0 -0.57 71 71
ADCY2 -0.067 0.24 -9999 0 -0.57 77 77
ADCY3 -0.057 0.22 -9999 0 -0.55 70 70
ADCY8 -0.06 0.22 -9999 0 -0.56 70 70
ADCY9 -0.057 0.22 -9999 0 -0.55 70 70
GSK3B 0.001 0.087 -9999 0 -0.3 24 24
arachidonic acid secretion -0.057 0.22 -9999 0 -0.54 72 72
GNG2 0.007 0.052 -9999 0 -0.47 6 6
TRIP6 0.017 0.047 -9999 0 -0.34 8 8
GNAO1 -0.063 0.19 -9999 0 -0.4 102 102
HRAS 0.006 0.064 -9999 0 -0.57 6 6
NFKBIA -0.015 0.13 -9999 0 -0.38 27 27
GAB1 0.012 0.022 -9999 0 -0.47 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.018 0.081 -9999 0 -0.88 4 4
JUN 0.006 0.06 -9999 0 -0.5 7 7
LPA/LPA2/NHERF2 0.015 0.041 -9999 0 -0.34 6 6
TIAM1 -0.007 0.093 -9999 0 -1 4 4
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
mol:IP3 -0.011 0.11 -9999 0 -0.34 24 24
PLCB3 0.021 0.037 -9999 0 -0.3 6 6
FOS -0.076 0.19 -9999 0 -0.47 91 91
positive regulation of mitosis -0.057 0.22 -9999 0 -0.54 72 72
LPA/LPA1-2-3 -0.043 0.15 -9999 0 -0.48 29 29
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation -0.012 0.11 -9999 0 -0.37 26 26
GNAZ -0.037 0.16 -9999 0 -0.38 74 74
EGFR/PI3K-beta/Gab1 -0.072 0.14 -9999 0 -0.46 44 44
positive regulation of dendritic cell cytokine production -0.044 0.15 -9999 0 -0.48 29 29
LPA/LPA2/MAGI-3 0.018 0.018 -9999 0 -0.31 1 1
ARHGEF1 0.005 0.093 -9999 0 -0.43 11 11
GNAI2 -0.01 0.11 -9999 0 -0.32 48 48
GNAI3 -0.01 0.11 -9999 0 -0.32 48 48
GNAI1 -0.014 0.12 -9999 0 -0.33 54 54
LPA/LPA3 -0.045 0.13 -9999 0 -0.34 79 79
LPA/LPA2 0.01 0.022 -9999 0 -0.37 1 1
LPA/LPA1 -0.023 0.13 -9999 0 -0.37 53 53
HB-EGF/EGFR -0.2 0.2 -9999 0 -0.36 292 292
HBEGF -0.22 0.22 -9999 0 -0.42 276 276
mol:DAG -0.011 0.11 -9999 0 -0.34 24 24
cAMP biosynthetic process -0.071 0.25 -9999 0 -0.62 70 70
NFKB1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
LYN -0.015 0.13 -9999 0 -0.38 27 27
GNAQ -0.02 0.098 -9999 0 -0.24 80 80
LPAR2 0.012 0.021 -9999 0 -0.47 1 1
LPAR3 -0.065 0.18 -9999 0 -0.48 79 79
LPAR1 -0.034 0.15 -9999 0 -0.5 48 48
IL8 -0.15 0.19 -9999 0 -0.45 108 108
PTK2 -0.035 0.14 -9999 0 -0.45 29 29
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
CASP3 -0.047 0.15 -9999 0 -0.53 24 24
EGFR -0.026 0.13 -9999 0 -0.47 40 40
PLCG1 -0.026 0.12 -9999 0 -0.28 81 81
PLD2 -0.035 0.14 -9999 0 -0.45 29 29
G12/G13 0 0.1 -9999 0 -0.46 11 11
PI3K-beta -0.026 0.081 -9999 0 -0.38 17 17
cell migration 0.011 0.068 -9999 0 -0.25 9 9
SLC9A3R2 0.007 0.059 -9999 0 -0.57 5 5
PXN -0.013 0.11 -9999 0 -0.38 26 26
HRAS/GTP -0.059 0.23 -9999 0 -0.56 72 72
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.31 0.29 -9999 0 -0.57 272 272
PRKCE 0.013 0 -9999 0 -10000 0 0
PRKCD -0.004 0.1 -9999 0 -0.33 21 21
Gi(beta/gamma) -0.052 0.22 -9999 0 -0.53 71 71
mol:LPA 0.001 0.022 -9999 0 -0.17 4 4
TRIP6/p130 Cas/FAK1/Paxillin -0.054 0.12 -9999 0 -0.46 28 28
MAPKKK cascade -0.057 0.22 -9999 0 -0.54 72 72
contractile ring contraction involved in cytokinesis 0.018 0.034 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.022 0.1 -9999 0 -0.25 81 81
GNA15 -0.034 0.12 -9999 0 -0.27 96 96
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.006 0.085 -9999 0 -0.32 14 14
GNA11 -0.03 0.12 -9999 0 -0.27 89 89
Rac1/GTP 0.019 0.086 -9999 0 -0.94 4 4
MMP2 -0.018 0.14 -9999 0 -0.69 16 16
HIF-1-alpha transcription factor network

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
PKM2 -0.11 0.43 -9999 0 -1.1 44 44
HDAC7 0.014 0.008 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.1 0.34 -9999 0 -0.92 40 40
SMAD4 0.015 0 -9999 0 -10000 0 0
ID2 -0.11 0.44 -9999 0 -1.1 48 48
AP1 -0.048 0.15 -9999 0 -0.36 91 91
ABCG2 -0.13 0.46 -9999 0 -1.2 49 49
HIF1A 0 0.077 -9999 0 -0.54 1 1
TFF3 -0.22 0.49 -9999 0 -1.1 77 77
GATA2 0.012 0.027 -9999 0 -0.57 1 1
AKT1 -0.002 0.086 -9999 0 -10000 0 0
response to hypoxia -0.02 0.09 -9999 0 -0.25 14 14
MCL1 -0.11 0.43 -9999 0 -1.1 44 44
NDRG1 -0.11 0.43 -9999 0 -1.1 44 44
SERPINE1 -0.14 0.46 -9999 0 -1.1 55 55
FECH -0.11 0.44 -9999 0 -1.1 46 46
FURIN -0.11 0.43 -9999 0 -1.1 45 45
NCOA2 -0.047 0.16 -9999 0 -0.47 60 60
EP300 0.01 0.13 -9999 0 -0.35 24 24
HMOX1 -0.11 0.44 -9999 0 -1.1 45 45
BHLHE40 -0.11 0.44 -9999 0 -1.1 48 48
BHLHE41 -0.11 0.44 -9999 0 -1.1 45 45
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.013 0.076 -9999 0 -10000 0 0
ENG 0.049 0.09 -9999 0 -10000 0 0
JUN 0.006 0.061 -9999 0 -0.5 7 7
RORA -0.11 0.43 -9999 0 -1.1 46 46
ABCB1 -0.056 0.18 -9999 0 -1.3 8 8
TFRC -0.11 0.43 -9999 0 -1.1 46 46
CXCR4 -0.11 0.44 -9999 0 -1.1 45 45
TF -0.16 0.48 -9999 0 -1.1 62 62
CITED2 -0.11 0.43 -9999 0 -1.1 45 45
HIF1A/ARNT -0.14 0.49 -9999 0 -1.2 49 49
LDHA -0.022 0.06 -9999 0 -0.53 3 3
ETS1 -0.11 0.44 -9999 0 -1.1 45 45
PGK1 -0.11 0.43 -9999 0 -1.1 45 45
NOS2 -0.14 0.46 -9999 0 -1.1 54 54
ITGB2 -0.11 0.44 -9999 0 -1.1 45 45
ALDOA -0.11 0.43 -9999 0 -1.1 45 45
Cbp/p300/CITED2 -0.11 0.46 -9999 0 -1.2 39 39
FOS -0.076 0.19 -9999 0 -0.48 91 91
HK2 -0.11 0.44 -9999 0 -1.1 43 43
SP1 0.022 0.003 -9999 0 -10000 0 0
GCK -0.039 0.35 -9999 0 -1.3 27 27
HK1 -0.11 0.43 -9999 0 -1.1 45 45
NPM1 -0.11 0.43 -9999 0 -1.1 46 46
EGLN1 -0.11 0.43 -9999 0 -1.1 45 45
CREB1 0.021 0.002 -9999 0 -10000 0 0
PGM1 -0.11 0.43 -9999 0 -1.1 45 45
SMAD3 0.015 0 -9999 0 -10000 0 0
EDN1 -0.054 0.33 -9999 0 -1.1 34 34
IGFBP1 -0.13 0.44 -9999 0 -1.1 51 51
VEGFA -0.053 0.35 -9999 0 -0.85 34 34
HIF1A/JAB1 -0.001 0.043 -9999 0 -0.39 1 1
CP -0.16 0.48 -9999 0 -1.1 63 63
CXCL12 -0.12 0.45 -9999 0 -1.1 46 46
COPS5 0.011 0.009 -9999 0 -10000 0 0
SMAD3/SMAD4 0.022 0 -9999 0 -10000 0 0
BNIP3 -0.11 0.43 -9999 0 -1.1 48 48
EGLN3 -0.11 0.44 -9999 0 -1.1 47 47
CA9 -0.12 0.44 -9999 0 -1.1 47 47
TERT -0.19 0.49 -9999 0 -1.1 73 73
ENO1 -0.11 0.43 -9999 0 -1.1 46 46
PFKL -0.11 0.43 -9999 0 -1.1 45 45
NCOA1 0.012 0.005 -9999 0 -10000 0 0
ADM -0.12 0.45 -9999 0 -1.1 53 53
ARNT 0.002 0.072 -9999 0 -10000 0 0
HNF4A -0.03 0.14 -9999 0 -0.57 29 29
ADFP -0.12 0.43 -9999 0 -1.1 48 48
SLC2A1 -0.041 0.33 -9999 0 -0.82 30 30
LEP -0.12 0.44 -9999 0 -1.1 46 46
HIF1A/ARNT/Cbp/p300 -0.069 0.39 -9999 0 -0.98 36 36
EPO -0.13 0.42 -9999 0 -0.96 65 65
CREBBP 0.011 0.13 -9999 0 -0.36 21 21
HIF1A/ARNT/Cbp/p300/HDAC7 -0.1 0.34 -9999 0 -0.93 39 39
PFKFB3 -0.11 0.44 -9999 0 -1.1 45 45
NT5E -0.13 0.47 -9999 0 -1.1 52 52
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.02 0.12 -9999 0 -0.35 51 51
PDGFRB 0.01 0.037 -9999 0 -0.58 2 2
SPHK1 -0.02 0.033 -9999 0 -10000 0 0
mol:S1P -0.023 0.038 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.11 0.26 -9999 0 -0.49 125 125
GNAO1 -0.081 0.19 -9999 0 -0.47 96 96
PDGFB-D/PDGFRB/PLCgamma1 -0.082 0.22 -9999 0 -0.52 74 74
PLCG1 -0.093 0.24 -9999 0 -0.54 81 81
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.037 -9999 0 -0.58 2 2
GNAI2 0.012 0.006 -9999 0 -10000 0 0
GNAI3 0.011 0.006 -9999 0 -10000 0 0
GNAI1 0.004 0.064 -9999 0 -0.53 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.018 0.097 -9999 0 -0.3 51 51
S1P1/S1P -0.024 0.1 -9999 0 -0.35 21 21
negative regulation of cAMP metabolic process -0.1 0.25 -9999 0 -0.48 125 125
MAPK3 -0.13 0.3 -9999 0 -0.62 118 118
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
KDR -0.01 0.1 -9999 0 -0.47 23 23
PLCB2 -0.016 0.096 -9999 0 -0.32 19 19
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.041 0.075 -9999 0 -0.31 19 19
receptor internalization -0.046 0.084 -9999 0 -0.33 21 21
PTGS2 -0.19 0.42 -9999 0 -1 99 99
Rac1/GTP -0.041 0.075 -9999 0 -0.31 19 19
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA -0.019 0.12 -9999 0 -0.49 31 31
negative regulation of T cell proliferation -0.1 0.25 -9999 0 -0.48 125 125
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.036 0.14 -9999 0 -0.47 49 49
MAPK1 -0.13 0.3 -9999 0 -0.6 125 125
S1P1/S1P/PDGFB-D/PDGFRB -0.024 0.12 -9999 0 -0.38 23 23
ABCC1 0.012 0.003 -9999 0 -10000 0 0
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS -0.036 0.14 -9999 0 -0.46 27 27
SMAD6-7/SMURF1 0.022 0.039 -9999 0 -0.27 9 9
NOG -0.045 0.16 -9999 0 -0.47 60 60
SMAD9 -0.042 0.17 -9999 0 -0.48 54 54
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.005 0.098 -9999 0 -0.38 17 17
BMP7/USAG1 -0.16 0.23 -9999 0 -0.41 207 207
SMAD5/SKI 0.002 0.094 -9999 0 -0.37 15 15
SMAD1 0.034 0.023 -9999 0 -10000 0 0
BMP2 -0.022 0.12 -9999 0 -0.47 36 36
SMAD1/SMAD1/SMAD4 -0.003 0.019 -9999 0 -10000 0 0
BMPR1A 0.012 0.022 -9999 0 -0.47 1 1
BMPR1B 0.006 0.062 -9999 0 -0.51 7 7
BMPR1A-1B/BAMBI 0.007 0.083 -9999 0 -0.33 28 28
AHSG -0.041 0.15 -9999 0 -0.57 38 38
CER1 -0.009 0.085 -9999 0 -0.57 11 11
BMP2-4/CER1 -0.024 0.13 -9999 0 -0.36 58 58
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.13 -9999 0 -0.42 32 32
BMP2-4 (homodimer) -0.022 0.14 -9999 0 -0.42 48 48
RGMB 0.006 0.06 -9999 0 -0.47 8 8
BMP6/BMPR2/BMPR1A-1B -0.016 0.12 -9999 0 -0.31 69 69
RGMA -0.011 0.1 -9999 0 -0.47 25 25
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.016 0.13 -9999 0 -0.44 32 32
BMP2-4/USAG1 -0.11 0.2 -9999 0 -0.34 178 178
SMAD6/SMURF1/SMAD5 0.002 0.094 -9999 0 -0.37 15 15
SOSTDC1 -0.15 0.23 -9999 0 -0.47 170 170
BMP7/BMPR2/BMPR1A-1B -0.023 0.11 -9999 0 -0.34 5 5
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.065 0.2 -9999 0 -0.57 66 66
HFE2 -0.052 0.18 -9999 0 -0.57 50 50
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0.001 -9999 0 -10000 0 0
BMP2-4/CHRD -0.043 0.16 -9999 0 -0.37 88 88
SMAD5/SMAD5/SMAD4 0.002 0.094 -9999 0 -0.37 15 15
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.038 0.097 -9999 0 -0.37 31 31
BMP7 (homodimer) -0.081 0.19 -9999 0 -0.47 97 97
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.076 0.18 -9999 0 -0.44 98 98
SMAD1/SKI 0.04 0.022 -9999 0 -10000 0 0
SMAD6 0.005 0.064 -9999 0 -0.47 9 9
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.043 0.15 -9999 0 -0.36 83 83
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.068 0.19 -9999 0 -0.51 77 77
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.024 0.033 -9999 0 -0.35 4 4
BMPR1A-1B (homodimer) 0.014 0.048 -9999 0 -0.36 8 8
CHRDL1 -0.11 0.21 -9999 0 -0.47 129 129
ENDOFIN/SMAD1 0.04 0.022 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.046 0.034 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.01 0.12 -9999 0 -0.57 20 20
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.082 0.2 -9999 0 -0.36 140 140
BMP2-4/GREM1 -0.059 0.17 -9999 0 -0.36 112 112
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.033 0.16 -9999 0 -0.44 54 54
SMAD1/SMAD6 0.04 0.022 -9999 0 -10000 0 0
TAK1/SMAD6 0.02 0 -9999 0 -10000 0 0
BMP7 -0.081 0.19 -9999 0 -0.47 97 97
BMP6 -0.065 0.2 -9999 0 -0.57 66 66
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.009 0.12 -9999 0 -0.41 32 32
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.04 0.022 -9999 0 -10000 0 0
SMAD7/SMURF1 0.02 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.009 0.052 -9999 0 -0.57 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.039 0.19 -9999 0 -0.59 42 42
CHRD -0.04 0.17 -9999 0 -0.57 46 46
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.022 0.14 -9999 0 -0.48 32 32
BMP4 -0.013 0.11 -9999 0 -0.47 27 27
FST -0.031 0.14 -9999 0 -0.47 45 45
BMP2-4/NOG -0.043 0.17 -9999 0 -0.37 88 88
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.014 0.1 -9999 0 -0.45 1 1
Signaling events mediated by PRL

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
CCNE1 0.006 0.064 -10000 0 -0.57 6 6
mol:Halofuginone 0.005 0.001 -10000 0 -10000 0 0
ITGA1 -0.024 0.13 -10000 0 -0.47 39 39
CDKN1A 0.009 0.067 -10000 0 -0.53 4 4
PRL-3/alpha Tubulin -0.069 0.18 -10000 0 -0.41 102 102
mol:Ca2+ -0.013 0.18 0.25 88 -0.39 73 161
AGT -0.068 0.2 -10000 0 -0.54 73 73
CCNA2 -0.049 0.15 -10000 0 -0.51 13 13
TUBA1B 0.013 0 -10000 0 -10000 0 0
EGR1 -0.028 0.13 -10000 0 -0.36 66 66
CDK2/Cyclin E1 0.019 0.07 -10000 0 -0.44 6 6
MAPK3 -0.068 0.18 -10000 0 -0.41 102 102
PRL-2 /Rab GGTase beta 0.02 0 -10000 0 -10000 0 0
MAPK1 -0.068 0.18 -10000 0 -0.41 102 102
PTP4A1 -0.005 0.099 -10000 0 -10000 0 0
PTP4A3 -0.11 0.24 -10000 0 -0.57 102 102
PTP4A2 0.013 0 -10000 0 -10000 0 0
ITGB1 -0.068 0.18 -10000 0 -0.41 102 102
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 -0.013 0.071 -10000 0 -0.24 4 4
Rab GGTase beta/Rab GGTase alpha 0.02 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.002 0.1 -10000 0 -0.51 1 1
RABGGTA 0.013 0 -10000 0 -10000 0 0
BCAR1 0.051 0.1 0.25 102 -10000 0 102
RHOC -0.013 0.071 -10000 0 -10000 0 0
RHOA -0.013 0.071 -10000 0 -10000 0 0
cell motility -0.011 0.074 -10000 0 -0.25 5 5
PRL-1/alpha Tubulin 0.002 0.092 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.094 0.2 -10000 0 -0.42 128 128
ROCK1 -0.011 0.075 -10000 0 -0.26 5 5
RABGGTB 0.013 0 -10000 0 -10000 0 0
CDK2 0.013 0 -10000 0 -10000 0 0
mitosis -0.005 0.098 -10000 0 -10000 0 0
ATF5 0.005 0.069 -10000 0 -0.57 7 7
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.012 0.14 -9999 0 -0.45 35 35
MAP4K1 -0.024 0.14 -9999 0 -0.55 33 33
MAP3K8 -0.001 0.084 -9999 0 -0.47 15 15
PRKCB -0.097 0.2 -9999 0 -0.47 114 114
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.015 0.085 -9999 0 -0.46 7 7
JUN -0.11 0.25 -9999 0 -0.53 125 125
MAP3K7 0.016 0.084 -9999 0 -0.46 7 7
GRAP2 -0.007 0.099 -9999 0 -0.48 21 21
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.019 0.091 -9999 0 -0.42 10 10
LAT -0.004 0.098 -9999 0 -0.56 15 15
LCP2 0.006 0.064 -9999 0 -0.53 7 7
MAPK8 -0.12 0.26 -9999 0 -0.56 123 123
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.01 0.089 -9999 0 -0.39 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.005 0.14 -9999 0 -0.42 35 35
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.022 0.041 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.063 0.11 -9999 0 -0.37 35 35
JUN -0.033 0.13 -9999 0 -0.4 34 34
HRAS 0.006 0.064 -9999 0 -0.57 6 6
RET51/GFRalpha1/GDNF/GRB10 -0.071 0.17 -9999 0 -0.36 101 101
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.072 0.17 -9999 0 -0.36 102 102
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.022 0.12 -9999 0 -0.3 71 71
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.086 0.14 -9999 0 -0.33 103 103
GRB7 0.012 0.026 -9999 0 -0.57 1 1
RET51/GFRalpha1/GDNF -0.071 0.17 -9999 0 -0.36 101 101
MAPKKK cascade -0.073 0.12 -9999 0 -0.44 28 28
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.023 0.12 -9999 0 -0.28 77 77
lamellipodium assembly -0.058 0.1 -9999 0 -0.34 35 35
RET51/GFRalpha1/GDNF/SHC -0.071 0.17 -9999 0 -0.36 101 101
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
RET9/GFRalpha1/GDNF/SHC -0.015 0.1 -9999 0 -0.26 67 67
RET9/GFRalpha1/GDNF/Shank3 -0.015 0.1 -9999 0 -0.26 67 67
MAPK3 -0.053 0.15 -9999 0 -0.47 25 25
DOK1 0.012 0.022 -9999 0 -0.47 1 1
DOK6 -0.026 0.14 -9999 0 -0.51 37 37
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.045 0.15 -9999 0 -0.45 29 29
DOK5 -0.021 0.13 -9999 0 -0.5 33 33
GFRA1 -0.031 0.14 -9999 0 -0.47 46 46
MAPK8 -0.037 0.13 -9999 0 -0.42 32 32
HRAS/GTP -0.085 0.14 -9999 0 -0.5 28 28
tube development -0.007 0.096 -9999 0 -0.43 7 7
MAPK1 -0.053 0.15 -9999 0 -0.47 25 25
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.007 0.093 -9999 0 -0.44 6 6
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PDLIM7 -0.002 0.085 -9999 0 -0.48 15 15
RET51/GFRalpha1/GDNF/Dok6 -0.08 0.18 -9999 0 -0.36 118 118
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.074 0.18 -9999 0 -0.37 103 103
RET51/GFRalpha1/GDNF/Dok5 -0.089 0.19 -9999 0 -0.39 113 113
PRKCA -0.009 0.1 -9999 0 -0.47 23 23
HRAS/GDP 0.005 0.047 -9999 0 -0.42 6 6
CREB1 -0.024 0.12 -9999 0 -0.41 23 23
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.007 0.095 -9999 0 -0.46 7 7
RET51/GFRalpha1/GDNF/Grb7 -0.072 0.17 -9999 0 -0.36 101 101
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.1 0.23 -9999 0 -0.56 98 98
DOK4 0.007 0.052 -9999 0 -0.47 6 6
JNK cascade -0.032 0.13 -9999 0 -0.4 34 34
RET9/GFRalpha1/GDNF/FRS2 -0.015 0.1 -9999 0 -0.26 67 67
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.011 0.03 -9999 0 -0.47 2 2
NCK1 0.012 0.026 -9999 0 -0.57 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.007 0.092 -9999 0 -0.44 6 6
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.039 0.13 -9999 0 -0.44 23 23
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.041 0.13 -9999 0 -0.45 24 24
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.04 0.13 -9999 0 -0.47 23 23
PI3K -0.046 0.18 -9999 0 -0.54 35 35
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.006 0.097 -9999 0 -0.43 7 7
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.036 0.12 -9999 0 -0.36 40 40
RET51/GFRalpha1/GDNF/FRS2 -0.071 0.17 -9999 0 -0.36 101 101
GAB1 0.012 0.022 -9999 0 -0.47 1 1
IRS1 -0.003 0.087 -9999 0 -0.47 17 17
IRS2 0.006 0.062 -9999 0 -0.56 6 6
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.041 0.14 -9999 0 -0.49 23 23
RET51/GFRalpha1/GDNF/PKC alpha -0.082 0.19 -9999 0 -0.39 107 107
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.015 0.11 -9999 0 -0.47 27 27
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.08 0.18 -9999 0 -0.37 106 106
Rac1/GTP -0.068 0.12 -9999 0 -0.42 35 35
RET9/GFRalpha1/GDNF -0.026 0.11 -9999 0 -0.3 67 67
GFRalpha1/GDNF -0.032 0.13 -9999 0 -0.35 67 67
S1P5 pathway

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.067 0.18 0.5 59 -10000 0 59
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.03 0.11 -10000 0 -0.27 82 82
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.08 0.19 -10000 0 -0.47 96 96
RhoA/GTP -0.069 0.19 -10000 0 -0.51 59 59
negative regulation of cAMP metabolic process -0.081 0.2 -10000 0 -0.56 59 59
GNAZ -0.034 0.14 -10000 0 -0.47 49 49
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 -0.066 0.18 -10000 0 -0.47 82 82
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.082 0.2 -10000 0 -0.56 59 59
RhoA/GDP 0.01 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.006 0.064 -10000 0 -0.53 7 7
TCGA08_p53

