PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C11V5BWP
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Breast Invasive Carcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C11V5BWP
Overview
Introduction

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

Summary

There were 48 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Class IB PI3K non-lipid kinase events 230
Signaling events mediated by Stem cell factor receptor (c-Kit) 220
Reelin signaling pathway 202
EGFR-dependent Endothelin signaling events 185
HIF-1-alpha transcription factor network 153
p75(NTR)-mediated signaling 136
FOXA2 and FOXA3 transcription factor networks 124
Glucocorticoid receptor regulatory network 122
Lissencephaly gene (LIS1) in neuronal migration and development 118
Signaling mediated by p38-alpha and p38-beta 110
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Class IB PI3K non-lipid kinase events 230 690 3 -0.23 -1000 1000 -1000 -0.028 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 220 17206 78 -0.62 0.19 1000 -1000 -0.082 -1000
Reelin signaling pathway 202 11357 56 -0.52 0 1000 -1000 -0.091 -1000
EGFR-dependent Endothelin signaling events 185 3893 21 -0.35 0 1000 -1000 -0.074 -1000
HIF-1-alpha transcription factor network 153 11640 76 -0.8 0.018 1000 -1000 -0.084 -1000
p75(NTR)-mediated signaling 136 17039 125 -0.44 0 1000 -1000 -0.095 -1000
FOXA2 and FOXA3 transcription factor networks 124 5733 46 -1.2 0.025 1000 -1000 -0.034 -1000
Glucocorticoid receptor regulatory network 122 13996 114 -1 0.37 1000 -1000 -0.076 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 118 6403 54 -0.52 0.022 1000 -1000 -0.092 -1000
Signaling mediated by p38-alpha and p38-beta 110 4882 44 -0.41 0 1000 -1000 -0.053 -1000
Wnt signaling 110 776 7 -0.2 -0.006 1000 -1000 -0.045 -1000
Arf6 signaling events 109 6764 62 -0.35 0.017 1000 -1000 -0.054 -1000
EPHB forward signaling 108 9256 85 -0.36 0.2 1000 -1000 -0.091 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 104 7086 68 -0.53 0.16 1000 -1000 -0.12 -1000
ErbB2/ErbB3 signaling events 102 6632 65 -0.44 0.018 1000 -1000 -0.058 -1000
Ephrin B reverse signaling 101 4848 48 -0.36 0.21 1000 -1000 -0.066 -1000
Endothelins 100 9680 96 -0.4 0.037 1000 -1000 -0.069 -1000
Angiopoietin receptor Tie2-mediated signaling 98 8671 88 -0.35 0.032 1000 -1000 -0.097 -1000
IL4-mediated signaling events 95 8731 91 -1 0.52 1000 -1000 -0.14 -1000
IGF1 pathway 93 5340 57 -0.19 0.081 1000 -1000 -0.086 -1000
ErbB4 signaling events 81 5657 69 -0.45 0.06 1000 -1000 -0.086 -1000
IL23-mediated signaling events 81 4909 60 -0.49 0.018 1000 -1000 -0.13 -1000
Calcium signaling in the CD4+ TCR pathway 78 2441 31 -0.38 0.011 1000 -1000 -0.09 -1000
Neurotrophic factor-mediated Trk receptor signaling 78 9464 120 -0.66 0.26 1000 -1000 -0.071 -1000
Noncanonical Wnt signaling pathway 77 2018 26 -0.2 0 1000 -1000 -0.07 -1000
Nongenotropic Androgen signaling 77 4018 52 -0.25 0.11 1000 -1000 -0.056 -1000
FOXM1 transcription factor network 77 3950 51 -0.46 0.012 1000 -1000 -0.16 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 75 6440 85 -0.27 0.012 1000 -1000 -0.075 -1000
BMP receptor signaling 75 6107 81 -0.58 0.024 1000 -1000 -0.093 -1000
Glypican 1 network 74 3574 48 -0.34 0.026 1000 -1000 -0.047 -1000
Visual signal transduction: Rods 74 3849 52 -0.53 0 1000 -1000 -0.08 -1000
Aurora B signaling 70 4731 67 -0.33 0.013 1000 -1000 -0.071 -1000
Signaling events regulated by Ret tyrosine kinase 69 5668 82 -0.17 0 1000 -1000 -0.091 -1000
Plasma membrane estrogen receptor signaling 68 5899 86 -0.2 0.081 1000 -1000 -0.074 -1000
Syndecan-1-mediated signaling events 65 2230 34 -0.22 0 1000 -1000 -0.074 -1000
Signaling events mediated by PTP1B 64 4935 76 -0.68 0.069 1000 -1000 -0.071 -1000
amb2 Integrin signaling 62 5116 82 -0.54 0 1000 -1000 -0.072 -1000
Integrins in angiogenesis 60 5063 84 -0.34 0 1000 -1000 -0.083 -1000
IL6-mediated signaling events 60 4556 75 -0.31 0.054 1000 -1000 -0.075 -1000
Ephrin A reverse signaling 59 415 7 -0.083 0 1000 -1000 -0.041 -1000
RXR and RAR heterodimerization with other nuclear receptor 59 3074 52 -0.2 0.03 1000 -1000 -0.062 -1000
Syndecan-3-mediated signaling events 54 1899 35 -0.37 0 1000 -1000 -0.06 -1000
Signaling events mediated by PRL 54 1866 34 -0.2 0.021 1000 -1000 -0.059 -1000
Fc-epsilon receptor I signaling in mast cells 52 5132 97 -0.27 0.028 1000 -1000 -0.085 -1000
PDGFR-alpha signaling pathway 49 2180 44 -0.4 0.02 1000 -1000 -0.058 -1000
LPA receptor mediated events 49 5089 102 -0.29 0.029 1000 -1000 -0.083 -1000
Signaling events mediated by the Hedgehog family 48 2538 52 -0.22 0.03 1000 -1000 -0.076 -1000
E-cadherin signaling in keratinocytes 45 1964 43 -0.29 0.044 1000 -1000 -0.069 -1000
Nephrin/Neph1 signaling in the kidney podocyte 42 1454 34 -0.076 0 1000 -1000 -0.065 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 42 1417 33 -0.6 0 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class III 40 1616 40 -0.61 0.03 1000 -1000 -0.042 -1000
Stabilization and expansion of the E-cadherin adherens junction 40 3000 74 -0.29 0.071 1000 -1000 -0.081 -1000
Rapid glucocorticoid signaling 39 780 20 -0.19 0.027 1000 -1000 -0.036 -1000
Presenilin action in Notch and Wnt signaling 37 2265 61 -0.44 0.013 1000 -1000 -0.063 -1000
S1P1 pathway 37 1354 36 -0.33 0.007 1000 -1000 -0.065 -1000
FAS signaling pathway (CD95) 37 1749 47 -0.5 0.01 1000 -1000 -0.05 -1000
LPA4-mediated signaling events 36 434 12 -0.17 0.02 1000 -1000 -0.021 -1000
TCGA08_rtk_signaling 36 936 26 -0.29 0.027 1000 -1000 -0.032 -1000
TCR signaling in naïve CD8+ T cells 33 3111 93 -0.18 0.086 1000 -1000 -0.073 -1000
Nectin adhesion pathway 31 1980 63 -0.067 0.015 1000 -1000 -0.078 -1000
Syndecan-4-mediated signaling events 29 1987 67 -0.34 0.004 1000 -1000 -0.085 -1000
Ras signaling in the CD4+ TCR pathway 29 499 17 -0.13 0 1000 -1000 -0.071 -1000
IL27-mediated signaling events 28 1458 51 -0.32 0.015 1000 -1000 -0.081 -1000
Coregulation of Androgen receptor activity 27 2083 76 -0.18 0.034 1000 -1000 -0.051 -1000
IL12-mediated signaling events 27 2412 87 -0.39 0.054 1000 -1000 -0.098 -1000
Canonical Wnt signaling pathway 27 1397 51 -0.44 0.15 1000 -1000 -0.055 -1000
BCR signaling pathway 27 2705 99 -0.15 0.043 1000 -1000 -0.078 -1000
Insulin Pathway 25 1868 74 -0.19 0.032 1000 -1000 -0.082 -1000
Regulation of nuclear SMAD2/3 signaling 23 3182 136 -0.34 0.05 1000 -1000 -0.088 -1000
Regulation of p38-alpha and p38-beta 23 1256 54 -0.38 0.028 1000 -1000 -0.066 -1000
Regulation of Telomerase 23 2442 102 -0.35 0.022 1000 -1000 -0.081 -1000
Aurora A signaling 22 1341 60 -0.2 0.006 1000 -1000 -0.054 -1000
Arf6 trafficking events 22 1620 71 -0.48 0.032 1000 -1000 -0.068 -1000
TCGA08_retinoblastoma 22 180 8 -0.045 0.008 1000 -1000 -0.027 -1000
Regulation of Androgen receptor activity 22 1584 70 -0.28 0.026 1000 -1000 -0.074 -1000
Thromboxane A2 receptor signaling 21 2300 105 -0.29 0.071 1000 -1000 -0.067 -1000
Syndecan-2-mediated signaling events 20 1404 69 -0.2 0.038 1000 -1000 -0.06 -1000
Effects of Botulinum toxin 20 522 26 -0.1 0 1000 -1000 -0.067 -1000
Ceramide signaling pathway 18 1414 76 -0.19 0.047 1000 -1000 -0.057 -1000
Osteopontin-mediated events 17 671 38 -0.27 0.028 1000 -1000 -0.094 -1000
PLK1 signaling events 16 1391 85 -0.22 0.036 1000 -1000 -0.059 -1000
Caspase cascade in apoptosis 14 1072 74 -0.055 0.045 1000 -1000 -0.049 -1000
Visual signal transduction: Cones 14 532 38 -0.18 0.007 1000 -1000 -0.07 -1000
Hedgehog signaling events mediated by Gli proteins 14 917 65 -0.063 0.041 1000 -1000 -0.081 -1000
Class I PI3K signaling events mediated by Akt 14 1012 68 -0.28 0.053 1000 -1000 -0.062 -1000
TRAIL signaling pathway 14 682 48 -0.079 0.048 1000 -1000 -0.065 -1000
E-cadherin signaling events 14 74 5 -0.024 0 1000 -1000 -0.045 -1000
Cellular roles of Anthrax toxin 12 481 39 -0.15 0.02 1000 -1000 -0.031 -1000
Signaling mediated by p38-gamma and p38-delta 12 186 15 -0.016 0.021 1000 -1000 -0.048 -1000
S1P4 pathway 12 324 25 -0.042 0 1000 -1000 -0.056 -1000
S1P5 pathway 11 196 17 -0.042 0.023 1000 -1000 -0.053 -1000
S1P3 pathway 10 444 42 -0.042 0.02 1000 -1000 -0.053 -1000
Retinoic acid receptors-mediated signaling 9 573 58 -0.1 0.039 1000 -1000 -0.076 -1000
E-cadherin signaling in the nascent adherens junction 9 738 76 -0.024 0.048 1000 -1000 -0.077 -1000
Sphingosine 1-phosphate (S1P) pathway 8 248 28 -0.042 0.019 1000 -1000 -0.055 -1000
JNK signaling in the CD4+ TCR pathway 8 151 17 -0.019 0.044 1000 -1000 -0.064 -1000
IL2 signaling events mediated by PI3K 8 518 58 -0.034 0.065 1000 -1000 -0.073 -1000
Glypican 2 network 8 33 4 -0.033 -0.027 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 7 260 37 -0.048 0.034 1000 -1000 -0.068 -1000
IL1-mediated signaling events 7 485 62 -0.038 0.033 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class II 6 466 75 -0.15 0.001 1000 -1000 -0.065 -1000
a4b1 and a4b7 Integrin signaling 6 33 5 -0.007 -0.002 1000 -1000 -0.031 -1000
mTOR signaling pathway 6 331 53 -0.016 0.028 1000 -1000 -0.055 -1000
p38 MAPK signaling pathway 6 299 44 -0.076 0.032 1000 -1000 -0.062 -1000
EPO signaling pathway 5 283 55 -0.037 0.059 1000 -1000 -0.086 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 5 441 83 -0.074 0.048 1000 -1000 -0.072 -1000
IL2 signaling events mediated by STAT5 5 113 22 -0.12 0.067 1000 -1000 -0.058 -1000
VEGFR1 specific signals 5 284 56 -0.17 0.063 1000 -1000 -0.084 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 4 224 45 -0.027 0.073 1000 -1000 -0.08 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 566 125 -0.17 0.086 1000 -1000 -0.1 -1000
ceramide signaling pathway 3 164 49 -0.024 0.053 1000 -1000 -0.044 -1000
HIF-2-alpha transcription factor network 3 134 43 -0.057 0.17 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class I 3 357 104 -0.097 0.046 1000 -1000 -0.07 -1000
FoxO family signaling 3 226 64 -0.047 0.093 1000 -1000 -0.074 -1000
Class I PI3K signaling events 3 272 73 -0.036 0.061 1000 -1000 -0.066 -1000
PDGFR-beta signaling pathway 3 358 97 -0.027 0.055 1000 -1000 -0.083 -1000
Canonical NF-kappaB pathway 2 95 39 -0.022 0.076 1000 -1000 -0.079 -1000
Insulin-mediated glucose transport 2 67 32 -0.14 0.021 1000 -1000 -0.057 -1000
Atypical NF-kappaB pathway 2 73 31 -0.019 0.024 1000 -1000 -0.06 -1000
Circadian rhythm pathway 1 29 22 -0.018 0.046 1000 -1000 -0.067 -1000
Arf6 downstream pathway 1 55 43 -0.013 0.021 1000 -1000 -0.042 -1000
IFN-gamma pathway 1 128 68 -0.076 0.075 1000 -1000 -0.088 -1000
Paxillin-dependent events mediated by a4b1 1 53 36 -0.009 0.022 1000 -1000 -0.061 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 4 23 -0.034 0.041 1000 -1000 -0.071 -1000
BARD1 signaling events 0 8 57 -0.11 0.022 1000 -1000 -0.072 -1000
PLK2 and PLK4 events 0 0 3 -0.014 0.013 1000 -1000 -0.032 -1000
Aurora C signaling 0 2 7 -0.16 0 1000 -1000 -0.049 -1000
TCGA08_p53 0 2 7 -0.02 0.014 1000 -1000 -0.022 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 7 27 -0.001 0.028 1000 -1000 -0.052 -1000
Arf1 pathway 0 1 54 0 0.025 1000 -1000 -0.047 -1000
Alternative NF-kappaB pathway 0 5 13 -0.002 0 1000 -1000 -0.068 -1000
Total 5677 343223 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 0.84 230 -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 -0.39 381 381
CRKL -0.16 0.23 -10000 0 -0.41 380 380
HRAS -0.16 0.18 -10000 0 -0.58 22 22
mol:PIP3 -0.17 0.21 -10000 0 -0.4 380 380
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.2 0.22 -10000 0 -0.44 381 381
FOXO3 -0.15 0.21 -10000 0 -0.38 380 380
AKT1 -0.16 0.22 -10000 0 -0.41 380 380
BAD -0.14 0.21 -10000 0 -0.37 380 380
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 381 381
GSK3B -0.14 0.21 -10000 0 -0.37 380 380
RAF1 -0.09 0.17 -10000 0 -0.47 19 19
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 381 381
STAT1 -0.45 0.56 -10000 0 -1.1 387 387
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.47 19 19
cell proliferation -0.18 0.24 -10000 0 -0.43 381 381
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 -0.44 381 381
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.46 20 20
LYN/TEC/p62DOK -0.18 0.2 -10000 0 -0.4 381 381
MAPK3 -0.053 0.13 -10000 0 -0.32 17 17
STAP1 -0.2 0.24 -10000 0 -0.46 383 383
GRAP2 -0.015 0.11 -10000 0 -0.74 17 17
JAK2 -0.4 0.44 -10000 0 -0.87 387 387
STAT1 (dimer) -0.44 0.55 -10000 0 -1 387 387
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.18 0.2 -10000 0 -0.41 381 381
actin filament polymerization -0.18 0.24 -10000 0 -0.44 381 381
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.34 -10000 0 -0.63 382 382
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.37 380 380
PI3K -0.19 0.2 -10000 0 -0.41 380 380
PTEN -0.002 0.041 -10000 0 -0.84 2 2
SCF/KIT/EPO/EPOR -0.6 0.68 -10000 0 -1.3 380 380
MAPK8 -0.18 0.24 -10000 0 -0.44 381 381
STAT3 (dimer) -0.18 0.24 -10000 0 -0.43 381 381
positive regulation of transcription -0.04 0.11 -10000 0 -0.26 15 15
mol:GDP -0.16 0.18 -10000 0 -0.6 24 24
PIK3C2B -0.18 0.24 -10000 0 -0.44 381 381
CBL/CRKL -0.18 0.19 -10000 0 -0.38 380 380
FER -0.18 0.24 -10000 0 -0.45 384 384
SH2B3 -0.18 0.24 -10000 0 -0.44 381 381
PDPK1 -0.15 0.2 -10000 0 -0.36 380 380
SNAI2 -0.18 0.24 -10000 0 -0.45 382 382
positive regulation of cell proliferation -0.32 0.41 -10000 0 -0.76 387 387
KITLG 0.001 0.068 -10000 0 -0.68 6 6
cell motility -0.32 0.41 -10000 0 -0.76 387 387
PTPN6 0.014 0.021 -10000 0 -10000 0 0
EPOR -0.095 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 388 388
SOCS1 -0.004 0.039 -10000 0 -0.34 9 9
cell migration 0.19 0.25 0.45 387 -10000 0 387
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.045 0.11 -10000 0 -0.28 147 147
VAV1 -0.002 0.032 -10000 0 -0.84 1 1
GRB10 -0.2 0.22 -10000 0 -0.44 381 381
PTPN11 0.012 0.013 -10000 0 -10000 0 0
SCF/KIT -0.21 0.24 -10000 0 -0.47 381 381
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.062 0.14 -10000 0 -0.36 17 17
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.74 -10000 0 -1.4 379 379
MAP2K2 -0.062 0.14 -10000 0 -0.36 17 17
SHC/Grb2/SOS1 -0.18 0.2 -10000 0 -0.4 380 380
STAT5A -0.27 0.35 -10000 0 -0.64 388 388
GRB2 0 0.01 -10000 0 -10000 0 0
response to radiation -0.18 0.24 -10000 0 -0.44 382 382
SHC/GRAP2 -0.011 0.083 -10000 0 -0.65 14 14
PTPRO -0.18 0.24 -10000 0 -0.44 381 381
SH2B2 -0.18 0.24 -10000 0 -0.44 381 381
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.19 0.25 -10000 0 -0.46 387 387
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.12 0.29 -10000 0 -1.6 24 24
Reelin signaling pathway

