PARADIGM pathway analysis of mRNASeq expression and copy number 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 and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1R78CG5
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 39 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 203
Signaling events mediated by Stem cell factor receptor (c-Kit) 133
Signaling events regulated by Ret tyrosine kinase 118
Reelin signaling pathway 104
Noncanonical Wnt signaling pathway 99
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 88
Wnt signaling 86
PDGFR-alpha signaling pathway 78
FOXA2 and FOXA3 transcription factor networks 76
Signaling events mediated by the Hedgehog family 74
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 203 1423 7 -0.43 0 1000 -1000 -0.011 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 133 10422 78 -0.73 0.23 1000 -1000 -0.045 -1000
Signaling events regulated by Ret tyrosine kinase 118 9700 82 -0.38 0.026 1000 -1000 -0.06 -1000
Reelin signaling pathway 104 5836 56 -0.48 0.064 1000 -1000 -0.041 -1000
Noncanonical Wnt signaling pathway 99 2583 26 -0.34 0.026 1000 -1000 -0.036 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 88 6031 68 -0.7 0.34 1000 -1000 -0.065 -1000
Wnt signaling 86 606 7 -0.34 0.01 1000 -1000 -0.012 -1000
PDGFR-alpha signaling pathway 78 3447 44 -0.41 0.043 1000 -1000 -0.049 -1000
FOXA2 and FOXA3 transcription factor networks 76 3517 46 -0.9 0.03 1000 -1000 -0.071 -1000
Signaling events mediated by the Hedgehog family 74 3894 52 -0.31 0.14 1000 -1000 -0.032 -1000
Nongenotropic Androgen signaling 70 3678 52 -0.26 0.19 1000 -1000 -0.031 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 60 3267 54 -0.48 0.038 1000 -1000 -0.055 -1000
Nephrin/Neph1 signaling in the kidney podocyte 55 1876 34 -0.11 0.027 1000 -1000 -0.034 -1000
Calcium signaling in the CD4+ TCR pathway 53 1657 31 -0.35 0.026 1000 -1000 -0.045 -1000
Endothelins 51 4968 96 -0.33 0.028 1000 -1000 -0.053 -1000
Glypican 1 network 50 2412 48 -0.31 0.05 1000 -1000 -0.036 -1000
IGF1 pathway 48 2756 57 -0.13 0.057 1000 -1000 -0.043 -1000
IL4-mediated signaling events 47 4356 91 -1.2 0.56 1000 -1000 -0.073 -1000
HIF-1-alpha transcription factor network 46 3542 76 -0.5 0.041 1000 -1000 -0.05 -1000
IL23-mediated signaling events 45 2717 60 -0.31 0.026 1000 -1000 -0.043 -1000
Ephrin B reverse signaling 44 2114 48 -0.24 0.13 1000 -1000 -0.031 -1000
BMP receptor signaling 42 3405 81 -0.45 0.051 1000 -1000 -0.054 -1000
TCR signaling in naïve CD8+ T cells 41 3815 93 -0.16 0.045 1000 -1000 -0.05 -1000
Glucocorticoid receptor regulatory network 39 4533 114 -0.46 0.26 1000 -1000 -0.06 -1000
Coregulation of Androgen receptor activity 38 2953 76 -0.67 0.074 1000 -1000 -0.015 -1000
EPHB forward signaling 37 3196 85 -0.24 0.11 1000 -1000 -0.07 -1000
Arf6 signaling events 36 2249 62 -0.26 0.06 1000 -1000 -0.034 -1000
Signaling mediated by p38-alpha and p38-beta 35 1582 44 -0.23 0.026 1000 -1000 -0.033 -1000
Thromboxane A2 receptor signaling 29 3093 105 -0.16 0.049 1000 -1000 -0.044 -1000
Hedgehog signaling events mediated by Gli proteins 29 1921 65 -0.61 0.063 1000 -1000 -0.043 -1000
IL12-mediated signaling events 27 2357 87 -0.37 0.026 1000 -1000 -0.07 -1000
EGFR-dependent Endothelin signaling events 25 527 21 -0.072 0.037 1000 -1000 -0.048 -1000
IL6-mediated signaling events 24 1850 75 -0.16 0.054 1000 -1000 -0.039 -1000
ErbB2/ErbB3 signaling events 22 1451 65 -0.17 0.037 1000 -1000 -0.053 -1000
Syndecan-1-mediated signaling events 22 756 34 -0.085 0.026 1000 -1000 -0.035 -1000
Ras signaling in the CD4+ TCR pathway 22 380 17 -0.11 0.034 1000 -1000 -0.03 -1000
Osteopontin-mediated events 21 802 38 -0.16 0.039 1000 -1000 -0.034 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 21 1857 85 -0.22 0.13 1000 -1000 -0.047 -1000
Regulation of p38-alpha and p38-beta 21 1151 54 -0.36 0.063 1000 -1000 -0.045 -1000
Plasma membrane estrogen receptor signaling 20 1799 86 -0.13 0.047 1000 -1000 -0.057 -1000
Regulation of Androgen receptor activity 20 1415 70 -0.44 0.034 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 19 921 47 -0.25 0.042 1000 -1000 -0.034 -1000
IFN-gamma pathway 18 1268 68 -0.16 0.035 1000 -1000 -0.053 -1000
LPA receptor mediated events 18 1888 102 -0.16 0.034 1000 -1000 -0.064 -1000
BCR signaling pathway 18 1879 99 -0.11 0.046 1000 -1000 -0.056 -1000
Syndecan-4-mediated signaling events 17 1197 67 -0.16 0.038 1000 -1000 -0.038 -1000
Ceramide signaling pathway 16 1217 76 -0.14 0.074 1000 -1000 -0.036 -1000
Fc-epsilon receptor I signaling in mast cells 15 1511 97 -0.16 0.045 1000 -1000 -0.059 -1000
Angiopoietin receptor Tie2-mediated signaling 15 1329 88 -0.26 0.038 1000 -1000 -0.06 -1000
p75(NTR)-mediated signaling 14 1785 125 -0.29 0.072 1000 -1000 -0.059 -1000
amb2 Integrin signaling 14 1191 82 -0.23 0.034 1000 -1000 -0.038 -1000
Integrins in angiogenesis 14 1215 84 -0.14 0.055 1000 -1000 -0.049 -1000
VEGFR1 specific signals 14 832 56 -0.048 0.058 1000 -1000 -0.045 -1000
Signaling events mediated by PRL 14 477 34 -0.088 0.038 1000 -1000 -0.047 -1000
Signaling events mediated by PTP1B 13 1026 76 -0.2 0.041 1000 -1000 -0.035 -1000
ceramide signaling pathway 13 645 49 -0.058 0.038 1000 -1000 -0.039 -1000
RXR and RAR heterodimerization with other nuclear receptor 13 695 52 -0.19 0.06 1000 -1000 -0.032 -1000
IL27-mediated signaling events 13 683 51 -0.12 0.039 1000 -1000 -0.044 -1000
Insulin Pathway 12 895 74 -0.048 0.065 1000 -1000 -0.051 -1000
LPA4-mediated signaling events 11 139 12 -0.059 0.005 1000 -1000 -0.023 -1000
Caspase cascade in apoptosis 11 860 74 -0.059 0.043 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 11 455 38 -0.047 0.043 1000 -1000 -0.017 -1000
IL1-mediated signaling events 11 736 62 -0.079 0.061 1000 -1000 -0.053 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 11 500 45 -0.059 0.073 1000 -1000 -0.048 -1000
Neurotrophic factor-mediated Trk receptor signaling 11 1403 120 -0.25 0.073 1000 -1000 -0.046 -1000
Regulation of nuclear SMAD2/3 signaling 10 1444 136 -0.26 0.051 1000 -1000 -0.049 -1000
JNK signaling in the CD4+ TCR pathway 10 184 17 -0.075 0.025 1000 -1000 -0.037 -1000
mTOR signaling pathway 10 578 53 -0.037 0.03 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class III 10 436 40 -0.28 0.046 1000 -1000 -0.017 -1000
ErbB4 signaling events 9 648 69 -0.063 0.036 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 9 359 39 -0.059 0.026 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 9 600 61 -0.16 0.069 1000 -1000 -0.054 -1000
Nectin adhesion pathway 9 590 63 -0.11 0.072 1000 -1000 -0.042 -1000
Syndecan-3-mediated signaling events 9 340 35 -0.12 0.069 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 9 547 58 -0.052 0.048 1000 -1000 -0.037 -1000
Rapid glucocorticoid signaling 9 196 20 -0.058 0.034 1000 -1000 -0.007 -1000
Visual signal transduction: Rods 9 503 52 -0.071 0.045 1000 -1000 -0.03 -1000
Sphingosine 1-phosphate (S1P) pathway 8 225 28 -0.13 0.055 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 8 587 69 -0.16 0.049 1000 -1000 -0.032 -1000
S1P1 pathway 8 298 36 -0.066 0.026 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 8 484 58 -0.027 0.052 1000 -1000 -0.041 -1000
TCGA08_rtk_signaling 8 225 26 -0.19 0.051 1000 -1000 -0.007 -1000
Stabilization and expansion of the E-cadherin adherens junction 8 599 74 -0.12 0.069 1000 -1000 -0.059 -1000
FOXM1 transcription factor network 8 424 51 -0.22 0.052 1000 -1000 -0.09 -1000
BARD1 signaling events 7 419 57 -0.041 0.051 1000 -1000 -0.046 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 558 83 -0.18 0.047 1000 -1000 -0.043 -1000
TCGA08_p53 6 42 7 -0.024 0.025 1000 -1000 -0.008 -1000
Class I PI3K signaling events 6 484 73 -0.2 0.049 1000 -1000 -0.039 -1000
Regulation of Telomerase 6 692 102 -0.2 0.071 1000 -1000 -0.039 -1000
S1P3 pathway 6 278 42 -0.13 0.046 1000 -1000 -0.036 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 219 33 -0.12 0.054 1000 -1000 -0.025 -1000
PLK1 signaling events 5 447 85 -0.007 0.056 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class I 5 559 104 -0.059 0.062 1000 -1000 -0.032 -1000
TCGA08_retinoblastoma 5 47 8 -0.035 0.03 1000 -1000 -0.002 -1000
Class IB PI3K non-lipid kinase events 5 15 3 -0.015 0.015 1000 -1000 -0.004 -1000
Effects of Botulinum toxin 4 104 26 -0.074 0.047 1000 -1000 -0.015 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 513 125 -0.012 0.069 1000 -1000 -0.054 -1000
IL2 signaling events mediated by STAT5 4 101 22 -0.027 0.033 1000 -1000 -0.039 -1000
Aurora B signaling 4 295 67 -0.33 0.1 1000 -1000 -0.042 -1000
Canonical NF-kappaB pathway 3 134 39 -0.059 0.06 1000 -1000 -0.027 -1000
a4b1 and a4b7 Integrin signaling 3 18 5 0.004 0.036 1000 -1000 0.003 -1000
Insulin-mediated glucose transport 3 103 32 -0.086 0.05 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 3 217 68 -0.086 0.049 1000 -1000 -0.036 -1000
S1P5 pathway 3 52 17 -0.008 0.032 1000 -1000 -0.015 -1000
Canonical Wnt signaling pathway 3 195 51 -0.038 0.063 1000 -1000 -0.049 -1000
PDGFR-beta signaling pathway 3 351 97 -0.15 0.078 1000 -1000 -0.055 -1000
S1P4 pathway 3 89 25 -0.001 0.046 1000 -1000 -0.028 -1000
p38 MAPK signaling pathway 3 135 44 -0.024 0.048 1000 -1000 -0.023 -1000
EPO signaling pathway 2 162 55 -0.024 0.06 1000 -1000 -0.047 -1000
FoxO family signaling 2 183 64 -0.086 0.11 1000 -1000 -0.042 -1000
Signaling mediated by p38-gamma and p38-delta 2 39 15 0 0.026 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 2 85 31 -0.009 0.038 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 2 97 43 -0.029 0.05 1000 -1000 -0.035 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 45 23 -0.015 0.048 1000 -1000 -0.028 -1000
Circadian rhythm pathway 1 34 22 -0.012 0.044 1000 -1000 -0.031 -1000
Aurora A signaling 1 103 60 -0.025 0.053 1000 -1000 -0.022 -1000
Paxillin-independent events mediated by a4b1 and a4b7 1 68 37 0 0.064 1000 -1000 -0.031 -1000
TRAIL signaling pathway 1 70 48 -0.018 0.072 1000 -1000 -0.036 -1000
HIF-2-alpha transcription factor network 1 76 43 -0.16 0.16 1000 -1000 -0.036 -1000
Paxillin-dependent events mediated by a4b1 1 46 36 -0.054 0.056 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 1 109 76 -0.058 0.064 1000 -1000 -0.058 -1000
Arf6 trafficking events 1 90 71 -0.046 0.048 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class II 0 61 75 -0.035 0.073 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 0 0 3 0.015 0.026 1000 -1000 -0.014 -1000
Arf6 downstream pathway 0 6 43 -0.059 0.045 1000 -1000 -0.02 -1000
Aurora C signaling 0 1 7 -0.006 0.047 1000 -1000 -0.016 -1000
Glypican 2 network 0 3 4 -0.021 0.012 1000 -1000 -0.009 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 12 27 0 0.065 1000 -1000 -0.037 -1000
E-cadherin signaling events 0 0 5 0.025 0.05 1000 -1000 0.002 -1000
Arf1 pathway 0 15 54 -0.001 0.05 1000 -1000 -0.02 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.071 1000 -1000 -0.003 -1000
Total 2828 163280 7203 -23 8 131000 -131000 -4.9 -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 -0.33 0.27 -9999 0 -0.5 278 278
EFNA5 -0.082 0.26 -9999 0 -0.69 61 61
FYN -0.31 0.24 -9999 0 -0.46 274 274
neuron projection morphogenesis -0.33 0.27 -9999 0 -0.5 278 278
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.33 0.27 -9999 0 -0.5 278 278
EPHA5 -0.43 0.34 -9999 0 -0.69 254 254
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 0.2 0.38 1 -0.39 224 225
CRKL -0.22 0.22 -10000 0 -0.41 225 225
HRAS -0.19 0.19 -10000 0 -0.4 86 86
mol:PIP3 -0.2 0.2 -10000 0 -0.39 207 207
SPRED1 0.026 0.003 -10000 0 -10000 0 0
SPRED2 0.026 0.005 -10000 0 -10000 0 0
GAB1 -0.23 0.23 -10000 0 -0.43 225 225
FOXO3 -0.18 0.2 0.44 1 -0.36 216 217
AKT1 -0.2 0.22 0.29 1 -0.39 218 219
BAD -0.18 0.2 0.29 2 -0.36 214 216
megakaryocyte differentiation -0.23 0.22 -10000 0 -0.42 234 234
GSK3B -0.18 0.21 0.32 2 -0.36 215 217
RAF1 -0.15 0.16 0.35 1 -0.34 59 60
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.23 0.23 -10000 0 -0.43 223 223
STAT1 -0.57 0.56 -10000 0 -1.1 228 228
HRAS/SPRED1 -0.15 0.16 -10000 0 -0.34 59 59
cell proliferation -0.23 0.23 -10000 0 -0.43 228 228
PIK3CA 0.024 0.036 -10000 0 -0.69 1 1
TEC 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.22 0.23 -10000 0 -0.42 226 226
HRAS/SPRED2 -0.15 0.16 -10000 0 -0.34 59 59
LYN/TEC/p62DOK -0.2 0.24 -10000 0 -0.41 224 224
MAPK3 -0.1 0.13 0.32 5 -0.29 11 16
STAP1 -0.24 0.23 -10000 0 -0.44 225 225
GRAP2 -0.02 0.15 -10000 0 -0.56 27 27
JAK2 -0.48 0.48 -10000 0 -0.88 228 228
STAT1 (dimer) -0.56 0.54 -10000 0 -1 228 228
mol:Gleevec 0.007 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.2 0.23 -10000 0 -0.41 215 215
actin filament polymerization -0.22 0.22 -10000 0 -0.42 223 223
LYN 0.026 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.33 0.32 0.35 1 -0.61 227 228
PIK3R1 0.025 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.18 0.21 -10000 0 -0.38 214 214
PI3K -0.2 0.23 -10000 0 -0.4 224 224
PTEN 0.025 0.021 -10000 0 -0.38 1 1
SCF/KIT/EPO/EPOR -0.68 0.66 -10000 0 -1.3 227 227
MAPK8 -0.23 0.23 -10000 0 -0.43 228 228
STAT3 (dimer) -0.22 0.22 -10000 0 -0.42 223 223
positive regulation of transcription -0.082 0.12 0.34 7 -0.23 11 18
mol:GDP -0.19 0.2 -10000 0 -0.38 194 194
PIK3C2B -0.22 0.23 -10000 0 -0.43 207 207
CBL/CRKL -0.2 0.21 -10000 0 -0.38 223 223
FER -0.23 0.23 -10000 0 -0.43 227 227
SH2B3 -0.23 0.23 -10000 0 -0.43 227 227
PDPK1 -0.18 0.2 0.29 2 -0.36 202 204
SNAI2 -0.23 0.23 -10000 0 -0.43 227 227
positive regulation of cell proliferation -0.4 0.39 -10000 0 -0.74 228 228
KITLG -0.011 0.069 -10000 0 -0.72 3 3
cell motility -0.4 0.39 -10000 0 -0.74 228 228
PTPN6 0.037 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.18 -10000 0 -1.1 3 3
STAT5A (dimer) -0.33 0.32 -10000 0 -0.61 227 227
SOCS1 0.024 0.014 -10000 0 -10000 0 0
cell migration 0.23 0.23 0.43 223 -10000 0 223
SOS1 0.026 0.005 -10000 0 -10000 0 0
EPO -0.006 0.028 -10000 0 -10000 0 0
VAV1 0.011 0.064 -10000 0 -0.58 3 3
GRB10 -0.23 0.23 -10000 0 -0.43 224 224
PTPN11 0.034 0.011 -10000 0 -10000 0 0
SCF/KIT -0.24 0.24 -10000 0 -0.45 227 227
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.12 0.14 0.34 4 -0.32 10 14
CBL 0.026 0.005 -10000 0 -10000 0 0
KIT -0.73 0.69 -10000 0 -1.3 227 227
MAP2K2 -0.12 0.13 0.37 3 -0.32 10 13
SHC/Grb2/SOS1 -0.19 0.23 -10000 0 -0.41 199 199
STAT5A -0.34 0.33 -10000 0 -0.63 227 227
GRB2 0.025 0.006 -10000 0 -10000 0 0
response to radiation -0.23 0.23 -10000 0 -0.42 227 227
SHC/GRAP2 0 0.11 -10000 0 -0.38 27 27
PTPRO -0.24 0.23 -10000 0 -0.43 234 234
SH2B2 -0.23 0.23 -10000 0 -0.43 223 223
DOK1 0.026 0.005 -10000 0 -10000 0 0
MATK -0.23 0.23 -10000 0 -0.44 223 223
CREBBP -0.04 0.077 -10000 0 -10000 0 0
BCL2 -0.2 0.38 -10000 0 -1.5 29 29
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.065 0.097 -10000 0 -0.6 6 6
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 210 210
JUN -0.26 0.26 -10000 0 -0.58 126 126
HRAS 0.025 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.27 0.29 -10000 0 -0.5 238 238
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.28 0.29 -10000 0 -0.5 240 240
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.21 0.23 -10000 0 -0.42 225 225
RHOA 0.026 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.25 0.27 -10000 0 -0.45 234 234
GRB7 0.003 0.054 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.27 0.29 -10000 0 -0.5 238 238
MAPKKK cascade -0.24 0.24 -10000 0 -0.43 233 233
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.26 0.27 -10000 0 -0.46 240 240
lamellipodium assembly -0.2 0.18 -10000 0 -0.35 212 212
RET51/GFRalpha1/GDNF/SHC -0.27 0.29 -10000 0 -0.5 227 227
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
RET9/GFRalpha1/GDNF/SHC -0.21 0.22 -10000 0 -0.4 224 224
RET9/GFRalpha1/GDNF/Shank3 -0.22 0.22 -10000 0 -0.41 228 228
MAPK3 -0.25 0.24 -10000 0 -0.43 231 231
DOK1 0.026 0.005 -10000 0 -10000 0 0
DOK6 -0.094 0.27 -10000 0 -0.69 68 68
PXN 0.026 0.005 -10000 0 -10000 0 0
neurite development -0.27 0.25 -10000 0 -0.46 236 236
DOK5 -0.064 0.24 -10000 0 -0.69 51 51
GFRA1 -0.38 0.35 -10000 0 -0.68 232 232
MAPK8 -0.2 0.2 -10000 0 -0.48 72 72
HRAS/GTP -0.26 0.28 -10000 0 -0.48 238 238
tube development -0.2 0.21 -10000 0 -0.39 215 215
MAPK1 -0.25 0.24 0.32 3 -0.43 233 236
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 215 215
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
PDLIM7 0.025 0.014 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.32 0.34 -10000 0 -0.55 249 249
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.27 0.29 -10000 0 -0.49 242 242
RET51/GFRalpha1/GDNF/Dok5 -0.32 0.34 -10000 0 -0.56 250 250
PRKCA -0.014 0.16 -10000 0 -0.69 22 22
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
CREB1 -0.2 0.21 -10000 0 -0.38 212 212
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.15 0.16 -10000 0 -0.3 202 202
RET51/GFRalpha1/GDNF/Grb7 -0.28 0.29 -10000 0 -0.5 238 238
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.11 0.26 -10000 0 -0.68 68 68
DOK4 0.026 0.006 -10000 0 -10000 0 0
JNK cascade -0.26 0.25 -10000 0 -0.56 126 126
RET9/GFRalpha1/GDNF/FRS2 -0.21 0.23 -10000 0 -0.41 226 226
SHANK3 0.019 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 204 204
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.36 237 237
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.36 242 242
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.23 0.26 -10000 0 -0.41 228 228
PI3K -0.31 0.29 -10000 0 -0.55 217 217
SOS1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.2 0.21 -10000 0 -0.39 216 216
GRB10 0.025 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.34 176 176
RET51/GFRalpha1/GDNF/FRS2 -0.27 0.29 -10000 0 -0.5 240 240
GAB1 0.026 0.004 -10000 0 -10000 0 0
IRS1 -0.048 0.22 -10000 0 -0.69 42 42
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.23 0.26 -10000 0 -0.41 226 226
RET51/GFRalpha1/GDNF/PKC alpha -0.29 0.32 -10000 0 -0.53 237 237
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
GDNF -0.006 0.024 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.32 0.32 -10000 0 -0.54 250 250
Rac1/GTP -0.24 0.22 -10000 0 -0.42 212 212
RET9/GFRalpha1/GDNF -0.24 0.24 -10000 0 -0.45 231 231
GFRalpha1/GDNF -0.28 0.27 -10000 0 -0.52 231 231
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.014 -10000 0 -10000 0 0
VLDLR 0.004 0.12 -10000 0 -0.66 12 12
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.026 0.004 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
ITGA3 0.024 0.016 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.31 0.24 -10000 0 -0.46 284 284
MAPK8IP1/MKK7/MAP3K11/JNK1 0.064 0.049 -10000 0 -0.39 3 3
AKT1 -0.2 0.15 -10000 0 -0.3 275 275
MAP2K7 0.025 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
DAB1 0.007 0.021 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.29 0.22 -10000 0 -0.43 278 278
LRPAP1/LRP8 0.019 0.1 -10000 0 -0.52 14 14
RELN/LRP8/DAB1/Fyn -0.27 0.22 -10000 0 -0.41 278 278
DAB1/alpha3/beta1 Integrin -0.26 0.21 -10000 0 -0.39 270 270
long-term memory -0.27 0.23 -10000 0 -0.41 277 277
DAB1/LIS1 -0.26 0.22 -10000 0 -0.4 273 273
DAB1/CRLK/C3G -0.26 0.21 -10000 0 -0.39 273 273
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
DAB1/NCK2 -0.26 0.22 -10000 0 -0.4 276 276
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0 0.13 -10000 0 -0.69 13 13
CDK5R1 0.024 0.012 -10000 0 -10000 0 0
RELN -0.48 0.32 -10000 0 -0.69 281 281
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.31 0.24 -10000 0 -0.46 284 284
GRIN2A/RELN/LRP8/DAB1/Fyn -0.28 0.24 -10000 0 -0.42 277 277
MAPK8 0.021 0.062 -10000 0 -0.69 3 3
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.42 284 284
ITGB1 0.026 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.42 278 278
RELN/LRP8 -0.31 0.24 -10000 0 -0.46 282 282
GRIN2B/RELN/LRP8/DAB1/Fyn -0.27 0.22 -10000 0 -0.41 278 278
PI3K 0.037 0.029 -10000 0 -0.52 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.036 0.015 -10000 0 -10000 0 0
RAP1A -0.24 0.21 0.48 3 -0.41 106 109
PAFAH1B1 0.025 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.018 -10000 0 -10000 0 0
GRIN2B -0.004 0.02 -10000 0 -10000 0 0
NCK2 0.026 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.44 24 24
neuron adhesion -0.22 0.22 0.46 9 -0.64 18 27
LRP8 0.001 0.13 -10000 0 -0.69 14 14
GSK3B -0.19 0.14 -10000 0 -0.42 23 23
RELN/VLDLR/DAB1/Fyn -0.27 0.21 -10000 0 -0.4 277 277
MAP3K11 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.32 277 277
CDK5 0.025 0.006 -10000 0 -10000 0 0
MAPT 0.046 0.15 0.81 13 -0.62 2 15
neuron migration -0.26 0.2 0.26 3 -0.39 268 271
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.44 24 24
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 280 280
Noncanonical Wnt 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
NFATC2 -0.075 0.25 -10000 0 -0.69 57 57
GNB1/GNG2 -0.21 0.24 -10000 0 -0.38 248 248
mol:DAG -0.2 0.21 -10000 0 -0.49 98 98
PLCG1 -0.21 0.21 -10000 0 -0.51 98 98
YES1 -0.23 0.23 -10000 0 -0.39 252 252
FZD3 0.026 0.004 -10000 0 -10000 0 0
FZD6 0.026 0.005 -10000 0 -10000 0 0
G protein -0.2 0.22 -10000 0 -0.52 98 98
MAP3K7 -0.17 0.18 0.31 1 -0.42 94 95
mol:Ca2+ -0.19 0.2 -10000 0 -0.48 98 98
mol:IP3 -0.2 0.21 -10000 0 -0.49 98 98
NLK -0.003 0.062 -10000 0 -0.86 2 2
GNB1 0.026 0.005 -10000 0 -10000 0 0
CAMK2A -0.18 0.19 0.31 1 -0.45 97 98
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.24 0.24 -10000 0 -0.41 254 254
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
GNAS -0.23 0.23 -10000 0 -0.39 250 250
GO:0007205 -0.2 0.2 -10000 0 -0.48 98 98
WNT6 0.02 0.024 -10000 0 -10000 0 0
WNT4 -0.21 0.33 -10000 0 -0.69 133 133
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.51 141 141
GNG2 0.026 0.005 -10000 0 -10000 0 0
WNT5A 0.01 0.11 -10000 0 -0.69 9 9
WNT11 -0.34 0.36 -10000 0 -0.68 210 210
CDC42 -0.22 0.22 -10000 0 -0.37 246 246
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.012 0.11 -10000 0 -0.49 14 14
NFATC2 -0.2 0.33 -10000 0 -0.74 89 89
NFATC3 -0.082 0.14 -10000 0 -0.29 92 92
CD40LG -0.62 0.56 -10000 0 -1.1 218 218
ITCH 0.037 0.017 -10000 0 -10000 0 0
CBLB 0.038 0.017 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.43 0.5 -10000 0 -1.2 97 97
JUNB 0.019 0.058 -10000 0 -0.53 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.041 0.02 -10000 0 -0.32 1 1
T cell anergy 0.012 0.076 0.39 5 -0.48 1 6
TLE4 -0.2 0.35 -10000 0 -0.75 97 97
Jun/NFAT1-c-4/p21SNFT -0.54 0.6 -10000 0 -1.1 187 187
AP-1/NFAT1-c-4 -0.7 0.75 -10000 0 -1.3 210 210
IKZF1 -0.15 0.28 -10000 0 -0.62 79 79
T-helper 2 cell differentiation -0.27 0.33 -10000 0 -0.86 71 71
AP-1/NFAT1 -0.31 0.41 -10000 0 -0.77 154 154
CALM1 0.037 0.013 -10000 0 -10000 0 0
EGR2 -0.7 0.78 -10000 0 -1.5 186 186
EGR3 -0.52 0.7 -10000 0 -1.3 136 136
NFAT1/FOXP3 -0.16 0.28 -10000 0 -0.6 93 93
EGR1 -0.12 0.28 -10000 0 -0.69 81 81
JUN -0.14 0.29 -10000 0 -0.69 87 87
EGR4 -0.025 0.16 -10000 0 -0.68 23 23
mol:Ca2+ 0.011 0.01 -10000 0 -10000 0 0
GBP3 -0.14 0.27 -10000 0 -0.7 53 53
FOSL1 0.003 0.054 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.47 0.56 -10000 0 -1 189 189
DGKA -0.14 0.24 -10000 0 -0.57 76 76
CREM 0.026 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.48 0.55 -10000 0 -1 187 187
CTLA4 -0.17 0.3 -10000 0 -0.72 72 72
NFAT1-c-4 (dimer)/EGR1 -0.54 0.63 -10000 0 -1.2 186 186
NFAT1-c-4 (dimer)/EGR4 -0.5 0.56 -10000 0 -1 191 191
FOS -0.17 0.31 -10000 0 -0.69 103 103
IFNG -0.36 0.5 -10000 0 -1.1 104 104
T cell activation -0.38 0.39 -10000 0 -0.88 130 130
MAF 0.025 0.006 -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 0.34 0.4 0.74 180 -10000 0 180
TNF -0.53 0.55 -10000 0 -1 204 204
FASLG -0.69 0.77 -10000 0 -1.4 197 197
TBX21 -0.023 0.16 -10000 0 -0.7 19 19
BATF3 0.016 0.048 -10000 0 -0.69 1 1
PRKCQ 0.014 0.084 -10000 0 -0.64 6 6
PTPN1 -0.14 0.25 -10000 0 -0.64 56 56
NFAT1-c-4/ICER1 -0.47 0.55 -10000 0 -1 186 186
GATA3 -0.01 0.16 -10000 0 -0.65 22 22
T-helper 1 cell differentiation -0.35 0.48 -10000 0 -1.1 104 104
IL2RA -0.39 0.46 -10000 0 -1 100 100
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.14 0.25 -10000 0 -0.63 56 56
E2F1 -0.014 0.068 -10000 0 -10000 0 0
PPARG 0.016 0.08 -10000 0 -0.69 5 5
SLC3A2 -0.14 0.25 -10000 0 -0.58 74 74
IRF4 -0.044 0.18 -10000 0 -0.68 26 26
PTGS2 -0.6 0.55 -10000 0 -1.1 208 208
CSF2 -0.6 0.54 -10000 0 -1.1 212 212
JunB/Fra1/NFAT1-c-4 -0.45 0.54 -10000 0 -0.98 184 184
IL4 -0.28 0.35 -10000 0 -0.92 69 69
IL5 -0.59 0.53 -10000 0 -1 208 208
IL2 -0.39 0.4 -10000 0 -0.9 130 130
IL3 -0.07 0.089 -10000 0 -1.1 1 1
RNF128 0.034 0.041 -10000 0 -0.76 1 1
NFATC1 -0.34 0.41 -10000 0 -0.74 180 180
CDK4 0.22 0.25 0.55 102 -10000 0 102
PTPRK -0.14 0.25 -10000 0 -0.57 77 77
IL8 -0.6 0.53 -10000 0 -1.1 207 207
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.24 0.24 -9999 0 -0.41 254 254
FZD6 0.026 0.005 -9999 0 -10000 0 0
WNT6 0.02 0.024 -9999 0 -10000 0 0
WNT4 -0.21 0.33 -9999 0 -0.69 133 133
FZD3 0.026 0.004 -9999 0 -10000 0 0
WNT5A 0.01 0.11 -9999 0 -0.69 9 9
WNT11 -0.34 0.36 -9999 0 -0.68 210 210
PDGFR-alpha 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
PDGFRA -0.21 0.33 -10000 0 -0.7 123 123
PDGF/PDGFRA/CRKL -0.14 0.25 -10000 0 -0.52 122 122
positive regulation of JUN kinase activity -0.079 0.2 -10000 0 -0.41 109 109
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.25 -10000 0 -0.53 122 122
AP1 -0.41 0.55 -10000 0 -1.3 110 110
mol:IP3 -0.16 0.25 -10000 0 -0.54 122 122
PLCG1 -0.16 0.25 -10000 0 -0.54 122 122
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.52 122 122
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.25 -10000 0 -0.53 122 122
CAV3 -0.011 0.02 -10000 0 -10000 0 0
CAV1 0.011 0.1 -10000 0 -0.69 8 8
SHC/Grb2/SOS1 -0.078 0.21 -10000 0 -0.41 109 109
PDGF/PDGFRA/Shf -0.14 0.25 -10000 0 -0.52 123 123
FOS -0.4 0.52 -10000 0 -1.2 110 110
JUN -0.15 0.23 -10000 0 -0.59 86 86
oligodendrocyte development -0.14 0.25 -10000 0 -0.52 122 122
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.25 -10000 0 -0.54 122 122
PDGF/PDGFRA -0.21 0.33 -10000 0 -0.7 123 123
actin cytoskeleton reorganization -0.14 0.25 -10000 0 -0.52 123 123
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K -0.1 0.22 -10000 0 -0.44 121 121
PDGF/PDGFRA/Crk/C3G -0.1 0.22 -10000 0 -0.44 120 120
JAK1 -0.15 0.24 -10000 0 -0.52 123 123
ELK1/SRF -0.12 0.19 0.32 1 -0.42 114 115
SHB 0.025 0.007 -10000 0 -10000 0 0
SHF 0.026 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.024 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.55 122 122
SOS1 0.026 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.079 0.2 -10000 0 -0.41 109 109
PDGF/PDGFRA/SHB -0.14 0.25 -10000 0 -0.52 123 123
PDGF/PDGFRA/Caveolin-1 -0.15 0.26 -10000 0 -0.52 125 125
ITGAV 0.024 0.036 -10000 0 -0.69 1 1
ELK1 -0.16 0.22 -10000 0 -0.5 119 119
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
PDGF/PDGFRA/Crk -0.14 0.24 -10000 0 -0.5 122 122
JAK-STAT cascade -0.15 0.24 -10000 0 -0.52 123 123
cell proliferation -0.14 0.25 -10000 0 -0.52 123 123
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 -0.5 0.5 -10000 0 -1 173 173
PCK1 -0.34 0.47 -10000 0 -1.4 54 54
HNF4A -0.65 0.62 -10000 0 -1.2 203 203
KCNJ11 -0.47 0.49 -10000 0 -1 150 150
AKT1 -0.067 0.14 -10000 0 -0.46 12 12
response to starvation -0.018 0.041 -10000 0 -0.37 2 2
DLK1 -0.48 0.49 -10000 0 -1 154 154
NKX2-1 -0.18 0.19 -10000 0 -10000 0 0
ACADM -0.5 0.5 -10000 0 -1 155 155
TAT -0.19 0.2 -10000 0 -0.57 15 15
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.071 -10000 0 -0.69 4 4
TTR -0.15 0.23 0.62 4 -0.74 24 28
PKLR -0.49 0.5 -10000 0 -1 165 165
APOA1 -0.9 0.85 -10000 0 -1.7 205 205
CPT1C -0.5 0.5 -10000 0 -1 172 172
ALAS1 -0.17 0.2 -10000 0 -1.2 1 1
TFRC -0.24 0.27 -10000 0 -0.7 32 32
FOXF1 0.013 0.071 -10000 0 -0.69 4 4
NF1 0.03 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.026 0.036 -10000 0 -0.69 1 1