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
CDKN2A -0.082 0.18 -10000 0 -0.42 106 106
TP53 -0.027 0.056 -10000 0 -0.32 6 6
Senescence -0.027 0.056 -10000 0 -0.32 6 6
Apoptosis -0.027 0.056 -10000 0 -0.32 6 6
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.045 0.087 0.21 106 -10000 0 106
MDM4 0.013 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.002 0.081 -10000 0 -0.24 50 50
regulation of S phase of mitotic cell cycle 0.002 0.087 -10000 0 -0.39 10 10
GNAO1 -0.08 0.19 -10000 0 -0.47 96 96
HRAS 0.006 0.064 -10000 0 -0.57 6 6
SHBG/T-DHT -0.001 0.056 -10000 0 -0.31 15 15
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.001 0.092 -10000 0 -0.39 12 12
T-DHT/AR -0.021 0.098 -10000 0 -0.34 44 44
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 89 89
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.006 0.064 -10000 0 -0.53 7 7
mol:GDP -0.035 0.12 -10000 0 -0.4 44 44
cell proliferation -0.037 0.17 -10000 0 -0.38 90 90
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
FOS -0.1 0.31 -10000 0 -0.77 86 86
mol:Ca2+ -0.019 0.033 -10000 0 -0.091 74 74
MAPK3 -0.02 0.13 -10000 0 -0.48 12 12
MAPK1 -0.013 0.089 -10000 0 -0.27 8 8
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
mol:IP3 -0.001 0.002 -10000 0 -0.004 91 91
cAMP biosynthetic process 0.006 0.057 -10000 0 -0.28 15 15
GNG2 0.007 0.052 -10000 0 -0.47 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 91 91
HRAS/GTP -0.027 0.079 -10000 0 -0.4 12 12
actin cytoskeleton reorganization -0.004 0.031 -10000 0 -0.43 1 1
SRC 0.013 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 91 91
PI3K 0.013 0.042 -10000 0 -0.31 8 8
apoptosis 0.04 0.17 0.39 87 -10000 0 87
T-DHT/AR/PELP1 -0.009 0.084 -10000 0 -0.28 44 44
HRAS/GDP -0.036 0.13 -10000 0 -0.42 43 43
CREB1 -0.044 0.18 -10000 0 -0.42 87 87
RAC1-CDC42/GTP 0 0.033 -10000 0 -0.44 1 1
AR -0.03 0.14 -10000 0 -0.47 44 44
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.002 0.089 -10000 0 -0.39 12 12
RAC1-CDC42/GDP -0.028 0.11 -10000 0 -0.36 43 43
T-DHT/AR/PELP1/Src -0.001 0.077 -10000 0 -0.24 44 44
MAP2K2 -0.001 0.095 -10000 0 -0.41 12 12
T-DHT/AR/PELP1/Src/PI3K 0.002 0.088 -10000 0 -0.39 10 10
GNAZ -0.034 0.14 -10000 0 -0.47 49 49
SHBG -0.003 0.09 -10000 0 -0.51 15 15
Gi family/GNB1/GNG2/GDP -0.052 0.18 -10000 0 -0.4 96 96
mol:T-DHT 0 0.001 0.002 2 -0.003 82 84
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.001 0.064 -10000 0 -0.42 11 11
Gi family/GTP -0.046 0.14 -10000 0 -0.38 56 56
CDC42 0.013 0 -10000 0 -10000 0 0
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 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.017 0.096 -10000 0 -0.26 41 41
NT3 (dimer)/TRKC -0.081 0.2 -10000 0 -0.42 113 113
NT3 (dimer)/TRKB -0.071 0.19 -10000 0 -0.37 124 124
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.037 -10000 0 -0.43 1 1
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.087 0.2 -10000 0 -0.47 104 104
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
DYNLT1 0.013 0.001 -10000 0 -10000 0 0
NTRK1 -0.027 0.14 -10000 0 -0.49 39 39
NTRK2 -0.057 0.17 -10000 0 -0.47 72 72
NTRK3 -0.079 0.19 -10000 0 -0.47 95 95
NT-4/5 (dimer)/TRKB -0.1 0.21 -10000 0 -0.37 163 163
neuron apoptosis 0.075 0.19 0.5 63 -10000 0 63
SHC 2-3/Grb2 -0.083 0.21 -10000 0 -0.56 63 63
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.091 0.17 -10000 0 -0.51 55 55
SHC3 -0.12 0.22 -10000 0 -0.58 71 71
STAT3 (dimer) 0.021 0.012 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.055 0.17 -10000 0 -0.35 109 109
RIN/GDP -0.01 0.097 -10000 0 -0.26 20 20
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.029 0.12 -10000 0 -0.36 46 46
RIN/GTP -0.024 0.11 -10000 0 -0.42 35 35
CCND1 0.028 0.022 -10000 0 -0.46 1 1
MAGED1 0.012 0.026 -10000 0 -0.57 1 1
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.099 0.2 -10000 0 -0.47 116 116
SHC/GRB2/SOS1 0.027 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.18 0.21 -10000 0 -0.38 233 233
TRKA/NEDD4-2 -0.022 0.13 -10000 0 -0.39 51 51
ELMO1 0.008 0.048 -10000 0 -0.47 5 5
RhoG/GTP/ELMO1/DOCK1 0.013 0.039 -10000 0 -0.27 9 9
NGF -0.01 0.1 -10000 0 -0.48 24 24
HRAS 0.006 0.064 -10000 0 -0.57 6 6
DOCK1 0.009 0.043 -10000 0 -0.47 4 4
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 -0.033 0.15 -10000 0 -0.57 35 35
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 0.011 0.034 -10000 0 -0.52 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.031 0.13 -10000 0 -0.36 46 46
mol:GDP -0.002 0.12 -10000 0 -0.35 22 22
NGF (dimer) -0.01 0.1 -10000 0 -0.48 24 24
RhoG/GDP 0.006 0.034 -10000 0 -0.33 5 5
RIT1/GDP 0.007 0.085 -10000 0 -0.24 13 13
TIAM1 0.009 0.043 -10000 0 -0.47 4 4
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
BDNF (dimer)/TRKB -0.074 0.18 -10000 0 -0.36 129 129
KIDINS220/CRKL/C3G 0.02 0 -10000 0 -10000 0 0
SHC/RasGAP 0.018 0.022 -10000 0 -0.32 2 2
FRS2 family/SHP2 0.027 0.013 -10000 0 -0.27 1 1
SHC/GRB2/SOS1/GAB1 0.034 0.012 -10000 0 -10000 0 0
RIT1/GTP 0.01 0 -10000 0 -10000 0 0
NT3 (dimer) -0.043 0.15 -10000 0 -0.47 58 58
RAP1/GDP -0.026 0.053 -10000 0 -0.21 7 7
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.087 0.2 -10000 0 -0.47 104 104
ubiquitin-dependent protein catabolic process -0.024 0.13 -10000 0 -0.4 29 29
Schwann cell development -0.026 0.034 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.034 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.038 0.011 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.13 0.21 -10000 0 -0.53 88 88
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
Rap1/GTP 0.004 0.079 -10000 0 -10000 0 0
STAT3 0.021 0.012 -10000 0 -10000 0 0
axon guidance -0.12 0.2 -10000 0 -0.5 88 88
MAPK3 -0.15 0.19 -10000 0 -0.34 233 233
MAPK1 -0.15 0.19 -10000 0 -0.34 233 233
CDC42/GDP 0.007 0.085 -10000 0 -0.23 18 18
NTF3 -0.043 0.15 -10000 0 -0.47 58 58
NTF4 -0.099 0.2 -10000 0 -0.47 116 116
NGF (dimer)/TRKA/FAIM -0.013 0.11 -10000 0 -0.3 61 61
PI3K 0.014 0.049 -10000 0 -0.36 8 8
FRS3 0.013 0.001 -10000 0 -10000 0 0
FAIM 0.012 0.026 -10000 0 -0.57 1 1
GAB1 0.012 0.022 -10000 0 -0.47 1 1
RASGRF1 -0.073 0.17 -10000 0 -0.44 62 62
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.061 0.17 -10000 0 -0.36 113 113
RGS19 0.012 0.026 -10000 0 -0.57 1 1
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.067 -10000 0 -10000 0 0
Rac1/GDP 0.007 0.085 -10000 0 -0.24 13 13
NGF (dimer)/TRKA/GRIT -0.021 0.11 -10000 0 -0.3 60 60
neuron projection morphogenesis -0.017 0.12 -10000 0 -0.48 17 17
NGF (dimer)/TRKA/NEDD4-2 -0.023 0.13 -10000 0 -0.4 29 29
MAP2K1 0.035 0.011 -10000 0 -10000 0 0
NGFR -0.028 0.14 -10000 0 -0.47 43 43
NGF (dimer)/TRKA/GIPC/GAIP 0.005 0.082 -10000 0 -0.43 3 3
RAS family/GTP/PI3K 0.022 0.049 -10000 0 -0.43 4 4
FRS2 family/SHP2/GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
NRAS 0.012 0.022 -10000 0 -0.47 1 1
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
PRKCI 0.012 0.026 -10000 0 -0.57 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.079 0.19 -10000 0 -0.64 49 49
RASA1 0.011 0.03 -10000 0 -0.47 2 2
TRKA/c-Abl -0.009 0.099 -10000 0 -0.35 39 39
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.059 0.17 -10000 0 -0.47 48 48
NGF (dimer)/TRKA/p62/Atypical PKCs 0.005 0.093 -10000 0 -0.32 15 15
MATK -0.25 0.29 -10000 0 -0.57 222 222
NEDD4L -0.006 0.1 -10000 0 -0.57 16 16
RAS family/GDP -0.026 0.051 -10000 0 -0.23 3 3
NGF (dimer)/TRKA -0.054 0.12 -10000 0 -0.38 47 47
Rac1/GTP -0.065 0.11 -10000 0 -0.35 42 42
FRS2 family/SHP2/CRK family 0.039 0.011 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.049 0.15 -9999 0 -0.44 21 21
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.14 -9999 0 -0.42 21 21
alphaV/beta3 Integrin/Osteopontin/Src -0.041 0.16 -9999 0 -0.4 79 79
AP1 -0.071 0.21 -9999 0 -0.56 43 43
ILK -0.06 0.16 -9999 0 -0.49 17 17
bone resorption -0.054 0.18 -9999 0 -0.44 56 56
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.045 0.15 -9999 0 -0.46 20 20
ITGAV 0.013 0.038 -9999 0 -0.47 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.018 0.11 -9999 0 -0.35 51 51
alphaV/beta3 Integrin/Osteopontin -0.076 0.18 -9999 0 -0.37 83 83
MAP3K1 -0.062 0.16 -9999 0 -0.47 21 21
JUN 0.006 0.061 -9999 0 -0.5 7 7
MAPK3 -0.049 0.16 -9999 0 -0.46 21 21
MAPK1 -0.049 0.16 -9999 0 -0.46 21 21
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.056 0.16 -9999 0 -0.46 26 26
ITGB3 -0.081 0.19 -9999 0 -0.46 101 101
NFKBIA -0.039 0.15 -9999 0 -0.47 21 21
FOS -0.075 0.19 -9999 0 -0.47 91 91
CD44 0.002 0.074 -9999 0 -0.47 12 12
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.05 0.23 -9999 0 -1.1 15 15
NF kappa B1 p50/RelA -0.07 0.11 -9999 0 -0.44 19 19
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.045 0.14 -9999 0 -0.33 101 101
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.066 0.16 -9999 0 -0.34 88 88
VAV3 -0.081 0.19 -9999 0 -0.52 43 43
MAP3K14 -0.061 0.16 -9999 0 -0.48 21 21
ROCK2 -0.028 0.14 -9999 0 -0.47 43 43
SPP1 -0.072 0.21 -9999 0 -0.56 76 76
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.069 0.17 -9999 0 -0.47 43 43
MMP2 -0.058 0.19 -9999 0 -0.63 26 26
Calcium 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
NFATC1 0.008 0.028 -9999 0 -10000 0 0
NFATC2 -0.044 0.12 -9999 0 -0.28 88 88
NFATC3 0.008 0.028 -9999 0 -10000 0 0
CD40LG -0.14 0.29 -9999 0 -0.7 71 71
PTGS2 -0.16 0.31 -9999 0 -0.69 94 94
JUNB -0.014 0.12 -9999 0 -0.52 25 25
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.016 -9999 0 -10000 0 0
CaM/Ca2+ 0 0.016 -9999 0 -10000 0 0
CALM1 0.011 0.008 -9999 0 -10000 0 0
JUN 0.004 0.062 -9999 0 -0.51 7 7
mol:Ca2+ -0.006 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.007 0.005 -9999 0 -10000 0 0
FOSL1 -0.1 0.22 -9999 0 -0.5 113 113
CREM 0.013 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.058 0.16 -9999 0 -0.46 25 25
FOS -0.08 0.19 -9999 0 -0.48 91 91
IFNG -0.14 0.28 -9999 0 -0.7 62 62
AP-1/NFAT1-c-4 -0.15 0.32 -9999 0 -0.72 73 73
FASLG -0.13 0.28 -9999 0 -0.71 58 58
NFAT1-c-4/ICER1 -0.043 0.11 -9999 0 -0.37 7 7
IL2RA -0.16 0.31 -9999 0 -0.7 80 80
FKBP12/FK506 0.01 0 -9999 0 -10000 0 0
CSF2 -0.12 0.26 -9999 0 -0.67 54 54
JunB/Fra1/NFAT1-c-4 -0.093 0.17 -9999 0 -0.44 49 49
IL4 -0.12 0.26 -9999 0 -0.65 54 54
IL2 -0.004 0.03 -9999 0 -0.41 2 2
IL3 -0.017 0.022 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.016 0.13 -9999 0 -0.57 25 25
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0.026 -9999 0 -0.57 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.13 -10000 0 -0.4 27 27
TBX21 -0.089 0.38 -10000 0 -0.95 55 55
B2M 0.012 0.009 -10000 0 -10000 0 0
TYK2 0.015 0.02 -10000 0 -10000 0 0
IL12RB1 -0.012 0.13 -10000 0 -0.57 24 24
GADD45B -0.059 0.31 -10000 0 -0.83 41 41
IL12RB2 -0.006 0.11 -10000 0 -0.5 21 21
GADD45G -0.078 0.32 -10000 0 -0.86 39 39
natural killer cell activation 0.002 0.021 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 0.001 0.082 -10000 0 -0.48 14 14
IL2RA -0.081 0.21 -10000 0 -0.57 81 81
IFNG -0.029 0.14 -10000 0 -0.57 33 33
STAT3 (dimer) -0.065 0.3 -10000 0 -0.71 58 58
HLA-DRB5 -0.012 0.11 -10000 0 -0.54 21 21
FASLG -0.092 0.38 -10000 0 -0.97 56 56
NF kappa B2 p52/RelB -0.16 0.29 -10000 0 -0.77 68 68
CD4 0.004 0.066 -10000 0 -0.54 7 7
SOCS1 0.008 0.055 -10000 0 -0.53 5 5
EntrezGene:6955 -0.005 0.014 -10000 0 -10000 0 0
CD3D -0.03 0.14 -10000 0 -0.54 36 36
CD3E -0.012 0.11 -10000 0 -0.52 21 21
CD3G -0.045 0.16 -10000 0 -0.51 53 53
IL12Rbeta2/JAK2 0.008 0.086 -10000 0 -0.36 22 22
CCL3 -0.1 0.38 -10000 0 -0.96 56 56
CCL4 -0.085 0.36 -10000 0 -0.87 59 59
HLA-A 0.001 0.078 -10000 0 -0.51 11 11
IL18/IL18R 0.014 0.12 -10000 0 -0.34 43 43
NOS2 -0.11 0.42 -10000 0 -1 64 64
IL12/IL12R/TYK2/JAK2/SPHK2 -0.001 0.12 -10000 0 -0.4 23 23
IL1R1 -0.076 0.35 -10000 0 -0.88 49 49
IL4 0 0.022 -10000 0 -10000 0 0
JAK2 0.014 0.03 -10000 0 -0.49 1 1
EntrezGene:6957 -0.004 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.069 0.29 -10000 0 -0.78 49 49
RAB7A -0.038 0.28 -10000 0 -0.74 28 28
lysosomal transport -0.034 0.27 -10000 0 -0.7 28 28
FOS -0.21 0.5 -10000 0 -1.1 102 102
STAT4 (dimer) -0.06 0.33 -10000 0 -0.81 51 51
STAT5A (dimer) -0.17 0.3 -10000 0 -0.82 69 69
GZMA -0.088 0.37 -10000 0 -1 43 43
GZMB -0.1 0.4 -10000 0 -0.96 66 66
HLX -0.006 0.1 -10000 0 -0.57 16 16
LCK -0.089 0.38 -10000 0 -0.88 65 65
TCR/CD3/MHC II/CD4 -0.056 0.18 -10000 0 -0.46 58 58
IL2/IL2R -0.057 0.18 -10000 0 -0.4 89 89
MAPK14 -0.063 0.33 -10000 0 -0.8 50 50
CCR5 -0.061 0.32 -10000 0 -0.87 40 40
IL1B -0.062 0.19 -10000 0 -0.52 74 74
STAT6 -0.005 0.11 0.21 2 -0.27 19 21
STAT4 -0.007 0.1 -10000 0 -0.54 18 18
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.003 0.078 -10000 0 -0.57 9 9
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.01 0.045 -10000 0 -0.57 3 3
IL12B -0.022 0.14 -10000 0 -0.59 30 30
CD8A -0.009 0.1 -10000 0 -0.5 21 21
CD8B -0.011 0.11 -10000 0 -0.52 22 22
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.002 0.13 0.4 27 -10000 0 27
IL2RB -0.019 0.12 -10000 0 -0.49 32 32
proteasomal ubiquitin-dependent protein catabolic process -0.05 0.3 -10000 0 -0.73 51 51
IL2RG -0.011 0.12 -10000 0 -0.55 22 22
IL12 -0.016 0.14 -10000 0 -0.45 42 42
STAT5A 0.012 0.022 -10000 0 -0.47 1 1
CD247 -0.015 0.12 -10000 0 -0.56 22 22
IL2 0.004 0.037 -10000 0 -0.57 2 2
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.003 0.098 -10000 0 -0.52 16 16
IL12/IL12R/TYK2/JAK2 -0.098 0.4 -10000 0 -0.91 67 67
MAP2K3 -0.066 0.33 -10000 0 -0.78 53 53
RIPK2 0.001 0.082 -10000 0 -0.57 10 10
MAP2K6 -0.069 0.33 -10000 0 -0.79 54 54
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.005 0.059 -10000 0 -0.52 6 6
IL18RAP -0.02 0.13 -10000 0 -0.53 32 32
IL12Rbeta1/TYK2 0.001 0.1 -10000 0 -0.43 24 24
EOMES -0.055 0.23 -10000 0 -1.1 19 19
STAT1 (dimer) -0.068 0.3 -10000 0 -0.72 60 60
T cell proliferation -0.042 0.26 -10000 0 -0.59 55 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.007 0.062 -10000 0 -0.47 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.13 0.22 -10000 0 -0.64 53 53
ATF2 -0.063 0.31 -10000 0 -0.76 49 49
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
Noncanonical Wnts/FZD -0.047 0.14 -9999 0 -0.46 29 29
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 -0.084 0.2 -9999 0 -0.48 99 99
WNT4 0.007 0.052 -9999 0 -0.47 6 6
FZD3 0.011 0.03 -9999 0 -0.47 2 2
WNT5A -0.026 0.14 -9999 0 -0.5 38 38
WNT11 -0.025 0.14 -9999 0 -0.55 34 34
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.019 0.11 -10000 0 -0.3 58 58
cell-cell adhesion 0.089 0.14 0.44 41 -10000 0 41
Ephrin B/EPHB2/RasGAP -0.011 0.13 -10000 0 -0.66 9 9
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.012 0.049 -10000 0 -0.34 9 9
Ephrin B1/EPHB1 -0.08 0.14 -10000 0 -0.28 161 161
HRAS/GDP -0.091 0.14 -10000 0 -0.44 42 42
Ephrin B/EPHB1/GRB7 -0.087 0.18 -10000 0 -0.48 47 47
Endophilin/SYNJ1 -0.012 0.12 -10000 0 -0.63 8 8
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.086 0.18 -10000 0 -0.48 47 47
endothelial cell migration 0.013 0.069 -10000 0 -0.31 18 18
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 0.012 0.026 -10000 0 -0.57 1 1
PAK1 -0.011 0.14 -10000 0 -0.67 10 10
HRAS 0.006 0.064 -10000 0 -0.57 6 6
RRAS -0.014 0.13 -10000 0 -0.42 24 24
DNM1 0.011 0.034 -10000 0 -0.52 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.084 0.17 -10000 0 -0.45 47 47
lamellipodium assembly -0.089 0.14 -10000 0 -0.44 41 41
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.076 0.16 -10000 0 -0.46 39 39
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
EPHB2 0.005 0.066 -10000 0 -0.51 8 8
EPHB3 0.009 0.052 -10000 0 -0.57 4 4
EPHB1 -0.14 0.22 -10000 0 -0.47 161 161
EPHB4 0.012 0.026 -10000 0 -0.57 1 1
mol:GDP -0.061 0.15 -10000 0 -0.45 39 39
Ephrin B/EPHB2 -0.018 0.13 -10000 0 -0.44 22 22
Ephrin B/EPHB3 -0.016 0.12 -10000 0 -0.41 21 21
JNK cascade -0.051 0.13 -10000 0 -0.51 11 11
Ephrin B/EPHB1 -0.094 0.18 -10000 0 -0.48 47 47
RAP1/GDP -0.042 0.14 -10000 0 -0.39 38 38
EFNB2 -0.006 0.1 -10000 0 -0.57 16 16
EFNB3 -0.049 0.16 -10000 0 -0.47 64 64
EFNB1 0.007 0.052 -10000 0 -0.47 6 6
Ephrin B2/EPHB1-2 -0.076 0.15 -10000 0 -0.27 171 171
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.095 0.15 -10000 0 -0.48 41 41
Rap1/GTP -0.088 0.14 -10000 0 -0.44 41 41
axon guidance -0.019 0.1 -10000 0 -0.3 58 58
MAPK3 -0.055 0.14 -10000 0 -0.4 39 39
MAPK1 -0.055 0.14 -10000 0 -0.4 39 39
Rac1/GDP -0.05 0.14 -10000 0 -0.41 39 39
actin cytoskeleton reorganization -0.069 0.11 -10000 0 -0.35 42 42
CDC42/GDP -0.05 0.14 -10000 0 -0.41 39 39
PI3K 0.016 0.07 -10000 0 -0.31 18 18
EFNA5 -0.04 0.15 -10000 0 -0.47 55 55
Ephrin B2/EPHB4 0.005 0.067 -10000 0 -0.35 17 17
Ephrin B/EPHB2/Intersectin/N-WASP -0.009 0.12 -10000 0 -0.68 8 8
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.089 0.14 -10000 0 -0.43 44 44
PTK2 0.023 0.034 -10000 0 -10000 0 0
MAP4K4 -0.052 0.14 -10000 0 -0.51 11 11
SRC 0.013 0 -10000 0 -10000 0 0
KALRN 0.01 0.045 -10000 0 -0.57 3 3
Intersectin/N-WASP 0.02 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.035 0.14 -10000 0 -0.37 42 42
MAP2K1 -0.065 0.15 -10000 0 -0.43 39 39
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.061 0.14 -10000 0 -0.55 11 11
cell migration -0.073 0.17 -10000 0 -0.48 39 39
NRAS 0.012 0.022 -10000 0 -0.47 1 1
SYNJ1 -0.012 0.12 -10000 0 -0.65 8 8
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.059 0.17 -10000 0 -0.48 45 45
HRAS/GTP -0.099 0.15 -10000 0 -0.46 44 44
Ephrin B1/EPHB1-2 -0.068 0.14 -10000 0 -0.26 163 163
cell adhesion mediated by integrin 0.026 0.11 0.39 20 -10000 0 20
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.079 0.18 -10000 0 -0.5 41 41
RAC1-CDC42/GTP -0.089 0.14 -10000 0 -0.44 44 44
RASA1 0.011 0.03 -10000 0 -0.47 2 2
RAC1-CDC42/GDP -0.042 0.14 -10000 0 -0.38 39 39
ruffle organization -0.056 0.16 -10000 0 -0.44 41 41
NCK1 0.012 0.026 -10000 0 -0.57 1 1
receptor internalization -0.006 0.12 -10000 0 -0.58 9 9
Ephrin B/EPHB2/KALRN -0.012 0.13 -10000 0 -0.66 9 9
ROCK1 0.017 0.046 -10000 0 -0.37 4 4
RAS family/GDP -0.065 0.1 -10000 0 -0.45 14 14
Rac1/GTP -0.094 0.15 -10000 0 -0.47 41 41
Ephrin B/EPHB1/Src/Paxillin -0.083 0.17 -10000 0 -0.5 39 39
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.08 0.19 -9999 0 -0.47 96 96
CDC42/GTP -0.034 0.14 -9999 0 -0.39 45 45
PLCG1 -0.035 0.14 -9999 0 -0.4 45 45
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
cell migration -0.034 0.13 -9999 0 -0.38 45 45
S1PR5 -0.066 0.18 -9999 0 -0.47 82 82
S1PR4 -0.012 0.12 -9999 0 -0.57 22 22
MAPK3 -0.035 0.14 -9999 0 -0.4 45 45
MAPK1 -0.035 0.14 -9999 0 -0.4 45 45
S1P/S1P5/Gi -0.082 0.2 -9999 0 -0.56 59 59
GNAI1 0.006 0.064 -9999 0 -0.53 7 7
CDC42/GDP 0.01 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.03 0.11 -9999 0 -0.27 82 82
RHOA 0.015 0.065 -9999 0 -0.29 21 21
S1P/S1P4/Gi -0.044 0.15 -9999 0 -0.43 45 45
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.034 0.14 -9999 0 -0.47 49 49
S1P/S1P4/G12/G13 0.011 0.069 -9999 0 -0.31 22 22
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.072 0.18 -9999 0 -0.47 88 88
GNB1/GNG2 -0.031 0.14 -9999 0 -0.44 28 28
mol:DAG -0.023 0.13 -9999 0 -0.4 28 28
PLCG1 -0.024 0.13 -9999 0 -0.41 28 28
YES1 -0.037 0.14 -9999 0 -0.44 27 27
FZD3 0.011 0.03 -9999 0 -0.47 2 2
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.023 0.13 -9999 0 -0.41 28 28
MAP3K7 -0.049 0.15 -9999 0 -0.4 40 40
mol:Ca2+ -0.022 0.12 -9999 0 -0.38 28 28
mol:IP3 -0.023 0.13 -9999 0 -0.4 28 28
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.06 0.16 -9999 0 -0.41 54 54
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.047 0.14 -9999 0 -0.46 29 29
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.037 0.14 -9999 0 -0.44 26 26
GO:0007205 -0.022 0.12 -9999 0 -0.39 28 28
WNT6 -0.084 0.2 -9999 0 -0.48 99 99
WNT4 0.007 0.052 -9999 0 -0.47 6 6
NFAT1/CK1 alpha -0.054 0.16 -9999 0 -0.41 44 44
GNG2 0.007 0.052 -9999 0 -0.47 6 6
WNT5A -0.026 0.14 -9999 0 -0.5 38 38
WNT11 -0.025 0.14 -9999 0 -0.55 34 34
CDC42 -0.029 0.13 -9999 0 -0.42 26 26
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.016 0.055 -9999 0 -0.26 2 2
BIRC5 -0.2 0.28 -9999 0 -0.57 184 184
NFKBIA 0.019 0.052 -9999 0 -10000 0 0
CPEB1 -0.12 0.21 -9999 0 -0.47 134 134
AKT1 0.019 0.052 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.015 0.055 -9999 0 -0.47 2 2
NDEL1/TACC3 -0.004 0.12 -9999 0 -0.37 44 44
GADD45A 0.011 0.03 -9999 0 -0.47 2 2
GSK3B 0.018 0.007 -9999 0 -10000 0 0
PAK1/Aurora A 0.013 0.066 -9999 0 -0.3 8 8
MDM2 0.013 0 -9999 0 -10000 0 0
JUB -0.015 0.11 -9999 0 -0.47 29 29
TPX2 -0.12 0.2 -9999 0 -0.42 156 156
TP53 0.019 0.047 -9999 0 -0.27 6 6
DLG7 0.01 0.052 -9999 0 -10000 0 0
AURKAIP1 0.003 0.078 -9999 0 -0.57 9 9
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.005 0.13 -9999 0 -0.39 44 44
G2/M transition of mitotic cell cycle 0.014 0.054 -9999 0 -0.47 2 2
AURKA 0.014 0.064 -9999 0 -10000 0 0
AURKB -0.048 0.077 -9999 0 -0.16 149 149
CDC25B 0.013 0.056 -9999 0 -0.31 3 3
G2/M transition checkpoint 0 0.076 -9999 0 -0.24 29 29
mRNA polyadenylation -0.056 0.13 -9999 0 -0.25 134 134
Aurora A/CPEB -0.056 0.13 -9999 0 -0.26 134 134
Aurora A/TACC1/TRAP/chTOG 0.026 0.062 -9999 0 -0.36 3 3
BRCA1 0.011 0.037 -9999 0 -0.57 2 2
centrosome duplication 0.013 0.066 -9999 0 -0.3 8 8
regulation of centrosome cycle -0.005 0.12 -9999 0 -0.36 44 44
spindle assembly 0.025 0.062 -9999 0 -0.36 3 3
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.087 0.17 -9999 0 -0.38 60 60
CENPA -0.045 0.075 -9999 0 -0.22 36 36
Aurora A/PP2A 0.018 0.052 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.024 0.044 -9999 0 -10000 0 0
negative regulation of DNA binding 0.019 0.047 -9999 0 -0.27 6 6
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.02 0 -9999 0 -10000 0 0
RASA1 0.011 0.03 -9999 0 -0.47 2 2
Ajuba/Aurora A 0 0.076 -9999 0 -0.24 29 29
mitotic prometaphase 0.013 0.02 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.064 -9999 0 -10000 0 0
TACC1 0.001 0.077 -9999 0 -0.47 13 13
TACC3 -0.039 0.17 -9999 0 -0.57 44 44
Aurora A/Antizyme1 0.019 0.065 -9999 0 -0.31 9 9
Aurora A/RasGAP 0.016 0.055 -9999 0 -0.26 2 2
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.018 0.007 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.022 0.037 -9999 0 -0.27 8 8
Importin alpha/Importin beta/TPX2 -0.12 0.2 -9999 0 -0.41 156 156
PPP2R5D 0.013 0.001 -9999 0 -10000 0 0
Aurora A/TPX2 -0.082 0.18 -9999 0 -0.34 156 156
PAK1 0.006 0.06 -9999 0 -0.47 8 8
CKAP5 0.013 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.007 0.043 -10000 0 -0.47 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.028 0.18 0.59 25 -10000 0 25
IL27/IL27R/JAK1 0.002 0.25 0.4 1 -0.84 21 22
TBX21 0.009 0.22 0.35 1 -0.62 33 34
IL12B -0.024 0.14 -10000 0 -0.58 30 30
IL12A -0.003 0.068 -10000 0 -0.37 16 16
IL6ST -0.083 0.2 -10000 0 -0.47 102 102
IL27RA/JAK1 0.003 0.17 -10000 0 -1.1 11 11
IL27 -0.012 0.12 -10000 0 -0.57 20 20
TYK2 0.015 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.086 0.15 -10000 0 -0.6 7 7
T-helper 2 cell differentiation 0.028 0.18 0.59 25 -10000 0 25
T cell proliferation during immune response 0.028 0.18 0.59 25 -10000 0 25
MAPKKK cascade -0.028 0.18 -10000 0 -0.59 25 25
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.005 0.079 -10000 0 -0.57 9 9
IL12RB1 -0.014 0.12 -10000 0 -0.55 24 24
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.011 0.22 0.36 1 -0.6 26 27
IL27/IL27R/JAK2/TYK2 -0.028 0.18 -10000 0 -0.6 25 25
positive regulation of T cell mediated cytotoxicity -0.028 0.18 -10000 0 -0.59 25 25
STAT1 (dimer) 0.022 0.32 0.49 106 -0.91 18 124
JAK2 0.012 0.022 -10000 0 -0.47 1 1
JAK1 0.016 0.004 -10000 0 -10000 0 0
STAT2 (dimer) -0.021 0.17 -10000 0 -0.58 23 23
T cell proliferation -0.11 0.21 -10000 0 -0.52 63 63
IL12/IL12R/TYK2/JAK2 0.009 0.086 -10000 0 -0.52 2 2
IL17A -0.089 0.14 -10000 0 -0.61 7 7
mast cell activation 0.028 0.18 0.59 25 -10000 0 25
IFNG -0.001 0.033 -10000 0 -0.089 25 25
T cell differentiation -0.003 0.006 0.015 1 -0.021 26 27
STAT3 (dimer) -0.021 0.17 -10000 0 -0.58 23 23
STAT5A (dimer) -0.021 0.17 -10000 0 -0.6 22 22
STAT4 (dimer) -0.031 0.19 -10000 0 -0.59 32 32
STAT4 -0.007 0.1 -10000 0 -0.54 18 18
T cell activation -0.007 0.02 0.12 12 -10000 0 12
IL27R/JAK2/TYK2 -0.05 0.19 -10000 0 -1 12 12
GATA3 -0.34 0.56 -10000 0 -1.2 148 148
IL18 0.001 0.057 -10000 0 -0.33 14 14
positive regulation of mast cell cytokine production -0.02 0.16 -10000 0 -0.57 23 23
IL27/EBI3 -0.007 0.11 -10000 0 -0.4 35 35
IL27RA -0.016 0.18 -10000 0 -1.2 11 11
IL6 -0.16 0.25 -10000 0 -0.51 159 159
STAT5A 0.012 0.022 -10000 0 -0.47 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.011 0.074 0.48 11 -10000 0 11
IL1B -0.045 0.13 -10000 0 -0.36 74 74
EBI3 -0.001 0.097 -10000 0 -0.55 15 15
TNF -0.018 0.099 -10000 0 -0.36 37 37
EGFR-dependent Endothelin 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
HRAS 0.006 0.064 -9999 0 -0.57 6 6
EGFR -0.025 0.13 -9999 0 -0.47 40 40
EGF/EGFR -0.091 0.16 -9999 0 -0.4 71 71
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.019 0.12 -9999 0 -0.45 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.038 0.15 -9999 0 -0.47 53 53
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.058 0.19 -9999 0 -0.53 65 65
EGF/EGFR dimer/SHC -0.041 0.14 -9999 0 -0.31 101 101
mol:GDP -0.022 0.12 -9999 0 -0.44 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.025 0.14 -9999 0 -0.5 37 37
GRB2/SOS1 0.02 0 -9999 0 -10000 0 0
HRAS/GTP -0.049 0.1 -9999 0 -0.48 7 7
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.05 0.1 -9999 0 -0.49 7 7
FRAP1 -0.023 0.11 -9999 0 -0.43 4 4
EGF/EGFR dimer -0.06 0.16 -9999 0 -0.37 101 101
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.043 0.16 -9999 0 -0.4 75 75
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.044 0.12 -10000 0 -0.24 129 129
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.002 0.033 -10000 0 -0.42 3 3
GNB1/GNG2 0.015 0.032 -10000 0 -0.27 6 6
GNB1 0.013 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 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.06 0.12 -10000 0 -0.26 129 129
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 0.018 0.03 0.069 129 -10000 0 129
GNAL -0.11 0.21 -10000 0 -0.47 129 129
GNG2 0.007 0.052 -10000 0 -0.47 6 6
CRH -0.003 0.045 -10000 0 -0.57 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.048 -10000 0 -0.31 12 12
MAPK11 0.004 0.031 -10000 0 -0.24 8 8
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.067 0.15 0.35 112 -10000 0 112
KIRREL -0.087 0.2 -10000 0 -0.47 102 102
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.067 0.15 -10000 0 -0.35 112 112
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.039 0.12 -10000 0 -0.32 16 16
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.029 0.1 -10000 0 -0.36 5 5
FYN -0.042 0.11 -10000 0 -0.31 16 16
mol:Ca2+ -0.04 0.11 -10000 0 -0.32 16 16
mol:DAG -0.039 0.12 -10000 0 -0.32 16 16
NPHS2 -0.011 0.049 -10000 0 -0.58 3 3
mol:IP3 -0.039 0.12 -10000 0 -0.32 16 16
regulation of endocytosis -0.031 0.1 -10000 0 -0.44 4 4
Nephrin/NEPH1/podocin/Cholesterol -0.048 0.12 -10000 0 -0.26 112 112
establishment of cell polarity -0.067 0.15 -10000 0 -0.35 112 112
Nephrin/NEPH1/podocin/NCK1-2 -0.028 0.11 -10000 0 -0.41 5 5
Nephrin/NEPH1/beta Arrestin2 -0.031 0.11 -10000 0 -0.45 4 4
NPHS1 -0.015 0.086 -10000 0 -0.57 11 11
Nephrin/NEPH1/podocin -0.042 0.11 -10000 0 -0.31 16 16
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.012 0.026 -10000 0 -0.57 1 1
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.039 0.12 -10000 0 -0.32 16 16
CD2AP 0.013 0.001 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.039 0.12 -10000 0 -0.32 15 15
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.079 0.16 -10000 0 -0.42 57 57
cytoskeleton organization -0.029 0.12 -10000 0 -0.39 5 5
Nephrin/NEPH1 -0.045 0.11 -10000 0 -0.24 112 112
Nephrin/NEPH1/ZO-1 -0.043 0.12 -10000 0 -0.33 14 14
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.02 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.003 0.1 -10000 0 -0.44 25 25
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.005 0.091 -10000 0 -0.38 5 5
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.18 -10000 0 -0.33 184 184
NT-4/5 (dimer)/p75(NTR) -0.087 0.19 -10000 0 -0.4 125 125
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.002 0.097 -10000 0 -0.44 6 6
IKBKG 0.013 0 -10000 0 -10000 0 0
BDNF -0.087 0.2 -10000 0 -0.47 104 104
MGDIs/NGR/p75(NTR)/LINGO1 -0.039 0.14 -10000 0 -0.33 93 93
FURIN 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.058 0.16 -10000 0 -0.31 124 124
LINGO1 -0.052 0.18 -10000 0 -0.57 55 55
Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.087 0.2 -10000 0 -0.47 104 104
NTRK1 -0.027 0.14 -10000 0 -0.49 39 39
RTN4R 0.013 0 -10000 0 -10000 0 0
neuron apoptosis -0.036 0.16 -10000 0 -0.45 39 39
IRAK1 0.012 0.026 -10000 0 -0.57 1 1
SHC1 -0.014 0.1 -10000 0 -0.45 5 5
ARHGDIA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP 0.01 0 -10000 0 -10000 0 0
Gamma Secretase 0.04 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.008 0.11 -10000 0 -0.4 13 13
MAGEH1 0.003 0.075 -10000 0 -0.55 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.004 0.1 -10000 0 -0.44 9 9
Mammalian IAPs/DIABLO 0.03 0.038 -10000 0 -0.31 3 3
proNGF (dimer) -0.01 0.1 -10000 0 -0.48 24 24
MAGED1 0.012 0.026 -10000 0 -0.57 1 1
APP 0.01 0.037 -10000 0 -0.47 3 3
NT-4/5 (dimer) -0.099 0.2 -10000 0 -0.47 116 116
ZNF274 0.013 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.003 0.089 -10000 0 -0.38 5 5
NGF -0.01 0.1 -10000 0 -0.48 24 24
cell cycle arrest 0.01 0.1 -10000 0 -0.4 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.001 0.092 -10000 0 -0.4 7 7
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.065 0.17 -10000 0 -0.34 125 125
NCSTN 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.013 0.1 -10000 0 -0.45 5 5
PSENEN 0.013 0 -10000 0 -10000 0 0
mol:ceramide -0.006 0.098 -10000 0 -0.41 7 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.009 0.08 -10000 0 -0.34 7 7
p75(NTR)/beta APP -0.012 0.1 -10000 0 -0.34 44 44
BEX1 -0.14 0.23 -10000 0 -0.47 158 158
mol:GDP -0.023 0.1 -10000 0 -0.29 64 64
NGF (dimer) -0.059 0.15 -10000 0 -0.33 82 82
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.026 0.13 -10000 0 -0.33 55 55
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
RAC1/GTP -0.01 0.09 -10000 0 -0.39 5 5
MYD88 0.013 0 -10000 0 -10000 0 0
CHUK 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.013 0.1 -10000 0 -0.45 5 5
RHOB 0.006 0.06 -10000 0 -0.47 8 8
RHOA 0.013 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0 0.091 -10000 0 -0.41 23 23
NT3 (dimer) -0.043 0.15 -10000 0 -0.47 58 58
TP53 -0.031 0.13 -10000 0 -0.44 26 26
PRDM4 -0.005 0.095 -10000 0 -0.41 5 5
BDNF (dimer) -0.15 0.2 -10000 0 -0.41 133 133
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
SORT1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity 0.002 0.089 -10000 0 -0.38 5 5
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.002 0.096 -10000 0 -0.41 5 5
RHOC 0.013 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
MAPK10 -0.018 0.14 -10000 0 -0.43 35 35
DIABLO 0.013 0 -10000 0 -10000 0 0
SMPD2 -0.006 0.098 -10000 0 -0.41 7 7
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.013 0.1 -10000 0 -0.28 64 64
PSEN1 0.013 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.048 0.16 -10000 0 -0.38 85 85
MAPK8 -0.021 0.14 -10000 0 -0.41 37 37
MAPK9 -0.016 0.14 -10000 0 -0.41 33 33
APAF1 0.013 0 -10000 0 -10000 0 0
NTF3 -0.043 0.15 -10000 0 -0.47 58 58
NTF4 -0.099 0.2 -10000 0 -0.47 116 116
NDN 0.008 0.048 -10000 0 -0.47 5 5
RAC1/GDP 0.01 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.03 0.078 -10000 0 -0.41 7 7
p75 CTF/Sortilin/TRAF6/NRIF 0.031 0.029 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.013 0.1 -10000 0 -0.45 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.034 0.14 -10000 0 -0.45 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.044 0.14 -10000 0 -0.48 23 23
PRKACB 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.056 0.15 -10000 0 -0.33 107 107
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.005 0.066 -10000 0 -0.51 8 8
BIRC2 0.013 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.011 0.12 0.18 5 -0.35 10 15
BAD -0.014 0.14 -10000 0 -0.41 36 36
RIPK2 0.001 0.082 -10000 0 -0.57 10 10
NGFR -0.028 0.14 -10000 0 -0.47 43 43
CYCS 0.002 0.091 -10000 0 -0.46 4 4
ADAM17 0.007 0.052 -10000 0 -0.47 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.009 0.11 -10000 0 -0.39 15 15
BCL2L11 -0.014 0.14 -10000 0 -0.41 37 37
BDNF (dimer)/p75(NTR) -0.079 0.18 -10000 0 -0.38 124 124
PI3K -0.007 0.1 -10000 0 -0.43 8 8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.002 0.096 -10000 0 -0.41 5 5
NDNL2 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKCI 0.012 0.026 -10000 0 -0.57 1 1
NGF (dimer)/p75(NTR) -0.027 0.12 -10000 0 -0.34 64 64
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.003 0.099 -10000 0 -0.43 6 6
TRAF6 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
PLG -0.022 0.12 -10000 0 -0.57 24 24
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.053 0.16 -10000 0 -0.5 32 32
SQSTM1 0.013 0 -10000 0 -10000 0 0
NGFRAP1 0.013 0 -10000 0 -10000 0 0
CASP3 -0.01 0.13 -10000 0 -0.38 37 37
E2F1 -0.014 0.12 -10000 0 -0.57 23 23
CASP9 0.013 0 -10000 0 -10000 0 0
IKK complex -0.039 0.091 -10000 0 -0.37 16 16
NGF (dimer)/TRKA -0.026 0.12 -10000 0 -0.36 60 60
MMP7 -0.09 0.21 -10000 0 -0.53 95 95
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.005 0.091 -10000 0 -0.38 5 5
MMP3 -0.074 0.2 -10000 0 -0.51 81 81
APAF-1/Caspase 9 -0.023 0.062 -10000 0 -0.44 2 2
Effects of Botulinum toxin

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
STX1A 0.009 0.027 -9999 0 -0.42 2 2
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.004 0.079 -9999 0 -0.38 20 20
STXBP1 0.01 0.04 -9999 0 -0.5 3 3
ACh/CHRNA1 -0.071 0.15 -9999 0 -0.38 91 91
RAB3GAP2/RIMS1/UNC13B 0.013 0.068 -9999 0 -0.35 12 12
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 -0.003 0.091 -9999 0 -0.52 15 15
mol:ACh -0.01 0.043 -9999 0 -0.11 77 77
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.029 0.07 -9999 0 -0.35 11 11
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.07 0.15 -9999 0 -0.38 91 91
UNC13B 0.007 0.059 -9999 0 -0.57 5 5
CHRNA1 -0.095 0.23 -9999 0 -0.57 91 91
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.056 0.14 -9999 0 -0.33 92 92
SNAP25 -0.035 0.099 -9999 0 -0.27 76 76
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.078 0.19 -9999 0 -0.48 92 92
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.014 0.034 -9999 0 -0.32 5 5
STX1A/SNAP25 fragment 1/VAMP2 -0.029 0.07 -9999 0 -0.35 11 11
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.029 0.13 -10000 0 -0.35 35 35
IKBKB 0.01 0.059 -10000 0 -0.22 7 7
AKT1 -0.015 0.097 0.2 8 -0.24 34 42
IKBKG 0.012 0.06 -10000 0 -0.24 7 7
CALM1 -0.007 0.083 0.23 11 -0.3 15 26
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
MAP3K1 -0.059 0.17 -10000 0 -0.42 70 70
MAP3K7 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.087 0.23 11 -0.29 24 35
DOK1 0.012 0.022 -10000 0 -0.47 1 1
AP-1 -0.015 0.08 -10000 0 -0.24 21 21
LYN 0.013 0 -10000 0 -10000 0 0
BLNK 0.012 0.022 -10000 0 -0.47 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
BCR complex -0.064 0.19 -10000 0 -0.46 87 87
CD22 -0.078 0.18 -10000 0 -0.53 51 51
CAMK2G 0 0.079 0.22 11 -0.38 5 16
CSNK2A1 0.013 0 -10000 0 -10000 0 0
INPP5D -0.014 0.11 -10000 0 -0.47 28 28
SHC/GRB2/SOS1 -0.05 0.12 -10000 0 -0.5 20 20
GO:0007205 -0.014 0.088 0.23 11 -0.3 24 35
SYK 0.006 0.059 -10000 0 -0.48 7 7
ELK1 -0.007 0.084 0.23 11 -0.34 10 21
NFATC1 -0.031 0.14 -10000 0 -0.34 64 64
B-cell antigen/BCR complex -0.064 0.19 -10000 0 -0.46 87 87
PAG1/CSK 0.018 0.027 -10000 0 -0.41 2 2
NFKBIB 0.014 0.023 0.082 4 -10000 0 4
HRAS -0.008 0.091 0.21 10 -0.32 19 29
NFKBIA 0.014 0.023 0.082 4 -10000 0 4
NF-kappa-B/RelA/I kappa B beta 0.018 0.02 0.084 4 -10000 0 4
RasGAP/Csk -0.038 0.17 -10000 0 -0.63 26 26
mol:GDP -0.013 0.083 0.24 11 -0.28 23 34
PTEN 0.001 0.077 -10000 0 -0.47 13 13
CD79B -0.017 0.12 -10000 0 -0.53 28 28
NF-kappa-B/RelA/I kappa B alpha 0.019 0.02 0.085 1 -10000 0 1
GRB2 0.013 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.057 0.17 -10000 0 -0.4 75 75
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
mol:IP3 -0.014 0.088 0.23 11 -0.3 24 35
CSK 0.013 0 -10000 0 -10000 0 0
FOS -0.041 0.12 0.23 5 -0.4 22 27
CHUK 0.012 0.06 -10000 0 -0.24 7 7
IBTK 0.012 0.022 -10000 0 -0.47 1 1
CARD11/BCL10/MALT1/TAK1 -0.029 0.079 -10000 0 -0.42 13 13
PTPN6 -0.044 0.18 -10000 0 -0.53 45 45
RELA 0.013 0 -10000 0 -10000 0 0
BCL2A1 0.016 0.023 -10000 0 -0.1 9 9
VAV2 -0.079 0.2 -10000 0 -0.49 72 72
ubiquitin-dependent protein catabolic process 0.018 0.022 0.085 4 -10000 0 4
BTK 0.008 0.088 -10000 0 -0.81 2 2
CD19 -0.12 0.2 -10000 0 -0.5 85 85
MAP4K1 -0.024 0.14 -10000 0 -0.55 33 33
CD72 -0.013 0.12 -10000 0 -0.56 23 23
PAG1 0.011 0.037 -10000 0 -0.57 2 2
MAPK14 -0.043 0.15 -10000 0 -0.39 47 47
SH3BP5 0.013 0 -10000 0 -10000 0 0
PIK3AP1 -0.014 0.095 -10000 0 -0.34 22 22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.015 0.13 -10000 0 -0.36 47 47
RAF1 -0.001 0.087 0.21 3 -0.34 11 14
RasGAP/p62DOK/SHIP -0.078 0.16 -10000 0 -0.56 37 37
CD79A -0.074 0.2 -10000 0 -0.54 78 78
re-entry into mitotic cell cycle -0.015 0.079 -10000 0 -0.24 18 18
RASA1 0.011 0.03 -10000 0 -0.47 2 2
MAPK3 0.012 0.076 -10000 0 -0.32 6 6
MAPK1 0.012 0.076 -10000 0 -0.33 5 5
CD72/SHP1 -0.046 0.2 -10000 0 -0.56 49 49
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.048 0.16 -10000 0 -0.4 51 51
actin cytoskeleton organization -0.061 0.17 -10000 0 -0.42 71 71
NF-kappa-B/RelA 0.042 0.037 0.16 4 -10000 0 4
Calcineurin 0.003 0.068 -10000 0 -0.34 5 5
PI3K -0.094 0.16 -10000 0 -0.43 77 77
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.018 0.093 -10000 0 -0.32 29 29
SOS1 0.013 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.13 0.3 -10000 0 -0.7 97 97
DAPP1 -0.15 0.32 -10000 0 -0.87 74 74
cytokine secretion -0.028 0.14 0.19 3 -0.32 64 67
mol:DAG -0.014 0.088 0.23 11 -0.3 24 35
PLCG2 0.003 0.071 -10000 0 -0.49 10 10
MAP2K1 0.006 0.082 -10000 0 -0.36 6 6
B-cell antigen/BCR complex/FcgammaRIIB -0.06 0.2 -10000 0 -0.49 63 63
mol:PI-3-4-5-P3 -0.064 0.12 0.25 8 -0.31 71 79
ETS1 0.004 0.08 0.22 11 -0.39 6 17
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.028 0.15 -10000 0 -0.57 20 20
B-cell antigen/BCR complex/LYN -0.063 0.14 -10000 0 -0.45 42 42
MALT1 0.009 0.05 -10000 0 -0.55 4 4
TRAF6 0.013 0 -10000 0 -10000 0 0
RAC1 -0.066 0.18 -10000 0 -0.45 71 71
B-cell antigen/BCR complex/LYN/SYK -0.08 0.18 -10000 0 -0.53 50 50
CARD11 -0.016 0.1 0.23 8 -0.4 20 28
FCGR2B -0.013 0.12 -10000 0 -0.53 24 24
PPP3CA 0.01 0.045 -10000 0 -0.57 3 3
BCL10 0.013 0 -10000 0 -10000 0 0
IKK complex 0.013 0.031 0.09 4 -10000 0 4
PTPRC -0.014 0.12 -10000 0 -0.5 27 27
PDPK1 -0.019 0.095 0.18 8 -0.23 38 46
PPP3CB 0.013 0 -10000 0 -10000 0 0
PPP3CC 0.013 0 -10000 0 -10000 0 0
POU2F2 0.016 0.021 -10000 0 -0.099 3 3
Syndecan-4-mediated signaling events

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
PTK2 -0.008 0.078 -9999 0 -0.41 16 16
Syndecan-4/Syndesmos -0.1 0.14 -9999 0 -0.46 30 30
positive regulation of JNK cascade -0.1 0.15 -9999 0 -0.48 30 30
Syndecan-4/ADAM12 -0.12 0.16 -9999 0 -0.48 47 47
CCL5 -0.009 0.1 -9999 0 -0.5 21 21
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 -0.002 0.086 -9999 0 -0.47 16 16
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG -0.017 0.12 -9999 0 -0.57 24 24
ADAM12 -0.017 0.13 -9999 0 -0.56 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.062 0.055 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.13 0.16 -9999 0 -0.49 42 42
Syndecan-4/CXCL12/CXCR4 -0.11 0.16 -9999 0 -0.52 29 29
Syndecan-4/Laminin alpha3 -0.12 0.16 -9999 0 -0.45 53 53
MDK -0.011 0.12 -9999 0 -0.56 21 21
Syndecan-4/FZD7 -0.11 0.15 -9999 0 -0.47 36 36
Syndecan-4/Midkine -0.11 0.16 -9999 0 -0.51 32 32
FZD7 -0.004 0.09 -9999 0 -0.47 18 18
Syndecan-4/FGFR1/FGF -0.12 0.13 -9999 0 -0.53 19 19
THBS1 -0.012 0.11 -9999 0 -0.49 25 25
integrin-mediated signaling pathway -0.11 0.15 -9999 0 -0.45 41 41
positive regulation of MAPKKK cascade -0.1 0.15 -9999 0 -0.48 30 30
Syndecan-4/TACI -0.13 0.18 -9999 0 -0.46 74 74
CXCR4 0.002 0.077 -9999 0 -0.53 10 10
cell adhesion 0.007 0.088 -9999 0 -0.4 15 15
Syndecan-4/Dynamin -0.1 0.14 -9999 0 -0.46 30 30
Syndecan-4/TSP1 -0.11 0.15 -9999 0 -0.49 34 34
Syndecan-4/GIPC -0.1 0.14 -9999 0 -0.46 30 30
Syndecan-4/RANTES -0.11 0.15 -9999 0 -0.47 40 40
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.038 0.16 -9999 0 -0.53 47 47
LAMA3 -0.031 0.14 -9999 0 -0.47 45 45
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.017 0.1 -9999 0 -0.41 23 23
Syndecan-4/alpha-Actinin -0.1 0.15 -9999 0 -0.46 33 33
TFPI -0.02 0.13 -9999 0 -0.52 31 31
F2 -0.033 0.14 -9999 0 -0.58 29 29
alpha5/beta1 Integrin 0.008 0.062 -9999 0 -0.33 16 16
positive regulation of cell adhesion -0.14 0.17 -9999 0 -0.5 48 48
ACTN1 0.007 0.052 -9999 0 -0.47 6 6
TNC -0.014 0.11 -9999 0 -0.47 28 28
Syndecan-4/CXCL12 -0.11 0.15 -9999 0 -0.47 37 37
FGF6 -0.001 0.037 -9999 0 -0.57 2 2
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.008 0.1 -9999 0 -0.47 22 22
TNFRSF13B -0.05 0.18 -9999 0 -0.56 53 53
FGF2 -0.024 0.13 -9999 0 -0.47 38 38
FGFR1 0.011 0.03 -9999 0 -0.47 2 2
Syndecan-4/PI-4-5-P2 -0.11 0.14 -9999 0 -0.46 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.004 0.088 -9999 0 -0.47 16 16
cell migration -0.024 0.021 -9999 0 -10000 0 0
PRKCD 0.02 0.009 -9999 0 -10000 0 0
vasculogenesis -0.11 0.15 -9999 0 -0.45 41 41
SDC4 -0.11 0.15 -9999 0 -0.49 30 30
Syndecan-4/Tenascin C -0.11 0.15 -9999 0 -0.47 41 41
Syndecan-4/PI-4-5-P2/PKC alpha -0.049 0.043 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.1 0.14 -9999 0 -0.46 30 30
MMP9 -0.31 0.29 -9999 0 -0.57 272 272
Rac1/GTP 0.007 0.091 -9999 0 -0.42 15 15
cytoskeleton organization -0.099 0.14 -9999 0 -0.44 30 30
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.12 0.16 -9999 0 -0.51 38 38
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR 0.012 0.022 -9999 0 -0.47 1 1
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.039 0.15 -9999 0 -0.35 86 86
CaM/Ca2+ 0.01 0 -9999 0 -10000 0 0
KATNA1 0.013 0.001 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.029 0.13 -9999 0 -0.32 81 81
IQGAP1/CaM 0.02 0 -9999 0 -10000 0 0
DAB1 -0.18 0.23 -9999 0 -0.47 193 193
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.13 0.25 -9999 0 -0.57 124 124
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.014 0.051 -9999 0 -0.41 7 7
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 -0.015 0.13 -9999 0 -0.57 24 24
LIS1/Poliovirus Protein 3A 0.016 0 -9999 0 -10000 0 0
CDK5R2 -0.05 0.18 -9999 0 -0.57 53 53
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.14 0.2 -9999 0 -0.34 232 232
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.021 0.13 -9999 0 -0.41 20 20
MAP1B -0.023 0.075 -9999 0 -0.27 42 42
RAC1 0.021 0 -9999 0 -10000 0 0
p35/CDK5 -0.026 0.14 -9999 0 -0.61 9 9
RELN -0.082 0.22 -9999 0 -0.57 82 82
PAFAH/LIS1 -0.067 0.16 -9999 0 -0.34 124 124
LIS1/CLIP170 0.026 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.045 0.083 -9999 0 -0.44 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.16 -9999 0 -0.44 59 59
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.03 0.14 -9999 0 -0.43 21 21
LIS1/IQGAP1 0.026 0 -9999 0 -10000 0 0
RHOA 0.021 0 -9999 0 -10000 0 0
PAFAH1B1 0.021 0 -9999 0 -10000 0 0
PAFAH1B3 -0.009 0.11 -9999 0 -0.57 19 19
PAFAH1B2 0 0.08 -9999 0 -0.47 14 14
MAP1B/LIS1/Dynein heavy chain 0.009 0.051 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.014 0.13 -9999 0 -0.39 20 20
LRP8 0.005 0.069 -9999 0 -0.57 7 7
NDEL1/Katanin 60 -0.021 0.13 -9999 0 -0.4 21 21
P39/CDK5 -0.044 0.15 -9999 0 -0.55 15 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0 -9999 0 -10000 0 0
CDK5 -0.02 0.12 -9999 0 -0.57 3 3
PPP2R5D 0.013 0.001 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.11 0.18 -9999 0 -0.52 44 44
RELN/VLDLR -0.027 0.14 -9999 0 -0.32 81 81
CDC42 0.021 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.016 0.1 -10000 0 -0.32 51 51
CRKL -0.004 0.11 -10000 0 -0.43 19 19
mol:PIP3 -0.006 0.072 0.43 13 -10000 0 13
AKT1 0.009 0.05 0.31 13 -10000 0 13
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 0.003 0.11 -10000 0 -0.41 18 18
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
HGF/MET/SHIP2 -0.026 0.14 -10000 0 -0.34 72 72
MAP3K5 0.003 0.11 -10000 0 -0.42 20 20
HGF/MET/CIN85/CBL/ENDOPHILINS -0.015 0.13 -10000 0 -0.42 28 28
AP1 -0.051 0.14 -10000 0 -0.33 91 91
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.12 0.29 -10000 0 -0.74 86 86
STAT3 (dimer) -0.002 0.11 -10000 0 -0.43 19 19
GAB1/CRKL/SHP2/PI3K 0.01 0.12 -10000 0 -0.42 23 23
INPP5D -0.014 0.11 -10000 0 -0.47 28 28
CBL/CRK 0.003 0.11 -10000 0 -0.42 18 18
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.001 0.077 -10000 0 -0.47 13 13
ELK1 -0.018 0.052 -10000 0 -0.17 51 51
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.024 0.066 -10000 0 -0.3 18 18
PAK1 0.011 0.055 0.3 13 -10000 0 13
HGF/MET/RANBP10 -0.026 0.14 -10000 0 -0.34 72 72
HRAS -0.043 0.21 -10000 0 -0.63 51 51
DOCK1 0.001 0.11 -10000 0 -0.42 19 19
GAB1 -0.011 0.12 -10000 0 -0.32 52 52
CRK -0.004 0.11 -10000 0 -0.43 19 19
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.045 0.21 -10000 0 -0.57 62 62
JUN 0.006 0.06 -10000 0 -0.5 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.024 0.1 -10000 0 -0.27 62 62
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
cell morphogenesis 0.016 0.13 -10000 0 -0.46 23 23
GRB2/SHC -0.005 0.091 -10000 0 -0.36 17 17
FOS -0.076 0.19 -10000 0 -0.47 91 91
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.018 0.052 -10000 0 -0.17 51 51
HGF/MET/MUC20 -0.035 0.13 -10000 0 -0.35 72 72
cell migration -0.006 0.09 -10000 0 -0.35 17 17
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.012 0.022 -10000 0 -0.47 1 1
MET/RANBP10 -0.016 0.1 -10000 0 -0.32 51 51
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.007 0.11 -10000 0 -0.44 19 19
MET/MUC20 -0.025 0.1 -10000 0 -0.33 51 51
RAP1B 0.009 0.1 -10000 0 -0.38 18 18
RAP1A 0.009 0.1 -10000 0 -0.38 18 18
HGF/MET/RANBP9 -0.026 0.14 -10000 0 -0.34 72 72
RAF1 -0.033 0.2 -10000 0 -0.59 51 51
STAT3 -0.003 0.11 -10000 0 -0.44 19 19
cell proliferation -0.008 0.16 -10000 0 -0.41 52 52
RPS6KB1 -0.001 0.039 -10000 0 -10000 0 0
MAPK3 -0.021 0.047 -10000 0 -10000 0 0
MAPK1 -0.021 0.047 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 0.01 0.13 -10000 0 -0.41 30 30
SRC 0 0.11 -10000 0 -0.41 19 19
PI3K -0.01 0.1 -10000 0 -0.39 23 23
MET/Glomulin -0.019 0.092 -10000 0 -0.29 51 51
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.023 0.18 -10000 0 -0.54 51 51
MET -0.036 0.15 -10000 0 -0.47 51 51
MAP4K1 -0.003 0.12 -10000 0 -0.44 19 19
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.024 0.18 -10000 0 -0.53 52 52
BAD 0.014 0.048 0.3 13 -0.3 1 14
MAP2K4 0.01 0.1 -10000 0 -0.38 20 20
SHP2/GRB2/SOS1/GAB1 -0.042 0.12 -10000 0 -0.36 51 51
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.015 0.094 -10000 0 -0.27 51 51
PLCgamma1/PKC 0.01 0 -10000 0 -10000 0 0
HGF -0.026 0.14 -10000 0 -0.5 38 38
RASA1 0.011 0.03 -10000 0 -0.47 2 2
NCK1 0.012 0.026 -10000 0 -0.57 1 1
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.005 0.095 -10000 0 -0.37 18 18
PDPK1 0.002 0.057 0.35 13 -10000 0 13
HGF/MET/SHIP -0.04 0.17 -10000 0 -0.4 78 78
Signaling events mediated by PTP1B

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
PDGFRB 0.011 0.037 -10000 0 -0.57 2 2
Jak2/Leptin Receptor -0.031 0.12 0.19 15 -0.4 24 39
PTP1B/AKT1 -0.037 0.081 -10000 0 -0.3 13 13
FYN 0.011 0.03 -10000 0 -0.47 2 2
p210 bcr-abl/PTP1B -0.048 0.088 -10000 0 -0.29 27 27
EGFR -0.028 0.13 -10000 0 -0.48 40 40
EGF/EGFR -0.079 0.14 -10000 0 -0.35 77 77
CSF1 0.002 0.074 -10000 0 -0.47 12 12
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.1 0.14 -10000 0 -0.33 107 107
Insulin Receptor/Insulin -0.041 0.066 -10000 0 -0.29 15 15
HCK 0.008 0.05 -10000 0 -0.49 5 5
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.039 0.084 -10000 0 -0.3 17 17
EGF -0.06 0.18 -10000 0 -0.54 65 65
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.062 0.12 -10000 0 -0.37 44 44
TXN 0.011 0.027 -10000 0 -0.58 1 1
PTP1B/IRS1/GRB2 -0.038 0.099 -10000 0 -0.36 20 20
cell migration 0.048 0.088 0.29 27 -10000 0 27
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.041 0.16 -10000 0 -0.52 51 51
ITGA2B -0.005 0.092 -10000 0 -0.51 16 16
CSF1R 0.01 0.04 -10000 0 -0.5 3 3
Prolactin Receptor/Prolactin -0.031 0.13 -10000 0 -0.38 56 56
FGR 0.01 0.04 -10000 0 -0.5 3 3
PTP1B/p130 Cas -0.039 0.084 -10000 0 -0.28 23 23
Crk/p130 Cas -0.031 0.082 -10000 0 -0.3 13 13
DOK1 -0.029 0.079 -10000 0 -0.29 12 12
JAK2 -0.033 0.1 -10000 0 -0.37 21 21
Jak2/Leptin Receptor/Leptin -0.084 0.14 -10000 0 -0.43 55 55
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
PTPN1 -0.048 0.089 -10000 0 -0.29 27 27
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.12 0.22 -10000 0 -0.48 136 136
SRC -0.004 0.035 -10000 0 -10000 0 0
ITGB3 -0.085 0.19 -10000 0 -0.47 101 101
CAT1/PTP1B -0.039 0.1 -10000 0 -0.36 15 15
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.035 0.074 -10000 0 -0.39 8 8
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.084 0.15 -10000 0 -0.42 72 72
negative regulation of transcription -0.03 0.1 -10000 0 -0.36 21 21
FCGR2A 0.009 0.048 -10000 0 -0.52 4 4
FER -0.008 0.098 -10000 0 -0.47 21 21
alphaIIb/beta3 Integrin -0.063 0.16 -10000 0 -0.34 112 112
BLK -0.1 0.22 -10000 0 -0.5 112 112
Insulin Receptor/Insulin/Shc 0.009 0.059 -10000 0 -0.34 14 14
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR -0.009 0.1 -10000 0 -0.46 24 24
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.014 0.1 -10000 0 -0.42 6 6
PRL -0.003 0.058 -10000 0 -0.57 5 5
SOCS3 -0.14 0.41 -10000 0 -1.2 67 67
SPRY2 0.01 0.049 -10000 0 -0.47 5 5
Insulin Receptor/Insulin/IRS1 -0.001 0.081 -10000 0 -0.32 30 30
CSF1/CSF1R -0.037 0.1 -10000 0 -0.42 18 18
Ras protein signal transduction 0.028 0.027 -10000 0 -10000 0 0
IRS1 -0.003 0.087 -10000 0 -0.47 17 17
INS -0.015 0.095 -10000 0 -0.57 14 14
LEP -0.006 0.082 -10000 0 -0.57 10 10
STAT5B -0.036 0.087 -10000 0 -0.26 29 29
STAT5A -0.037 0.086 -10000 0 -0.27 26 26
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.04 0.086 -10000 0 -0.32 15 15
CSN2 -0.002 0.054 -10000 0 -10000 0 0
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
LAT -0.012 0.064 -10000 0 -0.53 4 4
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK 0.003 0.078 -10000 0 -0.57 9 9
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.27 0.29 -10000 0 -0.57 242 242
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.019 0.12 -9999 0 -0.5 27 27
PDGF/PDGFRA/CRKL -0.002 0.081 -9999 0 -0.34 27 27
positive regulation of JUN kinase activity 0.017 0.062 -9999 0 -0.32 1 1
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.085 0.17 -9999 0 -0.36 135 135
AP1 -0.16 0.34 -9999 0 -0.87 91 91
mol:IP3 -0.006 0.09 -9999 0 -0.37 27 27
PLCG1 -0.006 0.09 -9999 0 -0.37 27 27
PDGF/PDGFRA/alphaV Integrin -0.004 0.091 -9999 0 -0.37 27 27
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.006 0.09 -9999 0 -0.37 27 27
CAV3 -0.1 0.21 -9999 0 -0.48 113 113
CAV1 -0.049 0.16 -9999 0 -0.47 64 64
SHC/Grb2/SOS1 0.018 0.062 -9999 0 -0.32 1 1
PDGF/PDGFRA/Shf -0.004 0.087 -9999 0 -0.35 28 28
FOS -0.13 0.35 -9999 0 -0.85 91 91
JUN -0.017 0.054 -9999 0 -0.42 7 7
oligodendrocyte development -0.004 0.091 -9999 0 -0.37 27 27
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
mol:DAG -0.006 0.09 -9999 0 -0.37 27 27
PDGF/PDGFRA -0.019 0.12 -9999 0 -0.5 27 27
actin cytoskeleton reorganization -0.004 0.089 -9999 0 -0.36 28 28
SRF 0.023 0.01 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K 0.004 0.085 -9999 0 -0.31 32 32
PDGF/PDGFRA/Crk/C3G 0.009 0.069 -9999 0 -0.28 27 27
JAK1 -0.001 0.082 -9999 0 -0.34 27 27
ELK1/SRF 0.017 0.069 -9999 0 -0.3 1 1
SHB 0.01 0.037 -9999 0 -0.47 3 3
SHF 0.011 0.034 -9999 0 -0.52 2 2
CSNK2A1 0.017 0.019 -9999 0 -10000 0 0
GO:0007205 -0.008 0.096 -9999 0 -0.4 27 27
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.017 0.062 -9999 0 -0.32 1 1
PDGF/PDGFRA/SHB -0.004 0.089 -9999 0 -0.36 28 28
PDGF/PDGFRA/Caveolin-1 -0.044 0.16 -9999 0 -0.42 70 70
ITGAV 0.01 0.037 -9999 0 -0.47 3 3
ELK1 -0.005 0.092 -9999 0 -0.36 27 27
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
PDGF/PDGFRA/Crk -0.002 0.081 -9999 0 -0.34 27 27
JAK-STAT cascade -0.001 0.082 -9999 0 -0.34 27 27
cell proliferation -0.004 0.087 -9999 0 -0.35 28 28
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.002 0.075 -9999 0 -0.24 46 46
RGS9BP 0.01 0.04 -9999 0 -0.5 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.001 0.052 -9999 0 -0.57 4 4
mol:Na + -0.016 0.09 -9999 0 -0.37 30 30
mol:ADP 0.005 0.039 -9999 0 -0.42 4 4
GNAT2 0.005 0.059 -9999 0 -0.57 5 5
RGS9-1/Gbeta5/R9AP -0.039 0.12 -9999 0 -0.27 110 110
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.003 0.053 -9999 0 -0.4 8 8
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 -0.015 0.1 -9999 0 -0.57 16 16
Cone Metarhodopsin II/X-Arrestin 0.001 0.027 -9999 0 -0.42 2 2
mol:Ca2+ -0.04 0.12 -9999 0 -0.33 74 74
Cone PDE6 -0.032 0.11 -9999 0 -0.42 5 5
Cone Metarhodopsin II 0.004 0.03 -9999 0 -0.32 4 4
Na + (4 Units) -0.04 0.12 -9999 0 -0.33 74 74
GNAT2/GDP -0.029 0.11 -9999 0 -0.38 10 10
GNB5 0.012 0.022 -9999 0 -0.47 1 1
mol:GMP (4 units) 0.004 0.049 -9999 0 -0.36 8 8
Cone Transducin -0.001 0.08 -9999 0 -0.25 46 46
SLC24A2 -0.046 0.17 -9999 0 -0.57 46 46
GNB3/GNGT2 -0.009 0.096 -9999 0 -0.33 41 41
GNB3 -0.021 0.12 -9999 0 -0.47 35 35
GNAT2/GTP 0.004 0.043 -9999 0 -0.42 5 5
CNGA3 -0.011 0.099 -9999 0 -0.57 15 15
ARR3 0.002 0.037 -9999 0 -0.57 2 2
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.016 0.091 -9999 0 -0.37 30 30
mol:Pi -0.039 0.12 -9999 0 -0.27 110 110
Cone CNG Channel -0.023 0.082 -9999 0 -0.3 38 38
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.046 0.17 -9999 0 -0.57 46 46
RGS9 -0.091 0.2 -9999 0 -0.47 107 107
PDE6C 0.003 0.006 -9999 0 -10000 0 0
GNGT2 0.007 0.055 -9999 0 -0.48 6 6
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.052 -9999 0 -0.57 4 4
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.05 0.14 -10000 0 -0.51 35 35
FYN -0.014 0.21 -10000 0 -0.69 35 35
LAT/GRAP2/SLP76 -0.062 0.17 -10000 0 -0.54 43 43
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 0 0.15 -10000 0 -0.44 38 38
B2M 0.014 0.003 -10000 0 -10000 0 0
IKBKG -0.013 0.037 -10000 0 -0.15 24 24
MAP3K8 -0.001 0.084 -10000 0 -0.47 15 15
mol:Ca2+ -0.003 0.013 -10000 0 -0.11 3 3
integrin-mediated signaling pathway 0.004 0.061 -10000 0 -0.27 23 23
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.019 0.21 -10000 0 -0.66 40 40
TRPV6 -0.002 0.048 -10000 0 -0.53 4 4
CD28 -0.04 0.17 -10000 0 -0.56 47 47
SHC1 -0.018 0.2 -10000 0 -0.66 35 35
receptor internalization -0.029 0.21 -10000 0 -0.6 45 45
PRF1 -0.017 0.23 -10000 0 -0.93 23 23
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 0.005 0.13 -10000 0 -0.39 33 33
LAT -0.025 0.22 -10000 0 -0.65 41 41
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.026 0.14 -10000 0 -0.54 36 36
CD3E -0.008 0.11 -10000 0 -0.52 21 21
CD3G -0.041 0.16 -10000 0 -0.5 53 53
RASGRP2 0.001 0.041 -10000 0 -0.17 23 23
RASGRP1 0.003 0.15 -10000 0 -0.44 39 39
HLA-A 0.003 0.078 -10000 0 -0.51 11 11
RASSF5 -0.009 0.1 -10000 0 -0.47 23 23
RAP1A/GTP/RAPL 0.005 0.061 -10000 0 -0.27 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.049 -10000 0 -0.12 28 28
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.066 -10000 0 -0.25 31 31
PRKCA -0.036 0.084 -10000 0 -0.29 38 38
GRAP2 -0.007 0.099 -10000 0 -0.48 21 21
mol:IP3 -0.049 0.12 0.2 3 -0.45 35 38
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.023 0.21 -10000 0 -0.64 36 36
ORAI1 0.005 0.026 0.29 4 -10000 0 4
CSK -0.02 0.2 -10000 0 -0.67 35 35
B7 family/CD28 -0.038 0.24 -10000 0 -0.73 39 39
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.032 0.24 -10000 0 -0.74 38 38
PTPN6 -0.017 0.2 -10000 0 -0.66 36 36
VAV1 -0.027 0.22 -10000 0 -0.68 40 40
Monovalent TCR/CD3 -0.029 0.16 -10000 0 -0.39 63 63
CBL 0.012 0.022 -10000 0 -0.47 1 1
LCK -0.017 0.21 -10000 0 -0.72 34 34
PAG1 -0.02 0.21 -10000 0 -0.68 35 35
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.027 0.23 -10000 0 -0.74 37 37
CD80 -0.029 0.15 -10000 0 -0.57 35 35
CD86 0.003 0.076 -10000 0 -0.56 9 9
PDK1/CARD11/BCL10/MALT1 -0.032 0.08 -10000 0 -0.3 32 32
HRAS 0.006 0.064 -10000 0 -0.57 6 6
GO:0035030 -0.026 0.19 -10000 0 -0.58 39 39
CD8A -0.007 0.1 -10000 0 -0.51 21 21
CD8B -0.009 0.11 -10000 0 -0.52 22 22
PTPRC -0.014 0.12 -10000 0 -0.5 27 27
PDK1/PKC theta -0.006 0.18 -10000 0 -0.56 39 39
CSK/PAG1 -0.015 0.2 -10000 0 -0.66 35 35
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.013 0.057 -10000 0 -0.36 11 11
GRAP2/SLP76 -0.068 0.19 -10000 0 -0.66 38 38
STIM1 0.003 0.013 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.065 -10000 0 -0.17 26 26
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.033 0.23 -10000 0 -0.64 45 45
mol:DAG -0.045 0.11 -10000 0 -0.38 39 39
RAP1A/GDP 0.01 0.022 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.011 0.12 -10000 0 -0.55 22 22
cytotoxic T cell degranulation -0.014 0.21 -10000 0 -0.86 23 23
RAP1A/GTP -0.004 0.013 -10000 0 -0.067 10 10
mol:PI-3-4-5-P3 -0.009 0.18 -10000 0 -0.52 40 40
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.062 0.16 0.22 2 -0.57 38 40
NRAS 0.012 0.022 -10000 0 -0.47 1 1
ZAP70 -0.051 0.18 -10000 0 -0.57 55 55
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.064 0.16 -10000 0 -0.57 39 39
MALT1 0.009 0.05 -10000 0 -0.55 4 4
TRAF6 0.013 0 -10000 0 -10000 0 0
CD8 heterodimer -0.01 0.12 -10000 0 -0.45 34 34
CARD11 -0.006 0.099 -10000 0 -0.52 18 18
PRKCB -0.059 0.1 -10000 0 -0.3 62 62
PRKCE -0.03 0.076 -10000 0 -0.28 32 32
PRKCQ -0.019 0.21 -10000 0 -0.64 40 40
LCP2 0.006 0.064 -10000 0 -0.53 7 7
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.004 0.13 -10000 0 -0.37 38 38
IKK complex 0.014 0.055 -10000 0 -0.11 35 35
RAS family/GDP -0.003 0.011 -10000 0 -0.078 4 4
MAP3K14 0.012 0.098 -10000 0 -0.3 29 29
PDPK1 0.003 0.14 -10000 0 -0.43 35 35
TCR/CD3/MHC I/CD8/Fyn -0.024 0.23 -10000 0 -0.74 37 37
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 0.012 0.075 -10000 0 -0.34 13 13
epithelial cell differentiation -0.031 0.074 -10000 0 -0.4 3 3
ITCH 0.018 0.013 -10000 0 -10000 0 0
WWP1 0.018 0.055 -10000 0 -0.56 1 1
FYN 0.011 0.03 -10000 0 -0.47 2 2
EGFR -0.025 0.13 -10000 0 -0.47 40 40
PRL -0.004 0.058 -10000 0 -0.57 5 5
neuron projection morphogenesis -0.019 0.12 -10000 0 -0.45 7 7
PTPRZ1 -0.16 0.24 -10000 0 -0.48 179 179
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.033 0.13 -10000 0 -0.46 12 12
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.054 0.14 -10000 0 -0.36 36 36
ADAM17 0.012 0.053 -10000 0 -0.45 6 6
ErbB4/ErbB4 0.015 0.069 -10000 0 -0.42 5 5
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.017 0.11 -10000 0 -0.36 25 25
NCOR1 0.012 0.022 -10000 0 -0.47 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.045 0.13 -10000 0 -0.33 33 33
GRIN2B -0.041 0.13 -10000 0 -0.57 3 3
ErbB4/ErbB2/betacellulin 0.007 0.1 -10000 0 -0.53 9 9
STAT1 0.003 0.078 -10000 0 -0.57 9 9
HBEGF 0.003 0.074 -10000 0 -0.54 9 9
PRLR -0.042 0.16 -10000 0 -0.52 51 51
E4ICDs/ETO2 0.015 0.066 -10000 0 -0.48 2 2
axon guidance 0.033 0.076 -10000 0 -0.3 2 2
NEDD4 0.006 0.07 -10000 0 -0.45 11 11
Prolactin receptor/Prolactin receptor/Prolactin -0.033 0.12 -10000 0 -0.38 56 56
CBFA2T3 0.008 0.048 -10000 0 -0.47 5 5
ErbB4/ErbB2/HBEGF 0.018 0.074 -10000 0 -0.37 7 7
MAPK3 -0.025 0.13 -10000 0 -0.43 12 12
STAT1 (dimer) 0.011 0.078 -10000 0 -0.36 14 14
MAPK1 -0.025 0.13 -10000 0 -0.43 12 12
JAK2 0.012 0.022 -10000 0 -0.47 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.047 0.14 -10000 0 -0.36 35 35
NRG1 -0.081 0.16 -10000 0 -0.33 145 145
NRG3 -0.045 0.16 -10000 0 -0.51 52 52
NRG2 -0.16 0.23 -10000 0 -0.47 174 174
NRG4 -0.15 0.23 -10000 0 -0.47 168 168
heart development 0.033 0.076 -10000 0 -0.3 2 2
neural crest cell migration -0.046 0.14 -10000 0 -0.35 35 35
ERBB2 0.016 0.052 -10000 0 -0.32 11 11
WWOX/E4ICDs 0.017 0.061 -10000 0 -0.36 5 5
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.082 0.17 -10000 0 -0.48 40 40
apoptosis 0.027 0.11 0.34 38 -10000 0 38
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.078 0.16 -10000 0 -0.4 41 41
ErbB4/ErbB2/epiregulin -0.009 0.096 -10000 0 -0.38 6 6
ErbB4/ErbB4/betacellulin/betacellulin 0 0.11 -10000 0 -0.44 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.006 0.12 -10000 0 -0.44 12 12
MDM2 0.02 0.06 -10000 0 -0.36 5 5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.048 0.13 -10000 0 -0.32 33 33
STAT5A 0.042 0.07 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.063 0.16 -10000 0 -0.4 50 50
DLG4 0 0.08 -10000 0 -0.47 14 14
GRB2/SHC 0.02 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.015 0.058 -10000 0 -0.38 5 5
STAT5A (dimer) -0.032 0.078 -10000 0 -0.42 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.041 0.068 -10000 0 -10000 0 0
LRIG1 0.012 0.026 -10000 0 -0.57 1 1
EREG -0.036 0.15 -10000 0 -0.51 44 44
BTC -0.019 0.12 -10000 0 -0.47 33 33
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.031 0.076 -10000 0 -0.3 2 2
ERBB4 0.015 0.07 -10000 0 -0.42 5 5
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 0.011 0.066 -10000 0 -0.72 4 4
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.061 0.14 -10000 0 -0.38 28 28
glial cell differentiation -0.015 0.058 0.38 5 -10000 0 5
WWOX 0.012 0.022 -10000 0 -0.47 1 1
cell proliferation -0.061 0.17 -10000 0 -0.51 27 27
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.013 0.038 -10000 0 -0.46 3 3
HSPA8 0.013 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.006 0.064 -10000 0 -0.35 5 5
AKT1 0.016 0.004 -10000 0 -10000 0 0
GSC -0.11 0.22 -10000 0 -0.52 44 44
NKX2-5 -0.045 0.16 -10000 0 -0.57 43 43
muscle cell differentiation 0.045 0.085 0.38 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.048 0.054 -10000 0 -0.41 1 1
SMAD4 0.011 0.035 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.037 0.13 -10000 0 -0.27 110 110
SMAD3/SMAD4/VDR 0.017 0.055 -10000 0 -0.34 1 1
MYC -0.035 0.16 -10000 0 -0.58 39 39
CDKN2B 0.035 0.096 -10000 0 -1.3 2 2
AP1 0.005 0.13 -10000 0 -0.72 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.048 0.036 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.035 0.049 -10000 0 -0.6 1 1
SP3 0.016 0 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.12 0.24 -10000 0 -0.6 99 99
SMAD3/SMAD4/GR 0.024 0.068 -10000 0 -0.35 6 6
GATA3 -0.13 0.22 -10000 0 -0.47 148 148
SKI/SIN3/HDAC complex/NCoR1 0.042 0.017 -10000 0 -10000 0 0
MEF2C/TIF2 -0.091 0.2 -10000 0 -0.49 70 70
endothelial cell migration 0.06 0.24 0.61 55 -10000 0 55
MAX 0.016 0.013 -10000 0 -10000 0 0
RBBP7 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.012 0.022 -10000 0 -0.47 1 1
RUNX2 0.01 0.04 -10000 0 -0.5 3 3
RUNX3 0.001 0.082 -10000 0 -0.55 11 11
RUNX1 0.008 0.05 -10000 0 -0.49 5 5
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.004 0.079 -10000 0 -0.47 13 13
VDR 0.005 0.064 -10000 0 -0.49 8 8
CDKN1A 0.049 0.12 -10000 0 -1.2 4 4
KAT2B 0.014 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.072 0.18 -10000 0 -0.4 100 100
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.013 0.001 -10000 0 -10000 0 0
SERPINE1 -0.061 0.24 -10000 0 -0.64 49 49
SMAD3/SMAD4/ATF2 0.011 0.082 -10000 0 -0.36 2 2
SMAD3/SMAD4/ATF3 -0.024 0.14 -10000 0 -0.35 62 62
SAP30 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.032 0.036 -10000 0 -0.27 1 1
JUN 0.003 0.13 -10000 0 -0.72 7 7
SMAD3/SMAD4/IRF7 0.01 0.097 -10000 0 -0.37 26 26
TFE3 0.015 0.013 -10000 0 -10000 0 0
COL1A2 0 0.072 -10000 0 -0.62 5 5
mesenchymal cell differentiation -0.028 0.048 0.34 3 -10000 0 3
DLX1 -0.51 0.18 -10000 0 -0.57 447 447
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.071 0.19 -10000 0 -0.47 91 91
SMAD3/SMAD4/Max 0.032 0.039 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.026 0.025 -10000 0 -0.26 3 3
ZBTB17 0.011 0.003 -10000 0 -10000 0 0
LAMC1 0.038 0.036 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.039 -10000 0 -10000 0 0
IRF7 -0.017 0.13 -10000 0 -0.57 26 26
ESR1 -0.005 0.088 -10000 0 -0.47 17 17
HNF4A -0.029 0.14 -10000 0 -0.57 29 29
MEF2C -0.075 0.18 -10000 0 -0.43 67 67
SMAD2-3/SMAD4 0.023 0.047 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.028 0.028 -10000 0 -0.26 3 3
IGHV3OR16-13 -0.002 0.013 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.014 0.008 -10000 0 -10000 0 0
SKIL 0.002 0.077 -10000 0 -0.51 11 11
HDAC1 0.013 0.001 -10000 0 -10000 0 0
HDAC2 0.012 0.022 -10000 0 -0.47 1 1
SNIP1 0.013 0.002 -10000 0 -10000 0 0
GCN5L2 0.001 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.04 0.044 -10000 0 -10000 0 0
MSG1/HSC70 -0.06 0.15 -10000 0 -0.34 108 108
SMAD2 0.006 0.023 -10000 0 -10000 0 0
SMAD3 0.02 0.03 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.02 0.068 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 0.014 0.022 -10000 0 -10000 0 0
NCOR1 0.012 0.022 -10000 0 -0.47 1 1
NCOA2 -0.045 0.16 -10000 0 -0.47 60 60
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.071 -10000 0 -0.39 16 16
SMAD2-3/SMAD4/SP1/MIZ-1 0.06 0.052 -10000 0 -0.38 1 1
IFNB1 0.012 0.085 -10000 0 -0.4 4 4
SMAD3/SMAD4/MEF2C -0.063 0.18 -10000 0 -0.5 29 29
CITED1 -0.094 0.2 -10000 0 -0.48 108 108
SMAD2-3/SMAD4/ARC105 0.031 0.043 -10000 0 -10000 0 0
RBL1 -0.015 0.11 -10000 0 -0.47 29 29
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.052 0.043 -10000 0 -0.53 2 2
RUNX1-3/PEBPB2 0.016 0.062 -10000 0 -0.33 15 15
SMAD7 0.028 0.12 -10000 0 -0.57 4 4
MYC/MIZ-1 -0.019 0.12 -10000 0 -0.42 39 39
SMAD3/SMAD4 0.017 0.12 0.35 1 -0.38 10 11
IL10 -0.061 0.18 -10000 0 -0.56 30 30
PIASy/HDAC complex 0.012 0.009 -10000 0 -10000 0 0
PIAS3 0.014 0.004 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.057 0.15 -10000 0 -0.48 18 18
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.012 0.009 -10000 0 -10000 0 0
ATF3 -0.072 0.19 -10000 0 -0.5 83 83
SMAD3/SMAD4/SP1 0.043 0.052 -10000 0 -0.39 1 1
FOXG1 -0.039 0.15 -10000 0 -0.57 35 35
FOXO3 0.025 0.006 -10000 0 -10000 0 0
FOXO1 0.025 0.006 -10000 0 -10000 0 0
FOXO4 0.024 0.02 -10000 0 -0.41 1 1
heart looping -0.074 0.18 -10000 0 -0.42 67 67
CEBPB 0.015 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.32 0.12 -10000 0 -0.36 447 447
MYOD1 -0.016 0.097 -10000 0 -0.55 16 16
SMAD3/SMAD4/HNF4 0.002 0.1 -10000 0 -0.37 29 29
SMAD3/SMAD4/GATA3 -0.067 0.16 -10000 0 -0.49 16 16
SnoN/SIN3/HDAC complex/NCoR1 0.002 0.077 -10000 0 -0.5 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.031 0.067 -10000 0 -0.4 3 3
SMAD3/SMAD4/SP1-3 0.054 0.049 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.021 0.016 -10000 0 -10000 0 0
SIN3B 0.013 0.001 -10000 0 -10000 0 0
SIN3A 0.013 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.083 0.19 -10000 0 -0.42 84 84
ITGB5 0.057 0.038 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.043 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR 0.002 0.096 -10000 0 -0.34 9 9
AR -0.029 0.14 -10000 0 -0.47 44 44
negative regulation of cell growth 0.008 0.086 -10000 0 -0.33 5 5
SMAD3/SMAD4/MYOD 0.011 0.075 -10000 0 -0.36 12 12
E2F5 -0.01 0.12 -10000 0 -0.57 20 20
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.044 0.15 -10000 0 -0.39 47 47
SMAD2-3/SMAD4/FOXO1-3a-4 0.047 0.039 -10000 0 -0.39 2 2
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.005 0.13 -10000 0 -0.73 7 7
SMAD3/SMAD4/RUNX2 0.028 0.048 -10000 0 -0.34 3 3
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.015 0.11 -10000 0 -0.47 29 29
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.009 0.1 -9999 0 -0.48 22 22
ITGA4 -0.012 0.11 -9999 0 -0.52 24 24
alpha4/beta7 Integrin -0.014 0.12 -9999 0 -0.4 40 40
alpha4/beta1 Integrin 0.001 0.083 -9999 0 -0.37 24 24
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.032 0.13 -10000 0 -0.56 26 26
HDAC1 0.011 0.006 -10000 0 -10000 0 0
AES 0.013 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.01 0.11 -10000 0 -0.56 20 20
LRP6/FZD1 0.019 0.015 -10000 0 -0.32 1 1
TLE1 0.013 0.001 -10000 0 -10000 0 0
AP1 -0.051 0.16 -10000 0 -0.32 103 103
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.008 0.099 -10000 0 -0.47 22 22
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.018 0.06 -10000 0 -10000 0 0
NICD/RBPSUH 0.004 0.13 -10000 0 -0.53 26 26
WIF1 -0.22 0.24 -10000 0 -0.47 242 242
NOTCH1 -0.03 0.13 -10000 0 -0.56 26 26
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.025 0.14 -10000 0 -0.53 35 35
DKK1 -0.09 0.2 -10000 0 -0.48 104 104
beta catenin/beta TrCP1 0.027 0.048 0.21 1 -10000 0 1
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 -0.009 0.048 -10000 0 -0.23 9 9
CtBP/CBP/TCF1/TLE1/AES 0.004 0.062 -10000 0 -10000 0 0
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.076 0.19 -10000 0 -0.47 91 91
JUN 0.006 0.06 -10000 0 -0.5 7 7
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.021 0.051 0.2 7 -10000 0 7
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.018 0.12 -10000 0 -0.32 64 64
HNF1A -0.057 0.19 -10000 0 -0.57 59 59
CTBP1 0.013 0.002 -10000 0 -10000 0 0
MYC -0.007 0.11 -10000 0 -10000 0 0
NKD1 -0.036 0.15 -10000 0 -0.48 49 49
FZD1 0.012 0.022 -10000 0 -0.47 1 1
NOTCH1 precursor/Deltex homolog 1 -0.009 0.14 -10000 0 -0.53 26 26
apoptosis -0.05 0.16 -10000 0 -0.31 103 103
Delta 1/NOTCHprecursor 0 0.13 -10000 0 -0.55 26 26
DLL1 0.006 0.06 -10000 0 -0.47 8 8
PPARD 0.021 0.014 -10000 0 -10000 0 0
Gamma Secretase 0.04 0.001 -10000 0 -10000 0 0
APC -0.012 0.057 -10000 0 -0.28 12 12
DVL1 -0.002 0.034 -10000 0 -10000 0 0
CSNK2A1 0.014 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.06 0.15 -10000 0 -0.3 130 130
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.001 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.021 0.023 -10000 0 -0.39 1 1
WNT1 -0.003 0.09 -10000 0 -0.57 12 12
Axin1/APC/beta catenin 0.018 0.051 -10000 0 -10000 0 0
DKK2 -0.021 0.13 -10000 0 -0.51 33 33
NOTCH1 precursor/DVL1 -0.028 0.11 -10000 0 -0.51 26 26
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.039 0.13 -10000 0 -0.54 26 26
PPP2R5D 0.016 0.075 0.24 49 -10000 0 49
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.11 0.14 -10000 0 -0.36 20 20
RBPJ 0.013 0 -10000 0 -10000 0 0
CREBBP 0.015 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.012 0.046 0.21 23 -10000 0 23
RFC1 0.012 0.046 0.21 23 -10000 0 23
PRKDC 0.011 0.049 0.21 23 -0.34 1 24
RIPK1 0.016 0.004 -10000 0 -10000 0 0
CASP7 -0.017 0.036 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.024 0.064 0.2 1 -0.26 25 26
MAP2K4 -0.038 0.14 -10000 0 -0.4 18 18
mol:ceramide -0.025 0.11 -10000 0 -0.36 20 20
GSN 0.01 0.045 0.21 20 -0.26 1 21
FASLG/FAS/FADD/FAF1/Caspase 8 -0.014 0.081 -10000 0 -0.3 20 20
FAS -0.001 0.071 -10000 0 -0.47 11 11
BID 0.003 0.021 -10000 0 -10000 0 0
MAP3K1 -0.011 0.081 -10000 0 -0.24 4 4
MAP3K7 0.01 0.005 -10000 0 -10000 0 0
RB1 0.011 0.048 0.21 23 -0.26 1 24
CFLAR 0.016 0.004 -10000 0 -10000 0 0
HGF/MET -0.027 0.14 -10000 0 -0.34 72 72
ARHGDIB 0.008 0.053 0.21 21 -0.31 4 25
FADD 0.01 0.007 -10000 0 -10000 0 0
actin filament polymerization -0.01 0.045 0.26 1 -0.21 20 21
NFKB1 -0.057 0.083 -10000 0 -0.25 16 16
MAPK8 -0.078 0.2 -10000 0 -0.42 110 110
DFFA 0.012 0.046 0.21 23 -10000 0 23
DNA fragmentation during apoptosis 0.012 0.046 0.21 23 -10000 0 23
FAS/FADD/MET -0.016 0.1 -10000 0 -0.29 58 58
CFLAR/RIP1 0.013 0.009 -10000 0 -10000 0 0
FAIM3 0.002 0.086 -10000 0 -0.57 11 11
FAF1 0.01 0.007 -10000 0 -10000 0 0
PARP1 0.012 0.046 0.21 23 -10000 0 23
DFFB 0.012 0.046 0.21 23 -10000 0 23
CHUK -0.05 0.073 -10000 0 -10000 0 0
FASLG -0.023 0.13 -10000 0 -0.54 29 29
FAS/FADD 0.005 0.053 -10000 0 -0.33 11 11
HGF -0.026 0.14 -10000 0 -0.5 38 38
LMNA 0.02 0.044 0.2 23 -0.31 1 24
CASP6 0.012 0.046 0.21 23 -10000 0 23
CASP10 0.002 0.063 -10000 0 -0.48 8 8
CASP3 0.014 0.054 0.25 23 -10000 0 23
PTPN13 0.011 0.03 -10000 0 -0.47 2 2
CASP8 0.005 0.036 0.24 11 -10000 0 11
IL6 -0.26 0.49 -10000 0 -1.2 106 106
MET -0.036 0.15 -10000 0 -0.47 51 51
ICAD/CAD 0.011 0.043 0.2 23 -10000 0 23
FASLG/FAS/FADD/FAF1/Caspase 10 -0.026 0.11 -10000 0 -0.36 20 20
activation of caspase activity by cytochrome c 0.01 0.02 -10000 0 -10000 0 0
PAK2 0.012 0.046 0.21 23 -10000 0 23
BCL2 -0.008 0.1 -10000 0 -0.47 23 23
Canonical Wnt signaling pathway

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
HDAC1 0.011 0.013 -10000 0 -10000 0 0
AES 0.012 0.011 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.02 0.015 -10000 0 -0.32 1 1
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.021 0.13 -10000 0 -0.51 33 33
TLE1 0.012 0.011 -10000 0 -10000 0 0
MACF1 0.014 0.001 -10000 0 -10000 0 0
CTNNB1 0.087 0.082 0.24 20 -10000 0 20
WIF1 -0.22 0.24 -10000 0 -0.47 242 242
beta catenin/RanBP3 0.018 0.086 0.32 28 -10000 0 28
KREMEN2 -0.025 0.14 -10000 0 -0.53 35 35
DKK1 -0.09 0.2 -10000 0 -0.48 104 104
beta catenin/beta TrCP1 0.09 0.077 0.25 15 -10000 0 15
FZD1 0.013 0.022 -10000 0 -0.47 1 1
AXIN2 0.004 0.14 -10000 0 -1.3 5 5
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.037 0.035 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.066 0.075 -10000 0 -0.44 1 1
Axin1/APC/GSK3 0.02 0.055 0.2 27 -10000 0 27
Axin1/APC/GSK3/beta catenin/Macf1 0.064 0.056 -10000 0 -10000 0 0
HNF1A -0.058 0.19 -10000 0 -0.57 59 59
CTBP1 0.012 0.011 -10000 0 -10000 0 0
MYC -0.01 0.12 -10000 0 -0.54 2 2
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.018 0.12 -10000 0 -0.32 64 64
NKD1 -0.036 0.15 -10000 0 -0.48 49 49
TCF4 0.008 0.042 -10000 0 -0.44 4 4
TCF3 0.012 0.011 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.026 0.054 -10000 0 -0.3 12 12
Ran/GTP 0.01 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.001 0.088 0.46 4 -0.42 1 5
LEF1 -0.02 0.13 -10000 0 -0.55 28 28
DVL1 0.066 0.043 0.19 1 -10000 0 1
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.069 0.082 -10000 0 -0.4 2 2
DKK1/LRP6/Kremen 2 -0.059 0.15 -10000 0 -0.3 130 130
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.012 0.013 -10000 0 -10000 0 0
NLK 0.014 0.002 -10000 0 -10000 0 0
CCND1 0.014 0.041 -10000 0 -10000 0 0
WNT1 -0.003 0.09 -10000 0 -0.57 12 12
GSK3A 0.013 0.022 -10000 0 -0.47 1 1
GSK3B 0.013 0 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.06 0.078 0.28 49 -10000 0 49
APC 0.028 0.053 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.11 0.1 0.21 232 -10000 0 232
CREBBP 0.012 0.011 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.011 0.037 -9999 0 -0.57 2 2
mol:S1P 0.001 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.034 0.14 -9999 0 -0.43 44 44
GNAO1 -0.078 0.19 -9999 0 -0.47 96 96
S1P/S1P3/G12/G13 0.018 0.052 -9999 0 -0.24 19 19
AKT1 0.003 0.063 -9999 0 -10000 0 0
AKT3 -0.013 0.13 -9999 0 -0.6 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.037 -9999 0 -0.57 2 2
GNAI2 0.015 0.001 -9999 0 -10000 0 0
GNAI3 0.015 0.001 -9999 0 -10000 0 0
GNAI1 0.007 0.064 -9999 0 -0.53 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.004 0.093 -9999 0 -0.47 19 19
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.038 0.17 -9999 0 -0.48 51 51
MAPK3 -0.03 0.16 -9999 0 -0.45 51 51
MAPK1 -0.03 0.16 -9999 0 -0.45 51 51
JAK2 -0.031 0.17 -9999 0 -0.46 53 53
CXCR4 -0.035 0.17 -9999 0 -0.44 58 58
FLT1 0.01 0.057 -9999 0 -0.5 6 6
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC -0.03 0.16 -9999 0 -0.45 51 51
S1P/S1P3/Gi -0.038 0.17 -9999 0 -0.48 51 51
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.029 0.16 -9999 0 -0.44 51 51
VEGFA -0.015 0.12 -9999 0 -0.48 31 31
S1P/S1P2/Gi -0.03 0.14 -9999 0 -0.42 44 44
VEGFR1 homodimer/VEGFA homodimer 0.001 0.1 -9999 0 -0.37 34 34
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.002 0.11 -9999 0 -0.29 50 50
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ -0.033 0.14 -9999 0 -0.47 49 49
G12/G13 0.02 0 -9999 0 -10000 0 0
GNA14 0.011 0.03 -9999 0 -0.47 2 2
GNA15 -0.011 0.1 -9999 0 -0.47 25 25
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.087 -9999 0 -0.47 17 17
Rac1/GTP -0.029 0.16 -9999 0 -0.44 51 51
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.012 0.026 -9999 0 -0.57 1 1
GNAT1/GTP 0.001 0.027 -9999 0 -0.42 2 2
Metarhodopsin II/Arrestin 0.002 0.028 -9999 0 -0.36 3 3
PDE6G/GNAT1/GTP -0.027 0.11 -9999 0 -0.36 51 51
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.037 -9999 0 -0.57 2 2
GRK1 -0.001 0.052 -9999 0 -0.57 4 4
CNG Channel -0.073 0.13 -9999 0 -0.48 20 20
mol:Na + -0.055 0.11 -9999 0 -0.53 7 7
mol:ADP -0.001 0.052 -9999 0 -0.57 4 4
RGS9-1/Gbeta5/R9AP -0.039 0.12 -9999 0 -0.27 110 110
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.056 0.12 -9999 0 -0.54 7 7
CNGB1 -0.003 0.078 -9999 0 -0.57 9 9
RDH5 -0.008 0.1 -9999 0 -0.48 21 21
SAG 0.001 0.026 -9999 0 -0.57 1 1
mol:Ca2+ -0.026 0.12 -9999 0 -0.51 7 7
Na + (4 Units) -0.051 0.1 -9999 0 -0.49 7 7
RGS9 -0.091 0.2 -9999 0 -0.47 107 107
GNB1/GNGT1 0.009 0.027 -9999 0 -0.41 2 2
GNAT1/GDP -0.032 0.11 -9999 0 -0.32 7 7
GUCY2D -0.067 0.2 -9999 0 -0.55 70 70
GNGT1 -0.002 0.036 -9999 0 -0.57 2 2
GUCY2F 0 0.026 -9999 0 -0.57 1 1
GNB5 0.012 0.022 -9999 0 -0.47 1 1
mol:GMP (4 units) -0.052 0.14 -9999 0 -0.34 64 64
mol:11-cis-retinal -0.008 0.1 -9999 0 -0.48 21 21
mol:cGMP -0.036 0.13 -9999 0 -0.32 71 71
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.004 0.077 -9999 0 -0.35 23 23
SLC24A1 0.012 0.026 -9999 0 -0.57 1 1
CNGA1 0.004 0.072 -9999 0 -0.53 9 9
Metarhodopsin II 0.001 0.037 -9999 0 -0.33 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.037 0.13 -9999 0 -0.34 70 70
RGS9BP 0.01 0.04 -9999 0 -0.5 3 3
Metarhodopsin II/Transducin 0.007 0.02 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0 0.066 -9999 0 -0.32 20 20
PDE6A/B -0.041 0.15 -9999 0 -0.37 78 78
mol:Pi -0.039 0.12 -9999 0 -0.27 110 110
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.009 0.03 -9999 0 -0.32 4 4
PDE6B -0.047 0.16 -9999 0 -0.47 62 62
PDE6A -0.013 0.11 -9999 0 -0.48 26 26
PDE6G -0.045 0.18 -9999 0 -0.57 49 49
RHO 0.002 0.037 -9999 0 -0.57 2 2
PDE6 -0.11 0.16 -9999 0 -0.46 55 55
GUCA1A 0.005 0.037 -9999 0 -0.57 2 2
GC2/GCAP Family 0 0.067 -9999 0 -0.32 20 20
GUCA1C -0.001 0.026 -9999 0 -0.57 1 1
GUCA1B -0.007 0.11 -9999 0 -0.57 17 17
Arf6 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
CENTA1/KIF3B 0.015 0.032 -9999 0 -0.33 4 4
ARNO/beta Arrestin1-2 0.013 0.035 -9999 0 -10000 0 0
EGFR -0.025 0.13 -9999 0 -0.47 40 40
EPHA2 -0.037 0.15 -9999 0 -0.47 51 51
USP6 0.012 0.026 -9999 0 -0.57 1 1
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.06 0.16 -9999 0 -0.37 101 101
ARRB2 0.008 0.022 -9999 0 -0.23 4 4
mol:GTP 0.012 0.019 -9999 0 -0.14 2 2
ARRB1 0.012 0.022 -9999 0 -0.47 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR -0.007 0.099 -9999 0 -0.5 19 19
EGF -0.058 0.19 -9999 0 -0.53 65 65
somatostatin receptor activity 0 0 -9999 0 -0.001 27 27
ARAP2 0.012 0.022 -9999 0 -0.47 1 1
mol:GDP -0.025 0.087 -9999 0 -0.26 35 35
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 15 15
ITGA2B -0.004 0.092 -9999 0 -0.51 16 16
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.006 0.084 -9999 0 -0.31 4 4
ADAP1 0.009 0.05 -9999 0 -0.55 4 4
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.042 0.16 -9999 0 -0.4 72 72
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.018 0.089 -9999 0 -0.26 26 26
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.041 0.14 -9999 0 -0.31 101 101
ADRB2 0.006 0.064 -9999 0 -0.57 6 6
receptor agonist activity 0 0 -9999 0 0 23 23
actin filament binding 0 0 -9999 0 0 26 26
SRC 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.084 0.19 -9999 0 -0.47 101 101
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 20 20
ARF6/GDP 0.014 0.067 -9999 0 -0.33 5 5
ARF6/GDP/GULP/ACAP1 -0.02 0.11 -9999 0 -0.34 24 24
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.03 0.12 -9999 0 -0.47 7 7
ACAP1 -0.017 0.13 -9999 0 -0.56 26 26
ACAP2 0.012 0.022 -9999 0 -0.47 1 1
LHCGR/beta Arrestin2 0.001 0.031 -9999 0 -0.33 4 4
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.026 0.14 -9999 0 -0.5 38 38
CYTH3 0.006 0.043 -9999 0 -0.42 5 5
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.012 0.026 -9999 0 -0.57 1 1
fibronectin binding 0 0 -9999 0 0 24 24
endosomal lumen acidification 0 0 -9999 0 0 31 31
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.009 0.048 -9999 0 -0.52 4 4
GNAQ/ARNO 0.017 0.004 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 11 11
MET -0.036 0.15 -9999 0 -0.47 51 51
GNA14 0.011 0.03 -9999 0 -0.47 2 2
GNA15 -0.011 0.1 -9999 0 -0.47 25 25
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 21 21
GNA11 -0.003 0.087 -9999 0 -0.47 17 17
LHCGR -0.001 0.052 -9999 0 -0.57 4 4
AGTR1 -0.12 0.24 -9999 0 -0.55 113 113
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.031 -9999 0 -0.33 4 4
IPCEF1/ARNO -0.029 0.11 -9999 0 -0.42 4 4
alphaIIb/beta3 Integrin -0.062 0.16 -9999 0 -0.34 112 112
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.002 0.096 -9999 0 -0.31 40 40
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DOCK1 0.009 0.043 -9999 0 -0.47 4 4
ITGA4 -0.012 0.11 -9999 0 -0.52 24 24
alpha4/beta7 Integrin/MAdCAM1 -0.058 0.16 -9999 0 -0.34 106 106
EPO -0.067 0.19 -9999 0 -0.51 76 76
alpha4/beta7 Integrin -0.014 0.12 -9999 0 -0.4 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.001 0.083 -9999 0 -0.37 24 24
EPO/EPOR (dimer) -0.047 0.15 -9999 0 -0.37 84 84
lamellipodium assembly 0.029 0.044 -9999 0 -0.39 3 3
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
PI3K 0.014 0.049 -9999 0 -0.36 8 8
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 -0.02 0.1 -9999 0 -0.42 7 7
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
MADCAM1 -0.1 0.23 -9999 0 -0.57 95 95
cell adhesion -0.058 0.16 -9999 0 -0.34 106 106
CRKL/CBL 0.019 0.015 -9999 0 -0.32 1 1
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.007 0.092 -9999 0 -0.39 17 17
ITGB7 -0.009 0.1 -9999 0 -0.48 22 22
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.001 0.1 -9999 0 -0.35 34 34
p130Cas/Crk/Dock1 0.026 0.085 -9999 0 -0.47 7 7
VCAM1 -0.003 0.094 -9999 0 -0.53 15 15
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.02 0.065 -9999 0 -0.31 11 11
BCAR1 0.014 0.086 -9999 0 -0.36 17 17
EPOR 0.001 0.082 -9999 0 -0.57 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.012 0.022 -9999 0 -0.47 1 1
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.003 0.043 -9999 0 -0.41 3 3
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.008 0.082 -10000 0 -0.3 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.048 0.19 -10000 0 -0.49 58 58
AKT1 -0.009 0.16 -10000 0 -0.78 19 19
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.16 -10000 0 -0.78 19 19
mol:Ca2+ 0.013 0.079 -10000 0 -0.49 4 4
IGF1R 0.011 0.034 -10000 0 -0.52 2 2
E2/ER alpha (dimer)/Striatin -0.014 0.097 -10000 0 -0.3 50 50
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.007 0.15 0.74 19 -10000 0 19
RhoA/GTP -0.01 0.047 -10000 0 -0.46 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.061 0.14 -10000 0 -0.38 58 58
regulation of stress fiber formation -0.016 0.088 0.37 14 -10000 0 14
E2/ERA-ERB (dimer) -0.006 0.088 -10000 0 -0.32 36 36
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP 0.008 0.049 -10000 0 -0.25 17 17
pseudopodium formation 0.016 0.088 -10000 0 -0.37 14 14
E2/ER alpha (dimer)/PELP1 0.008 0.054 -10000 0 -0.28 17 17
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.007 0.052 -10000 0 -0.47 6 6
GNAO1 -0.08 0.19 -10000 0 -0.47 96 96
HRAS 0.006 0.064 -10000 0 -0.57 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.017 0.14 -10000 0 -0.52 21 21
E2/ER beta (dimer) -0.007 0.083 -10000 0 -0.42 19 19
mol:GDP -0.021 0.073 -10000 0 -0.35 16 16
mol:NADP -0.017 0.14 -10000 0 -0.52 21 21
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
mol:IP3 0.013 0.082 -10000 0 -0.52 4 4
IGF-1R heterotetramer 0.011 0.034 -10000 0 -0.52 2 2
PLCB1 0.008 0.082 -10000 0 -0.43 7 7
PLCB2 0.009 0.079 -10000 0 -0.42 5 5
IGF1 -0.045 0.16 -10000 0 -0.5 56 56
mol:L-citrulline -0.017 0.14 -10000 0 -0.52 21 21
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.11 0.3 -10000 0 -0.7 96 96
JNK cascade -0.007 0.083 -10000 0 -0.42 19 19
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 -0.009 0.11 -10000 0 -0.57 19 19
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.003 0.089 -10000 0 -0.47 17 17
Gq family/GDP/Gbeta gamma 0.002 0.12 -10000 0 -0.39 42 42
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.017 0.057 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.061 0.14 -10000 0 -0.52 20 20
GNAZ -0.034 0.14 -10000 0 -0.47 49 49
E2/ER alpha (dimer) -0.002 0.064 -10000 0 -0.34 17 17
STRN -0.023 0.13 -10000 0 -0.47 37 37
GNAL -0.11 0.21 -10000 0 -0.47 129 129
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 -0.002 0.084 -10000 0 -0.35 27 27
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.006 0.064 -10000 0 -0.53 7 7
HBEGF -0.11 0.18 -10000 0 -0.47 78 78
cAMP biosynthetic process -0.074 0.11 -10000 0 -0.33 30 30
SRC -0.039 0.18 -10000 0 -0.48 50 50
PI3K 0.014 0.049 -10000 0 -0.36 8 8
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.069 -10000 0 -0.49 3 3
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.069 0.14 -10000 0 -0.43 47 47
Gs family/GTP -0.075 0.12 -10000 0 -0.34 30 30
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.039 -10000 0 -0.3 7 7
vasodilation -0.016 0.14 -10000 0 -0.5 21 21
mol:DAG 0.013 0.082 -10000 0 -0.52 4 4
Gs family/GDP/Gbeta gamma -0.061 0.1 -10000 0 -0.42 19 19
MSN 0.016 0.095 -10000 0 -0.41 14 14
Gq family/GTP 0.003 0.08 -10000 0 -0.45 5 5
mol:PI-3-4-5-P3 -0.008 0.15 -10000 0 -0.75 19 19
NRAS 0.012 0.022 -10000 0 -0.47 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.016 0.14 0.5 21 -10000 0 21
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
RhoA/GDP -0.019 0.068 -10000 0 -0.32 16 16
NOS3 -0.019 0.15 -10000 0 -0.56 21 21
GNA11 -0.003 0.087 -10000 0 -0.47 17 17
MAPKKK cascade -0.02 0.16 -10000 0 -0.58 24 24
E2/ER alpha (dimer)/PELP1/Src -0.065 0.14 -10000 0 -0.4 58 58
ruffle organization 0.016 0.088 -10000 0 -0.37 14 14
ROCK2 0.013 0.091 -10000 0 -0.43 10 10
GNA14 0.011 0.03 -10000 0 -0.47 2 2
GNA15 -0.011 0.1 -10000 0 -0.47 25 25
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.19 0.21 -10000 0 -0.51 85 85
MMP2 -0.036 0.19 -10000 0 -0.5 51 51
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.007 0.06 -10000 0 -0.54 6 6
LAT2 -0.007 0.11 -10000 0 -0.39 26 26
AP1 -0.07 0.14 -10000 0 -0.48 35 35
mol:PIP3 -0.006 0.15 -10000 0 -0.47 32 32
IKBKB -0.007 0.1 0.15 2 -0.25 52 54
AKT1 0.011 0.11 -10000 0 -0.38 13 13
IKBKG -0.007 0.1 0.15 2 -0.25 52 54
MS4A2 -0.016 0.12 -10000 0 -0.48 28 28
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.038 -10000 0 -0.47 3 3
MAP3K1 0.012 0.12 -10000 0 -0.4 24 24
mol:Ca2+ 0.001 0.12 -10000 0 -0.35 32 32
LYN 0.014 0.003 -10000 0 -10000 0 0
CBLB -0.002 0.11 -10000 0 -0.41 19 19
SHC1 0.013 0 -10000 0 -10000 0 0
RasGAP/p62DOK 0.013 0.056 -10000 0 -0.24 23 23
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.014 0.11 -10000 0 -0.47 28 28
PLD2 -0.009 0.11 -10000 0 -0.41 17 17
PTPN13 0.004 0.11 -10000 0 -0.43 18 18
PTPN11 0.012 0.023 -10000 0 -0.48 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.026 0.097 -10000 0 -0.3 20 20
SYK 0.007 0.061 -10000 0 -0.5 7 7
GRB2 0.013 0 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.057 0.13 -10000 0 -0.49 31 31
LAT -0.01 0.12 -10000 0 -0.38 29 29
PAK2 0.005 0.13 -10000 0 -0.42 30 30
NFATC2 -0.1 0.2 -10000 0 -0.52 88 88
HRAS -0.003 0.14 -10000 0 -0.45 31 31
GAB2 0.013 0 -10000 0 -10000 0 0
PLA2G1B 0.024 0.018 -10000 0 -10000 0 0
Fc epsilon R1 -0.052 0.12 -10000 0 -0.34 69 69
Antigen/IgE/Fc epsilon R1 -0.026 0.12 -10000 0 -0.31 69 69
mol:GDP -0.008 0.14 -10000 0 -0.48 30 30
JUN 0.006 0.06 -10000 0 -0.5 7 7
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.053 -10000 0 -0.47 6 6
FOS -0.076 0.19 -10000 0 -0.47 91 91
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.009 0.11 -10000 0 -0.37 28 28
CHUK -0.007 0.1 0.15 2 -0.25 52 54
KLRG1 -0.004 0.1 -10000 0 -0.41 18 18
VAV1 -0.013 0.14 -10000 0 -0.47 29 29
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.002 0.11 -10000 0 -0.42 19 19
negative regulation of mast cell degranulation -0.009 0.13 -10000 0 -0.45 30 30
BTK -0.006 0.13 -10000 0 -0.46 23 23
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.031 0.17 -10000 0 -0.54 37 37
GAB2/PI3K/SHP2 -0.039 0.096 -10000 0 -0.39 21 21
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.013 0.13 -10000 0 -0.51 21 21
RAF1 0.015 0.019 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.037 0.17 -10000 0 -0.54 37 37
FCER1G 0.008 0.053 -10000 0 -0.58 4 4
FCER1A -0.046 0.16 -10000 0 -0.48 61 61
Antigen/IgE/Fc epsilon R1/Fyn -0.018 0.12 -10000 0 -0.4 24 24
MAPK3 0.025 0.017 -10000 0 -10000 0 0
MAPK1 0.025 0.017 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.008 0.11 -10000 0 -0.65 12 12
DUSP1 -0.006 0.094 -10000 0 -0.47 20 20
NF-kappa-B/RelA -0.026 0.048 -10000 0 -0.2 1 1
actin cytoskeleton reorganization -0.001 0.11 -10000 0 -0.44 18 18
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.047 0.12 -10000 0 -0.44 34 34
FER -0.011 0.13 -10000 0 -0.43 26 26
RELA 0.013 0 -10000 0 -10000 0 0
ITK -0.028 0.076 -10000 0 -0.33 20 20
SOS1 0.013 0 -10000 0 -10000 0 0
PLCG1 -0.004 0.14 -10000 0 -0.48 30 30
cytokine secretion -0.019 0.035 -10000 0 -10000 0 0
SPHK1 -0.011 0.12 -10000 0 -0.36 34 34
PTK2 -0.002 0.11 -10000 0 -0.45 18 18
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.056 0.13 -10000 0 -0.5 30 30
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.15 -10000 0 -0.45 33 33
MAP2K2 0.02 0.021 -10000 0 -10000 0 0
MAP2K1 0.021 0.017 -10000 0 -10000 0 0
MAP2K7 0.013 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.003 0.098 -10000 0 -0.37 19 19
MAP2K4 0.021 0.008 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.033 0.15 -10000 0 -0.44 38 38
mol:Choline -0.009 0.11 -10000 0 -0.41 17 17
SHC/Grb2/SOS1 0.011 0.1 -10000 0 -0.4 17 17
FYN 0.011 0.03 -10000 0 -0.47 2 2
DOK1 0.012 0.022 -10000 0 -0.47 1 1
PXN 0.005 0.11 -10000 0 -0.44 16 16
HCLS1 -0.004 0.11 -10000 0 -0.42 22 22
PRKCB -0.023 0.14 -10000 0 -0.35 57 57
FCGR2B -0.013 0.12 -10000 0 -0.53 24 24
IGHE 0 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.009 0.14 -10000 0 -0.46 30 30
LCP2 0.006 0.064 -10000 0 -0.53 7 7
PLA2G4A -0.015 0.14 -10000 0 -0.48 29 29
RASA1 0.011 0.03 -10000 0 -0.47 2 2
mol:Phosphatidic acid -0.009 0.11 -10000 0 -0.41 17 17
IKK complex 0.008 0.082 0.15 2 -0.21 22 24
WIPF1 0.007 0.052 -10000 0 -0.47 6 6
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.052 0.14 -9999 0 -0.33 101 101
AKT1 0.026 0.16 -9999 0 -0.6 24 24
PTK2B -0.037 0.19 -9999 0 -0.65 30 30
VEGFR2 homodimer/Frs2 0.004 0.14 -9999 0 -0.61 24 24
CAV1 -0.049 0.16 -9999 0 -0.47 64 64
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.002 0.15 -9999 0 -0.6 23 23
endothelial cell proliferation 0.002 0.17 -9999 0 -0.6 26 26
mol:Ca2+ 0.005 0.15 -9999 0 -0.61 23 23
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.007 0.14 -9999 0 -0.56 23 23
RP11-342D11.1 -0.003 0.15 -9999 0 -0.61 23 23
CDH5 0.012 0.022 -9999 0 -0.47 1 1
VEGFA homodimer 0.017 0.07 -9999 0 -0.3 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 -0.002 0.091 -9999 0 -0.56 13 13
HRAS/GDP -0.037 0.12 -9999 0 -0.55 23 23
SH2D2A -0.017 0.13 -9999 0 -0.56 26 26
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.036 0.12 -9999 0 -0.51 23 23
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.019 0.16 -9999 0 -0.6 24 24
VEGFR1 homodimer 0.007 0.057 -9999 0 -0.5 6 6
SHC/GRB2/SOS1 -0.038 0.13 -9999 0 -0.58 23 23
GRB10 0.005 0.15 -9999 0 -0.61 23 23
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.006 0.06 -9999 0 -0.47 8 8
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.012 0.14 -9999 0 -0.55 23 23
HRAS 0.006 0.064 -9999 0 -0.57 6 6
VEGF/Rho/ROCK1/Integrin Complex -0.025 0.15 -9999 0 -0.51 30 30
HIF1A 0.012 0.022 -9999 0 -0.47 1 1
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.006 0.14 -9999 0 -0.55 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.009 0.046 -9999 0 -0.49 4 4
Nck/Pak 0.013 0.047 -9999 0 -0.34 9 9
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.003 0.15 -9999 0 -0.62 23 23
mol:GDP -0.037 0.12 -9999 0 -0.56 23 23
mol:NADP 0.031 0.12 -9999 0 -0.44 23 23
eNOS/Hsp90 0.036 0.11 -9999 0 -0.41 23 23
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
mol:IP3 0.005 0.15 -9999 0 -0.62 23 23
HIF1A/ARNT 0.019 0.015 -9999 0 -0.32 1 1
SHB 0.01 0.037 -9999 0 -0.47 3 3
VEGFA -0.016 0.12 -9999 0 -0.48 31 31
VEGFC 0.011 0.034 -9999 0 -0.52 2 2
FAK1/Vinculin -0.034 0.22 -9999 0 -0.64 43 43
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.044 0.2 -9999 0 -0.69 30 30
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.004 0.091 -9999 0 -0.38 24 24
mol:L-citrulline 0.031 0.12 -9999 0 -0.44 23 23
ITGAV 0.01 0.037 -9999 0 -0.47 3 3
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.007 0.14 -9999 0 -0.56 23 23
VEGFR2 homodimer/VEGFA homodimer -0.001 0.16 -9999 0 -0.67 23 23
VEGFR2/3 heterodimer 0.002 0.14 -9999 0 -0.61 25 25
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.002 0.16 -9999 0 -0.65 23 23
VEGFR2 homodimer -0.001 0.16 -9999 0 -0.69 24 24
FLT1 0.007 0.057 -9999 0 -0.5 6 6
NEDD4 0.005 0.071 -9999 0 -0.46 11 11
MAPK3 -0.018 0.16 -9999 0 -0.62 26 26
MAPK1 -0.018 0.16 -9999 0 -0.62 26 26
VEGFA145/NRP2 -0.024 0.12 -9999 0 -0.34 62 62
VEGFR1/2 heterodimer 0.001 0.15 -9999 0 -0.62 26 26
KDR -0.001 0.16 -9999 0 -0.7 24 24
VEGFA165/NRP1/VEGFR2 homodimer -0.009 0.18 -9999 0 -0.68 27 27
SRC 0.013 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.017 0.17 -9999 0 -0.64 26 26
PI3K 0.014 0.19 -9999 0 -0.73 23 23
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.002 0.15 -9999 0 -0.53 29 29
FES 0.001 0.16 -9999 0 -0.66 23 23
GAB1 -0.047 0.15 -9999 0 -0.64 25 25
VEGFR2 homodimer/VEGFA homodimer/Src -0.002 0.15 -9999 0 -0.6 23 23
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.011 0.15 -9999 0 -0.51 25 25
VEGFR2 homodimer/VEGFA homodimer/Yes -0.002 0.15 -9999 0 -0.6 23 23
PI3K/GAB1 0.026 0.17 -9999 0 -0.62 24 24
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.008 0.14 -9999 0 -0.56 23 23
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.009 0.14 -9999 0 -0.55 26 26
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.004 0.16 -9999 0 -0.63 23 23
actin cytoskeleton reorganization -0.019 0.16 -9999 0 -0.6 24 24
PTK2 -0.032 0.21 -9999 0 -0.73 30 30
EDG1 -0.003 0.15 -9999 0 -0.61 23 23
mol:DAG 0.005 0.15 -9999 0 -0.62 23 23
CaM/Ca2+ 0.01 0.14 -9999 0 -0.56 23 23
MAP2K3 0.005 0.16 -9999 0 -0.59 25 25
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.007 0.16 -9999 0 -0.63 23 23
PLCG1 0.004 0.16 -9999 0 -0.63 23 23
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.005 0.14 -9999 0 -0.56 23 23
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.002 0.15 -9999 0 -0.6 23 23
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.002 0.15 -9999 0 -0.6 23 23
cell migration -0.007 0.2 -9999 0 -0.65 29 29
mol:PI-3-4-5-P3 0.016 0.17 -9999 0 -0.66 23 23
FYN 0.011 0.03 -9999 0 -0.47 2 2
VEGFB/NRP1 0.004 0.14 -9999 0 -0.58 23 23
mol:NO 0.031 0.12 -9999 0 -0.44 23 23
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.037 0.12 -9999 0 -0.55 23 23
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.006 0.16 -9999 0 -0.63 23 23
VHL 0.012 0.022 -9999 0 -0.47 1 1
ITGB3 -0.084 0.19 -9999 0 -0.47 101 101
NOS3 0.029 0.13 -9999 0 -0.5 23 23
VEGFR2 homodimer/VEGFA homodimer/Sck -0.01 0.17 -9999 0 -0.68 24 24
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.001 0.16 -9999 0 -0.63 24 24
PRKCB -0.043 0.19 -9999 0 -0.67 29 29
VCL -0.017 0.12 -9999 0 -0.47 31 31
VEGFA165/NRP1 -0.002 0.15 -9999 0 -0.62 23 23
VEGFR1/2 heterodimer/VEGFA homodimer -0.005 0.16 -9999 0 -0.63 24 24
VEGFA165/NRP2 -0.024 0.12 -9999 0 -0.34 62 62
MAPKKK cascade 0.026 0.14 -9999 0 -0.54 23 23
NRP2 -0.02 0.12 -9999 0 -0.47 34 34
VEGFC homodimer 0.011 0.034 -9999 0 -0.52 2 2
NCK1 0.012 0.026 -9999 0 -0.57 1 1
ROCK1 0.012 0.022 -9999 0 -0.47 1 1
FAK1/Paxillin -0.021 0.19 -9999 0 -0.67 30 30
MAP3K13 -0.001 0.16 -9999 0 -0.63 25 25
PDPK1 0.024 0.15 -9999 0 -0.57 23 23
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.01 0.067 -9999 0 -0.31 20 20
EPHB2 0.005 0.066 -9999 0 -0.51 8 8
Syndecan-2/TACI -0.02 0.12 -9999 0 -0.33 59 59
LAMA1 -0.038 0.16 -9999 0 -0.53 47 47
Syndecan-2/alpha2 ITGB1 -0.019 0.13 -9999 0 -0.44 25 25
HRAS 0.006 0.064 -9999 0 -0.57 6 6
Syndecan-2/CASK 0.01 0.032 -9999 0 -0.27 6 6
ITGA5 -0.002 0.086 -9999 0 -0.47 16 16
BAX 0.025 0.06 -9999 0 -0.53 2 2
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.029 -9999 0 -0.24 6 6
LAMA3 -0.031 0.14 -9999 0 -0.47 45 45
EZR 0.013 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.035 0.14 -9999 0 -0.47 50 50
Syndecan-2/MMP2 0.01 0.065 -9999 0 -0.3 20 20
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.023 0.11 -9999 0 -0.32 62 62
dendrite morphogenesis 0.015 0.056 -9999 0 -0.33 12 12
Syndecan-2/GM-CSF 0.009 0.051 -9999 0 -0.31 12 12
determination of left/right symmetry 0.014 0.038 -9999 0 -0.32 6 6
Syndecan-2/PKC delta 0.02 0.032 -9999 0 -0.26 6 6
GNB2L1 0.009 0.052 -9999 0 -0.57 4 4
MAPK3 0.017 0.046 -9999 0 -0.31 6 6
MAPK1 0.017 0.046 -9999 0 -0.31 6 6
Syndecan-2/RACK1 0.019 0.056 -9999 0 -0.33 9 9
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.038 -9999 0 -0.32 6 6
ITGA2 -0.047 0.16 -9999 0 -0.47 62 62
MAPK8 0.02 0.059 -9999 0 -0.51 1 1
Syndecan-2/alpha2/beta1 Integrin -0.024 0.13 -9999 0 -0.35 39 39
Syndecan-2/Kininogen -0.035 0.13 -9999 0 -0.34 72 72
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.024 0.053 -9999 0 -0.3 9 9
Syndecan-2/CASK/Protein 4.1 0.018 0.029 -9999 0 -0.24 6 6
extracellular matrix organization 0.019 0.038 -9999 0 -0.31 6 6
actin cytoskeleton reorganization 0.01 0.067 -9999 0 -0.31 20 20
Syndecan-2/Caveolin-2/Ras -0.003 0.1 -9999 0 -0.42 13 13
Syndecan-2/Laminin alpha3 -0.007 0.093 -9999 0 -0.28 49 49
Syndecan-2/RasGAP 0.025 0.056 -9999 0 -0.31 9 9
alpha5/beta1 Integrin 0.008 0.062 -9999 0 -0.33 16 16
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.015 0.056 -9999 0 -0.33 12 12
GO:0007205 0.003 0.005 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.031 0.054 -9999 0 -0.54 1 1
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.05 0.18 -9999 0 -0.56 53 53
RASA1 0.011 0.03 -9999 0 -0.47 2 2
alpha2/beta1 Integrin -0.023 0.11 -9999 0 -0.32 62 62
Syndecan-2/Synbindin 0.02 0.032 -9999 0 -0.26 6 6
TGFB1 0.012 0.022 -9999 0 -0.47 1 1
CASP3 0.026 0.029 -9999 0 -10000 0 0
FN1 -0.003 0.09 -9999 0 -0.49 16 16
Syndecan-2/IL8 -0.02 0.11 -9999 0 -0.3 67 67
SDC2 0.014 0.038 -9999 0 -0.32 6 6
KNG1 -0.072 0.2 -9999 0 -0.57 66 66
Syndecan-2/Neurofibromin 0.02 0.032 -9999 0 -0.26 6 6
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.002 0.063 -9999 0 -0.57 6 6
Syndecan-2/TGFB1 0.019 0.038 -9999 0 -0.31 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.029 -9999 0 -0.24 6 6
Syndecan-2/Ezrin 0.027 0.029 -9999 0 -10000 0 0
PRKACA 0.026 0.029 -9999 0 -10000 0 0
angiogenesis -0.02 0.11 -9999 0 -0.3 67 67
MMP2 -0.002 0.086 -9999 0 -0.47 16 16
IL8 -0.052 0.17 -9999 0 -0.51 62 62
calcineurin-NFAT signaling pathway -0.02 0.12 -9999 0 -0.33 59 59
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.029 0.11 -9999 0 -0.4 13 13
CCNA2 -0.081 0.22 -9999 0 -0.57 80 80
PIK3CA 0.011 0.037 -9999 0 -0.47 3 3
JAK3 -0.003 0.096 -9999 0 -0.55 15 15
PIK3R1 0.008 0.053 -9999 0 -0.47 6 6
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.025 0.11 -9999 0 -0.49 12 12
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0 0.082 -9999 0 -0.32 31 31
IL2RA -0.058 0.19 -9999 0 -0.47 84 84
IL2RB -0.018 0.12 -9999 0 -0.49 32 32
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.011 0.12 -9999 0 -0.54 22 22
G1/S transition of mitotic cell cycle -0.05 0.23 -9999 0 -0.72 41 41
PTPN11 0.013 0.022 -9999 0 -0.47 1 1
CCND2 -0.017 0.18 -9999 0 -0.69 32 32
LCK 0.003 0.078 -9999 0 -0.57 9 9
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.004 0.037 -9999 0 -0.57 2 2
CDK6 -0.006 0.097 -9999 0 -0.49 19 19
CCND3 0.033 0.1 -9999 0 -0.44 9 9
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.016 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.03 0.11 -10000 0 -0.38 6 6
NFATC4 -0.021 0.097 -10000 0 -0.32 8 8
ERBB2IP 0.013 0.022 -10000 0 -0.46 1 1
HSP90 (dimer) 0.013 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.04 0.11 -10000 0 -0.4 5 5
JUN 0.003 0.073 -10000 0 -0.33 1 1
HRAS 0.006 0.064 -10000 0 -0.57 6 6
DOCK7 -0.034 0.11 -10000 0 -0.38 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.05 0.12 -10000 0 -0.48 5 5
AKT1 0.009 0.003 -10000 0 -10000 0 0
BAD 0.016 0.017 -10000 0 -0.36 1 1
MAPK10 -0.005 0.069 -10000 0 -0.28 4 4
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.042 0.12 -10000 0 -0.43 5 5
RAF1 -0.024 0.11 -10000 0 -0.39 5 5
ErbB2/ErbB3/neuregulin 2 -0.081 0.13 -10000 0 -0.26 175 175
STAT3 0.004 0.006 -10000 0 -10000 0 0
cell migration -0.001 0.073 -10000 0 -0.22 4 4
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.072 0.21 -10000 0 -0.59 22 22
FOS -0.075 0.22 -10000 0 -0.49 88 88
NRAS 0.012 0.022 -10000 0 -0.47 1 1
mol:Ca2+ -0.04 0.11 -10000 0 -0.4 5 5
MAPK3 -0.052 0.17 -10000 0 -0.5 17 17
MAPK1 -0.052 0.17 -10000 0 -0.5 17 17
JAK2 -0.034 0.11 -10000 0 -0.38 6 6
NF2 -0.002 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.047 0.12 -10000 0 -0.24 141 141
NRG1 -0.12 0.22 -10000 0 -0.47 141 141
GRB2/SOS1 0.02 0.001 -10000 0 -10000 0 0
MAPK8 -0.044 0.13 -10000 0 -0.36 8 8
MAPK9 -0.003 0.065 -10000 0 -0.2 1 1
ERBB2 -0.003 0.04 0.35 1 -0.36 5 6
ERBB3 0.011 0.022 -10000 0 -0.47 1 1
SHC1 0.013 0.001 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.004 0.015 0.21 1 -10000 0 1
STAT3 (dimer) 0.018 0.006 -10000 0 -10000 0 0
RNF41 0.02 0.007 -10000 0 -10000 0 0
FRAP1 0.008 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.042 0.067 -10000 0 -0.27 5 5
ErbB2/ErbB2/HSP90 (dimer) 0.006 0.033 0.24 1 -0.3 5 6
CHRNA1 -0.054 0.17 -10000 0 -0.42 38 38
myelination -0.018 0.095 -10000 0 -0.3 8 8
PPP3CB -0.032 0.1 -10000 0 -0.35 5 5
KRAS 0.013 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.026 0.11 -10000 0 -0.32 5 5
NRG2 -0.16 0.23 -10000 0 -0.47 174 174
mol:GDP -0.047 0.12 -10000 0 -0.23 141 141
SOS1 0.013 0.001 -10000 0 -10000 0 0
MAP2K2 -0.022 0.12 -10000 0 -0.41 5 5
SRC 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.031 0.11 -10000 0 -0.38 6 6
MAP2K1 -0.067 0.18 -10000 0 -0.51 19 19
heart morphogenesis -0.04 0.11 -10000 0 -0.4 5 5
RAS family/GDP -0.029 0.11 -10000 0 -0.4 5 5
GRB2 0.013 0.001 -10000 0 -10000 0 0
PRKACA -0.004 0.007 -10000 0 -10000 0 0
CHRNE 0.009 0.02 -10000 0 -0.2 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.009 0.003 -10000 0 -10000 0 0
nervous system development -0.04 0.11 -10000 0 -0.4 5 5
CDC42 0.013 0 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.006 0.1 -10000 0 -0.57 16 16
EPHB2 0.005 0.066 -10000 0 -0.51 8 8
EFNB1 0.014 0.046 -10000 0 -0.34 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.043 0.14 -10000 0 -0.59 10 10
Ephrin B2/EPHB1-2 -0.075 0.15 -10000 0 -0.27 169 169
neuron projection morphogenesis -0.068 0.11 -10000 0 -0.56 10 10
Ephrin B1/EPHB1-2/Tiam1 -0.052 0.15 -10000 0 -0.56 13 13
DNM1 0.011 0.034 -10000 0 -0.52 2 2
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.015 0.038 -10000 0 -0.57 2 2
YES1 -0.002 0.05 -10000 0 -0.78 2 2
Ephrin B1/EPHB1-2/NCK2 -0.05 0.14 -10000 0 -0.49 13 13
PI3K 0.014 0.061 -10000 0 -0.61 3 3
mol:GDP -0.052 0.14 -10000 0 -0.55 13 13
ITGA2B -0.004 0.092 -10000 0 -0.51 16 16
endothelial cell proliferation 0.005 0.067 -10000 0 -0.35 17 17
FYN -0.003 0.051 -10000 0 -0.78 2 2
MAP3K7 0.009 0.04 -10000 0 -0.6 2 2
FGR -0.001 0.051 -10000 0 -0.79 2 2
TIAM1 0.009 0.043 -10000 0 -0.47 4 4
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.029 0.13 -10000 0 -0.52 12 12
LYN -0.002 0.05 -10000 0 -0.78 2 2
Ephrin B1/EPHB1-2/Src Family Kinases -0.004 0.048 -10000 0 -0.75 2 2
Ephrin B1/EPHB1-2 -0.005 0.042 -10000 0 -0.66 2 2
SRC -0.001 0.05 -10000 0 -0.79 2 2
ITGB3 -0.084 0.19 -10000 0 -0.47 101 101
EPHB1 -0.14 0.22 -10000 0 -0.47 161 161
EPHB4 0.012 0.026 -10000 0 -0.57 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.005 0.068 -10000 0 -0.36 17 17
alphaIIb/beta3 Integrin -0.062 0.16 -10000 0 -0.34 112 112
BLK -0.029 0.076 -10000 0 -0.79 2 2
HCK -0.003 0.053 -10000 0 -0.79 2 2
regulation of stress fiber formation 0.05 0.14 0.48 13 -10000 0 13
MAPK8 0.016 0.056 -10000 0 -0.64 2 2
Ephrin B1/EPHB1-2/RGS3 -0.05 0.14 -10000 0 -0.49 13 13
endothelial cell migration 0.004 0.066 -10000 0 -0.32 19 19
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.012 0.038 -10000 0 -0.58 2 2
regulation of focal adhesion formation 0.05 0.14 0.48 13 -10000 0 13
chemotaxis 0.05 0.14 0.48 13 -10000 0 13
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
Rac1/GTP -0.068 0.12 -10000 0 -0.58 10 10
angiogenesis -0.005 0.042 -10000 0 -0.65 2 2
LCK -0.002 0.051 -10000 0 -0.79 2 2
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.018 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.003 0.094 -9999 0 -0.55 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.057 0.11 -9999 0 -0.19 191 191
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.011 0.03 -9999 0 -0.47 2 2
MAP3K12 0.007 0.057 -9999 0 -0.47 7 7
FGR 0.01 0.04 -9999 0 -0.5 3 3
p38 alpha/TAB1 -0.022 0.047 -9999 0 -0.29 6 6
PRKG1 -0.12 0.22 -9999 0 -0.47 143 143
DUSP8 0.007 0.059 -9999 0 -0.57 5 5
PGK/cGMP/p38 alpha -0.074 0.11 -9999 0 -0.3 53 53
apoptosis -0.021 0.046 -9999 0 -0.28 6 6
RAL/GTP 0.018 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.006 0.094 -9999 0 -0.47 20 20
PAK1 0.006 0.06 -9999 0 -0.47 8 8
SRC 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.034 0 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 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 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.018 0 -9999 0 -10000 0 0
MAPK11 -0.006 0.093 -9999 0 -0.38 9 9
BLK -0.1 0.22 -9999 0 -0.5 112 112
HCK 0.008 0.05 -9999 0 -0.49 5 5
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.012 0.022 -9999 0 -0.47 1 1
DUSP10 0.013 0 -9999 0 -10000 0 0
TRAF6/MEKK3 0.017 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.01 0.069 -9999 0 -0.31 6 6
positive regulation of innate immune response -0.001 0.099 -9999 0 -0.4 9 9
LCK 0.003 0.078 -9999 0 -0.57 9 9
p38alpha-beta/MKP7 0.006 0.097 -9999 0 -0.41 7 7
p38alpha-beta/MKP5 0.006 0.096 -9999 0 -0.41 7 7
PGK/cGMP -0.089 0.16 -9999 0 -0.33 143 143
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.002 0.11 -9999 0 -0.42 10 10
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.17 0.23 -9999 0 -0.47 185 185
Coregulation of Androgen receptor activity

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
NRIP1 0.012 0.033 -9999 0 -0.68 1 1
SVIL -0.009 0.1 -9999 0 -0.47 23 23
ZNF318 0.012 0.019 -9999 0 -10000 0 0
JMJD2C 0.006 0.011 -9999 0 -0.11 4 4
T-DHT/AR/Ubc9 0.002 0.089 -9999 0 -0.27 44 44
CARM1 0.013 0.001 -9999 0 -10000 0 0
PRDX1 0.013 0.001 -9999 0 -10000 0 0
PELP1 0.013 0.003 -9999 0 -10000 0 0
CTNNB1 0.014 0.006 -9999 0 -10000 0 0
AKT1 0.013 0.006 -9999 0 -10000 0 0
PTK2B 0.013 0.006 -9999 0 -10000 0 0
MED1 0.013 0.006 -9999 0 -10000 0 0
MAK -0.16 0.27 -9999 0 -0.57 144 144
response to oxidative stress 0 0.002 -9999 0 -10000 0 0
HIP1 0 0.08 -9999 0 -0.47 14 14
GSN 0.01 0.044 -9999 0 -0.47 4 4
NCOA2 -0.045 0.16 -9999 0 -0.47 60 60
NCOA6 0.014 0.008 -9999 0 -10000 0 0
DNA-PK 0.025 0.021 -9999 0 -10000 0 0
NCOA4 0.013 0.001 -9999 0 -10000 0 0
PIAS3 0.014 0.006 -9999 0 -10000 0 0
cell proliferation -0.075 0.11 -9999 0 -0.25 141 141
XRCC5 0.013 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.014 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.008 0.11 -9999 0 -0.3 56 56
FHL2 -0.014 0.2 -9999 0 -0.86 25 25
RANBP9 0.014 0.008 -9999 0 -10000 0 0
JMJD1A 0.013 0.016 -9999 0 -0.13 6 6
CDK6 -0.006 0.097 -9999 0 -0.49 19 19
TGFB1I1 -0.024 0.13 -9999 0 -0.47 39 39
T-DHT/AR/CyclinD1 0.002 0.09 -9999 0 -0.27 45 45
XRCC6 0.013 0.004 -9999 0 -10000 0 0
T-DHT/AR 0.017 0.1 -9999 0 -0.5 4 4
CTDSP1 0.013 0.003 -9999 0 -10000 0 0
CTDSP2 0.013 0.014 -9999 0 -10000 0 0
BRCA1 0.011 0.04 -9999 0 -0.61 2 2
TCF4 0.009 0.044 -9999 0 -0.47 4 4
CDKN2A -0.11 0.24 -9999 0 -0.57 106 106
SRF 0.013 0.032 -9999 0 -10000 0 0
NKX3-1 0.022 0.05 -9999 0 -10000 0 0
KLK3 0.021 0.16 -9999 0 -1.2 8 8
TMF1 0.013 0.002 -9999 0 -10000 0 0
HNRNPA1 0.013 0.008 -9999 0 -10000 0 0
AOF2 0 0.009 -9999 0 -0.07 7 7
APPL1 0.021 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.002 0.088 -9999 0 -0.27 44 44
AR -0.025 0.14 -9999 0 -0.46 44 44
UBA3 0.013 0.003 -9999 0 -10000 0 0
PATZ1 0.013 0.008 -9999 0 -10000 0 0
PAWR 0.013 0.002 -9999 0 -10000 0 0
PRKDC 0.012 0.024 -9999 0 -0.52 1 1
PA2G4 0.013 0.008 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.003 0.081 -9999 0 -0.24 44 44
RPS6KA3 0.013 0.023 -9999 0 -0.47 1 1
T-DHT/AR/ARA70 0.002 0.089 -9999 0 -0.27 44 44
LATS2 0.013 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.003 0.081 -9999 0 -0.24 44 44
Cyclin D3/CDK11 p58 0.01 0.002 -9999 0 -10000 0 0
VAV3 -0.041 0.15 -9999 0 -0.47 56 56
KLK2 0.013 0.091 -9999 0 -0.85 4 4
CASP8 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.018 0.15 -9999 0 -0.4 62 62
TMPRSS2 0.014 0.11 -9999 0 -0.88 6 6
CCND1 0.012 0.026 -9999 0 -0.57 1 1
PIAS1 0.013 0.025 -9999 0 -0.46 1 1
mol:T-DHT 0.004 0.017 -9999 0 -0.062 31 31
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.014 0.018 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.01 0.11 -9999 0 -0.29 61 61
CMTM2 0.008 0.048 -9999 0 -0.52 4 4
SNURF -0.005 0.09 -9999 0 -0.47 18 18
ZMIZ1 0.016 0.027 -9999 0 -0.46 1 1
CCND3 0.013 0.001 -9999 0 -10000 0 0
TGIF1 0.013 0.008 -9999 0 -10000 0 0
FKBP4 0.014 0.008 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.003 0.089 -10000 0 -0.47 17 17
ANTXR2 0.002 0.074 -10000 0 -0.47 12 12
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.015 -10000 0 -0.063 28 28
monocyte activation -0.015 0.1 -10000 0 -0.38 33 33
MAP2K2 -0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.003 0.012 -10000 0 -10000 0 0
MAP2K7 -0.003 0.012 -10000 0 -10000 0 0
MAP2K6 -0.011 0.051 -10000 0 -0.3 14 14
CYAA -0.001 0.06 -10000 0 -0.24 28 28
MAP2K4 -0.003 0.012 -10000 0 -10000 0 0
IL1B -0.034 0.11 -10000 0 -0.28 78 78
Channel 0.002 0.065 -10000 0 -0.26 28 28
NLRP1 -0.01 0.045 -10000 0 -0.26 14 14
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.016 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.015 0.063 28 -10000 0 28
MAPK3 -0.003 0.012 -10000 0 -10000 0 0
MAPK1 -0.003 0.012 -10000 0 -10000 0 0
PGR -0.037 0.09 -10000 0 -0.25 72 72
PA/Cellular Receptors 0.001 0.071 -10000 0 -0.29 28 28
apoptosis -0.004 0.015 -10000 0 -0.063 28 28
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.002 0.061 -10000 0 -0.24 28 28
macrophage activation 0.014 0.014 -10000 0 -10000 0 0
TNF -0.026 0.14 -10000 0 -0.5 37 37
VCAM1 -0.015 0.1 -10000 0 -0.38 33 33
platelet activation -0.004 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.02 0.12 2 -10000 0 2
IL18 -0.002 0.074 -10000 0 -0.32 21 21
negative regulation of macrophage activation -0.004 0.015 -10000 0 -0.063 28 28
LEF -0.004 0.015 -10000 0 -0.063 28 28
CASP1 -0.011 0.048 -10000 0 -0.22 20 20
mol:cAMP -0.004 0.016 -10000 0 -10000 0 0
necrosis -0.004 0.015 -10000 0 -0.063 28 28
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.002 0.061 -10000 0 -0.24 28 28
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.015 0.12 -9999 0 -0.5 6 6
CRKL -0.001 0.099 -9999 0 -0.43 3 3
mol:DAG 0.001 0.11 -9999 0 -0.36 8 8
HRAS 0.019 0.09 -9999 0 -0.39 2 2
MAPK8 -0.02 0.12 -9999 0 -0.31 39 39
RAP1A -0.001 0.099 -9999 0 -0.43 3 3
GAB1 -0.001 0.099 -9999 0 -0.4 4 4
MAPK14 -0.014 0.11 -9999 0 -0.3 38 38
EPO -0.065 0.19 -9999 0 -0.51 76 76
PLCG1 0.001 0.11 -9999 0 -0.37 8 8
EPOR/TRPC2/IP3 Receptors 0 0.083 -9999 0 -0.57 10 10
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.065 0.16 -9999 0 -0.34 96 96
GAB1/SHC/GRB2/SOS1 -0.031 0.068 -9999 0 -0.42 2 2
EPO/EPOR (dimer) -0.042 0.15 -9999 0 -0.37 84 84
IRS2 -0.004 0.1 -9999 0 -0.42 5 5
STAT1 0.001 0.12 -9999 0 -0.44 10 10
STAT5B 0.003 0.11 -9999 0 -0.4 8 8
cell proliferation -0.012 0.11 -9999 0 -0.47 5 5
GAB1/SHIP/PIK3R1/SHP2/SHC -0.042 0.087 -9999 0 -0.4 10 10
TEC -0.001 0.099 -9999 0 -0.43 3 3
SOCS3 -0.053 0.17 -9999 0 -0.48 67 67
STAT1 (dimer) 0.001 0.12 -9999 0 -0.43 10 10
JAK2 0.01 0.024 -9999 0 -0.46 1 1
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
EPO/EPOR (dimer)/JAK2 0.005 0.11 -9999 0 -0.35 8 8
EPO/EPOR -0.042 0.15 -9999 0 -0.37 84 84
LYN 0.014 0.003 -9999 0 -10000 0 0
TEC/VAV2 0.008 0.097 -9999 0 -0.46 2 2
elevation of cytosolic calcium ion concentration 0 0.083 -9999 0 -0.57 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.019 0.13 -9999 0 -0.33 43 43
mol:IP3 0.001 0.11 -9999 0 -0.36 8 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.006 0.12 -9999 0 -0.41 13 13
SH2B3 0.01 0.011 -9999 0 -10000 0 0
NFKB1 -0.014 0.11 -9999 0 -0.3 38 38
EPO/EPOR (dimer)/JAK2/SOCS3 -0.061 0.1 -9999 0 -0.28 57 57
PTPN6 -0.008 0.1 -9999 0 -0.35 8 8
TEC/VAV2/GRB2 0.014 0.094 -9999 0 -0.44 2 2
EPOR 0 0.083 -9999 0 -0.57 10 10
INPP5D -0.014 0.11 -9999 0 -0.47 28 28
mol:GDP -0.031 0.069 -9999 0 -0.42 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.003 0.071 -9999 0 -0.49 10 10
CRKL/CBL/C3G 0.013 0.096 -9999 0 -0.42 3 3
VAV2 -0.001 0.099 -9999 0 -0.43 3 3
CBL -0.001 0.1 -9999 0 -0.42 4 4
SHC/Grb2/SOS1 -0.033 0.072 -9999 0 -0.44 2 2
STAT5A 0.002 0.11 -9999 0 -0.4 8 8
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.017 0.12 -9999 0 -0.44 8 8
LYN/PLCgamma2 0.013 0.052 -9999 0 -0.34 10 10
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
BTK -0.008 0.11 -9999 0 -0.39 6 6
BCL2 -0.008 0.2 -9999 0 -0.83 23 23
Insulin Pathway

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
CBL/APS/CAP -0.06 0.12 -9999 0 -0.38 34 34
TC10/GTP -0.044 0.092 -9999 0 -0.46 6 6
Insulin Receptor/Insulin/IRS1/Shp2 0.01 0.075 -9999 0 -0.31 15 15
HRAS 0.006 0.064 -9999 0 -0.57 6 6
APS homodimer -0.01 0.11 -9999 0 -0.57 20 20
GRB14 -0.096 0.23 -9999 0 -0.57 93 93
FOXO3 -0.073 0.21 -9999 0 -0.57 72 72
AKT1 -0.023 0.13 -9999 0 -0.43 15 15
INSR 0.014 0.005 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.046 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 -0.072 0.18 -9999 0 -0.47 88 88
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.024 0.044 -9999 0 -10000 0 0
CAV1 -0.024 0.11 -9999 0 -0.36 23 23
CBL/APS/CAP/Crk-II/C3G -0.018 0.12 -9999 0 -0.35 20 20
Insulin Receptor/Insulin/IRS1/NCK2 0.011 0.072 -9999 0 -0.27 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.071 -9999 0 -0.48 5 5
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.024 0.049 -9999 0 -0.36 1 1
RPS6KB1 -0.015 0.12 -9999 0 -0.39 15 15
PARD6A 0.006 0.064 -9999 0 -0.57 6 6
CBL 0.012 0.022 -9999 0 -0.47 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.001 0.034 -9999 0 -0.74 1 1
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.052 0.1 -9999 0 -0.4 15 15
HRAS/GTP -0.024 0.074 -9999 0 -0.41 8 8
Insulin Receptor 0.014 0.005 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.018 0.068 -9999 0 -0.49 1 1
PRKCI -0.014 0.028 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.063 0.12 -9999 0 -0.47 15 15
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.023 0.036 -9999 0 -0.46 2 2
PI3K 0.01 0.079 -9999 0 -0.49 5 5
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 -0.001 0.005 -9999 0 -10000 0 0
HRAS/GDP 0.005 0.047 -9999 0 -0.42 6 6
AKT2 -0.023 0.13 -9999 0 -0.43 15 15
PRKCZ -0.014 0.027 -9999 0 -10000 0 0
SH2B2 -0.01 0.11 -9999 0 -0.57 20 20
SHC/SHIP 0.003 0.09 -9999 0 -0.44 8 8
F2RL2 -0.22 0.29 -9999 0 -0.57 197 197
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.012 0.051 -9999 0 -0.29 14 14
TC10/GTP/CIP4/Exocyst 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.027 0.048 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.011 0.03 -9999 0 -0.47 2 2
NCK1 0.012 0.026 -9999 0 -0.57 1 1
CBL/APS/CAP/Crk-II -0.027 0.12 -9999 0 -0.38 20 20
TC10/GDP 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.02 0.051 -9999 0 -0.28 14 14
INPP5D -0.005 0.095 -9999 0 -0.34 20 20
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.12 0.29 -9999 0 -0.82 72 72
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
IRS1 -0.003 0.087 -9999 0 -0.47 17 17
p62DOK/RasGAP 0.023 0.037 -9999 0 -0.46 2 2
INS -0.013 0.094 -9999 0 -0.57 14 14
mol:PI-3-4-P2 -0.005 0.094 -9999 0 -0.34 20 20
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.039 0.15 -9999 0 -0.46 30 30
PTPRA 0.014 0.005 -9999 0 -10000 0 0
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
TC10/GTP/CIP4 0.018 0 -9999 0 -10000 0 0
PDPK1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.019 0.053 -9999 0 -0.41 1 1
Insulin Receptor/Insulin/IRS1 0.002 0.072 -9999 0 -0.28 30 30
Insulin Receptor/Insulin/IRS3 0.002 0.07 -9999 0 -0.41 14 14
Par3/Par6 -0.1 0.16 -9999 0 -0.3 199 199
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.13 0.22 -9999 0 -0.47 144 144
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.005 0.069 -9999 0 -0.57 7 7
TCEB1 0.012 0.026 -9999 0 -0.57 1 1
HIF1A/p53 0.026 0.03 -9999 0 -0.27 1 1
HIF1A 0.021 0.015 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.034 0.045 -9999 0 -0.31 8 8
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.11 0.24 -9999 0 -0.57 106 106
ARNT/IPAS -0.08 0.16 -9999 0 -0.33 144 144
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.009 0.052 -9999 0 -0.57 4 4
HIF1A/ARNT 0.028 0.015 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.018 0.064 -9999 0 -0.41 10 10
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.028 0.015 -9999 0 -10000 0 0
PHD1-3/OS9 0.029 0.038 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.032 0.053 -9999 0 -0.48 3 3
VHL 0.012 0.022 -9999 0 -0.47 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.028 0.015 -9999 0 -10000 0 0
EGLN3 0.004 0.067 -9999 0 -0.47 10 10
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.007 0.052 -9999 0 -0.47 6 6
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.033 0.036 -9999 0 -0.65 1 1
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.034 0.12 -9999 0 -0.26 106 106
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.017 0.11 -10000 0 -0.32 53 53
ATM 0.012 0.022 -10000 0 -0.47 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.012 0.026 -10000 0 -0.57 1 1
ATR 0.012 0.026 -10000 0 -0.57 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.022 0.031 -10000 0 -0.34 3 3
protein ubiquitination 0.004 0.09 -10000 0 -0.53 3 3
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex 0.027 0 -10000 0 -10000 0 0
MRE11A 0.013 0 -10000 0 -10000 0 0
DNA-PK 0.026 0.017 -10000 0 -0.35 1 1
FA complex/FANCD2/Ubiquitin 0.033 0.044 -10000 0 -0.33 1 1
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.011 0.037 -10000 0 -0.57 2 2
CCNE1 0.006 0.064 -10000 0 -0.57 6 6
CDK2/Cyclin E1 0.015 0.047 -10000 0 -0.41 6 6
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.019 0.11 -10000 0 -0.33 55 55
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.012 0.026 -10000 0 -0.57 1 1
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.032 0.16 -10000 0 -0.57 39 39
DNA repair 0.01 0.12 -10000 0 -0.5 11 11
BRCA1/BARD1/ubiquitin -0.019 0.11 -10000 0 -0.33 55 55
BARD1/DNA-PK 0.005 0.084 -10000 0 -0.31 1 1
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.017 0.11 0.32 53 -10000 0 53
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.076 -10000 0 -0.34 2 2
BRCA1/BACH1/BARD1/TopBP1 -0.006 0.093 -10000 0 -0.27 55 55
BRCA1/BARD1/P53 0 0.092 -10000 0 -0.39 3 3
BARD1/CSTF1/BRCA1 -0.006 0.093 -10000 0 -0.27 55 55
BRCA1/BACH1 0.011 0.037 -10000 0 -0.57 2 2
BARD1 -0.038 0.15 -10000 0 -0.47 53 53
PCNA 0.012 0.026 -10000 0 -0.57 1 1
BRCA1/BARD1/UbcH5C -0.006 0.093 -10000 0 -0.27 55 55
BRCA1/BARD1/UbcH7 -0.006 0.093 -10000 0 -0.27 55 55
BRCA1/BARD1/RAD51/PCNA -0.024 0.13 -10000 0 -0.37 41 41
BARD1/DNA-PK/P53 0.009 0.083 -10000 0 -0.28 1 1
BRCA1/BARD1/Ubiquitin -0.019 0.11 -10000 0 -0.33 55 55
BRCA1/BARD1/CTIP 0.002 0.087 -10000 0 -0.36 3 3
FA complex 0.023 0.052 -10000 0 -0.29 1 1
BARD1/EWS -0.017 0.11 -10000 0 -0.32 53 53
RBBP8 0.02 0.022 -10000 0 -0.33 2 2
TP53 0.007 0.052 -10000 0 -0.47 6 6
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.001 0.091 0.38 3 -10000 0 3
BRCA1/BARD1 0.007 0.092 -10000 0 -0.54 3 3
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.027 0.11 -10000 0 -0.33 53 53
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.035 0.16 -10000 0 -0.57 41 41
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.019 0.11 -10000 0 -0.33 55 55
EWSR1 0.013 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 -0.004 0.1 -9999 0 -0.57 15 15
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.015 0.034 -9999 0 -0.18 15 15
GNAO1 -0.08 0.19 -9999 0 -0.47 96 96
mol:Sphinganine-1-P 0.008 0.074 -9999 0 -0.41 15 15
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.025 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
S1PR3 -0.005 0.093 -9999 0 -0.47 19 19
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.028 -9999 0 -10000 0 0
S1PR5 -0.066 0.18 -9999 0 -0.47 82 82
S1PR4 -0.012 0.12 -9999 0 -0.57 22 22
GNAI1 0.006 0.064 -9999 0 -0.53 7 7
S1P/S1P5/G12 -0.016 0.099 -9999 0 -0.37 1 1
S1P/S1P3/Gq 0.003 0.11 -9999 0 -0.51 13 13
S1P/S1P4/Gi -0.038 0.15 -9999 0 -0.42 45 45
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ -0.034 0.14 -9999 0 -0.47 49 49
GNA14 0.011 0.03 -9999 0 -0.47 2 2
GNA15 -0.011 0.1 -9999 0 -0.47 25 25
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.087 -9999 0 -0.47 17 17
ABCC1 0.013 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.022 0.16 -10000 0 -1.2 9 9
oxygen homeostasis -0.001 0.016 -10000 0 -10000 0 0
TCEB2 0.005 0.069 -10000 0 -0.57 7 7
TCEB1 0.012 0.026 -10000 0 -0.57 1 1
VHL/Elongin B/Elongin C/HIF2A -0.019 0.075 -10000 0 -0.39 11 11
EPO -0.053 0.29 -10000 0 -0.67 49 49
FIH (dimer) 0.014 0.015 -10000 0 -10000 0 0
APEX1 0.012 0.017 -10000 0 -10000 0 0
SERPINE1 -0.05 0.28 -10000 0 -0.65 45 45
FLT1 -0.022 0.15 -10000 0 -1.2 8 8
ADORA2A -0.019 0.24 -10000 0 -0.67 24 24
germ cell development -0.038 0.27 -10000 0 -0.66 43 43
SLC11A2 -0.014 0.24 -10000 0 -0.68 23 23
BHLHE40 -0.02 0.26 -10000 0 -0.7 29 29
HIF1AN 0.014 0.015 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.007 0.16 -10000 0 -0.47 7 7
ETS1 0.021 0.054 -10000 0 -0.49 5 5
CITED2 -0.003 0.034 -10000 0 -0.44 1 1
KDR -0.055 0.26 -10000 0 -1.2 24 24
PGK1 -0.014 0.25 -10000 0 -0.68 23 23
SIRT1 0.013 0.003 -10000 0 -10000 0 0
response to hypoxia -0.001 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.023 0.28 -10000 0 -0.75 30 30
EPAS1 0.014 0.11 -10000 0 -0.38 7 7
SP1 0.02 0.003 -10000 0 -10000 0 0
ABCG2 -0.041 0.29 -10000 0 -0.76 40 40
EFNA1 -0.014 0.24 -10000 0 -0.68 23 23
FXN -0.018 0.24 -10000 0 -0.67 23 23
POU5F1 -0.041 0.28 -10000 0 -0.69 43 43
neuron apoptosis 0.022 0.28 0.72 30 -10000 0 30
EP300 0.01 0.037 -10000 0 -0.47 3 3
EGLN3 0.004 0.069 -10000 0 -0.47 10 10
EGLN2 0.014 0.015 -10000 0 -10000 0 0
EGLN1 0.014 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.021 0.052 -10000 0 -0.38 8 8
VHL 0.012 0.022 -10000 0 -0.47 1 1
ARNT 0.012 0.018 -10000 0 -10000 0 0
SLC2A1 -0.018 0.24 -10000 0 -0.67 23 23
TWIST1 -0.089 0.31 -10000 0 -0.68 63 63
ELK1 0.02 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.018 0.15 -10000 0 -0.51 5 5
VEGFA -0.03 0.27 -10000 0 -0.69 33 33
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.021 0.041 -9999 0 -0.27 10 10
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.015 0.065 -9999 0 -0.34 15 15
MAPK12 -0.011 0.12 -9999 0 -0.39 35 35
CCND1 0.005 0.047 -9999 0 -0.2 10 10
p38 gamma/SNTA1 -0.003 0.11 -9999 0 -0.36 35 35
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.004 0.074 -9999 0 -0.57 8 8
G2/M transition checkpoint -0.01 0.12 -9999 0 -0.38 35 35
MAP2K6 -0.001 0.088 -9999 0 -0.32 31 31
MAPT 0.01 0.058 -9999 0 -0.26 13 13
MAPK13 0.014 0.049 -9999 0 -0.33 10 10
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0 0.072 -9999 0 -0.3 25 25
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.013 0.055 -10000 0 -1.1 1 1
VDR 0.005 0.064 -10000 0 -0.49 8 8
FAM120B 0.013 0.001 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.018 0.12 -10000 0 -0.41 8 8
RXRs/LXRs/DNA/Oxysterols -0.012 0.14 -10000 0 -0.42 26 26
MED1 0.013 0 -10000 0 -10000 0 0
mol:9cRA 0.002 0.013 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.025 0.049 -10000 0 -0.44 1 1
RXRs/NUR77 -0.037 0.14 -10000 0 -0.38 30 30
RXRs/PPAR -0.033 0.12 -10000 0 -0.37 20 20
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.004 0.046 -10000 0 -0.36 8 8
RARs/VDR/DNA/Vit D3 0.02 0.059 -10000 0 -0.39 5 5
RARA 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.005 0.064 -10000 0 -0.49 8 8
RARs/RARs/DNA/9cRA 0.018 0.042 -10000 0 -0.22 14 14
RARG 0.004 0.067 -10000 0 -0.47 10 10
RPS6KB1 0.022 0.04 -10000 0 -0.4 1 1
RARs/THRs/DNA/SMRT 0.025 0.049 -10000 0 -0.44 1 1
THRA 0.013 0 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.004 0.046 -10000 0 -0.36 8 8
RXRs/PPAR/9cRA/PGJ2/DNA -0.031 0.12 0.27 1 -0.32 12 13
NR1H4 -0.1 0.21 -10000 0 -0.49 109 109
RXRs/LXRs/DNA -0.009 0.12 -10000 0 -0.35 6 6
NR1H2 0.017 0.01 -10000 0 -10000 0 0
NR1H3 0.016 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.028 0.12 -10000 0 -0.3 17 17
NR4A1 -0.01 0.11 -10000 0 -0.51 22 22
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.07 0.13 -10000 0 -0.33 52 52
RXRG -0.1 0.21 -10000 0 -0.47 120 120
RXR alpha/CCPG 0.022 0.007 -10000 0 -10000 0 0
RXRA 0.016 0.01 -10000 0 -10000 0 0
RXRB 0.016 0.012 -10000 0 -10000 0 0
THRB 0.004 0.074 -10000 0 -0.57 8 8
PPARG -0.017 0.12 -10000 0 -0.48 31 31
PPARD 0.013 0 -10000 0 -10000 0 0
TNF -0.038 0.24 -10000 0 -0.97 26 26
mol:Oxysterols 0.003 0.012 -10000 0 -10000 0 0
cholesterol transport -0.011 0.13 -10000 0 -0.42 26 26
PPARA 0.013 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.009 0.043 -10000 0 -0.47 4 4
RXRs/NUR77/BCL2 -0.049 0.14 -10000 0 -0.4 35 35
SREBF1 -0.003 0.13 -10000 0 -0.57 7 7
RXRs/RXRs/DNA/9cRA -0.031 0.12 0.26 1 -0.32 12 13
ABCA1 -0.004 0.13 -10000 0 -0.61 8 8
RARs/THRs 0.027 0.06 -10000 0 -0.52 1 1
RXRs/FXR -0.088 0.17 -10000 0 -0.39 61 61
BCL2 -0.009 0.1 -10000 0 -0.47 23 23
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.005 0.064 -10000 0 -0.49 8 8
Cbp/p300/PCAF 0.025 0.023 -10000 0 -0.27 3 3
EP300 0.01 0.037 -10000 0 -0.47 3 3
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.027 0.057 -10000 0 -0.31 8 8
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.023 0.066 0.2 30 -0.23 13 43
RAR alpha/9cRA/Cyclin H -0.02 0.072 -10000 0 -0.46 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.025 0.055 -10000 0 -0.29 8 8
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0 0.086 -10000 0 -0.46 12 12
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.004 0.046 -10000 0 -0.36 8 8
RXRs/RARs/NRIP1/9cRA 0.004 0.12 -10000 0 -0.5 19 19
NCOA2 -0.045 0.16 -10000 0 -0.47 60 60
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.005 0.064 -10000 0 -0.49 8 8
RARG 0.004 0.068 -10000 0 -0.47 10 10
RAR gamma1/9cRA 0.013 0.041 -10000 0 -0.27 10 10
MAPK3 0.014 0 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.003 0.074 -10000 0 -0.47 12 12
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.011 0.12 -10000 0 -0.48 24 24
RARA 0.004 0.077 -10000 0 -0.26 32 32
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.001 0.1 -10000 0 -0.34 24 24
PRKCA -0.006 0.1 -10000 0 -0.47 23 23
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.007 0.13 -10000 0 -0.48 24 24
RXRG -0.075 0.17 -10000 0 -0.32 143 143
RXRA 0.011 0.07 -10000 0 -0.24 25 25
RXRB 0.003 0.078 -10000 0 -0.26 39 39
VDR/Vit D3/DNA 0.004 0.046 -10000 0 -0.36 8 8
RBP1 -0.034 0.14 -10000 0 -0.47 48 48
CRBP1/9-cic-RA -0.024 0.1 -10000 0 -0.34 48 48
RARB 0.012 0.043 -10000 0 -0.47 4 4
PRKCG -0.008 0.1 -10000 0 -0.57 16 16
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.008 0.12 -10000 0 -0.5 19 19
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.01 0.11 -10000 0 -0.43 19 19
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.068 -10000 0 -0.32 11 11
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.007 0.13 -10000 0 -0.48 24 24
positive regulation of DNA binding -0.019 0.068 -10000 0 -0.43 5 5
NRIP1 -0.005 0.12 -10000 0 -0.51 15 15
RXRs/RARs -0.013 0.13 -10000 0 -0.45 29 29
RXRs/RXRs/DNA/9cRA -0.025 0.12 -10000 0 -0.47 25 25
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0.024 0.033 -10000 0 -0.35 4 4
RAR alpha/9cRA -0.014 0.052 -10000 0 -0.45 3 3
CCNH 0.009 0.052 -10000 0 -0.57 4 4
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.006 0.035 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.027 0.1 -10000 0 -0.47 11 11
UGCG -0.041 0.19 -10000 0 -0.64 43 43
AKT1/mTOR/p70S6K/Hsp90/TERT -0.005 0.12 -10000 0 -0.36 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.039 0.19 -10000 0 -0.63 43 43
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.042 0.11 -10000 0 -0.39 34 34
FRAP1 0.012 0.16 -10000 0 -0.46 34 34
FOXO3 0.022 0.13 -10000 0 -0.47 14 14
AKT1 0.016 0.14 -10000 0 -0.5 15 15
GAB2 0.013 0.002 -10000 0 -10000 0 0
SMPD1 0.015 0.028 -10000 0 -10000 0 0
SGMS1 0.015 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 0.013 0.042 -10000 0 -0.3 8 8
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.012 0.13 -10000 0 -0.35 46 46
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.017 0.05 -10000 0 -0.36 8 8
RPS6KB1 0.016 0.032 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.001 0.096 -10000 0 -0.54 15 15
PIK3R1 0.01 0.053 -10000 0 -0.47 6 6
JAK1 0.015 0.002 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.011 0.15 -10000 0 -0.61 7 7
MYB 0.008 0.089 -10000 0 -0.47 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.016 0.12 -10000 0 -0.45 20 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.04 -10000 0 -0.32 3 3
mol:PI-3-4-5-P3 0.016 0.12 -10000 0 -0.44 20 20
Rac1/GDP 0.02 0.039 -10000 0 -0.27 8 8
T cell proliferation 0.022 0.12 -10000 0 -0.42 17 17
SHC1 0.013 0.002 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.009 -10000 0 -0.039 24 24
PRKCZ 0.022 0.12 -10000 0 -0.44 17 17
NF kappa B1 p50/RelA -0.038 0.11 -10000 0 -0.46 17 17
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.018 0.11 -10000 0 -0.46 20 20
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.081 0.21 -10000 0 -0.57 81 81
IL2RB -0.017 0.12 -10000 0 -0.49 32 32
TERT -0.18 0.27 -10000 0 -0.57 159 159
E2F1 0.01 0.059 -10000 0 -0.33 2 2
SOS1 0.013 0.002 -10000 0 -10000 0 0
RPS6 0.01 0.045 -10000 0 -0.57 3 3
mol:cAMP -0.002 0.005 0.018 24 -10000 0 24
PTPN11 0.012 0.022 -10000 0 -0.47 1 1
IL2RG -0.009 0.12 -10000 0 -0.54 22 22
actin cytoskeleton organization 0.022 0.12 -10000 0 -0.42 17 17
GRB2 0.013 0.002 -10000 0 -10000 0 0
IL2 0.006 0.037 -10000 0 -0.57 2 2
PIK3CA 0.012 0.037 -10000 0 -0.47 3 3
Rac1/GTP 0.027 0.039 -10000 0 -0.25 8 8
LCK 0.005 0.078 -10000 0 -0.57 9 9
BCL2 0.001 0.21 -10000 0 -0.83 24 24
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.015 0.026 -9999 0 -0.28 4 4
ADCY5 -0.029 0.11 -9999 0 -0.28 80 80
ADCY6 0.018 0 -9999 0 -10000 0 0
ADCY7 0.017 0.017 -9999 0 -0.35 1 1
ADCY1 -0.017 0.11 -9999 0 -0.35 47 47
ADCY2 0.005 0.06 -9999 0 -0.28 21 21
ADCY3 0.017 0.013 -9999 0 -0.28 1 1
ADCY8 0.008 0.037 -9999 0 -0.35 5 5
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.016 0.018 -9999 0 -0.28 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.006 0.052 -9999 0 -0.26 4 4
Caspase cascade in apoptosis

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
TOP1 0.001 0.094 -10000 0 -0.33 25 25
ACTA1 -0.06 0.13 -10000 0 -0.39 49 49
NUMA1 0.001 0.094 -10000 0 -0.33 25 25
SPTAN1 -0.009 0.11 0.22 1 -0.42 24 25
LIMK1 -0.009 0.11 0.22 1 -0.42 24 25
BIRC3 0.005 0.066 -10000 0 -0.51 8 8
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.011 0.037 -10000 0 -0.57 2 2
CASP10 -0.015 0.13 -10000 0 -0.37 51 51
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.001 0.094 -10000 0 -0.32 28 28
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.008 0.11 0.21 1 -0.41 24 25
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN -0.011 0.12 0.22 1 -0.43 26 27
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.01 0.13 -10000 0 -0.57 25 25
BID 0.003 0.063 -10000 0 -0.18 47 47
MAP3K1 0.003 0.046 -10000 0 -0.23 7 7
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.012 0.12 0.22 1 -0.44 27 28
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.002 0.032 -10000 0 -0.16 4 4
neuron apoptosis 0.016 0.055 -10000 0 -0.66 3 3
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.11 -10000 0 -0.41 23 23
APAF1 0.013 0 -10000 0 -10000 0 0
CASP6 0.014 0.065 -10000 0 -0.3 5 5
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD -0.002 0.11 -10000 0 -0.53 12 12
CASP7 -0.004 0.037 0.26 8 -0.2 1 9
KRT18 0.012 0.026 -10000 0 -0.18 1 1
apoptosis 0.005 0.098 0.23 1 -0.45 12 13
DFFA -0.009 0.11 0.22 1 -0.42 24 25
DFFB -0.009 0.11 0.22 1 -0.42 24 25
PARP1 0.002 0.032 0.16 4 -10000 0 4
actin filament polymerization 0.002 0.11 0.4 23 -0.21 1 24
TNF -0.026 0.14 -10000 0 -0.5 37 37
CYCS 0.005 0.05 -10000 0 -0.2 13 13
SATB1 0.016 0.072 -10000 0 -0.33 7 7
SLK -0.009 0.11 0.22 1 -0.42 24 25
p15 BID/BAX 0.008 0.06 -10000 0 -0.27 11 11
CASP2 0.025 0.063 -10000 0 -0.34 4 4
JNK cascade -0.003 0.046 0.23 7 -10000 0 7
CASP3 -0.016 0.12 0.22 1 -0.35 46 47
LMNB2 0.027 0.054 -10000 0 -0.24 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.012 0.022 -10000 0 -0.47 1 1
Mammalian IAPs/DIABLO 0.03 0.038 -10000 0 -0.31 3 3
negative regulation of DNA binding -0.01 0.13 -10000 0 -0.56 25 25
stress fiber formation -0.008 0.11 0.21 1 -0.41 24 25
GZMB -0.021 0.14 -10000 0 -0.43 47 47
CASP1 0.005 0.064 -10000 0 -0.32 17 17
LMNB1 0.024 0.057 -10000 0 -0.26 5 5
APP 0.016 0.056 -10000 0 -0.67 3 3
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0 0.096 0.21 2 -0.35 22 24
LMNA 0.027 0.054 -10000 0 -0.24 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.024 0.057 -10000 0 -0.34 1 1
LRDD 0.001 0.082 -10000 0 -0.57 10 10
SREBF1 -0.01 0.12 0.22 1 -0.42 25 26
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.001 0.093 -10000 0 -0.33 25 25
CFL2 -0.003 0.11 -10000 0 -0.41 23 23
GAS2 -0.025 0.14 -10000 0 -0.38 45 45
positive regulation of apoptosis 0.029 0.056 -10000 0 -0.25 5 5
PRF1 0 0.082 -10000 0 -0.5 13 13
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.037 -9999 0 -0.57 2 2
alphaV beta3 Integrin -0.052 0.14 -9999 0 -0.33 101 101
PTK2 -0.042 0.092 -9999 0 -0.47 14 14
positive regulation of JNK cascade -0.014 0.052 -9999 0 -0.31 14 14
CDC42/GDP 0.025 0.084 -9999 0 -0.41 14 14
Rac1/GDP 0.027 0.083 -9999 0 -0.41 14 14
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.017 0.064 -9999 0 -0.38 14 14
nectin-3/I-afadin -0.014 0.11 -9999 0 -0.38 41 41
RAPGEF1 0.017 0.091 -9999 0 -0.46 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.1 -9999 0 -0.53 14 14
PDGFB-D/PDGFRB 0.011 0.037 -9999 0 -0.57 2 2
TLN1 0.014 0.049 -9999 0 -10000 0 0
Rap1/GTP -0.014 0.055 -9999 0 -0.32 14 14
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.026 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.014 0.11 -9999 0 -0.38 41 41
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.021 0.1 -9999 0 -0.51 14 14
MLLT4 0.013 0.001 -9999 0 -10000 0 0
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
PI3K 0.009 0.097 -9999 0 -0.5 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.015 0.055 -9999 0 -0.32 14 14
PVRL1 0.013 0 -9999 0 -10000 0 0
PVRL3 -0.032 0.15 -9999 0 -0.54 41 41
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
CDH1 0.011 0.03 -9999 0 -0.47 2 2
CLDN1 -0.042 0.15 -9999 0 -0.47 57 57
JAM-A/CLDN1 -0.022 0.12 -9999 0 -0.35 31 31
SRC 0.003 0.11 -9999 0 -0.59 14 14
ITGB3 -0.084 0.19 -9999 0 -0.47 101 101
nectin-1(dimer)/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
FARP2 0.016 0.097 -9999 0 -0.5 14 14
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.001 0.096 -9999 0 -0.32 41 41
nectin-1/I-afadin 0.02 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0.02 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.001 0.096 -9999 0 -0.32 41 41
CDC42/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.014 0.052 -9999 0 -0.31 14 14
alphaV/beta3 Integrin/Talin -0.02 0.11 -9999 0 -0.35 17 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
PIP5K1C 0.007 0.053 -9999 0 -0.2 7 7
VAV2 0.015 0.099 -9999 0 -0.51 14 14
RAP1/GDP -0.015 0.064 -9999 0 -0.38 14 14
ITGAV 0.01 0.037 -9999 0 -0.47 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.001 0.096 -9999 0 -0.32 41 41
nectin-3(dimer)/I-afadin/I-afadin -0.014 0.11 -9999 0 -0.38 41 41
Rac1/GTP -0.017 0.067 -9999 0 -0.39 14 14
PTPRM 0 0.059 -9999 0 -0.23 7 7
E-cadherin/beta catenin/alpha catenin -0.001 0.012 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.004 0.091 -9999 0 -0.49 1 1
Syndecan-3/Neurocan -0.003 0.079 -9999 0 -0.29 33 33
POMC -0.046 0.16 -9999 0 -0.48 60 60
EGFR -0.025 0.13 -9999 0 -0.47 40 40
Syndecan-3/EGFR 0.004 0.07 -9999 0 -0.53 1 1
AGRP 0.002 0.045 -9999 0 -0.57 3 3
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.028 0.14 -9999 0 -0.57 32 32
long-term memory 0.029 0.028 -9999 0 -0.49 1 1
Syndecan-3/IL8 -0.01 0.092 -9999 0 -0.29 25 25
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0.02 0 -9999 0 -10000 0 0
FYN 0.011 0.03 -9999 0 -0.47 2 2
limb bud formation -0.001 0.025 -9999 0 -0.55 1 1
MC4R -0.001 0.052 -9999 0 -0.57 4 4
SRC 0.013 0 -9999 0 -10000 0 0
PTN -0.073 0.19 -9999 0 -0.47 88 88
FGFR/FGF/Syndecan-3 -0.001 0.025 -9999 0 -0.56 1 1
neuron projection morphogenesis -0.028 0.11 -9999 0 -0.46 6 6
Syndecan-3/AgRP 0.008 0.036 -9999 0 -0.35 4 4
Syndecan-3/AgRP/MC4R -0.002 0.041 -9999 0 -0.31 7 7
Fyn/Cortactin 0.018 0.022 -9999 0 -0.32 2 2
SDC3 -0.001 0.025 -9999 0 -0.56 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.01 0.091 -9999 0 -0.29 25 25
IL8 -0.052 0.17 -9999 0 -0.51 62 62
Syndecan-3/Fyn/Cortactin 0.03 0.028 -9999 0 -0.5 1 1
Syndecan-3/CASK -0.001 0.024 -9999 0 -0.53 1 1
alpha-MSH/MC4R -0.033 0.12 -9999 0 -0.35 63 63
Gamma Secretase 0.04 0 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.009 0.096 -10000 0 -0.41 13 13
GRB2/SOS1/SHC 0.027 0 -10000 0 -10000 0 0
HRAS 0.006 0.064 -10000 0 -0.57 6 6
IRS1/Crk -0.009 0.097 -10000 0 -0.42 13 13
IGF-1R heterotetramer/IGF1/PTP1B -0.011 0.1 -10000 0 -0.29 56 56
AKT1 0.007 0.094 -10000 0 -0.38 15 15
BAD 0.012 0.09 -10000 0 -0.38 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.009 0.096 -10000 0 -0.41 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.1 -10000 0 -0.43 13 13
RAF1 0.018 0.086 -10000 0 -0.56 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.001 0.093 -10000 0 -0.39 13 13
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.018 0.1 -10000 0 -0.29 56 56
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
RPS6KB1 0.007 0.094 -10000 0 -0.38 15 15
GNB2L1 0.009 0.052 -10000 0 -0.57 4 4
positive regulation of MAPKKK cascade 0.014 0.076 -10000 0 -0.47 2 2
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
HRAS/GTP -0.028 0.078 -10000 0 -0.37 13 13
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.01 0.083 -10000 0 -0.44 2 2
IGF-1R heterotetramer 0.003 0.044 -10000 0 -0.58 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.098 -10000 0 -0.26 56 56
Crk/p130 Cas/Paxillin 0.006 0.089 -10000 0 -0.37 13 13
IGF1R 0.003 0.044 -10000 0 -0.59 2 2
IGF1 -0.047 0.17 -10000 0 -0.52 56 56
IRS2/Crk -0.005 0.1 -10000 0 -0.38 18 18
PI3K -0.003 0.1 -10000 0 -0.43 15 15
apoptosis -0.019 0.081 0.33 10 -10000 0 10
HRAS/GDP 0.005 0.047 -10000 0 -0.42 6 6
PRKCD 0.001 0.11 -10000 0 -0.35 37 37
RAF1/14-3-3 E 0.025 0.077 -10000 0 -0.47 2 2
BAD/14-3-3 0.02 0.085 -10000 0 -0.35 10 10
PRKCZ 0.007 0.094 -10000 0 -0.38 15 15
Crk/p130 Cas/Paxillin/FAK1 -0.023 0.067 -10000 0 -0.46 3 3
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.006 0.12 -10000 0 -0.36 41 41
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.002 0.089 -10000 0 -0.38 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.009 0.097 -10000 0 -0.26 56 56
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.01 0.099 -10000 0 -0.43 13 13
IRS1 -0.018 0.1 -10000 0 -0.29 56 56
IRS2 -0.013 0.1 -10000 0 -0.41 18 18
IGF-1R heterotetramer/IGF1 -0.028 0.13 -10000 0 -0.39 56 56
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 0 0.099 -10000 0 -0.4 15 15
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 0 0.11 -10000 0 -0.35 37 37
SHC1 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.01 0.037 -10000 0 -0.47 3 3
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.056 0.42 8 -10000 0 8
CDKN1A -0.006 0.066 -10000 0 -0.53 7 7
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.011 0.037 -10000 0 -0.57 2 2
FOXO3 0.002 0.03 0.38 3 -10000 0 3
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.019 0.025 -10000 0 -0.25 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT -0.024 0.13 -10000 0 -0.57 28 28
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.001 0.072 -10000 0 -0.39 16 16
PPARGC1A -0.13 0.22 -10000 0 -0.47 151 151
FHL2 -0.011 0.1 -10000 0 -0.47 25 25
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.018 0.012 -10000 0 -10000 0 0
HIST2H4A 0.013 0.056 -10000 0 -0.42 8 8
SIRT1/FOXO3a 0.003 0.024 0.26 3 -10000 0 3
SIRT1 0.011 0.018 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.025 0.011 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.028 0.079 -10000 0 -10000 0 0
apoptosis -0.023 0.026 0.35 2 -10000 0 2
SIRT1/PGC1A -0.072 0.13 -10000 0 -0.27 151 151
p53/SIRT1 0.001 0.053 0.33 7 -0.33 6 13
SIRT1/FOXO4 0.021 0.025 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.011 0.058 -10000 0 -10000 0 0
HIST1H1E -0.04 0.093 -10000 0 -0.25 6 6
SIRT1/p300 0.016 0.029 -10000 0 -0.33 3 3
muscle cell differentiation -0.006 0.062 0.33 16 -10000 0 16
TP53 0.005 0.055 -10000 0 -0.47 6 6
KU70/SIRT1/BAX 0.024 0.026 -10000 0 -0.35 2 2
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.012 0.098 -10000 0 -0.41 28 28
ACSS2 0.02 0.011 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.006 0.062 -10000 0 -0.33 16 16
IL1-mediated signaling events

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.014 0.005 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.013 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.072 -10000 0 -0.28 11 11
IRAK/TOLLIP 0.026 0.015 -10000 0 -0.31 1 1
IKBKB 0.013 0 -10000 0 -10000 0 0
IKBKG 0.013 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.057 0.14 -10000 0 -0.33 104 104
IL1A 0.001 0.058 -10000 0 -0.52 6 6
IL1B -0.045 0.15 -10000 0 -0.38 81 81
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.019 -10000 0 -10000 0 0
IL1R2 -0.082 0.19 -10000 0 -0.47 98 98
IL1R1 0.011 0.03 -10000 0 -0.47 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.063 0.19 1 -10000 0 1
TOLLIP 0.013 0 -10000 0 -10000 0 0
TICAM2 0.006 0.057 -10000 0 -0.47 7 7
MAP3K3 0.013 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.009 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.059 0.01 -10000 0 -10000 0 0
JUN 0.023 0.063 -10000 0 -0.39 2 2
MAP3K7 0.013 0.001 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.12 -10000 0 -0.46 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88 0.024 0.047 -10000 0 -0.35 4 4
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.03 0.044 -10000 0 -0.32 4 4
IL1 beta fragment/IL1R1/IL1RAP -0.022 0.12 -10000 0 -0.36 33 33
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.021 0.056 -10000 0 -10000 0 0
IRAK1 0.02 0.017 -10000 0 -0.35 1 1
IL1RN/IL1R1 -0.004 0.09 -10000 0 -0.34 32 32
IRAK4 0.013 0 -10000 0 -10000 0 0
PRKCI 0.012 0.026 -10000 0 -0.57 1 1
TRAF6 0.013 0 -10000 0 -10000 0 0
PI3K 0.014 0.049 -10000 0 -0.36 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.081 -10000 0 -0.3 11 11
CHUK 0.013 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.022 0.12 -10000 0 -0.36 33 33
IL1 beta/IL1R2 -0.087 0.18 -10000 0 -0.47 49 49
IRAK/TRAF6/TAK1/TAB1/TAB2 0.028 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.04 0.093 -10000 0 -0.41 13 13
IRAK3 -0.013 0.11 -10000 0 -0.47 27 27
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.009 0.12 -10000 0 -0.42 11 11
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.027 0.038 -10000 0 -0.43 1 1
IL1 alpha/IL1R1/IL1RAP 0.016 0.051 -10000 0 -0.31 11 11
RELA 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
MYD88 0.013 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.034 0.015 -10000 0 -10000 0 0
IL1RAP 0.009 0.043 -10000 0 -0.47 4 4
UBE2N 0.013 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.036 0.081 -10000 0 -0.36 12 12
CASP1 -0.003 0.087 -10000 0 -0.47 17 17
IL1RN/IL1R2 -0.069 0.16 -10000 0 -0.35 118 118
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.012 0.12 -10000 0 -0.34 33 33
TMEM189-UBE2V1 0.005 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.034 0.036 -10000 0 -0.37 2 2
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
IL1RN -0.017 0.12 -10000 0 -0.49 30 30
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 0.022 0.047 -10000 0 -0.27 11 11
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.054 0.23 12 -0.41 1 13
DAPP1 -0.029 0.13 -10000 0 -0.39 40 40
Src family/SYK family/BLNK-LAT/BTK-ITK -0.009 0.14 -10000 0 -0.49 18 18
mol:DAG 0.018 0.082 0.18 10 -0.25 15 25
HRAS 0.007 0.064 -10000 0 -0.57 6 6
RAP1A 0.014 0.003 -10000 0 -10000 0 0
ARF5/GDP 0.031 0.055 -10000 0 -0.38 4 4
PLCG2 0.003 0.071 -10000 0 -0.49 10 10
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.049 0.22 12 -0.44 1 13
ARF1/GTP 0.034 0.05 0.22 12 -0.42 1 13
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0.025 0.048 0.21 12 -0.44 1 13
ADAP1 -0.001 0.053 0.21 12 -0.4 2 14
ARAP3 0 0.048 0.22 12 -0.44 1 13
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.011 0.03 -10000 0 -0.47 2 2
ARHGEF6 0.012 0.022 -10000 0 -0.47 1 1
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0.022 -10000 0 -0.47 1 1
FYN 0.011 0.03 -10000 0 -0.47 2 2
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.01 0.04 -10000 0 -0.5 3 3
mol:Ca2+ 0.016 0.043 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.009 0.043 -10000 0 -0.47 4 4
ZAP70 -0.051 0.18 -10000 0 -0.57 55 55
mol:IP3 0.018 0.057 -10000 0 -0.2 3 3
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.031 0.055 -10000 0 -0.35 5 5
RhoA/GDP -0.002 0.049 0.22 9 -0.34 2 11
PDK1/Src/Hsp90 0.027 0 -10000 0 -10000 0 0
BLNK 0.012 0.022 -10000 0 -0.47 1 1
actin cytoskeleton reorganization 0.048 0.064 0.22 9 -0.39 4 13
SRC 0.013 0 -10000 0 -10000 0 0
PLEKHA2 -0.002 0.11 -10000 0 -0.38 35 35
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.073 -10000 0 -0.44 13 13
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0.001 0.048 0.23 12 -0.41 1 13
RhoA/GTP 0.03 0.046 0.21 12 -0.42 1 13
Src family/SYK family/BLNK-LAT -0.013 0.12 -10000 0 -0.44 19 19
BLK -0.1 0.22 -10000 0 -0.5 112 112
PDPK1 0.013 0 -10000 0 -10000 0 0
CYTH1 0.001 0.047 0.21 12 -0.42 1 13
HCK 0.008 0.05 -10000 0 -0.49 5 5
CYTH3 -0.002 0.054 0.21 12 -0.42 1 13
CYTH2 0.001 0.047 0.21 12 -0.42 1 13
KRAS 0.014 0.003 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.025 0.16 -10000 0 -0.41 67 67
SGK1 -0.064 0.16 -10000 0 -0.44 72 72
INPP5D -0.014 0.11 -10000 0 -0.47 28 28
mol:GDP 0.025 0.057 -10000 0 -0.34 6 6
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.006 0.059 -10000 0 -0.48 7 7
ARF6/GDP -0.002 0.049 0.23 9 -0.34 2 11
mol:PI-3-4-5-P3 0.001 0.053 0.26 12 -0.44 1 13
ARAP3/RAP1A/GTP 0.025 0.048 0.21 12 -0.44 1 13
VAV1 -0.011 0.11 -10000 0 -0.47 25 25
mol:PI-3-4-P2 0.002 0.08 -10000 0 -0.32 28 28
RAS family/GTP/PI3K Class I 0.024 0.04 -10000 0 -0.45 1 1
PLEKHA1 0.01 0.067 -10000 0 -0.27 28 28
Rac1/GDP 0.031 0.055 -10000 0 -0.38 4 4
LAT -0.004 0.098 -10000 0 -0.56 15 15
Rac1/GTP 0.026 0.063 -10000 0 -0.39 6 6
ITK -0.021 0.087 0.21 12 -0.51 2 14
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.016 0.11 0.21 10 -0.35 18 28
LCK 0.003 0.078 -10000 0 -0.57 9 9
BTK -0.006 0.061 0.21 12 -0.42 1 13
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.21 -9999 0 -0.48 63 63
RAD9A 0.01 0.045 -9999 0 -0.57 3 3
AP1 -0.053 0.15 -9999 0 -0.36 91 91
IFNAR2 0.01 0.007 -9999 0 -10000 0 0
AKT1 0.004 0.042 -9999 0 -0.22 2 2
ER alpha/Oestrogen -0.004 0.064 -9999 0 -0.34 17 17
NFX1/SIN3/HDAC complex 0.031 0.024 -9999 0 -10000 0 0
EGF -0.06 0.19 -9999 0 -0.54 65 65
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.015 0.019 -9999 0 -0.32 1 1
TERT/c-Abl -0.11 0.2 -9999 0 -0.45 60 60
SAP18 0.013 0.002 -9999 0 -10000 0 0
MRN complex 0.027 0 -9999 0 -10000 0 0
WT1 -0.21 0.28 -9999 0 -0.56 192 192
WRN 0.012 0.022 -9999 0 -0.47 1 1
SP1 0.011 0.008 -9999 0 -10000 0 0
SP3 0.011 0.004 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.12 0.16 -9999 0 -0.46 22 22
Mad/Max 0.015 0.01 -9999 0 -10000 0 0
TERT -0.12 0.21 -9999 0 -0.49 63 63
CCND1 -0.1 0.19 -9999 0 -0.51 15 15
MAX 0.012 0.004 -9999 0 -10000 0 0
RBBP7 0.013 0.002 -9999 0 -10000 0 0
RBBP4 0.012 0.022 -9999 0 -0.47 1 1
TERF2 0.012 0.003 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0.002 -9999 0 -10000 0 0
Telomerase/911 0.018 0.035 -9999 0 -10000 0 0
CDKN1B -0.003 0.11 -9999 0 -0.36 42 42
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.013 0.002 -9999 0 -10000 0 0
TRF2/PARP2 0.02 0.003 -9999 0 -10000 0 0
UBE3A 0.012 0.003 -9999 0 -10000 0 0
JUN 0.005 0.06 -9999 0 -0.5 7 7
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.008 0.006 -9999 0 -10000 0 0
FOS -0.077 0.19 -9999 0 -0.48 91 91
IFN-gamma/IRF1 -0.019 0.13 -9999 0 -0.44 42 42
PARP2 0.013 0 -9999 0 -10000 0 0
BLM -0.016 0.13 -9999 0 -0.57 25 25
Telomerase -0.005 0.045 -9999 0 -0.28 2 2
IRF1 0.001 0.093 -9999 0 -0.57 13 13
ESR1 -0.004 0.089 -9999 0 -0.48 17 17
KU/TER 0.02 0 -9999 0 -10000 0 0
ATM/TRF2 0.02 0.014 -9999 0 -0.3 1 1
ubiquitin-dependent protein catabolic process 0.036 0.025 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.035 0.026 -9999 0 -10000 0 0
HDAC1 0.013 0.002 -9999 0 -10000 0 0
HDAC2 0.01 0.023 -9999 0 -0.47 1 1
ATM -0.001 0.017 -9999 0 -0.38 1 1
SMAD3 0.022 0.016 -9999 0 -0.33 1 1
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.012 0.004 -9999 0 -10000 0 0
MRE11A 0.013 0 -9999 0 -10000 0 0
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.09 0.19 -9999 0 -0.49 21 21
NR2F2 0.017 0.008 -9999 0 -10000 0 0
MAPK3 0.01 0.028 -9999 0 -0.41 2 2
MAPK1 0.01 0.028 -9999 0 -0.41 2 2
TGFB1/TGF beta receptor Type II 0.013 0.022 -9999 0 -0.47 1 1
NFKB1 0.013 0 -9999 0 -10000 0 0
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.017 -9999 0 -0.38 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR -0.027 0.13 -9999 0 -0.47 40 40
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.064 0.16 -9999 0 -0.38 101 101
MYC -0.036 0.16 -9999 0 -0.58 39 39
IL2 0 0.038 -9999 0 -0.57 2 2
KU 0.02 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.013 0.022 -9999 0 -0.47 1 1
TRF2/BLM -0.001 0.088 -9999 0 -0.38 25 25
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.1 0.2 -9999 0 -0.47 43 43
SP1/HDAC2 0.015 0.021 -9999 0 -0.32 1 1
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.12 0.16 -9999 0 -0.46 22 22
Smad3/Myc -0.002 0.1 -9999 0 -0.34 40 40
911 complex 0.025 0.029 -9999 0 -0.35 3 3
IFNG -0.025 0.14 -9999 0 -0.57 33 33
Telomerase/PinX1 -0.12 0.16 -9999 0 -0.46 22 22
Telomerase/AKT1/mTOR/p70S6K -0.003 0.061 -9999 0 -10000 0 0
SIN3B 0.013 0.002 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.12 0.16 -9999 0 -0.46 22 22
response to DNA damage stimulus 0.003 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.039 0.002 -9999 0 -10000 0 0
TRF2/WRN 0.019 0.015 -9999 0 -0.3 1 1
Telomerase/hnRNP C1/C2 -0.12 0.16 -9999 0 -0.46 23 23
E2F1 -0.017 0.12 -9999 0 -0.58 23 23
ZNFX1 0.013 0.002 -9999 0 -10000 0 0
PIF1 0.004 0.072 -9999 0 -0.56 8 8
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.064 -9999 0 -0.54 6 6
VEGFR1 homodimer/NRP1 0.014 0.064 -9999 0 -0.54 6 6
mol:DAG -0.005 0.1 -9999 0 -0.48 6 6
VEGFR1 homodimer/NRP1/VEGFR 121 0.005 0.096 -9999 0 -0.5 10 10
CaM/Ca2+ 0.003 0.099 -9999 0 -0.52 4 4
HIF1A 0.016 0.04 -9999 0 -0.34 5 5
GAB1 0.012 0.022 -9999 0 -0.47 1 1
AKT1 0.009 0.11 -9999 0 -0.49 7 7
PLCG1 -0.005 0.1 -9999 0 -0.48 6 6
NOS3 0.014 0.1 -9999 0 -0.5 4 4
CBL 0.012 0.022 -9999 0 -0.47 1 1
mol:NO 0.015 0.1 -9999 0 -0.48 4 4
FLT1 0.021 0.073 -9999 0 -0.58 7 7
PGF -0.05 0.16 -9999 0 -0.47 65 65
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.12 -9999 0 -0.56 10 10
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
eNOS/Hsp90 0.021 0.099 -9999 0 -0.46 4 4
endothelial cell proliferation -0.056 0.19 -9999 0 -0.51 57 57
mol:Ca2+ -0.005 0.1 -9999 0 -0.48 6 6
MAPK3 -0.002 0.12 -9999 0 -0.48 13 13
MAPK1 -0.002 0.12 -9999 0 -0.48 13 13
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
PLGF homodimer -0.05 0.16 -9999 0 -0.47 65 65
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.049 0.16 -9999 0 -0.47 64 64
VEGFA homodimer -0.018 0.12 -9999 0 -0.48 31 31
VEGFR1 homodimer/VEGFA homodimer 0.005 0.1 -9999 0 -0.54 10 10
platelet activating factor biosynthetic process 0.004 0.11 -9999 0 -0.46 13 13
PI3K 0 0.11 -9999 0 -0.52 7 7
PRKCA -0.009 0.12 -9999 0 -0.51 13 13
PRKCB -0.054 0.16 -9999 0 -0.45 47 47
VEGFR1 homodimer/PLGF homodimer -0.015 0.12 -9999 0 -0.49 8 8
VEGFA -0.018 0.12 -9999 0 -0.48 31 31
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.005 0.1 -9999 0 -0.48 6 6
RASA1 0.029 0.061 -9999 0 -0.48 6 6
NRP2 -0.02 0.12 -9999 0 -0.47 34 34
VEGFR1 homodimer 0.021 0.073 -9999 0 -0.57 7 7
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.012 0.026 -9999 0 -0.57 1 1
eNOS/Caveolin-1 -0.006 0.14 -9999 0 -0.42 32 32
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
mol:PI-3-4-5-P3 -0.001 0.11 -9999 0 -0.51 7 7
mol:L-citrulline 0.015 0.1 -9999 0 -0.48 4 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.021 0.094 -9999 0 -0.6 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.013 0.098 -9999 0 -0.47 11 11
CD2AP 0.013 0.001 -9999 0 -10000 0 0
PI3K/GAB1 0.006 0.1 -9999 0 -0.49 7 7
PDPK1 0.005 0.1 -9999 0 -0.48 7 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.013 0.099 -9999 0 -0.6 7 7
mol:NADP 0.015 0.1 -9999 0 -0.48 4 4
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.02 0.093 -9999 0 -0.59 6 6
VEGFR1 homodimer/NRP2 0.004 0.098 -9999 0 -0.53 7 7
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.013 0.022 -9999 0 -0.47 1 1
GNB1/GNG2 0.017 0.034 -9999 0 -0.27 6 6
forebrain development -0.038 0.13 -9999 0 -0.45 9 9
GNAO1 -0.081 0.19 -9999 0 -0.47 96 96
SMO/beta Arrestin2 0.016 0.011 -9999 0 -10000 0 0
SMO 0.01 0.007 -9999 0 -10000 0 0
ARRB2 0.01 0.006 -9999 0 -10000 0 0
GLI3/SPOP 0.033 0.065 -9999 0 -0.52 2 2
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.012 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.036 0.004 -9999 0 -10000 0 0
GNAI1 0.005 0.064 -9999 0 -0.53 7 7
XPO1 0.011 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.029 0.12 -9999 0 -0.42 2 2
SAP30 0.014 0.001 -9999 0 -10000 0 0
mol:GDP 0.01 0.007 -9999 0 -10000 0 0
MIM/GLI2A -0.007 0.06 -9999 0 -0.55 3 3
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.012 0.003 -9999 0 -10000 0 0
GLI2 0.035 0.037 -9999 0 -10000 0 0
GLI3 0.027 0.068 -9999 0 -0.56 2 2
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.007 0.052 -9999 0 -0.47 6 6
Gi family/GTP -0.045 0.15 -9999 0 -0.37 67 67
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.046 0.051 -9999 0 -0.38 2 2
GLI2/Su(fu) 0.036 0.04 -9999 0 -10000 0 0
FOXA2 -0.29 0.45 -9999 0 -1 141 141
neural tube patterning -0.038 0.13 -9999 0 -0.45 9 9
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.014 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.006 0.06 -9999 0 -0.55 3 3
embryonic limb morphogenesis -0.038 0.13 -9999 0 -0.45 9 9
SUFU 0.021 0.014 -9999 0 -10000 0 0
LGALS3 -0.024 0.13 -9999 0 -0.47 39 39
catabolic process 0.052 0.072 -9999 0 -0.49 2 2
GLI3A/CBP 0.014 0.038 -9999 0 -0.29 7 7
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.039 0.13 -9999 0 -0.46 9 9
RAB23 0.011 0.03 -9999 0 -0.47 2 2
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.008 0.071 -9999 0 -10000 0 0
GNAZ -0.035 0.14 -9999 0 -0.47 49 49
RBBP4 0.013 0.022 -9999 0 -0.47 1 1
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.012 0.022 -9999 0 -0.47 1 1
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.04 0.035 -9999 0 -10000 0 0
STK36 0.011 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.033 0.14 -9999 0 -0.41 46 46
PTCH1 -0.027 0.12 -9999 0 -0.49 4 4
MIM/GLI1 -0.099 0.24 -9999 0 -0.45 143 143
CREBBP 0.014 0.038 -9999 0 -0.29 7 7
Su(fu)/SIN3/HDAC complex 0.049 0.014 -9999 0 -10000 0 0
TCGA08_rtk_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
PDGFRA -0.013 0.11 -10000 0 -0.47 27 27
HRAS 0.006 0.064 -10000 0 -0.57 6 6
EGFR -0.025 0.13 -10000 0 -0.47 40 40
AKT 0.035 0.029 -10000 0 -0.41 1 1
FOXO3 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.012 0.022 -10000 0 -0.47 1 1
FOXO4 0.012 0.022 -10000 0 -0.47 1 1
MET -0.036 0.15 -10000 0 -0.47 51 51
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
PIK3CB 0.012 0.026 -10000 0 -0.57 1 1
NRAS 0.012 0.022 -10000 0 -0.47 1 1
PIK3CG -0.029 0.14 -10000 0 -0.48 43 43
PIK3R3 0.013 0 -10000 0 -10000 0 0
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.014 0.097 -10000 0 -0.34 28 28
ERBB2 0.008 0.05 -10000 0 -0.49 5 5
proliferation/survival/translation -0.024 0.04 0.22 4 -10000 0 4
PI3K -0.008 0.11 0.17 5 -0.32 40 45
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.043 0.024 0.15 5 -10000 0 5
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.001 0.077 -10000 0 -0.47 13 13
TRAIL signaling pathway

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
TNFSF10 0.008 0.055 -10000 0 -0.53 5 5
positive regulation of NF-kappaB transcription factor activity -0.011 0.11 -10000 0 -0.36 40 40
MAP2K4 0.04 0.024 -10000 0 -10000 0 0
IKBKB 0.013 0 -10000 0 -10000 0 0
TNFRSF10B 0.013 0 -10000 0 -10000 0 0
TNFRSF10A 0.007 0.052 -10000 0 -0.47 6 6
SMPD1 0.017 0.019 -10000 0 -10000 0 0
IKBKG 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.024 0.13 -10000 0 -0.47 39 39
TRAIL/TRAILR2 0.016 0.04 -10000 0 -0.38 5 5
TRAIL/TRAILR3 -0.02 0.12 -10000 0 -0.34 55 55
TRAIL/TRAILR1 0.012 0.055 -10000 0 -0.35 11 11
TRAIL/TRAILR4 -0.011 0.11 -10000 0 -0.36 40 40
TRAIL/TRAILR1/DAP3/GTP 0.019 0.042 -10000 0 -0.32 3 3
IKK complex -0.002 0.012 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.01 0 -10000 0 -10000 0 0
MAPK3 0.017 0.04 -10000 0 -0.38 5 5
MAP3K1 0.035 0.025 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.024 0.13 -10000 0 -0.47 39 39
TRADD 0.013 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.007 0.052 -10000 0 -0.47 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.03 0.033 -10000 0 -10000 0 0
CFLAR 0.013 0 -10000 0 -10000 0 0
MAPK1 0.017 0.04 -10000 0 -0.38 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.034 0.04 -10000 0 -10000 0 0
mol:ceramide 0.017 0.019 -10000 0 -10000 0 0
FADD 0.013 0 -10000 0 -10000 0 0
MAPK8 0.039 0.047 -10000 0 -0.3 4 4
TRAF2 0.013 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.037 0.15 -10000 0 -0.47 52 52
CHUK 0.013 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.02 0.047 -10000 0 -0.35 3 3
DAP3 0.013 0 -10000 0 -10000 0 0
CASP10 0.01 0.072 0.24 33 -10000 0 33
JNK cascade -0.011 0.11 -10000 0 -0.36 40 40
TRAIL (trimer) 0.008 0.054 -10000 0 -0.53 5 5
TNFRSF10C -0.037 0.15 -10000 0 -0.47 52 52
TRAIL/TRAILR1/DAP3/GTP/FADD 0.026 0.04 -10000 0 -0.29 3 3
TRAIL/TRAILR2/FADD 0.024 0.034 -10000 0 -0.35 3 3
cell death 0.017 0.019 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.033 0.021 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.013 0 -10000 0 -10000 0 0
CASP8 0.001 0.011 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.037 0.03 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.049 0.025 -10000 0 -10000 0 0
NFATC2 0.006 0.067 -10000 0 -0.25 14 14
NFATC3 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.038 0.14 -10000 0 -0.4 44 44
Exportin 1/Ran/NUP214 0.026 0.006 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.065 0.13 -10000 0 -0.4 52 52
BCL2/BAX 0.002 0.077 -10000 0 -0.33 25 25
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.004 -10000 0 -10000 0 0
BAX 0.011 0.037 -10000 0 -0.57 2 2
MAPK14 0.013 0.002 -10000 0 -10000 0 0
BAD 0.012 0.026 -10000 0 -0.57 1 1
CABIN1/MEF2D -0.029 0.13 -10000 0 -0.38 44 44
Calcineurin A alpha-beta B1/BCL2 -0.009 0.1 -10000 0 -0.47 23 23
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.029 0.13 0.37 44 -10000 0 44
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.006 0.064 -10000 0 -0.57 6 6
XPO1 0.013 0 -10000 0 -10000 0 0
SFN -0.035 0.14 -10000 0 -0.47 50 50
MAP3K8 -0.001 0.084 -10000 0 -0.47 15 15
NFAT4/CK1 alpha 0.032 0.013 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.024 0.087 -10000 0 -0.4 5 5
CABIN1 -0.038 0.14 -10000 0 -0.41 44 44
CALM1 0.013 0.002 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.012 0.022 -10000 0 -0.47 1 1
CAMK4 -0.024 0.13 -10000 0 -0.47 38 38
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.011 0.059 -10000 0 -0.4 10 10
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.002 0.074 -10000 0 -0.47 12 12
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.055 0.034 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.018 0.027 -10000 0 -0.32 3 3
CASP3 0.013 0.001 -10000 0 -10000 0 0
PIM1 0.005 0.067 -10000 0 -0.56 7 7
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.002 -10000 0 -10000 0 0
apoptosis -0.006 0.025 -10000 0 -0.22 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.055 -10000 0 -10000 0 0
PRKCB -0.097 0.2 -10000 0 -0.47 114 114
PRKCE 0.013 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.028 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0.019 0.019 -10000 0 -0.41 1 1
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.003 -10000 0 -10000 0 0
PRKCA -0.009 0.1 -10000 0 -0.47 23 23
PRKCG -0.011 0.1 -10000 0 -0.57 16 16
PRKCQ -0.031 0.14 -10000 0 -0.49 44 44
FKBP38/BCL2 0.004 0.073 -10000 0 -0.32 23 23
EP300 0.011 0.037 -10000 0 -0.47 3 3
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.048 0.042 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.019 0.004 -10000 0 -10000 0 0
FKBP12/FK506 0.01 0 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.004 0.078 -10000 0 -0.28 38 38
NFATc/ERK1 0.054 0.024 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.065 0.13 -10000 0 -0.4 53 53
NR4A1 0.017 0.12 -10000 0 -0.45 25 25
GSK3B 0.013 0.003 -10000 0 -10000 0 0
positive T cell selection 0.022 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.018 0.039 -10000 0 -0.27 1 1
RCH1/ KPNB1 0.015 0.047 -10000 0 -0.41 6 6
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0.001 -10000 0 -10000 0 0
AKAP5 0.002 0.08 -10000 0 -0.55 10 10
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.053 0.026 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
BCL2 -0.009 0.1 -10000 0 -0.47 23 23
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.001 -9999 0 -10000 0 0
SMARCC1 0.003 0.007 -9999 0 -10000 0 0
REL -0.034 0.14 -9999 0 -0.47 48 48
HDAC7 0.048 0.075 -9999 0 -10000 0 0
JUN 0.006 0.061 -9999 0 -0.5 7 7
EP300 0.01 0.037 -9999 0 -0.47 3 3
KAT2B 0.013 0 -9999 0 -10000 0 0
KAT5 0.013 0 -9999 0 -10000 0 0
MAPK14 0.014 0.069 -9999 0 -0.39 14 14
FOXO1 0.013 0 -9999 0 -10000 0 0
T-DHT/AR 0.05 0.081 -9999 0 -0.35 1 1
MAP2K6 -0.001 0.093 -9999 0 -0.55 14 14
BRM/BAF57 0.02 0.022 -9999 0 -0.32 2 2
MAP2K4 0.015 0.002 -9999 0 -10000 0 0
SMARCA2 0.012 0.03 -9999 0 -0.47 2 2
PDE9A -0.003 0.054 -9999 0 -0.97 1 1
NCOA2 -0.044 0.16 -9999 0 -0.47 60 60
CEBPA 0.013 0.001 -9999 0 -10000 0 0
EHMT2 0.014 0.002 -9999 0 -10000 0 0
cell proliferation 0.064 0.094 -9999 0 -0.42 5 5
NR0B1 -0.002 0.063 -9999 0 -0.57 6 6
EGR1 -0.056 0.18 -9999 0 -0.51 66 66
RXRs/9cRA -0.039 0.12 -9999 0 -0.24 120 120
AR/RACK1/Src 0.037 0.086 -9999 0 -0.49 5 5
AR/GR 0.005 0.11 -9999 0 -0.45 15 15
GNB2L1 0.009 0.052 -9999 0 -0.57 4 4
PKN1 0.004 0.074 -9999 0 -0.57 8 8
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 0.017 0.054 -9999 0 -0.33 12 12
T-DHT/AR/TIF2/CARM1 0.013 0.13 -9999 0 -0.48 15 15
SRC 0.031 0.064 -9999 0 -0.33 1 1
NR3C1 0.001 0.077 -9999 0 -0.47 13 13
KLK3 0.013 0.14 -9999 0 -1.1 7 7
APPBP2 0.015 0.002 -9999 0 -10000 0 0
TRIM24 0.014 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.028 0.077 -9999 0 -0.32 13 13
TMPRSS2 -0.011 0.11 -9999 0 -0.98 6 6
RXRG -0.1 0.21 -9999 0 -0.47 120 120
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.001 -9999 0 -10000 0 0
NR2C2 -0.002 0.085 -9999 0 -0.47 16 16
KLK2 0.025 0.13 -9999 0 -0.5 15 15
AR 0.008 0.1 -9999 0 -0.42 15 15
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.012 0.004 -9999 0 -10000 0 0
SRY 0.003 0.027 -9999 0 -0.57 1 1
GATA2 0.012 0.026 -9999 0 -0.57 1 1
MYST2 0.013 0.001 -9999 0 -10000 0 0
HOXB13 0.014 0.004 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.034 0.086 -9999 0 -0.48 5 5
positive regulation of transcription 0.012 0.026 -9999 0 -0.57 1 1
DNAJA1 0.015 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.001 -9999 0 -10000 0 0
NCOA1 0.017 0.003 -9999 0 -10000 0 0
SPDEF 0.014 0.026 -9999 0 -0.57 1 1
T-DHT/AR/TIF2 0.015 0.12 -9999 0 -0.44 18 18
T-DHT/AR/Hsp90 0.028 0.077 -9999 0 -0.32 13 13
GSK3B 0.014 0.001 -9999 0 -10000 0 0
NR2C1 0.013 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.025 0.068 -9999 0 -0.3 11 11
SIRT1 0.013 0 -9999 0 -10000 0 0
ZMIZ2 0.012 0.004 -9999 0 -10000 0 0
POU2F1 0.025 0.029 -9999 0 -0.56 1 1
T-DHT/AR/DAX-1 0.019 0.085 -9999 0 -0.35 13 13
CREBBP 0.013 0 -9999 0 -10000 0 0
SMARCE1 0.014 0.002 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.016 0.11 -9999 0 -0.47 30 30
Caspase 8 (4 units) 0.023 0.065 -9999 0 -0.38 3 3
NEF -0.004 0.036 -9999 0 -10000 0 0
NFKBIA 0.015 0.013 -9999 0 -10000 0 0
BIRC3 0.032 0.068 -9999 0 -0.5 8 8
CYCS 0.026 0.069 -9999 0 -0.44 2 2
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.017 0.13 -9999 0 -0.61 22 22
MAP2K7 0.03 0.066 -9999 0 -0.55 2 2
protein ubiquitination 0.05 0.053 -9999 0 -0.35 2 2
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.003 0.071 -9999 0 -0.47 11 11
BID 0.02 0.073 -9999 0 -0.41 3 3
NF-kappa-B/RelA/I kappa B alpha 0.033 0.036 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.01 0.04 -9999 0 -0.5 3 3
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.033 0.036 -9999 0 -10000 0 0
MAPK8 0.03 0.074 -9999 0 -0.6 2 2
APAF1 0.013 0 -9999 0 -10000 0 0
TRAF1 0.012 0.026 -9999 0 -0.57 1 1
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.014 0.076 -9999 0 -0.28 14 14
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.041 0.063 -9999 0 -0.39 4 4
CHUK 0.051 0.055 -9999 0 -0.38 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.032 0.045 -9999 0 -0.45 1 1
TCRz/NEF -0.016 0.12 -9999 0 -0.39 42 42
TNF -0.026 0.14 -9999 0 -0.5 37 37
FASLG -0.021 0.16 -9999 0 -0.53 42 42
NFKB1 0.015 0.013 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.015 0.11 -9999 0 -0.3 64 64
CASP6 0.039 0.052 -9999 0 -0.5 1 1
CASP7 0.057 0.081 -9999 0 -0.49 6 6
RELA 0.015 0.013 -9999 0 -10000 0 0
CASP2 0.007 0.057 -9999 0 -0.47 7 7
CASP3 0.058 0.08 -9999 0 -0.49 6 6
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.082 -9999 0 -0.32 30 30
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.046 0.06 -9999 0 -0.38 3 3
APAF-1/Caspase 9 -0.014 0.055 -9999 0 -0.44 4 4
BCL2 0.026 0.089 -9999 0 -0.39 10 10
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.028 0.015 -9999 0 -10000 0 0
epithelial cell differentiation 0.028 0.016 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.038 0.055 -9999 0 -10000 0 0
EGFR -0.025 0.13 -9999 0 -0.47 40 40
EPHA2 -0.037 0.15 -9999 0 -0.47 51 51
MYO6 0.001 0.096 -9999 0 -0.28 51 51
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0.027 0 -9999 0 -10000 0 0
AQP5 -0.18 0.2 -9999 0 -0.4 219 219
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.015 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.022 0.053 -9999 0 -0.27 3 3
EGF -0.058 0.19 -9999 0 -0.53 65 65
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.013 0.069 -9999 0 -0.4 15 15
cortical microtubule organization 0.028 0.016 -9999 0 -10000 0 0
GO:0000145 0.031 0.014 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.016 -9999 0 -10000 0 0
MLLT4 0.013 0.001 -9999 0 -10000 0 0
ARF6/GDP -0.018 0.051 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.006 0.084 -9999 0 -0.31 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.03 0.045 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.033 0.015 -9999 0 -10000 0 0
ARF6/GTP 0.011 0.078 -9999 0 -0.28 4 4
CDH1 0.011 0.03 -9999 0 -0.47 2 2
EGFR/EGFR/EGF/EGF -0.047 0.094 -9999 0 -0.41 4 4
RhoA/GDP -0.001 0.013 -9999 0 -10000 0 0
actin cytoskeleton organization -0.005 0.1 -9999 0 -0.46 3 3
IGF-1R heterotetramer 0.011 0.034 -9999 0 -0.52 2 2
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.011 0.034 -9999 0 -0.52 2 2
IGF1 -0.045 0.16 -9999 0 -0.5 56 56
DIAPH1 0.002 0.005 -9999 0 -10000 0 0
Wnt receptor signaling pathway -0.028 0.016 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.018 0.05 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL -0.005 0.1 -9999 0 -0.47 3 3
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.02 0.064 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.021 0.06 -9999 0 -10000 0 0
SEC6/SEC8 -0.001 0.011 -9999 0 -10000 0 0
MGAT3 0.022 0.053 -9999 0 -0.27 3 3
HGF/MET -0.037 0.097 -9999 0 -0.41 18 18
HGF -0.026 0.14 -9999 0 -0.5 38 38
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.028 0.015 -9999 0 -10000 0 0
actin cable formation 0.05 0.052 -9999 0 -10000 0 0
KIAA1543 0.038 0.018 -9999 0 -10000 0 0
KIFC3 0.031 0.028 -9999 0 -10000 0 0
NCK1 0.012 0.026 -9999 0 -0.57 1 1
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.031 0.03 -9999 0 -10000 0 0
NCK1/GIT1 0.019 0.019 -9999 0 -0.41 1 1
mol:GDP 0.028 0.016 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.033 0.015 -9999 0 -10000 0 0
PIP5K1C 0.033 0.015 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.034 0.062 -9999 0 -10000 0 0
adherens junction assembly 0.048 0.038 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.026 0.074 -9999 0 -0.48 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.02 0 -9999 0 -10000 0 0
MET -0.036 0.15 -9999 0 -0.47 51 51
PLEKHA7 0.033 0.018 -9999 0 -10000 0 0
mol:GTP 0.005 0.083 -9999 0 -0.31 4 4
establishment of epithelial cell apical/basal polarity 0.054 0.013 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.028 0.015 -9999 0 -10000 0 0
regulation of cell-cell adhesion -0.005 0.1 -9999 0 -0.46 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.028 0.015 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.012 0.021 -10000 0 -0.26 3 3
TRAF2/ASK1 0.016 0.025 -10000 0 -0.3 3 3
ATM 0.012 0.022 -10000 0 -0.47 1 1
MAP2K3 0.017 0.047 -10000 0 -0.32 3 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.013 0.062 -10000 0 -0.32 6 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.054 0.19 -10000 0 -0.57 57 57
TXN 0.008 0.011 -10000 0 -0.24 1 1
CALM1 0.013 0 -10000 0 -10000 0 0
GADD45A 0.011 0.03 -10000 0 -0.47 2 2
GADD45B -0.01 0.11 -10000 0 -0.57 20 20
MAP3K1 0.012 0.022 -10000 0 -0.47 1 1
MAP3K6 0.013 0 -10000 0 -10000 0 0
MAP3K7 0.013 0.001 -10000 0 -10000 0 0
MAP3K4 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.018 0.029 -10000 0 -0.36 3 3
TAK1/TAB family 0.002 0.017 0.14 8 -10000 0 8
RAC1/OSM/MEKK3 0.026 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.007 0.024 -10000 0 -0.29 1 1
TRAF6 0.008 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.025 0.14 -10000 0 -0.57 33 33
CCM2 0.013 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.006 0.091 -10000 0 -0.35 33 33
MAPK11 0.004 0.074 -10000 0 -0.57 8 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.002 0.088 -10000 0 -0.32 35 35
OSM/MEKK3 0.02 0 -10000 0 -10000 0 0
TAOK1 -0.041 0.12 -10000 0 -0.3 90 90
TAOK2 0.016 0.014 -10000 0 -0.3 1 1
TAOK3 0.015 0.018 -10000 0 -0.26 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.013 0.001 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.01 0.04 -10000 0 -0.5 3 3
MAP3K10 0.013 0 -10000 0 -10000 0 0
MAP3K3 0.013 0 -10000 0 -10000 0 0
TRX/ASK1 0.014 0.026 -10000 0 -0.27 4 4
GADD45/MTK1/MTK1 -0.018 0.14 -10000 0 -0.36 60 60
IFN-gamma pathway

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.016 0.075 -9999 0 -0.33 4 4
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.033 0.1 -9999 0 -0.52 9 9
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.023 0.024 -9999 0 -0.32 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.027 0.058 -9999 0 -0.25 16 16
CaM/Ca2+ 0.017 0.07 -9999 0 -0.32 3 3
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.016 0.093 -9999 0 -0.46 9 9
AKT1 0.027 0.074 -9999 0 -0.71 1 1
MAP2K1 0.027 0.071 -9999 0 -0.57 1 1
MAP3K11 0.02 0.071 -9999 0 -0.33 3 3
IFNGR1 0.013 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.065 0.14 -9999 0 -0.34 85 85
Rap1/GTP -0.012 0.046 -9999 0 -0.45 1 1
CRKL/C3G 0.02 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.019 0.078 -9999 0 -0.29 2 2
CEBPB 0.052 0.079 -9999 0 -0.44 3 3
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.019 0.11 -9999 0 -0.75 5 5
STAT1 0.014 0.092 -9999 0 -0.46 9 9
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.027 0.14 -9999 0 -0.57 33 33
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
STAT1 (dimer)/PIAS1 0.021 0.089 -9999 0 -0.44 9 9
CEBPB/PTGES2/Cbp/p300 -0.011 0.035 -9999 0 -0.34 1 1
mol:Ca2+ 0.014 0.074 -9999 0 -0.33 4 4
MAPK3 0.038 0.067 -9999 0 -0.58 1 1
STAT1 (dimer) -0.035 0.077 -9999 0 -0.35 15 15
MAPK1 0.038 0.067 -9999 0 -0.58 1 1
JAK2 0.012 0.024 -9999 0 -0.5 1 1
PIK3R1 0.008 0.052 -9999 0 -0.47 6 6
JAK1 0.013 0.008 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.047 0.08 -9999 0 -0.43 3 3
SMAD7 0.025 0.051 -9999 0 -10000 0 0
CBL/CRKL/C3G 0.031 0.069 -9999 0 -0.55 1 1
PI3K -0.019 0.068 -9999 0 -0.79 1 1
IFNG -0.027 0.14 -9999 0 -0.57 33 33
apoptosis 0.033 0.063 -9999 0 -0.33 3 3
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.085 0.2 -9999 0 -0.48 98 98
CAMK2B -0.025 0.14 -9999 0 -0.57 33 33
FRAP1 0.025 0.07 -9999 0 -0.65 1 1
PRKCD 0.028 0.076 -9999 0 -0.72 1 1
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.027 0.058 -9999 0 -0.25 16 16
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.011 0.037 -9999 0 -0.47 3 3
IRF1 0.034 0.12 -9999 0 -0.48 16 16
STAT1 (dimer)/PIASy 0.019 0.088 -9999 0 -0.44 9 9
SOCS1 -0.004 0.086 -9999 0 -0.74 5 5
mol:GDP 0.028 0.066 -9999 0 -0.52 1 1
CASP1 0.02 0.07 -9999 0 -0.27 17 17
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.045 0.032 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.019 0.066 -9999 0 -0.75 1 1
RAP1/GDP -0.012 0.047 -9999 0 -0.46 1 1
CBL 0.019 0.074 -9999 0 -0.4 3 3
MAP3K1 0.02 0.074 -9999 0 -0.4 3 3
PIAS1 0.012 0.022 -9999 0 -0.47 1 1
PIAS4 0.013 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.027 0.058 -9999 0 -0.25 16 16
PTPN11 0.013 0.073 -9999 0 -0.33 4 4
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.021 0 -10000 0 -10000 0 0
MAP4K4 0.029 0.055 -10000 0 -0.43 1 1
BAG4 -0.016 0.11 -10000 0 -0.47 30 30
PKC zeta/ceramide -0.008 0.026 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 0.005 0.066 -10000 0 -0.51 8 8
BAX -0.002 0.014 -10000 0 -0.12 2 2
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.018 0.005 -10000 0 -10000 0 0
BAD -0.01 0.029 -10000 0 -0.31 1 1
SMPD1 0.015 0.045 -10000 0 -0.22 1 1
RB1 -0.01 0.027 -10000 0 -0.24 1 1
FADD/Caspase 8 0.038 0.053 -10000 0 -0.41 1 1
MAP2K4 -0.003 0.026 -10000 0 -0.22 1 1
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.013 0.054 -10000 0 -0.25 21 21
EGF -0.058 0.19 -10000 0 -0.53 65 65
mol:ceramide -0.018 0.027 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0 -10000 0 -10000 0 0
ASAH1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.01 0.027 -10000 0 -0.24 1 1
cell proliferation -0.014 0.092 -10000 0 -0.38 12 12
BID 0.022 0.04 -10000 0 -0.28 1 1
MAP3K1 -0.01 0.027 -10000 0 -0.24 1 1
EIF2A 0.004 0.023 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.052 -10000 0 -0.26 7 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.052 -10000 0 -0.26 7 7
Cathepsin D/ceramide -0.008 0.026 -10000 0 -10000 0 0
FADD 0.029 0.055 -10000 0 -0.43 1 1
KSR1 -0.02 0.057 -10000 0 -0.26 21 21
MAPK8 -0.003 0.044 -10000 0 -0.24 12 12
PRKRA -0.009 0.025 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.045 0.16 -10000 0 -0.5 56 56
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.018 0.027 -10000 0 -10000 0 0
CTSD 0.013 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.02 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.014 0.099 -10000 0 -0.43 11 11
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0 -10000 0 -10000 0 0
RelA/NF kappa B1 0.02 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.023 0.058 -10000 0 -0.36 2 2
TNFR1A/BAG4/TNF-alpha -0.015 0.11 -10000 0 -0.3 64 64
mol:Sphingosine-1-phosphate 0.021 0 -10000 0 -10000 0 0
MAP2K1 -0.006 0.052 -10000 0 -0.27 7 7
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.002 0.035 0.15 18 -10000 0 18
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.082 -10000 0 -0.32 30 30
EIF2AK2 -0.003 0.024 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.003 0.085 -10000 0 -0.29 37 37
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.032 0.035 -10000 0 -0.23 1 1
MAP2K2 -0.006 0.054 -10000 0 -0.27 8 8
SMPD3 0.011 0.059 -10000 0 -0.27 7 7
TNF -0.026 0.14 -10000 0 -0.5 37 37
PKC zeta/PAR4 0.02 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.012 0.066 0.18 64 -10000 0 64
NF kappa B1/RelA/I kappa B alpha 0.04 0 -10000 0 -10000 0 0
AIFM1 0.002 0.035 0.15 18 -10000 0 18
BCL2 -0.009 0.1 -10000 0 -0.47 23 23
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.011 -10000 0 -10000 0 0
DOCK1 0.009 0.043 -10000 0 -0.47 4 4
ITGA4 -0.012 0.11 -10000 0 -0.52 24 24
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.014 0.12 -10000 0 -0.4 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.011 0.071 -10000 0 -0.3 24 24
alpha4/beta7 Integrin/Paxillin 0.006 0.095 -10000 0 -0.41 14 14
lamellipodium assembly -0.005 0.062 -10000 0 -0.45 8 8
PIK3CA 0.01 0.037 -10000 0 -0.47 3 3
PI3K 0.014 0.049 -10000 0 -0.36 8 8
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.021 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.052 -10000 0 -0.47 6 6
ARF6/GTP -0.011 0.048 -10000 0 -10000 0 0
cell adhesion 0.024 0.061 -10000 0 -0.28 11 11
CRKL/CBL 0.019 0.015 -10000 0 -0.32 1 1
alpha4/beta1 Integrin/Paxillin 0.018 0.065 -10000 0 -0.31 11 11
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.009 0.1 -10000 0 -0.48 22 22
ARF6/GDP 0.002 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.017 0.088 -10000 0 -0.36 17 17
p130Cas/Crk/Dock1 0.025 0.026 -10000 0 -0.27 4 4
VCAM1 -0.003 0.094 -10000 0 -0.53 15 15
alpha4/beta1 Integrin/Paxillin/Talin 0.026 0.062 -10000 0 -0.28 11 11
alpha4/beta1 Integrin/Paxillin/GIT1 0.026 0.062 -10000 0 -0.28 11 11
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.024 0.061 0.28 11 -10000 0 11
CBL 0.012 0.022 -10000 0 -0.47 1 1
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.026 0.062 -10000 0 -0.28 11 11
Rac1/GTP -0.006 0.071 -10000 0 -0.51 8 8
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.008 0.069 -9999 0 -0.41 13 13
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.003 0.086 -9999 0 -0.27 48 48
NF kappa B1 p50/RelA/I kappa B alpha 0.04 0.029 -9999 0 -10000 0 0
NFKBIA 0.022 0.032 -9999 0 -0.27 1 1
MAPK14 0.013 0.001 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.026 0 -9999 0 -10000 0 0
ARRB2 0.016 0 -9999 0 -10000 0 0
REL -0.033 0.14 -9999 0 -0.47 48 48
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.016 0.059 -9999 0 -0.35 13 13
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.026 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
NF kappa B1 p50 dimer 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
NFKB1 0.021 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.028 0.031 -9999 0 -0.24 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.043 0.028 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PI3K 0.014 0.049 -9999 0 -0.36 8 8
NF kappa B1 p50/RelA 0.028 0.031 -9999 0 -0.25 1 1
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.006 0.059 -9999 0 -0.48 7 7
I kappa B alpha/PIK3R1 0.025 0.04 -9999 0 -0.25 1 1
cell death 0.042 0.027 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.003 0.086 -9999 0 -0.27 48 48
LCK 0.003 0.078 -9999 0 -0.57 9 9
BCL3 -0.002 0.094 -9999 0 -0.57 13 13
PLK2 and PLK4 events

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
PLK2 0.007 0.052 -9999 0 -0.47 6 6
PLK4 0.009 0.052 -9999 0 -0.57 4 4
regulation of centriole replication 0.013 0.054 -9999 0 -0.36 10 10
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.006 0.075 0.25 12 -0.31 17 29
FRAP1 0.013 0.023 -10000 0 -10000 0 0
AKT1 0.018 0.067 0.21 12 -0.42 4 16
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.001 0.06 -10000 0 -0.35 14 14
mol:GTP 0.023 0.049 -10000 0 -0.38 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.003 0.014 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.037 -10000 0 -0.34 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.06 -10000 0 -0.32 17 17
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.042 0.17 12 -0.26 3 15
MAP3K5 0.008 0.025 -10000 0 -0.31 3 3
PIK3R1 0.008 0.053 -10000 0 -0.47 6 6
apoptosis 0.008 0.025 -10000 0 -0.31 3 3
mol:LY294002 0 0 -10000 0 -0.001 16 16
EIF4B 0.027 0.038 0.17 12 -0.23 3 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.039 -10000 0 -0.31 3 3
eIF4E/eIF4G1/eIF4A1 -0.001 0.006 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.01 0.074 -10000 0 -0.32 21 21
mTOR/RHEB/GTP/Raptor/GBL 0.027 0.032 0.15 12 -0.23 1 13
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.007 0.037 -10000 0 -0.33 3 3
mol:Amino Acids 0 0 -10000 0 -0.001 16 16
FKBP12/Rapamycin 0.01 0.002 -10000 0 -10000 0 0
PDPK1 -0.006 0.067 0.22 12 -0.28 17 29
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.019 0.041 -10000 0 -0.59 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.003 -10000 0 -10000 0 0
TSC1/TSC2 0.025 0.053 -10000 0 -0.41 3 3
tumor necrosis factor receptor activity 0 0 0.001 16 -10000 0 16
RPS6 0.01 0.045 -10000 0 -0.57 3 3
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.004 0.064 -10000 0 -0.34 17 17
INS -0.016 0.095 -10000 0 -0.57 14 14
PTEN 0 0.076 -10000 0 -0.47 13 13
PDK2 -0.007 0.069 0.22 12 -0.28 17 29
EIF4EBP1 -0.003 0.065 -10000 0 -1.1 1 1
PIK3CA 0.011 0.037 -10000 0 -0.47 3 3
PPP2R5D 0.019 0.021 -10000 0 -10000 0 0
peptide biosynthetic process 0.007 0.054 -10000 0 -0.31 14 14
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 12 -0.003 1 13
EEF2 0.007 0.055 -10000 0 -0.31 14 14
eIF4E/4E-BP1 0.005 0.059 -10000 0 -0.97 1 1
ceramide 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
MAP4K4 0.033 0.056 -10000 0 -0.44 1 1
BAG4 -0.016 0.11 -10000 0 -0.47 30 30
BAD 0.023 0.027 -10000 0 -0.26 1 1
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 0.005 0.066 -10000 0 -0.51 8 8
BAX 0.022 0.03 -10000 0 -0.26 2 2
EnzymeConsortium:3.1.4.12 0.01 0.018 -10000 0 -0.087 3 3
IKBKB 0.038 0.053 -10000 0 -0.41 1 1
MAP2K2 0.025 0.051 -10000 0 -0.25 5 5
MAP2K1 0.026 0.05 -10000 0 -0.26 4 4
SMPD1 0.015 0.018 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.039 0.055 -10000 0 -0.42 1 1
MAP2K4 0.028 0.027 -10000 0 -10000 0 0
protein ubiquitination 0.04 0.054 -10000 0 -0.41 1 1
EnzymeConsortium:2.7.1.37 0.029 0.053 -10000 0 -0.26 4 4
response to UV 0 0.001 -10000 0 -0.002 2 2
RAF1 0.021 0.052 -10000 0 -0.28 4 4
CRADD 0.013 0 -10000 0 -10000 0 0
mol:ceramide 0.018 0.025 -10000 0 -0.16 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.018 0 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.023 0.026 -10000 0 -0.19 1 1
TRADD 0.013 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.028 0.05 -10000 0 -0.25 4 4
MAPK1 0.028 0.05 -10000 0 -0.25 4 4
p50/RELA/I-kappa-B-alpha 0.02 0 -10000 0 -10000 0 0
FADD 0.033 0.056 -10000 0 -0.44 1 1
KSR1 0.016 0.053 -10000 0 -0.21 21 21
MAPK8 0.028 0.045 -10000 0 -0.3 3 3
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.038 0.053 -10000 0 -0.41 1 1
TNF R/SODD -0.001 0.082 -10000 0 -0.33 30 30
TNF -0.026 0.14 -10000 0 -0.5 37 37
CYCS 0.028 0.031 0.13 15 -10000 0 15
IKBKG 0.038 0.053 -10000 0 -0.41 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.027 0.058 -10000 0 -0.34 3 3
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.028 0.031 0.13 15 -10000 0 15
TNF/TNF R/SODD -0.015 0.11 -10000 0 -0.3 64 64
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.013 -10000 0 -10000 0 0
NSMAF 0.033 0.056 -10000 0 -0.32 3 3
response to hydrogen peroxide 0 0.001 -10000 0 -0.002 2 2
BCL2 -0.009 0.1 -10000 0 -0.47 23 23
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.006 0.064 0.57 6 -10000 0 6
PI3K Class IB/PDE3B 0.006 0.064 -10000 0 -0.57 6 6
PDE3B 0.006 0.064 -10000 0 -0.57 6 6
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.062 0.051 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.01 0.11 -9999 0 -0.39 36 36
NFKBIA 0.041 0 -9999 0 -10000 0 0
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.001 0.082 -9999 0 -0.57 10 10
IKBKG 0.027 0.058 -9999 0 -0.28 6 6
IKK complex/A20 0.024 0.087 -9999 0 -0.36 7 7
NEMO/A20/RIP2 0.001 0.082 -9999 0 -0.57 10 10
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.033 0.057 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.018 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.01 0.037 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.024 0.032 -9999 0 -0.33 4 4
NOD2 -0.017 0.12 -9999 0 -0.47 31 31
NFKB1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
MALT1 0.009 0.05 -9999 0 -0.55 4 4
cIAP1/UbcH5C 0.02 0 -9999 0 -10000 0 0
ATM 0.012 0.022 -9999 0 -0.47 1 1
TNF/TNFR1A -0.009 0.099 -9999 0 -0.36 37 37
TRAF6 0.013 0 -9999 0 -10000 0 0
PRKCA -0.009 0.1 -9999 0 -0.47 23 23
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.026 0.14 -9999 0 -0.5 37 37
NF kappa B1 p50/RelA 0.038 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex 0.04 0.055 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.033 0.077 -9999 0 -0.36 7 7
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.031 0.029 -9999 0 -10000 0 0
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.011 -9999 0 -0.25 1 1
GATA1/HDAC4 0.017 0.025 -9999 0 -0.37 2 2
GATA1/HDAC5 0.017 0.025 -9999 0 -0.37 2 2
GATA2/HDAC5 0.019 0.019 -9999 0 -0.41 1 1
HDAC5/BCL6/BCoR 0.027 0 -9999 0 -10000 0 0
HDAC9 -0.045 0.16 -9999 0 -0.5 56 56
Glucocorticoid receptor/Hsp90/HDAC6 0.019 0.047 -9999 0 -0.27 13 13
HDAC4/ANKRA2 0.02 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0.02 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.013 -9999 0 -10000 0 0
GATA2 0.012 0.026 -9999 0 -0.57 1 1
HDAC4/RFXANK 0.014 0.051 -9999 0 -0.41 7 7
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.009 0.052 -9999 0 -0.57 4 4
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 0.016 0.038 -9999 0 -0.32 6 6
Histones 0.015 0.064 -9999 0 -0.35 1 1
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.02 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0.02 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.02 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.014 0.051 -9999 0 -0.41 7 7
CAMK4 -0.024 0.13 -9999 0 -0.47 38 38
Tubulin/HDAC6 -0.009 0.11 -9999 0 -0.35 48 48
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.009 0.034 -9999 0 -0.52 2 2
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.001 0.077 -9999 0 -0.47 13 13
SUMO1/HDAC4 0.029 0.012 -9999 0 -10000 0 0
SRF 0.013 0.001 -9999 0 -10000 0 0
HDAC4/YWHAB 0.02 0 -9999 0 -10000 0 0
Tubulin -0.022 0.13 -9999 0 -0.41 48 48
HDAC4/14-3-3 E 0.02 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.01 0.045 -9999 0 -0.57 3 3
BCL6/BCoR 0.02 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.027 0 -9999 0 -10000 0 0
HDAC4/SRF 0.004 0.079 -9999 0 -0.27 38 38
HDAC4/ER alpha 0.008 0.064 -9999 0 -0.33 17 17
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.015 0.063 -9999 0 -0.35 1 1
cell motility -0.009 0.11 -9999 0 -0.34 48 48
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.02 0 -9999 0 -10000 0 0
BCL6 0.013 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.02 0 -9999 0 -10000 0 0
ESR1 -0.003 0.089 -9999 0 -0.47 17 17
HDAC6/HDAC11 0.02 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.012 -9999 0 -10000 0 0
NPC 0.007 0.014 -9999 0 -0.31 1 1
MEF2C 0.007 0.059 -9999 0 -0.52 6 6
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.036 0.032 -9999 0 -0.28 3 3
GNG2 0.007 0.052 -9999 0 -0.47 6 6
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A -0.043 0.17 -9999 0 -0.57 48 48
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.012 0.026 -9999 0 -0.57 1 1
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.005 0.069 -9999 0 -0.57 7 7
nuclear import -0.028 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.008 0.098 -9999 0 -10000 0 0
PLK1 -0.076 0.25 -9999 0 -0.76 19 19
CDKN1B 0.047 0.1 -9999 0 -0.34 1 1
FOXO3 -0.025 0.2 -9999 0 -0.67 18 18
KAT2B 0.016 0.015 -9999 0 -10000 0 0
FOXO1/SIRT1 0.011 0.052 -9999 0 -10000 0 0
CAT -0.015 0.18 -9999 0 -0.72 10 10
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.016 0.018 -9999 0 -10000 0 0
FOXO1 0.02 0.057 -9999 0 -10000 0 0
MAPK10 0.03 0.031 -9999 0 -0.3 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.08 0.054 -9999 0 -0.37 1 1
response to oxidative stress 0.002 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.069 0.14 -9999 0 -0.59 16 16
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.01 0.038 -9999 0 -0.47 3 3
BCL2L11 0.015 0.068 -9999 0 -1.3 1 1
FOXO1/SKP2 0.02 0.064 -9999 0 -0.42 2 2
mol:GDP 0.002 0.02 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.047 0.11 -9999 0 -0.93 2 2
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.051 0.05 -9999 0 -10000 0 0
MST1 -0.06 0.2 -9999 0 -0.58 64 64
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.027 0.084 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.028 0.042 -9999 0 -0.25 5 5
MAPK9 0.033 0.009 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.013 0.01 -9999 0 -10000 0 0
SOD2 0.047 0.13 -9999 0 -10000 0 0
RBL2 0.012 0.16 -9999 0 -0.94 6 6
RAL/GDP 0.024 0.014 -9999 0 -10000 0 0
CHUK 0.016 0.015 -9999 0 -10000 0 0
Ran/GTP 0.014 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.031 0.014 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.026 0.22 -9999 0 -0.78 29 29
SKP2 0.005 0.062 -9999 0 -0.48 8 8
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.016 0.015 -9999 0 -10000 0 0
CCNB1 -0.024 0.2 -9999 0 -0.8 14 14
FOXO1-3a-4/beta catenin 0.068 0.12 -9999 0 -0.41 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.063 -9999 0 -0.42 2 2
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.061 0.18 -9999 0 -0.48 78 78
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.004 -9999 0 -10000 0 0
ZFAND5 0.082 0.048 -9999 0 -10000 0 0
SFN -0.035 0.14 -9999 0 -0.47 50 50
CDK2 0.011 0.012 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.019 0.087 -9999 0 -0.32 8 8
CREBBP 0.011 0.012 -9999 0 -10000 0 0
FBXO32 -0.017 0.19 -9999 0 -0.85 9 9
BCL6 0.019 0.13 -9999 0 -0.57 2 2
RALB 0.014 0.001 -9999 0 -10000 0 0
RALA 0.014 0.001 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.091 0.2 -10000 0 -0.47 108 108
CLTC 0.024 0.032 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.017 0.033 -10000 0 -10000 0 0
Dynamin 2/GTP 0.016 0.05 -10000 0 -0.32 11 11
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.021 0.025 -10000 0 -10000 0 0
CPE 0.015 0.031 -10000 0 -0.29 5 5
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.017 0.034 -10000 0 -10000 0 0
CTNND1 0.022 0.047 -10000 0 -0.29 11 11
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.023 -10000 0 -10000 0 0
TSHR 0.005 0.061 -10000 0 -0.3 19 19
INS 0.006 0.021 -10000 0 -10000 0 0
BIN1 0.011 0.037 -10000 0 -0.57 2 2
mol:Choline 0.017 0.034 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.054 -10000 0 -0.35 11 11
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0.016 0.049 -10000 0 -0.31 11 11
JUP 0.021 0.025 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.024 0.022 -10000 0 -0.32 2 2
ARF6/GTP 0.01 0 -10000 0 -10000 0 0
CDH1 0.02 0.028 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.01 0 -10000 0 -10000 0 0
MAPK8IP3 0.009 0.052 -10000 0 -0.57 4 4
positive regulation of endocytosis 0.01 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.04 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.036 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.015 0.033 -10000 0 -0.35 4 4
ACAP1 0.016 0.032 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.029 0.085 -10000 0 -0.3 4 4
clathrin heavy chain/ACAP1 0.026 0.035 -10000 0 -10000 0 0
JIP4/KLC1 0.026 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.041 0 -10000 0 -10000 0 0
RALA/GTP 0.01 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.018 0 -10000 0 -10000 0 0
receptor recycling 0.01 0 -10000 0 -10000 0 0
CTNNA1 0.022 0.047 -10000 0 -0.29 11 11
NME1 0.009 0.055 -10000 0 -0.35 11 11
clathrin coat assembly 0.024 0.031 -10000 0 -10000 0 0
IL2RA -0.006 0.065 -10000 0 -0.3 2 2
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.046 0.084 -10000 0 -0.27 17 17
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0.008 0.058 -10000 0 -0.25 24 24
PLD2 0.021 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.024 0.023 -10000 0 -10000 0 0
SDC1 0.012 0.052 -10000 0 -0.27 7 7
ARF6/GDP 0.01 0.054 -10000 0 -0.35 11 11
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.005 0.037 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.017 0.034 -10000 0 -10000 0 0
endocytosis -0.023 0.021 0.31 2 -10000 0 2
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.025 0.044 -10000 0 -10000 0 0
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.013 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.017 0.05 -10000 0 -0.31 11 11
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.023 0.048 -10000 0 -10000 0 0
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.033 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.039 0.031 -10000 0 -10000 0 0
CLOCK -0.022 0.13 -10000 0 -0.46 40 40
TIMELESS/CRY2 0.035 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.011 0.029 -10000 0 -0.36 3 3
ATR 0.012 0.026 -10000 0 -0.57 1 1
NR1D1 0.033 0.025 -10000 0 -10000 0 0
ARNTL 0.014 0.03 -10000 0 -0.46 2 2
TIMELESS 0.032 0.029 -10000 0 -10000 0 0
NPAS2 0.014 0.034 -10000 0 -0.52 2 2
CRY2 0.013 0 -10000 0 -10000 0 0
mol:CO -0.013 0.004 0.077 1 -10000 0 1
CHEK1 0.012 0.026 -10000 0 -0.57 1 1
mol:HEME 0.013 0.004 -10000 0 -0.077 1 1
PER1 -0.001 0.082 -10000 0 -0.47 15 15
BMAL/CLOCK/NPAS2 0.016 0.088 -10000 0 -0.59 1 1
BMAL1/CLOCK 0.015 0.1 -10000 0 -0.51 3 3
S phase of mitotic cell cycle 0.039 0.031 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.04 0.032 -10000 0 -10000 0 0
mol:NADPH 0.013 0.004 -10000 0 -0.077 1 1
PER1/TIMELESS 0.027 0.052 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.001 0.026 -10000 0 -0.57 1 1
Arf6 downstream 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
PLAUR 0.032 0.055 -10000 0 -0.39 8 8
regulation of axonogenesis -0.017 0.042 -10000 0 -10000 0 0
myoblast fusion -0.016 0.029 0.2 8 -10000 0 8
mol:GTP 0.009 0.019 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.06 0.3 15 -10000 0 15
ARF1/GTP 0.017 0.014 -10000 0 -10000 0 0
mol:GM1 0.009 0.014 -10000 0 -10000 0 0
mol:Choline 0.012 0.061 -10000 0 -0.25 24 24
lamellipodium assembly -0.001 0.031 -10000 0 -10000 0 0
MAPK3 0.024 0.027 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.023 0.061 -10000 0 -0.3 15 15
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP 0.016 0.029 -10000 0 -0.2 8 8
ARF1/GDP 0.024 0.028 -10000 0 -10000 0 0
ARF6 0.012 0.01 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 0.011 0.043 -10000 0 -0.47 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.027 -10000 0 -10000 0 0
actin filament bundle formation -0.022 0.027 -10000 0 -10000 0 0
KALRN -0.002 0.032 -10000 0 -0.28 3 3
RAB11FIP3/RAB11A 0.02 0 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.027 -10000 0 -10000 0 0
NME1 0.002 0.086 -10000 0 -0.57 11 11
Rac1/GDP 0.022 0.027 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.019 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.031 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development 0.009 0.019 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.019 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.014 -10000 0 -10000 0 0
mol:GDP -0.001 0.03 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.025 0.013 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0.003 0.069 -10000 0 -0.3 24 24
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.031 -10000 0 -10000 0 0
ruffle organization 0.017 0.042 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.009 0.019 -10000 0 -10000 0 0
PLD2 0.019 0.014 -10000 0 -10000 0 0
PIP5K1A 0.017 0.042 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.012 0.061 -10000 0 -0.25 24 24
Rac1/GTP -0.001 0.032 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.015 0.094 -10000 0 -0.33 3 3
CaM/Ca2+ 0.01 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.012 0.022 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.007 0.097 0.24 8 -10000 0 8
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 0.019 0.034 -10000 0 -0.42 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip 0.027 0.013 -10000 0 -0.27 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.001 0.072 -10000 0 -0.53 9 9
PRKCI 0.012 0.026 -10000 0 -0.57 1 1
AS160/CaM/Ca2+ 0.01 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.029 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.018 0 -10000 0 -10000 0 0
AS160/14-3-3 0.022 0.062 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 -0.009 0.1 0.24 8 -10000 0 8
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.024 0 -10000 0 -10000 0 0
SFN -0.035 0.14 -10000 0 -0.47 50 50
LNPEP -0.021 0.12 -10000 0 -0.47 35 35
YWHAE 0.013 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.022 0.053 -9999 0 -0.34 2 2
PDGFB-D/PDGFRB/SLAP 0.004 0.087 -9999 0 -0.46 16 16
PDGFB-D/PDGFRB/APS/CBL 0.01 0.077 -9999 0 -0.34 23 23
AKT1 0.04 0.058 -9999 0 -0.37 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.022 0.055 -9999 0 -0.35 2 2
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
FGR -0.002 0.037 -9999 0 -0.48 2 2
mol:Ca2+ 0.023 0.029 -9999 0 -10000 0 0
MYC 0.016 0.1 -9999 0 -0.38 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.028 0.042 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.024 0.034 -9999 0 -0.31 5 5
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.022 -9999 0 -0.47 1 1
GO:0007205 0.023 0.029 -9999 0 -10000 0 0
PTEN 0.001 0.077 -9999 0 -0.47 13 13
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 0.012 0.026 -9999 0 -0.57 1 1
PDGFB-D/PDGFRB/SHP2 0.017 0.032 -9999 0 -0.38 3 3
PDGFB-D/PDGFRB/GRB10 0.017 0.027 -9999 0 -0.41 2 2
cell cycle arrest 0.004 0.087 -9999 0 -0.46 16 16
HRAS 0.006 0.064 -9999 0 -0.57 6 6
HIF1A 0.044 0.056 -9999 0 -0.44 2 2
GAB1 0.019 0.047 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.022 0.047 -9999 0 -0.28 1 1
PDGFB-D/PDGFRB 0.025 0.025 -9999 0 -0.34 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.027 -9999 0 -0.41 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.009 0.048 -9999 0 -0.35 2 2
positive regulation of MAPKKK cascade 0.017 0.031 -9999 0 -0.38 3 3
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
mol:IP3 0.023 0.029 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.013 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.017 0.034 -9999 0 -0.41 3 3
SHB 0.01 0.037 -9999 0 -0.47 3 3
BLK -0.084 0.17 -9999 0 -0.48 75 75
PTPN2 0.013 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.017 0.027 -9999 0 -0.41 2 2
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.02 0.056 -9999 0 -10000 0 0
CBL 0.012 0.022 -9999 0 -0.47 1 1
PDGFB-D/PDGFRB/DEP1 0.017 0.027 -9999 0 -0.41 2 2
LCK -0.002 0.026 -9999 0 -10000 0 0
PDGFRB 0.011 0.037 -9999 0 -0.57 2 2
ACP1 0.013 0 -9999 0 -10000 0 0
HCK -0.001 0.047 -9999 0 -0.46 4 4
ABL1 0.017 0.043 -9999 0 -0.27 1 1
PDGFB-D/PDGFRB/CBL 0.018 0.047 -9999 0 -10000 0 0
PTPN1 0.013 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.003 0.078 -9999 0 -0.57 9 9
cell proliferation 0.017 0.098 -9999 0 -0.34 10 10
SLA -0.006 0.1 -9999 0 -0.57 16 16
actin cytoskeleton reorganization 0.041 0.032 -9999 0 -10000 0 0
SRC 0.001 0.019 -9999 0 -10000 0 0
PI3K -0.011 0.052 -9999 0 -0.41 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.025 0.029 -9999 0 -0.34 3 3
SH2B2 -0.01 0.11 -9999 0 -0.57 20 20
PLCgamma1/SPHK1 0.023 0.056 -9999 0 -0.36 2 2
LYN 0.001 0.02 -9999 0 -10000 0 0
LRP1 0.01 0.04 -9999 0 -0.5 3 3
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.012 0.022 -9999 0 -0.47 1 1
NCK1-2/p130 Cas 0.036 0.026 -9999 0 -10000 0 0
SPHK1 -0.004 0.1 -9999 0 -0.57 15 15
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.023 0.029 -9999 0 -10000 0 0
PLCG1 0.023 0.03 -9999 0 -10000 0 0
NHERF/PDGFRB 0.022 0.044 -9999 0 -0.34 7 7
YES1 0.001 0.019 -9999 0 -10000 0 0
cell migration 0.022 0.044 -9999 0 -0.34 7 7
SHC/Grb2/SOS1 0.037 0.023 -9999 0 -10000 0 0
SLC9A3R2 0.007 0.059 -9999 0 -0.57 5 5
SLC9A3R1 0.013 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.023 0.058 -9999 0 -0.31 7 7
FYN -0.001 0.033 -9999 0 -0.43 2 2
DOK1 0.028 0.024 -9999 0 -0.3 2 2
HRAS/GTP 0.005 0.047 -9999 0 -0.42 6 6
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.024 0.074 -9999 0 -10000 0 0
PRKCD 0.028 0.023 -9999 0 -0.3 2 2
FER 0.017 0.058 -9999 0 -0.3 2 2
MAPKKK cascade 0.001 0.022 -9999 0 -10000 0 0
RASA1 0.027 0.028 -9999 0 -0.3 2 2
NCK1 0.012 0.026 -9999 0 -0.57 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.035 0.023 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.015 0.038 -9999 0 -0.36 5 5
chemotaxis 0.017 0.043 -9999 0 -0.27 1 1
STAT1-3-5/STAT1-3-5 -0.006 0.038 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.008 0.027 -9999 0 -0.42 2 2
PTPRJ 0.013 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.013 0.005 -9999 0 -10000 0 0
SMAD3 0.038 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.042 0.021 -9999 0 -0.33 1 1
SMAD4/Ubc9/PIASy 0.027 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.035 0.033 -9999 0 -10000 0 0
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.02 0.004 -9999 0 -10000 0 0
MAP3K1 0.012 0.022 -9999 0 -0.47 1 1
TRAP-1/SMAD4 0 0.08 -9999 0 -0.32 28 28
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.014 0.11 -9999 0 -0.47 28 28
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.022 -9999 0 -0.47 1 1
KPNA2 0.006 0.064 -9999 0 -0.57 6 6
PIAS4 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.041 0.04 -10000 0 -0.44 1 1
adherens junction organization 0.023 0.046 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.074 -10000 0 -0.4 6 6
FMN1 0.006 0.087 -10000 0 -0.29 4 4
mol:IP3 0.034 0.035 -10000 0 -0.4 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.033 0.02 -10000 0 -10000 0 0
CTNNB1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.04 0.035 -10000 0 -0.39 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.039 0.025 -10000 0 -0.34 2 2
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.038 0.019 -10000 0 -10000 0 0
VASP 0.038 0.02 -10000 0 -10000 0 0
ZYX 0.038 0.02 -10000 0 -10000 0 0
JUB 0.025 0.059 -10000 0 -0.3 2 2
EGFR(dimer) 0.02 0.07 -10000 0 -0.28 6 6
E-cadherin/beta catenin-gamma catenin 0.024 0.017 -10000 0 -0.25 2 2
mol:PI-3-4-5-P3 0.035 0.036 -10000 0 -0.42 1 1
PIK3CA 0.011 0.038 -10000 0 -0.47 3 3
PI3K 0.036 0.037 -10000 0 -0.42 1 1
FYN 0.041 0.044 -10000 0 -0.35 1 1
mol:Ca2+ 0.034 0.034 -10000 0 -0.39 1 1
JUP 0.013 0.001 -10000 0 -10000 0 0
PIK3R1 0.008 0.053 -10000 0 -0.47 6 6
mol:DAG 0.034 0.035 -10000 0 -0.4 1 1
CDH1 0.011 0.03 -10000 0 -0.47 2 2
RhoA/GDP 0.03 0.074 -10000 0 -0.4 6 6
establishment of polarity of embryonic epithelium 0.038 0.019 -10000 0 -10000 0 0
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR -0.025 0.13 -10000 0 -0.47 40 40
CASR 0.035 0.043 -10000 0 -0.37 1 1
RhoA/GTP 0.038 0.032 -10000 0 -0.36 1 1
AKT2 0.04 0.035 -10000 0 -0.39 1 1
actin cable formation 0.012 0.084 -10000 0 -0.31 1 1
apoptosis -0.038 0.037 0.41 1 -10000 0 1
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.023 0.078 -10000 0 -0.44 6 6
PIP5K1A 0.038 0.02 -10000 0 -10000 0 0
PLCG1 0.035 0.035 -10000 0 -0.41 1 1
Rac1/GTP 0.024 0.065 -10000 0 -0.3 1 1
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.021 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0.015 -9999 0 -0.31 1 1
CDKN1B 0.034 0.007 -9999 0 -10000 0 0
CDKN1A 0.03 0.032 -9999 0 -0.27 3 3
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.012 0.026 -9999 0 -0.57 1 1
FOXO3 0.034 0.007 -9999 0 -10000 0 0
AKT1 0.029 0.008 -9999 0 -10000 0 0
BAD 0.012 0.026 -9999 0 -0.57 1 1
AKT3 0.016 0.014 -9999 0 -0.3 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.033 0.013 -9999 0 -10000 0 0
AKT1/ASK1 0.032 0.021 -9999 0 -10000 0 0
BAD/YWHAZ 0.026 0.017 -9999 0 -0.35 1 1
RICTOR 0.013 0 -9999 0 -10000 0 0
RAF1 0.013 0 -9999 0 -10000 0 0
JNK cascade -0.031 0.02 -9999 0 -10000 0 0
TSC1 0.034 0.007 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
AKT1/RAF1 0.035 0.007 -9999 0 -10000 0 0
EP300 0.01 0.037 -9999 0 -0.47 3 3
mol:GDP 0.028 0.008 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.034 0.007 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
TBC1D4 0.02 0.028 -9999 0 -0.34 3 3
MAP3K5 0.01 0.04 -9999 0 -0.5 3 3
MAPKAP1 0.013 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.027 0.041 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
AKT1S1 0.034 0.007 -9999 0 -10000 0 0
CASP9 0.034 0.007 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.04 0.007 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.027 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0.034 0.031 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.003 -9999 0 -10000 0 0
CHUK 0.034 0.007 -9999 0 -10000 0 0
BAD/BCL-XL 0.046 0.015 -9999 0 -10000 0 0
mTORC2 0.017 0 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.039 0.048 -9999 0 -10000 0 0
PDPK1 0.013 0 -9999 0 -10000 0 0
MDM2 0.034 0.007 -9999 0 -10000 0 0
MAPKKK cascade -0.035 0.007 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.045 0.019 -9999 0 -10000 0 0
TSC1/TSC2 0.039 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.018 -9999 0 -10000 0 0
glucose import -0.031 0.11 -9999 0 -0.3 4 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.029 0.005 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.032 0.11 -9999 0 -0.31 4 4
GSK3A 0.033 0.013 -9999 0 -10000 0 0
FOXO1 0.034 0.007 -9999 0 -10000 0 0
GSK3B 0.034 0.007 -9999 0 -10000 0 0
SFN -0.035 0.14 -9999 0 -0.47 50 50
G1/S transition of mitotic cell cycle 0.039 0.012 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.026 0.058 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
KPNA1 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
RHEB 0.013 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.019 0.067 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -9999 0 -0.25 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.071 -9999 0 -10000 0 0
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.013 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones 0.032 0.043 -9999 0 -10000 0 0
YY1/LSF 0.028 0.022 -9999 0 -0.25 1 1
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.062 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.019 0.045 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA 0.018 0.06 -9999 0 -10000 0 0
HDAC1/Smad7 0.027 0 -9999 0 -10000 0 0
RANGAP1 0.01 0.045 -9999 0 -0.57 3 3
HDAC3/TR2 0.019 0.045 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.043 0.014 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.023 0.055 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.012 0.026 -9999 0 -0.57 1 1
GATA1 0.009 0.034 -9999 0 -0.52 2 2
Mad/Max 0.02 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.052 0.018 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0.007 0.014 -9999 0 -0.31 1 1
RBBP4 0.012 0.022 -9999 0 -0.47 1 1
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA 0.013 0.05 -9999 0 -10000 0 0
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.04 0.013 -9999 0 -10000 0 0
SIN3 complex 0.034 0 -9999 0 -10000 0 0
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.013 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.012 0.022 -9999 0 -0.47 1 1
YY1/HDAC3 0.028 0.044 -9999 0 -10000 0 0
YY1/HDAC2 0.028 0.022 -9999 0 -0.25 1 1
YY1/HDAC1 0.029 0.018 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.044 0.013 -9999 0 -10000 0 0
PPARG -0.002 0.1 -9999 0 -0.3 25 25
HDAC8/hEST1B 0.027 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.019 0.045 -9999 0 -10000 0 0
MBD3L2 0 0.002 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.047 0.015 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 0.013 0.05 -9999 0 -10000 0 0
HDAC2 0.012 0.022 -9999 0 -0.47 1 1
YY1 0.027 0.021 -9999 0 -0.25 3 3
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.023 0.024 -9999 0 -0.29 3 3
NFKB1 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0.026 -9999 0 -0.57 1 1
YY1/LSF/HDAC1 0.034 0.02 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.035 0.017 -9999 0 -10000 0 0
EP300 0.01 0.037 -9999 0 -0.47 3 3
STAT3 (dimer non-phopshorylated) 0.022 0.024 -9999 0 -0.29 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.05 -9999 0 -10000 0 0
histone deacetylation 0.044 0.013 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.026 0.045 -9999 0 -10000 0 0
nuclear export -0.027 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.018 0.047 -9999 0 -0.3 1 1
GATA1/HDAC1 0.017 0.025 -9999 0 -0.37 2 2
GATA1/HDAC3 0.016 0.049 -9999 0 -0.3 1 1
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.009 0.099 -9999 0 -0.36 37 37
SIN3/HDAC complex/Mad/Max 0.044 0.012 -9999 0 -10000 0 0
NuRD Complex 0.051 0.017 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.031 0.042 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.029 0.012 -9999 0 -10000 0 0
HDAC complex 0.033 0.017 -9999 0 -10000 0 0
GATA1/Fog1 0.017 0.025 -9999 0 -0.37 2 2
FKBP25/HDAC1/HDAC2 0.027 0.013 -9999 0 -0.27 1 1
TNF -0.026 0.14 -9999 0 -0.5 37 37
negative regulation of cell growth 0.044 0.012 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.044 0.013 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.012 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.018 0.074 -9999 0 -0.27 24 24
SIN3/HDAC complex/NCoR1 0.041 0.016 -9999 0 -10000 0 0
TFCP2 0.012 0.022 -9999 0 -0.47 1 1
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.011 0.037 -9999 0 -0.57 2 2
MBD2 0.012 0.026 -9999 0 -0.57 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.038 0.028 -9999 0 -0.4 2 2
KLHL20 -0.003 0.02 -9999 0 -0.22 1 1
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.056 0.018 -9999 0 -10000 0 0
ENAH 0.038 0.028 -9999 0 -0.4 2 2
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.009 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.002 0.011 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.021 0.062 -9999 0 -0.35 4 4
RAPGEF1 0.047 0.024 -9999 0 -0.34 2 2
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.032 0.028 -9999 0 -0.41 2 2
CRK 0.043 0.026 -9999 0 -0.37 2 2
E-cadherin/gamma catenin/alpha catenin 0.026 0.019 -9999 0 -0.27 2 2
alphaE/beta7 Integrin 0.004 0.074 -9999 0 -0.34 22 22
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.026 0 -9999 0 -10000 0 0
DLG1 0.038 0.028 -9999 0 -0.4 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.015 -9999 0 -10000 0 0
MLLT4 0.013 0.001 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.016 0.055 -9999 0 -0.3 15 15
PI3K -0.003 0.019 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.018 0.022 -9999 0 -0.32 2 2
TIAM1 0.009 0.043 -9999 0 -0.47 4 4
E-cadherin(dimer)/Ca2+ 0.031 0.016 -9999 0 -10000 0 0
AKT1 -0.002 0.011 -9999 0 -10000 0 0
PIK3R1 0.007 0.052 -9999 0 -0.47 6 6
CDH1 0.011 0.03 -9999 0 -0.47 2 2
RhoA/GDP 0.056 0.018 -9999 0 -10000 0 0
actin cytoskeleton organization 0.039 0.022 -9999 0 -0.16 1 1
CDC42/GDP 0.056 0.018 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.015 -9999 0 -0.22 2 2
ITGB7 -0.009 0.1 -9999 0 -0.48 22 22
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.034 0.017 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.023 0.016 -9999 0 -0.23 2 2
mol:GDP 0.053 0.02 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0.053 0.019 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.02 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.031 0.017 -9999 0 -0.2 1 1
NME1 0 0.086 -9999 0 -0.57 11 11
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.038 0.028 -9999 0 -0.4 2 2
regulation of cell-cell adhesion -0.001 0.008 -9999 0 -10000 0 0
WASF2 -0.001 0.006 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.011 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.058 -9999 0 -0.45 1 1
CCND1 0.036 0.021 -9999 0 -0.25 1 1
VAV2 0.048 0.026 -9999 0 -0.36 2 2
RAP1/GDP 0.05 0.018 -9999 0 -10000 0 0
adherens junction assembly 0.037 0.027 -9999 0 -0.38 2 2
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.032 0.056 -9999 0 -0.42 1 1
E-cadherin/beta catenin -0.001 0.021 -9999 0 -0.32 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.038 0.028 -9999 0 -0.4 2 2
PIK3CA 0.01 0.037 -9999 0 -0.47 3 3
Rac1/GTP -0.005 0.026 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.026 0.019 -9999 0 -0.27 2 2
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.029 -9999 0 -0.42 2 2
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.026 0.019 -9999 0 -0.27 2 2
E-cadherin/beta catenin 0.018 0.022 -9999 0 -0.32 2 2
CTNNB1 0.013 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
CDH1 0.011 0.03 -9999 0 -0.47 2 2
Sumoylation by RanBP2 regulates transcriptional repression

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.011 -9999 0 -10000 0 0
MDM2/SUMO1 0.029 0.012 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -9999 0 -10000 0 0
SUMO1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.015 0.016 -9999 0 -0.16 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.025 0.012 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0.026 -9999 0 -0.57 1 1
SUMO1/HDAC4 0.029 0.012 -9999 0 -10000 0 0
SUMO1/HDAC1 0.029 0.012 -9999 0 -10000 0 0
RANGAP1 0.01 0.045 -9999 0 -0.57 3 3
MDM2/SUMO1/SUMO1 0.034 0.012 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.019 0.013 -9999 0 -10000 0 0
Ran/GTP 0.025 0.012 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.012 -9999 0 -10000 0 0
NPC 0.007 0.014 -9999 0 -0.31 1 1
PIAS2 0.013 0 -9999 0 -10000 0 0
PIAS1 0.012 0.022 -9999 0 -0.47 1 1
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.018 -9999 0 -0.24 2 2
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.019 0 -9999 0 -10000 0 0
AP2 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.019 0 -9999 0 -10000 0 0
CLTB 0.012 0.026 -9999 0 -0.57 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.024 0.008 -9999 0 -10000 0 0
CD4 0.005 0.066 -9999 0 -0.54 7 7
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.009 0.027 -9999 0 -0.42 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.024 0.019 -9999 0 -0.26 2 2
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0.007 0.019 -9999 0 -0.29 2 2
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.016 0 -9999 0 -10000 0 0
Rac/GTP 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.023 0.021 -9999 0 -0.3 2 2
ARFIP2 0.012 0 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.024 0.005 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.01 0 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.018 0 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.025 0.013 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.018 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.017 0 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.019 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.01 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 0.031 0.021 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.009 0.027 -9999 0 -0.42 2 2
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.021 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.027 -9999 0 -0.42 2 2
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.019 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.022 0.042 -9999 0 -0.32 7 7
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.02 0 -9999 0 -10000 0 0
FBXW11 0.013 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 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.038 0.025 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.02 0 -9999 0 -10000 0 0
RELB 0.013 0 -9999 0 -10000 0 0
NFKB2 0.01 0.045 -9999 0 -0.57 3 3
NF kappa B2 p52/RelB 0.016 0.029 -9999 0 -0.35 3 3
regulation of B cell activation 0.016 0.029 -9999 0 -0.35 3 3
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 497 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZG.A9NI TCGA.ZG.A9ND TCGA.ZG.A9N3 TCGA.ZG.A9MC
109_MAP3K5 0.05 -0.18 -0.18 -0.049
47_PPARGC1A 0.013 -0.47 0.013 0.013
105_BMP4 0.013 0.013 -0.47 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 -0.47 -0.47 0.013
105_BMP2 0.013 0.013 -0.47 0.013
131_RELN/VLDLR 0.034 -0.31 0.034 0.034
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.017 0.013
84_STAT5B -0.024 -0.022 -0.16 -0.041
84_STAT5A -0.024 -0.022 -0.16 -0.041
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/PRAD-TP/22311258/PRAD-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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