Thyroid Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 38 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 205
Signaling events mediated by Stem cell factor receptor (c-Kit) 135
Signaling events regulated by Ret tyrosine kinase 119
Reelin signaling pathway 109
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 89
Wnt signaling 86
Noncanonical Wnt signaling pathway 82
FOXA2 and FOXA3 transcription factor networks 78
PDGFR-alpha signaling pathway 78
Nongenotropic Androgen signaling 70
Results
Summary Table

The following list describes the columns found in Table 2.

  • 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 205 1437 7 -0.43 0 1000 -1000 -0.01 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 135 10598 78 -0.73 0.23 1000 -1000 -0.046 -1000
Signaling events regulated by Ret tyrosine kinase 119 9831 82 -0.38 0.027 1000 -1000 -0.058 -1000
Reelin signaling pathway 109 6121 56 -0.48 0.065 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 89 6062 68 -0.7 0.34 1000 -1000 -0.063 -1000
Wnt signaling 86 607 7 -0.34 0.011 1000 -1000 -0.018 -1000
Noncanonical Wnt signaling pathway 82 2133 26 -0.34 0.027 1000 -1000 -0.048 -1000
FOXA2 and FOXA3 transcription factor networks 78 3621 46 -0.9 0.031 1000 -1000 -0.06 -1000
PDGFR-alpha signaling pathway 78 3462 44 -0.41 0.043 1000 -1000 -0.043 -1000
Nongenotropic Androgen signaling 70 3667 52 -0.26 0.19 1000 -1000 -0.035 -1000
Signaling events mediated by the Hedgehog family 62 3274 52 -0.3 0.14 1000 -1000 -0.046 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 60 3274 54 -0.48 0.039 1000 -1000 -0.06 -1000
Nephrin/Neph1 signaling in the kidney podocyte 54 1869 34 -0.11 0.027 1000 -1000 -0.038 -1000
Calcium signaling in the CD4+ TCR pathway 52 1638 31 -0.35 0.027 1000 -1000 -0.045 -1000
Glypican 1 network 50 2437 48 -0.3 0.051 1000 -1000 -0.024 -1000
Endothelins 50 4826 96 -0.32 0.028 1000 -1000 -0.048 -1000
IGF1 pathway 49 2805 57 -0.13 0.058 1000 -1000 -0.047 -1000
HIF-1-alpha transcription factor network 47 3574 76 -0.5 0.041 1000 -1000 -0.051 -1000
IL23-mediated signaling events 44 2677 60 -0.3 0.027 1000 -1000 -0.059 -1000
Ephrin B reverse signaling 43 2104 48 -0.24 0.13 1000 -1000 -0.039 -1000
EPHB forward signaling 42 3628 85 -0.24 0.11 1000 -1000 -0.062 -1000
IL4-mediated signaling events 41 3771 91 -1.2 0.55 1000 -1000 -0.095 -1000
BMP receptor signaling 40 3305 81 -0.45 0.052 1000 -1000 -0.056 -1000
Glucocorticoid receptor regulatory network 40 4621 114 -0.46 0.26 1000 -1000 -0.063 -1000
TCR signaling in naïve CD8+ T cells 40 3797 93 -0.15 0.045 1000 -1000 -0.05 -1000
Coregulation of Androgen receptor activity 37 2877 76 -0.67 0.074 1000 -1000 -0.028 -1000
Arf6 signaling events 37 2300 62 -0.26 0.061 1000 -1000 -0.029 -1000
Signaling mediated by p38-alpha and p38-beta 35 1553 44 -0.23 0.027 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 29 3063 105 -0.16 0.051 1000 -1000 -0.041 -1000
Hedgehog signaling events mediated by Gli proteins 29 1907 65 -0.6 0.064 1000 -1000 -0.042 -1000
IL12-mediated signaling events 27 2375 87 -0.37 0.029 1000 -1000 -0.07 -1000
Ras signaling in the CD4+ TCR pathway 26 449 17 -0.11 0.035 1000 -1000 -0.027 -1000
EGFR-dependent Endothelin signaling events 25 527 21 -0.071 0.038 1000 -1000 -0.043 -1000
IL6-mediated signaling events 24 1851 75 -0.15 0.055 1000 -1000 -0.04 -1000
Syndecan-1-mediated signaling events 23 786 34 -0.084 0.027 1000 -1000 -0.041 -1000
Plasma membrane estrogen receptor signaling 22 1934 86 -0.13 0.049 1000 -1000 -0.049 -1000
Osteopontin-mediated events 21 817 38 -0.15 0.04 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 21 1154 54 -0.36 0.064 1000 -1000 -0.05 -1000
ErbB2/ErbB3 signaling events 20 1351 65 -0.17 0.037 1000 -1000 -0.049 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 19 1666 85 -0.22 0.13 1000 -1000 -0.042 -1000
BCR signaling pathway 19 1933 99 -0.11 0.048 1000 -1000 -0.057 -1000
FAS signaling pathway (CD95) 18 884 47 -0.25 0.043 1000 -1000 -0.043 -1000
LPA receptor mediated events 18 1907 102 -0.16 0.035 1000 -1000 -0.06 -1000
Syndecan-4-mediated signaling events 18 1216 67 -0.16 0.039 1000 -1000 -0.043 -1000
Regulation of Androgen receptor activity 18 1262 70 -0.44 0.035 1000 -1000 -0.053 -1000
IFN-gamma pathway 17 1216 68 -0.16 0.035 1000 -1000 -0.055 -1000
Fc-epsilon receptor I signaling in mast cells 16 1570 97 -0.15 0.045 1000 -1000 -0.05 -1000
Ceramide signaling pathway 16 1216 76 -0.14 0.075 1000 -1000 -0.039 -1000
Signaling events mediated by PRL 16 563 34 -0.088 0.039 1000 -1000 -0.034 -1000
Integrins in angiogenesis 14 1207 84 -0.14 0.057 1000 -1000 -0.058 -1000
Angiopoietin receptor Tie2-mediated signaling 14 1318 88 -0.26 0.039 1000 -1000 -0.065 -1000
JNK signaling in the CD4+ TCR pathway 13 229 17 -0.073 0.027 1000 -1000 -0.029 -1000
Signaling events mediated by PTP1B 13 1030 76 -0.2 0.042 1000 -1000 -0.036 -1000
amb2 Integrin signaling 13 1136 82 -0.23 0.035 1000 -1000 -0.051 -1000
ceramide signaling pathway 13 663 49 -0.057 0.039 1000 -1000 -0.039 -1000
VEGFR1 specific signals 13 742 56 -0.048 0.06 1000 -1000 -0.053 -1000
Visual signal transduction: Cones 12 458 38 -0.047 0.051 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 12 1588 125 -0.29 0.072 1000 -1000 -0.062 -1000
RXR and RAR heterodimerization with other nuclear receptor 12 661 52 -0.18 0.061 1000 -1000 -0.049 -1000
IL27-mediated signaling events 12 632 51 -0.12 0.039 1000 -1000 -0.048 -1000
LPA4-mediated signaling events 11 140 12 -0.058 0.005 1000 -1000 -0.022 -1000
Regulation of nuclear SMAD2/3 signaling 11 1497 136 -0.26 0.053 1000 -1000 -0.042 -1000
mTOR signaling pathway 11 601 53 -0.039 0.029 1000 -1000 -0.039 -1000
IL1-mediated signaling events 11 736 62 -0.078 0.062 1000 -1000 -0.054 -1000
Syndecan-3-mediated signaling events 11 405 35 -0.12 0.07 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 11 527 45 -0.058 0.075 1000 -1000 -0.051 -1000
TCGA08_rtk_signaling 11 292 26 -0.19 0.047 1000 -1000 -0.006 -1000
Neurotrophic factor-mediated Trk receptor signaling 11 1399 120 -0.25 0.074 1000 -1000 -0.05 -1000
Class IB PI3K non-lipid kinase events 11 33 3 -0.016 0.016 1000 -1000 -0.012 -1000
Caspase cascade in apoptosis 10 812 74 -0.058 0.044 1000 -1000 -0.039 -1000
ErbB4 signaling events 10 694 69 -0.062 0.036 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 10 436 40 -0.28 0.047 1000 -1000 -0.024 -1000
Insulin Pathway 10 773 74 -0.049 0.066 1000 -1000 -0.045 -1000
Cellular roles of Anthrax toxin 9 366 39 -0.058 0.027 1000 -1000 -0.025 -1000
Presenilin action in Notch and Wnt signaling 9 609 61 -0.15 0.071 1000 -1000 -0.046 -1000
IL2 signaling events mediated by PI3K 9 567 58 -0.051 0.049 1000 -1000 -0.045 -1000
Rapid glucocorticoid signaling 9 196 20 -0.057 0.035 1000 -1000 -0.006 -1000
Visual signal transduction: Rods 9 502 52 -0.07 0.047 1000 -1000 -0.032 -1000
FOXM1 transcription factor network 9 491 51 -0.21 0.053 1000 -1000 -0.067 -1000
Sphingosine 1-phosphate (S1P) pathway 8 229 28 -0.13 0.056 1000 -1000 -0.023 -1000
Syndecan-2-mediated signaling events 8 581 69 -0.16 0.051 1000 -1000 -0.034 -1000
Nectin adhesion pathway 8 547 63 -0.11 0.074 1000 -1000 -0.051 -1000
S1P1 pathway 8 303 36 -0.066 0.027 1000 -1000 -0.045 -1000
Retinoic acid receptors-mediated signaling 8 480 58 -0.026 0.053 1000 -1000 -0.038 -1000
Stabilization and expansion of the E-cadherin adherens junction 8 601 74 -0.12 0.07 1000 -1000 -0.074 -1000
Class I PI3K signaling events 7 512 73 -0.2 0.05 1000 -1000 -0.039 -1000
BARD1 signaling events 6 388 57 -0.043 0.052 1000 -1000 -0.052 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 516 83 -0.17 0.048 1000 -1000 -0.031 -1000
TCGA08_p53 6 48 7 -0.024 0.025 1000 -1000 -0.009 -1000
Regulation of Telomerase 6 690 102 -0.19 0.073 1000 -1000 -0.043 -1000
S1P3 pathway 6 286 42 -0.13 0.047 1000 -1000 -0.034 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 211 33 -0.12 0.055 1000 -1000 -0.041 -1000
PLK1 signaling events 5 461 85 -0.006 0.057 1000 -1000 -0.032 -1000
TCGA08_retinoblastoma 5 45 8 -0.035 0.031 1000 -1000 -0.002 -1000
Canonical Wnt signaling pathway 4 206 51 -0.038 0.064 1000 -1000 -0.05 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 538 125 -0.011 0.071 1000 -1000 -0.055 -1000
IL2 signaling events mediated by STAT5 4 101 22 -0.027 0.033 1000 -1000 -0.041 -1000
Aurora B signaling 4 304 67 -0.33 0.11 1000 -1000 -0.044 -1000
Canonical NF-kappaB pathway 3 132 39 -0.058 0.061 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 3 18 5 0.005 0.037 1000 -1000 -0.002 -1000
EPO signaling pathway 3 166 55 -0.024 0.061 1000 -1000 -0.039 -1000
Insulin-mediated glucose transport 3 107 32 -0.085 0.05 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 3 216 68 -0.085 0.05 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class I 3 415 104 -0.058 0.064 1000 -1000 -0.036 -1000
Effects of Botulinum toxin 3 103 26 -0.075 0.048 1000 -1000 -0.009 -1000
PDGFR-beta signaling pathway 3 364 97 -0.15 0.079 1000 -1000 -0.056 -1000
p38 MAPK signaling pathway 3 137 44 -0.024 0.049 1000 -1000 -0.025 -1000
S1P5 pathway 2 39 17 -0.008 0.032 1000 -1000 -0.02 -1000
FoxO family signaling 2 181 64 -0.085 0.11 1000 -1000 -0.04 -1000
Signaling mediated by p38-gamma and p38-delta 2 41 15 0 0.027 1000 -1000 -0.031 -1000
Atypical NF-kappaB pathway 2 79 31 -0.009 0.038 1000 -1000 -0.026 -1000
S1P4 pathway 2 73 25 -0.002 0.047 1000 -1000 -0.033 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 45 23 -0.016 0.049 1000 -1000 -0.028 -1000
Circadian rhythm pathway 1 28 22 -0.012 0.045 1000 -1000 -0.038 -1000
Aurora A signaling 1 101 60 -0.024 0.054 1000 -1000 -0.018 -1000
Paxillin-independent events mediated by a4b1 and a4b7 1 68 37 0 0.065 1000 -1000 -0.031 -1000
TRAIL signaling pathway 1 71 48 -0.018 0.074 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 1 76 43 -0.16 0.16 1000 -1000 -0.038 -1000
Paxillin-dependent events mediated by a4b1 1 44 36 -0.055 0.057 1000 -1000 -0.046 -1000
E-cadherin signaling in the nascent adherens junction 1 97 76 -0.057 0.066 1000 -1000 -0.062 -1000
Arf6 trafficking events 1 104 71 -0.048 0.05 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 1 83 43 -0.029 0.051 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class II 0 64 75 -0.036 0.074 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 0 0 3 0.015 0.027 1000 -1000 -0.018 -1000
Arf6 downstream pathway 0 6 43 -0.058 0.046 1000 -1000 -0.033 -1000
Aurora C signaling 0 1 7 -0.006 0.048 1000 -1000 -0.014 -1000
Glypican 2 network 0 3 4 -0.02 0.013 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 16 27 0 0.066 1000 -1000 -0.036 -1000
E-cadherin signaling events 0 0 5 0.026 0.051 1000 -1000 -0.002 -1000
Arf1 pathway 0 16 54 -0.001 0.052 1000 -1000 -0.025 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.073 1000 -1000 -0.009 -1000
Total 2814 162197 7203 -23 8.1 131000 -131000 -5.1 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.33 0.27 -9999 0 -0.5 280 280
EFNA5 -0.083 0.26 -9999 0 -0.69 62 62
FYN -0.31 0.24 -9999 0 -0.46 279 279
neuron projection morphogenesis -0.33 0.27 -9999 0 -0.5 280 280
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.33 0.27 -9999 0 -0.5 280 280
EPHA5 -0.43 0.34 -9999 0 -0.69 256 256
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 -0.39 223 224
CRKL -0.22 0.22 -10000 0 -0.41 225 225
HRAS -0.19 0.19 -10000 0 -0.36 192 192
mol:PIP3 -0.2 0.2 -10000 0 -0.39 202 202
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.027 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 -0.39 222 223
BAD -0.18 0.2 0.29 2 -0.36 217 219
megakaryocyte differentiation -0.23 0.22 -10000 0 -0.42 234 234
GSK3B -0.18 0.2 0.32 2 -0.36 218 220
RAF1 -0.15 0.16 0.35 1 -0.33 71 72
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 -0.32 86 86
cell proliferation -0.23 0.23 -10000 0 -0.43 228 228
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
TEC 0.027 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 -0.32 86 86
LYN/TEC/p62DOK -0.2 0.24 -10000 0 -0.41 223 223
MAPK3 -0.1 0.13 0.32 5 -0.29 11 16
STAP1 -0.24 0.23 -10000 0 -0.44 225 225
GRAP2 -0.019 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 -0.41 216 216
actin filament polymerization -0.22 0.22 -10000 0 -0.42 223 223
LYN 0.027 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.33 0.32 0.35 1 -0.61 227 228
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.18 0.21 -10000 0 -0.38 213 213
PI3K -0.2 0.23 -10000 0 -0.4 222 222
PTEN 0.026 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 -0.081 0.12 0.34 7 -0.23 11 18
mol:GDP -0.19 0.2 -10000 0 -0.38 193 193
PIK3C2B -0.22 0.23 -10000 0 -0.43 205 205
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 -0.36 199 201
SNAI2 -0.23 0.23 -10000 0 -0.43 226 226
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 0.038 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.18 -10000 0 -1.1 3 3
STAT5A (dimer) -0.32 0.32 -10000 0 -0.61 227 227
SOCS1 0.025 0.014 -10000 0 -10000 0 0
cell migration 0.23 0.23 0.43 223 -10000 0 223
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.006 0.028 -10000 0 -10000 0 0
VAV1 0.012 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 0.13 0.28 2 -0.3 18 20
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.73 0.69 -10000 0 -1.3 228 228
MAP2K2 -0.12 0.13 0.44 2 -0.3 18 20
SHC/Grb2/SOS1 -0.19 0.23 -10000 0 -0.41 197 197
STAT5A -0.33 0.33 -10000 0 -0.63 227 227
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.23 0.23 -10000 0 -0.42 226 226
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 0.027 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 28 28
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 -0.068 0.11 -10000 0 -0.67 7 7
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 211 211
JUN -0.26 0.26 -10000 0 -0.58 126 126
HRAS 0.026 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.27 0.3 -10000 0 -0.49 244 244
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.27 0.3 -10000 0 -0.5 241 241
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 -0.42 224 224
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.27 -10000 0 -0.45 235 235
GRB7 0.004 0.053 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.27 0.29 -10000 0 -0.49 245 245
MAPKKK cascade -0.24 0.24 -10000 0 -0.43 234 234
BCAR1 0.026 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 -0.35 213 213
RET51/GFRalpha1/GDNF/SHC -0.27 0.29 -10000 0 -0.49 242 242
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
RET9/GFRalpha1/GDNF/SHC -0.21 0.22 -10000 0 -0.4 225 225
RET9/GFRalpha1/GDNF/Shank3 -0.22 0.22 -10000 0 -0.41 226 226
MAPK3 -0.25 0.24 -10000 0 -0.43 232 232
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.093 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 -0.065 0.24 -10000 0 -0.69 52 52
GFRA1 -0.38 0.35 -10000 0 -0.68 233 233
MAPK8 -0.2 0.2 -10000 0 -0.48 74 74
HRAS/GTP -0.26 0.29 -10000 0 -0.48 239 239
tube development -0.2 0.21 -10000 0 -0.39 216 216
MAPK1 -0.25 0.24 0.32 3 -0.43 234 237
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 216 216
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 -0.55 250 250
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.27 0.3 -10000 0 -0.49 244 244
RET51/GFRalpha1/GDNF/Dok5 -0.32 0.34 -10000 0 -0.55 254 254
PRKCA -0.013 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 -0.38 213 213
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.15 0.16 -10000 0 -0.3 203 203
RET51/GFRalpha1/GDNF/Grb7 -0.28 0.3 -10000 0 -0.5 245 245
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.11 0.26 -10000 0 -0.68 69 69
DOK4 0.026 0.006 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.56 126 126
RET9/GFRalpha1/GDNF/FRS2 -0.21 0.23 -10000 0 -0.41 228 228
SHANK3 0.02 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 205 205
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.36 238 238
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.36 243 243
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.23 0.26 -10000 0 -0.41 229 229
PI3K -0.31 0.29 -10000 0 -0.55 217 217
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.2 0.21 -10000 0 -0.39 216 216
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.33 223 223
RET51/GFRalpha1/GDNF/FRS2 -0.27 0.3 -10000 0 -0.5 243 243
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.049 0.22 -10000 0 -0.69 43 43
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.23 0.26 -10000 0 -0.41 228 228
RET51/GFRalpha1/GDNF/PKC alpha -0.29 0.32 -10000 0 -0.52 244 244
GRB2 0.026 0.007 -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 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.32 0.33 -10000 0 -0.54 255 255
Rac1/GTP -0.24 0.22 -10000 0 -0.43 212 212
RET9/GFRalpha1/GDNF -0.24 0.24 -10000 0 -0.45 232 232
GFRalpha1/GDNF -0.28 0.27 -10000 0 -0.52 232 232
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 0.037 0.014 -10000 0 -10000 0 0
VLDLR 0.005 0.12 -10000 0 -0.66 12 12
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 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 -0.46 286 286
MAPK8IP1/MKK7/MAP3K11/JNK1 0.065 0.05 -10000 0 -0.39 3 3
AKT1 -0.2 0.15 -10000 0 -0.3 276 276
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
DAB1 0.007 0.022 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.29 0.23 -10000 0 -0.43 279 279
LRPAP1/LRP8 0.018 0.11 -10000 0 -0.52 15 15
RELN/LRP8/DAB1/Fyn -0.27 0.22 -10000 0 -0.41 279 279
DAB1/alpha3/beta1 Integrin -0.26 0.21 -10000 0 -0.39 271 271
long-term memory -0.27 0.23 -10000 0 -0.42 278 278
DAB1/LIS1 -0.26 0.22 -10000 0 -0.4 274 274
DAB1/CRLK/C3G -0.26 0.21 -10000 0 -0.39 274 274
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
DAB1/NCK2 -0.26 0.23 -10000 0 -0.4 277 277
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 -0.001 0.13 -10000 0 -0.69 14 14
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
RELN -0.48 0.32 -10000 0 -0.69 283 283
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.31 0.24 -10000 0 -0.46 286 286
GRIN2A/RELN/LRP8/DAB1/Fyn -0.28 0.24 -10000 0 -0.43 278 278
MAPK8 0.021 0.061 -10000 0 -0.69 3 3
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.42 286 286
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.42 279 279
RELN/LRP8 -0.31 0.24 -10000 0 -0.46 284 284
GRIN2B/RELN/LRP8/DAB1/Fyn -0.27 0.23 -10000 0 -0.41 279 279
PI3K 0.038 0.029 -10000 0 -0.52 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.016 -10000 0 -10000 0 0
RAP1A -0.24 0.21 0.48 3 -0.38 233 236
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.019 -10000 0 -10000 0 0
GRIN2B -0.004 0.02 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.42 27 27
neuron adhesion -0.22 0.22 0.46 9 -0.59 23 32
LRP8 0 0.14 -10000 0 -0.69 15 15
GSK3B -0.19 0.14 -10000 0 -0.3 143 143
RELN/VLDLR/DAB1/Fyn -0.27 0.21 -10000 0 -0.4 278 278
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.32 279 279
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.048 0.15 0.81 14 -0.62 2 16
neuron migration -0.26 0.2 -10000 0 -0.39 269 269
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.43 27 27
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 281 281
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.012 0.11 -10000 0 -0.6 10 10
NFATC2 -0.2 0.33 -10000 0 -0.73 93 93
NFATC3 -0.082 0.14 -10000 0 -0.29 96 96
CD40LG -0.62 0.56 -10000 0 -1.1 220 220
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 -1.2 105 105
JUNB 0.02 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 0.011 0.075 0.39 5 -0.48 1 6
TLE4 -0.2 0.36 -10000 0 -0.76 97 97
Jun/NFAT1-c-4/p21SNFT -0.54 0.59 -10000 0 -1.1 188 188
AP-1/NFAT1-c-4 -0.7 0.74 -10000 0 -1.3 211 211
IKZF1 -0.15 0.28 -10000 0 -0.62 81 81
T-helper 2 cell differentiation -0.27 0.33 -10000 0 -0.87 69 69
AP-1/NFAT1 -0.31 0.41 -10000 0 -0.75 160 160
CALM1 0.038 0.013 -10000 0 -10000 0 0
EGR2 -0.7 0.78 -10000 0 -1.5 185 185
EGR3 -0.52 0.69 -10000 0 -1.3 135 135
NFAT1/FOXP3 -0.16 0.28 -10000 0 -0.6 95 95
EGR1 -0.12 0.29 -10000 0 -0.69 82 82
JUN -0.14 0.29 -10000 0 -0.68 87 87
EGR4 -0.025 0.17 -10000 0 -0.68 24 24
mol:Ca2+ 0.011 0.01 -10000 0 -10000 0 0
GBP3 -0.15 0.27 -10000 0 -0.61 75 75
FOSL1 0.004 0.054 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.47 0.56 -10000 0 -1 188 188
DGKA -0.14 0.24 -10000 0 -0.62 59 59
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.48 0.55 -10000 0 -1 188 188
CTLA4 -0.18 0.3 -10000 0 -0.7 77 77
NFAT1-c-4 (dimer)/EGR1 -0.54 0.63 -10000 0 -1.2 185 185
NFAT1-c-4 (dimer)/EGR4 -0.5 0.56 -10000 0 -1 191 191
FOS -0.16 0.31 -10000 0 -0.69 103 103
IFNG -0.36 0.5 -10000 0 -1.1 105 105
T cell activation -0.38 0.39 -10000 0 -0.9 118 118
MAF 0.026 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 0.74 181 -10000 0 181
TNF -0.54 0.55 -10000 0 -1 204 204
FASLG -0.69 0.76 -10000 0 -1.4 198 198
TBX21 -0.022 0.16 -10000 0 -0.7 19 19
BATF3 0.016 0.048 -10000 0 -0.69 1 1
PRKCQ 0.014 0.083 -10000 0 -0.64 6 6
PTPN1 -0.14 0.25 -10000 0 -0.58 77 77
NFAT1-c-4/ICER1 -0.47 0.55 -10000 0 -1 188 188
GATA3 -0.009 0.15 -10000 0 -0.64 22 22
T-helper 1 cell differentiation -0.35 0.48 -10000 0 -1.1 106 106
IL2RA -0.39 0.45 -10000 0 -1 109 109
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.14 0.25 -10000 0 -0.56 83 83
E2F1 -0.014 0.068 -10000 0 -10000 0 0
PPARG 0.017 0.08 -10000 0 -0.69 5 5
SLC3A2 -0.14 0.25 -10000 0 -0.6 67 67
IRF4 -0.043 0.18 -10000 0 -0.68 26 26
PTGS2 -0.6 0.55 -10000 0 -1.1 206 206
CSF2 -0.6 0.53 -10000 0 -1.1 212 212
JunB/Fra1/NFAT1-c-4 -0.45 0.53 -10000 0 -0.98 184 184
IL4 -0.28 0.35 -10000 0 -0.92 69 69
IL5 -0.58 0.53 -10000 0 -1 209 209
IL2 -0.39 0.4 -10000 0 -0.93 117 117
IL3 -0.069 0.09 -10000 0 -1.1 1 1
RNF128 0.034 0.041 -10000 0 -0.76 1 1
NFATC1 -0.34 0.41 -10000 0 -0.74 181 181
CDK4 0.22 0.25 0.6 62 -10000 0 62
PTPRK -0.14 0.25 -10000 0 -0.57 79 79
IL8 -0.6 0.53 -10000 0 -1.1 211 211
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.24 0.24 -9999 0 -0.41 255 255
FZD6 0.026 0.005 -9999 0 -10000 0 0
WNT6 0.021 0.024 -9999 0 -10000 0 0
WNT4 -0.21 0.33 -9999 0 -0.69 132 132
FZD3 0.027 0.004 -9999 0 -10000 0 0
WNT5A 0.011 0.1 -9999 0 -0.69 9 9
WNT11 -0.34 0.36 -9999 0 -0.68 211 211
Noncanonical Wnt signaling pathway

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
NFATC2 -0.075 0.25 -10000 0 -0.69 58 58
GNB1/GNG2 -0.21 0.23 -10000 0 -0.53 100 100
mol:DAG -0.2 0.21 -10000 0 -0.5 95 95
PLCG1 -0.2 0.21 -10000 0 -0.51 95 95
YES1 -0.23 0.23 -10000 0 -0.38 252 252
FZD3 0.027 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 95 95
MAP3K7 -0.17 0.17 0.31 1 -0.42 92 93
mol:Ca2+ -0.19 0.2 -10000 0 -0.48 95 95
mol:IP3 -0.2 0.21 -10000 0 -0.5 95 95
NLK -0.004 0.072 -10000 0 -0.82 3 3
GNB1 0.026 0.005 -10000 0 -10000 0 0
CAMK2A -0.18 0.19 0.31 1 -0.46 93 94
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.24 0.24 -10000 0 -0.41 255 255
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
GNAS -0.23 0.23 -10000 0 -0.51 116 116
GO:0007205 -0.2 0.2 -10000 0 -0.48 95 95
WNT6 0.021 0.024 -10000 0 -10000 0 0
WNT4 -0.21 0.33 -10000 0 -0.69 132 132
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.51 141 141
GNG2 0.027 0.005 -10000 0 -10000 0 0
WNT5A 0.011 0.1 -10000 0 -0.69 9 9
WNT11 -0.34 0.36 -10000 0 -0.68 211 211
CDC42 -0.22 0.22 -10000 0 -0.52 99 99
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.5 0.5 -10000 0 -1 172 172
PCK1 -0.33 0.47 -10000 0 -1.4 55 55
HNF4A -0.65 0.62 -10000 0 -1.2 204 204
KCNJ11 -0.47 0.49 -10000 0 -1 152 152
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 -0.47 0.48 -10000 0 -1 153 153
NKX2-1 -0.18 0.19 -10000 0 -10000 0 0
ACADM -0.49 0.5 -10000 0 -0.98 176 176
TAT -0.19 0.2 -10000 0 -0.6 7 7
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 0.59 5 -0.72 27 32
PKLR -0.49 0.5 -10000 0 -1 165 165
APOA1 -0.9 0.85 -10000 0 -1.7 208 208
CPT1C -0.5 0.5 -10000 0 -1 166 166
ALAS1 -0.17 0.2 -10000 0 -0.91 2 2
TFRC -0.24 0.26 -10000 0 -0.71 30 30
FOXF1 0.014 0.071 -10000 0 -0.69 4 4
NF1 0.031 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 -0.95 194 194
HMGCS1 -0.5 0.5 -10000 0 -0.98 179 179
NR3C1 0.032 0.009 -10000 0 -10000 0 0
CPT1B -0.5 0.49 -10000 0 -0.96 190 190
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.026 0.006 -10000 0 -10000 0 0
GCK -0.62 0.64 -10000 0 -1.2 195 195
CREB1 0.005 0.07 -10000 0 -0.25 15 15
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 -0.96 191 191
ALDOB -0.47 0.49 -10000 0 -1 146 146
AFP -0.02 0.088 -10000 0 -0.39 1 1
BDH1 -0.5 0.5 -10000 0 -1 158 158
HADH -0.47 0.49 -10000 0 -1 149 149
F2 -0.61 0.59 -10000 0 -1.2 191 191
HNF1A 0.026 0.036 -10000 0 -0.69 1 1
G6PC -0.003 0.07 -10000 0 -10000 0 0
SLC2A2 -0.23 0.25 -10000 0 -1 3 3
INS -0.022 0.013 -10000 0 -10000 0 0
FOXA1 -0.014 0.097 -10000 0 -0.32 27 27
FOXA3 -0.03 0.12 -10000 0 -0.37 19 19
FOXA2 -0.53 0.55 -10000 0 -1.1 172 172
ABCC8 -0.73 0.67 -10000 0 -1.3 214 214
ALB -0.067 0.28 -10000 0 -1.1 27 27
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.21 0.33 -10000 0 -0.7 123 123
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.51 124 124
positive regulation of JUN kinase activity -0.077 0.2 -10000 0 -0.4 112 112
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.25 -10000 0 -0.52 123 123
AP1 -0.41 0.55 -10000 0 -1.2 110 110
mol:IP3 -0.16 0.25 -10000 0 -0.53 122 122
PLCG1 -0.16 0.25 -10000 0 -0.54 122 122
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.52 123 123
RAPGEF1 0.025 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 -0.012 0.02 -10000 0 -10000 0 0
CAV1 0.012 0.099 -10000 0 -0.69 8 8
SHC/Grb2/SOS1 -0.077 0.21 -10000 0 -0.4 112 112
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 85 85
oligodendrocyte development -0.14 0.25 -10000 0 -0.52 123 123
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.25 -10000 0 -0.53 122 122
PDGF/PDGFRA -0.2 0.33 -10000 0 -0.7 123 123
actin cytoskeleton reorganization -0.14 0.25 -10000 0 -0.51 123 123
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K -0.098 0.22 -10000 0 -0.44 121 121
PDGF/PDGFRA/Crk/C3G -0.099 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 0.027 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 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.077 0.2 -10000 0 -0.4 112 112
PDGF/PDGFRA/SHB -0.14 0.25 -10000 0 -0.52 123 123
PDGF/PDGFRA/Caveolin-1 -0.15 0.26 -10000 0 -0.52 126 126
ITGAV 0.025 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 -0.5 123 123
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
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.14 0.22 -10000 0 -0.41 158 158
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.3 162 162
GNAO1 0.006 0.12 -10000 0 -0.69 11 11
HRAS 0.025 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 -0.15 0.2 0.46 3 -0.38 159 162
T-DHT/AR -0.2 0.26 -10000 0 -0.51 167 167
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 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.21 0.26 -10000 0 -0.53 163 163
cell proliferation -0.2 0.26 0.5 9 -0.52 116 125
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
FOS -0.26 0.37 0.52 7 -0.84 108 115
mol:Ca2+ -0.026 0.029 -10000 0 -0.066 84 84
MAPK3 -0.16 0.24 0.53 10 -0.54 64 74
MAPK1 -0.17 0.22 0.33 5 -0.42 139 144
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 0.027 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 -0.39 159 159
actin cytoskeleton reorganization 0.038 0.024 -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 0.52 123 -0.47 6 129
T-DHT/AR/PELP1 -0.16 0.24 -10000 0 -0.45 164 164
HRAS/GDP -0.2 0.26 -10000 0 -0.51 163 163
CREB1 -0.21 0.27 0.48 6 -0.56 123 129
RAC1-CDC42/GTP 0.048 0.026 -10000 0 -0.38 1 1
AR -0.26 0.35 -10000 0 -0.68 167 167
GNB1 0.026 0.005 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.55 5 -0.38 159 164
RAC1-CDC42/GDP -0.17 0.26 -10000 0 -0.49 162 162
T-DHT/AR/PELP1/Src -0.14 0.23 -10000 0 -0.42 159 159
MAP2K2 -0.15 0.2 0.5 3 -0.38 157 160
T-DHT/AR/PELP1/Src/PI3K -0.11 0.16 -10000 0 -0.3 162 162
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.011 0.099 -10000 0 -0.69 8 8
Gi family/GNB1/GNG2/GDP -0.031 0.097 -10000 0 -0.46 12 12
mol:T-DHT -0.001 0.003 0.001 44 -0.005 60 104
RAC1 0.026 0.006 -10000 0 -10000 0 0
GNRH1 0.007 0.026 -10000 0 -0.52 1 1
Gi family/GTP -0.086 0.11 -10000 0 -0.3 38 38
CDC42 0.026 0.005 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.092 0.21 -10000 0 -0.63 23 23
IHH -0.17 0.32 -10000 0 -0.72 105 105
SHH Np/Cholesterol/GAS1 -0.057 0.16 -10000 0 -0.4 70 70
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.056 0.16 0.4 70 -10000 0 70
SMO/beta Arrestin2 -0.081 0.21 -10000 0 -0.54 11 11
SMO -0.1 0.21 -10000 0 -0.45 92 92
AKT1 -0.016 0.099 -10000 0 -0.34 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.015 0.093 -10000 0 -0.69 7 7
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.099 0.21 -10000 0 -0.44 96 96
STIL -0.071 0.16 -10000 0 -0.47 11 11
DHH N/PTCH2 -0.052 0.21 -10000 0 -0.52 66 66
DHH N/PTCH1 -0.082 0.19 -10000 0 -0.38 102 102
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
DHH 0.021 0.061 -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 96 96
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 -0.3 0.34 -10000 0 -0.6 216 216
DHH N/Hhip -0.18 0.27 -10000 0 -0.52 155 155
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.099 0.21 -10000 0 -0.44 96 96
pancreas development -0.25 0.34 -10000 0 -0.68 155 155
HHAT 0.024 0.036 -10000 0 -0.69 1 1
PI3K 0.038 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 96 96
SHH Np/Cholesterol/PTCH1 -0.075 0.16 -10000 0 -0.51 10 10
SHH Np/Cholesterol/PTCH2 -0.045 0.15 -10000 0 -0.39 65 65
SHH Np/Cholesterol/Megalin -0.078 0.18 -10000 0 -0.39 97 97
SHH -0.005 0.031 -10000 0 -0.52 1 1
catabolic process -0.1 0.21 -10000 0 -0.42 108 108
SMO/Vitamin D3 -0.08 0.19 -10000 0 -0.55 9 9
SHH Np/Cholesterol/Hhip -0.14 0.21 -10000 0 -0.4 154 154
LRP2 -0.15 0.3 -10000 0 -0.68 100 100
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.6 33 33
SHH Np/Cholesterol/BOC 0.013 0.059 -10000 0 -0.38 8 8
SHH Np/Cholesterol/CDO -0.097 0.19 -10000 0 -0.39 117 117
mesenchymal cell differentiation 0.14 0.2 0.4 154 -10000 0 154
mol:Vitamin D3 -0.07 0.17 -10000 0 -0.51 10 10
IHH N/PTCH2 -0.18 0.3 -10000 0 -0.55 150 150
CDON -0.18 0.32 -10000 0 -0.69 117 117
IHH N/PTCH1 -0.097 0.21 -10000 0 -0.43 108 108
Megalin/LRPAP1 -0.096 0.24 -10000 0 -0.51 100 100
PTCH2 -0.087 0.26 -10000 0 -0.68 65 65
SHH Np/Cholesterol 0.009 0.025 -10000 0 -0.41 1 1
PTCH1 -0.1 0.21 -10000 0 -0.42 108 108
HHIP -0.25 0.34 -10000 0 -0.68 155 155
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 0.005 0.12 -10000 0 -0.66 12 12
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.31 0.24 -10000 0 -0.46 284 284
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.29 0.21 -10000 0 -0.43 276 276
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 0.007 0.022 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.078 0.25 -10000 0 -0.69 60 60
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.018 0.11 -10000 0 -0.52 15 15
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.005 -10000 0 -10000 0 0
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.004 -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 -0.46 286 286
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.22 0.19 0.46 2 -0.55 17 19
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.25 0.2 -10000 0 -0.38 270 270
RELN -0.48 0.32 -10000 0 -0.69 283 283
PAFAH/LIS1 -0.039 0.17 -10000 0 -0.44 60 60
LIS1/CLIP170 0.03 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.49 12 12
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.16 -10000 0 -0.3 272 272
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.24 0.19 0.64 1 -0.36 268 269
LIS1/IQGAP1 0.031 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 0.025 0.012 -10000 0 -10000 0 0
PAFAH1B2 0.023 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 -0.56 15 16
LRP8 0 0.14 -10000 0 -0.69 15 15
NDEL1/Katanin 60 -0.22 0.18 0.29 3 -0.55 17 20
P39/CDK5 -0.26 0.2 -10000 0 -0.39 275 275
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.2 -10000 0 -0.4 276 276
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 -0.4 271 271
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 281 281
CDC42 0.016 0.006 -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 0.098 0.24 0.54 92 -10000 0 92
KIRREL -0.036 0.18 -10000 0 -0.7 27 27
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.099 0.24 -10000 0 -0.54 92 92
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.053 0.2 -10000 0 -0.43 86 86
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.054 0.15 -10000 0 -0.34 84 84
FYN -0.063 0.19 0.27 19 -0.4 86 105
mol:Ca2+ -0.054 0.2 -10000 0 -0.43 85 85
mol:DAG -0.054 0.2 -10000 0 -0.43 85 85
NPHS2 -0.003 0.042 -10000 0 -10000 0 0
mol:IP3 -0.054 0.2 -10000 0 -0.43 85 85
regulation of endocytosis -0.049 0.18 -10000 0 -0.38 85 85
Nephrin/NEPH1/podocin/Cholesterol -0.065 0.19 -10000 0 -0.43 87 87
establishment of cell polarity -0.098 0.24 -10000 0 -0.54 92 92
Nephrin/NEPH1/podocin/NCK1-2 -0.037 0.19 -10000 0 -0.4 86 86
Nephrin/NEPH1/beta Arrestin2 -0.048 0.18 -10000 0 -0.39 85 85
NPHS1 -0.11 0.27 -10000 0 -0.69 70 70
Nephrin/NEPH1/podocin -0.058 0.19 -10000 0 -0.41 86 86
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.053 0.2 -10000 0 -0.43 85 85
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.054 0.2 -10000 0 -0.43 84 84
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.076 0.19 0.28 17 -0.41 87 104
cytoskeleton organization -0.08 0.2 -10000 0 -0.45 84 84
Nephrin/NEPH1 -0.07 0.18 -10000 0 -0.4 92 92
Nephrin/NEPH1/ZO-1 -0.067 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 -0.009 0.064 -9999 0 -0.46 6 6
NFATC2 -0.069 0.16 -9999 0 -0.46 58 58
NFATC3 -0.002 0.031 -9999 0 -10000 0 0
CD40LG -0.33 0.37 -9999 0 -0.76 148 148
PTGS2 -0.31 0.36 -9999 0 -0.75 134 134
JUNB 0.02 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 0.017 0.021 -9999 0 -10000 0 0
JUN -0.14 0.29 -9999 0 -0.69 86 86
mol:Ca2+ -0.008 0.019 -9999 0 -0.16 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -9999 0 -10000 0 0
FOSL1 0.004 0.054 -9999 0 -10000 0 0
CREM 0.027 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.24 -9999 0 -0.47 128 128
FOS -0.16 0.31 -9999 0 -0.69 103 103
IFNG -0.33 0.36 -9999 0 -0.74 152 152
AP-1/NFAT1-c-4 -0.35 0.45 -9999 0 -0.86 142 142
FASLG -0.31 0.35 -9999 0 -0.73 136 136
NFAT1-c-4/ICER1 -0.07 0.17 -9999 0 -0.42 62 62
IL2RA -0.31 0.34 -9999 0 -0.72 137 137
FKBP12/FK506 0.02 0.004 -9999 0 -10000 0 0
CSF2 -0.32 0.32 -9999 0 -0.7 139 139
JunB/Fra1/NFAT1-c-4 -0.061 0.17 -9999 0 -0.41 61 61
IL4 -0.3 0.32 -9999 0 -0.69 133 133
IL2 -0.001 0.086 -9999 0 -0.95 3 3
IL3 -0.009 0.057 -9999 0 -0.93 1 1
FKBP1A 0.027 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
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.028 -9999 0 -0.45 1 1
fibroblast growth factor receptor signaling pathway 0.051 0.028 -9999 0 -0.45 1 1
LAMA1 -0.026 0.18 -9999 0 -0.68 30 30
PRNP 0.027 0.005 -9999 0 -10000 0 0
GPC1/SLIT2 -0.04 0.19 -9999 0 -0.51 58 58
SMAD2 0.017 0.03 -9999 0 -0.41 1 1
GPC1/PrPc/Cu2+ 0.035 0.01 -9999 0 -10000 0 0
GPC1/Laminin alpha1 -0.002 0.14 -9999 0 -0.51 30 30
TDGF1 -0.27 0.35 -9999 0 -0.68 169 169
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.52 169 169
APP/GPC1 0.038 0.012 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.23 -9999 0 -0.45 167 167
FLT1 0.026 0.007 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.049 0.031 -9999 0 -0.45 1 1
SERPINC1 0.022 0.015 -9999 0 -10000 0 0
FYN -0.17 0.23 -9999 0 -0.45 167 167
FGR -0.17 0.23 -9999 0 -0.44 167 167
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.52 166 166
SLIT2 -0.075 0.25 -9999 0 -0.68 58 58
GPC1/NRG -0.016 0.16 -9999 0 -0.51 40 40
NRG1 -0.043 0.21 -9999 0 -0.68 40 40
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.039 -9999 0 -0.45 2 2
LYN -0.17 0.23 -9999 0 -0.45 167 167
mol:Spermine 0.008 0.005 -9999 0 -10000 0 0
cell growth 0.051 0.028 -9999 0 -0.45 1 1
BMP signaling pathway -0.026 0.009 -9999 0 -10000 0 0
SRC -0.17 0.23 -9999 0 -0.45 167 167
TGFBR1 0.021 0.026 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.19 0.31 -9999 0 -0.69 111 111
GPC1 0.026 0.009 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.021 0.026 -9999 0 -10000 0 0
VEGFA 0.024 0.05 -9999 0 -0.69 2 2
BLK -0.3 0.31 -9999 0 -0.55 229 229
HCK -0.18 0.23 -9999 0 -0.45 167 167
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.025 0.036 -9999 0 -0.69 1 1
VEGFR1 homodimer 0.026 0.007 -9999 0 -10000 0 0
TGFBR2 0.025 0.036 -9999 0 -0.69 1 1
cell death 0.038 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.036 0.015 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.13 0.24 -9999 0 -0.52 111 111
LCK -0.18 0.23 -9999 0 -0.44 172 172
neuron differentiation -0.016 0.16 -9999 0 -0.51 40 40
PrPc/Cu2+ 0.02 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
Endothelins