CPT1A -0.5 0.5 -10000 0 -1 164 164
HMGCS1 -0.5 0.5 -10000 0 -0.99 174 174
NR3C1 0.031 0.01 -10000 0 -10000 0 0
CPT1B -0.5 0.49 -10000 0 -1 173 173
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.026 0.006 -10000 0 -10000 0 0
GCK -0.63 0.64 -10000 0 -1.2 189 189
CREB1 0.005 0.07 -10000 0 -0.39 2 2
IGFBP1 -0.17 0.18 -10000 0 -10000 0 0
PDX1 -0.19 0.2 -10000 0 -0.7 4 4
UCP2 -0.5 0.5 -10000 0 -1 167 167
ALDOB -0.47 0.49 -10000 0 -1 155 155
AFP -0.021 0.088 -10000 0 -0.37 6 6
BDH1 -0.5 0.5 -10000 0 -1 168 168
HADH -0.47 0.49 -10000 0 -1 153 153
F2 -0.61 0.59 -10000 0 -1.2 168 168
HNF1A 0.026 0.036 -10000 0 -0.69 1 1
G6PC -0.004 0.071 -10000 0 -10000 0 0
SLC2A2 -0.23 0.25 -10000 0 -1.3 2 2
INS -0.022 0.013 -10000 0 -10000 0 0
FOXA1 -0.015 0.097 -10000 0 -0.32 27 27
FOXA3 -0.031 0.12 -10000 0 -0.38 17 17
FOXA2 -0.53 0.55 -10000 0 -1.1 172 172
ABCC8 -0.73 0.68 -10000 0 -1.3 218 218
ALB -0.068 0.29 -10000 0 -1.1 27 27
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.093 0.21 -10000 0 -0.42 107 107
IHH -0.17 0.33 -10000 0 -0.72 105 105
SHH Np/Cholesterol/GAS1 -0.058 0.16 -10000 0 -0.41 70 70
LRPAP1 0.026 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.057 0.16 0.4 70 -10000 0 70
SMO/beta Arrestin2 -0.082 0.21 -10000 0 -0.42 95 95
SMO -0.1 0.21 -10000 0 -0.44 99 99
AKT1 -0.017 0.099 -10000 0 -0.34 1 1
ARRB2 0.025 0.007 -10000 0 -10000 0 0
BOC 0.014 0.093 -10000 0 -0.69 7 7
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
heart looping -0.099 0.21 -10000 0 -0.44 100 100
STIL -0.072 0.16 0.27 1 -0.33 93 94
DHH N/PTCH2 -0.053 0.21 -10000 0 -0.52 66 66
DHH N/PTCH1 -0.083 0.19 -10000 0 -0.38 110 110
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
DHH 0.02 0.062 -10000 0 -0.69 3 3
PTHLH -0.14 0.31 -10000 0 -1.1 25 25
determination of left/right symmetry -0.099 0.21 -10000 0 -0.44 100 100
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development -0.14 0.31 -10000 0 -1 25 25
IHH N/Hhip -0.31 0.34 -10000 0 -0.6 216 216
DHH N/Hhip -0.18 0.27 -10000 0 -0.52 154 154
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.099 0.21 -10000 0 -0.44 100 100
pancreas development -0.25 0.34 -10000 0 -0.69 154 154
HHAT 0.023 0.036 -10000 0 -0.69 1 1
PI3K 0.037 0.029 -10000 0 -0.52 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.11 0.27 -10000 0 -0.64 80 80
somite specification -0.099 0.21 -10000 0 -0.44 100 100
SHH Np/Cholesterol/PTCH1 -0.076 0.16 -10000 0 -0.34 96 96
SHH Np/Cholesterol/PTCH2 -0.046 0.16 -10000 0 -0.39 65 65
SHH Np/Cholesterol/Megalin -0.08 0.18 -10000 0 -0.4 97 97
SHH -0.005 0.031 -10000 0 -0.52 1 1
catabolic process -0.1 0.21 -10000 0 -0.41 120 120
SMO/Vitamin D3 -0.081 0.19 -10000 0 -0.39 96 96
SHH Np/Cholesterol/Hhip -0.14 0.21 -10000 0 -0.4 154 154
LRP2 -0.15 0.31 -10000 0 -0.68 100 100
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.45 80 80
SHH Np/Cholesterol/BOC 0.012 0.059 -10000 0 -0.38 8 8
SHH Np/Cholesterol/CDO -0.098 0.19 -10000 0 -0.39 116 116
mesenchymal cell differentiation 0.14 0.2 0.4 154 -10000 0 154
mol:Vitamin D3 -0.071 0.17 -10000 0 -0.35 96 96
IHH N/PTCH2 -0.18 0.3 -10000 0 -0.55 151 151
CDON -0.18 0.32 -10000 0 -0.69 116 116
IHH N/PTCH1 -0.098 0.21 -10000 0 -0.42 120 120
Megalin/LRPAP1 -0.098 0.24 -10000 0 -0.51 100 100
PTCH2 -0.088 0.26 -10000 0 -0.68 65 65
SHH Np/Cholesterol 0.009 0.025 -10000 0 -0.42 1 1
PTCH1 -0.1 0.21 -10000 0 -0.41 120 120
HHIP -0.26 0.34 -10000 0 -0.69 154 154
Nongenotropic Androgen signaling

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
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.14 0.22 -10000 0 -0.4 164 164
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.3 161 161
GNAO1 0.007 0.11 -10000 0 -0.69 10 10
HRAS 0.024 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.008 0.065 -10000 0 -0.45 8 8
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.21 0.54 5 -0.38 158 163
T-DHT/AR -0.2 0.26 -10000 0 -0.52 166 166
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.006 106 106
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.21 0.26 -10000 0 -0.53 163 163
cell proliferation -0.2 0.27 0.52 9 -0.52 120 129
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
FOS -0.26 0.37 0.54 7 -0.85 107 114
mol:Ca2+ -0.026 0.029 -10000 0 -0.066 83 83
MAPK3 -0.16 0.24 0.52 11 -0.5 76 87
MAPK1 -0.17 0.22 0.35 5 -0.42 136 141
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 96 96
cAMP biosynthetic process 0.014 0.072 0.25 7 -0.42 8 15
GNG2 0.026 0.005 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 96 96
HRAS/GTP -0.14 0.21 -10000 0 -0.39 158 158
actin cytoskeleton reorganization 0.037 0.023 -10000 0 -0.37 1 1
SRC 0.025 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 96 96
PI3K 0.034 0.025 -10000 0 -0.45 1 1
apoptosis 0.19 0.25 0.52 121 -0.45 7 128
T-DHT/AR/PELP1 -0.16 0.24 -10000 0 -0.44 166 166
HRAS/GDP -0.2 0.26 -10000 0 -0.51 163 163
CREB1 -0.21 0.27 0.46 7 -0.57 121 128
RAC1-CDC42/GTP 0.047 0.026 -10000 0 -0.38 1 1
AR -0.26 0.35 -10000 0 -0.68 166 166
GNB1 0.026 0.005 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.55 5 -0.39 158 163
RAC1-CDC42/GDP -0.18 0.26 -10000 0 -0.49 162 162
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.42 158 158
MAP2K2 -0.15 0.2 0.5 3 -0.38 156 159
T-DHT/AR/PELP1/Src/PI3K -0.11 0.16 -10000 0 -0.3 161 161
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.011 0.1 -10000 0 -0.69 8 8
Gi family/GNB1/GNG2/GDP -0.031 0.094 -10000 0 -0.42 13 13
mol:T-DHT -0.001 0.003 0.001 44 -0.005 60 104
RAC1 0.025 0.006 -10000 0 -10000 0 0
GNRH1 0.007 0.027 -10000 0 -0.52 1 1
Gi family/GTP -0.086 0.11 -10000 0 -0.29 38 38
CDC42 0.026 0.005 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.005 -10000 0 -10000 0 0
VLDLR 0.004 0.12 -10000 0 -0.66 12 12
LRPAP1 0.026 0.004 -10000 0 -10000 0 0
NUDC 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.31 0.24 -10000 0 -0.46 282 282
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.29 0.21 -10000 0 -0.43 275 275
IQGAP1/CaM 0.038 0.008 -10000 0 -10000 0 0
DAB1 0.007 0.021 -10000 0 -10000 0 0
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
PLA2G7 -0.08 0.25 -10000 0 -0.69 60 60
CALM1 0.026 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.019 0.1 -10000 0 -0.52 14 14
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.005 -10000 0 -10000 0 0
CDK5R1 0.024 0.012 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.003 -10000 0 -10000 0 0
CDK5R2 0.001 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.31 0.24 -10000 0 -0.46 284 284
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.22 0.19 0.37 4 -0.52 18 22
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.016 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.25 0.19 -10000 0 -0.38 269 269
RELN -0.48 0.32 -10000 0 -0.69 281 281
PAFAH/LIS1 -0.04 0.17 -10000 0 -0.44 60 60
LIS1/CLIP170 0.03 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.49 11 11
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.16 -10000 0 -0.3 270 270
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.24 0.18 -10000 0 -0.36 268 268
LIS1/IQGAP1 0.03 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.012 -10000 0 -10000 0 0
PAFAH1B2 0.022 0.05 -10000 0 -0.69 2 2
MAP1B/LIS1/Dynein heavy chain 0.03 0.011 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.21 0.18 0.32 1 -0.58 12 13
LRP8 0.001 0.13 -10000 0 -0.69 14 14
NDEL1/Katanin 60 -0.22 0.18 0.29 3 -0.46 28 31
P39/CDK5 -0.26 0.19 -10000 0 -0.38 274 274
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.2 -10000 0 -0.4 275 275
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.026 0.008 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.21 -10000 0 -0.4 270 270
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 280 280
CDC42 0.016 0.005 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.1 0.24 0.54 92 -10000 0 92
KIRREL -0.037 0.18 -10000 0 -0.71 27 27
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.1 0.24 -10000 0 -0.54 92 92
PLCG1 0.026 0.005 -10000 0 -10000 0 0
ARRB2 0.025 0.007 -10000 0 -10000 0 0
WASL 0.025 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.055 0.2 -10000 0 -0.43 87 87
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.055 0.15 -10000 0 -0.34 84 84
FYN -0.064 0.19 0.26 18 -0.4 87 105
mol:Ca2+ -0.055 0.2 -10000 0 -0.42 86 86
mol:DAG -0.055 0.2 -10000 0 -0.43 86 86
NPHS2 -0.004 0.042 -10000 0 -10000 0 0
mol:IP3 -0.055 0.2 -10000 0 -0.43 86 86
regulation of endocytosis -0.05 0.18 -10000 0 -0.38 85 85
Nephrin/NEPH1/podocin/Cholesterol -0.067 0.19 -10000 0 -0.42 88 88
establishment of cell polarity -0.1 0.24 -10000 0 -0.54 92 92
Nephrin/NEPH1/podocin/NCK1-2 -0.039 0.19 -10000 0 -0.4 86 86
Nephrin/NEPH1/beta Arrestin2 -0.049 0.18 -10000 0 -0.39 85 85
NPHS1 -0.11 0.27 -10000 0 -0.69 70 70
Nephrin/NEPH1/podocin -0.06 0.19 -10000 0 -0.4 87 87
TJP1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.003 -10000 0 -10000 0 0
NCK2 0.026 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.055 0.2 -10000 0 -0.43 86 86
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.055 0.2 -10000 0 -0.43 85 85
GRB2 0.025 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.077 0.19 0.28 16 -0.41 87 103
cytoskeleton organization -0.081 0.2 -10000 0 -0.45 84 84
Nephrin/NEPH1 -0.071 0.18 -10000 0 -0.4 92 92
Nephrin/NEPH1/ZO-1 -0.068 0.21 -10000 0 -0.45 88 88
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.064 -9999 0 -0.46 6 6
NFATC2 -0.068 0.16 -9999 0 -0.47 57 57
NFATC3 -0.002 0.031 -9999 0 -10000 0 0
CD40LG -0.34 0.37 -9999 0 -0.76 149 149
PTGS2 -0.32 0.36 -9999 0 -0.74 138 138
JUNB 0.019 0.058 -9999 0 -0.53 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.025 -9999 0 -10000 0 0
CaM/Ca2+ 0.006 0.025 -9999 0 -10000 0 0
CALM1 0.016 0.021 -9999 0 -10000 0 0
JUN -0.14 0.29 -9999 0 -0.69 87 87
mol:Ca2+ -0.008 0.019 -9999 0 -0.16 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.011 -9999 0 -0.098 1 1
FOSL1 0.003 0.054 -9999 0 -10000 0 0
CREM 0.026 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.24 -9999 0 -0.47 129 129
FOS -0.17 0.31 -9999 0 -0.69 103 103
IFNG -0.33 0.36 -9999 0 -0.74 153 153
AP-1/NFAT1-c-4 -0.35 0.45 -9999 0 -0.85 145 145
FASLG -0.31 0.35 -9999 0 -0.73 138 138
NFAT1-c-4/ICER1 -0.07 0.17 -9999 0 -0.42 61 61
IL2RA -0.31 0.34 -9999 0 -0.72 136 136
FKBP12/FK506 0.019 0.004 -9999 0 -10000 0 0
CSF2 -0.33 0.32 -9999 0 -0.69 146 146
JunB/Fra1/NFAT1-c-4 -0.062 0.17 -9999 0 -0.41 62 62
IL4 -0.3 0.32 -9999 0 -0.69 135 135
IL2 0.003 0.062 -9999 0 -1.1 1 1
IL3 -0.01 0.057 -9999 0 -0.93 1 1
FKBP1A 0.026 0.005 -9999 0 -10000 0 0
BATF3 0.016 0.048 -9999 0 -0.69 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.025 0.01 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.033 0.094 -10000 0 -0.41 11 11
PTK2B 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.5 1 -0.68 56 57
EDN1 -0.007 0.1 -10000 0 -0.6 7 7
EDN3 -0.33 0.36 -10000 0 -0.69 198 198
EDN2 0.012 0.077 -10000 0 -0.69 4 4
HRAS/GDP -0.11 0.22 0.48 2 -0.49 74 76
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.15 -10000 0 -0.34 78 78
ADCY4 -0.072 0.15 0.35 1 -0.42 52 53
ADCY5 -0.12 0.2 0.35 1 -0.47 90 91
ADCY6 -0.069 0.15 0.35 1 -0.42 50 51
ADCY7 -0.07 0.15 0.35 1 -0.42 51 52
ADCY1 -0.072 0.15 0.35 1 -0.43 51 52
ADCY2 -0.1 0.18 -10000 0 -0.46 74 74
ADCY3 -0.071 0.15 0.35 1 -0.42 53 54
ADCY8 -0.1 0.16 0.35 1 -0.45 53 54
ADCY9 -0.07 0.15 0.35 1 -0.42 51 52
arachidonic acid secretion -0.19 0.31 0.43 5 -0.62 117 122
ETB receptor/Endothelin-1/Gq/GTP -0.082 0.18 -10000 0 -0.37 96 96
GNAO1 0.007 0.11 -10000 0 -0.69 10 10
HRAS 0.024 0.012 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.027 0.11 -10000 0 -0.36 10 10
ETA receptor/Endothelin-1/Gs/GTP -0.027 0.18 -10000 0 -0.44 54 54
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.039 0.1 -10000 0 -0.48 8 8
EDNRB 0.015 0.073 -10000 0 -0.69 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.074 0.16 -10000 0 -0.61 22 22
CYSLTR1 -0.036 0.12 -10000 0 -0.6 10 10
SLC9A1 -0.002 0.058 -10000 0 -0.28 10 10
mol:GDP -0.13 0.23 0.48 3 -0.51 76 79
SLC9A3 -0.052 0.2 0.39 1 -0.69 26 27
RAF1 -0.17 0.28 0.44 3 -0.54 113 116
JUN -0.29 0.49 0.48 1 -1.1 98 99
JAK2 -0.033 0.097 -10000 0 -0.46 10 10
mol:IP3 -0.1 0.2 -10000 0 -0.41 103 103
ETA receptor/Endothelin-1 0.008 0.14 -10000 0 -0.42 21 21
PLCB1 0.021 0.051 -10000 0 -0.69 2 2
PLCB2 0.019 0.023 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.25 0.28 -10000 0 -0.53 199 199
FOS -0.28 0.45 0.61 2 -1 106 108
Gai/GDP -0.008 0.14 -10000 0 -0.64 17 17
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.18 -10000 0 -0.46 55 55
BCAR1 0.025 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.41 99 99
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.058 0.23 -10000 0 -0.67 49 49
Gs family/GDP -0.15 0.25 0.28 1 -0.54 91 92
ETA receptor/Endothelin-1/Gq/GTP -0.089 0.18 -10000 0 -0.38 93 93
MAPK14 -0.069 0.15 -10000 0 -0.34 65 65
TRPC6 -0.16 0.29 0.5 1 -0.72 56 57
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.07 0.16 -10000 0 -0.34 78 78
ETB receptor/Endothelin-2 0.021 0.081 -10000 0 -0.52 8 8
ETB receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.52 200 200
ETB receptor/Endothelin-1 0.013 0.097 -10000 0 -0.54 9 9
MAPK3 -0.24 0.4 0.41 4 -0.86 111 115
MAPK1 -0.29 0.45 0.63 2 -0.96 112 114
Rac1/GDP -0.11 0.22 -10000 0 -0.49 70 70
cAMP biosynthetic process -0.078 0.19 0.47 9 -0.46 52 61
MAPK8 -0.18 0.33 0.51 1 -0.79 64 65
SRC 0.025 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.002 0.073 -10000 0 -0.3 15 15
p130Cas/CRK/Src/PYK2 -0.15 0.28 0.47 6 -0.55 103 109
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 -10000 0 -0.48 71 71
COL1A2 -0.008 0.096 -10000 0 -0.5 5 5
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.013 0.082 -10000 0 -0.55 5 5
mol:DAG -0.1 0.2 -10000 0 -0.41 103 103
MAP2K2 -0.2 0.33 0.4 7 -0.67 111 118
MAP2K1 -0.21 0.34 0.43 3 -0.69 115 118
EDNRA -0.002 0.074 -10000 0 -0.39 4 4
positive regulation of muscle contraction -0.026 0.078 -10000 0 -0.39 6 6
Gq family/GDP -0.15 0.28 0.38 1 -0.57 100 101
HRAS/GTP -0.14 0.24 0.49 2 -0.5 89 91
PRKCH -0.11 0.19 -10000 0 -0.44 83 83
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.22 -10000 0 -0.48 88 88
PRKCB -0.11 0.19 -10000 0 -0.45 77 77
PRKCE -0.11 0.2 -10000 0 -0.45 79 79
PRKCD -0.11 0.19 -10000 0 -0.44 78 78
PRKCG -0.1 0.19 -10000 0 -0.45 74 74
regulation of vascular smooth muscle contraction -0.32 0.52 0.64 2 -1.2 106 108
PRKCQ -0.11 0.2 -10000 0 -0.44 83 83
PLA2G4A -0.21 0.35 0.43 5 -0.69 117 122
GNA14 -0.14 0.29 -10000 0 -0.66 92 92
GNA15 0.006 0.053 -10000 0 -0.69 1 1
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.011 0.072 -10000 0 -0.69 4 4
Rac1/GTP 0.028 0.11 -10000 0 -0.36 10 10
MMP1 -0.035 0.082 0.63 2 -10000 0 2
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.051 0.028 -9999 0 -0.45 1 1
fibroblast growth factor receptor signaling pathway 0.05 0.028 -9999 0 -0.45 1 1
LAMA1 -0.026 0.18 -9999 0 -0.68 30 30
PRNP 0.026 0.005 -9999 0 -10000 0 0
GPC1/SLIT2 -0.04 0.19 -9999 0 -0.52 56 56
SMAD2 0.017 0.03 -9999 0 -0.41 1 1
GPC1/PrPc/Cu2+ 0.034 0.009 -9999 0 -10000 0 0
GPC1/Laminin alpha1 -0.003 0.14 -9999 0 -0.51 30 30
TDGF1 -0.27 0.35 -9999 0 -0.68 169 169
CRIPTO/GPC1 -0.2 0.27 -9999 0 -0.52 167 167
APP/GPC1 0.037 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.23 -9999 0 -0.45 165 165
FLT1 0.025 0.006 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.03 -9999 0 -0.45 1 1
SERPINC1 0.021 0.015 -9999 0 -10000 0 0
FYN -0.18 0.23 -9999 0 -0.45 167 167
FGR -0.17 0.23 -9999 0 -0.45 163 163
positive regulation of MAPKKK cascade -0.24 0.26 -9999 0 -0.53 166 166
SLIT2 -0.074 0.25 -9999 0 -0.68 57 57
GPC1/NRG -0.017 0.17 -9999 0 -0.52 39 39
NRG1 -0.044 0.21 -9999 0 -0.68 40 40
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.038 -9999 0 -0.45 2 2
LYN -0.18 0.23 -9999 0 -0.45 166 166
mol:Spermine 0.008 0.005 -9999 0 -10000 0 0
cell growth 0.05 0.028 -9999 0 -0.45 1 1
BMP signaling pathway -0.025 0.009 -9999 0 -10000 0 0
SRC -0.17 0.23 -9999 0 -0.45 164 164
TGFBR1 0.02 0.026 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.19 0.31 -9999 0 -0.69 112 112
GPC1 0.026 0.009 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.02 0.026 -9999 0 -10000 0 0
VEGFA 0.023 0.05 -9999 0 -0.69 2 2
BLK -0.31 0.31 -9999 0 -0.55 226 226
HCK -0.18 0.23 -9999 0 -0.45 164 164
FGF2 0.026 0.004 -9999 0 -10000 0 0
FGFR1 0.025 0.036 -9999 0 -0.69 1 1
VEGFR1 homodimer 0.025 0.006 -9999 0 -10000 0 0
TGFBR2 0.025 0.036 -9999 0 -0.69 1 1
cell death 0.037 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.035 0.014 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.13 0.24 -9999 0 -0.52 112 112
LCK -0.18 0.23 -9999 0 -0.45 168 168
neuron differentiation -0.017 0.16 -9999 0 -0.52 39 39
PrPc/Cu2+ 0.019 0.004 -9999 0 -10000 0 0
APP 0.026 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.025 0.036 -9999 0 -0.69 1 1
IGF1 pathway

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.026 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.005 -10000 0 -10000 0 0
CRKL -0.093 0.18 -10000 0 -0.37 113 113
GRB2/SOS1/SHC 0.047 0.019 -10000 0 -10000 0 0
HRAS 0.025 0.012 -10000 0 -10000 0 0
IRS1/Crk -0.085 0.19 -10000 0 -0.38 110 110
IGF-1R heterotetramer/IGF1/PTP1B -0.059 0.19 -10000 0 -0.44 81 81
AKT1 -0.082 0.16 -10000 0 -0.36 79 79
BAD -0.08 0.15 -10000 0 -0.34 76 76
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.09 0.18 -10000 0 -0.37 110 110
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.082 0.19 -10000 0 -0.38 113 113
RAF1 -0.061 0.15 0.39 1 -0.55 11 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.055 0.19 -10000 0 -0.36 109 109
YWHAZ 0.026 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.089 0.2 -10000 0 -0.4 115 115
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
RPS6KB1 -0.081 0.16 -10000 0 -0.36 78 78
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.051 0.14 0.32 5 -0.47 10 15
PXN 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.066 0.16 -10000 0 -0.36 76 76
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.024 0.17 -10000 0 -0.36 76 76
IGF-1R heterotetramer -0.007 0.057 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.071 0.2 -10000 0 -0.38 113 113
Crk/p130 Cas/Paxillin -0.051 0.19 -10000 0 -0.35 109 109
IGF1R -0.007 0.057 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.71 82 82
IRS2/Crk -0.079 0.18 -10000 0 -0.36 110 110
PI3K -0.057 0.2 -10000 0 -0.36 113 113
apoptosis 0.057 0.14 0.5 10 -0.39 1 11
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.084 0.19 -10000 0 -0.46 81 81
RAF1/14-3-3 E -0.039 0.14 0.34 2 -0.47 11 13
BAD/14-3-3 -0.06 0.15 0.4 1 -0.54 10 11
PRKCZ -0.081 0.16 0.25 1 -0.36 79 80
Crk/p130 Cas/Paxillin/FAK1 -0.051 0.16 -10000 0 -0.54 10 10
PTPN1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.088 0.2 -10000 0 -0.48 82 82
BCAR1 0.025 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.039 0.18 -10000 0 -0.38 79 79
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.08 0.19 -10000 0 -0.37 113 113
GRB10 0.025 0.006 -10000 0 -10000 0 0
PTPN11 -0.091 0.18 -10000 0 -0.37 113 113
IRS1 -0.1 0.2 -10000 0 -0.4 115 115
IRS2 -0.092 0.18 -10000 0 -0.37 114 114
IGF-1R heterotetramer/IGF1 -0.095 0.23 -10000 0 -0.55 82 82
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDPK1 -0.082 0.18 -10000 0 -0.38 80 80
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKD1 -0.084 0.19 -10000 0 -0.46 81 81
SHC1 0.025 0.007 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.5 0.4 -10000 0 -1.1 67 67
STAT6 (cleaved dimer) -0.52 0.41 -10000 0 -0.97 130 130
IGHG1 -0.18 0.13 -10000 0 -0.42 2 2
IGHG3 -0.49 0.38 -10000 0 -0.92 126 126
AKT1 -0.27 0.28 0.66 1 -0.82 51 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.98 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.3 -10000 0 -0.76 77 77
THY1 -0.5 0.4 -10000 0 -1.1 72 72
MYB 0.009 0.1 -10000 0 -0.65 9 9
HMGA1 0.026 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.32 -10000 0 -0.82 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.88 43 43
SP1 0.03 0.009 -10000 0 -10000 0 0
INPP5D 0.018 0.034 -10000 0 -10000 0 0
SOCS5 0.04 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.41 -10000 0 -1 103 103
SOCS1 -0.35 0.26 -10000 0 -0.72 59 59
SOCS3 -0.34 0.38 0.59 2 -1.2 54 56
FCER2 -0.51 0.42 -10000 0 -1 103 103
PARP14 0.026 0.006 -10000 0 -10000 0 0
CCL17 -0.53 0.42 -10000 0 -1.2 65 65
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.21 -10000 0 -0.7 35 35
T cell proliferation -0.5 0.41 -10000 0 -1.1 78 78
IL4R/JAK1 -0.5 0.4 -10000 0 -1.1 76 76
EGR2 -0.82 0.68 -10000 0 -1.6 177 177
JAK2 -0.03 0.034 -10000 0 -10000 0 0
JAK3 -0.01 0.063 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.003 0.021 -10000 0 -10000 0 0
COL1A2 -0.16 0.14 -10000 0 -0.97 2 2
CCL26 -0.5 0.4 -10000 0 -1.1 64 64
IL4R -0.53 0.43 -10000 0 -1.2 75 75
PTPN6 0.039 0.012 -10000 0 -10000 0 0
IL13RA2 -0.61 0.55 -10000 0 -1.4 95 95
IL13RA1 -0.03 0.033 -10000 0 -10000 0 0
IRF4 -0.29 0.48 -10000 0 -1.1 84 84
ARG1 -0.13 0.14 -10000 0 -1.2 2 2
CBL -0.32 0.3 -10000 0 -0.81 68 68
GTF3A 0.025 0.016 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
IL13RA1/JAK2 -0.036 0.046 -10000 0 -10000 0 0
IRF4/BCL6 -0.26 0.44 -10000 0 -1 84 84
CD40LG -0.077 0.24 -10000 0 -0.66 59 59
MAPK14 -0.34 0.34 -10000 0 -0.92 70 70
mitosis -0.26 0.26 0.61 2 -0.76 52 54
STAT6 -0.56 0.48 -10000 0 -1.1 111 111
SPI1 0.022 0.031 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 0.7 3 -0.72 47 50
STAT6 (dimer) -0.57 0.48 -10000 0 -1.1 111 111
STAT6 (dimer)/PARP14 -0.53 0.44 -10000 0 -1.1 105 105
mast cell activation 0.014 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.31 -10000 0 -0.97 46 46
FRAP1 -0.27 0.28 0.62 2 -0.81 52 54
LTA -0.51 0.4 -10000 0 -1.1 71 71
FES 0.026 0.003 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.56 0.46 1.1 112 -10000 0 112
CCL11 -0.49 0.38 -10000 0 -1.1 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.31 -10000 0 -0.93 50 50
IL2RG -0.012 0.14 -10000 0 -0.63 18 18
IL10 -0.51 0.43 -10000 0 -1.2 72 72
IRS1 -0.048 0.22 -10000 0 -0.69 42 42
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.091 -10000 0 -10000 0 0
IL5 -0.51 0.4 -10000 0 -1.1 66 66
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.44 0.35 -10000 0 -0.97 70 70
COL1A1 -0.21 0.23 -10000 0 -1.1 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.42 -10000 0 -1.2 56 56
IL2R gamma/JAK3 -0.02 0.12 -10000 0 -0.49 17 17
TFF3 -1.2 0.58 -10000 0 -1.4 327 327
ALOX15 -0.5 0.4 -10000 0 -1.1 64 64
MYBL1 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.43 0.35 -10000 0 -0.92 81 81
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.029 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.27 -10000 0 -0.88 40 40
mol:PI-3-4-5-P3 -0.27 0.28 0.62 2 -0.82 51 53
PI3K -0.28 0.3 0.67 1 -0.9 50 51
DOK2 0.019 0.055 -10000 0 -0.69 2 2
ETS1 0.038 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.2 -10000 0 -0.68 31 31
ITGB3 -0.52 0.43 -10000 0 -1.2 69 69
PIGR -0.53 0.45 -10000 0 -1.2 82 82
IGHE 0.046 0.045 0.24 8 -10000 0 8
MAPKKK cascade -0.2 0.2 0.58 1 -0.66 31 32
BCL6 0.025 0.036 -10000 0 -0.69 1 1
OPRM1 -0.51 0.4 -10000 0 -1.1 73 73
RETNLB -0.51 0.4 -10000 0 -1.1 68 68
SELP -0.5 0.41 -10000 0 -1.2 60 60
AICDA -0.49 0.38 -10000 0 -1.1 70 70
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.36 0.62 2 -0.85 45 47
HDAC7 0.027 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.25 0.41 -10000 0 -0.83 92 92
SMAD4 0.027 0.004 -10000 0 -10000 0 0
ID2 -0.2 0.36 0.62 2 -0.85 45 47
AP1 -0.2 0.38 -10000 0 -0.74 121 121
ABCG2 -0.21 0.36 0.61 1 -0.86 45 46
HIF1A -0.022 0.072 -10000 0 -10000 0 0
TFF3 -0.5 0.44 0.62 2 -0.92 156 158
GATA2 0.027 0.011 -10000 0 -10000 0 0
AKT1 -0.058 0.11 -10000 0 -0.24 34 34
response to hypoxia -0.073 0.11 -10000 0 -0.24 69 69
MCL1 -0.2 0.35 0.62 2 -0.89 36 38
NDRG1 -0.2 0.36 0.62 2 -0.85 44 46
SERPINE1 -0.21 0.35 -10000 0 -0.87 41 41
FECH -0.2 0.36 0.64 1 -0.86 43 44
FURIN -0.2 0.36 0.62 2 -0.86 43 45
NCOA2 -0.026 0.19 -10000 0 -0.69 30 30
EP300 -0.11 0.18 -10000 0 -0.35 133 133
HMOX1 -0.22 0.34 0.64 1 -0.87 41 42
BHLHE40 -0.21 0.36 0.62 2 -0.86 45 47
BHLHE41 -0.21 0.36 0.61 1 -0.86 43 44
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.026 0.099 -10000 0 -10000 0 0
ENG 0.01 0.094 0.48 3 -10000 0 3
JUN -0.13 0.29 -10000 0 -0.68 87 87
RORA -0.2 0.36 0.62 2 -0.86 45 47
ABCB1 -0.051 0.15 -10000 0 -1.2 5 5
TFRC -0.2 0.36 0.64 1 -0.86 43 44
CXCR4 -0.2 0.36 0.62 2 -0.85 45 47
TF -0.25 0.43 0.62 2 -0.97 69 71
CITED2 -0.23 0.4 0.62 2 -0.91 60 62
HIF1A/ARNT -0.23 0.39 -10000 0 -0.95 43 43
LDHA -0.036 0.11 -10000 0 -0.65 8 8
ETS1 -0.2 0.36 0.62 2 -0.85 44 46
PGK1 -0.21 0.35 0.61 1 -0.88 38 39
NOS2 -0.21 0.36 0.61 1 -0.86 44 45
ITGB2 -0.21 0.36 0.62 2 -0.87 43 45
ALDOA -0.21 0.35 0.61 1 -0.86 42 43
Cbp/p300/CITED2 -0.32 0.47 -10000 0 -0.98 97 97
FOS -0.16 0.31 -10000 0 -0.69 103 103
HK2 -0.21 0.36 0.64 1 -0.86 45 46
SP1 0.031 0.014 -10000 0 -10000 0 0
GCK -0.42 0.65 -10000 0 -1.4 116 116
HK1 -0.21 0.36 0.62 2 -0.86 43 45
NPM1 -0.21 0.35 -10000 0 -0.88 39 39
EGLN1 -0.2 0.35 0.64 1 -0.88 38 39
CREB1 0.032 0.006 -10000 0 -10000 0 0
PGM1 -0.2 0.36 0.64 1 -0.9 36 37
SMAD3 0.027 0.003 -10000 0 -10000 0 0
EDN1 -0.2 0.3 0.5 1 -0.68 70 71
IGFBP1 -0.21 0.35 0.61 1 -0.86 43 44
VEGFA -0.21 0.35 -10000 0 -0.73 78 78
HIF1A/JAB1 0.002 0.058 -10000 0 -10000 0 0
CP -0.34 0.47 0.62 2 -0.94 115 117
CXCL12 -0.24 0.41 0.62 2 -0.95 62 64
COPS5 0.027 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.007 -10000 0 -10000 0 0
BNIP3 -0.2 0.36 0.62 2 -0.85 45 47
EGLN3 -0.22 0.36 -10000 0 -0.86 50 50
CA9 -0.21 0.36 0.61 1 -0.84 48 49
TERT -0.21 0.35 -10000 0 -0.86 43 43
ENO1 -0.2 0.36 0.64 1 -0.9 36 37
PFKL -0.2 0.36 0.62 2 -0.85 44 46
NCOA1 0.026 0.005 -10000 0 -10000 0 0
ADM -0.21 0.36 0.64 1 -0.89 41 42
ARNT -0.016 0.071 -10000 0 -0.33 1 1
HNF4A -0.017 0.058 -10000 0 -10000 0 0
ADFP -0.22 0.34 -10000 0 -0.84 48 48
SLC2A1 -0.21 0.35 -10000 0 -0.72 82 82
LEP -0.21 0.35 -10000 0 -0.88 39 39
HIF1A/ARNT/Cbp/p300 -0.27 0.42 -10000 0 -0.84 98 98
EPO -0.14 0.26 -10000 0 -0.88 13 13
CREBBP -0.086 0.17 -10000 0 -0.33 115 115
HIF1A/ARNT/Cbp/p300/HDAC7 -0.24 0.41 -10000 0 -0.83 89 89
PFKFB3 -0.21 0.36 0.64 1 -0.86 43 44
NT5E -0.21 0.36 0.62 2 -0.88 42 44
IL23-mediated signaling events

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
CCL2 -0.2 0.54 -10000 0 -1.3 68 68
IL23A -0.22 0.55 -10000 0 -1.2 82 82
NF kappa B1 p50/RelA/I kappa B alpha -0.18 0.54 -10000 0 -1.2 75 75
positive regulation of T cell mediated cytotoxicity -0.24 0.62 -10000 0 -1.3 79 79
ITGA3 -0.19 0.51 -10000 0 -1.2 66 66
IL17F -0.1 0.34 0.69 2 -0.73 67 69
IL12B 0.003 0.087 -10000 0 -0.71 4 4
STAT1 (dimer) -0.22 0.58 -10000 0 -1.3 78 78
CD4 -0.18 0.5 -10000 0 -1.2 65 65
IL23 -0.2 0.53 -10000 0 -1.1 82 82
IL23R 0 0.11 -10000 0 -0.96 2 2
IL1B -0.23 0.58 -10000 0 -1.4 67 67
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.18 0.5 -10000 0 -1.2 65 65
TYK2 0.015 0.035 -10000 0 -10000 0 0
STAT4 0.002 0.099 -10000 0 -0.58 9 9
STAT3 0.025 0.006 -10000 0 -10000 0 0
IL18RAP -0.012 0.15 -10000 0 -0.69 18 18
IL12RB1 -0.002 0.074 -10000 0 -0.62 3 3
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
IL12Rbeta1/TYK2 0.014 0.067 -10000 0 -0.48 3 3
IL23R/JAK2 0.007 0.13 -10000 0 -0.87 2 2
positive regulation of chronic inflammatory response -0.24 0.62 -10000 0 -1.3 79 79
natural killer cell activation 0.001 0.009 -10000 0 -0.054 1 1
JAK2 0.015 0.045 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.5 -10000 0 -1.1 82 82
ALOX12B -0.19 0.5 -10000 0 -1.2 68 68
CXCL1 -0.2 0.52 -10000 0 -1.2 70 70
T cell proliferation -0.24 0.62 -10000 0 -1.3 79 79
NFKBIA 0.026 0.006 -10000 0 -10000 0 0
IL17A -0.062 0.27 -10000 0 -0.56 63 63
PI3K -0.2 0.55 -10000 0 -1.2 75 75
IFNG -0.015 0.054 0.16 2 -0.13 56 58
STAT3 (dimer) -0.18 0.51 -10000 0 -1.2 71 71
