Thyroid Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression 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 48 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 211
Signaling events mediated by Stem cell factor receptor (c-Kit) 133
Signaling events regulated by Ret tyrosine kinase 125
TCGA08_retinoblastoma 117
Reelin signaling pathway 113
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 92
FOXA2 and FOXA3 transcription factor networks 82
PDGFR-alpha signaling pathway 82
IL4-mediated signaling events 81
Noncanonical Wnt signaling pathway 73
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 211 1481 7 -0.54 0 1000 -1000 -0.025 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 133 10437 78 -0.78 0.23 1000 -1000 -0.066 -1000
Signaling events regulated by Ret tyrosine kinase 125 10288 82 -0.48 0.013 1000 -1000 -0.082 -1000
TCGA08_retinoblastoma 117 943 8 -0.13 0.073 1000 -1000 -0.017 -1000
Reelin signaling pathway 113 6335 56 -0.63 0.034 1000 -1000 -0.082 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 92 6292 68 -0.9 0.35 1000 -1000 -0.11 -1000
FOXA2 and FOXA3 transcription factor networks 82 3797 46 -0.97 0.021 1000 -1000 -0.053 -1000
PDGFR-alpha signaling pathway 82 3614 44 -0.51 0.033 1000 -1000 -0.08 -1000
IL4-mediated signaling events 81 7433 91 -1.3 0.66 1000 -1000 -0.13 -1000
Noncanonical Wnt signaling pathway 73 1898 26 -0.44 0.013 1000 -1000 -0.094 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 70 3791 54 -0.63 0.028 1000 -1000 -0.095 -1000
Signaling events mediated by the Hedgehog family 68 3572 52 -0.41 0.21 1000 -1000 -0.082 -1000
Nongenotropic Androgen signaling 68 3551 52 -0.35 0.16 1000 -1000 -0.061 -1000
Wnt signaling 67 475 7 -0.44 0.013 1000 -1000 -0.036 -1000
Calcium signaling in the CD4+ TCR pathway 64 2013 31 -0.53 0.013 1000 -1000 -0.076 -1000
Nephrin/Neph1 signaling in the kidney podocyte 58 2004 34 -0.16 0.013 1000 -1000 -0.058 -1000
Glypican 1 network 53 2559 48 -0.4 0.029 1000 -1000 -0.05 -1000
Ephrin B reverse signaling 51 2487 48 -0.31 0.2 1000 -1000 -0.083 -1000
Endothelins 50 4871 96 -0.42 0.013 1000 -1000 -0.079 -1000
Glypican 2 network 49 197 4 -0.087 -0.018 1000 -1000 -0.036 -1000
Glucocorticoid receptor regulatory network 48 5582 114 -0.58 0.38 1000 -1000 -0.079 -1000
IGF1 pathway 47 2683 57 -0.19 0.054 1000 -1000 -0.086 -1000
IL23-mediated signaling events 47 2846 60 -0.35 0.021 1000 -1000 -0.14 -1000
TCR signaling in naïve CD8+ T cells 46 4325 93 -0.2 0.088 1000 -1000 -0.08 -1000
BMP receptor signaling 44 3571 81 -0.6 0.024 1000 -1000 -0.086 -1000
HIF-1-alpha transcription factor network 42 3232 76 -0.6 0.041 1000 -1000 -0.11 -1000
Coregulation of Androgen receptor activity 39 3021 76 -0.78 0.061 1000 -1000 -0.053 -1000
Arf6 signaling events 39 2438 62 -0.33 0.021 1000 -1000 -0.063 -1000
Signaling mediated by p38-alpha and p38-beta 36 1618 44 -0.24 0.013 1000 -1000 -0.051 -1000
EPHB forward signaling 34 2951 85 -0.31 0.16 1000 -1000 -0.1 -1000
IL12-mediated signaling events 33 2898 87 -0.41 0.02 1000 -1000 -0.11 -1000
Syndecan-1-mediated signaling events 33 1129 34 -0.22 0.013 1000 -1000 -0.068 -1000
Syndecan-4-mediated signaling events 33 2212 67 -0.26 0.013 1000 -1000 -0.087 -1000
Hedgehog signaling events mediated by Gli proteins 32 2103 65 -0.69 0.064 1000 -1000 -0.062 -1000
amb2 Integrin signaling 31 2573 82 -0.26 0.013 1000 -1000 -0.08 -1000
IL6-mediated signaling events 30 2308 75 -0.21 0.062 1000 -1000 -0.085 -1000
EGFR-dependent Endothelin signaling events 27 572 21 -0.11 0.013 1000 -1000 -0.065 -1000
Osteopontin-mediated events 26 1004 38 -0.26 0.013 1000 -1000 -0.1 -1000
Thromboxane A2 receptor signaling 26 2789 105 -0.22 0.029 1000 -1000 -0.073 -1000
TCGA08_p53 24 169 7 -0.081 0.052 1000 -1000 -0.015 -1000
Ras signaling in the CD4+ TCR pathway 23 407 17 -0.097 0.012 1000 -1000 -0.048 -1000
IL27-mediated signaling events 22 1159 51 -0.19 0.058 1000 -1000 -0.076 -1000
Visual signal transduction: Rods 22 1149 52 -0.2 0.014 1000 -1000 -0.089 -1000
ErbB2/ErbB3 signaling events 21 1397 65 -0.13 0.027 1000 -1000 -0.067 -1000
Syndecan-2-mediated signaling events 21 1475 69 -0.22 0.037 1000 -1000 -0.063 -1000
Regulation of p38-alpha and p38-beta 21 1144 54 -0.49 0.013 1000 -1000 -0.061 -1000
Plasma membrane estrogen receptor signaling 21 1855 86 -0.18 0.02 1000 -1000 -0.077 -1000
Regulation of Androgen receptor activity 21 1488 70 -0.48 0.034 1000 -1000 -0.075 -1000
JNK signaling in the CD4+ TCR pathway 20 342 17 -0.1 0.018 1000 -1000 -0.058 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 20 1726 85 -0.29 0.013 1000 -1000 -0.073 -1000
FAS signaling pathway (CD95) 20 973 47 -0.28 0.027 1000 -1000 -0.054 -1000
Integrins in angiogenesis 20 1763 84 -0.23 0.032 1000 -1000 -0.09 -1000
LPA receptor mediated events 19 1967 102 -0.26 0.031 1000 -1000 -0.086 -1000
BCR signaling pathway 18 1872 99 -0.2 0.022 1000 -1000 -0.093 -1000
Angiopoietin receptor Tie2-mediated signaling 18 1610 88 -0.33 0.03 1000 -1000 -0.12 -1000
Signaling events mediated by PRL 18 645 34 -0.12 0.013 1000 -1000 -0.048 -1000
Signaling events mediated by PTP1B 17 1353 76 -0.26 0.021 1000 -1000 -0.075 -1000
Regulation of nuclear SMAD2/3 signaling 16 2255 136 -0.35 0.068 1000 -1000 -0.083 -1000
p75(NTR)-mediated signaling 16 2074 125 -0.38 0.07 1000 -1000 -0.1 -1000
Fc-epsilon receptor I signaling in mast cells 16 1572 97 -0.21 0.03 1000 -1000 -0.08 -1000
ErbB4 signaling events 15 1093 69 -0.14 0.059 1000 -1000 -0.077 -1000
Visual signal transduction: Cones 15 596 38 -0.095 0.013 1000 -1000 -0.075 -1000
Neurotrophic factor-mediated Trk receptor signaling 15 1877 120 -0.32 0.043 1000 -1000 -0.076 -1000
FOXM1 transcription factor network 15 783 51 -0.19 0.049 1000 -1000 -0.15 -1000
Aurora C signaling 14 103 7 -0.06 0.004 1000 -1000 -0.05 -1000
IFN-gamma pathway 14 977 68 -0.11 0.041 1000 -1000 -0.086 -1000
Nectin adhesion pathway 14 914 63 -0.26 0.037 1000 -1000 -0.071 -1000
RXR and RAR heterodimerization with other nuclear receptor 14 761 52 -0.28 0.054 1000 -1000 -0.071 -1000
Aurora B signaling 14 943 67 -0.38 0.014 1000 -1000 -0.074 -1000
IL1-mediated signaling events 13 860 62 -0.13 0.067 1000 -1000 -0.1 -1000
Effects of Botulinum toxin 13 342 26 -0.18 0.019 1000 -1000 -0.06 -1000
LPA4-mediated signaling events 12 148 12 -0.12 0.017 1000 -1000 -0.021 -1000
Syndecan-3-mediated signaling events 12 453 35 -0.17 0.013 1000 -1000 -0.071 -1000
Rapid glucocorticoid signaling 12 253 20 -0.09 0.014 1000 -1000 -0.042 -1000
Presenilin action in Notch and Wnt signaling 11 684 61 -0.21 0.046 1000 -1000 -0.072 -1000
Insulin-mediated glucose transport 11 370 32 -0.21 0.037 1000 -1000 -0.063 -1000
IL2 signaling events mediated by PI3K 11 648 58 -0.06 0.033 1000 -1000 -0.075 -1000
IL2 signaling events mediated by STAT5 11 253 22 -0.061 0.042 1000 -1000 -0.04 -1000
Insulin Pathway 11 876 74 -0.082 0.038 1000 -1000 -0.086 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 11 386 33 -0.17 0.035 1000 -1000 -0.066 -1000
Class IB PI3K non-lipid kinase events 11 33 3 -0.002 -1000 1000 -1000 -0.011 -1000
Ceramide signaling pathway 10 795 76 -0.18 0.024 1000 -1000 -0.063 -1000
Signaling events mediated by HDAC Class III 10 439 40 -0.36 0.024 1000 -1000 -0.055 -1000
Sphingosine 1-phosphate (S1P) pathway 9 268 28 -0.18 0.032 1000 -1000 -0.059 -1000
TCGA08_rtk_signaling 9 234 26 -0.25 0.024 1000 -1000 -0.024 -1000
Regulation of Telomerase 9 961 102 -0.3 0.054 1000 -1000 -0.1 -1000
a4b1 and a4b7 Integrin signaling 8 40 5 -0.03 0.007 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 8 333 39 -0.091 0.019 1000 -1000 -0.035 -1000
mTOR signaling pathway 8 458 53 -0.041 0.023 1000 -1000 -0.06 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 8 696 83 -0.21 0.053 1000 -1000 -0.084 -1000
Retinoic acid receptors-mediated signaling 8 499 58 -0.12 0.034 1000 -1000 -0.074 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 8 385 45 -0.091 0.039 1000 -1000 -0.097 -1000
Class I PI3K signaling events 8 636 73 -0.26 0.023 1000 -1000 -0.08 -1000
Caspase cascade in apoptosis 7 577 74 -0.091 0.029 1000 -1000 -0.06 -1000
BARD1 signaling events 7 451 57 -0.031 0.054 1000 -1000 -0.068 -1000
VEGFR1 specific signals 7 445 56 -0.072 0.043 1000 -1000 -0.086 -1000
Class I PI3K signaling events mediated by Akt 6 439 68 -0.21 0.052 1000 -1000 -0.06 -1000
TRAIL signaling pathway 6 313 48 -0.085 0.051 1000 -1000 -0.066 -1000
ceramide signaling pathway 6 327 49 -0.091 0.032 1000 -1000 -0.055 -1000
S1P1 pathway 6 223 36 -0.044 0.032 1000 -1000 -0.06 -1000
Stabilization and expansion of the E-cadherin adherens junction 6 512 74 -0.18 0.087 1000 -1000 -0.09 -1000
S1P3 pathway 6 291 42 -0.18 0.05 1000 -1000 -0.067 -1000
Arf6 downstream pathway 5 235 43 -0.17 0.094 1000 -1000 -0.039 -1000
FoxO family signaling 4 315 64 -0.21 0.16 1000 -1000 -0.073 -1000
Canonical Wnt signaling pathway 4 241 51 -0.047 0.068 1000 -1000 -0.057 -1000
E-cadherin signaling in the nascent adherens junction 4 326 76 -0.17 0.074 1000 -1000 -0.082 -1000
Canonical NF-kappaB pathway 3 131 39 -0.091 0.069 1000 -1000 -0.089 -1000
EPO signaling pathway 3 177 55 -0.054 0.065 1000 -1000 -0.087 -1000
Paxillin-independent events mediated by a4b1 and a4b7 3 113 37 -0.031 0.034 1000 -1000 -0.069 -1000
Signaling events mediated by HDAC Class I 3 399 104 -0.091 0.061 1000 -1000 -0.076 -1000
Atypical NF-kappaB pathway 3 104 31 -0.029 0.048 1000 -1000 -0.053 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 420 125 -0.037 0.086 1000 -1000 -0.11 -1000
PLK2 and PLK4 events 2 6 3 0.008 0.021 1000 -1000 -0.017 -1000
Circadian rhythm pathway 2 51 22 -0.053 0.013 1000 -1000 -0.059 -1000
Aurora A signaling 2 135 60 -0.052 0.038 1000 -1000 -0.061 -1000
PLK1 signaling events 2 238 85 -0.059 0.025 1000 -1000 -0.055 -1000
S1P5 pathway 2 45 17 -0.015 0.024 1000 -1000 -0.06 -1000
Paxillin-dependent events mediated by a4b1 2 73 36 -0.03 0.024 1000 -1000 -0.079 -1000
PDGFR-beta signaling pathway 2 253 97 -0.19 0.067 1000 -1000 -0.085 -1000
p38 MAPK signaling pathway 2 117 44 -0.029 0.028 1000 -1000 -0.068 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 38 23 -0.031 0.05 1000 -1000 -0.066 -1000
Signaling events mediated by HDAC Class II 1 136 75 -0.049 0.036 1000 -1000 -0.064 -1000
HIF-2-alpha transcription factor network 1 73 43 -0.2 0.21 1000 -1000 -0.082 -1000
Signaling mediated by p38-gamma and p38-delta 1 27 15 0 0.032 1000 -1000 -0.027 -1000
Arf6 trafficking events 1 85 71 -0.023 0.046 1000 -1000 -0.073 -1000
E-cadherin signaling in keratinocytes 1 81 43 -0.005 0.052 1000 -1000 -0.066 -1000
S1P4 pathway 1 49 25 -0.015 0.032 1000 -1000 -0.057 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.031 1000 -1000 -0.06 -1000
E-cadherin signaling events 0 0 5 0 0.013 1000 -1000 -0.049 -1000
Arf1 pathway 0 23 54 -0.005 0.036 1000 -1000 -0.041 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.013 1000 -1000 -0.063 -1000
Total 3301 182854 7203 -30 -990 131000 -131000 -9.2 -131000
Ephrin A reverse signaling

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

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

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

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.21 0.22 -10000 0 -0.4 234 234
CRKL -0.21 0.24 -10000 0 -0.42 227 227
HRAS -0.18 0.21 -10000 0 -0.45 55 55
mol:PIP3 -0.21 0.22 -10000 0 -0.4 227 227
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.23 0.25 -10000 0 -0.45 227 227
FOXO3 -0.19 0.22 -10000 0 -0.38 227 227
AKT1 -0.21 0.23 -10000 0 -0.41 227 227
BAD -0.19 0.22 -10000 0 -0.38 227 227
megakaryocyte differentiation -0.24 0.24 -10000 0 -0.44 234 234
GSK3B -0.19 0.22 -10000 0 -0.38 227 227
RAF1 -0.14 0.18 -10000 0 -0.41 30 30
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.23 0.25 -10000 0 -0.45 227 227
STAT1 -0.58 0.58 -10000 0 -1.1 228 228
HRAS/SPRED1 -0.17 0.14 -10000 0 -0.39 35 35
cell proliferation -0.23 0.25 -10000 0 -0.44 228 228
PIK3CA 0.01 0.043 -10000 0 -0.85 1 1
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.24 -10000 0 -0.44 227 227
HRAS/SPRED2 -0.17 0.14 -10000 0 -0.4 34 34
LYN/TEC/p62DOK -0.23 0.2 -10000 0 -0.41 227 227
MAPK3 -0.091 0.13 -10000 0 -0.31 17 17
STAP1 -0.25 0.25 -10000 0 -0.47 227 227
GRAP2 -0.046 0.22 -10000 0 -0.8 30 30
JAK2 -0.5 0.45 -10000 0 -0.89 228 228
STAT1 (dimer) -0.56 0.57 -10000 0 -1.1 228 228
mol:Gleevec 0.007 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.24 0.21 -10000 0 -0.42 230 230
actin filament polymerization -0.22 0.24 -10000 0 -0.44 227 227
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.34 -10000 0 -0.64 227 227
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.18 -10000 0 -0.37 227 227
PI3K -0.23 0.21 -10000 0 -0.42 227 227
PTEN 0.011 0.043 -10000 0 -0.85 1 1
SCF/KIT/EPO/EPOR -0.72 0.72 -10000 0 -1.4 227 227
MAPK8 -0.23 0.25 -10000 0 -0.45 228 228
STAT3 (dimer) -0.22 0.24 -10000 0 -0.44 227 227
positive regulation of transcription -0.073 0.11 -10000 0 -0.26 15 15
mol:GDP -0.22 0.19 -10000 0 -0.45 71 71
PIK3C2B -0.23 0.25 -10000 0 -0.45 227 227
CBL/CRKL -0.19 0.22 -10000 0 -0.39 227 227
FER -0.23 0.25 -10000 0 -0.45 228 228
SH2B3 -0.23 0.25 -10000 0 -0.45 227 227
PDPK1 -0.19 0.21 -10000 0 -0.37 227 227
SNAI2 -0.23 0.25 -10000 0 -0.45 227 227
positive regulation of cell proliferation -0.4 0.42 -10000 0 -0.77 228 228
KITLG 0.002 0.077 -10000 0 -0.88 3 3
cell motility -0.4 0.42 -10000 0 -0.77 228 228
PTPN6 0.02 0.018 -10000 0 -10000 0 0
EPOR -0.13 0.18 -10000 0 -0.67 1 1
STAT5A (dimer) -0.32 0.34 -10000 0 -0.63 227 227
SOCS1 0.011 0.028 -10000 0 -0.31 3 3
cell migration 0.23 0.25 0.45 228 -10000 0 228
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.002 0.027 -10000 0 -0.33 2 2
VAV1 -0.014 0.11 -10000 0 -0.37 29 29
GRB10 -0.23 0.25 -10000 0 -0.45 227 227
PTPN11 0.016 0.014 -10000 0 -10000 0 0
SCF/KIT -0.26 0.25 -10000 0 -0.48 227 227
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.1 0.15 -10000 0 -0.35 18 18
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.78 0.76 -10000 0 -1.5 227 227
MAP2K2 -0.1 0.15 -10000 0 -0.35 17 17
SHC/Grb2/SOS1 -0.23 0.2 -10000 0 -0.41 227 227
STAT5A -0.34 0.36 -10000 0 -0.65 227 227
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.23 0.24 -10000 0 -0.44 227 227
SHC/GRAP2 -0.045 0.16 -10000 0 -0.66 27 27
PTPRO -0.24 0.25 -10000 0 -0.45 234 234
SH2B2 -0.23 0.25 -10000 0 -0.45 227 227
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.24 0.26 -10000 0 -0.46 228 228
CREBBP 0.018 0.02 -10000 0 -10000 0 0
BCL2 -0.2 0.4 -10000 0 -1.6 26 26
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 -0.092 0.071 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -9999 0 -0.52 96 96
JUN -0.33 0.32 -9999 0 -0.68 147 147
HRAS 0.012 0.023 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.41 0.34 -9999 0 -0.64 254 254
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.41 0.34 -9999 0 -0.64 254 254
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.31 0.26 -9999 0 -0.54 234 234
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.36 0.31 -9999 0 -0.57 254 254
GRB7 -0.037 0.12 -9999 0 -0.31 63 63
RET51/GFRalpha1/GDNF -0.41 0.34 -9999 0 -0.64 254 254
MAPKKK cascade -0.32 0.27 -9999 0 -0.51 254 254
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.36 0.32 -9999 0 -0.6 245 245
lamellipodium assembly -0.24 0.19 -9999 0 -0.39 235 235
RET51/GFRalpha1/GDNF/SHC -0.41 0.34 -9999 0 -0.64 254 254
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
RET9/GFRalpha1/GDNF/SHC -0.31 0.26 -9999 0 -0.53 234 234
RET9/GFRalpha1/GDNF/Shank3 -0.31 0.26 -9999 0 -0.53 234 234
MAPK3 -0.33 0.3 -9999 0 -0.54 254 254
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.13 0.32 -9999 0 -0.85 68 68
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.33 0.29 -9999 0 -0.69 110 110
DOK5 -0.099 0.29 -9999 0 -0.85 53 53
GFRA1 -0.48 0.43 -9999 0 -0.85 235 235
MAPK8 -0.24 0.23 -9999 0 -0.59 72 72
HRAS/GTP -0.37 0.32 -9999 0 -0.59 254 254
tube development -0.29 0.25 -9999 0 -0.5 234 234
MAPK1 -0.33 0.3 -9999 0 -0.54 254 254
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.19 0.19 -9999 0 -0.35 234 234
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
PDLIM7 0.009 0.036 -9999 0 -0.31 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.46 0.4 -9999 0 -0.7 264 264
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.41 0.34 -9999 0 -0.64 254 254
RET51/GFRalpha1/GDNF/Dok5 -0.47 0.4 -9999 0 -0.71 264 264
PRKCA -0.038 0.2 -9999 0 -0.85 24 24
HRAS/GDP -0.001 0.015 -9999 0 -10000 0 0
CREB1 -0.25 0.24 -9999 0 -0.44 234 234
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.19 0.19 -9999 0 -0.35 234 234
RET51/GFRalpha1/GDNF/Grb7 -0.43 0.34 -9999 0 -0.66 254 254
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.17 0.33 -9999 0 -0.66 113 113
DOK4 0.013 0 -9999 0 -10000 0 0
JNK cascade -0.32 0.31 -9999 0 -0.66 147 147
RET9/GFRalpha1/GDNF/FRS2 -0.31 0.26 -9999 0 -0.53 234 234
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.19 0.19 -9999 0 -0.35 234 234
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.26 0.24 -9999 0 -0.42 254 254
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.26 0.24 -9999 0 -0.42 254 254
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.3 0.32 -9999 0 -0.48 254 254
PI3K -0.38 0.34 -9999 0 -0.63 235 235
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.29 0.25 -9999 0 -0.5 234 234
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.23 0.21 -9999 0 -0.39 234 234
RET51/GFRalpha1/GDNF/FRS2 -0.41 0.34 -9999 0 -0.64 254 254
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.078 0.26 -9999 0 -0.85 43 43
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.3 0.32 -9999 0 -0.48 254 254
RET51/GFRalpha1/GDNF/PKC alpha -0.43 0.38 -9999 0 -0.68 254 254
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.001 0.039 -9999 0 -0.31 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.46 0.38 -9999 0 -0.69 264 264
Rac1/GTP -0.3 0.23 -9999 0 -0.47 235 235
RET9/GFRalpha1/GDNF -0.34 0.29 -9999 0 -0.58 234 234
GFRalpha1/GDNF -0.38 0.33 -9999 0 -0.66 234 234
TCGA08_retinoblastoma

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
CDKN2B -0.13 0.16 -10000 0 -0.31 174 174
CDKN2C 0.025 0.038 -10000 0 -0.32 2 2
CDKN2A -0.12 0.16 -10000 0 -0.32 169 169
CCND2 0.07 0.072 0.17 119 -10000 0 119
RB1 -0.068 0.071 -10000 0 -0.17 119 119
CDK4 0.07 0.071 0.17 120 -10000 0 120
CDK6 0.073 0.077 0.18 119 -0.19 1 120
G1/S progression 0.06 0.079 0.17 120 -10000 0 120
Reelin signaling pathway

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.001 0.014 -9999 0 -10000 0 0
VLDLR -0.012 0.15 -9999 0 -0.85 12 12
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.009 0.036 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.44 0.27 -9999 0 -0.59 307 307
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.041 -9999 0 -0.48 3 3
AKT1 -0.24 0.17 -9999 0 -0.34 307 307
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.007 0.007 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.42 0.26 -9999 0 -0.55 307 307
LRPAP1/LRP8 -0.026 0.13 -9999 0 -0.66 16 16
RELN/LRP8/DAB1/Fyn -0.39 0.24 -9999 0 -0.52 307 307
DAB1/alpha3/beta1 Integrin -0.36 0.24 -9999 0 -0.48 309 309
long-term memory -0.39 0.25 -9999 0 -0.51 309 309
DAB1/LIS1 -0.37 0.24 -9999 0 -0.5 309 309
DAB1/CRLK/C3G -0.36 0.23 -9999 0 -0.48 309 309
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
DAB1/NCK2 -0.38 0.24 -9999 0 -0.5 309 309
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.026 0.17 -9999 0 -0.65 24 24
CDK5R1 0.012 0.023 -9999 0 -0.31 2 2
RELN -0.63 0.38 -9999 0 -0.85 305 305
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.44 0.27 -9999 0 -0.59 307 307
GRIN2A/RELN/LRP8/DAB1/Fyn -0.4 0.26 -9999 0 -0.54 309 309
MAPK8 0.007 0.074 -9999 0 -0.85 3 3
RELN/VLDLR/DAB1 -0.41 0.25 -9999 0 -0.55 307 307
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.39 0.26 -9999 0 -0.52 309 309
RELN/LRP8 -0.44 0.27 -9999 0 -0.59 307 307
GRIN2B/RELN/LRP8/DAB1/Fyn -0.39 0.24 -9999 0 -0.52 307 307
PI3K -0.002 0.032 -9999 0 -0.66 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.022 -9999 0 -10000 0 0
RAP1A -0.32 0.24 -9999 0 -0.83 23 23
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.017 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.13 -9999 0 -0.51 16 16
neuron adhesion -0.3 0.23 -9999 0 -0.74 27 27
LRP8 -0.021 0.17 -9999 0 -0.85 16 16
GSK3B -0.22 0.16 -9999 0 -0.62 11 11
RELN/VLDLR/DAB1/Fyn -0.38 0.23 -9999 0 -0.51 307 307
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.36 307 307
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.034 0.087 -9999 0 -0.53 4 4
neuron migration -0.31 0.22 -9999 0 -0.43 307 307
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.13 -9999 0 -0.52 16 16
RELN/VLDLR -0.42 0.27 -9999 0 -0.56 309 309
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.047 0.17 -10000 0 -0.51 35 35
NFATC2 -0.22 0.38 -10000 0 -0.84 91 91
NFATC3 -0.084 0.13 -10000 0 -10000 0 0
CD40LG -0.73 0.58 -10000 0 -1.2 223 223
ITCH 0.051 0.016 -10000 0 -10000 0 0
CBLB 0.051 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.51 0.52 -10000 0 -1.2 120 120
JUNB 0 0.1 -10000 0 -0.85 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.017 -10000 0 -0.34 1 1
T cell anergy 0.029 0.065 -10000 0 -0.5 1 1
TLE4 -0.23 0.44 -10000 0 -0.92 102 102
Jun/NFAT1-c-4/p21SNFT -0.66 0.62 -10000 0 -1.2 198 198
AP-1/NFAT1-c-4 -0.9 0.8 -10000 0 -1.5 218 218
IKZF1 -0.16 0.34 -10000 0 -0.82 66 66
T-helper 2 cell differentiation -0.3 0.34 -10000 0 -0.84 93 93
AP-1/NFAT1 -0.42 0.5 -10000 0 -0.95 170 170
CALM1 0.028 0.01 -10000 0 -10000 0 0
EGR2 -0.77 0.86 -10000 0 -1.7 184 184
EGR3 -0.56 0.75 -10000 0 -1.7 105 105
NFAT1/FOXP3 -0.2 0.34 -10000 0 -0.72 99 99
EGR1 -0.18 0.36 -10000 0 -0.85 89 89
JUN -0.2 0.36 -10000 0 -0.86 93 93
EGR4 -0.049 0.21 -10000 0 -0.74 32 32
mol:Ca2+ 0.016 0.011 -10000 0 -10000 0 0
GBP3 -0.15 0.32 -10000 0 -0.75 72 72
FOSL1 -0.036 0.12 -10000 0 -0.31 62 62
NFAT1-c-4/MAF/IRF4 -0.55 0.56 -10000 0 -1.1 183 183
DGKA -0.14 0.3 -10000 0 -0.7 71 71
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.54 0.56 -10000 0 -1.1 195 195
CTLA4 -0.22 0.38 -10000 0 -0.84 89 89
NFAT1-c-4 (dimer)/EGR1 -0.63 0.68 -10000 0 -1.3 193 193
NFAT1-c-4 (dimer)/EGR4 -0.57 0.57 -10000 0 -1.1 198 198
FOS -0.22 0.38 -10000 0 -0.86 106 106
IFNG -0.42 0.55 -10000 0 -1.2 110 110
T cell activation -0.43 0.43 -10000 0 -1 126 126
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.42 0.79 159 -10000 0 159
TNF -0.59 0.59 -10000 0 -1.1 195 195
FASLG -0.73 0.8 -10000 0 -1.5 199 199
TBX21 -0.04 0.19 -10000 0 -0.72 26 26
BATF3 -0.009 0.089 -10000 0 -0.33 26 26
PRKCQ 0 0.1 -10000 0 -0.85 6 6
PTPN1 -0.14 0.29 -10000 0 -0.71 66 66
NFAT1-c-4/ICER1 -0.53 0.56 -10000 0 -1 194 194
GATA3 -0.036 0.2 -10000 0 -0.83 24 24
T-helper 1 cell differentiation -0.4 0.52 -10000 0 -1.2 111 111
IL2RA -0.46 0.46 -10000 0 -1 125 125
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.14 0.29 -10000 0 -0.71 68 68
E2F1 -0.082 0.15 -10000 0 -0.31 80 80
PPARG -0.001 0.1 -10000 0 -0.58 10 10
SLC3A2 -0.14 0.29 -10000 0 -0.74 58 58
IRF4 -0.099 0.23 -10000 0 -0.46 98 98
PTGS2 -0.71 0.58 -10000 0 -1.2 213 213
CSF2 -0.77 0.54 -10000 0 -1.2 222 222
JunB/Fra1/NFAT1-c-4 -0.53 0.54 -10000 0 -1 191 191
IL4 -0.31 0.37 -10000 0 -0.93 84 84
IL5 -0.69 0.55 -10000 0 -1.2 211 211
IL2 -0.44 0.45 -10000 0 -1 123 123
IL3 -0.096 0.063 -10000 0 -10000 0 0
RNF128 0.049 0.047 -10000 0 -0.9 1 1
NFATC1 -0.35 0.42 -10000 0 -0.8 152 152
CDK4 0.21 0.24 0.61 39 -10000 0 39
PTPRK -0.14 0.29 -10000 0 -0.71 68 68
IL8 -0.72 0.56 -10000 0 -1.2 211 211
POU2F1 0.013 0.016 -10000 0 -0.31 1 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.55 0.56 -9999 0 -1.1 168 168
PCK1 -0.37 0.52 -9999 0 -1.5 61 61
HNF4A -0.71 0.67 -9999 0 -1.3 211 211
KCNJ11 -0.52 0.56 -9999 0 -1.1 165 165
AKT1 -0.042 0.13 -9999 0 -0.41 2 2
response to starvation -0.017 0.034 -9999 0 -10000 0 0
DLK1 -0.52 0.55 -9999 0 -1.1 169 169
NKX2-1 -0.17 0.21 -9999 0 -10000 0 0
ACADM -0.55 0.56 -9999 0 -1.1 189 189
TAT -0.21 0.23 -9999 0 -0.68 8 8
CEBPB 0.013 0.004 -9999 0 -10000 0 0
CEBPA 0.005 0.085 -9999 0 -0.85 4 4
TTR -0.2 0.22 -9999 0 -0.77 26 26
PKLR -0.55 0.56 -9999 0 -1.1 171 171
APOA1 -0.97 0.91 -9999 0 -1.8 220 220
CPT1C -0.56 0.56 -9999 0 -1.1 173 173
ALAS1 -0.17 0.21 -9999 0 -10000 0 0
TFRC -0.27 0.29 -9999 0 -0.78 19 19
FOXF1 -0.009 0.086 -9999 0 -0.75 5 5
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.013 0.043 -9999 0 -0.85 1 1
CPT1A -0.55 0.56 -9999 0 -1.1 189 189
HMGCS1 -0.55 0.56 -9999 0 -1.1 168 168
NR3C1 0.019 0.015 -9999 0 -10000 0 0
CPT1B -0.55 0.56 -9999 0 -1.1 189 189
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.7 0.72 -9999 0 -1.3 207 207
CREB1 -0.002 0.055 -9999 0 -10000 0 0
IGFBP1 -0.19 0.2 -9999 0 -0.59 1 1
PDX1 -0.19 0.22 -9999 0 -0.86 2 2
UCP2 -0.55 0.56 -9999 0 -1.1 178 178
ALDOB -0.52 0.55 -9999 0 -1.1 174 174
AFP -0.047 0.12 -9999 0 -0.45 15 15
BDH1 -0.55 0.56 -9999 0 -1.1 184 184
HADH -0.51 0.55 -9999 0 -1.1 174 174
F2 -0.66 0.65 -9999 0 -1.3 179 179
HNF1A 0.013 0.043 -9999 0 -0.85 1 1
G6PC -0.008 0.092 -9999 0 -10000 0 0
SLC2A2 -0.24 0.27 -9999 0 -1.5 1 1
INS -0.008 0.018 -9999 0 -10000 0 0
FOXA1 -0.055 0.14 -9999 0 -0.35 66 66
FOXA3 -0.077 0.18 -9999 0 -0.49 33 33
FOXA2 -0.59 0.63 -9999 0 -1.2 186 186
ABCC8 -0.83 0.78 -9999 0 -1.4 231 231
ALB -0.1 0.34 -9999 0 -1.3 27 27
PDGFR-alpha signaling pathway