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
AKT1 -0.033 0.094 -10000 0 -0.45 8 8
PTK2B 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.46 1 -0.67 62 63
EDN1 -0.007 0.1 -10000 0 -0.6 7 7
EDN3 -0.32 0.36 -10000 0 -0.69 199 199
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 -0.36 63 63
ADCY4 -0.071 0.15 0.35 1 -0.42 51 52
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 -0.069 0.15 0.35 1 -0.42 51 52
ADCY1 -0.072 0.15 0.35 1 -0.43 50 51
ADCY2 -0.1 0.18 -10000 0 -0.46 72 72
ADCY3 -0.07 0.15 0.35 1 -0.42 53 54
ADCY8 -0.1 0.16 0.35 1 -0.45 53 54
ADCY9 -0.069 0.15 0.35 1 -0.42 51 52
arachidonic acid secretion -0.19 0.31 0.45 4 -0.61 122 126
ETB receptor/Endothelin-1/Gq/GTP -0.081 0.18 -10000 0 -0.37 94 94
GNAO1 0.006 0.12 -10000 0 -0.69 11 11
HRAS 0.025 0.012 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.028 0.11 -10000 0 -0.4 7 7
ETA receptor/Endothelin-1/Gs/GTP -0.027 0.18 -10000 0 -0.44 54 54
mol:GTP -0.004 0.009 -10000 0 -10000 0 0
COL3A1 -0.039 0.1 -10000 0 -0.48 8 8
EDNRB 0.017 0.072 -10000 0 -0.69 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.074 0.15 -10000 0 -0.62 21 21
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 0.44 3 -0.51 76 79
SLC9A3 -0.051 0.2 -10000 0 -0.7 25 25
RAF1 -0.17 0.28 0.51 2 -0.54 112 114
JUN -0.29 0.49 0.45 1 -1.1 103 104
JAK2 -0.033 0.096 -10000 0 -0.47 9 9
mol:IP3 -0.1 0.2 -10000 0 -0.42 96 96
ETA receptor/Endothelin-1 0.009 0.13 -10000 0 -0.53 10 10
PLCB1 0.021 0.051 -10000 0 -0.69 2 2
PLCB2 0.02 0.023 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.25 0.28 -10000 0 -0.53 200 200
FOS -0.28 0.44 0.61 2 -1 106 108
Gai/GDP -0.009 0.14 -10000 0 -0.64 18 18
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.18 -10000 0 -0.49 43 43
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.19 -10000 0 -0.43 84 84
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.057 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 -0.39 82 82
MAPK14 -0.069 0.15 -10000 0 -0.37 47 47
TRPC6 -0.16 0.3 0.46 1 -0.71 62 63
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.07 0.16 -10000 0 -0.36 65 65
ETB receptor/Endothelin-2 0.022 0.081 -10000 0 -0.52 8 8
ETB receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.52 201 201
ETB receptor/Endothelin-1 0.014 0.097 -10000 0 -0.53 9 9
MAPK3 -0.24 0.4 0.41 4 -0.87 107 111
MAPK1 -0.29 0.44 0.63 2 -0.96 112 114
Rac1/GDP -0.11 0.21 -10000 0 -0.5 66 66
cAMP biosynthetic process -0.077 0.19 0.49 8 -0.46 52 60
MAPK8 -0.18 0.34 0.48 1 -0.76 74 75
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.002 0.074 -10000 0 -0.38 6 6
p130Cas/CRK/Src/PYK2 -0.16 0.28 0.45 5 -0.55 109 114
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.21 -10000 0 -0.5 66 66
COL1A2 -0.008 0.096 -10000 0 -0.5 5 5
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.014 0.082 -10000 0 -0.55 5 5
mol:DAG -0.1 0.2 -10000 0 -0.42 96 96
MAP2K2 -0.2 0.33 0.39 7 -0.67 111 118
MAP2K1 -0.21 0.34 0.5 2 -0.69 114 116
EDNRA -0.001 0.074 -10000 0 -0.39 4 4
positive regulation of muscle contraction -0.026 0.078 -10000 0 -0.4 5 5
Gq family/GDP -0.14 0.28 0.38 2 -0.56 101 103
HRAS/GTP -0.14 0.24 0.66 1 -0.51 86 87
PRKCH -0.11 0.19 -10000 0 -0.45 75 75
RAC1 0.026 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 -0.44 77 77
PRKCE -0.11 0.2 -10000 0 -0.45 78 78
PRKCD -0.11 0.19 -10000 0 -0.45 76 76
PRKCG -0.1 0.19 -10000 0 -0.46 69 69
regulation of vascular smooth muscle contraction -0.32 0.52 0.64 2 -1.2 106 108
PRKCQ -0.11 0.2 -10000 0 -0.46 73 73
PLA2G4A -0.22 0.35 0.46 4 -0.69 120 124
GNA14 -0.14 0.29 -10000 0 -0.66 92 92
GNA15 0.007 0.053 -10000 0 -0.69 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA11 0.012 0.072 -10000 0 -0.69 4 4
Rac1/GTP 0.028 0.11 -10000 0 -0.41 6 6
MMP1 -0.035 0.081 0.63 2 -10000 0 2
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 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.094 0.18 -10000 0 -0.37 116 116
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.012 -10000 0 -10000 0 0
IRS1/Crk -0.085 0.19 -10000 0 -0.37 112 112
IGF-1R heterotetramer/IGF1/PTP1B -0.059 0.2 -10000 0 -0.44 83 83
AKT1 -0.083 0.16 -10000 0 -0.36 80 80
BAD -0.081 0.15 -10000 0 -0.34 79 79
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.091 0.18 -10000 0 -0.37 112 112
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.082 0.19 -10000 0 -0.38 115 115
RAF1 -0.062 0.15 0.39 1 -0.55 11 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.056 0.19 -10000 0 -0.36 111 111
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.09 0.21 -10000 0 -0.4 117 117
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
RPS6KB1 -0.083 0.16 -10000 0 -0.36 79 79
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.052 0.14 0.33 4 -0.47 10 14
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 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.067 0.16 -10000 0 -0.36 77 77
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.024 0.17 -10000 0 -0.35 77 77
IGF-1R heterotetramer -0.006 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.071 0.2 -10000 0 -0.37 116 116
Crk/p130 Cas/Paxillin -0.051 0.19 -10000 0 -0.34 112 112
IGF1R -0.007 0.058 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.71 83 83
IRS2/Crk -0.08 0.18 -10000 0 -0.36 112 112
PI3K -0.057 0.2 -10000 0 -0.36 115 115
apoptosis 0.058 0.14 0.5 10 -0.32 2 12
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.085 0.19 -10000 0 -0.46 82 82
RAF1/14-3-3 E -0.039 0.14 0.34 2 -0.47 11 13
BAD/14-3-3 -0.061 0.15 0.39 2 -0.54 10 12
PRKCZ -0.082 0.16 0.25 1 -0.36 80 81
Crk/p130 Cas/Paxillin/FAK1 -0.052 0.16 -10000 0 -0.54 10 10
PTPN1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.089 0.2 -10000 0 -0.48 83 83
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.038 0.18 -10000 0 -0.38 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.081 0.19 -10000 0 -0.37 115 115
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.092 0.18 -10000 0 -0.37 115 115
IRS1 -0.1 0.2 -10000 0 -0.4 117 117
IRS2 -0.093 0.18 -10000 0 -0.37 116 116
IGF-1R heterotetramer/IGF1 -0.093 0.24 -10000 0 -0.55 83 83
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.083 0.18 -10000 0 -0.38 81 81
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKD1 -0.085 0.19 -10000 0 -0.46 82 82
SHC1 0.025 0.007 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.2 0.36 0.61 4 -0.85 45 49
HDAC7 0.027 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.25 0.41 -10000 0 -0.84 87 87
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.2 0.36 0.62 3 -0.85 45 48
AP1 -0.19 0.38 -10000 0 -0.74 121 121
ABCG2 -0.21 0.36 0.61 1 -0.85 47 48
HIF1A -0.022 0.072 -10000 0 -10000 0 0
TFF3 -0.5 0.44 0.62 3 -0.92 151 154
GATA2 0.027 0.011 -10000 0 -10000 0 0
AKT1 -0.058 0.11 -10000 0 -0.28 9 9
response to hypoxia -0.072 0.11 -10000 0 -0.24 77 77
MCL1 -0.2 0.35 0.61 3 -0.87 40 43
NDRG1 -0.2 0.35 0.61 1 -0.87 40 41
SERPINE1 -0.21 0.35 0.61 1 -0.86 43 44
FECH -0.2 0.36 0.61 4 -0.86 42 46
FURIN -0.2 0.36 0.61 4 -0.85 45 49
NCOA2 -0.025 0.19 -10000 0 -0.69 30 30
EP300 -0.11 0.19 -10000 0 -0.35 129 129
HMOX1 -0.22 0.34 0.62 2 -0.87 41 43
BHLHE40 -0.21 0.36 0.62 2 -0.86 44 46
BHLHE41 -0.21 0.35 0.61 1 -0.86 43 44
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.027 0.1 -10000 0 -10000 0 0
ENG 0.011 0.096 0.46 4 -10000 0 4
JUN -0.12 0.29 -10000 0 -0.68 86 86
RORA -0.2 0.36 0.61 4 -0.86 45 49
ABCB1 -0.05 0.15 -10000 0 -1.2 5 5
TFRC -0.2 0.36 0.62 2 -0.85 45 47
CXCR4 -0.2 0.36 0.62 3 -0.85 45 48
TF -0.25 0.42 0.62 2 -0.96 71 73
CITED2 -0.23 0.4 0.61 3 -0.91 60 63
HIF1A/ARNT -0.23 0.39 -10000 0 -0.94 45 45
LDHA -0.035 0.11 -10000 0 -0.7 6 6
ETS1 -0.2 0.36 0.62 3 -0.85 45 48
PGK1 -0.2 0.35 0.61 1 -0.85 43 44
NOS2 -0.21 0.36 0.62 2 -0.85 46 48
ITGB2 -0.21 0.36 0.62 3 -0.86 45 48
ALDOA -0.2 0.35 0.61 1 -0.85 44 45
Cbp/p300/CITED2 -0.32 0.47 -10000 0 -0.98 100 100
FOS -0.15 0.31 -10000 0 -0.68 103 103
HK2 -0.21 0.36 0.62 3 -0.85 47 50
SP1 0.032 0.015 -10000 0 -10000 0 0
GCK -0.42 0.65 -10000 0 -1.4 117 117
HK1 -0.2 0.36 0.62 3 -0.85 45 48
NPM1 -0.2 0.35 0.61 1 -0.86 41 42
EGLN1 -0.2 0.35 0.61 3 -0.88 38 41
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.2 0.36 0.61 3 -0.86 42 45
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.2 0.3 0.49 1 -0.73 55 56
IGFBP1 -0.21 0.35 0.61 1 -0.86 42 43
VEGFA -0.21 0.35 -10000 0 -0.73 79 79
HIF1A/JAB1 0.002 0.058 -10000 0 -10000 0 0
CP -0.34 0.47 0.62 2 -0.95 114 116
CXCL12 -0.24 0.41 0.62 3 -0.95 63 66
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.008 -10000 0 -10000 0 0
BNIP3 -0.2 0.36 0.62 3 -0.86 43 46
EGLN3 -0.22 0.36 -10000 0 -0.87 48 48
CA9 -0.21 0.36 0.61 1 -0.86 45 46
TERT -0.21 0.35 0.6 1 -0.85 44 45
ENO1 -0.2 0.36 0.61 3 -0.85 44 47
PFKL -0.2 0.36 0.62 3 -0.86 43 46
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.21 0.36 0.62 3 -0.84 50 53
ARNT -0.016 0.071 -10000 0 -0.33 1 1
HNF4A -0.016 0.058 -10000 0 -0.22 3 3
ADFP -0.22 0.34 -10000 0 -0.83 49 49
SLC2A1 -0.21 0.35 -10000 0 -0.74 72 72
LEP -0.21 0.35 0.61 1 -0.86 44 45
HIF1A/ARNT/Cbp/p300 -0.27 0.41 -10000 0 -0.85 95 95
EPO -0.14 0.26 -10000 0 -0.88 13 13
CREBBP -0.086 0.17 -10000 0 -0.33 114 114
HIF1A/ARNT/Cbp/p300/HDAC7 -0.24 0.41 -10000 0 -0.84 84 84
PFKFB3 -0.21 0.36 0.62 3 -0.86 43 46
NT5E -0.21 0.36 0.61 3 -0.86 45 48
IL23-mediated signaling events

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
CCL2 -0.2 0.54 -10000 0 -1.2 70 70
IL23A -0.21 0.55 -10000 0 -1.3 74 74
NF kappa B1 p50/RelA/I kappa B alpha -0.18 0.54 -10000 0 -1.2 74 74
positive regulation of T cell mediated cytotoxicity -0.24 0.62 -10000 0 -1.3 79 79
ITGA3 -0.18 0.51 -10000 0 -1.2 66 66
IL17F -0.1 0.33 0.69 2 -0.73 65 67
IL12B 0.004 0.087 -10000 0 -0.71 4 4
STAT1 (dimer) -0.22 0.58 -10000 0 -1.3 78 78
CD4 -0.18 0.49 -10000 0 -1.2 65 65
IL23 -0.2 0.53 -10000 0 -1.2 74 74
IL23R 0.001 0.11 -10000 0 -0.79 3 3
IL1B -0.22 0.57 -10000 0 -1.4 67 67
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.5 -10000 0 -1.2 66 66
TYK2 0.015 0.035 -10000 0 -10000 0 0
STAT4 0.001 0.1 -10000 0 -0.59 10 10
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.012 0.15 -10000 0 -0.69 18 18
IL12RB1 -0.001 0.074 -10000 0 -0.62 3 3
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
IL12Rbeta1/TYK2 0.015 0.067 -10000 0 -0.48 3 3
IL23R/JAK2 0.008 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 0.027 0.006 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.18 0.5 -10000 0 -1.1 74 74
ALOX12B -0.18 0.5 -10000 0 -1.2 65 65
CXCL1 -0.2 0.52 -10000 0 -1.2 69 69
T cell proliferation -0.24 0.62 -10000 0 -1.3 79 79
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.06 0.27 -10000 0 -0.55 65 65
PI3K -0.2 0.55 -10000 0 -1.2 74 74
IFNG -0.015 0.054 0.16 2 -0.13 57 59
STAT3 (dimer) -0.18 0.51 -10000 0 -1.2 71 71
IL18R1 -0.003 0.095 -10000 0 -0.58 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.35 -10000 0 -0.82 56 56
IL18/IL18R -0.002 0.15 -10000 0 -0.48 30 30
macrophage activation -0.009 0.021 -10000 0 -0.045 68 68
TNF -0.25 0.6 -10000 0 -1.4 81 81
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 -0.009 0.11 -10000 0 -0.66 9 9
IL19 -0.18 0.5 -10000 0 -1.2 65 65
STAT5A (dimer) -0.22 0.58 -10000 0 -1.3 77 77
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.024 0.18 -10000 0 -0.69 28 28
CXCL9 -0.26 0.61 -10000 0 -1.3 87 87
MPO -0.19 0.51 -10000 0 -1.1 73 73
positive regulation of humoral immune response -0.24 0.62 -10000 0 -1.3 79 79
IL23/IL23R/JAK2/TYK2 -0.28 0.76 -10000 0 -1.6 79 79
IL6 -0.3 0.64 -10000 0 -1.3 105 105
STAT5A 0.026 0.007 -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 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
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 -0.12 0.22 -10000 0 -0.41 152 152
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.39 155 155
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.24 -10000 0 -0.43 159 159
DNM1 -0.003 0.13 -10000 0 -0.63 17 17
cell-cell signaling -0.001 0.004 -10000 0 -10000 0 0
MAP2K4 0.001 0.071 0.41 1 -0.57 4 5
YES1 0.01 0.074 -10000 0 -0.84 3 3
Ephrin B1/EPHB1-2/NCK2 -0.13 0.22 -10000 0 -0.4 155 155
PI3K 0.03 0.072 -10000 0 -0.74 3 3
mol:GDP -0.13 0.24 -10000 0 -0.42 159 159
ITGA2B -0.051 0.22 -10000 0 -0.68 44 44
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN 0.009 0.08 -10000 0 -0.79 4 4
MAP3K7 -0.006 0.062 -10000 0 -0.6 4 4
FGR 0.007 0.08 -10000 0 -0.78 4 4
TIAM1 -0.057 0.08 -10000 0 -0.69 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.029 0.16 -10000 0 -0.46 29 29
LYN 0.009 0.081 -10000 0 -0.8 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.001 0.075 -10000 0 -0.74 4 4
Ephrin B1/EPHB1-2 -0.005 0.062 -10000 0 -0.71 3 3
SRC 0.007 0.08 -10000 0 -0.78 4 4
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
EPHB1 -0.24 0.34 -10000 0 -0.68 153 153
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.035 0.2 -10000 0 -0.54 51 51
BLK -0.044 0.12 -10000 0 -0.83 4 4
HCK 0.008 0.08 -10000 0 -0.78 4 4
regulation of stress fiber formation 0.13 0.22 0.39 155 -10000 0 155
MAPK8 0.002 0.094 0.37 4 -0.71 4 8
Ephrin B1/EPHB1-2/RGS3 -0.13 0.22 -10000 0 -0.4 155 155
endothelial cell migration -0.002 0.059 0.41 1 -0.56 3 4
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.03 0.059 -10000 0 -0.8 2 2
regulation of focal adhesion formation 0.13 0.22 0.39 155 -10000 0 155
chemotaxis 0.13 0.22 0.39 155 -10000 0 155
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
Rac1/GTP -0.12 0.22 -10000 0 -0.4 155 155
angiogenesis -0.006 0.066 -10000 0 -0.64 4 4
LCK 0.006 0.085 -10000 0 -0.82 4 4
EPHB forward 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
Ephrin A5/EPHB2 -0.042 0.18 -10000 0 -0.45 64 64
cell-cell adhesion 0.11 0.16 0.33 140 -10000 0 140
Ephrin B/EPHB2/RasGAP 0.066 0.058 -10000 0 -0.39 5 5
ITSN1 0.026 0.006 -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 -0.026 0.046 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.23 -10000 0 -0.44 152 152
HRAS/GDP -0.082 0.17 -10000 0 -0.33 41 41
Ephrin B/EPHB1/GRB7 -0.1 0.23 -10000 0 -0.41 144 144
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 -0.099 0.22 -10000 0 -0.4 145 145
endothelial cell migration 0.053 0.028 -10000 0 -0.39 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.004 0.053 -10000 0 -10000 0 0
PAK1 0.025 0.077 0.46 5 -0.36 5 10
HRAS 0.026 0.012 -10000 0 -10000 0 0
RRAS 0.022 0.069 0.42 5 -0.37 4 9
DNM1 -0.002 0.13 -10000 0 -0.63 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.13 0.19 -10000 0 -0.38 145 145
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 -0.3 135 135
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.021 0.061 -10000 0 -0.69 3 3
EPHB3 -0.066 0.073 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.68 153 153
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.074 0.14 -10000 0 -0.4 9 9
Ephrin B/EPHB2 0.052 0.054 -10000 0 -0.39 5 5
Ephrin B/EPHB3 0.065 0.046 -10000 0 -0.44 2 2
JNK cascade -0.13 0.2 -10000 0 -0.39 143 143
Ephrin B/EPHB1 -0.11 0.22 -10000 0 -0.39 146 146
RAP1/GDP -0.048 0.14 -10000 0 -0.36 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 -0.12 0.22 -10000 0 -0.41 153 153
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.087 0.19 -10000 0 -0.34 141 141
Rap1/GTP -0.1 0.18 -10000 0 -0.34 133 133
axon guidance -0.042 0.18 -10000 0 -0.45 64 64
MAPK3 -0.083 0.14 -10000 0 -0.48 6 6
MAPK1 -0.082 0.14 -10000 0 -0.46 7 7
Rac1/GDP -0.06 0.14 -10000 0 -0.37 8 8
actin cytoskeleton reorganization -0.082 0.13 -10000 0 -0.32 8 8
CDC42/GDP -0.057 0.14 0.37 1 -0.37 9 10
PI3K 0.058 0.029 -10000 0 -0.39 1 1
EFNA5 -0.083 0.26 -10000 0 -0.69 62 62
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.044 -10000 0 -0.34 5 5
CDC42 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.17 -10000 0 -0.33 137 137
PTK2 0.04 0.085 0.61 7 -10000 0 7
MAP4K4 -0.13 0.2 -10000 0 -0.39 143 143
SRC 0.026 0.009 -10000 0 -10000 0 0
KALRN 0.027 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.078 0.14 0.37 1 -10000 0 1
MAP2K1 -0.084 0.15 -10000 0 -0.41 12 12
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.11 0.23 -10000 0 -0.42 143 143
cell migration -0.085 0.18 0.53 4 -0.46 11 15
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.07 0.44 4 -0.36 5 9
PXN 0.026 0.005 -10000 0 -10000 0 0
TF -0.036 0.14 0.44 2 -0.38 51 53
HRAS/GTP -0.094 0.19 -10000 0 -0.35 141 141
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.4 153 153
cell adhesion mediated by integrin -0.007 0.066 0.39 2 -0.37 6 8
RAC1 0.026 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 -0.38 4 4
ruffle organization -0.11 0.18 0.54 4 -0.4 5 9
NCK1 0.027 0.004 -10000 0 -10000 0 0
receptor internalization -0.001 0.093 0.41 3 -0.38 16 19
Ephrin B/EPHB2/KALRN 0.066 0.058 -10000 0 -0.39 5 5
ROCK1 -0.024 0.045 -10000 0 -10000 0 0
RAS family/GDP -0.075 0.1 -10000 0 -0.33 5 5
Rac1/GTP -0.12 0.18 -10000 0 -0.35 140 140
Ephrin B/EPHB1/Src/Paxillin -0.092 0.16 -10000 0 -0.3 146 146
IL4-mediated signaling events

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.5 0.4 -10000 0 -1.2 56 56
STAT6 (cleaved dimer) -0.52 0.41 -10000 0 -1.1 99 99
IGHG1 -0.18 0.13 -10000 0 -0.4 5 5
IGHG3 -0.49 0.38 -10000 0 -1 90 90
AKT1 -0.27 0.28 0.66 1 -0.88 41 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.99 41 41
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.3 -10000 0 -0.85 53 53
THY1 -0.5 0.4 -10000 0 -1.2 58 58
MYB 0.01 0.1 -10000 0 -0.65 9 9
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.32 -10000 0 -0.9 63 63
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.28 -10000 0 -0.93 37 37
SP1 0.031 0.009 -10000 0 -10000 0 0
INPP5D 0.018 0.035 -10000 0 -10000 0 0
SOCS5 0.04 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.41 -10000 0 -1.1 82 82
SOCS1 -0.35 0.26 -10000 0 -0.73 56 56
SOCS3 -0.34 0.38 0.59 2 -1.2 54 56
FCER2 -0.51 0.42 -10000 0 -1.1 93 93
PARP14 0.027 0.006 -10000 0 -10000 0 0
CCL17 -0.54 0.42 -10000 0 -1.3 62 62
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.21 -10000 0 -0.71 32 32
T cell proliferation -0.5 0.41 -10000 0 -1.2 68 68
IL4R/JAK1 -0.5 0.4 -10000 0 -1.1 67 67
EGR2 -0.82 0.68 -10000 0 -1.6 178 178
JAK2 -0.031 0.034 -10000 0 -10000 0 0
JAK3 -0.009 0.063 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.003 0.022 -10000 0 -10000 0 0
COL1A2 -0.16 0.14 -10000 0 -0.97 2 2
CCL26 -0.5 0.4 -10000 0 -1.2 63 63
IL4R -0.53 0.42 -10000 0 -1.2 66 66
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.61 0.55 -10000 0 -1.5 85 85
IL13RA1 -0.03 0.033 -10000 0 -10000 0 0
IRF4 -0.28 0.47 -10000 0 -1.2 71 71
ARG1 -0.13 0.14 -10000 0 -1.2 2 2
CBL -0.32 0.3 -10000 0 -0.85 60 60
GTF3A 0.026 0.015 -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 -1.1 71 71
CD40LG -0.076 0.24 -10000 0 -0.66 59 59
MAPK14 -0.34 0.34 -10000 0 -0.98 62 62
mitosis -0.26 0.26 0.61 2 -0.81 42 44
STAT6 -0.56 0.48 -10000 0 -1.3 76 76
SPI1 0.023 0.031 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 0.7 3 -0.78 37 40
STAT6 (dimer) -0.57 0.48 -10000 0 -1.3 76 76
STAT6 (dimer)/PARP14 -0.53 0.43 -10000 0 -1.2 73 73
mast cell activation 0.014 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.31 -10000 0 -1 42 42
FRAP1 -0.27 0.28 0.62 2 -0.87 42 44
LTA -0.51 0.4 -10000 0 -1.2 60 60
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.55 0.46 1.2 77 -10000 0 77
CCL11 -0.48 0.38 -10000 0 -1.1 61 61
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.27 0.31 -10000 0 -1 42 42
IL2RG -0.011 0.14 -10000 0 -0.63 18 18
IL10 -0.51 0.42 -10000 0 -1.3 60 60
IRS1 -0.049 0.22 -10000 0 -0.69 43 43
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.091 -10000 0 -10000 0 0
IL5 -0.5 0.4 -10000 0 -1.1 65 65
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.44 0.35 -10000 0 -0.97 70 70
COL1A1 -0.21 0.23 -10000 0 -1 18 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.41 -10000 0 -1.2 55 55
IL2R gamma/JAK3 -0.019 0.12 -10000 0 -0.49 17 17
TFF3 -1.2 0.58 -10000 0 -1.4 326 326
ALOX15 -0.5 0.4 -10000 0 -1.2 61 61
MYBL1 0.026 0.009 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.43 0.35 -10000 0 -0.97 69 69
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.27 -10000 0 -0.94 34 34
mol:PI-3-4-5-P3 -0.27 0.28 0.62 2 -0.88 41 43
PI3K -0.28 0.3 0.67 1 -0.96 41 42
DOK2 0.02 0.055 -10000 0 -0.69 2 2
ETS1 0.039 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.2 -10000 0 -0.7 28 28
ITGB3 -0.52 0.43 -10000 0 -1.3 58 58
PIGR -0.53 0.44 -10000 0 -1.3 67 67
IGHE 0.046 0.046 0.27 6 -10000 0 6
MAPKKK cascade -0.2 0.2 0.58 1 -0.69 28 29
BCL6 0.025 0.036 -10000 0 -0.69 1 1
OPRM1 -0.51 0.4 -10000 0 -1.2 60 60
RETNLB -0.51 0.4 -10000 0 -1.2 58 58
SELP -0.5 0.41 -10000 0 -1.2 58 58
AICDA -0.49 0.38 -10000 0 -1.1 59 59
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.18 0.3 -10000 0 -0.5 179 179
SMAD6-7/SMURF1 0.052 0.014 -10000 0 -10000 0 0
NOG -0.028 0.18 -10000 0 -0.69 29 29
SMAD9 -0.19 0.28 -10000 0 -0.55 141 141
SMAD4 0.027 0.005 -10000 0 -10000 0 0
SMAD5 -0.089 0.17 -10000 0 -0.46 26 26
BMP7/USAG1 -0.25 0.28 -10000 0 -0.52 207 207
SMAD5/SKI -0.073 0.18 0.32 2 -0.44 26 28
SMAD1 -0.038 0.099 -10000 0 -0.53 2 2
BMP2 0.004 0.13 -10000 0 -0.69 13 13
SMAD1/SMAD1/SMAD4 -0.022 0.088 -10000 0 -0.53 1 1
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 -0.002 0.038 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.014 0.12 -10000 0 -0.46 23 23
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.07 0.17 -10000 0 -0.55 24 24
BMP2-4 (homodimer) 0.006 0.13 -10000 0 -0.52 23 23
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.096 0.23 -10000 0 -0.41 137 137
RGMA 0 0.14 -10000 0 -0.67 16 16
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.082 0.16 -10000 0 -0.46 29 29
BMP2-4/USAG1 -0.23 0.26 -10000 0 -0.47 219 219
SMAD6/SMURF1/SMAD5 -0.071 0.17 0.32 1 -0.44 23 24
SOSTDC1 -0.34 0.35 -10000 0 -0.69 207 207
BMP7/BMPR2/BMPR1A-1B -0.095 0.22 -10000 0 -0.41 134 134
SKI 0.026 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.003 -10000 0 -10000 0 0
HFE2 -0.003 0.022 -10000 0 -10000 0 0
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.14 -10000 0 -0.46 30 30
SMAD5/SMAD5/SMAD4 -0.071 0.18 0.3 3 -0.43 26 29
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.056 0.15 -10000 0 -0.43 23 23
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.029 0.028 -10000 0 -10000 0 0
SMAD1/SKI -0.028 0.1 0.33 1 -0.63 1 2
SMAD6 0.027 0.004 -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 23 23
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.67 90 90
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 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 -0.031 0.1 -10000 0 -0.51 2 2
SMAD6-7/SMURF1/SMAD1 -0.013 0.1 -10000 0 -0.59 1 1
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.046 -10000 0 -0.69 1 1
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.25 -10000 0 -0.46 280 280
BMP2-4/GREM1 -0.077 0.24 -10000 0 -0.49 97 97
SMAD7 0.027 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.17 0.27 -10000 0 -0.53 134 134
SMAD1/SMAD6 -0.028 0.1 -10000 0 -0.51 2 2
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 0.027 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 -0.06 0.14 -10000 0 -0.41 26 26
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.028 0.1 0.3 1 -0.51 2 3
SMAD7/SMURF1 0.038 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.004 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.017 0.079 -10000 0 -0.69 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.17 0.26 -10000 0 -0.64 76 76
CHRD 0.013 0.099 -10000 0 -0.69 8 8
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.083 0.16 -10000 0 -0.49 27 27
BMP4 0.006 0.11 -10000 0 -0.66 11 11
FST -0.15 0.3 -10000 0 -0.69 98 98
BMP2-4/NOG -0.013 0.17 -10000 0 -0.46 51 51
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.079 0.22 -10000 0 -0.39 131 131
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 -10000 0 -10000 0 0
SMARCC2 0.026 0.016 -10000 0 -10000 0 0
SMARCC1 0.027 0.016 -10000 0 -10000 0 0
TBX21 -0.13 0.25 -10000 0 -0.7 45 45
SUMO2 0.023 0.019 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.023 -10000 0 -10000 0 0
FKBP4 0.026 0.005 -10000 0 -10000 0 0
FKBP5 0.02 0.071 -10000 0 -0.69 4 4
GR alpha/HSP90/FKBP51/HSP90 0.13 0.11 0.34 43 -0.44 3 46
PRL -0.065 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.2 0.29 0.54 124 -0.48 16 140
RELA -0.032 0.1 -10000 0 -0.23 52 52
FGG 0.17 0.2 0.48 82 -10000 0 82
GR beta/TIF2 0.084 0.19 0.33 62 -0.47 30 92
IFNG -0.36 0.48 -10000 0 -1 114 114
apoptosis -0.013 0.24 0.5 29 -0.55 15 44
CREB1 0.026 0.013 -10000 0 -10000 0 0
histone acetylation -0.08 0.15 -10000 0 -0.41 52 52
BGLAP -0.078 0.13 -10000 0 -0.45 16 16
GR/PKAc 0.12 0.1 0.35 28 -10000 0 28
NF kappa B1 p50/RelA -0.052 0.18 -10000 0 -0.41 51 51
SMARCD1 0.026 0.016 -10000 0 -10000 0 0
MDM2 0.086 0.099 0.24 85 -10000 0 85
GATA3 -0.007 0.16 -10000 0 -0.64 22 22
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.11 0.13 -10000 0 -0.55 14 14
GSK3B 0.024 0.019 -10000 0 -10000 0 0
NR1I3 0.003 0.24 0.53 22 -0.66 6 28
CSN2 0.14 0.16 0.4 72 -10000 0 72
BRG1/BAF155/BAF170/BAF60A 0.065 0.047 -10000 0 -0.32 2 2
NFATC1 0.017 0.087 -10000 0 -0.69 6 6
POU2F1 0.026 0.01 -10000 0 -10000 0 0
CDKN1A 0.025 0.037 -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 -0.085 0.13 -10000 0 -0.69 12 12
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.13 0.13 0.35 43 -0.36 10 53
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.47 26 -0.84 85 111
JUN -0.24 0.26 -10000 0 -0.56 135 135
IL4 -0.1 0.16 -10000 0 -0.64 14 14
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 -0.69 120 120
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.11 0.34 37 -0.4 3 40
cortisol/GR alpha (monomer) 0.26 0.31 0.64 127 -10000 0 127
NCOA2 -0.026 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 -0.38 0.41 -10000 0 -0.78 182 182
AFP -0.17 0.2 -10000 0 -0.62 26 26
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.15 0.5 23 -10000 0 23
TP53 0.041 0.013 -10000 0 -10000 0 0
PPP5C 0.026 0.007 -10000 0 -10000 0 0
KRT17 -0.3 0.35 -10000 0 -0.73 113 113
KRT14 -0.085 0.12 -10000 0 -0.47 8 8
TBP 0.034 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 0.027 0.017 -10000 0 -10000 0 0
MAPK10 0.026 0.017 -10000 0 -10000 0 0
MAPK11 0.017 0.02 -10000 0 -10000 0 0
KRT5 -0.39 0.51 -10000 0 -1 130 130
interleukin-1 receptor activity 0.002 0.003 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.023 -10000 0 -10000 0 0
CGA -0.096 0.14 -10000 0 -0.49 15 15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.089 0.12 0.35 32 -10000 0 32
MAPK3 0.025 0.017 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.6 79 79
NFKB1 -0.03 0.1 -10000 0 -0.31 4 4
MAPK8 -0.14 0.17 -10000 0 -0.43 71 71
MAPK9 0.027 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.019 0.24 0.5 28 -0.58 15 43
BAX 0.035 0.083 0.85 3 -10000 0 3
POMC -0.46 0.64 -10000 0 -1.4 107 107
EP300 0.027 0.038 -10000 0 -0.26 5 5
cortisol/GR alpha (dimer)/p53 0.24 0.25 0.56 119 -10000 0 119
proteasomal ubiquitin-dependent protein catabolic process 0.081 0.13 0.32 70 -10000 0 70
SGK1 0.017 0.2 0.51 1 -1.4 7 8
IL13 -0.22 0.26 -10000 0 -0.75 46 46
IL6 -0.32 0.51 -10000 0 -1.2 100 100
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.19 0.21 -10000 0 -0.61 50 50
IL2 -0.26 0.28 -10000 0 -0.75 60 60
CDK5 0.027 0.009 -10000 0 -10000 0 0
PRKACB 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.28 -10000 0 -0.7 64 64
CDK5R1/CDK5 0.038 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.007 0.14 -10000 0 -0.38 21 21
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 0.15 0.39 77 -0.44 2 79
NF kappa B1 p50/RelA/Cbp -0.014 0.16 -10000 0 -0.41 22 22
JUN (dimer) -0.24 0.26 -10000 0 -0.56 135 135
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.22 0.37 -10000 0 -0.82 93 93
NR3C1 0.16 0.19 0.45 91 -10000 0 91
NR4A1 -0.27 0.37 -10000 0 -0.67 173 173
TIF2/SUV420H1 -0.003 0.15 -10000 0 -0.52 30 30
MAPKKK cascade -0.013 0.24 0.5 29 -0.55 15 44
cortisol/GR alpha (dimer)/Src-1 0.23 0.25 0.56 121 -10000 0 121
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 83 83
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.16 0.39 75 -0.44 2 77
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 115 -10000 0 115
mol:cortisol 0.14 0.19 0.38 126 -10000 0 126
MMP1 -0.098 0.13 -10000 0 -0.82 7 7
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.057 0.25 0.29 14 -0.6 58 72
FYN -0.1 0.32 0.67 2 -0.8 61 63
LAT/GRAP2/SLP76 -0.083 0.26 -10000 0 -0.62 65 65
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.059 0.22 0.55 9 -0.47 64 73
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.016 0.056 0.11 2 -0.16 24 26
MAP3K8 0.016 0.086 -10000 0 -0.69 6 6
mol:Ca2+ -0.03 0.043 0.091 5 -0.11 82 87
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.31 0.72 4 -0.72 68 72
TRPV6 -0.1 0.36 1 17 -0.69 83 100
CD28 -0.015 0.15 -10000 0 -0.65 21 21
SHC1 -0.1 0.32 0.31 16 -0.8 61 77
receptor internalization -0.13 0.35 -10000 0 -0.79 73 73
PRF1 -0.11 0.33 -10000 0 -0.83 59 59
KRAS 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.043 0.18 0.51 6 -0.38 65 71
LAT -0.11 0.32 0.3 3 -0.78 64 67
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.052 0.22 -10000 0 -0.66 44 44
CD3E -0.034 0.19 -10000 0 -0.65 35 35
CD3G -0.098 0.27 -10000 0 -0.66 72 72
RASGRP2 -0.003 0.031 0.093 3 -0.18 8 11
RASGRP1 -0.048 0.23 0.69 8 -0.47 63 71
HLA-A 0.027 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 0.4 22 -0.13 31 53
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.047 0.085 -10000 0 -0.24 49 49
PRKCA -0.04 0.13 -10000 0 -0.29 67 67
GRAP2 -0.019 0.15 -10000 0 -0.56 27 27
mol:IP3 -0.032 0.21 0.27 59 -0.44 61 120
EntrezGene:6957 0 0.005 0.058 1 -10000 0 1
TCR/CD3/MHC I/CD8 -0.13 0.36 -10000 0 -0.86 63 63
ORAI1 0.045 0.21 0.7 2 -0.78 14 16
CSK -0.11 0.32 -10000 0 -0.79 65 65
B7 family/CD28 -0.11 0.35 -10000 0 -0.82 66 66
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.39 -10000 0 -0.9 70 70
PTPN6 -0.12 0.33 0.25 1 -0.81 63 64
VAV1 -0.11 0.31 -10000 0 -0.77 64 64
Monovalent TCR/CD3 -0.12 0.33 -10000 0 -0.64 88 88
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.11 0.34 0.87 1 -0.84 61 62
PAG1 -0.11 0.32 -10000 0 -0.8 64 64
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.39 -10000 0 -0.93 66 66
CD80 -0.051 0.22 -10000 0 -0.68 44 44
CD86 0.012 0.077 -10000 0 -0.7 4 4
PDK1/CARD11/BCL10/MALT1 -0.04 0.11 -10000 0 -0.29 50 50
HRAS 0.026 0.012 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.64 66 66
CD8A -0.022 0.18 -10000 0 -0.66 29 29
CD8B -0.055 0.22 -10000 0 -0.66 46 46
PTPRC -0.01 0.15 -10000 0 -0.69 17 17
PDK1/PKC theta -0.074 0.27 0.66 10 -0.58 65 75
CSK/PAG1 -0.11 0.31 -10000 0 -0.79 61 61
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.039 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.31 -10000 0 -0.74 66 66
STIM1 0.018 0.17 1.2 2 -0.89 8 10
RAS family/GTP 0.012 0.12 0.3 19 -0.19 37 56
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.39 -10000 0 -0.88 73 73
mol:DAG -0.06 0.16 0.15 6 -0.39 64 70
RAP1A/GDP 0.012 0.09 0.32 12 -0.066 7 19
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.006 0.14 -10000 0 -0.7 16 16
cytotoxic T cell degranulation -0.1 0.32 0.44 1 -0.77 61 62
RAP1A/GTP 0 0.011 -10000 0 -0.066 7 7
mol:PI-3-4-5-P3 -0.081 0.25 0.66 6 -0.56 68 74
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.26 0.29 56 -0.58 63 119
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 -0.002 0.13 -10000 0 -0.67 15 15
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.082 0.24 -10000 0 -0.58 65 65
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.025 0.036 -10000 0 -0.69 1 1
CD8 heterodimer -0.057 0.24 -10000 0 -0.59 61 61
CARD11 -0.021 0.11 -10000 0 -0.69 8 8
PRKCB -0.03 0.12 -10000 0 -0.29 57 57
PRKCE -0.029 0.12 -10000 0 -0.28 59 59
PRKCQ -0.093 0.3 0.69 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 0.54 9 -0.39 64 73
IKK complex 0.019 0.15 0.47 18 -0.12 29 47
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.035 0.12 0.22 3 -0.28 60 63
PDPK1 -0.055 0.21 0.59 9 -0.45 63 72
TCR/CD3/MHC I/CD8/Fyn -0.15 0.42 -10000 0 -0.98 70 70
Coregulation of Androgen receptor activity

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
NRIP1 -0.004 0.052 -10000 0 -0.21 5 5
SVIL -0.001 0.047 -10000 0 -10000 0 0
ZNF318 0.074 0.079 0.24 7 -10000 0 7
JMJD2C -0.065 0.066 -10000 0 -0.12 228 228
T-DHT/AR/Ubc9 -0.23 0.24 -10000 0 -0.51 165 165
CARM1 0.023 0.009 -10000 0 -10000 0 0
PRDX1 0.028 0.007 -10000 0 -10000 0 0
PELP1 0.032 0.013 -10000 0 -10000 0 0
CTNNB1 0.003 0.039 -10000 0 -10000 0 0
AKT1 0.038 0.02 -10000 0 -10000 0 0
PTK2B 0.008 0.032 -10000 0 -10000 0 0
MED1 0.036 0.021 -10000 0 -10000 0 0
MAK 0.065 0.11 0.24 8 -0.66 5 13
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.004 0.058 -10000 0 -0.69 1 1
GSN 0.001 0.044 -10000 0 -10000 0 0
NCOA2 -0.029 0.19 -10000 0 -0.69 30 30
NCOA6 0 0.045 -10000 0 -10000 0 0
DNA-PK 0.072 0.076 -10000 0 -10000 0 0
NCOA4 0.025 0.005 -10000 0 -10000 0 0
PIAS3 0.004 0.038 -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 0.063 -10000 0 -0.18 1 1
T-DHT/AR/SNURF -0.24 0.26 -10000 0 -0.53 170 170
FHL2 -0.14 0.34 -10000 0 -1.2 35 35
RANBP9 0 0.045 -10000 0 -10000 0 0
JMJD1A -0.001 0.034 -10000 0 -0.12 27 27
CDK6 0.025 0.036 -10000 0 -0.68 1 1
TGFB1I1 -0.002 0.047 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.25 -10000 0 -0.52 167 167
XRCC6 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.27 -10000 0 -0.54 186 186
CTDSP1 0.013 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 0.003 0.084 -10000 0 -10000 0 0
SRF 0.033 0.051 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.67 9 9
KLK3 -0.37 0.64 -10000 0 -1.4 110 110
TMF1 0.02 0.015 -10000 0 -10000 0 0
HNRNPA1 0.043 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 -0.5 163 163
AR -0.31 0.35 -10000 0 -0.72 167 167
UBA3 0.013 0.023 -10000 0 -10000 0 0
PATZ1 0.032 0.03 -10000 0 -10000 0 0
PAWR 0.02 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 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.23 -10000 0 -0.47 163 163
RPS6KA3 -0.002 0.045 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.52 163 163
LATS2 0.041 0.028 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.19 0.22 -10000 0 -0.46 163 163
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.002 0.078 -10000 0 -0.69 4 4
KLK2 -0.67 0.56 -10000 0 -1.1 232 232
CASP8 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.54 167 167
TMPRSS2 -0.16 0.27 -10000 0 -1.1 27 27
CCND1 0.013 0.031 -10000 0 -10000 0 0
PIAS1 -0.011 0.063 -10000 0 -0.16 4 4
mol:T-DHT -0.032 0.039 -10000 0 -0.076 151 151
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.027 0.089 -10000 0 -0.19 20 20
T-DHT/AR/CDK6 -0.22 0.25 -10000 0 -0.51 165 165
CMTM2 0.028 0.012 -10000 0 -10000 0 0
SNURF -0.003 0.14 -10000 0 -0.65 17 17
ZMIZ1 -0.022 0.048 -10000 0 -10000 0 0
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.043 0.028 -10000 0 -10000 0 0
FKBP4 -0.001 0.045 -10000 0 -10000 0 0
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 0.035 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.016 0.15 -10000 0 -0.71 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 0.015 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.043 0.2 -10000 0 -0.52 59 59
ARRB2 -0.035 0.13 -10000 0 -0.39 48 48
mol:GTP 0.023 0.038 0.18 14 -0.14 1 15
ARRB1 0.025 0.036 -10000 0 -0.69 1 1
FBXO8 0.027 0.005 -10000 0 -10000 0 0
TSHR 0.023 0.05 -10000 0 -0.69 2 2
EGF -0.071 0.24 -10000 0 -0.68 55 55
somatostatin receptor activity 0 0.001 0.002 12 -0.001 116 128
ARAP2 0.025 0.036 -10000 0 -0.69 1 1
mol:GDP -0.11 0.14 0.26 6 -0.3 98 104
mol:PI-3-4-5-P3 0 0 0.002 10 -0.001 59 69
ITGA2B -0.051 0.22 -10000 0 -0.68 44 44
ARF6 0.026 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.024 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.004 -10000 0 -10000 0 0
HGF/MET -0.084 0.19 -10000 0 -0.54 58 58
PXN 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.16 0.53 8 -0.29 123 131
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.021 0.18 -10000 0 -0.45 59 59
ADRB2 0.01 0.1 -10000 0 -0.69 9 9
receptor agonist activity 0 0 0.001 15 0 123 138
actin filament binding 0 0 0.002 13 -0.001 118 131
SRC 0.026 0.009 -10000 0 -10000 0 0
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.005 13 -0.001 56 69
ARF6/GDP -0.008 0.092 0.24 1 -0.43 9 10
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.42 92 92
alphaIIb/beta3 Integrin/paxillin/GIT1 0.002 0.17 -10000 0 -0.44 51 51
ACAP1 0.019 0.047 -10000 0 -0.53 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.049 0.19 -10000 0 -0.57 48 48
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF -0.076 0.25 -10000 0 -0.69 58 58
CYTH3 0.007 0.026 -10000 0 -0.52 1 1
CYTH2 -0.007 0.15 -10000 0 -0.93 10 10
NCK1 0.027 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0.002 16 0 89 105
endosomal lumen acidification 0 0 0.002 7 -0.001 117 124
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 -0.095 0.27 -10000 0 -0.67 71 71
GNAQ/ARNO 0.007 0.14 -10000 0 -0.86 10 10
mol:Phosphatidic acid 0 0 0.001 12 -10000 0 12
PIP3-E 0 0 0.001 9 0 15 24
MET -0.034 0.073 -10000 0 -10000 0 0
GNA14 -0.13 0.29 -10000 0 -0.65 92 92
GNA15 0.013 0.052 -10000 0 -0.69 1 1
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 12 -0.001 98 110
GNA11 0.018 0.071 -10000 0 -0.69 4 4
LHCGR -0.073 0.23 -10000 0 -0.69 48 48
AGTR1 -0.26 0.35 -10000 0 -0.68 163 163
desensitization of G-protein coupled receptor protein signaling pathway -0.049 0.19 -10000 0 -0.57 48 48
IPCEF1/ARNO -0.033 0.18 -10000 0 -0.73 10 10
alphaIIb/beta3 Integrin -0.035 0.2 -10000 0 -0.54 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 -0.34 33 33
ATF2/c-Jun -0.2 0.35 -10000 0 -0.8 98 98
MAPK11 -0.016 0.1 -10000 0 -0.34 28 28
MITF -0.027 0.13 -10000 0 -0.41 35 35
MAPKAPK5 -0.022 0.12 -10000 0 -0.4 31 31
KRT8 -0.022 0.12 -10000 0 -0.4 31 31
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.031 0.16 -10000 0 -0.49 34 34
CEBPB -0.024 0.12 -10000 0 -0.4 33 33
SLC9A1 -0.028 0.12 -10000 0 -0.4 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.074 0.18 -10000 0 -0.41 67 67
p38alpha-beta/MNK1 -0.015 0.13 -10000 0 -0.41 31 31
JUN -0.2 0.35 -10000 0 -0.8 98 98
PPARGC1A -0.23 0.25 -10000 0 -0.45 210 210
USF1 -0.028 0.12 -10000 0 -0.4 36 36
RAB5/GDP/GDI1 -0.039 0.1 -10000 0 -0.34 17 17
NOS2 -0.033 0.12 -10000 0 -0.48 12 12
DDIT3 -0.023 0.12 -10000 0 -0.4 31 31
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.017 0.096 0.37 2 -0.36 15 17
p38alpha-beta/HBP1 -0.012 0.12 -10000 0 -0.41 26 26
CREB1 -0.056 0.16 -10000 0 -0.46 38 38
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.029 0.11 -10000 0 -0.43 11 11
RPS6KA4 -0.025 0.13 -10000 0 -0.41 33 33
PLA2G4A -0.062 0.17 -10000 0 -0.5 47 47
GDI1 -0.022 0.12 -10000 0 -0.41 30 30
TP53 -0.036 0.14 -10000 0 -0.49 30 30
RPS6KA5 -0.06 0.18 -10000 0 -0.44 61 61
ESR1 -0.056 0.19 -10000 0 -0.54 46 46
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.022 0.12 -10000 0 -0.4 31 31
MEF2A -0.028 0.13 -10000 0 -0.4 36 36
EIF4EBP1 -0.056 0.15 -10000 0 -0.44 39 39
KRT19 -0.057 0.18 -10000 0 -0.53 38 38
ELK4 -0.028 0.12 -10000 0 -0.4 36 36
ATF6 -0.028 0.12 -10000 0 -0.4 36 36
ATF1 -0.053 0.15 -10000 0 -0.44 36 36
p38alpha-beta/MAPKAPK2 -0.016 0.13 -10000 0 -0.41 31 31
p38alpha-beta/MAPKAPK3 -0.016 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 0.004 0.054 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.065 -10000 0 -0.19 53 53
AKT1 0.011 0.13 0.44 15 -0.22 11 26
EGF -0.071 0.24 -10000 0 -0.68 55 55
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.016 0.08 0.38 7 -0.44 2 9
mol:Ca2+ -0.018 0.14 0.42 10 -0.31 55 65
LYN 0.016 0.079 0.37 7 -0.44 2 9
RhoA/GTP -0.008 0.053 -10000 0 -0.14 3 3
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.018 0.16 0.43 14 -0.34 54 68
GNG2 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.027 0.11 0.27 1 -0.61 7 8
G beta5/gamma2 -0.042 0.089 -10000 0 -0.26 53 53
PRKCH -0.024 0.16 0.48 9 -0.36 54 63
DNM1 -0.002 0.13 -10000 0 -0.63 17 17
TXA2/TP beta/beta Arrestin3 -0.011 0.12 -10000 0 -0.41 27 27
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.003 0.14 -10000 0 -0.69 17 17
G12 family/GTP -0.032 0.12 -10000 0 -0.31 52 52
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.008 -10000 0 -10000 0 0
mol:GDP 0.051 0.15 0.4 34 -0.37 5 39
mol:NADP 0.026 0.006 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.68 108 108
mol:IP3 -0.028 0.17 0.47 9 -0.38 55 64
cell morphogenesis 0.035 0.007 -10000 0 -10000 0 0
PLCB2 -0.049 0.21 0.46 7 -0.52 55 62
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.083 0.18 0.4 5 -0.34 118 123
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.011 0.07 0.34 3 -0.44 2 5
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.018 0.071 -10000 0 -0.69 4 4
PRKCB1 -0.028 0.17 0.44 9 -0.38 55 64
GNAQ 0.025 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.045 0.22 0.5 10 -0.54 54 64
LCK 0.012 0.092 0.38 7 -0.48 5 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.026 0.079 -10000 0 -0.32 14 14
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 0.031 0.08 -10000 0 -0.32 14 14
MAPK14 -0.005 0.12 0.36 15 -0.23 50 65
TGM2/GTP -0.044 0.17 0.34 2 -0.43 54 56
MAPK11 -0.009 0.12 0.38 15 -0.23 52 67
ARHGEF1 -0.014 0.071 -10000 0 -0.18 47 47
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.024 0.18 0.43 14 -0.39 54 68
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.016 0.14 0.37 14 -0.29 55 69
cAMP biosynthetic process -0.029 0.16 0.45 10 -0.36 55 65
Gq family/GTP/EBP50 -0.044 0.11 0.24 1 -0.23 93 94
actin cytoskeleton reorganization 0.035 0.007 -10000 0 -10000 0 0
SRC 0.013 0.069 0.34 3 -0.44 2 5
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.025 0.13 0.51 9 -0.29 14 23
VCAM1 -0.012 0.14 0.38 13 -0.3 54 67
TP beta/Gq family/GDP/G beta5/gamma2 -0.027 0.11 0.27 1 -0.61 7 8
platelet activation -0.005 0.16 0.48 15 -0.3 53 68
PGI2/IP 0.014 0.054 -10000 0 -0.52 4 4
PRKACA 0.003 0.083 -10000 0 -0.36 18 18
Gq family/GDP/G beta5/gamma2 -0.028 0.11 0.28 1 -0.55 8 9
TXA2/TP beta/beta Arrestin2 -0.002 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 -0.033 0.19 0.47 9 -0.43 55 64
EGFR 0.017 0.079 -10000 0 -0.69 5 5
TXA2/TP alpha -0.045 0.21 0.54 8 -0.49 55 63
Gq family/GTP -0.062 0.13 0.22 2 -0.28 96 98
YES1 0.018 0.081 0.38 8 -0.44 2 10
GNAI2/GTP 0.008 0.069 -10000 0 -0.51 2 2
PGD2/DP -0.003 0.11 -10000 0 -0.52 17 17
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.019 0.083 0.36 10 -0.44 2 12
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.013 0.052 -10000 0 -0.69 1 1
PGK/cGMP -0.092 0.21 -10000 0 -0.44 107 107
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.042 0.085 -10000 0 -0.41 6 6
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.033 0.18 0.48 10 -0.38 57 67
PRKCB -0.026 0.17 0.46 11 -0.37 54 65
PRKCE -0.03 0.16 0.36 7 -0.37 55 62
PRKCD -0.028 0.17 0.46 8 -0.39 54 62
PRKCG -0.028 0.17 0.44 10 -0.39 52 62
muscle contraction -0.037 0.21 0.51 10 -0.49 54 64
PRKCZ -0.017 0.16 0.43 14 -0.34 52 66
ARR3 -0.001 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.016 0.078 -10000 0 -0.38 6 6
PRKCQ -0.029 0.16 0.43 9 -0.36 56 65
MAPKKK cascade -0.037 0.2 0.47 11 -0.46 55 66
SELE -0.028 0.18 0.38 13 -0.42 54 67
TP beta/GNAI2/GDP/G beta/gamma 0.04 0.082 -10000 0 -0.56 2 2
ROCK1 0.027 0.005 -10000 0 -10000 0 0
GNA14 -0.13 0.29 -10000 0 -0.65 92 92
chemotaxis -0.051 0.25 0.52 10 -0.61 54 64
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -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 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.047 0.016 -10000 0 -10000 0 0
forebrain development -0.3 0.28 0.34 1 -0.54 197 198
GNAO1 0.004 0.12 -10000 0 -0.69 11 11
SMO/beta Arrestin2 0.015 0.027 -10000 0 -10000 0 0
SMO 0.016 0.015 -10000 0 -10000 0 0
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.039 0.067 -10000 0 -0.34 5 5
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
GNAI2 0.025 0.008 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.034 -10000 0 -0.42 1 1
GNAI1 0.024 0.006 -10000 0 -10000 0 0
XPO1 0.015 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.22 0.22 -10000 0 -0.5 113 113
SAP30 0.026 0.036 -10000 0 -0.69 1 1
mol:GDP 0.016 0.015 -10000 0 -10000 0 0
MIM/GLI2A -0.033 0.067 -10000 0 -10000 0 0
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.024 0.008 -10000 0 -10000 0 0
GLI2 -0.001 0.082 0.28 2 -0.35 10 12
GLI3 0.029 0.069 0.27 2 -0.37 4 6
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.027 0.005 -10000 0 -10000 0 0
Gi family/GTP -0.014 0.065 -10000 0 -0.31 11 11
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.039 0.06 -10000 0 -0.41 3 3
GLI2/Su(fu) 0.007 0.079 -10000 0 -0.49 3 3
FOXA2 -0.6 0.62 -10000 0 -1.2 203 203
neural tube patterning -0.3 0.28 0.34 1 -0.54 197 198
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.034 0.028 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
MTSS1 -0.033 0.067 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.34 1 -0.54 197 198
SUFU 0.019 0.011 -10000 0 -10000 0 0
LGALS3 -0.027 0.072 -10000 0 -10000 0 0
catabolic process 0.033 0.099 -10000 0 -0.46 7 7
GLI3A/CBP -0.17 0.2 -10000 0 -0.38 200 200
KIF3A 0.026 0.005 -10000 0 -10000 0 0
GLI1 -0.31 0.29 0.34 1 -0.56 196 197
RAB23 0.022 0.061 -10000 0 -0.69 3 3
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.032 0.042 -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 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
GLI2/SPOP 0.008 0.084 -10000 0 -0.36 8 8
STK36 0.015 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.012 0.047 -10000 0 -0.31 2 2
PTCH1 -0.27 0.26 -10000 0 -0.59 112 112
MIM/GLI1 -0.43 0.38 -10000 0 -0.72 213 213
CREBBP -0.17 0.2 -10000 0 -0.38 200 200
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 52 52
B2M 0.023 0.018 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0.004 0.072 -10000 0 -0.6 3 3
GADD45B -0.11 0.4 -10000 0 -1 50 50
IL12RB2 -0.005 0.13 -10000 0 -0.69 14 14
GADD45G -0.094 0.35 -10000 0 -0.94 42 42
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 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 -0.073 0.23 -10000 0 -0.69 50 50
STAT3 (dimer) -0.083 0.31 -10000 0 -0.78 50 50
HLA-DRB5 -0.01 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 -0.95 50 50
CD4 0.011 0.033 -10000 0 -10000 0 0
SOCS1 0.025 0.014 -10000 0 -10000 0 0
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.066 0.21 -10000 0 -0.66 44 44
CD3E -0.047 0.19 -10000 0 -0.65 35 35
CD3G -0.11 0.26 -10000 0 -0.67 72 72
IL12Rbeta2/JAK2 0.01 0.11 -10000 0 -0.52 14 14
CCL3 -0.11 0.41 -10000 0 -1.2 40 40
CCL4 -0.15 0.49 -10000 0 -1.4 49 49
HLA-A 0.023 0.018 -10000 0 -10000 0 0
IL18/IL18R 0.029 0.16 -10000 0 -0.49 29 29
NOS2 -0.09 0.35 -10000 0 -0.96 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 -0.025 0.14 -10000 0 -0.36 34 34
IL1R1 -0.1 0.37 -10000 0 -1 43 43
IL4 0 0.034 -10000 0 -10000 0 0
JAK2 0.018 0.031 -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 -0.062 0.3 -10000 0 -0.75 44 44
lysosomal transport -0.056 0.28 -10000 0 -0.7 44 44
FOS -0.37 0.61 -10000 0 -1.2 130 130
STAT4 (dimer) -0.087 0.35 -10000 0 -0.84 55 55
STAT5A (dimer) -0.14 0.4 -10000 0 -0.95 61 61
GZMA -0.12 0.39 -10000 0 -1.1 41 41
GZMB -0.11 0.38 -10000 0 -1.1 41 41
HLX 0.021 0.025 -10000 0 -10000 0 0
LCK -0.12 0.42 -10000 0 -1.1 51 51
TCR/CD3/MHC II/CD4 -0.15 0.3 -10000 0 -0.56 93 93
IL2/IL2R -0.001 0.18 -10000 0 -0.59 28 28
MAPK14 -0.089 0.37 -10000 0 -0.89 54 54
CCR5 -0.097 0.39 -10000 0 -1.2 34 34
IL1B -0.036 0.2 -10000 0 -0.72 32 32
STAT6 -0.008 0.11 -10000 0 -0.46 5 5
STAT4 0.001 0.1 -10000 0 -0.59 10 10
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B 0.006 0.08 -10000 0 -0.7 4 4
CD8A -0.025 0.18 -10000 0 -0.66 29 29
CD8B -0.058 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 -0.074 0.32 -10000 0 -0.75 55 55
IL2RG -0.012 0.14 -10000 0 -0.64 18 18
IL12 -0.03 0.18 -10000 0 -0.53 42 42
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.018 0.14 -10000 0 -0.69 16 16
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.026 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.049 0.21 -10000 0 -0.69 39 39
IL12/IL12R/TYK2/JAK2 -0.14 0.48 -10000 0 -1.2 52 52
MAP2K3 -0.093 0.37 -10000 0 -0.9 52 52
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.099 0.38 -10000 0 -0.9 55 55
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 -0.006 0.15 -10000 0 -0.69 18 18
IL12Rbeta1/TYK2 0.024 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 72 72
T cell proliferation -0.055 0.26 -10000 0 -0.61 54 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.003 0.094 -10000 0 -0.56 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.068 0.28 -10000 0 -0.66 57 57
ATF2 -0.087 0.34 -10000 0 -0.81 53 53
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.23 -10000 0 -0.53 58 58
MAP3K8 0.014 0.087 -10000 0 -0.69 6 6
FOS -0.082 0.19 0.28 3 -0.47 52 55
PRKCA -0.023 0.16 -10000 0 -0.69 22 22
PTPN7 -0.023 0.14 -10000 0 -0.69 15 15
HRAS 0.025 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 0.035 0.031 -10000 0 -10000 0 0
MAPK3 -0.016 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 -0.43 97 97
RAF1 -0.017 0.13 -10000 0 -0.5 23 23
KRAS 0.026 0.006 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.026 0.012 -9999 0 -10000 0 0
EGFR 0.017 0.079 -9999 0 -0.69 5 5
EGF/EGFR -0.017 0.16 -9999 0 -0.38 62 62
EGF/EGFR dimer/SHC/GRB2/SOS1 0.004 0.16 -9999 0 -0.39 55 55
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.038 -9999 0 -0.69 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.071 0.24 -9999 0 -0.68 55 55
EGF/EGFR dimer/SHC -0.023 0.18 -9999 0 -0.44 59 59
mol:GDP -0.001 0.16 -9999 0 -0.39 55 55
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.018 0.079 -9999 0 -0.69 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.013 0.14 -9999 0 -0.36 55 55
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP 0 0.15 -9999 0 -0.37 55 55
FRAP1 -0.051 0.13 -9999 0 -0.37 55 55
EGF/EGFR dimer -0.043 0.2 -9999 0 -0.52 59 59
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.03 0.069 -9999 0 -0.52 6 6
IL6-mediated 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
BCL2L1 -0.002 0.2 0.6 5 -0.72 7 12
CRP 0.002 0.21 0.59 8 -0.71 10 18
cell cycle arrest -0.017 0.21 0.75 1 -0.72 18 19
TIMP1 -0.035 0.21 0.59 3 -0.64 23 26
IL6ST -0.052 0.22 -10000 0 -0.69 45 45
Rac1/GDP -0.051 0.2 -10000 0 -0.53 39 39
AP1 -0.11 0.27 -10000 0 -0.6 79 79
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.013 0.2 0.62 4 -0.67 12 16
HSP90B1 0.041 0.056 -10000 0 -0.64 1 1
GAB1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.1 0.26 -10000 0 -0.72 47 47
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 -0.6 49 50
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.038 0.19 0.34 3 -0.6 21 24
MITF -0.072 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 0.008 -10000 0 -10000 0 0
A2M 0.025 0.077 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.008 0.09 -10000 0 -0.51 4 4
STAT3 -0.027 0.22 0.75 1 -0.77 18 19
STAT1 0.009 0.11 -10000 0 -1 4 4
CEBPD -0.005 0.2 0.64 2 -0.73 8 10
PIK3CA 0.027 0.036 -10000 0 -0.69 1 1
PI3K 0.04 0.029 -10000 0 -0.52 1 1
JUN -0.12 0.29 -10000 0 -0.68 86 86
PIAS3/MITF -0.058 0.2 -10000 0 -0.54 38 38
MAPK11 -0.1 0.25 -10000 0 -0.73 44 44
STAT3 (dimer)/FOXO1 0.014 0.16 -10000 0 -0.59 9 9
GRB2/SOS1/GAB family -0.034 0.2 -10000 0 -0.5 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.075 0.21 -10000 0 -0.45 61 61
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.025 0.008 -10000 0 -10000 0 0
LBP 0.006 0.18 0.62 7 -0.58 7 14
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.025 0.016 -10000 0 -10000 0 0
MYC -0.016 0.24 0.63 3 -0.94 15 18
FGG -0.01 0.2 0.68 3 -0.72 9 12
macrophage differentiation -0.017 0.21 0.75 1 -0.72 18 19
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.074 0.25 -10000 0 -0.45 114 114
JUNB -0.007 0.21 0.6 3 -0.8 13 16
FOS -0.15 0.31 -10000 0 -0.68 103 103
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.072 0.22 -10000 0 -0.54 49 49
STAT1/PIAS1 -0.04 0.2 -10000 0 -0.49 39 39
GRB2/SOS1/GAB family/SHP2/PI3K 0.04 0.038 -10000 0 -0.29 2 2
STAT3 (dimer) -0.021 0.22 0.75 1 -0.75 18 19
PRKCD -0.025 0.19 0.44 3 -0.62 17 20
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 0.001 0.16 -10000 0 -0.45 43 43
Rac1/GTP -0.049 0.2 -10000 0 -0.52 39 39
HCK 0.017 0.036 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.091 0.34 1 -0.55 4 5
bone resorption -0.011 0.19 0.62 4 -0.62 13 17
IRF1 -0.002 0.2 0.64 6 -0.73 6 12
mol:GDP -0.071 0.21 -10000 0 -0.54 43 43
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.073 0.21 -10000 0 -0.55 43 43
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.095 0.26 -10000 0 -0.71 45 45
PTPN11 0.017 0.049 -10000 0 -0.85 1 1
IL6/IL6RA -0.087 0.24 -10000 0 -0.53 88 88
gp130 (dimer)/TYK2/TYK2/LMO4 -0.002 0.15 -10000 0 -0.43 45 45
gp130 (dimer)/JAK2/JAK2/LMO4 -0.004 0.16 -10000 0 -0.44 45 45
IL6 -0.12 0.29 -10000 0 -0.69 81 81
PIAS3 0.025 0.007 -10000 0 -10000 0 0
PTPRE -0.026 0.079 -10000 0 -0.69 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.075 0.21 -10000 0 -0.37 113 113
LMO4 0.026 0.02 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.024 0.21 -10000 0 -0.76 17 17
MCL1 0.055 0.058 -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 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.04 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 -0.53 22 22
Syndecan-1/Syntenin -0.032 0.15 0.25 2 -0.44 36 38
MAPK3 -0.03 0.13 -10000 0 -0.52 18 18
HGF/MET -0.084 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 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.033 0.14 -10000 0 -0.52 22 22
Syndecan-1/RANTES -0.053 0.2 -10000 0 -0.54 46 46
Syndecan-1/CD147 -0.015 0.15 -10000 0 -0.54 20 20
Syndecan-1/Syntenin/PIP2 -0.032 0.14 0.24 1 -0.42 36 37
LAMA5 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.032 0.14 0.24 1 -0.41 36 37
MMP7 -0.078 0.16 -10000 0 -0.67 21 21
HGF -0.076 0.25 -10000 0 -0.69 58 58
Syndecan-1/CASK -0.045 0.14 -10000 0 -0.41 42 42
Syndecan-1/HGF/MET -0.079 0.21 -10000 0 -0.49 67 67
regulation of cell adhesion -0.032 0.12 -10000 0 -0.52 16 16
HPSE 0.006 0.1 -10000 0 -0.65 9 9
positive regulation of cell migration -0.04 0.14 -10000 0 -0.42 39 39
SDC1 -0.039 0.14 -10000 0 -0.42 41 41
Syndecan-1/Collagen -0.04 0.14 -10000 0 -0.42 39 39
PPIB 0.027 0.004 -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 -0.04 0.19 -10000 0 -0.69 32 32
MAPK1 -0.032 0.13 -10000 0 -0.52 19 19
homophilic cell adhesion -0.038 0.14 0.43 2 -0.41 40 42
MMP1 -0.049 0.073 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.039 0.1 -10000 0 -0.41 19 19
ER alpha/Gai/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.53 20 20
AKT1 -0.013 0.2 -10000 0 -0.74 26 26
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.2 -10000 0 -0.76 25 25
mol:Ca2+ -0.093 0.19 -10000 0 -0.42 96 96
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.014 0.14 -10000 0 -0.45 37 37
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.19 0.7 26 -10000 0 26
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 0.078 0.29 21 -0.28 1 22
E2/ERA-ERB (dimer) 0.004 0.11 -10000 0 -0.45 21 21
KRAS 0.026 0.005 -10000 0 -10000 0 0
G13/GTP 0.009 0.087 -10000 0 -0.37 18 18
pseudopodium formation -0.004 0.078 0.28 1 -0.29 21 22
E2/ER alpha (dimer)/PELP1 0.009 0.094 -10000 0 -0.4 18 18
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.005 -10000 0 -10000 0 0
GNAO1 0.006 0.12 -10000 0 -0.69 11 11
HRAS 0.026 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.01 0.16 0.48 7 -0.59 19 26
E2/ER beta (dimer) 0.014 0.053 -10000 0 -0.52 4 4
mol:GDP 0.001 0.11 -10000 0 -0.48 20 20
mol:NADP 0.01 0.16 0.48 7 -0.59 19 26
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 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.097 0.2 -10000 0 -0.45 96 96
PLCB2 -0.097 0.2 -10000 0 -0.46 95 95
IGF1 -0.12 0.29 -10000 0 -0.68 83 83
mol:L-citrulline 0.01 0.16 0.48 7 -0.59 19 26
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP 0.005 0.15 -10000 0 -0.71 15 15
JNK cascade 0.014 0.053 -10000 0 -0.52 4 4
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.02 0.071 -10000 0 -0.69 4 4
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.015 0.15 -10000 0 -0.66 19 19
Gq family/GDP/Gbeta gamma -0.055 0.18 -10000 0 -0.62 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.11 -10000 0 -0.57 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.005 0.13 -10000 0 -0.55 16 16
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.01 0.11 -10000 0 -0.49 19 19
STRN -0.007 0.15 -10000 0 -0.69 19 19
GNAL -0.057 0.23 -10000 0 -0.67 49 49
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.008 0.045 -10000 0 -0.44 4 4
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.006 -10000 0 -10000 0 0
HBEGF -0.014 0.15 0.38 4 -0.49 23 27
cAMP biosynthetic process -0.04 0.16 -10000 0 -0.4 61 61
SRC -0.002 0.13 -10000 0 -0.5 19 19
PI3K 0.038 0.029 -10000 0 -0.52 1 1
GNB1 0.026 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.031 0.11 -10000 0 -0.43 19 19
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.065 0.16 -10000 0 -0.42 44 44
Gs family/GTP -0.03 0.17 -10000 0 -0.41 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 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 58 58
MSN -0.005 0.083 0.29 1 -0.32 21 22
Gq family/GTP -0.098 0.22 -10000 0 -0.47 98 98
mol:PI-3-4-5-P3 -0.008 0.19 -10000 0 -0.73 25 25
NRAS 0.027 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 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.11 -10000 0 -0.45 20 20
NOS3 0.002 0.16 0.39 2 -0.62 19 21
GNA11 0.018 0.071 -10000 0 -0.69 4 4
MAPKKK cascade -0.011 0.17 0.37 1 -0.5 39 40
E2/ER alpha (dimer)/PELP1/Src 0.002 0.14 -10000 0 -0.55 18 18
ruffle organization -0.004 0.078 0.28 1 -0.29 21 22
ROCK2 0.002 0.1 0.36 5 -0.34 21 26
GNA14 -0.13 0.29 -10000 0 -0.65 92 92
GNA15 0.013 0.052 -10000 0 -0.69 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.03 0.17 -10000 0 -0.46 43 43
MMP2 -0.001 0.12 -10000 0 -0.48 19 19
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 0.01 0.11 0.35 3 -0.39 10 13
alphaV/beta3 Integrin/Osteopontin/Src 0.003 0.13 -10000 0 -0.51 21 21
AP1 -0.14 0.3 -10000 0 -0.67 82 82
ILK -0.008 0.12 -10000 0 -0.41 26 26
bone resorption -0.003 0.12 -10000 0 -0.45 11 11
PTK2B 0.027 0.004 -10000 0 -10000 0 0
PYK2/p130Cas 0.04 0.12 -10000 0 -0.38 27 27
ITGAV 0.027 0.036 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.025 0.087 -10000 0 -0.52 10 10
alphaV/beta3 Integrin/Osteopontin 0.025 0.13 -10000 0 -0.45 28 28
MAP3K1 -0.01 0.12 -10000 0 -0.42 27 27
JUN -0.12 0.29 -10000 0 -0.68 86 86
MAPK3 -0.023 0.1 -10000 0 -0.39 27 27
MAPK1 -0.024 0.1 -10000 0 -0.38 27 27
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.027 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 -0.018 0.1 -10000 0 -0.38 27 27
FOS -0.15 0.31 -10000 0 -0.68 103 103
CD44 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.036 0.12 0.52 3 -0.62 1 4
NF kappa B1 p50/RelA 0.021 0.11 -10000 0 -0.47 3 3
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.026 0.096 -10000 0 -0.52 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.009 0.12 -10000 0 -0.42 27 27
VAV3 -0.016 0.12 0.4 1 -0.4 29 30
MAP3K14 -0.014 0.11 -10000 0 -0.42 27 27
ROCK2 0.009 0.11 -10000 0 -0.69 10 10
SPP1 -0.03 0.16 -10000 0 -0.68 20 20
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.11 -10000 0 -0.37 29 29
MMP2 -0.13 0.24 0.3 1 -0.56 73 74
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 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 0.015 0.087 -10000 0 -0.69 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 205 205
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -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 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.026 0.005 -10000 0 -10000 0 0
FGR 0.025 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 0.019 0.064 -10000 0 -0.69 3 3
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 109 109
apoptosis -0.044 0.067 -10000 0 -0.28 9 9
RAL/GTP 0.035 0.009 -10000 0 -10000 0 0
LYN 0.027 0.004 -10000 0 -10000 0 0
DUSP1 -0.083 0.26 -10000 0 -0.69 62 62
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.064 0.021 -10000 0 -10000 0 0
TRAF6 0.025 0.036 -10000 0 -0.69 1 1
RAC1 0.026 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 0.026 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.034 0.01 -10000 0 -10000 0 0
MAPK11 -0.054 0.16 0.43 16 -0.33 25 41
BLK -0.2 0.32 -10000 0 -0.68 123 123
HCK 0.018 0.036 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.026 0.005 -10000 0 -10000 0 0
DUSP10 0.023 0.038 -10000 0 -0.69 1 1
TRAF6/MEKK3 0.031 0.024 -10000 0 -0.41 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.013 0.12 0.38 15 -0.31 9 24
positive regulation of innate immune response -0.044 0.17 0.46 17 -0.42 9 26
LCK 0.012 0.083 -10000 0 -0.69 5 5
p38alpha-beta/MKP7 -0.048 0.14 0.35 6 -0.44 6 12
p38alpha-beta/MKP5 -0.038 0.16 0.45 14 -0.45 7 21
PGK/cGMP -0.12 0.24 -10000 0 -0.52 108 108
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.099 0.18 0.33 3 -0.42 53 56
CDC42 0.026 0.005 -10000 0 -10000 0 0
RALB 0.027 0.004 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.35 -10000 0 -0.67 224 224
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.004 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.12 -10000 0 -0.38 20 20
NFATC4 -0.024 0.091 0.29 3 -0.29 16 19
ERBB2IP 0.027 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 0.098 0.38 9 -0.29 2 11
HRAS 0.025 0.012 -10000 0 -10000 0 0
DOCK7 -0.028 0.11 -10000 0 -0.35 36 36
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 0.13 0.38 7 -0.39 19 26
ErbB2/ErbB3/neuregulin 2 -0.033 0.16 -10000 0 -0.43 54 54
STAT3 0.025 0.087 -10000 0 -0.84 4 4
cell migration 0.007 0.11 0.37 18 -0.24 2 20
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.16 0.32 0.47 1 -0.69 96 97
FOS -0.12 0.26 0.38 5 -0.5 123 128
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.12 -10000 0 -0.36 37 37
MAPK3 -0.082 0.24 0.47 2 -0.52 70 72
MAPK1 -0.17 0.31 0.44 2 -0.63 101 103
JAK2 -0.029 0.1 -10000 0 -0.35 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 -0.044 0.21 -10000 0 -0.68 40 40
GRB2/SOS1 0.037 0.011 -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 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.015 0.082 -10000 0 -0.64 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.002 0.015 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.085 -10000 0 -0.82 4 4
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 17 17
ErbB2/ErbB2/HSP90 (dimer) 0.013 0.014 -10000 0 -10000 0 0
CHRNA1 -0.077 0.2 0.47 1 -0.43 43 44
myelination -0.011 0.15 0.55 15 -0.29 1 16
PPP3CB -0.026 0.1 -10000 0 -0.32 37 37
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.016 0.11 -10000 0 -0.34 20 20
NRG2 -0.062 0.23 -10000 0 -0.69 49 49
mol:GDP -0.017 0.12 -10000 0 -0.35 38 38
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.028 0.13 0.4 4 -0.39 20 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 -0.077 0.23 -10000 0 -0.61 27 27
heart morphogenesis -0.019 0.12 -10000 0 -0.36 37 37
RAS family/GDP 0.012 0.12 -10000 0 -0.36 20 20
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.013 0.13 -10000 0 -0.66 16 16
CHRNE 0.008 0.039 0.19 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
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.009 0.057 -10000 0 -10000 0 0
CRKL -0.016 0.094 0.36 1 -0.33 4 5
mol:PIP3 -0.001 0.019 0.34 1 -10000 0 1
AKT1 0.004 0.055 0.37 2 -0.46 2 4
PTK2B 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0 0.11 0.43 7 -0.4 1 8
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
HGF/MET/SHIP2 -0.015 0.19 -10000 0 -0.47 58 58
MAP3K5 0.011 0.13 0.47 12 -0.42 5 17
HGF/MET/CIN85/CBL/ENDOPHILINS 0 0.18 -10000 0 -0.43 56 56
AP1 -0.18 0.34 -10000 0 -0.67 120 120
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 -0.81 122 122
STAT3 (dimer) -0.022 0.11 -10000 0 -0.3 25 25
GAB1/CRKL/SHP2/PI3K 0.026 0.1 -10000 0 -0.38 1 1
INPP5D 0.018 0.035 -10000 0 -10000 0 0
CBL/CRK 0.014 0.12 0.45 6 -0.41 1 7
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.021 -10000 0 -0.38 1 1
ELK1 0.033 0.14 0.43 24 -0.26 2 26
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.07 -10000 0 -0.24 4 4
PAK1 0.008 0.062 0.37 6 -0.4 1 7
HGF/MET/RANBP10 -0.016 0.19 -10000 0 -0.47 58 58
HRAS -0.019 0.13 -10000 0 -0.56 2 2
DOCK1 -0.001 0.12 0.45 8 -0.43 3 11
GAB1 -0.012 0.099 0.26 1 -0.35 4 5
CRK -0.008 0.1 0.29 4 -0.43 1 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.044 0.19 -10000 0 -0.52 58 58
JUN -0.12 0.29 -10000 0 -0.68 86 86
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 -0.009 0.12 0.5 4 -0.46 1 5
GRB2/SHC 0.002 0.088 -10000 0 -0.23 25 25
FOS -0.15 0.31 -10000 0 -0.68 103 103
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.033 0.14 0.43 24 -0.26 2 26
HGF/MET/MUC20 -0.071 0.17 -10000 0 -0.47 58 58
cell migration 0.002 0.087 -10000 0 -0.22 25 25
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.009 0.057 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.018 0.12 -10000 0 -0.3 55 55
MET/MUC20 -0.02 0.047 -10000 0 -10000 0 0
RAP1B 0.011 0.13 0.55 12 -0.37 1 13
RAP1A 0.008 0.11 0.4 10 -0.37 1 11
HGF/MET/RANBP9 -0.015 0.19 -10000 0 -0.47 58 58
RAF1 -0.017 0.13 -10000 0 -0.45 2 2
STAT3 -0.022 0.11 -10000 0 -0.3 25 25
cell proliferation -0.028 0.15 -10000 0 -0.4 53 53
RPS6KB1 0 0.033 -10000 0 -0.25 1 1
MAPK3 -0.021 0.11 0.52 12 -10000 0 12
MAPK1 0.13 0.29 0.61 105 -10000 0 105
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.027 0.16 0.63 14 -0.63 3 17
SRC -0.023 0.11 -10000 0 -0.3 25 25
PI3K 0.004 0.092 -10000 0 -0.23 27 27
MET/Glomulin -0.009 0.046 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.011 0.12 -10000 0 -0.46 1 1
MET -0.034 0.073 -10000 0 -10000 0 0
MAP4K1 0.005 0.12 0.48 7 -0.44 5 12
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.009 0.12 -10000 0 -0.42 2 2
BAD 0.008 0.062 0.37 6 -0.4 1 7
MAP2K4 0.021 0.15 0.53 17 -0.4 4 21
SHP2/GRB2/SOS1/GAB1 0.017 0.1 -10000 0 -0.38 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.026 0.005 -10000 0 -10000 0 0
SH3KBP1 0.025 0.008 -10000 0 -10000 0 0
HGS -0.03 0.08 -10000 0 -0.23 56 56
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.076 0.25 -10000 0 -0.69 58 58
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.002 0.1 -10000 0 -0.24 57 57
PDPK1 0 0.047 -10000 0 -0.49 2 2
HGF/MET/SHIP -0.02 0.19 -10000 0 -0.47 58 58
BCR signaling pathway