IL18R1 -0.004 0.095 -10000 0 -0.58 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.35 -10000 0 -0.81 57 57
IL18/IL18R -0.003 0.15 -10000 0 -0.48 30 30
macrophage activation -0.009 0.021 -10000 0 -0.044 82 82
TNF -0.25 0.6 -10000 0 -1.3 84 84
STAT3/STAT4 -0.2 0.55 -10000 0 -1.2 76 76
STAT4 (dimer) -0.22 0.59 -10000 0 -1.3 78 78
IL18 -0.01 0.11 -10000 0 -0.66 9 9
IL19 -0.18 0.5 -10000 0 -1.2 67 67
STAT5A (dimer) -0.22 0.58 -10000 0 -1.3 78 78
STAT1 0.023 0.022 -10000 0 -10000 0 0
SOCS3 -0.024 0.18 -10000 0 -0.69 28 28
CXCL9 -0.27 0.61 -10000 0 -1.4 87 87
MPO -0.19 0.51 -10000 0 -1.2 68 68
positive regulation of humoral immune response -0.24 0.62 -10000 0 -1.3 79 79
IL23/IL23R/JAK2/TYK2 -0.29 0.76 -10000 0 -1.6 79 79
IL6 -0.31 0.64 -10000 0 -1.3 105 105
STAT5A 0.025 0.006 -10000 0 -10000 0 0
IL2 0.003 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -10000 0 -0.054 1 1
CD3E -0.22 0.56 -10000 0 -1.3 72 72
keratinocyte proliferation -0.24 0.62 -10000 0 -1.3 79 79
NOS2 -0.18 0.5 -10000 0 -1.2 66 66
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.02 0.062 -10000 0 -0.69 3 3
EFNB1 -0.007 0.1 -10000 0 -0.49 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.23 -10000 0 -0.4 155 155
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.41 151 151
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.39 155 155
Ephrin B1/EPHB1-2/Tiam1 -0.14 0.24 -10000 0 -0.43 155 155
DNM1 -0.004 0.13 -10000 0 -0.63 17 17
cell-cell signaling -0.001 0.004 -10000 0 -10000 0 0
MAP2K4 0.001 0.072 0.41 1 -0.59 4 5
YES1 0.008 0.082 -10000 0 -0.8 4 4
Ephrin B1/EPHB1-2/NCK2 -0.13 0.22 -10000 0 -0.4 154 154
PI3K 0.029 0.073 -10000 0 -0.75 3 3
mol:GDP -0.14 0.24 -10000 0 -0.43 155 155
ITGA2B -0.052 0.22 -10000 0 -0.68 44 44
endothelial cell proliferation 0.032 0.01 -10000 0 -10000 0 0
FYN 0.009 0.082 -10000 0 -0.8 4 4
MAP3K7 -0.006 0.063 -10000 0 -0.62 4 4
FGR 0.006 0.081 -10000 0 -0.79 4 4
TIAM1 -0.058 0.08 -10000 0 -0.69 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.024 0.008 -10000 0 -10000 0 0
cell adhesion -0.029 0.16 -10000 0 -0.42 50 50
LYN 0.008 0.083 -10000 0 -0.81 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.001 0.077 -10000 0 -0.76 4 4
Ephrin B1/EPHB1-2 -0.007 0.068 -10000 0 -0.66 4 4
SRC 0.007 0.081 -10000 0 -0.79 4 4
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
EPHB1 -0.24 0.35 -10000 0 -0.69 152 152
EPHB4 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.036 0.2 -10000 0 -0.55 51 51
BLK -0.044 0.12 -10000 0 -0.85 4 4
HCK 0.008 0.081 -10000 0 -0.79 4 4
regulation of stress fiber formation 0.13 0.22 0.4 154 -10000 0 154
MAPK8 0.002 0.095 0.35 5 -0.65 5 10
Ephrin B1/EPHB1-2/RGS3 -0.13 0.22 -10000 0 -0.4 154 154
endothelial cell migration -0.002 0.06 0.41 1 -0.56 3 4
NCK2 0.026 0.005 -10000 0 -10000 0 0
PTPN13 0.029 0.059 -10000 0 -0.8 2 2
regulation of focal adhesion formation 0.13 0.22 0.4 154 -10000 0 154
chemotaxis 0.13 0.22 0.39 154 -10000 0 154
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
Rac1/GTP -0.12 0.22 -10000 0 -0.4 155 155
angiogenesis -0.007 0.067 -10000 0 -0.66 4 4
LCK 0.005 0.086 -10000 0 -0.84 4 4
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.18 0.3 -10000 0 -0.5 179 179
SMAD6-7/SMURF1 0.051 0.014 -10000 0 -10000 0 0
NOG -0.029 0.18 -10000 0 -0.69 29 29
SMAD9 -0.19 0.28 -10000 0 -0.55 141 141
SMAD4 0.026 0.004 -10000 0 -10000 0 0
SMAD5 -0.09 0.17 -10000 0 -0.32 132 132
BMP7/USAG1 -0.25 0.28 -10000 0 -0.52 207 207
SMAD5/SKI -0.074 0.18 0.32 3 -0.44 25 28
SMAD1 -0.036 0.092 -10000 0 -0.32 1 1
BMP2 0.003 0.13 -10000 0 -0.69 13 13
SMAD1/SMAD1/SMAD4 -0.021 0.083 -10000 0 -10000 0 0
BMPR1A 0.026 0.005 -10000 0 -10000 0 0
BMPR1B -0.22 0.34 -10000 0 -0.69 137 137
BMPR1A-1B/BAMBI -0.12 0.24 -10000 0 -0.46 137 137
AHSG -0.003 0.038 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.014 0.11 -10000 0 -0.46 22 22
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.07 0.17 -10000 0 -0.53 26 26
BMP2-4 (homodimer) 0.006 0.13 -10000 0 -0.52 22 22
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.098 0.23 -10000 0 -0.41 137 137
RGMA -0.002 0.14 -10000 0 -0.69 16 16
SMURF1 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.082 0.16 -10000 0 -0.47 28 28
BMP2-4/USAG1 -0.23 0.26 -10000 0 -0.47 218 218
SMAD6/SMURF1/SMAD5 -0.072 0.17 0.32 1 -0.44 23 24
SOSTDC1 -0.34 0.35 -10000 0 -0.69 207 207
BMP7/BMPR2/BMPR1A-1B -0.097 0.22 -10000 0 -0.41 135 135
SKI 0.026 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.003 -10000 0 -10000 0 0
HFE2 -0.003 0.021 -10000 0 -10000 0 0
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.14 -10000 0 -0.46 29 29
SMAD5/SMAD5/SMAD4 -0.072 0.18 0.32 3 -0.44 25 28
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.057 0.15 -10000 0 -0.43 23 23
BMP7 (homodimer) 0.026 0.005 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.028 0.028 -10000 0 -10000 0 0
SMAD1/SKI -0.027 0.1 0.33 1 -0.34 1 2
SMAD6 0.026 0.003 -10000 0 -10000 0 0
CTDSP2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.022 0.12 -10000 0 -0.46 22 22
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.68 90 90
BMPR2 (homodimer) 0.026 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.043 0.058 -10000 0 -0.45 5 5
BMPR1A-1B (homodimer) -0.15 0.26 -10000 0 -0.52 137 137
CHRDL1 -0.45 0.33 -10000 0 -0.67 277 277
ENDOFIN/SMAD1 -0.029 0.096 -10000 0 -0.33 1 1
SMAD6-7/SMURF1/SMAD1 -0.012 0.099 -10000 0 -10000 0 0
SMAD6/SMURF1 0.025 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.046 -10000 0 -0.69 1 1
SMURF2 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.31 0.25 -10000 0 -0.47 270 270
BMP2-4/GREM1 -0.078 0.24 -10000 0 -0.5 96 96
SMAD7 0.026 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.17 0.27 -10000 0 -0.52 139 139
SMAD1/SMAD6 -0.026 0.094 -10000 0 -10000 0 0
TAK1/SMAD6 0.037 0.01 -10000 0 -10000 0 0
BMP7 0.026 0.005 -10000 0 -10000 0 0
BMP6 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.061 0.14 -10000 0 -0.41 26 26
PPM1A 0.026 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.026 0.097 0.33 1 -0.34 1 2
SMAD7/SMURF1 0.037 0.01 -10000 0 -10000 0 0
CTDSPL 0.026 0.003 -10000 0 -10000 0 0
PPP1CA 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
CTDSP1 0.026 0.005 -10000 0 -10000 0 0
PPP1R15A 0.016 0.079 -10000 0 -0.69 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.17 0.26 -10000 0 -0.61 85 85
CHRD 0.012 0.1 -10000 0 -0.69 8 8
BMPR2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.085 0.16 -10000 0 -0.46 31 31
BMP4 0.007 0.11 -10000 0 -0.66 10 10
FST -0.15 0.3 -10000 0 -0.69 98 98
BMP2-4/NOG -0.012 0.17 -10000 0 -0.46 50 50
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.081 0.22 -10000 0 -0.39 131 131
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 -0.058 0.25 0.29 13 -0.6 59 72
FYN -0.1 0.33 0.56 3 -0.77 65 68
LAT/GRAP2/SLP76 -0.083 0.26 -10000 0 -0.62 65 65
IKBKB 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.058 0.22 0.67 7 -0.47 65 72
B2M 0.026 0.006 -10000 0 -10000 0 0
IKBKG -0.017 0.055 0.11 2 -0.15 27 29
MAP3K8 0.016 0.087 -10000 0 -0.69 6 6
mol:Ca2+ -0.03 0.044 0.092 5 -0.11 82 87
integrin-mediated signaling pathway 0.033 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.31 0.69 5 -0.72 68 73
TRPV6 -0.1 0.36 1 17 -0.69 83 100
CD28 -0.016 0.15 -10000 0 -0.65 21 21
SHC1 -0.1 0.32 0.31 14 -0.8 61 75
receptor internalization -0.13 0.35 -10000 0 -0.8 72 72
PRF1 -0.11 0.34 0.5 1 -0.8 63 64
KRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.043 0.18 0.68 4 -0.38 65 69
LAT -0.11 0.32 0.31 2 -0.78 64 66
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.053 0.22 -10000 0 -0.66 44 44
CD3E -0.035 0.19 -10000 0 -0.66 35 35
CD3G -0.098 0.26 -10000 0 -0.67 71 71
RASGRP2 -0.003 0.03 0.093 3 -0.18 7 10
RASGRP1 -0.048 0.23 0.71 8 -0.47 63 71
HLA-A 0.026 0.011 -10000 0 -10000 0 0
RASSF5 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.16 0.42 21 -0.13 31 52
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.048 0.085 -10000 0 -0.25 47 47
PRKCA -0.04 0.13 -10000 0 -0.3 65 65
GRAP2 -0.02 0.15 -10000 0 -0.56 27 27
mol:IP3 -0.032 0.21 0.27 60 -0.45 60 120
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.36 -10000 0 -0.87 63 63
ORAI1 0.045 0.21 0.7 2 -0.78 14 16
CSK -0.12 0.32 -10000 0 -0.79 65 65
B7 family/CD28 -0.11 0.36 0.3 1 -0.7 87 88
CHUK 0.026 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.39 -10000 0 -0.89 71 71
PTPN6 -0.12 0.33 -10000 0 -0.8 64 64
VAV1 -0.11 0.32 -10000 0 -0.77 65 65
Monovalent TCR/CD3 -0.12 0.33 -10000 0 -0.64 87 87
CBL 0.026 0.005 -10000 0 -10000 0 0
LCK -0.11 0.34 0.6 2 -0.84 61 63
PAG1 -0.12 0.32 -10000 0 -0.79 65 65
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.39 -10000 0 -0.9 69 69
CD80 -0.053 0.22 -10000 0 -0.69 44 44
CD86 0.012 0.078 -10000 0 -0.7 4 4
PDK1/CARD11/BCL10/MALT1 -0.041 0.11 -10000 0 -0.3 48 48
HRAS 0.025 0.012 -10000 0 -10000 0 0
GO:0035030 -0.1 0.27 0.26 1 -0.56 87 88
CD8A -0.023 0.18 -10000 0 -0.66 29 29
CD8B -0.056 0.22 -10000 0 -0.66 46 46
PTPRC -0.011 0.15 -10000 0 -0.7 17 17
PDK1/PKC theta -0.074 0.27 0.68 10 -0.58 66 76
CSK/PAG1 -0.11 0.31 -10000 0 -0.77 64 64
SOS1 0.026 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.014 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.31 -10000 0 -0.74 66 66
STIM1 0.019 0.17 1.2 2 -0.89 8 10
RAS family/GTP 0.011 0.12 0.32 17 -0.19 34 51
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.39 -10000 0 -0.9 71 71
mol:DAG -0.06 0.16 0.15 6 -0.39 63 69
RAP1A/GDP 0.013 0.093 0.34 12 -10000 0 12
PLCG1 0.026 0.005 -10000 0 -10000 0 0
CD247 -0.007 0.14 -10000 0 -0.7 16 16
cytotoxic T cell degranulation -0.1 0.32 0.5 1 -0.75 65 66
RAP1A/GTP 0 0.011 -10000 0 -0.068 5 5
mol:PI-3-4-5-P3 -0.081 0.26 0.69 6 -0.57 68 74
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.26 0.29 55 -0.59 62 117
NRAS 0.026 0.005 -10000 0 -10000 0 0
ZAP70 -0.003 0.13 -10000 0 -0.67 15 15
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.082 0.24 -10000 0 -0.58 65 65
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.036 -10000 0 -0.69 1 1
CD8 heterodimer -0.058 0.24 -10000 0 -0.59 61 61
CARD11 -0.022 0.11 -10000 0 -0.69 8 8
PRKCB -0.03 0.12 -10000 0 -0.29 55 55
PRKCE -0.03 0.12 -10000 0 -0.28 57 57
PRKCQ -0.093 0.3 0.72 7 -0.68 65 72
LCP2 0.023 0.021 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.045 0.19 0.6 8 -0.39 64 72
IKK complex 0.019 0.15 0.55 15 -0.12 19 34
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.035 0.12 0.24 2 -0.28 58 60
PDPK1 -0.054 0.22 0.58 10 -0.44 65 75
TCR/CD3/MHC I/CD8/Fyn -0.16 0.42 -10000 0 -0.98 70 70
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.086 0.088 0.36 1 -10000 0 1
SMARCC2 0.025 0.016 -10000 0 -10000 0 0
SMARCC1 0.026 0.015 -10000 0 -10000 0 0
TBX21 -0.13 0.25 -10000 0 -0.76 38 38
SUMO2 0.023 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.029 0.023 -10000 0 -10000 0 0
FKBP4 0.026 0.005 -10000 0 -10000 0 0
FKBP5 0.019 0.071 -10000 0 -0.69 4 4
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.33 46 -0.44 3 49
PRL -0.066 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.2 0.29 0.56 110 -0.48 16 126
RELA -0.032 0.1 -10000 0 -0.27 29 29
FGG 0.17 0.2 0.48 84 -10000 0 84
GR beta/TIF2 0.084 0.19 0.34 54 -0.47 30 84
IFNG -0.37 0.48 -10000 0 -1 113 113
apoptosis -0.011 0.24 0.47 41 -0.55 16 57
CREB1 0.026 0.013 -10000 0 -10000 0 0
histone acetylation -0.08 0.15 -10000 0 -0.38 60 60
BGLAP -0.08 0.13 -10000 0 -0.48 11 11
GR/PKAc 0.12 0.1 0.35 27 -10000 0 27
NF kappa B1 p50/RelA -0.054 0.18 -10000 0 -0.46 35 35
SMARCD1 0.025 0.016 -10000 0 -10000 0 0
MDM2 0.087 0.099 0.25 80 -10000 0 80
GATA3 -0.008 0.16 -10000 0 -0.65 22 22
AKT1 0.02 0.004 -10000 0 -10000 0 0
CSF2 -0.12 0.14 -10000 0 -0.48 25 25
GSK3B 0.024 0.019 -10000 0 -10000 0 0
NR1I3 0.005 0.24 0.52 25 -0.66 6 31
CSN2 0.14 0.16 0.4 72 -10000 0 72
BRG1/BAF155/BAF170/BAF60A 0.063 0.046 -10000 0 -0.3 4 4
NFATC1 0.017 0.087 -10000 0 -0.69 6 6
POU2F1 0.025 0.01 -10000 0 -10000 0 0
CDKN1A 0.025 0.036 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.014 -10000 0 -10000 0 0
SFN -0.086 0.13 -10000 0 -0.69 12 12
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.13 0.14 0.35 40 -0.36 10 50
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.47 25 -0.84 84 109
JUN -0.24 0.26 -10000 0 -0.57 135 135
IL4 -0.1 0.16 -10000 0 -0.62 16 16
CDK5R1 0.025 0.014 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.32 -10000 0 -0.69 121 121
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.11 0.34 41 -0.41 3 44
cortisol/GR alpha (monomer) 0.26 0.31 0.65 121 -10000 0 121
NCOA2 -0.027 0.19 -10000 0 -0.69 30 30
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.19 0.31 -10000 0 -0.7 104 104
AP-1/NFAT1-c-4 -0.39 0.42 -10000 0 -0.78 182 182
AFP -0.17 0.2 -10000 0 -0.59 35 35
SUV420H1 0.026 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.15 0.46 35 -10000 0 35
TP53 0.04 0.012 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
KRT17 -0.3 0.35 -10000 0 -0.77 102 102
KRT14 -0.087 0.12 -10000 0 -0.48 7 7
TBP 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.034 0.042 -10000 0 -0.26 7 7
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.029 0.005 -10000 0 -10000 0 0
AP-1 -0.39 0.42 -10000 0 -0.78 182 182
MAPK14 0.026 0.017 -10000 0 -10000 0 0
MAPK10 0.025 0.017 -10000 0 -10000 0 0
MAPK11 0.016 0.019 -10000 0 -10000 0 0
KRT5 -0.4 0.51 -10000 0 -1 126 126
interleukin-1 receptor activity 0.002 0.003 -10000 0 -10000 0 0
NCOA1 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.023 -10000 0 -10000 0 0
CGA -0.098 0.14 -10000 0 -0.53 10 10
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.091 0.12 0.35 35 -10000 0 35
MAPK3 0.024 0.017 -10000 0 -10000 0 0
MAPK1 0.019 0.017 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.67 55 55
NFKB1 -0.031 0.1 -10000 0 -0.3 6 6
MAPK8 -0.14 0.17 -10000 0 -0.42 74 74
MAPK9 0.026 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.017 0.24 0.47 39 -0.57 16 55
BAX 0.035 0.082 0.85 3 -10000 0 3
POMC -0.46 0.65 -10000 0 -1.5 101 101
EP300 0.026 0.038 -10000 0 -0.26 5 5
cortisol/GR alpha (dimer)/p53 0.24 0.25 0.57 117 -10000 0 117
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.13 0.34 65 -10000 0 65
SGK1 0.018 0.21 0.51 1 -1.4 7 8
IL13 -0.22 0.26 -10000 0 -0.72 51 51
IL6 -0.33 0.51 -10000 0 -1.2 97 97
PRKACG -0.008 0.016 -10000 0 -10000 0 0
IL5 -0.19 0.21 -10000 0 -0.68 33 33
IL2 -0.26 0.28 -10000 0 -0.66 92 92
CDK5 0.026 0.009 -10000 0 -10000 0 0
PRKACB 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.29 -10000 0 -0.7 63 63
CDK5R1/CDK5 0.037 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.008 0.14 -10000 0 -0.38 18 18
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 115 -10000 0 115
SMARCA4 0.025 0.016 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.16 0.4 67 -0.44 2 69
NF kappa B1 p50/RelA/Cbp -0.015 0.16 -10000 0 -0.41 22 22
JUN (dimer) -0.24 0.26 -10000 0 -0.57 135 135
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.22 0.37 -10000 0 -0.87 85 85
NR3C1 0.16 0.19 0.46 84 -10000 0 84
NR4A1 -0.27 0.37 -10000 0 -0.68 173 173
TIF2/SUV420H1 -0.003 0.15 -10000 0 -0.52 30 30
MAPKKK cascade -0.011 0.24 0.47 41 -0.55 16 57
cortisol/GR alpha (dimer)/Src-1 0.24 0.25 0.56 117 -10000 0 117
PBX1 0.024 0.036 -10000 0 -0.69 1 1
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.26 0.45 -10000 0 -1.2 68 68
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.16 0.4 66 -0.44 2 68
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 115 -10000 0 115
mol:cortisol 0.15 0.19 0.38 124 -10000 0 124
MMP1 -0.099 0.13 -10000 0 -0.86 6 6
Coregulation of Androgen receptor activity

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
NRIP1 -0.004 0.052 -10000 0 -10000 0 0
SVIL -0.002 0.046 -10000 0 -10000 0 0
ZNF318 0.074 0.079 0.25 4 -10000 0 4
JMJD2C -0.064 0.066 -10000 0 -0.12 226 226
T-DHT/AR/Ubc9 -0.23 0.24 -10000 0 -0.5 167 167
CARM1 0.022 0.01 -10000 0 -10000 0 0
PRDX1 0.028 0.006 -10000 0 -10000 0 0
PELP1 0.031 0.013 -10000 0 -10000 0 0
CTNNB1 0.003 0.039 -10000 0 -10000 0 0
AKT1 0.037 0.02 -10000 0 -10000 0 0
PTK2B 0.008 0.031 -10000 0 -10000 0 0
MED1 0.036 0.021 -10000 0 -10000 0 0
MAK 0.065 0.11 0.21 95 -0.66 5 100
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.005 0.058 -10000 0 -0.69 1 1
GSN 0 0.044 -10000 0 -10000 0 0
NCOA2 -0.03 0.19 -10000 0 -0.69 30 30
NCOA6 -0.001 0.044 -10000 0 -10000 0 0
DNA-PK 0.073 0.076 -10000 0 -10000 0 0
NCOA4 0.025 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.037 -10000 0 -10000 0 0
cell proliferation -0.001 0.14 -10000 0 -0.86 6 6
XRCC5 0.036 0.017 -10000 0 -10000 0 0
UBE3A -0.011 0.062 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.24 0.26 -10000 0 -0.53 171 171
FHL2 -0.14 0.34 -10000 0 -1.2 36 36
RANBP9 -0.001 0.045 -10000 0 -10000 0 0
JMJD1A -0.001 0.035 -10000 0 -0.12 27 27
CDK6 0.025 0.036 -10000 0 -0.69 1 1
TGFB1I1 -0.002 0.046 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.25 -10000 0 -0.51 173 173
XRCC6 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.27 -10000 0 -0.54 185 185
CTDSP1 0.012 0.023 -10000 0 -10000 0 0
CTDSP2 0.056 0.051 -10000 0 -10000 0 0
BRCA1 -0.002 0.046 -10000 0 -10000 0 0
TCF4 0.047 0.035 -10000 0 -10000 0 0
CDKN2A 0.002 0.083 -10000 0 -10000 0 0
SRF 0.033 0.051 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.56 13 13
KLK3 -0.37 0.65 -10000 0 -1.4 111 111
TMF1 0.02 0.014 -10000 0 -10000 0 0
HNRNPA1 0.042 0.029 -10000 0 -10000 0 0
AOF2 -0.019 0.032 -10000 0 -0.072 110 110
APPL1 0.041 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.5 164 164
AR -0.31 0.35 -10000 0 -0.72 166 166
UBA3 0.013 0.023 -10000 0 -10000 0 0
PATZ1 0.032 0.03 -10000 0 -10000 0 0
PAWR 0.019 0.015 -10000 0 -10000 0 0
PRKDC 0.036 0.017 -10000 0 -10000 0 0
PA2G4 0.047 0.036 -10000 0 -10000 0 0
UBE2I 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.23 -10000 0 -0.46 167 167
RPS6KA3 -0.002 0.045 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.5 172 172
LATS2 0.041 0.028 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.2 0.22 -10000 0 -0.46 163 163
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.003 0.078 -10000 0 -0.69 4 4
KLK2 -0.67 0.57 -10000 0 -1.2 228 228
CASP8 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.54 166 166
TMPRSS2 -0.16 0.27 -10000 0 -1.1 26 26
CCND1 0.013 0.031 -10000 0 -10000 0 0
PIAS1 -0.011 0.062 -10000 0 -10000 0 0
mol:T-DHT -0.032 0.039 -10000 0 -0.076 150 150
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.028 0.089 -10000 0 -0.22 1 1
T-DHT/AR/CDK6 -0.22 0.25 -10000 0 -0.5 168 168
CMTM2 0.028 0.012 -10000 0 -10000 0 0
SNURF -0.005 0.14 -10000 0 -0.67 17 17
ZMIZ1 -0.022 0.048 -10000 0 -10000 0 0
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.042 0.028 -10000 0 -10000 0 0
FKBP4 -0.001 0.044 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 -0.042 0.18 -10000 0 -0.46 63 63
cell-cell adhesion 0.11 0.16 0.33 140 -10000 0 140
Ephrin B/EPHB2/RasGAP 0.064 0.058 -10000 0 -0.39 5 5
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.027 0.046 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.23 -10000 0 -0.44 150 150
HRAS/GDP -0.083 0.17 -10000 0 -0.35 14 14
Ephrin B/EPHB1/GRB7 -0.1 0.23 -10000 0 -0.41 143 143
Endophilin/SYNJ1 0.023 0.07 0.44 4 -0.36 5 9
KRAS 0.026 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.22 -10000 0 -0.4 144 144
endothelial cell migration 0.051 0.028 -10000 0 -0.39 1 1
GRB2 0.025 0.006 -10000 0 -10000 0 0
GRB7 0.003 0.054 -10000 0 -10000 0 0
PAK1 0.025 0.076 0.46 5 -0.36 5 10
HRAS 0.025 0.012 -10000 0 -10000 0 0
RRAS 0.022 0.069 0.42 5 -0.37 4 9
DNM1 -0.003 0.13 -10000 0 -0.63 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.12 0.19 -10000 0 -0.38 144 144
lamellipodium assembly -0.11 0.16 -10000 0 -0.33 140 140
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.088 0.16 -10000 0 -0.3 134 134
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.02 0.062 -10000 0 -0.69 3 3
EPHB3 -0.067 0.072 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.68 152 152
EPHB4 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.073 0.14 0.24 1 -0.38 9 10
Ephrin B/EPHB2 0.05 0.054 -10000 0 -0.39 5 5
Ephrin B/EPHB3 0.06 0.05 -10000 0 -0.44 2 2
JNK cascade -0.13 0.2 0.36 1 -0.39 143 144
Ephrin B/EPHB1 -0.11 0.22 -10000 0 -0.4 145 145
RAP1/GDP -0.049 0.14 -10000 0 -0.34 8 8
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EFNB3 0.016 0.058 -10000 0 -0.69 2 2
EFNB1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.41 152 152
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.089 0.19 -10000 0 -0.4 15 15
Rap1/GTP -0.1 0.18 -10000 0 -0.46 6 6
axon guidance -0.042 0.18 -10000 0 -0.45 63 63
MAPK3 -0.083 0.14 -10000 0 -0.46 6 6
MAPK1 -0.082 0.14 -10000 0 -0.44 7 7
Rac1/GDP -0.06 0.14 -10000 0 -0.35 8 8
actin cytoskeleton reorganization -0.082 0.13 -10000 0 -0.34 4 4
CDC42/GDP -0.057 0.14 0.37 1 -0.35 9 10
PI3K 0.057 0.029 -10000 0 -0.39 1 1
EFNA5 -0.082 0.26 -10000 0 -0.69 61 61
Ephrin B2/EPHB4 0.033 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.04 -10000 0 -0.32 4 4
CDC42 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.17 -10000 0 -0.44 6 6
PTK2 0.037 0.072 0.59 5 -10000 0 5
MAP4K4 -0.13 0.2 0.36 1 -0.39 143 144
SRC 0.026 0.009 -10000 0 -10000 0 0
KALRN 0.026 0.003 -10000 0 -10000 0 0
Intersectin/N-WASP 0.037 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.079 0.14 0.29 4 -0.35 1 5
MAP2K1 -0.084 0.15 -10000 0 -0.47 7 7
WASL 0.025 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.23 -10000 0 -0.42 143 143
cell migration -0.085 0.18 0.55 4 -0.5 8 12
NRAS 0.026 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.07 0.44 4 -0.37 5 9
PXN 0.026 0.005 -10000 0 -10000 0 0
TF -0.035 0.14 0.41 3 -0.38 51 54
HRAS/GTP -0.095 0.19 -10000 0 -0.35 139 139
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.41 152 152
cell adhesion mediated by integrin -0.008 0.066 0.39 2 -0.37 6 8
RAC1 0.025 0.006 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.37 143 143
RAC1-CDC42/GTP -0.14 0.17 -10000 0 -0.38 108 108
RASA1 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.05 0.14 -10000 0 -0.34 7 7
ruffle organization -0.1 0.19 0.56 5 -0.4 5 10
NCK1 0.026 0.003 -10000 0 -10000 0 0
receptor internalization -0.001 0.093 0.41 3 -0.38 16 19
Ephrin B/EPHB2/KALRN 0.064 0.058 -10000 0 -0.39 5 5
ROCK1 -0.024 0.046 -10000 0 -10000 0 0
RAS family/GDP -0.075 0.1 -10000 0 -0.34 3 3
Rac1/GTP -0.12 0.18 -10000 0 -0.35 140 140
Ephrin B/EPHB1/Src/Paxillin -0.092 0.16 -10000 0 -0.3 145 145
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 0.034 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.017 0.15 -10000 0 -0.7 10 10
EGFR 0.017 0.079 -10000 0 -0.69 5 5
EPHA2 0.025 0.014 -10000 0 -10000 0 0
USP6 0.024 0.014 -10000 0 -10000 0 0
IQSEC1 0.026 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.044 0.2 -10000 0 -0.52 59 59
ARRB2 -0.036 0.13 -10000 0 -0.39 48 48
mol:GTP 0.024 0.037 0.18 15 -0.14 1 16
ARRB1 0.024 0.036 -10000 0 -0.69 1 1
FBXO8 0.026 0.004 -10000 0 -10000 0 0
TSHR 0.022 0.05 -10000 0 -0.69 2 2
EGF -0.072 0.24 -10000 0 -0.68 55 55
somatostatin receptor activity 0 0.001 0.002 12 -0.001 111 123
ARAP2 0.024 0.036 -10000 0 -0.69 1 1
mol:GDP -0.11 0.14 0.28 6 -0.3 96 102
mol:PI-3-4-5-P3 0 0 0.002 10 -0.001 48 58
ITGA2B -0.052 0.22 -10000 0 -0.68 44 44
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.023 -10000 0 -10000 0 0
ADAP1 0.025 0.006 -10000 0 -10000 0 0
KIF13B 0.026 0.004 -10000 0 -10000 0 0
HGF/MET -0.085 0.2 -10000 0 -0.54 58 58
PXN 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.17 0.55 8 -0.29 119 127
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.022 0.18 -10000 0 -0.45 59 59
ADRB2 0.01 0.11 -10000 0 -0.69 9 9
receptor agonist activity 0 0 0.001 16 0 122 138
actin filament binding 0 0.001 0.002 12 -0.001 112 124
SRC 0.025 0.009 -10000 0 -10000 0 0
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
GNAQ 0.024 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.006 12 -0.001 51 63
ARF6/GDP -0.006 0.088 0.38 2 -0.41 6 8
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.41 98 98
alphaIIb/beta3 Integrin/paxillin/GIT1 0 0.17 -10000 0 -0.44 51 51
ACAP1 0.019 0.047 -10000 0 -0.53 2 2
ACAP2 0.026 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.05 0.19 -10000 0 -0.57 48 48
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF -0.077 0.25 -10000 0 -0.69 58 58
CYTH3 0.007 0.026 -10000 0 -0.52 1 1
CYTH2 -0.008 0.15 -10000 0 -0.93 10 10
NCK1 0.026 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.002 17 0 79 96
endosomal lumen acidification 0 0 0.002 7 -0.001 117 124
microtubule-based process 0 0 -10000 0 0 9 9
GULP1 -0.096 0.27 -10000 0 -0.67 71 71
GNAQ/ARNO 0.006 0.14 -10000 0 -0.85 10 10
mol:Phosphatidic acid 0 0 0.001 11 -10000 0 11
PIP3-E 0 0 0.001 9 0 12 21
MET -0.035 0.073 -10000 0 -10000 0 0
GNA14 -0.13 0.29 -10000 0 -0.66 92 92
GNA15 0.012 0.052 -10000 0 -0.69 1 1
GIT1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 12 -0.001 90 102
GNA11 0.017 0.071 -10000 0 -0.69 4 4
LHCGR -0.076 0.23 -10000 0 -0.69 48 48
AGTR1 -0.26 0.35 -10000 0 -0.69 162 162
desensitization of G-protein coupled receptor protein signaling pathway -0.05 0.19 -10000 0 -0.57 48 48
IPCEF1/ARNO -0.034 0.18 -10000 0 -0.73 10 10
alphaIIb/beta3 Integrin -0.036 0.2 -10000 0 -0.55 51 51
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.35 -10000 0 -1.2 39 39
MKNK1 0.026 0.005 -10000 0 -10000 0 0
MAPK14 -0.022 0.11 -10000 0 -0.33 37 37
ATF2/c-Jun -0.21 0.36 -10000 0 -0.81 97 97
MAPK11 -0.016 0.1 -10000 0 -0.34 28 28
MITF -0.027 0.13 -10000 0 -0.4 35 35
MAPKAPK5 -0.023 0.12 -10000 0 -0.4 31 31
KRT8 -0.023 0.12 -10000 0 -0.4 31 31
MAPKAPK3 0.026 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.032 0.16 -10000 0 -0.51 31 31
CEBPB -0.025 0.12 -10000 0 -0.4 33 33
SLC9A1 -0.029 0.13 -10000 0 -0.4 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.074 0.18 -10000 0 -0.42 67 67
p38alpha-beta/MNK1 -0.016 0.13 -10000 0 -0.41 31 31
JUN -0.21 0.35 -10000 0 -0.81 97 97
PPARGC1A -0.23 0.25 -10000 0 -0.45 209 209
USF1 -0.029 0.12 -10000 0 -0.4 36 36
RAB5/GDP/GDI1 -0.039 0.1 -10000 0 -0.34 19 19
NOS2 -0.034 0.12 -10000 0 -0.49 9 9
DDIT3 -0.024 0.12 -10000 0 -0.4 31 31
RAB5A 0.026 0.003 -10000 0 -10000 0 0
HSPB1 -0.018 0.097 0.37 2 -0.33 29 31
p38alpha-beta/HBP1 -0.012 0.12 -10000 0 -0.41 26 26
CREB1 -0.056 0.16 -10000 0 -0.45 38 38
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.029 0.11 -10000 0 -0.37 28 28
RPS6KA4 -0.025 0.13 -10000 0 -0.41 33 33
PLA2G4A -0.061 0.17 -10000 0 -0.5 46 46
GDI1 -0.022 0.12 -10000 0 -0.41 30 30
TP53 -0.038 0.14 -10000 0 -0.49 31 31
RPS6KA5 -0.061 0.18 -10000 0 -0.45 61 61
ESR1 -0.057 0.19 -10000 0 -0.54 45 45
HBP1 0.025 0.006 -10000 0 -10000 0 0
MEF2C -0.023 0.12 -10000 0 -0.4 31 31
MEF2A -0.029 0.13 -10000 0 -0.4 36 36
EIF4EBP1 -0.056 0.15 -10000 0 -0.44 39 39
KRT19 -0.058 0.18 -10000 0 -0.52 40 40
ELK4 -0.029 0.12 -10000 0 -0.4 36 36
ATF6 -0.029 0.12 -10000 0 -0.4 36 36
ATF1 -0.054 0.15 -10000 0 -0.44 36 36
p38alpha-beta/MAPKAPK2 -0.017 0.13 -10000 0 -0.41 31 31
p38alpha-beta/MAPKAPK3 -0.017 0.14 -10000 0 -0.41 31 31
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.003 0.054 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.065 -10000 0 -0.19 53 53
AKT1 0.012 0.13 0.5 14 -0.23 4 18
EGF -0.072 0.24 -10000 0 -0.68 55 55
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.015 0.076 0.34 7 -0.44 2 9
mol:Ca2+ -0.016 0.15 0.46 11 -0.31 55 66
LYN 0.014 0.073 0.34 5 -0.44 2 7
RhoA/GTP -0.009 0.053 -10000 0 -0.14 25 25
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.017 0.17 0.49 13 -0.35 53 66
GNG2 0.026 0.005 -10000 0 -10000 0 0
ARRB2 0.025 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.028 0.11 0.27 1 -0.57 8 9
G beta5/gamma2 -0.042 0.089 -10000 0 -0.26 53 53
PRKCH -0.022 0.17 0.5 11 -0.36 54 65
DNM1 -0.003 0.13 -10000 0 -0.63 17 17
TXA2/TP beta/beta Arrestin3 -0.011 0.12 -10000 0 -0.46 21 21