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
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 -0.57 531 531
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.002 0.029 -9999 0 -0.48 3 3
AKT1 -0.21 0.17 -9999 0 -0.33 531 531
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 -0.54 527 527
LRPAP1/LRP8 -0.021 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.33 0.24 -9999 0 -0.51 527 527
DAB1/alpha3/beta1 Integrin -0.3 0.23 -9999 0 -0.47 534 534
long-term memory -0.4 0.31 -9999 0 -0.58 572 572
DAB1/LIS1 -0.31 0.24 -9999 0 -0.49 531 531
DAB1/CRLK/C3G -0.3 0.23 -9999 0 -0.47 531 531
PIK3CA 0 0.01 -9999 0 -10000 0 0
DAB1/NCK2 -0.32 0.24 -9999 0 -0.49 531 531
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.095 0.26 -9999 0 -0.78 102 102
CDK5R1 -0.009 0.048 -9999 0 -0.28 26 26
RELN -0.52 0.4 -9999 0 -0.84 529 529
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.37 0.28 -9999 0 -0.58 526 526
GRIN2A/RELN/LRP8/DAB1/Fyn -0.37 0.3 -9999 0 -0.57 540 540
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.34 0.27 -9999 0 -0.54 531 531
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.34 0.26 -9999 0 -0.52 534 534
RELN/LRP8 -0.37 0.28 -9999 0 -0.58 526 526
GRIN2B/RELN/LRP8/DAB1/Fyn -0.36 0.27 -9999 0 -0.54 559 559
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 -0.65 4 4
RAP1A -0.28 0.22 -9999 0 -0.55 119 119
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 -0.07 0.23 -9999 0 -0.84 70 70
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.14 0.11 -9999 0 -0.42 6 6
neuron adhesion -0.26 0.2 -9999 0 -0.52 119 119
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 -0.51 531 531
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.23 0.18 -9999 0 -0.36 531 531
CDK5 -0.001 0.019 -9999 0 -0.28 4 4
MAPT -0.042 0.25 -9999 0 -0.76 86 86
neuron migration -0.25 0.24 -9999 0 -0.43 527 527
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.11 -9999 0 -0.43 6 6
RELN/VLDLR -0.35 0.27 -9999 0 -0.54 531 531
EGFR-dependent Endothelin signaling events

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
HRAS 0 0.01 -9999 0 -0.28 1 1
EGFR -0.29 0.4 -9999 0 -0.84 293 293
EGF/EGFR -0.29 0.33 -9999 0 -0.58 420 420
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.29 -9999 0 -0.53 411 411
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 -0.62 411 411
mol:GDP -0.26 0.28 -9999 0 -0.53 411 411
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.067 0.23 -9999 0 -0.83 68 68
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.26 -9999 0 -0.49 411 411
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.24 0.26 -9999 0 -0.49 411 411
FRAP1 -0.25 0.27 -9999 0 -0.51 411 411
EGF/EGFR dimer -0.35 0.37 -9999 0 -0.71 411 411
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.01 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.052 0.18 -9999 0 -0.65 67 67
HIF-1-alpha transcription factor network

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
PKM2 -0.42 0.45 -9999 0 -1 213 213
HDAC7 0 0 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.31 -9999 0 -0.79 189 189
SMAD4 0 0 -9999 0 -10000 0 0
ID2 -0.42 0.45 -9999 0 -1 212 212
AP1 -0.22 0.32 -9999 0 -0.66 273 273
ABCG2 -0.45 0.49 -9999 0 -1.1 217 217
HIF1A -0.054 0.06 -9999 0 -10000 0 0
TFF3 -0.5 0.52 -9999 0 -1.1 256 256
GATA2 -0.017 0.13 -9999 0 -0.84 19 19
AKT1 -0.057 0.079 -9999 0 -10000 0 0
response to hypoxia -0.078 0.085 -9999 0 -0.25 33 33
MCL1 -0.42 0.45 -9999 0 -1 226 226
NDRG1 -0.43 0.46 -9999 0 -1 208 208
SERPINE1 -0.43 0.46 -9999 0 -1 212 212
FECH -0.42 0.45 -9999 0 -1 195 195
FURIN -0.42 0.45 -9999 0 -1 205 205
NCOA2 -0.004 0.077 -9999 0 -0.84 7 7
EP300 -0.058 0.12 -9999 0 -0.36 51 51
HMOX1 -0.43 0.45 -9999 0 -1 199 199
BHLHE40 -0.42 0.46 -9999 0 -1 205 205
BHLHE41 -0.43 0.47 -9999 0 -1 215 215
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.05 0.051 -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 -1 199 199
ABCB1 -0.34 0.55 -9999 0 -1.5 162 162
TFRC -0.43 0.46 -9999 0 -1 205 205
CXCR4 -0.43 0.46 -9999 0 -1 212 212
TF -0.69 0.57 -9999 0 -1.1 457 457
CITED2 -0.42 0.45 -9999 0 -1 203 203
HIF1A/ARNT -0.52 0.51 -9999 0 -1.2 229 229
LDHA -0.051 0.047 -9999 0 -10000 0 0
ETS1 -0.43 0.46 -9999 0 -1 211 211
PGK1 -0.42 0.45 -9999 0 -1 199 199
NOS2 -0.43 0.46 -9999 0 -1 207 207
ITGB2 -0.43 0.45 -9999 0 -1 213 213
ALDOA -0.43 0.45 -9999 0 -1 215 215
Cbp/p300/CITED2 -0.44 0.44 -9999 0 -1.1 200 200
FOS -0.27 0.39 -9999 0 -0.84 272 272
HK2 -0.42 0.45 -9999 0 -1 213 213
SP1 0.011 0.024 -9999 0 -10000 0 0
GCK -0.15 0.4 -9999 0 -1.6 52 52
HK1 -0.42 0.45 -9999 0 -1 202 202
NPM1 -0.42 0.45 -9999 0 -1 203 203
EGLN1 -0.42 0.45 -9999 0 -1 199 199
CREB1 0.018 0 -9999 0 -10000 0 0
PGM1 -0.42 0.45 -9999 0 -1 213 213
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.21 0.41 -9999 0 -1.2 104 104
IGFBP1 -0.53 0.53 -9999 0 -1.1 275 275
VEGFA -0.26 0.31 -9999 0 -0.75 108 108
HIF1A/JAB1 -0.029 0.026 -9999 0 -10000 0 0
CP -0.54 0.55 -9999 0 -1.2 292 292
CXCL12 -0.45 0.5 -9999 0 -1.1 222 222
COPS5 0.001 0.01 -9999 0 -0.28 1 1
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.42 0.46 -9999 0 -1 214 214
EGLN3 -0.43 0.46 -9999 0 -1 218 218
CA9 -0.47 0.48 -9999 0 -1.1 232 232
TERT -0.44 0.46 -9999 0 -1 226 226
ENO1 -0.42 0.45 -9999 0 -1 214 214
PFKL -0.42 0.45 -9999 0 -1 213 213
NCOA1 -0.001 0.029 -9999 0 -0.84 1 1
ADM -0.46 0.49 -9999 0 -1.1 232 232
ARNT -0.058 0.052 -9999 0 -10000 0 0
HNF4A -0.002 0.041 -9999 0 -0.28 13 13
ADFP -0.43 0.45 -9999 0 -1 229 229
SLC2A1 -0.26 0.31 -9999 0 -0.74 125 125
LEP -0.8 0.52 -9999 0 -1.2 468 468
HIF1A/ARNT/Cbp/p300 -0.35 0.32 -9999 0 -0.82 189 189
EPO -0.23 0.24 -9999 0 -0.68 16 16
CREBBP -0.058 0.12 -9999 0 -0.36 51 51
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.31 -9999 0 -0.78 187 187
PFKFB3 -0.43 0.46 -9999 0 -1 214 214
NT5E -0.43 0.46 -9999 0 -1.1 186 186
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.022 -9999 0 -0.65 1 1
Necdin/E2F1 -0.082 0.15 -9999 0 -0.72 30 30
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.17 0.24 -9999 0 -0.49 288 288
NGF (dimer)/p75(NTR)/BEX1 -0.29 0.34 -9999 0 -0.66 348 348
NT-4/5 (dimer)/p75(NTR) -0.44 0.44 -9999 0 -0.81 461 461
IKBKB -0.001 0.014 -9999 0 -0.28 2 2
AKT1 -0.16 0.23 -9999 0 -0.48 286 286
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.072 0.23 -9999 0 -0.84 65 65
MGDIs/NGR/p75(NTR)/LINGO1 -0.22 0.27 -9999 0 -0.59 279 279
FURIN -0.001 0.014 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.23 0.31 -9999 0 -0.61 313 313
LINGO1 -0.062 0.12 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.001 0.029 -9999 0 -0.84 1 1
proBDNF (dimer) -0.072 0.23 -9999 0 -0.84 65 65
NTRK1 -0.009 0.054 -9999 0 -0.84 1 1
RTN4R -0.007 0.043 -9999 0 -0.28 21 21
neuron apoptosis -0.16 0.28 -9999 0 -0.52 279 279
IRAK1 -0.001 0.014 -9999 0 -10000 0 0
SHC1 -0.18 0.29 -9999 0 -0.57 286 286
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 -0.52 286 286
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.2 0.28 -9999 0 -0.56 297 297
Mammalian IAPs/DIABLO -0.006 0.051 -9999 0 -0.51 8 8
proNGF (dimer) -0.017 0.11 -9999 0 -0.66 22 22
MAGED1 -0.001 0.014 -9999 0 -0.28 2 2
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 -0.49 286 286
NGF -0.017 0.11 -9999 0 -0.66 22 22
cell cycle arrest -0.14 0.25 -9999 0 -0.48 286 286
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.12 0.17 -9999 0 -0.35 286 286
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.39 0.4 -9999 0 -0.72 461 461
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.2 0.28 -9999 0 -0.58 286 286
PSENEN 0 0.01 -9999 0 -10000 0 0
mol:ceramide -0.18 0.25 -9999 0 -0.52 286 286
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.094 0.14 -9999 0 -0.5 13 13
p75(NTR)/beta APP -0.21 0.3 -9999 0 -0.65 279 279
BEX1 -0.16 0.28 -9999 0 -0.52 254 254
mol:GDP -0.19 0.29 -9999 0 -0.58 286 286
NGF (dimer) -0.087 0.19 -9999 0 -0.53 131 131
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.2 0.25 -9999 0 -0.54 279 279
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.17 0.24 -9999 0 -0.5 286 286
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 -0.59 286 286
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 -0.79 147 147
TP53 -0.18 0.25 -9999 0 -0.49 313 313
PRDM4 -0.18 0.25 -9999 0 -0.52 286 286
BDNF (dimer) -0.17 0.24 -9999 0 -0.61 175 175
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 -0.48 288 288
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.18 0.25 -9999 0 -0.52 286 286
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.18 0.28 -9999 0 -0.52 290 290
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.18 0.25 -9999 0 -0.52 286 286
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 -0.57 286 286
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 -0.74 355 355
MAPK8 -0.13 0.25 -9999 0 -0.46 279 279
MAPK9 -0.13 0.25 -9999 0 -0.46 279 279
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.14 0.31 -9999 0 -0.79 147 147
NTF4 -0.32 0.41 -9999 0 -0.84 324 324
NDN -0.03 0.16 -9999 0 -0.84 30 30
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.16 0.22 -9999 0 -0.46 286 286
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 -0.58 286 286
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.2 0.27 -9999 0 -0.53 313 313
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.21 0.28 -9999 0 -0.56 313 313
PRKACB -0.017 0.079 -9999 0 -0.31 47 47
proBDNF (dimer)/p75 ECD -0.054 0.17 -9999 0 -0.65 65 65
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.011 0.086 -9999 0 -0.53 18 18
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.15 0.28 -9999 0 -0.5 286 286
BAD -0.14 0.26 -9999 0 -0.47 281 281
RIPK2 -0.001 0.019 -9999 0 -0.28 4 4
NGFR -0.28 0.4 -9999 0 -0.84 279 279
CYCS -0.17 0.24 -9999 0 -0.49 286 286
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.18 0.25 -9999 0 -0.52 286 286
BCL2L11 -0.14 0.26 -9999 0 -0.47 281 281
BDNF (dimer)/p75(NTR) -0.26 0.35 -9999 0 -0.7 313 313
PI3K -0.18 0.25 -9999 0 -0.52 286 286
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.18 0.25 -9999 0 -0.52 286 286
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) -0.23 0.32 -9999 0 -0.66 286 286
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.18 0.25 -9999 0 -0.53 286 286
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 -0.001 0.019 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.22 0.29 -9999 0 -0.56 320 320
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 -0.43 281 281
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 17 17
NGF (dimer)/TRKA -0.019 0.093 -9999 0 -0.65 16 16
MMP7 -0.12 0.29 -9999 0 -0.84 118 118
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.17 0.24 -9999 0 -0.49 286 286
MMP3 -0.12 0.16 -9999 0 -0.3 328 328
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.69 14 14
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.24 0.28 -9999 0 -0.81 85 85
PCK1 -1.1 0.72 -9999 0 -1.6 519 519
HNF4A -0.25 0.28 -9999 0 -0.86 66 66
KCNJ11 -0.27 0.32 -9999 0 -0.84 117 117
AKT1 -0.14 0.14 -9999 0 -0.39 44 44
response to starvation -0.001 0.006 -9999 0 -10000 0 0
DLK1 -0.5 0.58 -9999 0 -1.3 275 275
NKX2-1 -0.055 0.15 -9999 0 -10000 0 0
ACADM -0.24 0.29 -9999 0 -0.82 88 88
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 -0.45 0.28 -9999 0 -0.73 316 316
PKLR -0.24 0.28 -9999 0 -0.76 116 116
APOA1 -0.29 0.3 -9999 0 -0.88 91 91
CPT1C -0.24 0.28 -9999 0 -0.78 105 105
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.75 247 247
FOXF1 -0.004 0.056 -9999 0 -0.84 3 3
NF1 0.016 0.029 -9999 0 -0.83 1 1
HNF1A (dimer) 0.003 0.025 -9999 0 -10000 0 0
CPT1A -0.24 0.28 -9999 0 -0.78 99 99
HMGCS1 -0.24 0.28 -9999 0 -0.83 79 79
NR3C1 -0.11 0.12 -9999 0 -0.46 34 34
CPT1B -0.24 0.29 -9999 0 -0.82 88 88
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.006 -9999 0 -10000 0 0
GCK -0.28 0.37 -9999 0 -0.97 132 132
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 -0.79 94 94
ALDOB -0.26 0.31 -9999 0 -0.87 92 92
AFP -0.7 0.62 -9999 0 -1.4 351 351
BDH1 -0.24 0.28 -9999 0 -0.83 81 81
HADH -0.26 0.3 -9999 0 -0.88 81 81
F2 -0.29 0.3 -9999 0 -0.9 79 79
HNF1A 0.003 0.025 -9999 0 -10000 0 0
G6PC -0.2 0.11 -9999 0 -0.64 7 7
SLC2A2 -0.16 0.17 -9999 0 -10000 0 0
INS 0.025 0.068 -9999 0 -10000 0 0
FOXA1 -0.25 0.28 -9999 0 -0.64 184 184
FOXA3 -0.43 0.22 -9999 0 -0.54 586 586
FOXA2 -0.32 0.34 -9999 0 -0.86 152 152
ABCC8 -0.34 0.44 -9999 0 -1.1 153 153
ALB -0.97 0.65 -9999 0 -1.4 548 548
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 0.27 -10000 0 -0.87 67 67
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 -0.013 0.1 -10000 0 -0.84 12 12
GR alpha/HSP90/FKBP51/HSP90 0.12 0.14 0.35 45 -0.45 12 57
PRL -0.096 0.12 -10000 0 -0.57 1 1
cortisol/GR alpha (dimer)/TIF2 0.31 0.26 0.54 404 -0.56 5 409
RELA -0.042 0.083 -10000 0 -10000 0 0
FGG 0.25 0.22 0.47 316 -0.51 1 317
GR beta/TIF2 0.14 0.14 0.35 90 -0.58 9 99
IFNG -0.45 0.35 -10000 0 -0.77 396 396
apoptosis -0.29 0.3 0.59 3 -0.69 209 212
CREB1 -0.008 0.028 -10000 0 -10000 0 0
histone acetylation 0.021 0.14 0.39 30 -0.37 29 59
BGLAP -0.11 0.15 -10000 0 -0.49 23 23
GR/PKAc 0.12 0.12 0.32 57 -0.44 4 61
NF kappa B1 p50/RelA -0.074 0.15 -10000 0 -0.41 30 30
SMARCD1 0.003 0.01 -10000 0 -10000 0 0
MDM2 0.13 0.1 0.27 169 -10000 0 169
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 -0.64 123 126
CSN2 0.21 0.17 0.4 234 -10000 0 234
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 0.34 36 -0.45 11 47
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.39 0.44 0.54 3 -0.93 304 307
JUN -0.33 0.29 -10000 0 -0.63 324 324
IL4 -0.14 0.15 -10000 0 -0.51 24 24
CDK5R1 -0.009 0.049 -10000 0 -0.28 26 26
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.46 0.42 -10000 0 -0.77 483 483
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.13 0.34 37 -0.5 2 39
cortisol/GR alpha (monomer) 0.37 0.31 0.63 432 -0.46 1 433
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 -1 538 538
AFP -0.63 0.71 -10000 0 -1.6 285 285
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.2 0.16 0.46 86 -10000 0 86
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 -1.7 403 403
KRT14 -0.9 0.78 -10000 0 -1.6 476 476
TBP 0.019 0.001 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.29 286 -10000 0 286
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 -1.1 540 540
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.14 0.31 -10000 0 -0.84 135 135
MAPK11 -0.002 0.042 -10000 0 -0.85 2 2
KRT5 -1 0.83 -10000 0 -1.7 480 480
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 -0.53 51 51
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.21 0.18 0.37 424 -10000 0 424
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 -0.58 174 174
NFKB1 -0.042 0.083 -10000 0 -0.26 1 1
MAPK8 -0.24 0.21 -10000 0 -0.48 265 265
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.3 0.32 0.59 3 -0.74 209 212
BAX 0.049 0.03 -10000 0 -10000 0 0
POMC -0.2 0.31 -10000 0 -0.93 73 73
EP300 0.15 0.14 0.29 249 -10000 0 249
cortisol/GR alpha (dimer)/p53 0.33 0.25 0.55 414 -10000 0 414
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.079 0.25 37 -10000 0 37
SGK1 0.24 0.2 0.42 21 -1.2 4 25
IL13 -0.34 0.28 -10000 0 -0.71 166 166
IL6 -0.54 0.64 -10000 0 -1.3 330 330
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.29 0.22 -10000 0 -0.71 65 65
IL2 -0.44 0.35 -10000 0 -0.75 410 410
CDK5 -0.001 0.02 -10000 0 -0.28 4 4
PRKACB -0.017 0.079 -10000 0 -0.31 47 47
HSP90AA1 0 0.01 -10000 0 -10000 0 0
IL8 -0.22 0.31 -10000 0 -0.64 204 204
CDK5R1/CDK5 -0.006 0.035 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.062 0.098 -10000 0 -0.48 9 9
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.53 348 -10000 0 348
SMARCA4 0.003 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.21 0.16 0.39 225 -10000 0 225
NF kappa B1 p50/RelA/Cbp 0.058 0.17 0.34 50 -0.42 1 51
JUN (dimer) -0.33 0.29 -10000 0 -0.63 325 325
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.14 0.26 -10000 0 -0.57 140 140
NR3C1 0.21 0.2 0.44 270 -0.63 2 272
NR4A1 -0.069 0.25 -10000 0 -0.79 90 90
TIF2/SUV420H1 -0.005 0.059 -10000 0 -0.65 7 7
MAPKKK cascade -0.29 0.3 0.59 3 -0.69 209 212
cortisol/GR alpha (dimer)/Src-1 0.32 0.25 0.54 402 -10000 0 402
PBX1 0.005 0.044 -10000 0 -0.56 4 4
POU1F1 0.003 0.012 -10000 0 -10000 0 0
SELE -0.23 0.36 -10000 0 -0.68 231 231
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.21 0.16 0.4 223 -10000 0 223
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.23 0.53 348 -10000 0 348
mol:cortisol 0.21 0.2 0.37 423 -10000 0 423
MMP1 -0.22 0.1 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
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 -0.37 0.28 -9999 0 -0.58 526 526
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 -0.52 526 526
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 -0.016 0.093 -9999 0 -0.84 8 8
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.01 -9999 0 -10000 0 0
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 -0.28 26 26
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.041 0.098 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.37 0.29 -9999 0 -0.58 531 531
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.26 0.2 -9999 0 -0.47 152 152
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 -0.46 526 526
RELN -0.52 0.4 -9999 0 -0.84 529 529
PAFAH/LIS1 -0.009 0.058 -9999 0 -0.56 8 8
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 -0.44 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.22 0.17 -9999 0 -0.34 531 531
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.28 0.22 -9999 0 -0.44 526 526
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 -0.024 0.078 -9999 0 -0.28 73 73
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 -0.25 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 -0.47 153 153
P39/CDK5 -0.3 0.24 -9999 0 -0.48 526 526
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.29 0.25 -9999 0 -0.49 526 526
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 -0.5 531 531
RELN/VLDLR -0.35 0.27 -9999 0 -0.54 531 531
CDC42 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.41 0.64 -9999 0 -1.3 282 282
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.082 0.16 -9999 0 -0.4 12 12
ATF2/c-Jun -0.056 0.17 -9999 0 -0.93 13 13
MAPK11 -0.084 0.16 -9999 0 -0.48 14 14
MITF -0.093 0.2 -9999 0 -0.36 288 288
MAPKAPK5 -0.09 0.19 -9999 0 -0.36 285 285
KRT8 -0.096 0.19 -9999 0 -0.36 286 286
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.01 -9999 0 -0.28 1 1
p38alpha-beta/CK2 -0.13 0.24 -9999 0 -0.45 285 285
CEBPB -0.09 0.19 -9999 0 -0.5 14 14
SLC9A1 -0.09 0.19 -9999 0 -0.5 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.083 0.19 -9999 0 -0.56 14 14
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.55 14 14
JUN -0.055 0.16 -9999 0 -0.91 13 13
PPARGC1A -0.22 0.38 -9999 0 -0.59 358 358
USF1 -0.09 0.19 -9999 0 -0.5 15 15
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.4 11 11
NOS2 -0.093 0.22 -9999 0 -1.3 6 6
DDIT3 -0.09 0.19 -9999 0 -0.5 14 14
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.069 0.16 -9999 0 -0.42 28 28
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.55 14 14
CREB1 -0.093 0.2 -9999 0 -0.37 285 285
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.07 0.17 -9999 0 -0.5 12 12
RPS6KA4 -0.09 0.19 -9999 0 -0.36 285 285
PLA2G4A -0.13 0.27 -9999 0 -0.75 100 100
GDI1 -0.09 0.19 -9999 0 -0.5 15 15
TP53 -0.12 0.24 -9999 0 -0.44 285 285
RPS6KA5 -0.093 0.19 -9999 0 -0.36 291 291
ESR1 -0.17 0.25 -9999 0 -0.42 384 384
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.19 -9999 0 -0.54 15 15
MEF2A -0.09 0.19 -9999 0 -0.36 285 285
EIF4EBP1 -0.092 0.2 -9999 0 -0.37 285 285
KRT19 -0.1 0.21 -9999 0 -0.53 44 44
ELK4 -0.09 0.19 -9999 0 -0.36 285 285
ATF6 -0.09 0.19 -9999 0 -0.5 15 15
ATF1 -0.093 0.2 -9999 0 -0.37 285 285
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.54 15 15
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.55 14 14
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 -0.45 322 322
FZD6 -0.006 0.071 -9999 0 -0.84 6 6
WNT6 -0.18 0.34 -9999 0 -0.78 198 198
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 -0.59 20 20
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 0.05 -9999 0 -0.69 4 4
ARNO/beta Arrestin1-2 -0.14 0.21 -9999 0 -0.46 214 214
EGFR -0.29 0.4 -9999 0 -0.84 293 293
EPHA2 -0.006 0.071 -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 -0.71 411 411
ARRB2 -0.062 0.16 -9999 0 -0.46 115 115
mol:GTP 0.017 0.019 -9999 0 -0.16 5 5
ARRB1 -0.002 0.042 -9999 0 -0.84 2 2
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.038 0.17 -9999 0 -0.84 37 37
EGF -0.17 0.33 -9999 0 -0.84 167 167
somatostatin receptor activity 0 0 -9999 0 -0.001 291 291
ARAP2 -0.005 0.064 -9999 0 -0.84 5 5
mol:GDP -0.14 0.18 -9999 0 -0.36 258 258
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 256 256
ITGA2B -0.016 0.072 -9999 0 -0.84 2 2
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 0.052 -9999 0 -0.61 5 5
KIF13B -0.002 0.041 -9999 0 -0.84 2 2
HGF/MET -0.15 0.29 -9999 0 -0.69 179 179
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.16 -9999 0 -0.32 287 287
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.3 0.33 -9999 0 -0.62 411 411
ADRB2 -0.21 0.36 -9999 0 -0.84 213 213
receptor agonist activity 0 0 -9999 0 0 299 299
actin filament binding 0 0 -9999 0 -0.001 292 292
SRC 0 0.01 -9999 0 -0.28 1 1
ITGB3 -0.016 0.11 -9999 0 -0.72 19 19
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 287 287
ARF6/GDP -0.016 0.088 -9999 0 -0.43 16 16
ARF6/GDP/GULP/ACAP1 -0.15 0.21 -9999 0 -0.49 174 174
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 -0.051 0.2 -9999 0 -0.84 51 51
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 0 312 312
endosomal lumen acidification 0 0 -9999 0 -0.001 239 239
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.054 0.2 -9999 0 -0.84 54 54
GNAQ/ARNO -0.001 0.024 -9999 0 -0.49 2 2
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 316 316
MET -0.14 0.32 -9999 0 -0.84 144 144
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 -0.28 4 4
mol:PI-4-5-P2 0 0 -9999 0 -0.001 288 288
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 -0.72 242 242
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 -0.5 411 411
alphaIIb/beta3 Integrin -0.022 0.099 -9999 0 -0.65 17 17
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.058 0.17 -10000 0 -0.57 83 83
cell-cell adhesion 0.2 0.23 0.72 60 -10000 0 60
Ephrin B/EPHB2/RasGAP -0.042 0.13 -10000 0 -0.48 72 72
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 76 76
Ephrin B/EPHB1/GRB7 -0.25 0.3 -10000 0 -0.56 380 380
Endophilin/SYNJ1 -0.04 0.12 -10000 0 -0.45 72 72
KRAS 0 0.01 -10000 0 -0.28 1 1
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 -0.046 0.15 -10000 0 -0.49 80 80
HRAS 0 0.01 -10000 0 -0.28 1 1
RRAS -0.04 0.13 -10000 0 -0.46 72 72
DNM1 -0.005 0.065 -10000 0 -0.84 5 5
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 60 60
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 -10000 0 0
EPHB1 -0.36 0.42 -10000 0 -0.84 364 364
EPHB4 0 0.01 -10000 0 -10000 0 0
mol:GDP -0.18 0.22 -10000 0 -0.69 73 73
Ephrin B/EPHB2 -0.043 0.14 -10000 0 -0.49 72 72
Ephrin B/EPHB3 -0.042 0.14 -10000 0 -0.49 72 72
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 -0.58 72 72
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.072 0.23 -10000 0 -0.84 72 72
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 -0.73 75 75
Rap1/GTP -0.2 0.24 -10000 0 -0.75 59 59
axon guidance -0.058 0.17 -10000 0 -0.56 83 83
MAPK3 -0.12 0.2 -10000 0 -0.55 56 56
MAPK1 -0.12 0.2 -10000 0 -0.55 56 56
Rac1/GDP -0.16 0.2 -10000 0 -0.61 73 73
actin cytoskeleton reorganization -0.15 0.18 -10000 0 -0.54 62 62
CDC42/GDP -0.16 0.2 -10000 0 -0.61 73 73
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 -0.031 0.1 -10000 0 -0.36 72 72
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.19 0.23 -10000 0 -0.71 60 60
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 -0.28 1 1
KALRN -0.015 0.11 -10000 0 -0.84 15 15
Intersectin/N-WASP -0.002 0.031 -10000 0 -0.65 2 2
neuron projection morphogenesis -0.15 0.18 -10000 0 -0.57 65 65
MAP2K1 -0.16 0.18 -10000 0 -0.35 363 363
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 -0.39 363 363
NRAS -0.001 0.014 -10000 0 -0.28 2 2
SYNJ1 -0.04 0.13 -10000 0 -0.46 72 72
PXN 0 0 -10000 0 -10000 0 0
TF -0.28 0.28 -10000 0 -0.49 506 506
HRAS/GTP -0.21 0.25 -10000 0 -0.47 379 379
Ephrin B1/EPHB1-2 -0.22 0.26 -10000 0 -0.52 363 363
cell adhesion mediated by integrin 0.007 0.14 0.45 72 -10000 0 72
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 60 60
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.15 0.19 -10000 0 -0.58 72 72
ruffle organization -0.2 0.24 -10000 0 -0.74 60 60
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.001 0.14 -10000 0 -0.45 73 73
Ephrin B/EPHB2/KALRN -0.051 0.16 -10000 0 -0.52 80 80
ROCK1 -0.001 0.012 -10000 0 -10000 0 0
RAS family/GDP -0.13 0.16 -10000 0 -0.55 57 57
Rac1/GTP -0.21 0.25 -10000 0 -0.79 60 60
Ephrin B/EPHB1/Src/Paxillin -0.18 0.21 -10000 0 -0.39 379 379
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.074 0.15 -10000 0 -0.37 107 107
NFATC2 -0.032 0.24 -10000 0 -0.78 67 67
NFATC3 -0.063 0.12 -10000 0 -10000 0 0
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 -1.1 65 65
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 -0.49 87 87
TLE4 -0.012 0.24 -10000 0 -0.78 60 60
Jun/NFAT1-c-4/p21SNFT -0.29 0.43 -10000 0 -1 150 150
AP-1/NFAT1-c-4 -0.53 0.66 -10000 0 -1.4 261 261
IKZF1 -0.001 0.19 -10000 0 -0.66 45 45
T-helper 2 cell differentiation -0.097 0.28 -10000 0 -0.88 64 64
AP-1/NFAT1 -0.24 0.34 -10000 0 -0.68 292 292
CALM1 -0.019 0.055 -10000 0 -10000 0 0
EGR2 -0.27 0.62 -10000 0 -1.6 116 116
EGR3 -0.38 0.73 -10000 0 -1.5 226 226
NFAT1/FOXP3 -0.09 0.2 -10000 0 -0.64 59 59
EGR1 -0.28 0.4 -10000 0 -0.84 285 285
JUN -0.012 0.087 -10000 0 -0.84 9 9
EGR4 -0.016 0.064 -10000 0 -0.28 48 48
mol:Ca2+ -0.022 0.063 -10000 0 -10000 0 0
GBP3 -0.008 0.21 -10000 0 -0.69 62 62
FOSL1 -0.007 0.055 -10000 0 -0.84 2 2
NFAT1-c-4/MAF/IRF4 -0.31 0.46 -10000 0 -1 191 191
DGKA 0 0.19 -10000 0 -0.63 54 54
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.39 0.52 -10000 0 -1.1 248 248
CTLA4 -0.069 0.22 -10000 0 -0.73 41 41
NFAT1-c-4 (dimer)/EGR1 -0.44 0.57 -10000 0 -1.2 254 254
NFAT1-c-4 (dimer)/EGR4 -0.28 0.44 -10000 0 -0.91 234 234
FOS -0.28 0.4 -10000 0 -0.85 272 272
IFNG -0.14 0.26 -10000 0 -0.88 69 69
T cell activation -0.17 0.35 -10000 0 -0.79 156 156
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 0.79 92 -10000 0 92
TNF -0.32 0.53 -10000 0 -1.1 245 245
FASLG -0.35 0.66 -10000 0 -1.2 269 269
TBX21 -0.028 0.17 -10000 0 -0.73 45 45
BATF3 -0.001 0.029 -10000 0 -0.84 1 1
PRKCQ -0.029 0.17 -10000 0 -0.72 43 43
PTPN1 -0.001 0.19 -10000 0 -0.63 54 54
NFAT1-c-4/ICER1 -0.29 0.43 -10000 0 -0.92 226 226
GATA3 -0.038 0.16 -10000 0 -0.84 30 30
T-helper 1 cell differentiation -0.14 0.25 -10000 0 -0.86 69 69
IL2RA -0.22 0.32 -10000 0 -0.96 80 80
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.001 0.19 -10000 0 -0.63 54 54
E2F1 -0.081 0.14 -10000 0 -10000 0 0
PPARG -0.2 0.36 -10000 0 -0.84 198 198
SLC3A2 0.001 0.19 -10000 0 -0.66 45 45
IRF4 -0.075 0.24 -10000 0 -0.76 83 83
PTGS2 -0.49 0.67 -10000 0 -1.3 308 308
CSF2 -0.37 0.56 -10000 0 -1.1 253 253
JunB/Fra1/NFAT1-c-4 -0.27 0.42 -10000 0 -0.98 145 145
IL4 -0.1 0.3 -10000 0 -0.96 60 60
IL5 -0.37 0.56 -10000 0 -1.1 253 253
IL2 -0.18 0.36 -10000 0 -0.81 154 154
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 -0.8 88 88
CDK4 0.078 0.23 0.63 17 -10000 0 17
PTPRK -0.003 0.2 -10000 0 -0.67 57 57
IL8 -0.38 0.57 -10000 0 -1.1 259 259
POU2F1 0.001 0.01 -10000 0 -0.28 1 1
ErbB2/ErbB3 signaling events