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
JUN -0.067 0.18 0.43 9 -0.45 27 36
IKBKB 0.009 0.12 0.47 14 -0.3 6 20
AKT1 -0.004 0.17 0.55 21 -0.25 12 33
IKBKG -0.003 0.12 0.43 15 -0.33 13 28
CALM1 -0.024 0.094 0.37 2 -0.42 7 9
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
MAP3K1 -0.018 0.17 0.48 9 -0.55 18 27
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.094 -10000 0 -0.42 8 8
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.058 0.16 0.56 10 -0.27 80 90
LYN 0.027 0.004 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex -0.076 0.19 -10000 0 -0.51 57 57
CD22 -0.074 0.18 -10000 0 -0.43 72 72
CAMK2G -0.02 0.092 0.32 3 -0.43 5 8
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
INPP5D 0.018 0.035 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.043 0.13 -10000 0 -0.35 51 51
GO:0007205 -0.027 0.097 -10000 0 -0.43 8 8
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.02 0.096 0.37 2 -0.44 6 8
NFATC1 -0.042 0.14 0.37 6 -0.44 18 24
B-cell antigen/BCR complex -0.076 0.19 -10000 0 -0.51 57 57
PAG1/CSK 0.038 0.029 -10000 0 -0.52 1 1
NFKBIB 0.019 0.044 0.2 11 -0.13 6 17
HRAS -0.02 0.098 0.3 3 -0.35 8 11
NFKBIA 0.019 0.044 0.2 11 -0.13 6 17
NF-kappa-B/RelA/I kappa B beta 0.023 0.041 0.2 11 -10000 0 11
RasGAP/Csk -0.007 0.19 -10000 0 -0.42 63 63
mol:GDP -0.024 0.094 -10000 0 -0.41 9 9
PTEN 0.026 0.021 -10000 0 -0.38 1 1
CD79B 0.007 0.049 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.023 0.041 0.2 11 -10000 0 11
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.041 0.16 0.5 3 -0.48 18 21
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.025 0.093 -10000 0 -0.42 7 7
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.1 0.18 0.45 6 -0.38 104 110
CHUK 0.007 0.11 0.39 15 -0.32 5 20
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.015 0.11 -10000 0 -0.46 8 8
PTPN6 -0.068 0.17 -10000 0 -0.5 35 35
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.013 0.037 0.15 6 -0.12 10 16
VAV2 -0.058 0.16 -10000 0 -0.68 12 12
ubiquitin-dependent protein catabolic process 0.022 0.044 0.2 11 -0.12 5 16
BTK -0.033 0.24 -10000 0 -0.99 23 23
CD19 -0.065 0.16 -10000 0 -0.41 59 59
MAP4K1 0.008 0.085 -10000 0 -0.69 5 5
CD72 0.024 0.015 -10000 0 -10000 0 0
PAG1 0.025 0.036 -10000 0 -0.69 1 1
MAPK14 -0.01 0.16 0.44 11 -0.48 15 26
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.018 0.098 -10000 0 -0.43 9 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.052 0.19 -10000 0 -0.43 66 66
RAF1 -0.016 0.098 0.33 6 -0.37 5 11
RasGAP/p62DOK/SHIP -0.01 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 -0.057 0.16 0.56 10 -0.26 80 90
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.005 0.1 0.38 13 -0.41 2 15
MAPK1 -0.011 0.09 0.37 7 -0.39 2 9
CD72/SHP1 -0.053 0.17 -10000 0 -0.47 36 36
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.013 0.16 0.49 10 -0.48 17 27
actin cytoskeleton organization -0.048 0.14 0.34 2 -0.57 11 13
NF-kappa-B/RelA 0.048 0.073 0.35 11 -0.22 1 12
Calcineurin 0.006 0.093 -10000 0 -0.41 4 4
PI3K -0.065 0.14 -10000 0 -0.45 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.021 0.1 -10000 0 -0.46 9 9
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.026 0.23 -10000 0 -0.96 17 17
DAPP1 -0.046 0.26 -10000 0 -1.2 16 16
cytokine secretion -0.039 0.13 0.37 6 -0.41 18 24
mol:DAG -0.025 0.093 -10000 0 -0.42 7 7
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.014 0.093 0.33 6 -0.45 2 8
B-cell antigen/BCR complex/FcgammaRIIB -0.06 0.2 -10000 0 -0.46 70 70
mol:PI-3-4-5-P3 -0.054 0.1 -10000 0 -0.36 13 13
ETS1 -0.016 0.09 0.41 3 -0.42 4 7
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.009 0.16 -10000 0 -0.39 54 54
B-cell antigen/BCR complex/LYN -0.05 0.18 -10000 0 -0.43 60 60
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.025 0.036 -10000 0 -0.69 1 1
RAC1 -0.051 0.15 0.36 1 -0.62 11 12
B-cell antigen/BCR complex/LYN/SYK -0.042 0.2 -10000 0 -0.46 59 59
CARD11 -0.038 0.12 0.37 3 -0.44 14 17
FCGR2B -0.011 0.16 -10000 0 -0.69 20 20
PPP3CA 0.027 0.005 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.018 0.099 0.43 16 -0.13 4 20
PTPRC -0.01 0.14 -10000 0 -0.69 17 17
PDPK1 -0.032 0.085 0.28 5 -0.26 13 18
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.004 -10000 0 -10000 0 0
POU2F2 0.019 0.033 0.16 13 -10000 0 13
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 0.01 0.057 0.25 21 -10000 0 21
RFC1 0.012 0.059 0.25 23 -10000 0 23
PRKDC 0.012 0.06 0.25 24 -10000 0 24
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.006 0.1 -10000 0 -0.77 5 5
FASLG/FAS/FADD/FAF1 -0.02 0.099 0.24 2 -0.35 29 31
MAP2K4 -0.04 0.18 0.32 2 -0.52 24 26
mol:ceramide -0.029 0.14 -10000 0 -0.44 31 31
GSN 0.01 0.057 0.25 21 -10000 0 21
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.13 -10000 0 -0.44 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 0.27 3 -0.53 9 12
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
RB1 0.012 0.062 0.26 22 -10000 0 22
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET -0.018 0.19 -10000 0 -0.47 59 59
ARHGDIB 0.012 0.063 0.24 26 -10000 0 26
FADD 0.018 0.02 -10000 0 -10000 0 0
actin filament polymerization -0.01 0.057 -10000 0 -0.25 21 21
NFKB1 -0.026 0.11 -10000 0 -0.63 3 3
MAPK8 -0.078 0.24 0.4 2 -0.48 90 92
DFFA 0.012 0.059 0.25 23 -10000 0 23
DNA fragmentation during apoptosis 0.012 0.059 0.25 23 -10000 0 23
FAS/FADD/MET 0.042 0.046 -10000 0 -10000 0 0
CFLAR/RIP1 0.043 0.01 -10000 0 -10000 0 0
FAIM3 0.016 0.067 -10000 0 -0.69 3 3
FAF1 0.017 0.022 -10000 0 -10000 0 0
PARP1 0.015 0.074 0.29 24 -10000 0 24
DFFB 0.012 0.059 0.25 23 -10000 0 23
CHUK -0.024 0.099 -10000 0 -0.58 3 3
FASLG -0.039 0.18 -10000 0 -0.7 29 29
FAS/FADD 0.027 0.028 -10000 0 -10000 0 0
HGF -0.076 0.25 -10000 0 -0.69 58 58
LMNA 0.011 0.065 0.26 23 -10000 0 23
CASP6 0.012 0.059 0.25 23 -10000 0 23
CASP10 0.018 0.019 -10000 0 -10000 0 0
CASP3 0.015 0.074 0.3 25 -10000 0 25
PTPN13 0.023 0.05 -10000 0 -0.69 2 2
CASP8 -0.014 0.037 0.4 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 0.01 0.053 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.03 0.14 -10000 0 -0.45 31 31
activation of caspase activity by cytochrome c -0.019 0.037 0.28 3 -10000 0 3
PAK2 0.011 0.06 0.24 24 -10000 0 24
BCL2 -0.018 0.17 -10000 0 -0.68 26 26
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.018 0.12 -10000 0 -0.41 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.083 0.41 1 -0.43 1 2
AP1 -0.16 0.3 -10000 0 -0.56 130 130
mol:PIP3 -0.013 0.1 -10000 0 -0.38 25 25
AKT1 0.028 0.094 0.33 2 -0.48 1 3
PTK2B -0.011 0.087 0.24 2 -0.28 25 27
RHOA 0.012 0.04 -10000 0 -10000 0 0
PIK3CB 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.069 0.3 5 -10000 0 5
MAGI3 0.025 0.036 -10000 0 -0.69 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.01 0.1 -10000 0 -0.35 33 33
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.002 0.1 0.37 9 -0.39 7 16
NF kappa B1 p50/RelA -0.019 0.1 -10000 0 -0.45 5 5
endothelial cell migration -0.015 0.14 -10000 0 -0.5 28 28
ADCY4 -0.029 0.15 -10000 0 -0.51 31 31
ADCY5 -0.056 0.16 -10000 0 -0.54 33 33
ADCY6 -0.029 0.15 -10000 0 -0.52 29 29
ADCY7 -0.029 0.15 -10000 0 -0.53 29 29
ADCY1 -0.031 0.15 -10000 0 -0.52 30 30
ADCY2 -0.051 0.17 -10000 0 -0.55 33 33
ADCY3 -0.029 0.15 -10000 0 -0.54 28 28
ADCY8 -0.037 0.15 -10000 0 -0.51 32 32
ADCY9 -0.03 0.15 -10000 0 -0.53 29 29
GSK3B -0.01 0.086 0.37 2 -0.38 7 9
arachidonic acid secretion -0.03 0.14 -10000 0 -0.44 39 39
GNG2 0.027 0.005 -10000 0 -10000 0 0
TRIP6 0.024 0.009 -10000 0 -10000 0 0
GNAO1 -0.025 0.15 -10000 0 -0.46 39 39
HRAS 0.026 0.012 -10000 0 -10000 0 0
NFKBIA -0.005 0.095 0.49 5 -0.49 1 6
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.017 0.18 -10000 0 -0.78 19 19
JUN -0.12 0.29 -10000 0 -0.68 86 86
LPA/LPA2/NHERF2 0.035 0.015 -10000 0 -10000 0 0
TIAM1 0.004 0.21 -10000 0 -0.93 19 19
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.008 0.065 0.36 2 -10000 0 2
PLCB3 0.026 0.031 -10000 0 -10000 0 0
FOS -0.15 0.31 -10000 0 -0.68 103 103
positive regulation of mitosis -0.03 0.14 -10000 0 -0.44 39 39
LPA/LPA1-2-3 0.017 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 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation -0.001 0.1 0.38 3 -0.32 25 28
GNAZ -0.016 0.12 -10000 0 -0.45 28 28
EGFR/PI3K-beta/Gab1 -0.002 0.11 -10000 0 -0.4 25 25
positive regulation of dendritic cell cytokine production 0.016 0.12 -10000 0 -0.4 28 28
LPA/LPA2/MAGI-3 0.035 0.029 -10000 0 -0.46 1 1
ARHGEF1 0.003 0.1 0.37 2 -0.39 22 24
GNAI2 -0.014 0.12 -10000 0 -0.42 33 33
GNAI3 -0.013 0.12 -10000 0 -0.46 28 28
GNAI1 -0.012 0.12 -10000 0 -0.42 31 31
LPA/LPA3 0.015 0.023 -10000 0 -0.14 1 1
LPA/LPA2 0.021 0.011 -10000 0 -10000 0 0
LPA/LPA1 -0.017 0.14 -10000 0 -0.48 34 34
HB-EGF/EGFR -0.021 0.13 -10000 0 -0.44 35 35
HBEGF -0.036 0.14 -10000 0 -0.5 32 32
mol:DAG -0.008 0.065 0.36 2 -10000 0 2
cAMP biosynthetic process -0.034 0.17 0.41 10 -0.47 40 50
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
LYN -0.008 0.091 0.38 6 -0.41 2 8
GNAQ 0.016 0.014 -10000 0 -10000 0 0
LPAR2 0.026 0.007 -10000 0 -10000 0 0
LPAR3 0.012 0.034 -10000 0 -10000 0 0
LPAR1 -0.026 0.18 -10000 0 -0.62 34 34
IL8 -0.084 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 -0.35 33 33
EGFR 0.017 0.079 -10000 0 -0.69 5 5
PLCG1 -0.012 0.063 -10000 0 -0.3 1 1
PLD2 -0.005 0.1 -10000 0 -0.38 25 25
G12/G13 0.019 0.12 -10000 0 -0.41 27 27
PI3K-beta 0.004 0.086 -10000 0 -0.56 1 1
cell migration 0.019 0.074 -10000 0 -0.25 13 13
SLC9A3R2 0.026 0.007 -10000 0 -10000 0 0
PXN -0.003 0.1 0.26 2 -0.33 25 27
HRAS/GTP -0.029 0.15 -10000 0 -0.45 39 39
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 -0.04 0.19 -10000 0 -0.69 32 32
PRKCE 0.022 0.061 -10000 0 -0.69 3 3
PRKCD -0.007 0.084 0.41 6 -10000 0 6
Gi(beta/gamma) -0.023 0.14 -10000 0 -0.51 28 28
mol:LPA 0.002 0.014 -10000 0 -0.2 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.016 0.12 -10000 0 -0.38 24 24
MAPKKK cascade -0.03 0.14 -10000 0 -0.44 39 39
contractile ring contraction involved in cytokinesis 0.014 0.047 0.27 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.064 0.15 -10000 0 -0.35 90 90
GNA15 0.014 0.027 -10000 0 -0.37 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.005 0.097 0.34 7 -0.4 7 14
GNA11 0.014 0.038 -10000 0 -0.33 4 4
Rac1/GTP 0.017 0.19 -10000 0 -0.82 19 19
MMP2 -0.015 0.14 -10000 0 -0.5 28 28
Syndecan-4-mediated signaling events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.11 -10000 0 -0.81 6 6
Syndecan-4/Syndesmos -0.034 0.16 -10000 0 -0.55 32 32
positive regulation of JNK cascade -0.05 0.19 -10000 0 -0.56 33 33
Syndecan-4/ADAM12 -0.034 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 0.008 -10000 0 -10000 0 0
ITGA5 0.026 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
PLG 0.01 0.029 -10000 0 -10000 0 0
ADAM12 -0.012 0.066 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 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 -0.058 0.18 -10000 0 -0.6 31 31
Syndecan-4/CXCL12/CXCR4 -0.052 0.2 -10000 0 -0.59 33 33
Syndecan-4/Laminin alpha3 -0.042 0.17 -10000 0 -0.57 31 31
MDK -0.02 0.076 -10000 0 -0.69 1 1
Syndecan-4/FZD7 -0.034 0.16 -10000 0 -0.56 32 32
Syndecan-4/Midkine -0.04 0.16 -10000 0 -0.57 31 31
FZD7 0.021 0.057 -10000 0 -0.53 4 4
Syndecan-4/FGFR1/FGF -0.009 0.15 -10000 0 -0.52 31 31
THBS1 0.017 0.038 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.042 0.16 -10000 0 -0.57 32 32
positive regulation of MAPKKK cascade -0.05 0.19 -10000 0 -0.56 33 33
Syndecan-4/TACI -0.13 0.22 -10000 0 -0.59 36 36
CXCR4 0.026 0.014 -10000 0 -10000 0 0
cell adhesion -0.001 0.08 -10000 0 -0.32 22 22
Syndecan-4/Dynamin -0.033 0.16 -10000 0 -0.55 32 32
Syndecan-4/TSP1 -0.033 0.16 -10000 0 -0.56 32 32
Syndecan-4/GIPC -0.033 0.16 -10000 0 -0.55 32 32
Syndecan-4/RANTES -0.055 0.2 -10000 0 -0.67 34 34
ITGB1 0.027 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 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.001 0.21 0.74 16 -0.64 22 38
Syndecan-4/alpha-Actinin -0.032 0.16 -10000 0 -0.55 31 31
TFPI -0.013 0.16 -10000 0 -0.67 23 23
F2 0.013 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.07 0.18 -10000 0 -0.6 30 30
ACTN1 0.026 0.009 -10000 0 -10000 0 0
TNC -0.035 0.096 -10000 0 -0.69 4 4
Syndecan-4/CXCL12 -0.071 0.2 -10000 0 -0.56 43 43
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.051 0.22 -10000 0 -0.69 44 44
TNFRSF13B -0.16 0.3 -10000 0 -0.68 100 100
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.025 0.036 -10000 0 -0.69 1 1
Syndecan-4/PI-4-5-P2 -0.045 0.15 -10000 0 -0.56 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.074 0.077 -10000 0 -10000 0 0
cell migration -0.027 0.013 -10000 0 -10000 0 0
PRKCD 0.026 0.023 -10000 0 -10000 0 0
vasculogenesis -0.031 0.15 -10000 0 -0.53 32 32
SDC4 -0.044 0.16 -10000 0 -0.59 32 32
Syndecan-4/Tenascin C -0.044 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 -0.68 32 32
Rac1/GTP -0.002 0.081 -10000 0 -0.32 22 22
cytoskeleton organization -0.032 0.15 -10000 0 -0.53 32 32
GIPC1 0.025 0.007 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.052 0.18 -10000 0 -0.55 38 38
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.014 -10000 0 -10000 0 0
REL -0.003 0.16 -10000 0 -0.68 20 20
HDAC7 -0.064 0.1 -10000 0 -0.47 9 9
JUN -0.13 0.29 -10000 0 -0.68 86 86
EP300 0.02 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 -0.53 6 6
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.062 0.11 -10000 0 -0.48 10 10
MAP2K6 0.008 0.088 -10000 0 -0.7 6 6
BRM/BAF57 0.018 0.032 -10000 0 -10000 0 0
MAP2K4 0.019 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.013 0.074 -10000 0 -0.59 1 1
NCOA2 -0.032 0.19 -10000 0 -0.69 30 30
CEBPA 0.02 0.071 -10000 0 -0.69 4 4
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.078 0.2 0.59 17 -0.45 11 28
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.13 0.28 -10000 0 -0.69 82 82
RXRs/9cRA 0.024 0.073 -10000 0 -0.41 3 3
AR/RACK1/Src -0.13 0.13 0.33 2 -0.49 10 12
AR/GR -0.12 0.17 0.25 5 -0.32 161 166
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.007 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.005 -10000 0 -0.019 13 13
MAPK8 -0.008 0.049 -10000 0 -0.52 3 3
T-DHT/AR/TIF2/CARM1 -0.12 0.16 0.35 2 -0.54 32 34
SRC -0.038 0.064 0.24 1 -0.4 8 9
NR3C1 0.026 0.005 -10000 0 -10000 0 0
KLK3 -0.34 0.54 -10000 0 -1.2 110 110
APPBP2 0.024 0.012 -10000 0 -10000 0 0
TRIM24 0.014 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.065 0.11 0.34 5 -0.5 9 14
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 -10000 0 0
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.019 0.071 -10000 0 -0.69 4 4
KLK2 -0.44 0.39 0.33 2 -0.77 232 234
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 0.035 0.016 -10000 0 -10000 0 0
SRY 0.008 0.014 0.031 110 -10000 0 110
GATA2 0.027 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.011 0.035 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.095 0.12 0.34 3 -0.52 8 11
positive regulation of transcription 0.027 0.008 -10000 0 -10000 0 0
DNAJA1 0.024 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 0.022 -10000 0 -10000 0 0
SPDEF -0.002 0.048 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.084 0.13 0.28 2 -0.43 30 32
T-DHT/AR/Hsp90 -0.066 0.11 0.33 5 -0.48 9 14
GSK3B 0.025 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.066 0.26 1 -0.41 9 10
SIRT1 0.026 0.005 -10000 0 -10000 0 0
ZMIZ2 0.035 0.017 -10000 0 -10000 0 0
POU2F1 0.032 0.036 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.07 0.11 0.33 5 -0.5 9 14
CREBBP 0.025 0.006 -10000 0 -10000 0 0
SMARCE1 0.013 0.022 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.008 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 -10000 0 0
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 -0.26 1 1
CaM/Ca2+ 0.013 0.14 -10000 0 -0.34 50 50
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.012 0.13 -10000 0 -0.35 50 50
AKT1 -0.015 0.12 0.38 5 -0.35 2 7
MAP2K1 -0.025 0.12 0.29 2 -0.33 48 50
MAP3K11 -0.022 0.13 0.3 4 -0.35 50 54
IFNGR1 0.02 0.026 -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 -0.3 1 1
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.015 0.15 -10000 0 -0.38 50 50
CEBPB -0.056 0.18 0.55 5 -0.48 30 35
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.019 0.15 -10000 0 -0.66 3 3
STAT1 -0.021 0.13 0.32 6 -0.34 50 56
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.066 0.23 -10000 0 -0.69 50 50
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
STAT1 (dimer)/PIAS1 -0.006 0.13 0.3 4 -0.33 50 54
CEBPB/PTGES2/Cbp/p300 -0.024 0.12 -10000 0 -0.38 6 6
mol:Ca2+ 0.006 0.14 -10000 0 -0.36 50 50
MAPK3 -0.009 0.12 -10000 0 -0.65 3 3
STAT1 (dimer) 0.016 0.097 -10000 0 -10000 0 0
MAPK1 -0.16 0.3 0.43 1 -0.67 97 98
JAK2 0.019 0.026 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.02 0.026 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.04 0.18 0.5 9 -0.6 22 31
SMAD7 0.018 0.068 0.46 5 -10000 0 5
CBL/CRKL/C3G -0.008 0.12 0.3 2 -0.32 36 38
PI3K 0.012 0.13 -10000 0 -0.34 49 49
IFNG -0.067 0.23 -10000 0 -0.69 50 50
apoptosis -0.035 0.16 0.55 6 -0.45 28 34
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.013 0.032 -10000 0 -10000 0 0
CAMK2B 0.019 0.071 -10000 0 -0.69 4 4
FRAP1 -0.022 0.11 0.37 5 -0.33 2 7
PRKCD -0.011 0.13 0.43 9 -0.36 2 11
RAP1B 0.026 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.007 0.071 -10000 0 -0.26 1 1
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.021 0.012 -10000 0 -10000 0 0
IRF1 -0.014 0.087 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.011 0.12 0.3 2 -0.33 49 51
SOCS1 0.021 0.098 -10000 0 -0.96 4 4
mol:GDP -0.009 0.12 0.28 2 -0.31 45 47
CASP1 0.015 0.066 0.52 3 -0.33 2 5
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.057 0.34 1 -10000 0 1
mol:PI-3-4-5-P3 -0.001 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 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.007 0.071 -10000 0 -0.26 1 1
PTPN11 -0.025 0.13 -10000 0 -0.36 50 50
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.002 0.065 -10000 0 -0.27 2 2
AP1 -0.12 0.26 -10000 0 -0.56 84 84
mol:PIP3 0.028 0.18 0.64 17 -0.38 16 33
IKBKB 0.039 0.17 0.64 21 -0.25 9 30
AKT1 -0.007 0.12 0.32 19 -0.36 13 32
IKBKG 0.043 0.18 0.66 23 -0.26 7 30
MS4A2 -0.012 0.061 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.036 -10000 0 -0.69 1 1
MAP3K1 0.025 0.12 0.51 10 -0.42 5 15
mol:Ca2+ 0.034 0.17 0.58 21 -0.32 10 31
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 -0.021 0.17 -10000 0 -0.41 62 62
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.018 0.035 -10000 0 -10000 0 0
PLD2 -0.009 0.13 0.32 27 -0.38 24 51
PTPN13 0.013 0.14 0.48 2 -0.68 10 12
PTPN11 0.024 0.015 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.032 0.17 0.65 17 -0.38 4 21
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.001 0.11 -10000 0 -0.38 23 23
LAT -0.003 0.07 -10000 0 -0.31 6 6
PAK2 0.017 0.1 0.34 6 -0.43 7 13
NFATC2 -0.09 0.22 -10000 0 -0.62 58 58
HRAS 0.011 0.094 -10000 0 -0.48 6 6
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.004 0.098 -10000 0 -0.69 6 6
Fc epsilon R1 0.011 0.13 -10000 0 -0.46 26 26
Antigen/IgE/Fc epsilon R1 0.012 0.12 -10000 0 -0.42 26 26
mol:GDP 0.003 0.1 -10000 0 -0.5 9 9
JUN -0.12 0.29 -10000 0 -0.68 86 86
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.15 0.31 -10000 0 -0.68 103 103
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.004 0.069 -10000 0 -0.24 21 21
CHUK 0.038 0.17 0.62 21 -0.27 6 27
KLRG1 -0.006 0.076 -10000 0 -0.3 13 13
VAV1 -0.003 0.073 -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 -0.25 1 1
negative regulation of mast cell degranulation 0.008 0.08 -10000 0 -0.31 7 7
BTK -0.003 0.12 -10000 0 -0.56 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.16 -10000 0 -0.5 32 32
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 -0.27 24 24
RAF1 0.012 0.092 -10000 0 -0.85 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.024 0.18 -10000 0 -0.52 34 34
FCER1G 0.018 0.035 -10000 0 -10000 0 0
FCER1A -0.033 0.18 -10000 0 -0.69 27 27
Antigen/IgE/Fc epsilon R1/Fyn 0.03 0.12 -10000 0 -0.39 26 26
MAPK3 0.019 0.088 -10000 0 -0.77 4 4
MAPK1 -0.015 0.11 -10000 0 -0.71 6 6
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.003 0.17 -10000 0 -0.63 22 22
DUSP1 -0.083 0.26 -10000 0 -0.69 62 62
NF-kappa-B/RelA 0.015 0.046 -10000 0 -0.18 2 2
actin cytoskeleton reorganization 0.013 0.14 0.4 2 -0.7 10 12
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 0.027 0.005 -10000 0 -10000 0 0
ITK -0.044 0.15 -10000 0 -0.47 46 46
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.011 0.12 0.41 6 -0.51 8 14
cytokine secretion 0.005 0.03 -10000 0 -10000 0 0
SPHK1 0 0.066 0.23 2 -0.26 2 4
PTK2 0.012 0.14 0.4 2 -0.75 10 12
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 0.034 0.18 0.72 15 -0.41 9 24
MAP2K2 0.015 0.093 -10000 0 -0.79 4 4
MAP2K1 0.009 0.085 -10000 0 -0.79 4 4
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 0 0.078 -10000 0 -0.3 12 12
MAP2K4 -0.012 0.21 -10000 0 -0.83 23 23
Fc epsilon R1/FcgammaRIIB 0.012 0.18 -10000 0 -0.55 34 34
mol:Choline -0.009 0.13 0.32 27 -0.38 24 51
SHC/Grb2/SOS1 0.037 0.076 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.017 0.14 0.5 3 -0.67 10 13
HCLS1 0 0.064 -10000 0 -0.28 2 2
PRKCB 0.037 0.18 0.66 21 -0.34 11 32
FCGR2B -0.011 0.16 -10000 0 -0.69 20 20
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.008 0.081 -10000 0 -0.32 7 7
LCP2 0.024 0.022 -10000 0 -10000 0 0
PLA2G4A -0.027 0.12 -10000 0 -0.4 32 32
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.13 0.32 27 -0.38 24 51
IKK complex 0.045 0.18 0.67 23 -0.21 3 26
WIPF1 0.027 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.016 0.12 -10000 0 -0.52 12 12
BAG4 0.025 0.036 -10000 0 -0.69 1 1
PKC zeta/ceramide -0.019 0.1 -10000 0 -0.4 16 16
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.011 0.15 -10000 0 -0.64 21 21
BAX -0.012 0.075 -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 0.091 0.18 1 -0.3 26 27
SMPD1 -0.011 0.092 0.29 6 -0.23 48 54
RB1 -0.031 0.093 0.19 1 -0.33 22 23
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.55 11 11
MAP2K4 -0.019 0.074 0.22 2 -0.39 7 9
NSMAF 0.027 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 -0.071 0.24 -10000 0 -0.68 55 55
mol:ceramide -0.036 0.1 -10000 0 -0.32 29 29
MADD 0.027 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 0.025 0.036 -10000 0 -0.69 1 1
negative regulation of cell cycle -0.031 0.092 0.19 1 -0.33 22 23
cell proliferation -0.056 0.15 -10000 0 -0.33 79 79
BID -0.14 0.28 -10000 0 -0.6 100 100
MAP3K1 -0.027 0.082 -10000 0 -0.32 19 19
EIF2A -0.028 0.081 -10000 0 -0.47 9 9
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.072 -10000 0 -0.37 8 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.042 0.088 -10000 0 -0.38 11 11
Cathepsin D/ceramide -0.017 0.096 -10000 0 -0.31 24 24
FADD -0.016 0.12 -10000 0 -0.53 12 12
KSR1 -0.026 0.089 0.18 5 -0.44 11 16
MAPK8 -0.015 0.087 -10000 0 -0.4 12 12
PRKRA -0.034 0.095 -10000 0 -0.46 12 12
PDGFA 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.008 -10000 0 -10000 0 0
IGF1 -0.12 0.29 -10000 0 -0.68 83 83
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 0.039 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 79 79
PRKCD 0.027 0.004 -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 0.039 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 -0.55 12 12
TNFR1A/BAG4/TNF-alpha -0.005 0.16 -10000 0 -0.45 47 47
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.022 0.079 -10000 0 -0.44 8 8
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.007 0.07 0.17 18 -0.25 15 33
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.029 -10000 0 -0.52 1 1
EIF2AK2 -0.03 0.088 -10000 0 -0.51 9 9
TNF-alpha/TNFR1A/FAN -0.004 0.16 -10000 0 -0.45 46 46
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.083 -10000 0 -0.57 3 3
MAP2K2 -0.015 0.068 -10000 0 -0.41 5 5
SMPD3 -0.02 0.11 -10000 0 -0.27 55 55
TNF -0.058 0.23 -10000 0 -0.69 46 46
PKC zeta/PAR4 0.038 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.014 0.11 0.26 54 -0.26 15 69
NF kappa B1/RelA/I kappa B alpha 0.075 0.023 -10000 0 -10000 0 0
AIFM1 -0.011 0.087 0.17 18 -0.28 21 39
BCL2 -0.018 0.17 -10000 0 -0.68 26 26
Signaling events mediated by PRL

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
CCNE1 0.025 0.007 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0.086 -10000 0 -0.69 6 6
CDKN1A -0.008 0.074 -10000 0 -0.62 1 1
PRL-3/alpha Tubulin 0.03 0.031 -10000 0 -10000 0 0
mol:Ca2+ -0.028 0.077 0.2 4 -0.53 8 12
AGT 0.004 0.1 -10000 0 -0.69 8 8
CCNA2 -0.07 0.15 -10000 0 -0.38 81 81
TUBA1B 0.026 0.005 -10000 0 -10000 0 0
EGR1 -0.088 0.21 -10000 0 -0.51 82 82
CDK2/Cyclin E1 0.018 0.078 -10000 0 -0.55 1 1
MAPK3 0.01 0.024 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.039 0.008 -10000 0 -10000 0 0
MAPK1 0.008 0.021 -10000 0 -10000 0 0
PTP4A1 -0.072 0.16 -10000 0 -0.4 82 82
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 -0.014 0.086 -10000 0 -0.62 2 2
Rab GGTase beta/Rab GGTase alpha 0.038 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.054 0.16 -10000 0 -0.38 81 81
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.007 -10000 0 -10000 0 0
RHOC -0.014 0.088 -10000 0 -0.4 7 7
RHOA -0.014 0.09 -10000 0 -0.42 8 8
cell motility -0.008 0.099 0.28 3 -0.38 9 12
PRL-1/alpha Tubulin -0.052 0.16 -10000 0 -0.38 82 82
PRL-3/alpha1 Integrin 0.022 0.075 -10000 0 -0.54 6 6
ROCK1 -0.009 0.097 0.26 2 -0.4 8 10
RABGGTB 0.027 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 82 82
ATF5 0.02 0.029 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.062 -10000 0 -0.52 5 5
alphaV beta3 Integrin 0.037 0.088 -10000 0 -0.49 10 10
PTK2 0.007 0.14 0.41 9 -0.52 10 19
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.008 0.05 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
CDKN1B -0.036 0.18 -10000 0 -0.55 42 42
VEGFA 0.024 0.05 -10000 0 -0.69 2 2
ILK -0.036 0.18 -10000 0 -0.54 43 43
ROCK1 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.037 0.16 -10000 0 -0.51 42 42
PTK2B 0.011 0.094 0.36 1 -0.44 13 14
alphaV/beta3 Integrin/JAM-A -0.001 0.15 -10000 0 -0.41 47 47
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.034 0.086 -10000 0 -0.47 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.079 0.24 -10000 0 -0.44 115 115
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.004 0.098 -10000 0 -0.4 5 5
alphaV/beta3 Integrin/Syndecan-1 0.038 0.088 -10000 0 -0.49 10 10
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.085 0.24 -10000 0 -0.44 117 117
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
alphaV/beta3 Integrin/Osteopontin 0.017 0.14 -10000 0 -0.44 31 31
RPS6KB1 -0.14 0.19 0.42 2 -0.42 117 119
TLN1 0.025 0.007 -10000 0 -10000 0 0
MAPK3 -0.054 0.14 -10000 0 -0.66 11 11
GPR124 0.027 0.004 -10000 0 -10000 0 0
MAPK1 -0.065 0.15 -10000 0 -0.59 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 0.024 0.13 -10000 0 -0.52 19 19
cell adhesion 0.028 0.084 -10000 0 -0.47 9 9
ANGPTL3 0.007 0.023 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.057 -10000 0 -0.45 5 5
IGF-1R heterotetramer 0.027 0.004 -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 83 83
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.037 0.087 -10000 0 -0.49 10 10
apoptosis 0.025 0.036 -10000 0 -0.69 1 1
CD47 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.038 0.088 -10000 0 -0.49 10 10
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.034 0.1 -10000 0 -0.51 13 13
CSF1 0.018 0.079 -10000 0 -0.69 5 5
PIK3C2A -0.036 0.18 -10000 0 -0.54 43 43
PI4 Kinase/Pyk2 -0.02 0.13 -10000 0 -0.62 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.046 0.1 -10000 0 -0.47 13 13
FAK1/Vinculin 0.019 0.13 0.39 8 -0.46 6 14
alphaV beta3/Integrin/ppsTEM5 0.038 0.088 -10000 0 -0.49 10 10
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN -0.048 0.22 -10000 0 -0.69 41 41
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.04 0.089 -10000 0 -0.49 10 10
alphaV/beta3 Integrin/TGFBR2 0.037 0.089 -10000 0 -0.47 11 11
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.057 0.061 -10000 0 -0.41 6 6
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.034 0.081 -10000 0 -0.45 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.081 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 -0.049 0.22 -10000 0 -0.69 43 43
FAK1/Paxillin 0.016 0.12 0.34 6 -0.46 6 12
cell migration 0.013 0.11 0.34 5 -0.41 6 11
ITGAV 0.025 0.036 -10000 0 -0.69 1 1
PI3K 0.01 0.15 -10000 0 -0.38 47 47
SPP1 -0.033 0.16 -10000 0 -0.69 20 20
KDR 0.022 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 0.025 0.036 -10000 0 -0.69 1 1
COL4A3 0.005 0.12 -10000 0 -0.66 13 13
angiogenesis -0.059 0.16 -10000 0 -0.63 17 17
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
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.013 0.19 -10000 0 -0.89 16 16
NCK1/PAK1/Dok-R -0.028 0.085 -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 0.027 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 0.25 13 -10000 0 13
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.013 0.22 -10000 0 -0.98 16 16
FN1 -0.081 0.067 -10000 0 -10000 0 0
PLD2 -0.021 0.22 -10000 0 -1.1 16 16
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GRB14 0 0.14 -10000 0 -0.69 15 15
ELK1 -0.022 0.2 -10000 0 -0.96 16 16
GRB7 0.004 0.053 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.015 0.24 -10000 0 -1.1 16 16
CDKN1A -0.024 0.16 0.5 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 0.22 -10000 0 -1 17 17
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.011 0.17 0.54 8 -0.65 16 24
PLG -0.027 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 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 0.42 1 -0.82 14 15
BMX -0.029 0.23 -10000 0 -1.1 16 16
ANGPT1 -0.041 0.25 -10000 0 -1.3 14 14
tube development -0.038 0.17 0.45 3 -0.7 16 19
ANGPT4 -0.033 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 0.039 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 0.54 8 -0.65 16 24
AGTR1 -0.26 0.35 -10000 0 -0.68 163 163
MAPK14 -0.022 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 -0.52 163 163
Tie2/Ang1/GRB2 -0.012 0.23 -10000 0 -1.1 16 16
MAPK3 -0.017 0.21 -10000 0 -0.98 16 16
MAPK1 -0.026 0.2 -10000 0 -0.99 16 16
Tie2/Ang1/GRB7 -0.012 0.24 -10000 0 -1.1 16 16
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.025 0.23 -10000 0 -1.1 16 16
PI3K -0.018 0.22 -10000 0 -1 16 16
FES -0.024 0.23 -10000 0 -1.1 16 16
Crk/Dok-R 0 0.22 -10000 0 -1 17 17
Tie2/Ang1/ABIN2 -0.012 0.23 -10000 0 -1.1 16 16
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.005 0.18 0.52 3 -0.8 16 19
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.011 0.19 -10000 0 -0.86 16 16
Tie2/Ang2 -0.054 0.21 -10000 0 -0.96 16 16
Tie2/Ang1 -0.022 0.24 -10000 0 -1.2 16 16
FOXO1 -0.001 0.18 0.57 3 -0.8 16 19
ELF1 0.03 0.039 -10000 0 -0.68 1 1
ELF2 -0.02 0.22 -10000 0 -1 16 16
mol:Choline -0.019 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 0.02 0.055 -10000 0 -0.69 2 2
negative regulation of cell cycle -0.02 0.14 0.5 3 -0.56 16 19
ETS1 0.025 0.047 -10000 0 -0.24 11 11
PXN 0.002 0.17 0.52 6 -0.7 16 22
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.004 0.18 0.6 5 -0.74 16 21
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.058 0.24 -10000 0 -0.7 46 46
MAPKKK cascade -0.019 0.21 -10000 0 -1 16 16
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.014 0.23 -10000 0 -1.1 16 16
NCK1 0.027 0.004 -10000 0 -10000 0 0
vasculogenesis 0.013 0.16 0.51 9 -0.58 16 25
mol:Phosphatidic acid -0.019 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 0.54 8 -0.65 16 24
Rac1/GTP -0.005 0.17 -10000 0 -0.79 16 16
MMP2 -0.025 0.22 -10000 0 -1.1 16 16
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.018 0.13 -10000 0 -0.44 22 22
MAP4K1 0.008 0.085 -10000 0 -0.69 5 5
MAP3K8 0.016 0.086 -10000 0 -0.69 6 6
PRKCB 0.008 0.066 -10000 0 -0.69 2 2
DBNL 0.026 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.001 0.083 -10000 0 -0.32 21 21
JUN -0.073 0.2 0.42 2 -0.46 43 45
MAP3K7 0.001 0.083 -10000 0 -0.32 21 21
GRAP2 -0.019 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 16 18
LAT 0.019 0.065 -10000 0 -0.61 4 4
LCP2 0.023 0.021 -10000 0 -10000 0 0
MAPK8 0.005 0.12 -10000 0 -0.57 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.004 0.088 -10000 0 -0.33 24 24
LAT/GRAP2/SLP76/HPK1/HIP-55 0.027 0.12 -10000 0 -0.44 20 20
Signaling events mediated by PTP1B

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
PDGFRB 0.026 0.005 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.001 0.12 0.32 1 -0.37 24 25
PTP1B/AKT1 0.007 0.071 0.32 2 -0.33 3 5
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.003 0.087 0.35 10 -0.31 5 15
EGFR 0.012 0.081 -10000 0 -0.7 5 5
EGF/EGFR -0.034 0.16 0.24 1 -0.4 58 59
CSF1 0.018 0.079 -10000 0 -0.69 5 5
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.026 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.002 0.12 0.33 6 -0.39 16 22
Insulin Receptor/Insulin 0.018 0.068 -10000 0 -0.32 2 2
HCK 0.018 0.036 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 0.01 0.093 0.35 15 -0.34 3 18
EGF -0.071 0.24 -10000 0 -0.69 55 55
YES1 0.027 0.005 -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 0.27 1 -0.38 44 45
cell migration -0.003 0.087 0.31 5 -0.35 10 15
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.01 0.15 -10000 0 -0.69 18 18
ITGA2B -0.051 0.22 -10000 0 -0.68 44 44
CSF1R 0.023 0.039 -10000 0 -0.69 1 1
Prolactin Receptor/Prolactin 0.005 0.12 -10000 0 -0.52 18 18
FGR 0.025 0.016 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.007 0.073 0.27 3 -0.33 3 6
Crk/p130 Cas 0.013 0.071 -10000 0 -0.34 2 2
DOK1 0.016 0.093 0.42 11 -0.32 3 14
JAK2 -0.005 0.13 0.31 8 -0.38 26 34
Jak2/Leptin Receptor/Leptin -0.024 0.16 -10000 0 -0.51 29 29
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.003 0.088 0.35 10 -0.31 5 15
LYN 0.027 0.004 -10000 0 -10000 0 0
CDH2 -0.073 0.14 -10000 0 -0.65 15 15
SRC 0.024 0.056 0.31 1 -0.43 3 4
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
CAT1/PTP1B -0.059 0.16 0.43 12 -0.36 29 41
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.025 0.072 -10000 0 -0.48 1 1
mol:H2O2 -0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.025 0.16 -10000 0 -0.54 29 29
negative regulation of transcription -0.004 0.13 0.31 8 -0.38 26 34
FCGR2A 0.017 0.048 -10000 0 -0.69 1 1
FER 0.022 0.051 -10000 0 -0.7 2 2
alphaIIb/beta3 Integrin -0.036 0.2 -10000 0 -0.55 51 51
BLK -0.2 0.32 -10000 0 -0.68 123 123
Insulin Receptor/Insulin/Shc 0.042 0.018 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.02 0.063 -10000 0 -0.59 4 4
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.092 0.18 0.4 3 -0.47 33 36
PRL -0.005 0.021 -10000 0 -10000 0 0
SOCS3 -0.087 0.38 -10000 0 -1.3 36 36
SPRY2 0.025 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.009 0.15 -10000 0 -0.46 43 43
CSF1/CSF1R 0.01 0.088 0.28 1 -0.4 8 9
Ras protein signal transduction 0.022 0.095 0.46 16 -10000 0 16
IRS1 -0.049 0.22 -10000 0 -0.69 43 43
INS 0.01 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 -0.29 11 21
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.07 0.28 1 -0.34 3 4
CSN2 0.001 0.064 0.81 1 -10000 0 1
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
LAT 0.02 0.08 0.29 3 -0.46 8 11
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.012 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
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.006 0.1 -10000 0 -0.55 8 8
alphaM/beta2 Integrin/GPIbA -0.004 0.12 -10000 0 -0.5 16 16
alphaM/beta2 Integrin/proMMP-9 -0.026 0.17 -10000 0 -0.53 34 34
PLAUR -0.024 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 -0.58 5 5
AGER -0.05 0.2 -10000 0 -0.71 32 32
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.017 0.036 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.05 0.21 -10000 0 -0.48 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.04 0.19 -10000 0 -0.69 32 32
CYR61 -0.18 0.32 -10000 0 -0.68 116 116
TLN1 0.025 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.005 0.096 -10000 0 -0.38 10 10
RHOA 0.027 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.013 0.087 -10000 0 -0.69 6 6
MYH2 -0.037 0.11 -10000 0 -0.44 10 10
MST1R 0.016 0.082 -10000 0 -0.64 6 6
leukocyte activation during inflammatory response 0.011 0.086 -10000 0 -0.51 5 5
APOB 0.01 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 0.02 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 -0.053 0.19 -10000 0 -0.48 60 60
alphaM/beta2 Integrin -0.029 0.1 -10000 0 -0.33 24 24
JAM3 homodimer 0.026 0.005 -10000 0 -10000 0 0
ICAM2 0.026 0.007 -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 -0.029 0.1 -10000 0 -0.33 24 24
cell adhesion -0.004 0.12 -10000 0 -0.5 16 16
NFKB1 -0.14 0.28 0.38 1 -0.7 51 52
THY1 0.026 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.023 0.025 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.025 0.1 -10000 0 -0.5 8 8
IL6 -0.23 0.41 -10000 0 -0.97 87 87
ITGB2 -0.006 0.061 -10000 0 -0.37 3 3
elevation of cytosolic calcium ion concentration 0.01 0.11 -10000 0 -0.53 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.023 0.1 -10000 0 -0.52 8 8
JAM2 0.019 0.071 -10000 0 -0.69 4 4
alphaM/beta2 Integrin/ICAM1 0.026 0.12 -10000 0 -0.54 8 8
alphaM/beta2 Integrin/uPA/Plg 0.013 0.1 -10000 0 -0.54 5 5
RhoA/GTP -0.032 0.12 -10000 0 -0.39 19 19
positive regulation of phagocytosis -0.012 0.1 -10000 0 -0.59 5 5
Ron/MSP 0.03 0.07 -10000 0 -0.48 7 7
alphaM/beta2 Integrin/uPAR/uPA 0.012 0.12 -10000 0 -0.54 5 5
alphaM/beta2 Integrin/uPAR 0.007 0.1 -10000 0 -0.57 5 5
PLAU -0.04 0.074 -10000 0 -10000 0 0
PLAT 0.02 0.054 -10000 0 -0.69 2 2
actin filament polymerization -0.035 0.1 -10000 0 -0.42 10 10
MST1 0.025 0.036 -10000 0 -0.69 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.015 0.089 -10000 0 -0.52 5 5
TNF -0.18 0.36 0.38 1 -0.94 61 62
RAP1B 0.026 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.11 -10000 0 -0.53 6 6
fibrinolysis 0.011 0.1 -10000 0 -0.54 5 5
HCK 0.018 0.036 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.029 0.1 -10000 0 -0.33 24 24
VTN -0.048 0.22 -10000 0 -0.69 41 41
alphaM/beta2 Integrin/CYR61 -0.12 0.24 -10000 0 -0.48 118 118
LPA -0.005 0.026 -10000 0 -10000 0 0
LRP1 0.025 0.036 -10000 0 -0.69 1 1
cell migration -0.033 0.16 -10000 0 -0.51 34 34
FN1 -0.081 0.067 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.01 0.094 -10000 0 -0.58 5 5
MPO 0.011 0.087 -10000 0 -0.69 6 6
KNG1 -0.004 0.037 -10000 0 -10000 0 0
RAP1/GDP 0.035 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 -0.073 0.25 -10000 0 -0.67 58 58
alphaM/beta2 Integrin/Hck 0.006 0.098 -10000 0 -0.53 6 6
ITGAM -0.009 0.088 -10000 0 -0.75 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.015 0.11 -10000 0 -0.54 10 10
HP -0.021 0.1 -10000 0 -0.69 6 6
leukocyte adhesion -0.038 0.18 -10000 0 -0.54 23 23
SELP 0.013 0.088 -10000 0 -0.69 6 6
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.016 0.12 -10000 0 -0.48 15 15
BAG4 0.025 0.036 -10000 0 -0.69 1 1
BAD 0.007 0.07 0.37 8 -10000 0 8
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.011 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 15 25
IKBKB -0.016 0.12 -10000 0 -0.46 14 14
MAP2K2 0.016 0.096 0.37 17 -0.31 1 18
MAP2K1 0.011 0.087 0.39 11 -0.31 1 12
SMPD1 0.005 0.048 0.27 6 -0.16 2 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.011 0.12 -10000 0 -0.48 15 15
MAP2K4 0.017 0.1 0.38 20 -10000 0 20
protein ubiquitination -0.011 0.13 0.41 5 -0.46 15 20
EnzymeConsortium:2.7.1.37 0.017 0.11 0.4 20 -0.31 1 21
response to UV 0 0.002 0.007 22 -0.002 2 24
RAF1 0.012 0.089 0.32 18 -0.32 1 19
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 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.08 0.32 15 -10000 0 15
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.017 0.091 0.34 17 -0.3 1 18
MAPK1 -0.005 0.095 0.36 13 -0.28 2 15
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.016 0.12 -10000 0 -0.47 15 15
KSR1 0.011 0.083 0.3 18 -0.34 1 19
MAPK8 0.015 0.11 0.39 19 -0.37 3 22
TRAF2 0.025 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 12 -10000 0 12
CHUK -0.015 0.12 0.33 1 -0.46 14 15
TNF R/SODD 0.038 0.029 -10000 0 -0.52 1 1
TNF -0.057 0.23 -10000 0 -0.69 46 46
CYCS 0.018 0.083 0.27 21 -0.18 1 22
IKBKG -0.013 0.12 0.32 2 -0.46 14 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.017 0.13 -10000 0 -0.5 15 15
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.016 0.082 0.28 17 -0.18 2 19
TNF/TNF R/SODD -0.005 0.16 -10000 0 -0.45 47 47
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 12 -10000 0 12
CASP8 0.01 0.12 -10000 0 -0.74 10 10
NSMAF -0.016 0.12 -10000 0 -0.47 15 15
response to hydrogen peroxide 0 0.002 0.007 22 -0.002 2 24
BCL2 -0.018 0.17 -10000 0 -0.68 26 26
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.035 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 -0.4 39 39
VEGFR1 homodimer/NRP1/VEGFR 121 0.03 0.032 -10000 0 -0.41 2 2
CaM/Ca2+ -0.005 0.12 -10000 0 -0.38 39 39
HIF1A 0.033 0.006 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.017 0.12 -10000 0 -0.52 3 3
PLCG1 -0.02 0.13 -10000 0 -0.41 39 39
NOS3 -0.013 0.12 -10000 0 -0.4 2 2
CBL 0.027 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 -0.043 0.21 -10000 0 -0.68 40 40
VEGFR1 homodimer/NRP2/VEGFR121 0.047 0.037 -10000 0 -0.41 2 2
CALM1 0.027 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 -10000 0 0
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 -0.045 0.14 0.35 2 -0.44 21 23
MAPK1 -0.047 0.14 0.35 1 -0.39 53 54
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.043 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 0.012 0.099 -10000 0 -0.69 8 8
VEGFA homodimer 0.024 0.05 -10000 0 -0.69 2 2
VEGFR1 homodimer/VEGFA homodimer 0.033 0.035 -10000 0 -0.45 2 2
platelet activating factor biosynthetic process -0.048 0.13 -10000 0 -0.68 4 4
PI3K 0.018 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 0.024 0.05 -10000 0 -0.69 2 2
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.02 0.13 -10000 0 -0.4 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 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.001 0.13 0.45 3 -0.56 2 5
PTPN11 0.026 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.016 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 0.06 0.038 -10000 0 -0.39 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.047 0.036 -10000 0 -0.41 2 2
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.028 0.13 -10000 0 -0.37 39 39
PDPK1 -0.014 0.12 0.34 3 -0.37 37 40
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.046 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 0.058 0.037 -10000 0 -0.38 2 2
VEGFR1 homodimer/NRP2 0.036 0.014 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.075 -9999 0 -0.39 12 12
RGS9BP -0.018 0.17 -9999 0 -0.68 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.044 0.21 -9999 0 -0.67 40 40
mol:Na + 0.018 0.033 -9999 0 -10000 0 0
mol:ADP -0.047 0.15 -9999 0 -0.52 39 39
GNAT2 0.017 0.021 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.024 0.18 -9999 0 -0.46 59 59
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.01 -9999 0 -10000 0 0
GRK7 0.006 0.022 -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 -0.005 0.17 -9999 0 -0.41 57 57
Cone Metarhodopsin II -0.013 0.13 -9999 0 -0.41 39 39
Na + (4 Units) 0.031 0.033 -9999 0 -10000 0 0
GNAT2/GDP -0.01 0.16 -9999 0 -0.4 55 55
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.001 0.024 -9999 0 -10000 0 0
Cone Transducin 0.033 0.079 -9999 0 -0.41 12 12
SLC24A2 -0.007 0.03 -9999 0 -10000 0 0
GNB3/GNGT2 0.021 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 0.008 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 0.018 0.033 -9999 0 -10000 0 0
mol:Pi -0.024 0.18 -9999 0 -0.46 59 59
Cone CNG Channel 0.051 0.021 -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 -0.04 0.2 -9999 0 -0.69 37 37
PDE6C -0.004 0.02 -9999 0 -10000 0 0
GNGT2 0.025 0.012 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.004 0.02 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.037 0.029 -10000 0 -0.52 1 1
Necdin/E2F1 0.001 0.067 -10000 0 -0.57 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.053 0.1 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.19 0.26 -10000 0 -0.46 192 192
NT-4/5 (dimer)/p75(NTR) -0.01 0.13 -10000 0 -0.53 23 23
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.003 0.1 0.36 1 -0.41 17 18
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.006 0.11 -10000 0 -0.69 10 10
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.1 -10000 0 -0.46 15 15
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.024 0.12 -10000 0 -0.43 25 25
LINGO1 0.021 0.03 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.032 0.024 -10000 0 -0.36 1 1
proBDNF (dimer) 0.006 0.11 -10000 0 -0.69 10 10
NTRK1 0.012 0.028 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.021 0.14 0.49 9 -0.52 6 15
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.01 0.099 -10000 0 -0.46 16 16
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.029 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.044 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 0.044 0.097 -10000 0 -0.41 16 16
proNGF (dimer) 0.021 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 0.026 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.009 0.093 -10000 0 -0.41 16 16
NGF 0.021 0.062 -10000 0 -0.69 3 3
cell cycle arrest 0.057 0.14 0.46 14 -0.39 16 30
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.015 0.075 -10000 0 -0.32 17 17
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.021 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 0.026 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 0.018 0.064 -10000 0 -0.36 5 5
p75(NTR)/beta APP 0.003 0.11 -10000 0 -0.52 15 15
BEX1 -0.29 0.35 -10000 0 -0.69 180 180
mol:GDP -0.02 0.097 -10000 0 -0.46 17 17
NGF (dimer) 0.041 0.11 -10000 0 -0.41 23 23
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.034 0.096 -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 0.027 0.004 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.032 0.11 -10000 0 -0.48 16 16
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -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 -0.002 0.098 -10000 0 -0.44 16 16
BDNF (dimer) 0.009 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 0.047 0.098 -10000 0 -0.41 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.044 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 0.38 13 -0.39 14 27
DIABLO 0.026 0.005 -10000 0 -10000 0 0
SMPD2 0 0.1 -10000 0 -0.44 16 16
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.032 0.11 -10000 0 -0.48 16 16
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 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 0.38 13 -0.41 15 28
MAPK9 0.007 0.11 0.35 9 -0.4 13 22
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 0.049 0.093 -10000 0 -0.39 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.061 0.048 -10000 0 -0.79 1 1
RhoA-B-C/GTP 0.031 0.1 -10000 0 -0.47 16 16
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.046 0.11 -10000 0 -0.39 22 22
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.037 0.12 -10000 0 -0.41 23 23
PRKACB 0.027 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.022 0.092 -10000 0 -0.52 11 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.011 0.15 -10000 0 -0.64 21 21
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.072 0.15 0.54 9 -0.4 16 25
BAD 0.028 0.16 0.48 23 -0.4 15 38
RIPK2 0.027 0.005 -10000 0 -10000 0 0
NGFR -0.018 0.14 -10000 0 -0.69 15 15
CYCS 0.006 0.11 0.36 10 -0.41 16 26
ADAM17 0.025 0.036 -10000 0 -0.69 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.043 0.11 -10000 0 -0.44 17 17
BCL2L11 0.028 0.16 0.47 23 -0.4 15 38
BDNF (dimer)/p75(NTR) -0.012 0.13 -10000 0 -0.51 25 25
PI3K 0.044 0.1 -10000 0 -0.44 17 17
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.046 0.1 -10000 0 -0.44 16 16
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.001 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 0.044 0.1 -10000 0 -0.44 16 16
TRAF6 0.025 0.036 -10000 0 -0.69 1 1
RAC1 0.026 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 -0.41 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 15 38
E2F1 -0.019 0.069 -10000 0 -10000 0 0
CASP9 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.048 0.08 -10000 0 -0.42 5 5
NGF (dimer)/TRKA 0.028 0.053 -10000 0 -0.52 3 3
MMP7 -0.078 0.16 -10000 0 -0.67 21 21
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 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
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.037 0.12 0.87 5 -10000 0 5
VDR 0.026 0.009 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.003 0.11 -10000 0 -0.41 6 6
RXRs/LXRs/DNA/Oxysterols -0.01 0.15 -10000 0 -0.42 44 44
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.001 0.018 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.023 0.06 -10000 0 -0.29 14 14
RXRs/NUR77 -0.091 0.24 -10000 0 -0.47 109 109
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 0.05 0.071 -10000 0 -0.4 9 9
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 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 0.049 0.12 0.55 21 -10000 0 21
RARs/THRs/DNA/SMRT 0.023 0.06 -10000 0 -0.29 14 14
THRA 0.026 0.007 -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 0.041 0.099 -10000 0 -0.43 4 4
NR1H4 -0.004 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.061 0.12 -10000 0 -0.5 3 3
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.023 0.026 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.052 0.081 -10000 0 -0.46 2 2
NR4A1 -0.18 0.33 -10000 0 -0.69 120 120
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.054 -10000 0 -0.32 2 2
RXRG -0.1 0.076 -10000 0 -0.59 4 4
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.02 0.025 -10000 0 -10000 0 0
RXRB 0.023 0.026 -10000 0 -10000 0 0
THRB 0.018 0.079 -10000 0 -0.69 5 5
PPARG 0.017 0.08 -10000 0 -0.69 5 5
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.098 0.38 -10000 0 -1.1 47 47
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.009 0.15 -10000 0 -0.41 44 44
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 -0.34 123 123
SREBF1 -0.01 0.14 -10000 0 -0.6 3 3
RXRs/RXRs/DNA/9cRA 0.041 0.099 -10000 0 -0.43 4 4
ABCA1 -0.009 0.14 -10000 0 -0.6 3 3
RARs/THRs 0.059 0.088 -10000 0 -0.39 14 14
RXRs/FXR 0.052 0.087 -10000 0 -0.49 2 2
BCL2 -0.018 0.17 -10000 0 -0.68 26 26
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 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 0.47 8 -10000 0 8
IL27/IL27R/JAK1 -0.005 0.16 -10000 0 -0.56 3 3
TBX21 -0.062 0.18 0.38 4 -0.58 23 27
IL12B 0.006 0.074 -10000 0 -0.69 4 4
IL12A -0.045 0.15 -10000 0 -0.52 39 39
IL6ST -0.058 0.22 -10000 0 -0.69 45 45
IL27RA/JAK1 0.018 0.052 0.55 1 -10000 0 1
IL27 0.011 0.027 -10000 0 -10000 0 0
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.053 0.14 -10000 0 -0.49 4 4
T-helper 2 cell differentiation 0.039 0.12 0.47 8 -10000 0 8
T cell proliferation during immune response 0.039 0.12 0.47 8 -10000 0 8
MAPKKK cascade -0.039 0.12 -10000 0 -0.47 8 8
STAT3 0.026 0.007 -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 0.008 0.067 -10000 0 -0.58 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.054 0.19 0.53 8 -0.6 14 22
IL27/IL27R/JAK2/TYK2 -0.039 0.12 -10000 0 -0.47 8 8
positive regulation of T cell mediated cytotoxicity -0.039 0.12 -10000 0 -0.47 8 8
STAT1 (dimer) -0.016 0.21 0.52 9 -0.75 5 14
JAK2 0.02 0.019 -10000 0 -10000 0 0
JAK1 0.027 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.028 0.13 -10000 0 -0.45 8 8
T cell proliferation -0.12 0.2 -10000 0 -0.55 36 36
IL12/IL12R/TYK2/JAK2 -0.067 0.23 -10000 0 -0.81 24 24
IL17A -0.054 0.14 -10000 0 -0.49 4 4
mast cell activation 0.039 0.12 0.47 8 -10000 0 8
IFNG -0.015 0.051 0.1 1 -0.13 55 56
T cell differentiation -0.004 0.008 -10000 0 -0.023 45 45
STAT3 (dimer) -0.028 0.13 -10000 0 -0.45 8 8
STAT5A (dimer) -0.028 0.13 -10000 0 -0.45 8 8
STAT4 (dimer) -0.034 0.14 -10000 0 -0.46 10 10
STAT4 0.001 0.1 -10000 0 -0.59 10 10
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.019 0.14 -10000 0 -0.53 3 3
GATA3 -0.065 0.31 -10000 0 -1.4 22 22
IL18 -0.012 0.078 -10000 0 -0.49 9 9
positive regulation of mast cell cytokine production -0.027 0.13 -10000 0 -0.44 8 8
IL27/EBI3 -0.028 0.06 -10000 0 -0.27 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.12 0.28 -10000 0 -0.69 81 81
STAT5A 0.026 0.007 -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 -0.05 0.074 -10000 0 -0.38 1 1
TNF -0.054 0.17 -10000 0 -0.52 46 46
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.003 0.039 -10000 0 -0.45 3 3
ADCY5 -0.058 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 0.045 -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 -0.035 0.095 0.35 6 -0.34 14 20
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.026 0.37 1 -10000 0 1
HSPA8 0.021 0.054 -10000 0 -0.58 3 3
SMAD3/SMAD4/ER alpha -0.003 0.13 -10000 0 -0.48 17 17
AKT1 0.026 0.006 -10000 0 -10000 0 0
GSC -0.2 0.52 -10000 0 -1.4 62 62
NKX2-5 0.018 0.015 -10000 0 -10000 0 0
muscle cell differentiation -0.01 0.081 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.037 0.095 -10000 0 -10000 0 0
SMAD4 -0.008 0.072 -10000 0 -0.26 1 1
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.048 0.069 -10000 0 -0.45 2 2
SMAD3/SMAD4/VDR 0.05 0.074 -10000 0 -10000 0 0
MYC 0.012 0.1 -10000 0 -0.66 9 9
CDKN2B -0.02 0.11 -10000 0 -10000 0 0
AP1 -0.2 0.42 -10000 0 -0.79 121 121
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.028 0.058 -10000 0 -0.67 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.036 -10000 0 -10000 0 0
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 0.004 0.053 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.021 0.079 -10000 0 -10000 0 0
GATA3 -0.012 0.16 -10000 0 -0.64 22 22
SKI/SIN3/HDAC complex/NCoR1 0.028 0.047 -10000 0 -0.77 1 1
MEF2C/TIF2 -0.029 0.13 -10000 0 -0.42 11 11
endothelial cell migration -0.024 0.084 1.3 1 -10000 0 1
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.007 -10000 0 -10000 0 0
RBBP4 0.026 0.005 -10000 0 -10000 0 0
RUNX2 -0.017 0.082 -10000 0 -0.69 2 2
RUNX3 0.012 0.095 -10000 0 -0.69 7 7
RUNX1 -0.042 0.074 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.026 0.009 -10000 0 -10000 0 0
CDKN1A 0.02 0.044 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.01 0.12 -10000 0 -0.29 24 24
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.026 0.005 -10000 0 -10000 0 0
SERPINE1 0.023 0.085 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 0.01 0.11 -10000 0 -0.48 10 10
SMAD3/SMAD4/ATF3 -0.079 0.24 -10000 0 -0.52 87 87
SAP30 0.024 0.036 -10000 0 -0.69 1 1
Cbp/p300/PIAS3 0.049 0.045 -10000 0 -10000 0 0
JUN -0.2 0.41 -10000 0 -0.78 121 121
SMAD3/SMAD4/IRF7 0.025 0.079 -10000 0 -10000 0 0
TFE3 0.03 0.01 -10000 0 -10000 0 0
COL1A2 0.028 0.039 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.016 0.099 0.41 3 -10000 0 3
DLX1 -0.016 0.17 -10000 0 -0.66 25 25
TCF3 0.025 0.008 -10000 0 -10000 0 0
FOS -0.17 0.34 -10000 0 -0.75 103 103
SMAD3/SMAD4/Max 0.02 0.08 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.03 -10000 0 -10000 0 0
ZBTB17 0.027 0.006 -10000 0 -10000 0 0
LAMC1 0.012 0.061 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.022 0.08 -10000 0 -10000 0 0
IRF7 0.027 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 -0.014 0.096 0.39 3 -10000 0 3
SMAD2-3/SMAD4 0.01 0.096 -10000 0 -0.3 1 1
Cbp/p300/Src-1 0.047 0.035 -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 0.03 0.011 -10000 0 -10000 0 0
SKIL 0.027 0.004 -10000 0 -10000 0 0
HDAC1 0.026 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 0.03 0.08 -10000 0 -10000 0 0
MSG1/HSC70 -0.064 0.066 -10000 0 -0.45 6 6
SMAD2 0.01 0.049 -10000 0 -10000 0 0
SMAD3 0.006 0.059 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.056 -10000 0 -0.31 4 4
SMAD2/SMAD2/SMAD4 0.002 0.035 0.24 2 -10000 0 2
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.026 0.19 -10000 0 -0.69 30 30
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.045 0.094 -10000 0 -10000 0 0
IFNB1 -0.001 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.003 0.11 -10000 0 -10000 0 0
CITED1 -0.096 0.073 -10000 0 -0.58 3 3
SMAD2-3/SMAD4/ARC105 0.012 0.087 -10000 0 -10000 0 0
RBL1 0.016 0.086 -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 0.048 0.072 -10000 0 -0.44 7 7
SMAD7 -0.088 0.25 -10000 0 -0.55 71 71
MYC/MIZ-1 0.028 0.08 -10000 0 -0.49 9 9
SMAD3/SMAD4 0.026 0.11 0.3 25 -0.52 1 26
IL10 -0.032 0.15 -10000 0 -0.53 29 29
PIASy/HDAC complex 0.017 0.021 -10000 0 -10000 0 0
PIAS3 0.027 0.009 -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 0.031 0.012 -10000 0 -10000 0 0
PIAS4 0.017 0.021 -10000 0 -10000 0 0
ATF3 -0.13 0.29 -10000 0 -0.68 88 88
SMAD3/SMAD4/SP1 0.033 0.082 -10000 0 -10000 0 0
FOXG1 0.005 0.057 -10000 0 -0.69 2 2
FOXO3 0.016 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 -0.014 0.095 0.38 3 -10000 0 3
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.008 0.14 -10000 0 -0.49 24 24
MYOD1 -0.014 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.017 0.081 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 -0.002 0.14 -10000 0 -0.43 28 28
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.032 0.12 -10000 0 -0.51 6 6
SMAD3/SMAD4/SP1-3 0.053 0.08 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.032 0.01 -10000 0 -10000 0 0
SIN3B 0.025 0.007 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.026 0.12 -10000 0 -0.33 1 1
ITGB5 0.015 0.06 -10000 0 -10000 0 0
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 -0.68 167 167
negative regulation of cell growth -0.021 0.11 -10000 0 -0.34 6 6
SMAD3/SMAD4/MYOD 0.016 0.08 -10000 0 -10000 0 0
E2F5 0.027 0.005 -10000 0 -10000 0 0
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.025 0.098 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.036 -10000 0 -10000 0 0
TFDP1 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.18 0.44 -10000 0 -0.8 121 121
SMAD3/SMAD4/RUNX2 0.016 0.1 -10000 0 -0.41 3 3
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.005 -10000 0 -10000 0 0
ATF2 0.009 0.11 -10000 0 -0.69 10 10
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.026 0.11 -10000 0 -0.33 42 42
FRAP1 0.011 0.046 0.39 2 -0.42 1 3
AKT1 -0.022 0.088 -10000 0 -0.28 40 40
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.007 0.083 -10000 0 -0.45 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.008 0.034 -10000 0 -0.24 1 1
TSC2 0.026 0.007 -10000 0 -10000 0 0
RHEB/GDP 0.002 0.069 -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 45 45
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.018 0.042 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.02 0.097 0.37 16 -0.36 3 19
MAP3K5 0.005 0.031 0.18 1 -0.22 6 7
PIK3R1 0.027 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 56 57
EIF4B 0.025 0.11 0.45 18 -0.31 3 21
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.029 0.068 0.36 4 -0.32 2 6
eIF4E/eIF4G1/eIF4A1 0.017 0.023 -10000 0 -0.25 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.002 0.12 -10000 0 -0.36 43 43
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.042 0.25 2 -0.23 1 3
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.015 0.075 -10000 0 -0.41 1 1
mol:Amino Acids 0 0.001 0.001 1 -0.002 56 57
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.028 0.099 -10000 0 -0.32 41 41
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.078 -10000 0 -0.48 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.009 0.09 0.28 1 -0.49 1 2
tumor necrosis factor receptor activity 0 0.001 0.002 56 -0.001 1 57
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.026 0.007 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.039 0.13 -10000 0 -0.37 51 51
INS -0.016 0.003 -10000 0 -10000 0 0
PTEN 0.025 0.021 -10000 0 -0.37 1 1
PDK2 -0.026 0.097 0.23 2 -0.31 41 43
EIF4EBP1 0.015 0.11 -10000 0 -0.93 5 5
PIK3CA 0.026 0.036 -10000 0 -0.69 1 1
PPP2R5D 0.02 0.074 0.38 11 -0.38 1 12
peptide biosynthetic process 0.014 0.017 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 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 0.029 0.097 -10000 0 -0.83 5 5
IL1-mediated signaling events

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
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 0.012 0.067 -9999 0 -0.39 2 2
IRAK/TOLLIP 0.029 0.011 -9999 0 -10000 0 0
IKBKB 0.027 0.004 -9999 0 -10000 0 0
IKBKG 0.025 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.061 0.22 -9999 0 -0.55 63 63
IL1A -0.034 0.19 -9999 0 -0.68 33 33
IL1B -0.029 0.15 -9999 0 -0.53 33 33
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.034 -9999 0 -0.37 1 1
IL1R2 -0.047 0.2 -9999 0 -0.67 36 36
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.053 -9999 0 -10000 0 0
TOLLIP 0.026 0.005 -9999 0 -10000 0 0
TICAM2 0.017 0.079 -9999 0 -0.69 5 5
MAP3K3 0.026 0.007 -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 -0.078 0.16 -9999 0 -0.37 86 86
MAP3K7 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.13 -9999 0 -0.4 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88 0.035 0.13 -9999 0 -0.42 32 32
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.045 0.13 -9999 0 -0.4 32 32
IL1 beta fragment/IL1R1/IL1RAP 0.011 0.13 -9999 0 -0.43 32 32
NFKB1 0.027 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 0.012 0.083 -9999 0 -0.48 8 8
IRAK4 0.026 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.004 -9999 0 -10000 0 0
TRAF6 0.025 0.036 -9999 0 -0.69 1 1
PI3K 0.038 0.029 -9999 0 -0.52 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.072 -9999 0 -0.42 2 2
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.011 0.13 -9999 0 -0.43 32 32
IL1 beta/IL1R2 -0.052 0.2 -9999 0 -0.5 60 60
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.024 -9999 0 -0.37 1 1
NF kappa B1 p50/RelA 0.024 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 0.032 0.14 -9999 0 -0.4 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.088 -9999 0 -0.3 32 32
IL1 alpha/IL1R1/IL1RAP 0.017 0.14 -9999 0 -0.46 32 32
RELA 0.027 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 0.027 0.004 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.029 -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 0.022 0.052 -9999 0 -0.69 2 2
IL1RN/IL1R2 -0.043 0.18 -9999 0 -0.52 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 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 0.008 0.074 -9999 0 -0.37 2 2
PIK3CA 0.025 0.036 -9999 0 -0.69 1 1
IL1RN -0.009 0.11 -9999 0 -0.65 8 8
TRAF6/TAK1/TAB1/TAB2 0.046 0.025 -9999 0 -0.38 1 1
MAP2K6 0.009 0.055 -9999 0 -0.37 7 7
Syndecan-3-mediated signaling events

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.023 0.12 -9999 0 -0.34 35 35
Syndecan-3/Neurocan -0.001 0.11 -9999 0 -0.37 29 29
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 0.049 -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 0.026 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.035 0.19 -9999 0 -0.68 33 33
long-term memory 0.049 0.03 -9999 0 -0.28 1 1
Syndecan-3/IL8 0.031 0.067 -9999 0 -0.36 9 9
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.038 0.011 -9999 0 -10000 0 0
FYN 0.027 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 -0.041 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 -0.35 58 58
Syndecan-3/AgRP 0.03 0.024 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.045 0.03 -9999 0 -0.29 1 1
Fyn/Cortactin 0.039 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 0.031 0.066 -9999 0 -0.36 9 9
IL8 -0.024 0.11 -9999 0 -0.69 8 8
Syndecan-3/Fyn/Cortactin 0.051 0.03 -9999 0 -0.28 1 1
Syndecan-3/CASK 0.011 0.024 -9999 0 -0.31 1 1
alpha-MSH/MC4R -0.081 0.22 -9999 0 -0.51 85 85
Gamma Secretase 0.07 0.029 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.036 -10000 0 -0.69 1 1
Caspase 8 (4 units) 0.021 0.095 -10000 0 -0.45 5 5
NEF -0.012 0.059 -10000 0 -0.22 24 24
NFKBIA 0.021 0.032 -10000 0 -10000 0 0
BIRC3 -0.006 0.16 -10000 0 -0.67 20 20
CYCS -0.011 0.096 -10000 0 -0.38 10 10
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CD247 -0.02 0.16 -10000 0 -0.44 38 38
MAP2K7 -0.003 0.17 0.36 1 -0.66 19 20
protein ubiquitination 0.007 0.098 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 0.027 0.005 -10000 0 -10000 0 0
BID -0.012 0.1 0.22 1 -0.34 22 23
NF-kappa-B/RelA/I kappa B alpha 0.041 0.082 -10000 0 -0.33 17 17
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.025 0.036 -10000 0 -0.69 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.041 0.082 -10000 0 -0.33 17 17
MAPK8 -0.003 0.16 0.35 2 -0.62 18 20
APAF1 0.026 0.005 -10000 0 -10000 0 0
TRAF1 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.003 0.1 -10000 0 -0.33 29 29
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.001 0.1 -10000 0 -0.37 14 14
CHUK 0.003 0.098 0.28 3 -0.39 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.032 -10000 0 -0.39 1 1
TCRz/NEF -0.026 0.16 -10000 0 -0.46 40 40
TNF -0.058 0.23 -10000 0 -0.69 46 46
FASLG -0.055 0.24 -10000 0 -0.76 38 38
NFKB1 0.021 0.034 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.005 0.16 -10000 0 -0.45 47 47
CASP6 0.036 0.1 -10000 0 -0.72 4 4
CASP7 0.009 0.16 0.38 3 -0.58 22 25
RELA 0.021 0.034 -10000 0 -0.18 2 2
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.008 0.15 0.35 1 -0.58 22 23
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.029 -10000 0 -0.52 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.026 0.005 -10000 0 -10000 0 0
MAP3K14 0 0.1 -10000 0 -0.38 7 7
APAF-1/Caspase 9 -0.005 0.12 -10000 0 -0.49 19 19
BCL2 -0.021 0.16 0.42 2 -0.57 17 19
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.19 0.33 -10000 0 -0.68 124 124
HRAS 0.026 0.012 -10000 0 -10000 0 0
EGFR 0.017 0.079 -10000 0 -0.69 5 5
AKT 0.014 0.088 0.32 9 -0.24 1 10
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.025 0.008 -10000 0 -10000 0 0
FOXO4 0.025 0.007 -10000 0 -10000 0 0
MET -0.034 0.073 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.009 0.11 -10000 0 -0.69 9 9
PIK3R3 0.026 0.005 -10000 0 -10000 0 0
PIK3R2 0.025 0.007 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.034 0.092 -10000 0 -0.18 109 109
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.037 0.06 0.33 6 -10000 0 6
PI3K -0.016 0.1 0.4 7 -0.26 13 20
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.026 0.005 -10000 0 -10000 0 0
FOXO 0.047 0.059 0.31 7 -10000 0 7
AKT2 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.021 -10000 0 -0.38 1 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.003 0.068 -10000 0 -0.24 18 18
NT3 (dimer)/TRKC -0.025 0.15 -10000 0 -0.51 32 32
NT3 (dimer)/TRKB 0.002 0.15 -10000 0 -0.45 38 38
SHC/Grb2/SOS1/GAB1/PI3K 0.031 0.021 -10000 0 -0.29 1 1
RAPGEF1 0.025 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 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.012 0.028 -10000 0 -10000 0 0
NTRK2 0.021 0.054 -10000 0 -0.58 3 3
NTRK3 -0.015 0.12 -10000 0 -0.66 12 12
NT-4/5 (dimer)/TRKB 0.016 0.13 -10000 0 -0.45 26 26
neuron apoptosis -0.007 0.11 0.4 15 -10000 0 15
SHC 2-3/Grb2 0.007 0.12 -10000 0 -0.43 15 15
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0 0.11 -10000 0 -0.54 10 10
SHC3 -0.007 0.12 -10000 0 -0.46 18 18
STAT3 (dimer) 0.03 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0 0.14 -10000 0 -0.46 34 34
RIN/GDP -0.005 0.081 0.31 6 -0.26 5 11
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 0.048 0.02 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.037 0.07 -10000 0 -0.45 7 7
TRKA/NEDD4-2 0.032 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 0.021 0.062 -10000 0 -0.69 3 3
HRAS 0.026 0.012 -10000 0 -10000 0 0
DOCK1 0.023 0.05 -10000 0 -0.69 2 2
GAB2 0.027 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 -0.002 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 -0.36 160 160
mol:GDP -0.013 0.12 0.44 7 -0.36 9 16
NGF (dimer) 0.021 0.062 -10000 0 -0.69 3 3
RhoG/GDP -0.19 0.26 -10000 0 -0.52 155 155
RIT1/GDP -0.003 0.086 0.36 7 -0.26 4 11
TIAM1 -0.057 0.08 -10000 0 -0.69 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.036 0.093 -10000 0 -0.5 11 11
KIDINS220/CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
SHC/RasGAP 0.036 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.06 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.16 -10000 0 -0.69 21 21
RAP1/GDP -0.007 0.059 -10000 0 -0.23 4 4
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 0.047 -10000 0 -0.45 3 3
Schwann cell development -0.031 0.029 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.064 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.038 -10000 0 -0.24 4 4
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 37 37
ABL1 0.025 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.1 -10000 0 -0.51 6 6
STAT3 0.03 0.015 -10000 0 -10000 0 0
axon guidance -0.018 0.12 -10000 0 -0.36 37 37
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 0.088 0.36 7 -0.26 4 11
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 0.046 0.047 -10000 0 -0.45 3 3
PI3K 0.038 0.029 -10000 0 -0.52 1 1
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.004 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.044 0.093 -10000 0 -0.41 20 20
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.03 0.12 -10000 0 -0.44 31 31
RGS19 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.034 0.071 -10000 0 -0.49 2 2
Rac1/GDP -0.006 0.069 -10000 0 -0.26 3 3
NGF (dimer)/TRKA/GRIT 0.026 0.046 -10000 0 -0.45 3 3
neuron projection morphogenesis 0.019 0.1 -10000 0 -0.75 3 3
NGF (dimer)/TRKA/NEDD4-2 0.045 0.047 -10000 0 -0.45 3 3
MAP2K1 0.037 0.055 0.36 3 -10000 0 3
NGFR -0.018 0.14 -10000 0 -0.69 15 15
NGF (dimer)/TRKA/GIPC/GAIP 0.013 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 0.074 0.024 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
MAPKKK cascade 0.019 0.083 -10000 0 -0.52 7 7
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.031 0.022 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.047 0.088 -10000 0 -0.46 10 10
NGF (dimer)/TRKA/p62/Atypical PKCs 0.067 0.049 -10000 0 -0.4 3 3
MATK 0.016 0.075 -10000 0 -0.62 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.043 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.001 0.084 -10000 0 -0.39 17 17
Rac1/GTP -0.12 0.12 -10000 0 -0.28 112 112
FRS2 family/SHP2/CRK family 0.058 0.038 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.016 0.08 0.38 11 -10000 0 11
PI3K Class IB/PDE3B 0.016 0.081 -10000 0 -0.38 11 11
PDE3B 0.016 0.081 -10000 0 -0.38 11 11
Caspase cascade in apoptosis

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
TOP1 0.021 0.088 0.32 5 -0.4 10 15
ACTA1 0.009 0.1 0.36 5 -0.46 10 15
NUMA1 0.016 0.1 0.28 6 -0.5 11 17
SPTAN1 0.007 0.098 0.36 5 -0.47 9 14
LIMK1 0.014 0.11 0.43 8 -0.49 8 16
BIRC3 -0.011 0.15 -10000 0 -0.64 21 21
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.026 0.007 -10000 0 -10000 0 0
CASP10 -0.011 0.088 -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 0.013 0.1 0.39 2 -0.43 14 16
DIABLO 0.026 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.007 0.097 0.36 5 -0.46 9 14
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
GSN 0.006 0.099 0.36 5 -0.48 9 14
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.041 0.22 -10000 0 -0.62 50 50
BID -0.012 0.061 -10000 0 -0.32 10 10
MAP3K1 0.018 0.042 0.27 3 -0.21 1 4
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 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 -0.49 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 0.005 0.12 -10000 0 -0.55 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.016 0.11 0.34 4 -0.5 11 15
APAF1 0.026 0.005 -10000 0 -10000 0 0
CASP6 0.019 0.097 0.36 2 -0.62 5 7
TRAF2 0.025 0.008 -10000 0 -10000 0 0
ICAD/CAD 0.013 0.11 0.4 13 -0.48 8 21
CASP7 0.007 0.097 0.32 18 -0.44 6 24
KRT18 0.021 0.044 -10000 0 -0.44 2 2
apoptosis 0.018 0.096 0.48 4 -0.43 8 12
DFFA 0.01 0.1 0.36 6 -0.47 9 15
DFFB 0.01 0.1 0.36 6 -0.49 8 14
PARP1 0.017 0.059 0.21 16 -0.35 3 19
actin filament polymerization -0.019 0.12 0.46 8 -0.54 10 18
TNF -0.058 0.23 -10000 0 -0.69 46 46
CYCS 0 0.05 0.24 4 -0.22 8 12
SATB1 0.02 0.096 0.45 3 -0.58 5 8
SLK 0.007 0.099 0.46 3 -0.47 9 12
p15 BID/BAX -0.01 0.07 0.19 1 -0.29 10 11
CASP2 -0.015 0.1 0.21 2 -0.39 14 16
JNK cascade -0.018 0.042 0.21 1 -0.27 3 4
CASP3 0.006 0.1 0.35 5 -0.44 12 17
LMNB2 0.006 0.12 0.37 9 -0.44 11 20
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.044 0.097 -10000 0 -0.41 16 16
negative regulation of DNA binding -0.04 0.22 -10000 0 -0.61 50 50
stress fiber formation 0.006 0.098 0.46 3 -0.46 9 12
GZMB -0.007 0.1 -10000 0 -0.6 10 10
CASP1 0.014 0.029 -10000 0 -0.39 2 2
LMNB1 0.02 0.096 0.34 11 -0.38 5 16
APP 0.005 0.12 -10000 0 -0.56 15 15
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 0.092 0.4 4 -0.41 9 13
LMNA 0.015 0.1 0.35 11 -0.41 7 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.014 0.11 -10000 0 -0.42 12 12
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.014 0.11 0.44 7 -0.49 8 15
APAF-1/Caspase 9 0.014 0.059 -10000 0 -0.53 3 3
nuclear fragmentation during apoptosis 0.016 0.1 0.28 6 -0.48 11 17
CFL2 0.019 0.12 0.54 10 -0.47 8 18
GAS2 0.004 0.1 0.39 3 -0.47 11 14
positive regulation of apoptosis 0.016 0.11 0.37 9 -0.4 8 17
PRF1 0.015 0.087 -10000 0 -0.69 6 6
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.002 0.085 -10000 0 -0.33 1 1
epithelial cell differentiation -0.001 0.097 -10000 0 -0.42 6 6
ITCH 0.036 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.067 -10000 0 -10000 0 0
FYN 0.027 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 -0.022 0.12 0.34 3 -0.49 5 8
PTPRZ1 0.001 0.11 -10000 0 -0.69 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.004 0.13 -10000 0 -0.38 33 33
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.043 0.14 -10000 0 -0.43 39 39
ADAM17 0.034 0.041 -10000 0 -0.69 1 1
ErbB4/ErbB4 -0.015 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.033 0.14 -10000 0 -0.46 28 28
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.03 0.14 -10000 0 -0.41 39 39
GRIN2B -0.039 0.13 -10000 0 -0.39 39 39
ErbB4/ErbB2/betacellulin 0.003 0.1 -10000 0 -0.5 9 9
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.018 0.034 -10000 0 -10000 0 0
PRLR -0.011 0.15 -10000 0 -0.69 18 18
E4ICDs/ETO2 -0.002 0.081 -10000 0 -0.33 1 1
axon guidance -0.006 0.068 -10000 0 -10000 0 0
NEDD4 0.035 0.04 -10000 0 -0.69 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.003 0.11 -10000 0 -0.52 18 18
CBFA2T3 0.025 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.011 0.07 -10000 0 -0.48 1 1
MAPK3 -0.019 0.12 -10000 0 -0.51 5 5
STAT1 (dimer) -0.001 0.085 -10000 0 -0.31 1 1
MAPK1 -0.022 0.12 -10000 0 -0.51 5 5
JAK2 0.025 0.008 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.035 0.13 -10000 0 -0.41 36 36
NRG1 -0.032 0.17 -10000 0 -0.54 39 39
NRG3 -0.024 0.18 -10000 0 -0.66 30 30
NRG2 -0.062 0.23 -10000 0 -0.69 49 49
NRG4 0.021 0.021 -10000 0 -10000 0 0
heart development -0.006 0.068 -10000 0 -10000 0 0
neural crest cell migration -0.035 0.13 -10000 0 -0.4 36 36
ERBB2 0.02 0.029 -10000 0 -0.51 1 1
WWOX/E4ICDs -0.003 0.082 -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 -0.45 5 5
apoptosis 0.024 0.13 0.41 30 -10000 0 30
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.056 0.17 -10000 0 -0.44 50 50
ErbB4/ErbB2/epiregulin 0.013 0.084 -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 -0.013 0.076 0.26 2 -10000 0 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.026 0.14 -10000 0 -0.41 38 38
STAT5A -0.002 0.066 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.033 0.15 -10000 0 -0.41 43 43
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.002 0.075 -10000 0 -0.28 1 1
STAT5A (dimer) 0.007 0.11 -10000 0 -0.45 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.005 0.069 -10000 0 -10000 0 0
LRIG1 0.022 0.061 -10000 0 -0.69 3 3
EREG -0.049 0.07 -10000 0 -10000 0 0
BTC 0.011 0.1 -10000 0 -0.69 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.006 0.068 -10000 0 -10000 0 0
ERBB4 -0.014 0.086 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.006 0.059 -10000 0 -0.43 6 6
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.01 0.069 -10000 0 -0.44 1 1
glial cell differentiation 0.003 0.074 0.28 1 -10000 0 1
WWOX 0.026 0.006 -10000 0 -10000 0 0
cell proliferation -0.027 0.14 -10000 0 -0.52 11 11
Signaling events mediated by HDAC Class III

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
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 0.005 -9999 0 -10000 0 0
CDKN1A -0.007 0.011 -9999 0 -10000 0 0
KAT2B 0.027 0.004 -9999 0 -10000 0 0
BAX 0.026 0.007 -9999 0 -10000 0 0
FOXO3 -0.005 0.004 -9999 0 -10000 0 0
FOXO1 0.026 0.007 -9999 0 -10000 0 0
FOXO4 0.014 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 0.022 -9999 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -10000 0 0
MYOD1 -0.009 0.01 -9999 0 -10000 0 0
PPARGC1A -0.28 0.35 -9999 0 -0.68 177 177
FHL2 -0.031 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 0.005 -9999 0 -10000 0 0
SIRT1/FOXO3a 0.038 0.047 -9999 0 -10000 0 0
SIRT1 0.023 0.005 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.017 -9999 0 -10000 0 0
SIRT1/Histone H1b -0.005 0.07 -9999 0 -0.31 8 8
apoptosis -0.038 0.024 -9999 0 -10000 0 0
SIRT1/PGC1A -0.18 0.24 -9999 0 -0.45 176 176
p53/SIRT1 0.029 0.013 -9999 0 -10000 0 0
SIRT1/FOXO4 -0.002 0.059 -9999 0 -0.27 2 2
FOXO1/FHL2/SIRT1 0.008 0.13 -9999 0 -0.42 33 33
HIST1H1E 0.006 0.05 -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 0.007 -9999 0 -10000 0 0
KU70/SIRT1/BAX 0.038 0.024 -9999 0 -10000 0 0
CREBBP 0.026 0.006 -9999 0 -10000 0 0
MEF2D 0.025 0.007 -9999 0 -10000 0 0
HIV-1 Tat/SIRT1 0.033 0.011 -9999 0 -10000 0 0
ACSS2 0.014 0.003 -9999 0 -10000 0 0
SIRT1/PCAF/MYOD 0.031 0.022 -9999 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.004 0.13 -10000 0 -0.37 43 43
TC10/GTP 0.042 0.035 -10000 0 -0.36 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.008 0.15 -10000 0 -0.43 42 42
HRAS 0.026 0.012 -10000 0 -10000 0 0
APS homodimer 0.025 0.01 -10000 0 -10000 0 0
GRB14 0 0.14 -10000 0 -0.69 15 15
FOXO3 0.002 0.11 -10000 0 -0.65 11 11
AKT1 -0.026 0.13 0.37 4 -0.37 13 17
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 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 -0.032 0.14 -10000 0 -0.4 48 48
CBL/APS/CAP/Crk-II/C3G 0.066 0.044 -10000 0 -0.39 2 2
Insulin Receptor/Insulin/IRS1/NCK2 0.009 0.15 -10000 0 -0.43 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.003 0.13 -10000 0 -0.38 43 43
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.004 0.098 -10000 0 -0.41 6 6
RPS6KB1 -0.031 0.12 0.32 2 -0.58 1 3
PARD6A 0.026 0.006 -10000 0 -10000 0 0
CBL 0.027 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 -0.01 0.13 -10000 0 -0.45 2 2
HRAS/GTP -0.021 0.1 -10000 0 -0.34 35 35
Insulin Receptor 0.027 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 -0.022 0.14 -10000 0 -0.36 53 53
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.045 0.043 -10000 0 -0.4 1 1
PI3K 0.011 0.14 -10000 0 -0.38 43 43
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 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 -0.028 0.13 0.39 5 -0.34 51 56
PRKCZ 0.015 0.066 -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 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.041 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.064 0.03 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.06 0.04 -10000 0 -0.42 2 2
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.055 0.025 -10000 0 -10000 0 0
INPP5D -0.028 0.13 0.31 1 -0.4 42 43
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.011 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 -0.049 0.22 -10000 0 -0.69 43 43
p62DOK/RasGAP 0.046 0.043 -10000 0 -0.41 1 1
INS 0.019 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.028 0.13 0.31 1 -0.4 42 43
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.031 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 0.034 0.011 -10000 0 -10000 0 0
PDPK1 0.024 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 43 43
Insulin Receptor/Insulin/IRS3 0.033 0.012 -10000 0 -10000 0 0
Par3/Par6 0.062 0.029 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.09 -10000 0 -0.61 8 8
ANTXR2 0.025 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 0.052 -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 0.025 0.061 -10000 0 -0.36 9 9
NLRP1 -0.003 0.029 -10000 0 -0.39 2 2
CALM1 0.027 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 0.06 -10000 0 -0.33 12 12
PA/Cellular Receptors 0.026 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) 0.025 0.057 -10000 0 -0.34 9 9
macrophage activation -0.001 0.01 -10000 0 -10000 0 0
TNF -0.058 0.23 -10000 0 -0.69 46 46
VCAM1 -0.035 0.15 -10000 0 -0.43 51 51
platelet activation 0.011 0.03 -10000 0 -0.52 1 1
MAPKKK cascade -0.003 0.026 0.11 5 -0.13 6 11
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 -0.098 11 11
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) 0.025 0.058 -10000 0 -0.34 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.012 0.12 -10000 0 -0.67 5 5
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.025 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
DTX1 0.023 0.05 -10000 0 -0.69 2 2
LRP6/FZD1 0.038 0.01 -10000 0 -10000 0 0
TLE1 0.021 0.05 -10000 0 -0.69 2 2
AP1 -0.13 0.24 -10000 0 -0.49 116 116
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 0.029 0.068 -10000 0 -0.52 3 3
NICD/RBPSUH 0.011 0.12 -10000 0 -0.66 5 5
WIF1 -0.014 0.045 -10000 0 -10000 0 0
NOTCH1 0.001 0.12 -10000 0 -0.68 5 5
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.014 0.039 -10000 0 -10000 0 0
DKK1 0 0.072 -10000 0 -0.69 2 2
beta catenin/beta TrCP1 0.046 0.048 0.29 2 -10000 0 2
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 -0.006 0.085 0.32 2 -0.39 11 13
CtBP/CBP/TCF1/TLE1/AES 0.019 0.032 -10000 0 -0.3 3 3
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.15 0.31 -10000 0 -0.68 103 103
JUN -0.12 0.29 -10000 0 -0.68 86 86
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.038 0.063 0.31 10 -10000 0 10
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.033 0.1 -10000 0 -0.45 16 16
HNF1A 0.024 0.036 -10000 0 -0.69 1 1
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC -0.018 0.25 -10000 0 -1.2 16 16
NKD1 0.004 0.12 -10000 0 -0.69 12 12
FZD1 0.026 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.01 0.12 -10000 0 -0.65 7 7
apoptosis -0.13 0.24 -10000 0 -0.49 116 116
Delta 1/NOTCHprecursor 0.012 0.12 -10000 0 -0.65 5 5
DLL1 0.027 0.008 -10000 0 -10000 0 0
PPARD 0.024 0.06 -10000 0 -0.77 2 2
Gamma Secretase 0.071 0.029 -10000 0 -10000 0 0
APC 0.003 0.058 0.3 3 -0.34 2 5
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.048 0.049 -10000 0 -0.48 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.013 0.007 -10000 0 -10000 0 0
CCND1 0.013 0.12 -10000 0 -0.85 7 7
WNT1 0.019 0.019 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.048 0.091 0.4 13 -0.33 1 14
DKK2 -0.007 0.14 -10000 0 -0.69 17 17
NOTCH1 precursor/DVL1 0.018 0.11 -10000 0 -0.56 6 6
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.13 -10000 0 -0.66 7 7
PPP2R5D 0.03 0.061 0.34 12 -0.34 2 14
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.065 0.019 -10000 0 -10000 0 0
RBPJ 0.026 0.009 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.76 4 4
UGCG -0.049 0.21 -10000 0 -0.62 43 43
AKT1/mTOR/p70S6K/Hsp90/TERT 0.017 0.13 0.42 5 -0.41 16 21
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.051 0.21 -10000 0 -0.6 46 46
mol:DAG -0.01 0.12 -10000 0 -0.79 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.16 -10000 0 -0.43 34 34
FRAP1 -0.009 0.18 0.44 2 -0.49 38 40
FOXO3 0.002 0.16 0.43 2 -0.58 18 20
AKT1 -0.003 0.17 -10000 0 -0.62 19 19
GAB2 0.027 0.005 -10000 0 -10000 0 0
SMPD1 0.012 0.077 -10000 0 -0.81 3 3
SGMS1 0.002 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 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.024 0.18 0.32 5 -0.52 31 36
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.041 0.03 -10000 0 -0.53 1 1
RPS6KB1 0.014 0.077 -10000 0 -0.74 3 3
mol:sphingomyelin -0.01 0.12 -10000 0 -0.79 10 10
natural killer cell activation 0 0.004 -10000 0 -0.018 7 7
JAK3 -0.007 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 0.027 0.004 -10000 0 -10000 0 0
MYC -0.003 0.2 0.46 4 -0.86 15 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 -0.59 17 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.04 0.077 -10000 0 -0.67 3 3
mol:PI-3-4-5-P3 -0.002 0.15 -10000 0 -0.57 17 17
Rac1/GDP 0.025 0.025 -10000 0 -0.42 1 1
T cell proliferation -0.003 0.14 -10000 0 -0.55 15 15
SHC1 0.025 0.009 -10000 0 -10000 0 0
RAC1 0.026 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 0.016 0.16 -10000 0 -0.5 19 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.003 0.11 -10000 0 -0.62 9 9
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.014 0.15 -10000 0 -0.66 20 20
IL2RB 0.004 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 0.027 0.006 -10000 0 -10000 0 0
RPS6 0.025 0.008 -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 0.14 -10000 0 -0.55 15 15
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.019 0.014 -10000 0 -10000 0 0
PIK3CA 0.027 0.036 -10000 0 -0.69 1 1
Rac1/GTP 0.049 0.032 -10000 0 -0.4 1 1
LCK 0.014 0.083 -10000 0 -0.69 5 5
BCL2 -0.03 0.26 0.47 4 -0.8 35 39
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.004 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 0.035 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 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.033 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 0.097 49 -10000 0 49
GNAL -0.057 0.23 -10000 0 -0.67 49 49
GNG2 0.027 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 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
mol:K + 0.027 0.004 -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 0.042 -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 0.023 -10000 0 -10000 0 0
GRK1 -0.044 0.21 -10000 0 -0.67 40 40
CNG Channel 0.037 0.057 -10000 0 -0.39 5 5
mol:Na + 0.027 0.076 -10000 0 -0.4 9 9
mol:ADP -0.044 0.21 -10000 0 -0.67 40 40
RGS9-1/Gbeta5/R9AP -0.024 0.18 -10000 0 -0.46 59 59
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.04 0.08 -10000 0 -0.41 9 9
CNGB1 0.017 0.03 -10000 0 -10000 0 0
RDH5 -0.07 0.071 -10000 0 -10000 0 0
SAG -0.008 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.11 0.53 9 -0.4 8 17
Na + (4 Units) 0.02 0.071 -10000 0 -0.38 9 9
RGS9 -0.04 0.2 -10000 0 -0.69 37 37
GNB1/GNGT1 0.029 0.013 -10000 0 -10000 0 0
GNAT1/GDP -0.012 0.16 -10000 0 -0.41 57 57
GUCY2D 0.011 0.085 -10000 0 -0.64 6 6
GNGT1 -0.015 0.012 -10000 0 -10000 0 0
GUCY2F -0.013 0.011 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.016 0.037 -10000 0 -0.39 1 1
mol:11-cis-retinal -0.07 0.071 -10000 0 -10000 0 0
mol:cGMP 0.031 0.063 -10000 0 -0.41 6 6
GNB1 0.026 0.005 -10000 0 -10000 0 0
Rhodopsin -0.041 0.055 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.016 0.08 -10000 0 -0.69 5 5
Metarhodopsin II -0.013 0.13 -10000 0 -0.41 40 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.047 0.069 -10000 0 -0.42 8 8
RGS9BP -0.018 0.17 -10000 0 -0.68 25 25
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.038 0.041 -10000 0 -0.42 3 3
PDE6A/B 0.031 0.028 -10000 0 -10000 0 0
mol:Pi -0.024 0.18 -10000 0 -0.46 59 59
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.014 -10000 0 -10000 0 0
PDE6B 0.027 0.005 -10000 0 -10000 0 0
PDE6A 0.012 0.037 -10000 0 -10000 0 0
PDE6G 0.012 0.061 -10000 0 -0.69 2 2
RHO 0.007 0.023 -10000 0 -10000 0 0
PDE6 0.005 0.17 -10000 0 -0.39 57 57
GUCA1A 0.006 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.04 -10000 0 -0.37 3 3
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.022 0.061 -10000 0 -0.69 3 3
FOXM1 transcription factor network

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
NFATC3 -0.004 0.31 0.79 2 -1 6 8
PLK1 0.03 0.089 -10000 0 -0.77 4 4
BIRC5 0.022 0.12 -10000 0 -0.92 5 5
HSPA1B -0.01 0.3 -10000 0 -1 6 6
MAP2K1 0.026 0.044 -10000 0 -10000 0 0
BRCA2 -0.015 0.32 0.79 1 -1.1 9 10
FOXM1 -0.035 0.33 -10000 0 -0.98 15 15
XRCC1 -0.003 0.3 -10000 0 -0.99 6 6
FOXM1B/p19 -0.033 0.32 -10000 0 -0.9 18 18
Cyclin D1/CDK4 0.01 0.28 -10000 0 -0.88 6 6
CDC2 -0.013 0.32 -10000 0 -0.87 15 15
TGFA -0.003 0.28 -10000 0 -0.85 7 7
SKP2 -0.004 0.31 0.79 2 -1 7 9
CCNE1 0.027 0.01 -10000 0 -10000 0 0
CKS1B 0.001 0.3 0.78 1 -0.95 8 9
RB1 0.035 0.17 -10000 0 -0.59 6 6
FOXM1C/SP1 -0.018 0.32 -10000 0 -0.94 14 14
AURKB 0.006 0.14 -10000 0 -0.86 9 9
CENPF 0 0.3 0.78 1 -1 6 7
CDK4 0.028 0.019 -10000 0 -10000 0 0
MYC -0.019 0.3 -10000 0 -0.88 13 13
CHEK2 0.021 0.04 -10000 0 -10000 0 0
ONECUT1 0 0.3 -10000 0 -0.96 6 6
CDKN2A -0.033 0.071 -10000 0 -10000 0 0
LAMA4 -0.01 0.3 -10000 0 -1 6 6
FOXM1B/HNF6 -0.007 0.32 -10000 0 -1.1 6 6
FOS -0.21 0.59 0.79 2 -1.2 104 106
SP1 0.026 0.01 -10000 0 -10000 0 0
CDC25B -0.005 0.3 0.79 1 -1 6 7
response to radiation 0.007 0.026 -10000 0 -10000 0 0
CENPB -0.005 0.3 0.79 1 -1 6 7
CENPA -0.013 0.3 -10000 0 -1 6 6
NEK2 0 0.3 0.78 1 -1 6 7
HIST1H2BA -0.016 0.3 -10000 0 -1 6 6
CCNA2 0.025 0.023 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.02 0.32 -10000 0 -1.1 7 7
CCNB2 -0.012 0.3 -10000 0 -0.94 8 8
CCNB1 -0.011 0.31 0.68 1 -1 7 8
ETV5 -0.01 0.3 -10000 0 -1 6 6
ESR1 -0.047 0.38 -10000 0 -1.1 24 24
CCND1 0.004 0.29 -10000 0 -0.91 6 6
GSK3A 0.023 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.053 0.043 -10000 0 -10000 0 0
CDK2 0.028 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.01 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.025 0.3 -10000 0 -1 8 8
GAS1 -0.16 0.55 0.79 1 -1.2 81 82
MMP2 -0.009 0.32 0.79 2 -1.1 9 11
RB1/FOXM1C 0.005 0.28 -10000 0 -0.89 7 7
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.026 0.007 -9999 0 -10000 0 0
SPHK1 0.023 0.021 -9999 0 -10000 0 0
GNAI2 0.027 0.004 -9999 0 -10000 0 0
mol:S1P 0.017 0.007 -9999 0 -10000 0 0
GNAO1 0.006 0.12 -9999 0 -0.69 11 11
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 0.056 0.028 -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 0.025 0.008 -9999 0 -10000 0 0
S1PR2 0.025 0.013 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.019 -9999 0 -0.2 2 2
S1PR5 0.024 0.016 -9999 0 -10000 0 0
S1PR4 0.024 0.016 -9999 0 -10000 0 0
GNAI1 0.026 0.006 -9999 0 -10000 0 0
S1P/S1P5/G12 0.044 0.025 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.053 0.16 -9999 0 -0.3 106 106
S1P/S1P4/Gi 0.003 0.081 -9999 0 -0.35 13 13
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.29 -9999 0 -0.65 92 92
GNA15 0.013 0.052 -9999 0 -0.69 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.018 0.071 -9999 0 -0.69 4 4
ABCC1 0.026 0.006 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.035 0.06 -9999 0 -0.4 5 5
EPHB2 0.021 0.061 -9999 0 -0.69 3 3
Syndecan-2/TACI -0.093 0.21 -9999 0 -0.45 99 99
LAMA1 -0.026 0.18 -9999 0 -0.68 30 30
Syndecan-2/alpha2 ITGB1 0.051 0.088 -9999 0 -0.39 14 14
HRAS 0.026 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 0.049 -9999 0 -0.4 6 6
EPB41 0.026 0.005 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.041 -9999 0 -0.4 3 3
LAMA3 0 0.12 -9999 0 -0.69 12 12
EZR 0.027 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 0.023 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 -0.033 0.056 -9999 0 -0.36 5 5
determination of left/right symmetry 0.009 0.05 -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 0.038 0.041 -9999 0 -0.38 3 3
NF1 0.026 0.007 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.009 0.05 -9999 0 -0.38 6 6
ITGA2 -0.034 0.073 -9999 0 -10000 0 0
MAPK8 0.009 0.057 -9999 0 -0.44 6 6
Syndecan-2/alpha2/beta1 Integrin 0.032 0.13 -9999 0 -0.43 27 27
Syndecan-2/Kininogen 0.017 0.049 -9999 0 -0.33 6 6
ITGB1 0.027 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 -0.32 5 5
extracellular matrix organization 0.024 0.043 -9999 0 -0.44 3 3
actin cytoskeleton reorganization -0.035 0.06 -9999 0 -0.4 5 5
Syndecan-2/Caveolin-2/Ras 0.04 0.046 -9999 0 -0.41 4 4
Syndecan-2/Laminin alpha3 0.009 0.092 -9999 0 -0.43 16 16
Syndecan-2/RasGAP 0.05 0.042 -9999 0 -0.37 3 3
alpha5/beta1 Integrin 0.039 0.009 -9999 0 -10000 0 0
PRKCD 0.027 0.004 -9999 0 -10000 0 0
Syndecan-2 dimer 0.022 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 0.027 0.004 -9999 0 -10000 0 0
SDCBP 0.027 0.004 -9999 0 -10000 0 0
TNFRSF13B -0.16 0.3 -9999 0 -0.68 100 100
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 -0.44 3 3
TGFB1 0.024 0.016 -9999 0 -10000 0 0
CASP3 0.017 0.043 -9999 0 -0.4 3 3
FN1 -0.081 0.067 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.005 0.085 -9999 0 -0.4 14 14
SDC2 0.009 0.051 -9999 0 -0.38 6 6
KNG1 -0.004 0.037 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.043 -9999 0 -0.44 3 3
TRAPPC4 0.027 0.005 -9999 0 -10000 0 0
CSF2 -0.08 0.064 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.025 0.043 -9999 0 -0.44 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.041 -9999 0 -0.41 3 3
Syndecan-2/Ezrin 0.041 0.043 -9999 0 -0.41 3 3
PRKACA 0.017 0.039 -9999 0 -0.4 3 3
angiogenesis -0.005 0.085 -9999 0 -0.39 14 14
MMP2 0.02 0.065 -9999 0 -0.61 4 4
IL8 -0.024 0.11 -9999 0 -0.69 8 8
calcineurin-NFAT signaling pathway -0.093 0.21 -9999 0 -0.45 99 99
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.026 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.022 0.096 -10000 0 -0.53 11 11
PTK2 0.012 0.14 -10000 0 -0.59 17 17
positive regulation of JNK cascade 0.017 0.091 -10000 0 -0.33 18 18
CDC42/GDP 0.033 0.13 0.44 1 -0.46 20 21
Rac1/GDP 0.031 0.13 -10000 0 -0.47 18 18
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.027 0.11 -10000 0 -0.41 18 18
nectin-3/I-afadin 0.012 0.12 -10000 0 -0.51 20 20
RAPGEF1 0.015 0.13 0.35 1 -0.52 18 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0.14 -10000 0 -0.6 18 18
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 0.015 0.087 -10000 0 -0.37 16 16
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.012 0.12 -10000 0 -0.51 20 20
PVR 0.026 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.018 0.16 0.47 1 -0.57 23 24
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
PI3K 0.056 0.1 -10000 0 -0.41 17 17
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.019 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.012 0.1 -10000 0 -0.37 19 19
PVRL1 0.023 0.024 -10000 0 -10000 0 0
PVRL3 -0.008 0.16 -10000 0 -0.69 20 20
PVRL2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.1 -10000 0 -0.62 10 10
JAM-A/CLDN1 0.047 0.12 -10000 0 -0.44 21 21
SRC 0.011 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 0.036 0.019 -10000 0 -10000 0 0
FARP2 0.022 0.15 -10000 0 -0.55 21 21
RAC1 0.026 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) 0.027 0.11 -10000 0 -0.44 20 20
nectin-1/I-afadin 0.036 0.019 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.03 0.11 -10000 0 -0.45 19 19
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.008 -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 18 18
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 0.038 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
PIP5K1C 0 0.065 -10000 0 -0.84 1 1
VAV2 0.002 0.18 0.36 1 -0.63 22 23
RAP1/GDP 0.035 0.12 -10000 0 -0.43 18 18
ITGAV 0.025 0.036 -10000 0 -0.69 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.027 0.11 -10000 0 -0.45 19 19
nectin-3(dimer)/I-afadin/I-afadin 0.012 0.12 -10000 0 -0.51 20 20
Rac1/GTP 0.018 0.13 -10000 0 -0.46 19 19
PTPRM 0.003 0.071 -10000 0 -0.28 19 19
E-cadherin/beta catenin/alpha catenin 0.074 0.026 -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
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.03 0.063 -10000 0 -0.52 5 5
PDGFRB 0.026 0.006 -10000 0 -10000 0 0
SPHK1 0.007 0.07 -10000 0 -0.73 3 3
mol:S1P 0.006 0.066 -10000 0 -0.65 3 3
S1P1/S1P/Gi -0.01 0.14 -10000 0 -0.44 31 31
GNAO1 0.003 0.12 -10000 0 -0.7 11 11
PDGFB-D/PDGFRB/PLCgamma1 -0.008 0.12 -10000 0 -0.52 12 12
PLCG1 -0.01 0.13 -10000 0 -0.42 28 28
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 0.024 0.014 -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 0.001 0.068 -10000 0 -0.44 5 5
negative regulation of cAMP metabolic process -0.009 0.13 -10000 0 -0.42 31 31
MAPK3 -0.024 0.18 -10000 0 -0.61 30 30
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 0.021 0.062 -10000 0 -0.69 3 3
PLCB2 0.011 0.076 0.38 4 -0.4 5 9
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.059 -10000 0 -0.38 5 5
receptor internalization 0.001 0.064 -10000 0 -0.41 5 5
PTGS2 -0.066 0.32 0.63 3 -1 39 42
Rac1/GTP 0.009 0.059 -10000 0 -0.38 5 5
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.05 -10000 0 -0.69 2 2
negative regulation of T cell proliferation -0.009 0.13 -10000 0 -0.42 31 31
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.016 -10000 0 -10000 0 0
MAPK1 -0.026 0.18 -10000 0 -0.63 32 32
S1P1/S1P/PDGFB-D/PDGFRB 0.011 0.076 -10000 0 -0.43 5 5
ABCC1 0.026 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.005 -10000 0 -10000 0 0
VDR 0.026 0.009 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 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 0.068 -10000 0 -0.3 6 6
KAT2B 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.012 0.078 0.26 9 -0.36 9 18
RAR alpha/9cRA/Cyclin H 0.028 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 0.065 0.24 1 -0.35 6 7
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.012 0.077 -10000 0 -0.48 4 4
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 -0.01 0.14 -10000 0 -0.52 24 24
NCOA2 -0.026 0.19 -10000 0 -0.69 30 30
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.009 -10000 0 -10000 0 0
RARG 0.027 0.006 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.022 0.061 -10000 0 -0.69 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.001 0.13 -10000 0 -0.51 23 23
RARA 0.003 0.07 -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 -0.01 0.11 -10000 0 -0.42 19 19
PRKCA -0.011 0.16 -10000 0 -0.69 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 0.003 0.15 0.39 4 -0.52 25 29
RXRG -0.023 0.095 -10000 0 -0.39 25 25
RXRA 0.004 0.076 -10000 0 -0.29 21 21
RXRB 0.001 0.091 -10000 0 -0.38 22 22
VDR/Vit D3/DNA 0.019 0.006 -10000 0 -10000 0 0
RBP1 0.017 0.08 -10000 0 -0.69 5 5
CRBP1/9-cic-RA 0.012 0.06 -10000 0 -0.52 5 5
RARB 0.011 0.11 -10000 0 -0.69 10 10
PRKCG 0.022 0.014 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.14 -10000 0 -0.56 24 24
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.006 0.13 -10000 0 -0.47 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.085 0.3 2 -0.39 8 10
RXRs/RARs/NRIP1/9cRA/HDAC3 0.002 0.15 0.4 3 -0.52 25 28
positive regulation of DNA binding 0.017 0.091 -10000 0 -0.33 20 20
NRIP1 0.004 0.14 0.49 1 -0.59 8 9
RXRs/RARs -0.004 0.14 -10000 0 -0.51 26 26
RXRs/RXRs/DNA/9cRA -0.018 0.13 -10000 0 -0.52 23 23
PRKACA 0.025 0.007 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.053 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.045 0.065 -10000 0 -10000 0 0
CCNH 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.05 0.017 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.028 0.009 -10000 0 -10000 0 0
epithelial cell differentiation 0.055 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.005 -10000 0 -10000 0 0
ENAH 0.022 0.082 0.48 9 -10000 0 9
EGFR 0.017 0.079 -10000 0 -0.69 5 5
EPHA2 0.025 0.014 -10000 0 -10000 0 0
MYO6 0.033 0.072 0.44 10 -10000 0 10
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.013 -10000 0 -10000 0 0
AQP5 0.002 0.11 -10000 0 -0.54 15 15
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.052 0.41 6 -10000 0 6
regulation of calcium-dependent cell-cell adhesion -0.008 0.061 0.39 6 -10000 0 6
EGF -0.071 0.24 -10000 0 -0.68 55 55
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
AQP3 -0.042 0.17 -10000 0 -0.54 40 40
cortical microtubule organization 0.055 0.016 -10000 0 -10000 0 0
GO:0000145 0.013 0.052 0.4 6 -10000 0 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.061 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.005 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.015 0.02 -10000 0 -10000 0 0
PVRL2 0.026 0.007 -10000 0 -10000 0 0
ZYX 0.02 0.019 -10000 0 -10000 0 0
ARF6/GTP 0.067 0.027 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.01 0.15 -10000 0 -0.37 58 58
RhoA/GDP 0.056 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization 0.022 0.056 0.41 7 -10000 0 7
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 -0.12 0.29 -10000 0 -0.68 83 83
DIAPH1 0.05 0.048 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.055 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
VCL 0.022 0.057 0.42 7 -10000 0 7
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.014 0.043 0.36 2 -0.37 2 4
Ephrin A1/EPHA2 0.047 0.019 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 -0.009 0.062 0.4 6 -10000 0 6
HGF/MET -0.007 0.15 -10000 0 -0.39 54 54
HGF -0.076 0.25 -10000 0 -0.69 58 58
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.028 0.009 -10000 0 -10000 0 0
actin cable formation 0.07 0.14 0.51 26 -0.33 1 27
KIAA1543 0.013 0.053 0.37 6 -0.36 1 7
KIFC3 0.021 0.023 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ACTN1 0.024 0.038 0.36 3 -10000 0 3
NCK1/GIT1 0.038 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.021 0.023 -10000 0 -10000 0 0
PIP5K1C 0.025 0.052 0.41 6 -10000 0 6
LIMA1 0.026 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.044 0.11 0.44 20 -10000 0 20
adherens junction assembly 0.028 0.091 0.48 11 -10000 0 11
IGF-1R heterotetramer/IGF1 -0.033 0.16 -10000 0 -0.37 78 78
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET -0.034 0.073 -10000 0 -10000 0 0
PLEKHA7 0.025 0.053 0.38 6 -0.38 1 7
mol:GTP 0.059 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.03 0.066 0.48 6 -10000 0 6
cortical actin cytoskeleton stabilization 0.028 0.009 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.022 0.056 0.41 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.028 0.009 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.027 0.05 0.29 10 -0.4 1 11
DAPP1 -0.04 0.13 0.4 2 -0.49 11 13
Src family/SYK family/BLNK-LAT/BTK-ITK -0.057 0.17 0.32 1 -0.52 18 19
mol:DAG -0.019 0.092 0.32 8 -0.26 11 19
HRAS 0.027 0.014 -10000 0 -10000 0 0
RAP1A 0.028 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.035 0.065 0.22 1 -0.34 4 5
PLCG2 0.026 0.006 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0.001 0.052 0.3 10 -10000 0 10
ARF1/GTP 0.003 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.018 0.016 -10000 0 -10000 0 0
ADAP1 0 0.048 0.29 10 -10000 0 10
ARAP3 0.001 0.051 0.3 10 -10000 0 10
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.025 0.007 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.025 0.008 -10000 0 -10000 0 0
NRAS 0.028 0.008 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.066 0.31 8 -10000 0 8
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.057 0.08 -10000 0 -0.69 1 1
ZAP70 -0.002 0.13 -10000 0 -0.67 15 15
mol:IP3 -0.014 0.068 0.23 9 -0.21 4 13
LYN 0.027 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.035 0.075 0.31 7 -0.34 6 13
RhoA/GDP 0.037 0.044 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.029 -10000 0 -0.45 1 1
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.079 0.36 13 -10000 0 13
SRC 0.026 0.009 -10000 0 -10000 0 0
PLEKHA2 0.005 0.017 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.022 0.023 -10000 0 -0.35 1 1
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.026 0.042 0.29 9 -10000 0 9
RhoA/GTP 0.024 0.043 0.3 8 -10000 0 8
Src family/SYK family/BLNK-LAT -0.048 0.14 -10000 0 -0.46 20 20
BLK -0.2 0.32 -10000 0 -0.68 123 123
PDPK1 0.024 0.036 -10000 0 -0.69 1 1
CYTH1 0.002 0.056 0.31 11 -10000 0 11
HCK 0.018 0.036 -10000 0 -10000 0 0
CYTH3 -0.001 0.052 0.29 10 -0.41 1 11
CYTH2 0.004 0.063 0.32 14 -10000 0 14
KRAS 0.028 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.019 0.087 -10000 0 -0.57 7 7
SGK1 0.019 0.097 -10000 0 -0.62 7 7
INPP5D 0.018 0.035 -10000 0 -10000 0 0
mol:GDP 0.027 0.085 0.31 11 -0.32 9 20
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.03 0.053 0.29 9 -10000 0 9
mol:PI-3-4-5-P3 -0.008 0.015 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.018 0.016 -10000 0 -10000 0 0
VAV1 0.012 0.064 -10000 0 -0.58 3 3
mol:PI-3-4-P2 0.011 0.022 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.029 0.33 1 -10000 0 1
PLEKHA1 0.005 0.017 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.065 -10000 0 -0.32 5 5
LAT 0.019 0.065 -10000 0 -0.61 4 4
Rac1/GTP 0.019 0.064 0.28 2 -0.48 3 5
ITK -0.041 0.12 0.28 9 -0.38 40 49
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.032 0.12 0.38 6 -0.36 13 19
LCK 0.012 0.083 -10000 0 -0.69 5 5
BTK -0.006 0.069 0.3 12 -0.38 5 17
BARD1 signaling events

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

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.015 0.11 -10000 0 -0.48 19 19
ATM 0.025 0.036 -10000 0 -0.69 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
ATR 0.027 0.004 -10000 0 -10000 0 0
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.024 0.021 -10000 0 -0.38 1 1
protein ubiquitination 0.045 0.094 -10000 0 -0.39 16 16
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.052 0.014 -10000 0 -10000 0 0
MRE11A 0.027 0.005 -10000 0 -10000 0 0
DNA-PK 0.04 0.025 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.006 0.12 -10000 0 -0.5 21 21
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
CCNE1 0.025 0.007 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.012 -10000 0 -10000 0 0
FANCG 0.025 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.014 0.11 -10000 0 -0.47 19 19
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.008 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA 0.018 0.033 -10000 0 -10000 0 0
DNA repair 0.018 0.089 0.4 2 -0.53 3 5
BRCA1/BARD1/ubiquitin 0.014 0.11 -10000 0 -0.47 19 19
BARD1/DNA-PK 0.032 0.096 -10000 0 -0.41 16 16
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.015 0.11 0.48 19 -10000 0 19
BRCA1/BARD1/CTIP/M/R/N Complex 0.016 0.072 -10000 0 -0.49 1 1
BRCA1/BACH1/BARD1/TopBP1 0.03 0.099 -10000 0 -0.45 15 15
BRCA1/BARD1/P53 0.045 0.095 -10000 0 -0.42 15 15
BARD1/CSTF1/BRCA1 0.03 0.099 -10000 0 -0.44 16 16
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.004 0.14 -10000 0 -0.64 19 19
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.03 0.099 -10000 0 -0.45 15 15
BRCA1/BARD1/UbcH7 0.019 0.098 -10000 0 -0.43 16 16
BRCA1/BARD1/RAD51/PCNA 0.045 0.096 -10000 0 -0.42 15 15
BARD1/DNA-PK/P53 0.039 0.095 -10000 0 -0.39 16 16
BRCA1/BARD1/Ubiquitin 0.014 0.11 -10000 0 -0.47 19 19
BRCA1/BARD1/CTIP 0.024 0.093 -10000 0 -0.42 16 16
FA complex 0.029 0.029 -10000 0 -10000 0 0
BARD1/EWS 0.006 0.11 -10000 0 -0.47 19 19
RBBP8 0.015 0.027 -10000 0 -0.52 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.043 0.094 0.41 15 -10000 0 15
BRCA1/BARD1 0.051 0.097 -10000 0 -0.39 16 16
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.004 0.11 -10000 0 -0.48 19 19
CDK2 0.026 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.025 0.015 -10000 0 -10000 0 0
RAD50 0.026 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.014 0.11 -10000 0 -0.47 19 19
EWSR1 0.02 0.012 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.035 0.094 0.45 8 -0.4 6 14
NFATC2 -0.017 0.093 0.28 9 -0.27 17 26
NFATC3 0.018 0.01 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.012 0.091 0.28 1 -0.37 10 11
Exportin 1/Ran/NUP214 0.047 0.018 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.002 0.1 -10000 0 -0.45 6 6
BCL2/BAX 0.003 0.13 -10000 0 -0.5 26 26
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.02 -10000 0 -10000 0 0
BAX 0.026 0.007 -10000 0 -10000 0 0
MAPK14 0.025 0.005 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.003 0.097 0.38 3 -0.37 9 12
Calcineurin A alpha-beta B1/BCL2 -0.018 0.17 -10000 0 -0.68 26 26
FKBP8 0.025 0.007 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.003 0.096 0.36 9 -0.38 3 12
KPNB1 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.69 12 12
MAP3K8 0.014 0.086 -10000 0 -0.69 6 6
NFAT4/CK1 alpha 0.019 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.07 0.17 -10000 0 -0.33 89 89
CABIN1 -0.012 0.088 0.28 1 -0.36 9 10
CALM1 0.023 0.009 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
CAMK4 0.016 0.074 -10000 0 -0.69 4 4
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.035 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.061 -10000 0 -0.69 3 3
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.022 0.081 0.28 1 -0.52 2 3
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.006 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.013 -10000 0 -10000 0 0
apoptosis 0.011 0.043 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.053 -10000 0 -0.33 3 3
PRKCB 0.008 0.066 -10000 0 -0.69 2 2
PRKCE 0.021 0.061 -10000 0 -0.69 3 3
JNK2/NFAT4 0.031 0.023 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.013 0.16 -10000 0 -0.69 22 22
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.017 0.081 -10000 0 -0.64 6 6
FKBP38/BCL2 0.003 0.13 -10000 0 -0.5 26 26
EP300 0.01 0.021 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.041 0.094 0.41 7 -0.39 6 13
CaM/Ca2+/FKBP38 0.019 0.026 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.014 0.055 -10000 0 -0.46 4 4
NFATc/ERK1 0.04 0.077 0.4 2 -0.44 3 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.006 0.1 -10000 0 -0.47 5 5
NR4A1 -0.17 0.3 -10000 0 -0.62 122 122
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection 0.018 0.01 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.019 0.067 -10000 0 -0.36 4 4
RCH1/ KPNB1 0.038 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.008 -10000 0 -10000 0 0
AKAP5 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.014 0.022 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.048 0.093 0.42 9 -0.39 6 15
CREBBP 0.012 0.023 -10000 0 -10000 0 0
BCL2 -0.018 0.17 -10000 0 -0.68 26 26
TCGA08_p53

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.024 0.042 -9999 0 -10000 0 0
TP53 -0.008 0.036 -9999 0 -0.18 16 16
Senescence -0.008 0.036 -9999 0 -0.18 16 16
Apoptosis -0.008 0.036 -9999 0 -0.18 16 16
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.01 0.019 -9999 0 -10000 0 0
MDM4 0.025 0.007 -9999 0 -10000 0 0
Regulation of Telomerase

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex 0 0.11 0.53 5 -10000 0 5
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.38 -10000 0 -0.74 121 121
IFNAR2 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.054 -10000 0 -0.24 16 16
ER alpha/Oestrogen -0.01 0.11 -10000 0 -0.49 19 19
NFX1/SIN3/HDAC complex 0.033 0.022 -10000 0 -10000 0 0
EGF -0.071 0.24 -10000 0 -0.68 55 55
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.025 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.001 0.089 0.54 2 -10000 0 2
SAP18 0.026 0.006 -10000 0 -10000 0 0
MRN complex 0.052 0.014 -10000 0 -10000 0 0
WT1 0.006 0.048 -10000 0 -10000 0 0
WRN 0.027 0.004 -10000 0 -10000 0 0
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.027 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.01 0.083 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT -0.001 0.11 0.54 5 -10000 0 5
CCND1 0.002 0.11 0.59 5 -10000 0 5
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.008 -10000 0 -10000 0 0
RBBP4 0.027 0.005 -10000 0 -10000 0 0
TERF2 0.023 0.009 -10000 0 -10000 0 0
PTGES3 0.026 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
Telomerase/911 0.025 0.06 -10000 0 -10000 0 0
CDKN1B -0.031 0.15 -10000 0 -0.44 47 47
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.025 0.036 -10000 0 -0.69 1 1
TRF2/PARP2 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.027 0.004 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.68 86 86
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.15 0.31 -10000 0 -0.68 103 103
IFN-gamma/IRF1 -0.021 0.18 -10000 0 -0.5 50 50
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.027 0.008 -10000 0 -10000 0 0
Telomerase 0.015 0.1 -10000 0 -0.46 10 10
IRF1 0.03 0.01 -10000 0 -10000 0 0
ESR1 -0.015 0.15 -10000 0 -0.66 19 19
KU/TER 0.029 0.018 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.027 -10000 0 -0.47 1 1
ubiquitin-dependent protein catabolic process 0.039 0.035 -10000 0 -0.46 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.039 0.036 -10000 0 -0.48 1 1
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
ATM 0.009 0.026 -10000 0 -0.49 1 1
SMAD3 0.015 0.01 -10000 0 -10000 0 0
ABL1 0.025 0.008 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
MRE11A 0.027 0.005 -10000 0 -10000 0 0
HUS1 0.026 0.006 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.015 0.082 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.013 -10000 0 -10000 0 0
MAPK1 0.001 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.016 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.026 -10000 0 -0.49 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.018 0.079 -10000 0 -0.69 5 5
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.042 0.2 -10000 0 -0.52 59 59
MYC 0.012 0.1 -10000 0 -0.65 9 9
IL2 0.02 0.009 -10000 0 -10000 0 0
KU 0.029 0.018 -10000 0 -10000 0 0
RAD50 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.016 -10000 0 -10000 0 0
TRF2/BLM 0.037 0.012 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.003 0.088 0.5 2 -10000 0 2
SP1/HDAC2 0.041 0.01 -10000 0 -10000 0 0
PINX1 0.027 0.004 -10000 0 -10000 0 0
Telomerase/EST1A 0.009 0.081 -10000 0 -10000 0 0
Smad3/Myc 0.02 0.066 -10000 0 -0.42 8 8
911 complex 0.052 0.015 -10000 0 -10000 0 0
IFNG -0.062 0.23 -10000 0 -0.68 50 50
Telomerase/PinX1 0.01 0.083 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.013 0.067 0.36 1 -0.42 3 4
SIN3B 0.026 0.007 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.007 0.079 -10000 0 -10000 0 0
response to DNA damage stimulus 0.004 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.073 0.021 -10000 0 -10000 0 0
TRF2/WRN 0.037 0.01 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.01 0.083 -10000 0 -10000 0 0
E2F1 -0.018 0.069 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.018 0.072 -10000 0 -0.69 4 4
NCL 0.026 0.005 -10000 0 -10000 0 0
DKC1 0.025 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
S1P3 pathway

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -9999 0 -10000 0 0
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.014 0.049 -9999 0 -0.26 11 11
GNAO1 0.007 0.12 -9999 0 -0.69 11 11
S1P/S1P3/G12/G13 0.047 0.02 -9999 0 -10000 0 0
AKT1 0.024 0.032 -9999 0 -0.31 1 1
AKT3 0.022 0.062 -9999 0 -0.46 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.026 0.005 -9999 0 -10000 0 0
GNAI2 0.028 0.004 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.027 0.006 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.025 0.013 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.008 0.065 -9999 0 -0.29 11 11
MAPK3 0.005 0.06 -9999 0 -0.34 2 2
MAPK1 0.015 0.052 -9999 0 -0.28 11 11
JAK2 0.009 0.061 -9999 0 -0.34 2 2
CXCR4 0.004 0.06 -9999 0 -0.28 11 11
FLT1 0.028 0.007 -9999 0 -10000 0 0
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.005 -9999 0 -10000 0 0
SRC 0.004 0.061 -9999 0 -0.34 2 2
S1P/S1P3/Gi 0.008 0.065 -9999 0 -0.3 11 11
RAC1 0.026 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.012 0.069 -9999 0 -0.33 2 2
VEGFA 0.026 0.05 -9999 0 -0.69 2 2
S1P/S1P2/Gi 0.006 0.074 -9999 0 -0.34 12 12
VEGFR1 homodimer/VEGFA homodimer 0.042 0.041 -9999 0 -0.52 2 2
RHOA 0.027 0.004 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.052 0.15 -9999 0 -0.32 94 94
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.013 -9999 0 -10000 0 0
G12/G13 0.037 0.011 -9999 0 -10000 0 0
GNA14 -0.13 0.29 -9999 0 -0.65 92 92
GNA15 0.013 0.052 -9999 0 -0.69 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.018 0.071 -9999 0 -0.69 4 4
Rac1/GTP 0.012 0.068 -9999 0 -0.33 2 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.12 0.28 -10000 0 -0.68 82 82
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.01 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.032 0.041 0.35 1 -10000 0 1
HIF1A 0.008 0.026 -10000 0 -10000 0 0
COPS5 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.049 -10000 0 -0.38 2 2
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.031 0.071 -10000 0 -10000 0 0
ARNT/IPAS -0.073 0.22 -10000 0 -0.5 82 82
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.032 0.052 0.3 7 -10000 0 7
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.026 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.031 0.04 0.28 1 -10000 0 1
PHD1-3/OS9 0.049 0.078 -10000 0 -0.42 10 10
HIF1A/RACK1/Elongin B/Elongin C 0.054 0.041 -10000 0 -10000 0 0
VHL 0.023 0.05 -10000 0 -0.69 2 2
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.05 0.34 4 -10000 0 4
EGLN3 0.002 0.11 -10000 0 -0.69 10 10
EGLN2 0.026 0.007 -10000 0 -10000 0 0
EGLN1 0.025 0.008 -10000 0 -10000 0 0
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.025 0.074 -10000 0 -0.57 4 4
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.039 0.056 0.31 6 -10000 0 6
PLK1 signaling events

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.006 0.023 0.14 4 -0.12 4 8
BUB1B 0.015 0.032 0.2 8 -10000 0 8
PLK1 0.013 0.032 0.16 12 -0.1 1 13
PLK1S1 0.016 0.027 0.18 9 -10000 0 9
KIF2A 0.019 0.066 0.33 16 -10000 0 16
regulation of mitotic centrosome separation 0.013 0.032 0.16 12 -0.1 1 13
GOLGA2 0.025 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.035 0.037 -10000 0 -10000 0 0
WEE1 0.023 0.047 0.28 6 -0.34 1 7
cytokinesis 0.015 0.056 0.27 8 -0.3 1 9
PP2A-alpha B56 0.057 0.069 -10000 0 -0.48 3 3
AURKA 0.015 0.025 0.17 7 -10000 0 7
PICH/PLK1 0.02 0.015 -10000 0 -10000 0 0
CENPE 0.013 0.05 0.26 11 -0.4 1 12
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.019 0.066 0.33 16 -10000 0 16
PPP2CA 0.026 0.005 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.016 0.029 0.19 9 -10000 0 9
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.037 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
CLSPN 0.014 0.026 0.17 2 -0.24 2 4
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.023 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.02 0.1 12 -0.05 1 13
G2 phase of mitotic cell cycle 0 0.004 0.018 11 -10000 0 11
STAG2 0.025 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.022 0.04 -10000 0 -0.43 3 3
spindle elongation 0.013 0.032 0.16 12 -0.1 1 13
ODF2 0.025 0.008 -10000 0 -10000 0 0
BUB1 0.031 0.074 -10000 0 -0.48 8 8
TPT1 0.006 0.044 0.16 5 -0.18 18 23
CDC25C 0.019 0.026 0.2 5 -10000 0 5
CDC25B 0.027 0.012 -10000 0 -10000 0 0
SGOL1 0.006 0.023 0.12 4 -0.14 4 8
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.013 -10000 0 -10000 0 0
CDC14B 0.004 0.042 -10000 0 -0.39 4 4
CDC20 0.025 0.017 -10000 0 -10000 0 0
PLK1/PBIP1 0.011 0.022 0.15 4 -10000 0 4
mitosis -0.001 0.003 0.019 5 -10000 0 5
FBXO5 0.014 0.036 0.22 8 -10000 0 8
CDC2 0.002 0.001 0.01 1 -10000 0 1
NDC80 0.003 0.054 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.028 0.21 1 -0.23 3 4
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.012 0.029 0.15 13 -10000 0 13
microtubule cytoskeleton organization 0.006 0.044 0.16 5 -0.18 18 23
G2/M transition DNA damage checkpoint 0 0.004 0.02 11 -10000 0 11
PPP1R12A 0.027 0.006 -10000 0 -10000 0 0
interphase 0 0.004 0.02 11 -10000 0 11
PLK1/PRC1-2 0.041 0.028 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.021 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.029 0.15 12 -10000 0 12
mitotic prometaphase 0 0.004 0.026 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.025 -10000 0 -10000 0 0
microtubule-based process 0.025 0.027 -10000 0 -10000 0 0
Golgi organization 0.013 0.032 0.16 12 -0.1 1 13
Cohesin/SA2 0.021 0.016 0.17 1 -10000 0 1
PPP1CB/MYPT1 0.039 0.009 -10000 0 -10000 0 0
KIF20A -0.006 0.061 -10000 0 -10000 0 0
APC/C/CDC20 0.026 0.026 0.19 4 -10000 0 4
PPP2R1A 0.026 0.007 -10000 0 -10000 0 0
chromosome segregation 0.011 0.021 0.15 4 -10000 0 4
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.012 0.034 0.22 8 -10000 0 8
C13orf34 0.01 0.028 0.14 12 -0.081 1 13
NUDC 0.014 0.028 0.21 1 -0.23 3 4
regulation of attachment of spindle microtubules to kinetochore 0.015 0.032 0.2 8 -10000 0 8
spindle assembly 0.014 0.039 0.17 17 -10000 0 17
spindle stabilization 0.016 0.027 0.18 9 -10000 0 9
APC/C/HCDH1 0.019 0.038 -10000 0 -0.33 4 4
MKLP2/PLK1 0.025 0.027 -10000 0 -10000 0 0
CCNB1 0.027 0.006 -10000 0 -10000 0 0
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 0.005 0.086 0.22 3 -0.36 18 21
TUBG1 0.015 0.032 0.18 9 -0.16 3 12
G2/M transition of mitotic cell cycle 0.013 0.008 -10000 0 -10000 0 0
MLF1IP 0.007 0.013 -10000 0 -10000 0 0
INCENP 0.027 0.005 -10000 0 -10000 0 0
TCGA08_retinoblastoma

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.035 0.075 -10000 0 -10000 0 0
CDKN2C 0.031 0.02 -10000 0 -10000 0 0
CDKN2A -0.032 0.076 -10000 0 -0.18 1 1
CCND2 0.009 0.023 -10000 0 -10000 0 0
RB1 -0.014 0.047 0.31 1 -0.24 11 12
CDK4 0.013 0.043 0.26 9 -10000 0 9
CDK6 0.015 0.044 0.26 9 -0.16 1 10
G1/S progression 0.015 0.049 0.24 12 -0.31 1 13
Canonical Wnt signaling pathway

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.024 0.25 2 -10000 0 2
AES 0.026 0.019 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.01 -10000 0 -10000 0 0
SMAD4 0.027 0.005 -10000 0 -10000 0 0
DKK2 -0.007 0.14 -10000 0 -0.69 17 17
TLE1 0.022 0.053 0.22 2 -0.66 2 4
MACF1 0.027 0.006 -10000 0 -10000 0 0
CTNNB1 0.049 0.095 0.49 14 -10000 0 14
WIF1 -0.014 0.046 -10000 0 -10000 0 0
beta catenin/RanBP3 0.03 0.084 0.38 20 -10000 0 20
KREMEN2 0.014 0.039 -10000 0 -10000 0 0
DKK1 0 0.072 -10000 0 -0.69 2 2
beta catenin/beta TrCP1 0.047 0.048 0.38 2 -10000 0 2
FZD1 0.026 0.006 -10000 0 -10000 0 0
AXIN2 -0.033 0.3 0.59 13 -1.4 16 29
AXIN1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.028 0.073 -10000 0 -0.42 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.036 0.095 0.29 1 -0.64 3 4
Axin1/APC/GSK3 0.033 0.046 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.036 0.044 0.51 2 -10000 0 2
HNF1A 0.025 0.041 0.23 1 -0.69 1 2
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.038 0.24 0.54 4 -1.4 11 15
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.033 0.1 -10000 0 -0.45 16 16
NKD1 0.004 0.12 -10000 0 -0.69 12 12
TCF4 0.027 0.019 0.22 1 -10000 0 1
TCF3 0.026 0.023 0.25 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.064 0.021 -10000 0 -10000 0 0
Ran/GTP 0.02 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.022 0.12 0.47 20 -10000 0 20
LEF1 0.025 0.028 -10000 0 -10000 0 0
DVL1 0.027 0.015 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.11 -10000 0 -0.59 5 5
DKK1/LRP6/Kremen 2 0.048 0.049 -10000 0 -0.48 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.018 -10000 0 -10000 0 0
NLK 0.025 0.008 -10000 0 -10000 0 0
CCND1 -0.011 0.09 0.58 2 -0.72 2 4
WNT1 0.023 0.014 -10000 0 -10000 0 0
GSK3A 0.026 0.007 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
PPP2R5D 0.032 0.059 0.33 12 -0.33 1 13
APC 0.024 0.039 0.36 4 -10000 0 4
WNT1/LRP6/FZD1 0.03 0.019 -10000 0 -10000 0 0
CREBBP 0.027 0.02 0.23 1 -10000 0 1
Signaling events mediated by VEGFR1 and VEGFR2

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.022 0.096 -10000 0 -0.53 11 11
AKT1 0.039 0.079 0.34 1 -0.56 4 5
PTK2B 0.017 0.11 0.35 1 -0.78 4 5
VEGFR2 homodimer/Frs2 0.032 0.075 -10000 0 -0.82 3 3
CAV1 0.012 0.099 -10000 0 -0.69 8 8
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.047 0.079 -10000 0 -0.62 5 5
endothelial cell proliferation 0.051 0.15 0.59 16 -0.53 4 20
mol:Ca2+ 0.024 0.073 -10000 0 -0.54 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.061 0.076 -10000 0 -0.65 4 4
RP11-342D11.1 0.013 0.072 -10000 0 -0.54 6 6
CDH5 0.026 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.06 0.049 -10000 0 -0.41 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.02 0.061 -10000 0 -0.69 3 3
HRAS/GDP 0.041 0.061 -10000 0 -0.49 4 4
SH2D2A -0.011 0.15 -10000 0 -0.69 19 19
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.055 0.089 -10000 0 -0.56 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.024 0.12 -10000 0 -0.44 24 24
VEGFR1 homodimer 0.026 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.068 0.072 -10000 0 -0.58 3 3
GRB10 0.025 0.071 -10000 0 -0.57 5 5
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.071 0.074 -10000 0 -0.54 5 5
HRAS 0.026 0.012 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.026 0.065 -10000 0 -0.43 4 4
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.059 0.075 -10000 0 -0.64 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.019 0.071 -10000 0 -0.69 4 4
Nck/Pak 0.039 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.048 0.079 -10000 0 -0.62 5 5
mol:GDP 0.053 0.066 -10000 0 -0.56 3 3
mol:NADP 0.04 0.097 0.48 6 -0.45 4 10
eNOS/Hsp90 0.043 0.078 -10000 0 -0.42 4 4
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.024 0.074 -10000 0 -0.54 6 6
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.025 0.05 -10000 0 -0.68 2 2
VEGFC 0.025 0.036 -10000 0 -0.69 1 1
FAK1/Vinculin 0.038 0.1 -10000 0 -0.7 4 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.11 -10000 0 -0.52 13 13
PTPN6 0.026 0.005 -10000 0 -10000 0 0
EPAS1 0.032 0.036 -10000 0 -0.38 3 3
mol:L-citrulline 0.04 0.097 0.48 6 -0.45 4 10
ITGAV 0.025 0.036 -10000 0 -0.69 1 1
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.059 0.077 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer 0.051 0.082 -10000 0 -0.58 6 6
VEGFR2/3 heterodimer 0.028 0.095 -10000 0 -0.7 6 6
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.008 0.077 0.38 1 -0.56 6 7
VEGFR2 homodimer 0.02 0.081 -10000 0 -0.92 3 3
FLT1 0.026 0.007 -10000 0 -10000 0 0
NEDD4 0.027 0.036 -10000 0 -0.68 1 1
MAPK3 0 0.08 0.37 1 -0.61 4 5
MAPK1 -0.004 0.081 0.37 1 -0.62 4 5
VEGFA145/NRP2 0.028 0.051 -10000 0 -0.52 2 2
VEGFR1/2 heterodimer 0.031 0.074 -10000 0 -0.82 3 3
KDR 0.02 0.081 -10000 0 -0.92 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.055 0.079 -10000 0 -0.54 6 6
SRC 0.026 0.009 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.012 0.11 0.42 11 -0.62 4 15
PI3K 0.044 0.079 -10000 0 -0.64 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.048 0.079 -10000 0 -0.62 5 5
FES 0.025 0.075 -10000 0 -0.73 3 3
GAB1 0.031 0.072 -10000 0 -0.6 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.079 -10000 0 -0.62 5 5
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.038 0.088 -10000 0 -0.51 4 4
VEGFR2 homodimer/VEGFA homodimer/Yes 0.047 0.079 -10000 0 -0.62 5 5
PI3K/GAB1 0.051 0.074 -10000 0 -0.54 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.071 0.077 -10000 0 -0.62 4 4
PRKACA 0.025 0.007 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.095 -10000 0 -0.62 7 7
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.024 0.071 -10000 0 -0.52 6 6
actin cytoskeleton reorganization 0.024 0.12 -10000 0 -0.43 24 24
PTK2 0.025 0.099 -10000 0 -0.69 5 5
EDG1 0.013 0.072 -10000 0 -0.54 6 6
mol:DAG 0.024 0.074 -10000 0 -0.54 6 6
CaM/Ca2+ 0.037 0.07 -10000 0 -0.66 3 3
MAP2K3 0.012 0.081 0.37 1 -0.69 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.079 -10000 0 -0.59 5 5
PLCG1 0.025 0.075 -10000 0 -0.55 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.058 0.078 -10000 0 -0.59 5 5
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.047 0.079 -10000 0 -0.62 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.047 0.079 -10000 0 -0.62 5 5
cell migration 0.045 0.083 0.34 1 -0.63 3 4
mol:PI-3-4-5-P3 0.043 0.073 -10000 0 -0.58 4 4
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.029 0.07 -10000 0 -0.51 6 6
mol:NO 0.04 0.097 0.48 6 -0.45 4 10
PXN 0.026 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.057 -10000 0 -0.49 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.044 0.076 -10000 0 -0.59 5 5
VHL 0.023 0.05 -10000 0 -0.69 2 2
ITGB3 0.007 0.11 -10000 0 -0.66 11 11
NOS3 0.039 0.1 0.52 5 -0.5 4 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.041 0.086 -10000 0 -0.56 7 7
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.005 0.12 0.36 1 -0.42 24 25
PRKCB 0.009 0.077 0.36 1 -0.55 5 6
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.031 0.074 -10000 0 -0.54 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.079 -10000 0 -0.62 5 5
VEGFA165/NRP2 0.028 0.051 -10000 0 -0.52 2 2
MAPKKK cascade 0.051 0.073 0.35 1 -0.53 3 4
NRP2 0.014 0.041 -10000 0 -10000 0 0
VEGFC homodimer 0.025 0.036 -10000 0 -0.69 1 1
NCK1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.027 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.038 0.1 -10000 0 -0.64 5 5
MAP3K13 0.021 0.085 -10000 0 -0.48 10 10
PDPK1 0.029 0.069 -10000 0 -0.57 4 4
IL2 signaling events mediated by STAT5

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.027 0.005 -10000 0 -10000 0 0
ELF1 0.008 0.093 -10000 0 -0.39 20 20
CCNA2 0.024 0.021 -10000 0 -10000 0 0
PIK3CA 0.026 0.036 -10000 0 -0.69 1 1
JAK3 -0.008 0.062 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.004 0.14 -10000 0 -0.62 13 13
SHC1 0.026 0.008 -10000 0 -10000 0 0
SP1 0.033 0.007 -10000 0 -10000 0 0
IL2RA -0.027 0.2 -10000 0 -0.89 20 20
IL2RB 0.003 0.099 -10000 0 -0.62 9 9
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG -0.012 0.14 -10000 0 -0.64 18 18
G1/S transition of mitotic cell cycle 0.032 0.06 0.43 5 -0.51 1 6
PTPN11 0.027 0.005 -10000 0 -10000 0 0
CCND2 0.023 0.005 -10000 0 -10000 0 0
LCK 0.013 0.083 -10000 0 -0.69 5 5
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.024 0.036 -10000 0 -0.69 1 1
CCND3 0.009 0.12 -10000 0 -0.62 8 8
Aurora B signaling

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.016 0.043 -10000 0 -0.25 3 3
STMN1 0.002 0.042 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.052 0.054 -10000 0 -0.45 1 1
Chromosomal passenger complex/Cul3 protein complex 0.013 0.052 -10000 0 -0.26 10 10
BIRC5 0.013 0.054 -10000 0 -0.7 1 1
DES -0.33 0.3 -10000 0 -0.57 237 237
Aurora C/Aurora B/INCENP 0.058 0.03 -10000 0 -10000 0 0
Aurora B/TACC1 0.036 0.032 -10000 0 -10000 0 0
Aurora B/PP2A 0.032 0.044 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.006 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.012 0.062 -10000 0 -10000 0 0
Cul3 protein complex 0.038 0.072 -10000 0 -0.45 8 8
KIF2C 0.016 0.029 -10000 0 -0.47 1 1
PEBP1 0.026 0.006 -10000 0 -10000 0 0
KIF20A -0.006 0.062 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.032 0.044 -10000 0 -10000 0 0
SEPT1 0.024 0.019 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.013 0.091 -10000 0 -0.54 9 9
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.012 0.015 -10000 0 -10000 0 0
AURKB 0.002 0.064 -10000 0 -10000 0 0
AURKC 0.021 0.025 -10000 0 -10000 0 0
CDCA8 0.027 0.015 -10000 0 -10000 0 0
cytokinesis -0.018 0.054 -10000 0 -0.37 3 3
Aurora B/Septin1 0.048 0.065 -10000 0 -0.38 2 2
AURKA 0.026 0.005 -10000 0 -10000 0 0
INCENP 0.028 0.007 -10000 0 -10000 0 0
KLHL13 0.008 0.1 -10000 0 -0.69 8 8
BUB1 -0.03 0.072 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.046 0.063 -10000 0 -0.42 2 2
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.052 0.043 -10000 0 -10000 0 0
SGOL1 0.018 0.047 -10000 0 -0.69 1 1
CENPA 0.021 0.034 0.19 1 -10000 0 1
NCAPG 0.009 0.049 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.032 0.044 -10000 0 -10000 0 0
NCAPD2 0.026 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.031 0.044 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.005 0.053 -10000 0 -10000 0 0
NPM1 0.011 0.047 -10000 0 -0.31 5 5
RASA1 0.026 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.044 -10000 0 -10000 0 0
PPP1CC 0.026 0.005 -10000 0 -10000 0 0
Centraspindlin 0.042 0.046 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 0.011 0.048 -10000 0 -0.33 2 2
MYLK 0.012 0.015 -10000 0 -10000 0 0
KIF23 0.02 0.035 -10000 0 -10000 0 0
VIM 0 0.038 -10000 0 -10000 0 0
RACGAP1 0.027 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.003 0.089 -10000 0 -0.55 7 7
Chromosomal passenger complex 0.017 0.033 -10000 0 -0.28 2 2
Chromosomal passenger complex/EVI5 0.11 0.059 -10000 0 -0.4 1 1
TACC1 0.027 0.004 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.026 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.072 0.4 2 -0.37 1 3
ERC1 0.026 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.022 0.049 -10000 0 -0.52 1 1
NFKBIA 0.022 0.015 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.027 0.004 -10000 0 -10000 0 0
RIPK2 0.027 0.005 -10000 0 -10000 0 0
IKBKG 0.034 0.022 -10000 0 -10000 0 0
IKK complex/A20 0.015 0.14 0.33 1 -0.55 3 4
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.034 0.074 -10000 0 -0.44 2 2
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.069 -10000 0 -0.52 1 1
BCL10/MALT1/TRAF6 0.051 0.029 -10000 0 -0.45 1 1
NOD2 0.005 0.061 -10000 0 -0.69 1 1
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.008 -10000 0 -10000 0 0
ATM 0.025 0.036 -10000 0 -0.69 1 1
TNF/TNFR1A -0.026 0.18 -10000 0 -0.52 46 46
TRAF6 0.025 0.036 -10000 0 -0.69 1 1
PRKCA -0.013 0.16 -10000 0 -0.69 22 22
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.058 0.23 -10000 0 -0.69 46 46
NF kappa B1 p50/RelA 0.061 0.015 -10000 0 -10000 0 0
BCL10 0.026 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.015 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.049 0.074 -10000 0 -0.55 1 1
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.034 0.12 -10000 0 -0.52 2 2
a4b1 and a4b7 Integrin signaling

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.005 0.1 -9999 0 -0.65 9 9
ITGA4 0.024 0.021 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.02 0.083 -9999 0 -0.49 9 9
alpha4/beta1 Integrin 0.037 0.018 -9999 0 -10000 0 0
EPO signaling pathway

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.033 0.093 -10000 0 -10000 0 0
CRKL 0.015 0.049 0.46 3 -10000 0 3
mol:DAG 0.029 0.045 -10000 0 -10000 0 0
HRAS 0.033 0.062 0.36 5 -10000 0 5
MAPK8 0.017 0.05 -10000 0 -0.45 3 3
RAP1A 0.025 0.067 0.48 6 -10000 0 6
GAB1 0.022 0.056 0.45 4 -10000 0 4
MAPK14 0.02 0.029 -10000 0 -10000 0 0
EPO 0.02 0.018 -10000 0 -10000 0 0
PLCG1 0.029 0.046 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.024 0.022 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.012 0.13 -10000 0 -0.44 28 28
GAB1/SHC/GRB2/SOS1 0.047 0.041 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.033 0.023 -10000 0 -10000 0 0
IRS2 0.023 0.062 0.46 5 -10000 0 5
STAT1 0.031 0.068 -10000 0 -10000 0 0
STAT5B 0.028 0.058 -10000 0 -10000 0 0
cell proliferation 0.015 0.063 0.34 6 -0.42 3 9
GAB1/SHIP/PIK3R1/SHP2/SHC 0.038 0.034 -10000 0 -10000 0 0
TEC 0.022 0.056 0.45 4 -10000 0 4
SOCS3 -0.024 0.18 -10000 0 -0.69 28 28
STAT1 (dimer) 0.03 0.067 -10000 0 -10000 0 0
JAK2 0.028 0.013 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.061 0.051 -10000 0 -10000 0 0
EPO/EPOR 0.033 0.023 -10000 0 -10000 0 0
LYN 0.025 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.032 0.038 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.024 0.022 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.05 0.031 -10000 0 -10000 0 0
mol:IP3 0.029 0.045 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.045 0.044 -10000 0 -10000 0 0
SH2B3 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.02 0.028 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.007 0.072 -10000 0 -0.26 28 28
PTPN6 0.022 0.044 0.3 1 -10000 0 1
TEC/VAV2/GRB2 0.042 0.041 -10000 0 -10000 0 0
EPOR 0.024 0.022 -10000 0 -10000 0 0
INPP5D 0.018 0.035 -10000 0 -10000 0 0
mol:GDP 0.047 0.041 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.031 0.04 -10000 0 -10000 0 0
VAV2 0.025 0.063 0.46 6 -10000 0 6
CBL 0.022 0.056 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.037 0.037 -10000 0 -10000 0 0
STAT5A 0.028 0.058 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.041 0.092 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.01 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
BTK 0.012 0.057 -10000 0 -0.37 5 5
BCL2 -0.007 0.24 -10000 0 -0.91 26 26
Insulin-mediated glucose transport

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.028 0.1 -10000 0 -0.51 4 4
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.026 0.007 -10000 0 -10000 0 0
STXBP4 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.02 0.11 0.36 7 -0.51 6 13
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.045 0.17 -10000 0 -0.51 47 47
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.017 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.007 0.045 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.017 0.012 0.24 1 -10000 0 1
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
TRIP10 0.025 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
AS160/14-3-3 -0.03 0.092 -10000 0 -0.36 10 10
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.018 0.12 0.4 5 -0.59 6 11
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.023 0.007 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.69 12 12
LNPEP 0.011 0.1 -10000 0 -0.69 9 9
YWHAE 0.025 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.044 0.015 -10000 0 -10000 0 0
CDKN1B 0.022 0.018 -10000 0 -10000 0 0
CDKN1A 0.02 0.02 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
FOXO3 0.022 0.018 -10000 0 -10000 0 0
AKT1 0.022 0.017 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.014 0.021 -10000 0 -0.39 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.022 0.022 -10000 0 -10000 0 0
AKT1/ASK1 0.038 0.036 -10000 0 -0.34 1 1
BAD/YWHAZ 0.05 0.017 -10000 0 -10000 0 0
RICTOR 0.026 0.006 -10000 0 -10000 0 0
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.034 0.33 1 -10000 0 1
TSC1 0.021 0.018 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.033 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.022 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.022 0.017 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.04 0.14 -10000 0 -0.44 46 46
MAP3K5 0.025 0.036 -10000 0 -0.69 1 1
MAPKAP1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.083 0.4 5 -0.39 6 11
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.025 0.031 -10000 0 -10000 0 0
CASP9 0.024 0.027 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.046 0.4 4 -10000 0 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.029 -10000 0 -0.45 1 1
YWHAE 0.025 0.007 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.023 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.009 -10000 0 -10000 0 0
CHUK 0.022 0.018 -10000 0 -10000 0 0
BAD/BCL-XL 0.047 0.031 0.28 1 -10000 0 1
mTORC2 0.031 0.012 -10000 0 -10000 0 0
AKT2 0.014 0.021 -10000 0 -0.39 1 1
FOXO1-3a-4/14-3-3 family 0.021 0.085 0.41 6 -0.36 4 10
PDPK1 0.024 0.036 -10000 0 -0.69 1 1
MDM2 0.023 0.02 -10000 0 -10000 0 0
MAPKKK cascade -0.041 0.032 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.04 0.03 -10000 0 -10000 0 0
TSC1/TSC2 0.023 0.033 0.32 3 -10000 0 3
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.029 -10000 0 -10000 0 0
glucose import -0.051 0.16 0.21 3 -0.43 56 59
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.026 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.053 0.16 -10000 0 -0.43 56 56
GSK3A 0.025 0.029 -10000 0 -10000 0 0
FOXO1 0.021 0.018 -10000 0 -10000 0 0
GSK3B 0.022 0.018 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.69 12 12
G1/S transition of mitotic cell cycle 0.028 0.04 0.32 2 -10000 0 2
p27Kip1/14-3-3 family 0.017 0.052 -10000 0 -0.34 3 3
PRKACA 0.025 0.007 -10000 0 -10000 0 0
KPNA1 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.006 0.16 -10000 0 -0.44 46 46
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.14 -10000 0 -0.39 45 45
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.025 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.036 0.084 -10000 0 -10000 0 0
YY1/LSF 0.007 0.065 -10000 0 -0.45 3 3
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.008 0.11 -10000 0 -0.32 44 44
I kappa B alpha/HDAC1 0.01 0.081 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
RELA -0.016 0.11 -10000 0 -0.32 46 46
HDAC1/Smad7 0.051 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.081 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.032 0.025 -10000 0 -0.32 1 1
NF kappa B1 p50/RelA -0.023 0.12 0.32 1 -0.44 11 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.008 -10000 0 -10000 0 0
GATA1 0.011 0.02 -10000 0 -10000 0 0
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.034 0.065 -10000 0 -0.47 4 4
RBBP7 0.025 0.008 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.005 -10000 0 -10000 0 0
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
NFKBIA -0.003 0.084 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.031 0.019 -10000 0 -10000 0 0
SIN3 complex 0.061 0.033 -10000 0 -0.42 1 1
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.025 0.036 -10000 0 -0.69 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.009 0.08 -10000 0 -10000 0 0
YY1/HDAC2 0.009 0.054 -10000 0 -0.28 1 1
YY1/HDAC1 0.01 0.052 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.032 0.023 -10000 0 -10000 0 0
PPARG -0.021 0.14 -10000 0 -0.39 49 49
HDAC8/hEST1B 0.046 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.011 0.081 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.05 0.016 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.035 0.058 -10000 0 -0.34 7 7
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC3 -0.003 0.084 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.018 0.012 -10000 0 -10000 0 0
HDAC8 0.025 0.007 -10000 0 -10000 0 0
SMAD7 0.027 0.004 -10000 0 -10000 0 0
NCOR2 0.026 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.018 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.02 0.064 -10000 0 -0.42 3 3
YY1/SAP30/HDAC1 0.021 0.057 -10000 0 -0.32 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.084 -10000 0 -10000 0 0
histone deacetylation 0.038 0.026 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.002 0.076 -10000 0 -0.3 1 1
nuclear export -0.046 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.007 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.007 -10000 0 -10000 0 0
GATA2/HDAC3 0.011 0.082 -10000 0 -10000 0 0
GATA1/HDAC1 0.034 0.012 -10000 0 -10000 0 0
GATA1/HDAC3 0.009 0.08 -10000 0 -10000 0 0
CHD4 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.026 0.18 -10000 0 -0.52 46 46
SIN3/HDAC complex/Mad/Max 0.032 0.041 -10000 0 -0.66 1 1
NuRD Complex 0.042 0.049 -10000 0 -0.42 2 2
positive regulation of chromatin silencing 0.033 0.082 -10000 0 -10000 0 0
SIN3B 0.025 0.007 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.014 0.057 -10000 0 -0.25 3 3
HDAC complex 0.064 0.022 -10000 0 -10000 0 0
GATA1/Fog1 0.034 0.013 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.052 0.014 -10000 0 -10000 0 0
TNF -0.058 0.23 -10000 0 -0.69 46 46
negative regulation of cell growth 0.034 0.042 -10000 0 -0.65 1 1
NuRD/MBD2/PRMT5 Complex 0.032 0.023 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.018 0.051 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.031 0.14 -10000 0 -0.4 45 45
SIN3/HDAC complex/NCoR1 0.03 0.048 -10000 0 -0.49 2 2
TFCP2 0.021 0.061 -10000 0 -0.69 3 3
NR2C1 0.026 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.008 -10000 0 -10000 0 0
MBD2 0.027 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.008 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.011 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.009 0.04 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.048 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.022 0.016 -10000 0 -10000 0 0
mol:ACh 0.002 0.045 0.14 16 -0.14 20 36
RAB3GAP2 0.025 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.056 -10000 0 -0.26 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.009 0.04 -10000 0 -10000 0 0
UNC13B 0.025 0.008 -10000 0 -10000 0 0
CHRNA1 0.008 0.044 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.046 0.12 -10000 0 -0.5 22 22
SNAP25 -0.016 0.077 -10000 0 -0.34 21 21
VAMP2 0.005 0.002 -10000 0 -10000 0 0
SYT1 -0.075 0.16 -10000 0 -0.69 22 22
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.056 -10000 0 -0.26 1 1
PDGFR-beta signaling pathway

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.041 0.31 1 -10000 0 1
PDGFB-D/PDGFRB/SLAP 0.038 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.052 0.015 -10000 0 -10000 0 0
AKT1 0.031 0.084 0.46 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.045 0.35 2 -10000 0 2
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
FGR 0.018 0.043 0.32 2 -0.65 1 3
mol:Ca2+ 0.034 0.072 0.4 9 -10000 0 9
MYC 0.029 0.18 0.54 17 -0.78 10 27
SHC1 0.025 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.013 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.039 0.035 -10000 0 -0.45 1 1
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GO:0007205 0.033 0.072 0.4 9 -10000 0 9
PTEN 0.026 0.021 -10000 0 -0.38 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.004 0.053 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.039 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.039 0.01 -10000 0 -10000 0 0
cell cycle arrest 0.038 0.012 -10000 0 -10000 0 0
HRAS 0.026 0.012 -10000 0 -10000 0 0
HIF1A 0.025 0.082 0.45 11 -10000 0 11
GAB1 0.027 0.081 0.4 9 -0.4 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.032 0.1 0.48 13 -0.32 1 14
PDGFB-D/PDGFRB 0.055 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.039 0.01 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.019 0.048 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.039 0.009 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.034 0.072 0.4 9 -10000 0 9
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.02 0.043 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
BLK -0.15 0.26 -10000 0 -0.56 120 120
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.039 0.009 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.032 0.1 0.46 12 -0.47 2 14
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.039 0.009 -10000 0 -10000 0 0
LCK 0.012 0.066 -10000 0 -0.56 5 5
PDGFRB 0.027 0.006 -10000 0 -10000 0 0
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.025 0.022 -10000 0 -10000 0 0
ABL1 0.025 0.087 0.39 12 -0.5 1 13
PDGFB-D/PDGFRB/CBL 0.022 0.07 0.4 3 -0.46 1 4
PTPN1 0.027 0.005 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
cell proliferation 0.031 0.16 0.53 17 -0.69 10 27
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.021 -10000 0 -10000 0 0
SRC 0.019 0.028 -10000 0 -10000 0 0
PI3K 0.014 0.021 -10000 0 -0.35 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.051 0.023 -10000 0 -10000 0 0
SH2B2 0.025 0.01 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.029 0.046 0.35 2 -10000 0 2
LYN 0.018 0.029 -10000 0 -0.44 1 1
LRP1 0.025 0.036 -10000 0 -0.69 1 1
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.079 0.025 -10000 0 -10000 0 0
SPHK1 0.024 0.02 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.034 0.072 0.4 9 -10000 0 9
PLCG1 0.034 0.072 0.4 9 -10000 0 9
NHERF/PDGFRB 0.051 0.017 -10000 0 -10000 0 0
YES1 0.015 0.058 0.36 1 -0.49 4 5
cell migration 0.05 0.017 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.073 0.032 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.026 -10000 0 -10000 0 0
FYN 0.016 0.05 0.29 1 -0.46 3 4
DOK1 0.022 0.017 -10000 0 -10000 0 0
HRAS/GTP 0.019 0.008 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.038 0.14 0.52 17 -0.45 7 24
PRKCD 0.024 0.021 -10000 0 -10000 0 0
FER 0.021 0.036 -10000 0 -0.42 2 2
MAPKKK cascade 0.015 0.055 0.37 1 -10000 0 1
RASA1 0.023 0.018 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.021 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.037 0.013 -10000 0 -10000 0 0
chemotaxis 0.025 0.087 0.38 12 -0.48 1 13
STAT1-3-5/STAT1-3-5 0.064 0.021 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.02 0.005 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
p38 MAPK signaling pathway

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.028 -10000 0 -0.34 2 2
TRAF2/ASK1 0.032 0.027 -10000 0 -0.45 1 1
ATM 0.025 0.036 -10000 0 -0.69 1 1
MAP2K3 0.038 0.097 0.4 15 -0.39 3 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.028 0.092 0.34 13 -0.45 3 16
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.013 0.087 -10000 0 -0.69 6 6
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.001 0.13 -10000 0 -0.65 15 15
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
MAP3K6 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.037 0.029 -10000 0 -0.52 1 1
TAK1/TAB family 0.011 0.032 -10000 0 -0.19 2 2
RAC1/OSM/MEKK3 0.049 0.015 -10000 0 -10000 0 0
TRAF2 0.025 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.037 0.055 -10000 0 -0.34 2 2
TRAF6 0.007 0.02 -10000 0 -0.4 1 1
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.019 0.071 -10000 0 -0.69 4 4
CCM2 0.026 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.03 0.049 -10000 0 -0.45 4 4
MAPK11 0.02 0.012 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.044 0.059 -10000 0 -0.51 4 4
OSM/MEKK3 0.037 0.011 -10000 0 -10000 0 0
TAOK1 -0.024 0.13 -10000 0 -0.41 38 38
TAOK2 0.015 0.021 -10000 0 -0.39 1 1
TAOK3 0.015 0.021 -10000 0 -0.39 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.025 0.036 -10000 0 -0.69 1 1
MAP3K10 0.026 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.016 0.038 -10000 0 -0.44 1 1
GADD45/MTK1/MTK1 0.034 0.1 -10000 0 -0.4 18 18
S1P5 pathway

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.008 0.073 0.48 3 -10000 0 3
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.015 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.006 0.12 -10000 0 -0.69 11 11
RhoA/GTP 0.008 0.075 -10000 0 -0.49 3 3
negative regulation of cAMP metabolic process 0.001 0.073 -10000 0 -0.35 11 11
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
S1PR5 0.024 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.074 -10000 0 -0.36 11 11
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.026 0.006 -10000 0 -10000 0 0
FoxO family signaling

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.026 0.12 0.67 9 -10000 0 9
PLK1 0.072 0.11 0.57 3 -0.56 1 4
CDKN1B 0.075 0.092 0.59 3 -10000 0 3
FOXO3 0.068 0.098 -10000 0 -0.61 1 1
KAT2B 0.032 0.018 -10000 0 -10000 0 0
FOXO1/SIRT1 0.02 0.053 0.41 2 -10000 0 2
CAT 0.068 0.097 0.53 1 -0.55 1 2
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.034 0.019 -10000 0 -10000 0 0
FOXO1 0.019 0.084 0.44 11 -10000 0 11
MAPK10 0.034 0.028 -10000 0 -10000 0 0
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.074 0.08 0.5 9 -0.4 1 10
response to oxidative stress 0.01 0.011 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.088 0.063 -10000 0 -0.41 1 1
XPO1 0.027 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.026 0.1 -10000 0 -0.66 7 7
FOXO1/SKP2 0.017 0.046 -10000 0 -0.38 1 1
mol:GDP 0.01 0.011 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
GADD45A 0.1 0.088 0.46 7 -0.55 2 9
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.1 -10000 0 -0.51 5 5
MST1 0.03 0.04 -10000 0 -0.68 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.007 0.11 -10000 0 -0.6 7 7
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.032 0.047 -10000 0 -0.4 3 3
MAPK9 0.031 0.019 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.027 0.019 -10000 0 -10000 0 0
SOD2 0.11 0.098 0.62 8 -10000 0 8
RBL2 0.082 0.12 0.56 1 -0.85 3 4
RAL/GDP 0.045 0.014 -10000 0 -10000 0 0
CHUK 0.032 0.018 -10000 0 -10000 0 0
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
RAL/GTP 0.049 0.015 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.07 0.38 -10000 0 -1.4 32 32
SKP2 0.024 0.036 -10000 0 -0.69 1 1
USP7 0.027 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.019 -10000 0 -10000 0 0
CCNB1 0.071 0.1 0.57 3 -10000 0 3
FOXO1-3a-4/beta catenin 0.1 0.094 0.44 6 -0.41 2 8
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.046 -10000 0 -0.37 1 1
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
SGK1 0.02 0.094 -10000 0 -0.68 7 7
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.01 -10000 0 -10000 0 0
ZFAND5 0.081 0.1 0.59 13 -10000 0 13
SFN -0.085 0.13 -10000 0 -0.69 12 12
CDK2 0.026 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.01 0.1 -10000 0 -0.54 7 7
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.068 0.1 0.56 2 -0.55 1 3
BCL6 0.083 0.12 0.52 2 -0.81 4 6
RALB 0.028 0.005 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.008 0.003 -10000 0 -10000 0 0
SNTA1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.008 0.004 -10000 0 -10000 0 0
MAPK12 0.001 0.045 -10000 0 -0.4 5 5
CCND1 0.009 0.038 -10000 0 -0.34 3 3
p38 gamma/SNTA1 0.023 0.057 -10000 0 -0.36 6 6
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.007 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.052 0.21 7 -0.39 5 12
MAP2K6 0.004 0.052 -10000 0 -0.42 6 6
MAPT 0.012 0.051 0.3 7 -0.37 2 9
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.016 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.037 0.012 -9999 0 -10000 0 0
FBXW11 0.026 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.008 0.1 -9999 0 -0.45 20 20
NF kappa B1 p50/RelA/I kappa B alpha 0.035 0.039 -9999 0 -10000 0 0
NFKBIA 0.014 0.029 -9999 0 -0.25 4 4
MAPK14 0.027 0.003 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.031 0.008 -9999 0 -10000 0 0
ARRB2 0.016 0.005 -9999 0 -10000 0 0
REL -0.009 0.16 -9999 0 -0.69 20 20
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.01 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.007 -9999 0 -10000 0 0
PIK3CA 0.025 0.036 -9999 0 -0.69 1 1
NF kappa B1 p50 dimer 0.025 0.025 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
NFKB1 0.017 0.003 -9999 0 -10000 0 0
RELA 0.027 0.005 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.02 0.039 -9999 0 -0.31 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.038 0.041 -9999 0 -10000 0 0
SRC 0.026 0.009 -9999 0 -10000 0 0
PI3K 0.038 0.029 -9999 0 -0.52 1 1
NF kappa B1 p50/RelA 0.02 0.039 -9999 0 -0.31 4 4
IKBKB 0.027 0.004 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.005 -9999 0 -10000 0 0
SYK 0.025 0.008 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.038 -9999 0 -10000 0 0
cell death 0.037 0.04 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.008 0.1 -9999 0 -0.45 20 20
LCK 0.012 0.083 -9999 0 -0.69 5 5
BCL3 0.025 0.01 -9999 0 -10000 0 0
S1P4 pathway

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.006 0.12 -10000 0 -0.69 11 11
CDC42/GTP 0.008 0.074 -10000 0 -0.49 3 3
PLCG1 -0.002 0.069 -10000 0 -0.34 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.011 -10000 0 -10000 0 0
cell migration 0.008 0.073 -10000 0 -0.48 3 3
S1PR5 0.024 0.016 -10000 0 -10000 0 0
S1PR4 0.024 0.016 -10000 0 -10000 0 0
MAPK3 -0.002 0.069 -10000 0 -0.5 3 3
MAPK1 0.01 0.061 -10000 0 -0.33 11 11
S1P/S1P5/Gi 0.001 0.074 -10000 0 -0.36 11 11
GNAI1 0.026 0.006 -10000 0 -10000 0 0
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.015 -10000 0 -10000 0 0
RHOA 0.033 0.068 0.42 9 -10000 0 9
S1P/S1P4/Gi 0.001 0.074 -10000 0 -0.36 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.017 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.027 0.005 -9999 0 -10000 0 0
SMAD2 -0.016 0.044 -9999 0 -0.24 1 1
SMAD3 0.021 0.016 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.05 -9999 0 -0.43 4 4
SMAD4/Ubc9/PIASy 0.049 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.061 -9999 0 -10000 0 0
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.003 0.055 -9999 0 -0.34 2 2
MAP3K1 0.026 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.013 0.12 -9999 0 -0.52 19 19
MAPK3 0.026 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.025 0.008 -9999 0 -10000 0 0
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.026 0.005 -9999 0 -10000 0 0
CTDSPL 0.027 0.004 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.007 0.15 -9999 0 -0.69 19 19
UBE2I 0.026 0.007 -9999 0 -10000 0 0
NUP153 0.027 0.003 -9999 0 -10000 0 0
KPNA2 0.026 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.008 -9999 0 -10000 0 0
Circadian rhythm pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.031 -9999 0 -10000 0 0
CLOCK 0.005 0.13 -9999 0 -0.69 13 13
TIMELESS/CRY2 0.03 0.031 -9999 0 -10000 0 0
DEC1/BMAL1 0.018 0.037 -9999 0 -10000 0 0
ATR 0.027 0.004 -9999 0 -10000 0 0
NR1D1 0.004 0.035 -9999 0 -10000 0 0
ARNTL 0.011 0.047 -9999 0 -10000 0 0
TIMELESS 0.014 0.025 -9999 0 -10000 0 0
NPAS2 0.026 0.023 -9999 0 -0.37 1 1
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.005 0.008 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.005 0.008 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.039 0.096 -9999 0 -0.46 13 13
BMAL1/CLOCK 0.009 0.086 -9999 0 -0.52 1 1
S phase of mitotic cell cycle 0.044 0.031 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.045 0.031 -9999 0 -10000 0 0
mol:NADPH 0.005 0.008 -9999 0 -10000 0 0
PER1/TIMELESS 0.029 0.028 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 0 -10000 0 0
Aurora A signaling

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.029 0.024 -10000 0 -10000 0 0
BIRC5 0.012 0.053 -10000 0 -0.69 1 1
NFKBIA 0.014 0.022 0.25 3 -10000 0 3
CPEB1 -0.024 0.18 -10000 0 -0.66 30 30
AKT1 0.014 0.025 0.25 4 -10000 0 4
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.026 0.02 -10000 0 -10000 0 0
NDEL1/TACC3 0.042 0.023 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.008 -10000 0 -10000 0 0
PAK1/Aurora A 0.029 0.024 -10000 0 -10000 0 0
MDM2 0.026 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.028 -10000 0 -10000 0 0
TP53 0.025 0.01 -10000 0 -10000 0 0
DLG7 0.012 0.007 -10000 0 -10000 0 0
AURKAIP1 0.026 0.009 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.044 0.023 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.025 0.02 -10000 0 -10000 0 0
AURKA 0.019 0.01 -10000 0 -10000 0 0
AURKB 0.014 0.019 -10000 0 -0.16 3 3
CDC25B 0.02 0.009 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.004 0.11 -10000 0 -0.41 28 28
Aurora A/CPEB -0.004 0.11 -10000 0 -0.41 28 28
Aurora A/TACC1/TRAP/chTOG 0.053 0.033 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
centrosome duplication 0.029 0.024 -10000 0 -10000 0 0
regulation of centrosome cycle 0.04 0.023 -10000 0 -10000 0 0
spindle assembly 0.052 0.033 -10000 0 -10000 0 0
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.054 0.035 -10000 0 -0.37 1 1
CENPA 0.019 0.02 -10000 0 -0.24 2 2
Aurora A/PP2A 0.029 0.024 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.02 0.017 -10000 0 -10000 0 0
negative regulation of DNA binding 0.024 0.014 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.009 0.018 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.01 -10000 0 -10000 0 0
TACC1 0.027 0.004 -10000 0 -10000 0 0
TACC3 0.026 0.009 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.045 0.018 -10000 0 -10000 0 0
Aurora A/RasGAP 0.029 0.024 -10000 0 -10000 0 0
OAZ1 0.025 0.008 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.008 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.017 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.028 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.016 0.031 0.21 1 -10000 0 1
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0.055 -9999 0 -0.36 8 8
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.005 -9999 0 -10000 0 0
DOCK1 0.023 0.05 -9999 0 -0.69 2 2
ITGA4 0.024 0.021 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.052 0.075 -9999 0 -0.42 9 9
EPO 0.004 0.023 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.02 0.083 -9999 0 -0.49 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.025 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.018 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.031 0.019 -9999 0 -10000 0 0
lamellipodium assembly 0.021 0.027 -9999 0 -0.42 1 1
PIK3CA 0.025 0.036 -9999 0 -0.69 1 1
PI3K 0.038 0.029 -9999 0 -0.52 1 1
ARF6 0.027 0.005 -9999 0 -10000 0 0
JAK2 0.025 0.012 -9999 0 -10000 0 0
PXN 0.026 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
MADCAM1 0.007 0.05 -9999 0 -0.69 1 1
cell adhesion 0.048 0.075 -9999 0 -0.41 9 9
CRKL/CBL 0.03 0.018 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.02 0.049 -9999 0 -0.41 3 3
ITGB7 0.005 0.1 -9999 0 -0.65 9 9
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.049 0.046 -9999 0 -0.45 3 3
p130Cas/Crk/Dock1 0.037 0.054 -9999 0 -0.36 5 5
VCAM1 0.019 0.063 -9999 0 -0.69 3 3
RHOA 0.027 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.065 0.02 -9999 0 -10000 0 0
BCAR1 0.011 0.045 -9999 0 -0.39 3 3
EPOR 0.023 0.018 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.021 0.028 -9999 0 -0.43 1 1
TRAIL signaling pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.023 0.051 -10000 0 -0.69 2 2
positive regulation of NF-kappaB transcription factor activity 0.036 0.04 -10000 0 -0.52 2 2
MAP2K4 0.026 0.045 -10000 0 -0.29 2 2
IKBKB 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.05 -10000 0 -0.69 2 2
SMPD1 0.016 0.019 -10000 0 -0.25 2 2
IKBKG 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.036 0.04 -10000 0 -0.52 2 2
TRAIL/TRAILR3 0.001 0.065 -10000 0 -0.52 2 2
TRAIL/TRAILR1 0.034 0.056 -10000 0 -0.52 4 4
TRAIL/TRAILR4 0.036 0.04 -10000 0 -0.52 2 2
TRAIL/TRAILR1/DAP3/GTP 0.043 0.048 -10000 0 -0.41 4 4
IKK complex 0.024 0.048 -10000 0 -10000 0 0
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.038 -10000 0 -0.52 2 2
MAP3K1 0.027 0.042 -10000 0 -0.29 4 4
TRAILR4 (trimer) 0.027 0.004 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.05 -10000 0 -0.69 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.029 0.034 -10000 0 -0.29 4 4
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.01 0.038 -10000 0 -0.52 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.071 0.051 -10000 0 -0.39 4 4
mol:ceramide 0.016 0.019 -10000 0 -0.25 2 2
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.059 0.28 1 -0.34 3 4
TRAF2 0.025 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.018 0.068 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.048 0.051 -10000 0 -0.45 4 4
DAP3 0.025 0.007 -10000 0 -10000 0 0
CASP10 0.011 0.038 -10000 0 -0.44 2 2
JNK cascade 0.036 0.04 -10000 0 -0.52 2 2
TRAIL (trimer) 0.023 0.051 -10000 0 -0.69 2 2
TNFRSF10C -0.018 0.069 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.054 0.049 -10000 0 -0.39 4 4
TRAIL/TRAILR2/FADD 0.05 0.037 -10000 0 -0.45 2 2
cell death 0.016 0.019 -10000 0 -0.25 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.026 -10000 0 -0.29 2 2
TRAILR2 (trimer) 0.027 0.004 -10000 0 -10000 0 0
CASP8 0.011 0.032 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.074 0.039 -10000 0 -0.39 2 2
HIF-2-alpha transcription factor network

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.015 0.035 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.01 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.099 0.077 -10000 0 -0.39 1 1
EPO 0.12 0.097 -10000 0 -10000 0 0
FIH (dimer) 0.036 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.1 -10000 0 -0.52 1 1
FLT1 0.002 0.093 -10000 0 -0.6 6 6
ADORA2A 0.1 0.1 0.43 1 -10000 0 1
germ cell development 0.12 0.098 -10000 0 -10000 0 0
SLC11A2 0.12 0.099 -10000 0 -10000 0 0
BHLHE40 0.13 0.1 -10000 0 -10000 0 0
HIF1AN 0.036 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.084 0.36 1 -10000 0 1
ETS1 0.038 0.012 -10000 0 -10000 0 0
CITED2 -0.031 0.3 -10000 0 -1.1 30 30
KDR 0.006 0.11 -10000 0 -0.99 4 4
PGK1 0.12 0.099 -10000 0 -10000 0 0
SIRT1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.12 -10000 0 -10000 0 0
EPAS1 0.06 0.064 -10000 0 -10000 0 0
SP1 0.032 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.11 -10000 0 -0.6 1 1
EFNA1 0.12 0.099 -10000 0 -10000 0 0
FXN 0.12 0.11 0.51 3 -10000 0 3
POU5F1 0.12 0.1 -10000 0 -10000 0 0
neuron apoptosis -0.16 0.12 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.012 0.11 -10000 0 -0.68 10 10
EGLN2 0.035 0.014 -10000 0 -10000 0 0
EGLN1 0.035 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.05 0.038 -10000 0 -0.45 2 2
VHL 0.023 0.05 -10000 0 -0.69 2 2
ARNT 0.034 0.015 -10000 0 -10000 0 0
SLC2A1 0.13 0.11 0.49 5 -10000 0 5
TWIST1 0.12 0.13 -10000 0 -0.55 7 7
ELK1 0.022 0.036 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.089 0.091 -10000 0 -10000 0 0
VEGFA 0.12 0.11 -10000 0 -0.56 2 2
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.008 -9999 0 -10000 0 0
DOCK1 0.023 0.05 -9999 0 -0.69 2 2
ITGA4 0.024 0.021 -9999 0 -10000 0 0
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.02 0.083 -9999 0 -0.49 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.025 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.051 0.016 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.036 0.067 -9999 0 -0.41 8 8
lamellipodium assembly 0.026 0.054 -9999 0 -0.47 3 3
PIK3CA 0.025 0.036 -9999 0 -0.69 1 1
PI3K 0.038 0.029 -9999 0 -0.52 1 1
ARF6 0.027 0.005 -9999 0 -10000 0 0
TLN1 0.025 0.007 -9999 0 -10000 0 0
PXN 0.016 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
ARF6/GTP 0.055 0.021 -9999 0 -10000 0 0
cell adhesion 0.053 0.023 -9999 0 -10000 0 0
CRKL/CBL 0.03 0.018 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.044 0.015 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.005 0.1 -9999 0 -0.65 9 9
ARF6/GDP 0.024 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.054 0.044 -9999 0 -0.39 3 3
p130Cas/Crk/Dock1 0.048 0.039 -9999 0 -0.45 2 2
VCAM1 0.019 0.063 -9999 0 -0.69 3 3
alpha4/beta1 Integrin/Paxillin/Talin 0.055 0.024 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.021 -9999 0 -10000 0 0
BCAR1 0.026 0.006 -9999 0 -10000 0 0
mol:GDP -0.055 0.021 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
PRKACA 0.025 0.007 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.055 0.024 -9999 0 -10000 0 0
Rac1/GTP 0.027 0.061 -9999 0 -0.54 3 3
E-cadherin signaling in the nascent adherens junction

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.03 0.029 -10000 0 -10000 0 0
KLHL20 0.013 0.051 -10000 0 -10000 0 0
CYFIP2 0.026 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.04 -10000 0 -10000 0 0
ENAH 0.027 0.026 -10000 0 -10000 0 0
AP1M1 0.025 0.007 -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
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.016 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.07 -10000 0 -0.42 8 8
RAPGEF1 0.026 0.035 -10000 0 -10000 0 0
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.032 0.034 -10000 0 -10000 0 0
CRK 0.025 0.028 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.016 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.022 0.081 -10000 0 -0.52 8 8
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.015 -10000 0 -10000 0 0
DLG1 0.029 0.034 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.009 0.012 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.057 0.034 -10000 0 -0.41 1 1
PI3K 0.017 0.016 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.037 0.012 -10000 0 -10000 0 0
TIAM1 -0.057 0.08 -10000 0 -0.69 1 1
E-cadherin(dimer)/Ca2+ 0.061 0.017 -10000 0 -10000 0 0
AKT1 0.018 0.02 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.046 0.072 0.49 6 -10000 0 6
actin cytoskeleton organization 0.012 0.041 0.26 1 -10000 0 1
CDC42/GDP 0.047 0.081 0.52 8 -10000 0 8
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.022 0.008 -10000 0 -10000 0 0
ITGB7 0.005 0.1 -10000 0 -0.65 9 9
RAC1 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.012 -10000 0 -10000 0 0
mol:GDP 0.037 0.087 0.55 8 -10000 0 8
CDC42/GTP/IQGAP1 0.035 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.045 0.044 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1 0.035 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.037 0.011 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.026 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.037 0.24 3 -10000 0 3
NME1 0.026 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.029 0.034 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.024 0.011 -10000 0 -10000 0 0
WASF2 0.007 0.022 -10000 0 -10000 0 0
Rap1/GTP 0.041 0.026 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.064 0.07 -10000 0 -0.39 8 8
CCND1 0.012 0.039 0.22 2 -10000 0 2
VAV2 0.007 0.14 -10000 0 -0.53 21 21
RAP1/GDP 0.047 0.038 0.32 2 -10000 0 2
adherens junction assembly 0.029 0.033 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.053 0.065 -10000 0 -0.38 8 8
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.03 0.029 -10000 0 -10000 0 0
PIK3CA 0.025 0.036 -10000 0 -0.69 1 1
Rac1/GTP -0.006 0.076 -10000 0 -0.31 2 2
E-cadherin/beta catenin/alpha catenin 0.052 0.014 -10000 0 -10000 0 0
ITGAE 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.035 -10000 0 -10000 0 0
Arf6 trafficking events

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.003 0.14 -10000 0 -0.67 16 16
CLTC 0.027 0.02 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.014 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.01 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
CD59 0.021 0.011 -10000 0 -10000 0 0
CPE 0.008 0.061 -10000 0 -0.45 7 7
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
membrane fusion 0.018 0.007 -10000 0 -10000 0 0
CTNND1 0.022 0.036 0.36 2 -10000 0 2
DNM2 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.021 0.027 -10000 0 -10000 0 0
TSHR 0.014 0.033 -10000 0 -0.45 2 2
INS 0.008 0.063 -10000 0 -0.45 7 7
BIN1 0.027 0.004 -10000 0 -10000 0 0
mol:Choline 0.018 0.007 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.01 -10000 0 -10000 0 0
JUP 0.021 0.01 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.049 0.026 -10000 0 -0.41 1 1
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.027 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0.014 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.046 0.024 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.01 -10000 0 -10000 0 0
ACAP1 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.009 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.028 0.022 -10000 0 -10000 0 0
JIP4/KLC1 0.049 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.014 -10000 0 -10000 0 0
RALA/GTP 0.019 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.02 0.029 0.36 1 -10000 0 1
NME1 0.016 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.03 0.036 0.32 2 -10000 0 2
IL2RA 0.008 0.055 -10000 0 -0.24 17 17
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.024 0.071 -10000 0 -0.33 15 15
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.005 -10000 0 -10000 0 0
PLD2 0.017 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.05 0.026 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.018 0.007 -10000 0 -10000 0 0
endocytosis -0.048 0.025 0.41 1 -10000 0 1
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 0.025 0.078 0.35 8 -0.34 9 17
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ASAP2 0.025 0.036 -10000 0 -0.69 1 1
Dynamin 2/GDP 0.03 0.011 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.027 0.078 0.39 7 -0.34 8 15
RALA 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.024 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.029 0.032 0.29 2 -0.37 1 3
adherens junction organization 0.022 0.041 0.25 3 -0.31 1 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.035 0.047 -10000 0 -10000 0 0
FMN1 0.012 0.074 -10000 0 -0.35 15 15
mol:IP3 0.028 0.025 -10000 0 -0.34 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.026 -10000 0 -0.3 1 1
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.034 0.03 0.25 1 -0.34 1 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.035 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.026 -10000 0 -0.34 1 1
VASP 0.025 0.023 -10000 0 -0.28 1 1
ZYX 0.025 0.024 -10000 0 -0.28 1 1
JUB 0.025 0.024 -10000 0 -0.28 1 1
EGFR(dimer) 0.037 0.052 -10000 0 -0.34 6 6
E-cadherin/beta catenin-gamma catenin 0.05 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.049 0.032 0.25 1 -0.35 1 2
PIK3CA 0.027 0.036 -10000 0 -0.69 1 1
PI3K 0.051 0.033 0.26 1 -0.36 1 2
FYN 0.026 0.029 0.28 2 -10000 0 2
mol:Ca2+ 0.028 0.025 -10000 0 -0.33 1 1
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:DAG 0.028 0.025 -10000 0 -0.34 1 1
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.036 0.048 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.024 0.023 -10000 0 -0.28 1 1
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.017 0.079 -10000 0 -0.69 5 5
CASR 0.019 0.024 -10000 0 -0.32 1 1
RhoA/GTP 0.04 0.025 -10000 0 -0.31 1 1
AKT2 0.032 0.027 -10000 0 -0.34 1 1
actin cable formation 0.01 0.071 -10000 0 -0.35 14 14
apoptosis -0.029 0.031 0.35 1 -0.37 1 2
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.021 0.047 -10000 0 -0.34 6 6
PIP5K1A 0.024 0.027 -10000 0 -0.35 1 1
PLCG1 0.029 0.026 -10000 0 -0.35 1 1
Rac1/GTP 0.046 0.051 -10000 0 -0.32 5 5
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.064 0.022 -9999 0 -10000 0 0
HDAC3 0.026 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.012 -9999 0 -10000 0 0
GATA2/HDAC5 0.038 0.011 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.03 -9999 0 -0.45 1 1
HDAC9 0.012 0.043 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.016 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.038 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.038 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -9999 0 -10000 0 0
GATA2 0.027 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.037 0.013 -9999 0 -10000 0 0
BCOR 0.025 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.012 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.038 0.01 -9999 0 -10000 0 0
Histones 0.007 0.048 -9999 0 -10000 0 0
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.026 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.026 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.026 0.005 -9999 0 -10000 0 0
HDAC6 0.025 0.007 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.014 -9999 0 -10000 0 0
CAMK4 0.016 0.074 -9999 0 -0.69 4 4
Tubulin/HDAC6 0.048 0.041 -9999 0 -0.39 3 3
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.005 -9999 0 -10000 0 0
GATA1 0.011 0.02 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.025 0.007 -9999 0 -10000 0 0
NR3C1 0.026 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.057 -9999 0 -0.24 3 3
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.035 0.049 -9999 0 -0.52 3 3
HDAC4/14-3-3 E 0.037 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.005 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.036 0.03 -9999 0 -0.52 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.048 0.052 -9999 0 -0.45 4 4
HDAC4/ER alpha 0.007 0.12 -9999 0 -0.49 19 19
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.007 0.048 -9999 0 -10000 0 0
cell motility 0.047 0.041 -9999 0 -0.39 3 3
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.025 0.036 -9999 0 -0.69 1 1
HDAC4/CaMK II delta B 0.026 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.012 -9999 0 -10000 0 0
ESR1 -0.015 0.15 -9999 0 -0.66 19 19
HDAC6/HDAC11 0.037 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.018 0.051 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
MEF2C 0.026 0.005 -9999 0 -10000 0 0
RAN 0.026 0.006 -9999 0 -10000 0 0
HDAC4/MEF2C 0.074 0.024 -9999 0 -10000 0 0
GNG2 0.027 0.005 -9999 0 -10000 0 0
NCOR2 0.026 0.005 -9999 0 -10000 0 0
TUBB2A 0.022 0.061 -9999 0 -0.69 3 3
HDAC11 0.027 0.004 -9999 0 -10000 0 0
HSP90AA1 0.026 0.005 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
ANKRA2 0.026 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.01 -9999 0 -10000 0 0
nuclear import -0.036 0.012 -9999 0 -10000 0 0
PLK2 and PLK4 events

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.019 -9999 0 -9999 0 0
PLK4 0.027 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.015 0.012 -9999 0 -9999 0 0
Arf6 downstream pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.003 0.039 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.016 0.27 1 -10000 0 1
myoblast fusion -0.013 0.025 -10000 0 -10000 0 0
mol:GTP 0.009 0.017 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.024 0.065 0.42 1 -10000 0 1
ARF1/GTP 0.03 0.013 -10000 0 -10000 0 0
mol:GM1 0.005 0.011 -10000 0 -10000 0 0
mol:Choline 0.008 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.016 0.025 -10000 0 -10000 0 0
MAPK3 0.008 0.025 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.025 0.066 -10000 0 -0.43 1 1
ARF1 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.013 0.025 -10000 0 -10000 0 0
ARF1/GDP 0.02 0.028 -10000 0 -10000 0 0
ARF6 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.058 0.081 -10000 0 -0.69 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.023 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.027 -10000 0 -10000 0 0
KALRN 0.011 0.018 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.028 -10000 0 -10000 0 0
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.023 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.017 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.016 0.024 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.009 0.017 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.017 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.008 0.019 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.015 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.012 0.016 -10000 0 -10000 0 0
RAB11FIP3 0.025 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.016 0.025 -10000 0 -10000 0 0
ruffle organization 0.012 0.016 -10000 0 -0.27 1 1
regulation of epithelial cell migration 0.009 0.017 -10000 0 -10000 0 0
PLD2 0.011 0.016 -10000 0 -10000 0 0
PIP5K1A 0.012 0.017 -10000 0 -0.27 1 1
mol:Phosphatidic acid 0.008 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.025 -10000 0 -10000 0 0
Aurora C signaling

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.027 0.005 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.048 0.029 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.02 -9999 0 -0.34 1 1
AURKB -0.006 0.06 -9999 0 -10000 0 0
AURKC 0.021 0.025 -9999 0 -10000 0 0
Glypican 2 network

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.02 0.076 -9999 0 -0.69 1 1
GPC2 0.013 0.042 -9999 0 -10000 0 0
GPC2/Midkine -0.006 0.063 -9999 0 -0.31 1 1
neuron projection morphogenesis -0.006 0.062 -9999 0 -0.31 1 1
Sumoylation by RanBP2 regulates transcriptional repression

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.001 0.014 -9999 0 -10000 0 0
MDM2/SUMO1 0.015 0.053 -9999 0 -0.22 1 1
HDAC4 0.026 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.001 0.013 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.006 0.037 -9999 0 -0.24 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.012 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.057 -9999 0 -0.24 3 3
SUMO1/HDAC1 0.014 0.057 -9999 0 -0.25 3 3
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.007 0.047 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.026 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.007 0.045 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
PIAS2 0.027 0.004 -9999 0 -10000 0 0
PIAS1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.038 0.01 -9999 0 -9999 0 0
CTNNB1 0.027 0.004 -9999 0 -9999 0 0
JUP 0.026 0.007 -9999 0 -9999 0 0
CDH1 0.026 0.006 -9999 0 -9999 0 0
Arf1 pathway

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.018 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.023 0.033 0.2 1 -0.2 2 3
AP2 0.038 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.035 0.011 -10000 0 -10000 0 0
CLTB 0.026 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.022 0.026 -10000 0 -10000 0 0
CLTA 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.019 -10000 0 -0.38 1 1
ARF1/GTP 0.029 0.018 -10000 0 -0.2 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.007 -10000 0 -10000 0 0
mol:Choline 0.006 0.019 -10000 0 -0.37 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.022 -10000 0 -0.38 1 1
ARF1/GDP 0.005 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.015 -10000 0 -10000 0 0
ARFIP2 0.022 0.013 -10000 0 -10000 0 0
COPA 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.036 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.018 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.023 -10000 0 -0.28 1 1
AP2A1 0.026 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.008 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.025 0.025 -10000 0 -0.31 1 1
Arfaptin 2/Rac/GDP 0.033 0.011 -10000 0 -10000 0 0
CYTH2 0.028 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.024 0.024 -10000 0 -10000 0 0
PLD2 0.006 0.019 -10000 0 -0.37 1 1
ARF-GAP1/v-SNARE 0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.007 0.019 -10000 0 -0.38 1 1
ARF1/GTP/Membrin/GBF1/p115 0.023 0.018 -10000 0 -0.2 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.019 -10000 0 -0.37 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.014 0.011 -10000 0 -10000 0 0
USO1 0.014 0.011 -10000 0 -10000 0 0
GBF1 0.012 0.025 -10000 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.035 0.014 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.052 0.016 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.038 0.011 -9999 0 -9999 0 0
FBXW11 0.026 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.005 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.073 0.026 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.026 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 407 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.KS.A41L TCGA.KS.A41J TCGA.KS.A41I TCGA.KS.A41F
109_MAP3K5 -0.19 -0.2 0.052 -0.19
47_PPARGC1A 0.027 -0.69 0.027 -0.69
105_BMP4 0.027 0.027 0.027 0.027
105_BMP6 0.027 0.027 0.027 0.027
105_BMP7 0.027 0.027 0.027 0.027
105_BMP2 0.027 0.027 0.027 0.027
131_RELN/VLDLR 0.064 -0.41 0.064 -0.41
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.038 0.035 0.033 -0.046
84_STAT5A 0.038 0.035 0.033 -0.046
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2845244/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/THCA-TP/2859958/all_data_by_genes.txt

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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