PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1V9867K
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1V9867K
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 49 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
Class IB PI3K non-lipid kinase events 230
Signaling events mediated by Stem cell factor receptor (c-Kit) 219
EGFR-dependent Endothelin signaling events 185
Reelin signaling pathway 178
Signaling mediated by p38-alpha and p38-beta 164
HIF-1-alpha transcription factor network 154
p75(NTR)-mediated signaling 134
Glucocorticoid receptor regulatory network 127
FOXA2 and FOXA3 transcription factor networks 126
Lissencephaly gene (LIS1) in neuronal migration and development 112
Results
Summary Table

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

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

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Class IB PI3K non-lipid kinase events 230 690 3 -0.23 -1000 1000 -1000 -0.022 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 219 17102 78 -0.62 0.19 1000 -1000 -0.086 -1000
EGFR-dependent Endothelin signaling events 185 3885 21 -0.35 0 1000 -1000 -0.074 -1000
Reelin signaling pathway 178 9975 56 -0.52 0 1000 -1000 -0.1 -1000
Signaling mediated by p38-alpha and p38-beta 164 7258 44 -0.4 0 1000 -1000 -0.055 -1000
HIF-1-alpha transcription factor network 154 11771 76 -0.8 0.018 1000 -1000 -0.089 -1000
p75(NTR)-mediated signaling 134 16822 125 -0.44 0 1000 -1000 -0.1 -1000
Glucocorticoid receptor regulatory network 127 14578 114 -1 0.37 1000 -1000 -0.068 -1000
FOXA2 and FOXA3 transcription factor networks 126 5806 46 -1.2 0.026 1000 -1000 -0.041 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 112 6057 54 -0.52 0.022 1000 -1000 -0.09 -1000
Wnt signaling 106 746 7 -0.2 -0.006 1000 -1000 -0.052 -1000
Arf6 signaling events 104 6479 62 -0.35 0.017 1000 -1000 -0.068 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 104 7125 68 -0.53 0.16 1000 -1000 -0.11 -1000
IL4-mediated signaling events 102 9283 91 -1 0.52 1000 -1000 -0.14 -1000
Endothelins 101 9745 96 -0.4 0.038 1000 -1000 -0.07 -1000
Ephrin B reverse signaling 100 4844 48 -0.36 0.21 1000 -1000 -0.067 -1000
FOXM1 transcription factor network 98 5041 51 -0.46 0.012 1000 -1000 -0.14 -1000
EPHB forward signaling 97 8263 85 -0.36 0.2 1000 -1000 -0.097 -1000
Angiopoietin receptor Tie2-mediated signaling 95 8433 88 -0.35 0.031 1000 -1000 -0.099 -1000
ErbB2/ErbB3 signaling events 93 6074 65 -0.44 0.018 1000 -1000 -0.068 -1000
IGF1 pathway 84 4812 57 -0.19 0.081 1000 -1000 -0.097 -1000
BMP receptor signaling 82 6698 81 -0.58 0.024 1000 -1000 -0.095 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 80 6879 85 -0.27 0.012 1000 -1000 -0.068 -1000
ErbB4 signaling events 79 5498 69 -0.45 0.061 1000 -1000 -0.085 -1000
Calcium signaling in the CD4+ TCR pathway 78 2445 31 -0.38 0.011 1000 -1000 -0.086 -1000
Neurotrophic factor-mediated Trk receptor signaling 78 9456 120 -0.66 0.26 1000 -1000 -0.072 -1000
Nongenotropic Androgen signaling 76 3986 52 -0.25 0.11 1000 -1000 -0.06 -1000
Noncanonical Wnt signaling pathway 75 1956 26 -0.2 0 1000 -1000 -0.077 -1000
Signaling events regulated by Ret tyrosine kinase 74 6094 82 -0.17 0 1000 -1000 -0.087 -1000
Visual signal transduction: Rods 74 3857 52 -0.53 0 1000 -1000 -0.08 -1000
Glypican 1 network 73 3532 48 -0.34 0.025 1000 -1000 -0.048 -1000
IL23-mediated signaling events 71 4290 60 -0.49 0.018 1000 -1000 -0.14 -1000
Syndecan-1-mediated signaling events 70 2387 34 -0.22 0 1000 -1000 -0.07 -1000
Aurora C signaling 70 494 7 -0.16 0 1000 -1000 -0.039 -1000
IL6-mediated signaling events 66 5011 75 -0.31 0.054 1000 -1000 -0.073 -1000
Plasma membrane estrogen receptor signaling 66 5725 86 -0.2 0.081 1000 -1000 -0.076 -1000
Aurora B signaling 62 4197 67 -0.33 0.013 1000 -1000 -0.068 -1000
Signaling events mediated by PTP1B 60 4593 76 -0.68 0.068 1000 -1000 -0.08 -1000
amb2 Integrin signaling 60 4921 82 -0.54 0 1000 -1000 -0.08 -1000
Ephrin A reverse signaling 59 415 7 -0.083 0 1000 -1000 -0.04 -1000
Signaling events mediated by PRL 59 2034 34 -0.2 0.021 1000 -1000 -0.059 -1000
Integrins in angiogenesis 56 4744 84 -0.34 0 1000 -1000 -0.089 -1000
LPA receptor mediated events 52 5395 102 -0.29 0.029 1000 -1000 -0.078 -1000
RXR and RAR heterodimerization with other nuclear receptor 50 2627 52 -0.2 0.03 1000 -1000 -0.067 -1000
Signaling events mediated by the Hedgehog family 48 2514 52 -0.22 0.031 1000 -1000 -0.087 -1000
PDGFR-alpha signaling pathway 48 2127 44 -0.4 0.02 1000 -1000 -0.058 -1000
Visual signal transduction: Cones 46 1775 38 -0.18 0.007 1000 -1000 -0.07 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 43 1419 33 -0.6 0 1000 -1000 -0.057 -1000
Ras signaling in the CD4+ TCR pathway 43 733 17 -0.13 0 1000 -1000 -0.065 -1000
Syndecan-3-mediated signaling events 42 1489 35 -0.37 0 1000 -1000 -0.072 -1000
Presenilin action in Notch and Wnt signaling 41 2550 61 -0.44 0.013 1000 -1000 -0.069 -1000
Fc-epsilon receptor I signaling in mast cells 41 4063 97 -0.27 0.028 1000 -1000 -0.087 -1000
Signaling events mediated by HDAC Class III 41 1644 40 -0.61 0.03 1000 -1000 -0.043 -1000
TCGA08_rtk_signaling 41 1071 26 -0.29 0.027 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 40 2967 74 -0.29 0.071 1000 -1000 -0.089 -1000
E-cadherin signaling in keratinocytes 40 1756 43 -0.29 0.044 1000 -1000 -0.073 -1000
Nephrin/Neph1 signaling in the kidney podocyte 38 1299 34 -0.075 0 1000 -1000 -0.072 -1000
Rapid glucocorticoid signaling 38 775 20 -0.19 0.027 1000 -1000 -0.032 -1000
LPA4-mediated signaling events 37 445 12 -0.17 0.019 1000 -1000 -0.016 -1000
FAS signaling pathway (CD95) 37 1781 47 -0.5 0.01 1000 -1000 -0.042 -1000
S1P1 pathway 35 1264 36 -0.33 0.007 1000 -1000 -0.068 -1000
Syndecan-4-mediated signaling events 33 2262 67 -0.34 0.004 1000 -1000 -0.082 -1000
Insulin-mediated glucose transport 31 994 32 -0.14 0.021 1000 -1000 -0.051 -1000
Nectin adhesion pathway 31 1994 63 -0.067 0.015 1000 -1000 -0.077 -1000
TCR signaling in naïve CD8+ T cells 31 2942 93 -0.18 0.085 1000 -1000 -0.068 -1000
Glypican 2 network 31 124 4 -0.033 -0.027 1000 -1000 -0.039 -1000
Canonical Wnt signaling pathway 30 1545 51 -0.44 0.15 1000 -1000 -0.058 -1000
IL27-mediated signaling events 29 1498 51 -0.32 0.014 1000 -1000 -0.065 -1000
IL12-mediated signaling events 28 2511 87 -0.39 0.055 1000 -1000 -0.1 -1000
Coregulation of Androgen receptor activity 27 2094 76 -0.18 0.034 1000 -1000 -0.049 -1000
PLK1 signaling events 27 2318 85 -0.22 0.036 1000 -1000 -0.055 -1000
Regulation of Androgen receptor activity 27 1921 70 -0.29 0.026 1000 -1000 -0.076 -1000
Regulation of p38-alpha and p38-beta 24 1310 54 -0.38 0.028 1000 -1000 -0.071 -1000
BCR signaling pathway 24 2379 99 -0.15 0.043 1000 -1000 -0.096 -1000
Insulin Pathway 24 1846 74 -0.19 0.032 1000 -1000 -0.084 -1000
Arf6 trafficking events 23 1657 71 -0.47 0.032 1000 -1000 -0.065 -1000
Thromboxane A2 receptor signaling 22 2341 105 -0.29 0.071 1000 -1000 -0.056 -1000
TCGA08_retinoblastoma 22 183 8 -0.046 0.008 1000 -1000 -0.021 -1000
IL2 signaling events mediated by STAT5 21 470 22 -0.12 0.067 1000 -1000 -0.054 -1000
Regulation of nuclear SMAD2/3 signaling 20 2780 136 -0.34 0.05 1000 -1000 -0.092 -1000
Effects of Botulinum toxin 20 524 26 -0.1 0 1000 -1000 -0.058 -1000
Regulation of Telomerase 20 2056 102 -0.35 0.022 1000 -1000 -0.08 -1000
TCGA08_p53 19 133 7 -0.02 0.014 1000 -1000 -0.022 -1000
Syndecan-2-mediated signaling events 18 1305 69 -0.2 0.038 1000 -1000 -0.067 -1000
Ceramide signaling pathway 17 1356 76 -0.18 0.047 1000 -1000 -0.064 -1000
E-cadherin signaling events 15 76 5 -0.024 0 1000 -1000 -0.044 -1000
Osteopontin-mediated events 14 532 38 -0.27 0.028 1000 -1000 -0.097 -1000
Hedgehog signaling events mediated by Gli proteins 14 953 65 -0.062 0.041 1000 -1000 -0.079 -1000
Class I PI3K signaling events mediated by Akt 14 1015 68 -0.28 0.053 1000 -1000 -0.057 -1000
TRAIL signaling pathway 14 701 48 -0.08 0.048 1000 -1000 -0.06 -1000
Caspase cascade in apoptosis 12 957 74 -0.054 0.046 1000 -1000 -0.056 -1000
Cellular roles of Anthrax toxin 12 471 39 -0.15 0.02 1000 -1000 -0.029 -1000
Signaling mediated by p38-gamma and p38-delta 12 188 15 -0.016 0.021 1000 -1000 -0.053 -1000
Retinoic acid receptors-mediated signaling 11 655 58 -0.1 0.039 1000 -1000 -0.069 -1000
JNK signaling in the CD4+ TCR pathway 10 171 17 -0.018 0.044 1000 -1000 -0.061 -1000
BARD1 signaling events 9 514 57 -0.11 0.022 1000 -1000 -0.064 -1000
Aurora A signaling 9 586 60 -0.2 0.005 1000 -1000 -0.061 -1000
S1P5 pathway 9 160 17 -0.043 0.024 1000 -1000 -0.052 -1000
E-cadherin signaling in the nascent adherens junction 9 708 76 -0.024 0.048 1000 -1000 -0.087 -1000
IL2 signaling events mediated by PI3K 8 502 58 -0.034 0.065 1000 -1000 -0.075 -1000
S1P3 pathway 8 362 42 -0.043 0.02 1000 -1000 -0.056 -1000
IL1-mediated signaling events 7 494 62 -0.039 0.032 1000 -1000 -0.097 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 7 582 83 -0.074 0.048 1000 -1000 -0.071 -1000
S1P4 pathway 7 181 25 -0.043 0 1000 -1000 -0.057 -1000
Signaling events mediated by HDAC Class II 6 484 75 -0.15 0.001 1000 -1000 -0.059 -1000
Sphingosine 1-phosphate (S1P) pathway 6 186 28 -0.043 0.019 1000 -1000 -0.051 -1000
p38 MAPK signaling pathway 6 269 44 -0.076 0.032 1000 -1000 -0.059 -1000
mTOR signaling pathway 5 301 53 -0.016 0.028 1000 -1000 -0.058 -1000
IFN-gamma pathway 5 340 68 -0.076 0.075 1000 -1000 -0.089 -1000
VEGFR1 specific signals 5 324 56 -0.17 0.063 1000 -1000 -0.085 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 4 106 23 -0.034 0.041 1000 -1000 -0.068 -1000
a4b1 and a4b7 Integrin signaling 4 23 5 -0.007 -0.002 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 4 220 45 -0.026 0.074 1000 -1000 -0.079 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 541 125 -0.17 0.086 1000 -1000 -0.1 -1000
Class I PI3K signaling events 4 294 73 -0.036 0.061 1000 -1000 -0.08 -1000
Circadian rhythm pathway 3 74 22 -0.018 0.046 1000 -1000 -0.052 -1000
HIF-2-alpha transcription factor network 3 155 43 -0.056 0.17 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class I 3 323 104 -0.095 0.046 1000 -1000 -0.066 -1000
FoxO family signaling 3 236 64 -0.048 0.092 1000 -1000 -0.074 -1000
PDGFR-beta signaling pathway 3 317 97 -0.027 0.055 1000 -1000 -0.085 -1000
Arf6 downstream pathway 2 91 43 -0.013 0.022 1000 -1000 -0.039 -1000
EPO signaling pathway 2 123 55 -0.037 0.058 1000 -1000 -0.087 -1000
ceramide signaling pathway 2 131 49 -0.024 0.053 1000 -1000 -0.05 -1000
Atypical NF-kappaB pathway 2 73 31 -0.019 0.024 1000 -1000 -0.068 -1000
Canonical NF-kappaB pathway 1 76 39 -0.022 0.076 1000 -1000 -0.075 -1000
Paxillin-independent events mediated by a4b1 and a4b7 1 63 37 -0.048 0.035 1000 -1000 -0.073 -1000
Paxillin-dependent events mediated by a4b1 1 43 36 -0.008 0.022 1000 -1000 -0.073 -1000
PLK2 and PLK4 events 0 0 3 -0.014 0.012 1000 -1000 -0.027 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 7 27 -0.001 0.028 1000 -1000 -0.051 -1000
Arf1 pathway 0 0 54 0 0.025 1000 -1000 -0.045 -1000
Alternative NF-kappaB pathway 0 5 13 -0.002 0 1000 -1000 -0.059 -1000
Total 5861 344851 7203 -32 -990 131000 -131000 -9 -131000
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.23 0.37 0.83 230 -10000 0 230
PI3K Class IB/PDE3B -0.23 0.37 -10000 0 -0.84 230 230
PDE3B -0.23 0.37 -10000 0 -0.84 230 230
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 -0.15 0.22 -10000 0 -0.39 380 380
CRKL -0.16 0.23 -10000 0 -0.41 379 379
HRAS -0.16 0.17 -10000 0 -0.57 21 21
mol:PIP3 -0.17 0.21 -10000 0 -0.4 379 379
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.2 0.22 -10000 0 -0.44 380 380
FOXO3 -0.14 0.21 -10000 0 -0.38 379 379
AKT1 -0.16 0.22 -10000 0 -0.41 379 379
BAD -0.14 0.21 -10000 0 -0.37 379 379
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 380 380
GSK3B -0.14 0.21 -10000 0 -0.37 379 379
RAF1 -0.089 0.17 -10000 0 -0.46 18 18
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 380 380
STAT1 -0.45 0.56 -10000 0 -1.1 386 386
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.46 19 19
cell proliferation -0.18 0.24 -10000 0 -0.43 380 380
PIK3CA 0 0.01 -10000 0 -10000 0 0
TEC -0.002 0.041 -10000 0 -0.84 2 2
RPS6KB1 -0.18 0.24 -10000 0 -0.44 380 380
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.46 19 19
LYN/TEC/p62DOK -0.18 0.2 -10000 0 -0.4 380 380
MAPK3 -0.052 0.13 -10000 0 -0.32 16 16
STAP1 -0.2 0.24 -10000 0 -0.46 382 382
GRAP2 -0.014 0.1 -10000 0 -0.73 16 16
JAK2 -0.4 0.44 -10000 0 -0.87 386 386
STAT1 (dimer) -0.44 0.55 -10000 0 -1 386 386
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.18 0.2 -10000 0 -0.41 380 380
actin filament polymerization -0.18 0.24 -10000 0 -0.44 380 380
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.34 -10000 0 -0.63 381 381
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.37 370 370
PI3K -0.19 0.2 -10000 0 -0.41 379 379
PTEN -0.002 0.041 -10000 0 -0.84 2 2
SCF/KIT/EPO/EPOR -0.59 0.68 -10000 0 -1.3 379 379
MAPK8 -0.18 0.24 -10000 0 -0.44 380 380
STAT3 (dimer) -0.18 0.24 -10000 0 -0.43 380 380
positive regulation of transcription -0.04 0.11 -10000 0 -0.26 16 16
mol:GDP -0.16 0.18 -10000 0 -0.51 38 38
PIK3C2B -0.18 0.24 -10000 0 -0.44 380 380
CBL/CRKL -0.18 0.19 -10000 0 -0.38 379 379
FER -0.18 0.24 -10000 0 -0.44 383 383
SH2B3 -0.18 0.24 -10000 0 -0.44 380 380
PDPK1 -0.15 0.2 -10000 0 -0.36 379 379
SNAI2 -0.18 0.24 -10000 0 -0.45 381 381
positive regulation of cell proliferation -0.32 0.41 -10000 0 -0.76 386 386
KITLG 0.001 0.068 -10000 0 -0.68 6 6
cell motility -0.32 0.41 -10000 0 -0.76 386 386
PTPN6 0.014 0.021 -10000 0 -0.27 2 2
EPOR -0.095 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 387 387
SOCS1 -0.004 0.039 -10000 0 -0.34 9 9
cell migration 0.19 0.25 0.45 386 -10000 0 386
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.045 0.11 -10000 0 -0.3 85 85
VAV1 -0.002 0.032 -10000 0 -0.46 3 3
GRB10 -0.2 0.22 -10000 0 -0.44 380 380
PTPN11 0.012 0.013 -10000 0 -10000 0 0
SCF/KIT -0.21 0.24 -10000 0 -0.47 380 380
GO:0007205 0.008 0.013 -10000 0 -10000 0 0
MAP2K1 -0.062 0.14 -10000 0 -0.36 16 16
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.74 -10000 0 -1.4 378 378
MAP2K2 -0.062 0.14 -10000 0 -0.36 16 16
SHC/Grb2/SOS1 -0.18 0.2 -10000 0 -0.4 379 379
STAT5A -0.27 0.35 -10000 0 -0.64 387 387
GRB2 0 0.01 -10000 0 -10000 0 0
response to radiation -0.18 0.24 -10000 0 -0.44 381 381
SHC/GRAP2 -0.011 0.08 -10000 0 -0.64 13 13
PTPRO -0.18 0.24 -10000 0 -0.44 380 380
SH2B2 -0.18 0.24 -10000 0 -0.44 380 380
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.19 0.25 -10000 0 -0.46 386 386
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.12 0.29 -10000 0 -1.6 24 24
EGFR-dependent Endothelin signaling events

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
HRAS 0 0.01 -9999 0 -10000 0 0
EGFR -0.29 0.4 -9999 0 -0.83 297 297
EGF/EGFR -0.29 0.33 -9999 0 -0.58 419 419
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.29 -9999 0 -0.53 410 410
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.17 0.33 -9999 0 -0.84 167 167
EGF/EGFR dimer/SHC -0.3 0.33 -9999 0 -0.62 410 410
mol:GDP -0.26 0.28 -9999 0 -0.52 410 410
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.066 0.22 -9999 0 -0.84 66 66
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.26 -9999 0 -0.48 410 410
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.24 0.26 -9999 0 -0.49 410 410
FRAP1 -0.25 0.27 -9999 0 -0.51 410 410
EGF/EGFR dimer -0.35 0.37 -9999 0 -0.71 410 410
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.01 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.051 0.17 -9999 0 -0.64 66 66
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 -0.006 0.032 -9999 0 -10000 0 0
VLDLR -0.021 0.13 -9999 0 -0.84 21 21
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.029 -9999 0 -0.84 1 1
ITGA3 -0.004 0.058 -9999 0 -0.84 4 4
RELN/VLDLR/Fyn -0.36 0.29 -9999 0 -0.57 529 529
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.002 0.029 -9999 0 -0.48 3 3
AKT1 -0.21 0.17 -9999 0 -0.33 527 527
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.066 -9999 0 -0.28 51 51
RELN/LRP8/DAB1 -0.35 0.26 -9999 0 -0.54 525 525
LRPAP1/LRP8 -0.021 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.32 0.24 -9999 0 -0.51 525 525
DAB1/alpha3/beta1 Integrin -0.3 0.23 -9999 0 -0.6 120 120
long-term memory -0.39 0.31 -9999 0 -0.57 571 571
DAB1/LIS1 -0.31 0.24 -9999 0 -0.49 529 529
DAB1/CRLK/C3G -0.3 0.23 -9999 0 -0.6 119 119
PIK3CA 0 0.01 -9999 0 -10000 0 0
DAB1/NCK2 -0.31 0.24 -9999 0 -0.49 529 529
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.093 0.26 -9999 0 -0.84 90 90
CDK5R1 -0.009 0.048 -9999 0 -10000 0 0
RELN -0.52 0.4 -9999 0 -0.84 524 524
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.36 0.28 -9999 0 -0.58 524 524
GRIN2A/RELN/LRP8/DAB1/Fyn -0.37 0.3 -9999 0 -0.57 538 538
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.34 0.27 -9999 0 -0.54 529 529
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.33 0.26 -9999 0 -0.52 532 532
RELN/LRP8 -0.36 0.28 -9999 0 -0.58 524 524
GRIN2B/RELN/LRP8/DAB1/Fyn -0.36 0.27 -9999 0 -0.54 558 558
PI3K 0 0.006 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.045 -9999 0 -0.64 4 4
RAP1A -0.28 0.22 -9999 0 -0.55 118 118
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.053 -9999 0 -0.52 7 7
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.071 0.23 -9999 0 -0.82 73 73
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.14 0.11 -9999 0 -0.56 3 3
neuron adhesion -0.26 0.2 -9999 0 -0.62 36 36
LRP8 -0.034 0.091 -9999 0 -10000 0 0
GSK3B -0.18 0.17 -9999 0 -0.44 48 48
RELN/VLDLR/DAB1/Fyn -0.32 0.25 -9999 0 -0.51 529 529
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.23 0.18 -9999 0 -0.36 529 529
CDK5 -0.001 0.019 -9999 0 -0.28 4 4
MAPT -0.043 0.25 -9999 0 -0.78 84 84
neuron migration -0.25 0.24 -9999 0 -0.5 135 135
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.11 -9999 0 -0.56 3 3
RELN/VLDLR -0.34 0.27 -9999 0 -0.54 529 529
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.4 0.64 -9999 0 -1.3 281 281
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.082 0.15 -9999 0 -0.39 11 11
ATF2/c-Jun -0.056 0.17 -9999 0 -0.97 12 12
MAPK11 -0.084 0.16 -9999 0 -0.48 13 13
MITF -0.092 0.2 -9999 0 -0.36 287 287
MAPKAPK5 -0.089 0.19 -9999 0 -0.35 284 284
KRT8 -0.095 0.19 -9999 0 -0.36 285 285
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.01 -9999 0 -0.28 1 1
p38alpha-beta/CK2 -0.12 0.23 -9999 0 -0.45 284 284
CEBPB -0.089 0.19 -9999 0 -0.35 284 284
SLC9A1 -0.089 0.19 -9999 0 -0.35 284 284
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.34 284 284
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.54 13 13
JUN -0.054 0.16 -9999 0 -0.95 12 12
PPARGC1A -0.22 0.37 -9999 0 -0.58 357 357
USF1 -0.089 0.19 -9999 0 -0.35 284 284
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.37 13 13
NOS2 -0.091 0.21 -9999 0 -1.1 7 7
DDIT3 -0.089 0.19 -9999 0 -0.35 284 284
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.069 0.16 -9999 0 -0.42 27 27
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.54 13 13
CREB1 -0.092 0.2 -9999 0 -0.37 284 284
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.07 0.17 -9999 0 -0.49 11 11
RPS6KA4 -0.089 0.19 -9999 0 -0.35 284 284
PLA2G4A -0.13 0.27 -9999 0 -0.74 99 99
GDI1 -0.089 0.19 -9999 0 -0.35 284 284
TP53 -0.12 0.24 -9999 0 -0.44 284 284
RPS6KA5 -0.092 0.19 -9999 0 -0.36 290 290
ESR1 -0.17 0.25 -9999 0 -0.42 383 383
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.19 -9999 0 -0.36 284 284
MEF2A -0.089 0.19 -9999 0 -0.35 284 284
EIF4EBP1 -0.092 0.2 -9999 0 -0.37 284 284
KRT19 -0.1 0.21 -9999 0 -0.37 288 288
ELK4 -0.089 0.19 -9999 0 -0.35 284 284
ATF6 -0.089 0.19 -9999 0 -0.35 284 284
ATF1 -0.092 0.2 -9999 0 -0.37 284 284
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.53 14 14
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.54 13 13
HIF-1-alpha transcription factor network

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
PKM2 -0.42 0.45 -9999 0 -1 221 221
HDAC7 0 0 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.31 -9999 0 -0.8 173 173
SMAD4 0 0 -9999 0 -10000 0 0
ID2 -0.42 0.45 -9999 0 -1 212 212
AP1 -0.22 0.31 -9999 0 -0.66 273 273
ABCG2 -0.45 0.48 -9999 0 -1.1 224 224
HIF1A -0.054 0.06 -9999 0 -10000 0 0
TFF3 -0.5 0.52 -9999 0 -1.1 269 269
GATA2 -0.017 0.13 -9999 0 -0.79 21 21
AKT1 -0.057 0.079 -9999 0 -10000 0 0
response to hypoxia -0.079 0.085 -9999 0 -0.25 25 25
MCL1 -0.42 0.45 -9999 0 -1 209 209
NDRG1 -0.43 0.45 -9999 0 -1 212 212
SERPINE1 -0.43 0.45 -9999 0 -1 210 210
FECH -0.42 0.45 -9999 0 -1 212 212
FURIN -0.42 0.45 -9999 0 -1 211 211
NCOA2 -0.004 0.077 -9999 0 -0.84 7 7
EP300 -0.058 0.12 -9999 0 -0.36 49 49
HMOX1 -0.43 0.45 -9999 0 -1 212 212
BHLHE40 -0.42 0.45 -9999 0 -1 224 224
BHLHE41 -0.43 0.47 -9999 0 -1 225 225
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.05 0.05 -9999 0 -10000 0 0
ENG -0.04 0.046 -9999 0 -10000 0 0
JUN -0.009 0.086 -9999 0 -0.84 9 9
RORA -0.42 0.45 -9999 0 -1 215 215
ABCB1 -0.34 0.55 -9999 0 -1.5 160 160
TFRC -0.43 0.45 -9999 0 -1 213 213
CXCR4 -0.43 0.45 -9999 0 -1 226 226
TF -0.69 0.57 -9999 0 -1.1 456 456
CITED2 -0.42 0.45 -9999 0 -1 212 212
HIF1A/ARNT -0.52 0.51 -9999 0 -1.2 227 227
LDHA -0.051 0.047 -9999 0 -10000 0 0
ETS1 -0.43 0.45 -9999 0 -1 201 201
PGK1 -0.42 0.45 -9999 0 -1 215 215
NOS2 -0.43 0.46 -9999 0 -1 211 211
ITGB2 -0.43 0.45 -9999 0 -1 221 221
ALDOA -0.43 0.45 -9999 0 -1 213 213
Cbp/p300/CITED2 -0.44 0.44 -9999 0 -1.1 196 196
FOS -0.27 0.39 -9999 0 -0.84 272 272
HK2 -0.42 0.45 -9999 0 -1 221 221
SP1 0.012 0.024 -9999 0 -10000 0 0
GCK -0.15 0.4 -9999 0 -1.6 53 53
HK1 -0.42 0.45 -9999 0 -1 200 200
NPM1 -0.42 0.45 -9999 0 -1 224 224
EGLN1 -0.42 0.45 -9999 0 -1 210 210
CREB1 0.018 0 -9999 0 -10000 0 0
PGM1 -0.42 0.45 -9999 0 -1 212 212
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.21 0.41 -9999 0 -1.2 100 100
IGFBP1 -0.53 0.53 -9999 0 -1.1 283 283
VEGFA -0.26 0.31 -9999 0 -0.76 100 100
HIF1A/JAB1 -0.029 0.026 -9999 0 -10000 0 0
CP -0.54 0.54 -9999 0 -1.2 295 295
CXCL12 -0.45 0.49 -9999 0 -1.1 236 236
COPS5 0.001 0.01 -9999 0 -0.28 1 1
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.42 0.45 -9999 0 -1 215 215
EGLN3 -0.43 0.46 -9999 0 -1 217 217
CA9 -0.47 0.48 -9999 0 -1.1 229 229
TERT -0.44 0.46 -9999 0 -1 229 229
ENO1 -0.42 0.45 -9999 0 -1 211 211
PFKL -0.42 0.45 -9999 0 -1 224 224
NCOA1 -0.001 0.029 -9999 0 -0.84 1 1
ADM -0.46 0.49 -9999 0 -1.1 232 232
ARNT -0.059 0.052 -9999 0 -10000 0 0
HNF4A -0.002 0.042 -9999 0 -0.28 14 14
ADFP -0.43 0.45 -9999 0 -1 227 227
SLC2A1 -0.26 0.31 -9999 0 -0.76 102 102
LEP -0.8 0.52 -9999 0 -1.1 484 484
HIF1A/ARNT/Cbp/p300 -0.36 0.32 -9999 0 -0.82 181 181
EPO -0.23 0.24 -9999 0 -0.69 14 14
CREBBP -0.058 0.12 -9999 0 -0.36 52 52
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.31 -9999 0 -0.83 144 144
PFKFB3 -0.43 0.46 -9999 0 -1 212 212
NT5E -0.43 0.46 -9999 0 -1 212 212
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.022 -9999 0 -0.64 1 1
Necdin/E2F1 -0.081 0.15 -9999 0 -0.72 29 29
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.17 0.24 -9999 0 -0.49 286 286
NGF (dimer)/p75(NTR)/BEX1 -0.29 0.34 -9999 0 -0.66 347 347
NT-4/5 (dimer)/p75(NTR) -0.44 0.44 -9999 0 -0.81 459 459
IKBKB -0.001 0.014 -9999 0 -0.28 2 2
AKT1 -0.16 0.23 -9999 0 -0.48 284 284
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.073 0.23 -9999 0 -0.7 87 87
MGDIs/NGR/p75(NTR)/LINGO1 -0.22 0.27 -9999 0 -0.59 277 277
FURIN -0.001 0.014 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.23 0.31 -9999 0 -0.61 312 312
LINGO1 -0.062 0.12 -9999 0 -0.28 187 187
Sortilin/TRAF6/NRIF -0.001 0.029 -9999 0 -0.84 1 1
proBDNF (dimer) -0.073 0.23 -9999 0 -0.7 87 87
NTRK1 -0.01 0.061 -9999 0 -0.84 2 2
RTN4R -0.007 0.042 -9999 0 -0.28 20 20
neuron apoptosis -0.16 0.28 -9999 0 -0.52 277 277
IRAK1 -0.001 0.014 -9999 0 -0.28 2 2
SHC1 -0.18 0.29 -9999 0 -0.57 284 284
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.017 -9999 0 -0.48 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.18 0.25 -9999 0 -0.52 284 284
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.2 0.28 -9999 0 -0.55 295 295
Mammalian IAPs/DIABLO -0.006 0.048 -9999 0 -0.51 7 7
proNGF (dimer) -0.017 0.11 -9999 0 -0.66 22 22
MAGED1 -0.001 0.014 -9999 0 -10000 0 0
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.32 0.41 -9999 0 -0.84 324 324
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.17 0.24 -9999 0 -0.49 284 284
NGF -0.017 0.11 -9999 0 -0.66 22 22
cell cycle arrest -0.14 0.25 -9999 0 -0.48 284 284
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.12 0.17 -9999 0 -0.35 284 284
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.39 0.4 -9999 0 -0.72 459 459
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.2 0.28 -9999 0 -0.58 284 284
PSENEN 0 0.01 -9999 0 -10000 0 0
mol:ceramide -0.18 0.25 -9999 0 -0.52 284 284
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.093 0.13 -9999 0 -0.5 13 13
p75(NTR)/beta APP -0.21 0.3 -9999 0 -0.64 277 277
BEX1 -0.16 0.29 -9999 0 -0.53 255 255
mol:GDP -0.18 0.29 -9999 0 -0.58 284 284
NGF (dimer) -0.086 0.19 -9999 0 -0.53 129 129
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.2 0.24 -9999 0 -0.54 277 277
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.17 0.24 -9999 0 -0.5 284 284
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.2 0.28 -9999 0 -0.59 284 284
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.06 0.083 -9999 0 -10000 0 0
NT3 (dimer) -0.14 0.31 -9999 0 -0.84 135 135
TP53 -0.18 0.25 -9999 0 -0.49 312 312
PRDM4 -0.18 0.25 -9999 0 -0.52 284 284
BDNF (dimer) -0.17 0.24 -9999 0 -0.61 174 174
PIK3CA 0 0.01 -9999 0 -10000 0 0
SORT1 -0.001 0.029 -9999 0 -0.84 1 1
activation of caspase activity -0.17 0.23 -9999 0 -0.48 286 286
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.18 0.25 -9999 0 -0.52 284 284
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.18 0.28 -9999 0 -0.52 288 288
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.18 0.25 -9999 0 -0.52 284 284
APH1B -0.001 0.029 -9999 0 -0.84 1 1
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.2 0.28 -9999 0 -0.57 284 284
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.31 0.38 -9999 0 -0.74 353 353
MAPK8 -0.13 0.25 -9999 0 -0.46 277 277
MAPK9 -0.13 0.25 -9999 0 -0.46 277 277
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.14 0.31 -9999 0 -0.84 135 135
NTF4 -0.32 0.41 -9999 0 -0.84 324 324
NDN -0.029 0.15 -9999 0 -0.84 29 29
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.16 0.22 -9999 0 -0.46 284 284
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.018 -9999 0 -0.51 1 1
RhoA-B-C/GTP -0.2 0.28 -9999 0 -0.58 284 284
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.2 0.27 -9999 0 -0.53 312 312
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.21 0.28 -9999 0 -0.56 312 312
PRKACB -0.017 0.078 -9999 0 -0.32 46 46
proBDNF (dimer)/p75 ECD -0.055 0.17 -9999 0 -0.64 66 66
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.082 -9999 0 -0.84 7 7
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.27 -9999 0 -0.5 284 284
BAD -0.14 0.26 -9999 0 -0.47 279 279
RIPK2 -0.001 0.019 -9999 0 -0.28 4 4
NGFR -0.28 0.39 -9999 0 -0.84 277 277
CYCS -0.16 0.24 -9999 0 -0.49 284 284
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.18 0.25 -9999 0 -0.52 284 284
BCL2L11 -0.14 0.26 -9999 0 -0.47 279 279
BDNF (dimer)/p75(NTR) -0.26 0.35 -9999 0 -0.7 312 312
PI3K -0.18 0.25 -9999 0 -0.52 284 284
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.18 0.25 -9999 0 -0.52 284 284
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0.01 -9999 0 -0.28 1 1
NGF (dimer)/p75(NTR) -0.22 0.32 -9999 0 -0.66 284 284
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.18 0.25 -9999 0 -0.52 284 284
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.029 -9999 0 -0.84 1 1
PLG -0.002 0.021 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.22 0.29 -9999 0 -0.56 319 319
SQSTM1 -0.001 0.014 -9999 0 -10000 0 0
NGFRAP1 -0.002 0.041 -9999 0 -0.84 2 2
CASP3 -0.12 0.24 -9999 0 -0.43 279 279
E2F1 -0.095 0.13 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.074 0.12 -9999 0 -0.6 18 18
NGF (dimer)/TRKA -0.019 0.096 -9999 0 -0.65 17 17
MMP7 -0.12 0.29 -9999 0 -0.84 116 116
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.17 0.24 -9999 0 -0.49 284 284
MMP3 -0.12 0.16 -9999 0 -0.84 12 12
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.69 13 13
Glucocorticoid receptor regulatory network

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
PCK2 0.025 0.079 0.34 3 -10000 0 3
SMARCC2 0.003 0.011 -10000 0 -10000 0 0
SMARCC1 0.003 0.01 -10000 0 -10000 0 0
TBX21 -0.15 0.26 -10000 0 -0.68 101 101
SUMO2 0 0.01 -10000 0 -0.28 1 1
STAT1 (dimer) 0.012 0.042 -10000 0 -0.34 1 1
FKBP4 -0.002 0.025 -10000 0 -10000 0 0
FKBP5 -0.012 0.096 -10000 0 -0.72 14 14
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.33 69 -0.44 13 82
PRL -0.096 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.31 0.26 0.53 412 -0.56 5 417
RELA -0.042 0.083 -10000 0 -10000 0 0
FGG 0.25 0.22 0.48 280 -0.51 1 281
GR beta/TIF2 0.14 0.14 0.34 102 -0.58 9 111
IFNG -0.45 0.35 -10000 0 -0.75 425 425
apoptosis -0.29 0.3 0.59 3 -0.67 234 237
CREB1 -0.008 0.028 -10000 0 -10000 0 0
histone acetylation 0.021 0.14 0.39 30 -0.36 30 60
BGLAP -0.11 0.15 -10000 0 -0.45 43 43
GR/PKAc 0.12 0.12 0.32 57 -0.44 4 61
NF kappa B1 p50/RelA -0.074 0.15 -10000 0 -0.42 25 25
SMARCD1 0.003 0.01 -10000 0 -10000 0 0
MDM2 0.13 0.1 0.26 198 -10000 0 198
GATA3 -0.029 0.16 -10000 0 -0.84 30 30
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.043 0.11 -10000 0 -0.57 5 5
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.22 0.27 0.56 3 -0.62 148 151
CSN2 0.21 0.17 0.41 213 -10000 0 213
BRG1/BAF155/BAF170/BAF60A -0.002 0.032 -10000 0 -0.46 4 4
NFATC1 0.001 0.03 -10000 0 -0.84 1 1
POU2F1 0.007 0.013 -10000 0 -10000 0 0
CDKN1A 0.047 0.061 -10000 0 -1.5 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.008 0.008 -10000 0 -10000 0 0
SFN -0.016 0.11 -10000 0 -0.62 21 21
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.14 0.33 50 -0.41 22 72
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.4 0.44 0.54 3 -0.9 325 328
JUN -0.33 0.29 -10000 0 -0.61 356 356
IL4 -0.14 0.15 -10000 0 -0.46 49 49
CDK5R1 -0.009 0.049 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.46 0.42 -10000 0 -0.77 484 484
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.13 0.33 51 -0.41 10 61
cortisol/GR alpha (monomer) 0.37 0.31 0.62 443 -0.46 1 444
NCOA2 -0.007 0.076 -10000 0 -0.84 7 7
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.32 0.41 -10000 0 -0.9 272 272
AP-1/NFAT1-c-4 -0.7 0.53 -10000 0 -1 549 549
AFP -0.63 0.71 -10000 0 -1.6 296 296
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.2 0.16 0.51 51 -10000 0 51
TP53 0.031 0.018 -10000 0 -0.5 1 1
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.89 0.82 -10000 0 -1.7 414 414
KRT14 -0.9 0.78 -10000 0 -1.6 475 475
TBP 0.019 0.001 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.28 361 -10000 0 361
HDAC1 0 0.003 -10000 0 -10000 0 0
HDAC2 0 0.003 -10000 0 -10000 0 0
AP-1 -0.71 0.54 -10000 0 -1 550 550
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.14 0.31 -10000 0 -0.84 137 137
MAPK11 -0.002 0.042 -10000 0 -0.85 2 2
KRT5 -1 0.83 -10000 0 -1.7 476 476
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.005 0.03 -10000 0 -0.83 1 1
STAT1 0.012 0.042 -10000 0 -0.34 1 1
CGA -0.17 0.18 -10000 0 -0.5 81 81
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.21 0.18 0.37 453 -10000 0 453
MAPK3 0 0.004 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.19 0.25 -10000 0 -0.61 138 138
NFKB1 -0.042 0.083 -10000 0 -10000 0 0
MAPK8 -0.24 0.21 -10000 0 -0.45 344 344
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.31 0.32 0.59 3 -0.71 235 238
BAX 0.049 0.03 -10000 0 -10000 0 0
POMC -0.2 0.31 -10000 0 -0.95 70 70
EP300 0.15 0.14 0.3 177 -10000 0 177
cortisol/GR alpha (dimer)/p53 0.33 0.25 0.55 413 -10000 0 413
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.079 0.24 47 -10000 0 47
SGK1 0.24 0.2 0.41 112 -1.2 4 116
IL13 -0.34 0.28 -10000 0 -0.76 125 125
IL6 -0.53 0.64 -10000 0 -1.3 333 333
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.29 0.22 -10000 0 -0.66 88 88
IL2 -0.44 0.35 -10000 0 -0.76 386 386
CDK5 -0.001 0.02 -10000 0 -0.29 4 4
PRKACB -0.017 0.078 -10000 0 -0.32 46 46
HSP90AA1 0 0.01 -10000 0 -0.28 1 1
IL8 -0.22 0.31 -10000 0 -0.76 116 116
CDK5R1/CDK5 -0.006 0.035 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.062 0.098 -10000 0 -0.57 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.51 397 -10000 0 397
SMARCA4 0.003 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.21 0.15 0.38 273 -10000 0 273
NF kappa B1 p50/RelA/Cbp 0.058 0.17 0.34 67 -0.42 1 68
JUN (dimer) -0.33 0.29 -10000 0 -0.61 356 356
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.14 0.26 -10000 0 -0.75 82 82
NR3C1 0.21 0.2 0.42 302 -0.63 2 304
NR4A1 -0.069 0.25 -10000 0 -0.79 90 90
TIF2/SUV420H1 -0.005 0.059 -10000 0 -0.64 7 7
MAPKKK cascade -0.29 0.3 0.59 3 -0.67 234 237
cortisol/GR alpha (dimer)/Src-1 0.32 0.25 0.54 421 -10000 0 421
PBX1 0.005 0.044 -10000 0 -0.83 2 2
POU1F1 0.003 0.012 -10000 0 -10000 0 0
SELE -0.23 0.36 -10000 0 -0.76 179 179
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.21 0.16 0.38 271 -10000 0 271
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.51 397 -10000 0 397
mol:cortisol 0.21 0.2 0.37 440 -10000 0 440
MMP1 -0.22 0.1 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.24 0.28 -9999 0 -0.8 91 91
PCK1 -1.1 0.72 -9999 0 -1.6 506 506
HNF4A -0.25 0.28 -9999 0 -0.9 56 56
KCNJ11 -0.27 0.32 -9999 0 -0.91 85 85
AKT1 -0.14 0.14 -9999 0 -0.4 28 28
response to starvation -0.001 0.006 -9999 0 -10000 0 0
DLK1 -0.5 0.57 -9999 0 -1.3 268 268
NKX2-1 -0.055 0.15 -9999 0 -10000 0 0
ACADM -0.24 0.29 -9999 0 -0.86 72 72
TAT -1.2 0.68 -9999 0 -1.6 616 616
CEBPB 0.002 0.005 -9999 0 -10000 0 0
CEBPA -0.003 0.077 -9999 0 -0.84 7 7
TTR -0.46 0.28 -9999 0 -0.74 303 303
PKLR -0.24 0.28 -9999 0 -0.79 98 98
APOA1 -0.3 0.3 -9999 0 -0.96 58 58
CPT1C -0.24 0.28 -9999 0 -0.82 82 82
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.46 0.26 -9999 0 -0.74 271 271
FOXF1 -0.004 0.056 -9999 0 -0.47 9 9
NF1 0.016 0.029 -9999 0 -0.83 1 1
HNF1A (dimer) 0.003 0.027 -9999 0 -0.28 7 7
CPT1A -0.24 0.28 -9999 0 -0.84 73 73
HMGCS1 -0.24 0.28 -9999 0 -0.83 79 79
NR3C1 -0.11 0.12 -9999 0 -0.39 46 46
CPT1B -0.24 0.29 -9999 0 -0.83 84 84
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.006 -9999 0 -10000 0 0
GCK -0.29 0.37 -9999 0 -1 117 117
CREB1 -0.057 0.066 -9999 0 -10000 0 0
IGFBP1 -0.46 0.61 -9999 0 -1.5 197 197
PDX1 -0.13 0.14 -9999 0 -10000 0 0
UCP2 -0.24 0.28 -9999 0 -0.82 81 81
ALDOB -0.27 0.31 -9999 0 -0.89 82 82
AFP -0.71 0.62 -9999 0 -1 539 539
BDH1 -0.24 0.28 -9999 0 -0.84 78 78
HADH -0.26 0.3 -9999 0 -0.86 90 90
F2 -0.29 0.3 -9999 0 -0.95 61 61
HNF1A 0.003 0.027 -9999 0 -0.28 7 7
G6PC -0.2 0.11 -9999 0 -0.64 7 7
SLC2A2 -0.16 0.17 -9999 0 -10000 0 0
INS 0.026 0.068 -9999 0 -10000 0 0
FOXA1 -0.25 0.28 -9999 0 -0.55 250 250
FOXA3 -0.43 0.22 -9999 0 -0.53 619 619
FOXA2 -0.32 0.34 -9999 0 -0.89 134 134
ABCC8 -0.34 0.44 -9999 0 -1.2 135 135
ALB -0.98 0.65 -9999 0 -1.4 569 569
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.021 0.13 -9999 0 -0.84 21 21
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.36 0.28 -9999 0 -0.58 524 524
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.01 -9999 0 -0.28 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.33 0.25 -9999 0 -0.52 524 524
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.066 -9999 0 -0.28 51 51
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.015 0.089 -9999 0 -0.84 7 7
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.01 -9999 0 -0.28 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.021 0.057 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.009 0.048 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.04 0.098 -9999 0 -0.28 122 122
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.37 0.29 -9999 0 -0.58 529 529
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.26 0.2 -9999 0 -0.47 151 151
MAP1B -0.006 0.046 -9999 0 -0.39 12 12
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.29 0.22 -9999 0 -0.46 524 524
RELN -0.52 0.4 -9999 0 -0.84 524 524
PAFAH/LIS1 -0.009 0.055 -9999 0 -0.56 7 7
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.2 0.16 -9999 0 -0.42 22 22
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.22 0.17 -9999 0 -0.41 98 98
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.28 0.22 -9999 0 -0.44 524 524
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 -0.023 0.077 -9999 0 -0.28 71 71
PAFAH1B2 0 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.004 0.029 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.24 0.19 -9999 0 -0.48 86 86
LRP8 -0.034 0.091 -9999 0 -10000 0 0
NDEL1/Katanin 60 -0.26 0.2 -9999 0 -0.47 152 152
P39/CDK5 -0.3 0.24 -9999 0 -0.48 524 524
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.29 0.25 -9999 0 -0.49 524 524
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.32 0.25 -9999 0 -0.5 529 529
RELN/VLDLR -0.34 0.27 -9999 0 -0.54 529 529
CDC42 0 0 -9999 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.18 0.26 -9999 0 -0.46 322 322
FZD6 -0.006 0.07 -9999 0 -0.84 6 6
WNT6 -0.18 0.34 -9999 0 -0.84 177 177
WNT4 -0.024 0.13 -9999 0 -0.84 19 19
FZD3 -0.008 0.081 -9999 0 -0.84 8 8
WNT5A -0.014 0.099 -9999 0 -0.84 11 11
WNT11 -0.2 0.35 -9999 0 -0.81 203 203
Arf6 signaling events

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
CENTA1/KIF3B -0.004 0.051 -9999 0 -0.69 4 4
ARNO/beta Arrestin1-2 -0.14 0.21 -9999 0 -0.46 215 215
EGFR -0.29 0.4 -9999 0 -0.83 297 297
EPHA2 -0.006 0.07 -9999 0 -0.84 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.35 0.37 -9999 0 -0.71 410 410
ARRB2 -0.062 0.16 -9999 0 -0.46 115 115
mol:GTP 0.017 0.02 -9999 0 -0.16 5 5
ARRB1 -0.002 0.042 -9999 0 -0.65 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.039 0.18 -9999 0 -0.84 38 38
EGF -0.17 0.33 -9999 0 -0.84 167 167
somatostatin receptor activity 0 0 -9999 0 -0.001 287 287
ARAP2 -0.006 0.071 -9999 0 -0.84 6 6
mol:GDP -0.14 0.18 -9999 0 -0.37 253 253
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 229 229
ITGA2B -0.017 0.078 -9999 0 -0.84 3 3
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.044 -9999 0 -0.51 6 6
ADAP1 -0.004 0.053 -9999 0 -0.84 3 3
KIF13B -0.002 0.041 -9999 0 -0.84 2 2
HGF/MET -0.15 0.29 -9999 0 -0.69 178 178
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.16 -9999 0 -0.32 281 281
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.3 0.33 -9999 0 -0.62 410 410
ADRB2 -0.21 0.36 -9999 0 -0.84 214 214
receptor agonist activity 0 0 -9999 0 0 286 286
actin filament binding 0 0 -9999 0 -0.001 279 279
SRC 0 0.01 -9999 0 -10000 0 0
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 259 259
ARF6/GDP -0.016 0.089 -9999 0 -0.44 16 16
ARF6/GDP/GULP/ACAP1 -0.15 0.21 -9999 0 -0.53 143 143
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.017 0.076 -9999 0 -0.52 17 17
ACAP1 -0.016 0.096 -9999 0 -0.44 31 31
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.095 0.24 -9999 0 -0.69 115 115
EFNA1 0 0.01 -9999 0 -10000 0 0
HGF -0.05 0.2 -9999 0 -0.84 50 50
CYTH3 0.011 0 -9999 0 -10000 0 0
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 259 259
endosomal lumen acidification 0 0 -9999 0 -0.001 218 218
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.052 0.2 -9999 0 -0.84 52 52
GNAQ/ARNO -0.001 0.024 -9999 0 -0.48 2 2
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 299 299
MET -0.14 0.32 -9999 0 -0.83 144 144
GNA14 -0.013 0.082 -9999 0 -0.4 27 27
GNA15 -0.002 0.035 -9999 0 -0.39 5 5
GIT1 -0.001 0.019 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 283 283
GNA11 0 0 -9999 0 -10000 0 0
LHCGR -0.12 0.29 -9999 0 -0.84 115 115
AGTR1 -0.21 0.35 -9999 0 -0.84 189 189
desensitization of G-protein coupled receptor protein signaling pathway -0.094 0.24 -9999 0 -0.69 115 115
IPCEF1/ARNO -0.24 0.26 -9999 0 -0.5 410 410
alphaIIb/beta3 Integrin -0.023 0.099 -9999 0 -0.65 17 17
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.074 0.15 -10000 0 -0.37 105 105
NFATC2 -0.031 0.24 -10000 0 -0.78 65 65
NFATC3 -0.063 0.12 -10000 0 -0.31 32 32
CD40LG -0.38 0.58 -10000 0 -1.2 258 258
ITCH 0.013 0.099 -10000 0 -10000 0 0
CBLB 0.013 0.099 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.34 -10000 0 -1 75 75
JUNB 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.1 -10000 0 -0.34 87 87
T cell anergy -0.024 0.16 -10000 0 -0.48 87 87
TLE4 -0.01 0.24 -10000 0 -0.85 47 47
Jun/NFAT1-c-4/p21SNFT -0.29 0.42 -10000 0 -0.93 213 213
AP-1/NFAT1-c-4 -0.53 0.66 -10000 0 -1.4 259 259
IKZF1 0.001 0.18 -10000 0 -0.63 52 52
T-helper 2 cell differentiation -0.096 0.28 -10000 0 -0.79 81 81
AP-1/NFAT1 -0.24 0.34 -10000 0 -0.67 291 291
CALM1 -0.019 0.055 -10000 0 -10000 0 0
EGR2 -0.26 0.62 -10000 0 -1.6 120 120
EGR3 -0.38 0.73 -10000 0 -1.5 224 224
NFAT1/FOXP3 -0.09 0.2 -10000 0 -0.65 56 56
EGR1 -0.29 0.4 -10000 0 -0.84 287 287
JUN -0.012 0.087 -10000 0 -0.84 9 9
EGR4 -0.016 0.064 -10000 0 -0.3 2 2
mol:Ca2+ -0.022 0.063 -10000 0 -10000 0 0
GBP3 -0.006 0.21 -10000 0 -0.72 53 53
FOSL1 -0.007 0.056 -10000 0 -0.84 2 2
NFAT1-c-4/MAF/IRF4 -0.31 0.46 -10000 0 -0.96 222 222
DGKA 0.002 0.18 -10000 0 -0.63 51 51
CREM 0 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.39 0.52 -10000 0 -1.1 253 253
CTLA4 -0.067 0.22 -10000 0 -0.66 50 50
NFAT1-c-4 (dimer)/EGR1 -0.44 0.57 -10000 0 -1.2 258 258
NFAT1-c-4 (dimer)/EGR4 -0.28 0.44 -10000 0 -0.91 232 232
FOS -0.28 0.4 -10000 0 -0.85 272 272
IFNG -0.14 0.25 -10000 0 -0.86 67 67
T cell activation -0.17 0.35 -10000 0 -0.81 144 144
MAF -0.001 0.029 -10000 0 -0.84 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.35 0.88 60 -10000 0 60
TNF -0.32 0.52 -10000 0 -1.1 243 243
FASLG -0.34 0.66 -10000 0 -1.2 267 267
TBX21 -0.026 0.17 -10000 0 -0.73 43 43
BATF3 -0.001 0.029 -10000 0 -0.84 1 1
PRKCQ -0.027 0.16 -10000 0 -0.68 45 45
PTPN1 0 0.18 -10000 0 -0.63 52 52
NFAT1-c-4/ICER1 -0.29 0.43 -10000 0 -0.9 234 234
GATA3 -0.037 0.16 -10000 0 -0.84 30 30
T-helper 1 cell differentiation -0.14 0.24 -10000 0 -0.83 70 70
IL2RA -0.22 0.32 -10000 0 -0.9 90 90
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.002 0.18 -10000 0 -0.63 51 51
E2F1 -0.081 0.14 -10000 0 -10000 0 0
PPARG -0.2 0.36 -10000 0 -0.84 197 197
SLC3A2 0.002 0.18 -10000 0 -0.63 52 52
IRF4 -0.074 0.23 -10000 0 -0.84 71 71
PTGS2 -0.48 0.66 -10000 0 -1.3 304 304
CSF2 -0.37 0.56 -10000 0 -1.1 251 251
JunB/Fra1/NFAT1-c-4 -0.27 0.41 -10000 0 -0.94 168 168
IL4 -0.1 0.3 -10000 0 -0.87 75 75
IL5 -0.37 0.56 -10000 0 -1.1 252 252
IL2 -0.17 0.36 -10000 0 -0.83 141 141
IL3 -0.064 0.066 -10000 0 -10000 0 0
RNF128 -0.063 0.28 -10000 0 -0.89 87 87
NFATC1 -0.16 0.35 -10000 0 -0.89 59 59
CDK4 0.077 0.22 0.61 23 -10000 0 23
PTPRK -0.002 0.2 -10000 0 -0.71 47 47
IL8 -0.38 0.57 -10000 0 -1.1 257 257
POU2F1 0.001 0.011 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.46 0.45 -10000 0 -1.1 180 180
STAT6 (cleaved dimer) -0.5 0.44 -10000 0 -1 290 290
IGHG1 -0.16 0.16 -10000 0 -0.35 131 131
IGHG3 -0.45 0.44 -10000 0 -0.94 286 286
AKT1 -0.21 0.24 -10000 0 -0.64 65 65
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.19 -10000 0 -0.62 36 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.61 96 96
THY1 -0.46 0.45 -10000 0 -1.1 193 193
MYB -0.015 0.11 -10000 0 -0.77 16 16
HMGA1 -0.009 0.05 -10000 0 -0.28 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.66 183 183
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.23 -10000 0 -0.57 85 85
SP1 0.017 0.004 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.025 0.015 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.43 -10000 0 -1 247 247
SOCS1 -0.3 0.3 -10000 0 -0.73 161 161
SOCS3 -0.23 0.26 -10000 0 -0.81 51 51
FCER2 -0.62 0.66 -10000 0 -1.5 276 276
PARP14 0 0.019 -10000 0 -0.31 1 1
CCL17 -0.47 0.45 -10000 0 -1.1 175 175
GRB2 0 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.57 23 23
T cell proliferation -0.46 0.47 -10000 0 -1.1 203 203
IL4R/JAK1 -0.46 0.45 -10000 0 -1.1 185 185
EGR2 -0.59 0.61 -10000 0 -1.3 264 264
JAK2 -0.007 0.025 -10000 0 -10000 0 0
JAK3 0.008 0.035 -10000 0 -0.28 5 5
PIK3R1 0 0 -10000 0 -10000 0 0
JAK1 0.005 0.011 -10000 0 -10000 0 0
COL1A2 -0.14 0.15 -10000 0 -1.7 1 1
CCL26 -0.46 0.45 -10000 0 -1.1 176 176
IL4R -0.49 0.48 -10000 0 -1.2 194 194
PTPN6 0.022 0.018 -10000 0 -0.26 2 2
IL13RA2 -0.46 0.45 -10000 0 -1.1 177 177
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.6 86 86
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.27 -10000 0 -0.64 154 154
GTF3A 0.013 0.016 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.013 0.036 -10000 0 -10000 0 0
IRF4/BCL6 -0.2 0.42 -10000 0 -1.4 87 87
CD40LG -0.035 0.19 -10000 0 -0.72 54 54
MAPK14 -0.26 0.27 -10000 0 -0.68 120 120
mitosis -0.2 0.23 -10000 0 -0.61 65 65
STAT6 -0.52 0.52 -10000 0 -1.1 259 259
SPI1 0.007 0.021 -10000 0 -0.27 4 4
RPS6KB1 -0.19 0.22 -10000 0 -0.59 60 60
STAT6 (dimer) -0.52 0.52 -10000 0 -1.1 265 265
STAT6 (dimer)/PARP14 -0.52 0.5 -10000 0 -1.1 286 286
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.23 -10000 0 -0.66 48 48
FRAP1 -0.21 0.24 -10000 0 -0.64 65 65
LTA -0.47 0.45 -10000 0 -1.1 174 174
FES -0.003 0.05 -10000 0 -0.84 3 3
T-helper 1 cell differentiation 0.52 0.51 1.1 265 -10000 0 265
CCL11 -0.48 0.43 -10000 0 -1.1 213 213
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.23 -10000 0 -0.67 49 49
IL2RG -0.004 0.085 -10000 0 -0.84 5 5
IL10 -0.46 0.46 -10000 0 -1.2 165 165
IRS1 -0.031 0.16 -10000 0 -0.84 31 31
IRS2 -0.038 0.17 -10000 0 -0.84 38 38
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.47 0.45 -10000 0 -1.1 187 187
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.35 -10000 0 -0.8 240 240
COL1A1 -0.18 0.16 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.46 -10000 0 -1.2 165 165
IL2R gamma/JAK3 -0.013 0.07 -10000 0 -0.44 17 17
TFF3 -0.56 0.58 -10000 0 -1.3 249 249
ALOX15 -0.55 0.57 -10000 0 -1.3 219 219
MYBL1 -0.046 0.1 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.4 0.37 -10000 0 -0.84 254 254
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.008 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.23 -10000 0 -0.63 66 66
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.64 65 65
PI3K -0.22 0.25 -10000 0 -0.69 64 64
DOK2 -0.002 0.041 -10000 0 -0.84 2 2
ETS1 0.02 0.042 -10000 0 -0.8 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.18 -10000 0 -0.73 9 9
ITGB3 -0.47 0.47 -10000 0 -1.2 170 170
PIGR -1 0.75 -10000 0 -1.6 548 548
IGHE 0.047 0.039 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.71 9 9
BCL6 0.003 0.042 -10000 0 -0.82 2 2
OPRM1 -0.47 0.45 -10000 0 -1.1 177 177
RETNLB -0.47 0.45 -10000 0 -1.1 180 180
SELP -0.65 0.68 -10000 0 -1.6 257 257
AICDA -0.45 0.44 -10000 0 -1.1 175 175
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 -0.019 0.19 -9999 0 -0.6 67 67
PTK2B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.029 0.16 -9999 0 -0.94 14 14
EDN1 -0.04 0.25 -9999 0 -0.86 66 66
EDN3 -0.4 0.42 -9999 0 -0.84 398 398
EDN2 -0.075 0.14 -9999 0 -0.29 214 214
HRAS/GDP -0.027 0.19 -9999 0 -0.51 68 68
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0 0.13 -9999 0 -0.39 44 44
ADCY4 -0.15 0.29 -9999 0 -0.58 232 232
ADCY5 -0.28 0.36 -9999 0 -0.63 393 393
ADCY6 -0.13 0.27 -9999 0 -0.55 219 219
ADCY7 -0.13 0.27 -9999 0 -0.55 219 219
ADCY1 -0.15 0.29 -9999 0 -0.58 228 228
ADCY2 -0.17 0.33 -9999 0 -0.63 243 243
ADCY3 -0.13 0.27 -9999 0 -0.55 219 219
ADCY8 -0.14 0.27 -9999 0 -0.56 219 219
ADCY9 -0.13 0.27 -9999 0 -0.55 219 219
arachidonic acid secretion -0.11 0.29 -9999 0 -0.46 289 289
ETB receptor/Endothelin-1/Gq/GTP -0.029 0.17 -9999 0 -0.39 108 108
GNAO1 -0.033 0.14 -9999 0 -0.84 21 21
HRAS 0 0.01 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.038 0.2 -9999 0 -0.56 67 67
ETA receptor/Endothelin-1/Gs/GTP -0.092 0.32 -9999 0 -0.59 219 219
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.028 0.2 -9999 0 -0.6 67 67
EDNRB -0.061 0.23 -9999 0 -0.84 69 69
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.027 0.22 -9999 0 -0.65 74 74
CYSLTR1 -0.025 0.21 -9999 0 -0.64 74 74
SLC9A1 0.002 0.099 -9999 0 -0.32 50 50
mol:GDP -0.035 0.21 -9999 0 -0.54 75 75
SLC9A3 -0.04 0.25 -9999 0 -0.6 127 127
RAF1 -0.086 0.24 -9999 0 -0.52 125 125
JUN 0.029 0.17 -9999 0 -0.98 15 15
JAK2 -0.019 0.19 -9999 0 -0.6 67 67
mol:IP3 -0.024 0.16 -9999 0 -0.47 56 56
ETA receptor/Endothelin-1 0.036 0.24 -9999 0 -0.69 67 67
PLCB1 -0.049 0.2 -9999 0 -0.84 49 49
PLCB2 -0.001 0.03 -9999 0 -0.84 1 1
ETA receptor/Endothelin-3 -0.29 0.34 -9999 0 -0.65 398 398
FOS -0.28 0.51 -9999 0 -0.99 278 278
Gai/GDP -0.04 0.15 -9999 0 -0.79 21 21
CRK 0 0 -9999 0 -10000 0 0
mol:Ca ++ -0.045 0.23 -9999 0 -0.65 81 81
BCAR1 0 0.002 -9999 0 -10000 0 0
PRKCB1 -0.028 0.16 -9999 0 -0.44 60 60
GNAQ 0.007 0.042 -9999 0 -0.84 2 2
GNAZ -0.006 0.07 -9999 0 -0.84 6 6
GNAL -0.19 0.35 -9999 0 -0.84 190 190
Gs family/GDP -0.17 0.26 -9999 0 -0.55 227 227
ETA receptor/Endothelin-1/Gq/GTP 0.017 0.12 -9999 0 -0.38 39 39
MAPK14 -0.025 0.16 -9999 0 -0.58 34 34
TRPC6 0.027 0.17 -9999 0 -1 14 14
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.17 -9999 0 -0.41 97 97
ETB receptor/Endothelin-2 -0.1 0.2 -9999 0 -0.69 74 74
ETB receptor/Endothelin-3 -0.35 0.36 -9999 0 -0.68 435 435
ETB receptor/Endothelin-1 -0.077 0.27 -9999 0 -0.69 127 127
MAPK3 -0.21 0.42 -9999 0 -0.79 280 280
MAPK1 -0.21 0.42 -9999 0 -0.79 280 280
Rac1/GDP -0.029 0.19 -9999 0 -0.52 63 63
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.62 227 227
MAPK8 0.027 0.14 -9999 0 -0.6 22 22
SRC 0 0.01 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.045 0.18 -9999 0 -0.6 48 48
p130Cas/CRK/Src/PYK2 -0.01 0.2 -9999 0 -0.58 47 47
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.029 0.19 -9999 0 -0.5 71 71
COL1A2 -0.048 0.24 -9999 0 -0.67 74 74
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.028 0.11 -9999 0 -0.64 6 6
mol:DAG -0.025 0.16 -9999 0 -0.47 56 56
MAP2K2 -0.14 0.31 -9999 0 -0.56 280 280
MAP2K1 -0.14 0.31 -9999 0 -0.56 280 280
EDNRA 0.028 0.056 -9999 0 -0.33 1 1
positive regulation of muscle contraction -0.01 0.17 -9999 0 -0.52 67 67
Gq family/GDP -0.071 0.15 -9999 0 -0.59 38 38
HRAS/GTP -0.05 0.2 -9999 0 -0.45 105 105
PRKCH -0.019 0.16 -9999 0 -0.54 36 36
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.031 0.19 -9999 0 -0.59 53 53
PRKCB -0.03 0.18 -9999 0 -0.55 51 51
PRKCE -0.02 0.16 -9999 0 -0.53 38 38
PRKCD -0.02 0.16 -9999 0 -0.53 37 37
PRKCG -0.028 0.16 -9999 0 -0.52 43 43
regulation of vascular smooth muscle contraction -0.32 0.58 -9999 0 -1.1 277 277
PRKCQ -0.041 0.2 -9999 0 -0.58 69 69
PLA2G4A -0.12 0.32 -9999 0 -0.5 289 289
GNA14 -0.004 0.084 -9999 0 -0.4 27 27
GNA15 0.006 0.036 -9999 0 -0.39 5 5
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.006 -9999 0 -10000 0 0
Rac1/GTP 0.038 0.2 -9999 0 -0.56 67 67
MMP1 -0.12 0.12 -9999 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 -0.004 0.037 -10000 0 -0.28 15 15
EFNB1 0.017 0.052 -10000 0 -0.65 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.19 0.22 -10000 0 -0.44 364 364
Ephrin B2/EPHB1-2 -0.22 0.25 -10000 0 -0.51 363 363
neuron projection morphogenesis -0.18 0.21 -10000 0 -0.42 364 364
Ephrin B1/EPHB1-2/Tiam1 -0.21 0.24 -10000 0 -0.48 364 364
DNM1 -0.005 0.065 -10000 0 -0.75 6 6
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.003 0.13 -10000 0 -0.77 23 23
YES1 -0.023 0.16 -10000 0 -1 22 22
Ephrin B1/EPHB1-2/NCK2 -0.21 0.24 -10000 0 -0.48 364 364
PI3K -0.021 0.13 -10000 0 -0.79 22 22
mol:GDP -0.21 0.24 -10000 0 -0.47 364 364
ITGA2B -0.017 0.078 -10000 0 -0.84 3 3
endothelial cell proliferation 0 0.005 -10000 0 -10000 0 0
FYN -0.023 0.16 -10000 0 -1 22 22
MAP3K7 -0.021 0.13 -10000 0 -0.83 22 22
FGR -0.025 0.16 -10000 0 -1 22 22
TIAM1 -0.001 0.019 -10000 0 -0.28 4 4
PIK3R1 0 0 -10000 0 -10000 0 0
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.033 0.14 -10000 0 -0.63 38 38
LYN -0.023 0.16 -10000 0 -1 22 22
Ephrin B1/EPHB1-2/Src Family Kinases -0.025 0.15 -10000 0 -0.95 22 22
Ephrin B1/EPHB1-2 -0.028 0.14 -10000 0 -0.9 22 22
SRC -0.025 0.16 -10000 0 -1 22 22
ITGB3 -0.015 0.11 -10000 0 -0.84 14 14
EPHB1 -0.36 0.41 -10000 0 -0.84 363 363
EPHB4 0 0.01 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.023 0.099 -10000 0 -0.65 17 17
BLK -0.025 0.16 -10000 0 -1 22 22
HCK -0.025 0.16 -10000 0 -1 22 22
regulation of stress fiber formation 0.21 0.24 0.47 364 -10000 0 364
MAPK8 0.005 0.12 -10000 0 -0.72 23 23
Ephrin B1/EPHB1-2/RGS3 -0.21 0.24 -10000 0 -0.48 364 364
endothelial cell migration -0.015 0.12 -10000 0 -0.73 22 22
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.015 0.15 -10000 0 -0.95 22 22
regulation of focal adhesion formation 0.21 0.24 0.47 364 -10000 0 364
chemotaxis 0.21 0.24 0.47 364 -10000 0 364
PIK3CA 0 0.01 -10000 0 -10000 0 0
Rac1/GTP -0.19 0.22 -10000 0 -0.44 364 364
angiogenesis -0.028 0.14 -10000 0 -0.89 22 22
LCK -0.027 0.16 -10000 0 -1 22 22
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.23 0.41 -9999 0 -0.93 115 115
PLK1 -0.082 0.095 -9999 0 -10000 0 0
BIRC5 -0.091 0.091 -9999 0 -10000 0 0
HSPA1B -0.23 0.41 -9999 0 -0.94 106 106
MAP2K1 0.007 0.028 -9999 0 -10000 0 0
BRCA2 -0.24 0.42 -9999 0 -0.95 112 112
FOXM1 -0.28 0.49 -9999 0 -1 172 172
XRCC1 -0.23 0.41 -9999 0 -0.96 100 100
FOXM1B/p19 -0.28 0.4 -9999 0 -0.92 161 161
Cyclin D1/CDK4 -0.22 0.39 -9999 0 -0.9 100 100
CDC2 -0.25 0.43 -9999 0 -0.89 172 172
TGFA -0.22 0.41 -9999 0 -0.92 113 113
SKP2 -0.23 0.41 -9999 0 -0.98 90 90
CCNE1 -0.051 0.12 -9999 0 -0.29 163 163
CKS1B -0.23 0.42 -9999 0 -0.96 101 101
RB1 -0.11 0.12 -9999 0 -1.3 1 1
FOXM1C/SP1 -0.31 0.4 -9999 0 -0.92 185 185
AURKB -0.072 0.097 -9999 0 -10000 0 0
CENPF -0.26 0.43 -9999 0 -0.92 149 149
CDK4 0.007 0.018 -9999 0 -0.3 1 1
MYC -0.21 0.4 -9999 0 -0.86 126 126
CHEK2 0.006 0.031 -9999 0 -0.3 2 2
ONECUT1 -0.23 0.41 -9999 0 -0.9 126 126
CDKN2A -0.032 0.1 -9999 0 -0.27 133 133
LAMA4 -0.23 0.42 -9999 0 -0.96 101 101
FOXM1B/HNF6 -0.26 0.46 -9999 0 -1 126 126
FOS -0.46 0.68 -9999 0 -1.3 290 290
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.23 0.42 -9999 0 -0.97 97 97
response to radiation -0.008 0.028 -9999 0 -10000 0 0
CENPB -0.23 0.41 -9999 0 -0.94 107 107
CENPA -0.26 0.43 -9999 0 -0.97 122 122
NEK2 -0.28 0.42 -9999 0 -0.97 122 122
HIST1H2BA -0.24 0.41 -9999 0 -0.96 100 100
CCNA2 -0.12 0.15 -9999 0 -0.29 369 369
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.27 0.46 -9999 0 -1.1 122 122
CCNB2 -0.26 0.43 -9999 0 -0.98 119 119
CCNB1 -0.25 0.44 -9999 0 -0.99 122 122
ETV5 -0.23 0.42 -9999 0 -0.92 119 119
ESR1 -0.33 0.56 -9999 0 -1.2 172 172
CCND1 -0.22 0.4 -9999 0 -0.91 107 107
GSK3A 0.012 0.02 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.083 0.13 -9999 0 -0.32 112 112
CDK2 0.005 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.011 0.034 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.32 0.36 -9999 0 -0.88 178 178
GAS1 -0.27 0.47 -9999 0 -1.1 118 118
MMP2 -0.24 0.42 -9999 0 -1 93 93
RB1/FOXM1C -0.23 0.42 -9999 0 -0.94 117 117
CREBBP 0 0 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.059 0.17 -10000 0 -0.57 83 83
cell-cell adhesion 0.2 0.23 0.72 59 -10000 0 59
Ephrin B/EPHB2/RasGAP -0.042 0.13 -10000 0 -0.48 71 71
ITSN1 -0.002 0.041 -10000 0 -0.84 2 2
PIK3CA 0 0.01 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.24 0.28 -10000 0 -0.57 363 363
HRAS/GDP -0.2 0.24 -10000 0 -0.69 75 75
Ephrin B/EPHB1/GRB7 -0.25 0.3 -10000 0 -0.55 380 380
Endophilin/SYNJ1 -0.039 0.12 -10000 0 -0.45 71 71
KRAS 0 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.25 0.29 -10000 0 -0.55 379 379
endothelial cell migration 0 0.005 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
GRB7 -0.021 0.077 -10000 0 -0.29 62 62
PAK1 -0.045 0.15 -10000 0 -0.48 79 79
HRAS 0 0.01 -10000 0 -10000 0 0
RRAS -0.04 0.13 -10000 0 -0.45 71 71
DNM1 -0.005 0.065 -10000 0 -0.74 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.23 0.28 -10000 0 -0.52 379 379
lamellipodium assembly -0.2 0.23 -10000 0 -0.72 59 59
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.17 0.2 -10000 0 -0.38 363 363
PIK3R1 0 0 -10000 0 -10000 0 0
EPHB2 -0.005 0.037 -10000 0 -0.28 15 15
EPHB3 -0.003 0.029 -10000 0 -0.28 9 9
EPHB1 -0.36 0.42 -10000 0 -0.84 363 363
EPHB4 0 0.01 -10000 0 -10000 0 0
mol:GDP -0.18 0.22 -10000 0 -0.69 72 72
Ephrin B/EPHB2 -0.043 0.14 -10000 0 -0.48 71 71
Ephrin B/EPHB3 -0.042 0.14 -10000 0 -0.48 71 71
JNK cascade -0.2 0.23 -10000 0 -0.47 363 363
Ephrin B/EPHB1 -0.25 0.3 -10000 0 -0.55 379 379
RAP1/GDP -0.15 0.19 -10000 0 -0.63 56 56
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.071 0.23 -10000 0 -0.84 71 71
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.22 0.26 -10000 0 -0.52 363 363
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.2 0.25 -10000 0 -0.8 59 59
Rap1/GTP -0.2 0.23 -10000 0 -0.75 58 58
axon guidance -0.058 0.17 -10000 0 -0.56 83 83
MAPK3 -0.12 0.2 -10000 0 -0.54 55 55
MAPK1 -0.12 0.2 -10000 0 -0.54 55 55
Rac1/GDP -0.16 0.2 -10000 0 -0.61 71 71
actin cytoskeleton reorganization -0.15 0.18 -10000 0 -0.56 56 56
CDC42/GDP -0.16 0.2 -10000 0 -0.61 71 71
PI3K 0 0.005 -10000 0 -10000 0 0
EFNA5 -0.083 0.25 -10000 0 -0.84 83 83
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.03 0.1 -10000 0 -0.36 71 71
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.19 0.23 -10000 0 -0.71 59 59
PTK2 0.047 0.053 -10000 0 -10000 0 0
MAP4K4 -0.2 0.23 -10000 0 -0.47 363 363
SRC 0 0.01 -10000 0 -10000 0 0
KALRN -0.014 0.11 -10000 0 -0.84 14 14
Intersectin/N-WASP -0.002 0.031 -10000 0 -0.64 2 2
neuron projection morphogenesis -0.15 0.18 -10000 0 -0.56 64 64
MAP2K1 -0.16 0.18 -10000 0 -0.57 56 56
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.22 0.25 -10000 0 -0.51 363 363
cell migration -0.14 0.23 -10000 0 -0.57 78 78
NRAS -0.001 0.014 -10000 0 -10000 0 0
SYNJ1 -0.04 0.13 -10000 0 -0.45 71 71
PXN 0 0 -10000 0 -10000 0 0
TF -0.28 0.28 -10000 0 -0.48 506 506
HRAS/GTP -0.21 0.25 -10000 0 -0.79 58 58
Ephrin B1/EPHB1-2 -0.22 0.26 -10000 0 -0.52 363 363
cell adhesion mediated by integrin 0.006 0.14 0.45 71 -10000 0 71
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.23 0.27 -10000 0 -0.5 379 379
RAC1-CDC42/GTP -0.2 0.23 -10000 0 -0.73 59 59
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.15 0.19 -10000 0 -0.63 56 56
ruffle organization -0.2 0.24 -10000 0 -0.74 59 59
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.001 0.14 -10000 0 -0.45 72 72
Ephrin B/EPHB2/KALRN -0.05 0.16 -10000 0 -0.51 79 79
ROCK1 -0.001 0.012 -10000 0 -10000 0 0
RAS family/GDP -0.13 0.16 -10000 0 -0.55 56 56
Rac1/GTP -0.21 0.25 -10000 0 -0.79 59 59
Ephrin B/EPHB1/Src/Paxillin -0.18 0.21 -10000 0 -0.39 379 379
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.086 0.39 -10000 0 -0.91 149 149
NCK1/PAK1/Dok-R -0.076 0.16 -10000 0 -0.42 149 149
NCK1/Dok-R -0.2 0.44 -10000 0 -1.1 149 149
PIK3CA 0.002 0.011 -10000 0 -10000 0 0
mol:beta2-estradiol 0.03 0.094 0.25 131 -10000 0 131
RELA 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.031 0.1 0.38 2 -0.3 6 8
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.19 0.41 -10000 0 -1.1 149 149
FN1 -0.12 0.14 -10000 0 -10000 0 0
PLD2 -0.15 0.49 -10000 0 -1.2 149 149
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.23 -10000 0 -0.47 183 183
ELK1 -0.12 0.44 -10000 0 -1 149 149
GRB7 -0.021 0.077 -10000 0 -0.29 62 62
PAK1 -0.006 0.04 -10000 0 -0.28 18 18
Tie2/Ang1/alpha5/beta1 Integrin -0.15 0.46 -10000 0 -1.1 149 149
CDKN1A -0.04 0.26 -10000 0 -0.59 120 120
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.2 0.44 -10000 0 -1.1 149 149
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.041 0.29 -10000 0 -0.66 149 149
PLG -0.16 0.49 -10000 0 -1.2 149 149
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.34 -10000 0 -0.88 149 149
GRB2 0 0.01 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
ANGPT2 -0.095 0.27 -10000 0 -0.78 74 74
BMX -0.35 0.56 -10000 0 -1.4 152 152
ANGPT1 -0.2 0.54 -10000 0 -1.4 136 136
tube development -0.055 0.29 -10000 0 -0.64 149 149
ANGPT4 -0.28 0.39 -10000 0 -0.84 277 277
response to hypoxia -0.007 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.24 0.51 -10000 0 -1.3 149 149
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.34 0.41 -10000 0 -0.84 337 337
STAT5A (dimer) -0.069 0.33 -10000 0 -0.78 120 120
mol:L-citrulline -0.041 0.29 -10000 0 -0.66 149 149
AGTR1 -0.2 0.35 -10000 0 -0.84 189 189
MAPK14 -0.14 0.47 -10000 0 -1.1 149 149
Tie2/SHP2 -0.075 0.24 -10000 0 -1.3 27 27
TEK -0.086 0.28 -10000 0 -1.5 27 27
RPS6KB1 -0.082 0.37 -10000 0 -0.87 149 149
Angiotensin II/AT1 -0.16 0.27 -10000 0 -0.65 189 189
Tie2/Ang1/GRB2 -0.22 0.48 -10000 0 -1.2 149 149
MAPK3 -0.13 0.45 -10000 0 -1.1 149 149
MAPK1 -0.13 0.45 -10000 0 -1.1 149 149
Tie2/Ang1/GRB7 -0.21 0.49 -10000 0 -1.2 149 149
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.15 0.49 -10000 0 -1.2 149 149
PI3K -0.12 0.44 -10000 0 -1.1 149 149
FES -0.14 0.46 -10000 0 -1.1 149 149
Crk/Dok-R -0.2 0.44 -10000 0 -1.1 149 149
Tie2/Ang1/ABIN2 -0.22 0.48 -10000 0 -1.2 149 149
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.069 0.34 -10000 0 -0.8 149 149
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.082 0.37 -10000 0 -0.87 149 149
Tie2/Ang2 -0.099 0.38 -10000 0 -0.92 124 124
Tie2/Ang1 -0.18 0.54 -10000 0 -1.3 149 149
FOXO1 -0.066 0.35 -10000 0 -0.81 150 150
ELF1 0.015 0.019 -10000 0 -10000 0 0
ELF2 -0.15 0.48 -10000 0 -1.2 149 149
mol:Choline -0.14 0.46 -10000 0 -1.1 149 149
cell migration -0.03 0.099 -10000 0 -0.25 30 30
FYN -0.069 0.32 -10000 0 -0.76 124 124
DOK2 -0.002 0.041 -10000 0 -0.84 2 2
negative regulation of cell cycle -0.032 0.24 -10000 0 -0.54 120 120
ETS1 -0.02 0.1 -10000 0 -1 2 2
PXN -0.051 0.31 -10000 0 -0.71 149 149
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.056 0.33 -10000 0 -0.75 149 149
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.033 0.14 -10000 0 -0.84 12 12
MAPKKK cascade -0.14 0.46 -10000 0 -1.1 149 149
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.2 0.49 -10000 0 -1.2 149 149
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.03 0.26 -10000 0 -0.59 149 149
mol:Phosphatidic acid -0.14 0.46 -10000 0 -1.1 149 149
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.041 0.29 -10000 0 -0.66 149 149
Rac1/GTP -0.14 0.31 -10000 0 -0.81 149 149
MMP2 -0.15 0.5 -10000 0 -1.2 150 150
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.4 1 1
NFATC4 -0.09 0.16 -9999 0 -0.37 20 20
ERBB2IP 0.007 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.01 -9999 0 -0.28 1 1
mammary gland morphogenesis -0.15 0.2 -9999 0 -0.41 299 299
JUN -0.019 0.079 -9999 0 -0.37 4 4
HRAS 0 0.01 -9999 0 -10000 0 0
DOCK7 -0.14 0.18 -9999 0 -0.39 299 299
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.24 -9999 0 -0.5 299 299
AKT1 0.007 0.006 -9999 0 -10000 0 0
BAD 0.018 0.004 -9999 0 -10000 0 0
MAPK10 -0.12 0.14 -9999 0 -0.37 137 137
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.21 -9999 0 -0.45 299 299
RAF1 -0.082 0.16 -9999 0 -0.42 1 1
ErbB2/ErbB3/neuregulin 2 -0.29 0.27 -9999 0 -0.54 448 448
STAT3 0 0.004 -9999 0 -10000 0 0
cell migration -0.064 0.13 -9999 0 -0.32 67 67
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.23 -9999 0 -0.52 138 138
FOS -0.17 0.27 -9999 0 -0.54 273 273
NRAS -0.001 0.014 -9999 0 -10000 0 0
mol:Ca2+ -0.15 0.2 -9999 0 -0.41 299 299
MAPK3 -0.11 0.19 -9999 0 -0.49 53 53
MAPK1 -0.11 0.19 -9999 0 -0.49 53 53
JAK2 -0.14 0.18 -9999 0 -0.39 299 299
NF2 -0.007 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.18 -9999 0 -0.37 299 299
NRG1 -0.3 0.4 -9999 0 -0.84 298 298
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.34 299 299
MAPK9 -0.07 0.091 -9999 0 -10000 0 0
ERBB2 -0.017 0.055 -9999 0 -10000 0 0
ERBB3 -0.001 0.029 -9999 0 -0.84 1 1
SHC1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.017 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.004 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.007 0.005 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.1 0.13 -9999 0 -0.33 19 19
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.043 -9999 0 -10000 0 0
CHRNA1 -0.097 0.16 -9999 0 -0.41 53 53
myelination -0.084 0.17 -9999 0 -0.36 20 20
PPP3CB -0.13 0.17 -9999 0 -0.36 299 299
KRAS 0 0.01 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.35 8 8
NRG2 -0.44 0.42 -9999 0 -0.84 447 447
mol:GDP -0.13 0.18 -9999 0 -0.37 299 299
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.075 0.15 -9999 0 -0.42 3 3
SRC 0 0.01 -9999 0 -10000 0 0
mol:cAMP -0.002 0.003 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.39 299 299
MAP2K1 -0.14 0.21 -9999 0 -0.49 137 137
heart morphogenesis -0.15 0.2 -9999 0 -0.41 299 299
RAS family/GDP -0.11 0.14 -9999 0 -10000 0 0
GRB2 0 0.01 -9999 0 -10000 0 0
PRKACA -0.011 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.022 -9999 0 -0.18 4 4
HSP90AA1 0 0.01 -9999 0 -0.28 1 1
activation of caspase activity -0.007 0.006 -9999 0 -10000 0 0
nervous system development -0.15 0.2 -9999 0 -0.41 299 299
CDC42 0 0 -9999 0 -10000 0 0
IGF1 pathway

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
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.12 0.24 -10000 0 -0.51 204 204
GRB2/SOS1/SHC 0 0.005 -10000 0 -10000 0 0
HRAS 0 0.01 -10000 0 -10000 0 0
IRS1/Crk -0.13 0.24 -10000 0 -0.52 204 204
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.24 -10000 0 -0.57 194 194
AKT1 -0.068 0.21 -10000 0 -0.75 29 29
BAD -0.055 0.2 -10000 0 -0.68 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.24 -10000 0 -0.51 204 204
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.24 -10000 0 -0.52 204 204
RAF1 -0.048 0.19 -10000 0 -0.65 27 27
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.23 -10000 0 -0.49 204 204
YWHAZ -0.001 0.017 -10000 0 -0.28 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.26 -10000 0 -0.56 204 204
PIK3CA 0 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.068 0.21 -10000 0 -0.75 29 29
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.041 0.16 -10000 0 -0.52 29 29
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.2 -10000 0 -0.78 29 29
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.2 -10000 0 -0.45 194 194
IGF-1R heterotetramer -0.042 0.13 -10000 0 -0.86 18 18
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.24 -10000 0 -0.52 204 204
Crk/p130 Cas/Paxillin -0.11 0.21 -10000 0 -0.83 29 29
IGF1R -0.042 0.13 -10000 0 -0.86 18 18
IGF1 -0.19 0.36 -10000 0 -0.86 186 186
IRS2/Crk -0.14 0.26 -10000 0 -0.55 209 209
PI3K -0.12 0.22 -10000 0 -0.48 204 204
apoptosis 0.081 0.15 0.56 30 -10000 0 30
HRAS/GDP 0 0.006 -10000 0 -10000 0 0
PRKCD -0.098 0.26 -10000 0 -0.55 194 194
RAF1/14-3-3 E -0.076 0.14 -10000 0 -0.54 27 27
BAD/14-3-3 -0.086 0.16 -10000 0 -0.61 30 30
PRKCZ -0.069 0.21 -10000 0 -0.74 30 30
Crk/p130 Cas/Paxillin/FAK1 -0.085 0.16 -10000 0 -0.64 27 27
PTPN1 -0.004 0.032 -10000 0 -0.28 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.14 0.26 -10000 0 -0.59 194 194
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.22 -10000 0 -0.49 194 194
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.23 -10000 0 -0.51 204 204
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.12 0.24 -10000 0 -0.51 204 204
IRS1 -0.14 0.25 -10000 0 -0.56 204 204
IRS2 -0.15 0.28 -10000 0 -0.57 216 216
IGF-1R heterotetramer/IGF1 -0.16 0.3 -10000 0 -0.7 194 194
GRB2 0 0.01 -10000 0 -10000 0 0
PDPK1 -0.11 0.21 -10000 0 -0.46 194 194
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.59 204 204
SHC1 0 0 -10000 0 -10000 0 0
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 -0.11 0.2 -9999 0 -0.63 95 95
SMAD6-7/SMURF1 -0.001 0.019 -9999 0 -0.56 1 1
NOG -0.025 0.13 -9999 0 -0.84 20 20
SMAD9 -0.096 0.25 -9999 0 -0.85 70 70
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.079 0.18 -9999 0 -0.49 109 109
BMP7/USAG1 -0.36 0.36 -9999 0 -0.7 434 434
SMAD5/SKI -0.089 0.16 -9999 0 -0.52 76 76
SMAD1 0.024 0.031 -9999 0 -10000 0 0
BMP2 -0.15 0.32 -9999 0 -0.83 153 153
SMAD1/SMAD1/SMAD4 -0.002 0.013 -9999 0 -10000 0 0
BMPR1A -0.001 0.029 -9999 0 -0.84 1 1
BMPR1B -0.14 0.17 -9999 0 -0.3 377 377
BMPR1A-1B/BAMBI -0.092 0.15 -9999 0 -0.64 45 45
AHSG -0.002 0.025 -9999 0 -10000 0 0
CER1 -0.001 0.014 -9999 0 -10000 0 0
BMP2-4/CER1 -0.14 0.26 -9999 0 -0.61 188 188
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.2 -9999 0 -0.52 116 116
BMP2-4 (homodimer) -0.15 0.29 -9999 0 -0.69 188 188
RGMB -0.001 0.029 -9999 0 -0.84 1 1
BMP6/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.57 89 89
RGMA -0.11 0.28 -9999 0 -0.84 112 112
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.55 107 107
BMP2-4/USAG1 -0.4 0.39 -9999 0 -0.69 483 483
SMAD6/SMURF1/SMAD5 -0.089 0.16 -9999 0 -0.52 76 76
SOSTDC1 -0.41 0.42 -9999 0 -0.84 410 410
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.6 77 77
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.072 0.23 -9999 0 -0.83 73 73
HFE2 -0.002 0.025 -9999 0 -0.28 7 7
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.01 -9999 0 -0.28 1 1
BMP2-4/CHRD -0.15 0.28 -9999 0 -0.64 190 190
SMAD5/SMAD5/SMAD4 -0.089 0.16 -9999 0 -0.52 76 76
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.088 0.17 -9999 0 -0.54 80 80
BMP7 (homodimer) -0.074 0.22 -9999 0 -0.63 99 99
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.057 0.18 -9999 0 -0.65 72 72
SMAD1/SKI -0.005 0.014 -9999 0 -10000 0 0
SMAD6 -0.001 0.029 -9999 0 -0.84 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.14 0.26 -9999 0 -0.61 188 188
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.041 0.12 -9999 0 -0.33 105 105
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.089 0.12 -9999 0 -0.65 19 19
CHRDL1 -0.58 0.39 -9999 0 -0.84 582 582
ENDOFIN/SMAD1 -0.005 0.014 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.004 0.016 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.036 0.15 -9999 0 -0.84 26 26
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.51 0.39 -9999 0 -0.72 597 597
BMP2-4/GREM1 -0.16 0.27 -9999 0 -0.62 191 191
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.091 0.23 -9999 0 -0.8 70 70
SMAD1/SMAD6 -0.005 0.014 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.074 0.22 -9999 0 -0.63 99 99
BMP6 -0.072 0.23 -9999 0 -0.83 73 73
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.19 -9999 0 -0.61 79 79
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.005 0.014 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA -0.002 0.021 -9999 0 -0.28 5 5
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.13 0.24 -9999 0 -0.47 202 202
CHRD -0.03 0.13 -9999 0 -0.43 59 59
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.24 -9999 0 -0.47 213 213
BMP4 -0.051 0.2 -9999 0 -0.83 52 52
FST -0.033 0.16 -9999 0 -0.79 35 35
BMP2-4/NOG -0.15 0.28 -9999 0 -0.62 199 199
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.092 0.16 -9999 0 -0.56 77 77
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.11 0.24 -10000 0 -0.64 143 143
CRKL -0.041 0.16 -10000 0 -0.36 143 143
mol:PIP3 -0.017 0.041 0.82 2 -10000 0 2
AKT1 0.004 0.025 0.5 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.031 0.15 -10000 0 -0.56 15 15
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.13 0.25 -10000 0 -0.6 178 178
MAP3K5 -0.021 0.15 -10000 0 -0.55 17 17
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.23 -10000 0 -0.55 178 178
AP1 -0.22 0.29 -10000 0 -0.62 273 273
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.25 0.37 -10000 0 -0.78 273 273
STAT3 (dimer) -0.073 0.15 -10000 0 -0.34 178 178
GAB1/CRKL/SHP2/PI3K -0.061 0.12 -10000 0 -0.53 15 15
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.067 0.13 -10000 0 -0.56 15 15
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.84 2 2
ELK1 -0.045 0.11 -10000 0 -0.28 143 143
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.047 0.095 -10000 0 -0.23 143 143
PAK1 0.009 0.03 0.46 2 -10000 0 2
HGF/MET/RANBP10 -0.13 0.25 -10000 0 -0.6 178 178
HRAS -0.15 0.3 -10000 0 -0.72 178 178
DOCK1 -0.031 0.15 -10000 0 -0.33 143 143
GAB1 -0.051 0.17 -10000 0 -0.36 178 178
CRK -0.041 0.16 -10000 0 -0.36 143 143
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.16 0.31 -10000 0 -0.73 178 178
JUN -0.009 0.086 -10000 0 -0.84 9 9
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.079 0.16 -10000 0 -0.37 178 178
PIK3R1 0 0 -10000 0 -10000 0 0
cell morphogenesis -0.015 0.17 -10000 0 -0.6 15 15
GRB2/SHC -0.068 0.14 -10000 0 -0.34 143 143
FOS -0.27 0.39 -10000 0 -0.84 272 272
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.045 0.11 -10000 0 -0.28 143 143
HGF/MET/MUC20 -0.13 0.26 -10000 0 -0.61 178 178
cell migration -0.067 0.13 -10000 0 -0.34 143 143
GRB2 0 0.01 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.11 0.24 -10000 0 -0.64 143 143
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.078 0.16 -10000 0 -0.37 178 178
MET/MUC20 -0.11 0.25 -10000 0 -0.65 144 144
RAP1B -0.021 0.14 -10000 0 -0.52 15 15
RAP1A -0.021 0.14 -10000 0 -0.52 15 15
HGF/MET/RANBP9 -0.13 0.25 -10000 0 -0.6 178 178
RAF1 -0.1 0.3 -10000 0 -0.73 143 143
STAT3 -0.074 0.15 -10000 0 -0.35 178 178
cell proliferation -0.062 0.23 -10000 0 -0.5 178 178
RPS6KB1 -0.027 0.054 -10000 0 -0.19 15 15
MAPK3 -0.045 0.095 -10000 0 -0.26 143 143
MAPK1 -0.045 0.095 -10000 0 -0.26 143 143
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.13 -10000 0 -0.43 16 16
SRC -0.072 0.14 -10000 0 -0.64 15 15
PI3K -0.068 0.14 -10000 0 -0.34 143 143
MET/Glomulin -0.1 0.22 -10000 0 -0.59 143 143
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.087 0.27 -10000 0 -0.66 143 143
MET -0.14 0.32 -10000 0 -0.83 144 144
MAP4K1 -0.03 0.15 -10000 0 -0.34 144 144
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.087 0.27 -10000 0 -0.66 143 143
BAD 0.012 0.023 0.46 2 -10000 0 2
MAP2K4 -0.011 0.14 -10000 0 -0.48 18 18
SHP2/GRB2/SOS1/GAB1 -0.099 0.2 -10000 0 -0.53 143 143
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.072 0.14 -10000 0 -0.34 178 178
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.05 0.2 -10000 0 -0.84 50 50
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.068 0.14 -10000 0 -0.34 143 143
PDPK1 -0.006 0.029 0.59 2 -10000 0 2
HGF/MET/SHIP -0.13 0.25 -10000 0 -0.6 178 178
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.025 0.063 -10000 0 -0.53 2 2
epithelial cell differentiation -0.018 0.054 -10000 0 -0.45 1 1
ITCH 0.008 0.021 -10000 0 -10000 0 0
WWP1 0.009 0.067 -10000 0 -10000 0 0
FYN -0.001 0.029 -10000 0 -0.84 1 1
EGFR -0.29 0.4 -10000 0 -0.83 297 297
PRL -0.004 0.032 -10000 0 -10000 0 0
neuron projection morphogenesis -0.11 0.22 -10000 0 -0.5 46 46
PTPRZ1 -0.45 0.42 -10000 0 -0.84 449 449
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.17 0.21 -10000 0 -0.55 53 53
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.2 0.25 -10000 0 -0.53 298 298
ADAM17 0.008 0.021 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.029 0.071 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.06 0.15 -10000 0 -0.57 52 52
NCOR1 -0.001 0.029 -10000 0 -0.84 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.18 0.23 -10000 0 -0.5 298 298
GRIN2B -0.21 0.25 -10000 0 -0.5 347 347
ErbB4/ErbB2/betacellulin -0.049 0.12 -10000 0 -0.5 45 45
STAT1 -0.006 0.04 -10000 0 -10000 0 0
HBEGF -0.002 0.041 -10000 0 -0.84 2 2
PRLR -0.002 0.025 -10000 0 -0.28 7 7
E4ICDs/ETO2 -0.035 0.096 -10000 0 -0.58 16 16
axon guidance 0.048 0.13 -10000 0 -0.39 1 1
NEDD4 0.008 0.021 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.004 0.026 -10000 0 -10000 0 0
CBFA2T3 -0.017 0.12 -10000 0 -0.84 16 16
ErbB4/ErbB2/HBEGF -0.025 0.052 -10000 0 -0.47 2 2
MAPK3 -0.15 0.2 -10000 0 -0.51 50 50
STAT1 (dimer) -0.027 0.064 -10000 0 -10000 0 0
MAPK1 -0.15 0.2 -10000 0 -0.51 50 50
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.23 -10000 0 -0.5 298 298
NRG1 -0.22 0.32 -10000 0 -0.65 298 298
NRG3 -0.059 0.2 -10000 0 -0.67 74 74
NRG2 -0.44 0.42 -10000 0 -0.84 447 447
NRG4 -0.004 0.034 -10000 0 -0.28 13 13
heart development 0.048 0.13 -10000 0 -0.39 1 1
neural crest cell migration -0.19 0.23 -10000 0 -0.5 298 298
ERBB2 0.008 0.058 -10000 0 -10000 0 0
WWOX/E4ICDs -0.024 0.058 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.19 0.23 -10000 0 -0.49 292 292
apoptosis 0.061 0.16 0.55 57 -10000 0 57
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.3 0.26 -10000 0 -0.54 447 447
ErbB4/ErbB2/epiregulin -0.087 0.16 -10000 0 -0.49 99 99
ErbB4/ErbB4/betacellulin/betacellulin -0.053 0.13 -10000 0 -0.54 45 45
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.018 0.051 -10000 0 -0.44 2 2
MDM2 0.011 0.073 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.19 0.24 -10000 0 -0.5 298 298
STAT5A 0.048 0.12 -10000 0 -0.46 6 6
ErbB4/EGFR/neuregulin 1 beta -0.35 0.38 -10000 0 -0.7 411 411
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.023 0.056 -10000 0 -0.5 1 1
STAT5A (dimer) -0.019 0.058 -10000 0 -0.49 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.025 0.061 -10000 0 -0.45 4 4
LRIG1 -0.001 0.029 -10000 0 -0.84 1 1
EREG -0.12 0.27 -10000 0 -0.62 162 162
BTC -0.045 0.19 -10000 0 -0.81 47 47
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.048 0.13 -10000 0 -0.4 1 1
ERBB4 -0.029 0.071 -10000 0 -10000 0 0
STAT5B -0.003 0.05 -10000 0 -0.84 3 3
YAP1 -0.009 0.038 -10000 0 -0.7 2 2
GRB2 0 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.025 0.051 -10000 0 -10000 0 0
glial cell differentiation 0.022 0.055 0.49 1 -10000 0 1
WWOX 0 0.01 -10000 0 -10000 0 0
cell proliferation -0.12 0.24 -10000 0 -0.48 155 155
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.032 -9999 0 -0.55 1 1
NFATC2 -0.022 0.14 -9999 0 -0.58 47 47
NFATC3 0.011 0.025 -9999 0 -10000 0 0
CD40LG -0.27 0.33 -9999 0 -0.74 234 234
PTGS2 -0.38 0.43 -9999 0 -0.88 327 327
JUNB 0 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.009 -9999 0 -10000 0 0
CALM1 0 0.002 -9999 0 -10000 0 0
JUN -0.009 0.087 -9999 0 -0.85 9 9
mol:Ca2+ -0.006 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
FOSL1 -0.007 0.056 -9999 0 -0.84 2 2
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.061 0.14 -9999 0 -0.52 46 46
FOS -0.28 0.4 -9999 0 -0.85 272 272
IFNG -0.27 0.31 -9999 0 -0.7 244 244
AP-1/NFAT1-c-4 -0.32 0.39 -9999 0 -0.84 249 249
FASLG -0.26 0.31 -9999 0 -0.7 228 228
NFAT1-c-4/ICER1 -0.042 0.12 -9999 0 -0.49 48 48
IL2RA -0.26 0.31 -9999 0 -0.71 232 232
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.23 0.33 -9999 0 -0.69 229 229
JunB/Fra1/NFAT1-c-4 -0.04 0.12 -9999 0 -0.48 46 46
IL4 -0.22 0.34 -9999 0 -0.69 230 230
IL2 -0.012 0.025 -9999 0 -10000 0 0
IL3 -0.024 0.027 -9999 0 -10000 0 0
FKBP1A 0 0.01 -9999 0 -10000 0 0
BATF3 -0.001 0.029 -9999 0 -0.84 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.011 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.13 -10000 0 -0.34 65 65
NT3 (dimer)/TRKC -0.32 0.39 -10000 0 -0.74 361 361
NT3 (dimer)/TRKB -0.55 0.48 -10000 0 -0.85 537 537
SHC/Grb2/SOS1/GAB1/PI3K 0 0.001 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.073 0.23 -10000 0 -0.7 87 87
PIK3CA 0 0.01 -10000 0 -10000 0 0
DYNLT1 0 0.01 -10000 0 -0.28 1 1
NTRK1 -0.01 0.061 -10000 0 -0.84 2 2
NTRK2 -0.44 0.42 -10000 0 -0.84 440 440
NTRK3 -0.29 0.4 -10000 0 -0.83 297 297
NT-4/5 (dimer)/TRKB -0.66 0.53 -10000 0 -0.95 584 584
neuron apoptosis 0.26 0.25 0.6 246 -10000 0 246
SHC 2-3/Grb2 -0.28 0.29 -10000 0 -0.68 246 246
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.26 0.3 -10000 0 -0.7 232 232
SHC3 -0.26 0.28 -10000 0 -0.6 293 293
STAT3 (dimer) -0.005 0.029 -10000 0 -0.39 3 3
NT3 (dimer)/TRKA -0.28 0.34 -10000 0 -0.65 353 353
RIN/GDP -0.072 0.13 -10000 0 -0.3 40 40
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0.01 -10000 0 -10000 0 0
DNAJA3 -0.15 0.21 -10000 0 -0.44 277 277
RIN/GTP 0 0.009 -10000 0 -10000 0 0
CCND1 0.017 0.075 -10000 0 -1 3 3
MAGED1 -0.001 0.014 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.32 0.41 -10000 0 -0.84 324 324
SHC/GRB2/SOS1 0 0.005 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.029 0.12 -10000 0 -0.58 33 33
TRKA/NEDD4-2 -0.007 0.048 -10000 0 -0.64 3 3
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.017 0.11 -10000 0 -0.66 22 22
HRAS 0 0.01 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.003 0.027 -10000 0 -0.28 8 8
RIT2 -0.001 0.014 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.03 -10000 0 -0.28 10 10
DNM1 -0.005 0.065 -10000 0 -0.74 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.15 0.21 -10000 0 -0.43 277 277
mol:GDP -0.11 0.19 -10000 0 -0.38 192 192
NGF (dimer) -0.017 0.11 -10000 0 -0.66 22 22
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.069 0.13 -10000 0 -0.3 40 40
TIAM1 -0.001 0.019 -10000 0 -0.28 4 4
PIK3R1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.34 0.32 -10000 0 -0.61 463 463
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.002 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0.004 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.14 0.31 -10000 0 -0.84 135 135
RAP1/GDP -0.077 0.089 -10000 0 -0.27 2 2
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.073 0.23 -10000 0 -0.7 87 87
ubiquitin-dependent protein catabolic process -0.017 0.084 -10000 0 -0.56 18 18
Schwann cell development -0.061 0.045 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0.001 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.46 0.41 -10000 0 -0.71 546 546
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.11 0.1 -10000 0 -10000 0 0
STAT3 -0.005 0.029 -10000 0 -0.38 3 3
axon guidance -0.43 0.37 -10000 0 -0.66 546 546
MAPK3 -0.026 0.1 -10000 0 -0.53 33 33
MAPK1 -0.026 0.1 -10000 0 -0.53 33 33
CDC42/GDP -0.069 0.13 -10000 0 -0.29 47 47
NTF3 -0.14 0.31 -10000 0 -0.84 135 135
NTF4 -0.32 0.41 -10000 0 -0.84 324 324
NGF (dimer)/TRKA/FAIM -0.016 0.082 -10000 0 -0.56 17 17
PI3K 0 0.006 -10000 0 -10000 0 0
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.17 0.22 -10000 0 -0.46 285 285
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.27 0.36 -10000 0 -0.65 362 362
RGS19 -0.001 0.014 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.007 0.084 -10000 0 -10000 0 0
Rac1/GDP -0.069 0.13 -10000 0 -0.29 43 43
NGF (dimer)/TRKA/GRIT -0.017 0.083 -10000 0 -0.57 17 17
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.6 17 17
NGF (dimer)/TRKA/NEDD4-2 -0.017 0.084 -10000 0 -0.56 18 18
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.28 0.39 -10000 0 -0.84 277 277
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.057 -10000 0 -0.35 21 21
RAS family/GTP/PI3K 0 0.002 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
NRAS -0.001 0.014 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.01 -10000 0 -0.28 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
MAPKKK cascade -0.068 0.12 -10000 0 -0.82 17 17
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.042 -10000 0 -0.64 2 2
SQSTM1 -0.001 0.014 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.31 0.3 -10000 0 -0.56 463 463
NGF (dimer)/TRKA/p62/Atypical PKCs -0.014 0.071 -10000 0 -0.48 18 18
MATK -0.02 0.12 -10000 0 -0.63 27 27
NEDD4L -0.001 0.029 -10000 0 -0.84 1 1
RAS family/GDP -0.07 0.083 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.16 0.22 -10000 0 -0.47 284 284
Rac1/GTP -0.13 0.15 -10000 0 -0.35 205 205
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.061 0.17 -10000 0 -0.52 97 97
regulation of S phase of mitotic cell cycle -0.038 0.11 -10000 0 -0.34 92 92
GNAO1 -0.033 0.14 -10000 0 -0.84 21 21
HRAS 0 0.01 -10000 0 -10000 0 0
SHBG/T-DHT 0 0.005 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.003 -10000 0 -10000 0 0
MAP2K1 -0.041 0.16 -10000 0 -0.46 92 92
T-DHT/AR -0.072 0.21 -10000 0 -0.65 93 93
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 272 272
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.84 43 43
mol:GDP -0.069 0.2 -10000 0 -0.63 92 92
cell proliferation -0.11 0.24 -10000 0 -0.57 82 82
PIK3CA 0 0.01 -10000 0 -10000 0 0
FOS -0.25 0.43 -10000 0 -0.87 272 272
mol:Ca2+ -0.016 0.028 -10000 0 -0.078 111 111
MAPK3 -0.076 0.2 -10000 0 -0.51 92 92
MAPK1 -0.049 0.12 -10000 0 -0.31 48 48
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.005 272 272
cAMP biosynthetic process 0.012 0.025 -10000 0 -10000 0 0
GNG2 -0.006 0.07 -10000 0 -0.84 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 272 272
HRAS/GTP -0.061 0.15 -10000 0 -0.49 92 92
actin cytoskeleton reorganization 0 0.003 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 272 272
PI3K 0 0.005 -10000 0 -10000 0 0
apoptosis 0.11 0.23 0.43 272 -10000 0 272
T-DHT/AR/PELP1 -0.063 0.18 -10000 0 -0.57 92 92
HRAS/GDP -0.066 0.19 -10000 0 -0.6 92 92
CREB1 -0.12 0.25 -10000 0 -0.46 272 272
RAC1-CDC42/GTP 0 0.003 -10000 0 -10000 0 0
AR -0.092 0.26 -10000 0 -0.84 93 93
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.04 0.16 -10000 0 -0.48 92 92
RAC1-CDC42/GDP -0.062 0.18 -10000 0 -0.57 92 92
T-DHT/AR/PELP1/Src -0.058 0.16 -10000 0 -0.53 92 92
MAP2K2 -0.041 0.16 -10000 0 -0.46 92 92
T-DHT/AR/PELP1/Src/PI3K -0.038 0.11 -10000 0 -0.35 92 92
GNAZ -0.006 0.071 -10000 0 -0.84 6 6
SHBG 0 0.01 -10000 0 -0.28 1 1
Gi family/GNB1/GNG2/GDP -0.036 0.1 -10000 0 -0.46 29 29
mol:T-DHT -0.001 0.001 0.002 48 -0.003 223 271
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.005 0.061 -10000 0 -0.66 7 7
Gi family/GTP -0.047 0.1 -10000 0 -0.31 70 70
CDC42 0 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.047 0.19 -9999 0 -0.84 47 47
GNB1/GNG2 -0.16 0.24 -9999 0 -0.72 86 86
mol:DAG -0.14 0.21 -9999 0 -0.64 86 86
PLCG1 -0.14 0.22 -9999 0 -0.67 86 86
YES1 -0.16 0.24 -9999 0 -0.69 95 95
FZD3 -0.008 0.081 -9999 0 -0.84 8 8
FZD6 -0.006 0.07 -9999 0 -0.84 6 6
G protein -0.15 0.22 -9999 0 -0.67 88 88
MAP3K7 -0.079 0.19 -9999 0 -0.51 87 87
mol:Ca2+ -0.14 0.2 -9999 0 -0.61 86 86
mol:IP3 -0.14 0.21 -9999 0 -0.64 86 86
NLK -0.006 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.094 0.21 -9999 0 -0.56 87 87
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.18 0.26 -9999 0 -0.46 322 322
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.16 0.24 -9999 0 -0.7 94 94
GO:0007205 -0.11 0.23 -9999 0 -0.62 86 86
WNT6 -0.18 0.34 -9999 0 -0.84 177 177
WNT4 -0.024 0.13 -9999 0 -0.84 19 19
NFAT1/CK1 alpha -0.16 0.24 -9999 0 -0.66 107 107
GNG2 -0.006 0.07 -9999 0 -0.84 6 6
WNT5A -0.014 0.099 -9999 0 -0.84 11 11
WNT11 -0.2 0.35 -9999 0 -0.81 203 203
CDC42 -0.12 0.25 -9999 0 -0.69 83 83
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.035 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.077 0.16 -9999 0 -0.48 65 65
JUN -0.047 0.14 -9999 0 -0.56 16 16
HRAS 0 0.01 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.21 -9999 0 -0.56 148 148
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.03 -9999 0 -0.28 10 10
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.21 -9999 0 -0.56 145 145
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.19 -9999 0 -0.52 139 139
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.5 145 145
GRB7 -0.021 0.077 -9999 0 -0.29 62 62
RET51/GFRalpha1/GDNF -0.15 0.21 -9999 0 -0.56 148 148
MAPKKK cascade -0.094 0.17 -9999 0 -0.56 35 35
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.24 -9999 0 -0.6 148 148
lamellipodium assembly -0.077 0.15 -9999 0 -0.38 145 145
RET51/GFRalpha1/GDNF/SHC -0.15 0.21 -9999 0 -0.56 148 148
PIK3CA 0 0.01 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.52 139 139
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.52 139 139
MAPK3 -0.12 0.17 -9999 0 -0.47 145 145
DOK1 0 0 -9999 0 -10000 0 0
DOK6 -0.01 0.084 -9999 0 -0.84 8 8
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.56 38 38
DOK5 -0.018 0.12 -9999 0 -0.84 16 16
GFRA1 -0.16 0.31 -9999 0 -0.84 139 139
MAPK8 -0.069 0.13 -9999 0 -0.42 35 35
HRAS/GTP -0.098 0.2 -9999 0 -0.52 145 145
tube development -0.094 0.18 -9999 0 -0.49 139 139
MAPK1 -0.12 0.17 -9999 0 -0.47 145 145
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.062 0.13 -9999 0 -0.35 139 139
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.2 -9999 0 -0.54 150 150
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.21 -9999 0 -0.56 148 148
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.58 158 158
PRKCA -0.022 0.13 -9999 0 -0.77 24 24
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
CREB1 -0.068 0.15 -9999 0 -0.39 139 139
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.13 -9999 0 -0.35 139 139
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.58 150 150
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.16 -9999 0 -0.3 335 335
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.046 0.14 -9999 0 -0.54 16 16
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.52 139 139
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.062 0.13 -9999 0 -0.35 139 139
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.079 0.14 -9999 0 -0.37 145 145
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.078 0.14 -9999 0 -0.37 145 145
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.08 0.15 -9999 0 -0.38 145 145
PI3K -0.12 0.24 -9999 0 -0.61 145 145
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.094 0.18 -9999 0 -0.49 139 139
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.075 0.13 -9999 0 -0.35 139 139
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.21 -9999 0 -0.56 148 148
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.031 0.16 -9999 0 -0.84 31 31
IRS2 -0.038 0.17 -9999 0 -0.84 38 38
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.08 0.15 -9999 0 -0.38 145 145
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.22 -9999 0 -0.57 169 169
GRB2 0 0.01 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.016 0.065 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.24 -9999 0 -0.63 156 156
Rac1/GTP -0.093 0.18 -9999 0 -0.46 145 145
RET9/GFRalpha1/GDNF -0.11 0.21 -9999 0 -0.57 143 143
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.65 143 143
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.022 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.038 -9999 0 -0.3 2 2
PDE6G/GNAT1/GTP -0.007 0.032 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.033 -9999 0 -0.28 12 12
GRK1 -0.003 0.027 -9999 0 -0.28 8 8
CNG Channel -0.16 0.22 -9999 0 -0.47 264 264
mol:Na + -0.15 0.2 -9999 0 -0.45 259 259
mol:ADP -0.003 0.027 -9999 0 -0.28 8 8
RGS9-1/Gbeta5/R9AP -0.071 0.18 -9999 0 -0.57 92 92
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.15 0.21 -9999 0 -0.46 259 259
CNGB1 -0.014 0.061 -9999 0 -10000 0 0
RDH5 -0.53 0.4 -9999 0 -0.84 533 533
SAG -0.014 0.061 -9999 0 -10000 0 0
mol:Ca2+ -0.14 0.2 -9999 0 -0.43 243 243
Na + (4 Units) -0.14 0.19 -9999 0 -0.42 243 243
RGS9 -0.095 0.26 -9999 0 -0.84 92 92
GNB1/GNGT1 -0.029 0.065 -9999 0 -10000 0 0
GNAT1/GDP -0.063 0.16 -9999 0 -0.5 92 92
GUCY2D -0.004 0.042 -9999 0 -0.33 11 11
GNGT1 -0.046 0.1 -9999 0 -10000 0 0
GUCY2F -0.001 0.014 -9999 0 -0.28 2 2
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.017 0.073 -9999 0 -0.48 17 17
mol:11-cis-retinal -0.53 0.4 -9999 0 -0.84 533 533
mol:cGMP -0.011 0.049 -9999 0 -0.49 6 6
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.41 0.31 -9999 0 -0.65 533 533
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.26 0.38 -9999 0 -0.83 261 261
Metarhodopsin II -0.003 0.021 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.011 0.052 -9999 0 -0.52 6 6
RGS9BP -0.017 0.066 -9999 0 -0.28 51 51
Metarhodopsin II/Transducin -0.008 0.018 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.01 0.049 -9999 0 -0.52 5 5
PDE6A/B -0.017 0.094 -9999 0 -0.65 17 17
mol:Pi -0.071 0.18 -9999 0 -0.57 92 92
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.022 0.048 -9999 0 -10000 0 0
PDE6B -0.017 0.12 -9999 0 -0.84 17 17
PDE6A -0.006 0.04 -9999 0 -10000 0 0
PDE6G -0.01 0.051 -9999 0 -0.28 29 29
RHO -0.005 0.036 -9999 0 -0.28 14 14
PDE6 -0.07 0.16 -9999 0 -0.48 105 105
GUCA1A -0.014 0.06 -9999 0 -0.28 41 41
GC2/GCAP Family -0.01 0.049 -9999 0 -0.52 5 5
GUCA1C 0 0.01 -9999 0 -10000 0 0
GUCA1B -0.005 0.064 -9999 0 -0.84 5 5
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.23 0.28 -10000 0 -0.56 341 341
fibroblast growth factor receptor signaling pathway -0.23 0.28 -10000 0 -0.56 341 341
LAMA1 -0.095 0.26 -10000 0 -0.83 97 97
PRNP -0.011 0.095 -10000 0 -0.84 11 11
GPC1/SLIT2 -0.049 0.17 -10000 0 -0.64 63 63
SMAD2 -0.014 0.081 -10000 0 -0.51 22 22
GPC1/PrPc/Cu2+ -0.008 0.065 -10000 0 -0.57 11 11
GPC1/Laminin alpha1 -0.074 0.2 -10000 0 -0.64 95 95
TDGF1 -0.019 0.12 -10000 0 -0.84 18 18
CRIPTO/GPC1 -0.015 0.094 -10000 0 -0.64 18 18
APP/GPC1 0 0.009 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.012 0.087 -10000 0 -0.56 19 19
FLT1 -0.001 0.029 -10000 0 -0.84 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.015 0.089 -10000 0 -0.56 22 22
SERPINC1 -0.014 0.06 -10000 0 -10000 0 0
FYN 0.012 0.087 -10000 0 -0.56 19 19
FGR 0.012 0.085 -10000 0 -0.56 18 18
positive regulation of MAPKKK cascade 0.025 0.095 -10000 0 -0.55 18 18
SLIT2 -0.063 0.22 -10000 0 -0.84 63 63
GPC1/NRG -0.23 0.31 -10000 0 -0.64 298 298
NRG1 -0.3 0.4 -10000 0 -0.84 298 298
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.002 0.024 -10000 0 -0.56 1 1
LYN 0.012 0.085 -10000 0 -0.56 18 18
mol:Spermine 0.011 0.01 -10000 0 -0.19 2 2
cell growth -0.23 0.28 -10000 0 -0.56 341 341
BMP signaling pathway 0.001 0.014 0.28 2 -10000 0 2
SRC 0.012 0.085 -10000 0 -0.56 18 18
TGFBR1 0 0.01 -10000 0 -0.28 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.29 0.4 -10000 0 -0.8 308 308
GPC1 -0.001 0.014 -10000 0 -0.28 2 2
TGFBR1 (dimer) 0 0.01 -10000 0 -0.28 1 1
VEGFA -0.003 0.029 -10000 0 -0.28 9 9
BLK -0.01 0.11 -10000 0 -0.59 20 20
HCK 0.01 0.087 -10000 0 -0.56 18 18
FGF2 -0.34 0.41 -10000 0 -0.84 337 337
FGFR1 -0.008 0.077 -10000 0 -0.71 9 9
VEGFR1 homodimer -0.001 0.029 -10000 0 -0.84 1 1
TGFBR2 -0.022 0.13 -10000 0 -0.84 22 22
cell death 0 0.009 -10000 0 -10000 0 0
ATIII/GPC1 -0.009 0.039 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.23 0.3 -10000 0 -0.65 289 289
LCK 0 0.11 -10000 0 -0.56 29 29
neuron differentiation -0.23 0.31 -10000 0 -0.64 298 298
PrPc/Cu2+ -0.009 0.074 -10000 0 -0.65 11 11
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.022 0.13 -10000 0 -0.84 22 22
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.4 -9999 0 -1 74 74
IL23A -0.18 0.4 -9999 0 -1.1 58 58
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.32 -9999 0 -0.87 119 119
positive regulation of T cell mediated cytotoxicity -0.2 0.43 -9999 0 -0.87 179 179
ITGA3 -0.17 0.39 -9999 0 -1 73 73
IL17F -0.11 0.29 -9999 0 -0.66 66 66
IL12B -0.041 0.11 -9999 0 -0.3 57 57
STAT1 (dimer) -0.23 0.38 -9999 0 -0.87 146 146
CD4 -0.17 0.38 -9999 0 -0.96 72 72
IL23 -0.19 0.38 -9999 0 -1.1 59 59
IL23R -0.015 0.088 -9999 0 -10000 0 0
IL1B -0.19 0.41 -9999 0 -1.1 75 75
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.18 0.38 -9999 0 -0.94 84 84
TYK2 0.011 0.016 -9999 0 -10000 0 0
STAT4 -0.033 0.16 -9999 0 -0.82 34 34
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.034 0.16 -9999 0 -0.84 33 33
IL12RB1 0.001 0.06 -9999 0 -0.3 26 26
PIK3CA 0 0.01 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.002 0.045 -9999 0 -0.69 1 1
IL23R/JAK2 -0.013 0.11 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.2 0.43 -9999 0 -0.87 179 179
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.018 0.021 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.18 0.37 -9999 0 -0.98 62 62
ALOX12B -0.18 0.38 -9999 0 -0.9 99 99
CXCL1 -0.38 0.66 -9999 0 -1.4 234 234
T cell proliferation -0.2 0.43 -9999 0 -0.87 179 179
NFKBIA 0 0 -9999 0 -10000 0 0
IL17A -0.074 0.24 -9999 0 -0.54 45 45
PI3K -0.25 0.33 -9999 0 -0.86 129 129
IFNG -0.005 0.026 -9999 0 -0.092 18 18
STAT3 (dimer) -0.24 0.31 -9999 0 -0.87 107 107
IL18R1 -0.011 0.095 -9999 0 -0.84 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 -0.088 0.24 -9999 0 -0.56 43 43
IL18/IL18R -0.033 0.13 -9999 0 -0.58 42 42
macrophage activation -0.014 0.017 -9999 0 -0.043 60 60
TNF -0.19 0.41 -9999 0 -1.1 76 76
STAT3/STAT4 -0.27 0.35 -9999 0 -0.88 157 157
STAT4 (dimer) -0.24 0.4 -9999 0 -0.88 183 183
IL18 -0.007 0.045 -9999 0 -0.28 22 22
IL19 -0.18 0.38 -9999 0 -0.92 95 95
STAT5A (dimer) -0.23 0.38 -9999 0 -0.85 165 165
STAT1 -0.006 0.04 -9999 0 -10000 0 0
SOCS3 -0.005 0.064 -9999 0 -0.84 5 5
CXCL9 -0.19 0.39 -9999 0 -0.95 90 90
MPO -0.22 0.48 -9999 0 -1.2 110 110
positive regulation of humoral immune response -0.2 0.43 -9999 0 -0.87 179 179
IL23/IL23R/JAK2/TYK2 -0.21 0.45 -9999 0 -0.91 174 174
IL6 -0.49 0.72 -9999 0 -1.4 328 328
STAT5A -0.007 0.076 -9999 0 -0.84 7 7
IL2 0.002 0.031 -9999 0 -0.3 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.19 0.42 -9999 0 -1.1 80 80
keratinocyte proliferation -0.2 0.43 -9999 0 -0.87 179 179
NOS2 -0.17 0.39 -9999 0 -0.98 74 74
Syndecan-1-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
TGFB1 0 0 -9999 0 -10000 0 0
CCL5 -0.011 0.063 -9999 0 -0.84 2 2
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.073 0.11 -9999 0 -0.35 82 82
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.067 0.099 -9999 0 -0.36 32 32
Syndecan-1/Syntenin -0.066 0.099 -9999 0 -0.36 32 32
MAPK3 -0.049 0.09 -9999 0 -0.52 4 4
HGF/MET -0.15 0.29 -9999 0 -0.69 178 178
TGFB1/TGF beta receptor Type II 0 0 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.066 0.098 -9999 0 -0.36 32 32
Syndecan-1/RANTES -0.072 0.11 -9999 0 -0.39 33 33
Syndecan-1/CD147 -0.057 0.096 -9999 0 -0.56 4 4
Syndecan-1/Syntenin/PIP2 -0.064 0.096 -9999 0 -0.35 32 32
LAMA5 0 0.01 -9999 0 -0.28 1 1
positive regulation of cell-cell adhesion -0.063 0.094 -9999 0 -0.34 32 32
MMP7 -0.12 0.29 -9999 0 -0.84 116 116
HGF -0.05 0.2 -9999 0 -0.84 50 50
Syndecan-1/CASK -0.069 0.1 -9999 0 -0.33 82 82
Syndecan-1/HGF/MET -0.17 0.26 -9999 0 -0.61 180 180
regulation of cell adhesion -0.036 0.093 -9999 0 -0.54 3 3
HPSE -0.008 0.056 -9999 0 -0.84 2 2
positive regulation of cell migration -0.073 0.11 -9999 0 -0.35 82 82
SDC1 -0.073 0.11 -9999 0 -0.35 82 82
Syndecan-1/Collagen -0.073 0.11 -9999 0 -0.35 82 82
PPIB 0 0.01 -9999 0 -10000 0 0
MET -0.14 0.32 -9999 0 -0.83 144 144
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.28 352 352
MAPK1 -0.049 0.09 -9999 0 -0.52 4 4
homophilic cell adhesion -0.072 0.11 -9999 0 -0.34 82 82
MMP1 -0.22 0.11 -9999 0 -0.28 662 662
Aurora C signaling

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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.072 0.064 -9999 0 -0.64 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.019 0.017 -9999 0 -10000 0 0
AURKB -0.16 0.14 -9999 0 -0.28 492 492
AURKC -0.005 0.045 -9999 0 -0.84 1 1
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.055 0.21 -9999 0 -0.64 39 39
CRP -0.059 0.21 -9999 0 -0.64 39 39
cell cycle arrest -0.072 0.24 -9999 0 -0.72 45 45
TIMP1 -0.054 0.2 -9999 0 -0.58 36 36
IL6ST -0.042 0.21 -9999 0 -0.82 56 56
Rac1/GDP -0.14 0.19 -9999 0 -0.65 54 54
AP1 -0.14 0.25 -9999 0 -0.49 266 266
GAB2 -0.002 0.027 -9999 0 -0.28 8 8
TNFSF11 -0.065 0.22 -9999 0 -0.64 39 39
HSP90B1 0.017 0.047 -9999 0 -10000 0 0
GAB1 0 0.002 -9999 0 -10000 0 0
MAPK14 -0.12 0.24 -9999 0 -0.73 55 55
AKT1 0.041 0.026 -9999 0 -10000 0 0
FOXO1 0.052 0.044 -9999 0 -0.44 6 6
MAP2K6 -0.14 0.24 -9999 0 -0.58 100 100
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.075 0.22 -9999 0 -0.63 52 52
MITF -0.13 0.24 -9999 0 -0.51 124 124
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.016 0.11 -9999 0 -1.5 4 4
CEBPB 0.015 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.052 0.069 -9999 0 -0.27 7 7
STAT3 -0.08 0.26 -9999 0 -0.78 45 45
STAT1 -0.012 0.023 -9999 0 -10000 0 0
CEBPD -0.057 0.22 -9999 0 -0.67 39 39
PIK3CA 0.01 0.011 -9999 0 -10000 0 0
PI3K 0 0.006 -9999 0 -10000 0 0
JUN -0.009 0.086 -9999 0 -0.84 9 9
PIAS3/MITF -0.14 0.2 -9999 0 -0.66 56 56
MAPK11 -0.12 0.24 -9999 0 -0.75 55 55
STAT3 (dimer)/FOXO1 -0.022 0.21 -9999 0 -0.57 42 42
GRB2/SOS1/GAB family -0.13 0.18 -9999 0 -0.72 37 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.15 0.24 -9999 0 -0.38 365 365
GRB2 0 0.01 -9999 0 -10000 0 0
JAK2 0 0 -9999 0 -10000 0 0
LBP -0.23 0.45 -9999 0 -0.96 210 210
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0 0.002 -9999 0 -10000 0 0
MYC -0.07 0.26 -9999 0 -0.87 44 44
FGG -0.064 0.22 -9999 0 -0.65 39 39
macrophage differentiation -0.072 0.24 -9999 0 -0.72 45 45
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.28 -9999 0 -0.52 366 366
JUNB -0.054 0.21 -9999 0 -0.61 40 40
FOS -0.27 0.39 -9999 0 -0.84 272 272
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.14 0.25 -9999 0 -0.38 364 364
STAT1/PIAS1 -0.14 0.2 -9999 0 -0.45 148 148
GRB2/SOS1/GAB family/SHP2/PI3K 0.001 0.009 -9999 0 -10000 0 0
STAT3 (dimer) -0.076 0.25 -9999 0 -0.76 44 44
PRKCD -0.05 0.21 -9999 0 -0.61 48 48
IL6R -0.022 0.13 -9999 0 -0.84 22 22
SOCS3 -0.11 0.23 -9999 0 -0.79 46 46
gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.14 -9999 0 -0.56 58 58
Rac1/GTP -0.14 0.19 -9999 0 -0.63 59 59
HCK -0.004 0.033 -9999 0 -10000 0 0
MAPKKK cascade 0 0.068 -9999 0 -10000 0 0
bone resorption -0.062 0.21 -9999 0 -0.61 40 40
IRF1 -0.055 0.21 -9999 0 -0.64 37 37
mol:GDP -0.12 0.23 -9999 0 -0.46 155 155
SOS1 0 0.002 -9999 0 -10000 0 0
VAV1 -0.12 0.24 -9999 0 -0.47 154 154
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.22 -9999 0 -0.8 51 51
PTPN11 -0.013 0.02 -9999 0 -10000 0 0
IL6/IL6RA -0.26 0.33 -9999 0 -0.66 332 332
gp130 (dimer)/TYK2/TYK2/LMO4 -0.032 0.14 -9999 0 -0.56 58 58
gp130 (dimer)/JAK2/JAK2/LMO4 -0.032 0.14 -9999 0 -0.56 58 58
IL6 -0.31 0.41 -9999 0 -0.83 324 324
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.002 0.03 -9999 0 -0.84 1 1
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.23 -9999 0 -0.39 365 365
LMO4 0.008 0.057 -9999 0 -0.46 9 9
STAT3 (dimer)/PIAS3 -0.14 0.2 -9999 0 -0.78 44 44
MCL1 0.054 0.014 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.099 0.19 -10000 0 -0.5 146 146
ER alpha/Gai/GDP/Gbeta gamma -0.086 0.19 -10000 0 -0.48 125 125
AKT1 -0.11 0.3 -10000 0 -0.85 117 117
PIK3CA 0 0.01 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.12 0.3 -10000 0 -0.86 117 117
mol:Ca2+ -0.023 0.14 -10000 0 -0.49 56 56
IGF1R -0.02 0.12 -10000 0 -0.84 16 16
E2/ER alpha (dimer)/Striatin -0.098 0.2 -10000 0 -0.57 117 117
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.081 0.29 0.81 117 -10000 0 117
RhoA/GTP -0.069 0.14 -10000 0 -0.42 117 117
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.087 0.21 -10000 0 -0.56 122 122
regulation of stress fiber formation 0.014 0.13 0.41 2 -10000 0 2
E2/ERA-ERB (dimer) -0.11 0.21 -10000 0 -0.58 141 141
KRAS 0 0.01 -10000 0 -10000 0 0
G13/GTP -0.09 0.18 -10000 0 -0.52 117 117
pseudopodium formation -0.014 0.13 -10000 0 -0.41 2 2
E2/ER alpha (dimer)/PELP1 -0.098 0.2 -10000 0 -0.57 117 117
GRB2 0 0.01 -10000 0 -10000 0 0
GNG2 -0.006 0.07 -10000 0 -0.84 6 6
GNAO1 -0.033 0.14 -10000 0 -0.84 21 21
HRAS 0 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.055 0.22 -10000 0 -0.55 125 125
E2/ER beta (dimer) -0.019 0.11 -10000 0 -0.65 25 25
mol:GDP -0.086 0.21 -10000 0 -0.55 141 141
mol:NADP -0.055 0.22 -10000 0 -0.55 125 125
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.025 0.15 -10000 0 -0.51 56 56
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.84 16 16
PLCB1 -0.059 0.14 -10000 0 -0.53 55 55
PLCB2 -0.033 0.088 -10000 0 -0.67 9 9
IGF1 -0.18 0.35 -10000 0 -0.84 186 186
mol:L-citrulline -0.055 0.22 -10000 0 -0.55 125 125
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.039 0.15 -10000 0 -0.84 21 21
JNK cascade -0.019 0.11 -10000 0 -0.65 25 25
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.025 0.14 -10000 0 -0.84 25 25
GNAQ -0.002 0.041 -10000 0 -0.84 2 2
ESR1 -0.15 0.29 -10000 0 -0.56 228 228
Gq family/GDP/Gbeta gamma -0.004 0.061 -10000 0 -0.54 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.022 0.13 -10000 0 -0.36 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.087 0.21 -10000 0 -0.56 122 122
GNAZ -0.006 0.07 -10000 0 -0.84 6 6
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.65 117 117
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.19 0.35 -10000 0 -0.84 190 190
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 -0.001 0.11 -10000 0 -0.58 26 26
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.84 43 43
HBEGF -0.063 0.19 -10000 0 -0.45 127 127
cAMP biosynthetic process -0.2 0.27 -10000 0 -0.54 291 291
SRC -0.047 0.19 -10000 0 -0.45 125 125
PI3K 0 0.006 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.077 0.19 -10000 0 -0.48 146 146
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.53 181 181
Gs family/GTP -0.2 0.28 -10000 0 -0.56 291 291
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.008 -10000 0 -10000 0 0
vasodilation -0.051 0.21 -10000 0 -0.52 125 125
mol:DAG -0.025 0.15 -10000 0 -0.51 56 56
Gs family/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.46 292 292
MSN -0.016 0.14 -10000 0 -0.45 2 2
Gq family/GTP -0.036 0.092 -10000 0 -0.67 9 9
mol:PI-3-4-5-P3 -0.087 0.3 -10000 0 -0.82 117 117
NRAS -0.001 0.014 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.051 0.21 0.52 125 -10000 0 125
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.079 0.2 -10000 0 -0.52 141 141
NOS3 -0.06 0.23 -10000 0 -0.58 125 125
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.054 0.25 -10000 0 -0.66 117 117
E2/ER alpha (dimer)/PELP1/Src -0.092 0.22 -10000 0 -0.59 122 122
ruffle organization -0.014 0.13 -10000 0 -0.41 2 2
ROCK2 -0.064 0.13 -10000 0 -0.47 3 3
GNA14 -0.013 0.082 -10000 0 -0.4 27 27
GNA15 -0.002 0.035 -10000 0 -0.39 5 5
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.087 0.19 -10000 0 -0.48 130 130
MMP2 -0.04 0.19 -10000 0 -0.67 23 23
Aurora B signaling

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
Condensin I complex -0.055 0.054 -9999 0 -10000 0 0
STMN1 -0.1 0.12 -9999 0 -0.35 65 65
Aurora B/RasGAP/Survivin -0.18 0.12 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.15 0.15 -9999 0 -0.33 330 330
BIRC5 -0.21 0.12 -9999 0 -10000 0 0
DES -0.31 0.34 -9999 0 -0.65 414 414
Aurora C/Aurora B/INCENP -0.065 0.073 -9999 0 -0.65 1 1
Aurora B/TACC1 -0.09 0.11 -9999 0 -0.63 20 20
Aurora B/PP2A -0.094 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.006 0.015 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.16 -9999 0 -0.35 451 451
Cul3 protein complex -0.22 0.27 -9999 0 -0.56 330 330
KIF2C -0.036 0.025 -9999 0 -10000 0 0
PEBP1 0 0 -9999 0 -10000 0 0
KIF20A -0.23 0.11 -9999 0 -0.28 676 676
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.094 0.091 -9999 0 -10000 0 0
SEPT1 -0.004 0.034 -9999 0 -0.28 13 13
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.006 0.039 -9999 0 -0.28 17 17
NSUN2/NPM1/Nucleolin 0.013 0.014 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.031 0.04 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -0.28 339 339
AURKC -0.005 0.045 -9999 0 -0.84 1 1
CDCA8 -0.1 0.14 -9999 0 -10000 0 0
cytokinesis -0.11 0.066 -9999 0 -10000 0 0
Aurora B/Septin1 -0.088 0.076 -9999 0 -10000 0 0
AURKA -0.14 0.14 -9999 0 -10000 0 0
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.33 0.41 -9999 0 -0.84 330 330
BUB1 -0.21 0.12 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.25 0.17 -9999 0 -0.39 455 455
EVI5 0.007 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.094 0.092 -9999 0 -10000 0 0
SGOL1 -0.19 0.13 -9999 0 -10000 0 0
CENPA -0.05 0.052 -9999 0 -10000 0 0
NCAPG -0.16 0.14 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome -0.094 0.091 -9999 0 -10000 0 0
NCAPD2 -0.003 0.027 -9999 0 -0.28 8 8
Aurora B/PP1-gamma -0.094 0.091 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.12 0.14 -9999 0 -0.28 363 363
NPM1 -0.012 0.019 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.001 0.029 -9999 0 -0.84 1 1
mitotic prometaphase -0.006 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.094 0.091 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.11 0.1 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.019 -9999 0 -10000 0 0
MYLK -0.073 0.14 -9999 0 -0.48 80 80
KIF23 -0.094 0.13 -9999 0 -0.28 281 281
VIM -0.091 0.1 -9999 0 -0.72 2 2
RACGAP1 -0.013 0.063 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.019 -9999 0 -10000 0 0
Chromosomal passenger complex -0.077 0.062 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.15 0.17 -9999 0 -10000 0 0
TACC1 -0.02 0.13 -9999 0 -0.84 20 20
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.002 0.041 -10000 0 -0.84 2 2
Jak2/Leptin Receptor -0.15 0.24 -10000 0 -0.55 202 202
PTP1B/AKT1 -0.067 0.099 -10000 0 -0.32 84 84
FYN -0.001 0.029 -10000 0 -0.84 1 1
p210 bcr-abl/PTP1B -0.068 0.12 -10000 0 -0.37 86 86
EGFR -0.3 0.4 -10000 0 -0.84 294 294
EGF/EGFR -0.3 0.32 -10000 0 -0.6 410 410
CSF1 -0.003 0.05 -10000 0 -0.84 3 3
AKT1 0 0 -10000 0 -10000 0 0
INSR 0 0.01 -10000 0 -0.28 1 1
PTP1B/N-cadherin -0.094 0.12 -10000 0 -0.36 88 88
Insulin Receptor/Insulin -0.047 0.073 -10000 0 -0.4 7 7
HCK -0.004 0.033 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.057 0.12 -10000 0 -0.35 84 84
EGF -0.17 0.34 -10000 0 -0.85 167 167
YES1 -0.001 0.029 -10000 0 -0.84 1 1
CAV1 -0.17 0.24 -10000 0 -0.51 214 214
TXN 0 0.01 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.083 0.14 -10000 0 -0.41 93 93
cell migration 0.068 0.12 0.37 86 -10000 0 86
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.001 0.026 -10000 0 -0.28 7 7
ITGA2B -0.017 0.078 -10000 0 -0.84 3 3
CSF1R 0 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin -0.003 0.027 -10000 0 -10000 0 0
FGR 0 0.01 -10000 0 -0.28 1 1
PTP1B/p130 Cas -0.072 0.11 -10000 0 -0.35 84 84
Crk/p130 Cas -0.066 0.1 -10000 0 -0.41 21 21
DOK1 -0.043 0.11 -10000 0 -0.32 65 65
JAK2 -0.038 0.07 -10000 0 -0.3 7 7
Jak2/Leptin Receptor/Leptin -0.39 0.18 -10000 0 -0.52 421 421
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 -0.069 0.12 -10000 0 -0.38 86 86
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.058 0.12 -10000 0 -0.84 2 2
SRC -0.013 0.046 -10000 0 -10000 0 0
ITGB3 -0.015 0.11 -10000 0 -0.84 14 14
CAT1/PTP1B -0.086 0.17 -10000 0 -0.44 76 76
CAPN1 0 0.002 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.037 0.064 -10000 0 -0.42 2 2
mol:H2O2 -0.005 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.34 0.16 -10000 0 -0.45 410 410
negative regulation of transcription -0.038 0.069 -10000 0 -0.3 7 7
FCGR2A 0 0.01 -10000 0 -10000 0 0
FER -0.006 0.071 -10000 0 -0.85 6 6
alphaIIb/beta3 Integrin -0.023 0.1 -10000 0 -0.66 17 17
BLK -0.036 0.1 -10000 0 -0.3 102 102
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0 0.002 -10000 0 -10000 0 0
LEPR -0.19 0.36 -10000 0 -0.84 201 201
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.01 -10000 0 -10000 0 0
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.036 0.13 -10000 0 -0.44 18 18
PRL -0.004 0.032 -10000 0 -10000 0 0
SOCS3 0.016 0.12 -10000 0 -1.5 5 5
SPRY2 -0.096 0.27 -10000 0 -0.85 95 95
Insulin Receptor/Insulin/IRS1 -0.021 0.11 -10000 0 -0.58 31 31
CSF1/CSF1R -0.068 0.1 -10000 0 -0.35 75 75
Ras protein signal transduction 0.036 0.035 -10000 0 -10000 0 0
IRS1 -0.031 0.16 -10000 0 -0.84 31 31
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.68 0.32 -10000 0 -0.84 687 687
STAT5B -0.056 0.1 -10000 0 -0.31 85 85
STAT5A -0.057 0.1 -10000 0 -0.31 87 87
GRB2 0 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.074 0.11 -10000 0 -0.36 86 86
CSN2 0.02 0.029 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -10000 0 0
LAT -0.014 0.054 -10000 0 -0.59 2 2
YBX1 -0.002 0.015 -10000 0 -0.27 1 1
LCK -0.019 0.1 -10000 0 -0.46 34 34
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.003 0.04 -10000 0 -0.85 1 1
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.023 0.062 -9999 0 -0.6 8 8
alphaM/beta2 Integrin/GPIbA -0.024 0.06 -9999 0 -0.57 7 7
alphaM/beta2 Integrin/proMMP-9 -0.076 0.077 -9999 0 -0.44 3 3
PLAUR -0.021 0.073 -9999 0 -0.28 63 63
HMGB1 -0.014 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.018 0.026 -9999 0 -10000 0 0
AGER -0.016 0.048 -9999 0 -0.71 3 3
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG 0 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.078 0.099 -9999 0 -0.73 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.28 352 352
CYR61 -0.047 0.19 -9999 0 -0.84 47 47
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.06 0.12 -9999 0 -0.55 20 20
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.21 0.36 -9999 0 -0.84 208 208
MYH2 -0.074 0.17 -9999 0 -0.53 41 41
MST1R -0.011 0.089 -9999 0 -0.84 9 9
leukocyte activation during inflammatory response -0.33 0.24 -9999 0 -0.5 542 542
APOB -0.54 0.4 -9999 0 -0.84 542 542
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.008 0.081 -9999 0 -0.84 8 8
JAM3 -0.003 0.05 -9999 0 -0.84 3 3
GP1BA -0.011 0.08 -9999 0 -0.43 22 22
alphaM/beta2 Integrin/CTGF -0.024 0.068 -9999 0 -0.63 9 9
alphaM/beta2 Integrin -0.075 0.14 -9999 0 -0.38 77 77
JAM3 homodimer -0.003 0.05 -9999 0 -0.84 3 3
ICAM2 -0.005 0.064 -9999 0 -0.84 5 5
ICAM1 -0.004 0.032 -9999 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.066 0.14 -9999 0 -0.38 77 77
cell adhesion -0.024 0.06 -9999 0 -0.57 7 7
NFKB1 -0.14 0.18 -9999 0 -0.65 12 12
THY1 -0.002 0.023 -9999 0 -0.28 6 6
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.37 0.28 -9999 0 -0.57 542 542
alphaM/beta2 Integrin/LRP/tPA -0.033 0.11 -9999 0 -0.58 31 31
IL6 -0.33 0.5 -9999 0 -0.96 323 323
ITGB2 -0.017 0.033 -9999 0 -0.34 1 1
elevation of cytosolic calcium ion concentration -0.024 0.047 -9999 0 -10000 0 0
alphaM/beta2 Integrin/JAM2/JAM3 -0.04 0.12 -9999 0 -0.55 45 45
JAM2 -0.043 0.18 -9999 0 -0.84 43 43
alphaM/beta2 Integrin/ICAM1 -0.022 0.082 -9999 0 -0.53 19 19
alphaM/beta2 Integrin/uPA/Plg -0.02 0.032 -9999 0 -10000 0 0
RhoA/GTP -0.093 0.17 -9999 0 -0.41 153 153
positive regulation of phagocytosis -0.052 0.095 -9999 0 -0.48 17 17
Ron/MSP -0.017 0.1 -9999 0 -0.67 19 19
alphaM/beta2 Integrin/uPAR/uPA -0.024 0.047 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR -0.028 0.044 -9999 0 -10000 0 0
PLAU -0.009 0.048 -9999 0 -0.28 26 26
PLAT -0.026 0.14 -9999 0 -0.78 28 28
actin filament polymerization -0.071 0.16 -9999 0 -0.44 63 63
MST1 -0.011 0.096 -9999 0 -0.84 11 11
alphaM/beta2 Integrin/lipoprotein(a) -0.34 0.24 -9999 0 -0.51 542 542
TNF -0.096 0.22 -9999 0 -0.95 14 14
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.022 0.035 -9999 0 -10000 0 0
fibrinolysis -0.02 0.032 -9999 0 -10000 0 0
HCK -0.004 0.033 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.066 0.14 -9999 0 -0.38 77 77
VTN -0.023 0.09 -9999 0 -0.32 61 61
alphaM/beta2 Integrin/CYR61 -0.05 0.14 -9999 0 -0.61 47 47
LPA -0.002 0.021 -9999 0 -0.28 5 5
LRP1 -0.009 0.086 -9999 0 -0.84 9 9
cell migration -0.067 0.082 -9999 0 -0.55 9 9
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.019 0.028 -9999 0 -10000 0 0
MPO -0.06 0.22 -9999 0 -0.84 60 60
KNG1 -0.004 0.033 -9999 0 -10000 0 0
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.069 0.17 -9999 0 -0.47 56 56
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.002 0.021 -9999 0 -10000 0 0
CTGF -0.01 0.087 -9999 0 -0.84 9 9
alphaM/beta2 Integrin/Hck -0.02 0.032 -9999 0 -10000 0 0
ITGAM -0.015 0.027 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.23 -9999 0 -0.54 208 208
HP -0.17 0.33 -9999 0 -0.75 189 189
leukocyte adhesion -0.076 0.13 -9999 0 -0.6 28 28
SELP -0.21 0.36 -9999 0 -0.84 208 208
Ephrin A reverse signaling

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.057 0.17 -9999 0 -0.57 83 83
EFNA5 -0.083 0.25 -9999 0 -0.84 83 83
FYN -0.052 0.16 -9999 0 -0.52 83 83
neuron projection morphogenesis -0.057 0.17 -9999 0 -0.57 83 83
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.057 0.17 -9999 0 -0.57 83 83
EPHA5 -0.001 0.019 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.054 0.11 -9999 0 -0.28 163 163
mol:Halofuginone 0 0.002 -9999 0 -10000 0 0
ITGA1 -0.002 0.041 -9999 0 -0.84 2 2
CDKN1A -0.064 0.093 -9999 0 -0.88 1 1
PRL-3/alpha Tubulin -0.001 0.012 -9999 0 -10000 0 0
mol:Ca2+ -0.036 0.1 -9999 0 -0.66 13 13
AGT -0.051 0.14 -9999 0 -0.34 128 128
CCNA2 -0.19 0.26 -9999 0 -0.53 287 287
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.2 0.32 -9999 0 -0.64 287 287
CDK2/Cyclin E1 -0.071 0.091 -9999 0 -0.79 1 1
MAPK3 0.021 0.014 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.009 -9999 0 -10000 0 0
MAPK1 0.021 0.014 -9999 0 -10000 0 0
PTP4A1 -0.15 0.25 -9999 0 -0.5 287 287
PTP4A3 -0.001 0.019 -9999 0 -10000 0 0
PTP4A2 -0.001 0.014 -9999 0 -0.28 2 2
ITGB1 0.021 0.014 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -10000 0 0
RAC1 -0.064 0.088 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.16 0.22 -9999 0 -0.46 287 287
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0 0.006 -9999 0 -10000 0 0
RHOC -0.064 0.088 -9999 0 -10000 0 0
RHOA -0.064 0.088 -9999 0 -10000 0 0
cell motility -0.044 0.11 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.16 0.22 -9999 0 -0.46 287 287
PRL-3/alpha1 Integrin -0.002 0.034 -9999 0 -0.64 2 2
ROCK1 -0.044 0.11 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.14 0.25 -9999 0 -0.49 287 287
ATF5 -0.001 0.019 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.003 0.036 -9999 0 -0.64 2 2
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.57 343 343
PTK2 -0.086 0.18 -9999 0 -0.67 17 17
IGF1R -0.02 0.12 -9999 0 -0.84 16 16
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.012 0.094 -9999 0 -0.63 16 16
SRC 0 0.01 -9999 0 -10000 0 0
CDKN1B -0.088 0.12 -9999 0 -0.94 7 7
VEGFA -0.003 0.029 -9999 0 -0.28 9 9
ILK -0.085 0.11 -9999 0 -0.84 4 4
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.075 0.099 -9999 0 -0.78 4 4
PTK2B -0.01 0.069 -9999 0 -0.5 15 15
alphaV/beta3 Integrin/JAM-A -0.21 0.25 -9999 0 -0.5 345 345
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.011 0.073 -9999 0 -0.56 14 14
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.26 -9999 0 -0.58 204 204
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.006 0.043 -9999 0 -0.43 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.08 -9999 0 -0.56 15 15
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.34 0.36 -9999 0 -0.78 273 273
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.048 0.093 -9999 0 -0.58 14 14
RPS6KB1 -0.31 0.33 -9999 0 -0.71 273 273
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.34 0.39 -9999 0 -0.79 343 343
GPR124 -0.008 0.081 -9999 0 -0.84 8 8
MAPK1 -0.34 0.39 -9999 0 -0.79 343 343
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.12 0.23 -9999 0 -0.56 178 178
cell adhesion -0.016 0.086 -9999 0 -0.5 24 24
ANGPTL3 -0.002 0.021 -9999 0 -0.28 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.031 -9999 0 -0.56 2 2
IGF-1R heterotetramer -0.02 0.12 -9999 0 -0.84 16 16
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.022 0.13 -9999 0 -0.84 22 22
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
IGF1 -0.18 0.35 -9999 0 -0.84 186 186
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.015 0.098 -9999 0 -0.63 19 19
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.029 -9999 0 -0.84 1 1
alphaV/beta3 Integrin/CD47 -0.011 0.074 -9999 0 -0.56 15 15
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.027 0.14 -9999 0 -0.7 29 29
CSF1 -0.003 0.05 -9999 0 -0.84 3 3
PIK3C2A -0.085 0.11 -9999 0 -0.84 4 4
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.59 42 42
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.011 0.074 -9999 0 -0.54 15 15
FAK1/Vinculin -0.064 0.15 -9999 0 -0.51 16 16
alphaV beta3/Integrin/ppsTEM5 -0.015 0.099 -9999 0 -0.64 19 19
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.023 0.09 -9999 0 -0.32 61 61
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.34 0.41 -9999 0 -0.84 337 337
F11R -0.24 0.33 -9999 0 -0.64 337 337
alphaV/beta3 Integrin/Lactadherin -0.017 0.097 -9999 0 -0.58 23 23
alphaV/beta3 Integrin/TGFBR2 -0.024 0.13 -9999 0 -0.64 31 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.03 -9999 0 -0.51 3 3
HSP90AA1 0 0.01 -9999 0 -0.28 1 1
alphaV/beta3 Integrin/Talin -0.009 0.067 -9999 0 -0.52 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.01 0.07 -9999 0 -0.51 15 15
SDC1 -0.02 0.075 -9999 0 -0.29 58 58
VAV3 -0.005 0.042 -9999 0 -0.47 6 6
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.031 0.16 -9999 0 -0.84 31 31
FAK1/Paxillin -0.064 0.15 -9999 0 -0.51 16 16
cell migration -0.05 0.14 -9999 0 -0.45 16 16
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.22 -9999 0 -0.45 345 345
SPP1 -0.08 0.13 -9999 0 -10000 0 0
KDR -0.002 0.041 -9999 0 -0.84 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.17 0.33 -9999 0 -0.84 166 166
angiogenesis -0.3 0.39 -9999 0 -0.76 345 345
Rac1/GTP -0.005 0.038 -9999 0 -0.43 6 6
EDIL3 -0.028 0.14 -9999 0 -0.84 23 23
cell proliferation -0.024 0.12 -9999 0 -0.64 31 31
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.013 0.083 -9999 0 -0.55 17 17
NF kappa B1 p50/RelA/I kappa B alpha -0.045 0.12 -9999 0 -0.42 12 12
AP1 -0.21 0.28 -9999 0 -0.52 339 339
mol:PIP3 -0.2 0.25 -9999 0 -0.49 294 294
AKT1 -0.009 0.054 -9999 0 -0.57 2 2
PTK2B 0.015 0.058 -9999 0 -0.31 14 14
RHOA 0.029 0.025 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.14 -9999 0 -0.37 101 101
MAGI3 -0.001 0.029 -9999 0 -0.84 1 1
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.063 0.16 -9999 0 -0.45 109 109
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.019 0.15 -9999 0 -0.44 88 88
NF kappa B1 p50/RelA -0.054 0.14 -9999 0 -0.52 17 17
endothelial cell migration 0.01 0.11 -9999 0 -0.69 20 20
ADCY4 0.001 0.14 -9999 0 -0.62 26 26
ADCY5 -0.068 0.18 -9999 0 -0.6 54 54
ADCY6 0.01 0.12 -9999 0 -0.6 19 19
ADCY7 0.01 0.12 -9999 0 -0.6 19 19
ADCY1 0.002 0.13 -9999 0 -0.61 23 23
ADCY2 -0.01 0.15 -9999 0 -0.62 31 31
ADCY3 0.01 0.12 -9999 0 -0.6 19 19
ADCY8 0.007 0.12 -9999 0 -0.6 19 19
ADCY9 0.01 0.12 -9999 0 -0.6 19 19
GSK3B 0.022 0.056 -9999 0 -0.4 5 5
arachidonic acid secretion 0.014 0.12 -9999 0 -0.57 19 19
GNG2 -0.006 0.07 -9999 0 -0.84 6 6
TRIP6 -0.001 0.019 -9999 0 -0.53 1 1
GNAO1 -0.005 0.12 -9999 0 -0.53 40 40
HRAS 0 0.01 -9999 0 -10000 0 0
NFKBIA -0.005 0.16 -9999 0 -0.42 101 101
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.033 -9999 0 -0.95 1 1
JUN -0.009 0.086 -9999 0 -0.84 9 9
LPA/LPA2/NHERF2 -0.001 0.011 -9999 0 -10000 0 0
TIAM1 -0.001 0.04 -9999 0 -1.1 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.01 0.14 -9999 0 -0.38 101 101
PLCB3 -0.001 0.009 -9999 0 -10000 0 0
FOS -0.27 0.39 -9999 0 -0.84 272 272
positive regulation of mitosis 0.014 0.12 -9999 0 -0.57 19 19
LPA/LPA1-2-3 -0.075 0.18 -9999 0 -0.53 109 109
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.1 -9999 0 -0.42 13 13
GNAZ 0.012 0.09 -9999 0 -0.48 26 26
EGFR/PI3K-beta/Gab1 -0.2 0.27 -9999 0 -0.52 292 292
positive regulation of dendritic cell cytokine production -0.075 0.18 -9999 0 -0.52 109 109
LPA/LPA2/MAGI-3 -0.002 0.022 -9999 0 -0.56 1 1
ARHGEF1 -0.009 0.06 -9999 0 -0.46 12 12
GNAI2 0.016 0.076 -9999 0 -0.45 20 20
GNAI3 0.016 0.076 -9999 0 -0.45 20 20
GNAI1 -0.013 0.16 -9999 0 -0.59 56 56
LPA/LPA3 -0.087 0.21 -9999 0 -0.65 101 101
LPA/LPA2 -0.001 0.014 -9999 0 -10000 0 0
LPA/LPA1 -0.013 0.084 -9999 0 -0.53 20 20
HB-EGF/EGFR -0.25 0.27 -9999 0 -0.61 292 292
HBEGF -0.063 0.1 -9999 0 -0.65 3 3
mol:DAG -0.01 0.14 -9999 0 -0.38 101 101
cAMP biosynthetic process -0.009 0.14 -9999 0 -0.56 38 38
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.005 0.16 -9999 0 -0.42 101 101
GNAQ -0.057 0.14 -9999 0 -0.43 103 103
LPAR2 0 0.01 -9999 0 -0.28 1 1
LPAR3 -0.11 0.27 -9999 0 -0.84 101 101
LPAR1 -0.014 0.1 -9999 0 -0.83 12 12
IL8 -0.19 0.23 -9999 0 -0.45 312 312
PTK2 -0.069 0.17 -9999 0 -0.49 109 109
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.064 0.16 -9999 0 -0.45 109 109
EGFR -0.29 0.4 -9999 0 -0.83 297 297
PLCG1 -0.058 0.15 -9999 0 -0.45 102 102
PLD2 -0.069 0.17 -9999 0 -0.49 109 109
G12/G13 -0.01 0.065 -9999 0 -0.5 12 12
PI3K-beta -0.01 0.063 -9999 0 -0.42 17 17
cell migration -0.022 0.056 -9999 0 -0.26 5 5
SLC9A3R2 0 0 -9999 0 -10000 0 0
PXN 0.002 0.1 -9999 0 -0.43 13 13
HRAS/GTP -0.031 0.11 -9999 0 -0.59 19 19
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.28 352 352
PRKCE -0.001 0.029 -9999 0 -0.84 1 1
PRKCD -0.001 0.13 -9999 0 -0.36 101 101
Gi(beta/gamma) -0.031 0.11 -9999 0 -0.6 21 21
mol:LPA -0.002 0.021 -9999 0 -0.22 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.057 0.14 -9999 0 -0.5 23 23
MAPKKK cascade 0.014 0.12 -9999 0 -0.57 19 19
contractile ring contraction involved in cytokinesis 0.029 0.025 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.061 0.15 -9999 0 -0.45 105 105
GNA15 -0.057 0.14 -9999 0 -0.43 102 102
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.02 0.16 -9999 0 -0.45 88 88
GNA11 -0.056 0.14 -9999 0 -0.43 101 101
Rac1/GTP -0.001 0.035 -9999 0 -1 1 1
MMP2 0.01 0.11 -9999 0 -0.69 20 20
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.03 -9999 0 -10000 0 0
VDR 0 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.037 0.16 -9999 0 -0.42 14 14
RXRs/LXRs/DNA/Oxysterols -0.015 0.14 -9999 0 -0.47 13 13
MED1 -0.008 0.045 -9999 0 -10000 0 0
mol:9cRA 0.005 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.019 0.087 -9999 0 -0.38 42 42
RXRs/NUR77 -0.17 0.26 -9999 0 -0.55 258 258
RXRs/PPAR -0.16 0.21 -9999 0 -0.52 114 114
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.006 0.048 -9999 0 -0.48 8 8
RARA -0.004 0.033 -9999 0 -10000 0 0
NCOA1 -0.001 0.029 -9999 0 -0.84 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.006 0.049 -9999 0 -0.49 8 8
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.03 0.053 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.018 0.081 -9999 0 -0.36 42 42
THRA -0.001 0.029 -9999 0 -0.84 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.22 -9999 0 -0.5 204 204
NR1H4 -0.002 0.025 -9999 0 -0.28 7 7
RXRs/LXRs/DNA -0.11 0.2 -9999 0 -0.46 204 204
NR1H2 0.016 0.005 -9999 0 -10000 0 0
NR1H3 0.016 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.2 -9999 0 -0.48 204 204
NR4A1 -0.079 0.24 -9999 0 -0.84 79 79
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.049 0.13 -9999 0 -0.28 204 204
RXRG -0.19 0.36 -9999 0 -0.83 204 204
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.005 -9999 0 -10000 0 0
RXRB 0.015 0.006 -9999 0 -10000 0 0
THRB -0.036 0.17 -9999 0 -0.84 36 36
PPARG -0.2 0.36 -9999 0 -0.84 197 197
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.015 0.19 -9999 0 -1.3 10 10
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.015 0.14 -9999 0 -0.47 13 13
PPARA -0.003 0.05 -9999 0 -0.84 3 3
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.008 0.081 -9999 0 -0.84 8 8
RXRs/NUR77/BCL2 -0.13 0.2 -9999 0 -0.4 270 270
SREBF1 -0.005 0.14 -9999 0 -0.68 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.22 -9999 0 -0.5 204 204
ABCA1 -0.007 0.15 -9999 0 -0.94 6 6
RARs/THRs -0.027 0.12 -9999 0 -0.51 42 42
RXRs/FXR -0.12 0.22 -9999 0 -0.51 204 204
BCL2 -0.024 0.14 -9999 0 -0.84 24 24
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.046 0.29 -10000 0 -0.84 91 91
IHH -0.011 0.076 -10000 0 -0.5 2 2
SHH Np/Cholesterol/GAS1 -0.031 0.12 -10000 0 -0.53 46 46
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.031 0.12 0.53 46 -10000 0 46
SMO/beta Arrestin2 -0.07 0.23 -10000 0 -0.87 57 57
SMO -0.046 0.25 -10000 0 -0.93 57 57
AKT1 0 0.093 -10000 0 -0.34 11 11
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.06 0.22 -10000 0 -0.84 60 60
ADRBK1 0 0.01 -10000 0 -0.28 1 1
heart looping -0.028 0.25 -10000 0 -0.9 57 57
STIL -0.035 0.21 -10000 0 -0.72 59 59
DHH N/PTCH2 -0.073 0.21 -10000 0 -0.68 91 91
DHH N/PTCH1 -0.084 0.24 -10000 0 -0.78 80 80
PIK3CA 0 0.01 -10000 0 -10000 0 0
DHH -0.023 0.14 -10000 0 -0.81 24 24
PTHLH -0.07 0.37 -10000 0 -1.1 91 91
determination of left/right symmetry -0.028 0.25 -10000 0 -0.9 57 57
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.067 0.36 -10000 0 -1.1 91 91
IHH N/Hhip -0.009 0.048 -10000 0 -0.7 1 1
DHH N/Hhip -0.021 0.11 -10000 0 -0.66 24 24
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.028 0.25 -10000 0 -0.9 57 57
pancreas development -0.004 0.042 -10000 0 -0.84 1 1
HHAT -0.001 0.029 -10000 0 -0.84 1 1
PI3K 0 0.006 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.045 0.19 -10000 0 -0.84 45 45
somite specification -0.028 0.25 -10000 0 -0.9 57 57
SHH Np/Cholesterol/PTCH1 -0.066 0.2 -10000 0 -0.78 56 56
SHH Np/Cholesterol/PTCH2 -0.049 0.15 -10000 0 -0.53 74 74
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.52 219 219
SHH 0.01 0.037 -10000 0 -0.65 1 1
catabolic process -0.041 0.25 -10000 0 -0.88 62 62
SMO/Vitamin D3 -0.069 0.22 -10000 0 -0.84 57 57
SHH Np/Cholesterol/Hhip -0.006 0.038 -10000 0 -0.53 2 2
LRP2 -0.22 0.36 -10000 0 -0.79 239 239
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.86 67 67
SHH Np/Cholesterol/BOC -0.041 0.14 -10000 0 -0.53 61 61
SHH Np/Cholesterol/CDO -0.01 0.062 -10000 0 -0.52 11 11
mesenchymal cell differentiation 0.006 0.037 0.52 2 -10000 0 2
mol:Vitamin D3 -0.025 0.22 -10000 0 -0.79 56 56
IHH N/PTCH2 -0.067 0.2 -10000 0 -0.72 73 73
CDON -0.01 0.091 -10000 0 -0.84 10 10
IHH N/PTCH1 -0.038 0.26 -10000 0 -0.89 62 62
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.64 218 218
PTCH2 -0.073 0.24 -10000 0 -0.84 73 73
SHH Np/Cholesterol -0.004 0.026 -10000 0 -0.53 1 1
PTCH1 -0.041 0.26 -10000 0 -0.89 62 62
HHIP -0.004 0.042 -10000 0 -0.84 1 1
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.056 0.2 -9999 0 -0.85 49 49
PDGF/PDGFRA/CRKL -0.037 0.15 -9999 0 -0.65 48 48
positive regulation of JUN kinase activity -0.029 0.12 -9999 0 -0.5 48 48
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.041 0.15 -9999 0 -0.66 48 48
AP1 -0.4 0.56 -9999 0 -1.2 272 272
mol:IP3 -0.034 0.16 -9999 0 -0.67 48 48
PLCG1 -0.034 0.16 -9999 0 -0.68 48 48
PDGF/PDGFRA/alphaV Integrin -0.037 0.15 -9999 0 -0.65 48 48
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.034 0.16 -9999 0 -0.67 48 48
CAV3 -0.001 0.017 -9999 0 -0.28 3 3
CAV1 -0.17 0.34 -9999 0 -0.84 174 174
SHC/Grb2/SOS1 -0.029 0.12 -9999 0 -0.5 48 48
PDGF/PDGFRA/Shf -0.038 0.15 -9999 0 -0.66 48 48
FOS -0.36 0.57 -9999 0 -1.2 272 272
JUN -0.028 0.077 -9999 0 -0.72 9 9
oligodendrocyte development -0.037 0.15 -9999 0 -0.65 48 48
GRB2 0 0.01 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG -0.034 0.16 -9999 0 -0.67 48 48
PDGF/PDGFRA -0.056 0.2 -9999 0 -0.85 49 49
actin cytoskeleton reorganization -0.038 0.15 -9999 0 -0.65 49 49
SRF 0.016 0.022 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.032 0.13 -9999 0 -0.56 48 48
PDGF/PDGFRA/Crk/C3G -0.032 0.13 -9999 0 -0.56 48 48
JAK1 -0.022 0.16 -9999 0 -0.65 48 48
ELK1/SRF -0.025 0.12 -9999 0 -0.51 48 48
SHB -0.001 0.03 -9999 0 -0.84 1 1
SHF -0.001 0.03 -9999 0 -0.56 2 2
CSNK2A1 0.02 0.027 -9999 0 -10000 0 0
GO:0007205 -0.035 0.16 -9999 0 -0.69 48 48
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.029 0.12 -9999 0 -0.5 48 48
PDGF/PDGFRA/SHB -0.038 0.15 -9999 0 -0.65 49 49
PDGF/PDGFRA/Caveolin-1 -0.17 0.33 -9999 0 -0.75 190 190
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.035 0.15 -9999 0 -0.62 48 48
PIK3CA 0 0.01 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.037 0.15 -9999 0 -0.65 48 48
JAK-STAT cascade -0.022 0.15 -9999 0 -0.64 48 48
cell proliferation -0.038 0.15 -9999 0 -0.66 48 48
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.008 0.061 -9999 0 -0.49 13 13
RGS9BP -0.017 0.066 -9999 0 -0.28 51 51
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.027 -9999 0 -0.28 8 8
mol:Na + -0.021 0.052 -9999 0 -10000 0 0
mol:ADP 0.007 0.026 -9999 0 -10000 0 0
GNAT2 -0.001 0.017 -9999 0 -0.28 3 3
RGS9-1/Gbeta5/R9AP -0.071 0.18 -9999 0 -0.57 92 92
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.013 -9999 0 -10000 0 0
GRK7 -0.002 0.025 -9999 0 -10000 0 0
CNGB3 -0.011 0.053 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin -0.001 0.016 -9999 0 -0.19 6 6
mol:Ca2+ -0.099 0.076 -9999 0 -10000 0 0
Cone PDE6 -0.061 0.16 -9999 0 -0.49 92 92
Cone Metarhodopsin II -0.002 0.018 -9999 0 -10000 0 0
Na + (4 Units) -0.099 0.076 -9999 0 -10000 0 0
GNAT2/GDP -0.061 0.15 -9999 0 -0.49 92 92
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.005 0.013 -9999 0 -10000 0 0
Cone Transducin -0.009 0.064 -9999 0 -0.52 13 13
SLC24A2 -0.18 0.13 -9999 0 -0.28 546 546
GNB3/GNGT2 -0.01 0.08 -9999 0 -0.64 13 13
GNB3 -0.013 0.1 -9999 0 -0.76 14 14
GNAT2/GTP -0.001 0.011 -9999 0 -0.19 3 3
CNGA3 -0.029 0.085 -9999 0 -0.28 88 88
ARR3 -0.002 0.023 -9999 0 -0.28 6 6
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.021 0.052 -9999 0 -10000 0 0
mol:Pi -0.071 0.18 -9999 0 -0.57 92 92
Cone CNG Channel -0.016 0.039 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.18 0.13 -9999 0 -0.28 546 546
RGS9 -0.095 0.26 -9999 0 -0.84 92 92
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.001 0.029 -9999 0 -0.84 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.019 -9999 0 -0.28 4 4
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.6 0.38 -9999 0 -0.84 601 601
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.001 0.019 -9999 0 -0.28 4 4
TCEB1 -0.001 0.017 -9999 0 -0.28 3 3
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.007 -9999 0 -10000 0 0
COPS5 0 0.01 -9999 0 -0.28 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.009 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.044 0.1 -9999 0 -0.28 133 133
ARNT/IPAS -0.46 0.29 -9999 0 -0.64 601 601
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.001 0.005 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0.01 -9999 0 -0.28 1 1
RACK1/Elongin B/Elongin C -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.006 -9999 0 -10000 0 0
PHD1-3/OS9 -0.01 0.035 -9999 0 -0.51 1 1
HIF1A/RACK1/Elongin B/Elongin C 0 0.008 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -0.28 1 1
HIF1A/JAB1 -0.001 0.006 -9999 0 -10000 0 0
EGLN3 -0.023 0.076 -9999 0 -0.28 69 69
EGLN2 -0.001 0.017 -9999 0 -0.28 3 3
EGLN1 -0.001 0.029 -9999 0 -0.84 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0.004 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.016 0.036 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.13 0.19 -9999 0 -0.39 274 274
MAP3K8 -0.005 0.066 -9999 0 -0.75 6 6
FOS -0.041 0.14 -9999 0 -0.46 27 27
PRKCA -0.022 0.13 -9999 0 -0.78 24 24
PTPN7 -0.007 0.068 -9999 0 -10000 0 0
HRAS 0 0.01 -9999 0 -10000 0 0
PRKCB -0.018 0.11 -9999 0 -0.57 27 27
NRAS -0.001 0.014 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.011 0.073 -9999 0 -10000 0 0
MAP2K1 -0.015 0.14 -9999 0 -0.6 37 37
ELK1 -0.003 0.005 -9999 0 -10000 0 0
BRAF -0.033 0.12 -9999 0 -0.61 33 33
mol:GTP -0.002 0.003 -9999 0 -0.006 272 272
MAPK1 -0.011 0.073 -9999 0 -10000 0 0
RAF1 -0.033 0.12 -9999 0 -0.61 33 33
KRAS 0 0.01 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN -0.003 0.027 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.2 0.22 -9999 0 -0.44 373 373
Syndecan-3/Neurocan -0.007 0.025 -9999 0 -10000 0 0
POMC -0.022 0.12 -9999 0 -0.52 35 35
EGFR -0.29 0.4 -9999 0 -0.83 297 297
Syndecan-3/EGFR -0.17 0.23 -9999 0 -0.48 292 292
AGRP -0.002 0.025 -9999 0 -10000 0 0
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0.01 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.029 -9999 0 -0.84 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.017 0.067 -9999 0 -10000 0 0
long-term memory -0.001 0.018 -9999 0 -0.44 1 1
Syndecan-3/IL8 -0.017 0.071 -9999 0 -0.48 17 17
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.001 0.029 -9999 0 -0.84 1 1
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.004 0.033 -9999 0 -0.28 12 12
SRC 0 0.01 -9999 0 -10000 0 0
PTN -0.37 0.42 -9999 0 -0.84 373 373
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.19 0.21 -9999 0 -0.52 33 33
Syndecan-3/AgRP -0.001 0.01 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.014 -9999 0 -10000 0 0
Fyn/Cortactin -0.002 0.028 -9999 0 -0.64 1 1
SDC3 0 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.017 0.07 -9999 0 -0.47 17 17
IL8 -0.036 0.14 -9999 0 -0.84 17 17
Syndecan-3/Fyn/Cortactin -0.001 0.018 -9999 0 -0.46 1 1
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.018 0.093 -9999 0 -0.62 17 17
Gamma Secretase -0.001 0.017 -9999 0 -0.48 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.002 0.032 -10000 0 -0.47 4 4
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.001 0.003 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.077 0.24 -10000 0 -0.84 77 77
LRP6/FZD1 0 0.009 -10000 0 -10000 0 0
TLE1 -0.006 0.071 -10000 0 -0.84 6 6
AP1 -0.13 0.19 -10000 0 -0.39 276 276
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 0 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.046 -10000 0 -0.34 1 1
NICD/RBPSUH 0 0.003 -10000 0 -10000 0 0
WIF1 -0.44 0.42 -10000 0 -0.84 440 440
NOTCH1 0 0.003 -10000 0 -10000 0 0
PSENEN 0 0.01 -10000 0 -10000 0 0
KREMEN2 -0.13 0.14 -10000 0 -0.28 389 389
DKK1 -0.08 0.2 -10000 0 -0.84 43 43
beta catenin/beta TrCP1 -0.011 0.024 0.23 2 -10000 0 2
APH1B -0.001 0.029 -10000 0 -0.84 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.009 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.003 0.04 -10000 0 -0.35 6 6
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.27 0.39 -10000 0 -0.84 272 272
JUN -0.009 0.086 -10000 0 -0.84 9 9
MAP3K7 0 0.011 -10000 0 -0.28 1 1
CTNNB1 -0.004 0.037 0.23 4 -10000 0 4
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.074 0.11 -10000 0 -0.66 17 17
HNF1A -0.002 0.026 -10000 0 -0.28 7 7
CTBP1 0.001 0.003 -10000 0 -10000 0 0
MYC -0.036 0.23 -10000 0 -1.5 20 20
NKD1 -0.011 0.08 -10000 0 -0.43 22 22
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.043 0.14 -10000 0 -0.47 77 77
apoptosis -0.13 0.19 -10000 0 -0.39 276 276
Delta 1/NOTCHprecursor -0.002 0.032 -10000 0 -0.47 4 4
DLL1 -0.004 0.058 -10000 0 -0.84 4 4
PPARD -0.001 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.017 -10000 0 -0.48 1 1
APC 0.003 0.009 -10000 0 -10000 0 0
DVL1 -0.04 0.038 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.6 45 45
LRP6 -0.001 0.014 -10000 0 -10000 0 0
CSNK1A1 0 0 -10000 0 -10000 0 0
NLK 0.002 0.011 -10000 0 -10000 0 0
CCND1 -0.011 0.094 -10000 0 -1.5 3 3
WNT1 0 0.01 -10000 0 -0.28 1 1
Axin1/APC/beta catenin 0.009 0.037 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.78 19 19
NOTCH1 precursor/DVL1 -0.019 0.019 -10000 0 -10000 0 0
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 0 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.043 0.14 -10000 0 -0.47 77 77
PPP2R5D -0.016 0.042 0.36 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.27 0.25 -10000 0 -0.51 440 440
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.004 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.001 0.029 -9999 0 -0.84 1 1
LAT2 -0.064 0.14 -9999 0 -0.44 66 66
AP1 -0.17 0.23 -9999 0 -0.6 118 118
mol:PIP3 -0.031 0.21 -9999 0 -0.52 68 68
IKBKB 0 0.12 -9999 0 -0.33 35 35
AKT1 -0.084 0.18 -9999 0 -0.7 28 28
IKBKG 0.001 0.12 -9999 0 -0.33 35 35
MS4A2 -0.066 0.22 -9999 0 -0.84 65 65
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
MAP3K1 0.006 0.13 -9999 0 -0.45 27 27
mol:Ca2+ -0.015 0.16 -9999 0 -0.38 68 68
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.063 0.14 -9999 0 -0.44 66 66
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.072 0.18 -9999 0 -0.52 117 117
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.1 0.22 -9999 0 -0.51 170 170
PTPN13 -0.032 0.17 -9999 0 -0.56 45 45
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.006 0.15 -9999 0 -0.42 27 27
SYK 0.01 0.011 -9999 0 -10000 0 0
GRB2 0 0.01 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.09 0.19 -9999 0 -0.54 68 68
LAT -0.065 0.14 -9999 0 -0.59 29 29
PAK2 -0.003 0.14 -9999 0 -0.5 28 28
NFATC2 -0.079 0.21 -9999 0 -0.89 47 47
HRAS -0.013 0.15 -9999 0 -0.56 28 28
GAB2 -0.003 0.027 -9999 0 -0.28 8 8
PLA2G1B 0.028 0.019 -9999 0 -10000 0 0
Fc epsilon R1 -0.13 0.27 -9999 0 -0.63 170 170
Antigen/IgE/Fc epsilon R1 -0.12 0.25 -9999 0 -0.59 170 170
mol:GDP -0.019 0.15 -9999 0 -0.57 28 28
JUN -0.009 0.086 -9999 0 -0.84 9 9
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
FOS -0.27 0.39 -9999 0 -0.84 272 272
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.068 0.15 -9999 0 -0.46 66 66
CHUK 0.001 0.12 -9999 0 -0.33 35 35
KLRG1 -0.063 0.14 -9999 0 -0.57 28 28
VAV1 -0.064 0.14 -9999 0 -0.59 29 29
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.063 0.14 -9999 0 -0.58 28 28
negative regulation of mast cell degranulation -0.057 0.12 -9999 0 -0.52 28 28
BTK -0.061 0.14 -9999 0 -0.57 28 28
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.089 0.2 -9999 0 -0.47 138 138
GAB2/PI3K/SHP2 -0.093 0.2 -9999 0 -0.76 30 30
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.072 0.16 -9999 0 -0.73 28 28
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.23 -9999 0 -0.54 171 171
FCER1G 0.003 0.013 -9999 0 -0.28 1 1
FCER1A -0.12 0.31 -9999 0 -0.85 131 131
Antigen/IgE/Fc epsilon R1/Fyn -0.11 0.23 -9999 0 -0.55 170 170
MAPK3 0.026 0.019 -9999 0 -10000 0 0
MAPK1 0.026 0.019 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.013 0.05 -9999 0 -0.61 1 1
DUSP1 -0.12 0.29 -9999 0 -0.84 117 117
NF-kappa-B/RelA -0.028 0.055 -9999 0 -0.24 1 1
actin cytoskeleton reorganization -0.028 0.15 -9999 0 -0.56 27 27
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.054 0.12 -9999 0 -0.53 27 27
FER -0.066 0.14 -9999 0 -0.59 32 32
RELA 0 0 -9999 0 -10000 0 0
ITK -0.033 0.11 -9999 0 -0.62 25 25
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.017 0.16 -9999 0 -0.59 28 28
cytokine secretion -0.02 0.04 -9999 0 -10000 0 0
SPHK1 -0.065 0.14 -9999 0 -0.59 30 30
PTK2 -0.03 0.16 -9999 0 -0.59 27 27
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.094 0.2 -9999 0 -0.55 74 74
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.026 0.2 -9999 0 -0.5 68 68
MAP2K2 0.023 0.019 -9999 0 -10000 0 0
MAP2K1 0.023 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.059 0.13 -9999 0 -0.53 28 28
MAP2K4 0.015 0.038 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.12 0.25 -9999 0 -0.58 171 171
mol:Choline -0.1 0.21 -9999 0 -0.5 170 170
SHC/Grb2/SOS1 -0.057 0.13 -9999 0 -0.55 27 27
FYN -0.001 0.029 -9999 0 -0.84 1 1
DOK1 0 0 -9999 0 -10000 0 0
PXN -0.02 0.15 -9999 0 -0.55 26 26
HCLS1 -0.063 0.14 -9999 0 -0.58 28 28
PRKCB -0.017 0.16 -9999 0 -0.39 72 72
FCGR2B -0.003 0.051 -9999 0 -0.84 3 3
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.058 0.13 -9999 0 -0.53 28 28
LCP2 0 0.01 -9999 0 -0.28 1 1
PLA2G4A -0.11 0.21 -9999 0 -0.53 142 142
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.1 0.21 -9999 0 -0.5 170 170
IKK complex 0.018 0.095 -9999 0 -0.23 34 34
WIPF1 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.029 -10000 0 -0.84 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.03 0.07 0.64 1 -10000 0 1
CDKN1A -0.001 0.034 -10000 0 -0.98 1 1
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
FOXO3 -0.001 0.017 -10000 0 -0.34 2 2
FOXO1 -0.006 0.07 -10000 0 -0.84 6 6
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.61 0.37 -10000 0 -0.82 626 626
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.02 -10000 0 -10000 0 0
PPARGC1A -0.19 0.35 -10000 0 -0.81 196 196
FHL2 -0.006 0.066 -10000 0 -0.68 7 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.005 -10000 0 -10000 0 0
HIST2H4A -0.03 0.07 -10000 0 -0.65 1 1
SIRT1/FOXO3a 0 0.014 -10000 0 -0.26 2 2
SIRT1 0 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.02 -10000 0 -0.56 1 1
SIRT1/Histone H1b -0.002 0.009 -10000 0 -10000 0 0
apoptosis 0 0.005 -10000 0 -10000 0 0
SIRT1/PGC1A -0.13 0.24 -10000 0 -0.57 186 186
p53/SIRT1 0.001 0.016 0.43 1 -10000 0 1
SIRT1/FOXO4 0 0.006 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.007 0.059 -10000 0 -0.52 11 11
HIST1H1E -0.004 0.012 -10000 0 -10000 0 0
SIRT1/p300 0 0.005 -10000 0 -10000 0 0
muscle cell differentiation 0.001 0.015 -10000 0 -10000 0 0
TP53 0 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.005 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.47 0.28 -10000 0 -0.65 602 602
ACSS2 0 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.001 0.015 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.048 0.19 -10000 0 -0.83 49 49
HRAS 0 0.01 -10000 0 -10000 0 0
EGFR -0.29 0.4 -10000 0 -0.83 297 297
AKT 0.016 0.073 -10000 0 -0.58 11 11
FOXO3 -0.002 0.041 -10000 0 -0.84 2 2
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.006 0.07 -10000 0 -0.84 6 6
AKT3 -0.011 0.095 -10000 0 -0.84 11 11
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.32 -10000 0 -0.83 144 144
PIK3CA 0 0.01 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.014 -10000 0 -10000 0 0
PIK3CG -0.008 0.078 -10000 0 -0.84 7 7
PIK3R3 0 0.01 -10000 0 -0.28 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.029 -10000 0 -0.84 1 1
RAS -0.091 0.16 0.26 1 -0.37 157 158
ERBB2 -0.025 0.079 -10000 0 -0.28 75 75
proliferation/survival/translation -0.006 0.054 0.28 4 -10000 0 4
PI3K -0.08 0.16 -10000 0 -0.27 303 303
PIK3R1 0 0 -10000 0 -10000 0 0
KRAS 0 0.01 -10000 0 -10000 0 0
FOXO 0.027 0.024 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.84 2 2
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.01 0.058 -10000 0 -0.34 25 25
epithelial cell differentiation -0.014 0.08 -10000 0 -0.48 24 24
CYFIP2 -0.009 0.06 -10000 0 -0.32 24 24
ENAH 0.056 0.064 -10000 0 -10000 0 0
EGFR -0.29 0.4 -10000 0 -0.83 297 297
EPHA2 -0.006 0.07 -10000 0 -0.84 6 6
MYO6 -0.014 0.077 -10000 0 -0.45 25 25
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.034 -10000 0 -0.56 2 2
AQP5 -0.26 0.31 -10000 0 -0.62 346 346
CTNND1 0 0.01 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.074 -10000 0 -0.44 24 24
regulation of calcium-dependent cell-cell adhesion -0.037 0.13 -10000 0 -0.46 68 68
EGF -0.17 0.33 -10000 0 -0.84 167 167
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.041 0.15 -10000 0 -0.61 44 44
cortical microtubule organization -0.014 0.08 -10000 0 -0.48 24 24
GO:0000145 0.024 0.077 -10000 0 -0.42 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.081 -10000 0 -0.48 24 24
MLLT4 -0.003 0.05 -10000 0 -0.84 3 3
ARF6/GDP -0.014 0.069 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.044 -10000 0 -0.51 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.079 -10000 0 -0.42 24 24
PVRL2 -0.001 0.017 -10000 0 -0.28 3 3
ZYX -0.013 0.075 -10000 0 -0.45 24 24
ARF6/GTP -0.004 0.04 -10000 0 -0.47 6 6
CDH1 -0.024 0.14 -10000 0 -0.84 24 24
EGFR/EGFR/EGF/EGF -0.25 0.28 -10000 0 -0.5 423 423
RhoA/GDP -0.013 0.075 -10000 0 -0.45 24 24
actin cytoskeleton organization 0.031 0.08 -10000 0 -0.42 25 25
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.84 16 16
GIT1 -0.001 0.019 -10000 0 -10000 0 0
IGF1R -0.02 0.12 -10000 0 -0.84 16 16
IGF1 -0.18 0.35 -10000 0 -0.84 186 186
DIAPH1 -0.001 0.035 -10000 0 -0.68 2 2
Wnt receptor signaling pathway 0.014 0.08 0.48 24 -10000 0 24
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.07 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL -0.013 0.074 -10000 0 -0.44 25 25
EFNA1 0 0.01 -10000 0 -10000 0 0
LPP 0.031 0.082 -10000 0 -0.42 26 26
Ephrin A1/EPHA2 -0.016 0.08 -10000 0 -0.43 30 30
SEC6/SEC8 -0.013 0.07 -10000 0 -10000 0 0
MGAT3 -0.038 0.13 -10000 0 -0.47 68 68
HGF/MET -0.11 0.22 -10000 0 -0.49 195 195
HGF -0.05 0.2 -10000 0 -0.84 50 50
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.01 0.058 -10000 0 -0.34 25 25
actin cable formation 0.071 0.06 -10000 0 -10000 0 0
KIAA1543 0.031 0.089 -10000 0 -0.46 24 24
KIFC3 -0.014 0.079 -10000 0 -0.45 26 26
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.014 0.077 -10000 0 -0.45 25 25
NCK1/GIT1 -0.001 0.012 -10000 0 -10000 0 0
mol:GDP -0.014 0.08 -10000 0 -0.48 24 24
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.013 0.075 -10000 0 -0.45 24 24
PIP5K1C -0.013 0.075 -10000 0 -0.45 24 24
LIMA1 -0.001 0.029 -10000 0 -0.84 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.012 0.06 -10000 0 -10000 0 0
adherens junction assembly 0.047 0.085 -10000 0 -0.63 3 3
IGF-1R heterotetramer/IGF1 -0.12 0.21 -10000 0 -0.46 215 215
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.04 -10000 0 -0.64 3 3
MET -0.14 0.32 -10000 0 -0.83 144 144
PLEKHA7 -0.014 0.08 -10000 0 -0.47 24 24
mol:GTP -0.004 0.043 -10000 0 -0.5 6 6
establishment of epithelial cell apical/basal polarity -0.012 0.066 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.01 0.058 -10000 0 -0.34 25 25
regulation of cell-cell adhesion 0.031 0.08 -10000 0 -0.42 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.01 0.058 -10000 0 -0.34 25 25
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.005 0.027 -9999 0 -10000 0 0
adherens junction organization 0.033 0.064 -9999 0 -0.31 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP -0.14 0.19 -9999 0 -0.57 11 11
FMN1 0.027 0.083 -9999 0 -0.48 11 11
mol:IP3 -0.005 0.029 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.056 -9999 0 -0.33 25 25
CTNNB1 0.001 0.004 -9999 0 -10000 0 0
AKT1 -0.006 0.033 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.015 0.087 -9999 0 -0.52 24 24
CTNND1 0 0.009 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.058 -9999 0 -0.3 25 25
VASP 0.033 0.059 -9999 0 -0.3 25 25
ZYX 0.033 0.059 -9999 0 -10000 0 0
JUB 0.031 0.068 -9999 0 -0.32 29 29
EGFR(dimer) -0.16 0.22 -9999 0 -0.46 293 293
E-cadherin/beta catenin-gamma catenin -0.016 0.092 -9999 0 -0.54 25 25
mol:PI-3-4-5-P3 -0.006 0.036 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -10000 0 0
PI3K -0.006 0.037 -9999 0 -10000 0 0
FYN 0.044 0.036 -9999 0 -0.4 1 1
mol:Ca2+ -0.005 0.028 -9999 0 -10000 0 0
JUP -0.001 0.032 -9999 0 -0.46 3 3
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG -0.005 0.029 -9999 0 -10000 0 0
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
RhoA/GDP -0.14 0.19 -9999 0 -0.4 292 292
establishment of polarity of embryonic epithelium 0.033 0.058 -9999 0 -0.3 25 25
SRC 0 0.01 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.4 -9999 0 -0.83 297 297
CASR -0.005 0.027 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.025 -9999 0 -10000 0 0
AKT2 -0.006 0.033 -9999 0 -10000 0 0
actin cable formation 0.034 0.081 -9999 0 -0.46 11 11
apoptosis 0.006 0.032 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
mol:GDP -0.15 0.2 -9999 0 -0.43 292 292
PIP5K1A 0.033 0.059 -9999 0 -0.3 25 25
PLCG1 -0.005 0.029 -9999 0 -10000 0 0
Rac1/GTP -0.15 0.2 -9999 0 -0.42 293 293
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.075 0.18 0.68 61 -10000 0 61
KIRREL -0.061 0.22 -10000 0 -0.84 61 61
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.075 0.18 -10000 0 -0.68 61 61
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.054 0.14 -10000 0 -0.52 61 61
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.03 0.098 -10000 0 -0.38 61 61
FYN -0.05 0.13 -10000 0 -0.5 61 61
mol:Ca2+ -0.054 0.14 -10000 0 -0.52 61 61
mol:DAG -0.054 0.14 -10000 0 -0.52 61 61
NPHS2 -0.008 0.03 -10000 0 -0.29 1 1
mol:IP3 -0.054 0.14 -10000 0 -0.52 61 61
regulation of endocytosis -0.022 0.13 -10000 0 -0.46 61 61
Nephrin/NEPH1/podocin/Cholesterol -0.056 0.14 -10000 0 -0.53 61 61
establishment of cell polarity -0.075 0.18 -10000 0 -0.68 61 61
Nephrin/NEPH1/podocin/NCK1-2 -0.021 0.13 -10000 0 -0.48 61 61
Nephrin/NEPH1/beta Arrestin2 -0.022 0.13 -10000 0 -0.47 61 61
NPHS1 -0.049 0.1 -10000 0 -0.35 10 10
Nephrin/NEPH1/podocin -0.044 0.13 -10000 0 -0.5 61 61
TJP1 -0.001 0.029 -10000 0 -0.84 1 1
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.054 0.14 -10000 0 -0.52 61 61
CD2AP 0 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.054 0.14 -10000 0 -0.52 61 61
GRB2 0 0.01 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.056 0.14 -10000 0 -0.52 67 67
cytoskeleton organization -0.039 0.12 -10000 0 -0.48 61 61
Nephrin/NEPH1 -0.054 0.14 -10000 0 -0.51 61 61
Nephrin/NEPH1/ZO-1 -0.059 0.15 -10000 0 -0.57 61 61
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.5 191 191
MAPK9 0 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.02 -10000 0 -10000 0 0
GNB1/GNG2 -0.004 0.048 -10000 0 -0.57 6 6
GNB1 0 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
Gs family/GTP -0.12 0.22 -10000 0 -0.53 190 190
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 0.027 0.049 0.12 190 -10000 0 190
GNAL -0.19 0.35 -10000 0 -0.84 190 190
GNG2 -0.006 0.07 -10000 0 -0.84 6 6
CRH -0.003 0.029 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0 -10000 0 -10000 0 0
MAPK11 -0.001 0.023 -10000 0 -0.46 2 2
LPA4-mediated signaling events

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
ADCY4 -0.002 0.11 -9999 0 -0.57 31 31
ADCY5 -0.17 0.28 -9999 0 -0.57 267 267
ADCY6 0.019 0.02 -9999 0 -0.57 1 1
ADCY7 0.019 0.02 -9999 0 -0.57 1 1
ADCY1 -0.007 0.097 -9999 0 -0.57 19 19
ADCY2 -0.034 0.16 -9999 0 -0.57 67 67
ADCY3 0.019 0.021 -9999 0 -0.57 1 1
ADCY8 0.009 0.033 -9999 0 -0.57 1 1
PRKCE 0.01 0.023 -9999 0 -0.66 1 1
ADCY9 0.019 0.02 -9999 0 -0.57 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.033 0.11 -9999 0 -0.33 55 55
FAS signaling pathway (CD95)

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
SPTAN1 0.009 0.049 0.29 24 -10000 0 24
RFC1 0.009 0.049 0.29 24 -10000 0 24
PRKDC 0.008 0.05 0.29 24 -10000 0 24
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.024 0.036 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.016 0.059 0.26 9 -0.4 7 16
MAP2K4 -0.063 0.16 -10000 0 -0.4 25 25
mol:ceramide -0.058 0.093 -10000 0 -0.6 10 10
GSN 0 0.082 0.29 23 -0.53 13 36
FASLG/FAS/FADD/FAF1/Caspase 8 -0.03 0.063 0.23 9 -0.49 7 16
FAS -0.002 0.041 -10000 0 -0.85 2 2
BID 0 0.005 -10000 0 -10000 0 0
MAP3K1 -0.024 0.093 -10000 0 -0.29 9 9
MAP3K7 0 0.01 -10000 0 -0.28 1 1
RB1 0.008 0.052 0.29 24 -0.55 1 25
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.14 0.28 -10000 0 -0.63 187 187
ARHGDIB 0.008 0.049 0.29 24 -10000 0 24
FADD -0.006 0.041 -10000 0 -0.3 16 16
actin filament polymerization 0 0.082 0.53 13 -0.29 23 36
NFKB1 -0.08 0.1 -10000 0 -0.3 7 7
MAPK8 -0.12 0.24 -10000 0 -0.43 323 323
DFFA 0.009 0.049 0.29 24 -10000 0 24
DNA fragmentation during apoptosis 0.009 0.049 0.29 24 -10000 0 24
FAS/FADD/MET -0.1 0.22 -10000 0 -0.59 143 143
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.001 0.047 -10000 0 -10000 0 0
FAF1 0 0 -10000 0 -10000 0 0
PARP1 0.009 0.049 0.29 24 -10000 0 24
DFFB 0.009 0.049 0.29 24 -10000 0 24
CHUK -0.069 0.089 -10000 0 -10000 0 0
FASLG -0.017 0.09 -10000 0 -0.37 39 39
FAS/FADD -0.005 0.044 -10000 0 -0.73 2 2
HGF -0.05 0.2 -10000 0 -0.84 50 50
LMNA 0.008 0.044 0.26 24 -10000 0 24
CASP6 0.009 0.049 0.29 24 -10000 0 24
CASP10 -0.003 0.051 -10000 0 -0.85 3 3
CASP3 0.01 0.059 0.36 24 -10000 0 24
PTPN13 -0.022 0.13 -10000 0 -0.84 22 22
CASP8 0.002 0.013 -10000 0 -10000 0 0
IL6 -0.5 0.69 -10000 0 -1.4 323 323
MET -0.14 0.32 -10000 0 -0.83 144 144
ICAD/CAD 0.008 0.045 0.27 24 -10000 0 24
FASLG/FAS/FADD/FAF1/Caspase 10 -0.058 0.094 -10000 0 -0.61 10 10
activation of caspase activity by cytochrome c 0 0.005 -10000 0 -10000 0 0
PAK2 0.009 0.048 0.29 24 -10000 0 24
BCL2 -0.02 0.14 -10000 0 -0.84 24 24
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.003 0.037 -9999 0 -0.66 2 2
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
SPHK1 -0.025 0.061 -9999 0 -1.1 2 2
mol:S1P -0.031 0.062 -9999 0 -0.99 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.61 67 67
GNAO1 -0.033 0.14 -9999 0 -0.85 21 21
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.61 51 51
PLCG1 -0.089 0.22 -9999 0 -0.65 50 50
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
GNAI2 0 0.001 -9999 0 -10000 0 0
GNAI3 0 0.001 -9999 0 -10000 0 0
GNAI1 -0.043 0.19 -9999 0 -0.85 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.007 0.035 -9999 0 -0.58 2 2
S1P1/S1P -0.044 0.073 -9999 0 -0.69 4 4
negative regulation of cAMP metabolic process -0.096 0.22 -9999 0 -0.59 67 67
MAPK3 -0.16 0.31 -9999 0 -0.57 281 281
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.002 0.041 -9999 0 -0.84 2 2
PLCB2 -0.007 0.085 -9999 0 -0.57 5 5
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.06 -9999 0 -0.55 4 4
receptor internalization -0.042 0.068 -9999 0 -0.62 4 4
PTGS2 -0.33 0.56 -9999 0 -1.1 281 281
Rac1/GTP -0.037 0.06 -9999 0 -0.55 4 4
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.029 -9999 0 -0.28 9 9
negative regulation of T cell proliferation -0.096 0.22 -9999 0 -0.59 67 67
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
MAPK1 -0.16 0.31 -9999 0 -0.57 281 281
S1P1/S1P/PDGFB-D/PDGFRB -0.052 0.086 -9999 0 -0.72 5 5
ABCC1 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0 0.031 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.019 0.034 -9999 0 -0.66 1 1
positive regulation of JNK cascade -0.048 0.11 -9999 0 -0.44 29 29
Syndecan-4/ADAM12 -0.03 0.055 -9999 0 -0.57 2 2
CCL5 -0.011 0.063 -9999 0 -0.84 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.023 -9999 0 -10000 0 0
ADAM12 -0.023 0.084 -9999 0 -0.3 67 67
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.001 0.014 -9999 0 -0.28 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.056 0.044 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.071 0.14 -9999 0 -0.49 49 49
Syndecan-4/CXCL12/CXCR4 -0.05 0.12 -9999 0 -0.46 29 29
Syndecan-4/Laminin alpha3 -0.13 0.2 -9999 0 -0.51 150 150
MDK -0.01 0.051 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.028 0.069 -9999 0 -0.5 10 10
Syndecan-4/Midkine -0.021 0.04 -9999 0 -0.66 1 1
FZD7 -0.016 0.11 -9999 0 -0.84 16 16
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.52 83 83
THBS1 -0.001 0.029 -9999 0 -0.84 1 1
integrin-mediated signaling pathway -0.029 0.072 -9999 0 -0.51 11 11
positive regulation of MAPKKK cascade -0.048 0.11 -9999 0 -0.44 29 29
Syndecan-4/TACI -0.03 0.068 -9999 0 -0.53 6 6
CXCR4 -0.009 0.048 -9999 0 -0.28 26 26
cell adhesion -0.027 0.058 -9999 0 -0.36 21 21
Syndecan-4/Dynamin -0.019 0.033 -9999 0 -0.66 1 1
Syndecan-4/TSP1 -0.02 0.036 -9999 0 -0.66 1 1
Syndecan-4/GIPC -0.019 0.033 -9999 0 -0.66 1 1
Syndecan-4/RANTES -0.024 0.045 -9999 0 -0.6 2 2
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.095 0.26 -9999 0 -0.83 97 97
LAMA3 -0.2 0.36 -9999 0 -0.84 201 201
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.003 0.13 -9999 0 -0.75 23 23
Syndecan-4/alpha-Actinin -0.02 0.037 -9999 0 -0.57 2 2
TFPI -0.034 0.16 -9999 0 -0.84 34 34
F2 0.001 0.028 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.24 -9999 0 -0.56 125 125
ACTN1 -0.001 0.029 -9999 0 -0.84 1 1
TNC -0.019 0.12 -9999 0 -0.69 23 23
Syndecan-4/CXCL12 -0.053 0.12 -9999 0 -0.48 29 29
FGF6 -0.002 0.041 -9999 0 -0.84 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.062 0.22 -9999 0 -0.84 62 62
TNFRSF13B -0.024 0.12 -9999 0 -0.84 13 13
FGF2 -0.34 0.41 -9999 0 -0.84 337 337
FGFR1 -0.008 0.077 -9999 0 -0.71 9 9
Syndecan-4/PI-4-5-P2 -0.014 0.044 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.15 -9999 0 -0.29 370 370
cell migration -0.025 0.019 -9999 0 -10000 0 0
PRKCD 0.004 0.014 -9999 0 -10000 0 0
vasculogenesis -0.019 0.035 -9999 0 -0.63 1 1
SDC4 -0.014 0.047 -9999 0 -0.71 1 1
Syndecan-4/Tenascin C -0.03 0.076 -9999 0 -0.53 11 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.044 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.019 0.033 -9999 0 -0.66 1 1
MMP9 -0.11 0.14 -9999 0 -0.28 348 348
Rac1/GTP -0.028 0.059 -9999 0 -0.37 21 21
cytoskeleton organization -0.019 0.033 -9999 0 -0.63 1 1
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.038 0.094 -9999 0 -0.53 9 9
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.38 14 14
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 -0.001 0.014 -9999 0 -0.28 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.13 0.15 -9999 0 -0.26 472 472
YWHAZ -0.001 0.017 -9999 0 -0.28 3 3
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.021 0.023 -9999 0 -0.65 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0.007 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.001 0.017 -9999 0 -0.28 3 3
PRKCI 0 0.01 -9999 0 -0.28 1 1
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.029 -9999 0 -0.84 1 1
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.004 0.032 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 -0.14 0.16 -9999 0 -0.28 472 472
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
SFN -0.016 0.11 -9999 0 -0.62 21 21
LNPEP -0.004 0.058 -9999 0 -0.84 4 4
YWHAE 0 0 -9999 0 -10000 0 0
Nectin adhesion pathway

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
alphaV beta3 Integrin -0.012 0.083 -9999 0 -0.64 14 14
PTK2 -0.047 0.16 -9999 0 -0.56 68 68
positive regulation of JNK cascade -0.028 0.093 -9999 0 -0.34 68 68
CDC42/GDP 0.013 0.14 -9999 0 -0.46 68 68
Rac1/GDP 0.015 0.14 -9999 0 -0.45 68 68
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.034 0.12 -9999 0 -0.42 68 68
nectin-3/I-afadin -0.053 0.18 -9999 0 -0.66 68 68
RAPGEF1 0.008 0.16 -9999 0 -0.52 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.004 0.18 -9999 0 -0.61 68 68
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
TLN1 -0.024 0.089 -9999 0 -0.7 6 6
Rap1/GTP -0.03 0.099 -9999 0 -0.36 68 68
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.031 -9999 0 -0.52 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.053 0.18 -9999 0 -0.66 68 68
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP 0.006 0.17 -9999 0 -0.58 68 68
MLLT4 -0.003 0.05 -9999 0 -0.84 3 3
PIK3CA 0 0.01 -9999 0 -10000 0 0
PI3K -0.041 0.14 -9999 0 -0.49 70 70
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.002 0.038 -9999 0 -0.64 3 3
positive regulation of lamellipodium assembly -0.029 0.097 -9999 0 -0.36 68 68
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.067 0.23 -9999 0 -0.84 67 67
PVRL2 -0.001 0.017 -9999 0 -0.28 3 3
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
CLDN1 -0.04 0.16 -9999 0 -0.6 56 56
JAM-A/CLDN1 -0.064 0.18 -9999 0 -0.56 93 93
SRC -0.057 0.19 -9999 0 -0.69 68 68
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.038 -9999 0 -0.64 3 3
FARP2 0 0.17 -9999 0 -0.57 68 68
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.046 0.16 -9999 0 -0.57 68 68
nectin-1/I-afadin -0.002 0.038 -9999 0 -0.64 3 3
nectin-2/I-afadin -0.003 0.04 -9999 0 -0.64 3 3
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.046 0.16 -9999 0 -0.57 68 68
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.028 0.093 -9999 0 -0.34 68 68
alphaV/beta3 Integrin/Talin -0.027 0.11 -9999 0 -0.64 17 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.04 -9999 0 -0.64 3 3
nectin-2(dimer)/I-afadin/I-afadin -0.003 0.04 -9999 0 -0.64 3 3
PIP5K1C -0.026 0.096 -9999 0 -0.66 8 8
VAV2 -0.001 0.17 -9999 0 -0.58 68 68
RAP1/GDP -0.035 0.12 -9999 0 -0.42 68 68
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.047 0.16 -9999 0 -0.57 68 68
nectin-3(dimer)/I-afadin/I-afadin -0.053 0.18 -9999 0 -0.66 68 68
Rac1/GTP -0.036 0.12 -9999 0 -0.44 68 68
PTPRM -0.029 0.11 -9999 0 -0.34 71 71
E-cadherin/beta catenin/alpha catenin -0.015 0.08 -9999 0 -0.45 27 27
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.035 0.13 -10000 0 -0.61 32 32
FYN 0.017 0.18 -10000 0 -0.77 33 33
LAT/GRAP2/SLP76 -0.027 0.15 -10000 0 -0.64 37 37
IKBKB -0.001 0.014 -10000 0 -0.28 2 2
AKT1 0.032 0.12 -10000 0 -0.47 35 35
B2M 0.008 0.006 -10000 0 -10000 0 0
IKBKG -0.008 0.027 -10000 0 -0.14 8 8
MAP3K8 -0.005 0.065 -10000 0 -0.74 6 6
mol:Ca2+ -0.028 0.051 -10000 0 -0.12 175 175
integrin-mediated signaling pathway -0.002 0.028 -10000 0 -0.56 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.023 0.18 -10000 0 -0.7 38 38
TRPV6 -0.18 0.34 -10000 0 -0.85 175 175
CD28 -0.006 0.063 -10000 0 -0.84 4 4
SHC1 0.011 0.19 -10000 0 -0.79 34 34
receptor internalization -0.001 0.21 -10000 0 -0.7 51 51
PRF1 -0.002 0.23 -10000 0 -1.2 25 25
KRAS 0 0.01 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
COT/AKT1 0.033 0.1 -10000 0 -0.38 36 36
LAT 0.01 0.19 -10000 0 -0.77 38 38
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.52 50 50
CD3E -0.018 0.14 -10000 0 -0.85 21 21
CD3G -0.038 0.16 -10000 0 -0.53 61 61
RASGRP2 -0.006 0.04 -10000 0 -0.19 37 37
RASGRP1 0.038 0.12 -10000 0 -0.46 37 37
HLA-A 0.01 0.015 -10000 0 -10000 0 0
RASSF5 -0.002 0.042 -10000 0 -0.65 3 3
RAP1A/GTP/RAPL -0.002 0.028 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.042 -10000 0 -0.12 32 32
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.048 -10000 0 -0.24 23 23
PRKCA -0.011 0.087 -10000 0 -0.31 49 49
GRAP2 -0.014 0.1 -10000 0 -0.73 16 16
mol:IP3 0.024 0.15 0.28 149 -0.45 35 184
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.007 0.22 -10000 0 -0.96 31 31
ORAI1 0.085 0.16 0.39 175 -10000 0 175
CSK 0.009 0.19 -10000 0 -0.81 34 34
B7 family/CD28 -0.019 0.18 -10000 0 -0.74 39 39
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.22 -10000 0 -0.81 46 46
PTPN6 0.008 0.19 -10000 0 -0.71 43 43
VAV1 0.011 0.19 -10000 0 -0.69 44 44
Monovalent TCR/CD3 -0.029 0.21 -10000 0 -0.73 49 49
CBL 0 0 -10000 0 -10000 0 0
LCK 0.01 0.2 -10000 0 -0.71 45 45
PAG1 0.008 0.19 -10000 0 -0.7 44 44
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.002 0.22 -10000 0 -0.82 43 43
CD80 -0.08 0.12 -10000 0 -0.28 12 12
CD86 -0.001 0.019 -10000 0 -0.28 4 4
PDK1/CARD11/BCL10/MALT1 -0.017 0.058 -10000 0 -0.28 28 28
HRAS 0 0.01 -10000 0 -10000 0 0
GO:0035030 -0.045 0.13 -10000 0 -0.59 39 39
CD8A -0.004 0.08 -10000 0 -0.39 26 26
CD8B -0.026 0.16 -10000 0 -0.6 51 51
PTPRC -0.007 0.06 -10000 0 -0.39 15 15
PDK1/PKC theta 0.036 0.16 -10000 0 -0.6 38 38
CSK/PAG1 0.013 0.18 -10000 0 -0.79 33 33
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0 0.008 -10000 0 -10000 0 0
GRAP2/SLP76 -0.034 0.17 -10000 0 -0.74 39 39
STIM1 0.045 0.083 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.053 -10000 0 -0.18 24 24
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.005 0.23 -10000 0 -0.78 51 51
mol:DAG -0.005 0.1 -10000 0 -0.41 35 35
RAP1A/GDP 0.016 0.018 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.022 0.13 -10000 0 -0.62 30 30
cytotoxic T cell degranulation 0.001 0.21 -10000 0 -1.1 27 27
RAP1A/GTP -0.003 0.014 -10000 0 -0.068 28 28
mol:PI-3-4-5-P3 0.028 0.14 -10000 0 -0.55 38 38
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.017 0.18 0.29 144 -0.61 35 179
NRAS -0.001 0.014 -10000 0 -10000 0 0
ZAP70 -0.027 0.13 -10000 0 -0.51 44 44
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.024 0.14 -10000 0 -0.63 35 35
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.035 0.15 -10000 0 -0.62 43 43
CARD11 -0.007 0.056 -10000 0 -0.84 2 2
PRKCB -0.01 0.086 -10000 0 -0.32 42 42
PRKCE -0.005 0.07 -10000 0 -0.28 33 33
PRKCQ 0.026 0.18 -10000 0 -0.68 40 40
LCP2 0 0.01 -10000 0 -0.28 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.033 0.1 -10000 0 -0.4 35 35
IKK complex 0.042 0.044 -10000 0 -0.12 26 26
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.037 0.08 -10000 0 -0.3 30 30
PDPK1 0.035 0.12 -10000 0 -0.45 34 34
TCR/CD3/MHC I/CD8/Fyn -0.007 0.24 -10000 0 -0.96 41 41
Glypican 2 network

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
MDK -0.01 0.051 -9999 0 -10000 0 0
GPC2 -0.033 0.099 -9999 0 -0.3 94 94
GPC2/Midkine -0.027 0.077 -9999 0 -0.41 15 15
neuron projection morphogenesis -0.027 0.077 -9999 0 -0.41 15 15
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.017 -10000 0 -10000 0 0
AES 0.003 0.014 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0.009 -10000 0 -10000 0 0
SMAD4 0 0 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.78 19 19
TLE1 -0.003 0.072 -10000 0 -0.84 6 6
MACF1 0 0 -10000 0 -10000 0 0
CTNNB1 0.11 0.088 -10000 0 -10000 0 0
WIF1 -0.44 0.42 -10000 0 -0.84 440 440
beta catenin/RanBP3 0.013 0.075 0.38 30 -10000 0 30
KREMEN2 -0.13 0.14 -10000 0 -0.28 389 389
DKK1 -0.08 0.2 -10000 0 -0.84 43 43
beta catenin/beta TrCP1 0.1 0.087 -10000 0 -10000 0 0
FZD1 0 0 -10000 0 -10000 0 0
AXIN2 -0.007 0.18 -10000 0 -1.6 11 11
AXIN1 0 0.002 -10000 0 -10000 0 0
RAN 0 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.004 0.017 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.095 0.073 -10000 0 -0.53 3 3
Axin1/APC/GSK3 0.001 0.015 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.078 0.034 -10000 0 -10000 0 0
HNF1A 0.001 0.029 -10000 0 -0.28 6 6
CTBP1 0.004 0.015 -10000 0 -10000 0 0
MYC -0.021 0.24 -10000 0 -1.6 20 20
RANBP3 0 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.074 0.11 -10000 0 -0.66 17 17
NKD1 -0.011 0.08 -10000 0 -0.43 22 22
TCF4 -0.001 0.067 -10000 0 -0.84 5 5
TCF3 0.004 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0 0 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.013 0.094 0.44 34 -0.44 1 35
LEF1 -0.037 0.1 -10000 0 -10000 0 0
DVL1 0.073 0.066 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.1 0.082 -10000 0 -0.58 2 2
DKK1/LRP6/Kremen 2 -0.11 0.15 -10000 0 -0.6 45 45
LRP6 -0.001 0.014 -10000 0 -10000 0 0
CSNK1A1 0.004 0.017 -10000 0 -10000 0 0
NLK 0 0.01 -10000 0 -10000 0 0
CCND1 0.002 0.11 -10000 0 -1.6 3 3
WNT1 0 0.01 -10000 0 -0.28 1 1
GSK3A 0 0 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.045 0.048 0.35 7 -10000 0 7
APC 0 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.15 0.14 0.28 440 -10000 0 440
CREBBP 0.004 0.015 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.002 0.007 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.014 0.1 0.44 17 -10000 0 17
IL27/IL27R/JAK1 -0.046 0.16 -10000 0 -0.63 29 29
TBX21 -0.024 0.2 -10000 0 -0.63 54 54
IL12B -0.052 0.11 -10000 0 -0.28 71 71
IL12A -0.031 0.16 -10000 0 -0.66 48 48
IL6ST -0.051 0.21 -10000 0 -0.84 56 56
IL27RA/JAK1 -0.006 0.068 -10000 0 -1.4 2 2
IL27 -0.023 0.084 -10000 0 -0.28 82 82
TYK2 0.008 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.14 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.014 0.1 0.44 17 -10000 0 17
T cell proliferation during immune response 0.014 0.1 0.44 17 -10000 0 17
MAPKKK cascade -0.014 0.1 -10000 0 -0.44 17 17
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.006 0.041 -10000 0 -10000 0 0
IL12RB1 -0.009 0.056 -10000 0 -0.3 26 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.039 0.22 -10000 0 -0.63 66 66
IL27/IL27R/JAK2/TYK2 -0.017 0.1 -10000 0 -0.44 17 17
positive regulation of T cell mediated cytotoxicity -0.014 0.1 -10000 0 -0.44 17 17
STAT1 (dimer) -0.064 0.2 0.47 19 -0.73 31 50
JAK2 0.004 0.006 -10000 0 -10000 0 0
JAK1 0 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.028 0.089 -10000 0 -0.45 11 11
T cell proliferation -0.19 0.25 -10000 0 -0.49 331 331
IL12/IL12R/TYK2/JAK2 0.013 0.071 -10000 0 -10000 0 0
IL17A -0.14 0.18 -10000 0 -10000 0 0
mast cell activation 0.014 0.1 0.44 17 -10000 0 17
IFNG 0.003 0.021 -10000 0 -0.078 4 4
T cell differentiation -0.003 0.005 -10000 0 -0.02 11 11
STAT3 (dimer) -0.028 0.089 -10000 0 -0.49 7 7
STAT5A (dimer) -0.032 0.1 -10000 0 -0.55 12 12
STAT4 (dimer) -0.047 0.13 -10000 0 -0.53 41 41
STAT4 -0.033 0.16 -10000 0 -0.82 34 34
T cell activation -0.008 0.008 0.13 2 -10000 0 2
IL27R/JAK2/TYK2 -0.036 0.14 -10000 0 -0.57 34 34
GATA3 -0.044 0.28 -10000 0 -1.5 30 30
IL18 0.006 0.032 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.027 0.087 -10000 0 -0.48 7 7
IL27/EBI3 -0.022 0.074 -10000 0 -0.57 7 7
IL27RA 0.001 0.074 -10000 0 -1.5 2 2
IL6 -0.32 0.41 -10000 0 -0.84 323 323
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.002 0.028 0.48 2 -10000 0 2
IL1B 0.003 0.069 -10000 0 -0.66 9 9
EBI3 -0.003 0.07 -10000 0 -0.54 11 11
TNF -0.001 0.077 -10000 0 -0.66 10 10
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.002 0.13 -10000 0 -0.41 42 42
TBX21 -0.01 0.35 -10000 0 -1.2 46 46
B2M 0.01 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.007 0.062 -10000 0 -0.31 26 26
GADD45B 0.038 0.21 -10000 0 -0.79 25 25
IL12RB2 -0.058 0.2 -10000 0 -0.48 115 115
GADD45G 0.034 0.21 -10000 0 -0.79 25 25
natural killer cell activation 0.007 0.017 -10000 0 -10000 0 0
RELB -0.002 0.021 -10000 0 -0.28 5 5
RELA 0 0 -10000 0 -10000 0 0
IL18 0.007 0.047 -10000 0 -0.27 22 22
IL2RA -0.028 0.11 -10000 0 -0.36 66 66
IFNG -0.041 0.099 -10000 0 -0.28 124 124
STAT3 (dimer) 0.032 0.21 -10000 0 -0.63 40 40
HLA-DRB5 -0.022 0.093 -10000 0 -0.42 23 23
FASLG 0.015 0.26 -10000 0 -1 27 27
NF kappa B2 p52/RelB -0.074 0.18 -10000 0 -0.69 48 48
CD4 0 0 -10000 0 -10000 0 0
SOCS1 -0.004 0.039 -10000 0 -0.34 9 9
EntrezGene:6955 -0.007 0.014 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.52 50 50
CD3E -0.022 0.14 -10000 0 -0.8 23 23
CD3G -0.031 0.16 -10000 0 -0.54 61 61
IL12Rbeta2/JAK2 -0.027 0.16 -10000 0 -0.66 40 40
CCL3 0.019 0.25 -10000 0 -0.9 33 33
CCL4 0.022 0.24 -10000 0 -0.94 24 24
HLA-A 0.009 0.015 -10000 0 -10000 0 0
IL18/IL18R 0.024 0.15 -10000 0 -0.59 42 42
NOS2 0.025 0.24 -10000 0 -0.97 24 24
IL12/IL12R/TYK2/JAK2/SPHK2 -0.001 0.13 -10000 0 -0.36 66 66
IL1R1 0.013 0.27 -10000 0 -1.1 31 31
IL4 -0.005 0.018 -10000 0 -10000 0 0
JAK2 0.017 0.015 -10000 0 -10000 0 0
EntrezGene:6957 -0.006 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.031 0.26 -10000 0 -1.1 36 36
RAB7A 0.054 0.19 -10000 0 -0.68 22 22
lysosomal transport 0.055 0.18 -10000 0 -0.64 22 22
FOS -0.39 0.69 -10000 0 -1.3 283 283
STAT4 (dimer) 0.028 0.26 -10000 0 -0.88 38 38
STAT5A (dimer) -0.077 0.2 -10000 0 -0.68 55 55
GZMA 0.01 0.27 -10000 0 -1.1 25 25
GZMB -0.002 0.3 -10000 0 -1.1 35 35
HLX 0 0.01 -10000 0 -0.28 1 1
LCK 0.013 0.27 -10000 0 -0.77 58 58
TCR/CD3/MHC II/CD4 -0.068 0.2 -10000 0 -0.59 61 61
IL2/IL2R -0.028 0.098 -10000 0 -0.47 31 31
MAPK14 0.044 0.22 -10000 0 -0.76 29 29
CCR5 0.032 0.22 -10000 0 -0.82 25 25
IL1B 0.007 0.092 -10000 0 -0.74 11 11
STAT6 0.027 0.085 -10000 0 -0.24 12 12
STAT4 -0.033 0.16 -10000 0 -0.82 34 34
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.006 0.04 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B -0.038 0.11 -10000 0 -0.29 74 74
CD8A -0.002 0.08 -10000 0 -0.39 26 26
CD8B -0.026 0.16 -10000 0 -0.6 51 51
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.002 0.13 0.41 42 -10000 0 42
IL2RB -0.011 0.055 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.24 -10000 0 -0.78 38 38
IL2RG -0.016 0.083 -10000 0 -0.84 5 5
IL12 -0.049 0.17 -10000 0 -0.63 52 52
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
CD247 -0.014 0.13 -10000 0 -0.62 30 30
IL2 -0.003 0.029 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.036 0.2 -10000 0 -0.78 54 54
IL12/IL12R/TYK2/JAK2 0.017 0.27 -10000 0 -0.77 54 54
MAP2K3 0.04 0.22 -10000 0 -0.79 27 27
RIPK2 -0.001 0.019 -10000 0 -0.28 4 4
MAP2K6 0.036 0.22 -10000 0 -0.75 33 33
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.032 -10000 0 -0.57 2 2
IL18RAP -0.02 0.17 -10000 0 -0.81 35 35
IL12Rbeta1/TYK2 0.016 0.05 -10000 0 -0.7 1 1
EOMES -0.023 0.18 -10000 0 -1.5 12 12
STAT1 (dimer) 0.036 0.21 -10000 0 -0.63 37 37
T cell proliferation 0.038 0.2 -10000 0 -0.62 39 39
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.004 0.097 -10000 0 -0.84 11 11
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.059 0.17 -10000 0 -0.73 35 35
ATF2 0.052 0.2 -10000 0 -0.72 27 27
Coregulation of Androgen receptor activity

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
NRIP1 -0.008 0.034 -10000 0 -0.84 1 1
SVIL -0.009 0.052 -10000 0 -0.84 3 3
ZNF318 0.022 0.058 -10000 0 -10000 0 0
JMJD2C -0.004 0.043 -10000 0 -0.13 81 81
T-DHT/AR/Ubc9 -0.075 0.18 -10000 0 -0.58 92 92
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.002 0.007 -10000 0 -10000 0 0
PELP1 0.005 0.012 -10000 0 -10000 0 0
CTNNB1 -0.005 0.012 -10000 0 -10000 0 0
AKT1 0.007 0.018 -10000 0 -10000 0 0
PTK2B -0.004 0.01 -10000 0 -10000 0 0
MED1 0 0.049 -10000 0 -10000 0 0
MAK 0.011 0.1 0.22 1 -0.54 16 17
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.017 -10000 0 -10000 0 0
GSN -0.02 0.1 -10000 0 -0.84 13 13
NCOA2 -0.007 0.076 -10000 0 -0.84 7 7
NCOA6 -0.002 0.021 -10000 0 -10000 0 0
DNA-PK 0.021 0.059 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 -0.005 0.012 -10000 0 -10000 0 0
cell proliferation -0.006 0.1 -10000 0 -0.86 8 8
XRCC5 0.006 0.016 -10000 0 -10000 0 0
UBE3A -0.006 0.031 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.09 0.21 -10000 0 -0.62 106 106
FHL2 -0.018 0.12 -10000 0 -1.2 5 5
RANBP9 -0.001 0.018 -10000 0 -10000 0 0
JMJD1A -0.012 0.057 -10000 0 -0.15 121 121
CDK6 -0.005 0.072 -10000 0 -0.84 6 6
TGFB1I1 -0.009 0.052 -10000 0 -0.84 3 3
T-DHT/AR/CyclinD1 -0.087 0.19 -10000 0 -0.58 98 98
XRCC6 0.006 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.063 0.21 -10000 0 -0.56 107 107
CTDSP1 0 0 -10000 0 -10000 0 0
CTDSP2 0.015 0.039 -10000 0 -10000 0 0
BRCA1 -0.007 0.023 -10000 0 -0.32 2 2
TCF4 0.006 0.071 -10000 0 -0.82 5 5
CDKN2A -0.035 0.1 -10000 0 -0.28 115 115
SRF 0.023 0.02 -10000 0 -10000 0 0
NKX3-1 -0.083 0.2 -10000 0 -1.3 17 17
KLK3 -0.18 0.52 -10000 0 -1.6 102 102
TMF1 0 0 -10000 0 -10000 0 0
HNRNPA1 0.008 0.022 -10000 0 -10000 0 0
AOF2 -0.008 0.024 -10000 0 -0.072 102 102
APPL1 0.034 0.033 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.067 0.19 -10000 0 -0.57 93 93
AR -0.09 0.27 -10000 0 -0.84 93 93
UBA3 0 0 -10000 0 -10000 0 0
PATZ1 0.008 0.022 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
PRKDC 0.004 0.025 -10000 0 -0.28 4 4
PA2G4 0.011 0.028 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.063 0.17 -10000 0 -0.53 93 93
RPS6KA3 -0.009 0.045 -10000 0 -0.84 2 2
T-DHT/AR/ARA70 -0.079 0.18 -10000 0 -0.58 92 92
LATS2 0.009 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.058 0.18 0.19 1 -0.53 92 93
Cyclin D3/CDK11 p58 0 0 -10000 0 -10000 0 0
VAV3 -0.013 0.064 -10000 0 -0.37 19 19
KLK2 -0.13 0.34 -10000 0 -1.2 70 70
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.075 0.17 -10000 0 -0.54 97 97
TMPRSS2 -0.18 0.4 -10000 0 -1.2 112 112
CCND1 -0.016 0.074 -10000 0 -0.33 36 36
PIAS1 -0.006 0.031 -10000 0 -10000 0 0
mol:T-DHT -0.01 0.035 -10000 0 -0.08 157 157
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.012 0.05 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.076 0.19 -10000 0 -0.58 98 98
CMTM2 0.003 0.013 -10000 0 -10000 0 0
SNURF -0.023 0.14 -10000 0 -0.84 23 23
ZMIZ1 0.002 0.032 -10000 0 -0.35 1 1
CCND3 0.002 0.005 -10000 0 -10000 0 0
TGIF1 0.008 0.022 -10000 0 -10000 0 0
FKBP4 -0.004 0.031 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.028 0.026 -9999 0 -10000 0 0
BUB1B -0.039 0.046 -9999 0 -10000 0 0
PLK1 -0.007 0.021 -9999 0 -10000 0 0
PLK1S1 0 0.012 -9999 0 -10000 0 0
KIF2A 0.003 0.019 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.007 0.021 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.16 0.11 -9999 0 -0.27 335 335
WEE1 -0.002 0.021 -9999 0 -10000 0 0
cytokinesis -0.045 0.042 -9999 0 -0.27 2 2
PP2A-alpha B56 0.036 0.022 -9999 0 -10000 0 0
AURKA 0.003 0.011 -9999 0 -10000 0 0
PICH/PLK1 -0.078 0.092 -9999 0 -0.32 10 10
CENPE -0.056 0.083 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.019 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.002 0.013 -9999 0 -10000 0 0
PAK1 -0.006 0.04 -9999 0 -0.27 18 18
SPC24 -0.17 0.14 -9999 0 -0.28 518 518
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.003 0.014 -9999 0 -10000 0 0
GORASP1 0 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.004 0.012 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.002 0.002 -9999 0 -10000 0 0
STAG2 0 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.007 0.021 -9999 0 -10000 0 0
ODF2 0 0 -9999 0 -10000 0 0
BUB1 0.031 0.019 -9999 0 -10000 0 0
TPT1 0 0.012 -9999 0 -10000 0 0
CDC25C -0.001 0.012 -9999 0 -10000 0 0
CDC25B -0.003 0.038 -9999 0 -10000 0 0
SGOL1 -0.028 0.026 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.022 0.041 -9999 0 -10000 0 0
CDC14B -0.01 0.12 -9999 0 -0.66 25 25
CDC20 -0.16 0.14 -9999 0 -10000 0 0
PLK1/PBIP1 -0.031 0.054 -9999 0 -10000 0 0
mitosis -0.007 0.007 -9999 0 -0.022 2 2
FBXO5 0 0.021 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.18 0.13 -9999 0 -10000 0 0
metaphase plate congression -0.002 0.014 -9999 0 -10000 0 0
ERCC6L -0.068 0.084 -9999 0 -10000 0 0
NLP/gamma Tubulin 0 0.012 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0 0.012 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.094 -9999 0 -0.27 237 237
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.002 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.002 0.022 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.05 -9999 0 -0.3 20 20
microtubule-based process -0.12 0.059 -9999 0 -0.18 7 7
Golgi organization -0.007 0.021 -9999 0 -10000 0 0
Cohesin/SA2 -0.008 0.009 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.11 -9999 0 -0.28 676 676
APC/C/CDC20 -0.085 0.075 -9999 0 -10000 0 0
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.03 0.053 -9999 0 -10000 0 0
PRC1 -0.078 0.12 -9999 0 -0.28 237 237
ECT2 -0.004 0.039 -9999 0 -0.2 2 2
C13orf34 0 0.02 -9999 0 -10000 0 0
NUDC -0.002 0.014 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.039 0.046 -9999 0 -10000 0 0
spindle assembly -0.003 0.018 -9999 0 -10000 0 0
spindle stabilization 0 0.012 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.097 -9999 0 -0.57 25 25
MKLP2/PLK1 -0.12 0.059 -9999 0 -0.18 7 7
CCNB1 -0.065 0.12 -9999 0 -0.28 195 195
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 0.005 0.031 -9999 0 -0.55 2 2
TUBG1 0 0.012 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.022 0.039 -9999 0 -10000 0 0
MLF1IP -0.032 0.077 -9999 0 -10000 0 0
INCENP 0 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.02 0.006 -9999 0 -10000 0 0
SMARCC1 0.004 0.022 -9999 0 -0.59 1 1
REL 0.003 0.031 -9999 0 -0.84 1 1
HDAC7 0.012 0.12 -9999 0 -0.64 6 6
JUN -0.009 0.086 -9999 0 -0.84 9 9
EP300 0 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0.001 0.004 -9999 0 -10000 0 0
MAPK14 0.005 0.098 -9999 0 -0.65 18 18
FOXO1 -0.006 0.07 -9999 0 -0.84 6 6
T-DHT/AR -0.002 0.13 -9999 0 -0.57 11 11
MAP2K6 -0.018 0.12 -9999 0 -0.81 19 19
BRM/BAF57 -0.001 0.009 -9999 0 -10000 0 0
MAP2K4 0 0.029 -9999 0 -0.84 1 1
SMARCA2 0 0 -9999 0 -10000 0 0
PDE9A -0.093 0.3 -9999 0 -1.1 64 64
NCOA2 -0.007 0.076 -9999 0 -0.84 7 7
CEBPA -0.006 0.076 -9999 0 -0.84 7 7
EHMT2 0 0 -9999 0 -10000 0 0
cell proliferation 0.021 0.14 -9999 0 -0.53 12 12
NR0B1 -0.01 0.052 -9999 0 -10000 0 0
EGR1 -0.29 0.4 -9999 0 -0.84 287 287
RXRs/9cRA -0.13 0.22 -9999 0 -0.52 204 204
AR/RACK1/Src -0.002 0.1 -9999 0 -0.54 12 12
AR/GR -0.043 0.11 -9999 0 -0.43 30 30
GNB2L1 0.001 0.003 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.019 0.027 -9999 0 -0.65 1 1
T-DHT/AR/TIF2/CARM1 -0.029 0.096 -9999 0 -0.51 21 21
SRC 0.024 0.088 -9999 0 -0.51 18 18
NR3C1 -0.007 0.076 -9999 0 -0.84 7 7
KLK3 -0.21 0.42 -9999 0 -1.2 119 119
APPBP2 -0.001 0.013 -9999 0 -0.27 2 2
TRIM24 0 0.01 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.024 0.088 -9999 0 -0.52 18 18
TMPRSS2 -0.17 0.43 -9999 0 -1.2 112 112
RXRG -0.2 0.36 -9999 0 -0.84 204 204
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0 0 -9999 0 -10000 0 0
NR2C2 0 0 -9999 0 -10000 0 0
KLK2 -0.035 0.25 -9999 0 -0.81 72 72
AR -0.02 0.13 -9999 0 -0.34 101 101
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -0.28 1 1
MDM2 0.004 0.024 -9999 0 -0.28 4 4
SRY 0.003 0.01 -9999 0 -10000 0 0
GATA2 -0.023 0.13 -9999 0 -0.84 19 19
MYST2 0 0.01 -9999 0 -0.28 1 1
HOXB13 -0.13 0.14 -9999 0 -0.28 384 384
T-DHT/AR/RACK1/Src -0.024 0.086 -9999 0 -0.54 12 12
positive regulation of transcription -0.023 0.13 -9999 0 -0.84 19 19
DNAJA1 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.013 -9999 0 -10000 0 0
NCOA1 0.011 0.031 -9999 0 -0.87 1 1
SPDEF -0.047 0.2 -9999 0 -0.81 50 50
T-DHT/AR/TIF2 0.026 0.067 -9999 0 -0.38 3 3
T-DHT/AR/Hsp90 -0.03 0.084 -9999 0 -0.52 18 18
GSK3B 0.001 0.004 -9999 0 -10000 0 0
NR2C1 0.002 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.017 0.092 -9999 0 -0.55 18 18
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.005 0.013 -9999 0 -10000 0 0
POU2F1 0.02 0.027 -9999 0 -0.41 1 1
T-DHT/AR/DAX-1 -0.031 0.089 -9999 0 -0.53 18 18
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.014 -9999 0 -0.28 2 2
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.018 0.12 -9999 0 -0.84 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.029 -9999 0 -0.84 1 1
RAC1-CDC42/GTP/PAK family -0.13 0.14 -9999 0 -0.28 377 377
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.029 -9999 0 -0.84 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.001 0.029 -9999 0 -0.84 1 1
MAP3K12 0 0 -9999 0 -10000 0 0
FGR 0 0.01 -9999 0 -0.28 1 1
p38 alpha/TAB1 -0.007 0.035 -9999 0 -0.38 2 2
PRKG1 -0.032 0.16 -9999 0 -0.84 32 32
DUSP8 -0.003 0.051 -9999 0 -0.7 4 4
PGK/cGMP/p38 alpha -0.022 0.088 -9999 0 -0.43 34 34
apoptosis -0.007 0.033 -9999 0 -0.37 2 2
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.29 -9999 0 -0.84 117 117
PAK1 -0.006 0.04 -9999 0 -0.28 18 18
SRC 0 0.01 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.004 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.017 0.07 -9999 0 -0.36 14 14
BLK -0.036 0.1 -9999 0 -0.3 102 102
HCK -0.004 0.033 -9999 0 -10000 0 0
MAP2K3 0 0.01 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.014 -9999 0 -10000 0 0
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.028 0.049 -9999 0 -0.41 2 2
positive regulation of innate immune response 0.023 0.075 -9999 0 -0.38 14 14
LCK -0.019 0.1 -9999 0 -0.46 34 34
p38alpha-beta/MKP7 -0.012 0.056 -9999 0 -0.43 4 4
p38alpha-beta/MKP5 -0.012 0.056 -9999 0 -0.43 4 4
PGK/cGMP -0.025 0.12 -9999 0 -0.65 32 32
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.066 0.15 -9999 0 -0.4 119 119
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.38 0.42 -9999 0 -0.84 377 377
BCR signaling pathway

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
JUN 0.004 0.12 -10000 0 -0.46 30 30
IKBKB 0.016 0.055 -10000 0 -0.25 3 3
AKT1 0.006 0.082 0.25 2 -0.28 15 17
IKBKG 0.018 0.057 -10000 0 -0.24 16 16
CALM1 -0.012 0.098 -10000 0 -0.46 26 26
PIK3CA 0 0.01 -10000 0 -10000 0 0
MAP3K1 -0.009 0.16 -10000 0 -0.67 28 28
MAP3K7 0 0.01 -10000 0 -0.28 1 1
mol:Ca2+ -0.021 0.1 -10000 0 -0.5 26 26
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.049 0.12 -10000 0 -0.28 55 55
LYN 0 0 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.082 0.22 -10000 0 -0.7 87 87
CD22 -0.063 0.19 -10000 0 -0.57 80 80
CAMK2G -0.004 0.092 -10000 0 -0.42 26 26
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.05 0.15 -10000 0 -0.82 14 14
GO:0007205 -0.022 0.1 -10000 0 -0.5 26 26
SYK 0 0.01 -10000 0 -10000 0 0
ELK1 -0.013 0.1 -10000 0 -0.47 26 26
NFATC1 -0.016 0.13 -10000 0 -0.56 28 28
B-cell antigen/BCR complex -0.082 0.22 -10000 0 -0.7 87 87
PAG1/CSK -0.001 0.013 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 -10000 0 -10000 0 0
HRAS -0.01 0.11 -10000 0 -0.49 26 26
NFKBIA 0.015 0.02 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.019 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.061 0.17 -10000 0 -0.56 80 80
mol:GDP -0.022 0.097 -10000 0 -0.47 26 26
PTEN -0.002 0.041 -10000 0 -0.84 2 2
CD79B -0.029 0.15 -10000 0 -0.84 26 26
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.01 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.024 0.16 -10000 0 -0.48 78 78
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.031 0.1 -10000 0 -0.51 26 26
CSK 0 0 -10000 0 -10000 0 0
FOS -0.15 0.24 -10000 0 -0.47 289 289
CHUK 0.018 0.057 -10000 0 -0.24 16 16
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.025 0.083 -10000 0 -0.48 16 16
PTPN6 -0.058 0.17 -10000 0 -0.77 32 32
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.13 1 1
VAV2 -0.07 0.18 -10000 0 -0.83 28 28
ubiquitin-dependent protein catabolic process 0.019 0.02 -10000 0 -10000 0 0
BTK -0.004 0.006 -10000 0 -10000 0 0
CD19 -0.08 0.18 -10000 0 -0.57 78 78
MAP4K1 -0.01 0.062 -10000 0 -0.32 27 27
CD72 -0.006 0.048 -10000 0 -0.84 1 1
PAG1 -0.002 0.021 -10000 0 -0.28 5 5
MAPK14 0.002 0.13 -10000 0 -0.55 27 27
SH3BP5 0 0 -10000 0 -10000 0 0
PIK3AP1 -0.013 0.11 -10000 0 -0.55 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.044 0.14 -10000 0 -0.5 67 67
RAF1 -0.002 0.1 -10000 0 -0.45 26 26
RasGAP/p62DOK/SHIP -0.058 0.17 -10000 0 -0.9 15 15
CD79A -0.084 0.23 -10000 0 -0.84 66 66
re-entry into mitotic cell cycle -0.048 0.12 -10000 0 -0.28 54 54
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.087 -10000 0 -0.44 14 14
MAPK1 0.015 0.087 -10000 0 -0.44 14 14
CD72/SHP1 -0.055 0.16 -10000 0 -0.7 34 34
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.13 -10000 0 -0.55 27 27
actin cytoskeleton organization -0.025 0.16 -10000 0 -0.67 28 28
NF-kappa-B/RelA 0.043 0.032 -10000 0 -10000 0 0
Calcineurin -0.022 0.076 -10000 0 -0.46 14 14
PI3K -0.055 0.13 -10000 0 -0.54 31 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.034 0.12 -10000 0 -0.59 26 26
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.055 0.18 -10000 0 -0.85 30 30
DAPP1 -0.054 0.21 -10000 0 -1 29 29
cytokine secretion -0.014 0.12 -10000 0 -0.52 28 28
mol:DAG -0.031 0.1 -10000 0 -0.51 26 26
PLCG2 -0.001 0.03 -10000 0 -0.56 2 2
MAP2K1 0.007 0.096 -10000 0 -0.5 14 14
B-cell antigen/BCR complex/FcgammaRIIB -0.073 0.2 -10000 0 -0.65 80 80
mol:PI-3-4-5-P3 -0.04 0.093 0.35 2 -0.38 27 29
ETS1 0.004 0.089 -10000 0 -0.48 15 15
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.06 0.17 -10000 0 -0.56 78 78
B-cell antigen/BCR complex/LYN -0.061 0.2 -10000 0 -0.6 78 78
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 -0.028 0.17 -10000 0 -0.73 28 28
B-cell antigen/BCR complex/LYN/SYK -0.059 0.19 -10000 0 -0.58 78 78
CARD11 -0.017 0.11 -10000 0 -0.49 27 27
FCGR2B -0.003 0.051 -10000 0 -0.84 3 3
PPP3CA 0 0.01 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -10000 0 0
PTPRC -0.007 0.06 -10000 0 -0.39 15 15
PDPK1 -0.026 0.063 0.23 2 -0.28 15 17
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.013 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.12 0.22 -9999 0 -0.5 202 202
TC10/GTP -0.1 0.18 -9999 0 -0.44 190 190
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.1 -9999 0 -0.53 31 31
HRAS 0 0.01 -9999 0 -10000 0 0
APS homodimer -0.01 0.051 -9999 0 -10000 0 0
GRB14 -0.1 0.23 -9999 0 -0.47 183 183
FOXO3 -0.013 0.065 -9999 0 -0.73 6 6
AKT1 -0.054 0.13 -9999 0 -0.54 6 6
INSR 0 0.009 -9999 0 -0.27 1 1
Insulin Receptor/Insulin -0.003 0.028 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.19 0.35 -9999 0 -0.84 190 190
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.032 0.032 -9999 0 -10000 0 0
CAV1 -0.12 0.24 -9999 0 -0.54 187 187
CBL/APS/CAP/Crk-II/C3G -0.11 0.2 -9999 0 -0.48 190 190
Insulin Receptor/Insulin/IRS1/NCK2 -0.02 0.1 -9999 0 -0.53 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.087 -9999 0 -0.46 31 31
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.005 0.13 -9999 0 -0.48 6 6
PARD6A -0.001 0.017 -9999 0 -0.28 3 3
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.001 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.047 0.11 -9999 0 -0.51 6 6
HRAS/GTP -0.015 0.075 -9999 0 -0.49 1 1
Insulin Receptor 0 0.009 -9999 0 -0.27 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.018 0.093 -9999 0 -0.49 31 31
PRKCI -0.012 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.059 0.14 -9999 0 -0.44 94 94
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.001 -9999 0 -10000 0 0
PI3K -0.017 0.089 -9999 0 -0.47 31 31
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
AKT2 -0.054 0.13 -9999 0 -0.54 6 6
PRKCZ -0.013 0.038 -9999 0 -0.63 1 1
SH2B2 -0.01 0.052 -9999 0 -10000 0 0
SHC/SHIP -0.017 0.087 -9999 0 -0.46 31 31
F2RL2 -0.06 0.14 -9999 0 -0.84 14 14
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0.005 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.12 0.22 -9999 0 -0.52 190 190
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.004 -9999 0 -10000 0 0
INPP5D -0.018 0.093 -9999 0 -0.5 31 31
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.008 0.071 -9999 0 -1 4 4
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.031 0.16 -9999 0 -0.84 31 31
p62DOK/RasGAP 0 0.001 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.018 0.093 -9999 0 -0.49 31 31
GRB2 0 0.01 -9999 0 -10000 0 0
EIF4EBP1 -0.01 0.14 -9999 0 -0.48 10 10
PTPRA 0 0.001 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.013 0.064 -9999 0 -0.34 31 31
Insulin Receptor/Insulin/IRS1 -0.02 0.1 -9999 0 -0.54 31 31
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.025 0.072 -9999 0 -0.49 14 14
Arf6 trafficking events

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.47 0.42 -10000 0 -0.84 476 476
CLTC 0.027 0.016 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.025 0.017 -10000 0 -10000 0 0
Dynamin 2/GTP -0.006 0.026 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.016 -10000 0 -0.28 1 1
CPE 0.006 0.083 -10000 0 -0.57 17 17
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.016 -10000 0 -10000 0 0
CTNND1 -0.005 0.022 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.012 -10000 0 -10000 0 0
TSHR -0.009 0.12 -10000 0 -0.57 38 38
INS 0.011 0.004 -10000 0 -10000 0 0
BIN1 -0.009 0.087 -10000 0 -0.84 9 9
mol:Choline -0.001 0.016 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.035 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.026 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -0.28 1 1
ASAP2/amphiphysin II -0.006 0.056 -10000 0 -0.52 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.017 0.052 -10000 0 -0.28 24 24
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.004 0.034 -10000 0 -0.28 13 13
substrate adhesion-dependent cell spreading 0 0.001 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.033 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.001 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.014 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.02 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0.001 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 -0.005 0.022 -10000 0 -10000 0 0
NME1 0.01 0.035 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.016 -10000 0 -10000 0 0
IL2RA 0.018 0.042 -10000 0 -0.33 10 10
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.24 0.21 -10000 0 -0.43 476 476
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.002 0.027 -10000 0 -0.35 5 5
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.023 -10000 0 -0.36 1 1
ARF6/GDP -0.007 0.031 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.009 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.016 -10000 0 -10000 0 0
endocytosis 0.006 0.056 0.51 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.091 0.22 -10000 0 -0.46 214 214
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.029 -10000 0 -0.84 1 1
Dynamin 2/GDP -0.006 0.026 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.17 0.24 -10000 0 -0.46 351 351
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.029 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.005 0.037 -10000 0 -0.28 15 15
GNB1/GNG2 -0.013 0.044 -10000 0 -0.19 43 43
AKT1 0.054 0.068 -10000 0 -0.2 43 43
EGF -0.17 0.33 -10000 0 -0.84 167 167
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.008 0.044 -10000 0 -0.34 2 2
mol:Ca2+ 0.052 0.092 -10000 0 -0.3 43 43
LYN -0.008 0.044 -10000 0 -0.34 2 2
RhoA/GTP -0.007 0.028 -10000 0 -0.14 2 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.058 0.1 -10000 0 -0.34 43 43
GNG2 -0.006 0.071 -10000 0 -0.84 6 6
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.031 0.047 -10000 0 -0.6 3 3
G beta5/gamma2 -0.016 0.058 -10000 0 -0.25 43 43
PRKCH 0.054 0.1 -10000 0 -0.35 43 43
DNM1 -0.005 0.065 -10000 0 -0.74 6 6
TXA2/TP beta/beta Arrestin3 -0.004 0.026 -10000 0 -0.31 5 5
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.027 0.14 -10000 0 -0.84 25 25
G12 family/GTP -0.018 0.068 -10000 0 -0.3 43 43
ADRBK1 0 0.01 -10000 0 -0.28 1 1
ADRBK2 -0.002 0.041 -10000 0 -0.84 2 2
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.041 0.072 0.36 12 -10000 0 12
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.014 -10000 0 -0.28 2 2
PRKG1 -0.032 0.16 -10000 0 -0.84 32 32
mol:IP3 0.054 0.11 -10000 0 -0.38 43 43
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.053 0.14 -10000 0 -0.51 43 43
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0 0.06 -10000 0 -0.4 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.008 0.045 -10000 0 -0.34 2 2
RHOA 0 0 -10000 0 -10000 0 0
PTGIR 0 0.01 -10000 0 -0.28 1 1
PRKCB1 0.051 0.11 -10000 0 -0.37 43 43
GNAQ -0.002 0.041 -10000 0 -0.84 2 2
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.055 0.15 -10000 0 -0.54 43 43
LCK -0.011 0.07 -10000 0 -0.46 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.01 0.054 -10000 0 -0.31 25 25
TXA2-R family/G12 family/GDP/G beta/gamma 0.026 0.028 -10000 0 -0.3 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.009 0.053 -10000 0 -10000 0 0
MAPK14 0.055 0.074 -10000 0 -0.22 43 43
TGM2/GTP 0.054 0.12 -10000 0 -0.42 43 43
MAPK11 0.055 0.077 -10000 0 -0.23 43 43
ARHGEF1 0.041 0.058 -10000 0 -0.17 43 43
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.055 0.12 -10000 0 -0.39 43 43
RAB11/GDP -0.001 0.013 -10000 0 -0.28 2 2
ICAM1 0.051 0.087 -10000 0 -0.28 43 43
cAMP biosynthetic process 0.05 0.11 -10000 0 -0.35 43 43
Gq family/GTP/EBP50 -0.006 0.027 -10000 0 -0.25 9 9
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.008 0.044 -10000 0 -0.34 2 2
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.1 -10000 0 -0.31 32 32
VCAM1 0.049 0.094 -10000 0 -0.31 43 43
TP beta/Gq family/GDP/G beta5/gamma2 0.031 0.047 -10000 0 -0.6 3 3
platelet activation 0.071 0.098 -10000 0 -0.3 43 43
PGI2/IP 0 0.006 -10000 0 -0.19 1 1
PRKACA -0.012 0.066 -10000 0 -0.39 25 25
Gq family/GDP/G beta5/gamma2 0.029 0.049 -10000 0 -0.6 3 3
TXA2/TP beta/beta Arrestin2 -0.005 0.052 -10000 0 -0.67 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.061 -10000 0 -0.36 25 25
mol:DAG 0.053 0.12 -10000 0 -0.42 43 43
EGFR -0.29 0.4 -10000 0 -0.83 297 297
TXA2/TP alpha 0.056 0.14 -10000 0 -0.48 43 43
Gq family/GTP -0.003 0.031 -10000 0 -0.29 9 9
YES1 -0.009 0.046 -10000 0 -0.36 3 3
GNAI2/GTP -0.009 0.051 -10000 0 -0.39 2 2
PGD2/DP -0.021 0.11 -10000 0 -0.65 25 25
SLC9A3R1 -0.027 0.082 -10000 0 -10000 0 0
FYN -0.009 0.046 -10000 0 -0.36 3 3
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.002 0.035 -10000 0 -0.39 5 5
PGK/cGMP -0.022 0.11 -10000 0 -0.57 32 32
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.011 0.068 -10000 0 -0.52 6 6
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.047 0.12 -10000 0 -0.37 57 57
PRKCB 0.049 0.11 -10000 0 -0.36 53 53
PRKCE 0.055 0.1 -10000 0 -0.34 44 44
PRKCD 0.054 0.11 -10000 0 -0.37 43 43
PRKCG 0.05 0.11 -10000 0 -0.38 43 43
muscle contraction 0.058 0.14 -10000 0 -0.49 44 44
PRKCZ 0.058 0.1 -10000 0 -0.34 44 44
ARR3 -0.002 0.023 -10000 0 -0.28 6 6
TXA2/TP beta -0.01 0.057 -10000 0 -0.34 10 10
PRKCQ 0.043 0.13 -10000 0 -0.37 66 66
MAPKKK cascade 0.052 0.13 -10000 0 -0.46 44 44
SELE 0.043 0.12 -10000 0 -0.42 43 43
TP beta/GNAI2/GDP/G beta/gamma -0.012 0.067 -10000 0 -0.52 6 6
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.013 0.082 -10000 0 -0.4 27 27
chemotaxis 0.054 0.17 -10000 0 -0.62 43 43
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 0 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.002 0.057 -10000 0 -0.7 5 5
CDKN2C 0.006 0.032 -10000 0 -0.82 1 1
CDKN2A -0.046 0.11 -10000 0 -0.29 133 133
CCND2 0.005 0.028 0.25 5 -0.17 6 11
RB1 -0.006 0.028 0.14 4 -0.26 5 9
CDK4 0.008 0.026 0.26 5 -10000 0 5
CDK6 0.006 0.032 0.28 5 -0.22 6 11
G1/S progression -0.008 0.031 0.24 6 -0.17 2 8
IL2 signaling events mediated by STAT5

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
GAB2 -0.003 0.027 -9999 0 -0.28 8 8
ELF1 -0.011 0.047 -9999 0 -0.39 10 10
CCNA2 -0.12 0.14 -9999 0 -0.28 369 369
PIK3CA 0 0.01 -9999 0 -10000 0 0
JAK3 -0.004 0.033 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.027 0.069 -9999 0 -0.61 4 4
SHC1 0 0 -9999 0 -10000 0 0
SP1 -0.003 0.033 -9999 0 -0.39 6 6
IL2RA 0.004 0.13 -9999 0 -1 10 10
IL2RB -0.011 0.055 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
IL2RG -0.016 0.083 -9999 0 -0.84 5 5
G1/S transition of mitotic cell cycle 0.012 0.1 -9999 0 -0.84 10 10
PTPN11 0 0 -9999 0 -10000 0 0
CCND2 0.021 0.091 -9999 0 -1 6 6
LCK -0.019 0.1 -9999 0 -0.46 34 34
GRB2 0 0.01 -9999 0 -10000 0 0
IL2 -0.003 0.029 -9999 0 -10000 0 0
CDK6 -0.007 0.072 -9999 0 -0.84 6 6
CCND3 0.067 0.059 -9999 0 -0.63 2 2
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.1 0.21 -10000 0 -0.6 117 117
AKT1 0.013 0.005 -10000 0 -10000 0 0
GSC -0.053 0.33 -10000 0 -1.5 39 39
NKX2-5 -0.038 0.095 -10000 0 -0.27 116 116
muscle cell differentiation 0.006 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.002 0.029 -10000 0 -10000 0 0
SMAD4 0.012 0.033 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.23 0.27 -10000 0 -0.56 343 343
SMAD3/SMAD4/VDR 0.006 0.03 -10000 0 -0.49 1 1
MYC -0.02 0.13 -10000 0 -0.84 20 20
CDKN2B 0.031 0.11 -10000 0 -1.5 4 4
AP1 -0.14 0.23 -10000 0 -0.57 58 58
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.012 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.038 -10000 0 -0.35 1 1
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.04 0.093 -10000 0 -0.4 4 4
SMAD3/SMAD4/GR -0.007 0.062 -10000 0 -0.63 7 7
GATA3 -0.039 0.16 -10000 0 -0.83 30 30
SKI/SIN3/HDAC complex/NCoR1 0.002 0.013 -10000 0 -10000 0 0
MEF2C/TIF2 -0.03 0.075 -10000 0 -0.65 5 5
endothelial cell migration -0.01 0.035 -10000 0 -10000 0 0
MAX 0.001 0.004 -10000 0 -10000 0 0
RBBP7 -0.003 0.027 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
RUNX2 -0.004 0.033 -10000 0 -10000 0 0
RUNX3 -0.004 0.052 -10000 0 -0.84 3 3
RUNX1 -0.001 0.029 -10000 0 -0.84 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.006 0.077 -10000 0 -0.84 7 7
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.049 0.065 -10000 0 -1.4 1 1
KAT2B 0.001 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.014 0.069 -10000 0 -0.43 3 3
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 0.01 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.001 0.023 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.09 0.22 -10000 0 -0.6 126 126
SAP30 -0.001 0.017 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.006 0.024 -10000 0 -10000 0 0
JUN -0.099 0.25 -10000 0 -0.58 50 50
SMAD3/SMAD4/IRF7 -0.011 0.058 -10000 0 -10000 0 0
TFE3 0.011 0.01 -10000 0 -10000 0 0
COL1A2 0.028 0.092 -10000 0 -1.2 1 1
mesenchymal cell differentiation 0.004 0.029 -10000 0 -10000 0 0
DLX1 -0.05 0.13 -10000 0 -0.84 8 8
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.26 0.4 -10000 0 -0.83 272 272
SMAD3/SMAD4/Max -0.002 0.024 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 0 0.005 -10000 0 -10000 0 0
LAMC1 0.041 0.048 -10000 0 -0.82 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.023 -10000 0 -10000 0 0
IRF7 -0.019 0.071 -10000 0 -0.35 18 18
ESR1 -0.15 0.29 -10000 0 -0.57 227 227
HNF4A -0.005 0.036 -10000 0 -0.28 14 14
MEF2C 0.001 0.086 -10000 0 -0.94 1 1
SMAD2-3/SMAD4 -0.003 0.03 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.003 0.025 -10000 0 -0.56 1 1
IGHV3OR16-13 0 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.002 0.007 -10000 0 -10000 0 0
SKIL -0.004 0.032 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 0 0 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.002 0.026 -10000 0 -10000 0 0
MSG1/HSC70 -0.26 0.32 -10000 0 -0.64 343 343
SMAD2 0.014 0.022 -10000 0 -10000 0 0
SMAD3 0.012 0.03 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.005 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.021 -10000 0 -10000 0 0
NCOR1 -0.001 0.029 -10000 0 -0.84 1 1
NCOA2 -0.007 0.076 -10000 0 -0.84 7 7
NCOA1 -0.001 0.029 -10000 0 -0.84 1 1
MYOD/E2A -0.002 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.006 0.031 -10000 0 -10000 0 0
IFNB1 0.016 0.083 -10000 0 -0.41 1 1
SMAD3/SMAD4/MEF2C -0.021 0.068 -10000 0 -0.92 1 1
CITED1 -0.34 0.41 -10000 0 -0.82 352 352
SMAD2-3/SMAD4/ARC105 0 0.026 -10000 0 -10000 0 0
RBL1 -0.001 0.014 -10000 0 -0.28 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.007 0.05 -10000 0 -0.5 4 4
RUNX1-3/PEBPB2 -0.003 0.046 -10000 0 -0.73 3 3
SMAD7 -0.087 0.14 -10000 0 -0.57 8 8
MYC/MIZ-1 -0.015 0.1 -10000 0 -0.65 20 20
SMAD3/SMAD4 0.02 0.061 0.3 15 -10000 0 15
IL10 0.015 0.12 -10000 0 -0.57 24 24
PIASy/HDAC complex 0.001 0.003 -10000 0 -10000 0 0
PIAS3 0.001 0.005 -10000 0 -10000 0 0
CDK2 0.002 0.008 -10000 0 -10000 0 0
IL5 0.011 0.12 -10000 0 -0.54 30 30
CDK4 0.001 0.016 -10000 0 -10000 0 0
PIAS4 0.001 0.003 -10000 0 -10000 0 0
ATF3 -0.12 0.3 -10000 0 -0.84 126 126
SMAD3/SMAD4/SP1 0.001 0.025 -10000 0 -10000 0 0
FOXG1 -0.02 0.071 -10000 0 -0.28 59 59
FOXO3 0.025 0.033 -10000 0 -0.64 2 2
FOXO1 0.021 0.057 -10000 0 -0.64 6 6
FOXO4 0.026 0.007 -10000 0 -10000 0 0
heart looping 0.002 0.085 -10000 0 -0.92 1 1
CEBPB 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.027 0.081 -10000 0 -0.6 8 8
MYOD1 -0.003 0.029 -10000 0 -0.28 9 9
SMAD3/SMAD4/HNF4 -0.006 0.03 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.024 0.12 -10000 0 -0.6 30 30
SnoN/SIN3/HDAC complex/NCoR1 -0.004 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.001 0.048 -10000 0 -0.68 3 3
SMAD3/SMAD4/SP1-3 0.004 0.023 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.012 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.008 0.082 -10000 0 -0.46 3 3
ITGB5 0.05 0.043 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.067 0.19 -10000 0 -0.6 92 92
AR -0.092 0.26 -10000 0 -0.83 93 93
negative regulation of cell growth -0.027 0.076 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.006 0.03 -10000 0 -10000 0 0
E2F5 -0.006 0.041 -10000 0 -0.28 19 19
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.002 0.05 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.04 -10000 0 -0.35 1 1
TFDP1 -0.001 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.14 0.23 -10000 0 -0.65 37 37
SMAD3/SMAD4/RUNX2 -0.004 0.029 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.003 0.038 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.048 0.14 -9999 0 -0.64 37 37
STXBP1 -0.004 0.058 -9999 0 -0.84 4 4
ACh/CHRNA1 -0.065 0.079 -9999 0 -0.27 9 9
RAB3GAP2/RIMS1/UNC13B -0.04 0.12 -9999 0 -0.56 37 37
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.068 0.19 -9999 0 -0.84 37 37
mol:ACh 0 0.033 -9999 0 -0.15 30 30
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.099 -9999 0 -0.42 41 41
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.065 0.079 -9999 0 -0.27 9 9
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.1 0.14 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.059 0.13 -9999 0 -0.48 46 46
SNAP25 -0.017 0.072 -9999 0 -0.39 30 30
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.086 0.18 -9999 0 -0.36 199 199
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.008 0.048 -9999 0 -0.57 4 4
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.099 -9999 0 -0.42 41 41
Regulation of Telomerase

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
Telomerase catalytic core complex -0.051 0.11 -9999 0 -0.65 3 3
RAD9A 0 0.01 -9999 0 -10000 0 0
AP1 -0.21 0.31 -9999 0 -0.66 273 273
IFNAR2 0.009 0.006 -9999 0 -10000 0 0
AKT1 -0.037 0.11 -9999 0 -0.3 79 79
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.65 117 117
NFX1/SIN3/HDAC complex 0 0.001 -9999 0 -10000 0 0
EGF -0.17 0.33 -9999 0 -0.84 167 167
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.064 0.085 -9999 0 -0.6 3 3
SAP18 0 0 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.15 0.14 -9999 0 -0.29 3 3
WRN 0 0 -9999 0 -10000 0 0
SP1 0.01 0.006 -9999 0 -10000 0 0
SP3 0 0 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.049 0.074 -9999 0 -0.54 3 3
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.051 0.12 -9999 0 -0.66 3 3
CCND1 -0.044 0.13 -9999 0 -1.3 3 3
MAX 0 0 -9999 0 -10000 0 0
RBBP7 -0.003 0.027 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
Telomerase/911 -0.001 0.005 -9999 0 -10000 0 0
CDKN1B 0.006 0.079 -9999 0 -0.91 3 3
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.017 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0 0 -9999 0 -10000 0 0
JUN -0.009 0.086 -9999 0 -0.84 9 9
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.27 0.39 -9999 0 -0.84 272 272
IFN-gamma/IRF1 -0.025 0.062 -9999 0 -0.36 4 4
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.032 0.089 -9999 0 -0.28 98 98
Telomerase -0.003 0.025 -9999 0 -10000 0 0
IRF1 -0.001 0.018 -9999 0 -10000 0 0
ESR1 -0.15 0.29 -9999 0 -0.56 228 228
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.002 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC2 0.009 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.022 0.002 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0 0.01 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.014 -9999 0 -0.28 2 2
TERT/NF kappa B1/14-3-3 -0.062 0.098 -9999 0 -0.67 3 3
NR2F2 -0.001 0.05 -9999 0 -0.84 3 3
MAPK3 0.014 0.021 -9999 0 -10000 0 0
MAPK1 0.014 0.021 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0 0.001 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.4 -9999 0 -0.83 297 297
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.35 0.37 -9999 0 -0.71 410 410
MYC -0.02 0.13 -9999 0 -0.84 20 20
IL2 0.003 0.03 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -0.28 1 1
TGFB1 0 0.001 -9999 0 -10000 0 0
TRF2/BLM -0.018 0.05 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.059 0.083 -9999 0 -0.6 3 3
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.049 0.074 -9999 0 -0.54 3 3
Smad3/Myc -0.013 0.085 -9999 0 -0.56 20 20
911 complex 0 0.005 -9999 0 -10000 0 0
IFNG -0.039 0.096 -9999 0 -0.27 15 15
Telomerase/PinX1 -0.049 0.074 -9999 0 -0.54 3 3
Telomerase/AKT1/mTOR/p70S6K 0.004 0.054 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.049 0.074 -9999 0 -0.54 3 3
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.049 0.074 -9999 0 -0.54 3 3
E2F1 -0.088 0.14 -9999 0 -10000 0 0
ZNFX1 0 0 -9999 0 -10000 0 0
PIF1 -0.052 0.11 -9999 0 -10000 0 0
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.014 -9999 0 -0.28 2 2
telomeric DNA binding 0 0 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.02 0.072 -9999 0 -0.19 133 133
TP53 -0.007 0.018 -9999 0 -10000 0 0
Senescence -0.007 0.018 -9999 0 -10000 0 0
Apoptosis -0.007 0.018 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.014 0.037 -9999 0 -10000 0 0
MDM4 0 0 -9999 0 -10000 0 0
Syndecan-2-mediated 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
Syndecan-2/Fibronectin -0.064 0.075 -9999 0 -0.42 6 6
EPHB2 -0.005 0.037 -9999 0 -0.28 15 15
Syndecan-2/TACI -0.017 0.081 -9999 0 -0.56 16 16
LAMA1 -0.095 0.26 -9999 0 -0.83 97 97
Syndecan-2/alpha2 ITGB1 -0.12 0.22 -9999 0 -0.49 213 213
HRAS 0 0.01 -9999 0 -10000 0 0
Syndecan-2/CASK -0.003 0.035 -9999 0 -0.56 3 3
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.038 0.033 -9999 0 -0.49 3 3
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.032 -9999 0 -0.51 3 3
LAMA3 -0.2 0.36 -9999 0 -0.84 201 201
EZR -0.001 0.014 -9999 0 -0.28 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.11 0.28 -9999 0 -0.84 106 106
Syndecan-2/MMP2 -0.008 0.077 -9999 0 -0.75 8 8
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.012 0.088 -9999 0 -0.64 16 16
dendrite morphogenesis -0.005 0.039 -9999 0 -0.55 3 3
Syndecan-2/GM-CSF -0.005 0.039 -9999 0 -0.56 3 3
determination of left/right symmetry 0.016 0.042 -9999 0 -0.64 3 3
Syndecan-2/PKC delta -0.003 0.035 -9999 0 -0.56 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.039 -9999 0 -0.51 3 3
MAPK1 0.022 0.039 -9999 0 -0.51 3 3
Syndecan-2/RACK1 -0.002 0.03 -9999 0 -0.48 3 3
NF1 -0.001 0.029 -9999 0 -0.84 1 1
FGFR/FGF/Syndecan-2 0.016 0.042 -9999 0 -0.64 3 3
ITGA2 -0.016 0.11 -9999 0 -0.84 16 16
MAPK8 0.032 0.037 -9999 0 -0.55 3 3
Syndecan-2/alpha2/beta1 Integrin -0.065 0.19 -9999 0 -0.55 99 99
Syndecan-2/Kininogen -0.005 0.038 -9999 0 -0.56 3 3
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.002 0.028 -9999 0 -0.45 3 3
Syndecan-2/CASK/Protein 4.1 -0.002 0.032 -9999 0 -0.52 3 3
extracellular matrix organization -0.003 0.034 -9999 0 -0.55 3 3
actin cytoskeleton reorganization -0.063 0.075 -9999 0 -0.42 6 6
Syndecan-2/Caveolin-2/Ras -0.067 0.18 -9999 0 -0.52 106 106
Syndecan-2/Laminin alpha3 -0.14 0.24 -9999 0 -0.56 204 204
Syndecan-2/RasGAP -0.002 0.028 -9999 0 -0.46 3 3
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0.01 -9999 0 -10000 0 0
Syndecan-2 dimer -0.005 0.039 -9999 0 -0.56 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.027 -9999 0 -0.44 3 3
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.024 0.12 -9999 0 -0.84 13 13
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.012 0.088 -9999 0 -0.64 16 16
Syndecan-2/Synbindin -0.003 0.034 -9999 0 -0.56 3 3
TGFB1 0 0 -9999 0 -10000 0 0
CASP3 0.029 0.034 -9999 0 -0.5 3 3
FN1 -0.12 0.14 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.023 0.091 -9999 0 -0.56 20 20
SDC2 0.016 0.042 -9999 0 -0.64 3 3
KNG1 -0.004 0.033 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin -0.003 0.039 -9999 0 -0.56 4 4
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.005 0.038 -9999 0 -10000 0 0
Syndecan-2/TGFB1 -0.003 0.034 -9999 0 -0.56 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.032 -9999 0 -0.52 3 3
Syndecan-2/Ezrin -0.003 0.032 -9999 0 -0.51 3 3
PRKACA 0.029 0.038 -9999 0 -0.5 4 4
angiogenesis -0.023 0.091 -9999 0 -0.56 20 20
MMP2 -0.008 0.081 -9999 0 -0.84 8 8
IL8 -0.036 0.14 -9999 0 -0.84 17 17
calcineurin-NFAT signaling pathway -0.016 0.08 -9999 0 -0.56 16 16
Ceramide signaling pathway

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
SPHK2 0.021 0.023 -10000 0 -0.64 1 1
MAP4K4 -0.005 0.034 -10000 0 -10000 0 0
BAG4 -0.003 0.03 -10000 0 -0.28 10 10
PKC zeta/ceramide -0.025 0.05 -10000 0 -0.61 1 1
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.082 -10000 0 -0.84 7 7
BAX -0.009 0.022 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.01 -10000 0 -10000 0 0
BAD -0.023 0.047 0.21 1 -10000 0 1
SMPD1 0.025 0.032 -10000 0 -0.25 10 10
RB1 -0.024 0.05 0.21 1 -0.51 1 2
FADD/Caspase 8 -0.005 0.035 -10000 0 -0.34 2 2
MAP2K4 -0.015 0.047 -10000 0 -0.49 1 1
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.015 0.048 -10000 0 -0.48 1 1
EGF -0.17 0.33 -10000 0 -0.84 167 167
mol:ceramide -0.034 0.05 0.22 1 -0.13 148 149
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.026 -10000 0 -0.64 1 1
ASAH1 -0.001 0.017 -10000 0 -0.28 3 3
negative regulation of cell cycle -0.023 0.05 0.21 1 -0.5 1 2
cell proliferation -0.1 0.17 -10000 0 -0.41 186 186
BID 0.023 0.033 -10000 0 -10000 0 0
MAP3K1 -0.023 0.047 0.21 1 -10000 0 1
EIF2A -0.006 0.043 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.003 0.046 -10000 0 -0.44 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.046 -10000 0 -0.44 1 1
Cathepsin D/ceramide -0.029 0.05 -10000 0 -10000 0 0
FADD -0.007 0.038 -10000 0 -0.37 2 2
KSR1 -0.024 0.051 0.21 1 -0.34 3 4
MAPK8 -0.011 0.046 0.2 1 -0.32 2 3
PRKRA -0.023 0.047 0.21 1 -10000 0 1
PDGFA -0.001 0.029 -10000 0 -0.84 1 1
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.18 0.35 -10000 0 -0.84 186 186
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.034 0.05 0.22 1 -0.13 148 149
CTSD -0.01 0.052 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.11 0.18 -10000 0 -0.44 186 186
PRKCD 0 0.01 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.026 -10000 0 -0.64 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.005 0.037 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.011 0.065 -10000 0 -0.56 10 10
mol:Sphingosine-1-phosphate 0.021 0.023 -10000 0 -0.64 1 1
MAP2K1 -0.007 0.046 -10000 0 -0.45 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.009 0.044 0.19 18 -10000 0 18
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.019 -10000 0 -10000 0 0
EIF2AK2 -0.014 0.044 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.009 0.063 -10000 0 -0.56 10 10
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0.02 -10000 0 -10000 0 0
MAP2K2 -0.007 0.046 -10000 0 -0.45 1 1
SMPD3 0.026 0.039 -10000 0 -0.27 12 12
TNF -0.016 0.098 -10000 0 -0.84 10 10
PKC zeta/PAR4 -0.001 0.022 -10000 0 -0.64 1 1
mol:PHOSPHOCHOLINE 0.047 0.12 0.28 168 -10000 0 168
NF kappa B1/RelA/I kappa B alpha -0.001 0.016 -10000 0 -0.47 1 1
AIFM1 -0.009 0.044 0.19 18 -10000 0 18
BCL2 -0.024 0.14 -10000 0 -0.84 24 24
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.017 0.095 -9999 0 -0.56 25 25
E-cadherin/beta catenin -0.018 0.11 -9999 0 -0.64 24 24
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.002 0.032 -9999 0 -0.46 3 3
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.03 0.068 -9999 0 -0.47 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.054 -9999 0 -0.49 2 2
alphaV/beta3 Integrin/Osteopontin/Src -0.046 0.073 -9999 0 -10000 0 0
AP1 -0.16 0.22 -9999 0 -0.79 24 24
ILK -0.01 0.088 -9999 0 -0.5 14 14
bone resorption -0.022 0.063 -9999 0 -0.7 2 2
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.014 0.076 -9999 0 -0.52 3 3
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.002 0.033 -9999 0 -0.64 2 2
alphaV/beta3 Integrin/Osteopontin -0.042 0.086 -9999 0 -0.56 14 14
MAP3K1 -0.035 0.075 -9999 0 -0.51 14 14
JUN -0.009 0.086 -9999 0 -0.84 9 9
MAPK3 0.015 0.089 -9999 0 -0.46 14 14
MAPK1 0.015 0.089 -9999 0 -0.46 14 14
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.012 0.088 -9999 0 -0.47 14 14
ITGB3 -0.015 0.11 -9999 0 -0.83 14 14
NFKBIA 0.028 0.086 -9999 0 -0.45 14 14
FOS -0.27 0.39 -9999 0 -0.84 272 272
CD44 -0.001 0.017 -9999 0 -0.28 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.025 0.087 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.016 0.052 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.011 0.082 -9999 0 -0.63 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.035 0.076 -9999 0 -0.51 14 14
VAV3 0.005 0.095 -9999 0 -0.48 17 17
MAP3K14 0.002 0.094 -9999 0 -0.5 14 14
ROCK2 -0.002 0.041 -9999 0 -0.84 2 2
SPP1 -0.077 0.12 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.028 0.067 -9999 0 -0.5 4 4
MMP2 -0.13 0.18 -9999 0 -0.7 24 24
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.003 -9999 0 -10000 0 0
HDAC2 0.001 0.003 -9999 0 -10000 0 0
GNB1/GNG2 -0.009 0.073 -9999 0 -0.6 12 12
forebrain development -0.026 0.2 -9999 0 -0.53 101 101
GNAO1 -0.033 0.14 -9999 0 -0.84 21 21
SMO/beta Arrestin2 -0.006 0.059 -9999 0 -0.65 7 7
SMO -0.005 0.077 -9999 0 -0.84 7 7
ARRB2 0 0.001 -9999 0 -10000 0 0
GLI3/SPOP -0.003 0.038 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
XPO1 0.011 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.053 0.16 -9999 0 -0.53 57 57
SAP30 0 0.017 -9999 0 -10000 0 0
mol:GDP -0.005 0.077 -9999 0 -0.84 7 7
MIM/GLI2A 0.001 0.03 -9999 0 -0.28 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GLI2 0.041 0.032 -9999 0 -10000 0 0
GLI3 0.038 0.043 -9999 0 -0.31 11 11
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.003 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.006 0.07 -9999 0 -0.84 6 6
Gi family/GTP -0.031 0.095 -9999 0 -0.38 37 37
SIN3B 0.001 0.003 -9999 0 -10000 0 0
SIN3A 0.001 0.003 -9999 0 -10000 0 0
GLI3/Su(fu) -0.002 0.024 -9999 0 -10000 0 0
GLI2/Su(fu) -0.004 0.035 -9999 0 -0.41 4 4
FOXA2 -0.013 0.033 -9999 0 -10000 0 0
neural tube patterning -0.026 0.2 -9999 0 -0.53 101 101
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.023 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 0.001 0.03 -9999 0 -0.28 9 9
embryonic limb morphogenesis -0.026 0.2 -9999 0 -0.53 101 101
SUFU -0.002 0.027 -9999 0 -0.31 1 1
LGALS3 -0.009 0.086 -9999 0 -0.84 9 9
catabolic process -0.004 0.029 -9999 0 -10000 0 0
GLI3A/CBP -0.027 0.099 -9999 0 -0.39 59 59
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.027 0.21 -9999 0 -0.54 101 101
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.029 -9999 0 -0.84 1 1
RBBP7 -0.002 0.027 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.008 0.063 -9999 0 -0.57 9 9
GNAZ -0.006 0.07 -9999 0 -0.84 6 6
RBBP4 0.001 0.003 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.003 0.024 -9999 0 -10000 0 0
STK36 0.011 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.027 0.095 -9999 0 -0.55 10 10
PTCH1 -0.062 0.34 -9999 0 -1.2 64 64
MIM/GLI1 -0.053 0.19 -9999 0 -0.5 101 101
CREBBP -0.027 0.099 -9999 0 -0.39 59 59
Su(fu)/SIN3/HDAC complex 0.006 0.019 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.007 -10000 0 -10000 0 0
CDKN1B 0.035 0.03 -10000 0 -0.46 3 3
CDKN1A 0.036 0.018 -10000 0 -0.46 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.019 -10000 0 -0.28 4 4
FOXO3 0.036 0.024 -10000 0 -0.46 2 2
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
AKT3 -0.006 0.052 -10000 0 -0.46 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.002 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.022 -10000 0 -0.44 2 2
BAD/YWHAZ 0 0.008 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.021 0.43 2 -10000 0 2
TSC1 0.037 0.002 -10000 0 -10000 0 0
YWHAZ -0.001 0.017 -10000 0 -0.28 3 3
AKT1/RAF1 0 0.001 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.037 0.002 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.024 0.02 -10000 0 -0.55 1 1
MAP3K5 -0.002 0.041 -10000 0 -0.84 2 2
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.039 0.024 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.002 -10000 0 -10000 0 0
CASP9 0.037 0.002 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.026 -10000 0 -0.43 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0.007 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.015 -10000 0 -0.44 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.002 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.002 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.031 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.009 -10000 0 -10000 0 0
MAPKKK cascade 0 0.001 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.005 -10000 0 -10000 0 0
TSC1/TSC2 0.043 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.005 -10000 0 -10000 0 0
glucose import -0.27 0.27 -10000 0 -0.5 476 476
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.031 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.28 0.27 -10000 0 -0.51 476 476
GSK3A 0.037 0.002 -10000 0 -10000 0 0
FOXO1 0.033 0.042 -10000 0 -0.46 6 6
GSK3B 0.037 0.002 -10000 0 -10000 0 0
SFN -0.016 0.11 -10000 0 -0.62 21 21
G1/S transition of mitotic cell cycle 0.044 0.002 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.041 0.035 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0.01 -10000 0 -0.28 1 1
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.007 0.077 -10000 0 -0.84 7 7
positive regulation of NF-kappaB transcription factor activity -0.067 0.2 -10000 0 -0.64 87 87
MAP2K4 -0.004 0.033 -10000 0 -0.46 1 1
IKBKB -0.001 0.014 -10000 0 -0.28 2 2
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.004 0.058 -10000 0 -0.84 4 4
SMPD1 -0.003 0.027 -10000 0 -0.3 7 7
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.08 0.25 -10000 0 -0.84 80 80
TRAIL/TRAILR2 -0.006 0.059 -10000 0 -0.64 7 7
TRAIL/TRAILR3 -0.009 0.076 -10000 0 -0.7 9 9
TRAIL/TRAILR1 -0.009 0.074 -10000 0 -0.64 11 11
TRAIL/TRAILR4 -0.067 0.2 -10000 0 -0.64 87 87
TRAIL/TRAILR1/DAP3/GTP -0.007 0.059 -10000 0 -0.52 11 11
IKK complex -0.003 0.02 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0.006 -10000 0 -10000 0 0
MAPK3 0.016 0.061 -10000 0 -0.64 7 7
MAP3K1 -0.004 0.032 -10000 0 -0.33 7 7
TRAILR4 (trimer) -0.08 0.24 -10000 0 -0.84 80 80
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.004 0.058 -10000 0 -0.84 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.039 -10000 0 -0.34 11 11
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.061 -10000 0 -0.64 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.057 -10000 0 -0.49 11 11
mol:ceramide -0.003 0.027 -10000 0 -0.3 7 7
FADD -0.005 0.038 -10000 0 -0.28 16 16
MAPK8 0.048 0.037 -10000 0 -0.43 1 1
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.006 0.057 -10000 0 -0.84 3 3
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.067 -10000 0 -0.57 11 11
DAP3 0 0.01 -10000 0 -0.28 1 1
CASP10 0.021 0.11 0.31 76 -0.53 10 86
JNK cascade -0.067 0.2 -10000 0 -0.64 87 87
TRAIL (trimer) -0.007 0.077 -10000 0 -0.84 7 7
TNFRSF10C -0.006 0.057 -10000 0 -0.84 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD -0.009 0.058 -10000 0 -0.49 11 11
TRAIL/TRAILR2/FADD -0.007 0.054 -10000 0 -0.56 7 7
cell death -0.003 0.027 -10000 0 -0.3 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.031 -10000 0 -0.34 7 7
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.015 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.006 0.045 -10000 0 -0.48 7 7
Caspase cascade in apoptosis

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
TOP1 0.005 0.096 -10000 0 -0.46 29 29
ACTA1 -0.018 0.14 -10000 0 -0.64 30 30
NUMA1 0.005 0.096 -10000 0 -0.46 29 29
SPTAN1 -0.005 0.13 -10000 0 -0.65 26 26
LIMK1 -0.005 0.13 -10000 0 -0.65 26 26
BIRC3 -0.01 0.082 -10000 0 -0.84 7 7
BIRC2 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.016 0.15 -10000 0 -0.69 30 30
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.096 -10000 0 -0.46 29 29
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.13 -10000 0 -0.63 26 26
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.012 0.15 -10000 0 -0.66 35 35
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.014 0.08 -10000 0 -0.67 11 11
BID 0.005 0.064 -10000 0 -0.3 29 29
MAP3K1 0.004 0.04 -10000 0 -0.24 6 6
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.005 0.13 -10000 0 -0.65 26 26
CASP9 0 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.19 1 -0.22 3 4
neuron apoptosis 0.021 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.12 -10000 0 -0.62 26 26
APAF1 0 0 -10000 0 -10000 0 0
CASP6 0.022 0.056 -10000 0 -0.36 3 3
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD 0.003 0.13 -10000 0 -0.62 26 26
CASP7 -0.007 0.037 0.36 7 -10000 0 7
KRT18 0.015 0.017 -10000 0 -10000 0 0
apoptosis 0.008 0.11 -10000 0 -0.55 26 26
DFFA -0.005 0.13 -10000 0 -0.65 26 26
DFFB -0.005 0.13 -10000 0 -0.65 26 26
PARP1 0.002 0.031 0.22 3 -0.19 1 4
actin filament polymerization -0.003 0.12 0.6 26 -10000 0 26
TNF -0.016 0.098 -10000 0 -0.84 10 10
CYCS 0.007 0.051 -10000 0 -0.22 29 29
SATB1 0.019 0.095 -10000 0 -0.5 19 19
SLK -0.005 0.13 -10000 0 -0.65 26 26
p15 BID/BAX -0.013 0.05 -10000 0 -0.35 6 6
CASP2 0.043 0.039 -10000 0 -10000 0 0
JNK cascade -0.004 0.039 0.24 6 -10000 0 6
CASP3 -0.014 0.14 -10000 0 -0.65 30 30
LMNB2 0.04 0.035 -10000 0 -0.26 2 2
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.029 -10000 0 -0.84 1 1
Mammalian IAPs/DIABLO -0.006 0.048 -10000 0 -0.51 7 7
negative regulation of DNA binding 0.014 0.079 -10000 0 -0.66 11 11
stress fiber formation -0.004 0.13 -10000 0 -0.63 26 26
GZMB -0.029 0.16 -10000 0 -0.66 38 38
CASP1 -0.002 0.027 -10000 0 -0.46 3 3
LMNB1 0.045 0.036 -10000 0 -0.28 1 1
APP 0.021 0.013 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.003 0.11 -10000 0 -0.54 26 26
LMNA 0.04 0.035 -10000 0 -0.28 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.034 -10000 0 -10000 0 0
LRDD 0 0.01 -10000 0 -10000 0 0
SREBF1 -0.007 0.13 -10000 0 -0.66 26 26
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.005 0.094 -10000 0 -0.45 29 29
CFL2 0.003 0.13 -10000 0 -0.62 26 26
GAS2 -0.054 0.2 -10000 0 -0.54 103 103
positive regulation of apoptosis 0.046 0.035 -10000 0 -0.28 1 1
PRF1 -0.02 0.12 -10000 0 -0.84 17 17
Cellular roles of Anthrax toxin

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
ANTXR1 0 0.01 -10000 0 -0.28 1 1
ANTXR2 -0.009 0.086 -10000 0 -0.84 9 9
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.011 -10000 0 -0.1 9 9
monocyte activation 0.006 0.065 -10000 0 -0.46 16 16
MAP2K2 0 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.012 0.074 -10000 0 -0.51 18 18
CYAA -0.005 0.051 -10000 0 -0.5 9 9
MAP2K4 -0.002 0.02 -10000 0 -0.5 1 1
IL1B 0.009 0.06 -10000 0 -0.35 20 20
Channel -0.006 0.054 -10000 0 -0.52 9 9
NLRP1 -0.008 0.06 -10000 0 -0.52 11 11
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.011 0.1 9 -10000 0 9
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.15 0.22 -10000 0 -0.5 230 230
PA/Cellular Receptors -0.006 0.059 -10000 0 -0.57 9 9
apoptosis -0.001 0.011 -10000 0 -0.1 9 9
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.005 0.051 -10000 0 -0.49 9 9
macrophage activation 0.02 0.01 -10000 0 -10000 0 0
TNF -0.016 0.098 -10000 0 -0.84 10 10
VCAM1 -0.009 0.064 -10000 0 -0.46 16 16
platelet activation -0.001 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.023 0.11 18 -10000 0 18
IL18 0.011 0.036 -10000 0 -0.22 11 11
negative regulation of macrophage activation -0.001 0.011 -10000 0 -0.1 9 9
LEF -0.001 0.011 -10000 0 -0.1 9 9
CASP1 -0.004 0.029 -10000 0 -0.25 11 11
mol:cAMP -0.001 0.013 -10000 0 -10000 0 0
necrosis -0.001 0.011 -10000 0 -0.1 9 9
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.005 0.051 -10000 0 -0.5 9 9
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.03 0.01 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.045 -9999 0 -10000 0 0
MAPK12 0.017 0.086 -9999 0 -0.51 21 21
CCND1 0.015 0.043 -9999 0 -0.23 20 20
p38 gamma/SNTA1 -0.012 0.076 -9999 0 -0.5 18 18
MAP2K3 0 0.01 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.017 0.086 -9999 0 -0.5 21 21
MAP2K6 0.01 0.087 -9999 0 -0.53 21 21
MAPT -0.016 0.13 -9999 0 -0.41 84 84
MAPK13 0.021 0.012 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.002 0.027 -9999 0 -0.46 3 3
Retinoic acid receptors-mediated signaling

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
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR 0 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.039 0.034 -10000 0 -0.33 2 2
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.021 0.043 0.24 3 -0.36 6 9
RAR alpha/9cRA/Cyclin H -0.01 0.06 -10000 0 -0.39 21 21
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.035 0.046 -10000 0 -0.36 8 8
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.007 0.039 -10000 0 -0.29 1 1
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.007 0.12 -10000 0 -0.58 24 24
NCOA2 -0.007 0.076 -10000 0 -0.84 7 7
NCOA3 0 0.01 -10000 0 -0.28 1 1
NCOA1 -0.001 0.029 -10000 0 -0.84 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.042 0.11 -10000 0 -0.64 21 21
RARA 0.016 0.054 -10000 0 -0.31 21 21
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.033 0.047 -10000 0 -0.28 11 11
PRKCA -0.008 0.13 -10000 0 -0.77 24 24
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.004 0.13 -10000 0 -0.6 25 25
RXRG -0.1 0.22 -10000 0 -0.46 221 221
RXRA 0.024 0.06 -10000 0 -0.34 21 21
RXRB 0.01 0.076 -10000 0 -0.45 21 21
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.022 0.094 -10000 0 -0.84 6 6
CRBP1/9-cic-RA -0.015 0.069 -10000 0 -0.65 6 6
RARB 0.004 0.083 -10000 0 -0.84 8 8
PRKCG -0.002 0.056 -10000 0 -0.28 34 34
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.027 0.12 -10000 0 -0.64 22 22
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.014 0.1 -10000 0 -0.5 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.048 -10000 0 -0.43 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.004 0.13 -10000 0 -0.6 25 25
positive regulation of DNA binding -0.009 0.057 -10000 0 -0.36 21 21
NRIP1 -0.003 0.12 -10000 0 -0.6 22 22
RXRs/RARs -0.011 0.13 -10000 0 -0.59 25 25
RXRs/RXRs/DNA/9cRA -0.045 0.12 -10000 0 -0.65 22 22
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.029 -10000 0 -10000 0 0
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.015 0.085 -9999 0 -0.55 18 18
MAP4K1 -0.01 0.062 -9999 0 -0.32 27 27
MAP3K8 -0.005 0.065 -9999 0 -0.74 6 6
PRKCB -0.018 0.11 -9999 0 -0.57 27 27
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 -0.006 0.047 -9999 0 -0.58 2 2
JUN 0.02 0.1 -9999 0 -0.58 23 23
MAP3K7 -0.006 0.047 -9999 0 -0.58 2 2
GRAP2 -0.014 0.1 -9999 0 -0.73 16 16
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.044 0.058 -9999 0 -0.52 4 4
LAT -0.004 0.048 -9999 0 -0.84 2 2
LCP2 0 0.01 -9999 0 -0.28 1 1
MAPK8 0.018 0.094 -9999 0 -0.68 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.007 0.05 -9999 0 -0.38 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.014 0.08 -9999 0 -0.54 16 16
BARD1 signaling events

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
BARD1/CSTF1 0 0.009 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
PRKDC -0.001 0.019 -9999 0 -0.28 4 4
ATR 0 0 -9999 0 -10000 0 0
UBE2L3 0 0 -9999 0 -10000 0 0
FANCD2 -0.001 0.007 -9999 0 -10000 0 0
protein ubiquitination -0.018 0.038 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
M/R/N Complex 0 0 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
DNA-PK -0.001 0.009 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.002 0.01 -9999 0 -10000 0 0
FANCF 0 0.01 -9999 0 -0.28 1 1
BRCA1 -0.001 0.014 -9999 0 -0.28 2 2
CCNE1 -0.054 0.11 -9999 0 -0.28 163 163
CDK2/Cyclin E1 -0.034 0.069 -9999 0 -10000 0 0
FANCG 0 0 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.001 0.01 -9999 0 -10000 0 0
FANCE 0 0 -9999 0 -10000 0 0
FANCC 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
FANCA -0.052 0.11 -9999 0 -10000 0 0
DNA repair 0.013 0.074 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin -0.001 0.01 -9999 0 -10000 0 0
BARD1/DNA-PK -0.001 0.008 -9999 0 -10000 0 0
FANCL 0 0 -9999 0 -10000 0 0
mRNA polyadenylation 0 0.009 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0 0.001 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0 0.007 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.001 0.009 -9999 0 -10000 0 0
BRCA1/BACH1 -0.001 0.014 -9999 0 -0.28 2 2
BARD1 0 0.01 -9999 0 -0.28 1 1
PCNA -0.001 0.017 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.046 0.056 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 -0.001 0.007 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.001 0.01 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP -0.001 0.008 -9999 0 -10000 0 0
FA complex -0.004 0.009 -9999 0 -10000 0 0
BARD1/EWS 0 0.006 -9999 0 -10000 0 0
RBBP8 0.022 0.007 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
TOPBP1 0 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle 0 0.007 -9999 0 -10000 0 0
BRCA1/BARD1 -0.019 0.038 -9999 0 -10000 0 0
CSTF1 0 0.01 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0 0.006 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 -0.11 0.14 -9999 0 -0.28 341 341
RAD50 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.001 0.01 -9999 0 -10000 0 0
EWSR1 0 0 -9999 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A -0.027 0.029 -9999 0 -10000 0 0
BIRC5 -0.2 0.12 -9999 0 -10000 0 0
NFKBIA -0.025 0.031 -9999 0 -10000 0 0
CPEB1 -0.16 0.33 -9999 0 -0.84 163 163
AKT1 -0.025 0.031 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.024 0.026 -9999 0 -10000 0 0
NDEL1/TACC3 -0.038 0.056 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.001 0.003 -9999 0 -10000 0 0
PAK1/Aurora A -0.03 0.037 -9999 0 -10000 0 0
MDM2 -0.001 0.019 -9999 0 -0.28 4 4
JUB -0.004 0.058 -9999 0 -0.84 4 4
TPX2 -0.11 0.093 -9999 0 -10000 0 0
TP53 -0.011 0.015 -9999 0 -10000 0 0
DLG7 -0.033 0.033 -9999 0 -10000 0 0
AURKAIP1 0 0.01 -9999 0 -0.28 1 1
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.041 0.06 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.026 -9999 0 -10000 0 0
AURKA -0.039 0.042 -9999 0 -10000 0 0
AURKB -0.003 0.008 -9999 0 -10000 0 0
CDC25B -0.018 0.024 -9999 0 -10000 0 0
G2/M transition checkpoint -0.026 0.043 -9999 0 -0.53 4 4
mRNA polyadenylation -0.13 0.21 -9999 0 -0.56 163 163
Aurora A/CPEB -0.13 0.22 -9999 0 -0.56 163 163
Aurora A/TACC1/TRAP/chTOG -0.026 0.077 -9999 0 -0.51 20 20
BRCA1 -0.001 0.014 -9999 0 -0.28 2 2
centrosome duplication -0.03 0.037 -9999 0 -10000 0 0
regulation of centrosome cycle -0.038 0.056 -9999 0 -10000 0 0
spindle assembly -0.025 0.076 -9999 0 -0.5 20 20
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.065 -9999 0 -10000 0 0
CENPA 0.002 0.011 -9999 0 -10000 0 0
Aurora A/PP2A -0.027 0.029 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.005 0.027 -9999 0 -10000 0 0
negative regulation of DNA binding -0.011 0.015 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.012 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.026 0.043 -9999 0 -0.53 4 4
mitotic prometaphase -0.014 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.042 -9999 0 -10000 0 0
TACC1 -0.02 0.13 -9999 0 -0.84 20 20
TACC3 -0.041 0.099 -9999 0 -10000 0 0
Aurora A/Antizyme1 -0.02 0.02 -9999 0 -10000 0 0
Aurora A/RasGAP -0.027 0.029 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.001 0.003 -9999 0 -10000 0 0
GIT1 -0.001 0.019 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.003 0.021 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.11 0.093 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.11 0.081 -9999 0 -10000 0 0
PAK1 -0.006 0.04 -9999 0 -0.28 18 18
CKAP5 0 0 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.079 0.51 5 -10000 0 5
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.038 -10000 0 -0.57 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.033 0.14 -10000 0 -0.84 21 21
RhoA/GTP -0.024 0.081 -10000 0 -0.53 5 5
negative regulation of cAMP metabolic process -0.027 0.09 -10000 0 -0.37 30 30
GNAZ -0.006 0.07 -10000 0 -0.84 6 6
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.061 -10000 0 -0.38 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.028 0.091 -10000 0 -0.38 30 30
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.043 0.18 -10000 0 -0.84 43 43
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.018 0.099 -9999 0 -0.6 24 24
KLHL20 -0.008 0.033 -9999 0 -0.25 2 2
CYFIP2 -0.009 0.06 -9999 0 -0.32 24 24
Rac1/GDP 0.048 0.07 -9999 0 -10000 0 0
ENAH -0.017 0.098 -9999 0 -0.59 24 24
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.009 0.049 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.023 -9999 0 -0.17 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.089 -9999 0 -0.51 26 26
RAPGEF1 0.038 0.091 -9999 0 -0.49 24 24
CTNND1 0 0.01 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.018 0.1 -9999 0 -0.61 24 24
CRK 0.029 0.099 -9999 0 -0.55 24 24
E-cadherin/gamma catenin/alpha catenin -0.017 0.095 -9999 0 -0.56 25 25
alphaE/beta7 Integrin -0.005 0.039 -9999 0 -0.64 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.031 -9999 0 -0.52 3 3
DLG1 -0.017 0.098 -9999 0 -0.59 24 24
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.035 -9999 0 -10000 0 0
MLLT4 -0.003 0.05 -9999 0 -0.84 3 3
ARF6/GTP/NME1/Tiam1 -0.006 0.027 -9999 0 -10000 0 0
PI3K -0.008 0.046 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.02 0.11 -9999 0 -0.64 25 25
TIAM1 -0.001 0.019 -9999 0 -0.28 4 4
E-cadherin(dimer)/Ca2+ -0.014 0.081 -9999 0 -0.48 24 24
AKT1 -0.005 0.026 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
RhoA/GDP 0.048 0.07 -9999 0 -10000 0 0
actin cytoskeleton organization -0.006 0.024 -9999 0 -0.18 2 2
CDC42/GDP 0.048 0.07 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.011 0.06 -9999 0 -0.35 25 25
ITGB7 -0.007 0.055 -9999 0 -0.34 17 17
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.015 0.085 -9999 0 -0.51 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin -0.014 0.082 -9999 0 -0.49 24 24
mol:GDP 0.046 0.081 -9999 0 -0.42 24 24
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.002 0.032 -9999 0 -0.46 3 3
p120 catenin/RhoA/GDP -0.011 0.06 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.029 -9999 0 -0.21 6 6
NME1 -0.014 0.06 -9999 0 -0.28 41 41
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.018 0.099 -9999 0 -0.58 25 25
regulation of cell-cell adhesion -0.008 0.043 -9999 0 -10000 0 0
WASF2 -0.003 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.01 0.057 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.085 -9999 0 -0.48 27 27
CCND1 -0.009 0.035 -9999 0 -0.26 6 6
VAV2 0.034 0.096 -9999 0 -0.52 24 24
RAP1/GDP -0.01 0.057 -9999 0 -10000 0 0
adherens junction assembly -0.017 0.096 -9999 0 -0.56 25 25
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.016 0.08 -9999 0 -0.45 27 27
E-cadherin/beta catenin -0.015 0.085 -9999 0 -0.51 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.017 0.098 -9999 0 -0.59 24 24
PIK3CA 0 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.011 0.054 -9999 0 -0.37 4 4
E-cadherin/beta catenin/alpha catenin -0.016 0.093 -9999 0 -0.56 24 24
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.018 0.1 -9999 0 -0.63 24 24
IL2 signaling events mediated by PI3K

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
BCL2L1 0.049 0.051 -10000 0 -10000 0 0
UGCG 0 0.027 -10000 0 -0.64 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.058 0.082 -10000 0 -0.38 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.024 0.03 -10000 0 -0.63 1 1
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.022 0.08 -10000 0 -0.36 26 26
FRAP1 0.058 0.12 -10000 0 -0.38 47 47
FOXO3 0.065 0.099 -10000 0 -0.55 5 5
AKT1 0.06 0.1 -10000 0 -0.41 24 24
GAB2 -0.003 0.027 -10000 0 -0.28 8 8
SMPD1 -0.001 0.013 -10000 0 -10000 0 0
SGMS1 -0.001 0.013 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.008 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.039 0.056 -10000 0 -0.25 21 21
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0 0.006 -10000 0 -10000 0 0
RPS6KB1 0.022 0.03 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 20 20
JAK3 0.008 0.034 -10000 0 -10000 0 0
PIK3R1 0.013 0.004 -10000 0 -10000 0 0
JAK1 0.013 0.004 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.048 0.18 -10000 0 -1 22 22
MYB 0.014 0.18 -10000 0 -1.3 14 14
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.057 0.08 -10000 0 -0.6 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.02 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.057 0.079 -10000 0 -0.58 4 4
Rac1/GDP 0 0.004 -10000 0 -10000 0 0
T cell proliferation 0.062 0.076 -10000 0 -0.5 5 5
SHC1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.009 -10000 0 -0.067 14 14
PRKCZ 0.062 0.078 -10000 0 -0.52 5 5
NF kappa B1 p50/RelA -0.021 0.078 -10000 0 -0.44 7 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.007 0.043 -10000 0 -0.54 2 2
HSP90AA1 0 0.01 -10000 0 -0.28 1 1
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.028 0.11 -10000 0 -0.36 66 66
IL2RB 0.001 0.057 -10000 0 -10000 0 0
TERT -0.034 0.091 -10000 0 -0.28 103 103
E2F1 0.025 0.061 -10000 0 -0.43 14 14
SOS1 0 0 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.004 0.03 14 -10000 0 14
PTPN11 0 0 -10000 0 -10000 0 0
IL2RG -0.003 0.085 -10000 0 -0.84 5 5
actin cytoskeleton organization 0.062 0.076 -10000 0 -0.5 5 5
GRB2 0 0.01 -10000 0 -10000 0 0
IL2 0.005 0.03 -10000 0 -10000 0 0
PIK3CA 0.013 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.03 0.009 -10000 0 -10000 0 0
LCK -0.006 0.11 -10000 0 -0.46 34 34
BCL2 0.046 0.18 -10000 0 -0.9 26 26
S1P3 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
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.029 0.096 -9999 0 -0.37 50 50
GNAO1 -0.033 0.14 -9999 0 -0.84 21 21
S1P/S1P3/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.01 0.046 -9999 0 -0.68 2 2
AKT3 0.018 0.17 -9999 0 -1.4 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
GNAI2 0.001 0.003 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.002 0.029 -9999 0 -0.28 9 9
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.1 -9999 0 -0.39 31 31
MAPK3 0.018 0.1 -9999 0 -0.53 9 9
MAPK1 0.018 0.1 -9999 0 -0.53 9 9
JAK2 0.02 0.1 -9999 0 -0.48 12 12
CXCR4 0.014 0.1 -9999 0 -0.48 14 14
FLT1 0.012 0.03 -9999 0 -0.85 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.018 0.1 -9999 0 -0.53 9 9
S1P/S1P3/Gi 0.01 0.11 -9999 0 -0.4 30 30
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.084 -9999 0 -0.51 9 9
VEGFA 0.01 0.03 -9999 0 -0.28 9 9
S1P/S1P2/Gi -0.027 0.089 -9999 0 -0.38 30 30
VEGFR1 homodimer/VEGFA homodimer 0.02 0.031 -9999 0 -0.67 1 1
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.005 0.037 -9999 0 -0.35 9 9
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.013 0.082 -9999 0 -0.4 27 27
GNA15 -0.002 0.035 -9999 0 -0.39 5 5
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.024 0.084 -9999 0 -0.51 9 9
IL1-mediated signaling events

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
UBC13/UEV1A 0 0.009 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.034 -10000 0 -0.28 9 9
IRAK/TOLLIP -0.001 0.008 -10000 0 -10000 0 0
IKBKB -0.001 0.014 -10000 0 -0.28 2 2
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.033 0.13 -10000 0 -0.62 36 36
IL1A -0.006 0.039 -10000 0 -0.28 17 17
IL1B 0.013 0.081 -10000 0 -0.7 10 10
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.016 -10000 0 -0.43 1 1
IL1R2 -0.039 0.17 -10000 0 -0.84 33 33
IL1R1 -0.01 0.091 -10000 0 -0.84 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.057 0.24 23 -0.33 9 32
TOLLIP 0 0.01 -10000 0 -0.28 1 1
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.005 -10000 0 -10000 0 0
JUN 0.032 0.081 -10000 0 -0.41 26 26
MAP3K7 0 0.01 -10000 0 -0.28 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.012 0.08 -10000 0 -0.5 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.008 0.057 -10000 0 -0.51 10 10
PIK3R1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.053 -10000 0 -0.48 10 10
IL1 beta fragment/IL1R1/IL1RAP -0.013 0.089 -10000 0 -0.56 19 19
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.03 0.067 -10000 0 -0.42 18 18
IRAK1 0.021 0.012 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.015 0.082 -10000 0 -0.64 12 12
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.01 -10000 0 -0.28 1 1
TRAF6 0 0 -10000 0 -10000 0 0
PI3K 0 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.05 -10000 0 -0.37 10 10
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.013 0.089 -10000 0 -0.56 19 19
IL1 beta/IL1R2 -0.033 0.13 -10000 0 -0.58 42 42
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.01 0.07 -10000 0 -1.1 1 1
IRAK3 -0.025 0.14 -10000 0 -0.82 26 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.012 0.079 -10000 0 -0.5 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.037 -10000 0 -0.34 10 10
IL1 alpha/IL1R1/IL1RAP -0.009 0.063 -10000 0 -0.56 10 10
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 -0.001 0.014 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0.006 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.009 0.063 -10000 0 -0.98 1 1
CASP1 -0.002 0.041 -10000 0 -0.84 2 2
IL1RN/IL1R2 -0.037 0.13 -10000 0 -0.63 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.012 0.084 -10000 0 -0.52 19 19
TMEM189-UBE2V1 -0.001 0.014 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.004 0.042 -10000 0 -0.38 10 10
PIK3CA 0 0.01 -10000 0 -10000 0 0
IL1RN -0.012 0.065 -10000 0 -0.84 2 2
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.01 0.065 -10000 0 -0.45 18 18
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.048 0.025 -10000 0 -0.36 1 1
NFATC2 0.023 0.052 -10000 0 -0.26 4 4
NFATC3 -0.001 0.018 -10000 0 -0.53 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.096 -10000 0 -0.4 27 27
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.017 0.075 -10000 0 -0.53 10 10
BCL2/BAX -0.018 0.11 -10000 0 -0.64 24 24
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.019 0.082 -10000 0 -0.56 11 11
Calcineurin A alpha-beta B1/BCL2 -0.024 0.14 -10000 0 -0.84 24 24
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.019 0.081 0.55 11 -10000 0 11
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.034 0.091 -10000 0 -0.28 102 102
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.016 0.11 -10000 0 -0.62 21 21
MAP3K8 -0.005 0.065 -10000 0 -0.74 6 6
NFAT4/CK1 alpha 0 0.012 -10000 0 -0.35 1 1
MEF2D/NFAT1/Cbp/p300 -0.036 0.097 -10000 0 -0.48 3 3
CABIN1 0.012 0.097 -10000 0 -0.4 27 27
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.011 0.053 -10000 0 -0.28 32 32
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.041 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0 0 -10000 0 -10000 0 0
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.01 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.018 -10000 0 -0.42 1 1
PRKCH -0.001 0.029 -10000 0 -0.84 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0 0 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -10000 0 -10000 0 0
apoptosis -0.006 0.033 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.027 -10000 0 -10000 0 0
PRKCB -0.018 0.11 -10000 0 -0.57 27 27
PRKCE -0.001 0.029 -10000 0 -0.84 1 1
JNK2/NFAT4 -0.001 0.017 -10000 0 -0.48 1 1
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0.01 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.029 -10000 0 -0.84 1 1
PRKCA -0.022 0.13 -10000 0 -0.77 24 24
PRKCG -0.011 0.055 -10000 0 -0.28 34 34
PRKCQ -0.036 0.16 -10000 0 -0.68 45 45
FKBP38/BCL2 -0.018 0.11 -10000 0 -0.64 24 24
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.047 0.031 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.005 0.027 -10000 0 -10000 0 0
NFATc/ERK1 -0.001 0.016 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.017 0.074 -10000 0 -0.53 10 10
NR4A1 -0.074 0.22 -10000 0 -0.74 79 79
GSK3B 0 0 -10000 0 -10000 0 0
positive T cell selection -0.001 0.018 -10000 0 -0.53 1 1
NFAT1/CK1 alpha -0.011 0.031 -10000 0 -0.3 1 1
RCH1/ KPNB1 -0.021 0.057 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 -0.016 0.065 -10000 0 -10000 0 0
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.017 -10000 0 -0.28 3 3
NFATc/p38 alpha 0.047 0.03 -10000 0 -10000 0 0
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.024 0.14 -10000 0 -0.84 24 24
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.033 0.14 -9999 0 -0.84 21 21
CDC42/GTP -0.025 0.08 -9999 0 -0.57 2 2
PLCG1 -0.026 0.082 -9999 0 -0.58 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.025 0.078 -9999 0 -0.55 2 2
S1PR5 -0.008 0.061 -9999 0 -0.38 17 17
S1PR4 -0.011 0.08 -9999 0 -0.84 6 6
MAPK3 -0.026 0.082 -9999 0 -0.58 2 2
MAPK1 -0.026 0.082 -9999 0 -0.5 3 3
S1P/S1P5/Gi -0.028 0.091 -9999 0 -0.38 30 30
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.038 -9999 0 -0.57 3 3
RHOA -0.005 0.043 -9999 0 -0.48 6 6
S1P/S1P4/Gi -0.029 0.089 -9999 0 -0.36 32 32
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.006 0.07 -9999 0 -0.84 6 6
S1P/S1P4/G12/G13 -0.006 0.046 -9999 0 -0.52 6 6
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.004 0.043 -10000 0 -0.51 6 6
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.015 -10000 0 -0.43 1 1
GATA1/HDAC4 -0.003 0.029 -10000 0 -0.64 1 1
GATA1/HDAC5 -0.002 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 -0.017 0.098 -10000 0 -0.64 19 19
HDAC5/BCL6/BCoR -0.002 0.033 -10000 0 -0.56 3 3
HDAC9 -0.01 0.078 -10000 0 -0.84 6 6
Glucocorticoid receptor/Hsp90/HDAC6 -0.005 0.051 -10000 0 -0.56 7 7
HDAC4/ANKRA2 -0.001 0.022 -10000 0 -0.64 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.023 0.13 -10000 0 -0.84 19 19
HDAC4/RFXANK -0.001 0.023 -10000 0 -0.64 1 1
BCOR -0.001 0.029 -10000 0 -0.84 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.005 0.054 -10000 0 -0.64 6 6
Histones -0.002 0.024 -10000 0 -10000 0 0
ADRBK1 0 0.01 -10000 0 -0.28 1 1
HDAC4 -0.001 0.029 -10000 0 -0.84 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.022 -10000 0 -0.64 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0 0.006 -10000 0 -10000 0 0
CAMK4 -0.011 0.053 -10000 0 -0.28 32 32
Tubulin/HDAC6 0 0.007 -10000 0 -10000 0 0
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 -0.003 0.03 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.007 0.076 -10000 0 -0.84 7 7
SUMO1/HDAC4 -0.001 0.016 -10000 0 -0.47 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.022 -10000 0 -0.64 1 1
Tubulin 0 0.009 -10000 0 -10000 0 0
HDAC4/14-3-3 E -0.001 0.022 -10000 0 -0.64 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR -0.002 0.038 -10000 0 -0.64 3 3
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.019 -10000 0 -0.56 1 1
HDAC4/SRF -0.006 0.032 -10000 0 -0.56 1 1
HDAC4/ER alpha -0.11 0.22 -10000 0 -0.64 118 118
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.002 0.024 -10000 0 -10000 0 0
cell motility 0 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.002 0.041 -10000 0 -0.84 2 2
HDAC4/CaMK II delta B -0.001 0.029 -10000 0 -0.84 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.15 0.29 -10000 0 -0.56 228 228
HDAC6/HDAC11 0 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.001 0.029 -10000 0 -0.84 1 1
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.023 -10000 0 -0.48 2 2
GNG2 -0.006 0.07 -10000 0 -0.84 6 6
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.014 -10000 0 -0.28 2 2
HDAC11 -0.001 0.014 -10000 0 -10000 0 0
HSP90AA1 0 0.01 -10000 0 -0.28 1 1
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK 0 0.01 -10000 0 -0.28 1 1
nuclear import 0.001 0.016 0.45 1 -10000 0 1
Sphingosine 1-phosphate (S1P) 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
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.004 0.048 -9999 0 -0.84 2 2
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.018 -9999 0 -0.37 2 2
GNAO1 -0.033 0.14 -9999 0 -0.84 21 21
mol:Sphinganine-1-P 0.019 0.037 -9999 0 -0.64 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.029 -9999 0 -0.28 9 9
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.016 -9999 0 -0.32 2 2
S1PR5 -0.008 0.061 -9999 0 -0.38 17 17
S1PR4 -0.011 0.08 -9999 0 -0.84 6 6
GNAI1 -0.043 0.18 -9999 0 -0.84 43 43
S1P/S1P5/G12 -0.004 0.036 -9999 0 -0.41 5 5
S1P/S1P3/Gq -0.003 0.032 -9999 0 -0.29 9 9
S1P/S1P4/Gi -0.027 0.086 -9999 0 -0.35 28 28
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
GNAZ -0.006 0.07 -9999 0 -0.84 6 6
GNA14 -0.013 0.082 -9999 0 -0.4 27 27
GNA15 -0.002 0.035 -9999 0 -0.39 5 5
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
ABCC1 0 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.001 0.024 -10000 0 -0.5 2 2
TRAF2/ASK1 -0.001 0.028 -10000 0 -0.57 2 2
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.029 0.036 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.053 -10000 0 -0.37 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.015 0.063 -10000 0 -0.28 45 45
TXN 0 0.003 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A 0 0 -10000 0 -10000 0 0
GADD45B 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
MAP3K6 -0.001 0.029 -10000 0 -0.84 1 1
MAP3K7 0 0.01 -10000 0 -0.28 1 1
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.002 0.038 -10000 0 -0.64 3 3
TAK1/TAB family 0 0.011 0.22 2 -10000 0 2
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.004 0.015 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.076 0.23 -10000 0 -0.84 65 65
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.05 0.15 -10000 0 -0.57 65 65
MAPK11 -0.002 0.041 -10000 0 -0.84 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.046 0.14 -10000 0 -0.52 67 67
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 -0.003 0.038 -10000 0 -0.46 6 6
TAOK2 0 0 -10000 0 -10000 0 0
TAOK3 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.002 0.041 -10000 0 -0.84 2 2
MAP3K10 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.001 0.027 -10000 0 -0.56 2 2
GADD45/MTK1/MTK1 -0.005 0.023 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.012 0.067 0.34 1 -0.35 30 31
FRAP1 0.012 0.015 -10000 0 -10000 0 0
AKT1 -0.011 0.057 0.24 1 -0.52 1 2
INSR 0 0.01 -10000 0 -0.28 1 1
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.009 0.042 -10000 0 -0.41 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.002 0.012 -10000 0 -10000 0 0
TSC2 0 0 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.036 -10000 0 -0.36 1 1
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.016 0.081 -10000 0 -0.43 31 31
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.015 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.034 -10000 0 -0.28 1 1
MAP3K5 0.009 0.023 -10000 0 -0.45 2 2
PIK3R1 0 0 -10000 0 -10000 0 0
apoptosis 0.009 0.023 -10000 0 -0.45 2 2
mol:LY294002 0 0 -10000 0 -0.002 31 31
EIF4B 0.028 0.031 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.022 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.003 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.014 0.072 -10000 0 -0.38 31 31
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.023 0.18 1 -10000 0 1
FKBP1A 0 0.01 -10000 0 -10000 0 0
RHEB/GTP -0.007 0.035 -10000 0 -0.35 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 31 31
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.011 0.06 0.26 1 -0.32 30 31
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.002 0.031 -10000 0 -0.63 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.009 0.045 -10000 0 -0.44 1 1
tumor necrosis factor receptor activity 0 0 0.002 31 -10000 0 31
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 -0.009 0.088 -10000 0 -0.46 31 31
INS 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.84 2 2
PDK2 -0.013 0.069 0.26 1 -0.34 33 34
EIF4EBP1 0.013 0.014 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -10000 0 0
PPP2R5D 0.019 0.014 -10000 0 -10000 0 0
peptide biosynthetic process 0 0.004 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -10000 0 2
EEF2 0 0.004 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.013 0.033 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.006 0.024 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.001 0.003 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.008 0.031 -9999 0 -10000 0 0
CaM/Ca2+ 0.012 0.029 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.031 -9999 0 -10000 0 0
AKT1 -0.006 0.014 -9999 0 -10000 0 0
MAP2K1 0.041 0.037 -9999 0 -10000 0 0
MAP3K11 -0.003 0.028 -9999 0 -10000 0 0
IFNGR1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.027 0.1 -9999 0 -0.42 20 20
Rap1/GTP -0.003 0.008 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.013 0.032 -9999 0 -10000 0 0
CEBPB 0.075 0.033 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.011 0.058 -9999 0 -1.3 1 1
STAT1 -0.011 0.031 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.039 0.096 -9999 0 -0.27 124 124
PIK3CA 0 0.01 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.008 0.028 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0 0.006 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.031 -9999 0 -10000 0 0
MAPK3 0.055 0.033 -9999 0 -10000 0 0
STAT1 (dimer) -0.002 0.046 -9999 0 -10000 0 0
MAPK1 0.055 0.033 -9999 0 -10000 0 0
JAK2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0 0 -9999 0 -10000 0 0
CAMK2D -0.003 0.05 -9999 0 -0.84 3 3
DAPK1 0.069 0.031 -9999 0 -10000 0 0
SMAD7 0.051 0.035 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.006 0.014 -9999 0 -10000 0 0
PI3K 0.01 0.026 -9999 0 -10000 0 0
IFNG -0.039 0.096 -9999 0 -0.27 124 124
apoptosis 0.054 0.025 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.008 0.046 -9999 0 -10000 0 0
CAMK2B -0.076 0.23 -9999 0 -0.84 65 65
FRAP1 0.043 0.033 -9999 0 -10000 0 0
PRKCD -0.006 0.014 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.008 0.031 -9999 0 -10000 0 0
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.065 0.044 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.008 0.029 -9999 0 -10000 0 0
SOCS1 0.001 0.055 -9999 0 -1.5 1 1
mol:GDP -0.006 0.014 -9999 0 -10000 0 0
CASP1 0.05 0.039 -9999 0 -0.36 2 2
PTGES2 0 0 -9999 0 -10000 0 0
IRF9 0.057 0.018 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.007 0.02 -9999 0 -10000 0 0
RAP1/GDP -0.003 0.008 -9999 0 -10000 0 0
CBL -0.009 0.021 -9999 0 -10000 0 0
MAP3K1 0.031 0.038 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.008 0.031 -9999 0 -10000 0 0
PTPN11 -0.01 0.025 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.001 0.032 -9999 0 -0.94 1 1
VEGFR1 homodimer/NRP1 -0.001 0.033 -9999 0 -0.95 1 1
mol:DAG 0.038 0.036 -9999 0 -0.68 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.033 -9999 0 -0.88 1 1
CaM/Ca2+ -0.002 0.032 -9999 0 -0.64 2 2
HIF1A 0 0.013 -9999 0 -0.39 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.03 -9999 0 -0.74 1 1
PLCG1 0.038 0.036 -9999 0 -0.68 2 2
NOS3 0.063 0.032 -9999 0 -0.58 2 2
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.062 0.031 -9999 0 -0.56 2 2
FLT1 0.028 0.037 -9999 0 -1 1 1
PGF -0.001 0.029 -9999 0 -0.84 1 1
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.047 -9999 0 -1.3 1 1
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
eNOS/Hsp90 -0.001 0.027 -9999 0 -0.67 1 1
endothelial cell proliferation 0.037 0.094 -9999 0 -0.89 3 3
mol:Ca2+ 0.038 0.036 -9999 0 -0.67 2 2
MAPK3 0.039 0.088 -9999 0 -0.48 21 21
MAPK1 0.039 0.088 -9999 0 -0.48 21 21
PIK3R1 0 0 -9999 0 -10000 0 0
PLGF homodimer -0.001 0.029 -9999 0 -0.84 1 1
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.17 0.34 -9999 0 -0.84 174 174
VEGFA homodimer -0.003 0.029 -9999 0 -0.28 9 9
VEGFR1 homodimer/VEGFA homodimer -0.002 0.035 -9999 0 -0.94 1 1
platelet activating factor biosynthetic process 0.046 0.085 -9999 0 -1.1 1 1
PI3K -0.002 0.033 -9999 0 -0.65 2 2
PRKCA 0.032 0.093 -9999 0 -0.51 22 22
PRKCB 0.035 0.081 -9999 0 -0.52 15 15
VEGFR1 homodimer/PLGF homodimer -0.002 0.038 -9999 0 -0.75 2 2
VEGFA -0.003 0.029 -9999 0 -0.28 9 9
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.036 -9999 0 -0.68 2 2
RASA1 0.039 0.031 -9999 0 -0.87 1 1
NRP2 -0.001 0.03 -9999 0 -0.56 2 2
VEGFR1 homodimer 0.028 0.037 -9999 0 -1 1 1
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.083 0.17 -9999 0 -0.93 2 2
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.032 -9999 0 -0.64 2 2
mol:L-citrulline 0.062 0.031 -9999 0 -0.56 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.031 -9999 0 -0.83 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.032 -9999 0 -0.88 1 1
CD2AP 0 0.01 -9999 0 -10000 0 0
PI3K/GAB1 -0.001 0.031 -9999 0 -0.78 1 1
PDPK1 -0.002 0.03 -9999 0 -0.76 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.032 -9999 0 -0.88 1 1
mol:NADP 0.062 0.031 -9999 0 -0.56 2 2
HSP90AA1 0 0.01 -9999 0 -0.28 1 1
ubiquitin-dependent protein catabolic process -0.002 0.03 -9999 0 -0.82 1 1
VEGFR1 homodimer/NRP2 -0.002 0.049 -9999 0 -1.4 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0 0 -9999 0 -10000 0 0
SMAD2 0.014 0 -9999 0 -10000 0 0
SMAD3 0.041 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.01 0.027 -9999 0 -10000 0 0
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
MAP3K1 0 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.002 0.031 -9999 0 -0.64 2 2
MAPK3 0 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
NUP214 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 -0.002 0.041 -9999 0 -0.84 2 2
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.01 -9999 0 -10000 0 0
KPNA2 -0.034 0.091 -9999 0 -0.28 102 102
PIAS4 0 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.007 0.055 -9999 0 -0.34 17 17
ITGA4 -0.003 0.03 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.45 6 6
alpha4/beta1 Integrin -0.002 0.019 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.003 0.03 -9999 0 -0.28 10 10
Caspase 8 (4 units) -0.007 0.045 -9999 0 -1 1 1
NEF -0.004 0.022 -9999 0 -0.22 4 4
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 -0.01 0.08 -9999 0 -0.84 7 7
CYCS 0.042 0.055 -9999 0 -0.98 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.026 0.13 -9999 0 -0.64 30 30
MAP2K7 0.043 0.046 -9999 0 -0.82 1 1
protein ubiquitination 0.066 0.033 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.002 0.041 -9999 0 -0.84 2 2
BID -0.008 0.05 -9999 0 -1.1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.034 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.002 0.041 -9999 0 -0.84 2 2
CFLAR 0 0 -9999 0 -10000 0 0
FADD -0.005 0.038 -9999 0 -0.28 16 16
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.034 -9999 0 -0.34 7 7
MAPK8 0.049 0.043 -9999 0 -0.75 1 1
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.017 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.009 0.054 -9999 0 -0.43 7 7
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.03 -9999 0 -0.39 1 1
CHUK 0.068 0.034 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.004 0.045 -9999 0 -0.67 3 3
TCRz/NEF -0.024 0.11 -9999 0 -0.55 29 29
TNF -0.016 0.098 -9999 0 -0.84 10 10
FASLG -0.003 0.13 -9999 0 -0.61 29 29
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.011 0.065 -9999 0 -0.56 10 10
CASP6 -0.003 0.03 -9999 0 -0.72 1 1
CASP7 0.074 0.075 -9999 0 -0.64 7 7
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.074 0.075 -9999 0 -0.64 7 7
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.019 -9999 0 -10000 0 0
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.037 -9999 0 -0.36 1 1
APAF-1/Caspase 9 -0.008 0.054 -9999 0 -0.54 7 7
BCL2 0.042 0.089 -9999 0 -0.43 25 25
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.012 0.083 -9999 0 -0.64 14 14
AKT1 0.085 0.044 -9999 0 -0.69 2 2
PTK2B -0.01 0.072 -9999 0 -0.98 2 2
VEGFR2 homodimer/Frs2 -0.004 0.047 -9999 0 -0.93 2 2
CAV1 -0.17 0.34 -9999 0 -0.84 174 174
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.004 0.044 -9999 0 -0.87 2 2
endothelial cell proliferation 0.086 0.071 -9999 0 -0.65 3 3
mol:Ca2+ 0.054 0.043 -9999 0 -0.78 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.001 0.041 -9999 0 -0.82 2 2
RP11-342D11.1 0.046 0.043 -9999 0 -0.78 2 2
CDH5 -0.004 0.058 -9999 0 -0.84 4 4
VEGFA homodimer -0.001 0.011 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.024 0.14 -9999 0 -0.84 24 24
HRAS/GDP -0.001 0.033 -9999 0 -0.66 2 2
SH2D2A -0.029 0.088 -9999 0 -0.28 86 86
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0 0.034 -9999 0 -0.63 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.013 0.056 -9999 0 -0.78 3 3
VEGFR1 homodimer -0.001 0.029 -9999 0 -0.84 1 1
SHC/GRB2/SOS1 -0.001 0.037 -9999 0 -0.75 2 2
GRB10 -0.003 0.039 -9999 0 -0.78 2 2
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.01 -9999 0 -10000 0 0
PAK1 -0.006 0.04 -9999 0 -0.28 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.003 0.064 -9999 0 -1.2 2 2
HRAS 0 0.01 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.005 0.04 -9999 0 -0.52 2 2
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.03 -9999 0 -0.28 10 10
oxygen and reactive oxygen species metabolic process -0.001 0.04 -9999 0 -0.81 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.041 -9999 0 -0.84 2 2
Nck/Pak -0.004 0.025 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.004 0.055 -9999 0 -1.1 2 2
mol:GDP -0.001 0.036 -9999 0 -0.72 2 2
mol:NADP 0.076 0.031 -9999 0 -0.52 2 2
eNOS/Hsp90 0.077 0.029 -9999 0 -0.49 2 2
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.003 0.039 -9999 0 -0.79 2 2
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.03 -9999 0 -0.84 1 1
VEGFA -0.003 0.028 -9999 0 -10000 0 0
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin -0.006 0.055 -9999 0 -0.9 2 2
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.008 0.078 -9999 0 -1 2 2
PTPN6 -0.001 0.014 -9999 0 -0.28 2 2
EPAS1 -0.001 0.019 -9999 0 -0.38 2 2
mol:L-citrulline 0.076 0.031 -9999 0 -0.52 2 2
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0 0.042 -9999 0 -0.82 2 2
VEGFR2 homodimer/VEGFA homodimer -0.001 0.043 -9999 0 -0.86 2 2
VEGFR2/3 heterodimer -0.003 0.061 -9999 0 -0.96 3 3
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.059 0.044 -9999 0 -0.8 2 2
VEGFR2 homodimer 0.032 0.052 -9999 0 -1 2 2
FLT1 -0.001 0.029 -9999 0 -0.84 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.055 0.064 -9999 0 -0.8 3 3
MAPK1 0.055 0.064 -9999 0 -0.8 3 3
VEGFA145/NRP2 -0.003 0.029 -9999 0 -0.64 1 1
VEGFR1/2 heterodimer -0.003 0.058 -9999 0 -1.2 2 2
KDR 0.032 0.052 -9999 0 -1 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.001 0.051 -9999 0 -1 2 2
SRC 0 0.01 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.057 0.064 -9999 0 -1 2 2
PI3K -0.003 0.049 -9999 0 -0.91 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.003 0.043 -9999 0 -0.87 2 2
FES -0.004 0.048 -9999 0 -0.81 2 2
GAB1 -0.002 0.047 -9999 0 -0.95 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.043 -9999 0 -0.87 2 2
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.009 0.17 -9999 0 -0.55 5 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.004 0.046 -9999 0 -0.74 3 3
PI3K/GAB1 -0.002 0.038 -9999 0 -0.71 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.002 0.043 -9999 0 -0.79 2 2
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.057 -9999 0 -0.9 3 3
HSP90AA1 0 0.01 -9999 0 -0.28 1 1
CDC42 -0.003 0.04 -9999 0 -0.81 2 2
actin cytoskeleton reorganization -0.013 0.056 -9999 0 -0.77 3 3
PTK2 0.061 0.07 -9999 0 -1 2 2
EDG1 0.046 0.043 -9999 0 -0.78 2 2
mol:DAG -0.003 0.039 -9999 0 -0.79 2 2
CaM/Ca2+ -0.002 0.036 -9999 0 -0.72 2 2
MAP2K3 0.062 0.042 -9999 0 -0.76 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.001 0.041 -9999 0 -0.82 2 2
PLCG1 -0.003 0.04 -9999 0 -0.81 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.001 0.044 -9999 0 -0.82 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.029 -9999 0 -0.84 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.003 0.043 -9999 0 -0.87 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.003 0.044 -9999 0 -0.87 2 2
cell migration 0.086 0.059 -9999 0 -0.79 2 2
mol:PI-3-4-5-P3 -0.002 0.043 -9999 0 -0.8 2 2
FYN -0.001 0.029 -9999 0 -0.84 1 1
VEGFB/NRP1 -0.002 0.037 -9999 0 -0.74 2 2
mol:NO 0.076 0.031 -9999 0 -0.52 2 2
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.033 -9999 0 -0.66 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.001 0.041 -9999 0 -0.82 2 2
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.015 0.11 -9999 0 -0.84 14 14
NOS3 0.078 0.035 -9999 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/Sck -0.017 0.093 -9999 0 -0.52 26 26
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.049 0.092 -9999 0 -0.95 2 2
PRKCB 0.051 0.087 -9999 0 -1.2 2 2
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.001 0.04 -9999 0 -0.79 2 2
VEGFR1/2 heterodimer/VEGFA homodimer -0.004 0.055 -9999 0 -1.1 2 2
VEGFA165/NRP2 -0.003 0.029 -9999 0 -0.64 1 1
MAPKKK cascade 0 0.034 -9999 0 -0.66 2 2
NRP2 -0.001 0.03 -9999 0 -0.56 2 2
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.006 0.055 -9999 0 -0.9 2 2
MAP3K13 -0.003 0.04 -9999 0 -0.81 2 2
PDPK1 0.078 0.043 -9999 0 -0.68 2 2
Class I PI3K signaling events

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
ARF5/GTP 0 0.021 0.3 2 -10000 0 2
DAPP1 0.036 0.051 -10000 0 -0.54 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.047 0.079 -10000 0 -0.54 8 8
mol:DAG 0.054 0.049 0.21 1 -0.27 5 6
HRAS 0 0.009 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.001 0.016 -10000 0 -10000 0 0
PLCG2 -0.001 0.03 -10000 0 -0.56 2 2
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.01 -10000 0 -10000 0 0
mol:GTP 0 0.02 -10000 0 -0.42 1 1
ARF1/GTP 0 0.02 0.28 2 -10000 0 2
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.029 -10000 0 -0.84 1 1
RAP1A/GTP 0 0.02 -10000 0 -0.42 1 1
ADAP1 -0.002 0.033 -10000 0 -0.44 3 3
ARAP3 0 0.02 0.27 2 -0.42 1 3
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.052 -10000 0 -10000 0 0
ARHGEF6 -0.005 0.064 -10000 0 -0.84 5 5
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -10000 0 0
FYN -0.001 0.029 -10000 0 -0.84 1 1
ARF6 0 0 -10000 0 -10000 0 0
FGR 0 0.01 -10000 0 -0.28 1 1
mol:Ca2+ 0.04 0.028 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.019 -10000 0 -0.28 4 4
ZAP70 -0.027 0.13 -10000 0 -0.51 44 44
mol:IP3 0.049 0.037 -10000 0 -10000 0 0
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.015 -10000 0 -10000 0 0
RhoA/GDP 0 0.019 0.28 2 -10000 0 2
PDK1/Src/Hsp90 0 0.007 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.064 0.024 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -10000 0 0
PLEKHA2 0.03 0.006 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.002 0.04 -10000 0 -0.82 2 2
HSP90AA1 0 0.01 -10000 0 -0.28 1 1
ARF6/GTP 0 0.02 0.3 2 -10000 0 2
RhoA/GTP 0 0.019 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.01 0.057 -10000 0 -0.55 4 4
BLK -0.036 0.1 -10000 0 -0.3 102 102
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 0 0.019 -10000 0 -10000 0 0
HCK -0.004 0.033 -10000 0 -10000 0 0
CYTH3 0 0.019 -10000 0 -10000 0 0
CYTH2 0 0.019 -10000 0 -10000 0 0
KRAS 0 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.003 0.049 -10000 0 -0.56 6 6
SGK1 -0.003 0.05 0.24 2 -0.69 4 6
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.036 0.021 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.01 -10000 0 -10000 0 0
ARF6/GDP 0 0.02 0.29 2 -10000 0 2
mol:PI-3-4-5-P3 0 0.024 0.37 2 -0.42 1 3
ARAP3/RAP1A/GTP 0 0.02 -10000 0 -0.42 1 1
VAV1 -0.002 0.032 -10000 0 -0.46 3 3
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.016 -10000 0 -0.42 1 1
PLEKHA1 0.029 0.021 -10000 0 -0.56 1 1
Rac1/GDP -0.001 0.015 -10000 0 -10000 0 0
LAT -0.004 0.048 -10000 0 -0.84 2 2
Rac1/GTP -0.002 0.028 -10000 0 -0.34 5 5
ITK -0.017 0.08 -10000 0 -0.46 24 24
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.061 0.063 0.24 1 -0.38 5 6
LCK -0.019 0.1 -10000 0 -0.46 34 34
BTK 0 0.02 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.001 0.019 -9999 0 -10000 0 0
CLOCK 0 0.001 -9999 0 -10000 0 0
TIMELESS/CRY2 -0.001 0.008 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.01 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.042 0.011 -9999 0 -10000 0 0
ARNTL 0 0.001 -9999 0 -10000 0 0
TIMELESS 0.041 0.014 -9999 0 -10000 0 0
NPAS2 -0.005 0.06 -9999 0 -0.59 7 7
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.013 0.003 -9999 0 -10000 0 0
CHEK1 -0.008 0.046 -9999 0 -0.28 24 24
mol:HEME 0.013 0.003 -9999 0 -10000 0 0
PER1 -0.018 0.12 -9999 0 -0.84 18 18
BMAL/CLOCK/NPAS2 -0.003 0.038 -9999 0 -0.55 4 4
BMAL1/CLOCK 0.046 0.026 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.001 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.001 0.019 -9999 0 -10000 0 0
mol:NADPH 0.013 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.011 0.071 -9999 0 -0.49 18 18
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.001 0.017 -9999 0 -0.28 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.001 0.014 -10000 0 -10000 0 0
oxygen homeostasis 0.013 0.012 -10000 0 -10000 0 0
TCEB2 -0.001 0.019 -10000 0 -0.28 4 4
TCEB1 -0.001 0.017 -10000 0 -0.28 3 3
VHL/Elongin B/Elongin C/HIF2A -0.003 0.023 -10000 0 -10000 0 0
EPO 0.16 0.14 -10000 0 -10000 0 0
FIH (dimer) 0.023 0.011 -10000 0 -10000 0 0
APEX1 0.022 0.009 -10000 0 -10000 0 0
SERPINE1 0.17 0.14 -10000 0 -0.59 1 1
FLT1 -0.001 0.073 -10000 0 -1.4 2 2
ADORA2A 0.15 0.14 -10000 0 -0.55 2 2
germ cell development 0.17 0.13 -10000 0 -0.66 1 1
SLC11A2 0.17 0.13 -10000 0 -0.59 1 1
BHLHE40 0.17 0.14 -10000 0 -0.98 2 2
HIF1AN 0.023 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.02 0.064 -10000 0 -0.39 1 1
ETS1 0.024 0.044 -10000 0 -0.87 2 2
CITED2 0.001 0.009 -10000 0 -10000 0 0
KDR -0.002 0.086 -10000 0 -1.7 2 2
PGK1 0.17 0.13 -10000 0 -0.59 1 1
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.17 0.15 -10000 0 -0.57 4 4
EPAS1 0.1 0.072 -10000 0 -0.41 1 1
SP1 0.018 0.002 -10000 0 -10000 0 0
ABCG2 0.14 0.23 -10000 0 -0.71 50 50
EFNA1 0.17 0.13 -10000 0 -0.59 1 1
FXN 0.16 0.13 -10000 0 -0.57 1 1
POU5F1 0.17 0.14 -10000 0 -0.69 1 1
neuron apoptosis -0.056 0.13 0.56 4 -10000 0 4
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.08 -10000 0 -0.28 39 39
EGLN2 0.022 0.02 -10000 0 -0.26 3 3
EGLN1 0.022 0.032 -10000 0 -0.85 1 1
VHL/Elongin B/Elongin C -0.001 0.012 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.023 0.009 -10000 0 -10000 0 0
SLC2A1 0.16 0.14 -10000 0 -0.55 2 2
TWIST1 0.15 0.19 -10000 0 -0.7 25 25
ELK1 0.018 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.012 0.056 -10000 0 -10000 0 0
VEGFA 0.17 0.14 -10000 0 -0.59 1 1
CREBBP 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.005 0.057 -9999 0 -0.52 10 10
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.046 -9999 0 -0.42 10 10
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.001 0.014 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.023 -9999 0 -10000 0 0
YY1/LSF 0 0 -9999 0 -10000 0 0
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.041 -9999 0 -0.38 10 10
I kappa B alpha/HDAC1 -0.004 0.028 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.004 0.035 -9999 0 -0.33 10 10
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.028 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.032 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.023 0.13 -9999 0 -0.84 19 19
GATA1 -0.003 0.03 -9999 0 -10000 0 0
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.003 -9999 0 -10000 0 0
RBBP7 -0.003 0.027 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.032 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.001 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.017 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.029 -9999 0 -0.84 1 1
YY1/HDAC3 -0.003 0.024 -9999 0 -10000 0 0
YY1/HDAC2 0 0 -9999 0 -10000 0 0
YY1/HDAC1 0 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0.001 -9999 0 -10000 0 0
PPARG -0.095 0.17 -9999 0 -0.39 204 204
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.028 -9999 0 -10000 0 0
MBD3L2 -0.001 0.014 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.002 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.032 -9999 0 -0.29 10 10
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0 0 -9999 0 -10000 0 0
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 0 0 -9999 0 -10000 0 0
MXD1 0 0.01 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0 0.006 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.032 -9999 0 -10000 0 0
histone deacetylation 0.046 0.003 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.025 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.017 0.081 -9999 0 -0.51 19 19
GATA1/HDAC1 -0.002 0.019 -9999 0 -10000 0 0
GATA1/HDAC3 -0.005 0.031 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.011 0.074 -9999 0 -0.64 10 10
SIN3/HDAC complex/Mad/Max 0 0.002 -9999 0 -10000 0 0
NuRD Complex 0 0.002 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.023 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.011 -9999 0 -10000 0 0
GATA1/Fog1 -0.003 0.021 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.016 0.098 -9999 0 -0.84 10 10
negative regulation of cell growth 0.045 0.004 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.001 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.049 -9999 0 -0.45 10 10
SIN3/HDAC complex/NCoR1 0 0.007 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0 -9999 0 -10000 0 0
MBD2 0 0 -9999 0 -10000 0 0
FoxO family 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
G6PC 0.03 0.033 -9999 0 -10000 0 0
PLK1 0.011 0.11 -9999 0 -0.6 1 1
CDKN1B 0.082 0.067 -9999 0 -0.55 3 3
FOXO3 0.043 0.096 -9999 0 -0.49 6 6
KAT2B 0.008 0.012 -9999 0 -10000 0 0
FOXO1/SIRT1 0.008 0.035 -9999 0 -0.34 6 6
CAT 0.046 0.11 -9999 0 -1.1 3 3
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.014 0.011 -9999 0 -10000 0 0
FOXO1 0.033 0.035 -9999 0 -0.37 6 6
MAPK10 -0.048 0.19 -9999 0 -0.48 137 137
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.062 0.088 -9999 0 -10000 0 0
response to oxidative stress 0.005 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.013 0.059 -9999 0 -0.48 5 5
XPO1 0 0 -9999 0 -10000 0 0
EP300 0.002 0.005 -9999 0 -10000 0 0
BCL2L11 0.029 0.018 -9999 0 -10000 0 0
FOXO1/SKP2 -0.002 0.028 -9999 0 -0.34 5 5
mol:GDP 0.005 0.011 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
GADD45A 0.068 0.058 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.068 0.029 -9999 0 -10000 0 0
MST1 -0.004 0.098 -9999 0 -0.84 11 11
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.001 0.044 -9999 0 -0.36 4 4
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.037 0.006 -9999 0 -10000 0 0
MAPK9 0.036 0.005 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ -0.001 0.017 -9999 0 -0.28 3 3
SIRT1 0.002 0.007 -9999 0 -10000 0 0
SOD2 0.092 0.069 -9999 0 -10000 0 0
RBL2 0.062 0.072 -9999 0 -10000 0 0
RAL/GDP 0.01 0.015 -9999 0 -10000 0 0
CHUK 0.008 0.012 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.029 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.013 0.14 -9999 0 -1.5 6 6
SKP2 0 0 -9999 0 -10000 0 0
USP7 0 0 -9999 0 -10000 0 0
IKBKB 0.007 0.018 -9999 0 -0.26 2 2
CCNB1 0.035 0.1 -9999 0 -0.6 1 1
FOXO1-3a-4/beta catenin -0.007 0.032 -9999 0 -0.41 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.028 -9999 0 -0.34 5 5
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.004 0.06 -9999 0 -0.84 4 4
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.067 0.078 -9999 0 -10000 0 0
SFN -0.016 0.11 -9999 0 -0.62 21 21
CDK2 0.002 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.051 -9999 0 -10000 0 0
CREBBP 0.002 0.005 -9999 0 -10000 0 0
FBXO32 0.045 0.12 -9999 0 -1.4 3 3
BCL6 0.059 0.095 -9999 0 -1.2 2 2
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.004 0.041 -9999 0 -0.55 4 4
PDGFB-D/PDGFRB/SLAP -0.003 0.036 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/APS/CBL -0.006 0.037 -9999 0 -0.55 2 2
AKT1 -0.007 0.031 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.004 0.042 -9999 0 -0.57 4 4
PIK3CA 0 0.01 -9999 0 -10000 0 0
FGR -0.003 0.029 -9999 0 -0.53 2 2
mol:Ca2+ 0.033 0.04 -9999 0 -0.68 2 2
MYC 0.038 0.14 -9999 0 -0.83 22 22
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.024 -9999 0 -0.45 2 2
LRP1/PDGFRB/PDGFB -0.007 0.072 -9999 0 -0.67 9 9
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.041 -9999 0 -0.69 2 2
PTEN -0.002 0.041 -9999 0 -0.84 2 2
GRB2 0 0.01 -9999 0 -10000 0 0
GRB7 -0.021 0.077 -9999 0 -0.29 62 62
PDGFB-D/PDGFRB/SHP2 -0.002 0.031 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/GRB10 -0.002 0.031 -9999 0 -0.64 2 2
cell cycle arrest -0.003 0.036 -9999 0 -0.64 2 2
HRAS 0 0.01 -9999 0 -10000 0 0
HIF1A 0.055 0.043 -9999 0 -10000 0 0
GAB1 0.036 0.048 -9999 0 -0.66 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.04 0.047 -9999 0 -0.61 2 2
PDGFB-D/PDGFRB -0.003 0.032 -9999 0 -0.56 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.031 -9999 0 -0.64 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.006 0.046 -9999 0 -0.57 4 4
positive regulation of MAPKKK cascade -0.002 0.031 -9999 0 -0.64 2 2
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0.033 0.041 -9999 0 -0.7 2 2
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.015 0.059 -9999 0 -0.64 3 3
SHB -0.001 0.03 -9999 0 -0.84 1 1
BLK -0.002 0.052 -9999 0 -0.63 5 5
PTPN2 0 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.031 -9999 0 -0.64 2 2
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.057 -9999 0 -0.56 3 3
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.031 -9999 0 -0.64 2 2
LCK -0.01 0.076 -9999 0 -0.61 13 13
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.002 0.029 -9999 0 -0.53 2 2
ABL1 0.034 0.042 -9999 0 -0.62 2 2
PDGFB-D/PDGFRB/CBL 0.035 0.051 -9999 0 -0.76 2 2
PTPN1 -0.003 0.031 -9999 0 -0.28 11 11
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.006 0.04 -9999 0 -10000 0 0
cell proliferation 0.039 0.13 -9999 0 -0.72 22 22
SLA -0.003 0.027 -9999 0 -0.28 8 8
actin cytoskeleton reorganization -0.002 0.027 -9999 0 -10000 0 0
SRC -0.002 0.028 -9999 0 -0.53 2 2
PI3K -0.009 0.035 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.012 0.048 -9999 0 -0.56 3 3
SH2B2 -0.01 0.052 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.004 0.043 -9999 0 -0.6 4 4
LYN -0.002 0.029 -9999 0 -0.53 2 2
LRP1 -0.009 0.086 -9999 0 -0.84 9 9
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.003 0.05 -9999 0 -0.84 3 3
STAT5A -0.007 0.076 -9999 0 -0.84 7 7
NCK1-2/p130 Cas -0.002 0.024 -9999 0 -0.45 2 2
SPHK1 -0.004 0.048 -9999 0 -0.84 2 2
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.033 0.041 -9999 0 -0.7 2 2
PLCG1 0.034 0.042 -9999 0 -0.72 2 2
NHERF/PDGFRB -0.014 0.048 -9999 0 -0.55 2 2
YES1 -0.003 0.035 -9999 0 -0.56 3 3
cell migration -0.014 0.047 -9999 0 -0.55 2 2
SHC/Grb2/SOS1 -0.002 0.024 -9999 0 -0.45 2 2
SLC9A3R2 0 0 -9999 0 -10000 0 0
SLC9A3R1 -0.027 0.082 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.013 0.047 -9999 0 -0.51 4 4
FYN -0.003 0.05 -9999 0 -0.92 2 2
DOK1 -0.001 0.028 -9999 0 -0.51 2 2
HRAS/GTP 0 0.006 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.046 0.081 -9999 0 -0.43 22 22
PRKCD 0.002 0.031 -9999 0 -0.51 2 2
FER -0.001 0.053 -9999 0 -0.52 8 8
MAPKKK cascade -0.002 0.023 -9999 0 -0.44 2 2
RASA1 0.002 0.031 -9999 0 -0.51 2 2
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.025 -9999 0 -0.47 2 2
PDGFB-D/PDGFRB/SHB -0.003 0.039 -9999 0 -0.64 3 3
chemotaxis 0.034 0.041 -9999 0 -0.6 2 2
STAT1-3-5/STAT1-3-5 -0.009 0.057 -9999 0 -0.67 2 2
Bovine Papilomavirus E5/PDGFRB -0.002 0.032 -9999 0 -0.65 2 2
PTPRJ 0 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.029 0.041 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.025 0.33 5 -10000 0 5
myoblast fusion 0.007 0.025 -10000 0 -10000 0 0
mol:GTP -0.005 0.014 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.028 -10000 0 -10000 0 0
ARF1/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GM1 0.006 0.013 -10000 0 -10000 0 0
mol:Choline 0.022 0.045 -10000 0 -0.55 5 5
lamellipodium assembly -0.004 0.03 -10000 0 -10000 0 0
MAPK3 0.02 0.023 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.008 0.028 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.007 0.025 -10000 0 -10000 0 0
ARF1/GDP -0.005 0.02 -10000 0 -10000 0 0
ARF6 0.007 0.007 -10000 0 -10000 0 0
RAB11A -0.001 0.014 -10000 0 -0.28 2 2
TIAM1 -0.001 0.019 -10000 0 -0.28 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.023 -10000 0 -10000 0 0
actin filament bundle formation 0.005 0.02 -10000 0 -10000 0 0
KALRN -0.01 0.067 -10000 0 -0.51 14 14
RAB11FIP3/RAB11A 0 0.009 -10000 0 -10000 0 0
RhoA/GDP -0.005 0.02 -10000 0 -10000 0 0
NME1 -0.013 0.059 -10000 0 -0.28 41 41
Rac1/GDP -0.005 0.02 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.014 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.004 0.03 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.005 0.014 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.007 -10000 0 -10000 0 0
mol:GDP -0.005 0.027 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.013 0.05 -10000 0 -0.62 5 5
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.03 -10000 0 -10000 0 0
ruffle organization -0.003 0.025 -10000 0 -0.33 5 5
regulation of epithelial cell migration -0.005 0.014 -10000 0 -10000 0 0
PLD2 0.016 0.013 -10000 0 -10000 0 0
PIP5K1A -0.003 0.025 -10000 0 -0.33 5 5
mol:Phosphatidic acid 0.022 0.045 -10000 0 -0.55 5 5
Rac1/GTP -0.004 0.03 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.06 0.071 -9999 0 -10000 0 0
CRKL 0.029 0.046 -9999 0 -10000 0 0
mol:DAG 0 0.024 -9999 0 -10000 0 0
HRAS -0.005 0.015 -9999 0 -10000 0 0
MAPK8 0.014 0.05 -9999 0 -10000 0 0
RAP1A 0.029 0.046 -9999 0 -10000 0 0
GAB1 0.029 0.046 -9999 0 -10000 0 0
MAPK14 0.014 0.05 -9999 0 -10000 0 0
EPO -0.037 0.11 -9999 0 -0.3 9 9
PLCG1 0 0.024 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.012 0.004 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.024 0.067 -9999 0 -0.68 5 5
GAB1/SHC/GRB2/SOS1 -0.006 0.017 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.029 0.063 -9999 0 -10000 0 0
IRS2 0.006 0.12 -9999 0 -0.5 38 38
STAT1 0.05 0.051 -9999 0 -10000 0 0
STAT5B -0.003 0.043 -9999 0 -0.46 3 3
cell proliferation 0.024 0.047 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.005 0.014 -9999 0 -10000 0 0
TEC 0.027 0.052 -9999 0 -0.5 2 2
SOCS3 -0.005 0.064 -9999 0 -0.84 5 5
STAT1 (dimer) 0.05 0.051 -9999 0 -10000 0 0
JAK2 0.001 0.002 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.055 0.038 -9999 0 -10000 0 0
EPO/EPOR -0.029 0.063 -9999 0 -10000 0 0
LYN 0.002 0.005 -9999 0 -10000 0 0
TEC/VAV2 -0.011 0.033 -9999 0 -0.47 2 2
elevation of cytosolic calcium ion concentration 0.012 0.004 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.017 0.047 -9999 0 -10000 0 0
mol:IP3 0 0.024 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.027 0.095 -9999 0 -0.52 16 16
SH2B3 0.001 0.002 -9999 0 -10000 0 0
NFKB1 0.014 0.05 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.009 0.029 -9999 0 -0.32 5 5
PTPN6 0.021 0.047 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.009 0.03 -9999 0 -0.5 1 1
EPOR 0.012 0.004 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.006 0.018 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.001 0.03 -9999 0 -0.56 2 2
CRKL/CBL/C3G -0.008 0.02 -9999 0 -10000 0 0
VAV2 0.028 0.046 -9999 0 -10000 0 0
CBL 0.029 0.046 -9999 0 -10000 0 0
SHC/Grb2/SOS1 0.006 0.026 -9999 0 -10000 0 0
STAT5A -0.005 0.057 -9999 0 -0.5 7 7
GRB2 0 0.01 -9999 0 -10000 0 0
STAT5 (dimer) 0.058 0.085 -9999 0 -0.63 3 3
LYN/PLCgamma2 -0.001 0.023 -9999 0 -0.64 1 1
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.028 0.047 -9999 0 -10000 0 0
BCL2 0.041 0.18 -9999 0 -1 24 24
ceramide signaling pathway

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
MAP4K4 0.045 0.045 -10000 0 -10000 0 0
BAG4 -0.003 0.03 -10000 0 -0.28 10 10
BAD 0.032 0.017 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.082 -10000 0 -0.84 7 7
BAX 0.032 0.017 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.012 -10000 0 -0.09 1 1
IKBKB 0.051 0.043 -10000 0 -10000 0 0
MAP2K2 0.044 0.026 -10000 0 -0.49 1 1
MAP2K1 0.044 0.026 -10000 0 -0.49 1 1
SMPD1 0.021 0.012 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.049 0.049 -10000 0 -0.42 2 2
MAP2K4 0.038 0.023 -10000 0 -0.42 1 1
protein ubiquitination 0.053 0.044 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.049 0.028 -10000 0 -0.52 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.039 0.026 -10000 0 -0.53 1 1
CRADD 0 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.018 -10000 0 -0.13 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.032 0.017 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.046 0.025 -10000 0 -0.48 1 1
MAPK1 0.046 0.025 -10000 0 -0.48 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.043 0.05 -10000 0 -0.44 2 2
KSR1 0.032 0.027 -10000 0 -0.56 1 1
MAPK8 0.044 0.022 -10000 0 -0.38 1 1
TRAF2 0 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.052 0.043 -10000 0 -10000 0 0
TNF R/SODD -0.002 0.019 -10000 0 -10000 0 0
TNF -0.016 0.098 -10000 0 -0.84 10 10
CYCS 0.037 0.024 0.15 22 -10000 0 22
IKBKG 0.052 0.043 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.038 0.047 -10000 0 -0.34 7 7
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.024 0.15 22 -10000 0 22
TNF/TNF R/SODD -0.011 0.064 -10000 0 -0.56 10 10
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.027 0.013 -10000 0 -10000 0 0
NSMAF 0.045 0.045 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.024 0.14 -10000 0 -0.84 24 24
Atypical NF-kappaB pathway

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
BCL3/RelA 0 0.006 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.02 -9999 0 -0.56 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.026 -9999 0 -10000 0 0
NFKBIA 0.024 0.036 -9999 0 -0.28 11 11
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0.007 -9999 0 -10000 0 0
ARRB2 0 0 -9999 0 -10000 0 0
REL -0.001 0.029 -9999 0 -0.84 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0 0.008 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0 0.009 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0.022 0.01 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.004 0.031 -9999 0 -0.28 11 11
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.025 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -10000 0 0
PI3K 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.032 -9999 0 -0.28 11 11
IKBKB -0.001 0.014 -9999 0 -0.28 2 2
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.01 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 -0.004 0.029 -9999 0 -10000 0 0
cell death -0.003 0.024 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.001 0.02 -9999 0 -0.56 1 1
LCK -0.019 0.1 -9999 0 -0.46 34 34
BCL3 0 0.01 -9999 0 -0.28 1 1
Canonical NF-kappaB 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
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.076 0.036 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.006 0.033 -9999 0 -0.35 1 1
NFKBIA 0.047 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.014 -9999 0 -0.28 2 2
RIPK2 -0.001 0.019 -9999 0 -0.28 4 4
IKBKG 0 0.001 -9999 0 -10000 0 0
IKK complex/A20 -0.003 0.046 -9999 0 -10000 0 0
NEMO/A20/RIP2 -0.001 0.019 -9999 0 -0.28 4 4
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.002 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.004 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.008 0.046 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.011 0.074 -9999 0 -0.64 10 10
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.022 0.13 -9999 0 -0.77 24 24
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.016 0.098 -9999 0 -0.84 10 10
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex 0.001 0.005 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.01 0.063 -9999 0 -0.4 21 21
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.003 0.026 -9999 0 -0.43 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.03 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 -0.009 0.042 -9999 0 -0.45 4 4
EPO -0.048 0.1 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.019 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.03 0.066 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
PI3K 0 0.006 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.009 0.018 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
MADCAM1 -0.01 0.052 -9999 0 -10000 0 0
cell adhesion -0.009 0.042 -9999 0 -0.44 4 4
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.006 0.045 -9999 0 -0.51 6 6
ITGB7 -0.007 0.055 -9999 0 -0.34 17 17
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.007 0.05 -9999 0 -0.56 6 6
p130Cas/Crk/Dock1 -0.004 0.036 -9999 0 -10000 0 0
VCAM1 -0.008 0.074 -9999 0 -0.56 12 12
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.035 0.047 -9999 0 -0.47 6 6
EPOR 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.019 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.006 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.03 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.007 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.015 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.034 -9999 0 -0.51 2 2
lamellipodium assembly 0.001 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
PI3K 0 0.006 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.022 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.012 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.007 0.055 -9999 0 -0.34 17 17
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.005 0.042 -9999 0 -0.48 6 6
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.008 0.074 -9999 0 -0.56 12 12
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.012 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.002 0.012 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.019 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.01 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.007 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0 0 -9999 0 -9999 0 0
PLK4 -0.014 0.06 -9999 0 -9999 0 0
regulation of centriole replication 0.012 0.042 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.014 -9999 0 -0.4 1 1
MDM2/SUMO1 0 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.029 -9999 0 -0.84 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.028 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 -0.001 0.016 -9999 0 -0.47 1 1
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.019 -9999 0 -0.28 4 4
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.004 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -9999 0 0
AP2 0 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -9999 0 0
CLTB 0 0.01 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -9999 0 0
CD4 0 0 -9999 0 -9999 0 0
CLTA 0 0 -9999 0 -9999 0 0
mol:GTP 0.002 0 -9999 0 -9999 0 0
ARFGAP1 0.011 0.01 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
ARF1/GTP 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0.004 -9999 0 -9999 0 0
mol:Choline 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0 0 -9999 0 -9999 0 0
DDEF1 0 0 -9999 0 -9999 0 0
ARF1/GDP 0 0.005 -9999 0 -9999 0 0
AP2M1 0 0 -9999 0 -9999 0 0
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0 0 -9999 0 -9999 0 0
Rac/GTP 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.005 -9999 0 -9999 0 0
ARFIP2 0 0 -9999 0 -9999 0 0
COPA 0 0 -9999 0 -9999 0 0
RAC1 0 0 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.025 0.001 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -9999 0 0
GGA3 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -9999 0 0
AP2A1 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.002 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -9999 0 0
CYTH2 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0 0 -9999 0 -9999 0 0
mol:Brefeldin A 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0 0 -9999 0 -9999 0 0
PLD2 0 0 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.011 0.01 -9999 0 -9999 0 0
PIP5K1A 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0 0 -9999 0 -9999 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.011 0.01 -9999 0 -9999 0 0
GOSR2 0 0 -9999 0 -9999 0 0
USO1 0 0 -9999 0 -9999 0 0
GBF1 0 0 -9999 0 -9999 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.007 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.013 -9999 0 -10000 0 0
RELB -0.002 0.021 -9999 0 -0.28 5 5
NFKB2 0 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.001 0.011 -9999 0 -10000 0 0
regulation of B cell activation -0.001 0.011 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 841 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.HN.A2NL TCGA.GM.A3NY TCGA.GM.A2DO TCGA.GM.A2DN
109_MAP3K5 0.053 0.053 0.043 0.053
47_PPARGC1A -0.28 0 0 0
105_BMP4 -0.84 0 -0.84 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 0 0 0 0
131_RELN/VLDLR 0 -1 -0.51 -0.51
30_TGFB1/TGF beta receptor Type II 0.015 0 0 0
84_STAT5B -0.013 -0.076 -0.16 0.019
84_STAT5A -0.013 -0.076 -0.16 0.019
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/BRCA-TP/2587659/0.mRNAseq_preprocessor.Finished/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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