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
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.36 17 17
NFATC4 -0.091 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 -10000 0 0
mammary gland morphogenesis -0.15 0.2 -9999 0 -0.41 301 301
JUN -0.019 0.079 -9999 0 -0.37 4 4
HRAS 0 0.01 -9999 0 -0.28 1 1
DOCK7 -0.14 0.18 -9999 0 -0.39 301 301
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.19 0.24 -9999 0 -0.5 301 301
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 -0.36 150 150
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.21 -9999 0 -0.45 301 301
RAF1 -0.083 0.16 -9999 0 -0.37 13 13
ErbB2/ErbB3/neuregulin 2 -0.29 0.27 -9999 0 -0.54 446 446
STAT3 0 0.004 -9999 0 -10000 0 0
cell migration -0.064 0.13 -9999 0 -0.3 80 80
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.23 -9999 0 -0.52 139 139
FOS -0.17 0.27 -9999 0 -0.54 273 273
NRAS -0.001 0.014 -9999 0 -0.28 2 2
mol:Ca2+ -0.15 0.2 -9999 0 -0.41 301 301
MAPK3 -0.11 0.19 -9999 0 -0.48 57 57
MAPK1 -0.11 0.19 -9999 0 -0.49 53 53
JAK2 -0.14 0.18 -9999 0 -0.39 301 301
NF2 -0.007 0.01 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.18 -9999 0 -0.37 301 301
NRG1 -0.3 0.4 -9999 0 -0.83 304 304
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.34 301 301
MAPK9 -0.071 0.092 -9999 0 -0.23 19 19
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 -0.28 144 144
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 -0.31 145 145
PPP3CB -0.13 0.17 -9999 0 -0.36 301 301
KRAS 0 0.01 -9999 0 -0.28 1 1
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.32 190 190
NRG2 -0.44 0.42 -9999 0 -0.84 445 445
mol:GDP -0.13 0.18 -9999 0 -0.37 301 301
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.075 0.15 -9999 0 -0.41 6 6
SRC 0 0.01 -9999 0 -0.28 1 1
mol:cAMP -0.002 0.003 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.39 301 301
MAP2K1 -0.14 0.21 -9999 0 -0.49 139 139
heart morphogenesis -0.15 0.2 -9999 0 -0.41 301 301
RAS family/GDP -0.11 0.14 -9999 0 -0.35 12 12
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 -10000 0 0
activation of caspase activity -0.007 0.006 -9999 0 -10000 0 0
nervous system development -0.15 0.2 -9999 0 -0.41 301 301
CDC42 0 0 -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 -0.84 5 5
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 -0.016 0.072 -10000 0 -0.84 2 2
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 -0.016 0.11 -10000 0 -0.72 19 19
EPHB1 -0.36 0.42 -10000 0 -0.84 364 364
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 -0.022 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
Endothelins

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
AKT1 -0.02 0.19 -9999 0 -0.6 68 68
PTK2B 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.029 0.16 -9999 0 -0.94 14 14
EDN1 -0.041 0.25 -9999 0 -0.86 68 68
EDN3 -0.4 0.42 -9999 0 -0.84 399 399
EDN2 -0.075 0.14 -9999 0 -0.84 6 6
HRAS/GDP -0.027 0.19 -9999 0 -0.51 71 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.001 0.13 -9999 0 -0.39 45 45
ADCY4 -0.15 0.3 -9999 0 -0.58 232 232
ADCY5 -0.28 0.37 -9999 0 -0.63 392 392
ADCY6 -0.13 0.27 -9999 0 -0.56 219 219
ADCY7 -0.13 0.27 -9999 0 -0.56 219 219
ADCY1 -0.15 0.29 -9999 0 -0.59 229 229
ADCY2 -0.17 0.33 -9999 0 -0.63 244 244
ADCY3 -0.13 0.27 -9999 0 -0.56 219 219
ADCY8 -0.14 0.27 -9999 0 -0.56 219 219
ADCY9 -0.13 0.27 -9999 0 -0.56 219 219
arachidonic acid secretion -0.11 0.29 -9999 0 -0.46 290 290
ETB receptor/Endothelin-1/Gq/GTP -0.029 0.17 -9999 0 -0.38 125 125
GNAO1 -0.033 0.14 -9999 0 -0.48 58 58
HRAS 0 0.01 -9999 0 -0.28 1 1
ETA receptor/Endothelin-1/G12/GTP 0.036 0.2 -9999 0 -0.56 68 68
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 -0.029 0.2 -9999 0 -0.6 68 68
EDNRB -0.06 0.23 -9999 0 -0.84 68 68
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.029 0.22 -9999 0 -0.66 75 75
CYSLTR1 -0.026 0.21 -9999 0 -0.64 75 75
SLC9A1 0.002 0.1 -9999 0 -0.31 68 68
mol:GDP -0.036 0.21 -9999 0 -0.55 76 76
SLC9A3 -0.04 0.26 -9999 0 -0.61 127 127
RAF1 -0.087 0.24 -9999 0 -0.52 127 127
JUN 0.029 0.17 -9999 0 -0.98 15 15
JAK2 -0.02 0.19 -9999 0 -0.6 68 68
mol:IP3 -0.025 0.16 -9999 0 -0.46 58 58
ETA receptor/Endothelin-1 0.034 0.25 -9999 0 -0.69 69 69
PLCB1 -0.05 0.2 -9999 0 -0.84 50 50
PLCB2 -0.001 0.03 -9999 0 -0.56 2 2
ETA receptor/Endothelin-3 -0.29 0.34 -9999 0 -0.65 398 398
FOS -0.28 0.51 -9999 0 -1 277 277
Gai/GDP -0.039 0.15 -9999 0 -0.69 28 28
CRK 0 0 -9999 0 -10000 0 0
mol:Ca ++ -0.046 0.24 -9999 0 -0.66 82 82
BCAR1 0 0.002 -9999 0 -10000 0 0
PRKCB1 -0.028 0.16 -9999 0 -0.43 65 65
GNAQ 0.007 0.042 -9999 0 -0.84 2 2
GNAZ -0.006 0.071 -9999 0 -0.84 6 6
GNAL -0.19 0.35 -9999 0 -0.84 189 189
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 40 40
MAPK14 -0.025 0.16 -9999 0 -0.48 54 54
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 -0.042 0.18 -9999 0 -0.84 42 42
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.17 -9999 0 -0.41 100 100
ETB receptor/Endothelin-2 -0.099 0.2 -9999 0 -0.69 73 73
ETB receptor/Endothelin-3 -0.35 0.35 -9999 0 -0.68 435 435
ETB receptor/Endothelin-1 -0.078 0.27 -9999 0 -0.7 127 127
MAPK3 -0.21 0.42 -9999 0 -0.79 278 278
MAPK1 -0.21 0.42 -9999 0 -0.79 278 278
Rac1/GDP -0.03 0.19 -9999 0 -0.51 70 70
cAMP biosynthetic process -0.18 0.3 -9999 0 -0.62 229 229
MAPK8 0.026 0.15 -9999 0 -0.6 22 22
SRC 0 0.01 -9999 0 -0.28 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.045 0.18 -9999 0 -0.41 118 118
p130Cas/CRK/Src/PYK2 -0.011 0.2 -9999 0 -0.56 54 54
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.03 0.19 -9999 0 -0.52 66 66
COL1A2 -0.049 0.24 -9999 0 -0.67 75 75
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.64 6 6
mol:DAG -0.025 0.16 -9999 0 -0.46 59 59
MAP2K2 -0.14 0.32 -9999 0 -0.56 280 280
MAP2K1 -0.14 0.32 -9999 0 -0.56 280 280
EDNRA 0.028 0.056 -9999 0 -0.33 1 1
positive regulation of muscle contraction -0.011 0.17 -9999 0 -0.53 68 68
Gq family/GDP -0.072 0.15 -9999 0 -0.6 38 38
HRAS/GTP -0.051 0.2 -9999 0 -0.46 105 105
PRKCH -0.02 0.16 -9999 0 -0.54 37 37
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.032 0.19 -9999 0 -0.59 53 53
PRKCB -0.031 0.18 -9999 0 -0.55 53 53
PRKCE -0.019 0.16 -9999 0 -0.52 38 38
PRKCD -0.021 0.16 -9999 0 -0.54 36 36
PRKCG -0.029 0.16 -9999 0 -0.52 44 44
regulation of vascular smooth muscle contraction -0.32 0.58 -9999 0 -1.1 277 277
PRKCQ -0.042 0.21 -9999 0 -0.61 67 67
PLA2G4A -0.12 0.32 -9999 0 -0.56 218 218
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 0.037 0.2 -9999 0 -0.56 68 68
MMP1 -0.12 0.12 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.088 0.39 -10000 0 -0.91 151 151
NCK1/PAK1/Dok-R -0.076 0.16 -10000 0 -0.42 151 151
NCK1/Dok-R -0.21 0.44 -10000 0 -1.1 151 151
PIK3CA 0.002 0.011 -10000 0 -10000 0 0
mol:beta2-estradiol 0.03 0.094 0.24 138 -10000 0 138
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 0.032 0.1 0.27 26 -0.3 6 32
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.19 0.41 -10000 0 -1.1 151 151
FN1 -0.12 0.14 -10000 0 -10000 0 0
PLD2 -0.15 0.49 -10000 0 -1.2 151 151
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.23 -10000 0 -0.84 65 65
ELK1 -0.12 0.44 -10000 0 -1 151 151
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 -0.16 0.46 -10000 0 -1.1 151 151
CDKN1A -0.041 0.26 -10000 0 -0.61 104 104
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.21 0.44 -10000 0 -1.1 151 151
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.043 0.29 -10000 0 -0.66 151 151
PLG -0.16 0.49 -10000 0 -1.2 151 151
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.34 -10000 0 -0.88 151 151
GRB2 0 0.01 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
ANGPT2 -0.095 0.27 -10000 0 -0.74 84 84
BMX -0.35 0.57 -10000 0 -1.4 152 152
ANGPT1 -0.2 0.55 -10000 0 -1.4 138 138
tube development -0.056 0.29 -10000 0 -0.64 151 151
ANGPT4 -0.27 0.39 -10000 0 -0.84 275 275
response to hypoxia -0.008 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.24 0.52 -10000 0 -1.3 151 151
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.34 0.41 -10000 0 -0.84 337 337
STAT5A (dimer) -0.07 0.33 -10000 0 -0.77 122 122
mol:L-citrulline -0.043 0.29 -10000 0 -0.66 151 151
AGTR1 -0.2 0.35 -10000 0 -0.71 242 242
MAPK14 -0.14 0.47 -10000 0 -1.1 151 151
Tie2/SHP2 -0.076 0.24 -10000 0 -1.3 27 27
TEK -0.086 0.28 -10000 0 -1.5 27 27
RPS6KB1 -0.084 0.37 -10000 0 -0.87 151 151
Angiotensin II/AT1 -0.16 0.27 -10000 0 -0.55 242 242
Tie2/Ang1/GRB2 -0.22 0.48 -10000 0 -1.2 151 151
MAPK3 -0.13 0.45 -10000 0 -1.1 151 151
MAPK1 -0.13 0.45 -10000 0 -1.1 151 151
Tie2/Ang1/GRB7 -0.22 0.49 -10000 0 -1.2 151 151
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.15 0.49 -10000 0 -1.2 151 151
PI3K -0.12 0.44 -10000 0 -1.1 151 151
FES -0.14 0.47 -10000 0 -1.1 151 151
Crk/Dok-R -0.21 0.44 -10000 0 -1.1 151 151
Tie2/Ang1/ABIN2 -0.22 0.48 -10000 0 -1.2 151 151
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.071 0.35 -10000 0 -0.8 151 151
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.084 0.37 -10000 0 -0.87 151 151
Tie2/Ang2 -0.1 0.38 -10000 0 -0.92 126 126
Tie2/Ang1 -0.18 0.54 -10000 0 -1.3 151 151
FOXO1 -0.068 0.35 -10000 0 -0.81 152 152
ELF1 0.015 0.019 -10000 0 -10000 0 0
ELF2 -0.15 0.48 -10000 0 -1.2 151 151
mol:Choline -0.14 0.46 -10000 0 -1.1 151 151
cell migration -0.03 0.099 -10000 0 -0.24 151 151
FYN -0.071 0.32 -10000 0 -0.76 126 126
DOK2 -0.002 0.041 -10000 0 -0.84 2 2
negative regulation of cell cycle -0.033 0.24 -10000 0 -0.54 122 122
ETS1 -0.02 0.1 -10000 0 -1 2 2
PXN -0.052 0.31 -10000 0 -0.71 151 151
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.058 0.33 -10000 0 -0.75 151 151
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.035 0.14 -10000 0 -0.53 28 28
MAPKKK cascade -0.14 0.46 -10000 0 -1.1 151 151
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.2 0.5 -10000 0 -1.2 151 151
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.032 0.26 -10000 0 -0.59 151 151
mol:Phosphatidic acid -0.14 0.46 -10000 0 -1.1 151 151
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.043 0.29 -10000 0 -0.66 151 151
Rac1/GTP -0.15 0.31 -10000 0 -0.81 151 151
MMP2 -0.16 0.5 -10000 0 -1.2 152 152
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.46 0.45 -10000 0 -1.2 167 167
STAT6 (cleaved dimer) -0.5 0.44 -10000 0 -1 277 277
IGHG1 -0.16 0.16 -10000 0 -0.36 60 60
IGHG3 -0.45 0.44 -10000 0 -0.99 247 247
AKT1 -0.21 0.24 -10000 0 -0.65 65 65
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.19 -10000 0 -0.64 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.67 62 62
THY1 -0.46 0.45 -10000 0 -1.2 166 166
MYB -0.015 0.11 -10000 0 -0.84 14 14
HMGA1 -0.009 0.049 -10000 0 -0.28 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.66 181 181
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.23 -10000 0 -0.66 39 39
SP1 0.017 0.005 -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 -1.1 221 221
SOCS1 -0.3 0.3 -10000 0 -0.73 161 161
SOCS3 -0.23 0.26 -10000 0 -0.8 55 55
FCER2 -0.62 0.66 -10000 0 -1.4 302 302
PARP14 0 0.019 -10000 0 -0.29 3 3
CCL17 -0.47 0.45 -10000 0 -1.2 170 170
GRB2 0 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.76 9 9
T cell proliferation -0.46 0.47 -10000 0 -1.2 182 182
IL4R/JAK1 -0.46 0.45 -10000 0 -1.2 170 170
EGR2 -0.6 0.62 -10000 0 -1.5 214 214
JAK2 -0.007 0.025 -10000 0 -10000 0 0
JAK3 0.008 0.035 -10000 0 -0.28 2 2
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 -1.2 176 176
PTPN6 0.022 0.018 -10000 0 -10000 0 0
IL13RA2 -0.46 0.46 -10000 0 -1.1 179 179
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.23 0.48 -10000 0 -1.6 87 87
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.27 -10000 0 -0.64 158 158
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 0.43 -10000 0 -1.4 88 88
CD40LG -0.037 0.19 -10000 0 -0.85 43 43
MAPK14 -0.26 0.27 -10000 0 -0.69 116 116
mitosis -0.2 0.23 -10000 0 -0.61 65 65
STAT6 -0.52 0.52 -10000 0 -1.2 233 233
SPI1 0.007 0.021 -10000 0 -10000 0 0
RPS6KB1 -0.19 0.22 -10000 0 -0.64 40 40
STAT6 (dimer) -0.53 0.52 -10000 0 -1.2 233 233
STAT6 (dimer)/PARP14 -0.52 0.5 -10000 0 -1.1 256 256
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 -0.65 50 50
FRAP1 -0.21 0.24 -10000 0 -0.65 65 65
LTA -0.47 0.45 -10000 0 -1.2 170 170
FES -0.003 0.05 -10000 0 -0.84 3 3
T-helper 1 cell differentiation 0.52 0.51 1.2 239 -10000 0 239
CCL11 -0.48 0.43 -10000 0 -1.1 181 181
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.23 -10000 0 -0.66 50 50
IL2RG -0.004 0.085 -10000 0 -0.84 5 5
IL10 -0.46 0.46 -10000 0 -1.1 180 180
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 -1.2 167 167
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.84 200 200
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 -1.2 156 156
IL2R gamma/JAK3 -0.013 0.069 -10000 0 -0.44 17 17
TFF3 -0.56 0.58 -10000 0 -1.3 243 243
ALOX15 -0.55 0.57 -10000 0 -1.4 218 218
MYBL1 -0.046 0.1 -10000 0 -0.28 139 139
T-helper 2 cell differentiation -0.4 0.37 -10000 0 -0.88 216 216
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 -0.68 51 51
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.65 65 65
PI3K -0.22 0.25 -10000 0 -0.7 62 62
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 -0.97 5 5
ITGB3 -0.47 0.48 -10000 0 -1.2 186 186
PIGR -1 0.75 -10000 0 -1.6 549 549
IGHE 0.047 0.039 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.94 5 5
BCL6 0.003 0.042 -10000 0 -0.83 2 2
OPRM1 -0.47 0.45 -10000 0 -1.2 163 163
RETNLB -0.47 0.45 -10000 0 -1.2 173 173
SELP -0.65 0.68 -10000 0 -1.6 257 257
AICDA -0.45 0.44 -10000 0 -1.1 165 165
IGF1 pathway

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
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.13 0.24 -10000 0 -0.51 205 205
GRB2/SOS1/SHC 0 0.005 -10000 0 -10000 0 0
HRAS 0 0.01 -10000 0 -0.28 1 1
IRS1/Crk -0.13 0.24 -10000 0 -0.52 205 205
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.24 -10000 0 -0.57 195 195
AKT1 -0.068 0.21 -10000 0 -0.43 195 195
BAD -0.056 0.2 -10000 0 -0.69 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.13 0.24 -10000 0 -0.51 205 205
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.24 -10000 0 -0.52 205 205
RAF1 -0.048 0.19 -10000 0 -0.64 29 29
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.23 -10000 0 -0.49 205 205
YWHAZ -0.001 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.26 -10000 0 -0.56 205 205
PIK3CA 0 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.069 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 -0.45 195 195
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 -0.52 205 205
Crk/p130 Cas/Paxillin -0.11 0.21 -10000 0 -0.47 195 195
IGF1R -0.043 0.13 -10000 0 -0.86 18 18
IGF1 -0.19 0.36 -10000 0 -0.86 187 187
IRS2/Crk -0.14 0.26 -10000 0 -0.54 217 217
PI3K -0.12 0.22 -10000 0 -0.48 205 205
apoptosis 0.081 0.15 0.56 30 -10000 0 30
HRAS/GDP 0 0.006 -10000 0 -10000 0 0
PRKCD -0.099 0.26 -10000 0 -0.55 195 195
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 -0.43 196 196
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 -0.59 195 195
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.22 -10000 0 -0.5 195 195
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 -0.51 205 205
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.51 205 205
IRS1 -0.14 0.25 -10000 0 -0.56 205 205
IRS2 -0.15 0.28 -10000 0 -0.57 217 217
IGF-1R heterotetramer/IGF1 -0.16 0.3 -10000 0 -0.7 195 195
GRB2 0 0.01 -10000 0 -10000 0 0
PDPK1 -0.11 0.21 -10000 0 -0.46 195 195
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.12 0.28 -10000 0 -0.59 206 206
SHC1 0 0 -10000 0 -10000 0 0
ErbB4 signaling events

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
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 -0.84 293 293
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 -0.83 458 458
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.17 0.21 -10000 0 -0.45 300 300
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.2 0.25 -10000 0 -0.53 300 300
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 -0.059 0.15 -10000 0 -0.57 51 51
NCOR1 -0.001 0.029 -10000 0 -0.84 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.19 0.24 -10000 0 -0.5 300 300
GRIN2B -0.21 0.25 -10000 0 -0.5 348 348
ErbB4/ErbB2/betacellulin -0.05 0.12 -10000 0 -0.5 46 46
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 -10000 0 0
E4ICDs/ETO2 -0.035 0.096 -10000 0 -0.58 16 16
axon guidance 0.048 0.13 -10000 0 -0.4 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 -0.73 20 20
ErbB4/ErbB2/HBEGF -0.024 0.052 -10000 0 -0.47 2 2
MAPK3 -0.16 0.2 -10000 0 -0.51 50 50
STAT1 (dimer) -0.027 0.064 -10000 0 -10000 0 0
MAPK1 -0.16 0.2 -10000 0 -0.51 50 50
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.2 0.24 -10000 0 -0.5 300 300
NRG1 -0.22 0.32 -10000 0 -0.65 300 300
NRG3 -0.058 0.2 -10000 0 -0.84 51 51
NRG2 -0.44 0.42 -10000 0 -0.84 445 445
NRG4 -0.004 0.034 -10000 0 -10000 0 0
heart development 0.048 0.13 -10000 0 -0.4 1 1
neural crest cell migration -0.19 0.23 -10000 0 -0.5 300 300
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 -0.49 293 293
apoptosis 0.06 0.16 0.56 51 -10000 0 51
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.3 0.26 -10000 0 -0.54 445 445
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 46 46
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 -0.5 300 300
STAT5A 0.048 0.12 -10000 0 -0.46 6 6
ErbB4/EGFR/neuregulin 1 beta -0.35 0.38 -10000 0 -0.7 413 413
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.022 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 -0.84 99 99
BTC -0.046 0.19 -10000 0 -0.82 48 48
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 -0.01 0.044 -10000 0 -0.67 3 3
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 -0.28 1 1
cell proliferation -0.12 0.24 -10000 0 -0.48 154 154
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.4 -9999 0 -0.92 101 101
IL23A -0.18 0.4 -9999 0 -1 70 70
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.32 -9999 0 -0.82 149 149
positive regulation of T cell mediated cytotoxicity -0.2 0.43 -9999 0 -0.85 195 195
ITGA3 -0.18 0.39 -9999 0 -0.98 79 79
IL17F -0.11 0.29 -9999 0 -0.65 73 73
IL12B -0.041 0.11 -9999 0 -0.29 82 82
STAT1 (dimer) -0.23 0.38 -9999 0 -0.83 181 181
CD4 -0.17 0.38 -9999 0 -0.96 73 73
IL23 -0.19 0.38 -9999 0 -1 64 64
IL23R -0.015 0.088 -9999 0 -10000 0 0
IL1B -0.19 0.41 -9999 0 -1 81 81
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.18 0.39 -9999 0 -0.88 111 111
TYK2 0.011 0.016 -9999 0 -10000 0 0
STAT4 -0.033 0.16 -9999 0 -0.84 33 33
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.034 0.16 -9999 0 -0.78 37 37
IL12RB1 0.001 0.06 -9999 0 -0.3 25 25
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 -0.85 195 195
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 -0.97 67 67
ALOX12B -0.18 0.39 -9999 0 -0.9 100 100
CXCL1 -0.38 0.66 -9999 0 -1.4 238 238
T cell proliferation -0.2 0.43 -9999 0 -0.85 195 195
NFKBIA 0 0 -9999 0 -10000 0 0
IL17A -0.074 0.24 -9999 0 -0.53 52 52
PI3K -0.25 0.33 -9999 0 -0.78 194 194
IFNG -0.005 0.026 -9999 0 -0.089 29 29
STAT3 (dimer) -0.24 0.32 -9999 0 -0.82 131 131
IL18R1 -0.011 0.095 -9999 0 -0.84 11 11
IL23/IL23R/JAK2/TYK2/SOCS3 -0.089 0.24 -9999 0 -0.54 55 55
IL18/IL18R -0.033 0.13 -9999 0 -0.58 42 42
macrophage activation -0.014 0.017 -9999 0 -0.042 83 83
TNF -0.19 0.41 -9999 0 -1 94 94
STAT3/STAT4 -0.27 0.36 -9999 0 -0.84 188 188
STAT4 (dimer) -0.24 0.4 -9999 0 -0.86 203 203
IL18 -0.007 0.044 -9999 0 -10000 0 0
IL19 -0.18 0.39 -9999 0 -0.93 90 90
STAT5A (dimer) -0.23 0.38 -9999 0 -0.82 198 198
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 -0.92 104 104
MPO -0.22 0.48 -9999 0 -1.1 142 142
positive regulation of humoral immune response -0.2 0.43 -9999 0 -0.85 195 195
IL23/IL23R/JAK2/TYK2 -0.21 0.45 -9999 0 -0.88 195 195
IL6 -0.49 0.72 -9999 0 -1.4 329 329
STAT5A -0.007 0.076 -9999 0 -0.84 7 7
IL2 0.003 0.03 -9999 0 -0.29 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.19 0.42 -9999 0 -0.95 119 119
keratinocyte proliferation -0.2 0.43 -9999 0 -0.85 195 195
NOS2 -0.18 0.39 -9999 0 -0.94 90 90
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.01 0.032 -9999 0 -0.55 1 1
NFATC2 -0.023 0.14 -9999 0 -0.59 48 48
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 -0.88 328 328
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 0.055 -9999 0 -0.84 2 2
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.062 0.14 -9999 0 -0.53 47 47
FOS -0.28 0.4 -9999 0 -0.85 272 272
IFNG -0.27 0.31 -9999 0 -0.7 241 241
AP-1/NFAT1-c-4 -0.32 0.39 -9999 0 -0.85 250 250
FASLG -0.26 0.31 -9999 0 -0.71 229 229
NFAT1-c-4/ICER1 -0.043 0.12 -9999 0 -0.5 49 49
IL2RA -0.26 0.31 -9999 0 -0.71 233 233
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.23 0.33 -9999 0 -0.7 230 230
JunB/Fra1/NFAT1-c-4 -0.04 0.12 -9999 0 -0.5 39 39
IL4 -0.22 0.34 -9999 0 -0.7 227 227
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 0.01 -9999 0 -0.28 1 1
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.13 -10000 0 -0.34 73 73
NT3 (dimer)/TRKC -0.32 0.39 -10000 0 -0.74 362 362
NT3 (dimer)/TRKB -0.55 0.48 -10000 0 -0.85 538 538
SHC/Grb2/SOS1/GAB1/PI3K 0 0.001 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.072 0.23 -10000 0 -0.84 65 65
PIK3CA 0 0.01 -10000 0 -10000 0 0
DYNLT1 0 0.01 -10000 0 -10000 0 0
NTRK1 -0.009 0.054 -10000 0 -0.84 1 1
NTRK2 -0.44 0.42 -10000 0 -0.84 439 439
NTRK3 -0.29 0.4 -10000 0 -0.83 298 298
NT-4/5 (dimer)/TRKB -0.66 0.53 -10000 0 -0.95 585 585
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 -0.67 237 237
STAT3 (dimer) -0.005 0.029 -10000 0 -0.39 3 3
NT3 (dimer)/TRKA -0.28 0.34 -10000 0 -0.65 355 355
RIN/GDP -0.073 0.13 -10000 0 -0.27 77 77
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0.01 -10000 0 -0.28 1 1
DNAJA3 -0.15 0.21 -10000 0 -0.44 286 286
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 -0.28 2 2
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 -0.028 0.12 -10000 0 -0.58 32 32
TRKA/NEDD4-2 -0.006 0.042 -10000 0 -0.65 2 2
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 -0.28 1 1
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 -0.28 2 2
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.03 -10000 0 -10000 0 0
DNM1 -0.005 0.065 -10000 0 -0.84 5 5
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 0.2 -10000 0 -0.43 279 279
mol:GDP -0.11 0.19 -10000 0 -0.38 191 191
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 -0.29 49 49
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 -0.61 461 461
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.002 0.014 -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 -0.79 147 147
RAP1/GDP -0.077 0.089 -10000 0 -0.26 7 7
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.072 0.23 -10000 0 -0.84 65 65
ubiquitin-dependent protein catabolic process -0.016 0.081 -10000 0 -0.56 17 17
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 0.012 -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 -0.71 545 545
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 -0.66 545 545
MAPK3 -0.025 0.1 -10000 0 -0.53 32 32
MAPK1 -0.025 0.1 -10000 0 -0.53 32 32
CDC42/GDP -0.069 0.13 -10000 0 -0.28 56 56
NTF3 -0.14 0.31 -10000 0 -0.79 147 147
NTF4 -0.32 0.41 -10000 0 -0.84 324 324
NGF (dimer)/TRKA/FAIM -0.015 0.08 -10000 0 -0.56 16 16
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 -0.46 286 286
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.27 0.36 -10000 0 -0.65 363 363
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 -0.28 53 53
NGF (dimer)/TRKA/GRIT -0.016 0.081 -10000 0 -0.57 16 16
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.59 16 16
NGF (dimer)/TRKA/NEDD4-2 -0.016 0.082 -10000 0 -0.56 17 17
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.28 0.4 -10000 0 -0.84 279 279
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.055 -10000 0 -0.36 20 20
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 -0.28 2 2
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 -0.067 0.12 -10000 0 -0.81 16 16
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.006 0.036 -10000 0 -0.65 1 1
SQSTM1 -0.001 0.014 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.31 0.3 -10000 0 -0.56 461 461
NGF (dimer)/TRKA/p62/Atypical PKCs -0.013 0.069 -10000 0 -0.48 17 17
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 -0.47 286 286
Rac1/GTP -0.13 0.14 -10000 0 -0.35 214 214
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
Noncanonical Wnt signaling 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
NFATC2 -0.048 0.19 -9999 0 -0.84 48 48
GNB1/GNG2 -0.16 0.24 -9999 0 -0.68 95 95
mol:DAG -0.14 0.21 -9999 0 -0.64 85 85
PLCG1 -0.14 0.22 -9999 0 -0.67 85 85
YES1 -0.16 0.24 -9999 0 -0.69 94 94
FZD3 -0.008 0.081 -9999 0 -0.84 8 8
FZD6 -0.006 0.071 -9999 0 -0.84 6 6
G protein -0.15 0.22 -9999 0 -0.67 87 87
MAP3K7 -0.079 0.19 -9999 0 -0.51 85 85
mol:Ca2+ -0.14 0.2 -9999 0 -0.61 85 85
mol:IP3 -0.14 0.21 -9999 0 -0.64 85 85
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 -0.55 89 89
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.18 0.26 -9999 0 -0.45 322 322
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.16 0.24 -9999 0 -0.69 95 95
GO:0007205 -0.11 0.23 -9999 0 -0.62 85 85
WNT6 -0.18 0.34 -9999 0 -0.78 198 198
WNT4 -0.024 0.13 -9999 0 -0.84 19 19
NFAT1/CK1 alpha -0.16 0.24 -9999 0 -0.62 126 126
GNG2 -0.006 0.071 -9999 0 -0.84 6 6
WNT5A -0.014 0.099 -9999 0 -0.59 20 20
WNT11 -0.2 0.35 -9999 0 -0.81 203 203
CDC42 -0.12 0.25 -9999 0 -0.66 92 92
Nongenotropic Androgen 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
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 -0.48 58 58
HRAS 0 0.01 -10000 0 -0.28 1 1
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 -0.04 0.16 -10000 0 -0.46 92 92
T-DHT/AR -0.072 0.21 -10000 0 -0.66 92 92
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 -0.042 0.18 -10000 0 -0.84 42 42
mol:GDP -0.069 0.2 -10000 0 -0.63 92 92
cell proliferation -0.11 0.24 -10000 0 -0.58 81 81
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 -0.078 110 110
MAPK3 -0.075 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 0.071 -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 -0.28 1 1
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 92 92
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 -0.04 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 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.035 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 69 69
CDC42 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.23 0.41 -9999 0 -0.99 86 86
PLK1 -0.081 0.095 -9999 0 -10000 0 0
BIRC5 -0.09 0.091 -9999 0 -10000 0 0
HSPA1B -0.23 0.41 -9999 0 -0.98 89 89
MAP2K1 0.007 0.028 -9999 0 -10000 0 0
BRCA2 -0.23 0.42 -9999 0 -1 86 86
FOXM1 -0.28 0.48 -9999 0 -1.1 126 126
XRCC1 -0.23 0.41 -9999 0 -0.96 95 95
FOXM1B/p19 -0.27 0.4 -9999 0 -0.94 152 152
Cyclin D1/CDK4 -0.22 0.39 -9999 0 -0.91 92 92
CDC2 -0.25 0.43 -9999 0 -0.96 126 126
TGFA -0.22 0.4 -9999 0 -0.93 107 107
SKP2 -0.23 0.41 -9999 0 -0.98 89 89
CCNE1 -0.051 0.12 -9999 0 -0.29 158 158
CKS1B -0.23 0.41 -9999 0 -0.99 87 87
RB1 -0.11 0.12 -9999 0 -10000 0 0
FOXM1C/SP1 -0.3 0.4 -9999 0 -0.96 155 155
AURKB -0.071 0.097 -9999 0 -10000 0 0
CENPF -0.26 0.43 -9999 0 -1 103 103
CDK4 0.007 0.018 -9999 0 -10000 0 0
MYC -0.21 0.4 -9999 0 -0.91 103 103
CHEK2 0.006 0.031 -9999 0 -0.32 1 1
ONECUT1 -0.23 0.41 -9999 0 -0.94 108 108
CDKN2A -0.032 0.1 -9999 0 -0.27 118 118
LAMA4 -0.23 0.42 -9999 0 -0.99 89 89
FOXM1B/HNF6 -0.26 0.46 -9999 0 -1.1 107 107
FOS -0.46 0.68 -9999 0 -1.4 278 278
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.23 0.42 -9999 0 -0.98 90 90
response to radiation -0.008 0.028 -9999 0 -10000 0 0
CENPB -0.23 0.41 -9999 0 -0.98 87 87
CENPA -0.26 0.43 -9999 0 -1 99 99
NEK2 -0.28 0.42 -9999 0 -1 107 107
HIST1H2BA -0.24 0.41 -9999 0 -0.99 87 87
CCNA2 -0.12 0.15 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.27 0.46 -9999 0 -1.1 107 107
CCNB2 -0.26 0.43 -9999 0 -0.97 119 119
CCNB1 -0.25 0.44 -9999 0 -1 112 112
ETV5 -0.23 0.42 -9999 0 -1 80 80
ESR1 -0.32 0.56 -9999 0 -1.3 165 165
CCND1 -0.22 0.4 -9999 0 -0.93 95 95
GSK3A 0.012 0.02 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.083 0.13 -9999 0 -10000 0 0
CDK2 0.005 0.008 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.01 0.034 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.31 0.36 -9999 0 -0.92 152 152
GAS1 -0.26 0.47 -9999 0 -1.1 111 111
MMP2 -0.23 0.42 -9999 0 -1 88 88
RB1/FOXM1C -0.23 0.42 -9999 0 -0.98 96 96
CREBBP 0 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.11 0.24 -10000 0 -0.65 144 144
CRKL -0.042 0.16 -10000 0 -0.36 144 144
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 -0.032 0.15 -10000 0 -0.56 16 16
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.01 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.13 0.26 -10000 0 -0.6 179 179
MAP3K5 -0.022 0.15 -10000 0 -0.54 18 18
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.24 -10000 0 -0.55 179 179
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) -0.074 0.15 -10000 0 -0.35 179 179
GAB1/CRKL/SHP2/PI3K -0.062 0.12 -10000 0 -0.53 16 16
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.067 0.14 -10000 0 -0.56 16 16
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 -0.28 144 144
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.047 0.095 -10000 0 -0.43 16 16
PAK1 0.009 0.03 0.46 2 -10000 0 2
HGF/MET/RANBP10 -0.13 0.26 -10000 0 -0.6 179 179
HRAS -0.15 0.31 -10000 0 -0.8 144 144
DOCK1 -0.032 0.15 -10000 0 -0.56 16 16
GAB1 -0.052 0.17 -10000 0 -0.36 179 179
CRK -0.042 0.16 -10000 0 -0.36 144 144
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.16 0.31 -10000 0 -0.74 179 179
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 -0.37 179 179
PIK3R1 0 0 -10000 0 -10000 0 0
cell morphogenesis -0.016 0.17 -10000 0 -0.6 16 16
GRB2/SHC -0.068 0.14 -10000 0 -0.34 144 144
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 -0.28 144 144
HGF/MET/MUC20 -0.13 0.26 -10000 0 -0.61 179 179
cell migration -0.067 0.13 -10000 0 -0.34 144 144
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 -0.65 144 144
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.078 0.16 -10000 0 -0.37 179 179
MET/MUC20 -0.11 0.25 -10000 0 -0.66 144 144
RAP1B -0.022 0.14 -10000 0 -0.52 16 16
RAP1A -0.022 0.14 -10000 0 -0.52 16 16
HGF/MET/RANBP9 -0.13 0.26 -10000 0 -0.6 179 179
RAF1 -0.11 0.3 -10000 0 -0.73 144 144
STAT3 -0.074 0.15 -10000 0 -0.35 179 179
cell proliferation -0.063 0.24 -10000 0 -0.5 179 179
RPS6KB1 -0.027 0.054 -10000 0 -10000 0 0
MAPK3 -0.045 0.096 -10000 0 -0.26 144 144
MAPK1 -0.045 0.096 -10000 0 -10000 0 0
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.13 -10000 0 -0.43 17 17
SRC -0.072 0.15 -10000 0 -0.64 16 16
PI3K -0.068 0.14 -10000 0 -0.34 144 144
MET/Glomulin -0.1 0.22 -10000 0 -0.59 144 144
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.088 0.27 -10000 0 -0.66 144 144
MET -0.14 0.32 -10000 0 -0.84 144 144
MAP4K1 -0.031 0.16 -10000 0 -0.34 145 145
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.088 0.27 -10000 0 -0.66 144 144
BAD 0.012 0.023 0.46 2 -10000 0 2
MAP2K4 -0.012 0.14 -10000 0 -0.48 19 19
SHP2/GRB2/SOS1/GAB1 -0.1 0.2 -10000 0 -0.53 144 144
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 -0.073 0.14 -10000 0 -0.37 144 144
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.051 0.2 -10000 0 -0.84 51 51
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 -0.069 0.14 -10000 0 -0.34 144 144
PDPK1 -0.006 0.029 0.59 2 -10000 0 2
HGF/MET/SHIP -0.13 0.26 -10000 0 -0.6 179 179
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.11 0.2 -9999 0 -0.63 97 97
SMAD6-7/SMURF1 -0.001 0.019 -9999 0 -0.56 1 1
NOG -0.025 0.13 -9999 0 -0.61 34 34
SMAD9 -0.098 0.25 -9999 0 -0.86 71 71
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.08 0.19 -9999 0 -0.49 111 111
BMP7/USAG1 -0.36 0.36 -9999 0 -0.7 433 433
SMAD5/SKI -0.09 0.16 -9999 0 -0.52 78 78
SMAD1 0.024 0.031 -9999 0 -10000 0 0
BMP2 -0.15 0.32 -9999 0 -0.84 154 154
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 -0.84 20 20
BMPR1A-1B/BAMBI -0.093 0.15 -9999 0 -0.63 47 47
AHSG -0.002 0.025 -9999 0 -0.28 7 7
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 -0.61 81 81
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 91 91
RGMA -0.11 0.29 -9999 0 -0.84 114 114
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.63 84 84
BMP2-4/USAG1 -0.4 0.39 -9999 0 -0.7 481 481
SMAD6/SMURF1/SMAD5 -0.09 0.16 -9999 0 -0.52 78 78
SOSTDC1 -0.41 0.42 -9999 0 -0.83 412 412
BMP7/BMPR2/BMPR1A-1B -0.1 0.17 -9999 0 -0.6 79 79
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 -10000 0 0
BMP2-4/CHRD -0.15 0.28 -9999 0 -0.65 190 190
SMAD5/SMAD5/SMAD4 -0.09 0.16 -9999 0 -0.52 78 78
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.089 0.17 -9999 0 -0.55 81 81
BMP7 (homodimer) -0.075 0.22 -9999 0 -0.63 100 100
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 -0.84 10 10
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.091 0.12 -9999 0 -0.65 21 21
CHRDL1 -0.58 0.39 -9999 0 -0.84 584 584
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 -0.72 599 599
BMP2-4/GREM1 -0.16 0.27 -9999 0 -0.62 191 191
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.092 0.23 -9999 0 -0.8 71 71
SMAD1/SMAD6 -0.005 0.014 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.075 0.22 -9999 0 -0.63 100 100
BMP6 -0.072 0.24 -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 81 81
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 -10000 0 0
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 -0.59 131 131
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 -0.55 156 156
BMP4 -0.05 0.2 -9999 0 -0.83 51 51
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 -0.093 0.16 -9999 0 -0.57 79 79
Glypican 1 network

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
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 -0.05 0.17 -10000 0 -0.65 64 64
SMAD2 -0.015 0.084 -10000 0 -0.51 24 24
GPC1/PrPc/Cu2+ -0.008 0.065 -10000 0 -0.57 11 11
GPC1/Laminin alpha1 -0.074 0.2 -10000 0 -0.65 95 95
TDGF1 -0.018 0.12 -10000 0 -0.84 18 18
CRIPTO/GPC1 -0.014 0.094 -10000 0 -0.65 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 -0.016 0.093 -10000 0 -0.56 24 24
SERPINC1 -0.014 0.06 -10000 0 -0.28 41 41
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 0.026 0.095 -10000 0 -0.56 18 18
SLIT2 -0.064 0.22 -10000 0 -0.84 64 64
GPC1/NRG -0.23 0.31 -10000 0 -0.65 300 300
NRG1 -0.3 0.4 -10000 0 -0.83 304 304
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 -10000 0 0
cell growth -0.23 0.28 -10000 0 -0.56 341 341
BMP signaling pathway 0.001 0.013 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 -0.3 0.4 -10000 0 -0.84 291 291
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 -0.009 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 -0.84 7 7
VEGFR1 homodimer -0.001 0.029 -10000 0 -0.84 1 1
TGFBR2 -0.024 0.14 -10000 0 -0.84 24 24
cell death 0 0.008 -10000 0 -10000 0 0
ATIII/GPC1 -0.009 0.039 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.23 0.31 -10000 0 -0.65 291 291
LCK 0 0.11 -10000 0 -0.56 29 29
neuron differentiation -0.23 0.31 -10000 0 -0.64 300 300
PrPc/Cu2+ -0.009 0.074 -10000 0 -0.66 11 11
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.024 0.14 -10000 0 -0.84 24 24
Visual signal transduction: Rods

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
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 -0.29 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 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -10000 0 0
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 0.028 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.071 0.18 -9999 0 -0.57 93 93
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 0.06 -9999 0 -0.28 42 42
RDH5 -0.53 0.4 -9999 0 -0.84 533 533
SAG -0.014 0.061 -9999 0 -0.28 43 43
mol:Ca2+ -0.14 0.2 -9999 0 -0.44 153 153
Na + (4 Units) -0.14 0.19 -9999 0 -0.43 153 153
RGS9 -0.096 0.26 -9999 0 -0.78 103 103
GNB1/GNGT1 -0.029 0.065 -9999 0 -10000 0 0
GNAT1/GDP -0.063 0.16 -9999 0 -0.5 93 93
GUCY2D -0.004 0.042 -9999 0 -0.33 11 11
GNGT1 -0.045 0.1 -9999 0 -0.28 138 138
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 -0.84 256 256
Metarhodopsin II -0.004 0.022 -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 -10000 0 0
Metarhodopsin II/Transducin -0.008 0.018 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.009 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 93 93
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.022 0.047 -9999 0 -10000 0 0
PDE6B -0.017 0.12 -9999 0 -0.81 18 18
PDE6A -0.006 0.039 -9999 0 -0.28 17 17
PDE6G -0.01 0.051 -9999 0 -0.28 29 29
RHO -0.005 0.035 -9999 0 -0.28 14 14
PDE6 -0.07 0.16 -9999 0 -0.48 106 106
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
Aurora B signaling

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
Condensin I complex -0.055 0.053 -9999 0 -10000 0 0
STMN1 -0.1 0.12 -9999 0 -0.35 65 65
Aurora B/RasGAP/Survivin -0.17 0.12 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.15 0.15 -9999 0 -0.33 332 332
BIRC5 -0.2 0.12 -9999 0 -0.28 528 528
DES -0.31 0.34 -9999 0 -0.65 415 415
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 21 21
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 0.28 -9999 0 -0.56 332 332
KIF2C -0.035 0.025 -9999 0 -10000 0 0
PEBP1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.11 -9999 0 -10000 0 0
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 -10000 0 0
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.006 0.039 -9999 0 -10000 0 0
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 0.039 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -10000 0 0
AURKC -0.005 0.045 -9999 0 -0.84 1 1
CDCA8 -0.1 0.14 -9999 0 -0.28 114 114
cytokinesis -0.1 0.066 -9999 0 -10000 0 0
Aurora B/Septin1 -0.087 0.076 -9999 0 -10000 0 0
AURKA -0.14 0.14 -9999 0 -0.28 433 433
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.33 0.41 -9999 0 -0.84 332 332
BUB1 -0.2 0.12 -9999 0 -0.28 619 619
hSgo1/Aurora B/Survivin -0.25 0.17 -9999 0 -0.38 455 455
EVI5 0.007 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.094 0.091 -9999 0 -10000 0 0
SGOL1 -0.19 0.13 -9999 0 -10000 0 0
CENPA -0.049 0.052 -9999 0 -10000 0 0
NCAPG -0.16 0.14 -9999 0 -0.28 470 470
Aurora B/HC8 Proteasome -0.094 0.091 -9999 0 -10000 0 0
NCAPD2 -0.003 0.027 -9999 0 -10000 0 0
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 -10000 0 0
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 -0.34 16 16
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.019 -9999 0 -10000 0 0
MYLK -0.072 0.14 -9999 0 -0.48 79 79
KIF23 -0.094 0.13 -9999 0 -10000 0 0
VIM -0.091 0.1 -9999 0 -0.72 2 2
RACGAP1 -0.013 0.062 -9999 0 -0.28 43 43
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.019 -9999 0 -10000 0 0
Chromosomal passenger complex -0.076 0.062 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.15 0.17 -9999 0 -10000 0 0
TACC1 -0.021 0.13 -9999 0 -0.84 21 21
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 regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.035 0.05 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.076 0.16 -9999 0 -0.48 65 65
JUN -0.046 0.14 -9999 0 -0.56 16 16
HRAS 0 0.01 -9999 0 -0.28 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.21 -9999 0 -0.56 147 147
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.03 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.21 -9999 0 -0.56 144 144
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 -0.53 138 138
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.51 144 144
GRB7 -0.021 0.077 -9999 0 -0.29 62 62
RET51/GFRalpha1/GDNF -0.15 0.21 -9999 0 -0.56 147 147
MAPKKK cascade -0.094 0.17 -9999 0 -0.47 92 92
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.24 -9999 0 -0.6 147 147
lamellipodium assembly -0.076 0.15 -9999 0 -0.38 144 144
RET51/GFRalpha1/GDNF/SHC -0.15 0.21 -9999 0 -0.56 147 147
PIK3CA 0 0.01 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.53 138 138
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.53 138 138
MAPK3 -0.12 0.17 -9999 0 -0.47 144 144
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 -0.68 192 192
MAPK8 -0.069 0.13 -9999 0 -0.46 23 23
HRAS/GTP -0.098 0.2 -9999 0 -0.52 144 144
tube development -0.093 0.18 -9999 0 -0.49 138 138
MAPK1 -0.12 0.17 -9999 0 -0.47 144 144
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.061 0.13 -9999 0 -0.35 138 138
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.2 -9999 0 -0.54 149 149
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.21 -9999 0 -0.56 147 147
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.58 157 157
PRKCA -0.022 0.13 -9999 0 -0.84 21 21
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
CREB1 -0.067 0.15 -9999 0 -0.39 138 138
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.061 0.13 -9999 0 -0.35 138 138
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.58 149 149
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.12 0.16 -9999 0 -0.84 13 13
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.045 0.14 -9999 0 -0.54 16 16
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.53 138 138
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 -0.061 0.13 -9999 0 -0.35 138 138
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.078 0.14 -9999 0 -0.38 98 98
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.078 0.14 -9999 0 -0.37 144 144
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.079 0.15 -9999 0 -0.38 144 144
PI3K -0.12 0.24 -9999 0 -0.61 144 144
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.093 0.18 -9999 0 -0.49 138 138
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.074 0.13 -9999 0 -0.42 35 35
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.2 -9999 0 -0.56 144 144
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 -0.079 0.15 -9999 0 -0.38 144 144
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.22 -9999 0 -0.57 168 168
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 -0.64 152 152
Rac1/GTP -0.092 0.18 -9999 0 -0.46 144 144
RET9/GFRalpha1/GDNF -0.11 0.21 -9999 0 -0.57 142 142
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.65 142 142
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.098 0.19 -10000 0 -0.5 144 144
ER alpha/Gai/GDP/Gbeta gamma -0.086 0.19 -10000 0 -0.47 136 136
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 -0.48 57 57
IGF1R -0.02 0.12 -10000 0 -0.59 29 29
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 -0.58 139 139
KRAS 0 0.01 -10000 0 -0.28 1 1
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 0.071 -10000 0 -0.84 6 6
GNAO1 -0.033 0.14 -10000 0 -0.48 58 58
HRAS 0 0.01 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.054 0.22 -10000 0 -0.55 125 125
E2/ER beta (dimer) -0.018 0.11 -10000 0 -0.66 23 23
mol:GDP -0.084 0.21 -10000 0 -0.56 139 139
mol:NADP -0.054 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 57 57
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.59 29 29
PLCB1 -0.059 0.14 -10000 0 -0.53 56 56
PLCB2 -0.032 0.088 -10000 0 -0.68 9 9
IGF1 -0.19 0.35 -10000 0 -0.84 187 187
mol:L-citrulline -0.054 0.22 -10000 0 -0.55 125 125
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.038 0.15 -10000 0 -0.85 21 21
JNK cascade -0.018 0.11 -10000 0 -0.65 23 23
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.023 0.14 -10000 0 -0.84 23 23
GNAQ -0.002 0.041 -10000 0 -0.84 2 2
ESR1 -0.15 0.29 -10000 0 -0.56 230 230
Gq family/GDP/Gbeta gamma -0.004 0.061 -10000 0 -0.78 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.022 0.13 -10000 0 -0.36 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.087 0.21 -10000 0 -0.56 122 122
GNAZ -0.006 0.071 -10000 0 -0.84 6 6
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.66 117 117
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.19 0.35 -10000 0 -0.84 189 189
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.001 0.1 -10000 0 -0.59 24 24
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.84 42 42
HBEGF -0.063 0.19 -10000 0 -0.44 134 134
cAMP biosynthetic process -0.2 0.27 -10000 0 -0.55 288 288
SRC -0.046 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 -0.076 0.19 -10000 0 -0.48 144 144
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.53 184 184
Gs family/GTP -0.2 0.28 -10000 0 -0.56 288 288
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.008 -10000 0 -10000 0 0
vasodilation -0.05 0.21 -10000 0 -0.52 125 125
mol:DAG -0.025 0.15 -10000 0 -0.51 57 57
Gs family/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.46 289 289
MSN -0.017 0.14 -10000 0 -0.45 2 2
Gq family/GTP -0.036 0.091 -10000 0 -0.67 9 9
mol:PI-3-4-5-P3 -0.086 0.3 -10000 0 -0.82 117 117
NRAS -0.001 0.014 -10000 0 -0.28 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.05 0.21 0.52 125 -10000 0 125
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.077 0.2 -10000 0 -0.52 139 139
NOS3 -0.059 0.23 -10000 0 -0.58 125 125
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.053 0.25 -10000 0 -0.66 117 117
E2/ER alpha (dimer)/PELP1/Src -0.091 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 -0.086 0.19 -10000 0 -0.48 135 135
MMP2 -0.039 0.19 -10000 0 -0.43 131 131
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0 0 -9999 0 -10000 0 0
CCL5 -0.012 0.07 -9999 0 -0.84 3 3
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.073 0.11 -9999 0 -0.35 83 83
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 0.1 -9999 0 -0.63 3 3
Syndecan-1/Syntenin -0.067 0.1 -9999 0 -0.63 3 3
MAPK3 -0.049 0.091 -9999 0 -0.52 4 4
HGF/MET -0.15 0.29 -9999 0 -0.69 179 179
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 0.099 -9999 0 -0.62 3 3
Syndecan-1/RANTES -0.072 0.11 -9999 0 -0.68 7 7
Syndecan-1/CD147 -0.057 0.097 -9999 0 -0.56 4 4
Syndecan-1/Syntenin/PIP2 -0.064 0.097 -9999 0 -0.61 3 3
LAMA5 0 0.01 -9999 0 -0.28 1 1
positive regulation of cell-cell adhesion -0.063 0.095 -9999 0 -0.59 3 3
MMP7 -0.12 0.29 -9999 0 -0.84 118 118
HGF -0.051 0.2 -9999 0 -0.84 51 51
Syndecan-1/CASK -0.069 0.1 -9999 0 -0.33 83 83
Syndecan-1/HGF/MET -0.17 0.26 -9999 0 -0.62 181 181
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 83 83
SDC1 -0.073 0.11 -9999 0 -0.35 83 83
Syndecan-1/Collagen -0.073 0.11 -9999 0 -0.35 83 83
PPIB 0 0.01 -9999 0 -0.28 1 1
MET -0.14 0.32 -9999 0 -0.84 144 144
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.28 353 353
MAPK1 -0.049 0.091 -9999 0 -0.52 4 4
homophilic cell adhesion -0.072 0.11 -9999 0 -0.34 83 83
MMP1 -0.22 0.11 -9999 0 -0.28 662 662
Signaling events mediated by PTP1B

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
PDGFRB -0.002 0.041 -10000 0 -0.84 2 2
Jak2/Leptin Receptor -0.15 0.24 -10000 0 -0.55 205 205
PTP1B/AKT1 -0.068 0.1 -10000 0 -0.33 84 84
FYN -0.001 0.029 -10000 0 -0.84 1 1
p210 bcr-abl/PTP1B -0.069 0.12 -10000 0 -0.37 90 90
EGFR -0.3 0.4 -10000 0 -0.84 295 295
EGF/EGFR -0.3 0.32 -10000 0 -0.6 411 411
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 89 89
Insulin Receptor/Insulin -0.047 0.073 -10000 0 -0.4 8 8
HCK -0.004 0.033 -10000 0 -0.28 12 12
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 -0.51 215 215
TXN 0 0.01 -10000 0 -0.28 1 1
PTP1B/IRS1/GRB2 -0.084 0.14 -10000 0 -0.42 93 93
cell migration 0.069 0.12 0.37 90 -10000 0 90
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.001 0.026 -10000 0 -10000 0 0
ITGA2B -0.016 0.072 -10000 0 -0.84 2 2
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 -0.073 0.11 -10000 0 -0.35 85 85
Crk/p130 Cas -0.066 0.1 -10000 0 -0.34 72 72
DOK1 -0.043 0.11 -10000 0 -0.32 65 65
JAK2 -0.039 0.07 -10000 0 -0.3 8 8
Jak2/Leptin Receptor/Leptin -0.39 0.19 -10000 0 -0.46 693 693
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 -0.069 0.12 -10000 0 -0.37 90 90
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 -0.016 0.11 -10000 0 -0.72 19 19
CAT1/PTP1B -0.087 0.17 -10000 0 -0.38 150 150
CAPN1 0 0.002 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.037 0.065 -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 -0.45 420 420
negative regulation of transcription -0.038 0.07 -10000 0 -0.3 8 8
FCGR2A 0 0.01 -10000 0 -0.28 1 1
FER -0.006 0.071 -10000 0 -0.85 6 6
alphaIIb/beta3 Integrin -0.023 0.099 -10000 0 -0.66 17 17
BLK -0.036 0.1 -10000 0 -0.84 3 3
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 -0.84 202 202
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 -0.45 17 17
PRL -0.004 0.032 -10000 0 -0.31 1 1
SOCS3 0.016 0.12 -10000 0 -1.5 5 5
SPRY2 -0.097 0.27 -10000 0 -0.85 96 96
Insulin Receptor/Insulin/IRS1 -0.021 0.11 -10000 0 -0.58 31 31
CSF1/CSF1R -0.068 0.11 -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 85 85
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 -10000 0 0
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 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
alphaM/beta2 Integrin/proMMP-2 -0.023 0.063 -9999 0 -0.6 8 8
alphaM/beta2 Integrin/GPIbA -0.025 0.06 -9999 0 -0.54 8 8
alphaM/beta2 Integrin/proMMP-9 -0.076 0.077 -9999 0 -0.39 5 5
PLAUR -0.02 0.072 -9999 0 -0.28 62 62
HMGB1 -0.014 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.018 0.026 -9999 0 -10000 0 0
AGER -0.017 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 0.1 -9999 0 -0.73 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.28 353 353
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 -0.84 209 209
MYH2 -0.074 0.17 -9999 0 -0.42 94 94
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 -0.012 0.08 -9999 0 -0.42 23 23
alphaM/beta2 Integrin/CTGF -0.025 0.071 -9999 0 -0.63 10 10
alphaM/beta2 Integrin -0.075 0.14 -9999 0 -0.38 81 81
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 -0.28 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.066 0.14 -9999 0 -0.33 118 118
cell adhesion -0.025 0.06 -9999 0 -0.53 8 8
NFKB1 -0.14 0.18 -9999 0 -0.66 13 13
THY1 -0.002 0.023 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.37 0.28 -9999 0 -0.58 542 542
alphaM/beta2 Integrin/LRP/tPA -0.033 0.11 -9999 0 -0.59 31 31
IL6 -0.33 0.5 -9999 0 -0.97 324 324
ITGB2 -0.017 0.033 -9999 0 -0.28 9 9
elevation of cytosolic calcium ion concentration -0.024 0.046 -9999 0 -10000 0 0
alphaM/beta2 Integrin/JAM2/JAM3 -0.042 0.13 -9999 0 -0.55 47 47
JAM2 -0.045 0.19 -9999 0 -0.84 45 45
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 -0.4 162 162
positive regulation of phagocytosis -0.051 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 0.043 -9999 0 -0.31 1 1
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 -0.07 0.16 -9999 0 -0.4 95 95
MST1 -0.012 0.096 -9999 0 -0.84 11 11
alphaM/beta2 Integrin/lipoprotein(a) -0.34 0.24 -9999 0 -0.51 542 542
TNF -0.097 0.22 -9999 0 -0.86 19 19
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.022 0.035 -9999 0 -10000 0 0
fibrinolysis -0.019 0.031 -9999 0 -10000 0 0
HCK -0.004 0.033 -9999 0 -0.28 12 12
dendritic cell antigen processing and presentation -0.066 0.14 -9999 0 -0.33 118 118
VTN -0.023 0.09 -9999 0 -0.84 4 4
alphaM/beta2 Integrin/CYR61 -0.05 0.14 -9999 0 -0.61 47 47
LPA -0.001 0.019 -9999 0 -0.28 4 4
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 -0.82 62 62
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 -0.41 102 102
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.001 0.019 -9999 0 -10000 0 0
CTGF -0.011 0.092 -9999 0 -0.74 12 12
alphaM/beta2 Integrin/Hck -0.02 0.032 -9999 0 -0.31 2 2
ITGAM -0.015 0.027 -9999 0 -0.3 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.14 0.23 -9999 0 -0.54 209 209
HP -0.17 0.33 -9999 0 -0.84 159 159
leukocyte adhesion -0.077 0.13 -9999 0 -0.6 30 30
SELP -0.21 0.36 -9999 0 -0.84 209 209
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.003 0.036 -9999 0 -0.65 2 2
alphaV beta3 Integrin -0.23 0.29 -9999 0 -0.57 343 343
PTK2 -0.086 0.18 -9999 0 -0.66 19 19
IGF1R -0.02 0.12 -9999 0 -0.59 29 29
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.013 0.098 -9999 0 -0.84 11 11
SRC 0 0.01 -9999 0 -0.28 1 1
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 -0.011 0.071 -9999 0 -0.5 16 16
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 0.076 -9999 0 -0.56 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.26 -9999 0 -0.58 205 205
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.006 0.044 -9999 0 -0.43 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.083 -9999 0 -0.56 16 16
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.34 0.36 -9999 0 -0.66 412 412
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.049 0.094 -9999 0 -0.58 15 15
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 -0.017 0.092 -9999 0 -0.52 25 25
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 -0.59 29 29
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.024 0.14 -9999 0 -0.84 24 24
ITGB3 -0.016 0.11 -9999 0 -0.72 19 19
IGF1 -0.19 0.35 -9999 0 -0.84 187 187
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.016 0.1 -9999 0 -0.63 20 20
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 0.077 -9999 0 -0.56 16 16
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.028 0.14 -9999 0 -0.69 30 30
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 -0.6 43 43
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.012 0.076 -9999 0 -0.54 16 16
FAK1/Vinculin -0.064 0.15 -9999 0 -0.5 18 18
alphaV beta3/Integrin/ppsTEM5 -0.016 0.1 -9999 0 -0.64 20 20
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.023 0.09 -9999 0 -0.84 4 4
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 -0.65 337 337
alphaV/beta3 Integrin/Lactadherin -0.019 0.1 -9999 0 -0.6 24 24
alphaV/beta3 Integrin/TGFBR2 -0.026 0.13 -9999 0 -0.65 33 33
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.03 -9999 0 -0.51 3 3
HSP90AA1 0 0.01 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.01 0.069 -9999 0 -0.52 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.011 0.072 -9999 0 -0.51 16 16
SDC1 -0.02 0.075 -9999 0 -0.84 1 1
VAV3 -0.005 0.042 -9999 0 -0.48 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 -0.5 18 18
cell migration -0.05 0.14 -9999 0 -0.45 17 17
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.22 -9999 0 -0.45 345 345
SPP1 -0.079 0.12 -9999 0 -0.28 240 240
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 -0.84 165 165
angiogenesis -0.31 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 -0.026 0.13 -9999 0 -0.65 33 33
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.056 0.22 -9999 0 -0.64 37 37
CRP -0.06 0.22 -9999 0 -0.64 38 38
cell cycle arrest -0.073 0.24 -9999 0 -0.73 44 44
TIMP1 -0.055 0.2 -9999 0 -0.56 42 42
IL6ST -0.043 0.21 -9999 0 -0.83 57 57
Rac1/GDP -0.14 0.19 -9999 0 -0.66 54 54
AP1 -0.14 0.25 -9999 0 -0.51 228 228
GAB2 -0.002 0.027 -9999 0 -0.28 8 8
TNFSF11 -0.066 0.22 -9999 0 -0.66 36 36
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 0.051 0.047 -9999 0 -0.44 7 7
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 53 53
MITF -0.13 0.24 -9999 0 -0.51 125 125
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 -10000 0 0
STAT3 -0.08 0.26 -9999 0 -0.8 44 44
STAT1 -0.012 0.023 -9999 0 -10000 0 0
CEBPD -0.058 0.22 -9999 0 -0.67 40 40
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 -0.15 0.2 -9999 0 -0.66 57 57
MAPK11 -0.12 0.24 -9999 0 -0.75 55 55
STAT3 (dimer)/FOXO1 -0.023 0.21 -9999 0 -0.58 40 40
GRB2/SOS1/GAB family -0.13 0.18 -9999 0 -0.75 35 35
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 -0.98 202 202
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0 0.002 -9999 0 -10000 0 0
MYC -0.07 0.26 -9999 0 -0.86 45 45
FGG -0.065 0.22 -9999 0 -0.64 40 40
macrophage differentiation -0.073 0.24 -9999 0 -0.73 44 44
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.28 -9999 0 -0.52 367 367
JUNB -0.055 0.21 -9999 0 -0.63 35 35
FOS -0.27 0.39 -9999 0 -0.84 272 272
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.14 0.25 -9999 0 -0.45 207 207
STAT1/PIAS1 -0.14 0.2 -9999 0 -0.62 63 63
GRB2/SOS1/GAB family/SHP2/PI3K 0.001 0.009 -9999 0 -10000 0 0
STAT3 (dimer) -0.076 0.25 -9999 0 -0.77 44 44
PRKCD -0.051 0.22 -9999 0 -0.61 49 49
IL6R -0.022 0.13 -9999 0 -0.84 22 22
SOCS3 -0.11 0.23 -9999 0 -0.8 46 46
gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.15 -9999 0 -0.56 59 59
Rac1/GTP -0.14 0.19 -9999 0 -0.66 55 55
HCK -0.004 0.033 -9999 0 -0.28 12 12
MAPKKK cascade 0 0.068 -9999 0 -10000 0 0
bone resorption -0.062 0.21 -9999 0 -0.62 37 37
IRF1 -0.056 0.22 -9999 0 -0.63 40 40
mol:GDP -0.12 0.24 -9999 0 -0.62 69 69
SOS1 0 0.002 -9999 0 -10000 0 0
VAV1 -0.12 0.24 -9999 0 -0.64 69 69
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.23 -9999 0 -0.81 51 51
PTPN11 -0.013 0.02 -9999 0 -10000 0 0
IL6/IL6RA -0.26 0.33 -9999 0 -0.66 333 333
gp130 (dimer)/TYK2/TYK2/LMO4 -0.033 0.15 -9999 0 -0.56 59 59
gp130 (dimer)/JAK2/JAK2/LMO4 -0.033 0.15 -9999 0 -0.56 59 59
IL6 -0.31 0.41 -9999 0 -0.84 324 324
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 -0.4 366 366
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
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
RXR and RAR heterodimerization with other nuclear receptor

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
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 0.17 -9999 0 -0.32 206 206
RXRs/LXRs/DNA/Oxysterols -0.016 0.15 -9999 0 -0.43 25 25
MED1 -0.008 0.045 -9999 0 -10000 0 0
mol:9cRA 0.005 0.008 -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 -0.39 347 347
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 -10000 0 0
RXRs/LXRs/DNA -0.11 0.2 -9999 0 -0.46 204 204
NR1H2 0.016 0.006 -9999 0 -10000 0 0
NR1H3 0.016 0.007 -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 0.006 -9999 0 -10000 0 0
RXRB 0.015 0.007 -9999 0 -10000 0 0
THRB -0.036 0.17 -9999 0 -0.84 36 36
PPARG -0.2 0.36 -9999 0 -0.84 198 198
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.017 0.2 -9999 0 -1.3 11 11
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.016 0.15 -9999 0 -0.42 25 25
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 -0.006 0.14 -9999 0 -0.66 5 5
RXRs/RXRs/DNA/9cRA -0.12 0.22 -9999 0 -0.5 204 204
ABCA1 -0.009 0.16 -9999 0 -1 7 7
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
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.003 0.027 -9999 0 -0.28 8 8
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 -0.84 293 293
Syndecan-3/EGFR -0.17 0.23 -9999 0 -0.48 293 293
AGRP -0.002 0.025 -9999 0 -0.28 7 7
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 -0.28 1 1
PTN -0.37 0.42 -9999 0 -0.84 374 374
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.19 0.21 -9999 0 -0.43 373 373
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 -0.65 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 -0.016 0.07 -9999 0 -0.47 17 17
IL8 -0.035 0.13 -9999 0 -0.41 73 73
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
Signaling events mediated by PRL

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
CCNE1 -0.053 0.11 -9999 0 -10000 0 0
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 -0.33 128 128
CCNA2 -0.18 0.26 -9999 0 -0.53 285 285
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.2 0.32 -9999 0 -0.64 285 285
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 -0.14 0.25 -9999 0 -0.5 285 285
PTP4A3 -0.001 0.019 -9999 0 -10000 0 0
PTP4A2 -0.001 0.014 -9999 0 -10000 0 0
ITGB1 0.021 0.014 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
RAC1 -0.063 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 -0.46 285 285
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0 0.006 -9999 0 -10000 0 0
RHOC -0.063 0.088 -9999 0 -10000 0 0
RHOA -0.063 0.088 -9999 0 -10000 0 0
cell motility -0.043 0.11 -9999 0 -0.25 2 2
PRL-1/alpha Tubulin -0.16 0.22 -9999 0 -0.46 285 285
PRL-3/alpha1 Integrin -0.002 0.034 -9999 0 -0.65 2 2
ROCK1 -0.044 0.11 -9999 0 -0.25 2 2
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.14 0.25 -9999 0 -0.5 285 285
ATF5 -0.001 0.019 -9999 0 -0.28 4 4
Fc-epsilon receptor I signaling in mast cells

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
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 -0.46 284 284
mol:PIP3 -0.03 0.21 -9999 0 -0.43 169 169
IKBKB 0.001 0.12 -9999 0 -0.33 36 36
AKT1 -0.084 0.18 -9999 0 -0.68 30 30
IKBKG 0.001 0.12 -9999 0 -0.33 36 36
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 0.007 0.13 -9999 0 -0.45 27 27
mol:Ca2+ -0.015 0.16 -9999 0 -0.32 169 169
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 -0.51 169 169
PTPN13 -0.031 0.17 -9999 0 -0.57 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 0.18 -9999 0 -0.44 169 169
LAT -0.065 0.14 -9999 0 -0.44 67 67
PAK2 -0.003 0.14 -9999 0 -0.5 28 28
NFATC2 -0.08 0.22 -9999 0 -0.89 48 48
HRAS -0.013 0.15 -9999 0 -0.55 29 29
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 -0.64 169 169
Antigen/IgE/Fc epsilon R1 -0.12 0.25 -9999 0 -0.59 169 169
mol:GDP -0.019 0.15 -9999 0 -0.56 29 29
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 68 68
CHUK 0.001 0.12 -9999 0 -0.33 36 36
KLRG1 -0.063 0.14 -9999 0 -0.41 68 68
VAV1 -0.064 0.14 -9999 0 -0.44 67 67
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.063 0.14 -9999 0 -0.44 66 66
negative regulation of mast cell degranulation -0.058 0.12 -9999 0 -0.52 29 29
BTK -0.061 0.14 -9999 0 -0.43 66 66
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.089 0.2 -9999 0 -0.44 170 170
GAB2/PI3K/SHP2 -0.093 0.2 -9999 0 -0.77 30 30
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.072 0.16 -9999 0 -0.36 169 169
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.23 -9999 0 -0.54 170 170
FCER1G 0.003 0.013 -9999 0 -0.28 1 1
FCER1A -0.12 0.31 -9999 0 -0.85 130 130
Antigen/IgE/Fc epsilon R1/Fyn -0.11 0.23 -9999 0 -0.55 169 169
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 28 28
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.054 0.12 -9999 0 -0.52 29 29
FER -0.066 0.14 -9999 0 -0.45 70 70
RELA 0 0 -9999 0 -10000 0 0
ITK -0.034 0.11 -9999 0 -0.62 27 27
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.017 0.16 -9999 0 -0.54 35 35
cytokine secretion -0.02 0.04 -9999 0 -10000 0 0
SPHK1 -0.065 0.14 -9999 0 -0.44 69 69
PTK2 -0.03 0.16 -9999 0 -0.58 28 28
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.093 0.19 -9999 0 -0.46 169 169
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.025 0.2 -9999 0 -0.49 75 75
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 -0.52 29 29
MAP2K4 0.015 0.038 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.12 0.25 -9999 0 -0.58 170 170
mol:Choline -0.1 0.21 -9999 0 -0.5 169 169
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 -0.54 27 27
HCLS1 -0.063 0.14 -9999 0 -0.44 66 66
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 -0.059 0.13 -9999 0 -0.53 29 29
LCP2 0 0.01 -9999 0 -10000 0 0
PLA2G4A -0.11 0.21 -9999 0 -0.53 143 143
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.1 0.21 -9999 0 -0.5 169 169
IKK complex 0.018 0.095 -9999 0 -0.23 34 34
WIPF1 0 0 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.058 0.2 -9999 0 -0.85 51 51
PDGF/PDGFRA/CRKL -0.039 0.15 -9999 0 -0.65 50 50
positive regulation of JUN kinase activity -0.03 0.12 -9999 0 -0.5 50 50
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.043 0.16 -9999 0 -0.66 50 50
AP1 -0.4 0.56 -9999 0 -1.2 272 272
mol:IP3 -0.035 0.16 -9999 0 -0.67 50 50
PLCG1 -0.035 0.16 -9999 0 -0.68 50 50
PDGF/PDGFRA/alphaV Integrin -0.039 0.15 -9999 0 -0.65 50 50
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.035 0.16 -9999 0 -0.67 50 50
CAV3 -0.001 0.017 -9999 0 -0.28 3 3
CAV1 -0.17 0.34 -9999 0 -0.84 175 175
SHC/Grb2/SOS1 -0.03 0.12 -9999 0 -0.5 50 50
PDGF/PDGFRA/Shf -0.04 0.16 -9999 0 -0.66 50 50
FOS -0.36 0.57 -9999 0 -1.2 272 272
JUN -0.028 0.077 -9999 0 -0.72 9 9
oligodendrocyte development -0.039 0.15 -9999 0 -0.65 50 50
GRB2 0 0.01 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG -0.035 0.16 -9999 0 -0.67 50 50
PDGF/PDGFRA -0.058 0.2 -9999 0 -0.85 51 51
actin cytoskeleton reorganization -0.04 0.16 -9999 0 -0.65 51 51
SRF 0.016 0.022 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.033 0.13 -9999 0 -0.56 50 50
PDGF/PDGFRA/Crk/C3G -0.033 0.13 -9999 0 -0.56 50 50
JAK1 -0.023 0.16 -9999 0 -0.65 50 50
ELK1/SRF -0.026 0.12 -9999 0 -0.51 50 50
SHB -0.001 0.03 -9999 0 -0.56 2 2
SHF -0.001 0.03 -9999 0 -0.56 2 2
CSNK2A1 0.02 0.027 -9999 0 -10000 0 0
GO:0007205 -0.037 0.17 -9999 0 -0.69 50 50
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.03 0.12 -9999 0 -0.5 50 50
PDGF/PDGFRA/SHB -0.04 0.16 -9999 0 -0.65 51 51
PDGF/PDGFRA/Caveolin-1 -0.17 0.33 -9999 0 -0.76 191 191
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.036 0.16 -9999 0 -0.62 50 50
PIK3CA 0 0.01 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.039 0.15 -9999 0 -0.65 50 50
JAK-STAT cascade -0.023 0.16 -9999 0 -0.65 50 50
cell proliferation -0.04 0.16 -9999 0 -0.66 50 50
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.013 0.081 -9999 0 -0.55 16 16
NF kappa B1 p50/RelA/I kappa B alpha -0.045 0.12 -9999 0 -0.5 4 4
AP1 -0.21 0.28 -9999 0 -0.52 339 339
mol:PIP3 -0.2 0.25 -9999 0 -0.49 294 294
AKT1 -0.008 0.053 -9999 0 -0.57 2 2
PTK2B 0.016 0.057 -9999 0 -0.31 12 12
RHOA 0.029 0.024 -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 -0.062 0.15 -9999 0 -0.44 110 110
HRAS/GDP 0 0.006 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.018 0.15 -9999 0 -0.44 87 87
NF kappa B1 p50/RelA -0.054 0.14 -9999 0 -0.55 11 11
endothelial cell migration 0.011 0.11 -9999 0 -0.7 19 19
ADCY4 0.002 0.14 -9999 0 -0.62 25 25
ADCY5 -0.067 0.18 -9999 0 -0.6 53 53
ADCY6 0.011 0.12 -9999 0 -0.6 18 18
ADCY7 0.011 0.12 -9999 0 -0.6 18 18
ADCY1 0.003 0.13 -9999 0 -0.61 22 22
ADCY2 -0.009 0.15 -9999 0 -0.64 28 28
ADCY3 0.011 0.12 -9999 0 -0.6 18 18
ADCY8 0.008 0.12 -9999 0 -0.61 18 18
ADCY9 0.011 0.12 -9999 0 -0.6 18 18
GSK3B 0.023 0.054 -9999 0 -0.4 4 4
arachidonic acid secretion 0.015 0.11 -9999 0 -0.57 18 18
GNG2 -0.006 0.071 -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 39 39
HRAS 0 0.01 -9999 0 -0.28 1 1
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 0.003 -9999 0 -10000 0 0
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 0.005 -9999 0 -10000 0 0
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 0.015 0.11 -9999 0 -0.57 18 18
LPA/LPA1-2-3 -0.075 0.18 -9999 0 -0.52 109 109
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 0.003 0.1 -9999 0 -0.41 12 12
GNAZ 0.013 0.088 -9999 0 -0.48 25 25
EGFR/PI3K-beta/Gab1 -0.2 0.27 -9999 0 -0.65 130 130
positive regulation of dendritic cell cytokine production -0.074 0.18 -9999 0 -0.52 109 109
LPA/LPA2/MAGI-3 -0.002 0.022 -9999 0 -0.56 1 1
ARHGEF1 -0.008 0.058 -9999 0 -0.47 11 11
GNAI2 0.017 0.073 -9999 0 -0.46 18 18
GNAI3 0.017 0.073 -9999 0 -0.45 19 19
GNAI1 -0.012 0.16 -9999 0 -0.61 50 50
LPA/LPA3 -0.086 0.21 -9999 0 -0.65 101 101
LPA/LPA2 -0.001 0.014 -9999 0 -10000 0 0
LPA/LPA1 -0.012 0.081 -9999 0 -0.53 19 19
HB-EGF/EGFR -0.25 0.27 -9999 0 -0.61 293 293
HBEGF -0.062 0.1 -9999 0 -0.65 3 3
mol:DAG -0.01 0.14 -9999 0 -0.38 101 101
cAMP biosynthetic process -0.008 0.14 -9999 0 -0.56 37 37
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
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 -10000 0 0
LPAR3 -0.11 0.27 -9999 0 -0.7 134 134
LPAR1 -0.013 0.096 -9999 0 -0.83 11 11
IL8 -0.19 0.23 -9999 0 -0.45 314 314
PTK2 -0.069 0.17 -9999 0 -0.49 109 109
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.063 0.16 -9999 0 -0.44 110 110
EGFR -0.29 0.4 -9999 0 -0.84 293 293
PLCG1 -0.058 0.15 -9999 0 -0.45 101 101
PLD2 -0.069 0.17 -9999 0 -0.49 109 109
G12/G13 -0.009 0.063 -9999 0 -0.5 11 11
PI3K-beta -0.01 0.061 -9999 0 -0.68 2 2
cell migration -0.022 0.055 -9999 0 -0.24 5 5
SLC9A3R2 0 0 -9999 0 -10000 0 0
PXN 0.003 0.1 -9999 0 -0.42 12 12
HRAS/GTP -0.03 0.1 -9999 0 -0.59 18 18
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.14 -9999 0 -0.28 353 353
PRKCE 0 0.001 -9999 0 -10000 0 0
PRKCD -0.001 0.13 -9999 0 -0.42 8 8
Gi(beta/gamma) -0.031 0.11 -9999 0 -0.61 20 20
mol:LPA -0.002 0.021 -9999 0 -0.22 8 8
TRIP6/p130 Cas/FAK1/Paxillin -0.057 0.14 -9999 0 -0.55 13 13
MAPKKK cascade 0.015 0.11 -9999 0 -0.57 18 18
contractile ring contraction involved in cytokinesis 0.029 0.024 -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 -0.019 0.15 -9999 0 -0.45 86 86
GNA11 -0.056 0.14 -9999 0 -0.43 101 101
Rac1/GTP 0 0.003 -9999 0 -10000 0 0
MMP2 0.011 0.11 -9999 0 -0.7 19 19
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.047 0.29 -10000 0 -0.84 92 92
IHH -0.011 0.076 -10000 0 -0.43 3 3
SHH Np/Cholesterol/GAS1 -0.03 0.12 -10000 0 -0.53 45 45
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.03 0.12 0.53 45 -10000 0 45
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 14 14
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.062 0.22 -10000 0 -0.84 62 62
ADRBK1 0 0.01 -10000 0 -10000 0 0
heart looping -0.029 0.25 -10000 0 -0.9 57 57
STIL -0.035 0.21 -10000 0 -0.73 59 59
DHH N/PTCH2 -0.073 0.21 -10000 0 -0.67 91 91
DHH N/PTCH1 -0.085 0.24 -10000 0 -0.8 75 75
PIK3CA 0 0.01 -10000 0 -10000 0 0
DHH -0.023 0.14 -10000 0 -0.84 23 23
PTHLH -0.071 0.37 -10000 0 -1.1 92 92
determination of left/right symmetry -0.029 0.25 -10000 0 -0.9 57 57
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.069 0.36 -10000 0 -1.1 92 92
IHH N/Hhip -0.009 0.047 -10000 0 -0.49 2 2
DHH N/Hhip -0.02 0.11 -10000 0 -0.66 24 24
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.029 0.25 -10000 0 -0.9 57 57
pancreas development -0.004 0.04 -10000 0 -0.33 10 10
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 -0.044 0.19 -10000 0 -0.84 44 44
somite specification -0.029 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 -0.048 0.15 -10000 0 -0.52 73 73
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.52 220 220
SHH 0.01 0.036 -10000 0 -0.66 1 1
catabolic process -0.041 0.25 -10000 0 -0.89 62 62
SMO/Vitamin D3 -0.069 0.22 -10000 0 -0.84 58 58
SHH Np/Cholesterol/Hhip -0.005 0.036 -10000 0 -0.53 2 2
LRP2 -0.22 0.37 -10000 0 -0.79 240 240
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.84 70 70
SHH Np/Cholesterol/BOC -0.042 0.14 -10000 0 -0.53 63 63
SHH Np/Cholesterol/CDO -0.009 0.061 -10000 0 -0.52 11 11
mesenchymal cell differentiation 0.005 0.036 0.52 2 -10000 0 2
mol:Vitamin D3 -0.025 0.22 -10000 0 -0.79 56 56
IHH N/PTCH2 -0.066 0.2 -10000 0 -0.72 72 72
CDON -0.01 0.091 -10000 0 -0.84 10 10
IHH N/PTCH1 -0.039 0.26 -10000 0 -0.89 62 62
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.65 219 219
PTCH2 -0.072 0.23 -10000 0 -0.84 72 72
SHH Np/Cholesterol -0.003 0.026 -10000 0 -0.53 1 1
PTCH1 -0.041 0.26 -10000 0 -0.89 62 62
HHIP -0.004 0.041 -10000 0 -0.33 10 10
E-cadherin signaling in keratinocytes

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
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 -0.4 293 293
FMN1 0.026 0.085 -9999 0 -0.48 12 12
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 -10000 0 0
ZYX 0.033 0.059 -9999 0 -10000 0 0
JUB 0.031 0.068 -9999 0 -0.45 4 4
EGFR(dimer) -0.16 0.22 -9999 0 -0.46 294 294
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 -0.84 1 1
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 -0.4 293 293
establishment of polarity of embryonic epithelium 0.033 0.058 -9999 0 -10000 0 0
SRC 0 0.01 -9999 0 -0.28 1 1
RAC1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.4 -9999 0 -0.84 293 293
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 0.082 -9999 0 -0.46 12 12
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 -0.43 293 293
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 -0.42 294 294
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.075 0.18 0.68 62 -10000 0 62
KIRREL -0.062 0.22 -10000 0 -0.84 62 62
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.076 0.18 -10000 0 -0.68 62 62
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 -0.055 0.14 -10000 0 -0.52 62 62
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.03 0.099 -10000 0 -0.38 62 62
FYN -0.05 0.13 -10000 0 -0.5 62 62
mol:Ca2+ -0.054 0.14 -10000 0 -0.52 62 62
mol:DAG -0.054 0.14 -10000 0 -0.52 62 62
NPHS2 -0.008 0.03 -10000 0 -0.27 6 6
mol:IP3 -0.054 0.14 -10000 0 -0.52 62 62
regulation of endocytosis -0.022 0.13 -10000 0 -0.46 62 62
Nephrin/NEPH1/podocin/Cholesterol -0.057 0.14 -10000 0 -0.53 62 62
establishment of cell polarity -0.075 0.18 -10000 0 -0.68 62 62
Nephrin/NEPH1/podocin/NCK1-2 -0.022 0.13 -10000 0 -0.48 62 62
Nephrin/NEPH1/beta Arrestin2 -0.022 0.13 -10000 0 -0.47 62 62
NPHS1 -0.049 0.1 -10000 0 -0.28 139 139
Nephrin/NEPH1/podocin -0.045 0.13 -10000 0 -0.5 62 62
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 -0.055 0.14 -10000 0 -0.52 62 62
CD2AP 0 0.01 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.055 0.14 -10000 0 -0.52 62 62
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 68 68
cytoskeleton organization -0.04 0.12 -10000 0 -0.48 62 62
Nephrin/NEPH1 -0.054 0.14 -10000 0 -0.51 62 62
Nephrin/NEPH1/ZO-1 -0.059 0.15 -10000 0 -0.57 62 62
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.6 0.38 -9999 0 -0.84 603 603
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.001 0.019 -9999 0 -10000 0 0
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 -0.043 0.1 -9999 0 -0.28 132 132
ARNT/IPAS -0.46 0.29 -9999 0 -0.65 603 603
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 0.005 -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 -10000 0 0
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
Signaling events mediated by HDAC Class III