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.004 0.14 -10000 0 -0.69 17 17
G12 family/GTP -0.033 0.12 -10000 0 -0.31 51 51
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.035 0.007 -10000 0 -10000 0 0
mol:GDP 0.049 0.15 0.4 35 -0.36 8 43
mol:NADP 0.025 0.006 -10000 0 -10000 0 0
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.68 108 108
mol:IP3 -0.026 0.18 0.49 11 -0.38 55 66
cell morphogenesis 0.034 0.007 -10000 0 -10000 0 0
PLCB2 -0.049 0.22 0.49 8 -0.52 55 63
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.085 0.17 0.32 4 -0.34 117 121
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.01 0.07 0.32 4 -0.44 2 6
RHOA 0.026 0.003 -10000 0 -10000 0 0
PTGIR 0.018 0.071 -10000 0 -0.69 4 4
PRKCB1 -0.026 0.17 0.47 11 -0.38 54 65
GNAQ 0.024 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.025 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.044 0.23 0.54 11 -0.54 54 65
LCK 0.011 0.089 0.34 7 -0.48 5 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.025 0.079 -10000 0 -0.31 16 16
TXA2-R family/G12 family/GDP/G beta/gamma 0.032 0.025 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.03 0.081 -10000 0 -0.32 14 14
MAPK14 -0.005 0.12 0.42 13 -0.23 49 62
TGM2/GTP -0.046 0.17 0.35 1 -0.43 52 53
MAPK11 -0.008 0.13 0.45 13 -0.23 47 60
ARHGEF1 -0.015 0.071 -10000 0 -0.18 47 47
GNAI2 0.026 0.003 -10000 0 -10000 0 0
JNK cascade -0.024 0.18 0.49 13 -0.39 54 67
RAB11/GDP 0.026 0.006 -10000 0 -10000 0 0
ICAM1 -0.016 0.14 0.43 13 -0.29 54 67
cAMP biosynthetic process -0.027 0.17 0.5 11 -0.36 53 64
Gq family/GTP/EBP50 -0.044 0.11 0.24 1 -0.23 93 94
actin cytoskeleton reorganization 0.034 0.007 -10000 0 -10000 0 0
SRC 0.012 0.07 0.32 4 -0.44 2 6
GNB5 0.026 0.003 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.023 0.13 0.48 12 -0.29 15 27
VCAM1 -0.011 0.14 0.42 13 -0.3 54 67
TP beta/Gq family/GDP/G beta5/gamma2 -0.028 0.11 0.27 1 -0.57 8 9
platelet activation -0.004 0.17 0.55 14 -0.3 52 66
PGI2/IP 0.013 0.054 -10000 0 -0.52 4 4
PRKACA 0.003 0.084 -10000 0 -0.37 18 18
Gq family/GDP/G beta5/gamma2 -0.028 0.11 0.28 1 -0.55 8 9
TXA2/TP beta/beta Arrestin2 -0.001 0.12 -10000 0 -0.54 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.001 0.075 -10000 0 -0.35 16 16
mol:DAG -0.031 0.19 0.51 10 -0.43 54 64
EGFR 0.017 0.079 -10000 0 -0.69 5 5
TXA2/TP alpha -0.043 0.22 0.57 10 -0.49 53 63
Gq family/GTP -0.063 0.13 0.22 1 -0.27 102 103
YES1 0.016 0.075 0.35 6 -0.44 2 8
GNAI2/GTP 0.007 0.069 -10000 0 -0.34 7 7
PGD2/DP -0.004 0.11 -10000 0 -0.52 17 17
SLC9A3R1 0.025 0.006 -10000 0 -10000 0 0
FYN 0.018 0.08 0.34 9 -0.44 2 11
mol:NO 0.025 0.006 -10000 0 -10000 0 0
GNA15 0.013 0.052 -10000 0 -0.69 1 1
PGK/cGMP -0.094 0.21 -10000 0 -0.45 107 107
RhoA/GDP 0.026 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.085 -10000 0 -0.41 6 6
NOS3 0.025 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.032 0.18 0.51 10 -0.38 57 67
PRKCB -0.024 0.17 0.5 12 -0.37 54 66
PRKCE -0.028 0.16 0.42 9 -0.37 55 64
PRKCD -0.026 0.17 0.48 10 -0.39 54 64
PRKCG -0.026 0.18 0.5 10 -0.39 51 61
muscle contraction -0.037 0.22 0.54 12 -0.49 54 66
PRKCZ -0.017 0.17 0.49 13 -0.35 52 65
ARR3 -0.001 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.015 0.079 -10000 0 -0.31 17 17
PRKCQ -0.027 0.17 0.46 11 -0.36 56 67
MAPKKK cascade -0.036 0.2 0.49 13 -0.46 54 67
SELE -0.028 0.18 0.42 13 -0.42 54 67
TP beta/GNAI2/GDP/G beta/gamma 0.039 0.082 -10000 0 -0.56 2 2
ROCK1 0.026 0.004 -10000 0 -10000 0 0
GNA14 -0.13 0.29 -10000 0 -0.66 92 92
chemotaxis -0.05 0.25 0.58 10 -0.61 54 64
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.018 0.071 -10000 0 -0.69 4 4
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.015 -10000 0 -10000 0 0
forebrain development -0.3 0.28 0.34 1 -0.54 197 198
GNAO1 0.005 0.11 -10000 0 -0.69 10 10
SMO/beta Arrestin2 0.014 0.027 -10000 0 -10000 0 0
SMO 0.016 0.015 -10000 0 -10000 0 0
ARRB2 0.02 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.038 0.067 -10000 0 -0.34 5 5
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.003 -10000 0 -10000 0 0
GNAI2 0.024 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.063 0.034 -10000 0 -0.42 1 1
GNAI1 0.023 0.006 -10000 0 -10000 0 0
XPO1 0.015 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.21 0.21 -10000 0 -0.49 112 112
SAP30 0.025 0.036 -10000 0 -0.69 1 1
mol:GDP 0.016 0.015 -10000 0 -10000 0 0
MIM/GLI2A -0.033 0.066 -10000 0 -10000 0 0
IFT88 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.023 0.008 -10000 0 -10000 0 0
GLI2 0 0.084 0.3 3 -0.39 6 9
GLI3 0.029 0.069 0.26 3 -0.37 4 7
CSNK1D 0.025 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.026 0.005 -10000 0 -10000 0 0
Gi family/GTP -0.014 0.064 -10000 0 -0.31 10 10
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.038 0.061 -10000 0 -0.46 2 2
GLI2/Su(fu) 0.007 0.078 -10000 0 -0.57 2 2
FOXA2 -0.61 0.62 -10000 0 -1.2 204 204
neural tube patterning -0.3 0.28 0.34 1 -0.54 197 198
SPOP 0.025 0.006 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.034 0.026 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.007 -10000 0 -10000 0 0
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
MTSS1 -0.033 0.066 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.34 1 -0.54 197 198
SUFU 0.018 0.011 -10000 0 -10000 0 0
LGALS3 -0.028 0.072 -10000 0 -10000 0 0
catabolic process 0.032 0.098 0.27 2 -0.47 6 8
GLI3A/CBP -0.18 0.2 -10000 0 -0.38 199 199
KIF3A 0.026 0.005 -10000 0 -10000 0 0
GLI1 -0.31 0.29 0.34 1 -0.56 197 198
RAB23 0.021 0.061 -10000 0 -0.69 3 3
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
IFT172 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.02 0.048 -10000 0 -10000 0 0
GNAZ 0.018 0.012 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
CSNK1G1 0.026 0.003 -10000 0 -10000 0 0
PIAS1 0.026 0.003 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
GLI2/SPOP 0.008 0.083 -10000 0 -0.37 7 7
STK36 0.015 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.013 0.046 -10000 0 -0.25 10 10
PTCH1 -0.27 0.26 0.41 1 -0.59 111 112
MIM/GLI1 -0.43 0.38 -10000 0 -0.7 226 226
CREBBP -0.17 0.2 -10000 0 -0.38 199 199
Su(fu)/SIN3/HDAC complex 0.038 0.06 -10000 0 -0.66 2 2
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.024 0.13 -10000 0 -0.38 24 24
TBX21 -0.13 0.42 -10000 0 -1.1 49 49
B2M 0.023 0.017 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0.003 0.072 -10000 0 -0.6 3 3
GADD45B -0.11 0.4 -10000 0 -1 50 50
IL12RB2 -0.006 0.13 -10000 0 -0.69 14 14
GADD45G -0.093 0.35 -10000 0 -0.94 41 41
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.025 0.007 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
IL18 -0.004 0.11 -10000 0 -0.66 9 9
IL2RA -0.014 0.15 -10000 0 -0.66 20 20
IFNG -0.074 0.23 -10000 0 -0.69 50 50
STAT3 (dimer) -0.083 0.31 -10000 0 -0.78 50 50
HLA-DRB5 -0.011 0.081 -10000 0 -0.69 3 3
FASLG -0.14 0.46 -10000 0 -1.2 50 50
NF kappa B2 p52/RelB -0.1 0.38 -10000 0 -0.97 48 48
CD4 0.011 0.032 -10000 0 -10000 0 0
SOCS1 0.024 0.014 -10000 0 -10000 0 0
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.067 0.21 -10000 0 -0.66 44 44
CD3E -0.048 0.19 -10000 0 -0.65 35 35
CD3G -0.11 0.26 -10000 0 -0.67 71 71
IL12Rbeta2/JAK2 0.009 0.11 -10000 0 -0.52 14 14
CCL3 -0.12 0.41 -10000 0 -1.2 42 42
CCL4 -0.16 0.49 -10000 0 -1.4 49 49
HLA-A 0.023 0.018 -10000 0 -10000 0 0
IL18/IL18R 0.026 0.16 -10000 0 -0.49 29 29
NOS2 -0.088 0.34 -10000 0 -0.96 38 38
IL12/IL12R/TYK2/JAK2/SPHK2 -0.025 0.14 -10000 0 -0.36 34 34
IL1R1 -0.1 0.37 -10000 0 -1 40 40
IL4 0 0.034 -10000 0 -10000 0 0
JAK2 0.018 0.03 -10000 0 -10000 0 0
EntrezGene:6957 -0.007 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.22 0.51 -10000 0 -1.1 81 81
RAB7A -0.061 0.3 -10000 0 -0.74 43 43
lysosomal transport -0.055 0.28 -10000 0 -0.7 43 43
FOS -0.37 0.61 -10000 0 -1.2 130 130
STAT4 (dimer) -0.086 0.35 -10000 0 -0.82 57 57
STAT5A (dimer) -0.14 0.4 -10000 0 -0.95 61 61
GZMA -0.12 0.39 -10000 0 -1.1 43 43
GZMB -0.11 0.38 -10000 0 -1 44 44
HLX 0.021 0.025 -10000 0 -10000 0 0
LCK -0.12 0.42 -10000 0 -1.1 50 50
TCR/CD3/MHC II/CD4 -0.15 0.3 -10000 0 -0.72 62 62
IL2/IL2R -0.007 0.18 -10000 0 -0.59 28 28
MAPK14 -0.088 0.37 0.46 1 -0.86 56 57
CCR5 -0.096 0.39 -10000 0 -1.1 38 38
IL1B -0.037 0.2 -10000 0 -0.72 32 32
STAT6 -0.009 0.11 -10000 0 -0.47 5 5
STAT4 0.002 0.099 -10000 0 -0.58 9 9
STAT3 0.025 0.006 -10000 0 -10000 0 0
STAT1 0.023 0.022 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
NFKB2 0.026 0.004 -10000 0 -10000 0 0
IL12B 0.006 0.08 -10000 0 -0.7 4 4
CD8A -0.026 0.18 -10000 0 -0.66 29 29
CD8B -0.059 0.22 -10000 0 -0.66 46 46
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.024 0.13 0.38 24 -10000 0 24
IL2RB 0.002 0.099 -10000 0 -0.62 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.073 0.32 0.39 1 -0.74 57 58
IL2RG -0.013 0.14 -10000 0 -0.64 18 18
IL12 -0.03 0.18 -10000 0 -0.54 41 41
STAT5A 0.025 0.006 -10000 0 -10000 0 0
CD247 -0.019 0.14 -10000 0 -0.7 16 16
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.049 0.21 -10000 0 -0.69 38 38
IL12/IL12R/TYK2/JAK2 -0.14 0.48 -10000 0 -1.2 51 51
MAP2K3 -0.091 0.36 -10000 0 -0.85 56 56
RIPK2 0.026 0.004 -10000 0 -10000 0 0
MAP2K6 -0.097 0.37 -10000 0 -0.86 58 58
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.01 0.1 -10000 0 -0.69 7 7
IL18RAP -0.007 0.15 -10000 0 -0.7 18 18
IL12Rbeta1/TYK2 0.023 0.064 -10000 0 -0.46 3 3
EOMES -0.13 0.41 -10000 0 -1.3 42 42
STAT1 (dimer) -0.13 0.35 -10000 0 -0.78 71 71
T cell proliferation -0.055 0.26 -10000 0 -0.6 54 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.002 0.095 -10000 0 -0.57 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.069 0.28 -10000 0 -0.66 57 57
ATF2 -0.086 0.33 0.44 1 -0.77 58 59
EGFR-dependent Endothelin 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
HRAS 0.025 0.012 -9999 0 -10000 0 0
EGFR 0.017 0.079 -9999 0 -0.69 5 5
EGF/EGFR -0.018 0.16 -9999 0 -0.38 62 62
EGF/EGFR dimer/SHC/GRB2/SOS1 0.002 0.16 -9999 0 -0.39 55 55
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.023 0.038 -9999 0 -0.69 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.072 0.24 -9999 0 -0.68 55 55
EGF/EGFR dimer/SHC -0.024 0.18 -9999 0 -0.44 59 59
mol:GDP -0.002 0.16 -9999 0 -0.39 55 55
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.017 0.08 -9999 0 -0.69 5 5
GRB2/SOS1 0.037 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.015 0.14 -9999 0 -0.36 55 55
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.15 -9999 0 -0.37 55 55
FRAP1 -0.051 0.13 -9999 0 -0.37 55 55
EGF/EGFR dimer -0.044 0.2 -9999 0 -0.52 59 59
SOS1 0.026 0.005 -9999 0 -10000 0 0
GRB2 0.025 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.029 0.069 -9999 0 -0.52 6 6
IL6-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
BCL2L1 -0.002 0.2 0.6 5 -0.64 13 18
CRP 0 0.21 0.62 6 -0.71 10 16
cell cycle arrest -0.018 0.21 0.6 2 -0.72 18 20
TIMP1 -0.037 0.21 0.6 3 -0.63 24 27
IL6ST -0.053 0.22 -10000 0 -0.69 45 45
Rac1/GDP -0.053 0.2 -10000 0 -0.53 39 39
AP1 -0.12 0.27 -10000 0 -0.61 76 76
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.014 0.2 0.62 4 -0.67 12 16
HSP90B1 0.04 0.056 -10000 0 -0.64 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.1 0.26 -10000 0 -0.74 45 45
AKT1 0.042 0.038 -10000 0 -10000 0 0
FOXO1 0.041 0.039 -10000 0 -10000 0 0
MAP2K6 -0.087 0.24 0.24 1 -0.62 47 48
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.039 0.19 0.34 3 -0.53 31 34
MITF -0.073 0.21 -10000 0 -0.54 43 43
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.007 -10000 0 -10000 0 0
A2M 0.024 0.078 -10000 0 -1.1 2 2
CEBPB 0.032 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.008 0.089 -10000 0 -0.51 4 4
STAT3 -0.028 0.22 0.76 1 -0.77 18 19
STAT1 0.011 0.09 -10000 0 -0.99 3 3
CEBPD -0.007 0.19 0.64 2 -0.67 12 14
PIK3CA 0.026 0.036 -10000 0 -0.69 1 1
PI3K 0.039 0.029 -10000 0 -0.52 1 1
JUN -0.13 0.29 -10000 0 -0.69 87 87
PIAS3/MITF -0.059 0.2 -10000 0 -0.54 38 38
MAPK11 -0.11 0.25 -10000 0 -0.74 43 43
STAT3 (dimer)/FOXO1 0.014 0.16 -10000 0 -0.58 10 10
GRB2/SOS1/GAB family -0.034 0.2 -10000 0 -0.62 18 18
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.076 0.21 -10000 0 -0.47 54 54
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.025 0.007 -10000 0 -10000 0 0
LBP 0.005 0.18 0.62 7 -0.6 6 13
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.025 0.016 -10000 0 -10000 0 0
MYC -0.018 0.24 0.62 3 -1 13 16
FGG -0.011 0.2 0.63 4 -0.67 12 16
macrophage differentiation -0.018 0.21 0.6 2 -0.72 18 20
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.076 0.25 -10000 0 -0.45 112 112
JUNB -0.008 0.21 0.6 3 -0.78 14 17
FOS -0.16 0.31 -10000 0 -0.69 103 103
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.072 0.23 -10000 0 -0.53 50 50
STAT1/PIAS1 -0.041 0.2 -10000 0 -0.49 39 39
GRB2/SOS1/GAB family/SHP2/PI3K 0.04 0.036 -10000 0 -0.29 2 2
STAT3 (dimer) -0.022 0.22 0.76 1 -0.75 18 19
PRKCD -0.025 0.19 0.47 5 -0.58 21 26
IL6R 0.006 0.11 -10000 0 -0.69 10 10
SOCS3 -0.13 0.37 0.43 2 -1.1 45 47
gp130 (dimer)/JAK1/JAK1/LMO4 0 0.16 -10000 0 -0.45 43 43
Rac1/GTP -0.05 0.2 -10000 0 -0.52 39 39
HCK 0.017 0.036 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.089 0.34 1 -0.55 4 5
bone resorption -0.012 0.19 0.62 4 -0.64 12 16
IRF1 -0.002 0.2 0.64 6 -0.66 10 16
mol:GDP -0.072 0.21 -10000 0 -0.54 42 42
SOS1 0.026 0.005 -10000 0 -10000 0 0
VAV1 -0.074 0.21 -10000 0 -0.55 42 42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.096 0.26 -10000 0 -0.72 45 45
PTPN11 0.016 0.049 -10000 0 -0.85 1 1
IL6/IL6RA -0.089 0.24 -10000 0 -0.53 88 88
gp130 (dimer)/TYK2/TYK2/LMO4 -0.004 0.15 -10000 0 -0.43 45 45
gp130 (dimer)/JAK2/JAK2/LMO4 -0.005 0.16 -10000 0 -0.45 43 43
IL6 -0.12 0.29 -10000 0 -0.69 81 81
PIAS3 0.025 0.007 -10000 0 -10000 0 0
PTPRE -0.027 0.079 -10000 0 -0.69 1 1
PIAS1 0.026 0.003 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.076 0.21 -10000 0 -0.37 113 113
LMO4 0.026 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.025 0.21 -10000 0 -0.75 18 18
MCL1 0.054 0.058 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.005 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.12 -10000 0 -0.38 19 19
NFATC4 -0.024 0.09 0.32 2 -0.28 35 37
ERBB2IP 0.026 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.019 0.12 -10000 0 -0.36 37 37
JUN -0.003 0.1 0.38 10 -0.4 1 11
HRAS 0.024 0.012 -10000 0 -10000 0 0
DOCK7 -0.028 0.11 -10000 0 -0.34 37 37
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.003 0.14 -10000 0 -0.41 38 38
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.005 -10000 0 -10000 0 0
MAPK10 -0.011 0.063 0.25 2 -10000 0 2
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.02 0.12 -10000 0 -0.39 37 37
RAF1 -0.014 0.14 0.43 7 -0.39 19 26
ErbB2/ErbB3/neuregulin 2 -0.034 0.16 -10000 0 -0.43 54 54
STAT3 0.026 0.076 -10000 0 -0.84 3 3
cell migration 0.006 0.11 0.39 16 -0.24 2 18
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.15 0.33 0.52 4 -0.69 95 99
FOS -0.12 0.27 0.49 6 -0.5 123 129
NRAS 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.12 -10000 0 -0.36 37 37
MAPK3 -0.081 0.24 0.5 4 -0.52 69 73
MAPK1 -0.17 0.31 0.54 3 -0.64 97 100
JAK2 -0.028 0.1 -10000 0 -0.34 36 36
NF2 -0.014 0.12 -10000 0 -0.63 15 15
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.017 0.12 -10000 0 -0.35 38 38
NRG1 -0.045 0.21 -10000 0 -0.68 40 40
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
MAPK8 -0.019 0.11 -10000 0 -0.33 38 38
MAPK9 -0.011 0.063 0.25 2 -10000 0 2
ERBB2 -0.016 0.006 -10000 0 -10000 0 0
ERBB3 0.014 0.082 -10000 0 -0.64 6 6
SHC1 0.024 0.007 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.015 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.074 -10000 0 -0.82 3 3
RNF41 0 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.018 0.079 -10000 0 -0.26 35 35
ErbB2/ErbB2/HSP90 (dimer) 0.013 0.013 -10000 0 -10000 0 0
CHRNA1 -0.076 0.2 0.46 4 -0.4 78 82
myelination -0.011 0.14 0.55 15 -0.28 16 31
PPP3CB -0.026 0.1 -10000 0 -0.32 37 37
KRAS 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.015 0.11 -10000 0 -0.31 37 37
NRG2 -0.063 0.23 -10000 0 -0.69 49 49
mol:GDP -0.017 0.12 -10000 0 -0.35 38 38
SOS1 0.025 0.005 -10000 0 -10000 0 0
MAP2K2 -0.028 0.13 0.43 5 -0.39 19 24
SRC 0.026 0.009 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.027 0.11 0.25 1 -0.34 37 38
MAP2K1 -0.075 0.23 0.52 3 -0.61 27 30
heart morphogenesis -0.019 0.12 -10000 0 -0.36 37 37
RAS family/GDP 0.01 0.12 -10000 0 -0.38 14 14
GRB2 0.025 0.006 -10000 0 -10000 0 0
PRKACA -0.014 0.13 -10000 0 -0.66 16 16
CHRNE 0.008 0.04 0.2 10 -0.23 1 11
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.006 -10000 0 -10000 0 0
nervous system development -0.019 0.12 -10000 0 -0.36 37 37
CDC42 0.026 0.005 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.016 -10000 0 -10000 0 0
CCL5 -0.019 0.17 -10000 0 -0.69 24 24
SDCBP 0.026 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.041 0.14 -10000 0 -0.42 39 39
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.034 0.15 -10000 0 -0.56 20 20
Syndecan-1/Syntenin -0.032 0.15 0.25 2 -0.52 24 26
MAPK3 -0.031 0.13 -10000 0 -0.52 18 18
HGF/MET -0.085 0.19 -10000 0 -0.54 58 58
TGFB1/TGF beta receptor Type II 0.024 0.016 -10000 0 -10000 0 0
BSG 0.025 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.034 0.14 -10000 0 -0.55 20 20
Syndecan-1/RANTES -0.054 0.2 -10000 0 -0.53 47 47
Syndecan-1/CD147 -0.015 0.15 0.46 1 -0.54 20 21
Syndecan-1/Syntenin/PIP2 -0.033 0.14 0.24 1 -0.5 24 25
LAMA5 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.032 0.14 0.23 1 -0.46 28 29
MMP7 -0.079 0.16 -10000 0 -0.67 21 21
HGF -0.077 0.25 -10000 0 -0.69 58 58
Syndecan-1/CASK -0.046 0.14 -10000 0 -0.41 42 42
Syndecan-1/HGF/MET -0.081 0.21 0.26 1 -0.48 70 71
regulation of cell adhesion -0.033 0.12 -10000 0 -0.5 18 18
HPSE 0.005 0.1 -10000 0 -0.65 9 9
positive regulation of cell migration -0.041 0.14 -10000 0 -0.42 39 39
SDC1 -0.04 0.14 -10000 0 -0.43 39 39
Syndecan-1/Collagen -0.041 0.14 -10000 0 -0.42 39 39
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET -0.034 0.073 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
MMP9 -0.041 0.19 -10000 0 -0.69 32 32
MAPK1 -0.032 0.13 -10000 0 -0.52 19 19
homophilic cell adhesion -0.038 0.15 0.43 2 -0.42 40 42
MMP1 -0.049 0.073 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.23 -10000 0 -0.54 54 54
MAP3K8 0.013 0.087 -10000 0 -0.69 6 6
FOS -0.083 0.19 0.33 2 -0.53 35 37
PRKCA -0.024 0.16 -10000 0 -0.69 22 22
PTPN7 -0.024 0.14 -10000 0 -0.69 15 15
HRAS 0.024 0.012 -10000 0 -10000 0 0
PRKCB -0.002 0.066 -10000 0 -0.69 2 2
NRAS 0.025 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.034 0.03 -10000 0 -10000 0 0
MAPK3 -0.017 0.12 -10000 0 -0.48 18 18
MAP2K1 -0.025 0.14 -10000 0 -0.51 24 24
ELK1 0.012 0.025 -10000 0 -10000 0 0
BRAF -0.019 0.13 -10000 0 -0.52 23 23
mol:GTP -0.002 0.004 -10000 0 -0.007 106 106
MAPK1 -0.1 0.21 -10000 0 -0.55 50 50
RAF1 -0.018 0.13 -10000 0 -0.51 23 23
KRAS 0.025 0.006 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.001 0.11 -10000 0 -0.39 27 27
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.11 0.35 3 -0.39 9 12
alphaV/beta3 Integrin/Osteopontin/Src 0.002 0.13 -10000 0 -0.51 21 21
AP1 -0.14 0.31 -10000 0 -0.71 73 73
ILK -0.008 0.12 -10000 0 -0.41 26 26
bone resorption -0.003 0.12 -10000 0 -0.48 8 8
PTK2B 0.026 0.004 -10000 0 -10000 0 0
PYK2/p130Cas 0.039 0.12 -10000 0 -0.38 27 27
ITGAV 0.026 0.036 -10000 0 -0.69 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.087 -10000 0 -0.52 10 10
alphaV/beta3 Integrin/Osteopontin 0.024 0.14 -10000 0 -0.46 27 27
MAP3K1 -0.01 0.12 -10000 0 -0.42 27 27
JUN -0.13 0.29 -10000 0 -0.69 87 87
MAPK3 -0.022 0.1 -10000 0 -0.39 27 27
MAPK1 -0.024 0.1 -10000 0 -0.39 27 27
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.017 0.12 -10000 0 -0.42 28 28
ITGB3 0.009 0.11 -10000 0 -0.66 11 11
NFKBIA -0.019 0.1 -10000 0 -0.38 27 27
FOS -0.16 0.31 -10000 0 -0.69 103 103
CD44 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.026 0.004 -10000 0 -10000 0 0
PLAU -0.036 0.12 0.52 3 -0.62 1 4
NF kappa B1 p50/RelA 0.02 0.11 -10000 0 -0.52 2 2
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.026 0.096 -10000 0 -0.56 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.01 0.12 -10000 0 -0.42 27 27
VAV3 -0.016 0.12 0.4 1 -0.4 29 30
MAP3K14 -0.014 0.12 -10000 0 -0.42 27 27
ROCK2 0.008 0.11 -10000 0 -0.69 10 10
SPP1 -0.031 0.16 -10000 0 -0.68 20 20
RAC1 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.11 -10000 0 -0.37 29 29
MMP2 -0.13 0.24 -10000 0 -0.56 74 74
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.009 0.057 -10000 0 -10000 0 0
CRKL -0.015 0.093 0.36 1 -0.3 3 4
mol:PIP3 -0.002 0.018 0.34 1 -10000 0 1
AKT1 0.005 0.058 0.37 3 -0.46 2 5
PTK2B 0.026 0.004 -10000 0 -10000 0 0
RAPGEF1 0.002 0.11 0.44 8 -10000 0 8
RANBP10 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
HGF/MET/SHIP2 -0.017 0.19 -10000 0 -0.47 58 58
MAP3K5 0.011 0.13 0.49 11 -0.43 4 15
HGF/MET/CIN85/CBL/ENDOPHILINS -0.002 0.18 -10000 0 -0.43 57 57
AP1 -0.18 0.34 -10000 0 -0.68 120 120
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis -0.22 0.4 -10000 0 -0.81 121 121
STAT3 (dimer) -0.022 0.11 -10000 0 -0.29 55 55
GAB1/CRKL/SHP2/PI3K 0.026 0.1 -10000 0 -10000 0 0
INPP5D 0.018 0.034 -10000 0 -10000 0 0
CBL/CRK 0.014 0.11 0.49 5 -10000 0 5
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.005 -10000 0 -10000 0 0
PTEN 0.025 0.021 -10000 0 -0.38 1 1
ELK1 0.032 0.14 0.29 61 -0.24 3 64
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.069 -10000 0 -0.25 3 3
PAK1 0.008 0.062 0.37 6 -0.4 1 7
HGF/MET/RANBP10 -0.018 0.19 -10000 0 -0.47 58 58
HRAS -0.02 0.13 -10000 0 -0.56 2 2
DOCK1 0.001 0.12 0.44 9 -0.45 2 11
GAB1 -0.012 0.098 0.26 1 -0.32 3 4
CRK -0.007 0.099 0.29 3 -0.3 2 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.045 0.2 -10000 0 -0.52 58 58
JUN -0.13 0.29 -10000 0 -0.69 87 87
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.032 0.087 -10000 0 -0.24 57 57
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.007 0.13 0.48 6 -0.46 1 7
GRB2/SHC 0.002 0.088 -10000 0 -0.23 25 25
FOS -0.16 0.31 -10000 0 -0.69 103 103
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.032 0.14 0.29 61 -0.24 3 64
HGF/MET/MUC20 -0.071 0.17 -10000 0 -0.47 58 58
cell migration 0.001 0.086 -10000 0 -0.22 25 25
GRB2 0.025 0.006 -10000 0 -10000 0 0
CBL 0.026 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.009 0.056 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.019 0.12 -10000 0 -0.3 56 56
MET/MUC20 -0.02 0.047 -10000 0 -10000 0 0
RAP1B 0.011 0.13 0.57 11 -10000 0 11
RAP1A 0.008 0.11 0.42 9 -10000 0 9
HGF/MET/RANBP9 -0.017 0.19 -10000 0 -0.47 58 58
RAF1 -0.017 0.13 -10000 0 -0.46 2 2
STAT3 -0.023 0.11 -10000 0 -0.29 55 55
cell proliferation -0.028 0.15 -10000 0 -0.4 55 55
RPS6KB1 0 0.031 -10000 0 -10000 0 0
MAPK3 -0.021 0.11 0.51 12 -10000 0 12
MAPK1 0.13 0.29 0.61 103 -10000 0 103
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.028 0.16 0.61 15 -0.63 3 18
SRC -0.024 0.11 -10000 0 -0.29 56 56
PI3K 0.003 0.092 -10000 0 -0.22 57 57
MET/Glomulin -0.01 0.045 -10000 0 -0.14 1 1
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K1 -0.012 0.12 0.3 2 -0.42 2 4
MET -0.034 0.073 -10000 0 -10000 0 0
MAP4K1 0.005 0.12 0.52 6 -0.46 4 10
PTK2 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.01 0.12 0.31 1 -0.42 2 3
BAD 0.008 0.062 0.37 6 -0.4 1 7
MAP2K4 0.022 0.15 0.53 17 -0.42 3 20
SHP2/GRB2/SOS1/GAB1 0.018 0.099 -10000 0 -10000 0 0
INPPL1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.026 0.005 -10000 0 -10000 0 0
SH3KBP1 0.025 0.007 -10000 0 -10000 0 0
HGS -0.03 0.08 -10000 0 -0.23 56 56
PLCgamma1/PKC 0.019 0.004 -10000 0 -10000 0 0
HGF -0.077 0.25 -10000 0 -0.69 58 58
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.003 -10000 0 -10000 0 0
PTPRJ 0.026 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.001 0.1 -10000 0 -0.25 57 57
PDPK1 0 0.047 -10000 0 -0.49 2 2
HGF/MET/SHIP -0.021 0.19 -10000 0 -0.47 58 58
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.014 0.087 -10000 0 -0.69 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 204 204
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.004 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.006 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
MAP3K12 0.026 0.005 -10000 0 -10000 0 0
FGR 0.024 0.016 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.045 0.07 -10000 0 -0.29 9 9
PRKG1 -0.16 0.31 -10000 0 -0.68 108 108
DUSP8 0.018 0.064 -10000 0 -0.69 3 3
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 111 111
apoptosis -0.043 0.067 -10000 0 -0.29 8 8
RAL/GTP 0.034 0.008 -10000 0 -10000 0 0
LYN 0.026 0.004 -10000 0 -10000 0 0
DUSP1 -0.084 0.26 -10000 0 -0.69 62 62
PAK1 0.026 0.005 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.063 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.036 -10000 0 -0.69 1 1
RAC1 0.025 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.025 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.01 -10000 0 -10000 0 0
MAPK11 -0.054 0.16 0.43 16 -0.33 24 40
BLK -0.2 0.32 -10000 0 -0.68 122 122
HCK 0.017 0.036 -10000 0 -10000 0 0
MAP2K3 0.025 0.007 -10000 0 -10000 0 0
DUSP16 0.026 0.005 -10000 0 -10000 0 0
DUSP10 0.022 0.038 -10000 0 -0.69 1 1
TRAF6/MEKK3 0.031 0.024 -10000 0 -0.42 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.013 0.12 0.38 15 -0.33 8 23
positive regulation of innate immune response -0.044 0.17 0.48 16 -0.43 9 25
LCK 0.011 0.083 -10000 0 -0.69 5 5
p38alpha-beta/MKP7 -0.049 0.14 0.34 5 -0.44 6 11
p38alpha-beta/MKP5 -0.039 0.16 0.46 13 -0.46 7 20
PGK/cGMP -0.12 0.24 -10000 0 -0.52 108 108
PAK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.1 0.18 0.28 3 -0.41 58 61
CDC42 0.026 0.005 -10000 0 -10000 0 0
RALB 0.026 0.004 -10000 0 -10000 0 0
RALA 0.025 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.35 -10000 0 -0.67 222 222
Plasma membrane estrogen 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
GNB1/GNG2 0.038 0.1 -10000 0 -0.41 19 19
ER alpha/Gai/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.54 20 20
AKT1 -0.014 0.2 -10000 0 -0.77 24 24
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.01 0.2 -10000 0 -0.79 23 23
mol:Ca2+ -0.094 0.19 -10000 0 -0.42 96 96
IGF1R 0.026 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.016 0.14 -10000 0 -0.46 36 36
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.012 0.19 0.73 24 -10000 0 24
RhoA/GTP 0.005 0.073 -10000 0 -0.36 14 14
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.006 0.13 -10000 0 -0.55 16 16
regulation of stress fiber formation 0.004 0.077 0.31 7 -0.28 1 8
E2/ERA-ERB (dimer) 0.003 0.11 -10000 0 -0.45 21 21
KRAS 0.026 0.005 -10000 0 -10000 0 0
G13/GTP 0.008 0.087 -10000 0 -0.37 18 18
pseudopodium formation -0.004 0.077 0.28 1 -0.31 7 8
E2/ER alpha (dimer)/PELP1 0.008 0.094 -10000 0 -0.4 18 18
GRB2 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.026 0.005 -10000 0 -10000 0 0
GNAO1 0.007 0.11 -10000 0 -0.69 10 10
HRAS 0.025 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.011 0.16 0.52 6 -0.59 19 25
E2/ER beta (dimer) 0.014 0.054 -10000 0 -0.52 4 4
mol:GDP 0.001 0.11 -10000 0 -0.48 20 20
mol:NADP 0.011 0.16 0.52 6 -0.59 19 25
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.098 0.2 -10000 0 -0.44 96 96
IGF-1R heterotetramer 0.026 0.003 -10000 0 -10000 0 0
PLCB1 -0.098 0.2 -10000 0 -0.45 96 96
PLCB2 -0.098 0.2 -10000 0 -0.46 95 95
IGF1 -0.12 0.29 -10000 0 -0.68 82 82
mol:L-citrulline 0.011 0.16 0.52 6 -0.59 19 25
RHOA 0.026 0.003 -10000 0 -10000 0 0
Gai/GDP 0.006 0.14 -10000 0 -0.71 14 14
JNK cascade 0.014 0.053 -10000 0 -0.52 4 4
BCAR1 0.025 0.006 -10000 0 -10000 0 0
ESR2 0.019 0.071 -10000 0 -0.69 4 4
GNAQ 0.024 0.008 -10000 0 -10000 0 0
ESR1 -0.016 0.15 -10000 0 -0.66 19 19
Gq family/GDP/Gbeta gamma -0.056 0.18 -10000 0 -0.61 23 23
