PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
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 (2013): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1W0945F
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 48 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 211
Signaling events mediated by Stem cell factor receptor (c-Kit) 129
TCGA08_retinoblastoma 117
Signaling events regulated by Ret tyrosine kinase 116
Reelin signaling pathway 108
Wnt signaling 91
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 91
Noncanonical Wnt signaling pathway 87
FOXA2 and FOXA3 transcription factor networks 86
PDGFR-alpha signaling pathway 82
Results
Summary Table

The following list describes the columns found in ##REF##406.

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

  • 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.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Ephrin A reverse signaling 211 1481 7 -0.54 0 1000 -1000 -0.032 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 129 10104 78 -0.78 0.23 1000 -1000 -0.09 -1000
TCGA08_retinoblastoma 117 941 8 -0.13 0.073 1000 -1000 -0.018 -1000
Signaling events regulated by Ret tyrosine kinase 116 9567 82 -0.48 0.013 1000 -1000 -0.089 -1000
Reelin signaling pathway 108 6052 56 -0.63 0.034 1000 -1000 -0.079 -1000
Wnt signaling 91 637 7 -0.44 0.013 1000 -1000 -0.022 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 91 6219 68 -0.9 0.35 1000 -1000 -0.12 -1000
Noncanonical Wnt signaling pathway 87 2266 26 -0.44 0.013 1000 -1000 -0.079 -1000
FOXA2 and FOXA3 transcription factor networks 86 3987 46 -0.97 0.021 1000 -1000 -0.054 -1000
PDGFR-alpha signaling pathway 82 3614 44 -0.51 0.033 1000 -1000 -0.066 -1000
IL4-mediated signaling events 73 6673 91 -1.3 0.66 1000 -1000 -0.15 -1000
Nongenotropic Androgen signaling 70 3669 52 -0.35 0.16 1000 -1000 -0.059 -1000
Signaling events mediated by the Hedgehog family 68 3581 52 -0.41 0.21 1000 -1000 -0.081 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 66 3609 54 -0.63 0.028 1000 -1000 -0.089 -1000
Calcium signaling in the CD4+ TCR pathway 63 1956 31 -0.53 0.013 1000 -1000 -0.089 -1000
Nephrin/Neph1 signaling in the kidney podocyte 58 2004 34 -0.16 0.013 1000 -1000 -0.063 -1000
Endothelins 54 5187 96 -0.42 0.013 1000 -1000 -0.071 -1000
Glypican 1 network 52 2535 48 -0.4 0.029 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 51 2487 48 -0.31 0.2 1000 -1000 -0.077 -1000
Glucocorticoid receptor regulatory network 49 5633 114 -0.58 0.38 1000 -1000 -0.067 -1000
Glypican 2 network 49 197 4 -0.087 -0.018 1000 -1000 -0.036 -1000
IL23-mediated signaling events 49 2999 60 -0.35 0.021 1000 -1000 -0.14 -1000
TCR signaling in naïve CD8+ T cells 47 4380 93 -0.2 0.088 1000 -1000 -0.076 -1000
IGF1 pathway 45 2572 57 -0.19 0.054 1000 -1000 -0.097 -1000
HIF-1-alpha transcription factor network 44 3365 76 -0.6 0.041 1000 -1000 -0.12 -1000
BMP receptor signaling 44 3572 81 -0.6 0.024 1000 -1000 -0.091 -1000
Arf6 signaling events 41 2561 62 -0.33 0.021 1000 -1000 -0.068 -1000
Coregulation of Androgen receptor activity 39 3016 76 -0.78 0.061 1000 -1000 -0.045 -1000
Syndecan-1-mediated signaling events 39 1350 34 -0.22 0.013 1000 -1000 -0.064 -1000
EPHB forward signaling 39 3349 85 -0.31 0.16 1000 -1000 -0.099 -1000
Signaling mediated by p38-alpha and p38-beta 35 1576 44 -0.24 0.013 1000 -1000 -0.05 -1000
Syndecan-4-mediated signaling events 33 2235 67 -0.26 0.013 1000 -1000 -0.096 -1000
IL12-mediated signaling events 32 2852 87 -0.41 0.02 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 32 2115 65 -0.69 0.064 1000 -1000 -0.062 -1000
amb2 Integrin signaling 29 2436 82 -0.26 0.013 1000 -1000 -0.085 -1000
IL6-mediated signaling events 29 2239 75 -0.21 0.062 1000 -1000 -0.084 -1000
Ras signaling in the CD4+ TCR pathway 28 485 17 -0.097 0.012 1000 -1000 -0.045 -1000
EGFR-dependent Endothelin signaling events 27 572 21 -0.11 0.013 1000 -1000 -0.075 -1000
Osteopontin-mediated events 26 1000 38 -0.26 0.013 1000 -1000 -0.097 -1000
Thromboxane A2 receptor signaling 26 2760 105 -0.22 0.029 1000 -1000 -0.074 -1000
TCGA08_p53 24 169 7 -0.081 0.052 1000 -1000 -0.01 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 23 2018 85 -0.29 0.013 1000 -1000 -0.071 -1000
FAS signaling pathway (CD95) 23 1118 47 -0.28 0.027 1000 -1000 -0.048 -1000
Syndecan-2-mediated signaling events 22 1546 69 -0.22 0.037 1000 -1000 -0.062 -1000
BCR signaling pathway 22 2220 99 -0.2 0.022 1000 -1000 -0.091 -1000
Regulation of p38-alpha and p38-beta 21 1178 54 -0.49 0.013 1000 -1000 -0.056 -1000
Visual signal transduction: Rods 21 1100 52 -0.2 0.014 1000 -1000 -0.093 -1000
Regulation of Androgen receptor activity 21 1505 70 -0.48 0.034 1000 -1000 -0.061 -1000
JNK signaling in the CD4+ TCR pathway 20 341 17 -0.1 0.018 1000 -1000 -0.06 -1000
RXR and RAR heterodimerization with other nuclear receptor 20 1043 52 -0.28 0.054 1000 -1000 -0.061 -1000
Integrins in angiogenesis 20 1703 84 -0.23 0.032 1000 -1000 -0.1 -1000
LPA receptor mediated events 20 2075 102 -0.26 0.031 1000 -1000 -0.083 -1000
Plasma membrane estrogen receptor signaling 20 1747 86 -0.18 0.02 1000 -1000 -0.083 -1000
IL27-mediated signaling events 19 987 51 -0.19 0.058 1000 -1000 -0.074 -1000
Signaling events mediated by PRL 19 670 34 -0.12 0.013 1000 -1000 -0.048 -1000
ErbB2/ErbB3 signaling events 18 1219 65 -0.13 0.027 1000 -1000 -0.07 -1000
Signaling events mediated by PTP1B 18 1378 76 -0.26 0.021 1000 -1000 -0.079 -1000
Angiopoietin receptor Tie2-mediated signaling 18 1605 88 -0.33 0.03 1000 -1000 -0.11 -1000
p75(NTR)-mediated signaling 17 2214 125 -0.38 0.07 1000 -1000 -0.094 -1000
Fc-epsilon receptor I signaling in mast cells 17 1729 97 -0.21 0.03 1000 -1000 -0.076 -1000
VEGFR1 specific signals 17 979 56 -0.072 0.043 1000 -1000 -0.073 -1000
Regulation of nuclear SMAD2/3 signaling 15 2046 136 -0.35 0.068 1000 -1000 -0.077 -1000
Visual signal transduction: Cones 15 600 38 -0.095 0.013 1000 -1000 -0.063 -1000
IFN-gamma pathway 15 1030 68 -0.11 0.041 1000 -1000 -0.09 -1000
Syndecan-3-mediated signaling events 15 556 35 -0.17 0.013 1000 -1000 -0.067 -1000
TCGA08_rtk_signaling 15 399 26 -0.25 0.024 1000 -1000 -0.02 -1000
Neurotrophic factor-mediated Trk receptor signaling 15 1863 120 -0.32 0.043 1000 -1000 -0.082 -1000
Aurora B signaling 15 1009 67 -0.38 0.014 1000 -1000 -0.066 -1000
ErbB4 signaling events 14 997 69 -0.14 0.059 1000 -1000 -0.083 -1000
Aurora C signaling 14 103 7 -0.06 0.004 1000 -1000 -0.045 -1000
Nectin adhesion pathway 14 914 63 -0.26 0.037 1000 -1000 -0.076 -1000
FOXM1 transcription factor network 14 758 51 -0.19 0.049 1000 -1000 -0.16 -1000
Presenilin action in Notch and Wnt signaling 12 748 61 -0.21 0.046 1000 -1000 -0.079 -1000
Insulin-mediated glucose transport 12 395 32 -0.21 0.037 1000 -1000 -0.061 -1000
IL1-mediated signaling events 12 803 62 -0.13 0.067 1000 -1000 -0.1 -1000
LPA4-mediated signaling events 11 135 12 -0.12 0.017 1000 -1000 -0.029 -1000
Insulin Pathway 11 819 74 -0.082 0.038 1000 -1000 -0.094 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 11 386 33 -0.17 0.035 1000 -1000 -0.062 -1000
Rapid glucocorticoid signaling 11 226 20 -0.09 0.014 1000 -1000 -0.046 -1000
Class IB PI3K non-lipid kinase events 11 33 3 -0.002 -1000 1000 -1000 -0.015 -1000
Ceramide signaling pathway 10 804 76 -0.18 0.024 1000 -1000 -0.061 -1000
Signaling events mediated by HDAC Class III 10 439 40 -0.36 0.024 1000 -1000 -0.048 -1000
Sphingosine 1-phosphate (S1P) pathway 9 268 28 -0.18 0.032 1000 -1000 -0.06 -1000
a4b1 and a4b7 Integrin signaling 9 48 5 -0.03 0.007 1000 -1000 -0.041 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 9 812 83 -0.21 0.053 1000 -1000 -0.077 -1000
IL2 signaling events mediated by PI3K 9 528 58 -0.06 0.033 1000 -1000 -0.087 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 9 425 45 -0.091 0.039 1000 -1000 -0.087 -1000
Stabilization and expansion of the E-cadherin adherens junction 9 676 74 -0.18 0.087 1000 -1000 -0.085 -1000
IL2 signaling events mediated by STAT5 9 219 22 -0.061 0.042 1000 -1000 -0.048 -1000
Class I PI3K signaling events 9 679 73 -0.26 0.023 1000 -1000 -0.067 -1000
Caspase cascade in apoptosis 8 623 74 -0.091 0.029 1000 -1000 -0.052 -1000
Cellular roles of Anthrax toxin 8 342 39 -0.091 0.019 1000 -1000 -0.035 -1000
Retinoic acid receptors-mediated signaling 8 486 58 -0.12 0.034 1000 -1000 -0.07 -1000
BARD1 signaling events 7 450 57 -0.031 0.054 1000 -1000 -0.065 -1000
mTOR signaling pathway 7 415 53 -0.041 0.023 1000 -1000 -0.061 -1000
Canonical NF-kappaB pathway 6 255 39 -0.091 0.069 1000 -1000 -0.079 -1000
Class I PI3K signaling events mediated by Akt 6 438 68 -0.21 0.052 1000 -1000 -0.066 -1000
TRAIL signaling pathway 6 313 48 -0.085 0.051 1000 -1000 -0.066 -1000
ceramide signaling pathway 6 336 49 -0.091 0.032 1000 -1000 -0.047 -1000
S1P1 pathway 6 235 36 -0.044 0.032 1000 -1000 -0.054 -1000
Regulation of Telomerase 6 711 102 -0.3 0.054 1000 -1000 -0.11 -1000
S1P3 pathway 6 291 42 -0.18 0.05 1000 -1000 -0.053 -1000
Arf6 downstream pathway 5 235 43 -0.17 0.094 1000 -1000 -0.04 -1000
Canonical Wnt signaling pathway 5 270 51 -0.047 0.068 1000 -1000 -0.059 -1000
Effects of Botulinum toxin 5 146 26 -0.18 0.019 1000 -1000 -0.064 -1000
FoxO family signaling 4 316 64 -0.21 0.16 1000 -1000 -0.079 -1000
E-cadherin signaling in the nascent adherens junction 4 326 76 -0.17 0.074 1000 -1000 -0.085 -1000
S1P4 pathway 4 109 25 -0.015 0.032 1000 -1000 -0.049 -1000
Circadian rhythm pathway 3 82 22 -0.053 0.013 1000 -1000 -0.063 -1000
Paxillin-independent events mediated by a4b1 and a4b7 3 133 37 -0.031 0.034 1000 -1000 -0.077 -1000
S1P5 pathway 3 57 17 -0.015 0.024 1000 -1000 -0.052 -1000
Signaling events mediated by HDAC Class I 3 399 104 -0.091 0.061 1000 -1000 -0.071 -1000
Atypical NF-kappaB pathway 3 99 31 -0.029 0.048 1000 -1000 -0.061 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 460 125 -0.037 0.086 1000 -1000 -0.11 -1000
PLK2 and PLK4 events 2 6 3 0.008 0.021 1000 -1000 -0.017 -1000
Aurora A signaling 2 135 60 -0.052 0.038 1000 -1000 -0.057 -1000
EPO signaling pathway 2 157 55 -0.054 0.065 1000 -1000 -0.1 -1000
PLK1 signaling events 2 243 85 -0.059 0.025 1000 -1000 -0.058 -1000
Paxillin-dependent events mediated by a4b1 2 79 36 -0.03 0.024 1000 -1000 -0.077 -1000
PDGFR-beta signaling pathway 2 254 97 -0.19 0.067 1000 -1000 -0.079 -1000
p38 MAPK signaling pathway 2 120 44 -0.029 0.028 1000 -1000 -0.059 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 38 23 -0.031 0.05 1000 -1000 -0.068 -1000
Signaling events mediated by HDAC Class II 1 110 75 -0.049 0.036 1000 -1000 -0.071 -1000
HIF-2-alpha transcription factor network 1 72 43 -0.2 0.21 1000 -1000 -0.083 -1000
Signaling mediated by p38-gamma and p38-delta 1 27 15 0 0.032 1000 -1000 -0.03 -1000
E-cadherin signaling in keratinocytes 1 68 43 -0.005 0.052 1000 -1000 -0.066 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.031 1000 -1000 -0.059 -1000
Arf6 trafficking events 0 65 71 -0.023 0.046 1000 -1000 -0.075 -1000
E-cadherin signaling events 0 0 5 0 0.013 1000 -1000 -0.038 -1000
Arf1 pathway 0 19 54 -0.005 0.036 1000 -1000 -0.045 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.013 1000 -1000 -0.057 -1000
Total 3363 184015 7203 -30 -990 131000 -131000 -9.1 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.46 0.33 -9999 0 -0.65 288 288
EFNA5 -0.13 0.32 -9999 0 -0.84 69 69
FYN -0.41 0.32 -9999 0 -0.59 288 288
neuron projection morphogenesis -0.46 0.33 -9999 0 -0.65 288 288
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.46 0.33 -9999 0 -0.65 288 288
EPHA5 -0.54 0.41 -9999 0 -0.85 260 260
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.21 0.22 -10000 0 -0.4 234 234
CRKL -0.21 0.24 -10000 0 -0.42 227 227
HRAS -0.18 0.21 -10000 0 -0.58 20 20
mol:PIP3 -0.21 0.22 -10000 0 -0.4 227 227
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.23 0.25 -10000 0 -0.45 227 227
FOXO3 -0.19 0.22 -10000 0 -0.38 227 227
AKT1 -0.21 0.23 -10000 0 -0.41 227 227
BAD -0.19 0.22 -10000 0 -0.38 227 227
megakaryocyte differentiation -0.24 0.24 -10000 0 -0.44 234 234
GSK3B -0.19 0.22 -10000 0 -0.38 227 227
RAF1 -0.14 0.18 -10000 0 -0.47 17 17
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.23 0.25 -10000 0 -0.45 227 227
STAT1 -0.58 0.58 -10000 0 -1.1 227 227
HRAS/SPRED1 -0.17 0.14 -10000 0 -0.46 18 18
cell proliferation -0.23 0.25 -10000 0 -0.44 228 228
PIK3CA 0.01 0.043 -10000 0 -0.85 1 1
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.24 -10000 0 -0.44 227 227
HRAS/SPRED2 -0.17 0.14 -10000 0 -0.46 18 18
LYN/TEC/p62DOK -0.23 0.2 -10000 0 -0.41 227 227
MAPK3 -0.091 0.13 -10000 0 -0.32 15 15
STAP1 -0.25 0.25 -10000 0 -0.47 227 227
GRAP2 -0.046 0.22 -10000 0 -0.8 30 30
JAK2 -0.5 0.45 -10000 0 -0.9 227 227
STAT1 (dimer) -0.56 0.57 -10000 0 -1.1 227 227
mol:Gleevec 0.007 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.24 0.21 -10000 0 -0.42 230 230
actin filament polymerization -0.22 0.24 -10000 0 -0.44 227 227
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.34 -10000 0 -0.64 227 227
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.18 -10000 0 -0.42 26 26
PI3K -0.23 0.21 -10000 0 -0.42 227 227
PTEN 0.011 0.043 -10000 0 -0.85 1 1
SCF/KIT/EPO/EPOR -0.72 0.72 -10000 0 -1.4 227 227
MAPK8 -0.23 0.25 -10000 0 -0.45 228 228
STAT3 (dimer) -0.22 0.24 -10000 0 -0.44 227 227
positive regulation of transcription -0.073 0.11 -10000 0 -0.26 15 15
mol:GDP -0.22 0.19 -10000 0 -0.56 32 32
PIK3C2B -0.23 0.25 -10000 0 -0.45 227 227
CBL/CRKL -0.19 0.22 -10000 0 -0.39 227 227
FER -0.23 0.25 -10000 0 -0.45 228 228
SH2B3 -0.23 0.25 -10000 0 -0.45 227 227
PDPK1 -0.19 0.21 -10000 0 -0.37 227 227
SNAI2 -0.23 0.25 -10000 0 -0.45 227 227
positive regulation of cell proliferation -0.4 0.42 -10000 0 -0.77 227 227
KITLG 0.002 0.077 -10000 0 -0.88 3 3
cell motility -0.4 0.42 -10000 0 -0.77 227 227
PTPN6 0.02 0.018 -10000 0 -10000 0 0
EPOR -0.13 0.18 -10000 0 -0.67 1 1
STAT5A (dimer) -0.32 0.34 -10000 0 -0.63 227 227
SOCS1 0.011 0.028 -10000 0 -0.31 3 3
cell migration 0.23 0.25 0.45 228 -10000 0 228
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.002 0.027 -10000 0 -0.33 2 2
VAV1 -0.014 0.11 -10000 0 -0.37 29 29
GRB10 -0.23 0.25 -10000 0 -0.45 227 227
PTPN11 0.016 0.014 -10000 0 -10000 0 0
SCF/KIT -0.26 0.25 -10000 0 -0.48 227 227
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.1 0.15 -10000 0 -0.36 15 15
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.78 0.76 -10000 0 -1.5 227 227
MAP2K2 -0.1 0.15 -10000 0 -0.36 15 15
SHC/Grb2/SOS1 -0.23 0.2 -10000 0 -0.41 227 227
STAT5A -0.34 0.36 -10000 0 -0.65 227 227
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.23 0.24 -10000 0 -0.44 227 227
SHC/GRAP2 -0.045 0.16 -10000 0 -0.66 27 27
PTPRO -0.24 0.25 -10000 0 -0.45 234 234
SH2B2 -0.23 0.25 -10000 0 -0.45 227 227
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.24 0.26 -10000 0 -0.46 228 228
CREBBP 0.018 0.02 -10000 0 -10000 0 0
BCL2 -0.2 0.4 -10000 0 -1.6 26 26
TCGA08_retinoblastoma

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
CDKN2B -0.13 0.16 -10000 0 -0.31 174 174
CDKN2C 0.025 0.038 -10000 0 -0.32 2 2
CDKN2A -0.12 0.16 -10000 0 -0.32 169 169
CCND2 0.07 0.072 0.17 119 -10000 0 119
RB1 -0.068 0.071 -10000 0 -0.17 119 119
CDK4 0.07 0.071 0.17 119 -10000 0 119
CDK6 0.073 0.077 0.18 119 -0.19 1 120
G1/S progression 0.06 0.079 0.17 119 -10000 0 119
Signaling events regulated by Ret tyrosine kinase

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 -0.092 0.071 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -9999 0 -0.52 96 96
JUN -0.33 0.32 -9999 0 -0.71 134 134
HRAS 0.012 0.023 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.41 0.34 -9999 0 -0.64 254 254
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.41 0.34 -9999 0 -0.64 254 254
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.31 0.26 -9999 0 -0.54 234 234
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.36 0.31 -9999 0 -0.57 254 254
GRB7 -0.037 0.12 -9999 0 -0.31 63 63
RET51/GFRalpha1/GDNF -0.41 0.34 -9999 0 -0.64 254 254
MAPKKK cascade -0.32 0.27 -9999 0 -0.54 185 185
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.36 0.32 -9999 0 -0.6 245 245
lamellipodium assembly -0.24 0.19 -9999 0 -0.39 235 235
RET51/GFRalpha1/GDNF/SHC -0.41 0.34 -9999 0 -0.64 254 254
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
RET9/GFRalpha1/GDNF/SHC -0.31 0.26 -9999 0 -0.53 234 234
RET9/GFRalpha1/GDNF/Shank3 -0.31 0.26 -9999 0 -0.53 234 234
MAPK3 -0.33 0.3 -9999 0 -0.54 254 254
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.13 0.32 -9999 0 -0.85 68 68
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.33 0.29 -9999 0 -0.69 110 110
DOK5 -0.099 0.29 -9999 0 -0.85 53 53
GFRA1 -0.48 0.43 -9999 0 -0.85 235 235
MAPK8 -0.24 0.23 -9999 0 -0.59 72 72
HRAS/GTP -0.37 0.32 -9999 0 -0.59 254 254
tube development -0.29 0.25 -9999 0 -0.5 234 234
MAPK1 -0.33 0.3 -9999 0 -0.54 254 254
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.19 0.19 -9999 0 -0.35 234 234
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
PDLIM7 0.009 0.036 -9999 0 -0.31 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.46 0.4 -9999 0 -0.7 264 264
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.41 0.34 -9999 0 -0.64 254 254
RET51/GFRalpha1/GDNF/Dok5 -0.47 0.4 -9999 0 -0.71 264 264
PRKCA -0.038 0.2 -9999 0 -0.85 24 24
HRAS/GDP -0.001 0.015 -9999 0 -10000 0 0
CREB1 -0.25 0.24 -9999 0 -0.44 234 234
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.19 0.19 -9999 0 -0.35 234 234
RET51/GFRalpha1/GDNF/Grb7 -0.43 0.34 -9999 0 -0.66 254 254
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.17 0.33 -9999 0 -0.85 72 72
DOK4 0.013 0 -9999 0 -10000 0 0
JNK cascade -0.32 0.31 -9999 0 -0.69 134 134
RET9/GFRalpha1/GDNF/FRS2 -0.31 0.26 -9999 0 -0.53 234 234
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.19 0.19 -9999 0 -0.35 234 234
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.26 0.24 -9999 0 -0.44 203 203
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.26 0.24 -9999 0 -0.42 254 254
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.3 0.32 -9999 0 -0.86 70 70
PI3K -0.38 0.34 -9999 0 -0.63 235 235
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.29 0.25 -9999 0 -0.5 234 234
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.23 0.21 -9999 0 -0.54 69 69
RET51/GFRalpha1/GDNF/FRS2 -0.41 0.34 -9999 0 -0.64 254 254
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.078 0.26 -9999 0 -0.85 43 43
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.3 0.32 -9999 0 -0.87 69 69
RET51/GFRalpha1/GDNF/PKC alpha -0.43 0.38 -9999 0 -0.68 254 254
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.001 0.039 -9999 0 -0.31 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.46 0.38 -9999 0 -0.69 264 264
Rac1/GTP -0.3 0.23 -9999 0 -0.47 235 235
RET9/GFRalpha1/GDNF -0.34 0.29 -9999 0 -0.58 234 234
GFRalpha1/GDNF -0.38 0.33 -9999 0 -0.66 234 234
Reelin 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
CDK5R1/CDK5 -0.001 0.014 -9999 0 -10000 0 0
VLDLR -0.012 0.15 -9999 0 -0.85 12 12
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.009 0.036 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.44 0.27 -9999 0 -0.59 307 307
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.041 -9999 0 -0.48 3 3
AKT1 -0.24 0.17 -9999 0 -0.66 11 11
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.007 0.007 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.42 0.26 -9999 0 -0.55 307 307
LRPAP1/LRP8 -0.026 0.13 -9999 0 -0.66 16 16
RELN/LRP8/DAB1/Fyn -0.39 0.24 -9999 0 -0.52 307 307
DAB1/alpha3/beta1 Integrin -0.36 0.24 -9999 0 -0.48 309 309
long-term memory -0.39 0.25 -9999 0 -0.51 309 309
DAB1/LIS1 -0.37 0.24 -9999 0 -0.5 309 309
DAB1/CRLK/C3G -0.36 0.23 -9999 0 -0.48 309 309
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
DAB1/NCK2 -0.38 0.24 -9999 0 -0.5 309 309
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.026 0.17 -9999 0 -0.65 24 24
CDK5R1 0.012 0.023 -9999 0 -0.31 2 2
RELN -0.63 0.38 -9999 0 -0.85 305 305
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.44 0.27 -9999 0 -0.59 307 307
GRIN2A/RELN/LRP8/DAB1/Fyn -0.4 0.26 -9999 0 -0.54 309 309
MAPK8 0.007 0.074 -9999 0 -0.85 3 3
RELN/VLDLR/DAB1 -0.41 0.25 -9999 0 -0.55 307 307
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.39 0.26 -9999 0 -0.52 309 309
RELN/LRP8 -0.44 0.27 -9999 0 -0.59 307 307
GRIN2B/RELN/LRP8/DAB1/Fyn -0.39 0.24 -9999 0 -0.52 307 307
PI3K -0.002 0.032 -9999 0 -0.66 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.022 -9999 0 -10000 0 0
RAP1A -0.32 0.24 -9999 0 -0.83 23 23
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.017 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.13 -9999 0 -0.51 16 16
neuron adhesion -0.3 0.23 -9999 0 -0.74 27 27
LRP8 -0.021 0.17 -9999 0 -0.85 16 16
GSK3B -0.22 0.16 -9999 0 -0.62 11 11
RELN/VLDLR/DAB1/Fyn -0.38 0.23 -9999 0 -0.51 307 307
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.36 307 307
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.034 0.087 -9999 0 -0.32 18 18
neuron migration -0.31 0.22 -9999 0 -0.43 306 306
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.13 -9999 0 -0.52 16 16
RELN/VLDLR -0.42 0.27 -9999 0 -0.56 309 309
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.3 0.29 -9999 0 -0.48 261 261
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.005 0.048 -9999 0 -0.31 9 9
WNT4 -0.28 0.41 -9999 0 -0.84 142 142
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.009 0.13 -9999 0 -0.8 11 11
WNT11 -0.44 0.43 -9999 0 -0.85 214 214
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.047 0.17 -10000 0 -0.51 35 35
NFATC2 -0.22 0.38 -10000 0 -0.86 85 85
NFATC3 -0.084 0.13 -10000 0 -10000 0 0
CD40LG -0.73 0.58 -10000 0 -1.2 223 223
ITCH 0.051 0.016 -10000 0 -10000 0 0
CBLB 0.051 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.51 0.52 -10000 0 -1.2 109 109
JUNB 0 0.1 -10000 0 -0.85 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.017 -10000 0 -0.34 1 1
T cell anergy 0.029 0.065 -10000 0 -0.5 1 1
TLE4 -0.23 0.44 -10000 0 -0.93 99 99
Jun/NFAT1-c-4/p21SNFT -0.66 0.62 -10000 0 -1.2 196 196
AP-1/NFAT1-c-4 -0.9 0.8 -10000 0 -1.5 221 221
IKZF1 -0.16 0.34 -10000 0 -0.78 74 74
T-helper 2 cell differentiation -0.3 0.34 -10000 0 -0.85 90 90
AP-1/NFAT1 -0.42 0.5 -10000 0 -0.95 170 170
CALM1 0.028 0.01 -10000 0 -10000 0 0
EGR2 -0.77 0.86 -10000 0 -1.7 184 184
EGR3 -0.56 0.75 -10000 0 -1.6 118 118
NFAT1/FOXP3 -0.2 0.34 -10000 0 -0.73 94 94
EGR1 -0.18 0.36 -10000 0 -0.85 89 89
JUN -0.2 0.36 -10000 0 -0.86 93 93
EGR4 -0.049 0.21 -10000 0 -0.74 32 32
mol:Ca2+ 0.016 0.011 -10000 0 -10000 0 0
GBP3 -0.15 0.32 -10000 0 -0.81 58 58
FOSL1 -0.036 0.12 -10000 0 -0.31 62 62
NFAT1-c-4/MAF/IRF4 -0.55 0.56 -10000 0 -1.1 194 194
DGKA -0.14 0.3 -10000 0 -0.72 65 65
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.54 0.56 -10000 0 -1.1 195 195
CTLA4 -0.22 0.38 -10000 0 -0.86 86 86
NFAT1-c-4 (dimer)/EGR1 -0.63 0.68 -10000 0 -1.3 193 193
NFAT1-c-4 (dimer)/EGR4 -0.57 0.57 -10000 0 -1.1 198 198
FOS -0.22 0.38 -10000 0 -0.86 106 106
IFNG -0.42 0.55 -10000 0 -1.2 117 117
T cell activation -0.43 0.43 -10000 0 -0.98 132 132
MAF 0.013 0 -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 0.35 0.42 0.8 149 -10000 0 149
TNF -0.59 0.59 -10000 0 -1.1 195 195
FASLG -0.73 0.8 -10000 0 -1.5 199 199
TBX21 -0.04 0.19 -10000 0 -0.72 26 26
BATF3 -0.009 0.089 -10000 0 -0.33 26 26
PRKCQ 0 0.1 -10000 0 -0.85 6 6
PTPN1 -0.14 0.29 -10000 0 -0.71 68 68
NFAT1-c-4/ICER1 -0.53 0.56 -10000 0 -1.1 193 193
GATA3 -0.036 0.2 -10000 0 -0.83 24 24
T-helper 1 cell differentiation -0.4 0.52 -10000 0 -1.1 119 119
IL2RA -0.46 0.46 -10000 0 -1 117 117
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.14 0.29 -10000 0 -0.7 69 69
E2F1 -0.082 0.15 -10000 0 -10000 0 0
PPARG -0.001 0.1 -10000 0 -0.58 10 10
SLC3A2 -0.14 0.29 -10000 0 -0.74 58 58
IRF4 -0.099 0.23 -10000 0 -0.46 98 98
PTGS2 -0.71 0.58 -10000 0 -1.2 215 215
CSF2 -0.77 0.54 -10000 0 -1.2 221 221
JunB/Fra1/NFAT1-c-4 -0.53 0.54 -10000 0 -1 189 189
IL4 -0.31 0.37 -10000 0 -0.93 84 84
IL5 -0.69 0.55 -10000 0 -1.2 212 212
IL2 -0.44 0.45 -10000 0 -1 132 132
IL3 -0.096 0.063 -10000 0 -10000 0 0
RNF128 0.049 0.047 -10000 0 -0.9 1 1
NFATC1 -0.35 0.42 -10000 0 -0.81 146 146
CDK4 0.21 0.24 0.57 64 -10000 0 64
PTPRK -0.14 0.29 -10000 0 -0.74 58 58
IL8 -0.72 0.56 -10000 0 -1.2 213 213
POU2F1 0.013 0.016 -10000 0 -0.31 1 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.11 0.3 -9999 0 -0.85 59 59
GNB1/GNG2 -0.27 0.24 -9999 0 -0.62 109 109
mol:DAG -0.23 0.24 -9999 0 -0.57 102 102
PLCG1 -0.24 0.25 -9999 0 -0.59 102 102
YES1 -0.27 0.28 -9999 0 -0.45 261 261
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.26 0.23 -9999 0 -0.6 102 102
MAP3K7 -0.18 0.21 -9999 0 -0.46 103 103
mol:Ca2+ -0.22 0.24 -9999 0 -0.55 102 102
mol:IP3 -0.23 0.24 -9999 0 -0.57 102 102
NLK -0.011 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.21 0.22 -9999 0 -0.51 103 103
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.3 0.29 -9999 0 -0.48 261 261
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.27 0.28 -9999 0 -0.61 122 122
GO:0007205 -0.22 0.24 -9999 0 -0.56 102 102
WNT6 0.005 0.048 -9999 0 -0.31 9 9
WNT4 -0.28 0.41 -9999 0 -0.84 142 142
NFAT1/CK1 alpha -0.31 0.26 -9999 0 -0.6 151 151
GNG2 0.013 0 -9999 0 -10000 0 0
WNT5A -0.009 0.13 -9999 0 -0.8 11 11
WNT11 -0.44 0.43 -9999 0 -0.85 214 214
CDC42 -0.25 0.26 -9999 0 -0.6 109 109
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.55 0.56 -9999 0 -1.1 190 190
PCK1 -0.37 0.52 -9999 0 -1.5 59 59
HNF4A -0.71 0.67 -9999 0 -1.3 208 208
KCNJ11 -0.52 0.56 -9999 0 -1.1 165 165
AKT1 -0.042 0.13 -9999 0 -10000 0 0
response to starvation -0.017 0.034 -9999 0 -10000 0 0
DLK1 -0.52 0.55 -9999 0 -1.1 177 177
NKX2-1 -0.17 0.21 -9999 0 -10000 0 0
ACADM -0.55 0.56 -9999 0 -1.1 190 190
TAT -0.21 0.23 -9999 0 -0.6 21 21
CEBPB 0.013 0.004 -9999 0 -10000 0 0
CEBPA 0.005 0.085 -9999 0 -0.85 4 4
TTR -0.2 0.22 -9999 0 -0.78 25 25
PKLR -0.55 0.56 -9999 0 -1.1 191 191
APOA1 -0.97 0.91 -9999 0 -1.8 217 217
CPT1C -0.56 0.56 -9999 0 -1.1 178 178
ALAS1 -0.17 0.21 -9999 0 -10000 0 0
TFRC -0.27 0.29 -9999 0 -0.73 29 29
FOXF1 -0.009 0.086 -9999 0 -0.86 4 4
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.013 0.043 -9999 0 -0.85 1 1
CPT1A -0.55 0.56 -9999 0 -1.1 183 183
HMGCS1 -0.55 0.56 -9999 0 -1.1 182 182
NR3C1 0.019 0.015 -9999 0 -10000 0 0
CPT1B -0.55 0.56 -9999 0 -1.1 190 190
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.7 0.72 -9999 0 -1.3 206 206
CREB1 -0.002 0.055 -9999 0 -10000 0 0
IGFBP1 -0.19 0.2 -9999 0 -0.58 3 3
PDX1 -0.19 0.22 -9999 0 -0.86 2 2
UCP2 -0.55 0.56 -9999 0 -1.1 192 192
ALDOB -0.52 0.55 -9999 0 -1.1 167 167
AFP -0.047 0.12 -9999 0 -0.46 12 12
BDH1 -0.55 0.56 -9999 0 -1.1 180 180
HADH -0.51 0.55 -9999 0 -1.1 174 174
F2 -0.66 0.65 -9999 0 -1.3 179 179
HNF1A 0.013 0.043 -9999 0 -0.85 1 1
G6PC -0.008 0.092 -9999 0 -10000 0 0
SLC2A2 -0.24 0.27 -9999 0 -0.55 77 77
INS -0.008 0.018 -9999 0 -10000 0 0
FOXA1 -0.055 0.14 -9999 0 -0.35 66 66
FOXA3 -0.077 0.18 -9999 0 -0.39 67 67
FOXA2 -0.59 0.63 -9999 0 -1.2 190 190
ABCC8 -0.83 0.78 -9999 0 -1.4 229 229
ALB -0.1 0.34 -9999 0 -1.3 28 28
PDGFR-alpha signaling pathway

