PARADIGM pathway analysis of mRNASeq expression and copy number data
Thymoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C14T6HV8
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 47 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
Angiopoietin receptor Tie2-mediated signaling 36
Signaling mediated by p38-alpha and p38-beta 34
Class IB PI3K non-lipid kinase events 33
Nongenotropic Androgen signaling 32
PDGFR-alpha signaling pathway 26
Endothelins 26
IL4-mediated signaling events 25
Nephrin/Neph1 signaling in the kidney podocyte 22
Reelin signaling pathway 22
HIF-1-alpha transcription factor network 21
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 120 . 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 ( 120 ).

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
Angiopoietin receptor Tie2-mediated signaling 0.3000 36 3196 88 -0.54 0.11 1000 -1000 -0.057 -1000
Signaling mediated by p38-alpha and p38-beta 0.2833 34 1533 44 -0.35 0.032 1000 -1000 -0.006 -1000
Class IB PI3K non-lipid kinase events 0.2750 33 99 3 -0.12 -1000 1000 -1000 -0.019 -1000
Nongenotropic Androgen signaling 0.2667 32 1673 52 -0.44 0.28 1000 -1000 -0.022 -1000
PDGFR-alpha signaling pathway 0.2167 26 1181 44 -0.56 0.058 1000 -1000 -0.027 -1000
Endothelins 0.2167 26 2542 96 -0.58 0.059 1000 -1000 -0.037 -1000
IL4-mediated signaling events 0.2083 25 2293 91 -0.87 0.56 1000 -1000 -0.025 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1833 22 771 34 -0.12 0.033 1000 -1000 -0.022 -1000
Reelin signaling pathway 0.1833 22 1253 56 -0.19 0.062 1000 -1000 -0.014 -1000
HIF-1-alpha transcription factor network 0.1750 21 1611 76 -0.29 0.047 1000 -1000 -0.032 -1000
Calcium signaling in the CD4+ TCR pathway 0.1750 21 652 31 -0.35 0.032 1000 -1000 -0.048 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1667 20 1406 68 -0.49 0.11 1000 -1000 -0.036 -1000
Thromboxane A2 receptor signaling 0.1583 19 2077 105 -0.26 0.076 1000 -1000 -0.031 -1000
Signaling events mediated by the Hedgehog family 0.1500 18 968 52 -0.34 0.037 1000 -1000 -0.015 -1000
Signaling events regulated by Ret tyrosine kinase 0.1500 18 1534 82 -0.26 0.051 1000 -1000 -0.042 -1000
IL6-mediated signaling events 0.1417 17 1349 75 -0.24 0.054 1000 -1000 -0.022 -1000
IL23-mediated signaling events 0.1417 17 1028 60 -0.55 0.063 1000 -1000 -0.014 -1000
Osteopontin-mediated events 0.1333 16 639 38 -0.24 0.035 1000 -1000 -0.015 -1000
TCGA08_retinoblastoma 0.1167 14 114 8 -0.028 0.028 1000 -1000 -0.003 -1000
FOXM1 transcription factor network 0.1167 14 743 51 -0.54 0.032 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 0.1083 13 1022 76 -0.29 0.059 1000 -1000 -0.01 -1000
IL12-mediated signaling events 0.1000 12 1114 87 -0.59 0.086 1000 -1000 -0.041 -1000
Glucocorticoid receptor regulatory network 0.1000 12 1442 114 -0.5 0.18 1000 -1000 -0.042 -1000
S1P1 pathway 0.1000 12 450 36 -0.35 0.031 1000 -1000 -0.022 -1000
Ras signaling in the CD4+ TCR pathway 0.1000 12 208 17 -0.19 0.042 1000 -1000 -0.012 -1000
amb2 Integrin signaling 0.0917 11 950 82 -0.28 0.04 1000 -1000 -0.024 -1000
TCR signaling in naïve CD8+ T cells 0.0917 11 1047 93 -0.13 0.045 1000 -1000 -0.036 -1000
Wnt signaling 0.0917 11 78 7 -0.12 0.022 1000 -1000 -0.003 -1000
ErbB2/ErbB3 signaling events 0.0833 10 660 65 -0.23 0.044 1000 -1000 -0.056 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0833 10 568 54 -0.19 0.047 1000 -1000 -0.022 -1000
Fc-epsilon receptor I signaling in mast cells 0.0833 10 1055 97 -0.24 0.033 1000 -1000 -0.051 -1000
Integrins in angiogenesis 0.0833 10 893 84 -0.1 0.054 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 0.0750 9 248 26 -0.14 0.032 1000 -1000 -0.021 -1000
Signaling events mediated by PTP1B 0.0750 9 722 76 -0.2 0.048 1000 -1000 -0.034 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0750 9 486 52 -0.16 0.068 1000 -1000 -0.021 -1000
PDGFR-beta signaling pathway 0.0750 9 965 97 -0.099 0.039 1000 -1000 -0.032 -1000
BARD1 signaling events 0.0667 8 501 57 -0.066 0.06 1000 -1000 -0.035 -1000
JNK signaling in the CD4+ TCR pathway 0.0667 8 136 17 -0.12 0.032 1000 -1000 -0.023 -1000
Arf6 signaling events 0.0667 8 534 62 -0.22 0.063 1000 -1000 -0.021 -1000
BMP receptor signaling 0.0667 8 685 81 -0.2 0.062 1000 -1000 -0.023 -1000
Glypican 1 network 0.0667 8 387 48 -0.13 0.053 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0667 8 473 58 -0.14 0.062 1000 -1000 -0.019 -1000
Regulation of Androgen receptor activity 0.0667 8 575 70 -0.16 0.044 1000 -1000 -0.041 -1000
FOXA2 and FOXA3 transcription factor networks 0.0583 7 327 46 -0.65 0.036 1000 -1000 -0.016 -1000
BCR signaling pathway 0.0583 7 731 99 -0.16 0.059 1000 -1000 -0.046 -1000
Insulin Pathway 0.0583 7 549 74 -0.32 0.074 1000 -1000 -0.028 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0583 7 957 120 -0.37 0.17 1000 -1000 -0.033 -1000
Regulation of nuclear SMAD2/3 signaling 0.0500 6 886 136 -0.28 0.073 1000 -1000 -0.032 -1000
Nectin adhesion pathway 0.0500 6 395 63 -0.073 0.08 1000 -1000 -0.04 -1000
LPA receptor mediated events 0.0500 6 612 102 -0.24 0.033 1000 -1000 -0.055 -1000
Syndecan-4-mediated signaling events 0.0500 6 441 67 -0.19 0.046 1000 -1000 -0.025 -1000
Aurora B signaling 0.0500 6 435 67 -0.45 0.072 1000 -1000 -0.027 -1000
Syndecan-2-mediated signaling events 0.0417 5 412 69 -0.19 0.046 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 0.0417 5 29 5 -0.008 0.023 1000 -1000 0.017 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0417 5 437 85 -0.4 0.063 1000 -1000 -0.029 -1000
Presenilin action in Notch and Wnt signaling 0.0417 5 360 61 -0.24 0.082 1000 -1000 -0.036 -1000
FAS signaling pathway (CD95) 0.0417 5 263 47 -0.44 0.048 1000 -1000 -0.022 -1000
IL2 signaling events mediated by PI3K 0.0417 5 327 58 -0.19 0.05 1000 -1000 -0.029 -1000
LPA4-mediated signaling events 0.0333 4 59 12 -0.12 0.009 1000 -1000 -0.018 -1000
Syndecan-1-mediated signaling events 0.0333 4 157 34 -0.13 0.032 1000 -1000 -0.017 -1000
Plasma membrane estrogen receptor signaling 0.0333 4 402 86 -0.062 0.057 1000 -1000 -0.039 -1000
p75(NTR)-mediated signaling 0.0250 3 495 125 -0.13 0.081 1000 -1000 -0.048 -1000
PLK1 signaling events 0.0250 3 273 85 -0.034 0.052 1000 -1000 -0.03 -1000
Ceramide signaling pathway 0.0250 3 256 76 -0.062 0.089 1000 -1000 -0.02 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0250 3 118 37 -0.026 0.051 1000 -1000 -0.018 -1000
IL1-mediated signaling events 0.0250 3 201 62 -0.053 0.076 1000 -1000 -0.022 -1000
ceramide signaling pathway 0.0250 3 154 49 -0.019 0.046 1000 -1000 -0.016 -1000
HIF-2-alpha transcription factor network 0.0250 3 143 43 -0.1 0.1 1000 -1000 -0.047 -1000
Ephrin B reverse signaling 0.0250 3 172 48 -0.073 0.051 1000 -1000 -0.02 -1000
Paxillin-dependent events mediated by a4b1 0.0250 3 111 36 -0.043 0.054 1000 -1000 -0.022 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0250 3 137 45 -0.035 0.082 1000 -1000 -0.029 -1000
Canonical Wnt signaling pathway 0.0250 3 154 51 -0.07 0.074 1000 -1000 -0.033 -1000
Glypican 2 network 0.0250 3 12 4 0.013 0.023 1000 -1000 0.016 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0250 3 377 125 -0.073 0.062 1000 -1000 -0.03 -1000
IL27-mediated signaling events 0.0250 3 189 51 -0.19 0.061 1000 -1000 -0.029 -1000
IL2 signaling events mediated by STAT5 0.0250 3 72 22 -0.052 0.036 1000 -1000 -0.02 -1000
IGF1 pathway 0.0250 3 194 57 -0.021 0.068 1000 -1000 -0.021 -1000
Caspase cascade in apoptosis 0.0167 2 160 74 -0.071 0.078 1000 -1000 -0.027 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0167 2 51 23 -0.057 0.061 1000 -1000 -0.01 -1000
ErbB4 signaling events 0.0167 2 200 69 -0.1 0.062 1000 -1000 -0.017 -1000
Cellular roles of Anthrax toxin 0.0167 2 101 39 -0.1 0.044 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 0.0167 2 153 65 -0.013 0.077 1000 -1000 -0.028 -1000
Aurora C signaling 0.0167 2 16 7 -0.006 0.027 1000 -1000 -0.008 -1000
mTOR signaling pathway 0.0167 2 155 53 -0.022 0.042 1000 -1000 -0.032 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0167 2 216 83 -0.094 0.062 1000 -1000 -0.018 -1000
Atypical NF-kappaB pathway 0.0167 2 68 31 -0.008 0.036 1000 -1000 -0.011 -1000
EPHB forward signaling 0.0167 2 199 85 -0.13 0.076 1000 -1000 -0.047 -1000
Regulation of p38-alpha and p38-beta 0.0167 2 154 54 -0.049 0.074 1000 -1000 -0.044 -1000
TCGA08_rtk_signaling 0.0167 2 64 26 -0.16 0.043 1000 -1000 -0.01 -1000
Class I PI3K signaling events 0.0167 2 165 73 -0.055 0.058 1000 -1000 -0.027 -1000
Regulation of Telomerase 0.0167 2 227 102 -0.24 0.079 1000 -1000 -0.019 -1000
S1P3 pathway 0.0167 2 91 42 -0.04 0.048 1000 -1000 -0.022 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0167 2 78 33 -0.036 0.078 1000 -1000 -0.021 -1000
Rapid glucocorticoid signaling 0.0167 2 47 20 -0.011 0.034 1000 -1000 -0.004 -1000
Visual signal transduction: Rods 0.0167 2 143 52 -0.16 0.078 1000 -1000 -0.01 -1000
Signaling events mediated by PRL 0.0167 2 99 34 -0.087 0.047 1000 -1000 -0.035 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0167 2 232 78 -0.028 0.066 1000 -1000 -0.031 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0083 1 33 28 0 0.064 1000 -1000 -0.012 -1000
Aurora A signaling 0.0083 1 73 60 -0.016 0.072 1000 -1000 -0.009 -1000
EPO signaling pathway 0.0083 1 77 55 -0.009 0.085 1000 -1000 -0.021 -1000
IFN-gamma pathway 0.0083 1 116 68 0 0.081 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class III 0.0083 1 55 40 -0.051 0.051 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class I 0.0083 1 146 104 -0.055 0.077 1000 -1000 -0.032 -1000
FoxO family signaling 0.0083 1 100 64 -0.032 0.082 1000 -1000 -0.028 -1000
Effects of Botulinum toxin 0.0083 1 39 26 -0.015 0.05 1000 -1000 -0.002 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0083 1 79 74 -0.06 0.07 1000 -1000 -0.048 -1000
Arf6 trafficking events 0.0083 1 72 71 -0.055 0.057 1000 -1000 -0.025 -1000
VEGFR1 specific signals 0.0083 1 79 56 -0.019 0.072 1000 -1000 -0.026 -1000
E-cadherin signaling in keratinocytes 0.0083 1 69 43 -0.024 0.052 1000 -1000 -0.015 -1000
S1P4 pathway 0.0083 1 40 25 0 0.049 1000 -1000 -0.017 -1000
Canonical NF-kappaB pathway 0.0000 0 31 39 -0.015 0.072 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class II 0.0000 0 61 75 -0.045 0.087 1000 -1000 -0.017 -1000
PLK2 and PLK4 events 0.0000 0 1 3 0.019 -1000 1000 -1000 -0.004 -1000
Visual signal transduction: Cones 0.0000 0 5 38 -0.007 0.072 1000 -1000 -0.006 -1000
Circadian rhythm pathway 0.0000 0 7 22 -0.012 0.065 1000 -1000 -0.024 -1000
Ephrin A reverse signaling 0.0000 0 2 7 0 0.032 1000 -1000 0 -1000
Arf6 downstream pathway 0.0000 0 22 43 -0.056 0.058 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 0.0000 0 14 32 0 0.06 1000 -1000 -0.016 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 38 68 -0.045 0.06 1000 -1000 -0.022 -1000
TRAIL signaling pathway 0.0000 0 33 48 0 0.078 1000 -1000 -0.017 -1000
S1P5 pathway 0.0000 0 5 17 -0.035 0.039 1000 -1000 -0.008 -1000
TCGA08_p53 0.0000 0 0 7 -0.007 0.027 1000 -1000 -0.008 -1000
Signaling mediated by p38-gamma and p38-delta 0.0000 0 11 15 -0.008 0.032 1000 -1000 -0.025 -1000
Syndecan-3-mediated signaling events 0.0000 0 20 35 -0.023 0.081 1000 -1000 -0.021 -1000
E-cadherin signaling in the nascent adherens junction 0.0000 0 47 76 -0.005 0.079 1000 -1000 -0.04 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 4 27 0 0.078 1000 -1000 -0.023 -1000
EGFR-dependent Endothelin signaling events 0.0000 0 12 21 -0.008 0.076 1000 -1000 -0.033 -1000
E-cadherin signaling events 0.0000 0 0 5 0.028 0.053 1000 -1000 0.018 -1000
p38 MAPK signaling pathway 0.0000 0 26 44 -0.003 0.065 1000 -1000 -0.01 -1000
Arf1 pathway 0.0000 0 16 54 -0.001 0.058 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.088 1000 -1000 0 -1000
Total NA 878 56650 7203 -20 -2000 131000 -131000 -3.1 -131000
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.39 0.44 -10000 0 -0.83 58 58
NCK1/PAK1/Dok-R -0.2 0.2 -10000 0 -0.41 56 56
NCK1/Dok-R -0.46 0.54 -10000 0 -1 58 58
PIK3CA 0.028 0.049 -10000 0 -0.5 1 1
mol:beta2-estradiol 0.095 0.12 0.23 52 -10000 0 52
RELA 0.032 0.004 -10000 0 -10000 0 0
SHC1 0.026 0.012 -10000 0 -10000 0 0
Rac/GDP 0.023 0.006 -10000 0 -10000 0 0
F2 0.11 0.13 0.26 52 -10000 0 52
TNIP2 0.032 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.44 0.52 -10000 0 -0.96 58 58
FN1 -0.058 0.2 -10000 0 -0.5 20 20
PLD2 -0.5 0.55 -10000 0 -1 58 58
PTPN11 0.032 0.007 -10000 0 -10000 0 0
GRB14 -0.046 0.19 -10000 0 -0.5 17 17
ELK1 -0.45 0.49 -10000 0 -0.94 58 58
GRB7 0.029 0.011 -10000 0 -10000 0 0
PAK1 0.032 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.49 0.53 -10000 0 -1 58 58
CDKN1A -0.27 0.28 -10000 0 -0.58 40 40
ITGA5 0.032 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.47 0.55 -10000 0 -1 58 58
CRK 0.03 0.009 -10000 0 -10000 0 0
mol:NO -0.28 0.35 0.42 2 -0.62 57 59
PLG -0.5 0.55 -10000 0 -1.1 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.38 0.42 -10000 0 -0.81 58 58
GRB2 0.03 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.069 -10000 0 -0.5 2 2
ANGPT2 -0.29 0.27 -10000 0 -0.65 34 34
BMX -0.53 0.55 -10000 0 -1.1 58 58
ANGPT1 -0.54 0.62 -10000 0 -1.2 52 52
tube development -0.31 0.32 -10000 0 -0.63 54 54
ANGPT4 -0.085 0.2 -10000 0 -0.5 23 23
response to hypoxia -0.033 0.033 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.54 0.58 -10000 0 -1.1 58 58
alpha5/beta1 Integrin 0.046 0.012 -10000 0 -10000 0 0
FGF2 0.024 0.068 -10000 0 -0.5 2 2
STAT5A (dimer) -0.33 0.37 -10000 0 -0.71 53 53
mol:L-citrulline -0.28 0.35 0.42 2 -0.62 57 59
AGTR1 -0.22 0.26 -10000 0 -0.5 56 56
MAPK14 -0.51 0.52 -10000 0 -1 59 59
Tie2/SHP2 -0.18 0.35 -10000 0 -1.1 14 14
TEK -0.21 0.38 -10000 0 -1.2 14 14
RPS6KB1 -0.37 0.43 -10000 0 -0.8 58 58
Angiotensin II/AT1 -0.16 0.19 -10000 0 -0.36 56 56
Tie2/Ang1/GRB2 -0.5 0.57 -10000 0 -1.1 58 58
MAPK3 -0.47 0.5 -10000 0 -0.97 58 58
MAPK1 -0.46 0.5 -10000 0 -0.96 58 58
Tie2/Ang1/GRB7 -0.51 0.57 -10000 0 -1.1 58 58
NFKB1 0.033 0.003 -10000 0 -10000 0 0
MAPK8 -0.51 0.56 -10000 0 -1.1 59 59
PI3K -0.45 0.5 -10000 0 -0.95 58 58
FES -0.48 0.53 -10000 0 -1 59 59
Crk/Dok-R -0.47 0.54 -10000 0 -1 58 58
Tie2/Ang1/ABIN2 -0.51 0.58 -10000 0 -1.1 58 58
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.34 0.4 -10000 0 -0.75 58 58
STAT5A 0.031 0.008 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.37 0.43 -10000 0 -0.8 58 58
Tie2/Ang2 -0.4 0.43 -10000 0 -0.84 54 54
Tie2/Ang1 -0.54 0.6 -10000 0 -1.1 58 58
FOXO1 -0.35 0.4 -10000 0 -0.75 58 58
ELF1 -0.012 0.082 -10000 0 -0.52 2 2
ELF2 -0.49 0.54 -10000 0 -1 58 58
mol:Choline -0.48 0.52 -10000 0 -1 58 58
cell migration -0.12 0.11 -10000 0 -0.23 56 56
FYN -0.35 0.36 -10000 0 -0.72 54 54
DOK2 0.032 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.24 0.26 -10000 0 -0.51 51 51
ETS1 -0.098 0.15 -10000 0 -0.26 54 54
PXN -0.3 0.36 -10000 0 -0.67 57 57
ITGB1 0.032 0.005 -10000 0 -10000 0 0
NOS3 -0.32 0.39 0.45 1 -0.71 57 58
RAC1 0.031 0.008 -10000 0 -10000 0 0
TNF -0.13 0.19 -10000 0 -0.31 55 55
MAPKKK cascade -0.48 0.52 -10000 0 -1 58 58
RASA1 0.018 0.084 -10000 0 -0.5 3 3
Tie2/Ang1/Shc -0.51 0.57 -10000 0 -1.1 58 58
NCK1 0.027 0.049 -10000 0 -0.5 1 1
vasculogenesis -0.25 0.31 0.41 2 -0.56 57 59
mol:Phosphatidic acid -0.48 0.52 -10000 0 -1 58 58
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP -0.28 0.35 0.42 2 -0.62 57 59
Rac1/GTP -0.35 0.4 -10000 0 -0.75 58 58
MMP2 -0.52 0.55 -10000 0 -1.1 58 58
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.35 0.53 -10000 0 -1.1 42 42
MKNK1 0.032 0.006 -10000 0 -10000 0 0
MAPK14 -0.094 0.19 -10000 0 -0.34 42 42
ATF2/c-Jun -0.17 0.3 -10000 0 -0.65 26 26
MAPK11 -0.091 0.19 -10000 0 -0.34 41 41
MITF -0.12 0.22 -10000 0 -0.4 42 42
MAPKAPK5 -0.11 0.21 -10000 0 -0.39 42 42
KRT8 -0.11 0.21 -10000 0 -0.38 42 42
MAPKAPK3 0.031 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.012 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.15 0.28 -10000 0 -0.5 44 44
CEBPB -0.12 0.21 -10000 0 -0.39 42 42
SLC9A1 -0.12 0.21 -10000 0 -0.39 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.13 0.24 -10000 0 -0.43 42 42
p38alpha-beta/MNK1 -0.11 0.24 -10000 0 -0.41 43 43
JUN -0.17 0.3 -10000 0 -0.64 26 26
PPARGC1A -0.14 0.22 -10000 0 -0.4 48 48
USF1 -0.12 0.2 -10000 0 -0.38 42 42
RAB5/GDP/GDI1 -0.085 0.16 -10000 0 -0.29 43 43
NOS2 -0.12 0.25 -10000 0 -0.42 41 41
DDIT3 -0.11 0.21 -10000 0 -0.39 42 42
RAB5A 0.031 0.008 -10000 0 -10000 0 0
HSPB1 -0.09 0.18 0.29 2 -0.32 40 42
p38alpha-beta/HBP1 -0.1 0.24 -10000 0 -0.41 42 42
CREB1 -0.12 0.22 -10000 0 -0.41 42 42
RAB5/GDP 0.023 0.006 -10000 0 -10000 0 0
EIF4E -0.12 0.2 -10000 0 -0.38 41 41
RPS6KA4 -0.11 0.21 -10000 0 -0.39 42 42
PLA2G4A -0.14 0.22 -10000 0 -0.41 44 44
GDI1 -0.11 0.21 -10000 0 -0.39 42 42
TP53 -0.16 0.26 -10000 0 -0.5 42 42
RPS6KA5 -0.12 0.23 -10000 0 -0.41 42 42
ESR1 -0.12 0.22 -10000 0 -0.4 43 43
HBP1 0.031 0.008 -10000 0 -10000 0 0
MEF2C -0.12 0.21 -10000 0 -0.39 42 42
MEF2A -0.12 0.22 -10000 0 -0.4 42 42
EIF4EBP1 -0.12 0.22 -10000 0 -0.41 42 42
KRT19 -0.11 0.21 -10000 0 -0.39 42 42
ELK4 -0.12 0.2 -10000 0 -0.38 42 42
ATF6 -0.12 0.2 -10000 0 -0.38 42 42
ATF1 -0.12 0.23 -10000 0 -0.42 42 42
p38alpha-beta/MAPKAPK2 -0.1 0.23 -10000 0 -0.4 42 42
p38alpha-beta/MAPKAPK3 -0.11 0.24 -10000 0 -0.41 43 43
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.12 0.24 0.5 33 -10000 0 33
PI3K Class IB/PDE3B -0.12 0.24 -10000 0 -0.5 33 33
PDE3B -0.12 0.24 -10000 0 -0.5 33 33
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.15 0.17 -10000 0 -0.29 71 71
regulation of S phase of mitotic cell cycle -0.14 0.14 -10000 0 -0.25 71 71
GNAO1 0.025 0.049 -10000 0 -0.5 1 1
HRAS 0.029 0.008 -10000 0 -10000 0 0
SHBG/T-DHT 0.018 0.009 -10000 0 -10000 0 0
PELP1 0.029 0.009 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.19 0.14 -10000 0 -0.29 66 66
T-DHT/AR -0.21 0.18 -10000 0 -0.36 70 70
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.003 -10000 0 -0.005 62 62
GNAI2 0.031 0.008 -10000 0 -10000 0 0
GNAI3 0.031 0.007 -10000 0 -10000 0 0
GNAI1 0.03 0.008 -10000 0 -10000 0 0
mol:GDP -0.25 0.2 -10000 0 -0.42 71 71
cell proliferation -0.3 0.23 0.37 1 -0.49 64 65
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
FOS -0.44 0.39 0.42 1 -0.8 63 64
mol:Ca2+ -0.029 0.024 -10000 0 -0.054 41 41
MAPK3 -0.25 0.18 0.3 1 -0.39 60 61
MAPK1 -0.16 0.16 -10000 0 -0.32 38 38
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
mol:IP3 -0.002 0.002 -10000 0 -0.004 62 62
cAMP biosynthetic process 0.022 0.03 0.11 6 -10000 0 6
GNG2 0.018 0.084 -10000 0 -0.5 3 3
potassium channel inhibitor activity -0.002 0.002 -10000 0 -0.004 62 62
HRAS/GTP -0.17 0.14 -10000 0 -0.28 69 69
actin cytoskeleton reorganization 0.038 0.057 -10000 0 -0.36 2 2
SRC 0.03 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.002 0.002 -10000 0 -0.004 62 62
PI3K 0.034 0.066 -10000 0 -0.44 2 2
apoptosis 0.28 0.24 0.48 63 -0.28 1 64
T-DHT/AR/PELP1 -0.18 0.16 -10000 0 -0.31 70 70
HRAS/GDP -0.24 0.2 -10000 0 -0.4 71 71
CREB1 -0.3 0.26 0.28 1 -0.52 63 64
RAC1-CDC42/GTP 0.049 0.061 -10000 0 -0.37 2 2
AR -0.29 0.25 -10000 0 -0.5 70 70
GNB1 0.032 0.007 -10000 0 -10000 0 0
RAF1 -0.18 0.14 -10000 0 -0.29 67 67
RAC1-CDC42/GDP -0.22 0.21 -10000 0 -0.38 71 71
T-DHT/AR/PELP1/Src -0.16 0.16 -10000 0 -0.29 69 69
MAP2K2 -0.19 0.14 -10000 0 -0.3 61 61
T-DHT/AR/PELP1/Src/PI3K -0.14 0.14 -10000 0 -0.25 71 71
GNAZ 0.029 0.01 -10000 0 -10000 0 0
SHBG 0.027 0.013 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.064 0.17 -10000 0 -0.66 7 7
mol:T-DHT 0 0.001 -10000 0 -0.002 27 27
RAC1 0.031 0.008 -10000 0 -10000 0 0
GNRH1 0.008 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.084 0.093 -10000 0 -0.29 7 7
CDC42 0.032 0.007 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.19 0.25 -9999 0 -0.53 42 42
PDGF/PDGFRA/CRKL -0.12 0.18 -9999 0 -0.37 40 40
positive regulation of JUN kinase activity -0.048 0.16 -9999 0 -0.29 33 33
CRKL 0.03 0.009 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.13 0.18 -9999 0 -0.38 42 42
AP1 -0.56 0.5 -9999 0 -1 61 61
mol:IP3 -0.15 0.18 -9999 0 -0.4 41 41
PLCG1 -0.15 0.18 -9999 0 -0.4 41 41
PDGF/PDGFRA/alphaV Integrin -0.12 0.19 -9999 0 -0.37 42 42
RAPGEF1 0.032 0.007 -9999 0 -10000 0 0
CRK 0.03 0.009 -9999 0 -10000 0 0
mol:Ca2+ -0.15 0.18 -9999 0 -0.4 41 41
CAV3 0.019 0.007 -9999 0 -10000 0 0
CAV1 0.004 0.12 -9999 0 -0.5 6 6
SHC/Grb2/SOS1 -0.048 0.16 -9999 0 -0.29 33 33
PDGF/PDGFRA/Shf -0.12 0.18 -9999 0 -0.37 40 40
FOS -0.55 0.49 -9999 0 -1 61 61
JUN -0.1 0.13 -9999 0 -0.43 16 16
oligodendrocyte development -0.12 0.19 -9999 0 -0.37 42 42
GRB2 0.03 0.009 -9999 0 -10000 0 0
PIK3R1 0.023 0.069 -9999 0 -0.5 2 2
mol:DAG -0.15 0.18 -9999 0 -0.4 41 41
PDGF/PDGFRA -0.19 0.25 -9999 0 -0.53 42 42
actin cytoskeleton reorganization -0.12 0.18 -9999 0 -0.37 40 40
SRF 0.027 0.015 -9999 0 -10000 0 0
SHC1 0.028 0.012 -9999 0 -10000 0 0
PI3K -0.078 0.18 -9999 0 -0.33 40 40
PDGF/PDGFRA/Crk/C3G -0.073 0.17 -9999 0 -0.32 40 40
JAK1 -0.13 0.18 -9999 0 -0.37 40 40
ELK1/SRF -0.12 0.14 -9999 0 -0.32 40 40
SHB 0.031 0.007 -9999 0 -10000 0 0
SHF 0.029 0.011 -9999 0 -10000 0 0
CSNK2A1 0.058 0.023 -9999 0 -10000 0 0
GO:0007205 -0.16 0.2 -9999 0 -0.43 41 41
SOS1 0.033 0.003 -9999 0 -10000 0 0
Ras protein signal transduction -0.048 0.16 -9999 0 -0.29 33 33
PDGF/PDGFRA/SHB -0.12 0.18 -9999 0 -0.38 40 40
PDGF/PDGFRA/Caveolin-1 -0.13 0.21 -9999 0 -0.42 39 39
ITGAV 0.032 0.004 -9999 0 -10000 0 0
ELK1 -0.16 0.17 -9999 0 -0.4 39 39
PIK3CA 0.027 0.049 -9999 0 -0.5 1 1
PDGF/PDGFRA/Crk -0.12 0.18 -9999 0 -0.37 42 42
JAK-STAT cascade -0.13 0.17 -9999 0 -0.37 40 40
cell proliferation -0.12 0.18 -9999 0 -0.37 40 40
Endothelins

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
AKT1 -0.14 0.25 0.23 1 -0.43 43 44
PTK2B 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.28 -10000 0 -0.63 22 22
EDN1 -0.081 0.18 -10000 0 -0.32 34 34
EDN3 -0.045 0.17 -10000 0 -0.5 15 15
EDN2 0.028 0.012 -10000 0 -10000 0 0
HRAS/GDP -0.18 0.21 -10000 0 -0.41 43 43
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.096 0.16 -10000 0 -0.34 28 28
ADCY4 -0.12 0.22 -10000 0 -0.4 39 39
ADCY5 -0.21 0.28 -10000 0 -0.46 56 56
ADCY6 -0.12 0.22 -10000 0 -0.41 38 38
ADCY7 -0.12 0.22 -10000 0 -0.42 36 36
ADCY1 -0.13 0.22 -10000 0 -0.4 39 39
ADCY2 -0.15 0.22 -10000 0 -0.42 41 41
ADCY3 -0.12 0.23 -10000 0 -0.4 40 40
ADCY8 -0.13 0.22 -10000 0 -0.42 37 37
ADCY9 -0.12 0.22 -10000 0 -0.4 39 39
arachidonic acid secretion -0.29 0.33 0.36 3 -0.54 67 70
ETB receptor/Endothelin-1/Gq/GTP -0.069 0.14 -10000 0 -0.4 14 14
GNAO1 0.025 0.049 -10000 0 -0.5 1 1
HRAS 0.029 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.12 0.24 0.31 1 -0.4 43 44
ETA receptor/Endothelin-1/Gs/GTP -0.13 0.23 0.29 1 -0.39 47 48
mol:GTP -0.004 0.008 -10000 0 -10000 0 0
COL3A1 -0.22 0.36 -10000 0 -0.71 39 39
EDNRB -0.003 0.11 -10000 0 -0.53 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.21 0.35 -10000 0 -0.64 42 42
CYSLTR1 -0.14 0.25 -10000 0 -0.49 33 33
SLC9A1 -0.069 0.13 -10000 0 -0.27 30 30
mol:GDP -0.19 0.23 0.41 1 -0.44 44 45
SLC9A3 -0.16 0.3 -10000 0 -0.82 15 15
RAF1 -0.25 0.27 0.35 1 -0.47 63 64
JUN -0.21 0.42 -10000 0 -1 23 23
JAK2 -0.14 0.24 0.23 1 -0.43 43 44
mol:IP3 -0.1 0.17 -10000 0 -0.4 20 20
ETA receptor/Endothelin-1 -0.16 0.28 0.39 1 -0.5 43 44
PLCB1 0.024 0.049 -10000 0 -0.5 1 1
PLCB2 0.021 0.049 -10000 0 -0.5 1 1
ETA receptor/Endothelin-3 -0.088 0.15 -10000 0 -0.28 35 35
FOS -0.49 0.48 0.38 2 -0.93 64 66
Gai/GDP -0.057 0.23 -10000 0 -0.68 13 13
CRK 0.03 0.009 -10000 0 -10000 0 0
mol:Ca ++ -0.19 0.29 0.3 1 -0.56 40 41
BCAR1 0.03 0.01 -10000 0 -10000 0 0
PRKCB1 -0.11 0.18 -10000 0 -0.41 20 20
GNAQ 0.02 0.022 -10000 0 -10000 0 0
GNAZ 0.03 0.01 -10000 0 -10000 0 0
GNAL 0 0.12 -10000 0 -0.5 7 7
Gs family/GDP -0.18 0.21 0.38 1 -0.41 44 45
ETA receptor/Endothelin-1/Gq/GTP -0.1 0.18 -10000 0 -0.34 35 35
MAPK14 -0.06 0.13 -10000 0 -0.38 11 11
TRPC6 -0.15 0.29 -10000 0 -0.7 18 18
GNAI2 0.031 0.008 -10000 0 -10000 0 0
GNAI3 0.032 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.064 0.14 -10000 0 -0.4 11 11
ETB receptor/Endothelin-2 0.014 0.08 -10000 0 -0.36 4 4
ETB receptor/Endothelin-3 -0.044 0.16 -10000 0 -0.41 17 17
ETB receptor/Endothelin-1 -0.067 0.17 -10000 0 -0.31 32 32
MAPK3 -0.43 0.43 0.36 2 -0.8 66 68
MAPK1 -0.45 0.45 0.4 2 -0.82 66 68
Rac1/GDP -0.18 0.21 -10000 0 -0.42 42 42
cAMP biosynthetic process -0.15 0.24 -10000 0 -0.44 41 41
MAPK8 -0.17 0.33 -10000 0 -0.69 27 27
SRC 0.032 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.03 0.088 -10000 0 -0.28 7 7
p130Cas/CRK/Src/PYK2 -0.18 0.24 0.35 1 -0.5 32 33
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.18 0.21 -10000 0 -0.42 42 42
COL1A2 -0.2 0.37 -10000 0 -0.75 33 33
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.04 0.1 -10000 0 -0.2 25 25
mol:DAG -0.1 0.17 -10000 0 -0.4 20 20
MAP2K2 -0.34 0.35 0.46 2 -0.62 66 68
MAP2K1 -0.33 0.33 0.35 2 -0.61 66 68
EDNRA -0.072 0.14 -10000 0 -0.26 35 35
positive regulation of muscle contraction -0.12 0.22 0.22 2 -0.42 35 37
Gq family/GDP -0.17 0.22 -10000 0 -0.42 37 37
HRAS/GTP -0.18 0.22 0.36 1 -0.41 46 47
PRKCH -0.11 0.17 -10000 0 -0.42 19 19
RAC1 0.031 0.008 -10000 0 -10000 0 0
PRKCA -0.1 0.17 0.25 1 -0.41 18 19
PRKCB -0.13 0.18 -10000 0 -0.4 23 23
PRKCE -0.11 0.17 -10000 0 -0.41 20 20
PRKCD -0.11 0.17 -10000 0 -0.42 17 17
PRKCG -0.16 0.18 -10000 0 -0.4 31 31
regulation of vascular smooth muscle contraction -0.58 0.57 0.46 1 -1.1 63 64
PRKCQ -0.12 0.18 -10000 0 -0.43 22 22
PLA2G4A -0.32 0.37 0.39 2 -0.6 67 69
GNA14 0.007 0.085 -10000 0 -0.5 3 3
GNA15 0.023 0.02 -10000 0 -10000 0 0
GNA12 0.031 0.008 -10000 0 -10000 0 0
GNA11 -0.004 0.12 -10000 0 -0.5 6 6
Rac1/GTP -0.12 0.24 0.31 1 -0.4 43 44
MMP1 0.059 0.13 0.23 18 -0.86 1 19
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.49 0.6 -10000 0 -1.2 42 42
STAT6 (cleaved dimer) -0.57 0.6 -10000 0 -1.2 48 48
IGHG1 -0.13 0.2 -10000 0 -0.35 22 22
IGHG3 -0.48 0.57 -10000 0 -1.1 47 47
AKT1 -0.26 0.37 -10000 0 -0.74 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.36 -10000 0 -0.77 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.38 -10000 0 -0.8 23 23
THY1 -0.53 0.62 -10000 0 -1.2 45 45
MYB -0.047 0.18 -10000 0 -0.5 17 17
HMGA1 0.03 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.36 0.43 -10000 0 -0.74 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.26 0.38 -10000 0 -0.78 24 24
SP1 0.017 0.052 -10000 0 -0.2 1 1
INPP5D 0.032 0.006 -10000 0 -10000 0 0
SOCS5 0.043 0.036 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.61 -10000 0 -1.2 49 49
SOCS1 -0.34 0.38 -10000 0 -0.71 50 50
SOCS3 -0.31 0.39 -10000 0 -0.84 28 28
FCER2 -0.87 0.75 -10000 0 -1.4 76 76
PARP14 0.008 0.036 -10000 0 -10000 0 0
CCL17 -0.55 0.66 -10000 0 -1.3 45 45
GRB2 0.03 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.18 0.3 0.46 2 -0.66 16 18
T cell proliferation -0.52 0.62 -10000 0 -1.2 48 48
IL4R/JAK1 -0.51 0.6 -10000 0 -1.2 44 44
EGR2 -0.63 0.65 -10000 0 -1.3 51 51
JAK2 -0.02 0.058 -10000 0 -10000 0 0
JAK3 0.013 0.054 -10000 0 -0.48 1 1
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
JAK1 0.004 0.034 -10000 0 -10000 0 0
COL1A2 -0.3 0.53 -10000 0 -1.4 20 20
CCL26 -0.51 0.63 0.82 1 -1.2 44 45
IL4R -0.53 0.65 -10000 0 -1.2 44 44
PTPN6 0.036 0.026 -10000 0 -10000 0 0
IL13RA2 -0.52 0.64 0.82 1 -1.2 44 45
IL13RA1 -0.021 0.058 -10000 0 -10000 0 0
IRF4 -0.49 0.65 -10000 0 -1.3 42 42
ARG1 -0.11 0.21 -10000 0 -0.82 4 4
CBL -0.34 0.41 -10000 0 -0.71 51 51
GTF3A 0.027 0.039 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
IL13RA1/JAK2 -0.02 0.083 -10000 0 -10000 0 0
IRF4/BCL6 -0.41 0.6 -10000 0 -1.2 42 42
CD40LG -0.07 0.18 -10000 0 -0.51 16 16
MAPK14 -0.34 0.4 -10000 0 -0.73 47 47
mitosis -0.25 0.34 -10000 0 -0.69 28 28
STAT6 -0.59 0.74 -10000 0 -1.4 47 47
SPI1 0.037 0.008 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.32 -10000 0 -0.66 26 26
STAT6 (dimer) -0.59 0.74 -10000 0 -1.4 46 46
STAT6 (dimer)/PARP14 -0.61 0.66 -10000 0 -1.2 53 53
mast cell activation 0.011 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.39 -10000 0 -0.76 27 27
FRAP1 -0.26 0.37 -10000 0 -0.74 28 28
LTA -0.51 0.61 -10000 0 -1.2 42 42
FES 0.031 0.007 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.56 0.7 1.3 46 -10000 0 46
CCL11 -0.47 0.57 -10000 0 -1.1 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.39 -10000 0 -0.79 25 25
IL2RG -0.003 0.11 -10000 0 -0.49 5 5
IL10 -0.47 0.62 0.79 2 -1.2 41 43
IRS1 0.01 0.11 -10000 0 -0.5 5 5
IRS2 0.027 0.049 -10000 0 -0.5 1 1
IL4 -0.081 0.19 -10000 0 -1.3 1 1
IL5 -0.5 0.6 -10000 0 -1.2 42 42
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.46 -10000 0 -0.86 45 45
COL1A1 -0.24 0.47 -10000 0 -1.3 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.52 0.62 -10000 0 -1.2 42 42
IL2R gamma/JAK3 0.007 0.088 -10000 0 -0.36 5 5
TFF3 -0.51 0.62 0.77 1 -1.2 43 44
ALOX15 -0.54 0.65 -10000 0 -1.3 44 44
MYBL1 0.032 0.007 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.44 0.53 -10000 0 -0.98 45 45
SHC1 0.028 0.012 -10000 0 -10000 0 0
CEBPB 0.036 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.38 0.48 1 -0.8 22 23
mol:PI-3-4-5-P3 -0.26 0.37 -10000 0 -0.74 28 28
PI3K -0.28 0.4 -10000 0 -0.81 28 28
DOK2 0.032 0.007 -10000 0 -10000 0 0
ETS1 0.021 0.086 -10000 0 -0.46 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.27 0.44 2 -0.64 14 16
ITGB3 -0.63 0.69 -10000 0 -1.3 53 53
PIGR -0.5 0.66 0.79 2 -1.3 42 44
IGHE 0.016 0.071 0.16 2 -0.26 3 5
MAPKKK cascade -0.17 0.27 0.44 2 -0.62 14 16
BCL6 0.038 0.014 -10000 0 -10000 0 0
OPRM1 -0.5 0.6 -10000 0 -1.2 43 43
RETNLB -0.5 0.6 -10000 0 -1.2 44 44
SELP -0.64 0.77 0.79 2 -1.4 51 53
AICDA -0.59 0.66 -10000 0 -1.3 51 51
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.087 0.19 0.37 36 -10000 0 36
KIRREL -0.12 0.24 -10000 0 -0.51 33 33
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.087 0.19 -10000 0 -0.37 36 36
PLCG1 0.032 0.006 -10000 0 -10000 0 0
ARRB2 0.03 0.009 -10000 0 -10000 0 0
WASL 0.03 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.046 0.16 -10000 0 -0.28 36 36
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.059 0.13 -10000 0 -0.25 35 35
FYN -0.05 0.16 0.3 8 -0.26 36 44
mol:Ca2+ -0.045 0.15 -10000 0 -0.28 36 36
mol:DAG -0.045 0.16 -10000 0 -0.28 36 36
NPHS2 -0.009 0.039 -10000 0 -10000 0 0
mol:IP3 -0.045 0.16 -10000 0 -0.28 36 36
regulation of endocytosis -0.042 0.14 -10000 0 -0.25 36 36
Nephrin/NEPH1/podocin/Cholesterol -0.056 0.15 -10000 0 -0.28 36 36
establishment of cell polarity -0.087 0.19 -10000 0 -0.37 36 36
Nephrin/NEPH1/podocin/NCK1-2 -0.033 0.16 -10000 0 -0.26 35 35
Nephrin/NEPH1/beta Arrestin2 -0.042 0.14 -10000 0 -0.25 36 36
NPHS1 -0.013 0.11 -10000 0 -0.45 6 6
Nephrin/NEPH1/podocin -0.052 0.14 -10000 0 -0.26 36 36
TJP1 0.032 0.007 -10000 0 -10000 0 0
NCK1 0.027 0.049 -10000 0 -0.5 1 1
NCK2 0.033 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.044 0.16 -10000 0 -0.28 36 36
CD2AP 0.03 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.044 0.15 -10000 0 -0.28 35 35
GRB2 0.03 0.009 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.054 0.15 0.33 6 -0.26 37 43
cytoskeleton organization -0.074 0.14 -10000 0 -0.29 35 35
Nephrin/NEPH1 -0.058 0.13 -10000 0 -0.26 36 36
Nephrin/NEPH1/ZO-1 -0.057 0.16 -10000 0 -0.3 36 36
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.035 0.055 -10000 0 -0.36 2 2
VLDLR -0.036 0.18 -10000 0 -0.5 15 15
CRKL 0.03 0.009 -10000 0 -10000 0 0
LRPAP1 0.032 0.004 -10000 0 -10000 0 0
FYN 0.029 0.01 -10000 0 -10000 0 0
ITGA3 0.029 0.011 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.14 0.2 -10000 0 -0.34 58 58
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.085 -10000 0 -0.27 6 6
AKT1 -0.12 0.16 -10000 0 -0.26 58 58
MAP2K7 0.032 0.007 -10000 0 -10000 0 0
RAPGEF1 0.032 0.007 -10000 0 -10000 0 0
DAB1 0.024 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.088 0.16 -10000 0 -0.28 49 49
LRPAP1/LRP8 0.047 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.073 0.16 -10000 0 -0.26 49 49
DAB1/alpha3/beta1 Integrin -0.1 0.17 -10000 0 -0.28 52 52
long-term memory -0.11 0.19 -10000 0 -0.3 53 53
DAB1/LIS1 -0.1 0.18 -10000 0 -0.28 56 56
DAB1/CRLK/C3G -0.1 0.18 -10000 0 -0.28 56 56
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
DAB1/NCK2 -0.1 0.19 -10000 0 -0.29 56 56
ARHGEF2 0.028 0.012 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.051 0.19 -10000 0 -0.5 18 18
CDK5R1 0.021 0.069 -10000 0 -0.5 2 2
RELN -0.19 0.26 -10000 0 -0.5 49 49
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
RELN/LRP8/Fyn -0.095 0.18 -10000 0 -0.31 49 49
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.2 -10000 0 -0.3 56 56
MAPK8 0.001 0.12 -10000 0 -0.5 7 7
RELN/VLDLR/DAB1 -0.13 0.18 -10000 0 -0.31 58 58
ITGB1 0.032 0.005 -10000 0 -10000 0 0
MAP1B -0.14 0.19 0.22 1 -0.31 59 60
RELN/LRP8 -0.095 0.18 -10000 0 -0.31 49 49
GRIN2B/RELN/LRP8/DAB1/Fyn -0.068 0.17 -10000 0 -0.27 48 48
PI3K 0.036 0.075 -10000 0 -0.51 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.042 0.017 -10000 0 -10000 0 0
RAP1A -0.12 0.18 0.36 5 -0.3 30 35
PAFAH1B1 0.03 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.032 0.007 -10000 0 -10000 0 0
CRLK/C3G 0.044 0.015 -10000 0 -10000 0 0
GRIN2B 0.019 0.007 -10000 0 -10000 0 0
NCK2 0.033 0.003 -10000 0 -10000 0 0
neuron differentiation -0.061 0.13 -10000 0 -0.44 5 5
neuron adhesion -0.1 0.18 0.44 4 -0.43 7 11
LRP8 0.032 0.006 -10000 0 -10000 0 0
GSK3B -0.12 0.15 -10000 0 -0.26 56 56
RELN/VLDLR/DAB1/Fyn -0.11 0.18 -10000 0 -0.29 58 58
MAP3K11 0.032 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.12 0.17 -10000 0 -0.28 58 58
CDK5 0.03 0.009 -10000 0 -10000 0 0
MAPT 0.058 0.19 0.86 6 -10000 0 6
neuron migration -0.14 0.18 0.34 1 -0.33 49 50
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.061 0.13 -10000 0 -0.45 5 5
RELN/VLDLR -0.12 0.2 -10000 0 -0.31 58 58
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.31 -10000 0 -0.56 30 30
HDAC7 0.033 0.007 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.11 0.27 -10000 0 -0.58 10 10
SMAD4 0.032 0.007 -10000 0 -10000 0 0
ID2 -0.13 0.35 0.67 1 -0.57 29 30
AP1 -0.2 0.25 -10000 0 -0.42 63 63
ABCG2 -0.14 0.36 0.67 1 -0.57 30 31
HIF1A -0.028 0.1 -10000 0 -0.42 2 2
TFF3 -0.17 0.32 -10000 0 -0.57 30 30
GATA2 0.008 0.11 -10000 0 -0.5 5 5
AKT1 -0.021 0.087 -10000 0 -0.2 1 1
response to hypoxia -0.037 0.079 0.17 1 -0.22 6 7
MCL1 -0.17 0.3 -10000 0 -0.57 28 28
NDRG1 -0.15 0.34 -10000 0 -0.56 30 30
SERPINE1 -0.16 0.33 -10000 0 -0.56 30 30
FECH -0.15 0.34 -10000 0 -0.6 21 21
FURIN -0.14 0.34 -10000 0 -0.56 29 29
NCOA2 -0.14 0.25 -10000 0 -0.5 38 38
EP300 -0.006 0.11 0.29 1 -0.28 4 5
HMOX1 -0.14 0.35 0.67 1 -0.56 30 31
BHLHE40 -0.15 0.34 0.67 1 -0.56 30 31
BHLHE41 -0.15 0.33 -10000 0 -0.56 30 30
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.007 0.12 -10000 0 -0.46 1 1
ENG 0.003 0.13 0.38 3 -0.42 1 4
JUN -0.04 0.18 -10000 0 -0.5 16 16
RORA -0.14 0.34 -10000 0 -0.57 29 29
ABCB1 -0.032 0.067 -10000 0 -10000 0 0
TFRC -0.14 0.35 0.67 1 -0.57 29 30
CXCR4 -0.14 0.36 0.67 1 -0.58 31 32
TF -0.29 0.41 0.67 1 -0.64 55 56
CITED2 -0.16 0.33 -10000 0 -0.57 30 30
HIF1A/ARNT -0.19 0.34 -10000 0 -0.82 10 10
LDHA -0.014 0.1 -10000 0 -0.67 2 2
ETS1 -0.14 0.35 0.67 1 -0.57 30 31
PGK1 -0.13 0.36 0.67 1 -0.56 30 31
NOS2 -0.16 0.32 -10000 0 -0.58 27 27
ITGB2 -0.15 0.34 -10000 0 -0.57 29 29
ALDOA -0.14 0.35 0.67 1 -0.56 30 31
Cbp/p300/CITED2 -0.15 0.32 -10000 0 -0.71 11 11
FOS -0.24 0.26 -10000 0 -0.5 60 60
HK2 -0.13 0.35 0.67 1 -0.57 29 30
SP1 0.038 0.008 -10000 0 -10000 0 0
GCK -0.004 0.14 -10000 0 -10000 0 0
HK1 -0.14 0.35 0.67 1 -0.56 30 31
NPM1 -0.13 0.36 0.67 1 -0.56 30 31
EGLN1 -0.17 0.3 -10000 0 -0.57 28 28
CREB1 0.039 0.004 -10000 0 -10000 0 0
PGM1 -0.14 0.35 0.67 1 -0.57 29 30
SMAD3 0.032 0.007 -10000 0 -10000 0 0
EDN1 -0.14 0.26 -10000 0 -0.78 11 11
IGFBP1 -0.16 0.32 -10000 0 -0.57 29 29
VEGFA -0.09 0.25 -10000 0 -0.52 10 10
HIF1A/JAB1 -0.009 0.082 -10000 0 -0.48 1 1
CP -0.24 0.4 0.66 1 -0.64 45 46
CXCL12 -0.15 0.36 0.67 1 -0.59 33 34
COPS5 0.033 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.047 0.013 -10000 0 -10000 0 0
BNIP3 -0.14 0.35 0.67 1 -0.56 30 31
EGLN3 -0.16 0.36 -10000 0 -0.57 34 34
CA9 -0.18 0.3 -10000 0 -0.57 29 29
TERT -0.15 0.35 0.67 1 -0.58 30 31
ENO1 -0.14 0.35 0.67 1 -0.56 30 31
PFKL -0.15 0.34 -10000 0 -0.57 29 29
NCOA1 0.033 0.003 -10000 0 -10000 0 0
ADM -0.16 0.38 0.67 1 -0.61 33 34
ARNT -0.029 0.073 -10000 0 -10000 0 0
HNF4A 0.021 0.005 -10000 0 -10000 0 0
ADFP -0.18 0.31 -10000 0 -0.56 30 30
SLC2A1 -0.086 0.26 0.57 1 -0.52 10 11
LEP -0.26 0.39 -10000 0 -0.65 44 44
HIF1A/ARNT/Cbp/p300 -0.12 0.27 -10000 0 -0.59 11 11
EPO -0.18 0.31 -10000 0 -0.66 25 25
CREBBP -0.004 0.094 0.29 1 -0.34 1 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.11 0.27 -10000 0 -0.58 10 10
PFKFB3 -0.18 0.39 0.67 1 -0.64 35 36
NT5E -0.18 0.36 -10000 0 -0.65 30 30
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.002 0.036 0.17 1 -10000 0 1
NFATC2 -0.098 0.16 -10000 0 -0.33 37 37
NFATC3 -0.002 0.029 -10000 0 -10000 0 0
CD40LG -0.3 0.32 0.42 2 -0.57 60 62
PTGS2 -0.35 0.36 -10000 0 -0.71 53 53
JUNB 0.032 0.007 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.024 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.024 -10000 0 -10000 0 0
CALM1 0.03 0.012 -10000 0 -10000 0 0
JUN -0.043 0.18 -10000 0 -0.51 16 16
mol:Ca2+ -0.005 0.011 -10000 0 -0.1 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.021 0.006 -10000 0 -10000 0 0
FOSL1 0.031 0.007 -10000 0 -10000 0 0
CREM 0.032 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.13 0.22 0.33 1 -0.44 29 30
FOS -0.24 0.27 -10000 0 -0.51 60 60
IFNG -0.29 0.29 0.37 1 -0.58 51 52
AP-1/NFAT1-c-4 -0.34 0.37 -10000 0 -0.68 53 53
FASLG -0.3 0.3 -10000 0 -0.59 51 51
NFAT1-c-4/ICER1 -0.091 0.16 0.26 1 -0.3 37 38
IL2RA -0.28 0.36 0.48 5 -0.62 51 56
FKBP12/FK506 0.024 0.004 -10000 0 -10000 0 0
CSF2 -0.27 0.32 0.49 3 -0.58 51 54
JunB/Fra1/NFAT1-c-4 -0.078 0.16 -10000 0 -0.3 35 35
IL4 -0.28 0.3 0.41 2 -0.57 51 53
IL2 0.014 0.017 -10000 0 -10000 0 0
IL3 -0.01 0.057 -10000 0 -10000 0 0
FKBP1A 0.032 0.006 -10000 0 -10000 0 0
BATF3 0.027 0.012 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.013 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.068 0.2 -10000 0 -0.4 26 26
NFATC2 -0.16 0.3 -10000 0 -0.52 43 43
NFATC3 0.023 0.093 -10000 0 -0.28 5 5
CD40LG -0.39 0.41 -10000 0 -0.88 39 39
ITCH -0.016 0.11 -10000 0 -0.24 24 24
CBLB -0.017 0.11 -10000 0 -0.24 24 24
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.49 0.58 -10000 0 -1.1 51 51
JUNB 0.032 0.007 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.023 0.13 -10000 0 -0.28 24 24
T cell anergy -0.075 0.19 0.48 1 -0.41 24 25
TLE4 -0.12 0.21 0.34 1 -0.43 22 23
Jun/NFAT1-c-4/p21SNFT -0.19 0.35 -10000 0 -0.76 25 25
AP-1/NFAT1-c-4 -0.42 0.48 -10000 0 -0.99 39 39
IKZF1 -0.15 0.28 0.35 2 -0.52 32 34
T-helper 2 cell differentiation -0.2 0.33 -10000 0 -0.66 31 31
AP-1/NFAT1 -0.3 0.33 0.33 1 -0.57 60 61
CALM1 0.001 0.087 -10000 0 -10000 0 0
EGR2 -0.18 0.39 -10000 0 -1.1 13 13
EGR3 -0.18 0.38 -10000 0 -1.1 13 13
NFAT1/FOXP3 -0.18 0.3 -10000 0 -0.53 39 39
EGR1 -0.078 0.21 -10000 0 -0.5 24 24
JUN -0.057 0.18 -10000 0 -0.49 17 17
EGR4 0.025 0.019 -10000 0 -10000 0 0
mol:Ca2+ -0.025 0.07 -10000 0 -0.16 24 24
GBP3 -0.12 0.21 -10000 0 -0.44 20 20
FOSL1 0.031 0.007 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.19 0.35 -10000 0 -0.76 24 24
DGKA -0.13 0.24 -10000 0 -0.5 23 23
CREM 0.032 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.19 0.34 -10000 0 -0.85 18 18
CTLA4 -0.24 0.35 -10000 0 -0.68 40 40
NFAT1-c-4 (dimer)/EGR1 -0.2 0.37 -10000 0 -0.84 22 22
NFAT1-c-4 (dimer)/EGR4 -0.15 0.33 -10000 0 -0.89 14 14
FOS -0.25 0.27 -10000 0 -0.51 60 60
IFNG -0.17 0.26 -10000 0 -0.57 22 22
T cell activation -0.17 0.26 -10000 0 -0.69 13 13
MAF 0.03 0.01 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.098 0.22 0.63 12 -10000 0 12
TNF -0.23 0.35 -10000 0 -0.78 27 27
FASLG -0.24 0.47 -10000 0 -1.3 18 18
TBX21 0.037 0.016 -10000 0 -10000 0 0
BATF3 0.028 0.012 -10000 0 -10000 0 0
PRKCQ 0.002 0.12 -10000 0 -0.5 6 6
PTPN1 -0.11 0.21 -10000 0 -0.44 20 20
NFAT1-c-4/ICER1 -0.15 0.33 -10000 0 -0.88 14 14
GATA3 0.017 0.097 -10000 0 -0.5 4 4
T-helper 1 cell differentiation -0.16 0.25 -10000 0 -0.56 23 23
IL2RA -0.4 0.5 -10000 0 -0.94 46 46
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.12 0.21 -10000 0 -0.42 25 25
E2F1 0.027 0.069 -10000 0 -0.5 2 2
PPARG -0.05 0.19 -10000 0 -0.5 18 18
SLC3A2 -0.12 0.21 -10000 0 -0.44 20 20
IRF4 -0.083 0.22 -10000 0 -0.5 25 25
PTGS2 -0.44 0.45 -10000 0 -0.88 54 54
CSF2 -0.36 0.4 -10000 0 -0.86 38 38
JunB/Fra1/NFAT1-c-4 -0.13 0.32 -10000 0 -0.87 13 13
IL4 -0.2 0.34 -10000 0 -0.7 28 28
IL5 -0.37 0.4 -10000 0 -0.86 38 38
IL2 -0.17 0.26 -10000 0 -0.71 12 12
IL3 -0.05 0.071 -10000 0 -10000 0 0
RNF128 -0.095 0.25 -10000 0 -0.6 24 24
NFATC1 -0.098 0.22 -10000 0 -0.64 12 12
CDK4 0.11 0.18 0.53 8 -10000 0 8
PTPRK -0.12 0.2 -10000 0 -0.44 20 20
IL8 -0.38 0.41 -10000 0 -0.87 39 39
POU2F1 0.027 0.013 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 -0.002 0.12 -10000 0 -0.5 7 7
GNB1/GNG2 -0.092 0.089 -10000 0 -0.19 53 53
AKT1 -0.072 0.12 0.3 2 -0.26 2 4
EGF 0.025 0.011 -10000 0 -10000 0 0
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR -0.01 0.083 0.33 2 -10000 0 2
mol:Ca2+ -0.12 0.17 0.37 1 -0.29 53 54
LYN -0.011 0.082 0.33 2 -10000 0 2
RhoA/GTP -0.055 0.071 -10000 0 -0.13 47 47
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.14 0.2 0.4 3 -0.34 52 55
GNG2 0.018 0.084 -10000 0 -0.5 3 3
ARRB2 0.03 0.009 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.005 0.13 0.31 2 -0.43 7 9
G beta5/gamma2 -0.11 0.13 -10000 0 -0.25 53 53
PRKCH -0.14 0.19 0.34 2 -0.34 52 54
DNM1 0.009 0.11 -10000 0 -0.5 5 5
TXA2/TP beta/beta Arrestin3 -0.002 0.058 -10000 0 -0.4 1 1
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
PTGDR 0 0.12 -10000 0 -0.5 7 7
G12 family/GTP -0.13 0.16 -10000 0 -0.3 50 50
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
ADRBK2 0.03 0.009 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.04 0.013 -10000 0 -10000 0 0
mol:GDP 0.076 0.14 0.31 16 -0.35 1 17
mol:NADP 0.03 0.009 -10000 0 -10000 0 0
RAB11A 0.032 0.007 -10000 0 -10000 0 0
PRKG1 -0.045 0.19 -10000 0 -0.5 17 17
mol:IP3 -0.16 0.2 0.39 1 -0.37 53 54
cell morphogenesis 0.039 0.013 -10000 0 -10000 0 0
PLCB2 -0.22 0.27 0.42 1 -0.5 53 54
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.039 0.11 0.33 2 -0.24 13 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.01 0.083 0.33 2 -10000 0 2
RHOA 0.031 0.008 -10000 0 -10000 0 0
PTGIR -0.006 0.13 -10000 0 -0.5 8 8
PRKCB1 -0.16 0.2 0.36 1 -0.37 52 53
GNAQ 0.031 0.007 -10000 0 -10000 0 0
mol:L-citrulline 0.03 0.009 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.23 0.28 0.41 1 -0.52 52 53
LCK -0.022 0.098 0.33 2 -0.27 5 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.008 0.086 -10000 0 -0.22 14 14
TXA2-R family/G12 family/GDP/G beta/gamma 0.02 0.082 -10000 0 -0.45 3 3
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.085 -10000 0 -0.21 14 14
MAPK14 -0.092 0.14 0.34 3 -0.23 52 55
TGM2/GTP -0.18 0.23 0.41 1 -0.42 53 54
MAPK11 -0.091 0.14 0.34 3 -0.23 51 54
ARHGEF1 -0.077 0.095 -10000 0 -0.18 50 50
GNAI2 0.031 0.008 -10000 0 -10000 0 0
JNK cascade -0.16 0.21 0.39 1 -0.38 52 53
RAB11/GDP 0.032 0.007 -10000 0 -10000 0 0
ICAM1 -0.12 0.16 0.32 1 -0.28 51 52
cAMP biosynthetic process -0.15 0.19 0.38 1 -0.35 54 55
Gq family/GTP/EBP50 0.007 0.071 0.24 2 -0.22 6 8
actin cytoskeleton reorganization 0.039 0.013 -10000 0 -10000 0 0
SRC -0.009 0.083 0.33 2 -10000 0 2
GNB5 0.031 0.007 -10000 0 -10000 0 0
GNB1 0.032 0.007 -10000 0 -10000 0 0
EGF/EGFR -0.015 0.099 0.3 3 -0.25 7 10
VCAM1 -0.12 0.16 0.33 1 -0.29 50 51
TP beta/Gq family/GDP/G beta5/gamma2 -0.005 0.13 0.31 2 -0.43 7 9
platelet activation -0.12 0.18 0.42 3 -0.3 51 54
PGI2/IP -0.004 0.096 -10000 0 -0.36 8 8
PRKACA -0.01 0.088 -10000 0 -0.25 14 14
Gq family/GDP/G beta5/gamma2 -0.008 0.12 0.28 1 -0.4 7 8
TXA2/TP beta/beta Arrestin2 -0.018 0.11 -10000 0 -0.47 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.017 0.082 -10000 0 -0.24 14 14
mol:DAG -0.17 0.22 0.4 1 -0.41 52 53
EGFR 0.026 0.049 -10000 0 -0.5 1 1
TXA2/TP alpha -0.21 0.26 0.44 1 -0.47 54 55
Gq family/GTP 0 0.062 0.22 1 -0.19 10 11
YES1 -0.005 0.1 0.44 3 -10000 0 3
GNAI2/GTP 0 0.078 -10000 0 -0.21 11 11
PGD2/DP 0 0.09 -10000 0 -0.36 7 7
SLC9A3R1 0.031 0.008 -10000 0 -10000 0 0
FYN -0.007 0.1 0.44 3 -10000 0 3
mol:NO 0.03 0.009 -10000 0 -10000 0 0
GNA15 0.032 0.007 -10000 0 -10000 0 0
PGK/cGMP -0.009 0.12 -10000 0 -0.31 16 16
RhoA/GDP 0.032 0.008 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.008 0.12 -10000 0 -0.22 21 21
NOS3 0.03 0.009 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
PRKCA -0.14 0.19 0.36 1 -0.35 50 51
PRKCB -0.16 0.2 0.35 1 -0.36 53 54
PRKCE -0.14 0.19 0.36 1 -0.35 52 53
PRKCD -0.16 0.2 0.36 1 -0.37 52 53
PRKCG -0.18 0.22 0.4 1 -0.4 52 53
muscle contraction -0.21 0.26 0.44 1 -0.48 52 53
PRKCZ -0.14 0.19 0.36 1 -0.34 52 53
ARR3 0.023 0.007 -10000 0 -10000 0 0
TXA2/TP beta 0.012 0.09 -10000 0 -0.22 14 14
PRKCQ -0.16 0.2 0.36 1 -0.35 54 55
MAPKKK cascade -0.19 0.24 0.39 1 -0.44 52 53
SELE -0.17 0.21 0.33 1 -0.39 52 53
TP beta/GNAI2/GDP/G beta/gamma 0.023 0.1 -10000 0 -0.22 15 15
ROCK1 0.031 0.007 -10000 0 -10000 0 0
GNA14 0.018 0.084 -10000 0 -0.5 3 3
chemotaxis -0.26 0.32 0.41 1 -0.6 52 53
GNA12 0.031 0.008 -10000 0 -10000 0 0
GNA13 0.031 0.008 -10000 0 -10000 0 0
GNA11 0.005 0.12 -10000 0 -0.5 6 6
Rac1/GTP 0.022 0.006 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.19 0.28 -10000 0 -0.55 43 43
IHH -0.023 0.086 -10000 0 -0.16 4 4
SHH Np/Cholesterol/GAS1 0.017 0.042 -10000 0 -0.29 2 2
LRPAP1 0.032 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.017 0.042 0.28 2 -10000 0 2
SMO/beta Arrestin2 -0.082 0.17 -10000 0 -0.3 42 42
SMO -0.094 0.17 -10000 0 -0.31 43 43
AKT1 -0.022 0.1 -10000 0 -0.49 2 2
ARRB2 0.03 0.009 -10000 0 -10000 0 0
BOC 0.014 0.096 -10000 0 -0.5 4 4
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
heart looping -0.093 0.17 -10000 0 -0.31 43 43
STIL -0.067 0.15 0.3 1 -0.24 42 43
DHH N/PTCH2 0.02 0.097 -10000 0 -0.36 7 7
DHH N/PTCH1 -0.089 0.19 -10000 0 -0.3 47 47
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
DHH 0.013 0.096 -10000 0 -0.5 4 4
PTHLH -0.34 0.47 -10000 0 -0.92 47 47
determination of left/right symmetry -0.093 0.17 -10000 0 -0.31 43 43
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
skeletal system development -0.34 0.47 -10000 0 -0.91 47 47
IHH N/Hhip -0.071 0.16 -10000 0 -0.41 21 21
DHH N/Hhip -0.04 0.17 -10000 0 -0.38 24 24
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.093 0.17 -10000 0 -0.31 43 43
pancreas development -0.062 0.2 -10000 0 -0.5 21 21
HHAT 0.027 0.012 -10000 0 -10000 0 0
PI3K 0.036 0.075 -10000 0 -0.51 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.018 0.084 -10000 0 -0.5 3 3
somite specification -0.093 0.17 -10000 0 -0.31 43 43
SHH Np/Cholesterol/PTCH1 -0.077 0.14 -10000 0 -0.25 45 45
SHH Np/Cholesterol/PTCH2 0.015 0.05 -10000 0 -0.29 3 3
SHH Np/Cholesterol/Megalin 0.015 0.007 -10000 0 -10000 0 0
SHH -0.012 0.005 -10000 0 -10000 0 0
catabolic process -0.1 0.18 -10000 0 -0.32 47 47
SMO/Vitamin D3 -0.079 0.16 -10000 0 -0.28 45 45
SHH Np/Cholesterol/Hhip -0.017 0.1 -10000 0 -0.28 14 14
LRP2 0.018 0.002 -10000 0 -10000 0 0
receptor-mediated endocytosis -0.081 0.16 -10000 0 -0.28 43 43
SHH Np/Cholesterol/BOC 0.012 0.057 -10000 0 -0.29 4 4
SHH Np/Cholesterol/CDO 0.023 0.011 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.017 0.1 0.28 14 -10000 0 14
mol:Vitamin D3 -0.057 0.17 0.38 4 -0.25 45 49
IHH N/PTCH2 -0.006 0.086 -10000 0 -0.4 3 3
CDON 0.032 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 -0.096 0.19 -10000 0 -0.32 47 47
Megalin/LRPAP1 0.037 0.007 -10000 0 -10000 0 0
PTCH2 0.018 0.084 -10000 0 -0.5 3 3
SHH Np/Cholesterol 0.014 0.006 -10000 0 -10000 0 0
PTCH1 -0.1 0.18 -10000 0 -0.32 47 47
HHIP -0.062 0.2 -10000 0 -0.5 21 21
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.031 0.084 -10000 0 -0.42 3 3
Crk/p130 Cas/Paxillin -0.12 0.12 -10000 0 -0.33 8 8
JUN -0.16 0.19 -10000 0 -0.37 41 41
HRAS 0.03 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.13 0.18 -10000 0 -0.29 61 61
RAP1A 0.027 0.049 -10000 0 -0.5 1 1
FRS2 0.032 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.035 -10000 0 -0.36 1 1
RET51/GFRalpha1/GDNF/DOK1 -0.12 0.18 -10000 0 -0.28 65 65
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.032 0.063 -10000 0 -0.27 4 4
RHOA 0.031 0.008 -10000 0 -10000 0 0
RAP1A/GTP -0.12 0.16 -10000 0 -0.26 63 63
GRB7 0.029 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.13 0.18 -10000 0 -0.29 62 62
MAPKKK cascade -0.13 0.15 -10000 0 -0.27 57 57
BCAR1 0.03 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.02 0.093 -10000 0 -0.3 8 8
lamellipodium assembly -0.089 0.12 -10000 0 -0.3 9 9
RET51/GFRalpha1/GDNF/SHC -0.12 0.17 -10000 0 -0.28 59 59
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
RET9/GFRalpha1/GDNF/SHC 0.033 0.045 -10000 0 -0.28 1 1
RET9/GFRalpha1/GDNF/Shank3 0.032 0.063 -10000 0 -0.27 4 4
MAPK3 -0.12 0.15 0.31 3 -0.26 54 57
DOK1 0.033 0.003 -10000 0 -10000 0 0
DOK6 -0.01 0.14 -10000 0 -0.5 9 9
PXN 0.032 0.007 -10000 0 -10000 0 0
neurite development -0.12 0.14 0.33 1 -0.36 8 9
DOK5 0.019 0.069 -10000 0 -0.5 2 2
GFRA1 0.008 0.11 -10000 0 -0.5 5 5
MAPK8 -0.14 0.16 -10000 0 -0.28 55 55
HRAS/GTP -0.13 0.18 -10000 0 -0.29 61 61
tube development 0.035 0.061 0.22 3 -0.27 3 6
MAPK1 -0.13 0.14 0.35 2 -0.26 54 56
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.021 0.044 -10000 0 -0.23 3 3
Rac1/GDP 0.023 0.006 -10000 0 -10000 0 0
SRC 0.032 0.006 -10000 0 -10000 0 0
PDLIM7 0.032 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.18 -10000 0 -0.29 65 65
SHC1 0.028 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.13 0.18 -10000 0 -0.29 62 62
RET51/GFRalpha1/GDNF/Dok5 -0.13 0.18 -10000 0 -0.28 63 63
PRKCA 0.031 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.006 -10000 0 -10000 0 0
CREB1 -0.042 0.083 -10000 0 -0.41 3 3
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.029 -10000 0 -0.23 1 1
RET51/GFRalpha1/GDNF/Grb7 -0.12 0.18 -10000 0 -0.29 61 61
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.26 0.26 -10000 0 -0.5 65 65
DOK4 0.03 0.01 -10000 0 -10000 0 0
JNK cascade -0.16 0.19 -10000 0 -0.45 26 26
RET9/GFRalpha1/GDNF/FRS2 0.032 0.059 -10000 0 -0.28 3 3
SHANK3 0.03 0.009 -10000 0 -10000 0 0
RASA1 0.018 0.084 -10000 0 -0.5 3 3
NCK1 0.027 0.049 -10000 0 -0.5 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.024 0.029 -10000 0 -0.23 1 1
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.14 -10000 0 -0.24 60 60
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.15 -10000 0 -0.25 64 64
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.14 -10000 0 -0.24 57 57
PI3K -0.13 0.17 -10000 0 -0.45 9 9
SOS1 0.033 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.051 0.059 -10000 0 -0.27 3 3
GRB10 0.031 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.065 0.11 -10000 0 -0.38 4 4
RET51/GFRalpha1/GDNF/FRS2 -0.12 0.18 -10000 0 -0.28 63 63
GAB1 0.033 0.003 -10000 0 -10000 0 0
IRS1 0.01 0.11 -10000 0 -0.5 5 5
IRS2 0.027 0.049 -10000 0 -0.5 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.14 -10000 0 -0.24 59 59
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.18 -10000 0 -0.29 61 61
GRB2 0.03 0.009 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GDNF 0.019 0.011 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.14 0.19 -10000 0 -0.3 64 64
Rac1/GTP -0.1 0.14 -10000 0 -0.36 9 9
RET9/GFRalpha1/GDNF 0.016 0.063 -10000 0 -0.3 4 4
GFRalpha1/GDNF 0.017 0.074 -10000 0 -0.36 4 4
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.097 0.26 0.64 1 -0.68 5 6
CRP -0.08 0.29 0.58 4 -0.69 5 9
cell cycle arrest -0.12 0.29 -10000 0 -0.64 13 13
TIMP1 -0.092 0.24 -10000 0 -0.59 6 6
IL6ST -0.19 0.26 -10000 0 -0.5 49 49
Rac1/GDP -0.17 0.26 -10000 0 -0.5 37 37
AP1 -0.13 0.22 -10000 0 -0.47 19 19
GAB2 0.024 0.068 -10000 0 -0.5 2 2
TNFSF11 -0.15 0.36 -10000 0 -1 12 12
HSP90B1 0.016 0.095 -10000 0 -0.64 1 1
GAB1 0.033 0.003 -10000 0 -10000 0 0
MAPK14 -0.2 0.26 -10000 0 -0.58 32 32
AKT1 0.028 0.067 -10000 0 -0.4 2 2
FOXO1 0.03 0.071 0.33 1 -0.38 2 3
MAP2K6 -0.2 0.26 -10000 0 -0.54 37 37
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.16 0.25 -10000 0 -0.48 36 36
MITF -0.2 0.26 -10000 0 -0.53 37 37
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.032 0.007 -10000 0 -10000 0 0
A2M 0.004 0.17 -10000 0 -1 3 3
CEBPB 0.036 0.011 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.033 0.089 -10000 0 -0.3 1 1
STAT3 -0.14 0.29 -10000 0 -0.68 13 13
STAT1 0.003 0.089 -10000 0 -0.92 1 1
CEBPD -0.096 0.27 0.58 2 -0.68 5 7
PIK3CA 0.028 0.049 -10000 0 -0.5 1 1
PI3K 0.038 0.075 -10000 0 -0.51 2 2
JUN -0.04 0.18 -10000 0 -0.5 16 16
PIAS3/MITF -0.18 0.25 -10000 0 -0.5 37 37
MAPK11 -0.2 0.26 -10000 0 -0.58 32 32
STAT3 (dimer)/FOXO1 -0.097 0.23 0.44 1 -0.52 9 10
GRB2/SOS1/GAB family -0.16 0.26 -10000 0 -0.53 30 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.2 0.26 -10000 0 -0.42 58 58
GRB2 0.031 0.009 -10000 0 -10000 0 0
JAK2 0.031 0.008 -10000 0 -10000 0 0
LBP -0.12 0.3 0.58 1 -0.77 10 11
PIK3R1 0.024 0.069 -10000 0 -0.5 2 2
JAK1 0.033 0.011 -10000 0 -10000 0 0
MYC -0.1 0.28 0.58 2 -0.73 6 8
FGG -0.11 0.26 -10000 0 -0.69 5 5
macrophage differentiation -0.12 0.29 -10000 0 -0.64 13 13
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.19 0.26 -10000 0 -0.39 66 66
JUNB -0.097 0.26 0.61 1 -0.66 5 6
FOS -0.24 0.26 -10000 0 -0.5 60 60
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.21 0.27 -10000 0 -0.55 38 38
STAT1/PIAS1 -0.16 0.25 -10000 0 -0.48 36 36
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.083 -10000 0 -0.51 2 2
STAT3 (dimer) -0.13 0.29 -10000 0 -0.66 13 13
PRKCD -0.13 0.26 0.55 3 -0.49 28 31
IL6R -0.03 0.16 -10000 0 -0.5 13 13
SOCS3 -0.2 0.3 0.44 1 -0.61 32 33
gp130 (dimer)/JAK1/JAK1/LMO4 -0.085 0.18 -10000 0 -0.3 49 49
Rac1/GTP -0.17 0.26 -10000 0 -0.5 36 36
HCK 0.031 0.008 -10000 0 -10000 0 0
MAPKKK cascade 0 0.11 -10000 0 -0.5 2 2
bone resorption -0.14 0.34 -10000 0 -0.94 12 12
IRF1 -0.099 0.27 0.6 2 -0.68 5 7
mol:GDP -0.19 0.26 -10000 0 -0.51 38 38
SOS1 0.033 0.003 -10000 0 -10000 0 0
VAV1 -0.19 0.26 -10000 0 -0.52 38 38
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.22 0.3 -10000 0 -0.66 32 32
PTPN11 0.006 0.06 -10000 0 -0.58 1 1
IL6/IL6RA -0.14 0.22 -10000 0 -0.38 50 50
gp130 (dimer)/TYK2/TYK2/LMO4 -0.087 0.18 -10000 0 -0.3 49 49
gp130 (dimer)/JAK2/JAK2/LMO4 -0.089 0.18 -10000 0 -0.3 49 49
IL6 -0.16 0.26 -10000 0 -0.5 44 44
PIAS3 0.029 0.011 -10000 0 -10000 0 0
PTPRE 0.019 0.052 -10000 0 -0.51 1 1
PIAS1 0.032 0.007 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.21 0.27 -10000 0 -0.4 66 66
LMO4 0.034 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.15 0.27 -10000 0 -0.59 25 25
MCL1 0.054 0.089 0.51 1 -10000 0 1
IL23-mediated signaling events

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
CCL2 -0.33 0.54 0.77 1 -1.1 28 29
IL23A -0.33 0.52 -10000 0 -1.1 25 25
NF kappa B1 p50/RelA/I kappa B alpha -0.3 0.51 -10000 0 -1 26 26
positive regulation of T cell mediated cytotoxicity -0.34 0.56 0.78 1 -1.1 28 29
ITGA3 -0.3 0.49 0.74 1 -1 25 26
IL17F -0.21 0.34 0.55 1 -0.67 25 26
IL12B -0.015 0.12 0.23 1 -0.53 4 5
STAT1 (dimer) -0.33 0.54 -10000 0 -1.1 28 28
CD4 -0.3 0.51 -10000 0 -1 26 26
IL23 -0.32 0.5 -10000 0 -1 27 27
IL23R -0.054 0.24 -10000 0 -1 5 5
IL1B -0.32 0.52 -10000 0 -1.1 26 26
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.3 0.53 0.74 3 -1 28 31
TYK2 0.001 0.05 -10000 0 -10000 0 0
STAT4 0.033 0.003 -10000 0 -10000 0 0
STAT3 0.031 0.009 -10000 0 -10000 0 0
IL18RAP 0.025 0.068 -10000 0 -0.5 2 2
IL12RB1 0.001 0.05 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
IL12Rbeta1/TYK2 0.004 0.063 -10000 0 -10000 0 0
IL23R/JAK2 -0.055 0.24 -10000 0 -0.96 5 5
positive regulation of chronic inflammatory response -0.34 0.56 0.78 1 -1.1 28 29
natural killer cell activation 0.003 0.01 -10000 0 -0.037 1 1
JAK2 0 0.062 0.23 1 -10000 0 1
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
NFKB1 0.032 0.006 -10000 0 -10000 0 0
RELA 0.032 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.31 0.48 -10000 0 -0.98 27 27
ALOX12B -0.3 0.5 0.75 1 -1 26 27
CXCL1 -0.38 0.6 0.75 1 -1.2 35 36
T cell proliferation -0.34 0.56 0.78 1 -1.1 28 29
NFKBIA 0.031 0.008 -10000 0 -10000 0 0
IL17A -0.16 0.28 0.53 1 -0.52 25 26
PI3K -0.31 0.52 -10000 0 -1 29 29
IFNG 0.003 0.034 0.14 2 -0.12 1 3
STAT3 (dimer) -0.29 0.49 -10000 0 -1 25 25
IL18R1 0.03 0.049 -10000 0 -0.5 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.17 0.36 0.57 2 -0.64 26 28
IL18/IL18R 0.063 0.062 -10000 0 -0.3 3 3
macrophage activation -0.017 0.022 -10000 0 -0.043 26 26
TNF -0.36 0.56 -10000 0 -1.1 30 30
STAT3/STAT4 -0.31 0.51 -10000 0 -1.1 26 26
STAT4 (dimer) -0.33 0.54 -10000 0 -1.1 28 28
IL18 0.034 0.007 -10000 0 -10000 0 0
IL19 -0.27 0.5 0.76 2 -0.98 26 28
STAT5A (dimer) -0.33 0.52 -10000 0 -1.1 27 27
STAT1 0.033 0.003 -10000 0 -10000 0 0
SOCS3 0.013 0.096 -10000 0 -0.5 4 4
CXCL9 -0.32 0.53 0.75 1 -1.1 27 28
MPO -0.46 0.64 0.77 1 -1.2 45 46
positive regulation of humoral immune response -0.34 0.56 0.78 1 -1.1 28 29
IL23/IL23R/JAK2/TYK2 -0.36 0.59 0.78 1 -1.2 27 28
IL6 -0.55 0.69 0.72 1 -1.2 56 57
STAT5A 0.031 0.008 -10000 0 -10000 0 0
IL2 0.028 0.02 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.01 -10000 0 -0.037 1 1
CD3E -0.35 0.56 -10000 0 -1.1 29 29
keratinocyte proliferation -0.34 0.56 0.78 1 -1.1 28 29
NOS2 -0.3 0.51 0.78 1 -1 27 28
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.027 0.15 -10000 0 -0.29 27 27
NF kappa B1 p50/RelA/I kappa B alpha 0 0.16 0.36 5 -0.45 3 8
alphaV/beta3 Integrin/Osteopontin/Src 0.02 0.1 -10000 0 -0.36 8 8
AP1 -0.2 0.3 0.31 1 -0.62 33 34
ILK -0.037 0.16 0.28 3 -0.3 27 30
bone resorption -0.044 0.18 0.32 2 -0.36 20 22
PTK2B 0.031 0.007 -10000 0 -10000 0 0
PYK2/p130Cas -0.002 0.16 -10000 0 -0.28 28 28
ITGAV 0.035 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.006 0.12 -10000 0 -0.36 12 12
alphaV/beta3 Integrin/Osteopontin -0.028 0.18 -10000 0 -0.33 28 28
MAP3K1 -0.041 0.16 0.27 3 -0.3 28 31
JUN -0.04 0.18 -10000 0 -0.5 16 16
MAPK3 -0.048 0.14 -10000 0 -0.28 27 27
MAPK1 -0.05 0.13 -10000 0 -0.28 27 27
Rac1/GDP 0.023 0.006 -10000 0 -10000 0 0
NFKB1 0.033 0.003 -10000 0 -10000 0 0
MAPK8 -0.063 0.17 0.28 3 -0.33 30 33
ITGB3 -0.071 0.21 -10000 0 -0.5 23 23
NFKBIA -0.033 0.16 0.46 4 -0.32 10 14
FOS -0.24 0.26 -10000 0 -0.5 60 60
CD44 0.032 0.006 -10000 0 -10000 0 0
CHUK 0.032 0.006 -10000 0 -10000 0 0
PLAU -0.04 0.2 0.56 3 -0.63 4 7
NF kappa B1 p50/RelA 0 0.15 0.35 1 -0.41 4 5
BCAR1 0.03 0.01 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.03 0.16 -10000 0 -0.36 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.039 0.16 0.27 3 -0.3 28 31
VAV3 -0.041 0.15 0.31 4 -0.28 27 31
MAP3K14 -0.042 0.15 -10000 0 -0.3 27 27
ROCK2 -0.021 0.16 -10000 0 -0.5 12 12
SPP1 -0.004 0.13 -10000 0 -0.5 8 8
RAC1 0.031 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.026 0.14 0.28 4 -0.27 26 30
MMP2 -0.2 0.26 0.3 3 -0.55 34 37
TCGA08_retinoblastoma

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
CDKN2B -0.028 0.16 -10000 0 -0.47 14 14
CDKN2C -0.002 0.11 -10000 0 -0.48 6 6
CDKN2A 0.028 0.016 -10000 0 -10000 0 0
CCND2 0.021 0.074 0.19 18 -10000 0 18
RB1 -0.024 0.082 -10000 0 -0.21 18 18
CDK4 0.024 0.084 0.21 19 -10000 0 19
CDK6 0.027 0.088 0.22 19 -10000 0 19
G1/S progression 0.027 0.084 0.21 20 -10000 0 20
FOXM1 transcription factor network

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
NFATC3 -0.17 0.46 -10000 0 -1 19 19
PLK1 -0.057 0.34 -10000 0 -1.4 7 7
BIRC5 -0.069 0.37 -10000 0 -1.3 10 10
HSPA1B -0.17 0.46 -10000 0 -1 19 19
MAP2K1 0.007 0.055 -10000 0 -10000 0 0
BRCA2 -0.2 0.48 -10000 0 -1 23 23
FOXM1 -0.25 0.66 -10000 0 -1.4 19 19
XRCC1 -0.17 0.46 -10000 0 -1 19 19
FOXM1B/p19 -0.22 0.43 -10000 0 -1.1 18 18
Cyclin D1/CDK4 -0.14 0.42 -10000 0 -0.9 18 18
CDC2 -0.18 0.48 -10000 0 -1.1 19 19
TGFA -0.16 0.38 -10000 0 -0.87 17 17
SKP2 -0.17 0.46 -10000 0 -1 19 19
CCNE1 0.027 0.018 -10000 0 -10000 0 0
CKS1B -0.17 0.45 -10000 0 -1 19 19
RB1 -0.069 0.3 -10000 0 -0.94 9 9
FOXM1C/SP1 -0.2 0.52 -10000 0 -1.2 19 19
AURKB -0.15 0.47 -10000 0 -1.2 17 17
CENPF -0.17 0.5 -10000 0 -1 21 21
CDK4 0.021 0.03 -10000 0 -10000 0 0
MYC -0.17 0.39 -10000 0 -0.88 19 19
CHEK2 0.005 0.052 -10000 0 -10000 0 0
ONECUT1 -0.18 0.42 -10000 0 -0.95 19 19
CDKN2A 0.025 0.013 -10000 0 -10000 0 0
LAMA4 -0.24 0.55 -10000 0 -1.2 24 24
FOXM1B/HNF6 -0.22 0.49 -10000 0 -1.1 19 19
FOS -0.54 0.67 0.74 1 -1.1 66 67
SP1 0.032 0.007 -10000 0 -10000 0 0
CDC25B -0.17 0.46 0.74 1 -1 19 20
response to radiation -0.002 0.031 -10000 0 -10000 0 0
CENPB -0.17 0.46 -10000 0 -1 19 19
CENPA -0.2 0.5 -10000 0 -1.1 20 20
NEK2 -0.16 0.5 0.74 1 -1.1 19 20
HIST1H2BA -0.18 0.45 -10000 0 -1 19 19
CCNA2 0.01 0.1 -10000 0 -0.52 4 4
EP300 0.03 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 -0.21 0.53 -10000 0 -1.2 19 19
CCNB2 -0.19 0.49 -10000 0 -1.1 20 20
CCNB1 -0.18 0.48 -10000 0 -1.1 19 19
ETV5 -0.17 0.46 -10000 0 -1 19 19
ESR1 -0.19 0.47 -10000 0 -1 21 21
CCND1 -0.16 0.41 -10000 0 -0.92 18 18
GSK3A 0.008 0.048 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.032 0.089 -10000 0 -0.34 4 4
CDK2 0.027 0.018 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.037 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.2 0.48 -10000 0 -1.1 19 19
GAS1 -0.18 0.48 -10000 0 -1.1 20 20
MMP2 -0.23 0.55 -10000 0 -1.2 23 23
RB1/FOXM1C -0.15 0.45 -10000 0 -0.99 19 19
CREBBP 0.032 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.031 0.009 -10000 0 -10000 0 0
SVIL 0.027 0.049 -10000 0 -0.5 1 1
ZNF318 0.028 0.014 -10000 0 -10000 0 0
JMJD2C 0 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 -0.18 0.17 -10000 0 -0.31 70 70
CARM1 0.032 0.007 -10000 0 -10000 0 0
PRDX1 0.032 0.006 -10000 0 -10000 0 0
PELP1 0.03 0.009 -10000 0 -10000 0 0
CTNNB1 0.031 0.008 -10000 0 -10000 0 0
AKT1 0.031 0.007 -10000 0 -10000 0 0
PTK2B 0.031 0.007 -10000 0 -10000 0 0
MED1 0.03 0.009 -10000 0 -10000 0 0
MAK 0.025 0.015 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 -0.009 0.14 -10000 0 -0.5 9 9
GSN -0.008 0.14 -10000 0 -0.5 9 9
NCOA2 -0.14 0.25 -10000 0 -0.5 38 38
NCOA6 0.032 0.006 -10000 0 -10000 0 0
DNA-PK 0.059 0.021 -10000 0 -10000 0 0
NCOA4 0.032 0.005 -10000 0 -10000 0 0
PIAS3 0.029 0.011 -10000 0 -10000 0 0
cell proliferation -0.072 0.15 -10000 0 -0.48 13 13
XRCC5 0.032 0.003 -10000 0 -10000 0 0
UBE3A 0.032 0.007 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.18 0.17 -10000 0 -0.32 69 69
FHL2 -0.072 0.1 -10000 0 -0.44 5 5
RANBP9 0.03 0.011 -10000 0 -10000 0 0
JMJD1A -0.016 0.049 0.053 1 -0.12 21 22
CDK6 0.017 0.084 -10000 0 -0.5 3 3
TGFB1I1 0.024 0.069 -10000 0 -0.5 2 2
T-DHT/AR/CyclinD1 -0.18 0.16 -10000 0 -0.31 70 70
XRCC6 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.18 0.18 -10000 0 -0.3 79 79
CTDSP1 0.033 0.003 -10000 0 -10000 0 0
CTDSP2 0.03 0.011 -10000 0 -10000 0 0
BRCA1 0.031 0.009 -10000 0 -10000 0 0
TCF4 0.031 0.007 -10000 0 -10000 0 0
CDKN2A 0.026 0.013 -10000 0 -10000 0 0
SRF 0.035 0.012 -10000 0 -10000 0 0
NKX3-1 -0.11 0.099 -10000 0 -0.17 79 79
KLK3 0.019 0.062 -10000 0 -10000 0 0
TMF1 0.031 0.009 -10000 0 -10000 0 0
HNRNPA1 0.031 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 0.014 0.008 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.18 0.17 -10000 0 -0.31 70 70
AR -0.29 0.25 -10000 0 -0.5 70 70
UBA3 0.031 0.009 -10000 0 -10000 0 0
PATZ1 0.03 0.009 -10000 0 -10000 0 0
PAWR 0.032 0.007 -10000 0 -10000 0 0
PRKDC 0.031 0.007 -10000 0 -10000 0 0
PA2G4 0.031 0.007 -10000 0 -10000 0 0
UBE2I 0.032 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.16 0.15 -10000 0 -0.28 70 70
RPS6KA3 0.028 0.049 -10000 0 -0.5 1 1
T-DHT/AR/ARA70 -0.17 0.17 -10000 0 -0.31 68 68
LATS2 0.023 0.069 -10000 0 -0.5 2 2
T-DHT/AR/PRX1 -0.16 0.15 -10000 0 -0.28 70 70
Cyclin D3/CDK11 p58 0.022 0.007 -10000 0 -10000 0 0
VAV3 0.031 0.008 -10000 0 -10000 0 0
KLK2 -0.083 0.08 -10000 0 -0.56 1 1
CASP8 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.21 -10000 0 -0.36 83 83
TMPRSS2 -0.22 0.36 -10000 0 -0.95 22 22
CCND1 0.03 0.009 -10000 0 -10000 0 0
PIAS1 0.032 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.007 0.021 -10000 0 -0.049 21 21
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.032 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.18 0.17 -10000 0 -0.32 71 71
CMTM2 0.016 0.084 -10000 0 -0.5 3 3
SNURF 0.025 0.049 -10000 0 -0.5 1 1
ZMIZ1 0.018 0.036 -10000 0 -10000 0 0
CCND3 0.03 0.01 -10000 0 -10000 0 0
TGIF1 0.031 0.007 -10000 0 -10000 0 0
FKBP4 0.032 0.008 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.027 0.13 0.29 8 -0.32 7 15
TBX21 0.018 0.32 0.66 5 -0.87 5 10
B2M 0.007 0.042 -10000 0 -10000 0 0
TYK2 0.033 0.042 0.17 1 -10000 0 1
IL12RB1 0.033 0.042 -10000 0 -10000 0 0
GADD45B 0.041 0.26 0.62 3 -0.62 7 10
IL12RB2 0.018 0.11 -10000 0 -0.52 4 4
GADD45G 0.048 0.28 0.61 8 -0.62 7 15
natural killer cell activation 0.01 0.032 0.082 12 -0.04 9 21
RELB 0.031 0.007 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
IL18 0.033 0.027 -10000 0 -10000 0 0
IL2RA -0.017 0.15 -10000 0 -0.5 11 11
IFNG 0.028 0.01 -10000 0 -10000 0 0
STAT3 (dimer) 0.013 0.28 0.53 6 -0.6 11 17
HLA-DRB5 -0.01 0.011 -10000 0 -0.022 54 54
FASLG -0.002 0.42 0.75 7 -1.3 7 14
NF kappa B2 p52/RelB -0.014 0.29 0.48 3 -0.64 14 17
CD4 -0.006 0.071 -10000 0 -0.5 2 2
SOCS1 0.023 0.069 -10000 0 -0.5 2 2
EntrezGene:6955 -0.025 0.029 -10000 0 -0.046 67 67
CD3D -0.065 0.15 -10000 0 -0.5 11 11
CD3E -0.063 0.15 -10000 0 -0.5 11 11
CD3G -0.083 0.16 -10000 0 -0.5 15 15
IL12Rbeta2/JAK2 0.037 0.1 0.23 3 -0.4 4 7
CCL3 0.02 0.32 0.65 6 -0.82 6 12
CCL4 0.01 0.35 0.67 6 -1 6 12
HLA-A -0.014 0.024 -10000 0 -0.052 33 33
IL18/IL18R 0.086 0.099 0.28 3 -0.3 3 6
NOS2 0.008 0.34 0.62 7 -0.86 9 16
IL12/IL12R/TYK2/JAK2/SPHK2 0.032 0.12 0.29 8 -0.28 6 14
IL1R1 -0.023 0.38 0.62 5 -0.96 11 16
IL4 -0.002 0.049 -10000 0 -10000 0 0
JAK2 0.031 0.042 0.17 1 -10000 0 1
EntrezGene:6957 -0.024 0.028 -10000 0 -0.043 67 67
TCR/CD3/MHC I/CD8 -0.38 0.51 -10000 0 -0.95 47 47
RAB7A 0.054 0.27 0.65 5 -0.61 4 9
lysosomal transport 0.056 0.26 0.64 5 -0.59 4 9
FOS -0.59 0.67 0.49 2 -1.2 63 65
STAT4 (dimer) 0.041 0.31 0.58 10 -0.63 11 21
STAT5A (dimer) -0.019 0.28 0.47 2 -0.64 14 16
GZMA -0.022 0.39 0.69 2 -1.2 7 9
GZMB 0.014 0.3 0.65 5 -0.87 5 10
HLX 0.027 0.012 -10000 0 -10000 0 0
LCK -0.014 0.32 0.57 8 -0.67 14 22
TCR/CD3/MHC II/CD4 -0.22 0.3 -10000 0 -0.39 68 68
IL2/IL2R 0.021 0.13 -10000 0 -0.3 16 16
MAPK14 0.051 0.28 0.6 6 -0.65 8 14
CCR5 -0.064 0.46 0.62 3 -1.2 15 18
IL1B 0.03 0.065 -10000 0 -0.52 1 1
STAT6 0.026 0.16 0.36 7 -0.5 3 10
STAT4 0.033 0.003 -10000 0 -10000 0 0
STAT3 0.03 0.009 -10000 0 -10000 0 0
STAT1 0.033 0.003 -10000 0 -10000 0 0
NFKB1 0.033 0.003 -10000 0 -10000 0 0
NFKB2 0.032 0.006 -10000 0 -10000 0 0
IL12B 0.016 0.1 -10000 0 -0.49 4 4
CD8A -0.046 0.16 -10000 0 -0.5 12 12
CD8B -0.033 0.14 -10000 0 -0.5 9 9
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.028 0.13 0.32 7 -0.29 8 15
IL2RB 0.021 0.069 -10000 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.3 0.58 10 -0.59 11 21
IL2RG 0.01 0.11 -10000 0 -0.5 5 5
IL12 0.029 0.1 0.24 2 -0.34 5 7
STAT5A 0.031 0.008 -10000 0 -10000 0 0
CD247 -0.052 0.13 -10000 0 -0.5 8 8
IL2 0.026 0.008 -10000 0 -10000 0 0
SPHK2 0.032 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.024 0.065 -10000 0 -0.52 1 1
IL12/IL12R/TYK2/JAK2 -0.016 0.33 0.65 7 -0.71 14 21
MAP2K3 0.049 0.28 0.58 8 -0.66 7 15
RIPK2 0.031 0.007 -10000 0 -10000 0 0
MAP2K6 0.05 0.28 0.58 8 -0.66 7 15
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.012 0.013 -10000 0 -0.025 54 54
IL18RAP 0.023 0.074 -10000 0 -0.5 2 2
IL12Rbeta1/TYK2 0.049 0.056 0.22 1 -10000 0 1
EOMES -0.43 0.58 -10000 0 -1.2 43 43
STAT1 (dimer) 0.022 0.28 0.54 6 -0.6 10 16
T cell proliferation 0.06 0.25 0.53 11 -0.47 10 21
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.029 0.054 -10000 0 -0.48 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.005 0.22 -10000 0 -0.54 12 12
ATF2 0.04 0.27 0.58 5 -0.61 8 13
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 0.072 0.082 -10000 0 -10000 0 0
SMARCC2 0.033 0.007 -10000 0 -10000 0 0
SMARCC1 0.032 0.009 -10000 0 -10000 0 0
TBX21 -0.055 0.11 -10000 0 -0.37 5 5
SUMO2 0.022 0.021 -10000 0 -10000 0 0
STAT1 (dimer) 0.04 0.004 -10000 0 -10000 0 0
FKBP4 0.031 0.007 -10000 0 -10000 0 0
FKBP5 0.025 0.049 -10000 0 -0.5 1 1
GR alpha/HSP90/FKBP51/HSP90 0.097 0.1 0.3 9 -0.25 1 10
PRL -0.19 0.43 -10000 0 -1.3 16 16
cortisol/GR alpha (dimer)/TIF2 0.058 0.25 0.51 16 -0.39 6 22
RELA -0.098 0.13 -10000 0 -0.24 39 39
FGG 0.14 0.18 0.42 22 -10000 0 22
GR beta/TIF2 -0.031 0.2 0.28 13 -0.31 31 44
IFNG -0.17 0.21 -10000 0 -0.59 11 11
apoptosis -0.023 0.2 0.81 1 -0.5 6 7
CREB1 0.036 0.009 -10000 0 -10000 0 0
histone acetylation 0.039 0.15 0.39 14 -10000 0 14
BGLAP -0.043 0.1 -10000 0 -10000 0 0
GR/PKAc 0.11 0.099 0.3 8 -10000 0 8
NF kappa B1 p50/RelA -0.18 0.24 -10000 0 -0.38 63 63
SMARCD1 0.033 0.007 -10000 0 -10000 0 0
MDM2 0.068 0.081 0.2 22 -10000 0 22
GATA3 0.02 0.096 -10000 0 -0.5 4 4
AKT1 0.026 0.01 -10000 0 -10000 0 0
CSF2 0 0.083 -10000 0 -10000 0 0
GSK3B 0.023 0.021 -10000 0 -10000 0 0
NR1I3 -0.001 0.18 0.96 1 -10000 0 1
CSN2 0.098 0.2 0.35 21 -0.48 6 27
BRG1/BAF155/BAF170/BAF60A 0.079 0.03 -10000 0 -10000 0 0
NFATC1 0.038 0.014 -10000 0 -10000 0 0
POU2F1 0.003 0.088 -10000 0 -0.27 11 11
CDKN1A 0.02 0.037 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.008 -10000 0 -10000 0 0
SFN 0.026 0.013 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.099 0.3 9 -10000 0 9
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.36 0.74 1 -0.79 25 26
JUN -0.084 0.18 -10000 0 -0.4 22 22
IL4 -0.06 0.11 -10000 0 -0.38 1 1
CDK5R1 0.019 0.069 -10000 0 -0.5 2 2
PRKACA 0.032 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.12 0.14 -10000 0 -0.36 26 26
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.099 0.31 8 -0.22 1 9
cortisol/GR alpha (monomer) 0.18 0.25 0.55 25 -10000 0 25
NCOA2 -0.14 0.25 -10000 0 -0.5 38 38
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.23 0.27 -10000 0 -0.49 60 60
AP-1/NFAT1-c-4 -0.2 0.28 -10000 0 -0.58 28 28
AFP -0.071 0.18 0.6 1 -0.65 2 3
SUV420H1 0.032 0.004 -10000 0 -10000 0 0
IRF1 0.12 0.13 0.4 5 -10000 0 5
TP53 0.045 0.014 -10000 0 -10000 0 0
PPP5C 0.032 0.007 -10000 0 -10000 0 0
KRT17 -0.22 0.33 -10000 0 -0.86 17 17
KRT14 -0.47 0.6 -10000 0 -1.3 42 42
TBP 0.039 0.018 -10000 0 -10000 0 0
CREBBP 0.13 0.15 0.32 41 -10000 0 41
HDAC1 0.03 0.007 -10000 0 -10000 0 0
HDAC2 0.029 0.01 -10000 0 -10000 0 0
AP-1 -0.2 0.28 -10000 0 -0.58 28 28
MAPK14 0.024 0.02 -10000 0 -10000 0 0
MAPK10 0.011 0.085 -10000 0 -0.5 3 3
MAPK11 0.022 0.021 -10000 0 -10000 0 0
KRT5 -0.17 0.21 -10000 0 -0.56 13 13
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.035 0.004 -10000 0 -10000 0 0
STAT1 0.04 0.004 -10000 0 -10000 0 0
CGA -0.062 0.11 -10000 0 -0.37 3 3
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.067 0.13 0.3 19 -10000 0 19
MAPK3 0.025 0.02 -10000 0 -10000 0 0
MAPK1 0.025 0.019 -10000 0 -10000 0 0
ICAM1 -0.2 0.24 -10000 0 -0.5 34 34
NFKB1 -0.097 0.13 -10000 0 -0.22 55 55
MAPK8 -0.066 0.16 -10000 0 -0.39 16 16
MAPK9 0.025 0.019 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.027 0.2 0.82 1 -0.53 6 7
BAX 0.024 0.036 -10000 0 -10000 0 0
POMC -0.098 0.19 -10000 0 -0.77 4 4
EP300 0.12 0.14 0.32 38 -10000 0 38
cortisol/GR alpha (dimer)/p53 0.16 0.21 0.51 20 -10000 0 20
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.08 0.21 13 -10000 0 13
SGK1 0.14 0.16 -10000 0 -10000 0 0
IL13 -0.14 0.18 -10000 0 -0.53 7 7
IL6 -0.47 0.55 -10000 0 -1.1 50 50
PRKACG 0.02 0.007 -10000 0 -10000 0 0
IL5 -0.13 0.16 -10000 0 -0.56 2 2
IL2 -0.17 0.21 -10000 0 -0.57 13 13
CDK5 0.029 0.009 -10000 0 -10000 0 0
PRKACB 0.032 0.006 -10000 0 -10000 0 0
HSP90AA1 0.032 0.007 -10000 0 -10000 0 0
IL8 -0.23 0.31 -10000 0 -0.56 41 41
CDK5R1/CDK5 0.032 0.055 -10000 0 -0.37 2 2
NF kappa B1 p50/RelA/PKAc -0.11 0.2 -10000 0 -0.35 36 36
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.48 24 -10000 0 24
SMARCA4 0.033 0.007 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.13 0.34 17 -10000 0 17
NF kappa B1 p50/RelA/Cbp -0.063 0.24 0.4 12 -0.38 24 36
JUN (dimer) -0.084 0.18 -10000 0 -0.4 22 22
YWHAH 0.03 0.009 -10000 0 -10000 0 0
VIPR1 -0.068 0.16 -10000 0 -0.61 6 6
NR3C1 0.12 0.15 0.37 20 -10000 0 20
NR4A1 0.012 0.12 -10000 0 -0.51 6 6
TIF2/SUV420H1 -0.085 0.19 -10000 0 -0.36 38 38
MAPKKK cascade -0.023 0.2 0.81 1 -0.5 6 7
cortisol/GR alpha (dimer)/Src-1 0.18 0.22 0.5 24 -10000 0 24
PBX1 0.001 0.091 -10000 0 -0.27 12 12
POU1F1 -0.019 0.12 -10000 0 -0.31 17 17
SELE -0.5 0.55 -10000 0 -1 58 58
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.13 0.34 17 -10000 0 17
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.48 24 -10000 0 24
mol:cortisol 0.095 0.15 0.31 27 -0.21 1 28
MMP1 -0.041 0.13 -10000 0 -1.2 1 1
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.024 0.059 -10000 0 -0.38 2 2
PDGFRB -0.042 0.18 -10000 0 -0.51 16 16
SPHK1 -0.028 0.12 -10000 0 -0.74 3 3
mol:S1P -0.035 0.12 -10000 0 -0.65 3 3
S1P1/S1P/Gi -0.12 0.2 -10000 0 -0.36 45 45
GNAO1 0.005 0.054 -10000 0 -0.5 1 1
PDGFB-D/PDGFRB/PLCgamma1 -0.13 0.22 -10000 0 -0.37 49 49
PLCG1 -0.12 0.19 -10000 0 -0.36 45 45
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.042 0.18 -10000 0 -0.5 16 16
GNAI2 0.012 0.028 -10000 0 -10000 0 0
GNAI3 0.012 0.027 -10000 0 -10000 0 0
GNAI1 0.012 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.048 -10000 0 -0.33 2 2
S1P1/S1P -0.054 0.11 -10000 0 -0.43 4 4
negative regulation of cAMP metabolic process -0.12 0.19 -10000 0 -0.36 45 45
MAPK3 -0.2 0.29 -10000 0 -0.55 46 46
calcium-dependent phospholipase C activity -0.003 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
KDR 0.02 0.07 -10000 0 -0.51 2 2
PLCB2 -0.046 0.11 0.22 1 -0.37 5 6
RAC1 0.031 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.046 0.098 -10000 0 -0.37 4 4
receptor internalization -0.052 0.1 -10000 0 -0.4 4 4
PTGS2 -0.35 0.5 0.36 1 -0.98 45 46
Rac1/GTP -0.045 0.096 -10000 0 -0.39 3 3
RHOA 0.031 0.008 -10000 0 -10000 0 0
VEGFA 0.025 0.012 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.12 0.19 -10000 0 -0.36 45 45
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.012 0.026 -10000 0 -10000 0 0
MAPK1 -0.18 0.28 -10000 0 -0.54 44 44
S1P1/S1P/PDGFB-D/PDGFRB -0.073 0.16 -10000 0 -0.37 19 19
ABCC1 0.03 0.006 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.19 0.27 -9999 0 -0.39 60 60
MAP3K8 0.027 0.009 -9999 0 -10000 0 0
FOS -0.11 0.22 -9999 0 -0.62 14 14
PRKCA 0.005 0.028 -9999 0 -10000 0 0
PTPN7 -0.037 0.13 -9999 0 -0.5 8 8
HRAS 0.029 0.008 -9999 0 -10000 0 0
PRKCB -0.04 0.14 -9999 0 -0.5 10 10
NRAS 0.03 0.007 -9999 0 -10000 0 0
RAS family/GTP 0.042 0.023 -9999 0 -10000 0 0
MAPK3 -0.073 0.2 -9999 0 -0.65 12 12
MAP2K1 -0.041 0.12 -9999 0 -0.41 9 9
ELK1 0 0.035 -9999 0 -10000 0 0
BRAF -0.032 0.11 -9999 0 -0.38 10 10
mol:GTP -0.003 0.003 -9999 0 -0.005 62 62
MAPK1 -0.076 0.21 -9999 0 -0.63 13 13
RAF1 -0.035 0.12 -9999 0 -0.41 10 10
KRAS 0.03 0.006 -9999 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.03 0.12 -10000 0 -0.34 12 12
alphaM/beta2 Integrin/GPIbA -0.005 0.086 -10000 0 -0.34 3 3
alphaM/beta2 Integrin/proMMP-9 -0.006 0.093 -10000 0 -0.36 4 4
PLAUR 0.032 0.006 -10000 0 -10000 0 0
HMGB1 -0.006 0.045 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.007 0.068 -10000 0 -10000 0 0
AGER -0.005 0.044 -10000 0 -10000 0 0
RAP1A 0.027 0.049 -10000 0 -0.5 1 1
SELPLG 0.027 0.049 -10000 0 -0.5 1 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.043 0.15 -10000 0 -0.22 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.013 0.096 -10000 0 -0.5 4 4
CYR61 -0.12 0.24 -10000 0 -0.5 34 34
TLN1 0.032 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.088 0.16 -10000 0 -0.35 22 22
RHOA 0.031 0.008 -10000 0 -10000 0 0
P-selectin oligomer -0.12 0.23 -10000 0 -0.5 32 32
MYH2 -0.13 0.18 -10000 0 -0.42 22 22
MST1R 0.031 0.008 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.079 0.15 -10000 0 -0.3 33 33
APOB -0.11 0.23 -10000 0 -0.5 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.024 0.16 -10000 0 -0.5 12 12
JAM3 0.032 0.006 -10000 0 -10000 0 0
GP1BA 0.017 0.084 -10000 0 -0.5 3 3
alphaM/beta2 Integrin/CTGF -0.043 0.14 -10000 0 -0.34 17 17
alphaM/beta2 Integrin -0.11 0.16 -10000 0 -0.39 22 22
JAM3 homodimer 0.032 0.006 -10000 0 -10000 0 0
ICAM2 0.031 0.008 -10000 0 -10000 0 0
ICAM1 0.031 0.007 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.11 0.16 -10000 0 -0.38 22 22
cell adhesion -0.005 0.086 -10000 0 -0.34 3 3
NFKB1 -0.13 0.22 0.4 1 -0.38 50 51
THY1 0.014 0.096 -10000 0 -0.5 4 4
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
Lipoprotein(a) -0.075 0.17 -10000 0 -0.33 36 36
alphaM/beta2 Integrin/LRP/tPA -0.041 0.16 -10000 0 -0.38 18 18
IL6 -0.28 0.38 0.4 1 -0.72 49 50
ITGB2 -0.004 0.044 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.013 0.078 -10000 0 -0.33 1 1
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 -10000 0 -0.31 7 7
JAM2 -0.001 0.12 -10000 0 -0.5 7 7
alphaM/beta2 Integrin/ICAM1 0.028 0.076 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA/Plg 0.008 0.076 -10000 0 -0.34 1 1
RhoA/GTP -0.14 0.19 -10000 0 -0.43 24 24
positive regulation of phagocytosis -0.085 0.13 -10000 0 -0.31 18 18
Ron/MSP 0.04 0.019 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.015 0.08 -10000 0 -0.33 1 1
alphaM/beta2 Integrin/uPAR 0.007 0.068 -10000 0 -10000 0 0
PLAU 0.027 0.049 -10000 0 -0.5 1 1
PLAT -0.014 0.15 -10000 0 -0.5 10 10
actin filament polymerization -0.12 0.17 -10000 0 -0.41 22 22
MST1 0.027 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.077 0.16 -10000 0 -0.31 33 33
TNF -0.17 0.26 -10000 0 -0.43 48 48
RAP1B 0.032 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.001 0.075 -10000 0 -0.36 1 1
fibrinolysis 0.007 0.075 -10000 0 -0.33 1 1
HCK 0.031 0.008 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.11 0.16 -10000 0 -0.38 22 22
VTN 0.025 0.049 -10000 0 -0.5 1 1
alphaM/beta2 Integrin/CYR61 -0.085 0.18 -10000 0 -0.34 34 34
LPA -0.008 0.13 -10000 0 -0.5 8 8
LRP1 -0.027 0.17 -10000 0 -0.5 13 13
cell migration -0.037 0.12 -10000 0 -0.31 16 16
FN1 -0.058 0.2 -10000 0 -0.5 20 20
alphaM/beta2 Integrin/Thy1 -0.004 0.095 -10000 0 -0.37 4 4
MPO -0.1 0.23 -10000 0 -0.5 29 29
KNG1 0.02 0.007 -10000 0 -10000 0 0
RAP1/GDP 0.039 0.034 -10000 0 -0.31 1 1
ROCK1 -0.13 0.18 -10000 0 -0.43 21 21
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.008 -10000 0 -10000 0 0
CTGF -0.049 0.18 -10000 0 -0.5 17 17
alphaM/beta2 Integrin/Hck 0.005 0.067 -10000 0 -10000 0 0
ITGAM -0.005 0.046 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.066 0.16 -10000 0 -0.32 32 32
HP -0.092 0.22 -10000 0 -0.5 27 27
leukocyte adhesion -0.057 0.16 -10000 0 -0.36 14 14
SELP -0.12 0.23 -10000 0 -0.5 32 32
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.012 0.26 0.34 10 -0.65 14 24
FYN -0.086 0.34 0.32 3 -0.95 14 17
LAT/GRAP2/SLP76 -0.061 0.28 -10000 0 -0.69 17 17
IKBKB 0.031 0.007 -10000 0 -10000 0 0
AKT1 -0.04 0.2 0.26 3 -0.52 16 19
B2M 0.032 0.007 -10000 0 -10000 0 0
IKBKG -0.004 0.055 0.11 2 -0.15 11 13
MAP3K8 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.025 0.088 1 -0.071 17 18
integrin-mediated signaling pathway 0.034 0.035 -10000 0 -0.31 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.081 0.32 0.3 3 -0.81 17 20
TRPV6 0.032 0.31 1.2 7 -0.5 8 15
CD28 -0.026 0.17 -10000 0 -0.5 13 13
SHC1 -0.062 0.34 0.34 10 -0.92 14 24
receptor internalization -0.1 0.4 0.27 2 -0.96 18 20
PRF1 -0.074 0.33 -10000 0 -0.95 14 14
KRAS 0.032 0.007 -10000 0 -10000 0 0
GRB2 0.03 0.009 -10000 0 -10000 0 0
COT/AKT1 -0.014 0.16 0.25 3 -0.39 16 19
LAT -0.094 0.36 0.3 3 -0.93 16 19
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D -0.017 0.16 -10000 0 -0.51 11 11
CD3E -0.016 0.16 -10000 0 -0.51 11 11
CD3G -0.035 0.18 -10000 0 -0.5 15 15
RASGRP2 -0.005 0.047 -10000 0 -0.18 7 7
RASGRP1 -0.043 0.22 0.3 3 -0.56 16 19
HLA-A 0 0.005 -10000 0 -10000 0 0
RASSF5 0.027 0.012 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.036 -10000 0 -0.31 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.086 0.2 11 -0.15 14 25
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.023 0.085 -10000 0 -0.24 14 14
PRKCA -0.021 0.1 -10000 0 -0.28 15 15
GRAP2 -0.028 0.16 -10000 0 -0.5 13 13
mol:IP3 -0.041 0.19 0.25 3 -0.48 16 19
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.11 0.38 -10000 0 -1 15 15
ORAI1 -0.036 0.24 -10000 0 -0.96 7 7
CSK -0.08 0.34 0.32 4 -0.97 14 18
B7 family/CD28 -0.077 0.36 0.33 1 -0.81 19 20
CHUK 0.032 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.41 0.33 1 -1.1 15 16
PTPN6 -0.093 0.34 0.25 1 -0.98 14 15
VAV1 -0.082 0.33 0.3 4 -0.9 15 19
Monovalent TCR/CD3 -0.095 0.33 -10000 0 -0.86 16 16
CBL 0.023 0.069 -10000 0 -0.5 2 2
LCK -0.096 0.38 0.32 3 -1.1 14 17
PAG1 -0.084 0.34 0.32 3 -0.92 15 18
RAP1A 0.027 0.049 -10000 0 -0.5 1 1
TCR/CD3/MHC I/CD8/LCK -0.12 0.42 0.34 2 -1 17 19
CD80 -0.014 0.15 -10000 0 -0.5 10 10
CD86 0.031 0.007 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.018 0.11 -10000 0 -0.28 14 14
HRAS 0.03 0.009 -10000 0 -10000 0 0
GO:0035030 -0.084 0.26 0.28 1 -0.63 19 20
CD8A -0.021 0.16 -10000 0 -0.51 12 12
CD8B -0.007 0.14 -10000 0 -0.51 9 9
PTPRC -0.004 0.13 -10000 0 -0.5 7 7
PDK1/PKC theta -0.06 0.25 0.29 3 -0.64 16 19
CSK/PAG1 -0.074 0.33 0.35 5 -0.92 14 19
SOS1 0.033 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.021 0.015 -10000 0 -10000 0 0
GRAP2/SLP76 -0.07 0.33 0.28 2 -0.78 18 20
STIM1 0.001 0.046 -10000 0 -10000 0 0
RAS family/GTP 0.016 0.094 0.2 7 -0.2 14 21
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.13 0.46 0.27 2 -1.1 18 20
mol:DAG -0.051 0.16 0.14 1 -0.43 16 17
RAP1A/GDP 0.014 0.042 0.1 10 -0.069 12 22
PLCG1 0.032 0.006 -10000 0 -10000 0 0
CD247 -0.008 0.13 -10000 0 -0.51 8 8
cytotoxic T cell degranulation -0.069 0.32 -10000 0 -0.9 14 14
RAP1A/GTP -0.001 0.019 -10000 0 -0.068 8 8
mol:PI-3-4-5-P3 -0.055 0.25 0.28 3 -0.62 17 20
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.056 0.25 0.27 3 -0.66 16 19
NRAS 0.032 0.007 -10000 0 -10000 0 0
ZAP70 -0.012 0.15 -10000 0 -0.5 10 10
GRB2/SOS1 0.045 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.064 0.25 -10000 0 -0.67 16 16
MALT1 0.031 0.007 -10000 0 -10000 0 0
TRAF6 0.032 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.016 0.19 -10000 0 -0.52 14 14
CARD11 0.031 0.008 -10000 0 -10000 0 0
PRKCB -0.033 0.14 -10000 0 -0.36 16 16
PRKCE -0.024 0.11 -10000 0 -0.3 15 15
PRKCQ -0.074 0.29 0.29 3 -0.74 17 20
LCP2 0.032 0.006 -10000 0 -10000 0 0
BCL10 0.032 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.029 0.17 0.25 3 -0.43 16 19
IKK complex 0.011 0.063 0.19 5 -0.12 12 17
RAS family/GDP 0 0.014 -10000 0 -10000 0 0
MAP3K14 -0.005 0.12 0.21 3 -0.28 14 17
PDPK1 -0.039 0.19 0.26 3 -0.47 17 20
TCR/CD3/MHC I/CD8/Fyn -0.12 0.43 0.27 2 -1.1 16 18
Wnt signaling

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
Noncanonical Wnts/FZD -0.051 0.15 -9999 0 -0.26 36 36
FZD6 0.031 0.008 -9999 0 -10000 0 0
WNT6 0.021 0.069 -9999 0 -0.5 2 2
WNT4 0.022 0.015 -9999 0 -10000 0 0
FZD3 0.031 0.008 -9999 0 -10000 0 0
WNT5A 0.008 0.11 -9999 0 -0.5 5 5
WNT11 -0.12 0.24 -9999 0 -0.5 35 35
ErbB2/ErbB3 signaling events

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
USP8 -0.005 0.012 -10000 0 -10000 0 0
RAS family/GTP -0.026 0.13 -10000 0 -0.29 15 15
NFATC4 -0.029 0.11 0.37 3 -0.24 15 18
ERBB2IP 0.023 0.068 -10000 0 -0.5 2 2
HSP90 (dimer) 0.032 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.044 0.11 -10000 0 -0.29 17 17
JUN -0.017 0.1 0.26 4 -10000 0 4
HRAS 0.03 0.009 -10000 0 -10000 0 0
DOCK7 -0.048 0.11 -10000 0 -0.28 17 17
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.006 0.13 0.24 1 -0.3 17 18
AKT1 0.006 0.009 -10000 0 -10000 0 0
BAD -0.004 0.011 -10000 0 -10000 0 0
MAPK10 -0.025 0.086 0.23 4 -0.26 3 7
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.047 0.12 -10000 0 -0.31 17 17
RAF1 -0.032 0.16 0.33 7 -0.31 15 22
ErbB2/ErbB3/neuregulin 2 -0.023 0.13 -10000 0 -0.31 18 18
STAT3 0.032 0.074 -10000 0 -0.76 1 1
cell migration -0.01 0.11 0.32 7 -0.22 4 11
mol:PI-3-4-5-P3 -0.001 0.003 -10000 0 -10000 0 0
cell proliferation -0.22 0.33 0.51 2 -0.61 37 39
FOS -0.23 0.3 0.44 4 -0.48 69 73
NRAS 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.044 0.11 -10000 0 -0.29 17 17
MAPK3 -0.14 0.26 0.49 2 -0.52 24 26
MAPK1 -0.16 0.28 0.48 2 -0.54 28 30
JAK2 -0.05 0.1 -10000 0 -0.28 17 17
NF2 0.009 0.01 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.021 0.12 0.21 2 -0.29 17 19
NRG1 0.021 0.051 -10000 0 -0.51 1 1
GRB2/SOS1 0.044 0.013 -10000 0 -10000 0 0
MAPK8 -0.052 0.13 -10000 0 -0.3 22 22
MAPK9 -0.023 0.076 0.22 3 -0.23 1 4
ERBB2 -0.02 0.036 0.35 1 -10000 0 1
ERBB3 -0.05 0.19 -10000 0 -0.5 17 17
SHC1 0.027 0.012 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
apoptosis 0.005 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.032 0.073 -10000 0 -0.74 1 1
RNF41 -0.009 0.01 -10000 0 -10000 0 0
FRAP1 -0.002 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.041 0.078 -10000 0 -0.22 17 17
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.034 0.26 1 -10000 0 1
CHRNA1 -0.13 0.26 0.47 2 -0.5 26 28
myelination -0.008 0.15 0.4 8 -0.35 1 9
PPP3CB -0.046 0.1 -10000 0 -0.26 17 17
KRAS 0.031 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.013 0.12 -10000 0 -0.26 15 15
NRG2 0.017 0.084 -10000 0 -0.5 3 3
mol:GDP -0.021 0.12 0.21 2 -0.28 17 19
SOS1 0.032 0.003 -10000 0 -10000 0 0
MAP2K2 -0.056 0.16 0.32 6 -0.34 14 20
SRC 0.032 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.003 -10000 0 -10000 0 0
PTPN11 -0.043 0.11 -10000 0 -0.28 17 17
MAP2K1 -0.14 0.24 0.43 2 -0.47 27 29
heart morphogenesis -0.044 0.11 -10000 0 -0.29 17 17
RAS family/GDP 0.004 0.13 0.28 1 -0.28 15 16
GRB2 0.03 0.009 -10000 0 -10000 0 0
PRKACA 0.012 0.011 -10000 0 -10000 0 0
CHRNE 0.001 0.024 0.13 1 -10000 0 1
HSP90AA1 0.032 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.006 0.009 -10000 0 -10000 0 0
nervous system development -0.044 0.11 -10000 0 -0.29 17 17
CDC42 0.032 0.007 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.032 0.007 -10000 0 -10000 0 0
VLDLR -0.036 0.18 -10000 0 -0.5 15 15
LRPAP1 0.032 0.004 -10000 0 -10000 0 0
NUDC 0.032 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.095 0.18 -10000 0 -0.31 49 49
CaM/Ca2+ 0.023 0.005 -10000 0 -10000 0 0
KATNA1 0.029 0.011 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.1 0.15 0.18 4 -0.28 49 53
IQGAP1/CaM 0.046 0.012 -10000 0 -10000 0 0
DAB1 0.024 0.01 -10000 0 -10000 0 0
IQGAP1 0.031 0.007 -10000 0 -10000 0 0
PLA2G7 0.028 0.012 -10000 0 -10000 0 0
CALM1 0.032 0.007 -10000 0 -10000 0 0
DYNLT1 0.029 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.047 0.01 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.032 0.007 -10000 0 -10000 0 0
CDK5R1 0.021 0.069 -10000 0 -0.5 2 2
LIS1/Poliovirus Protein 3A 0.011 0.004 -10000 0 -10000 0 0
CDK5R2 0.022 0.008 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.14 0.2 -10000 0 -0.34 58 58
YWHAE 0.03 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.071 0.14 0.32 3 -0.28 2 5
MAP1B -0.007 0.063 -10000 0 -0.28 6 6
RAC1 0.016 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.092 0.13 -10000 0 -0.26 47 47
RELN -0.19 0.26 -10000 0 -0.5 49 49
PAFAH/LIS1 0.03 0.014 -10000 0 -10000 0 0
LIS1/CLIP170 0.033 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.061 0.12 -10000 0 -0.25 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.11 0.15 -10000 0 -0.26 57 57
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.082 0.14 0.32 3 -0.29 2 5
LIS1/IQGAP1 0.032 0.012 -10000 0 -10000 0 0
RHOA 0.016 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.015 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.019 0.084 -10000 0 -0.5 3 3
MAP1B/LIS1/Dynein heavy chain 0.024 0.054 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.068 0.13 0.33 1 -0.28 2 3
LRP8 0.032 0.006 -10000 0 -10000 0 0
NDEL1/Katanin 60 -0.074 0.13 0.32 2 -0.28 2 4
P39/CDK5 -0.1 0.13 -10000 0 -0.26 47 47
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.012 -10000 0 -10000 0 0
CDK5 -0.11 0.13 0.18 1 -0.27 49 50
PPP2R5D 0.03 0.01 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0.01 -10000 0 -10000 0 0
CSNK2A1 0.032 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.12 0.18 -10000 0 -0.3 56 56
RELN/VLDLR -0.12 0.2 -10000 0 -0.31 58 58
CDC42 0.016 0.006 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.007 -10000 0 -10000 0 0
LAT2 -0.027 0.11 -10000 0 -0.26 20 20
AP1 -0.14 0.2 -10000 0 -0.42 30 30
mol:PIP3 -0.004 0.19 0.41 8 -0.31 19 27
IKBKB 0.013 0.15 0.34 12 -0.28 3 15
AKT1 -0.012 0.16 0.35 12 -0.34 4 16
IKBKG 0.012 0.15 0.37 10 -0.28 3 13
MS4A2 -0.077 0.21 -10000 0 -0.48 25 25
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
MAP3K1 0.011 0.14 0.37 7 -0.36 1 8
mol:Ca2+ 0.004 0.16 0.36 9 -0.24 19 28
LYN 0.033 0.01 -10000 0 -10000 0 0
CBLB -0.027 0.1 -10000 0 -0.25 20 20
SHC1 0.028 0.012 -10000 0 -10000 0 0
RasGAP/p62DOK 0.028 0.11 -10000 0 -0.31 10 10
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.032 0.006 -10000 0 -10000 0 0
PLD2 -0.013 0.15 0.34 12 -0.24 20 32
PTPN13 -0.006 0.12 -10000 0 -0.41 1 1
PTPN11 0.033 0.013 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.013 0.15 0.4 7 -0.29 2 9
SYK 0.032 0.01 -10000 0 -10000 0 0
GRB2 0.031 0.009 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.039 0.14 -10000 0 -0.31 21 21
LAT -0.044 0.12 -10000 0 -0.27 26 26
PAK2 0.003 0.13 0.3 6 -0.4 1 7
NFATC2 -0.16 0.25 -10000 0 -0.55 34 34
HRAS -0.011 0.12 0.23 1 -0.34 2 3
GAB2 0.023 0.069 -10000 0 -0.5 2 2
PLA2G1B -0.022 0.2 -10000 0 -0.8 7 7
Fc epsilon R1 -0.013 0.14 -10000 0 -0.3 21 21
Antigen/IgE/Fc epsilon R1 -0.009 0.13 -10000 0 -0.27 21 21
mol:GDP -0.019 0.11 -10000 0 -0.43 1 1
JUN -0.04 0.18 -10000 0 -0.5 16 16
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.068 -10000 0 -0.5 2 2
FOS -0.24 0.26 -10000 0 -0.5 60 60
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.023 0.11 -10000 0 -0.26 20 20
CHUK 0.006 0.13 0.31 9 -0.28 3 12
KLRG1 -0.02 0.09 -10000 0 -0.21 19 19
VAV1 -0.03 0.11 -10000 0 -0.25 21 21
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.029 0.11 -10000 0 -0.25 21 21
negative regulation of mast cell degranulation 0.004 0.1 0.26 2 -0.37 1 3
BTK -0.015 0.11 -10000 0 -0.43 1 1
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.035 0.12 -10000 0 -0.25 26 26
GAB2/PI3K/SHP2 -0.034 0.1 -10000 0 -0.24 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.015 0.091 -10000 0 -0.49 1 1
RAF1 -0.029 0.22 -10000 0 -0.89 7 7
Fc epsilon R1/FcgammaRIIB/SHIP 0.002 0.15 -10000 0 -0.27 25 25
FCER1G 0.031 0.017 -10000 0 -10000 0 0
FCER1A 0.015 0.07 -10000 0 -0.51 2 2
Antigen/IgE/Fc epsilon R1/Fyn 0.005 0.12 -10000 0 -0.25 21 21
MAPK3 -0.021 0.2 -10000 0 -0.8 7 7
MAPK1 -0.026 0.2 -10000 0 -0.82 7 7
NFKB1 0.033 0.003 -10000 0 -10000 0 0
MAPK8 -0.024 0.2 -10000 0 -0.55 13 13
DUSP1 -0.008 0.14 -10000 0 -0.5 9 9
NF-kappa-B/RelA 0.002 0.072 0.17 4 -0.17 3 7
actin cytoskeleton reorganization -0.001 0.13 -10000 0 -0.42 1 1
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.005 0.13 0.36 1 -0.41 2 3
FER -0.027 0.1 -10000 0 -0.25 20 20
RELA 0.032 0.004 -10000 0 -10000 0 0
ITK -0.038 0.12 -10000 0 -0.38 12 12
SOS1 0.033 0.003 -10000 0 -10000 0 0
PLCG1 -0.002 0.14 0.3 5 -0.35 2 7
cytokine secretion -0.006 0.045 -10000 0 -10000 0 0
SPHK1 -0.027 0.1 -10000 0 -0.25 20 20
PTK2 -0.003 0.13 -10000 0 -0.44 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.02 0.13 -10000 0 -0.31 20 20
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.012 0.18 0.41 9 -0.3 18 27
MAP2K2 -0.029 0.2 -10000 0 -0.81 7 7
MAP2K1 -0.027 0.21 -10000 0 -0.83 7 7
MAP2K7 0.032 0.007 -10000 0 -10000 0 0
KLRG1/SHP2 -0.005 0.081 -10000 0 -0.35 1 1
MAP2K4 -0.034 0.25 -10000 0 -0.82 11 11
Fc epsilon R1/FcgammaRIIB -0.008 0.15 -10000 0 -0.28 25 25
mol:Choline -0.012 0.15 0.33 12 -0.24 20 32
SHC/Grb2/SOS1 0.014 0.12 -10000 0 -0.41 1 1
FYN 0.029 0.01 -10000 0 -10000 0 0
DOK1 0.033 0.003 -10000 0 -10000 0 0
PXN -0.001 0.13 -10000 0 -0.41 1 1
HCLS1 -0.027 0.1 -10000 0 -0.25 20 20
PRKCB -0.001 0.16 0.35 9 -0.25 23 32
FCGR2B 0.005 0.11 -10000 0 -0.5 5 5
IGHE 0.001 0.009 -10000 0 -10000 0 0
KLRG1/SHIP 0.004 0.1 0.26 2 -0.38 1 3
LCP2 0.032 0.006 -10000 0 -10000 0 0
PLA2G4A -0.052 0.14 -10000 0 -0.28 28 28
RASA1 0.018 0.084 -10000 0 -0.5 3 3
mol:Phosphatidic acid -0.012 0.15 0.33 12 -0.24 20 32
IKK complex 0.022 0.15 0.36 13 -0.21 3 16
WIPF1 0.032 0.004 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.035 0.055 -10000 0 -0.36 2 2
alphaV beta3 Integrin -0.016 0.16 -10000 0 -0.32 24 24
PTK2 -0.05 0.23 0.44 7 -0.42 23 30
IGF1R 0.03 0.009 -10000 0 -10000 0 0
PI4KB 0.028 0.012 -10000 0 -10000 0 0
MFGE8 0.031 0.007 -10000 0 -10000 0 0
SRC 0.032 0.006 -10000 0 -10000 0 0
CDKN1B -0.005 0.082 -10000 0 -0.46 2 2
VEGFA 0.029 0.011 -10000 0 -10000 0 0
ILK -0.005 0.08 -10000 0 -0.45 2 2
ROCK1 0.031 0.007 -10000 0 -10000 0 0
AKT1 -0.011 0.073 -10000 0 -0.42 2 2
PTK2B -0.034 0.13 0.34 2 -0.27 24 26
alphaV/beta3 Integrin/JAM-A 0.011 0.15 -10000 0 -0.28 22 22
CBL 0.023 0.069 -10000 0 -0.5 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.019 0.14 -10000 0 -0.31 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.052 0.092 -10000 0 -0.28 8 8
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.021 0.11 -10000 0 -0.42 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.016 0.14 -10000 0 -0.31 22 22
PI4KA 0.03 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.059 0.21 -10000 0 -0.35 35 35
PI4 Kinase 0.039 0.019 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
alphaV/beta3 Integrin/Osteopontin -0.037 0.17 -10000 0 -0.34 28 28
RPS6KB1 -0.1 0.17 -10000 0 -0.51 12 12
TLN1 0.032 0.007 -10000 0 -10000 0 0
MAPK3 -0.084 0.23 -10000 0 -0.54 22 22
GPR124 0.027 0.049 -10000 0 -0.5 1 1
MAPK1 -0.082 0.23 -10000 0 -0.54 22 22
PXN 0.032 0.007 -10000 0 -10000 0 0
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
alphaV/beta3 Integrin/Tumstatin -0.078 0.21 -10000 0 -0.39 36 36
cell adhesion -0.019 0.14 -10000 0 -0.31 22 22
ANGPTL3 0.017 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.053 -10000 0 -0.31 2 2
IGF-1R heterotetramer 0.03 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.017 0.084 -10000 0 -0.5 3 3
ITGB3 -0.073 0.21 -10000 0 -0.5 23 23
IGF1 0.014 0.096 -10000 0 -0.5 4 4
RAC1 0.031 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.017 0.15 -10000 0 -0.31 24 24
apoptosis 0.032 0.004 -10000 0 -10000 0 0
CD47 0.032 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.012 0.15 -10000 0 -0.31 23 23
VCL 0.032 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.08 0.2 -10000 0 -0.36 36 36
CSF1 0.009 0.11 -10000 0 -0.5 5 5
PIK3C2A -0.005 0.08 -10000 0 -0.45 2 2
PI4 Kinase/Pyk2 -0.018 0.13 -10000 0 -0.28 22 22
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0 0.15 -10000 0 -0.29 24 24
FAK1/Vinculin -0.03 0.19 0.35 7 -0.34 22 29
alphaV beta3/Integrin/ppsTEM5 -0.017 0.15 -10000 0 -0.31 24 24
RHOA 0.031 0.008 -10000 0 -10000 0 0
VTN 0.025 0.049 -10000 0 -0.5 1 1
BCAR1 0.03 0.01 -10000 0 -10000 0 0
FGF2 0.024 0.069 -10000 0 -0.5 2 2
F11R 0.008 0.049 -10000 0 -0.36 2 2
alphaV/beta3 Integrin/Lactadherin -0.01 0.14 -10000 0 -0.31 22 22
alphaV/beta3 Integrin/TGFBR2 -0.021 0.16 -10000 0 -0.33 24 24
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.054 0.089 -10000 0 -0.29 7 7
HSP90AA1 0.032 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.01 0.13 -10000 0 -0.28 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.058 0.2 -10000 0 -0.5 20 20
alphaV/beta3 Integrin/Pyk2 -0.015 0.14 -10000 0 -0.28 24 24
SDC1 0.028 0.012 -10000 0 -10000 0 0
VAV3 0.001 0.069 -10000 0 -0.27 7 7
PTPN11 0.032 0.007 -10000 0 -10000 0 0
IRS1 0.01 0.11 -10000 0 -0.5 5 5
FAK1/Paxillin -0.026 0.2 0.4 7 -0.34 22 29
cell migration -0.033 0.17 0.34 6 -0.31 22 28
ITGAV 0.032 0.004 -10000 0 -10000 0 0
PI3K 0.011 0.15 -10000 0 -0.28 22 22
SPP1 -0.006 0.13 -10000 0 -0.5 8 8
KDR 0.024 0.069 -10000 0 -0.5 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.032 0.004 -10000 0 -10000 0 0
COL4A3 -0.072 0.21 -10000 0 -0.5 23 23
angiogenesis -0.072 0.24 -10000 0 -0.56 22 22
Rac1/GTP 0.016 0.067 -10000 0 -0.25 7 7
EDIL3 -0.066 0.2 -10000 0 -0.5 20 20
cell proliferation -0.021 0.16 -10000 0 -0.33 24 24
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.14 0.25 -9999 0 -0.5 37 37
GNB1/GNG2 -0.027 0.16 -9999 0 -0.39 8 8
mol:DAG -0.041 0.13 -9999 0 -0.37 7 7
PLCG1 -0.043 0.14 -9999 0 -0.38 7 7
YES1 -0.053 0.14 -9999 0 -0.29 20 20
FZD3 0.031 0.008 -9999 0 -10000 0 0
FZD6 0.031 0.008 -9999 0 -10000 0 0
G protein -0.027 0.15 -9999 0 -0.39 7 7
MAP3K7 -0.045 0.11 -9999 0 -0.35 5 5
mol:Ca2+ -0.04 0.13 -9999 0 -0.36 7 7
mol:IP3 -0.041 0.13 -9999 0 -0.37 7 7
NLK -0.003 0.12 -9999 0 -0.72 3 3
GNB1 0.032 0.007 -9999 0 -10000 0 0
CAMK2A -0.042 0.12 -9999 0 -0.35 6 6
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.051 0.15 -9999 0 -0.26 36 36
CSNK1A1 0.032 0.006 -9999 0 -10000 0 0
GNAS -0.054 0.14 -9999 0 -0.29 20 20
GO:0007205 -0.046 0.12 -9999 0 -0.37 7 7
WNT6 0.021 0.069 -9999 0 -0.5 2 2
WNT4 0.022 0.015 -9999 0 -10000 0 0
NFAT1/CK1 alpha -0.1 0.19 -9999 0 -0.42 21 21
GNG2 0.018 0.084 -9999 0 -0.5 3 3
WNT5A 0.008 0.11 -9999 0 -0.5 5 5
WNT11 -0.12 0.24 -9999 0 -0.5 35 35
CDC42 -0.049 0.13 -9999 0 -0.43 5 5
Signaling events mediated by PTP1B

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
PDGFRB -0.04 0.18 -10000 0 -0.5 16 16
Jak2/Leptin Receptor -0.11 0.17 -10000 0 -0.38 22 22
PTP1B/AKT1 0.004 0.12 0.3 6 -0.27 8 14
FYN 0.029 0.01 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.005 0.14 0.31 8 -0.3 9 17
EGFR 0.027 0.051 -10000 0 -0.51 1 1
EGF/EGFR 0.003 0.11 0.27 5 -0.31 5 10
CSF1 0.009 0.11 -10000 0 -0.5 5 5
AKT1 0.032 0.007 -10000 0 -10000 0 0
INSR 0.032 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.11 0.34 4 -0.28 7 11
Insulin Receptor/Insulin 0.019 0.12 0.3 6 -0.28 3 9
HCK 0.031 0.008 -10000 0 -10000 0 0
CRK 0.03 0.009 -10000 0 -10000 0 0
TYK2 -0.004 0.14 0.31 9 -0.3 8 17
EGF 0.023 0.019 -10000 0 -10000 0 0
YES1 0.031 0.007 -10000 0 -10000 0 0
CAV1 0.008 0.14 0.31 11 -0.31 5 16
TXN 0.034 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0 0.13 0.26 5 -0.29 10 15
cell migration 0.005 0.14 0.3 9 -0.31 8 17
STAT3 0.03 0.009 -10000 0 -10000 0 0
PRLR -0.11 0.23 -10000 0 -0.48 31 31
ITGA2B 0.019 0.068 -10000 0 -0.5 2 2
CSF1R 0.032 0.007 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin -0.12 0.22 -10000 0 -0.4 42 42
FGR 0.027 0.049 -10000 0 -0.5 1 1
PTP1B/p130 Cas -0.004 0.12 0.24 6 -0.3 8 14
Crk/p130 Cas 0.005 0.12 0.25 6 -0.28 8 14
DOK1 -0.022 0.16 0.31 8 -0.32 14 22
JAK2 -0.089 0.17 0.32 1 -0.39 18 19
Jak2/Leptin Receptor/Leptin -0.13 0.15 -10000 0 -0.35 23 23
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
PTPN1 -0.006 0.14 0.31 8 -0.3 9 17
LYN 0.032 0.007 -10000 0 -10000 0 0
CDH2 0.02 0.016 -10000 0 -10000 0 0
SRC 0.026 0.097 0.36 1 -0.54 2 3
ITGB3 -0.073 0.21 -10000 0 -0.5 23 23
CAT1/PTP1B -0.025 0.16 0.3 8 -0.36 11 19
CAPN1 0.034 0.01 -10000 0 -10000 0 0
CSK 0.032 0.006 -10000 0 -10000 0 0
PI3K 0.019 0.12 0.26 1 -0.38 4 5
mol:H2O2 0.003 0.011 -10000 0 -10000 0 0
STAT3 (dimer) -0.12 0.14 -10000 0 -0.33 22 22
negative regulation of transcription -0.088 0.17 0.32 1 -0.38 18 19
FCGR2A 0.027 0.013 -10000 0 -10000 0 0
FER 0.034 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.04 0.16 -10000 0 -0.36 24 24
BLK -0.04 0.18 -10000 0 -0.5 16 16
Insulin Receptor/Insulin/Shc 0.048 0.023 -10000 0 -10000 0 0
RHOA 0.033 0.012 -10000 0 -10000 0 0
LEPR -0.033 0.17 -10000 0 -0.5 14 14
BCAR1 0.03 0.01 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.03 0.009 -10000 0 -10000 0 0
mol:NADPH 0.002 0.009 -10000 0 -10000 0 0
TRPV6 -0.044 0.19 -10000 0 -0.54 12 12
PRL -0.052 0.18 -10000 0 -0.47 18 18
SOCS3 -0.018 0.25 -10000 0 -1.2 5 5
SPRY2 0.016 0.098 -10000 0 -0.5 4 4
Insulin Receptor/Insulin/IRS1 0.038 0.075 -10000 0 -0.31 5 5
CSF1/CSF1R 0.005 0.15 0.31 6 -0.32 11 17
Ras protein signal transduction 0.021 0.13 0.55 6 -10000 0 6
IRS1 0.01 0.11 -10000 0 -0.5 5 5
INS 0.011 0.017 -10000 0 -10000 0 0
LEP -0.2 0.25 -10000 0 -0.5 49 49
STAT5B -0.032 0.14 0.29 5 -0.3 13 18
STAT5A -0.032 0.14 0.29 5 -0.3 13 18
GRB2 0.03 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.03 0.17 0.3 6 -0.34 17 23
CSN2 -0.14 0.35 -10000 0 -1.4 8 8
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
LAT -0.013 0.14 -10000 0 -0.43 10 10
YBX1 0.041 0.011 -10000 0 -10000 0 0
LCK -0.004 0.13 -10000 0 -0.5 8 8
SHC1 0.028 0.012 -10000 0 -10000 0 0
NOX4 -0.024 0.17 -10000 0 -0.5 13 13
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.02 0.053 -10000 0 -10000 0 0
VDR 0.031 0.008 -10000 0 -10000 0 0
FAM120B 0.029 0.01 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.065 0.14 -10000 0 -0.33 9 9
RXRs/LXRs/DNA/Oxysterols -0.059 0.15 -10000 0 -0.43 10 10
MED1 0.03 0.009 -10000 0 -10000 0 0
mol:9cRA 0.001 0.014 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.01 0.079 -10000 0 -0.23 11 11
RXRs/NUR77 -0.065 0.17 -10000 0 -0.29 41 41
RXRs/PPAR -0.098 0.16 -10000 0 -0.27 48 48
NCOR2 0.032 0.007 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.068 0.027 -10000 0 -10000 0 0
RARA 0.03 0.009 -10000 0 -10000 0 0
NCOA1 0.033 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.031 0.008 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.049 0.024 -10000 0 -10000 0 0
RARG 0.032 0.007 -10000 0 -10000 0 0
RPS6KB1 0.043 0.11 0.67 3 -10000 0 3
RARs/THRs/DNA/SMRT 0.009 0.085 -10000 0 -0.25 11 11
THRA 0.03 0.009 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.065 0.16 -10000 0 -0.28 39 39
NR1H4 0.019 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA -0.045 0.17 -10000 0 -0.27 39 39
NR1H2 0.03 0.023 -10000 0 -10000 0 0
NR1H3 0.03 0.025 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.054 0.15 -10000 0 -0.27 39 39
NR4A1 0.009 0.11 -10000 0 -0.5 5 5
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.054 0.11 -10000 0 -0.29 4 4
RXRG -0.16 0.24 -10000 0 -0.5 39 39
RXR alpha/CCPG 0.038 0.028 -10000 0 -10000 0 0
RXRA 0.028 0.025 -10000 0 -10000 0 0
RXRB 0.026 0.026 -10000 0 -10000 0 0
THRB -0.014 0.15 -10000 0 -0.5 10 10
PPARG -0.05 0.19 -10000 0 -0.5 18 18
PPARD 0.03 0.01 -10000 0 -10000 0 0
TNF -0.11 0.3 -10000 0 -1 10 10
mol:Oxysterols 0.001 0.013 -10000 0 -10000 0 0
cholesterol transport -0.059 0.15 -10000 0 -0.42 10 10
PPARA 0.03 0.009 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.03 0.01 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.077 0.13 -10000 0 -0.24 44 44
SREBF1 -0.056 0.14 -10000 0 -0.54 3 3
RXRs/RXRs/DNA/9cRA -0.065 0.16 -10000 0 -0.28 39 39
ABCA1 -0.056 0.14 -10000 0 -0.54 3 3
RARs/THRs 0.055 0.1 -10000 0 -0.26 10 10
RXRs/FXR -0.062 0.16 -10000 0 -0.29 39 39
BCL2 0.022 0.069 -10000 0 -0.5 2 2
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.031 0.17 0.26 1 -0.44 17 18
PDGFB-D/PDGFRB/SLAP -0.028 0.16 -10000 0 -0.35 22 22
PDGFB-D/PDGFRB/APS/CBL 0.009 0.13 -10000 0 -0.3 17 17
AKT1 -0.02 0.13 0.4 5 -0.38 1 6
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.033 0.19 -10000 0 -0.47 17 17
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
FGR -0.033 0.14 -10000 0 -0.36 17 17
mol:Ca2+ -0.045 0.19 -10000 0 -0.5 17 17
MYC -0.002 0.18 0.42 4 -0.44 6 10
SHC1 0.028 0.012 -10000 0 -10000 0 0
HRAS/GDP -0.006 0.11 -10000 0 -0.24 19 19
LRP1/PDGFRB/PDGFB -0.024 0.18 -10000 0 -0.4 21 21
GRB10 0.031 0.008 -10000 0 -10000 0 0
PTPN11 0.032 0.007 -10000 0 -10000 0 0
GO:0007205 -0.046 0.2 -10000 0 -0.51 17 17
PTEN 0.032 0.006 -10000 0 -10000 0 0
GRB2 0.03 0.009 -10000 0 -10000 0 0
GRB7 0.029 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 -0.009 0.14 -10000 0 -0.36 16 16
PDGFB-D/PDGFRB/GRB10 -0.007 0.14 -10000 0 -0.36 15 15
cell cycle arrest -0.028 0.16 -10000 0 -0.35 22 22
HRAS 0.03 0.009 -10000 0 -10000 0 0
HIF1A -0.021 0.12 0.38 5 -0.53 1 6
GAB1 -0.04 0.19 0.26 1 -0.47 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.034 0.17 0.28 2 -0.43 17 19
PDGFB-D/PDGFRB 0.012 0.13 -10000 0 -0.32 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.008 0.14 -10000 0 -0.36 16 16
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.028 0.16 -10000 0 -0.4 18 18
positive regulation of MAPKKK cascade -0.009 0.14 -10000 0 -0.36 16 16
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
mol:IP3 -0.046 0.2 -10000 0 -0.52 17 17
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.012 0.14 -10000 0 -0.36 16 16
SHB 0.031 0.007 -10000 0 -10000 0 0
BLK -0.099 0.24 -10000 0 -0.58 18 18
PTPN2 0.031 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.007 0.14 -10000 0 -0.36 16 16
BCAR1 0.03 0.01 -10000 0 -10000 0 0
VAV2 -0.035 0.19 0.28 1 -0.46 18 19
CBL 0.023 0.069 -10000 0 -0.5 2 2
PDGFB-D/PDGFRB/DEP1 -0.008 0.14 -10000 0 -0.36 16 16
LCK -0.066 0.2 -10000 0 -0.57 11 11
PDGFRB -0.04 0.18 -10000 0 -0.5 16 16
ACP1 0.033 0.003 -10000 0 -10000 0 0
HCK -0.021 0.11 -10000 0 -0.32 3 3
ABL1 -0.039 0.17 -10000 0 -0.41 18 18
PDGFB-D/PDGFRB/CBL -0.051 0.21 -10000 0 -0.54 17 17
PTPN1 0.032 0.007 -10000 0 -10000 0 0
SNX15 0.032 0.004 -10000 0 -10000 0 0
STAT3 0.03 0.009 -10000 0 -10000 0 0
STAT1 0.033 0.003 -10000 0 -10000 0 0
cell proliferation 0.001 0.17 0.39 5 -0.4 6 11
SLA 0.004 0.12 -10000 0 -0.5 6 6
actin cytoskeleton reorganization -0.001 0.11 0.36 1 -0.25 16 17
SRC -0.022 0.12 -10000 0 -0.33 4 4
PI3K -0.023 0.096 -10000 0 -0.25 17 17
PDGFB-D/PDGFRB/GRB7/SHC 0.009 0.12 -10000 0 -0.31 14 14
SH2B2 0.03 0.009 -10000 0 -10000 0 0
PLCgamma1/SPHK1 -0.034 0.19 -10000 0 -0.49 17 17
LYN -0.021 0.12 -10000 0 -0.31 15 15
LRP1 -0.027 0.17 -10000 0 -0.5 13 13
SOS1 0.033 0.003 -10000 0 -10000 0 0
STAT5B 0.031 0.008 -10000 0 -10000 0 0
STAT5A 0.031 0.008 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.038 0.12 -10000 0 -0.26 17 17
SPHK1 0.025 0.049 -10000 0 -0.5 1 1
EDG1 -0.001 0.004 -10000 0 -10000 0 0
mol:DAG -0.046 0.2 -10000 0 -0.52 17 17
PLCG1 -0.048 0.2 -10000 0 -0.53 17 17
NHERF/PDGFRB 0.009 0.13 -10000 0 -0.31 16 16
YES1 -0.033 0.15 0.36 1 -0.44 7 8
cell migration 0.009 0.13 -10000 0 -0.31 16 16
SHC/Grb2/SOS1 0.039 0.12 -10000 0 -0.26 14 14
SLC9A3R2 0.031 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.031 0.008 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.027 0.12 -10000 0 -0.28 16 16
FYN -0.051 0.18 0.34 1 -0.38 22 23
DOK1 -0.018 0.11 0.18 1 -0.28 16 17
HRAS/GTP 0.023 0.006 -10000 0 -10000 0 0
PDGFB 0.03 0.01 -10000 0 -10000 0 0
RAC1 -0.023 0.19 0.35 3 -0.42 18 21
PRKCD -0.018 0.11 0.2 1 -0.28 16 17
FER -0.018 0.11 0.2 1 -0.28 16 17
MAPKKK cascade -0.01 0.13 0.4 4 -0.26 13 17
RASA1 -0.025 0.12 0.2 1 -0.28 19 20
NCK1 0.027 0.049 -10000 0 -0.5 1 1
NCK2 0.033 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.001 0.11 -10000 0 -0.26 16 16
PDGFB-D/PDGFRB/SHB -0.009 0.14 -10000 0 -0.36 16 16
chemotaxis -0.038 0.17 -10000 0 -0.4 18 18
STAT1-3-5/STAT1-3-5 0.031 0.11 -10000 0 -0.25 15 15
Bovine Papilomavirus E5/PDGFRB -0.029 0.13 -10000 0 -0.36 16 16
PTPRJ 0.032 0.005 -10000 0 -10000 0 0
BARD1 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
BARD1/CSTF1 -0.029 0.16 -10000 0 -0.36 22 22
ATM 0.028 0.049 -10000 0 -0.5 1 1
UBE2D3 0.033 0.003 -10000 0 -10000 0 0
PRKDC 0.032 0.007 -10000 0 -10000 0 0
ATR 0.027 0.049 -10000 0 -0.5 1 1
UBE2L3 0.03 0.009 -10000 0 -10000 0 0
FANCD2 0.019 0.07 -10000 0 -0.74 1 1
protein ubiquitination 0.012 0.14 -10000 0 -0.28 22 22
XRCC5 0.033 0.003 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.059 0.038 -10000 0 -0.31 1 1
MRE11A 0.028 0.049 -10000 0 -0.5 1 1
DNA-PK 0.06 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.016 0.079 -10000 0 -0.34 4 4
FANCF 0.032 0.006 -10000 0 -10000 0 0
BRCA1 0.03 0.009 -10000 0 -10000 0 0
CCNE1 0.032 0.007 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.045 0.013 -10000 0 -10000 0 0
FANCG 0.032 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.032 0.16 -10000 0 -0.36 22 22
FANCE 0.029 0.01 -10000 0 -10000 0 0
FANCC 0.032 0.007 -10000 0 -10000 0 0
NBN 0.031 0.007 -10000 0 -10000 0 0
FANCA 0.03 0.01 -10000 0 -10000 0 0
DNA repair -0.019 0.12 0.29 2 -0.39 4 6
BRCA1/BARD1/ubiquitin -0.032 0.16 -10000 0 -0.36 22 22
BARD1/DNA-PK 0.008 0.14 -10000 0 -0.28 22 22
FANCL 0.033 0.003 -10000 0 -10000 0 0
mRNA polyadenylation 0.029 0.16 0.36 22 -10000 0 22
BRCA1/BARD1/CTIP/M/R/N Complex -0.018 0.13 -10000 0 -0.26 21 21
BRCA1/BACH1/BARD1/TopBP1 -0.011 0.14 -10000 0 -0.31 22 22
BRCA1/BARD1/P53 0.004 0.15 -10000 0 -0.3 22 22
BARD1/CSTF1/BRCA1 -0.01 0.14 -10000 0 -0.31 22 22
BRCA1/BACH1 0.03 0.009 -10000 0 -10000 0 0
BARD1 -0.066 0.21 -10000 0 -0.5 22 22
PCNA 0.032 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.009 0.14 -10000 0 -0.31 22 22
BRCA1/BARD1/UbcH7 -0.011 0.14 -10000 0 -0.31 22 22
BRCA1/BARD1/RAD51/PCNA 0.004 0.14 -10000 0 -0.28 23 23
BARD1/DNA-PK/P53 0.016 0.14 -10000 0 -0.27 22 22
BRCA1/BARD1/Ubiquitin -0.032 0.16 -10000 0 -0.36 22 22
BRCA1/BARD1/CTIP -0.014 0.14 -10000 0 -0.29 22 22
FA complex 0.031 0.027 -10000 0 -10000 0 0
BARD1/EWS -0.032 0.16 -10000 0 -0.36 22 22
RBBP8 0.013 0.035 -10000 0 -0.36 1 1
TP53 0.03 0.01 -10000 0 -10000 0 0
TOPBP1 0.031 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.003 0.14 0.29 22 -10000 0 22
BRCA1/BARD1 0.018 0.15 -10000 0 -0.28 22 22
CSTF1 0.032 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.047 0.15 -10000 0 -0.36 22 22
CDK2 0.032 0.007 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.027 0.049 -10000 0 -0.5 1 1
RAD50 0.032 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.032 0.16 -10000 0 -0.36 22 22
EWSR1 0.029 0.01 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.015 0.17 -9999 0 -0.44 13 13
MAP4K1 0.032 0.006 -9999 0 -10000 0 0
MAP3K8 0.032 0.005 -9999 0 -10000 0 0
PRKCB -0.013 0.15 -9999 0 -0.5 10 10
DBNL 0.031 0.008 -9999 0 -10000 0 0
CRKL 0.03 0.009 -9999 0 -10000 0 0
MAP3K1 -0.022 0.13 -9999 0 -0.44 9 9
JUN -0.12 0.27 -9999 0 -0.71 18 18
MAP3K7 -0.016 0.12 -9999 0 -0.45 8 8
GRAP2 -0.028 0.17 -9999 0 -0.5 13 13
CRK 0.03 0.009 -9999 0 -10000 0 0
MAP2K4 -0.023 0.13 -9999 0 -0.46 8 8
LAT -0.017 0.15 -9999 0 -0.5 11 11
LCP2 0.032 0.006 -9999 0 -10000 0 0
MAPK8 -0.082 0.28 -9999 0 -0.68 20 20
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.015 0.14 -9999 0 -0.39 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 0.026 0.17 -9999 0 -0.42 13 13
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.034 0.019 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 0.003 0.15 -10000 0 -0.78 3 3
EGFR 0.026 0.049 -10000 0 -0.5 1 1
EPHA2 0.027 0.049 -10000 0 -0.5 1 1
USP6 0.03 0.01 -10000 0 -10000 0 0
IQSEC1 0.031 0.008 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.036 0.04 -10000 0 -0.36 1 1
ARRB2 -0.036 0.12 -10000 0 -0.34 16 16
mol:GTP 0.014 0.041 0.16 2 -0.13 2 4
ARRB1 0.032 0.004 -10000 0 -10000 0 0
FBXO8 0.032 0.004 -10000 0 -10000 0 0
TSHR -0.059 0.2 -10000 0 -0.5 20 20
EGF 0.025 0.011 -10000 0 -10000 0 0
somatostatin receptor activity 0 0 0.001 6 -0.001 17 23
ARAP2 0.032 0.004 -10000 0 -10000 0 0
mol:GDP -0.092 0.16 0.25 3 -0.32 23 26
mol:PI-3-4-5-P3 0 0 0.001 3 -0.001 7 10
ITGA2B 0.019 0.069 -10000 0 -0.5 2 2
ARF6 0.031 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.063 0.065 -10000 0 -0.54 1 1
ADAP1 0.026 0.013 -10000 0 -10000 0 0
KIF13B 0.031 0.007 -10000 0 -10000 0 0
HGF/MET 0.023 0.091 -10000 0 -0.44 4 4
PXN 0.032 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.069 0.13 0.31 4 -0.26 19 23
EGFR/EGFR/EGF/EGF/ARFGEP100 0.05 0.041 -10000 0 -0.31 1 1
ADRB2 0.032 0.006 -10000 0 -10000 0 0
receptor agonist activity 0 0 0 5 0 18 23
actin filament binding 0 0 0.001 6 0 16 22
SRC 0.032 0.006 -10000 0 -10000 0 0
ITGB3 -0.073 0.21 -10000 0 -0.5 23 23
GNAQ 0.031 0.007 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.003 6 -0.001 7 13
ARF6/GDP -0.021 0.15 0.24 2 -0.42 11 13
ARF6/GDP/GULP/ACAP1 -0.11 0.18 0.28 2 -0.34 34 36
alphaIIb/beta3 Integrin/paxillin/GIT1 0.005 0.14 -10000 0 -0.28 24 24
ACAP1 0.003 0.12 -10000 0 -0.5 6 6
ACAP2 0.027 0.049 -10000 0 -0.5 1 1
LHCGR/beta Arrestin2 -0.043 0.15 -10000 0 -0.43 16 16
EFNA1 0.027 0.013 -10000 0 -10000 0 0
HGF 0.017 0.084 -10000 0 -0.5 3 3
CYTH3 0.008 0.002 -10000 0 -10000 0 0
CYTH2 -0.003 0.16 -10000 0 -0.98 3 3
NCK1 0.027 0.049 -10000 0 -0.5 1 1
fibronectin binding 0 0 0.001 6 0 9 15
endosomal lumen acidification 0 0 0.001 4 0 20 24
microtubule-based process 0 0 -10000 0 0 2 2
GULP1 -0.04 0.18 -10000 0 -0.5 16 16
GNAQ/ARNO 0.015 0.15 -10000 0 -0.91 3 3
mol:Phosphatidic acid 0 0 0.001 2 -10000 0 2
PIP3-E 0 0 0 4 0 3 7
MET 0.017 0.069 -10000 0 -0.5 2 2
GNA14 0.018 0.084 -10000 0 -0.5 3 3
GNA15 0.031 0.007 -10000 0 -10000 0 0
GIT1 0.03 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.002 6 -0.001 13 19
GNA11 0.005 0.12 -10000 0 -0.5 6 6
LHCGR -0.051 0.18 -10000 0 -0.5 16 16
AGTR1 -0.22 0.26 -10000 0 -0.5 56 56
desensitization of G-protein coupled receptor protein signaling pathway -0.043 0.15 -10000 0 -0.43 16 16
IPCEF1/ARNO 0.021 0.15 -10000 0 -0.9 3 3
alphaIIb/beta3 Integrin -0.041 0.16 -10000 0 -0.36 24 24
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.006 0.17 -10000 0 -0.29 29 29
SMAD6-7/SMURF1 0.057 0.039 -10000 0 -0.31 1 1
NOG 0.026 0.049 -10000 0 -0.5 1 1
SMAD9 -0.072 0.21 -10000 0 -0.49 22 22
SMAD4 0.031 0.007 -10000 0 -10000 0 0
SMAD5 -0.018 0.11 -10000 0 -0.46 3 3
BMP7/USAG1 0.014 0.097 -10000 0 -0.34 8 8
SMAD5/SKI -0.008 0.13 0.27 2 -0.44 5 7
SMAD1 0.015 0.064 -10000 0 -0.36 2 2
BMP2 0.004 0.12 -10000 0 -0.5 6 6
SMAD1/SMAD1/SMAD4 0.036 0.068 -10000 0 -0.36 1 1
BMPR1A 0.027 0.049 -10000 0 -0.5 1 1
BMPR1B -0.043 0.19 -10000 0 -0.5 17 17
BMPR1A-1B/BAMBI 0.001 0.14 -10000 0 -0.31 20 20
AHSG 0.02 0.007 -10000 0 -10000 0 0
CER1 0.017 0.005 -10000 0 -10000 0 0
BMP2-4/CER1 -0.019 0.15 -10000 0 -0.36 19 19
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.018 0.12 -10000 0 -0.38 6 6
BMP2-4 (homodimer) -0.031 0.17 -10000 0 -0.41 19 19
RGMB 0.031 0.008 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.023 0.13 -10000 0 -0.27 18 18
RGMA 0.03 0.009 -10000 0 -10000 0 0
SMURF1 0.031 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.022 0.12 -10000 0 -0.37 7 7
BMP2-4/USAG1 -0.023 0.17 -10000 0 -0.37 21 21
SMAD6/SMURF1/SMAD5 -0.01 0.13 0.28 1 -0.45 4 5
SOSTDC1 0.01 0.096 -10000 0 -0.5 4 4
BMP7/BMPR2/BMPR1A-1B 0.024 0.14 -10000 0 -0.3 17 17
SKI 0.032 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.028 0.012 -10000 0 -10000 0 0
HFE2 0.021 0.011 -10000 0 -10000 0 0
ZFYVE16 0.032 0.007 -10000 0 -10000 0 0
MAP3K7 0.03 0.01 -10000 0 -10000 0 0
BMP2-4/CHRD -0.15 0.23 -10000 0 -0.37 58 58
SMAD5/SMAD5/SMAD4 -0.009 0.12 0.28 1 -0.4 5 6
MAPK1 0.03 0.009 -10000 0 -10000 0 0
TAK1/TAB family -0.01 0.12 -10000 0 -0.34 7 7
BMP7 (homodimer) 0.013 0.096 -10000 0 -0.5 4 4
NUP214 0.032 0.007 -10000 0 -10000 0 0
BMP6/FETUA 0.032 0.016 -10000 0 -10000 0 0
SMAD1/SKI 0.026 0.078 -10000 0 -0.34 2 2
SMAD6 0.032 0.007 -10000 0 -10000 0 0
CTDSP2 0.032 0.007 -10000 0 -10000 0 0
BMP2-4/FETUA -0.015 0.15 -10000 0 -0.35 19 19
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.11 0.23 -10000 0 -0.5 31 31
BMPR2 (homodimer) 0.033 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.062 0.018 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.014 0.15 -10000 0 -0.36 18 18
CHRDL1 -0.11 0.24 -10000 0 -0.5 32 32
ENDOFIN/SMAD1 0.025 0.075 -10000 0 -0.35 2 2
SMAD6-7/SMURF1/SMAD1 0.053 0.081 -10000 0 -0.39 1 1
SMAD6/SMURF1 0.031 0.008 -10000 0 -10000 0 0
BAMBI 0.018 0.084 -10000 0 -0.5 3 3
SMURF2 0.031 0.008 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.1 0.22 -10000 0 -0.37 44 44
BMP2-4/GREM1 -0.1 0.21 -10000 0 -0.35 46 46
SMAD7 0.027 0.049 -10000 0 -0.5 1 1
SMAD8A/SMAD8A/SMAD4 -0.06 0.21 -10000 0 -0.47 22 22
SMAD1/SMAD6 0.025 0.078 -10000 0 -0.33 3 3
TAK1/SMAD6 0.042 0.017 -10000 0 -10000 0 0
BMP7 0.013 0.096 -10000 0 -0.5 4 4
BMP6 0.028 0.012 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.016 0.11 -10000 0 -0.32 7 7
PPM1A 0.031 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.027 0.07 -10000 0 -0.34 2 2
SMAD7/SMURF1 0.041 0.04 -10000 0 -0.36 1 1
CTDSPL 0.031 0.008 -10000 0 -10000 0 0
PPP1CA 0.032 0.004 -10000 0 -10000 0 0
XIAP 0.032 0.006 -10000 0 -10000 0 0
CTDSP1 0.033 0.003 -10000 0 -10000 0 0
PPP1R15A 0.032 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.059 0.18 -10000 0 -0.47 15 15
CHRD -0.2 0.26 -10000 0 -0.5 52 52
BMPR2 0.033 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.027 0.12 -10000 0 -0.38 7 7
BMP4 -0.042 0.18 -10000 0 -0.5 16 16
FST -0.042 0.18 -10000 0 -0.5 16 16
BMP2-4/NOG -0.01 0.16 -10000 0 -0.37 17 17
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.038 0.13 -10000 0 -0.29 15 15
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.042 0.075 -10000 0 -0.3 5 5
fibroblast growth factor receptor signaling pathway 0.041 0.074 -10000 0 -0.3 5 5
LAMA1 0.016 0.069 -10000 0 -0.5 2 2
PRNP 0.032 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.075 0.18 -10000 0 -0.35 36 36
SMAD2 0.014 0.052 0.18 1 -0.28 3 4
GPC1/PrPc/Cu2+ 0.039 0.015 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.027 0.056 -10000 0 -0.36 2 2
TDGF1 -0.059 0.19 -10000 0 -0.5 18 18
CRIPTO/GPC1 -0.033 0.14 -10000 0 -0.36 18 18
APP/GPC1 0.04 0.019 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.013 0.12 -10000 0 -0.3 17 17
FLT1 0.031 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.063 -10000 0 -0.31 3 3
SERPINC1 0.027 0.012 -10000 0 -10000 0 0
FYN -0.012 0.12 -10000 0 -0.3 17 17
FGR -0.017 0.13 -10000 0 -0.3 19 19
positive regulation of MAPKKK cascade -0.06 0.17 0.21 1 -0.37 23 24
SLIT2 -0.13 0.24 -10000 0 -0.5 36 36
GPC1/NRG 0.035 0.041 -10000 0 -0.36 1 1
NRG1 0.024 0.049 -10000 0 -0.5 1 1
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.053 0.027 -10000 0 -10000 0 0
LYN -0.007 0.12 -10000 0 -0.3 15 15
mol:Spermine 0.008 0.003 -10000 0 -10000 0 0
cell growth 0.041 0.074 -10000 0 -0.3 5 5
BMP signaling pathway -0.03 0.01 -10000 0 -10000 0 0
SRC -0.009 0.12 -10000 0 -0.3 16 16
TGFBR1 0.031 0.007 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.11 0.23 -10000 0 -0.5 30 30
GPC1 0.03 0.01 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.031 0.007 -10000 0 -10000 0 0
VEGFA 0.029 0.011 -10000 0 -10000 0 0
BLK -0.049 0.16 -10000 0 -0.31 29 29
HCK -0.008 0.12 -10000 0 -0.3 16 16
FGF2 0.024 0.069 -10000 0 -0.5 2 2
FGFR1 0.018 0.084 -10000 0 -0.5 3 3
VEGFR1 homodimer 0.031 0.007 -10000 0 -10000 0 0
TGFBR2 0.017 0.084 -10000 0 -0.5 3 3
cell death 0.04 0.019 -10000 0 -10000 0 0
ATIII/GPC1 0.038 0.02 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.065 0.17 -10000 0 -0.36 30 30
LCK -0.036 0.14 -10000 0 -0.3 26 26
neuron differentiation 0.035 0.041 -10000 0 -0.36 1 1
PrPc/Cu2+ 0.024 0.004 -10000 0 -10000 0 0
APP 0.029 0.011 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.017 0.083 -10000 0 -0.5 3 3
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.032 0.007 -9999 0 -10000 0 0
HDAC3 0.032 0.006 -9999 0 -10000 0 0
VDR 0.031 0.008 -9999 0 -10000 0 0
Cbp/p300/PCAF 0.054 0.05 -9999 0 -0.3 2 2
EP300 0.03 0.009 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.013 0.11 -9999 0 -0.43 6 6
KAT2B 0.022 0.069 -9999 0 -0.5 2 2
MAPK14 0.03 0.01 -9999 0 -10000 0 0
AKT1 -0.02 0.073 -9999 0 -0.25 4 4
RAR alpha/9cRA/Cyclin H -0.006 0.13 -9999 0 -0.28 2 2
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.001 0.082 -9999 0 -0.29 6 6
CDC2 0 0 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.037 0.14 -9999 0 -0.41 8 8
NCOR2 0.032 0.007 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.023 0.006 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.096 0.2 -9999 0 -0.46 24 24
NCOA2 -0.14 0.25 -9999 0 -0.5 38 38
NCOA3 0.032 0.006 -9999 0 -10000 0 0
NCOA1 0.033 0.003 -9999 0 -10000 0 0
VDR/VDR/DNA 0.031 0.008 -9999 0 -10000 0 0
RARG 0.032 0.007 -9999 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.011 -9999 0 -10000 0 0
MAPK3 0.033 0.005 -9999 0 -10000 0 0
MAPK1 0.03 0.009 -9999 0 -10000 0 0
MAPK8 0.002 0.12 -9999 0 -0.5 7 7
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.099 0.21 -9999 0 -0.47 24 24
RARA -0.045 0.11 -9999 0 -0.23 32 32
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.073 0.14 -9999 0 -0.33 15 15
PRKCA 0.033 0.009 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.11 0.21 -9999 0 -0.47 25 25
RXRG -0.14 0.23 -9999 0 -0.4 45 45
RXRA -0.032 0.099 -9999 0 -0.2 30 30
RXRB -0.052 0.15 -9999 0 -0.33 26 26
VDR/Vit D3/DNA 0.023 0.006 -9999 0 -10000 0 0
RBP1 0.028 0.012 -9999 0 -10000 0 0
CRBP1/9-cic-RA 0.021 0.009 -9999 0 -10000 0 0
RARB 0.031 0.01 -9999 0 -10000 0 0
PRKCG -0.092 0.23 -9999 0 -0.5 28 28
MNAT1 0.031 0.007 -9999 0 -10000 0 0
RAR alpha/RXRs -0.099 0.2 -9999 0 -0.48 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.083 0.18 -9999 0 -0.4 26 26
proteasomal ubiquitin-dependent protein catabolic process -0.031 0.12 -9999 0 -0.39 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.1 0.21 -9999 0 -0.46 25 25
positive regulation of DNA binding -0.013 0.11 -9999 0 -0.27 2 2
NRIP1 -0.093 0.2 -9999 0 -0.52 13 13
RXRs/RARs -0.11 0.22 -9999 0 -0.46 28 28
RXRs/RXRs/DNA/9cRA -0.11 0.21 -9999 0 -0.48 24 24
PRKACA 0.032 0.006 -9999 0 -10000 0 0
CDK7 0.032 0.007 -9999 0 -10000 0 0
TFIIH 0.062 0.018 -9999 0 -10000 0 0
RAR alpha/9cRA 0.011 0.11 -9999 0 -0.29 1 1
CCNH 0.032 0.007 -9999 0 -10000 0 0
CREBBP 0.032 0.005 -9999 0 -10000 0 0
RAR gamma2/9cRA 0.058 0.023 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.016 0.004 -10000 0 -10000 0 0
SMARCC1 0.015 0.009 -10000 0 -10000 0 0
REL -0.008 0.14 -10000 0 -0.5 9 9
HDAC7 -0.079 0.11 -10000 0 -0.29 14 14
JUN -0.04 0.18 -10000 0 -0.5 16 16
EP300 0.03 0.009 -10000 0 -10000 0 0
KAT2B 0.022 0.069 -10000 0 -0.5 2 2
KAT5 0.032 0.004 -10000 0 -10000 0 0
MAPK14 0 0.049 -10000 0 -0.35 2 2
FOXO1 0.031 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.073 0.12 -10000 0 -0.29 19 19
MAP2K6 0.013 0.069 -10000 0 -0.49 2 2
BRM/BAF57 0.044 0.016 -10000 0 -10000 0 0
MAP2K4 0.022 0.022 -10000 0 -10000 0 0
SMARCA2 0.031 0.008 -10000 0 -10000 0 0
PDE9A -0.019 0.12 -10000 0 -0.61 1 1
NCOA2 -0.14 0.25 -10000 0 -0.5 38 38
CEBPA 0.027 0.049 -10000 0 -0.5 1 1
EHMT2 0.03 0.01 -10000 0 -10000 0 0
cell proliferation -0.063 0.17 0.47 4 -0.39 10 14
NR0B1 -0.017 0.14 -10000 0 -0.5 9 9
EGR1 -0.075 0.21 -10000 0 -0.5 24 24
RXRs/9cRA -0.064 0.15 -10000 0 -0.28 39 39
AR/RACK1/Src -0.071 0.083 -10000 0 -0.28 8 8
AR/GR -0.15 0.13 -10000 0 -0.25 66 66
GNB2L1 0.032 0.007 -10000 0 -10000 0 0
PKN1 0.032 0.007 -10000 0 -10000 0 0
RCHY1 0.033 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.011 0.084 -10000 0 -0.36 6 6
T-DHT/AR/TIF2/CARM1 -0.14 0.17 -10000 0 -0.35 39 39
SRC -0.035 0.065 -10000 0 -0.27 7 7
NR3C1 0.032 0.006 -10000 0 -10000 0 0
KLK3 -0.029 0.11 -10000 0 -0.39 1 1
APPBP2 0.022 0.023 -10000 0 -10000 0 0
TRIM24 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.073 0.094 -10000 0 -0.3 8 8
TMPRSS2 -0.16 0.39 -10000 0 -0.97 22 22
RXRG -0.15 0.24 -10000 0 -0.5 39 39
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.032 0.007 -10000 0 -10000 0 0
RXRB 0.03 0.01 -10000 0 -10000 0 0
CARM1 0.032 0.007 -10000 0 -10000 0 0
NR2C2 -0.014 0.15 -10000 0 -0.5 10 10
KLK2 -0.12 0.14 0.27 1 -0.32 25 26
AR -0.15 0.14 -10000 0 -0.27 62 62
SENP1 0.032 0.007 -10000 0 -10000 0 0
HSP90AA1 0.032 0.007 -10000 0 -10000 0 0
MDM2 0.031 0.008 -10000 0 -10000 0 0
SRY 0 0.002 -10000 0 -0.013 3 3
GATA2 0.008 0.11 -10000 0 -0.5 5 5
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.02 0.01 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.07 0.092 -10000 0 -0.29 8 8
positive regulation of transcription 0.008 0.11 -10000 0 -0.5 5 5
DNAJA1 0.024 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.043 0.018 -10000 0 -10000 0 0
SPDEF 0.026 0.013 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.12 0.17 0.26 1 -0.33 33 34
T-DHT/AR/Hsp90 -0.071 0.093 -10000 0 -0.3 8 8
GSK3B 0.032 0.008 -10000 0 -10000 0 0
NR2C1 0.031 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.035 0.07 -10000 0 -0.28 8 8
SIRT1 0.023 0.069 -10000 0 -0.5 2 2
ZMIZ2 0.03 0.011 -10000 0 -10000 0 0
POU2F1 0.02 0.046 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.096 0.12 -10000 0 -0.31 18 18
CREBBP 0.032 0.005 -10000 0 -10000 0 0
SMARCE1 0.031 0.009 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.041 0.21 -10000 0 -0.72 3 3
PCK1 -0.65 0.61 -10000 0 -1.1 71 71
HNF4A -0.049 0.22 -10000 0 -0.83 3 3
KCNJ11 -0.044 0.24 -10000 0 -0.73 3 3
AKT1 -0.034 0.15 -10000 0 -0.38 4 4
response to starvation 0.001 0.02 -10000 0 -0.21 1 1
DLK1 -0.19 0.44 -10000 0 -0.92 29 29
NKX2-1 -0.009 0.14 0.34 1 -0.35 4 5
ACADM -0.049 0.23 -10000 0 -0.7 5 5
TAT -0.054 0.16 -10000 0 -0.58 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
CEBPA 0.028 0.049 -10000 0 -0.5 1 1
TTR -0.04 0.16 -10000 0 -0.66 1 1
PKLR -0.036 0.21 0.52 1 -0.72 3 4
APOA1 -0.066 0.28 -10000 0 -0.99 4 4
CPT1C -0.058 0.26 -10000 0 -0.9 5 5
ALAS1 -0.002 0.13 -10000 0 -10000 0 0
TFRC -0.084 0.24 -10000 0 -0.8 3 3
FOXF1 -0.029 0.16 -10000 0 -0.5 13 13
NF1 0.036 0.01 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.011 -10000 0 -10000 0 0
CPT1A -0.045 0.22 -10000 0 -0.72 3 3
HMGCS1 -0.047 0.22 -10000 0 -0.72 3 3
NR3C1 0.043 0.014 -10000 0 -10000 0 0
CPT1B -0.043 0.22 -10000 0 -0.72 3 3
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.033 0.01 -10000 0 -10000 0 0
GCK -0.044 0.22 -10000 0 -0.72 3 3
CREB1 -0.12 0.13 -10000 0 -0.23 70 70
IGFBP1 -0.001 0.12 -10000 0 -10000 0 0
PDX1 -0.017 0.15 -10000 0 -0.52 1 1
UCP2 -0.064 0.26 -10000 0 -0.9 5 5
ALDOB -0.062 0.26 -10000 0 -0.78 6 6
AFP -0.035 0.1 -10000 0 -0.36 3 3
BDH1 -0.047 0.22 0.52 1 -0.72 3 4
HADH -0.049 0.24 -10000 0 -0.73 3 3
F2 -0.055 0.24 -10000 0 -0.84 3 3
HNF1A 0.034 0.011 -10000 0 -10000 0 0
G6PC -0.083 0.11 -10000 0 -10000 0 0
SLC2A2 -0.022 0.16 -10000 0 -10000 0 0
INS -0.028 0.016 -10000 0 -10000 0 0
FOXA1 0.004 0.095 -10000 0 -0.27 12 12
FOXA3 -0.081 0.13 -10000 0 -0.25 30 30
FOXA2 -0.058 0.28 -10000 0 -0.77 4 4
ABCC8 -0.033 0.24 -10000 0 -0.73 3 3
ALB -0.11 0.29 -10000 0 -0.89 14 14
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.064 0.18 0.38 3 -0.35 21 24
IKBKB 0.01 0.097 0.36 5 -0.27 1 6
AKT1 -0.046 0.17 0.46 7 -0.24 14 21
IKBKG 0.01 0.088 0.35 4 -10000 0 4
CALM1 0.002 0.074 0.36 1 -10000 0 1
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
MAP3K1 -0.034 0.18 0.4 4 -0.46 8 12
MAP3K7 0.03 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.073 -10000 0 -10000 0 0
DOK1 0.033 0.003 -10000 0 -10000 0 0
AP-1 -0.076 0.13 0.34 4 -0.24 20 24
LYN 0.032 0.007 -10000 0 -10000 0 0
BLNK 0.032 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.012 -10000 0 -10000 0 0
BCR complex -0.012 0.14 -10000 0 -0.35 16 16
CD22 -0.14 0.19 -10000 0 -0.45 21 21
CAMK2G 0.004 0.075 0.34 1 -10000 0 1
CSNK2A1 0.032 0.006 -10000 0 -10000 0 0
INPP5D 0.032 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.004 0.091 -10000 0 -0.25 13 13
GO:0007205 -0.003 0.073 -10000 0 -10000 0 0
SYK 0.032 0.007 -10000 0 -10000 0 0
ELK1 -0.002 0.072 -10000 0 -10000 0 0
NFATC1 -0.045 0.17 0.34 7 -0.36 11 18
B-cell antigen/BCR complex -0.012 0.14 -10000 0 -0.35 16 16
PAG1/CSK 0.046 0.012 -10000 0 -10000 0 0
NFKBIB 0.026 0.046 0.18 6 -0.12 2 8
HRAS 0.005 0.082 0.26 2 -10000 0 2
NFKBIA 0.026 0.046 0.18 6 -0.13 1 7
NF-kappa-B/RelA/I kappa B beta 0.029 0.045 0.18 6 -10000 0 6
RasGAP/Csk 0.011 0.14 -10000 0 -0.28 20 20
mol:GDP 0.003 0.072 -10000 0 -10000 0 0
PTEN 0.032 0.006 -10000 0 -10000 0 0
CD79B 0.022 0.069 -10000 0 -0.5 2 2
NF-kappa-B/RelA/I kappa B alpha 0.029 0.044 0.18 6 -10000 0 6
GRB2 0.03 0.009 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.078 0.2 0.37 5 -0.49 11 16
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
mol:IP3 -0.003 0.069 -10000 0 -10000 0 0
CSK 0.032 0.006 -10000 0 -10000 0 0
FOS -0.12 0.13 0.34 1 -0.38 7 8
CHUK 0.004 0.1 0.34 4 -0.33 3 7
IBTK 0.03 0.01 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.029 0.078 0.25 1 -10000 0 1
PTPN6 -0.14 0.19 -10000 0 -0.47 17 17
RELA 0.032 0.004 -10000 0 -10000 0 0
BCL2A1 0.024 0.037 0.17 4 -10000 0 4
VAV2 -0.1 0.2 -10000 0 -0.54 13 13
ubiquitin-dependent protein catabolic process 0.029 0.046 0.18 6 -0.12 2 8
BTK 0.016 0.075 -10000 0 -0.79 1 1
CD19 -0.12 0.2 -10000 0 -0.44 22 22
MAP4K1 0.032 0.006 -10000 0 -10000 0 0
CD72 0.031 0.007 -10000 0 -10000 0 0
PAG1 0.032 0.007 -10000 0 -10000 0 0
MAPK14 -0.028 0.16 0.39 4 -0.5 4 8
SH3BP5 0.027 0.049 -10000 0 -0.5 1 1
PIK3AP1 0 0.072 -10000 0 -0.29 1 1
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.017 0.13 -10000 0 -0.37 6 6
RAF1 0.005 0.078 0.25 2 -10000 0 2
RasGAP/p62DOK/SHIP 0.013 0.14 -10000 0 -0.27 20 20
CD79A -0.044 0.19 -10000 0 -0.5 17 17
re-entry into mitotic cell cycle -0.074 0.12 0.34 4 -0.24 20 24
RASA1 0.018 0.084 -10000 0 -0.5 3 3
MAPK3 0.009 0.086 0.28 5 -10000 0 5
MAPK1 0.011 0.073 0.28 3 -10000 0 3
CD72/SHP1 -0.11 0.19 0.26 1 -0.46 16 17
NFKB1 0.033 0.003 -10000 0 -10000 0 0
MAPK8 -0.043 0.17 0.38 5 -0.46 7 12
actin cytoskeleton organization -0.084 0.18 0.33 1 -0.46 13 14
NF-kappa-B/RelA 0.059 0.078 0.31 6 -0.19 1 7
Calcineurin 0.035 0.077 -10000 0 -10000 0 0
PI3K -0.16 0.2 -10000 0 -0.4 40 40
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.002 0.071 -10000 0 -0.3 2 2
SOS1 0.033 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.004 0.18 -10000 0 -0.74 4 4
DAPP1 -0.024 0.19 -10000 0 -0.86 4 4
cytokine secretion -0.041 0.16 0.34 7 -0.34 11 18
mol:DAG -0.003 0.069 -10000 0 -10000 0 0
PLCG2 0.03 0.01 -10000 0 -10000 0 0
MAP2K1 0.007 0.084 0.3 3 -10000 0 3
B-cell antigen/BCR complex/FcgammaRIIB -0.006 0.14 -10000 0 -0.33 17 17
mol:PI-3-4-5-P3 -0.12 0.14 0.2 1 -0.29 39 40
ETS1 -0.001 0.076 0.33 1 -10000 0 1
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.036 0.12 -10000 0 -0.27 15 15
B-cell antigen/BCR complex/LYN -0.035 0.15 -10000 0 -0.36 16 16
MALT1 0.031 0.007 -10000 0 -10000 0 0
TRAF6 0.032 0.006 -10000 0 -10000 0 0
RAC1 -0.094 0.19 0.33 1 -0.49 13 14
B-cell antigen/BCR complex/LYN/SYK -0.12 0.2 -10000 0 -0.44 20 20
CARD11 0.005 0.08 0.31 2 -10000 0 2
FCGR2B 0.005 0.11 -10000 0 -0.5 5 5
PPP3CA 0.033 0.003 -10000 0 -10000 0 0
BCL10 0.032 0.006 -10000 0 -10000 0 0
IKK complex 0.015 0.079 0.26 8 -0.13 1 9
PTPRC -0.004 0.12 -10000 0 -0.5 7 7
PDPK1 -0.07 0.14 0.32 6 -0.21 37 43
PPP3CB 0.032 0.005 -10000 0 -10000 0 0
PPP3CC 0.031 0.007 -10000 0 -10000 0 0
POU2F2 0.021 0.036 0.19 3 -10000 0 3
Insulin 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
CBL/APS/CAP -0.16 0.16 -10000 0 -0.27 77 77
TC10/GTP -0.14 0.14 -10000 0 -0.25 76 76
Insulin Receptor/Insulin/IRS1/Shp2 0.057 0.068 -10000 0 -0.28 4 4
HRAS 0.03 0.009 -10000 0 -10000 0 0
APS homodimer 0.03 0.009 -10000 0 -10000 0 0
GRB14 -0.046 0.19 -10000 0 -0.5 17 17
FOXO3 -0.029 0.18 -10000 0 -0.67 9 9
AKT1 -0.052 0.11 -10000 0 -0.8 1 1
INSR 0.034 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.061 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.031 0.008 -10000 0 -10000 0 0
SORBS1 -0.32 0.25 -10000 0 -0.5 78 78
CRK 0.03 0.009 -10000 0 -10000 0 0
PTPN1 0.008 0.015 -10000 0 -10000 0 0
CAV1 -0.012 0.081 -10000 0 -0.26 11 11
CBL/APS/CAP/Crk-II/C3G -0.15 0.17 -10000 0 -0.27 76 76
Insulin Receptor/Insulin/IRS1/NCK2 0.057 0.072 -10000 0 -0.27 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.09 -10000 0 -0.34 5 5
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.029 0.029 -10000 0 -10000 0 0
RPS6KB1 -0.05 0.099 -10000 0 -0.71 1 1
PARD6A 0.03 0.01 -10000 0 -10000 0 0
CBL 0.023 0.069 -10000 0 -0.5 2 2
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.023 0.011 -10000 0 -10000 0 0
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.006 0.12 -10000 0 -0.26 16 16
HRAS/GTP 0.016 0.026 -10000 0 -10000 0 0
Insulin Receptor 0.034 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.068 0.054 -10000 0 -0.27 1 1
PRKCI 0.026 0.045 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.018 0.13 -10000 0 -0.28 20 20
SHC1 0.028 0.012 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.045 0.068 -10000 0 -0.5 1 1
PI3K 0.052 0.095 -10000 0 -0.34 5 5
NCK2 0.033 0.003 -10000 0 -10000 0 0
RHOQ 0.033 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.006 -10000 0 -10000 0 0
AKT2 -0.054 0.11 -10000 0 -0.27 18 18
PRKCZ 0.017 0.07 -10000 0 -0.33 2 2
SH2B2 0.03 0.009 -10000 0 -10000 0 0
SHC/SHIP 0.026 0.036 -10000 0 -0.26 1 1
F2RL2 0.031 0.008 -10000 0 -10000 0 0
TRIP10 0.032 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.047 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.043 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.037 -10000 0 -10000 0 0
RAPGEF1 0.032 0.007 -10000 0 -10000 0 0
RASA1 0.018 0.084 -10000 0 -0.5 3 3
NCK1 0.027 0.049 -10000 0 -0.5 1 1
CBL/APS/CAP/Crk-II -0.16 0.17 -10000 0 -0.29 76 76
TC10/GDP 0.024 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.064 0.03 -10000 0 -10000 0 0
INPP5D 0.004 0.056 0.19 1 -0.25 5 6
SOS1 0.033 0.003 -10000 0 -10000 0 0
SGK1 -0.054 0.2 -10000 0 -0.64 13 13
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.007 -10000 0 -10000 0 0
IRS1 0.01 0.11 -10000 0 -0.5 5 5
p62DOK/RasGAP 0.046 0.069 -10000 0 -0.5 1 1
INS 0.021 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.004 0.056 0.19 1 -0.25 5 6
GRB2 0.03 0.009 -10000 0 -10000 0 0
EIF4EBP1 -0.047 0.1 0.21 1 -0.66 1 2
PTPRA 0.033 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
TC10/GTP/CIP4 0.043 0.009 -10000 0 -10000 0 0
PDPK1 0.028 0.049 -10000 0 -0.5 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.023 0.034 -10000 0 -0.22 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.066 -10000 0 -0.27 5 5
Insulin Receptor/Insulin/IRS3 0.04 0.014 -10000 0 -10000 0 0
Par3/Par6 0.068 0.027 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.03 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.009 0.081 -10000 0 -0.27 4 4
NT3 (dimer)/TRKC -0.035 0.15 -10000 0 -0.37 18 18
NT3 (dimer)/TRKB -0.23 0.17 -10000 0 -0.31 90 90
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.048 -10000 0 -0.46 1 1
RAPGEF1 0.032 0.007 -10000 0 -10000 0 0
BDNF 0.031 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
DYNLT1 0.029 0.011 -10000 0 -10000 0 0
NTRK1 0.008 0.096 -10000 0 -0.5 4 4
NTRK2 -0.37 0.23 -10000 0 -0.5 90 90
NTRK3 -0.019 0.15 -10000 0 -0.5 11 11
NT-4/5 (dimer)/TRKB -0.22 0.16 -10000 0 -0.31 89 89
neuron apoptosis 0.17 0.19 0.51 23 -10000 0 23
SHC 2-3/Grb2 -0.19 0.21 -10000 0 -0.56 23 23
SHC1 0.028 0.012 -10000 0 -10000 0 0
SHC2 -0.11 0.12 -10000 0 -0.45 8 8
SHC3 -0.21 0.26 -10000 0 -0.65 26 26
STAT3 (dimer) 0.038 0.012 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.012 0.11 -10000 0 -0.33 12 12
RIN/GDP 0.011 0.081 -10000 0 -0.29 3 3
GIPC1 0.032 0.007 -10000 0 -10000 0 0
KRAS 0.032 0.007 -10000 0 -10000 0 0
DNAJA3 -0.013 0.095 -10000 0 -0.3 10 10
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.022 0.008 -10000 0 -10000 0 0
MAGED1 0.032 0.004 -10000 0 -10000 0 0
PTPN11 0.032 0.007 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.006 0.095 -10000 0 -0.5 4 4
SHC/GRB2/SOS1 0.054 0.026 -10000 0 -10000 0 0
GRB2 0.03 0.009 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.026 0.094 -10000 0 -0.31 8 8
TRKA/NEDD4-2 0.023 0.075 -10000 0 -0.36 4 4
ELMO1 0.031 0.008 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.037 0.034 -10000 0 -0.31 1 1
NGF 0.013 0.096 -10000 0 -0.5 4 4
HRAS 0.03 0.009 -10000 0 -10000 0 0
DOCK1 0.027 0.049 -10000 0 -0.5 1 1
GAB2 0.023 0.069 -10000 0 -0.5 2 2
RIT2 0.017 0.004 -10000 0 -10000 0 0
RIT1 0.028 0.012 -10000 0 -10000 0 0
FRS2 0.032 0.007 -10000 0 -10000 0 0
DNM1 0.009 0.11 -10000 0 -0.5 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.008 0.1 -10000 0 -0.29 10 10
mol:GDP 0.007 0.12 0.4 1 -0.48 3 4
NGF (dimer) 0.013 0.096 -10000 0 -0.5 4 4
RhoG/GDP 0.023 0.006 -10000 0 -10000 0 0
RIT1/GDP 0.015 0.065 -10000 0 -0.24 2 2
TIAM1 0.026 0.049 -10000 0 -0.5 1 1
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
BDNF (dimer)/TRKB -0.22 0.15 -10000 0 -0.31 90 90
KIDINS220/CRKL/C3G 0.044 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.03 0.066 -10000 0 -0.36 3 3
FRS2 family/SHP2 0.06 0.02 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.068 0.034 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.009 -10000 0 -10000 0 0
NT3 (dimer) -0.021 0.14 -10000 0 -0.5 9 9
RAP1/GDP 0.012 0.071 -10000 0 -0.24 3 3
KIDINS220/CRKL 0.03 0.009 -10000 0 -10000 0 0
BDNF (dimer) 0.031 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.025 0.094 -10000 0 -0.31 8 8
Schwann cell development -0.036 0.023 -10000 0 -10000 0 0
EHD4 0.032 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.073 0.03 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.027 0.033 -10000 0 -0.19 1 1
RAP1B 0.032 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.049 -10000 0 -0.5 1 1
CDC42/GTP -0.19 0.14 -10000 0 -0.3 60 60
ABL1 0.032 0.007 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.045 0.013 -10000 0 -10000 0 0
Rap1/GTP -0.089 0.096 -10000 0 -0.38 7 7
STAT3 0.039 0.012 -10000 0 -10000 0 0
axon guidance -0.19 0.14 -10000 0 -0.29 60 60
MAPK3 0.02 0.098 0.25 1 -0.28 8 9
MAPK1 0.022 0.1 0.25 1 -0.28 8 9
CDC42/GDP 0.02 0.089 0.27 2 -0.29 3 5
NTF3 -0.021 0.14 -10000 0 -0.5 9 9
NTF4 0.006 0.096 -10000 0 -0.5 4 4
NGF (dimer)/TRKA/FAIM 0.026 0.095 -10000 0 -0.31 8 8
PI3K 0.036 0.075 -10000 0 -0.51 2 2
FRS3 0.03 0.01 -10000 0 -10000 0 0
FAIM 0.032 0.007 -10000 0 -10000 0 0
GAB1 0.033 0.003 -10000 0 -10000 0 0
RASGRF1 -0.013 0.095 -10000 0 -0.3 10 10
SOS1 0.033 0.003 -10000 0 -10000 0 0
MCF2L -0.015 0.13 -10000 0 -0.32 18 18
RGS19 0.032 0.006 -10000 0 -10000 0 0
CDC42 0.032 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.055 0.056 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.08 -10000 0 -0.27 3 3
NGF (dimer)/TRKA/GRIT 0.011 0.087 -10000 0 -0.31 8 8
neuron projection morphogenesis 0.016 0.14 0.43 1 -0.54 4 5
NGF (dimer)/TRKA/NEDD4-2 0.025 0.094 -10000 0 -0.31 8 8
MAP2K1 0.049 0.084 0.43 3 -10000 0 3
NGFR 0.012 0.096 -10000 0 -0.5 4 4
NGF (dimer)/TRKA/GIPC/GAIP 0.004 0.089 -10000 0 -0.25 12 12
RAS family/GTP/PI3K 0.026 0.043 -10000 0 -0.43 1 1
FRS2 family/SHP2/GRB2/SOS1 0.084 0.034 -10000 0 -10000 0 0
NRAS 0.032 0.007 -10000 0 -10000 0 0
GRB2/SOS1 0.045 0.013 -10000 0 -10000 0 0
PRKCI 0.032 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
PRKCZ 0.031 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.058 0.17 -10000 0 -0.6 10 10
RASA1 0.018 0.084 -10000 0 -0.5 3 3
TRKA/c-Abl 0.024 0.075 -10000 0 -0.36 4 4
SQSTM1 0.032 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.2 0.14 -10000 0 -0.28 89 89
NGF (dimer)/TRKA/p62/Atypical PKCs 0.056 0.095 -10000 0 -0.27 8 8
MATK 0.031 0.007 -10000 0 -10000 0 0
NEDD4L 0.03 0.009 -10000 0 -10000 0 0
RAS family/GDP -0.015 0.044 -10000 0 -0.21 2 2
NGF (dimer)/TRKA -0.008 0.1 -10000 0 -0.31 10 10
Rac1/GTP -0.007 0.072 -10000 0 -0.25 6 6
FRS2 family/SHP2/CRK family 0.081 0.038 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.039 0.029 0.29 1 -10000 0 1
HSPA8 0.03 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.019 0.099 0.24 1 -0.36 1 2
AKT1 0.02 0.038 -10000 0 -10000 0 0
GSC -0.14 0.45 -10000 0 -1.3 15 15
NKX2-5 0.001 0 -10000 0 -10000 0 0
muscle cell differentiation 0.007 0.11 0.44 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0 0.14 -10000 0 -0.26 12 12
SMAD4 -0.02 0.07 -10000 0 -0.16 4 4
CBFB 0.03 0.01 -10000 0 -10000 0 0
SAP18 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.073 0.044 0.4 1 -10000 0 1
SMAD3/SMAD4/VDR 0.065 0.073 -10000 0 -10000 0 0
MYC 0.034 0.057 -10000 0 -0.5 1 1
CDKN2B -0.18 0.45 -10000 0 -1.3 16 16
AP1 -0.17 0.26 -10000 0 -0.38 61 61
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.005 0.11 -10000 0 -0.51 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.031 0.12 -10000 0 -0.32 14 14
SP3 0.029 0.049 -10000 0 -0.5 1 1
CREB1 0.033 0.003 -10000 0 -10000 0 0
FOXH1 0.014 0.057 -10000 0 -0.17 5 5
SMAD3/SMAD4/GR -0.004 0.082 -10000 0 -10000 0 0
GATA3 0.018 0.096 -10000 0 -0.49 4 4
SKI/SIN3/HDAC complex/NCoR1 0.018 0.079 -10000 0 -0.73 1 1
MEF2C/TIF2 -0.089 0.16 -10000 0 -0.28 45 45
endothelial cell migration -0.049 0.042 -10000 0 -10000 0 0
MAX 0.026 0.016 -10000 0 -10000 0 0
RBBP7 0.031 0.007 -10000 0 -10000 0 0
RBBP4 0.031 0.008 -10000 0 -10000 0 0
RUNX2 0.029 0.01 -10000 0 -10000 0 0
RUNX3 0.027 0.049 -10000 0 -0.5 1 1
RUNX1 0.03 0.009 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
NR3C1 0.027 0.015 -10000 0 -10000 0 0
VDR 0.031 0.008 -10000 0 -10000 0 0
CDKN1A -0.029 0.12 -10000 0 -0.56 2 2
KAT2B 0.024 0.069 -10000 0 -0.5 2 2
SMAD2/SMAD2/SMAD4/FOXH1 0.009 0.14 -10000 0 -0.31 15 15
DCP1A 0.031 0.008 -10000 0 -10000 0 0
SKI 0.03 0.008 -10000 0 -10000 0 0
SERPINE1 0.047 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.005 0.095 -10000 0 -0.36 2 2
SMAD3/SMAD4/ATF3 -0.1 0.2 -10000 0 -0.39 36 36
SAP30 0.031 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.068 0.044 -10000 0 -10000 0 0
JUN -0.17 0.26 0.39 1 -0.37 61 62
SMAD3/SMAD4/IRF7 0.009 0.083 -10000 0 -10000 0 0
TFE3 0.038 0.006 -10000 0 -10000 0 0
COL1A2 -0.11 0.33 -10000 0 -0.9 18 18
mesenchymal cell differentiation 0.001 0.081 -10000 0 -10000 0 0
DLX1 -0.007 0.13 -10000 0 -0.5 8 8
TCF3 0.032 0.007 -10000 0 -10000 0 0
FOS -0.25 0.28 -10000 0 -0.52 60 60
SMAD3/SMAD4/Max -0.005 0.082 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.067 0.03 0.27 1 -10000 0 1
ZBTB17 0.038 0.022 -10000 0 -10000 0 0
LAMC1 -0.014 0.055 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0 0.082 -10000 0 -10000 0 0
IRF7 0.033 0.008 -10000 0 -10000 0 0
ESR1 0.032 0.056 -10000 0 -0.5 1 1
HNF4A 0.018 0.003 -10000 0 -10000 0 0
MEF2C -0.009 0.11 0.39 1 -0.26 12 13
SMAD2-3/SMAD4 -0.001 0.11 -10000 0 -0.21 7 7
Cbp/p300/Src-1 0.072 0.041 0.38 1 -10000 0 1
IGHV3OR16-13 0.008 0.014 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.032 0.006 -10000 0 -10000 0 0
CREBBP 0.038 0.019 0.2 1 -10000 0 1
SKIL 0.032 0.007 -10000 0 -10000 0 0
HDAC1 0.031 0.008 -10000 0 -10000 0 0
HDAC2 0.029 0.01 -10000 0 -10000 0 0
SNIP1 0.03 0.01 -10000 0 -10000 0 0
GCN5L2 0.007 0.019 0.18 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.022 0.087 -10000 0 -10000 0 0
MSG1/HSC70 0.044 0.013 -10000 0 -10000 0 0
SMAD2 0.008 0.055 -10000 0 -10000 0 0
SMAD3 -0.009 0.063 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.009 0.038 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.009 0.075 0.4 1 -0.41 2 3
NCOR1 0.029 0.009 -10000 0 -10000 0 0
NCOA2 -0.14 0.25 -10000 0 -0.5 38 38
NCOA1 0.033 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.037 0.01 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.015 0.14 -10000 0 -0.27 7 7
IFNB1 -0.018 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.002 0.12 -10000 0 -0.26 8 8
CITED1 0.032 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.015 0.1 -10000 0 -10000 0 0
RBL1 0.032 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.041 0.17 -10000 0 -0.51 14 14
RUNX1-3/PEBPB2 0.055 0.028 -10000 0 -10000 0 0
SMAD7 -0.14 0.23 -10000 0 -0.49 22 22
MYC/MIZ-1 0.053 0.063 0.19 14 -0.37 1 15
SMAD3/SMAD4 0.042 0.094 0.25 10 -10000 0 10
IL10 -0.027 0.082 -10000 0 -0.38 3 3
PIASy/HDAC complex 0.015 0.033 -10000 0 -0.19 1 1
PIAS3 0.03 0.013 -10000 0 -10000 0 0
CDK2 0.036 0.012 -10000 0 -10000 0 0
IL5 -0.019 0.081 0.28 1 -0.3 3 4
CDK4 0.037 0.013 -10000 0 -10000 0 0
PIAS4 0.015 0.033 -10000 0 -0.19 1 1
ATF3 -0.13 0.24 -10000 0 -0.5 36 36
SMAD3/SMAD4/SP1 -0.005 0.12 -10000 0 -0.24 13 13
FOXG1 0.002 0.12 -10000 0 -0.5 6 6
FOXO3 0.004 0.039 -10000 0 -10000 0 0
FOXO1 0.005 0.038 -10000 0 -10000 0 0
FOXO4 0.005 0.039 -10000 0 -10000 0 0
heart looping -0.009 0.11 0.39 1 -0.25 12 13
CEBPB 0.023 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.023 0.12 -10000 0 -0.36 8 8
MYOD1 0.019 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.009 0.08 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.001 0.11 -10000 0 -0.34 5 5
SnoN/SIN3/HDAC complex/NCoR1 0.032 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.03 0.083 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.016 0.12 -10000 0 -0.26 6 6
MED15 0.03 0.009 -10000 0 -10000 0 0
SP1 0.007 0.06 -10000 0 -10000 0 0
SIN3B 0.031 0.008 -10000 0 -10000 0 0
SIN3A 0.031 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.016 0.13 -10000 0 -0.28 15 15
ITGB5 -0.03 0.085 -10000 0 -0.3 2 2
TGIF/SIN3/HDAC complex/CtBP 0.03 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.21 0.18 -10000 0 -0.35 68 68
AR -0.28 0.26 -10000 0 -0.5 70 70
negative regulation of cell growth -0.037 0.1 -10000 0 -0.23 9 9
SMAD3/SMAD4/MYOD -0.007 0.082 -10000 0 -10000 0 0
E2F5 0.032 0.007 -10000 0 -10000 0 0
E2F4 0.03 0.01 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.042 0.12 -10000 0 -0.24 10 10
SMAD2-3/SMAD4/FOXO1-3a-4 -0.025 0.12 -10000 0 -0.34 15 15
TFDP1 0.031 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.16 0.28 -10000 0 -0.38 61 61
SMAD3/SMAD4/RUNX2 -0.001 0.081 -10000 0 -10000 0 0
TGIF2 0.032 0.006 -10000 0 -10000 0 0
TGIF1 0.031 0.007 -10000 0 -10000 0 0
ATF2 0.023 0.069 -10000 0 -0.5 2 2
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.04 0.18 -10000 0 -0.5 16 16
alphaV beta3 Integrin -0.034 0.16 -10000 0 -0.36 23 23
PTK2 -0.035 0.16 -10000 0 -0.5 10 10
positive regulation of JNK cascade -0.005 0.12 -10000 0 -0.33 10 10
CDC42/GDP 0.006 0.17 -10000 0 -0.44 10 10
Rac1/GDP 0.004 0.16 -10000 0 -0.44 10 10
RAP1B 0.032 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.049 -10000 0 -0.5 1 1
CTNNB1 0.031 0.008 -10000 0 -10000 0 0
CDC42/GTP -0.001 0.15 -10000 0 -0.4 10 10
nectin-3/I-afadin 0.01 0.11 -10000 0 -0.36 9 9
RAPGEF1 -0.025 0.16 0.36 1 -0.47 11 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.033 0.18 -10000 0 -0.54 11 11
PDGFB-D/PDGFRB -0.04 0.18 -10000 0 -0.5 16 16
TLN1 -0.006 0.043 -10000 0 -0.17 8 8
Rap1/GTP -0.015 0.12 -10000 0 -0.35 10 10
IQGAP1 0.031 0.007 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.053 0.037 -10000 0 -0.28 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.11 -10000 0 -0.36 9 9
PVR 0.032 0.006 -10000 0 -10000 0 0
Necl-5(dimer) 0.032 0.006 -10000 0 -10000 0 0
mol:GDP -0.014 0.19 -10000 0 -0.54 10 10
MLLT4 0.029 0.01 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
PI3K 0.002 0.16 -10000 0 -0.28 26 26
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.04 0.019 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.004 0.12 -10000 0 -0.34 10 10
PVRL1 0.029 0.011 -10000 0 -10000 0 0
PVRL3 -0.01 0.14 -10000 0 -0.5 9 9
PVRL2 0.032 0.007 -10000 0 -10000 0 0
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
CDH1 0.028 0.012 -10000 0 -10000 0 0
CLDN1 0.028 0.012 -10000 0 -10000 0 0
JAM-A/CLDN1 0.041 0.094 -10000 0 -0.28 8 8
SRC -0.035 0.2 -10000 0 -0.59 11 11
ITGB3 -0.073 0.21 -10000 0 -0.5 23 23
nectin-1(dimer)/I-afadin/I-afadin 0.04 0.019 -10000 0 -10000 0 0
FARP2 -0.013 0.2 -10000 0 -0.54 10 10
RAC1 0.031 0.008 -10000 0 -10000 0 0
CTNNA1 0.032 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.027 0.098 -10000 0 -0.3 9 9
nectin-1/I-afadin 0.04 0.019 -10000 0 -10000 0 0
nectin-2/I-afadin 0.043 0.016 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.04 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.026 0.097 -10000 0 -0.3 9 9
CDC42/GTP/IQGAP1/filamentous actin 0.041 0.012 -10000 0 -10000 0 0
F11R 0.027 0.012 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.005 0.12 -10000 0 -0.33 10 10
alphaV/beta3 Integrin/Talin -0.024 0.14 0.32 2 -0.28 23 25
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.016 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.043 0.016 -10000 0 -10000 0 0
PIP5K1C -0.002 0.047 -10000 0 -0.18 8 8
VAV2 -0.014 0.19 -10000 0 -0.52 10 10
RAP1/GDP 0.012 0.16 0.29 1 -0.41 10 11
ITGAV 0.032 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.028 0.096 -10000 0 -0.3 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.11 -10000 0 -0.36 9 9
Rac1/GTP -0.003 0.15 -10000 0 -0.41 10 10
PTPRM -0.001 0.065 -10000 0 -0.22 9 9
E-cadherin/beta catenin/alpha catenin 0.08 0.039 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.032 0.007 -10000 0 -10000 0 0
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 0.025 0.1 -10000 0 -0.24 16 16
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.098 0.33 3 -0.35 1 4
AP1 -0.16 0.21 -10000 0 -0.33 64 64
mol:PIP3 -0.015 0.087 -10000 0 -0.33 4 4
AKT1 -0.005 0.087 0.37 1 -0.31 1 2
PTK2B 0.004 0.078 0.31 1 -0.26 2 3
RHOA -0.006 0.074 0.35 1 -0.27 4 5
PIK3CB 0.031 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.058 -10000 0 -0.26 2 2
MAGI3 0.032 0.007 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
apoptosis -0.006 0.095 -10000 0 -0.24 15 15
HRAS/GDP 0.023 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.019 0.09 0.31 4 -10000 0 4
NF kappa B1 p50/RelA 0.006 0.097 -10000 0 -0.32 3 3
endothelial cell migration -0.044 0.19 -10000 0 -0.58 13 13
ADCY4 -0.008 0.085 -10000 0 -0.36 1 1
ADCY5 -0.069 0.13 -10000 0 -0.41 10 10
ADCY6 -0.009 0.085 -10000 0 -0.36 1 1
ADCY7 -0.006 0.088 0.23 1 -0.36 1 2
ADCY1 -0.01 0.083 -10000 0 -0.36 1 1
ADCY2 -0.013 0.099 -10000 0 -0.4 3 3
ADCY3 -0.006 0.088 0.23 1 -0.36 1 2
ADCY8 -0.01 0.085 -10000 0 -0.36 1 1
ADCY9 -0.006 0.088 0.23 1 -0.36 1 2
GSK3B 0.009 0.084 0.29 3 -0.24 2 5
arachidonic acid secretion -0.013 0.099 -10000 0 -0.48 2 2
GNG2 0.018 0.083 -10000 0 -0.5 3 3
TRIP6 0.019 0.021 -10000 0 -10000 0 0
GNAO1 -0.012 0.091 -10000 0 -0.26 14 14
HRAS 0.03 0.009 -10000 0 -10000 0 0
NFKBIA 0.009 0.091 0.32 4 -0.38 1 5
GAB1 0.033 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.014 0.18 -10000 0 -0.78 5 5
JUN -0.04 0.18 -10000 0 -0.5 16 16
LPA/LPA2/NHERF2 0.03 0.043 -10000 0 -10000 0 0
TIAM1 -0.004 0.21 -10000 0 -0.9 6 6
PIK3R1 0.022 0.069 -10000 0 -0.5 2 2
mol:IP3 -0.004 0.057 -10000 0 -0.27 2 2
PLCB3 0.014 0.043 0.19 2 -10000 0 2
FOS -0.24 0.26 -10000 0 -0.5 60 60
positive regulation of mitosis -0.013 0.099 -10000 0 -0.48 2 2
LPA/LPA1-2-3 0.022 0.11 -10000 0 -0.25 14 14
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.03 0.01 -10000 0 -10000 0 0
stress fiber formation 0.013 0.089 0.35 1 -0.28 2 3
GNAZ -0.009 0.087 -10000 0 -0.26 13 13
EGFR/PI3K-beta/Gab1 -0.004 0.096 -10000 0 -0.34 4 4
positive regulation of dendritic cell cytokine production 0.019 0.11 -10000 0 -0.25 14 14
LPA/LPA2/MAGI-3 0.03 0.043 -10000 0 -10000 0 0
ARHGEF1 0.01 0.098 0.36 2 -0.22 13 15
GNAI2 -0.008 0.088 -10000 0 -0.26 13 13
GNAI3 -0.008 0.088 -10000 0 -0.26 13 13
GNAI1 -0.007 0.088 -10000 0 -0.26 13 13
LPA/LPA3 0 0.075 -10000 0 -0.17 14 14
LPA/LPA2 0.012 0.042 -10000 0 -10000 0 0
LPA/LPA1 -0.006 0.1 -10000 0 -0.3 13 13
HB-EGF/EGFR 0.023 0.064 -10000 0 -0.31 4 4
HBEGF 0.005 0.069 -10000 0 -0.36 4 4
mol:DAG -0.004 0.057 -10000 0 -0.27 2 2
cAMP biosynthetic process -0.011 0.11 0.3 2 -0.28 11 13
NFKB1 0.033 0.003 -10000 0 -10000 0 0
SRC 0.032 0.006 -10000 0 -10000 0 0
GNB1 0.031 0.009 -10000 0 -10000 0 0
LYN 0.01 0.09 0.3 4 -0.38 1 5
GNAQ 0.008 0.055 -10000 0 -0.31 2 2
LPAR2 0.031 0.007 -10000 0 -10000 0 0
LPAR3 0.015 0.084 -10000 0 -0.5 3 3
LPAR1 0.009 0.08 -10000 0 -0.2 13 13
IL8 -0.078 0.16 0.38 2 -0.43 10 12
PTK2 -0.001 0.099 0.31 2 -0.24 14 16
Rac1/GDP 0.023 0.006 -10000 0 -10000 0 0
CASP3 -0.007 0.095 -10000 0 -0.24 15 15
EGFR 0.026 0.049 -10000 0 -0.5 1 1
PLCG1 -0.001 0.063 -10000 0 -0.25 4 4
PLD2 0 0.1 0.31 2 -0.24 14 16
G12/G13 0.03 0.095 -10000 0 -0.23 13 13
PI3K-beta -0.008 0.086 -10000 0 -0.34 1 1
cell migration 0.017 0.068 -10000 0 -0.23 4 4
SLC9A3R2 0.031 0.007 -10000 0 -10000 0 0
PXN 0.012 0.09 0.35 1 -0.29 2 3
HRAS/GTP -0.013 0.1 -10000 0 -0.49 2 2
RAC1 0.031 0.008 -10000 0 -10000 0 0
MMP9 0.013 0.096 -10000 0 -0.5 4 4
PRKCE 0.032 0.007 -10000 0 -10000 0 0
PRKCD -0.005 0.056 -10000 0 -0.3 1 1
Gi(beta/gamma) -0.012 0.1 -10000 0 -0.42 3 3
mol:LPA -0.014 0.052 -10000 0 -0.17 12 12
TRIP6/p130 Cas/FAK1/Paxillin 0.026 0.096 -10000 0 -0.42 1 1
MAPKKK cascade -0.013 0.099 -10000 0 -0.48 2 2
contractile ring contraction involved in cytokinesis -0.005 0.084 0.28 3 -0.27 4 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.001 0.073 -10000 0 -0.31 5 5
GNA15 0.009 0.055 -10000 0 -0.31 2 2
GNA12 0.031 0.008 -10000 0 -10000 0 0
GNA13 0.031 0.008 -10000 0 -10000 0 0
MAPT 0.019 0.092 0.32 4 -0.22 1 5
GNA11 -0.006 0.082 -10000 0 -0.28 8 8
Rac1/GTP 0.014 0.19 -10000 0 -0.82 5 5
MMP2 -0.044 0.19 -10000 0 -0.58 13 13
Syndecan-4-mediated 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
PTK2 -0.053 0.18 -10000 0 -0.45 20 20
Syndecan-4/Syndesmos -0.016 0.14 -10000 0 -0.43 6 6
positive regulation of JNK cascade -0.024 0.16 -10000 0 -0.43 8 8
Syndecan-4/ADAM12 -0.034 0.16 -10000 0 -0.43 11 11
CCL5 0.011 0.096 -10000 0 -0.5 4 4
Rac1/GDP 0.023 0.006 -10000 0 -10000 0 0
DNM2 0.032 0.007 -10000 0 -10000 0 0
ITGA5 0.032 0.007 -10000 0 -10000 0 0
SDCBP 0.032 0.007 -10000 0 -10000 0 0
PLG 0.011 0.021 -10000 0 -10000 0 0
ADAM12 0 0.12 -10000 0 -0.5 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.032 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.029 0.14 -10000 0 -0.43 6 6
Syndecan-4/CXCL12/CXCR4 -0.025 0.16 -10000 0 -0.45 8 8
Syndecan-4/Laminin alpha3 -0.021 0.15 -10000 0 -0.45 7 7
MDK 0.026 0.013 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.035 0.16 -10000 0 -0.43 12 12
Syndecan-4/Midkine -0.022 0.14 -10000 0 -0.43 6 6
FZD7 -0.005 0.13 -10000 0 -0.5 8 8
Syndecan-4/FGFR1/FGF -0.012 0.16 -10000 0 -0.43 9 9
THBS1 -0.12 0.24 -10000 0 -0.5 34 34
integrin-mediated signaling pathway -0.043 0.17 -10000 0 -0.46 11 11
positive regulation of MAPKKK cascade -0.024 0.16 -10000 0 -0.43 8 8
Syndecan-4/TACI -0.12 0.17 -10000 0 -0.51 10 10
CXCR4 0.014 0.096 -10000 0 -0.5 4 4
cell adhesion -0.02 0.11 0.2 3 -0.28 18 21
Syndecan-4/Dynamin -0.016 0.14 -10000 0 -0.43 6 6
Syndecan-4/TSP1 -0.087 0.19 -10000 0 -0.45 15 15
Syndecan-4/GIPC -0.016 0.14 -10000 0 -0.43 6 6
Syndecan-4/RANTES -0.029 0.15 -10000 0 -0.47 6 6
ITGB1 0.032 0.005 -10000 0 -10000 0 0
LAMA1 0.016 0.069 -10000 0 -0.5 2 2
LAMA3 0.018 0.084 -10000 0 -0.5 3 3
RAC1 0.031 0.008 -10000 0 -10000 0 0
PRKCA 0.04 0.17 0.75 6 -10000 0 6
Syndecan-4/alpha-Actinin -0.013 0.14 -10000 0 -0.45 5 5
TFPI 0.024 0.069 -10000 0 -0.5 2 2
F2 0.027 0.016 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.046 0.012 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.035 0.14 -10000 0 -0.42 8 8
ACTN1 0.031 0.007 -10000 0 -10000 0 0
TNC -0.04 0.18 -10000 0 -0.5 16 16
Syndecan-4/CXCL12 -0.028 0.15 -10000 0 -0.47 6 6
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.031 0.008 -10000 0 -10000 0 0
CXCL12 0.01 0.11 -10000 0 -0.5 5 5
TNFRSF13B -0.19 0.26 -10000 0 -0.5 48 48
FGF2 0.024 0.069 -10000 0 -0.5 2 2
FGFR1 0.018 0.084 -10000 0 -0.5 3 3
Syndecan-4/PI-4-5-P2 -0.036 0.13 -10000 0 -0.43 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.061 0.19 -10000 0 -0.48 20 20
cell migration -0.014 0.01 -10000 0 -10000 0 0
PRKCD 0.027 0.024 -10000 0 -10000 0 0
vasculogenesis -0.084 0.18 -10000 0 -0.44 15 15
SDC4 -0.028 0.14 -10000 0 -0.45 6 6
Syndecan-4/Tenascin C -0.045 0.18 -10000 0 -0.48 11 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.017 0.14 -10000 0 -0.45 5 5
MMP9 0.015 0.096 -10000 0 -0.5 4 4
Rac1/GTP -0.021 0.12 0.2 3 -0.29 18 21
cytoskeleton organization -0.015 0.14 -10000 0 -0.42 6 6
GIPC1 0.032 0.007 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.02 0.15 -10000 0 -0.44 8 8
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.014 0.16 -9999 0 -0.48 10 10
STMN1 -0.013 0.12 -9999 0 -0.41 9 9
Aurora B/RasGAP/Survivin 0.017 0.16 -9999 0 -0.45 11 11
Chromosomal passenger complex/Cul3 protein complex -0.007 0.13 -9999 0 -0.45 8 8
BIRC5 -0.003 0.13 -9999 0 -0.53 7 7
DES -0.45 0.39 -9999 0 -0.65 85 85
Aurora C/Aurora B/INCENP 0.039 0.091 -9999 0 -0.28 8 8
Aurora B/TACC1 0.018 0.091 -9999 0 -0.31 8 8
Aurora B/PP2A 0.02 0.1 -9999 0 -0.36 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.002 0.042 -9999 0 -0.15 8 8
mitotic metaphase/anaphase transition 0 0.004 -9999 0 -10000 0 0
NDC80 -0.01 0.11 -9999 0 -0.41 8 8
Cul3 protein complex 0.06 0.024 -9999 0 -10000 0 0
KIF2C -0.001 0.11 -9999 0 -0.35 7 7
PEBP1 0.029 0.015 -9999 0 -10000 0 0
KIF20A 0.023 0.069 -9999 0 -0.5 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.012 0.12 -9999 0 -0.37 10 10
SEPT1 -0.022 0.16 -9999 0 -0.5 12 12
SMC2 0.032 0.007 -9999 0 -10000 0 0
SMC4 0.032 0.007 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.074 0.25 -9999 0 -0.62 19 19
PSMA3 0.031 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 -9999 0 -10000 0 0
H3F3B -0.003 0.086 -9999 0 -0.32 8 8
AURKB 0.001 0.14 -9999 0 -0.52 8 8
AURKC 0.027 0.012 -9999 0 -10000 0 0
CDCA8 0.021 0.074 -9999 0 -0.53 2 2
cytokinesis -0.069 0.24 -9999 0 -0.79 10 10
Aurora B/Septin1 -0.042 0.27 -9999 0 -0.71 13 13
AURKA 0.033 0.008 -9999 0 -10000 0 0
INCENP 0.03 0.017 -9999 0 -10000 0 0
KLHL13 0.028 0.049 -9999 0 -0.5 1 1
BUB1 0.015 0.097 -9999 0 -0.51 4 4
hSgo1/Aurora B/Survivin 0.012 0.18 -9999 0 -0.58 9 9
EVI5 0.033 0.007 -9999 0 -10000 0 0
RhoA/GTP 0.011 0.2 -9999 0 -0.62 9 9
SGOL1 0.013 0.096 -9999 0 -0.5 4 4
CENPA -0.04 0.21 -9999 0 -0.64 11 11
NCAPG 0.001 0.12 -9999 0 -0.5 7 7
Aurora B/HC8 Proteasome 0.024 0.1 -9999 0 -0.36 7 7
NCAPD2 0.031 0.007 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.021 0.11 -9999 0 -0.37 8 8
RHOA 0.031 0.008 -9999 0 -10000 0 0
NCAPH 0.019 0.084 -9999 0 -0.5 3 3
NPM1 -0.044 0.17 -9999 0 -0.44 17 17
RASA1 0.018 0.084 -9999 0 -0.5 3 3
KLHL9 0.031 0.008 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.1 -9999 0 -0.36 7 7
PPP1CC 0.032 0.007 -9999 0 -10000 0 0
Centraspindlin 0.001 0.22 -9999 0 -0.68 9 9
RhoA/GDP 0.023 0.006 -9999 0 -10000 0 0
NSUN2 -0.046 0.17 -9999 0 -0.44 17 17
MYLK -0.024 0.11 -9999 0 -0.32 15 15
KIF23 0.022 0.071 -9999 0 -0.52 2 2
VIM -0.007 0.097 -9999 0 -0.37 8 8
RACGAP1 0.031 0.012 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.05 0.19 -9999 0 -0.47 17 17
Chromosomal passenger complex -0.024 0.2 -9999 0 -0.7 8 8
Chromosomal passenger complex/EVI5 0.072 0.19 -9999 0 -0.57 8 8
TACC1 0.031 0.007 -9999 0 -10000 0 0
PPP2R5D 0.03 0.01 -9999 0 -10000 0 0
CUL3 0.032 0.005 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin -0.029 0.14 -10000 0 -0.32 21 21
EPHB2 0.026 0.049 -10000 0 -0.5 1 1
Syndecan-2/TACI -0.11 0.16 -10000 0 -0.3 50 50
LAMA1 0.016 0.069 -10000 0 -0.5 2 2
Syndecan-2/alpha2 ITGB1 0.041 0.081 -10000 0 -0.26 7 7
HRAS 0.03 0.009 -10000 0 -10000 0 0
Syndecan-2/CASK 0.003 0.049 -10000 0 -0.3 3 3
ITGA5 0.032 0.007 -10000 0 -10000 0 0
BAX -0.011 0.074 -10000 0 -10000 0 0
EPB41 0.032 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.023 0.048 -10000 0 -0.27 3 3
LAMA3 0.018 0.084 -10000 0 -0.5 3 3
EZR 0.029 0.011 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.017 0.084 -10000 0 -0.5 3 3
Syndecan-2/MMP2 -0.01 0.12 -10000 0 -0.34 13 13
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.039 0.041 -10000 0 -0.36 1 1
dendrite morphogenesis 0.021 0.061 -10000 0 -0.3 4 4
Syndecan-2/GM-CSF 0.02 0.053 -10000 0 -0.3 3 3
determination of left/right symmetry 0.005 0.058 -10000 0 -0.35 3 3
Syndecan-2/PKC delta 0.024 0.054 -10000 0 -0.3 3 3
GNB2L1 0.032 0.007 -10000 0 -10000 0 0
MAPK3 0.015 0.057 0.19 4 -0.28 3 7
MAPK1 0.016 0.06 0.19 5 -0.28 3 8
Syndecan-2/RACK1 0.038 0.051 -10000 0 -0.26 3 3
NF1 0.03 0.009 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.005 0.058 -10000 0 -0.35 3 3
ITGA2 0.025 0.049 -10000 0 -0.5 1 1
MAPK8 -0.012 0.087 -10000 0 -0.3 10 10
Syndecan-2/alpha2/beta1 Integrin 0.042 0.082 -10000 0 -0.31 5 5
Syndecan-2/Kininogen 0.017 0.053 -10000 0 -0.3 3 3
ITGB1 0.032 0.005 -10000 0 -10000 0 0
SRC 0.022 0.056 0.19 4 -0.25 3 7
Syndecan-2/CASK/Protein 4.1 0.021 0.05 -10000 0 -0.27 3 3
extracellular matrix organization 0.025 0.054 -10000 0 -0.3 3 3
actin cytoskeleton reorganization -0.029 0.14 -10000 0 -0.32 21 21
Syndecan-2/Caveolin-2/Ras 0.03 0.074 -10000 0 -0.28 6 6
Syndecan-2/Laminin alpha3 0.016 0.074 -10000 0 -0.3 6 6
Syndecan-2/RasGAP 0.046 0.066 -10000 0 -0.22 6 6
alpha5/beta1 Integrin 0.046 0.012 -10000 0 -10000 0 0
PRKCD 0.031 0.008 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.062 -10000 0 -0.3 4 4
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.03 0.059 -10000 0 -0.22 6 6
RHOA 0.031 0.008 -10000 0 -10000 0 0
SDCBP 0.032 0.007 -10000 0 -10000 0 0
TNFRSF13B -0.19 0.26 -10000 0 -0.5 48 48
RASA1 0.018 0.084 -10000 0 -0.5 3 3
alpha2/beta1 Integrin 0.039 0.041 -10000 0 -0.36 1 1
Syndecan-2/Synbindin 0.025 0.054 -10000 0 -0.3 3 3
TGFB1 0.032 0.006 -10000 0 -10000 0 0
CASP3 0.019 0.062 0.2 6 -0.28 3 9
FN1 -0.058 0.2 -10000 0 -0.5 20 20
Syndecan-2/IL8 0.011 0.085 -10000 0 -0.3 8 8
SDC2 0.005 0.058 -10000 0 -0.35 3 3
KNG1 0.02 0.007 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.023 0.054 -10000 0 -0.3 3 3
TRAPPC4 0.032 0.004 -10000 0 -10000 0 0
CSF2 0.025 0.009 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.025 0.054 -10000 0 -0.3 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.049 -10000 0 -0.27 3 3
Syndecan-2/Ezrin 0.039 0.055 -10000 0 -0.28 3 3
PRKACA 0.016 0.057 0.19 4 -0.28 3 7
angiogenesis 0.011 0.085 -10000 0 -0.3 8 8
MMP2 -0.024 0.16 -10000 0 -0.5 12 12
IL8 0.005 0.12 -10000 0 -0.5 6 6
calcineurin-NFAT signaling pathway -0.11 0.16 -10000 0 -0.3 50 50
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.032 0.005 -9999 0 -10000 0 0
ITGB7 0.023 0.069 -9999 0 -0.5 2 2
ITGA4 -0.008 0.14 -9999 0 -0.5 9 9
alpha4/beta7 Integrin 0.009 0.12 -9999 0 -0.39 10 10
alpha4/beta1 Integrin 0.019 0.1 -9999 0 -0.36 8 8
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.029 0.056 -10000 0 -0.36 2 2
CRKL 0.033 0.08 0.25 3 -0.39 2 5
mol:PIP3 -0.008 0.078 -10000 0 -0.86 1 1
AKT1 -0.006 0.083 -10000 0 -0.75 1 1
PTK2B 0.031 0.007 -10000 0 -10000 0 0
RAPGEF1 0.043 0.11 0.41 5 -0.38 2 7
RANBP10 0.03 0.01 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
HGF/MET/SHIP2 0.038 0.085 -10000 0 -0.38 4 4
MAP3K5 0.041 0.1 0.37 2 -0.44 3 5
HGF/MET/CIN85/CBL/ENDOPHILINS 0.057 0.099 -10000 0 -0.38 5 5
AP1 -0.18 0.23 -10000 0 -0.38 62 62
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.012 -10000 0 -10000 0 0
apoptosis -0.4 0.42 -10000 0 -0.76 66 66
STAT3 (dimer) 0.013 0.089 -10000 0 -0.32 6 6
GAB1/CRKL/SHP2/PI3K 0.063 0.1 -10000 0 -0.56 2 2
INPP5D 0.032 0.006 -10000 0 -10000 0 0
CBL/CRK 0.049 0.097 0.36 2 -0.49 2 4
PTPN11 0.032 0.007 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.032 0.006 -10000 0 -10000 0 0
PTEN 0.032 0.006 -10000 0 -10000 0 0
ELK1 0.013 0.097 0.31 8 -0.2 1 9
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.019 0.044 -10000 0 -0.24 2 2
PAK1 -0.007 0.079 -10000 0 -0.72 1 1
HGF/MET/RANBP10 0.035 0.085 -10000 0 -0.38 4 4
HRAS 0.004 0.12 -10000 0 -0.52 4 4
DOCK1 0.039 0.11 0.38 3 -0.49 2 5
GAB1 0.03 0.074 0.24 1 -0.41 2 3
CRK 0.03 0.082 0.45 1 -0.39 2 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.006 0.13 -10000 0 -0.58 4 4
JUN -0.04 0.18 -10000 0 -0.5 16 16
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.003 0.054 -10000 0 -0.26 4 4
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
cell morphogenesis 0.041 0.16 0.61 4 -0.64 2 6
GRB2/SHC 0.038 0.062 -10000 0 -0.31 2 2
FOS -0.24 0.26 -10000 0 -0.5 60 60
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.013 0.096 0.31 8 -0.2 1 9
HGF/MET/MUC20 0.021 0.079 -10000 0 -0.38 4 4
cell migration 0.037 0.061 -10000 0 -0.31 2 2
GRB2 0.03 0.009 -10000 0 -10000 0 0
CBL 0.023 0.069 -10000 0 -0.5 2 2
MET/RANBP10 0.029 0.056 -10000 0 -0.36 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.018 0.089 -10000 0 -0.33 6 6
MET/MUC20 0.013 0.05 -10000 0 -0.36 2 2
RAP1B 0.042 0.11 0.4 6 -0.36 2 8
RAP1A 0.039 0.12 0.43 5 -0.46 2 7
HGF/MET/RANBP9 0.035 0.085 -10000 0 -0.38 4 4
RAF1 0.001 0.12 -10000 0 -0.5 4 4
STAT3 0.012 0.09 -10000 0 -0.33 6 6
cell proliferation 0.032 0.13 0.33 7 -0.48 4 11
RPS6KB1 0.015 0.022 -10000 0 -10000 0 0
MAPK3 -0.005 0.084 0.42 2 -10000 0 2
MAPK1 0.018 0.14 0.61 5 -10000 0 5
RANBP9 0.029 0.01 -10000 0 -10000 0 0
MAPK8 0.025 0.16 0.41 2 -0.48 8 10
SRC 0.01 0.083 -10000 0 -0.31 6 6
PI3K 0.039 0.095 -10000 0 -0.34 5 5
MET/Glomulin 0.013 0.049 -10000 0 -0.26 3 3
SOS1 0.033 0.003 -10000 0 -10000 0 0
MAP2K1 0.005 0.12 -10000 0 -0.46 4 4
MET 0.017 0.069 -10000 0 -0.5 2 2
MAP4K1 0.043 0.1 0.37 2 -0.4 3 5
PTK2 0.031 0.008 -10000 0 -10000 0 0
MAP2K2 0.003 0.12 0.36 1 -0.46 4 5
BAD -0.006 0.078 -10000 0 -0.72 1 1
MAP2K4 0.036 0.098 0.36 2 -0.46 2 4
SHP2/GRB2/SOS1/GAB1 0.045 0.08 -10000 0 -0.46 2 2
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PXN 0.032 0.007 -10000 0 -10000 0 0
SH3KBP1 0.032 0.004 -10000 0 -10000 0 0
HGS 0.003 0.051 -10000 0 -0.25 4 4
PLCgamma1/PKC 0.024 0.004 -10000 0 -10000 0 0
HGF 0.017 0.084 -10000 0 -0.5 3 3
RASA1 0.018 0.084 -10000 0 -0.5 3 3
NCK1 0.027 0.049 -10000 0 -0.5 1 1
PTPRJ 0.032 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.044 0.079 -10000 0 -0.32 4 4
PDPK1 -0.009 0.082 -10000 0 -0.79 1 1
HGF/MET/SHIP 0.036 0.085 -10000 0 -0.38 4 4
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0 0.18 -10000 0 -0.63 8 8
HDAC1 0.026 0.013 -10000 0 -10000 0 0
AES 0.031 0.006 -10000 0 -10000 0 0
FBXW11 0.032 0.006 -10000 0 -10000 0 0
DTX1 -0.004 0.13 -10000 0 -0.5 8 8
LRP6/FZD1 0.045 0.014 -10000 0 -10000 0 0
TLE1 0.03 0.008 -10000 0 -10000 0 0
AP1 -0.15 0.19 -10000 0 -0.31 62 62
NCSTN 0.027 0.012 -10000 0 -10000 0 0
ADAM10 -0.009 0.14 -10000 0 -0.5 9 9
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.044 0.048 -10000 0 -10000 0 0
NICD/RBPSUH 0.011 0.17 -10000 0 -0.58 8 8
WIF1 0.017 0.012 -10000 0 -10000 0 0
NOTCH1 -0.016 0.16 -10000 0 -0.61 8 8
PSENEN 0.032 0.006 -10000 0 -10000 0 0
KREMEN2 0.01 0.083 -10000 0 -0.5 3 3
DKK1 0.029 0.008 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.043 0.06 0.27 2 -0.26 1 3
APH1B 0.032 0.007 -10000 0 -10000 0 0
APH1A 0.028 0.012 -10000 0 -10000 0 0
AXIN1 0.014 0.082 0.32 2 -10000 0 2
CtBP/CBP/TCF1/TLE1/AES 0.019 0.033 -10000 0 -10000 0 0
PSEN1 0.031 0.007 -10000 0 -10000 0 0
FOS -0.24 0.26 -10000 0 -0.5 60 60
JUN -0.04 0.18 -10000 0 -0.5 16 16
MAP3K7 0.028 0.01 -10000 0 -10000 0 0
CTNNB1 0.027 0.07 0.29 3 -0.26 2 5
MAPK3 0.032 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.023 0.14 -10000 0 -0.32 20 20
HNF1A 0.031 0.006 -10000 0 -10000 0 0
CTBP1 0.031 0.006 -10000 0 -10000 0 0
MYC 0.023 0.12 -10000 0 -1.3 1 1
NKD1 0.021 0.069 -10000 0 -0.5 2 2
FZD1 0.031 0.008 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0 0.17 -10000 0 -0.58 8 8
apoptosis -0.15 0.18 -10000 0 -0.31 62 62
Delta 1/NOTCHprecursor 0.006 0.17 -10000 0 -0.61 8 8
DLL1 0.025 0.049 -10000 0 -0.5 1 1
PPARD -0.034 0.22 -10000 0 -0.72 11 11
Gamma Secretase 0.082 0.038 -10000 0 -10000 0 0
APC 0.015 0.089 0.31 3 -0.32 1 4
DVL1 0.029 0.014 -10000 0 -10000 0 0
CSNK2A1 0.032 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.034 0.063 -10000 0 -0.3 3 3
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.032 0.006 -10000 0 -10000 0 0
NLK 0.012 0.007 -10000 0 -10000 0 0
CCND1 0.026 0.1 -10000 0 -0.72 2 2
WNT1 0.027 0.049 -10000 0 -0.5 1 1
Axin1/APC/beta catenin 0.054 0.1 0.51 3 -10000 0 3
DKK2 -0.06 0.2 -10000 0 -0.5 20 20
NOTCH1 precursor/DVL1 0.008 0.14 -10000 0 -0.51 8 8
GSK3B 0.031 0.007 -10000 0 -10000 0 0
FRAT1 0.031 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.009 0.17 -10000 0 -0.6 8 8
PPP2R5D 0.023 0.06 0.28 2 -0.28 3 5
MAPK1 0.03 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.069 0.041 -10000 0 -0.29 1 1
RBPJ 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.035 0.007 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.003 0.047 -10000 0 -10000 0 0
RFC1 0.003 0.047 0.17 5 -10000 0 5
PRKDC 0.003 0.047 -10000 0 -10000 0 0
RIPK1 0.032 0.014 -10000 0 -10000 0 0
CASP7 -0.006 0.11 -10000 0 -0.54 3 3
FASLG/FAS/FADD/FAF1 -0.006 0.087 0.21 6 -0.27 6 12
MAP2K4 -0.091 0.18 0.29 1 -0.44 11 12
mol:ceramide -0.043 0.12 -10000 0 -0.38 6 6
GSN -0.018 0.091 0.17 5 -0.29 9 14
FASLG/FAS/FADD/FAF1/Caspase 8 -0.023 0.098 -10000 0 -0.35 6 6
FAS 0.012 0.029 -10000 0 -10000 0 0
BID 0.004 0.094 0.33 8 -10000 0 8
MAP3K1 -0.036 0.13 0.44 1 -0.38 4 5
MAP3K7 0.027 0.01 -10000 0 -10000 0 0
RB1 0.001 0.054 -10000 0 -0.29 1 1
CFLAR 0.036 0.006 -10000 0 -10000 0 0
HGF/MET 0.031 0.1 -10000 0 -0.42 5 5
ARHGDIB 0.001 0.047 -10000 0 -10000 0 0
FADD 0.012 0.029 -10000 0 -10000 0 0
actin filament polymerization 0.018 0.091 0.29 9 -0.17 5 14
NFKB1 -0.045 0.1 -10000 0 -10000 0 0
MAPK8 -0.17 0.27 0.28 2 -0.48 48 50
DFFA 0.002 0.044 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.044 0.17 4 -10000 0 4
FAS/FADD/MET 0.021 0.061 -10000 0 -0.32 2 2
CFLAR/RIP1 0.048 0.021 -10000 0 -10000 0 0
FAIM3 -0.007 0.13 -10000 0 -0.5 8 8
FAF1 0.008 0.032 -10000 0 -10000 0 0
PARP1 0.005 0.044 0.17 5 -10000 0 5
DFFB 0.002 0.044 0.17 4 -10000 0 4
CHUK -0.042 0.094 -10000 0 -10000 0 0
FASLG -0.02 0.12 -10000 0 -0.51 6 6
FAS/FADD 0.018 0.041 -10000 0 -10000 0 0
HGF 0.017 0.084 -10000 0 -0.5 3 3
LMNA 0 0.042 -10000 0 -10000 0 0
CASP6 0.003 0.047 -10000 0 -10000 0 0
CASP10 0.012 0.029 -10000 0 -10000 0 0
CASP3 0.009 0.054 0.21 8 -10000 0 8
PTPN13 0.018 0.084 -10000 0 -0.5 3 3
CASP8 0.003 0.095 0.36 8 -10000 0 8
IL6 -0.44 0.61 -10000 0 -1.2 46 46
MET 0.017 0.069 -10000 0 -0.5 2 2
ICAD/CAD 0.001 0.044 0.2 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.044 0.12 -10000 0 -0.39 6 6
activation of caspase activity by cytochrome c 0.004 0.094 0.33 8 -10000 0 8
PAK2 0.004 0.051 0.18 6 -10000 0 6
BCL2 0.023 0.069 -10000 0 -0.5 2 2
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.094 -10000 0 -10000 0 0
UGCG -0.12 0.28 -10000 0 -0.63 26 26
AKT1/mTOR/p70S6K/Hsp90/TERT 0.006 0.16 -10000 0 -0.43 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.12 0.27 -10000 0 -0.62 26 26
mol:DAG 0.008 0.083 -10000 0 -0.83 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.17 -10000 0 -0.53 7 7
FRAP1 0.002 0.19 -10000 0 -0.66 7 7
FOXO3 0.006 0.17 0.27 1 -0.55 7 8
AKT1 0.005 0.18 0.29 1 -0.6 7 8
GAB2 0.024 0.069 -10000 0 -0.5 2 2
SMPD1 -0.006 0.15 -10000 0 -0.68 5 5
SGMS1 0.017 0.072 -10000 0 -0.69 1 1
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 0.06 -10000 0 -0.44 2 2
CALM1 0.032 0.007 -10000 0 -10000 0 0
cell proliferation -0.045 0.18 0.26 1 -0.34 27 28
EIF3A 0.032 0.006 -10000 0 -10000 0 0
PI3K 0.04 0.075 -10000 0 -0.51 2 2
RPS6KB1 -0.013 0.12 -10000 0 -0.77 1 1
mol:sphingomyelin 0.008 0.083 -10000 0 -0.83 1 1
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.029 0.049 -10000 0 -0.5 1 1
PIK3R1 0.025 0.069 -10000 0 -0.5 2 2
JAK1 0.034 0.007 -10000 0 -10000 0 0
NFKB1 0.033 0.003 -10000 0 -10000 0 0
MYC 0.017 0.18 0.41 1 -0.61 5 6
MYB -0.19 0.47 -10000 0 -1.2 21 21
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.002 0.16 0.25 1 -0.47 9 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.12 -10000 0 -0.72 1 1
mol:PI-3-4-5-P3 0.003 0.16 0.25 1 -0.46 9 10
Rac1/GDP 0.02 0.059 -10000 0 -0.4 2 2
T cell proliferation 0.007 0.14 0.24 2 -0.44 7 9
SHC1 0.028 0.012 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.008 0.026 -10000 0 -0.062 21 21
PRKCZ 0.004 0.14 0.24 1 -0.46 7 8
NF kappa B1 p50/RelA 0.026 0.18 -10000 0 -0.55 7 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.015 0.1 -10000 0 -0.35 7 7
HSP90AA1 0.032 0.007 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
IL2RA -0.017 0.15 -10000 0 -0.5 11 11
IL2RB 0.023 0.069 -10000 0 -0.5 2 2
TERT 0.017 0.084 -10000 0 -0.5 3 3
E2F1 -0.053 0.2 -10000 0 -0.47 21 21
SOS1 0.033 0.003 -10000 0 -10000 0 0
RPS6 0.03 0.009 -10000 0 -10000 0 0
mol:cAMP 0.004 0.013 0.031 21 -10000 0 21
PTPN11 0.032 0.007 -10000 0 -10000 0 0
IL2RG 0.012 0.11 -10000 0 -0.5 5 5
actin cytoskeleton organization 0.007 0.14 0.24 2 -0.44 7 9
GRB2 0.031 0.009 -10000 0 -10000 0 0
IL2 0.027 0.012 -10000 0 -10000 0 0
PIK3CA 0.029 0.049 -10000 0 -0.5 1 1
Rac1/GTP 0.05 0.063 -10000 0 -0.38 2 2
LCK -0.002 0.13 -10000 0 -0.5 8 8
BCL2 0.006 0.18 -10000 0 -0.68 5 5
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.006 0.001 -10000 0 -10000 0 0
ADCY5 -0.12 0.14 -10000 0 -0.31 43 43
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.003 0.014 -10000 0 -10000 0 0
ADCY2 0 0.079 -10000 0 -0.31 6 6
ADCY3 -0.005 0.007 -10000 0 -10000 0 0
ADCY8 -0.004 0.021 -10000 0 -10000 0 0
PRKCE 0.009 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.001 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.001 0.088 0.26 7 -0.2 3 10
Syndecan-1-mediated signaling events

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
TGFB1 0.032 0.006 -10000 0 -10000 0 0
CCL5 0.011 0.096 -10000 0 -0.5 4 4
SDCBP 0.032 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.036 0.12 -10000 0 -0.36 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.025 0.12 -10000 0 -0.33 4 4
Syndecan-1/Syntenin -0.021 0.13 0.28 1 -0.39 3 4
MAPK3 -0.021 0.12 0.26 1 -0.37 3 4
HGF/MET 0.023 0.091 -10000 0 -0.44 4 4
TGFB1/TGF beta receptor Type II 0.032 0.006 -10000 0 -10000 0 0
BSG 0.032 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.025 0.12 -10000 0 -0.33 4 4
Syndecan-1/RANTES -0.032 0.14 0.32 1 -0.41 6 7
Syndecan-1/CD147 -0.008 0.13 0.28 1 -0.38 3 4
Syndecan-1/Syntenin/PIP2 -0.021 0.12 0.26 1 -0.38 3 4
LAMA5 0.031 0.008 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.021 0.12 0.25 1 -0.37 3 4
MMP7 -0.13 0.24 -10000 0 -0.5 35 35
HGF 0.017 0.084 -10000 0 -0.5 3 3
Syndecan-1/CASK -0.039 0.11 -10000 0 -0.35 4 4
Syndecan-1/HGF/MET -0.025 0.15 0.28 1 -0.49 4 5
regulation of cell adhesion -0.025 0.11 0.26 2 -0.36 3 5
HPSE 0.03 0.01 -10000 0 -10000 0 0
positive regulation of cell migration -0.036 0.12 -10000 0 -0.36 4 4
SDC1 -0.036 0.12 -10000 0 -0.21 34 34
Syndecan-1/Collagen -0.036 0.12 -10000 0 -0.36 4 4
PPIB 0.032 0.007 -10000 0 -10000 0 0
MET 0.017 0.069 -10000 0 -0.5 2 2
PRKACA 0.032 0.006 -10000 0 -10000 0 0
MMP9 0.013 0.096 -10000 0 -0.5 4 4
MAPK1 -0.022 0.12 0.26 1 -0.37 3 4
homophilic cell adhesion -0.032 0.13 0.3 1 -0.36 4 5
MMP1 0.024 0.049 -10000 0 -0.5 1 1
Plasma membrane estrogen receptor signaling

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.056 0.077 -10000 0 -0.33 4 4
ER alpha/Gai/GDP/Gbeta gamma -0.022 0.21 -10000 0 -0.57 11 11
AKT1 -0.062 0.27 -10000 0 -0.74 15 15
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.057 0.28 -10000 0 -0.76 15 15
mol:Ca2+ -0.005 0.088 -10000 0 -0.36 5 5
IGF1R 0.03 0.009 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.005 0.12 -10000 0 -0.32 14 14
SHC1 0.028 0.012 -10000 0 -10000 0 0
apoptosis 0.057 0.26 0.7 15 -10000 0 15
RhoA/GTP 0.024 0.029 -10000 0 -0.24 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.008 0.16 -10000 0 -0.49 8 8
regulation of stress fiber formation 0.018 0.081 -10000 0 -0.29 1 1
E2/ERA-ERB (dimer) 0.032 0.047 -10000 0 -0.3 2 2
KRAS 0.032 0.007 -10000 0 -10000 0 0
G13/GTP 0.033 0.033 -10000 0 -0.28 1 1
pseudopodium formation -0.018 0.081 0.29 1 -10000 0 1
E2/ER alpha (dimer)/PELP1 0.033 0.037 -10000 0 -0.31 1 1
GRB2 0.03 0.009 -10000 0 -10000 0 0
GNG2 0.018 0.084 -10000 0 -0.5 3 3
GNAO1 0.025 0.049 -10000 0 -0.5 1 1
HRAS 0.03 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.024 0.22 0.4 1 -0.56 13 14
E2/ER beta (dimer) 0.02 0.035 -10000 0 -0.36 1 1
mol:GDP 0.014 0.061 -10000 0 -0.37 2 2
mol:NADP -0.024 0.22 0.4 1 -0.56 13 14
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
mol:IP3 -0.008 0.089 -10000 0 -0.37 5 5
IGF-1R heterotetramer 0.03 0.009 -10000 0 -10000 0 0
PLCB1 -0.003 0.092 -10000 0 -0.38 5 5
PLCB2 -0.001 0.085 -10000 0 -0.36 4 4
IGF1 0.014 0.096 -10000 0 -0.5 4 4
mol:L-citrulline -0.024 0.22 0.4 1 -0.56 13 14
RHOA 0.031 0.008 -10000 0 -10000 0 0
Gai/GDP -0.019 0.2 -10000 0 -0.58 11 11
JNK cascade 0.02 0.035 -10000 0 -0.36 1 1
BCAR1 0.03 0.01 -10000 0 -10000 0 0
ESR2 0.027 0.049 -10000 0 -0.5 1 1
GNAQ 0.031 0.007 -10000 0 -10000 0 0
ESR1 0.024 0.049 -10000 0 -0.5 1 1
Gq family/GDP/Gbeta gamma -0.008 0.17 -10000 0 -0.51 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.13 -10000 0 -0.71 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.018 0.14 -10000 0 -0.54 5 5
GNAZ 0.03 0.01 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.018 0.036 -10000 0 -0.36 1 1
STRN -0.03 0.17 -10000 0 -0.5 14 14
GNAL 0 0.12 -10000 0 -0.5 7 7
PELP1 0.03 0.009 -10000 0 -10000 0 0
MAPK11 0.014 0.028 -10000 0 -0.28 1 1
GNAI2 0.031 0.008 -10000 0 -10000 0 0
GNAI3 0.032 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.008 -10000 0 -10000 0 0
HBEGF -0.031 0.18 -10000 0 -0.55 9 9
cAMP biosynthetic process 0.011 0.076 -10000 0 -0.24 9 9
SRC -0.023 0.2 -10000 0 -0.56 10 10
PI3K 0.036 0.075 -10000 0 -0.51 2 2
GNB1 0.032 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.045 0.078 -10000 0 -0.42 2 2
SOS1 0.033 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.006 0.1 -10000 0 -0.4 5 5
Gs family/GTP 0.018 0.08 -10000 0 -0.25 9 9
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.056 0.02 -10000 0 -10000 0 0
vasodilation -0.021 0.2 0.4 1 -0.52 13 14
mol:DAG -0.008 0.089 -10000 0 -0.37 5 5
Gs family/GDP/Gbeta gamma 0.007 0.088 -10000 0 -0.26 9 9
MSN -0.019 0.085 0.3 1 -10000 0 1
Gq family/GTP 0.007 0.091 -10000 0 -0.38 4 4
mol:PI-3-4-5-P3 -0.052 0.27 -10000 0 -0.72 15 15
NRAS 0.032 0.007 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.021 0.2 0.52 13 -0.4 1 14
GRB2/SOS1 0.045 0.013 -10000 0 -10000 0 0
RhoA/GDP 0.034 0.066 -10000 0 -0.34 2 2
NOS3 -0.032 0.24 -10000 0 -0.61 13 13
GNA11 0.005 0.12 -10000 0 -0.5 6 6
MAPKKK cascade -0.045 0.21 0.34 1 -0.54 12 13
E2/ER alpha (dimer)/PELP1/Src -0.001 0.17 -10000 0 -0.5 9 9
ruffle organization -0.018 0.081 0.29 1 -10000 0 1
ROCK2 -0.016 0.093 0.31 1 -0.24 10 11
GNA14 0.018 0.084 -10000 0 -0.5 3 3
GNA15 0.032 0.007 -10000 0 -10000 0 0
GNA13 0.031 0.008 -10000 0 -10000 0 0
MMP9 -0.025 0.18 -10000 0 -0.52 10 10
MMP2 -0.036 0.18 -10000 0 -0.54 8 8
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.011 -10000 0 -10000 0 0
Necdin/E2F1 0.038 0.056 -10000 0 -0.36 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.065 0.1 -10000 0 -0.35 6 6
NGF (dimer)/p75(NTR)/BEX1 0.018 0.12 -10000 0 -0.36 10 10
NT-4/5 (dimer)/p75(NTR) 0.007 0.097 -10000 0 -0.34 8 8
IKBKB 0.031 0.007 -10000 0 -10000 0 0
AKT1 0.004 0.11 0.36 1 -0.35 8 9
IKBKG 0.032 0.007 -10000 0 -10000 0 0
BDNF 0.031 0.008 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.041 0.071 -10000 0 -0.31 4 4
FURIN 0.031 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.043 0.07 -10000 0 -0.31 4 4
LINGO1 0.031 0.008 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.039 0.018 -10000 0 -10000 0 0
proBDNF (dimer) 0.031 0.008 -10000 0 -10000 0 0
NTRK1 0.008 0.096 -10000 0 -0.5 4 4
RTN4R 0.03 0.009 -10000 0 -10000 0 0
neuron apoptosis 0.01 0.095 -10000 0 -0.42 3 3
IRAK1 0.032 0.007 -10000 0 -10000 0 0
SHC1 -0.002 0.097 -10000 0 -0.4 6 6
ARHGDIA 0.031 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.023 0.006 -10000 0 -10000 0 0
Gamma Secretase 0.081 0.038 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.05 0.11 -10000 0 -0.36 7 7
MAGEH1 0.023 0.069 -10000 0 -0.5 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.049 0.11 -10000 0 -0.36 7 7
Mammalian IAPs/DIABLO 0.078 0.022 -10000 0 -10000 0 0
proNGF (dimer) 0.013 0.096 -10000 0 -0.5 4 4
MAGED1 0.032 0.004 -10000 0 -10000 0 0
APP 0.029 0.011 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.006 0.095 -10000 0 -0.5 4 4
ZNF274 0.032 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.026 0.091 -10000 0 -0.35 6 6
NGF 0.013 0.096 -10000 0 -0.5 4 4
cell cycle arrest -0.004 0.12 0.3 9 -0.32 6 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.017 0.08 -10000 0 -0.31 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.021 0.09 -10000 0 -0.29 8 8
NCSTN 0.027 0.012 -10000 0 -10000 0 0
mol:GTP 0.034 0.11 -10000 0 -0.4 6 6
PSENEN 0.032 0.006 -10000 0 -10000 0 0
mol:ceramide 0.005 0.095 -10000 0 -0.36 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.018 0.068 -10000 0 -0.39 2 2
p75(NTR)/beta APP 0.026 0.075 -10000 0 -0.36 4 4
BEX1 0 0.12 -10000 0 -0.5 7 7
mol:GDP -0.015 0.092 -10000 0 -0.4 6 6
NGF (dimer) -0.047 0.17 -10000 0 -0.3 36 36
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.06 0.071 -10000 0 -0.28 4 4
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
RAC1/GTP 0.028 0.092 -10000 0 -0.34 6 6
MYD88 0.031 0.008 -10000 0 -10000 0 0
CHUK 0.032 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.035 0.11 -10000 0 -0.4 6 6
RHOB 0.033 0.003 -10000 0 -10000 0 0
RHOA 0.031 0.008 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.039 0.054 -10000 0 -0.36 2 2
NT3 (dimer) -0.021 0.14 -10000 0 -0.5 9 9
TP53 -0.009 0.059 -10000 0 -0.26 4 4
PRDM4 0.008 0.097 -10000 0 -0.37 6 6
BDNF (dimer) -0.033 0.15 -10000 0 -0.25 35 35
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
SORT1 0.032 0.007 -10000 0 -10000 0 0
activation of caspase activity 0.058 0.1 -10000 0 -0.35 6 6
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.054 0.1 -10000 0 -0.37 6 6
RHOC 0.032 0.007 -10000 0 -10000 0 0
XIAP 0.032 0.006 -10000 0 -10000 0 0
MAPK10 0.001 0.1 0.34 2 -0.39 4 6
DIABLO 0.032 0.007 -10000 0 -10000 0 0
SMPD2 0.005 0.096 -10000 0 -0.37 6 6
APH1B 0.032 0.007 -10000 0 -10000 0 0
APH1A 0.028 0.012 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.035 0.11 -10000 0 -0.4 6 6
PSEN1 0.031 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.045 0.013 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.013 0.12 -10000 0 -0.38 11 11
MAPK8 -0.006 0.11 0.34 2 -0.39 4 6
MAPK9 0.004 0.09 0.3 1 -0.39 4 5
APAF1 0.032 0.007 -10000 0 -10000 0 0
NTF3 -0.021 0.14 -10000 0 -0.5 9 9
NTF4 0.006 0.096 -10000 0 -0.5 4 4
NDN 0.027 0.049 -10000 0 -0.5 1 1
RAC1/GDP 0.023 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.057 0.096 -10000 0 -0.33 6 6
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.061 -10000 0 -0.28 3 3
RhoA-B-C/GTP 0.034 0.1 -10000 0 -0.4 6 6
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.075 0.071 -10000 0 -0.27 4 4
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.064 0.069 -10000 0 -0.28 4 4
PRKACB 0.032 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.035 0.066 -10000 0 -0.36 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.032 0.005 -10000 0 -10000 0 0
BIRC2 0.032 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.012 0.1 0.27 3 -0.35 7 10
BAD 0.004 0.11 0.39 3 -0.39 4 7
RIPK2 0.031 0.007 -10000 0 -10000 0 0
NGFR 0.012 0.096 -10000 0 -0.5 4 4
CYCS 0.006 0.093 -10000 0 -0.35 6 6
ADAM17 0.019 0.084 -10000 0 -0.5 3 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.05 0.1 -10000 0 -0.37 6 6
BCL2L11 0.004 0.11 0.39 3 -0.39 4 7
BDNF (dimer)/p75(NTR) 0.027 0.075 -10000 0 -0.36 4 4
PI3K 0.044 0.12 -10000 0 -0.38 8 8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.052 0.1 -10000 0 -0.37 6 6
NDNL2 0.032 0.007 -10000 0 -10000 0 0
YWHAE 0.03 0.009 -10000 0 -10000 0 0
PRKCI 0.032 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.017 0.12 -10000 0 -0.46 6 6
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.054 0.1 -10000 0 -0.37 6 6
TRAF6 0.032 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
PRKCZ 0.031 0.007 -10000 0 -10000 0 0
PLG 0.018 0.008 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.009 0.093 -10000 0 -0.37 6 6
SQSTM1 0.032 0.007 -10000 0 -10000 0 0
NGFRAP1 0.032 0.004 -10000 0 -10000 0 0
CASP3 0.006 0.11 0.42 2 -0.36 4 6
E2F1 0.023 0.069 -10000 0 -0.5 2 2
CASP9 0.031 0.007 -10000 0 -10000 0 0
IKK complex 0.044 0.11 -10000 0 -0.39 4 4
NGF (dimer)/TRKA 0.01 0.1 -10000 0 -0.36 8 8
MMP7 -0.13 0.24 -10000 0 -0.5 35 35
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.065 0.1 -10000 0 -0.35 6 6
MMP3 0.017 0.014 -10000 0 -10000 0 0
APAF-1/Caspase 9 0.007 0.073 -10000 0 -0.42 2 2
PLK1 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
regulation of centriole-centriole cohesion 0.01 0.056 0.18 11 -10000 0 11
BUB1B -0.001 0.074 0.13 2 -0.29 6 8
PLK1 0.006 0.029 0.095 3 -0.12 2 5
PLK1S1 0.012 0.021 0.11 3 -10000 0 3
KIF2A 0.008 0.042 0.21 3 -10000 0 3
regulation of mitotic centrosome separation 0.006 0.029 0.095 3 -0.12 2 5
GOLGA2 0.032 0.007 -10000 0 -10000 0 0
Hec1/SPC24 0.027 0.089 -10000 0 -0.36 5 5
WEE1 0.013 0.06 -10000 0 -0.31 3 3
cytokinesis -0.006 0.087 0.2 1 -0.2 14 15
PP2A-alpha B56 0.044 0.14 -10000 0 -0.58 5 5
AURKA 0.011 0.018 -10000 0 -10000 0 0
PICH/PLK1 0.018 0.024 -10000 0 -10000 0 0
CENPE 0 0.053 0.25 1 -0.32 2 3
RhoA/GTP 0.023 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.042 0.21 3 -10000 0 3
PPP2CA 0.032 0.006 -10000 0 -10000 0 0
FZR1 0.032 0.007 -10000 0 -10000 0 0
TPX2 0.006 0.054 0.12 1 -0.31 3 4
PAK1 0.033 0.005 -10000 0 -10000 0 0
SPC24 0.009 0.11 -10000 0 -0.5 5 5
FBXW11 0.032 0.006 -10000 0 -10000 0 0
CLSPN -0.034 0.11 -10000 0 -0.29 19 19
GORASP1 0.031 0.008 -10000 0 -10000 0 0
metaphase 0 0.005 0.016 2 -0.017 7 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.016 0.057 3 -0.066 2 5
G2 phase of mitotic cell cycle -0.001 0.002 0.011 2 -10000 0 2
STAG2 0.032 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.001 0.12 -10000 0 -0.49 7 7
spindle elongation 0.006 0.029 0.095 3 -0.12 2 5
ODF2 0.032 0.007 -10000 0 -10000 0 0
BUB1 0.008 0.15 -10000 0 -0.63 6 6
TPT1 0.003 0.044 -10000 0 -0.2 5 5
CDC25C -0.008 0.1 -10000 0 -0.37 8 8
CDC25B 0.033 0.007 -10000 0 -10000 0 0
SGOL1 -0.01 0.056 -10000 0 -0.18 11 11
RHOA 0.031 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 0.046 0.03 -10000 0 -10000 0 0
CDC14B 0.005 0.034 -10000 0 -0.37 1 1
CDC20 0.009 0.11 -10000 0 -0.5 5 5
PLK1/PBIP1 0.006 0.028 -10000 0 -0.12 2 2
mitosis -0.002 0.003 0.019 1 -10000 0 1
FBXO5 0 0.029 0.12 1 -10000 0 1
CDC2 0.002 0.001 -10000 0 -10000 0 0
NDC80 0.027 0.049 -10000 0 -0.5 1 1
metaphase plate congression 0.004 0.046 -10000 0 -0.2 5 5
ERCC6L 0.023 0.028 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.006 0.023 0.088 2 -0.084 3 5
microtubule cytoskeleton organization 0.003 0.044 -10000 0 -0.19 5 5
G2/M transition DNA damage checkpoint 0 0.003 0.017 3 -10000 0 3
PPP1R12A 0.032 0.007 -10000 0 -10000 0 0
interphase 0 0.003 0.017 3 -10000 0 3
PLK1/PRC1-2 0.036 0.053 -10000 0 -0.29 2 2
GRASP65/GM130/RAB1/GTP/PLK1 0.052 0.036 -10000 0 -10000 0 0
RAB1A 0.033 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.021 0.1 3 -10000 0 3
mitotic prometaphase -0.001 0.005 0.02 5 -0.012 4 9
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.043 -10000 0 -10000 0 0
microtubule-based process 0.02 0.05 -10000 0 -0.2 4 4
Golgi organization 0.006 0.029 0.095 3 -0.12 2 5
Cohesin/SA2 0.021 0.029 -10000 0 -0.12 2 2
PPP1CB/MYPT1 0.046 0.011 -10000 0 -10000 0 0
KIF20A 0.023 0.069 -10000 0 -0.5 2 2
APC/C/CDC20 0.014 0.076 -10000 0 -0.33 5 5
PPP2R1A 0.032 0.006 -10000 0 -10000 0 0
chromosome segregation 0.005 0.028 -10000 0 -0.12 2 2
PRC1 0.031 0.007 -10000 0 -10000 0 0
ECT2 0.007 0.058 0.26 4 -0.26 1 5
C13orf34 0.006 0.022 0.09 3 -0.082 2 5
NUDC 0.004 0.047 -10000 0 -0.2 5 5
regulation of attachment of spindle microtubules to kinetochore -0.001 0.073 0.13 2 -0.29 6 8
spindle assembly 0.008 0.03 0.11 4 -0.1 2 6
spindle stabilization 0.012 0.021 0.11 3 -10000 0 3
APC/C/HCDH1 0.026 0.032 -10000 0 -0.31 1 1
MKLP2/PLK1 0.02 0.051 -10000 0 -0.2 4 4
CCNB1 0.033 0.007 -10000 0 -10000 0 0
PPP1CB 0.033 0.003 -10000 0 -10000 0 0
BTRC 0.032 0.006 -10000 0 -10000 0 0
ROCK2 -0.031 0.13 -10000 0 -0.4 12 12
TUBG1 0.008 0.031 0.12 1 -0.18 2 3
G2/M transition of mitotic cell cycle 0.01 0.021 -10000 0 -10000 0 0
MLF1IP 0.007 0.006 -10000 0 -10000 0 0
INCENP 0.032 0.005 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.03 0.027 -10000 0 -10000 0 0
MAP4K4 0.001 0.061 -10000 0 -10000 0 0
BAG4 0.031 0.007 -10000 0 -10000 0 0
PKC zeta/ceramide -0.007 0.1 -10000 0 -0.35 6 6
NFKBIA 0.032 0.007 -10000 0 -10000 0 0
BIRC3 0.032 0.005 -10000 0 -10000 0 0
BAX -0.004 0.067 -10000 0 -0.31 5 5
RIPK1 0.028 0.012 -10000 0 -10000 0 0
AKT1 0.023 0.16 0.85 4 -10000 0 4
BAD -0.023 0.097 -10000 0 -0.39 5 5
SMPD1 -0.011 0.071 0.14 1 -0.2 12 13
RB1 -0.027 0.099 -10000 0 -0.36 6 6
FADD/Caspase 8 0.007 0.067 -10000 0 -10000 0 0
MAP2K4 -0.02 0.087 0.19 2 -0.6 2 4
NSMAF 0.032 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.1 0.21 5 -0.51 3 8
EGF 0.025 0.011 -10000 0 -10000 0 0
mol:ceramide -0.023 0.1 -10000 0 -0.37 6 6
MADD 0.032 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.03 0.028 -10000 0 -10000 0 0
ASAH1 0.032 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.097 -10000 0 -0.36 6 6
cell proliferation 0.006 0.098 0.21 4 -0.32 6 10
BID -0.011 0.16 -10000 0 -0.78 4 4
MAP3K1 -0.019 0.092 0.2 2 -0.36 5 7
EIF2A -0.019 0.087 0.2 3 -0.56 2 5
TRADD 0.03 0.01 -10000 0 -10000 0 0
CRADD 0.032 0.007 -10000 0 -10000 0 0
MAPK3 -0.004 0.094 0.21 6 -0.56 2 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.09 0.22 4 -0.53 2 6
Cathepsin D/ceramide -0.007 0.1 -10000 0 -0.38 5 5
FADD 0.001 0.061 -10000 0 -10000 0 0
KSR1 -0.013 0.11 0.2 7 -0.38 5 12
MAPK8 -0.026 0.11 -10000 0 -0.33 10 10
PRKRA -0.024 0.097 -10000 0 -0.39 5 5
PDGFA 0.023 0.015 -10000 0 -10000 0 0
TRAF2 0.032 0.006 -10000 0 -10000 0 0
IGF1 0.014 0.096 -10000 0 -0.5 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.023 0.1 -10000 0 -0.36 6 6
CTSD 0.031 0.007 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.047 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.007 0.11 0.23 4 -0.34 6 10
PRKCD 0.031 0.008 -10000 0 -10000 0 0
PRKCZ 0.031 0.007 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.03 0.028 -10000 0 -10000 0 0
RelA/NF kappa B1 0.048 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.032 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.012 0.061 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.029 0.1 -10000 0 -0.31 9 9
mol:Sphingosine-1-phosphate 0.03 0.027 -10000 0 -10000 0 0
MAP2K1 -0.01 0.1 0.2 6 -0.64 2 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
CYCS -0.006 0.055 0.17 1 -0.24 4 5
TNFRSF1A 0.031 0.007 -10000 0 -10000 0 0
NFKB1 0.033 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.045 0.014 -10000 0 -10000 0 0
EIF2AK2 -0.024 0.094 0.2 1 -0.43 4 5
TNF-alpha/TNFR1A/FAN 0.03 0.1 -10000 0 -0.31 9 9
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.025 0.077 -10000 0 -0.7 1 1
MAP2K2 -0.01 0.089 0.22 6 -0.48 2 8
SMPD3 -0.062 0.16 -10000 0 -0.3 30 30
TNF -0.015 0.15 -10000 0 -0.5 10 10
PKC zeta/PAR4 0.045 0.013 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.043 0.081 -10000 0 -0.26 9 9
NF kappa B1/RelA/I kappa B alpha 0.089 0.028 -10000 0 -10000 0 0
AIFM1 -0.007 0.058 0.17 1 -0.24 4 5
BCL2 0.022 0.069 -10000 0 -0.5 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.004 0.1 -9999 0 -0.36 9 9
CRKL 0.03 0.009 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.006 -9999 0 -10000 0 0
DOCK1 0.027 0.049 -9999 0 -0.5 1 1
ITGA4 -0.008 0.14 -9999 0 -0.5 9 9
alpha4/beta7 Integrin/MAdCAM1 0.046 0.1 -9999 0 -0.28 10 10
EPO 0.029 0.01 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.009 0.12 -9999 0 -0.39 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.03 0.009 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.019 0.1 -9999 0 -0.36 8 8
EPO/EPOR (dimer) 0.043 0.015 -9999 0 -10000 0 0
lamellipodium assembly 0.012 0.11 -9999 0 -0.51 4 4
PIK3CA 0.027 0.049 -9999 0 -0.5 1 1
PI3K 0.036 0.075 -9999 0 -0.51 2 2
ARF6 0.031 0.007 -9999 0 -10000 0 0
JAK2 0.014 0.065 -9999 0 -0.24 7 7
PXN 0.032 0.007 -9999 0 -10000 0 0
PIK3R1 0.023 0.069 -9999 0 -0.5 2 2
MADCAM1 0.028 0.011 -9999 0 -10000 0 0
cell adhesion 0.044 0.1 -9999 0 -0.28 10 10
CRKL/CBL 0.039 0.052 -9999 0 -0.35 2 2
ITGB1 0.032 0.005 -9999 0 -10000 0 0
SRC 0.001 0.072 -9999 0 -0.28 7 7
ITGB7 0.023 0.069 -9999 0 -0.5 2 2
RAC1 0.031 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.037 0.096 -9999 0 -0.31 8 8
p130Cas/Crk/Dock1 0.021 0.08 -9999 0 -0.29 6 6
VCAM1 0.031 0.007 -9999 0 -10000 0 0
RHOA 0.031 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.094 -9999 0 -0.28 8 8
BCAR1 -0.026 0.061 -9999 0 -0.28 6 6
EPOR 0.032 0.007 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.023 0.069 -9999 0 -0.5 2 2
GIT1 0.03 0.009 -9999 0 -10000 0 0
Rac1/GTP 0.011 0.11 -9999 0 -0.53 4 4
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.023 0.005 -10000 0 -10000 0 0
PRKCZ 0.031 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.019 0.056 -10000 0 -0.31 1 1
IRAK/TOLLIP 0.035 0.011 -10000 0 -10000 0 0
IKBKB 0.031 0.007 -10000 0 -10000 0 0
IKBKG 0.032 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.019 0.09 -10000 0 -0.36 6 6
IL1A 0.028 0.008 -10000 0 -10000 0 0
IL1B 0.014 0.035 -10000 0 -0.36 1 1
IRAK/TRAF6/p62/Atypical PKCs 0.076 0.026 -10000 0 -10000 0 0
IL1R2 0.002 0.12 -10000 0 -0.5 6 6
IL1R1 0.01 0.11 -10000 0 -0.5 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.069 -10000 0 -0.27 5 5
TOLLIP 0.032 0.007 -10000 0 -10000 0 0
TICAM2 0.032 0.007 -10000 0 -10000 0 0
MAP3K3 0.031 0.008 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.02 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.034 -10000 0 -10000 0 0
JUN -0.053 0.1 0.18 1 -0.26 22 23
MAP3K7 0.03 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.058 0.11 -10000 0 -0.33 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88 0.059 0.077 -10000 0 -0.29 5 5
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.069 0.078 -10000 0 -0.27 5 5
IL1 beta fragment/IL1R1/IL1RAP 0.036 0.075 -10000 0 -0.28 6 6
NFKB1 0.033 0.003 -10000 0 -10000 0 0
MAPK8 -0.021 0.063 0.19 1 -0.24 8 9
IRAK1 0.017 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.019 0.15 -10000 0 -0.36 19 19
IRAK4 0.032 0.007 -10000 0 -10000 0 0
PRKCI 0.032 0.007 -10000 0 -10000 0 0
TRAF6 0.032 0.006 -10000 0 -10000 0 0
PI3K 0.036 0.075 -10000 0 -0.51 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.018 0.062 -10000 0 -0.22 5 5
CHUK 0.032 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.036 0.075 -10000 0 -0.28 6 6
IL1 beta/IL1R2 0.018 0.084 -10000 0 -0.31 7 7
IRAK/TRAF6/TAK1/TAB1/TAB2 0.042 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.043 0.098 -10000 0 -0.31 7 7
IRAK3 0.023 0.069 -10000 0 -0.5 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.062 0.08 -10000 0 -0.26 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.061 -10000 0 -0.24 6 6
IL1 alpha/IL1R1/IL1RAP 0.044 0.077 -10000 0 -0.31 5 5
RELA 0.032 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.032 0.007 -10000 0 -10000 0 0
MYD88 0.031 0.008 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.052 0.022 -10000 0 -10000 0 0
IL1RAP 0.031 0.007 -10000 0 -10000 0 0
UBE2N 0.032 0.007 -10000 0 -10000 0 0
IRAK/TRAF6 0.03 0.063 -10000 0 -0.24 6 6
CASP1 0.032 0.004 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.026 0.16 -10000 0 -0.37 19 19
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.05 0.078 -10000 0 -0.27 6 6
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.089 -10000 0 -0.32 7 7
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
IL1RN -0.031 0.17 -10000 0 -0.5 14 14
TRAF6/TAK1/TAB1/TAB2 0.043 0.016 -10000 0 -10000 0 0
MAP2K6 0.013 0.039 -10000 0 -0.25 2 2
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.014 0.13 -10000 0 -0.5 5 5
BAG4 0.031 0.007 -10000 0 -10000 0 0
BAD -0.004 0.042 -10000 0 -0.17 3 3
NFKBIA 0.032 0.007 -10000 0 -10000 0 0
BIRC3 0.032 0.005 -10000 0 -10000 0 0
BAX -0.002 0.048 0.16 2 -0.18 3 5
EnzymeConsortium:3.1.4.12 -0.002 0.031 -10000 0 -0.097 6 6
IKBKB -0.01 0.12 -10000 0 -0.5 4 4
MAP2K2 0.002 0.06 0.23 3 -0.23 1 4
MAP2K1 0.001 0.054 0.19 4 -0.22 1 5
SMPD1 -0.002 0.039 -10000 0 -0.16 4 4
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.012 0.14 -10000 0 -0.48 6 6
MAP2K4 -0.001 0.042 0.18 1 -0.23 1 2
protein ubiquitination -0.017 0.13 -10000 0 -0.44 6 6
EnzymeConsortium:2.7.1.37 0.002 0.061 0.22 3 -0.26 1 4
response to UV 0 0.001 0.002 4 -0.002 1 5
RAF1 0.001 0.052 0.2 3 -0.23 1 4
CRADD 0.032 0.007 -10000 0 -10000 0 0
mol:ceramide -0.004 0.047 -10000 0 -0.18 4 4
I-kappa-B-alpha/RELA/p50/ubiquitin 0.042 0.01 -10000 0 -10000 0 0
MADD 0.032 0.005 -10000 0 -10000 0 0
MAP3K1 0 0.049 0.16 2 -0.2 2 4
TRADD 0.03 0.01 -10000 0 -10000 0 0
RELA/p50 0.032 0.004 -10000 0 -10000 0 0
MAPK3 0.007 0.057 0.22 3 -0.22 1 4
MAPK1 0.004 0.061 0.22 3 -0.24 2 5
p50/RELA/I-kappa-B-alpha 0.046 0.011 -10000 0 -10000 0 0
FADD -0.014 0.13 -10000 0 -0.5 5 5
KSR1 0.002 0.053 0.18 4 -0.2 2 6
MAPK8 -0.015 0.073 0.19 1 -0.24 8 9
TRAF2 0.032 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.019 0.12 -10000 0 -0.47 5 5
TNF R/SODD 0.045 0.014 -10000 0 -10000 0 0
TNF -0.015 0.15 -10000 0 -0.5 10 10
CYCS -0.001 0.044 0.18 2 -0.15 2 4
IKBKG -0.01 0.11 -10000 0 -0.42 5 5
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.008 0.14 -10000 0 -0.59 4 4
RELA 0.032 0.004 -10000 0 -10000 0 0
RIPK1 0.028 0.011 -10000 0 -10000 0 0
AIFM1 -0.001 0.042 0.21 1 -0.16 1 2
TNF/TNF R/SODD 0.029 0.1 -10000 0 -0.31 9 9
TNFRSF1A 0.031 0.007 -10000 0 -10000 0 0
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.014 0.14 -10000 0 -0.84 3 3
NSMAF -0.008 0.12 -10000 0 -0.6 3 3
response to hydrogen peroxide 0 0.001 0.002 4 -0.002 1 5
BCL2 0.022 0.069 -10000 0 -0.5 2 2
HIF-2-alpha transcription factor network

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
MMP14 0.037 0.061 -10000 0 -10000 0 0
oxygen homeostasis 0.01 0.017 -10000 0 -10000 0 0
TCEB2 0.031 0.008 -10000 0 -10000 0 0
TCEB1 0.032 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.063 0.14 0.31 3 -0.39 5 8
EPO 0.074 0.18 -10000 0 -0.62 2 2
FIH (dimer) 0.041 0.021 -10000 0 -10000 0 0
APEX1 0.035 0.03 -10000 0 -10000 0 0
SERPINE1 0.069 0.18 0.48 1 -0.62 2 3
FLT1 0.022 0.12 -10000 0 -0.6 3 3
ADORA2A 0.085 0.24 0.51 8 -0.52 7 15
germ cell development 0.074 0.18 0.47 1 -0.59 2 3
SLC11A2 0.082 0.19 0.48 1 -0.62 2 3
BHLHE40 0.084 0.19 0.45 2 -0.62 2 4
HIF1AN 0.041 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.062 0.15 -10000 0 -0.45 4 4
ETS1 0.028 0.086 -10000 0 -0.5 3 3
CITED2 0.019 0.11 -10000 0 -0.61 2 2
KDR 0.015 0.18 -10000 0 -0.85 4 4
PGK1 0.085 0.19 0.48 1 -0.62 2 3
SIRT1 0.024 0.068 -10000 0 -0.49 2 2
response to hypoxia 0.001 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.1 0.22 -10000 0 -0.71 2 2
EPAS1 0.044 0.14 0.35 6 -0.34 6 12
SP1 0.039 0.013 -10000 0 -10000 0 0
ABCG2 0.079 0.2 -10000 0 -0.74 2 2
EFNA1 0.067 0.18 0.42 1 -0.62 2 3
FXN 0.095 0.21 0.52 7 -0.6 2 9
POU5F1 0.075 0.19 0.48 1 -0.62 2 3
neuron apoptosis -0.1 0.21 0.69 2 -10000 0 2
EP300 0.03 0.009 -10000 0 -10000 0 0
EGLN3 0.01 0.12 -10000 0 -0.49 7 7
EGLN2 0.041 0.022 -10000 0 -10000 0 0
EGLN1 0.034 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.053 0.044 -10000 0 -0.24 2 2
VHL 0.022 0.069 -10000 0 -0.5 2 2
ARNT 0.028 0.029 -10000 0 -10000 0 0
SLC2A1 0.096 0.2 0.5 7 -0.6 2 9
TWIST1 0.048 0.28 0.53 6 -0.51 18 24
ELK1 0.037 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.069 0.15 -10000 0 -0.4 4 4
VEGFA 0.078 0.19 0.48 1 -0.62 2 3
CREBBP 0.032 0.005 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.03 0.009 -10000 0 -10000 0 0
EPHB2 0.026 0.05 -10000 0 -0.5 1 1
EFNB1 0.001 0.077 -10000 0 -0.37 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.051 0.085 -10000 0 -0.3 5 5
Ephrin B2/EPHB1-2 0.046 0.04 -10000 0 -0.29 1 1
neuron projection morphogenesis 0.032 0.076 -10000 0 -0.29 5 5
Ephrin B1/EPHB1-2/Tiam1 0.044 0.086 -10000 0 -0.32 5 5
DNM1 0.009 0.11 -10000 0 -0.5 5 5
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.01 0.088 -10000 0 -0.56 3 3
YES1 0.001 0.13 -10000 0 -0.78 3 3
Ephrin B1/EPHB1-2/NCK2 0.048 0.084 -10000 0 -0.32 5 5
PI3K 0.029 0.13 -10000 0 -0.71 3 3
mol:GDP 0.041 0.084 -10000 0 -0.32 5 5
ITGA2B 0.019 0.069 -10000 0 -0.5 2 2
endothelial cell proliferation 0.039 0.014 -10000 0 -10000 0 0
FYN 0 0.13 -10000 0 -0.78 3 3
MAP3K7 -0.009 0.093 -10000 0 -0.58 3 3
FGR 0.001 0.13 -10000 0 -0.78 3 3
TIAM1 0.026 0.049 -10000 0 -0.5 1 1
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
RGS3 0.032 0.006 -10000 0 -10000 0 0
cell adhesion -0.036 0.16 -10000 0 -0.54 5 5
LYN 0.001 0.13 -10000 0 -0.78 3 3
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.12 -10000 0 -0.72 3 3
Ephrin B1/EPHB1-2 -0.007 0.1 -10000 0 -0.63 3 3
SRC 0.003 0.13 -10000 0 -0.78 3 3
ITGB3 -0.073 0.21 -10000 0 -0.5 23 23
EPHB1 0.028 0.011 -10000 0 -10000 0 0
EPHB4 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.031 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.039 0.014 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.041 0.16 -10000 0 -0.36 24 24
BLK -0.021 0.14 -10000 0 -0.77 3 3
HCK 0.003 0.12 -10000 0 -0.77 3 3
regulation of stress fiber formation -0.045 0.081 0.32 5 -10000 0 5
MAPK8 -0.023 0.11 -10000 0 -0.61 3 3
Ephrin B1/EPHB1-2/RGS3 0.047 0.083 -10000 0 -0.32 5 5
endothelial cell migration -0.002 0.079 0.21 1 -0.44 3 4
NCK2 0.033 0.003 -10000 0 -10000 0 0
PTPN13 0.017 0.1 -10000 0 -0.61 3 3
regulation of focal adhesion formation -0.045 0.081 0.32 5 -10000 0 5
chemotaxis -0.045 0.081 0.32 5 -10000 0 5
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
Rac1/GTP 0.043 0.081 -10000 0 -0.3 5 5
angiogenesis -0.007 0.1 -10000 0 -0.62 3 3
LCK -0.009 0.13 -10000 0 -0.78 3 3
Paxillin-dependent events mediated by a4b1

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
CRKL 0.03 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.031 0.015 -10000 0 -10000 0 0
DOCK1 0.027 0.049 -10000 0 -0.5 1 1
ITGA4 -0.008 0.14 -10000 0 -0.5 9 9
RAC1 0.031 0.008 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.009 0.12 -10000 0 -0.39 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.03 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.091 -10000 0 -0.31 7 7
alpha4/beta7 Integrin/Paxillin 0.024 0.097 -10000 0 -0.29 10 10
lamellipodium assembly 0.021 0.1 -10000 0 -0.53 3 3
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
PI3K 0.036 0.075 -10000 0 -0.51 2 2
ARF6 0.031 0.007 -10000 0 -10000 0 0
TLN1 0.032 0.007 -10000 0 -10000 0 0
PXN 0.016 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
ARF6/GTP 0.044 0.078 -10000 0 -0.25 7 7
cell adhesion 0.043 0.083 -10000 0 -0.27 7 7
CRKL/CBL 0.039 0.052 -10000 0 -0.35 2 2
alpha4/beta1 Integrin/Paxillin 0.029 0.082 -10000 0 -0.28 7 7
ITGB1 0.032 0.005 -10000 0 -10000 0 0
ITGB7 0.023 0.069 -10000 0 -0.5 2 2
ARF6/GDP 0.031 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.085 -10000 0 -0.27 7 7
p130Cas/Crk/Dock1 0.054 0.041 -10000 0 -0.31 1 1
VCAM1 0.031 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin 0.046 0.085 -10000 0 -0.27 7 7
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.085 -10000 0 -0.27 7 7
BCAR1 0.03 0.01 -10000 0 -10000 0 0
mol:GDP -0.043 0.082 0.27 7 -10000 0 7
CBL 0.023 0.069 -10000 0 -0.5 2 2
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GIT1 0.03 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.046 0.085 -10000 0 -0.27 7 7
Rac1/GTP 0.019 0.12 -10000 0 -0.62 3 3
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.031 0.007 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.033 0.077 -10000 0 -10000 0 0
NEF -0.005 0.038 -10000 0 -0.17 6 6
NFKBIA 0.034 0.008 -10000 0 -10000 0 0
BIRC3 0.031 0.03 -10000 0 -10000 0 0
CYCS 0.003 0.076 0.23 2 -0.24 6 8
RIPK1 0.028 0.012 -10000 0 -10000 0 0
CD247 -0.016 0.14 -10000 0 -0.36 14 14
MAP2K7 -0.005 0.17 -10000 0 -0.75 4 4
protein ubiquitination -0.005 0.1 0.29 1 -0.32 6 7
CRADD 0.032 0.007 -10000 0 -10000 0 0
DAXX 0.03 0.01 -10000 0 -10000 0 0
FAS 0.032 0.006 -10000 0 -10000 0 0
BID 0.007 0.082 0.24 2 -0.25 6 8
NF-kappa-B/RelA/I kappa B alpha 0.072 0.019 -10000 0 -10000 0 0
TRADD 0.03 0.01 -10000 0 -10000 0 0
MAP3K5 0.025 0.049 -10000 0 -0.5 1 1
CFLAR 0.033 0.003 -10000 0 -10000 0 0
FADD 0.032 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.072 0.019 -10000 0 -10000 0 0
MAPK8 -0.016 0.17 0.35 1 -0.74 4 5
APAF1 0.032 0.007 -10000 0 -10000 0 0
TRAF1 0.032 0.007 -10000 0 -10000 0 0
TRAF2 0.032 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.009 0.082 -10000 0 -0.25 7 7
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.007 0.12 -10000 0 -0.44 6 6
CHUK -0.007 0.099 -10000 0 -0.34 5 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.082 0.047 -10000 0 -0.27 1 1
TCRz/NEF -0.016 0.12 -10000 0 -0.33 14 14
TNF -0.015 0.15 -10000 0 -0.5 10 10
FASLG -0.035 0.15 -10000 0 -0.43 14 14
NFKB1 0.035 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.029 0.1 -10000 0 -0.31 9 9
CASP6 0.046 0.082 -10000 0 -0.4 1 1
CASP7 0.039 0.097 0.38 3 -0.41 1 4
RELA 0.035 0.005 -10000 0 -10000 0 0
CASP2 0.03 0.009 -10000 0 -10000 0 0
CASP3 0.042 0.084 0.38 3 -10000 0 3
TNFRSF1A 0.031 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.045 0.014 -10000 0 -10000 0 0
CASP8 0.033 0.003 -10000 0 -10000 0 0
CASP9 0.031 0.007 -10000 0 -10000 0 0
MAP3K14 -0.002 0.11 -10000 0 -0.38 5 5
APAF-1/Caspase 9 0.024 0.067 -10000 0 -10000 0 0
BCL2 -0.017 0.16 0.33 1 -0.66 4 5
Canonical Wnt signaling 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
HDAC1 0.032 0.031 0.29 1 -10000 0 1
AES 0.035 0.036 0.27 2 -10000 0 2
FBXW11 0.032 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.045 0.014 -10000 0 -10000 0 0
SMAD4 0.031 0.007 -10000 0 -10000 0 0
DKK2 -0.06 0.2 -10000 0 -0.5 20 20
TLE1 0.034 0.025 0.2 1 -10000 0 1
MACF1 0.032 0.006 -10000 0 -10000 0 0
CTNNB1 0.03 0.098 0.37 5 -10000 0 5
WIF1 0.015 0.014 -10000 0 -10000 0 0
beta catenin/RanBP3 0.032 0.14 0.45 9 -10000 0 9
KREMEN2 0.011 0.083 -10000 0 -0.5 3 3
DKK1 0.029 0.008 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.04 0.094 0.38 4 -10000 0 4
FZD1 0.031 0.009 -10000 0 -10000 0 0
AXIN2 -0.07 0.35 0.66 3 -1.2 9 12
AXIN1 0.033 0.006 -10000 0 -10000 0 0
RAN 0.032 0.007 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.035 0.068 -10000 0 -0.58 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.009 0.13 -10000 0 -0.5 4 4
Axin1/APC/GSK3 0.026 0.044 0.23 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.038 0.067 0.45 1 -10000 0 1
HNF1A 0.034 0.028 0.2 2 -10000 0 2
CTBP1 0.034 0.025 0.2 1 -10000 0 1
MYC 0.002 0.18 0.52 3 -0.85 3 6
RANBP3 0.032 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.023 0.14 -10000 0 -0.32 20 20
NKD1 0.021 0.069 -10000 0 -0.5 2 2
TCF4 0.035 0.037 0.28 2 -10000 0 2
TCF3 0.034 0.026 0.2 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.074 0.043 -10000 0 -0.28 1 1
Ran/GTP 0.024 0.007 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.003 0.13 0.49 4 -0.35 2 6
LEF1 -0.064 0.2 -10000 0 -0.48 22 22
DVL1 0.029 0.033 0.28 1 -10000 0 1
CSNK2A1 0.032 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.013 0.14 0.28 1 -0.7 2 3
DKK1/LRP6/Kremen 2 0.035 0.062 -10000 0 -0.3 3 3
LRP6 0.032 0.007 -10000 0 -10000 0 0
CSNK1A1 0.037 0.044 0.32 2 -10000 0 2
NLK 0.03 0.01 -10000 0 -10000 0 0
CCND1 -0.006 0.094 -10000 0 -0.62 2 2
WNT1 0.027 0.049 -10000 0 -0.5 1 1
GSK3A 0.032 0.006 -10000 0 -10000 0 0
GSK3B 0.032 0.008 -10000 0 -10000 0 0
FRAT1 0.031 0.01 -10000 0 -10000 0 0
PPP2R5D 0.02 0.073 0.29 3 -0.3 4 7
APC 0.022 0.053 0.3 2 -0.27 1 3
WNT1/LRP6/FZD1 0.021 0.031 -10000 0 -0.2 1 1
CREBBP 0.034 0.027 0.2 2 -10000 0 2
Glypican 2 network

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.026 0.013 -9999 0 -10000 0 0
GPC2 0.013 0.096 -9999 0 -0.5 4 4
GPC2/Midkine 0.023 0.073 -9999 0 -0.35 4 4
neuron projection morphogenesis 0.023 0.073 -9999 0 -0.35 4 4
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.034 0.16 -10000 0 -0.36 23 23
AKT1 0.022 0.12 0.37 1 -0.76 2 3
PTK2B -0.038 0.16 0.32 2 -0.63 4 6
VEGFR2 homodimer/Frs2 0.02 0.12 -10000 0 -0.49 5 5
CAV1 0.004 0.12 -10000 0 -0.5 6 6
CALM1 0.032 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.035 0.12 -10000 0 -0.46 5 5
endothelial cell proliferation 0.027 0.12 0.35 3 -0.6 2 5
mol:Ca2+ 0.008 0.1 -10000 0 -0.67 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.051 0.12 -10000 0 -0.43 5 5
RP11-342D11.1 -0.002 0.098 -10000 0 -0.67 2 2
CDH5 0.025 0.049 -10000 0 -0.5 1 1
VEGFA homodimer 0.061 0.072 -10000 0 -0.41 2 2
SHC1 0.028 0.012 -10000 0 -10000 0 0
SHC2 0.032 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.091 -10000 0 -0.54 2 2
SH2D2A 0.01 0.096 -10000 0 -0.5 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.049 0.12 0.44 1 -0.55 3 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.12 -10000 0 -0.42 6 6
VEGFR1 homodimer 0.031 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.059 0.11 -10000 0 -0.65 2 2
GRB10 0.01 0.1 -10000 0 -0.67 2 2
PTPN11 0.032 0.007 -10000 0 -10000 0 0
GRB2 0.03 0.009 -10000 0 -10000 0 0
PAK1 0.032 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.056 0.12 -10000 0 -0.68 2 2
HRAS 0.03 0.009 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.019 0.12 -10000 0 -0.4 7 7
HIF1A 0.027 0.049 -10000 0 -0.5 1 1
FRS2 0.032 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.047 0.11 -10000 0 -0.43 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.007 -10000 0 -10000 0 0
Nck/Pak 0.042 0.039 -10000 0 -0.36 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.034 0.12 -10000 0 -0.46 5 5
mol:GDP 0.045 0.1 -10000 0 -0.63 2 2
mol:NADP 0.03 0.12 0.37 3 -0.49 4 7
eNOS/Hsp90 0.036 0.11 0.34 1 -0.46 4 5
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
mol:IP3 0.008 0.1 -10000 0 -0.68 2 2
HIF1A/ARNT 0.038 0.041 -10000 0 -0.36 1 1
SHB 0.031 0.007 -10000 0 -10000 0 0
VEGFA 0.03 0.012 -10000 0 -10000 0 0
VEGFC 0.03 0.01 -10000 0 -10000 0 0
FAK1/Vinculin -0.015 0.16 -10000 0 -0.56 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.031 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.009 0.18 -10000 0 -0.33 22 22
PTPN6 0.031 0.007 -10000 0 -10000 0 0
EPAS1 0.015 0.13 -10000 0 -0.6 5 5
mol:L-citrulline 0.03 0.12 0.37 3 -0.49 4 7
ITGAV 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.05 0.12 -10000 0 -0.43 5 5
VEGFR2 homodimer/VEGFA homodimer 0.038 0.12 -10000 0 -0.45 5 5
VEGFR2/3 heterodimer 0.02 0.12 -10000 0 -0.49 5 5
VEGFB 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.008 0.1 -10000 0 -0.57 3 3
VEGFR2 homodimer 0.003 0.13 -10000 0 -0.56 5 5
FLT1 0.031 0.007 -10000 0 -10000 0 0
NEDD4 0.033 0.007 -10000 0 -10000 0 0
MAPK3 -0.012 0.1 0.4 1 -0.61 2 3
MAPK1 -0.012 0.092 -10000 0 -0.61 2 2
VEGFA145/NRP2 0.039 0.041 -10000 0 -0.36 1 1
VEGFR1/2 heterodimer 0.02 0.12 -10000 0 -0.49 5 5
KDR 0.003 0.13 -10000 0 -0.56 5 5
VEGFA165/NRP1/VEGFR2 homodimer 0.039 0.11 -10000 0 -0.67 2 2
SRC 0.032 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.003 0.11 0.34 2 -0.62 2 4
PI3K 0.024 0.14 -10000 0 -0.87 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.031 0.13 -10000 0 -0.5 5 5
FES 0.01 0.1 -10000 0 -0.69 2 2
GAB1 0.023 0.12 -10000 0 -0.73 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.034 0.12 -10000 0 -0.46 5 5
CTNNB1 0.031 0.008 -10000 0 -10000 0 0
SOS1 0.033 0.003 -10000 0 -10000 0 0
ARNT 0.028 0.012 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.022 0.12 0.34 1 -0.46 4 5
VEGFR2 homodimer/VEGFA homodimer/Yes 0.035 0.12 -10000 0 -0.46 5 5
PI3K/GAB1 0.034 0.12 -10000 0 -0.72 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.062 0.13 -10000 0 -0.79 2 2
PRKACA 0.032 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.033 0.11 -10000 0 -0.46 5 5
HSP90AA1 0.032 0.007 -10000 0 -10000 0 0
CDC42 0.008 0.1 -10000 0 -0.69 2 2
actin cytoskeleton reorganization 0.022 0.12 -10000 0 -0.42 6 6
PTK2 -0.031 0.16 0.39 1 -0.56 6 7
EDG1 -0.002 0.098 -10000 0 -0.67 2 2
mol:DAG 0.008 0.1 -10000 0 -0.68 2 2
CaM/Ca2+ 0.025 0.098 -10000 0 -0.63 2 2
MAP2K3 -0.014 0.11 -10000 0 -0.6 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.045 0.12 -10000 0 -0.7 2 2
PLCG1 0.008 0.1 -10000 0 -0.69 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.05 0.12 -10000 0 -0.43 5 5
IQGAP1 0.031 0.007 -10000 0 -10000 0 0
YES1 0.031 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.035 0.12 -10000 0 -0.46 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.035 0.12 -10000 0 -0.46 5 5
cell migration -0.003 0.14 0.36 1 -0.5 5 6
mol:PI-3-4-5-P3 0.025 0.12 0.28 1 -0.77 2 3
FYN 0.029 0.01 -10000 0 -10000 0 0
VEGFB/NRP1 0.016 0.098 -10000 0 -0.64 2 2
mol:NO 0.03 0.12 0.37 3 -0.49 4 7
PXN 0.032 0.007 -10000 0 -10000 0 0
HRAS/GTP 0.013 0.085 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.029 0.11 -10000 0 -0.7 2 2
VHL 0.022 0.069 -10000 0 -0.5 2 2
ITGB3 -0.073 0.21 -10000 0 -0.5 23 23
NOS3 0.029 0.14 0.38 3 -0.56 4 7
VEGFR2 homodimer/VEGFA homodimer/Sck 0.033 0.12 -10000 0 -0.46 5 5
RAC1 0.031 0.008 -10000 0 -10000 0 0
PRKCA -0.003 0.094 -10000 0 -0.64 2 2
PRKCB -0.019 0.11 -10000 0 -0.64 2 2
VCL 0.032 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 0.017 0.1 -10000 0 -0.67 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.033 0.12 -10000 0 -0.46 5 5
VEGFA165/NRP2 0.039 0.041 -10000 0 -0.36 1 1
MAPKKK cascade 0.03 0.097 -10000 0 -0.55 2 2
NRP2 0.027 0.049 -10000 0 -0.5 1 1
VEGFC homodimer 0.03 0.01 -10000 0 -10000 0 0
NCK1 0.027 0.049 -10000 0 -0.5 1 1
ROCK1 0.031 0.007 -10000 0 -10000 0 0
FAK1/Paxillin -0.01 0.16 0.38 1 -0.52 6 7
MAP3K13 -0.003 0.12 -10000 0 -0.63 3 3
PDPK1 0.011 0.12 0.27 2 -0.74 2 4
IL27-mediated signaling events

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
TGFB1 0.032 0.006 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.061 0.13 0.47 1 -10000 0 1
IL27/IL27R/JAK1 -0.052 0.18 -10000 0 -0.37 1 1
TBX21 -0.064 0.16 0.59 2 -0.42 3 5
IL12B 0.015 0.096 -10000 0 -0.5 4 4
IL12A 0.004 0.034 -10000 0 -0.36 1 1
IL6ST -0.19 0.27 -10000 0 -0.51 49 49
IL27RA/JAK1 0.016 0.05 -10000 0 -10000 0 0
IL27 0.022 0.02 -10000 0 -10000 0 0
TYK2 0.033 0.009 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.1 0.15 -10000 0 -0.52 3 3
T-helper 2 cell differentiation 0.061 0.13 0.47 1 -10000 0 1
T cell proliferation during immune response 0.061 0.13 0.47 1 -10000 0 1
MAPKKK cascade -0.061 0.13 -10000 0 -0.47 1 1
STAT3 0.03 0.009 -10000 0 -10000 0 0
STAT2 0.032 0.007 -10000 0 -10000 0 0
STAT1 0.034 0.004 -10000 0 -10000 0 0
IL12RB1 0.032 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.067 0.18 0.51 3 -0.56 4 7
IL27/IL27R/JAK2/TYK2 -0.061 0.13 -10000 0 -0.48 1 1
positive regulation of T cell mediated cytotoxicity -0.061 0.13 -10000 0 -0.47 1 1
STAT1 (dimer) -0.058 0.21 0.54 3 -0.54 3 6
JAK2 0.031 0.009 -10000 0 -10000 0 0
JAK1 0.032 0.007 -10000 0 -10000 0 0
STAT2 (dimer) -0.048 0.14 -10000 0 -0.46 1 1
T cell proliferation -0.15 0.19 -10000 0 -0.46 23 23
IL12/IL12R/TYK2/JAK2 0.005 0.2 -10000 0 -0.74 7 7
IL17A -0.1 0.15 -10000 0 -0.52 3 3
mast cell activation 0.061 0.13 0.47 1 -10000 0 1
IFNG -0.001 0.035 0.13 3 -0.083 3 6
T cell differentiation -0.004 0.006 -10000 0 -0.016 3 3
STAT3 (dimer) -0.049 0.13 -10000 0 -10000 0 0
STAT5A (dimer) -0.05 0.13 -10000 0 -0.46 1 1
STAT4 (dimer) -0.049 0.14 -10000 0 -0.44 1 1
STAT4 0.033 0.003 -10000 0 -10000 0 0
T cell activation -0.011 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.072 0.16 -10000 0 -10000 0 0
GATA3 -0.033 0.27 0.57 1 -1.3 5 6
IL18 0.009 0.002 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.048 0.13 -10000 0 -10000 0 0
IL27/EBI3 0.039 0.02 -10000 0 -10000 0 0
IL27RA -0.002 0.025 -10000 0 -10000 0 0
IL6 -0.17 0.26 -10000 0 -0.5 44 44
STAT5A 0.031 0.008 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.006 0.031 -10000 0 -10000 0 0
IL1B 0.006 0.034 -10000 0 -0.36 1 1
EBI3 0.032 0.008 -10000 0 -10000 0 0
TNF -0.023 0.1 -10000 0 -0.36 10 10
IL2 signaling events mediated by STAT5

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
GAB2 0.024 0.069 -10000 0 -0.5 2 2
ELF1 -0.006 0.13 -10000 0 -0.37 13 13
CCNA2 0.015 0.096 -10000 0 -0.5 4 4
PIK3CA 0.028 0.049 -10000 0 -0.5 1 1
JAK3 0.028 0.049 -10000 0 -0.5 1 1
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
JAK1 0.032 0.007 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.001 0.15 -10000 0 -0.46 8 8
SHC1 0.028 0.012 -10000 0 -10000 0 0
SP1 0.036 0.036 -10000 0 -0.34 1 1
IL2RA -0.052 0.23 -10000 0 -0.73 12 12
IL2RB 0.022 0.069 -10000 0 -0.5 2 2
SOS1 0.033 0.003 -10000 0 -10000 0 0
IL2RG 0.011 0.11 -10000 0 -0.5 5 5
G1/S transition of mitotic cell cycle -0.003 0.15 0.33 1 -0.57 6 7
PTPN11 0.032 0.007 -10000 0 -10000 0 0
CCND2 0.016 0.072 -10000 0 -0.76 1 1
LCK -0.004 0.13 -10000 0 -0.5 8 8
GRB2 0.031 0.009 -10000 0 -10000 0 0
IL2 0.027 0.008 -10000 0 -10000 0 0
CDK6 0.017 0.084 -10000 0 -0.5 3 3
CCND3 -0.001 0.13 -10000 0 -0.54 2 2
IGF1 pathway

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
NCK2 0.033 0.003 -10000 0 -10000 0 0
PTK2 0.031 0.008 -10000 0 -10000 0 0
CRKL 0.003 0.061 -10000 0 -0.22 7 7
GRB2/SOS1/SHC 0.054 0.026 -10000 0 -10000 0 0
HRAS 0.03 0.009 -10000 0 -10000 0 0
IRS1/Crk 0.014 0.063 -10000 0 -0.23 7 7
IGF-1R heterotetramer/IGF1/PTP1B 0.042 0.07 -10000 0 -0.3 4 4
AKT1 -0.02 0.095 0.21 1 -0.33 6 7
BAD -0.021 0.082 0.2 1 -0.31 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.003 0.059 -10000 0 -0.22 7 7
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.019 0.066 -10000 0 -0.23 7 7
RAF1 -0.001 0.1 -10000 0 -0.51 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.051 0.074 -10000 0 -0.25 4 4
YWHAZ 0.031 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.072 -10000 0 -0.23 8 8
PIK3CA 0.027 0.049 -10000 0 -0.5 1 1
RPS6KB1 -0.014 0.099 0.31 2 -0.34 5 7
GNB2L1 0.032 0.007 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.009 0.11 0.37 4 -0.42 3 7
PXN 0.032 0.007 -10000 0 -10000 0 0
PIK3R1 0.023 0.069 -10000 0 -0.5 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.045 0.013 -10000 0 -10000 0 0
HRAS/GTP 0.024 0.053 -10000 0 -0.23 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.068 0.07 -10000 0 -0.24 4 4
IGF-1R heterotetramer 0.026 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.038 0.073 -10000 0 -0.23 7 7
Crk/p130 Cas/Paxillin 0.05 0.07 -10000 0 -0.24 4 4
IGF1R 0.026 0.027 -10000 0 -10000 0 0
IGF1 0.012 0.1 -10000 0 -0.52 4 4
IRS2/Crk 0.011 0.066 -10000 0 -0.25 5 5
PI3K 0.044 0.1 -10000 0 -0.29 8 8
apoptosis -0.008 0.082 0.56 1 -0.39 1 2
HRAS/GDP 0.023 0.006 -10000 0 -10000 0 0
PRKCD 0.007 0.066 -10000 0 -0.34 4 4
RAF1/14-3-3 E 0.018 0.11 0.43 2 -0.43 3 5
BAD/14-3-3 0.009 0.087 0.41 1 -0.61 1 2
PRKCZ -0.015 0.1 0.27 3 -0.33 6 9
Crk/p130 Cas/Paxillin/FAK1 0.029 0.083 -10000 0 -0.31 5 5
PTPN1 0.032 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.011 0.07 -10000 0 -0.36 4 4
BCAR1 0.03 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.057 0.067 -10000 0 -0.26 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.033 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.023 0.069 -10000 0 -0.22 7 7
GRB10 0.031 0.008 -10000 0 -10000 0 0
PTPN11 0.003 0.061 -10000 0 -0.22 7 7
IRS1 0.005 0.068 -10000 0 -0.24 7 7
IRS2 0.001 0.066 -10000 0 -0.23 8 8
IGF-1R heterotetramer/IGF1 0.026 0.08 -10000 0 -0.38 4 4
GRB2 0.03 0.009 -10000 0 -10000 0 0
PDPK1 0.008 0.11 0.28 3 -0.35 6 9
YWHAE 0.03 0.009 -10000 0 -10000 0 0
PRKD1 0.003 0.073 -10000 0 -0.34 4 4
SHC1 0.028 0.012 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.032 0.042 -10000 0 -10000 0 0
ACTA1 0.015 0.08 0.3 5 -10000 0 5
NUMA1 0.032 0.039 -10000 0 -10000 0 0
SPTAN1 0.019 0.059 0.32 3 -10000 0 3
LIMK1 0.026 0.077 0.39 4 -10000 0 4
BIRC3 0.032 0.005 -10000 0 -10000 0 0
BIRC2 0.032 0.004 -10000 0 -10000 0 0
BAX 0.032 0.007 -10000 0 -10000 0 0
CASP10 0 0.026 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.032 0.006 -10000 0 -10000 0 0
PTK2 0.034 0.036 -10000 0 -10000 0 0
DIABLO 0.032 0.007 -10000 0 -10000 0 0
apoptotic nuclear changes 0.019 0.059 0.32 3 -10000 0 3
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.007 -10000 0 -10000 0 0
GSN 0 0.092 0.33 3 -0.24 9 12
MADD 0.032 0.005 -10000 0 -10000 0 0
TFAP2A -0.071 0.24 -10000 0 -0.53 25 25
BID 0.013 0.013 -10000 0 -10000 0 0
MAP3K1 0.021 0.042 -10000 0 -0.36 1 1
TRADD 0.03 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.045 0.013 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.016 0.058 0.25 2 -0.25 1 3
CASP9 0.031 0.007 -10000 0 -10000 0 0
DNA repair -0.017 0.039 0.26 1 -0.18 1 2
neuron apoptosis 0.006 0.13 -10000 0 -0.59 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.028 0.037 -10000 0 -10000 0 0
APAF1 0.032 0.007 -10000 0 -10000 0 0
CASP6 0.029 0.038 -10000 0 -10000 0 0
TRAF2 0.032 0.006 -10000 0 -10000 0 0
ICAD/CAD 0.013 0.045 0.26 1 -10000 0 1
CASP7 -0.014 0.065 -10000 0 -0.34 2 2
KRT18 0.01 0.093 -10000 0 -0.47 4 4
apoptosis 0.023 0.06 0.47 1 -0.28 1 2
DFFA 0.016 0.045 0.25 1 -10000 0 1
DFFB 0.016 0.045 0.25 1 -10000 0 1
PARP1 0.017 0.039 0.18 1 -0.26 1 2
actin filament polymerization -0.03 0.1 -10000 0 -0.56 4 4
TNF -0.015 0.15 -10000 0 -0.5 10 10
CYCS 0.021 0.049 0.23 2 -0.22 2 4
SATB1 0.005 0.076 -10000 0 -0.34 1 1
SLK 0.016 0.058 0.3 2 -0.25 1 3
p15 BID/BAX 0.036 0.031 0.2 1 -10000 0 1
CASP2 0.001 0.072 0.22 1 -0.31 2 3
JNK cascade -0.021 0.042 0.35 1 -10000 0 1
CASP3 0.019 0.048 0.25 1 -10000 0 1
LMNB2 0.013 0.091 -10000 0 -0.4 3 3
RIPK1 0.028 0.012 -10000 0 -10000 0 0
CASP4 0.032 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.078 0.022 -10000 0 -10000 0 0
negative regulation of DNA binding -0.07 0.24 -10000 0 -0.52 25 25
stress fiber formation 0.016 0.058 0.3 2 -0.24 1 3
GZMB 0.022 0.02 -10000 0 -10000 0 0
CASP1 0.018 0.002 -10000 0 -10000 0 0
LMNB1 0.015 0.08 -10000 0 -0.35 2 2
APP 0.006 0.13 -10000 0 -0.6 5 5
TNFRSF1A 0.031 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM 0.026 0.043 0.3 1 -10000 0 1
LMNA 0.013 0.076 -10000 0 -0.26 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.008 0.062 -10000 0 -10000 0 0
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.019 0.047 0.25 1 -10000 0 1
APAF-1/Caspase 9 0.004 0.11 -10000 0 -0.55 4 4
nuclear fragmentation during apoptosis 0.032 0.038 -10000 0 -10000 0 0
CFL2 0.03 0.1 0.56 4 -10000 0 4
GAS2 0.024 0.057 0.25 1 -10000 0 1
positive regulation of apoptosis 0.018 0.087 -10000 0 -0.32 4 4
PRF1 0.032 0.005 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.031 0.007 -9999 0 -10000 0 0
SMAD2 0 0.039 -9999 0 -0.24 1 1
SMAD3 0.028 0.023 -9999 0 -10000 0 0
SMAD3/SMAD4 0.018 0.11 -9999 0 -0.4 6 6
SMAD4/Ubc9/PIASy 0.061 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.057 0.058 -9999 0 -0.24 1 1
PPM1A 0.031 0.007 -9999 0 -10000 0 0
CALM1 0.032 0.007 -9999 0 -10000 0 0
SMAD2/SMAD4 0.018 0.048 -9999 0 -0.22 2 2
MAP3K1 0.032 0.007 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.023 0.15 -9999 0 -0.36 20 20
MAPK3 0.032 0.005 -9999 0 -10000 0 0
MAPK1 0.03 0.009 -9999 0 -10000 0 0
NUP214 0.032 0.007 -9999 0 -10000 0 0
CTDSP1 0.033 0.003 -9999 0 -10000 0 0
CTDSP2 0.032 0.007 -9999 0 -10000 0 0
CTDSPL 0.031 0.008 -9999 0 -10000 0 0
KPNB1 0.031 0.008 -9999 0 -10000 0 0
TGFBRAP1 -0.057 0.2 -9999 0 -0.5 20 20
UBE2I 0.032 0.005 -9999 0 -10000 0 0
NUP153 0.025 0.049 -9999 0 -0.5 1 1
KPNA2 0.031 0.008 -9999 0 -10000 0 0
PIAS4 0.032 0.007 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.051 0.039 -10000 0 -10000 0 0
epithelial cell differentiation -0.036 0.13 -10000 0 -0.37 5 5
ITCH 0.03 0.01 -10000 0 -10000 0 0
WWP1 0.032 0.038 -10000 0 -10000 0 0
FYN 0.029 0.01 -10000 0 -10000 0 0
EGFR 0.026 0.049 -10000 0 -0.5 1 1
PRL -0.04 0.18 -10000 0 -0.5 15 15
neuron projection morphogenesis 0.05 0.11 0.41 6 -0.28 3 9
PTPRZ1 -0.006 0.12 -10000 0 -0.5 7 7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.062 0.076 -10000 0 -0.3 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.023 0.066 -10000 0 -0.32 4 4
ADAM17 0.016 0.083 -10000 0 -0.5 3 3
ErbB4/ErbB4 0.034 0.035 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.043 0.038 -10000 0 -10000 0 0
NCOR1 0.03 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.04 0.068 -10000 0 -0.3 4 4
GRIN2B 0.026 0.071 0.27 2 -0.31 3 5
ErbB4/ErbB2/betacellulin 0.043 0.063 -10000 0 -0.32 3 3
STAT1 0.033 0.003 -10000 0 -10000 0 0
HBEGF 0.032 0.007 -10000 0 -10000 0 0
PRLR -0.096 0.22 -10000 0 -0.5 28 28
E4ICDs/ETO2 0.045 0.046 -10000 0 -0.25 1 1
axon guidance 0.026 0.055 -10000 0 -10000 0 0
NEDD4 0.03 0.01 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.1 0.2 -10000 0 -0.39 39 39
CBFA2T3 0.025 0.049 -10000 0 -0.5 1 1
ErbB4/ErbB2/HBEGF 0.043 0.062 -10000 0 -0.32 3 3
MAPK3 0.048 0.098 0.41 4 -0.29 3 7
STAT1 (dimer) 0.054 0.039 -10000 0 -10000 0 0
MAPK1 0.044 0.097 0.4 4 -0.29 3 7
JAK2 0.031 0.008 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.025 0.064 -10000 0 -0.3 4 4
NRG1 0.002 0.069 -10000 0 -0.36 4 4
NRG3 0.024 0.01 -10000 0 -10000 0 0
NRG2 0.017 0.084 -10000 0 -0.5 3 3
NRG4 0.026 0.013 -10000 0 -10000 0 0
heart development 0.026 0.055 -10000 0 -10000 0 0
neural crest cell migration 0.025 0.064 -10000 0 -0.3 4 4
ERBB2 0.005 0.058 -10000 0 -0.36 3 3
WWOX/E4ICDs 0.047 0.038 -10000 0 -10000 0 0
SHC1 0.028 0.012 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.05 0.052 -10000 0 -0.25 1 1
apoptosis -0.04 0.043 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.042 0.064 -10000 0 -0.27 3 3
ErbB4/ErbB2/epiregulin 0.041 0.062 -10000 0 -0.32 3 3
ErbB4/ErbB4/betacellulin/betacellulin 0.048 0.041 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.028 0.16 -10000 0 -0.43 4 4
MDM2 0.028 0.037 0.28 1 -10000 0 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.037 0.064 -10000 0 -0.29 4 4
STAT5A 0.031 0.07 0.33 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta 0.041 0.068 -10000 0 -0.3 4 4
DLG4 0.03 0.01 -10000 0 -10000 0 0
GRB2/SHC 0.039 0.019 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.044 0.035 -10000 0 -10000 0 0
STAT5A (dimer) -0.031 0.15 -10000 0 -0.4 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.045 0.066 -10000 0 -10000 0 0
LRIG1 0.026 0.049 -10000 0 -0.5 1 1
EREG 0.025 0.008 -10000 0 -10000 0 0
BTC 0.028 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.025 0.054 -10000 0 -10000 0 0
ERBB4 0.034 0.035 -10000 0 -10000 0 0
STAT5B 0.031 0.008 -10000 0 -10000 0 0
YAP1 0.023 0.069 -10000 0 -0.48 2 2
GRB2 0.03 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.036 0.063 -10000 0 -0.32 3 3
glial cell differentiation -0.043 0.035 -10000 0 -10000 0 0
WWOX 0.03 0.01 -10000 0 -10000 0 0
cell proliferation 0.04 0.096 0.31 2 -0.41 3 5
Cellular roles of Anthrax toxin

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
ANTXR1 0.033 0.003 -9999 0 -10000 0 0
ANTXR2 0.033 0.003 -9999 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 -9999 0 -10000 0 0
monocyte activation -0.04 0.15 -9999 0 -0.36 21 21
MAP2K2 0.011 0.069 -9999 0 -0.52 2 2
MAP2K1 -0.003 0.001 -9999 0 -10000 0 0
MAP2K7 -0.003 0.001 -9999 0 -10000 0 0
MAP2K6 -0.007 0.033 -9999 0 -0.26 2 2
CYAA -0.005 0.001 -9999 0 -10000 0 0
MAP2K4 -0.003 0.001 -9999 0 -10000 0 0
IL1B -0.002 0.024 -9999 0 -0.25 1 1
Channel 0.042 0.005 -9999 0 -10000 0 0
NLRP1 -0.003 0.001 -9999 0 -10000 0 0
CALM1 0.032 0.007 -9999 0 -10000 0 0
negative regulation of phagocytosis 0.015 0.004 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0 -9999 0 -10000 0 0
MAPK3 -0.003 0.001 -9999 0 -10000 0 0
MAPK1 -0.003 0.001 -9999 0 -10000 0 0
PGR -0.1 0.12 -9999 0 -0.26 45 45
PA/Cellular Receptors 0.044 0.006 -9999 0 -10000 0 0
apoptosis -0.001 0 -9999 0 -10000 0 0
LOC728358 0 0 -9999 0 -10000 0 0
Lethal toxin (unfolded) 0.041 0.005 -9999 0 -10000 0 0
macrophage activation -0.005 0.002 -9999 0 -10000 0 0
TNF -0.015 0.15 -9999 0 -0.5 10 10
VCAM1 -0.035 0.14 -9999 0 -0.36 19 19
platelet activation 0.015 0.004 -9999 0 -10000 0 0
MAPKKK cascade -0.003 0.023 -9999 0 -0.13 1 1
IL18 0 0.009 -9999 0 -10000 0 0
negative regulation of macrophage activation -0.001 0 -9999 0 -10000 0 0
LEF -0.001 0 -9999 0 -10000 0 0
CASP1 0.002 0.001 -9999 0 -10000 0 0
mol:cAMP 0.015 0.004 -9999 0 -10000 0 0
necrosis -0.001 0 -9999 0 -10000 0 0
intracellular pH reduction 0 0 -9999 0 -10000 0 0
PAGA 0 0 -9999 0 -10000 0 0
Edema toxin (unfolded) 0.041 0.005 -9999 0 -10000 0