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.11 -10000 0 -0.66 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.004 0.13 -10000 0 -0.55 16 16
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.011 0.11 -10000 0 -0.49 19 19
STRN -0.008 0.15 -10000 0 -0.69 19 19
GNAL -0.058 0.23 -10000 0 -0.67 49 49
PELP1 0.025 0.007 -10000 0 -10000 0 0
MAPK11 0.008 0.045 -10000 0 -0.44 4 4
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.006 -10000 0 -10000 0 0
HBEGF -0.014 0.15 0.38 4 -0.55 17 21
cAMP biosynthetic process -0.041 0.16 -10000 0 -0.4 61 61
SRC -0.002 0.13 -10000 0 -0.51 18 18
PI3K 0.037 0.029 -10000 0 -0.52 1 1
GNB1 0.026 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.03 0.11 -10000 0 -0.43 19 19
SOS1 0.026 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.065 0.16 -10000 0 -0.43 40 40
Gs family/GTP -0.031 0.17 -10000 0 -0.41 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.015 -10000 0 -10000 0 0
vasodilation 0.011 0.15 0.48 7 -0.55 20 27
mol:DAG -0.098 0.2 -10000 0 -0.44 96 96
Gs family/GDP/Gbeta gamma -0.026 0.14 -10000 0 -0.36 57 57
MSN -0.005 0.082 0.29 1 -0.33 7 8
Gq family/GTP -0.099 0.22 -10000 0 -0.48 96 96
mol:PI-3-4-5-P3 -0.008 0.19 -10000 0 -0.76 23 23
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.011 0.15 0.55 20 -0.48 7 27
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.11 -10000 0 -0.45 20 20
NOS3 0.002 0.16 0.51 1 -0.63 19 20
GNA11 0.018 0.071 -10000 0 -0.69 4 4
MAPKKK cascade -0.011 0.17 0.37 1 -0.59 24 25
E2/ER alpha (dimer)/PELP1/Src 0.001 0.14 -10000 0 -0.58 16 16
ruffle organization -0.004 0.077 0.28 1 -0.31 7 8
ROCK2 0.001 0.099 0.36 5 -0.34 21 26
GNA14 -0.13 0.29 -10000 0 -0.66 92 92
GNA15 0.013 0.052 -10000 0 -0.69 1 1
GNA13 0.025 0.006 -10000 0 -10000 0 0
MMP9 -0.03 0.17 -10000 0 -0.6 21 21
MMP2 -0.001 0.12 -10000 0 -0.58 11 11
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.014 -10000 0 -10000 0 0
REL -0.004 0.16 -10000 0 -0.69 20 20
HDAC7 -0.064 0.1 -10000 0 -0.46 10 10
JUN -0.13 0.29 -10000 0 -0.69 87 87
EP300 0.019 0.012 -10000 0 -10000 0 0
KAT2B 0.026 0.004 -10000 0 -10000 0 0
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.012 0.067 -10000 0 -0.54 6 6
FOXO1 0.024 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.062 0.11 -10000 0 -0.47 11 11
MAP2K6 0.008 0.088 -10000 0 -0.7 6 6
BRM/BAF57 0.018 0.032 -10000 0 -10000 0 0
MAP2K4 0.018 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.021 -10000 0 -10000 0 0
PDE9A 0.014 0.07 -10000 0 -0.59 1 1
NCOA2 -0.033 0.19 -10000 0 -0.69 30 30
CEBPA 0.019 0.071 -10000 0 -0.69 4 4
EHMT2 0.024 0.005 -10000 0 -10000 0 0
cell proliferation -0.078 0.2 0.57 18 -0.44 12 30
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.13 0.28 -10000 0 -0.69 81 81
RXRs/9cRA 0.022 0.072 -10000 0 -0.41 3 3
AR/RACK1/Src -0.13 0.13 0.33 2 -0.48 11 13
AR/GR -0.12 0.17 0.25 5 -0.32 161 166
GNB2L1 0.021 0.008 -10000 0 -10000 0 0
PKN1 0.024 0.007 -10000 0 -10000 0 0
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.005 -10000 0 -0.01 148 148
MAPK8 -0.008 0.049 -10000 0 -0.52 3 3
T-DHT/AR/TIF2/CARM1 -0.12 0.16 0.35 2 -0.53 33 35
SRC -0.037 0.064 0.24 1 -0.41 8 9
NR3C1 0.026 0.005 -10000 0 -10000 0 0
KLK3 -0.34 0.54 0.38 2 -1.2 111 113
APPBP2 0.023 0.012 -10000 0 -10000 0 0
TRIM24 0.013 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.065 0.11 0.33 5 -0.48 10 15
TMPRSS2 -0.044 0.28 -10000 0 -1.1 24 24
RXRG -0.1 0.075 -10000 0 -0.69 3 3
mol:9cRA -0.002 0.003 -10000 0 -0.01 6 6
RXRA 0.023 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.008 -10000 0 -10000 0 0
NR2C2 0.018 0.071 -10000 0 -0.69 4 4
KLK2 -0.44 0.39 0.33 2 -0.77 230 232
AR -0.14 0.18 -10000 0 -0.35 160 160
SENP1 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
MDM2 0.034 0.016 -10000 0 -10000 0 0
SRY 0.008 0.014 0.031 110 -10000 0 110
GATA2 0.026 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.012 0.035 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.094 0.12 0.34 3 -0.5 9 12
positive regulation of transcription 0.026 0.008 -10000 0 -10000 0 0
DNAJA1 0.023 0.013 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.008 -10000 0 -10000 0 0
NCOA1 0.018 0.021 -10000 0 -10000 0 0
SPDEF -0.003 0.047 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.083 0.13 0.28 2 -0.42 32 34
T-DHT/AR/Hsp90 -0.066 0.11 0.33 5 -0.46 10 15
GSK3B 0.024 0.006 -10000 0 -10000 0 0
NR2C1 0.027 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.066 0.26 1 -0.42 9 10
SIRT1 0.025 0.005 -10000 0 -10000 0 0
ZMIZ2 0.034 0.017 -10000 0 -10000 0 0
POU2F1 0.031 0.035 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.069 0.11 0.32 5 -0.5 9 14
CREBBP 0.025 0.006 -10000 0 -10000 0 0
SMARCE1 0.013 0.021 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.058 0.25 21 -10000 0 21
RFC1 0.012 0.06 0.25 23 -10000 0 23
PRKDC 0.012 0.06 0.25 23 -10000 0 23
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.006 0.099 -10000 0 -0.77 5 5
FASLG/FAS/FADD/FAF1 -0.02 0.098 0.24 2 -0.34 29 31
MAP2K4 -0.04 0.18 0.32 2 -0.43 36 38
mol:ceramide -0.029 0.14 -10000 0 -0.43 31 31
GSN 0.011 0.058 0.25 21 -10000 0 21
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.12 -10000 0 -0.43 29 29
FAS 0.018 0.019 -10000 0 -10000 0 0
BID -0.019 0.037 0.28 3 -10000 0 3
MAP3K1 -0.016 0.12 0.26 4 -0.39 18 22
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
RB1 0.013 0.063 0.26 22 -10000 0 22
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET -0.019 0.19 -10000 0 -0.47 59 59
ARHGDIB 0.013 0.063 0.24 26 -10000 0 26
FADD 0.017 0.019 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.058 -10000 0 -0.25 21 21
NFKB1 -0.025 0.11 -10000 0 -0.68 2 2
MAPK8 -0.078 0.23 0.4 2 -0.48 91 93
DFFA 0.012 0.06 0.25 23 -10000 0 23
DNA fragmentation during apoptosis 0.012 0.06 0.25 23 -10000 0 23
FAS/FADD/MET 0.041 0.045 -10000 0 -10000 0 0
CFLAR/RIP1 0.042 0.01 -10000 0 -10000 0 0
FAIM3 0.015 0.067 -10000 0 -0.69 3 3
FAF1 0.017 0.021 -10000 0 -10000 0 0
PARP1 0.015 0.074 0.29 24 -10000 0 24
DFFB 0.012 0.06 0.25 23 -10000 0 23
CHUK -0.023 0.096 -10000 0 -0.63 2 2
FASLG -0.04 0.18 -10000 0 -0.7 29 29
FAS/FADD 0.026 0.028 -10000 0 -10000 0 0
HGF -0.077 0.25 -10000 0 -0.69 58 58
LMNA 0.012 0.065 0.26 23 -10000 0 23
CASP6 0.012 0.06 0.25 23 -10000 0 23
CASP10 0.018 0.019 -10000 0 -10000 0 0
CASP3 0.016 0.075 0.3 26 -10000 0 26
PTPN13 0.023 0.05 -10000 0 -0.69 2 2
CASP8 -0.014 0.037 0.41 3 -10000 0 3
IL6 -0.25 0.55 -10000 0 -1.3 89 89
MET -0.034 0.073 -10000 0 -10000 0 0
ICAD/CAD 0.011 0.054 0.23 15 -10000 0 15
FASLG/FAS/FADD/FAF1/Caspase 10 -0.03 0.14 -10000 0 -0.44 31 31
activation of caspase activity by cytochrome c -0.019 0.037 0.28 3 -10000 0 3
PAK2 0.013 0.062 0.24 25 -10000 0 25
BCL2 -0.019 0.17 -10000 0 -0.68 26 26
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.14 -10000 0 -0.36 50 50
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.002 0.12 -10000 0 -0.34 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.05 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.007 0.071 -10000 0 -0.25 2 2
CaM/Ca2+ 0.012 0.14 -10000 0 -0.34 50 50
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.013 0.13 -10000 0 -0.35 50 50
AKT1 -0.016 0.12 0.38 5 -0.32 48 53
MAP2K1 -0.025 0.12 0.29 2 -0.33 47 49
MAP3K11 -0.022 0.13 0.3 4 -0.35 50 54
IFNGR1 0.02 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.016 0.076 -10000 0 -0.38 4 4
Rap1/GTP -0.021 0.096 -10000 0 -10000 0 0
CRKL/C3G 0.028 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.014 0.15 -10000 0 -0.38 50 50
CEBPB -0.053 0.19 0.58 6 -0.53 18 24
STAT3 0.025 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.017 0.15 -10000 0 -0.66 3 3
STAT1 -0.021 0.13 0.32 6 -0.35 50 56
CALM1 0.026 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.068 0.24 -10000 0 -0.69 50 50
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
STAT1 (dimer)/PIAS1 -0.005 0.13 0.32 6 -0.33 50 56
CEBPB/PTGES2/Cbp/p300 -0.024 0.12 -10000 0 -0.38 6 6
mol:Ca2+ 0.005 0.14 -10000 0 -0.36 50 50
MAPK3 -0.008 0.12 0.42 1 -0.65 3 4
STAT1 (dimer) 0.016 0.097 -10000 0 -0.35 1 1
MAPK1 -0.16 0.3 0.43 1 -0.67 94 95
JAK2 0.018 0.025 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.019 0.025 -10000 0 -10000 0 0
CAMK2D 0.026 0.004 -10000 0 -10000 0 0
DAPK1 -0.039 0.19 0.54 8 -0.6 22 30
SMAD7 0.02 0.076 0.5 6 -10000 0 6
CBL/CRKL/C3G -0.008 0.12 0.3 2 -0.35 1 3
PI3K 0.011 0.13 -10000 0 -0.34 49 49
IFNG -0.068 0.24 -10000 0 -0.69 50 50
apoptosis -0.034 0.16 0.56 6 -0.45 27 33
CAMK2G 0.026 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.006 -10000 0 -10000 0 0
CAMK2A 0.012 0.032 -10000 0 -10000 0 0
CAMK2B 0.018 0.071 -10000 0 -0.69 4 4
FRAP1 -0.022 0.11 0.37 5 -0.3 48 53
PRKCD -0.01 0.14 0.44 10 -0.32 48 58
RAP1B 0.026 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.007 0.071 -10000 0 -0.25 2 2
PTPN2 0.026 0.004 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
IRF1 -0.013 0.088 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.012 0.12 0.3 2 -0.33 49 51
SOCS1 0.021 0.099 -10000 0 -0.96 4 4
mol:GDP -0.009 0.12 0.28 2 -0.34 1 3
CASP1 0.017 0.075 0.57 4 -0.33 2 6
PTGES2 0.024 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.058 0.34 1 -10000 0 1
mol:PI-3-4-5-P3 -0.002 0.12 -10000 0 -0.33 49 49
RAP1/GDP -0.006 0.1 -10000 0 -10000 0 0
CBL -0.022 0.13 0.29 5 -0.35 50 55
MAP3K1 -0.023 0.12 0.3 2 -0.35 48 50
PIAS1 0.026 0.003 -10000 0 -10000 0 0
PIAS4 0.024 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.007 0.071 -10000 0 -0.25 2 2
PTPN11 -0.025 0.13 -10000 0 -0.36 50 50
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.016 0.12 -10000 0 -0.42 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.008 0.083 0.41 1 -0.43 1 2
AP1 -0.16 0.31 -10000 0 -0.57 130 130
mol:PIP3 -0.013 0.1 -10000 0 -0.38 25 25
AKT1 0.028 0.094 0.28 8 -0.48 1 9
PTK2B -0.011 0.088 0.23 3 -0.4 7 10
RHOA 0.011 0.039 0.18 1 -10000 0 1
PIK3CB 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.069 0.3 5 -10000 0 5
MAGI3 0.024 0.036 -10000 0 -0.69 1 1
RELA 0.026 0.005 -10000 0 -10000 0 0
apoptosis -0.01 0.1 -10000 0 -0.36 31 31
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.003 0.1 0.38 9 -0.39 7 16
NF kappa B1 p50/RelA -0.02 0.1 -10000 0 -0.45 5 5
endothelial cell migration -0.015 0.14 -10000 0 -0.5 28 28
ADCY4 -0.028 0.15 -10000 0 -0.51 31 31
ADCY5 -0.056 0.17 -10000 0 -0.55 33 33
ADCY6 -0.028 0.15 -10000 0 -0.52 29 29
ADCY7 -0.029 0.15 -10000 0 -0.53 29 29
ADCY1 -0.03 0.15 -10000 0 -0.5 32 32
ADCY2 -0.05 0.17 -10000 0 -0.52 36 36
ADCY3 -0.028 0.15 -10000 0 -0.51 31 31
ADCY8 -0.037 0.15 -10000 0 -0.51 33 33
ADCY9 -0.029 0.15 -10000 0 -0.51 32 32
GSK3B -0.01 0.086 0.37 2 -0.42 5 7
arachidonic acid secretion -0.029 0.14 -10000 0 -0.44 38 38
GNG2 0.026 0.005 -10000 0 -10000 0 0
TRIP6 0.024 0.009 -10000 0 -10000 0 0
GNAO1 -0.024 0.15 -10000 0 -0.46 38 38
HRAS 0.025 0.012 -10000 0 -10000 0 0
NFKBIA -0.005 0.095 0.45 6 -0.49 1 7
GAB1 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.019 0.17 -10000 0 -0.78 17 17
JUN -0.13 0.29 -10000 0 -0.69 87 87
LPA/LPA2/NHERF2 0.034 0.014 -10000 0 -10000 0 0
TIAM1 0.005 0.2 -10000 0 -0.93 18 18
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.009 0.065 0.36 2 -10000 0 2
PLCB3 0.025 0.03 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.69 103 103
positive regulation of mitosis -0.029 0.14 -10000 0 -0.44 38 38
LPA/LPA1-2-3 0.016 0.12 -10000 0 -0.4 28 28
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.006 -10000 0 -10000 0 0
stress fiber formation -0.001 0.1 0.35 4 -0.32 25 29
GNAZ -0.016 0.12 -10000 0 -0.44 29 29
EGFR/PI3K-beta/Gab1 -0.004 0.11 -10000 0 -0.4 25 25
positive regulation of dendritic cell cytokine production 0.014 0.12 -10000 0 -0.4 28 28
LPA/LPA2/MAGI-3 0.034 0.028 -10000 0 -0.46 1 1
ARHGEF1 0.002 0.1 0.36 1 -0.39 22 23
GNAI2 -0.014 0.13 -10000 0 -0.44 30 30
GNAI3 -0.013 0.12 -10000 0 -0.46 28 28
GNAI1 -0.013 0.12 -10000 0 -0.45 28 28
LPA/LPA3 0.015 0.023 -10000 0 -10000 0 0
LPA/LPA2 0.02 0.011 -10000 0 -10000 0 0
LPA/LPA1 -0.018 0.14 -10000 0 -0.48 34 34
HB-EGF/EGFR -0.022 0.13 -10000 0 -0.45 35 35
HBEGF -0.036 0.14 -10000 0 -0.5 32 32
mol:DAG -0.009 0.065 0.36 2 -10000 0 2
cAMP biosynthetic process -0.034 0.17 0.41 10 -0.48 39 49
NFKB1 0.026 0.004 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.008 0.09 0.41 5 -0.41 2 7
GNAQ 0.016 0.014 -10000 0 -10000 0 0
LPAR2 0.025 0.007 -10000 0 -10000 0 0
LPAR3 0.012 0.034 -10000 0 -10000 0 0
LPAR1 -0.027 0.18 -10000 0 -0.63 33 33
IL8 -0.085 0.17 -10000 0 -0.47 32 32
PTK2 -0.005 0.11 -10000 0 -0.39 25 25
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
CASP3 -0.01 0.1 -10000 0 -0.36 31 31
EGFR 0.017 0.079 -10000 0 -0.69 5 5
PLCG1 -0.012 0.063 -10000 0 -0.3 1 1
PLD2 -0.006 0.1 -10000 0 -0.38 25 25
G12/G13 0.018 0.12 -10000 0 -0.41 27 27
PI3K-beta 0.004 0.086 -10000 0 -0.32 23 23
cell migration 0.019 0.072 -10000 0 -0.25 12 12
SLC9A3R2 0.025 0.006 -10000 0 -10000 0 0
PXN -0.003 0.1 0.26 3 -0.37 13 16
HRAS/GTP -0.028 0.15 -10000 0 -0.46 38 38
RAC1 0.025 0.006 -10000 0 -10000 0 0
MMP9 -0.041 0.19 -10000 0 -0.69 32 32
PRKCE 0.021 0.062 -10000 0 -0.69 3 3
PRKCD -0.007 0.084 0.37 8 -10000 0 8
Gi(beta/gamma) -0.023 0.14 -10000 0 -0.48 31 31
mol:LPA 0.002 0.014 -10000 0 -0.2 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.015 0.12 -10000 0 -0.42 12 12
MAPKKK cascade -0.029 0.14 -10000 0 -0.44 38 38
contractile ring contraction involved in cytokinesis 0.013 0.046 0.27 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.065 0.15 -10000 0 -0.35 90 90
GNA15 0.014 0.027 -10000 0 -0.37 1 1
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.025 0.006 -10000 0 -10000 0 0
MAPT -0.006 0.097 0.38 6 -0.4 7 13
GNA11 0.014 0.038 -10000 0 -0.33 4 4
Rac1/GTP 0.019 0.18 -10000 0 -0.83 17 17
MMP2 -0.016 0.14 -10000 0 -0.51 28 28
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 -0.069 0.18 0.43 8 -0.46 26 34
IKBKB 0.008 0.12 0.49 13 -0.31 5 18
AKT1 -0.004 0.17 0.54 21 -0.25 12 33
IKBKG -0.004 0.12 0.43 14 -0.31 15 29
CALM1 -0.024 0.093 0.34 3 -0.47 4 7
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
MAP3K1 -0.018 0.17 0.47 9 -0.55 17 26
MAP3K7 0.026 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.027 0.092 -10000 0 -0.41 7 7
DOK1 0.026 0.005 -10000 0 -10000 0 0
AP-1 -0.059 0.16 0.55 10 -0.27 81 91
LYN 0.026 0.004 -10000 0 -10000 0 0
BLNK 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex -0.077 0.19 -10000 0 -0.51 57 57
CD22 -0.074 0.18 -10000 0 -0.43 71 71
CAMK2G -0.02 0.09 0.33 3 -0.43 4 7
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
INPP5D 0.018 0.034 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.044 0.13 -10000 0 -0.35 51 51
GO:0007205 -0.028 0.095 -10000 0 -0.45 6 6
SYK 0.024 0.008 -10000 0 -10000 0 0
ELK1 -0.02 0.094 0.34 3 -0.48 4 7
NFATC1 -0.044 0.14 0.38 5 -0.45 17 22
B-cell antigen/BCR complex -0.077 0.19 -10000 0 -0.51 57 57
PAG1/CSK 0.037 0.029 -10000 0 -0.52 1 1
NFKBIB 0.018 0.043 0.2 11 -0.13 4 15
HRAS -0.021 0.095 0.3 3 -0.38 4 7
NFKBIA 0.018 0.044 0.2 11 -0.13 5 16
NF-kappa-B/RelA/I kappa B beta 0.023 0.04 0.2 11 -10000 0 11
RasGAP/Csk -0.009 0.19 -10000 0 -0.42 63 63
mol:GDP -0.025 0.092 -10000 0 -0.48 5 5
PTEN 0.025 0.021 -10000 0 -0.38 1 1
CD79B 0.006 0.05 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.023 0.04 0.2 11 -10000 0 11
GRB2 0.025 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.04 0.16 0.5 4 -0.49 15 19
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.025 0.09 -10000 0 -0.41 6 6
CSK 0.026 0.003 -10000 0 -10000 0 0
FOS -0.1 0.18 0.46 6 -0.38 103 109
CHUK 0.006 0.1 0.42 12 -0.32 5 17
IBTK 0.026 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.015 0.11 0.32 1 -0.47 7 8
PTPN6 -0.068 0.17 -10000 0 -0.41 68 68
RELA 0.026 0.005 -10000 0 -10000 0 0
BCL2A1 0.013 0.038 0.2 4 -0.12 11 15
VAV2 -0.058 0.16 -10000 0 -0.7 11 11
ubiquitin-dependent protein catabolic process 0.022 0.043 0.2 11 -0.12 4 15
BTK -0.034 0.24 -10000 0 -0.99 23 23
CD19 -0.065 0.16 -10000 0 -0.41 56 56
MAP4K1 0.008 0.085 -10000 0 -0.69 5 5
CD72 0.024 0.015 -10000 0 -10000 0 0
PAG1 0.024 0.036 -10000 0 -0.69 1 1
MAPK14 -0.01 0.15 0.43 11 -0.47 16 27
SH3BP5 0.026 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.019 0.096 -10000 0 -0.66 3 3
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.053 0.19 -10000 0 -0.44 61 61
RAF1 -0.017 0.096 0.37 4 -0.4 2 6
RasGAP/p62DOK/SHIP -0.012 0.18 -10000 0 -0.4 63 63
CD79A -0.11 0.24 -10000 0 -0.67 58 58
re-entry into mitotic cell cycle -0.058 0.16 0.54 10 -0.26 81 91
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.006 0.1 0.41 10 -0.4 1 11
MAPK1 -0.012 0.087 0.4 5 -0.38 1 6
CD72/SHP1 -0.054 0.17 -10000 0 -0.52 25 25
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.013 0.16 0.47 10 -0.48 17 27
actin cytoskeleton organization -0.046 0.15 0.39 4 -0.56 11 15
NF-kappa-B/RelA 0.046 0.072 0.34 11 -0.22 1 12
Calcineurin 0.006 0.091 -10000 0 -0.42 3 3
PI3K -0.065 0.14 -10000 0 -0.46 20 20
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.021 0.1 -10000 0 -0.61 4 4
SOS1 0.026 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.027 0.23 -10000 0 -0.98 16 16
DAPP1 -0.047 0.26 -10000 0 -1.2 15 15
cytokine secretion -0.04 0.13 0.37 5 -0.42 17 22
mol:DAG -0.025 0.09 -10000 0 -0.41 6 6
PLCG2 0.025 0.006 -10000 0 -10000 0 0
MAP2K1 -0.015 0.091 0.36 4 -0.38 2 6
B-cell antigen/BCR complex/FcgammaRIIB -0.062 0.2 -10000 0 -0.46 70 70
mol:PI-3-4-5-P3 -0.056 0.1 -10000 0 -0.35 15 15
ETS1 -0.016 0.089 0.37 4 -0.42 3 7
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.007 0.16 -10000 0 -0.39 54 54
B-cell antigen/BCR complex/LYN -0.05 0.17 -10000 0 -0.43 58 58
MALT1 0.026 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.036 -10000 0 -0.69 1 1
RAC1 -0.051 0.15 0.35 2 -0.61 11 13
B-cell antigen/BCR complex/LYN/SYK -0.043 0.2 -10000 0 -0.46 59 59
CARD11 -0.038 0.11 0.34 3 -0.49 10 13
FCGR2B -0.011 0.16 -10000 0 -0.69 20 20
PPP3CA 0.026 0.004 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.018 0.098 0.42 16 -0.13 4 20
PTPRC -0.01 0.14 -10000 0 -0.69 17 17
PDPK1 -0.031 0.085 0.28 5 -0.26 13 18
PPP3CB 0.026 0.005 -10000 0 -10000 0 0
PPP3CC 0.026 0.004 -10000 0 -10000 0 0
POU2F2 0.019 0.032 0.18 10 -10000 0 10
Syndecan-4-mediated signaling events

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.005 0.1 -10000 0 -0.85 4 4
Syndecan-4/Syndesmos -0.035 0.16 -10000 0 -0.55 32 32
positive regulation of JNK cascade -0.051 0.19 -10000 0 -0.56 33 33
Syndecan-4/ADAM12 -0.044 0.16 -10000 0 -0.56 32 32
CCL5 -0.019 0.17 -10000 0 -0.69 24 24
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DNM2 0.025 0.007 -10000 0 -10000 0 0
ITGA5 0.026 0.005 -10000 0 -10000 0 0
SDCBP 0.026 0.004 -10000 0 -10000 0 0
PLG 0.01 0.028 -10000 0 -10000 0 0
ADAM12 -0.013 0.066 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.059 0.032 -10000 0 -0.18 2 2
Syndecan-4/Laminin alpha1 -0.06 0.19 -10000 0 -0.61 31 31
Syndecan-4/CXCL12/CXCR4 -0.054 0.2 -10000 0 -0.59 33 33
Syndecan-4/Laminin alpha3 -0.045 0.17 -10000 0 -0.58 31 31
MDK -0.021 0.076 -10000 0 -0.69 1 1
Syndecan-4/FZD7 -0.035 0.16 -10000 0 -0.56 32 32
Syndecan-4/Midkine -0.047 0.16 -10000 0 -0.57 31 31
FZD7 0.021 0.058 -10000 0 -0.53 4 4
Syndecan-4/FGFR1/FGF -0.01 0.15 -10000 0 -0.52 31 31
THBS1 0.016 0.038 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.052 0.16 -10000 0 -0.57 32 32
positive regulation of MAPKKK cascade -0.051 0.19 -10000 0 -0.56 33 33
Syndecan-4/TACI -0.13 0.22 -10000 0 -0.62 31 31
CXCR4 0.025 0.014 -10000 0 -10000 0 0
cell adhesion -0.008 0.079 0.19 5 -0.32 22 27
Syndecan-4/Dynamin -0.034 0.16 -10000 0 -0.55 32 32
Syndecan-4/TSP1 -0.036 0.16 -10000 0 -0.56 32 32
Syndecan-4/GIPC -0.034 0.16 -10000 0 -0.55 32 32
Syndecan-4/RANTES -0.056 0.2 -10000 0 -0.68 32 32
ITGB1 0.026 0.004 -10000 0 -10000 0 0
LAMA1 -0.026 0.18 -10000 0 -0.68 30 30
LAMA3 0 0.12 -10000 0 -0.69 12 12
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCA -0.002 0.2 0.74 14 -0.64 22 36
Syndecan-4/alpha-Actinin -0.033 0.16 -10000 0 -0.56 31 31
TFPI -0.014 0.16 -10000 0 -0.68 23 23
F2 0.013 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.038 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.072 0.19 -10000 0 -0.61 30 30
ACTN1 0.026 0.009 -10000 0 -10000 0 0
TNC -0.036 0.096 -10000 0 -0.69 4 4
Syndecan-4/CXCL12 -0.072 0.2 -10000 0 -0.61 33 33
FGF6 -0.015 0.005 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
CXCL12 -0.052 0.22 -10000 0 -0.69 44 44
TNFRSF13B -0.16 0.3 -10000 0 -0.69 100 100
FGF2 0.026 0.004 -10000 0 -10000 0 0
FGFR1 0.025 0.036 -10000 0 -0.69 1 1
Syndecan-4/PI-4-5-P2 -0.046 0.15 -10000 0 -0.56 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.075 0.077 -10000 0 -10000 0 0
cell migration -0.027 0.012 -10000 0 -10000 0 0
PRKCD 0.025 0.022 -10000 0 -10000 0 0
vasculogenesis -0.034 0.15 -10000 0 -0.54 32 32
SDC4 -0.045 0.16 -10000 0 -0.59 32 32
Syndecan-4/Tenascin C -0.054 0.17 -10000 0 -0.59 32 32
Syndecan-4/PI-4-5-P2/PKC alpha -0.047 0.025 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.033 0.16 -10000 0 -0.56 32 32
MMP9 -0.04 0.19 -10000 0 -0.69 32 32
Rac1/GTP -0.009 0.081 0.2 3 -0.32 22 25
cytoskeleton organization -0.033 0.15 -10000 0 -0.53 32 32
GIPC1 0.025 0.007 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.053 0.18 -10000 0 -0.58 32 32
Ceramide signaling pathway

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
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.016 0.12 -10000 0 -0.53 12 12
BAG4 0.025 0.036 -10000 0 -0.69 1 1
PKC zeta/ceramide -0.02 0.1 -10000 0 -0.31 26 26
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 -0.012 0.15 -10000 0 -0.64 21 21
BAX -0.013 0.076 -10000 0 -0.34 17 17
RIPK1 0.027 0.002 -10000 0 -10000 0 0
AKT1 0.027 0.14 0.78 13 -10000 0 13
BAD -0.032 0.092 0.18 1 -0.39 15 16
SMPD1 -0.011 0.092 0.29 6 -0.23 49 55
RB1 -0.032 0.093 0.19 1 -0.34 21 22
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.54 11 11
MAP2K4 -0.019 0.074 0.22 2 -0.37 8 10
NSMAF 0.026 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.023 0.084 -10000 0 -0.43 10 10
EGF -0.072 0.24 -10000 0 -0.68 55 55
mol:ceramide -0.036 0.1 -10000 0 -0.32 29 29
MADD 0.026 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.027 -10000 0 -0.52 1 1
ASAH1 0.024 0.036 -10000 0 -0.69 1 1
negative regulation of cell cycle -0.031 0.092 0.19 1 -0.33 21 22
cell proliferation -0.056 0.15 -10000 0 -0.33 78 78
BID -0.14 0.28 -10000 0 -0.6 97 97
MAP3K1 -0.028 0.082 -10000 0 -0.37 14 14
EIF2A -0.028 0.081 -10000 0 -0.47 9 9
TRADD 0.025 0.006 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.073 -10000 0 -0.37 8 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.041 0.088 -10000 0 -0.38 11 11
Cathepsin D/ceramide -0.018 0.096 -10000 0 -0.3 26 26
FADD -0.016 0.12 -10000 0 -0.53 12 12
KSR1 -0.026 0.089 0.18 7 -0.33 20 27
MAPK8 -0.016 0.087 -10000 0 -0.39 13 13
PRKRA -0.034 0.095 -10000 0 -0.52 10 10
PDGFA 0.025 0.006 -10000 0 -10000 0 0
TRAF2 0.024 0.008 -10000 0 -10000 0 0
IGF1 -0.12 0.29 -10000 0 -0.68 82 82
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.036 0.1 -10000 0 -0.32 29 29
CTSD 0.026 0.005 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.059 0.16 -10000 0 -0.36 78 78
PRKCD 0.026 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.027 -10000 0 -0.52 1 1
RelA/NF kappa B1 0.038 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.014 0.13 -10000 0 -0.56 12 12
TNFR1A/BAG4/TNF-alpha -0.007 0.16 -10000 0 -0.45 47 47
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.022 0.08 -10000 0 -0.4 10 10
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
CYCS -0.007 0.07 0.17 19 -0.25 15 34
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.037 0.029 -10000 0 -0.52 1 1
EIF2AK2 -0.03 0.088 -10000 0 -0.51 9 9
TNF-alpha/TNFR1A/FAN -0.005 0.16 -10000 0 -0.45 46 46
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.072 -10000 0 -0.55 1 1
MAP2K2 -0.015 0.069 -10000 0 -0.41 5 5
SMPD3 -0.02 0.11 -10000 0 -0.27 55 55
TNF -0.059 0.23 -10000 0 -0.69 46 46
PKC zeta/PAR4 0.037 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.013 0.11 0.26 54 -0.26 15 69
NF kappa B1/RelA/I kappa B alpha 0.074 0.022 -10000 0 -10000 0 0
AIFM1 -0.011 0.086 0.17 18 -0.28 21 39
BCL2 -0.019 0.17 -10000 0 -0.68 26 26
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.025 0.009 -10000 0 -10000 0 0
LAT2 -0.001 0.066 -10000 0 -0.28 1 1
AP1 -0.12 0.26 -10000 0 -0.56 85 85
mol:PIP3 0.027 0.18 0.63 17 -0.42 10 27
IKBKB 0.038 0.17 0.63 21 -0.27 6 27
AKT1 -0.005 0.12 0.32 18 -0.36 13 31
IKBKG 0.043 0.18 0.65 23 -0.26 7 30
MS4A2 -0.013 0.061 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
MAP3K1 0.025 0.12 0.52 10 -0.42 5 15
mol:Ca2+ 0.033 0.17 0.57 21 -0.32 9 30
LYN 0.027 0.01 -10000 0 -10000 0 0
CBLB 0 0.063 -10000 0 -0.28 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK -0.022 0.17 -10000 0 -0.42 62 62
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.018 0.034 -10000 0 -10000 0 0
PLD2 -0.01 0.13 0.32 26 -0.38 24 50
PTPN13 0.016 0.13 0.52 4 -0.65 9 13
PTPN11 0.023 0.015 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.034 0.17 0.65 18 -0.36 3 21
SYK 0.024 0.012 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0 0.11 -10000 0 -0.38 23 23
LAT -0.002 0.071 -10000 0 -0.34 4 4
PAK2 0.017 0.1 0.37 5 -0.45 6 11
NFATC2 -0.089 0.22 -10000 0 -0.62 57 57
HRAS 0.01 0.094 -10000 0 -0.48 6 6
GAB2 0.026 0.005 -10000 0 -10000 0 0
PLA2G1B 0.005 0.092 -10000 0 -0.7 5 5
Fc epsilon R1 0.008 0.13 -10000 0 -0.46 26 26
Antigen/IgE/Fc epsilon R1 0.011 0.12 -10000 0 -0.42 26 26
mol:GDP 0.003 0.1 -10000 0 -0.5 9 9
JUN -0.13 0.29 -10000 0 -0.69 87 87
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.69 103 103
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.004 0.069 -10000 0 -0.26 7 7
CHUK 0.037 0.17 0.61 21 -0.27 6 27
KLRG1 -0.007 0.076 -10000 0 -0.3 12 12
VAV1 -0.003 0.074 -10000 0 -0.38 5 5
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0 0.063 -10000 0 -10000 0 0
negative regulation of mast cell degranulation 0.007 0.08 -10000 0 -0.32 7 7
BTK -0.004 0.12 -10000 0 -0.51 15 15
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.16 -10000 0 -0.59 21 21
GAB2/PI3K/SHP2 -0.026 0.091 -10000 0 -0.37 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0 0.074 -10000 0 -0.28 23 23
RAF1 0.014 0.085 -10000 0 -0.9 3 3
Fc epsilon R1/FcgammaRIIB/SHIP 0.022 0.18 -10000 0 -0.53 33 33
FCER1G 0.017 0.035 -10000 0 -10000 0 0
FCER1A -0.034 0.18 -10000 0 -0.69 27 27
Antigen/IgE/Fc epsilon R1/Fyn 0.028 0.12 -10000 0 -0.39 26 26
MAPK3 0.02 0.082 -10000 0 -0.82 3 3
MAPK1 -0.013 0.1 -10000 0 -0.72 5 5
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.002 0.17 -10000 0 -0.63 22 22
DUSP1 -0.084 0.26 -10000 0 -0.69 62 62
NF-kappa-B/RelA 0.014 0.046 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.016 0.13 0.4 4 -0.67 9 13
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.093 -10000 0 -0.44 5 5
FER -0.002 0.067 -10000 0 -0.36 2 2
RELA 0.026 0.005 -10000 0 -10000 0 0
ITK -0.045 0.15 -10000 0 -0.47 46 46
SOS1 0.026 0.005 -10000 0 -10000 0 0
PLCG1 0.01 0.12 0.42 6 -0.52 8 14
cytokine secretion 0.005 0.029 -10000 0 -10000 0 0
SPHK1 0 0.066 0.27 1 -0.28 1 2
PTK2 0.015 0.14 0.4 4 -0.71 9 13
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.007 0.11 -10000 0 -0.39 22 22
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.033 0.18 0.74 14 -0.42 9 23
MAP2K2 0.016 0.087 -10000 0 -0.84 3 3
MAP2K1 0.011 0.079 -10000 0 -0.84 3 3
MAP2K7 0.025 0.007 -10000 0 -10000 0 0
KLRG1/SHP2 0 0.078 -10000 0 -0.32 9 9
MAP2K4 -0.012 0.2 -10000 0 -0.81 23 23
Fc epsilon R1/FcgammaRIIB 0.009 0.18 -10000 0 -0.56 34 34
mol:Choline -0.01 0.13 0.32 26 -0.38 24 50
SHC/Grb2/SOS1 0.037 0.076 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
DOK1 0.026 0.005 -10000 0 -10000 0 0
PXN 0.02 0.13 0.53 5 -0.63 9 14
HCLS1 0 0.064 -10000 0 -0.28 2 2
PRKCB 0.037 0.18 0.65 21 -0.34 10 31
FCGR2B -0.011 0.16 -10000 0 -0.69 20 20
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.007 0.081 -10000 0 -0.32 7 7