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
PDGFRA -0.26 0.4 -9999 0 -0.86 126 126
PDGF/PDGFRA/CRKL -0.2 0.3 -9999 0 -0.65 126 126
positive regulation of JUN kinase activity -0.16 0.23 -9999 0 -0.5 126 126
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.21 0.3 -9999 0 -0.66 126 126
AP1 -0.51 0.64 -9999 0 -1.5 110 110
mol:IP3 -0.2 0.32 -9999 0 -0.68 126 126
PLCG1 -0.2 0.32 -9999 0 -0.68 126 126
PDGF/PDGFRA/alphaV Integrin -0.2 0.3 -9999 0 -0.66 126 126
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.2 0.32 -9999 0 -0.67 126 126
CAV3 -0.002 0.035 -9999 0 -0.31 5 5
CAV1 -0.01 0.14 -9999 0 -0.85 11 11
SHC/Grb2/SOS1 -0.16 0.24 -9999 0 -0.51 126 126
PDGF/PDGFRA/Shf -0.2 0.3 -9999 0 -0.65 126 126
FOS -0.46 0.62 -9999 0 -1.4 110 110
JUN -0.18 0.3 -9999 0 -0.73 93 93
oligodendrocyte development -0.2 0.3 -9999 0 -0.66 126 126
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.2 0.32 -9999 0 -0.68 126 126
PDGF/PDGFRA -0.26 0.4 -9999 0 -0.86 126 126
actin cytoskeleton reorganization -0.2 0.3 -9999 0 -0.65 126 126
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.17 0.26 -9999 0 -0.56 127 127
PDGF/PDGFRA/Crk/C3G -0.17 0.26 -9999 0 -0.56 126 126
JAK1 -0.19 0.31 -9999 0 -0.65 126 126
ELK1/SRF -0.15 0.24 -9999 0 -0.51 126 126
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.012 0.016 -9999 0 -0.31 1 1
CSNK2A1 0.027 0.028 -9999 0 -10000 0 0
GO:0007205 -0.21 0.32 -9999 0 -0.69 126 126
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.23 -9999 0 -0.5 126 126
PDGF/PDGFRA/SHB -0.2 0.3 -9999 0 -0.65 126 126
PDGF/PDGFRA/Caveolin-1 -0.22 0.32 -9999 0 -0.68 131 131
ITGAV 0.011 0.043 -9999 0 -0.85 1 1
ELK1 -0.19 0.29 -9999 0 -0.62 126 126
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
PDGF/PDGFRA/Crk -0.2 0.3 -9999 0 -0.65 126 126
JAK-STAT cascade -0.19 0.31 -9999 0 -0.65 126 126
cell proliferation -0.2 0.3 -9999 0 -0.65 126 126
IL4-mediated signaling events

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
BCL2L1 -0.59 0.44 -10000 0 -1.1 138 138
STAT6 (cleaved dimer) -0.65 0.45 -10000 0 -1 192 192
IGHG1 -0.2 0.14 -10000 0 -0.37 11 11
IGHG3 -0.58 0.43 -10000 0 -0.99 172 172
AKT1 -0.32 0.26 -10000 0 -0.7 72 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.26 -10000 0 -0.72 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.35 0.28 -10000 0 -0.71 97 97
THY1 -0.59 0.45 -10000 0 -1.1 118 118
MYB -0.009 0.13 -10000 0 -0.68 13 13
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.42 0.32 -10000 0 -0.75 138 138
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.72 61 61
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.005 0.075 -10000 0 -0.31 23 23
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.62 0.44 -10000 0 -1 177 177
SOCS1 -0.4 0.29 -10000 0 -0.73 104 104
SOCS3 -0.4 0.39 -10000 0 -1.1 67 67
FCER2 -0.58 0.43 -10000 0 -0.97 181 181
PARP14 0.012 0.004 -10000 0 -10000 0 0
CCL17 -0.67 0.49 -10000 0 -1.1 169 169
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.22 -10000 0 -0.69 38 38
T cell proliferation -0.6 0.46 -10000 0 -1.1 130 130
IL4R/JAK1 -0.59 0.44 -10000 0 -1.2 106 106
EGR2 -0.92 0.73 -10000 0 -1.6 199 199
JAK2 -0.015 0.024 -10000 0 -10000 0 0
JAK3 -0.06 0.14 -10000 0 -0.31 94 94
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.009 -10000 0 -10000 0 0
COL1A2 -0.19 0.16 -10000 0 -0.55 17 17
CCL26 -0.61 0.46 -10000 0 -1.1 130 130
IL4R -0.63 0.47 -10000 0 -1.2 106 106
PTPN6 0.028 0.009 -10000 0 -10000 0 0
IL13RA2 -0.71 0.58 -10000 0 -1.4 138 138
IL13RA1 -0.015 0.024 -10000 0 -10000 0 0
IRF4 -0.34 0.47 -10000 0 -1.2 79 79
ARG1 -0.14 0.12 -10000 0 -10000 0 0
CBL -0.38 0.3 -10000 0 -0.75 110 110
GTF3A 0.016 0.01 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
IL13RA1/JAK2 -0.022 0.034 -10000 0 -10000 0 0
IRF4/BCL6 -0.31 0.43 -10000 0 -1.1 69 69
CD40LG -0.12 0.32 -10000 0 -0.83 68 68
MAPK14 -0.4 0.33 -10000 0 -0.79 114 114
mitosis -0.3 0.25 -10000 0 -0.66 70 70
STAT6 -0.68 0.52 -10000 0 -1.2 154 154
SPI1 0.002 0.069 -10000 0 -0.31 19 19
RPS6KB1 -0.29 0.24 -10000 0 -0.67 53 53
STAT6 (dimer) -0.68 0.52 -10000 0 -1.2 154 154
STAT6 (dimer)/PARP14 -0.63 0.48 -10000 0 -1.1 152 152
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.28 -10000 0 -0.74 68 68
FRAP1 -0.32 0.26 -10000 0 -0.7 72 72
LTA -0.62 0.46 -10000 0 -1.2 120 120
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.66 0.5 1.2 155 -10000 0 155
CCL11 -0.59 0.44 -10000 0 -1.1 131 131
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.72 71 71
IL2RG -0.044 0.2 -10000 0 -0.85 20 20
IL10 -0.61 0.48 -10000 0 -1.2 125 125
IRS1 -0.078 0.26 -10000 0 -0.85 43 43
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.098 -10000 0 -10000 0 0
IL5 -0.6 0.44 -10000 0 -1.1 138 138
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.48 0.34 -10000 0 -0.84 138 138
COL1A1 -0.26 0.23 -10000 0 -1.7 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.6 0.46 -10000 0 -1.2 101 101
IL2R gamma/JAK3 -0.077 0.18 -10000 0 -0.53 43 43
TFF3 -1.3 0.62 -10000 0 -1.6 328 328
ALOX15 -0.6 0.45 -10000 0 -1.2 112 112
MYBL1 0.012 0.016 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.51 0.36 -10000 0 -0.87 162 162
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.017 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.3 0.26 -10000 0 -0.67 68 68
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.7 72 72
PI3K -0.33 0.28 -10000 0 -0.75 72 72
DOK2 0.001 0.078 -10000 0 -0.4 12 12
ETS1 0.029 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.24 0.21 -10000 0 -0.67 38 38
ITGB3 -0.62 0.48 -10000 0 -1.2 134 134
PIGR -0.64 0.5 -10000 0 -1.3 119 119
IGHE 0.051 0.036 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.21 -10000 0 -0.66 38 38
BCL6 0.011 0.043 -10000 0 -0.85 1 1
OPRM1 -0.6 0.44 -10000 0 -1.1 120 120
RETNLB -0.6 0.44 -10000 0 -1.1 125 125
SELP -0.6 0.46 -10000 0 -1.1 126 126
AICDA -0.58 0.43 -10000 0 -1.1 130 130
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.22 0.26 -10000 0 -0.53 170 170
regulation of S phase of mitotic cell cycle -0.13 0.18 -10000 0 -0.34 171 171
GNAO1 -0.016 0.15 -10000 0 -0.72 16 16
HRAS 0.011 0.023 -10000 0 -0.31 2 2
SHBG/T-DHT -0.011 0.081 -10000 0 -0.59 8 8
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.17 0.24 -10000 0 -0.45 170 170
T-DHT/AR -0.28 0.33 -10000 0 -0.67 170 170
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 106 106
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.27 0.31 -10000 0 -0.64 170 170
cell proliferation -0.2 0.28 -10000 0 -0.67 67 67
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
FOS -0.25 0.39 -10000 0 -0.89 106 106
mol:Ca2+ -0.027 0.03 -10000 0 -0.071 71 71
MAPK3 -0.19 0.26 -10000 0 -0.47 170 170
MAPK1 -0.084 0.13 -10000 0 -0.31 59 59
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 106 106
cAMP biosynthetic process 0.014 0.084 -10000 0 -0.55 8 8
GNG2 0.013 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 106 106
HRAS/GTP -0.21 0.24 -10000 0 -0.49 170 170
actin cytoskeleton reorganization -0.001 0.023 -10000 0 -0.46 1 1
SRC 0.012 0.017 -10000 0 -0.32 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 106 106
PI3K -0.001 0.029 -10000 0 -0.58 1 1
apoptosis 0.16 0.25 0.52 106 -10000 0 106
T-DHT/AR/PELP1 -0.24 0.29 -10000 0 -0.58 170 170
HRAS/GDP -0.25 0.3 -10000 0 -0.6 171 171
CREB1 -0.18 0.27 -10000 0 -0.57 106 106
RAC1-CDC42/GTP -0.001 0.023 -10000 0 -0.47 1 1
AR -0.35 0.43 -10000 0 -0.85 170 170
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.18 0.25 -10000 0 -0.47 170 170
RAC1-CDC42/GDP -0.24 0.28 -10000 0 -0.57 170 170
T-DHT/AR/PELP1/Src -0.22 0.26 -10000 0 -0.54 170 170
MAP2K2 -0.17 0.24 -10000 0 -0.45 170 170
T-DHT/AR/PELP1/Src/PI3K -0.13 0.19 -10000 0 -0.35 171 171
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG -0.004 0.12 -10000 0 -0.85 8 8
Gi family/GNB1/GNG2/GDP -0.018 0.11 -10000 0 -0.54 12 12
mol:T-DHT 0 0.001 0.002 59 -0.003 46 105
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.01 0.034 -10000 0 -0.67 1 1
Gi family/GTP -0.095 0.12 -10000 0 -0.48 12 12
CDC42 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.12 0.27 -10000 0 -0.71 29 29
IHH -0.22 0.39 -10000 0 -0.87 108 108
SHH Np/Cholesterol/GAS1 -0.11 0.22 -10000 0 -0.54 82 82
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.21 0.54 82 -10000 0 82
SMO/beta Arrestin2 -0.11 0.25 -10000 0 -0.5 109 109
SMO -0.12 0.26 -10000 0 -0.53 110 110
AKT1 -0.029 0.12 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.004 0.12 -10000 0 -0.85 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.12 0.26 -10000 0 -0.52 110 110
STIL -0.087 0.2 -10000 0 -0.59 16 16
DHH N/PTCH2 -0.11 0.25 -10000 0 -0.66 68 68
DHH N/PTCH1 -0.11 0.24 -10000 0 -0.48 112 112
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
DHH 0.007 0.074 -10000 0 -0.85 3 3
PTHLH -0.17 0.38 -10000 0 -1.2 29 29
determination of left/right symmetry -0.12 0.26 -10000 0 -0.52 110 110
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.17 0.37 -10000 0 -1.2 29 29
IHH N/Hhip -0.41 0.42 -10000 0 -0.77 221 221
DHH N/Hhip -0.26 0.32 -10000 0 -0.66 160 160
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.12 0.26 -10000 0 -0.52 110 110
pancreas development -0.33 0.42 -10000 0 -0.84 161 161
HHAT 0.011 0.043 -10000 0 -0.85 1 1
PI3K -0.002 0.032 -10000 0 -0.66 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.16 0.34 -10000 0 -0.85 81 81
somite specification -0.12 0.26 -10000 0 -0.52 110 110
SHH Np/Cholesterol/PTCH1 -0.099 0.21 -10000 0 -0.64 15 15
SHH Np/Cholesterol/PTCH2 -0.092 0.2 -10000 0 -0.54 67 67
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.54 102 102
SHH 0.007 0.052 -10000 0 -0.66 1 1
catabolic process -0.13 0.26 -10000 0 -0.53 109 109
SMO/Vitamin D3 -0.1 0.23 -10000 0 -0.68 15 15
SHH Np/Cholesterol/Hhip -0.21 0.26 -10000 0 -0.53 160 160
LRP2 -0.2 0.37 -10000 0 -0.85 101 101
receptor-mediated endocytosis -0.2 0.24 -10000 0 -0.74 38 38
SHH Np/Cholesterol/BOC -0.016 0.084 -10000 0 -0.55 9 9
SHH Np/Cholesterol/CDO -0.16 0.24 -10000 0 -0.54 119 119
mesenchymal cell differentiation 0.21 0.26 0.53 160 -10000 0 160
mol:Vitamin D3 -0.098 0.22 -10000 0 -0.65 15 15
IHH N/PTCH2 -0.25 0.36 -10000 0 -0.69 154 154
CDON -0.24 0.39 -10000 0 -0.85 118 118
IHH N/PTCH1 -0.13 0.26 -10000 0 -0.54 109 109
Megalin/LRPAP1 -0.16 0.28 -10000 0 -0.66 101 101
PTCH2 -0.13 0.32 -10000 0 -0.85 66 66
SHH Np/Cholesterol -0.006 0.038 -10000 0 -0.54 1 1
PTCH1 -0.13 0.26 -10000 0 -0.54 109 109
HHIP -0.33 0.42 -10000 0 -0.84 161 161
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.012 0.15 -9999 0 -0.85 12 12
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.44 0.27 -9999 0 -0.59 307 307
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.4 0.26 -9999 0 -0.54 307 307
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.007 0.007 -9999 0 -10000 0 0
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.12 0.31 -9999 0 -0.85 61 61
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.026 0.13 -9999 0 -0.66 16 16
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.012 0.023 -9999 0 -0.31 2 2
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.023 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.44 0.27 -9999 0 -0.59 307 307
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.29 0.21 -9999 0 -0.76 14 14
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.34 0.24 -9999 0 -0.47 307 307
RELN -0.63 0.38 -9999 0 -0.85 305 305
PAFAH/LIS1 -0.061 0.21 -9999 0 -0.57 61 61
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.24 0.14 -9999 0 -0.56 14 14
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.25 0.18 -9999 0 -0.34 308 308
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.32 0.22 -9999 0 -0.44 307 307
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0.023 -9999 0 -0.31 2 2
PAFAH1B2 0.009 0.06 -9999 0 -0.85 2 2
MAP1B/LIS1/Dynein heavy chain 0.026 0.004 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.29 0.18 -9999 0 -0.72 14 14
LRP8 -0.021 0.17 -9999 0 -0.85 16 16
NDEL1/Katanin 60 -0.29 0.21 -9999 0 -0.73 15 15
P39/CDK5 -0.34 0.24 -9999 0 -0.47 307 307
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.36 0.25 -9999 0 -0.5 307 307
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.38 0.23 -9999 0 -0.5 307 307
RELN/VLDLR -0.42 0.27 -9999 0 -0.56 309 309
CDC42 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.009 0.076 -9999 0 -0.59 6 6
NFATC2 -0.09 0.21 -9999 0 -0.61 59 59
NFATC3 0 0.028 -9999 0 -10000 0 0
CD40LG -0.44 0.42 -9999 0 -0.89 169 169
PTGS2 -0.42 0.41 -9999 0 -0.87 156 156
JUNB 0 0.1 -9999 0 -0.85 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.014 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.014 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.19 0.36 -9999 0 -0.86 93 93
mol:Ca2+ -0.01 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.002 -9999 0 -10000 0 0
FOSL1 -0.036 0.12 -9999 0 -0.31 62 62
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.6 135 135
FOS -0.22 0.38 -9999 0 -0.86 106 106
IFNG -0.44 0.41 -9999 0 -0.86 172 172
AP-1/NFAT1-c-4 -0.53 0.52 -9999 0 -1 174 174
FASLG -0.42 0.4 -9999 0 -0.85 161 161
NFAT1-c-4/ICER1 -0.11 0.2 -9999 0 -0.54 64 64
IL2RA -0.41 0.39 -9999 0 -0.84 154 154
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.37 -9999 0 -0.82 191 191
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.54 67 67
IL4 -0.4 0.37 -9999 0 -0.81 154 154
IL2 -0.013 0.026 -9999 0 -10000 0 0
IL3 -0.032 0.031 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.009 0.089 -9999 0 -0.33 26 26
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.016 -9999 0 -0.31 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.16 0.3 0.7 95 -10000 0 95
KIRREL -0.06 0.22 -10000 0 -0.87 29 29
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.16 0.3 -10000 0 -0.7 95 95
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.13 0.24 -10000 0 -0.54 95 95
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.071 0.19 -10000 0 -0.4 95 95
FYN -0.11 0.23 -10000 0 -0.51 95 95
mol:Ca2+ -0.12 0.23 -10000 0 -0.53 95 95
mol:DAG -0.12 0.23 -10000 0 -0.54 95 95
NPHS2 -0.014 0.034 -10000 0 -10000 0 0
mol:IP3 -0.12 0.23 -10000 0 -0.54 95 95
regulation of endocytosis -0.11 0.21 -10000 0 -0.48 95 95
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.55 95 95
establishment of cell polarity -0.16 0.3 -10000 0 -0.7 95 95
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.49 95 95
Nephrin/NEPH1/beta Arrestin2 -0.11 0.21 -10000 0 -0.48 95 95
NPHS1 -0.15 0.33 -10000 0 -0.85 73 73
Nephrin/NEPH1/podocin -0.12 0.22 -10000 0 -0.51 95 95
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.13 0.24 -10000 0 -0.54 95 95
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 95 95
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.24 -10000 0 -0.52 97 97
cytoskeleton organization -0.096 0.25 -10000 0 -0.53 95 95
Nephrin/NEPH1 -0.12 0.23 -10000 0 -0.53 95 95
Nephrin/NEPH1/ZO-1 -0.14 0.25 -10000 0 -0.58 95 95
Endothelins

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
AKT1 -0.057 0.15 -9999 0 -0.58 9 9
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.68 51 51
EDN1 -0.049 0.13 -9999 0 -0.77 7 7
EDN3 -0.42 0.43 -9999 0 -0.85 207 207
EDN2 -0.012 0.11 -9999 0 -0.4 25 25
HRAS/GDP -0.1 0.24 -9999 0 -0.51 77 77
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.084 0.18 -9999 0 -0.38 85 85
ADCY4 -0.1 0.2 -9999 0 -0.53 55 55
ADCY5 -0.17 0.26 -9999 0 -0.59 96 96
ADCY6 -0.1 0.2 -9999 0 -0.53 55 55
ADCY7 -0.1 0.2 -9999 0 -0.53 55 55
ADCY1 -0.11 0.21 -9999 0 -0.56 56 56
ADCY2 -0.15 0.25 -9999 0 -0.59 82 82
ADCY3 -0.1 0.2 -9999 0 -0.53 55 55
ADCY8 -0.21 0.21 -9999 0 -0.56 79 79
ADCY9 -0.1 0.2 -9999 0 -0.53 55 55
arachidonic acid secretion -0.18 0.32 -9999 0 -0.62 120 120
ETB receptor/Endothelin-1/Gq/GTP -0.093 0.21 -9999 0 -0.44 95 95
GNAO1 -0.015 0.15 -9999 0 -0.72 16 16
HRAS 0.009 0.023 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.021 0.16 -9999 0 -0.54 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.086 0.23 -9999 0 -0.56 56 56
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.075 0.18 -9999 0 -0.52 32 32
EDNRB 0.002 0.088 -9999 0 -0.85 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.17 0.24 -9999 0 -0.64 49 49
CYSLTR1 -0.063 0.17 -9999 0 -0.74 11 11
SLC9A1 -0.024 0.077 -9999 0 -0.31 7 7
mol:GDP -0.12 0.25 -9999 0 -0.54 80 80
SLC9A3 -0.051 0.19 -9999 0 -0.78 19 19
RAF1 -0.15 0.29 -9999 0 -0.56 114 114
JUN -0.28 0.52 -9999 0 -1.2 97 97
JAK2 -0.057 0.15 -9999 0 -0.58 9 9
mol:IP3 -0.11 0.22 -9999 0 -0.49 89 89
ETA receptor/Endothelin-1 -0.041 0.2 -9999 0 -0.48 33 33
PLCB1 0.006 0.061 -9999 0 -0.85 2 2
PLCB2 0.005 0.043 -9999 0 -0.32 4 4
ETA receptor/Endothelin-3 -0.35 0.34 -9999 0 -0.69 206 206
FOS -0.26 0.48 -9999 0 -1 108 108
Gai/GDP -0.001 0.12 -9999 0 -0.65 12 12
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.23 -9999 0 -0.54 66 66
BCAR1 0.013 0.002 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.48 90 90
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.09 0.28 -9999 0 -0.85 49 49
Gs family/GDP -0.19 0.25 -9999 0 -0.56 107 107
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.45 90 90
MAPK14 -0.061 0.17 -9999 0 -0.38 61 61
TRPC6 -0.14 0.29 -9999 0 -0.74 48 48
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.013 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.073 0.18 -9999 0 -0.37 87 87
ETB receptor/Endothelin-2 -0.024 0.1 -9999 0 -0.63 9 9
ETB receptor/Endothelin-3 -0.34 0.33 -9999 0 -0.66 207 207
ETB receptor/Endothelin-1 -0.023 0.12 -9999 0 -0.62 11 11
MAPK3 -0.23 0.43 -9999 0 -0.89 113 113
MAPK1 -0.23 0.43 -9999 0 -0.89 113 113
Rac1/GDP -0.1 0.23 -9999 0 -0.52 73 73
cAMP biosynthetic process -0.14 0.22 -9999 0 -0.58 62 62
MAPK8 -0.16 0.32 -9999 0 -0.6 113 113
SRC 0.012 0.016 -9999 0 -0.32 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.009 0.074 -9999 0 -0.32 9 9
p130Cas/CRK/Src/PYK2 -0.13 0.29 -9999 0 -0.56 100 100
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.23 -9999 0 -0.52 73 73
COL1A2 -0.042 0.16 -9999 0 -0.58 10 10
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.1 -9999 0 -0.52 9 9
mol:DAG -0.11 0.23 -9999 0 -0.49 89 89
MAP2K2 -0.18 0.35 -9999 0 -0.68 116 116
MAP2K1 -0.18 0.35 -9999 0 -0.68 115 115
EDNRA -0.041 0.099 -9999 0 -0.53 4 4
positive regulation of muscle contraction -0.041 0.13 -9999 0 -0.55 7 7
Gq family/GDP -0.19 0.29 -9999 0 -0.67 98 98
HRAS/GTP -0.13 0.26 -9999 0 -0.54 91 91
PRKCH -0.1 0.22 -9999 0 -0.48 87 87
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.13 0.26 -9999 0 -0.55 91 91
PRKCB -0.12 0.22 -9999 0 -0.49 83 83
PRKCE -0.1 0.23 -9999 0 -0.51 78 78
PRKCD -0.1 0.22 -9999 0 -0.5 77 77
PRKCG -0.11 0.22 -9999 0 -0.49 83 83
regulation of vascular smooth muscle contraction -0.3 0.55 -9999 0 -1.2 108 108
PRKCQ -0.11 0.23 -9999 0 -0.51 81 81
PLA2G4A -0.2 0.36 -9999 0 -0.69 120 120
GNA14 -0.18 0.36 -9999 0 -0.86 92 92
GNA15 -0.015 0.093 -9999 0 -0.33 30 30
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 0.002 0.085 -9999 0 -0.85 4 4
Rac1/GTP -0.021 0.16 -9999 0 -0.54 9 9
MMP1 -0.099 0.16 -9999 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.002 0.029 -10000 0 -0.57 1 1
fibroblast growth factor receptor signaling pathway -0.002 0.029 -10000 0 -0.57 1 1
LAMA1 -0.053 0.23 -10000 0 -0.83 32 32
PRNP 0.013 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.096 0.23 -10000 0 -0.66 59 59
SMAD2 0.029 0.04 -10000 0 -0.52 1 1
GPC1/PrPc/Cu2+ 0 0.008 -10000 0 -10000 0 0
GPC1/Laminin alpha1 -0.051 0.17 -10000 0 -0.66 31 31
TDGF1 -0.35 0.42 -10000 0 -0.85 170 170
CRIPTO/GPC1 -0.27 0.32 -10000 0 -0.66 170 170
APP/GPC1 0 0.01 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.22 0.29 -10000 0 -0.57 170 170
FLT1 0.013 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.039 -10000 0 -0.57 1 1
SERPINC1 0.011 0.016 -10000 0 -10000 0 0
FYN -0.22 0.29 -10000 0 -0.57 170 170
FGR -0.22 0.29 -10000 0 -0.57 170 170
positive regulation of MAPKKK cascade -0.28 0.32 -10000 0 -0.64 172 172
SLIT2 -0.11 0.3 -10000 0 -0.84 60 60
GPC1/NRG -0.066 0.2 -10000 0 -0.66 40 40
NRG1 -0.073 0.26 -10000 0 -0.82 42 42
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.04 -10000 0 -0.57 2 2
LYN -0.22 0.29 -10000 0 -0.57 170 170
mol:Spermine 0.012 0.011 -10000 0 -10000 0 0
cell growth -0.002 0.029 -10000 0 -0.57 1 1
BMP signaling pathway -0.012 0.016 0.31 1 -10000 0 1
SRC -0.22 0.29 -10000 0 -0.57 170 170
TGFBR1 0.004 0.055 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.27 0.38 -10000 0 -0.72 158 158
GPC1 0.012 0.016 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.004 0.055 -10000 0 -10000 0 0
VEGFA 0.009 0.06 -10000 0 -0.85 2 2
BLK -0.4 0.39 -10000 0 -0.7 234 234
HCK -0.23 0.29 -10000 0 -0.57 170 170
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.011 0.043 -10000 0 -0.85 1 1
VEGFR1 homodimer 0.013 0 -10000 0 -10000 0 0
TGFBR2 0.011 0.043 -10000 0 -0.85 1 1
cell death 0 0.01 -10000 0 -10000 0 0
ATIII/GPC1 -0.001 0.014 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.21 0.29 -10000 0 -0.66 118 118
LCK -0.23 0.29 -10000 0 -0.57 175 175
neuron differentiation -0.066 0.2 -10000 0 -0.66 40 40
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.011 0.043 -10000 0 -0.85 1 1
Ephrin B reverse signaling

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
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.006 0.074 -10000 0 -0.85 3 3
EFNB1 -0.009 0.14 -10000 0 -0.66 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.26 0.26 -10000 0 -0.55 170 170
Ephrin B2/EPHB1-2 -0.2 0.26 -10000 0 -0.53 156 156
neuron projection morphogenesis -0.24 0.24 -10000 0 -0.52 170 170
Ephrin B1/EPHB1-2/Tiam1 -0.28 0.28 -10000 0 -0.59 170 170
DNM1 -0.027 0.18 -10000 0 -0.82 19 19
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.011 0.056 -10000 0 -0.76 2 2
YES1 -0.003 0.07 -10000 0 -1 2 2
Ephrin B1/EPHB1-2/NCK2 -0.2 0.26 -10000 0 -0.5 170 170
PI3K 0.01 0.074 -10000 0 -1 2 2
mol:GDP -0.28 0.27 -10000 0 -0.58 170 170
ITGA2B -0.088 0.28 -10000 0 -0.85 48 48
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.003 0.07 -10000 0 -1 2 2
MAP3K7 -0.006 0.057 -10000 0 -0.81 2 2
FGR -0.005 0.07 -10000 0 -1 2 2
TIAM1 -0.17 0.16 -10000 0 -0.32 230 230
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.047 0.21 -10000 0 -0.54 55 55
LYN -0.003 0.07 -10000 0 -1 2 2
Ephrin B1/EPHB1-2/Src Family Kinases -0.007 0.065 -10000 0 -0.94 2 2
Ephrin B1/EPHB1-2 -0.014 0.061 -10000 0 -0.87 2 2
SRC -0.005 0.07 -10000 0 -1 2 2
ITGB3 -0.014 0.15 -10000 0 -0.85 13 13
EPHB1 -0.31 0.42 -10000 0 -0.85 154 154
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.096 0.25 -10000 0 -0.72 55 55
BLK -0.061 0.11 -10000 0 -1 2 2
HCK -0.006 0.07 -10000 0 -1 2 2
regulation of stress fiber formation 0.2 0.25 0.49 170 -10000 0 170
MAPK8 0.015 0.087 -10000 0 -0.93 3 3
Ephrin B1/EPHB1-2/RGS3 -0.2 0.26 -10000 0 -0.5 170 170
endothelial cell migration -0.001 0.05 -10000 0 -0.71 2 2
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.012 0.069 -10000 0 -0.96 2 2
regulation of focal adhesion formation 0.2 0.25 0.49 170 -10000 0 170
chemotaxis 0.2 0.25 0.49 170 -10000 0 170
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
Rac1/GTP -0.25 0.25 -10000 0 -0.54 170 170
angiogenesis -0.014 0.061 -10000 0 -0.87 2 2
LCK -0.008 0.073 -10000 0 -1 2 2
Glucocorticoid receptor regulatory 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
PCK2 0.047 0.096 -10000 0 -10000 0 0
SMARCC2 0.014 0.012 -10000 0 -10000 0 0
SMARCC1 0.014 0.012 -10000 0 -10000 0 0
TBX21 -0.16 0.29 -10000 0 -0.61 80 80
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.05 -10000 0 -0.32 9 9
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.003 0.095 -10000 0 -0.85 5 5
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.35 36 -0.54 5 41
PRL -0.092 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.27 0.31 0.58 140 -0.54 16 156
RELA -0.038 0.09 -10000 0 -10000 0 0
FGG 0.25 0.19 0.52 93 -10000 0 93
GR beta/TIF2 0.098 0.23 0.36 56 -0.6 30 86
IFNG -0.51 0.52 -10000 0 -1.1 141 141
apoptosis 0.035 0.24 0.49 58 -0.54 1 59
CREB1 0.011 0.022 -10000 0 -10000 0 0
histone acetylation -0.075 0.16 -10000 0 -0.4 52 52
BGLAP -0.1 0.15 -10000 0 -0.56 4 4
GR/PKAc 0.14 0.1 0.35 27 -10000 0 27
NF kappa B1 p50/RelA -0.075 0.16 -10000 0 -0.44 26 26
SMARCD1 0.014 0.012 -10000 0 -10000 0 0
MDM2 0.12 0.096 0.28 80 -10000 0 80
GATA3 -0.032 0.2 -10000 0 -0.83 24 24
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.62 21 21
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.061 0.24 0.51 39 -0.78 4 43
CSN2 0.21 0.14 0.44 56 -10000 0 56
BRG1/BAF155/BAF170/BAF60A 0.008 0.04 -10000 0 -10000 0 0
NFATC1 0.002 0.1 -10000 0 -0.85 6 6
POU2F1 0.013 0.016 -10000 0 -0.3 1 1
CDKN1A 0.022 0.057 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 265 265
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.047 0.17 0.35 12 -0.47 15 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.079 0.45 0.49 40 -0.9 89 129
JUN -0.34 0.3 -10000 0 -0.7 143 143
IL4 -0.13 0.17 -10000 0 -0.61 23 23
CDK5R1 0.011 0.024 -10000 0 -0.32 2 2
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.37 0.43 -10000 0 -0.86 150 150
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.13 0.35 33 -0.49 5 38
cortisol/GR alpha (monomer) 0.38 0.31 0.68 164 -10000 0 164
NCOA2 -0.05 0.22 -10000 0 -0.85 30 30
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.26 0.37 -10000 0 -0.88 106 106
AP-1/NFAT1-c-4 -0.57 0.5 -10000 0 -0.99 198 198
AFP -0.23 0.21 -10000 0 -0.63 53 53
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.52 31 -10000 0 31
TP53 0.032 0.023 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.48 0.38 -10000 0 -0.82 165 165
KRT14 -0.24 0.18 -10000 0 -0.56 35 35
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.063 -10000 0 -10000 0 0
HDAC1 0.01 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.014 -10000 0 -10000 0 0
AP-1 -0.58 0.5 -10000 0 -0.99 200 200
MAPK14 0.014 0.012 -10000 0 -10000 0 0
MAPK10 0.014 0.013 -10000 0 -10000 0 0
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.56 0.55 -10000 0 -1.1 161 161
interleukin-1 receptor activity 0.017 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.015 0.05 -10000 0 -0.32 9 9
CGA -0.13 0.16 -10000 0 -0.56 17 17
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.38 155 -10000 0 155
MAPK3 0.014 0.013 -10000 0 -10000 0 0
MAPK1 0.014 0.012 -10000 0 -10000 0 0
ICAM1 -0.27 0.27 -10000 0 -0.68 89 89
NFKB1 -0.038 0.09 -10000 0 -10000 0 0
MAPK8 -0.19 0.19 -10000 0 -0.48 86 86
MAPK9 0.014 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.03 0.25 0.5 57 -0.56 1 58
BAX 0.028 0.031 -10000 0 -10000 0 0
POMC -0.56 0.7 -10000 0 -1.4 134 134
EP300 0.064 0.064 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.34 0.24 0.59 156 -10000 0 156
proteasomal ubiquitin-dependent protein catabolic process 0.089 0.073 0.25 25 -10000 0 25
SGK1 0.11 0.21 -10000 0 -1.4 7 7
IL13 -0.31 0.26 -10000 0 -0.81 55 55
IL6 -0.43 0.56 -10000 0 -1.3 109 109
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.27 0.21 -10000 0 -0.71 43 43
IL2 -0.37 0.27 -10000 0 -0.73 105 105
CDK5 0.012 0.008 -10000 0 -10000 0 0
PRKACB 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.28 0.32 -10000 0 -0.77 78 78
CDK5R1/CDK5 0.007 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.033 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.56 146 -10000 0 146
SMARCA4 0.014 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.21 0.15 0.4 106 -0.36 2 108
NF kappa B1 p50/RelA/Cbp 0.017 0.16 -10000 0 -0.49 3 3
JUN (dimer) -0.34 0.3 -10000 0 -0.69 143 143
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.25 0.43 -10000 0 -1 85 85
NR3C1 0.22 0.2 0.5 106 -10000 0 106
NR4A1 -0.32 0.42 -10000 0 -0.76 179 179
TIF2/SUV420H1 -0.048 0.17 -10000 0 -0.66 30 30
MAPKKK cascade 0.035 0.24 0.49 58 -0.54 1 59
cortisol/GR alpha (dimer)/Src-1 0.33 0.24 0.58 158 -10000 0 158
PBX1 0.012 0.043 -10000 0 -0.85 1 1
POU1F1 0.006 0.008 -10000 0 -10000 0 0
SELE -0.35 0.5 -10000 0 -1.2 88 88
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.21 0.15 0.4 106 -0.36 2 108
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.56 146 -10000 0 146
mol:cortisol 0.22 0.2 0.4 167 -10000 0 167
MMP1 -0.22 0.15 -10000 0 -0.44 50 50
Glypican 2 network

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
MDK -0.087 0.15 -9999 0 -0.32 124 124
GPC2 -0.018 0.096 -9999 0 -0.31 39 39
GPC2/Midkine -0.081 0.12 -9999 0 -0.41 17 17
neuron projection morphogenesis -0.081 0.12 -9999 0 -0.41 17 17
IL23-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
CCL2 -0.23 0.55 -9999 0 -1.2 73 73
IL23A -0.24 0.56 -9999 0 -1.3 74 74
NF kappa B1 p50/RelA/I kappa B alpha -0.3 0.47 -9999 0 -1.2 76 76
positive regulation of T cell mediated cytotoxicity -0.26 0.62 -9999 0 -1.3 85 85
ITGA3 -0.21 0.51 -9999 0 -1.2 69 69
IL17F -0.11 0.34 -9999 0 -0.73 66 66
IL12B -0.003 0.1 -9999 0 -0.55 10 10
STAT1 (dimer) -0.25 0.58 -9999 0 -1.2 83 83
CD4 -0.2 0.5 -9999 0 -1.1 74 74
IL23 -0.24 0.53 -9999 0 -1.2 74 74
IL23R -0.006 0.098 -9999 0 -10000 0 0
IL1B -0.25 0.59 -9999 0 -1.4 69 69
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.21 0.5 -9999 0 -1.1 77 77
TYK2 0.013 0.022 -9999 0 -10000 0 0
STAT4 -0.031 0.15 -9999 0 -0.45 39 39
STAT3 0.013 0 -9999 0 -10000 0 0
IL18RAP -0.03 0.18 -9999 0 -0.82 20 20
IL12RB1 -0.022 0.12 -9999 0 -0.38 35 35
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
IL12Rbeta1/TYK2 -0.01 0.092 -9999 0 -0.7 3 3
IL23R/JAK2 -0.003 0.12 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.26 0.62 -9999 0 -1.3 85 85
natural killer cell activation 0.002 0.009 -9999 0 -10000 0 0
JAK2 0.021 0.026 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.013 0.004 -9999 0 -10000 0 0
RELA 0.013 0.004 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.22 0.5 -9999 0 -1.1 74 74
ALOX12B -0.22 0.51 -9999 0 -1.2 71 71
CXCL1 -0.23 0.53 -9999 0 -1.2 78 78
T cell proliferation -0.26 0.62 -9999 0 -1.3 85 85
NFKBIA 0.013 0.004 -9999 0 -10000 0 0
IL17A -0.067 0.28 -9999 0 -0.57 54 54
PI3K -0.31 0.48 -9999 0 -1.2 80 80
IFNG -0.021 0.055 -9999 0 -0.13 69 69
STAT3 (dimer) -0.29 0.45 -9999 0 -1.1 77 77
IL18R1 -0.032 0.15 -9999 0 -0.42 41 41
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.33 -9999 0 -0.74 52 52
IL18/IL18R -0.074 0.19 -9999 0 -0.6 38 38
macrophage activation -0.015 0.018 -9999 0 -0.044 76 76
TNF -0.28 0.62 -9999 0 -1.4 86 86
STAT3/STAT4 -0.32 0.49 -9999 0 -1.2 85 85
STAT4 (dimer) -0.26 0.59 -9999 0 -1.3 82 82
IL18 -0.041 0.16 -9999 0 -0.42 50 50
IL19 -0.21 0.5 -9999 0 -1.1 75 75
STAT5A (dimer) -0.24 0.58 -9999 0 -1.3 79 79
STAT1 0.006 0.048 -9999 0 -0.31 9 9
SOCS3 -0.054 0.23 -9999 0 -0.85 32 32
CXCL9 -0.3 0.63 -9999 0 -1.3 95 95
MPO -0.21 0.52 -9999 0 -1.1 79 79
positive regulation of humoral immune response -0.26 0.62 -9999 0 -1.3 85 85
IL23/IL23R/JAK2/TYK2 -0.31 0.75 -9999 0 -1.5 85 85
IL6 -0.35 0.67 -9999 0 -1.4 108 108
STAT5A 0.013 0 -9999 0 -10000 0 0
IL2 0.001 0.017 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.009 -9999 0 -10000 0 0
CD3E -0.24 0.58 -9999 0 -1.3 78 78
keratinocyte proliferation -0.26 0.62 -9999 0 -1.3 85 85
NOS2 -0.22 0.51 -9999 0 -1.1 78 78
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.62 65 65
FYN -0.11 0.35 -10000 0 -0.79 74 74
LAT/GRAP2/SLP76 -0.13 0.28 -10000 0 -0.66 78 78
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.055 0.22 -10000 0 -0.47 77 77
B2M 0.012 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.05 -10000 0 -0.19 9 9
MAP3K8 0 0.1 -10000 0 -0.85 6 6
mol:Ca2+ -0.032 0.051 -10000 0 -0.13 86 86
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.33 -10000 0 -0.72 79 79
TRPV6 -0.18 0.35 -10000 0 -0.86 84 84
CD28 -0.048 0.2 -10000 0 -0.61 40 40
SHC1 -0.12 0.35 -10000 0 -0.8 73 73
receptor internalization -0.14 0.39 -10000 0 -0.83 81 81
PRF1 -0.12 0.35 -10000 0 -0.85 64 64
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.038 0.18 -10000 0 -0.38 76 76
LAT -0.12 0.35 -10000 0 -0.82 73 73
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.097 0.28 -10000 0 -0.74 60 60
CD3E -0.074 0.26 -10000 0 -0.77 46 46
CD3G -0.15 0.33 -10000 0 -0.81 80 80
RASGRP2 0 0.03 -10000 0 -0.19 4 4
RASGRP1 -0.052 0.22 -10000 0 -0.47 78 78
HLA-A 0.011 0.017 -10000 0 -10000 0 0
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.068 -10000 0 -0.12 53 53
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.057 0.09 -10000 0 -0.25 54 54
PRKCA -0.066 0.14 -10000 0 -0.32 79 79
GRAP2 -0.046 0.22 -10000 0 -0.8 30 30
mol:IP3 -0.053 0.24 0.28 71 -0.47 74 145
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.16 0.43 -10000 0 -0.96 72 72
ORAI1 0.088 0.16 0.4 84 -10000 0 84
CSK -0.12 0.36 -10000 0 -0.82 73 73
B7 family/CD28 -0.2 0.36 -10000 0 -0.76 97 97
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.43 -10000 0 -0.94 80 80
PTPN6 -0.13 0.36 -10000 0 -0.83 73 73
VAV1 -0.13 0.35 -10000 0 -0.79 77 77
Monovalent TCR/CD3 -0.17 0.43 -10000 0 -0.76 101 101
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.85 72 72
PAG1 -0.12 0.36 -10000 0 -0.82 73 73
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.43 -10000 0 -0.95 78 78
CD80 -0.086 0.27 -10000 0 -0.83 48 48
CD86 -0.011 0.11 -10000 0 -0.41 23 23
PDK1/CARD11/BCL10/MALT1 -0.07 0.11 -10000 0 -0.3 60 60
HRAS 0.012 0.023 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.3 -10000 0 -0.6 97 97
CD8A -0.049 0.22 -10000 0 -0.86 29 29
CD8B -0.096 0.28 -10000 0 -0.75 59 59
PTPRC -0.036 0.18 -10000 0 -0.6 32 32
PDK1/PKC theta -0.071 0.27 -10000 0 -0.58 78 78
CSK/PAG1 -0.11 0.35 -10000 0 -0.83 67 67
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.014 0.016 -10000 0 -10000 0 0
GRAP2/SLP76 -0.16 0.33 -10000 0 -0.78 78 78
STIM1 0.047 0.083 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.092 -10000 0 -0.18 48 48
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.44 -10000 0 -0.94 81 81
mol:DAG -0.072 0.18 -10000 0 -0.41 78 78
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.029 0.18 -10000 0 -0.65 26 26
cytotoxic T cell degranulation -0.11 0.33 -10000 0 -0.78 67 67
RAP1A/GTP -0.003 0.009 -10000 0 -0.07 3 3
mol:PI-3-4-5-P3 -0.076 0.26 -10000 0 -0.57 79 79
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.083 0.3 0.3 65 -0.62 77 142
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.025 0.17 -10000 0 -0.67 23 23
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.26 -10000 0 -0.62 78 78
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.011 0.043 -10000 0 -0.85 1 1
CD8 heterodimer -0.11 0.3 -10000 0 -0.78 62 62
CARD11 -0.076 0.17 -10000 0 -0.36 98 98
PRKCB -0.059 0.13 -10000 0 -0.31 69 69
PRKCE -0.052 0.12 -10000 0 -0.3 61 61
PRKCQ -0.095 0.31 -10000 0 -0.68 79 79
LCP2 0.007 0.045 -10000 0 -0.31 8 8
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.041 0.19 -10000 0 -0.4 77 77
IKK complex 0.012 0.07 -10000 0 -0.12 44 44
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.017 0.14 -10000 0 -0.3 58 58
PDPK1 -0.048 0.21 -10000 0 -0.44 78 78
TCR/CD3/MHC I/CD8/Fyn -0.17 0.46 -10000 0 -1.1 73 73
IGF1 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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.12 0.24 -10000 0 -0.48 122 122
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.023 -10000 0 -0.31 2 2
IRS1/Crk -0.12 0.24 -10000 0 -0.48 122 122
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.23 -10000 0 -0.55 89 89
AKT1 -0.086 0.22 -10000 0 -0.8 11 11
BAD -0.072 0.2 -10000 0 -0.72 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.24 -10000 0 -0.48 122 122
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.23 -10000 0 -0.48 122 122
RAF1 -0.063 0.19 -10000 0 -0.67 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.22 -10000 0 -0.45 122 122
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.25 -10000 0 -0.52 122 122
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
RPS6KB1 -0.086 0.22 -10000 0 -0.8 11 11
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.054 0.17 -10000 0 -0.54 11 11
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.76 11 11
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.18 -10000 0 -0.44 89 89
IGF-1R heterotetramer -0.018 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.14 0.23 -10000 0 -0.48 122 122
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.46 89 89
IGF1R -0.018 0.048 -10000 0 -10000 0 0
IGF1 -0.19 0.36 -10000 0 -0.84 94 94
IRS2/Crk -0.11 0.23 -10000 0 -0.48 89 89
PI3K -0.14 0.22 -10000 0 -0.45 122 122
apoptosis 0.054 0.18 0.59 11 -10000 0 11
HRAS/GDP -0.001 0.015 -10000 0 -10000 0 0
PRKCD -0.1 0.25 -10000 0 -0.55 89 89
RAF1/14-3-3 E -0.046 0.17 -10000 0 -0.55 11 11
BAD/14-3-3 -0.058 0.19 -10000 0 -0.64 11 11
PRKCZ -0.086 0.22 -10000 0 -0.8 11 11
Crk/p130 Cas/Paxillin/FAK1 -0.099 0.16 -10000 0 -0.66 11 11
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.26 -10000 0 -0.59 89 89
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.2 -10000 0 -0.48 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.24 -10000 0 -0.48 122 122
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.12 0.24 -10000 0 -0.48 122 122
IRS1 -0.14 0.26 -10000 0 -0.52 122 122
IRS2 -0.12 0.24 -10000 0 -0.48 122 122
IGF-1R heterotetramer/IGF1 -0.16 0.28 -10000 0 -0.69 89 89
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.099 0.23 -10000 0 -0.46 89 89
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.1 0.25 -10000 0 -0.55 89 89
SHC1 0.013 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.43 -9999 0 -0.98 44 44
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.35 -9999 0 -0.84 92 92
SMAD4 0.015 0.002 -9999 0 -10000 0 0
ID2 -0.2 0.43 -9999 0 -0.99 42 42
AP1 -0.3 0.47 -9999 0 -0.98 124 124
ABCG2 -0.2 0.43 -9999 0 -1 43 43
HIF1A -0.014 0.066 -9999 0 -10000 0 0
TFF3 -0.6 0.53 -9999 0 -1.1 168 168
GATA2 0.014 0.017 -9999 0 -0.31 1 1
AKT1 -0.043 0.1 -9999 0 -10000 0 0
response to hypoxia -0.064 0.11 -9999 0 -0.25 10 10
MCL1 -0.2 0.43 -9999 0 -0.99 42 42
NDRG1 -0.2 0.43 -9999 0 -0.99 42 42
SERPINE1 -0.22 0.43 -9999 0 -1 45 45
FECH -0.2 0.43 -9999 0 -0.97 46 46
FURIN -0.2 0.43 -9999 0 -0.99 42 42
NCOA2 -0.049 0.22 -9999 0 -0.85 30 30
EP300 -0.069 0.18 -9999 0 -0.34 93 93
HMOX1 -0.21 0.43 -9999 0 -0.99 46 46
BHLHE40 -0.21 0.43 -9999 0 -1 46 46
BHLHE41 -0.2 0.43 -9999 0 -0.97 48 48
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.036 -9999 0 -10000 0 0
ENG 0.041 0.091 -9999 0 -10000 0 0
JUN -0.18 0.36 -9999 0 -0.85 93 93
RORA -0.2 0.43 -9999 0 -0.99 46 46
ABCB1 -0.071 0.16 -9999 0 -1.5 4 4
TFRC -0.2 0.43 -9999 0 -0.99 42 42
CXCR4 -0.2 0.43 -9999 0 -0.98 44 44
TF -0.27 0.51 -9999 0 -1.1 76 76
CITED2 -0.24 0.47 -9999 0 -1.1 58 58
HIF1A/ARNT -0.31 0.39 -9999 0 -1 61 61
LDHA -0.041 0.05 -9999 0 -10000 0 0
ETS1 -0.2 0.43 -9999 0 -0.98 45 45
PGK1 -0.2 0.43 -9999 0 -0.99 43 43
NOS2 -0.22 0.44 -9999 0 -0.98 53 53
ITGB2 -0.21 0.43 -9999 0 -1 47 47
ALDOA -0.2 0.43 -9999 0 -0.99 42 42
Cbp/p300/CITED2 -0.34 0.51 -9999 0 -1.1 91 91
FOS -0.21 0.38 -9999 0 -0.85 106 106
HK2 -0.21 0.43 -9999 0 -1 44 44
SP1 0.022 0.006 -9999 0 -10000 0 0
GCK -0.42 0.73 -9999 0 -1.5 118 118
HK1 -0.2 0.43 -9999 0 -0.99 43 43
NPM1 -0.2 0.43 -9999 0 -0.99 43 43
EGLN1 -0.2 0.43 -9999 0 -0.99 43 43
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.2 0.43 -9999 0 -1 34 34
SMAD3 0.015 0.002 -9999 0 -10000 0 0
EDN1 -0.17 0.32 -9999 0 -0.76 53 53
IGFBP1 -0.22 0.43 -9999 0 -1 43 43
VEGFA -0.17 0.39 -9999 0 -0.77 61 61
HIF1A/JAB1 -0.012 0.02 -9999 0 -10000 0 0
CP -0.38 0.57 -9999 0 -1.1 119 119
CXCL12 -0.25 0.49 -9999 0 -1.1 61 61
COPS5 0.014 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.2 0.43 -9999 0 -0.99 42 42
EGLN3 -0.22 0.44 -9999 0 -1 48 48
CA9 -0.22 0.43 -9999 0 -1 45 45
TERT -0.21 0.42 -9999 0 -1 43 43
ENO1 -0.2 0.43 -9999 0 -0.99 42 42
PFKL -0.2 0.43 -9999 0 -0.99 42 42
NCOA1 0.013 0 -9999 0 -10000 0 0
ADM -0.24 0.45 -9999 0 -1 45 45
ARNT -0.014 0.066 -9999 0 -10000 0 0
HNF4A -0.027 0.065 -9999 0 -0.34 9 9
ADFP -0.22 0.42 -9999 0 -0.93 59 59
SLC2A1 -0.17 0.38 -9999 0 -0.77 55 55
LEP -0.22 0.43 -9999 0 -1 45 45
HIF1A/ARNT/Cbp/p300 -0.31 0.36 -9999 0 -0.87 93 93
EPO -0.14 0.31 -9999 0 -1 11 11
CREBBP -0.069 0.18 -9999 0 -0.34 93 93
HIF1A/ARNT/Cbp/p300/HDAC7 -0.29 0.34 -9999 0 -0.84 88 88
PFKFB3 -0.2 0.43 -9999 0 -1 42 42
NT5E -0.21 0.43 -9999 0 -1 46 46
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.29 0.34 -9999 0 -0.63 187 187
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.06 0.23 -9999 0 -0.73 40 40
SMAD9 -0.22 0.29 -9999 0 -0.61 132 132
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.1 0.21 -9999 0 -0.38 139 139
BMP7/USAG1 -0.34 0.33 -9999 0 -0.66 213 213
SMAD5/SKI -0.09 0.2 -9999 0 -0.54 23 23
SMAD1 0.017 0.046 -9999 0 -10000 0 0
BMP2 -0.014 0.15 -9999 0 -0.85 13 13
SMAD1/SMAD1/SMAD4 -0.002 0.002 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.28 0.41 -9999 0 -0.85 139 139
BMPR1A-1B/BAMBI -0.2 0.28 -9999 0 -0.58 139 139
AHSG -0.014 0.078 -9999 0 -0.31 26 26
CER1 0.001 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.037 0.14 -9999 0 -0.58 25 25
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.083 0.2 -9999 0 -0.65 27 27
BMP2-4 (homodimer) -0.043 0.16 -9999 0 -0.66 25 25
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.18 0.25 -9999 0 -0.52 139 139
RGMA -0.021 0.17 -9999 0 -0.85 16 16
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.093 0.19 -9999 0 -0.58 25 25
BMP2-4/USAG1 -0.33 0.31 -9999 0 -0.6 227 227
SMAD6/SMURF1/SMAD5 -0.09 0.2 -9999 0 -0.54 23 23
SOSTDC1 -0.44 0.43 -9999 0 -0.85 214 214
BMP7/BMPR2/BMPR1A-1B -0.18 0.25 -9999 0 -0.52 139 139
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0 -9999 0 -10000 0 0
HFE2 0.001 0.032 -9999 0 -0.31 4 4
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.048 0.16 -9999 0 -0.58 32 32
SMAD5/SMAD5/SMAD4 -0.09 0.2 -9999 0 -0.54 23 23
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.098 0.14 -9999 0 -0.49 25 25
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.013 0.049 -9999 0 -10000 0 0
SMAD1/SKI 0.024 0.044 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.047 0.14 -9999 0 -0.59 25 25
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.36 -9999 0 -0.74 115 115
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.01 0.074 -9999 0 -0.57 7 7
BMPR1A-1B (homodimer) -0.22 0.31 -9999 0 -0.66 139 139
CHRDL1 -0.6 0.39 -9999 0 -0.85 290 290
ENDOFIN/SMAD1 0.024 0.044 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.007 0.009 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.076 -9999 0 -0.34 17 17
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.44 0.29 -9999 0 -0.61 295 295
BMP2-4/GREM1 -0.17 0.29 -9999 0 -0.64 104 104
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.19 0.28 -9999 0 -0.57 132 132
SMAD1/SMAD6 0.024 0.044 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.07 0.16 -9999 0 -0.5 25 25
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.024 0.044 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A -0.002 0.11 -9999 0 -0.85 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.21 0.33 -9999 0 -0.82 73 73
CHRD -0.004 0.12 -9999 0 -0.85 8 8
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.098 0.2 -9999 0 -0.62 25 25
BMP4 -0.016 0.15 -9999 0 -0.69 17 17
FST -0.21 0.37 -9999 0 -0.85 103 103
BMP2-4/NOG -0.083 0.2 -9999 0 -0.57 56 56
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.16 0.23 -9999 0 -0.48 139 139
Arf6 signaling events

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
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.042 0.11 -9999 0 -0.51 10 10
EGFR 0.002 0.095 -9999 0 -0.85 5 5
EPHA2 0.011 0.028 -9999 0 -0.31 3 3
USP6 0.011 0.028 -9999 0 -10000 0 0
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.099 0.23 -9999 0 -0.66 60 60
ARRB2 -0.043 0.15 -9999 0 -0.46 48 48
mol:GTP 0.021 0.011 -9999 0 -10000 0 0
ARRB1 0.011 0.043 -9999 0 -0.85 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.009 0.06 -9999 0 -0.85 2 2
EGF -0.11 0.3 -9999 0 -0.8 61 61
somatostatin receptor activity 0 0 -9999 0 -0.001 113 113
ARAP2 0.011 0.043 -9999 0 -0.85 1 1
mol:GDP -0.12 0.15 -9999 0 -0.31 114 114
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 98 98
ITGA2B -0.088 0.28 -9999 0 -0.85 48 48
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.011 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.18 0.25 -9999 0 -0.72 62 62
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.31 115 115
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.086 0.2 -9999 0 -0.57 60 60
ADRB2 -0.008 0.13 -9999 0 -0.85 10 10
receptor agonist activity 0 0 -9999 0 0 122 122
actin filament binding 0 0 -9999 0 -0.001 112 112
SRC 0.012 0.016 -9999 0 -0.31 1 1
ITGB3 -0.014 0.15 -9999 0 -0.85 13 13
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 108 108
ARF6/GDP 0.001 0.069 -9999 0 -0.37 1 1
ARF6/GDP/GULP/ACAP1 -0.19 0.2 -9999 0 -0.51 93 93
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.077 0.2 -9999 0 -0.57 55 55
ACAP1 0.001 0.078 -9999 0 -0.4 12 12
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.085 0.23 -9999 0 -0.7 48 48
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.12 0.31 -9999 0 -0.85 62 62
CYTH3 0.01 0.034 -9999 0 -0.67 1 1
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 108 108
endosomal lumen acidification 0 0 -9999 0 -0.001 121 121
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.33 -9999 0 -0.85 74 74
GNAQ/ARNO 0.008 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 34 34
MET -0.12 0.16 -9999 0 -0.31 164 164
GNA14 -0.18 0.36 -9999 0 -0.85 92 92
GNA15 -0.012 0.094 -9999 0 -0.33 30 30
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 114 114
GNA11 0.004 0.085 -9999 0 -0.85 4 4
LHCGR -0.098 0.28 -9999 0 -0.79 54 54
AGTR1 -0.33 0.42 -9999 0 -0.85 164 164
desensitization of G-protein coupled receptor protein signaling pathway -0.085 0.22 -9999 0 -0.7 48 48
IPCEF1/ARNO -0.064 0.16 -9999 0 -0.45 60 60
alphaIIb/beta3 Integrin -0.096 0.25 -9999 0 -0.72 55 55
Coregulation of Androgen receptor activity

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
NRIP1 -0.014 0.063 -10000 0 -0.37 8 8
SVIL -0.006 0.03 -10000 0 -10000 0 0
ZNF318 0.061 0.083 0.24 1 -10000 0 1
JMJD2C -0.064 0.069 -10000 0 -0.12 231 231
T-DHT/AR/Ubc9 -0.29 0.3 -10000 0 -0.65 170 170
CARM1 0.011 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.01 -10000 0 -10000 0 0
CTNNB1 -0.002 0.023 -10000 0 -10000 0 0
AKT1 0.025 0.019 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.025 0.019 -10000 0 -10000 0 0
MAK 0.049 0.13 -10000 0 -0.82 5 5
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.008 0.052 -10000 0 -0.85 1 1
GSN -0.005 0.03 -10000 0 -10000 0 0
NCOA2 -0.052 0.22 -10000 0 -0.85 30 30
NCOA6 -0.005 0.028 -10000 0 -10000 0 0
DNA-PK 0.057 0.083 0.26 1 -10000 0 1
NCOA4 0.011 0.004 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.013 0.15 -10000 0 -1.1 5 5
XRCC5 0.024 0.017 -10000 0 -10000 0 0
UBE3A -0.015 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.32 0.33 -10000 0 -0.68 174 174
FHL2 -0.16 0.38 -10000 0 -1.4 33 33
RANBP9 -0.005 0.028 -10000 0 -10000 0 0
JMJD1A 0.003 0.037 -10000 0 -0.12 29 29
CDK6 0.012 0.043 -10000 0 -0.85 1 1
TGFB1I1 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.3 0.31 -10000 0 -0.66 171 171
XRCC6 0.024 0.017 -10000 0 -10000 0 0
T-DHT/AR -0.34 0.33 -10000 0 -0.66 191 191
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.045 0.05 -10000 0 -10000 0 0
BRCA1 -0.006 0.03 -10000 0 -10000 0 0
TCF4 0.035 0.034 -10000 0 -10000 0 0
CDKN2A -0.1 0.16 -10000 0 -0.31 117 117
SRF 0.028 0.039 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -0.66 10 10
KLK3 -0.43 0.71 -10000 0 -1.6 111 111
TMF1 0.009 0.006 -10000 0 -10000 0 0
HNRNPA1 0.03 0.027 -10000 0 -10000 0 0
AOF2 -0.021 0.033 -10000 0 -0.075 111 111
APPL1 0.051 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.28 0.31 -10000 0 -0.64 170 170
AR -0.39 0.43 -10000 0 -0.9 170 170
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.03 0.027 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.024 0.017 -10000 0 -10000 0 0
PA2G4 0.035 0.035 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.26 0.29 -10000 0 -0.6 170 170
RPS6KA3 -0.005 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.29 0.31 -10000 0 -0.65 170 170
LATS2 0.03 0.027 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.26 0.29 -10000 0 -0.59 170 170
Cyclin D3/CDK11 p58 0 0 -10000 0 -10000 0 0
VAV3 -0.01 0.087 -10000 0 -0.86 4 4
KLK2 -0.78 0.64 -10000 0 -1.3 231 231
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.67 176 176
TMPRSS2 -0.18 0.31 -10000 0 -1.2 28 28
CCND1 0 0.053 -10000 0 -10000 0 0
PIAS1 -0.015 0.046 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.041 -10000 0 -0.083 138 138
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.034 0.076 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.29 0.31 -10000 0 -0.65 170 170
CMTM2 0.015 0.024 -10000 0 -0.31 2 2
SNURF -0.023 0.17 -10000 0 -0.85 17 17
ZMIZ1 -0.011 0.037 -10000 0 -10000 0 0
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -10000 0 0
FKBP4 -0.005 0.028 -10000 0 -10000 0 0
Syndecan-1-mediated 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
TGFB1 0.008 0.039 -9999 0 -0.31 6 6
CCL5 -0.047 0.21 -9999 0 -0.75 32 32
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.17 -9999 0 -0.49 43 43
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.095 0.16 -9999 0 -0.69 17 17
Syndecan-1/Syntenin -0.095 0.16 -9999 0 -0.69 17 17
MAPK3 -0.072 0.15 -9999 0 -0.63 16 16
HGF/MET -0.18 0.25 -9999 0 -0.72 62 62
TGFB1/TGF beta receptor Type II 0.008 0.039 -9999 0 -0.31 6 6
BSG 0.012 0.016 -9999 0 -0.31 1 1
keratinocyte migration -0.094 0.16 -9999 0 -0.67 17 17
Syndecan-1/RANTES -0.13 0.23 -9999 0 -0.75 38 38
Syndecan-1/CD147 -0.094 0.15 -9999 0 -0.66 17 17
Syndecan-1/Syntenin/PIP2 -0.1 0.15 -9999 0 -0.66 17 17
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.1 0.14 -9999 0 -0.64 17 17
MMP7 -0.18 0.23 -9999 0 -0.37 203 203
HGF -0.12 0.31 -9999 0 -0.85 62 62
Syndecan-1/CASK -0.1 0.16 -9999 0 -0.47 43 43
Syndecan-1/HGF/MET -0.22 0.24 -9999 0 -0.66 74 74
regulation of cell adhesion -0.062 0.14 -9999 0 -0.6 16 16
HPSE -0.022 0.15 -9999 0 -0.51 27 27
positive regulation of cell migration -0.11 0.17 -9999 0 -0.49 43 43
SDC1 -0.11 0.17 -9999 0 -0.5 43 43
Syndecan-1/Collagen -0.11 0.17 -9999 0 -0.49 43 43
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.12 0.16 -9999 0 -0.31 164 164
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.084 0.25 -9999 0 -0.59 66 66
MAPK1 -0.072 0.15 -9999 0 -0.63 16 16
homophilic cell adhesion -0.11 0.17 -9999 0 -0.49 43 43
MMP1 -0.15 0.16 -9999 0 -0.31 201 201
EPHB forward signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.1 0.22 -10000 0 -0.58 70 70
cell-cell adhesion 0.16 0.19 0.56 8 -10000 0 8
Ephrin B/EPHB2/RasGAP -0.013 0.066 -10000 0 -0.48 7 7
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.081 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.22 0.28 -10000 0 -0.58 154 154
HRAS/GDP -0.14 0.18 -10000 0 -0.41 48 48
Ephrin B/EPHB1/GRB7 -0.21 0.25 -10000 0 -0.52 157 157
Endophilin/SYNJ1 0.026 0.069 -10000 0 -0.45 7 7
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.19 0.24 -10000 0 -0.5 157 157
endothelial cell migration -0.001 0.024 -10000 0 -0.49 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.037 0.12 -10000 0 -0.31 63 63
PAK1 0.034 0.071 -10000 0 -0.46 7 7
HRAS 0.012 0.023 -10000 0 -0.31 2 2
RRAS 0.026 0.071 -10000 0 -0.46 7 7
DNM1 -0.026 0.18 -10000 0 -0.82 19 19
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.25 -10000 0 -0.47 157 157
lamellipodium assembly -0.16 0.19 -10000 0 -0.56 8 8
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.18 -10000 0 -0.34 154 154
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.007 0.074 -10000 0 -0.85 3 3
EPHB3 -0.19 0.16 -10000 0 -0.31 254 254
EPHB1 -0.31 0.42 -10000 0 -0.85 154 154
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.07 0.18 -10000 0 -0.47 8 8
Ephrin B/EPHB2 -0.013 0.068 -10000 0 -0.49 7 7
Ephrin B/EPHB3 -0.086 0.082 -10000 0 -0.6 4 4
JNK cascade -0.16 0.25 -10000 0 -0.48 156 156
Ephrin B/EPHB1 -0.2 0.24 -10000 0 -0.5 157 157
RAP1/GDP -0.054 0.16 -10000 0 -0.5 2 2
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.008 0.1 -10000 0 -0.42 20 20
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.2 0.26 -10000 0 -0.53 156 156
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.2 -10000 0 -0.53 13 13
Rap1/GTP -0.16 0.19 -10000 0 -0.57 8 8
axon guidance -0.1 0.22 -10000 0 -0.58 70 70
MAPK3 -0.078 0.17 -10000 0 -0.55 1 1
MAPK1 -0.078 0.17 -10000 0 -0.55 1 1
Rac1/GDP -0.045 0.17 -10000 0 -0.44 6 6
actin cytoskeleton reorganization -0.11 0.14 -10000 0 -0.45 5 5
CDC42/GDP -0.045 0.17 -10000 0 -0.44 6 6
PI3K -0.001 0.024 -10000 0 -0.49 1 1
EFNA5 -0.13 0.32 -10000 0 -0.84 69 69
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.052 -10000 0 -0.34 7 7
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.15 0.19 -10000 0 -0.55 9 9
PTK2 0.042 0.053 -10000 0 -10000 0 0
MAP4K4 -0.16 0.26 -10000 0 -0.48 156 156
SRC 0.012 0.016 -10000 0 -0.31 1 1
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.071 0.18 -10000 0 -0.56 2 2
MAP2K1 -0.091 0.18 -10000 0 -0.4 8 8
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.2 0.26 -10000 0 -0.52 156 156
cell migration -0.086 0.19 -10000 0 -0.43 8 8
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.071 -10000 0 -0.46 7 7
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.036 0.19 -10000 0 -0.46 62 62
HRAS/GTP -0.17 0.21 -10000 0 -0.42 159 159
Ephrin B1/EPHB1-2 -0.2 0.26 -10000 0 -0.53 156 156
cell adhesion mediated by integrin 0.012 0.07 0.52 4 -10000 0 4
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.18 0.22 -10000 0 -0.46 159 159
RAC1-CDC42/GTP -0.21 0.22 -10000 0 -0.51 119 119
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.054 0.16 -10000 0 -0.46 3 3
ruffle organization -0.12 0.23 -10000 0 -0.57 8 8
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.012 0.13 -10000 0 -0.48 23 23
Ephrin B/EPHB2/KALRN -0.013 0.066 -10000 0 -0.48 7 7
ROCK1 -0.076 0.081 -10000 0 -10000 0 0
RAS family/GDP -0.086 0.11 -10000 0 -0.54 2 2
Rac1/GTP -0.16 0.2 -10000 0 -0.61 8 8
Ephrin B/EPHB1/Src/Paxillin -0.11 0.19 -10000 0 -0.34 157 157
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.13 0.41 -9999 0 -1.4 39 39
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.04 0.11 -9999 0 -0.39 16 16
ATF2/c-Jun -0.22 0.43 -9999 0 -1 93 93
MAPK11 -0.04 0.11 -9999 0 -0.39 16 16
MITF -0.034 0.14 -9999 0 -0.4 39 39
MAPKAPK5 -0.034 0.14 -9999 0 -0.4 39 39
KRT8 -0.034 0.14 -9999 0 -0.4 39 39
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.055 0.17 -9999 0 -0.51 39 39
CEBPB -0.034 0.14 -9999 0 -0.4 39 39
SLC9A1 -0.034 0.14 -9999 0 -0.4 39 39
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.07 0.18 -9999 0 -0.42 58 58
p38alpha-beta/MNK1 -0.031 0.14 -9999 0 -0.5 16 16
JUN -0.22 0.43 -9999 0 -0.99 93 93
PPARGC1A -0.24 0.25 -9999 0 -0.47 216 216
USF1 -0.034 0.14 -9999 0 -0.4 39 39
RAB5/GDP/GDI1 -0.041 0.086 -9999 0 -0.35 16 16
NOS2 -0.055 0.16 -9999 0 -0.55 16 16
DDIT3 -0.036 0.14 -9999 0 -0.41 39 39
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.017 0.11 -9999 0 -0.39 16 16
p38alpha-beta/HBP1 -0.031 0.14 -9999 0 -0.5 16 16
CREB1 -0.049 0.16 -9999 0 -0.44 39 39
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.019 0.12 -9999 0 -0.44 16 16
RPS6KA4 -0.034 0.14 -9999 0 -0.4 39 39
PLA2G4A -0.061 0.22 -9999 0 -0.63 43 43
GDI1 -0.034 0.14 -9999 0 -0.4 39 39
TP53 -0.044 0.16 -9999 0 -0.5 39 39
RPS6KA5 -0.073 0.19 -9999 0 -0.46 68 68
ESR1 -0.07 0.2 -9999 0 -0.52 50 50
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.034 0.14 -9999 0 -0.4 39 39
MEF2A -0.034 0.14 -9999 0 -0.4 39 39
EIF4EBP1 -0.05 0.16 -9999 0 -0.44 39 39
KRT19 -0.11 0.22 -9999 0 -0.56 54 54
ELK4 -0.034 0.14 -9999 0 -0.4 39 39
ATF6 -0.034 0.14 -9999 0 -0.4 39 39
ATF1 -0.049 0.16 -9999 0 -0.44 39 39
p38alpha-beta/MAPKAPK2 -0.031 0.14 -9999 0 -0.5 16 16
p38alpha-beta/MAPKAPK3 -0.031 0.14 -9999 0 -0.5 16 16
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.081 0.061 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.18 -9999 0 -0.66 34 34
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.61 60 60
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.66 34 34
CCL5 -0.047 0.21 -9999 0 -0.75 32 32
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG 0.002 0.025 -9999 0 -0.31 2 2
ADAM12 -0.072 0.14 -9999 0 -0.31 106 106
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.066 0.046 -9999 0 -0.23 2 2
Syndecan-4/Laminin alpha1 -0.17 0.22 -9999 0 -0.7 42 42
Syndecan-4/CXCL12/CXCR4 -0.18 0.22 -9999 0 -0.66 55 55
Syndecan-4/Laminin alpha3 -0.15 0.19 -9999 0 -0.68 36 36
MDK -0.087 0.15 -9999 0 -0.32 124 124
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.65 36 36
Syndecan-4/Midkine -0.18 0.19 -9999 0 -0.67 34 34
FZD7 0.005 0.085 -9999 0 -0.85 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 35 35
THBS1 -0.009 0.082 -9999 0 -0.31 28 28
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.68 34 34
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.61 60 60
Syndecan-4/TACI -0.26 0.27 -9999 0 -0.64 114 114
CXCR4 0.011 0.028 -9999 0 -0.31 3 3
cell adhesion -0.077 0.1 -9999 0 -0.46 24 24
Syndecan-4/Dynamin -0.13 0.18 -9999 0 -0.66 34 34
Syndecan-4/TSP1 -0.14 0.18 -9999 0 -0.66 34 34
Syndecan-4/GIPC -0.13 0.18 -9999 0 -0.66 34 34
Syndecan-4/RANTES -0.16 0.23 -9999 0 -0.78 39 39
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.053 0.23 -9999 0 -0.83 32 32
LAMA3 -0.023 0.16 -9999 0 -0.56 26 26
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.003 0.2 -9999 0 -0.78 24 24
Syndecan-4/alpha-Actinin -0.13 0.18 -9999 0 -0.66 34 34
TFPI -0.035 0.2 -9999 0 -0.85 23 23
F2 -0.002 0.04 -9999 0 -0.33 4 4
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.18 0.22 -9999 0 -0.69 43 43
ACTN1 0.012 0.016 -9999 0 -0.31 1 1
TNC -0.12 0.17 -9999 0 -0.33 161 161
Syndecan-4/CXCL12 -0.18 0.24 -9999 0 -0.68 60 60
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.082 0.27 -9999 0 -0.85 45 45
TNFRSF13B -0.22 0.38 -9999 0 -0.85 105 105
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.011 0.043 -9999 0 -0.85 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.66 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 293 293
cell migration -0.021 0.017 -9999 0 -10000 0 0
PRKCD 0.009 0.016 -9999 0 -10000 0 0
vasculogenesis -0.14 0.17 -9999 0 -0.63 34 34
SDC4 -0.15 0.19 -9999 0 -0.71 34 34
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.71 34 34
Syndecan-4/PI-4-5-P2/PKC alpha -0.052 0.036 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.18 -9999 0 -0.66 34 34
MMP9 -0.086 0.24 -9999 0 -0.59 65 65
Rac1/GTP -0.079 0.11 -9999 0 -0.47 24 24
cytoskeleton organization -0.13 0.17 -9999 0 -0.63 34 34
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.21 -9999 0 -0.66 50 50
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.02 0.15 -10000 0 -0.42 23 23
TBX21 -0.12 0.44 -10000 0 -1.1 57 57
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.015 0.02 -10000 0 -10000 0 0
IL12RB1 -0.019 0.12 -10000 0 -0.38 35 35
GADD45B -0.1 0.4 -10000 0 -1 48 48
IL12RB2 -0.016 0.16 -10000 0 -0.76 17 17
GADD45G -0.079 0.35 -10000 0 -0.9 40 40
natural killer cell activation 0.002 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.037 0.16 -10000 0 -0.41 50 50
IL2RA -0.044 0.2 -10000 0 -0.85 20 20
IFNG -0.11 0.29 -10000 0 -0.76 65 65
STAT3 (dimer) -0.075 0.32 -10000 0 -0.74 55 55
HLA-DRB5 -0.043 0.14 -10000 0 -0.35 62 62
FASLG -0.15 0.49 -10000 0 -1.2 58 58
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.88 55 55
CD4 0.001 0.056 -10000 0 -0.32 12 12
SOCS1 0.011 0.028 -10000 0 -0.31 3 3
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.1 0.28 -10000 0 -0.74 60 60
CD3E -0.077 0.25 -10000 0 -0.76 46 46
CD3G -0.15 0.33 -10000 0 -0.82 80 80
IL12Rbeta2/JAK2 -0.001 0.13 -10000 0 -0.66 14 14
CCL3 -0.11 0.43 -10000 0 -1.1 43 43
CCL4 -0.16 0.52 -10000 0 -1.4 53 53
HLA-A 0.011 0.018 -10000 0 -10000 0 0
IL18/IL18R -0.037 0.2 -10000 0 -0.59 39 39
NOS2 -0.093 0.35 -10000 0 -0.83 51 51
IL12/IL12R/TYK2/JAK2/SPHK2 -0.02 0.15 -10000 0 -0.42 22 22
IL1R1 -0.089 0.37 -10000 0 -0.98 42 42
IL4 0.001 0.028 -10000 0 -0.34 1 1
JAK2 0.015 0.02 -10000 0 -10000 0 0
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.25 0.58 -10000 0 -1.2 89 89
RAB7A -0.046 0.3 -10000 0 -0.75 28 28
lysosomal transport -0.041 0.28 -10000 0 -0.7 31 31
FOS -0.41 0.65 -10000 0 -1.3 133 133
STAT4 (dimer) -0.083 0.35 -10000 0 -0.83 51 51
STAT5A (dimer) -0.22 0.36 -10000 0 -0.87 79 79
GZMA -0.1 0.4 -10000 0 -1 47 47
GZMB -0.1 0.39 -10000 0 -0.99 47 47
HLX 0.004 0.053 -10000 0 -0.31 11 11
LCK -0.11 0.42 -10000 0 -1 56 56
TCR/CD3/MHC II/CD4 -0.19 0.36 -10000 0 -0.61 118 118
IL2/IL2R -0.08 0.23 -10000 0 -0.74 36 36
MAPK14 -0.076 0.35 -10000 0 -0.81 54 54
CCR5 -0.1 0.4 -10000 0 -1 48 48
IL1B -0.057 0.24 -10000 0 -0.85 34 34
STAT6 -0.005 0.11 0.23 4 -0.24 29 33
STAT4 -0.031 0.15 -10000 0 -0.45 39 39
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.048 -10000 0 -0.31 9 9
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.001 0.098 -10000 0 -0.57 9 9
CD8A -0.049 0.22 -10000 0 -0.86 29 29
CD8B -0.097 0.28 -10000 0 -0.74 59 59
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.02 0.15 0.41 23 -10000 0 23
IL2RB -0.015 0.14 -10000 0 -0.85 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.071 0.32 -10000 0 -0.75 51 51
IL2RG -0.048 0.2 -10000 0 -0.85 20 20
IL12 -0.055 0.22 -10000 0 -0.67 43 43
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.032 0.17 -10000 0 -0.65 26 26
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.071 0.26 -10000 0 -0.82 42 42
IL12/IL12R/TYK2/JAK2 -0.12 0.47 -10000 0 -1.1 58 58
MAP2K3 -0.078 0.35 -10000 0 -0.8 54 54
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.084 0.36 -10000 0 -0.82 56 56
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.031 0.14 -10000 0 -0.41 41 41
IL18RAP -0.026 0.18 -10000 0 -0.83 20 20
IL12Rbeta1/TYK2 -0.004 0.093 -10000 0 -0.68 3 3
EOMES -0.16 0.45 -10000 0 -1.5 39 39
STAT1 (dimer) -0.14 0.37 -10000 0 -0.77 79 79
T cell proliferation -0.055 0.27 -10000 0 -0.6 50 50
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.028 0.15 -10000 0 -0.42 41 41
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.25 -10000 0 -0.68 54 54
ATF2 -0.072 0.33 -10000 0 -0.75 52 52
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
forebrain development -0.32 0.28 -9999 0 -0.56 214 214
GNAO1 -0.019 0.15 -9999 0 -0.72 16 16
SMO/beta Arrestin2 0.012 0.012 -9999 0 -10000 0 0
SMO 0.008 0.008 -9999 0 -10000 0 0
ARRB2 0.007 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.048 0.044 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.032 -9999 0 -0.52 1 1
GNAI1 0.01 0.005 -9999 0 -10000 0 0
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.25 0.19 -9999 0 -0.51 113 113
SAP30 0.012 0.043 -9999 0 -0.85 1 1
mol:GDP 0.008 0.008 -9999 0 -10000 0 0
MIM/GLI2A -0.009 0.044 -9999 0 -10000 0 0
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GLI2 0.033 0.063 -9999 0 -10000 0 0
GLI3 0.043 0.046 -9999 0 -0.31 7 7
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.013 0 -9999 0 -10000 0 0
Gi family/GTP 0.009 0.065 -9999 0 -0.34 12 12
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.03 0.045 -9999 0 -10000 0 0
GLI2/Su(fu) 0.022 0.059 -9999 0 -10000 0 0
FOXA2 -0.69 0.67 -9999 0 -1.4 203 203
neural tube patterning -0.32 0.28 -9999 0 -0.56 214 214
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.018 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.008 0.044 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.32 0.28 -9999 0 -0.56 214 214
SUFU 0.017 0.017 -9999 0 -10000 0 0
LGALS3 -0.11 0.16 -9999 0 -0.31 149 149
catabolic process 0.064 0.061 -9999 0 -0.4 1 1
GLI3A/CBP -0.2 0.2 -9999 0 -0.39 214 214
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.33 0.29 -9999 0 -0.57 214 214
RAB23 0.007 0.074 -9999 0 -0.85 3 3
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.036 0.077 -9999 0 -10000 0 0
GNAZ 0.01 0.005 -9999 0 -10000 0 0
RBBP4 0.014 0.001 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.037 0.058 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.015 0.055 -9999 0 -10000 0 0
PTCH1 -0.29 0.26 -9999 0 -0.62 113 113
MIM/GLI1 -0.46 0.39 -9999 0 -0.76 212 212
CREBBP -0.2 0.2 -9999 0 -0.39 214 214
Su(fu)/SIN3/HDAC complex 0.057 0.017 -9999 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.044 0.12 -9999 0 -0.55 15 15
alphaM/beta2 Integrin/GPIbA -0.057 0.15 -9999 0 -0.59 24 24
alphaM/beta2 Integrin/proMMP-9 -0.097 0.21 -9999 0 -0.62 47 47
PLAUR -0.095 0.15 -9999 0 -0.31 136 136
HMGB1 0.002 0.024 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.037 0.11 -9999 0 -0.44 20 20
AGER -0.072 0.24 -9999 0 -0.83 36 36
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.007 0.078 -9999 0 -0.31 25 25
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.21 -9999 0 -0.66 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.084 0.25 -9999 0 -0.59 66 66
CYR61 -0.25 0.4 -9999 0 -0.85 124 124
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.076 0.098 -9999 0 -0.45 10 10
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.004 0.11 -9999 0 -0.6 11 11
MYH2 -0.11 0.12 -9999 0 -0.42 34 34
MST1R -0.006 0.12 -9999 0 -0.7 11 11
leukocyte activation during inflammatory response -0.041 0.1 -9999 0 -0.64 5 5
APOB -0.006 0.07 -9999 0 -0.31 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.002 0.089 -9999 0 -0.62 7 7
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.019 0.15 -9999 0 -0.64 20 20
alphaM/beta2 Integrin/CTGF -0.12 0.23 -9999 0 -0.61 69 69
alphaM/beta2 Integrin -0.1 0.12 -9999 0 -0.36 44 44
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.087 0.15 -9999 0 -0.31 125 125
phagocytosis triggered by activation of immune response cell surface activating receptor -0.099 0.12 -9999 0 -0.36 44 44
cell adhesion -0.057 0.15 -9999 0 -0.59 24 24
NFKB1 -0.15 0.31 -9999 0 -0.76 56 56
THY1 0.011 0.028 -9999 0 -0.31 3 3
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.012 0.047 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/LRP/tPA -0.036 0.11 -9999 0 -0.62 8 8
IL6 -0.26 0.48 -9999 0 -1.1 91 91
ITGB2 -0.021 0.091 -9999 0 -0.34 26 26
elevation of cytosolic calcium ion concentration -0.14 0.17 -9999 0 -0.55 31 31
alphaM/beta2 Integrin/JAM2/JAM3 -0.035 0.11 -9999 0 -0.63 9 9
JAM2 0.004 0.086 -9999 0 -0.74 5 5
alphaM/beta2 Integrin/ICAM1 -0.076 0.14 -9999 0 -0.51 25 25
alphaM/beta2 Integrin/uPA/Plg -0.098 0.13 -9999 0 -0.52 20 20
RhoA/GTP -0.11 0.13 -9999 0 -0.43 39 39
positive regulation of phagocytosis -0.074 0.12 -9999 0 -0.49 17 17
Ron/MSP -0.016 0.098 -9999 0 -0.66 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.17 -9999 0 -0.56 31 31
alphaM/beta2 Integrin/uPAR -0.09 0.14 -9999 0 -0.47 31 31
PLAU -0.14 0.16 -9999 0 -10000 0 0
PLAT 0.002 0.075 -9999 0 -0.42 10 10
actin filament polymerization -0.1 0.12 -9999 0 -0.4 34 34
MST1 0.01 0.046 -9999 0 -0.58 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.041 0.1 -9999 0 -0.65 5 5
TNF -0.19 0.41 -9999 0 -1 64 64
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.14 -9999 0 -0.56 20 20
fibrinolysis -0.098 0.13 -9999 0 -0.51 20 20
HCK -0.008 0.08 -9999 0 -0.31 26 26
dendritic cell antigen processing and presentation -0.099 0.12 -9999 0 -0.36 44 44
VTN -0.078 0.26 -9999 0 -0.79 46 46
alphaM/beta2 Integrin/CYR61 -0.21 0.29 -9999 0 -0.6 138 138
LPA -0.003 0.047 -9999 0 -0.31 9 9
LRP1 0.011 0.043 -9999 0 -0.85 1 1
cell migration -0.091 0.21 -9999 0 -0.62 45 45
FN1 -0.22 0.15 -9999 0 -0.31 295 295
alphaM/beta2 Integrin/Thy1 -0.038 0.11 -9999 0 -0.53 11 11
MPO -0.005 0.11 -9999 0 -0.73 9 9
KNG1 -0.013 0.075 -9999 0 -10000 0 0
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.099 0.12 -9999 0 -0.43 27 27
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0.022 -9999 0 -0.31 2 2
CTGF -0.11 0.3 -9999 0 -0.85 59 59
alphaM/beta2 Integrin/Hck -0.048 0.13 -9999 0 -0.55 20 20
ITGAM -0.026 0.12 -9999 0 -0.4 27 27
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.049 0.14 -9999 0 -0.53 25 25
HP -0.077 0.17 -9999 0 -0.34 103 103
leukocyte adhesion -0.1 0.17 -9999 0 -0.64 24 24
SELP -0.004 0.11 -9999 0 -0.61 11 11
IL6-mediated signaling events

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
BCL2L1 -0.055 0.2 -9999 0 -0.62 21 21
CRP -0.06 0.2 -9999 0 -0.66 17 17
cell cycle arrest -0.076 0.23 -9999 0 -0.72 23 23
TIMP1 -0.15 0.2 -9999 0 -0.58 30 30
IL6ST -0.092 0.28 -9999 0 -0.85 49 49
Rac1/GDP -0.087 0.24 -9999 0 -0.58 51 51
AP1 -0.2 0.33 -9999 0 -0.7 114 114
GAB2 0.014 0.001 -9999 0 -10000 0 0
TNFSF11 -0.099 0.22 -9999 0 -0.64 21 21
HSP90B1 0.022 0.041 -9999 0 -10000 0 0
GAB1 0.014 0 -9999 0 -10000 0 0
MAPK14 -0.1 0.31 -9999 0 -0.82 48 48
AKT1 0.055 0.021 -9999 0 -10000 0 0
FOXO1 0.062 0.02 -9999 0 -10000 0 0
MAP2K6 -0.1 0.29 -9999 0 -0.7 53 53
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.077 0.23 -9999 0 -0.63 34 34
MITF -0.089 0.26 -9999 0 -0.57 57 57
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.025 0.006 -9999 0 -10000 0 0
CEBPB 0.022 0.002 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.026 0.078 -9999 0 -10000 0 0
STAT3 -0.088 0.24 -9999 0 -0.78 23 23
STAT1 -0.011 0.022 -9999 0 -10000 0 0
CEBPD -0.055 0.2 -9999 0 -0.68 13 13
PIK3CA 0.013 0.043 -9999 0 -0.85 1 1
PI3K -0.002 0.032 -9999 0 -0.66 1 1
JUN -0.18 0.36 -9999 0 -0.85 93 93
PIAS3/MITF -0.078 0.24 -9999 0 -0.58 47 47
MAPK11 -0.1 0.31 -9999 0 -0.83 47 47
STAT3 (dimer)/FOXO1 -0.005 0.19 -9999 0 -0.59 12 12
GRB2/SOS1/GAB family -0.11 0.19 -9999 0 -0.77 16 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.25 -9999 0 -0.48 92 92
GRB2 0.014 0 -9999 0 -10000 0 0
JAK2 0.013 0 -9999 0 -10000 0 0
LBP -0.061 0.19 -9999 0 -0.58 13 13
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.013 0.005 -9999 0 -10000 0 0
MYC -0.069 0.25 -9999 0 -1 14 14
FGG -0.063 0.2 -9999 0 -0.63 22 22
macrophage differentiation -0.076 0.23 -9999 0 -0.72 23 23
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.19 0.28 -9999 0 -0.56 130 130
JUNB -0.062 0.23 -9999 0 -0.72 24 24
FOS -0.21 0.38 -9999 0 -0.85 106 106
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.099 0.27 -9999 0 -0.54 76 76
STAT1/PIAS1 -0.081 0.23 -9999 0 -0.6 37 37
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.027 -9999 0 -0.32 1 1
STAT3 (dimer) -0.085 0.23 -9999 0 -0.76 23 23
PRKCD -0.064 0.22 -9999 0 -0.64 27 27
IL6R -0.01 0.14 -9999 0 -0.85 11 11
SOCS3 -0.13 0.41 -9999 0 -1.2 46 46
gp130 (dimer)/JAK1/JAK1/LMO4 -0.052 0.19 -9999 0 -0.57 49 49
Rac1/GTP -0.11 0.23 -9999 0 -0.58 51 51
HCK -0.008 0.08 -9999 0 -0.31 26 26
MAPKKK cascade 0.011 0.06 -9999 0 -10000 0 0
bone resorption -0.094 0.21 -9999 0 -0.6 23 23
IRF1 -0.055 0.2 -9999 0 -0.66 15 15
mol:GDP -0.099 0.26 -9999 0 -0.58 59 59
SOS1 0.013 0.001 -9999 0 -10000 0 0
VAV1 -0.1 0.26 -9999 0 -0.6 59 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.31 -9999 0 -0.8 49 49
PTPN11 -0.009 0.018 -9999 0 -10000 0 0
IL6/IL6RA -0.16 0.29 -9999 0 -0.68 96 96
gp130 (dimer)/TYK2/TYK2/LMO4 -0.057 0.19 -9999 0 -0.57 49 49
gp130 (dimer)/JAK2/JAK2/LMO4 -0.057 0.19 -9999 0 -0.57 49 49
IL6 -0.19 0.35 -9999 0 -0.77 104 104
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE -0.095 0.15 -9999 0 -0.33 57 57
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.099 0.26 -9999 0 -0.44 114 114
LMO4 0.011 0.01 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.22 -9999 0 -0.77 23 23
MCL1 0.061 0.019 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.097 0.22 -9999 0 -0.41 122 122
MAP3K8 -0.003 0.1 -9999 0 -0.86 6 6
FOS -0.062 0.17 -9999 0 -0.5 30 30
PRKCA -0.04 0.2 -9999 0 -0.85 24 24
PTPN7 -0.047 0.18 -9999 0 -0.49 48 48
HRAS 0.011 0.023 -9999 0 -0.31 2 2
PRKCB -0.026 0.11 -9999 0 -0.34 42 42
NRAS 0.012 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.01 -9999 0 -10000 0 0
MAPK3 -0.034 0.13 -9999 0 -0.54 15 15
MAP2K1 -0.029 0.16 -9999 0 -0.58 25 25
ELK1 0.008 0.01 -9999 0 -10000 0 0
BRAF -0.049 0.14 -9999 0 -0.58 25 25
mol:GTP -0.001 0.003 -9999 0 -0.006 106 106
MAPK1 -0.034 0.13 -9999 0 -0.54 15 15
RAF1 -0.049 0.14 -9999 0 -0.58 25 25
KRAS 0.012 0.002 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.023 -9999 0 -0.31 2 2
EGFR 0.003 0.095 -9999 0 -0.85 5 5
EGF/EGFR -0.08 0.18 -9999 0 -0.48 66 66
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.073 0.17 -9999 0 -0.48 60 60
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.009 0.051 -9999 0 -0.45 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.8 61 61
EGF/EGFR dimer/SHC -0.086 0.2 -9999 0 -0.57 60 60
mol:GDP -0.072 0.17 -9999 0 -0.48 60 60
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.001 0.097 -9999 0 -0.7 7 7
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.067 0.16 -9999 0 -0.44 60 60
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.068 0.16 -9999 0 -0.45 60 60
FRAP1 -0.036 0.18 -9999 0 -0.46 60 60
EGF/EGFR dimer -0.099 0.23 -9999 0 -0.66 60 60
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.012 0.083 -9999 0 -0.62 7 7
Osteopontin-mediated 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
IKK alpha homodimer -0.034 0.15 -9999 0 -0.49 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.055 0.12 -9999 0 -0.57 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.067 0.15 -9999 0 -0.64 21 21
AP1 -0.26 0.37 -9999 0 -0.88 94 94
ILK -0.038 0.16 -9999 0 -0.52 33 33
bone resorption -0.057 0.14 -9999 0 -0.63 9 9
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.054 0.13 -9999 0 -0.47 33 33
ITGAV 0.011 0.043 -9999 0 -0.85 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.016 0.1 -9999 0 -0.66 10 10
alphaV/beta3 Integrin/Osteopontin -0.072 0.16 -9999 0 -0.58 33 33
MAP3K1 -0.035 0.16 -9999 0 -0.53 33 33
JUN -0.18 0.36 -9999 0 -0.85 93 93
MAPK3 -0.034 0.16 -9999 0 -0.49 33 33
MAPK1 -0.034 0.16 -9999 0 -0.49 33 33
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.027 0.16 -9999 0 -0.52 34 34
ITGB3 -0.014 0.15 -9999 0 -0.84 13 13
NFKBIA -0.027 0.15 -9999 0 -0.47 33 33
FOS -0.21 0.38 -9999 0 -0.85 106 106
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.1 0.18 -9999 0 -0.72 4 4
NF kappa B1 p50/RelA -0.06 0.11 -9999 0 -0.56 6 6
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.022 0.12 -9999 0 -0.69 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.034 0.16 -9999 0 -0.53 33 33
VAV3 -0.028 0.16 -9999 0 -0.5 36 36
MAP3K14 -0.042 0.16 -9999 0 -0.53 33 33
ROCK2 -0.008 0.13 -9999 0 -0.85 10 10
SPP1 -0.083 0.21 -9999 0 -0.43 88 88
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.056 0.14 -9999 0 -0.46 36 36
MMP2 -0.17 0.3 -9999 0 -0.67 90 90
Thromboxane A2 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
TGM2 -0.039 0.12 -10000 0 -0.31 62 62
GNB1/GNG2 -0.044 0.067 -10000 0 -0.2 33 33
AKT1 -0.014 0.1 -10000 0 -0.21 26 26
EGF -0.11 0.3 -10000 0 -0.8 61 61
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.008 0.069 -10000 0 -0.59 1 1
mol:Ca2+ -0.044 0.14 -10000 0 -0.31 59 59
LYN 0.01 0.068 -10000 0 -0.59 1 1
RhoA/GTP -0.031 0.044 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.044 0.16 -10000 0 -0.35 56 56
GNG2 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.02 0.11 -10000 0 -0.55 5 5
G beta5/gamma2 -0.059 0.091 -10000 0 -0.27 38 38
PRKCH -0.052 0.16 -10000 0 -0.36 57 57
DNM1 -0.026 0.18 -10000 0 -0.82 19 19
TXA2/TP beta/beta Arrestin3 -0.016 0.064 -10000 0 -0.31 18 18
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.023 0.17 -10000 0 -0.85 17 17
G12 family/GTP -0.077 0.11 -10000 0 -0.31 56 56
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.1 0.34 14 -10000 0 14
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.22 0.38 -10000 0 -0.85 108 108
mol:IP3 -0.06 0.17 -10000 0 -0.39 59 59
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.087 0.22 -10000 0 -0.53 59 59
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.12 0.2 -10000 0 -0.41 123 123
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.002 0.071 -10000 0 -0.59 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.005 0.085 -10000 0 -0.85 4 4
PRKCB1 -0.06 0.17 -10000 0 -0.39 59 59
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.084 0.23 -10000 0 -0.54 60 60
LCK 0 0.088 -10000 0 -0.5 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.017 0.078 -10000 0 -0.84 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.025 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.077 -10000 0 -0.83 1 1
MAPK14 -0.019 0.11 -10000 0 -0.23 47 47
TGM2/GTP -0.073 0.2 -10000 0 -0.44 59 59
MAPK11 -0.019 0.11 -10000 0 -0.23 37 37
ARHGEF1 -0.015 0.087 -10000 0 -0.2 2 2
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.057 0.18 -10000 0 -0.39 60 60
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.052 0.15 -10000 0 -0.3 64 64
cAMP biosynthetic process -0.059 0.16 -10000 0 -0.36 57 57
Gq family/GTP/EBP50 -0.039 0.12 -10000 0 -0.25 95 95
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.009 0.068 -10000 0 -0.59 1 1
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.02 0.1 -10000 0 -0.31 14 14
VCAM1 -0.038 0.14 -10000 0 -0.3 59 59
TP beta/Gq family/GDP/G beta5/gamma2 -0.02 0.11 -10000 0 -0.55 5 5
platelet activation -0.026 0.15 -10000 0 -0.31 55 55
PGI2/IP -0.007 0.066 -10000 0 -0.67 4 4
PRKACA -0.001 0.1 -10000 0 -0.43 20 20
Gq family/GDP/G beta5/gamma2 -0.022 0.11 -10000 0 -0.52 5 5
TXA2/TP beta/beta Arrestin2 -0.031 0.14 -10000 0 -0.68 18 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.009 0.097 -10000 0 -0.4 20 20
mol:DAG -0.068 0.19 -10000 0 -0.44 58 58
EGFR 0.003 0.095 -10000 0 -0.85 5 5
TXA2/TP alpha -0.082 0.22 -10000 0 -0.5 57 57
Gq family/GTP -0.073 0.13 -10000 0 -0.31 95 95
YES1 0.01 0.068 -10000 0 -0.59 1 1
GNAI2/GTP -0.015 0.07 -10000 0 -0.72 1 1
PGD2/DP -0.028 0.13 -10000 0 -0.67 17 17
SLC9A3R1 0.012 0.023 -10000 0 -0.31 2 2
FYN 0.01 0.068 -10000 0 -0.59 1 1
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.012 0.094 -10000 0 -0.33 30 30
PGK/cGMP -0.15 0.26 -10000 0 -0.58 108 108
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.03 0.087 -10000 0 -0.54 5 5
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.068 0.18 -10000 0 -0.39 71 71
PRKCB -0.061 0.16 -10000 0 -0.37 60 60
PRKCE -0.054 0.17 -10000 0 -0.38 57 57
PRKCD -0.054 0.17 -10000 0 -0.39 57 57
PRKCG -0.059 0.17 -10000 0 -0.4 58 58
muscle contraction -0.074 0.21 -10000 0 -0.49 60 60
PRKCZ -0.044 0.16 -10000 0 -0.35 56 56
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.017 0.079 -10000 0 -0.85 1 1
PRKCQ -0.054 0.17 -10000 0 -0.37 61 61
MAPKKK cascade -0.075 0.2 -10000 0 -0.47 60 60
SELE -0.057 0.17 -10000 0 -0.43 57 57
TP beta/GNAI2/GDP/G beta/gamma -0.017 0.076 -10000 0 -0.83 1 1
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.36 -10000 0 -0.85 92 92
chemotaxis -0.096 0.25 -10000 0 -0.62 59 59
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 0.005 0.085 -10000 0 -0.85 4 4
Rac1/GTP 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.081 0.11 -9999 0 -0.21 169 169
TP53 -0.027 0.032 -9999 0 -10000 0 0
Senescence -0.027 0.032 -9999 0 -10000 0 0
Apoptosis -0.027 0.032 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.052 0.062 -9999 0 -10000 0 0
MDM4 0.013 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.081 0.099 -10000 0 -10000 0 0
CRKL -0.035 0.12 -10000 0 -0.34 25 25
mol:PIP3 -0.018 0.036 0.71 1 -10000 0 1
AKT1 0.002 0.036 0.46 1 -0.56 1 2
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.026 0.11 -10000 0 -10000 0 0
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
HGF/MET/SHIP2 -0.15 0.22 -10000 0 -0.63 62 62
MAP3K5 -0.023 0.12 -10000 0 -0.49 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.13 0.2 -10000 0 -0.58 62 62
AP1 -0.29 0.44 -10000 0 -0.93 124 124
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.26 0.4 -10000 0 -0.86 124 124
STAT3 (dimer) -0.044 0.14 -10000 0 -0.35 62 62
GAB1/CRKL/SHP2/PI3K -0.043 0.089 -10000 0 -0.4 1 1
INPP5D -0.005 0.075 -10000 0 -0.31 23 23
CBL/CRK -0.026 0.11 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.043 -10000 0 -0.85 1 1
ELK1 -0.053 0.063 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.041 0.074 -10000 0 -0.25 25 25
PAK1 0.01 0.034 0.43 1 -0.52 1 2
HGF/MET/RANBP10 -0.15 0.22 -10000 0 -0.63 62 62
HRAS -0.064 0.17 -10000 0 -0.44 62 62
DOCK1 -0.028 0.12 -10000 0 -0.58 2 2
GAB1 -0.046 0.12 -10000 0 -0.31 62 62
CRK -0.035 0.12 -10000 0 -0.34 25 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.12 0.22 -10000 0 -0.62 62 62
JUN -0.18 0.36 -10000 0 -0.85 93 93
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.075 0.1 -10000 0 -0.3 62 62
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.013 0.14 -10000 0 -10000 0 0
GRB2/SHC -0.058 0.088 -10000 0 -10000 0 0
FOS -0.21 0.38 -10000 0 -0.85 106 106
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.053 0.063 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.15 0.22 -10000 0 -0.64 62 62
cell migration -0.058 0.087 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.081 0.099 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.056 0.14 -10000 0 -0.38 62 62
MET/MUC20 -0.085 0.1 -10000 0 -0.21 164 164
RAP1B -0.016 0.1 -10000 0 -10000 0 0
RAP1A -0.016 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.15 0.22 -10000 0 -0.63 62 62
RAF1 -0.053 0.16 -10000 0 -0.46 26 26
STAT3 -0.045 0.14 -10000 0 -0.35 62 62
cell proliferation -0.053 0.18 -10000 0 -0.47 62 62
RPS6KB1 -0.017 0.041 -10000 0 -10000 0 0
MAPK3 -0.053 0.058 -10000 0 -10000 0 0
MAPK1 -0.053 0.058 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.11 -10000 0 -0.51 7 7
SRC -0.045 0.14 -10000 0 -0.4 25 25
PI3K -0.059 0.091 -10000 0 -0.48 1 1
MET/Glomulin -0.065 0.095 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.041 0.15 -10000 0 -0.43 26 26
MET -0.12 0.16 -10000 0 -0.31 164 164
MAP4K1 -0.031 0.12 -10000 0 -0.34 30 30
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.041 0.15 -10000 0 -0.43 26 26
BAD 0.01 0.034 0.43 1 -0.52 1 2
MAP2K4 -0.013 0.11 -10000 0 -0.44 5 5
SHP2/GRB2/SOS1/GAB1 -0.06 0.094 -10000 0 -10000 0 0
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.053 0.1 -10000 0 -0.33 25 25
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.12 0.31 -10000 0 -0.85 62 62
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.045 0.11 -10000 0 -0.34 25 25
PDPK1 -0.008 0.04 0.53 1 -0.6 1 2
HGF/MET/SHIP -0.16 0.22 -10000 0 -0.63 62 62
FAS signaling pathway (CD95)

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
SPTAN1 0.023 0.074 0.3 26 -10000 0 26
RFC1 0.023 0.074 0.3 26 -10000 0 26
PRKDC 0.023 0.074 0.3 26 -10000 0 26
RIPK1 0.014 0.005 -10000 0 -10000 0 0
CASP7 -0.015 0.047 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.033 0.11 0.26 2 -0.38 31 33
MAP2K4 -0.031 0.16 -10000 0 -0.54 15 15
mol:ceramide -0.029 0.15 -10000 0 -0.5 31 31
GSN 0.023 0.074 0.3 26 -10000 0 26
FASLG/FAS/FADD/FAF1/Caspase 8 -0.026 0.14 -10000 0 -0.48 31 31
FAS 0.01 0.006 -10000 0 -10000 0 0
BID -0.035 0.083 0.32 3 -10000 0 3
MAP3K1 -0.001 0.1 -10000 0 -10000 0 0
MAP3K7 0.01 0.006 -10000 0 -10000 0 0
RB1 0.023 0.074 0.3 26 -10000 0 26
CFLAR 0.014 0.005 -10000 0 -10000 0 0
HGF/MET -0.15 0.22 -10000 0 -0.64 63 63
ARHGDIB 0.019 0.079 0.3 26 -10000 0 26
FADD 0.01 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.023 0.074 -10000 0 -0.3 26 26
NFKB1 -0.055 0.09 -10000 0 -0.29 15 15
MAPK8 -0.063 0.22 -10000 0 -0.46 83 83
DFFA 0.023 0.074 0.3 26 -10000 0 26
DNA fragmentation during apoptosis 0.023 0.074 0.3 26 -10000 0 26
FAS/FADD/MET -0.064 0.078 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.004 0.095 -10000 0 -0.85 3 3
FAF1 0.011 0.007 -10000 0 -10000 0 0
PARP1 0.023 0.074 0.3 26 -10000 0 26
DFFB 0.023 0.074 0.3 26 -10000 0 26
CHUK -0.047 0.079 -10000 0 -10000 0 0
FASLG -0.065 0.23 -10000 0 -0.71 43 43
FAS/FADD 0 0.001 -10000 0 -10000 0 0
HGF -0.12 0.31 -10000 0 -0.85 62 62
LMNA 0.021 0.068 0.27 26 -10000 0 26
CASP6 0.023 0.074 0.3 26 -10000 0 26
CASP10 0.01 0.006 -10000 0 -10000 0 0
CASP3 0.027 0.09 0.35 29 -10000 0 29
PTPN13 0.009 0.06 -10000 0 -0.85 2 2
CASP8 0.009 0.048 0.46 3 -10000 0 3
IL6 -0.28 0.58 -10000 0 -1.4 88 88
MET -0.12 0.16 -10000 0 -0.31 164 164
ICAD/CAD 0.021 0.069 0.28 26 -10000 0 26
FASLG/FAS/FADD/FAF1/Caspase 10 -0.03 0.16 -10000 0 -0.5 31 31
activation of caspase activity by cytochrome c -0.035 0.083 0.32 3 -10000 0 3
PAK2 0.023 0.074 0.3 26 -10000 0 26
BCL2 -0.041 0.21 -10000 0 -0.85 26 26
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.12 0.11 -9999 0 -0.67 6 6
EPHB2 0.007 0.074 -9999 0 -0.85 3 3
Syndecan-2/TACI -0.14 0.27 -9999 0 -0.59 108 108
LAMA1 -0.053 0.23 -9999 0 -0.83 32 32
Syndecan-2/alpha2 ITGB1 -0.073 0.11 -9999 0 -0.49 18 18
HRAS 0.012 0.023 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.069 -9999 0 -0.57 6 6
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.031 0.08 -9999 0 -0.5 9 9
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.008 0.063 -9999 0 -0.52 6 6
LAMA3 -0.023 0.16 -9999 0 -0.56 26 26
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.009 0.06 -9999 0 -0.85 2 2
Syndecan-2/MMP2 0.01 0.093 -9999 0 -0.57 10 10
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.082 0.099 -9999 0 -10000 0 0
dendrite morphogenesis 0.013 0.087 -9999 0 -0.57 9 9
Syndecan-2/GM-CSF -0.11 0.1 -9999 0 -0.6 6 6
determination of left/right symmetry 0.011 0.081 -9999 0 -0.65 6 6
Syndecan-2/PKC delta 0.017 0.071 -9999 0 -0.57 6 6
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.087 0.094 -9999 0 -0.54 6 6
MAPK1 -0.087 0.094 -9999 0 -0.54 6 6
Syndecan-2/RACK1 -0.008 0.06 -9999 0 -0.49 6 6
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.011 0.081 -9999 0 -0.65 6 6
ITGA2 -0.12 0.16 -9999 0 -0.31 166 166
MAPK8 0.024 0.088 -9999 0 -0.56 9 9
Syndecan-2/alpha2/beta1 Integrin -0.091 0.15 -9999 0 -0.55 34 34
Syndecan-2/Kininogen -0.007 0.081 -9999 0 -0.57 6 6
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.061 -9999 0 -0.46 6 6
Syndecan-2/CASK/Protein 4.1 -0.008 0.063 -9999 0 -0.52 6 6
extracellular matrix organization 0.014 0.074 -9999 0 -0.56 6 6
actin cytoskeleton reorganization -0.12 0.11 -9999 0 -0.66 6 6
Syndecan-2/Caveolin-2/Ras -0.011 0.08 -9999 0 -0.59 7 7
Syndecan-2/Laminin alpha3 -0.007 0.12 -9999 0 -0.57 18 18
Syndecan-2/RasGAP -0.007 0.056 -9999 0 -0.47 6 6
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.013 0.087 -9999 0 -0.57 9 9
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.037 0.06 -9999 0 -0.44 6 6
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.22 0.38 -9999 0 -0.85 105 105
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.082 0.099 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.017 0.071 -9999 0 -0.57 6 6
TGFB1 0.008 0.039 -9999 0 -0.31 6 6
CASP3 0.027 0.066 -9999 0 -0.51 6 6
FN1 -0.22 0.15 -9999 0 -0.31 295 295
Syndecan-2/IL8 -0.04 0.13 -9999 0 -0.57 14 14
SDC2 0.011 0.081 -9999 0 -0.66 6 6
KNG1 -0.013 0.075 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.017 0.071 -9999 0 -0.57 6 6
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 277 277
Syndecan-2/TGFB1 0.014 0.074 -9999 0 -0.57 6 6
Syndecan-2/Syntenin/PI-4-5-P2 -0.008 0.063 -9999 0 -0.52 6 6
Syndecan-2/Ezrin -0.008 0.062 -9999 0 -0.52 6 6
PRKACA 0.027 0.066 -9999 0 -0.51 6 6
angiogenesis -0.04 0.13 -9999 0 -0.57 14 14
MMP2 0.002 0.089 -9999 0 -0.62 7 7
IL8 -0.084 0.18 -9999 0 -0.35 108 108
calcineurin-NFAT signaling pathway -0.14 0.27 -9999 0 -0.58 108 108
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 -0.11 0.19 -9999 0 -0.46 56 56
IKBKB -0.02 0.071 -9999 0 -0.28 5 5
AKT1 -0.044 0.1 -9999 0 -0.27 19 19
IKBKG -0.019 0.074 -9999 0 -0.29 5 5
CALM1 -0.037 0.088 -9999 0 -0.36 2 2
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
MAP3K1 -0.079 0.19 -9999 0 -0.66 15 15
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.047 0.092 -9999 0 -0.38 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.083 0.14 -9999 0 -0.28 99 99
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.18 0.25 -9999 0 -0.54 119 119
CD22 -0.16 0.23 -9999 0 -0.53 91 91
CAMK2G -0.027 0.083 -9999 0 -0.33 2 2
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.005 0.075 -9999 0 -0.31 23 23
SHC/GRB2/SOS1 -0.1 0.16 -9999 0 -10000 0 0
GO:0007205 -0.048 0.093 -9999 0 -0.39 2 2
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.038 0.089 -9999 0 -0.36 2 2
NFATC1 -0.073 0.16 -9999 0 -0.56 16 16
B-cell antigen/BCR complex -0.18 0.25 -9999 0 -0.54 119 119
PAG1/CSK -0.002 0.032 -9999 0 -0.66 1 1
NFKBIB 0.002 0.027 -9999 0 -0.1 1 1
HRAS -0.041 0.1 -9999 0 -0.35 2 2
NFKBIA 0.002 0.027 -9999 0 -0.1 1 1
NF-kappa-B/RelA/I kappa B beta 0.008 0.023 -9999 0 -10000 0 0
RasGAP/Csk -0.15 0.21 -9999 0 -0.52 83 83
mol:GDP -0.043 0.085 -9999 0 -0.35 2 2
PTEN 0.011 0.043 -9999 0 -0.85 1 1
CD79B -0.029 0.11 -9999 0 -0.31 53 53
NF-kappa-B/RelA/I kappa B alpha 0.008 0.022 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.092 0.18 -9999 0 -0.44 67 67
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.054 0.09 -9999 0 -0.39 2 2
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.15 0.22 -9999 0 -0.49 108 108
CHUK -0.019 0.074 -9999 0 -0.28 6 6
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.069 0.099 -9999 0 -0.51 8 8
PTPN6 -0.15 0.22 -9999 0 -0.5 91 91
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.003 0.037 -9999 0 -0.14 18 18
VAV2 -0.14 0.2 -9999 0 -0.48 63 63
ubiquitin-dependent protein catabolic process 0.007 0.026 -9999 0 -0.095 1 1
BTK -0.016 0.15 -9999 0 -1.2 6 6
CD19 -0.16 0.21 -9999 0 -0.46 87 87
MAP4K1 -0.02 0.13 -9999 0 -0.44 30 30
CD72 0.011 0.028 -9999 0 -0.31 3 3
PAG1 0.011 0.043 -9999 0 -0.85 1 1
MAPK14 -0.059 0.16 -9999 0 -0.53 15 15
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.037 0.091 -9999 0 -0.33 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.068 0.18 -9999 0 -0.44 64 64
RAF1 -0.031 0.097 -9999 0 -0.33 1 1
RasGAP/p62DOK/SHIP -0.15 0.21 -9999 0 -0.5 82 82
CD79A -0.2 0.32 -9999 0 -0.53 163 163
re-entry into mitotic cell cycle -0.081 0.13 -9999 0 -0.28 97 97
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.011 0.086 -9999 0 -10000 0 0
MAPK1 -0.011 0.086 -9999 0 -10000 0 0
CD72/SHP1 -0.11 0.22 -9999 0 -0.58 45 45
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.062 0.17 -9999 0 -0.54 18 18
actin cytoskeleton organization -0.093 0.18 -9999 0 -0.7 10 10
NF-kappa-B/RelA 0.022 0.043 -9999 0 -10000 0 0
Calcineurin -0.037 0.061 -9999 0 -10000 0 0
PI3K -0.14 0.17 -9999 0 -0.54 28 28
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.058 0.088 -9999 0 -0.35 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.25 -9999 0 -1 18 18
DAPP1 -0.14 0.27 -9999 0 -1.3 14 14
cytokine secretion -0.068 0.15 -9999 0 -0.51 16 16
mol:DAG -0.054 0.09 -9999 0 -0.39 2 2
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.021 0.092 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.18 0.25 -9999 0 -0.61 83 83
mol:PI-3-4-5-P3 -0.1 0.12 -9999 0 -0.37 26 26
ETS1 -0.018 0.078 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.18 -9999 0 -0.48 67 67
B-cell antigen/BCR complex/LYN -0.13 0.21 -9999 0 -0.51 72 72
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
RAC1 -0.1 0.2 -9999 0 -0.77 10 10
B-cell antigen/BCR complex/LYN/SYK -0.16 0.23 -9999 0 -0.56 84 84
CARD11 -0.078 0.13 -9999 0 -0.55 11 11
FCGR2B -0.032 0.19 -9999 0 -0.76 24 24
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex -0.001 0.035 -9999 0 -0.14 1 1
PTPRC -0.035 0.18 -9999 0 -0.6 32 32
PDPK1 -0.046 0.1 -9999 0 -0.27 19 19
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.024 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0 0.1 -9999 0 -0.77 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.16 -9999 0 -0.28 236 236
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.01 0.032 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.048 0.067 -9999 0 -0.28 3 3
PRKG1 -0.22 0.38 -9999 0 -0.85 108 108
DUSP8 0.002 0.083 -9999 0 -0.49 9 9
PGK/cGMP/p38 alpha -0.16 0.21 -9999 0 -0.48 110 110
apoptosis -0.046 0.065 -9999 0 -0.29 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.32 -9999 0 -0.85 65 65
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.062 0.12 -9999 0 -0.36 9 9
BLK -0.26 0.39 -9999 0 -0.78 143 143
HCK -0.008 0.08 -9999 0 -0.31 26 26
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.009 0.048 -9999 0 -0.85 1 1
TRAF6/MEKK3 -0.001 0.026 -9999 0 -0.54 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.09 -9999 0 -0.3 3 3
positive regulation of innate immune response -0.06 0.13 -9999 0 -0.39 7 7
LCK -0.009 0.11 -9999 0 -0.45 20 20
p38alpha-beta/MKP7 -0.051 0.13 -9999 0 -0.38 6 6
p38alpha-beta/MKP5 -0.053 0.13 -9999 0 -0.49 4 4
PGK/cGMP -0.18 0.29 -9999 0 -0.67 108 108
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.48 68 68
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.49 0.43 -9999 0 -0.85 236 236
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.015 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.012 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.016 0.065 -9999 0 -0.58 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.023 -9999 0 -0.31 2 2
GRK1 -0.072 0.26 -9999 0 -0.84 41 41
CNG Channel -0.028 0.088 -9999 0 -0.6 5 5
mol:Na + -0.025 0.09 -9999 0 -0.5 8 8
mol:ADP -0.072 0.26 -9999 0 -0.84 41 41
RGS9-1/Gbeta5/R9AP -0.095 0.22 -9999 0 -0.58 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.026 0.093 -9999 0 -0.62 3 3
CNGB1 -0.001 0.063 -9999 0 -0.31 16 16
RDH5 -0.2 0.16 -9999 0 -0.31 264 264
SAG 0.002 0.016 -9999 0 -0.31 1 1
mol:Ca2+ 0.014 0.096 -9999 0 -0.84 1 1
Na + (4 Units) -0.023 0.083 -9999 0 -0.8 1 1
RGS9 -0.077 0.26 -9999 0 -0.83 44 44
GNB1/GNGT1 -0.003 0.026 -9999 0 -10000 0 0
GNAT1/GDP -0.084 0.19 -9999 0 -0.51 66 66
GUCY2D -0.011 0.12 -9999 0 -0.48 20 20
GNGT1 -0.005 0.041 -9999 0 -0.31 7 7
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.003 0.068 -9999 0 -0.5 3 3
mol:11-cis-retinal -0.2 0.16 -9999 0 -0.31 264 264
mol:cGMP -0.017 0.078 -9999 0 -0.5 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.099 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.001 0.1 -9999 0 -0.58 10 10
Metarhodopsin II -0.053 0.16 -9999 0 -0.54 40 40
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.018 0.082 -9999 0 -0.53 9 9
RGS9BP -0.042 0.21 -9999 0 -0.85 26 26
Metarhodopsin II/Transducin 0.01 0.016 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.048 -9999 0 -0.54 3 3
PDE6A/B -0.012 0.048 -9999 0 -10000 0 0
mol:Pi -0.095 0.22 -9999 0 -0.58 66 66
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.024 -9999 0 -10000 0 0
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.009 0.078 -9999 0 -10000 0 0
PDE6G -0.013 0.11 -9999 0 -0.85 3 3
RHO 0.006 0.017 -9999 0 -0.31 1 1
PDE6 -0.094 0.19 -9999 0 -0.5 68 68
GUCA1A 0.005 0.028 -9999 0 -0.31 3 3
GC2/GCAP Family -0.005 0.048 -9999 0 -0.54 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.007 0.074 -9999 0 -0.85 3 3
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.014 0.014 -9999 0 -10000 0 0
REL -0.024 0.19 -9999 0 -0.85 20 20
HDAC7 -0.024 0.12 -9999 0 -0.57 9 9
JUN -0.19 0.36 -9999 0 -0.85 93 93
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B 0.012 0.003 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 0.001 0.084 -9999 0 -0.67 6 6
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.037 0.13 -9999 0 -0.61 9 9
MAP2K6 -0.006 0.11 -9999 0 -0.78 7 7
BRM/BAF57 -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 0.008 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.011 0.057 -9999 0 -10000 0 0
NCOA2 -0.057 0.22 -9999 0 -0.85 30 30
CEBPA 0.006 0.085 -9999 0 -0.85 4 4
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.061 0.14 -9999 0 -0.47 11 11
NR0B1 -0.002 0.038 -9999 0 -0.31 6 6
EGR1 -0.18 0.36 -9999 0 -0.86 89 89
RXRs/9cRA -0.13 0.06 -9999 0 -0.53 3 3
AR/RACK1/Src -0.11 0.14 -9999 0 -0.61 9 9
AR/GR -0.12 0.19 -9999 0 -0.35 122 122
GNB2L1 0.006 0.007 -9999 0 -10000 0 0
PKN1 0.012 0.003 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 0.007 0.059 -9999 0 -0.66 3 3
T-DHT/AR/TIF2/CARM1 -0.11 0.2 -9999 0 -0.65 35 35
SRC 0.006 0.083 -9999 0 -0.5 9 9
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.39 0.57 -9999 0 -1.3 111 111
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.046 0.12 -9999 0 -0.63 9 9
TMPRSS2 -0.056 0.31 -9999 0 -1.3 25 25
RXRG -0.28 0.12 -9999 0 -0.32 359 359
mol:9cRA -0.002 0.002 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.006 0.007 -9999 0 -10000 0 0
NR2C2 0.004 0.085 -9999 0 -0.85 4 4
KLK2 -0.48 0.43 -9999 0 -0.84 235 235
AR -0.15 0.2 -9999 0 -0.38 172 172
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.022 0.014 -9999 0 -10000 0 0
SRY 0.009 0.014 -9999 0 -10000 0 0
GATA2 0.012 0.016 -9999 0 -0.31 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.016 0.058 -9999 0 -0.32 13 13
T-DHT/AR/RACK1/Src -0.069 0.12 -9999 0 -0.62 9 9
positive regulation of transcription 0.012 0.016 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.004 -9999 0 -10000 0 0
NCOA1 0.012 0.009 -9999 0 -10000 0 0
SPDEF -0.026 0.1 -9999 0 -0.32 44 44
T-DHT/AR/TIF2 -0.043 0.13 -9999 0 -0.42 29 29
T-DHT/AR/Hsp90 -0.048 0.12 -9999 0 -0.63 9 9
GSK3B 0.009 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT 0.003 0.087 -9999 0 -0.54 9 9
SIRT1 0.013 0.001 -9999 0 -10000 0 0
ZMIZ2 0.022 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.02 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.067 0.11 -9999 0 -0.63 9 9
CREBBP 0.012 0.003 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.06 0.17 -9999 0 -0.57 37 37
MAP4K1 -0.02 0.13 -9999 0 -0.44 30 30
MAP3K8 0 0.1 -9999 0 -0.85 6 6
PRKCB -0.023 0.11 -9999 0 -0.34 42 42
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.011 0.11 -9999 0 -0.57 5 5
JUN -0.1 0.24 -9999 0 -0.51 97 97
MAP3K7 0.011 0.11 -9999 0 -0.57 5 5
GRAP2 -0.046 0.22 -9999 0 -0.8 30 30
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.11 -9999 0 -0.54 6 6
LAT 0.004 0.086 -9999 0 -0.74 5 5
LCP2 0.007 0.045 -9999 0 -0.31 8 8
MAPK8 0.009 0.092 -9999 0 -0.74 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.002 0.12 -9999 0 -0.38 28 28
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.056 0.16 -9999 0 -0.54 37 37
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.036 -9999 0 -10000 0 0
VDR 0.012 0.016 -9999 0 -0.31 1 1
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.057 0.1 -9999 0 -0.58 2 2
RXRs/LXRs/DNA/Oxysterols -0.046 0.15 -9999 0 -0.45 47 47
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.025 0.073 -9999 0 -0.34 16 16
RXRs/NUR77 -0.27 0.26 -9999 0 -0.66 123 123
RXRs/PPAR -0.053 0.062 -9999 0 -0.4 8 8
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.011 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.012 0.079 -9999 0 -0.51 10 10
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0.016 -9999 0 -0.31 1 1
RARs/RARs/DNA/9cRA -0.012 0.077 -9999 0 -0.5 10 10
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.054 0.03 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.025 0.073 -9999 0 -0.34 16 16
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.011 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.081 -9999 0 -0.6 3 3
NR1H4 0 0.035 -9999 0 -0.31 5 5
RXRs/LXRs/DNA -0.097 0.089 -9999 0 -0.59 3 3
NR1H2 0.015 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.1 0.067 -9999 0 -0.54 3 3
NR4A1 -0.24 0.39 -9999 0 -0.85 122 122
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.046 0.047 -9999 0 -0.32 3 3
RXRG -0.28 0.12 -9999 0 -0.32 359 359
RXR alpha/CCPG 0 0.003 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.014 0.014 -9999 0 -10000 0 0
THRB 0 0.1 -9999 0 -0.85 6 6
PPARG -0.001 0.1 -9999 0 -0.58 10 10
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.41 -9999 0 -1.3 47 47
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.046 0.15 -9999 0 -0.45 47 47
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.008 0.13 -9999 0 -0.85 10 10
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.46 139 139
SREBF1 -0.036 0.14 -9999 0 -0.63 2 2
RXRs/RXRs/DNA/9cRA -0.12 0.081 -9999 0 -0.6 3 3
ABCA1 -0.035 0.14 -9999 0 -0.63 2 2
RARs/THRs -0.019 0.094 -9999 0 -0.48 16 16
RXRs/FXR -0.12 0.071 -9999 0 -0.57 3 3
BCL2 -0.042 0.21 -9999 0 -0.85 26 26
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.008 0.072 -9999 0 -0.66 5 5
alphaV beta3 Integrin -0.019 0.11 -9999 0 -0.61 13 13
PTK2 0.013 0.16 -9999 0 -0.55 15 15
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.028 0.11 -9999 0 -0.31 51 51
SRC 0.012 0.016 -9999 0 -0.31 1 1
CDKN1B -0.07 0.19 -9999 0 -0.63 41 41
VEGFA 0.009 0.06 -9999 0 -0.85 2 2
ILK -0.07 0.19 -9999 0 -0.63 41 41
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.065 0.18 -9999 0 -0.59 41 41
PTK2B 0.018 0.12 -9999 0 -0.54 17 17
alphaV/beta3 Integrin/JAM-A -0.067 0.17 -9999 0 -0.5 53 53
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.02 0.11 -9999 0 -0.61 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.17 0.27 -9999 0 -0.56 122 122
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.12 -9999 0 -0.55 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.11 -9999 0 -0.61 13 13
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.23 0.26 -9999 0 -0.58 129 129
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
alphaV/beta3 Integrin/Osteopontin -0.073 0.17 -9999 0 -0.6 33 33
RPS6KB1 -0.2 0.25 -9999 0 -0.6 88 88
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.096 0.16 -9999 0 -0.8 13 13
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.096 0.16 -9999 0 -0.8 13 13
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.037 0.16 -9999 0 -0.66 23 23
cell adhesion -0.031 0.1 -9999 0 -0.56 13 13
ANGPTL3 0.006 0.017 -9999 0 -0.31 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.063 -9999 0 -0.57 5 5
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.043 -9999 0 -0.85 1 1
ITGB3 -0.014 0.15 -9999 0 -0.85 13 13
IGF1 -0.18 0.36 -9999 0 -0.82 94 94
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.019 0.11 -9999 0 -0.6 13 13
apoptosis 0.011 0.042 -9999 0 -0.85 1 1
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.019 0.11 -9999 0 -0.61 13 13
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.035 0.13 -9999 0 -0.63 16 16
CSF1 0.003 0.095 -9999 0 -0.85 5 5
PIK3C2A -0.07 0.19 -9999 0 -0.63 41 41
PI4 Kinase/Pyk2 -0.06 0.15 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.024 0.12 -9999 0 -0.58 17 17
FAK1/Vinculin 0.022 0.13 -9999 0 -0.51 6 6
alphaV beta3/Integrin/ppsTEM5 -0.019 0.11 -9999 0 -0.61 13 13
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.078 0.26 -9999 0 -0.79 46 46
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.039 0.12 -9999 0 -0.61 13 13
alphaV/beta3 Integrin/TGFBR2 -0.021 0.11 -9999 0 -0.61 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.008 0.062 -9999 0 -0.52 6 6
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.018 0.1 -9999 0 -0.56 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 295 295
alphaV/beta3 Integrin/Pyk2 -0.022 0.11 -9999 0 -0.54 17 17
SDC1 0.011 0.028 -9999 0 -0.31 3 3
VAV3 0.029 0.081 -9999 0 -0.48 10 10
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.078 0.26 -9999 0 -0.85 43 43
FAK1/Paxillin 0.022 0.13 -9999 0 -0.51 6 6
cell migration 0.032 0.12 -9999 0 -0.46 6 6
ITGAV 0.011 0.043 -9999 0 -0.85 1 1
PI3K -0.061 0.16 -9999 0 -0.46 53 53
SPP1 -0.083 0.21 -9999 0 -0.44 88 88
KDR 0.007 0.074 -9999 0 -0.85 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.011 0.043 -9999 0 -0.85 1 1
COL4A3 -0.014 0.15 -9999 0 -0.85 13 13
angiogenesis -0.087 0.19 -9999 0 -0.62 31 31
Rac1/GTP -0.011 0.068 -9999 0 -0.44 10 10
EDIL3 -0.017 0.12 -9999 0 -0.38 31 31
cell proliferation -0.021 0.11 -9999 0 -0.6 14 14
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.045 0.15 -9999 0 -0.54 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.022 0.041 -9999 0 -10000 0 0
AP1 -0.26 0.38 -9999 0 -0.73 144 144
mol:PIP3 -0.044 0.14 -9999 0 -0.47 32 32
AKT1 -0.028 0.095 -9999 0 -0.56 3 3
PTK2B 0.001 0.084 -9999 0 -0.27 33 33
RHOA 0.031 0.046 -9999 0 -0.27 1 1
PIK3CB 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.073 -9999 0 -10000 0 0
MAGI3 0.011 0.043 -9999 0 -0.85 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.015 0.14 -9999 0 -0.45 33 33
HRAS/GDP -0.001 0.015 -9999 0 -0.21 2 2
positive regulation of microtubule depolymerization 0.009 0.086 -9999 0 -0.34 8 8
NF kappa B1 p50/RelA -0.048 0.12 -9999 0 -0.54 7 7
endothelial cell migration -0.027 0.2 -9999 0 -0.64 34 34
ADCY4 -0.014 0.19 -9999 0 -0.63 33 33
ADCY5 -0.048 0.21 -9999 0 -0.65 36 36
ADCY6 -0.014 0.19 -9999 0 -0.63 33 33
ADCY7 -0.014 0.19 -9999 0 -0.63 33 33
ADCY1 -0.017 0.2 -9999 0 -0.64 33 33
ADCY2 -0.038 0.21 -9999 0 -0.67 34 34
ADCY3 -0.014 0.19 -9999 0 -0.63 33 33
ADCY8 -0.056 0.19 -9999 0 -0.66 34 34
ADCY9 -0.014 0.19 -9999 0 -0.63 33 33
GSK3B 0.009 0.08 -9999 0 -0.3 7 7
arachidonic acid secretion -0.007 0.18 -9999 0 -0.54 39 39
GNG2 0.013 0.001 -9999 0 -10000 0 0
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.04 0.2 -9999 0 -0.61 44 44
HRAS 0.012 0.023 -9999 0 -0.31 2 2
NFKBIA 0.012 0.076 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.032 0.097 -9999 0 -0.98 4 4
JUN -0.18 0.36 -9999 0 -0.85 93 93
LPA/LPA2/NHERF2 -0.001 0.006 -9999 0 -10000 0 0
TIAM1 -0.042 0.12 -9999 0 -1.2 4 4
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:IP3 0.006 0.074 -9999 0 -10000 0 0
PLCB3 0.03 0.007 -9999 0 -10000 0 0
FOS -0.21 0.38 -9999 0 -0.85 106 106
positive regulation of mitosis -0.007 0.18 -9999 0 -0.54 39 39
LPA/LPA1-2-3 -0.052 0.16 -9999 0 -0.55 33 33
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.004 0.11 -9999 0 -0.36 33 33
GNAZ -0.022 0.17 -9999 0 -0.59 34 34
EGFR/PI3K-beta/Gab1 -0.046 0.14 -9999 0 -0.51 28 28
positive regulation of dendritic cell cytokine production -0.051 0.15 -9999 0 -0.55 33 33
LPA/LPA2/MAGI-3 -0.002 0.031 -9999 0 -0.62 1 1
ARHGEF1 -0.002 0.15 -9999 0 -0.5 33 33
GNAI2 -0.022 0.17 -9999 0 -0.59 34 34
GNAI3 -0.022 0.17 -9999 0 -0.59 34 34
GNAI1 -0.022 0.17 -9999 0 -0.59 34 34
LPA/LPA3 -0.01 0.044 -9999 0 -0.27 1 1
LPA/LPA2 -0.001 0.008 -9999 0 -10000 0 0
LPA/LPA1 -0.057 0.19 -9999 0 -0.68 34 34
HB-EGF/EGFR -0.057 0.18 -9999 0 -0.57 39 39
HBEGF -0.062 0.2 -9999 0 -0.64 36 36
mol:DAG 0.006 0.074 -9999 0 -10000 0 0
cAMP biosynthetic process -0.027 0.2 -9999 0 -0.58 43 43
NFKB1 0.013 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
GNB1 0.013 0.001 -9999 0 -10000 0 0
LYN 0.012 0.076 -9999 0 -10000 0 0
GNAQ 0.019 0.029 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.004 0.067 -9999 0 -0.31 18 18
LPAR1 -0.054 0.24 -9999 0 -0.86 33 33
IL8 -0.13 0.2 -9999 0 -0.48 52 52
PTK2 -0.011 0.16 -9999 0 -0.52 33 33
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.016 0.14 -9999 0 -0.46 33 33
EGFR 0.002 0.095 -9999 0 -0.85 5 5
PLCG1 -0.013 0.084 -9999 0 -0.29 11 11
PLD2 -0.011 0.16 -9999 0 -0.52 33 33
G12/G13 -0.045 0.15 -9999 0 -0.54 33 33
PI3K-beta -0.033 0.11 -9999 0 -0.67 3 3
cell migration -0.016 0.058 -9999 0 -0.26 7 7
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.003 0.11 -9999 0 -0.36 33 33
HRAS/GTP -0.019 0.19 -9999 0 -0.6 33 33
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.084 0.25 -9999 0 -0.59 66 66
PRKCE 0.007 0.074 -9999 0 -0.85 3 3
PRKCD 0.014 0.071 -9999 0 -10000 0 0
Gi(beta/gamma) -0.008 0.18 -9999 0 -0.59 33 33
mol:LPA 0.003 0.016 -9999 0 -0.22 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.031 0.13 -9999 0 -0.46 33 33
MAPKKK cascade -0.007 0.18 -9999 0 -0.54 39 39
contractile ring contraction involved in cytokinesis 0.031 0.046 -9999 0 -0.27 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.086 0.2 -9999 0 -0.45 92 92
GNA15 0.009 0.055 -9999 0 -0.25 9 9
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.009 0.088 -9999 0 -0.36 7 7
GNA11 0.014 0.054 -9999 0 -0.44 4 4
Rac1/GTP -0.033 0.1 -9999 0 -1.1 4 4
MMP2 -0.027 0.2 -9999 0 -0.64 34 34
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.036 0.12 -10000 0 -0.52 22 22
ER alpha/Gai/GDP/Gbeta gamma 0.007 0.15 -10000 0 -0.57 19 19
AKT1 -0.011 0.2 -10000 0 -0.87 20 20
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.012 0.2 -10000 0 -0.88 20 20
mol:Ca2+ -0.097 0.23 -10000 0 -0.5 94 94
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.064 0.18 -10000 0 -0.6 37 37
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.009 0.19 0.82 20 -10000 0 20
RhoA/GTP -0.027 0.092 -10000 0 -0.43 19 19
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.035 0.13 -10000 0 -0.61 19 19
regulation of stress fiber formation -0.02 0.1 0.44 2 -10000 0 2
E2/ERA-ERB (dimer) -0.043 0.14 -10000 0 -0.6 22 22
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.035 0.12 -10000 0 -0.53 19 19
pseudopodium formation 0.02 0.1 -10000 0 -0.44 2 2
E2/ER alpha (dimer)/PELP1 -0.038 0.13 -10000 0 -0.58 19 19
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.013 0 -10000 0 -10000 0 0
GNAO1 -0.015 0.15 -10000 0 -0.72 16 16
HRAS 0.012 0.023 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.15 -10000 0 -0.62 19 19
E2/ER beta (dimer) -0.007 0.066 -10000 0 -0.67 4 4
mol:GDP -0.037 0.13 -10000 0 -0.58 22 22
mol:NADP 0.014 0.15 -10000 0 -0.62 19 19
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.1 0.24 -10000 0 -0.52 94 94
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.24 -10000 0 -0.54 94 94
PLCB2 -0.11 0.24 -10000 0 -0.55 92 92
IGF1 -0.18 0.36 -10000 0 -0.82 94 94
mol:L-citrulline 0.014 0.15 -10000 0 -0.62 19 19
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.024 0.14 -10000 0 -0.82 12 12
JNK cascade -0.006 0.065 -10000 0 -0.66 4 4
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.005 0.085 -10000 0 -0.85 4 4
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.049 0.2 -10000 0 -0.85 19 19
Gq family/GDP/Gbeta gamma -0.049 0.16 -10000 0 -0.49 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.082 -10000 0 -0.37 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.035 0.13 -10000 0 -0.61 19 19
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.045 0.15 -10000 0 -0.67 19 19
STRN -0.027 0.18 -10000 0 -0.85 19 19
GNAL -0.09 0.28 -10000 0 -0.85 49 49
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.014 0.059 -10000 0 -0.58 4 4
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.013 0 -10000 0 -10000 0 0
HBEGF -0.002 0.16 -10000 0 -0.67 13 13
cAMP biosynthetic process -0.091 0.2 -10000 0 -0.51 67 67
SRC 0.015 0.14 -10000 0 -0.53 19 19
PI3K -0.002 0.032 -10000 0 -0.66 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.031 0.12 -10000 0 -0.52 19 19
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -10000 0 -0.54 31 31
Gs family/GTP -0.093 0.2 -10000 0 -0.52 67 67
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.01 -10000 0 -10000 0 0
vasodilation 0.015 0.14 -10000 0 -0.59 19 19
mol:DAG -0.1 0.24 -10000 0 -0.52 94 94
Gs family/GDP/Gbeta gamma -0.073 0.16 -10000 0 -0.52 23 23
MSN 0.019 0.11 -10000 0 -0.48 2 2
Gq family/GTP -0.14 0.24 -10000 0 -0.57 95 95
mol:PI-3-4-5-P3 -0.01 0.19 -10000 0 -0.83 20 20
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.015 0.14 0.59 19 -10000 0 19
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.034 0.12 -10000 0 -0.54 22 22
NOS3 0.012 0.16 -10000 0 -0.66 19 19
GNA11 0.005 0.085 -10000 0 -0.85 4 4
MAPKKK cascade 0 0.19 -10000 0 -0.56 37 37
E2/ER alpha (dimer)/PELP1/Src -0.038 0.14 -10000 0 -0.65 19 19
ruffle organization 0.02 0.1 -10000 0 -0.44 2 2
ROCK2 0.01 0.12 -10000 0 -0.44 10 10
GNA14 -0.18 0.36 -10000 0 -0.85 92 92
GNA15 -0.012 0.094 -10000 0 -0.33 30 30
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.027 0.2 -10000 0 -0.56 38 38
MMP2 0.018 0.14 -10000 0 -0.72 8 8
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.04 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.058 0.14 0.43 19 -10000 0 19
IL27/IL27R/JAK1 -0.11 0.19 -10000 0 -0.61 33 33
TBX21 -0.084 0.22 -10000 0 -0.65 29 29
IL12B -0.005 0.093 -10000 0 -0.53 10 10
IL12A -0.056 0.2 -10000 0 -0.64 42 42
IL6ST -0.093 0.28 -10000 0 -0.86 49 49
IL27RA/JAK1 0.013 0.026 -10000 0 -10000 0 0
IL27 0.002 0.037 -10000 0 -0.32 5 5
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.07 0.16 -10000 0 -0.52 1 1
T-helper 2 cell differentiation 0.058 0.14 0.43 19 -10000 0 19
T cell proliferation during immune response 0.058 0.14 0.43 19 -10000 0 19
MAPKKK cascade -0.058 0.14 -10000 0 -0.43 19 19
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.048 -10000 0 -0.31 9 9
IL12RB1 -0.022 0.12 -10000 0 -0.36 37 37
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.083 0.21 -10000 0 -0.65 23 23
IL27/IL27R/JAK2/TYK2 -0.059 0.14 -10000 0 -0.44 18 18
positive regulation of T cell mediated cytotoxicity -0.058 0.14 -10000 0 -0.43 19 19
STAT1 (dimer) -0.11 0.24 0.52 14 -0.81 11 25
JAK2 0.014 0.007 -10000 0 -10000 0 0
JAK1 0.013 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.048 0.13 -10000 0 -0.52 6 6
T cell proliferation -0.16 0.24 -10000 0 -0.54 94 94
IL12/IL12R/TYK2/JAK2 -0.054 0.16 -10000 0 -0.7 11 11
IL17A -0.071 0.16 -10000 0 -0.52 1 1
mast cell activation 0.058 0.14 0.43 19 -10000 0 19
IFNG -0.019 0.049 -10000 0 -0.13 56 56
T cell differentiation -0.005 0.008 -10000 0 -0.022 54 54
STAT3 (dimer) -0.048 0.13 -10000 0 -0.52 6 6
STAT5A (dimer) -0.048 0.13 -10000 0 -0.52 6 6
STAT4 (dimer) -0.07 0.16 -10000 0 -0.52 19 19
STAT4 -0.031 0.15 -10000 0 -0.45 39 39
T cell activation -0.011 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.053 0.17 -10000 0 -0.59 9 9
GATA3 -0.054 0.36 -10000 0 -1.5 23 23
IL18 -0.026 0.12 -10000 0 -0.3 50 50
positive regulation of mast cell cytokine production -0.047 0.13 -10000 0 -0.51 6 6
IL27/EBI3 -0.098 0.12 -10000 0 -0.44 6 6
IL27RA 0.004 0.027 -10000 0 -10000 0 0
IL6 -0.19 0.35 -10000 0 -0.85 88 88
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.013 -10000 0 -10000 0 0
IL1B -0.044 0.18 -10000 0 -0.67 32 32
EBI3 -0.15 0.17 -10000 0 -0.34 33 33
TNF -0.07 0.22 -10000 0 -0.62 53 53
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0 0.1 -9999 0 -0.85 6 6
CDKN1A -0.015 0.092 -9999 0 -0.26 2 2
PRL-3/alpha Tubulin -0.013 0.05 -9999 0 -10000 0 0
mol:Ca2+ -0.017 0.11 -9999 0 -0.39 21 21
AGT -0.021 0.14 -9999 0 -0.46 29 29
CCNA2 -0.07 0.22 -9999 0 -0.48 89 89
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.12 0.28 -9999 0 -0.65 89 89
CDK2/Cyclin E1 -0.033 0.061 -9999 0 -10000 0 0
MAPK3 0.009 0.056 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.009 0.056 -9999 0 -10000 0 0
PTP4A1 -0.079 0.22 -9999 0 -0.51 89 89
PTP4A3 -0.008 0.081 -9999 0 -0.31 27 27
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.009 0.056 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
RAC1 -0.017 0.094 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.075 0.21 -9999 0 -0.48 89 89
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.01 0.036 -9999 0 -10000 0 0
RHOC -0.017 0.094 -9999 0 -10000 0 0
RHOA -0.017 0.094 -9999 0 -0.26 9 9
cell motility -0.016 0.1 -9999 0 -0.27 9 9
PRL-1/alpha Tubulin -0.068 0.21 -9999 0 -0.47 89 89
PRL-3/alpha1 Integrin -0.023 0.097 -9999 0 -0.71 6 6
ROCK1 -0.016 0.1 -9999 0 -0.27 9 9
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.078 0.22 -9999 0 -0.5 89 89
ATF5 0 0.065 -9999 0 -0.31 17 17
ErbB2/ErbB3 signaling events

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
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.045 0.11 -9999 0 -0.4 19 19
NFATC4 -0.003 0.12 -9999 0 -0.58 2 2
ERBB2IP 0.013 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.05 0.14 -9999 0 -0.42 48 48
JUN 0.005 0.094 -9999 0 -0.27 7 7
HRAS 0.011 0.023 -9999 0 -0.31 2 2
DOCK7 -0.017 0.14 -9999 0 -0.42 18 18
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.061 0.17 -9999 0 -0.51 48 48
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.023 0.063 -9999 0 -0.29 1 1
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.16 -9999 0 -0.46 48 48
RAF1 -0.006 0.13 -9999 0 -0.41 19 19
ErbB2/ErbB3/neuregulin 2 -0.079 0.19 -9999 0 -0.54 59 59
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.023 0.08 -9999 0 -0.28 2 2
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.13 0.33 -9999 0 -0.68 97 97
FOS -0.11 0.28 -9999 0 -0.52 124 124
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.05 0.14 -9999 0 -0.42 48 48
MAPK3 -0.086 0.26 -9999 0 -0.51 94 94
MAPK1 -0.086 0.26 -9999 0 -0.51 94 94
JAK2 -0.017 0.14 -9999 0 -0.41 22 22
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.022 0.14 -9999 0 -0.39 48 48
NRG1 -0.075 0.26 -9999 0 -0.83 42 42
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.01 0.13 -9999 0 -0.35 50 50
MAPK9 -0.023 0.063 -9999 0 -0.29 1 1
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.011 0.13 -9999 0 -0.76 11 11
SHC1 0.012 0.003 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.003 -9999 0 -10000 0 0
RNF41 0.027 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.033 0.09 -9999 0 -0.44 1 1
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.058 0.2 -9999 0 -0.46 26 26
myelination 0.006 0.12 -9999 0 -0.53 2 2
PPP3CB -0.015 0.13 -9999 0 -0.61 1 1
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.039 0.11 -9999 0 -0.92 1 1
NRG2 -0.095 0.28 -9999 0 -0.82 53 53
mol:GDP -0.02 0.14 -9999 0 -0.38 48 48
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.009 0.14 -9999 0 -0.42 19 19
SRC 0.012 0.016 -9999 0 -0.31 1 1
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.017 0.14 -9999 0 -0.4 30 30
MAP2K1 -0.079 0.23 -9999 0 -0.62 24 24
heart morphogenesis -0.05 0.14 -9999 0 -0.42 48 48
RAS family/GDP -0.039 0.11 -9999 0 -0.68 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.009 -9999 0 -10000 0 0
CHRNE 0.011 0.032 -9999 0 -0.13 11 11
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.05 0.14 -9999 0 -0.42 48 48
CDC42 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.013 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.016 0.094 0.21 4 -0.38 10 14
PTP1B/AKT1 -0.002 0.064 -10000 0 -0.39 2 2
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.011 0.071 -10000 0 -0.38 3 3
EGFR 0.001 0.096 -10000 0 -0.86 5 5
EGF/EGFR -0.084 0.18 -10000 0 -0.52 60 60
CSF1 0.003 0.095 -10000 0 -0.85 5 5
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.099 0.12 -10000 0 -0.45 23 23
Insulin Receptor/Insulin -0.013 0.042 -10000 0 -10000 0 0
HCK -0.008 0.08 -10000 0 -0.31 26 26
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.002 0.067 -10000 0 -0.4 2 2
EGF -0.11 0.3 -10000 0 -0.8 61 61
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.017 0.1 -10000 0 -0.48 4 4
TXN 0.011 0.017 -10000 0 -0.32 1 1
PTP1B/IRS1/GRB2 -0.067 0.16 -10000 0 -0.5 45 45
cell migration 0.011 0.071 0.38 3 -10000 0 3
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.042 0.19 -10000 0 -0.58 38 38
ITGA2B -0.089 0.28 -10000 0 -0.85 48 48
CSF1R 0.007 0.056 -10000 0 -0.4 6 6
Prolactin Receptor/Prolactin -0.037 0.15 -10000 0 -0.67 19 19
FGR 0.01 0.032 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.003 0.066 -10000 0 -0.4 2 2
Crk/p130 Cas -0.016 0.049 -10000 0 -0.38 2 2
DOK1 0.008 0.062 -10000 0 -0.36 2 2
JAK2 -0.007 0.084 -10000 0 -0.37 9 9
Jak2/Leptin Receptor/Leptin -0.069 0.16 -10000 0 -0.61 32 32
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.011 0.071 -10000 0 -0.38 3 3
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.19 0.21 -10000 0 -0.35 227 227
SRC 0.012 0.03 -10000 0 -10000 0 0
ITGB3 -0.016 0.15 -10000 0 -0.85 13 13
CAT1/PTP1B -0.091 0.15 -10000 0 -0.39 47 47
CAPN1 0.013 0.003 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.014 0.043 -10000 0 -0.62 1 1
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.069 0.18 -10000 0 -0.65 32 32
negative regulation of transcription -0.006 0.083 -10000 0 -0.36 9 9
FCGR2A -0.008 0.087 -10000 0 -0.34 25 25
FER 0.008 0.061 -10000 0 -0.86 2 2
alphaIIb/beta3 Integrin -0.095 0.25 -10000 0 -0.72 55 55
BLK -0.26 0.39 -10000 0 -0.78 143 143
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.013 0.003 -10000 0 -10000 0 0
LEPR 0.004 0.087 -10000 0 -0.84 4 4
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.5 39 39
PRL 0.001 0.017 -10000 0 -0.31 1 1
SOCS3 -0.1 0.41 -10000 0 -1.5 32 32
SPRY2 0.012 0.017 -10000 0 -0.31 1 1
Insulin Receptor/Insulin/IRS1 -0.061 0.18 -10000 0 -0.58 43 43
CSF1/CSF1R -0.025 0.078 -10000 0 -0.47 8 8
Ras protein signal transduction 0.02 0.023 -10000 0 -10000 0 0
IRS1 -0.078 0.26 -10000 0 -0.85 43 43
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.009 0.069 -10000 0 -0.31 20 20
STAT5B -0.004 0.069 -10000 0 -0.29 5 5
STAT5A -0.004 0.069 -10000 0 -0.29 5 5
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.066 -10000 0 -0.4 2 2
CSN2 -0.006 0.053 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
LAT 0.001 0.071 -10000 0 -0.55 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.009 0.11 -10000 0 -0.45 20 20
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 176 176
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.013 0.21 -10000 0 -0.94 16 16
NCK1/PAK1/Dok-R -0.027 0.086 -10000 0 -0.42 17 17
NCK1/Dok-R -0.062 0.22 -10000 0 -1.1 16 16
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
mol:beta2-estradiol -0.004 0.046 0.25 12 -10000 0 12
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.008 0.062 -10000 0 -0.33 6 6
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.054 0.2 -10000 0 -1 16 16
FN1 -0.22 0.15 -10000 0 -0.31 295 295
PLD2 0.007 0.25 -10000 0 -1.2 16 16
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.019 0.16 -10000 0 -0.85 15 15
ELK1 0.021 0.22 -10000 0 -1 16 16
GRB7 -0.037 0.12 -10000 0 -0.31 63 63
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.099 0.22 -10000 0 -1.2 16 16
CDKN1A -0.011 0.17 -10000 0 -0.63 16 16
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.062 0.22 -10000 0 -1.1 16 16
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.028 0.16 -10000 0 -0.68 16 16
PLG -0.002 0.25 -10000 0 -1.2 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.01 0.2 -10000 0 -0.9 16 16
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0.002 -10000 0 -10000 0 0
ANGPT2 -0.11 0.23 -10000 0 -0.8 18 18
BMX -0.006 0.26 -10000 0 -1.2 18 18
ANGPT1 -0.035 0.28 -10000 0 -1.5 14 14
tube development -0.017 0.18 -10000 0 -0.72 16 16
ANGPT4 -0.064 0.24 -10000 0 -0.75 42 42
response to hypoxia 0 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.018 0.27 -10000 0 -1.2 16 16
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.001 -10000 0 -10000 0 0
STAT5A (dimer) -0.019 0.2 -10000 0 -0.82 16 16
mol:L-citrulline 0.028 0.16 -10000 0 -0.68 16 16
AGTR1 -0.33 0.42 -10000 0 -0.85 164 164
MAPK14 -0.006 0.24 -10000 0 -1.2 16 16
Tie2/SHP2 -0.018 0.095 -10000 0 -1.2 2 2
TEK 0.023 0.12 -10000 0 -1.4 2 2
RPS6KB1 0.013 0.2 -10000 0 -0.9 16 16
Angiotensin II/AT1 -0.26 0.33 -10000 0 -0.66 163 163
Tie2/Ang1/GRB2 0.001 0.25 -10000 0 -1.2 16 16
MAPK3 0.017 0.23 -10000 0 -1.1 16 16
MAPK1 0.017 0.23 -10000 0 -1.1 16 16
Tie2/Ang1/GRB7 -0.021 0.26 -10000 0 -1.2 16 16
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.003 0.25 -10000 0 -1.1 17 17
PI3K -0.001 0.24 -10000 0 -1.1 16 16
FES -0.006 0.24 -10000 0 -1.2 16 16
Crk/Dok-R -0.062 0.22 -10000 0 -1.1 16 16
Tie2/Ang1/ABIN2 0.001 0.25 -10000 0 -1.2 16 16
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.017 0.19 -10000 0 -0.83 16 16
STAT5A 0.013 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.013 0.2 -10000 0 -0.9 16 16
Tie2/Ang2 -0.037 0.23 -10000 0 -0.99 16 16
Tie2/Ang1 -0.004 0.26 -10000 0 -1.3 16 16
FOXO1 0.023 0.19 -10000 0 -0.83 16 16
ELF1 0.02 0.043 -10000 0 -0.84 1 1
ELF2 0.003 0.24 -10000 0 -1.1 16 16
mol:Choline 0.009 0.24 -10000 0 -1.1 16 16
cell migration -0.023 0.054 -10000 0 -0.25 2 2
FYN -0.022 0.2 -10000 0 -0.82 16 16
DOK2 0.001 0.078 -10000 0 -0.4 12 12
negative regulation of cell cycle -0.007 0.16 -10000 0 -0.57 16 16
ETS1 0.016 0.043 -10000 0 -10000 0 0
PXN 0.025 0.17 -10000 0 -0.73 16 16
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.025 0.18 -10000 0 -0.78 16 16
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.089 0.28 -10000 0 -0.8 53 53
MAPKKK cascade 0.009 0.24 -10000 0 -1.1 16 16
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.002 0.26 -10000 0 -1.2 16 16
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.03 0.14 -10000 0 -0.6 16 16
mol:Phosphatidic acid 0.009 0.24 -10000 0 -1.1 16 16
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.028 0.16 -10000 0 -0.68 16 16
Rac1/GTP -0.048 0.16 -10000 0 -0.83 16 16
MMP2 0.001 0.25 -10000 0 -1.2 16 16
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.002 0.032 -10000 0 -0.66 1 1
Necdin/E2F1 -0.066 0.11 -10000 0 -0.82 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.038 0.11 -10000 0 -0.51 19 19
NGF (dimer)/p75(NTR)/BEX1 -0.3 0.3 -10000 0 -0.6 201 201
NT-4/5 (dimer)/p75(NTR) -0.075 0.19 -10000 0 -0.69 30 30
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.004 0.13 -10000 0 -0.51 20 20
IKBKG 0.013 0 -10000 0 -10000 0 0
BDNF -0.018 0.15 -10000 0 -0.85 12 12
MGDIs/NGR/p75(NTR)/LINGO1 -0.05 0.13 -10000 0 -0.56 20 20
FURIN 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.062 0.15 -10000 0 -0.59 28 28
LINGO1 -0.001 0.067 -10000 0 -0.31 18 18
Sortilin/TRAF6/NRIF -0.001 0.021 -10000 0 -10000 0 0
proBDNF (dimer) -0.018 0.15 -10000 0 -0.85 12 12
NTRK1 0 0.055 -10000 0 -0.31 12 12
RTN4R 0.013 0 -10000 0 -10000 0 0
neuron apoptosis -0.014 0.14 -10000 0 -0.52 22 22
IRAK1 0.013 0 -10000 0 -10000 0 0
SHC1 -0.022 0.14 -10000 0 -0.59 19 19
ARHGDIA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.042 0.12 -10000 0 -0.55 19 19
MAGEH1 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.044 0.13 -10000 0 -0.54 21 21
Mammalian IAPs/DIABLO -0.03 0.12 -10000 0 -0.52 21 21
proNGF (dimer) 0.006 0.075 -10000 0 -0.72 4 4
MAGED1 0.013 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.15 -10000 0 -0.6 22 22
ZNF274 0.013 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.039 0.11 -10000 0 -0.51 19 19
NGF 0.006 0.075 -10000 0 -0.72 4 4
cell cycle arrest 0.044 0.17 -10000 0 -0.5 19 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.091 -10000 0 -0.36 20 20
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.065 0.16 -10000 0 -0.61 31 31
NCSTN 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.047 0.13 -10000 0 -0.59 19 19
PSENEN 0.013 0 -10000 0 -10000 0 0
mol:ceramide -0.012 0.13 -10000 0 -0.54 19 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.02 0.075 -10000 0 -0.45 2 2
p75(NTR)/beta APP -0.052 0.14 -10000 0 -0.66 17 17
BEX1 -0.38 0.43 -10000 0 -0.85 186 186
mol:GDP -0.033 0.14 -10000 0 -0.6 19 19
NGF (dimer) -0.096 0.13 -10000 0 -0.53 26 26
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.044 0.12 -10000 0 -0.55 17 17
PIK3R1 0.013 0 -10000 0 -10000 0 0
RAC1/GTP -0.041 0.12 -10000 0 -0.52 19 19
MYD88 0.013 0 -10000 0 -10000 0 0
CHUK 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.047 0.13 -10000 0 -0.6 19 19
RHOB 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.063 0.093 -10000 0 -10000 0 0
NT3 (dimer) -0.051 0.21 -10000 0 -0.63 41 41
TP53 -0.009 0.14 -10000 0 -0.48 29 29
PRDM4 -0.012 0.13 -10000 0 -0.54 19 19
BDNF (dimer) -0.13 0.17 -10000 0 -0.58 34 34
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
SORT1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.037 0.11 -10000 0 -0.5 19 19
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.043 0.12 -10000 0 -0.55 20 20
RHOC 0.013 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
MAPK10 0.021 0.13 -10000 0 -0.46 18 18
DIABLO 0.013 0 -10000 0 -10000 0 0
SMPD2 -0.012 0.13 -10000 0 -0.54 19 19
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.047 0.13 -10000 0 -0.6 19 19
PSEN1 0.013 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.098 0.21 -10000 0 -0.69 40 40
MAPK8 0.019 0.13 -10000 0 -0.47 18 18
MAPK9 0.021 0.13 -10000 0 -0.45 20 20
APAF1 0.013 0 -10000 0 -10000 0 0
NTF3 -0.051 0.21 -10000 0 -0.63 41 41
NTF4 -0.02 0.15 -10000 0 -0.61 22 22
NDN 0.009 0.06 -10000 0 -0.85 2 2
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.034 0.1 -10000 0 -0.47 19 19
p75 CTF/Sortilin/TRAF6/NRIF -0.002 0.05 -10000 0 -1 1 1
RhoA-B-C/GTP -0.047 0.13 -10000 0 -0.59 19 19
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.051 0.13 -10000 0 -0.51 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.056 0.14 -10000 0 -0.54 29 29
PRKACB 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.024 0.12 -10000 0 -0.66 13 13
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.038 0.2 -10000 0 -0.69 30 30
BIRC2 0.013 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.07 0.18 0.25 161 -0.5 19 180
BAD 0.028 0.13 -10000 0 -0.45 18 18
RIPK2 0.013 0 -10000 0 -10000 0 0
NGFR -0.063 0.2 -10000 0 -0.45 67 67
CYCS -0.003 0.12 -10000 0 -0.51 19 19
ADAM17 0.011 0.043 -10000 0 -0.85 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.043 0.12 -10000 0 -0.55 20 20
BCL2L11 0.028 0.13 -10000 0 -0.45 18 18
BDNF (dimer)/p75(NTR) -0.074 0.18 -10000 0 -0.68 28 28
PI3K -0.043 0.12 -10000 0 -0.55 20 20
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.042 0.12 -10000 0 -0.55 19 19
NDNL2 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.057 0.16 -10000 0 -0.68 19 19
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.042 0.12 -10000 0 -0.55 19 19
TRAF6 0.011 0.043 -10000 0 -0.85 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
PLG 0 0.022 -10000 0 -0.31 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.021 0.15 -10000 0 -0.51 30 30
SQSTM1 0.013 0 -10000 0 -10000 0 0
NGFRAP1 0.013 0 -10000 0 -10000 0 0
CASP3 0.03 0.12 -10000 0 -0.41 18 18
E2F1 -0.089 0.15 -10000 0 -10000 0 0
CASP9 0.013 0 -10000 0 -10000 0 0
IKK complex -0.014 0.063 -10000 0 -0.55 3 3
NGF (dimer)/TRKA -0.011 0.066 -10000 0 -0.66 3 3
MMP7 -0.18 0.23 -10000 0 -0.37 203 203
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.039 0.12 -10000 0 -0.52 20 20
MMP3 -0.041 0.11 -10000 0 -0.31 59 59
APAF-1/Caspase 9 -0.043 0.12 -10000 0 -0.66 6 6
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0.016 -9999 0 -0.31 1 1
LAT2 -0.016 0.1 -9999 0 -0.3 13 13
AP1 -0.21 0.29 -9999 0 -0.6 131 131
mol:PIP3 -0.015 0.16 -9999 0 -0.44 33 33
IKBKB 0.006 0.093 -9999 0 -0.28 16 16
AKT1 -0.013 0.13 -9999 0 -0.48 5 5
IKBKG 0.006 0.093 -9999 0 -0.28 16 16
MS4A2 -0.063 0.13 -9999 0 -0.31 91 91
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
MAP3K1 0.012 0.1 -9999 0 -0.45 7 7
mol:Ca2+ -0.006 0.12 -9999 0 -0.33 33 33
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.008 0.088 -9999 0 -0.33 3 3
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.084 0.19 -9999 0 -0.53 65 65
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.005 0.075 -9999 0 -0.31 23 23
PLD2 -0.046 0.15 -9999 0 -0.46 34 34
PTPN13 0.003 0.087 -9999 0 -0.46 2 2
PTPN11 0.012 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.021 0.1 -9999 0 -0.32 4 4
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.45 33 33
LAT -0.014 0.1 -9999 0 -0.45 7 7
PAK2 0.004 0.11 -9999 0 -0.51 7 7
NFATC2 -0.13 0.27 -9999 0 -0.78 59 59
HRAS -0.005 0.12 -9999 0 -0.5 10 10
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.097 0.17 -9999 0 -0.49 54 54
Antigen/IgE/Fc epsilon R1 -0.088 0.16 -9999 0 -0.45 54 54
mol:GDP -0.014 0.13 -9999 0 -0.53 12 12
JUN -0.18 0.36 -9999 0 -0.85 93 93
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.21 0.38 -9999 0 -0.85 106 106
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.042 0.078 -9999 0 -0.27 28 28
CHUK 0.006 0.093 -9999 0 -0.27 17 17
KLRG1 -0.02 0.11 -9999 0 -0.39 13 13
VAV1 -0.02 0.12 -9999 0 -0.45 10 10
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.008 0.088 -9999 0 -0.33 3 3
negative regulation of mast cell degranulation -0.019 0.1 -9999 0 -0.38 12 12
BTK -0.045 0.12 -9999 0 -0.6 10 10
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.049 0.2 -9999 0 -0.55 38 38
GAB2/PI3K/SHP2 -0.062 0.12 -9999 0 -0.44 29 29
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.017 0.095 -9999 0 -0.3 28 28
RAF1 0.017 0.021 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.21 -9999 0 -0.61 47 47
FCER1G -0.009 0.083 -9999 0 -0.32 27 27
FCER1A -0.073 0.23 -9999 0 -0.57 59 59
Antigen/IgE/Fc epsilon R1/Fyn -0.079 0.15 -9999 0 -0.5 34 34
MAPK3 0.029 0.018 -9999 0 -10000 0 0
MAPK1 0.029 0.018 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.015 0.064 -9999 0 -0.6 3 3
DUSP1 -0.12 0.32 -9999 0 -0.85 65 65
NF-kappa-B/RelA -0.018 0.042 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.003 0.082 -9999 0 -10000 0 0
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.04 0.099 -9999 0 -0.52 8 8
FER -0.011 0.093 -9999 0 -0.39 5 5
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.077 0.18 -9999 0 -0.54 53 53
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.01 0.13 -9999 0 -0.52 12 12
cytokine secretion -0.013 0.031 -9999 0 -10000 0 0
SPHK1 -0.011 0.09 -9999 0 -0.33 4 4
PTK2 -0.003 0.085 -9999 0 -10000 0 0
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.065 0.14 -9999 0 -0.46 36 36
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.009 0.15 -9999 0 -0.42 33 33
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.045 0.089 -9999 0 -0.4 11 11
MAP2K4 0.021 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.22 -9999 0 -0.66 43 43
mol:Choline -0.045 0.15 -9999 0 -0.46 34 34
SHC/Grb2/SOS1 -0.03 0.064 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.005 0.08 -9999 0 -10000 0 0
HCLS1 -0.01 0.093 -9999 0 -0.35 5 5
PRKCB -0.007 0.12 -9999 0 -0.34 33 33
FCGR2B -0.032 0.19 -9999 0 -0.76 24 24
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.019 0.11 -9999 0 -0.38 12 12
LCP2 0.007 0.046 -9999 0 -0.32 8 8
PLA2G4A -0.046 0.17 -9999 0 -0.52 34 34
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.045 0.15 -9999 0 -0.46 34 34
IKK complex 0.02 0.075 -9999 0 -0.23 4 4
WIPF1 0.013 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG -0.011 0.16 -9999 0 -0.51 40 40
VEGFR1 homodimer/NRP1/VEGFR 121 -0.003 0.036 -9999 0 -0.52 2 2
CaM/Ca2+ -0.004 0.16 -9999 0 -0.47 40 40
HIF1A 0.021 0 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.011 0.16 -9999 0 -0.92 1 1
PLCG1 -0.012 0.16 -9999 0 -0.51 40 40
NOS3 0.018 0.15 -9999 0 -0.44 40 40
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.019 0.15 -9999 0 -0.42 40 40
FLT1 0.033 0 -9999 0 -10000 0 0
PGF -0.072 0.26 -9999 0 -0.84 41 41
VEGFR1 homodimer/NRP2/VEGFR121 -0.013 0.049 -9999 0 -0.51 2 2
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
eNOS/Hsp90 0.025 0.14 -9999 0 -10000 0 0
endothelial cell proliferation -0.031 0.2 -9999 0 -0.55 41 41
mol:Ca2+ -0.011 0.16 -9999 0 -0.5 40 40
MAPK3 -0.022 0.19 -9999 0 -0.47 60 60
MAPK1 -0.022 0.19 -9999 0 -0.47 60 60
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.072 0.26 -9999 0 -0.84 41 41
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.01 0.14 -9999 0 -0.85 11 11
VEGFA homodimer 0.009 0.06 -9999 0 -0.85 2 2
VEGFR1 homodimer/VEGFA homodimer 0.031 0.042 -9999 0 -0.56 2 2
platelet activating factor biosynthetic process -0.014 0.19 -9999 0 -0.86 4 4
PI3K -0.048 0.14 -9999 0 -0.48 41 41
PRKCA -0.032 0.2 -9999 0 -0.5 60 60
PRKCB -0.019 0.16 -9999 0 -0.48 42 42
VEGFR1 homodimer/PLGF homodimer -0.025 0.18 -9999 0 -0.56 40 40
VEGFA 0.009 0.06 -9999 0 -0.85 2 2
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.011 0.16 -9999 0 -0.51 40 40
RASA1 0.043 0 -9999 0 -10000 0 0
NRP2 -0.013 0.089 -9999 0 -0.31 33 33
VEGFR1 homodimer 0.033 0 -9999 0 -10000 0 0
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.013 0.16 -9999 0 -0.83 2 2
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.048 0.14 -9999 0 -0.47 41 41
mol:L-citrulline 0.019 0.15 -9999 0 -0.42 40 40
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.033 -9999 0 -0.48 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.003 0.036 -9999 0 -0.51 2 2
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.045 0.13 -9999 0 -0.45 41 41
PDPK1 0.003 0.15 -9999 0 -0.45 41 41
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.003 0.036 -9999 0 -0.51 2 2
mol:NADP 0.019 0.15 -9999 0 -0.42 40 40
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.033 -9999 0 -0.47 2 2
VEGFR1 homodimer/NRP2 0.019 0.05 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.021 0.016 -10000 0 -10000 0 0
HSPA8 0.005 0.074 -10000 0 -0.85 3 3
SMAD3/SMAD4/ER alpha -0.052 0.14 -10000 0 -0.61 19 19
AKT1 0.009 0.01 -10000 0 -10000 0 0
GSC -0.22 0.57 -10000 0 -1.6 63 63
NKX2-5 0.001 0.031 -10000 0 -10000 0 0
muscle cell differentiation 0.025 0.047 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.003 0.08 -10000 0 -10000 0 0
SMAD4 -0.016 0.059 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.011 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.078 -10000 0 -0.57 4 4
SMAD3/SMAD4/VDR 0.011 0.045 -10000 0 -10000 0 0
MYC 0.002 0.14 -10000 0 -0.86 10 10
CDKN2B -0.079 0.14 -10000 0 -10000 0 0
AP1 -0.27 0.53 -10000 0 -1 124 124
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.033 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.065 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.009 0.067 -10000 0 -0.3 14 14
SMAD3/SMAD4/GR -0.017 0.046 -10000 0 -10000 0 0
GATA3 -0.037 0.2 -10000 0 -0.84 23 23
SKI/SIN3/HDAC complex/NCoR1 0.041 0.023 -10000 0 -10000 0 0
MEF2C/TIF2 -0.052 0.14 -10000 0 -0.53 19 19
endothelial cell migration -0.009 0.11 1.4 1 -10000 0 1
MAX 0.013 0.006 -10000 0 -10000 0 0
RBBP7 0.011 0.004 -10000 0 -10000 0 0
RBBP4 0.011 0.004 -10000 0 -10000 0 0
RUNX2 -0.08 0.16 -10000 0 -0.32 113 113
RUNX3 -0.007 0.12 -10000 0 -0.58 14 14
RUNX1 -0.14 0.16 -10000 0 -10000 0 0
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.012 0.016 -10000 0 -0.31 1 1
CDKN1A 0.023 0.074 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.04 0.09 -10000 0 -0.35 1 1
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.011 0.004 -10000 0 -10000 0 0
SERPINE1 0.008 0.11 -10000 0 -1.5 1 1
SMAD3/SMAD4/ATF2 -0.032 0.1 -10000 0 -0.61 10 10
SMAD3/SMAD4/ATF3 -0.16 0.28 -10000 0 -0.65 96 96
SAP30 0.009 0.043 -10000 0 -0.85 1 1
Cbp/p300/PIAS3 0.035 0.046 -10000 0 -10000 0 0
JUN -0.26 0.52 -10000 0 -0.99 124 124
SMAD3/SMAD4/IRF7 -0.017 0.046 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.002 0.092 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.068 0.098 0.48 4 -10000 0 4
DLX1 -0.04 0.21 -10000 0 -0.85 25 25
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.23 0.41 -10000 0 -0.92 106 106
SMAD3/SMAD4/Max -0.017 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.009 0.021 -10000 0 -10000 0 0
ZBTB17 0.021 0.012 -10000 0 -10000 0 0
LAMC1 0.025 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.017 0.045 -10000 0 -10000 0 0
IRF7 0.014 0.005 -10000 0 -10000 0 0
ESR1 -0.049 0.2 -10000 0 -0.85 19 19
HNF4A -0.004 0.047 -10000 0 -0.31 9 9
MEF2C 0.005 0.087 -10000 0 -10000 0 0
SMAD2-3/SMAD4 -0.033 0.056 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.025 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.017 0.024 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.018 0.011 -10000 0 -10000 0 0
SKIL 0.013 0 -10000 0 -10000 0 0
HDAC1 0.011 0.004 -10000 0 -10000 0 0
HDAC2 0.011 0.004 -10000 0 -10000 0 0
SNIP1 0.011 0.005 -10000 0 -10000 0 0
GCN5L2 0.006 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.012 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.18 0.1 -10000 0 -0.7 7 7
SMAD2 -0.004 0.04 -10000 0 -10000 0 0
SMAD3 -0.005 0.048 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.059 -10000 0 -0.37 4 4
SMAD2/SMAD2/SMAD4 0.013 0.026 -10000 0 -10000 0 0
NCOR1 0.011 0.004 -10000 0 -10000 0 0
NCOA2 -0.05 0.22 -10000 0 -0.85 30 30
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.011 0.076 -10000 0 -10000 0 0
IFNB1 0.015 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.088 -10000 0 -10000 0 0
CITED1 -0.26 0.14 -10000 0 -0.32 335 335
SMAD2-3/SMAD4/ARC105 -0.024 0.045 -10000 0 -10000 0 0
RBL1 0 0.1 -10000 0 -0.85 6 6
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.007 0.081 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.085 0.11 -10000 0 -0.61 7 7
SMAD7 -0.11 0.28 -10000 0 -0.6 83 83
MYC/MIZ-1 0.014 0.11 -10000 0 -0.66 10 10
SMAD3/SMAD4 0.066 0.1 0.31 38 -0.35 1 39
IL10 -0.031 0.2 -10000 0 -0.64 34 34
PIASy/HDAC complex 0.007 0.009 -10000 0 -10000 0 0
PIAS3 0.015 0.006 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.02 0.15 -10000 0 -0.53 23 23
CDK4 0.019 0.013 -10000 0 -10000 0 0
PIAS4 0.007 0.009 -10000 0 -10000 0 0
ATF3 -0.19 0.37 -10000 0 -0.82 102 102
SMAD3/SMAD4/SP1 -0.018 0.053 -10000 0 -10000 0 0
FOXG1 -0.007 0.09 -10000 0 -0.43 14 14
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.005 0.087 -10000 0 -10000 0 0
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.055 0.15 -10000 0 -0.63 25 25
MYOD1 -0.002 0.031 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.054 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.055 0.15 -10000 0 -0.56 28 28
SnoN/SIN3/HDAC complex/NCoR1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.079 0.11 -10000 0 -0.57 9 9
SMAD3/SMAD4/SP1-3 -0.006 0.047 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.014 0.022 -10000 0 -10000 0 0
SIN3B 0.011 0.004 -10000 0 -10000 0 0
SIN3A 0.011 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.031 0.082 -10000 0 -10000 0 0
ITGB5 0.035 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.27 0.3 -10000 0 -0.62 170 170
AR -0.35 0.43 -10000 0 -0.85 170 170
negative regulation of cell growth -0.038 0.12 -10000 0 -0.4 3 3
SMAD3/SMAD4/MYOD -0.023 0.051 -10000 0 -10000 0 0
E2F5 0.013 0 -10000 0 -10000 0 0
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.02 0.058 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.067 -10000 0 -10000 0 0
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.28 0.54 -10000 0 -1 124 124
SMAD3/SMAD4/RUNX2 -0.068 0.099 -10000 0 -0.48 4 4
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.008 0.13 -10000 0 -0.85 10 10
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.089 -9999 0 -0.5 13 13
RGS9BP -0.042 0.21 -9999 0 -0.85 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.072 0.26 -9999 0 -0.84 41 41
mol:Na + -0.022 0.057 -9999 0 -10000 0 0
mol:ADP -0.049 0.2 -9999 0 -0.66 40 40
GNAT2 0.009 0.023 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.095 0.22 -9999 0 -0.58 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.065 -9999 0 -0.31 2 2
Cone PDE6 -0.083 0.19 -9999 0 -0.51 66 66
Cone Metarhodopsin II -0.053 0.16 -9999 0 -0.54 40 40
Na + (4 Units) -0.025 0.06 -9999 0 -10000 0 0
GNAT2/GDP -0.083 0.19 -9999 0 -0.51 66 66
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.012 0.014 -9999 0 -10000 0 0
Cone Transducin -0.018 0.093 -9999 0 -0.53 13 13
SLC24A2 -0.01 0.065 -9999 0 -0.31 18 18
GNB3/GNGT2 -0.022 0.12 -9999 0 -0.66 13 13
GNB3 -0.014 0.15 -9999 0 -0.85 13 13
GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
CNGA3 -0.028 0.11 -9999 0 -0.31 51 51
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.022 0.057 -9999 0 -10000 0 0
mol:Pi -0.095 0.22 -9999 0 -0.58 66 66
Cone CNG Channel -0.016 0.043 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.01 0.065 -9999 0 -0.31 18 18
RGS9 -0.077 0.26 -9999 0 -0.83 44 44
PDE6C 0.004 0.006 -9999 0 -10000 0 0
GNGT2 0.012 0.023 -9999 0 -0.31 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.062 0.15 -9999 0 -0.45 54 54
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.051 0.12 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.009 0.023 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -0.27 1 1
CaM/Ca2+ -0.057 0.14 -9999 0 -0.42 54 54
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.022 0.16 -9999 0 -0.42 54 54
AKT1 -0.004 0.15 -9999 0 -0.41 3 3
MAP2K1 -0.007 0.15 -9999 0 -0.39 54 54
MAP3K11 -0.018 0.16 -9999 0 -0.42 54 54
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.026 0.07 -9999 0 -0.66 1 1
Rap1/GTP -0.042 0.1 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.065 0.16 -9999 0 -0.47 54 54
CEBPB 0.016 0.17 -9999 0 -0.78 2 2
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.058 0.14 -9999 0 -10000 0 0
STAT1 -0.021 0.16 -9999 0 -0.42 54 54
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.11 0.29 -9999 0 -0.75 65 65
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
STAT1 (dimer)/PIAS1 -0.048 0.14 -9999 0 -0.39 54 54
CEBPB/PTGES2/Cbp/p300 -0.036 0.081 -9999 0 -0.43 2 2
mol:Ca2+ -0.061 0.15 -9999 0 -0.44 54 54
MAPK3 0.008 0.14 -9999 0 -0.49 2 2
STAT1 (dimer) -0.031 0.081 -9999 0 -0.37 1 1
MAPK1 0.008 0.14 -9999 0 -0.49 2 2
JAK2 0.009 0.014 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.013 0.18 -9999 0 -0.66 20 20
SMAD7 0.041 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.051 0.13 -9999 0 -10000 0 0
PI3K -0.056 0.14 -9999 0 -0.4 55 55
IFNG -0.11 0.29 -9999 0 -0.76 65 65
apoptosis 0.011 0.13 -9999 0 -0.44 20 20
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.003 0.065 -9999 0 -0.31 17 17
CAMK2B 0.003 0.095 -9999 0 -0.85 5 5
FRAP1 0 0.14 -9999 0 -0.38 3 3
PRKCD -0.002 0.15 -9999 0 -0.41 3 3
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.024 0.061 -9999 0 -0.27 1 1
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.029 0.12 -9999 0 -0.4 1 1
STAT1 (dimer)/PIASy -0.056 0.14 -9999 0 -0.4 54 54
SOCS1 0.005 0.025 -9999 0 -10000 0 0
mol:GDP -0.049 0.12 -9999 0 -10000 0 0
CASP1 0.039 0.064 -9999 0 -0.36 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.041 0.058 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.055 0.13 -9999 0 -0.39 55 55
RAP1/GDP -0.042 0.11 -9999 0 -10000 0 0
CBL -0.019 0.16 -9999 0 -0.42 54 54
MAP3K1 -0.018 0.16 -9999 0 -0.42 54 54
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.061 -9999 0 -0.27 1 1
PTPN11 -0.028 0.16 -9999 0 -0.45 54 54
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.044 0.13 -9999 0 -0.44 40 40
Syndecan-3/Neurocan -0.043 0.14 -9999 0 -0.49 35 35
POMC -0.17 0.35 -9999 0 -0.83 88 88
EGFR 0.003 0.095 -9999 0 -0.85 5 5
Syndecan-3/EGFR -0.006 0.054 -9999 0 -0.49 5 5
AGRP -0.003 0.059 -9999 0 -0.31 14 14
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.064 0.24 -9999 0 -0.81 38 38
long-term memory 0 0.004 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.04 0.082 -9999 0 -0.49 8 8
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0 0.01 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation 0 0.006 -9999 0 -10000 0 0
MC4R 0.001 0.039 -9999 0 -0.31 6 6
SRC 0.012 0.016 -9999 0 -0.31 1 1
PTN -0.072 0.26 -9999 0 -0.84 41 41
FGFR/FGF/Syndecan-3 0 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.079 0.17 -9999 0 -0.43 74 74
Syndecan-3/AgRP -0.005 0.023 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.006 0.025 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 0 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.039 0.081 -9999 0 -0.48 8 8
IL8 -0.084 0.18 -9999 0 -0.35 108 108
Syndecan-3/Fyn/Cortactin 0 0.004 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.006 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.14 0.27 -9999 0 -0.66 85 85
Gamma Secretase 0 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.25 0.4 -10000 0 -0.85 126 126
HRAS 0.012 0.023 -10000 0 -0.31 2 2
EGFR 0.003 0.095 -10000 0 -0.85 5 5
AKT 0.018 0.025 0.21 1 -10000 0 1
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.12 0.16 -10000 0 -0.31 164 164
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.008 0.13 -10000 0 -0.75 11 11
PIK3R3 0.011 0.043 -10000 0 -0.85 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.063 0.1 -10000 0 -0.28 40 40
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.025 0.022 0.17 1 -0.17 1 2
PI3K -0.041 0.098 0.23 1 -0.23 43 44
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.024 0.026 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.043 -10000 0 -0.85 1 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.067 0.085 -10000 0 -0.35 20 20
NT3 (dimer)/TRKC -0.095 0.2 -10000 0 -0.7 35 35
NT3 (dimer)/TRKB -0.087 0.19 -10000 0 -0.6 43 43
SHC/Grb2/SOS1/GAB1/PI3K 0.039 0.019 -10000 0 -0.34 1 1
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.018 0.15 -10000 0 -0.85 12 12
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 0 0.055 -10000 0 -0.31 12 12
NTRK2 0.007 0.074 -10000 0 -0.85 3 3
NTRK3 -0.061 0.18 -10000 0 -0.4 73 73
NT-4/5 (dimer)/TRKB -0.067 0.17 -10000 0 -0.6 33 33
neuron apoptosis 0.042 0.096 0.45 11 -10000 0 11
SHC 2-3/Grb2 -0.045 0.1 -10000 0 -0.49 11 11
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.031 0.098 -10000 0 -0.68 5 5
SHC3 -0.049 0.1 -10000 0 -0.57 10 10
STAT3 (dimer) 0.017 0.026 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.088 0.18 -10000 0 -0.6 41 41
RIN/GDP -0.01 0.064 -10000 0 -0.29 2 2
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.032 0.098 -10000 0 -0.44 20 20
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.025 0.047 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.15 -10000 0 -0.6 22 22
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.018 0.085 -10000 0 -0.57 8 8
TRKA/NEDD4-2 -0.006 0.034 -10000 0 -10000 0 0
ELMO1 -0.32 0.42 -10000 0 -0.85 159 159
RhoG/GTP/ELMO1/DOCK1 -0.23 0.29 -10000 0 -0.58 159 159
NGF 0.006 0.075 -10000 0 -0.72 4 4
HRAS 0.012 0.023 -10000 0 -0.31 2 2
DOCK1 0.009 0.06 -10000 0 -0.85 2 2
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.026 0.18 -10000 0 -0.82 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.21 0.24 -10000 0 -0.49 174 174
mol:GDP -0.017 0.093 -10000 0 -0.41 4 4
NGF (dimer) 0.006 0.075 -10000 0 -0.72 4 4
RhoG/GDP -0.26 0.32 -10000 0 -0.67 159 159
RIT1/GDP -0.005 0.065 -10000 0 -0.28 2 2
TIAM1 -0.17 0.16 -10000 0 -0.32 230 230
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.023 0.12 -10000 0 -0.65 13 13
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.051 0.21 -10000 0 -0.63 41 41
RAP1/GDP -0.019 0.044 -10000 0 -0.26 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.018 0.15 -10000 0 -0.85 12 12
ubiquitin-dependent protein catabolic process -0.009 0.055 -10000 0 -0.57 3 3
Schwann cell development -0.043 0.033 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.043 0 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.072 0.16 -10000 0 -0.71 12 12
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.037 -10000 0 -10000 0 0
STAT3 0.017 0.026 -10000 0 -10000 0 0
axon guidance -0.069 0.16 -10000 0 -0.48 45 45
MAPK3 0.016 0.083 -10000 0 -0.52 8 8
MAPK1 0.016 0.083 -10000 0 -0.52 8 8
CDC42/GDP -0.005 0.065 -10000 0 -0.28 2 2
NTF3 -0.051 0.21 -10000 0 -0.63 41 41
NTF4 -0.02 0.15 -10000 0 -0.61 22 22
NGF (dimer)/TRKA/FAIM -0.009 0.056 -10000 0 -0.57 3 3
PI3K -0.002 0.032 -10000 0 -0.66 1 1
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.12 -10000 0 -0.51 24 24
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.058 0.19 -10000 0 -0.61 35 35
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.045 -10000 0 -10000 0 0
Rac1/GDP -0.005 0.065 -10000 0 -0.28 2 2
NGF (dimer)/TRKA/GRIT -0.01 0.057 -10000 0 -0.58 3 3
neuron projection morphogenesis 0 0.1 -10000 0 -0.53 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.009 0.056 -10000 0 -0.57 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.063 0.2 -10000 0 -0.45 67 67
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.088 -10000 0 -0.36 20 20
RAS family/GTP/PI3K 0.032 0.024 -10000 0 -0.44 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.061 -10000 0 -0.62 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.034 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.021 0.11 -10000 0 -0.6 13 13
NGF (dimer)/TRKA/p62/Atypical PKCs -0.007 0.046 -10000 0 -0.49 3 3
MATK -0.001 0.1 -10000 0 -0.58 10 10
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.016 0.043 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.036 0.1 -10000 0 -0.47 20 20
Rac1/GTP -0.19 0.15 -10000 0 -0.36 163 163
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.002 0.082 -9999 0 -10000 0 0
STMN1 -0.021 0.094 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.026 0.11 -9999 0 -0.33 33 33
Chromosomal passenger complex/Cul3 protein complex 0.008 0.068 -9999 0 -0.29 10 10
BIRC5 -0.018 0.1 -9999 0 -0.34 36 36
DES -0.38 0.3 -9999 0 -0.62 249 249
Aurora C/Aurora B/INCENP -0.013 0.077 -9999 0 -10000 0 0
Aurora B/TACC1 -0.02 0.075 -9999 0 -10000 0 0
Aurora B/PP2A -0.027 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.025 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.053 0.15 -9999 0 -0.39 56 56
Cul3 protein complex -0.016 0.086 -9999 0 -0.57 9 9
KIF2C -0.002 0.043 -9999 0 -10000 0 0
PEBP1 0.01 0.005 -9999 0 -10000 0 0
KIF20A -0.058 0.14 -9999 0 -0.31 90 90
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.027 0.091 -9999 0 -10000 0 0
SEPT1 0.008 0.039 -9999 0 -0.31 6 6
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.006 0.044 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.001 -9999 0 -10000 0 0
H3F3B -0.007 0.055 -9999 0 -10000 0 0
AURKB -0.05 0.14 -9999 0 -0.31 91 91
AURKC 0.004 0.055 -9999 0 -0.31 12 12
CDCA8 0.009 0.029 -9999 0 -0.33 3 3
cytokinesis -0.069 0.08 -9999 0 -0.38 9 9
Aurora B/Septin1 -0.029 0.1 -9999 0 -0.42 6 6
AURKA 0.012 0.002 -9999 0 -10000 0 0
INCENP 0.012 0.006 -9999 0 -10000 0 0
KLHL13 -0.014 0.14 -9999 0 -0.57 19 19
BUB1 -0.11 0.16 -9999 0 -0.31 154 154
hSgo1/Aurora B/Survivin -0.03 0.12 -9999 0 -0.46 17 17
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.033 0.074 -9999 0 -0.36 3 3
SGOL1 -0.003 0.079 -9999 0 -0.34 19 19
CENPA -0.008 0.069 -9999 0 -0.21 10 10
NCAPG -0.028 0.11 -9999 0 -0.31 51 51
Aurora B/HC8 Proteasome -0.027 0.091 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.027 0.091 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.036 0.12 -9999 0 -0.31 61 61
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.09 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.037 0.082 -9999 0 -0.35 16 16
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.007 0.055 -9999 0 -10000 0 0
KIF23 -0.006 0.076 -9999 0 -0.32 23 23
VIM -0.021 0.093 -9999 0 -10000 0 0
RACGAP1 0.012 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.016 0.084 -9999 0 -0.25 21 21
Chromosomal passenger complex/EVI5 0.012 0.12 -9999 0 -0.43 4 4
TACC1 0.013 0 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.015 0.093 -10000 0 -0.33 4 4
epithelial cell differentiation -0.044 0.097 -10000 0 -0.5 8 8
ITCH 0.024 0.021 -10000 0 -10000 0 0
WWP1 -0.002 0.08 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.003 0.095 -10000 0 -0.85 5 5
PRL 0.001 0.016 -10000 0 -0.31 1 1
neuron projection morphogenesis -0.001 0.15 -10000 0 -0.54 8 8
PTPRZ1 -0.02 0.15 -10000 0 -0.6 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.062 0.14 -10000 0 -0.61 8 8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.049 0.18 -10000 0 -0.55 40 40
ADAM17 0.022 0.048 -10000 0 -0.85 1 1
ErbB4/ErbB4 -0.012 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.049 0.18 -10000 0 -0.59 31 31
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.072 0.16 -10000 0 -0.52 40 40
GRIN2B -0.034 0.16 -10000 0 -0.49 40 40
ErbB4/ErbB2/betacellulin -0.035 0.1 -10000 0 -0.63 9 9
STAT1 0.006 0.048 -10000 0 -0.31 9 9
HBEGF -0.004 0.072 -10000 0 -0.31 21 21
PRLR -0.042 0.19 -10000 0 -0.58 38 38
E4ICDs/ETO2 -0.006 0.086 -10000 0 -0.33 1 1
axon guidance 0 0.082 -10000 0 -0.33 2 2
NEDD4 0.022 0.048 -10000 0 -0.85 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.041 0.14 -10000 0 -0.67 19 19
CBFA2T3 0.012 0.016 -10000 0 -0.31 1 1
ErbB4/ErbB2/HBEGF -0.029 0.058 -10000 0 -0.67 1 1
MAPK3 -0.01 0.15 -10000 0 -0.57 8 8
STAT1 (dimer) -0.009 0.09 -10000 0 -0.33 3 3
MAPK1 -0.01 0.15 -10000 0 -0.57 8 8
JAK2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.072 0.16 -10000 0 -0.52 40 40
NRG1 -0.039 0.21 -10000 0 -0.68 40 40
NRG3 -0.053 0.23 -10000 0 -0.85 31 31
NRG2 -0.095 0.28 -10000 0 -0.82 53 53
NRG4 0.007 0.039 -10000 0 -0.31 6 6
heart development 0 0.082 -10000 0 -0.33 2 2
neural crest cell migration -0.071 0.15 -10000 0 -0.51 40 40
ERBB2 0.029 0.035 -10000 0 -0.64 1 1
WWOX/E4ICDs -0.006 0.085 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.04 0.089 -10000 0 -0.59 5 5
apoptosis 0.059 0.14 0.48 31 -10000 0 31
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.077 0.2 -10000 0 -0.57 51 51
ErbB4/ErbB2/epiregulin -0.078 0.085 -10000 0 -0.67 1 1
ErbB4/ErbB4/betacellulin/betacellulin -0.018 0.13 -10000 0 -0.67 9 9
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.059 0.12 -10000 0 -0.5 19 19
MDM2 -0.001 0.088 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.066 0.16 -10000 0 -0.53 40 40
STAT5A 0.008 0.077 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.078 0.17 -10000 0 -0.53 44 44
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.033 0.063 -10000 0 -10000 0 0
STAT5A (dimer) -0.047 0.1 -10000 0 -0.54 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.007 0.075 -10000 0 -10000 0 0
LRIG1 0.007 0.074 -10000 0 -0.85 3 3
EREG -0.14 0.16 -10000 0 -0.31 189 189
BTC -0.006 0.13 -10000 0 -0.85 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0 0.083 -10000 0 -0.33 2 2
ERBB4 -0.012 0.1 -10000 0 -10000 0 0
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.011 0.021 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.054 -10000 0 -0.53 1 1
glial cell differentiation 0.033 0.063 -10000 0 -10000 0 0
WWOX 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.024 0.17 -10000 0 -0.47 44 44
Aurora C signaling

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
INCENP 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.035 0.065 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.01 0.018 -9999 0 -10000 0 0
AURKB -0.06 0.14 -9999 0 -0.31 91 91
AURKC 0.004 0.055 -9999 0 -0.31 12 12
Nectin adhesion pathway

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.022 0.12 -9999 0 -0.7 13 13
PTK2 -0.036 0.15 -9999 0 -0.64 20 20
positive regulation of JNK cascade -0.018 0.076 -9999 0 -0.35 20 20
CDC42/GDP 0.035 0.12 -9999 0 -0.48 20 20
Rac1/GDP 0.037 0.12 -9999 0 -0.48 20 20
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.022 0.095 -9999 0 -0.44 20 20
nectin-3/I-afadin -0.032 0.14 -9999 0 -0.66 20 20
RAPGEF1 0.028 0.13 -9999 0 -0.55 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.018 0.15 -9999 0 -0.65 20 20
PDGFB-D/PDGFRB 0.013 0 -9999 0 -10000 0 0
TLN1 0.021 0.076 -9999 0 -0.97 1 1
Rap1/GTP -0.019 0.082 -9999 0 -0.38 20 20
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.032 0.14 -9999 0 -0.66 20 20
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.029 0.15 -9999 0 -0.61 20 20
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
PI3K -0.025 0.11 -9999 0 -0.51 20 20
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.031 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.019 0.08 -9999 0 -0.37 20 20
PVRL1 0.005 0.05 -9999 0 -0.31 10 10
PVRL3 -0.029 0.19 -9999 0 -0.85 20 20
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.26 0.16 -9999 0 -0.33 331 331
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.58 30 30
SRC -0.038 0.16 -9999 0 -0.74 20 20
ITGB3 -0.014 0.15 -9999 0 -0.85 13 13
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.031 -9999 0 -10000 0 0
FARP2 0.023 0.14 -9999 0 -0.6 20 20
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.028 0.12 -9999 0 -0.57 20 20
nectin-1/I-afadin -0.005 0.031 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.032 0.12 -9999 0 -0.57 20 20
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.018 0.076 -9999 0 -0.35 20 20
alphaV/beta3 Integrin/Talin 0.018 0.13 -9999 0 -0.63 13 13
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0.08 -9999 0 -1 1 1
VAV2 0.022 0.14 -9999 0 -0.61 20 20
RAP1/GDP -0.022 0.096 -9999 0 -0.44 20 20
ITGAV 0.011 0.043 -9999 0 -0.85 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.028 0.12 -9999 0 -0.57 20 20
nectin-3(dimer)/I-afadin/I-afadin -0.032 0.14 -9999 0 -0.66 20 20
Rac1/GTP -0.023 0.099 -9999 0 -0.46 20 20
PTPRM -0.017 0.083 -9999 0 -0.34 20 20
E-cadherin/beta catenin/alpha catenin -0.002 0.015 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.049 0.35 -9999 0 -0.94 11 11
PLK1 0.042 0.073 -9999 0 -10000 0 0
BIRC5 0.023 0.13 -9999 0 -1.6 1 1
HSPA1B 0.049 0.35 -9999 0 -0.94 11 11
MAP2K1 0.032 0.037 -9999 0 -10000 0 0
BRCA2 0.042 0.36 -9999 0 -1 14 14
FOXM1 0.037 0.39 -9999 0 -1.1 13 13
XRCC1 0.049 0.35 -9999 0 -0.94 11 11
FOXM1B/p19 -0.094 0.3 -9999 0 -0.92 19 19
Cyclin D1/CDK4 0.034 0.33 -9999 0 -0.88 10 10
CDC2 0.042 0.36 -9999 0 -0.95 13 13
TGFA 0.016 0.34 -9999 0 -0.86 13 13
SKP2 0.046 0.35 -9999 0 -0.95 12 12
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.049 0.35 -9999 0 -0.94 11 11
RB1 -0.052 0.095 -9999 0 -10000 0 0
FOXM1C/SP1 0.034 0.36 -9999 0 -1 12 12
AURKB -0.005 0.13 -9999 0 -10000 0 0
CENPF 0.042 0.36 -9999 0 -0.97 12 12
CDK4 0.018 0.015 -9999 0 -10000 0 0
MYC 0.041 0.35 -9999 0 -0.9 16 16
CHEK2 0.032 0.037 -9999 0 -10000 0 0
ONECUT1 0.031 0.34 -9999 0 -0.93 11 11
CDKN2A -0.12 0.16 -9999 0 -0.31 165 165
LAMA4 0.049 0.35 -9999 0 -0.94 11 11
FOXM1B/HNF6 0.024 0.37 -9999 0 -1.1 11 11
FOS -0.19 0.66 -9999 0 -1.2 107 107
SP1 0.014 0.006 -9999 0 -10000 0 0
CDC25B 0.048 0.35 -9999 0 -0.95 11 11
response to radiation 0.015 0.034 -9999 0 -10000 0 0
CENPB 0.049 0.35 -9999 0 -0.94 11 11
CENPA 0.041 0.36 -9999 0 -0.98 12 12
NEK2 0.039 0.36 -9999 0 -0.98 12 12
HIST1H2BA 0.04 0.35 -9999 0 -0.95 11 11
CCNA2 0.008 0.051 -9999 0 -0.33 9 9
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.037 0.37 -9999 0 -1.1 11 11
CCNB2 0.045 0.36 -9999 0 -0.98 11 11
CCNB1 0.044 0.36 -9999 0 -0.99 11 11
ETV5 0.048 0.35 -9999 0 -0.94 12 12
ESR1 0 0.43 -9999 0 -1.1 27 27
CCND1 0.037 0.34 -9999 0 -0.9 10 10
GSK3A 0.03 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.036 0.052 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.12 0.23 -9999 0 -0.91 16 16
GAS1 -0.13 0.62 -9999 0 -1.2 86 86
MMP2 0.042 0.37 -9999 0 -1.1 13 13
RB1/FOXM1C 0.045 0.34 -9999 0 -0.93 11 11
CREBBP 0.013 0 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.01 0.085 -10000 0 -0.77 5 5
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.002 0.11 -10000 0 -0.85 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.008 0.06 -10000 0 -0.85 2 2
AP1 -0.15 0.27 -10000 0 -0.5 134 134
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.002 0.095 -10000 0 -0.85 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.054 -10000 0 -10000 0 0
NICD/RBPSUH -0.009 0.084 -10000 0 -0.77 5 5
WIF1 -0.034 0.1 -10000 0 -0.31 50 50
NOTCH1 -0.01 0.086 -10000 0 -0.79 5 5
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.011 0.085 -10000 0 -10000 0 0
DKK1 -0.041 0.13 -10000 0 -0.33 64 64
beta catenin/beta TrCP1 0.036 0.039 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0.002 0.029 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.04 -10000 0 -0.36 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.21 0.38 -10000 0 -0.85 106 106
JUN -0.18 0.36 -10000 0 -0.85 93 93
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.03 0.042 0.24 12 -10000 0 12
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.039 0.12 -10000 0 -0.6 17 17
HNF1A 0.01 0.043 -10000 0 -0.85 1 1
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.012 0.24 -10000 0 -1.5 10 10
NKD1 -0.017 0.15 -10000 0 -0.75 16 16
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.017 0.1 -10000 0 -0.59 12 12
apoptosis -0.15 0.26 -10000 0 -0.5 134 134
Delta 1/NOTCHprecursor -0.009 0.081 -10000 0 -0.74 5 5
DLL1 0.012 0.016 -10000 0 -0.31 1 1
PPARD 0.024 0.016 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC 0.002 0.029 -10000 0 -10000 0 0
DVL1 0 0.002 -10000 0 -10000 0 0
CSNK2A1 0.013 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.038 0.083 -10000 0 -0.65 2 2
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.002 -10000 0 -10000 0 0
NLK 0.015 0.007 -10000 0 -10000 0 0
CCND1 0.018 0.045 -10000 0 -10000 0 0
WNT1 0.009 0.023 -10000 0 -0.31 2 2
Axin1/APC/beta catenin 0.046 0.035 -10000 0 -10000 0 0
DKK2 -0.031 0.18 -10000 0 -0.65 27 27
NOTCH1 precursor/DVL1 -0.005 0.073 -10000 0 -0.66 5 5
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.018 0.1 -10000 0 -0.6 12 12
PPP2R5D 0.013 0.068 0.38 13 -10000 0 13
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.017 0.044 -10000 0 -10000 0 0
RBPJ 0.012 0.016 -10000 0 -0.31 1 1
CREBBP 0.016 0.004 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.005 0.074 -10000 0 -0.37 5 5
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.036 0.075 0.23 7 -0.28 9 16
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.054 0.22 -10000 0 -0.66 47 47
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.023 0.1 -10000 0 -0.31 44 44
PRKCI 0.013 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.035 0.099 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.037 0.079 -10000 0 -0.31 9 9
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.027 0 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 265 265
LNPEP -0.006 0.13 -10000 0 -0.85 9 9
YWHAE 0.013 0 -10000 0 -10000 0 0
IL1-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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.031 0.071 -9999 0 -0.32 7 7
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.13 0.26 -9999 0 -0.7 65 65
IL1A -0.06 0.24 -9999 0 -0.81 36 36
IL1B -0.036 0.19 -9999 0 -0.67 34 34
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.022 -9999 0 -0.45 1 1
IL1R2 -0.089 0.25 -9999 0 -0.62 66 66
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.059 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.002 0.095 -9999 0 -0.85 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.067 0.022 -9999 0 -10000 0 0
JUN -0.07 0.21 -9999 0 -0.44 98 98
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.069 0.14 -9999 0 -0.5 34 34
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.079 0.15 -9999 0 -0.53 33 33
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.071 0.14 -9999 0 -0.5 33 33
IL1 beta fragment/IL1R1/IL1RAP -0.082 0.16 -9999 0 -0.56 33 33
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.029 0.08 -9999 0 -0.48 9 9
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.042 0.11 -9999 0 -0.66 8 8
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
PI3K -0.002 0.032 -9999 0 -0.66 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.09 -9999 0 -0.35 7 7
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.082 0.16 -9999 0 -0.56 33 33
IL1 beta/IL1R2 -0.11 0.24 -9999 0 -0.64 64 64
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.023 -9999 0 -0.46 1 1
NF kappa B1 p50/RelA -0.059 0.12 -9999 0 -0.58 7 7
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.074 0.15 -9999 0 -0.51 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.11 -9999 0 -0.35 33 33
IL1 alpha/IL1R1/IL1RAP -0.09 0.16 -9999 0 -0.58 33 33
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.024 -9999 0 -0.49 1 1
IL1RAP -0.076 0.15 -9999 0 -10000 0 0
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.057 0.12 -9999 0 -0.52 11 11
CASP1 0.006 0.066 -9999 0 -0.53 5 5
IL1RN/IL1R2 -0.12 0.22 -9999 0 -0.63 53 53
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.074 0.15 -9999 0 -0.52 33 33
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.081 -9999 0 -0.34 3 3
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
IL1RN -0.052 0.16 -9999 0 -0.85 8 8
TRAF6/TAK1/TAB1/TAB2 -0.001 0.024 -9999 0 -0.48 1 1
MAP2K6 0.025 0.065 -9999 0 -0.46 7 7
LPA4-mediated signaling events

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
ADCY4 0.017 0.051 -9999 0 -0.58 3 3
ADCY5 -0.064 0.21 -9999 0 -0.58 57 57
ADCY6 0.017 0.051 -9999 0 -0.58 3 3
ADCY7 0.017 0.051 -9999 0 -0.58 3 3
ADCY1 0.01 0.078 -9999 0 -0.6 6 6
ADCY2 -0.041 0.18 -9999 0 -0.59 38 38
ADCY3 0.017 0.051 -9999 0 -0.58 3 3
ADCY8 -0.12 0.099 -9999 0 -0.73 3 3
PRKCE 0.007 0.058 -9999 0 -0.67 3 3
ADCY9 0.017 0.051 -9999 0 -0.58 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.056 0.1 -9999 0 -0.45 13 13
Insulin 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
CBL/APS/CAP -0.05 0.14 -9999 0 -0.45 45 45
TC10/GTP -0.002 0.031 -9999 0 -0.44 2 2
Insulin Receptor/Insulin/IRS1/Shp2 -0.056 0.16 -9999 0 -0.54 43 43
HRAS 0.012 0.023 -9999 0 -0.31 2 2
APS homodimer 0.012 0.016 -9999 0 -0.31 1 1
GRB14 -0.019 0.16 -9999 0 -0.85 15 15
FOXO3 -0.021 0.098 -9999 0 -0.72 7 7
AKT1 -0.011 0.16 -9999 0 -0.78 1 1
INSR 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.009 0.06 -9999 0 -0.85 2 2
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.038 0 -9999 0 -10000 0 0
CAV1 -0.041 0.18 -9999 0 -0.5 54 54
CBL/APS/CAP/Crk-II/C3G -0.003 0.034 -9999 0 -0.48 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.056 0.16 -9999 0 -0.54 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.05 0.14 -9999 0 -0.47 44 44
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.006 0.1 -9999 0 -10000 0 0
RPS6KB1 0 0.15 -9999 0 -0.69 1 1
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.054 0.13 -9999 0 -0.67 1 1
HRAS/GTP -0.047 0.12 -9999 0 -0.52 2 2
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.052 0.15 -9999 0 -0.5 43 43
PRKCI -0.014 0.035 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.063 0.16 -9999 0 -0.44 59 59
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.051 0.15 -9999 0 -0.48 44 44
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.015 -9999 0 -10000 0 0
AKT2 -0.011 0.16 -9999 0 -0.43 16 16
PRKCZ -0.014 0.035 -9999 0 -10000 0 0
SH2B2 0.012 0.016 -9999 0 -0.31 1 1
SHC/SHIP -0.026 0.16 -9999 0 -0.48 43 43
F2RL2 -0.082 0.15 -9999 0 -0.32 118 118
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.003 0.037 -9999 0 -0.52 2 2
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.036 0.17 -9999 0 -0.51 43 43
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.022 0.14 -9999 0 -1.1 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.078 0.26 -9999 0 -0.85 43 43
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.035 0.16 -9999 0 -0.5 43 43
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.002 0.15 -9999 0 -0.55 3 3
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.011 0.043 -9999 0 -0.85 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.004 0.12 -9999 0 -0.34 43 43
Insulin Receptor/Insulin/IRS1 -0.057 0.17 -9999 0 -0.54 43 43
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.036 0.059 -9999 0 -0.49 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.17 0.35 -9999 0 -0.85 86 86
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0.016 -9999 0 -0.31 1 1
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.023 -9999 0 -10000 0 0
HIF1A 0.022 0.024 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.034 -9999 0 -0.48 2 2
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.12 0.16 -9999 0 -0.31 169 169
ARNT/IPAS -0.14 0.27 -9999 0 -0.66 86 86
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.023 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0.008 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.084 -9999 0 -0.52 10 10
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.014 -9999 0 -10000 0 0
VHL 0.009 0.06 -9999 0 -0.85 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.023 -9999 0 -10000 0 0
EGLN3 -0.022 0.15 -9999 0 -0.5 28 28
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.044 -9999 0 -0.59 2 2
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.03 0.073 -9999 0 -10000 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.06 0.16 -10000 0 -0.5 49 49
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.055 -10000 0 -10000 0 0
GNB1/GNG2 0 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.065 0.18 -10000 0 -0.54 49 49
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.014 0.039 0.12 49 -10000 0 49
GNAL -0.09 0.28 -10000 0 -0.85 49 49
GNG2 0.013 0 -10000 0 -10000 0 0
CRH -0.014 0.08 -10000 0 -0.31 27 27
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.041 -10000 0 -0.47 3 3
MAPK11 0.009 0 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.002 0.1 0.56 11 -10000 0 11
PI3K Class IB/PDE3B -0.002 0.1 -10000 0 -0.56 11 11
PDE3B -0.002 0.1 -10000 0 -0.56 11 11
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.004 0.15 -10000 0 -0.72 10 10
BAG4 0.011 0.043 -10000 0 -0.85 1 1
PKC zeta/ceramide -0.017 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.038 0.2 -10000 0 -0.69 30 30
BAX -0.005 0.019 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.009 -10000 0 -10000 0 0
BAD -0.017 0.041 -10000 0 -10000 0 0
SMPD1 -0.006 0.098 -10000 0 -0.27 47 47
RB1 -0.017 0.041 -10000 0 -10000 0 0
FADD/Caspase 8 0.008 0.14 -10000 0 -0.68 10 10
MAP2K4 -0.008 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.01 0.048 -10000 0 -0.59 1 1
EGF -0.11 0.3 -10000 0 -0.8 61 61
mol:ceramide -0.028 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.034 -10000 0 -0.66 1 1
ASAH1 0.011 0.043 -10000 0 -0.85 1 1
negative regulation of cell cycle -0.017 0.04 -10000 0 -10000 0 0
cell proliferation -0.097 0.17 -10000 0 -0.41 89 89
BID -0.018 0.093 -10000 0 -0.41 10 10
MAP3K1 -0.017 0.041 -10000 0 -10000 0 0
EIF2A 0 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.003 0.045 -10000 0 -0.54 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.003 0.045 -10000 0 -0.54 1 1
Cathepsin D/ceramide -0.017 0.04 -10000 0 -10000 0 0
FADD -0.004 0.15 -10000 0 -0.72 10 10
KSR1 -0.018 0.05 -10000 0 -0.63 1 1
MAPK8 -0.005 0.048 -10000 0 -0.35 3 3
PRKRA -0.017 0.041 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.36 -10000 0 -0.82 94 94
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.043 -10000 0 -10000 0 0
CTSD 0.013 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.084 0.19 -10000 0 -0.44 89 89
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.034 -10000 0 -0.66 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.16 -10000 0 -0.77 10 10
TNFR1A/BAG4/TNF-alpha -0.069 0.18 -10000 0 -0.57 48 48
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.001 0.046 -10000 0 -0.55 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.002 0.049 0.18 19 -10000 0 19
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.032 -10000 0 -0.66 1 1
EIF2AK2 -0.008 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.068 0.18 -10000 0 -0.57 47 47
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.081 -10000 0 -0.34 10 10
MAP2K2 -0.001 0.046 -10000 0 -0.55 1 1
SMPD3 -0.014 0.12 -10000 0 -0.31 53 53
TNF -0.091 0.28 -10000 0 -0.79 53 53
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.021 0.11 0.28 55 -10000 0 55
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.002 0.05 0.18 19 -10000 0 19
BCL2 -0.042 0.21 -10000 0 -0.85 26 26
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
induction of apoptosis 0 0 -9999 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.022 0.005 -9999 0 -10000 0 0
CDKN1A -0.008 0.039 -9999 0 -10000 0 0
KAT2B 0.013 0 -9999 0 -10000 0 0
BAX 0.013 0 -9999 0 -10000 0 0
FOXO3 0 0 -9999 0 -10000 0 0
FOXO1 0.013 0 -9999 0 -10000 0 0
FOXO4 0.024 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
TAT 0.008 0.017 -9999 0 -0.31 1 1
mol:Lysophosphatidic acid 0 0 -9999 0 -10000 0 0
MYOD1 0.011 0.021 -9999 0 -10000 0 0
PPARGC1A -0.36 0.43 -9999 0 -0.85 178 178
FHL2 -0.057 0.24 -9999 0 -0.85 33 33
response to nutrient levels 0 0 -9999 0 -10000 0 0
KU70/SIRT1 0.002 0.012 -9999 0 -10000 0 0
HIST2H4A 0.022 0.005 -9999 0 -10000 0 0
SIRT1/FOXO3a 0.002 0.009 -9999 0 -10000 0 0
SIRT1 0.003 0.013 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.003 0.012 -9999 0 -10000 0 0
SIRT1/Histone H1b -0.005 0.047 -9999 0 -0.32 8 8
apoptosis -0.002 0.012 -9999 0 -10000 0 0
SIRT1/PGC1A -0.25 0.29 -9999 0 -0.58 178 178
p53/SIRT1 0.007 0.035 -9999 0 -10000 0 0
SIRT1/FOXO4 0.003 0.013 -9999 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.04 0.14 -9999 0 -0.53 33 33
HIST1H1E 0.014 0.057 -9999 0 -0.37 8 8
SIRT1/p300 0.002 0.012 -9999 0 -10000 0 0
muscle cell differentiation -0.001 0.019 -9999 0 -10000 0 0
TP53 0.003 0.013 -9999 0 -10000 0 0
KU70/SIRT1/BAX 0.003 0.012 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
MEF2D 0.013 0 -9999 0 -10000 0 0
HIV-1 Tat/SIRT1 0.002 0.015 -9999 0 -10000 0 0
ACSS2 0.022 0.005 -9999 0 -10000 0 0
SIRT1/PCAF/MYOD 0.001 0.019 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.007 0.045 -9999 0 -0.31 8 8
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.015 -9999 0 -10000 0 0
GNAO1 -0.015 0.15 -9999 0 -0.72 16 16
mol:Sphinganine-1-P 0.02 0.031 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.012 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.012 0.023 -9999 0 -0.31 2 2
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.01 -9999 0 -10000 0 0
S1PR5 0.009 0.036 -9999 0 -0.31 5 5
S1PR4 0.01 0.032 -9999 0 -0.31 4 4
GNAI1 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.017 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.044 0.15 -9999 0 -0.31 95 95
S1P/S1P4/Gi 0.032 0.064 -9999 0 -0.32 12 12
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.18 0.36 -9999 0 -0.85 92 92
GNA15 -0.012 0.094 -9999 0 -0.33 30 30
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.005 0.085 -9999 0 -0.85 4 4
ABCC1 0.013 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.52 28 28
ITGA4 0.007 0.045 -9999 0 -0.31 8 8
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.64 12 12
alpha4/beta1 Integrin -0.004 0.028 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.048 0.054 -10000 0 -0.39 5 5
NFATC2 -0.012 0.088 -10000 0 -0.29 16 16
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.008 0.094 -10000 0 -0.3 26 26
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.027 0.09 -10000 0 -0.57 5 5
BCL2/BAX -0.042 0.16 -10000 0 -0.66 26 26
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.007 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.007 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.012 0.089 -10000 0 -0.53 3 3
Calcineurin A alpha-beta B1/BCL2 -0.042 0.21 -10000 0 -0.85 26 26
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.012 0.088 0.52 3 -10000 0 3
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 265 265
MAP3K8 -0.003 0.1 -10000 0 -0.85 6 6
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.11 0.16 -10000 0 -0.34 123 123
CABIN1 0.008 0.094 -10000 0 -0.31 26 26
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.003 0.097 -10000 0 -0.48 13 13
mol:Ca2+ -0.005 0.01 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.003 0.074 -10000 0 -0.85 3 3
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.007 0.044 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.003 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.013 0.049 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.049 -10000 0 -10000 0 0
PRKCB -0.023 0.11 -10000 0 -0.34 42 42
PRKCE 0.007 0.074 -10000 0 -0.85 3 3
JNK2/NFAT4 0.021 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.038 0.2 -10000 0 -0.85 24 24
PRKCG 0.005 0.023 -10000 0 -0.31 2 2
PRKCQ 0 0.1 -10000 0 -0.85 6 6
FKBP38/BCL2 -0.042 0.16 -10000 0 -0.66 26 26
EP300 0.009 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.038 0.07 -10000 0 -0.41 3 3
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.01 0.063 -10000 0 -0.59 4 4
NFATc/ERK1 0.053 0.051 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.026 0.088 -10000 0 -0.56 5 5
NR4A1 -0.19 0.37 -10000 0 -0.75 123 123
GSK3B 0.01 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.032 0.057 -10000 0 -0.48 2 2
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.009 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.042 0.058 -10000 0 -10000 0 0
CREBBP 0.009 0.007 -10000 0 -10000 0 0
BCL2 -0.042 0.21 -10000 0 -0.85 26 26
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.013 0.12 -10000 0 -0.59 9 9
UGCG -0.034 0.16 -10000 0 -0.82 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.025 0.13 -10000 0 -0.41 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.013 0.16 -10000 0 -0.81 15 15
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.054 0.13 -10000 0 -0.46 25 25
FRAP1 0.01 0.19 -10000 0 -0.54 25 25
FOXO3 0.025 0.16 -10000 0 -0.61 13 13
AKT1 0.017 0.17 -10000 0 -0.65 14 14
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 -0.005 0.022 -10000 0 -10000 0 0
SGMS1 -0.005 0.022 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.031 -10000 0 -0.58 1 1
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.005 0.15 -10000 0 -0.47 23 23
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.022 0.035 -10000 0 -0.66 1 1
RPS6KB1 0.017 0.042 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.012 6 6
JAK3 -0.06 0.14 -10000 0 -0.31 94 94
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.013 0.21 -10000 0 -0.91 15 15
MYB -0.017 0.2 -10000 0 -1.4 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.013 0.16 -10000 0 -0.62 17 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.013 0.16 -10000 0 -0.59 17 17
Rac1/GDP 0.026 0.029 -10000 0 -0.53 1 1
T cell proliferation 0.022 0.15 -10000 0 -0.55 16 16
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.054 13 13
PRKCZ 0.021 0.15 -10000 0 -0.58 16 16
NF kappa B1 p50/RelA -0.053 0.13 -10000 0 -0.51 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.004 0.13 -10000 0 -0.63 10 10
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.044 0.2 -10000 0 -0.85 20 20
IL2RB -0.013 0.14 -10000 0 -0.85 9 9
TERT 0 0.032 -10000 0 -10000 0 0
E2F1 -0.005 0.077 -10000 0 -0.45 9 9
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.026 13 -10000 0 13
PTPN11 0.013 0.004 -10000 0 -10000 0 0
IL2RG -0.045 0.2 -10000 0 -0.85 20 20
actin cytoskeleton organization 0.022 0.15 -10000 0 -0.55 16 16
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.013 0.043 -10000 0 -0.85 1 1
Rac1/GTP 0.033 0.029 -10000 0 -0.51 1 1
LCK -0.007 0.11 -10000 0 -0.44 20 20
BCL2 -0.015 0.27 -10000 0 -0.83 35 35
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for