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

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

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

Figure 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
BCL2L1 -0.59 0.44 -10000 0 -1.1 145 145
STAT6 (cleaved dimer) -0.65 0.45 -10000 0 -1 214 214
IGHG1 -0.2 0.14 -10000 0 -0.36 35 35
IGHG3 -0.58 0.43 -10000 0 -0.96 192 192
AKT1 -0.32 0.26 -10000 0 -0.69 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.26 -10000 0 -0.76 46 46
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.35 0.28 -10000 0 -0.71 98 98
THY1 -0.59 0.45 -10000 0 -1.1 141 141
MYB -0.009 0.13 -10000 0 -0.68 13 13
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.42 0.32 -10000 0 -0.73 150 150
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.69 72 72
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.005 0.075 -10000 0 -0.31 23 23
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.62 0.44 -10000 0 -1 196 196
SOCS1 -0.4 0.29 -10000 0 -0.73 112 112
SOCS3 -0.4 0.39 -10000 0 -1 73 73
FCER2 -0.58 0.43 -10000 0 -0.99 167 167
PARP14 0.012 0.004 -10000 0 -10000 0 0
CCL17 -0.67 0.49 -10000 0 -1.1 175 175
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.22 -10000 0 -0.65 47 47
T cell proliferation -0.6 0.46 -10000 0 -1.1 157 157
IL4R/JAK1 -0.59 0.44 -10000 0 -1.1 145 145
EGR2 -0.92 0.73 -10000 0 -1.6 201 201
JAK2 -0.015 0.024 -10000 0 -10000 0 0
JAK3 -0.06 0.14 -10000 0 -0.31 94 94
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.009 -10000 0 -10000 0 0
COL1A2 -0.19 0.16 -10000 0 -0.55 16 16
CCL26 -0.61 0.46 -10000 0 -1.1 142 142
IL4R -0.63 0.47 -10000 0 -1.1 145 145
PTPN6 0.028 0.009 -10000 0 -10000 0 0
IL13RA2 -0.71 0.58 -10000 0 -1.3 167 167
IL13RA1 -0.015 0.024 -10000 0 -10000 0 0
IRF4 -0.34 0.47 -10000 0 -1.2 77 77
ARG1 -0.14 0.12 -10000 0 -0.5 1 1
CBL -0.38 0.3 -10000 0 -0.7 134 134
GTF3A 0.016 0.01 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
IL13RA1/JAK2 -0.022 0.034 -10000 0 -10000 0 0
IRF4/BCL6 -0.31 0.43 -10000 0 -1.2 67 67
CD40LG -0.12 0.32 -10000 0 -0.83 68 68
MAPK14 -0.4 0.33 -10000 0 -0.76 125 125
mitosis -0.3 0.25 -10000 0 -0.65 75 75
STAT6 -0.68 0.52 -10000 0 -1.1 186 186
SPI1 0.002 0.069 -10000 0 -0.31 19 19
RPS6KB1 -0.29 0.24 -10000 0 -0.65 59 59
STAT6 (dimer) -0.68 0.52 -10000 0 -1.1 186 186
STAT6 (dimer)/PARP14 -0.63 0.48 -10000 0 -1.1 176 176
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.28 -10000 0 -0.7 80 80
FRAP1 -0.32 0.26 -10000 0 -0.69 75 75
LTA -0.62 0.46 -10000 0 -1.1 154 154
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.66 0.5 1.1 186 -10000 0 186
CCL11 -0.59 0.44 -10000 0 -1.1 144 144
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.73 68 68
IL2RG -0.044 0.2 -10000 0 -0.56 43 43
IL10 -0.61 0.48 -10000 0 -1.1 146 146
IRS1 -0.078 0.26 -10000 0 -0.85 43 43
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.098 -10000 0 -10000 0 0
IL5 -0.6 0.44 -10000 0 -1.1 139 139
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.48 0.34 -10000 0 -0.82 149 149
COL1A1 -0.26 0.23 -10000 0 -0.77 19 19
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.6 0.46 -10000 0 -1.2 114 114
IL2R gamma/JAK3 -0.077 0.18 -10000 0 -0.53 43 43
TFF3 -1.3 0.62 -10000 0 -1.6 328 328
ALOX15 -0.6 0.45 -10000 0 -1.1 128 128
MYBL1 0.012 0.016 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.51 0.36 -10000 0 -0.86 169 169
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.017 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.3 0.26 -10000 0 -0.68 64 64
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.69 75 75
PI3K -0.33 0.28 -10000 0 -0.74 75 75
DOK2 0.001 0.078 -10000 0 -0.4 12 12
ETS1 0.029 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.24 0.21 -10000 0 -0.62 49 49
ITGB3 -0.62 0.48 -10000 0 -1.1 147 147
PIGR -0.64 0.5 -10000 0 -1.2 134 134
IGHE 0.051 0.036 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.21 -10000 0 -0.61 49 49
BCL6 0.011 0.043 -10000 0 -0.85 1 1
OPRM1 -0.6 0.44 -10000 0 -1.1 150 150
RETNLB -0.6 0.44 -10000 0 -1.1 138 138
SELP -0.6 0.46 -10000 0 -1.1 151 151
AICDA -0.58 0.43 -10000 0 -1 144 144
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.11 0.3 -9999 0 -0.85 59 59
GNB1/GNG2 -0.27 0.24 -9999 0 -0.63 102 102
mol:DAG -0.23 0.24 -9999 0 -0.57 102 102
PLCG1 -0.24 0.25 -9999 0 -0.59 102 102
YES1 -0.27 0.28 -9999 0 -0.64 109 109
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.26 0.23 -9999 0 -0.6 102 102
MAP3K7 -0.18 0.21 -9999 0 -0.46 102 102
mol:Ca2+ -0.22 0.24 -9999 0 -0.55 102 102
mol:IP3 -0.23 0.24 -9999 0 -0.57 102 102
NLK -0.011 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.21 0.22 -9999 0 -0.51 103 103
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.3 0.29 -9999 0 -0.69 109 109
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.27 0.28 -9999 0 -0.64 109 109
GO:0007205 -0.22 0.24 -9999 0 -0.56 102 102
WNT6 0.005 0.048 -9999 0 -10000 0 0
WNT4 -0.28 0.41 -9999 0 -0.84 142 142
NFAT1/CK1 alpha -0.31 0.26 -9999 0 -0.64 125 125
GNG2 0.013 0 -9999 0 -10000 0 0
WNT5A -0.009 0.13 -9999 0 -0.85 10 10
WNT11 -0.44 0.43 -9999 0 -0.85 214 214
CDC42 -0.25 0.26 -9999 0 -0.62 102 102
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.012 0.15 -9999 0 -0.85 12 12
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.44 0.27 -9999 0 -0.59 307 307
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.4 0.26 -9999 0 -0.54 307 307
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.007 0.007 -9999 0 -10000 0 0
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.12 0.31 -9999 0 -0.85 61 61
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.026 0.13 -9999 0 -0.66 16 16
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.012 0.023 -9999 0 -0.31 2 2
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.023 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.44 0.27 -9999 0 -0.59 307 307
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.29 0.21 -9999 0 -0.42 196 196
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.34 0.24 -9999 0 -0.47 307 307
RELN -0.63 0.38 -9999 0 -0.85 305 305
PAFAH/LIS1 -0.061 0.21 -9999 0 -0.57 61 61
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.24 0.14 -9999 0 -0.56 14 14
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.25 0.18 -9999 0 -0.34 308 308
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.32 0.22 -9999 0 -0.44 307 307
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0.023 -9999 0 -0.31 2 2
PAFAH1B2 0.009 0.06 -9999 0 -0.85 2 2
MAP1B/LIS1/Dynein heavy chain 0.026 0.004 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.29 0.18 -9999 0 -0.72 14 14
LRP8 -0.021 0.17 -9999 0 -0.85 16 16
NDEL1/Katanin 60 -0.29 0.21 -9999 0 -0.73 15 15
P39/CDK5 -0.34 0.24 -9999 0 -0.47 307 307
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.36 0.25 -9999 0 -0.5 307 307
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.38 0.23 -9999 0 -0.5 307 307
RELN/VLDLR -0.42 0.27 -9999 0 -0.56 309 309
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.12 0.27 -10000 0 -0.71 29 29
IHH -0.22 0.39 -10000 0 -0.87 107 107
SHH Np/Cholesterol/GAS1 -0.11 0.22 -10000 0 -0.54 82 82
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.21 0.54 82 -10000 0 82
SMO/beta Arrestin2 -0.11 0.25 -10000 0 -0.5 109 109
SMO -0.12 0.26 -10000 0 -0.53 109 109
AKT1 -0.029 0.12 -10000 0 -0.33 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.004 0.12 -10000 0 -0.85 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.12 0.26 -10000 0 -0.52 109 109
STIL -0.087 0.2 -10000 0 -0.59 16 16
DHH N/PTCH2 -0.11 0.25 -10000 0 -0.66 68 68
DHH N/PTCH1 -0.11 0.24 -10000 0 -0.48 112 112
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
DHH 0.007 0.074 -10000 0 -0.85 3 3
PTHLH -0.17 0.38 -10000 0 -1.2 29 29
determination of left/right symmetry -0.12 0.26 -10000 0 -0.52 109 109
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.17 0.37 -10000 0 -1.2 29 29
IHH N/Hhip -0.41 0.42 -10000 0 -0.77 221 221
DHH N/Hhip -0.26 0.32 -10000 0 -0.66 160 160
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.12 0.26 -10000 0 -0.52 109 109
pancreas development -0.33 0.42 -10000 0 -0.85 159 159
HHAT 0.011 0.043 -10000 0 -0.85 1 1
PI3K -0.002 0.032 -10000 0 -0.66 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.16 0.34 -10000 0 -0.85 81 81
somite specification -0.12 0.26 -10000 0 -0.52 109 109
SHH Np/Cholesterol/PTCH1 -0.099 0.21 -10000 0 -0.64 15 15
SHH Np/Cholesterol/PTCH2 -0.092 0.2 -10000 0 -0.54 67 67
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.54 102 102
SHH 0.007 0.052 -10000 0 -0.66 1 1
catabolic process -0.13 0.26 -10000 0 -0.53 109 109
SMO/Vitamin D3 -0.1 0.23 -10000 0 -0.68 15 15
SHH Np/Cholesterol/Hhip -0.21 0.26 -10000 0 -0.53 160 160
LRP2 -0.2 0.37 -10000 0 -0.85 101 101
receptor-mediated endocytosis -0.2 0.24 -10000 0 -0.74 38 38
SHH Np/Cholesterol/BOC -0.016 0.084 -10000 0 -0.55 9 9
SHH Np/Cholesterol/CDO -0.16 0.24 -10000 0 -0.54 119 119
mesenchymal cell differentiation 0.21 0.26 0.53 160 -10000 0 160
mol:Vitamin D3 -0.098 0.22 -10000 0 -0.65 15 15
IHH N/PTCH2 -0.25 0.36 -10000 0 -0.69 154 154
CDON -0.24 0.39 -10000 0 -0.85 118 118
IHH N/PTCH1 -0.13 0.26 -10000 0 -0.54 109 109
Megalin/LRPAP1 -0.16 0.28 -10000 0 -0.66 101 101
PTCH2 -0.13 0.32 -10000 0 -0.85 66 66
SHH Np/Cholesterol -0.006 0.038 -10000 0 -0.54 1 1
PTCH1 -0.13 0.26 -10000 0 -0.54 109 109
HHIP -0.33 0.42 -10000 0 -0.85 159 159
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.22 0.26 -10000 0 -0.53 170 170
regulation of S phase of mitotic cell cycle -0.13 0.18 -10000 0 -0.34 171 171
GNAO1 -0.016 0.15 -10000 0 -0.72 16 16
HRAS 0.011 0.023 -10000 0 -0.31 2 2
SHBG/T-DHT -0.011 0.081 -10000 0 -0.59 8 8
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.17 0.24 -10000 0 -0.45 170 170
T-DHT/AR -0.28 0.33 -10000 0 -0.67 170 170
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 47 47
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.27 0.31 -10000 0 -0.64 170 170
cell proliferation -0.2 0.28 -10000 0 -0.67 67 67
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
FOS -0.25 0.39 -10000 0 -0.89 106 106
mol:Ca2+ -0.027 0.03 -10000 0 -0.071 71 71
MAPK3 -0.19 0.26 -10000 0 -0.47 170 170
MAPK1 -0.084 0.13 -10000 0 -0.31 59 59
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 106 106
cAMP biosynthetic process 0.014 0.084 -10000 0 -0.55 8 8
GNG2 0.013 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 106 106
HRAS/GTP -0.21 0.24 -10000 0 -0.49 170 170
actin cytoskeleton reorganization -0.001 0.023 -10000 0 -0.46 1 1
SRC 0.012 0.017 -10000 0 -0.32 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 106 106
PI3K -0.001 0.029 -10000 0 -0.58 1 1
apoptosis 0.16 0.25 0.52 106 -10000 0 106
T-DHT/AR/PELP1 -0.24 0.29 -10000 0 -0.58 170 170
HRAS/GDP -0.25 0.3 -10000 0 -0.6 171 171
CREB1 -0.18 0.27 -10000 0 -0.57 106 106
RAC1-CDC42/GTP -0.001 0.023 -10000 0 -0.47 1 1
AR -0.35 0.43 -10000 0 -0.85 170 170
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.18 0.25 -10000 0 -0.47 170 170
RAC1-CDC42/GDP -0.24 0.28 -10000 0 -0.57 170 170
T-DHT/AR/PELP1/Src -0.22 0.26 -10000 0 -0.54 170 170
MAP2K2 -0.17 0.24 -10000 0 -0.45 170 170
T-DHT/AR/PELP1/Src/PI3K -0.13 0.19 -10000 0 -0.35 171 171
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG -0.004 0.12 -10000 0 -0.85 8 8
Gi family/GNB1/GNG2/GDP -0.018 0.11 -10000 0 -0.54 12 12
mol:T-DHT 0 0.001 -10000 0 -0.003 46 46
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.01 0.034 -10000 0 -0.67 1 1
Gi family/GTP -0.095 0.12 -10000 0 -0.48 12 12
CDC42 0.013 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.3 0.29 -9999 0 -0.69 109 109
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.005 0.048 -9999 0 -10000 0 0
WNT4 -0.28 0.41 -9999 0 -0.84 142 142
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.009 0.13 -9999 0 -0.85 10 10
WNT11 -0.44 0.43 -9999 0 -0.85 214 214
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.076 -9999 0 -0.59 6 6
NFATC2 -0.09 0.21 -9999 0 -0.61 59 59
NFATC3 0 0.028 -9999 0 -10000 0 0
CD40LG -0.44 0.42 -9999 0 -0.88 170 170
PTGS2 -0.42 0.41 -9999 0 -0.87 157 157
JUNB 0 0.1 -9999 0 -0.85 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.014 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.014 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.19 0.36 -9999 0 -0.86 93 93
mol:Ca2+ -0.01 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.002 -9999 0 -10000 0 0
FOSL1 -0.036 0.12 -9999 0 -0.31 62 62
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.6 142 142
FOS -0.22 0.38 -9999 0 -0.86 106 106
IFNG -0.44 0.41 -9999 0 -0.86 172 172
AP-1/NFAT1-c-4 -0.53 0.52 -9999 0 -0.99 191 191
FASLG -0.42 0.4 -9999 0 -0.85 162 162
NFAT1-c-4/ICER1 -0.11 0.2 -9999 0 -0.54 64 64
IL2RA -0.41 0.39 -9999 0 -0.84 155 155
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.37 -9999 0 -0.78 218 218
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.53 69 69
IL4 -0.4 0.37 -9999 0 -0.81 154 154
IL2 -0.013 0.026 -9999 0 -10000 0 0
IL3 -0.032 0.031 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.009 0.089 -9999 0 -0.33 26 26
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.016 -9999 0 -0.31 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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

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

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

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
GPC1/FGF2 dimer/FGFR1 dimer -0.002 0.029 -10000 0 -0.57 1 1
fibroblast growth factor receptor signaling pathway -0.002 0.029 -10000 0 -0.57 1 1
LAMA1 -0.053 0.23 -10000 0 -0.83 32 32
PRNP 0.013 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.096 0.23 -10000 0 -0.66 59 59
SMAD2 0.029 0.04 -10000 0 -0.52 1 1
GPC1/PrPc/Cu2+ 0 0.008 -10000 0 -10000 0 0
GPC1/Laminin alpha1 -0.051 0.17 -10000 0 -0.66 31 31
TDGF1 -0.35 0.42 -10000 0 -0.85 170 170
CRIPTO/GPC1 -0.27 0.32 -10000 0 -0.66 170 170
APP/GPC1 0 0.01 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.22 0.29 -10000 0 -0.57 170 170
FLT1 0.013 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.006 0.039 -10000 0 -0.57 1 1
SERPINC1 0.011 0.016 -10000 0 -0.31 1 1
FYN -0.22 0.29 -10000 0 -0.57 170 170
FGR -0.22 0.29 -10000 0 -0.57 170 170
positive regulation of MAPKKK cascade -0.28 0.32 -10000 0 -0.64 172 172
SLIT2 -0.11 0.3 -10000 0 -0.85 59 59
GPC1/NRG -0.066 0.2 -10000 0 -0.66 40 40
NRG1 -0.073 0.26 -10000 0 -0.82 42 42
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.04 -10000 0 -0.57 2 2
LYN -0.22 0.29 -10000 0 -0.57 170 170
mol:Spermine 0.012 0.011 -10000 0 -10000 0 0
cell growth -0.002 0.029 -10000 0 -0.57 1 1
BMP signaling pathway -0.012 0.016 0.31 1 -10000 0 1
SRC -0.22 0.29 -10000 0 -0.57 170 170
TGFBR1 0.004 0.055 -10000 0 -0.31 12 12
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.27 0.38 -10000 0 -0.72 158 158
GPC1 0.012 0.016 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.004 0.055 -10000 0 -0.31 12 12
VEGFA 0.009 0.06 -10000 0 -0.85 2 2
BLK -0.4 0.39 -10000 0 -0.7 234 234
HCK -0.23 0.29 -10000 0 -0.57 170 170
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.011 0.043 -10000 0 -0.85 1 1
VEGFR1 homodimer 0.013 0 -10000 0 -10000 0 0
TGFBR2 0.011 0.043 -10000 0 -0.85 1 1
cell death 0 0.01 -10000 0 -10000 0 0
ATIII/GPC1 -0.001 0.014 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.21 0.29 -10000 0 -0.66 118 118
LCK -0.23 0.29 -10000 0 -0.57 175 175
neuron differentiation -0.066 0.2 -10000 0 -0.66 40 40
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.011 0.043 -10000 0 -0.85 1 1
Ephrin B reverse signaling

Figure 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
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.006 0.074 -10000 0 -0.85 3 3
EFNB1 -0.009 0.14 -10000 0 -0.66 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.26 0.26 -10000 0 -0.55 170 170
Ephrin B2/EPHB1-2 -0.2 0.26 -10000 0 -0.53 156 156
neuron projection morphogenesis -0.24 0.24 -10000 0 -0.52 170 170
Ephrin B1/EPHB1-2/Tiam1 -0.28 0.28 -10000 0 -0.59 170 170
DNM1 -0.027 0.18 -10000 0 -0.82 19 19
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.011 0.056 -10000 0 -0.76 2 2
YES1 -0.003 0.07 -10000 0 -1 2 2
Ephrin B1/EPHB1-2/NCK2 -0.2 0.26 -10000 0 -0.5 170 170
PI3K 0.01 0.074 -10000 0 -1 2 2
mol:GDP -0.28 0.27 -10000 0 -0.58 170 170
ITGA2B -0.088 0.28 -10000 0 -0.85 48 48
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.003 0.07 -10000 0 -1 2 2
MAP3K7 -0.006 0.057 -10000 0 -0.81 2 2
FGR -0.005 0.07 -10000 0 -1 2 2
TIAM1 -0.17 0.16 -10000 0 -0.32 230 230
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.047 0.21 -10000 0 -0.54 55 55
LYN -0.003 0.07 -10000 0 -1 2 2
Ephrin B1/EPHB1-2/Src Family Kinases -0.007 0.065 -10000 0 -0.94 2 2
Ephrin B1/EPHB1-2 -0.014 0.061 -10000 0 -0.87 2 2
SRC -0.005 0.07 -10000 0 -1 2 2
ITGB3 -0.014 0.15 -10000 0 -0.85 13 13
EPHB1 -0.31 0.42 -10000 0 -0.85 154 154
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.096 0.25 -10000 0 -0.72 55 55
BLK -0.061 0.11 -10000 0 -1 2 2
HCK -0.006 0.07 -10000 0 -1 2 2
regulation of stress fiber formation 0.2 0.25 0.49 170 -10000 0 170
MAPK8 0.015 0.087 -10000 0 -0.93 3 3
Ephrin B1/EPHB1-2/RGS3 -0.2 0.26 -10000 0 -0.5 170 170
endothelial cell migration -0.001 0.05 -10000 0 -0.71 2 2
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.012 0.069 -10000 0 -0.96 2 2
regulation of focal adhesion formation 0.2 0.25 0.49 170 -10000 0 170
chemotaxis 0.2 0.25 0.49 170 -10000 0 170
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
Rac1/GTP -0.25 0.25 -10000 0 -0.54 170 170
angiogenesis -0.014 0.061 -10000 0 -0.87 2 2
LCK -0.008 0.073 -10000 0 -1 2 2
Endothelins

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
AKT1 -0.057 0.15 -9999 0 -0.6 8 8
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.64 60 60
EDN1 -0.049 0.13 -9999 0 -0.77 7 7
EDN3 -0.42 0.43 -9999 0 -0.85 207 207
EDN2 -0.012 0.11 -9999 0 -0.4 25 25
HRAS/GDP -0.1 0.24 -9999 0 -0.53 71 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.084 0.18 -9999 0 -0.4 73 73
ADCY4 -0.1 0.2 -9999 0 -0.53 55 55
ADCY5 -0.17 0.26 -9999 0 -0.59 96 96
ADCY6 -0.1 0.2 -9999 0 -0.53 55 55
ADCY7 -0.1 0.2 -9999 0 -0.53 55 55
ADCY1 -0.11 0.21 -9999 0 -0.56 55 55
ADCY2 -0.15 0.25 -9999 0 -0.59 81 81
ADCY3 -0.1 0.2 -9999 0 -0.53 55 55
ADCY8 -0.21 0.21 -9999 0 -0.56 78 78
ADCY9 -0.1 0.2 -9999 0 -0.53 55 55
arachidonic acid secretion -0.18 0.32 -9999 0 -0.65 107 107
ETB receptor/Endothelin-1/Gq/GTP -0.093 0.21 -9999 0 -0.44 94 94
GNAO1 -0.015 0.15 -9999 0 -0.72 16 16
HRAS 0.009 0.023 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.021 0.16 -9999 0 -0.59 7 7
ETA receptor/Endothelin-1/Gs/GTP -0.086 0.23 -9999 0 -0.57 55 55
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.075 0.18 -9999 0 -0.55 18 18
EDNRB 0.002 0.088 -9999 0 -0.67 6 6
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.17 0.24 -9999 0 -0.73 32 32
CYSLTR1 -0.063 0.17 -9999 0 -0.74 11 11
SLC9A1 -0.024 0.077 -9999 0 -0.31 7 7
mol:GDP -0.12 0.25 -9999 0 -0.56 75 75
SLC9A3 -0.051 0.19 -9999 0 -0.78 19 19
RAF1 -0.15 0.29 -9999 0 -0.6 93 93
JUN -0.28 0.52 -9999 0 -1.1 101 101
JAK2 -0.057 0.15 -9999 0 -0.6 8 8
mol:IP3 -0.11 0.22 -9999 0 -0.49 87 87
ETA receptor/Endothelin-1 -0.041 0.2 -9999 0 -0.66 9 9
PLCB1 0.006 0.061 -9999 0 -0.85 2 2
PLCB2 0.005 0.043 -9999 0 -0.33 3 3
ETA receptor/Endothelin-3 -0.35 0.34 -9999 0 -0.69 206 206
FOS -0.26 0.48 -9999 0 -1 106 106
Gai/GDP -0.001 0.12 -9999 0 -0.65 12 12
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.23 -9999 0 -0.6 45 45
BCAR1 0.013 0.002 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.48 87 87
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.09 0.28 -9999 0 -0.85 49 49
Gs family/GDP -0.19 0.25 -9999 0 -0.58 97 97
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.46 86 86
MAPK14 -0.061 0.17 -9999 0 -0.39 54 54
TRPC6 -0.14 0.29 -9999 0 -0.72 51 51
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.013 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.073 0.18 -9999 0 -0.4 70 70
ETB receptor/Endothelin-2 -0.024 0.1 -9999 0 -0.63 9 9
ETB receptor/Endothelin-3 -0.34 0.33 -9999 0 -0.66 207 207
ETB receptor/Endothelin-1 -0.023 0.12 -9999 0 -0.62 11 11
MAPK3 -0.23 0.43 -9999 0 -0.91 108 108
MAPK1 -0.23 0.43 -9999 0 -0.91 108 108
Rac1/GDP -0.1 0.23 -9999 0 -0.53 66 66
cAMP biosynthetic process -0.14 0.22 -9999 0 -0.58 61 61
MAPK8 -0.16 0.32 -9999 0 -0.62 103 103
SRC 0.012 0.016 -9999 0 -0.32 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.009 0.074 -9999 0 -0.33 7 7
p130Cas/CRK/Src/PYK2 -0.13 0.29 -9999 0 -0.57 94 94
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.23 -9999 0 -0.53 66 66
COL1A2 -0.042 0.16 -9999 0 -0.63 7 7
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.1 -9999 0 -0.69 5 5
mol:DAG -0.11 0.23 -9999 0 -0.49 87 87
MAP2K2 -0.18 0.35 -9999 0 -0.69 112 112
MAP2K1 -0.18 0.35 -9999 0 -0.69 113 113
EDNRA -0.041 0.099 -9999 0 -0.53 4 4
positive regulation of muscle contraction -0.041 0.13 -9999 0 -0.55 7 7
Gq family/GDP -0.19 0.29 -9999 0 -0.67 98 98
HRAS/GTP -0.13 0.26 -9999 0 -0.57 79 79
PRKCH -0.1 0.22 -9999 0 -0.51 72 72
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.13 0.26 -9999 0 -0.56 86 86
PRKCB -0.12 0.22 -9999 0 -0.51 74 74
PRKCE -0.1 0.23 -9999 0 -0.53 70 70
PRKCD -0.1 0.22 -9999 0 -0.5 77 77
PRKCG -0.11 0.22 -9999 0 -0.52 69 69
regulation of vascular smooth muscle contraction -0.3 0.55 -9999 0 -1.2 106 106
PRKCQ -0.11 0.23 -9999 0 -0.52 73 73
PLA2G4A -0.2 0.36 -9999 0 -0.73 107 107
GNA14 -0.18 0.36 -9999 0 -0.86 92 92
GNA15 -0.015 0.093 -9999 0 -0.33 30 30
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 0.002 0.085 -9999 0 -0.85 4 4
Rac1/GTP -0.021 0.16 -9999 0 -0.58 7 7
MMP1 -0.099 0.16 -9999 0 -10000 0 0
Glypican 2 network

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.087 0.15 -9999 0 -0.32 124 124
GPC2 -0.018 0.096 -9999 0 -0.31 39 39
GPC2/Midkine -0.081 0.12 -9999 0 -0.41 17 17
neuron projection morphogenesis -0.081 0.12 -9999 0 -0.41 17 17
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.047 0.096 0.33 11 -10000 0 11
SMARCC2 0.014 0.012 -10000 0 -10000 0 0
SMARCC1 0.014 0.012 -10000 0 -10000 0 0
TBX21 -0.16 0.29 -10000 0 -0.81 46 46
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.05 -10000 0 -0.32 9 9
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.003 0.095 -10000 0 -0.85 5 5
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.35 38 -0.54 5 43
PRL -0.092 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.27 0.31 0.58 143 -0.53 17 160
RELA -0.038 0.09 -10000 0 -10000 0 0
FGG 0.25 0.19 0.54 82 -10000 0 82
GR beta/TIF2 0.098 0.23 0.36 56 -0.6 30 86
IFNG -0.51 0.52 -10000 0 -1.1 123 123
apoptosis 0.035 0.24 0.49 60 -0.54 1 61
CREB1 0.011 0.022 -10000 0 -10000 0 0
histone acetylation -0.075 0.16 -10000 0 -0.4 51 51
BGLAP -0.1 0.15 -10000 0 -0.49 21 21
GR/PKAc 0.14 0.1 0.34 31 -10000 0 31
NF kappa B1 p50/RelA -0.075 0.16 -10000 0 -0.44 25 25
SMARCD1 0.014 0.012 -10000 0 -10000 0 0
MDM2 0.12 0.096 0.27 89 -10000 0 89
GATA3 -0.032 0.2 -10000 0 -0.83 24 24
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.55 41 41
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.061 0.24 0.5 43 -0.78 4 47
CSN2 0.21 0.14 0.42 77 -10000 0 77
BRG1/BAF155/BAF170/BAF60A 0.008 0.04 -10000 0 -10000 0 0
NFATC1 0.002 0.1 -10000 0 -0.85 6 6
POU2F1 0.013 0.016 -10000 0 -0.3 1 1
CDKN1A 0.022 0.057 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 265 265
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.047 0.17 0.35 12 -0.48 14 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.079 0.45 0.48 43 -0.9 89 132
JUN -0.34 0.3 -10000 0 -0.69 147 147
IL4 -0.13 0.17 -10000 0 -0.6 24 24
CDK5R1 0.011 0.024 -10000 0 -0.32 2 2
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.37 0.43 -10000 0 -0.88 143 143
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.13 0.35 33 -0.49 5 38
cortisol/GR alpha (monomer) 0.38 0.31 0.68 166 -10000 0 166
NCOA2 -0.05 0.22 -10000 0 -0.85 30 30
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.26 0.37 -10000 0 -0.88 106 106
AP-1/NFAT1-c-4 -0.57 0.5 -10000 0 -1 184 184
AFP -0.23 0.21 -10000 0 -0.59 75 75
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.51 36 -10000 0 36
TP53 0.032 0.023 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.48 0.38 -10000 0 -0.86 146 146
KRT14 -0.24 0.18 -10000 0 -0.56 33 33
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.063 -10000 0 -10000 0 0
HDAC1 0.01 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.014 -10000 0 -10000 0 0
AP-1 -0.58 0.5 -10000 0 -1 184 184
MAPK14 0.014 0.012 -10000 0 -10000 0 0
MAPK10 0.014 0.013 -10000 0 -10000 0 0
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.56 0.55 -10000 0 -1.2 130 130
interleukin-1 receptor activity 0.017 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.015 0.05 -10000 0 -0.32 9 9
CGA -0.13 0.16 -10000 0 -0.57 16 16
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.38 168 -10000 0 168
MAPK3 0.014 0.013 -10000 0 -10000 0 0
MAPK1 0.014 0.012 -10000 0 -10000 0 0
ICAM1 -0.27 0.27 -10000 0 -0.64 107 107
NFKB1 -0.038 0.09 -10000 0 -10000 0 0
MAPK8 -0.19 0.19 -10000 0 -0.5 75 75
MAPK9 0.014 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.03 0.25 0.49 60 -0.56 1 61
BAX 0.028 0.031 -10000 0 -10000 0 0
POMC -0.56 0.7 -10000 0 -1.3 145 145
EP300 0.064 0.064 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.34 0.24 0.58 163 -10000 0 163
proteasomal ubiquitin-dependent protein catabolic process 0.089 0.073 0.24 30 -10000 0 30
SGK1 0.11 0.21 -10000 0 -1.4 7 7
IL13 -0.31 0.26 -10000 0 -0.8 58 58
IL6 -0.43 0.56 -10000 0 -1.3 109 109
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.27 0.21 -10000 0 -0.74 38 38
IL2 -0.37 0.27 -10000 0 -0.78 84 84
CDK5 0.012 0.008 -10000 0 -10000 0 0
PRKACB 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.28 0.32 -10000 0 -0.82 65 65
CDK5R1/CDK5 0.007 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.033 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.55 149 -10000 0 149
SMARCA4 0.014 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.21 0.15 0.4 107 -0.36 2 109
NF kappa B1 p50/RelA/Cbp 0.017 0.16 -10000 0 -0.49 3 3
JUN (dimer) -0.34 0.3 -10000 0 -0.68 147 147
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.25 0.43 -10000 0 -1.1 74 74
NR3C1 0.22 0.2 0.49 108 -10000 0 108
NR4A1 -0.32 0.42 -10000 0 -0.78 171 171
TIF2/SUV420H1 -0.048 0.17 -10000 0 -0.66 30 30
MAPKKK cascade 0.035 0.24 0.49 60 -0.54 1 61
cortisol/GR alpha (dimer)/Src-1 0.33 0.24 0.58 158 -10000 0 158
PBX1 0.012 0.043 -10000 0 -0.85 1 1
POU1F1 0.006 0.008 -10000 0 -10000 0 0
SELE -0.35 0.5 -10000 0 -1.1 97 97
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.21 0.15 0.4 106 -0.36 2 108
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.55 149 -10000 0 149
mol:cortisol 0.22 0.2 0.4 176 -10000 0 176
MMP1 -0.22 0.15 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.12 0.24 -10000 0 -0.48 122 122
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.023 -10000 0 -0.31 2 2
IRS1/Crk -0.12 0.24 -10000 0 -0.48 122 122
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.23 -10000 0 -0.55 89 89
AKT1 -0.086 0.22 -10000 0 -0.8 11 11
BAD -0.072 0.2 -10000 0 -0.72 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.24 -10000 0 -0.48 122 122
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.23 -10000 0 -0.48 122 122
RAF1 -0.063 0.19 -10000 0 -0.67 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.22 -10000 0 -0.45 122 122
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.25 -10000 0 -0.52 122 122
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
RPS6KB1 -0.086 0.22 -10000 0 -0.8 11 11
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.054 0.17 -10000 0 -0.54 11 11
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.43 89 89
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.18 -10000 0 -0.44 89 89
IGF-1R heterotetramer -0.018 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.14 0.23 -10000 0 -0.48 122 122
Crk/p130 Cas/Paxillin -0.13 0.21 -10000 0 -0.46 89 89
IGF1R -0.018 0.048 -10000 0 -10000 0 0
IGF1 -0.19 0.36 -10000 0 -0.84 94 94
IRS2/Crk -0.11 0.23 -10000 0 -0.45 122 122
PI3K -0.14 0.22 -10000 0 -0.45 122 122
apoptosis 0.054 0.18 0.59 11 -10000 0 11
HRAS/GDP -0.001 0.015 -10000 0 -10000 0 0
PRKCD -0.1 0.25 -10000 0 -0.55 89 89
RAF1/14-3-3 E -0.046 0.17 -10000 0 -0.55 11 11
BAD/14-3-3 -0.058 0.19 -10000 0 -0.64 11 11
PRKCZ -0.086 0.22 -10000 0 -0.8 11 11
Crk/p130 Cas/Paxillin/FAK1 -0.099 0.16 -10000 0 -0.66 11 11
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.26 -10000 0 -0.59 89 89
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.2 -10000 0 -0.48 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.24 -10000 0 -0.48 122 122
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.12 0.24 -10000 0 -0.48 122 122
IRS1 -0.14 0.26 -10000 0 -0.52 122 122
IRS2 -0.12 0.24 -10000 0 -0.48 122 122
IGF-1R heterotetramer/IGF1 -0.16 0.28 -10000 0 -0.69 89 89
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.099 0.23 -10000 0 -0.46 89 89
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.1 0.25 -10000 0 -0.55 89 89
SHC1 0.013 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.23 0.55 -9999 0 -1.3 70 70
IL23A -0.24 0.56 -9999 0 -1.3 74 74
NF kappa B1 p50/RelA/I kappa B alpha -0.3 0.47 -9999 0 -1.2 75 75
positive regulation of T cell mediated cytotoxicity -0.26 0.62 -9999 0 -1.4 77 77
ITGA3 -0.21 0.51 -9999 0 -1.2 67 67
IL17F -0.11 0.34 -9999 0 -0.72 68 68
IL12B -0.003 0.1 -9999 0 -0.55 10 10
STAT1 (dimer) -0.25 0.58 -9999 0 -1.3 77 77
CD4 -0.2 0.5 -9999 0 -1.2 67 67
IL23 -0.24 0.53 -9999 0 -1.2 74 74
IL23R -0.006 0.098 -9999 0 -10000 0 0
IL1B -0.25 0.59 -9999 0 -1.4 68 68
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.21 0.5 -9999 0 -1.1 72 72
TYK2 0.013 0.022 -9999 0 -10000 0 0
STAT4 -0.031 0.15 -9999 0 -0.45 39 39
STAT3 0.013 0 -9999 0 -10000 0 0
IL18RAP -0.03 0.18 -9999 0 -0.82 20 20
IL12RB1 -0.022 0.12 -9999 0 -0.47 13 13
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
IL12Rbeta1/TYK2 -0.01 0.092 -9999 0 -0.7 3 3
IL23R/JAK2 -0.003 0.12 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.26 0.62 -9999 0 -1.4 77 77
natural killer cell activation 0.002 0.009 -9999 0 -10000 0 0
JAK2 0.021 0.026 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.013 0.004 -9999 0 -10000 0 0
RELA 0.013 0.004 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.22 0.5 -9999 0 -1.1 74 74
ALOX12B -0.22 0.51 -9999 0 -1.2 69 69
CXCL1 -0.23 0.53 -9999 0 -1.2 76 76
T cell proliferation -0.26 0.62 -9999 0 -1.4 77 77
NFKBIA 0.013 0.004 -9999 0 -10000 0 0
IL17A -0.067 0.28 -9999 0 -0.58 51 51
PI3K -0.31 0.48 -9999 0 -1.2 78 78
IFNG -0.021 0.055 -9999 0 -0.13 63 63
STAT3 (dimer) -0.29 0.45 -9999 0 -1.1 74 74
IL18R1 -0.032 0.15 -9999 0 -0.42 41 41
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.33 -9999 0 -0.76 47 47
IL18/IL18R -0.074 0.19 -9999 0 -0.58 40 40
macrophage activation -0.015 0.018 -9999 0 -0.044 75 75
TNF -0.28 0.62 -9999 0 -1.4 83 83
STAT3/STAT4 -0.32 0.49 -9999 0 -1.2 79 79
STAT4 (dimer) -0.26 0.59 -9999 0 -1.3 79 79
IL18 -0.041 0.16 -9999 0 -0.42 50 50
IL19 -0.21 0.5 -9999 0 -1.2 65 65
STAT5A (dimer) -0.24 0.58 -9999 0 -1.3 76 76
STAT1 0.006 0.048 -9999 0 -0.31 9 9
SOCS3 -0.054 0.23 -9999 0 -0.85 32 32
CXCL9 -0.3 0.63 -9999 0 -1.4 92 92
MPO -0.21 0.52 -9999 0 -1.1 75 75
positive regulation of humoral immune response -0.26 0.62 -9999 0 -1.4 77 77
IL23/IL23R/JAK2/TYK2 -0.31 0.75 -9999 0 -1.6 76 76
IL6 -0.35 0.67 -9999 0 -1.4 108 108
STAT5A 0.013 0 -9999 0 -10000 0 0
IL2 0.001 0.017 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.009 -9999 0 -10000 0 0
CD3E -0.24 0.58 -9999 0 -1.3 78 78
keratinocyte proliferation -0.26 0.62 -9999 0 -1.4 77 77
NOS2 -0.22 0.51 -9999 0 -1.1 73 73
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.61 67 67
FYN -0.11 0.35 -10000 0 -0.79 73 73
LAT/GRAP2/SLP76 -0.13 0.28 -10000 0 -0.66 77 77
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.055 0.22 -10000 0 -0.47 77 77
B2M 0.012 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.05 -10000 0 -0.19 9 9
MAP3K8 0 0.1 -10000 0 -0.85 6 6
mol:Ca2+ -0.032 0.051 -10000 0 -0.13 88 88
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.33 -10000 0 -0.72 79 79
TRPV6 -0.18 0.35 -10000 0 -0.82 91 91
CD28 -0.048 0.2 -10000 0 -0.68 33 33
SHC1 -0.12 0.35 -10000 0 -0.8 73 73
receptor internalization -0.14 0.39 -10000 0 -0.83 81 81
PRF1 -0.12 0.35 -10000 0 -0.88 60 60
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.038 0.18 -10000 0 -0.38 76 76
LAT -0.12 0.35 -10000 0 -0.82 73 73
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.097 0.28 -10000 0 -0.74 60 60
CD3E -0.074 0.26 -10000 0 -0.77 46 46
CD3G -0.15 0.33 -10000 0 -0.81 80 80
RASGRP2 0 0.03 -10000 0 -0.19 4 4
RASGRP1 -0.052 0.22 -10000 0 -0.47 78 78
HLA-A 0.011 0.017 -10000 0 -10000 0 0
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.068 -10000 0 -0.12 57 57
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.057 0.09 -10000 0 -0.26 49 49
PRKCA -0.066 0.14 -10000 0 -0.32 79 79
GRAP2 -0.046 0.22 -10000 0 -0.8 30 30
mol:IP3 -0.053 0.24 0.28 71 -0.46 75 146
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.16 0.43 -10000 0 -0.99 69 69
ORAI1 0.088 0.16 0.4 84 -10000 0 84
CSK -0.12 0.36 -10000 0 -0.82 73 73
B7 family/CD28 -0.2 0.36 -10000 0 -0.76 96 96
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.43 -10000 0 -0.94 80 80
PTPN6 -0.13 0.36 -10000 0 -0.85 70 70
VAV1 -0.13 0.35 -10000 0 -0.8 76 76
Monovalent TCR/CD3 -0.17 0.43 -10000 0 -0.76 101 101
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.85 71 71
PAG1 -0.12 0.36 -10000 0 -0.82 73 73
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.43 -10000 0 -0.95 78 78
CD80 -0.086 0.27 -10000 0 -0.83 48 48
CD86 -0.011 0.11 -10000 0 -0.41 23 23
PDK1/CARD11/BCL10/MALT1 -0.07 0.11 -10000 0 -0.3 59 59
HRAS 0.012 0.023 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.3 -10000 0 -0.65 80 80
CD8A -0.049 0.22 -10000 0 -0.86 29 29
CD8B -0.096 0.28 -10000 0 -0.75 59 59
PTPRC -0.036 0.18 -10000 0 -0.6 32 32
PDK1/PKC theta -0.071 0.27 -10000 0 -0.59 76 76
CSK/PAG1 -0.11 0.35 -10000 0 -0.82 68 68
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.014 0.016 -10000 0 -10000 0 0
GRAP2/SLP76 -0.16 0.33 -10000 0 -0.78 78 78
STIM1 0.047 0.083 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.092 -10000 0 -0.18 45 45
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.44 -10000 0 -0.94 81 81
mol:DAG -0.072 0.18 -10000 0 -0.41 78 78
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.029 0.18 -10000 0 -0.65 26 26
cytotoxic T cell degranulation -0.11 0.33 -10000 0 -0.83 60 60
RAP1A/GTP -0.003 0.009 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.076 0.26 -10000 0 -0.57 78 78
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.083 0.3 0.3 65 -0.62 77 142
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.025 0.17 -10000 0 -0.67 23 23
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.26 -10000 0 -0.62 78 78
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.011 0.043 -10000 0 -0.85 1 1
CD8 heterodimer -0.11 0.3 -10000 0 -0.78 62 62
CARD11 -0.076 0.17 -10000 0 -0.36 98 98
PRKCB -0.059 0.13 -10000 0 -0.32 67 67
PRKCE -0.052 0.12 -10000 0 -0.3 60 60
PRKCQ -0.095 0.31 -10000 0 -0.69 77 77
LCP2 0.007 0.045 -10000 0 -0.31 8 8
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.041 0.19 -10000 0 -0.4 77 77
IKK complex 0.012 0.07 -10000 0 -0.12 43 43
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.017 0.14 -10000 0 -0.3 56 56
PDPK1 -0.048 0.21 -10000 0 -0.45 75 75
TCR/CD3/MHC I/CD8/Fyn -0.17 0.46 -10000 0 -1.1 73 73
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.29 0.34 -9999 0 -0.63 187 187
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.06 0.23 -9999 0 -0.73 40 40
SMAD9 -0.22 0.29 -9999 0 -0.61 132 132
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.1 0.21 -9999 0 -0.38 139 139
BMP7/USAG1 -0.34 0.33 -9999 0 -0.66 213 213
SMAD5/SKI -0.09 0.2 -9999 0 -0.54 23 23
SMAD1 0.017 0.046 -9999 0 -10000 0 0
BMP2 -0.014 0.15 -9999 0 -0.85 13 13
SMAD1/SMAD1/SMAD4 -0.002 0.002 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.28 0.41 -9999 0 -0.85 139 139
BMPR1A-1B/BAMBI -0.2 0.28 -9999 0 -0.58 139 139
AHSG -0.014 0.078 -9999 0 -0.31 26 26
CER1 0.001 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.037 0.14 -9999 0 -0.58 25 25
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.083 0.2 -9999 0 -0.65 27 27
BMP2-4 (homodimer) -0.043 0.16 -9999 0 -0.66 25 25
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.18 0.25 -9999 0 -0.52 139 139
RGMA -0.021 0.17 -9999 0 -0.85 16 16
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.093 0.19 -9999 0 -0.58 25 25
BMP2-4/USAG1 -0.33 0.31 -9999 0 -0.6 227 227
SMAD6/SMURF1/SMAD5 -0.09 0.2 -9999 0 -0.54 23 23
SOSTDC1 -0.44 0.43 -9999 0 -0.85 214 214
BMP7/BMPR2/BMPR1A-1B -0.18 0.25 -9999 0 -0.52 139 139
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0 -9999 0 -10000 0 0
HFE2 0.001 0.032 -9999 0 -0.31 4 4
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.048 0.16 -9999 0 -0.58 32 32
SMAD5/SMAD5/SMAD4 -0.09 0.2 -9999 0 -0.54 23 23
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.098 0.14 -9999 0 -0.49 25 25
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.013 0.049 -9999 0 -10000 0 0
SMAD1/SKI 0.024 0.044 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.047 0.14 -9999 0 -0.59 25 25
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.36 -9999 0 -0.74 115 115
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.01 0.074 -9999 0 -0.57 7 7
BMPR1A-1B (homodimer) -0.22 0.31 -9999 0 -0.66 139 139
CHRDL1 -0.6 0.39 -9999 0 -0.85 290 290
ENDOFIN/SMAD1 0.024 0.044 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.007 0.009 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.076 -9999 0 -0.34 17 17
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.44 0.29 -9999 0 -0.61 295 295
BMP2-4/GREM1 -0.17 0.29 -9999 0 -0.64 104 104
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.19 0.28 -9999 0 -0.57 132 132
SMAD1/SMAD6 0.024 0.044 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.07 0.16 -9999 0 -0.5 25 25
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.024 0.044 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A -0.002 0.11 -9999 0 -0.85 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.21 0.33 -9999 0 -0.82 73 73
CHRD -0.004 0.12 -9999 0 -0.85 8 8
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.098 0.2 -9999 0 -0.62 25 25
BMP4 -0.016 0.15 -9999 0 -0.69 17 17
FST -0.21 0.37 -9999 0 -0.85 103 103
BMP2-4/NOG -0.083 0.2 -9999 0 -0.58 55 55
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.16 0.23 -9999 0 -0.48 139 139
HIF-1-alpha transcription factor network