LCP2 0.023 0.022 -10000 0 -10000 0 0
PLA2G4A -0.026 0.12 -10000 0 -0.42 28 28
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.01 0.13 0.32 26 -0.38 24 50
IKK complex 0.045 0.18 0.66 23 -0.21 3 26
WIPF1 0.026 0.004 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.012 0.19 -10000 0 -0.9 16 16
NCK1/PAK1/Dok-R -0.028 0.086 -10000 0 -0.41 17 17
NCK1/Dok-R 0 0.23 -10000 0 -1 17 17
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
mol:beta2-estradiol 0 0.044 0.23 14 -10000 0 14
RELA 0.026 0.005 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
F2 -0.011 0.053 0.26 11 -10000 0 11
TNIP2 0.026 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.012 0.22 -10000 0 -0.98 16 16
FN1 -0.082 0.067 -10000 0 -10000 0 0
PLD2 -0.023 0.22 -10000 0 -1.1 16 16
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GRB14 0.001 0.13 -10000 0 -0.69 14 14
ELK1 -0.023 0.2 -10000 0 -0.96 16 16
GRB7 0.003 0.054 -10000 0 -10000 0 0
PAK1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.013 0.24 -10000 0 -1.1 16 16
CDKN1A -0.023 0.16 0.54 3 -0.62 16 19
ITGA5 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.001 0.23 -10000 0 -1 17 17
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.011 0.17 0.58 8 -0.65 16 24
PLG -0.028 0.22 -10000 0 -1.1 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.011 0.18 -10000 0 -0.85 16 16
GRB2 0.025 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 0.41 2 -0.8 15 17
BMX -0.03 0.23 -10000 0 -1.1 16 16
ANGPT1 -0.041 0.26 -10000 0 -1.3 14 14
tube development -0.038 0.17 0.54 2 -0.7 16 18
ANGPT4 -0.034 0.2 -10000 0 -0.69 33 33
response to hypoxia -0.004 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.025 0.25 -10000 0 -1.1 16 16
alpha5/beta1 Integrin 0.038 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.037 0.18 -10000 0 -0.8 16 16
mol:L-citrulline 0.011 0.17 0.58 8 -0.65 16 24
AGTR1 -0.26 0.35 -10000 0 -0.68 162 162
MAPK14 -0.023 0.23 -10000 0 -1.1 16 16
Tie2/SHP2 0.003 0.14 -10000 0 -1 5 5
TEK 0.011 0.14 -10000 0 -1.1 5 5
RPS6KB1 -0.007 0.19 0.53 1 -0.85 16 17
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.52 162 162
Tie2/Ang1/GRB2 -0.013 0.23 -10000 0 -1.1 16 16
MAPK3 -0.017 0.21 -10000 0 -0.98 16 16
MAPK1 -0.025 0.2 -10000 0 -0.99 16 16
Tie2/Ang1/GRB7 -0.012 0.24 -10000 0 -1.1 16 16
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.026 0.23 -10000 0 -1.1 16 16
PI3K -0.018 0.22 -10000 0 -1 16 16
FES -0.023 0.23 -10000 0 -1.1 16 16
Crk/Dok-R -0.001 0.22 -10000 0 -1 17 17
Tie2/Ang1/ABIN2 -0.012 0.24 -10000 0 -1.1 16 16
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.004 0.18 0.54 3 -0.8 16 19
STAT5A 0.025 0.006 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.01 0.19 0.53 1 -0.86 16 17
Tie2/Ang2 -0.054 0.21 -10000 0 -0.96 16 16
Tie2/Ang1 -0.023 0.24 -10000 0 -1.2 16 16
FOXO1 0 0.18 0.6 3 -0.8 16 19
ELF1 0.029 0.039 -10000 0 -0.68 1 1
ELF2 -0.02 0.22 -10000 0 -1.1 16 16
mol:Choline -0.02 0.21 -10000 0 -1 16 16
cell migration -0.014 0.054 -10000 0 -0.24 16 16
FYN -0.046 0.18 0.52 1 -0.8 16 17
DOK2 0.019 0.055 -10000 0 -0.69 2 2
negative regulation of cell cycle -0.02 0.15 0.53 3 -0.56 16 19
ETS1 0.025 0.047 -10000 0 -0.24 11 11
PXN 0.003 0.17 0.56 6 -0.7 16 22
ITGB1 0.026 0.004 -10000 0 -10000 0 0
NOS3 0.005 0.18 0.58 7 -0.74 16 23
RAC1 0.025 0.006 -10000 0 -10000 0 0
TNF -0.059 0.24 -10000 0 -0.61 58 58
MAPKKK cascade -0.02 0.21 -10000 0 -1 16 16
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.015 0.23 -10000 0 -1.1 16 16
NCK1 0.026 0.003 -10000 0 -10000 0 0
vasculogenesis 0.014 0.16 0.55 9 -0.58 16 25
mol:Phosphatidic acid -0.02 0.21 -10000 0 -1 16 16
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.011 0.17 0.58 8 -0.65 16 24
Rac1/GTP -0.005 0.17 -10000 0 -0.8 16 16
MMP2 -0.026 0.22 -10000 0 -1.1 16 16
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.036 0.029 -10000 0 -0.52 1 1
Necdin/E2F1 0 0.067 -10000 0 -0.58 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.052 0.1 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.19 0.26 -10000 0 -0.46 190 190
NT-4/5 (dimer)/p75(NTR) -0.011 0.14 -10000 0 -0.54 23 23
IKBKB 0.026 0.004 -10000 0 -10000 0 0
AKT1 0.003 0.1 0.36 1 -0.41 17 18
IKBKG 0.024 0.008 -10000 0 -10000 0 0
BDNF 0.006 0.11 -10000 0 -0.69 10 10
MGDIs/NGR/p75(NTR)/LINGO1 0.02 0.1 -10000 0 -0.46 15 15
FURIN 0.026 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.023 0.12 -10000 0 -0.43 25 25
LINGO1 0.02 0.03 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.024 -10000 0 -0.36 1 1
proBDNF (dimer) 0.006 0.11 -10000 0 -0.69 10 10
NTRK1 0.012 0.027 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.021 0.13 0.4 17 -0.4 17 34
IRAK1 0.024 0.008 -10000 0 -10000 0 0
SHC1 -0.01 0.099 -10000 0 -0.46 16 16
ARHGDIA 0.025 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.042 0.1 -10000 0 -0.44 16 16
MAGEH1 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.044 0.1 -10000 0 -0.44 17 17
Mammalian IAPs/DIABLO 0.043 0.097 -10000 0 -0.41 16 16
proNGF (dimer) 0.02 0.062 -10000 0 -0.69 3 3
MAGED1 0.025 0.007 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.007 0.1 -10000 0 -0.65 9 9
ZNF274 0.025 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.009 0.093 -10000 0 -0.41 16 16
NGF 0.02 0.062 -10000 0 -0.69 3 3
cell cycle arrest 0.056 0.14 0.39 18 -0.39 16 34
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.014 0.074 -10000 0 -0.32 17 17
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.019 0.12 -10000 0 -0.46 24 24
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.031 0.11 -10000 0 -0.47 16 16
PSENEN 0.025 0.007 -10000 0 -10000 0 0
mol:ceramide 0 0.099 -10000 0 -0.43 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.017 0.064 -10000 0 -0.27 17 17
p75(NTR)/beta APP 0.002 0.11 -10000 0 -0.52 15 15
BEX1 -0.29 0.35 -10000 0 -0.69 178 178
mol:GDP -0.02 0.098 -10000 0 -0.46 17 17
NGF (dimer) 0.038 0.11 -10000 0 -0.42 22 22
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.032 0.097 -10000 0 -0.42 15 15
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.027 0.092 -10000 0 -0.41 16 16
MYD88 0.026 0.003 -10000 0 -10000 0 0
CHUK 0.026 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.031 0.11 -10000 0 -0.48 16 16
RHOB 0.026 0.005 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.003 0.054 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.16 -10000 0 -0.69 21 21
TP53 -0.005 0.1 0.35 1 -0.37 22 23
PRDM4 -0.003 0.097 -10000 0 -0.44 16 16
BDNF (dimer) 0.004 0.14 -10000 0 -0.46 28 28
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
SORT1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.046 0.098 -10000 0 -0.41 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.043 0.1 -10000 0 -0.44 17 17
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
MAPK10 0.013 0.12 0.37 14 -0.38 17 31
DIABLO 0.026 0.005 -10000 0 -10000 0 0
SMPD2 0 0.1 -10000 0 -0.44 16 16
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.031 0.11 -10000 0 -0.48 16 16
PSEN1 0.026 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.03 0.16 -10000 0 -0.53 35 35
MAPK8 0.011 0.12 0.37 14 -0.4 17 31
MAPK9 0.007 0.11 0.36 8 -0.39 17 25
APAF1 0.026 0.005 -10000 0 -10000 0 0
NTF3 -0.018 0.16 -10000 0 -0.69 21 21
NTF4 0.007 0.1 -10000 0 -0.65 9 9
NDN 0.023 0.05 -10000 0 -0.69 2 2
RAC1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.048 0.093 -10000 0 -0.39 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.06 0.048 -10000 0 -0.79 1 1
RhoA-B-C/GTP 0.03 0.1 -10000 0 -0.47 16 16
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.045 0.11 -10000 0 -0.37 25 25
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.036 0.12 -10000 0 -0.39 26 26
PRKACB 0.026 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.021 0.092 -10000 0 -0.52 11 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.012 0.15 -10000 0 -0.64 21 21
BIRC2 0.026 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.072 0.15 0.21 155 -0.4 16 171
BAD 0.028 0.16 0.48 23 -0.39 17 40
RIPK2 0.026 0.004 -10000 0 -10000 0 0
NGFR -0.019 0.14 -10000 0 -0.69 15 15
CYCS 0.005 0.11 0.36 9 -0.41 16 25
ADAM17 0.024 0.036 -10000 0 -0.69 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.043 0.11 -10000 0 -0.43 18 18
BCL2L11 0.028 0.15 0.47 23 -0.39 17 40
BDNF (dimer)/p75(NTR) -0.013 0.14 -10000 0 -0.51 25 25
PI3K 0.043 0.1 -10000 0 -0.44 17 17
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.045 0.1 -10000 0 -0.44 16 16
NDNL2 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.002 0.12 -10000 0 -0.53 17 17
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.042 0.1 -10000 0 -0.44 16 16
TRAF6 0.024 0.036 -10000 0 -0.69 1 1
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
PLG -0.012 0.016 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.009 0.11 -10000 0 -0.42 24 24
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.025 0.007 -10000 0 -10000 0 0
CASP3 0.031 0.15 0.46 23 -0.36 17 40
E2F1 -0.019 0.069 -10000 0 -10000 0 0
CASP9 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.047 0.078 -10000 0 -0.44 4 4
NGF (dimer)/TRKA 0.027 0.053 -10000 0 -0.52 3 3
MMP7 -0.079 0.16 -10000 0 -0.67 21 21
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.051 0.1 -10000 0 -0.42 17 17
MMP3 -0.017 0.048 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.016 0.1 -10000 0 -0.55 6 6
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.005 0.1 -10000 0 -0.55 8 8
alphaM/beta2 Integrin/GPIbA -0.005 0.12 -10000 0 -0.5 16 16
alphaM/beta2 Integrin/proMMP-9 -0.027 0.17 -10000 0 -0.53 34 34
PLAUR -0.025 0.07 -10000 0 -10000 0 0
HMGB1 0.006 0.038 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.008 0.093 -10000 0 -0.59 5 5
AGER -0.051 0.2 -10000 0 -0.71 32 32
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.016 0.036 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.052 0.21 -10000 0 -0.48 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.041 0.19 -10000 0 -0.69 32 32
CYR61 -0.18 0.32 -10000 0 -0.69 117 117
TLN1 0.025 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.006 0.093 -10000 0 -0.38 9 9
RHOA 0.026 0.003 -10000 0 -10000 0 0
P-selectin oligomer 0.012 0.088 -10000 0 -0.69 6 6
MYH2 -0.035 0.11 -10000 0 -0.43 10 10
MST1R 0.017 0.075 -10000 0 -0.63 5 5
leukocyte activation during inflammatory response 0.009 0.086 -10000 0 -0.51 5 5
APOB 0.009 0.035 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.019 0.065 -10000 0 -0.61 4 4
JAM3 0.026 0.005 -10000 0 -10000 0 0
GP1BA 0.002 0.12 -10000 0 -0.64 12 12
alphaM/beta2 Integrin/CTGF -0.054 0.19 -10000 0 -0.48 59 59
alphaM/beta2 Integrin -0.029 0.099 -10000 0 -0.38 15 15
JAM3 homodimer 0.026 0.005 -10000 0 -10000 0 0
ICAM2 0.025 0.006 -10000 0 -10000 0 0
ICAM1 -0.021 0.068 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.028 0.098 -10000 0 -0.38 15 15
cell adhesion -0.005 0.12 -10000 0 -0.5 16 16
NFKB1 -0.14 0.28 0.38 1 -0.51 120 121
THY1 0.025 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.022 0.025 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.023 0.099 -10000 0 -0.5 8 8
IL6 -0.23 0.41 -10000 0 -0.97 87 87
ITGB2 -0.006 0.061 -10000 0 -0.46 2 2
elevation of cytosolic calcium ion concentration 0.008 0.11 -10000 0 -0.53 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.022 0.1 -10000 0 -0.5 9 9
JAM2 0.018 0.071 -10000 0 -0.69 4 4
alphaM/beta2 Integrin/ICAM1 0.026 0.12 -10000 0 -0.56 7 7
alphaM/beta2 Integrin/uPA/Plg 0.011 0.1 -10000 0 -0.54 5 5
RhoA/GTP -0.032 0.11 -10000 0 -0.37 21 21
positive regulation of phagocytosis -0.012 0.1 -10000 0 -0.59 5 5
Ron/MSP 0.031 0.064 -10000 0 -0.47 6 6
alphaM/beta2 Integrin/uPAR/uPA 0.01 0.12 -10000 0 -0.54 5 5
alphaM/beta2 Integrin/uPAR 0 0.1 -10000 0 -0.57 5 5
PLAU -0.041 0.074 -10000 0 -10000 0 0
PLAT 0.02 0.054 -10000 0 -0.69 2 2
actin filament polymerization -0.034 0.1 -10000 0 -0.41 10 10
MST1 0.025 0.036 -10000 0 -0.69 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.014 0.089 -10000 0 -0.52 5 5
TNF -0.18 0.36 0.38 1 -0.92 63 64
RAP1B 0.026 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.001 0.11 -10000 0 -0.53 6 6
fibrinolysis 0.009 0.1 -10000 0 -0.54 5 5
HCK 0.017 0.036 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.028 0.098 -10000 0 -0.38 15 15
VTN -0.047 0.21 -10000 0 -0.69 40 40
alphaM/beta2 Integrin/CYR61 -0.13 0.24 -10000 0 -0.48 119 119
LPA -0.005 0.025 -10000 0 -10000 0 0
LRP1 0.024 0.036 -10000 0 -0.69 1 1
cell migration -0.034 0.16 -10000 0 -0.51 34 34
FN1 -0.082 0.067 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.009 0.094 -10000 0 -0.58 5 5
MPO 0.01 0.087 -10000 0 -0.69 6 6
KNG1 -0.004 0.037 -10000 0 -10000 0 0
RAP1/GDP 0.034 0.009 -10000 0 -10000 0 0
ROCK1 -0.029 0.11 -10000 0 -0.43 10 10
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.012 0.016 -10000 0 -10000 0 0
CTGF -0.074 0.25 -10000 0 -0.67 58 58
alphaM/beta2 Integrin/Hck 0.004 0.098 -10000 0 -0.53 6 6
ITGAM -0.01 0.088 -10000 0 -0.75 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.014 0.11 -10000 0 -0.54 10 10
HP -0.021 0.1 -10000 0 -0.69 6 6
leukocyte adhesion -0.039 0.18 -10000 0 -0.46 36 36
SELP 0.012 0.088 -10000 0 -0.69 6 6
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.032 0.062 -10000 0 -0.52 5 5
alphaV beta3 Integrin 0.036 0.088 -10000 0 -0.49 10 10
PTK2 0.01 0.15 0.43 10 -0.52 10 20
IGF1R 0.026 0.003 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.007 0.05 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
CDKN1B -0.035 0.18 -10000 0 -0.55 41 41
VEGFA 0.023 0.05 -10000 0 -0.69 2 2
ILK -0.035 0.18 -10000 0 -0.54 42 42
ROCK1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.036 0.16 -10000 0 -0.51 41 41
PTK2B 0.012 0.096 0.36 2 -0.44 13 15
alphaV/beta3 Integrin/JAM-A -0.001 0.15 -10000 0 -0.41 46 46
CBL 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.086 -10000 0 -0.48 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.078 0.24 -10000 0 -0.44 113 113
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.004 0.099 -10000 0 -0.38 6 6
alphaV/beta3 Integrin/Syndecan-1 0.037 0.088 -10000 0 -0.49 10 10
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.084 0.24 -10000 0 -0.44 115 115
PI4 Kinase 0.028 0.018 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
alphaV/beta3 Integrin/Osteopontin 0.016 0.14 -10000 0 -0.44 31 31
RPS6KB1 -0.14 0.19 0.42 2 -0.42 115 117
TLN1 0.025 0.007 -10000 0 -10000 0 0
MAPK3 -0.053 0.13 -10000 0 -0.68 10 10
GPR124 0.026 0.004 -10000 0 -10000 0 0
MAPK1 -0.063 0.15 -10000 0 -0.58 19 19
PXN 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.023 0.13 -10000 0 -0.52 19 19
cell adhesion 0.028 0.084 -10000 0 -0.47 9 9
ANGPTL3 0.007 0.022 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.057 -10000 0 -0.45 5 5
IGF-1R heterotetramer 0.026 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
TGFBR2 0.025 0.036 -10000 0 -0.69 1 1
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
IGF1 -0.12 0.29 -10000 0 -0.68 82 82
RAC1 0.025 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.036 0.087 -10000 0 -0.49 10 10
apoptosis 0.024 0.036 -10000 0 -0.69 1 1
CD47 0.026 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.037 0.088 -10000 0 -0.49 10 10
VCL 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.033 0.1 -10000 0 -0.51 13 13
CSF1 0.017 0.079 -10000 0 -0.69 5 5
PIK3C2A -0.035 0.18 -10000 0 -0.54 42 42
PI4 Kinase/Pyk2 -0.019 0.13 -10000 0 -0.62 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.1 -10000 0 -0.47 13 13
FAK1/Vinculin 0.022 0.13 0.43 10 -0.41 10 20
alphaV beta3/Integrin/ppsTEM5 0.037 0.088 -10000 0 -0.49 10 10
RHOA 0.026 0.003 -10000 0 -10000 0 0
VTN -0.047 0.21 -10000 0 -0.69 40 40
BCAR1 0.025 0.006 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.039 0.089 -10000 0 -0.49 10 10
alphaV/beta3 Integrin/TGFBR2 0.036 0.089 -10000 0 -0.47 11 11
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.061 -10000 0 -0.42 6 6
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.081 -10000 0 -0.45 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.082 0.067 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.032 0.093 -10000 0 -0.45 13 13
SDC1 0.025 0.014 -10000 0 -10000 0 0
VAV3 0.013 0.07 0.36 1 -0.39 10 11
PTPN11 0.026 0.005 -10000 0 -10000 0 0
IRS1 -0.048 0.22 -10000 0 -0.69 42 42
FAK1/Paxillin 0.017 0.12 0.34 6 -0.41 10 16
cell migration 0.013 0.11 0.34 5 -0.41 6 11
ITGAV 0.024 0.036 -10000 0 -0.69 1 1
PI3K 0.01 0.15 -10000 0 -0.38 46 46
SPP1 -0.034 0.16 -10000 0 -0.69 20 20
KDR 0.021 0.061 -10000 0 -0.69 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.036 -10000 0 -0.69 1 1
COL4A3 0.005 0.12 -10000 0 -0.69 12 12
angiogenesis -0.057 0.16 -10000 0 -0.53 29 29
Rac1/GTP 0.023 0.062 -10000 0 -0.36 10 10
EDIL3 0.01 0.078 -10000 0 -0.69 4 4
cell proliferation 0.036 0.089 -10000 0 -0.47 11 11
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0.011 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.016 0.005 -10000 0 -10000 0 0
mol:DAG -0.02 0.13 -10000 0 -0.41 39 39
VEGFR1 homodimer/NRP1/VEGFR 121 0.029 0.032 -10000 0 -0.41 2 2
CaM/Ca2+ -0.005 0.12 -10000 0 -0.38 39 39
HIF1A 0.032 0.006 -10000 0 -10000 0 0
GAB1 0.026 0.004 -10000 0 -10000 0 0
AKT1 -0.018 0.12 -10000 0 -0.39 38 38
PLCG1 -0.021 0.13 -10000 0 -0.41 39 39
NOS3 -0.013 0.12 -10000 0 -0.4 2 2
CBL 0.026 0.005 -10000 0 -10000 0 0
mol:NO -0.007 0.12 0.46 3 -0.38 2 5
FLT1 0.022 0.007 -10000 0 -10000 0 0
PGF -0.044 0.21 -10000 0 -0.68 40 40
VEGFR1 homodimer/NRP2/VEGFR121 0.047 0.037 -10000 0 -0.41 2 2
CALM1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
eNOS/Hsp90 0.005 0.12 -10000 0 -0.37 2 2
endothelial cell proliferation -0.041 0.15 0.36 2 -0.45 39 41
mol:Ca2+ -0.02 0.12 -10000 0 -0.4 39 39
MAPK3 -0.044 0.14 0.35 2 -0.39 56 58
MAPK1 -0.047 0.14 0.35 1 -0.39 56 57
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.044 0.21 -10000 0 -0.68 40 40
PRKACA 0.025 0.007 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.011 0.1 -10000 0 -0.69 8 8
VEGFA homodimer 0.023 0.05 -10000 0 -0.69 2 2
VEGFR1 homodimer/VEGFA homodimer 0.032 0.035 -10000 0 -0.45 2 2
platelet activating factor biosynthetic process -0.048 0.14 -10000 0 -0.44 16 16
PI3K 0.017 0.13 -10000 0 -0.39 39 39
PRKCA -0.046 0.15 -10000 0 -0.41 56 56
PRKCB -0.032 0.12 -10000 0 -0.38 41 41
VEGFR1 homodimer/PLGF homodimer -0.012 0.14 -10000 0 -0.45 39 39
VEGFA 0.023 0.05 -10000 0 -0.69 2 2
VEGFB 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.02 0.13 -10000 0 -0.41 39 39
RASA1 0.021 0.014 -10000 0 -10000 0 0
NRP2 0.014 0.041 -10000 0 -10000 0 0
VEGFR1 homodimer 0.022 0.007 -10000 0 -10000 0 0
VEGFB homodimer 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0 0.13 0.45 3 -0.5 3 6
PTPN11 0.026 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.015 0.13 -10000 0 -0.38 39 39
mol:L-citrulline -0.007 0.12 0.46 3 -0.38 2 5
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.037 -10000 0 -0.39 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.046 0.035 -10000 0 -0.41 2 2
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.027 0.13 -10000 0 -0.37 39 39
PDPK1 -0.014 0.12 0.34 3 -0.37 39 42
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.045 0.036 -10000 0 -0.41 2 2
mol:NADP -0.007 0.12 0.46 3 -0.38 2 5
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.037 -10000 0 -0.38 2 2
VEGFR1 homodimer/NRP2 0.035 0.014 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.025 0.007 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.015 0.087 -10000 0 -0.69 6 6
CDKN1A -0.008 0.074 -10000 0 -0.62 1 1
PRL-3/alpha Tubulin 0.029 0.03 -10000 0 -10000 0 0
mol:Ca2+ -0.029 0.075 0.23 1 -0.53 8 9
AGT 0.003 0.1 -10000 0 -0.69 8 8
CCNA2 -0.069 0.15 -10000 0 -0.42 4 4
TUBA1B 0.026 0.005 -10000 0 -10000 0 0
EGR1 -0.088 0.21 -10000 0 -0.51 81 81
CDK2/Cyclin E1 0.017 0.078 -10000 0 -0.55 1 1
MAPK3 0.01 0.024 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.038 0.008 -10000 0 -10000 0 0
MAPK1 0.008 0.021 -10000 0 -10000 0 0
PTP4A1 -0.071 0.16 -10000 0 -0.4 81 81
PTP4A3 0.016 0.038 -10000 0 -10000 0 0
PTP4A2 0.026 0.005 -10000 0 -10000 0 0
ITGB1 0.01 0.024 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1 -0.013 0.081 -10000 0 -0.34 7 7
Rab GGTase beta/Rab GGTase alpha 0.038 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.053 0.16 -10000 0 -0.38 78 78
RABGGTA 0.026 0.005 -10000 0 -10000 0 0
BCAR1 -0.016 0.007 -10000 0 -10000 0 0
RHOC -0.012 0.082 -10000 0 -0.37 6 6
RHOA -0.013 0.085 -10000 0 -0.39 7 7
cell motility -0.007 0.096 0.28 4 -0.35 8 12
PRL-1/alpha Tubulin -0.052 0.16 -10000 0 -0.38 80 80
PRL-3/alpha1 Integrin 0.021 0.075 -10000 0 -0.54 6 6
ROCK1 -0.008 0.093 0.28 2 -0.37 7 9
RABGGTB 0.026 0.005 -10000 0 -10000 0 0
CDK2 0.026 0.005 -10000 0 -10000 0 0
mitosis -0.071 0.16 -10000 0 -0.4 81 81
ATF5 0.019 0.029 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.026 0.005 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.001 0.12 0.32 1 -0.38 20 21
PTP1B/AKT1 0.006 0.07 0.31 2 -0.29 5 7
FYN 0.026 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.003 0.087 0.36 10 -0.29 6 16
EGFR 0.011 0.081 -10000 0 -0.7 5 5
EGF/EGFR -0.035 0.16 -10000 0 -0.4 58 58
CSF1 0.017 0.079 -10000 0 -0.69 5 5
AKT1 0.026 0.005 -10000 0 -10000 0 0
INSR 0.025 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.003 0.12 0.34 6 -0.39 16 22
Insulin Receptor/Insulin 0.016 0.067 -10000 0 -0.31 3 3
HCK 0.017 0.036 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 0.01 0.094 0.35 15 -0.34 3 18
EGF -0.072 0.24 -10000 0 -0.69 55 55
YES1 0.026 0.004 -10000 0 -10000 0 0
CAV1 0 0.12 0.45 11 -0.38 5 16
TXN 0.024 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.025 0.14 0.32 1 -0.38 43 44
cell migration -0.003 0.087 0.29 6 -0.36 10 16
STAT3 0.025 0.006 -10000 0 -10000 0 0
PRLR -0.011 0.15 -10000 0 -0.69 18 18
ITGA2B -0.052 0.22 -10000 0 -0.68 44 44
CSF1R 0.022 0.039 -10000 0 -0.69 1 1
Prolactin Receptor/Prolactin 0.004 0.12 -10000 0 -0.52 18 18
FGR 0.024 0.016 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.007 0.072 0.27 3 -0.33 3 6
Crk/p130 Cas 0.012 0.07 -10000 0 -0.32 3 3
DOK1 0.016 0.093 0.42 11 -0.32 3 14
JAK2 -0.005 0.13 0.35 6 -0.39 25 31
Jak2/Leptin Receptor/Leptin -0.024 0.16 -10000 0 -0.52 28 28
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.003 0.088 0.36 10 -0.3 6 16
LYN 0.026 0.004 -10000 0 -10000 0 0
CDH2 -0.075 0.14 -10000 0 -0.65 15 15
SRC 0.025 0.058 0.29 3 -0.43 3 6
ITGB3 0.006 0.11 -10000 0 -0.66 11 11
CAT1/PTP1B -0.06 0.16 0.44 12 -0.35 32 44
CAPN1 0.026 0.005 -10000 0 -10000 0 0
CSK 0.026 0.003 -10000 0 -10000 0 0
PI3K 0.023 0.071 -10000 0 -0.4 2 2
mol:H2O2 -0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.025 0.16 -10000 0 -0.55 28 28
negative regulation of transcription -0.004 0.13 0.35 6 -0.38 25 31
FCGR2A 0.016 0.048 -10000 0 -0.69 1 1
FER 0.022 0.051 -10000 0 -0.7 2 2
alphaIIb/beta3 Integrin -0.037 0.2 -10000 0 -0.55 51 51
BLK -0.2 0.32 -10000 0 -0.68 122 122
Insulin Receptor/Insulin/Shc 0.041 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
LEPR 0.02 0.064 -10000 0 -0.59 4 4
BCAR1 0.025 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.025 0.006 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.093 0.18 0.42 3 -0.46 34 37
PRL -0.005 0.02 -10000 0 -10000 0 0
SOCS3 -0.085 0.38 -10000 0 -1.3 35 35
SPRY2 0.025 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.009 0.15 -10000 0 -0.46 42 42
CSF1/CSF1R 0.01 0.088 0.28 1 -0.4 8 9
Ras protein signal transduction 0.02 0.089 0.43 16 -10000 0 16
IRS1 -0.048 0.22 -10000 0 -0.69 42 42
INS 0.009 0.014 -10000 0 -10000 0 0
LEP 0.008 0.033 -10000 0 -10000 0 0
STAT5B 0.006 0.095 0.33 10 -0.29 10 20
STAT5A 0.006 0.095 0.33 10 -0.28 11 21
GRB2 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.006 0.069 0.28 1 -0.34 3 4
CSN2 0.002 0.063 0.81 1 -10000 0 1
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
LAT 0.02 0.08 0.3 3 -0.46 8 11
YBX1 0.032 0.007 -10000 0 -10000 0 0
LCK 0.011 0.083 -10000 0 -0.69 5 5
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.038 0.074 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.015 0.12 -10000 0 -0.48 14 14
BAG4 0.025 0.036 -10000 0 -0.69 1 1
BAD 0.007 0.07 0.37 8 -10000 0 8
NFKBIA 0.026 0.005 -10000 0 -10000 0 0
BIRC3 -0.012 0.15 -10000 0 -0.64 21 21
BAX 0.012 0.071 0.27 16 -10000 0 16
EnzymeConsortium:3.1.4.12 0.002 0.042 0.16 10 -0.11 14 24
IKBKB -0.014 0.12 0.33 1 -0.47 13 14
MAP2K2 0.017 0.096 0.38 16 -0.31 1 17
MAP2K1 0.012 0.086 0.39 11 -0.31 1 12
SMPD1 0.006 0.049 0.27 6 -0.15 3 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.48 14 14
MAP2K4 0.017 0.1 0.38 20 -10000 0 20
protein ubiquitination -0.01 0.13 0.44 4 -0.47 13 17
EnzymeConsortium:2.7.1.37 0.018 0.11 0.4 20 -0.32 1 21
response to UV 0 0.002 0.007 21 -0.002 2 23
RAF1 0.012 0.089 0.31 19 -0.32 1 20
CRADD 0.026 0.005 -10000 0 -10000 0 0
mol:ceramide 0.005 0.062 0.26 9 -0.16 13 22
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.008 -10000 0 -10000 0 0
MADD 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.08 0.34 14 -10000 0 14
TRADD 0.025 0.006 -10000 0 -10000 0 0
RELA/p50 0.026 0.005 -10000 0 -10000 0 0
MAPK3 0.017 0.09 0.37 14 -0.3 1 15
MAPK1 -0.004 0.095 0.36 13 -0.27 3 16
p50/RELA/I-kappa-B-alpha 0.038 0.008 -10000 0 -10000 0 0
FADD -0.015 0.12 -10000 0 -0.48 14 14
KSR1 0.011 0.083 0.28 20 -0.26 2 22
MAPK8 0.015 0.11 0.39 19 -0.37 3 22
TRAF2 0.024 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 12 -10000 0 12
CHUK -0.014 0.12 0.33 1 -0.46 13 14
TNF R/SODD 0.037 0.029 -10000 0 -0.52 1 1
TNF -0.058 0.23 -10000 0 -0.69 46 46
CYCS 0.019 0.083 0.27 20 -10000 0 20
IKBKG -0.013 0.12 0.37 1 -0.46 13 14
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.016 0.13 -10000 0 -0.51 14 14
RELA 0.026 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.017 0.082 0.28 17 -0.18 1 18
TNF/TNF R/SODD -0.006 0.16 -10000 0 -0.45 47 47
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 12 -10000 0 12
CASP8 0.013 0.11 -10000 0 -0.73 8 8
NSMAF -0.016 0.12 -10000 0 -0.48 14 14
response to hydrogen peroxide 0 0.002 0.007 21 -0.002 2 23
BCL2 -0.019 0.17 -10000 0 -0.68 26 26
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.036 0.11 0.87 5 -10000 0 5
VDR 0.025 0.009 -10000 0 -10000 0 0
FAM120B 0.026 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.005 0.11 -10000 0 -0.3 34 34
RXRs/LXRs/DNA/Oxysterols -0.01 0.15 -10000 0 -0.41 46 46
MED1 0.025 0.006 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.023 0.06 -10000 0 -0.29 14 14
RXRs/NUR77 -0.094 0.24 -10000 0 -0.47 110 110
RXRs/PPAR -0.017 0.081 -10000 0 -0.4 8 8
NCOR2 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.048 0.071 -10000 0 -0.4 9 9
RARA 0.025 0.006 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.009 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.03 0.069 -10000 0 -0.37 10 10
RARG 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 0.047 0.11 0.55 19 -10000 0 19
RARs/THRs/DNA/SMRT 0.023 0.06 -10000 0 -0.29 14 14
THRA 0.025 0.006 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.04 0.098 -10000 0 -0.43 4 4
NR1H4 -0.004 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.06 0.12 -10000 0 -0.5 3 3
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.022 0.026 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.051 0.08 -10000 0 -0.46 2 2
NR4A1 -0.19 0.33 -10000 0 -0.69 120 120
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.003 0.053 -10000 0 -0.32 2 2
RXRG -0.1 0.076 -10000 0 -0.59 4 4
RXR alpha/CCPG 0.031 0.024 -10000 0 -10000 0 0
RXRA 0.02 0.025 -10000 0 -10000 0 0
RXRB 0.022 0.026 -10000 0 -10000 0 0
THRB 0.018 0.079 -10000 0 -0.69 5 5
PPARG 0.016 0.08 -10000 0 -0.69 5 5
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.099 0.38 -10000 0 -1.1 47 47
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.01 0.15 -10000 0 -0.41 46 46
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.009 0.11 -10000 0 -0.69 10 10
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 124 124
SREBF1 -0.011 0.14 -10000 0 -0.54 5 5
RXRs/RXRs/DNA/9cRA 0.04 0.098 -10000 0 -0.43 4 4
ABCA1 -0.01 0.14 -10000 0 -0.6 3 3
RARs/THRs 0.058 0.088 -10000 0 -0.39 14 14
RXRs/FXR 0.051 0.086 -10000 0 -0.49 2 2
BCL2 -0.019 0.17 -10000 0 -0.68 26 26
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.017 -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 0.039 0.12 0.46 9 -10000 0 9
IL27/IL27R/JAK1 -0.006 0.16 -10000 0 -0.53 6 6
TBX21 -0.063 0.18 0.38 4 -0.58 23 27
IL12B 0.005 0.074 -10000 0 -0.69 4 4
IL12A -0.044 0.15 -10000 0 -0.52 38 38
IL6ST -0.059 0.23 -10000 0 -0.7 45 45
IL27RA/JAK1 0.018 0.052 0.55 1 -10000 0 1
IL27 0.01 0.026 -10000 0 -10000 0 0
TYK2 0.018 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.054 0.14 -10000 0 -0.49 4 4
T-helper 2 cell differentiation 0.039 0.12 0.46 9 -10000 0 9
T cell proliferation during immune response 0.039 0.12 0.46 9 -10000 0 9
MAPKKK cascade -0.039 0.12 -10000 0 -0.46 9 9
STAT3 0.025 0.006 -10000 0 -10000 0 0
STAT2 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
IL12RB1 0.007 0.067 -10000 0 -0.59 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.054 0.19 0.5 10 -0.57 18 28
IL27/IL27R/JAK2/TYK2 -0.039 0.13 -10000 0 -0.46 9 9
positive regulation of T cell mediated cytotoxicity -0.039 0.12 -10000 0 -0.46 9 9
STAT1 (dimer) -0.018 0.21 0.52 9 -0.65 9 18
JAK2 0.02 0.019 -10000 0 -10000 0 0
JAK1 0.026 0.008 -10000 0 -10000 0 0
STAT2 (dimer) -0.029 0.13 -10000 0 -0.45 8 8
T cell proliferation -0.12 0.2 -10000 0 -0.52 45 45
IL12/IL12R/TYK2/JAK2 -0.068 0.23 -10000 0 -0.75 29 29
IL17A -0.054 0.14 -10000 0 -0.5 4 4
mast cell activation 0.039 0.12 0.46 9 -10000 0 9
IFNG -0.016 0.051 0.087 4 -0.13 56 60
T cell differentiation -0.004 0.008 0.013 1 -0.022 51 52
STAT3 (dimer) -0.029 0.13 -10000 0 -0.45 8 8
STAT5A (dimer) -0.029 0.13 -10000 0 -0.45 8 8
STAT4 (dimer) -0.034 0.14 0.33 1 -0.44 14 15
STAT4 0.002 0.099 -10000 0 -0.58 9 9
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.02 0.14 -10000 0 -0.49 6 6
GATA3 -0.065 0.31 -10000 0 -1.4 22 22
IL18 -0.012 0.078 -10000 0 -0.5 9 9
positive regulation of mast cell cytokine production -0.028 0.13 -10000 0 -0.44 8 8
IL27/EBI3 -0.029 0.059 -10000 0 -0.27 1 1
IL27RA 0 0.025 -10000 0 -10000 0 0
IL6 -0.12 0.28 -10000 0 -0.69 81 81
STAT5A 0.025 0.006 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.011 0.023 -10000 0 -10000 0 0
IL1B -0.035 0.14 -10000 0 -0.52 32 32
EBI3 -0.051 0.074 -10000 0 -0.39 1 1
TNF -0.055 0.17 -10000 0 -0.52 46 46
Insulin Pathway

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
CBL/APS/CAP 0.003 0.13 -10000 0 -0.37 42 42
TC10/GTP 0.041 0.035 -10000 0 -0.36 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.008 0.15 -10000 0 -0.43 41 41
HRAS 0.025 0.012 -10000 0 -10000 0 0
APS homodimer 0.025 0.01 -10000 0 -10000 0 0
GRB14 0.001 0.13 -10000 0 -0.69 14 14
FOXO3 0.002 0.11 -10000 0 -0.65 11 11
AKT1 -0.024 0.13 0.35 5 -0.34 51 56
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.051 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.006 -10000 0 -10000 0 0
SORBS1 0.023 0.05 -10000 0 -0.69 2 2
CRK 0.025 0.007 -10000 0 -10000 0 0
PTPN1 0.016 0.024 -10000 0 -10000 0 0
CAV1 -0.031 0.14 -10000 0 -0.4 47 47
CBL/APS/CAP/Crk-II/C3G 0.065 0.044 -10000 0 -0.39 2 2
Insulin Receptor/Insulin/IRS1/NCK2 0.009 0.15 -10000 0 -0.43 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.002 0.13 -10000 0 -0.38 42 42
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.004 0.098 -10000 0 -0.41 6 6
RPS6KB1 -0.029 0.12 0.29 3 -0.32 48 51
PARD6A 0.025 0.006 -10000 0 -10000 0 0
CBL 0.026 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.027 -10000 0 -0.5 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.008 0.12 -10000 0 -0.33 50 50
HRAS/GTP -0.02 0.1 -10000 0 -0.34 35 35
Insulin Receptor 0.026 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.019 0.14 -10000 0 -0.4 35 35
PRKCI 0.014 0.068 -10000 0 -0.51 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.021 0.13 -10000 0 -0.36 51 51
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.044 0.043 -10000 0 -0.4 1 1
PI3K 0.011 0.14 -10000 0 -0.38 42 42
NCK2 0.026 0.005 -10000 0 -10000 0 0
RHOQ 0.026 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
AKT2 -0.026 0.13 0.39 5 -0.34 51 56
PRKCZ 0.015 0.065 -10000 0 -0.51 2 2
SH2B2 0.025 0.01 -10000 0 -10000 0 0
SHC/SHIP -0.011 0.12 0.3 1 -0.38 36 37
F2RL2 -0.018 0.075 -10000 0 -0.69 1 1
TRIP10 0.025 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.04 0.017 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.033 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.063 0.029 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.059 0.04 -10000 0 -0.42 2 2
TC10/GDP 0.019 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.054 0.024 -10000 0 -10000 0 0
INPP5D -0.027 0.13 0.31 1 -0.4 41 42
SOS1 0.026 0.005 -10000 0 -10000 0 0
SGK1 -0.012 0.14 -10000 0 -0.81 12 12
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
IRS1 -0.048 0.22 -10000 0 -0.69 42 42
p62DOK/RasGAP 0.044 0.043 -10000 0 -0.41 1 1
INS 0.019 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.027 0.13 0.31 1 -0.4 41 42
GRB2 0.025 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.029 0.12 0.36 3 -0.47 2 5
PTPRA 0.028 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
TC10/GTP/CIP4 0.033 0.01 -10000 0 -10000 0 0
PDPK1 0.023 0.036 -10000 0 -0.69 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.004 0.095 -10000 0 -0.3 35 35
Insulin Receptor/Insulin/IRS1 -0.006 0.14 -10000 0 -0.42 42 42
Insulin Receptor/Insulin/IRS3 0.032 0.012 -10000 0 -10000 0 0
Par3/Par6 0.06 0.028 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.003 0.039 -10000 0 -0.45 3 3
ADCY5 -0.059 0.16 -10000 0 -0.45 57 57
ADCY6 0.003 0.039 -10000 0 -0.45 3 3
ADCY7 0.003 0.039 -10000 0 -0.45 3 3
ADCY1 0 0.052 -10000 0 -0.46 5 5
ADCY2 -0.039 0.14 -10000 0 -0.46 37 37
ADCY3 0.003 0.039 -10000 0 -0.45 3 3
ADCY8 -0.047 0.049 -10000 0 -0.5 3 3
PRKCE 0.005 0.046 -10000 0 -0.52 3 3
ADCY9 0.003 0.039 -10000 0 -0.45 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.034 0.097 0.38 6 -0.35 13 19
Caspase cascade in apoptosis

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
TOP1 0.021 0.088 0.32 5 -0.38 11 16
ACTA1 0.009 0.1 0.33 6 -0.43 12 18
NUMA1 0.018 0.093 0.28 6 -0.43 11 17
SPTAN1 0.007 0.099 0.36 5 -0.46 10 15
LIMK1 0.014 0.11 0.43 8 -0.45 10 18
BIRC3 -0.012 0.15 -10000 0 -0.64 21 21
BIRC2 0.026 0.005 -10000 0 -10000 0 0
BAX 0.025 0.007 -10000 0 -10000 0 0
CASP10 -0.01 0.089 -10000 0 -0.53 10 10
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
PTK2 0.015 0.1 0.32 4 -0.43 14 18
DIABLO 0.026 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.007 0.098 0.36 5 -0.45 10 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
GSN 0.007 0.1 0.36 5 -0.43 12 17
MADD 0.026 0.005 -10000 0 -10000 0 0
TFAP2A -0.042 0.22 -10000 0 -0.61 51 51
BID -0.012 0.061 -10000 0 -0.22 25 25
MAP3K1 0.017 0.042 0.27 3 -10000 0 3
TRADD 0.025 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.01 0.11 0.46 7 -0.51 8 15
CASP9 0.026 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.059 0.34 3 -0.21 16 19
neuron apoptosis 0.008 0.11 -10000 0 -0.55 13 13
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.018 0.1 0.34 4 -0.48 10 14
APAF1 0.026 0.005 -10000 0 -10000 0 0
CASP6 0.021 0.087 0.34 4 -0.57 4 8
TRAF2 0.024 0.008 -10000 0 -10000 0 0
ICAD/CAD 0.013 0.11 0.41 12 -0.49 8 20
CASP7 0.007 0.097 0.32 18 -0.41 7 25
KRT18 0.021 0.043 -10000 0 -0.44 2 2
apoptosis 0.018 0.097 0.48 4 -0.42 9 13
DFFA 0.009 0.1 0.33 8 -0.48 9 17
DFFB 0.009 0.1 0.33 8 -0.46 10 18
PARP1 0.017 0.06 0.21 16 -0.35 3 19
actin filament polymerization -0.019 0.12 0.47 8 -0.54 10 18
TNF -0.059 0.23 -10000 0 -0.69 46 46
CYCS 0 0.05 0.24 4 -0.2 12 16
SATB1 0.022 0.086 0.45 3 -0.53 4 7
SLK 0.007 0.1 0.46 3 -0.44 11 14
p15 BID/BAX -0.01 0.07 0.19 1 -0.29 10 11
CASP2 -0.015 0.1 -10000 0 -0.39 14 14
JNK cascade -0.018 0.042 -10000 0 -0.27 3 3
CASP3 0.006 0.1 0.28 11 -0.45 12 23
LMNB2 0.007 0.12 0.36 9 -0.42 11 20
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CASP4 0.026 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.043 0.097 -10000 0 -0.41 16 16
negative regulation of DNA binding -0.041 0.22 -10000 0 -0.6 51 51
stress fiber formation 0.007 0.099 0.4 4 -0.43 11 15
GZMB -0.007 0.1 -10000 0 -0.6 10 10
CASP1 0.014 0.029 -10000 0 -0.4 2 2
LMNB1 0.02 0.092 0.34 11 -0.34 4 15
APP 0.008 0.11 -10000 0 -0.56 13 13
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM 0.018 0.093 0.4 4 -0.41 10 14
LMNA 0.016 0.1 0.35 11 -0.38 6 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.013 0.11 -10000 0 -0.42 12 12
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.014 0.11 0.44 7 -0.51 8 15
APAF-1/Caspase 9 0.013 0.059 -10000 0 -0.53 3 3
nuclear fragmentation during apoptosis 0.018 0.092 0.28 6 -0.42 11 17
CFL2 0.019 0.12 0.54 10 -0.48 8 18
GAS2 0.004 0.1 0.33 5 -0.42 14 19
positive regulation of apoptosis 0.017 0.1 0.37 9 -0.35 9 18
PRF1 0.014 0.087 -10000 0 -0.69 6 6
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.029 0.075 -9999 0 -0.39 12 12
RGS9BP -0.019 0.17 -9999 0 -0.68 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.045 0.21 -9999 0 -0.67 40 40
mol:Na + 0.017 0.032 -9999 0 -10000 0 0
mol:ADP -0.047 0.16 -9999 0 -0.52 39 39
GNAT2 0.016 0.02 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.025 0.18 -9999 0 -0.46 58 58
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.01 -9999 0 -10000 0 0
GRK7 0.006 0.021 -9999 0 -10000 0 0
CNGB3 -0.007 0.018 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.027 -9999 0 -10000 0 0
Cone PDE6 -0.006 0.17 -9999 0 -0.41 57 57
Cone Metarhodopsin II -0.014 0.13 -9999 0 -0.41 39 39
Na + (4 Units) 0.03 0.033 -9999 0 -10000 0 0
GNAT2/GDP -0.01 0.16 -9999 0 -0.4 55 55
GNB5 0.026 0.003 -9999 0 -10000 0 0
mol:GMP (4 units) -0.001 0.024 -9999 0 -10000 0 0
Cone Transducin 0.032 0.079 -9999 0 -0.41 12 12
SLC24A2 -0.007 0.03 -9999 0 -10000 0 0
GNB3/GNGT2 0.02 0.095 -9999 0 -0.52 12 12
GNB3 0.005 0.12 -9999 0 -0.69 12 12
GNAT2/GTP 0.017 0.008 -9999 0 -10000 0 0
CNGA3 0.007 0.049 -9999 0 -10000 0 0
ARR3 -0.001 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.017 0.033 -9999 0 -10000 0 0
mol:Pi -0.025 0.18 -9999 0 -0.46 58 58
Cone CNG Channel 0.043 0.032 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.007 0.03 -9999 0 -10000 0 0
RGS9 -0.039 0.2 -9999 0 -0.69 36 36
PDE6C -0.004 0.019 -9999 0 -10000 0 0
GNGT2 0.024 0.012 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.004 0.019 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.033 0.008 -9999 0 -10000 0 0
PRKCZ 0.026 0.005 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.026 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.013 0.063 -9999 0 -0.32 1 1
IRAK/TOLLIP 0.029 0.011 -9999 0 -10000 0 0
IKBKB 0.026 0.004 -9999 0 -10000 0 0
IKBKG 0.024 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.062 0.22 -9999 0 -0.55 63 63
IL1A -0.035 0.19 -9999 0 -0.68 33 33
IL1B -0.03 0.15 -9999 0 -0.53 33 33
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.033 -9999 0 -0.37 1 1
IL1R2 -0.047 0.2 -9999 0 -0.67 36 36
IL1R1 0.026 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.053 -9999 0 -0.28 1 1
TOLLIP 0.026 0.005 -9999 0 -10000 0 0
TICAM2 0.016 0.079 -9999 0 -0.69 5 5
MAP3K3 0.025 0.006 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.033 0.057 -9999 0 -10000 0 0
JUN -0.079 0.16 -9999 0 -0.37 87 87
MAP3K7 0.026 0.003 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.035 0.13 -9999 0 -0.4 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88 0.031 0.13 -9999 0 -0.42 32 32
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.043 0.13 -9999 0 -0.4 32 32
IL1 beta fragment/IL1R1/IL1RAP 0.01 0.13 -9999 0 -0.44 32 32
NFKB1 0.026 0.004 -9999 0 -10000 0 0
MAPK8 -0.007 0.064 -9999 0 -0.39 9 9
IRAK1 0.015 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 0.011 0.083 -9999 0 -0.49 8 8
IRAK4 0.026 0.005 -9999 0 -10000 0 0
PRKCI 0.026 0.003 -9999 0 -10000 0 0
TRAF6 0.024 0.036 -9999 0 -0.69 1 1
PI3K 0.037 0.029 -9999 0 -0.52 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.069 -9999 0 -0.36 1 1
CHUK 0.026 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.01 0.13 -9999 0 -0.44 32 32
IL1 beta/IL1R2 -0.052 0.2 -9999 0 -0.5 60 60
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.024 -9999 0 -0.37 1 1
NF kappa B1 p50/RelA 0.023 0.12 -9999 0 -0.37 31 31
IRAK3 0.026 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.03 0.14 -9999 0 -0.4 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.088 -9999 0 -0.3 32 32
IL1 alpha/IL1R1/IL1RAP 0.016 0.14 -9999 0 -0.46 32 32
RELA 0.026 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.026 0.003 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.041 0.028 -9999 0 -0.4 1 1
IL1RAP -0.015 0.067 -9999 0 -10000 0 0
UBE2N 0.026 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.013 0.11 -9999 0 -0.4 10 10
CASP1 0.021 0.052 -9999 0 -0.69 2 2
IL1RN/IL1R2 -0.044 0.18 -9999 0 -0.52 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.025 0.13 -9999 0 -0.41 32 32
TMEM189-UBE2V1 -0.003 0.02 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.074 -9999 0 -0.37 2 2
PIK3CA 0.025 0.036 -9999 0 -0.69 1 1
IL1RN -0.01 0.11 -9999 0 -0.65 8 8
TRAF6/TAK1/TAB1/TAB2 0.045 0.025 -9999 0 -0.38 1 1
MAP2K6 0.01 0.055 -9999 0 -0.37 7 7
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.036 -10000 0 -0.69 1 1
Caspase 8 (4 units) 0.021 0.091 -10000 0 -0.48 3 3
NEF -0.012 0.059 -10000 0 -0.22 24 24
NFKBIA 0.02 0.032 -10000 0 -10000 0 0
BIRC3 -0.006 0.16 -10000 0 -0.67 20 20
CYCS -0.01 0.093 -10000 0 -0.36 8 8
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CD247 -0.02 0.16 -10000 0 -0.77 16 16
MAP2K7 -0.003 0.17 0.36 1 -0.68 17 18
protein ubiquitination 0.007 0.097 0.33 5 -0.36 4 9
CRADD 0.026 0.005 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.026 0.005 -10000 0 -10000 0 0
BID -0.011 0.099 0.22 1 -0.32 22 23
NF-kappa-B/RelA/I kappa B alpha 0.04 0.082 -10000 0 -0.33 17 17
TRADD 0.025 0.006 -10000 0 -10000 0 0
MAP3K5 0.024 0.036 -10000 0 -0.69 1 1
CFLAR 0.026 0.004 -10000 0 -10000 0 0
FADD 0.026 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.082 -10000 0 -0.33 17 17
MAPK8 -0.003 0.16 0.35 2 -0.63 17 19
APAF1 0.026 0.005 -10000 0 -10000 0 0
TRAF1 0.024 0.008 -10000 0 -10000 0 0
TRAF2 0.024 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.002 0.099 -10000 0 -0.32 29 29
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.002 0.1 -10000 0 -0.37 14 14
CHUK 0.003 0.097 0.28 3 -0.39 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.073 0.031 -10000 0 -0.39 1 1
TCRz/NEF -0.027 0.16 -10000 0 -0.46 40 40
TNF -0.059 0.23 -10000 0 -0.69 46 46
FASLG -0.056 0.24 -10000 0 -0.76 38 38
NFKB1 0.02 0.034 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.007 0.16 -10000 0 -0.45 47 47
CASP6 0.037 0.092 -10000 0 -0.7 3 3
CASP7 0.01 0.16 0.38 3 -0.59 21 24
RELA 0.02 0.034 -10000 0 -10000 0 0
CASP2 0.025 0.006 -10000 0 -10000 0 0
CASP3 0.009 0.15 0.35 1 -0.58 21 22
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.037 0.029 -10000 0 -0.52 1 1
CASP8 0.026 0.005 -10000 0 -10000 0 0
CASP9 0.026 0.005 -10000 0 -10000 0 0
MAP3K14 -0.002 0.1 -10000 0 -0.34 14 14
APAF-1/Caspase 9 -0.005 0.12 -10000 0 -0.49 19 19
BCL2 -0.022 0.16 0.42 2 -0.58 17 19
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.003 0.067 -10000 0 -0.38 2 2
NT3 (dimer)/TRKC -0.025 0.15 -10000 0 -0.5 32 32
NT3 (dimer)/TRKB 0.001 0.15 -10000 0 -0.46 37 37
SHC/Grb2/SOS1/GAB1/PI3K 0.031 0.02 -10000 0 -0.29 1 1
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
BDNF 0.006 0.11 -10000 0 -0.69 10 10
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
DYNLT1 0.026 0.004 -10000 0 -10000 0 0
NTRK1 0.012 0.027 -10000 0 -10000 0 0
NTRK2 0.02 0.054 -10000 0 -0.58 3 3
NTRK3 -0.015 0.12 -10000 0 -0.69 11 11
NT-4/5 (dimer)/TRKB 0.014 0.13 -10000 0 -0.46 25 25
neuron apoptosis -0.006 0.11 0.39 16 -10000 0 16
SHC 2-3/Grb2 0.006 0.12 -10000 0 -0.42 16 16
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 -0.001 0.11 -10000 0 -0.5 12 12
SHC3 -0.007 0.12 -10000 0 -0.42 24 24
STAT3 (dimer) 0.029 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.001 0.14 -10000 0 -0.46 34 34
RIN/GDP -0.006 0.08 0.34 5 -0.26 3 8
GIPC1 0.025 0.007 -10000 0 -10000 0 0
KRAS 0.026 0.005 -10000 0 -10000 0 0
DNAJA3 -0.006 0.078 -10000 0 -0.39 15 15
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.019 0.018 -10000 0 -10000 0 0
MAGED1 0.025 0.007 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.007 0.1 -10000 0 -0.65 9 9
SHC/GRB2/SOS1 0.047 0.019 -10000 0 -10000 0 0
GRB2 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.036 0.07 -10000 0 -0.46 7 7
TRKA/NEDD4-2 0.031 0.022 -10000 0 -10000 0 0
ELMO1 -0.25 0.35 -10000 0 -0.69 155 155
RhoG/GTP/ELMO1/DOCK1 -0.15 0.24 -10000 0 -0.46 155 155
NGF 0.02 0.062 -10000 0 -0.69 3 3
HRAS 0.025 0.012 -10000 0 -10000 0 0
DOCK1 0.023 0.05 -10000 0 -0.69 2 2
GAB2 0.026 0.005 -10000 0 -10000 0 0
RIT2 -0.009 0.016 -10000 0 -10000 0 0
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
DNM1 -0.003 0.13 -10000 0 -0.63 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.13 0.19 -10000 0 -0.36 161 161
mol:GDP -0.013 0.11 0.45 7 -0.39 4 11
NGF (dimer) 0.02 0.062 -10000 0 -0.69 3 3
RhoG/GDP -0.19 0.26 -10000 0 -0.52 155 155
RIT1/GDP -0.003 0.085 0.4 6 -0.28 2 8
TIAM1 -0.058 0.08 -10000 0 -0.69 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.034 0.093 -10000 0 -0.5 11 11
KIDINS220/CRKL/C3G 0.028 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.036 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2 0.052 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.06 0.024 -10000 0 -10000 0 0
RIT1/GTP 0.018 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.16 -10000 0 -0.69 21 21
RAP1/GDP -0.007 0.057 -10000 0 -0.23 2 2
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.006 0.11 -10000 0 -0.69 10 10
ubiquitin-dependent protein catabolic process 0.044 0.046 -10000 0 -0.45 3 3
Schwann cell development -0.031 0.029 -10000 0 -10000 0 0
EHD4 0.026 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.063 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.038 -10000 0 -10000 0 0
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.01 0.13 -10000 0 -0.38 38 38
ABL1 0.024 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.1 -10000 0 -0.51 6 6
STAT3 0.029 0.015 -10000 0 -10000 0 0
axon guidance -0.018 0.12 -10000 0 -0.36 38 38
MAPK3 0.015 0.07 -10000 0 -0.42 7 7
MAPK1 0.009 0.066 -10000 0 -0.41 7 7
CDC42/GDP -0.001 0.087 0.4 6 -0.28 2 8
NTF3 -0.018 0.16 -10000 0 -0.69 21 21
NTF4 0.007 0.1 -10000 0 -0.65 9 9
NGF (dimer)/TRKA/FAIM 0.045 0.047 -10000 0 -0.45 3 3
PI3K 0.037 0.029 -10000 0 -0.52 1 1
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.026 0.003 -10000 0 -10000 0 0
GAB1 0.026 0.004 -10000 0 -10000 0 0
RASGRF1 -0.045 0.094 -10000 0 -0.41 20 20
SOS1 0.026 0.005 -10000 0 -10000 0 0
MCF2L -0.03 0.12 -10000 0 -0.45 30 30
RGS19 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.033 0.068 -10000 0 -0.49 2 2
Rac1/GDP -0.006 0.068 -10000 0 -0.26 2 2
NGF (dimer)/TRKA/GRIT 0.025 0.046 -10000 0 -0.45 3 3
neuron projection morphogenesis 0.02 0.093 -10000 0 -0.69 2 2
NGF (dimer)/TRKA/NEDD4-2 0.044 0.047 -10000 0 -0.45 3 3
MAP2K1 0.038 0.057 0.36 4 -10000 0 4
NGFR -0.019 0.14 -10000 0 -0.69 15 15
NGF (dimer)/TRKA/GIPC/GAIP 0.012 0.082 -10000 0 -0.36 16 16
RAS family/GTP/PI3K 0.027 0.019 -10000 0 -0.32 1 1
FRS2 family/SHP2/GRB2/SOS1 0.073 0.023 -10000 0 -10000 0 0
NRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.01 -10000 0 -10000 0 0
PRKCI 0.026 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.075 -10000 0 -0.49 6 6
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.022 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.046 0.088 -10000 0 -0.44 11 11
NGF (dimer)/TRKA/p62/Atypical PKCs 0.066 0.048 -10000 0 -0.4 3 3
MATK 0.015 0.075 -10000 0 -0.63 5 5
NEDD4L 0.026 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.002 0.084 -10000 0 -0.39 17 17
Rac1/GTP -0.12 0.12 -10000 0 -0.27 144 144
FRS2 family/SHP2/CRK family 0.057 0.036 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.026 0.026 0.37 1 -10000 0 1
HSPA8 0.02 0.054 -10000 0 -0.58 3 3
SMAD3/SMAD4/ER alpha -0.004 0.13 -10000 0 -0.48 17 17
AKT1 0.025 0.006 -10000 0 -10000 0 0
GSC -0.2 0.52 -10000 0 -1.4 62 62
NKX2-5 0.017 0.015 -10000 0 -10000 0 0
muscle cell differentiation -0.009 0.081 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.034 0.095 -10000 0 -10000 0 0
SMAD4 -0.009 0.072 -10000 0 -0.26 1 1
CBFB 0.025 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.044 0.069 -10000 0 -0.45 2 2
SMAD3/SMAD4/VDR 0.049 0.073 -10000 0 -10000 0 0
MYC 0.011 0.11 -10000 0 -0.69 9 9
CDKN2B -0.02 0.11 -10000 0 -0.5 1 1
AP1 -0.2 0.42 -10000 0 -0.87 104 104
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.027 0.059 -10000 0 -0.67 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.009 0.037 -10000 0 -10000 0 0
SP3 0.028 0.005 -10000 0 -10000 0 0
CREB1 0.026 0.005 -10000 0 -10000 0 0
FOXH1 0.004 0.053 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.02 0.078 -10000 0 -10000 0 0
GATA3 -0.013 0.16 -10000 0 -0.64 22 22
SKI/SIN3/HDAC complex/NCoR1 0.025 0.061 -10000 0 -0.76 2 2
MEF2C/TIF2 -0.029 0.14 -10000 0 -0.41 16 16
endothelial cell migration -0.023 0.085 1.3 1 -10000 0 1
MAX 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.024 0.007 -10000 0 -10000 0 0
RBBP4 0.025 0.005 -10000 0 -10000 0 0
RUNX2 -0.018 0.082 -10000 0 -0.69 2 2
RUNX3 0.011 0.095 -10000 0 -0.69 7 7
RUNX1 -0.043 0.074 -10000 0 -10000 0 0
CTBP1 0.026 0.004 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.025 0.009 -10000 0 -10000 0 0
CDKN1A 0.02 0.044 -10000 0 -10000 0 0
KAT2B 0.028 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.009 0.12 -10000 0 -0.29 27 27
DCP1A 0.026 0.003 -10000 0 -10000 0 0
SKI 0.025 0.005 -10000 0 -10000 0 0
SERPINE1 0.023 0.086 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 0.009 0.11 -10000 0 -0.48 10 10
SMAD3/SMAD4/ATF3 -0.084 0.24 -10000 0 -0.53 89 89
SAP30 0.024 0.036 -10000 0 -0.69 1 1
Cbp/p300/PIAS3 0.048 0.045 -10000 0 -10000 0 0
JUN -0.2 0.41 -10000 0 -0.91 95 95
SMAD3/SMAD4/IRF7 0.024 0.079 -10000 0 -10000 0 0
TFE3 0.029 0.009 -10000 0 -10000 0 0
COL1A2 0.028 0.039 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.014 0.099 0.48 2 -10000 0 2
DLX1 -0.016 0.17 -10000 0 -0.66 25 25
TCF3 0.025 0.007 -10000 0 -10000 0 0
FOS -0.17 0.34 -10000 0 -0.75 103 103
SMAD3/SMAD4/Max 0.018 0.08 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.029 -10000 0 -10000 0 0
ZBTB17 0.027 0.006 -10000 0 -10000 0 0
LAMC1 0.011 0.061 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.021 0.079 -10000 0 -10000 0 0
IRF7 0.026 0.008 -10000 0 -10000 0 0
ESR1 -0.017 0.15 -10000 0 -0.66 19 19
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.015 0.092 0.33 2 -10000 0 2
SMAD2-3/SMAD4 0.009 0.095 -10000 0 -0.3 1 1
Cbp/p300/Src-1 0.046 0.034 -10000 0 -10000 0 0
IGHV3OR16-13 0.001 0.031 -10000 0 -0.32 2 2
TGIF2/HDAC complex 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.029 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.003 -10000 0 -10000 0 0
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
SNIP1 0.025 0.006 -10000 0 -10000 0 0
GCN5L2 0.005 0.014 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.028 0.08 -10000 0 -10000 0 0
MSG1/HSC70 -0.065 0.066 -10000 0 -0.45 6 6
SMAD2 0.009 0.048 -10000 0 -10000 0 0
SMAD3 0.005 0.06 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.056 -10000 0 -0.29 6 6
SMAD2/SMAD2/SMAD4 0.002 0.035 0.24 2 -10000 0 2
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.027 0.19 -10000 0 -0.69 30 30
NCOA1 0.026 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.043 0.093 -10000 0 -10000 0 0
IFNB1 -0.001 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.002 0.11 -10000 0 -10000 0 0
CITED1 -0.097 0.073 -10000 0 -0.58 3 3
SMAD2-3/SMAD4/ARC105 0.011 0.086 -10000 0 -10000 0 0
RBL1 0.015 0.087 -10000 0 -0.69 6 6
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.013 0.034 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.047 0.072 -10000 0 -0.44 7 7
SMAD7 -0.091 0.25 -10000 0 -0.56 71 71
MYC/MIZ-1 0.027 0.084 -10000 0 -0.52 9 9
SMAD3/SMAD4 0.027 0.11 0.29 28 -0.53 1 29
IL10 -0.033 0.16 -10000 0 -0.53 29 29
PIASy/HDAC complex 0.016 0.02 -10000 0 -10000 0 0
PIAS3 0.027 0.008 -10000 0 -10000 0 0
CDK2 0.03 0.011 -10000 0 -10000 0 0
IL5 -0.024 0.11 -10000 0 -0.41 20 20
CDK4 0.03 0.012 -10000 0 -10000 0 0
PIAS4 0.016 0.02 -10000 0 -10000 0 0
ATF3 -0.14 0.3 -10000 0 -0.69 90 90
SMAD3/SMAD4/SP1 0.031 0.081 -10000 0 -10000 0 0
FOXG1 0.004 0.057 -10000 0 -0.69 2 2
FOXO3 0.015 0.007 -10000 0 -10000 0 0
FOXO1 0.015 0.007 -10000 0 -10000 0 0
FOXO4 0.015 0.007 -10000 0 -10000 0 0
heart looping -0.015 0.091 0.32 2 -10000 0 2
CEBPB 0.025 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.009 0.14 -10000 0 -0.49 24 24
MYOD1 -0.013 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.016 0.081 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 -0.004 0.14 -10000 0 -0.44 27 27
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.03 0.12 -10000 0 -0.51 6 6
SMAD3/SMAD4/SP1-3 0.051 0.079 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.031 0.01 -10000 0 -10000 0 0
SIN3B 0.024 0.007 -10000 0 -10000 0 0
SIN3A 0.026 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.025 0.11 -10000 0 -0.33 1 1
ITGB5 0.017 0.063 0.36 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.03 0.042 -10000 0 -0.66 1 1
SMAD3/SMAD4/AR -0.18 0.26 -10000 0 -0.49 161 161
AR -0.26 0.35 -10000 0 -0.68 166 166
negative regulation of cell growth -0.023 0.11 -10000 0 -0.34 5 5
SMAD3/SMAD4/MYOD 0.015 0.08 -10000 0 -10000 0 0
E2F5 0.026 0.004 -10000 0 -10000 0 0
E2F4 0.025 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.025 0.098 -10000 0 -0.29 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.036 -10000 0 -10000 0 0
TFDP1 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.19 0.44 -10000 0 -0.92 97 97
SMAD3/SMAD4/RUNX2 0.014 0.099 -10000 0 -0.48 2 2
TGIF2 0.026 0.005 -10000 0 -10000 0 0
TGIF1 0.026 0.004 -10000 0 -10000 0 0
ATF2 0.008 0.11 -10000 0 -0.69 10 10
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.015 0.13 -10000 0 -0.46 20 20
MAP4K1 0.008 0.085 -10000 0 -0.69 5 5
MAP3K8 0.016 0.087 -10000 0 -0.69 6 6
PRKCB 0.008 0.066 -10000 0 -0.69 2 2
DBNL 0.025 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.002 0.082 -10000 0 -0.44 6 6
JUN -0.075 0.2 0.42 2 -0.48 37 39
MAP3K7 0.002 0.082 -10000 0 -0.44 6 6
GRAP2 -0.02 0.15 -10000 0 -0.56 27 27
CRK 0.025 0.007 -10000 0 -10000 0 0
MAP2K4 -0.006 0.1 0.38 2 -0.38 14 16
LAT 0.019 0.065 -10000 0 -0.61 4 4
LCP2 0.023 0.021 -10000 0 -10000 0 0
MAPK8 0.004 0.12 -10000 0 -0.57 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.004 0.087 -10000 0 -0.34 20 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.025 0.12 -10000 0 -0.45 19 19
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.025 0.1 -10000 0 -0.33 41 41
FRAP1 0.012 0.041 0.34 3 -10000 0 3
AKT1 -0.021 0.088 -10000 0 -0.28 39 39
INSR 0.025 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0.008 0.082 -10000 0 -0.45 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.008 0.031 -10000 0 -10000 0 0
TSC2 0.025 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.003 0.068 -10000 0 -0.42 1 1
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.019 0.13 -10000 0 -0.38 43 43
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.018 0.039 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.021 0.093 0.36 17 -0.3 2 19
MAP3K5 0.005 0.032 0.18 1 -0.21 7 8
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
apoptosis 0.005 0.033 0.17 2 -0.21 7 9
mol:LY294002 0 0.001 0.001 1 -0.002 54 55
EIF4B 0.027 0.11 0.45 18 -0.27 2 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.03 0.065 0.36 4 -0.25 2 6
eIF4E/eIF4G1/eIF4A1 0.017 0.019 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.002 0.12 -10000 0 -0.36 42 42
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.039 0.22 1 -0.24 1 2
FKBP1A 0.026 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.016 0.074 -10000 0 -0.41 1 1
mol:Amino Acids 0 0.001 0.001 1 -0.002 54 55
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.026 0.099 -10000 0 -0.32 40 40
EIF4E 0.026 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.076 -10000 0 -0.5 7 7
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.01 0.089 0.28 1 -0.49 1 2
tumor necrosis factor receptor activity 0 0.001 0.002 54 -0.001 1 55
RPS6 0.025 0.007 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
EIF4G1 0.026 0.004 -10000 0 -10000 0 0
IRS1 -0.037 0.13 -10000 0 -0.38 49 49
INS -0.016 0.003 -10000 0 -10000 0 0
PTEN 0.024 0.021 -10000 0 -0.38 1 1
PDK2 -0.024 0.096 0.23 2 -0.31 40 42
EIF4EBP1 0.016 0.097 -10000 0 -0.95 4 4
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
PPP2R5D 0.021 0.071 0.38 11 -10000 0 11
peptide biosynthetic process 0.014 0.017 -10000 0 -10000 0 0
RHEB 0.025 0.006 -10000 0 -10000 0 0
EIF4A1 0.025 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.008 16 -0.004 1 17
EEF2 0.014 0.017 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.03 0.091 -10000 0 -0.88 4 4
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.012 -9999 0 -10000 0 0
HDAC4 0.026 0.005 -9999 0 -10000 0 0
induction of apoptosis 0 0 -9999 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.014 0.004 -9999 0 -10000 0 0
CDKN1A -0.007 0.011 -9999 0 -10000 0 0
KAT2B 0.026 0.003 -9999 0 -10000 0 0
BAX 0.025 0.007 -9999 0 -10000 0 0
FOXO3 -0.004 0.004 -9999 0 -10000 0 0
FOXO1 0.025 0.007 -9999 0 -10000 0 0
FOXO4 0.013 0.009 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
XRCC6 0.02 0.012 -9999 0 -10000 0 0
TAT 0.011 0.021 -9999 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -10000 0 0
MYOD1 -0.008 0.01 -9999 0 -10000 0 0
PPARGC1A -0.28 0.35 -9999 0 -0.69 176 176
FHL2 -0.032 0.2 -9999 0 -0.69 33 33
response to nutrient levels 0 0 -9999 0 -10000 0 0
KU70/SIRT1 0.027 0.017 -9999 0 -10000 0 0
HIST2H4A 0.014 0.004 -9999 0 -10000 0 0
SIRT1/FOXO3a 0.038 0.046 -9999 0 -0.18 1 1
SIRT1 0.023 0.005 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.046 0.017 -9999 0 -10000 0 0
SIRT1/Histone H1b -0.005 0.069 -9999 0 -0.31 8 8
apoptosis -0.037 0.023 -9999 0 -10000 0 0
SIRT1/PGC1A -0.18 0.24 -9999 0 -0.45 176 176
p53/SIRT1 0.028 0.013 -9999 0 -10000 0 0
SIRT1/FOXO4 -0.002 0.059 -9999 0 -0.27 2 2
FOXO1/FHL2/SIRT1 0.007 0.13 -9999 0 -0.42 33 33
HIST1H1E 0.006 0.051 -9999 0 -0.35 7 7
SIRT1/p300 0.027 0.017 -9999 0 -10000 0 0
muscle cell differentiation -0.03 0.022 -9999 0 -10000 0 0
TP53 0.022 0.006 -9999 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.024 -9999 0 -10000 0 0
CREBBP 0.025 0.006 -9999 0 -10000 0 0
MEF2D 0.025 0.007 -9999 0 -10000 0 0
HIV-1 Tat/SIRT1 0.032 0.011 -9999 0 -10000 0 0
ACSS2 0.014 0.003 -9999 0 -10000 0 0
SIRT1/PCAF/MYOD 0.03 0.022 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.002 0.084 -10000 0 -0.33 1 1
epithelial cell differentiation -0.002 0.097 -10000 0 -0.42 6 6
ITCH 0.036 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.066 -10000 0 -10000 0 0
FYN 0.026 0.004 -10000 0 -10000 0 0
EGFR 0.017 0.079 -10000 0 -0.69 5 5
PRL -0.012 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis -0.021 0.12 0.34 3 -0.49 5 8
PTPRZ1 0 0.11 -10000 0 -0.69 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.004 0.13 -10000 0 -0.54 5 5
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.042 0.14 -10000 0 -0.43 39 39
ADAM17 0.033 0.04 -10000 0 -0.69 1 1
ErbB4/ErbB4 -0.014 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.032 0.14 -10000 0 -0.46 27 27
NCOR1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.03 0.14 -10000 0 -0.41 38 38
GRIN2B -0.04 0.13 -10000 0 -0.39 37 37
ErbB4/ErbB2/betacellulin 0.003 0.1 -10000 0 -0.5 9 9
STAT1 0.023 0.022 -10000 0 -10000 0 0
HBEGF 0.018 0.034 -10000 0 -10000 0 0
PRLR -0.012 0.15 -10000 0 -0.69 18 18
E4ICDs/ETO2 -0.001 0.08 -10000 0 -0.33 1 1
axon guidance -0.007 0.068 -10000 0 -10000 0 0
NEDD4 0.035 0.041 -10000 0 -0.69 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.002 0.12 -10000 0 -0.52 18 18
CBFA2T3 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.011 0.069 -10000 0 -0.48 1 1
MAPK3 -0.019 0.12 -10000 0 -0.51 5 5
STAT1 (dimer) -0.001 0.084 -10000 0 -0.31 1 1
MAPK1 -0.021 0.12 -10000 0 -0.51 5 5
JAK2 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.035 0.13 -10000 0 -0.41 35 35
NRG1 -0.032 0.17 -10000 0 -0.54 39 39
NRG3 -0.023 0.18 -10000 0 -0.66 29 29
NRG2 -0.063 0.23 -10000 0 -0.69 49 49
NRG4 0.021 0.02 -10000 0 -10000 0 0
heart development -0.007 0.068 -10000 0 -10000 0 0
neural crest cell migration -0.034 0.13 -10000 0 -0.4 35 35
ERBB2 0.02 0.029 -10000 0 -0.51 1 1
WWOX/E4ICDs -0.002 0.081 -10000 0 -0.33 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.007 0.097 -10000 0 -0.46 5 5
apoptosis 0.023 0.13 0.41 29 -10000 0 29
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.056 0.17 -10000 0 -0.45 50 50
ErbB4/ErbB2/epiregulin 0.013 0.083 -10000 0 -0.48 1 1
ErbB4/ErbB4/betacellulin/betacellulin -0.012 0.11 -10000 0 -0.52 10 10
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.008 0.12 -10000 0 -0.39 18 18
MDM2 -0.011 0.077 0.26 3 -10000 0 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.027 0.14 -10000 0 -0.41 38 38
STAT5A -0.003 0.065 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.033 0.15 -10000 0 -0.42 41 41
DLG4 0.025 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.002 0.074 -10000 0 -0.28 1 1
STAT5A (dimer) 0.006 0.11 -10000 0 -0.45 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.005 0.068 -10000 0 -10000 0 0
LRIG1 0.021 0.061 -10000 0 -0.69 3 3
EREG -0.049 0.07 -10000 0 -10000 0 0
BTC 0.01 0.11 -10000 0 -0.69 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.007 0.068 -10000 0 -10000 0 0
ERBB4 -0.014 0.086 -10000 0 -10000 0 0
STAT5B 0.025 0.006 -10000 0 -10000 0 0
YAP1 0.006 0.056 -10000 0 -0.43 5 5
GRB2 0.025 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.011 0.068 -10000 0 -0.44 1 1
glial cell differentiation 0.002 0.074 0.28 1 -10000 0 1
WWOX 0.025 0.006 -10000 0 -10000 0 0
cell proliferation -0.025 0.14 0.4 1 -1 2 3
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.091 -10000 0 -0.61 8 8
ANTXR2 0.024 0.036 -10000 0 -0.69 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.012 -10000 0 -0.081 9 9
monocyte activation -0.035 0.15 -10000 0 -0.43 51 51
MAP2K2 -0.01 0.12 -10000 0 -0.54 19 19
MAP2K1 -0.001 0.011 -10000 0 -10000 0 0
MAP2K7 -0.001 0.011 -10000 0 -10000 0 0
MAP2K6 -0.007 0.05 -10000 0 -0.41 6 6
CYAA -0.006 0.053 -10000 0 -0.34 9 9
MAP2K4 -0.001 0.011 -10000 0 -10000 0 0
IL1B -0.027 0.1 0.18 1 -0.36 34 35
Channel 0.024 0.061 -10000 0 -0.37 9 9
NLRP1 -0.003 0.03 -10000 0 -0.39 2 2
CALM1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.03 -10000 0 -0.52 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.012 0.081 9 -10000 0 9
MAPK3 -0.001 0.011 -10000 0 -10000 0 0
MAPK1 -0.001 0.011 -10000 0 -10000 0 0
PGR -0.013 0.061 -10000 0 -0.37 10 10
PA/Cellular Receptors 0.025 0.066 -10000 0 -0.4 9 9
apoptosis -0.001 0.012 -10000 0 -0.081 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.024 0.057 -10000 0 -0.34 9 9
macrophage activation -0.001 0.01 -10000 0 -10000 0 0
TNF -0.059 0.23 -10000 0 -0.69 46 46
VCAM1 -0.036 0.16 -10000 0 -0.43 51 51
platelet activation 0.011 0.03 -10000 0 -0.52 1 1
MAPKKK cascade -0.004 0.027 0.18 1 -0.14 7 8
IL18 -0.01 0.061 -10000 0 -0.33 11 11
negative regulation of macrophage activation -0.001 0.012 -10000 0 -0.081 9 9
LEF -0.001 0.012 -10000 0 -0.081 9 9
CASP1 0.001 0.018 -10000 0 -0.1 9 9
mol:cAMP 0.011 0.03 -10000 0 -0.52 1 1
necrosis -0.001 0.012 -10000 0 -0.081 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.024 0.058 -10000 0 -0.35 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.014 0.12 -10000 0 -0.67 5 5
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.024 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
DTX1 0.022 0.05 -10000 0 -0.69 2 2
LRP6/FZD1 0.038 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.051 -10000 0 -0.69 2 2
AP1 -0.13 0.24 -10000 0 -0.5 114 114
NCSTN 0.025 0.007 -10000 0 -10000 0 0
ADAM10 0.018 0.079 -10000 0 -0.69 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.072 -10000 0 -0.52 3 3
NICD/RBPSUH 0.013 0.12 -10000 0 -0.66 5 5
WIF1 -0.015 0.045 -10000 0 -10000 0 0
NOTCH1 0.003 0.11 -10000 0 -0.68 5 5
PSENEN 0.025 0.007 -10000 0 -10000 0 0
KREMEN2 0.014 0.039 -10000 0 -10000 0 0
DKK1 -0.001 0.072 -10000 0 -0.69 2 2
beta catenin/beta TrCP1 0.045 0.047 0.29 2 -10000 0 2
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 -0.004 0.08 0.24 2 -0.37 11 13
CtBP/CBP/TCF1/TLE1/AES 0.019 0.034 -10000 0 -0.3 3 3
PSEN1 0.026 0.005 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.69 103 103
JUN -0.13 0.29 -10000 0 -0.69 87 87
MAP3K7 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.039 0.064 0.3 11 -10000 0 11
MAPK3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.032 0.1 -10000 0 -0.45 16 16
HNF1A 0.023 0.036 -10000 0 -0.69 1 1
CTBP1 0.025 0.004 -10000 0 -10000 0 0
MYC -0.015 0.24 -10000 0 -1.2 15 15
NKD1 0.005 0.12 -10000 0 -0.69 11 11
FZD1 0.025 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.011 0.12 -10000 0 -0.65 7 7
apoptosis -0.13 0.24 -10000 0 -0.49 114 114
Delta 1/NOTCHprecursor 0.014 0.11 -10000 0 -0.65 5 5
DLL1 0.026 0.008 -10000 0 -10000 0 0
PPARD 0.024 0.059 -10000 0 -0.76 2 2
Gamma Secretase 0.069 0.028 -10000 0 -10000 0 0
APC 0.005 0.053 0.28 1 -0.3 1 2
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.046 0.049 -10000 0 -0.48 2 2
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
NLK 0.013 0.007 -10000 0 -10000 0 0
CCND1 0.014 0.11 -10000 0 -0.87 6 6
WNT1 0.018 0.019 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.048 0.091 0.4 13 -0.33 1 14
DKK2 -0.008 0.14 -10000 0 -0.69 17 17
NOTCH1 precursor/DVL1 0.019 0.1 -10000 0 -0.56 6 6
GSK3B 0.026 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.012 0.12 -10000 0 -0.66 7 7
PPP2R5D 0.028 0.059 0.34 11 -0.34 2 13
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.063 0.019 -10000 0 -10000 0 0
RBPJ 0.026 0.008 -10000 0 -10000 0 0
CREBBP 0.027 0.008 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.026 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.022 0.097 -10000 0 -0.53 11 11
PTK2 0.011 0.14 -10000 0 -0.56 19 19
positive regulation of JNK cascade 0.017 0.091 -10000 0 -0.33 19 19
CDC42/GDP 0.033 0.13 0.4 2 -0.45 22 24
Rac1/GDP 0.031 0.13 -10000 0 -0.46 19 19
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.026 0.11 -10000 0 -0.41 19 19
nectin-3/I-afadin 0.011 0.12 -10000 0 -0.51 20 20
RAPGEF1 0.014 0.13 0.32 2 -0.51 19 21
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0.14 -10000 0 -0.58 20 20
PDGFB-D/PDGFRB 0.026 0.005 -10000 0 -10000 0 0
TLN1 -0.002 0.06 -10000 0 -0.8 1 1
Rap1/GTP 0.014 0.088 -10000 0 -0.36 17 17
IQGAP1 0.026 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.011 0.12 -10000 0 -0.51 20 20
PVR 0.025 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.007 -10000 0 -10000 0 0
mol:GDP 0.018 0.16 0.44 2 -0.57 24 26
MLLT4 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
PI3K 0.055 0.1 -10000 0 -0.41 17 17
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.035 0.019 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.012 0.1 -10000 0 -0.37 19 19
PVRL1 0.022 0.024 -10000 0 -10000 0 0
PVRL3 -0.009 0.16 -10000 0 -0.69 20 20
PVRL2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.025 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.1 -10000 0 -0.63 10 10
JAM-A/CLDN1 0.045 0.12 -10000 0 -0.41 25 25
SRC 0.01 0.16 -10000 0 -0.66 19 19
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
nectin-1(dimer)/I-afadin/I-afadin 0.035 0.019 -10000 0 -10000 0 0
FARP2 0.022 0.15 -10000 0 -0.55 22 22
RAC1 0.025 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.026 0.11 -10000 0 -0.44 20 20
nectin-1/I-afadin 0.035 0.019 -10000 0 -10000 0 0
nectin-2/I-afadin 0.037 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.034 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.029 0.11 -10000 0 -0.45 19 19
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.007 -10000 0 -10000 0 0
F11R 0.025 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.017 0.091 -10000 0 -0.33 19 19
alphaV/beta3 Integrin/Talin 0.022 0.11 -10000 0 -0.56 10 10
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.037 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.037 0.01 -10000 0 -10000 0 0
PIP5K1C 0 0.065 -10000 0 -0.26 19 19
VAV2 0.002 0.18 0.36 1 -0.62 24 25
RAP1/GDP 0.035 0.12 -10000 0 -0.43 19 19
ITGAV 0.024 0.036 -10000 0 -0.69 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.026 0.11 -10000 0 -0.44 20 20
nectin-3(dimer)/I-afadin/I-afadin 0.011 0.12 -10000 0 -0.51 20 20
Rac1/GTP 0.017 0.13 -10000 0 -0.46 19 19
PTPRM 0.003 0.071 -10000 0 -0.29 19 19
E-cadherin/beta catenin/alpha catenin 0.072 0.025 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.026 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.022 0.12 -9999 0 -0.35 31 31
Syndecan-3/Neurocan -0.001 0.1 -9999 0 -0.37 28 28
POMC -0.12 0.29 -9999 0 -0.68 85 85
EGFR 0.017 0.079 -9999 0 -0.69 5 5
Syndecan-3/EGFR 0.025 0.05 -9999 0 -0.35 6 6
AGRP 0.004 0.032 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.025 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.026 0.003 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.034 0.19 -9999 0 -0.68 32 32
long-term memory 0.049 0.029 -9999 0 -10000 0 0
Syndecan-3/IL8 0.03 0.067 -9999 0 -0.36 9 9
PSEN1 0.026 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.038 0.01 -9999 0 -10000 0 0
FYN 0.026 0.004 -9999 0 -10000 0 0
limb bud formation 0.015 0.006 -9999 0 -10000 0 0
MC4R 0.001 0.026 -9999 0 -10000 0 0
SRC 0.026 0.009 -9999 0 -10000 0 0
PTN -0.042 0.21 -9999 0 -0.69 38 38
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.03 0.14 -9999 0 -0.52 2 2
Syndecan-3/AgRP 0.029 0.024 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.044 0.03 -9999 0 -10000 0 0
Fyn/Cortactin 0.038 0.008 -9999 0 -10000 0 0
SDC3 0.015 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.03 0.066 -9999 0 -0.36 9 9
IL8 -0.025 0.11 -9999 0 -0.69 8 8
Syndecan-3/Fyn/Cortactin 0.05 0.03 -9999 0 -10000 0 0
Syndecan-3/CASK 0.011 0.024 -9999 0 -0.31 1 1
alpha-MSH/MC4R -0.083 0.22 -9999 0 -0.52 85 85
Gamma Secretase 0.069 0.028 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.6 8 8
UGCG -0.05 0.21 -10000 0 -0.62 43 43
AKT1/mTOR/p70S6K/Hsp90/TERT 0.017 0.13 0.43 5 -0.42 15 20
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.052 0.21 -10000 0 -0.6 46 46
mol:DAG -0.011 0.12 -10000 0 -0.79 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.16 -10000 0 -0.46 27 27
FRAP1 -0.01 0.18 0.44 2 -0.49 37 39
FOXO3 0.002 0.16 0.43 2 -0.6 16 18
AKT1 -0.003 0.17 -10000 0 -0.63 18 18
GAB2 0.026 0.005 -10000 0 -10000 0 0
SMPD1 0.011 0.078 -10000 0 -0.81 3 3
SGMS1 0.001 0.11 -10000 0 -0.64 10 10
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 0.009 0.024 -10000 0 -0.46 1 1
CALM1 0.026 0.005 -10000 0 -10000 0 0
cell proliferation -0.025 0.18 0.33 5 -0.56 26 31
EIF3A 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.03 -10000 0 -0.53 1 1
RPS6KB1 0.016 0.066 -10000 0 -0.7 2 2
mol:sphingomyelin -0.011 0.12 -10000 0 -0.79 10 10
natural killer cell activation 0 0.004 -10000 0 -0.017 7 7
JAK3 -0.008 0.062 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.004 -10000 0 -10000 0 0
MYC -0.002 0.2 0.48 5 -0.9 14 19
MYB 0.003 0.19 -10000 0 -1.3 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.003 0.15 -10000 0 -0.61 16 16
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.066 -10000 0 -0.63 2 2
mol:PI-3-4-5-P3 -0.002 0.15 -10000 0 -0.59 16 16
Rac1/GDP 0.024 0.025 -10000 0 -0.42 1 1
T cell proliferation -0.003 0.13 -10000 0 -0.56 15 15
SHC1 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.025 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.066 9 9
PRKCZ -0.004 0.14 -10000 0 -0.58 15 15
NF kappa B1 p50/RelA 0.015 0.16 -10000 0 -0.54 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.002 0.11 -10000 0 -0.59 10 10
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.005 -10000 0 -10000 0 0
IL2RA -0.014 0.15 -10000 0 -0.66 20 20
IL2RB 0.003 0.099 -10000 0 -0.62 9 9
TERT -0.006 0.021 -10000 0 -10000 0 0
E2F1 0.023 0.071 -10000 0 -0.43 9 9
SOS1 0.026 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 9 -10000 0 9
PTPN11 0.026 0.006 -10000 0 -10000 0 0
IL2RG -0.011 0.14 -10000 0 -0.64 18 18
actin cytoskeleton organization -0.003 0.13 -10000 0 -0.56 15 15
GRB2 0.025 0.007 -10000 0 -10000 0 0
IL2 0.018 0.013 -10000 0 -10000 0 0
PIK3CA 0.026 0.036 -10000 0 -0.69 1 1
Rac1/GTP 0.048 0.032 -10000 0 -0.4 1 1
LCK 0.013 0.084 -10000 0 -0.69 5 5
BCL2 -0.031 0.26 0.48 4 -0.8 35 39
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.005 0.14 -10000 0 -0.38 46 46
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.021 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.009 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.034 0.14 -10000 0 -0.4 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 0.012 0.032 0.098 49 -10000 0 49
GNAL -0.058 0.23 -10000 0 -0.67 49 49
GNG2 0.026 0.005 -10000 0 -10000 0 0
CRH 0 0.038 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.035 -10000 0 -0.4 3 3
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.008 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.01 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.021 0.041 -10000 0 -0.44 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.002 0.022 -10000 0 -10000 0 0
GRK1 -0.045 0.21 -10000 0 -0.67 40 40
CNG Channel 0.037 0.057 -10000 0 -0.39 5 5
mol:Na + 0.026 0.076 -10000 0 -0.4 9 9
mol:ADP -0.044 0.21 -10000 0 -0.67 40 40
RGS9-1/Gbeta5/R9AP -0.025 0.18 -10000 0 -0.46 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.038 0.08 -10000 0 -0.41 9 9
CNGB1 0.017 0.03 -10000 0 -10000 0 0
RDH5 -0.071 0.071 -10000 0 -10000 0 0
SAG -0.008 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.12 0.49 12 -0.39 9 21
Na + (4 Units) 0.019 0.071 -10000 0 -0.38 9 9
RGS9 -0.039 0.2 -10000 0 -0.69 36 36
GNB1/GNGT1 0.029 0.013 -10000 0 -10000 0 0
GNAT1/GDP -0.013 0.16 -10000 0 -0.41 57 57
GUCY2D 0.01 0.085 -10000 0 -0.64 6 6
GNGT1 -0.015 0.012 -10000 0 -10000 0 0
GUCY2F -0.013 0.01 -10000 0 -10000 0 0
GNB5 0.026 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.037 -10000 0 -0.39 1 1
mol:11-cis-retinal -0.071 0.071 -10000 0 -10000 0 0
mol:cGMP 0.03 0.063 -10000 0 -0.41 6 6
GNB1 0.026 0.005 -10000 0 -10000 0 0
Rhodopsin -0.042 0.055 -10000 0 -10000 0 0
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 0.016 0.081 -10000 0 -0.69 5 5
Metarhodopsin II -0.014 0.13 -10000 0 -0.41 40 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.045 0.069 -10000 0 -0.42 8 8
RGS9BP -0.019 0.17 -10000 0 -0.68 25 25
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.037 0.041 -10000 0 -0.42 3 3
PDE6A/B 0.03 0.027 -10000 0 -10000 0 0
mol:Pi -0.025 0.18 -10000 0 -0.46 58 58
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.037 0.014 -10000 0 -10000 0 0
PDE6B 0.026 0.004 -10000 0 -10000 0 0
PDE6A 0.011 0.036 -10000 0 -10000 0 0
PDE6G 0.012 0.061 -10000 0 -0.69 2 2
RHO 0.006 0.022 -10000 0 -10000 0 0
PDE6 0.004 0.17 -10000 0 -0.39 57 57
GUCA1A 0.006 0.024 -10000 0 -10000 0 0
GC2/GCAP Family 0.045 0.04 -10000 0 -0.37 3 3
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.021 0.061 -10000 0 -0.69 3 3
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.025 0.007 -9999 0 -10000 0 0
SPHK1 0.023 0.02 -9999 0 -10000 0 0
GNAI2 0.026 0.003 -9999 0 -10000 0 0
mol:S1P 0.017 0.007 -9999 0 -10000 0 0
GNAO1 0.007 0.11 -9999 0 -0.69 10 10
mol:Sphinganine-1-P 0.014 0.013 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.055 0.026 -9999 0 -10000 0 0
GNAI3 0.026 0.005 -9999 0 -10000 0 0
G12/G13 0.037 0.011 -9999 0 -10000 0 0
S1PR3 0.024 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.013 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.017 -9999 0 -0.2 1 1
S1PR5 0.023 0.016 -9999 0 -10000 0 0
S1PR4 0.023 0.016 -9999 0 -10000 0 0
GNAI1 0.025 0.006 -9999 0 -10000 0 0
S1P/S1P5/G12 0.043 0.023 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.053 0.16 -9999 0 -0.3 106 106
S1P/S1P4/Gi 0.004 0.079 -9999 0 -0.36 11 11
GNAQ 0.024 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.29 -9999 0 -0.66 92 92
GNA15 0.013 0.052 -9999 0 -0.69 1 1
GNA12 0.025 0.006 -9999 0 -10000 0 0
GNA13 0.025 0.006 -9999 0 -10000 0 0
GNA11 0.018 0.071 -9999 0 -0.69 4 4
ABCC1 0.025 0.006 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.036 0.059 -9999 0 -0.4 5 5
EPHB2 0.02 0.062 -9999 0 -0.69 3 3
Syndecan-2/TACI -0.095 0.21 -9999 0 -0.45 101 101
LAMA1 -0.026 0.18 -9999 0 -0.68 30 30
Syndecan-2/alpha2 ITGB1 0.049 0.088 -9999 0 -0.39 14 14
HRAS 0.025 0.012 -9999 0 -10000 0 0
Syndecan-2/CASK 0.006 0.043 -9999 0 -0.33 6 6
ITGA5 0.026 0.005 -9999 0 -10000 0 0
BAX 0.007 0.05 -9999 0 -0.4 6 6
EPB41 0.026 0.005 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.023 0.041 -9999 0 -0.35 4 4
LAMA3 0 0.12 -9999 0 -0.69 12 12
EZR 0.026 0.004 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.024 0.036 -9999 0 -0.69 1 1
Syndecan-2/MMP2 0.022 0.059 -9999 0 -0.41 7 7
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.009 0.057 -9999 0 -10000 0 0
dendrite morphogenesis 0.021 0.061 -9999 0 -0.38 8 8
Syndecan-2/GM-CSF -0.034 0.056 -9999 0 -0.36 5 5
determination of left/right symmetry 0.01 0.051 -9999 0 -0.38 6 6
Syndecan-2/PKC delta 0.026 0.046 -9999 0 -0.33 6 6
GNB2L1 0.026 0.006 -9999 0 -10000 0 0
MAPK3 -0.032 0.046 -9999 0 -0.42 3 3
MAPK1 -0.026 0.045 -9999 0 -0.42 3 3
Syndecan-2/RACK1 0.037 0.041 -9999 0 -0.39 3 3
NF1 0.025 0.006 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.051 -9999 0 -0.38 6 6
ITGA2 -0.035 0.073 -9999 0 -10000 0 0
MAPK8 0.009 0.057 -9999 0 -0.44 6 6
Syndecan-2/alpha2/beta1 Integrin 0.03 0.13 -9999 0 -0.43 27 27
Syndecan-2/Kininogen 0.017 0.049 -9999 0 -0.33 6 6
ITGB1 0.026 0.004 -9999 0 -10000 0 0
SRC 0.02 0.041 -9999 0 -0.37 3 3
Syndecan-2/CASK/Protein 4.1 0.023 0.042 -9999 0 -0.41 3 3
extracellular matrix organization 0.024 0.043 -9999 0 -0.44 3 3
actin cytoskeleton reorganization -0.036 0.059 -9999 0 -0.4 5 5
Syndecan-2/Caveolin-2/Ras 0.039 0.047 -9999 0 -0.41 4 4
Syndecan-2/Laminin alpha3 0.008 0.093 -9999 0 -0.43 16 16
Syndecan-2/RasGAP 0.049 0.042 -9999 0 -0.37 3 3
alpha5/beta1 Integrin 0.038 0.009 -9999 0 -10000 0 0
PRKCD 0.026 0.003 -9999 0 -10000 0 0
Syndecan-2 dimer 0.021 0.061 -9999 0 -0.39 8 8
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.039 0.041 -9999 0 -0.36 3 3
RHOA 0.026 0.003 -9999 0 -10000 0 0
SDCBP 0.026 0.004 -9999 0 -10000 0 0
TNFRSF13B -0.16 0.3 -9999 0 -0.69 100 100
RASA1 0.026 0.005 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.009 0.057 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.044 -9999 0 -0.35 5 5
TGFB1 0.024 0.016 -9999 0 -10000 0 0
CASP3 0.017 0.043 -9999 0 -0.41 3 3
FN1 -0.082 0.067 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.005 0.085 -9999 0 -0.4 14 14
SDC2 0.01 0.051 -9999 0 -0.38 6 6
KNG1 -0.004 0.037 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.025 0.043 -9999 0 -0.44 3 3
TRAPPC4 0.026 0.005 -9999 0 -10000 0 0
CSF2 -0.08 0.064 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.044 -9999 0 -0.44 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.041 -9999 0 -0.35 4 4
Syndecan-2/Ezrin 0.041 0.043 -9999 0 -0.41 3 3
PRKACA 0.016 0.038 -9999 0 -0.41 3 3
angiogenesis -0.005 0.085 -9999 0 -0.39 14 14
MMP2 0.019 0.065 -9999 0 -0.61 4 4
IL8 -0.025 0.11 -9999 0 -0.69 8 8
calcineurin-NFAT signaling pathway -0.094 0.21 -9999 0 -0.45 101 101
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.029 0.063 -10000 0 -0.52 5 5
PDGFRB 0.026 0.006 -10000 0 -10000 0 0
SPHK1 0.009 0.057 -10000 0 -0.7 2 2
mol:S1P 0.007 0.055 -10000 0 -0.62 2 2
S1P1/S1P/Gi -0.009 0.14 -10000 0 -0.43 31 31
GNAO1 0.004 0.11 -10000 0 -0.7 10 10
PDGFB-D/PDGFRB/PLCgamma1 -0.007 0.12 -10000 0 -0.52 12 12
PLCG1 -0.01 0.12 -10000 0 -0.42 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.026 0.006 -10000 0 -10000 0 0
GNAI2 0.024 0.013 -10000 0 -10000 0 0
GNAI3 0.023 0.013 -10000 0 -10000 0 0
GNAI1 0.024 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.051 -10000 0 -0.44 5 5
S1P1/S1P 0.002 0.062 -10000 0 -0.38 5 5
negative regulation of cAMP metabolic process -0.008 0.13 -10000 0 -0.42 31 31
MAPK3 -0.023 0.18 -10000 0 -0.59 32 32
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.02 0.062 -10000 0 -0.69 3 3
PLCB2 0.013 0.072 0.43 3 -0.37 4 7
RAC1 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.009 0.054 -10000 0 -0.35 4 4
receptor internalization 0.002 0.059 -10000 0 -0.36 5 5
PTGS2 -0.066 0.32 0.63 3 -1 39 42
Rac1/GTP 0.01 0.054 -10000 0 -0.35 4 4
RHOA 0.026 0.003 -10000 0 -10000 0 0
VEGFA 0.022 0.05 -10000 0 -0.69 2 2
negative regulation of T cell proliferation -0.008 0.13 -10000 0 -0.42 31 31
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.015 -10000 0 -10000 0 0
MAPK1 -0.025 0.18 -10000 0 -0.62 32 32
S1P1/S1P/PDGFB-D/PDGFRB 0.012 0.072 -10000 0 -0.41 4 4
ABCC1 0.025 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.005 -10000 0 -10000 0 0
VDR 0.025 0.009 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.039 0.025 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.067 -10000 0 -0.32 5 5
KAT2B 0.026 0.003 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.012 0.076 0.25 8 -0.36 9 17
RAR alpha/9cRA/Cyclin H 0.027 0.1 -10000 0 -0.35 20 20
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.064 0.24 1 -0.3 10 11
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.011 0.076 -10000 0 -0.56 3 3
NCOR2 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.011 0.14 -10000 0 -0.53 22 22
NCOA2 -0.027 0.19 -10000 0 -0.69 30 30
NCOA3 0.026 0.005 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.009 -10000 0 -10000 0 0
RARG 0.026 0.006 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.011 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.022 0.062 -10000 0 -0.69 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0 0.13 -10000 0 -0.52 22 22
RARA 0.003 0.071 -10000 0 -0.28 23 23
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.009 0.11 0.24 1 -0.33 37 38
PRKCA -0.011 0.16 -10000 0 -0.69 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 0.003 0.15 0.41 3 -0.52 24 27
RXRG -0.025 0.096 -10000 0 -0.39 25 25
RXRA 0.002 0.075 -10000 0 -0.29 23 23
RXRB 0.001 0.092 -10000 0 -0.38 22 22
VDR/Vit D3/DNA 0.019 0.006 -10000 0 -10000 0 0
RBP1 0.016 0.08 -10000 0 -0.69 5 5
CRBP1/9-cic-RA 0.012 0.06 -10000 0 -0.52 5 5
RARB 0.01 0.11 -10000 0 -0.69 10 10
PRKCG 0.021 0.014 -10000 0 -10000 0 0
MNAT1 0.026 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.14 -10000 0 -0.57 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.007 0.13 -10000 0 -0.47 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.083 0.3 2 -0.39 7 9
RXRs/RARs/NRIP1/9cRA/HDAC3 0.001 0.15 0.45 2 -0.53 23 25
positive regulation of DNA binding 0.017 0.091 -10000 0 -0.33 20 20
NRIP1 0.004 0.14 0.49 1 -0.72 4 5
RXRs/RARs -0.004 0.14 -10000 0 -0.52 24 24
RXRs/RXRs/DNA/9cRA -0.019 0.13 -10000 0 -0.53 22 22
PRKACA 0.025 0.007 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.052 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.044 0.064 -10000 0 -10000 0 0
CCNH 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.048 0.017 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturb