PARADIGM pathway analysis of mRNASeq expression data
Stomach Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C19Z93C3
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 43 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
Syndecan-1-mediated signaling events 60
TCGA08_retinoblastoma 58
FOXA2 and FOXA3 transcription factor networks 53
IL23-mediated signaling events 53
Lissencephaly gene (LIS1) in neuronal migration and development 49
IL4-mediated signaling events 49
Osteopontin-mediated events 47
EPHB forward signaling 47
Aurora C signaling 39
Ephrin B reverse signaling 37
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 274 . 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 ( 274 ).

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
Syndecan-1-mediated signaling events 0.2190 60 2059 34 -0.31 0.012 1000 -1000 -0.061 -1000
TCGA08_retinoblastoma 0.2117 58 467 8 -0.2 0.061 1000 -1000 -0.014 -1000
FOXA2 and FOXA3 transcription factor networks 0.1934 53 2460 46 -0.78 0.026 1000 -1000 -0.13 -1000
IL23-mediated signaling events 0.1934 53 3232 60 -0.75 0.012 1000 -1000 -0.19 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1788 49 2671 54 -0.38 0.016 1000 -1000 -0.1 -1000
IL4-mediated signaling events 0.1788 49 4517 91 -0.85 0.74 1000 -1000 -0.18 -1000
Osteopontin-mediated events 0.1715 47 1823 38 -0.39 0.015 1000 -1000 -0.1 -1000
EPHB forward signaling 0.1715 47 4051 85 -0.4 0.24 1000 -1000 -0.098 -1000
Aurora C signaling 0.1423 39 277 7 -0.46 0.005 1000 -1000 -0.028 -1000
Ephrin B reverse signaling 0.1350 37 1803 48 -0.4 0.28 1000 -1000 -0.073 -1000
Effects of Botulinum toxin 0.1277 35 921 26 -0.36 0.012 1000 -1000 -0.064 -1000
Reelin signaling pathway 0.1241 34 1916 56 -0.28 0.019 1000 -1000 -0.076 -1000
Syndecan-4-mediated signaling events 0.1204 33 2238 67 -0.38 0.051 1000 -1000 -0.099 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1131 31 1061 34 -0.14 0.012 1000 -1000 -0.058 -1000
Syndecan-2-mediated signaling events 0.1095 30 2084 69 -0.4 0.041 1000 -1000 -0.045 -1000
Wnt signaling 0.1095 30 211 7 -0.14 -0.037 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1058 29 2263 78 -0.18 0.047 1000 -1000 -0.092 -1000
Aurora B signaling 0.0949 26 1743 67 -0.34 0.013 1000 -1000 -0.079 -1000
Fc-epsilon receptor I signaling in mast cells 0.0912 25 2487 97 -0.16 0.032 1000 -1000 -0.094 -1000
TCGA08_p53 0.0912 25 181 7 -0.15 0.058 1000 -1000 -0.012 -1000
Ephrin A reverse signaling 0.0839 23 163 7 -0.045 0 1000 -1000 -0.031 -1000
Glypican 1 network 0.0839 23 1116 48 -0.25 0.02 1000 -1000 -0.048 -1000
Glucocorticoid receptor regulatory network 0.0839 23 2699 114 -0.62 0.26 1000 -1000 -0.076 -1000
FOXM1 transcription factor network 0.0839 23 1189 51 -0.32 0.024 1000 -1000 -0.22 -1000
Signaling events mediated by the Hedgehog family 0.0803 22 1162 52 -0.13 0.083 1000 -1000 -0.074 -1000
Noncanonical Wnt signaling pathway 0.0803 22 580 26 -0.14 0.012 1000 -1000 -0.071 -1000
amb2 Integrin signaling 0.0803 22 1807 82 -0.23 0.012 1000 -1000 -0.092 -1000
BCR signaling pathway 0.0803 22 2238 99 -0.38 0.078 1000 -1000 -0.089 -1000
HIF-1-alpha transcription factor network 0.0766 21 1654 76 -0.41 0.02 1000 -1000 -0.19 -1000
Presenilin action in Notch and Wnt signaling 0.0766 21 1289 61 -0.38 0.036 1000 -1000 -0.082 -1000
Endothelins 0.0766 21 2096 96 -0.23 0.028 1000 -1000 -0.089 -1000
Canonical Wnt signaling pathway 0.0766 21 1097 51 -0.38 0.064 1000 -1000 -0.071 -1000
Glypican 2 network 0.0766 21 85 4 -0.051 -0.041 1000 -1000 -0.029 -1000
p75(NTR)-mediated signaling 0.0730 20 2614 125 -0.39 0.03 1000 -1000 -0.11 -1000
Signaling events regulated by Ret tyrosine kinase 0.0657 18 1525 82 -0.18 0.012 1000 -1000 -0.087 -1000
BMP receptor signaling 0.0620 17 1398 81 -0.3 0.041 1000 -1000 -0.092 -1000
PLK1 signaling events 0.0584 16 1409 85 -0.13 0.028 1000 -1000 -0.044 -1000
PDGFR-alpha signaling pathway 0.0584 16 707 44 -0.36 0.27 1000 -1000 -0.058 -1000
Visual signal transduction: Cones 0.0547 15 602 38 -0.14 0.017 1000 -1000 -0.059 -1000
Syndecan-3-mediated signaling events 0.0547 15 528 35 -0.37 0.016 1000 -1000 -0.061 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0547 15 1084 68 -0.46 0.034 1000 -1000 -0.14 -1000
EGFR-dependent Endothelin signaling events 0.0547 15 322 21 -0.093 0.019 1000 -1000 -0.075 -1000
PLK2 and PLK4 events 0.0511 14 43 3 -0.034 -0.026 1000 -1000 -0.014 -1000
Nectin adhesion pathway 0.0474 13 867 63 -0.55 0.034 1000 -1000 -0.08 -1000
Retinoic acid receptors-mediated signaling 0.0474 13 755 58 -0.29 0.016 1000 -1000 -0.08 -1000
Calcium signaling in the CD4+ TCR pathway 0.0474 13 410 31 -0.26 0.012 1000 -1000 -0.099 -1000
Regulation of Telomerase 0.0474 13 1345 102 -0.3 0.036 1000 -1000 -0.11 -1000
Visual signal transduction: Rods 0.0474 13 712 52 -0.17 0.013 1000 -1000 -0.079 -1000
IL1-mediated signaling events 0.0438 12 770 62 -0.16 0.058 1000 -1000 -0.081 -1000
LPA receptor mediated events 0.0438 12 1265 102 -0.24 0.041 1000 -1000 -0.092 -1000
Arf6 signaling events 0.0401 11 731 62 -0.16 0.021 1000 -1000 -0.072 -1000
TCR signaling in naïve CD8+ T cells 0.0401 11 1080 93 -0.16 0.089 1000 -1000 -0.087 -1000
IL27-mediated signaling events 0.0401 11 611 51 -0.33 0.032 1000 -1000 -0.087 -1000
ErbB4 signaling events 0.0365 10 755 69 -0.16 0.082 1000 -1000 -0.1 -1000
IFN-gamma pathway 0.0365 10 684 68 -0.19 0.025 1000 -1000 -0.1 -1000
Integrins in angiogenesis 0.0365 10 872 84 -0.39 0.03 1000 -1000 -0.096 -1000
LPA4-mediated signaling events 0.0328 9 108 12 -0.058 0.018 1000 -1000 -0.026 -1000
IL12-mediated signaling events 0.0328 9 821 87 -0.21 0.034 1000 -1000 -0.14 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0328 9 829 85 -0.092 0.027 1000 -1000 -0.072 -1000
S1P1 pathway 0.0328 9 334 36 -0.049 0.012 1000 -1000 -0.059 -1000
IL6-mediated signaling events 0.0328 9 714 75 -0.24 0.05 1000 -1000 -0.1 -1000
PDGFR-beta signaling pathway 0.0328 9 942 97 -0.14 0.032 1000 -1000 -0.092 -1000
ErbB2/ErbB3 signaling events 0.0292 8 556 65 -0.2 0.019 1000 -1000 -0.079 -1000
Signaling events mediated by PTP1B 0.0292 8 610 76 -0.24 0.028 1000 -1000 -0.086 -1000
IL2 signaling events mediated by PI3K 0.0292 8 465 58 -0.2 0.054 1000 -1000 -0.093 -1000
Nongenotropic Androgen signaling 0.0292 8 427 52 -0.043 0.021 1000 -1000 -0.058 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0292 8 1075 120 -0.17 0.081 1000 -1000 -0.074 -1000
Aurora A signaling 0.0255 7 432 60 -0.12 0.025 1000 -1000 -0.059 -1000
IGF1 pathway 0.0255 7 451 57 -0.076 0.019 1000 -1000 -0.099 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0255 7 262 33 -0.19 0.036 1000 -1000 -0.06 -1000
Regulation of Androgen receptor activity 0.0255 7 513 70 -0.5 0.048 1000 -1000 -0.075 -1000
Ras signaling in the CD4+ TCR pathway 0.0255 7 131 17 -0.023 0.018 1000 -1000 -0.039 -1000
Coregulation of Androgen receptor activity 0.0219 6 504 76 -0.19 0.023 1000 -1000 -0.042 -1000
Circadian rhythm pathway 0.0219 6 135 22 -0.015 0.037 1000 -1000 -0.056 -1000
Cellular roles of Anthrax toxin 0.0219 6 251 39 -0.031 0.015 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0219 6 344 52 -0.17 0.031 1000 -1000 -0.064 -1000
FAS signaling pathway (CD95) 0.0219 6 306 47 -0.098 0.023 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 0.0219 6 290 44 -0.095 0.012 1000 -1000 -0.051 -1000
Caspase cascade in apoptosis 0.0182 5 429 74 -0.085 0.034 1000 -1000 -0.043 -1000
Regulation of nuclear SMAD2/3 signaling 0.0182 5 734 136 -0.13 0.079 1000 -1000 -0.074 -1000
BARD1 signaling events 0.0182 5 310 57 -0.083 0.033 1000 -1000 -0.069 -1000
Thromboxane A2 receptor signaling 0.0182 5 616 105 -0.11 0.036 1000 -1000 -0.074 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0182 5 483 83 -0.38 0.054 1000 -1000 -0.072 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0182 5 439 74 -0.16 0.06 1000 -1000 -0.088 -1000
Signaling events mediated by PRL 0.0182 5 199 34 -0.086 0.03 1000 -1000 -0.035 -1000
E-cadherin signaling events 0.0182 5 29 5 -0.019 0.01 1000 -1000 -0.053 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0146 4 121 28 -0.043 0.025 1000 -1000 -0.044 -1000
EPO signaling pathway 0.0146 4 269 55 -0.021 0.051 1000 -1000 -0.092 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0146 4 178 37 -0.18 0.038 1000 -1000 -0.057 -1000
S1P5 pathway 0.0146 4 77 17 -0.043 0.034 1000 -1000 -0.043 -1000
Signaling mediated by p38-gamma and p38-delta 0.0146 4 70 15 -0.017 0.024 1000 -1000 -0.036 -1000
TCGA08_rtk_signaling 0.0146 4 115 26 -0.092 0.038 1000 -1000 -0.02 -1000
Plasma membrane estrogen receptor signaling 0.0146 4 394 86 -0.12 0.033 1000 -1000 -0.09 -1000
S1P3 pathway 0.0146 4 172 42 -0.048 0.022 1000 -1000 -0.05 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0146 4 437 88 -0.2 0.078 1000 -1000 -0.11 -1000
Class IB PI3K non-lipid kinase events 0.0146 4 12 3 -0.001 0.001 1000 -1000 -0.013 -1000
JNK signaling in the CD4+ TCR pathway 0.0109 3 60 17 -0.016 0.045 1000 -1000 -0.062 -1000
Ceramide signaling pathway 0.0109 3 273 76 -0.077 0.043 1000 -1000 -0.059 -1000
Signaling events mediated by HDAC Class III 0.0109 3 124 40 -0.062 0.021 1000 -1000 -0.049 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0109 3 388 125 -0.02 0.07 1000 -1000 -0.094 -1000
IL2 signaling events mediated by STAT5 0.0109 3 69 22 -0.026 0.057 1000 -1000 -0.06 -1000
Class I PI3K signaling events 0.0109 3 270 73 -0.11 0.034 1000 -1000 -0.074 -1000
Insulin Pathway 0.0109 3 252 74 -0.11 0.036 1000 -1000 -0.087 -1000
VEGFR1 specific signals 0.0109 3 212 56 -0.016 0.044 1000 -1000 -0.064 -1000
S1P4 pathway 0.0109 3 96 25 -0.043 0.027 1000 -1000 -0.048 -1000
Hedgehog signaling events mediated by Gli proteins 0.0073 2 164 65 -0.083 0.055 1000 -1000 -0.082 -1000
Class I PI3K signaling events mediated by Akt 0.0073 2 140 68 -0.058 0.043 1000 -1000 -0.05 -1000
TRAIL signaling pathway 0.0073 2 99 48 -0.009 0.047 1000 -1000 -0.062 -1000
HIF-2-alpha transcription factor network 0.0073 2 101 43 -0.088 0.09 1000 -1000 -0.093 -1000
FoxO family signaling 0.0073 2 185 64 -0.031 0.12 1000 -1000 -0.083 -1000
Regulation of p38-alpha and p38-beta 0.0073 2 146 54 -0.11 0.032 1000 -1000 -0.07 -1000
E-cadherin signaling in the nascent adherens junction 0.0073 2 153 76 -0.017 0.05 1000 -1000 -0.088 -1000
Rapid glucocorticoid signaling 0.0073 2 47 20 -0.012 0.012 1000 -1000 -0.043 -1000
E-cadherin signaling in keratinocytes 0.0073 2 121 43 -0.034 0.036 1000 -1000 -0.067 -1000
p38 MAPK signaling pathway 0.0073 2 116 44 -0.086 0.033 1000 -1000 -0.073 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0036 1 24 23 -0.018 0.039 1000 -1000 -0.065 -1000
Canonical NF-kappaB pathway 0.0036 1 46 39 -0.019 0.073 1000 -1000 -0.085 -1000
Signaling events mediated by HDAC Class II 0.0036 1 93 75 -0.028 0.031 1000 -1000 -0.068 -1000
Insulin-mediated glucose transport 0.0036 1 52 32 -0.036 0.032 1000 -1000 -0.068 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0036 1 70 45 -0.021 0.07 1000 -1000 -0.093 -1000
Arf6 trafficking events 0.0036 1 119 71 -0.1 0.041 1000 -1000 -0.065 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 4 5 0.009 0.019 1000 -1000 -0.026 -1000
Arf6 downstream pathway 0.0000 0 41 43 -0.025 0.025 1000 -1000 -0.042 -1000
mTOR signaling pathway 0.0000 0 18 53 -0.014 0.027 1000 -1000 -0.061 -1000
ceramide signaling pathway 0.0000 0 38 49 -0.021 0.045 1000 -1000 -0.051 -1000
Signaling events mediated by HDAC Class I 0.0000 0 83 104 -0.019 0.053 1000 -1000 -0.075 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 34 36 -0.034 0.035 1000 -1000 -0.071 -1000
Atypical NF-kappaB pathway 0.0000 0 8 31 -0.003 0.044 1000 -1000 -0.044 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 26 27 -0.009 0.031 1000 -1000 -0.06 -1000
Arf1 pathway 0.0000 0 2 54 -0.001 0.033 1000 -1000 -0.043 -1000
Alternative NF-kappaB pathway 0.0000 0 5 13 -0.002 0.016 1000 -1000 -0.06 -1000
Total NA 1686 95992 7203 -23 6 131000 -131000 -9.5 -131000
Syndecan-1-mediated signaling events

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
TGFB1 0.011 0.03 -9999 0 -0.48 1 1
CCL5 0.002 0.072 -9999 0 -0.48 6 6
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.26 0.22 -9999 0 -0.5 99 99
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 -0.26 0.23 -9999 0 -0.5 110 110
Syndecan-1/Syntenin -0.24 0.21 -9999 0 -0.47 99 99
MAPK3 -0.2 0.19 -9999 0 -0.5 44 44
HGF/MET -0.073 0.21 -9999 0 -0.56 43 43
TGFB1/TGF beta receptor Type II 0.011 0.03 -9999 0 -0.48 1 1
BSG 0.012 0 -9999 0 -10000 0 0
keratinocyte migration -0.26 0.23 -9999 0 -0.49 110 110
Syndecan-1/RANTES -0.24 0.2 -9999 0 -0.47 102 102
Syndecan-1/CD147 -0.22 0.2 -9999 0 -0.45 99 99
Syndecan-1/Syntenin/PIP2 -0.23 0.2 -9999 0 -0.45 99 99
LAMA5 -0.037 0.19 -9999 0 -0.74 18 18
positive regulation of cell-cell adhesion -0.23 0.18 -9999 0 -0.44 99 99
MMP7 -0.31 0.37 -9999 0 -0.72 121 121
HGF -0.003 0.1 -9999 0 -0.7 6 6
Syndecan-1/CASK -0.24 0.2 -9999 0 -0.48 99 99
Syndecan-1/HGF/MET -0.28 0.25 -9999 0 -0.51 126 126
regulation of cell adhesion -0.19 0.18 -9999 0 -0.55 28 28
HPSE -0.037 0.19 -9999 0 -0.74 18 18
positive regulation of cell migration -0.26 0.22 -9999 0 -0.5 99 99
SDC1 -0.26 0.22 -9999 0 -0.5 99 99
Syndecan-1/Collagen -0.26 0.22 -9999 0 -0.5 99 99
PPIB 0.012 0 -9999 0 -10000 0 0
MET -0.092 0.26 -9999 0 -0.74 38 38
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.23 0.35 -9999 0 -0.74 89 89
MAPK1 -0.2 0.19 -9999 0 -0.42 96 96
homophilic cell adhesion -0.25 0.21 -9999 0 -0.49 99 99
MMP1 -0.29 0.36 -9999 0 -0.72 112 112
TCGA08_retinoblastoma

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
CDKN2B -0.014 0.11 -10000 0 -0.52 12 12
CDKN2C 0.026 0.027 -10000 0 -10000 0 0
CDKN2A -0.2 0.34 -10000 0 -0.74 75 75
CCND2 0.049 0.084 0.18 74 -0.13 1 75
RB1 -0.043 0.097 -10000 0 -0.19 74 74
CDK4 0.061 0.096 0.2 82 -10000 0 82
CDK6 0.053 0.094 0.2 75 -10000 0 75
G1/S progression 0.043 0.096 0.19 74 -10000 0 74
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.49 0.4 -9999 0 -0.98 84 84
PCK1 -0.45 0.42 -9999 0 -0.97 84 84
HNF4A -0.63 0.52 -9999 0 -1.2 108 108
KCNJ11 -0.48 0.42 -9999 0 -1.1 66 66
AKT1 -0.22 0.15 -9999 0 -0.45 4 4
response to starvation -0.02 0.031 -9999 0 -10000 0 0
DLK1 -0.5 0.41 -9999 0 -1 72 72
NKX2-1 -0.2 0.23 -9999 0 -0.87 16 16
ACADM -0.49 0.4 -9999 0 -0.98 85 85
TAT -0.32 0.26 -9999 0 -0.78 39 39
CEBPB 0.003 0.02 -9999 0 -10000 0 0
CEBPA -0.016 0.12 -9999 0 -0.71 8 8
TTR -0.68 0.57 -9999 0 -1.3 125 125
PKLR -0.51 0.42 -9999 0 -1 82 82
APOA1 -0.78 0.65 -9999 0 -1.4 120 120
CPT1C -0.51 0.41 -9999 0 -1 87 87
ALAS1 -0.22 0.16 -9999 0 -10000 0 0
TFRC -0.38 0.34 -9999 0 -0.96 44 44
FOXF1 0.003 0.083 -9999 0 -0.48 7 7
NF1 0.019 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.059 0.13 -9999 0 -0.68 8 8
CPT1A -0.49 0.4 -9999 0 -0.99 81 81
HMGCS1 -0.49 0.4 -9999 0 -0.98 83 83
NR3C1 -0.021 0.074 -9999 0 -0.48 3 3
CPT1B -0.49 0.4 -9999 0 -0.98 83 83
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.014 0.026 -9999 0 -10000 0 0
GCK -0.51 0.43 -9999 0 -1 88 88
CREB1 -0.015 0.056 -9999 0 -10000 0 0
IGFBP1 -0.37 0.31 -9999 0 -0.83 70 70
PDX1 -0.31 0.35 -9999 0 -1.4 18 18
UCP2 -0.49 0.4 -9999 0 -1 78 78
ALDOB -0.62 0.51 -9999 0 -1.2 109 109
AFP -0.15 0.24 -9999 0 -0.66 33 33
BDH1 -0.5 0.41 -9999 0 -0.99 85 85
HADH -0.47 0.4 -9999 0 -1 69 69
F2 -0.64 0.52 -9999 0 -1.2 103 103
HNF1A -0.059 0.13 -9999 0 -0.68 8 8
G6PC -0.15 0.29 -9999 0 -1 23 23
SLC2A2 -0.71 0.6 -9999 0 -1.3 130 130
INS 0.026 0.056 -9999 0 -10000 0 0
FOXA1 -0.094 0.18 -9999 0 -0.54 24 24
FOXA3 -0.12 0.18 -9999 0 -0.46 39 39
FOXA2 -0.55 0.45 -9999 0 -1.1 78 78
ABCC8 -0.67 0.5 -9999 0 -1.1 135 135
ALB -0.26 0.39 -9999 0 -0.82 81 81
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.53 0.43 -10000 0 -1 79 79
IL23A -0.59 0.48 -10000 0 -1.2 84 84
NF kappa B1 p50/RelA/I kappa B alpha -0.58 0.42 -10000 0 -1 102 102
positive regulation of T cell mediated cytotoxicity -0.6 0.49 -10000 0 -1.1 103 103
ITGA3 -0.54 0.43 -10000 0 -1.1 74 74
IL17F -0.42 0.3 -10000 0 -0.74 85 85
IL12B -0.02 0.11 -10000 0 -0.57 9 9
STAT1 (dimer) -0.59 0.48 -10000 0 -1.1 91 91
CD4 -0.53 0.42 -10000 0 -1 79 79
IL23 -0.57 0.46 -10000 0 -1.1 85 85
IL23R -0.097 0.19 -10000 0 -1.3 6 6
IL1B -0.59 0.48 -10000 0 -1.1 92 92
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.56 0.44 -10000 0 -1.1 83 83
TYK2 -0.007 0.016 -10000 0 -10000 0 0
STAT4 0.006 0.062 -10000 0 -0.57 3 3
STAT3 0.012 0.002 -10000 0 -10000 0 0
IL18RAP -0.001 0.079 -10000 0 -0.52 6 6
IL12RB1 -0.007 0.016 -10000 0 -10000 0 0
PIK3CA 0.009 0.045 -10000 0 -0.74 1 1
IL12Rbeta1/TYK2 -0.01 0.02 -10000 0 -10000 0 0
IL23R/JAK2 -0.12 0.2 -10000 0 -1 9 9
positive regulation of chronic inflammatory response -0.6 0.49 -10000 0 -1.1 103 103
natural killer cell activation 0.008 0.012 0.074 6 -10000 0 6
JAK2 -0.007 0.084 -10000 0 -0.79 3 3
PIK3R1 0.012 0.002 -10000 0 -10000 0 0
NFKB1 0.008 0.003 -10000 0 -10000 0 0
RELA 0.008 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.55 0.43 -10000 0 -1.1 85 85
ALOX12B -0.58 0.46 -10000 0 -1.1 95 95
CXCL1 -0.66 0.48 -10000 0 -1.2 108 108
T cell proliferation -0.6 0.49 -10000 0 -1.1 103 103
NFKBIA 0.008 0.003 -10000 0 -10000 0 0
IL17A -0.37 0.25 -10000 0 -0.63 72 72
PI3K -0.59 0.42 -10000 0 -1 111 111
IFNG -0.033 0.048 0.14 4 -0.1 72 76
STAT3 (dimer) -0.58 0.41 -10000 0 -1 99 99
IL18R1 0.008 0.045 -10000 0 -0.73 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.3 0.24 -10000 0 -0.7 20 20
IL18/IL18R 0.003 0.087 -10000 0 -0.49 5 5
macrophage activation -0.029 0.016 -10000 0 -0.045 72 72
TNF -0.58 0.47 -10000 0 -1.1 87 87
STAT3/STAT4 -0.58 0.42 -10000 0 -1 104 104
STAT4 (dimer) -0.58 0.47 -10000 0 -1.1 90 90
IL18 -0.003 0.094 -10000 0 -0.62 6 6
IL19 -0.75 0.57 -10000 0 -1.3 133 133
STAT5A (dimer) -0.58 0.47 -10000 0 -1.1 92 92
STAT1 -0.009 0.13 -10000 0 -0.74 8 8
SOCS3 0.011 0.03 -10000 0 -0.48 1 1
CXCL9 -0.64 0.48 -10000 0 -1.1 108 108
MPO -0.53 0.42 -10000 0 -1 81 81
positive regulation of humoral immune response -0.6 0.49 -10000 0 -1.1 103 103
IL23/IL23R/JAK2/TYK2 -0.63 0.53 -10000 0 -1.2 98 98
IL6 -0.6 0.48 -10000 0 -1.2 92 92
STAT5A 0.012 0 -10000 0 -10000 0 0
IL2 0.011 0.011 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.012 0.074 6 -10000 0 6
CD3E -0.53 0.43 -10000 0 -1.1 78 78
keratinocyte proliferation -0.6 0.49 -10000 0 -1.1 103 103
NOS2 -0.57 0.46 -10000 0 -1.1 92 92
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR -0.036 0.15 -9999 0 -0.48 27 27
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.22 0.26 -9999 0 -0.55 93 93
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.19 0.25 -9999 0 -0.5 93 93
IQGAP1/CaM 0.016 0.035 -9999 0 -0.56 1 1
DAB1 0.009 0.042 -9999 0 -0.48 2 2
IQGAP1 0.01 0.045 -9999 0 -0.74 1 1
PLA2G7 -0.24 0.35 -9999 0 -0.74 91 91
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.18 0.27 -9999 0 -0.56 92 92
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0 -9999 0 -10000 0 0
CDK5R1 -0.004 0.11 -9999 0 -0.74 6 6
LIS1/Poliovirus Protein 3A -0.22 0.12 -9999 0 -0.28 215 215
CDK5R2 -0.13 0.23 -9999 0 -0.51 72 72
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.096 0.16 -9999 0 -0.56 16 16
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.18 0.24 -9999 0 -0.54 57 57
MAP1B -0.22 0.13 -9999 0 -0.28 216 216
RAC1 -0.1 0.053 -9999 0 -0.26 1 1
p35/CDK5 -0.16 0.23 -9999 0 -0.44 97 97
RELN -0.11 0.21 -9999 0 -0.49 66 66
PAFAH/LIS1 -0.37 0.24 -9999 0 -0.67 91 91
LIS1/CLIP170 -0.21 0.12 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.27 0.17 -9999 0 -0.49 87 87
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.18 -9999 0 -0.46 64 64
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.2 0.25 -9999 0 -0.56 66 66
LIS1/IQGAP1 -0.21 0.13 -9999 0 -0.73 1 1
RHOA -0.1 0.053 -9999 0 -0.26 1 1
PAFAH1B1 -0.26 0.15 -9999 0 -0.34 215 215
PAFAH1B3 0.01 0.045 -9999 0 -0.74 1 1
PAFAH1B2 0.012 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.26 0.15 -9999 0 -0.34 215 215
NDEL1/Katanin 60/Dynein heavy chain -0.17 0.23 -9999 0 -0.52 56 56
LRP8 -0.24 0.36 -9999 0 -0.74 92 92
NDEL1/Katanin 60 -0.18 0.24 -9999 0 -0.54 57 57
P39/CDK5 -0.22 0.27 -9999 0 -0.52 106 106
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.21 0.12 -9999 0 -10000 0 0
CDK5 -0.17 0.24 -9999 0 -0.46 93 93
PPP2R5D 0.012 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.18 0.1 -9999 0 -10000 0 0
CSNK2A1 -0.38 0.2 -9999 0 -0.48 215 215
RELN/VLDLR/DAB1/LIS1 -0.25 0.18 -9999 0 -0.51 64 64
RELN/VLDLR -0.21 0.28 -9999 0 -0.53 100 100
CDC42 -0.1 0.053 -9999 0 -0.26 1 1
IL4-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
BCL2L1 -0.65 0.54 -10000 0 -1.2 98 98
STAT6 (cleaved dimer) -0.7 0.52 -10000 0 -1.2 122 122
IGHG1 -0.33 0.38 -10000 0 -1 47 47
IGHG3 -0.63 0.52 -10000 0 -1.1 114 114
AKT1 -0.29 0.29 -10000 0 -0.82 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.23 0.27 -10000 0 -0.8 26 26
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.3 -10000 0 -0.89 23 23
THY1 -0.68 0.57 -10000 0 -1.3 99 99
MYB -0.22 0.34 -10000 0 -0.74 82 82
HMGA1 -0.001 0.084 -10000 0 -0.77 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.35 -10000 0 -0.85 55 55
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.3 0.3 -10000 0 -0.89 24 24
SP1 0.015 0.014 -10000 0 -10000 0 0
INPP5D 0.005 0.07 -10000 0 -0.65 3 3
SOCS5 0.029 0.016 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.68 0.53 -10000 0 -1.2 121 121
SOCS1 -0.41 0.35 -10000 0 -0.78 84 84
SOCS3 -0.31 0.29 -10000 0 -0.88 25 25
FCER2 -0.64 0.6 -10000 0 -1.4 80 80
PARP14 0.003 0.078 -10000 0 -0.74 3 3
CCL17 -0.68 0.57 -10000 0 -1.3 103 103
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.24 0.23 -10000 0 -0.74 16 16
T cell proliferation -0.66 0.56 -10000 0 -1.2 103 103
IL4R/JAK1 -0.65 0.54 -10000 0 -1.2 104 104
EGR2 -0.68 0.57 -10000 0 -1.3 103 103
JAK2 -0.027 0.08 -10000 0 -0.73 3 3
JAK3 -0.012 0.14 -10000 0 -0.74 10 10
PIK3R1 0.012 0 -10000 0 -10000 0 0
JAK1 0.005 0.012 -10000 0 -10000 0 0
COL1A2 -0.29 0.31 -10000 0 -0.83 56 56
CCL26 -0.68 0.57 -10000 0 -1.3 108 108
IL4R -0.69 0.58 -10000 0 -1.3 104 104
PTPN6 0.025 0.046 -10000 0 -0.71 1 1
IL13RA2 -0.71 0.57 -10000 0 -1.3 102 102
IL13RA1 -0.021 0.058 -10000 0 -0.81 1 1
IRF4 -0.26 0.48 -10000 0 -1.5 33 33
ARG1 -0.18 0.26 -10000 0 -1.4 8 8
CBL -0.36 0.34 -10000 0 -0.87 43 43
GTF3A 0.003 0.051 -10000 0 -0.73 1 1
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
IL13RA1/JAK2 -0.033 0.08 -10000 0 -0.57 4 4
IRF4/BCL6 -0.22 0.44 -10000 0 -1.4 32 32
CD40LG -0.007 0.11 -10000 0 -0.52 11 11
MAPK14 -0.35 0.34 -10000 0 -0.95 33 33
mitosis -0.28 0.28 -10000 0 -0.76 29 29
STAT6 -0.76 0.66 -10000 0 -1.4 111 111
SPI1 0.013 0.048 -10000 0 -0.73 1 1
RPS6KB1 -0.27 0.27 -10000 0 -0.76 25 25
STAT6 (dimer) -0.76 0.66 -10000 0 -1.4 110 110
STAT6 (dimer)/PARP14 -0.72 0.61 -10000 0 -1.3 116 116
mast cell activation 0.014 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.31 -10000 0 -0.85 30 30
FRAP1 -0.3 0.29 -10000 0 -0.82 30 30
LTA -0.66 0.56 -10000 0 -1.3 101 101
FES 0.01 0.045 -10000 0 -0.74 1 1
T-helper 1 cell differentiation 0.74 0.62 1.4 110 -10000 0 110
CCL11 -0.67 0.57 -10000 0 -1.3 104 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.3 0.3 -10000 0 -0.84 31 31
IL2RG -0.002 0.099 -10000 0 -0.5 10 10
IL10 -0.65 0.55 -10000 0 -1.2 97 97
IRS1 0.011 0.03 -10000 0 -0.48 1 1
IRS2 -0.016 0.13 -10000 0 -0.58 13 13
IL4 -0.14 0.14 -10000 0 -0.75 4 4
IL5 -0.65 0.54 -10000 0 -1.2 95 95
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.51 0.4 -10000 0 -0.91 98 98
COL1A1 -0.44 0.38 -10000 0 -0.86 109 109
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.66 0.56 -10000 0 -1.3 91 91
IL2R gamma/JAK3 -0.017 0.13 -10000 0 -0.46 20 20
TFF3 -0.79 0.61 -10000 0 -1.4 122 122
ALOX15 -0.7 0.59 -10000 0 -1.3 111 111
MYBL1 -0.012 0.16 0.24 4 -0.66 13 17
T-helper 2 cell differentiation -0.54 0.44 -10000 0 -0.98 100 100
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB -0.005 0.081 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.3 0.3 -10000 0 -0.86 28 28
mol:PI-3-4-5-P3 -0.3 0.29 -10000 0 -0.82 30 30
PI3K -0.31 0.32 -10000 0 -0.89 30 30
DOK2 0.011 0.03 -10000 0 -0.48 1 1
ETS1 0.024 0.046 -10000 0 -0.71 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.22 0.22 -10000 0 -0.74 14 14
ITGB3 -0.65 0.54 -10000 0 -1.2 95 95
PIGR -0.85 0.68 -10000 0 -1.5 136 136
IGHE -0.083 0.37 -10000 0 -1.1 31 31
MAPKKK cascade -0.22 0.22 -10000 0 -0.72 14 14
BCL6 0.009 0.024 -10000 0 -10000 0 0
OPRM1 -0.65 0.54 -10000 0 -1.2 95 95
RETNLB -0.75 0.61 -10000 0 -1.3 120 120
SELP -0.71 0.61 -10000 0 -1.3 108 108
AICDA -0.66 0.55 -10000 0 -1.2 109 109
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.19 0.22 -9999 0 -0.39 148 148
NF kappa B1 p50/RelA/I kappa B alpha -0.15 0.21 -9999 0 -0.5 19 19
alphaV/beta3 Integrin/Osteopontin/Src -0.3 0.27 -9999 0 -0.55 147 147
AP1 -0.16 0.22 -9999 0 -0.6 10 10
ILK -0.2 0.23 -9999 0 -0.41 148 148
bone resorption -0.16 0.2 -9999 0 -0.7 1 1
PTK2B 0.012 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.2 0.19 -9999 0 -0.43 19 19
ITGAV 0.015 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.006 0.084 -9999 0 -0.56 6 6
alphaV/beta3 Integrin/Osteopontin -0.25 0.23 -9999 0 -0.47 148 148
MAP3K1 -0.21 0.23 -9999 0 -0.42 148 148
JUN 0.011 0.03 -9999 0 -0.48 1 1
MAPK3 -0.19 0.23 -9999 0 -0.54 19 19
MAPK1 -0.19 0.23 -9999 0 -0.4 148 148
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.18 0.22 -9999 0 -0.39 148 148
ITGB3 0.012 0.045 -9999 0 -0.73 1 1
NFKBIA -0.17 0.22 -9999 0 -0.55 19 19
FOS -0.017 0.12 -9999 0 -0.5 16 16
CD44 -0.001 0.1 -9999 0 -0.74 5 5
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU -0.18 0.26 -9999 0 -0.78 24 24
NF kappa B1 p50/RelA -0.18 0.17 -9999 0 -0.54 19 19
BCAR1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.008 0.035 -9999 0 -0.54 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.21 0.23 -9999 0 -0.42 148 148
VAV3 -0.21 0.24 -9999 0 -0.41 155 155
MAP3K14 -0.21 0.24 -9999 0 -0.42 148 148
ROCK2 0.01 0.045 -9999 0 -0.74 1 1
SPP1 -0.39 0.37 -9999 0 -0.73 147 147
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.19 0.22 -9999 0 -0.49 26 26
MMP2 -0.13 0.19 -9999 0 -0.66 3 3
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.28 0.26 -10000 0 -0.51 150 150
cell-cell adhesion 0.24 0.23 0.65 45 -10000 0 45
Ephrin B/EPHB2/RasGAP -0.24 0.22 -10000 0 -0.42 151 151
ITSN1 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.012 0.073 -10000 0 -0.46 7 7
Ephrin B1/EPHB1 -0.081 0.18 -10000 0 -0.48 46 46
HRAS/GDP -0.12 0.17 -10000 0 -0.47 43 43
Ephrin B/EPHB1/GRB7 -0.14 0.22 -10000 0 -0.45 80 80
Endophilin/SYNJ1 -0.21 0.22 -10000 0 -0.4 151 151
KRAS -0.023 0.16 -10000 0 -0.74 13 13
Ephrin B/EPHB1/Src -0.084 0.17 -10000 0 -0.43 51 51
endothelial cell migration -0.007 0.054 -10000 0 -0.4 5 5
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 -0.09 0.26 -10000 0 -0.72 38 38
PAK1 -0.21 0.23 -10000 0 -0.4 151 151
HRAS 0.012 0 -10000 0 -10000 0 0
RRAS -0.21 0.22 -10000 0 -0.4 151 151
DNM1 -0.018 0.15 -10000 0 -0.74 11 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.052 0.18 -10000 0 -0.41 51 51
lamellipodium assembly -0.24 0.23 -10000 0 -0.65 45 45
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.018 0.11 -10000 0 -0.43 4 4
PIK3R1 0.012 0 -10000 0 -10000 0 0
EPHB2 -0.4 0.37 -10000 0 -0.74 149 149
EPHB3 -0.006 0.11 -10000 0 -0.7 7 7
EPHB1 -0.11 0.28 -10000 0 -0.73 46 46
EPHB4 0.004 0.078 -10000 0 -0.74 3 3
mol:GDP -0.099 0.18 -10000 0 -0.44 44 44
Ephrin B/EPHB2 -0.24 0.22 -10000 0 -0.43 151 151
Ephrin B/EPHB3 -0.028 0.11 -10000 0 -0.48 12 12
JNK cascade -0.27 0.29 -10000 0 -0.49 157 157
Ephrin B/EPHB1 -0.086 0.17 -10000 0 -0.43 51 51
RAP1/GDP -0.096 0.14 -10000 0 -0.48 9 9
EFNB2 0.01 0.045 -10000 0 -0.74 1 1
EFNB3 -0.019 0.14 -10000 0 -0.61 14 14
EFNB1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.3 0.31 -10000 0 -0.54 157 157
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.24 0.24 -10000 0 -0.67 44 44
Rap1/GTP -0.24 0.24 -10000 0 -0.66 44 44
axon guidance -0.28 0.26 -10000 0 -0.51 150 150
MAPK3 -0.002 0.1 -10000 0 -0.37 4 4
MAPK1 -0.002 0.1 -10000 0 -0.37 4 4
Rac1/GDP -0.085 0.16 -10000 0 -0.4 43 43
actin cytoskeleton reorganization -0.2 0.18 -10000 0 -0.5 52 52
CDC42/GDP -0.085 0.16 -10000 0 -0.4 43 43
PI3K -0.007 0.055 -10000 0 -0.41 5 5
EFNA5 -0.017 0.12 -10000 0 -0.52 15 15
Ephrin B2/EPHB4 -0.007 0.058 -10000 0 -0.48 4 4
Ephrin B/EPHB2/Intersectin/N-WASP -0.12 0.15 -10000 0 -0.5 8 8
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.25 0.23 -10000 0 -0.64 51 51
PTK2 0.058 0.051 -10000 0 -10000 0 0
MAP4K4 -0.27 0.3 -10000 0 -0.5 157 157
SRC 0.012 0 -10000 0 -10000 0 0
KALRN 0.007 0.051 -10000 0 -0.48 3 3
Intersectin/N-WASP 0.019 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.15 0.2 -10000 0 -0.48 46 46
MAP2K1 -0.009 0.11 -10000 0 -0.4 4 4
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.29 0.31 -10000 0 -0.53 157 157
cell migration -0.009 0.11 -10000 0 -0.44 4 4
NRAS 0.012 0 -10000 0 -10000 0 0
SYNJ1 -0.21 0.23 -10000 0 -0.4 151 151
PXN 0.008 0.054 -10000 0 -0.61 2 2
TF -0.27 0.26 -10000 0 -0.46 154 154
HRAS/GTP -0.26 0.25 -10000 0 -0.71 44 44
Ephrin B1/EPHB1-2 -0.3 0.31 -10000 0 -0.54 157 157
cell adhesion mediated by integrin 0.011 0.099 0.46 9 -10000 0 9
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.28 0.27 -10000 0 -0.48 158 158
RAC1-CDC42/GTP -0.25 0.24 -10000 0 -0.66 46 46
RASA1 0.012 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.096 0.14 -10000 0 -0.38 43 43
ruffle organization -0.22 0.26 -10000 0 -0.67 45 45
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.21 0.24 -10000 0 -0.4 151 151
Ephrin B/EPHB2/KALRN -0.24 0.22 -10000 0 -0.42 151 151
ROCK1 0.013 0.069 -10000 0 -0.44 6 6
RAS family/GDP -0.2 0.18 -10000 0 -0.49 52 52
Rac1/GTP -0.26 0.25 -10000 0 -0.71 45 45
Ephrin B/EPHB1/Src/Paxillin -0.025 0.12 -10000 0 -0.47 4 4
Aurora C signaling

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
INCENP 0.01 0.045 -9999 0 -0.74 1 1
Aurora C/Aurora B/INCENP 0 0.1 -9999 0 -0.44 13 13
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.46 0.16 -9999 0 -0.51 249 249
AURKB -0.017 0.14 -9999 0 -0.72 11 11
AURKC 0.005 0.07 -9999 0 -0.65 3 3
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.01 0.045 -10000 0 -0.74 1 1
EPHB2 -0.4 0.37 -10000 0 -0.74 149 149
EFNB1 -0.004 0.11 -10000 0 -0.56 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.28 0.28 -10000 0 -0.72 53 53
Ephrin B2/EPHB1-2 -0.3 0.31 -10000 0 -0.54 157 157
neuron projection morphogenesis -0.27 0.26 -10000 0 -0.58 78 78
Ephrin B1/EPHB1-2/Tiam1 -0.29 0.32 -10000 0 -0.53 157 157
DNM1 -0.019 0.15 -10000 0 -0.74 11 11
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.004 0.1 -10000 0 -0.66 6 6
YES1 -0.019 0.13 -10000 0 -0.87 6 6
Ephrin B1/EPHB1-2/NCK2 -0.28 0.31 -10000 0 -0.52 157 157
PI3K -0.004 0.1 -10000 0 -0.63 7 7
mol:GDP -0.28 0.31 -10000 0 -0.52 157 157
ITGA2B 0.001 0.08 -10000 0 -0.52 6 6
endothelial cell proliferation -0.005 0.058 -10000 0 -0.48 4 4
FYN -0.019 0.13 -10000 0 -0.87 6 6
MAP3K7 -0.019 0.1 -10000 0 -0.7 6 6
FGR -0.02 0.13 -10000 0 -0.87 6 6
TIAM1 0.008 0.054 -10000 0 -0.61 2 2
PIK3R1 0.012 0 -10000 0 -10000 0 0
RGS3 0.012 0 -10000 0 -10000 0 0
cell adhesion 0.003 0.11 -10000 0 -0.57 7 7
LYN -0.019 0.13 -10000 0 -0.87 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.022 0.12 -10000 0 -0.81 6 6
Ephrin B1/EPHB1-2 -0.026 0.11 -10000 0 -0.7 7 7
SRC -0.02 0.13 -10000 0 -0.87 6 6
ITGB3 0.01 0.045 -10000 0 -0.74 1 1
EPHB1 -0.11 0.28 -10000 0 -0.74 46 46
EPHB4 0.004 0.078 -10000 0 -0.74 3 3
RAC1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.005 0.059 -10000 0 -0.48 4 4
alphaIIb/beta3 Integrin 0.008 0.068 -10000 0 -0.4 7 7
BLK -0.054 0.15 -10000 0 -0.96 6 6
HCK -0.019 0.13 -10000 0 -0.86 6 6
regulation of stress fiber formation 0.28 0.31 0.52 157 -10000 0 157
MAPK8 0.003 0.096 -10000 0 -0.62 6 6
Ephrin B1/EPHB1-2/RGS3 -0.28 0.31 -10000 0 -0.52 157 157
endothelial cell migration -0.017 0.11 -10000 0 -0.57 9 9
NCK2 0.012 0 -10000 0 -10000 0 0
PTPN13 -0.001 0.1 -10000 0 -0.62 7 7
regulation of focal adhesion formation 0.28 0.31 0.52 157 -10000 0 157
chemotaxis 0.28 0.31 0.52 157 -10000 0 157
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
Rac1/GTP -0.28 0.28 -10000 0 -0.7 54 54
angiogenesis -0.026 0.11 -10000 0 -0.69 7 7
LCK -0.022 0.13 -10000 0 -0.87 6 6
Effects of Botulinum toxin

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
STX1A 0 0.077 -9999 0 -0.57 5 5
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.11 0.17 -9999 0 -0.34 95 95
STXBP1 -0.014 0.14 -9999 0 -0.71 10 10
ACh/CHRNA1 -0.26 0.26 -9999 0 -0.53 134 134
RAB3GAP2/RIMS1/UNC13B -0.097 0.13 -9999 0 -0.48 1 1
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 -0.16 0.24 -9999 0 -0.48 95 95
mol:ACh -0.017 0.053 -9999 0 -0.12 57 57
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.11 0.14 -9999 0 -0.4 38 38
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.26 0.26 -9999 0 -0.52 134 134
UNC13B 0.012 0 -9999 0 -10000 0 0
CHRNA1 -0.36 0.38 -9999 0 -0.74 134 134
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.098 0.2 -9999 0 -0.48 55 55
SNAP25 -0.05 0.11 -9999 0 -0.27 56 56
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.12 0.28 -9999 0 -0.67 55 55
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.009 0.12 -9999 0 -0.5 14 14
STX1A/SNAP25 fragment 1/VAMP2 -0.11 0.14 -9999 0 -0.4 38 38
Reelin signaling pathway

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.006 0.084 -9999 0 -0.56 6 6
VLDLR -0.036 0.15 -9999 0 -0.48 27 27
CRKL 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
ITGA3 0.007 0.064 -9999 0 -0.74 2 2
RELN/VLDLR/Fyn -0.094 0.16 -9999 0 -0.54 15 15
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.017 0.064 -9999 0 -0.4 2 2
AKT1 -0.046 0.14 -9999 0 -0.44 15 15
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 0.009 0.042 -9999 0 -0.48 2 2
RELN/LRP8/DAB1 -0.2 0.25 -9999 0 -0.51 95 95
LRPAP1/LRP8 -0.18 0.27 -9999 0 -0.56 92 92
RELN/LRP8/DAB1/Fyn -0.2 0.23 -9999 0 -0.48 95 95
DAB1/alpha3/beta1 Integrin -0.2 0.23 -9999 0 -0.6 42 42
long-term memory -0.28 0.33 -9999 0 -0.7 76 76
DAB1/LIS1 -0.2 0.23 -9999 0 -0.48 101 101
DAB1/CRLK/C3G -0.2 0.23 -9999 0 -0.6 42 42
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
DAB1/NCK2 -0.2 0.24 -9999 0 -0.48 101 101
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.099 0.22 -9999 0 -0.51 58 58
CDK5R1 -0.004 0.11 -9999 0 -0.74 6 6
RELN -0.11 0.21 -9999 0 -0.49 66 66
PIK3R1 0.012 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.22 0.26 -9999 0 -0.55 93 93
GRIN2A/RELN/LRP8/DAB1/Fyn -0.25 0.27 -9999 0 -0.53 112 112
MAPK8 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.07 0.16 -9999 0 -0.51 16 16
ITGB1 0.012 0 -9999 0 -10000 0 0
MAP1B -0.2 0.25 -9999 0 -0.46 109 109
RELN/LRP8 -0.22 0.26 -9999 0 -0.55 93 93
GRIN2B/RELN/LRP8/DAB1/Fyn -0.25 0.29 -9999 0 -0.55 113 113
PI3K 0.016 0.035 -9999 0 -0.56 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.049 -9999 0 -0.56 2 2
RAP1A -0.16 0.23 -9999 0 -0.59 35 35
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 -0.026 0.14 -9999 0 -0.51 20 20
CRLK/C3G 0.019 0 -9999 0 -10000 0 0
GRIN2B -0.1 0.26 -9999 0 -0.69 45 45
NCK2 0.012 0 -9999 0 -10000 0 0
neuron differentiation -0.091 0.16 -9999 0 -0.4 39 39
neuron adhesion -0.14 0.23 -9999 0 -0.55 35 35
LRP8 -0.24 0.36 -9999 0 -0.74 92 92
GSK3B -0.037 0.13 -9999 0 -0.41 15 15
RELN/VLDLR/DAB1/Fyn -0.08 0.14 -9999 0 -0.48 16 16
MAP3K11 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.057 0.15 -9999 0 -0.47 15 15
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.055 0.18 -9999 0 -0.48 38 38
neuron migration -0.14 0.22 -9999 0 -0.51 44 44
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.092 0.16 -9999 0 -0.4 39 39
RELN/VLDLR -0.21 0.28 -9999 0 -0.53 100 100
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.1 0.18 -9999 0 -0.4 76 76
Syndecan-4/Syndesmos -0.18 0.23 -9999 0 -0.58 46 46
positive regulation of JNK cascade -0.19 0.22 -9999 0 -0.54 53 53
Syndecan-4/ADAM12 -0.38 0.34 -9999 0 -0.74 109 109
CCL5 0.002 0.072 -9999 0 -0.48 6 6
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 -0.012 0.13 -9999 0 -0.74 9 9
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG 0.008 0.045 -9999 0 -0.71 1 1
ADAM12 -0.38 0.38 -9999 0 -0.74 142 142
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.068 0.066 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.23 0.28 -9999 0 -0.65 62 62
Syndecan-4/CXCL12/CXCR4 -0.19 0.24 -9999 0 -0.58 53 53
Syndecan-4/Laminin alpha3 -0.2 0.25 -9999 0 -0.61 50 50
MDK -0.003 0.1 -9999 0 -0.7 6 6
Syndecan-4/FZD7 -0.18 0.24 -9999 0 -0.59 47 47
Syndecan-4/Midkine -0.18 0.24 -9999 0 -0.58 49 49
FZD7 0.003 0.076 -9999 0 -0.61 4 4
Syndecan-4/FGFR1/FGF -0.19 0.2 -9999 0 -0.55 47 47
THBS1 -0.013 0.13 -9999 0 -0.69 10 10
integrin-mediated signaling pathway -0.21 0.26 -9999 0 -0.61 62 62
positive regulation of MAPKKK cascade -0.19 0.22 -9999 0 -0.54 53 53
Syndecan-4/TACI -0.25 0.25 -9999 0 -0.58 77 77
CXCR4 -0.007 0.12 -9999 0 -0.74 7 7
cell adhesion -0.061 0.15 -9999 0 -0.29 76 76
Syndecan-4/Dynamin -0.18 0.23 -9999 0 -0.58 46 46
Syndecan-4/TSP1 -0.19 0.25 -9999 0 -0.6 50 50
Syndecan-4/GIPC -0.18 0.23 -9999 0 -0.58 46 46
Syndecan-4/RANTES -0.18 0.23 -9999 0 -0.58 48 48
ITGB1 0.012 0 -9999 0 -10000 0 0
LAMA1 -0.088 0.26 -9999 0 -0.73 37 37
LAMA3 -0.033 0.17 -9999 0 -0.68 18 18
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.051 0.06 -9999 0 -0.46 1 1
Syndecan-4/alpha-Actinin -0.18 0.24 -9999 0 -0.58 49 49
TFPI 0.003 0.076 -9999 0 -0.61 4 4
F2 -0.087 0.25 -9999 0 -0.74 35 35
alpha5/beta1 Integrin 0 0.1 -9999 0 -0.56 9 9
positive regulation of cell adhesion -0.24 0.29 -9999 0 -0.66 65 65
ACTN1 0.004 0.078 -9999 0 -0.74 3 3
TNC -0.066 0.23 -9999 0 -0.73 29 29
Syndecan-4/CXCL12 -0.19 0.23 -9999 0 -0.57 50 50
FGF6 -0.006 0.077 -9999 0 -0.74 3 3
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.018 0.12 -9999 0 -0.48 17 17
TNFRSF13B -0.15 0.23 -9999 0 -0.48 91 91
FGF2 0.008 0.054 -9999 0 -0.61 2 2
FGFR1 0.003 0.076 -9999 0 -0.61 4 4
Syndecan-4/PI-4-5-P2 -0.18 0.23 -9999 0 -0.58 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.19 0.34 -9999 0 -0.74 76 76
cell migration -0.024 0.023 -9999 0 -10000 0 0
PRKCD 0.016 0.011 -9999 0 -10000 0 0
vasculogenesis -0.18 0.24 -9999 0 -0.58 50 50
SDC4 -0.19 0.25 -9999 0 -0.62 47 47
Syndecan-4/Tenascin C -0.22 0.28 -9999 0 -0.64 61 61
Syndecan-4/PI-4-5-P2/PKC alpha -0.054 0.052 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.18 0.23 -9999 0 -0.58 46 46
MMP9 -0.23 0.35 -9999 0 -0.74 89 89
Rac1/GTP -0.063 0.15 -9999 0 -0.3 76 76
cytoskeleton organization -0.17 0.22 -9999 0 -0.56 46 46
GIPC1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.18 0.24 -9999 0 -0.58 48 48
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.11 0.24 0.57 56 -10000 0 56
KIRREL -0.018 0.11 -10000 0 -0.79 5 5
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.11 0.24 -10000 0 -0.57 56 56
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.13 0.2 -10000 0 -0.49 50 50
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.072 0.15 -10000 0 -0.52 12 12
FYN -0.1 0.19 -10000 0 -0.44 50 50
mol:Ca2+ -0.13 0.2 -10000 0 -0.48 50 50
mol:DAG -0.13 0.2 -10000 0 -0.48 50 50
NPHS2 -0.094 0.19 -10000 0 -0.5 51 51
mol:IP3 -0.13 0.2 -10000 0 -0.48 50 50
regulation of endocytosis -0.092 0.18 -10000 0 -0.41 50 50
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.2 -10000 0 -0.49 50 50
establishment of cell polarity -0.11 0.24 -10000 0 -0.57 56 56
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.18 -10000 0 -0.44 50 50
Nephrin/NEPH1/beta Arrestin2 -0.092 0.19 -10000 0 -0.42 50 50
NPHS1 -0.14 0.29 -10000 0 -0.72 55 55
Nephrin/NEPH1/podocin -0.1 0.2 -10000 0 -0.44 50 50
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.012 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.13 0.2 -10000 0 -0.48 50 50
CD2AP 0.01 0.045 -10000 0 -0.74 1 1
Nephrin/NEPH1/podocin/GRB2 -0.13 0.2 -10000 0 -0.48 50 50
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.1 0.2 -10000 0 -0.46 51 51
cytoskeleton organization -0.086 0.19 -10000 0 -0.64 12 12
Nephrin/NEPH1 -0.081 0.18 -10000 0 -0.42 56 56
Nephrin/NEPH1/ZO-1 -0.098 0.2 -10000 0 -0.49 50 50
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.12 0.22 -9999 0 -0.48 76 76
EPHB2 -0.4 0.37 -9999 0 -0.74 149 149
Syndecan-2/TACI -0.077 0.14 -9999 0 -0.28 91 91
LAMA1 -0.088 0.26 -9999 0 -0.73 37 37
Syndecan-2/alpha2 ITGB1 -0.021 0.17 -9999 0 -0.47 29 29
HRAS 0.012 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.012 0.13 -9999 0 -0.74 9 9
BAX 0.037 0 -9999 0 -10000 0 0
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 -0.033 0.17 -9999 0 -0.68 18 18
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0 0.095 -9999 0 -0.69 5 5
Syndecan-2/MMP2 0.022 0.03 -9999 0 -0.48 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.023 0.15 -9999 0 -0.56 20 20
dendrite morphogenesis -0.25 0.25 -9999 0 -0.48 149 149
Syndecan-2/GM-CSF -0.15 0.24 -9999 0 -0.48 95 95
determination of left/right symmetry 0.019 0 -9999 0 -10000 0 0
Syndecan-2/PKC delta 0.023 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.13 0.22 -9999 0 -0.43 95 95
MAPK1 -0.13 0.22 -9999 0 -0.43 95 95
Syndecan-2/RACK1 0.028 0 -9999 0 -10000 0 0
NF1 0.012 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.019 0 -9999 0 -10000 0 0
ITGA2 -0.042 0.2 -9999 0 -0.74 20 20
MAPK8 0.032 0 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.054 0.18 -9999 0 -0.41 55 55
Syndecan-2/Kininogen -0.055 0.18 -9999 0 -0.48 42 42
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.034 0 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.021 0 -9999 0 -10000 0 0
extracellular matrix organization 0.022 0.018 -9999 0 -0.28 1 1
actin cytoskeleton reorganization -0.12 0.22 -9999 0 -0.48 76 76
Syndecan-2/Caveolin-2/Ras 0.022 0.058 -9999 0 -0.43 4 4
Syndecan-2/Laminin alpha3 -0.007 0.12 -9999 0 -0.43 18 18
Syndecan-2/RasGAP 0 0 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0.1 -9999 0 -0.56 9 9
PRKCD 0.012 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.25 0.25 -9999 0 -0.48 149 149
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.041 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.15 0.23 -9999 0 -0.48 91 91
RASA1 0.012 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.023 0.15 -9999 0 -0.56 20 20
Syndecan-2/Synbindin 0.023 0 -9999 0 -10000 0 0
TGFB1 0.011 0.03 -9999 0 -0.48 1 1
CASP3 0.03 0 -9999 0 -10000 0 0
FN1 -0.2 0.34 -9999 0 -0.74 76 76
Syndecan-2/IL8 -0.24 0.25 -9999 0 -0.48 141 141
SDC2 0.019 0 -9999 0 -10000 0 0
KNG1 -0.1 0.27 -9999 0 -0.74 42 42
Syndecan-2/Neurofibromin 0.023 0 -9999 0 -10000 0 0
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 -0.25 0.36 -9999 0 -0.74 95 95
Syndecan-2/TGFB1 0.022 0.018 -9999 0 -0.28 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.021 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0.03 0 -9999 0 -10000 0 0
PRKACA 0.03 0 -9999 0 -10000 0 0
angiogenesis -0.23 0.25 -9999 0 -0.48 141 141
MMP2 0.01 0.045 -9999 0 -0.74 1 1
IL8 -0.37 0.38 -9999 0 -0.74 141 141
calcineurin-NFAT signaling pathway -0.077 0.14 -9999 0 -0.28 91 91
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.13 0.2 -9999 0 -0.53 37 37
FZD6 0.002 0.083 -9999 0 -0.67 4 4
WNT6 -0.073 0.19 -9999 0 -0.5 45 45
WNT4 -0.066 0.18 -9999 0 -0.49 43 43
FZD3 0.008 0.054 -9999 0 -0.61 2 2
WNT5A -0.037 0.19 -9999 0 -0.74 18 18
WNT11 -0.14 0.29 -9999 0 -0.66 62 62
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.034 0.17 -10000 0 -0.38 50 50
CRKL -0.039 0.17 -10000 0 -0.4 49 49
HRAS -0.013 0.16 -10000 0 -0.48 6 6
mol:PIP3 -0.048 0.15 -10000 0 -0.38 47 47
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.049 0.18 -10000 0 -0.42 49 49
FOXO3 -0.032 0.16 -10000 0 -0.36 48 48
AKT1 -0.042 0.16 -10000 0 -0.39 48 48
BAD -0.032 0.16 -10000 0 -0.36 48 48
megakaryocyte differentiation -0.081 0.2 -10000 0 -0.42 69 69
GSK3B -0.032 0.16 -10000 0 -0.36 48 48
RAF1 0 0.13 -10000 0 -0.38 6 6
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.047 0.17 -10000 0 -0.42 48 48
STAT1 -0.13 0.39 -10000 0 -0.95 49 49
HRAS/SPRED1 -0.003 0.13 -10000 0 -0.38 6 6
cell proliferation -0.046 0.17 -10000 0 -0.41 48 48
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
TEC 0.011 0.03 -10000 0 -0.48 1 1
RPS6KB1 -0.047 0.17 -10000 0 -0.42 48 48
HRAS/SPRED2 -0.003 0.13 -10000 0 -0.38 6 6
LYN/TEC/p62DOK -0.074 0.15 -10000 0 -0.39 48 48
MAPK3 0.014 0.1 -10000 0 -0.28 2 2
STAP1 -0.07 0.21 -10000 0 -0.47 54 54
GRAP2 0.009 0.042 -10000 0 -0.48 2 2
JAK2 -0.14 0.32 -10000 0 -0.8 49 49
STAT1 (dimer) -0.13 0.38 -10000 0 -0.93 49 49
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.082 0.17 -10000 0 -0.41 53 53
actin filament polymerization -0.047 0.18 -10000 0 -0.42 49 49
LYN 0.01 0.045 -10000 0 -0.74 1 1
STAP1/STAT5A (dimer) -0.083 0.26 -10000 0 -0.62 49 49
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.024 0.16 -10000 0 -0.36 48 48
PI3K -0.036 0.17 -10000 0 -0.39 49 49
PTEN 0.012 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.47 -10000 0 -1.2 49 49
MAPK8 -0.047 0.17 -10000 0 -0.42 48 48
STAT3 (dimer) -0.046 0.17 -10000 0 -0.41 48 48
positive regulation of transcription 0.016 0.085 -10000 0 -10000 0 0
mol:GDP -0.069 0.14 -10000 0 -0.54 6 6
PIK3C2B -0.047 0.18 -10000 0 -0.42 49 49
CBL/CRKL -0.031 0.17 -10000 0 -0.38 49 49
FER -0.047 0.17 -10000 0 -0.42 48 48
SH2B3 -0.047 0.17 -10000 0 -0.42 48 48
PDPK1 -0.05 0.15 -10000 0 -0.36 50 50
SNAI2 -0.051 0.18 -10000 0 -0.43 50 50
positive regulation of cell proliferation -0.087 0.29 -10000 0 -0.7 49 49
KITLG 0.014 0.008 -10000 0 -10000 0 0
cell motility -0.087 0.29 -10000 0 -0.7 49 49
PTPN6 0.011 0.045 -10000 0 -0.72 1 1
EPOR -0.009 0.13 -10000 0 -0.71 2 2
STAT5A (dimer) -0.067 0.24 -10000 0 -0.58 49 49
SOCS1 -0.005 0.11 -10000 0 -0.66 7 7
cell migration 0.047 0.17 0.42 48 -10000 0 48
SOS1 0.012 0 -10000 0 -10000 0 0
EPO -0.022 0.15 -10000 0 -0.74 11 11
VAV1 0.005 0.07 -10000 0 -0.65 3 3
GRB10 -0.049 0.18 -10000 0 -0.43 48 48
PTPN11 0.013 0.007 -10000 0 -10000 0 0
SCF/KIT -0.057 0.18 -10000 0 -0.44 49 49
GO:0007205 0.002 0.01 -10000 0 -10000 0 0
MAP2K1 0.01 0.11 -10000 0 -0.3 4 4
CBL 0.01 0.045 -10000 0 -0.74 1 1
KIT -0.18 0.49 -10000 0 -1.2 49 49
MAP2K2 0.01 0.11 -10000 0 -0.31 3 3
SHC/Grb2/SOS1 -0.071 0.15 -10000 0 -0.38 48 48
STAT5A -0.07 0.25 -10000 0 -0.6 49 49
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.05 0.18 -10000 0 -0.42 50 50
SHC/GRAP2 0.016 0.03 -10000 0 -0.34 2 2
PTPRO -0.083 0.2 -10000 0 -0.42 69 69
SH2B2 -0.048 0.18 -10000 0 -0.42 49 49
DOK1 0.01 0.045 -10000 0 -0.74 1 1
MATK -0.049 0.18 -10000 0 -0.42 48 48
CREBBP 0.03 0.014 -10000 0 -10000 0 0
BCL2 -0.008 0.14 -10000 0 -1.4 1 1
Aurora B signaling

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
Condensin I complex -0.014 0.14 -9999 0 -0.51 15 15
STMN1 -0.001 0.13 -9999 0 -0.62 11 11
Aurora B/RasGAP/Survivin -0.02 0.16 -9999 0 -0.56 21 21
Chromosomal passenger complex/Cul3 protein complex -0.028 0.14 -9999 0 -0.45 18 18
BIRC5 -0.03 0.17 -9999 0 -0.74 15 15
DES -0.34 0.34 -9999 0 -0.64 139 139
Aurora C/Aurora B/INCENP -0.001 0.1 -9999 0 -0.44 13 13
Aurora B/TACC1 -0.003 0.096 -9999 0 -0.44 12 12
Aurora B/PP2A -0.004 0.11 -9999 0 -0.53 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.14 0.056 -9999 0 -0.16 240 240
mitotic metaphase/anaphase transition 0.003 0.006 -9999 0 -10000 0 0
NDC80 -0.085 0.25 -9999 0 -0.63 46 46
Cul3 protein complex -0.045 0.11 -9999 0 -0.49 4 4
KIF2C -0.06 0.14 -9999 0 -0.32 54 54
PEBP1 0.01 0.005 -9999 0 -10000 0 0
KIF20A -0.1 0.27 -9999 0 -0.74 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.004 0.11 -9999 0 -0.53 11 11
SEPT1 0.005 0.07 -9999 0 -0.65 3 3
SMC2 0.007 0.064 -9999 0 -0.74 2 2
SMC4 0.007 0.064 -9999 0 -0.74 2 2
NSUN2/NPM1/Nucleolin -0.019 0.089 -9999 0 -0.43 8 8
PSMA3 0.012 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.004 -9999 0 -10000 0 0
H3F3B -0.29 0.12 -9999 0 -0.32 251 251
AURKB -0.01 0.15 -9999 0 -0.72 11 11
AURKC 0.005 0.07 -9999 0 -0.65 3 3
CDCA8 -0.028 0.17 -9999 0 -0.75 14 14
cytokinesis -0.14 0.22 -9999 0 -0.5 57 57
Aurora B/Septin1 -0.11 0.22 -9999 0 -0.54 37 37
AURKA -0.025 0.16 -9999 0 -0.74 13 13
INCENP 0.008 0.047 -9999 0 -0.76 1 1
KLHL13 -0.063 0.18 -9999 0 -0.5 40 40
BUB1 -0.22 0.35 -9999 0 -0.74 83 83
hSgo1/Aurora B/Survivin -0.092 0.26 -9999 0 -0.57 53 53
EVI5 0.013 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.15 0.25 -9999 0 -0.54 71 71
SGOL1 -0.11 0.28 -9999 0 -0.74 44 44
CENPA -0.037 0.13 -9999 0 -0.37 30 30
NCAPG -0.04 0.19 -9999 0 -0.74 19 19
Aurora B/HC8 Proteasome -0.004 0.11 -9999 0 -0.53 11 11
NCAPD2 0.01 0.045 -9999 0 -0.74 1 1
Aurora B/PP1-gamma -0.004 0.11 -9999 0 -0.53 11 11
RHOA 0.012 0 -9999 0 -10000 0 0
NCAPH -0.045 0.2 -9999 0 -0.74 21 21
NPM1 -0.018 0.077 -9999 0 -0.39 11 11
RASA1 0.012 0 -9999 0 -10000 0 0
KLHL9 0.009 0.042 -9999 0 -0.48 2 2
mitotic prometaphase -0.003 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.11 -9999 0 -0.53 11 11
PPP1CC 0.012 0 -9999 0 -10000 0 0
Centraspindlin -0.17 0.28 -9999 0 -0.58 73 73
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 -0.019 0.079 -9999 0 -0.38 12 12
MYLK -0.018 0.11 -9999 0 -0.33 29 29
KIF23 -0.18 0.33 -9999 0 -0.74 69 69
VIM 0.001 0.11 -9999 0 -0.52 12 12
RACGAP1 0.004 0.065 -9999 0 -0.75 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.018 0.077 -9999 0 -0.39 11 11
Chromosomal passenger complex -0.067 0.18 -9999 0 -0.41 43 43
Chromosomal passenger complex/EVI5 -0.005 0.22 -9999 0 -0.58 28 28
TACC1 0.011 0.03 -9999 0 -0.48 1 1
PPP2R5D 0.012 0 -9999 0 -10000 0 0
CUL3 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0 -9999 0 -10000 0 0
LAT2 -0.098 0.2 -9999 0 -0.46 51 51
AP1 -0.11 0.17 -9999 0 -0.43 51 51
mol:PIP3 -0.1 0.23 -9999 0 -0.5 51 51
IKBKB -0.045 0.13 -9999 0 -0.33 19 19
AKT1 -0.076 0.18 -9999 0 -0.53 15 15
IKBKG -0.048 0.13 -9999 0 -0.33 19 19
MS4A2 -0.092 0.2 -9999 0 -0.5 56 56
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.045 -9999 0 -0.74 1 1
MAP3K1 -0.058 0.17 -9999 0 -0.52 15 15
mol:Ca2+ -0.071 0.17 -9999 0 -0.37 51 51
LYN 0.009 0.046 -9999 0 -0.74 1 1
CBLB -0.094 0.2 -9999 0 -0.46 49 49
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.003 0.075 -9999 0 -0.44 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.005 0.07 -9999 0 -0.65 3 3
PLD2 -0.11 0.21 -9999 0 -0.47 53 53
PTPN13 -0.094 0.21 -9999 0 -0.48 47 47
PTPN11 0.008 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.047 0.16 -9999 0 -0.39 15 15
SYK 0.011 0.004 -9999 0 -10000 0 0
GRB2 0.012 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.2 -9999 0 -0.51 51 51
LAT -0.094 0.2 -9999 0 -0.46 49 49
PAK2 -0.073 0.19 -9999 0 -0.42 50 50
NFATC2 -0.056 0.097 -9999 0 -0.91 2 2
HRAS -0.087 0.21 -9999 0 -0.47 51 51
GAB2 0.012 0 -9999 0 -10000 0 0
PLA2G1B 0.015 0.032 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.21 -9999 0 -0.54 46 46
Antigen/IgE/Fc epsilon R1 -0.16 0.22 -9999 0 -0.54 57 57
mol:GDP -0.095 0.22 -9999 0 -0.49 51 51
JUN 0.011 0.03 -9999 0 -0.48 1 1
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
FOS -0.017 0.12 -9999 0 -0.5 16 16
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.2 -9999 0 -0.49 49 49
CHUK -0.045 0.13 -9999 0 -0.33 19 19
KLRG1 -0.093 0.19 -9999 0 -0.43 50 50
VAV1 -0.098 0.2 -9999 0 -0.47 51 51
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.095 0.2 -9999 0 -0.46 50 50
negative regulation of mast cell degranulation -0.084 0.18 -9999 0 -0.4 52 52
BTK -0.1 0.22 -9999 0 -0.5 50 50
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.23 -9999 0 -0.57 44 44
GAB2/PI3K/SHP2 -0.12 0.17 -9999 0 -0.58 15 15
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.24 -9999 0 -0.57 49 49
RAF1 0.023 0.024 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.19 -9999 0 -0.47 49 49
FCER1G 0.005 0.079 -9999 0 -0.74 3 3
FCER1A -0.15 0.24 -9999 0 -0.49 86 86
Antigen/IgE/Fc epsilon R1/Fyn -0.15 0.2 -9999 0 -0.5 57 57
MAPK3 0.032 0.021 -9999 0 -10000 0 0
MAPK1 0.032 0.021 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.005 0.058 -9999 0 -10000 0 0
DUSP1 -0.022 0.13 -9999 0 -0.48 19 19
NF-kappa-B/RelA -0.047 0.062 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.097 0.2 -9999 0 -0.47 49 49
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.11 0.17 -9999 0 -0.43 50 50
FER -0.094 0.2 -9999 0 -0.46 49 49
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.042 0.089 -9999 0 -0.44 10 10
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.094 0.22 -9999 0 -0.49 51 51
cytokine secretion -0.034 0.045 -9999 0 -10000 0 0
SPHK1 -0.12 0.22 -9999 0 -0.49 58 58
PTK2 -0.1 0.21 -9999 0 -0.5 49 49
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.15 0.21 -9999 0 -0.54 51 51
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.095 0.22 -9999 0 -0.48 51 51
MAP2K2 0.028 0.021 -9999 0 -10000 0 0
MAP2K1 0.028 0.021 -9999 0 -10000 0 0
MAP2K7 0.012 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.16 -9999 0 -0.39 50 50
MAP2K4 0.015 0.011 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.13 0.2 -9999 0 -0.5 47 47
mol:Choline -0.11 0.21 -9999 0 -0.47 53 53
SHC/Grb2/SOS1 -0.11 0.16 -9999 0 -0.42 49 49
FYN 0.012 0 -9999 0 -10000 0 0
DOK1 0.01 0.045 -9999 0 -0.74 1 1
PXN -0.09 0.2 -9999 0 -0.47 47 47
HCLS1 -0.097 0.2 -9999 0 -0.46 51 51
PRKCB -0.075 0.18 -9999 0 -0.39 50 50
FCGR2B 0.003 0.066 -9999 0 -0.48 5 5
IGHE -0.053 0.18 -9999 0 -0.54 32 32
KLRG1/SHIP -0.085 0.18 -9999 0 -0.41 52 52
LCP2 0.012 0.001 -9999 0 -10000 0 0
PLA2G4A -0.11 0.21 -9999 0 -0.48 55 55
RASA1 0.012 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.11 0.21 -9999 0 -0.47 53 53
IKK complex -0.022 0.1 -9999 0 -0.26 7 7
WIPF1 0.009 0.042 -9999 0 -0.48 2 2
TCGA08_p53

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
CDKN2A -0.15 0.26 -10000 0 -0.56 75 75
TP53 -0.033 0.082 0.24 8 -10000 0 8
Senescence -0.033 0.081 0.24 8 -10000 0 8
Apoptosis -0.033 0.081 0.24 8 -10000 0 8
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.058 0.16 0.28 74 -0.55 8 82
MDM4 0.012 0 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.044 0.11 -9999 0 -0.31 39 39
EFNA5 -0.017 0.12 -9999 0 -0.52 15 15
FYN -0.019 0.11 -9999 0 -0.46 5 5
neuron projection morphogenesis -0.044 0.11 -9999 0 -0.31 39 39
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.045 0.11 -9999 0 -0.31 39 39
EPHA5 -0.036 0.15 -9999 0 -0.49 26 26
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.019 0.089 -10000 0 -0.48 9 9
fibroblast growth factor receptor signaling pathway -0.019 0.089 -10000 0 -0.48 9 9
LAMA1 -0.088 0.26 -10000 0 -0.73 37 37
PRNP 0.012 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.038 0.15 -10000 0 -0.4 37 37
SMAD2 0.02 0.073 -10000 0 -0.43 7 7
GPC1/PrPc/Cu2+ -0.011 0.071 -10000 0 -0.48 6 6
GPC1/Laminin alpha1 -0.07 0.22 -10000 0 -0.57 41 41
TDGF1 -0.11 0.24 -10000 0 -0.58 57 57
CRIPTO/GPC1 -0.084 0.2 -10000 0 -0.45 60 60
APP/GPC1 0.006 0.084 -10000 0 -0.56 6 6
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.063 0.18 -10000 0 -0.5 27 27
FLT1 0.01 0.045 -10000 0 -0.74 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.012 0.075 -10000 0 -0.48 7 7
SERPINC1 0.003 0.078 -10000 0 -0.74 3 3
FYN -0.063 0.18 -10000 0 -0.5 27 27
FGR -0.063 0.18 -10000 0 -0.5 27 27
positive regulation of MAPKKK cascade -0.078 0.19 -10000 0 -0.47 38 38
SLIT2 -0.048 0.17 -10000 0 -0.52 31 31
GPC1/NRG -0.098 0.18 -10000 0 -0.36 85 85
NRG1 -0.13 0.23 -10000 0 -0.48 80 80
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.026 0.12 -10000 0 -0.54 13 13
LYN -0.064 0.18 -10000 0 -0.5 28 28
mol:Spermine -0.002 0.084 -10000 0 -0.56 6 6
cell growth -0.019 0.089 -10000 0 -0.48 9 9
BMP signaling pathway 0.004 0.11 0.74 6 -10000 0 6
SRC -0.063 0.18 -10000 0 -0.5 27 27
TGFBR1 0.01 0.045 -10000 0 -0.74 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.34 -10000 0 -0.68 102 102
GPC1 -0.004 0.11 -10000 0 -0.74 6 6
TGFBR1 (dimer) 0.01 0.045 -10000 0 -0.74 1 1
VEGFA -0.009 0.13 -10000 0 -0.74 8 8
BLK -0.14 0.24 -10000 0 -0.59 46 46
HCK -0.063 0.18 -10000 0 -0.5 27 27
FGF2 0.008 0.054 -10000 0 -0.61 2 2
FGFR1 0.003 0.076 -10000 0 -0.61 4 4
VEGFR1 homodimer 0.01 0.045 -10000 0 -0.74 1 1
TGFBR2 0.012 0 -10000 0 -10000 0 0
cell death 0.006 0.084 -10000 0 -0.56 6 6
ATIII/GPC1 -0.001 0.1 -10000 0 -0.56 9 9
PLA2G2A/GPC1 -0.19 0.28 -10000 0 -0.54 102 102
LCK -0.073 0.19 -10000 0 -0.52 32 32
neuron differentiation -0.098 0.18 -10000 0 -0.36 85 85
PrPc/Cu2+ 0.009 0 -10000 0 -10000 0 0
APP 0.012 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.012 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.015 0.074 -10000 0 -10000 0 0
SMARCC2 0.013 0.009 -10000 0 -10000 0 0
SMARCC1 0.013 0.009 -10000 0 -10000 0 0
TBX21 -0.077 0.16 -10000 0 -0.47 19 19
SUMO2 0.013 0.008 -10000 0 -10000 0 0
STAT1 (dimer) -0.001 0.13 -10000 0 -0.73 8 8
FKBP4 0.01 0.045 -10000 0 -0.74 1 1
FKBP5 0.009 0.042 -10000 0 -0.48 2 2
GR alpha/HSP90/FKBP51/HSP90 0.1 0.11 0.3 15 -0.32 1 16
PRL -0.065 0.15 -10000 0 -0.68 6 6
cortisol/GR alpha (dimer)/TIF2 0.23 0.24 0.55 64 -10000 0 64
RELA -0.055 0.08 -10000 0 -10000 0 0
FGG 0.087 0.32 0.49 33 -0.54 37 70
GR beta/TIF2 0.11 0.11 0.31 25 -10000 0 25
IFNG -0.42 0.36 -10000 0 -0.83 98 98
apoptosis 0.025 0.15 0.52 10 -0.55 1 11
CREB1 -0.003 0.073 -10000 0 -0.33 1 1
histone acetylation -0.014 0.14 0.39 8 -0.35 11 19
BGLAP -0.064 0.13 -10000 0 -0.43 2 2
GR/PKAc 0.094 0.12 0.29 14 -0.4 4 18
NF kappa B1 p50/RelA -0.099 0.14 -10000 0 -0.41 16 16
SMARCD1 0.013 0.009 -10000 0 -10000 0 0
MDM2 0.082 0.11 0.25 31 -0.29 7 38
GATA3 0.003 0.11 -10000 0 -0.69 7 7
AKT1 0.001 0.002 -10000 0 -10000 0 0
CSF2 -0.2 0.26 -10000 0 -0.54 87 87
GSK3B 0.013 0.008 -10000 0 -10000 0 0
NR1I3 0.05 0.14 0.5 9 -10000 0 9
CSN2 0.14 0.18 0.42 20 -0.58 3 23
BRG1/BAF155/BAF170/BAF60A 0.036 0.032 -10000 0 -10000 0 0
NFATC1 0.014 0.03 -10000 0 -10000 0 0
POU2F1 0.012 0.051 -10000 0 -0.73 1 1
CDKN1A 0.01 0.16 -10000 0 -1.3 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 -10000 0 -10000 0 0
SFN -0.01 0.11 -10000 0 -0.55 11 11
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.089 0.12 0.31 7 -0.36 2 9
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.033 0.18 0.48 10 -0.77 6 16
JUN -0.26 0.18 -10000 0 -0.53 46 46
IL4 -0.08 0.15 -10000 0 -0.62 6 6
CDK5R1 -0.004 0.11 -10000 0 -0.74 6 6
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.29 0.26 0.23 4 -0.57 98 102
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.1 0.3 13 -10000 0 13
cortisol/GR alpha (monomer) 0.26 0.29 0.64 68 -10000 0 68
NCOA2 0.012 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.11 0.13 -10000 0 -0.57 16 16
AP-1/NFAT1-c-4 -0.46 0.31 -10000 0 -0.77 106 106
AFP -0.19 0.2 -10000 0 -0.76 19 19
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.14 0.15 0.42 14 -10000 0 14
TP53 0.026 0.058 -10000 0 -0.45 4 4
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.62 0.37 -10000 0 -0.83 189 189
KRT14 -0.26 0.39 -10000 0 -1 49 49
TBP 0.021 0 -10000 0 -10000 0 0
CREBBP 0.066 0.097 0.3 22 -10000 0 22
HDAC1 0.007 0.011 -10000 0 -10000 0 0
HDAC2 0.029 0.026 -10000 0 -10000 0 0
AP-1 -0.46 0.32 -10000 0 -0.77 109 109
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.013 0.11 -10000 0 -0.48 14 14
MAPK11 0.013 0.008 -10000 0 -10000 0 0
KRT5 -0.39 0.36 -10000 0 -0.88 74 74
interleukin-1 receptor activity 0.017 0.026 -10000 0 -10000 0 0
NCOA1 0.015 0.001 -10000 0 -10000 0 0
STAT1 -0.001 0.13 -10000 0 -0.73 8 8
CGA -0.13 0.26 -10000 0 -0.82 25 25
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.18 0.2 0.43 83 -0.46 1 84
MAPK3 0.013 0.008 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.19 0.25 -10000 0 -0.67 36 36
NFKB1 -0.055 0.08 -10000 0 -10000 0 0
MAPK8 -0.19 0.15 -10000 0 -0.42 46 46
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.017 0.16 0.52 10 -0.58 1 11
BAX 0.024 0.048 -10000 0 -10000 0 0
POMC -0.17 0.32 -10000 0 -1.2 18 18
EP300 0.069 0.098 0.32 14 -10000 0 14
cortisol/GR alpha (dimer)/p53 0.24 0.24 0.55 68 -10000 0 68
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.087 0.22 5 -0.26 6 11
SGK1 0.1 0.21 -10000 0 -1.2 5 5
IL13 -0.23 0.19 -10000 0 -0.66 15 15
IL6 -0.26 0.35 -10000 0 -0.91 49 49
PRKACG -0.002 0.09 -10000 0 -0.74 4 4
IL5 -0.2 0.17 -10000 0 -0.75 8 8
IL2 -0.3 0.23 -10000 0 -0.67 45 45
CDK5 0.013 0.004 -10000 0 -10000 0 0
PRKACB 0.007 0.051 -10000 0 -0.48 3 3
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.4 0.38 -10000 0 -0.73 142 142
CDK5R1/CDK5 0.006 0.084 -10000 0 -0.55 6 6
NF kappa B1 p50/RelA/PKAc -0.055 0.12 -10000 0 -0.48 6 6
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 59 -10000 0 59
SMARCA4 0.013 0.009 -10000 0 -10000 0 0
chromatin remodeling 0.16 0.15 0.39 35 -0.44 1 36
NF kappa B1 p50/RelA/Cbp -0.01 0.15 0.38 7 -0.44 3 10
JUN (dimer) -0.25 0.18 -10000 0 -0.53 46 46
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.096 0.2 -10000 0 -0.64 23 23
NR3C1 0.15 0.17 0.43 42 -0.31 1 43
NR4A1 -0.017 0.14 -10000 0 -0.49 19 19
TIF2/SUV420H1 0.019 0 -10000 0 -10000 0 0
MAPKKK cascade 0.025 0.15 0.52 10 -0.55 1 11
cortisol/GR alpha (dimer)/Src-1 0.24 0.24 0.56 62 -10000 0 62
PBX1 0 0.086 -10000 0 -0.48 8 8
POU1F1 0.01 0.024 -10000 0 -10000 0 0
SELE -0.24 0.32 -10000 0 -0.79 54 54
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.15 0.39 35 -0.45 1 36
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 59 -10000 0 59
mol:cortisol 0.15 0.17 0.36 75 -0.22 4 79
MMP1 -0.35 0.36 -10000 0 -0.76 112 112
FOXM1 transcription factor network

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
NFATC3 -0.085 0.48 -9999 0 -1.2 24 24
PLK1 -0.018 0.21 -9999 0 -0.66 24 24
BIRC5 0.001 0.18 -9999 0 -0.7 15 15
HSPA1B -0.087 0.48 -9999 0 -1.2 25 25
MAP2K1 0.024 0.037 -9999 0 -10000 0 0
BRCA2 -0.12 0.52 -9999 0 -1.2 30 30
FOXM1 -0.15 0.64 -9999 0 -1.5 32 32
XRCC1 -0.085 0.48 -9999 0 -1.2 24 24
FOXM1B/p19 -0.32 0.46 -9999 0 -1.2 43 43
Cyclin D1/CDK4 -0.12 0.47 -9999 0 -1.1 26 26
CDC2 -0.098 0.51 -9999 0 -1.2 30 30
TGFA -0.1 0.46 -9999 0 -1 25 25
SKP2 -0.099 0.51 -9999 0 -1.2 29 29
CCNE1 -0.082 0.25 -9999 0 -0.74 35 35
CKS1B -0.088 0.49 -9999 0 -1.2 24 24
RB1 -0.13 0.19 -9999 0 -0.61 21 21
FOXM1C/SP1 -0.12 0.54 -9999 0 -1.3 29 29
AURKB 0.011 0.16 -9999 0 -0.71 11 11
CENPF -0.2 0.57 -9999 0 -1.2 44 44
CDK4 0.01 0.068 -9999 0 -0.76 2 2
MYC -0.063 0.44 -9999 0 -0.99 25 25
CHEK2 0.016 0.092 -9999 0 -0.78 3 3
ONECUT1 -0.13 0.5 -9999 0 -1.2 28 28
CDKN2A -0.2 0.33 -9999 0 -0.73 75 75
LAMA4 -0.088 0.49 -9999 0 -1.2 24 24
FOXM1B/HNF6 -0.17 0.59 -9999 0 -1.4 30 30
FOS -0.12 0.53 -9999 0 -1.2 32 32
SP1 0.013 0.001 -9999 0 -10000 0 0
CDC25B -0.094 0.5 -9999 0 -1.2 27 27
response to radiation 0.009 0.035 -9999 0 -10000 0 0
CENPB -0.085 0.48 -9999 0 -1.1 28 28
CENPA -0.1 0.51 -9999 0 -1.2 29 29
NEK2 -0.12 0.54 -9999 0 -1.3 31 31
HIST1H2BA -0.093 0.48 -9999 0 -1.2 25 25
CCNA2 -0.022 0.16 -9999 0 -0.75 13 13
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.12 0.56 -9999 0 -1.4 28 28
CCNB2 -0.091 0.5 -9999 0 -1.2 24 24
CCNB1 -0.098 0.52 -9999 0 -1.2 28 28
ETV5 -0.093 0.49 -9999 0 -1.2 24 24
ESR1 -0.097 0.51 -9999 0 -1.2 27 27
CCND1 -0.12 0.48 -9999 0 -1.1 26 26
GSK3A 0.024 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.053 0.22 -9999 0 -0.52 45 45
CDK2 0.014 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.01 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.24 0.42 -9999 0 -1.2 35 35
GAS1 -0.12 0.54 -9999 0 -1.2 33 33
MMP2 -0.086 0.49 -9999 0 -1.2 25 25
RB1/FOXM1C -0.12 0.5 -9999 0 -1.1 31 31
CREBBP 0.012 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.067 0.26 -10000 0 -0.69 34 34
IHH -0.067 0.2 -10000 0 -0.56 37 37
SHH Np/Cholesterol/GAS1 -0.036 0.13 -10000 0 -0.5 10 10
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.13 0.5 10 -10000 0 10
SMO/beta Arrestin2 -0.035 0.18 -10000 0 -0.6 11 11
SMO -0.043 0.18 -10000 0 -0.55 18 18
AKT1 0.001 0.085 -10000 0 -0.34 1 1
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC -0.019 0.13 -10000 0 -0.53 16 16
ADRBK1 0.01 0.045 -10000 0 -0.74 1 1
heart looping -0.042 0.18 -10000 0 -0.54 18 18
STIL -0.13 0.24 -10000 0 -0.59 36 36
DHH N/PTCH2 -0.052 0.19 -10000 0 -0.53 35 35
DHH N/PTCH1 -0.037 0.17 -10000 0 -0.64 9 9
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
DHH 0 0.087 -10000 0 -0.57 6 6
PTHLH -0.07 0.27 -10000 0 -0.96 14 14
determination of left/right symmetry -0.042 0.18 -10000 0 -0.54 18 18
PIK3R1 0.012 0 -10000 0 -10000 0 0
skeletal system development -0.069 0.27 -10000 0 -0.94 14 14
IHH N/Hhip -0.13 0.22 -10000 0 -0.43 88 88
DHH N/Hhip -0.084 0.17 -10000 0 -0.35 76 76
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.042 0.18 -10000 0 -0.54 18 18
pancreas development -0.12 0.22 -10000 0 -0.48 72 72
HHAT 0.009 0.042 -10000 0 -0.48 2 2
PI3K 0.016 0.035 -10000 0 -0.56 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.028 0.15 -10000 0 -0.55 20 20
somite specification -0.042 0.18 -10000 0 -0.54 18 18
SHH Np/Cholesterol/PTCH1 -0.05 0.17 -10000 0 -0.53 18 18
SHH Np/Cholesterol/PTCH2 -0.062 0.16 -10000 0 -0.44 33 33
SHH Np/Cholesterol/Megalin -0.092 0.19 -10000 0 -0.46 47 47
SHH -0.025 0.13 -10000 0 -0.37 33 33
catabolic process -0.04 0.18 -10000 0 -0.66 8 8
SMO/Vitamin D3 -0.05 0.18 -10000 0 -0.55 18 18
SHH Np/Cholesterol/Hhip -0.083 0.17 -10000 0 -0.52 19 19
LRP2 -0.12 0.28 -10000 0 -0.71 48 48
receptor-mediated endocytosis -0.087 0.2 -10000 0 -0.52 30 30
SHH Np/Cholesterol/BOC -0.031 0.12 -10000 0 -0.46 9 9
SHH Np/Cholesterol/CDO -0.023 0.11 -10000 0 -0.45 8 8
mesenchymal cell differentiation 0.083 0.17 0.51 19 -10000 0 19
mol:Vitamin D3 -0.048 0.18 -10000 0 -0.53 18 18
IHH N/PTCH2 -0.094 0.22 -10000 0 -0.47 64 64
CDON -0.004 0.1 -10000 0 -0.63 7 7
IHH N/PTCH1 -0.041 0.18 -10000 0 -0.67 8 8
Megalin/LRPAP1 -0.079 0.21 -10000 0 -0.53 48 48
PTCH2 -0.068 0.23 -10000 0 -0.72 30 30
SHH Np/Cholesterol -0.034 0.095 -10000 0 -0.28 33 33
PTCH1 -0.041 0.18 -10000 0 -0.67 8 8
HHIP -0.12 0.22 -10000 0 -0.48 72 72
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.009 0.042 -9999 0 -0.48 2 2
GNB1/GNG2 -0.1 0.19 -9999 0 -0.49 37 37
mol:DAG -0.089 0.18 -9999 0 -0.46 29 29
PLCG1 -0.092 0.18 -9999 0 -0.48 29 29
YES1 -0.11 0.19 -9999 0 -0.5 37 37
FZD3 0.008 0.054 -9999 0 -0.61 2 2
FZD6 0.002 0.083 -9999 0 -0.67 4 4
G protein -0.094 0.18 -9999 0 -0.48 29 29
MAP3K7 -0.081 0.16 -9999 0 -0.5 15 15
mol:Ca2+ -0.086 0.17 -9999 0 -0.45 29 29
mol:IP3 -0.089 0.18 -9999 0 -0.46 29 29
NLK -0.005 0.008 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.095 0.18 -9999 0 -0.54 16 16
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.2 -9999 0 -0.53 37 37
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.12 0.19 -9999 0 -0.5 38 38
GO:0007205 -0.087 0.17 -9999 0 -0.45 29 29
WNT6 -0.073 0.19 -9999 0 -0.5 45 45
WNT4 -0.066 0.18 -9999 0 -0.49 43 43
NFAT1/CK1 alpha -0.086 0.18 -9999 0 -0.6 12 12
GNG2 0.01 0.045 -9999 0 -0.74 1 1
WNT5A -0.037 0.19 -9999 0 -0.74 18 18
WNT11 -0.14 0.29 -9999 0 -0.66 62 62
CDC42 -0.1 0.18 -9999 0 -0.47 37 37
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.023 0.1 -9999 0 -0.54 9 9
alphaM/beta2 Integrin/GPIbA -0.041 0.13 -9999 0 -0.53 14 14
alphaM/beta2 Integrin/proMMP-9 -0.18 0.25 -9999 0 -0.51 92 92
PLAUR 0.004 0.078 -9999 0 -0.74 3 3
HMGB1 0.008 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.022 0.097 -9999 0 -0.55 8 8
AGER 0.008 0.018 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG 0.012 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.042 0.11 -9999 0 -0.54 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.23 0.35 -9999 0 -0.74 89 89
CYR61 0.002 0.082 -9999 0 -0.58 5 5
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.099 0.13 -9999 0 -0.52 10 10
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.045 0.16 -9999 0 -0.48 32 32
MYH2 -0.13 0.19 -9999 0 -0.45 50 50
MST1R 0.001 0.08 -9999 0 -0.52 6 6
leukocyte activation during inflammatory response -0.14 0.18 -9999 0 -0.47 42 42
APOB -0.22 0.28 -9999 0 -0.55 114 114
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.01 0.045 -9999 0 -0.74 1 1
JAM3 0.01 0.045 -9999 0 -0.74 1 1
GP1BA -0.021 0.14 -9999 0 -0.56 16 16
alphaM/beta2 Integrin/CTGF -0.026 0.1 -9999 0 -0.55 9 9
alphaM/beta2 Integrin -0.11 0.17 -9999 0 -0.39 50 50
JAM3 homodimer 0.01 0.045 -9999 0 -0.74 1 1
ICAM2 0.01 0.045 -9999 0 -0.74 1 1
ICAM1 -0.015 0.14 -9999 0 -0.74 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.1 0.16 -9999 0 -0.38 50 50
cell adhesion -0.041 0.13 -9999 0 -0.53 14 14
NFKB1 -0.012 0.18 -9999 0 -0.72 7 7
THY1 -0.075 0.24 -9999 0 -0.74 32 32
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.15 0.19 -9999 0 -0.35 119 119
alphaM/beta2 Integrin/LRP/tPA -0.022 0.095 -9999 0 -0.5 9 9
IL6 -0.052 0.27 -9999 0 -0.69 38 38
ITGB2 -0.006 0.1 -9999 0 -0.75 5 5
elevation of cytosolic calcium ion concentration -0.061 0.16 -9999 0 -0.48 33 33
alphaM/beta2 Integrin/JAM2/JAM3 -0.034 0.11 -9999 0 -0.5 9 9
JAM2 -0.016 0.12 -9999 0 -0.48 16 16
alphaM/beta2 Integrin/ICAM1 -0.054 0.15 -9999 0 -0.46 29 29
alphaM/beta2 Integrin/uPA/Plg -0.059 0.16 -9999 0 -0.48 32 32
RhoA/GTP -0.13 0.2 -9999 0 -0.47 48 48
positive regulation of phagocytosis -0.083 0.12 -9999 0 -0.52 10 10
Ron/MSP -0.015 0.13 -9999 0 -0.5 18 18
alphaM/beta2 Integrin/uPAR/uPA -0.061 0.17 -9999 0 -0.48 33 33
alphaM/beta2 Integrin/uPAR -0.027 0.11 -9999 0 -0.54 11 11
PLAU -0.053 0.21 -9999 0 -0.74 24 24
PLAT 0.009 0.042 -9999 0 -0.48 2 2
actin filament polymerization -0.12 0.18 -9999 0 -0.43 50 50
MST1 -0.02 0.15 -9999 0 -0.74 12 12
alphaM/beta2 Integrin/lipoprotein(a) -0.14 0.18 -9999 0 -0.47 42 42
TNF -0.018 0.21 -9999 0 -0.76 14 14
RAP1B 0.012 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.063 0.17 -9999 0 -0.52 31 31
fibrinolysis -0.058 0.16 -9999 0 -0.47 32 32
HCK 0.012 0 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.1 0.16 -9999 0 -0.38 50 50
VTN -0.067 0.22 -9999 0 -0.67 32 32
alphaM/beta2 Integrin/CYR61 -0.029 0.11 -9999 0 -0.53 11 11
LPA -0.01 0.12 -9999 0 -0.74 7 7
LRP1 0.01 0.045 -9999 0 -0.74 1 1
cell migration -0.14 0.24 -9999 0 -0.46 93 93
FN1 -0.2 0.34 -9999 0 -0.74 76 76
alphaM/beta2 Integrin/Thy1 -0.077 0.18 -9999 0 -0.51 39 39
MPO 0.008 0.054 -9999 0 -0.61 2 2
KNG1 -0.1 0.27 -9999 0 -0.74 42 42
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.12 0.18 -9999 0 -0.44 48 48
ELA2 0 0 -9999 0 -10000 0 0
PLG 0.005 0.045 -9999 0 -0.74 1 1
CTGF 0.006 0.062 -9999 0 -0.57 3 3
alphaM/beta2 Integrin/Hck -0.022 0.097 -9999 0 -0.55 8 8
ITGAM -0.003 0.093 -9999 0 -0.75 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.047 0.12 -9999 0 -0.5 8 8
HP -0.1 0.26 -9999 0 -0.66 48 48
leukocyte adhesion -0.082 0.15 -9999 0 -0.59 11 11
SELP -0.045 0.16 -9999 0 -0.48 32 32
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.075 0.17 0.21 140 -0.4 13 153
IKBKB -0.027 0.08 -10000 0 -0.24 8 8
AKT1 -0.05 0.11 -10000 0 -0.26 32 32
IKBKG -0.03 0.083 -10000 0 -0.26 9 9
CALM1 -0.06 0.13 -10000 0 -0.43 19 19
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
MAP3K1 -0.083 0.21 -10000 0 -0.61 23 23
MAP3K7 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.071 0.14 -10000 0 -0.46 19 19
DOK1 0.01 0.045 -10000 0 -0.74 1 1
AP-1 0.078 0.13 0.19 135 -0.26 8 143
LYN 0.01 0.045 -10000 0 -0.74 1 1
BLNK -0.004 0.088 -10000 0 -0.48 9 9
SHC1 0.012 0 -10000 0 -10000 0 0
BCR complex -0.13 0.22 -10000 0 -0.4 95 95
CD22 -0.15 0.24 -10000 0 -0.68 34 34
CAMK2G -0.05 0.12 -10000 0 -0.41 18 18
CSNK2A1 -0.38 0.2 -10000 0 -0.48 215 215
INPP5D 0.005 0.07 -10000 0 -0.65 3 3
SHC/GRB2/SOS1 -0.087 0.14 -10000 0 -0.65 5 5
GO:0007205 -0.072 0.14 -10000 0 -0.47 19 19
SYK 0.012 0 -10000 0 -10000 0 0
ELK1 -0.061 0.13 -10000 0 -0.44 19 19
NFATC1 -0.078 0.18 -10000 0 -0.44 42 42
B-cell antigen/BCR complex -0.13 0.22 -10000 0 -0.4 95 95
PAG1/CSK 0.016 0.035 -10000 0 -0.56 1 1
NFKBIB 0 0.029 -10000 0 -10000 0 0
HRAS -0.059 0.13 -10000 0 -0.44 18 18
NFKBIA 0 0.029 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.006 0.024 -10000 0 -10000 0 0
RasGAP/Csk -0.099 0.16 -10000 0 -0.52 21 21
mol:GDP -0.068 0.13 -10000 0 -0.44 19 19
PTEN 0.012 0 -10000 0 -10000 0 0
CD79B -0.032 0.16 -10000 0 -0.6 20 20
NF-kappa-B/RelA/I kappa B alpha 0.007 0.024 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.13 0.23 -10000 0 -0.52 51 51
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.072 0.14 -10000 0 -0.48 19 19
CSK 0.012 0 -10000 0 -10000 0 0
FOS -0.065 0.14 -10000 0 -0.41 26 26
CHUK -0.027 0.084 -10000 0 -0.26 9 9
IBTK 0.012 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.09 0.14 -10000 0 -0.47 22 22
PTPN6 -0.12 0.24 -10000 0 -0.64 34 34
RELA 0.012 0 -10000 0 -10000 0 0
BCL2A1 0.001 0.036 -10000 0 -0.12 18 18
VAV2 -0.15 0.25 -10000 0 -0.64 44 44
ubiquitin-dependent protein catabolic process 0.004 0.028 -10000 0 -10000 0 0
BTK -0.01 0.081 -10000 0 -0.94 2 2
CD19 -0.15 0.25 -10000 0 -0.65 41 41
MAP4K1 0.003 0.076 -10000 0 -0.61 4 4
CD72 -0.015 0.14 -10000 0 -0.74 10 10
PAG1 0.01 0.045 -10000 0 -0.74 1 1
MAPK14 -0.062 0.18 -10000 0 -0.54 19 19
SH3BP5 0.012 0 -10000 0 -10000 0 0
PIK3AP1 -0.097 0.19 -10000 0 -0.5 39 39
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.1 0.2 -10000 0 -0.54 25 25
RAF1 -0.049 0.13 -10000 0 -0.41 18 18
RasGAP/p62DOK/SHIP -0.098 0.17 -10000 0 -0.56 21 21
CD79A -0.15 0.24 -10000 0 -0.49 88 88
re-entry into mitotic cell cycle 0.074 0.13 0.19 135 -0.26 8 143
RASA1 0.012 0 -10000 0 -10000 0 0
MAPK3 -0.029 0.11 -10000 0 -0.4 7 7
MAPK1 -0.029 0.11 -10000 0 -0.4 7 7
CD72/SHP1 -0.11 0.26 -10000 0 -0.67 35 35
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.062 0.18 -10000 0 -0.54 19 19
actin cytoskeleton organization -0.098 0.22 -10000 0 -0.53 44 44
NF-kappa-B/RelA 0.019 0.045 -10000 0 -10000 0 0
Calcineurin -0.058 0.1 -10000 0 -0.46 8 8
PI3K -0.13 0.19 -10000 0 -0.56 30 30
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.083 0.15 -10000 0 -0.53 19 19
SOS1 0.012 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.11 0.25 -10000 0 -0.83 22 22
DAPP1 -0.14 0.27 -10000 0 -0.93 22 22
cytokine secretion -0.072 0.17 -10000 0 -0.41 42 42
mol:DAG -0.072 0.14 -10000 0 -0.48 19 19
PLCG2 0 0.095 -10000 0 -0.69 5 5
MAP2K1 -0.039 0.12 -10000 0 -0.38 17 17
B-cell antigen/BCR complex/FcgammaRIIB -0.12 0.19 -10000 0 -0.6 21 21
mol:PI-3-4-5-P3 -0.092 0.13 -10000 0 -0.38 30 30
ETS1 -0.041 0.12 -10000 0 -0.42 13 13
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.1 0.17 -10000 0 -0.5 26 26
B-cell antigen/BCR complex/LYN -0.12 0.2 -10000 0 -0.67 21 21
MALT1 0.01 0.045 -10000 0 -0.74 1 1
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 -0.11 0.24 -10000 0 -0.57 44 44
B-cell antigen/BCR complex/LYN/SYK -0.14 0.22 -10000 0 -0.73 24 24
CARD11 -0.099 0.18 -10000 0 -0.47 41 41
FCGR2B 0.003 0.066 -10000 0 -0.48 5 5
PPP3CA 0.012 0 -10000 0 -10000 0 0
BCL10 0.012 0 -10000 0 -10000 0 0
IKK complex -0.005 0.037 -10000 0 -10000 0 0
PTPRC -0.012 0.13 -10000 0 -0.74 9 9
PDPK1 -0.05 0.11 -10000 0 -0.26 26 26
PPP3CB 0.012 0 -10000 0 -10000 0 0
PPP3CC 0.011 0.03 -10000 0 -0.48 1 1
POU2F2 0.009 0.023 -10000 0 -0.12 4 4
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.26 0.44 -9999 0 -1.1 28 28
HDAC7 0.012 0.008 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.33 -9999 0 -0.9 28 28
SMAD4 0.014 0 -9999 0 -10000 0 0
ID2 -0.26 0.44 -9999 0 -1.1 28 28
AP1 -0.002 0.094 -9999 0 -0.37 16 16
ABCG2 -0.27 0.46 -9999 0 -1.1 31 31
HIF1A -0.029 0.073 -9999 0 -10000 0 0
TFF3 -0.41 0.54 -9999 0 -1.2 62 62
GATA2 0.01 0.042 -9999 0 -0.48 2 2
AKT1 -0.03 0.084 -9999 0 -10000 0 0
response to hypoxia -0.048 0.089 -9999 0 -0.25 5 5
MCL1 -0.26 0.44 -9999 0 -1.1 28 28
NDRG1 -0.26 0.44 -9999 0 -1.1 28 28
SERPINE1 -0.32 0.48 -9999 0 -1.2 35 35
FECH -0.26 0.44 -9999 0 -1.1 28 28
FURIN -0.26 0.44 -9999 0 -1.1 28 28
NCOA2 0.013 0.004 -9999 0 -10000 0 0
EP300 -0.023 0.13 -9999 0 -0.35 11 11
HMOX1 -0.26 0.44 -9999 0 -1.1 28 28
BHLHE40 -0.26 0.44 -9999 0 -1.1 28 28
BHLHE41 -0.27 0.45 -9999 0 -1.1 30 30
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.026 0.053 -9999 0 -10000 0 0
ENG 0.017 0.091 -9999 0 -10000 0 0
JUN 0.011 0.03 -9999 0 -0.48 1 1
RORA -0.26 0.44 -9999 0 -1.1 28 28
ABCB1 -0.081 0.14 -9999 0 -0.8 7 7
TFRC -0.27 0.46 -9999 0 -1.1 29 29
CXCR4 -0.27 0.44 -9999 0 -1.1 29 29
TF -0.33 0.5 -9999 0 -1.1 50 50
CITED2 -0.26 0.44 -9999 0 -1.1 28 28
HIF1A/ARNT -0.33 0.46 -9999 0 -1.2 35 35
LDHA -0.034 0.049 -9999 0 -10000 0 0
ETS1 -0.26 0.44 -9999 0 -1.1 28 28
PGK1 -0.26 0.44 -9999 0 -1.1 28 28
NOS2 -0.33 0.5 -9999 0 -1.2 42 42
ITGB2 -0.27 0.44 -9999 0 -1.1 29 29
ALDOA -0.26 0.44 -9999 0 -1.1 28 28
Cbp/p300/CITED2 -0.26 0.46 -9999 0 -1.1 35 35
FOS -0.017 0.12 -9999 0 -0.5 16 16
HK2 -0.28 0.47 -9999 0 -1.2 29 29
SP1 0.019 0.015 -9999 0 -10000 0 0
GCK -0.09 0.34 -9999 0 -1.2 17 17
HK1 -0.26 0.44 -9999 0 -1.1 28 28
NPM1 -0.26 0.44 -9999 0 -1.1 28 28
EGLN1 -0.26 0.44 -9999 0 -1.1 28 28
CREB1 0.02 0 -9999 0 -10000 0 0
PGM1 -0.26 0.44 -9999 0 -1.1 30 30
SMAD3 0.014 0 -9999 0 -10000 0 0
EDN1 -0.026 0.2 -9999 0 -0.85 7 7
IGFBP1 -0.38 0.52 -9999 0 -1.2 52 52
VEGFA -0.18 0.36 -9999 0 -0.9 24 24
HIF1A/JAB1 -0.017 0.033 -9999 0 -10000 0 0
CP -0.29 0.47 -9999 0 -1.1 36 36
CXCL12 -0.27 0.45 -9999 0 -1.1 31 31
COPS5 0.013 0.003 -9999 0 -10000 0 0
SMAD3/SMAD4 0.001 0.003 -9999 0 -10000 0 0
BNIP3 -0.26 0.45 -9999 0 -1.1 28 28
EGLN3 -0.26 0.44 -9999 0 -1.1 28 28
CA9 -0.34 0.48 -9999 0 -1.1 46 46
TERT -0.36 0.52 -9999 0 -1.2 51 51
ENO1 -0.26 0.44 -9999 0 -1.1 28 28
PFKL -0.26 0.44 -9999 0 -1.1 28 28
NCOA1 0.013 0.001 -9999 0 -10000 0 0
ADM -0.26 0.45 -9999 0 -1.1 28 28
ARNT -0.029 0.072 -9999 0 -10000 0 0
HNF4A -0.025 0.15 -9999 0 -0.65 15 15
ADFP -0.27 0.44 -9999 0 -1.1 32 32
SLC2A1 -0.21 0.39 -9999 0 -1 28 28
LEP -0.28 0.46 -9999 0 -1.1 30 30
HIF1A/ARNT/Cbp/p300 -0.24 0.34 -9999 0 -0.88 36 36
EPO -0.12 0.3 -9999 0 -0.92 9 9
CREBBP -0.023 0.13 -9999 0 -0.35 11 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.24 0.35 -9999 0 -0.99 28 28
PFKFB3 -0.26 0.44 -9999 0 -1.1 28 28
NT5E -0.27 0.46 -9999 0 -1.1 33 33
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.008 0.05 -10000 0 -0.4 1 1
HDAC1 0.009 0.005 -10000 0 -10000 0 0
AES 0.011 0.001 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 0.002 0.083 -10000 0 -0.67 4 4
LRP6/FZD1 0.019 0 -10000 0 -10000 0 0
TLE1 0.012 0.001 -10000 0 -10000 0 0
AP1 -0.027 0.13 -10000 0 -0.3 40 40
NCSTN 0.012 0 -10000 0 -10000 0 0
ADAM10 0.012 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.002 0.056 -10000 0 -0.42 2 2
NICD/RBPSUH -0.005 0.044 -10000 0 -10000 0 0
WIF1 -0.15 0.24 -10000 0 -0.51 86 86
NOTCH1 -0.007 0.047 -10000 0 -10000 0 0
PSENEN 0.012 0 -10000 0 -10000 0 0
KREMEN2 -0.14 0.3 -10000 0 -0.74 57 57
DKK1 -0.29 0.35 -10000 0 -0.68 118 118
beta catenin/beta TrCP1 -0.1 0.1 0.23 2 -10000 0 2
APH1B 0.012 0 -10000 0 -10000 0 0
APH1A 0.012 0 -10000 0 -10000 0 0
AXIN1 -0.018 0.031 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.015 0.043 -10000 0 -10000 0 0
PSEN1 0.012 0 -10000 0 -10000 0 0
FOS -0.017 0.12 -10000 0 -0.5 16 16
JUN 0.011 0.03 -10000 0 -0.48 1 1
MAP3K7 0.011 0.002 -10000 0 -10000 0 0
CTNNB1 -0.12 0.11 0.22 7 -10000 0 7
MAPK3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.26 0.28 -10000 0 -0.52 138 138
HNF1A -0.008 0.11 -10000 0 -0.64 8 8
CTBP1 0.011 0.001 -10000 0 -10000 0 0
MYC 0.011 0.087 -10000 0 -0.94 2 2
NKD1 -0.069 0.22 -10000 0 -0.64 34 34
FZD1 0.012 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.011 0.061 -10000 0 -0.4 3 3
apoptosis -0.027 0.13 -10000 0 -0.3 40 40
Delta 1/NOTCHprecursor -0.007 0.05 -10000 0 -0.4 1 1
DLL1 0.01 0.045 -10000 0 -0.74 1 1
PPARD 0.018 0.012 -10000 0 -10000 0 0
Gamma Secretase 0.036 0.008 -10000 0 -10000 0 0
APC -0.018 0.031 -10000 0 -10000 0 0
DVL1 -0.32 0.16 -10000 0 -0.4 215 215
CSNK2A1 -0.38 0.2 -10000 0 -0.48 215 215
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.28 0.28 -10000 0 -0.54 133 133
LRP6 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.001 -10000 0 -10000 0 0
NLK 0.013 0.005 -10000 0 -10000 0 0
CCND1 0.003 0.097 -10000 0 -0.59 7 7
WNT1 -0.026 0.14 -10000 0 -0.51 20 20
Axin1/APC/beta catenin -0.17 0.11 -10000 0 -10000 0 0
DKK2 -0.25 0.36 -10000 0 -0.74 97 97
NOTCH1 precursor/DVL1 -0.25 0.13 -10000 0 -0.42 6 6
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.012 0.061 -10000 0 -0.4 3 3
PPP2R5D -0.1 0.13 0.26 19 -10000 0 19
MAPK1 0.012 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.084 0.15 -10000 0 -0.45 13 13
RBPJ 0.012 0 -10000 0 -10000 0 0
CREBBP 0.016 0.003 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.06 0.27 -10000 0 -0.63 31 31
PTK2B 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.12 -10000 0 -0.75 1 1
EDN1 -0.019 0.18 -10000 0 -0.78 7 7
EDN3 -0.14 0.23 -10000 0 -0.48 84 84
EDN2 -0.072 0.2 -10000 0 -0.51 44 44
HRAS/GDP -0.017 0.14 -10000 0 -0.39 6 6
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.01 0.12 -10000 0 -0.32 8 8
ADCY4 -0.064 0.23 -10000 0 -0.65 21 21
ADCY5 -0.12 0.26 -10000 0 -0.59 44 44
ADCY6 -0.064 0.23 -10000 0 -0.66 20 20
ADCY7 -0.064 0.23 -10000 0 -0.64 22 22
ADCY1 -0.082 0.24 -10000 0 -0.59 32 32
ADCY2 -0.089 0.24 -10000 0 -0.53 41 41
ADCY3 -0.064 0.23 -10000 0 -0.64 22 22
ADCY8 -0.07 0.23 -10000 0 -0.63 23 23
ADCY9 -0.064 0.23 -10000 0 -0.65 21 21
arachidonic acid secretion -0.011 0.16 -10000 0 -0.48 16 16
ETB receptor/Endothelin-1/Gq/GTP 0.01 0.087 -10000 0 -0.29 9 9
GNAO1 -0.043 0.18 -10000 0 -0.57 26 26
HRAS 0.012 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.034 0.28 0.32 60 -0.59 31 91
ETA receptor/Endothelin-1/Gs/GTP -0.045 0.28 0.3 58 -0.56 35 93
mol:GTP 0.002 0.003 -10000 0 -10000 0 0
COL3A1 -0.12 0.38 -10000 0 -0.8 56 56
EDNRB -0.015 0.087 -10000 0 -0.49 7 7
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.072 0.29 -10000 0 -0.78 24 24
CYSLTR1 -0.089 0.3 -10000 0 -0.62 50 50
SLC9A1 -0.03 0.14 0.19 5 -0.4 14 19
mol:GDP -0.025 0.15 -10000 0 -0.38 12 12
SLC9A3 -0.21 0.31 -10000 0 -0.54 107 107
RAF1 -0.025 0.14 -10000 0 -0.43 15 15
JUN 0.028 0.13 -10000 0 -0.95 1 1
JAK2 -0.066 0.27 -10000 0 -0.62 34 34
mol:IP3 0.007 0.11 -10000 0 -0.34 3 3
ETA receptor/Endothelin-1 -0.058 0.34 0.38 60 -0.61 51 111
PLCB1 -0.008 0.12 -10000 0 -0.68 8 8
PLCB2 0.012 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.14 0.24 -10000 0 -0.42 96 96
FOS -0.033 0.24 -10000 0 -0.9 16 16
Gai/GDP -0.034 0.18 -10000 0 -0.67 17 17
CRK 0.013 0 -10000 0 -10000 0 0
mol:Ca ++ -0.05 0.25 -10000 0 -0.63 25 25
BCAR1 0.013 0 -10000 0 -10000 0 0
PRKCB1 0.006 0.11 -10000 0 -0.33 3 3
GNAQ 0.014 0.004 -10000 0 -10000 0 0
GNAZ -0.013 0.11 -10000 0 -0.48 14 14
GNAL -0.008 0.1 -10000 0 -0.5 11 11
Gs family/GDP -0.07 0.11 -10000 0 -0.4 13 13
ETA receptor/Endothelin-1/Gq/GTP 0.006 0.14 -10000 0 -0.38 15 15
MAPK14 0.02 0.075 -10000 0 -10000 0 0
TRPC6 0.026 0.12 -10000 0 -0.79 1 1
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.003 0.066 -10000 0 -0.48 5 5
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.014 0.08 -10000 0 -10000 0 0
ETB receptor/Endothelin-2 -0.06 0.16 -10000 0 -0.38 50 50
ETB receptor/Endothelin-3 -0.11 0.18 -10000 0 -0.36 88 88
ETB receptor/Endothelin-1 -0.031 0.17 -10000 0 -0.57 11 11
MAPK3 -0.03 0.21 -10000 0 -0.77 16 16
MAPK1 -0.03 0.21 -10000 0 -0.77 16 16
Rac1/GDP -0.017 0.14 -10000 0 -0.39 6 6
cAMP biosynthetic process -0.082 0.22 -10000 0 -0.57 27 27
MAPK8 0.023 0.13 -10000 0 -0.54 2 2
SRC 0.012 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.02 0.12 -10000 0 -0.39 14 14
p130Cas/CRK/Src/PYK2 -0.029 0.15 -10000 0 -0.49 2 2
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.017 0.14 -10000 0 -0.4 5 5
COL1A2 -0.13 0.37 -10000 0 -0.75 62 62
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.096 0.23 -10000 0 -0.5 51 51
mol:DAG 0.007 0.11 -10000 0 -0.34 3 3
MAP2K2 -0.024 0.17 -10000 0 -0.57 16 16
MAP2K1 -0.024 0.17 -10000 0 -0.57 16 16
EDNRA -0.047 0.24 -10000 0 -0.86 17 17
positive regulation of muscle contraction -0.045 0.24 -10000 0 -0.74 16 16
Gq family/GDP -0.052 0.097 -10000 0 -0.41 3 3
HRAS/GTP -0.029 0.13 -10000 0 -0.36 10 10
PRKCH 0.013 0.11 -10000 0 -0.39 1 1
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA 0.012 0.11 -10000 0 -0.39 1 1
PRKCB -0.001 0.13 -10000 0 -0.46 6 6
PRKCE 0.013 0.1 -10000 0 -0.38 1 1
PRKCD 0.013 0.11 -10000 0 -0.39 1 1
PRKCG -0.15 0.23 -10000 0 -0.43 88 88
regulation of vascular smooth muscle contraction -0.041 0.27 -10000 0 -1 16 16
PRKCQ 0.008 0.11 -10000 0 -0.38 1 1
PLA2G4A -0.014 0.17 -10000 0 -0.52 16 16
GNA14 0.006 0.068 -10000 0 -0.55 4 4
GNA15 0.008 0.064 -10000 0 -0.74 2 2
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 0.014 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.28 0.32 60 -0.59 31 91
MMP1 -0.23 0.34 -10000 0 -0.63 112 112
Canonical Wnt signaling 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
HDAC1 0.007 0.02 -10000 0 -10000 0 0
AES 0.013 0.015 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.016 0.006 -10000 0 -10000 0 0
SMAD4 0.012 0 -10000 0 -10000 0 0
DKK2 -0.25 0.36 -10000 0 -0.74 97 97
TLE1 0.012 0.015 -10000 0 -10000 0 0
MACF1 0.012 0.001 -10000 0 -10000 0 0
CTNNB1 -0.066 0.11 0.27 2 -0.36 3 5
WIF1 -0.15 0.24 -10000 0 -0.5 86 86
beta catenin/RanBP3 -0.049 0.12 0.36 8 -10000 0 8
KREMEN2 -0.14 0.3 -10000 0 -0.74 57 57
DKK1 -0.29 0.35 -10000 0 -0.68 118 118
beta catenin/beta TrCP1 -0.054 0.1 0.29 1 -10000 0 1
FZD1 0.012 0.001 -10000 0 -10000 0 0
AXIN2 -0.037 0.2 -10000 0 -0.7 21 21
AXIN1 0.012 0.001 -10000 0 -10000 0 0
RAN 0.012 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.011 0.026 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.038 0.072 -10000 0 -10000 0 0
Axin1/APC/GSK3 -0.077 0.088 0.22 3 -10000 0 3
Axin1/APC/GSK3/beta catenin/Macf1 0 0.078 -10000 0 -10000 0 0
HNF1A -0.007 0.11 -10000 0 -0.63 8 8
CTBP1 0.006 0.018 -10000 0 -10000 0 0
MYC 0.001 0.096 -10000 0 -0.91 2 2
RANBP3 0.012 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.26 0.28 -10000 0 -0.52 138 138
NKD1 -0.069 0.22 -10000 0 -0.64 34 34
TCF4 0.008 0.018 -10000 0 -10000 0 0
TCF3 0.01 0.046 -10000 0 -0.71 1 1
WNT1/LRP6/FZD1/Axin1 0.001 0.077 -10000 0 -0.44 2 2
Ran/GTP 0.009 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.02 0.1 0.46 5 -10000 0 5
LEF1 -0.033 0.16 -10000 0 -0.71 15 15
DVL1 -0.17 0.14 -10000 0 -0.37 13 13
CSNK2A1 -0.38 0.2 -10000 0 -0.48 215 215
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.036 0.093 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.28 0.28 -10000 0 -0.54 133 133
LRP6 0.012 0.001 -10000 0 -10000 0 0
CSNK1A1 0.01 0.019 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 -0.005 0.11 -10000 0 -0.62 7 7
WNT1 -0.026 0.14 -10000 0 -0.51 20 20
GSK3A 0.012 0.001 -10000 0 -10000 0 0
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
PPP2R5D -0.051 0.13 0.28 23 -10000 0 23
APC 0.015 0.073 -10000 0 -0.4 2 2
WNT1/LRP6/FZD1 0.064 0.11 0.22 83 -10000 0 83
CREBBP 0.012 0.015 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.003 0.1 -9999 0 -0.7 6 6
GPC2 -0.051 0.21 -9999 0 -0.74 23 23
GPC2/Midkine -0.041 0.18 -9999 0 -0.56 28 28
neuron projection morphogenesis -0.041 0.18 -9999 0 -0.56 28 28
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.019 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.019 0.14 -9999 0 -0.5 20 20
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.093 0.15 -9999 0 -0.47 26 26
NGF (dimer)/p75(NTR)/BEX1 -0.24 0.23 -9999 0 -0.57 68 68
NT-4/5 (dimer)/p75(NTR) -0.13 0.22 -9999 0 -0.42 93 93
IKBKB 0.012 0 -9999 0 -10000 0 0
AKT1 -0.065 0.16 -9999 0 -0.44 25 25
IKBKG 0.005 0.006 -9999 0 -10000 0 0
BDNF -0.004 0.11 -9999 0 -0.74 6 6
MGDIs/NGR/p75(NTR)/LINGO1 -0.14 0.21 -9999 0 -0.54 43 43
FURIN 0.01 0.045 -9999 0 -0.74 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.094 0.15 -9999 0 -0.48 19 19
LINGO1 -0.062 0.22 -9999 0 -0.74 27 27
Sortilin/TRAF6/NRIF -0.001 0.015 -9999 0 -10000 0 0
proBDNF (dimer) -0.004 0.11 -9999 0 -0.74 6 6
NTRK1 0.007 0.051 -9999 0 -0.48 3 3
RTN4R -0.007 0.12 -9999 0 -0.74 7 7
neuron apoptosis -0.064 0.17 -9999 0 -0.49 17 17
IRAK1 0.012 0 -9999 0 -10000 0 0
SHC1 -0.09 0.18 -9999 0 -0.52 24 24
ARHGDIA 0.012 0 -9999 0 -10000 0 0
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.077 0.18 -9999 0 -0.5 25 25
MAGEH1 0.007 0.051 -9999 0 -0.48 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.079 0.18 -9999 0 -0.5 26 26
Mammalian IAPs/DIABLO 0.025 0.053 -9999 0 -0.43 3 3
proNGF (dimer) -0.034 0.15 -9999 0 -0.49 25 25
MAGED1 0.009 0.042 -9999 0 -0.48 2 2
APP 0.012 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.045 0.2 -9999 0 -0.74 21 21
ZNF274 0.009 0.042 -9999 0 -0.48 2 2
RhoA/GDP/RHOGDI -0.07 0.16 -9999 0 -0.45 24 24
NGF -0.034 0.15 -9999 0 -0.49 25 25
cell cycle arrest -0.042 0.18 -9999 0 -0.45 24 24
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.056 0.14 -9999 0 -0.44 13 13
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.12 0.18 -9999 0 -0.49 33 33
NCSTN 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.11 0.18 -9999 0 -0.54 24 24
PSENEN 0.012 0 -9999 0 -10000 0 0
mol:ceramide -0.074 0.17 -9999 0 -0.47 24 24
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.039 0.12 -9999 0 -0.37 15 15
p75(NTR)/beta APP -0.087 0.18 -9999 0 -0.38 73 73
BEX1 -0.21 0.26 -9999 0 -0.51 117 117
mol:GDP -0.099 0.18 -9999 0 -0.35 86 86
NGF (dimer) -0.2 0.24 -9999 0 -0.46 116 116
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.11 0.21 -9999 0 -0.49 43 43
PIK3R1 0.012 0 -9999 0 -10000 0 0
RAC1/GTP -0.093 0.15 -9999 0 -0.46 24 24
MYD88 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.11 0.18 -9999 0 -0.55 24 24
RHOB 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.013 0.13 -9999 0 -0.56 15 15
NT3 (dimer) -0.034 0.15 -9999 0 -0.49 25 25
TP53 -0.042 0.14 -9999 0 -0.38 21 21
PRDM4 -0.075 0.17 -9999 0 -0.48 24 24
BDNF (dimer) -0.39 0.3 -9999 0 -0.55 194 194
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
SORT1 0.012 0 -9999 0 -10000 0 0
activation of caspase activity -0.092 0.15 -9999 0 -0.46 26 26
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.075 0.17 -9999 0 -0.48 24 24
RHOC 0.012 0 -9999 0 -10000 0 0
XIAP 0.01 0.045 -9999 0 -0.74 1 1
MAPK10 -0.057 0.18 -9999 0 -0.49 22 22
DIABLO 0.012 0 -9999 0 -10000 0 0
SMPD2 -0.075 0.17 -9999 0 -0.48 24 24
APH1B 0.012 0 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.11 0.17 -9999 0 -0.53 24 24
PSEN1 0.012 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.12 0.21 -9999 0 -0.4 88 88
MAPK8 -0.046 0.16 -9999 0 -0.46 13 13
MAPK9 -0.046 0.16 -9999 0 -0.46 13 13
APAF1 0.012 0 -9999 0 -10000 0 0
NTF3 -0.034 0.15 -9999 0 -0.49 25 25
NTF4 -0.045 0.2 -9999 0 -0.74 21 21
NDN 0.003 0.066 -9999 0 -0.48 5 5
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.083 0.14 -9999 0 -0.49 12 12
p75 CTF/Sortilin/TRAF6/NRIF 0.03 0.023 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.18 -9999 0 -0.54 24 24
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.078 0.13 -9999 0 -0.41 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.06 0.15 -9999 0 -0.43 19 19
PRKACB 0.007 0.051 -9999 0 -0.48 3 3
proBDNF (dimer)/p75 ECD 0.006 0.084 -9999 0 -0.56 6 6
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 0.003 0.076 -9999 0 -0.61 4 4
BIRC2 0.012 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.038 0.2 -9999 0 -0.48 21 21
BAD -0.046 0.17 -9999 0 -0.47 14 14
RIPK2 0.004 0.078 -9999 0 -0.74 3 3
NGFR -0.13 0.24 -9999 0 -0.53 73 73
CYCS -0.065 0.16 -9999 0 -0.45 25 25
ADAM17 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.08 0.18 -9999 0 -0.48 27 27
BCL2L11 -0.046 0.17 -9999 0 -0.47 14 14
BDNF (dimer)/p75(NTR) -0.099 0.19 -9999 0 -0.39 79 79
PI3K -0.076 0.17 -9999 0 -0.48 25 25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.075 0.17 -9999 0 -0.48 24 24
NDNL2 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKCI 0.004 0.078 -9999 0 -0.74 3 3
NGF (dimer)/p75(NTR) -0.12 0.21 -9999 0 -0.41 86 86
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.077 0.18 -9999 0 -0.49 25 25
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
PLG 0.005 0.045 -9999 0 -0.74 1 1
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.08 0.18 -9999 0 -0.44 30 30
SQSTM1 0.012 0 -9999 0 -10000 0 0
NGFRAP1 0.005 0.059 -9999 0 -0.48 4 4
CASP3 -0.041 0.16 -9999 0 -0.43 14 14
E2F1 -0.029 0.17 -9999 0 -0.74 15 15
CASP9 0.012 0 -9999 0 -10000 0 0
IKK complex -0.063 0.11 -9999 0 -0.43 12 12
NGF (dimer)/TRKA -0.019 0.11 -9999 0 -0.34 28 28
MMP7 -0.31 0.37 -9999 0 -0.72 121 121
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.091 0.15 -9999 0 -0.47 24 24
MMP3 -0.34 0.37 -9999 0 -0.72 130 130
APAF-1/Caspase 9 -0.067 0.11 -9999 0 -0.56 4 4
Signaling events regulated by Ret tyrosine kinase

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 -0.035 0.047 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.11 0.14 -9999 0 -0.4 32 32
JUN -0.069 0.16 -9999 0 -0.43 27 27
HRAS 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.12 0.21 -9999 0 -0.55 35 35
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.007 0.064 -9999 0 -0.74 2 2
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.12 0.21 -9999 0 -0.55 35 35
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.095 0.17 -9999 0 -0.54 14 14
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.12 0.18 -9999 0 -0.49 35 35
GRB7 -0.09 0.26 -9999 0 -0.72 38 38
RET51/GFRalpha1/GDNF -0.12 0.21 -9999 0 -0.54 35 35
MAPKKK cascade -0.11 0.16 -9999 0 -0.49 26 26
BCAR1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.092 0.16 -9999 0 -0.53 13 13
lamellipodium assembly -0.1 0.13 -9999 0 -0.37 32 32
RET51/GFRalpha1/GDNF/SHC -0.12 0.21 -9999 0 -0.54 35 35
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/SHC -0.092 0.16 -9999 0 -0.52 13 13
RET9/GFRalpha1/GDNF/Shank3 -0.092 0.16 -9999 0 -0.52 13 13
MAPK3 -0.088 0.18 -9999 0 -0.49 26 26
DOK1 0.01 0.045 -9999 0 -0.74 1 1
DOK6 -0.001 0.1 -9999 0 -0.74 5 5
PXN 0.008 0.054 -9999 0 -0.61 2 2
neurite development -0.075 0.17 -9999 0 -0.46 27 27
DOK5 -0.012 0.13 -9999 0 -0.74 9 9
GFRA1 -0.16 0.24 -9999 0 -0.48 95 95
MAPK8 -0.079 0.16 -9999 0 -0.46 26 26
HRAS/GTP -0.13 0.18 -9999 0 -0.57 26 26
tube development -0.079 0.15 -9999 0 -0.48 13 13
MAPK1 -0.088 0.18 -9999 0 -0.46 35 35
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.074 0.14 -9999 0 -0.45 10 10
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.007 0.064 -9999 0 -0.74 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.19 -9999 0 -0.51 39 39
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.12 0.21 -9999 0 -0.55 35 35
RET51/GFRalpha1/GDNF/Dok5 -0.13 0.22 -9999 0 -0.53 43 43
PRKCA 0.011 0.03 -9999 0 -0.48 1 1
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
CREB1 -0.094 0.17 -9999 0 -0.46 26 26
PIK3R1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.074 0.14 -9999 0 -0.46 12 12
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.26 -9999 0 -0.57 70 70
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.047 0.19 -9999 0 -0.61 26 26
DOK4 0.011 0.03 -9999 0 -0.48 1 1
JNK cascade -0.068 0.16 -9999 0 -0.42 27 27
RET9/GFRalpha1/GDNF/FRS2 -0.095 0.16 -9999 0 -0.5 15 15
SHANK3 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.072 0.14 -9999 0 -0.45 10 10
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.092 0.17 -9999 0 -0.48 26 26
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.092 0.17 -9999 0 -0.49 26 26
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.096 0.18 -9999 0 -0.53 26 26
PI3K -0.12 0.24 -9999 0 -0.6 32 32
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.098 0.14 -9999 0 -0.48 13 13
GRB10 0.01 0.045 -9999 0 -0.74 1 1
activation of MAPKK activity -0.087 0.16 -9999 0 -0.46 26 26
RET51/GFRalpha1/GDNF/FRS2 -0.12 0.21 -9999 0 -0.53 37 37
GAB1 0.009 0.042 -9999 0 -0.48 2 2
IRS1 0.011 0.03 -9999 0 -0.48 1 1
IRS2 -0.016 0.13 -9999 0 -0.58 13 13
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.098 0.19 -9999 0 -0.55 27 27
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.21 -9999 0 -0.54 36 36
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF -0.025 0.14 -9999 0 -0.55 18 18
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.21 -9999 0 -0.55 35 35
Rac1/GTP -0.12 0.16 -9999 0 -0.45 32 32
RET9/GFRalpha1/GDNF -0.12 0.17 -9999 0 -0.32 103 103
GFRalpha1/GDNF -0.13 0.2 -9999 0 -0.38 103 103
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.11 0.17 -9999 0 -0.46 39 39
SMAD6-7/SMURF1 -0.004 0.044 -9999 0 -0.48 2 2
NOG -0.029 0.15 -9999 0 -0.58 19 19
SMAD9 -0.022 0.13 -9999 0 -0.67 8 8
SMAD4 0.012 0 -9999 0 -10000 0 0
SMAD5 -0.023 0.12 -9999 0 -0.35 21 21
BMP7/USAG1 -0.28 0.24 -9999 0 -0.42 187 187
SMAD5/SKI -0.015 0.12 -9999 0 -0.45 3 3
SMAD1 0.036 0.022 -9999 0 -10000 0 0
BMP2 0.007 0.051 -9999 0 -0.48 3 3
SMAD1/SMAD1/SMAD4 -0.003 0.026 -9999 0 -10000 0 0
BMPR1A 0.011 0.03 -9999 0 -0.48 1 1
BMPR1B -0.06 0.19 -9999 0 -0.52 37 37
BMPR1A-1B/BAMBI -0.13 0.22 -9999 0 -0.53 54 54
AHSG -0.041 0.18 -9999 0 -0.74 18 18
CER1 -0.004 0.078 -9999 0 -0.74 3 3
BMP2-4/CER1 -0.021 0.094 -9999 0 -0.48 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.14 -9999 0 -0.39 24 24
BMP2-4 (homodimer) 0 0.097 -9999 0 -0.49 10 10
RGMB 0.011 0.03 -9999 0 -0.48 1 1
BMP6/BMPR2/BMPR1A-1B -0.01 0.11 -9999 0 -0.44 7 7
RGMA -0.1 0.21 -9999 0 -0.5 62 62
SMURF1 0.007 0.064 -9999 0 -0.74 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.14 -9999 0 -0.38 24 24
BMP2-4/USAG1 -0.19 0.15 -9999 0 -0.57 10 10
SMAD6/SMURF1/SMAD5 -0.018 0.12 -9999 0 -0.42 5 5
SOSTDC1 -0.3 0.24 -9999 0 -0.48 173 173
BMP7/BMPR2/BMPR1A-1B -0.078 0.18 -9999 0 -0.47 28 28
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.012 0 -9999 0 -10000 0 0
HFE2 0.001 0.064 -9999 0 -0.74 2 2
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.019 0.092 -9999 0 -0.51 8 8
SMAD5/SMAD5/SMAD4 -0.015 0.12 -9999 0 -0.45 3 3
MAPK1 0.012 0 -9999 0 -10000 0 0
TAK1/TAB family -0.058 0.1 -9999 0 -0.43 6 6
BMP7 (homodimer) -0.11 0.24 -9999 0 -0.56 57 57
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.022 0.14 -9999 0 -0.56 18 18
SMAD1/SKI 0.041 0.021 -9999 0 -10000 0 0
SMAD6 0.011 0.03 -9999 0 -0.48 1 1
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.047 0.14 -9999 0 -0.48 25 25
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.15 0.3 -9999 0 -0.71 60 60
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.035 0.14 -9999 0 -0.38 37 37
CHRDL1 -0.15 0.23 -9999 0 -0.48 92 92
ENDOFIN/SMAD1 0.041 0.021 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.002 0.03 -9999 0 -10000 0 0
SMAD6/SMURF1 0.007 0.064 -9999 0 -0.74 2 2
BAMBI -0.12 0.29 -9999 0 -0.74 50 50
SMURF2 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.11 0.17 -9999 0 -0.69 9 9
BMP2-4/GREM1 -0.12 0.2 -9999 0 -0.48 61 61
SMAD7 0.012 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.014 0.12 -9999 0 -0.68 7 7
SMAD1/SMAD6 0.038 0.04 -9999 0 -0.36 2 2
TAK1/SMAD6 0.014 0.049 -9999 0 -0.56 2 2
BMP7 -0.11 0.24 -9999 0 -0.56 57 57
BMP6 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.035 0.13 -9999 0 -0.35 24 24
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.041 0.021 -9999 0 -10000 0 0
SMAD7/SMURF1 0.014 0.049 -9999 0 -0.56 2 2
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.01 0.045 -9999 0 -0.74 1 1
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.067 0.17 -9999 0 -0.5 28 28
CHRD 0.006 0.062 -9999 0 -0.57 3 3
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.049 0.15 -9999 0 -0.42 24 24
BMP4 -0.007 0.12 -9999 0 -0.74 7 7
FST -0.025 0.16 -9999 0 -0.67 15 15
BMP2-4/NOG -0.039 0.12 -9999 0 -0.5 14 14
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.095 0.15 -9999 0 -0.44 30 30
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.028 0.085 0.22 44 -10000 0 44
BUB1B -0.086 0.16 -10000 0 -0.32 83 83
PLK1 -0.005 0.042 -10000 0 -0.12 22 22
PLK1S1 0.003 0.021 -10000 0 -10000 0 0
KIF2A 0.003 0.038 -10000 0 -0.19 3 3
regulation of mitotic centrosome separation -0.005 0.042 -10000 0 -0.12 22 22
GOLGA2 0.012 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.061 0.19 -10000 0 -0.48 43 43
WEE1 -0.002 0.05 -10000 0 -0.27 4 4
cytokinesis -0.065 0.17 -10000 0 -0.42 45 45
PP2A-alpha B56 -0.078 0.12 -10000 0 -0.5 1 1
AURKA -0.005 0.046 -10000 0 -0.19 13 13
PICH/PLK1 -0.099 0.23 -10000 0 -0.49 66 66
CENPE -0.11 0.21 -10000 0 -0.48 68 68
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.038 -10000 0 -0.19 3 3
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0.012 0 -10000 0 -10000 0 0
TPX2 -0.038 0.085 -10000 0 -0.19 66 66
PAK1 0.009 0.045 -10000 0 -0.74 1 1
SPC24 0.001 0.09 -10000 0 -0.74 4 4
FBXW11 0.012 0 -10000 0 -10000 0 0
CLSPN -0.044 0.097 -10000 0 -0.21 65 65
GORASP1 0.012 0 -10000 0 -10000 0 0
metaphase -0.001 0.005 -10000 0 -0.015 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.002 0.021 -10000 0 -0.065 18 18
G2 phase of mitotic cell cycle 0 0.003 0.011 1 -0.012 13 14
STAG2 0.012 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.013 -10000 0 -10000 0 0
spindle elongation -0.005 0.042 -10000 0 -0.12 22 22
ODF2 0.009 0.045 -10000 0 -0.73 1 1
BUB1 -0.088 0.14 -10000 0 -0.55 1 1
TPT1 0.003 0.021 -10000 0 -0.11 1 1
CDC25C -0.003 0.051 -10000 0 -0.27 8 8
CDC25B -0.015 0.14 -10000 0 -0.74 10 10
SGOL1 -0.028 0.085 -10000 0 -0.22 44 44
RHOA 0.012 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.034 0.1 -10000 0 -0.42 17 17
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.017 0.14 -10000 0 -0.72 11 11
PLK1/PBIP1 -0.005 0.064 -10000 0 -0.3 8 8
mitosis 0.001 0.008 0.034 13 -10000 0 13
FBXO5 0 0.048 -10000 0 -0.28 4 4
CDC2 -0.001 0.005 -10000 0 -0.017 17 17
NDC80 -0.1 0.27 -10000 0 -0.74 42 42
metaphase plate congression 0.001 0.027 -10000 0 -10000 0 0
ERCC6L -0.097 0.23 -10000 0 -0.48 66 66
NLP/gamma Tubulin 0 0.023 -10000 0 -0.091 7 7
microtubule cytoskeleton organization 0.003 0.021 -10000 0 -0.11 1 1
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.012 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.12 0.27 -10000 0 -0.57 66 66
GRASP65/GM130/RAB1/GTP/PLK1 -0.005 0.025 -10000 0 -10000 0 0
RAB1A 0.012 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.003 0.036 -10000 0 -0.13 13 13
mitotic prometaphase -0.001 0.003 -10000 0 -0.011 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.034 -10000 0 -10000 0 0
microtubule-based process -0.067 0.18 -10000 0 -0.46 44 44
Golgi organization -0.005 0.042 -10000 0 -0.12 22 22
Cohesin/SA2 -0.012 0.032 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.017 0.006 -10000 0 -10000 0 0
KIF20A -0.1 0.27 -10000 0 -0.74 43 43
APC/C/CDC20 -0.014 0.11 -10000 0 -0.48 12 12
PPP2R1A 0.012 0 -10000 0 -10000 0 0
chromosome segregation -0.017 0.059 -10000 0 -0.3 8 8
PRC1 -0.1 0.27 -10000 0 -0.74 43 43
ECT2 -0.13 0.22 -10000 0 -0.47 82 82
C13orf34 -0.003 0.034 -10000 0 -0.12 12 12
NUDC 0.001 0.027 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.085 0.16 -10000 0 -0.32 83 83
spindle assembly -0.001 0.033 -10000 0 -0.13 8 8
spindle stabilization 0.003 0.021 -10000 0 -10000 0 0
APC/C/HCDH1 0.017 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 -0.068 0.18 -10000 0 -0.46 44 44
CCNB1 -0.007 0.12 -10000 0 -0.74 7 7
PPP1CB 0.012 0.001 -10000 0 -10000 0 0
BTRC 0.012 0 -10000 0 -10000 0 0
ROCK2 0.007 0.032 -10000 0 -0.26 1 1
TUBG1 0.003 0.021 -10000 0 -0.11 1 1
G2/M transition of mitotic cell cycle -0.033 0.099 -10000 0 -0.41 17 17
MLF1IP 0.002 0.07 -10000 0 -0.57 4 4
INCENP 0.007 0.046 -10000 0 -0.74 1 1
PDGFR-alpha signaling 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
PDGFRA 0.022 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/CRKL 0.004 0.008 -10000 0 -10000 0 0
positive regulation of JUN kinase activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.012 0 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.002 0.006 -10000 0 -10000 0 0
AP1 0.14 0.25 -10000 0 -0.79 15 15
mol:IP3 0.043 0.023 -10000 0 -10000 0 0
PLCG1 0.043 0.023 -10000 0 -10000 0 0
PDGF/PDGFRA/alphaV Integrin 0.004 0.008 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0.043 0.023 -10000 0 -10000 0 0
CAV3 0.006 0.006 -10000 0 -10000 0 0
CAV1 0.004 0.078 -10000 0 -0.74 3 3
SHC/Grb2/SOS1 0.007 0.013 -10000 0 -10000 0 0
PDGF/PDGFRA/Shf -0.006 0.059 -10000 0 -0.34 8 8
FOS 0.12 0.23 -10000 0 -0.76 16 16
JUN 0.27 0.15 0.35 214 -10000 0 214
oligodendrocyte development 0.004 0.008 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:DAG 0.043 0.023 -10000 0 -10000 0 0
PDGF/PDGFRA 0.022 0.012 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.004 0.008 -10000 0 -10000 0 0
SRF -0.25 0.14 -10000 0 -0.32 215 215
SHC1 0.012 0 -10000 0 -10000 0 0
PI3K -0.002 0.029 -10000 0 -0.48 1 1
PDGF/PDGFRA/Crk/C3G 0 0.001 -10000 0 -10000 0 0
JAK1 0.03 0.009 -10000 0 -10000 0 0
ELK1/SRF -0.12 0.086 -10000 0 -10000 0 0
SHB 0.012 0 -10000 0 -10000 0 0
SHF -0.002 0.083 -10000 0 -0.48 8 8
CSNK2A1 -0.36 0.19 -10000 0 -0.46 215 215
GO:0007205 0.045 0.025 -10000 0 -10000 0 0
SOS1 0.012 0 -10000 0 -10000 0 0
Ras protein signal transduction 0 0.001 -10000 0 -10000 0 0
PDGF/PDGFRA/SHB 0.004 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-1 -0.002 0.059 -10000 0 -0.56 3 3
ITGAV 0.012 0 -10000 0 -10000 0 0
ELK1 0.06 0.036 -10000 0 -10000 0 0
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
PDGF/PDGFRA/Crk 0.004 0.008 -10000 0 -10000 0 0
JAK-STAT cascade 0.03 0.009 -10000 0 -10000 0 0
cell proliferation -0.006 0.058 -10000 0 -0.34 8 8
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.007 0.062 -9999 0 -0.55 3 3
RGS9BP -0.054 0.17 -9999 0 -0.5 35 35
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.004 0.077 -9999 0 -0.74 3 3
mol:Na + -0.094 0.18 -9999 0 -0.4 64 64
mol:ADP 0.002 0.077 -9999 0 -0.56 5 5
GNAT2 0.005 0.07 -9999 0 -0.65 3 3
RGS9-1/Gbeta5/R9AP -0.055 0.13 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.01 0.067 -9999 0 -0.45 6 6
GRK7 0.005 0.064 -9999 0 -0.74 2 2
CNGB3 -0.069 0.23 -9999 0 -0.74 29 29
Cone Metarhodopsin II/X-Arrestin 0.009 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.14 0.25 -9999 0 -0.52 68 68
Cone PDE6 -0.05 0.12 -9999 0 -0.45 12 12
Cone Metarhodopsin II 0.001 0.061 -9999 0 -0.45 5 5
Na + (4 Units) -0.14 0.25 -9999 0 -0.52 68 68
GNAT2/GDP -0.05 0.12 -9999 0 -0.46 11 11
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.063 -9999 0 -0.44 5 5
Cone Transducin 0.017 0.068 -9999 0 -0.58 3 3
SLC24A2 -0.11 0.28 -9999 0 -0.71 47 47
GNB3/GNGT2 0.015 0.062 -9999 0 -1 1 1
GNB3 0.01 0.045 -9999 0 -0.74 1 1
GNAT2/GTP 0.004 0.053 -9999 0 -0.49 3 3
CNGA3 -0.062 0.18 -9999 0 -0.51 39 39
ARR3 0.012 0.001 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.094 0.18 -9999 0 -0.4 64 64
mol:Pi -0.055 0.13 -9999 0 -0.54 9 9
Cone CNG Channel -0.083 0.15 -9999 0 -0.42 39 39
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.11 0.27 -9999 0 -0.71 47 47
RGS9 -0.019 0.12 -9999 0 -0.5 17 17
PDE6C 0.011 0.003 -9999 0 -10000 0 0
GNGT2 0.01 0.045 -9999 0 -0.74 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.078 -9999 0 -0.74 3 3
Syndecan-3-mediated signaling 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
CTTN 0.01 0.045 -9999 0 -0.74 1 1
Syndecan-3/Src/Cortactin -0.022 0.064 -9999 0 -0.37 1 1
Syndecan-3/Neurocan -0.003 0.03 -9999 0 -0.35 2 2
POMC -0.015 0.12 -9999 0 -0.52 14 14
EGFR -0.021 0.14 -9999 0 -0.6 15 15
Syndecan-3/EGFR -0.018 0.075 -9999 0 -0.39 8 8
AGRP 0.004 0.078 -9999 0 -0.74 3 3
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.012 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.012 0 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN 0.008 0.045 -9999 0 -0.74 1 1
long-term memory -0.002 0.028 -9999 0 -0.38 1 1
Syndecan-3/IL8 -0.21 0.2 -9999 0 -0.4 142 142
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.016 0.035 -9999 0 -0.56 1 1
FYN 0.012 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.02 -9999 0 -0.32 1 1
MC4R 0.007 0.006 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.036 0.15 -9999 0 -0.48 27 27
FGFR/FGF/Syndecan-3 -0.001 0.02 -9999 0 -0.33 1 1
neuron projection morphogenesis -0.022 0.064 -9999 0 -0.35 2 2
Syndecan-3/AgRP -0.006 0.046 -9999 0 -0.38 4 4
Syndecan-3/AgRP/MC4R -0.005 0.044 -9999 0 -0.39 3 3
Fyn/Cortactin 0.016 0.035 -9999 0 -0.56 1 1
SDC3 -0.001 0.02 -9999 0 -0.33 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.2 0.2 -9999 0 -0.4 142 142
IL8 -0.37 0.38 -9999 0 -0.74 141 141
Syndecan-3/Fyn/Cortactin -0.002 0.029 -9999 0 -0.38 1 1
Syndecan-3/CASK -0.001 0.019 -9999 0 -0.31 1 1
alpha-MSH/MC4R -0.006 0.088 -9999 0 -0.38 14 14
Gamma Secretase 0 0 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.033 0.16 -10000 0 -0.93 7 7
NFATC2 0.007 0.13 -10000 0 -0.76 2 2
NFATC3 -0.02 0.066 -10000 0 -10000 0 0
CD40LG -0.28 0.37 -10000 0 -0.86 45 45
ITCH 0.034 0.051 -10000 0 -10000 0 0
CBLB 0.034 0.051 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.22 0.31 -10000 0 -0.93 34 34
JUNB 0.009 0.042 -10000 0 -0.48 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.053 -10000 0 -10000 0 0
T cell anergy 0.027 0.094 -10000 0 -0.43 5 5
TLE4 0.021 0.1 -10000 0 -0.69 2 2
Jun/NFAT1-c-4/p21SNFT -0.12 0.23 -10000 0 -0.8 13 13
AP-1/NFAT1-c-4 -0.31 0.41 -10000 0 -0.92 53 53
IKZF1 0.016 0.13 -10000 0 -0.78 5 5
T-helper 2 cell differentiation -0.047 0.15 -10000 0 -0.66 5 5
AP-1/NFAT1 -0.072 0.13 -10000 0 -0.57 5 5
CALM1 0.019 0.034 -10000 0 -10000 0 0
EGR2 -0.026 0.21 -10000 0 -0.88 8 8
EGR3 -0.057 0.31 -10000 0 -1.2 16 16
NFAT1/FOXP3 -0.029 0.2 -10000 0 -0.78 10 10
EGR1 -0.003 0.09 -10000 0 -0.51 8 8
JUN -0.024 0.047 -10000 0 -0.48 1 1
EGR4 -0.14 0.3 -10000 0 -0.7 60 60
mol:Ca2+ 0.006 0.036 -10000 0 -10000 0 0
GBP3 0.013 0.14 -10000 0 -0.74 6 6
FOSL1 -0.05 0.2 -10000 0 -0.71 24 24
NFAT1-c-4/MAF/IRF4 -0.083 0.24 -10000 0 -0.87 15 15
DGKA 0.023 0.093 -10000 0 -0.69 1 1
CREM 0.012 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.084 0.2 -10000 0 -0.79 12 12
CTLA4 -0.083 0.31 -10000 0 -0.76 44 44
NFAT1-c-4 (dimer)/EGR1 -0.06 0.24 -10000 0 -0.86 14 14
NFAT1-c-4 (dimer)/EGR4 -0.15 0.28 -10000 0 -0.81 22 22
FOS -0.053 0.12 -10000 0 -0.52 16 16
IFNG -0.19 0.28 -10000 0 -0.63 65 65
T cell activation -0.057 0.15 -10000 0 -0.66 2 2
MAF 0.005 0.059 -10000 0 -0.48 4 4
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.031 0.17 0.62 11 -10000 0 11
TNF -0.13 0.29 -10000 0 -0.92 21 21
FASLG -0.078 0.32 -10000 0 -1 22 22
TBX21 -0.014 0.077 -10000 0 -0.6 3 3
BATF3 0.013 0 -10000 0 -10000 0 0
PRKCQ 0.004 0.075 -10000 0 -0.49 6 6
PTPN1 0.023 0.093 -10000 0 -0.69 1 1
NFAT1-c-4/ICER1 -0.082 0.2 -10000 0 -0.78 13 13
GATA3 -0.004 0.11 -10000 0 -0.7 7 7
T-helper 1 cell differentiation -0.16 0.29 -10000 0 -0.62 64 64
IL2RA -0.18 0.24 -10000 0 -0.9 17 17
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.023 0.093 -10000 0 -0.69 1 1
E2F1 -0.024 0.17 -10000 0 -0.73 15 15
PPARG 0.009 0.042 -10000 0 -0.48 2 2
SLC3A2 0.023 0.093 -10000 0 -0.69 1 1
IRF4 -0.043 0.16 -10000 0 -0.48 31 31
PTGS2 -0.3 0.41 -10000 0 -0.97 45 45
CSF2 -0.4 0.48 -10000 0 -0.94 104 104
JunB/Fra1/NFAT1-c-4 -0.082 0.24 -10000 0 -0.8 13 13
IL4 -0.049 0.15 -10000 0 -0.68 5 5
IL5 -0.28 0.36 -10000 0 -0.85 44 44
IL2 -0.057 0.15 -10000 0 -0.67 2 2
IL3 -0.059 0.056 -10000 0 -10000 0 0
RNF128 0.017 0.12 -10000 0 -0.56 12 12
NFATC1 -0.031 0.17 -10000 0 -0.62 11 11
CDK4 0.006 0.13 -10000 0 -0.57 2 2
PTPRK 0.023 0.093 -10000 0 -0.69 1 1
IL8 -0.46 0.49 -10000 0 -0.92 123 123
POU2F1 0.011 0.045 -10000 0 -0.74 1 1
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR -0.021 0.14 -9999 0 -0.6 15 15
EGF/EGFR -0.093 0.18 -9999 0 -0.44 51 51
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.061 0.15 -9999 0 -0.44 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.034 0.18 -9999 0 -0.74 17 17
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.074 0.23 -9999 0 -0.69 33 33
EGF/EGFR dimer/SHC -0.073 0.18 -9999 0 -0.52 31 31
mol:GDP -0.061 0.15 -9999 0 -0.44 31 31
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.005 0.11 -9999 0 -0.66 7 7
GRB2/SOS1 0.019 0 -9999 0 -10000 0 0
HRAS/GTP -0.056 0.14 -9999 0 -0.74 3 3
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.057 0.14 -9999 0 -0.75 3 3
FRAP1 -0.031 0.15 -9999 0 -0.42 31 31
EGF/EGFR dimer -0.071 0.21 -9999 0 -0.52 45 45
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.03 0.16 -9999 0 -0.54 24 24
PLK2 and PLK4 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
PLK2 -0.004 0.11 -9999 0 -0.74 6 6
PLK4 -0.034 0.18 -9999 0 -0.74 17 17
regulation of centriole replication -0.026 0.17 -9999 0 -0.62 20 20
Nectin adhesion pathway

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
PDGFRB -0.048 0.2 -9999 0 -0.74 22 22
alphaV beta3 Integrin 0.016 0.035 -9999 0 -0.56 1 1
PTK2 -0.029 0.085 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.017 0.059 -9999 0 -0.27 13 13
CDC42/GDP 0.028 0.094 -9999 0 -0.36 13 13
Rac1/GDP 0.03 0.094 -9999 0 -0.36 13 13
RAP1B 0.012 0 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.045 -9999 0 -0.74 1 1
CDC42/GTP -0.02 0.071 -9999 0 -0.33 13 13
nectin-3/I-afadin 0.002 0.076 -9999 0 -0.34 13 13
RAPGEF1 0.023 0.1 -9999 0 -0.39 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0.11 -9999 0 -0.45 13 13
PDGFB-D/PDGFRB -0.048 0.2 -9999 0 -0.74 22 22
TLN1 0.023 0.036 -9999 0 -10000 0 0
Rap1/GTP -0.017 0.061 -9999 0 -0.34 1 1
IQGAP1 0.01 0.045 -9999 0 -0.74 1 1
Rap1/GTP/I-afadin 0.024 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.002 0.076 -9999 0 -0.34 13 13
PVR -0.001 0.1 -9999 0 -0.74 5 5
Necl-5(dimer) -0.001 0.1 -9999 0 -0.74 5 5
mol:GDP 0.024 0.11 -9999 0 -0.44 13 13
MLLT4 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
PI3K -0.044 0.12 -9999 0 -0.4 23 23
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.015 0.14 -9999 0 -0.56 16 16
positive regulation of lamellipodium assembly -0.02 0.066 -9999 0 -0.29 14 14
PVRL1 -0.031 0.18 -9999 0 -0.74 16 16
PVRL3 -0.011 0.1 -9999 0 -0.48 13 13
PVRL2 0.001 0.09 -9999 0 -0.74 4 4
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 0.002 0.072 -9999 0 -0.48 6 6
CLDN1 -0.55 0.32 -9999 0 -0.74 207 207
JAM-A/CLDN1 -0.33 0.2 -9999 0 -0.44 206 206
SRC -0.031 0.11 -9999 0 -0.5 13 13
ITGB3 0.01 0.045 -9999 0 -0.74 1 1
nectin-1(dimer)/I-afadin/I-afadin -0.015 0.14 -9999 0 -0.56 16 16
FARP2 0.02 0.11 -9999 0 -0.43 13 13
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.022 0.09 -9999 0 -0.53 5 5
nectin-1/I-afadin -0.015 0.14 -9999 0 -0.56 16 16
nectin-2/I-afadin 0.01 0.069 -9999 0 -0.56 4 4
RAC1/GTP/IQGAP1/filamentous actin -0.002 0.029 -9999 0 -0.48 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.041 0.12 -9999 0 -0.39 29 29
CDC42/GTP/IQGAP1/filamentous actin -0.002 0.029 -9999 0 -0.48 1 1
F11R 0.012 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.017 0.059 -9999 0 -0.27 13 13
alphaV/beta3 Integrin/Talin 0.034 0.041 -9999 0 -0.37 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.01 0.069 -9999 0 -0.56 4 4
nectin-2(dimer)/I-afadin/I-afadin 0.01 0.069 -9999 0 -0.56 4 4
PIP5K1C 0.017 0.039 -9999 0 -10000 0 0
VAV2 0.015 0.12 -9999 0 -0.45 14 14
RAP1/GDP -0.02 0.073 -9999 0 -0.43 1 1
ITGAV 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.02 0.081 -9999 0 -0.48 4 4
nectin-3(dimer)/I-afadin/I-afadin 0.002 0.076 -9999 0 -0.34 13 13
Rac1/GTP -0.023 0.08 -9999 0 -0.35 14 14
PTPRM 0.009 0.043 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.034 0.11 -9999 0 -0.42 19 19
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0 -10000 0 -10000 0 0
HDAC3 0.012 0 -10000 0 -10000 0 0
VDR 0.01 0.045 -10000 0 -0.74 1 1
Cbp/p300/PCAF -0.003 0.029 -10000 0 -10000 0 0
EP300 0.012 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.004 0.054 -10000 0 -0.39 1 1
KAT2B 0.007 0.051 -10000 0 -0.48 3 3
MAPK14 0.012 0 -10000 0 -10000 0 0
AKT1 -0.013 0.069 0.2 2 -10000 0 2
RAR alpha/9cRA/Cyclin H -0.065 0.079 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.054 -10000 0 -0.38 1 1
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.057 0.098 -10000 0 -0.38 2 2
NCOR2 0.012 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.007 0.035 -10000 0 -0.56 1 1
RXRs/RARs/NRIP1/9cRA -0.095 0.16 -10000 0 -0.52 3 3
NCOA2 0.012 0 -10000 0 -10000 0 0
NCOA3 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.01 0.045 -10000 0 -0.74 1 1
RARG 0.01 0.045 -10000 0 -0.74 1 1
RAR gamma1/9cRA 0.016 0.03 -10000 0 -0.48 1 1
MAPK3 0.013 0 -10000 0 -10000 0 0
MAPK1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.14 0.15 -10000 0 -0.38 44 44
RARA -0.069 0.12 -10000 0 -0.21 113 113
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.001 0.054 -10000 0 -0.38 1 1
PRKCA 0.013 0.03 -10000 0 -0.48 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.11 0.16 -10000 0 -0.37 42 42
RXRG -0.24 0.24 -10000 0 -0.4 174 174
RXRA -0.055 0.11 -10000 0 -0.41 1 1
RXRB -0.11 0.17 -10000 0 -0.32 113 113
VDR/Vit D3/DNA 0.007 0.035 -10000 0 -0.56 1 1
RBP1 -0.023 0.16 -10000 0 -0.68 14 14
CRBP1/9-cic-RA -0.018 0.12 -10000 0 -0.52 14 14
RARB 0.013 0.03 -10000 0 -0.48 1 1
PRKCG -0.29 0.37 -10000 0 -0.73 112 112
MNAT1 0.012 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.096 0.16 -10000 0 -0.47 6 6
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.084 0.14 -10000 0 -0.43 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.087 -10000 0 -0.33 3 3
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.11 0.16 -10000 0 -0.5 4 4
positive regulation of DNA binding -0.062 0.076 -10000 0 -10000 0 0
NRIP1 -0.1 0.15 -10000 0 -0.5 3 3
RXRs/RARs -0.12 0.16 -10000 0 -0.38 44 44
RXRs/RXRs/DNA/9cRA -0.14 0.16 -10000 0 -0.39 44 44
PRKACA 0.012 0 -10000 0 -10000 0 0
CDK7 0.012 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.047 0.059 -10000 0 -10000 0 0
CCNH 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.022 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.007 0.036 -9999 0 -10000 0 0
NFATC2 -0.009 0.043 -9999 0 -0.29 2 2
NFATC3 -0.007 0.036 -9999 0 -10000 0 0
CD40LG -0.15 0.26 -9999 0 -0.72 20 20
PTGS2 -0.17 0.3 -9999 0 -0.77 36 36
JUNB 0.009 0.042 -9999 0 -0.48 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.014 0.014 -9999 0 -10000 0 0
CaM/Ca2+ -0.014 0.014 -9999 0 -10000 0 0
CALM1 0.006 0.011 -9999 0 -10000 0 0
JUN 0.004 0.032 -9999 0 -0.49 1 1
mol:Ca2+ -0.013 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.003 -9999 0 -10000 0 0
FOSL1 -0.051 0.2 -9999 0 -0.71 24 24
CREM 0.012 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.094 0.099 -9999 0 -10000 0 0
FOS -0.024 0.12 -9999 0 -0.51 16 16
IFNG -0.23 0.35 -9999 0 -0.71 78 78
AP-1/NFAT1-c-4 -0.17 0.3 -9999 0 -0.7 46 46
FASLG -0.15 0.26 -9999 0 -0.76 19 19
NFAT1-c-4/ICER1 -0.052 0.058 -9999 0 -10000 0 0
IL2RA -0.15 0.28 -9999 0 -0.83 21 21
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.26 0.37 -9999 0 -0.69 99 99
JunB/Fra1/NFAT1-c-4 -0.08 0.12 -9999 0 -0.47 16 16
IL4 -0.15 0.26 -9999 0 -0.66 29 29
IL2 0.002 0.012 -9999 0 -10000 0 0
IL3 -0.018 0.027 -9999 0 -10000 0 0
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 0.012 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.011 0.045 -9999 0 -0.74 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.19 0.3 -10000 0 -0.64 78 78
RAD9A 0.012 0 -10000 0 -10000 0 0
AP1 -0.008 0.093 -10000 0 -0.37 16 16
IFNAR2 0.01 0.007 -10000 0 -10000 0 0
AKT1 0.007 0.039 -10000 0 -10000 0 0
ER alpha/Oestrogen -0.002 0.057 -10000 0 -0.35 7 7
NFX1/SIN3/HDAC complex 0.033 0.021 -10000 0 -10000 0 0
EGF -0.076 0.23 -10000 0 -0.69 33 33
SMG5 0.012 0 -10000 0 -10000 0 0
SMG6 0.012 0 -10000 0 -10000 0 0
SP3/HDAC2 0.015 0.011 -10000 0 -10000 0 0
TERT/c-Abl -0.19 0.27 -10000 0 -0.59 78 78
SAP18 0.011 0.002 -10000 0 -10000 0 0
MRN complex -0.003 0.041 -10000 0 -0.48 2 2
WT1 -0.3 0.37 -10000 0 -0.74 111 111
WRN 0.012 0 -10000 0 -10000 0 0
SP1 0.011 0.008 -10000 0 -10000 0 0
SP3 0.009 0.006 -10000 0 -10000 0 0
TERF2IP 0.012 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.17 0.24 -10000 0 -0.56 64 64
Mad/Max 0.012 0.031 -10000 0 -0.34 2 2
TERT -0.2 0.31 -10000 0 -0.65 78 78
CCND1 -0.17 0.28 -10000 0 -0.61 66 66
MAX 0.009 0.006 -10000 0 -10000 0 0
RBBP7 0.011 0.002 -10000 0 -10000 0 0
RBBP4 0.011 0.002 -10000 0 -10000 0 0
TERF2 -0.003 0.046 -10000 0 -0.77 1 1
PTGES3 0.012 0 -10000 0 -10000 0 0
SIN3A 0.011 0.002 -10000 0 -10000 0 0
Telomerase/911 0.011 0.045 -10000 0 -0.36 1 1
CDKN1B -0.1 0.22 -10000 0 -0.46 73 73
RAD1 0.01 0.045 -10000 0 -0.74 1 1
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
SAP30 0.011 0.002 -10000 0 -10000 0 0
TRF2/PARP2 -0.002 0.038 -10000 0 -0.63 1 1
UBE3A 0.009 0.006 -10000 0 -10000 0 0
JUN 0.008 0.03 -10000 0 -0.48 1 1
E6 -0.002 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.007 0.007 -10000 0 -10000 0 0
FOS -0.02 0.12 -10000 0 -0.5 16 16
IFN-gamma/IRF1 -0.13 0.25 -10000 0 -0.54 74 74
PARP2 0.012 0 -10000 0 -10000 0 0
BLM -0.064 0.23 -10000 0 -0.74 28 28
Telomerase 0.015 0.071 -10000 0 -0.38 2 2
IRF1 0.012 0.013 -10000 0 -10000 0 0
ESR1 -0.001 0.078 -10000 0 -0.48 7 7
KU/TER 0.019 0 -10000 0 -10000 0 0
ATM/TRF2 0.017 0.038 -10000 0 -0.61 1 1
ubiquitin-dependent protein catabolic process 0.036 0.024 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.036 0.024 -10000 0 -10000 0 0
HDAC1 0.011 0.002 -10000 0 -10000 0 0
HDAC2 0.01 0.009 -10000 0 -10000 0 0
ATM 0.001 0.013 0.22 1 -10000 0 1
SMAD3 0.023 0.023 -10000 0 -0.34 1 1
ABL1 0.012 0 -10000 0 -10000 0 0
MXD1 0.006 0.042 -10000 0 -0.48 2 2
MRE11A 0.01 0.045 -10000 0 -0.74 1 1
HUS1 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.17 0.26 -10000 0 -0.58 66 66
NR2F2 0.017 0.01 -10000 0 -10000 0 0
MAPK3 0.015 0.01 -10000 0 -10000 0 0
MAPK1 0.015 0.01 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.012 0.03 -10000 0 -0.48 1 1
NFKB1 0.012 0 -10000 0 -10000 0 0
HNRNPC 0.012 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.001 0.013 0.22 1 -10000 0 1
NBN 0.01 0.045 -10000 0 -0.74 1 1
EGFR -0.023 0.14 -10000 0 -0.6 15 15
mol:Oestrogen -0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.075 0.21 -10000 0 -0.52 45 45
MYC 0.005 0.054 -10000 0 -0.61 2 2
IL2 0.007 0.012 -10000 0 -10000 0 0
KU 0.019 0 -10000 0 -10000 0 0
RAD50 0.012 0 -10000 0 -10000 0 0
HSP90AA1 0.012 0 -10000 0 -10000 0 0
TGFB1 0.012 0.03 -10000 0 -0.48 1 1
TRF2/BLM -0.055 0.17 -10000 0 -0.54 28 28
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.17 0.28 -10000 0 -0.59 78 78
SP1/HDAC2 0.014 0.017 -10000 0 -10000 0 0
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.17 0.24 -10000 0 -0.55 65 65
Smad3/Myc 0.023 0.04 -10000 0 -0.48 1 1
911 complex -0.002 0.029 -10000 0 -0.48 1 1
IFNG -0.19 0.33 -10000 0 -0.72 74 74
Telomerase/PinX1 -0.17 0.24 -10000 0 -0.55 69 69
Telomerase/AKT1/mTOR/p70S6K -0.011 0.072 -10000 0 -10000 0 0
SIN3B 0.011 0.002 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Telomerase/EST1B -0.17 0.24 -10000 0 -0.55 65 65
response to DNA damage stimulus 0.003 0.004 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.005 0.045 -10000 0 -0.43 3 3
TRF2/WRN -0.002 0.038 -10000 0 -0.63 1 1
Telomerase/hnRNP C1/C2 -0.17 0.24 -10000 0 -0.55 65 65
E2F1 -0.031 0.17 -10000 0 -0.75 15 15
ZNFX1 0.011 0.002 -10000 0 -10000 0 0
PIF1 0.008 0.054 -10000 0 -0.61 2 2
NCL 0.012 0 -10000 0 -10000 0 0
DKC1 0.012 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.012 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.084 -9999 0 -0.56 6 6
Metarhodopsin II/Arrestin 0 0 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.016 0.086 -9999 0 -0.48 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.009 0.11 -9999 0 -0.74 6 6
GRK1 -0.004 0.077 -9999 0 -0.74 3 3
CNG Channel -0.059 0.14 -9999 0 -0.44 25 25
mol:Na + -0.083 0.15 -9999 0 -0.64 6 6
mol:ADP -0.004 0.077 -9999 0 -0.74 3 3
RGS9-1/Gbeta5/R9AP -0.055 0.13 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.085 0.16 -9999 0 -0.67 6 6
CNGB1 -0.022 0.15 -9999 0 -0.65 14 14
RDH5 0.012 0 -9999 0 -10000 0 0
SAG 0.008 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.048 0.16 -9999 0 -0.62 6 6
Na + (4 Units) -0.077 0.14 -9999 0 -0.6 6 6
RGS9 -0.019 0.12 -9999 0 -0.5 17 17
GNB1/GNGT1 -0.12 0.25 -9999 0 -0.56 68 68
GNAT1/GDP -0.056 0.13 -9999 0 -0.46 15 15
GUCY2D -0.015 0.14 -9999 0 -0.74 10 10
GNGT1 -0.17 0.32 -9999 0 -0.74 68 68
GUCY2F 0.002 0.045 -9999 0 -0.74 1 1
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.007 0.12 -9999 0 -0.46 17 17
mol:11-cis-retinal 0.012 0 -9999 0 -10000 0 0
mol:cGMP -0.04 0.16 -9999 0 -0.45 30 30
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin 0.013 0.005 -9999 0 -10000 0 0
SLC24A1 0.012 0 -9999 0 -10000 0 0
CNGA1 -0.022 0.13 -9999 0 -0.48 19 19
Metarhodopsin II 0.001 0.048 -9999 0 -0.45 3 3
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.043 0.16 -9999 0 -0.47 29 29
RGS9BP -0.054 0.17 -9999 0 -0.5 35 35
Metarhodopsin II/Transducin -0.054 0.12 -9999 0 -0.26 71 71
GCAP Family/Ca ++ -0.034 0.14 -9999 0 -0.36 37 37
PDE6A/B -0.008 0.12 -9999 0 -0.49 14 14
mol:Pi -0.055 0.13 -9999 0 -0.54 9 9
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.1 0.21 -9999 0 -0.46 71 71
PDE6B -0.003 0.097 -9999 0 -0.59 7 7
PDE6A -0.007 0.12 -9999 0 -0.74 7 7
PDE6G 0.004 0.078 -9999 0 -0.74 3 3
RHO 0.005 0.006 -9999 0 -10000 0 0
PDE6 -0.063 0.13 -9999 0 -0.44 22 22
GUCA1A -0.034 0.17 -9999 0 -0.68 18 18
GC2/GCAP Family -0.033 0.14 -9999 0 -0.47 21 21
GUCA1C -0.027 0.12 -9999 0 -0.51 16 16
GUCA1B 0.001 0.088 -9999 0 -0.64 5 5
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.019 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.01 0.045 -9999 0 -0.74 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.027 0.066 -9999 0 -0.31 2 2
IRAK/TOLLIP 0.031 0 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.005 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.16 0.25 -9999 0 -0.49 95 95
IL1A -0.15 0.31 -9999 0 -0.73 61 61
IL1B -0.038 0.18 -9999 0 -0.52 30 30
IRAK/TRAF6/p62/Atypical PKCs -0.004 0.038 -9999 0 -10000 0 0
IL1R2 -0.056 0.18 -9999 0 -0.51 36 36
IL1R1 0.01 0.045 -9999 0 -0.74 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.014 0.072 -9999 0 -0.38 1 1
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.058 0.021 -9999 0 -10000 0 0
JUN 0.041 0.032 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.021 0.16 -9999 0 -0.4 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.09 0.22 -9999 0 -0.46 68 68
PIK3R1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.11 0.19 -9999 0 -0.43 68 68
IL1 beta fragment/IL1R1/IL1RAP -0.036 0.17 -9999 0 -0.46 34 34
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.037 0.031 -9999 0 -10000 0 0
IRAK1 0.026 0 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.018 0.11 -9999 0 -0.36 26 26
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.004 0.078 -9999 0 -0.74 3 3
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0.016 0.035 -9999 0 -0.56 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.086 -9999 0 -0.39 2 2
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.036 0.17 -9999 0 -0.46 34 34
IL1 beta/IL1R2 -0.068 0.19 -9999 0 -0.53 28 28
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.051 0.13 -9999 0 -0.7 2 2
IRAK3 0.002 0.082 -9999 0 -0.58 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.056 0.14 -9999 0 -0.41 34 34
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.035 0.12 -9999 0 -0.46 4 4
IL1 alpha/IL1R1/IL1RAP -0.13 0.22 -9999 0 -0.5 68 68
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.012 0 -9999 0 -10000 0 0
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.038 0 -9999 0 -10000 0 0
IL1RAP -0.018 0.15 -9999 0 -0.74 11 11
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.046 0.12 -9999 0 -0.64 2 2
CASP1 0.008 0.054 -9999 0 -0.61 2 2
IL1RN/IL1R2 -0.063 0.18 -9999 0 -0.42 51 51
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.026 0.16 -9999 0 -0.43 34 34
TMEM189-UBE2V1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.01 0.097 -9999 0 -0.39 4 4
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
IL1RN -0.035 0.15 -9999 0 -0.5 25 25
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.031 0.032 -9999 0 -0.38 1 1
LPA receptor mediated 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
GNB1/GNG2 -0.017 0.064 -9999 0 -0.43 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.042 0.087 -9999 0 -0.37 1 1
AP1 -0.067 0.12 -9999 0 -0.42 13 13
mol:PIP3 -0.063 0.12 -9999 0 -0.48 10 10
AKT1 0.041 0.055 -9999 0 -0.38 1 1
PTK2B 0.005 0.058 -9999 0 -0.27 2 2
RHOA 0.024 0.023 -9999 0 -10000 0 0
PIK3CB 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.1 -9999 0 -0.42 2 2
MAGI3 0.011 0.03 -9999 0 -0.48 1 1
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.042 0.12 -9999 0 -0.39 7 7
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.018 0.11 -9999 0 -0.36 12 12
NF kappa B1 p50/RelA -0.052 0.097 -9999 0 -0.42 3 3
endothelial cell migration 0.005 0.083 -9999 0 -0.68 1 1
ADCY4 -0.013 0.13 -9999 0 -0.39 21 21
ADCY5 -0.061 0.19 -9999 0 -0.51 31 31
ADCY6 -0.013 0.13 -9999 0 -0.39 21 21
ADCY7 -0.013 0.13 -9999 0 -0.39 21 21
ADCY1 -0.02 0.13 -9999 0 -0.39 23 23
ADCY2 -0.032 0.16 -9999 0 -0.47 25 25
ADCY3 -0.013 0.13 -9999 0 -0.39 21 21
ADCY8 -0.015 0.13 -9999 0 -0.39 22 22
ADCY9 -0.013 0.13 -9999 0 -0.4 20 20
GSK3B 0.012 0.055 -9999 0 -10000 0 0
arachidonic acid secretion -0.009 0.13 -9999 0 -0.37 21 21
GNG2 0.009 0.045 -9999 0 -0.74 1 1
TRIP6 0.021 0.032 -9999 0 -0.35 2 2
GNAO1 -0.029 0.14 -9999 0 -0.49 12 12
HRAS 0.012 0 -9999 0 -10000 0 0
NFKBIA -0.013 0.12 -9999 0 -0.43 1 1
GAB1 0.009 0.042 -9999 0 -0.48 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.003 0.055 -9999 0 -0.87 1 1
JUN 0.01 0.03 -9999 0 -0.48 1 1
LPA/LPA2/NHERF2 0 0.005 -9999 0 -10000 0 0
TIAM1 -0.004 0.064 -9999 0 -1 1 1
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.009 0.1 -9999 0 -0.43 2 2
PLCB3 0.024 0.017 -9999 0 -10000 0 0
FOS -0.018 0.12 -9999 0 -0.5 16 16
positive regulation of mitosis -0.009 0.13 -9999 0 -0.37 21 21
LPA/LPA1-2-3 -0.064 0.12 -9999 0 -0.45 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade -0.001 0.001 -9999 0 -10000 0 0
BCAR1 0.012 0 -9999 0 -10000 0 0
stress fiber formation -0.007 0.093 -9999 0 -0.43 4 4
GNAZ -0.009 0.099 -9999 0 -0.54 1 1
EGFR/PI3K-beta/Gab1 -0.065 0.12 -9999 0 -0.51 10 10
positive regulation of dendritic cell cytokine production -0.064 0.12 -9999 0 -0.45 7 7
LPA/LPA2/MAGI-3 -0.001 0.017 -9999 0 -0.28 1 1
ARHGEF1 0.02 0.063 -9999 0 -10000 0 0
GNAI2 0.006 0.074 -9999 0 -0.27 17 17
GNAI3 0.006 0.074 -9999 0 -0.27 17 17
GNAI1 0.001 0.092 -9999 0 -0.32 19 19
LPA/LPA3 -0.067 0.14 -9999 0 -0.36 50 50
LPA/LPA2 0 0.007 -9999 0 -10000 0 0
LPA/LPA1 -0.022 0.082 -9999 0 -0.33 18 18
HB-EGF/EGFR -0.17 0.24 -9999 0 -0.49 94 94
HBEGF -0.17 0.27 -9999 0 -0.55 91 91
mol:DAG -0.009 0.1 -9999 0 -0.43 2 2
cAMP biosynthetic process -0.026 0.15 -9999 0 -0.44 21 21
NFKB1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
LYN -0.014 0.12 -9999 0 -0.43 1 1
GNAQ -0.029 0.11 -9999 0 -0.26 49 49
LPAR2 0.012 0.001 -9999 0 -10000 0 0
LPAR3 -0.084 0.2 -9999 0 -0.51 50 50
LPAR1 -0.015 0.12 -9999 0 -0.47 17 17
IL8 -0.24 0.21 -9999 0 -0.47 85 85
PTK2 -0.032 0.12 -9999 0 -0.42 7 7
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.042 0.12 -9999 0 -0.4 7 7
EGFR -0.022 0.14 -9999 0 -0.6 15 15
PLCG1 -0.026 0.12 -9999 0 -0.27 50 50
PLD2 -0.032 0.12 -9999 0 -0.42 7 7
G12/G13 -0.016 0.059 -9999 0 -10000 0 0
PI3K-beta -0.012 0.048 -9999 0 -0.44 1 1
cell migration -0.022 0.043 -9999 0 -0.28 1 1
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
PXN -0.007 0.095 -9999 0 -0.44 4 4
HRAS/GTP -0.01 0.13 -9999 0 -0.38 21 21
RAC1 0.012 0 -9999 0 -10000 0 0
MMP9 -0.23 0.35 -9999 0 -0.74 89 89
PRKCE 0.012 0 -9999 0 -10000 0 0
PRKCD -0.003 0.098 -9999 0 -0.41 2 2
Gi(beta/gamma) -0.008 0.12 -9999 0 -0.43 10 10
mol:LPA 0.003 0.012 -9999 0 -0.19 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.052 0.1 -9999 0 -0.48 4 4
MAPKKK cascade -0.009 0.13 -9999 0 -0.37 21 21
contractile ring contraction involved in cytokinesis 0.024 0.023 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.034 0.11 -9999 0 -0.26 54 54
GNA15 -0.032 0.12 -9999 0 -0.4 6 6
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
MAPT -0.019 0.11 -9999 0 -0.37 12 12
GNA11 -0.029 0.11 -9999 0 -0.26 50 50
Rac1/GTP 0.02 0.059 -9999 0 -0.92 1 1
MMP2 0.005 0.083 -9999 0 -0.68 1 1
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.004 0.041 -9999 0 -0.48 2 2
ARNO/beta Arrestin1-2 -0.072 0.095 -9999 0 -10000 0 0
EGFR -0.021 0.14 -9999 0 -0.6 15 15
EPHA2 0.008 0.054 -9999 0 -0.61 2 2
USP6 -0.012 0.13 -9999 0 -0.66 10 10
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.071 0.21 -9999 0 -0.52 45 45
ARRB2 0.006 0.05 -9999 0 -0.33 6 6
mol:GTP 0.016 0.015 -9999 0 -10000 0 0
ARRB1 0.012 0 -9999 0 -10000 0 0
FBXO8 0.012 0 -9999 0 -10000 0 0
TSHR -0.017 0.12 -9999 0 -0.48 16 16
EGF -0.074 0.23 -9999 0 -0.69 33 33
somatostatin receptor activity 0 0 -9999 0 -0.001 19 19
ARAP2 0.007 0.064 -9999 0 -0.74 2 2
mol:GDP -0.067 0.11 -9999 0 -0.26 42 42
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 10 10
ITGA2B 0.001 0.08 -9999 0 -0.52 6 6
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.021 0.07 -9999 0 -0.43 6 6
ADAP1 0.007 0.064 -9999 0 -0.74 2 2
KIF13B 0.012 0 -9999 0 -10000 0 0
HGF/MET -0.073 0.21 -9999 0 -0.56 43 43
PXN 0.008 0.054 -9999 0 -0.61 2 2
ARF6/GTP -0.057 0.1 -9999 0 -0.27 19 19
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.072 0.18 -9999 0 -0.52 31 31
ADRB2 -0.16 0.24 -9999 0 -0.48 94 94
receptor agonist activity 0 0 -9999 0 0 23 23
actin filament binding 0 0 -9999 0 -0.001 22 22
SRC 0.012 0 -9999 0 -10000 0 0
ITGB3 0.01 0.045 -9999 0 -0.74 1 1
GNAQ 0.012 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 16 16
ARF6/GDP 0.005 0.061 -9999 0 -0.29 1 1
ARF6/GDP/GULP/ACAP1 -0.073 0.11 -9999 0 -0.44 12 12
alphaIIb/beta3 Integrin/paxillin/GIT1 0.021 0.062 -9999 0 -0.43 3 3
ACAP1 0.007 0.064 -9999 0 -0.74 2 2
ACAP2 0.012 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.073 -9999 0 -0.48 6 6
EFNA1 -0.001 0.1 -9999 0 -0.74 5 5
HGF -0.003 0.1 -9999 0 -0.7 6 6
CYTH3 0.011 0 -9999 0 -10000 0 0
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 15 15
endosomal lumen acidification 0 0 0 1 0 10 11
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.011 0.1 -9999 0 -0.48 13 13
GNAQ/ARNO 0.014 0.006 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 8 8
MET -0.092 0.26 -9999 0 -0.74 38 38
GNA14 0.004 0.068 -9999 0 -0.55 4 4
GNA15 0.007 0.064 -9999 0 -0.74 2 2
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 17 17
GNA11 0.012 0 -9999 0 -10000 0 0
LHCGR -0.008 0.11 -9999 0 -0.74 6 6
AGTR1 -0.13 0.24 -9999 0 -0.53 71 71
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.072 -9999 0 -0.48 6 6
IPCEF1/ARNO -0.046 0.14 -9999 0 -0.41 31 31
alphaIIb/beta3 Integrin 0.008 0.068 -9999 0 -0.4 7 7
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.034 0.11 -10000 0 -0.54 10 10
FYN 0.004 0.17 -10000 0 -0.63 14 14
LAT/GRAP2/SLP76 -0.018 0.12 -10000 0 -0.55 10 10
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 0.015 0.12 -10000 0 -0.42 13 13
B2M 0.013 0.003 -10000 0 -10000 0 0
IKBKG -0.019 0.04 -10000 0 -0.15 5 5
MAP3K8 0.007 0.064 -10000 0 -0.74 2 2
mol:Ca2+ -0.017 0.027 -10000 0 -0.12 6 6
integrin-mediated signaling pathway -0.001 0.017 -10000 0 -0.28 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.013 0.16 -10000 0 -0.59 14 14
TRPV6 -0.16 0.23 -10000 0 -0.5 86 86
CD28 0 0.095 -10000 0 -0.69 5 5
SHC1 0.005 0.17 -10000 0 -0.61 14 14
receptor internalization 0.004 0.18 -10000 0 -0.63 15 15
PRF1 0.014 0.15 -10000 0 -0.72 8 8
KRAS -0.023 0.16 -10000 0 -0.74 13 13
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 0.019 0.1 -10000 0 -0.35 14 14
LAT 0.005 0.17 -10000 0 -0.63 13 13
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.001 0.079 -10000 0 -0.49 7 7
CD3E 0.006 0.061 -10000 0 -0.49 4 4
CD3G 0.002 0.073 -10000 0 -0.48 6 6
RASGRP2 0.007 0.033 -10000 0 -0.15 9 9
RASGRP1 0.028 0.12 -10000 0 -0.43 12 12
HLA-A 0.01 0.042 -10000 0 -0.48 2 2
RASSF5 0.011 0.03 -10000 0 -0.48 1 1
RAP1A/GTP/RAPL -0.001 0.017 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.043 -10000 0 -0.12 8 8
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.034 0.069 -10000 0 -0.23 13 13
PRKCA 0 0.068 -10000 0 -0.28 7 7
GRAP2 0.009 0.042 -10000 0 -0.48 2 2
mol:IP3 0.034 0.14 0.21 74 -0.41 10 84
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.002 0.18 -10000 0 -0.68 13 13
ORAI1 0.089 0.13 0.28 86 -10000 0 86
CSK 0.002 0.17 -10000 0 -0.64 13 13
B7 family/CD28 -0.094 0.18 -10000 0 -0.61 19 19
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.006 0.19 -10000 0 -0.69 15 15
PTPN6 -0.001 0.17 -10000 0 -0.64 14 14
VAV1 0.002 0.18 -10000 0 -0.64 15 15
Monovalent TCR/CD3 0.004 0.14 -10000 0 -0.94 5 5
CBL 0.01 0.045 -10000 0 -0.74 1 1
LCK -0.002 0.18 -10000 0 -0.68 14 14
PAG1 0.001 0.17 -10000 0 -0.64 14 14
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.007 0.19 -10000 0 -0.7 14 14
CD80 -0.12 0.29 -10000 0 -0.73 50 50
CD86 0.007 0.064 -10000 0 -0.74 2 2
PDK1/CARD11/BCL10/MALT1 -0.041 0.083 -10000 0 -0.28 15 15
HRAS 0.012 0 -10000 0 -10000 0 0
GO:0035030 -0.033 0.18 -10000 0 -0.51 19 19
CD8A -0.011 0.11 -10000 0 -0.51 13 13
CD8B -0.022 0.14 -10000 0 -0.56 17 17
PTPRC -0.012 0.13 -10000 0 -0.74 9 9
PDK1/PKC theta 0.016 0.15 -10000 0 -0.53 13 13
CSK/PAG1 0.005 0.17 -10000 0 -0.62 14 14
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.031 -10000 0 -0.34 2 2
GRAP2/SLP76 -0.027 0.15 -10000 0 -0.64 11 11
STIM1 0.044 0.064 -10000 0 -10000 0 0
RAS family/GTP 0.032 0.059 -10000 0 -0.18 5 5
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.001 0.2 -10000 0 -0.68 15 15
mol:DAG 0 0.096 -10000 0 -0.36 12 12
RAP1A/GDP 0.015 0.019 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 0.002 0.073 -10000 0 -0.49 6 6
cytotoxic T cell degranulation 0.015 0.14 -10000 0 -0.69 8 8
RAP1A/GTP -0.002 0.01 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.017 0.14 -10000 0 -0.48 14 14
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.029 0.16 0.23 57 -0.53 11 68
NRAS 0.012 0 -10000 0 -10000 0 0
ZAP70 -0.003 0.098 -10000 0 -0.59 7 7
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.016 0.13 -10000 0 -0.53 12 12
MALT1 0.01 0.045 -10000 0 -0.74 1 1
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.021 0.16 -10000 0 -0.55 20 20
CARD11 -0.058 0.22 -10000 0 -0.73 26 26
PRKCB -0.008 0.087 -10000 0 -0.31 15 15
PRKCE 0.001 0.067 -10000 0 -0.26 9 9
PRKCQ 0.019 0.16 -10000 0 -0.62 12 12
LCP2 0.012 0 -10000 0 -10000 0 0
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.017 0.1 -10000 0 -0.36 13 13
IKK complex 0.032 0.044 -10000 0 -0.12 4 4
RAS family/GDP -0.005 0.018 -10000 0 -0.08 13 13
MAP3K14 0.024 0.082 -10000 0 -0.3 7 7
PDPK1 0.012 0.12 -10000 0 -0.4 13 13
TCR/CD3/MHC I/CD8/Fyn -0.003 0.21 -10000 0 -0.84 13 13
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.076 0.17 -10000 0 -0.4 53 53
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.004 0.11 0.44 5 -10000 0 5
IL27/IL27R/JAK1 0.005 0.14 -10000 0 -0.55 3 3
TBX21 0.032 0.17 -10000 0 -0.68 3 3
IL12B -0.009 0.1 -10000 0 -0.54 9 9
IL12A -0.007 0.073 -10000 0 -0.35 12 12
IL6ST 0.012 0.008 -10000 0 -10000 0 0
IL27RA/JAK1 0.018 0.045 -10000 0 -0.54 1 1
IL27 -0.019 0.15 -10000 0 -0.74 11 11
TYK2 0.011 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.32 0.57 -10000 0 -1.3 64 64
T-helper 2 cell differentiation 0.004 0.11 0.44 5 -10000 0 5
T cell proliferation during immune response 0.004 0.11 0.44 5 -10000 0 5
MAPKKK cascade -0.004 0.11 -10000 0 -0.44 5 5
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.01 0.045 -10000 0 -0.74 1 1
STAT1 -0.008 0.13 -10000 0 -0.74 8 8
IL12RB1 0.009 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.013 0.2 -10000 0 -0.67 9 9
IL27/IL27R/JAK2/TYK2 -0.005 0.11 -10000 0 -0.44 5 5
positive regulation of T cell mediated cytotoxicity -0.004 0.11 -10000 0 -0.44 5 5
STAT1 (dimer) 0.016 0.22 0.4 8 -0.75 6 14
JAK2 0.002 0.081 -10000 0 -0.76 3 3
JAK1 0.014 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.002 0.11 -10000 0 -0.47 4 4
T cell proliferation -0.07 0.15 -10000 0 -0.54 8 8
IL12/IL12R/TYK2/JAK2 -0.043 0.16 -10000 0 -0.62 9 9
IL17A -0.33 0.57 -10000 0 -1.4 64 64
mast cell activation 0.004 0.11 0.44 5 -10000 0 5
IFNG -0.016 0.05 -10000 0 -0.095 74 74
T cell differentiation -0.004 0.007 -10000 0 -0.018 40 40
STAT3 (dimer) 0 0.1 -10000 0 -0.46 3 3
STAT5A (dimer) 0 0.1 -10000 0 -0.46 3 3
STAT4 (dimer) -0.004 0.1 -10000 0 -0.46 3 3
STAT4 0.006 0.062 -10000 0 -0.57 3 3
T cell activation -0.007 0.006 0.088 1 -10000 0 1
IL27R/JAK2/TYK2 -0.005 0.075 -10000 0 -0.52 4 4
GATA3 -0.001 0.11 -10000 0 -0.62 7 7
IL18 0 0.07 -10000 0 -0.46 6 6
positive regulation of mast cell cytokine production 0 0.1 -10000 0 -0.45 3 3
IL27/EBI3 -0.015 0.13 -10000 0 -0.51 17 17
IL27RA -0.005 0.041 -10000 0 -0.59 1 1
IL6 -0.15 0.26 -10000 0 -0.5 87 87
STAT5A 0.012 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.003 0.023 -10000 0 -10000 0 0
IL1B -0.046 0.17 -10000 0 -0.52 29 29
EBI3 -0.001 0.087 -10000 0 -0.57 6 6
TNF -0.014 0.11 -10000 0 -0.5 13 13
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.002 0.068 -10000 0 -10000 0 0
epithelial cell differentiation -0.051 0.11 -10000 0 -0.62 4 4
ITCH 0.02 0.016 -10000 0 -10000 0 0
WWP1 0.006 0.066 -10000 0 -0.59 1 1
FYN 0.012 0 -10000 0 -10000 0 0
EGFR -0.021 0.14 -10000 0 -0.6 15 15
PRL -0.007 0.11 -10000 0 -0.74 6 6
neuron projection morphogenesis -0.022 0.11 -10000 0 -10000 0 0
PTPRZ1 -0.16 0.24 -10000 0 -0.48 97 97
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.069 0.097 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.068 0.14 -10000 0 -0.43 1 1
ADAM17 0.02 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.001 0.076 -10000 0 -0.44 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.033 0.12 -10000 0 -0.45 7 7
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.057 0.13 -10000 0 -10000 0 0
GRIN2B -0.11 0.19 -10000 0 -0.57 18 18
ErbB4/ErbB2/betacellulin -0.026 0.13 -10000 0 -0.53 5 5
STAT1 -0.009 0.13 -10000 0 -0.74 8 8
HBEGF 0.009 0.042 -10000 0 -0.48 2 2
PRLR -0.077 0.21 -10000 0 -0.53 45 45
E4ICDs/ETO2 -0.016 0.096 -10000 0 -0.45 1 1
axon guidance 0.029 0.088 -10000 0 -10000 0 0
NEDD4 0.014 0.066 -10000 0 -0.74 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.061 0.18 -10000 0 -0.42 48 48
CBFA2T3 -0.021 0.13 -10000 0 -0.5 18 18
ErbB4/ErbB2/HBEGF -0.014 0.12 -10000 0 -0.42 18 18
MAPK3 -0.029 0.12 -10000 0 -10000 0 0
STAT1 (dimer) -0.01 0.1 -10000 0 -0.48 8 8
MAPK1 -0.029 0.12 -10000 0 -10000 0 0
JAK2 0.004 0.078 -10000 0 -0.74 3 3
ErbB4/ErbB2/neuregulin 1 beta -0.087 0.16 -10000 0 -0.49 9 9
NRG1 -0.082 0.17 -10000 0 -0.34 80 80
NRG3 -0.047 0.18 -10000 0 -0.54 29 29
NRG2 -0.14 0.23 -10000 0 -0.48 82 82
NRG4 -0.067 0.18 -10000 0 -0.48 44 44
heart development 0.029 0.088 -10000 0 -10000 0 0
neural crest cell migration -0.086 0.16 -10000 0 -0.48 9 9
ERBB2 -0.015 0.15 -10000 0 -0.54 20 20
WWOX/E4ICDs 0.004 0.064 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.05 0.14 -10000 0 -0.5 3 3
apoptosis 0.082 0.14 0.6 12 -10000 0 12
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.081 0.15 -10000 0 -0.63 1 1
ErbB4/ErbB2/epiregulin -0.11 0.22 -10000 0 -0.59 18 18
ErbB4/ErbB4/betacellulin/betacellulin -0.012 0.093 -10000 0 -0.63 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.07 0.14 -10000 0 -0.63 8 8
MDM2 -0.007 0.1 -10000 0 -0.45 8 8
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.077 0.11 -10000 0 -0.41 1 1
STAT5A 0.036 0.082 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.075 0.16 -10000 0 -0.54 10 10
DLG4 0.012 0 -10000 0 -10000 0 0
GRB2/SHC 0.019 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.022 0.046 -10000 0 -10000 0 0
STAT5A (dimer) -0.054 0.12 -10000 0 -0.68 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.033 0.078 -10000 0 -10000 0 0
LRIG1 0.009 0.042 -10000 0 -0.48 2 2
EREG -0.16 0.31 -10000 0 -0.72 63 63
BTC -0.015 0.11 -10000 0 -0.48 15 15
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.021 0.086 -10000 0 -10000 0 0
ERBB4 -0.001 0.077 -10000 0 -0.44 1 1
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 -0.003 0.033 -10000 0 -0.53 1 1
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.053 0.15 -10000 0 -0.44 19 19
glial cell differentiation 0.022 0.046 -10000 0 -10000 0 0
WWOX 0.012 0 -10000 0 -10000 0 0
cell proliferation -0.077 0.17 -10000 0 -0.62 7 7
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.07 0.18 -9999 0 -0.37 71 71
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.043 0.19 -9999 0 -0.71 9 9
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.021 0.062 -9999 0 -0.56 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.054 0.077 -9999 0 -0.32 5 5
CaM/Ca2+ -0.091 0.16 -9999 0 -0.68 3 3
RAP1A 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.07 0.21 -9999 0 -0.8 9 9
AKT1 -0.043 0.16 -9999 0 -0.6 3 3
MAP2K1 -0.048 0.17 -9999 0 -0.64 3 3
MAP3K11 -0.06 0.18 -9999 0 -0.69 3 3
IFNGR1 0.004 0.017 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.1 0.14 -9999 0 -0.46 23 23
Rap1/GTP -0.07 0.12 -9999 0 -0.5 3 3
CRKL/C3G 0.019 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.077 0.2 -9999 0 -0.4 72 72
CEBPB -0.01 0.15 -9999 0 -0.51 3 3
STAT3 0.012 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.079 0.21 -9999 0 -0.77 9 9
STAT1 -0.07 0.21 -9999 0 -0.8 9 9
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.19 0.33 -9999 0 -0.73 74 74
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
STAT1 (dimer)/PIAS1 -0.06 0.2 -9999 0 -0.74 9 9
CEBPB/PTGES2/Cbp/p300 -0.042 0.071 -9999 0 -10000 0 0
mol:Ca2+ -0.072 0.18 -9999 0 -0.37 71 71
MAPK3 -0.026 0.15 -9999 0 -0.53 3 3
STAT1 (dimer) -0.071 0.1 -9999 0 -0.46 5 5
MAPK1 -0.026 0.15 -9999 0 -0.53 3 3
JAK2 -0.004 0.083 -9999 0 -0.78 3 3
PIK3R1 0.012 0 -9999 0 -10000 0 0
JAK1 0.004 0.017 -9999 0 -10000 0 0
CAMK2D 0.012 0 -9999 0 -10000 0 0
DAPK1 0.007 0.12 -9999 0 -0.59 3 3
SMAD7 0.007 0.065 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.047 0.16 -9999 0 -0.62 3 3
PI3K -0.089 0.15 -9999 0 -0.66 3 3
IFNG -0.19 0.33 -9999 0 -0.73 74 74
apoptosis -0.002 0.1 -9999 0 -0.42 3 3
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.027 0.16 -9999 0 -0.62 17 17
CAMK2B -0.086 0.2 -9999 0 -0.5 53 53
FRAP1 -0.039 0.15 -9999 0 -0.55 3 3
PRKCD -0.043 0.16 -9999 0 -0.61 3 3
RAP1B 0.012 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.054 0.077 -9999 0 -0.32 5 5
PTPN2 0.012 0 -9999 0 -10000 0 0
EP300 0.013 0.001 -9999 0 -10000 0 0
IRF1 -0.021 0.16 -9999 0 -0.53 10 10
STAT1 (dimer)/PIASy -0.061 0.2 -9999 0 -0.74 9 9
SOCS1 -0.012 0.14 -9999 0 -0.79 7 7
mol:GDP -0.081 0.14 -9999 0 -0.59 3 3
CASP1 0.006 0.069 -9999 0 -0.3 2 2
PTGES2 0.012 0 -9999 0 -10000 0 0
IRF9 0.025 0.055 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.087 0.15 -9999 0 -0.64 3 3
RAP1/GDP -0.07 0.12 -9999 0 -0.51 3 3
CBL -0.063 0.18 -9999 0 -0.6 4 4
MAP3K1 -0.06 0.18 -9999 0 -0.69 3 3
PIAS1 0.012 0 -9999 0 -10000 0 0
PIAS4 0.012 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.054 0.077 -9999 0 -0.32 5 5
PTPN11 -0.071 0.18 -9999 0 -0.37 71 71
CREBBP 0.013 0.001 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.004 0.12 -9999 0 -0.66 9 9
alphaV beta3 Integrin -0.004 0.044 -9999 0 -0.48 2 2
PTK2 0.015 0.12 -9999 0 -0.49 5 5
IGF1R 0.01 0.045 -9999 0 -0.74 1 1
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B -0.045 0.12 -9999 0 -0.36 33 33
VEGFA -0.009 0.13 -9999 0 -0.74 8 8
ILK -0.044 0.12 -9999 0 -0.36 32 32
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.01 0.12 -9999 0 -0.37 9 9
PTK2B 0.018 0.1 -9999 0 -0.48 10 10
alphaV/beta3 Integrin/JAM-A -0.012 0.13 -9999 0 -0.4 25 25
CBL 0.01 0.045 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.037 0.1 -9999 0 -0.48 4 4
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.024 0.15 -9999 0 -0.44 26 26
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.088 -9999 0 -0.38 5 5
alphaV/beta3 Integrin/Syndecan-1 -0.003 0.033 -9999 0 -0.48 1 1
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.22 -9999 0 -0.71 19 19
PI4 Kinase 0.019 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
alphaV/beta3 Integrin/Osteopontin -0.26 0.24 -9999 0 -0.48 148 148
RPS6KB1 -0.1 0.23 -9999 0 -0.68 17 17
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.034 0.1 -9999 0 -0.49 2 2
GPR124 0.007 0.064 -9999 0 -0.74 2 2
MAPK1 -0.034 0.1 -9999 0 -0.49 2 2
PXN 0.008 0.054 -9999 0 -0.61 2 2
PIK3R1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.039 0.12 -9999 0 -0.48 12 12
cell adhesion -0.029 0.079 -9999 0 -0.36 4 4
ANGPTL3 -0.051 0.17 -9999 0 -0.5 33 33
VEGFR2 homodimer/VEGFA homodimer/Src -0.019 0.11 -9999 0 -0.57 9 9
IGF-1R heterotetramer 0.01 0.045 -9999 0 -0.74 1 1
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.012 0 -9999 0 -10000 0 0
ITGB3 0.01 0.045 -9999 0 -0.74 1 1
IGF1 -0.077 0.23 -9999 0 -0.65 37 37
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.005 0.049 -9999 0 -0.48 3 3
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.002 0.029 -9999 0 -0.48 1 1
VCL 0.01 0.045 -9999 0 -0.74 1 1
alphaV/beta3 Integrin/Del1 -0.007 0.047 -9999 0 -0.48 1 1
CSF1 0.012 0 -9999 0 -10000 0 0
PIK3C2A -0.044 0.12 -9999 0 -0.36 32 32
PI4 Kinase/Pyk2 -0.05 0.13 -9999 0 -0.65 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.012 0.11 -9999 0 -0.52 10 10
FAK1/Vinculin 0.02 0.1 -9999 0 -0.4 4 4
alphaV beta3/Integrin/ppsTEM5 -0.005 0.05 -9999 0 -0.48 3 3
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.067 0.22 -9999 0 -0.67 32 32
BCAR1 0.012 0 -9999 0 -10000 0 0
FGF2 0.008 0.054 -9999 0 -0.61 2 2
F11R 0.018 0.041 -9999 0 -0.45 2 2
alphaV/beta3 Integrin/Lactadherin -0.002 0.029 -9999 0 -0.48 1 1
alphaV/beta3 Integrin/TGFBR2 -0.002 0.029 -9999 0 -0.48 1 1
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.03 0.028 -9999 0 -0.43 1 1
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.022 0.028 -9999 0 -0.44 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.2 0.34 -9999 0 -0.74 76 76
alphaV/beta3 Integrin/Pyk2 0.019 0.1 -9999 0 -0.48 10 10
SDC1 0.011 0.03 -9999 0 -0.48 1 1
VAV3 0.011 0.1 -9999 0 -0.4 15 15
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.011 0.03 -9999 0 -0.48 1 1
FAK1/Paxillin 0.019 0.1 -9999 0 -0.4 4 4
cell migration 0.026 0.098 -9999 0 -0.37 3 3
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.041 0.11 -9999 0 -10000 0 0
SPP1 -0.39 0.37 -9999 0 -0.74 147 147
KDR 0.004 0.078 -9999 0 -0.74 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.05 0.19 -9999 0 -0.58 29 29
angiogenesis -0.031 0.11 -9999 0 -0.56 1 1
Rac1/GTP 0.016 0.094 -9999 0 -0.37 15 15
EDIL3 0.003 0.066 -9999 0 -0.48 5 5
cell proliferation -0.002 0.029 -9999 0 -0.48 1 1
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.018 0 -9999 0 -10000 0 0
ADCY5 -0.058 0.14 -9999 0 -0.29 67 67
ADCY6 0.018 0 -9999 0 -10000 0 0
ADCY7 0.018 0 -9999 0 -10000 0 0
ADCY1 -0.004 0.1 -9999 0 -0.49 12 12
ADCY2 -0.013 0.1 -9999 0 -0.32 26 26
ADCY3 0.018 0 -9999 0 -10000 0 0
ADCY8 0.012 0.03 -9999 0 -0.49 1 1
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.018 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.001 0.066 -9999 0 -0.36 2 2
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.007 0.12 -10000 0 -0.46 8 8
TBX21 -0.039 0.32 -10000 0 -1.1 12 12
B2M 0.011 0.009 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 0.016 0.02 -10000 0 -10000 0 0
GADD45B -0.009 0.24 -10000 0 -0.72 9 9
IL12RB2 -0.011 0.15 -10000 0 -0.72 11 11
GADD45G -0.013 0.25 -10000 0 -0.76 10 10
natural killer cell activation 0.004 0.021 -10000 0 -10000 0 0
RELB 0.01 0.045 -10000 0 -0.74 1 1
RELA 0.012 0 -10000 0 -10000 0 0
IL18 0.001 0.093 -10000 0 -0.61 6 6
IL2RA -0.02 0.15 -10000 0 -0.74 12 12
IFNG -0.19 0.33 -10000 0 -0.73 74 74
STAT3 (dimer) -0.014 0.25 -10000 0 -0.74 12 12
HLA-DRB5 0.001 0.08 -10000 0 -0.53 6 6
FASLG -0.047 0.34 -10000 0 -1.1 14 14
NF kappa B2 p52/RelB -0.13 0.24 -10000 0 -0.8 21 21
CD4 0.013 0.003 -10000 0 -10000 0 0
SOCS1 -0.005 0.11 -10000 0 -0.66 7 7
EntrezGene:6955 -0.002 0.012 -10000 0 -10000 0 0
CD3D -0.001 0.079 -10000 0 -0.48 7 7
CD3E 0.004 0.06 -10000 0 -0.48 4 4
CD3G 0.001 0.073 -10000 0 -0.48 6 6
IL12Rbeta2/JAK2 0 0.14 -10000 0 -0.62 12 12
CCL3 -0.1 0.38 -10000 0 -0.92 31 31
CCL4 -0.045 0.32 -10000 0 -0.98 17 17
HLA-A 0.008 0.043 -10000 0 -0.48 2 2
IL18/IL18R 0.034 0.094 -10000 0 -0.47 5 5
NOS2 -0.072 0.33 -10000 0 -0.87 21 21
IL12/IL12R/TYK2/JAK2/SPHK2 0.014 0.11 -10000 0 -0.47 5 5
IL1R1 -0.037 0.3 -10000 0 -1 12 12
IL4 -0.006 0.093 -10000 0 -0.75 4 4
JAK2 0.008 0.081 -10000 0 -0.74 3 3
EntrezGene:6957 -0.002 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.038 0.25 -10000 0 -0.82 17 17
RAB7A 0.012 0.22 -10000 0 -0.64 4 4
lysosomal transport 0.014 0.22 -10000 0 -0.61 4 4
FOS -0.044 0.33 -10000 0 -1.2 18 18
STAT4 (dimer) -0.005 0.27 -10000 0 -0.75 14 14
STAT5A (dimer) -0.21 0.3 -10000 0 -0.78 44 44
GZMA -0.051 0.34 -10000 0 -1 18 18
GZMB -0.051 0.34 -10000 0 -1 19 19
HLX 0.007 0.064 -10000 0 -0.74 2 2
LCK -0.051 0.33 -10000 0 -0.91 20 20
TCR/CD3/MHC II/CD4 -0.001 0.14 -10000 0 -0.61 10 10
IL2/IL2R -0.001 0.11 -10000 0 -0.47 12 12
MAPK14 -0.002 0.25 -10000 0 -0.68 10 10
CCR5 -0.015 0.26 -10000 0 -0.86 9 9
IL1B -0.058 0.22 -10000 0 -0.7 29 29
STAT6 0.009 0.1 0.22 1 -0.24 6 7
STAT4 0.006 0.062 -10000 0 -0.57 3 3
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 -0.009 0.13 -10000 0 -0.74 8 8
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B -0.001 0.1 -10000 0 -0.52 9 9
CD8A -0.013 0.11 -10000 0 -0.51 13 13
CD8B -0.024 0.14 -10000 0 -0.56 17 17
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.007 0.12 0.46 8 -10000 0 8
IL2RB 0.012 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.25 -10000 0 -0.69 14 14
IL2RG -0.007 0.099 -10000 0 -0.51 10 10
IL12 -0.001 0.11 -10000 0 -0.37 20 20
STAT5A 0.012 0 -10000 0 -10000 0 0
CD247 0.001 0.074 -10000 0 -0.49 6 6
IL2 0.01 0.005 -10000 0 -10000 0 0
SPHK2 0.012 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.006 0.11 -10000 0 -0.49 12 12
IL12/IL12R/TYK2/JAK2 -0.051 0.34 -10000 0 -0.96 20 20
MAP2K3 -0.006 0.24 -10000 0 -0.68 10 10
RIPK2 0.004 0.078 -10000 0 -0.74 3 3
MAP2K6 -0.007 0.25 -10000 0 -0.68 11 11
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.005 0.068 -10000 0 -0.55 4 4
IL18RAP 0.003 0.08 -10000 0 -0.52 6 6
IL12Rbeta1/TYK2 0.024 0.028 -10000 0 -10000 0 0
EOMES -0.045 0.21 -10000 0 -0.63 26 26
STAT1 (dimer) -0.086 0.3 -10000 0 -0.76 24 24
T cell proliferation 0.005 0.22 -10000 0 -0.56 12 12
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.046 -10000 0 -0.74 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.093 0.16 -10000 0 -0.62 9 9
ATF2 0.006 0.24 -10000 0 -0.68 6 6
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.061 0.2 -9999 0 -0.56 38 38
CRKL -0.003 0.097 -9999 0 -0.5 3 3
mol:PIP3 -0.018 0.006 -9999 0 -10000 0 0
AKT1 -0.014 0.062 -9999 0 -0.44 1 1
PTK2B 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.004 0.093 -9999 0 -0.46 3 3
RANBP10 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
HGF/MET/SHIP2 -0.076 0.18 -9999 0 -0.49 42 42
MAP3K5 0.01 0.098 -9999 0 -0.47 4 4
HGF/MET/CIN85/CBL/ENDOPHILINS -0.043 0.17 -9999 0 -0.44 43 43
AP1 -0.024 0.097 -9999 0 -0.33 16 16
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
apoptosis -0.036 0.17 -9999 0 -0.72 15 15
STAT3 (dimer) 0 0.092 -9999 0 -0.43 1 1
GAB1/CRKL/SHP2/PI3K -0.03 0.073 -9999 0 -0.41 4 4
INPP5D 0.005 0.07 -9999 0 -0.65 3 3
CBL/CRK 0.003 0.1 -9999 0 -0.59 3 3
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.012 0 -9999 0 -10000 0 0
PTEN 0.012 0 -9999 0 -10000 0 0
ELK1 -0.035 0.091 -9999 0 -0.26 38 38
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.023 0.054 -9999 0 -0.3 2 2
PAK1 -0.008 0.069 -9999 0 -0.53 2 2
HGF/MET/RANBP10 -0.076 0.18 -9999 0 -0.49 42 42
HRAS -0.014 0.12 -9999 0 -0.56 1 1
DOCK1 0.004 0.093 -9999 0 -0.46 3 3
GAB1 -0.011 0.1 -9999 0 -0.53 3 3
CRK -0.003 0.097 -9999 0 -0.5 3 3
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.048 0.11 -9999 0 -0.49 2 2
JUN 0.011 0.03 -9999 0 -0.48 1 1
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.03 0.1 -9999 0 -0.26 45 45
PIK3R1 0.012 0 -9999 0 -10000 0 0
cell morphogenesis 0.024 0.093 -9999 0 -0.37 1 1
GRB2/SHC -0.011 0.091 -9999 0 -0.39 1 1
FOS -0.017 0.12 -9999 0 -0.5 16 16
GLMN -0.002 0.02 -9999 0 -0.24 2 2
cell motility -0.035 0.091 -9999 0 -0.26 38 38
HGF/MET/MUC20 -0.077 0.18 -9999 0 -0.49 43 43
cell migration -0.011 0.09 -9999 0 -0.38 1 1
GRB2 0.012 0 -9999 0 -10000 0 0
CBL 0.01 0.045 -9999 0 -0.74 1 1
MET/RANBP10 -0.061 0.2 -9999 0 -0.56 38 38
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.009 0.1 -9999 0 -0.48 1 1
MET/MUC20 -0.07 0.2 -9999 0 -0.56 38 38
RAP1B 0.011 0.089 -9999 0 -0.48 2 2
RAP1A 0.011 0.089 -9999 0 -0.43 3 3
HGF/MET/RANBP9 -0.076 0.18 -9999 0 -0.49 42 42
RAF1 -0.006 0.11 -9999 0 -0.52 1 1
STAT3 0 0.093 -9999 0 -0.43 1 1
cell proliferation 0.003 0.11 -9999 0 -0.49 1 1
RPS6KB1 -0.004 0.039 -9999 0 -10000 0 0
MAPK3 -0.036 0.083 -9999 0 -0.24 38 38
MAPK1 -0.036 0.083 -9999 0 -0.24 38 38
RANBP9 0.012 0 -9999 0 -10000 0 0
MAPK8 0.027 0.083 -9999 0 -0.45 2 2
SRC -0.001 0.096 -9999 0 -0.45 1 1
PI3K -0.013 0.094 -9999 0 -0.39 2 2
MET/Glomulin -0.061 0.18 -9999 0 -0.5 38 38
SOS1 0.012 0 -9999 0 -10000 0 0
MAP2K1 0.002 0.11 -9999 0 -0.48 1 1
MET -0.092 0.26 -9999 0 -0.74 38 38
MAP4K1 0.003 0.1 -9999 0 -0.52 4 4
PTK2 0.012 0 -9999 0 -10000 0 0
MAP2K2 0.002 0.11 -9999 0 -0.48 1 1
BAD -0.007 0.059 -9999 0 -0.41 1 1
MAP2K4 0.017 0.091 -9999 0 -0.47 3 3
SHP2/GRB2/SOS1/GAB1 -0.047 0.11 -9999 0 -0.47 3 3
INPPL1 0.012 0 -9999 0 -10000 0 0
PXN 0.008 0.054 -9999 0 -0.61 2 2
SH3KBP1 0.012 0 -9999 0 -10000 0 0
HGS -0.02 0.095 -9999 0 -0.24 40 40
PLCgamma1/PKC 0.009 0 -9999 0 -10000 0 0
HGF -0.003 0.1 -9999 0 -0.7 6 6
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
PTPRJ 0.007 0.064 -9999 0 -0.74 2 2
NCK/PLCgamma1 -0.009 0.091 -9999 0 -0.4 1 1
PDPK1 -0.024 0.067 -9999 0 -0.3 15 15
HGF/MET/SHIP -0.08 0.18 -9999 0 -0.49 44 44
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.13 -9999 0 -0.66 9 9
PDGFRB -0.048 0.2 -9999 0 -0.74 22 22
SPHK1 -0.024 0.064 -9999 0 -0.28 14 14
mol:S1P -0.025 0.062 -9999 0 -0.32 5 5
S1P1/S1P/Gi -0.031 0.15 -9999 0 -0.49 15 15
GNAO1 -0.043 0.18 -9999 0 -0.57 26 26
PDGFB-D/PDGFRB/PLCgamma1 -0.041 0.17 -9999 0 -0.5 18 18
PLCG1 -0.025 0.15 -9999 0 -0.46 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.048 0.2 -9999 0 -0.74 22 22
GNAI2 0.012 0.004 -9999 0 -10000 0 0
GNAI3 0.012 0.004 -9999 0 -10000 0 0
GNAI1 0.003 0.067 -9999 0 -0.49 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.003 0.11 -9999 0 -0.58 9 9
S1P1/S1P -0.038 0.1 -9999 0 -0.45 11 11
negative regulation of cAMP metabolic process -0.029 0.15 -9999 0 -0.48 15 15
MAPK3 -0.032 0.18 -9999 0 -0.52 21 21
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR 0.004 0.079 -9999 0 -0.74 3 3
PLCB2 -0.001 0.1 -9999 0 -0.51 5 5
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.032 0.086 -9999 0 -0.48 5 5
receptor internalization -0.036 0.096 -9999 0 -0.41 11 11
PTGS2 -0.049 0.24 -9999 0 -0.67 29 29
Rac1/GTP -0.032 0.086 -9999 0 -0.48 5 5
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA -0.01 0.13 -9999 0 -0.74 8 8
negative regulation of T cell proliferation -0.029 0.15 -9999 0 -0.48 15 15
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.014 0.11 -9999 0 -0.49 14 14
MAPK1 -0.032 0.18 -9999 0 -0.52 21 21
S1P1/S1P/PDGFB-D/PDGFRB -0.026 0.16 -9999 0 -0.59 11 11
ABCC1 0.012 0.002 -9999 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.13 0.25 -10000 0 -0.75 12 12
CRP -0.14 0.27 -10000 0 -0.83 16 16
cell cycle arrest -0.15 0.28 -10000 0 -0.72 30 30
TIMP1 -0.12 0.24 -10000 0 -0.66 22 22
IL6ST 0.009 0.011 -10000 0 -10000 0 0
Rac1/GDP -0.033 0.13 -10000 0 -0.45 9 9
AP1 0.011 0.093 -10000 0 -0.47 3 3
GAB2 0.013 0.001 -10000 0 -10000 0 0
TNFSF11 -0.24 0.34 -10000 0 -0.78 46 46
HSP90B1 0.003 0.05 -10000 0 -10000 0 0
GAB1 0.009 0.042 -10000 0 -0.48 2 2
MAPK14 0 0.11 -10000 0 -0.59 3 3
AKT1 0.045 0.024 -10000 0 -10000 0 0
FOXO1 0.05 0.023 -10000 0 -10000 0 0
MAP2K6 -0.019 0.12 -10000 0 -0.5 5 5
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.05 0.16 -10000 0 -0.51 8 8
MITF -0.03 0.12 -10000 0 -0.42 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.012 0 -10000 0 -10000 0 0
A2M 0.02 0.004 -10000 0 -10000 0 0
CEBPB 0.018 0.005 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.003 0.056 -10000 0 -10000 0 0
STAT3 -0.16 0.3 -10000 0 -0.76 30 30
STAT1 -0.012 0.053 -10000 0 -0.34 5 5
CEBPD -0.13 0.26 -10000 0 -0.84 12 12
PIK3CA 0.011 0.045 -10000 0 -0.74 1 1
PI3K 0.019 0.035 -10000 0 -0.56 1 1
JUN 0.01 0.03 -10000 0 -0.48 1 1
PIAS3/MITF -0.022 0.11 -10000 0 -0.46 4 4
MAPK11 0 0.11 -10000 0 -0.54 4 4
STAT3 (dimer)/FOXO1 -0.077 0.22 0.49 1 -0.62 10 11
GRB2/SOS1/GAB family -0.03 0.075 -10000 0 -0.41 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.11 -10000 0 -0.38 8 8
GRB2 0.013 0.001 -10000 0 -10000 0 0
JAK2 0.004 0.078 -10000 0 -0.74 3 3
LBP -0.17 0.3 -10000 0 -0.69 48 48
PIK3R1 0.014 0 -10000 0 -10000 0 0
JAK1 0.012 0.005 -10000 0 -10000 0 0
MYC -0.13 0.26 -10000 0 -0.78 12 12
FGG -0.24 0.4 -10000 0 -0.97 52 52
macrophage differentiation -0.15 0.28 -10000 0 -0.72 30 30
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.041 0.13 -10000 0 -0.45 17 17
JUNB -0.13 0.25 -10000 0 -0.76 13 13
FOS -0.018 0.12 -10000 0 -0.5 16 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.039 0.12 0.29 2 -0.41 12 14
STAT1/PIAS1 -0.053 0.13 0.36 1 -0.42 10 11
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.029 -10000 0 -10000 0 0
STAT3 (dimer) -0.16 0.3 -10000 0 -0.76 30 30
PRKCD -0.069 0.19 -10000 0 -0.61 7 7
IL6R -0.001 0.078 -10000 0 -0.48 7 7
SOCS3 0.013 0.12 -10000 0 -1.2 1 1
gp130 (dimer)/JAK1/JAK1/LMO4 0.015 0.041 -10000 0 -0.46 1 1
Rac1/GTP -0.046 0.14 -10000 0 -0.48 9 9
HCK 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade 0.017 0.049 -10000 0 -10000 0 0
bone resorption -0.23 0.33 -10000 0 -0.73 46 46
IRF1 -0.13 0.25 -10000 0 -0.75 12 12
mol:GDP -0.036 0.13 0.27 1 -0.44 11 12
SOS1 0.012 0.001 -10000 0 -10000 0 0
VAV1 -0.036 0.13 -10000 0 -0.45 11 11
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.002 0.11 -10000 0 -0.56 4 4
PTPN11 -0.003 0.014 -10000 0 -10000 0 0
IL6/IL6RA -0.051 0.16 -10000 0 -0.41 41 41
gp130 (dimer)/TYK2/TYK2/LMO4 0.012 0.039 -10000 0 -0.46 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.007 0.064 -10000 0 -0.47 4 4
IL6 -0.066 0.2 -10000 0 -0.56 36 36
PIAS3 0.012 0 -10000 0 -10000 0 0
PTPRE 0.009 0.081 -10000 0 -0.75 3 3
PIAS1 0.012 0 -10000 0 -10000 0 0
RAC1 0.012 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.028 0.11 0.26 2 -0.34 11 13
LMO4 0.004 0.054 -10000 0 -0.6 2 2
STAT3 (dimer)/PIAS3 -0.19 0.23 0.45 1 -0.86 13 14
MCL1 0.05 0.022 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.036 0.11 -9999 0 -0.49 6 6
PDGFB-D/PDGFRB/SLAP -0.029 0.16 -9999 0 -0.55 23 23
PDGFB-D/PDGFRB/APS/CBL -0.035 0.14 -9999 0 -0.49 23 23
AKT1 0.026 0.098 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.01 0.12 -9999 0 -0.51 6 6
PIK3CA 0.01 0.045 -9999 0 -0.74 1 1
FGR -0.026 0.099 -9999 0 -0.41 3 3
mol:Ca2+ -0.002 0.089 -9999 0 -0.35 3 3
MYC 0.015 0.095 -9999 0 -0.64 2 2
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.002 0.11 -9999 0 -0.37 22 22
LRP1/PDGFRB/PDGFB -0.036 0.14 -9999 0 -0.49 24 24
GRB10 0.01 0.045 -9999 0 -0.74 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 -0.002 0.09 -9999 0 -0.36 3 3
PTEN 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
GRB7 -0.09 0.26 -9999 0 -0.72 38 38
PDGFB-D/PDGFRB/SHP2 -0.027 0.15 -9999 0 -0.55 22 22
PDGFB-D/PDGFRB/GRB10 -0.029 0.16 -9999 0 -0.55 23 23
cell cycle arrest -0.029 0.16 -9999 0 -0.55 23 23
HRAS 0.012 0 -9999 0 -10000 0 0
HIF1A 0.032 0.09 -9999 0 -10000 0 0
GAB1 -0.005 0.098 -9999 0 -0.42 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.001 0.099 -9999 0 -0.43 3 3
PDGFB-D/PDGFRB -0.031 0.13 -9999 0 -0.47 22 22
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.027 0.15 -9999 0 -0.55 22 22
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.035 0.11 -9999 0 -0.57 4 4
positive regulation of MAPKKK cascade -0.027 0.15 -9999 0 -0.55 22 22
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.002 0.09 -9999 0 -0.36 3 3
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.1 0.24 -9999 0 -0.56 59 59
SHB 0.012 0 -9999 0 -10000 0 0
BLK -0.14 0.21 -9999 0 -0.46 77 77
PTPN2 0.012 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.027 0.15 -9999 0 -0.55 22 22
BCAR1 0.012 0 -9999 0 -10000 0 0
VAV2 -0.002 0.1 -9999 0 -0.41 3 3
CBL 0.01 0.045 -9999 0 -0.74 1 1
PDGFB-D/PDGFRB/DEP1 -0.031 0.16 -9999 0 -0.55 24 24
LCK -0.033 0.11 -9999 0 -0.43 4 4
PDGFRB -0.047 0.2 -9999 0 -0.74 22 22
ACP1 0.012 0 -9999 0 -10000 0 0
HCK -0.022 0.1 -9999 0 -0.36 22 22
ABL1 -0.01 0.1 -9999 0 -0.41 3 3
PDGFB-D/PDGFRB/CBL -0.006 0.094 -9999 0 -0.39 3 3
PTPN1 0.012 0.002 -9999 0 -10000 0 0
SNX15 0.012 0 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
STAT1 -0.009 0.13 -9999 0 -0.74 8 8
cell proliferation 0.016 0.089 -9999 0 -0.57 2 2
SLA 0.01 0.045 -9999 0 -0.74 1 1
actin cytoskeleton reorganization 0.014 0.11 -9999 0 -10000 0 0
SRC -0.025 0.099 -9999 0 -0.41 3 3
PI3K -0.028 0.091 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.098 0.2 -9999 0 -0.48 57 57
SH2B2 0.01 0.045 -9999 0 -0.74 1 1
PLCgamma1/SPHK1 -0.011 0.13 -9999 0 -0.53 6 6
LYN -0.026 0.1 -9999 0 -0.35 22 22
LRP1 0.01 0.045 -9999 0 -0.74 1 1
SOS1 0.012 0 -9999 0 -10000 0 0
STAT5B 0.012 0 -9999 0 -10000 0 0
STAT5A 0.012 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.02 0.1 -9999 0 -0.37 22 22
SPHK1 -0.026 0.16 -9999 0 -0.74 14 14
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.002 0.09 -9999 0 -0.36 3 3
PLCG1 -0.002 0.092 -9999 0 -0.37 3 3
NHERF/PDGFRB -0.031 0.13 -9999 0 -0.47 22 22
YES1 -0.026 0.099 -9999 0 -0.36 22 22
cell migration -0.031 0.13 -9999 0 -0.46 22 22
SHC/Grb2/SOS1 -0.02 0.1 -9999 0 -10000 0 0
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.005 0.12 -9999 0 -0.42 22 22
FYN -0.025 0.099 -9999 0 -0.41 3 3
DOK1 -0.007 0.13 -9999 0 -0.42 23 23
HRAS/GTP 0.009 0 -9999 0 -10000 0 0
PDGFB 0.007 0.064 -9999 0 -0.74 2 2
RAC1 0.01 0.098 -9999 0 -0.4 2 2
PRKCD -0.005 0.12 -9999 0 -0.42 22 22
FER -0.005 0.12 -9999 0 -0.42 22 22
MAPKKK cascade -0.029 0.099 -9999 0 -10000 0 0
RASA1 -0.005 0.12 -9999 0 -0.42 22 22
NCK1 0.012 0 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
p62DOK/Csk 0.001 0.12 -9999 0 -0.39 23 23
PDGFB-D/PDGFRB/SHB -0.027 0.15 -9999 0 -0.55 22 22
chemotaxis -0.01 0.098 -9999 0 -0.4 3 3
STAT1-3-5/STAT1-3-5 -0.039 0.12 -9999 0 -0.75 1 1
Bovine Papilomavirus E5/PDGFRB -0.036 0.15 -9999 0 -0.56 22 22
PTPRJ 0.007 0.064 -9999 0 -0.74 2 2
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.015 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.077 0.15 -10000 0 -0.52 13 13
NFATC4 -0.043 0.11 -10000 0 -0.39 4 4
ERBB2IP 0.012 0.03 -10000 0 -0.48 1 1
HSP90 (dimer) 0.012 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.077 0.14 -10000 0 -0.51 5 5
JUN -0.019 0.063 0.17 1 -10000 0 1
HRAS 0.012 0.001 -10000 0 -10000 0 0
DOCK7 -0.07 0.13 -10000 0 -0.48 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.098 0.16 -10000 0 -0.46 25 25
AKT1 0.009 0.003 -10000 0 -10000 0 0
BAD 0.017 0.003 -10000 0 -10000 0 0
MAPK10 -0.04 0.078 -10000 0 -0.26 8 8
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.082 0.15 -10000 0 -0.56 5 5
RAF1 -0.078 0.15 -10000 0 -0.5 13 13
ErbB2/ErbB3/neuregulin 2 -0.12 0.17 -10000 0 -0.53 23 23
STAT3 0.002 0.004 -10000 0 -10000 0 0
cell migration -0.02 0.085 -10000 0 -0.24 2 2
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.19 0.23 -10000 0 -0.67 8 8
FOS -0.12 0.17 -10000 0 -0.48 17 17
NRAS 0.012 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.077 0.14 -10000 0 -0.51 5 5
MAPK3 -0.16 0.2 -10000 0 -0.57 13 13
MAPK1 -0.16 0.2 -10000 0 -0.57 13 13
JAK2 -0.074 0.14 -10000 0 -0.49 6 6
NF2 -0.003 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.068 0.13 -10000 0 -0.38 9 9
NRG1 -0.13 0.23 -10000 0 -0.49 80 80
GRB2/SOS1 0.017 0.003 -10000 0 -10000 0 0
MAPK8 -0.068 0.13 -10000 0 -0.39 5 5
MAPK9 -0.033 0.069 -10000 0 -0.26 1 1
ERBB2 -0.039 0.15 0.36 1 -0.55 20 21
ERBB3 -0.005 0.099 -10000 0 -0.66 6 6
SHC1 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.005 0.013 -10000 0 -10000 0 0
STAT3 (dimer) 0.015 0.007 -10000 0 -10000 0 0
RNF41 0.019 0.008 -10000 0 -10000 0 0
FRAP1 0.008 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.061 0.085 -10000 0 -0.35 4 4
ErbB2/ErbB2/HSP90 (dimer) -0.033 0.12 0.24 1 -0.47 20 21
CHRNA1 -0.2 0.24 -10000 0 -0.5 51 51
myelination -0.041 0.11 -10000 0 -0.38 4 4
PPP3CB -0.066 0.12 -10000 0 -0.44 5 5
KRAS -0.024 0.16 -10000 0 -0.74 13 13
RAC1-CDC42/GDP -0.046 0.12 -10000 0 -0.58 2 2
NRG2 -0.14 0.23 -10000 0 -0.48 82 82
mol:GDP -0.068 0.13 -10000 0 -0.38 9 9
SOS1 0.012 0.001 -10000 0 -10000 0 0
MAP2K2 -0.084 0.15 -10000 0 -0.49 12 12
SRC 0.012 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.07 0.13 -10000 0 -0.48 5 5
MAP2K1 -0.16 0.19 -10000 0 -0.48 36 36
heart morphogenesis -0.077 0.14 -10000 0 -0.51 5 5
RAS family/GDP -0.072 0.14 -10000 0 -0.51 13 13
GRB2 0.012 0.001 -10000 0 -10000 0 0
PRKACA -0.006 0.009 -10000 0 -10000 0 0
CHRNE 0.005 0.015 -10000 0 -10000 0 0
HSP90AA1 0.012 0 -10000 0 -10000 0 0
activation of caspase activity -0.009 0.003 -10000 0 -10000 0 0
nervous system development -0.077 0.14 -10000 0 -0.51 5 5
CDC42 0.012 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.048 0.2 -10000 0 -0.74 22 22
Jak2/Leptin Receptor -0.056 0.084 -10000 0 -0.37 3 3
PTP1B/AKT1 -0.018 0.078 0.22 2 -10000 0 2
FYN 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.028 0.088 0.23 3 -0.27 3 6
EGFR -0.023 0.14 -10000 0 -0.61 15 15
EGF/EGFR -0.09 0.15 -10000 0 -0.45 34 34
CSF1 0.012 0 -10000 0 -10000 0 0
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.039 0.11 0.22 1 -0.4 12 13
Insulin Receptor/Insulin -0.027 0.043 0.17 1 -10000 0 1
HCK 0.012 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.02 0.083 0.23 2 -0.29 1 3
EGF -0.075 0.23 -10000 0 -0.69 33 33
YES1 0.012 0 -10000 0 -10000 0 0
CAV1 -0.025 0.097 0.22 3 -0.34 5 8
TXN 0.01 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.016 0.077 -10000 0 -10000 0 0
cell migration 0.028 0.088 0.27 3 -0.23 3 6
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR -0.079 0.21 -10000 0 -0.54 45 45
ITGA2B 0 0.08 -10000 0 -0.53 6 6
CSF1R 0.007 0.051 -10000 0 -0.48 3 3
Prolactin Receptor/Prolactin -0.073 0.18 -10000 0 -0.43 48 48
FGR 0.012 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.02 0.083 0.22 2 -0.29 1 3
Crk/p130 Cas -0.015 0.076 -10000 0 -10000 0 0
DOK1 -0.025 0.1 0.23 2 -0.33 9 11
JAK2 -0.046 0.1 -10000 0 -0.33 13 13
Jak2/Leptin Receptor/Leptin -0.05 0.082 -10000 0 -0.4 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
PTPN1 -0.028 0.088 0.23 3 -0.27 3 6
LYN 0.01 0.045 -10000 0 -0.74 1 1
CDH2 -0.022 0.15 -10000 0 -0.66 14 14
SRC 0.004 0.037 -10000 0 -10000 0 0
ITGB3 0.009 0.045 -10000 0 -0.74 1 1
CAT1/PTP1B -0.081 0.12 0.24 1 -0.36 11 12
CAPN1 0.012 0.003 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.022 0.041 -10000 0 -0.39 1 1
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.045 0.074 -10000 0 -0.37 2 2
negative regulation of transcription -0.045 0.1 -10000 0 -0.33 13 13
FCGR2A -0.009 0.13 -10000 0 -0.74 8 8
FER 0.01 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.004 0.067 -10000 0 -0.4 7 7
BLK -0.11 0.23 -10000 0 -0.52 65 65
Insulin Receptor/Insulin/Shc 0.011 0.009 -10000 0 -10000 0 0
RHOA 0.012 0.003 -10000 0 -10000 0 0
LEPR 0.012 0.001 -10000 0 -10000 0 0
BCAR1 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.082 0.14 -10000 0 -0.38 27 27
PRL -0.008 0.11 -10000 0 -0.74 6 6
SOCS3 0.012 0.076 -10000 0 -1.2 1 1
SPRY2 0.012 0.031 -10000 0 -0.49 1 1
Insulin Receptor/Insulin/IRS1 0.01 0.02 -10000 0 -0.29 1 1
CSF1/CSF1R -0.018 0.079 -10000 0 -10000 0 0
Ras protein signal transduction 0.023 0.029 -10000 0 -10000 0 0
IRS1 0.011 0.03 -10000 0 -0.48 1 1
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.033 0.16 -10000 0 -0.57 21 21
STAT5B -0.032 0.081 0.19 2 -0.29 4 6
STAT5A -0.032 0.081 0.19 2 -0.29 4 6
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.054 0.16 0.22 2 -0.51 23 25
CSN2 -0.023 0.11 -10000 0 -0.65 5 5
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
LAT -0.003 0.058 -10000 0 -0.29 3 3
YBX1 0.019 0.002 -10000 0 -10000 0 0
LCK -0.003 0.1 -10000 0 -0.7 6 6
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.24 0.35 -10000 0 -0.74 92 92
IL2 signaling events mediated by PI3K

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
BCL2L1 0.04 0.064 -10000 0 -10000 0 0
UGCG 0.016 0.021 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT -0.009 0.11 -10000 0 -0.36 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.021 0.019 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.051 -10000 0 -0.45 1 1
FRAP1 0.044 0.084 -10000 0 -0.52 1 1
FOXO3 0.054 0.075 -10000 0 -10000 0 0
AKT1 0.049 0.079 -10000 0 -10000 0 0
GAB2 0.013 0.001 -10000 0 -10000 0 0
SMPD1 0.016 0.021 -10000 0 -10000 0 0
SGMS1 0.016 0.021 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.03 -10000 0 -0.48 1 1
CALM1 0.012 0 -10000 0 -10000 0 0
cell proliferation 0.036 0.04 -10000 0 -10000 0 0
EIF3A 0.012 0 -10000 0 -10000 0 0
PI3K 0.021 0.035 -10000 0 -0.55 1 1
RPS6KB1 -0.019 0.071 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.001 -10000 0 -10000 0 0
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 -0.013 0.14 -10000 0 -0.74 10 10
PIK3R1 0.015 0.002 -10000 0 -10000 0 0
JAK1 0.015 0.002 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
MYC 0.051 0.094 -10000 0 -0.72 2 2
MYB -0.15 0.28 -10000 0 -0.57 82 82
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.034 0.078 -10000 0 -0.39 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.066 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.075 -10000 0 -0.38 1 1
Rac1/GDP 0.024 0.028 -10000 0 -0.43 1 1
T cell proliferation 0.05 0.071 -10000 0 -0.36 1 1
SHC1 0.013 0.001 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.011 0.025 -10000 0 -0.048 82 82
PRKCZ 0.05 0.073 -10000 0 -0.37 1 1
NF kappa B1 p50/RelA -0.006 0.051 -10000 0 -0.44 1 1
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.035 0.069 -10000 0 -0.36 2 2
HSP90AA1 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL2RA -0.02 0.15 -10000 0 -0.74 12 12
IL2RB 0.015 0.002 -10000 0 -10000 0 0
TERT -0.2 0.33 -10000 0 -0.72 78 78
E2F1 -0.077 0.16 -10000 0 -0.31 82 82
SOS1 0.013 0.001 -10000 0 -10000 0 0
RPS6 0.012 0 -10000 0 -10000 0 0
mol:cAMP 0.005 0.012 0.023 82 -10000 0 82
PTPN11 0.013 0.002 -10000 0 -10000 0 0
IL2RG -0.004 0.099 -10000 0 -0.51 10 10
actin cytoskeleton organization 0.05 0.071 -10000 0 -0.36 1 1
GRB2 0.013 0.001 -10000 0 -10000 0 0
IL2 0.012 0.006 -10000 0 -10000 0 0
PIK3CA 0.012 0.045 -10000 0 -0.73 1 1
Rac1/GTP 0.023 0.031 -10000 0 -0.41 1 1
LCK -0.001 0.1 -10000 0 -0.69 6 6
BCL2 0.048 0.087 -10000 0 -0.87 1 1
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.001 0.087 -10000 0 -0.69 1 1
regulation of S phase of mitotic cell cycle 0.007 0.071 -10000 0 -10000 0 0
GNAO1 -0.043 0.18 -10000 0 -0.57 26 26
HRAS 0.012 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.025 0.096 -10000 0 -0.37 19 19
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 0.019 0.074 -10000 0 -10000 0 0
T-DHT/AR -0.022 0.1 -10000 0 -0.35 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.007 16 16
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.003 0.066 -10000 0 -0.48 5 5
mol:GDP -0.034 0.11 -10000 0 -0.38 24 24
cell proliferation 0.02 0.12 -10000 0 -0.48 6 6
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
FOS 0 0.2 -10000 0 -0.76 16 16
mol:Ca2+ -0.012 0.024 -10000 0 -0.089 15 15
MAPK3 0.021 0.097 -10000 0 -0.44 4 4
MAPK1 0.016 0.061 -10000 0 -0.26 4 4
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 16 16
cAMP biosynthetic process -0.014 0.096 -10000 0 -0.34 19 19
GNG2 0.01 0.045 -10000 0 -0.74 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 16 16
HRAS/GTP -0.021 0.063 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.001 0.023 -10000 0 -0.38 1 1
SRC 0.012 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 16 16
PI3K -0.001 0.03 -10000 0 -0.48 1 1
apoptosis -0.017 0.11 0.41 15 -10000 0 15
T-DHT/AR/PELP1 -0.025 0.081 -10000 0 -0.29 24 24
HRAS/GDP -0.031 0.1 -10000 0 -0.36 24 24
CREB1 0.016 0.12 -10000 0 -0.44 15 15
RAC1-CDC42/GTP -0.001 0.024 -10000 0 -0.39 1 1
AR -0.031 0.14 -10000 0 -0.48 24 24
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 0.014 0.073 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.029 0.096 -10000 0 -0.34 24 24
T-DHT/AR/PELP1/Src 0 0.078 -10000 0 -10000 0 0
MAP2K2 0.019 0.074 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.007 0.071 -10000 0 -10000 0 0
GNAZ -0.013 0.11 -10000 0 -0.48 14 14
SHBG -0.028 0.15 -10000 0 -0.58 19 19
Gi family/GNB1/GNG2/GDP -0.008 0.12 -10000 0 -0.47 9 9
mol:T-DHT 0 0.001 -10000 0 -0.003 12 12
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 0.008 0.03 -10000 0 -0.35 2 2
Gi family/GTP -0.02 0.11 -10000 0 -0.38 13 13
CDC42 0.012 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.012 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.026 0.1 -10000 0 -0.47 2 2
NT3 (dimer)/TRKC -0.071 0.17 -10000 0 -0.37 64 64
NT3 (dimer)/TRKB -0.16 0.22 -10000 0 -0.55 52 52
SHC/Grb2/SOS1/GAB1/PI3K 0.033 0.026 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.004 0.11 -10000 0 -0.74 6 6
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 0.007 0.051 -10000 0 -0.48 3 3
NTRK2 -0.078 0.2 -10000 0 -0.53 46 46
NTRK3 -0.067 0.18 -10000 0 -0.49 43 43
NT-4/5 (dimer)/TRKB -0.17 0.23 -10000 0 -0.52 65 65
neuron apoptosis 0.081 0.18 0.44 38 -10000 0 38
SHC 2-3/Grb2 -0.089 0.19 -10000 0 -0.48 38 38
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.11 0.18 -10000 0 -0.47 44 44
SHC3 -0.11 0.17 -10000 0 -0.45 45 45
STAT3 (dimer) 0.012 0.051 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.11 0.17 -10000 0 -0.51 23 23
RIN/GDP -0.005 0.082 -10000 0 -0.28 1 1
GIPC1 0.012 0 -10000 0 -10000 0 0
KRAS -0.023 0.16 -10000 0 -0.74 13 13
DNAJA3 -0.093 0.14 -10000 0 -0.48 11 11
RIN/GTP -0.001 0.048 -10000 0 -0.56 2 2
CCND1 0.012 0.11 -10000 0 -0.65 7 7
MAGED1 0.009 0.042 -10000 0 -0.48 2 2
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.045 0.2 -10000 0 -0.74 21 21
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.031 0.089 -10000 0 -0.48 1 1
TRKA/NEDD4-2 0.013 0.043 -10000 0 -0.34 4 4
ELMO1 0.01 0.045 -10000 0 -0.74 1 1
RhoG/GTP/ELMO1/DOCK1 -0.002 0.029 -10000 0 -0.48 1 1
NGF -0.034 0.15 -10000 0 -0.49 25 25
HRAS 0.012 0 -10000 0 -10000 0 0
DOCK1 0.012 0 -10000 0 -10000 0 0
GAB2 0.012 0 -10000 0 -10000 0 0
RIT2 -0.002 0.063 -10000 0 -0.74 2 2
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 0.007 0.064 -10000 0 -0.74 2 2
DNM1 -0.018 0.15 -10000 0 -0.74 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.091 0.14 -10000 0 -0.47 13 13
mol:GDP -0.008 0.11 -10000 0 -10000 0 0
NGF (dimer) -0.034 0.15 -10000 0 -0.49 25 25
RhoG/GDP 0.007 0.035 -10000 0 -0.56 1 1
RIT1/GDP 0.001 0.079 -10000 0 -10000 0 0
TIAM1 0.008 0.054 -10000 0 -0.61 2 2
PIK3R1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.063 0.14 -10000 0 -0.48 14 14
KIDINS220/CRKL/C3G 0.019 0 -10000 0 -10000 0 0
SHC/RasGAP 0.019 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.003 0.041 -10000 0 -0.48 2 2
SHC/GRB2/SOS1/GAB1 0.03 0.023 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.034 0.15 -10000 0 -0.49 25 25
RAP1/GDP -0.027 0.047 -10000 0 -10000 0 0
KIDINS220/CRKL 0.012 0 -10000 0 -10000 0 0
BDNF (dimer) -0.004 0.11 -10000 0 -0.74 6 6
ubiquitin-dependent protein catabolic process -0.03 0.088 -10000 0 -0.48 1 1
Schwann cell development -0.028 0.032 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.029 0.039 -10000 0 -0.43 2 2
FRS2 family/SHP2/CRK family/C3G/GAB2 0.037 0.018 -10000 0 -10000 0 0
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.17 -10000 0 -0.48 29 29
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
Rap1/GTP -0.021 0.044 -10000 0 -10000 0 0
STAT3 0.012 0.051 -10000 0 -10000 0 0
axon guidance -0.097 0.16 -10000 0 -0.46 29 29
MAPK3 0.001 0.088 -10000 0 -0.43 1 1
MAPK1 0.001 0.088 -10000 0 -0.43 1 1
CDC42/GDP 0.001 0.079 -10000 0 -10000 0 0
NTF3 -0.034 0.15 -10000 0 -0.49 25 25
NTF4 -0.045 0.2 -10000 0 -0.74 21 21
NGF (dimer)/TRKA/FAIM -0.031 0.091 -10000 0 -0.48 2 2
PI3K 0.016 0.035 -10000 0 -0.56 1 1
FRS3 0.012 0 -10000 0 -10000 0 0
FAIM 0.01 0.045 -10000 0 -0.74 1 1
GAB1 0.009 0.042 -10000 0 -0.48 2 2
RASGRF1 -0.11 0.16 -10000 0 -0.45 26 26
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.058 0.16 -10000 0 -0.55 11 11
RGS19 0.01 0.045 -10000 0 -0.74 1 1
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.084 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.079 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT -0.03 0.089 -10000 0 -0.29 28 28
neuron projection morphogenesis -0.065 0.15 -10000 0 -0.47 10 10
NGF (dimer)/TRKA/NEDD4-2 -0.03 0.088 -10000 0 -0.48 1 1
MAP2K1 0.035 0.022 -10000 0 -10000 0 0
NGFR -0.13 0.24 -10000 0 -0.53 73 73
NGF (dimer)/TRKA/GIPC/GAIP -0.002 0.092 -10000 0 -0.48 1 1
RAS family/GTP/PI3K 0.016 0.059 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.003 0.034 -10000 0 -0.4 2 2
NRAS 0.012 0 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
PRKCI 0.004 0.078 -10000 0 -0.74 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade -0.072 0.17 -10000 0 -0.57 27 27
RASA1 0.012 0 -10000 0 -10000 0 0
TRKA/c-Abl 0.014 0.037 -10000 0 -0.34 3 3
SQSTM1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.03 0.13 -10000 0 -0.43 14 14
NGF (dimer)/TRKA/p62/Atypical PKCs -0.028 0.08 -10000 0 -0.4 4 4
MATK 0.009 0.042 -10000 0 -0.48 2 2
NEDD4L 0.011 0.03 -10000 0 -0.48 1 1
RAS family/GDP -0.03 0.051 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.099 0.15 -10000 0 -0.33 72 72
Rac1/GTP -0.083 0.1 -10000 0 -0.32 17 17
FRS2 family/SHP2/CRK family -0.003 0.034 -10000 0 -0.4 2 2
Aurora A signaling

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
Aurora A/GADD45A 0.012 0.066 -9999 0 -0.45 1 1
BIRC5 -0.028 0.17 -9999 0 -0.72 15 15
NFKBIA 0.017 0.06 -9999 0 -10000 0 0
CPEB1 -0.069 0.18 -9999 0 -0.48 45 45
AKT1 0.017 0.06 -9999 0 -10000 0 0
NDEL1 0.012 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.014 0.081 -9999 0 -0.54 4 4
NDEL1/TACC3 -0.015 0.075 -9999 0 -0.43 5 5
GADD45A 0.01 0.045 -9999 0 -0.74 1 1
GSK3B 0.013 0.007 -9999 0 -10000 0 0
PAK1/Aurora A 0.012 0.072 -9999 0 -0.72 1 1
MDM2 -0.009 0.13 -9999 0 -0.74 8 8
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.12 0.25 -9999 0 -0.56 66 66
TP53 0.013 0.061 -9999 0 -0.38 2 2
DLG7 0.007 0.06 -9999 0 -0.26 13 13
AURKAIP1 0.012 0 -9999 0 -10000 0 0
ARHGEF7 0.01 0.045 -9999 0 -0.74 1 1
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.011 0.085 -9999 0 -0.46 5 5
G2/M transition of mitotic cell cycle -0.014 0.08 -9999 0 -0.53 4 4
AURKA 0.009 0.072 -9999 0 -0.31 13 13
AURKB -0.015 0.049 -9999 0 -0.2 14 14
CDC25B 0.004 0.077 -9999 0 -0.3 8 8
G2/M transition checkpoint -0.008 0.051 -9999 0 -0.23 13 13
mRNA polyadenylation -0.048 0.11 -9999 0 -0.49 2 2
Aurora A/CPEB -0.048 0.11 -9999 0 -0.49 2 2
Aurora A/TACC1/TRAP/chTOG 0.025 0.059 -9999 0 -0.4 1 1
BRCA1 0.001 0.09 -9999 0 -0.74 4 4
centrosome duplication 0.012 0.072 -9999 0 -0.71 1 1
regulation of centrosome cycle -0.014 0.074 -9999 0 -0.43 5 5
spindle assembly -0.007 0.053 -9999 0 -0.4 1 1
TDRD7 0.012 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.032 0.12 -9999 0 -0.46 16 16
CENPA -0.002 0.058 -9999 0 -0.27 7 7
Aurora A/PP2A 0.013 0.06 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.02 0.057 -9999 0 -0.3 2 2
negative regulation of DNA binding 0.013 0.061 -9999 0 -0.38 2 2
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.016 0.035 -9999 0 -0.56 1 1
RASA1 0.012 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.008 0.051 -9999 0 -0.23 13 13
mitotic prometaphase 0.002 0.014 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.072 -9999 0 -0.31 13 13
TACC1 0.011 0.03 -9999 0 -0.48 1 1
TACC3 -0.003 0.1 -9999 0 -0.7 6 6
Aurora A/Antizyme1 0.021 0.054 -9999 0 -10000 0 0
Aurora A/RasGAP 0.013 0.06 -9999 0 -10000 0 0
OAZ1 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.007 -9999 0 -10000 0 0
GIT1 0.012 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.003 0.041 -9999 0 -0.48 2 2
Importin alpha/Importin beta/TPX2 -0.12 0.25 -9999 0 -0.56 66 66
PPP2R5D 0.012 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.09 0.21 -9999 0 -0.45 66 66
PAK1 0.01 0.045 -9999 0 -0.74 1 1
CKAP5 0.01 0.045 -9999 0 -0.74 1 1
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.012 0 -10000 0 -10000 0 0
PTK2 0.012 0 -10000 0 -10000 0 0
CRKL -0.02 0.12 -10000 0 -0.34 26 26
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0 -10000 0 -10000 0 0
IRS1/Crk -0.02 0.12 -10000 0 -0.34 26 26
IGF-1R heterotetramer/IGF1/PTP1B -0.051 0.14 -10000 0 -0.44 25 25
AKT1 -0.012 0.11 -10000 0 -0.5 1 1
BAD -0.005 0.11 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.12 -10000 0 -0.34 26 26
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.02 0.12 -10000 0 -0.35 26 26
RAF1 -0.002 0.11 -10000 0 -0.44 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.011 0.11 -10000 0 -0.49 2 2
YWHAZ 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.03 0.13 -10000 0 -0.38 26 26
PIK3CA 0.01 0.045 -10000 0 -0.74 1 1
RPS6KB1 -0.012 0.11 -10000 0 -0.41 3 3
GNB2L1 0.012 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.003 0.096 -10000 0 -0.38 1 1
PXN 0.008 0.054 -10000 0 -0.61 2 2
PIK3R1 0.012 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
HRAS/GTP -0.034 0.089 -10000 0 -0.52 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.008 0.12 -10000 0 -0.58 1 1
IGF-1R heterotetramer 0 0.056 -10000 0 -0.81 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.019 0.12 -10000 0 -0.35 26 26
Crk/p130 Cas/Paxillin -0.007 0.11 -10000 0 -0.44 3 3
IGF1R 0 0.056 -10000 0 -0.81 1 1
IGF1 -0.076 0.23 -10000 0 -0.65 37 37
IRS2/Crk -0.026 0.13 -10000 0 -0.43 8 8
PI3K -0.013 0.11 -10000 0 -0.46 3 3
apoptosis -0.003 0.097 0.4 1 -10000 0 1
HRAS/GDP 0.009 0 -10000 0 -10000 0 0
PRKCD -0.004 0.11 -10000 0 -0.52 2 2
RAF1/14-3-3 E 0.006 0.099 -10000 0 -0.38 1 1
BAD/14-3-3 0.003 0.1 -10000 0 -0.43 1 1
PRKCZ -0.012 0.11 -10000 0 -0.43 2 2
Crk/p130 Cas/Paxillin/FAK1 -0.038 0.081 -10000 0 -0.43 1 1
PTPN1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.012 0.12 -10000 0 -0.37 13 13
BCAR1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.046 0.12 -10000 0 -0.38 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.012 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.02 0.12 -10000 0 -0.34 26 26
GRB10 0.01 0.045 -10000 0 -0.74 1 1
PTPN11 -0.02 0.12 -10000 0 -0.34 26 26
IRS1 -0.03 0.13 -10000 0 -0.38 26 26
IRS2 -0.036 0.14 -10000 0 -0.36 32 32
IGF-1R heterotetramer/IGF1 -0.052 0.18 -10000 0 -0.49 37 37
GRB2 0.012 0 -10000 0 -10000 0 0
PDPK1 -0.02 0.12 -10000 0 -0.42 4 4
YWHAE 0.012 0 -10000 0 -10000 0 0
PRKD1 -0.008 0.12 -10000 0 -0.59 4 4
SHC1 0.012 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.1 0.23 -9999 0 -0.54 57 57
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0 -9999 0 -10000 0 0
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 0.031 0 -9999 0 -10000 0 0
HIF1A 0.024 0 -9999 0 -10000 0 0
COPS5 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.19 0.33 -9999 0 -0.73 75 75
ARNT/IPAS -0.066 0.17 -9999 0 -0.39 57 57
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.031 0 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.031 0 -9999 0 -10000 0 0
PHD1-3/OS9 0.032 0 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.031 0 -9999 0 -10000 0 0
EGLN3 0.012 0 -9999 0 -10000 0 0
EGLN2 0.012 0 -9999 0 -10000 0 0
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.036 0 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.079 0.18 -9999 0 -0.38 73 73
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.001 -9999 0 -10000 0 0
SMARCC1 0.004 0.008 -9999 0 -10000 0 0
REL 0.013 0.003 -9999 0 -10000 0 0
HDAC7 0.033 0.098 -9999 0 -0.53 2 2
JUN 0.01 0.03 -9999 0 -0.48 1 1
EP300 0.012 0 -9999 0 -10000 0 0
KAT2B 0.007 0.051 -9999 0 -0.48 3 3
KAT5 0.012 0 -9999 0 -10000 0 0
MAPK14 0.017 0.049 -9999 0 -0.43 3 3
FOXO1 0.012 0 -9999 0 -10000 0 0
T-DHT/AR 0.031 0.1 -9999 0 -0.56 2 2
MAP2K6 0.006 0.063 -9999 0 -0.58 3 3
BRM/BAF57 0.011 0.064 -9999 0 -0.51 4 4
MAP2K4 0.012 0.006 -9999 0 -10000 0 0
SMARCA2 0.01 0.031 -9999 0 -0.5 1 1
PDE9A -0.088 0.28 -9999 0 -1 22 22
NCOA2 0.012 0.003 -9999 0 -10000 0 0
CEBPA -0.009 0.12 -9999 0 -0.71 8 8
EHMT2 0.009 0.045 -9999 0 -0.74 1 1
cell proliferation 0.048 0.11 -9999 0 -0.51 2 2
NR0B1 -0.001 0.064 -9999 0 -0.74 2 2
EGR1 -0.003 0.09 -9999 0 -0.51 8 8
RXRs/9cRA -0.08 0.13 -9999 0 -10000 0 0
AR/RACK1/Src 0.013 0.069 -9999 0 -0.42 1 1
AR/GR 0.009 0.095 -9999 0 -0.49 4 4
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
RCHY1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.021 0.012 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.034 0.068 -9999 0 -0.44 1 1
SRC 0.033 0.045 -9999 0 -0.39 1 1
NR3C1 0.007 0.051 -9999 0 -0.48 3 3
KLK3 -0.16 0.18 -9999 0 -0.73 15 15
APPBP2 0.012 0.005 -9999 0 -10000 0 0
TRIM24 0.01 0.045 -9999 0 -0.74 1 1
T-DHT/AR/TIP60 0.026 0.066 -9999 0 -0.44 2 2
TMPRSS2 -0.083 0.27 -9999 0 -1 20 20
RXRG -0.17 0.24 -9999 0 -0.48 102 102
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.011 0.03 -9999 0 -0.49 1 1
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.012 0.003 -9999 0 -10000 0 0
NR2C2 0.012 0 -9999 0 -10000 0 0
KLK2 0.024 0.13 -9999 0 -0.53 12 12
AR 0.008 0.096 -9999 0 -0.32 14 14
SENP1 0.012 0.001 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 -0.009 0.13 -9999 0 -0.74 8 8
SRY -0.005 0.059 -9999 0 -0.48 4 4
GATA2 0.009 0.042 -9999 0 -0.48 2 2
MYST2 0 0.001 -9999 0 -10000 0 0
HOXB13 -0.5 0.34 -9999 0 -0.73 190 190
T-DHT/AR/RACK1/Src 0.032 0.067 -9999 0 -0.44 1 1
positive regulation of transcription 0.009 0.042 -9999 0 -0.48 2 2
DNAJA1 0.012 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.045 -9999 0 -10000 0 0
NCOA1 0.015 0.004 -9999 0 -10000 0 0
SPDEF -0.088 0.2 -9999 0 -0.48 56 56
T-DHT/AR/TIF2 0.039 0.053 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.026 0.066 -9999 0 -0.44 2 2
GSK3B 0.012 0.003 -9999 0 -10000 0 0
NR2C1 0.012 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.028 0.048 -9999 0 -0.42 1 1
SIRT1 0.012 0 -9999 0 -10000 0 0
ZMIZ2 0.013 0.004 -9999 0 -10000 0 0
POU2F1 0.019 0.048 -9999 0 -0.73 1 1
T-DHT/AR/DAX-1 -0.002 0.073 -9999 0 -0.43 4 4
CREBBP 0.012 0 -9999 0 -10000 0 0
SMARCE1 0.004 0.078 -9999 0 -0.74 3 3
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.018 0.12 -9999 0 -0.53 5 5
MAP3K8 0.007 0.064 -9999 0 -0.74 2 2
FOS 0.016 0.091 -9999 0 -0.38 6 6
PRKCA 0.011 0.03 -9999 0 -0.48 1 1
PTPN7 0 0.1 -9999 0 -0.74 5 5
HRAS 0.012 0.001 -9999 0 -10000 0 0
PRKCB -0.016 0.12 -9999 0 -0.48 16 16
NRAS 0.012 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.002 0.099 -9999 0 -0.44 13 13
MAPK3 0.016 0.059 -9999 0 -0.29 1 1
MAP2K1 0.007 0.11 -9999 0 -0.4 17 17
ELK1 0.012 0.005 -9999 0 -10000 0 0
BRAF 0 0.1 -9999 0 -0.38 17 17
mol:GTP 0 0.001 -9999 0 -0.005 15 15
MAPK1 0.016 0.059 -9999 0 -0.26 3 3
RAF1 0 0.1 -9999 0 -0.38 17 17
KRAS -0.023 0.16 -9999 0 -0.74 13 13
Coregulation of Androgen receptor activity

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
NRIP1 0.011 0.009 -9999 0 -10000 0 0
SVIL -0.007 0.12 -9999 0 -0.71 7 7
ZNF318 0.01 0.068 -9999 0 -0.74 2 2
JMJD2C 0 0.025 -9999 0 -0.12 12 12
T-DHT/AR/Ubc9 -0.007 0.098 -9999 0 -0.3 24 24
CARM1 0.012 0.001 -9999 0 -10000 0 0
PRDX1 0.013 0.002 -9999 0 -10000 0 0
PELP1 0.013 0.003 -9999 0 -10000 0 0
CTNNB1 0.009 0.046 -9999 0 -0.74 1 1
AKT1 0.013 0.006 -9999 0 -10000 0 0
PTK2B 0.012 0.005 -9999 0 -10000 0 0
MED1 0.005 0.079 -9999 0 -0.74 3 3
MAK 0.001 0.1 -9999 0 -0.74 5 5
response to oxidative stress 0 0.002 -9999 0 -10000 0 0
HIP1 0.012 0.008 -9999 0 -10000 0 0
GSN -0.001 0.078 -9999 0 -0.48 7 7
NCOA2 0.012 0.001 -9999 0 -10000 0 0
NCOA6 0.012 0.008 -9999 0 -10000 0 0
DNA-PK 0 0.054 -9999 0 -0.46 3 3
NCOA4 0.012 0.001 -9999 0 -10000 0 0
PIAS3 0.012 0.006 -9999 0 -10000 0 0
cell proliferation -0.011 0.062 -9999 0 -0.42 5 5
XRCC5 0.013 0.004 -9999 0 -10000 0 0
UBE3A 0.011 0.013 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.015 0.098 -9999 0 -0.31 24 24
FHL2 0.011 0.13 -9999 0 -0.97 4 4
RANBP9 0.012 0.008 -9999 0 -10000 0 0
JMJD1A 0.002 0.043 -9999 0 -0.14 23 23
CDK6 -0.026 0.16 -9999 0 -0.74 14 14
TGFB1I1 0.005 0.062 -9999 0 -0.57 3 3
T-DHT/AR/CyclinD1 -0.021 0.13 -9999 0 -0.35 30 30
XRCC6 0.013 0.004 -9999 0 -10000 0 0
T-DHT/AR 0.001 0.12 -9999 0 -0.45 8 8
CTDSP1 0.012 0.003 -9999 0 -10000 0 0
CTDSP2 0.014 0.014 -9999 0 -10000 0 0
BRCA1 0.001 0.09 -9999 0 -0.74 4 4
TCF4 0.014 0.01 -9999 0 -10000 0 0
CDKN2A -0.19 0.33 -9999 0 -0.73 75 75
SRF 0.019 0.017 -9999 0 -10000 0 0
NKX3-1 -0.014 0.16 -9999 0 -1 5 5
KLK3 -0.007 0.14 -9999 0 -0.59 14 14
TMF1 0.012 0.003 -9999 0 -10000 0 0
HNRNPA1 0.013 0.008 -9999 0 -10000 0 0
AOF2 -0.001 0.009 -9999 0 -10000 0 0
APPL1 0.023 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.006 0.099 -9999 0 -0.3 24 24
AR -0.032 0.15 -9999 0 -0.5 24 24
UBA3 0.012 0.003 -9999 0 -10000 0 0
PATZ1 0.013 0.008 -9999 0 -10000 0 0
PAWR 0.012 0.003 -9999 0 -10000 0 0
PRKDC 0.005 0.077 -9999 0 -0.73 3 3
PA2G4 0.014 0.009 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.004 0.09 -9999 0 -0.34 8 8
RPS6KA3 0.011 0.009 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.008 0.098 -9999 0 -0.33 15 15
LATS2 0.013 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.004 0.09 -9999 0 -0.28 24 24
Cyclin D3/CDK11 p58 0.009 0.002 -9999 0 -10000 0 0
VAV3 -0.03 0.17 -9999 0 -0.71 16 16
KLK2 -0.04 0.13 -9999 0 -0.63 12 12
CASP8 0.013 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.002 0.09 -9999 0 -0.34 8 8
TMPRSS2 -0.051 0.25 -9999 0 -0.93 20 20
CCND1 -0.007 0.12 -9999 0 -0.74 7 7
PIAS1 0.011 0.013 -9999 0 -10000 0 0
mol:T-DHT -0.001 0.023 -9999 0 -0.064 30 30
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.01 0.019 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.032 0.15 -9999 0 -0.39 36 36
CMTM2 0.004 0.078 -9999 0 -0.73 3 3
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.012 0.021 -9999 0 -10000 0 0
CCND3 0.013 0.001 -9999 0 -10000 0 0
TGIF1 0.013 0.008 -9999 0 -10000 0 0
FKBP4 0.009 0.046 -9999 0 -0.74 1 1
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.007 0.17 -10000 0 -0.68 12 12
CLOCK 0.014 0.008 -10000 0 -10000 0 0
TIMELESS/CRY2 0.017 0.12 -10000 0 -0.53 12 12
DEC1/BMAL1 0.012 0.049 -10000 0 -0.56 2 2
ATR 0.01 0.045 -10000 0 -0.74 1 1
NR1D1 0.029 0.057 -10000 0 -10000 0 0
ARNTL 0.014 0.008 -10000 0 -10000 0 0
TIMELESS 0.014 0.13 -10000 0 -0.58 12 12
NPAS2 0.014 0.008 -10000 0 -10000 0 0
CRY2 0.012 0 -10000 0 -10000 0 0
mol:CO -0.008 0.023 0.1 12 -10000 0 12
CHEK1 -0.015 0.14 -10000 0 -0.74 10 10
mol:HEME 0.008 0.023 -10000 0 -0.1 12 12
PER1 -0.009 0.1 -10000 0 -0.48 12 12
BMAL/CLOCK/NPAS2 0.037 0.023 -10000 0 -10000 0 0
BMAL1/CLOCK 0.029 0.078 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.007 0.17 -10000 0 -0.68 12 12
TIMELESS/CHEK1/ATR 0.007 0.17 -10000 0 -0.7 12 12
mol:NADPH 0.008 0.023 -10000 0 -0.1 12 12
PER1/TIMELESS 0.005 0.13 -10000 0 -0.53 12 12
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.002 0.064 -10000 0 -0.74 2 2
Cellular roles of Anthrax toxin

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
ANTXR1 -0.007 0.12 -10000 0 -0.74 7 7
ANTXR2 0.007 0.051 -10000 0 -0.48 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.015 -10000 0 -0.082 10 10
monocyte activation -0.005 0.075 -10000 0 -0.27 19 19
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.002 0.013 -10000 0 -10000 0 0
MAP2K7 -0.002 0.013 -10000 0 -10000 0 0
MAP2K6 -0.006 0.035 -10000 0 -0.31 3 3
CYAA 0 0.073 -10000 0 -0.37 10 10
MAP2K4 -0.002 0.013 -10000 0 -10000 0 0
IL1B -0.031 0.12 -10000 0 -0.36 33 33
Channel 0.001 0.078 -10000 0 -0.39 10 10
NLRP1 -0.01 0.057 -10000 0 -0.41 5 5
CALM1 0.012 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.018 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.015 0.082 10 -10000 0 10
MAPK3 -0.002 0.013 -10000 0 -10000 0 0
MAPK1 -0.002 0.013 -10000 0 -10000 0 0
PGR -0.028 0.083 -10000 0 -0.28 25 25
PA/Cellular Receptors -0.015 0.081 -10000 0 -0.42 10 10
apoptosis -0.003 0.015 -10000 0 -0.082 10 10
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.002 0.07 -10000 0 -0.35 10 10
macrophage activation 0.015 0.014 -10000 0 -10000 0 0
TNF -0.019 0.14 -10000 0 -0.66 13 13
VCAM1 -0.005 0.075 -10000 0 -0.27 19 19
platelet activation -0.003 0.018 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.018 -10000 0 -10000 0 0
IL18 0.003 0.067 -10000 0 -0.32 9 9
negative regulation of macrophage activation -0.003 0.015 -10000 0 -0.082 10 10
LEF -0.003 0.016 -10000 0 -0.082 10 10
CASP1 -0.006 0.03 -10000 0 -0.2 5 5
mol:cAMP -0.004 0.018 -10000 0 -10000 0 0
necrosis -0.003 0.015 -10000 0 -0.082 10 10
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.002 0.074 -10000 0 -0.37 10 10
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.073 -10000 0 -1.1 1 1
VDR 0.01 0.045 -10000 0 -0.74 1 1
FAM120B 0.012 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.049 0.13 -10000 0 -0.41 8 8
RXRs/LXRs/DNA/Oxysterols -0.036 0.14 -10000 0 -0.5 8 8
MED1 0.004 0.078 -10000 0 -0.74 3 3
mol:9cRA 0.003 0.01 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.011 0.082 -10000 0 -0.52 2 2
RXRs/NUR77 -0.073 0.15 -10000 0 -0.51 4 4
RXRs/PPAR -0.055 0.12 -10000 0 -0.43 1 1
NCOR2 0.012 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.007 0.035 -10000 0 -0.56 1 1
RARs/VDR/DNA/Vit D3 -0.007 0.051 -10000 0 -0.41 4 4
RARA 0.007 0.064 -10000 0 -0.74 2 2
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.01 0.045 -10000 0 -0.74 1 1
RARs/RARs/DNA/9cRA 0.018 0.049 -10000 0 -0.42 3 3
RARG 0.01 0.045 -10000 0 -0.74 1 1
RPS6KB1 0.031 0.048 -10000 0 -0.4 1 1
RARs/THRs/DNA/SMRT 0.011 0.082 -10000 0 -0.52 2 2
THRA 0.01 0.045 -10000 0 -0.74 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.007 0.035 -10000 0 -0.56 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.07 0.14 0.27 1 -0.34 8 9
NR1H4 -0.09 0.24 -10000 0 -0.61 45 45
RXRs/LXRs/DNA -0.046 0.14 -10000 0 -10000 0 0
NR1H2 0.016 0.007 -10000 0 -10000 0 0
NR1H3 0.016 0.008 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.062 0.13 -10000 0 -0.4 1 1
NR4A1 -0.004 0.088 -10000 0 -0.48 9 9
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.092 0.15 -10000 0 -0.38 28 28
RXRG -0.17 0.24 -10000 0 -0.48 102 102
RXR alpha/CCPG 0.02 0.022 -10000 0 -0.33 1 1
RXRA 0.014 0.031 -10000 0 -0.48 1 1
RXRB 0.016 0.008 -10000 0 -10000 0 0
THRB -0.026 0.14 -10000 0 -0.49 21 21
PPARG 0.009 0.042 -10000 0 -0.48 2 2
PPARD 0.012 0 -10000 0 -10000 0 0
TNF -0.044 0.19 -10000 0 -0.76 13 13
mol:Oxysterols 0.003 0.009 -10000 0 -10000 0 0
cholesterol transport -0.036 0.13 -10000 0 -0.49 8 8
PPARA 0.012 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.011 0.03 -10000 0 -0.48 1 1
RXRs/NUR77/BCL2 -0.07 0.13 -10000 0 -0.48 5 5
SREBF1 -0.025 0.12 -10000 0 -0.52 2 2
RXRs/RXRs/DNA/9cRA -0.069 0.14 -10000 0 -0.34 8 8
ABCA1 -0.03 0.14 -10000 0 -0.63 4 4
RARs/THRs -0.024 0.09 -10000 0 -0.56 4 4
RXRs/FXR -0.12 0.2 -10000 0 -0.51 34 34
BCL2 0.011 0.03 -10000 0 -0.48 1 1
FAS signaling pathway (CD95)

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
SPTAN1 0.007 0.032 0.22 1 -10000 0 1
RFC1 0.007 0.032 0.22 1 -10000 0 1
PRKDC 0.002 0.059 0.22 1 -0.46 3 4
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 0 0.048 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 0.002 0.067 0.36 1 -0.28 2 3
MAP2K4 0.017 0.11 -10000 0 -0.38 4 4
mol:ceramide 0.015 0.085 -10000 0 -0.42 4 4
GSN 0 0.051 0.22 1 -0.27 6 7
FASLG/FAS/FADD/FAF1/Caspase 8 0.017 0.065 -10000 0 -0.36 2 2
FAS 0.009 0.045 -10000 0 -0.74 1 1
BID 0.008 0.055 0.22 12 -0.49 1 13
MAP3K1 0.023 0.068 -10000 0 -10000 0 0
MAP3K7 0.011 0.004 -10000 0 -10000 0 0
RB1 0.007 0.032 0.22 1 -10000 0 1
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.084 0.18 -10000 0 -0.49 43 43
ARHGDIB 0.005 0.043 0.22 1 -0.46 1 2
FADD 0.012 0.005 -10000 0 -10000 0 0
actin filament polymerization 0 0.051 0.27 6 -0.22 1 7
NFKB1 -0.026 0.064 -10000 0 -0.26 2 2
MAPK8 0.006 0.15 -10000 0 -0.41 26 26
DFFA 0.007 0.032 0.22 1 -10000 0 1
DNA fragmentation during apoptosis 0.007 0.032 0.22 1 -10000 0 1
FAS/FADD/MET -0.048 0.18 -10000 0 -0.49 38 38
CFLAR/RIP1 0.015 0.006 -10000 0 -10000 0 0
FAIM3 -0.018 0.15 -10000 0 -0.7 12 12
FAF1 0.012 0.005 -10000 0 -10000 0 0
PARP1 0.005 0.043 0.22 1 -0.46 1 2
DFFB 0.007 0.032 0.22 1 -10000 0 1
CHUK -0.023 0.056 -10000 0 -10000 0 0
FASLG -0.003 0.093 -10000 0 -0.56 7 7
FAS/FADD 0.015 0.036 -10000 0 -0.56 1 1
HGF -0.003 0.1 -10000 0 -0.7 6 6
LMNA 0.007 0.03 -10000 0 -10000 0 0
CASP6 0.007 0.032 0.22 1 -10000 0 1
CASP10 0.008 0.042 -10000 0 -0.48 2 2
CASP3 0.008 0.038 0.26 1 -10000 0 1
PTPN13 -0.001 0.085 -10000 0 -0.52 7 7
CASP8 0.015 0.07 0.34 12 -10000 0 12
IL6 -0.098 0.37 -10000 0 -1 36 36
MET -0.092 0.26 -10000 0 -0.74 38 38
ICAD/CAD 0.007 0.031 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 0.015 0.085 -10000 0 -0.43 4 4
activation of caspase activity by cytochrome c 0.008 0.055 0.22 12 -0.49 1 13
PAK2 0.007 0.032 0.22 1 -10000 0 1
BCL2 0.011 0.03 -10000 0 -0.48 1 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.072 0.24 -9999 0 -0.69 29 29
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.035 0.11 -9999 0 -0.39 4 4
ATF2/c-Jun -0.007 0.09 -9999 0 -0.59 1 1
MAPK11 -0.035 0.11 -9999 0 -0.39 4 4
MITF -0.03 0.13 -9999 0 -0.41 9 9
MAPKAPK5 -0.028 0.13 -9999 0 -0.47 4 4
KRT8 -0.03 0.13 -9999 0 -0.45 8 8
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.05 0.16 -9999 0 -0.51 8 8
CEBPB -0.028 0.13 -9999 0 -0.47 4 4
SLC9A1 -0.029 0.13 -9999 0 -0.47 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.024 0.13 -9999 0 -0.47 4 4
p38alpha-beta/MNK1 -0.027 0.13 -9999 0 -0.51 4 4
JUN -0.007 0.089 -9999 0 -0.59 1 1
PPARGC1A -0.074 0.18 -9999 0 -0.58 16 16
USF1 -0.028 0.13 -9999 0 -0.47 4 4
RAB5/GDP/GDI1 -0.042 0.074 -9999 0 -0.35 4 4
NOS2 -0.095 0.26 -9999 0 -0.62 49 49
DDIT3 -0.032 0.13 -9999 0 -0.4 11 11
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.017 0.11 -9999 0 -0.42 5 5
p38alpha-beta/HBP1 -0.027 0.13 -9999 0 -0.51 4 4
CREB1 -0.023 0.13 -9999 0 -0.4 8 8
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.017 0.11 -9999 0 -0.45 4 4
RPS6KA4 -0.028 0.13 -9999 0 -0.47 4 4
PLA2G4A -0.034 0.14 -9999 0 -0.52 12 12
GDI1 -0.028 0.13 -9999 0 -0.39 8 8
TP53 -0.039 0.15 -9999 0 -0.49 8 8
RPS6KA5 -0.028 0.13 -9999 0 -0.47 4 4
ESR1 -0.036 0.13 -9999 0 -0.47 4 4
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.03 0.13 -9999 0 -0.53 5 5
MEF2A -0.028 0.13 -9999 0 -0.39 8 8
EIF4EBP1 -0.024 0.13 -9999 0 -0.4 8 8
KRT19 -0.037 0.13 -9999 0 -0.4 8 8
ELK4 -0.037 0.13 -9999 0 -0.4 8 8
ATF6 -0.028 0.13 -9999 0 -0.39 8 8
ATF1 -0.023 0.13 -9999 0 -0.4 8 8
p38alpha-beta/MAPKAPK2 -0.027 0.13 -9999 0 -0.51 4 4
p38alpha-beta/MAPKAPK3 -0.027 0.13 -9999 0 -0.51 4 4
Caspase cascade in apoptosis

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
TOP1 0.012 0.071 -10000 0 -0.28 13 13
ACTA1 -0.005 0.092 -10000 0 -0.34 16 16
NUMA1 0.012 0.071 -10000 0 -0.28 13 13
SPTAN1 0.005 0.086 -10000 0 -0.34 14 14
LIMK1 0.002 0.093 -10000 0 -0.35 16 16
BIRC3 0.003 0.076 -10000 0 -0.61 4 4
BIRC2 0.012 0 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
CASP10 -0.002 0.11 -10000 0 -0.48 13 13
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0.045 -10000 0 -0.74 1 1
PTK2 0.012 0.071 -10000 0 -0.28 13 13
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.005 0.085 -10000 0 -0.34 14 14
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN -0.001 0.098 -10000 0 -0.36 15 15
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.085 0.15 -10000 0 -0.58 10 10
BID 0.009 0.056 -10000 0 -0.22 14 14
MAP3K1 0.008 0.034 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.003 0.089 -10000 0 -0.35 15 15
CASP9 0.012 0 -10000 0 -10000 0 0
DNA repair -0.005 0.032 0.2 1 -0.18 2 3
neuron apoptosis 0.022 0.012 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.012 0.083 -10000 0 -0.33 13 13
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 0.023 0.047 -10000 0 -10000 0 0
TRAF2 0.012 0 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.083 -10000 0 -0.34 12 12
CASP7 -0.005 0.039 0.27 5 -10000 0 5
KRT18 0.013 0.038 -10000 0 -0.52 1 1
apoptosis 0.016 0.079 -10000 0 -10000 0 0
DFFA 0.005 0.086 -10000 0 -0.34 14 14
DFFB 0.005 0.086 -10000 0 -0.34 15 15
PARP1 0.005 0.032 0.18 2 -0.21 1 3
actin filament polymerization 0 0.1 0.34 18 -10000 0 18
TNF -0.019 0.14 -10000 0 -0.66 13 13
CYCS 0.011 0.044 -10000 0 -0.17 13 13
SATB1 0.027 0.049 -10000 0 -10000 0 0
SLK 0.005 0.086 -10000 0 -0.35 13 13
p15 BID/BAX 0.014 0.05 -10000 0 -10000 0 0
CASP2 0.032 0.047 -10000 0 -10000 0 0
JNK cascade -0.008 0.034 -10000 0 -10000 0 0
CASP3 -0.002 0.091 -10000 0 -0.36 15 15
LMNB2 0.032 0.042 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.012 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.023 0.054 -10000 0 -0.43 3 3
negative regulation of DNA binding -0.084 0.15 -10000 0 -0.57 10 10
stress fiber formation 0.005 0.085 -10000 0 -0.34 13 13
GZMB -0.01 0.13 -10000 0 -0.52 16 16
CASP1 0.014 0.028 -10000 0 -0.32 2 2
LMNB1 0.03 0.043 -10000 0 -10000 0 0
APP 0.022 0.012 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.011 0.077 -10000 0 -0.31 12 12
LMNA 0.034 0.037 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.026 0.05 -10000 0 -10000 0 0
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.005 0.086 -10000 0 -0.35 12 12
APAF-1/Caspase 9 -0.001 0.021 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.012 0.071 -10000 0 -0.28 13 13
CFL2 0 0.1 -10000 0 -0.35 18 18
GAS2 -0.015 0.12 -10000 0 -0.38 21 21
positive regulation of apoptosis 0.034 0.041 -10000 0 -10000 0 0
PRF1 0.012 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.013 0.013 -10000 0 -10000 0 0
HSPA8 0.012 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.032 0.098 -10000 0 -0.36 1 1
AKT1 0.012 0.015 -10000 0 -10000 0 0
GSC -0.073 0.32 -10000 0 -0.91 30 30
NKX2-5 -0.12 0.28 -10000 0 -0.73 48 48
muscle cell differentiation 0.034 0.089 0.49 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.024 0.084 -10000 0 -10000 0 0
SMAD4 0.019 0.032 -10000 0 -10000 0 0
CBFB 0.007 0.064 -10000 0 -0.74 2 2
SAP18 0.012 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.041 0.15 -10000 0 -0.48 27 27
SMAD3/SMAD4/VDR 0.017 0.048 -10000 0 -0.38 1 1
MYC 0.008 0.057 -10000 0 -0.62 2 2
CDKN2B -0.014 0.24 -10000 0 -1.1 12 12
AP1 0.039 0.082 -10000 0 -0.57 2 2
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.055 0.029 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.034 0.07 -10000 0 -0.29 1 1
SP3 0.015 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.037 0.18 -10000 0 -0.77 16 16
SMAD3/SMAD4/GR 0.015 0.057 -10000 0 -10000 0 0
GATA3 -0.002 0.11 -10000 0 -0.69 7 7
SKI/SIN3/HDAC complex/NCoR1 0.042 0.017 -10000 0 -10000 0 0
MEF2C/TIF2 -0.054 0.2 -10000 0 -0.57 14 14
endothelial cell migration 0.079 0.22 0.59 43 -10000 0 43
MAX 0.016 0.014 -10000 0 -10000 0 0
RBBP7 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.012 0.001 -10000 0 -10000 0 0
RUNX2 0.011 0.03 -10000 0 -0.48 1 1
RUNX3 0.01 0.045 -10000 0 -0.74 1 1
RUNX1 -0.001 0.1 -10000 0 -0.74 5 5
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 0.011 0.054 -10000 0 -0.48 3 3
VDR 0.01 0.045 -10000 0 -0.74 1 1
CDKN1A 0.023 0.16 -10000 0 -1.2 4 4
KAT2B 0.007 0.051 -10000 0 -0.47 3 3
SMAD2/SMAD2/SMAD4/FOXH1 -0.009 0.15 -10000 0 -0.54 16 16
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.012 0.001 -10000 0 -10000 0 0
SERPINE1 -0.08 0.22 -10000 0 -0.59 43 43
SMAD3/SMAD4/ATF2 0.013 0.037 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.006 0.059 -10000 0 -0.35 2 2
SAP30 0.012 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.011 0.035 -10000 0 -10000 0 0
JUN 0.038 0.08 -10000 0 -0.56 2 2
SMAD3/SMAD4/IRF7 0.013 0.037 -10000 0 -10000 0 0
TFE3 0.011 0.023 -10000 0 -10000 0 0
COL1A2 -0.13 0.26 -10000 0 -0.62 59 59
mesenchymal cell differentiation -0.012 0.042 -10000 0 -10000 0 0
DLX1 -0.022 0.15 -10000 0 -0.68 13 13
TCF3 0.01 0.045 -10000 0 -0.74 1 1
FOS -0.012 0.12 -10000 0 -0.5 16 16
SMAD3/SMAD4/Max 0.019 0.047 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.007 0.016 -10000 0 -10000 0 0
ZBTB17 0.013 0.012 -10000 0 -10000 0 0
LAMC1 0.034 0.094 -10000 0 -0.68 4 4
TGIF2/HDAC complex/SMAD3/SMAD4 0.013 0.037 -10000 0 -10000 0 0
IRF7 0.014 0.002 -10000 0 -10000 0 0
ESR1 0.007 0.081 -10000 0 -0.48 7 7
HNF4A -0.024 0.15 -10000 0 -0.65 15 15
MEF2C -0.065 0.21 -10000 0 -0.58 16 16
SMAD2-3/SMAD4 0.006 0.043 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.009 0.023 -10000 0 -10000 0 0
IGHV3OR16-13 -0.003 0.016 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0 -10000 0 -10000 0 0
CREBBP 0.013 0.009 -10000 0 -10000 0 0
SKIL 0.01 0.045 -10000 0 -0.74 1 1
HDAC1 0.012 0.001 -10000 0 -10000 0 0
HDAC2 0.012 0.001 -10000 0 -10000 0 0
SNIP1 0.012 0.003 -10000 0 -10000 0 0
GCN5L2 0 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.037 0.059 -10000 0 -0.38 1 1
MSG1/HSC70 -0.043 0.17 -10000 0 -0.54 30 30
SMAD2 0.008 0.03 -10000 0 -10000 0 0
SMAD3 0.022 0.03 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.035 0.052 -10000 0 -0.31 2 2
SMAD2/SMAD2/SMAD4 0.011 0.036 -10000 0 -0.28 3 3
NCOR1 0.012 0.001 -10000 0 -10000 0 0
NCOA2 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A 0.005 0.059 -10000 0 -0.56 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.031 0.08 -10000 0 -10000 0 0
IFNB1 0.039 0.034 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.049 0.2 -10000 0 -0.58 13 13
CITED1 -0.067 0.23 -10000 0 -0.71 30 30
SMAD2-3/SMAD4/ARC105 0.044 0.046 -10000 0 -10000 0 0
RBL1 0.004 0.078 -10000 0 -0.74 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.038 0.1 -10000 0 -0.46 10 10
RUNX1-3/PEBPB2 -0.014 0.08 -10000 0 -0.48 8 8
SMAD7 0.048 0.086 -10000 0 -10000 0 0
MYC/MIZ-1 0.003 0.05 -10000 0 -0.45 2 2
SMAD3/SMAD4 -0.007 0.13 0.29 9 -0.41 2 11
IL10 0.035 0.1 -10000 0 -0.53 5 5
PIASy/HDAC complex 0.014 0.01 -10000 0 -10000 0 0
PIAS3 0.012 0.006 -10000 0 -10000 0 0
CDK2 0.013 0.008 -10000 0 -10000 0 0
IL5 0.031 0.11 -10000 0 -0.54 6 6
CDK4 0.008 0.066 -10000 0 -0.75 2 2
PIAS4 0.014 0.01 -10000 0 -10000 0 0
ATF3 0.002 0.072 -10000 0 -0.48 6 6
SMAD3/SMAD4/SP1 0.015 0.087 -10000 0 -10000 0 0
FOXG1 -0.011 0.11 -10000 0 -0.74 6 6
FOXO3 0.022 0.02 -10000 0 -10000 0 0
FOXO1 0.022 0.02 -10000 0 -10000 0 0
FOXO4 0.022 0.02 -10000 0 -10000 0 0
heart looping -0.064 0.21 -10000 0 -0.57 16 16
CEBPB 0.012 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.009 0.11 -10000 0 -0.51 11 11
MYOD1 -0.003 0.063 -10000 0 -0.74 2 2
SMAD3/SMAD4/HNF4 -0.011 0.11 -10000 0 -0.49 11 11
SMAD3/SMAD4/GATA3 0.001 0.091 -10000 0 -0.47 6 6
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.045 -10000 0 -0.74 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.015 0.083 -10000 0 -0.41 8 8
SMAD3/SMAD4/SP1-3 0.029 0.077 -10000 0 -10000 0 0
MED15 0.012 0 -10000 0 -10000 0 0
SP1 -0.009 0.058 -10000 0 -10000 0 0
SIN3B 0.012 0.001 -10000 0 -10000 0 0
SIN3A 0.012 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.077 0.22 -10000 0 -0.47 61 61
ITGB5 0.036 0.068 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.045 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.013 0.096 -10000 0 -0.38 3 3
AR -0.031 0.14 -10000 0 -0.48 24 24
negative regulation of cell growth 0.042 0.053 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.007 0.06 -10000 0 -0.56 2 2
E2F5 0.004 0.078 -10000 0 -0.74 3 3
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.005 0.12 -10000 0 -0.45 16 16
SMAD2-3/SMAD4/FOXO1-3a-4 0.039 0.076 -10000 0 -0.34 5 5
TFDP1 0.01 0.045 -10000 0 -0.74 1 1
SMAD3/SMAD4/AP1 0.045 0.085 -10000 0 -0.57 2 2
SMAD3/SMAD4/RUNX2 0.012 0.042 -10000 0 -10000 0 0
TGIF2 0.012 0 -10000 0 -10000 0 0
TGIF1 0.012 0 -10000 0 -10000 0 0
ATF2 0.012 0 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.016 0.035 -10000 0 -0.56 1 1
ATM 0.012 0 -10000 0 -10000 0 0
UBE2D3 0.012 0 -10000 0 -10000 0 0
PRKDC 0.004 0.078 -10000 0 -0.74 3 3
ATR 0.01 0.045 -10000 0 -0.74 1 1
UBE2L3 0.012 0 -10000 0 -10000 0 0
FANCD2 0.002 0.088 -10000 0 -0.34 17 17
protein ubiquitination -0.058 0.15 -10000 0 -0.42 38 38
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.041 -10000 0 -0.48 2 2
MRE11A 0.01 0.045 -10000 0 -0.74 1 1
DNA-PK -0.005 0.05 -10000 0 -0.48 3 3
FA complex/FANCD2/Ubiquitin 0.028 0.065 -10000 0 -0.37 4 4
FANCF 0.012 0 -10000 0 -10000 0 0
BRCA1 0.001 0.09 -10000 0 -0.74 4 4
CCNE1 -0.083 0.25 -10000 0 -0.74 35 35
CDK2/Cyclin E1 -0.055 0.19 -10000 0 -0.56 35 35
FANCG 0.012 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.008 0.077 -10000 0 -0.56 5 5
FANCE 0.012 0 -10000 0 -10000 0 0
FANCC 0.012 0 -10000 0 -10000 0 0
NBN 0.01 0.045 -10000 0 -0.74 1 1
FANCA -0.007 0.12 -10000 0 -0.74 7 7
DNA repair 0.014 0.15 -10000 0 -0.57 11 11
BRCA1/BARD1/ubiquitin 0.008 0.077 -10000 0 -0.56 5 5
BARD1/DNA-PK 0.026 0.066 -10000 0 -0.57 3 3
FANCL 0.012 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.016 0.035 0.56 1 -10000 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.033 0.031 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.009 0.064 -10000 0 -0.48 5 5
BRCA1/BARD1/P53 0.022 0.077 -10000 0 -0.52 5 5
BARD1/CSTF1/BRCA1 -0.009 0.064 -10000 0 -0.48 5 5
BRCA1/BACH1 0.001 0.09 -10000 0 -0.74 4 4
BARD1 0.01 0.045 -10000 0 -0.74 1 1
PCNA -0.001 0.1 -10000 0 -0.74 5 5
BRCA1/BARD1/UbcH5C -0.009 0.064 -10000 0 -0.48 5 5
BRCA1/BARD1/UbcH7 -0.009 0.064 -10000 0 -0.48 5 5
BRCA1/BARD1/RAD51/PCNA -0.008 0.15 -10000 0 -0.51 20 20
BARD1/DNA-PK/P53 -0.006 0.059 -10000 0 -0.54 3 3
BRCA1/BARD1/Ubiquitin 0.008 0.077 -10000 0 -0.56 5 5
BRCA1/BARD1/CTIP 0.023 0.062 -10000 0 -0.43 5 5
FA complex 0.031 0.048 -10000 0 -0.43 1 1
BARD1/EWS 0.016 0.035 -10000 0 -0.56 1 1
RBBP8 0.021 0 -10000 0 -10000 0 0
TP53 0.012 0 -10000 0 -10000 0 0
TOPBP1 0.012 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.009 0.072 0.51 5 -10000 0 5
BRCA1/BARD1 -0.059 0.15 -10000 0 -0.42 38 38
CSTF1 0.012 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.007 0.035 -10000 0 -0.56 1 1
CDK2 0.012 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.026 0.16 -10000 0 -0.74 14 14
RAD50 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.008 0.077 -10000 0 -0.56 5 5
EWSR1 0.012 0 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.014 0.13 -10000 0 -0.69 10 10
GNB1/GNG2 -0.045 0.053 -10000 0 -0.2 7 7
AKT1 -0.015 0.088 -10000 0 -0.21 4 4
EGF -0.074 0.23 -10000 0 -0.69 33 33
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.036 0.036 -10000 0 -10000 0 0
mol:Ca2+ -0.038 0.12 -10000 0 -0.3 13 13
LYN 0.034 0.042 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.036 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.042 0.13 -10000 0 -0.34 12 12
GNG2 0.01 0.045 -10000 0 -0.74 1 1
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.033 0.032 -10000 0 -10000 0 0
G beta5/gamma2 -0.053 0.068 -10000 0 -0.26 8 8
PRKCH -0.041 0.13 -10000 0 -0.35 12 12
DNM1 -0.018 0.15 -10000 0 -0.74 11 11
TXA2/TP beta/beta Arrestin3 -0.01 0.043 -10000 0 -0.22 11 11
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.002 0.083 -10000 0 -0.48 8 8
G12 family/GTP -0.073 0.085 -10000 0 -0.3 12 12
ADRBK1 0.01 0.045 -10000 0 -0.74 1 1
ADRBK2 0.012 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.008 0.009 -10000 0 -10000 0 0
mol:GDP 0.014 0.076 0.25 1 -10000 0 1
mol:NADP 0.001 0.09 -10000 0 -0.74 4 4
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 0.007 0.064 -10000 0 -0.74 2 2
mol:IP3 -0.05 0.14 -10000 0 -0.38 13 13
cell morphogenesis 0.007 0.009 -10000 0 -10000 0 0
PLCB2 -0.071 0.18 -10000 0 -0.51 13 13
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.021 0.11 -10000 0 -0.38 4 4
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.036 0.036 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.012 0 -10000 0 -10000 0 0
PRKCB1 -0.048 0.14 -10000 0 -0.36 14 14
GNAQ 0.012 0 -10000 0 -10000 0 0
mol:L-citrulline 0.001 0.09 -10000 0 -0.74 4 4
TXA2/TXA2-R family -0.075 0.18 -10000 0 -0.48 22 22
LCK 0.028 0.061 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.005 0.03 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.016 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.005 0.03 -10000 0 -10000 0 0
MAPK14 -0.021 0.096 -10000 0 -0.24 4 4
TGM2/GTP -0.066 0.16 -10000 0 -0.45 14 14
MAPK11 -0.021 0.096 -10000 0 -0.23 8 8
ARHGEF1 -0.018 0.076 -10000 0 -0.19 1 1
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.053 0.15 -10000 0 -0.35 22 22
RAB11/GDP 0.012 0.001 -10000 0 -10000 0 0
ICAM1 -0.038 0.12 -10000 0 -0.34 15 15
cAMP biosynthetic process -0.056 0.14 -10000 0 -0.35 16 16
Gq family/GTP/EBP50 0.023 0.03 -10000 0 -0.21 2 2
actin cytoskeleton reorganization 0.007 0.009 -10000 0 -10000 0 0
SRC 0.036 0.036 -10000 0 -10000 0 0
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR 0.008 0.079 -10000 0 -10000 0 0
VCAM1 -0.041 0.12 -10000 0 -0.33 14 14
TP beta/Gq family/GDP/G beta5/gamma2 0.033 0.032 -10000 0 -10000 0 0
platelet activation -0.028 0.13 -10000 0 -0.3 12 12
PGI2/IP 0.007 0.004 -10000 0 -10000 0 0
PRKACA 0.013 0.043 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.031 0.033 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2 -0.013 0.061 -10000 0 -0.31 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.019 0.04 -10000 0 -10000 0 0
mol:DAG -0.053 0.15 -10000 0 -0.42 12 12
EGFR -0.021 0.14 -10000 0 -0.6 15 15
TXA2/TP alpha -0.075 0.18 -10000 0 -0.48 15 15
Gq family/GTP -0.004 0.03 -10000 0 -0.2 6 6
YES1 0.036 0.036 -10000 0 -10000 0 0
GNAI2/GTP -0.006 0.033 -10000 0 -10000 0 0
PGD2/DP -0.003 0.06 -10000 0 -0.35 8 8
SLC9A3R1 0.012 0 -10000 0 -10000 0 0
FYN 0.036 0.036 -10000 0 -10000 0 0
mol:NO 0.001 0.09 -10000 0 -0.74 4 4
GNA15 0.007 0.064 -10000 0 -0.74 2 2
PGK/cGMP -0.002 0.073 -10000 0 -0.48 6 6
RhoA/GDP 0.012 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.022 0.082 -10000 0 -0.39 1 1
NOS3 0.001 0.09 -10000 0 -0.74 4 4
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.042 0.13 -10000 0 -0.35 12 12
PRKCB -0.049 0.14 -10000 0 -0.37 14 14
PRKCE -0.039 0.13 -10000 0 -0.35 12 12
PRKCD -0.043 0.14 -10000 0 -0.37 12 12
PRKCG -0.11 0.19 -10000 0 -0.46 26 26
muscle contraction -0.068 0.17 -10000 0 -0.45 22 22
PRKCZ -0.042 0.13 -10000 0 -0.34 12 12
ARR3 0.012 0.001 -10000 0 -10000 0 0
TXA2/TP beta 0.01 0.044 -10000 0 -10000 0 0
PRKCQ -0.043 0.13 -10000 0 -0.36 12 12
MAPKKK cascade -0.061 0.16 -10000 0 -0.45 13 13
SELE -0.053 0.14 -10000 0 -0.32 43 43
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.043 -10000 0 -10000 0 0
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 0.004 0.068 -10000 0 -0.55 4 4
chemotaxis -0.085 0.2 -10000 0 -0.54 22 22
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.012 0 -10000 0 -10000 0 0
GNA11 0.012 0 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.005 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.012 0 -10000 0 -10000 0 0
NFATC1 -0.19 0.13 -10000 0 -0.47 6 6
NFATC2 0.036 0.02 -10000 0 -10000 0 0
NFATC3 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.05 0.1 -10000 0 -0.38 6 6
Exportin 1/Ran/NUP214 0.025 0.005 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.056 0.078 -10000 0 -0.39 7 7
BCL2/BAX 0.017 0.021 -10000 0 -0.34 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.003 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
MAPK14 0.012 0.002 -10000 0 -10000 0 0
BAD 0.012 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.041 0.095 -10000 0 -0.36 6 6
Calcineurin A alpha-beta B1/BCL2 0.011 0.03 -10000 0 -0.48 1 1
FKBP8 0.012 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.04 0.094 0.35 6 -10000 0 6
KPNB1 0.012 0 -10000 0 -10000 0 0
KPNA2 -0.018 0.15 -10000 0 -0.74 11 11
XPO1 0.012 0 -10000 0 -10000 0 0
SFN -0.01 0.11 -10000 0 -0.55 11 11
MAP3K8 0.007 0.064 -10000 0 -0.74 2 2
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.054 0.053 -10000 0 -10000 0 0
CABIN1 -0.051 0.1 -10000 0 -0.38 6 6
CALM1 0.013 0.002 -10000 0 -10000 0 0
RAN 0.012 0 -10000 0 -10000 0 0
MAP3K1 0.012 0 -10000 0 -10000 0 0
CAMK4 0.002 0.072 -10000 0 -0.48 6 6
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
MAPK3 0.012 0 -10000 0 -10000 0 0
YWHAH 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.008 0.077 -10000 0 -0.56 5 5
YWHAB 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0.002 -10000 0 -10000 0 0
MAPK9 0.012 0 -10000 0 -10000 0 0
YWHAG 0.012 0 -10000 0 -10000 0 0
FKBP1A 0.012 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.13 0.1 -10000 0 -10000 0 0
PRKCH 0.012 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.019 0.005 -10000 0 -10000 0 0
CASP3 0.012 0.002 -10000 0 -10000 0 0
PIM1 0.011 0.03 -10000 0 -0.48 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.002 -10000 0 -10000 0 0
apoptosis 0 0.006 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.036 -10000 0 -10000 0 0
PRKCB -0.016 0.12 -10000 0 -0.48 16 16
PRKCE 0.012 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.027 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0.019 0 -10000 0 -10000 0 0
PRKCD 0.012 0 -10000 0 -10000 0 0
NUP214 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.002 -10000 0 -10000 0 0
PRKCA 0.011 0.03 -10000 0 -0.48 1 1
PRKCG -0.29 0.37 -10000 0 -0.73 112 112
PRKCQ 0.002 0.072 -10000 0 -0.48 6 6
FKBP38/BCL2 0.017 0.021 -10000 0 -0.34 1 1
EP300 0.013 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 -0.38 0.2 -10000 0 -0.48 215 215
NFATc/JNK1 -0.18 0.12 -10000 0 -0.44 6 6
CaM/Ca2+/FKBP38 0.018 0.003 -10000 0 -10000 0 0
FKBP12/FK506 0.009 0 -10000 0 -10000 0 0
CSNK1A1 0.019 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.011 0.045 -10000 0 -0.29 6 6
NFATc/ERK1 -0.18 0.12 -10000 0 -0.44 6 6
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.056 0.078 -10000 0 -0.39 7 7
NR4A1 0.049 0.092 -10000 0 -0.45 9 9
GSK3B 0.013 0.002 -10000 0 -10000 0 0
positive T cell selection 0.022 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.002 0.01 -10000 0 -10000 0 0
RCH1/ KPNB1 -0.005 0.11 -10000 0 -0.56 11 11
YWHAQ 0.012 0 -10000 0 -10000 0 0
PRKACA 0.012 0.002 -10000 0 -10000 0 0
AKAP5 -0.001 0.1 -10000 0 -0.74 5 5
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.012 0 -10000 0 -10000 0 0
NFATc/p38 alpha -0.18 0.12 -10000 0 -0.44 6 6
CREBBP 0.013 0.002 -10000 0 -10000 0 0
BCL2 0.011 0.03 -10000 0 -0.48 1 1
Stabilization and expansion of the E-cadherin adherens junction

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 a