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
PKM2 -0.2 0.43 -9999 0 -1 39 39
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.35 -9999 0 -0.84 91 91
SMAD4 0.015 0.002 -9999 0 -10000 0 0
ID2 -0.2 0.43 -9999 0 -1 40 40
AP1 -0.3 0.47 -9999 0 -0.98 124 124
ABCG2 -0.2 0.43 -9999 0 -1 39 39
HIF1A -0.014 0.066 -9999 0 -10000 0 0
TFF3 -0.6 0.53 -9999 0 -1.1 147 147
GATA2 0.014 0.017 -9999 0 -0.31 1 1
AKT1 -0.043 0.1 -9999 0 -10000 0 0
response to hypoxia -0.064 0.11 -9999 0 -0.24 21 21
MCL1 -0.2 0.43 -9999 0 -1 39 39
NDRG1 -0.2 0.43 -9999 0 -0.99 42 42
SERPINE1 -0.22 0.43 -9999 0 -1 44 44
FECH -0.2 0.43 -9999 0 -0.99 43 43
FURIN -0.2 0.43 -9999 0 -0.99 42 42
NCOA2 -0.049 0.22 -9999 0 -0.85 30 30
EP300 -0.069 0.18 -9999 0 -0.34 93 93
HMOX1 -0.21 0.43 -9999 0 -1 42 42
BHLHE40 -0.21 0.43 -9999 0 -1 44 44
BHLHE41 -0.2 0.43 -9999 0 -1 42 42
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.036 -9999 0 -10000 0 0
ENG 0.041 0.091 -9999 0 -10000 0 0
JUN -0.18 0.36 -9999 0 -0.85 93 93
RORA -0.2 0.43 -9999 0 -1 42 42
ABCB1 -0.071 0.16 -9999 0 -1.5 4 4
TFRC -0.2 0.43 -9999 0 -1 34 34
CXCR4 -0.2 0.43 -9999 0 -1 39 39
TF -0.27 0.51 -9999 0 -1.1 73 73
CITED2 -0.24 0.47 -9999 0 -1.1 56 56
HIF1A/ARNT -0.31 0.39 -9999 0 -1 61 61
LDHA -0.041 0.05 -9999 0 -10000 0 0
ETS1 -0.2 0.43 -9999 0 -1 39 39
PGK1 -0.2 0.43 -9999 0 -0.99 42 42
NOS2 -0.22 0.44 -9999 0 -1 45 45
ITGB2 -0.21 0.43 -9999 0 -1 44 44
ALDOA -0.2 0.43 -9999 0 -1 39 39
Cbp/p300/CITED2 -0.34 0.51 -9999 0 -1.1 91 91
FOS -0.21 0.38 -9999 0 -0.85 106 106
HK2 -0.21 0.43 -9999 0 -0.99 45 45
SP1 0.022 0.006 -9999 0 -10000 0 0
GCK -0.42 0.73 -9999 0 -1.5 118 118
HK1 -0.2 0.43 -9999 0 -0.99 42 42
NPM1 -0.2 0.43 -9999 0 -0.99 42 42
EGLN1 -0.2 0.43 -9999 0 -1 34 34
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.2 0.43 -9999 0 -0.99 42 42
SMAD3 0.015 0.002 -9999 0 -10000 0 0
EDN1 -0.17 0.32 -9999 0 -0.76 53 53
IGFBP1 -0.22 0.43 -9999 0 -1 40 40
VEGFA -0.17 0.39 -9999 0 -0.77 61 61
HIF1A/JAB1 -0.012 0.02 -9999 0 -10000 0 0
CP -0.38 0.57 -9999 0 -1.1 110 110
CXCL12 -0.25 0.49 -9999 0 -1.1 60 60
COPS5 0.014 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.2 0.43 -9999 0 -1 39 39
EGLN3 -0.22 0.44 -9999 0 -1 46 46
CA9 -0.22 0.43 -9999 0 -1 41 41
TERT -0.21 0.42 -9999 0 -1 43 43
ENO1 -0.2 0.43 -9999 0 -0.99 42 42
PFKL -0.2 0.43 -9999 0 -1 39 39
NCOA1 0.013 0 -9999 0 -10000 0 0
ADM -0.24 0.45 -9999 0 -1 45 45
ARNT -0.014 0.066 -9999 0 -10000 0 0
HNF4A -0.027 0.065 -9999 0 -0.34 9 9
ADFP -0.22 0.42 -9999 0 -0.94 56 56
SLC2A1 -0.17 0.38 -9999 0 -0.76 65 65
LEP -0.22 0.43 -9999 0 -1 39 39
HIF1A/ARNT/Cbp/p300 -0.31 0.36 -9999 0 -0.88 92 92
EPO -0.14 0.31 -9999 0 -0.96 13 13
CREBBP -0.069 0.18 -9999 0 -0.35 80 80
HIF1A/ARNT/Cbp/p300/HDAC7 -0.29 0.34 -9999 0 -0.86 81 81
PFKFB3 -0.2 0.43 -9999 0 -1 42 42
NT5E -0.21 0.43 -9999 0 -1 42 42
Coregulation of Androgen receptor activity

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
NRIP1 -0.014 0.063 -10000 0 -0.36 10 10
SVIL -0.006 0.03 -10000 0 -10000 0 0
ZNF318 0.061 0.083 -10000 0 -10000 0 0
JMJD2C -0.064 0.069 -10000 0 -0.12 232 232
T-DHT/AR/Ubc9 -0.29 0.3 -10000 0 -0.65 170 170
CARM1 0.011 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.01 -10000 0 -10000 0 0
CTNNB1 -0.002 0.023 -10000 0 -10000 0 0
AKT1 0.025 0.019 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.025 0.019 -10000 0 -10000 0 0
MAK 0.049 0.13 -10000 0 -0.82 5 5
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.008 0.052 -10000 0 -0.85 1 1
GSN -0.005 0.03 -10000 0 -10000 0 0
NCOA2 -0.052 0.22 -10000 0 -0.85 30 30
NCOA6 -0.005 0.028 -10000 0 -10000 0 0
DNA-PK 0.057 0.083 0.26 1 -10000 0 1
NCOA4 0.011 0.004 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.013 0.15 -10000 0 -1.1 5 5
XRCC5 0.024 0.017 -10000 0 -10000 0 0
UBE3A -0.015 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.32 0.33 -10000 0 -0.68 174 174
FHL2 -0.16 0.38 -10000 0 -1.4 33 33
RANBP9 -0.005 0.028 -10000 0 -10000 0 0
JMJD1A 0.003 0.037 -10000 0 -0.13 28 28
CDK6 0.012 0.043 -10000 0 -0.85 1 1
TGFB1I1 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.3 0.31 -10000 0 -0.66 171 171
XRCC6 0.024 0.017 -10000 0 -10000 0 0
T-DHT/AR -0.34 0.33 -10000 0 -0.66 191 191
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.045 0.05 -10000 0 -10000 0 0
BRCA1 -0.006 0.03 -10000 0 -10000 0 0
TCF4 0.035 0.034 -10000 0 -10000 0 0
CDKN2A -0.1 0.16 -10000 0 -0.31 117 117
SRF 0.028 0.039 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -1.1 4 4
KLK3 -0.43 0.71 -10000 0 -1.6 111 111
TMF1 0.009 0.006 -10000 0 -10000 0 0
HNRNPA1 0.03 0.027 -10000 0 -10000 0 0
AOF2 -0.021 0.033 -10000 0 -0.075 111 111
APPL1 0.051 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.28 0.31 -10000 0 -0.64 170 170
AR -0.39 0.43 -10000 0 -0.9 170 170
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.03 0.027 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.024 0.017 -10000 0 -10000 0 0
PA2G4 0.035 0.035 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.26 0.29 -10000 0 -0.6 170 170
RPS6KA3 -0.005 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.29 0.31 -10000 0 -0.65 170 170
LATS2 0.03 0.027 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.26 0.29 -10000 0 -0.59 170 170
Cyclin D3/CDK11 p58 0 0 -10000 0 -10000 0 0
VAV3 -0.01 0.087 -10000 0 -0.86 4 4
KLK2 -0.78 0.64 -10000 0 -1.3 231 231
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.67 176 176
TMPRSS2 -0.18 0.31 -10000 0 -1.2 28 28
CCND1 0 0.053 -10000 0 -0.31 11 11
PIAS1 -0.015 0.046 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.041 -10000 0 -0.083 137 137
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.034 0.076 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.29 0.31 -10000 0 -0.65 170 170
CMTM2 0.015 0.024 -10000 0 -0.31 2 2
SNURF -0.023 0.17 -10000 0 -0.85 17 17
ZMIZ1 -0.011 0.037 -10000 0 -10000 0 0
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.03 0.027 -10000 0 -10000 0 0
FKBP4 -0.005 0.028 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.042 0.11 -9999 0 -0.51 10 10
EGFR 0.002 0.095 -9999 0 -0.85 5 5
EPHA2 0.011 0.028 -9999 0 -0.31 3 3
USP6 0.011 0.028 -9999 0 -0.31 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.099 0.23 -9999 0 -0.66 60 60
ARRB2 -0.043 0.15 -9999 0 -0.46 48 48
mol:GTP 0.021 0.011 -9999 0 -10000 0 0
ARRB1 0.011 0.043 -9999 0 -0.85 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.009 0.06 -9999 0 -0.85 2 2
EGF -0.11 0.3 -9999 0 -0.8 61 61
somatostatin receptor activity 0 0 -9999 0 -0.001 113 113
ARAP2 0.011 0.043 -9999 0 -0.85 1 1
mol:GDP -0.12 0.15 -9999 0 -0.31 117 117
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 104 104
ITGA2B -0.088 0.28 -9999 0 -0.85 48 48
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.011 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.18 0.25 -9999 0 -0.72 62 62
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.31 115 115
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.086 0.2 -9999 0 -0.57 60 60
ADRB2 -0.008 0.13 -9999 0 -0.85 10 10
receptor agonist activity 0 0 -9999 0 0 131 131
actin filament binding 0 0 -9999 0 -0.001 113 113
SRC 0.012 0.016 -9999 0 -0.31 1 1
ITGB3 -0.014 0.15 -9999 0 -0.85 13 13
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 110 110
ARF6/GDP 0.001 0.069 -9999 0 -0.34 2 2
ARF6/GDP/GULP/ACAP1 -0.19 0.2 -9999 0 -0.51 97 97
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.077 0.2 -9999 0 -0.57 55 55
ACAP1 0.001 0.078 -9999 0 -0.4 12 12
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.085 0.23 -9999 0 -0.7 48 48
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.12 0.31 -9999 0 -0.85 62 62
CYTH3 0.01 0.034 -9999 0 -0.67 1 1
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 109 109
endosomal lumen acidification 0 0 -9999 0 -0.001 126 126
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.33 -9999 0 -0.85 74 74
GNAQ/ARNO 0.008 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 39 39
MET -0.12 0.16 -9999 0 -10000 0 0
GNA14 -0.18 0.36 -9999 0 -0.85 92 92
GNA15 -0.012 0.094 -9999 0 -0.33 30 30
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 115 115
GNA11 0.004 0.085 -9999 0 -0.85 4 4
LHCGR -0.098 0.28 -9999 0 -0.79 54 54
AGTR1 -0.33 0.42 -9999 0 -0.85 164 164
desensitization of G-protein coupled receptor protein signaling pathway -0.085 0.22 -9999 0 -0.7 48 48
IPCEF1/ARNO -0.064 0.16 -9999 0 -0.45 60 60
alphaIIb/beta3 Integrin -0.096 0.25 -9999 0 -0.72 55 55
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.13 0.41 -9999 0 -1.4 39 39
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.04 0.11 -9999 0 -0.33 39 39
ATF2/c-Jun -0.22 0.43 -9999 0 -1 93 93
MAPK11 -0.04 0.11 -9999 0 -0.39 16 16
MITF -0.034 0.14 -9999 0 -0.4 39 39
MAPKAPK5 -0.034 0.14 -9999 0 -0.4 39 39
KRT8 -0.034 0.14 -9999 0 -0.4 39 39
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.055 0.17 -9999 0 -0.51 39 39
CEBPB -0.034 0.14 -9999 0 -0.4 39 39
SLC9A1 -0.034 0.14 -9999 0 -0.4 39 39
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.07 0.18 -9999 0 -0.42 58 58
p38alpha-beta/MNK1 -0.031 0.14 -9999 0 -0.5 16 16
JUN -0.22 0.43 -9999 0 -0.99 93 93
PPARGC1A -0.24 0.25 -9999 0 -0.47 216 216
USF1 -0.034 0.14 -9999 0 -0.4 39 39
RAB5/GDP/GDI1 -0.041 0.086 -9999 0 -0.35 16 16
NOS2 -0.055 0.16 -9999 0 -0.55 16 16
DDIT3 -0.036 0.14 -9999 0 -0.41 39 39
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.017 0.11 -9999 0 -0.39 16 16
p38alpha-beta/HBP1 -0.031 0.14 -9999 0 -0.5 16 16
CREB1 -0.049 0.16 -9999 0 -0.42 45 45
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.019 0.12 -9999 0 -0.44 16 16
RPS6KA4 -0.034 0.14 -9999 0 -0.4 39 39
PLA2G4A -0.061 0.22 -9999 0 -0.63 43 43
GDI1 -0.034 0.14 -9999 0 -0.4 39 39
TP53 -0.044 0.16 -9999 0 -0.5 39 39
RPS6KA5 -0.073 0.19 -9999 0 -0.46 68 68
ESR1 -0.07 0.2 -9999 0 -0.52 51 51
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.034 0.14 -9999 0 -0.4 39 39
MEF2A -0.034 0.14 -9999 0 -0.4 39 39
EIF4EBP1 -0.05 0.16 -9999 0 -0.42 45 45
KRT19 -0.11 0.22 -9999 0 -0.56 54 54
ELK4 -0.034 0.14 -9999 0 -0.4 39 39
ATF6 -0.034 0.14 -9999 0 -0.4 39 39
ATF1 -0.049 0.16 -9999 0 -0.42 45 45
p38alpha-beta/MAPKAPK2 -0.031 0.14 -9999 0 -0.5 16 16
p38alpha-beta/MAPKAPK3 -0.031 0.14 -9999 0 -0.5 16 16
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.1 0.22 -10000 0 -0.58 70 70
cell-cell adhesion 0.16 0.19 0.56 8 -10000 0 8
Ephrin B/EPHB2/RasGAP -0.013 0.066 -10000 0 -0.48 7 7
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.081 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.22 0.28 -10000 0 -0.58 154 154
HRAS/GDP -0.14 0.18 -10000 0 -0.5 10 10
Ephrin B/EPHB1/GRB7 -0.21 0.25 -10000 0 -0.52 157 157
Endophilin/SYNJ1 0.026 0.069 -10000 0 -0.45 7 7
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.19 0.24 -10000 0 -0.5 157 157
endothelial cell migration -0.001 0.024 -10000 0 -0.49 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.037 0.12 -10000 0 -0.31 63 63
PAK1 0.034 0.071 -10000 0 -0.46 7 7
HRAS 0.012 0.023 -10000 0 -0.31 2 2
RRAS 0.026 0.071 -10000 0 -0.46 7 7
DNM1 -0.026 0.18 -10000 0 -0.82 19 19
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.25 -10000 0 -0.47 157 157
lamellipodium assembly -0.16 0.19 -10000 0 -0.56 8 8
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.18 -10000 0 -0.34 154 154
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.007 0.074 -10000 0 -0.85 3 3
EPHB3 -0.19 0.16 -10000 0 -10000 0 0
EPHB1 -0.31 0.42 -10000 0 -0.85 154 154
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.07 0.18 -10000 0 -0.47 8 8
Ephrin B/EPHB2 -0.013 0.068 -10000 0 -0.49 7 7
Ephrin B/EPHB3 -0.086 0.082 -10000 0 -0.6 4 4
JNK cascade -0.16 0.25 -10000 0 -0.48 156 156
Ephrin B/EPHB1 -0.2 0.24 -10000 0 -0.5 157 157
RAP1/GDP -0.054 0.16 -10000 0 -0.5 2 2
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.008 0.1 -10000 0 -0.42 20 20
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.2 0.26 -10000 0 -0.53 156 156
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.2 -10000 0 -0.59 8 8
Rap1/GTP -0.16 0.19 -10000 0 -0.57 8 8
axon guidance -0.1 0.22 -10000 0 -0.58 70 70
MAPK3 -0.078 0.17 -10000 0 -0.38 8 8
MAPK1 -0.078 0.17 -10000 0 -0.38 8 8
Rac1/GDP -0.045 0.17 -10000 0 -0.44 6 6
actin cytoskeleton reorganization -0.11 0.14 -10000 0 -0.56 2 2
CDC42/GDP -0.045 0.17 -10000 0 -0.44 6 6
PI3K -0.001 0.024 -10000 0 -0.49 1 1
EFNA5 -0.13 0.32 -10000 0 -0.84 69 69
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.052 -10000 0 -0.34 7 7
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.15 0.19 -10000 0 -0.55 9 9
PTK2 0.042 0.053 -10000 0 -10000 0 0
MAP4K4 -0.16 0.26 -10000 0 -0.48 156 156
SRC 0.012 0.016 -10000 0 -0.31 1 1
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.071 0.18 -10000 0 -0.56 2 2
MAP2K1 -0.091 0.18 -10000 0 -0.4 8 8
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.2 0.26 -10000 0 -0.52 156 156
cell migration -0.086 0.19 -10000 0 -0.35 47 47
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.071 -10000 0 -0.46 7 7
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.036 0.19 -10000 0 -0.46 62 62
HRAS/GTP -0.17 0.21 -10000 0 -0.6 9 9
Ephrin B1/EPHB1-2 -0.2 0.26 -10000 0 -0.53 156 156
cell adhesion mediated by integrin 0.012 0.07 0.52 4 -10000 0 4
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.18 0.22 -10000 0 -0.46 159 159
RAC1-CDC42/GTP -0.21 0.22 -10000 0 -0.51 119 119
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.054 0.16 -10000 0 -0.5 2 2
ruffle organization -0.12 0.23 -10000 0 -0.57 8 8
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.012 0.13 -10000 0 -0.48 23 23
Ephrin B/EPHB2/KALRN -0.013 0.066 -10000 0 -0.48 7 7
ROCK1 -0.076 0.081 -10000 0 -10000 0 0
RAS family/GDP -0.086 0.11 -10000 0 -0.54 2 2
Rac1/GTP -0.16 0.2 -10000 0 -0.61 8 8
Ephrin B/EPHB1/Src/Paxillin -0.11 0.19 -10000 0 -0.34 157 157
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 -0.02 0.15 -10000 0 -0.41 24 24
TBX21 -0.12 0.44 -10000 0 -1.1 54 54
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.015 0.02 -10000 0 -10000 0 0
IL12RB1 -0.019 0.12 -10000 0 -0.45 16 16
GADD45B -0.1 0.4 -10000 0 -0.99 50 50
IL12RB2 -0.016 0.16 -10000 0 -0.73 18 18
GADD45G -0.079 0.35 -10000 0 -0.9 40 40
natural killer cell activation 0.002 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.037 0.16 -10000 0 -0.41 50 50
IL2RA -0.044 0.2 -10000 0 -0.59 39 39
IFNG -0.11 0.29 -10000 0 -0.76 65 65
STAT3 (dimer) -0.075 0.32 -10000 0 -0.74 55 55
HLA-DRB5 -0.043 0.14 -10000 0 -0.35 62 62
FASLG -0.15 0.49 -10000 0 -1.2 61 61
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.88 55 55
CD4 0.001 0.056 -10000 0 -0.32 12 12
SOCS1 0.011 0.028 -10000 0 -0.31 3 3
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.1 0.28 -10000 0 -0.74 60 60
CD3E -0.077 0.25 -10000 0 -0.76 46 46
CD3G -0.15 0.33 -10000 0 -0.82 80 80
IL12Rbeta2/JAK2 -0.001 0.13 -10000 0 -0.66 14 14
CCL3 -0.11 0.43 -10000 0 -1.1 43 43
CCL4 -0.16 0.52 -10000 0 -1.3 55 55
HLA-A 0.011 0.018 -10000 0 -10000 0 0
IL18/IL18R -0.037 0.2 -10000 0 -0.59 39 39
NOS2 -0.093 0.35 -10000 0 -0.86 46 46
IL12/IL12R/TYK2/JAK2/SPHK2 -0.02 0.15 -10000 0 -0.42 22 22
IL1R1 -0.089 0.37 -10000 0 -0.97 43 43
IL4 0.001 0.028 -10000 0 -0.34 1 1
JAK2 0.015 0.02 -10000 0 -10000 0 0
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.25 0.58 -10000 0 -1.2 89 89
RAB7A -0.046 0.3 -10000 0 -0.68 46 46
lysosomal transport -0.041 0.28 -10000 0 -0.64 48 48
FOS -0.41 0.65 -10000 0 -1.3 130 130
STAT4 (dimer) -0.083 0.35 -10000 0 -0.83 51 51
STAT5A (dimer) -0.22 0.36 -10000 0 -0.87 79 79
GZMA -0.1 0.4 -10000 0 -1 49 49
GZMB -0.1 0.39 -10000 0 -0.99 47 47
HLX 0.004 0.053 -10000 0 -0.31 11 11
LCK -0.11 0.42 -10000 0 -0.99 57 57
TCR/CD3/MHC II/CD4 -0.19 0.36 -10000 0 -0.64 110 110
IL2/IL2R -0.08 0.23 -10000 0 -0.74 36 36
MAPK14 -0.076 0.35 -10000 0 -0.79 58 58
CCR5 -0.1 0.4 -10000 0 -1.1 40 40
IL1B -0.057 0.24 -10000 0 -0.8 37 37
STAT6 -0.005 0.11 -10000 0 -0.25 13 13
STAT4 -0.031 0.15 -10000 0 -0.45 39 39
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.048 -10000 0 -0.31 9 9
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.001 0.098 -10000 0 -0.57 9 9
CD8A -0.049 0.22 -10000 0 -0.86 29 29
CD8B -0.097 0.28 -10000 0 -0.74 59 59
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.02 0.15 0.41 24 -10000 0 24
IL2RB -0.015 0.14 -10000 0 -0.56 20 20
proteasomal ubiquitin-dependent protein catabolic process -0.071 0.32 -10000 0 -0.75 51 51
IL2RG -0.048 0.2 -10000 0 -0.56 43 43
IL12 -0.055 0.22 -10000 0 -0.67 43 43
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.032 0.17 -10000 0 -0.65 26 26
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.071 0.26 -10000 0 -0.82 42 42
IL12/IL12R/TYK2/JAK2 -0.12 0.47 -10000 0 -1.1 58 58
MAP2K3 -0.078 0.35 -10000 0 -0.79 56 56
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.084 0.36 -10000 0 -0.82 56 56
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.031 0.14 -10000 0 -0.41 41 41
IL18RAP -0.026 0.18 -10000 0 -0.83 20 20
IL12Rbeta1/TYK2 -0.004 0.093 -10000 0 -0.68 3 3
EOMES -0.16 0.45 -10000 0 -1.5 39 39
STAT1 (dimer) -0.14 0.37 -10000 0 -0.77 79 79
T cell proliferation -0.055 0.27 -10000 0 -0.6 50 50
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.028 0.15 -10000 0 -0.42 41 41
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.25 -10000 0 -0.68 54 54
ATF2 -0.072 0.33 -10000 0 -0.74 53 53
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.039 -9999 0 -0.31 6 6
CCL5 -0.047 0.21 -9999 0 -0.85 26 26
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.17 -9999 0 -0.49 43 43
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.095 0.16 -9999 0 -0.69 17 17
Syndecan-1/Syntenin -0.095 0.16 -9999 0 -0.69 17 17
MAPK3 -0.072 0.15 -9999 0 -0.63 16 16
HGF/MET -0.18 0.25 -9999 0 -0.72 62 62
TGFB1/TGF beta receptor Type II 0.008 0.039 -9999 0 -0.31 6 6
BSG 0.012 0.016 -9999 0 -0.31 1 1
keratinocyte migration -0.094 0.16 -9999 0 -0.67 17 17
Syndecan-1/RANTES -0.13 0.23 -9999 0 -0.75 38 38
Syndecan-1/CD147 -0.094 0.15 -9999 0 -0.68 16 16
Syndecan-1/Syntenin/PIP2 -0.1 0.15 -9999 0 -0.66 17 17
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.1 0.14 -9999 0 -0.64 17 17
MMP7 -0.18 0.23 -9999 0 -0.37 203 203
HGF -0.12 0.31 -9999 0 -0.85 62 62
Syndecan-1/CASK -0.1 0.16 -9999 0 -0.47 43 43
Syndecan-1/HGF/MET -0.22 0.24 -9999 0 -0.66 73 73
regulation of cell adhesion -0.062 0.14 -9999 0 -0.6 16 16
HPSE -0.022 0.15 -9999 0 -0.85 10 10
positive regulation of cell migration -0.11 0.17 -9999 0 -0.49 43 43
SDC1 -0.11 0.17 -9999 0 -0.5 43 43
Syndecan-1/Collagen -0.11 0.17 -9999 0 -0.49 43 43
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.12 0.16 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.084 0.25 -9999 0 -0.85 34 34
MAPK1 -0.072 0.15 -9999 0 -0.63 16 16
homophilic cell adhesion -0.11 0.17 -9999 0 -0.49 43 43
MMP1 -0.15 0.16 -9999 0 -0.31 201 201
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.081 0.061 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.18 -9999 0 -0.66 34 34
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.61 60 60
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.66 34 34
CCL5 -0.047 0.21 -9999 0 -0.85 26 26
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG 0.002 0.025 -9999 0 -0.31 2 2
ADAM12 -0.072 0.14 -9999 0 -0.31 106 106
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.066 0.046 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.17 0.22 -9999 0 -0.7 42 42
Syndecan-4/CXCL12/CXCR4 -0.18 0.22 -9999 0 -0.65 60 60
Syndecan-4/Laminin alpha3 -0.15 0.19 -9999 0 -0.67 37 37
MDK -0.087 0.15 -9999 0 -0.32 124 124
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.65 36 36
Syndecan-4/Midkine -0.18 0.19 -9999 0 -0.67 34 34
FZD7 0.005 0.085 -9999 0 -0.85 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 35 35
THBS1 -0.009 0.082 -9999 0 -0.31 28 28
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.68 34 34
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.61 60 60
Syndecan-4/TACI -0.26 0.27 -9999 0 -0.64 114 114
CXCR4 0.011 0.028 -9999 0 -0.31 3 3
cell adhesion -0.077 0.1 -9999 0 -0.46 24 24
Syndecan-4/Dynamin -0.13 0.18 -9999 0 -0.66 34 34
Syndecan-4/TSP1 -0.14 0.18 -9999 0 -0.66 34 34
Syndecan-4/GIPC -0.13 0.18 -9999 0 -0.66 34 34
Syndecan-4/RANTES -0.16 0.23 -9999 0 -0.78 39 39
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.053 0.23 -9999 0 -0.83 32 32
LAMA3 -0.023 0.16 -9999 0 -0.56 26 26
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.003 0.2 -9999 0 -0.78 24 24
Syndecan-4/alpha-Actinin -0.13 0.18 -9999 0 -0.66 34 34
TFPI -0.035 0.2 -9999 0 -0.85 23 23
F2 -0.002 0.04 -9999 0 -0.32 5 5
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.18 0.22 -9999 0 -0.69 44 44
ACTN1 0.012 0.016 -9999 0 -0.31 1 1
TNC -0.12 0.17 -9999 0 -0.33 161 161
Syndecan-4/CXCL12 -0.18 0.24 -9999 0 -0.68 61 61
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.082 0.27 -9999 0 -0.85 45 45
TNFRSF13B -0.22 0.38 -9999 0 -0.83 110 110
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.011 0.043 -9999 0 -0.85 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.66 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 295 295
cell migration -0.021 0.017 -9999 0 -10000 0 0
PRKCD 0.009 0.016 -9999 0 -10000 0 0
vasculogenesis -0.14 0.17 -9999 0 -0.63 34 34
SDC4 -0.15 0.19 -9999 0 -0.71 34 34
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.71 34 34
Syndecan-4/PI-4-5-P2/PKC alpha -0.052 0.036 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.18 -9999 0 -0.66 34 34
MMP9 -0.086 0.24 -9999 0 -0.85 34 34
Rac1/GTP -0.079 0.11 -9999 0 -0.47 24 24
cytoskeleton organization -0.13 0.17 -9999 0 -0.63 34 34
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.21 -9999 0 -0.66 50 50
Hedgehog signaling events mediated by Gli proteins

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
forebrain development -0.32 0.28 -9999 0 -0.56 213 213
GNAO1 -0.019 0.15 -9999 0 -0.72 16 16
SMO/beta Arrestin2 0.012 0.012 -9999 0 -10000 0 0
SMO 0.008 0.008 -9999 0 -10000 0 0
ARRB2 0.007 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.048 0.044 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.032 -9999 0 -0.52 1 1
GNAI1 0.01 0.005 -9999 0 -10000 0 0
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.25 0.19 -9999 0 -0.51 113 113
SAP30 0.012 0.043 -9999 0 -0.85 1 1
mol:GDP 0.008 0.008 -9999 0 -10000 0 0
MIM/GLI2A -0.009 0.044 -9999 0 -10000 0 0
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GLI2 0.033 0.063 -9999 0 -10000 0 0
GLI3 0.043 0.046 -9999 0 -10000 0 0
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.013 0 -9999 0 -10000 0 0
Gi family/GTP 0.009 0.065 -9999 0 -0.34 12 12
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.03 0.045 -9999 0 -10000 0 0
GLI2/Su(fu) 0.022 0.059 -9999 0 -10000 0 0
FOXA2 -0.69 0.67 -9999 0 -1.4 203 203
neural tube patterning -0.32 0.28 -9999 0 -0.56 213 213
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.018 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.008 0.044 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.32 0.28 -9999 0 -0.56 213 213
SUFU 0.017 0.017 -9999 0 -10000 0 0
LGALS3 -0.11 0.16 -9999 0 -0.31 149 149
catabolic process 0.064 0.061 -9999 0 -10000 0 0
GLI3A/CBP -0.2 0.2 -9999 0 -0.39 214 214
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.33 0.29 -9999 0 -0.57 213 213
RAB23 0.007 0.074 -9999 0 -0.85 3 3
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.036 0.077 -9999 0 -10000 0 0
GNAZ 0.01 0.005 -9999 0 -10000 0 0
RBBP4 0.014 0.001 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.037 0.058 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.015 0.055 -9999 0 -10000 0 0
PTCH1 -0.29 0.26 -9999 0 -0.62 113 113
MIM/GLI1 -0.46 0.39 -9999 0 -0.76 212 212
CREBBP -0.2 0.2 -9999 0 -0.39 214 214
Su(fu)/SIN3/HDAC complex 0.057 0.017 -9999 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.044 0.12 -9999 0 -0.55 15 15
alphaM/beta2 Integrin/GPIbA -0.057 0.15 -9999 0 -0.59 24 24
alphaM/beta2 Integrin/proMMP-9 -0.097 0.21 -9999 0 -0.63 45 45
PLAUR -0.095 0.15 -9999 0 -0.31 136 136
HMGB1 0.002 0.024 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.037 0.11 -9999 0 -0.53 11 11
AGER -0.072 0.24 -9999 0 -0.83 36 36
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.007 0.078 -9999 0 -0.31 25 25
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.13 0.21 -9999 0 -0.66 39 39
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.084 0.25 -9999 0 -0.85 34 34
CYR61 -0.25 0.4 -9999 0 -0.85 124 124
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.076 0.098 -9999 0 -0.44 11 11
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.004 0.11 -9999 0 -0.6 11 11
MYH2 -0.11 0.12 -9999 0 -0.41 36 36
MST1R -0.006 0.12 -9999 0 -0.7 11 11
leukocyte activation during inflammatory response -0.041 0.1 -9999 0 -0.71 4 4
APOB -0.006 0.07 -9999 0 -0.31 20 20
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.002 0.089 -9999 0 -0.62 7 7
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.019 0.15 -9999 0 -0.64 20 20
alphaM/beta2 Integrin/CTGF -0.12 0.23 -9999 0 -0.61 69 69
alphaM/beta2 Integrin -0.1 0.12 -9999 0 -0.36 47 47
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.087 0.15 -9999 0 -0.31 125 125
phagocytosis triggered by activation of immune response cell surface activating receptor -0.099 0.12 -9999 0 -0.35 47 47
cell adhesion -0.057 0.15 -9999 0 -0.59 24 24
NFKB1 -0.15 0.31 -9999 0 -0.76 56 56
THY1 0.011 0.028 -9999 0 -0.31 3 3
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.012 0.047 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/LRP/tPA -0.036 0.11 -9999 0 -0.62 8 8
IL6 -0.26 0.48 -9999 0 -1.1 90 90
ITGB2 -0.021 0.091 -9999 0 -0.34 26 26
elevation of cytosolic calcium ion concentration -0.14 0.17 -9999 0 -0.55 31 31
alphaM/beta2 Integrin/JAM2/JAM3 -0.035 0.11 -9999 0 -0.63 9 9
JAM2 0.004 0.086 -9999 0 -0.74 5 5
alphaM/beta2 Integrin/ICAM1 -0.076 0.14 -9999 0 -0.55 18 18
alphaM/beta2 Integrin/uPA/Plg -0.098 0.13 -9999 0 -0.52 20 20
RhoA/GTP -0.11 0.13 -9999 0 -0.41 44 44
positive regulation of phagocytosis -0.074 0.12 -9999 0 -0.5 16 16
Ron/MSP -0.016 0.098 -9999 0 -0.66 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.17 -9999 0 -0.56 31 31
alphaM/beta2 Integrin/uPAR -0.09 0.14 -9999 0 -0.57 19 19
PLAU -0.14 0.16 -9999 0 -0.31 185 185
PLAT 0.002 0.075 -9999 0 -0.42 10 10
actin filament polymerization -0.1 0.12 -9999 0 -0.4 36 36
MST1 0.01 0.046 -9999 0 -0.58 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.041 0.1 -9999 0 -0.73 4 4
TNF -0.19 0.41 -9999 0 -1 63 63
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.14 -9999 0 -0.56 20 20
fibrinolysis -0.098 0.13 -9999 0 -0.51 20 20
HCK -0.008 0.08 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.099 0.12 -9999 0 -0.35 47 47
VTN -0.078 0.26 -9999 0 -0.79 46 46
alphaM/beta2 Integrin/CYR61 -0.21 0.29 -9999 0 -0.61 131 131
LPA -0.003 0.047 -9999 0 -0.31 9 9
LRP1 0.011 0.043 -9999 0 -0.85 1 1
cell migration -0.091 0.21 -9999 0 -0.62 45 45
FN1 -0.22 0.15 -9999 0 -0.31 295 295
alphaM/beta2 Integrin/Thy1 -0.038 0.11 -9999 0 -0.53 11 11
MPO -0.005 0.11 -9999 0 -0.73 9 9
KNG1 -0.013 0.075 -9999 0 -0.31 24 24
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.099 0.12 -9999 0 -0.41 36 36
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0.022 -9999 0 -0.31 2 2
CTGF -0.11 0.3 -9999 0 -0.85 59 59
alphaM/beta2 Integrin/Hck -0.048 0.13 -9999 0 -0.56 19 19
ITGAM -0.026 0.12 -9999 0 -0.4 27 27
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.049 0.14 -9999 0 -0.53 25 25
HP -0.077 0.17 -9999 0 -0.34 103 103
leukocyte adhesion -0.1 0.17 -9999 0 -0.63 25 25
SELP -0.004 0.11 -9999 0 -0.61 11 11
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.055 0.2 -9999 0 -0.64 18 18
CRP -0.06 0.2 -9999 0 -0.7 12 12
cell cycle arrest -0.076 0.23 -9999 0 -0.72 23 23
TIMP1 -0.15 0.2 -9999 0 -0.6 26 26
IL6ST -0.092 0.28 -9999 0 -0.85 49 49
Rac1/GDP -0.087 0.24 -9999 0 -0.58 51 51
AP1 -0.2 0.33 -9999 0 -0.69 116 116
GAB2 0.014 0.001 -9999 0 -10000 0 0
TNFSF11 -0.099 0.22 -9999 0 -0.63 23 23
HSP90B1 0.022 0.041 -9999 0 -10000 0 0
GAB1 0.014 0 -9999 0 -10000 0 0
MAPK14 -0.1 0.31 -9999 0 -0.82 48 48
AKT1 0.055 0.021 -9999 0 -10000 0 0
FOXO1 0.062 0.02 -9999 0 -10000 0 0
MAP2K6 -0.1 0.29 -9999 0 -0.7 53 53
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.077 0.23 -9999 0 -0.65 31 31
MITF -0.089 0.26 -9999 0 -0.57 57 57
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.025 0.006 -9999 0 -10000 0 0
CEBPB 0.022 0.002 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.026 0.078 -9999 0 -10000 0 0
STAT3 -0.088 0.24 -9999 0 -0.78 23 23
STAT1 -0.011 0.022 -9999 0 -10000 0 0
CEBPD -0.055 0.2 -9999 0 -0.64 18 18
PIK3CA 0.013 0.043 -9999 0 -0.85 1 1
PI3K -0.002 0.032 -9999 0 -0.66 1 1
JUN -0.18 0.36 -9999 0 -0.85 93 93
PIAS3/MITF -0.078 0.24 -9999 0 -0.58 46 46
MAPK11 -0.1 0.31 -9999 0 -0.8 51 51
STAT3 (dimer)/FOXO1 -0.005 0.19 -9999 0 -0.58 13 13
GRB2/SOS1/GAB family -0.11 0.19 -9999 0 -0.69 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.25 -9999 0 -0.48 95 95
GRB2 0.014 0 -9999 0 -10000 0 0
JAK2 0.013 0 -9999 0 -10000 0 0
LBP -0.061 0.19 -9999 0 -0.59 12 12
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.013 0.005 -9999 0 -10000 0 0
MYC -0.069 0.25 -9999 0 -0.88 21 21
FGG -0.063 0.2 -9999 0 -0.76 8 8
macrophage differentiation -0.076 0.23 -9999 0 -0.72 23 23
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.19 0.28 -9999 0 -0.56 130 130
JUNB -0.062 0.23 -9999 0 -0.76 20 20
FOS -0.21 0.38 -9999 0 -0.85 106 106
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.099 0.27 -9999 0 -0.49 97 97
STAT1/PIAS1 -0.081 0.23 -9999 0 -0.52 54 54
GRB2/SOS1/GAB family/SHP2/PI3K 0.036 0.027 -9999 0 -0.32 1 1
STAT3 (dimer) -0.085 0.23 -9999 0 -0.76 23 23
PRKCD -0.064 0.22 -9999 0 -0.64 27 27
IL6R -0.01 0.14 -9999 0 -0.85 11 11
SOCS3 -0.13 0.41 -9999 0 -1.2 46 46
gp130 (dimer)/JAK1/JAK1/LMO4 -0.052 0.19 -9999 0 -0.57 49 49
Rac1/GTP -0.11 0.23 -9999 0 -0.58 51 51
HCK -0.008 0.08 -9999 0 -10000 0 0
MAPKKK cascade 0.011 0.06 -9999 0 -10000 0 0
bone resorption -0.094 0.21 -9999 0 -0.6 24 24
IRF1 -0.055 0.2 -9999 0 -0.66 15 15
mol:GDP -0.099 0.26 -9999 0 -0.58 59 59
SOS1 0.013 0.001 -9999 0 -10000 0 0
VAV1 -0.1 0.26 -9999 0 -0.6 59 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.31 -9999 0 -0.8 49 49
PTPN11 -0.009 0.018 -9999 0 -10000 0 0
IL6/IL6RA -0.16 0.29 -9999 0 -0.68 96 96
gp130 (dimer)/TYK2/TYK2/LMO4 -0.057 0.19 -9999 0 -0.57 49 49
gp130 (dimer)/JAK2/JAK2/LMO4 -0.057 0.19 -9999 0 -0.57 49 49
IL6 -0.19 0.35 -9999 0 -0.83 92 92
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE -0.095 0.15 -9999 0 -0.32 131 131
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.099 0.26 -9999 0 -0.44 114 114
LMO4 0.011 0.01 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.22 -9999 0 -0.77 23 23
MCL1 0.061 0.019 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0.023 -9999 0 -0.31 2 2
EGFR 0.003 0.095 -9999 0 -0.85 5 5
EGF/EGFR -0.08 0.18 -9999 0 -0.48 66 66
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.073 0.17 -9999 0 -0.48 60 60
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.009 0.051 -9999 0 -0.45 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.8 61 61
EGF/EGFR dimer/SHC -0.086 0.2 -9999 0 -0.57 60 60
mol:GDP -0.072 0.17 -9999 0 -0.48 60 60
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.001 0.097 -9999 0 -0.7 7 7
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.067 0.16 -9999 0 -0.44 60 60
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.068 0.16 -9999 0 -0.45 60 60
FRAP1 -0.036 0.18 -9999 0 -0.46 60 60
EGF/EGFR dimer -0.099 0.23 -9999 0 -0.66 60 60
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.012 0.083 -9999 0 -0.62 7 7
Osteopontin-mediated events

Figure 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
IKK alpha homodimer -0.034 0.15 -9999 0 -0.49 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.055 0.12 -9999 0 -0.57 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.067 0.15 -9999 0 -0.64 21 21
AP1 -0.26 0.37 -9999 0 -0.88 94 94
ILK -0.038 0.16 -9999 0 -0.52 33 33
bone resorption -0.057 0.14 -9999 0 -0.58 12 12
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.054 0.13 -9999 0 -0.47 33 33
ITGAV 0.011 0.043 -9999 0 -0.85 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.016 0.1 -9999 0 -0.66 10 10
alphaV/beta3 Integrin/Osteopontin -0.072 0.16 -9999 0 -0.58 33 33
MAP3K1 -0.035 0.16 -9999 0 -0.53 33 33
JUN -0.18 0.36 -9999 0 -0.85 93 93
MAPK3 -0.034 0.16 -9999 0 -0.49 33 33
MAPK1 -0.034 0.16 -9999 0 -0.49 33 33
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.027 0.16 -9999 0 -0.52 34 34
ITGB3 -0.014 0.15 -9999 0 -0.84 13 13
NFKBIA -0.027 0.15 -9999 0 -0.47 33 33
FOS -0.21 0.38 -9999 0 -0.85 106 106
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.1 0.18 -9999 0 -0.68 5 5
NF kappa B1 p50/RelA -0.06 0.11 -9999 0 -0.56 6 6
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.022 0.12 -9999 0 -0.69 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.034 0.16 -9999 0 -0.53 33 33
VAV3 -0.028 0.16 -9999 0 -0.5 36 36
MAP3K14 -0.042 0.16 -9999 0 -0.53 33 33
ROCK2 -0.008 0.13 -9999 0 -0.85 10 10
SPP1 -0.083 0.21 -9999 0 -0.43 88 88
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.056 0.14 -9999 0 -0.46 36 36
MMP2 -0.17 0.3 -9999 0 -0.67 90 90
Thromboxane A2 receptor signaling

Figure 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
TGM2 -0.039 0.12 -10000 0 -0.31 62 62
GNB1/GNG2 -0.044 0.067 -10000 0 -0.2 38 38
AKT1 -0.014 0.1 -10000 0 -0.21 21 21
EGF -0.11 0.3 -10000 0 -0.8 61 61
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.008 0.069 -10000 0 -0.59 1 1
mol:Ca2+ -0.044 0.14 -10000 0 -0.31 59 59
LYN 0.01 0.068 -10000 0 -0.59 1 1
RhoA/GTP -0.031 0.044 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.044 0.16 -10000 0 -0.35 56 56
GNG2 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.02 0.11 -10000 0 -0.55 5 5
G beta5/gamma2 -0.059 0.091 -10000 0 -0.27 38 38
PRKCH -0.052 0.16 -10000 0 -0.36 55 55
DNM1 -0.026 0.18 -10000 0 -0.82 19 19
TXA2/TP beta/beta Arrestin3 -0.016 0.064 -10000 0 -0.31 17 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.023 0.17 -10000 0 -0.85 17 17
G12 family/GTP -0.077 0.11 -10000 0 -0.31 56 56
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.1 0.35 13 -10000 0 13
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.22 0.38 -10000 0 -0.85 108 108
mol:IP3 -0.06 0.17 -10000 0 -0.39 59 59
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.087 0.22 -10000 0 -0.54 56 56
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.12 0.2 -10000 0 -0.41 123 123
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.002 0.071 -10000 0 -0.59 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.005 0.085 -10000 0 -0.85 4 4
PRKCB1 -0.06 0.17 -10000 0 -0.39 58 58
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.084 0.23 -10000 0 -0.54 60 60
LCK 0 0.088 -10000 0 -0.5 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.017 0.078 -10000 0 -0.84 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.025 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.077 -10000 0 -0.83 1 1
MAPK14 -0.019 0.11 -10000 0 -0.23 55 55
TGM2/GTP -0.073 0.2 -10000 0 -0.44 57 57
MAPK11 -0.019 0.11 -10000 0 -0.23 55 55
ARHGEF1 -0.015 0.087 -10000 0 -0.19 16 16
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.057 0.18 -10000 0 -0.39 60 60
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.052 0.15 -10000 0 -0.3 66 66
cAMP biosynthetic process -0.059 0.16 -10000 0 -0.36 57 57
Gq family/GTP/EBP50 -0.039 0.12 -10000 0 -0.25 95 95
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.009 0.068 -10000 0 -0.59 1 1
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.02 0.1 -10000 0 -0.31 14 14
VCAM1 -0.038 0.14 -10000 0 -0.3 58 58
TP beta/Gq family/GDP/G beta5/gamma2 -0.02 0.11 -10000 0 -0.55 5 5
platelet activation -0.026 0.15 -10000 0 -0.3 56 56
PGI2/IP -0.007 0.066 -10000 0 -0.67 4 4
PRKACA -0.001 0.1 -10000 0 -0.43 20 20
Gq family/GDP/G beta5/gamma2 -0.022 0.11 -10000 0 -0.52 5 5
TXA2/TP beta/beta Arrestin2 -0.031 0.14 -10000 0 -0.68 18 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.009 0.097 -10000 0 -0.4 20 20
mol:DAG -0.068 0.19 -10000 0 -0.44 58 58
EGFR 0.003 0.095 -10000 0 -0.85 5 5
TXA2/TP alpha -0.082 0.22 -10000 0 -0.5 57 57
Gq family/GTP -0.073 0.13 -10000 0 -0.31 95 95
YES1 0.01 0.068 -10000 0 -0.59 1 1
GNAI2/GTP -0.015 0.07 -10000 0 -0.72 1 1
PGD2/DP -0.028 0.13 -10000 0 -0.67 17 17
SLC9A3R1 0.012 0.023 -10000 0 -0.31 2 2
FYN 0.01 0.068 -10000 0 -0.59 1 1
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.012 0.094 -10000 0 -0.33 30 30
PGK/cGMP -0.15 0.26 -10000 0 -0.58 108 108
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.03 0.087 -10000 0 -0.54 5 5
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.068 0.18 -10000 0 -0.39 71 71
PRKCB -0.061 0.16 -10000 0 -0.37 60 60
PRKCE -0.054 0.17 -10000 0 -0.38 57 57
PRKCD -0.054 0.17 -10000 0 -0.39 57 57
PRKCG -0.059 0.17 -10000 0 -0.4 55 55
muscle contraction -0.074 0.21 -10000 0 -0.49 60 60
PRKCZ -0.044 0.16 -10000 0 -0.35 56 56
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.017 0.079 -10000 0 -0.85 1 1
PRKCQ -0.054 0.17 -10000 0 -0.37 61 61
MAPKKK cascade -0.075 0.2 -10000 0 -0.47 60 60
SELE -0.057 0.17 -10000 0 -0.43 57 57
TP beta/GNAI2/GDP/G beta/gamma -0.017 0.076 -10000 0 -0.83 1 1
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.36 -10000 0 -0.85 92 92
chemotaxis -0.096 0.25 -10000 0 -0.62 59 59
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 0.005 0.085 -10000 0 -0.85 4 4
Rac1/GTP 0 0 -10000 0 -10000 0 0
TCGA08_p53

Figure 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
CDKN2A -0.081 0.11 -9999 0 -0.21 169 169
TP53 -0.027 0.032 -9999 0 -10000 0 0
Senescence -0.027 0.032 -9999 0 -10000 0 0
Apoptosis -0.027 0.032 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.052 0.062 -9999 0 -10000 0 0
MDM4 0.013 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.097 0.22 -9999 0 -0.54 37 37
MAP3K8 -0.003 0.1 -9999 0 -0.86 6 6
FOS -0.062 0.17 -9999 0 -0.5 30 30
PRKCA -0.04 0.2 -9999 0 -0.85 24 24
PTPN7 -0.047 0.18 -9999 0 -0.49 48 48
HRAS 0.011 0.023 -9999 0 -0.31 2 2
PRKCB -0.026 0.11 -9999 0 -0.34 42 42
NRAS 0.012 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.01 -9999 0 -10000 0 0
MAPK3 -0.034 0.13 -9999 0 -0.54 15 15
MAP2K1 -0.029 0.16 -9999 0 -0.58 25 25
ELK1 0.008 0.01 -9999 0 -10000 0 0
BRAF -0.049 0.14 -9999 0 -0.58 25 25
mol:GTP -0.001 0.003 -9999 0 -0.006 106 106
MAPK1 -0.034 0.13 -9999 0 -0.45 22 22
RAF1 -0.049 0.14 -9999 0 -0.58 25 25
KRAS 0.012 0.002 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.04 -10000 0 -0.31 6 6
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.058 0.14 0.42 23 -10000 0 23
IL27/IL27R/JAK1 -0.11 0.19 -10000 0 -0.61 33 33
TBX21 -0.084 0.22 -10000 0 -0.65 29 29
IL12B -0.005 0.093 -10000 0 -0.53 10 10
IL12A -0.056 0.2 -10000 0 -0.64 42 42
IL6ST -0.093 0.28 -10000 0 -0.86 49 49
IL27RA/JAK1 0.013 0.026 -10000 0 -10000 0 0
IL27 0.002 0.037 -10000 0 -0.32 5 5
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.07 0.16 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.058 0.14 0.42 23 -10000 0 23
T cell proliferation during immune response 0.058 0.14 0.42 23 -10000 0 23
MAPKKK cascade -0.058 0.14 -10000 0 -0.42 23 23
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.048 -10000 0 -0.31 9 9
IL12RB1 -0.022 0.12 -10000 0 -0.85 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.083 0.21 -10000 0 -0.65 23 23
IL27/IL27R/JAK2/TYK2 -0.059 0.14 -10000 0 -0.42 23 23
positive regulation of T cell mediated cytotoxicity -0.058 0.14 -10000 0 -0.42 23 23
STAT1 (dimer) -0.11 0.24 0.52 14 -0.81 11 25
JAK2 0.014 0.007 -10000 0 -10000 0 0
JAK1 0.013 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.048 0.13 -10000 0 -0.52 6 6
T cell proliferation -0.16 0.24 -10000 0 -0.54 94 94
IL12/IL12R/TYK2/JAK2 -0.054 0.16 -10000 0 -0.7 11 11
IL17A -0.071 0.16 -10000 0 -10000 0 0
mast cell activation 0.058 0.14 0.42 23 -10000 0 23
IFNG -0.019 0.049 -10000 0 -0.13 56 56
T cell differentiation -0.005 0.008 -10000 0 -0.022 53 53
STAT3 (dimer) -0.048 0.13 -10000 0 -0.52 6 6
STAT5A (dimer) -0.048 0.13 -10000 0 -0.52 6 6
STAT4 (dimer) -0.07 0.16 -10000 0 -0.52 19 19
STAT4 -0.031 0.15 -10000 0 -0.45 39 39
T cell activation -0.011 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.053 0.17 -10000 0 -0.54 20 20
GATA3 -0.054 0.36 -10000 0 -1.5 23 23
IL18 -0.026 0.12 -10000 0 -0.3 50 50
positive regulation of mast cell cytokine production -0.047 0.13 -10000 0 -0.51 6 6
IL27/EBI3 -0.098 0.12 -10000 0 -0.44 6 6
IL27RA 0.004 0.027 -10000 0 -10000 0 0
IL6 -0.19 0.35 -10000 0 -0.85 88 88
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.013 -10000 0 -10000 0 0
IL1B -0.044 0.18 -10000 0 -0.61 37 37
EBI3 -0.15 0.17 -10000 0 -0.32 197 197
TNF -0.07 0.22 -10000 0 -0.67 47 47
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.015 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.012 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.016 0.065 -9999 0 -0.58 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.023 -9999 0 -10000 0 0
GRK1 -0.072 0.26 -9999 0 -0.84 41 41
CNG Channel -0.028 0.088 -9999 0 -0.56 7 7
mol:Na + -0.025 0.09 -9999 0 -0.48 13 13
mol:ADP -0.072 0.26 -9999 0 -0.84 41 41
RGS9-1/Gbeta5/R9AP -0.095 0.22 -9999 0 -0.58 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.026 0.093 -9999 0 -0.49 13 13
CNGB1 -0.001 0.063 -9999 0 -10000 0 0
RDH5 -0.2 0.16 -9999 0 -0.31 264 264
SAG 0.002 0.016 -9999 0 -0.31 1 1
mol:Ca2+ 0.014 0.096 -9999 0 -0.84 1 1
Na + (4 Units) -0.023 0.083 -9999 0 -0.8 1 1
RGS9 -0.077 0.26 -9999 0 -0.83 44 44
GNB1/GNGT1 -0.003 0.026 -9999 0 -10000 0 0
GNAT1/GDP -0.084 0.19 -9999 0 -0.51 66 66
GUCY2D -0.011 0.12 -9999 0 -0.48 20 20
GNGT1 -0.005 0.041 -9999 0 -0.31 7 7
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.003 0.068 -9999 0 -0.5 3 3
mol:11-cis-retinal -0.2 0.16 -9999 0 -0.31 264 264
mol:cGMP -0.017 0.078 -9999 0 -0.5 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.099 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.001 0.1 -9999 0 -0.58 10 10
Metarhodopsin II -0.053 0.16 -9999 0 -0.54 40 40
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.018 0.082 -9999 0 -0.53 9 9
RGS9BP -0.042 0.21 -9999 0 -0.85 26 26
Metarhodopsin II/Transducin 0.01 0.016 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.048 -9999 0 -0.54 3 3
PDE6A/B -0.012 0.048 -9999 0 -10000 0 0
mol:Pi -0.095 0.22 -9999 0 -0.58 66 66
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.024 -9999 0 -10000 0 0
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.009 0.078 -9999 0 -0.31 25 25
PDE6G -0.013 0.11 -9999 0 -0.37 28 28
RHO 0.006 0.017 -9999 0 -0.31 1 1
PDE6 -0.094 0.19 -9999 0 -0.5 68 68
GUCA1A 0.005 0.028 -9999 0 -0.31 3 3
GC2/GCAP Family -0.005 0.048 -9999 0 -0.54 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.007 0.074 -9999 0 -0.85 3 3
ErbB2/ErbB3 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
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.045 0.11 -9999 0 -0.4 19 19
NFATC4 -0.003 0.12 -9999 0 -0.58 2 2
ERBB2IP 0.013 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.05 0.14 -9999 0 -0.42 48 48
JUN 0.005 0.094 -9999 0 -0.29 6 6
HRAS 0.011 0.023 -9999 0 -0.31 2 2
DOCK7 -0.017 0.14 -9999 0 -0.4 48 48
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.061 0.17 -9999 0 -0.51 48 48
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.023 0.063 -9999 0 -0.29 1 1
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.16 -9999 0 -0.46 48 48
RAF1 -0.006 0.13 -9999 0 -0.41 19 19
ErbB2/ErbB3/neuregulin 2 -0.079 0.19 -9999 0 -0.54 59 59
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.023 0.08 -9999 0 -0.28 2 2
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.13 0.33 -9999 0 -0.68 97 97
FOS -0.11 0.28 -9999 0 -0.54 112 112
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.05 0.14 -9999 0 -0.42 48 48
MAPK3 -0.086 0.26 -9999 0 -0.51 95 95
MAPK1 -0.086 0.26 -9999 0 -0.51 95 95
JAK2 -0.017 0.14 -9999 0 -0.4 48 48
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.022 0.14 -9999 0 -0.39 48 48
NRG1 -0.075 0.26 -9999 0 -0.83 42 42
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.01 0.13 -9999 0 -0.35 50 50
MAPK9 -0.023 0.063 -9999 0 -0.29 1 1
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.011 0.13 -9999 0 -0.76 11 11
SHC1 0.012 0.003 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.003 -9999 0 -10000 0 0
RNF41 0.027 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.033 0.09 -9999 0 -0.44 1 1
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.058 0.2 -9999 0 -0.43 34 34
myelination 0.006 0.12 -9999 0 -0.53 2 2
PPP3CB -0.015 0.13 -9999 0 -0.37 48 48
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.039 0.11 -9999 0 -0.92 1 1
NRG2 -0.095 0.28 -9999 0 -0.82 53 53
mol:GDP -0.02 0.14 -9999 0 -0.38 48 48
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.009 0.14 -9999 0 -0.42 19 19
SRC 0.012 0.016 -9999 0 -0.31 1 1
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.017 0.14 -9999 0 -0.4 48 48
MAP2K1 -0.079 0.23 -9999 0 -0.45 84 84
heart morphogenesis -0.05 0.14 -9999 0 -0.42 48 48
RAS family/GDP -0.039 0.11 -9999 0 -0.68 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.009 -9999 0 -10000 0 0
CHRNE 0.011 0.032 -9999 0 -0.13 11 11
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.05 0.14 -9999 0 -0.42 48 48
CDC42 0.013 0 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.12 0.11 -9999 0 -0.67 6 6
EPHB2 0.007 0.074 -9999 0 -0.85 3 3
Syndecan-2/TACI -0.14 0.27 -9999 0 -0.59 108 108
LAMA1 -0.053 0.23 -9999 0 -0.83 32 32
Syndecan-2/alpha2 ITGB1 -0.073 0.11 -9999 0 -0.49 18 18
HRAS 0.012 0.023 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.069 -9999 0 -0.57 6 6
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.031 0.08 -9999 0 -0.5 9 9
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.008 0.063 -9999 0 -0.52 6 6
LAMA3 -0.023 0.16 -9999 0 -0.56 26 26
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.009 0.06 -9999 0 -0.85 2 2
Syndecan-2/MMP2 0.01 0.093 -9999 0 -0.57 10 10
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.082 0.099 -9999 0 -10000 0 0
dendrite morphogenesis 0.013 0.087 -9999 0 -0.57 9 9
Syndecan-2/GM-CSF -0.11 0.1 -9999 0 -0.6 6 6
determination of left/right symmetry 0.011 0.081 -9999 0 -0.65 6 6
Syndecan-2/PKC delta 0.017 0.071 -9999 0 -0.57 6 6
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.087 0.094 -9999 0 -0.54 6 6
MAPK1 -0.087 0.094 -9999 0 -0.54 6 6
Syndecan-2/RACK1 -0.008 0.06 -9999 0 -0.49 6 6
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.011 0.081 -9999 0 -0.65 6 6
ITGA2 -0.12 0.16 -9999 0 -0.31 166 166
MAPK8 0.024 0.088 -9999 0 -0.56 9 9
Syndecan-2/alpha2/beta1 Integrin -0.091 0.15 -9999 0 -0.55 34 34
Syndecan-2/Kininogen -0.007 0.081 -9999 0 -0.57 6 6
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.061 -9999 0 -0.46 6 6
Syndecan-2/CASK/Protein 4.1 -0.008 0.063 -9999 0 -0.52 6 6
extracellular matrix organization 0.014 0.074 -9999 0 -0.56 6 6
actin cytoskeleton reorganization -0.12 0.11 -9999 0 -0.66 6 6
Syndecan-2/Caveolin-2/Ras -0.011 0.08 -9999 0 -0.59 7 7
Syndecan-2/Laminin alpha3 -0.007 0.12 -9999 0 -0.57 18 18
Syndecan-2/RasGAP -0.007 0.056 -9999 0 -0.47 6 6
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.013 0.087 -9999 0 -0.57 9 9
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.037 0.06 -9999 0 -0.44 6 6
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.22 0.38 -9999 0 -0.83 110 110
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.082 0.099 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.017 0.071 -9999 0 -0.57 6 6
TGFB1 0.008 0.039 -9999 0 -0.31 6 6
CASP3 0.027 0.066 -9999 0 -0.51 6 6
FN1 -0.22 0.15 -9999 0 -0.31 295 295
Syndecan-2/IL8 -0.04 0.13 -9999 0 -0.57 14 14
SDC2 0.011 0.081 -9999 0 -0.66 6 6
KNG1 -0.013 0.075 -9999 0 -0.31 24 24
Syndecan-2/Neurofibromin 0.017 0.071 -9999 0 -0.57 6 6
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 277 277
Syndecan-2/TGFB1 0.014 0.074 -9999 0 -0.57 6 6
Syndecan-2/Syntenin/PI-4-5-P2 -0.008 0.063 -9999 0 -0.52 6 6
Syndecan-2/Ezrin -0.008 0.062 -9999 0 -0.52 6 6
PRKACA 0.027 0.066 -9999 0 -0.51 6 6
angiogenesis -0.04 0.13 -9999 0 -0.57 14 14
MMP2 0.002 0.089 -9999 0 -0.62 7 7
IL8 -0.084 0.18 -9999 0 -0.85 8 8
calcineurin-NFAT signaling pathway -0.14 0.27 -9999 0 -0.58 108 108
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0 0.1 -9999 0 -0.77 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.16 -9999 0 -0.28 236 236
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.01 0.032 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.048 0.067 -9999 0 -0.3 2 2
PRKG1 -0.22 0.38 -9999 0 -0.85 108 108
DUSP8 0.002 0.083 -9999 0 -0.49 9 9
PGK/cGMP/p38 alpha -0.16 0.21 -9999 0 -0.48 109 109
apoptosis -0.046 0.065 -9999 0 -0.29 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.32 -9999 0 -0.85 65 65
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.062 0.12 -9999 0 -0.37 7 7
BLK -0.26 0.39 -9999 0 -0.78 143 143
HCK -0.008 0.08 -9999 0 -10000 0 0
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.009 0.048 -9999 0 -0.49 3 3
TRAF6/MEKK3 -0.001 0.026 -9999 0 -0.54 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.09 -9999 0 -0.32 2 2
positive regulation of innate immune response -0.06 0.13 -9999 0 -0.4 6 6
LCK -0.009 0.11 -9999 0 -0.45 20 20
p38alpha-beta/MKP7 -0.051 0.13 -9999 0 -0.42 3 3
p38alpha-beta/MKP5 -0.053 0.13 -9999 0 -0.54 3 3
PGK/cGMP -0.18 0.29 -9999 0 -0.67 108 108
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.48 68 68
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.49 0.43 -9999 0 -0.85 236 236
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.036 0.12 -10000 0 -0.52 22 22
ER alpha/Gai/GDP/Gbeta gamma 0.007 0.15 -10000 0 -0.57 19 19
AKT1 -0.011 0.2 -10000 0 -0.87 20 20
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.012 0.2 -10000 0 -0.88 20 20
mol:Ca2+ -0.097 0.23 -10000 0 -0.5 94 94
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.064 0.18 -10000 0 -0.6 37 37
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.009 0.19 0.82 20 -10000 0 20
RhoA/GTP -0.027 0.092 -10000 0 -0.43 19 19
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.035 0.13 -10000 0 -0.61 19 19
regulation of stress fiber formation -0.02 0.1 0.44 2 -10000 0 2
E2/ERA-ERB (dimer) -0.043 0.14 -10000 0 -0.6 22 22
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.035 0.12 -10000 0 -0.53 19 19
pseudopodium formation 0.02 0.1 -10000 0 -0.44 2 2
E2/ER alpha (dimer)/PELP1 -0.038 0.13 -10000 0 -0.58 19 19
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.013 0 -10000 0 -10000 0 0
GNAO1 -0.015 0.15 -10000 0 -0.72 16 16
HRAS 0.012 0.023 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.014 0.15 -10000 0 -0.62 19 19
E2/ER beta (dimer) -0.007 0.066 -10000 0 -0.67 4 4
mol:GDP -0.037 0.13 -10000 0 -0.58 22 22
mol:NADP 0.014 0.15 -10000 0 -0.62 19 19
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.1 0.24 -10000 0 -0.52 94 94
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.24 -10000 0 -0.54 94 94
PLCB2 -0.11 0.24 -10000 0 -0.55 92 92
IGF1 -0.18 0.36 -10000 0 -0.82 94 94
mol:L-citrulline 0.014 0.15 -10000 0 -0.62 19 19
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.024 0.14 -10000 0 -0.82 12 12
JNK cascade -0.006 0.065 -10000 0 -0.66 4 4
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.005 0.085 -10000 0 -0.85 4 4
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.049 0.2 -10000 0 -0.54 46 46
Gq family/GDP/Gbeta gamma -0.049 0.16 -10000 0 -0.49 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.082 -10000 0 -0.34 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.035 0.13 -10000 0 -0.61 19 19
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.045 0.15 -10000 0 -0.67 19 19
STRN -0.027 0.18 -10000 0 -0.85 19 19
GNAL -0.09 0.28 -10000 0 -0.85 49 49
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.014 0.059 -10000 0 -0.58 4 4
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.013 0 -10000 0 -10000 0 0
HBEGF -0.002 0.16 -10000 0 -0.67 13 13
cAMP biosynthetic process -0.091 0.2 -10000 0 -0.51 67 67
SRC 0.015 0.14 -10000 0 -0.53 19 19
PI3K -0.002 0.032 -10000 0 -0.66 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.031 0.12 -10000 0 -0.5 22 22
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -10000 0 -0.54 31 31
Gs family/GTP -0.093 0.2 -10000 0 -0.52 67 67
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.01 -10000 0 -10000 0 0
vasodilation 0.015 0.14 -10000 0 -0.59 19 19
mol:DAG -0.1 0.24 -10000 0 -0.52 94 94
Gs family/GDP/Gbeta gamma -0.073 0.16 -10000 0 -0.43 67 67
MSN 0.019 0.11 -10000 0 -0.48 2 2
Gq family/GTP -0.14 0.24 -10000 0 -0.57 95 95
mol:PI-3-4-5-P3 -0.01 0.19 -10000 0 -0.83 20 20
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.015 0.14 0.59 19 -10000 0 19
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.034 0.12 -10000 0 -0.54 22 22
NOS3 0.012 0.16 -10000 0 -0.66 19 19
GNA11 0.005 0.085 -10000 0 -0.85 4 4
MAPKKK cascade 0 0.19 -10000 0 -0.56 37 37
E2/ER alpha (dimer)/PELP1/Src -0.038 0.14 -10000 0 -0.65 19 19
ruffle organization 0.02 0.1 -10000 0 -0.44 2 2
ROCK2 0.01 0.12 -10000 0 -0.41 29 29
GNA14 -0.18 0.36 -10000 0 -0.85 92 92
GNA15 -0.012 0.094 -10000 0 -0.33 30 30
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.027 0.2 -10000 0 -0.56 38 38
MMP2 0.018 0.14 -10000 0 -0.72 8 8
Regulation of Androgen receptor activity

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.014 0.014 -9999 0 -10000 0 0
REL -0.024 0.19 -9999 0 -0.85 20 20
HDAC7 -0.024 0.12 -9999 0 -0.59 8 8
JUN -0.19 0.36 -9999 0 -0.85 93 93
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B 0.012 0.003 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 0.001 0.084 -9999 0 -0.67 6 6
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.037 0.13 -9999 0 -0.61 9 9
MAP2K6 -0.006 0.11 -9999 0 -0.78 7 7
BRM/BAF57 -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 0.008 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.011 0.057 -9999 0 -10000 0 0
NCOA2 -0.057 0.22 -9999 0 -0.85 30 30
CEBPA 0.006 0.085 -9999 0 -0.85 4 4
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.061 0.14 -9999 0 -0.52 6 6
NR0B1 -0.002 0.038 -9999 0 -0.31 6 6
EGR1 -0.18 0.36 -9999 0 -0.86 89 89
RXRs/9cRA -0.13 0.06 -9999 0 -0.53 3 3
AR/RACK1/Src -0.11 0.14 -9999 0 -0.61 9 9
AR/GR -0.12 0.19 -9999 0 -0.36 111 111
GNB2L1 0.006 0.007 -9999 0 -10000 0 0
PKN1 0.012 0.003 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 0.007 0.059 -9999 0 -0.66 3 3
T-DHT/AR/TIF2/CARM1 -0.11 0.2 -9999 0 -0.66 34 34
SRC 0.006 0.083 -9999 0 -0.5 9 9
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.39 0.57 -9999 0 -1.3 111 111
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.046 0.12 -9999 0 -0.63 9 9
TMPRSS2 -0.056 0.31 -9999 0 -1.3 25 25
RXRG -0.28 0.12 -9999 0 -0.32 359 359
mol:9cRA -0.002 0.002 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.006 0.007 -9999 0 -10000 0 0
NR2C2 0.004 0.085 -9999 0 -0.85 4 4
KLK2 -0.48 0.43 -9999 0 -0.84 236 236
AR -0.15 0.2 -9999 0 -0.38 172 172
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.022 0.014 -9999 0 -10000 0 0
SRY 0.009 0.014 -9999 0 -10000 0 0
GATA2 0.012 0.016 -9999 0 -0.31 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.016 0.058 -9999 0 -0.32 13 13
T-DHT/AR/RACK1/Src -0.069 0.12 -9999 0 -0.62 9 9
positive regulation of transcription 0.012 0.016 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.004 -9999 0 -10000 0 0
NCOA1 0.012 0.009 -9999 0 -10000 0 0
SPDEF -0.026 0.1 -9999 0 -0.32 44 44
T-DHT/AR/TIF2 -0.043 0.13 -9999 0 -0.42 29 29
T-DHT/AR/Hsp90 -0.048 0.12 -9999 0 -0.63 9 9
GSK3B 0.009 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT 0.003 0.087 -9999 0 -0.54 9 9
SIRT1 0.013 0.001 -9999 0 -10000 0 0
ZMIZ2 0.022 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.02 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.067 0.11 -9999 0 -0.63 9 9
CREBBP 0.012 0.003 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.06 0.17 -9999 0 -0.57 37 37
MAP4K1 -0.02 0.13 -9999 0 -0.44 30 30
MAP3K8 0 0.1 -9999 0 -0.85 6 6
PRKCB -0.023 0.11 -9999 0 -0.34 42 42
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.011 0.11 -9999 0 -0.57 5 5
JUN -0.1 0.24 -9999 0 -0.51 97 97
MAP3K7 0.011 0.11 -9999 0 -0.57 5 5
GRAP2 -0.046 0.22 -9999 0 -0.8 30 30
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.11 -9999 0 -0.54 6 6
LAT 0.004 0.086 -9999 0 -0.74 5 5
LCP2 0.007 0.045 -9999 0 -0.31 8 8
MAPK8 0.009 0.092 -9999 0 -0.74 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.002 0.12 -9999 0 -0.38 29 29
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.056 0.16 -9999 0 -0.54 37 37
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.081 0.099 -10000 0 -10000 0 0
CRKL -0.035 0.12 -10000 0 -0.34 25 25
mol:PIP3 -0.018 0.036 0.71 1 -10000 0 1
AKT1 0.002 0.036 0.46 1 -0.56 1 2
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.026 0.11 -10000 0 -10000 0 0
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
HGF/MET/SHIP2 -0.15 0.22 -10000 0 -0.63 62 62
MAP3K5 -0.023 0.12 -10000 0 -0.49 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.13 0.2 -10000 0 -0.58 62 62
AP1 -0.29 0.44 -10000 0 -0.93 124 124
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.26 0.4 -10000 0 -0.86 124 124
STAT3 (dimer) -0.044 0.14 -10000 0 -0.35 62 62
GAB1/CRKL/SHP2/PI3K -0.043 0.089 -10000 0 -0.4 1 1
INPP5D -0.005 0.075 -10000 0 -0.31 23 23
CBL/CRK -0.026 0.11 -10000 0 -0.31 25 25
PTPN11 0.013 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.043 -10000 0 -0.85 1 1
ELK1 -0.053 0.063 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.041 0.074 -10000 0 -0.25 25 25
PAK1 0.01 0.034 0.43 1 -0.52 1 2
HGF/MET/RANBP10 -0.15 0.22 -10000 0 -0.63 62 62
HRAS -0.064 0.17 -10000 0 -0.5 26 26
DOCK1 -0.028 0.12 -10000 0 -0.58 2 2
GAB1 -0.046 0.12 -10000 0 -0.31 62 62
CRK -0.035 0.12 -10000 0 -0.34 25 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.12 0.22 -10000 0 -0.62 62 62
JUN -0.18 0.36 -10000 0 -0.85 93 93
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.075 0.1 -10000 0 -0.3 62 62
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.013 0.14 -10000 0 -10000 0 0
GRB2/SHC -0.058 0.088 -10000 0 -0.3 25 25
FOS -0.21 0.38 -10000 0 -0.85 106 106
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.053 0.063 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.15 0.22 -10000 0 -0.64 62 62
cell migration -0.058 0.087 -10000 0 -0.3 25 25
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.081 0.099 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.056 0.14 -10000 0 -0.38 62 62
MET/MUC20 -0.085 0.1 -10000 0 -10000 0 0
RAP1B -0.016 0.1 -10000 0 -10000 0 0
RAP1A -0.016 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.15 0.22 -10000 0 -0.63 62 62
RAF1 -0.053 0.16 -10000 0 -0.46 26 26
STAT3 -0.045 0.14 -10000 0 -0.35 62 62
cell proliferation -0.053 0.18 -10000 0 -0.47 62 62
RPS6KB1 -0.017 0.041 -10000 0 -10000 0 0
MAPK3 -0.053 0.058 -10000 0 -10000 0 0
MAPK1 -0.053 0.058 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.11 -10000 0 -0.51 7 7
SRC -0.045 0.14 -10000 0 -0.4 25 25
PI3K -0.059 0.091 -10000 0 -0.31 26 26
MET/Glomulin -0.065 0.095 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.041 0.15 -10000 0 -0.43 25 25
MET -0.12 0.16 -10000 0 -10000 0 0
MAP4K1 -0.031 0.12 -10000 0 -0.34 29 29
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.041 0.15 -10000 0 -10000 0 0
BAD 0.01 0.034 0.43 1 -0.52 1 2
MAP2K4 -0.013 0.11 -10000 0 -0.44 5 5
SHP2/GRB2/SOS1/GAB1 -0.06 0.094 -10000 0 -10000 0 0
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.053 0.1 -10000 0 -0.33 25 25
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.12 0.31 -10000 0 -0.85 62 62
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.045 0.11 -10000 0 -0.34 25 25
PDPK1 -0.008 0.04 0.53 1 -0.6 1 2
HGF/MET/SHIP -0.16 0.22 -10000 0 -0.63 62 62
FAS signaling pathway (CD95)

Figure 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
SPTAN1 0.023 0.074 0.3 26 -10000 0 26
RFC1 0.023 0.074 0.3 26 -10000 0 26
PRKDC 0.023 0.074 0.3 26 -10000 0 26
RIPK1 0.014 0.005 -10000 0 -10000 0 0
CASP7 -0.015 0.047 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.033 0.11 0.26 2 -0.38 31 33
MAP2K4 -0.031 0.16 -10000 0 -0.42 33 33
mol:ceramide -0.029 0.15 -10000 0 -0.5 31 31
GSN 0.023 0.074 0.3 26 -10000 0 26
FASLG/FAS/FADD/FAF1/Caspase 8 -0.026 0.14 -10000 0 -0.48 31 31
FAS 0.01 0.006 -10000 0 -10000 0 0
BID -0.035 0.083 0.32 3 -10000 0 3
MAP3K1 -0.001 0.1 -10000 0 -10000 0 0
MAP3K7 0.01 0.006 -10000 0 -10000 0 0
RB1 0.023 0.074 0.3 26 -10000 0 26
CFLAR 0.014 0.005 -10000 0 -10000 0 0
HGF/MET -0.15 0.22 -10000 0 -0.64 63 63
ARHGDIB 0.019 0.079 0.3 26 -10000 0 26
FADD 0.01 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.023 0.074 -10000 0 -0.3 26 26
NFKB1 -0.055 0.09 -10000 0 -10000 0 0
MAPK8 -0.063 0.22 -10000 0 -0.46 84 84
DFFA 0.023 0.074 0.3 26 -10000 0 26
DNA fragmentation during apoptosis 0.023 0.074 0.3 26 -10000 0 26
FAS/FADD/MET -0.064 0.078 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.004 0.095 -10000 0 -0.4 18 18
FAF1 0.011 0.007 -10000 0 -10000 0 0
PARP1 0.023 0.074 0.3 26 -10000 0 26
DFFB 0.023 0.074 0.3 26 -10000 0 26
CHUK -0.047 0.079 -10000 0 -10000 0 0
FASLG -0.065 0.23 -10000 0 -0.71 43 43
FAS/FADD 0 0.001 -10000 0 -10000 0 0
HGF -0.12 0.31 -10000 0 -0.85 62 62
LMNA 0.021 0.068 0.27 26 -10000 0 26
CASP6 0.023 0.074 0.3 26 -10000 0 26
CASP10 0.01 0.006 -10000 0 -10000 0 0
CASP3 0.027 0.09 0.35 29 -10000 0 29
PTPN13 0.009 0.06 -10000 0 -0.85 2 2
CASP8 0.009 0.048 0.46 3 -10000 0 3
IL6 -0.28 0.58 -10000 0 -1.4 88 88
MET -0.12 0.16 -10000 0 -10000 0 0
ICAD/CAD 0.021 0.069 0.28 26 -10000 0 26
FASLG/FAS/FADD/FAF1/Caspase 10 -0.03 0.16 -10000 0 -0.5 31 31
activation of caspase activity by cytochrome c -0.035 0.083 0.32 3 -10000 0 3
PAK2 0.023 0.074 0.3 26 -10000 0 26
BCL2 -0.041 0.21 -10000 0 -0.85 26 26
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.008 0.072 -9999 0 -0.66 5 5
alphaV beta3 Integrin -0.019 0.11 -9999 0 -0.61 13 13
PTK2 0.013 0.16 -9999 0 -0.53 18 18
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.028 0.11 -9999 0 -0.31 51 51
SRC 0.012 0.016 -9999 0 -0.31 1 1
CDKN1B -0.07 0.19 -9999 0 -0.63 41 41
VEGFA 0.009 0.06 -9999 0 -0.85 2 2
ILK -0.07 0.19 -9999 0 -0.63 41 41
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.065 0.18 -9999 0 -0.59 41 41
PTK2B 0.018 0.12 -9999 0 -0.54 17 17
alphaV/beta3 Integrin/JAM-A -0.067 0.17 -9999 0 -0.5 53 53
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.02 0.11 -9999 0 -0.61 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.17 0.27 -9999 0 -0.56 122 122
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.12 -9999 0 -0.55 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.11 -9999 0 -0.61 13 13
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.23 0.26 -9999 0 -0.58 129 129
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
alphaV/beta3 Integrin/Osteopontin -0.073 0.17 -9999 0 -0.6 33 33
RPS6KB1 -0.2 0.25 -9999 0 -0.54 129 129
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.096 0.16 -9999 0 -0.77 14 14
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.096 0.16 -9999 0 -0.77 14 14
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.037 0.16 -9999 0 -0.66 23 23
cell adhesion -0.031 0.1 -9999 0 -0.56 13 13
ANGPTL3 0.006 0.017 -9999 0 -0.31 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.063 -9999 0 -0.57 5 5
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.043 -9999 0 -0.85 1 1
ITGB3 -0.014 0.15 -9999 0 -0.85 13 13
IGF1 -0.18 0.36 -9999 0 -0.82 94 94
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.019 0.11 -9999 0 -0.6 13 13
apoptosis 0.011 0.042 -9999 0 -0.85 1 1
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.019 0.11 -9999 0 -0.61 13 13
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.035 0.13 -9999 0 -0.63 16 16
CSF1 0.003 0.095 -9999 0 -0.85 5 5
PIK3C2A -0.07 0.19 -9999 0 -0.63 41 41
PI4 Kinase/Pyk2 -0.06 0.15 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.024 0.12 -9999 0 -0.58 17 17
FAK1/Vinculin 0.022 0.13 -9999 0 -0.43 13 13
alphaV beta3/Integrin/ppsTEM5 -0.019 0.11 -9999 0 -0.61 13 13
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.078 0.26 -9999 0 -0.79 46 46
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.039 0.12 -9999 0 -0.61 13 13
alphaV/beta3 Integrin/TGFBR2 -0.021 0.11 -9999 0 -0.61 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.008 0.062 -9999 0 -0.52 6 6
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.018 0.1 -9999 0 -0.56 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 295 295
alphaV/beta3 Integrin/Pyk2 -0.022 0.11 -9999 0 -0.54 17 17
SDC1 0.011 0.028 -9999 0 -0.31 3 3
VAV3 0.029 0.081 -9999 0 -0.48 10 10
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.078 0.26 -9999 0 -0.85 43 43
FAK1/Paxillin 0.022 0.13 -9999 0 -0.43 13 13
cell migration 0.032 0.12 -9999 0 -0.46 6 6
ITGAV 0.011 0.043 -9999 0 -0.85 1 1
PI3K -0.061 0.16 -9999 0 -0.46 53 53
SPP1 -0.083 0.21 -9999 0 -0.44 88 88
KDR 0.007 0.074 -9999 0 -0.85 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.011 0.043 -9999 0 -0.85 1 1
COL4A3 -0.014 0.15 -9999 0 -0.85 13 13
angiogenesis -0.087 0.19 -9999 0 -0.62 31 31
Rac1/GTP -0.011 0.068 -9999 0 -0.44 10 10
EDIL3 -0.017 0.12 -9999 0 -0.38 31 31
cell proliferation -0.021 0.11 -9999 0 -0.6 14 14
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.045 0.15 -9999 0 -0.54 33 33
NF kappa B1 p50/RelA/I kappa B alpha -0.022 0.041 -9999 0 -10000 0 0
AP1 -0.26 0.38 -9999 0 -0.73 144 144
mol:PIP3 -0.044 0.14 -9999 0 -0.66 9 9
AKT1 -0.028 0.095 -9999 0 -0.56 3 3
PTK2B 0.001 0.084 -9999 0 -0.29 16 16
RHOA 0.031 0.046 -9999 0 -0.27 1 1
PIK3CB 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.073 -9999 0 -10000 0 0
MAGI3 0.011 0.043 -9999 0 -0.85 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.015 0.14 -9999 0 -0.45 33 33
HRAS/GDP -0.001 0.015 -9999 0 -0.21 2 2
positive regulation of microtubule depolymerization 0.009 0.086 -9999 0 -0.41 4 4
NF kappa B1 p50/RelA -0.048 0.12 -9999 0 -0.54 7 7
endothelial cell migration -0.027 0.2 -9999 0 -0.64 34 34
ADCY4 -0.014 0.19 -9999 0 -0.63 33 33
ADCY5 -0.048 0.21 -9999 0 -0.65 36 36
ADCY6 -0.014 0.19 -9999 0 -0.63 33 33
ADCY7 -0.014 0.19 -9999 0 -0.63 33 33
ADCY1 -0.017 0.2 -9999 0 -0.64 33 33
ADCY2 -0.038 0.21 -9999 0 -0.67 34 34
ADCY3 -0.014 0.19 -9999 0 -0.63 33 33
ADCY8 -0.056 0.19 -9999 0 -0.66 34 34
ADCY9 -0.014 0.19 -9999 0 -0.63 33 33
GSK3B 0.009 0.08 -9999 0 -0.3 7 7
arachidonic acid secretion -0.007 0.18 -9999 0 -0.58 33 33
GNG2 0.013 0.001 -9999 0 -10000 0 0
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.04 0.2 -9999 0 -0.61 44 44
HRAS 0.012 0.023 -9999 0 -0.31 2 2
NFKBIA 0.012 0.076 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.032 0.097 -9999 0 -0.98 4 4
JUN -0.18 0.36 -9999 0 -0.85 93 93
LPA/LPA2/NHERF2 -0.001 0.006 -9999 0 -10000 0 0
TIAM1 -0.042 0.12 -9999 0 -1.2 4 4
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:IP3 0.006 0.074 -9999 0 -10000 0 0
PLCB3 0.03 0.007 -9999 0 -10000 0 0
FOS -0.21 0.38 -9999 0 -0.85 106 106
positive regulation of mitosis -0.007 0.18 -9999 0 -0.58 33 33
LPA/LPA1-2-3 -0.052 0.16 -9999 0 -0.55 33 33
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.004 0.11 -9999 0 -0.36 33 33
GNAZ -0.022 0.17 -9999 0 -0.59 34 34
EGFR/PI3K-beta/Gab1 -0.046 0.14 -9999 0 -0.71 9 9
positive regulation of dendritic cell cytokine production -0.051 0.15 -9999 0 -0.55 33 33
LPA/LPA2/MAGI-3 -0.002 0.031 -9999 0 -0.62 1 1
ARHGEF1 -0.002 0.15 -9999 0 -0.5 33 33
GNAI2 -0.022 0.17 -9999 0 -0.59 34 34
GNAI3 -0.022 0.17 -9999 0 -0.59 34 34
GNAI1 -0.022 0.17 -9999 0 -0.59 34 34
LPA/LPA3 -0.01 0.044 -9999 0 -0.21 18 18
LPA/LPA2 -0.001 0.008 -9999 0 -10000 0 0
LPA/LPA1 -0.057 0.19 -9999 0 -0.68 34 34
HB-EGF/EGFR -0.057 0.18 -9999 0 -0.57 39 39
HBEGF -0.062 0.2 -9999 0 -0.64 36 36
mol:DAG 0.006 0.074 -9999 0 -10000 0 0
cAMP biosynthetic process -0.027 0.2 -9999 0 -0.58 43 43
NFKB1 0.013 0 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
GNB1 0.013 0.001 -9999 0 -10000 0 0
LYN 0.012 0.076 -9999 0 -10000 0 0
GNAQ 0.019 0.029 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.004 0.067 -9999 0 -0.31 18 18
LPAR1 -0.054 0.24 -9999 0 -0.86 33 33
IL8 -0.13 0.2 -9999 0 -0.48 51 51
PTK2 -0.011 0.16 -9999 0 -0.52 33 33
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.016 0.14 -9999 0 -0.46 33 33
EGFR 0.002 0.095 -9999 0 -0.85 5 5
PLCG1 -0.013 0.084 -9999 0 -0.29 11 11
PLD2 -0.011 0.16 -9999 0 -0.52 33 33
G12/G13 -0.045 0.15 -9999 0 -0.54 33 33
PI3K-beta -0.033 0.11 -9999 0 -0.67 3 3
cell migration -0.016 0.058 -9999 0 -0.26 7 7
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.003 0.11 -9999 0 -0.36 33 33
HRAS/GTP -0.019 0.19 -9999 0 -0.6 33 33
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.084 0.25 -9999 0 -0.85 34 34
PRKCE 0.007 0.074 -9999 0 -0.85 3 3
PRKCD 0.014 0.071 -9999 0 -10000 0 0
Gi(beta/gamma) -0.008 0.18 -9999 0 -0.59 33 33
mol:LPA 0.003 0.016 -9999 0 -0.22 1 1
TRIP6/p130 Cas/FAK1/Paxillin -0.031 0.13 -9999 0 -0.46 33 33
MAPKKK cascade -0.007 0.18 -9999 0 -0.58 33 33
contractile ring contraction involved in cytokinesis 0.031 0.046 -9999 0 -0.27 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.086 0.2 -9999 0 -0.45 92 92
GNA15 0.009 0.055 -9999 0 -0.45 1 1
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.009 0.088 -9999 0 -0.42 4 4
GNA11 0.014 0.054 -9999 0 -0.44 4 4
Rac1/GTP -0.033 0.1 -9999 0 -1.1 4 4
MMP2 -0.027 0.2 -9999 0 -0.64 34 34
BCR signaling pathway

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
JUN -0.11 0.19 -9999 0 -0.47 53 53
IKBKB -0.02 0.071 -9999 0 -0.33 2 2
AKT1 -0.044 0.1 -9999 0 -0.27 18 18
IKBKG -0.019 0.074 -9999 0 -0.36 2 2
CALM1 -0.037 0.088 -9999 0 -0.36 2 2
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
MAP3K1 -0.079 0.19 -9999 0 -0.66 15 15
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.047 0.092 -9999 0 -0.38 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.083 0.14 -9999 0 -0.29 90 90
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.18 0.25 -9999 0 -0.54 119 119
CD22 -0.16 0.23 -9999 0 -0.69 43 43
CAMK2G -0.027 0.083 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.005 0.075 -9999 0 -0.31 23 23
SHC/GRB2/SOS1 -0.1 0.16 -9999 0 -10000 0 0
GO:0007205 -0.048 0.093 -9999 0 -0.39 2 2
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.038 0.089 -9999 0 -0.36 2 2
NFATC1 -0.073 0.16 -9999 0 -0.57 15 15
B-cell antigen/BCR complex -0.18 0.25 -9999 0 -0.54 119 119
PAG1/CSK -0.002 0.032 -9999 0 -0.66 1 1
NFKBIB 0.002 0.027 -9999 0 -0.1 1 1
HRAS -0.041 0.1 -9999 0 -0.35 2 2
NFKBIA 0.002 0.027 -9999 0 -0.1 1 1
NF-kappa-B/RelA/I kappa B beta 0.008 0.023 -9999 0 -10000 0 0
RasGAP/Csk -0.15 0.21 -9999 0 -0.52 80 80
mol:GDP -0.043 0.085 -9999 0 -0.35 2 2
PTEN 0.011 0.043 -9999 0 -0.85 1 1
CD79B -0.029 0.11 -9999 0 -0.31 53 53
NF-kappa-B/RelA/I kappa B alpha 0.008 0.022 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.092 0.18 -9999 0 -0.44 65 65
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.054 0.09 -9999 0 -0.39 2 2
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.15 0.22 -9999 0 -0.5 106 106
CHUK -0.019 0.074 -9999 0 -0.32 3 3
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.069 0.099 -9999 0 -0.51 8 8
PTPN6 -0.15 0.22 -9999 0 -0.66 39 39
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.003 0.037 -9999 0 -0.14 18 18
VAV2 -0.14 0.2 -9999 0 -0.88 10 10
ubiquitin-dependent protein catabolic process 0.007 0.026 -9999 0 -0.095 1 1
BTK -0.016 0.15 -9999 0 -1.2 6 6
CD19 -0.16 0.21 -9999 0 -0.73 18 18
MAP4K1 -0.02 0.13 -9999 0 -0.44 30 30
CD72 0.011 0.028 -9999 0 -10000 0 0
PAG1 0.011 0.043 -9999 0 -0.85 1 1
MAPK14 -0.059 0.16 -9999 0 -0.53 15 15
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.037 0.091 -9999 0 -10000 0 0
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.068 0.18 -9999 0 -0.44 64 64
RAF1 -0.031 0.097 -9999 0 -10000 0 0
RasGAP/p62DOK/SHIP -0.15 0.21 -9999 0 -0.5 82 82
CD79A -0.2 0.32 -9999 0 -0.53 163 163
re-entry into mitotic cell cycle -0.081 0.13 -9999 0 -0.28 90 90
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.011 0.086 -9999 0 -10000 0 0
MAPK1 -0.011 0.086 -9999 0 -10000 0 0
CD72/SHP1 -0.11 0.22 -9999 0 -0.69 28 28
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.062 0.17 -9999 0 -0.55 17 17
actin cytoskeleton organization -0.093 0.18 -9999 0 -0.7 10 10
NF-kappa-B/RelA 0.022 0.043 -9999 0 -10000 0 0
Calcineurin -0.037 0.061 -9999 0 -10000 0 0
PI3K -0.14 0.17 -9999 0 -0.56 25 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.058 0.088 -9999 0 -0.35 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.25 -9999 0 -1 17 17
DAPP1 -0.14 0.27 -9999 0 -1.3 14 14
cytokine secretion -0.068 0.15 -9999 0 -0.53 15 15
mol:DAG -0.054 0.09 -9999 0 -0.39 2 2
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.021 0.092 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.18 0.25 -9999 0 -0.61 83 83
mol:PI-3-4-5-P3 -0.1 0.12 -9999 0 -0.38 25 25
ETS1 -0.018 0.078 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.18 -9999 0 -0.48 67 67
B-cell antigen/BCR complex/LYN -0.13 0.21 -9999 0 -0.51 72 72
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
RAC1 -0.1 0.2 -9999 0 -0.77 10 10
B-cell antigen/BCR complex/LYN/SYK -0.16 0.23 -9999 0 -0.78 27 27
CARD11 -0.078 0.13 -9999 0 -0.55 11 11
FCGR2B -0.032 0.19 -9999 0 -0.76 24 24
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex -0.001 0.035 -9999 0 -0.14 1 1
PTPRC -0.035 0.18 -9999 0 -0.6 32 32
PDPK1 -0.046 0.1 -9999 0 -0.27 19 19
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.024 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.013 0.21 -10000 0 -0.94 16 16
NCK1/PAK1/Dok-R -0.027 0.086 -10000 0 -0.42 16 16
NCK1/Dok-R -0.062 0.22 -10000 0 -1.1 16 16
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
mol:beta2-estradiol -0.004 0.046 0.25 12 -10000 0 12
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.008 0.062 -10000 0 -0.33 6 6
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.054 0.2 -10000 0 -1 16 16
FN1 -0.22 0.15 -10000 0 -0.31 295 295
PLD2 0.007 0.25 -10000 0 -1.2 16 16
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.019 0.16 -10000 0 -0.85 15 15
ELK1 0.021 0.22 -10000 0 -1 16 16
GRB7 -0.037 0.12 -10000 0 -0.31 63 63
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.099 0.22 -10000 0 -1.2 16 16
CDKN1A -0.011 0.17 -10000 0 -0.63 16 16
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.062 0.22 -10000 0 -1.1 16 16
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.028 0.16 -10000 0 -0.68 16 16
PLG -0.002 0.25 -10000 0 -1.2 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.01 0.2 -10000 0 -0.9 16 16
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0.002 -10000 0 -10000 0 0
ANGPT2 -0.11 0.23 -10000 0 -0.8 18 18
BMX -0.006 0.26 -10000 0 -1.2 16 16
ANGPT1 -0.035 0.28 -10000 0 -1.5 14 14
tube development -0.017 0.18 -10000 0 -0.72 16 16
ANGPT4 -0.064 0.24 -10000 0 -0.75 42 42
response to hypoxia 0 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.018 0.27 -10000 0 -1.2 16 16
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.001 -10000 0 -10000 0 0
STAT5A (dimer) -0.019 0.2 -10000 0 -0.82 16 16
mol:L-citrulline 0.028 0.16 -10000 0 -0.68 16 16
AGTR1 -0.33 0.42 -10000 0 -0.85 164 164
MAPK14 -0.006 0.24 -10000 0 -1.2 16 16
Tie2/SHP2 -0.018 0.095 -10000 0 -1.2 2 2
TEK 0.023 0.12 -10000 0 -1.4 2 2
RPS6KB1 0.013 0.2 -10000 0 -0.9 16 16
Angiotensin II/AT1 -0.26 0.33 -10000 0 -0.66 164 164
Tie2/Ang1/GRB2 0.001 0.25 -10000 0 -1.2 16 16
MAPK3 0.017 0.23 -10000 0 -1.1 16 16
MAPK1 0.017 0.23 -10000 0 -1.1 16 16
Tie2/Ang1/GRB7 -0.021 0.26 -10000 0 -1.2 16 16
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.003 0.25 -10000 0 -1.2 16 16
PI3K -0.001 0.24 -10000 0 -1.1 16 16
FES -0.006 0.24 -10000 0 -1.2 16 16
Crk/Dok-R -0.062 0.22 -10000 0 -1.1 16 16
Tie2/Ang1/ABIN2 0.001 0.25 -10000 0 -1.2 16 16
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.017 0.19 -10000 0 -0.83 16 16
STAT5A 0.013 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.013 0.2 -10000 0 -0.9 16 16
Tie2/Ang2 -0.037 0.23 -10000 0 -0.99 16 16
Tie2/Ang1 -0.004 0.26 -10000 0 -1.3 16 16
FOXO1 0.023 0.19 -10000 0 -0.83 16 16
ELF1 0.02 0.043 -10000 0 -0.84 1 1
ELF2 0.003 0.24 -10000 0 -1.1 16 16
mol:Choline 0.009 0.24 -10000 0 -1.1 16 16
cell migration -0.023 0.054 -10000 0 -0.24 16 16
FYN -0.022 0.2 -10000 0 -0.82 16 16
DOK2 0.001 0.078 -10000 0 -0.4 12 12
negative regulation of cell cycle -0.007 0.16 -10000 0 -0.57 16 16
ETS1 0.016 0.043 -10000 0 -10000 0 0
PXN 0.025 0.17 -10000 0 -0.73 16 16
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.025 0.18 -10000 0 -0.78 16 16
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.089 0.28 -10000 0 -0.86 47 47
MAPKKK cascade 0.009 0.24 -10000 0 -1.1 16 16
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.002 0.26 -10000 0 -1.2 16 16
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.03 0.14 -10000 0 -0.6 16 16
mol:Phosphatidic acid 0.009 0.24 -10000 0 -1.1 16 16
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.028 0.16 -10000 0 -0.68 16 16
Rac1/GTP -0.048 0.16 -10000 0 -0.83 16 16
MMP2 0.001 0.25 -10000 0 -1.2 16 16
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0 0.1 -9999 0 -0.85 6 6
CDKN1A -0.015 0.092 -9999 0 -0.26 2 2
PRL-3/alpha Tubulin -0.013 0.05 -9999 0 -10000 0 0
mol:Ca2+ -0.017 0.11 -9999 0 -0.67 8 8
AGT -0.021 0.14 -9999 0 -0.85 8 8
CCNA2 -0.07 0.22 -9999 0 -0.48 89 89
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.12 0.28 -9999 0 -0.65 89 89
CDK2/Cyclin E1 -0.033 0.061 -9999 0 -10000 0 0
MAPK3 0.009 0.056 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.009 0.056 -9999 0 -10000 0 0
PTP4A1 -0.079 0.22 -9999 0 -0.51 89 89
PTP4A3 -0.008 0.081 -9999 0 -0.31 27 27
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.009 0.056 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
RAC1 -0.017 0.094 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.075 0.21 -9999 0 -0.48 89 89
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.01 0.036 -9999 0 -10000 0 0
RHOC -0.017 0.094 -9999 0 -0.26 9 9
RHOA -0.017 0.094 -9999 0 -0.26 9 9
cell motility -0.016 0.1 -9999 0 -0.27 9 9
PRL-1/alpha Tubulin -0.068 0.21 -9999 0 -0.47 89 89
PRL-3/alpha1 Integrin -0.023 0.097 -9999 0 -0.71 6 6
ROCK1 -0.016 0.1 -9999 0 -0.27 9 9
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.078 0.22 -9999 0 -0.5 89 89
ATF5 0 0.065 -9999 0 -0.31 17 17
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.013 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.016 0.094 0.2 19 -0.36 13 32
PTP1B/AKT1 -0.002 0.064 -10000 0 -0.39 2 2
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.011 0.071 -10000 0 -0.38 3 3
EGFR 0.001 0.096 -10000 0 -0.86 5 5
EGF/EGFR -0.084 0.18 -10000 0 -0.52 60 60
CSF1 0.003 0.095 -10000 0 -0.85 5 5
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.099 0.12 -10000 0 -0.45 23 23
Insulin Receptor/Insulin -0.013 0.042 -10000 0 -10000 0 0
HCK -0.008 0.08 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.002 0.067 -10000 0 -0.4 2 2
EGF -0.11 0.3 -10000 0 -0.8 61 61
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.017 0.1 -10000 0 -0.48 4 4
TXN 0.011 0.017 -10000 0 -0.32 1 1
PTP1B/IRS1/GRB2 -0.067 0.16 -10000 0 -0.5 45 45
cell migration 0.011 0.071 0.38 3 -10000 0 3
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.042 0.19 -10000 0 -0.58 38 38
ITGA2B -0.089 0.28 -10000 0 -0.85 48 48
CSF1R 0.007 0.056 -10000 0 -0.4 6 6
Prolactin Receptor/Prolactin -0.037 0.15 -10000 0 -0.67 19 19
FGR 0.01 0.032 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.003 0.066 -10000 0 -0.35 3 3
Crk/p130 Cas -0.016 0.049 -10000 0 -0.38 2 2
DOK1 0.008 0.062 -10000 0 -0.36 2 2
JAK2 -0.007 0.084 -10000 0 -0.37 9 9
Jak2/Leptin Receptor/Leptin -0.069 0.16 -10000 0 -0.61 32 32
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.011 0.071 -10000 0 -0.38 3 3
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.19 0.21 -10000 0 -0.35 227 227
SRC 0.012 0.03 -10000 0 -10000 0 0
ITGB3 -0.016 0.15 -10000 0 -0.85 13 13
CAT1/PTP1B -0.091 0.15 -10000 0 -0.39 47 47
CAPN1 0.013 0.003 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.014 0.043 -10000 0 -0.62 1 1
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.069 0.18 -10000 0 -0.65 32 32
negative regulation of transcription -0.006 0.083 -10000 0 -0.36 9 9
FCGR2A -0.008 0.087 -10000 0 -0.34 25 25
FER 0.008 0.061 -10000 0 -0.86 2 2
alphaIIb/beta3 Integrin -0.095 0.25 -10000 0 -0.72 55 55
BLK -0.26 0.39 -10000 0 -0.78 143 143
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.013 0.003 -10000 0 -10000 0 0
LEPR 0.004 0.087 -10000 0 -0.67 6 6
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.5 39 39
PRL 0.001 0.017 -10000 0 -0.31 1 1
SOCS3 -0.1 0.41 -10000 0 -1.5 32 32
SPRY2 0.012 0.017 -10000 0 -0.31 1 1
Insulin Receptor/Insulin/IRS1 -0.061 0.18 -10000 0 -0.58 43 43
CSF1/CSF1R -0.025 0.078 -10000 0 -0.47 8 8
Ras protein signal transduction 0.02 0.023 -10000 0 -10000 0 0
IRS1 -0.078 0.26 -10000 0 -0.85 43 43
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.009 0.069 -10000 0 -10000 0 0
STAT5B -0.004 0.069 -10000 0 -0.29 5 5
STAT5A -0.004 0.069 -10000 0 -0.29 5 5
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.066 -10000 0 -0.4 2 2
CSN2 -0.006 0.053 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
LAT 0.001 0.071 -10000 0 -0.55 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.009 0.11 -10000 0 -0.45 20 20
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 176 176
Regulation of nuclear SMAD2/3 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
EP300 0.021 0.016 -10000 0 -10000 0 0
HSPA8 0.005 0.074 -10000 0 -0.85 3 3
SMAD3/SMAD4/ER alpha -0.052 0.14 -10000 0 -0.6 20 20
AKT1 0.009 0.01 -10000 0 -10000 0 0
GSC -0.22 0.57 -10000 0 -1.6 63 63
NKX2-5 0.001 0.031 -10000 0 -0.31 4 4
muscle cell differentiation 0.025 0.047 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.003 0.08 -10000 0 -10000 0 0
SMAD4 -0.016 0.059 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.011 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.078 -10000 0 -0.57 4 4
SMAD3/SMAD4/VDR 0.011 0.045 -10000 0 -10000 0 0
MYC 0.002 0.14 -10000 0 -0.86 10 10
CDKN2B -0.079 0.14 -10000 0 -10000 0 0
AP1 -0.27 0.53 -10000 0 -1 124 124
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.033 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.065 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.009 0.067 -10000 0 -0.3 14 14
SMAD3/SMAD4/GR -0.017 0.046 -10000 0 -10000 0 0
GATA3 -0.037 0.2 -10000 0 -0.82 24 24
SKI/SIN3/HDAC complex/NCoR1 0.041 0.023 -10000 0 -10000 0 0
MEF2C/TIF2 -0.052 0.14 -10000 0 -0.56 14 14
endothelial cell migration -0.009 0.11 1.4 1 -10000 0 1
MAX 0.013 0.006 -10000 0 -10000 0 0
RBBP7 0.011 0.004 -10000 0 -10000 0 0
RBBP4 0.011 0.004 -10000 0 -10000 0 0
RUNX2 -0.08 0.16 -10000 0 -0.32 113 113
RUNX3 -0.007 0.12 -10000 0 -0.58 14 14
RUNX1 -0.14 0.16 -10000 0 -0.31 190 190
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.012 0.016 -10000 0 -0.31 1 1
CDKN1A 0.023 0.074 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.04 0.09 -10000 0 -10000 0 0
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.011 0.004 -10000 0 -10000 0 0
SERPINE1 0.008 0.11 -10000 0 -1.5 1 1
SMAD3/SMAD4/ATF2 -0.032 0.1 -10000 0 -0.61 10 10
SMAD3/SMAD4/ATF3 -0.16 0.28 -10000 0 -0.65 96 96
SAP30 0.009 0.043 -10000 0 -0.85 1 1
Cbp/p300/PIAS3 0.035 0.046 -10000 0 -10000 0 0
JUN -0.26 0.52 -10000 0 -0.99 124 124
SMAD3/SMAD4/IRF7 -0.017 0.046 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.002 0.092 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.068 0.098 0.48 4 -10000 0 4
DLX1 -0.04 0.21 -10000 0 -0.85 25 25
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.23 0.41 -10000 0 -0.92 106 106
SMAD3/SMAD4/Max -0.017 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.009 0.021 -10000 0 -10000 0 0
ZBTB17 0.021 0.012 -10000 0 -10000 0 0
LAMC1 0.025 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.017 0.045 -10000 0 -10000 0 0
IRF7 0.014 0.005 -10000 0 -10000 0 0
ESR1 -0.049 0.2 -10000 0 -0.54 46 46
HNF4A -0.004 0.047 -10000 0 -0.31 9 9
MEF2C 0.005 0.087 -10000 0 -10000 0 0
SMAD2-3/SMAD4 -0.033 0.056 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.025 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.017 0.024 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.018 0.011 -10000 0 -10000 0 0
SKIL 0.013 0 -10000 0 -10000 0 0
HDAC1 0.011 0.004 -10000 0 -10000 0 0
HDAC2 0.011 0.004 -10000 0 -10000 0 0
SNIP1 0.011 0.005 -10000 0 -10000 0 0
GCN5L2 0.006 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.012 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.18 0.1 -10000 0 -0.7 7 7
SMAD2 -0.004 0.04 -10000 0 -10000 0 0
SMAD3 -0.005 0.048 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.059 -10000 0 -0.36 5 5
SMAD2/SMAD2/SMAD4 0.013 0.026 -10000 0 -10000 0 0
NCOR1 0.011 0.004 -10000 0 -10000 0 0
NCOA2 -0.05 0.22 -10000 0 -0.85 30 30
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.011 0.076 -10000 0 -10000 0 0
IFNB1 0.015 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.088 -10000 0 -10000 0 0
CITED1 -0.26 0.14 -10000 0 -0.32 335 335
SMAD2-3/SMAD4/ARC105 -0.024 0.045 -10000 0 -10000 0 0
RBL1 0 0.1 -10000 0 -0.85 6 6
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.007 0.081 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.085 0.11 -10000 0 -0.61 7 7
SMAD7 -0.11 0.28 -10000 0 -0.6 85 85
MYC/MIZ-1 0.014 0.11 -10000 0 -0.66 10 10
SMAD3/SMAD4 0.066 0.1 0.31 40 -0.35 1 41
IL10 -0.031 0.2 -10000 0 -0.64 34 34
PIASy/HDAC complex 0.007 0.009 -10000 0 -10000 0 0
PIAS3 0.015 0.006 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.02 0.15 -10000 0 -0.53 23 23
CDK4 0.019 0.013 -10000 0 -10000 0 0
PIAS4 0.007 0.009 -10000 0 -10000 0 0
ATF3 -0.19 0.37 -10000 0 -0.82 102 102
SMAD3/SMAD4/SP1 -0.018 0.053 -10000 0 -10000 0 0
FOXG1 -0.007 0.09 -10000 0 -0.85 3 3
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.005 0.087 -10000 0 -10000 0 0
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.055 0.15 -10000 0 -0.63 25 25
MYOD1 -0.002 0.031 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.054 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.055 0.15 -10000 0 -0.57 27 27
SnoN/SIN3/HDAC complex/NCoR1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.079 0.11 -10000 0 -0.57 9 9
SMAD3/SMAD4/SP1-3 -0.006 0.047 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.014 0.022 -10000 0 -10000 0 0
SIN3B 0.011 0.004 -10000 0 -10000 0 0
SIN3A 0.011 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.031 0.082 -10000 0 -10000 0 0
ITGB5 0.035 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.27 0.3 -10000 0 -0.62 170 170
AR -0.35 0.43 -10000 0 -0.85 170 170
negative regulation of cell growth -0.038 0.12 -10000 0 -0.43 2 2
SMAD3/SMAD4/MYOD -0.023 0.051 -10000 0 -10000 0 0
E2F5 0.013 0 -10000 0 -10000 0 0
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.02 0.058 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.067 -10000 0 -10000 0 0
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.28 0.54 -10000 0 -1 124 124
SMAD3/SMAD4/RUNX2 -0.068 0.099 -10000 0 -0.48 4 4
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.008 0.13 -10000 0 -0.85 10 10
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.002 0.032 -9999 0 -0.66 1 1
Necdin/E2F1 -0.066 0.11 -9999 0 -0.82 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.038 0.11 -9999 0 -0.51 19 19
NGF (dimer)/p75(NTR)/BEX1 -0.3 0.3 -9999 0 -0.6 201 201
NT-4/5 (dimer)/p75(NTR) -0.075 0.19 -9999 0 -0.69 30 30
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.004 0.13 -9999 0 -0.51 20 20
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.018 0.15 -9999 0 -0.65 19 19
MGDIs/NGR/p75(NTR)/LINGO1 -0.05 0.13 -9999 0 -0.56 20 20
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.062 0.15 -9999 0 -0.59 28 28
LINGO1 -0.001 0.067 -9999 0 -0.31 18 18
Sortilin/TRAF6/NRIF -0.001 0.021 -9999 0 -10000 0 0
proBDNF (dimer) -0.018 0.15 -9999 0 -0.65 19 19
NTRK1 0 0.055 -9999 0 -0.31 12 12
RTN4R 0.013 0 -9999 0 -10000 0 0
neuron apoptosis -0.014 0.14 -9999 0 -0.52 22 22
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.022 0.14 -9999 0 -0.59 19 19
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.042 0.12 -9999 0 -0.55 19 19
MAGEH1 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.044 0.13 -9999 0 -0.54 21 21
Mammalian IAPs/DIABLO -0.03 0.12 -9999 0 -0.52 21 21
proNGF (dimer) 0.006 0.075 -9999 0 -0.72 4 4
MAGED1 0.013 0 -9999 0 -10000 0 0
APP 0.013 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.15 -9999 0 -0.6 22 22
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.039 0.11 -9999 0 -0.51 19 19
NGF 0.006 0.075 -9999 0 -0.72 4 4
cell cycle arrest 0.044 0.17 -9999 0 -0.5 19 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.091 -9999 0 -0.36 20 20
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.065 0.16 -9999 0 -0.62 30 30
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.047 0.13 -9999 0 -0.59 19 19
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide -0.012 0.13 -9999 0 -0.54 19 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.02 0.075 -9999 0 -0.45 2 2
p75(NTR)/beta APP -0.052 0.14 -9999 0 -0.66 17 17
BEX1 -0.38 0.43 -9999 0 -0.85 186 186
mol:GDP -0.033 0.14 -9999 0 -0.6 19 19
NGF (dimer) -0.096 0.13 -9999 0 -0.53 26 26
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.044 0.12 -9999 0 -0.55 17 17
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.041 0.12 -9999 0 -0.52 19 19
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.047 0.13 -9999 0 -0.6 19 19
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.063 0.093 -9999 0 -10000 0 0
NT3 (dimer) -0.051 0.21 -9999 0 -0.85 24 24
TP53 -0.009 0.14 -9999 0 -0.48 29 29
PRDM4 -0.012 0.13 -9999 0 -0.54 19 19
BDNF (dimer) -0.13 0.17 -9999 0 -0.58 34 34
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.037 0.11 -9999 0 -0.5 19 19
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.043 0.12 -9999 0 -0.55 20 20
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 0.021 0.13 -9999 0 -0.46 18 18
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.012 0.13 -9999 0 -0.54 19 19
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.047 0.13 -9999 0 -0.6 19 19
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.098 0.21 -9999 0 -0.69 40 40
MAPK8 0.019 0.13 -9999 0 -0.7 3 3
MAPK9 0.021 0.13 -9999 0 -0.62 3 3
APAF1 0.013 0 -9999 0 -10000 0 0
NTF3 -0.051 0.21 -9999 0 -0.85 24 24
NTF4 -0.02 0.15 -9999 0 -0.61 22 22
NDN 0.009 0.06 -9999 0 -0.85 2 2
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.034 0.1 -9999 0 -0.47 19 19
p75 CTF/Sortilin/TRAF6/NRIF -0.002 0.05 -9999 0 -1 1 1
RhoA-B-C/GTP -0.047 0.13 -9999 0 -0.59 19 19
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.051 0.13 -9999 0 -0.51 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.056 0.14 -9999 0 -0.54 29 29
PRKACB 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.024 0.12 -9999 0 -0.66 13 13
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.038 0.2 -9999 0 -0.85 21 21
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.07 0.18 -9999 0 -0.5 19 19
BAD 0.028 0.13 -9999 0 -0.62 3 3
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.063 0.2 -9999 0 -0.45 67 67
CYCS -0.003 0.12 -9999 0 -0.51 19 19
ADAM17 0.011 0.043 -9999 0 -0.85 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.043 0.12 -9999 0 -0.55 20 20
BCL2L11 0.028 0.13 -9999 0 -0.62 3 3
BDNF (dimer)/p75(NTR) -0.074 0.18 -9999 0 -0.68 28 28
PI3K -0.043 0.12 -9999 0 -0.55 20 20
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.042 0.12 -9999 0 -0.55 19 19
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.057 0.16 -9999 0 -0.68 19 19
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.042 0.12 -9999 0 -0.55 19 19
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG 0 0.022 -9999 0 -0.31 2 2
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.021 0.15 -9999 0 -0.51 30 30
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.013 0 -9999 0 -10000 0 0
CASP3 0.03 0.12 -9999 0 -0.56 3 3
E2F1 -0.089 0.15 -9999 0 -0.31 128 128
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.014 0.063 -9999 0 -0.55 3 3
NGF (dimer)/TRKA -0.011 0.066 -9999 0 -0.66 3 3
MMP7 -0.18 0.23 -9999 0 -0.37 203 203
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.039 0.12 -9999 0 -0.52 20 20
MMP3 -0.041 0.11 -9999 0 -0.31 59 59
APAF-1/Caspase 9 -0.043 0.12 -9999 0 -0.66 6 6
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.012 0.016 -9999 0 -0.31 1 1
LAT2 -0.016 0.1 -9999 0 -0.34 5 5
AP1 -0.21 0.29 -9999 0 -0.68 99 99
mol:PIP3 -0.015 0.16 -9999 0 -0.47 23 23
IKBKB 0.006 0.093 -9999 0 -0.28 14 14
AKT1 -0.013 0.13 -9999 0 -0.47 6 6
IKBKG 0.006 0.093 -9999 0 -0.29 12 12
MS4A2 -0.063 0.13 -9999 0 -0.31 91 91
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
MAP3K1 0.012 0.1 -9999 0 -0.47 6 6
mol:Ca2+ -0.006 0.12 -9999 0 -0.33 33 33
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.008 0.088 -9999 0 -0.33 3 3
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.084 0.19 -9999 0 -0.53 65 65
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.005 0.075 -9999 0 -0.31 23 23
PLD2 -0.046 0.15 -9999 0 -0.46 34 34
PTPN13 0.003 0.087 -9999 0 -0.46 2 2
PTPN11 0.012 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.021 0.1 -9999 0 -0.31 5 5
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.45 33 33
LAT -0.014 0.1 -9999 0 -0.45 7 7
PAK2 0.004 0.11 -9999 0 -0.51 7 7
NFATC2 -0.13 0.27 -9999 0 -0.78 59 59
HRAS -0.005 0.12 -9999 0 -0.54 8 8
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.097 0.17 -9999 0 -0.53 43 43
Antigen/IgE/Fc epsilon R1 -0.088 0.16 -9999 0 -0.51 39 39
mol:GDP -0.014 0.13 -9999 0 -0.55 11 11
JUN -0.18 0.36 -9999 0 -0.85 93 93
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.21 0.38 -9999 0 -0.85 106 106
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.042 0.078 -9999 0 -0.33 5 5
CHUK 0.006 0.093 -9999 0 -0.28 14 14
KLRG1 -0.02 0.11 -9999 0 -0.41 11 11
VAV1 -0.02 0.12 -9999 0 -0.49 8 8
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.008 0.088 -9999 0 -0.33 3 3
negative regulation of mast cell degranulation -0.019 0.1 -9999 0 -0.4 9 9
BTK -0.045 0.12 -9999 0 -0.67 8 8
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.049 0.2 -9999 0 -0.55 38 38
GAB2/PI3K/SHP2 -0.062 0.12 -9999 0 -0.44 29 29
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.017 0.095 -9999 0 -0.39 3 3
RAF1 0.017 0.021 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.21 -9999 0 -0.61 47 47
FCER1G -0.009 0.083 -9999 0 -0.32 27 27
FCER1A -0.073 0.23 -9999 0 -0.57 59 59
Antigen/IgE/Fc epsilon R1/Fyn -0.079 0.15 -9999 0 -0.5 34 34
MAPK3 0.029 0.018 -9999 0 -10000 0 0
MAPK1 0.029 0.018 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.015 0.064 -9999 0 -0.6 3 3
DUSP1 -0.12 0.32 -9999 0 -0.85 65 65
NF-kappa-B/RelA -0.018 0.042 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.003 0.082 -9999 0 -0.32 2 2
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.04 0.099 -9999 0 -0.52 8 8
FER -0.011 0.093 -9999 0 -0.39 5 5
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.077 0.18 -9999 0 -0.54 53 53
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.01 0.13 -9999 0 -0.59 9 9
cytokine secretion -0.013 0.031 -9999 0 -10000 0 0
SPHK1 -0.011 0.09 -9999 0 -0.33 4 4
PTK2 -0.003 0.085 -9999 0 -0.33 2 2
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.065 0.14 -9999 0 -0.46 33 33
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.009 0.15 -9999 0 -0.42 33 33
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.045 0.089 -9999 0 -0.4 11 11
MAP2K4 0.021 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.22 -9999 0 -0.66 43 43
mol:Choline -0.045 0.15 -9999 0 -0.46 34 34
SHC/Grb2/SOS1 -0.03 0.064 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.005 0.08 -9999 0 -10000 0 0
HCLS1 -0.01 0.093 -9999 0 -0.37 4 4
PRKCB -0.007 0.12 -9999 0 -0.36 26 26
FCGR2B -0.032 0.19 -9999 0 -0.76 24 24
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.019 0.11 -9999 0 -0.4 9 9
LCP2 0.007 0.046 -9999 0 -0.32 8 8
PLA2G4A -0.046 0.17 -9999 0 -0.52 34 34
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.045 0.15 -9999 0 -0.46 34 34
IKK complex 0.02 0.075 -9999 0 -0.23 4 4
WIPF1 0.013 0 -9999 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.015 0.093 -10000 0 -0.33 4 4
epithelial cell differentiation -0.044 0.097 -10000 0 -0.5 8 8
ITCH 0.024 0.021 -10000 0 -10000 0 0
WWP1 -0.002 0.08 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.003 0.095 -10000 0 -0.85 5 5
PRL 0.001 0.016 -10000 0 -0.31 1 1
neuron projection morphogenesis -0.001 0.15 -10000 0 -0.54 8 8
PTPRZ1 -0.02 0.15 -10000 0 -0.6 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.062 0.14 -10000 0 -0.47 40 40
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.049 0.18 -10000 0 -0.55 40 40
ADAM17 0.022 0.048 -10000 0 -0.85 1 1
ErbB4/ErbB4 -0.012 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.049 0.18 -10000 0 -0.59 31 31
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.072 0.16 -10000 0 -0.52 40 40
GRIN2B -0.034 0.16 -10000 0 -0.49 40 40
ErbB4/ErbB2/betacellulin -0.035 0.1 -10000 0 -0.63 9 9
STAT1 0.006 0.048 -10000 0 -0.31 9 9
HBEGF -0.004 0.072 -10000 0 -0.31 21 21
PRLR -0.042 0.19 -10000 0 -0.58 38 38
E4ICDs/ETO2 -0.006 0.086 -10000 0 -0.33 1 1
axon guidance 0 0.082 -10000 0 -0.33 2 2
NEDD4 0.022 0.048 -10000 0 -0.85 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.041 0.14 -10000 0 -0.67 19 19
CBFA2T3 0.012 0.016 -10000 0 -0.31 1 1
ErbB4/ErbB2/HBEGF -0.029 0.058 -10000 0 -0.67 1 1
MAPK3 -0.01 0.15 -10000 0 -0.44 40 40
STAT1 (dimer) -0.009 0.09 -10000 0 -0.33 3 3
MAPK1 -0.01 0.15 -10000 0 -0.44 40 40
JAK2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.072 0.16 -10000 0 -0.52 40 40
NRG1 -0.039 0.21 -10000 0 -0.68 40 40
NRG3 -0.053 0.23 -10000 0 -0.85 31 31
NRG2 -0.095 0.28 -10000 0 -0.82 53 53
NRG4 0.007 0.039 -10000 0 -0.31 6 6
heart development 0 0.082 -10000 0 -0.33 2 2
neural crest cell migration -0.071 0.15 -10000 0 -0.51 40 40
ERBB2 0.029 0.035 -10000 0 -0.64 1 1
WWOX/E4ICDs -0.006 0.085 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.04 0.089 -10000 0 -0.59 5 5
apoptosis 0.059 0.14 0.48 31 -10000 0 31
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.077 0.2 -10000 0 -0.57 51 51
ErbB4/ErbB2/epiregulin -0.078 0.085 -10000 0 -0.67 1 1
ErbB4/ErbB4/betacellulin/betacellulin -0.018 0.13 -10000 0 -0.67 9 9
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.059 0.12 -10000 0 -0.5 19 19
MDM2 -0.001 0.088 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.066 0.16 -10000 0 -0.53 40 40
STAT5A 0.008 0.077 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.078 0.17 -10000 0 -0.53 44 44
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.033 0.063 -10000 0 -10000 0 0
STAT5A (dimer) -0.047 0.1 -10000 0 -0.54 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.007 0.075 -10000 0 -10000 0 0
LRIG1 0.007 0.074 -10000 0 -0.85 3 3
EREG -0.14 0.16 -10000 0 -0.31 189 189
BTC -0.006 0.13 -10000 0 -0.85 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0 0.083 -10000 0 -0.33 2 2
ERBB4 -0.012 0.1 -10000 0 -10000 0 0
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.011 0.021 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.054 -10000 0 -0.53 1 1
glial cell differentiation 0.033 0.063 -10000 0 -10000 0 0
WWOX 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.024 0.17 -10000 0 -0.47 44 44
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.017 0.089 -9999 0 -0.5 13 13
RGS9BP -0.042 0.21 -9999 0 -0.85 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.072 0.26 -9999 0 -0.84 41 41
mol:Na + -0.022 0.057 -9999 0 -10000 0 0
mol:ADP -0.049 0.2 -9999 0 -0.66 40 40
GNAT2 0.009 0.023 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.095 0.22 -9999 0 -0.58 66 66
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.012 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.065 -9999 0 -0.31 2 2
Cone PDE6 -0.083 0.19 -9999 0 -0.51 66 66
Cone Metarhodopsin II -0.053 0.16 -9999 0 -0.54 40 40
Na + (4 Units) -0.025 0.06 -9999 0 -10000 0 0
GNAT2/GDP -0.083 0.19 -9999 0 -0.51 66 66
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.012 0.014 -9999 0 -10000 0 0
Cone Transducin -0.018 0.093 -9999 0 -0.53 13 13
SLC24A2 -0.01 0.065 -9999 0 -0.31 18 18
GNB3/GNGT2 -0.022 0.12 -9999 0 -0.66 13 13
GNB3 -0.014 0.15 -9999 0 -0.85 13 13
GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
CNGA3 -0.028 0.11 -9999 0 -0.31 51 51
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.022 0.057 -9999 0 -10000 0 0
mol:Pi -0.095 0.22 -9999 0 -0.58 66 66
Cone CNG Channel -0.016 0.043 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.01 0.065 -9999 0 -0.31 18 18
RGS9 -0.077 0.26 -9999 0 -0.83 44 44
PDE6C 0.004 0.006 -9999 0 -10000 0 0
GNGT2 0.012 0.023 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.067 0.085 -10000 0 -0.35 20 20
NT3 (dimer)/TRKC -0.095 0.2 -10000 0 -0.7 35 35
NT3 (dimer)/TRKB -0.087 0.19 -10000 0 -0.6 42 42
SHC/Grb2/SOS1/GAB1/PI3K 0.039 0.019 -10000 0 -0.34 1 1
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.018 0.15 -10000 0 -0.65 19 19
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 0 0.055 -10000 0 -0.31 12 12
NTRK2 0.007 0.074 -10000 0 -0.85 3 3
NTRK3 -0.061 0.18 -10000 0 -0.4 73 73
NT-4/5 (dimer)/TRKB -0.067 0.17 -10000 0 -0.61 32 32
neuron apoptosis 0.042 0.096 0.43 13 -10000 0 13
SHC 2-3/Grb2 -0.045 0.1 -10000 0 -0.47 13 13
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.031 0.098 -10000 0 -0.68 5 5
SHC3 -0.049 0.1 -10000 0 -0.57 10 10
STAT3 (dimer) 0.017 0.026 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.088 0.18 -10000 0 -0.61 39 39
RIN/GDP -0.01 0.064 -10000 0 -0.28 3 3
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.032 0.098 -10000 0 -0.44 20 20
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.025 0.047 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.15 -10000 0 -0.6 22 22
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.018 0.085 -10000 0 -0.57 8 8
TRKA/NEDD4-2 -0.006 0.034 -10000 0 -10000 0 0
ELMO1 -0.32 0.42 -10000 0 -0.85 159 159
RhoG/GTP/ELMO1/DOCK1 -0.23 0.29 -10000 0 -0.58 159 159
NGF 0.006 0.075 -10000 0 -0.72 4 4
HRAS 0.012 0.023 -10000 0 -0.31 2 2
DOCK1 0.009 0.06 -10000 0 -0.85 2 2
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.026 0.18 -10000 0 -0.82 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.21 0.24 -10000 0 -0.49 174 174
mol:GDP -0.017 0.093 -10000 0 -0.39 5 5
NGF (dimer) 0.006 0.075 -10000 0 -0.72 4 4
RhoG/GDP -0.26 0.32 -10000 0 -0.67 159 159
RIT1/GDP -0.005 0.065 -10000 0 -0.27 3 3
TIAM1 -0.17 0.16 -10000 0 -0.32 230 230
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.023 0.12 -10000 0 -0.65 13 13
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.051 0.21 -10000 0 -0.85 24 24
RAP1/GDP -0.019 0.044 -10000 0 -10000 0 0
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.018 0.15 -10000 0 -0.65 19 19
ubiquitin-dependent protein catabolic process -0.009 0.055 -10000 0 -0.57 3 3
Schwann cell development -0.043 0.033 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.043 0 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.072 0.16 -10000 0 -0.5 45 45
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.037 -10000 0 -10000 0 0
STAT3 0.017 0.026 -10000 0 -10000 0 0
axon guidance -0.069 0.16 -10000 0 -0.48 45 45
MAPK3 0.016 0.083 -10000 0 -0.52 8 8
MAPK1 0.016 0.083 -10000 0 -0.52 8 8
CDC42/GDP -0.005 0.065 -10000 0 -0.27 3 3
NTF3 -0.051 0.21 -10000 0 -0.85 24 24
NTF4 -0.02 0.15 -10000 0 -0.61 22 22
NGF (dimer)/TRKA/FAIM -0.009 0.056 -10000 0 -0.57 3 3
PI3K -0.002 0.032 -10000 0 -0.66 1 1
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.12 -10000 0 -0.52 23 23
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.058 0.19 -10000 0 -0.62 34 34
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.045 -10000 0 -10000 0 0
Rac1/GDP -0.005 0.065 -10000 0 -0.28 2 2
NGF (dimer)/TRKA/GRIT -0.01 0.057 -10000 0 -0.58 3 3
neuron projection morphogenesis 0 0.1 -10000 0 -0.53 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.009 0.056 -10000 0 -0.57 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.063 0.2 -10000 0 -0.45 67 67
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.088 -10000 0 -0.36 20 20
RAS family/GTP/PI3K 0.032 0.024 -10000 0 -0.44 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.061 -10000 0 -0.62 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.034 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.021 0.11 -10000 0 -0.6 13 13
NGF (dimer)/TRKA/p62/Atypical PKCs -0.007 0.046 -10000 0 -0.49 3 3
MATK -0.001 0.1 -10000 0 -0.58 10 10
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.016 0.043 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.036 0.1 -10000 0 -0.47 20 20
Rac1/GTP -0.19 0.15 -10000 0 -0.36 163 163
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.049 0.35 -9999 0 -0.94 11 11
PLK1 0.042 0.073 -9999 0 -10000 0 0
BIRC5 0.023 0.13 -9999 0 -1.6 1 1
HSPA1B 0.049 0.35 -9999 0 -0.94 11 11
MAP2K1 0.032 0.037 -9999 0 -10000 0 0
BRCA2 0.042 0.36 -9999 0 -1 14 14
FOXM1 0.037 0.39 -9999 0 -1 16 16
XRCC1 0.049 0.35 -9999 0 -0.94 11 11
FOXM1B/p19 -0.094 0.3 -9999 0 -0.9 21 21
Cyclin D1/CDK4 0.034 0.33 -9999 0 -0.87 11 11
CDC2 0.042 0.36 -9999 0 -0.91 16 16
TGFA 0.016 0.34 -9999 0 -0.86 13 13
SKP2 0.046 0.35 -9999 0 -0.95 12 12
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.049 0.35 -9999 0 -0.94 11 11
RB1 -0.052 0.095 -9999 0 -10000 0 0
FOXM1C/SP1 0.034 0.36 -9999 0 -0.99 15 15
AURKB -0.005 0.13 -9999 0 -10000 0 0
CENPF 0.042 0.36 -9999 0 -0.97 12 12
CDK4 0.018 0.015 -9999 0 -10000 0 0
MYC 0.041 0.35 -9999 0 -0.9 16 16
CHEK2 0.032 0.037 -9999 0 -10000 0 0
ONECUT1 0.031 0.34 -9999 0 -0.91 12 12
CDKN2A -0.12 0.16 -9999 0 -0.31 169 169
LAMA4 0.049 0.35 -9999 0 -0.94 11 11
FOXM1B/HNF6 0.024 0.37 -9999 0 -1 12 12
FOS -0.19 0.66 -9999 0 -1.2 107 107
SP1 0.014 0.006 -9999 0 -10000 0 0
CDC25B 0.048 0.35 -9999 0 -0.95 11 11
response to radiation 0.015 0.034 -9999 0 -10000 0 0
CENPB 0.049 0.35 -9999 0 -0.94 11 11
CENPA 0.041 0.36 -9999 0 -0.96 13 13
NEK2 0.039 0.36 -9999 0 -0.96 13 13
HIST1H2BA 0.04 0.35 -9999 0 -0.95 11 11
CCNA2 0.008 0.051 -9999 0 -0.33 9 9
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.037 0.37 -9999 0 -1 12 12
CCNB2 0.045 0.36 -9999 0 -0.98 11 11
CCNB1 0.044 0.36 -9999 0 -0.97 12 12
ETV5 0.048 0.35 -9999 0 -0.94 12 12
ESR1 0 0.43 -9999 0 -1.1 29 29
CCND1 0.037 0.34 -9999 0 -0.89 11 11
GSK3A 0.03 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.036 0.052 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.12 0.23 -9999 0 -0.91 16 16
GAS1 -0.13 0.62 -9999 0 -1.2 86 86
MMP2 0.042 0.37 -9999 0 -1.1 13 13
RB1/FOXM1C 0.045 0.34 -9999 0 -0.93 11 11
CREBBP 0.013 0 -9999 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.035 0.065 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.01 0.018 -9999 0 -10000 0 0
AURKB -0.06 0.14 -9999 0 -0.31 91 91
AURKC 0.004 0.055 -9999 0 -0.31 12 12
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.062 0.15 -9999 0 -0.45 54 54
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.051 0.12 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.009 0.023 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -10000 0 0
CaM/Ca2+ -0.057 0.14 -9999 0 -0.42 54 54
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.022 0.16 -9999 0 -0.42 54 54
AKT1 -0.004 0.15 -9999 0 -0.41 3 3
MAP2K1 -0.007 0.15 -9999 0 -0.39 54 54
MAP3K11 -0.018 0.16 -9999 0 -0.42 54 54
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.026 0.07 -9999 0 -0.66 1 1
Rap1/GTP -0.042 0.1 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.065 0.16 -9999 0 -0.47 54 54
CEBPB 0.016 0.17 -9999 0 -0.78 2 2
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.058 0.14 -9999 0 -10000 0 0
STAT1 -0.021 0.16 -9999 0 -0.42 54 54
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.11 0.29 -9999 0 -0.75 65 65
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
STAT1 (dimer)/PIAS1 -0.048 0.14 -9999 0 -0.39 54 54
CEBPB/PTGES2/Cbp/p300 -0.036 0.081 -9999 0 -0.43 2 2
mol:Ca2+ -0.061 0.15 -9999 0 -0.44 54 54
MAPK3 0.008 0.14 -9999 0 -0.49 2 2
STAT1 (dimer) -0.031 0.081 -9999 0 -10000 0 0
MAPK1 0.008 0.14 -9999 0 -0.49 2 2
JAK2 0.009 0.014 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.013 0.18 -9999 0 -0.66 20 20
SMAD7 0.041 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.051 0.13 -9999 0 -0.4 2 2
PI3K -0.056 0.14 -9999 0 -0.4 55 55
IFNG -0.11 0.29 -9999 0 -0.76 65 65
apoptosis 0.011 0.13 -9999 0 -0.44 20 20
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.003 0.065 -9999 0 -0.31 17 17
CAMK2B 0.003 0.095 -9999 0 -0.85 5 5
FRAP1 0 0.14 -9999 0 -0.38 3 3
PRKCD -0.002 0.15 -9999 0 -0.41 3 3
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.024 0.061 -9999 0 -10000 0 0
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.029 0.12 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.056 0.14 -9999 0 -0.42 2 2
SOCS1 0.005 0.025 -9999 0 -10000 0 0
mol:GDP -0.049 0.12 -9999 0 -0.39 2 2
CASP1 0.039 0.064 -9999 0 -0.36 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.041 0.058 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.055 0.13 -9999 0 -0.39 55 55
RAP1/GDP -0.042 0.11 -9999 0 -10000 0 0
CBL -0.019 0.16 -9999 0 -0.42 54 54
MAP3K1 -0.018 0.16 -9999 0 -0.42 54 54
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.061 -9999 0 -10000 0 0
PTPN11 -0.028 0.16 -9999 0 -0.45 54 54
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

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

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
TGFB1 0.038 0.036 -9999 0 -10000 0 0
VDR 0.012 0.016 -9999 0 -0.31 1 1
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.057 0.1 -9999 0 -0.35 36 36
RXRs/LXRs/DNA/Oxysterols -0.046 0.15 -9999 0 -0.45 47 47
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.025 0.073 -9999 0 -0.34 16 16
RXRs/NUR77 -0.27 0.26 -9999 0 -0.66 123 123
RXRs/PPAR -0.053 0.062 -9999 0 -0.4 8 8
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.011 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.012 0.079 -9999 0 -0.51 10 10
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0.016 -9999 0 -0.31 1 1
RARs/RARs/DNA/9cRA -0.012 0.077 -9999 0 -0.5 10 10
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.054 0.03 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.025 0.073 -9999 0 -0.34 16 16
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.011 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.081 -9999 0 -0.6 3 3
NR1H4 0 0.035 -9999 0 -0.31 5 5
RXRs/LXRs/DNA -0.097 0.089 -9999 0 -0.59 3 3
NR1H2 0.015 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.1 0.067 -9999 0 -0.54 3 3
NR4A1 -0.24 0.39 -9999 0 -0.85 121 121
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.046 0.047 -9999 0 -0.32 3 3
RXRG -0.28 0.12 -9999 0 -0.39 44 44
RXR alpha/CCPG 0 0.003 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.014 0.014 -9999 0 -10000 0 0
THRB 0 0.1 -9999 0 -0.85 6 6
PPARG -0.001 0.1 -9999 0 -0.58 10 10
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.41 -9999 0 -1.3 47 47
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.046 0.15 -9999 0 -0.45 47 47
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.008 0.13 -9999 0 -0.85 10 10
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.46 139 139
SREBF1 -0.036 0.14 -9999 0 -0.63 2 2
RXRs/RXRs/DNA/9cRA -0.12 0.081 -9999 0 -0.6 3 3
ABCA1 -0.035 0.14 -9999 0 -0.63 2 2
RARs/THRs -0.019 0.094 -9999 0 -0.48 16 16
RXRs/FXR -0.12 0.071 -9999 0 -0.57 3 3
BCL2 -0.042 0.21 -9999 0 -0.85 26 26
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.002 0.082 -9999 0 -10000 0 0
STMN1 -0.021 0.094 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.026 0.11 -9999 0 -0.57 1 1
Chromosomal passenger complex/Cul3 protein complex 0.008 0.068 -9999 0 -0.29 10 10
BIRC5 -0.018 0.1 -9999 0 -0.34 36 36
DES -0.38 0.3 -9999 0 -0.62 249 249
Aurora C/Aurora B/INCENP -0.013 0.077 -9999 0 -10000 0 0
Aurora B/TACC1 -0.02 0.075 -9999 0 -10000 0 0
Aurora B/PP2A -0.027 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.025 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.053 0.15 -9999 0 -0.39 56 56
Cul3 protein complex -0.016 0.086 -9999 0 -0.57 9 9
KIF2C -0.002 0.043 -9999 0 -10000 0 0
PEBP1 0.01 0.005 -9999 0 -10000 0 0
KIF20A -0.058 0.14 -9999 0 -0.31 90 90
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.027 0.091 -9999 0 -10000 0 0
SEPT1 0.008 0.039 -9999 0 -0.31 6 6
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.006 0.044 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.001 -9999 0 -10000 0 0
H3F3B -0.007 0.055 -9999 0 -10000 0 0
AURKB -0.05 0.14 -9999 0 -0.31 90 90
AURKC 0.004 0.055 -9999 0 -0.31 12 12
CDCA8 0.009 0.029 -9999 0 -0.33 3 3
cytokinesis -0.069 0.08 -9999 0 -0.42 3 3
Aurora B/Septin1 -0.029 0.1 -9999 0 -0.44 3 3
AURKA 0.012 0.002 -9999 0 -10000 0 0
INCENP 0.012 0.006 -9999 0 -10000 0 0
KLHL13 -0.014 0.14 -9999 0 -0.57 19 19
BUB1 -0.11 0.16 -9999 0 -0.31 154 154
hSgo1/Aurora B/Survivin -0.03 0.12 -9999 0 -0.46 17 17
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.033 0.074 -9999 0 -0.37 1 1
SGOL1 -0.003 0.079 -9999 0 -0.34 19 19
CENPA -0.008 0.069 -9999 0 -0.23 3 3
NCAPG -0.028 0.11 -9999 0 -0.31 51 51
Aurora B/HC8 Proteasome -0.027 0.091 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.027 0.091 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.036 0.12 -9999 0 -0.31 61 61
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.09 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.037 0.082 -9999 0 -0.4 3 3
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.007 0.055 -9999 0 -10000 0 0
KIF23 -0.006 0.076 -9999 0 -0.32 23 23
VIM -0.021 0.093 -9999 0 -10000 0 0
RACGAP1 0.012 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.016 0.084 -9999 0 -0.25 19 19
Chromosomal passenger complex/EVI5 0.012 0.12 -9999 0 -0.43 4 4
TACC1 0.013 0 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
IL1-mediated signaling events

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.031 0.071 -9999 0 -0.32 7 7
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.13 0.26 -9999 0 -0.7 65 65
IL1A -0.06 0.24 -9999 0 -0.81 36 36
IL1B -0.036 0.19 -9999 0 -0.67 34 34
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.022 -9999 0 -0.45 1 1
IL1R2 -0.089 0.25 -9999 0 -0.62 66 66
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.026 0.059 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.002 0.095 -9999 0 -0.85 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.067 0.022 -9999 0 -10000 0 0
JUN -0.07 0.21 -9999 0 -0.44 98 98
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.069 0.14 -9999 0 -0.5 34 34
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.079 0.15 -9999 0 -0.53 33 33
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.071 0.14 -9999 0 -0.5 33 33
IL1 beta fragment/IL1R1/IL1RAP -0.082 0.16 -9999 0 -0.56 33 33
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.029 0.08 -9999 0 -0.48 9 9
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.042 0.11 -9999 0 -0.66 8 8
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
PI3K -0.002 0.032 -9999 0 -0.66 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.09 -9999 0 -0.35 7 7
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.082 0.16 -9999 0 -0.56 33 33
IL1 beta/IL1R2 -0.11 0.24 -9999 0 -0.64 64 64
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.023 -9999 0 -0.46 1 1
NF kappa B1 p50/RelA -0.059 0.12 -9999 0 -0.58 7 7
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.074 0.15 -9999 0 -0.51 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.11 -9999 0 -0.35 33 33
IL1 alpha/IL1R1/IL1RAP -0.09 0.16 -9999 0 -0.58 33 33
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.024 -9999 0 -0.49 1 1
IL1RAP -0.076 0.15 -9999 0 -10000 0 0
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.057 0.12 -9999 0 -0.52 11 11
CASP1 0.006 0.066 -9999 0 -0.53 5 5
IL1RN/IL1R2 -0.12 0.22 -9999 0 -0.63 53 53
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.074 0.15 -9999 0 -0.52 33 33
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.081 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
IL1RN -0.052 0.16 -9999 0 -0.38 68 68
TRAF6/TAK1/TAB1/TAB2 -0.001 0.024 -9999 0 -0.48 1 1
MAP2K6 0.025 0.065 -9999 0 -0.46 7 7
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.012 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0 0.01 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.016 0.065 -9999 0 -0.29 2 2
RAB3GAP2/RIMS1/UNC13B 0 0.008 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.011 0.017 -9999 0 -0.31 1 1
mol:ACh -0.007 0.041 -9999 0 -0.16 24 24
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.016 0.065 -9999 0 -0.29 2 2
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.02 0.095 -9999 0 -0.31 39 39
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.12 0.17 -9999 0 -0.42 55 55
SNAP25 -0.032 0.098 -9999 0 -0.39 24 24
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.18 0.24 -9999 0 -0.39 195 195
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.017 0.051 -9999 0 -0.58 3 3
ADCY5 -0.064 0.21 -9999 0 -0.58 57 57
ADCY6 0.017 0.051 -9999 0 -0.58 3 3
ADCY7 0.017 0.051 -9999 0 -0.58 3 3
ADCY1 0.01 0.078 -9999 0 -0.6 6 6
ADCY2 -0.041 0.18 -9999 0 -0.59 38 38
ADCY3 0.017 0.051 -9999 0 -0.58 3 3
ADCY8 -0.12 0.099 -9999 0 -0.73 3 3
PRKCE 0.007 0.058 -9999 0 -0.67 3 3
ADCY9 0.017 0.051 -9999 0 -0.58 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.056 0.1 -9999 0 -0.37 26 26
Syndecan-3-mediated signaling events

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

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
Gs family/GDP/Gbeta gamma -0.06 0.16 -10000 0 -0.5 49 49
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.055 -10000 0 -0.21 27 27
GNB1/GNG2 0 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.065 0.18 -10000 0 -0.54 49 49
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.014 0.039 0.12 49 -10000 0 49
GNAL -0.09 0.28 -10000 0 -0.85 49 49
GNG2 0.013 0 -10000 0 -10000 0 0
CRH -0.014 0.08 -10000 0 -0.31 27 27
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.041 -10000 0 -0.47 3 3
MAPK11 0.009 0 -10000 0 -10000 0 0
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) -0.01 0.085 -10000 0 -0.77 5 5
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.002 0.11 -10000 0 -0.85 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.008 0.06 -10000 0 -0.85 2 2
AP1 -0.15 0.27 -10000 0 -0.54 118 118
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.002 0.095 -10000 0 -0.85 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.054 -10000 0 -10000 0 0
NICD/RBPSUH -0.009 0.084 -10000 0 -0.77 5 5
WIF1 -0.034 0.1 -10000 0 -0.31 50 50
NOTCH1 -0.01 0.086 -10000 0 -0.79 5 5
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.011 0.085 -10000 0 -0.31 30 30
DKK1 -0.041 0.13 -10000 0 -0.85 2 2
beta catenin/beta TrCP1 0.036 0.039 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0.002 0.029 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.04 -10000 0 -0.36 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.21 0.38 -10000 0 -0.85 106 106
JUN -0.18 0.36 -10000 0 -0.85 93 93
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.03 0.042 0.24 12 -10000 0 12
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.039 0.12 -10000 0 -0.6 17 17
HNF1A 0.01 0.043 -10000 0 -0.85 1 1
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.012 0.24 -10000 0 -1.5 10 10
NKD1 -0.017 0.15 -10000 0 -0.75 16 16
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.017 0.1 -10000 0 -0.59 12 12
apoptosis -0.15 0.26 -10000 0 -0.54 118 118
Delta 1/NOTCHprecursor -0.009 0.081 -10000 0 -0.74 5 5
DLL1 0.012 0.016 -10000 0 -0.31 1 1
PPARD 0.024 0.016 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC 0.002 0.029 -10000 0 -10000 0 0
DVL1 0 0.002 -10000 0 -10000 0 0
CSNK2A1 0.013 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.038 0.083 -10000 0 -0.65 2 2
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.002 -10000 0 -10000 0 0
NLK 0.015 0.007 -10000 0 -10000 0 0
CCND1 0.018 0.045 -10000 0 -10000 0 0
WNT1 0.009 0.023 -10000 0 -0.31 2 2
Axin1/APC/beta catenin 0.046 0.035 -10000 0 -10000 0 0
DKK2 -0.031 0.18 -10000 0 -0.65 27 27
NOTCH1 precursor/DVL1 -0.005 0.073 -10000 0 -0.66 5 5
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.018 0.1 -10000 0 -0.6 12 12
PPP2R5D 0.013 0.068 0.38 13 -10000 0 13
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.017 0.044 -10000 0 -10000 0 0
RBPJ 0.012 0.016 -10000 0 -0.31 1 1
CREBBP 0.016 0.004 -10000 0 -10000 0 0
Insulin-mediated glucose transport

Figure 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
Insulin responsive Vesicles 0.005 0.074 -9999 0 -0.37 5 5
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0.013 0 -9999 0 -10000 0 0
AKT2 0.013 0 -9999 0 -10000 0 0
STXBP4 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.036 0.075 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
TBC1D4 -0.054 0.22 -9999 0 -0.66 47 47
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
SNARE/Synip 0 0 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
ASIP -0.023 0.1 -9999 0 -0.31 44 44
PRKCI 0.013 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
GYS1 0.034 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
TRIP10 0.013 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.035 0.099 -9999 0 -10000 0 0
VAMP2 0.013 0 -9999 0 -10000 0 0
SLC2A4 0.037 0.079 -9999 0 -10000 0 0
STX4 0.013 0 -9999 0 -10000 0 0
GSK3B 0.027 0 -9999 0 -10000 0 0
SFN -0.21 0.19 -9999 0 -0.34 265 265
LNPEP -0.006 0.13 -9999 0 -0.85 9 9
YWHAE 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.013 0.12 -10000 0 -0.59 9 9
UGCG -0.034 0.16 -10000 0 -0.82 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.025 0.13 -10000 0 -0.39 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.013 0.16 -10000 0 -0.81 15 15
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.054 0.13 -10000 0 -0.41 39 39
FRAP1 0.01 0.19 -10000 0 -0.45 48 48
FOXO3 0.025 0.16 -10000 0 -0.58 15 15
AKT1 0.017 0.17 -10000 0 -0.53 24 24
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 -0.005 0.022 -10000 0 -10000 0 0
SGMS1 -0.005 0.022 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.031 -10000 0 -0.58 1 1
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.005 0.15 -10000 0 -0.55 17 17
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.022 0.035 -10000 0 -0.66 1 1
RPS6KB1 0.017 0.042 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.012 6 6
JAK3 -0.06 0.14 -10000 0 -0.31 94 94
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.013 0.21 -10000 0 -0.88 16 16
MYB -0.017 0.2 -10000 0 -1.4 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.013 0.16 -10000 0 -0.6 18 18
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.013 0.16 -10000 0 -0.58 18 18
Rac1/GDP 0.026 0.029 -10000 0 -0.53 1 1
T cell proliferation 0.022 0.15 -10000 0 -0.54 17 17
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.054 13 13
PRKCZ 0.021 0.15 -10000 0 -0.57 17 17
NF kappa B1 p50/RelA -0.053 0.13 -10000 0 -0.45 25 25
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.004 0.13 -10000 0 -0.6 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.044 0.2 -10000 0 -0.59 39 39
IL2RB -0.013 0.14 -10000 0 -0.55 20 20
TERT 0 0.032 -10000 0 -0.31 4 4
E2F1 -0.005 0.077 -10000 0 -0.45 9 9
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.026 13 -10000 0 13
PTPN11 0.013 0.004 -10000 0 -10000 0 0
IL2RG -0.045 0.2 -10000 0 -0.56 43 43
actin cytoskeleton organization 0.022 0.15 -10000 0 -0.54 17 17
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.013 0.043 -10000 0 -0.85 1 1
Rac1/GTP 0.033 0.029 -10000 0 -0.51 1 1
LCK -0.007 0.11 -10000 0 -0.44 20 20
BCL2 -0.015 0.27 -10000 0 -0.83 35 35
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.008 0.1 -9999 0 -0.41 21 21
CCNA2 0.006 0.048 -9999 0 -0.31 9 9
PIK3CA 0.012 0.043 -9999 0 -0.85 1 1
JAK3 -0.061 0.14 -9999 0 -0.31 94 94
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.022 0.15 -9999 0 -0.6 15 15
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.021 0 -9999 0 -10000 0 0
IL2RA -0.035 0.24 -9999 0 -1 21 21
IL2RB -0.014 0.14 -9999 0 -0.56 20 20
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.047 0.2 -9999 0 -0.56 43 43
G1/S transition of mitotic cell cycle 0.042 0.04 -9999 0 -0.62 1 1
PTPN11 0.014 0 -9999 0 -10000 0 0
CCND2 0.033 0 -9999 0 -10000 0 0
LCK -0.009 0.11 -9999 0 -0.45 20 20
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.011 0.043 -9999 0 -0.85 1 1
CCND3 0.033 0.13 -9999 0 -0.64 7 7
Insulin Pathway

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
CBL/APS/CAP -0.05 0.14 -9999 0 -0.45 45 45
TC10/GTP -0.002 0.031 -9999 0 -0.44 2 2
Insulin Receptor/Insulin/IRS1/Shp2 -0.056 0.16 -9999 0 -0.54 43 43
HRAS 0.012 0.023 -9999 0 -0.31 2 2
APS homodimer 0.012 0.016 -9999 0 -0.31 1 1
GRB14 -0.019 0.16 -9999 0 -0.85 15 15
FOXO3 -0.021 0.098 -9999 0 -0.72 7 7
AKT1 -0.011 0.16 -9999 0 -0.43 16 16
INSR 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.009 0.06 -9999 0 -0.85 2 2
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.038 0 -9999 0 -10000 0 0
CAV1 -0.041 0.18 -9999 0 -0.5 54 54
CBL/APS/CAP/Crk-II/C3G -0.003 0.034 -9999 0 -0.48 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.056 0.16 -9999 0 -0.54 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.05 0.14 -9999 0 -0.47 44 44
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.006 0.1 -9999 0 -10000 0 0
RPS6KB1 0 0.15 -9999 0 -0.69 1 1
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.054 0.13 -9999 0 -0.67 1 1
HRAS/GTP -0.047 0.12 -9999 0 -0.41 43 43
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.052 0.15 -9999 0 -0.5 43 43
PRKCI -0.014 0.035 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.063 0.16 -9999 0 -0.44 59 59
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.051 0.15 -9999 0 -0.48 44 44
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.015 -9999 0 -10000 0 0
AKT2 -0.011 0.16 -9999 0 -0.43 17 17
PRKCZ -0.014 0.035 -9999 0 -10000 0 0
SH2B2 0.012 0.016 -9999 0 -0.31 1 1
SHC/SHIP -0.026 0.16 -9999 0 -0.48 43 43
F2RL2 -0.082 0.15 -9999 0 -0.32 118 118
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.003 0.037 -9999 0 -0.52 2 2
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.036 0.17 -9999 0 -0.51 43 43
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.022 0.14 -9999 0 -1.1 7 7
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.078 0.26 -9999 0 -0.85 43 43
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.035 0.16 -9999 0 -0.5 43 43
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.002 0.15 -9999 0 -0.55 3 3
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.011 0.043 -9999 0 -0.85 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.004 0.12 -9999 0 -0.34 43 43
Insulin Receptor/Insulin/IRS1 -0.057 0.17 -9999 0 -0.54 43 43
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.036 0.059 -9999 0 -0.49 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure 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
HIF3A -0.17 0.35 -9999 0 -0.85 86 86
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0.016 -9999 0 -0.31 1 1
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.023 -9999 0 -10000 0 0
HIF1A 0.022 0.024 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.034 -9999 0 -0.48 2 2
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.12 0.16 -9999 0 -0.31 169 169
ARNT/IPAS -0.14 0.27 -9999 0 -0.66 86 86
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.023 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0.008 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.084 -9999 0 -0.52 10 10
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.014 -9999 0 -10000 0 0
VHL 0.009 0.06 -9999 0 -0.85 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.023 -9999 0 -10000 0 0
EGLN3 -0.022 0.15 -9999 0 -0.5 28 28
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.044 -9999 0 -0.59 2 2
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.03 0.073 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.002 0.1 0.56 11 -10000 0 11
PI3K Class IB/PDE3B -0.002 0.1 -10000 0 -0.56 11 11
PDE3B -0.002 0.1 -10000 0 -0.56 11 11
Ceramide signaling pathway

Figure 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
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.004 0.15 -10000 0 -0.72 10 10
BAG4 0.011 0.043 -10000 0 -0.85 1 1
PKC zeta/ceramide -0.017 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.038 0.2 -10000 0 -0.85 21 21
BAX -0.005 0.019 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.009 -10000 0 -10000 0 0
BAD -0.017 0.041 -10000 0 -10000 0 0
SMPD1 -0.006 0.098 -10000 0 -0.27 47 47
RB1 -0.017 0.041 -10000 0 -10000 0 0
FADD/Caspase 8 0.008 0.14 -10000 0 -0.68 10 10
MAP2K4 -0.008 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.01 0.048 -10000 0 -0.59 1 1
EGF -0.11 0.3 -10000 0 -0.8 61 61
mol:ceramide -0.028 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.034 -10000 0 -0.66 1 1
ASAH1 0.011 0.043 -10000 0 -0.85 1 1
negative regulation of cell cycle -0.017 0.04 -10000 0 -10000 0 0
cell proliferation -0.097 0.17 -10000 0 -0.41 89 89
BID -0.018 0.093 -10000 0 -0.41 10 10
MAP3K1 -0.017 0.041 -10000 0 -10000 0 0
EIF2A 0 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.003 0.045 -10000 0 -0.54 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.003 0.045 -10000 0 -0.54 1 1
Cathepsin D/ceramide -0.017 0.04 -10000 0 -10000 0 0
FADD -0.004 0.15 -10000 0 -0.72 10 10
KSR1 -0.018 0.05 -10000 0 -0.63 1 1
MAPK8 -0.005 0.048 -10000 0 -0.35 3 3
PRKRA -0.017 0.041 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.36 -10000 0 -0.82 94 94
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.043 -10000 0 -10000 0 0
CTSD 0.013 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.084 0.19 -10000 0 -0.44 89 89
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.034 -10000 0 -0.66 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.16 -10000 0 -0.77 10 10
TNFR1A/BAG4/TNF-alpha -0.069 0.18 -10000 0 -0.57 48 48
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.001 0.046 -10000 0 -0.55 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.002 0.049 0.18 19 -10000 0 19
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.032 -10000 0 -0.66 1 1
EIF2AK2 -0.008 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.068 0.18 -10000 0 -0.57 47 47
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.081 -10000 0 -0.34 10 10
MAP2K2 -0.001 0.046 -10000 0 -0.55 1 1
SMPD3 -0.014 0.12 -10000 0 -0.31 53 53
TNF -0.091 0.28 -10000 0 -0.79 53 53
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.021 0.11 0.28 55 -10000 0 55
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.002 0.05 0.18 19 -10000 0 19
BCL2 -0.042 0.21 -10000 0 -0.85 26 26
Signaling events mediated by HDAC Class III

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

Figure 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
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.007 0.045 -9999 0 -0.31 8 8
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.015 -9999 0 -10000 0 0
GNAO1 -0.015 0.15 -9999 0 -0.72 16 16
mol:Sphinganine-1-P 0.02 0.031 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.012 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.012 0.023 -9999 0 -0.31 2 2
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.01 -9999 0 -10000 0 0
S1PR5 0.009 0.036 -9999 0 -0.31 5 5
S1PR4 0.01 0.032 -9999 0 -0.31 4 4
GNAI1 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.017 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.044 0.15 -9999 0 -0.31 95 95
S1P/S1P4/Gi 0.032 0.064 -9999 0 -0.32 12 12
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.18 0.36 -9999 0 -0.85 92 92
GNA15 -0.012 0.094 -9999 0 -0.33 30 30
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.005 0.085 -9999 0 -0.85 4 4
ABCC1 0.013 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.25 0.4 -10000 0 -0.85 126 126
HRAS 0.012 0.023 -10000 0 -0.31 2 2
EGFR 0.003 0.095 -10000 0 -0.85 5 5
AKT 0.018 0.025 0.21 1 -10000 0 1
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.12 0.16 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.008 0.13 -10000 0 -0.75 11 11
PIK3R3 0.011 0.043 -10000 0 -0.85 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.063 0.1 -10000 0 -0.28 40 40
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.025 0.022 -10000 0 -0.17 1 1
PI3K -0.041 0.098 0.23 1 -0.23 43 44
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.024 0.026 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.043 -10000 0 -0.85 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.024 0.091 -9999 0 -10000 0 0
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.3 0.47 -9999 0 -0.98 124 124
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.071 -9999 0 -0.3 18 18
ER alpha/Oestrogen -0.045 0.15 -9999 0 -0.4 46 46
NFX1/SIN3/HDAC complex 0.048 0.018 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.8 61 61
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.005 0.01 -9999 0 -10000 0 0
TERT/c-Abl -0.037 0.066 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.03 0.11 -9999 0 -0.31 51 51
WRN 0.013 0 -9999 0 -10000 0 0
SP1 0.015 0.003 -9999 0 -10000 0 0
SP3 0.013 0.002 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.029 0.051 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.025 0.092 -9999 0 -10000 0 0
CCND1 -0.017 0.091 -9999 0 -10000 0 0
MAX 0.013 0.002 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
RBBP4 0.013 0 -9999 0 -10000 0 0
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
Telomerase/911 0.035 0.02 -9999 0 -10000 0 0
CDKN1B -0.043 0.2 -9999 0 -0.55 54 54
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.011 0.043 -9999 0 -0.85 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.013 0.002 -9999 0 -10000 0 0
JUN -0.18 0.36 -9999 0 -0.85 93 93
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.005 -9999 0 -10000 0 0
FOS -0.21 0.38 -9999 0 -0.85 106 106
IFN-gamma/IRF1 -0.09 0.22 -9999 0 -0.64 55 55
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.012 0.016 -9999 0 -0.31 1 1
Telomerase 0.014 0.071 -9999 0 -0.48 4 4
IRF1 0.017 0.016 -9999 0 -0.3 1 1
ESR1 -0.048 0.2 -9999 0 -0.54 46 46
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.029 -9999 0 -0.58 1 1
ubiquitin-dependent protein catabolic process 0.053 0.017 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.054 0.018 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC2 0.014 0.003 -9999 0 -10000 0 0
ATM -0.001 0.028 -9999 0 -0.58 1 1
SMAD3 0.02 0.027 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0.002 -9999 0 -10000 0 0
MRE11A 0.013 0 -9999 0 -10000 0 0
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.031 0.059 -9999 0 -10000 0 0
NR2F2 0.012 0.002 -9999 0 -10000 0 0
MAPK3 0.017 0.006 -9999 0 -10000 0 0
MAPK1 0.017 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.039 -9999 0 -0.31 6 6
NFKB1 0.013 0 -9999 0 -10000 0 0
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.028 -9999 0 -0.57 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.003 0.095 -9999 0 -0.85 5 5
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.099 0.23 -9999 0 -0.66 60 60
MYC -0.008 0.13 -9999 0 -0.85 10 10
IL2 0.006 0.007 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.008 0.039 -9999 0 -0.31 6 6
TRF2/BLM 0 0.01 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.032 0.065 -9999 0 -10000 0 0
SP1/HDAC2 0.007 0.012 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.029 0.051 -9999 0 -10000 0 0
Smad3/Myc 0.006 0.096 -9999 0 -0.58 10 10
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.1 0.29 -9999 0 -0.75 65 65
Telomerase/PinX1 -0.029 0.051 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.021 0.037 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.029 0.051 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.008 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.005 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.029 0.051 -9999 0 -10000 0 0
E2F1 -0.088 0.15 -9999 0 -0.31 128 128
ZNFX1 0.013 0 -9999 0 -10000 0 0
PIF1 0.002 0.089 -9999 0 -0.62 7 7
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.52 28 28
ITGA4 0.007 0.045 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.64 12 12
alpha4/beta1 Integrin -0.004 0.028 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.004 0.12 -10000 0 -0.85 8 8
ANTXR2 0.011 0.043 -10000 0 -0.85 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.015 -10000 0 -0.1 9 9
monocyte activation -0.045 0.16 -10000 0 -0.48 49 49
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.002 0.013 -10000 0 -10000 0 0
MAP2K7 -0.002 0.013 -10000 0 -10000 0 0
MAP2K6 -0.01 0.065 -10000 0 -0.53 6 6
CYAA 0.005 0.076 -10000 0 -0.5 9 9
MAP2K4 -0.002 0.013 -10000 0 -10000 0 0
IL1B -0.027 0.14 -10000 0 -0.48 34 34
Channel -0.012 0.079 -10000 0 -0.54 9 9
NLRP1 -0.004 0.038 -10000 0 -0.52 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.018 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.015 0.1 9 -10000 0 9
MAPK3 -0.002 0.013 -10000 0 -10000 0 0
MAPK1 -0.002 0.013 -10000 0 -10000 0 0
PGR -0.024 0.087 -10000 0 -0.47 12 12
PA/Cellular Receptors -0.013 0.085 -10000 0 -0.58 9 9
apoptosis -0.002 0.015 -10000 0 -0.1 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.005 0.076 -10000 0 -0.5 9 9
macrophage activation 0.019 0.014 -10000 0 -10000 0 0
TNF -0.091 0.28 -10000 0 -0.79 53 53
VCAM1 -0.046 0.16 -10000 0 -0.48 49 49
platelet activation -0.003 0.018 -10000 0 -10000 0 0
MAPKKK cascade -0.014 0.022 0.12 6 -10000 0 6
IL18 -0.011 0.089 -10000 0 -0.43 12 12
negative regulation of macrophage activation -0.002 0.015 -10000 0 -0.1 9 9
LEF -0.002 0.015 -10000 0 -0.1 9 9
CASP1 -0.003 0.021 -10000 0 -0.23 2 2
mol:cAMP -0.003 0.018 -10000 0 -10000 0 0
necrosis -0.002 0.015 -10000 0 -0.1 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.011 0.075 -10000 0 -0.51 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.038 0.11 0.34 1 -0.36 44 45
FRAP1 0.009 0.024 -10000 0 -10000 0 0
AKT1 -0.031 0.094 0.25 1 -0.29 44 45
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.024 0.07 -10000 0 -0.53 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.02 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.02 0.059 -10000 0 -0.48 1 1
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.03 0.14 -10000 0 -0.43 43 43
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.008 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0.055 -10000 0 -0.38 1 1
MAP3K5 0.011 0.023 -10000 0 -0.46 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.01 0.023 -10000 0 -0.46 1 1
mol:LY294002 0 0.001 0.001 1 -0.002 43 44
EIF4B 0.02 0.05 -10000 0 -0.32 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.012 0.035 -10000 0 -0.3 1 1
eIF4E/eIF4G1/eIF4A1 -0.001 0.006 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.019 0.13 -10000 0 -0.39 44 44
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.037 0.18 1 -0.27 1 2
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.02 0.058 -10000 0 -0.48 1 1
mol:Amino Acids 0 0.001 0.001 1 -0.002 43 44
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.035 0.11 0.26 1 -0.33 44 45
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.036 -10000 0 -0.63 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.025 0.075 -10000 0 -0.59 1 1
tumor necrosis factor receptor activity 0 0.001 0.002 43 -0.001 1 44
RPS6 0.013 0 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.041 0.15 -10000 0 -0.47 43 43
INS 0 0 -10000 0 -10000 0 0
PTEN 0.011 0.043 -10000 0 -0.85 1 1
PDK2 -0.034 0.1 0.26 1 -0.32 44 45
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.011 0.043 -10000 0 -0.85 1 1
PPP2R5D 0.016 0.022 -10000 0 -10000 0 0
peptide biosynthetic process 0.018 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.004 1 2
EEF2 0.018 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.018 0.009 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.048 0.054 -10000 0 -10000 0 0
NFATC2 -0.012 0.088 -10000 0 -0.29 16 16
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.008 0.094 -10000 0 -0.3 26 26
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.027 0.09 -10000 0 -0.57 5 5
BCL2/BAX -0.042 0.16 -10000 0 -0.66 26 26
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.007 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.007 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.012 0.089 -10000 0 -0.53 3 3
Calcineurin A alpha-beta B1/BCL2 -0.042 0.21 -10000 0 -0.85 26 26
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.012 0.088 0.52 3 -10000 0 3
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 265 265
MAP3K8 -0.003 0.1 -10000 0 -0.85 6 6
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.11 0.16 -10000 0 -0.48 15 15
CABIN1 0.008 0.094 -10000 0 -0.31 26 26
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.003 0.097 -10000 0 -0.48 13 13
mol:Ca2+ -0.005 0.01 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.003 0.074 -10000 0 -0.85 3 3
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.007 0.044 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.003 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.013 0.049 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.049 -10000 0 -10000 0 0
PRKCB -0.023 0.11 -10000 0 -0.34 42 42
PRKCE 0.007 0.074 -10000 0 -0.85 3 3
JNK2/NFAT4 0.021 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.038 0.2 -10000 0 -0.85 24 24
PRKCG 0.005 0.023 -10000 0 -0.31 2 2
PRKCQ 0 0.1 -10000 0 -0.85 6 6
FKBP38/BCL2 -0.042 0.16 -10000 0 -0.66 26 26
EP300 0.009 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.038 0.07 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.01 0.063 -10000 0 -0.59 4 4
NFATc/ERK1 0.053 0.051 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.026 0.088 -10000 0 -0.56 5 5
NR4A1 -0.19 0.37 -10000 0 -0.75 123 123
GSK3B 0.01 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.032 0.057 -10000 0 -0.48 2 2
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.009 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.042 0.058 -10000 0 -10000 0 0
CREBBP 0.009 0.007 -10000 0 -10000 0 0
BCL2 -0.042 0.21 -10000 0 -0.85 26 26
Retinoic acid receptors-mediated signaling

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
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.012 0.016 -10000 0 -0.31 1 1
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.058 -10000 0 -0.33 5 5
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.011 0.081 0.24 4 -0.42 10 14
RAR alpha/9cRA/Cyclin H -0.025 0.094 -10000 0 -0.39 24 24
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.03 0.064 -10000 0 -0.38 5 5
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.02 0.082 -10000 0 -0.68 3 3
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.011 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.024 0.17 -10000 0 -0.64 25 25
NCOA2 -0.05 0.22 -10000 0 -0.85 30 30
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.012 0.016 -10000 0 -0.31 1 1
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.008 0.074 -10000 0 -0.85 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.043 0.16 -10000 0 -0.66 24 24
RARA 0.006 0.085 -10000 0 -0.31 27 27
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.006 0.12 -10000 0 -0.51 11 11
PRKCA -0.034 0.2 -10000 0 -0.85 24 24
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.035 0.17 -10000 0 -0.66 25 25
RXRG -0.12 0.12 -10000 0 -0.54 27 27
RXRA 0.011 0.094 -10000 0 -0.34 27 27
RXRB -0.002 0.11 -10000 0 -0.46 24 24
VDR/Vit D3/DNA -0.001 0.011 -10000 0 -10000 0 0
RBP1 -0.001 0.1 -10000 0 -0.61 9 9
CRBP1/9-cic-RA -0.01 0.076 -10000 0 -0.67 5 5
RARB -0.006 0.13 -10000 0 -0.85 10 10
PRKCG 0.008 0.024 -10000 0 -0.31 2 2
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.032 0.18 -10000 0 -0.7 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.012 0.15 -10000 0 -0.55 25 25
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.081 -10000 0 -0.43 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.035 0.17 -10000 0 -0.66 25 25
positive regulation of DNA binding -0.024 0.089 -10000 0 -0.37 24 24
NRIP1 -0.033 0.16 -10000 0 -0.63 20 20
RXRs/RARs -0.042 0.17 -10000 0 -0.66 25 25
RXRs/RXRs/DNA/9cRA -0.055 0.16 -10000 0 -0.69 24 24
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.012 0.046 -10000 0 -10000 0 0
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-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
BAG4 0.011 0.043 -9999 0 -0.85 1 1
Caspase 8 (4 units) -0.023 0.064 -9999 0 -10000 0 0
NEF -0.012 0.056 -9999 0 -10000 0 0
NFKBIA 0.009 0.03 -9999 0 -10000 0 0
BIRC3 -0.005 0.2 -9999 0 -0.85 21 21
CYCS -0.009 0.1 -9999 0 -0.4 5 5
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.043 0.2 -9999 0 -0.72 26 26
MAP2K7 0.023 0.082 -9999 0 -10000 0 0
protein ubiquitination 0.039 0.088 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID -0.019 0.11 -9999 0 -0.42 5 5
NF-kappa-B/RelA/I kappa B alpha -0.021 0.078 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.011 0.043 -9999 0 -0.85 1 1
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.079 -9999 0 -10000 0 0
MAPK8 0.027 0.088 -9999 0 -0.44 3 3
APAF1 0.013 0 -9999 0 -10000 0 0
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.1 -9999 0 -0.31 25 25
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.11 -9999 0 -0.37 10 10
CHUK 0.039 0.094 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.024 -9999 0 -0.48 1 1
TCRz/NEF -0.064 0.19 -9999 0 -0.53 46 46
TNF -0.091 0.28 -9999 0 -0.79 53 53
FASLG -0.077 0.3 -9999 0 -0.87 46 46
NFKB1 0.009 0.03 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.069 0.18 -9999 0 -0.57 48 48
CASP6 -0.005 0.047 -9999 0 -10000 0 0
CASP7 0.028 0.17 -9999 0 -0.64 21 21
RELA 0.009 0.03 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.028 0.17 -9999 0 -0.64 21 21
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.032 -9999 0 -0.66 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.1 -9999 0 -0.38 2 2
APAF-1/Caspase 9 -0.048 0.12 -9999 0 -0.54 21 21
BCL2 0.004 0.14 -9999 0 -0.42 28 28
Class I PI3K 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
ARF5/GTP -0.001 0.031 0.31 1 -0.55 1 2
DAPP1 -0.058 0.14 -10000 0 -0.51 11 11
Src family/SYK family/BLNK-LAT/BTK-ITK -0.064 0.18 -10000 0 -0.58 17 17
mol:DAG -0.008 0.098 -10000 0 -0.28 13 13
HRAS 0.013 0.023 -10000 0 -0.31 2 2
RAP1A 0.014 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.023 0.036 -10000 0 -0.47 1 1
PLCG2 0.013 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.015 0.27 1 -10000 0 1
ARF1/GTP 0 0.022 0.29 1 -10000 0 1
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0 0.015 -10000 0 -10000 0 0
ADAP1 0 0.014 -10000 0 -10000 0 0
ARAP3 0 0.015 0.27 1 -10000 0 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.013 0 -10000 0 -10000 0 0
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.01 0.032 -10000 0 -0.31 4 4
mol:Ca2+ 0.005 0.055 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.32 230 230
ZAP70 -0.025 0.17 -10000 0 -0.66 23 23
mol:IP3 0.002 0.073 -10000 0 -10000 0 0
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.036 -10000 0 -0.47 1 1
RhoA/GDP -0.001 0.021 0.29 1 -10000 0 1
PDK1/Src/Hsp90 -0.002 0.029 -10000 0 -0.57 1 1
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.039 0.039 -10000 0 -10000 0 0
SRC 0.012 0.016 -10000 0 -0.31 1 1
PLEKHA2 0.021 0.043 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.83 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.016 0.31 1 -10000 0 1
RhoA/GTP 0 0.014 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.055 0.16 -10000 0 -0.63 11 11
BLK -0.26 0.39 -10000 0 -0.78 143 143
PDPK1 0.011 0.043 -10000 0 -0.85 1 1
CYTH1 0 0.014 -10000 0 -10000 0 0
HCK -0.008 0.08 -10000 0 -10000 0 0
CYTH3 -0.001 0.031 -10000 0 -0.57 1 1
CYTH2 0 0.014 -10000 0 -10000 0 0
KRAS 0.014 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.01 0.084 -10000 0 -0.63 7 7
SGK1 -0.011 0.095 0.24 1 -0.7 7 8
INPP5D -0.005 0.075 -10000 0 -0.31 23 23
mol:GDP 0.016 0.038 -10000 0 -0.5 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.021 0.3 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.02 0.37 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.015 -10000 0 -10000 0 0
VAV1 -0.014 0.11 -10000 0 -0.37 29 29
mol:PI-3-4-P2 0.012 0.052 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.007 -10000 0 -10000 0 0
PLEKHA1 0.021 0.043 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.036 -10000 0 -0.47 1 1
LAT 0.004 0.086 -10000 0 -0.74 5 5
Rac1/GTP -0.005 0.055 -10000 0 -0.62 1 1
ITK -0.061 0.15 -10000 0 -0.46 52 52
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.019 0.13 -10000 0 -0.41 13 13
LCK -0.009 0.11 -10000 0 -0.45 20 20
BTK -0.013 0.062 -10000 0 -0.46 6 6
Caspase cascade in apoptosis

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
TOP1 0.018 0.094 -10000 0 -0.47 10 10
ACTA1 0.01 0.11 -10000 0 -0.57 10 10
NUMA1 0.018 0.094 -10000 0 -0.47 10 10
SPTAN1 0.015 0.11 -10000 0 -0.56 10 10
LIMK1 0.015 0.11 -10000 0 -0.59 9 9
BIRC3 -0.038 0.2 -10000 0 -0.85 21 21
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
CASP10 -0.001 0.12 -10000 0 -0.59 13 13
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.018 0.094 -10000 0 -0.47 10 10
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.015 0.11 -10000 0 -0.55 10 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.015 0.11 -10000 0 -0.62 8 8
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.057 0.23 -10000 0 -0.67 49 49
BID -0.013 0.07 -10000 0 -0.32 10 10
MAP3K1 0.014 0.042 -10000 0 -0.23 2 2
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.012 0.12 -10000 0 -0.57 10 10
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.016 0.052 -10000 0 -0.23 18 18
neuron apoptosis 0.023 0.016 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.021 0.11 -10000 0 -0.6 8 8
APAF1 0.013 0 -10000 0 -10000 0 0
CASP6 0.021 0.07 -10000 0 -0.49 4 4
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.022 0.11 -10000 0 -0.6 8 8
CASP7 0.01 0.082 0.34 21 -10000 0 21
KRT18 0.016 0.019 -10000 0 -10000 0 0
apoptosis 0.028 0.1 -10000 0 -0.52 8 8
DFFA 0.015 0.11 -10000 0 -0.59 9 9
DFFB 0.015 0.11 -10000 0 -0.59 9 9
PARP1 0.016 0.052 0.23 18 -10000 0 18
actin filament polymerization -0.023 0.1 0.56 8 -10000 0 8
TNF -0.091 0.28 -10000 0 -0.79 53 53
CYCS 0.004 0.046 -10000 0 -0.23 10 10
SATB1 0.029 0.067 -10000 0 -0.46 4 4
SLK 0.015 0.11 -10000 0 -0.56 10 10
p15 BID/BAX -0.004 0.062 -10000 0 -0.35 4 4
CASP2 0.006 0.12 -10000 0 -0.47 10 10
JNK cascade -0.014 0.042 0.23 2 -10000 0 2
CASP3 0.007 0.12 -10000 0 -0.6 10 10
LMNB2 0.02 0.08 -10000 0 -0.39 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.03 0.12 -10000 0 -0.52 21 21
negative regulation of DNA binding -0.056 0.22 -10000 0 -0.66 49 49
stress fiber formation 0.015 0.11 -10000 0 -0.55 10 10
GZMB -0.014 0.14 -10000 0 -0.68 13 13
CASP1 0.015 0.035 -10000 0 -0.46 2 2
LMNB1 0.02 0.081 -10000 0 -0.39 4 4
APP 0.023 0.016 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM 0.022 0.098 -10000 0 -0.51 8 8
LMNA 0.02 0.08 -10000 0 -0.39 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.003 0.12 -10000 0 -0.5 10 10
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.014 0.11 -10000 0 -0.56 10 10
APAF-1/Caspase 9 0.005 0.038 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.018 0.093 -10000 0 -0.46 10 10
CFL2 0.022 0.11 -10000 0 -0.58 8 8
GAS2 0.009 0.13 -10000 0 -0.55 15 15
positive regulation of apoptosis 0.022 0.083 -10000 0 -0.38 4 4
PRF1 -0.002 0.11 -10000 0 -0.67 9 9
BARD1 signaling events

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
BARD1/CSTF1 -0.031 0.14 -10000 0 -0.66 19 19
ATM 0.011 0.043 -10000 0 -0.85 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.013 0 -10000 0 -10000 0 0
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.024 -10000 0 -0.45 1 1
protein ubiquitination -0.023 0.1 -10000 0 -0.48 20 20
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.013 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.011 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.031 0.14 -10000 0 -0.66 19 19
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.004 0.072 -10000 0 -0.31 21 21
DNA repair 0.054 0.099 -10000 0 -0.43 1 1
BRCA1/BARD1/ubiquitin -0.031 0.14 -10000 0 -0.66 19 19
BARD1/DNA-PK -0.024 0.11 -10000 0 -0.52 19 19
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.03 0.14 0.66 19 -10000 0 19
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.085 -10000 0 -0.34 20 20
BRCA1/BACH1/BARD1/TopBP1 -0.026 0.12 -10000 0 -0.57 19 19
BRCA1/BARD1/P53 -0.024 0.11 -10000 0 -0.52 19 19
BARD1/CSTF1/BRCA1 -0.026 0.12 -10000 0 -0.57 19 19
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.027 0.18 -10000 0 -0.85 19 19
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.026 0.12 -10000 0 -0.57 19 19
BRCA1/BARD1/UbcH7 -0.026 0.12 -10000 0 -0.57 19 19
BRCA1/BARD1/RAD51/PCNA -0.025 0.11 -10000 0 -0.52 19 19
BARD1/DNA-PK/P53 -0.023 0.1 -10000 0 -0.48 19 19
BRCA1/BARD1/Ubiquitin -0.031 0.14 -10000 0 -0.66 19 19
BRCA1/BARD1/CTIP -0.025 0.11 -10000 0 -0.52 20 20
FA complex 0.038 0.022 -10000 0 -10000 0 0
BARD1/EWS -0.031 0.14 -10000 0 -0.66 19 19
RBBP8 0.023 0.034 -10000 0 -0.66 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.024 0.11 0.52 19 -10000 0 19
BRCA1/BARD1 -0.024 0.1 -10000 0 -0.49 20 20
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.031 0.14 -10000 0 -0.67 19 19
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.01 0.032 -10000 0 -0.31 4 4
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.031 0.14 -10000 0 -0.66 19 19
EWSR1 0.013 0 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG -0.011 0.16 -9999 0 -0.51 40 40
VEGFR1 homodimer/NRP1/VEGFR 121 -0.003 0.036 -9999 0 -0.52 2 2
CaM/Ca2+ -0.004 0.16 -9999 0 -10000 0 0
HIF1A 0.021 0 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.011 0.16 -9999 0 -0.92 1 1
PLCG1 -0.012 0.16 -9999 0 -0.51 40 40
NOS3 0.018 0.15 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.019 0.15 -9999 0 -10000 0 0
FLT1 0.033 0 -9999 0 -10000 0 0
PGF -0.072 0.26 -9999 0 -0.85 40 40
VEGFR1 homodimer/NRP2/VEGFR121 -0.013 0.049 -9999 0 -0.51 2 2
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
eNOS/Hsp90 0.025 0.14 -9999 0 -10000 0 0
endothelial cell proliferation -0.031 0.2 -9999 0 -0.75 8 8
mol:Ca2+ -0.011 0.16 -9999 0 -0.5 40 40
MAPK3 -0.022 0.19 -9999 0 -0.9 4 4
MAPK1 -0.022 0.19 -9999 0 -0.9 4 4
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.072 0.26 -9999 0 -0.85 40 40
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.01 0.14 -9999 0 -0.85 11 11
VEGFA homodimer 0.009 0.06 -9999 0 -0.85 2 2
VEGFR1 homodimer/VEGFA homodimer 0.031 0.042 -9999 0 -0.56 2 2
platelet activating factor biosynthetic process -0.014 0.19 -9999 0 -0.86 4 4
PI3K -0.048 0.14 -9999 0 -0.48 41 41
PRKCA -0.032 0.2 -9999 0 -0.56 24 24
PRKCB -0.019 0.16 -9999 0 -0.56 5 5
VEGFR1 homodimer/PLGF homodimer -0.025 0.18 -9999 0 -0.56 40 40
VEGFA 0.009 0.06 -9999 0 -0.85 2 2
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.011 0.16 -9999 0 -0.51 40 40
RASA1 0.043 0 -9999 0 -10000 0 0
NRP2 -0.013 0.089 -9999 0 -10000 0 0
VEGFR1 homodimer 0.033 0 -9999 0 -10000 0 0
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.013 0.16 -9999 0 -0.83 2 2
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.048 0.14 -9999 0 -0.47 41 41
mol:L-citrulline 0.019 0.15 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.033 -9999 0 -0.48 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.003 0.036 -9999 0 -0.51 2 2
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.045 0.13 -9999 0 -10000 0 0
PDPK1 0.003 0.15 -9999 0 -0.92 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.003 0.036 -9999 0 -0.51 2 2
mol:NADP 0.019 0.15 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.002 0.033 -9999 0 -0.47 2 2
VEGFR1 homodimer/NRP2 0.019 0.05 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.009 -10000 0 -10000 0 0
CDKN1A 0.034 0.03 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.009 -10000 0 -10000 0 0
AKT1 0 0.008 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.017 0.024 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.009 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.023 -10000 0 -0.45 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.013 0 -10000 0 -10000 0 0
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.023 0.44 1 -10000 0 1
TSC1 0.039 0.009 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.009 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.009 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.043 0.19 -10000 0 -0.57 47 47
MAP3K5 0.011 0.043 -10000 0 -0.85 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.01 0.036 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.039 0.009 -10000 0 -10000 0 0
CASP9 0.039 0.009 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.009 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.002 0.029 -10000 0 -0.57 1 1
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.012 0.016 -10000 0 -0.31 1 1
AKT2/p21CIP1 -0.005 0.025 -10000 0 -0.33 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.003 -10000 0 -10000 0 0
CHUK 0.039 0.009 -10000 0 -10000 0 0
BAD/BCL-XL 0.052 0.009 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0.024 -10000 0 -0.46 1 1
FOXO1-3a-4/14-3-3 family 0.024 0.041 -10000 0 -10000 0 0
PDPK1 0.011 0.043 -10000 0 -0.85 1 1
MDM2 0.039 0.009 -10000 0 -10000 0 0
MAPKKK cascade -0.038 0.009 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.006 -10000 0 -10000 0 0
TSC1/TSC2 0.046 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.006 -10000 0 -10000 0 0
glucose import -0.052 0.21 -10000 0 -0.55 59 59
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.034 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.053 0.21 -10000 0 -0.56 59 59
GSK3A 0.039 0.009 -10000 0 -10000 0 0
FOXO1 0.039 0.009 -10000 0 -10000 0 0
GSK3B 0.039 0.009 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 265 265
G1/S transition of mitotic cell cycle 0.046 0.009 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.002 0.053 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.008 0.062 -9999 0 -0.67 3 3
positive regulation of NF-kappaB transcription factor activity -0.004 0.047 -9999 0 -0.66 2 2
MAP2K4 0.048 0.028 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.009 0.06 -9999 0 -0.85 2 2
SMPD1 -0.002 0.021 -9999 0 -0.3 2 2
IKBKG 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.004 0.047 -9999 0 -0.66 2 2
TRAIL/TRAILR3 -0.064 0.1 -9999 0 -0.66 2 2
TRAIL/TRAILR1 -0.007 0.065 -9999 0 -0.66 4 4
TRAIL/TRAILR4 -0.004 0.047 -9999 0 -0.66 2 2
TRAIL/TRAILR1/DAP3/GTP -0.005 0.052 -9999 0 -0.53 4 4
IKK complex -0.002 0.016 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.02 0.049 -9999 0 -0.66 2 2
MAP3K1 -0.002 0.025 -9999 0 -0.33 2 2
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.009 0.06 -9999 0 -0.85 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.036 0.037 -9999 0 -0.34 4 4
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.02 0.049 -9999 0 -0.66 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP -0.005 0.048 -9999 0 -0.48 4 4
mol:ceramide -0.002 0.021 -9999 0 -0.3 2 2
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.051 0.05 -9999 0 -0.44 3 3
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.085 0.15 -9999 0 -0.31 123 123
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.006 0.057 -9999 0 -0.57 4 4
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.004 0.043 -9999 0 -0.54 2 2
JNK cascade -0.004 0.047 -9999 0 -0.66 2 2
TRAIL (trimer) 0.008 0.062 -9999 0 -0.67 3 3
TNFRSF10C -0.085 0.15 -9999 0 -0.31 123 123
TRAIL/TRAILR1/DAP3/GTP/FADD -0.005 0.049 -9999 0 -0.49 4 4
TRAIL/TRAILR2/FADD -0.003 0.04 -9999 0 -0.57 2 2
cell death -0.002 0.021 -9999 0 -0.3 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.037 0.027 -9999 0 -0.34 2 2
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.012 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.003 0.034 -9999 0 -0.48 2 2
ceramide signaling 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
MAP4K4 0.004 0.13 -10000 0 -0.57 10 10
BAG4 0.011 0.043 -10000 0 -0.85 1 1
BAD 0.018 0.047 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.039 0.2 -10000 0 -0.85 21 21
BAX 0.018 0.047 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.004 0.034 -10000 0 -0.12 10 10
IKBKB 0.013 0.13 -10000 0 -0.53 10 10
MAP2K2 0.028 0.055 -10000 0 -0.38 1 1
MAP2K1 0.028 0.055 -10000 0 -0.38 1 1
SMPD1 0.01 0.034 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.013 0.13 -10000 0 -0.55 10 10
MAP2K4 0.024 0.047 -10000 0 -10000 0 0
protein ubiquitination 0.014 0.13 -10000 0 -0.54 10 10
EnzymeConsortium:2.7.1.37 0.032 0.061 -10000 0 -0.39 1 1
response to UV 0 0.001 -10000 0 -0.003 1 1
RAF1 0.023 0.055 -10000 0 -0.42 1 1
CRADD 0.013 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.049 -10000 0 -0.17 10 10
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.018 0.048 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.031 0.055 -10000 0 -0.37 1 1
MAPK1 0.031 0.055 -10000 0 -0.37 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.004 0.13 -10000 0 -0.57 10 10
KSR1 0.016 0.054 -10000 0 -0.45 1 1
MAPK8 0.028 0.062 -10000 0 -0.47 3 3
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.013 0.13 -10000 0 -0.53 10 10
TNF R/SODD -0.002 0.032 -10000 0 -0.66 1 1
TNF -0.091 0.28 -10000 0 -0.79 53 53
CYCS 0.027 0.056 0.16 22 -10000 0 22
IKBKG 0.013 0.13 -10000 0 -0.53 10 10
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.004 0.14 -10000 0 -0.47 21 21
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.027 0.056 0.16 22 -10000 0 22
TNF/TNF R/SODD -0.069 0.18 -10000 0 -0.57 48 48
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.034 -10000 0 -10000 0 0
NSMAF 0.005 0.13 -10000 0 -0.56 10 10
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 1 1
BCL2 -0.042 0.21 -10000 0 -0.85 26 26
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.008 0.072 -9999 0 -0.66 5 5
PDGFRB 0.013 0.004 -9999 0 -10000 0 0
SPHK1 -0.008 0.022 -9999 0 -10000 0 0
mol:S1P -0.009 0.026 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.011 0.16 -9999 0 -0.72 9 9
GNAO1 -0.015 0.15 -9999 0 -0.72 16 16
PDGFB-D/PDGFRB/PLCgamma1 0.022 0.14 -9999 0 -0.6 9 9
PLCG1 0.018 0.15 -9999 0 -0.66 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.004 -9999 0 -10000 0 0
GNAI2 0.013 0.005 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GNAI1 0.013 0.005 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.065 -9999 0 -0.57 5 5
S1P1/S1P -0.017 0.059 -9999 0 -0.43 5 5
negative regulation of cAMP metabolic process 0.012 0.15 -9999 0 -0.7 9 9
MAPK3 0.003 0.21 -9999 0 -0.6 39 39
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.006 0.074 -9999 0 -0.85 3 3
PLCB2 0.029 0.068 -9999 0 -0.38 5 5
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.049 -9999 0 -0.36 5 5
receptor internalization -0.016 0.055 -9999 0 -0.4 5 5
PTGS2 -0.044 0.36 -9999 0 -1.1 39 39
Rac1/GTP -0.014 0.049 -9999 0 -0.36 5 5
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.06 -9999 0 -0.85 2 2
negative regulation of T cell proliferation 0.012 0.15 -9999 0 -0.7 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.005 -9999 0 -10000 0 0
MAPK1 0.003 0.21 -9999 0 -0.6 39 39
S1P1/S1P/PDGFB-D/PDGFRB 0.032 0.079 -9999 0 -0.44 5 5
ABCC1 0.013 0.002 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.033 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.071 0.01 -9999 0 -10000 0 0
EGFR 0.003 0.095 -9999 0 -0.85 5 5
EPHA2 0.011 0.028 -9999 0 -0.31 3 3
MYO6 0.041 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.04 0.14 -9999 0 -0.61 22 22
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.074 -9999 0 -10000 0 0
EGF -0.11 0.3 -9999 0 -0.8 61 61
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.073 0.2 -9999 0 -0.61 49 49
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.006 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.011 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.051 0.024 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.041 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.067 0.16 -9999 0 -0.45 60 60
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.047 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.18 0.36 -9999 0 -0.82 94 94
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.006 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.048 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.044 0.043 -9999 0 -0.45 3 3
Ephrin A1/EPHA2 -0.001 0.008 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.038 0.074 -9999 0 -10000 0 0
HGF/MET -0.11 0.17 -9999 0 -0.5 62 62
HGF -0.12 0.31 -9999 0 -0.85 62 62
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.087 0.016 -9999 0 -10000 0 0
KIAA1543 0.047 0.024 -9999 0 -0.44 1 1
KIFC3 0.041 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.04 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.041 0 -9999 0 -10000 0 0
PIP5K1C 0.041 0 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0 0.005 -9999 0 -10000 0 0
adherens junction assembly 0.064 0.022 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.099 0.18 -9999 0 -0.45 89 89
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.12 0.16 -9999 0 -10000 0 0
PLEKHA7 0.04 0.025 -9999 0 -0.47 1 1
mol:GTP -0.001 0.011 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.067 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.033 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.047 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.033 0 -9999 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.027 0.054 -9999 0 -0.28 12 12
GNAO1 -0.013 0.15 -9999 0 -0.72 16 16
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.003 0.018 -9999 0 -10000 0 0
AKT3 0.05 0.041 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0 -9999 0 -10000 0 0
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.015 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.012 0.023 -9999 0 -0.31 2 2
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.037 0.064 -9999 0 -0.33 12 12
MAPK3 0.044 0.061 -9999 0 -10000 0 0
MAPK1 0.044 0.061 -9999 0 -10000 0 0
JAK2 0.047 0.061 -9999 0 -10000 0 0
CXCR4 0.043 0.062 -9999 0 -10000 0 0
FLT1 0.016 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.043 0.061 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.037 0.064 -9999 0 -0.33 12 12
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.009 0.049 -9999 0 -10000 0 0
VEGFA 0.012 0.06 -9999 0 -0.85 2 2
S1P/S1P2/Gi 0.032 0.065 -9999 0 -0.33 12 12
VEGFR1 homodimer/VEGFA homodimer 0.025 0.048 -9999 0 -0.66 2 2
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.062 0.17 -9999 0 -0.36 95 95
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.36 -9999 0 -0.85 92 92
GNA15 -0.012 0.094 -9999 0 -0.33 30 30
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.005 0.085 -9999 0 -0.85 4 4
Rac1/GTP -0.009 0.049 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR -0.064 0.13 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.034 0.3 1 -10000 0 1
myoblast fusion 0.032 0.047 -10000 0 -10000 0 0
mol:GTP -0.028 0.04 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.094 0.11 0.54 1 -10000 0 1
ARF1/GTP -0.016 0.023 -10000 0 -10000 0 0
mol:GM1 -0.012 0.034 -10000 0 -10000 0 0
mol:Choline 0.011 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.005 0.064 -10000 0 -10000 0 0
MAPK3 -0.02 0.066 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.095 0.11 -10000 0 -0.55 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.032 0.047 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.059 -10000 0 -10000 0 0
ARF6 -0.003 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.17 -10000 0 -0.32 230 230
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.02 0.066 -10000 0 -10000 0 0
actin filament bundle formation 0.026 0.038 -10000 0 -10000 0 0
KALRN -0.008 0.051 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.038 -10000 0 -10000 0 0
NME1 0.01 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.026 0.038 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.028 0.04 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.005 0.064 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.028 0.04 -10000 0 -10000 0 0
ARF6/GTP -0.028 0.04 -10000 0 -10000 0 0
RhoA/GTP -0.016 0.023 -10000 0 -10000 0 0
mol:GDP -0.014 0.065 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.01 0.014 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 -0.001 0.034 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.005 0.064 -10000 0 -10000 0 0
ruffle organization 0.01 0.034 -10000 0 -0.3 1 1
regulation of epithelial cell migration -0.028 0.04 -10000 0 -10000 0 0
PLD2 -0.001 0.034 -10000 0 -10000 0 0
PIP5K1A 0.009 0.034 -10000 0 -0.3 1 1
mol:Phosphatidic acid 0.011 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.064 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.04 0.017 -9999 0 -10000 0 0
PLK1 0.11 0.096 -9999 0 -10000 0 0
CDKN1B 0.15 0.033 -9999 0 -10000 0 0
FOXO3 0.11 0.096 -9999 0 -10000 0 0
KAT2B 0.025 0.009 -9999 0 -10000 0 0
FOXO1/SIRT1 0.011 0.027 -9999 0 -10000 0 0
CAT 0.11 0.089 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.028 0.01 -9999 0 -10000 0 0
FOXO1 0.043 0.012 -9999 0 -10000 0 0
MAPK10 0.044 0.006 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.039 -9999 0 -0.47 1 1
response to oxidative stress 0.015 0.012 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.015 0.059 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.001 -9999 0 -10000 0 0
BCL2L11 0.041 0.027 -9999 0 -10000 0 0
FOXO1/SKP2 0.042 0.028 -9999 0 -0.49 1 1
mol:GDP 0.015 0.012 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.13 0.035 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.04 0.042 -9999 0 -10000 0 0
MST1 0.022 0.046 -9999 0 -0.84 1 1
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.066 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.041 0.047 -9999 0 -0.51 3 3
MAPK9 0.044 0.006 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.008 0.021 -9999 0 -10000 0 0
SOD2 0.16 0.047 -9999 0 -10000 0 0
RBL2 0.12 0.098 -9999 0 -1.2 1 1
RAL/GDP 0.033 0.012 -9999 0 -10000 0 0
CHUK 0.025 0.009 -9999 0 -10000 0 0
Ran/GTP 0.015 0.001 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.042 0.009 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.079 0.42 -9999 0 -1.5 31 31
SKP2 0.011 0.043 -9999 0 -0.85 1 1
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.025 0.009 -9999 0 -10000 0 0
CCNB1 0.11 0.089 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.003 0.036 -9999 0 -0.41 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.028 -9999 0 -0.48 1 1
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.01 0.11 -9999 0 -0.84 7 7
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.002 -9999 0 -10000 0 0
ZFAND5 0.11 0.034 -9999 0 -10000 0 0
SFN -0.21 0.19 -9999 0 -0.34 265 265
CDK2 0.014 0.002 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.016 0.063 -9999 0 -10000 0 0
CREBBP 0.014 0.002 -9999 0 -10000 0 0
FBXO32 0.11 0.091 -9999 0 -10000 0 0
BCL6 0.12 0.097 -9999 0 -1.2 1 1
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.006 0.022 -10000 0 -10000 0 0
AES 0.005 0.019 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.031 0.18 -10000 0 -0.65 27 27
TLE1 0.001 0.061 -10000 0 -0.82 2 2
MACF1 0.013 0 -10000 0 -10000 0 0
CTNNB1 0.047 0.042 -10000 0 -10000 0 0
WIF1 -0.034 0.1 -10000 0 -0.31 50 50
beta catenin/RanBP3 0.021 0.09 0.37 20 -10000 0 20
KREMEN2 -0.011 0.085 -10000 0 -0.31 30 30
DKK1 -0.041 0.13 -10000 0 -0.85 2 2
beta catenin/beta TrCP1 0.052 0.04 -10000 0 -10000 0 0
FZD1 0.014 0.001 -10000 0 -10000 0 0
AXIN2 -0.047 0.31 -10000 0 -1.6 15 15
AXIN1 0.014 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.063 0.041 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.007 0.032 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.016 -10000 0 -10000 0 0
HNF1A 0.004 0.047 -10000 0 -0.86 1 1
CTBP1 0.006 0.02 -10000 0 -10000 0 0
MYC -0.029 0.25 -10000 0 -1.6 10 10
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.039 0.12 -10000 0 -0.6 17 17
NKD1 -0.017 0.15 -10000 0 -0.75 16 16
TCF4 0.006 0.02 -10000 0 -10000 0 0
TCF3 0.006 0.02 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.009 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.11 0.46 24 -10000 0 24
LEF1 0 0.046 -10000 0 -0.32 6 6
DVL1 0.014 0.027 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.067 -10000 0 -0.53 2 2
DKK1/LRP6/Kremen 2 -0.038 0.083 -10000 0 -0.65 2 2
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.006 0.022 -10000 0 -10000 0 0
NLK 0.013 0.004 -10000 0 -10000 0 0
CCND1 0 0.071 -10000 0 -0.47 2 2
WNT1 0.009 0.023 -10000 0 -0.31 2 2
GSK3A 0.014 0 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.031 0.064 0.37 13 -10000 0 13
APC 0.039 0.013 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.035 0.037 -10000 0 -10000 0 0
CREBBP 0.006 0.02 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.044 0.007 -9999 0 -10000 0 0
KLHL20 -0.01 0.023 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.074 0.009 -9999 0 -10000 0 0
ENAH 0.044 0.007 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.002 0.016 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.087 -9999 0 -0.52 11 11
RAPGEF1 0.058 0.007 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.052 0.007 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.026 0.11 -9999 0 -0.66 11 11
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.044 0.007 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.011 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.079 0.073 -9999 0 -0.53 1 1
PI3K -0.001 0.014 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.17 0.16 -9999 0 -0.32 230 230
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0.008 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.073 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.017 -9999 0 -10000 0 0
CDC42/GDP 0.073 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.026 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.52 28 28
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.072 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.034 -9999 0 -0.15 11 11
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.044 0.007 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.009 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.081 -9999 0 -0.48 11 11
CCND1 0.014 0.041 -9999 0 -0.18 11 11
VAV2 0.056 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.002 -9999 0 -10000 0 0
adherens junction assembly 0.045 0.001 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.017 0.076 -9999 0 -0.46 11 11
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.044 0.01 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
Rac1/GTP -0.018 0.036 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.069 0.057 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.028 0.075 -9999 0 -0.66 1 1
NFKBIA 0.05 0 -9999 0 -10000 0 0
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.005 0.017 -9999 0 -10000 0 0
IKK complex/A20 -0.05 0.13 -9999 0 -0.67 1 1
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.042 0.038 -9999 0 -0.45 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.001 0.011 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.028 -9999 0 -0.57 1 1
NOD2 -0.032 0.12 -9999 0 -0.85 1 1
NFKB1 0.017 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.011 0.043 -9999 0 -0.85 1 1
TNF/TNFR1A -0.078 0.21 -9999 0 -0.66 47 47
TRAF6 0.011 0.043 -9999 0 -0.85 1 1
PRKCA -0.038 0.2 -9999 0 -0.85 24 24
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.091 0.28 -9999 0 -0.79 53 53
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.05 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.002 0.013 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.025 0.097 -9999 0 -10000 0 0
EPO signaling 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
BCL2L1 0.057 0.096 -9999 0 -10000 0 0
CRKL 0.042 0.033 -9999 0 -10000 0 0
mol:DAG 0.045 0.042 -9999 0 -10000 0 0
HRAS 0.065 0.032 -9999 0 -10000 0 0
MAPK8 0.029 0.057 -9999 0 -0.58 3 3
RAP1A 0.042 0.033 -9999 0 -10000 0 0
GAB1 0.042 0.033 -9999 0 -10000 0 0
MAPK14 0.033 0.023 -9999 0 -10000 0 0
EPO 0.008 0.023 -9999 0 -0.3 2 2
PLCG1 0.045 0.042 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.011 0.039 -9999 0 -0.31 6 6
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.049 0.16 -9999 0 -0.6 32 32
GAB1/SHC/GRB2/SOS1 -0.003 0.012 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.016 0.031 -9999 0 -10000 0 0
IRS2 0.042 0.033 -9999 0 -10000 0 0
STAT1 0.047 0.069 -9999 0 -10000 0 0
STAT5B 0.047 0.057 -9999 0 -10000 0 0
cell proliferation 0.036 0.054 -9999 0 -0.54 3 3
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.017 -9999 0 -10000 0 0
TEC 0.042 0.033 -9999 0 -10000 0 0
SOCS3 -0.054 0.23 -9999 0 -0.85 32 32
STAT1 (dimer) 0.046 0.069 -9999 0 -10000 0 0
JAK2 0.014 0.004 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.047 0.038 -9999 0 -10000 0 0
EPO/EPOR 0.016 0.031 -9999 0 -10000 0 0
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.05 0.032 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.011 0.039 -9999 0 -0.31 6 6
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.031 0.027 -9999 0 -10000 0 0
mol:IP3 0.045 0.042 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.008 0.023 -9999 0 -10000 0 0
SH2B3 0.014 0.004 -9999 0 -10000 0 0
NFKB1 0.033 0.023 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.024 0.079 -9999 0 -0.29 32 32
PTPN6 0.035 0.034 -9999 0 -10000 0 0
TEC/VAV2/GRB2 0.024 0.036 -9999 0 -10000 0 0
EPOR 0.011 0.039 -9999 0 -0.31 6 6
INPP5D -0.005 0.075 -9999 0 -0.31 23 23
mol:GDP -0.003 0.012 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.024 0.036 -9999 0 -10000 0 0
VAV2 0.042 0.033 -9999 0 -10000 0 0
CBL 0.042 0.033 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.004 0.014 -9999 0 -10000 0 0
STAT5A 0.047 0.057 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.058 0.089 -9999 0 -10000 0 0
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
BTK 0.025 0.076 -9999 0 -0.46 6 6
BCL2 0.014 0.26 -9999 0 -0.99 26 26
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.082 -9999 0 -0.43 11 11
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.009 0.06 -9999 0 -0.85 2 2
ITGA4 0.007 0.045 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 -0.031 0.097 -9999 0 -0.52 12 12
EPO 0.005 0.023 -9999 0 -0.31 2 2
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.64 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.004 0.028 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.004 0.028 -9999 0 -10000 0 0
lamellipodium assembly 0 0.027 -9999 0 -0.52 1 1
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
PI3K -0.002 0.032 -9999 0 -0.66 1 1
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 -0.003 0.015 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.01 0.086 -9999 0 -0.85 1 1
cell adhesion -0.031 0.097 -9999 0 -0.52 12 12
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.026 0.058 -9999 0 -0.52 3 3
ITGB7 -0.024 0.15 -9999 0 -0.52 28 28
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.01 0.058 -9999 0 -0.57 3 3
p130Cas/Crk/Dock1 -0.009 0.052 -9999 0 -0.43 5 5
VCAM1 0.002 0.083 -9999 0 -0.49 9 9
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.003 0.018 -9999 0 -10000 0 0
BCAR1 0.034 0.055 -9999 0 -0.48 3 3
EPOR 0.008 0.039 -9999 0 -0.31 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.027 -9999 0 -0.54 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.062 0.17 -9999 0 -0.52 47 47
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.05 0.14 -9999 0 -0.43 47 47
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.025 0.068 -9999 0 -10000 0 0
YY1/LSF 0.028 0.05 -9999 0 -0.55 3 3
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.044 0.12 -9999 0 -0.38 47 47
I kappa B alpha/HDAC1 -0.029 0.082 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.003 0.12 -9999 0 -0.33 47 47
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.029 0.082 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.051 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.003 0.11 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.012 0.016 -9999 0 -0.31 1 1
GATA1 0.009 0.006 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.061 0.002 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.013 0 -9999 0 -10000 0 0
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.008 0.1 -9999 0 -10000 0 0
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.046 0.015 -9999 0 -10000 0 0
SIN3 complex -0.001 0.026 -9999 0 -0.52 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.011 0.043 -9999 0 -0.85 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.024 0.072 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0 -9999 0 -10000 0 0
YY1/HDAC1 0.033 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.051 0 -9999 0 -10000 0 0
PPARG -0.06 0.16 -9999 0 -0.47 51 51
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.029 0.082 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.054 0 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.008 0.1 -9999 0 -10000 0 0
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.027 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.004 0.043 -9999 0 -0.51 3 3
YY1/SAP30/HDAC1 -0.001 0.025 -9999 0 -0.51 1 1
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.1 -9999 0 -10000 0 0
histone deacetylation 0.051 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.025 0.073 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.029 0.082 -9999 0 -10000 0 0
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 -0.03 0.083 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.078 0.21 -9999 0 -0.66 47 47
SIN3/HDAC complex/Mad/Max 0.05 0.013 -9999 0 -10000 0 0
NuRD Complex 0.059 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.025 0.067 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 0 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.091 0.28 -9999 0 -0.79 53 53
negative regulation of cell growth 0.05 0.013 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.051 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.053 0.14 -9999 0 -0.45 47 47
SIN3/HDAC complex/NCoR1 0.048 0.013 -9999 0 -10000 0 0
TFCP2 0.007 0.074 -9999 0 -0.85 3 3
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 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 0.01 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.13 -9999 0 -0.57 20 20
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.033 -9999 0 -10000 0 0
NFKBIA 0.025 0.038 -9999 0 -0.28 5 5
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0 -9999 0 -10000 0 0
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.029 0.19 -9999 0 -0.85 20 20
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.009 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
NF kappa B1 p50 dimer 0.021 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.024 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.032 0.037 -9999 0 -0.28 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.048 0.032 -9999 0 -10000 0 0
SRC 0.012 0.016 -9999 0 -0.31 1 1
PI3K -0.002 0.032 -9999 0 -0.66 1 1
NF kappa B1 p50/RelA 0.032 0.037 -9999 0 -0.28 5 5
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.03 0.035 -9999 0 -0.26 5 5
cell death -0.003 0.023 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.001 0.13 -9999 0 -0.57 20 20
LCK -0.009 0.11 -9999 0 -0.45 20 20
BCL3 0.012 0.016 -9999 0 -0.31 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.022 0.12 -9999 0 -0.7 13 13
AKT1 0.085 0.081 -9999 0 -0.61 4 4
PTK2B 0.037 0.13 -9999 0 -0.92 4 4
VEGFR2 homodimer/Frs2 -0.007 0.081 -9999 0 -0.94 3 3
CAV1 -0.01 0.14 -9999 0 -0.85 11 11
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.009 0.083 -9999 0 -0.73 5 5
endothelial cell proliferation 0.073 0.1 -9999 0 -0.62 3 3
mol:Ca2+ 0.051 0.084 -9999 0 -0.79 3 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.008 0.078 -9999 0 -0.84 3 3
RP11-342D11.1 0.042 0.084 -9999 0 -0.63 6 6
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.005 0.051 -9999 0 -0.52 4 4
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.007 0.074 -9999 0 -0.85 3 3
HRAS/GDP -0.008 0.068 -9999 0 -0.63 4 4
SH2D2A -0.037 0.19 -9999 0 -0.85 20 20
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.007 0.061 -9999 0 -0.62 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.036 0.14 -9999 0 -0.55 25 25
VEGFR1 homodimer 0.013 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.009 0.073 -9999 0 -0.76 3 3
GRB10 0.052 0.084 -9999 0 -0.79 3 3
PTPN11 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.008 0.075 -9999 0 -0.8 3 3
HRAS 0.012 0.023 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.077 -9999 0 -0.5 4 4
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.008 0.077 -9999 0 -0.82 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.005 0.085 -9999 0 -0.85 4 4
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.083 -9999 0 -0.73 5 5
mol:GDP -0.008 0.071 -9999 0 -0.73 3 3
mol:NADP 0.077 0.062 -9999 0 -0.51 3 3
eNOS/Hsp90 0.079 0.058 -9999 0 -0.48 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.052 0.086 -9999 0 -0.8 3 3
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.06 -9999 0 -0.85 2 2
VEGFC 0.011 0.043 -9999 0 -0.85 1 1
FAK1/Vinculin 0.059 0.11 -9999 0 -0.79 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.13 -9999 0 -0.61 15 15
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.021 0.035 -9999 0 -0.39 3 3
mol:L-citrulline 0.077 0.062 -9999 0 -0.51 3 3
ITGAV 0.011 0.043 -9999 0 -0.85 1 1
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.008 0.078 -9999 0 -0.69 5 5
VEGFR2 homodimer/VEGFA homodimer -0.01 0.086 -9999 0 -0.69 6 6
VEGFR2/3 heterodimer -0.012 0.11 -9999 0 -0.83 6 6
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.054 0.089 -9999 0 -0.65 6 6
VEGFR2 homodimer 0.031 0.093 -9999 0 -1 3 3
FLT1 0.013 0 -9999 0 -10000 0 0
NEDD4 0.014 0.043 -9999 0 -0.85 1 1
MAPK3 0.042 0.094 -9999 0 -0.76 3 3
MAPK1 0.042 0.094 -9999 0 -0.76 3 3
VEGFA145/NRP2 -0.019 0.07 -9999 0 -0.65 2 2
VEGFR1/2 heterodimer -0.007 0.081 -9999 0 -0.94 3 3
KDR 0.031 0.093 -9999 0 -1.1 3 3
VEGFA165/NRP1/VEGFR2 homodimer -0.016 0.084 -9999 0 -0.85 3 3
SRC 0.012 0.016 -9999 0 -0.31 1 1
platelet activating factor biosynthetic process 0.045 0.094 -9999 0 -0.78 3 3
PI3K -0.01 0.078 -9999 0 -0.76 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.009 0.083 -9999 0 -0.73 5 5
FES 0.052 0.087 -9999 0 -0.82 3 3
GAB1 -0.009 0.076 -9999 0 -0.79 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.009 0.083 -9999 0 -0.73 5 5
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.068 0.093 -9999 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.009 0.083 -9999 0 -0.73 5 5
PI3K/GAB1 0.086 0.079 -9999 0 -0.64 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.008 0.075 -9999 0 -0.8 3 3
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.013 0.1 -9999 0 -0.74 7 7
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.052 0.087 -9999 0 -0.82 3 3
actin cytoskeleton reorganization -0.036 0.13 -9999 0 -0.55 25 25
PTK2 0.053 0.12 -9999 0 -0.75 6 6
EDG1 0.042 0.084 -9999 0 -0.63 6 6
mol:DAG 0.052 0.086 -9999 0 -0.8 3 3
CaM/Ca2+ -0.008 0.072 -9999 0 -0.74 3 3
MAP2K3 0.054 0.097 -9999 0 -0.77 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.01 0.081 -9999 0 -0.83 3 3
PLCG1 0.052 0.087 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.009 0.079 -9999 0 -0.84 3 3
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.009 0.083 -9999 0 -0.73 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.009 0.083 -9999 0 -0.73 5 5
cell migration 0.083 0.095 -9999 0 -0.69 3 3
mol:PI-3-4-5-P3 -0.009 0.071 -9999 0 -0.69 3 3
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.009 0.073 -9999 0 -0.75 3 3
mol:NO 0.077 0.062 -9999 0 -0.51 3 3
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.068 -9999 0 -0.63 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.05 0.088 -9999 0 -0.83 3 3
VHL 0.009 0.06 -9999 0 -0.85 2 2
ITGB3 -0.014 0.15 -9999 0 -0.85 13 13
NOS3 0.079 0.069 -9999 0 -0.58 3 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.013 0.093 -9999 0 -0.64 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.029 0.15 -9999 0 -0.89 3 3
PRKCB 0.041 0.097 -9999 0 -0.74 3 3
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.042 0.085 -9999 0 -0.63 6 6
VEGFR1/2 heterodimer/VEGFA homodimer -0.009 0.083 -9999 0 -0.73 5 5
VEGFA165/NRP2 -0.019 0.07 -9999 0 -0.65 2 2
MAPKKK cascade -0.008 0.067 -9999 0 -0.67 3 3
NRP2 -0.013 0.089 -9999 0 -10000 0 0
VEGFC homodimer 0.011 0.043 -9999 0 -0.85 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.059 0.11 -9999 0 -0.68 6 6
MAP3K13 0.047 0.1 -9999 0 -0.82 3 3
PDPK1 0.077 0.081 -9999 0 -0.63 4 4
PLK2 and PLK4 events

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
PLK2 0.008 0.039 -9999 0 -0.31 6 6
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.021 0.027 -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 -0.023 0.037 -9999 0 -10000 0 0
CLOCK -0.017 0.15 -9999 0 -0.86 13 13
TIMELESS/CRY2 -0.002 0.062 -9999 0 -10000 0 0
DEC1/BMAL1 -0.024 0.067 -9999 0 -10000 0 0
ATR 0.013 0 -9999 0 -10000 0 0
NR1D1 -0.053 0.13 -9999 0 -10000 0 0
ARNTL -0.024 0.1 -9999 0 -0.34 14 14
TIMELESS -0.009 0.071 -9999 0 -10000 0 0
NPAS2 0.007 0.049 -9999 0 -0.58 2 2
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.007 0.03 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.007 0.03 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.017 0.13 -9999 0 -0.6 14 14
BMAL1/CLOCK -0.041 0.13 -9999 0 -0.63 7 7
S phase of mitotic cell cycle -0.023 0.037 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.023 0.037 -9999 0 -10000 0 0
mol:NADPH -0.007 0.03 -9999 0 -10000 0 0
PER1/TIMELESS -0.002 0.062 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.016 -9999 0 -0.31 1 1
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 0.006 0.012 -9999 0 -10000 0 0
BIRC5 -0.017 0.1 -9999 0 -0.33 36 36
NFKBIA 0.032 0.003 -9999 0 -10000 0 0
CPEB1 -0.052 0.23 -9999 0 -0.85 31 31
AKT1 0.032 0.003 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.009 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.012 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.012 0.002 -9999 0 -10000 0 0
PAK1/Aurora A 0.006 0.012 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.011 0.043 -9999 0 -0.85 1 1
TPX2 0.001 0.069 -9999 0 -10000 0 0
TP53 0.007 0.013 -9999 0 -10000 0 0
DLG7 0.021 0.003 -9999 0 -10000 0 0
AURKAIP1 0.012 0.016 -9999 0 -0.31 1 1
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.003 0.013 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.009 -9999 0 -10000 0 0
AURKA 0.025 0.004 -9999 0 -10000 0 0
AURKB -0.013 0.025 -9999 0 -10000 0 0
CDC25B 0.006 0.017 -9999 0 -10000 0 0
G2/M transition checkpoint 0.001 0.027 -9999 0 -0.52 1 1
mRNA polyadenylation -0.037 0.14 -9999 0 -0.52 31 31
Aurora A/CPEB -0.038 0.14 -9999 0 -0.53 31 31
Aurora A/TACC1/TRAP/chTOG 0.004 0.013 -9999 0 -10000 0 0
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.006 0.012 -9999 0 -10000 0 0
regulation of centrosome cycle 0.002 0.011 -9999 0 -10000 0 0
spindle assembly 0 0 -9999 0 -10000 0 0
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.01 0.037 -9999 0 -0.47 1 1
CENPA -0.008 0.017 -9999 0 -10000 0 0
Aurora A/PP2A 0.006 0.012 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.038 0.004 -9999 0 -10000 0 0
negative regulation of DNA binding 0.031 0.002 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.001 0.028 -9999 0 -0.53 1 1
mitotic prometaphase 0.006 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.004 -9999 0 -10000 0 0
TACC1 0.013 0 -9999 0 -10000 0 0
TACC3 0.012 0.016 -9999 0 -0.31 1 1
Aurora A/Antizyme1 0.003 0.013 -9999 0 -10000 0 0
Aurora A/RasGAP 0.006 0.012 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.002 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.001 0.069 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.018 0.05 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.008 0.024 0.3 1 -10000 0 1
BUB1B 0.017 0.029 -10000 0 -10000 0 0
PLK1 0.017 0.01 -10000 0 -0.1 1 1
PLK1S1 0.015 0.006 -10000 0 -10000 0 0
KIF2A 0.025 0.009 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.017 0.01 -10000 0 -0.1 1 1
GOLGA2 0.013 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.005 0.078 -10000 0 -0.28 14 14
WEE1 0.022 0.01 -10000 0 -10000 0 0
cytokinesis 0 0.065 -10000 0 -0.31 1 1
PP2A-alpha B56 -0.015 0.02 -10000 0 -10000 0 0
AURKA 0.016 0.007 -10000 0 -10000 0 0
PICH/PLK1 0.006 0.017 -10000 0 -10000 0 0
CENPE 0.021 0.036 -10000 0 -0.52 1 1
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.025 0.009 -10000 0 -10000 0 0
PPP2CA 0.013 0 -10000 0 -10000 0 0
FZR1 0.013 0 -10000 0 -10000 0 0
TPX2 0.009 0.021 -10000 0 -10000 0 0
PAK1 0.013 0 -10000 0 -10000 0 0
SPC24 -0.009 0.081 -10000 0 -0.31 27 27
FBXW11 0.013 0 -10000 0 -10000 0 0
CLSPN 0.005 0.028 -10000 0 -10000 0 0
GORASP1 0.013 0 -10000 0 -10000 0 0
metaphase 0.001 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.009 0.006 -10000 0 -0.068 1 1
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
STAG2 0.013 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.003 -10000 0 -10000 0 0
spindle elongation 0.017 0.01 -10000 0 -0.1 1 1
ODF2 0.013 0.001 -10000 0 -10000 0 0
BUB1 -0.023 0.03 -10000 0 -10000 0 0
TPT1 0.015 0.006 -10000 0 -10000 0 0
CDC25C 0.011 0.023 -10000 0 -10000 0 0
CDC25B 0.011 0.028 -10000 0 -0.31 3 3
SGOL1 0.008 0.024 -10000 0 -0.3 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.006 0.014 -10000 0 -10000 0 0
CDC14B 0.006 0.068 -10000 0 -0.68 4 4
CDC20 0.009 0.036 -10000 0 -0.31 5 5
PLK1/PBIP1 0.003 0.023 -10000 0 -10000 0 0
mitosis 0 0.001 -10000 0 -0.022 1 1
FBXO5 0.022 0.008 -10000 0 -10000 0 0
CDC2 0.001 0.001 -10000 0 -10000 0 0
NDC80 -0.039 0.12 -10000 0 -0.31 65 65
metaphase plate congression 0.016 0.006 -10000 0 -10000 0 0
ERCC6L 0.007 0.017 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.014 0.007 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.006 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -0.011 1 1
PPP1R12A 0.013 0 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -0.011 1 1
PLK1/PRC1-2 -0.003 0.066 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0 0.003 -10000 0 -10000 0 0
RAB1A 0.013 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.02 0.026 -10000 0 -0.5 1 1
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.035 -10000 0 -0.33 2 2
microtubule-based process -0.013 0.07 -10000 0 -10000 0 0
Golgi organization 0.017 0.01 -10000 0 -0.1 1 1
Cohesin/SA2 -0.001 0.004 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.059 0.14 -10000 0 -0.31 90 90
APC/C/CDC20 0.021 0.022 -10000 0 -10000 0 0
PPP2R1A 0.013 0 -10000 0 -10000 0 0
chromosome segregation 0.002 0.023 -10000 0 -10000 0 0
PRC1 0.013 0 -10000 0 -10000 0 0
ECT2 0.025 0.009 -10000 0 -10000 0 0
C13orf34 0.02 0.027 -10000 0 -0.5 1 1
NUDC 0.016 0.006 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.029 -10000 0 -10000 0 0
spindle assembly 0.017 0.008 -10000 0 -10000 0 0
spindle stabilization 0.015 0.006 -10000 0 -10000 0 0
APC/C/HCDH1 0.013 0.059 -10000 0 -0.58 4 4
MKLP2/PLK1 -0.013 0.071 -10000 0 -10000 0 0
CCNB1 0.014 0.001 -10000 0 -10000 0 0
PPP1CB 0.013 0 -10000 0 -10000 0 0
BTRC 0.013 0 -10000 0 -10000 0 0
ROCK2 0.011 0.085 -10000 0 -0.53 10 10
TUBG1 0.015 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.01 -10000 0 -10000 0 0
MLF1IP 0.007 0.034 -10000 0 -10000 0 0
INCENP 0.012 0.001 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.01 0.05 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.002 0.018 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 -0.015 0.15 -9999 0 -0.72 16 16
RhoA/GTP -0.01 0.051 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process 0.024 0.064 -9999 0 -0.34 12 12
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
S1PR5 0.009 0.036 -9999 0 -0.31 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi 0.024 0.065 -9999 0 -0.34 12 12
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
GNAI1 0.013 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.001 0.004 -9999 0 -10000 0 0
DOCK1 0.009 0.06 -9999 0 -0.85 2 2
ITGA4 0.007 0.045 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.64 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.003 0.022 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.022 0.089 -9999 0 -0.52 11 11
lamellipodium assembly -0.002 0.042 -9999 0 -0.57 2 2
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
PI3K -0.002 0.032 -9999 0 -0.66 1 1
ARF6 0.013 0 -9999 0 -10000 0 0
TLN1 0.013 0 -9999 0 -10000 0 0
PXN 0.024 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.013 -9999 0 -10000 0 0
cell adhesion -0.002 0.016 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.003 0.018 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.52 28 28
ARF6/GDP 0.001 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.008 0.048 -9999 0 -0.48 3 3
p130Cas/Crk/Dock1 -0.003 0.04 -9999 0 -0.57 2 2
VCAM1 0.002 0.083 -9999 0 -0.49 9 9
alpha4/beta1 Integrin/Paxillin/Talin -0.002 0.016 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.016 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.002 0.016 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.002 0.016 -9999 0 -10000 0 0
Rac1/GTP -0.002 0.05 -9999 0 -0.67 2 2
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.001 0.02 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SLAP 0 0.01 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0 0.008 -9999 0 -10000 0 0
AKT1 0.061 0.032 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.025 0.034 -9999 0 -10000 0 0
PIK3CA 0.011 0.043 -9999 0 -0.85 1 1
FGR 0.003 0.012 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.03 -9999 0 -10000 0 0
MYC 0.02 0.14 -9999 0 -0.87 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.019 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB -0.001 0.028 -9999 0 -0.57 1 1
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 0.021 0.03 -9999 0 -10000 0 0
PTEN 0.011 0.043 -9999 0 -0.85 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.037 0.12 -9999 0 -0.31 63 63
PDGFB-D/PDGFRB/SHP2 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0 0.001 -9999 0 -10000 0 0
cell cycle arrest -0.001 0.01 -9999 0 -10000 0 0
HRAS 0.012 0.023 -9999 0 -0.31 2 2
HIF1A 0.067 0.029 -9999 0 -10000 0 0
GAB1 0.014 0.049 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.021 0.046 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.016 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0.001 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.003 0.03 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.021 0.03 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.013 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.031 0.074 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.19 0.28 -9999 0 -0.62 123 123
PTPN2 0.013 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0.001 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.018 0.057 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0 0.001 -9999 0 -10000 0 0
LCK -0.006 0.07 -9999 0 -0.62 5 5
PDGFRB 0.014 0.002 -9999 0 -10000 0 0
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.007 0.024 -9999 0 -10000 0 0
ABL1 0.01 0.048 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.01 0.052 -9999 0 -10000 0 0
PTPN1 0.013 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.006 0.048 -9999 0 -0.31 9 9
cell proliferation 0.022 0.13 -9999 0 -0.75 10 10
SLA 0.012 0.016 -9999 0 -0.31 1 1
actin cytoskeleton reorganization 0.021 0.026 -9999 0 -10000 0 0
SRC 0.006 0.012 -9999 0 -10000 0 0
PI3K -0.002 0.03 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.024 0.057 -9999 0 -10000 0 0
SH2B2 0.012 0.016 -9999 0 -0.31 1 1
PLCgamma1/SPHK1 0.025 0.034 -9999 0 -10000 0 0
LYN 0.007 0.013 -9999 0 -10000 0 0
LRP1 0.011 0.043 -9999 0 -0.85 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0.001 0.007 -9999 0 -10000 0 0
SPHK1 0.007 0.045 -9999 0 -0.31 8 8
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.021 0.03 -9999 0 -10000 0 0
PLCG1 0.022 0.03 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.011 -9999 0 -10000 0 0
YES1 0.005 0.01 -9999 0 -10000 0 0
cell migration -0.001 0.011 -9999 0 -10000 0 0
SHC/Grb2/SOS1 0.001 0.007 -9999 0 -10000 0 0
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0.023 -9999 0 -0.31 2 2
NHERF1-2/PDGFRB/PTEN -0.002 0.027 -9999 0 -0.52 1 1
FYN 0.007 0.012 -9999 0 -10000 0 0
DOK1 0.035 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.015 -9999 0 -0.21 2 2
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.029 0.078 -9999 0 -0.4 10 10
PRKCD 0.035 0.006 -9999 0 -10000 0 0
FER 0.033 0.04 -9999 0 -0.53 2 2
MAPKKK cascade 0 0.006 -9999 0 -10000 0 0
RASA1 0.035 0.006 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.016 0.02 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0 0.001 -9999 0 -10000 0 0
chemotaxis 0.01 0.047 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 -0.002 0.013 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.003 0.004 -9999 0 -10000 0 0
PTPRJ 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 -0.002 0.03 -9999 0 -0.43 2 2
TRAF2/ASK1 -0.001 0.029 -9999 0 -0.58 1 1
ATM 0.011 0.043 -9999 0 -0.85 1 1
MAP2K3 0.028 0.057 -9999 0 -0.54 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.028 0.074 -9999 0 -0.53 3 3
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.002 0.11 -9999 0 -0.67 9 9
TXN 0.009 0.007 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.021 0.17 -9999 0 -0.85 16 16
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.002 0.032 -9999 0 -0.66 1 1
TAK1/TAB family -0.001 0.011 -9999 0 -0.22 1 1
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.007 0.033 -9999 0 -0.48 1 1
TRAF6 0.008 0.024 -9999 0 -0.47 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.003 0.095 -9999 0 -0.85 5 5
CCM2 0.013 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.007 0.064 -9999 0 -0.58 5 5
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.008 0.072 -9999 0 -0.63 5 5
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 -0.029 0.15 -9999 0 -0.48 39 39
TAOK2 0.017 0.024 -9999 0 -0.46 1 1
TAOK3 0.017 0.024 -9999 0 -0.46 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.011 0.043 -9999 0 -0.85 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.029 -9999 0 -0.57 1 1
GADD45/MTK1/MTK1 -0.027 0.12 -9999 0 -0.52 21 21
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.05 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.031 0.14 -9999 0 -0.66 19 19
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.027 0.18 -9999 0 -0.85 19 19
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.013 0 -9999 0 -10000 0 0
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0 0 -9999 0 -10000 0 0
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC5 0 0 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.01 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.028 -9999 0 -0.57 1 1
HDAC9 -0.017 0.095 -9999 0 -0.31 38 38
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.012 0.016 -9999 0 -0.31 1 1
HDAC4/RFXANK 0 0.01 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones 0.036 0.023 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0.01 -9999 0 -10000 0 0
CAMK4 -0.003 0.097 -9999 0 -0.48 13 13
Tubulin/HDAC6 -0.004 0.049 -9999 0 -0.57 3 3
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.009 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.005 0.056 -9999 0 -0.66 3 3
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.002 0.032 -9999 0 -0.66 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.009 0.06 -9999 0 -0.57 4 4
HDAC4/ER alpha -0.044 0.14 -9999 0 -0.66 19 19
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.023 -9999 0 -10000 0 0
cell motility -0.004 0.048 -9999 0 -0.57 3 3
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.011 0.043 -9999 0 -0.85 1 1
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.049 0.2 -9999 0 -0.54 46 46
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0 0 -9999 0 -10000 0 0
GNG2 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.007 0.074 -9999 0 -0.85 3 3
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.012 0.016 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.001 0.024 -9999 0 -10000 0 0
oxygen homeostasis 0.015 0.011 -9999 0 -10000 0 0
TCEB2 0.012 0.016 -9999 0 -0.31 1 1
TCEB1 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.008 0.043 -9999 0 -0.52 1 1
EPO 0.19 0.12 -9999 0 -10000 0 0
FIH (dimer) 0.028 0.011 -9999 0 -10000 0 0
APEX1 0.026 0.011 -9999 0 -10000 0 0
SERPINE1 0.18 0.16 -9999 0 -0.65 1 1
FLT1 0.001 0.016 -9999 0 -10000 0 0
ADORA2A 0.19 0.13 -9999 0 -10000 0 0
germ cell development 0.19 0.13 -9999 0 -10000 0 0
SLC11A2 0.19 0.13 -9999 0 -10000 0 0
BHLHE40 0.18 0.15 -9999 0 -10000 0 0
HIF1AN 0.028 0.011 -9999 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.001 0.043 -9999 0 -10000 0 0
ETS1 0.03 0.003 -9999 0 -10000 0 0
CITED2 -0.086 0.31 -9999 0 -1.2 30 30
KDR -0.007 0.11 -9999 0 -1.3 3 3
PGK1 0.19 0.13 -9999 0 -10000 0 0
SIRT1 0.013 0.001 -9999 0 -10000 0 0
response to hypoxia 0 0.001 -9999 0 -10000 0 0
HIF2A/ARNT 0.21 0.14 -9999 0 -10000 0 0
EPAS1 0.11 0.089 -9999 0 -0.32 1 1
SP1 0.021 0.002 -9999 0 -10000 0 0
ABCG2 0.19 0.14 -9999 0 -0.76 2 2
EFNA1 0.19 0.13 -9999 0 -10000 0 0
FXN 0.19 0.13 -9999 0 -10000 0 0
POU5F1 0.19 0.13 -9999 0 -10000 0 0
neuron apoptosis -0.2 0.14 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
EGLN3 -0.007 0.15 -9999 0 -0.57 20 20
EGLN2 0.028 0.011 -9999 0 -10000 0 0
EGLN1 0.028 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.04 -9999 0 -0.57 2 2
VHL 0.009 0.06 -9999 0 -0.85 2 2
ARNT 0.027 0.011 -9999 0 -10000 0 0
SLC2A1 0.19 0.13 -9999 0 -10000 0 0
TWIST1 0.18 0.17 -9999 0 -0.63 8 8
ELK1 0.014 0.027 -9999 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.002 0.042 -9999 0 -10000 0 0
VEGFA 0.19 0.14 -9999 0 -0.69 2 2
CREBBP 0.013 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.032 0.009 -9999 0 -10000 0 0
MAPK12 0.024 0.067 -9999 0 -0.52 6 6
CCND1 0.018 0.03 -9999 0 -0.26 1 1
p38 gamma/SNTA1 0.029 0.063 -9999 0 -0.48 6 6
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.024 0.067 -9999 0 -0.51 6 6
MAP2K6 0.017 0.071 -9999 0 -0.56 6 6
MAPT 0.026 0.041 -9999 0 -0.41 2 2
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.018 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.023 0.17 -10000 0 -0.77 19 19
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.01 0.078 -10000 0 -0.58 7 7
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.017 0.042 -10000 0 -0.58 2 2
INS 0.013 0 -10000 0 -10000 0 0
BIN1 0.013 0 -10000 0 -10000 0 0
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.031 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.026 -10000 0 -0.53 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.031 0 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.026 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.002 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.012 0.069 -10000 0 -0.28 20 20
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.017 0.083 -10000 0 -0.43 16 16
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.001 0.026 0.52 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.029 0.077 -10000 0 -0.46 10 10
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.011 0.043 -10000 0 -0.85 1 1
Dynamin 2/GDP 0.026 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.031 0.07 -10000 0 -0.46 8 8
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.052 0.025 -10000 0 -0.46 1 1
adherens junction organization 0.044 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.052 0.055 -10000 0 -0.4 6 6
FMN1 0.029 0.097 -10000 0 -0.46 15 15
mol:IP3 -0.001 0.021 -10000 0 -0.43 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.008 -10000 0 -10000 0 0
CTNNB1 0.013 0 -10000 0 -10000 0 0
AKT1 0.051 0.023 -10000 0 -0.42 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.046 0.025 -10000 0 -0.44 1 1
VASP 0.047 0.007 -10000 0 -10000 0 0
ZYX 0.047 0.007 -10000 0 -10000 0 0
JUB 0.046 0.026 -10000 0 -0.46 1 1
EGFR(dimer) 0.04 0.055 -10000 0 -0.45 5 5
E-cadherin/beta catenin-gamma catenin 0 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.022 -10000 0 -0.45 1 1
PIK3CA 0.012 0.043 -10000 0 -0.85 1 1
PI3K -0.001 0.023 -10000 0 -0.46 1 1
FYN 0.052 0.026 -10000 0 -0.37 1 1
mol:Ca2+ -0.001 0.021 -10000 0 -0.42 1 1
JUP 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.001 0.021 -10000 0 -0.43 1 1
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.052 0.055 -10000 0 -0.4 6 6
establishment of polarity of embryonic epithelium 0.047 0.007 -10000 0 -10000 0 0
SRC 0.012 0.016 -10000 0 -0.31 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.003 0.095 -10000 0 -0.85 5 5
CASR 0.044 0.028 -10000 0 -0.4 1 1
RhoA/GTP -0.001 0.019 -10000 0 -0.38 1 1
AKT2 0.051 0.023 -10000 0 -0.42 1 1
actin cable formation 0.036 0.094 -10000 0 -0.44 15 15
apoptosis 0.001 0.021 0.43 1 -10000 0 1
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.047 0.058 -10000 0 -0.43 6 6
PIP5K1A 0.046 0.026 -10000 0 -0.46 1 1
PLCG1 -0.001 0.022 -10000 0 -0.44 1 1
Rac1/GTP -0.005 0.046 -10000 0 -0.41 5 5
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.015 0.15 -9999 0 -0.72 16 16
CDC42/GTP -0.01 0.051 -9999 0 -10000 0 0
PLCG1 0.032 0.061 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.01 0.05 -9999 0 -10000 0 0
S1PR5 0.009 0.036 -9999 0 -0.31 5 5
S1PR4 0.01 0.032 -9999 0 -0.31 4 4
MAPK3 0.032 0.061 -9999 0 -10000 0 0
MAPK1 0.032 0.061 -9999 0 -10000 0 0
S1P/S1P5/Gi 0.024 0.065 -9999 0 -0.34 12 12
GNAI1 0.013 0 -9999 0 -10000 0 0
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.002 0.018 -9999 0 -10000 0 0
RHOA 0.032 0.015 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.024 0.065 -9999 0 -0.34 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.001 0.014 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
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 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 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 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0.013 0 -9999 0 -9999 0 0
JUP 0.013 0 -9999 0 -9999 0 0
CDH1 0.013 0 -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 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.012 -9999 0 -0.21 1 1
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.003 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.004 0.055 -9999 0 -0.31 12 12
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.022 -9999 0 -0.44 1 1
ARF1/GTP -0.001 0.013 -9999 0 -0.26 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline -0.001 0.021 -9999 0 -0.44 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
DDEF1 -0.001 0.022 -9999 0 -0.44 1 1
ARF1/GDP 0 0.006 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.002 -9999 0 -10000 0 0
ARFIP2 0 0.004 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0.006 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.008 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.007 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.003 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.014 -9999 0 -10000 0 0
PLD2 -0.001 0.022 -9999 0 -0.44 1 1
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.001 0.022 -9999 0 -0.44 1 1
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.012 -9999 0 -0.25 1 1
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.021 -9999 0 -0.44 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 0 0.009 -9999 0 -0.17 1 1
USO1 0 0.009 -9999 0 -10000 0 0
GBF1 0 0.009 -9999 0 -0.17 1 1
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.026 -9999 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 0 -9999 0 -9999 0 0
FBXW11 0.013 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -9999 0 0
CHUK 0.013 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -9999 0 0
NFKB1 0.013 0 -9999 0 -9999 0 0
MAP3K14 0.013 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0 0 -9999 0 -9999 0 0
RELB 0.013 0 -9999 0 -9999 0 0
NFKB2 0.013 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -9999 0 0
regulation of B cell activation 0 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 409 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.KS.A41L TCGA.KS.A41J TCGA.KS.A41I TCGA.KS.A41F
109_MAP3K5 -0.22 -0.28 0.058 -0.22
47_PPARGC1A 0.013 -0.85 0.013 -0.85
105_BMP4 0.013 0.013 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR 0 -0.52 0 -0.52
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B 0.045 0.0028 0 -0.053
84_STAT5A 0.045 0.0028 0 -0.053
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 = Copy number data was not used in this analysis.

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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle