PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1XS5SD5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Thyroid Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1XS5SD5
Overview
Introduction

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

Summary

There were 39 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 226
Signaling events mediated by Stem cell factor receptor (c-Kit) 155
Signaling events regulated by Ret tyrosine kinase 135
Reelin signaling pathway 117
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 104
Wnt signaling 95
Noncanonical Wnt signaling pathway 89
PDGFR-alpha signaling pathway 89
Nongenotropic Androgen signaling 81
FOXA2 and FOXA3 transcription factor networks 79
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 226 1583 7 -0.42 0 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 155 12156 78 -0.74 0.23 1000 -1000 -0.04 -1000
Signaling events regulated by Ret tyrosine kinase 135 11114 82 -0.38 0.027 1000 -1000 -0.064 -1000
Reelin signaling pathway 117 6557 56 -0.46 0.063 1000 -1000 -0.043 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 104 7103 68 -0.74 0.35 1000 -1000 -0.058 -1000
Wnt signaling 95 671 7 -0.33 0.013 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 89 2322 26 -0.33 0.027 1000 -1000 -0.044 -1000
PDGFR-alpha signaling pathway 89 3935 44 -0.42 0.044 1000 -1000 -0.046 -1000
Nongenotropic Androgen signaling 81 4248 52 -0.27 0.2 1000 -1000 -0.034 -1000
FOXA2 and FOXA3 transcription factor networks 79 3636 46 -0.87 0.031 1000 -1000 -0.076 -1000
Signaling events mediated by the Hedgehog family 72 3777 52 -0.3 0.14 1000 -1000 -0.042 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 71 3842 54 -0.46 0.04 1000 -1000 -0.053 -1000
Calcium signaling in the CD4+ TCR pathway 62 1935 31 -0.36 0.027 1000 -1000 -0.029 -1000
Nephrin/Neph1 signaling in the kidney podocyte 60 2055 34 -0.1 0.028 1000 -1000 -0.037 -1000
Endothelins 57 5477 96 -0.33 0.031 1000 -1000 -0.051 -1000
Glypican 1 network 56 2727 48 -0.3 0.052 1000 -1000 -0.03 -1000
EPHB forward signaling 54 4595 85 -0.25 0.12 1000 -1000 -0.056 -1000
IGF1 pathway 54 3120 57 -0.14 0.063 1000 -1000 -0.048 -1000
IL4-mediated signaling events 53 4888 91 -1.2 0.56 1000 -1000 -0.075 -1000
HIF-1-alpha transcription factor network 51 3896 76 -0.48 0.042 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 51 2456 48 -0.25 0.12 1000 -1000 -0.026 -1000
BMP receptor signaling 46 3749 81 -0.44 0.053 1000 -1000 -0.052 -1000
IL23-mediated signaling events 45 2717 60 -0.29 0.028 1000 -1000 -0.065 -1000
Coregulation of Androgen receptor activity 44 3354 76 -0.67 0.075 1000 -1000 -0.021 -1000
Glucocorticoid receptor regulatory network 44 5090 114 -0.46 0.26 1000 -1000 -0.055 -1000
TCR signaling in naïve CD8+ T cells 44 4175 93 -0.15 0.047 1000 -1000 -0.048 -1000
Signaling mediated by p38-alpha and p38-beta 42 1852 44 -0.23 0.027 1000 -1000 -0.021 -1000
Arf6 signaling events 40 2489 62 -0.26 0.062 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 34 2240 65 -0.59 0.064 1000 -1000 -0.038 -1000
Thromboxane A2 receptor signaling 33 3479 105 -0.16 0.052 1000 -1000 -0.046 -1000
IL12-mediated signaling events 30 2686 87 -0.38 0.032 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 28 606 21 -0.076 0.038 1000 -1000 -0.046 -1000
IL6-mediated signaling events 27 2082 75 -0.16 0.053 1000 -1000 -0.031 -1000
Syndecan-1-mediated signaling events 26 895 34 -0.08 0.027 1000 -1000 -0.034 -1000
Plasma membrane estrogen receptor signaling 26 2258 86 -0.13 0.049 1000 -1000 -0.064 -1000
ErbB2/ErbB3 signaling events 25 1630 65 -0.17 0.038 1000 -1000 -0.044 -1000
Ras signaling in the CD4+ TCR pathway 25 433 17 -0.11 0.041 1000 -1000 -0.029 -1000
Osteopontin-mediated events 24 917 38 -0.16 0.043 1000 -1000 -0.028 -1000
Regulation of p38-alpha and p38-beta 24 1311 54 -0.36 0.066 1000 -1000 -0.047 -1000
FAS signaling pathway (CD95) 22 1044 47 -0.22 0.043 1000 -1000 -0.03 -1000
Regulation of Androgen receptor activity 22 1549 70 -0.44 0.036 1000 -1000 -0.049 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 21 1839 85 -0.23 0.14 1000 -1000 -0.042 -1000
BCR signaling pathway 21 2153 99 -0.1 0.05 1000 -1000 -0.053 -1000
IFN-gamma pathway 20 1414 68 -0.17 0.036 1000 -1000 -0.052 -1000
LPA receptor mediated events 20 2041 102 -0.16 0.035 1000 -1000 -0.074 -1000
Syndecan-4-mediated signaling events 19 1313 67 -0.14 0.039 1000 -1000 -0.046 -1000
Fc-epsilon receptor I signaling in mast cells 18 1811 97 -0.16 0.045 1000 -1000 -0.055 -1000
Ceramide signaling pathway 18 1423 76 -0.15 0.076 1000 -1000 -0.036 -1000
Signaling events mediated by PRL 18 624 34 -0.089 0.04 1000 -1000 -0.033 -1000
Angiopoietin receptor Tie2-mediated signaling 17 1542 88 -0.26 0.039 1000 -1000 -0.064 -1000
ceramide signaling pathway 16 791 49 -0.056 0.039 1000 -1000 -0.037 -1000
Integrins in angiogenesis 16 1373 84 -0.14 0.056 1000 -1000 -0.048 -1000
Signaling events mediated by PTP1B 15 1196 76 -0.19 0.042 1000 -1000 -0.03 -1000
JNK signaling in the CD4+ TCR pathway 14 247 17 -0.08 0.03 1000 -1000 -0.028 -1000
mTOR signaling pathway 14 758 53 -0.044 0.031 1000 -1000 -0.042 -1000
amb2 Integrin signaling 14 1187 82 -0.21 0.035 1000 -1000 -0.041 -1000
RXR and RAR heterodimerization with other nuclear receptor 14 745 52 -0.18 0.059 1000 -1000 -0.049 -1000
IL27-mediated signaling events 14 761 51 -0.11 0.044 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 14 364 26 -0.19 0.047 1000 -1000 -0.007 -1000
VEGFR1 specific signals 14 799 56 -0.047 0.058 1000 -1000 -0.052 -1000
LPA4-mediated signaling events 13 160 12 -0.056 0.004 1000 -1000 -0.023 -1000
Regulation of nuclear SMAD2/3 signaling 13 1798 136 -0.26 0.052 1000 -1000 -0.039 -1000
Visual signal transduction: Cones 13 531 38 -0.046 0.044 1000 -1000 -0.018 -1000
p75(NTR)-mediated signaling 13 1692 125 -0.28 0.07 1000 -1000 -0.063 -1000
Signaling events mediated by HDAC Class III 13 522 40 -0.28 0.047 1000 -1000 -0.018 -1000
IL1-mediated signaling events 13 847 62 -0.083 0.061 1000 -1000 -0.047 -1000
ErbB4 signaling events 12 850 69 -0.052 0.036 1000 -1000 -0.042 -1000
Presenilin action in Notch and Wnt signaling 12 741 61 -0.16 0.07 1000 -1000 -0.053 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 12 578 45 -0.056 0.076 1000 -1000 -0.049 -1000
Insulin Pathway 12 896 74 -0.058 0.066 1000 -1000 -0.053 -1000
Neurotrophic factor-mediated Trk receptor signaling 12 1527 120 -0.24 0.075 1000 -1000 -0.049 -1000
FOXM1 transcription factor network 12 643 51 -0.23 0.052 1000 -1000 -0.064 -1000
Nectin adhesion pathway 11 736 63 -0.11 0.074 1000 -1000 -0.045 -1000
IL2 signaling events mediated by PI3K 11 643 58 -0.056 0.048 1000 -1000 -0.038 -1000
Rapid glucocorticoid signaling 11 235 20 -0.06 0.034 1000 -1000 -0.008 -1000
Caspase cascade in apoptosis 10 809 74 -0.056 0.046 1000 -1000 -0.045 -1000
Cellular roles of Anthrax toxin 10 416 39 -0.056 0.027 1000 -1000 -0.023 -1000
S1P1 pathway 10 373 36 -0.067 0.027 1000 -1000 -0.032 -1000
Syndecan-3-mediated signaling events 10 369 35 -0.12 0.07 1000 -1000 -0.032 -1000
Visual signal transduction: Rods 10 571 52 -0.071 0.048 1000 -1000 -0.029 -1000
Syndecan-2-mediated signaling events 9 644 69 -0.14 0.05 1000 -1000 -0.041 -1000
Retinoic acid receptors-mediated signaling 9 535 58 -0.035 0.054 1000 -1000 -0.037 -1000
Stabilization and expansion of the E-cadherin adherens junction 9 693 74 -0.12 0.07 1000 -1000 -0.064 -1000
BARD1 signaling events 8 498 57 -0.043 0.052 1000 -1000 -0.04 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 8 664 83 -0.17 0.048 1000 -1000 -0.033 -1000
Class I PI3K signaling events 8 597 73 -0.19 0.05 1000 -1000 -0.039 -1000
Regulation of Telomerase 8 819 102 -0.2 0.072 1000 -1000 -0.046 -1000
TCGA08_p53 7 55 7 -0.024 0.026 1000 -1000 -0.009 -1000
S1P3 pathway 7 329 42 -0.13 0.048 1000 -1000 -0.041 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 7 237 33 -0.11 0.055 1000 -1000 -0.039 -1000
Sphingosine 1-phosphate (S1P) pathway 6 185 28 -0.13 0.056 1000 -1000 -0.023 -1000
PLK1 signaling events 6 548 85 -0.006 0.051 1000 -1000 -0.032 -1000
TCGA08_retinoblastoma 6 50 8 -0.034 0.031 1000 -1000 -0.001 -1000
Class IB PI3K non-lipid kinase events 6 18 3 -0.016 0.016 1000 -1000 0 -1000
IL2 signaling events mediated by STAT5 5 119 22 -0.026 0.033 1000 -1000 -0.033 -1000
S1P4 pathway 5 129 25 -0.003 0.047 1000 -1000 -0.026 -1000
Aurora B signaling 5 380 67 -0.32 0.1 1000 -1000 -0.029 -1000
Insulin-mediated glucose transport 4 135 32 -0.084 0.05 1000 -1000 -0.026 -1000
S1P5 pathway 4 79 17 -0.006 0.032 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class I 4 479 104 -0.056 0.063 1000 -1000 -0.029 -1000
Canonical Wnt signaling pathway 4 223 51 -0.037 0.065 1000 -1000 -0.052 -1000
Effects of Botulinum toxin 4 117 26 -0.069 0.048 1000 -1000 -0.014 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 601 125 -0.008 0.072 1000 -1000 -0.048 -1000
PDGFR-beta signaling pathway 4 471 97 -0.14 0.079 1000 -1000 -0.061 -1000
Canonical NF-kappaB pathway 3 148 39 -0.056 0.062 1000 -1000 -0.028 -1000
Circadian rhythm pathway 3 68 22 -0.013 0.041 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 3 19 5 0.009 0.036 1000 -1000 -0.002 -1000
Class I PI3K signaling events mediated by Akt 3 268 68 -0.084 0.051 1000 -1000 -0.038 -1000
FoxO family signaling 3 253 64 -0.084 0.1 1000 -1000 -0.036 -1000
Signaling mediated by p38-gamma and p38-delta 3 47 15 -0.001 0.027 1000 -1000 -0.034 -1000
Atypical NF-kappaB pathway 3 113 31 -0.014 0.039 1000 -1000 -0.025 -1000
p38 MAPK signaling pathway 3 152 44 -0.028 0.05 1000 -1000 -0.021 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 2 59 23 -0.016 0.049 1000 -1000 -0.027 -1000
EPO signaling pathway 2 162 55 -0.014 0.06 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 2 93 37 0 0.065 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 2 108 43 -0.16 0.16 1000 -1000 -0.044 -1000
E-cadherin signaling in keratinocytes 2 126 43 -0.029 0.051 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class II 1 89 75 -0.036 0.074 1000 -1000 -0.023 -1000
Aurora A signaling 1 116 60 -0.023 0.055 1000 -1000 -0.025 -1000
TRAIL signaling pathway 1 58 48 -0.015 0.076 1000 -1000 -0.036 -1000
Paxillin-dependent events mediated by a4b1 1 65 36 -0.055 0.057 1000 -1000 -0.041 -1000
E-cadherin signaling in the nascent adherens junction 1 124 76 -0.058 0.068 1000 -1000 -0.059 -1000
Arf6 trafficking events 1 93 71 -0.049 0.05 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 0 0 3 0.016 0.027 1000 -1000 -0.014 -1000
Arf6 downstream pathway 0 9 43 -0.059 0.046 1000 -1000 -0.023 -1000
Aurora C signaling 0 3 7 -0.006 0.047 1000 -1000 -0.012 -1000
Glypican 2 network 0 0 4 -0.018 0.016 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 19 27 0 0.067 1000 -1000 -0.032 -1000
E-cadherin signaling events 0 0 5 0.026 0.052 1000 -1000 -0.001 -1000
Arf1 pathway 0 23 54 -0.001 0.052 1000 -1000 -0.02 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.073 1000 -1000 -0.005 -1000
Total 3199 184787 7203 -23 8.1 131000 -131000 -4.9 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.32 0.26 -9999 0 -0.48 310 310
EFNA5 -0.074 0.25 -9999 0 -0.68 65 65
FYN -0.3 0.24 -9999 0 -0.45 303 303
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.48 310 310
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.27 -9999 0 -0.49 310 310
EPHA5 -0.42 0.33 -9999 0 -0.68 285 285
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.21 0.2 0.38 1 -0.39 252 253
CRKL -0.22 0.22 -10000 0 -0.41 257 257
HRAS -0.19 0.19 -10000 0 -0.36 217 217
mol:PIP3 -0.2 0.21 -10000 0 -0.39 233 233
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.025 0.033 -10000 0 -0.68 1 1
GAB1 -0.23 0.23 -10000 0 -0.44 257 257
FOXO3 -0.19 0.21 0.37 2 -0.37 246 248
AKT1 -0.2 0.22 0.29 2 -0.39 251 253
BAD -0.18 0.21 0.29 3 -0.37 246 249
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 266 266
GSK3B -0.19 0.21 0.31 3 -0.37 246 249
RAF1 -0.16 0.16 0.35 1 -0.33 96 97
SHC1 0.026 0.008 -10000 0 -10000 0 0
STAT3 -0.23 0.23 -10000 0 -0.43 257 257
STAT1 -0.58 0.56 -10000 0 -1.1 260 260
HRAS/SPRED1 -0.15 0.16 -10000 0 -0.33 96 96
cell proliferation -0.23 0.23 -10000 0 -0.43 261 261
PIK3CA 0.022 0.057 -10000 0 -0.68 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.22 0.23 -10000 0 -0.42 258 258
HRAS/SPRED2 -0.15 0.16 -10000 0 -0.34 66 66
LYN/TEC/p62DOK -0.2 0.24 -10000 0 -0.41 256 256
MAPK3 -0.1 0.13 0.3 6 -0.27 27 33
STAP1 -0.24 0.24 -10000 0 -0.44 257 257
GRAP2 -0.017 0.14 -10000 0 -0.55 29 29
JAK2 -0.49 0.48 -10000 0 -0.89 259 259
STAT1 (dimer) -0.57 0.54 -10000 0 -1 260 260
mol:Gleevec 0.007 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.2 0.24 -10000 0 -0.41 247 247
actin filament polymerization -0.23 0.23 -10000 0 -0.43 256 256
LYN 0.027 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.33 0.32 0.35 1 -0.61 259 260
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 249 249
PI3K -0.2 0.24 -10000 0 -0.4 254 254
PTEN 0.026 0.019 -10000 0 -0.37 1 1
SCF/KIT/EPO/EPOR -0.69 0.66 -10000 0 -1.3 259 259
MAPK8 -0.24 0.24 -10000 0 -0.44 261 261
STAT3 (dimer) -0.23 0.23 -10000 0 -0.42 257 257
positive regulation of transcription -0.083 0.12 0.33 8 -0.24 17 25
mol:GDP -0.19 0.2 -10000 0 -0.38 220 220
PIK3C2B -0.22 0.23 -10000 0 -0.44 235 235
CBL/CRKL -0.2 0.22 -10000 0 -0.39 255 255
FER -0.24 0.23 -10000 0 -0.44 257 257
SH2B3 -0.23 0.23 -10000 0 -0.43 259 259
PDPK1 -0.18 0.2 0.3 3 -0.36 228 231
SNAI2 -0.24 0.24 -10000 0 -0.44 259 259
positive regulation of cell proliferation -0.4 0.4 -10000 0 -0.74 260 260
KITLG -0.013 0.08 -10000 0 -0.71 5 5
cell motility -0.4 0.4 -10000 0 -0.74 260 260
PTPN6 0.038 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.2 -10000 0 -1.2 5 5
STAT5A (dimer) -0.33 0.33 -10000 0 -0.61 259 259
SOCS1 0.024 0.036 -10000 0 -0.68 1 1
cell migration 0.23 0.23 0.43 253 -10000 0 253
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.007 0.029 -10000 0 -10000 0 0
VAV1 0.012 0.061 -10000 0 -0.57 3 3
GRB10 -0.23 0.23 -10000 0 -0.44 257 257
PTPN11 0.033 0.034 -10000 0 -0.66 1 1
SCF/KIT -0.24 0.25 -10000 0 -0.46 259 259
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.12 0.13 0.27 3 -0.27 63 66
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.74 0.69 -10000 0 -1.3 259 259
MAP2K2 -0.12 0.13 0.37 3 -0.3 23 26
SHC/Grb2/SOS1 -0.19 0.23 -10000 0 -0.41 223 223
STAT5A -0.34 0.34 -10000 0 -0.63 259 259
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.23 0.23 -10000 0 -0.43 259 259
SHC/GRAP2 0.002 0.1 -10000 0 -0.38 29 29
PTPRO -0.24 0.23 -10000 0 -0.44 266 266
SH2B2 -0.23 0.23 -10000 0 -0.43 256 256
DOK1 0.027 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.44 253 253
CREBBP -0.042 0.078 -10000 0 -10000 0 0
BCL2 -0.22 0.4 -10000 0 -1.5 37 37
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 -0.064 0.1 -10000 0 -0.66 7 7
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 234 234
JUN -0.26 0.26 -10000 0 -0.58 143 143
HRAS 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.26 0.29 -10000 0 -0.49 267 267
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.27 0.29 -10000 0 -0.49 270 270
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.21 0.22 -10000 0 -0.41 252 252
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.27 -10000 0 -0.45 263 263
GRB7 0.002 0.055 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.27 0.29 -10000 0 -0.49 265 265
MAPKKK cascade -0.24 0.24 -10000 0 -0.42 262 262
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.26 0.27 -10000 0 -0.47 267 267
lamellipodium assembly -0.2 0.18 -10000 0 -0.35 239 239
RET51/GFRalpha1/GDNF/SHC -0.26 0.29 -10000 0 -0.49 256 256
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.4 254 254
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.22 -10000 0 -0.4 257 257
MAPK3 -0.24 0.24 -10000 0 -0.43 260 260
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.083 0.26 -10000 0 -0.68 71 71
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.25 -10000 0 -0.47 240 240
DOK5 -0.066 0.24 -10000 0 -0.68 60 60
GFRA1 -0.38 0.35 -10000 0 -0.68 262 262
MAPK8 -0.2 0.2 -10000 0 -0.34 272 272
HRAS/GTP -0.26 0.28 -10000 0 -0.47 267 267
tube development -0.2 0.21 -10000 0 -0.39 243 243
MAPK1 -0.24 0.24 0.32 3 -0.42 262 265
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 243 243
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
SRC 0.027 0.009 -10000 0 -10000 0 0
PDLIM7 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.34 -10000 0 -0.54 278 278
SHC1 0.026 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.27 0.29 -10000 0 -0.49 269 269
RET51/GFRalpha1/GDNF/Dok5 -0.32 0.34 -10000 0 -0.55 283 283
PRKCA -0.005 0.14 -10000 0 -0.68 20 20
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
CREB1 -0.2 0.21 -10000 0 -0.38 238 238
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.15 0.16 -10000 0 -0.3 226 226
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.29 -10000 0 -0.5 268 268
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.1 0.26 -10000 0 -0.67 77 77
DOK4 0.026 0.009 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.57 143 143
RET9/GFRalpha1/GDNF/FRS2 -0.21 0.22 -10000 0 -0.41 253 253
SHANK3 0.02 0.013 -10000 0 -10000 0 0
RASA1 0.027 0.006 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 227 227
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.36 266 266
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.35 271 271
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.41 253 253
PI3K -0.31 0.29 -10000 0 -0.55 241 241
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.21 -10000 0 -0.39 243 243
GRB10 0.027 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.33 250 250
RET51/GFRalpha1/GDNF/FRS2 -0.27 0.29 -10000 0 -0.49 270 270
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.058 0.23 -10000 0 -0.68 55 55
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.41 253 253
RET51/GFRalpha1/GDNF/PKC alpha -0.28 0.31 -10000 0 -0.51 269 269
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.026 0.008 -10000 0 -10000 0 0
GDNF -0.007 0.024 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.32 0.33 -10000 0 -0.54 281 281
Rac1/GTP -0.24 0.23 -10000 0 -0.43 235 235
RET9/GFRalpha1/GDNF -0.24 0.23 -10000 0 -0.44 261 261
GFRalpha1/GDNF -0.28 0.27 -10000 0 -0.51 261 261
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.038 0.014 -10000 0 -10000 0 0
VLDLR -0.005 0.14 -10000 0 -0.65 21 21
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.025 0.015 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.31 0.24 -10000 0 -0.46 320 320
MAPK8IP1/MKK7/MAP3K11/JNK1 0.063 0.06 -10000 0 -0.38 6 6
AKT1 -0.2 0.16 -10000 0 -0.3 307 307
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.023 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.28 0.23 -10000 0 -0.43 309 309
LRPAP1/LRP8 0.016 0.11 -10000 0 -0.51 19 19
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.41 309 309
DAB1/alpha3/beta1 Integrin -0.25 0.22 -10000 0 -0.4 301 301
long-term memory -0.26 0.24 -10000 0 -0.41 308 308
DAB1/LIS1 -0.26 0.23 -10000 0 -0.4 304 304
DAB1/CRLK/C3G -0.25 0.22 -10000 0 -0.39 301 301
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
DAB1/NCK2 -0.26 0.23 -10000 0 -0.4 309 309
ARHGEF2 0.026 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.001 0.13 -10000 0 -0.68 16 16
CDK5R1 0.026 0.012 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.68 313 313
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.46 317 317
GRIN2A/RELN/LRP8/DAB1/Fyn -0.27 0.24 -10000 0 -0.42 308 308
MAPK8 0.017 0.082 -10000 0 -0.63 7 7
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.42 320 320
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.22 -10000 0 -0.42 308 308
RELN/LRP8 -0.3 0.24 -10000 0 -0.46 315 315
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.23 -10000 0 -0.41 308 308
PI3K 0.036 0.045 -10000 0 -0.51 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.038 0.015 -10000 0 -10000 0 0
RAP1A -0.24 0.21 0.48 3 -0.42 121 124
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.019 -10000 0 -10000 0 0
GRIN2B -0.005 0.02 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.43 34 34
neuron adhesion -0.22 0.22 0.45 10 -0.65 25 35
LRP8 -0.002 0.14 -10000 0 -0.68 19 19
GSK3B -0.19 0.15 -10000 0 -0.43 33 33
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.4 310 310
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.17 -10000 0 -0.32 309 309
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.047 0.16 0.81 16 -0.61 3 19
neuron migration -0.26 0.2 0.26 3 -0.4 293 296
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.14 -10000 0 -0.44 34 34
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 312 312
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.009 0.11 -10000 0 -0.48 14 14
NFATC2 -0.22 0.33 -10000 0 -0.73 109 109
NFATC3 -0.085 0.14 -10000 0 -0.28 116 116
CD40LG -0.63 0.56 -10000 0 -1.1 249 249
ITCH 0.038 0.017 -10000 0 -10000 0 0
CBLB 0.038 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.44 0.51 -10000 0 -1.1 125 125
JUNB 0.02 0.06 -10000 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.042 0.019 -10000 0 -0.32 1 1
T cell anergy 0.009 0.078 0.4 6 -0.44 2 8
TLE4 -0.21 0.35 -10000 0 -0.79 99 99
Jun/NFAT1-c-4/p21SNFT -0.56 0.6 -10000 0 -1.1 218 218
AP-1/NFAT1-c-4 -0.72 0.75 -10000 0 -1.3 242 242
IKZF1 -0.16 0.27 -10000 0 -0.67 73 73
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.81 99 99
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.76 185 185
CALM1 0.038 0.013 -10000 0 -10000 0 0
EGR2 -0.74 0.79 -10000 0 -1.5 215 215
EGR3 -0.54 0.7 -10000 0 -1.2 183 183
NFAT1/FOXP3 -0.16 0.28 -10000 0 -0.58 113 113
EGR1 -0.12 0.28 -10000 0 -0.68 94 94
JUN -0.14 0.29 -10000 0 -0.67 100 100
EGR4 -0.018 0.15 -10000 0 -0.67 23 23
mol:Ca2+ 0.012 0.009 -10000 0 -10000 0 0
GBP3 -0.15 0.26 -10000 0 -0.63 78 78
FOSL1 0.007 0.061 -10000 0 -0.52 2 2
NFAT1-c-4/MAF/IRF4 -0.48 0.56 -10000 0 -1 222 222
DGKA -0.15 0.24 -10000 0 -0.58 83 83
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.5 0.55 -10000 0 -1 219 219
CTLA4 -0.18 0.29 -10000 0 -0.7 87 87
NFAT1-c-4 (dimer)/EGR1 -0.56 0.63 -10000 0 -1.2 215 215
NFAT1-c-4 (dimer)/EGR4 -0.52 0.56 -10000 0 -1 222 222
FOS -0.17 0.31 -10000 0 -0.68 122 122
IFNG -0.37 0.51 -10000 0 -1.1 119 119
T cell activation -0.4 0.39 -10000 0 -0.88 154 154
MAF 0.026 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.41 0.74 212 -10000 0 212
TNF -0.55 0.55 -10000 0 -1 236 236
FASLG -0.71 0.77 -10000 0 -1.4 230 230
TBX21 -0.02 0.15 -10000 0 -0.69 21 21
BATF3 0.018 0.045 -10000 0 -0.68 1 1
PRKCQ 0.016 0.078 -10000 0 -0.63 6 6
PTPN1 -0.15 0.25 -10000 0 -0.61 74 74
NFAT1-c-4/ICER1 -0.49 0.55 -10000 0 -1 218 218
GATA3 -0.006 0.15 -10000 0 -0.64 23 23
T-helper 1 cell differentiation -0.36 0.48 -10000 0 -1.1 119 119
IL2RA -0.4 0.46 -10000 0 -0.95 143 143
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.15 0.25 -10000 0 -0.57 86 86
E2F1 -0.012 0.068 -10000 0 -10000 0 0
PPARG 0.017 0.081 -10000 0 -0.68 6 6
SLC3A2 -0.15 0.25 -10000 0 -0.62 70 70
IRF4 -0.044 0.18 -10000 0 -0.67 30 30
PTGS2 -0.61 0.55 0.5 1 -1.1 241 242
CSF2 -0.62 0.53 -10000 0 -1.1 245 245
JunB/Fra1/NFAT1-c-4 -0.46 0.54 -10000 0 -0.98 215 215
IL4 -0.29 0.35 -10000 0 -0.88 94 94
IL5 -0.6 0.53 -10000 0 -1.1 238 238
IL2 -0.4 0.4 -10000 0 -0.9 154 154
IL3 -0.07 0.087 -10000 0 -1.1 1 1
RNF128 0.035 0.039 -10000 0 -0.75 1 1
NFATC1 -0.36 0.42 -10000 0 -0.75 212 212
CDK4 0.24 0.25 0.57 95 -10000 0 95
PTPRK -0.15 0.25 -10000 0 -0.56 95 95
IL8 -0.61 0.54 0.5 1 -1.1 242 243
POU2F1 0.026 0.01 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.4 283 283
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.021 0.024 -9999 0 -10000 0 0
WNT4 -0.2 0.33 -9999 0 -0.68 146 146
FZD3 0.027 0.004 -9999 0 -10000 0 0
WNT5A 0.013 0.098 -9999 0 -0.68 9 9
WNT11 -0.33 0.35 -9999 0 -0.67 233 233
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.085 0.26 -10000 0 -0.68 73 73
GNB1/GNG2 -0.2 0.23 -10000 0 -0.53 106 106
mol:DAG -0.19 0.2 -10000 0 -0.49 103 103
PLCG1 -0.2 0.21 -10000 0 -0.51 103 103
YES1 -0.22 0.22 -10000 0 -0.38 280 280
FZD3 0.027 0.004 -10000 0 -10000 0 0
FZD6 0.027 0.005 -10000 0 -10000 0 0
G protein -0.19 0.22 -10000 0 -0.51 103 103
MAP3K7 -0.17 0.17 0.31 1 -0.42 100 101
mol:Ca2+ -0.18 0.2 -10000 0 -0.48 103 103
mol:IP3 -0.19 0.2 -10000 0 -0.49 103 103
NLK -0.003 0.068 -10000 0 -0.82 3 3
GNB1 0.027 0.006 -10000 0 -10000 0 0
CAMK2A -0.18 0.19 0.32 1 -0.45 101 102
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.24 -10000 0 -0.4 283 283
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
GNAS -0.22 0.22 -10000 0 -0.5 127 127
GO:0007205 -0.19 0.2 -10000 0 -0.48 103 103
WNT6 0.021 0.024 -10000 0 -10000 0 0
WNT4 -0.2 0.33 -10000 0 -0.68 146 146
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.54 133 133
GNG2 0.025 0.033 -10000 0 -0.68 1 1
WNT5A 0.013 0.098 -10000 0 -0.68 9 9
WNT11 -0.33 0.35 -10000 0 -0.67 233 233
CDC42 -0.21 0.21 -10000 0 -0.52 107 107
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 -0.2 0.32 -10000 0 -0.69 139 139
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 139 139
positive regulation of JUN kinase activity -0.076 0.2 -10000 0 -0.39 128 128
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.25 -10000 0 -0.52 139 139
AP1 -0.42 0.55 -10000 0 -1.2 131 131
mol:IP3 -0.16 0.24 -10000 0 -0.53 137 137
PLCG1 -0.16 0.24 -10000 0 -0.53 137 137
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.51 140 140
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.53 137 137
CAV3 -0.012 0.019 -10000 0 -10000 0 0
CAV1 0.014 0.093 -10000 0 -0.68 8 8
SHC/Grb2/SOS1 -0.075 0.2 -10000 0 -0.39 128 128
PDGF/PDGFRA/Shf -0.14 0.25 -10000 0 -0.51 139 139
FOS -0.41 0.52 -10000 0 -1.2 131 131
JUN -0.15 0.23 -10000 0 -0.58 98 98
oligodendrocyte development -0.14 0.25 -10000 0 -0.51 140 140
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.53 137 137
PDGF/PDGFRA -0.2 0.32 -10000 0 -0.69 139 139
actin cytoskeleton reorganization -0.14 0.24 -10000 0 -0.51 139 139
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
PI3K -0.099 0.22 -10000 0 -0.44 139 139
PDGF/PDGFRA/Crk/C3G -0.098 0.22 -10000 0 -0.43 136 136
JAK1 -0.15 0.24 -10000 0 -0.51 139 139
ELK1/SRF -0.12 0.19 0.32 1 -0.41 131 132
SHB 0.026 0.008 -10000 0 -10000 0 0
SHF 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.044 0.025 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.55 138 138
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.076 0.2 -10000 0 -0.39 128 128
PDGF/PDGFRA/SHB -0.14 0.25 -10000 0 -0.51 139 139
PDGF/PDGFRA/Caveolin-1 -0.14 0.26 -10000 0 -0.52 141 141
ITGAV 0.024 0.047 -10000 0 -0.68 2 2
ELK1 -0.16 0.22 -10000 0 -0.5 135 135
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
PDGF/PDGFRA/Crk -0.14 0.24 -10000 0 -0.5 139 139
JAK-STAT cascade -0.15 0.24 -10000 0 -0.51 139 139
cell proliferation -0.14 0.25 -10000 0 -0.51 139 139
Nongenotropic Androgen signaling

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
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.13 0.22 -10000 0 -0.41 172 172
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.3 182 182
GNAO1 0.004 0.12 -10000 0 -0.68 14 14
HRAS 0.026 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.061 -10000 0 -0.44 8 8
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.15 0.2 0.47 4 -0.38 178 182
T-DHT/AR -0.2 0.26 -10000 0 -0.51 188 188
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.005 125 125
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.034 -10000 0 -0.68 1 1
mol:GDP -0.21 0.26 -10000 0 -0.53 185 185
cell proliferation -0.2 0.27 0.5 10 -0.52 142 152
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
FOS -0.27 0.38 0.53 8 -0.85 126 134
mol:Ca2+ -0.026 0.03 -10000 0 -0.067 102 102
MAPK3 -0.16 0.25 0.53 12 -0.41 172 184
MAPK1 -0.18 0.22 0.34 5 -0.42 164 169
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 112 112
cAMP biosynthetic process 0.016 0.071 0.26 9 -0.42 8 17
GNG2 0.025 0.033 -10000 0 -0.68 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 112 112
HRAS/GTP -0.14 0.21 -10000 0 -0.39 178 178
actin cytoskeleton reorganization 0.037 0.035 -10000 0 -0.36 3 3
SRC 0.026 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 112 112
PI3K 0.033 0.04 -10000 0 -0.44 3 3
apoptosis 0.2 0.25 0.52 144 -0.46 7 151
T-DHT/AR/PELP1 -0.16 0.23 -10000 0 -0.44 186 186
HRAS/GDP -0.2 0.26 -10000 0 -0.51 185 185
CREB1 -0.21 0.28 0.47 7 -0.57 144 151
RAC1-CDC42/GTP 0.047 0.037 -10000 0 -0.37 3 3
AR -0.26 0.34 -10000 0 -0.67 188 188
GNB1 0.027 0.006 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.54 6 -0.38 178 184
RAC1-CDC42/GDP -0.17 0.26 -10000 0 -0.48 184 184
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.42 178 178
MAP2K2 -0.15 0.2 0.51 3 -0.38 174 177
T-DHT/AR/PELP1/Src/PI3K -0.1 0.16 -10000 0 -0.3 182 182
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.014 0.093 -10000 0 -0.68 8 8
Gi family/GNB1/GNG2/GDP -0.033 0.1 -10000 0 -0.46 16 16
mol:T-DHT 0 0.003 0.002 2 -0.005 66 68
RAC1 0.027 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.035 -10000 0 -0.51 2 2
Gi family/GTP -0.088 0.11 -10000 0 -0.3 46 46
CDC42 0.027 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.48 0.49 -10000 0 -1 172 172
PCK1 -0.31 0.45 -10000 0 -1.3 60 60
HNF4A -0.63 0.61 -10000 0 -1.2 223 223
KCNJ11 -0.46 0.48 -10000 0 -1 160 160
AKT1 -0.065 0.14 -10000 0 -0.46 13 13
response to starvation -0.018 0.04 -10000 0 -0.38 2 2
DLK1 -0.46 0.48 -10000 0 -1 160 160
NKX2-1 -0.17 0.19 -10000 0 -10000 0 0
ACADM -0.48 0.49 -10000 0 -1 160 160
TAT -0.18 0.2 -10000 0 -0.58 10 10
CEBPB 0.028 0.006 -10000 0 -10000 0 0
CEBPA 0.019 0.074 -10000 0 -0.68 5 5
TTR -0.14 0.23 0.71 5 -0.74 24 29
PKLR -0.47 0.49 -10000 0 -1 169 169
APOA1 -0.87 0.84 -10000 0 -1.7 224 224
CPT1C -0.48 0.49 -10000 0 -1 170 170
ALAS1 -0.16 0.2 -10000 0 -0.91 2 2
TFRC -0.23 0.27 -10000 0 -0.72 32 32
FOXF1 0.013 0.074 -10000 0 -0.68 5 5
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.007 -10000 0 -10000 0 0
CPT1A -0.48 0.49 -10000 0 -1.1 160 160
HMGCS1 -0.48 0.49 -10000 0 -1 163 163
NR3C1 0.032 0.01 -10000 0 -10000 0 0
CPT1B -0.48 0.49 -10000 0 -1.1 159 159
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
GCK -0.6 0.63 -10000 0 -1.3 193 193
CREB1 0.008 0.067 -10000 0 -0.25 14 14
IGFBP1 -0.17 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -0.61 3 3
UCP2 -0.48 0.49 -10000 0 -1 173 173
ALDOB -0.45 0.48 -10000 0 -1 164 164
AFP -0.02 0.087 -10000 0 -0.37 5 5
BDH1 -0.48 0.49 -10000 0 -1 171 171
HADH -0.45 0.48 -10000 0 -1 159 159
F2 -0.59 0.59 -10000 0 -1.2 177 177
HNF1A 0.029 0.007 -10000 0 -10000 0 0
G6PC -0.001 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.24 -10000 0 -1.2 1 1
INS -0.022 0.014 -10000 0 -10000 0 0
FOXA1 -0.015 0.097 -10000 0 -0.34 22 22
FOXA3 -0.028 0.12 -10000 0 -0.32 34 34
FOXA2 -0.51 0.55 -10000 0 -1.1 176 176
ABCC8 -0.71 0.67 -10000 0 -1.3 236 236
ALB -0.066 0.28 -10000 0 -1.1 30 30
Signaling events mediated by the Hedgehog family

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.089 0.21 -10000 0 -0.63 26 26
IHH -0.16 0.32 -10000 0 -0.7 116 116
SHH Np/Cholesterol/GAS1 -0.055 0.16 -10000 0 -0.41 74 74
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.054 0.16 0.4 74 -10000 0 74
SMO/beta Arrestin2 -0.078 0.21 -10000 0 -0.42 105 105
SMO -0.098 0.21 -10000 0 -0.44 109 109
AKT1 -0.017 0.11 -10000 0 -0.61 2 2
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.015 0.093 -10000 0 -0.68 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.097 0.21 -10000 0 -0.44 109 109
STIL -0.068 0.16 -10000 0 -0.49 14 14
DHH N/PTCH2 -0.052 0.21 -10000 0 -0.51 76 76
DHH N/PTCH1 -0.078 0.19 -10000 0 -0.38 119 119
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
DHH 0.022 0.057 -10000 0 -0.68 3 3
PTHLH -0.14 0.31 -10000 0 -1 29 29
determination of left/right symmetry -0.097 0.21 -10000 0 -0.44 109 109
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
skeletal system development -0.14 0.3 -10000 0 -1 29 29
IHH N/Hhip -0.3 0.34 -10000 0 -0.6 240 240
DHH N/Hhip -0.17 0.27 -10000 0 -0.51 174 174
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.097 0.21 -10000 0 -0.44 109 109
pancreas development -0.25 0.33 -10000 0 -0.68 174 174
HHAT 0.024 0.034 -10000 0 -0.68 1 1
PI3K 0.036 0.045 -10000 0 -0.51 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.1 0.27 -10000 0 -0.63 90 90
somite specification -0.097 0.21 -10000 0 -0.44 109 109
SHH Np/Cholesterol/PTCH1 -0.073 0.16 -10000 0 -0.5 13 13
SHH Np/Cholesterol/PTCH2 -0.045 0.15 -10000 0 -0.41 61 61
SHH Np/Cholesterol/Megalin -0.084 0.18 -10000 0 -0.41 100 100
SHH -0.005 0.03 -10000 0 -0.51 1 1
catabolic process -0.097 0.21 -10000 0 -0.42 120 120
SMO/Vitamin D3 -0.079 0.19 -10000 0 -0.55 12 12
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.4 173 173
LRP2 -0.16 0.31 -10000 0 -0.67 123 123
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.61 40 40
SHH Np/Cholesterol/BOC 0.013 0.059 -10000 0 -0.38 9 9
SHH Np/Cholesterol/CDO -0.097 0.19 -10000 0 -0.41 110 110
mesenchymal cell differentiation 0.14 0.2 0.39 173 -10000 0 173
mol:Vitamin D3 -0.067 0.17 -10000 0 -0.51 13 13
IHH N/PTCH2 -0.18 0.29 -10000 0 -0.54 168 168
CDON -0.18 0.32 -10000 0 -0.68 135 135
IHH N/PTCH1 -0.094 0.21 -10000 0 -0.42 128 128
Megalin/LRPAP1 -0.11 0.24 -10000 0 -0.5 123 123
PTCH2 -0.088 0.26 -10000 0 -0.68 75 75
SHH Np/Cholesterol 0.009 0.024 -10000 0 -0.41 1 1
PTCH1 -0.098 0.21 -10000 0 -0.42 120 120
HHIP -0.25 0.33 -10000 0 -0.68 174 174
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR -0.005 0.14 -10000 0 -0.65 21 21
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.3 0.24 -10000 0 -0.46 315 315
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.28 0.22 -10000 0 -0.42 305 305
IQGAP1/CaM 0.04 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.023 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.07 0.24 -10000 0 -0.68 63 63
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.016 0.11 -10000 0 -0.51 19 19
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.026 0.012 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.004 -10000 0 -10000 0 0
CDK5R2 0.001 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.3 0.24 -10000 0 -0.45 320 320
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.19 0.36 5 -0.35 194 199
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.25 0.2 -10000 0 -0.38 297 297
RELN -0.46 0.32 -10000 0 -0.68 313 313
PAFAH/LIS1 -0.033 0.16 -10000 0 -0.44 63 63
LIS1/CLIP170 0.031 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.49 15 15
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.17 -10000 0 -0.31 304 304
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.23 0.19 0.64 1 -0.36 296 297
LIS1/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.025 0.014 -10000 0 -10000 0 0
PAFAH1B2 0.017 0.082 -10000 0 -0.63 7 7
MAP1B/LIS1/Dynein heavy chain 0.031 0.013 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.18 0.32 1 -0.54 20 21
LRP8 -0.002 0.14 -10000 0 -0.68 19 19
NDEL1/Katanin 60 -0.22 0.18 0.29 4 -0.45 39 43
P39/CDK5 -0.25 0.2 -10000 0 -0.38 304 304
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.2 -10000 0 -0.4 305 305
PPP2R5D 0.028 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.21 -10000 0 -0.4 300 300
RELN/VLDLR -0.29 0.24 -10000 0 -0.44 312 312
CDC42 0.017 0.006 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.067 -9999 0 -0.46 8 8
NFATC2 -0.075 0.17 -9999 0 -0.45 73 73
NFATC3 -0.002 0.031 -9999 0 -10000 0 0
CD40LG -0.34 0.37 -9999 0 -0.76 167 167
PTGS2 -0.32 0.35 -9999 0 -0.73 160 160
JUNB 0.02 0.06 -9999 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.024 -9999 0 -10000 0 0
CaM/Ca2+ 0.007 0.024 -9999 0 -10000 0 0
CALM1 0.017 0.021 -9999 0 -10000 0 0
JUN -0.14 0.29 -9999 0 -0.68 99 99
mol:Ca2+ -0.008 0.02 -9999 0 -0.19 3 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -9999 0 -10000 0 0
FOSL1 0.007 0.061 -9999 0 -0.52 2 2
CREM 0.027 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.24 -9999 0 -0.46 152 152
FOS -0.17 0.31 -9999 0 -0.68 122 122
IFNG -0.34 0.36 -9999 0 -0.73 176 176
AP-1/NFAT1-c-4 -0.36 0.45 -9999 0 -0.85 166 166
FASLG -0.32 0.34 -9999 0 -0.72 160 160
NFAT1-c-4/ICER1 -0.075 0.17 -9999 0 -0.41 78 78
IL2RA -0.31 0.34 -9999 0 -0.71 161 161
FKBP12/FK506 0.02 0.004 -9999 0 -10000 0 0
CSF2 -0.33 0.32 -9999 0 -0.69 165 165
JunB/Fra1/NFAT1-c-4 -0.067 0.17 -9999 0 -0.4 78 78
IL4 -0.31 0.32 -9999 0 -0.68 156 156
IL2 0.001 0.082 -9999 0 -0.95 3 3
IL3 -0.009 0.053 -9999 0 -0.88 1 1
FKBP1A 0.027 0.005 -9999 0 -10000 0 0
BATF3 0.018 0.045 -9999 0 -0.68 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.026 0.01 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.098 0.24 0.54 100 -10000 0 100
KIRREL -0.041 0.19 -10000 0 -0.7 34 34
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.098 0.24 -10000 0 -0.54 100 100
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.053 0.2 -10000 0 -0.43 94 94
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.055 0.16 -10000 0 -0.35 93 93
FYN -0.061 0.19 0.27 24 -0.41 94 118
mol:Ca2+ -0.053 0.2 -10000 0 -0.43 93 93
mol:DAG -0.052 0.2 -10000 0 -0.43 93 93
NPHS2 -0.003 0.042 -10000 0 -10000 0 0
mol:IP3 -0.052 0.2 -10000 0 -0.43 93 93
regulation of endocytosis -0.047 0.18 -10000 0 -0.38 93 93
Nephrin/NEPH1/podocin/Cholesterol -0.065 0.2 -10000 0 -0.43 95 95
establishment of cell polarity -0.098 0.24 -10000 0 -0.54 100 100
Nephrin/NEPH1/podocin/NCK1-2 -0.037 0.19 -10000 0 -0.4 94 94
Nephrin/NEPH1/beta Arrestin2 -0.047 0.18 -10000 0 -0.39 93 93
NPHS1 -0.1 0.26 -10000 0 -0.68 78 78
Nephrin/NEPH1/podocin -0.058 0.19 -10000 0 -0.41 95 95
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.052 0.2 -10000 0 -0.43 93 93
CD2AP 0.028 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.052 0.2 -10000 0 -0.43 92 92
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.073 0.19 0.28 22 -0.41 96 118
cytoskeleton organization -0.08 0.2 -10000 0 -0.45 93 93
Nephrin/NEPH1 -0.069 0.18 -10000 0 -0.4 98 98
Nephrin/NEPH1/ZO-1 -0.067 0.21 -10000 0 -0.46 95 95
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.029 0.091 -10000 0 -0.42 10 10
PTK2B 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.47 1 -0.66 69 70
EDN1 -0.002 0.098 -10000 0 -0.55 8 8
EDN3 -0.32 0.35 -10000 0 -0.68 221 221
EDN2 0.01 0.086 -10000 0 -0.68 6 6
HRAS/GDP -0.11 0.23 0.44 3 -0.5 81 84
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.15 -10000 0 -0.36 64 64
ADCY4 -0.069 0.15 0.35 1 -0.4 61 62
ADCY5 -0.12 0.2 0.35 1 -0.46 103 104
ADCY6 -0.067 0.14 0.35 1 -0.4 61 62
ADCY7 -0.067 0.15 0.35 1 -0.4 61 62
ADCY1 -0.07 0.15 0.35 1 -0.41 61 62
ADCY2 -0.099 0.18 -10000 0 -0.44 87 87
ADCY3 -0.069 0.15 0.35 1 -0.41 63 64
ADCY8 -0.097 0.16 0.35 1 -0.44 62 63
ADCY9 -0.067 0.15 0.35 1 -0.41 60 61
arachidonic acid secretion -0.19 0.32 0.37 9 -0.62 136 145
ETB receptor/Endothelin-1/Gq/GTP -0.084 0.18 -10000 0 -0.36 111 111
GNAO1 0.004 0.12 -10000 0 -0.68 14 14
HRAS 0.025 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.031 0.1 -10000 0 -0.39 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.026 0.18 -10000 0 -0.42 64 64
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.033 0.099 -10000 0 -0.48 8 8
EDNRB 0.016 0.075 -10000 0 -0.68 5 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.068 0.15 -10000 0 -0.6 22 22
CYSLTR1 -0.032 0.12 -10000 0 -0.62 11 11
SLC9A1 0 0.056 -10000 0 -0.27 10 10
mol:GDP -0.13 0.24 0.41 5 -0.52 85 90
SLC9A3 -0.054 0.2 0.37 1 -0.67 35 36
RAF1 -0.17 0.28 0.44 3 -0.57 115 118
JUN -0.29 0.49 0.45 1 -1.1 116 117
JAK2 -0.029 0.094 -10000 0 -0.46 10 10
mol:IP3 -0.1 0.2 -10000 0 -0.45 88 88
ETA receptor/Endothelin-1 0.014 0.13 -10000 0 -0.42 21 21
PLCB1 0.023 0.034 -10000 0 -0.68 1 1
PLCB2 0.02 0.023 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.52 222 222
FOS -0.28 0.45 0.61 2 -0.99 126 128
Gai/GDP -0.014 0.15 -10000 0 -0.65 23 23
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.18 -10000 0 -0.48 50 50
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.44 89 89
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.06 0.23 -10000 0 -0.66 58 58
Gs family/GDP -0.15 0.25 0.28 1 -0.54 105 106
ETA receptor/Endothelin-1/Gq/GTP -0.09 0.18 -10000 0 -0.38 94 94
MAPK14 -0.071 0.15 -10000 0 -0.37 55 55
TRPC6 -0.16 0.3 0.47 1 -0.71 67 68
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.034 -10000 0 -0.68 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.072 0.16 -10000 0 -0.36 77 77
ETB receptor/Endothelin-2 0.021 0.088 -10000 0 -0.52 11 11
ETB receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.52 224 224
ETB receptor/Endothelin-1 0.016 0.095 -10000 0 -0.53 10 10
MAPK3 -0.25 0.41 0.4 5 -0.88 125 130
MAPK1 -0.3 0.45 0.63 2 -0.98 127 129
Rac1/GDP -0.11 0.22 0.37 1 -0.5 77 78
cAMP biosynthetic process -0.075 0.18 0.45 10 -0.44 65 75
MAPK8 -0.18 0.35 0.48 1 -0.71 100 101
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.002 0.076 -10000 0 -0.32 14 14
p130Cas/CRK/Src/PYK2 -0.15 0.29 0.44 8 -0.56 113 121
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.5 74 75
COL1A2 -0.005 0.096 -10000 0 -0.48 6 6
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.014 0.086 -10000 0 -0.54 7 7
mol:DAG -0.1 0.2 -10000 0 -0.45 88 88
MAP2K2 -0.2 0.34 0.39 10 -0.68 127 137
MAP2K1 -0.21 0.34 0.5 2 -0.7 131 133
EDNRA 0.002 0.072 -10000 0 -0.36 5 5
positive regulation of muscle contraction -0.023 0.076 -10000 0 -0.38 6 6
Gq family/GDP -0.15 0.28 0.38 3 -0.57 109 112
HRAS/GTP -0.14 0.24 0.48 2 -0.53 90 92
PRKCH -0.11 0.2 0.3 1 -0.45 86 87
RAC1 0.027 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.22 0.3 1 -0.49 91 92
PRKCB -0.11 0.2 0.3 1 -0.46 79 80
PRKCE -0.11 0.2 -10000 0 -0.47 79 79
PRKCD -0.11 0.2 -10000 0 -0.46 82 82
PRKCG -0.1 0.19 -10000 0 -0.46 81 81
regulation of vascular smooth muscle contraction -0.33 0.53 0.64 2 -1.2 126 128
PRKCQ -0.11 0.2 -10000 0 -0.46 84 84
PLA2G4A -0.21 0.35 0.38 9 -0.68 136 145
GNA14 -0.14 0.29 -10000 0 -0.65 107 107
GNA15 0.007 0.051 -10000 0 -0.68 1 1
GNA12 0.027 0.006 -10000 0 -10000 0 0
GNA11 0.009 0.083 -10000 0 -0.64 7 7
Rac1/GTP 0.031 0.1 -10000 0 -0.38 8 8
MMP1 -0.035 0.079 0.63 2 -10000 0 2
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.053 0.027 -9999 0 -0.44 1 1
fibroblast growth factor receptor signaling pathway 0.052 0.026 -9999 0 -0.44 1 1
LAMA1 -0.019 0.17 -9999 0 -0.67 30 30
PRNP 0.025 0.033 -9999 0 -0.68 1 1
GPC1/SLIT2 -0.039 0.19 -9999 0 -0.51 65 65
SMAD2 0.017 0.035 -9999 0 -0.41 2 2
GPC1/PrPc/Cu2+ 0.035 0.024 -9999 0 -0.44 1 1
GPC1/Laminin alpha1 0.003 0.14 -9999 0 -0.5 30 30
TDGF1 -0.27 0.35 -9999 0 -0.68 193 193
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.51 192 192
APP/GPC1 0.039 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.23 -9999 0 -0.44 188 188
FLT1 0.025 0.034 -9999 0 -0.68 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.038 -9999 0 -0.44 2 2
SERPINC1 0.021 0.019 -9999 0 -10000 0 0
FYN -0.17 0.23 -9999 0 -0.44 191 191
FGR -0.17 0.22 -9999 0 -0.44 185 185
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.52 186 186
SLIT2 -0.073 0.24 -9999 0 -0.67 65 65
GPC1/NRG -0.014 0.16 -9999 0 -0.51 44 44
NRG1 -0.042 0.21 -9999 0 -0.67 45 45
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.048 0.055 -9999 0 -0.57 3 3
LYN -0.17 0.23 -9999 0 -0.44 190 190
mol:Spermine 0.009 0.004 -9999 0 -10000 0 0
cell growth 0.052 0.026 -9999 0 -0.44 1 1
BMP signaling pathway -0.027 0.009 -9999 0 -10000 0 0
SRC -0.17 0.23 -9999 0 -0.44 187 187
TGFBR1 0.022 0.024 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.18 0.3 -9999 0 -0.68 119 119
GPC1 0.027 0.009 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.022 0.024 -9999 0 -10000 0 0
VEGFA 0.023 0.057 -9999 0 -0.68 3 3
BLK -0.3 0.3 -9999 0 -0.55 254 254
HCK -0.18 0.22 -9999 0 -0.44 187 187
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.026 0.033 -9999 0 -0.68 1 1
VEGFR1 homodimer 0.025 0.034 -9999 0 -0.68 1 1
TGFBR2 0.024 0.047 -9999 0 -0.68 2 2
cell death 0.039 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.035 0.017 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.24 -9999 0 -0.51 119 119
LCK -0.18 0.23 -9999 0 -0.45 190 190
neuron differentiation -0.014 0.16 -9999 0 -0.51 44 44
PrPc/Cu2+ 0.019 0.025 -9999 0 -0.51 1 1
APP 0.027 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.047 -9999 0 -0.68 2 2
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.036 0.17 -10000 0 -0.45 67 67
cell-cell adhesion 0.12 0.16 0.33 165 -10000 0 165
Ephrin B/EPHB2/RasGAP 0.065 0.063 -10000 0 -0.38 7 7
ITSN1 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
SHC1 0.026 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.026 0.047 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.15 0.23 -10000 0 -0.44 177 177
HRAS/GDP -0.085 0.17 -10000 0 -0.3 162 162
Ephrin B/EPHB1/GRB7 -0.1 0.23 -10000 0 -0.4 170 170
Endophilin/SYNJ1 0.023 0.075 0.46 5 -0.36 7 12
KRAS 0.027 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.22 -10000 0 -0.39 170 170
endothelial cell migration 0.052 0.039 -10000 0 -0.38 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.002 0.055 -10000 0 -10000 0 0
PAK1 0.024 0.077 0.46 5 -0.36 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.02 0.069 0.44 4 -0.36 6 10
DNM1 0.003 0.12 -10000 0 -0.62 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.13 0.19 -10000 0 -0.37 170 170
lamellipodium assembly -0.12 0.16 -10000 0 -0.33 165 165
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.09 0.16 -10000 0 -0.3 154 154
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
EPHB2 0.022 0.057 -10000 0 -0.68 3 3
EPHB3 -0.066 0.073 -10000 0 -10000 0 0
EPHB1 -0.25 0.34 -10000 0 -0.68 178 178
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.076 0.14 0.24 1 -0.36 15 16
Ephrin B/EPHB2 0.051 0.059 -10000 0 -0.38 7 7
Ephrin B/EPHB3 0.059 0.058 -10000 0 -0.43 4 4
JNK cascade -0.13 0.2 -10000 0 -0.38 167 167
Ephrin B/EPHB1 -0.11 0.22 -10000 0 -0.38 174 174
RAP1/GDP -0.051 0.14 -10000 0 -0.34 12 12
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EFNB3 0.015 0.071 -10000 0 -0.68 4 4
EFNB1 0.026 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.4 178 178
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.091 0.19 -10000 0 -0.33 166 166
Rap1/GTP -0.11 0.17 -10000 0 -0.33 165 165
axon guidance -0.036 0.17 -10000 0 -0.44 67 67
MAPK3 -0.086 0.14 -10000 0 -0.46 9 9
MAPK1 -0.083 0.14 -10000 0 -0.45 9 9
Rac1/GDP -0.062 0.14 -10000 0 -0.35 11 11
actin cytoskeleton reorganization -0.083 0.13 -10000 0 -0.29 19 19
CDC42/GDP -0.06 0.14 0.31 2 -0.35 12 14
PI3K 0.057 0.041 -10000 0 -0.38 3 3
EFNA5 -0.074 0.25 -10000 0 -0.68 65 65
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.046 -10000 0 -0.32 7 7
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.17 -10000 0 -0.33 162 162
PTK2 0.041 0.089 0.64 8 -10000 0 8
MAP4K4 -0.13 0.2 -10000 0 -0.39 167 167
SRC 0.027 0.009 -10000 0 -10000 0 0
KALRN 0.027 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.081 0.14 0.32 5 -0.33 2 7
MAP2K1 -0.086 0.15 -10000 0 -0.28 152 152
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.23 -10000 0 -0.41 167 167
cell migration -0.088 0.18 0.52 5 -0.36 39 44
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.076 0.46 5 -0.36 7 12
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.026 0.14 0.47 3 -0.38 49 52
HRAS/GTP -0.098 0.19 -10000 0 -0.35 166 166
Ephrin B1/EPHB1-2 -0.13 0.22 -10000 0 -0.4 178 178
cell adhesion mediated by integrin -0.007 0.075 0.4 4 -0.35 9 13
RAC1 0.027 0.006 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.36 168 168
RAC1-CDC42/GTP -0.14 0.17 -10000 0 -0.36 164 164
RASA1 0.027 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.053 0.14 -10000 0 -0.34 11 11
ruffle organization -0.11 0.18 0.58 4 -0.39 6 10
NCK1 0.027 0.004 -10000 0 -10000 0 0
receptor internalization 0.001 0.089 0.41 3 -0.37 17 20
Ephrin B/EPHB2/KALRN 0.065 0.063 -10000 0 -0.38 7 7
ROCK1 -0.024 0.044 -10000 0 -10000 0 0
RAS family/GDP -0.077 0.1 -10000 0 -0.3 10 10
Rac1/GTP -0.12 0.17 -10000 0 -0.34 165 165
Ephrin B/EPHB1/Src/Paxillin -0.095 0.16 -10000 0 -0.3 171 171
IGF1 pathway

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
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.099 0.18 -10000 0 -0.36 138 138
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.09 0.19 -10000 0 -0.37 134 134
IGF-1R heterotetramer/IGF1/PTP1B -0.061 0.2 -10000 0 -0.43 95 95
AKT1 -0.089 0.17 -10000 0 -0.37 91 91
BAD -0.087 0.16 -10000 0 -0.6 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.096 0.18 -10000 0 -0.37 134 134
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.087 0.2 -10000 0 -0.37 138 138
RAF1 -0.068 0.15 0.39 1 -0.55 16 17
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.061 0.2 -10000 0 -0.35 133 133
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.095 0.21 -10000 0 -0.39 139 139
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
RPS6KB1 -0.088 0.17 -10000 0 -0.37 90 90
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.057 0.14 0.32 6 -0.45 15 21
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.07 0.16 -10000 0 -0.35 90 90
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.026 0.17 -10000 0 -0.35 87 87
IGF-1R heterotetramer -0.008 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.076 0.2 -10000 0 -0.37 138 138
Crk/p130 Cas/Paxillin -0.055 0.19 -10000 0 -0.37 92 92
IGF1R -0.008 0.058 -10000 0 -10000 0 0
IGF1 -0.14 0.29 -10000 0 -0.7 96 96
IRS2/Crk -0.084 0.18 -10000 0 -0.35 132 132
PI3K -0.064 0.2 -10000 0 -0.36 138 138
apoptosis 0.063 0.15 0.5 14 -0.32 2 16
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.088 0.19 -10000 0 -0.46 94 94
RAF1/14-3-3 E -0.044 0.14 0.33 3 -0.46 16 19
BAD/14-3-3 -0.067 0.16 0.4 2 -0.55 14 16
PRKCZ -0.087 0.17 0.25 1 -0.63 14 15
Crk/p130 Cas/Paxillin/FAK1 -0.058 0.16 -10000 0 -0.55 14 14
PTPN1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.092 0.2 -10000 0 -0.48 96 96
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.04 0.18 -10000 0 -0.38 92 92
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.086 0.19 -10000 0 -0.36 138 138
GRB10 0.027 0.006 -10000 0 -10000 0 0
PTPN11 -0.098 0.19 -10000 0 -0.37 138 138
IRS1 -0.11 0.2 -10000 0 -0.39 139 139
IRS2 -0.098 0.18 -10000 0 -0.36 138 138
IGF-1R heterotetramer/IGF1 -0.098 0.23 -10000 0 -0.54 96 96
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.089 0.18 -10000 0 -0.38 95 95
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKD1 -0.088 0.19 -10000 0 -0.46 94 94
SHC1 0.026 0.008 -10000 0 -10000 0 0
IL4-mediated signaling events

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.5 0.4 -10000 0 -1.2 64 64
STAT6 (cleaved dimer) -0.51 0.41 -10000 0 -1 130 130
IGHG1 -0.18 0.13 -10000 0 -0.37 36 36
IGHG3 -0.49 0.38 -10000 0 -0.92 137 137
AKT1 -0.27 0.27 0.62 2 -0.81 56 58
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.29 -10000 0 -0.96 47 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.29 -10000 0 -0.73 96 96
THY1 -0.51 0.4 -10000 0 -1.2 71 71
MYB 0.012 0.096 -10000 0 -0.64 9 9
HMGA1 0.028 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.31 -10000 0 -0.84 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.28 -10000 0 -0.82 54 54
SP1 0.031 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.41 -10000 0 -1 107 107
SOCS1 -0.35 0.26 -10000 0 -0.72 69 69
SOCS3 -0.32 0.35 0.6 2 -1.1 55 57
FCER2 -0.51 0.42 -10000 0 -1 110 110
PARP14 0.027 0.006 -10000 0 -10000 0 0
CCL17 -0.54 0.42 -10000 0 -1.2 85 85
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.2 -10000 0 -0.67 39 39
T cell proliferation -0.5 0.41 -10000 0 -1.1 83 83
IL4R/JAK1 -0.5 0.4 -10000 0 -1.1 79 79
EGR2 -0.84 0.69 -10000 0 -1.6 209 209
JAK2 -0.031 0.039 -10000 0 -0.4 1 1
JAK3 -0.01 0.065 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.004 0.022 -10000 0 -10000 0 0
COL1A2 -0.15 0.13 -10000 0 -0.97 2 2
CCL26 -0.5 0.4 -10000 0 -1.1 83 83
IL4R -0.53 0.42 -10000 0 -1.2 77 77
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.6 0.53 -10000 0 -1.4 111 111
IL13RA1 -0.031 0.034 -10000 0 -10000 0 0
IRF4 -0.28 0.47 -10000 0 -1.1 91 91
ARG1 -0.13 0.14 -10000 0 -0.78 6 6
CBL -0.32 0.29 -10000 0 -0.81 71 71
GTF3A 0.026 0.016 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
IL13RA1/JAK2 -0.037 0.047 -10000 0 -10000 0 0
IRF4/BCL6 -0.26 0.44 -10000 0 -1 90 90
CD40LG -0.07 0.24 -10000 0 -0.64 64 64
MAPK14 -0.33 0.33 -10000 0 -0.92 70 70
mitosis -0.26 0.26 0.62 2 -0.75 57 59
STAT6 -0.57 0.48 -10000 0 -1.1 126 126
SPI1 0.023 0.032 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 0.78 2 -0.7 55 57
STAT6 (dimer) -0.57 0.48 -10000 0 -1.1 126 126
STAT6 (dimer)/PARP14 -0.53 0.44 -10000 0 -1.1 117 117
mast cell activation 0.014 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.3 -10000 0 -0.9 58 58
FRAP1 -0.27 0.27 0.62 2 -0.81 57 59
LTA -0.51 0.4 -10000 0 -1.1 94 94
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.56 0.46 1.1 128 -10000 0 128
CCL11 -0.49 0.38 -10000 0 -1.1 80 80
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.27 0.3 -10000 0 -0.89 59 59
IL2RG -0.009 0.14 -10000 0 -0.62 19 19
IL10 -0.51 0.42 -10000 0 -1.2 82 82
IRS1 -0.058 0.23 -10000 0 -0.68 55 55
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.09 -10000 0 -10000 0 0
IL5 -0.51 0.4 -10000 0 -1.1 72 72
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.44 0.36 -10000 0 -0.95 88 88
COL1A1 -0.21 0.23 -10000 0 -1 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.41 -10000 0 -1.2 59 59
IL2R gamma/JAK3 -0.018 0.12 -10000 0 -0.48 18 18
TFF3 -1.2 0.58 -10000 0 -1.4 370 370
ALOX15 -0.5 0.4 -10000 0 -1.2 67 67
MYBL1 0.027 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.43 0.35 -10000 0 -0.93 86 86
SHC1 0.026 0.008 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.27 -10000 0 -0.81 54 54
mol:PI-3-4-5-P3 -0.27 0.27 0.62 2 -0.81 56 58
PI3K -0.28 0.3 0.67 1 -0.88 56 57
DOK2 0.02 0.053 -10000 0 -0.68 2 2
ETS1 0.039 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.66 33 33
ITGB3 -0.52 0.43 -10000 0 -1.2 81 81
PIGR -0.53 0.44 -10000 0 -1.3 79 79
IGHE 0.046 0.045 0.25 8 -10000 0 8
MAPKKK cascade -0.19 0.19 0.58 1 -0.64 33 34
BCL6 0.026 0.033 -10000 0 -0.68 1 1
OPRM1 -0.51 0.4 -10000 0 -1.2 73 73
RETNLB -0.51 0.4 -10000 0 -1.1 84 84
SELP -0.5 0.41 -10000 0 -1.2 72 72
AICDA -0.49 0.38 -10000 0 -1.1 67 67
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.18 0.35 0.61 4 -0.84 44 48
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.4 -10000 0 -0.81 104 104
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.19 0.35 0.62 3 -0.84 45 48
AP1 -0.2 0.37 -10000 0 -0.72 144 144
ABCG2 -0.19 0.35 0.61 1 -0.84 47 48
HIF1A -0.018 0.072 -10000 0 -10000 0 0
TFF3 -0.48 0.43 0.62 3 -0.89 170 173
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.053 0.11 -10000 0 -0.25 24 24
response to hypoxia -0.069 0.11 -10000 0 -0.24 77 77
MCL1 -0.18 0.34 0.61 3 -0.86 40 43
NDRG1 -0.19 0.34 0.6 2 -0.85 42 44
SERPINE1 -0.19 0.35 0.61 1 -0.86 42 43
FECH -0.18 0.35 0.61 4 -0.85 43 47
FURIN -0.18 0.35 0.61 4 -0.84 44 48
NCOA2 -0.034 0.2 -10000 0 -0.68 40 40
EP300 -0.1 0.18 -10000 0 -0.34 150 150
HMOX1 -0.2 0.33 0.62 2 -0.84 45 47
BHLHE40 -0.19 0.35 0.62 2 -0.85 44 46
BHLHE41 -0.19 0.35 0.61 1 -0.84 45 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.031 0.1 -10000 0 -10000 0 0
ENG 0.014 0.095 0.47 4 -10000 0 4
JUN -0.12 0.29 -10000 0 -0.68 99 99
RORA -0.19 0.36 0.61 4 -0.85 45 49
ABCB1 -0.047 0.15 -10000 0 -1.2 6 6
TFRC -0.19 0.35 0.62 2 -0.84 46 48
CXCR4 -0.19 0.35 0.62 3 -0.84 44 47
TF -0.23 0.4 0.62 2 -0.94 70 72
CITED2 -0.21 0.39 0.61 3 -0.92 60 63
HIF1A/ARNT -0.21 0.38 -10000 0 -0.93 44 44
LDHA -0.031 0.11 -10000 0 -0.67 8 8
ETS1 -0.19 0.35 0.62 3 -0.84 45 48
PGK1 -0.19 0.34 0.61 1 -0.85 42 43
NOS2 -0.19 0.35 0.62 2 -0.84 44 46
ITGB2 -0.19 0.35 0.62 3 -0.86 43 46
ALDOA -0.19 0.34 0.61 1 -0.85 42 43
Cbp/p300/CITED2 -0.3 0.46 -10000 0 -0.96 109 109
FOS -0.16 0.31 -10000 0 -0.68 122 122
HK2 -0.19 0.35 0.62 3 -0.84 46 49
SP1 0.032 0.016 -10000 0 -10000 0 0
GCK -0.4 0.64 -10000 0 -1.4 128 128
HK1 -0.19 0.35 0.62 3 -0.84 44 47
NPM1 -0.19 0.34 0.61 1 -0.85 42 43
EGLN1 -0.18 0.34 0.61 3 -0.86 40 43
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.18 0.35 0.61 3 -0.85 43 46
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.2 0.29 0.5 1 -0.68 79 80
IGFBP1 -0.19 0.34 0.61 1 -0.85 43 44
VEGFA -0.2 0.35 -10000 0 -0.72 93 93
HIF1A/JAB1 0.005 0.059 -10000 0 -10000 0 0
CP -0.31 0.46 0.62 2 -0.92 126 128
CXCL12 -0.22 0.4 0.62 3 -0.93 67 70
COPS5 0.028 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.042 0.009 -10000 0 -10000 0 0
BNIP3 -0.19 0.35 0.62 3 -0.84 45 48
EGLN3 -0.2 0.35 -10000 0 -0.86 49 49
CA9 -0.19 0.35 0.6 2 -0.84 48 50
TERT -0.19 0.34 0.6 1 -0.85 43 44
ENO1 -0.18 0.35 0.61 3 -0.84 45 48
PFKL -0.18 0.35 0.62 3 -0.84 45 48
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.2 0.36 0.62 3 -0.8 59 62
ARNT -0.013 0.072 -10000 0 -0.31 2 2
HNF4A -0.016 0.058 -10000 0 -0.22 3 3
ADFP -0.2 0.34 -10000 0 -0.8 54 54
SLC2A1 -0.2 0.35 -10000 0 -0.71 89 89
LEP -0.19 0.34 0.61 1 -0.84 44 45
HIF1A/ARNT/Cbp/p300 -0.25 0.41 -10000 0 -0.8 120 120
EPO -0.13 0.28 -10000 0 -0.82 23 23
CREBBP -0.081 0.17 -10000 0 -0.33 128 128
HIF1A/ARNT/Cbp/p300/HDAC7 -0.23 0.4 -10000 0 -0.81 100 100
PFKFB3 -0.19 0.35 0.62 3 -0.84 46 49
NT5E -0.19 0.35 0.61 3 -0.86 43 46
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.021 0.057 -10000 0 -0.68 3 3
EFNB1 -0.004 0.09 -10000 0 -0.48 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.23 -10000 0 -0.4 176 176
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.4 178 178
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.38 176 176
Ephrin B1/EPHB1-2/Tiam1 -0.14 0.24 -10000 0 -0.42 178 178
DNM1 0.002 0.12 -10000 0 -0.62 16 16
cell-cell signaling -0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.002 0.093 0.41 1 -0.65 7 8
YES1 0.005 0.1 -10000 0 -0.9 6 6
Ephrin B1/EPHB1-2/NCK2 -0.13 0.22 -10000 0 -0.39 177 177
PI3K 0.024 0.11 -10000 0 -0.87 6 6
mol:GDP -0.14 0.24 -10000 0 -0.42 180 180
ITGA2B -0.046 0.21 -10000 0 -0.67 47 47
endothelial cell proliferation 0.033 0.011 -10000 0 -10000 0 0
FYN 0.004 0.11 -10000 0 -0.86 7 7
MAP3K7 -0.011 0.087 -10000 0 -0.69 7 7
FGR 0.002 0.11 -10000 0 -0.85 7 7
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.031 0.17 -10000 0 -0.44 56 56
LYN 0.004 0.11 -10000 0 -0.87 7 7
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.1 -10000 0 -0.82 7 7
Ephrin B1/EPHB1-2 -0.01 0.09 -10000 0 -0.78 6 6
SRC 0.002 0.11 -10000 0 -0.85 7 7
ITGB3 0.008 0.11 -10000 0 -0.65 12 12
EPHB1 -0.25 0.34 -10000 0 -0.68 178 178
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.03 0.19 -10000 0 -0.54 55 55
BLK -0.048 0.14 -10000 0 -0.93 7 7
HCK 0.003 0.11 -10000 0 -0.85 7 7
regulation of stress fiber formation 0.12 0.22 0.39 177 -10000 0 177
MAPK8 -0.004 0.12 0.34 6 -0.71 9 15
Ephrin B1/EPHB1-2/RGS3 -0.12 0.22 -10000 0 -0.39 176 176
endothelial cell migration -0.006 0.081 0.41 1 -0.63 6 7
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.025 0.087 -10000 0 -0.8 5 5
regulation of focal adhesion formation 0.12 0.22 0.39 177 -10000 0 177
chemotaxis 0.12 0.22 0.39 176 -10000 0 176
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
Rac1/GTP -0.12 0.22 -10000 0 -0.39 176 176
angiogenesis -0.011 0.092 -10000 0 -0.73 7 7
LCK 0 0.12 -10000 0 -0.9 7 7
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.17 0.3 -10000 0 -0.49 193 193
SMAD6-7/SMURF1 0.053 0.015 -10000 0 -10000 0 0
NOG -0.024 0.18 -10000 0 -0.68 30 30
SMAD9 -0.19 0.27 -10000 0 -0.53 164 164
SMAD4 0.027 0.005 -10000 0 -10000 0 0
SMAD5 -0.083 0.17 -10000 0 -0.33 103 103
BMP7/USAG1 -0.24 0.27 -10000 0 -0.51 233 233
SMAD5/SKI -0.068 0.17 0.3 4 -0.44 29 33
SMAD1 -0.037 0.096 -10000 0 -0.53 2 2
BMP2 -0.001 0.14 -10000 0 -0.68 18 18
SMAD1/SMAD1/SMAD4 -0.022 0.086 -10000 0 -0.53 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.2 0.33 -10000 0 -0.68 147 147
BMPR1A-1B/BAMBI -0.11 0.24 -10000 0 -0.45 147 147
AHSG -0.003 0.039 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.012 0.12 -10000 0 -0.44 29 29
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.067 0.17 -10000 0 -0.55 27 27
BMP2-4 (homodimer) 0.003 0.14 -10000 0 -0.51 29 29
RGMB 0.027 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.086 0.22 -10000 0 -0.41 147 147
RGMA 0.002 0.13 -10000 0 -0.66 17 17
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.079 0.16 -10000 0 -0.47 32 32
BMP2-4/USAG1 -0.23 0.27 -10000 0 -0.47 245 245
SMAD6/SMURF1/SMAD5 -0.066 0.17 0.32 1 -0.44 27 28
SOSTDC1 -0.34 0.35 -10000 0 -0.68 233 233
BMP7/BMPR2/BMPR1A-1B -0.085 0.22 -10000 0 -0.41 144 144
SKI 0.027 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.007 -10000 0 -10000 0 0
HFE2 -0.004 0.022 -10000 0 -10000 0 0
ZFYVE16 0.027 0.006 -10000 0 -10000 0 0
MAP3K7 0.028 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.014 0.14 -10000 0 -0.46 36 36
SMAD5/SMAD5/SMAD4 -0.066 0.17 0.3 4 -0.44 29 33
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.053 0.15 -10000 0 -0.43 27 27
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.029 0.03 -10000 0 -10000 0 0
SMAD1/SKI -0.027 0.1 0.34 1 -0.63 1 2
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.019 0.12 -10000 0 -0.45 29 29
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.66 105 105
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.045 0.054 -10000 0 -0.44 5 5
BMPR1A-1B (homodimer) -0.14 0.26 -10000 0 -0.51 147 147
CHRDL1 -0.44 0.33 -10000 0 -0.66 310 310
ENDOFIN/SMAD1 -0.029 0.1 -10000 0 -0.5 2 2
SMAD6-7/SMURF1/SMAD1 -0.013 0.1 -10000 0 -0.59 1 1
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.054 -10000 0 -0.68 2 2
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.25 -10000 0 -0.47 302 302
BMP2-4/GREM1 -0.081 0.24 -10000 0 -0.49 114 114
SMAD7 0.027 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.17 0.26 -10000 0 -0.51 156 156
SMAD1/SMAD6 -0.027 0.098 -10000 0 -0.5 2 2
TAK1/SMAD6 0.039 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.027 0.008 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.057 0.14 -10000 0 -0.42 28 28
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.027 0.1 0.31 1 -0.44 3 4
SMAD7/SMURF1 0.039 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.004 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.008 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.018 0.074 -10000 0 -0.68 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -10000 0 -0.64 82 82
CHRD 0.015 0.093 -10000 0 -0.68 8 8
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.08 0.16 -10000 0 -0.51 29 29
BMP4 0.007 0.11 -10000 0 -0.65 12 12
FST -0.14 0.3 -10000 0 -0.68 107 107
BMP2-4/NOG -0.011 0.17 -10000 0 -0.45 58 58
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.07 0.21 -10000 0 -0.39 141 141
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 -0.19 0.53 -10000 0 -1.3 73 73
IL23A -0.21 0.55 -10000 0 -1.3 75 75
NF kappa B1 p50/RelA/I kappa B alpha -0.17 0.54 -10000 0 -1.3 73 73
positive regulation of T cell mediated cytotoxicity -0.22 0.61 -10000 0 -1.4 74 74
ITGA3 -0.18 0.5 -10000 0 -1.2 73 73
IL17F -0.099 0.33 0.64 3 -0.74 71 74
IL12B 0.003 0.096 -10000 0 -0.7 6 6
STAT1 (dimer) -0.21 0.58 -10000 0 -1.4 74 74
CD4 -0.17 0.49 -10000 0 -1.2 70 70
IL23 -0.2 0.53 -10000 0 -1.2 75 75
IL23R 0.004 0.11 -10000 0 -0.96 2 2
IL1B -0.22 0.57 -10000 0 -1.4 75 75
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.5 -10000 0 -1.2 70 70
TYK2 0.016 0.036 -10000 0 -10000 0 0
STAT4 0.003 0.1 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.009 0.14 -10000 0 -0.68 19 19
IL12RB1 0 0.072 -10000 0 -0.61 3 3
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
IL12Rbeta1/TYK2 0.016 0.065 -10000 0 -0.47 3 3
IL23R/JAK2 0.01 0.13 -10000 0 -0.87 2 2
positive regulation of chronic inflammatory response -0.22 0.61 -10000 0 -1.4 74 74
natural killer cell activation 0.001 0.008 -10000 0 -0.055 1 1
JAK2 0.016 0.049 -10000 0 -0.4 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.18 0.5 -10000 0 -1.2 75 75
ALOX12B -0.18 0.5 -10000 0 -1.2 71 71
CXCL1 -0.19 0.52 -10000 0 -1.2 75 75
T cell proliferation -0.22 0.61 -10000 0 -1.4 74 74
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.056 0.27 -10000 0 -0.58 59 59
PI3K -0.19 0.54 -10000 0 -1.3 72 72
IFNG -0.015 0.054 0.16 2 -0.13 62 64
STAT3 (dimer) -0.17 0.51 -10000 0 -1.2 72 72
IL18R1 -0.001 0.09 -10000 0 -0.57 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.096 0.34 -10000 0 -0.83 53 53
IL18/IL18R 0.001 0.14 -10000 0 -0.47 32 32
macrophage activation -0.008 0.021 -10000 0 -0.045 67 67
TNF -0.24 0.6 -10000 0 -1.4 87 87
STAT3/STAT4 -0.19 0.55 -10000 0 -1.3 74 74
STAT4 (dimer) -0.21 0.58 -10000 0 -1.4 75 75
IL18 -0.008 0.11 -10000 0 -0.65 10 10
IL19 -0.17 0.5 -10000 0 -1.2 69 69
STAT5A (dimer) -0.21 0.57 -10000 0 -1.4 74 74
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.008 0.15 -10000 0 -0.68 22 22
CXCL9 -0.26 0.61 -10000 0 -1.4 96 96
MPO -0.18 0.5 -10000 0 -1.2 74 74
positive regulation of humoral immune response -0.22 0.61 -10000 0 -1.4 74 74
IL23/IL23R/JAK2/TYK2 -0.27 0.73 -10000 0 -1.7 74 74
IL6 -0.29 0.63 -10000 0 -1.3 112 112
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.003 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.008 -10000 0 -0.055 1 1
CD3E -0.21 0.55 -10000 0 -1.3 79 79
keratinocyte proliferation -0.22 0.61 -10000 0 -1.4 74 74
NOS2 -0.17 0.49 -10000 0 -1.2 69 69
Coregulation of Androgen receptor activity

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
NRIP1 -0.005 0.052 -10000 0 -10000 0 0
SVIL -0.002 0.048 -10000 0 -10000 0 0
ZNF318 0.075 0.088 0.22 58 -0.68 1 59
JMJD2C -0.065 0.067 -10000 0 -0.12 258 258
T-DHT/AR/Ubc9 -0.22 0.24 -10000 0 -0.5 188 188
CARM1 0.023 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.007 -10000 0 -10000 0 0
PELP1 0.032 0.014 -10000 0 -10000 0 0
CTNNB1 0.003 0.04 -10000 0 -10000 0 0
AKT1 0.038 0.021 -10000 0 -10000 0 0
PTK2B 0.008 0.032 -10000 0 -10000 0 0
MED1 0.037 0.021 -10000 0 -10000 0 0
MAK 0.067 0.12 0.22 57 -0.66 6 63
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.065 -10000 0 -0.68 2 2
GSN 0 0.045 -10000 0 -10000 0 0
NCOA2 -0.037 0.2 -10000 0 -0.68 40 40
NCOA6 -0.003 0.055 -10000 0 -0.68 1 1
DNA-PK 0.074 0.077 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.038 -10000 0 -10000 0 0
cell proliferation 0.001 0.14 -10000 0 -0.89 7 7
XRCC5 0.037 0.018 -10000 0 -10000 0 0
UBE3A -0.012 0.064 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.24 0.26 -10000 0 -0.53 194 194
FHL2 -0.13 0.33 -10000 0 -1.2 38 38
RANBP9 -0.001 0.046 -10000 0 -10000 0 0
JMJD1A -0.001 0.035 -10000 0 -0.12 31 31
CDK6 0.025 0.047 -10000 0 -0.68 2 2
TGFB1I1 -0.003 0.048 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.5 194 194
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.53 211 211
CTDSP1 0.012 0.024 -10000 0 -10000 0 0
CTDSP2 0.058 0.052 -10000 0 -10000 0 0
BRCA1 -0.003 0.047 -10000 0 -10000 0 0
TCF4 0.048 0.035 -10000 0 -10000 0 0
CDKN2A 0.003 0.083 -10000 0 -10000 0 0
SRF 0.035 0.051 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.64 13 13
KLK3 -0.39 0.65 -10000 0 -1.4 129 129
TMF1 0.017 0.048 -10000 0 -0.68 2 2
HNRNPA1 0.044 0.029 -10000 0 -10000 0 0
AOF2 -0.02 0.033 -10000 0 -0.072 129 129
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.5 184 184
AR -0.31 0.34 -10000 0 -0.71 188 188
UBA3 0.013 0.024 -10000 0 -10000 0 0
PATZ1 0.033 0.03 -10000 0 -10000 0 0
PAWR 0.02 0.015 -10000 0 -10000 0 0
PRKDC 0.037 0.017 -10000 0 -10000 0 0
PA2G4 0.049 0.037 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.22 -10000 0 -0.45 190 190
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.5 191 191
LATS2 0.041 0.044 -10000 0 -0.68 1 1
T-DHT/AR/PRX1 -0.19 0.22 -10000 0 -0.45 184 184
Cyclin D3/CDK11 p58 0.023 0.005 -10000 0 -10000 0 0
VAV3 -0.004 0.081 -10000 0 -0.68 5 5
KLK2 -0.67 0.56 -10000 0 -1.1 260 260
CASP8 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.53 192 192
TMPRSS2 -0.16 0.27 -10000 0 -1.1 31 31
CCND1 0.014 0.03 -10000 0 -10000 0 0
PIAS1 -0.012 0.064 -10000 0 -10000 0 0
mol:T-DHT -0.032 0.039 -10000 0 -0.077 158 158
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.03 0.09 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.22 0.24 -10000 0 -0.5 185 185
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF -0.008 0.15 -10000 0 -0.64 23 23
ZMIZ1 -0.023 0.057 -10000 0 -0.67 1 1
CCND3 0.029 0.004 -10000 0 -10000 0 0
TGIF1 0.044 0.029 -10000 0 -10000 0 0
FKBP4 -0.002 0.046 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.084 0.086 0.36 1 -10000 0 1
SMARCC2 0.026 0.019 -10000 0 -10000 0 0
SMARCC1 0.026 0.018 -10000 0 -10000 0 0
TBX21 -0.12 0.24 0.32 1 -0.69 49 50
SUMO2 0.024 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.024 -10000 0 -10000 0 0
FKBP4 0.027 0.005 -10000 0 -10000 0 0
FKBP5 0.021 0.066 -10000 0 -0.68 4 4
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.33 51 -0.43 3 54
PRL -0.062 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.29 0.55 127 -0.47 18 145
RELA -0.029 0.1 -10000 0 -0.28 25 25
FGG 0.17 0.2 0.47 99 -10000 0 99
GR beta/TIF2 0.075 0.2 0.33 63 -0.46 40 103
IFNG -0.37 0.48 -10000 0 -1.1 116 116
apoptosis -0.016 0.23 0.5 31 -0.54 19 50
CREB1 0.027 0.014 -10000 0 -10000 0 0
histone acetylation -0.075 0.16 -10000 0 -0.4 62 62
BGLAP -0.077 0.13 -10000 0 -0.47 14 14
GR/PKAc 0.11 0.1 0.35 27 -0.34 1 28
NF kappa B1 p50/RelA -0.05 0.17 -10000 0 -0.46 36 36
SMARCD1 0.026 0.019 -10000 0 -10000 0 0
MDM2 0.085 0.096 0.26 76 -10000 0 76
GATA3 -0.004 0.15 -10000 0 -0.64 23 23
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.11 0.14 -10000 0 -0.51 23 23
GSK3B 0.025 0.019 -10000 0 -10000 0 0
NR1I3 0.003 0.23 0.51 26 -0.56 12 38
CSN2 0.13 0.16 0.39 87 -10000 0 87
BRG1/BAF155/BAF170/BAF60A 0.063 0.055 -10000 0 -0.3 7 7
NFATC1 0.016 0.093 -10000 0 -0.68 8 8
POU2F1 0.026 0.011 -10000 0 -10000 0 0
CDKN1A 0.026 0.036 -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 -0.084 0.12 -10000 0 -0.68 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.13 0.13 0.34 45 -0.37 10 55
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.47 27 -0.83 97 124
JUN -0.24 0.27 -10000 0 -0.57 154 154
IL4 -0.099 0.16 -10000 0 -0.65 18 18
CDK5R1 0.026 0.014 -10000 0 -10000 0 0
PRKACA 0.026 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.31 -10000 0 -0.65 150 150
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.11 0.35 34 -0.4 3 37
cortisol/GR alpha (monomer) 0.26 0.3 0.64 135 -10000 0 135
NCOA2 -0.035 0.2 -10000 0 -0.68 40 40
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.19 0.31 -10000 0 -0.69 123 123
AP-1/NFAT1-c-4 -0.39 0.41 -10000 0 -0.77 209 209
AFP -0.17 0.21 0.47 1 -0.6 41 42
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.46 38 -10000 0 38
TP53 0.041 0.013 -10000 0 -10000 0 0
PPP5C 0.026 0.008 -10000 0 -10000 0 0
KRT17 -0.3 0.34 -10000 0 -0.82 91 91
KRT14 -0.083 0.12 -10000 0 -0.49 6 6
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.034 0.047 -10000 0 -0.26 10 10
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.005 -10000 0 -10000 0 0
AP-1 -0.39 0.41 -10000 0 -0.77 209 209
MAPK14 0.027 0.016 -10000 0 -10000 0 0
MAPK10 0.025 0.037 -10000 0 -0.68 1 1
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.39 0.5 -10000 0 -1 141 141
interleukin-1 receptor activity 0.003 0.003 -10000 0 -10000 0 0
NCOA1 0.03 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.024 -10000 0 -10000 0 0
CGA -0.094 0.14 -10000 0 -0.46 24 24
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.087 0.12 0.34 34 -10000 0 34
MAPK3 0.025 0.016 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.17 0.24 -10000 0 -0.64 68 68
NFKB1 -0.028 0.099 -10000 0 -0.27 21 21
MAPK8 -0.14 0.17 -10000 0 -0.43 84 84
MAPK9 0.027 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.021 0.23 0.5 30 -0.57 19 49
BAX 0.037 0.088 0.84 4 -10000 0 4
POMC -0.46 0.64 -10000 0 -1.4 128 128
EP300 0.026 0.044 -10000 0 -0.26 8 8
cortisol/GR alpha (dimer)/p53 0.23 0.25 0.56 132 -10000 0 132
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.13 0.34 76 -10000 0 76
SGK1 0.009 0.22 0.45 3 -1.3 11 14
IL13 -0.21 0.25 -10000 0 -0.75 47 47
IL6 -0.3 0.49 -10000 0 -1.1 104 104
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.21 -10000 0 -0.71 30 30
IL2 -0.26 0.28 -10000 0 -0.68 93 93
CDK5 0.027 0.009 -10000 0 -10000 0 0
PRKACB 0.025 0.033 -10000 0 -0.68 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.28 -10000 0 -0.76 59 59
CDK5R1/CDK5 0.039 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.003 0.14 -10000 0 -0.4 18 18
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.52 132 -10000 0 132
SMARCA4 0.025 0.019 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.37 90 -0.44 2 92
NF kappa B1 p50/RelA/Cbp -0.012 0.16 -10000 0 -0.42 24 24
JUN (dimer) -0.24 0.27 -10000 0 -0.57 154 154
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.21 0.36 -10000 0 -0.93 82 82
NR3C1 0.16 0.19 0.44 101 -10000 0 101
NR4A1 -0.27 0.37 -10000 0 -0.67 193 193
TIF2/SUV420H1 -0.009 0.16 -10000 0 -0.51 40 40
MAPKKK cascade -0.016 0.23 0.5 31 -0.54 19 50
cortisol/GR alpha (dimer)/Src-1 0.23 0.24 0.56 130 -10000 0 130
PBX1 0.025 0.034 -10000 0 -0.68 1 1
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.25 0.45 -10000 0 -1.1 85 85
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.37 89 -0.44 2 91
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.52 132 -10000 0 132
mol:cortisol 0.14 0.18 0.38 135 -10000 0 135
MMP1 -0.1 0.14 -10000 0 -0.88 9 9
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.053 0.25 0.29 19 -0.59 66 85
FYN -0.099 0.32 0.9 1 -0.78 68 69
LAT/GRAP2/SLP76 -0.08 0.25 -10000 0 -0.61 73 73
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.059 0.21 0.58 7 -0.46 72 79
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.015 0.056 0.11 2 -0.16 27 29
MAP3K8 0.016 0.089 -10000 0 -0.64 8 8
mol:Ca2+ -0.031 0.043 0.092 5 -0.11 95 100
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.3 0.72 4 -0.71 76 80
TRPV6 -0.1 0.36 1 19 -0.68 97 116
CD28 -0.012 0.15 -10000 0 -0.66 21 21
SHC1 -0.096 0.32 0.31 20 -0.78 68 88
receptor internalization -0.12 0.35 -10000 0 -0.78 82 82
PRF1 -0.1 0.33 -10000 0 -0.88 56 56
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.042 0.18 0.58 5 -0.37 74 79
LAT -0.1 0.31 0.3 3 -0.77 71 74
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.049 0.21 -10000 0 -0.64 49 49
CD3E -0.029 0.19 -10000 0 -0.63 38 38
CD3G -0.1 0.27 -10000 0 -0.66 84 84
RASGRP2 -0.003 0.032 0.095 3 -0.18 10 13
RASGRP1 -0.047 0.22 0.6 10 -0.46 71 81
HLA-A 0.027 0.013 -10000 0 -10000 0 0
RASSF5 0.026 0.008 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.035 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.15 0.35 28 -0.13 33 61
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.047 0.084 -10000 0 -0.24 56 56
PRKCA -0.035 0.12 -10000 0 -0.29 72 72
GRAP2 -0.016 0.14 -10000 0 -0.55 29 29
mol:IP3 -0.029 0.21 0.26 67 -0.44 67 134
EntrezGene:6957 0 0.005 0.059 1 -10000 0 1
TCR/CD3/MHC I/CD8 -0.12 0.35 -10000 0 -0.86 70 70
ORAI1 0.047 0.21 0.7 2 -0.8 15 17
CSK -0.11 0.32 -10000 0 -0.79 72 72
B7 family/CD28 -0.1 0.35 -10000 0 -0.79 75 75
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.13 0.38 -10000 0 -0.92 74 74
PTPN6 -0.11 0.32 -10000 0 -0.79 71 71
VAV1 -0.11 0.31 -10000 0 -0.76 71 71
Monovalent TCR/CD3 -0.12 0.32 -10000 0 -0.62 100 100
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.1 0.33 0.88 1 -0.82 68 69
PAG1 -0.11 0.32 -10000 0 -0.79 72 72
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.13 0.38 -10000 0 -0.93 72 72
CD80 -0.043 0.21 -10000 0 -0.68 45 45
CD86 0.015 0.072 -10000 0 -0.69 4 4
PDK1/CARD11/BCL10/MALT1 -0.039 0.11 -10000 0 -0.29 57 57
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.62 75 75
CD8A -0.02 0.18 -10000 0 -0.66 32 32
CD8B -0.052 0.22 -10000 0 -0.66 51 51
PTPRC -0.008 0.14 -10000 0 -0.69 18 18
PDK1/PKC theta -0.072 0.26 0.64 11 -0.59 69 80
CSK/PAG1 -0.1 0.31 -10000 0 -0.76 71 71
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.039 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.099 0.3 -10000 0 -0.73 74 74
STIM1 0.018 0.17 1.2 2 -0.9 9 11
RAS family/GTP 0.013 0.11 0.27 25 -0.18 42 67
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.39 -10000 0 -0.87 82 82
mol:DAG -0.058 0.16 0.15 5 -0.39 70 75
RAP1A/GDP 0.012 0.084 0.26 16 -10000 0 16
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.002 0.13 -10000 0 -0.69 16 16
cytotoxic T cell degranulation -0.096 0.31 0.44 1 -0.82 58 59
RAP1A/GTP -0.001 0.012 -10000 0 -0.068 8 8
mol:PI-3-4-5-P3 -0.08 0.25 0.58 6 -0.56 76 82
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.046 0.26 0.29 60 -0.58 69 129
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 -0.001 0.13 -10000 0 -0.66 16 16
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.078 0.24 -10000 0 -0.58 72 72
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.047 -10000 0 -0.68 2 2
CD8 heterodimer -0.054 0.23 -10000 0 -0.59 67 67
CARD11 -0.019 0.11 -10000 0 -0.68 8 8
PRKCB -0.028 0.12 -10000 0 -0.29 61 61
PRKCE -0.028 0.12 -10000 0 -0.28 62 62
PRKCQ -0.09 0.29 0.63 8 -0.67 73 81
LCP2 0.024 0.019 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.045 0.19 0.54 9 -0.39 72 81
IKK complex 0.02 0.14 0.46 20 -0.13 11 31
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.034 0.12 0.26 3 -0.29 62 65
PDPK1 -0.055 0.21 0.56 10 -0.45 69 79
TCR/CD3/MHC I/CD8/Fyn -0.15 0.41 -10000 0 -0.98 78 78
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.34 -10000 0 -1.1 43 43
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.021 0.11 -10000 0 -0.33 41 41
ATF2/c-Jun -0.21 0.35 -10000 0 -0.8 112 112
MAPK11 -0.014 0.099 -10000 0 -0.35 29 29
MITF -0.027 0.13 -10000 0 -0.41 39 39
MAPKAPK5 -0.023 0.12 -10000 0 -0.4 35 35
KRT8 -0.023 0.12 -10000 0 -0.4 35 35
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.029 0.16 -10000 0 -0.48 40 40
CEBPB -0.024 0.12 -10000 0 -0.4 37 37
SLC9A1 -0.027 0.13 -10000 0 -0.4 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.076 0.18 -10000 0 -0.42 78 78
p38alpha-beta/MNK1 -0.014 0.13 -10000 0 -0.4 34 34
JUN -0.21 0.35 -10000 0 -0.8 112 112
PPARGC1A -0.23 0.25 -10000 0 -0.45 236 236
USF1 -0.028 0.12 -10000 0 -0.39 42 42
RAB5/GDP/GDI1 -0.039 0.1 -10000 0 -0.36 20 20
NOS2 -0.033 0.12 -10000 0 -0.49 11 11
DDIT3 -0.023 0.12 -10000 0 -0.39 38 38
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.018 0.097 0.38 2 -0.33 33 35
p38alpha-beta/HBP1 -0.01 0.12 -10000 0 -0.41 28 28
CREB1 -0.059 0.16 -10000 0 -0.44 51 51
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.029 0.11 -10000 0 -0.37 30 30
RPS6KA4 -0.025 0.13 -10000 0 -0.41 37 37
PLA2G4A -0.055 0.16 -10000 0 -0.49 48 48
GDI1 -0.023 0.12 -10000 0 -0.42 34 34
TP53 -0.036 0.14 0.25 1 -0.49 34 35
RPS6KA5 -0.065 0.19 -10000 0 -0.44 76 76
ESR1 -0.058 0.2 -10000 0 -0.54 55 55
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.023 0.12 -10000 0 -0.4 36 36
MEF2A -0.029 0.13 -10000 0 -0.42 41 41
EIF4EBP1 -0.059 0.16 -10000 0 -0.37 73 73
KRT19 -0.055 0.17 -10000 0 -0.46 54 54
ELK4 -0.028 0.12 -10000 0 -0.4 40 40
ATF6 -0.028 0.12 -10000 0 -0.4 40 40
ATF1 -0.057 0.16 -10000 0 -0.43 49 49
p38alpha-beta/MAPKAPK2 -0.015 0.13 -10000 0 -0.4 34 34
p38alpha-beta/MAPKAPK3 -0.014 0.13 -10000 0 -0.41 34 34
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 0.036 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.021 0.16 -10000 0 -0.67 15 15
EGFR 0.02 0.066 -10000 0 -0.68 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
USP6 0.025 0.014 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.044 0.2 -10000 0 -0.51 69 69
ARRB2 -0.037 0.13 -10000 0 -0.39 56 56
mol:GTP 0.024 0.038 0.18 17 -0.13 1 18
ARRB1 0.025 0.033 -10000 0 -0.68 1 1
FBXO8 0.027 0.004 -10000 0 -10000 0 0
TSHR 0.024 0.047 -10000 0 -0.68 2 2
EGF -0.076 0.25 -10000 0 -0.68 66 66
somatostatin receptor activity 0 0.001 0.002 15 -0.001 125 140
ARAP2 0.024 0.047 -10000 0 -0.68 2 2
mol:GDP -0.11 0.15 0.27 5 -0.32 96 101
mol:PI-3-4-5-P3 0 0.001 0.002 11 -0.001 71 82
ITGA2B -0.046 0.21 -10000 0 -0.67 47 47
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.025 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.004 -10000 0 -10000 0 0
HGF/MET -0.076 0.19 -10000 0 -0.53 62 62
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.17 0.51 9 -0.3 129 138
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.021 0.18 -10000 0 -0.44 67 67
ADRB2 0.009 0.11 -10000 0 -0.68 11 11
receptor agonist activity 0 0 0.001 17 0 117 134
actin filament binding 0 0 0.002 16 -0.001 122 138
SRC 0.026 0.009 -10000 0 -10000 0 0
ITGB3 0.008 0.11 -10000 0 -0.65 12 12
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.005 16 -0.001 62 78
ARF6/GDP -0.008 0.095 0.23 4 -0.44 10 14
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.42 104 104
alphaIIb/beta3 Integrin/paxillin/GIT1 0.006 0.16 -10000 0 -0.43 55 55
ACAP1 0.019 0.045 -10000 0 -0.52 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.051 0.19 -10000 0 -0.57 56 56
EFNA1 0.026 0.008 -10000 0 -10000 0 0
HGF -0.07 0.24 -10000 0 -0.68 62 62
CYTH3 0.006 0.035 -10000 0 -0.52 2 2
CYTH2 -0.012 0.16 -10000 0 -0.93 14 14
NCK1 0.027 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0.002 19 0 80 99
endosomal lumen acidification 0 0 0.002 7 -0.001 129 136
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 -0.094 0.26 -10000 0 -0.66 81 81
GNAQ/ARNO 0.002 0.15 -10000 0 -0.85 14 14
mol:Phosphatidic acid 0 0 0.001 13 -10000 0 13
PIP3-E 0 0 0.001 11 0 6 17
MET -0.03 0.072 -10000 0 -10000 0 0
GNA14 -0.13 0.29 -10000 0 -0.64 107 107
GNA15 0.013 0.05 -10000 0 -0.68 1 1
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 15 -0.001 74 89
GNA11 0.015 0.082 -10000 0 -0.64 7 7
LHCGR -0.077 0.23 -10000 0 -0.68 56 56
AGTR1 -0.26 0.34 -10000 0 -0.68 184 184
desensitization of G-protein coupled receptor protein signaling pathway -0.051 0.19 -10000 0 -0.57 56 56
IPCEF1/ARNO -0.038 0.19 -10000 0 -0.76 14 14
alphaIIb/beta3 Integrin -0.03 0.19 -10000 0 -0.54 55 55
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.044 -10000 0 -0.83 1 1
forebrain development -0.3 0.28 0.35 1 -0.54 233 234
GNAO1 0.002 0.12 -10000 0 -0.68 14 14
SMO/beta Arrestin2 0.015 0.037 -10000 0 -0.51 1 1
SMO 0.015 0.036 -10000 0 -0.68 1 1
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.037 0.074 -10000 0 -0.39 2 2
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.034 -10000 0 -0.41 1 1
GNAI1 0.023 0.034 -10000 0 -0.69 1 1
XPO1 0.016 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.22 0.22 -10000 0 -0.49 130 130
SAP30 0.026 0.033 -10000 0 -0.68 1 1
mol:GDP 0.015 0.036 -10000 0 -0.68 1 1
MIM/GLI2A -0.031 0.067 -10000 0 -10000 0 0
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.025 0.008 -10000 0 -10000 0 0
GLI2 0 0.08 0.28 2 -0.34 11 13
GLI3 0.027 0.078 0.28 3 -0.37 4 7
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.033 -10000 0 -0.68 1 1
Gi family/GTP -0.017 0.071 -10000 0 -0.3 16 16
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.066 -10000 0 -0.46 2 2
GLI2/Su(fu) 0.008 0.078 -10000 0 -0.44 4 4
FOXA2 -0.59 0.62 -10000 0 -1.2 226 226
neural tube patterning -0.3 0.28 0.35 1 -0.54 233 234
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.034 0.03 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
MTSS1 -0.031 0.067 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.35 1 -0.54 233 234
SUFU 0.018 0.017 -10000 0 -0.24 1 1
LGALS3 -0.027 0.072 -10000 0 -10000 0 0
catabolic process 0.031 0.1 0.29 1 -0.44 8 9
GLI3A/CBP -0.18 0.2 -10000 0 -0.38 229 229
KIF3A 0.027 0.006 -10000 0 -10000 0 0
GLI1 -0.31 0.29 0.35 1 -0.55 233 234
RAB23 0.023 0.057 -10000 0 -0.68 3 3
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.018 0.05 -10000 0 -0.26 1 1
GNAZ 0.019 0.012 -10000 0 -10000 0 0
RBBP4 0.025 0.047 -10000 0 -0.68 2 2
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.008 -10000 0 -10000 0 0
GLI2/SPOP 0.01 0.083 -10000 0 -0.36 8 8
STK36 0.016 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.056 -10000 0 -0.34 4 4
PTCH1 -0.27 0.26 -10000 0 -0.6 129 129
MIM/GLI1 -0.43 0.38 0.34 1 -0.7 262 263
CREBBP -0.18 0.2 -10000 0 -0.38 229 229
Su(fu)/SIN3/HDAC complex 0.036 0.066 -10000 0 -0.54 4 4
Thromboxane A2 receptor 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
TGM2 0.006 0.052 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.065 -10000 0 -0.19 62 62
AKT1 0.011 0.13 0.41 19 -0.23 5 24
EGF -0.076 0.25 -10000 0 -0.68 66 66
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.018 0.093 0.37 13 -0.51 3 16
mol:Ca2+ -0.018 0.15 0.38 14 -0.3 62 76
LYN 0.018 0.092 0.38 12 -0.51 3 15
RhoA/GTP -0.009 0.054 -10000 0 -0.15 3 3
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.018 0.16 0.39 18 -0.34 62 80
GNG2 0.025 0.033 -10000 0 -0.68 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.033 0.13 0.27 1 -0.61 12 13
G beta5/gamma2 -0.043 0.089 -10000 0 -0.26 60 60
PRKCH -0.024 0.16 0.44 12 -0.36 63 75
DNM1 0.003 0.12 -10000 0 -0.62 16 16
TXA2/TP beta/beta Arrestin3 -0.01 0.12 -10000 0 -0.42 31 31
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.004 0.14 -10000 0 -0.68 20 20
G12 family/GTP -0.034 0.12 -10000 0 -0.31 60 60
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP 0.052 0.14 0.39 40 -0.35 6 46
mol:NADP 0.026 0.006 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.67 123 123
mol:IP3 -0.028 0.17 0.43 12 -0.38 62 74
cell morphogenesis 0.036 0.007 -10000 0 -10000 0 0
PLCB2 -0.05 0.21 0.45 8 -0.52 62 70
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.079 0.18 0.36 9 -0.33 129 138
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.011 0.081 0.33 8 -0.51 3 11
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.018 0.074 -10000 0 -0.68 5 5
PRKCB1 -0.028 0.17 0.44 10 -0.38 63 73
GNAQ 0.025 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.045 0.23 0.49 11 -0.53 63 74
LCK 0.013 0.1 0.37 13 -0.54 6 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.024 0.09 -10000 0 -0.34 19 19
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.03 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.029 0.091 -10000 0 -0.33 20 20
MAPK14 -0.005 0.12 0.32 20 -0.23 54 74
TGM2/GTP -0.045 0.17 0.34 3 -0.43 58 61
MAPK11 -0.01 0.12 0.34 19 -0.23 56 75
ARHGEF1 -0.015 0.073 0.17 1 -0.19 29 30
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.025 0.18 0.41 16 -0.39 63 79
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.017 0.14 0.37 15 -0.29 63 78
cAMP biosynthetic process -0.03 0.16 0.43 12 -0.36 58 70
Gq family/GTP/EBP50 -0.044 0.12 0.24 2 -0.36 18 20
actin cytoskeleton reorganization 0.036 0.007 -10000 0 -10000 0 0
SRC 0.013 0.081 0.33 8 -0.51 3 11
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.022 0.13 0.45 14 -0.3 16 30
VCAM1 -0.013 0.14 0.35 17 -0.3 63 80
TP beta/Gq family/GDP/G beta5/gamma2 -0.033 0.13 0.27 1 -0.61 12 13
platelet activation -0.005 0.16 0.44 20 -0.3 60 80
PGI2/IP 0.013 0.056 -10000 0 -0.51 5 5
PRKACA 0.002 0.089 -10000 0 -0.38 21 21
Gq family/GDP/G beta5/gamma2 -0.033 0.12 0.28 1 -0.58 12 13
TXA2/TP beta/beta Arrestin2 0.004 0.11 -10000 0 -0.54 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.09 -10000 0 -0.38 19 19
mol:DAG -0.034 0.19 0.46 10 -0.43 63 73
EGFR 0.02 0.066 -10000 0 -0.68 4 4
TXA2/TP alpha -0.046 0.21 0.51 10 -0.49 58 68
Gq family/GTP -0.064 0.13 0.22 2 -0.28 110 112
YES1 0.019 0.094 0.38 13 -0.51 3 16
GNAI2/GTP 0.006 0.077 -10000 0 -0.36 10 10
PGD2/DP -0.003 0.11 -10000 0 -0.51 20 20
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.022 0.098 0.38 16 -0.51 3 19
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.013 0.05 -10000 0 -0.68 1 1
PGK/cGMP -0.091 0.21 -10000 0 -0.44 122 122
RhoA/GDP 0.028 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.038 0.1 -10000 0 -0.51 7 7
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
PRKCA -0.031 0.18 0.44 13 -0.38 66 79
PRKCB -0.027 0.17 0.44 13 -0.37 62 75
PRKCE -0.031 0.16 0.37 8 -0.37 64 72
PRKCD -0.029 0.17 0.44 9 -0.38 62 71
PRKCG -0.029 0.17 0.41 13 -0.39 61 74
muscle contraction -0.038 0.21 0.5 11 -0.49 63 74
PRKCZ -0.018 0.16 0.41 16 -0.34 60 76
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.013 0.089 -10000 0 -0.34 21 21
PRKCQ -0.029 0.16 0.41 11 -0.36 64 75
MAPKKK cascade -0.037 0.2 0.46 12 -0.46 63 75
SELE -0.03 0.18 0.35 17 -0.42 63 80
TP beta/GNAI2/GDP/G beta/gamma 0.037 0.099 -10000 0 -0.76 3 3
ROCK1 0.027 0.005 -10000 0 -10000 0 0
GNA14 -0.13 0.29 -10000 0 -0.64 107 107
chemotaxis -0.053 0.25 0.53 10 -0.61 63 73
GNA12 0.027 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.082 -10000 0 -0.63 7 7
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
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 -0.028 0.14 -10000 0 -0.4 32 32
TBX21 -0.12 0.42 -10000 0 -1.1 54 54
B2M 0.023 0.018 -10000 0 -10000 0 0
TYK2 0.02 0.03 -10000 0 -10000 0 0
IL12RB1 0.004 0.069 -10000 0 -0.58 3 3
GADD45B -0.1 0.4 -10000 0 -1 59 59
IL12RB2 -0.004 0.13 -10000 0 -0.68 16 16
GADD45G -0.092 0.35 -10000 0 -0.92 51 51
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 -0.002 0.11 -10000 0 -0.66 10 10
IL2RA -0.012 0.15 -10000 0 -0.64 22 22
IFNG -0.073 0.23 -10000 0 -0.68 57 57
STAT3 (dimer) -0.08 0.31 -10000 0 -0.78 58 58
HLA-DRB5 -0.009 0.077 -10000 0 -0.68 3 3
FASLG -0.14 0.46 -10000 0 -1.2 57 57
NF kappa B2 p52/RelB -0.1 0.38 -10000 0 -0.97 55 55
CD4 0.011 0.034 -10000 0 -10000 0 0
SOCS1 0.024 0.036 -10000 0 -0.68 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.064 0.21 -10000 0 -0.64 49 49
CD3E -0.043 0.18 -10000 0 -0.62 38 38
CD3G -0.12 0.26 -10000 0 -0.66 84 84
IL12Rbeta2/JAK2 0.011 0.11 -10000 0 -0.5 17 17
CCL3 -0.12 0.41 -10000 0 -1.2 44 44
CCL4 -0.15 0.49 -10000 0 -1.4 55 55
HLA-A 0.023 0.02 -10000 0 -10000 0 0
IL18/IL18R 0.032 0.15 -10000 0 -0.48 31 31
NOS2 -0.088 0.35 -10000 0 -0.99 43 43
IL12/IL12R/TYK2/JAK2/SPHK2 -0.029 0.14 -10000 0 -0.4 30 30
IL1R1 -0.1 0.37 -10000 0 -1.1 45 45
IL4 0 0.034 -10000 0 -10000 0 0
JAK2 0.018 0.036 -10000 0 -0.4 1 1
EntrezGene:6957 -0.007 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.21 0.5 -10000 0 -1.1 91 91
RAB7A -0.058 0.3 -10000 0 -0.74 53 53
lysosomal transport -0.052 0.28 -10000 0 -0.69 54 54
FOS -0.38 0.62 -10000 0 -1.2 151 151
STAT4 (dimer) -0.084 0.36 -10000 0 -0.87 58 58
STAT5A (dimer) -0.14 0.4 -10000 0 -0.97 66 66
GZMA -0.11 0.39 -10000 0 -1.1 45 45
GZMB -0.11 0.38 -10000 0 -1.1 45 45
HLX 0.021 0.026 -10000 0 -10000 0 0
LCK -0.13 0.43 -10000 0 -1.1 55 55
TCR/CD3/MHC II/CD4 -0.15 0.29 -10000 0 -0.54 107 107
IL2/IL2R -0.004 0.17 -10000 0 -0.55 31 31
MAPK14 -0.085 0.37 0.46 1 -0.88 63 64
CCR5 -0.093 0.39 -10000 0 -1.1 43 43
IL1B -0.033 0.2 -10000 0 -0.71 35 35
STAT6 -0.008 0.11 -10000 0 -0.46 5 5
STAT4 0.003 0.1 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B 0.005 0.088 -10000 0 -0.69 6 6
CD8A -0.023 0.18 -10000 0 -0.66 32 32
CD8B -0.056 0.22 -10000 0 -0.65 51 51
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.028 0.14 0.39 32 -10000 0 32
IL2RB 0.003 0.093 -10000 0 -0.61 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.072 0.32 -10000 0 -0.78 58 58
IL2RG -0.011 0.14 -10000 0 -0.63 19 19
IL12 -0.037 0.18 -10000 0 -0.53 54 54
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.015 0.13 -10000 0 -0.68 16 16
IL2 -0.003 0.021 -10000 0 -10000 0 0
SPHK2 0.026 0.008 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.056 0.22 -10000 0 -0.68 49 49
IL12/IL12R/TYK2/JAK2 -0.14 0.5 -10000 0 -1.2 58 58
MAP2K3 -0.087 0.37 -10000 0 -0.89 60 60
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.094 0.38 -10000 0 -0.9 63 63
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.006 0.09 -10000 0 -0.68 6 6
IL18RAP -0.003 0.14 -10000 0 -0.68 19 19
IL12Rbeta1/TYK2 0.025 0.061 -10000 0 -0.44 3 3
EOMES -0.13 0.41 -10000 0 -1.3 47 47
STAT1 (dimer) -0.12 0.35 -10000 0 -0.79 79 79
T cell proliferation -0.052 0.26 -10000 0 -0.62 59 59
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.006 0.089 -10000 0 -0.56 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.064 0.28 -10000 0 -0.67 63 63
ATF2 -0.086 0.34 0.44 1 -0.79 65 66
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.011 -9999 0 -10000 0 0
EGFR 0.02 0.066 -9999 0 -0.68 4 4
EGF/EGFR -0.016 0.16 -9999 0 -0.37 71 71
EGF/EGFR dimer/SHC/GRB2/SOS1 0.004 0.16 -9999 0 -0.39 63 63
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.025 0.035 -9999 0 -0.68 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.076 0.25 -9999 0 -0.68 66 66
EGF/EGFR dimer/SHC -0.024 0.18 -9999 0 -0.44 69 69
mol:GDP -0.001 0.16 -9999 0 -0.38 63 63
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.02 0.074 -9999 0 -0.68 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.013 0.14 -9999 0 -0.36 63 63
SHC1 0.026 0.008 -9999 0 -10000 0 0
HRAS/GDP 0 0.15 -9999 0 -0.36 63 63
FRAP1 -0.054 0.13 -9999 0 -0.37 63 63
EGF/EGFR dimer -0.044 0.2 -9999 0 -0.51 69 69
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.064 -9999 0 -0.51 6 6
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.001 0.2 0.6 5 -0.67 8 13
CRP 0.005 0.21 0.58 10 -0.62 17 27
cell cycle arrest -0.014 0.21 0.75 1 -0.67 23 24
TIMP1 -0.036 0.22 0.6 3 -0.64 28 31
IL6ST -0.061 0.24 -10000 0 -0.68 58 58
Rac1/GDP -0.046 0.2 -10000 0 -0.54 41 41
AP1 -0.12 0.27 0.34 1 -0.6 88 89
GAB2 0.028 0.005 -10000 0 -10000 0 0
TNFSF11 -0.01 0.2 0.62 4 -0.67 10 14
HSP90B1 0.041 0.07 -10000 0 -0.78 2 2
GAB1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 -0.09 0.24 -10000 0 -0.71 45 45
AKT1 0.039 0.064 -10000 0 -0.64 2 2
FOXO1 0.038 0.061 -10000 0 -0.91 1 1
MAP2K6 -0.081 0.23 -10000 0 -0.6 50 50
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.032 0.19 0.35 3 -0.53 35 38
MITF -0.069 0.21 -10000 0 -0.57 43 43
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.008 -10000 0 -10000 0 0
A2M 0.026 0.073 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.007 0.097 -10000 0 -0.5 7 7
STAT3 -0.023 0.22 0.76 1 -0.72 23 24
STAT1 0.009 0.1 -10000 0 -0.94 5 5
CEBPD -0.002 0.2 0.64 2 -0.6 19 21
PIK3CA 0.024 0.057 -10000 0 -0.68 3 3
PI3K 0.038 0.046 -10000 0 -0.51 3 3
JUN -0.12 0.29 -10000 0 -0.68 99 99
PIAS3/MITF -0.053 0.2 -10000 0 -0.56 39 39
MAPK11 -0.092 0.23 -10000 0 -0.69 45 45
STAT3 (dimer)/FOXO1 0.016 0.16 -10000 0 -0.53 16 16
GRB2/SOS1/GAB family -0.029 0.2 -10000 0 -0.6 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.072 0.21 -10000 0 -0.52 49 49
GRB2 0.027 0.007 -10000 0 -10000 0 0
JAK2 0.025 0.02 -10000 0 -0.36 1 1
LBP 0.007 0.18 0.6 8 -0.55 13 21
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.015 -10000 0 -10000 0 0
MYC -0.014 0.24 0.63 3 -0.84 21 24
FGG -0.008 0.2 0.63 4 -0.62 17 21
macrophage differentiation -0.014 0.21 0.75 1 -0.67 23 24
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.07 0.25 -10000 0 -0.45 123 123
JUNB -0.003 0.21 0.6 3 -0.72 18 21
FOS -0.16 0.31 -10000 0 -0.68 122 122
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.067 0.22 -10000 0 -0.53 55 55
STAT1/PIAS1 -0.037 0.2 -10000 0 -0.54 37 37
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.067 -10000 0 -0.44 5 5
STAT3 (dimer) -0.018 0.22 0.75 1 -0.7 23 24
PRKCD -0.019 0.19 0.41 6 -0.58 24 30
IL6R 0.005 0.12 -10000 0 -0.68 13 13
SOCS3 -0.11 0.32 0.43 2 -0.96 45 47
gp130 (dimer)/JAK1/JAK1/LMO4 -0.004 0.17 -10000 0 -0.44 56 56
Rac1/GTP -0.044 0.2 -10000 0 -0.54 40 40
HCK 0.018 0.036 -10000 0 -10000 0 0
MAPKKK cascade 0.024 0.1 0.34 1 -0.57 7 8
bone resorption -0.008 0.19 0.62 4 -0.64 10 14
IRF1 0.002 0.2 0.64 6 -0.64 10 16
mol:GDP -0.066 0.2 -10000 0 -0.54 47 47
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.068 0.21 -10000 0 -0.55 47 47
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.085 0.24 -10000 0 -0.69 46 46
PTPN11 0.014 0.077 -10000 0 -0.87 3 3
IL6/IL6RA -0.078 0.23 -10000 0 -0.52 92 92
gp130 (dimer)/TYK2/TYK2/LMO4 -0.007 0.16 -10000 0 -0.42 58 58
gp130 (dimer)/JAK2/JAK2/LMO4 -0.01 0.16 -10000 0 -0.44 56 56
IL6 -0.11 0.27 -10000 0 -0.68 83 83
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.022 0.076 -10000 0 -0.68 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.074 0.21 -10000 0 -0.39 109 109
LMO4 0.028 0.019 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.021 0.21 -10000 0 -0.71 22 22
MCL1 0.053 0.075 -10000 0 -0.82 1 1
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CCL5 -0.015 0.16 -10000 0 -0.68 25 25
SDCBP 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.039 0.14 -10000 0 -0.4 44 44
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.032 0.14 -10000 0 -0.42 40 40
Syndecan-1/Syntenin -0.031 0.14 0.26 2 -0.42 40 42
MAPK3 -0.03 0.12 -10000 0 -0.51 19 19
HGF/MET -0.076 0.19 -10000 0 -0.53 62 62
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
BSG 0.025 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.032 0.14 -10000 0 -0.41 40 40
Syndecan-1/RANTES -0.05 0.19 -10000 0 -0.51 53 53
Syndecan-1/CD147 -0.015 0.14 -10000 0 -0.5 24 24
Syndecan-1/Syntenin/PIP2 -0.031 0.14 0.24 1 -0.41 40 41
LAMA5 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.031 0.14 0.24 1 -0.4 40 41
MMP7 -0.08 0.16 -10000 0 -0.67 24 24
HGF -0.069 0.24 -10000 0 -0.68 62 62
Syndecan-1/CASK -0.045 0.14 -10000 0 -0.4 46 46
Syndecan-1/HGF/MET -0.073 0.21 -10000 0 -0.5 67 67
regulation of cell adhesion -0.032 0.12 -10000 0 -0.49 19 19
HPSE 0.008 0.098 -10000 0 -0.64 9 9
positive regulation of cell migration -0.039 0.14 -10000 0 -0.4 44 44
SDC1 -0.039 0.14 -10000 0 -0.4 48 48
Syndecan-1/Collagen -0.039 0.14 -10000 0 -0.4 44 44
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET -0.03 0.072 -10000 0 -10000 0 0
PRKACA 0.026 0.008 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 36 36
MAPK1 -0.031 0.12 -10000 0 -0.51 20 20
homophilic cell adhesion -0.036 0.14 0.43 2 -0.41 43 45
MMP1 -0.045 0.073 -10000 0 -10000 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.038 0.11 -10000 0 -0.42 23 23
ER alpha/Gai/GDP/Gbeta gamma -0.008 0.14 -10000 0 -0.52 25 25
AKT1 -0.019 0.21 -10000 0 -0.77 31 31
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.015 0.21 -10000 0 -0.79 30 30
mol:Ca2+ -0.097 0.19 -10000 0 -0.43 109 109
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.021 0.15 -10000 0 -0.45 48 48
SHC1 0.026 0.008 -10000 0 -10000 0 0
apoptosis 0.017 0.2 0.73 31 -10000 0 31
RhoA/GTP 0.003 0.078 -10000 0 -0.35 19 19
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.002 0.14 -10000 0 -0.54 21 21
regulation of stress fiber formation 0.009 0.087 0.3 30 -0.28 1 31
E2/ERA-ERB (dimer) 0.004 0.11 -10000 0 -0.44 25 25
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.007 0.092 -10000 0 -0.37 23 23
pseudopodium formation -0.009 0.087 0.28 1 -0.3 30 31
E2/ER alpha (dimer)/PELP1 0.007 0.1 -10000 0 -0.41 23 23
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.033 -10000 0 -0.68 1 1
GNAO1 0.004 0.12 -10000 0 -0.68 14 14
HRAS 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.007 0.16 0.48 8 -0.58 24 32
E2/ER beta (dimer) 0.017 0.043 -10000 0 -0.51 3 3
mol:GDP 0 0.12 -10000 0 -0.48 24 24
mol:NADP 0.007 0.16 0.48 8 -0.58 24 32
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.44 109 109
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.1 0.2 -10000 0 -0.45 110 110
PLCB2 -0.1 0.21 -10000 0 -0.46 110 110
IGF1 -0.12 0.29 -10000 0 -0.68 96 96
mol:L-citrulline 0.007 0.16 0.48 8 -0.58 24 32
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP 0.001 0.15 -10000 0 -0.68 20 20
JNK cascade 0.016 0.043 -10000 0 -0.51 3 3
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.022 0.057 -10000 0 -0.68 3 3
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.018 0.16 -10000 0 -0.65 24 24
Gq family/GDP/Gbeta gamma -0.06 0.2 -10000 0 -0.67 26 26
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.11 -10000 0 -0.57 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0 0.14 -10000 0 -0.54 21 21
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.013 0.12 -10000 0 -0.49 24 24
STRN -0.014 0.16 -10000 0 -0.67 27 27
GNAL -0.06 0.23 -10000 0 -0.66 58 58
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.037 -10000 0 -0.44 3 3
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.034 -10000 0 -0.68 1 1
HBEGF -0.019 0.15 0.38 4 -0.55 20 24
cAMP biosynthetic process -0.042 0.16 -10000 0 -0.39 74 74
SRC -0.007 0.13 -10000 0 -0.51 22 22
PI3K 0.036 0.045 -10000 0 -0.51 3 3
GNB1 0.027 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.029 0.12 -10000 0 -0.46 21 21
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.07 0.16 -10000 0 -0.51 30 30
Gs family/GTP -0.032 0.16 -10000 0 -0.39 74 74
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.015 -10000 0 -10000 0 0
vasodilation 0.007 0.16 0.48 8 -0.55 25 33
mol:DAG -0.1 0.2 -10000 0 -0.44 109 109
Gs family/GDP/Gbeta gamma -0.029 0.15 -10000 0 -0.36 67 67
MSN -0.01 0.093 0.29 1 -0.32 30 31
Gq family/GTP -0.1 0.22 -10000 0 -0.47 111 111
mol:PI-3-4-5-P3 -0.013 0.2 -10000 0 -0.75 30 30
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.007 0.16 0.55 25 -0.48 8 33
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.12 -10000 0 -0.45 24 24
NOS3 -0.001 0.16 0.42 3 -0.62 24 27
GNA11 0.015 0.082 -10000 0 -0.63 7 7
MAPKKK cascade -0.018 0.18 0.37 1 -0.51 48 49
E2/ER alpha (dimer)/PELP1/Src -0.003 0.14 -10000 0 -0.57 21 21
ruffle organization -0.009 0.087 0.28 1 -0.3 30 31
ROCK2 -0.004 0.11 0.36 5 -0.35 31 36
GNA14 -0.13 0.29 -10000 0 -0.64 107 107
GNA15 0.013 0.05 -10000 0 -0.68 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.034 0.16 -10000 0 -0.58 24 24
MMP2 -0.005 0.13 0.34 1 -0.59 14 15
ErbB2/ErbB3 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
USP8 0.004 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.12 -10000 0 -0.36 22 22
NFATC4 -0.024 0.09 0.29 3 -0.28 39 42
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.019 0.12 -10000 0 -0.36 41 41
JUN -0.006 0.098 0.37 10 -0.22 5 15
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK7 -0.03 0.11 -10000 0 -0.34 43 43
ErbB2/ErbB3/neuregulin 1 beta/SHC 0 0.13 -10000 0 -0.4 42 42
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.005 -10000 0 -10000 0 0
MAPK10 -0.012 0.067 0.28 3 -0.39 1 4
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.02 0.12 -10000 0 -0.38 41 41
RAF1 -0.014 0.13 0.36 10 -0.38 21 31
ErbB2/ErbB3/neuregulin 2 -0.026 0.15 -10000 0 -0.42 55 55
STAT3 0.024 0.093 -10000 0 -0.85 5 5
cell migration 0.007 0.12 0.41 21 -0.28 4 25
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.16 0.32 0.48 1 -0.68 110 111
FOS -0.13 0.27 0.37 7 -0.5 146 153
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.019 0.12 -10000 0 -0.36 41 41
MAPK3 -0.084 0.24 0.41 4 -0.52 80 84
MAPK1 -0.17 0.31 0.44 2 -0.64 114 116
JAK2 -0.029 0.1 -10000 0 -0.34 40 40
NF2 -0.012 0.12 -10000 0 -0.62 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.015 0.11 -10000 0 -0.35 42 42
NRG1 -0.042 0.21 -10000 0 -0.67 45 45
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
MAPK8 -0.021 0.11 -10000 0 -0.33 45 45
MAPK9 -0.012 0.063 0.26 2 -10000 0 2
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.017 0.076 -10000 0 -0.63 6 6
SHC1 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.091 -10000 0 -0.83 5 5
RNF41 -0.001 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.02 0.08 -10000 0 -0.26 40 40
ErbB2/ErbB2/HSP90 (dimer) 0.011 0.016 -10000 0 -10000 0 0
CHRNA1 -0.08 0.2 0.4 2 -0.4 92 94
myelination -0.011 0.14 0.57 16 -0.28 19 35
PPP3CB -0.027 0.099 -10000 0 -0.32 41 41
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.018 0.11 -10000 0 -0.33 19 19
NRG2 -0.052 0.22 -10000 0 -0.68 50 50
mol:GDP -0.015 0.11 -10000 0 -0.34 42 42
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K2 -0.029 0.13 0.38 6 -0.39 20 26
SRC 0.027 0.009 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.028 0.11 0.25 1 -0.34 42 43
MAP2K1 -0.08 0.23 0.36 1 -0.59 35 36
heart morphogenesis -0.019 0.12 -10000 0 -0.36 41 41
RAS family/GDP 0.014 0.12 -10000 0 -0.36 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA -0.013 0.13 -10000 0 -0.65 18 18
CHRNE 0.007 0.038 0.19 11 -0.23 1 12
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.006 -10000 0 -10000 0 0
nervous system development -0.019 0.12 -10000 0 -0.36 41 41
CDC42 0.027 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.23 -10000 0 -0.54 58 58
MAP3K8 0.013 0.089 -10000 0 -0.64 8 8
FOS -0.08 0.18 0.3 3 -0.47 53 56
PRKCA -0.016 0.14 -10000 0 -0.68 20 20
PTPN7 -0.021 0.13 -10000 0 -0.68 15 15
HRAS 0.025 0.012 -10000 0 -10000 0 0
PRKCB -0.003 0.072 -10000 0 -0.68 3 3
NRAS 0.026 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.022 -10000 0 -10000 0 0
MAPK3 -0.016 0.12 -10000 0 -0.49 20 20
MAP2K1 -0.022 0.13 -10000 0 -0.5 25 25
ELK1 0.012 0.026 -10000 0 -10000 0 0
BRAF -0.015 0.12 -10000 0 -0.51 23 23
mol:GTP -0.002 0.004 -10000 0 -0.007 125 125
MAPK1 -0.1 0.21 -10000 0 -0.53 57 57
RAF1 -0.014 0.11 -10000 0 -0.49 23 23
KRAS 0.026 0.006 -10000 0 -10000 0 0
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 0.11 -10000 0 -0.4 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.008 0.11 0.35 3 -0.46 6 9
alphaV/beta3 Integrin/Osteopontin/Src -0.002 0.12 -10000 0 -0.5 22 22
AP1 -0.15 0.3 -10000 0 -0.67 92 92
ILK -0.007 0.12 -10000 0 -0.42 27 27
bone resorption -0.006 0.13 -10000 0 -0.42 23 23
PTK2B 0.027 0.004 -10000 0 -10000 0 0
PYK2/p130Cas 0.043 0.12 -10000 0 -0.39 28 28
ITGAV 0.026 0.047 -10000 0 -0.68 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.018 0.1 -10000 0 -0.5 18 18
alphaV/beta3 Integrin/Osteopontin 0.028 0.13 -10000 0 -0.45 29 29
MAP3K1 -0.009 0.12 -10000 0 -0.42 28 28
JUN -0.12 0.29 -10000 0 -0.68 99 99
MAPK3 -0.023 0.1 -10000 0 -0.39 28 28
MAPK1 -0.024 0.1 -10000 0 -0.39 28 28
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.019 0.12 -10000 0 -0.43 31 31
ITGB3 0.01 0.11 -10000 0 -0.65 12 12
NFKBIA -0.019 0.1 -10000 0 -0.38 28 28
FOS -0.16 0.31 -10000 0 -0.68 122 122
CD44 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.039 0.12 0.52 3 -0.54 4 7
NF kappa B1 p50/RelA 0.021 0.1 -10000 0 -0.5 4 4
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.027 0.1 -10000 0 -0.55 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.009 0.12 -10000 0 -0.42 28 28
VAV3 -0.016 0.12 0.4 1 -0.41 31 32
MAP3K14 -0.014 0.11 -10000 0 -0.42 28 28
ROCK2 0 0.14 -10000 0 -0.66 18 18
SPP1 -0.028 0.15 -10000 0 -0.67 20 20
RAC1 0.027 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.11 -10000 0 -0.38 31 31
MMP2 -0.13 0.24 -10000 0 -0.56 83 83
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.035 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.028 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.013 0.093 -10000 0 -0.68 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 232 232
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.026 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.045 0.073 -10000 0 -0.31 11 11
PRKG1 -0.16 0.31 -10000 0 -0.67 123 123
DUSP8 0.019 0.068 -10000 0 -0.68 4 4
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 120 120
apoptosis -0.043 0.07 -10000 0 -0.3 11 11
RAL/GTP 0.036 0.009 -10000 0 -10000 0 0
LYN 0.027 0.004 -10000 0 -10000 0 0
DUSP1 -0.085 0.26 -10000 0 -0.68 72 72
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.027 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.066 0.021 -10000 0 -10000 0 0
TRAF6 0.024 0.047 -10000 0 -0.68 2 2
RAC1 0.027 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.01 -10000 0 -10000 0 0
MAPK11 -0.053 0.16 0.44 17 -0.34 30 47
BLK -0.19 0.32 -10000 0 -0.67 136 136
HCK 0.018 0.036 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.023 0.035 -10000 0 -0.68 1 1
TRAF6/MEKK3 0.031 0.031 -10000 0 -0.41 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.011 0.13 0.38 17 -0.34 11 28
positive regulation of innate immune response -0.043 0.17 0.49 17 -0.44 12 29
LCK 0.011 0.085 -10000 0 -0.68 6 6
p38alpha-beta/MKP7 -0.046 0.14 0.34 7 -0.47 8 15
p38alpha-beta/MKP5 -0.035 0.16 0.47 14 -0.48 8 22
PGK/cGMP -0.12 0.23 -10000 0 -0.51 123 123
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.099 0.18 0.28 3 -0.42 63 66
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.005 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.34 -10000 0 -0.66 253 253
FAS signaling pathway (CD95)

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
SPTAN1 0.014 0.062 0.25 27 -10000 0 27
RFC1 0.014 0.063 0.24 31 -10000 0 31
PRKDC 0.015 0.067 0.25 32 -10000 0 32
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.005 0.1 -10000 0 -0.76 6 6
FASLG/FAS/FADD/FAF1 -0.017 0.098 0.24 4 -0.34 32 36
MAP2K4 -0.032 0.17 0.32 2 -0.5 27 29
mol:ceramide -0.023 0.14 -10000 0 -0.43 33 33
GSN 0.014 0.062 0.24 30 -10000 0 30
FASLG/FAS/FADD/FAF1/Caspase 8 -0.022 0.12 -10000 0 -0.43 32 32
FAS 0.019 0.019 -10000 0 -10000 0 0
BID -0.019 0.036 0.28 3 -10000 0 3
MAP3K1 -0.012 0.12 0.27 3 -0.54 10 13
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
RB1 0.014 0.066 0.25 29 -10000 0 29
CFLAR 0.029 0.007 -10000 0 -10000 0 0
HGF/MET -0.016 0.19 -10000 0 -0.47 64 64
ARHGDIB 0.015 0.069 0.25 34 -10000 0 34
FADD 0.019 0.019 -10000 0 -10000 0 0
actin filament polymerization -0.014 0.062 -10000 0 -0.24 30 30
NFKB1 -0.019 0.1 -10000 0 -0.57 3 3
MAPK8 -0.07 0.23 0.4 2 -0.48 93 95
DFFA 0.014 0.063 0.24 31 -10000 0 31
DNA fragmentation during apoptosis 0.014 0.063 0.24 31 -10000 0 31
FAS/FADD/MET 0.043 0.043 -10000 0 -10000 0 0
CFLAR/RIP1 0.043 0.01 -10000 0 -10000 0 0
FAIM3 0.017 0.063 -10000 0 -0.68 3 3
FAF1 0.018 0.021 -10000 0 -10000 0 0
PARP1 0.018 0.078 0.28 32 -10000 0 32
DFFB 0.014 0.063 0.24 31 -10000 0 31
CHUK -0.018 0.092 -10000 0 -0.53 3 3
FASLG -0.035 0.18 -10000 0 -0.69 31 31
FAS/FADD 0.029 0.028 -10000 0 -10000 0 0
HGF -0.069 0.24 -10000 0 -0.68 62 62
LMNA 0.013 0.069 0.42 5 -10000 0 5
CASP6 0.014 0.063 0.24 30 -10000 0 30
CASP10 0.019 0.019 -10000 0 -10000 0 0
CASP3 0.019 0.079 0.3 33 -10000 0 33
PTPN13 0.02 0.074 -10000 0 -0.68 5 5
CASP8 -0.015 0.035 0.4 3 -10000 0 3
IL6 -0.22 0.53 -10000 0 -1.3 91 91
MET -0.03 0.072 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.057 0.22 25 -10000 0 25
FASLG/FAS/FADD/FAF1/Caspase 10 -0.024 0.14 -10000 0 -0.44 33 33
activation of caspase activity by cytochrome c -0.019 0.036 0.28 3 -10000 0 3
PAK2 0.014 0.064 0.24 31 -10000 0 31
BCL2 -0.024 0.18 -10000 0 -0.67 34 34
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.009 0.014 -10000 0 -10000 0 0
SMARCC1 0.011 0.013 -10000 0 -10000 0 0
REL -0.009 0.16 -10000 0 -0.66 27 27
HDAC7 -0.067 0.11 -10000 0 -0.5 12 12
JUN -0.13 0.29 -10000 0 -0.68 99 99
EP300 0.02 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
KAT5 0.028 0.005 -10000 0 -10000 0 0
MAPK14 -0.014 0.072 -10000 0 -0.53 8 8
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.065 0.12 -10000 0 -0.49 15 15
MAP2K6 0.006 0.094 -10000 0 -0.69 8 8
BRM/BAF57 0.018 0.033 -10000 0 -10000 0 0
MAP2K4 0.019 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.014 0.073 -10000 0 -0.52 4 4
NCOA2 -0.041 0.2 -10000 0 -0.68 40 40
CEBPA 0.019 0.074 -10000 0 -0.68 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.081 0.19 0.58 18 -0.45 17 35
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.13 0.28 -10000 0 -0.68 94 94
RXRs/9cRA 0.021 0.071 -10000 0 -0.41 3 3
AR/RACK1/Src -0.13 0.14 0.33 2 -0.52 14 16
AR/GR -0.12 0.18 0.25 5 -0.32 179 184
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.006 -10000 0 -0.014 61 61
MAPK8 -0.011 0.062 -10000 0 -0.52 6 6
T-DHT/AR/TIF2/CARM1 -0.13 0.18 0.35 2 -0.55 42 44
SRC -0.041 0.075 0.23 1 -0.43 12 13
NR3C1 0.027 0.006 -10000 0 -10000 0 0
KLK3 -0.35 0.55 0.39 1 -1.2 129 130
APPBP2 0.024 0.012 -10000 0 -10000 0 0
TRIM24 0.014 0.022 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.067 0.12 0.34 5 -0.53 12 17
TMPRSS2 -0.043 0.28 -10000 0 -1.1 28 28
RXRG -0.1 0.073 -10000 0 -0.68 3 3
mol:9cRA -0.002 0.003 -10000 0 -0.012 7 7
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.027 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.014 0.093 -10000 0 -0.68 8 8
KLK2 -0.44 0.38 0.34 2 -0.77 258 260
AR -0.14 0.18 -10000 0 -0.35 180 180
SENP1 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.036 0.016 -10000 0 -10000 0 0
SRY 0.009 0.014 0.031 129 -10000 0 129
GATA2 0.027 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.012 0.035 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.097 0.12 0.34 3 -0.54 12 15
positive regulation of transcription 0.027 0.008 -10000 0 -10000 0 0
DNAJA1 0.024 0.013 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.018 0.022 -10000 0 -10000 0 0
SPDEF -0.003 0.049 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.091 0.14 0.28 2 -0.43 46 48
T-DHT/AR/Hsp90 -0.069 0.12 0.33 5 -0.52 12 17
GSK3B 0.025 0.006 -10000 0 -10000 0 0
NR2C1 0.028 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.035 0.078 0.26 1 -0.44 13 14
SIRT1 0.025 0.033 -10000 0 -0.68 1 1
ZMIZ2 0.036 0.017 -10000 0 -10000 0 0
POU2F1 0.033 0.035 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.072 0.12 0.33 5 -0.52 13 18
CREBBP 0.026 0.006 -10000 0 -10000 0 0
SMARCE1 0.013 0.022 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.006 0.057 -10000 0 -10000 0 0
CRKL -0.014 0.09 0.36 1 -0.42 1 2
mol:PIP3 -0.002 0.018 0.34 1 -10000 0 1
AKT1 0.003 0.057 0.37 2 -0.45 3 5
PTK2B 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.004 0.11 0.46 8 -0.4 1 9
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
HGF/MET/SHIP2 -0.011 0.18 -10000 0 -0.46 62 62
MAP3K5 0.015 0.13 0.5 14 -0.4 6 20
HGF/MET/CIN85/CBL/ENDOPHILINS 0.006 0.17 -10000 0 -0.42 58 58
AP1 -0.18 0.34 -10000 0 -0.65 143 143
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
apoptosis -0.23 0.4 -10000 0 -0.8 144 144
STAT3 (dimer) -0.018 0.1 -10000 0 -0.28 57 57
GAB1/CRKL/SHP2/PI3K 0.026 0.11 -10000 0 -0.5 3 3
INPP5D 0.019 0.033 -10000 0 -10000 0 0
CBL/CRK 0.018 0.12 0.5 7 -0.41 1 8
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.019 -10000 0 -0.36 1 1
ELK1 0.037 0.15 0.44 28 -0.26 2 30
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.068 -10000 0 -0.24 5 5
PAK1 0.007 0.063 0.37 6 -0.41 2 8
HGF/MET/RANBP10 -0.011 0.18 -10000 0 -0.46 62 62
HRAS -0.017 0.13 -10000 0 -0.55 3 3
DOCK1 0.002 0.12 0.48 9 -0.48 2 11
GAB1 -0.01 0.096 0.26 1 -0.35 4 5
CRK -0.005 0.098 0.33 3 -0.43 1 4
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.04 0.19 -10000 0 -0.51 62 62
JUN -0.12 0.29 -10000 0 -0.68 99 99
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.029 0.085 -10000 0 -0.24 60 60
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
cell morphogenesis -0.008 0.12 0.45 5 -0.52 3 8
GRB2/SHC 0.005 0.084 -10000 0 -0.28 1 1
FOS -0.16 0.31 -10000 0 -0.68 122 122
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.036 0.15 0.44 28 -0.26 2 30
HGF/MET/MUC20 -0.064 0.16 -10000 0 -0.46 62 62
cell migration 0.005 0.083 -10000 0 -0.27 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.006 0.057 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.014 0.11 -10000 0 -0.3 57 57
MET/MUC20 -0.017 0.047 -10000 0 -10000 0 0
RAP1B 0.013 0.13 0.57 13 -0.37 1 14
RAP1A 0.01 0.11 0.42 12 -0.37 1 13
HGF/MET/RANBP9 -0.01 0.18 -10000 0 -0.46 62 62
RAF1 -0.015 0.12 -10000 0 -0.47 3 3
STAT3 -0.018 0.1 -10000 0 -0.28 57 57
cell proliferation -0.022 0.15 -10000 0 -0.39 56 56
RPS6KB1 0.001 0.033 -10000 0 -0.22 2 2
MAPK3 -0.019 0.11 0.54 13 -10000 0 13
MAPK1 0.14 0.29 0.61 123 -10000 0 123
RANBP9 0.028 0.003 -10000 0 -10000 0 0
MAPK8 0.026 0.17 0.63 16 -0.65 6 22
SRC -0.019 0.1 -10000 0 -0.28 57 57
PI3K 0.005 0.094 -10000 0 -0.39 4 4
MET/Glomulin -0.007 0.045 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.008 0.12 0.43 2 -0.44 3 5
MET -0.03 0.072 -10000 0 -10000 0 0
MAP4K1 0.009 0.12 0.52 8 -0.43 6 14
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.005 0.12 0.43 2 -0.44 1 3
BAD 0.007 0.063 0.37 6 -0.41 2 8
MAP2K4 0.023 0.15 0.54 19 -0.4 4 23
SHP2/GRB2/SOS1/GAB1 0.02 0.099 -10000 0 -0.36 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.026 0.008 -10000 0 -10000 0 0
HGS -0.027 0.076 -10000 0 -0.24 26 26
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.069 0.24 -10000 0 -0.68 62 62
RASA1 0.027 0.006 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.005 0.098 -10000 0 -0.24 59 59
PDPK1 -0.001 0.049 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.015 0.18 -10000 0 -0.46 62 62
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.065 0.17 0.43 10 -0.41 39 49
IKBKB 0.011 0.12 0.48 15 -0.32 6 21
AKT1 0 0.17 0.54 24 -0.25 14 38
IKBKG -0.002 0.12 0.44 15 -0.32 16 31
CALM1 -0.021 0.094 0.42 3 -0.42 7 10
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
MAP3K1 -0.011 0.17 0.48 11 -0.54 19 30
MAP3K7 0.027 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.093 0.34 1 -0.44 7 8
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.059 0.16 0.56 11 -0.26 88 99
LYN 0.027 0.004 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
BCR complex -0.066 0.18 -10000 0 -0.5 58 58
CD22 -0.066 0.18 -10000 0 -0.43 74 74
CAMK2G -0.017 0.092 0.36 4 -0.43 5 9
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.036 0.12 -10000 0 -0.35 51 51
GO:0007205 -0.024 0.096 0.34 1 -0.45 7 8
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.018 0.093 0.36 3 -0.47 5 8
NFATC1 -0.038 0.14 0.39 7 -0.44 20 27
B-cell antigen/BCR complex -0.066 0.18 -10000 0 -0.5 58 58
PAG1/CSK 0.039 0.027 -10000 0 -0.51 1 1
NFKBIB 0.02 0.047 0.22 12 -0.13 7 19
HRAS -0.017 0.095 0.31 4 -0.36 8 12
NFKBIA 0.02 0.047 0.22 12 -0.13 7 19
NF-kappa-B/RelA/I kappa B beta 0.024 0.043 0.22 12 -10000 0 12
RasGAP/Csk 0 0.18 -10000 0 -0.41 65 65
mol:GDP -0.022 0.093 0.3 1 -0.46 7 8
PTEN 0.026 0.019 -10000 0 -0.36 1 1
CD79B 0.008 0.049 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.043 0.22 12 -10000 0 12
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.034 0.16 0.45 5 -0.48 18 23
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.022 0.091 0.34 1 -0.44 6 7
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.1 0.18 0.46 7 -0.37 123 130
CHUK 0.008 0.11 0.43 14 -0.34 7 21
IBTK 0.028 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.012 0.1 -10000 0 -0.46 8 8
PTPN6 -0.061 0.16 -10000 0 -0.41 71 71
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.014 0.037 0.18 6 -0.12 10 16
VAV2 -0.048 0.16 -10000 0 -0.41 54 54
ubiquitin-dependent protein catabolic process 0.023 0.046 0.22 12 -0.12 7 19
BTK -0.036 0.24 -10000 0 -0.98 27 27
CD19 -0.058 0.15 -10000 0 -0.4 60 60
MAP4K1 0.009 0.081 -10000 0 -0.68 5 5
CD72 0.025 0.012 -10000 0 -10000 0 0
PAG1 0.026 0.033 -10000 0 -0.68 1 1
MAPK14 -0.004 0.15 0.45 13 -0.45 19 32
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.015 0.094 -10000 0 -0.54 5 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.047 0.18 -10000 0 -0.42 69 69
RAF1 -0.014 0.095 0.33 7 -0.4 4 11
RasGAP/p62DOK/SHIP -0.003 0.17 -10000 0 -0.4 64 64
CD79A -0.097 0.23 -10000 0 -0.66 59 59
re-entry into mitotic cell cycle -0.058 0.16 0.55 11 -0.26 87 98
RASA1 0.027 0.006 -10000 0 -10000 0 0
MAPK3 -0.003 0.1 0.4 13 -0.42 2 15
MAPK1 -0.01 0.087 0.38 7 -0.4 2 9
CD72/SHP1 -0.045 0.17 -10000 0 -0.53 26 26
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.009 0.16 0.49 12 -0.46 21 33
actin cytoskeleton organization -0.042 0.14 0.34 2 -0.55 12 14
NF-kappa-B/RelA 0.05 0.077 0.38 12 -0.2 2 14
Calcineurin 0.009 0.09 -10000 0 -0.41 4 4
PI3K -0.059 0.14 -10000 0 -0.45 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.018 0.098 -10000 0 -0.46 9 9
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.019 0.22 -10000 0 -0.92 19 19
DAPP1 -0.04 0.25 -10000 0 -1.1 18 18
cytokine secretion -0.035 0.13 0.38 7 -0.4 20 27
mol:DAG -0.022 0.091 0.34 1 -0.44 6 7
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.012 0.091 0.34 6 -0.4 3 9
B-cell antigen/BCR complex/FcgammaRIIB -0.051 0.19 -10000 0 -0.45 73 73
mol:PI-3-4-5-P3 -0.05 0.1 -10000 0 -0.34 18 18
ETS1 -0.014 0.089 0.42 4 -0.42 4 8
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.014 0.15 -10000 0 -0.39 55 55
B-cell antigen/BCR complex/LYN -0.046 0.16 -10000 0 -0.42 61 61
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.047 -10000 0 -0.68 2 2
RAC1 -0.046 0.14 0.36 1 -0.59 12 13
B-cell antigen/BCR complex/LYN/SYK -0.034 0.19 -10000 0 -0.44 69 69
CARD11 -0.035 0.11 0.4 4 -0.46 12 16
FCGR2B -0.009 0.15 -10000 0 -0.68 22 22
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.019 0.097 0.42 18 -0.12 7 25
PTPRC -0.007 0.14 -10000 0 -0.68 18 18
PDPK1 -0.028 0.086 0.25 8 -0.26 16 24
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.004 -10000 0 -10000 0 0
POU2F2 0.02 0.034 0.19 11 -10000 0 11
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.009 0.14 -10000 0 -0.36 57 57
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.001 0.12 -10000 0 -0.37 3 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.053 -10000 0 -0.3 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.007 0.072 -10000 0 -0.26 2 2
CaM/Ca2+ 0.014 0.14 -10000 0 -0.34 57 57
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.013 0.13 -10000 0 -0.34 57 57
AKT1 -0.017 0.12 0.38 5 -0.32 53 58
MAP2K1 -0.025 0.12 0.29 2 -0.33 55 57
MAP3K11 -0.023 0.13 0.3 5 -0.34 57 62
IFNGR1 0.02 0.026 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.017 0.075 -10000 0 -0.44 2 2
Rap1/GTP -0.021 0.096 -10000 0 -0.36 1 1
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.017 0.15 -10000 0 -0.38 56 56
CEBPB -0.058 0.19 0.52 6 -0.51 33 39
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.016 0.16 -10000 0 -0.7 6 6
STAT1 -0.022 0.13 0.32 6 -0.34 57 63
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.067 0.23 -10000 0 -0.68 57 57
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
STAT1 (dimer)/PIAS1 -0.007 0.13 0.3 4 -0.33 53 57
CEBPB/PTGES2/Cbp/p300 -0.025 0.12 -10000 0 -0.4 10 10
mol:Ca2+ 0.006 0.14 -10000 0 -0.36 57 57
MAPK3 -0.011 0.13 -10000 0 -0.69 5 5
STAT1 (dimer) 0.017 0.098 -10000 0 -0.35 2 2
MAPK1 -0.17 0.3 0.44 1 -0.67 113 114
JAK2 0.018 0.032 -10000 0 -0.41 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.02 0.026 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.04 0.18 0.5 9 -0.59 25 34
SMAD7 0.018 0.066 0.42 6 -10000 0 6
CBL/CRKL/C3G -0.01 0.12 0.3 1 -0.37 3 4
PI3K 0.011 0.14 -10000 0 -0.34 57 57
IFNG -0.067 0.23 -10000 0 -0.68 57 57
apoptosis -0.034 0.16 0.56 6 -0.44 33 39
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.012 0.034 -10000 0 -10000 0 0
CAMK2B 0.02 0.066 -10000 0 -0.68 4 4
FRAP1 -0.024 0.11 0.37 5 -0.3 52 57
PRKCD -0.012 0.14 0.43 10 -0.39 6 16
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.007 0.072 -10000 0 -0.26 2 2
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
IRF1 -0.016 0.087 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.011 0.12 0.36 2 -0.33 56 58
SOCS1 0.017 0.12 -10000 0 -1 6 6
mol:GDP -0.011 0.11 -10000 0 -0.36 3 3
CASP1 0.016 0.065 0.45 4 -0.32 2 6
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.002 0.058 0.34 1 -10000 0 1
mol:PI-3-4-5-P3 -0.002 0.13 -10000 0 -0.33 57 57
RAP1/GDP -0.006 0.1 -10000 0 -0.37 1 1
CBL -0.023 0.13 0.29 6 -0.34 57 63
MAP3K1 -0.023 0.12 0.3 2 -0.34 55 57
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.007 0.072 -10000 0 -0.26 2 2
PTPN11 -0.026 0.13 -10000 0 -0.36 57 57
CREBBP 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.018 0.13 -10000 0 -0.43 30 30
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.088 0.34 2 -0.46 1 3
AP1 -0.16 0.3 -10000 0 -0.56 151 151
mol:PIP3 -0.012 0.095 -10000 0 -0.36 29 29
AKT1 0.03 0.1 0.32 5 -0.57 2 7
PTK2B -0.01 0.089 0.24 2 -0.32 17 19
RHOA 0.013 0.042 -10000 0 -10000 0 0
PIK3CB 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.072 0.29 7 -10000 0 7
MAGI3 0.026 0.033 -10000 0 -0.68 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.009 0.1 -10000 0 -0.36 34 34
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.002 0.1 0.38 9 -0.38 9 18
NF kappa B1 p50/RelA -0.02 0.1 -10000 0 -0.46 8 8
endothelial cell migration -0.015 0.14 -10000 0 -0.51 31 31
ADCY4 -0.031 0.15 -10000 0 -0.53 33 33
ADCY5 -0.058 0.17 -10000 0 -0.54 39 39
ADCY6 -0.031 0.15 -10000 0 -0.53 33 33
ADCY7 -0.031 0.15 -10000 0 -0.54 33 33
ADCY1 -0.033 0.15 -10000 0 -0.52 35 35
ADCY2 -0.052 0.17 -10000 0 -0.55 37 37
ADCY3 -0.031 0.15 -10000 0 -0.54 32 32
ADCY8 -0.039 0.15 -10000 0 -0.53 34 34
ADCY9 -0.031 0.15 -10000 0 -0.54 33 33
GSK3B -0.009 0.087 0.37 2 -0.35 10 12
arachidonic acid secretion -0.031 0.15 -10000 0 -0.49 35 35
GNG2 0.026 0.033 -10000 0 -0.68 1 1
TRIP6 0.024 0.009 -10000 0 -10000 0 0
GNAO1 -0.026 0.15 -10000 0 -0.48 43 43
HRAS 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.005 0.098 0.45 6 -0.53 1 7
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.18 -10000 0 -0.79 20 20
JUN -0.12 0.29 -10000 0 -0.68 99 99
LPA/LPA2/NHERF2 0.035 0.015 -10000 0 -10000 0 0
TIAM1 0.001 0.21 -10000 0 -0.92 22 22
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.01 0.066 0.36 2 -10000 0 2
PLCB3 0.027 0.033 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.68 122 122
positive regulation of mitosis -0.031 0.15 -10000 0 -0.49 35 35
LPA/LPA1-2-3 0.018 0.12 -10000 0 -0.41 29 29
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation 0.001 0.1 0.38 3 -0.41 10 13
GNAZ -0.016 0.12 -10000 0 -0.45 31 31
EGFR/PI3K-beta/Gab1 -0.002 0.1 -10000 0 -0.37 29 29
positive regulation of dendritic cell cytokine production 0.016 0.12 -10000 0 -0.41 29 29
LPA/LPA2/MAGI-3 0.035 0.027 -10000 0 -0.46 1 1
ARHGEF1 0.003 0.11 0.36 3 -0.4 25 28
GNAI2 -0.013 0.12 -10000 0 -0.46 31 31
GNAI3 -0.013 0.12 -10000 0 -0.46 31 31
GNAI1 -0.013 0.12 -10000 0 -0.45 32 32
LPA/LPA3 0.016 0.023 -10000 0 -10000 0 0
LPA/LPA2 0.021 0.011 -10000 0 -10000 0 0
LPA/LPA1 -0.016 0.14 -10000 0 -0.48 38 38
HB-EGF/EGFR -0.019 0.13 -10000 0 -0.44 36 36
HBEGF -0.035 0.14 -10000 0 -0.49 36 36
mol:DAG -0.01 0.066 0.36 2 -10000 0 2
cAMP biosynthetic process -0.037 0.17 0.41 11 -0.48 45 56
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.027 0.009 -10000 0 -10000 0 0
GNB1 0.027 0.007 -10000 0 -10000 0 0
LYN -0.007 0.094 0.37 7 -0.43 2 9
GNAQ 0.016 0.014 -10000 0 -10000 0 0
LPAR2 0.026 0.008 -10000 0 -10000 0 0
LPAR3 0.013 0.033 -10000 0 -10000 0 0
LPAR1 -0.024 0.18 -10000 0 -0.62 37 37
IL8 -0.084 0.17 0.36 1 -0.49 32 33
PTK2 -0.003 0.11 -10000 0 -0.4 26 26
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
CASP3 -0.009 0.1 -10000 0 -0.36 34 34
EGFR 0.02 0.066 -10000 0 -0.68 4 4
PLCG1 -0.012 0.063 -10000 0 -0.3 2 2
PLD2 -0.003 0.11 -10000 0 -0.4 26 26
G12/G13 0.02 0.12 -10000 0 -0.41 30 30
PI3K-beta 0.004 0.092 -10000 0 -0.69 2 2
cell migration 0.019 0.074 -10000 0 -0.26 9 9
SLC9A3R2 0.026 0.007 -10000 0 -10000 0 0
PXN -0.001 0.1 0.26 2 -0.42 10 12
HRAS/GTP -0.031 0.15 -10000 0 -0.5 35 35
RAC1 0.027 0.006 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 36 36
PRKCE 0.021 0.066 -10000 0 -0.68 4 4
PRKCD -0.007 0.086 0.34 11 -10000 0 11
Gi(beta/gamma) -0.025 0.14 -10000 0 -0.51 32 32
mol:LPA 0.002 0.013 -10000 0 -0.2 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.018 0.12 -10000 0 -0.42 14 14
MAPKKK cascade -0.031 0.15 -10000 0 -0.49 35 35
contractile ring contraction involved in cytokinesis 0.015 0.048 0.27 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.066 0.15 -10000 0 -0.34 105 105
GNA15 0.014 0.026 -10000 0 -0.36 1 1
GNA12 0.027 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.005 0.098 0.35 7 -0.39 9 16
GNA11 0.012 0.045 -10000 0 -0.33 7 7
Rac1/GTP 0.015 0.19 -10000 0 -0.84 20 20
MMP2 -0.015 0.14 -10000 0 -0.51 31 31
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.008 0.11 -10000 0 -0.75 7 7
Syndecan-4/Syndesmos -0.035 0.16 -10000 0 -0.56 36 36
positive regulation of JNK cascade -0.049 0.19 -10000 0 -0.57 37 37
Syndecan-4/ADAM12 -0.044 0.16 -10000 0 -0.56 36 36
CCL5 -0.015 0.16 -10000 0 -0.68 25 25
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
DNM2 0.025 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
PLG 0.009 0.03 -10000 0 -10000 0 0
ADAM12 -0.012 0.066 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.058 0.031 -10000 0 -0.18 3 3
Syndecan-4/Laminin alpha1 -0.056 0.18 -10000 0 -0.61 34 34
Syndecan-4/CXCL12/CXCR4 -0.052 0.2 -10000 0 -0.61 37 37
Syndecan-4/Laminin alpha3 -0.045 0.17 -10000 0 -0.58 34 34
MDK -0.018 0.069 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.035 0.16 -10000 0 -0.56 36 36
Syndecan-4/Midkine -0.046 0.16 -10000 0 -0.56 35 35
FZD7 0.022 0.053 -10000 0 -0.52 4 4
Syndecan-4/FGFR1/FGF -0.01 0.16 -10000 0 -0.52 35 35
THBS1 0.016 0.04 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.05 0.16 -10000 0 -0.57 36 36
positive regulation of MAPKKK cascade -0.049 0.19 -10000 0 -0.57 37 37
Syndecan-4/TACI -0.12 0.22 -10000 0 -0.64 35 35
CXCR4 0.026 0.011 -10000 0 -10000 0 0
cell adhesion -0.005 0.073 0.2 3 -0.32 20 23
Syndecan-4/Dynamin -0.034 0.16 -10000 0 -0.56 35 35
Syndecan-4/TSP1 -0.036 0.16 -10000 0 -0.56 36 36
Syndecan-4/GIPC -0.034 0.16 -10000 0 -0.56 35 35
Syndecan-4/RANTES -0.054 0.2 -10000 0 -0.67 37 37
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 -0.019 0.17 -10000 0 -0.67 30 30
LAMA3 0.001 0.12 -10000 0 -0.68 14 14
RAC1 0.027 0.006 -10000 0 -10000 0 0
PRKCA 0.007 0.2 0.75 17 -0.62 20 37
Syndecan-4/alpha-Actinin -0.033 0.16 -10000 0 -0.56 35 35
TFPI -0.009 0.16 -10000 0 -0.67 24 24
F2 0.012 0.026 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.069 0.18 -10000 0 -0.6 34 34
ACTN1 0.027 0.009 -10000 0 -10000 0 0
TNC -0.033 0.093 -10000 0 -0.68 4 4
Syndecan-4/CXCL12 -0.07 0.2 -10000 0 -0.63 37 37
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.047 0.22 -10000 0 -0.68 48 48
TNFRSF13B -0.14 0.29 -10000 0 -0.67 103 103
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.026 0.033 -10000 0 -0.68 1 1
Syndecan-4/PI-4-5-P2 -0.046 0.16 -10000 0 -0.56 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.076 0.075 -10000 0 -0.19 2 2
cell migration -0.027 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.023 -10000 0 -10000 0 0
vasculogenesis -0.035 0.16 -10000 0 -0.54 36 36
SDC4 -0.046 0.16 -10000 0 -0.59 36 36
Syndecan-4/Tenascin C -0.052 0.17 -10000 0 -0.59 36 36
Syndecan-4/PI-4-5-P2/PKC alpha -0.047 0.024 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.034 0.16 -10000 0 -0.56 36 36
MMP9 -0.038 0.19 -10000 0 -0.67 36 36
Rac1/GTP -0.005 0.074 0.2 3 -0.32 20 23
cytoskeleton organization -0.033 0.15 -10000 0 -0.53 36 36
GIPC1 0.026 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.051 0.18 -10000 0 -0.58 36 36
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.003 0.067 -10000 0 -0.28 3 3
AP1 -0.12 0.26 -10000 0 -0.55 98 98
mol:PIP3 0.028 0.18 0.66 18 -0.39 20 38
IKBKB 0.039 0.18 0.66 23 -0.25 11 34
AKT1 -0.007 0.13 0.32 25 -0.44 8 33
IKBKG 0.043 0.18 0.67 25 -0.26 7 32
MS4A2 -0.014 0.063 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
MAP3K1 0.025 0.12 0.49 12 -0.42 6 18
mol:Ca2+ 0.034 0.17 0.59 23 -0.32 13 36
LYN 0.027 0.011 -10000 0 -10000 0 0
CBLB -0.001 0.065 -10000 0 -0.28 1 1
SHC1 0.026 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK -0.022 0.17 -10000 0 -0.41 72 72
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
PLD2 -0.008 0.13 0.32 33 -0.38 28 61
PTPN13 0.011 0.14 0.48 2 -0.63 14 16
PTPN11 0.022 0.037 -10000 0 -0.7 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.031 0.17 0.63 20 -0.36 7 27
SYK 0.025 0.013 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.001 0.11 -10000 0 -0.38 27 27
LAT -0.004 0.071 -10000 0 -0.32 5 5
PAK2 0.017 0.11 0.37 5 -0.42 9 14
NFATC2 -0.1 0.23 -10000 0 -0.61 73 73
HRAS 0.012 0.1 0.25 1 -0.44 9 10
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.004 0.1 -10000 0 -0.72 7 7
Fc epsilon R1 0.007 0.13 -10000 0 -0.46 30 30
Antigen/IgE/Fc epsilon R1 0.01 0.12 -10000 0 -0.41 30 30
mol:GDP 0.003 0.11 -10000 0 -0.5 11 11
JUN -0.12 0.29 -10000 0 -0.68 99 99
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.68 122 122
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.003 0.07 -10000 0 -0.26 9 9
CHUK 0.038 0.17 0.63 23 -0.26 8 31
KLRG1 -0.009 0.079 -10000 0 -0.31 14 14
VAV1 -0.004 0.075 0.21 1 -0.36 6 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.001 0.064 -10000 0 -0.26 1 1
negative regulation of mast cell degranulation 0.005 0.082 -10000 0 -0.31 10 10
BTK -0.005 0.12 -10000 0 -0.55 15 15
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.16 -10000 0 -0.48 37 37
GAB2/PI3K/SHP2 -0.029 0.1 -10000 0 -0.39 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.073 -10000 0 -0.27 27 27
RAF1 0.011 0.097 -10000 0 -0.86 5 5
Fc epsilon R1/FcgammaRIIB/SHIP 0.024 0.18 -10000 0 -0.51 39 39
FCER1G 0.018 0.034 -10000 0 -10000 0 0
FCER1A -0.034 0.18 -10000 0 -0.68 31 31
Antigen/IgE/Fc epsilon R1/Fyn 0.024 0.12 -10000 0 -0.39 30 30
MAPK3 0.018 0.095 -10000 0 -0.78 5 5
MAPK1 -0.016 0.11 -10000 0 -0.74 7 7
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.001 0.18 -10000 0 -0.64 28 28
DUSP1 -0.085 0.26 -10000 0 -0.68 72 72
NF-kappa-B/RelA 0.015 0.048 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.013 0.14 0.4 2 -0.69 11 13
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.099 -10000 0 -0.47 7 7
FER -0.004 0.072 -10000 0 -0.39 4 4
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.043 0.15 -10000 0 -0.47 50 50
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.011 0.12 0.4 8 -0.52 10 18
cytokine secretion 0.005 0.031 -10000 0 -10000 0 0
SPHK1 -0.002 0.067 0.27 1 -0.27 3 4
PTK2 0.012 0.14 0.41 2 -0.74 11 13
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.006 0.11 -10000 0 -0.39 27 27
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.035 0.18 0.73 17 -0.42 12 29
MAP2K2 0.016 0.1 -10000 0 -0.8 5 5
MAP2K1 0.008 0.09 -10000 0 -0.8 5 5
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 -0.002 0.084 -10000 0 -0.33 12 12
MAP2K4 -0.012 0.21 -10000 0 -0.83 26 26
Fc epsilon R1/FcgammaRIIB 0.006 0.18 -10000 0 -0.54 39 39
mol:Choline -0.008 0.13 0.32 33 -0.37 28 61
SHC/Grb2/SOS1 0.036 0.078 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.018 0.13 0.49 4 -0.68 10 14
HCLS1 -0.002 0.065 -10000 0 -0.28 2 2
PRKCB 0.037 0.18 0.67 23 -0.34 13 36
FCGR2B -0.009 0.15 -10000 0 -0.68 22 22
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.005 0.084 -10000 0 -0.31 10 10
LCP2 0.024 0.019 -10000 0 -10000 0 0
PLA2G4A -0.024 0.12 -10000 0 -0.42 29 29
RASA1 0.027 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.008 0.13 0.32 33 -0.37 28 61
IKK complex 0.045 0.18 0.69 25 -0.21 3 28
WIPF1 0.027 0.005 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.014 0.12 -10000 0 -0.48 14 14
BAG4 0.026 0.033 -10000 0 -0.68 1 1
PKC zeta/ceramide -0.02 0.099 -10000 0 -0.3 32 32
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.009 0.15 -10000 0 -0.62 23 23
BAX -0.015 0.08 -10000 0 -0.35 21 21
RIPK1 0.028 0.002 -10000 0 -10000 0 0
AKT1 0.028 0.14 0.79 15 -10000 0 15
BAD -0.033 0.09 0.18 1 -0.29 31 32
SMPD1 -0.011 0.092 0.29 7 -0.23 56 63
RB1 -0.033 0.092 0.19 1 -0.33 25 26
FADD/Caspase 8 -0.004 0.12 -10000 0 -0.5 13 13
MAP2K4 -0.02 0.072 0.22 2 -0.42 6 8
NSMAF 0.027 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.025 0.083 -10000 0 -0.42 11 11
EGF -0.076 0.25 -10000 0 -0.68 66 66
mol:ceramide -0.037 0.099 -10000 0 -0.3 35 35
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.025 -10000 0 -0.51 1 1
ASAH1 0.026 0.033 -10000 0 -0.68 1 1
negative regulation of cell cycle -0.033 0.091 0.19 1 -0.33 24 25
cell proliferation -0.058 0.15 -10000 0 -0.33 93 93
BID -0.15 0.28 -10000 0 -0.6 118 118
MAP3K1 -0.028 0.079 0.19 1 -0.36 14 15
EIF2A -0.03 0.079 -10000 0 -0.5 8 8
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.015 0.071 -10000 0 -0.37 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.044 0.086 -10000 0 -0.38 12 12
Cathepsin D/ceramide -0.018 0.095 -10000 0 -0.28 32 32
FADD -0.013 0.11 -10000 0 -0.49 13 13
KSR1 -0.027 0.088 0.18 7 -0.37 17 24
MAPK8 -0.017 0.089 -10000 0 -0.39 15 15
PRKRA -0.035 0.092 -10000 0 -0.37 19 19
PDGFA 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
IGF1 -0.12 0.29 -10000 0 -0.68 96 96
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.037 0.098 -10000 0 -0.3 35 35
CTSD 0.027 0.009 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.04 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.061 0.16 -10000 0 -0.35 93 93
PRKCD 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.027 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.025 -10000 0 -0.51 1 1
RelA/NF kappa B1 0.04 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.12 -10000 0 -0.5 14 14
TNFR1A/BAG4/TNF-alpha -0.004 0.16 -10000 0 -0.44 53 53
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.024 0.078 -10000 0 -0.39 11 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.007 0.072 0.17 21 -0.28 12 33
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.027 -10000 0 -0.51 1 1
EIF2AK2 -0.032 0.086 -10000 0 -0.49 10 10
TNF-alpha/TNFR1A/FAN -0.003 0.16 -10000 0 -0.44 52 52
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.086 -10000 0 -0.54 5 5
MAP2K2 -0.016 0.068 -10000 0 -0.4 6 6
SMPD3 -0.018 0.11 -10000 0 -0.26 61 61
TNF -0.056 0.22 -10000 0 -0.68 52 52
PKC zeta/PAR4 0.039 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.016 0.11 0.25 65 -0.24 18 83
NF kappa B1/RelA/I kappa B alpha 0.076 0.024 -10000 0 -10000 0 0
AIFM1 -0.011 0.087 0.17 21 -0.32 17 38
BCL2 -0.025 0.18 -10000 0 -0.67 34 34
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.026 0.008 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.02 0.066 -10000 0 -0.68 4 4
CDKN1A -0.007 0.067 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.029 0.033 -10000 0 -10000 0 0
mol:Ca2+ -0.025 0.066 0.24 4 -0.49 7 11
AGT 0.008 0.091 -10000 0 -0.68 7 7
CCNA2 -0.069 0.15 -10000 0 -0.37 92 92
TUBA1B 0.027 0.005 -10000 0 -10000 0 0
EGR1 -0.089 0.21 -10000 0 -0.5 94 94
CDK2/Cyclin E1 0.018 0.078 -10000 0 -0.54 1 1
MAPK3 0.009 0.025 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.008 -10000 0 -10000 0 0
MAPK1 0.007 0.022 -10000 0 -10000 0 0
PTP4A1 -0.071 0.16 -10000 0 -0.39 93 93
PTP4A3 0.015 0.041 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.009 0.026 -10000 0 -10000 0 0
SRC 0.027 0.009 -10000 0 -10000 0 0
RAC1 -0.011 0.079 -10000 0 -0.34 7 7
Rab GGTase beta/Rab GGTase alpha 0.039 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.053 0.16 -10000 0 -0.37 92 92
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.006 -10000 0 -10000 0 0
RHOC -0.011 0.078 -10000 0 -0.35 6 6
RHOA -0.012 0.083 -10000 0 -0.62 2 2
cell motility -0.006 0.1 0.3 5 -0.4 8 13
PRL-1/alpha Tubulin -0.052 0.16 -10000 0 -0.37 94 94
PRL-3/alpha1 Integrin 0.024 0.061 -10000 0 -0.53 4 4
ROCK1 -0.007 0.097 0.3 3 -0.4 8 11
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.005 -10000 0 -10000 0 0
mitosis -0.071 0.16 -10000 0 -0.39 93 93
ATF5 0.021 0.028 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.014 0.2 -10000 0 -0.92 19 19
NCK1/PAK1/Dok-R -0.028 0.088 -10000 0 -0.42 19 19
NCK1/Dok-R -0.004 0.24 -10000 0 -1.1 20 20
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
mol:beta2-estradiol 0 0.045 0.23 16 -10000 0 16
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
Rac/GDP 0.02 0.005 -10000 0 -10000 0 0
F2 -0.01 0.056 0.27 13 -10000 0 13
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.01 0.23 -10000 0 -1 19 19
FN1 -0.081 0.067 -10000 0 -10000 0 0
PLD2 -0.025 0.24 -10000 0 -1.1 19 19
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
GRB14 0.006 0.12 -10000 0 -0.66 14 14
ELK1 -0.025 0.21 -10000 0 -1 19 19
GRB7 0.002 0.055 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.009 0.25 -10000 0 -1.1 19 19
CDKN1A -0.023 0.16 0.49 4 -0.62 19 23
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.004 0.24 -10000 0 -1.1 20 20
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.011 0.17 0.52 11 -0.66 19 30
PLG -0.031 0.24 -10000 0 -1.1 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.012 0.19 -10000 0 -0.87 19 19
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 -10000 0 -0.82 16 16
BMX -0.034 0.25 -10000 0 -1.2 19 19
ANGPT1 -0.045 0.26 -10000 0 -1.3 17 17
tube development -0.037 0.17 0.48 2 -0.71 19 21
ANGPT4 -0.029 0.19 -10000 0 -0.68 35 35
response to hypoxia -0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.026 0.26 -10000 0 -1.2 19 19
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.038 0.19 -10000 0 -0.81 19 19
mol:L-citrulline 0.011 0.17 0.52 11 -0.66 19 30
AGTR1 -0.26 0.34 -10000 0 -0.68 184 184
MAPK14 -0.025 0.24 -10000 0 -1.1 19 19
Tie2/SHP2 0 0.16 -10000 0 -1.1 6 6
TEK 0.009 0.17 -10000 0 -1.3 6 6
RPS6KB1 -0.009 0.2 0.5 2 -0.88 19 21
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.51 184 184
Tie2/Ang1/GRB2 -0.016 0.25 -10000 0 -1.2 19 19
MAPK3 -0.021 0.22 -10000 0 -1 19 19
MAPK1 -0.03 0.22 -10000 0 -1 19 19
Tie2/Ang1/GRB7 -0.017 0.25 -10000 0 -1.2 19 19
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.03 0.25 -10000 0 -1.1 19 19
PI3K -0.021 0.23 -10000 0 -1.1 19 19
FES -0.028 0.24 -10000 0 -1.1 19 19
Crk/Dok-R -0.004 0.24 -10000 0 -1.1 20 20
Tie2/Ang1/ABIN2 -0.015 0.25 -10000 0 -1.2 19 19
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.005 0.19 0.5 4 -0.81 19 23
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.012 0.2 0.48 1 -0.88 19 20
Tie2/Ang2 -0.055 0.22 -10000 0 -0.98 19 19
Tie2/Ang1 -0.026 0.26 -10000 0 -1.2 19 19
FOXO1 -0.001 0.19 0.56 4 -0.82 19 23
ELF1 0.028 0.055 -10000 0 -0.6 3 3
ELF2 -0.023 0.23 -10000 0 -1.1 19 19
mol:Choline -0.022 0.23 -10000 0 -1.1 19 19
cell migration -0.014 0.056 -10000 0 -0.24 19 19
FYN -0.046 0.19 0.53 1 -0.82 19 20
DOK2 0.02 0.053 -10000 0 -0.68 2 2
negative regulation of cell cycle -0.019 0.15 0.48 4 -0.56 19 23
ETS1 0.026 0.048 -10000 0 -0.24 13 13
PXN 0.002 0.18 0.57 6 -0.72 19 25
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.005 0.19 0.57 7 -0.76 19 26
RAC1 0.027 0.006 -10000 0 -10000 0 0
TNF -0.057 0.23 -10000 0 -0.68 53 53
MAPKKK cascade -0.022 0.23 -10000 0 -1.1 19 19
RASA1 0.027 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.017 0.25 -10000 0 -1.1 19 19
NCK1 0.027 0.004 -10000 0 -10000 0 0
vasculogenesis 0.013 0.16 0.5 12 -0.59 19 31
mol:Phosphatidic acid -0.022 0.23 -10000 0 -1.1 19 19
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.011 0.17 0.52 11 -0.66 19 30
Rac1/GTP -0.006 0.18 -10000 0 -0.81 19 19
MMP2 -0.029 0.24 -10000 0 -1.1 19 19
ceramide signaling pathway

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
MAP4K4 -0.015 0.12 -10000 0 -0.45 17 17
BAG4 0.026 0.033 -10000 0 -0.68 1 1
BAD 0.007 0.069 0.36 9 -10000 0 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.009 0.15 -10000 0 -0.62 23 23
BAX 0.013 0.072 0.26 20 -10000 0 20
EnzymeConsortium:3.1.4.12 0.002 0.041 0.16 11 -0.1 16 27
IKBKB -0.015 0.12 0.29 1 -0.43 16 17
MAP2K2 0.016 0.097 0.34 22 -0.3 2 24
MAP2K1 0.011 0.087 0.33 18 -0.3 2 20
SMPD1 0.005 0.048 0.26 7 -0.15 3 10
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.46 17 17
MAP2K4 0.017 0.1 0.38 22 -10000 0 22
protein ubiquitination -0.011 0.13 0.41 5 -0.44 16 21
EnzymeConsortium:2.7.1.37 0.017 0.11 0.38 24 -0.31 2 26
response to UV 0 0.002 0.006 26 -0.002 4 30
RAF1 0.011 0.089 0.32 20 -0.32 2 22
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.005 0.061 0.24 12 -0.15 15 27
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.008 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.08 0.33 17 -10000 0 17
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.091 0.35 18 -0.28 3 21
MAPK1 -0.005 0.094 0.34 16 -0.27 5 21
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.015 0.12 -10000 0 -0.44 17 17
KSR1 0.01 0.084 0.28 23 -0.34 2 25
MAPK8 0.013 0.11 0.4 21 -0.35 6 27
TRAF2 0.025 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 13 -10000 0 13
CHUK -0.014 0.12 0.33 1 -0.43 16 17
TNF R/SODD 0.039 0.027 -10000 0 -0.51 1 1
TNF -0.056 0.22 -10000 0 -0.68 52 52
CYCS 0.02 0.084 0.27 24 -0.18 1 25
IKBKG -0.012 0.11 0.32 2 -0.44 14 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.016 0.13 -10000 0 -0.41 26 26
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.028 0.002 -10000 0 -10000 0 0
AIFM1 0.018 0.082 0.29 19 -0.18 2 21
TNF/TNF R/SODD -0.004 0.16 -10000 0 -0.44 53 53
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.009 0.13 -10000 0 -0.76 12 12
NSMAF -0.016 0.12 -10000 0 -0.44 17 17
response to hydrogen peroxide 0 0.002 0.006 26 -0.002 4 30
BCL2 -0.025 0.18 -10000 0 -0.67 34 34
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 0.033 0.068 -10000 0 -0.6 5 5
alphaV beta3 Integrin 0.038 0.092 -10000 0 -0.51 11 11
PTK2 0.01 0.14 0.4 11 -0.52 12 23
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.026 0.008 -10000 0 -10000 0 0
MFGE8 0.01 0.048 -10000 0 -10000 0 0
SRC 0.027 0.009 -10000 0 -10000 0 0
CDKN1B -0.03 0.17 -10000 0 -0.54 43 43
VEGFA 0.023 0.057 -10000 0 -0.68 3 3
ILK -0.03 0.17 -10000 0 -0.54 44 44
ROCK1 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.031 0.16 -10000 0 -0.51 43 43
PTK2B 0.01 0.097 0.36 1 -0.45 15 16
alphaV/beta3 Integrin/JAM-A 0.003 0.15 -10000 0 -0.41 49 49
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.035 0.09 -10000 0 -0.5 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.086 0.24 -10000 0 -0.44 138 138
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.001 0.097 -10000 0 -0.42 6 6
alphaV/beta3 Integrin/Syndecan-1 0.039 0.092 -10000 0 -0.51 11 11
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.093 0.24 -10000 0 -0.44 139 139
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
alphaV/beta3 Integrin/Osteopontin 0.02 0.13 -10000 0 -0.45 32 32
RPS6KB1 -0.14 0.19 0.42 2 -0.42 136 138
TLN1 0.026 0.008 -10000 0 -10000 0 0
MAPK3 -0.053 0.14 -10000 0 -0.69 12 12
GPR124 0.027 0.004 -10000 0 -10000 0 0
MAPK1 -0.063 0.15 -10000 0 -0.63 19 19
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.025 0.13 -10000 0 -0.53 21 21
cell adhesion 0.029 0.087 -10000 0 -0.5 10 10
ANGPTL3 0.007 0.024 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.063 -10000 0 -0.52 5 5
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.024 0.047 -10000 0 -0.68 2 2
ITGB3 0.008 0.11 -10000 0 -0.65 12 12
IGF1 -0.12 0.29 -10000 0 -0.68 96 96
RAC1 0.027 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.038 0.091 -10000 0 -0.51 11 11
apoptosis 0.024 0.047 -10000 0 -0.68 2 2
CD47 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.038 0.092 -10000 0 -0.51 11 11
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.033 0.11 -10000 0 -0.52 15 15
CSF1 0.016 0.087 -10000 0 -0.68 7 7
PIK3C2A -0.031 0.17 -10000 0 -0.54 45 45
PI4 Kinase/Pyk2 -0.016 0.13 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.1 -10000 0 -0.48 15 15
FAK1/Vinculin 0.021 0.12 0.38 9 -0.42 11 20
alphaV beta3/Integrin/ppsTEM5 0.038 0.092 -10000 0 -0.51 11 11
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN -0.04 0.2 -10000 0 -0.68 42 42
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.04 0.092 -10000 0 -0.51 11 11
alphaV/beta3 Integrin/TGFBR2 0.036 0.095 -10000 0 -0.49 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.073 -10000 0 -0.45 8 8
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.034 0.085 -10000 0 -0.47 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.081 0.067 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.032 0.096 -10000 0 -0.46 15 15
SDC1 0.026 0.015 -10000 0 -10000 0 0
VAV3 0.01 0.082 0.36 1 -0.44 12 13
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
IRS1 -0.058 0.23 -10000 0 -0.68 55 55
FAK1/Paxillin 0.02 0.12 0.35 8 -0.42 11 19
cell migration 0.016 0.11 0.34 6 -0.42 7 13
ITGAV 0.024 0.047 -10000 0 -0.68 2 2
PI3K 0.013 0.15 -10000 0 -0.39 50 50
SPP1 -0.031 0.15 -10000 0 -0.68 20 20
KDR 0.023 0.057 -10000 0 -0.68 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.047 -10000 0 -0.68 2 2
COL4A3 0.006 0.12 -10000 0 -0.66 14 14
angiogenesis -0.057 0.16 -10000 0 -0.64 18 18
Rac1/GTP 0.021 0.074 -10000 0 -0.41 12 12
EDIL3 0.01 0.081 -10000 0 -0.68 5 5
cell proliferation 0.036 0.095 -10000 0 -0.49 13 13
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.033 -10000 0 -0.68 1 1
Jak2/Leptin Receptor -0.004 0.12 0.32 1 -0.4 23 24
PTP1B/AKT1 0.005 0.074 0.32 2 -0.3 8 10
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0 0.089 0.34 11 -0.31 9 20
EGFR 0.014 0.068 -10000 0 -0.69 4 4
EGF/EGFR -0.036 0.16 -10000 0 -0.39 69 69
CSF1 0.016 0.087 -10000 0 -0.68 7 7
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.026 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.006 0.12 0.32 7 -0.36 21 28
Insulin Receptor/Insulin 0.015 0.069 -10000 0 -0.33 2 2
HCK 0.018 0.036 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.007 0.097 0.32 21 -0.32 5 26
EGF -0.076 0.25 -10000 0 -0.68 66 66
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.003 0.12 0.44 12 -0.32 9 21
TXN 0.025 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.032 0.15 0.27 1 -0.38 57 58
cell migration 0 0.089 0.31 9 -0.34 11 20
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.011 0.15 -10000 0 -0.68 21 21
ITGA2B -0.046 0.21 -10000 0 -0.68 47 47
CSF1R 0.023 0.037 -10000 0 -0.68 1 1
Prolactin Receptor/Prolactin 0.005 0.12 -10000 0 -0.51 21 21
FGR 0.026 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.004 0.076 0.28 3 -0.32 6 9
Crk/p130 Cas 0.011 0.075 -10000 0 -0.32 5 5
DOK1 0.013 0.097 0.41 12 -0.36 5 17
JAK2 -0.01 0.13 0.37 5 -0.4 27 32
Jak2/Leptin Receptor/Leptin -0.013 0.14 -10000 0 -0.5 24 24
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
PTPN1 0 0.09 0.34 11 -0.31 9 20
LYN 0.027 0.004 -10000 0 -10000 0 0
CDH2 -0.073 0.13 -10000 0 -0.64 15 15
SRC 0.022 0.061 0.32 1 -0.47 4 5
ITGB3 0.008 0.11 -10000 0 -0.66 12 12
CAT1/PTP1B -0.061 0.16 0.43 14 -0.37 40 54
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.021 0.081 -10000 0 -0.54 3 3
mol:H2O2 -0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.014 0.14 -10000 0 -0.52 24 24
negative regulation of transcription -0.008 0.13 0.37 5 -0.39 27 32
FCGR2A 0.017 0.046 -10000 0 -0.68 1 1
FER 0.021 0.058 -10000 0 -0.69 3 3
alphaIIb/beta3 Integrin -0.031 0.19 -10000 0 -0.54 55 55
BLK -0.19 0.32 -10000 0 -0.67 136 136
Insulin Receptor/Insulin/Shc 0.042 0.019 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.02 0.068 -10000 0 -0.6 5 5
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.092 0.18 0.41 4 -0.47 39 43
PRL -0.006 0.02 -10000 0 -10000 0 0
SOCS3 -0.055 0.33 -10000 0 -1.3 30 30
SPRY2 0.022 0.048 -10000 0 -0.69 2 2
Insulin Receptor/Insulin/IRS1 -0.015 0.16 -10000 0 -0.45 54 54
CSF1/CSF1R 0.007 0.098 0.28 1 -0.44 11 12
Ras protein signal transduction 0.023 0.098 0.46 19 -10000 0 19
IRS1 -0.058 0.23 -10000 0 -0.68 55 55
INS 0.01 0.015 -10000 0 -10000 0 0
LEP 0.009 0.032 -10000 0 -10000 0 0
STAT5B 0.002 0.097 0.32 11 -0.29 15 26
STAT5A 0.002 0.097 0.32 11 -0.29 15 26
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.077 0.28 1 -0.36 7 8
CSN2 0.002 0.063 0.81 1 -10000 0 1
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
LAT 0.019 0.083 0.29 3 -0.46 10 13
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.011 0.085 -10000 0 -0.68 6 6
SHC1 0.026 0.008 -10000 0 -10000 0 0
NOX4 -0.04 0.075 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.02 0.12 -10000 0 -0.45 21 21
MAP4K1 0.009 0.081 -10000 0 -0.68 5 5
MAP3K8 0.016 0.089 -10000 0 -0.64 8 8
PRKCB 0.008 0.071 -10000 0 -0.68 3 3
DBNL 0.027 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.002 0.079 -10000 0 -0.32 21 21
JUN -0.08 0.2 0.42 2 -0.49 50 52
MAP3K7 0.002 0.079 -10000 0 -0.32 22 22
GRAP2 -0.017 0.14 -10000 0 -0.55 29 29
CRK 0.026 0.007 -10000 0 -10000 0 0
MAP2K4 -0.004 0.098 0.38 2 -0.38 16 18
LAT 0.021 0.06 -10000 0 -0.6 4 4
LCP2 0.024 0.019 -10000 0 -10000 0 0
MAPK8 -0.002 0.13 -10000 0 -0.58 21 21
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.085 -10000 0 -0.34 22 22
LAT/GRAP2/SLP76/HPK1/HIP-55 0.03 0.12 -10000 0 -0.43 21 21
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.032 0.11 -10000 0 -0.34 55 55
FRAP1 0.009 0.052 0.36 3 -0.42 2 5
AKT1 -0.027 0.097 -10000 0 -0.29 52 52
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.003 0.091 0.26 1 -0.42 3 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.037 -10000 0 -0.24 1 1
TSC2 0.026 0.007 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.076 -10000 0 -0.39 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.025 0.13 -10000 0 -0.38 55 55
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.015 0.045 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.017 0.1 0.36 20 -0.35 4 24
MAP3K5 0.005 0.03 0.18 1 -0.21 7 8
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.031 0.17 2 -0.21 7 9
mol:LY294002 0 0.001 0.001 1 -0.002 68 69
EIF4B 0.023 0.12 0.45 21 -0.33 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.073 0.34 6 -0.31 3 9
eIF4E/eIF4G1/eIF4A1 0.015 0.028 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.009 0.13 -10000 0 -0.36 56 56
mTOR/RHEB/GTP/Raptor/GBL 0.003 0.048 0.28 3 -0.24 2 5
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.011 0.082 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 68 69
FKBP12/Rapamycin 0.02 0.005 -10000 0 -10000 0 0
PDPK1 -0.033 0.11 0.18 1 -0.32 53 54
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.077 -10000 0 -0.47 9 9
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.009 -10000 0 -10000 0 0
TSC1/TSC2 0.004 0.098 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 68 -0.001 1 69
RPS6 0.026 0.008 -10000 0 -10000 0 0
PPP5C 0.026 0.008 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.044 0.14 -10000 0 -0.38 63 63
INS -0.016 0.003 -10000 0 -10000 0 0
PTEN 0.025 0.02 -10000 0 -0.36 1 1
PDK2 -0.031 0.1 0.22 3 -0.31 52 55
EIF4EBP1 0.016 0.1 -10000 0 -0.93 5 5
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
PPP2R5D 0.019 0.076 0.37 13 -0.38 2 15
peptide biosynthetic process 0.013 0.016 -10000 0 -10000 0 0
RHEB 0.027 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.008 18 -0.003 3 21
EEF2 0.014 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.031 0.091 -10000 0 -0.83 5 5
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.009 0.1 -10000 0 -0.53 9 9
alphaM/beta2 Integrin/GPIbA -0.001 0.12 -10000 0 -0.5 17 17
alphaM/beta2 Integrin/proMMP-9 -0.022 0.16 -10000 0 -0.5 39 39
PLAUR -0.022 0.069 -10000 0 -10000 0 0
HMGB1 0.008 0.037 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.012 0.089 -10000 0 -0.57 5 5
AGER -0.042 0.19 -10000 0 -0.7 32 32
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.017 0.037 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.04 0.2 -10000 0 -0.48 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 36 36
CYR61 -0.18 0.32 -10000 0 -0.68 135 135
TLN1 0.026 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.002 0.091 -10000 0 -0.38 9 9
RHOA 0.027 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.014 0.082 -10000 0 -0.68 6 6
MYH2 -0.033 0.1 -10000 0 -0.41 11 11
MST1R 0.02 0.067 -10000 0 -0.68 4 4
leukocyte activation during inflammatory response 0.013 0.083 -10000 0 -0.5 5 5
APOB 0.008 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.019 0.069 -10000 0 -0.62 5 5
JAM3 0.027 0.005 -10000 0 -10000 0 0
GP1BA 0.002 0.12 -10000 0 -0.63 14 14
alphaM/beta2 Integrin/CTGF -0.05 0.19 -10000 0 -0.48 67 67
alphaM/beta2 Integrin -0.025 0.093 -10000 0 -0.38 14 14
JAM3 homodimer 0.027 0.005 -10000 0 -10000 0 0
ICAM2 0.026 0.007 -10000 0 -10000 0 0
ICAM1 -0.019 0.068 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.025 0.094 -10000 0 -0.37 15 15
cell adhesion -0.001 0.12 -10000 0 -0.5 17 17
NFKB1 -0.12 0.26 0.38 1 -0.69 52 53
THY1 0.026 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.022 0.026 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.026 0.1 -10000 0 -0.48 10 10
IL6 -0.21 0.39 -10000 0 -0.96 89 89
ITGB2 -0.004 0.059 -10000 0 -0.71 1 1
elevation of cytosolic calcium ion concentration -0.02 0.11 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.027 0.098 -10000 0 -0.51 8 8
JAM2 0.02 0.066 -10000 0 -0.68 4 4
alphaM/beta2 Integrin/ICAM1 0.03 0.11 -10000 0 -0.52 8 8
alphaM/beta2 Integrin/uPA/Plg 0.013 0.1 -10000 0 -0.53 5 5
RhoA/GTP -0.028 0.11 -10000 0 -0.38 18 18
positive regulation of phagocytosis -0.009 0.1 -10000 0 -0.57 5 5
Ron/MSP 0.034 0.059 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/uPAR/uPA 0.013 0.11 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/uPAR 0.004 0.097 -10000 0 -0.55 5 5
PLAU -0.043 0.075 -10000 0 -10000 0 0
PLAT 0.018 0.069 -10000 0 -0.68 4 4
actin filament polymerization -0.031 0.1 0.31 1 -0.4 11 12
MST1 0.026 0.033 -10000 0 -0.68 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.018 0.085 -10000 0 -0.5 5 5
TNF -0.17 0.35 0.38 1 -0.92 68 69
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.002 0.1 -10000 0 -0.52 6 6
fibrinolysis 0.01 0.099 -10000 0 -0.52 5 5
HCK 0.018 0.036 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.025 0.094 -10000 0 -0.37 15 15
VTN -0.04 0.2 -10000 0 -0.68 42 42
alphaM/beta2 Integrin/CYR61 -0.12 0.24 -10000 0 -0.47 137 137
LPA -0.006 0.026 -10000 0 -10000 0 0
LRP1 0.025 0.033 -10000 0 -0.68 1 1
cell migration -0.029 0.16 -10000 0 -0.48 38 38
FN1 -0.081 0.067 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.013 0.09 -10000 0 -0.57 5 5
MPO 0.014 0.075 -10000 0 -0.68 5 5
KNG1 -0.004 0.037 -10000 0 -10000 0 0
RAP1/GDP 0.035 0.009 -10000 0 -10000 0 0
ROCK1 -0.026 0.1 -10000 0 -0.44 8 8
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.013 0.017 -10000 0 -10000 0 0
CTGF -0.072 0.24 -10000 0 -0.66 66 66
alphaM/beta2 Integrin/Hck 0.009 0.094 -10000 0 -0.57 5 5
ITGAM -0.007 0.083 -10000 0 -0.73 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.02 0.11 -10000 0 -0.53 10 10
HP -0.02 0.099 -10000 0 -0.68 6 6
leukocyte adhesion -0.032 0.17 -10000 0 -0.53 24 24
SELP 0.014 0.082 -10000 0 -0.68 6 6
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.038 0.12 0.88 6 -10000 0 6
VDR 0.027 0.009 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.004 0.1 -10000 0 -0.42 5 5
RXRs/LXRs/DNA/Oxysterols -0.009 0.15 -10000 0 -0.42 47 47
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.022 0.063 -10000 0 -0.29 18 18
RXRs/NUR77 -0.088 0.24 -10000 0 -0.45 122 122
RXRs/PPAR -0.018 0.08 -10000 0 -0.4 9 9
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.051 0.07 -10000 0 -0.38 11 11
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.009 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.034 0.067 -10000 0 -0.37 11 11
RARG 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 0.049 0.12 0.56 24 -10000 0 24
RARs/THRs/DNA/SMRT 0.022 0.063 -10000 0 -0.29 18 18
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.039 0.096 -10000 0 -0.48 3 3
NR1H4 -0.005 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.059 0.12 -10000 0 -0.49 3 3
NR1H2 0.023 0.024 -10000 0 -10000 0 0
NR1H3 0.023 0.027 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.05 0.079 -10000 0 -0.46 2 2
NR4A1 -0.18 0.32 -10000 0 -0.68 134 134
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.054 -10000 0 -0.31 2 2
RXRG -0.1 0.074 -10000 0 -0.58 4 4
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.021 0.026 -10000 0 -10000 0 0
RXRB 0.023 0.027 -10000 0 -10000 0 0
THRB 0.014 0.094 -10000 0 -0.64 9 9
PPARG 0.017 0.081 -10000 0 -0.68 6 6
PPARD 0.028 0.003 -10000 0 -10000 0 0
TNF -0.097 0.37 -10000 0 -1.1 53 53
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.008 0.15 -10000 0 -0.41 47 47
PPARA 0.02 0.013 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.01 0.11 -10000 0 -0.68 11 11
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 135 135
SREBF1 -0.01 0.13 -10000 0 -0.59 3 3
RXRs/RXRs/DNA/9cRA 0.039 0.096 -10000 0 -0.48 3 3
ABCA1 -0.009 0.14 -10000 0 -0.53 5 5
RARs/THRs 0.059 0.091 -10000 0 -0.39 17 17
RXRs/FXR 0.05 0.084 -10000 0 -0.48 2 2
BCL2 -0.025 0.18 -10000 0 -0.67 34 34
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.018 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.044 0.13 0.52 11 -10000 0 11
IL27/IL27R/JAK1 -0.012 0.17 -10000 0 -0.55 3 3
TBX21 -0.064 0.18 0.39 5 -0.59 26 31
IL12B 0.004 0.083 -10000 0 -0.68 6 6
IL12A -0.05 0.16 -10000 0 -0.51 49 49
IL6ST -0.068 0.24 -10000 0 -0.68 58 58
IL27RA/JAK1 0.019 0.053 0.55 1 -10000 0 1
IL27 0.011 0.027 -10000 0 -10000 0 0
TYK2 0.019 0.021 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.046 0.14 -10000 0 -0.49 4 4
T-helper 2 cell differentiation 0.044 0.13 0.52 11 -10000 0 11
T cell proliferation during immune response 0.044 0.13 0.52 11 -10000 0 11
MAPKKK cascade -0.044 0.13 -10000 0 -0.52 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.024 -10000 0 -10000 0 0
IL12RB1 0.008 0.064 -10000 0 -0.58 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.058 0.19 0.5 10 -0.58 21 31
IL27/IL27R/JAK2/TYK2 -0.045 0.13 -10000 0 -0.52 11 11
positive regulation of T cell mediated cytotoxicity -0.044 0.13 -10000 0 -0.52 11 11
STAT1 (dimer) -0.025 0.21 0.53 9 -0.67 10 19
JAK2 0.02 0.027 -10000 0 -0.37 1 1
JAK1 0.027 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.033 0.14 -10000 0 -0.5 11 11
T cell proliferation -0.11 0.19 -10000 0 -0.54 46 46
IL12/IL12R/TYK2/JAK2 -0.074 0.24 -10000 0 -0.84 26 26
IL17A -0.046 0.13 -10000 0 -0.49 4 4
mast cell activation 0.044 0.13 0.52 11 -10000 0 11
IFNG -0.016 0.051 0.099 2 -0.13 64 66
T cell differentiation -0.004 0.008 0.014 1 -0.023 54 55
STAT3 (dimer) -0.032 0.14 -10000 0 -0.48 11 11
STAT5A (dimer) -0.032 0.14 -10000 0 -0.48 11 11
STAT4 (dimer) -0.039 0.15 -10000 0 -0.5 15 15
STAT4 0.003 0.1 -10000 0 -0.59 11 11
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.023 0.15 -10000 0 -0.52 4 4
GATA3 -0.059 0.3 -10000 0 -1.3 23 23
IL18 -0.012 0.077 -10000 0 -0.49 10 10
positive regulation of mast cell cytokine production -0.031 0.13 -10000 0 -0.47 11 11
IL27/EBI3 -0.028 0.059 -10000 0 -0.26 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.11 0.27 -10000 0 -0.68 83 83
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.011 0.022 -10000 0 -10000 0 0
IL1B -0.033 0.14 -10000 0 -0.52 35 35
EBI3 -0.05 0.073 -10000 0 -0.38 1 1
TNF -0.054 0.16 -10000 0 -0.52 52 52
TCGA08_rtk_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
PDGFRA -0.19 0.32 -10000 0 -0.68 140 140
HRAS 0.026 0.011 -10000 0 -10000 0 0
EGFR 0.02 0.066 -10000 0 -0.68 4 4
AKT 0.016 0.087 0.34 10 -10000 0 10
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.026 0.008 -10000 0 -10000 0 0
FOXO4 0.026 0.008 -10000 0 -10000 0 0
MET -0.03 0.072 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.011 0.099 -10000 0 -0.68 9 9
PIK3R3 0.027 0.005 -10000 0 -10000 0 0
PIK3R2 0.026 0.008 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.033 0.088 -10000 0 -0.17 125 125
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.037 0.069 0.36 8 -10000 0 8
PI3K -0.016 0.1 0.41 8 -0.18 48 56
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
FOXO 0.047 0.061 0.32 8 -10000 0 8
AKT2 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.019 -10000 0 -0.36 1 1
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.042 -10000 0 -0.82 1 1
VEGFR1 homodimer/NRP1 0.015 0.039 -10000 0 -0.82 1 1
mol:DAG -0.024 0.13 -10000 0 -0.41 48 48
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.062 -10000 0 -0.64 3 3
CaM/Ca2+ -0.008 0.13 -10000 0 -0.38 48 48
HIF1A 0.033 0.02 -10000 0 -0.38 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.023 0.14 -10000 0 -0.7 4 4
PLCG1 -0.024 0.13 -10000 0 -0.41 48 48
NOS3 -0.016 0.12 -10000 0 -0.82 1 1
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:NO -0.011 0.13 0.47 3 -0.77 1 4
FLT1 0.02 0.044 -10000 0 -0.92 1 1
PGF -0.047 0.22 -10000 0 -0.67 48 48
VEGFR1 homodimer/NRP2/VEGFR121 0.045 0.065 -10000 0 -0.64 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
eNOS/Hsp90 0.002 0.13 -10000 0 -0.74 1 1
endothelial cell proliferation -0.043 0.16 0.36 2 -0.44 45 47
mol:Ca2+ -0.024 0.13 -10000 0 -0.4 48 48
MAPK3 -0.044 0.14 0.35 2 -0.42 18 20
MAPK1 -0.047 0.14 0.35 1 -0.43 14 15
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
PLGF homodimer -0.047 0.21 -10000 0 -0.67 48 48
PRKACA 0.026 0.008 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.014 0.093 -10000 0 -0.68 8 8
VEGFA homodimer 0.023 0.057 -10000 0 -0.68 3 3
VEGFR1 homodimer/VEGFA homodimer 0.031 0.066 -10000 0 -0.69 3 3
platelet activating factor biosynthetic process -0.047 0.13 -10000 0 -0.81 2 2
PI3K 0.013 0.15 -10000 0 -0.39 49 49
PRKCA -0.045 0.15 -10000 0 -0.39 63 63
PRKCB -0.036 0.13 -10000 0 -0.39 47 47
VEGFR1 homodimer/PLGF homodimer -0.016 0.15 -10000 0 -0.45 48 48
VEGFA 0.023 0.057 -10000 0 -0.68 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.024 0.13 -10000 0 -0.41 48 48
RASA1 0.019 0.039 -10000 0 -0.77 1 1
NRP2 0.014 0.042 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.044 -10000 0 -0.91 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.001 0.14 0.55 4 -0.63 4 8
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
mol:PI-3-4-5-P3 0.012 0.14 -10000 0 -0.39 49 49
mol:L-citrulline -0.011 0.13 0.47 3 -0.77 1 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.064 -10000 0 -0.62 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.064 -10000 0 -0.64 3 3
CD2AP 0.028 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.024 0.14 -10000 0 -0.38 46 46
PDPK1 -0.02 0.14 0.34 3 -1 2 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.078 -10000 0 -0.75 3 3
mol:NADP -0.011 0.13 0.47 3 -0.77 1 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.063 -10000 0 -0.6 3 3
VEGFR1 homodimer/NRP2 0.025 0.048 -10000 0 -0.82 1 1
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.002 0.042 -10000 0 -0.44 4 4
ADCY5 -0.056 0.15 -10000 0 -0.44 63 63
ADCY6 0.002 0.042 -10000 0 -0.44 4 4
ADCY7 0.002 0.042 -10000 0 -0.44 4 4
ADCY1 -0.001 0.056 -10000 0 -0.45 7 7
ADCY2 -0.037 0.13 -10000 0 -0.45 41 41
ADCY3 0.002 0.042 -10000 0 -0.44 4 4
ADCY8 -0.048 0.051 -10000 0 -0.5 4 4
PRKCE 0.004 0.049 -10000 0 -0.51 4 4
ADCY9 0.002 0.042 -10000 0 -0.44 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.035 0.095 0.37 6 -0.35 15 21
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.026 0.37 1 -10000 0 1
HSPA8 0.02 0.06 -10000 0 -0.6 4 4
SMAD3/SMAD4/ER alpha -0.007 0.14 -10000 0 -0.48 22 22
AKT1 0.026 0.006 -10000 0 -10000 0 0
GSC -0.18 0.5 -10000 0 -1.4 66 66
NKX2-5 0.018 0.015 -10000 0 -10000 0 0
muscle cell differentiation -0.009 0.082 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.037 0.095 -10000 0 -10000 0 0
SMAD4 -0.008 0.071 -10000 0 -0.26 1 1
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.042 0.071 -10000 0 -0.44 3 3
SMAD3/SMAD4/VDR 0.049 0.075 -10000 0 -10000 0 0
MYC 0.013 0.1 -10000 0 -0.65 10 10
CDKN2B -0.02 0.11 -10000 0 -0.49 2 2
AP1 -0.2 0.41 -10000 0 -0.76 143 143
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.027 0.067 -10000 0 -0.56 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.035 -10000 0 -10000 0 0
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 0.005 0.053 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.02 0.079 -10000 0 -10000 0 0
GATA3 -0.009 0.15 -10000 0 -0.63 23 23
SKI/SIN3/HDAC complex/NCoR1 0.028 0.057 -10000 0 -0.71 2 2
MEF2C/TIF2 -0.033 0.14 -10000 0 -0.41 35 35
endothelial cell migration -0.023 0.081 1.3 1 -10000 0 1
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.008 -10000 0 -10000 0 0
RBBP4 0.023 0.047 -10000 0 -0.68 2 2
RUNX2 -0.015 0.08 -10000 0 -0.68 2 2
RUNX3 0.012 0.094 -10000 0 -0.68 8 8
RUNX1 -0.04 0.074 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.026 0.006 -10000 0 -10000 0 0
VDR 0.027 0.009 -10000 0 -10000 0 0
CDKN1A 0.02 0.043 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.013 0.12 -10000 0 -0.28 44 44
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 0.023 0.082 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.006 0.12 -10000 0 -0.48 14 14
SMAD3/SMAD4/ATF3 -0.08 0.24 -10000 0 -0.51 100 100
SAP30 0.025 0.033 -10000 0 -0.68 1 1
Cbp/p300/PIAS3 0.049 0.045 -10000 0 -10000 0 0
JUN -0.2 0.4 0.3 1 -0.75 143 144
SMAD3/SMAD4/IRF7 0.024 0.08 -10000 0 -10000 0 0
TFE3 0.03 0.01 -10000 0 -10000 0 0
COL1A2 0.029 0.041 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.014 0.098 0.4 3 -10000 0 3
DLX1 -0.012 0.16 -10000 0 -0.66 26 26
TCF3 0.025 0.008 -10000 0 -10000 0 0
FOS -0.18 0.34 -10000 0 -0.74 122 122
SMAD3/SMAD4/Max 0.019 0.08 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.037 -10000 0 -0.43 1 1
ZBTB17 0.028 0.006 -10000 0 -10000 0 0
LAMC1 0.011 0.06 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.021 0.08 -10000 0 -10000 0 0
IRF7 0.027 0.01 -10000 0 -10000 0 0
ESR1 -0.02 0.16 -10000 0 -0.66 24 24
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.015 0.1 0.39 3 -0.89 1 4
SMAD2-3/SMAD4 0.01 0.095 -10000 0 -0.29 2 2
Cbp/p300/Src-1 0.047 0.035 -10000 0 -10000 0 0
IGHV3OR16-13 0.002 0.03 -10000 0 -0.32 2 2
TGIF2/HDAC complex 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.03 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.033 -10000 0 -0.68 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
SNIP1 0.024 0.033 -10000 0 -0.68 1 1
GCN5L2 0.005 0.014 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.029 0.081 -10000 0 -10000 0 0
MSG1/HSC70 -0.066 0.07 -10000 0 -0.47 8 8
SMAD2 0.011 0.048 -10000 0 -10000 0 0
SMAD3 0.005 0.059 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.012 0.068 -10000 0 -0.45 4 4
SMAD2/SMAD2/SMAD4 0.003 0.036 0.23 3 -10000 0 3
NCOR1 0.026 0.007 -10000 0 -10000 0 0
NCOA2 -0.035 0.2 -10000 0 -0.68 40 40
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.03 0.014 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.045 0.094 -10000 0 -10000 0 0
IFNB1 -0.002 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.002 0.11 -10000 0 -0.62 2 2
CITED1 -0.097 0.076 -10000 0 -0.6 4 4
SMAD2-3/SMAD4/ARC105 0.011 0.086 -10000 0 -10000 0 0
RBL1 0.013 0.098 -10000 0 -0.68 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.012 0.034 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.047 0.071 -10000 0 -0.43 8 8
SMAD7 -0.092 0.25 -10000 0 -0.54 87 87
MYC/MIZ-1 0.029 0.079 -10000 0 -0.49 10 10
SMAD3/SMAD4 0.023 0.11 0.29 33 -0.52 1 34
IL10 -0.03 0.15 -10000 0 -0.52 31 31
PIASy/HDAC complex 0.017 0.02 -10000 0 -10000 0 0
PIAS3 0.027 0.009 -10000 0 -10000 0 0
CDK2 0.031 0.011 -10000 0 -10000 0 0
IL5 -0.023 0.11 -10000 0 -0.41 21 21
CDK4 0.031 0.012 -10000 0 -10000 0 0
PIAS4 0.017 0.02 -10000 0 -10000 0 0
ATF3 -0.13 0.29 -10000 0 -0.68 101 101
SMAD3/SMAD4/SP1 0.032 0.082 -10000 0 -10000 0 0
FOXG1 0.007 0.044 -10000 0 -0.68 1 1
FOXO3 0.015 0.008 -10000 0 -10000 0 0
FOXO1 0.014 0.008 -10000 0 -10000 0 0
FOXO4 0.015 0.008 -10000 0 -10000 0 0
heart looping -0.014 0.1 0.39 3 -0.88 1 4
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.006 0.14 -10000 0 -0.49 24 24
MYOD1 -0.014 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.015 0.081 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 -0.001 0.14 -10000 0 -0.42 31 31
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.033 -10000 0 -0.68 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.03 0.12 -10000 0 -0.5 7 7
SMAD3/SMAD4/SP1-3 0.052 0.081 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.032 0.01 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.028 0.12 -10000 0 -0.46 2 2
ITGB5 0.014 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.031 0.049 -10000 0 -0.57 2 2
SMAD3/SMAD4/AR -0.18 0.26 -10000 0 -0.49 182 182
AR -0.26 0.34 -10000 0 -0.67 188 188
negative regulation of cell growth -0.024 0.12 -10000 0 -0.42 8 8
SMAD3/SMAD4/MYOD 0.015 0.081 -10000 0 -10000 0 0
E2F5 0.026 0.033 -10000 0 -0.68 1 1
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.026 0.098 -10000 0 -0.33 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.036 -10000 0 -10000 0 0
TFDP1 0.025 0.019 -10000 0 -0.36 1 1
SMAD3/SMAD4/AP1 -0.19 0.43 -10000 0 -0.77 143 143
SMAD3/SMAD4/RUNX2 0.015 0.098 -10000 0 -0.41 3 3
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.005 -10000 0 -10000 0 0
ATF2 0.005 0.12 -10000 0 -0.66 15 15
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.03 0.075 -9999 0 -0.38 14 14
RGS9BP -0.017 0.17 -9999 0 -0.67 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.042 0.2 -9999 0 -0.66 45 45
mol:Na + 0.018 0.032 -9999 0 -10000 0 0
mol:ADP -0.046 0.15 -9999 0 -0.5 44 44
GNAT2 0.016 0.021 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.026 0.18 -9999 0 -0.45 69 69
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.029 0.01 -9999 0 -10000 0 0
GRK7 0.006 0.022 -9999 0 -10000 0 0
CNGB3 -0.008 0.018 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.026 -9999 0 -10000 0 0
Cone PDE6 -0.006 0.17 -9999 0 -0.4 67 67
Cone Metarhodopsin II -0.012 0.13 -9999 0 -0.4 44 44
Na + (4 Units) 0.024 0.038 -9999 0 -10000 0 0
GNAT2/GDP -0.011 0.16 -9999 0 -0.4 65 65
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.002 0.024 -9999 0 -10000 0 0
Cone Transducin 0.033 0.08 -9999 0 -0.41 14 14
SLC24A2 -0.006 0.029 -9999 0 -10000 0 0
GNB3/GNGT2 0.021 0.096 -9999 0 -0.51 14 14
GNB3 0.007 0.12 -9999 0 -0.68 13 13
GNAT2/GTP 0.018 0.008 -9999 0 -10000 0 0
CNGA3 0.009 0.049 -9999 0 -10000 0 0
ARR3 -0.002 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.019 0.032 -9999 0 -10000 0 0
mol:Pi -0.026 0.18 -9999 0 -0.45 69 69
Cone CNG Channel 0.044 0.033 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.006 0.029 -9999 0 -10000 0 0
RGS9 -0.042 0.21 -9999 0 -0.68 44 44
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.024 0.036 -9999 0 -0.68 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.004 0.02 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

Figure 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
Sortilin/TRAF6 0.037 0.038 -10000 0 -0.51 2 2
Necdin/E2F1 -0.001 0.079 -10000 0 -0.56 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.057 0.094 -10000 0 -0.41 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.25 -10000 0 -0.45 209 209
NT-4/5 (dimer)/p75(NTR) -0.011 0.14 -10000 0 -0.53 27 27
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.004 0.099 0.36 1 -0.41 18 19
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.68 10 10
MGDIs/NGR/p75(NTR)/LINGO1 0.023 0.094 -10000 0 -0.45 15 15
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.027 0.11 -10000 0 -0.43 25 25
LINGO1 0.02 0.032 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.029 -10000 0 -0.35 2 2
proBDNF (dimer) 0.009 0.1 -10000 0 -0.68 10 10
NTRK1 0.012 0.028 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.022 0.14 0.47 10 -0.5 10 20
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.007 0.091 -10000 0 -0.46 15 15
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.031 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.095 -10000 0 -0.42 16 16
MAGEH1 0.026 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.045 0.1 -10000 0 -0.43 19 19
Mammalian IAPs/DIABLO 0.046 0.094 -10000 0 -0.4 18 18
proNGF (dimer) 0.021 0.058 -10000 0 -0.68 3 3
MAGED1 0.026 0.008 -10000 0 -10000 0 0
APP 0.027 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.12 -10000 0 -0.65 13 13
ZNF274 0.026 0.008 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.086 -10000 0 -0.4 15 15
NGF 0.021 0.058 -10000 0 -0.68 3 3
cell cycle arrest 0.056 0.14 0.46 15 -0.39 15 30
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.071 -10000 0 -0.32 17 17
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.019 0.13 -10000 0 -0.46 29 29
NCSTN 0.026 0.008 -10000 0 -10000 0 0
mol:GTP 0.034 0.1 -10000 0 -0.45 17 17
PSENEN 0.026 0.007 -10000 0 -10000 0 0
mol:ceramide 0.003 0.093 -10000 0 -0.43 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.06 -10000 0 -0.39 4 4
p75(NTR)/beta APP 0.005 0.1 -10000 0 -0.51 15 15
BEX1 -0.28 0.35 -10000 0 -0.68 200 200
mol:GDP -0.018 0.089 -10000 0 -0.44 17 17
NGF (dimer) 0.038 0.11 -10000 0 -0.42 25 25
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.034 0.091 -10000 0 -0.42 15 15
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
RAC1/GTP 0.031 0.085 -10000 0 -0.4 16 16
MYD88 0.027 0.004 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.034 0.1 -10000 0 -0.46 17 17
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.005 0.054 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.16 -10000 0 -0.68 23 23
TP53 -0.003 0.1 0.35 1 -0.37 24 25
PRDM4 0 0.091 -10000 0 -0.43 15 15
BDNF (dimer) 0.008 0.14 -10000 0 -0.44 31 31
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.051 0.091 -10000 0 -0.41 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.047 0.099 -10000 0 -0.43 17 17
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.008 -10000 0 -10000 0 0
MAPK10 0.015 0.12 0.38 15 -0.4 14 29
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.003 0.094 -10000 0 -0.43 15 15
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.036 0.098 -10000 0 -0.46 16 16
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.028 -10000 0 -0.51 1 1
NT3 (dimer)/p75(NTR) -0.026 0.16 -10000 0 -0.52 37 37
MAPK8 0.011 0.12 0.39 13 -0.41 15 28
MAPK9 0.009 0.1 0.35 9 -0.39 13 22
APAF1 0.025 0.033 -10000 0 -0.68 1 1
NTF3 -0.016 0.16 -10000 0 -0.68 23 23
NTF4 0.003 0.12 -10000 0 -0.66 13 13
NDN 0.019 0.074 -10000 0 -0.68 5 5
RAC1/GDP 0.02 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.053 0.087 -10000 0 -0.38 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.06 0.055 -10000 0 -0.52 3 3
RhoA-B-C/GTP 0.033 0.099 -10000 0 -0.45 17 17
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.11 -10000 0 -0.39 24 24
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.04 0.11 -10000 0 -0.41 25 25
PRKACB 0.025 0.033 -10000 0 -0.68 1 1
proBDNF (dimer)/p75 ECD 0.023 0.089 -10000 0 -0.51 12 12
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.009 0.15 -10000 0 -0.62 23 23
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.07 0.15 0.55 10 -0.4 15 25
BAD 0.029 0.15 0.47 25 -0.4 15 40
RIPK2 0.027 0.005 -10000 0 -10000 0 0
NGFR -0.016 0.13 -10000 0 -0.68 15 15
CYCS 0.008 0.1 0.36 12 -0.41 15 27
ADAM17 0.024 0.047 -10000 0 -0.68 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.046 0.1 -10000 0 -0.43 17 17
BCL2L11 0.03 0.15 0.46 25 -0.4 15 40
BDNF (dimer)/p75(NTR) -0.008 0.13 -10000 0 -0.51 25 25
PI3K 0.046 0.1 -10000 0 -0.43 18 18
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.05 0.094 -10000 0 -0.43 15 15
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.002 0.11 -10000 0 -0.51 17 17
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.047 0.095 -10000 0 -0.43 15 15
TRAF6 0.024 0.047 -10000 0 -0.68 2 2
RAC1 0.027 0.006 -10000 0 -10000 0 0
PRKCZ 0.027 0.006 -10000 0 -10000 0 0
PLG -0.013 0.017 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.006 0.1 -10000 0 -0.4 24 24
SQSTM1 0.027 0.006 -10000 0 -10000 0 0
NGFRAP1 0.026 0.008 -10000 0 -10000 0 0
CASP3 0.032 0.15 0.46 25 -0.37 15 40
E2F1 -0.017 0.068 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.05 0.076 -10000 0 -0.47 3 3
NGF (dimer)/TRKA 0.028 0.05 -10000 0 -0.52 3 3
MMP7 -0.08 0.16 -10000 0 -0.67 24 24
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.098 -10000 0 -0.41 17 17
MMP3 -0.016 0.047 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.014 0.096 -10000 0 -0.54 5 5
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.012 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.025 0.51 1 -10000 0 1
CDKN1A -0.007 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
BAX 0.026 0.008 -10000 0 -10000 0 0
FOXO3 -0.004 0.008 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
TAT 0.011 0.023 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.009 0.009 -10000 0 -10000 0 0
PPARGC1A -0.28 0.35 -10000 0 -0.68 201 201
FHL2 -0.027 0.19 -10000 0 -0.68 35 35
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.026 0.031 -10000 0 -0.51 1 1
HIST2H4A 0.013 0.025 -10000 0 -0.51 1 1
SIRT1/FOXO3a 0.039 0.052 -10000 0 -0.31 2 2
SIRT1 0.022 0.033 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.029 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.007 0.072 -10000 0 -0.28 14 14
apoptosis -0.037 0.033 0.44 1 -10000 0 1
SIRT1/PGC1A -0.18 0.24 -10000 0 -0.44 201 201
p53/SIRT1 0.028 0.028 -10000 0 -0.52 1 1
SIRT1/FOXO4 -0.004 0.064 -10000 0 -0.24 12 12
FOXO1/FHL2/SIRT1 0.01 0.12 -10000 0 -0.41 36 36
HIST1H1E 0.007 0.049 -10000 0 -0.35 8 8
SIRT1/p300 0.026 0.031 -10000 0 -0.51 1 1
muscle cell differentiation -0.03 0.03 0.45 1 -10000 0 1
TP53 0.023 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.034 -10000 0 -0.44 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.026 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.032 0.028 -10000 0 -0.51 1 1
ACSS2 0.013 0.025 -10000 0 -0.51 1 1
SIRT1/PCAF/MYOD 0.03 0.031 -10000 0 -0.45 1 1
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.034 0.009 -9999 0 -10000 0 0
PRKCZ 0.027 0.006 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.013 0.065 -9999 0 -0.38 2 2
IRAK/TOLLIP 0.03 0.012 -9999 0 -10000 0 0
IKBKB 0.027 0.004 -9999 0 -10000 0 0
IKBKG 0.025 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.055 0.21 -9999 0 -0.54 68 68
IL1A -0.032 0.19 -9999 0 -0.67 36 36
IL1B -0.027 0.15 -9999 0 -0.52 36 36
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.039 -9999 0 -0.37 2 2
IL1R2 -0.042 0.19 -9999 0 -0.66 38 38
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.052 -9999 0 -0.28 1 1
TOLLIP 0.027 0.005 -9999 0 -10000 0 0
TICAM2 0.018 0.074 -9999 0 -0.68 5 5
MAP3K3 0.026 0.007 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.033 0.06 -9999 0 -10000 0 0
JUN -0.083 0.16 -9999 0 -0.37 102 102
MAP3K7 0.028 0.003 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.13 -9999 0 -0.39 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88 0.035 0.13 -9999 0 -0.41 35 35
PIK3R1 0.027 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.13 -9999 0 -0.39 35 35
IL1 beta fragment/IL1R1/IL1RAP 0.013 0.13 -9999 0 -0.42 35 35
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAPK8 -0.011 0.078 -9999 0 -0.43 13 13
IRAK1 0.015 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 0.01 0.087 -9999 0 -0.48 10 10
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.004 -9999 0 -10000 0 0
TRAF6 0.024 0.047 -9999 0 -0.68 2 2
PI3K 0.036 0.045 -9999 0 -0.51 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.072 -9999 0 -0.39 3 3
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.013 0.13 -9999 0 -0.42 35 35
IL1 beta/IL1R2 -0.046 0.19 -9999 0 -0.49 65 65
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.03 -9999 0 -0.37 2 2
NF kappa B1 p50/RelA 0.025 0.12 -9999 0 -0.36 35 35
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.035 0.13 -9999 0 -0.39 37 37
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.086 -9999 0 -0.29 35 35
IL1 alpha/IL1R1/IL1RAP 0.019 0.14 -9999 0 -0.45 35 35
RELA 0.027 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.027 0.006 -9999 0 -10000 0 0
MYD88 0.027 0.004 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.034 -9999 0 -0.39 2 2
IL1RAP -0.012 0.066 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.01 0.11 -9999 0 -0.35 31 31
CASP1 0.023 0.048 -9999 0 -0.68 2 2
IL1RN/IL1R2 -0.04 0.17 -9999 0 -0.52 46 46
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.028 0.13 -9999 0 -0.4 35 35
TMEM189-UBE2V1 -0.003 0.02 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.071 -9999 0 -0.37 1 1
PIK3CA 0.023 0.057 -9999 0 -0.68 3 3
IL1RN -0.011 0.11 -9999 0 -0.65 10 10
TRAF6/TAK1/TAB1/TAB2 0.046 0.031 -9999 0 -0.38 2 2
MAP2K6 0.007 0.06 -9999 0 -0.36 10 10
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.001 0.087 -10000 0 -0.43 2 2
epithelial cell differentiation -0.004 0.1 -10000 0 -0.44 8 8
ITCH 0.036 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.069 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.02 0.066 -10000 0 -0.68 4 4
PRL -0.012 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis -0.022 0.12 0.34 3 -0.47 7 10
PTPRZ1 0.003 0.1 -10000 0 -0.68 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.002 0.14 -10000 0 -0.38 37 37
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.043 0.14 -10000 0 -0.42 46 46
ADAM17 0.033 0.051 -10000 0 -0.68 2 2
ErbB4/ErbB4 -0.014 0.088 -10000 0 -0.38 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.032 0.14 -10000 0 -0.46 34 34
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.03 0.14 -10000 0 -0.4 46 46
GRIN2B -0.039 0.13 -10000 0 -0.39 45 45
ErbB4/ErbB2/betacellulin 0.003 0.1 -10000 0 -0.49 12 12
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.018 0.035 -10000 0 -10000 0 0
PRLR -0.011 0.15 -10000 0 -0.68 21 21
E4ICDs/ETO2 -0.003 0.088 -10000 0 -0.43 4 4
axon guidance -0.009 0.08 -10000 0 -0.52 3 3
NEDD4 0.034 0.05 -10000 0 -0.67 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.003 0.12 -10000 0 -0.51 21 21
CBFA2T3 0.024 0.034 -10000 0 -0.68 1 1
ErbB4/ErbB2/HBEGF 0.011 0.074 -10000 0 -0.39 4 4
MAPK3 -0.017 0.12 -10000 0 -0.49 7 7
STAT1 (dimer) -0.001 0.087 -10000 0 -0.37 3 3
MAPK1 -0.022 0.12 -10000 0 -0.48 7 7
JAK2 0.025 0.02 -10000 0 -0.36 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.035 0.13 -10000 0 -0.4 43 43
NRG1 -0.032 0.16 -10000 0 -0.53 45 45
NRG3 -0.026 0.18 -10000 0 -0.65 35 35
NRG2 -0.052 0.22 -10000 0 -0.68 50 50
NRG4 0.022 0.02 -10000 0 -10000 0 0
heart development -0.009 0.08 -10000 0 -0.52 3 3
neural crest cell migration -0.035 0.13 -10000 0 -0.4 43 43
ERBB2 0.019 0.037 -10000 0 -0.5 2 2
WWOX/E4ICDs -0.003 0.091 -10000 0 -0.62 2 2
SHC1 0.026 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.009 0.098 -10000 0 -0.5 5 5
apoptosis 0.024 0.14 0.41 36 -10000 0 36
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.049 0.16 -10000 0 -0.44 53 53
ErbB4/ErbB2/epiregulin 0.012 0.087 -10000 0 -0.4 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.012 0.12 -10000 0 -0.52 13 13
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.008 0.12 -10000 0 -0.38 21 21
MDM2 -0.012 0.078 0.26 2 -0.41 1 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.026 0.14 -10000 0 -0.41 44 44
STAT5A -0.004 0.078 -10000 0 -0.6 2 2
ErbB4/EGFR/neuregulin 1 beta -0.031 0.15 -10000 0 -0.42 48 48
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.036 0.015 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.002 0.077 -10000 0 -0.4 2 2
STAT5A (dimer) 0.004 0.11 -10000 0 -0.47 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.003 0.081 -10000 0 -0.6 2 2
LRIG1 0.017 0.087 -10000 0 -0.68 7 7
EREG -0.049 0.07 -10000 0 -10000 0 0
BTC 0.01 0.11 -10000 0 -0.68 11 11
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.009 0.08 -10000 0 -0.53 3 3
ERBB4 -0.014 0.088 -10000 0 -0.39 2 2
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.005 0.068 -10000 0 -0.46 8 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.01 0.073 -10000 0 -0.38 4 4
glial cell differentiation 0.002 0.077 0.39 2 -10000 0 2
WWOX 0.025 0.034 -10000 0 -0.68 1 1
cell proliferation -0.028 0.15 0.3 1 -0.51 16 17
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.009 0.14 -10000 0 -0.68 9 9
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.025 0.008 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.047 -10000 0 -0.68 2 2
LRP6/FZD1 0.039 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.057 -10000 0 -0.68 3 3
AP1 -0.14 0.25 -10000 0 -0.46 149 149
NCSTN 0.026 0.008 -10000 0 -10000 0 0
ADAM10 0.013 0.098 -10000 0 -0.68 9 9
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.029 0.074 -10000 0 -0.55 4 4
NICD/RBPSUH 0.007 0.13 -10000 0 -0.63 9 9
WIF1 -0.014 0.045 -10000 0 -10000 0 0
NOTCH1 -0.003 0.13 -10000 0 -0.68 8 8
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.038 -10000 0 -10000 0 0
DKK1 0 0.07 -10000 0 -0.68 2 2
beta catenin/beta TrCP1 0.047 0.048 0.28 3 -10000 0 3
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.008 -10000 0 -10000 0 0
AXIN1 -0.006 0.085 0.38 1 -0.55 4 5
CtBP/CBP/TCF1/TLE1/AES 0.019 0.032 -10000 0 -0.3 3 3
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.68 122 122
JUN -0.12 0.29 -10000 0 -0.68 99 99
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.04 0.065 0.3 13 -10000 0 13
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.095 -10000 0 -0.44 17 17
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC -0.015 0.24 -10000 0 -1.2 17 17
NKD1 0.005 0.12 -10000 0 -0.68 13 13
FZD1 0.027 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.006 0.14 -10000 0 -0.63 11 11
apoptosis -0.14 0.24 -10000 0 -0.46 149 149
Delta 1/NOTCHprecursor 0.007 0.13 -10000 0 -0.67 9 9
DLL1 0.026 0.034 -10000 0 -0.68 1 1
PPARD 0.025 0.057 -10000 0 -0.77 2 2
Gamma Secretase 0.07 0.031 -10000 0 -10000 0 0
APC 0.001 0.075 0.33 2 -0.68 2 4
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.048 0.046 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -10000 0 0
CCND1 0.011 0.12 -10000 0 -0.82 9 9
WNT1 0.018 0.02 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.048 0.099 0.41 14 -0.61 1 15
DKK2 -0.004 0.14 -10000 0 -0.68 18 18
NOTCH1 precursor/DVL1 0.013 0.12 -10000 0 -0.59 9 9
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.008 0.14 -10000 0 -0.65 11 11
PPP2R5D 0.029 0.059 0.34 13 -0.44 1 14
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.065 0.018 -10000 0 -10000 0 0
RBPJ 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.033 -10000 0 -0.68 1 1
Caspase 8 (4 units) 0.023 0.092 -10000 0 -0.45 5 5
NEF -0.014 0.066 -10000 0 -0.24 28 28
NFKBIA 0.022 0.031 -10000 0 -10000 0 0
BIRC3 -0.003 0.15 -10000 0 -0.66 21 21
CYCS -0.01 0.093 0.22 1 -0.37 10 11
RIPK1 0.028 0.002 -10000 0 -10000 0 0
CD247 -0.015 0.15 -10000 0 -0.76 16 16
MAP2K7 -0.003 0.17 0.32 2 -0.62 24 26
protein ubiquitination 0.008 0.1 0.36 6 -0.36 5 11
CRADD 0.027 0.005 -10000 0 -10000 0 0
DAXX 0.028 0.003 -10000 0 -10000 0 0
FAS 0.027 0.005 -10000 0 -10000 0 0
BID -0.011 0.099 0.22 1 -0.31 32 33
NF-kappa-B/RelA/I kappa B alpha 0.043 0.079 -10000 0 -0.33 17 17
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.026 0.033 -10000 0 -0.68 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.08 -10000 0 -0.33 17 17
MAPK8 -0.006 0.16 0.32 3 -0.56 26 29
APAF1 0.025 0.033 -10000 0 -0.68 1 1
TRAF1 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.001 0.1 -10000 0 -0.32 32 32
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.37 17 17
CHUK 0.003 0.098 0.28 3 -0.39 5 8
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.076 0.031 -10000 0 -0.39 1 1
TCRz/NEF -0.023 0.15 -10000 0 -0.44 44 44
TNF -0.056 0.22 -10000 0 -0.68 52 52
FASLG -0.05 0.23 -10000 0 -0.75 40 40
NFKB1 0.022 0.034 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.004 0.16 -10000 0 -0.44 53 53
CASP6 0.039 0.097 -10000 0 -0.72 4 4
CASP7 0.011 0.16 0.38 3 -0.58 24 27
RELA 0.022 0.033 -10000 0 -10000 0 0
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.01 0.15 0.35 1 -0.57 24 25
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.027 -10000 0 -0.51 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
MAP3K14 0 0.1 -10000 0 -0.38 9 9
APAF-1/Caspase 9 -0.002 0.12 -10000 0 -0.49 20 20
BCL2 -0.027 0.17 0.42 2 -0.52 26 28
Insulin Pathway

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
CBL/APS/CAP -0.002 0.14 -10000 0 -0.37 55 55
TC10/GTP 0.042 0.038 -10000 0 -0.36 3 3
Insulin Receptor/Insulin/IRS1/Shp2 0.001 0.16 -10000 0 -0.43 54 54
HRAS 0.026 0.011 -10000 0 -10000 0 0
APS homodimer 0.026 0.009 -10000 0 -10000 0 0
GRB14 0.006 0.12 -10000 0 -0.66 14 14
FOXO3 0 0.12 -10000 0 -0.66 14 14
AKT1 -0.029 0.14 0.36 5 -0.76 2 7
INSR 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.027 0.006 -10000 0 -10000 0 0
SORBS1 0.023 0.057 -10000 0 -0.68 3 3
CRK 0.026 0.007 -10000 0 -10000 0 0
PTPN1 0.017 0.027 -10000 0 -10000 0 0
CAV1 -0.036 0.14 -10000 0 -0.39 59 59
CBL/APS/CAP/Crk-II/C3G 0.066 0.048 -10000 0 -0.39 3 3
Insulin Receptor/Insulin/IRS1/NCK2 0.003 0.16 -10000 0 -0.42 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.14 -10000 0 -0.38 56 56
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.007 0.1 -10000 0 -0.47 3 3
RPS6KB1 -0.042 0.12 0.32 2 -0.67 2 4
PARD6A 0.026 0.006 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.026 -10000 0 -0.5 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.13 -10000 0 -0.68 2 2
HRAS/GTP -0.024 0.11 -10000 0 -0.34 40 40
Insulin Receptor 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.015 0.14 -10000 0 -0.4 43 43
PRKCI 0.012 0.074 -10000 0 -0.5 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.026 0.14 -10000 0 -0.37 64 64
SHC1 0.026 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.046 0.042 -10000 0 -0.4 1 1
PI3K 0.004 0.15 -10000 0 -0.38 56 56
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
AKT2 -0.031 0.14 0.38 7 -0.76 2 9
PRKCZ 0.013 0.073 -10000 0 -0.52 4 4
SH2B2 0.026 0.01 -10000 0 -10000 0 0
SHC/SHIP -0.014 0.13 0.3 1 -0.38 45 46
F2RL2 -0.018 0.08 -10000 0 -0.68 2 2
TRIP10 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.041 0.019 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.065 0.031 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.006 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.06 0.045 -10000 0 -0.41 3 3
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.055 0.026 -10000 0 -10000 0 0
INPP5D -0.032 0.14 0.31 1 -0.39 54 55
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.015 0.16 -10000 0 -0.83 15 15
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
IRS1 -0.058 0.23 -10000 0 -0.68 55 55
p62DOK/RasGAP 0.047 0.043 -10000 0 -0.4 1 1
INS 0.02 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.032 0.14 0.31 1 -0.39 54 55
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.042 0.12 0.36 3 -0.57 3 6
PTPRA 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
TC10/GTP/CIP4 0.034 0.011 -10000 0 -10000 0 0
PDPK1 0.023 0.047 -10000 0 -0.68 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.008 0.099 -10000 0 -0.29 43 43
Insulin Receptor/Insulin/IRS1 -0.012 0.15 -10000 0 -0.42 54 54
Insulin Receptor/Insulin/IRS3 0.033 0.013 -10000 0 -10000 0 0
Par3/Par6 0.06 0.035 -10000 0 -0.3 2 2
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.002 0.066 -10000 0 -0.28 6 6
NT3 (dimer)/TRKC -0.02 0.14 -10000 0 -0.51 33 33
NT3 (dimer)/TRKB 0.005 0.15 -10000 0 -0.45 40 40
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.029 -10000 0 -0.29 3 3
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.68 10 10
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.012 0.028 -10000 0 -10000 0 0
NTRK2 0.02 0.06 -10000 0 -0.6 4 4
NTRK3 -0.011 0.12 -10000 0 -0.63 12 12
NT-4/5 (dimer)/TRKB 0.014 0.13 -10000 0 -0.46 30 30
neuron apoptosis -0.011 0.11 0.38 18 -10000 0 18
SHC 2-3/Grb2 0.01 0.12 -10000 0 -0.42 18 18
SHC1 0.026 0.008 -10000 0 -10000 0 0
SHC2 0.001 0.1 -10000 0 -0.47 15 15
SHC3 -0.006 0.12 -10000 0 -0.46 21 21
STAT3 (dimer) 0.031 0.014 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.003 0.14 -10000 0 -0.44 36 36
RIN/GDP -0.004 0.081 0.29 8 -0.26 4 12
GIPC1 0.026 0.008 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
DNAJA3 -0.005 0.072 -10000 0 -0.38 14 14
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.02 0.017 -10000 0 -10000 0 0
MAGED1 0.026 0.008 -10000 0 -10000 0 0
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.12 -10000 0 -0.65 13 13
SHC/GRB2/SOS1 0.048 0.02 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.037 0.066 -10000 0 -0.45 7 7
TRKA/NEDD4-2 0.032 0.023 -10000 0 -10000 0 0
ELMO1 -0.24 0.34 -10000 0 -0.68 172 172
RhoG/GTP/ELMO1/DOCK1 -0.15 0.24 -10000 0 -0.45 172 172
NGF 0.021 0.058 -10000 0 -0.68 3 3
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.057 -10000 0 -0.68 3 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 -0.009 0.017 -10000 0 -10000 0 0
RIT1 0.026 0.008 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.003 0.12 -10000 0 -0.62 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.19 -10000 0 -0.36 174 174
mol:GDP -0.012 0.11 0.39 10 -0.36 8 18
NGF (dimer) 0.021 0.058 -10000 0 -0.68 3 3
RhoG/GDP -0.18 0.26 -10000 0 -0.51 172 172
RIT1/GDP -0.001 0.084 0.35 8 -0.26 4 12
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.037 0.089 -10000 0 -0.48 12 12
KIDINS220/CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.026 -10000 0 -0.44 1 1
SHC/GRB2/SOS1/GAB1 0.061 0.026 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.006 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.16 -10000 0 -0.68 23 23
RAP1/GDP -0.006 0.059 -10000 0 -0.22 4 4
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.1 -10000 0 -0.68 10 10
ubiquitin-dependent protein catabolic process 0.045 0.045 -10000 0 -0.44 3 3
Schwann cell development -0.03 0.029 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.066 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.04 -10000 0 -0.28 1 1
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.006 0.12 -10000 0 -0.37 42 42
ABL1 0.025 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.009 0.1 -10000 0 -0.5 6 6
STAT3 0.031 0.014 -10000 0 -10000 0 0
axon guidance -0.015 0.12 -10000 0 -0.36 42 42
MAPK3 0.018 0.07 -10000 0 -0.41 7 7
MAPK1 0.01 0.063 -10000 0 -0.41 7 7
CDC42/GDP 0 0.086 0.35 8 -0.26 4 12
NTF3 -0.016 0.16 -10000 0 -0.68 23 23
NTF4 0.003 0.12 -10000 0 -0.66 13 13
NGF (dimer)/TRKA/FAIM 0.046 0.045 -10000 0 -0.45 3 3
PI3K 0.036 0.045 -10000 0 -0.51 3 3
FRS3 0.028 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.004 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.042 0.085 -10000 0 -0.38 21 21
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.027 0.12 -10000 0 -0.44 32 32
RGS19 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.07 -10000 0 -0.49 2 2
Rac1/GDP -0.005 0.069 0.22 1 -0.26 3 4
NGF (dimer)/TRKA/GRIT 0.026 0.044 -10000 0 -0.45 3 3
neuron projection morphogenesis 0.022 0.097 -10000 0 -0.73 3 3
NGF (dimer)/TRKA/NEDD4-2 0.046 0.045 -10000 0 -0.45 3 3
MAP2K1 0.038 0.056 0.36 3 -10000 0 3
NGFR -0.016 0.13 -10000 0 -0.68 15 15
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.075 -10000 0 -0.36 15 15
RAS family/GTP/PI3K 0.026 0.028 -10000 0 -0.3 3 3
FRS2 family/SHP2/GRB2/SOS1 0.075 0.032 -10000 0 -0.39 1 1
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
PRKCZ 0.027 0.006 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.078 -10000 0 -0.52 7 7
RASA1 0.027 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.031 0.023 -10000 0 -10000 0 0
SQSTM1 0.027 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.048 0.085 -10000 0 -0.45 11 11
NGF (dimer)/TRKA/p62/Atypical PKCs 0.068 0.047 -10000 0 -0.39 3 3
MATK 0.016 0.07 -10000 0 -0.62 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.043 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0 0.078 -10000 0 -0.38 17 17
Rac1/GTP -0.11 0.12 -10000 0 -0.27 124 124
FRS2 family/SHP2/CRK family 0.057 0.044 -10000 0 -0.39 1 1
FOXM1 transcription factor network

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.015 0.31 0.8 2 -0.94 9 11
PLK1 0.029 0.097 -10000 0 -0.81 5 5
BIRC5 0.023 0.11 -10000 0 -0.91 5 5
HSPA1B -0.022 0.31 -10000 0 -0.94 9 9
MAP2K1 0.024 0.046 -10000 0 -10000 0 0
BRCA2 -0.026 0.32 0.8 1 -1 12 13
FOXM1 -0.047 0.34 -10000 0 -0.95 20 20
XRCC1 -0.014 0.31 -10000 0 -0.92 9 9
FOXM1B/p19 -0.047 0.33 -10000 0 -0.88 23 23
Cyclin D1/CDK4 0 0.29 -10000 0 -0.83 9 9
CDC2 -0.025 0.32 -10000 0 -0.85 19 19
TGFA -0.014 0.29 -10000 0 -0.81 10 10
SKP2 -0.019 0.33 0.8 2 -1 11 13
CCNE1 0.027 0.011 -10000 0 -10000 0 0
CKS1B -0.011 0.31 0.79 1 -0.93 9 10
RB1 0.025 0.19 -10000 0 -0.69 9 9
FOXM1C/SP1 -0.029 0.33 -10000 0 -0.93 18 18
AURKB 0.007 0.14 -10000 0 -0.8 11 11
CENPF -0.011 0.31 0.79 1 -0.93 9 10
CDK4 0.027 0.02 -10000 0 -10000 0 0
MYC -0.027 0.31 -10000 0 -0.9 16 16
CHEK2 0.02 0.04 -10000 0 -10000 0 0
ONECUT1 -0.012 0.3 -10000 0 -0.86 11 11
CDKN2A -0.032 0.071 -10000 0 -10000 0 0
LAMA4 -0.022 0.31 -10000 0 -0.92 10 10
FOXM1B/HNF6 -0.019 0.32 -10000 0 -0.98 11 11
FOS -0.23 0.6 0.8 2 -1.2 124 126
SP1 0.027 0.009 -10000 0 -10000 0 0
CDC25B -0.017 0.31 0.8 1 -0.93 9 10
response to radiation 0.006 0.026 -10000 0 -10000 0 0
CENPB -0.017 0.31 0.8 1 -0.93 9 10
CENPA -0.03 0.32 -10000 0 -0.93 14 14
NEK2 -0.012 0.31 0.79 1 -0.95 8 9
HIST1H2BA -0.028 0.31 -10000 0 -0.95 9 9
CCNA2 0.026 0.022 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.032 0.33 -10000 0 -1 12 12
CCNB2 -0.023 0.31 -10000 0 -0.94 9 9
CCNB1 -0.023 0.32 0.68 1 -0.94 11 12
ETV5 -0.022 0.31 -10000 0 -0.94 9 9
ESR1 -0.063 0.39 -10000 0 -1.2 27 27
CCND1 -0.006 0.3 -10000 0 -0.86 9 9
GSK3A 0.021 0.039 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.052 0.044 -10000 0 -10000 0 0
CDK2 0.028 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.009 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.037 0.31 -10000 0 -0.86 18 18
GAS1 -0.17 0.55 0.8 1 -1.2 94 95
MMP2 -0.022 0.33 0.8 2 -1.1 10 12
RB1/FOXM1C -0.005 0.29 -10000 0 -0.88 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.033 -10000 0 -0.68 1 1
alphaV beta3 Integrin 0.023 0.1 -10000 0 -0.56 12 12
PTK2 0.01 0.14 -10000 0 -0.56 24 24
positive regulation of JNK cascade 0.016 0.095 -10000 0 -0.33 25 25
CDC42/GDP 0.032 0.14 0.44 1 -0.45 27 28
Rac1/GDP 0.031 0.13 -10000 0 -0.46 23 23
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.025 0.12 -10000 0 -0.41 25 25
nectin-3/I-afadin 0.011 0.12 -10000 0 -0.5 25 25
RAPGEF1 0.013 0.13 0.36 1 -0.52 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.15 -10000 0 -0.58 25 25
PDGFB-D/PDGFRB 0.025 0.033 -10000 0 -0.68 1 1
TLN1 -0.004 0.06 -10000 0 -0.79 1 1
Rap1/GTP 0.013 0.093 -10000 0 -0.36 22 22
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.011 0.12 -10000 0 -0.5 25 25
PVR 0.026 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.017 0.17 0.47 1 -0.55 30 31
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
PI3K 0.052 0.12 -10000 0 -0.43 23 23
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.037 0.019 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.01 0.11 -10000 0 -0.36 24 24
PVRL1 0.023 0.024 -10000 0 -10000 0 0
PVRL3 -0.011 0.16 -10000 0 -0.68 25 25
PVRL2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.097 -10000 0 -0.62 10 10
JAM-A/CLDN1 0.043 0.13 -10000 0 -0.41 30 30
SRC 0.007 0.17 -10000 0 -0.65 25 25
ITGB3 0.008 0.11 -10000 0 -0.65 12 12
nectin-1(dimer)/I-afadin/I-afadin 0.037 0.019 -10000 0 -10000 0 0
FARP2 0.021 0.16 -10000 0 -0.54 28 28
RAC1 0.027 0.006 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.025 0.11 -10000 0 -0.44 25 25
nectin-1/I-afadin 0.037 0.019 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.036 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.028 0.11 -10000 0 -0.44 24 24
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.026 0.008 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.016 0.095 -10000 0 -0.33 25 25
alphaV/beta3 Integrin/Talin 0.022 0.11 -10000 0 -0.57 11 11
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
PIP5K1C -0.001 0.065 -10000 0 -0.25 24 24
VAV2 0.001 0.18 0.37 1 -0.59 29 30
RAP1/GDP 0.035 0.12 -10000 0 -0.42 25 25
ITGAV 0.024 0.047 -10000 0 -0.68 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.025 0.11 -10000 0 -0.44 25 25
nectin-3(dimer)/I-afadin/I-afadin 0.011 0.12 -10000 0 -0.5 25 25
Rac1/GTP 0.016 0.13 -10000 0 -0.45 24 24
PTPRM 0.002 0.072 -10000 0 -0.28 24 24
E-cadherin/beta catenin/alpha catenin 0.074 0.028 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.72 5 5
UGCG -0.054 0.21 -10000 0 -0.63 51 51
AKT1/mTOR/p70S6K/Hsp90/TERT 0.015 0.14 0.42 5 -0.41 20 25
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.056 0.21 -10000 0 -0.61 55 55
mol:DAG -0.009 0.12 -10000 0 -0.77 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.16 -10000 0 -0.46 34 34
FRAP1 -0.013 0.19 0.44 2 -0.5 44 46
FOXO3 0 0.16 0.44 2 -0.62 18 20
AKT1 -0.005 0.17 -10000 0 -0.67 19 19
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.011 0.079 -10000 0 -0.75 4 4
SGMS1 0.003 0.1 -10000 0 -0.61 11 11
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 0.007 0.038 -10000 0 -0.45 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.026 0.18 0.33 5 -0.5 36 41
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.047 -10000 0 -0.52 3 3
RPS6KB1 0.015 0.073 -10000 0 -0.74 3 3
mol:sphingomyelin -0.009 0.12 -10000 0 -0.77 11 11
natural killer cell activation 0 0.004 -10000 0 -0.017 7 7
JAK3 -0.009 0.064 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.029 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.003 0.2 0.47 4 -0.92 15 19
MYB 0.005 0.18 -10000 0 -1.3 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.004 0.15 -10000 0 -0.58 19 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.074 -10000 0 -0.67 3 3
mol:PI-3-4-5-P3 -0.003 0.14 -10000 0 -0.56 19 19
Rac1/GDP 0.023 0.038 -10000 0 -0.41 3 3
T cell proliferation -0.003 0.13 -10000 0 -0.54 17 17
SHC1 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.009 -10000 0 -0.062 9 9
PRKCZ -0.004 0.14 -10000 0 -0.57 17 17
NF kappa B1 p50/RelA 0.013 0.17 -10000 0 -0.51 23 23
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.11 -10000 0 -0.59 11 11
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.012 0.15 -10000 0 -0.64 22 22
IL2RB 0.004 0.093 -10000 0 -0.61 9 9
TERT -0.006 0.021 -10000 0 -10000 0 0
E2F1 0.023 0.076 -10000 0 -0.48 9 9
SOS1 0.027 0.005 -10000 0 -10000 0 0
RPS6 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.031 9 -10000 0 9
PTPN11 0.025 0.034 -10000 0 -0.69 1 1
IL2RG -0.009 0.14 -10000 0 -0.63 19 19
actin cytoskeleton organization -0.003 0.13 -10000 0 -0.54 17 17
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.019 0.014 -10000 0 -10000 0 0
PIK3CA 0.024 0.058 -10000 0 -0.68 3 3
Rac1/GTP 0.048 0.043 -10000 0 -0.4 3 3
LCK 0.013 0.085 -10000 0 -0.68 6 6
BCL2 -0.038 0.27 0.47 4 -0.82 43 47
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.006 0.14 -10000 0 -0.39 52 52
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.021 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.024 -10000 0 -0.44 1 1
GNB1 0.027 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.035 0.14 -10000 0 -0.4 58 58
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.012 0.032 0.097 58 -10000 0 58
GNAL -0.06 0.23 -10000 0 -0.66 58 58
GNG2 0.025 0.033 -10000 0 -0.68 1 1
CRH 0 0.039 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.048 -10000 0 -0.38 7 7
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.023 0.081 0.32 5 -0.41 8 13
ACTA1 0.012 0.096 0.34 6 -0.48 8 14
NUMA1 0.018 0.096 0.28 6 -0.5 10 16
SPTAN1 0.009 0.092 0.37 5 -0.5 7 12
LIMK1 0.016 0.1 0.47 7 -0.5 7 14
BIRC3 -0.009 0.15 -10000 0 -0.63 23 23
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.026 0.008 -10000 0 -10000 0 0
CASP10 -0.008 0.08 -10000 0 -0.53 9 9
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.008 -10000 0 -10000 0 0
PTK2 0.016 0.094 0.39 2 -0.43 13 15
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.009 0.091 0.35 6 -0.49 7 13
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN 0.009 0.093 0.36 5 -0.48 8 13
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.039 0.22 -10000 0 -0.61 56 56
BID -0.01 0.056 -10000 0 -0.32 9 9
MAP3K1 0.019 0.04 0.27 3 -10000 0 3
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.028 -10000 0 -0.51 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.012 0.1 0.44 8 -0.5 7 15
CASP9 0.027 0.006 -10000 0 -10000 0 0
DNA repair -0.018 0.056 0.42 2 -0.21 17 19
neuron apoptosis 0.007 0.11 -10000 0 -0.55 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.019 0.099 0.35 4 -0.51 10 14
APAF1 0.025 0.033 -10000 0 -0.68 1 1
CASP6 0.022 0.091 0.37 2 -0.64 4 6
TRAF2 0.025 0.009 -10000 0 -10000 0 0
ICAD/CAD 0.016 0.11 0.4 14 -0.49 7 21
CASP7 0.006 0.096 0.32 19 -0.42 8 27
KRT18 0.022 0.042 -10000 0 -0.44 2 2
apoptosis 0.018 0.093 0.48 4 -0.43 8 12
DFFA 0.012 0.096 0.36 6 -0.5 7 13
DFFB 0.012 0.096 0.36 6 -0.5 7 13
PARP1 0.018 0.056 0.21 17 -0.43 2 19
actin filament polymerization -0.021 0.12 0.46 7 -0.52 12 19
TNF -0.056 0.22 -10000 0 -0.68 52 52
CYCS 0 0.047 0.23 4 -0.23 7 11
SATB1 0.022 0.09 0.52 2 -0.6 4 6
SLK 0.007 0.097 0.41 4 -0.46 10 14
p15 BID/BAX -0.009 0.067 -10000 0 -0.36 5 5
CASP2 -0.014 0.1 0.21 3 -0.37 16 19
JNK cascade -0.019 0.04 -10000 0 -0.27 3 3
CASP3 0.008 0.095 0.36 5 -0.48 9 14
LMNB2 0.007 0.12 0.37 10 -0.42 11 21
RIPK1 0.028 0.002 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.046 0.094 -10000 0 -0.4 18 18
negative regulation of DNA binding -0.038 0.21 -10000 0 -0.6 56 56
stress fiber formation 0.007 0.096 0.41 4 -0.45 10 14
GZMB -0.004 0.092 -10000 0 -0.6 9 9
CASP1 0.015 0.027 -10000 0 -0.39 2 2
LMNB1 0.021 0.094 0.35 11 -0.39 3 14
APP 0.007 0.12 -10000 0 -0.56 16 16
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM 0.02 0.085 0.45 3 -0.45 6 9
LMNA 0.017 0.1 0.36 12 -0.42 5 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.013 0.11 -10000 0 -0.4 14 14
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.017 0.1 0.47 7 -0.5 7 14
APAF-1/Caspase 9 0.014 0.058 -10000 0 -0.53 3 3
nuclear fragmentation during apoptosis 0.018 0.094 0.28 6 -0.49 10 16
CFL2 0.021 0.12 0.53 12 -0.48 7 19
GAS2 0.006 0.096 0.36 4 -0.47 10 14
positive regulation of apoptosis 0.017 0.1 0.37 10 -0.41 6 16
PRF1 0.019 0.074 -10000 0 -0.68 5 5
Cellular roles of Anthrax toxin

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
ANTXR1 0.015 0.09 -10000 0 -0.61 9 9
ANTXR2 0.023 0.057 -10000 0 -0.68 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.082 12 12
monocyte activation -0.035 0.16 -10000 0 -0.44 57 57
MAP2K2 -0.011 0.12 -10000 0 -0.54 22 22
MAP2K1 -0.001 0.012 -10000 0 -10000 0 0
MAP2K7 -0.001 0.012 -10000 0 -10000 0 0
MAP2K6 -0.008 0.053 -10000 0 -0.4 8 8
CYAA -0.008 0.057 -10000 0 -0.38 10 10
MAP2K4 -0.001 0.012 -10000 0 -10000 0 0
IL1B -0.026 0.1 0.18 1 -0.36 37 38
Channel 0.024 0.066 -10000 0 -0.41 10 10
NLRP1 -0.003 0.028 -10000 0 -0.39 2 2
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.029 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.082 12 -10000 0 12
MAPK3 -0.001 0.012 -10000 0 -10000 0 0
MAPK1 -0.001 0.012 -10000 0 -10000 0 0
PGR -0.013 0.059 -10000 0 -0.37 11 11
PA/Cellular Receptors 0.025 0.072 -10000 0 -0.44 10 10
apoptosis -0.002 0.013 -10000 0 -0.082 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.024 0.063 -10000 0 -0.35 12 12
macrophage activation -0.002 0.011 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.68 52 52
VCAM1 -0.036 0.16 -10000 0 -0.44 57 57
platelet activation 0.011 0.029 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.03 0.12 7 -0.14 8 15
IL18 -0.009 0.06 -10000 0 -0.33 12 12
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.082 12 12
LEF -0.002 0.013 -10000 0 -0.082 12 12
CASP1 0 0.019 -10000 0 -0.17 3 3
mol:cAMP 0.011 0.03 -10000 0 -0.52 1 1
necrosis -0.002 0.013 -10000 0 -0.082 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.024 0.063 -10000 0 -0.38 10 10
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P1 pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.03 0.07 -10000 0 -0.59 5 5
PDGFRB 0.025 0.034 -10000 0 -0.68 1 1
SPHK1 0.008 0.066 -10000 0 -0.73 3 3
mol:S1P 0.006 0.063 -10000 0 -0.65 3 3
S1P1/S1P/Gi -0.012 0.14 -10000 0 -0.42 39 39
GNAO1 0.002 0.12 -10000 0 -0.69 14 14
PDGFB-D/PDGFRB/PLCgamma1 -0.01 0.12 -10000 0 -0.48 17 17
PLCG1 -0.012 0.13 -10000 0 -0.41 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.034 -10000 0 -0.68 1 1
GNAI2 0.025 0.014 -10000 0 -10000 0 0
GNAI3 0.024 0.014 -10000 0 -10000 0 0
GNAI1 0.023 0.035 -10000 0 -0.68 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.057 -10000 0 -0.51 5 5
S1P1/S1P 0.001 0.072 -10000 0 -0.48 6 6
negative regulation of cAMP metabolic process -0.011 0.13 -10000 0 -0.41 39 39
MAPK3 -0.026 0.18 -10000 0 -0.58 38 38
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.022 0.057 -10000 0 -0.68 3 3
PLCB2 0.012 0.079 0.37 6 -0.42 6 12
RAC1 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.062 -10000 0 -0.4 6 6
receptor internalization 0.001 0.067 -10000 0 -0.44 6 6
PTGS2 -0.067 0.31 0.64 3 -0.99 44 47
Rac1/GTP 0.009 0.061 -10000 0 -0.4 6 6
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.022 0.057 -10000 0 -0.68 3 3
negative regulation of T cell proliferation -0.011 0.13 -10000 0 -0.41 39 39
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.016 -10000 0 -10000 0 0
MAPK1 -0.027 0.18 -10000 0 -0.6 38 38
S1P1/S1P/PDGFB-D/PDGFRB 0.01 0.082 -10000 0 -0.46 7 7
ABCC1 0.026 0.006 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.028 0.11 -9999 0 -0.34 31 31
Syndecan-3/Neurocan 0.003 0.098 -9999 0 -0.36 28 28
POMC -0.12 0.28 -9999 0 -0.67 96 96
EGFR 0.02 0.066 -9999 0 -0.68 4 4
Syndecan-3/EGFR 0.027 0.043 -9999 0 -0.34 5 5
AGRP 0.004 0.033 -9999 0 -10000 0 0
NCSTN 0.026 0.008 -9999 0 -10000 0 0
PSENEN 0.026 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.026 0.008 -9999 0 -10000 0 0
NCAN -0.028 0.18 -9999 0 -0.67 33 33
long-term memory 0.051 0.03 -9999 0 -10000 0 0
Syndecan-3/IL8 0.03 0.068 -9999 0 -0.36 11 11
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.011 -9999 0 -10000 0 0
FYN 0.027 0.004 -9999 0 -10000 0 0
limb bud formation 0.015 0.006 -9999 0 -10000 0 0
MC4R 0.001 0.027 -9999 0 -10000 0 0
SRC 0.027 0.009 -9999 0 -10000 0 0
PTN -0.036 0.2 -9999 0 -0.68 40 40
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.023 0.13 -9999 0 -0.52 2 2
Syndecan-3/AgRP 0.03 0.024 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.046 0.03 -9999 0 -10000 0 0
Fyn/Cortactin 0.04 0.008 -9999 0 -10000 0 0
SDC3 0.015 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.03 0.067 -9999 0 -0.35 11 11
IL8 -0.024 0.12 -9999 0 -0.68 10 10
Syndecan-3/Fyn/Cortactin 0.052 0.03 -9999 0 -10000 0 0
Syndecan-3/CASK 0.011 0.023 -9999 0 -0.31 1 1
alpha-MSH/MC4R -0.08 0.22 -9999 0 -0.51 96 96
Gamma Secretase 0.07 0.031 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.015 0.009 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.027 0.01 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.021 0.04 -10000 0 -0.44 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.001 0.024 -10000 0 -10000 0 0
GRK1 -0.042 0.2 -10000 0 -0.66 45 45
CNG Channel 0.039 0.054 -10000 0 -0.38 5 5
mol:Na + 0.029 0.072 -10000 0 -0.4 9 9
mol:ADP -0.042 0.2 -10000 0 -0.66 45 45
RGS9-1/Gbeta5/R9AP -0.026 0.18 -10000 0 -0.45 69 69
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.041 0.076 -10000 0 -0.41 9 9
CNGB1 0.018 0.03 -10000 0 -10000 0 0
RDH5 -0.071 0.071 -10000 0 -10000 0 0
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.11 0.51 10 -0.39 9 19
Na + (4 Units) 0.022 0.068 -10000 0 -0.38 9 9
RGS9 -0.042 0.21 -10000 0 -0.68 44 44
GNB1/GNGT1 0.03 0.013 -10000 0 -10000 0 0
GNAT1/GDP -0.014 0.16 -10000 0 -0.39 69 69
GUCY2D 0.012 0.08 -10000 0 -0.63 6 6
GNGT1 -0.015 0.012 -10000 0 -10000 0 0
GUCY2F -0.014 0.01 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.016 0.037 -10000 0 -0.38 1 1
mol:11-cis-retinal -0.071 0.071 -10000 0 -10000 0 0
mol:cGMP 0.032 0.059 -10000 0 -0.4 6 6
GNB1 0.027 0.006 -10000 0 -10000 0 0
Rhodopsin -0.042 0.055 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.018 0.075 -10000 0 -0.68 5 5
Metarhodopsin II -0.012 0.13 -10000 0 -0.4 45 45
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.048 0.065 -10000 0 -0.41 8 8
RGS9BP -0.017 0.17 -10000 0 -0.67 28 28
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.04 0.038 -10000 0 -0.42 3 3
PDE6A/B 0.032 0.028 -10000 0 -10000 0 0
mol:Pi -0.026 0.18 -10000 0 -0.45 69 69
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.039 0.015 -10000 0 -10000 0 0
PDE6B 0.027 0.005 -10000 0 -10000 0 0
PDE6A 0.012 0.036 -10000 0 -10000 0 0
PDE6G 0.013 0.059 -10000 0 -0.68 2 2
RHO 0.007 0.023 -10000 0 -10000 0 0
PDE6 0.003 0.17 -10000 0 -0.39 67 67
GUCA1A 0.006 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.047 0.038 -10000 0 -0.36 3 3
GUCA1C -0.017 0.002 -10000 0 -10000 0 0
GUCA1B 0.023 0.057 -10000 0 -0.68 3 3
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.037 0.06 -10000 0 -0.37 7 7
EPHB2 0.022 0.057 -10000 0 -0.68 3 3
Syndecan-2/TACI -0.082 0.2 -10000 0 -0.44 106 106
LAMA1 -0.019 0.17 -10000 0 -0.67 30 30
Syndecan-2/alpha2 ITGB1 0.045 0.091 -10000 0 -0.38 17 17
HRAS 0.026 0.011 -10000 0 -10000 0 0
Syndecan-2/CASK 0.006 0.045 -10000 0 -0.34 7 7
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.004 0.059 -10000 0 -10000 0 0
EPB41 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.043 -10000 0 -0.4 4 4
LAMA3 0.001 0.12 -10000 0 -0.68 14 14
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.025 0.034 -10000 0 -0.68 1 1
Syndecan-2/MMP2 0.022 0.068 -10000 0 -0.46 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.008 0.058 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.06 -10000 0 -0.38 9 9
Syndecan-2/GM-CSF -0.035 0.056 -10000 0 -0.37 6 6
determination of left/right symmetry 0.009 0.053 -10000 0 -0.39 7 7
Syndecan-2/PKC delta 0.026 0.048 -10000 0 -0.34 7 7
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
MAPK3 -0.032 0.048 -10000 0 -0.41 4 4
MAPK1 -0.026 0.047 -10000 0 -0.41 4 4
Syndecan-2/RACK1 0.038 0.043 -10000 0 -0.38 4 4
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.009 0.053 -10000 0 -0.39 7 7
ITGA2 -0.033 0.073 -10000 0 -10000 0 0
MAPK8 0.006 0.068 -10000 0 -0.42 11 11
Syndecan-2/alpha2/beta1 Integrin 0.034 0.12 -10000 0 -0.42 28 28
Syndecan-2/Kininogen 0.017 0.051 -10000 0 -0.34 7 7
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.02 0.045 0.35 1 -0.36 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.044 -10000 0 -0.3 7 7
extracellular matrix organization 0.024 0.046 -10000 0 -0.44 4 4
actin cytoskeleton reorganization -0.037 0.06 -10000 0 -0.37 7 7
Syndecan-2/Caveolin-2/Ras 0.04 0.048 -10000 0 -0.4 5 5
Syndecan-2/Laminin alpha3 0.009 0.094 -10000 0 -0.44 18 18
Syndecan-2/RasGAP 0.05 0.044 -10000 0 -0.36 4 4
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.061 -10000 0 -0.38 9 9
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.039 0.043 -10000 0 -0.36 4 4
RHOA 0.027 0.004 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
TNFRSF13B -0.14 0.29 -10000 0 -0.67 103 103
RASA1 0.027 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.008 0.058 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.046 -10000 0 -0.36 6 6
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CASP3 0.017 0.045 -10000 0 -0.4 4 4
FN1 -0.081 0.067 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.005 0.088 -10000 0 -0.44 14 14
SDC2 0.009 0.053 -10000 0 -0.39 7 7
KNG1 -0.004 0.037 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.045 -10000 0 -0.38 5 5
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 -0.079 0.064 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.046 -10000 0 -0.44 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.043 -10000 0 -0.4 4 4
Syndecan-2/Ezrin 0.042 0.045 -10000 0 -0.4 4 4
PRKACA 0.016 0.041 -10000 0 -0.4 4 4
angiogenesis -0.005 0.087 -10000 0 -0.44 14 14
MMP2 0.019 0.069 -10000 0 -0.62 5 5
IL8 -0.024 0.12 -10000 0 -0.68 10 10
calcineurin-NFAT signaling pathway -0.082 0.2 -10000 0 -0.44 106 106
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.027 0.006 -10000 0 -10000 0 0
VDR 0.027 0.009 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.026 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.069 -10000 0 -0.31 7 7
KAT2B 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.028 0.003 -10000 0 -10000 0 0
AKT1 0.013 0.079 0.25 12 -0.36 11 23
RAR alpha/9cRA/Cyclin H 0.031 0.1 -10000 0 -0.39 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.065 0.24 1 -0.3 11 12
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.012 0.093 -10000 0 -0.51 9 9
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.006 0.14 -10000 0 -0.55 23 23
NCOA2 -0.035 0.2 -10000 0 -0.68 40 40
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.009 -10000 0 -10000 0 0
RARG 0.028 0.006 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.035 0.012 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.018 0.082 -10000 0 -0.63 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.006 0.13 -10000 0 -0.52 22 22
RARA 0.004 0.077 -10000 0 -0.3 24 24
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.014 0.12 -10000 0 -0.33 47 47
PRKCA -0.002 0.14 -10000 0 -0.68 20 20
RXRs/RARs/NRIP1/9cRA/HDAC1 0.007 0.15 0.39 4 -0.53 24 28
RXRG -0.029 0.084 -10000 0 -0.39 23 23
RXRA 0.005 0.079 -10000 0 -0.32 22 22
RXRB 0.006 0.082 -10000 0 -0.37 20 20
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RBP1 0.015 0.088 -10000 0 -0.68 7 7
CRBP1/9-cic-RA 0.011 0.066 -10000 0 -0.51 7 7
RARB 0.012 0.11 -10000 0 -0.68 11 11
PRKCG 0.022 0.014 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.14 -10000 0 -0.58 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.002 0.13 -10000 0 -0.49 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.091 0.41 2 -0.42 10 12
RXRs/RARs/NRIP1/9cRA/HDAC3 0.008 0.15 0.42 5 -0.53 24 29
positive regulation of DNA binding 0.02 0.093 -10000 0 -0.37 19 19
NRIP1 0.008 0.13 0.5 1 -0.66 7 8
RXRs/RARs 0.002 0.14 -10000 0 -0.52 25 25
RXRs/RXRs/DNA/9cRA -0.014 0.12 -10000 0 -0.54 22 22
PRKACA 0.026 0.008 -10000 0 -10000 0 0
CDK7 0.027 0.006 -10000 0 -10000 0 0
TFIIH 0.054 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.046 0.07 -10000 0 -0.42 3 3
CCNH 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.05 0.018 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.029 0.009 -10000 0 -10000 0 0
epithelial cell differentiation 0.056 0.017 -10000 0 -10000 0 0
CYFIP2 0.027 0.006 -10000 0 -10000 0 0
ENAH 0.022 0.081 0.46 11 -10000 0 11
EGFR 0.02 0.066 -10000 0 -0.68 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
MYO6 0.033 0.071 0.43 12 -10000 0 12
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.014 -10000 0 -10000 0 0
AQP5 0.003 0.11 -10000 0 -0.54 16 16
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.054 0.4 8 -10000 0 8
regulation of calcium-dependent cell-cell adhesion -0.009 0.059 0.39 6 -10000 0 6
EGF -0.076 0.25 -10000 0 -0.68 66 66
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.042 0.17 -10000 0 -0.54 45 45
cortical microtubule organization 0.056 0.017 -10000 0 -10000 0 0
GO:0000145 0.013 0.054 0.39 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.061 0.018 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.014 0.025 -10000 0 -10000 0 0
PVRL2 0.026 0.007 -10000 0 -10000 0 0
ZYX 0.021 0.021 -10000 0 -10000 0 0
ARF6/GTP 0.068 0.028 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.01 0.15 -10000 0 -0.36 67 67
RhoA/GDP 0.057 0.017 -10000 0 -10000 0 0
actin cytoskeleton organization 0.022 0.057 0.4 9 -10000 0 9
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 -0.12 0.29 -10000 0 -0.68 96 96
DIAPH1 0.051 0.046 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.056 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
VCL 0.022 0.058 0.4 9 -10000 0 9
EFNA1 0.026 0.008 -10000 0 -10000 0 0
LPP 0.012 0.05 0.35 3 -0.36 4 7
Ephrin A1/EPHA2 0.047 0.02 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 -0.01 0.059 0.4 6 -10000 0 6
HGF/MET -0.003 0.14 -10000 0 -0.38 56 56
HGF -0.069 0.24 -10000 0 -0.68 62 62
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.009 -10000 0 -10000 0 0
actin cable formation 0.07 0.14 0.5 31 -0.33 1 32
KIAA1543 0.013 0.055 0.37 8 -0.36 1 9
KIFC3 0.021 0.024 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ACTN1 0.024 0.039 0.36 4 -10000 0 4
NCK1/GIT1 0.039 0.01 -10000 0 -10000 0 0
mol:GDP 0.056 0.017 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.021 0.024 -10000 0 -10000 0 0
PIP5K1C 0.026 0.054 0.4 8 -10000 0 8
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.045 0.11 0.43 23 -10000 0 23
adherens junction assembly 0.027 0.095 0.48 13 -0.56 1 14
IGF-1R heterotetramer/IGF1 -0.034 0.16 -10000 0 -0.36 90 90
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET -0.03 0.072 -10000 0 -10000 0 0
PLEKHA7 0.026 0.055 0.38 8 -0.37 1 9
mol:GTP 0.06 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.032 0.068 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.009 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.022 0.057 0.4 9 -10000 0 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.009 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.014 0.11 -10000 0 -0.47 23 23
ATM 0.025 0.033 -10000 0 -0.68 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
ATR 0.026 0.033 -10000 0 -0.68 1 1
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.023 0.027 -10000 0 -0.38 2 2
protein ubiquitination 0.046 0.094 -10000 0 -0.38 18 18
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.051 0.036 -10000 0 -0.44 2 2
MRE11A 0.024 0.047 -10000 0 -0.68 2 2
DNA-PK 0.04 0.026 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.007 0.12 -10000 0 -0.5 24 24
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
CCNE1 0.026 0.008 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.012 -10000 0 -10000 0 0
FANCG 0.026 0.008 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.014 0.11 -10000 0 -0.45 23 23
FANCE 0.028 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.008 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA 0.019 0.031 -10000 0 -10000 0 0
DNA repair 0.017 0.087 0.41 2 -0.48 4 6
BRCA1/BARD1/ubiquitin 0.014 0.11 -10000 0 -0.45 23 23
BARD1/DNA-PK 0.03 0.099 -10000 0 -0.4 20 20
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.014 0.11 0.47 23 -10000 0 23
BRCA1/BARD1/CTIP/M/R/N Complex 0.014 0.074 -10000 0 -0.3 20 20
BRCA1/BACH1/BARD1/TopBP1 0.031 0.1 -10000 0 -0.42 20 20
BRCA1/BARD1/P53 0.045 0.097 -10000 0 -0.41 18 18
BARD1/CSTF1/BRCA1 0.031 0.099 -10000 0 -0.42 19 19
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.007 0.15 -10000 0 -0.63 24 24
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.03 0.1 -10000 0 -0.39 23 23
BRCA1/BARD1/UbcH7 0.019 0.098 -10000 0 -0.39 22 22
BRCA1/BARD1/RAD51/PCNA 0.046 0.095 -10000 0 -0.41 17 17
BARD1/DNA-PK/P53 0.039 0.096 -10000 0 -0.38 18 18
BRCA1/BARD1/Ubiquitin 0.014 0.11 -10000 0 -0.45 23 23
BRCA1/BARD1/CTIP 0.025 0.092 -10000 0 -0.41 18 18
FA complex 0.028 0.034 -10000 0 -10000 0 0
BARD1/EWS 0.004 0.11 -10000 0 -0.46 24 24
RBBP8 0.016 0.025 -10000 0 -0.51 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.043 0.096 0.41 18 -10000 0 18
BRCA1/BARD1 0.052 0.097 -10000 0 -0.39 18 18
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.006 0.11 -10000 0 -0.47 24 24
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.027 0.011 -10000 0 -10000 0 0
RAD50 0.027 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.014 0.11 -10000 0 -0.45 23 23
EWSR1 0.02 0.012 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.035 0.098 0.45 10 -0.39 8 18
NFATC2 -0.02 0.095 0.27 10 -0.27 22 32
NFATC3 0.018 0.011 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.011 0.089 0.28 1 -0.3 25 26
Exportin 1/Ran/NUP214 0.047 0.019 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.003 0.1 -10000 0 -0.45 9 9
BCL2/BAX -0.002 0.14 -10000 0 -0.49 34 34
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.02 -10000 0 -10000 0 0
BAX 0.026 0.008 -10000 0 -10000 0 0
MAPK14 0.026 0.005 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.005 0.094 0.33 4 -0.37 10 14
Calcineurin A alpha-beta B1/BCL2 -0.025 0.18 -10000 0 -0.67 34 34
FKBP8 0.026 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.005 0.093 0.37 10 -0.33 4 14
KPNB1 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.007 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SFN -0.084 0.12 -10000 0 -0.68 13 13
MAP3K8 0.014 0.089 -10000 0 -0.64 8 8
NFAT4/CK1 alpha 0.019 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.071 0.17 -10000 0 -0.32 116 116
CABIN1 -0.01 0.086 0.28 1 -0.29 24 25
CALM1 0.024 0.01 -10000 0 -10000 0 0
RAN 0.026 0.006 -10000 0 -10000 0 0
MAP3K1 0.027 0.006 -10000 0 -10000 0 0
CAMK4 0.014 0.083 -10000 0 -0.68 6 6
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.014 0.082 -10000 0 -0.64 7 7
MAPK9 0.027 0.006 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.02 0.086 0.46 1 -0.47 3 4
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.028 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.013 -10000 0 -10000 0 0
apoptosis 0.01 0.044 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.002 0.058 -10000 0 -0.35 5 5
PRKCB 0.008 0.071 -10000 0 -0.68 3 3
PRKCE 0.021 0.066 -10000 0 -0.68 4 4
JNK2/NFAT4 0.031 0.026 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.008 -10000 0 -10000 0 0
PRKCA -0.005 0.14 -10000 0 -0.68 20 20
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.019 0.076 -10000 0 -0.63 6 6
FKBP38/BCL2 -0.002 0.14 -10000 0 -0.49 34 34
EP300 0.01 0.021 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.039 0.1 0.41 8 -0.4 9 17
CaM/Ca2+/FKBP38 0.019 0.026 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.061 -10000 0 -0.45 6 6
NFATc/ERK1 0.041 0.082 0.44 3 -0.37 8 11
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.007 0.1 -10000 0 -0.51 7 7
NR4A1 -0.17 0.29 -10000 0 -0.61 136 136
GSK3B 0.025 0.007 -10000 0 -10000 0 0
positive T cell selection 0.018 0.011 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.022 0.068 -10000 0 -0.32 6 6
RCH1/ KPNB1 0.039 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.024 0.008 -10000 0 -10000 0 0
AKAP5 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.014 0.022 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.048 0.097 0.42 11 -0.42 4 15
CREBBP 0.013 0.023 -10000 0 -10000 0 0
BCL2 -0.025 0.18 -10000 0 -0.67 34 34
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.027 0.05 0.29 11 -0.36 1 12
DAPP1 -0.037 0.13 0.34 4 -0.5 12 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.053 0.17 0.29 5 -0.53 20 25
mol:DAG -0.016 0.097 0.34 11 -0.26 13 24
HRAS 0.028 0.013 -10000 0 -10000 0 0
RAP1A 0.028 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.034 0.069 0.28 2 -0.33 6 8
PLCG2 0.026 0.006 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.051 0.3 11 -10000 0 11
ARF1/GTP 0.003 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.016 -10000 0 -10000 0 0
ADAP1 0 0.049 0.29 11 -10000 0 11
ARAP3 0 0.051 0.3 11 -10000 0 11
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.026 0.008 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.026 0.008 -10000 0 -10000 0 0
NRAS 0.028 0.008 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.026 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.066 0.31 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
ZAP70 -0.001 0.13 -10000 0 -0.66 16 16
mol:IP3 -0.012 0.07 0.23 12 -0.2 7 19
LYN 0.027 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.079 0.33 7 -0.33 8 15
RhoA/GDP 0.037 0.044 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.036 -10000 0 -0.44 2 2
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.035 0.088 0.38 17 -10000 0 17
SRC 0.027 0.009 -10000 0 -10000 0 0
PLEKHA2 0.005 0.016 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.022 -10000 0 -0.34 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.03 0.046 0.29 10 -10000 0 10
RhoA/GTP 0.024 0.043 0.3 9 -10000 0 9
Src family/SYK family/BLNK-LAT -0.046 0.14 -10000 0 -0.46 23 23
BLK -0.19 0.32 -10000 0 -0.67 136 136
PDPK1 0.023 0.047 -10000 0 -0.68 2 2
CYTH1 0.002 0.056 0.31 12 -10000 0 12
HCK 0.018 0.036 -10000 0 -10000 0 0
CYTH3 -0.002 0.053 0.29 11 -0.37 1 12
CYTH2 0.004 0.061 0.3 15 -10000 0 15
KRAS 0.028 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.017 0.096 -10000 0 -0.57 10 10
SGK1 0.017 0.11 -10000 0 -0.57 12 12
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.026 0.087 0.32 12 -0.33 10 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.029 0.053 0.29 9 -10000 0 9
mol:PI-3-4-5-P3 -0.008 0.016 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.016 -10000 0 -10000 0 0
VAV1 0.012 0.061 -10000 0 -0.57 3 3
mol:PI-3-4-P2 0.012 0.021 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.045 0.031 0.33 1 -10000 0 1
PLEKHA1 0.005 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.069 0.35 1 -0.32 7 8
LAT 0.021 0.06 -10000 0 -0.6 4 4
Rac1/GTP 0.018 0.063 0.28 2 -0.48 3 5
ITK -0.039 0.12 0.28 11 -0.37 45 56
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.37 9 -0.37 14 23
LCK 0.011 0.085 -10000 0 -0.68 6 6
BTK -0.004 0.068 0.29 14 -0.37 5 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.002 0.11 0.54 5 -0.48 1 6
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.2 0.37 -10000 0 -0.72 144 144
IFNAR2 0.028 0.006 -10000 0 -10000 0 0
AKT1 0.006 0.057 -10000 0 -0.24 21 21
ER alpha/Oestrogen -0.012 0.12 -10000 0 -0.49 24 24
NFX1/SIN3/HDAC complex 0.03 0.048 -10000 0 -0.45 3 3
EGF -0.075 0.25 -10000 0 -0.67 66 66
SMG5 0.026 0.008 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.042 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.004 0.089 0.55 2 -10000 0 2
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.051 0.036 -10000 0 -0.44 2 2
WT1 0.008 0.046 -10000 0 -10000 0 0
WRN 0.026 0.033 -10000 0 -0.68 1 1
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.028 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.01 0.085 -10000 0 -10000 0 0
Mad/Max 0.041 0.009 -10000 0 -10000 0 0
TERT -0.002 0.11 0.54 5 -10000 0 5
CCND1 0.001 0.11 0.6 5 -10000 0 5
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
RBBP4 0.024 0.047 -10000 0 -0.68 2 2
TERF2 0.024 0.009 -10000 0 -10000 0 0
PTGES3 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
Telomerase/911 0.025 0.06 -10000 0 -10000 0 0
CDKN1B -0.03 0.15 -10000 0 -0.43 52 52
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.026 0.033 -10000 0 -0.68 1 1
TRF2/PARP2 0.038 0.011 -10000 0 -10000 0 0
UBE3A 0.028 0.004 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.68 99 99
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.68 122 122
IFN-gamma/IRF1 -0.019 0.18 -10000 0 -0.48 57 57
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.027 0.008 -10000 0 -10000 0 0
Telomerase 0.014 0.11 -10000 0 -0.55 9 9
IRF1 0.03 0.01 -10000 0 -10000 0 0
ESR1 -0.018 0.16 -10000 0 -0.65 24 24
KU/TER 0.03 0.019 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.026 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.037 0.043 -10000 0 -0.37 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.037 0.044 -10000 0 -0.38 3 3
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.029 0.004 -10000 0 -10000 0 0
ATM 0.01 0.024 -10000 0 -0.49 1 1
SMAD3 0.015 0.011 -10000 0 -10000 0 0
ABL1 0.025 0.008 -10000 0 -10000 0 0
MXD1 0.028 0.005 -10000 0 -10000 0 0
MRE11A 0.024 0.047 -10000 0 -0.68 2 2
HUS1 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.014 0.085 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.001 0.013 -10000 0 -10000 0 0
MAPK1 0.001 0.012 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.024 -10000 0 -0.48 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.021 0.066 -10000 0 -0.68 4 4
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.043 0.2 -10000 0 -0.51 69 69
MYC 0.013 0.1 -10000 0 -0.65 10 10
IL2 0.02 0.008 -10000 0 -10000 0 0
KU 0.03 0.019 -10000 0 -10000 0 0
RAD50 0.027 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.017 -10000 0 -10000 0 0
TRF2/BLM 0.038 0.013 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.001 0.089 0.51 2 -10000 0 2
SP1/HDAC2 0.042 0.01 -10000 0 -10000 0 0
PINX1 0.027 0.004 -10000 0 -10000 0 0
Telomerase/EST1A 0.009 0.083 -10000 0 -10000 0 0
Smad3/Myc 0.02 0.065 -10000 0 -0.42 9 9
911 complex 0.053 0.015 -10000 0 -10000 0 0
IFNG -0.063 0.23 -10000 0 -0.67 57 57
Telomerase/PinX1 0.009 0.085 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.012 0.067 0.37 1 -0.42 3 4
SIN3B 0.026 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.008 0.081 -10000 0 -10000 0 0
response to DNA damage stimulus 0.004 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.072 0.037 -10000 0 -0.38 2 2
TRF2/WRN 0.037 0.027 -10000 0 -0.48 1 1
Telomerase/hnRNP C1/C2 0.01 0.085 -10000 0 -10000 0 0
E2F1 -0.016 0.068 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.018 0.075 -10000 0 -0.68 5 5
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.025 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.024 0.042 -10000 0 -10000 0 0
TP53 -0.008 0.036 -10000 0 -0.18 18 18
Senescence -0.008 0.036 -10000 0 -0.18 18 18
Apoptosis -0.008 0.036 -10000 0 -0.18 18 18
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.011 0.025 0.35 1 -10000 0 1
MDM4 0.026 0.008 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.025 0.033 -9999 0 -0.68 1 1
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.054 -9999 0 -0.26 15 15
GNAO1 0.006 0.12 -9999 0 -0.68 14 14
S1P/S1P3/G12/G13 0.048 0.02 -9999 0 -10000 0 0
AKT1 0.022 0.042 -9999 0 -0.44 1 1
AKT3 0.019 0.068 -9999 0 -0.51 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.033 -9999 0 -0.68 1 1
GNAI2 0.029 0.004 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.034 -9999 0 -0.68 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.027 0.008 -9999 0 -10000 0 0
S1PR2 0.025 0.013 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.005 0.071 -9999 0 -0.31 14 14
MAPK3 0.002 0.066 -9999 0 -0.4 3 3
MAPK1 0.013 0.059 -9999 0 -0.38 3 3
JAK2 0.006 0.067 -9999 0 -0.41 3 3
CXCR4 0.003 0.065 -9999 0 -0.4 3 3
FLT1 0.027 0.034 -9999 0 -0.68 1 1
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.005 -9999 0 -10000 0 0
SRC 0.003 0.063 -9999 0 -0.34 3 3
S1P/S1P3/Gi 0.005 0.071 -9999 0 -0.31 14 14
RAC1 0.027 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.01 0.074 -9999 0 -0.38 3 3
VEGFA 0.025 0.057 -9999 0 -0.68 3 3
S1P/S1P2/Gi 0.004 0.075 -9999 0 -0.33 14 14
VEGFR1 homodimer/VEGFA homodimer 0.04 0.059 -9999 0 -0.65 3 3
RHOA 0.027 0.004 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.055 0.15 -9999 0 -0.31 110 110
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.013 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
GNA14 -0.13 0.29 -9999 0 -0.64 107 107
GNA15 0.013 0.05 -9999 0 -0.68 1 1
GNA12 0.027 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.082 -9999 0 -0.63 7 7
Rac1/GTP 0.009 0.074 -9999 0 -0.38 3 3
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.28 -10000 0 -0.67 90 90
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.014 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.033 0.04 0.35 1 -10000 0 1
HIF1A 0.016 0.032 -10000 0 -0.25 2 2
COPS5 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.053 -10000 0 -0.4 3 3
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.03 0.072 -10000 0 -10000 0 0
ARNT/IPAS -0.067 0.21 -10000 0 -0.49 90 90
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.032 0.051 0.3 8 -10000 0 8
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.027 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.053 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.033 0.039 0.28 1 -10000 0 1
PHD1-3/OS9 0.049 0.076 -10000 0 -0.41 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.055 0.041 -10000 0 -10000 0 0
VHL 0.023 0.057 -10000 0 -0.68 3 3
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.048 0.34 4 -10000 0 4
EGLN3 0.006 0.11 -10000 0 -0.68 10 10
EGLN2 0.026 0.007 -10000 0 -10000 0 0
EGLN1 0.024 0.034 -10000 0 -0.68 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.024 0.08 -10000 0 -0.57 6 6
ARNT 0.026 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.039 0.054 0.31 7 -10000 0 7
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.026 0.008 -9999 0 -10000 0 0
SPHK1 0.023 0.023 -9999 0 -10000 0 0
GNAI2 0.027 0.004 -9999 0 -10000 0 0
mol:S1P 0.017 0.007 -9999 0 -10000 0 0
GNAO1 0.004 0.12 -9999 0 -0.68 14 14
mol:Sphinganine-1-P 0.014 0.015 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.056 0.029 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
S1PR3 0.025 0.008 -9999 0 -10000 0 0
S1PR2 0.025 0.013 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.019 -9999 0 -0.2 2 2
S1PR5 0.023 0.035 -9999 0 -0.68 1 1
S1PR4 0.024 0.017 -9999 0 -10000 0 0
GNAI1 0.025 0.034 -9999 0 -0.68 1 1
S1P/S1P5/G12 0.043 0.033 -9999 0 -0.39 1 1
S1P/S1P3/Gq -0.054 0.16 -9999 0 -0.39 35 35
S1P/S1P4/Gi 0.002 0.08 -9999 0 -0.33 16 16
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.29 -9999 0 -0.64 107 107
GNA15 0.013 0.05 -9999 0 -0.68 1 1
GNA12 0.027 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.082 -9999 0 -0.63 7 7
ABCC1 0.027 0.006 -9999 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.006 0.018 0.12 2 -0.13 4 6
BUB1B 0.015 0.031 0.18 9 -0.17 1 10
PLK1 0.012 0.032 0.16 13 -0.13 1 14
PLK1S1 0.016 0.027 0.18 10 -10000 0 10
KIF2A 0.019 0.07 0.32 20 -0.39 1 21
regulation of mitotic centrosome separation 0.012 0.032 0.16 13 -0.12 1 14
GOLGA2 0.025 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.034 0.038 -10000 0 -10000 0 0
WEE1 0.023 0.045 0.3 5 -0.29 2 7
cytokinesis 0.013 0.06 0.26 9 -0.25 3 12
PP2A-alpha B56 0.051 0.088 -10000 0 -0.53 7 7
AURKA 0.014 0.027 0.16 9 -0.26 1 10
PICH/PLK1 0.019 0.015 -10000 0 -10000 0 0
CENPE 0.011 0.051 0.25 11 -0.39 2 13
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.019 0.07 0.32 20 -0.39 1 21
PPP2CA 0.027 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.015 0.031 0.18 11 -0.25 1 12
PAK1 0.027 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.037 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
CLSPN 0.014 0.026 0.17 2 -0.26 2 4
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.022 27 -10000 0 27
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.02 0.096 14 -0.049 1 15
G2 phase of mitotic cell cycle 0 0.004 0.019 12 -10000 0 12
STAG2 0.026 0.008 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.023 0.038 -10000 0 -0.43 3 3
spindle elongation 0.012 0.032 0.16 13 -0.12 1 14
ODF2 0.025 0.008 -10000 0 -10000 0 0
BUB1 0.027 0.087 -10000 0 -0.54 10 10
TPT1 0.004 0.047 0.16 5 -0.18 23 28
CDC25C 0.019 0.027 0.18 7 -10000 0 7
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.018 0.13 4 -0.12 2 6
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.043 0.013 -10000 0 -10000 0 0
CDC14B 0.003 0.046 -10000 0 -0.41 5 5
CDC20 0.025 0.018 -10000 0 -10000 0 0
PLK1/PBIP1 0.011 0.022 0.14 6 -10000 0 6
mitosis -0.001 0.003 0.02 6 -10000 0 6
FBXO5 0.013 0.039 0.22 9 -0.35 1 10
CDC2 0.002 0.001 -10000 0 -10000 0 0
NDC80 0.006 0.053 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.028 0.17 2 -0.24 3 5
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.011 0.029 0.14 16 -10000 0 16
microtubule cytoskeleton organization 0.004 0.047 0.16 5 -0.18 23 28
G2/M transition DNA damage checkpoint 0 0.004 0.019 14 -10000 0 14
PPP1R12A 0.027 0.006 -10000 0 -10000 0 0
interphase 0 0.004 0.019 14 -10000 0 14
PLK1/PRC1-2 0.039 0.028 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.022 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.029 0.14 14 -0.11 1 15
mitotic prometaphase 0 0.003 0.026 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.027 -10000 0 -10000 0 0
microtubule-based process 0.023 0.026 -10000 0 -10000 0 0
Golgi organization 0.012 0.032 0.16 13 -0.12 1 14
Cohesin/SA2 0.021 0.018 0.17 1 -10000 0 1
PPP1CB/MYPT1 0.04 0.009 -10000 0 -10000 0 0
KIF20A 0.002 0.055 -10000 0 -10000 0 0
APC/C/CDC20 0.026 0.026 0.19 4 -10000 0 4
PPP2R1A 0.026 0.008 -10000 0 -10000 0 0
chromosome segregation 0.011 0.022 0.14 6 -10000 0 6
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.043 0.22 8 -0.41 2 10
C13orf34 0.01 0.028 0.14 13 -0.11 1 14
NUDC 0.014 0.028 0.17 2 -0.24 3 5
regulation of attachment of spindle microtubules to kinetochore 0.014 0.031 0.18 9 -0.17 1 10
spindle assembly 0.014 0.039 0.17 19 -0.087 1 20
spindle stabilization 0.016 0.027 0.18 10 -10000 0 10
APC/C/HCDH1 0.019 0.042 -10000 0 -0.35 5 5
MKLP2/PLK1 0.023 0.026 -10000 0 -10000 0 0
CCNB1 0.028 0.006 -10000 0 -10000 0 0
PPP1CB 0.028 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.001 0.1 0.26 2 -0.4 25 27
TUBG1 0.015 0.031 0.18 10 -0.16 3 13
G2/M transition of mitotic cell cycle 0.013 0.009 -10000 0 -10000 0 0
MLF1IP 0.007 0.013 -10000 0 -10000 0 0
INCENP 0.025 0.034 -10000 0 -0.68 1 1
TCGA08_retinoblastoma

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
CDKN2B -0.034 0.075 -10000 0 -10000 0 0
CDKN2C 0.031 0.02 -10000 0 -10000 0 0
CDKN2A -0.031 0.076 -10000 0 -10000 0 0
CCND2 0.01 0.023 -10000 0 -10000 0 0
RB1 -0.014 0.049 0.32 2 -0.24 12 14
CDK4 0.014 0.043 0.26 10 -10000 0 10
CDK6 0.016 0.044 0.26 10 -0.16 1 11
G1/S progression 0.015 0.05 0.24 13 -0.32 2 15
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.016 0.077 0.62 6 -10000 0 6
PI3K Class IB/PDE3B 0.016 0.078 -10000 0 -0.63 6 6
PDE3B 0.016 0.078 -10000 0 -0.63 6 6
IL2 signaling events mediated by STAT5

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
GAB2 0.028 0.005 -10000 0 -10000 0 0
ELF1 0.007 0.097 -10000 0 -0.4 23 23
CCNA2 0.025 0.02 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
JAK3 -0.01 0.063 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.004 0.14 -10000 0 -0.56 17 17
SHC1 0.026 0.008 -10000 0 -10000 0 0
SP1 0.033 0.007 -10000 0 -10000 0 0
IL2RA -0.026 0.19 -10000 0 -0.87 22 22
IL2RB 0.004 0.093 -10000 0 -0.61 9 9
SOS1 0.028 0.005 -10000 0 -10000 0 0
IL2RG -0.01 0.14 -10000 0 -0.63 19 19
G1/S transition of mitotic cell cycle 0.032 0.065 0.43 6 -0.51 2 8
PTPN11 0.026 0.033 -10000 0 -0.68 1 1
CCND2 0.023 0.005 -10000 0 -10000 0 0
LCK 0.012 0.085 -10000 0 -0.68 6 6
GRB2 0.027 0.007 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.023 0.047 -10000 0 -0.68 2 2
CCND3 0.008 0.12 -10000 0 -0.6 9 9
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.68 14 14
CDC42/GTP 0.006 0.076 -10000 0 -0.31 14 14
PLCG1 -0.002 0.068 -10000 0 -0.32 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.011 -10000 0 -10000 0 0
cell migration 0.006 0.074 -10000 0 -0.3 14 14
S1PR5 0.023 0.035 -10000 0 -0.68 1 1
S1PR4 0.024 0.017 -10000 0 -10000 0 0
MAPK3 -0.003 0.07 -10000 0 -0.32 14 14
MAPK1 0.009 0.062 -10000 0 -0.32 13 13
S1P/S1P5/Gi -0.001 0.076 -10000 0 -0.32 17 17
GNAI1 0.025 0.034 -10000 0 -0.68 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.026 -10000 0 -0.44 1 1
RHOA 0.034 0.069 0.41 11 -10000 0 11
S1P/S1P4/Gi 0 0.075 -10000 0 -0.33 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.018 -10000 0 -10000 0 0
GNA12 0.027 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.017 0.044 -10000 0 -0.28 3 3
STMN1 0.001 0.041 0.2 2 -10000 0 2
Aurora B/RasGAP/Survivin 0.049 0.057 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.013 0.052 -10000 0 -0.26 11 11
BIRC5 0.014 0.052 -10000 0 -0.69 1 1
DES -0.32 0.3 -10000 0 -0.56 274 274
Aurora C/Aurora B/INCENP 0.055 0.04 -10000 0 -0.46 1 1
Aurora B/TACC1 0.031 0.044 -10000 0 -0.5 1 1
Aurora B/PP2A 0.028 0.045 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.006 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.011 0.06 0.18 1 -10000 0 1
Cul3 protein complex 0.04 0.069 -10000 0 -0.42 9 9
KIF2C 0.015 0.03 -10000 0 -0.52 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.002 0.055 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.029 0.045 -10000 0 -10000 0 0
SEPT1 0.024 0.021 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.015 0.086 0.28 2 -0.54 9 11
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.012 0.016 -10000 0 -10000 0 0
AURKB 0.003 0.064 -10000 0 -10000 0 0
AURKC 0.021 0.027 -10000 0 -10000 0 0
CDCA8 0.028 0.015 -10000 0 -10000 0 0
cytokinesis -0.019 0.058 -10000 0 -0.36 5 5
Aurora B/Septin1 0.046 0.068 -10000 0 -0.36 4 4
AURKA 0.027 0.006 -10000 0 -10000 0 0
INCENP 0.027 0.034 -10000 0 -0.69 1 1
KLHL13 0.009 0.096 -10000 0 -0.64 9 9
BUB1 -0.027 0.078 -10000 0 -0.68 1 1
hSgo1/Aurora B/Survivin 0.048 0.057 -10000 0 -0.41 1 1
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.05 0.048 -10000 0 -0.28 1 1
SGOL1 0.021 0.03 -10000 0 -10000 0 0
CENPA 0.019 0.039 0.19 1 -0.22 6 7
NCAPG 0.012 0.045 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.028 0.045 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.028 0.046 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.006 0.052 -10000 0 -10000 0 0
NPM1 0.011 0.045 -10000 0 -0.3 8 8
RASA1 0.027 0.006 -10000 0 -10000 0 0
KLHL9 0.026 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.049 -10000 0 -10000 0 0
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin 0.042 0.049 -10000 0 -0.3 1 1
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 0.011 0.046 -10000 0 -0.3 9 9
MYLK 0.012 0.016 -10000 0 -10000 0 0
KIF23 0.021 0.034 -10000 0 -10000 0 0
VIM 0 0.038 -10000 0 -10000 0 0
RACGAP1 0.028 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.085 -10000 0 -0.45 11 11
Chromosomal passenger complex 0.016 0.036 -10000 0 -0.28 3 3
Chromosomal passenger complex/EVI5 0.1 0.064 -10000 0 -0.44 2 2
TACC1 0.026 0.033 -10000 0 -0.68 1 1
PPP2R5D 0.028 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.028 0.1 -10000 0 -0.5 6 6
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.026 0.007 -10000 0 -10000 0 0
STXBP4 0.025 0.034 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.022 0.11 0.37 7 -0.5 7 14
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.051 0.17 -10000 0 -0.49 60 60
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.029 -10000 0 -0.44 1 1
YWHAG 0.027 0.006 -10000 0 -10000 0 0
ASIP 0.007 0.047 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.017 0.012 0.25 1 -10000 0 1
PRKCZ 0.027 0.006 -10000 0 -10000 0 0
TRIP10 0.025 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
AS160/14-3-3 -0.032 0.093 -10000 0 -0.35 13 13
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.02 0.12 0.41 5 -0.54 8 13
STX4 0.027 0.006 -10000 0 -10000 0 0
GSK3B 0.023 0.008 -10000 0 -10000 0 0
SFN -0.084 0.12 -10000 0 -0.68 13 13
LNPEP 0.007 0.12 -10000 0 -0.68 13 13
YWHAE 0.026 0.007 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.006 0.076 0.3 14 -10000 0 14
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.026 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.68 14 14
RhoA/GTP 0.006 0.077 -10000 0 -0.31 14 14
negative regulation of cAMP metabolic process -0.001 0.076 -10000 0 -0.32 17 17
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.027 0.006 -10000 0 -10000 0 0
S1PR5 0.023 0.035 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.076 -10000 0 -0.32 17 17
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.025 0.034 -10000 0 -0.68 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.006 0.16 -10000 0 -0.44 52 52
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.14 -10000 0 -0.39 51 51
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.008 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.036 0.084 -10000 0 -10000 0 0
YY1/LSF 0.006 0.064 -10000 0 -0.44 3 3
SMG5 0.026 0.008 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.11 -10000 0 -0.31 50 50
I kappa B alpha/HDAC1 0.011 0.081 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA -0.016 0.11 -10000 0 -0.32 52 52
HDAC1/Smad7 0.052 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.081 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.041 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.024 0.12 0.32 1 -0.43 14 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.008 -10000 0 -10000 0 0
GATA1 0.012 0.021 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.033 0.07 -10000 0 -0.49 5 5
RBBP7 0.026 0.008 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.047 -10000 0 -0.68 2 2
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
NFKBIA -0.003 0.083 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.035 -10000 0 -0.34 3 3
SIN3 complex 0.062 0.033 -10000 0 -0.41 1 1
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.026 0.033 -10000 0 -0.68 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.009 0.08 -10000 0 -10000 0 0
YY1/HDAC2 0.008 0.056 -10000 0 -0.28 1 1
YY1/HDAC1 0.009 0.054 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.038 0.035 -10000 0 -0.4 1 1
PPARG -0.021 0.14 -10000 0 -0.39 55 55
HDAC8/hEST1B 0.046 0.022 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.012 0.081 -10000 0 -10000 0 0
MBD3L2 -0.016 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.016 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.034 0.064 -10000 0 -0.45 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 -0.003 0.083 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.018 0.012 -10000 0 -10000 0 0
HDAC8 0.026 0.008 -10000 0 -10000 0 0
SMAD7 0.027 0.004 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.018 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.02 0.064 -10000 0 -0.41 3 3
YY1/SAP30/HDAC1 0.021 0.058 -10000 0 -0.28 2 2
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.083 -10000 0 -10000 0 0
histone deacetylation 0.038 0.035 -10000 0 -0.4 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.002 0.075 -10000 0 -0.3 1 1
nuclear export -0.046 0.022 -10000 0 -10000 0 0
PRKACA 0.026 0.008 -10000 0 -10000 0 0
GATAD2B 0.026 0.008 -10000 0 -10000 0 0
GATAD2A 0.026 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.012 0.081 -10000 0 -10000 0 0
GATA1/HDAC1 0.035 0.012 -10000 0 -10000 0 0
GATA1/HDAC3 0.009 0.08 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.025 0.18 -10000 0 -0.51 52 52
SIN3/HDAC complex/Mad/Max 0.033 0.049 -10000 0 -0.57 2 2
NuRD Complex 0.041 0.054 -10000 0 -0.49 2 2
positive regulation of chromatin silencing 0.034 0.082 -10000 0 -10000 0 0
SIN3B 0.026 0.008 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.013 0.058 -10000 0 -0.27 2 2
HDAC complex 0.063 0.037 -10000 0 -0.4 2 2
GATA1/Fog1 0.034 0.013 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.053 0.014 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.68 52 52
negative regulation of cell growth 0.033 0.048 -10000 0 -0.57 2 2
NuRD/MBD2/PRMT5 Complex 0.038 0.035 -10000 0 -0.4 1 1
Ran/GTP/Exportin 1 0.017 0.052 -10000 0 -0.21 1 1
NF kappa B/RelA/I kappa B alpha -0.031 0.14 -10000 0 -0.4 51 51
SIN3/HDAC complex/NCoR1 0.029 0.055 -10000 0 -0.51 3 3
TFCP2 0.022 0.057 -10000 0 -0.68 3 3
NR2C1 0.027 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.008 -10000 0 -10000 0 0
MBD2 0.027 0.004 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.025 0.25 2 -10000 0 2
AES 0.026 0.02 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.01 -10000 0 -10000 0 0
SMAD4 0.027 0.005 -10000 0 -10000 0 0
DKK2 -0.004 0.14 -10000 0 -0.68 18 18
TLE1 0.021 0.06 0.22 2 -0.66 3 5
MACF1 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.05 0.095 0.47 17 -10000 0 17
WIF1 -0.014 0.045 -10000 0 -10000 0 0
beta catenin/RanBP3 0.029 0.084 0.39 21 -10000 0 21
KREMEN2 0.016 0.038 -10000 0 -10000 0 0
DKK1 0.001 0.07 -10000 0 -0.68 2 2
beta catenin/beta TrCP1 0.047 0.047 0.38 2 -10000 0 2
FZD1 0.027 0.006 -10000 0 -10000 0 0
AXIN2 -0.033 0.3 0.61 14 -1.4 18 32
AXIN1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.028 0.073 -10000 0 -0.5 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.037 0.099 0.3 1 -0.59 4 5
Axin1/APC/GSK3 0.034 0.046 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.035 0.044 0.51 2 -10000 0 2
HNF1A 0.027 0.021 0.23 1 -10000 0 1
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.037 0.23 0.53 4 -1.4 12 16
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.095 -10000 0 -0.44 17 17
NKD1 0.005 0.12 -10000 0 -0.68 13 13
TCF4 0.027 0.019 0.22 1 -10000 0 1
TCF3 0.026 0.023 0.25 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.065 0.021 -10000 0 -10000 0 0
Ran/GTP 0.02 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.023 0.13 0.53 21 -10000 0 21
LEF1 0.024 0.041 0.2 3 -0.63 1 4
DVL1 0.028 0.016 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.12 -10000 0 -0.53 8 8
DKK1/LRP6/Kremen 2 0.049 0.046 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.019 -10000 0 -10000 0 0
NLK 0.026 0.009 -10000 0 -10000 0 0
CCND1 -0.012 0.089 0.58 2 -0.68 3 5
WNT1 0.023 0.014 -10000 0 -10000 0 0
GSK3A 0.026 0.008 -10000 0 -10000 0 0
GSK3B 0.028 0.004 -10000 0 -10000 0 0
FRAT1 0.027 0.006 -10000 0 -10000 0 0
PPP2R5D 0.033 0.057 0.33 13 -0.33 1 14
APC 0.022 0.04 0.36 3 -0.39 1 4
WNT1/LRP6/FZD1 0.031 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.02 0.23 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.037 0.013 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.01 0.039 -10000 0 -0.17 3 3
RAB3GAP2/RIMS1/UNC13B 0.048 0.02 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.021 0.018 -10000 0 -10000 0 0
mol:ACh 0.002 0.045 0.15 17 -0.14 23 40
RAB3GAP2 0.026 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.056 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.01 0.039 -10000 0 -0.17 3 3
UNC13B 0.026 0.008 -10000 0 -10000 0 0
CHRNA1 0.01 0.042 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.042 0.12 -10000 0 -0.48 24 24
SNAP25 -0.016 0.077 -10000 0 -0.34 24 24
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 -0.069 0.16 -10000 0 -0.68 23 23
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.056 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.023 0.1 -10000 0 -0.56 12 12
AKT1 0.039 0.089 0.39 2 -0.58 6 8
PTK2B 0.016 0.11 0.35 1 -0.51 15 16
VEGFR2 homodimer/Frs2 0.033 0.078 -10000 0 -0.91 3 3
CAV1 0.014 0.093 -10000 0 -0.68 8 8
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.048 0.092 -10000 0 -0.74 5 5
endothelial cell proliferation 0.053 0.15 0.6 18 -0.6 4 22
mol:Ca2+ 0.024 0.088 -10000 0 -0.64 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.062 0.089 -10000 0 -0.79 4 4
RP11-342D11.1 0.013 0.087 -10000 0 -0.64 6 6
CDH5 0.026 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.059 0.061 -10000 0 -0.5 4 4
SHC1 0.026 0.008 -10000 0 -10000 0 0
SHC2 0.021 0.057 -10000 0 -0.68 3 3
HRAS/GDP 0.041 0.076 -10000 0 -0.65 4 4
SH2D2A -0.008 0.14 -10000 0 -0.68 20 20
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.055 0.097 -10000 0 -0.63 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.025 0.13 -10000 0 -0.46 25 25
VEGFR1 homodimer 0.025 0.034 -10000 0 -0.68 1 1
SHC/GRB2/SOS1 0.067 0.093 -10000 0 -0.86 3 3
GRB10 0.025 0.087 -10000 0 -0.92 3 3
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.071 0.089 -10000 0 -0.68 5 5
HRAS 0.026 0.011 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.069 -10000 0 -0.44 6 6
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.06 0.086 -10000 0 -0.77 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.019 0.074 -10000 0 -0.68 5 5
Nck/Pak 0.04 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.048 0.091 -10000 0 -0.74 5 5
mol:GDP 0.053 0.084 -10000 0 -0.81 3 3
mol:NADP 0.04 0.1 0.46 8 -0.48 6 14
eNOS/Hsp90 0.043 0.082 -10000 0 -0.49 4 4
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.024 0.091 -10000 0 -0.66 6 6
HIF1A/ARNT 0.037 0.013 -10000 0 -10000 0 0
SHB 0.026 0.008 -10000 0 -10000 0 0
VEGFA 0.025 0.057 -10000 0 -0.68 3 3
VEGFC 0.026 0.033 -10000 0 -0.68 1 1
FAK1/Vinculin 0.038 0.1 -10000 0 -0.65 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.12 -10000 0 -0.54 15 15
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.031 0.056 -10000 0 -0.58 3 3
mol:L-citrulline 0.04 0.1 0.46 8 -0.48 6 14
ITGAV 0.024 0.047 -10000 0 -0.68 2 2
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.06 0.089 -10000 0 -0.79 4 4
VEGFR2 homodimer/VEGFA homodimer 0.051 0.1 -10000 0 -0.73 6 6
VEGFR2/3 heterodimer 0.028 0.1 -10000 0 -0.79 6 6
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.007 0.097 0.38 1 -0.7 6 7
VEGFR2 homodimer 0.02 0.084 -10000 0 -1 3 3
FLT1 0.025 0.034 -10000 0 -0.68 1 1
NEDD4 0.026 0.047 -10000 0 -0.68 2 2
MAPK3 0.001 0.089 0.37 1 -0.89 3 4
MAPK1 -0.003 0.089 0.37 1 -0.9 3 4
VEGFA145/NRP2 0.028 0.055 -10000 0 -0.51 3 3
VEGFR1/2 heterodimer 0.031 0.089 -10000 0 -1 3 3
KDR 0.02 0.084 -10000 0 -1 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.055 0.098 -10000 0 -0.67 6 6
SRC 0.027 0.009 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.013 0.12 0.41 13 -0.94 3 16
PI3K 0.042 0.095 -10000 0 -0.8 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.048 0.091 -10000 0 -0.74 5 5
FES 0.025 0.095 -10000 0 -0.68 6 6
GAB1 0.03 0.091 -10000 0 -0.79 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.092 -10000 0 -0.74 5 5
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.026 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.039 0.092 0.4 1 -0.51 6 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.092 -10000 0 -0.74 5 5
PI3K/GAB1 0.051 0.081 -10000 0 -0.62 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.072 0.089 -10000 0 -0.68 5 5
PRKACA 0.026 0.008 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.1 -10000 0 -0.69 7 7
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.094 -10000 0 -0.68 6 6
actin cytoskeleton reorganization 0.025 0.13 -10000 0 -0.46 25 25
PTK2 0.024 0.1 0.32 1 -0.72 6 7
EDG1 0.013 0.087 -10000 0 -0.64 6 6
mol:DAG 0.024 0.091 -10000 0 -0.66 6 6
CaM/Ca2+ 0.037 0.084 -10000 0 -0.86 3 3
MAP2K3 0.011 0.1 0.37 1 -0.98 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.1 -10000 0 -1 3 3
PLCG1 0.024 0.095 -10000 0 -0.68 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.058 0.091 -10000 0 -0.7 5 5
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.047 0.1 -10000 0 -0.8 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.048 0.092 -10000 0 -0.74 5 5
cell migration 0.045 0.085 0.34 1 -0.57 5 6
mol:PI-3-4-5-P3 0.042 0.083 -10000 0 -0.7 4 4
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.029 0.084 -10000 0 -0.6 6 6
mol:NO 0.04 0.1 0.46 8 -0.48 6 14
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.073 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.044 0.098 -10000 0 -1 3 3
VHL 0.023 0.057 -10000 0 -0.68 3 3
ITGB3 0.008 0.11 -10000 0 -0.65 12 12
NOS3 0.039 0.11 0.49 7 -0.55 6 13
VEGFR2 homodimer/VEGFA homodimer/Sck 0.042 0.097 -10000 0 -0.64 7 7
RAC1 0.027 0.006 -10000 0 -10000 0 0
PRKCA -0.001 0.12 0.36 1 -0.46 21 22
PRKCB 0.008 0.09 0.36 1 -0.61 6 7
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.031 0.094 -10000 0 -0.67 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.1 -10000 0 -0.8 5 5
VEGFA165/NRP2 0.028 0.055 -10000 0 -0.51 3 3
MAPKKK cascade 0.053 0.087 0.35 1 -0.75 3 4
NRP2 0.014 0.042 -10000 0 -10000 0 0
VEGFC homodimer 0.026 0.033 -10000 0 -0.68 1 1
NCK1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.027 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.039 0.1 -10000 0 -0.65 6 6
MAP3K13 0.018 0.12 -10000 0 -0.53 13 13
PDPK1 0.028 0.079 -10000 0 -0.69 4 4
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.024 0.058 0.35 2 -0.56 2 4
PDGFB-D/PDGFRB/SLAP 0.038 0.029 -10000 0 -0.52 1 1
PDGFB-D/PDGFRB/APS/CBL 0.052 0.027 -10000 0 -0.43 1 1
AKT1 0.029 0.089 0.5 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.061 0.35 2 -0.62 2 4
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
FGR 0.017 0.049 0.33 2 -0.59 2 4
mol:Ca2+ 0.034 0.088 0.42 11 -0.68 2 13
MYC 0.031 0.18 0.56 19 -0.76 12 31
SHC1 0.026 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.026 -10000 0 -0.38 1 1
LRP1/PDGFRB/PDGFB 0.038 0.041 -10000 0 -0.45 2 2
GRB10 0.027 0.006 -10000 0 -10000 0 0
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
GO:0007205 0.034 0.089 0.42 11 -0.69 2 13
PTEN 0.026 0.019 -10000 0 -0.36 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.002 0.055 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.037 0.038 -10000 0 -0.52 2 2
PDGFB-D/PDGFRB/GRB10 0.039 0.028 -10000 0 -0.52 1 1
cell cycle arrest 0.038 0.029 -10000 0 -0.52 1 1
HRAS 0.026 0.011 -10000 0 -10000 0 0
HIF1A 0.02 0.087 0.48 11 -10000 0 11
GAB1 0.029 0.096 0.43 11 -0.64 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.034 0.11 0.5 15 -0.56 2 17
PDGFB-D/PDGFRB 0.054 0.03 -10000 0 -0.46 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.039 0.028 -10000 0 -0.52 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.021 0.06 -10000 0 -0.67 1 1
positive regulation of MAPKKK cascade 0.037 0.038 -10000 0 -0.52 2 2
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 0.034 0.089 0.42 11 -0.7 2 13
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.018 0.052 -10000 0 -0.57 1 1
SHB 0.026 0.008 -10000 0 -10000 0 0
BLK -0.14 0.26 -10000 0 -0.56 132 132
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.039 0.027 -10000 0 -0.5 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.034 0.12 0.49 13 -0.61 3 16
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.028 -10000 0 -0.52 1 1
LCK 0.01 0.085 -10000 0 -0.67 6 6
PDGFRB 0.026 0.034 -10000 0 -0.69 1 1
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.023 0.047 -10000 0 -0.59 2 2
ABL1 0.027 0.1 0.42 13 -0.68 2 15
PDGFB-D/PDGFRB/CBL 0.023 0.086 0.45 4 -0.72 2 6
PTPN1 0.028 0.006 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
cell proliferation 0.033 0.17 0.55 19 -0.67 12 31
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.033 0.027 -10000 0 -0.37 1 1
SRC 0.017 0.05 -10000 0 -0.59 2 2
PI3K 0.012 0.035 -10000 0 -0.36 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.029 -10000 0 -0.31 1 1
SH2B2 0.026 0.01 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.029 0.063 0.36 2 -0.64 2 4
LYN 0.018 0.036 -10000 0 -0.44 2 2
LRP1 0.025 0.033 -10000 0 -0.68 1 1
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.079 0.033 -10000 0 -0.38 1 1
SPHK1 0.023 0.023 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.034 0.089 0.42 11 -0.7 2 13
PLCG1 0.034 0.09 0.42 11 -0.73 2 13
NHERF/PDGFRB 0.05 0.029 -10000 0 -0.45 1 1
YES1 0.015 0.061 0.37 1 -0.54 4 5
cell migration 0.05 0.029 -10000 0 -0.44 1 1
SHC/Grb2/SOS1 0.073 0.036 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.034 -10000 0 -0.41 1 1
FYN 0.016 0.055 -10000 0 -0.52 3 3
DOK1 0.023 0.03 -10000 0 -0.42 1 1
HRAS/GTP 0.019 0.008 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.04 0.14 0.54 19 -0.49 9 28
PRKCD 0.024 0.031 -10000 0 -0.42 1 1
FER 0.019 0.045 -10000 0 -0.42 4 4
MAPKKK cascade 0.014 0.056 0.37 1 -10000 0 1
RASA1 0.022 0.028 -10000 0 -0.42 1 1
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.03 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.029 -10000 0 -0.52 1 1
chemotaxis 0.027 0.098 0.42 13 -0.65 2 15
STAT1-3-5/STAT1-3-5 0.064 0.03 -10000 0 -0.37 1 1
Bovine Papilomavirus E5/PDGFRB 0.019 0.026 -10000 0 -0.52 1 1
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.069 0.38 1 -0.37 1 2
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.023 0.047 -10000 0 -0.51 1 1
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.027 0.004 -10000 0 -10000 0 0
RIPK2 0.027 0.005 -10000 0 -10000 0 0
IKBKG 0.034 0.023 -10000 0 -10000 0 0
IKK complex/A20 0.015 0.14 0.33 1 -0.52 6 7
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.033 0.075 -10000 0 -0.44 2 2
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.071 -10000 0 -0.52 1 1
BCL10/MALT1/TRAF6 0.051 0.036 -10000 0 -0.44 2 2
NOD2 0.006 0.059 -10000 0 -0.68 1 1
NFKB1 0.03 0.004 -10000 0 -10000 0 0
RELA 0.03 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.04 0.008 -10000 0 -10000 0 0
ATM 0.025 0.033 -10000 0 -0.68 1 1
TNF/TNFR1A -0.025 0.18 -10000 0 -0.51 52 52
TRAF6 0.024 0.047 -10000 0 -0.68 2 2
PRKCA -0.005 0.14 -10000 0 -0.68 20 20
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.68 52 52
NF kappa B1 p50/RelA 0.062 0.016 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.048 0.076 -10000 0 -0.55 1 1
CYLD 0.027 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.039 0.11 -10000 0 -0.52 4 4
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.041 0.042 -9999 0 -0.46 1 1
CLOCK -0.01 0.16 -9999 0 -0.68 25 25
TIMELESS/CRY2 0.028 0.034 -9999 0 -10000 0 0
DEC1/BMAL1 0.019 0.036 -9999 0 -10000 0 0
ATR 0.026 0.033 -9999 0 -0.68 1 1
NR1D1 0.001 0.038 -9999 0 -10000 0 0
ARNTL 0.013 0.045 -9999 0 -10000 0 0
TIMELESS 0.011 0.029 -9999 0 -10000 0 0
NPAS2 0.025 0.038 -9999 0 -0.52 2 2
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.005 0.009 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.005 0.009 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.028 0.12 -9999 0 -0.44 26 26
BMAL1/CLOCK -0.002 0.1 -9999 0 -0.43 11 11
S phase of mitotic cell cycle 0.041 0.042 -9999 0 -0.46 1 1
TIMELESS/CHEK1/ATR 0.041 0.042 -9999 0 -0.46 1 1
mol:NADPH 0.005 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.027 0.032 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.013 0.013 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.009 0.093 -9999 0 -0.64 8 8
ITGA4 0.023 0.039 -9999 0 -0.68 1 1
alpha4/beta7 Integrin 0.022 0.078 -9999 0 -0.48 9 9
alpha4/beta1 Integrin 0.036 0.032 -9999 0 -0.51 1 1
Class I PI3K signaling events mediated by Akt

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 0.016 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.044 0.016 -10000 0 -10000 0 0
CDKN1B 0.022 0.024 -10000 0 -10000 0 0
CDKN1A 0.02 0.025 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
FOXO3 0.022 0.024 -10000 0 -10000 0 0
AKT1 0.021 0.024 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.013 0.027 -10000 0 -0.39 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.022 0.027 -10000 0 -10000 0 0
AKT1/ASK1 0.038 0.038 -10000 0 -0.33 1 1
BAD/YWHAZ 0.051 0.018 -10000 0 -10000 0 0
RICTOR 0.025 0.034 -10000 0 -0.68 1 1
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.037 0.32 1 -10000 0 1
TSC1 0.02 0.025 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.042 0.04 0.28 2 -10000 0 2
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.022 0.024 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.021 0.023 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.044 0.15 -10000 0 -0.44 56 56
MAP3K5 0.026 0.033 -10000 0 -0.68 1 1
MAPKAP1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.084 0.46 4 -0.36 8 12
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.026 0.038 -10000 0 -10000 0 0
CASP9 0.023 0.031 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.049 0.38 5 -10000 0 5
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.036 -10000 0 -0.44 2 2
YWHAE 0.026 0.007 -10000 0 -10000 0 0
SRC 0.027 0.009 -10000 0 -10000 0 0
AKT2/p21CIP1 0.021 0.03 -10000 0 -0.36 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.011 -10000 0 -10000 0 0
CHUK 0.022 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.035 0.28 1 -10000 0 1
mTORC2 0.03 0.024 -10000 0 -0.41 1 1
AKT2 0.014 0.027 -10000 0 -0.39 2 2
FOXO1-3a-4/14-3-3 family 0.021 0.089 0.4 9 -0.38 4 13
PDPK1 0.023 0.047 -10000 0 -0.68 2 2
MDM2 0.022 0.026 -10000 0 -10000 0 0
MAPKKK cascade -0.042 0.039 -10000 0 -0.28 2 2
MDM2/Cbp/p300 0.039 0.035 -10000 0 -10000 0 0
TSC1/TSC2 0.023 0.041 0.3 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.033 -10000 0 -10000 0 0
glucose import -0.056 0.16 0.21 3 -0.42 69 72
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.029 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.057 0.16 -10000 0 -0.42 69 69
GSK3A 0.025 0.037 -10000 0 -10000 0 0
FOXO1 0.02 0.024 -10000 0 -10000 0 0
GSK3B 0.022 0.024 -10000 0 -10000 0 0
SFN -0.084 0.12 -10000 0 -0.68 13 13
G1/S transition of mitotic cell cycle 0.027 0.044 0.32 2 -10000 0 2
p27Kip1/14-3-3 family 0.015 0.063 -10000 0 -0.77 1 1
PRKACA 0.026 0.008 -10000 0 -10000 0 0
KPNA1 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.024 0.12 0.62 12 -10000 0 12
PLK1 0.068 0.12 0.58 3 -0.58 4 7
CDKN1B 0.073 0.096 0.53 4 -0.35 2 6
FOXO3 0.065 0.11 -10000 0 -0.59 5 5
KAT2B 0.032 0.019 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.057 0.42 2 -0.4 1 3
CAT 0.061 0.14 0.53 1 -0.97 4 5
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.034 0.02 -10000 0 -10000 0 0
FOXO1 0.017 0.084 0.44 12 -10000 0 12
MAPK10 0.033 0.034 -10000 0 -0.41 1 1
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.071 0.091 0.52 10 -0.51 3 13
response to oxidative stress 0.01 0.011 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.084 0.09 -10000 0 -0.6 4 4
XPO1 0.028 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.026 0.1 -10000 0 -0.67 8 8
FOXO1/SKP2 0.014 0.056 -10000 0 -0.44 3 3
mol:GDP 0.01 0.011 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.099 0.097 0.52 4 -0.6 3 7
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0 0.11 -10000 0 -0.48 8 8
MST1 0.031 0.038 -10000 0 -0.67 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.008 0.12 -10000 0 -0.58 9 9
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.057 0.21 2 -0.4 6 8
MAPK9 0.03 0.017 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.026 0.038 -10000 0 -0.67 1 1
SOD2 0.1 0.11 0.56 11 -0.62 2 13
RBL2 0.074 0.16 0.57 1 -0.89 8 9
RAL/GDP 0.046 0.015 -10000 0 -10000 0 0
CHUK 0.032 0.019 -10000 0 -10000 0 0
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
RAL/GTP 0.05 0.016 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.07 0.38 -10000 0 -1.4 37 37
SKP2 0.022 0.057 -10000 0 -0.68 3 3
USP7 0.028 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.019 -10000 0 -10000 0 0
CCNB1 0.069 0.12 0.58 3 -0.63 2 5
FOXO1-3a-4/beta catenin 0.097 0.1 0.45 6 -0.42 4 10
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.056 -10000 0 -0.43 3 3
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
SGK1 0.017 0.11 -10000 0 -0.68 10 10
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.01 -10000 0 -10000 0 0
ZFAND5 0.078 0.11 0.61 13 -0.44 2 15
SFN -0.084 0.12 -10000 0 -0.68 13 13
CDK2 0.027 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.008 0.11 -10000 0 -0.55 9 9
CREBBP 0.027 0.006 -10000 0 -10000 0 0
FBXO32 0.065 0.11 0.56 2 -0.57 4 6
BCL6 0.082 0.13 0.53 2 -0.78 5 7
RALB 0.028 0.005 -10000 0 -10000 0 0
RALA 0.028 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.008 0.003 -10000 0 -10000 0 0
SNTA1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.008 0.004 -10000 0 -10000 0 0
MAPK12 -0.001 0.052 -10000 0 -0.39 8 8
CCND1 0.007 0.046 -10000 0 -0.4 4 4
p38 gamma/SNTA1 0.022 0.062 -10000 0 -0.37 8 8
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.026 0.008 -10000 0 -10000 0 0
G2/M transition checkpoint 0.002 0.058 -10000 0 -0.38 8 8
MAP2K6 0.002 0.06 -10000 0 -0.42 9 9
MAPT 0.013 0.051 0.32 6 -0.37 3 9
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.02 -10000 0 -0.39 1 1
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 0.038 0.013 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.005 0.11 -10000 0 -0.44 26 26
NF kappa B1 p50/RelA/I kappa B alpha 0.035 0.041 -10000 0 -10000 0 0
NFKBIA 0.014 0.03 -10000 0 -0.24 5 5
MAPK14 0.028 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.016 0.005 -10000 0 -10000 0 0
REL -0.014 0.16 -10000 0 -0.67 27 27
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.031 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
NF kappa B1 p50 dimer 0.025 0.024 0.25 5 -10000 0 5
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.019 0.042 -10000 0 -0.31 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.039 0.042 -10000 0 -10000 0 0
SRC 0.027 0.009 -10000 0 -10000 0 0
PI3K 0.036 0.045 -10000 0 -0.51 3 3
NF kappa B1 p50/RelA 0.019 0.042 -10000 0 -0.31 6 6
IKBKB 0.027 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.006 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.039 -10000 0 -10000 0 0
cell death 0.038 0.04 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.005 0.11 -10000 0 -0.44 26 26
LCK 0.011 0.085 -10000 0 -0.68 6 6
BCL3 0.025 0.01 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.031 -10000 0 -0.33 3 3
TRAF2/ASK1 0.032 0.025 -10000 0 -0.44 1 1
ATM 0.025 0.033 -10000 0 -0.68 1 1
MAP2K3 0.037 0.096 0.42 15 -0.39 3 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.094 0.34 14 -0.45 4 18
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.015 0.081 -10000 0 -0.68 6 6
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.004 0.12 -10000 0 -0.64 15 15
MAP3K1 0.027 0.006 -10000 0 -10000 0 0
MAP3K6 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.028 0.003 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.027 -10000 0 -0.51 1 1
TAK1/TAB family 0.011 0.033 -10000 0 -0.17 4 4
RAC1/OSM/MEKK3 0.05 0.015 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.037 0.056 -10000 0 -0.34 2 2
TRAF6 0.007 0.027 -10000 0 -0.4 2 2
RAC1 0.027 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.02 0.066 -10000 0 -0.68 4 4
CCM2 0.026 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.032 0.045 -10000 0 -0.44 4 4
MAPK11 0.02 0.013 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.046 0.055 -10000 0 -0.5 4 4
OSM/MEKK3 0.038 0.013 -10000 0 -10000 0 0
TAOK1 -0.028 0.13 -10000 0 -0.4 48 48
TAOK2 0.015 0.019 -10000 0 -0.39 1 1
TAOK3 0.016 0.019 -10000 0 -0.39 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.028 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.033 -10000 0 -0.68 1 1
MAP3K10 0.026 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.038 -10000 0 -0.43 1 1
GADD45/MTK1/MTK1 0.037 0.094 -10000 0 -0.41 17 17
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.027 0.005 -9999 0 -10000 0 0
SMAD2 -0.016 0.044 -9999 0 -0.24 1 1
SMAD3 0.02 0.016 -9999 0 -10000 0 0
SMAD3/SMAD4 0.031 0.053 -9999 0 -0.43 5 5
SMAD4/Ubc9/PIASy 0.049 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.026 0.065 -9999 0 -0.42 1 1
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.004 0.055 -9999 0 -0.43 1 1
MAP3K1 0.027 0.006 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.011 0.12 -9999 0 -0.49 25 25
MAPK3 0.026 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.025 0.008 -9999 0 -10000 0 0
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
CTDSPL 0.027 0.004 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.011 0.16 -9999 0 -0.67 25 25
UBE2I 0.026 0.007 -9999 0 -10000 0 0
NUP153 0.026 0.033 -9999 0 -0.68 1 1
KPNA2 0.026 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.008 -9999 0 -10000 0 0
EPO signaling 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
BCL2L1 0.031 0.098 -10000 0 -10000 0 0
CRKL 0.013 0.047 0.46 3 -10000 0 3
mol:DAG 0.028 0.047 -10000 0 -10000 0 0
HRAS 0.034 0.063 0.36 5 -10000 0 5
MAPK8 0.015 0.061 -10000 0 -0.44 6 6
RAP1A 0.024 0.065 0.48 6 -10000 0 6
GAB1 0.022 0.056 0.45 4 -10000 0 4
MAPK14 0.021 0.032 -10000 0 -10000 0 0
EPO 0.02 0.02 -10000 0 -10000 0 0
PLCG1 0.028 0.048 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.024 0.021 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.023 0.1 -10000 0 -0.42 22 22
GAB1/SHC/GRB2/SOS1 0.047 0.044 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.031 0.026 -10000 0 -10000 0 0
IRS2 0.022 0.061 0.47 5 -10000 0 5
STAT1 0.029 0.071 -10000 0 -10000 0 0
STAT5B 0.027 0.061 -10000 0 -10000 0 0
cell proliferation 0.013 0.072 0.37 6 -0.42 6 12
GAB1/SHIP/PIK3R1/SHP2/SHC 0.037 0.041 -10000 0 -0.41 1 1
TEC 0.022 0.056 0.45 4 -10000 0 4
SOCS3 -0.008 0.15 -10000 0 -0.68 22 22
STAT1 (dimer) 0.029 0.071 -10000 0 -10000 0 0
JAK2 0.027 0.021 -10000 0 -0.34 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.053 -10000 0 -10000 0 0
EPO/EPOR 0.031 0.026 -10000 0 -10000 0 0
LYN 0.025 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.031 0.04 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.024 0.021 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.05 0.033 -10000 0 -10000 0 0
mol:IP3 0.028 0.047 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.044 0.045 -10000 0 -10000 0 0
SH2B3 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.02 0.031 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.001 0.062 -10000 0 -0.26 19 19
PTPN6 0.022 0.046 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.042 0.044 -10000 0 -10000 0 0
EPOR 0.024 0.021 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.047 0.044 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.03 0.041 -10000 0 -10000 0 0
VAV2 0.024 0.062 0.46 6 -10000 0 6
CBL 0.021 0.056 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.036 0.038 -10000 0 -10000 0 0
STAT5A 0.027 0.061 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.098 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.011 -10000 0 -10000 0 0
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
BTK 0.011 0.057 0.26 1 -0.36 5 6
BCL2 -0.014 0.25 -10000 0 -0.91 33 33
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 0.054 -9999 0 -0.37 8 8
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.005 -9999 0 -10000 0 0
DOCK1 0.023 0.057 -9999 0 -0.68 3 3
ITGA4 0.023 0.039 -9999 0 -0.68 1 1
alpha4/beta7 Integrin/MAdCAM1 0.051 0.075 -9999 0 -0.41 10 10
EPO 0.004 0.025 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.022 0.078 -9999 0 -0.48 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.032 -9999 0 -0.51 1 1
EPO/EPOR (dimer) 0.031 0.019 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.038 -9999 0 -0.4 3 3
PIK3CA 0.023 0.057 -9999 0 -0.68 3 3
PI3K 0.036 0.045 -9999 0 -0.51 3 3
ARF6 0.027 0.005 -9999 0 -10000 0 0
JAK2 0.025 0.02 -9999 0 -0.31 1 1
PXN 0.027 0.005 -9999 0 -10000 0 0
PIK3R1 0.027 0.006 -9999 0 -10000 0 0
MADCAM1 0.006 0.058 -9999 0 -0.68 2 2
cell adhesion 0.049 0.074 -9999 0 -0.4 10 10
CRKL/CBL 0.03 0.019 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.018 0.054 -9999 0 -0.41 5 5
ITGB7 0.009 0.093 -9999 0 -0.64 8 8
RAC1 0.027 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.048 0.054 -9999 0 -0.44 5 5
p130Cas/Crk/Dock1 0.035 0.061 -9999 0 -0.36 8 8
VCAM1 0.019 0.068 -9999 0 -0.68 4 4
RHOA 0.027 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.065 0.03 -9999 0 -0.41 1 1
BCAR1 0.009 0.05 -9999 0 -0.38 5 5
EPOR 0.024 0.016 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.039 -9999 0 -0.41 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.015 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.014 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.089 -10000 0 -0.54 3 3
EPO 0.12 0.11 -10000 0 -0.92 1 1
FIH (dimer) 0.037 0.012 -10000 0 -10000 0 0
APEX1 0.036 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.12 -10000 0 -0.75 2 2
FLT1 0.021 0.12 -10000 0 -0.88 4 4
ADORA2A 0.1 0.12 0.43 1 -0.96 1 2
germ cell development 0.12 0.11 -10000 0 -0.94 1 1
SLC11A2 0.12 0.11 -10000 0 -1 1 1
BHLHE40 0.13 0.11 -10000 0 -1 1 1
HIF1AN 0.037 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.098 0.36 1 -0.66 2 3
ETS1 0.038 0.015 -10000 0 -10000 0 0
CITED2 -0.031 0.31 -10000 0 -1.1 35 35
KDR 0.028 0.12 -10000 0 -1.1 4 4
PGK1 0.12 0.11 -10000 0 -1 1 1
SIRT1 0.026 0.033 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.14 -10000 0 -1.3 1 1
EPAS1 0.06 0.07 -10000 0 -0.46 2 2
SP1 0.033 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.12 -10000 0 -0.76 3 3
EFNA1 0.12 0.11 -10000 0 -1 1 1
FXN 0.12 0.12 0.51 3 -0.96 1 4
POU5F1 0.12 0.11 -10000 0 -1 1 1
neuron apoptosis -0.16 0.13 1.2 1 -10000 0 1
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.016 0.11 -10000 0 -0.67 10 10
EGLN2 0.035 0.014 -10000 0 -10000 0 0
EGLN1 0.034 0.036 -10000 0 -0.68 1 1
VHL/Elongin B/Elongin C 0.05 0.044 -10000 0 -0.46 3 3
VHL 0.023 0.057 -10000 0 -0.68 3 3
ARNT 0.035 0.015 -10000 0 -10000 0 0
SLC2A1 0.14 0.12 0.49 6 -0.96 1 7
TWIST1 0.12 0.14 0.46 1 -0.59 7 8
ELK1 0.022 0.036 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.089 0.098 -10000 0 -0.64 1 1
VEGFA 0.12 0.12 -10000 0 -0.77 3 3
CREBBP 0.026 0.006 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.027 0.044 0.29 3 -0.38 3 6
adherens junction organization 0.02 0.043 0.25 4 -0.31 1 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.036 0.052 -10000 0 -0.37 6 6
FMN1 0.01 0.077 -10000 0 -0.35 18 18
mol:IP3 0.027 0.034 -10000 0 -0.34 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.027 -10000 0 -0.3 1 1
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.032 0.038 0.25 1 -0.33 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.036 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.034 -10000 0 -0.39 2 2
VASP 0.024 0.023 -10000 0 -0.28 1 1
ZYX 0.024 0.025 -10000 0 -10000 0 0
JUB 0.024 0.025 -10000 0 -0.28 1 1
EGFR(dimer) 0.038 0.049 -10000 0 -0.37 4 4
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.041 0.25 1 -0.34 3 4
PIK3CA 0.024 0.058 -10000 0 -0.68 3 3
PI3K 0.049 0.042 0.26 1 -0.35 3 4
FYN 0.026 0.038 0.29 3 -10000 0 3
mol:Ca2+ 0.026 0.034 -10000 0 -0.33 3 3
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.027 0.034 -10000 0 -0.34 3 3
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.037 0.052 -10000 0 -0.62 1 1
establishment of polarity of embryonic epithelium 0.024 0.023 -10000 0 -0.28 1 1
SRC 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.02 0.066 -10000 0 -0.68 4 4
CASR 0.017 0.033 -10000 0 -0.32 3 3
RhoA/GTP 0.039 0.034 -10000 0 -0.3 3 3
AKT2 0.03 0.035 -10000 0 -0.32 3 3
actin cable formation 0.007 0.074 -10000 0 -0.34 18 18
apoptosis -0.029 0.046 0.36 3 -0.32 4 7
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.021 0.052 -10000 0 -0.39 6 6
PIP5K1A 0.022 0.035 -10000 0 -0.4 2 2
PLCG1 0.027 0.035 -10000 0 -0.34 3 3
Rac1/GTP 0.048 0.049 -10000 0 -0.34 4 4
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.031 -9999 0 -0.39 1 1
HDAC3 0.027 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.035 0.013 -9999 0 -10000 0 0
GATA2/HDAC5 0.039 0.011 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.05 0.029 -9999 0 -0.44 1 1
HDAC9 0.013 0.044 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.017 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.039 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.039 0.011 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -9999 0 -10000 0 0
GATA2 0.027 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.037 0.014 -9999 0 -10000 0 0
BCOR 0.026 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.013 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.028 -9999 0 -0.51 1 1
Histones 0.007 0.049 -9999 0 -10000 0 0
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.027 0.005 -9999 0 -10000 0 0
HDAC6 0.026 0.008 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.015 -9999 0 -10000 0 0
CAMK4 0.014 0.083 -9999 0 -0.68 6 6
Tubulin/HDAC6 0.048 0.045 -9999 0 -0.4 4 4
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.005 -9999 0 -10000 0 0
GATA1 0.012 0.021 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.007 -9999 0 -10000 0 0
NR3C1 0.027 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.013 0.059 -9999 0 -0.25 4 4
SRF 0.028 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.035 0.052 -9999 0 -0.51 4 4
HDAC4/14-3-3 E 0.038 0.012 -9999 0 -10000 0 0
GNB1 0.027 0.006 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.037 0.028 -9999 0 -0.51 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 0.015 -9999 0 -10000 0 0
HDAC4/SRF 0.047 0.058 -9999 0 -0.44 6 6
HDAC4/ER alpha 0.005 0.12 -9999 0 -0.49 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.007 0.048 -9999 0 -10000 0 0
cell motility 0.047 0.045 -9999 0 -0.4 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.026 0.033 -9999 0 -0.68 1 1
HDAC4/CaMK II delta B 0.027 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.038 0.012 -9999 0 -10000 0 0
ESR1 -0.018 0.16 -9999 0 -0.65 24 24
HDAC6/HDAC11 0.038 0.012 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.052 -9999 0 -0.21 1 1
NPC 0.016 0.003 -9999 0 -10000 0 0
MEF2C 0.025 0.033 -9999 0 -0.68 1 1
RAN 0.027 0.006 -9999 0 -10000 0 0
HDAC4/MEF2C 0.074 0.032 -9999 0 -0.39 1 1
GNG2 0.025 0.033 -9999 0 -0.68 1 1
NCOR2 0.027 0.005 -9999 0 -10000 0 0
TUBB2A 0.022 0.066 -9999 0 -0.68 4 4
HDAC11 0.027 0.004 -9999 0 -10000 0 0
HSP90AA1 0.027 0.005 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
ANKRA2 0.027 0.006 -9999 0 -10000 0 0
RFXANK 0.025 0.012 -9999 0 -10000 0 0
nuclear import -0.036 0.012 -9999 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.029 0.025 -10000 0 -10000 0 0
BIRC5 0.013 0.052 -10000 0 -0.68 1 1
NFKBIA 0.014 0.022 0.25 3 -10000 0 3
CPEB1 -0.023 0.18 -10000 0 -0.65 34 34
AKT1 0.015 0.024 0.25 4 -10000 0 4
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.027 0.021 -10000 0 -10000 0 0
NDEL1/TACC3 0.043 0.024 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.029 0.025 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.027 -10000 0 -10000 0 0
TP53 0.025 0.011 -10000 0 -10000 0 0
DLG7 0.012 0.009 -10000 0 -10000 0 0
AURKAIP1 0.026 0.011 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.046 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.026 0.021 -10000 0 -10000 0 0
AURKA 0.02 0.013 -10000 0 -10000 0 0
AURKB 0.013 0.021 -10000 0 -0.15 6 6
CDC25B 0.02 0.011 -10000 0 -10000 0 0
G2/M transition checkpoint 0.009 0.019 -10000 0 -10000 0 0
mRNA polyadenylation -0.003 0.11 -10000 0 -0.41 30 30
Aurora A/CPEB -0.003 0.11 -10000 0 -0.41 30 30
Aurora A/TACC1/TRAP/chTOG 0.054 0.04 -10000 0 -0.38 1 1
BRCA1 0.026 0.007 -10000 0 -10000 0 0
centrosome duplication 0.029 0.025 -10000 0 -10000 0 0
regulation of centrosome cycle 0.042 0.023 -10000 0 -10000 0 0
spindle assembly 0.052 0.039 -10000 0 -0.38 1 1
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.055 0.035 -10000 0 -0.36 1 1
CENPA 0.017 0.027 -10000 0 -0.25 4 4
Aurora A/PP2A 0.03 0.025 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.021 0.018 -10000 0 -10000 0 0
negative regulation of DNA binding 0.025 0.011 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A 0.009 0.019 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.013 -10000 0 -10000 0 0
TACC1 0.026 0.033 -10000 0 -0.68 1 1
TACC3 0.027 0.009 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.046 0.021 -10000 0 -10000 0 0
Aurora A/RasGAP 0.029 0.025 -10000 0 -10000 0 0
OAZ1 0.025 0.008 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.01 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.051 0.018 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.027 -10000 0 -10000 0 0
PPP2R5D 0.028 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.016 0.03 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
TRAIL 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
TNFSF10 0.026 0.034 -10000 0 -0.68 1 1
positive regulation of NF-kappaB transcription factor activity 0.038 0.027 -10000 0 -0.51 1 1
MAP2K4 0.027 0.042 -10000 0 -10000 0 0
IKBKB 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.057 -10000 0 -0.68 3 3
SMPD1 0.017 0.013 -10000 0 -0.25 1 1
IKBKG 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.039 0.027 -10000 0 -0.51 1 1
TRAIL/TRAILR3 0.005 0.059 -10000 0 -0.51 1 1
TRAIL/TRAILR1 0.035 0.052 -10000 0 -0.51 4 4
TRAIL/TRAILR4 0.039 0.027 -10000 0 -0.51 1 1
TRAIL/TRAILR1/DAP3/GTP 0.044 0.046 -10000 0 -0.41 4 4
IKK complex 0.024 0.049 -10000 0 -0.35 1 1
RIPK1 0.028 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.006 -10000 0 -10000 0 0
MAPK3 0.015 0.025 -10000 0 -0.51 1 1
MAP3K1 0.028 0.039 -10000 0 -0.3 3 3
TRAILR4 (trimer) 0.027 0.004 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.057 -10000 0 -0.68 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.029 0.033 -10000 0 -0.29 4 4
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.011 0.026 -10000 0 -0.51 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.073 0.049 -10000 0 -0.39 4 4
mol:ceramide 0.017 0.013 -10000 0 -0.25 1 1
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.017 0.064 0.28 1 -0.36 6 7
TRAF2 0.025 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.015 0.067 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.049 0.048 -10000 0 -0.44 4 4
DAP3 0.026 0.008 -10000 0 -10000 0 0
CASP10 0.011 0.031 -10000 0 -0.44 1 1
JNK cascade 0.038 0.027 -10000 0 -0.51 1 1
TRAIL (trimer) 0.026 0.034 -10000 0 -0.68 1 1
TNFRSF10C -0.015 0.067 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.055 0.047 -10000 0 -0.39 4 4
TRAIL/TRAILR2/FADD 0.053 0.027 -10000 0 -0.44 1 1
cell death 0.016 0.013 -10000 0 -0.25 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.031 0.02 -10000 0 -0.29 1 1
TRAILR2 (trimer) 0.027 0.004 -10000 0 -10000 0 0
CASP8 0.011 0.03 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.076 0.031 -10000 0 -0.39 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.057 -10000 0 -0.68 3 3
ITGA4 0.023 0.039 -10000 0 -0.68 1 1
RAC1 0.027 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.022 0.078 -10000 0 -0.48 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.051 0.029 -10000 0 -0.44 1 1
alpha4/beta7 Integrin/Paxillin 0.037 0.062 -10000 0 -0.41 8 8
lamellipodium assembly 0.024 0.067 -10000 0 -0.54 5 5
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
PI3K 0.036 0.045 -10000 0 -0.51 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.026 0.008 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.054 0.029 -10000 0 -0.36 1 1
cell adhesion 0.052 0.031 -10000 0 -0.38 1 1
CRKL/CBL 0.03 0.019 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.044 0.026 -10000 0 -0.41 1 1
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.009 0.093 -10000 0 -0.64 8 8
ARF6/GDP 0.024 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.052 0.051 -10000 0 -0.38 5 5
p130Cas/Crk/Dock1 0.048 0.043 -10000 0 -0.44 3 3
VCAM1 0.019 0.068 -10000 0 -0.68 4 4
alpha4/beta1 Integrin/Paxillin/Talin 0.054 0.032 -10000 0 -0.39 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.03 -10000 0 -0.39 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.055 0.029 0.38 1 -10000 0 1
CBL 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.008 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.054 0.032 -10000 0 -0.39 1 1
Rac1/GTP 0.024 0.077 -10000 0 -0.62 5 5
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.029 0.033 -10000 0 -10000 0 0
KLHL20 0.013 0.051 0.2 1 -10000 0 1
CYFIP2 0.027 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.043 0.28 1 -10000 0 1
ENAH 0.027 0.03 -10000 0 -10000 0 0
AP1M1 0.026 0.008 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.016 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.058 0.062 -10000 0 -0.41 7 7
RAPGEF1 0.025 0.037 -10000 0 -10000 0 0
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.032 0.037 -10000 0 -10000 0 0
CRK 0.025 0.03 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.017 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.025 0.071 -10000 0 -0.51 7 7
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
DLG1 0.028 0.036 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.056 0.032 -10000 0 -0.41 1 1
PI3K 0.016 0.023 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.012 -10000 0 -10000 0 0
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
E-cadherin(dimer)/Ca2+ 0.061 0.018 -10000 0 -10000 0 0
AKT1 0.018 0.023 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.047 0.075 0.47 8 -10000 0 8
actin cytoskeleton organization 0.012 0.041 0.19 3 -10000 0 3
CDC42/GDP 0.048 0.082 0.5 10 -10000 0 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.008 -10000 0 -10000 0 0
ITGB7 0.009 0.093 -10000 0 -0.64 8 8
RAC1 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.02 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.013 -10000 0 -10000 0 0
mol:GDP 0.038 0.089 0.53 10 -10000 0 10
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.045 0.045 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1 0.036 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.038 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.036 0.21 4 -10000 0 4
NME1 0.026 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.028 0.036 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.025 0.012 -10000 0 -10000 0 0
WASF2 0.007 0.022 -10000 0 -10000 0 0
Rap1/GTP 0.042 0.027 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.068 0.062 -10000 0 -0.39 7 7
CCND1 0.012 0.039 0.2 3 -10000 0 3
VAV2 0.006 0.14 -10000 0 -0.51 30 30
RAP1/GDP 0.048 0.04 0.32 3 -10000 0 3
adherens junction assembly 0.028 0.036 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.056 0.058 -10000 0 -0.37 7 7
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.029 0.033 -10000 0 -10000 0 0
PIK3CA 0.023 0.057 -10000 0 -0.68 3 3
Rac1/GTP -0.006 0.077 -10000 0 -0.31 10 10
E-cadherin/beta catenin/alpha catenin 0.053 0.015 -10000 0 -10000 0 0
ITGAE 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.038 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.002 0.14 -10000 0 -0.66 18 18
CLTC 0.028 0.02 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.015 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.01 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
CD59 0.021 0.011 -10000 0 -10000 0 0
CPE 0.01 0.056 -10000 0 -0.44 7 7
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
membrane fusion 0.019 0.013 -10000 0 -10000 0 0
CTNND1 0.021 0.036 0.36 3 -10000 0 3
DNM2 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.031 0.24 1 -10000 0 1
TSHR 0.015 0.031 -10000 0 -0.44 2 2
INS 0.01 0.06 -10000 0 -0.45 7 7
BIN1 0.027 0.005 -10000 0 -10000 0 0
mol:Choline 0.019 0.013 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.01 -10000 0 -10000 0 0
JUP 0.021 0.01 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.05 0.024 -10000 0 -0.41 1 1
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.027 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0.014 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.046 0.023 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.01 -10000 0 -10000 0 0
ACAP1 0.023 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.009 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.028 0.023 -10000 0 -10000 0 0
JIP4/KLC1 0.05 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.014 -10000 0 -10000 0 0
RALA/GTP 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.019 0.027 0.36 1 -10000 0 1
NME1 0.016 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.038 0.34 3 -10000 0 3
IL2RA 0.009 0.052 -10000 0 -10000 0 0
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.024 0.071 -10000 0 -0.32 17 17
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.005 -10000 0 -10000 0 0
PLD2 0.018 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.02 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.049 0.025 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.013 -10000 0 -10000 0 0
endocytosis -0.049 0.024 0.4 1 -10000 0 1
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 0.028 0.087 0.46 7 -0.34 10 17
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ASAP2 0.026 0.033 -10000 0 -0.68 1 1
Dynamin 2/GDP 0.03 0.011 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.029 0.079 0.48 6 -0.34 8 14
RALA 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.024 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.025 0.017 -9999 0 -9999 0 0
PLK4 0.027 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.016 0.011 -9999 0 -9999 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.002 0.039 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.021 0.27 2 -10000 0 2
myoblast fusion -0.011 0.027 -10000 0 -10000 0 0
mol:GTP 0.009 0.018 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.025 0.064 0.42 1 -10000 0 1
ARF1/GTP 0.03 0.014 -10000 0 -10000 0 0
mol:GM1 0.005 0.011 -10000 0 -10000 0 0
mol:Choline 0.008 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.026 -10000 0 -10000 0 0
MAPK3 0.009 0.026 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.026 0.064 -10000 0 -0.42 1 1
ARF1 0.026 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.027 -10000 0 -10000 0 0
ARF1/GDP 0.021 0.029 -10000 0 -10000 0 0
ARF6 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.059 0.08 -10000 0 -0.68 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.024 0.03 -10000 0 -10000 0 0
KALRN 0.009 0.02 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.03 -10000 0 -10000 0 0
NME1 0.026 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.027 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.018 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.015 0.026 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
liver development 0.009 0.018 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.018 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.008 0.02 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.013 0.017 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.015 0.026 -10000 0 -10000 0 0
ruffle organization 0.012 0.021 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.009 0.018 -10000 0 -10000 0 0
PLD2 0.012 0.017 -10000 0 -10000 0 0
PIP5K1A 0.012 0.021 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.008 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.026 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.025 0.033 -9999 0 -0.68 1 1
Aurora C/Aurora B/INCENP 0.047 0.037 -9999 0 -0.46 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.02 -9999 0 -0.34 1 1
AURKB -0.006 0.061 -9999 0 -10000 0 0
AURKC 0.021 0.027 -9999 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.018 0.069 -9999 0 -9999 0 0
GPC2 0.016 0.037 -9999 0 -9999 0 0
GPC2/Midkine -0.004 0.059 -9999 0 -9999 0 0
neuron projection morphogenesis -0.004 0.059 -9999 0 -9999 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 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.014 -9999 0 -10000 0 0
MDM2/SUMO1 0.014 0.055 -9999 0 -0.27 2 2
HDAC4 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.001 0.014 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.006 0.039 -9999 0 -0.25 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.012 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.027 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.013 0.059 -9999 0 -0.25 4 4
SUMO1/HDAC1 0.013 0.058 -9999 0 -0.27 2 2
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.067 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.006 0.048 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.046 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
PIAS2 0.027 0.004 -9999 0 -10000 0 0
PIAS1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.052 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.01 -9999 0 -9999 0 0
CTNNB1 0.027 0.004 -9999 0 -9999 0 0
JUP 0.026 0.007 -9999 0 -9999 0 0
CDH1 0.026 0.006 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.018 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0.036 0.2 1 -0.22 1 2
AP2 0.038 0.012 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.036 0.011 -10000 0 -10000 0 0
CLTB 0.027 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.022 0.027 -10000 0 -10000 0 0
CLTA 0.026 0.008 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.028 -10000 0 -0.37 2 2
ARF1/GTP 0.028 0.02 -10000 0 -0.2 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.007 -10000 0 -10000 0 0
mol:Choline 0.008 0.028 -10000 0 -0.37 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.027 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.028 -10000 0 -0.38 2 2
ARF1/GDP 0.005 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.006 -10000 0 -10000 0 0
Rac/GTP 0.022 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.016 -10000 0 -10000 0 0
ARFIP2 0.022 0.014 -10000 0 -10000 0 0
COPA 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.035 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.018 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.023 -10000 0 -0.28 1 1
AP2A1 0.026 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.009 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.026 -10000 0 -0.31 1 1
Arfaptin 2/Rac/GDP 0.034 0.011 -10000 0 -10000 0 0
CYTH2 0.028 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.02 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.024 0.025 -10000 0 -10000 0 0
PLD2 0.005 0.025 -10000 0 -0.37 2 2
ARF-GAP1/v-SNARE 0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.006 0.026 -10000 0 -0.38 2 2
ARF1/GTP/Membrin/GBF1/p115 0.023 0.021 -10000 0 -0.2 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.028 -10000 0 -0.37 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.014 0.013 -10000 0 -10000 0 0
USO1 0.014 0.013 -10000 0 -10000 0 0
GBF1 0.012 0.025 -10000 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.035 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.052 0.017 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.039 0.011 -9999 0 -9999 0 0
FBXW11 0.027 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.073 0.028 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.026 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.035 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 458 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU TCGA.L6.A4ET
109_MAP3K5 0.027 0.027 0.027 -0.19
47_PPARGC1A -0.68 -0.68 0.028 -0.68
105_BMP4 -0.12 0.028 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR -0.41 -0.41 -0.41 -0.41
30_TGFB1/TGF beta receptor Type II 0.028 0.028 0.028 0.028
84_STAT5B -0.049 0.033 -0.048 -0.16
84_STAT5A -0.049 0.033 -0.048 -0.16
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/3033031/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/THCA-TP/3141197/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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