PARADIGM pathway analysis of mRNASeq expression data
Prostate Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C11R6PST
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 54 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 90
Aurora B signaling 88
Angiopoietin receptor Tie2-mediated signaling 87
Syndecan-1-mediated signaling events 71
Signaling mediated by p38-alpha and p38-beta 67
Endothelins 65
IL23-mediated signaling events 64
IL4-mediated signaling events 60
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 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 -0.019 -1000
FOXM1 transcription factor network 0.1811 90 4603 51 -0.42 0.013 1000 -1000 -0.18 -1000
Aurora B signaling 0.1771 88 5908 67 -0.26 0.013 1000 -1000 -0.051 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1751 87 7736 88 -0.32 0.06 1000 -1000 -0.085 -1000
Syndecan-1-mediated signaling events 0.1429 71 2442 34 -0.31 0.013 1000 -1000 -0.038 -1000
Signaling mediated by p38-alpha and p38-beta 0.1348 67 2990 44 -0.18 0.013 1000 -1000 -0.037 -1000
Endothelins 0.1308 65 6279 96 -0.17 0.013 1000 -1000 -0.075 -1000
IL23-mediated signaling events 0.1288 64 3888 60 -0.41 0.013 1000 -1000 -0.16 -1000
IL4-mediated signaling events 0.1207 60 5547 91 -0.61 0.51 1000 -1000 -0.14 -1000
Glucocorticoid receptor regulatory network 0.1207 60 6857 114 -0.52 0.28 1000 -1000 -0.072 -1000
Aurora C signaling 0.0966 48 340 7 -0.18 0.008 1000 -1000 -0.022 -1000
Integrins in angiogenesis 0.0966 48 4055 84 -0.22 0.026 1000 -1000 -0.076 -1000
Thromboxane A2 receptor signaling 0.0946 47 4981 105 -0.12 0.033 1000 -1000 -0.055 -1000
Glypican 1 network 0.0905 45 2191 48 -0.2 0.023 1000 -1000 -0.031 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0905 45 3127 68 -0.26 0.077 1000 -1000 -0.12 -1000
Ras signaling in the CD4+ TCR pathway 0.0885 44 752 17 -0.098 0.018 1000 -1000 -0.036 -1000
LPA receptor mediated events 0.0845 42 4360 102 -0.31 0.026 1000 -1000 -0.074 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0845 42 3315 78 -0.17 0.17 1000 -1000 -0.072 -1000
Signaling events mediated by the Hedgehog family 0.0825 41 2170 52 -0.09 0.088 1000 -1000 -0.044 -1000
IL6-mediated signaling events 0.0825 41 3128 75 -0.2 0.05 1000 -1000 -0.066 -1000
FOXA2 and FOXA3 transcription factor networks 0.0805 40 1857 46 -0.22 0.02 1000 -1000 -0.087 -1000
PLK1 signaling events 0.0805 40 3422 85 -0.21 0.03 1000 -1000 -0.035 -1000
Reelin signaling pathway 0.0805 40 2245 56 -0.18 0.032 1000 -1000 -0.069 -1000
amb2 Integrin signaling 0.0785 39 3278 82 -0.31 0.018 1000 -1000 -0.065 -1000
HIF-1-alpha transcription factor network 0.0744 37 2872 76 -0.22 0.049 1000 -1000 -0.15 -1000
S1P1 pathway 0.0744 37 1359 36 -0.19 0.013 1000 -1000 -0.052 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0684 34 1173 34 -0.087 0.013 1000 -1000 -0.034 -1000
Signaling events mediated by PRL 0.0684 34 1182 34 -0.11 0.051 1000 -1000 -0.031 -1000
TCGA08_retinoblastoma 0.0664 33 270 8 -0.12 0.029 1000 -1000 -0.015 -1000
IL12-mediated signaling events 0.0644 32 2788 87 -0.21 0.015 1000 -1000 -0.12 -1000
JNK signaling in the CD4+ TCR pathway 0.0644 32 554 17 -0.12 0.019 1000 -1000 -0.036 -1000
S1P5 pathway 0.0644 32 554 17 -0.082 0.067 1000 -1000 -0.027 -1000
TCGA08_p53 0.0644 32 230 7 -0.082 0.045 1000 -1000 -0.01 -1000
Nongenotropic Androgen signaling 0.0644 32 1705 52 -0.1 0.04 1000 -1000 -0.045 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0644 32 3958 120 -0.25 0.075 1000 -1000 -0.067 -1000
Aurora A signaling 0.0624 31 1892 60 -0.2 0.026 1000 -1000 -0.026 -1000
Calcium signaling in the CD4+ TCR pathway 0.0624 31 976 31 -0.16 0.013 1000 -1000 -0.055 -1000
Signaling events regulated by Ret tyrosine kinase 0.0604 30 2515 82 -0.1 0.013 1000 -1000 -0.078 -1000
Osteopontin-mediated events 0.0584 29 1122 38 -0.081 0.013 1000 -1000 -0.091 -1000
p75(NTR)-mediated signaling 0.0584 29 3732 125 -0.15 0.04 1000 -1000 -0.082 -1000
Wnt signaling 0.0584 29 208 7 -0.084 0.013 1000 -1000 -0.025 -1000
Syndecan-4-mediated signaling events 0.0584 29 1951 67 -0.31 0.02 1000 -1000 -0.06 -1000
BMP receptor signaling 0.0563 28 2290 81 -0.16 0.046 1000 -1000 -0.087 -1000
S1P4 pathway 0.0563 28 711 25 -0.082 0.02 1000 -1000 -0.027 -1000
Noncanonical Wnt signaling pathway 0.0543 27 720 26 -0.084 0.013 1000 -1000 -0.044 -1000
Effects of Botulinum toxin 0.0543 27 702 26 -0.095 0.014 1000 -1000 -0.058 -1000
IL27-mediated signaling events 0.0543 27 1400 51 -0.34 0.028 1000 -1000 -0.068 -1000
BCR signaling pathway 0.0543 27 2715 99 -0.15 0.042 1000 -1000 -0.073 -1000
EGFR-dependent Endothelin signaling events 0.0543 27 575 21 -0.091 0.02 1000 -1000 -0.064 -1000
Rapid glucocorticoid signaling 0.0543 27 554 20 -0.11 0.018 1000 -1000 -0.016 -1000
EPHB forward signaling 0.0523 26 2264 85 -0.14 0.089 1000 -1000 -0.079 -1000
PDGFR-alpha signaling pathway 0.0503 25 1141 44 -0.16 0.023 1000 -1000 -0.057 -1000
TCR signaling in naïve CD8+ T cells 0.0503 25 2328 93 -0.068 0.025 1000 -1000 -0.071 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0483 24 1315 54 -0.18 0.026 1000 -1000 -0.08 -1000
Signaling events mediated by PTP1B 0.0483 24 1896 76 -0.27 0.048 1000 -1000 -0.07 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0463 23 2009 85 -0.12 0.016 1000 -1000 -0.063 -1000
a4b1 and a4b7 Integrin signaling 0.0443 22 110 5 -0.014 0.001 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 0.0443 22 1359 61 -0.22 0.04 1000 -1000 -0.072 -1000
Canonical Wnt signaling pathway 0.0443 22 1138 51 -0.22 0.11 1000 -1000 -0.053 -1000
Regulation of nuclear SMAD2/3 signaling 0.0423 21 2888 136 -0.51 0.06 1000 -1000 -0.062 -1000
Arf6 signaling events 0.0423 21 1323 62 -0.12 0.017 1000 -1000 -0.044 -1000
Fc-epsilon receptor I signaling in mast cells 0.0402 20 1980 97 -0.1 0.026 1000 -1000 -0.071 -1000
Plasma membrane estrogen receptor signaling 0.0402 20 1797 86 -0.19 0.021 1000 -1000 -0.074 -1000
S1P3 pathway 0.0402 20 863 42 -0.078 0.02 1000 -1000 -0.033 -1000
ErbB4 signaling events 0.0382 19 1330 69 -0.16 0.042 1000 -1000 -0.08 -1000
Visual signal transduction: Cones 0.0382 19 723 38 -0.091 0.012 1000 -1000 -0.051 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0382 19 736 37 -0.1 0.029 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 0.0382 19 927 47 -0.26 0.02 1000 -1000 -0.045 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0382 19 2403 125 -0.084 0.036 1000 -1000 -0.083 -1000
IL2 signaling events mediated by STAT5 0.0382 19 420 22 -0.081 0.033 1000 -1000 -0.045 -1000
Syndecan-2-mediated signaling events 0.0362 18 1268 69 -0.072 0.031 1000 -1000 -0.028 -1000
Visual signal transduction: Rods 0.0362 18 950 52 -0.11 0.013 1000 -1000 -0.068 -1000
ErbB2/ErbB3 signaling events 0.0342 17 1135 65 -0.16 0.02 1000 -1000 -0.06 -1000
Signaling events mediated by HDAC Class III 0.0342 17 682 40 -0.13 0.025 1000 -1000 -0.024 -1000
Regulation of p38-alpha and p38-beta 0.0342 17 956 54 -0.17 0.034 1000 -1000 -0.057 -1000
Coregulation of Androgen receptor activity 0.0322 16 1264 76 -0.16 0.025 1000 -1000 -0.027 -1000
Cellular roles of Anthrax toxin 0.0322 16 660 39 -0.037 0.014 1000 -1000 -0.026 -1000
EPO signaling pathway 0.0322 16 907 55 -0.065 0.019 1000 -1000 -0.083 -1000
Ephrin B reverse signaling 0.0322 16 810 48 -0.14 0.05 1000 -1000 -0.057 -1000
Insulin Pathway 0.0322 16 1193 74 -0.22 0.027 1000 -1000 -0.083 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0322 16 558 33 -0.13 0.034 1000 -1000 -0.03 -1000
BARD1 signaling events 0.0302 15 889 57 -0.038 0.033 1000 -1000 -0.043 -1000
HIF-2-alpha transcription factor network 0.0302 15 662 43 -0.089 0.022 1000 -1000 -0.064 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0282 14 408 28 -0.08 0.034 1000 -1000 -0.026 -1000
Nectin adhesion pathway 0.0282 14 883 63 -0.084 0.027 1000 -1000 -0.059 -1000
Signaling mediated by p38-gamma and p38-delta 0.0282 14 224 15 -0.011 0.015 1000 -1000 -0.024 -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 -0.025 -1000
IL1-mediated signaling events 0.0262 13 864 62 -0.087 0.059 1000 -1000 -0.089 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0262 13 715 52 -0.1 0.027 1000 -1000 -0.039 -1000
Retinoic acid receptors-mediated signaling 0.0262 13 776 58 -0.075 0.027 1000 -1000 -0.068 -1000
Syndecan-3-mediated signaling events 0.0262 13 458 35 -0.073 0.04 1000 -1000 -0.04 -1000
Caspase cascade in apoptosis 0.0241 12 924 74 -0.06 0.03 1000 -1000 -0.037 -1000
Class I PI3K signaling events 0.0241 12 906 73 -0.1 0.034 1000 -1000 -0.053 -1000
IGF1 pathway 0.0241 12 693 57 -0.047 0.027 1000 -1000 -0.085 -1000
VEGFR1 specific signals 0.0241 12 713 56 -0.056 0.029 1000 -1000 -0.039 -1000
Hedgehog signaling events mediated by Gli proteins 0.0221 11 750 65 -0.29 0.052 1000 -1000 -0.05 -1000
TRAIL signaling pathway 0.0201 10 482 48 -0.037 0.04 1000 -1000 -0.058 -1000
TCGA08_rtk_signaling 0.0201 10 276 26 -0.036 0.043 1000 -1000 -0.017 -1000
Regulation of Telomerase 0.0201 10 1070 102 -0.21 0.039 1000 -1000 -0.1 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0181 9 819 83 -0.097 0.055 1000 -1000 -0.068 -1000
Regulation of Androgen receptor activity 0.0181 9 655 70 -0.1 0.064 1000 -1000 -0.056 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0161 8 635 74 -0.18 0.054 1000 -1000 -0.076 -1000
p38 MAPK signaling pathway 0.0161 8 377 44 -0.054 0.026 1000 -1000 -0.064 -1000
Ceramide signaling pathway 0.0141 7 578 76 -0.058 0.04 1000 -1000 -0.038 -1000
Atypical NF-kappaB pathway 0.0141 7 220 31 -0.033 0.043 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0141 7 346 45 -0.026 0.058 1000 -1000 -0.084 -1000
PLK2 and PLK4 events 0.0121 6 20 3 0.007 0.013 1000 -1000 -0.014 -1000
mTOR signaling pathway 0.0121 6 336 53 -0.016 0.027 1000 -1000 -0.057 -1000
IFN-gamma pathway 0.0121 6 465 68 -0.085 0.052 1000 -1000 -0.092 -1000
Paxillin-dependent events mediated by a4b1 0.0121 6 232 36 -0.024 0.026 1000 -1000 -0.059 -1000
Class IB PI3K non-lipid kinase events 0.0121 6 18 3 -0.006 0.006 1000 -1000 -0.013 -1000
Canonical NF-kappaB pathway 0.0101 5 212 39 -0.026 0.062 1000 -1000 -0.073 -1000
Signaling events mediated by HDAC Class II 0.0101 5 406 75 -0.045 0.036 1000 -1000 -0.036 -1000
Circadian rhythm pathway 0.0101 5 114 22 -0.022 0.04 1000 -1000 -0.031 -1000
ceramide signaling pathway 0.0101 5 292 49 -0.026 0.04 1000 -1000 -0.041 -1000
FoxO family signaling 0.0101 5 351 64 -0.076 0.082 1000 -1000 -0.072 -1000
Arf6 trafficking events 0.0080 4 289 71 -0.091 0.041 1000 -1000 -0.066 -1000
Insulin-mediated glucose transport 0.0060 3 119 32 -0.035 0.029 1000 -1000 -0.041 -1000
PDGFR-beta signaling pathway 0.0060 3 346 97 -0.084 0.044 1000 -1000 -0.076 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 65 23 -0.014 0.042 1000 -1000 -0.05 -1000
Arf6 downstream pathway 0.0040 2 120 43 -0.022 0.025 1000 -1000 -0.034 -1000
E-cadherin signaling in keratinocytes 0.0040 2 115 43 -0.038 0.041 1000 -1000 -0.039 -1000
Class I PI3K signaling events mediated by Akt 0.0020 1 80 68 -0.035 0.046 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class I 0.0020 1 186 104 -0.027 0.052 1000 -1000 -0.057 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 129 76 -0.009 0.056 1000 -1000 -0.07 -1000
E-cadherin signaling events 0.0020 1 6 5 0.011 0.026 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 10 27 -0.001 0.034 1000 -1000 -0.042 -1000
Arf1 pathway 0.0000 0 30 54 -0.001 0.031 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0.0000 0 9 13 0 0.038 1000 -1000 -0.034 -1000
Total NA 3254 185050 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 -1.1 110 110
PLK1 -0.12 0.23 -9999 0 -0.45 148 148
BIRC5 -0.14 0.24 -9999 0 -0.45 175 175
HSPA1B -0.29 0.57 -9999 0 -1.2 104 104
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 -1.6 124 124
XRCC1 -0.28 0.57 -9999 0 -1.1 101 101
FOXM1B/p19 -0.4 0.5 -9999 0 -1.2 120 120
Cyclin D1/CDK4 -0.25 0.52 -9999 0 -1 104 104
CDC2 -0.3 0.6 -9999 0 -1.2 123 123
TGFA -0.25 0.52 -9999 0 -1 109 109
SKP2 -0.29 0.58 -9999 0 -1.2 105 105
CCNE1 0.005 0.066 -9999 0 -0.59 6 6
CKS1B -0.28 0.57 -9999 0 -1.1 103 103
RB1 -0.16 0.18 -9999 0 -0.49 45 45
FOXM1C/SP1 -0.35 0.66 -9999 0 -1.3 125 125
AURKB -0.12 0.23 -9999 0 -0.44 166 166
CENPF -0.33 0.62 -9999 0 -1.2 145 145
CDK4 0.012 0.015 -9999 0 -10000 0 0
MYC -0.25 0.52 -9999 0 -1 111 111
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 -1.2 107 107
FOXM1B/HNF6 -0.35 0.67 -9999 0 -1.3 115 115
FOS -0.36 0.64 -9999 0 -1.2 143 143
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 -1.1 101 101
CENPA -0.36 0.63 -9999 0 -1.2 138 138
NEK2 -0.36 0.63 -9999 0 -1.2 135 135
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 -1.4 111 111
CCNB2 -0.3 0.6 -9999 0 -1.2 112 112
CCNB1 -0.31 0.61 -9999 0 -1.2 110 110
ETV5 -0.3 0.6 -9999 0 -1.2 118 118
ESR1 -0.29 0.58 -9999 0 -1.2 106 106
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 -1.2 113 113
MMP2 -0.29 0.58 -9999 0 -1.2 107 107
RB1/FOXM1C -0.28 0.57 -9999 0 -1.1 113 113
CREBBP 0.013 0 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.11 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 -0.24 29 29
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 -0.45 160 160
Aurora B/Septin1 -0.16 0.22 -9999 0 -0.46 153 153
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 -0.48 127 127
SGOL1 -0.11 0.24 -9999 0 -0.57 107 107
CENPA -0.14 0.19 -9999 0 -0.35 188 188
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 -0.22 165 165
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 -0.49 149 149
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
NSUN2 -0.062 0.11 -9999 0 -0.22 147 147
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 -0.22 165 165
Chromosomal passenger complex -0.15 0.22 -9999 0 -0.41 187 187
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
Angiopoietin receptor Tie2-mediated 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
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 0.24 125 -0.5 29 154
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 -0.6 60 60
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 52 52
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 -0.58 135 135
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 -0.67 113 113
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 -0.22 148 148
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 -0.54 63 63
ETS1 -0.05 0.12 -10000 0 -0.38 13 13
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
Syndecan-1-mediated signaling events

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
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 -0.34 119 119
Syndecan-1/Syntenin -0.14 0.15 -9999 0 -0.34 119 119
MAPK3 -0.12 0.14 -9999 0 -0.39 59 59
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 -0.34 119 119
Syndecan-1/RANTES -0.15 0.16 -9999 0 -0.36 130 130
Syndecan-1/CD147 -0.13 0.15 -9999 0 -0.42 59 59
Syndecan-1/Syntenin/PIP2 -0.13 0.14 -9999 0 -0.33 119 119
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.13 0.14 -9999 0 -0.32 119 119
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 -0.39 59 59
homophilic cell adhesion -0.15 0.15 -9999 0 -0.36 119 119
MMP1 -0.09 0.22 -9999 0 -0.54 93 93
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.18 0.41 -9999 0 -1 96 96
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 31 31
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 -0.39 116 116
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 -0.4 19 19
NOS2 -0.11 0.3 -9999 0 -1 33 33
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 -0.48 25 25
p38alpha-beta/HBP1 -0.056 0.18 -9999 0 -0.49 29 29
CREB1 -0.065 0.19 -9999 0 -0.38 112 112
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 -0.47 31 31
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 -0.39 113 113
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 -0.38 113 113
p38alpha-beta/MAPKAPK2 -0.056 0.18 -9999 0 -0.51 26 26
p38alpha-beta/MAPKAPK3 -0.056 0.18 -9999 0 -0.49 29 29
Endothelins

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
AKT1 -0.041 0.22 0.27 22 -0.59 44 66
PTK2B 0.013 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.41 -10000 0 -0.96 93 93
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 -0.56 70 70
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 -0.39 69 69
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 60 -0.56 43 103
ETA receptor/Endothelin-1/Gs/GTP -0.1 0.26 0.28 54 -0.57 87 141
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 -0.57 74 74
SLC9A3 -0.15 0.38 -10000 0 -0.91 82 82
RAF1 -0.077 0.26 -10000 0 -0.59 72 72
JUN -0.069 0.29 -10000 0 -0.73 58 58
JAK2 -0.041 0.22 0.27 22 -0.59 44 66
mol:IP3 -0.031 0.18 -10000 0 -0.44 50 50
ETA receptor/Endothelin-1 -0.067 0.26 0.34 62 -0.61 56 118
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 87 87
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 -0.57 109 109
ETA receptor/Endothelin-1/Gq/GTP -0.04 0.2 0.21 19 -0.48 65 84
MAPK14 -0.021 0.15 -10000 0 -0.42 37 37
TRPC6 -0.15 0.45 -10000 0 -1.1 93 93
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 -0.4 49 49
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 89 89
MAPK3 -0.12 0.36 -10000 0 -0.82 90 90
MAPK1 -0.12 0.36 -10000 0 -0.82 90 90
Rac1/GDP -0.057 0.24 -10000 0 -0.54 70 70
cAMP biosynthetic process -0.099 0.26 0.22 1 -0.57 93 94
MAPK8 -0.098 0.36 -10000 0 -0.71 101 101
SRC 0.013 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.075 0.22 -10000 0 -0.5 81 81
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 -0.55 66 66
COL1A2 -0.065 0.26 -10000 0 -0.68 54 54
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 50 50
MAP2K2 -0.095 0.3 -10000 0 -0.64 92 92
MAP2K1 -0.095 0.3 -10000 0 -0.63 94 94
EDNRA -0.042 0.19 -10000 0 -0.52 53 53
positive regulation of muscle contraction -0.029 0.19 0.24 19 -0.52 43 62
Gq family/GDP -0.11 0.21 -10000 0 -0.56 71 71
HRAS/GTP -0.065 0.23 -10000 0 -0.52 71 71
PRKCH -0.027 0.17 -10000 0 -0.46 41 41
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.037 0.19 -10000 0 -0.48 56 56
PRKCB -0.081 0.24 -10000 0 -0.52 86 86
PRKCE -0.025 0.17 -10000 0 -0.46 38 38
PRKCD -0.027 0.17 -10000 0 -0.45 43 43
PRKCG -0.04 0.18 -10000 0 -0.45 54 54
regulation of vascular smooth muscle contraction -0.16 0.44 -10000 0 -1.1 87 87
PRKCQ -0.049 0.2 -10000 0 -0.51 53 53
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 60 -0.54 45 105
MMP1 -0.066 0.26 0.29 11 -0.56 93 104
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 -1.1 113 113
IL23A -0.3 0.54 -10000 0 -1.2 96 96
NF kappa B1 p50/RelA/I kappa B alpha -0.35 0.47 -10000 0 -1.1 105 105
positive regulation of T cell mediated cytotoxicity -0.33 0.6 -10000 0 -1.3 105 105
ITGA3 -0.29 0.52 -10000 0 -1.1 107 107
IL17F -0.18 0.34 -10000 0 -0.73 86 86
IL12B -0.029 0.15 -10000 0 -0.6 30 30
STAT1 (dimer) -0.32 0.57 -10000 0 -1.2 107 107
CD4 -0.28 0.5 -10000 0 -1.1 104 104
IL23 -0.3 0.53 -10000 0 -1.2 98 98
IL23R -0.031 0.11 -10000 0 -0.54 5 5
IL1B -0.33 0.58 -10000 0 -1.3 111 111
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.28 0.5 -10000 0 -1.1 105 105
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 -1.3 105 105
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 98 98
ALOX12B -0.29 0.51 -10000 0 -1.1 113 113
CXCL1 -0.4 0.62 -10000 0 -1.3 139 139
T cell proliferation -0.33 0.6 -10000 0 -1.3 105 105
NFKBIA 0.012 0.004 -10000 0 -10000 0 0
IL17A -0.13 0.28 -10000 0 -0.59 72 72
PI3K -0.36 0.48 -10000 0 -1.2 107 107
IFNG -0.008 0.031 0.1 1 -0.11 6 7
STAT3 (dimer) -0.35 0.45 -10000 0 -1.1 107 107
IL18R1 0.006 0.06 -10000 0 -0.46 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.35 -10000 0 -0.78 81 81
IL18/IL18R -0.004 0.11 -10000 0 -0.31 50 50
macrophage activation -0.018 0.018 -10000 0 -0.045 65 65
TNF -0.32 0.56 -10000 0 -1.2 107 107
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 -1.1 104 104
STAT5A (dimer) -0.32 0.56 -10000 0 -1.2 105 105
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 -1.1 102 102
MPO -0.32 0.55 -10000 0 -1.1 125 125
positive regulation of humoral immune response -0.33 0.6 -10000 0 -1.3 105 105
IL23/IL23R/JAK2/TYK2 -0.36 0.68 -10000 0 -1.4 105 105
IL6 -0.41 0.62 -10000 0 -1.2 153 153
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 -1.1 107 107
keratinocyte proliferation -0.33 0.6 -10000 0 -1.3 105 105
NOS2 -0.31 0.54 -10000 0 -1.2 109 109
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 -1.1 106 106
STAT6 (cleaved dimer) -0.49 0.47 -10000 0 -1.1 153 153
IGHG1 -0.16 0.15 -10000 0 -0.39 17 17
IGHG3 -0.44 0.43 -10000 0 -1 145 145
AKT1 -0.22 0.26 -10000 0 -0.7 62 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.23 -10000 0 -0.69 40 40
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 -0.82 98 98
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.27 -10000 0 -0.72 64 64
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 -1.1 129 129
SOCS1 -0.29 0.3 -10000 0 -0.75 96 96
SOCS3 -0.33 0.43 -10000 0 -1.1 90 90
FCER2 -0.4 0.41 -10000 0 -1.1 87 87
PARP14 0.013 0.005 -10000 0 -10000 0 0
CCL17 -0.49 0.48 -10000 0 -1.2 122 122
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.23 -10000 0 -0.69 44 44
T cell proliferation -0.45 0.48 -10000 0 -1.2 107 107
IL4R/JAK1 -0.45 0.46 -10000 0 -1.1 108 108
EGR2 -0.49 0.49 -10000 0 -1.2 109 109
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 -1.2 108 108
PTPN6 0.025 0.009 -10000 0 -10000 0 0
IL13RA2 -0.53 0.55 -10000 0 -1.3 127 127
IL13RA1 -0.014 0.024 -10000 0 -10000 0 0
IRF4 -0.18 0.34 -10000 0 -1 55 55
ARG1 -0.14 0.16 -10000 0 -0.63 16 16
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 -0.96 54 54
CD40LG -0.037 0.17 -10000 0 -0.54 49 49
MAPK14 -0.3 0.35 -10000 0 -0.88 95 95
mitosis -0.21 0.25 -10000 0 -0.66 62 62
STAT6 -0.52 0.55 -10000 0 -1.2 144 144
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 -1.2 144 144
STAT6 (dimer)/PARP14 -0.48 0.5 -10000 0 -1.1 140 140
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 -0.7 62 62
LTA -0.47 0.47 -10000 0 -1.1 126 126
FES 0.007 0.057 -10000 0 -0.47 7 7
T-helper 1 cell differentiation 0.51 0.52 1.2 144 -10000 0 144
CCL11 -0.47 0.46 -10000 0 -1.1 125 125
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 -1.1 115 115
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 98 98
IL2R gamma/JAK3 -0.009 0.13 -10000 0 -0.54 26 26
TFF3 -0.53 0.48 -10000 0 -1.2 145 145
ALOX15 -0.58 0.49 -10000 0 -1.2 149 149
MYBL1 0.012 0.022 -10000 0 -0.47 1 1
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.93 113 113
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 -0.68 52 52
mol:PI-3-4-5-P3 -0.22 0.26 -10000 0 -0.7 62 62
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 -1.3 172 172
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 99 99
RETNLB -0.46 0.45 -10000 0 -1.2 98 98
SELP -0.46 0.47 -10000 0 -1.2 104 104
AICDA -0.44 0.44 -10000 0 -1.1 106 106
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 0.34 5 -10000 0 5
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 -0.49 83 83
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 0.29 85 -0.32 2 87
PRL -0.077 0.14 -10000 0 -0.57 6 6
cortisol/GR alpha (dimer)/TIF2 0.2 0.29 0.56 147 -0.48 9 156
RELA -0.053 0.1 -10000 0 -0.25 40 40
FGG 0.19 0.24 0.51 108 -0.55 14 122
GR beta/TIF2 0.071 0.19 0.31 95 -0.35 42 137
IFNG -0.29 0.34 -10000 0 -0.74 138 138
apoptosis 0.062 0.23 0.52 61 -0.53 10 71
CREB1 -0.039 0.11 -10000 0 -0.33 26 26
histone acetylation -0.056 0.18 0.36 10 -0.4 76 86
BGLAP -0.083 0.18 -10000 0 -0.54 27 27
GR/PKAc 0.11 0.11 0.29 68 -0.32 1 69
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 0.27 98 -10000 0 98
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 -0.45 23 23
GSK3B 0.016 0.014 -10000 0 -10000 0 0
NR1I3 0.081 0.22 0.51 58 -0.61 8 66
CSN2 0.17 0.19 0.42 105 -0.5 3 108
BRG1/BAF155/BAF170/BAF60A -0.003 0.11 -10000 0 -0.35 27 27
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 0.29 62 -0.32 1 63
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 -0.52 92 92
IL4 -0.09 0.16 -10000 0 -0.48 20 20
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 14 -0.52 74 88
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.11 0.29 77 -0.32 1 78
cortisol/GR alpha (monomer) 0.28 0.32 0.66 159 -0.52 1 160
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 -0.78 150 150
AFP -0.14 0.19 -10000 0 -0.63 31 31
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.15 0.18 0.44 74 -0.57 3 77
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 -1.1 143 143
KRT14 -0.39 0.58 0.42 3 -1.2 156 159
TBP 0.017 0.032 -10000 0 -0.24 1 1
CREBBP 0.049 0.13 0.27 84 -0.24 24 108
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 -0.78 150 150
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 -1.2 199 199
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 -0.86 105 105
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.11 0.18 0.38 112 -0.5 6 118
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 -0.6 126 126
NFKB1 -0.053 0.1 -10000 0 -0.29 6 6
MAPK8 -0.15 0.2 -10000 0 -0.45 107 107
MAPK9 0.016 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.054 0.23 0.53 61 -0.55 10 71
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 74 -0.41 5 79
cortisol/GR alpha (dimer)/p53 0.24 0.26 0.57 151 -0.52 1 152
proteasomal ubiquitin-dependent protein catabolic process 0.072 0.081 0.23 45 -10000 0 45
SGK1 -0.05 0.46 -10000 0 -1.1 72 72
IL13 -0.36 0.42 -10000 0 -0.89 162 162
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 -0.74 156 156
IL2 -0.28 0.32 -10000 0 -0.72 136 136
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 -0.78 130 130
CDK5R1/CDK5 0.001 0.094 -10000 0 -0.41 24 24
NF kappa B1 p50/RelA/PKAc -0.046 0.14 -10000 0 -0.38 20 20
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.24 0.24 0.53 151 -0.4 1 152
SMARCA4 0.002 0.032 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.21 0.4 89 -0.42 16 105
NF kappa B1 p50/RelA/Cbp -0.038 0.21 0.35 21 -0.51 35 56
JUN (dimer) -0.17 0.21 -10000 0 -0.51 92 92
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.076 0.17 -10000 0 -0.42 67 67
NR3C1 0.17 0.2 0.45 126 -0.41 5 131
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 -0.53 10 71
cortisol/GR alpha (dimer)/Src-1 0.24 0.26 0.56 155 -0.44 1 156
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 -0.99 154 154
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.21 0.4 89 -0.43 16 105
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.24 0.24 0.53 151 -0.4 1 152
mol:cortisol 0.16 0.2 0.4 160 -0.21 4 164
MMP1 -0.18 0.31 -10000 0 -0.71 93 93
Aurora C signaling

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
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
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.018 0.12 -9999 0 -0.35 51 51
alphaV beta3 Integrin -0.054 0.17 -9999 0 -0.36 105 105
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 -0.44 70 70
PTK2B -0.043 0.14 -9999 0 -0.45 31 31
alphaV/beta3 Integrin/JAM-A -0.092 0.2 -9999 0 -0.43 91 91
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 -0.39 78 78
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 -0.59 104 104
GPR124 -0.01 0.1 -9999 0 -0.47 24 24
MAPK1 -0.11 0.28 -9999 0 -0.59 104 104
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 -0.33 102 102
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 -0.4 138 138
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 -0.33 102 102
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 -0.25 101 101
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 73 73
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
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.001 0.081 -10000 0 -0.54 11 11
GNB1/GNG2 -0.057 0.078 -10000 0 -0.19 118 118
AKT1 -0.021 0.11 -10000 0 -0.2 57 57
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 22 22
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 -0.24 119 119
PRKCH -0.06 0.17 -10000 0 -0.34 119 119
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 0.29 37 -10000 0 37
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 -0.5 119 119
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 -0.36 120 120
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 -0.52 120 120
LCK 0.004 0.085 -10000 0 -0.34 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.024 0.079 -10000 0 -0.38 6 6
TXA2-R family/G12 family/GDP/G beta/gamma 0.017 0.035 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.003 0.084 -10000 0 -0.38 6 6
MAPK14 -0.03 0.12 -10000 0 -0.22 116 116
TGM2/GTP -0.083 0.21 -10000 0 -0.42 119 119
MAPK11 -0.033 0.12 -10000 0 -0.23 120 120
ARHGEF1 -0.023 0.094 -10000 0 -0.18 82 82
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.071 0.19 -10000 0 -0.38 120 120
RAB11/GDP 0.014 0.002 -10000 0 -10000 0 0
ICAM1 -0.046 0.14 -10000 0 -0.28 121 121
cAMP biosynthetic process -0.069 0.18 -10000 0 -0.35 119 119
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 -0.27 18 18
VCAM1 -0.051 0.15 -10000 0 -0.29 122 122
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 -0.3 117 117
PGI2/IP -0.031 0.13 -10000 0 -0.42 48 48
PRKACA -0.02 0.089 -10000 0 -0.23 39 39
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 -0.44 6 6
mol:DAG -0.078 0.2 -10000 0 -0.41 120 120
EGFR -0.025 0.13 -10000 0 -0.47 40 40
TXA2/TP alpha -0.098 0.24 -10000 0 -0.48 119 119
Gq family/GTP -0.011 0.054 -10000 0 -0.18 40 40
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 -0.35 120 120
PRKCB -0.091 0.2 -10000 0 -0.39 125 125
PRKCE -0.057 0.17 -10000 0 -0.34 118 118
PRKCD -0.067 0.18 -10000 0 -0.37 120 120
PRKCG -0.073 0.19 -10000 0 -0.38 122 122
muscle contraction -0.096 0.24 -10000 0 -0.48 120 120
PRKCZ -0.057 0.17 -10000 0 -0.34 119 119
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 -0.39 122 122
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 -0.6 120 120
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 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
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 -0.28 14 14
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 65 65
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
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 -0.7 35 35
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 -0.89 108 108
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 -0.44 68 68
TLE4 -0.048 0.18 -10000 0 -0.66 17 17
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 -0.71 26 26
T-helper 2 cell differentiation -0.21 0.31 -10000 0 -0.78 72 72
AP-1/NFAT1 -0.1 0.23 -10000 0 -0.58 61 61
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 -1.1 57 57
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 -0.9 52 52
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 66 66
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 -0.8 41 41
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 -0.87 91 91
FASLG -0.19 0.45 -10000 0 -1.2 55 55
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 -0.61 18 18
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 -0.78 41 41
IL2RA -0.26 0.33 -10000 0 -0.8 105 105
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 -0.65 15 15
IRF4 -0.037 0.16 -10000 0 -0.53 46 46
PTGS2 -0.24 0.42 -10000 0 -0.98 86 86
CSF2 -0.2 0.38 -10000 0 -0.95 67 67
JunB/Fra1/NFAT1-c-4 -0.17 0.35 -10000 0 -0.94 61 61
IL4 -0.22 0.32 -10000 0 -0.82 72 72
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 0.58 10 -10000 0 10
PTPRK -0.046 0.18 -10000 0 -0.61 18 18
IL8 -0.22 0.41 -10000 0 -0.97 83 83
POU2F1 0.012 0.026 -10000 0 -0.57 1 1
Ras signaling in the CD4+ TCR pathway

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
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 -0.41 56 56
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 -0.3 10 10
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 81 81
MAPK1 -0.027 0.093 -9999 0 -0.3 10 10
RAF1 -0.089 0.23 -9999 0 -0.46 116 116
KRAS 0.013 0.001 -9999 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 -0.003 0.11 -9999 0 -0.46 15 15
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.12 -9999 0 -0.39 12 12
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 -0.36 9 9
PTK2B -0.006 0.092 -9999 0 -0.3 32 32
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 -0.34 22 22
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 -0.3 111 111
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 -0.48 21 21
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 -0.56 73 73
ADCY2 -0.067 0.24 -9999 0 -0.57 78 78
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 25 25
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 -0.32 9 9
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 26 26
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 -0.35 22 22
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 -0.3 111 111
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 76 76
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 -0.3 111 111
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 -0.31 52 52
GNAI3 -0.01 0.11 -9999 0 -0.31 53 53
GNAI1 -0.014 0.12 -9999 0 -0.33 56 56
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 -0.35 22 22
cAMP biosynthetic process -0.071 0.25 -9999 0 -0.6 75 75
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 26 26
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 -0.45 111 111
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 -0.3 111 111
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 19 19
Gi(beta/gamma) -0.052 0.22 -9999 0 -0.53 71 71
mol:LPA 0.001 0.022 -9999 0 -0.17 5 5
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
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
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 -0.53 36 36
mol:PIP3 -0.038 0.15 -10000 0 -0.43 57 57
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 -0.48 67 67
GSK3B -0.021 0.15 -10000 0 -0.41 59 59
RAF1 -0.004 0.14 -10000 0 -0.44 30 30
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.04 0.18 -10000 0 -0.48 59 59
STAT1 -0.11 0.38 -10000 0 -1.1 60 60
HRAS/SPRED1 -0.007 0.15 -10000 0 -0.45 31 31
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 -0.49 59 59
HRAS/SPRED2 -0.007 0.15 -10000 0 -0.44 32 32
LYN/TEC/p62DOK -0.024 0.17 -10000 0 -0.45 59 59
MAPK3 0.011 0.1 -10000 0 -0.31 26 26
STAP1 -0.11 0.22 -10000 0 -0.53 80 80
GRAP2 -0.007 0.099 -10000 0 -0.48 21 21
JAK2 -0.091 0.32 -10000 0 -0.91 61 61
STAT1 (dimer) -0.11 0.37 -10000 0 -1 61 61
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.037 0.19 -10000 0 -0.49 61 61
actin filament polymerization -0.05 0.18 -10000 0 -0.49 62 62
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.12 0.28 -10000 0 -0.7 75 75
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 59 59
MAPK8 -0.045 0.18 -10000 0 -0.5 61 61
STAT3 (dimer) -0.038 0.17 -10000 0 -0.48 59 59
positive regulation of transcription 0.013 0.088 -10000 0 -0.26 19 19
mol:GDP -0.023 0.18 -10000 0 -0.53 39 39
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 67 67
SH2B3 -0.04 0.18 -10000 0 -0.48 59 59
PDPK1 -0.029 0.14 -10000 0 -0.4 54 54
SNAI2 -0.096 0.23 -10000 0 -0.6 73 73
positive regulation of cell proliferation -0.075 0.29 -10000 0 -0.79 64 64
KITLG -0.014 0.12 -10000 0 -0.49 27 27
cell motility -0.075 0.29 -10000 0 -0.79 64 64
PTPN6 0.014 0.009 -10000 0 -10000 0 0
EPOR -0.008 0.13 -10000 0 -10000 0 0
STAT5A (dimer) -0.062 0.25 -10000 0 -0.64 68 68
SOCS1 0.008 0.055 -10000 0 -0.53 5 5
cell migration 0.17 0.24 0.52 102 -10000 0 102
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 -0.52 59 59
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 -0.35 27 27
SHC/Grb2/SOS1 -0.023 0.17 -10000 0 -0.45 59 59
STAT5A -0.065 0.25 -10000 0 -0.67 67 67
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 -0.49 67 67
SH2B2 -0.052 0.19 -10000 0 -0.5 62 62
DOK1 0.012 0.022 -10000 0 -0.47 1 1
MATK -0.17 0.24 -10000 0 -0.54 102 102
CREBBP 0.028 0.026 -10000 0 -10000 0 0
BCL2 -0.047 0.3 -10000 0 -1.3 23 23
Signaling events mediated by the Hedgehog family

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
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 -0.39 68 68
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.088 0.16 0.38 68 -10000 0 68
SMO/beta Arrestin2 0.002 0.12 -10000 0 -0.46 16 16
SMO -0.005 0.12 -10000 0 -0.47 19 19
AKT1 0.014 0.081 -10000 0 -0.42 8 8
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 -0.46 19 19
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 -0.46 19 19
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 -0.46 19 19
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 -0.46 19 19
SHH Np/Cholesterol/PTCH1 -0.059 0.16 -10000 0 -0.46 28 28
SHH Np/Cholesterol/PTCH2 -0.063 0.14 -10000 0 -0.28 142 142
SHH Np/Cholesterol/Megalin -0.09 0.16 -10000 0 -0.38 72 72
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 -0.32 62 62
mesenchymal cell differentiation 0.085 0.17 0.31 161 -10000 0 161
mol:Vitamin D3 -0.056 0.16 -10000 0 -0.46 28 28
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
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 -0.66 18 18
CRP -0.077 0.24 -10000 0 -0.71 27 27
cell cycle arrest -0.072 0.24 -10000 0 -0.66 38 38
TIMP1 -0.054 0.22 -10000 0 -0.71 22 22
IL6ST -0.084 0.2 -10000 0 -0.47 102 102
Rac1/GDP -0.11 0.23 -10000 0 -0.5 94 94
AP1 -0.017 0.14 -10000 0 -0.49 11 11
GAB2 0.014 0.002 -10000 0 -10000 0 0
TNFSF11 -0.065 0.23 -10000 0 -0.72 22 22
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 -0.64 110 110
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 -0.56 114 114
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.087 0.23 -10000 0 -0.53 74 74
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 -0.4 3 3
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 -0.69 39 39
STAT1 -0.009 0.025 -10000 0 -10000 0 0
CEBPD -0.062 0.23 -10000 0 -0.69 25 25
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 -0.46 105 105
MAPK11 -0.15 0.31 -10000 0 -0.65 112 112
STAT3 (dimer)/FOXO1 -0.013 0.2 -10000 0 -0.57 12 12
GRB2/SOS1/GAB family -0.11 0.16 -10000 0 -0.46 65 65
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 -0.6 25 25
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 -0.74 16 16
FGG -0.072 0.23 -10000 0 -0.7 24 24
macrophage differentiation -0.072 0.24 -10000 0 -0.66 38 38
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.12 0.21 -10000 0 -0.44 104 104
JUNB -0.072 0.25 -10000 0 -0.82 28 28
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 84 84
GRB2/SOS1/GAB family/SHP2/PI3K 0.034 0.06 -10000 0 -0.68 2 2
STAT3 (dimer) -0.072 0.25 -10000 0 -0.69 38 38
PRKCD -0.07 0.24 -10000 0 -0.59 45 45
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 -0.29 51 51
Rac1/GTP -0.1 0.23 -10000 0 -0.53 81 81
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 -0.68 22 22
IRF1 -0.062 0.23 -10000 0 -0.73 19 19
mol:GDP -0.12 0.24 -10000 0 -0.49 117 117
SOS1 0.014 0.002 -10000 0 -10000 0 0
VAV1 -0.12 0.24 -10000 0 -0.49 117 117
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 51 51
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 -0.42 121 122
LMO4 0.014 0.025 -10000 0 -0.51 1 1
STAT3 (dimer)/PIAS3 -0.076 0.24 -10000 0 -0.66 37 37
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 -0.93 46 46
PCK1 -0.14 0.25 -10000 0 -0.71 41 41
HNF4A -0.2 0.41 -10000 0 -1.2 46 46
KCNJ11 -0.16 0.36 -10000 0 -0.96 46 46
AKT1 -0.032 0.13 -10000 0 -0.44 9 9
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 -0.65 43 44
ACADM -0.16 0.34 -10000 0 -0.93 49 49
TAT -0.14 0.27 -10000 0 -0.79 45 45
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 -0.86 78 78
PKLR -0.18 0.37 -10000 0 -0.94 61 61
APOA1 -0.22 0.45 -10000 0 -1.2 59 59
CPT1C -0.16 0.36 -10000 0 -0.96 53 53
ALAS1 -0.045 0.16 -10000 0 -10000 0 0
TFRC -0.15 0.29 -10000 0 -0.79 46 46
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 -0.91 49 49
NR3C1 -0.001 0.082 -10000 0 -0.47 13 13
CPT1B -0.19 0.37 -10000 0 -0.93 66 66
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 -0.7 28 28
PDX1 -0.093 0.22 -10000 0 -0.66 28 28
UCP2 -0.16 0.34 -10000 0 -0.93 51 51
ALDOB -0.17 0.38 -10000 0 -1 48 48
AFP -0.089 0.19 -10000 0 -0.55 51 51
BDH1 -0.15 0.34 -10000 0 -0.91 50 50
HADH -0.15 0.35 -10000 0 -0.96 44 44
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 -0.55 27 27
SLC2A2 -0.12 0.24 -10000 0 -0.8 20 20
INS -0.02 0.097 -10000 0 -0.58 14 14
FOXA1 -0.014 0.12 -10000 0 -0.32 16 16
FOXA3 -0.11 0.21 -10000 0 -0.54 70 70
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 -0.5 115 115
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 -0.14 37 37
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 -0.14 37 37
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 -0.13 139 139
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 68 68
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 -0.068 37 37
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 -0.14 37 37
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 -0.16 156 156
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 45 45
NLP/gamma Tubulin -0.003 0.027 -10000 0 -0.11 5 5
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 -0.22 3 3
mitotic prometaphase -0.002 0.003 -10000 0 -0.009 20 20
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 -0.14 37 37
Cohesin/SA2 -0.007 0.044 -10000 0 -0.18 4 4
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 -0.22 3 3
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 -0.12 21 21
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
Reelin signaling pathway

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
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 -10000 0 0
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 -0.32 234 234
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 -0.44 81 81
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.14 0.2 -9999 0 -0.54 65 65
RELN/LRP8 -0.039 0.15 -9999 0 -0.35 86 86
GRIN2B/RELN/LRP8/DAB1/Fyn -0.12 0.18 -9999 0 -0.43 84 84
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 48 48
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 -0.4 48 48
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 60 60
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
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.01 0.1 -9999 0 -0.4 23 23
alphaM/beta2 Integrin/GPIbA -0.008 0.097 -9999 0 -0.45 15 15
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 -0.47 9 9
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 -0.53 17 17
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 -0.33 37 37
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 94 94
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 -0.35 55 55
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 -0.34 55 55
cell adhesion -0.009 0.096 -9999 0 -0.45 15 15
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 -0.7 119 119
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 -0.4 22 22
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 -0.41 51 51
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 -0.44 17 17
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 94 94
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 -0.34 55 55
VTN -0.1 0.22 -9999 0 -0.52 107 107
alphaM/beta2 Integrin/CYR61 -0.012 0.1 -9999 0 -0.41 24 24
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 -0.45 16 16
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 -0.41 43 43
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 -0.46 12 12
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 -0.47 25 25
SELP 0.005 0.064 -9999 0 -0.47 9 9
HIF-1-alpha transcription factor network

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
PKM2 -0.11 0.43 -10000 0 -1.1 48 48
HDAC7 0.014 0.008 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.1 0.34 0.39 1 -0.91 42 43
SMAD4 0.015 0 -10000 0 -10000 0 0
ID2 -0.11 0.44 -10000 0 -1.1 48 48
AP1 -0.048 0.15 -10000 0 -0.36 91 91
ABCG2 -0.13 0.46 -10000 0 -1.1 54 54
HIF1A 0 0.077 -10000 0 -0.54 1 1
TFF3 -0.22 0.49 -10000 0 -1.1 78 78
GATA2 0.012 0.027 -10000 0 -0.57 1 1
AKT1 -0.002 0.086 -10000 0 -10000 0 0
response to hypoxia -0.02 0.09 -10000 0 -0.25 14 14
MCL1 -0.11 0.43 -10000 0 -1.1 47 47
NDRG1 -0.11 0.43 -10000 0 -1.1 47 47
SERPINE1 -0.14 0.46 -10000 0 -1.1 59 59
FECH -0.11 0.44 -10000 0 -1.1 50 50
FURIN -0.11 0.43 -10000 0 -1.1 47 47
NCOA2 -0.047 0.16 -10000 0 -0.47 60 60
EP300 0.01 0.13 -10000 0 -0.35 24 24
HMOX1 -0.11 0.44 -10000 0 -1.1 47 47
BHLHE40 -0.11 0.44 -10000 0 -1.1 50 50
BHLHE41 -0.11 0.44 -10000 0 -1.1 47 47
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.013 0.076 -10000 0 -10000 0 0
ENG 0.049 0.09 -10000 0 -10000 0 0
JUN 0.006 0.061 -10000 0 -0.5 7 7
RORA -0.11 0.43 -10000 0 -1.1 47 47
ABCB1 -0.056 0.18 -10000 0 -1.3 8 8
TFRC -0.11 0.43 -10000 0 -1.1 48 48
CXCR4 -0.11 0.44 -10000 0 -1.1 48 48
TF -0.16 0.48 -10000 0 -1.1 69 69
CITED2 -0.11 0.43 -10000 0 -1.1 47 47
HIF1A/ARNT -0.14 0.49 -10000 0 -1.2 51 51
LDHA -0.022 0.06 -10000 0 -0.53 3 3
ETS1 -0.11 0.44 -10000 0 -1.1 47 47
PGK1 -0.11 0.43 -10000 0 -1.1 47 47
NOS2 -0.14 0.46 -10000 0 -1.1 61 61
ITGB2 -0.11 0.44 -10000 0 -1.1 47 47
ALDOA -0.11 0.43 -10000 0 -1.1 47 47
Cbp/p300/CITED2 -0.11 0.46 -10000 0 -1.2 41 41
FOS -0.076 0.19 -10000 0 -0.48 91 91
HK2 -0.11 0.44 -10000 0 -1.1 47 47
SP1 0.022 0.003 -10000 0 -10000 0 0
GCK -0.039 0.35 -10000 0 -1.3 27 27
HK1 -0.11 0.43 -10000 0 -1.1 48 48
NPM1 -0.11 0.43 -10000 0 -1.1 48 48
EGLN1 -0.11 0.43 -10000 0 -1.1 48 48
CREB1 0.021 0.002 -10000 0 -10000 0 0
PGM1 -0.11 0.43 -10000 0 -1.1 47 47
SMAD3 0.015 0 -10000 0 -10000 0 0
EDN1 -0.054 0.33 -10000 0 -1.1 33 33
IGFBP1 -0.13 0.44 -10000 0 -1.1 55 55
VEGFA -0.053 0.35 -10000 0 -0.84 35 35
HIF1A/JAB1 -0.001 0.043 -10000 0 -0.39 1 1
CP -0.16 0.48 -10000 0 -1.1 65 65
CXCL12 -0.12 0.45 -10000 0 -1.1 49 49
COPS5 0.011 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.022 0 -10000 0 -10000 0 0
BNIP3 -0.11 0.43 -10000 0 -1.1 49 49
EGLN3 -0.11 0.44 -10000 0 -1.1 50 50
CA9 -0.12 0.44 -10000 0 -1.1 48 48
TERT -0.19 0.49 -10000 0 -1.1 73 73
ENO1 -0.11 0.43 -10000 0 -1.1 48 48
PFKL -0.11 0.43 -10000 0 -1.1 47 47
NCOA1 0.012 0.005 -10000 0 -10000 0 0
ADM -0.12 0.45 -10000 0 -1.1 55 55
ARNT 0.002 0.072 -10000 0 -10000 0 0
HNF4A -0.03 0.14 -10000 0 -0.57 29 29
ADFP -0.12 0.43 -10000 0 -1.1 49 49
SLC2A1 -0.041 0.33 -10000 0 -0.81 31 31
LEP -0.12 0.44 -10000 0 -1.1 48 48
HIF1A/ARNT/Cbp/p300 -0.069 0.39 -10000 0 -0.95 39 39
EPO -0.13 0.42 -10000 0 -0.93 70 70
CREBBP 0.011 0.13 -10000 0 -0.36 21 21
HIF1A/ARNT/Cbp/p300/HDAC7 -0.1 0.34 0.4 1 -0.92 41 42
PFKFB3 -0.11 0.44 -10000 0 -1.1 48 48
NT5E -0.13 0.47 -10000 0 -1.1 57 57
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.5 81 81
PLCG1 -0.093 0.24 -9999 0 -0.45 125 125
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 -0.36 19 19
negative regulation of cAMP metabolic process -0.1 0.25 -9999 0 -0.48 125 125
MAPK3 -0.13 0.3 -9999 0 -0.6 125 125
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 -0.34 19 19
PTGS2 -0.19 0.42 -9999 0 -0.99 100 100
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 -0.39 21 21
ABCC1 0.012 0.003 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
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 -0.25 69 69
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 -0.25 114 114
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 -0.24 112 112
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 16 16
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 -0.37 82 82
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 -0.27 112 112
Signaling events mediated by PRL

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
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 -0.23 15 15
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 -0.23 15 15
RHOA -0.013 0.071 -10000 0 -0.24 4 4
cell motility -0.011 0.074 -10000 0 -0.24 16 16
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 -0.24 16 16
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
TCGA08_retinoblastoma

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
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 -0.23 4 9
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 0.23 4 -0.14 5 9
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.13 -10000 0 -0.41 26 26
TBX21 -0.089 0.38 -10000 0 -0.93 58 58
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 -0.8 46 46
IL12RB2 -0.006 0.11 -10000 0 -0.5 21 21
GADD45G -0.078 0.32 -10000 0 -0.75 59 59
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 -0.68 66 66
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 -0.76 70 70
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 -0.93 60 60
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 -0.33 50 50
NOS2 -0.11 0.42 -10000 0 -1 62 62
IL12/IL12R/TYK2/JAK2/SPHK2 -0.001 0.12 -10000 0 -0.4 23 23
IL1R1 -0.076 0.35 -10000 0 -0.85 54 54
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 -0.72 56 56
RAB7A -0.038 0.28 -10000 0 -0.74 29 29
lysosomal transport -0.034 0.27 -10000 0 -0.69 31 31
FOS -0.21 0.5 -10000 0 -1.1 101 101
STAT4 (dimer) -0.06 0.33 -10000 0 -0.78 57 57
STAT5A (dimer) -0.17 0.3 -10000 0 -0.8 73 73
GZMA -0.088 0.37 -10000 0 -0.89 62 62
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 -0.86 68 68
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 -0.78 54 54
CCR5 -0.061 0.32 -10000 0 -0.92 35 35
IL1B -0.062 0.19 -10000 0 -0.52 74 74
STAT6 -0.005 0.11 -10000 0 -0.28 15 15
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 26 -10000 0 26
IL2RB -0.019 0.12 -10000 0 -0.49 32 32
proteasomal ubiquitin-dependent protein catabolic process -0.05 0.3 -10000 0 -0.71 56 56
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 -0.88 72 72
MAP2K3 -0.066 0.33 -10000 0 -0.77 56 56
RIPK2 0.001 0.082 -10000 0 -0.57 10 10
MAP2K6 -0.069 0.33 -10000 0 -0.78 57 57
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 -0.67 43 43
STAT1 (dimer) -0.068 0.3 -10000 0 -0.71 61 61
T cell proliferation -0.042 0.26 -10000 0 -0.58 60 60
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 -0.63 59 59
ATF2 -0.063 0.31 -10000 0 -0.73 55 55
JNK signaling in the CD4+ TCR pathway

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
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 -0.5 6 6
JUN -0.11 0.25 -9999 0 -0.53 124 124
MAP3K7 0.016 0.084 -9999 0 -0.5 6 6
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 -0.49 7 7
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
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 -0.55 60 60
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 60 60
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 80 82
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 -0.37 58 58
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 -0.24 1 1
NT3 (dimer)/TRKA -0.055 0.17 -10000 0 -0.35 109 109
RIN/GDP -0.01 0.097 -10000 0 -0.24 29 29
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 -0.37 255 255
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 -0.34 25 25
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 -0.23 20 20
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 -0.52 48 48
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 -0.22 4 4
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 -0.32 72 72
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 -0.24 1 1
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 21 21
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 -0.23 21 21
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 -0.32 72 72
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 -0.32 54 54
FRS2 family/SHP2/CRK family 0.039 0.011 -10000 0 -10000 0 0
Aurora A signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.17 36 36
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 -0.21 36 36
AURKB -0.048 0.077 -9999 0 -0.16 149 149
CDC25B 0.013 0.056 -9999 0 -0.29 4 4
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 -0.3 183 183
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 -0.21 36 36
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
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 24 24
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 -0.73 71 71
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
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.022 0.041 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.063 0.11 -9999 0 -0.37 34 34
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 -0.5 17 17
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 -0.37 27 27
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 -0.46 28 28
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 -0.36 34 34
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 -0.32 22 22
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 -0.28 21 21
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
Osteopontin-mediated events

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
IKK alpha homodimer -0.049 0.15 -9999 0 -0.45 20 20
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 -0.47 19 19
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 -0.48 20 20
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 16 16
NF kappa B1 p50/RelA -0.07 0.11 -9999 0 -0.44 18 18
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 -0.49 23 23
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 42 42
MMP2 -0.058 0.19 -9999 0 -0.62 27 27
p75(NTR)-mediated 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
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 -0.4 8 8
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 -0.28 64 64
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 -0.37 5 5
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 -0.28 64 64
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 -0.24 64 64
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 -0.28 64 64
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 -0.28 64 64
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 0.17 117 -0.35 10 127
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 -0.4 6 6
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 -0.39 4 4
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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
Syndecan-4-mediated signaling events

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
PTK2 -0.008 0.078 -9999 0 -0.44 13 13
Syndecan-4/Syndesmos -0.1 0.14 -9999 0 -0.46 30 30
positive regulation of JNK cascade -0.1 0.15 -9999 0 -0.44 45 45
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 -0.17 13 13
Syndecan-4/Laminin alpha1 -0.13 0.16 -9999 0 -0.46 54 54
Syndecan-4/CXCL12/CXCR4 -0.11 0.16 -9999 0 -0.46 45 45
Syndecan-4/Laminin alpha3 -0.12 0.16 -9999 0 -0.45 54 54
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 -0.48 42 42
FZD7 -0.004 0.09 -9999 0 -0.47 18 18
Syndecan-4/FGFR1/FGF -0.12 0.13 -9999 0 -0.48 28 28
THBS1 -0.012 0.11 -9999 0 -0.49 25 25
integrin-mediated signaling pathway -0.11 0.15 -9999 0 -0.44 43 43
positive regulation of MAPKKK cascade -0.1 0.15 -9999 0 -0.44 45 45
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 -0.47 41 41
Syndecan-4/GIPC -0.1 0.14 -9999 0 -0.46 30 30
Syndecan-4/RANTES -0.11 0.15 -9999 0 -0.46 41 41
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 -0.45 76 76
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 -0.43 42 42
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 -0.45 42 42
Syndecan-4/Tenascin C -0.11 0.15 -9999 0 -0.46 43 43
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 -0.49 45 45
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.036 0.14 -9999 0 -0.43 33 33
SMAD6-7/SMURF1 0.022 0.039 -9999 0 -10000 0 0
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 -0.37 50 50
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 -0.6 42 42
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 -0.42 57 57
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 -0.41 53 53
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 -0.6 40 40
BMP2-4/GREM1 -0.059 0.17 -9999 0 -0.44 56 56
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 -0.6 27 27
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.014 0.1 -9999 0 -0.32 5 5
S1P4 pathway

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
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 60 60
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 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
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 -0.42 29 29
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 -0.42 29 29
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
Effects of Botulinum toxin

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
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 -0.31 20 20
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
IL27-mediated signaling events

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
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 -0.82 22 23
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 -0.89 19 125
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 -0.51 64 64
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 -0.092 20 20
T cell differentiation -0.003 0.006 0.015 1 -0.021 25 26
STAT3 (dimer) -0.021 0.17 -10000 0 -0.56 25 25
STAT5A (dimer) -0.021 0.17 -10000 0 -0.59 23 23
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 -0.55 25 25
IL27/EBI3 -0.007 0.11 -10000 0 -0.4 35 35
IL27RA -0.016 0.18 -10000 0 -1.1 12 12
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
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.029 0.13 -10000 0 -0.34 39 39
IKBKB 0.01 0.059 -10000 0 -0.24 2 2
AKT1 -0.015 0.097 0.2 8 -0.24 36 44
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 -0.23 24 24
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 -0.31 15 26
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 0.081 5 -10000 0 5
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 -0.42 64 64
mol:GDP -0.013 0.083 0.24 11 -0.28 24 35
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 0.084 4 -10000 0 4
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 -0.38 26 31
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 73 73
ubiquitin-dependent protein catabolic process 0.018 0.022 0.083 5 -10000 0 5
BTK 0.008 0.088 0.31 1 -0.81 2 3
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 46 46
SH3BP5 0.013 0 -10000 0 -10000 0 0
PIK3AP1 -0.014 0.095 -10000 0 -0.33 23 23
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 -0.23 24 24
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 -0.32 6 6
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 -0.42 45 45
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 -0.42 78 78
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 -0.41 99 99
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 -0.38 60 60
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 -0.54 48 48
CARD11 -0.016 0.1 0.23 8 -0.41 19 27
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 39 47
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
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 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
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
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.43 23 23
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 -0.52 39 39
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 -0.62 10 10
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 -0.56 9 9
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 41 41
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 -0.56 9 9
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 -0.38 37 37
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 -0.53 11 11
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 -0.42 25 25
ROCK1 0.017 0.046 -10000 0 -0.35 5 5
RAS family/GDP -0.065 0.1 -10000 0 -0.46 13 13
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
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.88 88 88
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 -0.87 88 88
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 -0.29 17 17
JAK1 -0.001 0.082 -9999 0 -0.34 27 27
ELK1/SRF 0.017 0.069 -9999 0 -0.29 17 17
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
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.05 0.14 -10000 0 -0.51 35 35
FYN -0.014 0.21 -10000 0 -0.66 37 37
LAT/GRAP2/SLP76 -0.062 0.17 -10000 0 -0.54 44 44
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 0 0.15 -10000 0 -0.44 39 39
B2M 0.014 0.003 -10000 0 -10000 0 0
IKBKG -0.013 0.037 -10000 0 -0.15 19 19
MAP3K8 -0.001 0.084 -10000 0 -0.47 15 15
mol:Ca2+ -0.003 0.013 -10000 0 -0.13 2 2
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 -0.65 41 41
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 -0.63 38 38
receptor internalization -0.029 0.21 -10000 0 -0.6 45 45
PRF1 -0.017 0.23 -10000 0 -1 20 20
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 -0.38 34 34
LAT -0.025 0.22 -10000 0 -0.63 44 44
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 30 30
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.066 -10000 0 -0.26 29 29
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 -0.43 38 41
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.023 0.21 -10000 0 -0.63 37 37
ORAI1 0.005 0.026 0.29 4 -10000 0 4
CSK -0.02 0.2 -10000 0 -0.64 38 38
B7 family/CD28 -0.038 0.24 -10000 0 -0.72 40 40
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.032 0.24 -10000 0 -0.73 39 39
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 -0.69 37 37
PAG1 -0.02 0.21 -10000 0 -0.65 38 38
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.027 0.23 -10000 0 -0.73 38 38
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 -0.31 31 31
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 -0.063 4 4
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 -0.94 20 20
RAP1A/GTP -0.004 0.013 -10000 0 -0.066 15 15
mol:PI-3-4-5-P3 -0.009 0.18 -10000 0 -0.52 41 41
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 -0.56 41 41
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 39 39
IKK complex 0.014 0.055 -10000 0 -0.12 34 34
RAS family/GDP -0.003 0.011 -10000 0 -0.076 5 5
MAP3K14 0.012 0.098 -10000 0 -0.3 30 30
PDPK1 0.003 0.14 -10000 0 -0.42 38 38
TCR/CD3/MHC I/CD8/Fyn -0.024 0.23 -10000 0 -0.74 37 37
Lissencephaly gene (LIS1) in neuronal migration and development

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
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 -0.48 81 81
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.021 0.13 -9999 0 -0.4 21 21
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 -0.29 81 81
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 -0.5 46 46
RELN/VLDLR -0.027 0.14 -9999 0 -0.32 81 81
CDC42 0.021 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.011 0.037 -10000 0 -0.57 2 2
Jak2/Leptin Receptor -0.031 0.12 0.19 1 -0.41 22 23
PTP1B/AKT1 -0.037 0.081 -10000 0 -0.31 12 12
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 -0.3 13 13
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 -0.32 13 13
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 -0.36 46 46
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 -0.3 16 16
Crk/p130 Cas -0.031 0.082 -10000 0 -0.32 11 11
DOK1 -0.029 0.079 -10000 0 -0.29 12 12
JAK2 -0.033 0.1 -10000 0 -0.4 17 17
Jak2/Leptin Receptor/Leptin -0.084 0.14 -10000 0 -0.43 56 56
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 -0.34 19 19
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 -0.42 6 6
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 -0.4 17 17
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 -0.28 23 23
STAT5A -0.037 0.086 -10000 0 -0.28 22 22
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.04 0.086 -10000 0 -0.31 17 17
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
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.016 0.1 -10000 0 -0.32 51 51
CRKL -0.004 0.11 -10000 0 -0.44 18 18
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 -0.44 18 18
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 -0.29 51 51
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 -0.46 27 27
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 -0.5 17 17
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 -0.49 18 18
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 -0.55 38 38
a4b1 and a4b7 Integrin signaling

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
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 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
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 0.22 1 -10000 0 1
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
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.25 15 -10000 0 15
WIF1 -0.22 0.24 -10000 0 -0.47 242 242
beta catenin/RanBP3 0.018 0.086 0.32 26 -10000 0 26
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 0.22 8 -10000 0 8
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 -10000 0 -10000 0 0
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 0.21 235 -10000 0 235
CREBBP 0.012 0.011 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
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 0.4 4 -10000 0 4
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 -0.34 9 9
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 -0.55 50 50
endothelial cell migration 0.06 0.24 1.2 14 -10000 0 14
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 -1.3 14 14
SMAD3/SMAD4/ATF2 0.011 0.082 -10000 0 -0.33 5 5
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 -0.49 33 33
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 -10000 0 0
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 -0.54 22 22
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 -0.62 3 3
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 -0.57 28 28
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 -0.49 33 33
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 -0.51 14 14
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 -0.34 1 1
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 -0.46 65 65
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 -0.34 4 4
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 -0.4 46 46
SMAD2-3/SMAD4/FOXO1-3a-4 0.047 0.039 -10000 0 -0.49 1 1
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
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.13 3 3
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 31 31
ARAP2 0.012 0.022 -9999 0 -0.47 1 1
mol:GDP -0.025 0.087 -9999 0 -0.25 39 39
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 16 16
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 -0.25 28 28
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 25 25
actin filament binding 0 0 -9999 0 0 28 28
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 -0.33 28 28
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 25 25
endosomal lumen acidification 0 0 -9999 0 0 32 32
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 13 13
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
Fc-epsilon receptor I signaling in mast cells

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
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 -0.43 47 47
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 -0.36 21 21
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 -0.41 23 23
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 -0.42 18 18
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 -0.38 23 23
PTPN13 0.004 0.11 -10000 0 -0.45 16 16
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 18 18
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 -0.48 33 33
LAT -0.01 0.12 -10000 0 -0.38 30 30
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 -0.33 79 79
Antigen/IgE/Fc epsilon R1 -0.026 0.12 -10000 0 -0.3 73 73
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 -0.48 28 28
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 -0.46 29 29
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 -0.53 20 20
RAF1 0.015 0.019 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.037 0.17 -10000 0 -0.48 49 49
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 -0.39 25 25
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 -0.45 16 16
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 -0.45 24 24
RELA 0.013 0 -10000 0 -10000 0 0
ITK -0.028 0.076 -10000 0 -0.36 16 16
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 33 33
PTK2 -0.002 0.11 -10000 0 -0.47 16 16
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 -0.44 34 34
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 40 40
mol:Choline -0.009 0.11 -10000 0 -0.37 23 23
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 -0.43 21 21
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 -0.47 29 29
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 -0.37 23 23
IKK complex 0.008 0.082 0.15 2 -0.21 22 24
WIPF1 0.007 0.052 -10000 0 -0.47 6 6
Plasma membrane estrogen receptor signaling

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.52 20 20
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 -0.38 58 58
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 -0.32 6 6
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
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 -0.4 50 50
GNAO1 -0.078 0.19 -9999 0 -0.47 96 96
S1P/S1P3/G12/G13 0.018 0.052 -9999 0 -0.31 1 1
AKT1 0.003 0.063 -9999 0 -10000 0 0
AKT3 -0.013 0.13 -9999 0 -0.85 4 4
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 -0.46 52 52
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 -0.54 12 12
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
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.012 0.075 -10000 0 -0.44 3 3
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 -0.47 6 6
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 33 33
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 -0.46 7 7
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 -0.6 3 3
GRIN2B -0.041 0.13 -10000 0 -0.57 3 3
ErbB4/ErbB2/betacellulin 0.007 0.1 -10000 0 -0.55 8 8
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 -10000 0 0
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 -0.45 3 3
MAPK3 -0.025 0.13 -10000 0 -0.43 12 12
STAT1 (dimer) 0.011 0.078 -10000 0 -0.48 4 4
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 -0.55 7 7
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 -10000 0 0
neural crest cell migration -0.046 0.14 -10000 0 -0.54 7 7
ERBB2 0.016 0.052 -10000 0 -0.32 11 11
WWOX/E4ICDs 0.017 0.061 -10000 0 -0.58 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.082 0.17 -10000 0 -0.56 24 24
apoptosis 0.027 0.11 0.52 7 -10000 0 7
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 -0.45 3 3
ErbB4/ErbB4/betacellulin/betacellulin 0 0.11 -10000 0 -0.44 17 17
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 -0.58 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.048 0.13 -10000 0 -0.55 3 3
STAT5A 0.042 0.07 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.063 0.16 -10000 0 -0.54 20 20
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 -0.53 2 2
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 -10000 0 0
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 -0.51 10 10
glial cell differentiation -0.015 0.058 0.53 2 -10000 0 2
WWOX 0.012 0.022 -10000 0 -0.47 1 1
cell proliferation -0.061 0.17 -10000 0 -0.52 26 26
Visual signal transduction: Cones

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
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 -0.38 5 5
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 -0.5 3 3
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 -0.38 5 5
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
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 -0.36 24 24
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 -0.55 5 5
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
FAS signaling pathway (CD95)

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
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 -0.34 24 24
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 -0.47 28 28
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 -10000 0 0
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 -0.32 26 26
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 -10000 0 -0.31 1 1
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 -0.35 24 24
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
Signaling events mediated by VEGFR1 and VEGFR2

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
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 -0.77 30 30
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 -0.6 23 23
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 -0.49 28 28
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 -0.59 23 23
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 -0.66 28 28
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 -0.7 27 27
MAP3K13 -0.001 0.16 -9999 0 -0.63 25 25
PDPK1 0.024 0.15 -9999 0 -0.57 23 23
IL2 signaling events mediated by STAT5

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
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 -0.45 16 16
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 -0.46 89 89
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
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 -0.27 12 12
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 -0.3 10 10
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
Visual signal transduction: Rods

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
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 -0.38 5 5
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 -0.38 5 5
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
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 -0.4 5 5
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 -0.41 4 4
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 -0.23 3 3
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.072 0.21 -10000 0 -0.6 20 20
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 -0.51 16 16
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 -10000 0 0
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 37 37
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 -0.43 49 49
heart morphogenesis -0.04 0.11 -10000 0 -0.4 5 5
RAS family/GDP -0.029 0.11 -10000 0 -0.42 4 4
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
Signaling events mediated by HDAC Class III

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
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 -0.21 6 6
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 -0.21 4 4
FOXO1/FHL2/SIRT1 0.011 0.058 -10000 0 -0.24 24 24
HIST1H1E -0.04 0.093 -10000 0 -0.18 153 153
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
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 -0.3 5 5
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 -0.31 49 49
apoptosis -0.021 0.046 -9999 0 -0.29 5 5
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 -0.4 8 8
p38alpha-beta/MKP5 0.006 0.096 -9999 0 -0.4 8 8
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 -0.44 9 9
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 -0.27 44 44
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 -0.39 63 63
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 -0.23 19 19
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 38 38
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 -0.49 3 3
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 -0.31 139 139
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 -0.51 4 4
GAB1/SHIP/PIK3R1/SHP2/SHC -0.042 0.087 -9999 0 -0.39 13 13
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 -0.41 3 3
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 45 45
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
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.55 10 10
PI3K 0.014 0.061 -10000 0 -0.79 2 2
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 0.54 10 -10000 0 10
MAPK8 0.016 0.056 -10000 0 -0.64 2 2
Ephrin B1/EPHB1-2/RGS3 -0.05 0.14 -10000 0 -0.55 10 10
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 0.54 10 -10000 0 10
chemotaxis 0.05 0.14 0.54 10 -10000 0 10
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
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.06 0.12 -9999 0 -0.46 20 20
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 -0.3 14 14
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 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
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 -0.21 6 6
HIF1A 0.021 0.015 -9999 0 -0.2 1 1
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 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
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 -0.56 1 1
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
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 -1.1 10 10
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 -0.66 51 51
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 -1.1 9 9
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 -0.42 12 12
ETS1 0.021 0.054 -10000 0 -0.49 5 5
CITED2 -0.003 0.034 -10000 0 -0.41 2 2
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 -0.49 6 6
VEGFA -0.03 0.27 -10000 0 -0.69 33 33
CREBBP 0.013 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
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 -10000 0 0
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
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.31 33 33
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