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
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 0.069 0.65 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 -0.007 0.076 -10000 0 -0.84 7 7
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 -0.84 603 603
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 -0.84 187 187
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 -0.57 187 187
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 0.062 -10000 0 -0.52 12 12
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 -0.65 603 603
ACSS2 0 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.001 0.015 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
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 -0.01 0.061 -10000 0 -0.32 25 25
ENAH 0.056 0.064 -10000 0 -10000 0 0
EGFR -0.29 0.4 -10000 0 -0.84 293 293
EPHA2 -0.006 0.071 -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 0.035 -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 0.12 -10000 0 -0.46 67 67
EGF -0.17 0.33 -10000 0 -0.84 167 167
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.042 0.15 -10000 0 -0.6 47 47
cortical microtubule organization -0.014 0.08 -10000 0 -0.48 24 24
GO:0000145 0.025 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 -0.5 424 424
RhoA/GDP -0.013 0.075 -10000 0 -0.45 24 24
actin cytoskeleton organization 0.031 0.08 -10000 0 -0.43 25 25
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.59 29 29
GIT1 -0.001 0.019 -10000 0 -0.28 4 4
IGF1R -0.02 0.12 -10000 0 -0.59 29 29
IGF1 -0.19 0.35 -10000 0 -0.84 187 187
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 -0.43 26 26
Ephrin A1/EPHA2 -0.016 0.081 -10000 0 -0.43 30 30
SEC6/SEC8 -0.013 0.07 -10000 0 -10000 0 0
MGAT3 -0.037 0.13 -10000 0 -0.47 67 67
HGF/MET -0.12 0.22 -10000 0 -0.49 196 196
HGF -0.051 0.2 -10000 0 -0.84 51 51
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 -0.64 3 3
IGF-1R heterotetramer/IGF1 -0.12 0.21 -10000 0 -0.46 216 216
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.04 -10000 0 -0.65 3 3
MET -0.14 0.32 -10000 0 -0.84 144 144
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 -0.43 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
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.5 190 190
MAPK9 0 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 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 -0.53 189 189
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 0.12 189 -10000 0 189
GNAL -0.19 0.35 -10000 0 -0.84 189 189
GNG2 -0.006 0.071 -10000 0 -0.84 6 6
CRH -0.003 0.029 -10000 0 -0.28 9 9
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
Presenilin action in Notch and Wnt 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
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 -0.076 0.24 -10000 0 -0.84 76 76
LRP6/FZD1 0 0.008 -10000 0 -10000 0 0
TLE1 -0.006 0.071 -10000 0 -0.84 6 6
AP1 -0.13 0.19 -10000 0 -0.39 275 275
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 -10000 0 0
NICD/RBPSUH 0 0.003 -10000 0 -10000 0 0
WIF1 -0.44 0.42 -10000 0 -0.82 451 451
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 -10000 0 0
DKK1 -0.08 0.2 -10000 0 -0.43 157 157
beta catenin/beta TrCP1 -0.011 0.024 0.22 3 -10000 0 3
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 -0.38 1 1
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 -10000 0 0
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 -0.001 0.024 -10000 0 -10000 0 0
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 76 76
apoptosis -0.13 0.19 -10000 0 -0.39 275 275
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 0.013 -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 -10000 0 0
Axin1/APC/beta catenin 0.009 0.037 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.84 17 17
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 76 76
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
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.57 78 78
GNAO1 -0.034 0.14 -9999 0 -0.49 58 58
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.61 51 51
PLCG1 -0.088 0.22 -9999 0 -0.57 68 68
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 -0.042 0.18 -9999 0 -0.85 42 42
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 -0.55 78 78
MAPK3 -0.16 0.31 -9999 0 -0.57 282 282
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 -0.85 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 -1.1 282 282
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 -0.55 78 78
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.006 0.071 -9999 0 -0.85 6 6
MAPK1 -0.16 0.31 -9999 0 -0.57 282 282
S1P1/S1P/PDGFB-D/PDGFRB -0.052 0.086 -9999 0 -0.72 5 5
ABCC1 0 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
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 0.061 0.26 9 -0.4 8 17
MAP2K4 -0.063 0.16 -10000 0 -0.53 12 12
mol:ceramide -0.058 0.094 -10000 0 -0.59 11 11
GSN 0 0.082 0.29 23 -0.53 13 36
FASLG/FAS/FADD/FAF1/Caspase 8 -0.03 0.064 -10000 0 -0.47 8 8
FAS -0.003 0.051 -10000 0 -0.85 3 3
BID 0 0.004 -10000 0 -10000 0 0
MAP3K1 -0.025 0.093 -10000 0 -0.38 1 1
MAP3K7 0 0.01 -10000 0 -10000 0 0
RB1 0.009 0.049 0.29 24 -10000 0 24
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.14 0.28 -10000 0 -0.64 188 188
ARHGDIB 0.008 0.049 0.29 24 -10000 0 24
FADD -0.006 0.04 -10000 0 -0.3 11 11
actin filament polymerization 0 0.082 0.53 13 -0.29 23 36
NFKB1 -0.08 0.1 -10000 0 -0.29 11 11
MAPK8 -0.12 0.24 -10000 0 -0.43 313 313
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 -0.59 144 144
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 -0.018 0.09 -10000 0 -0.37 40 40
FAS/FADD -0.006 0.05 -10000 0 -0.71 3 3
HGF -0.051 0.2 -10000 0 -0.84 51 51
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 -1.4 324 324
MET -0.14 0.32 -10000 0 -0.84 144 144
ICAD/CAD 0.008 0.045 0.27 24 -10000 0 24
FASLG/FAS/FADD/FAF1/Caspase 10 -0.059 0.095 -10000 0 -0.6 11 11
activation of caspase activity by cytochrome c 0 0.004 -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
LPA4-mediated signaling events

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
ADCY4 -0.001 0.11 -9999 0 -0.57 30 30
ADCY5 -0.17 0.27 -9999 0 -0.57 266 266
ADCY6 0.02 0 -9999 0 -10000 0 0
ADCY7 0.02 0 -9999 0 -10000 0 0
ADCY1 -0.007 0.095 -9999 0 -0.57 18 18
ADCY2 -0.033 0.16 -9999 0 -0.57 66 66
ADCY3 0.02 0.006 -9999 0 -10000 0 0
ADCY8 0.01 0.027 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.032 0.1 -9999 0 -0.32 54 54
TCGA08_rtk_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
PDGFRA -0.05 0.2 -10000 0 -0.83 51 51
HRAS 0 0.01 -10000 0 -0.28 1 1
EGFR -0.29 0.4 -10000 0 -0.84 293 293
AKT 0.015 0.077 -10000 0 -0.59 12 12
FOXO3 -0.002 0.041 -10000 0 -0.84 2 2
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.007 0.076 -10000 0 -0.84 7 7
AKT3 -0.012 0.099 -10000 0 -0.84 12 12
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.32 -10000 0 -0.84 144 144
PIK3CA 0 0.01 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.014 -10000 0 -0.28 2 2
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 -0.092 0.17 0.26 1 -0.37 159 160
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 -0.081 0.16 -10000 0 -0.36 161 161
PIK3R1 0 0 -10000 0 -10000 0 0
KRAS 0 0.01 -10000 0 -0.28 1 1
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
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.036 0.13 -10000 0 -0.63 31 31
FYN 0.015 0.18 -10000 0 -0.79 33 33
LAT/GRAP2/SLP76 -0.028 0.15 -10000 0 -0.66 36 36
IKBKB -0.001 0.014 -10000 0 -0.28 2 2
AKT1 0.031 0.12 -10000 0 -0.48 36 36
B2M 0.008 0.006 -10000 0 -10000 0 0
IKBKG -0.008 0.027 -10000 0 -0.19 1 1
MAP3K8 -0.005 0.065 -10000 0 -0.84 5 5
mol:Ca2+ -0.028 0.051 -10000 0 -0.13 176 176
integrin-mediated signaling pathway -0.002 0.028 -10000 0 -0.56 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.022 0.18 -10000 0 -0.72 38 38
TRPV6 -0.18 0.35 -10000 0 -0.81 188 188
CD28 -0.007 0.069 -10000 0 -0.51 12 12
SHC1 0.01 0.19 -10000 0 -0.81 34 34
receptor internalization -0.002 0.21 -10000 0 -0.86 38 38
PRF1 -0.004 0.24 -10000 0 -1.1 30 30
KRAS 0 0.01 -10000 0 -0.28 1 1
GRB2 0 0.01 -10000 0 -10000 0 0
COT/AKT1 0.032 0.1 -10000 0 -0.39 36 36
LAT 0.008 0.19 -10000 0 -0.78 38 38
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.024 0.14 -10000 0 -0.56 45 45
CD3E -0.019 0.14 -10000 0 -0.55 46 46
CD3G -0.038 0.16 -10000 0 -0.53 61 61
RASGRP2 -0.006 0.04 -10000 0 -0.19 36 36
RASGRP1 0.038 0.13 -10000 0 -0.46 38 38
HLA-A 0.01 0.015 -10000 0 -0.27 2 2
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 33 33
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.048 -10000 0 -0.24 22 22
PRKCA -0.011 0.087 -10000 0 -0.32 44 44
GRAP2 -0.015 0.11 -10000 0 -0.74 17 17
mol:IP3 0.023 0.15 0.27 150 -0.45 36 186
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.22 -10000 0 -0.97 32 32
ORAI1 0.086 0.16 0.39 176 -10000 0 176
CSK 0.007 0.19 -10000 0 -0.82 35 35
B7 family/CD28 -0.021 0.19 -10000 0 -0.74 41 41
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.004 0.23 -10000 0 -0.82 47 47
PTPN6 0.006 0.19 -10000 0 -0.82 35 35
VAV1 0.01 0.19 -10000 0 -0.8 36 36
Monovalent TCR/CD3 -0.031 0.21 -10000 0 -0.74 50 50
CBL 0 0 -10000 0 -10000 0 0
LCK 0.008 0.2 -10000 0 -0.78 40 40
PAG1 0.007 0.19 -10000 0 -0.84 34 34
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.004 0.23 -10000 0 -0.85 43 43
CD80 -0.08 0.12 -10000 0 -0.28 243 243
CD86 -0.001 0.019 -10000 0 -0.28 4 4
PDK1/CARD11/BCL10/MALT1 -0.017 0.059 -10000 0 -0.28 30 30
HRAS 0 0.01 -10000 0 -0.28 1 1
GO:0035030 -0.046 0.14 -10000 0 -0.59 41 41
CD8A -0.004 0.079 -10000 0 -0.85 5 5
CD8B -0.027 0.16 -10000 0 -0.61 52 52
PTPRC -0.008 0.067 -10000 0 -0.84 4 4
PDK1/PKC theta 0.035 0.16 -10000 0 -0.6 39 39
CSK/PAG1 0.012 0.19 -10000 0 -0.8 34 34
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0 0.008 -10000 0 -10000 0 0
GRAP2/SLP76 -0.036 0.18 -10000 0 -0.74 40 40
STIM1 0.045 0.083 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.054 -10000 0 -0.18 28 28
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.007 0.24 -10000 0 -0.96 38 38
mol:DAG -0.005 0.11 -10000 0 -0.41 36 36
RAP1A/GDP 0.015 0.018 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.023 0.13 -10000 0 -0.84 19 19
cytotoxic T cell degranulation -0.001 0.22 -10000 0 -0.98 33 33
RAP1A/GTP -0.003 0.014 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.15 -10000 0 -0.56 38 38
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.017 0.18 0.29 144 -0.61 36 180
NRAS -0.001 0.014 -10000 0 -0.28 2 2
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 -0.025 0.14 -10000 0 -0.63 36 36
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 44 44
CARD11 -0.007 0.055 -10000 0 -0.84 2 2
PRKCB -0.01 0.088 -10000 0 -0.34 41 41
PRKCE -0.005 0.07 -10000 0 -0.28 33 33
PRKCQ 0.025 0.18 -10000 0 -0.71 39 39
LCP2 0 0.01 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.032 0.11 -10000 0 -0.4 36 36
IKK complex 0.042 0.044 -10000 0 -0.12 20 20
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.037 0.081 -10000 0 -0.3 31 31
PDPK1 0.034 0.12 -10000 0 -0.45 35 35
TCR/CD3/MHC I/CD8/Fyn -0.009 0.24 -10000 0 -0.97 42 42
Nectin adhesion pathway

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
PDGFRB -0.002 0.041 -9999 0 -0.84 2 2
alphaV beta3 Integrin -0.012 0.086 -9999 0 -0.65 15 15
PTK2 -0.048 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 -0.46 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 -0.035 0.12 -9999 0 -0.42 68 68
nectin-3/I-afadin -0.053 0.18 -9999 0 -0.66 68 68
RAPGEF1 0.007 0.16 -9999 0 -0.53 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.005 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 -0.61 8 8
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 0.18 -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 -0.65 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 -0.84 32 32
JAM-A/CLDN1 -0.064 0.18 -9999 0 -0.56 93 93
SRC -0.057 0.19 -9999 0 -0.7 68 68
ITGB3 -0.016 0.11 -9999 0 -0.72 19 19
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.038 -9999 0 -0.65 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 -0.65 3 3
nectin-2/I-afadin -0.003 0.04 -9999 0 -0.65 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 -0.028 0.11 -9999 0 -0.63 19 19
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.003 0.04 -9999 0 -0.65 3 3
nectin-2(dimer)/I-afadin/I-afadin -0.003 0.04 -9999 0 -0.65 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
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0 0.03 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.019 0.033 -9999 0 -0.66 1 1
positive regulation of JNK cascade -0.048 0.11 -9999 0 -0.48 5 5
Syndecan-4/ADAM12 -0.03 0.055 -9999 0 -0.66 1 1
CCL5 -0.012 0.07 -9999 0 -0.84 3 3
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 0.021 -9999 0 -10000 0 0
ADAM12 -0.023 0.084 -9999 0 -0.84 2 2
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 -0.07 0.14 -9999 0 -0.49 49 49
Syndecan-4/CXCL12/CXCR4 -0.05 0.12 -9999 0 -0.56 2 2
Syndecan-4/Laminin alpha3 -0.13 0.2 -9999 0 -0.51 151 151
MDK -0.01 0.051 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.028 0.07 -9999 0 -0.49 11 11
Syndecan-4/Midkine -0.021 0.039 -9999 0 -0.66 1 1
FZD7 -0.017 0.12 -9999 0 -0.84 17 17
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.52 88 88
THBS1 -0.001 0.029 -9999 0 -0.84 1 1
integrin-mediated signaling pathway -0.028 0.072 -9999 0 -0.51 11 11
positive regulation of MAPKKK cascade -0.048 0.11 -9999 0 -0.48 5 5
Syndecan-4/TACI -0.03 0.07 -9999 0 -0.52 7 7
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 -0.025 0.047 -9999 0 -0.56 3 3
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 -0.84 202 202
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.002 0.13 -9999 0 -0.8 21 21
Syndecan-4/alpha-Actinin -0.02 0.037 -9999 0 -0.57 2 2
TFPI -0.035 0.17 -9999 0 -0.84 35 35
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 -0.56 124 124
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 -0.49 29 29
FGF6 -0.002 0.041 -9999 0 -0.84 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.063 0.22 -9999 0 -0.84 63 63
TNFRSF13B -0.024 0.12 -9999 0 -0.45 46 46
FGF2 -0.34 0.41 -9999 0 -0.84 337 337
FGFR1 -0.008 0.077 -9999 0 -0.84 7 7
Syndecan-4/PI-4-5-P2 -0.013 0.044 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.15 -9999 0 -0.29 184 184
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 -0.029 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 -0.28 350 350
Rac1/GTP -0.027 0.059 -9999 0 -0.37 21 21
cytoskeleton organization -0.019 0.032 -9999 0 -0.63 1 1
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.038 0.095 -9999 0 -0.5 17 17
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.13 0.19 -9999 0 -0.63 26 26
MAP3K8 -0.005 0.066 -9999 0 -0.85 5 5
FOS -0.041 0.14 -9999 0 -0.48 24 24
PRKCA -0.022 0.13 -9999 0 -0.85 21 21
PTPN7 -0.008 0.068 -9999 0 -0.31 17 17
HRAS 0 0.01 -9999 0 -0.28 1 1
PRKCB -0.019 0.12 -9999 0 -0.58 28 28
NRAS -0.001 0.014 -9999 0 -0.28 2 2
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.011 0.074 -9999 0 -10000 0 0
MAP2K1 -0.016 0.14 -9999 0 -0.63 34 34
ELK1 -0.003 0.005 -9999 0 -10000 0 0
BRAF -0.033 0.12 -9999 0 -0.61 34 34
mol:GTP -0.002 0.003 -9999 0 -0.006 272 272
MAPK1 -0.011 0.074 -9999 0 -10000 0 0
RAF1 -0.033 0.12 -9999 0 -0.61 34 34
KRAS 0 0.01 -9999 0 -0.28 1 1
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.015 0.1 0.47 11 -10000 0 11
IL27/IL27R/JAK1 -0.047 0.16 -10000 0 -0.77 13 13
TBX21 -0.025 0.21 -10000 0 -0.69 45 45
IL12B -0.052 0.11 -10000 0 -0.28 157 157
IL12A -0.031 0.16 -10000 0 -0.66 48 48
IL6ST -0.052 0.21 -10000 0 -0.85 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 0.015 0.1 0.47 11 -10000 0 11
T cell proliferation during immune response 0.015 0.1 0.47 11 -10000 0 11
MAPKKK cascade -0.015 0.1 -10000 0 -0.47 11 11
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 0.055 -10000 0 -0.3 26 26
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.04 0.22 -10000 0 -0.66 63 63
IL27/IL27R/JAK2/TYK2 -0.018 0.1 -10000 0 -0.48 11 11
positive regulation of T cell mediated cytotoxicity -0.015 0.1 -10000 0 -0.47 11 11
STAT1 (dimer) -0.066 0.21 0.52 7 -0.84 22 29
JAK2 0.004 0.006 -10000 0 -10000 0 0
JAK1 0 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.028 0.09 -10000 0 -0.56 4 4
T cell proliferation -0.2 0.25 -10000 0 -0.49 327 327
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 0.015 0.1 0.47 11 -10000 0 11
IFNG 0.002 0.021 -10000 0 -0.08 3 3
T cell differentiation -0.003 0.005 -10000 0 -0.02 9 9
STAT3 (dimer) -0.028 0.09 -10000 0 -0.56 4 4
STAT5A (dimer) -0.032 0.1 -10000 0 -0.56 11 11
STAT4 (dimer) -0.047 0.13 -10000 0 -0.54 37 37
STAT4 -0.033 0.16 -10000 0 -0.84 33 33
T cell activation -0.008 0.008 0.13 2 -10000 0 2
IL27R/JAK2/TYK2 -0.037 0.14 -10000 0 -0.94 4 4
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 -0.028 0.088 -10000 0 -0.55 4 4
IL27/EBI3 -0.022 0.078 -10000 0 -0.58 8 8
IL27RA 0.001 0.074 -10000 0 -1.5 2 2
IL6 -0.32 0.41 -10000 0 -0.84 324 324
STAT5A -0.007 0.076 -10000 0 -0.84 7 7
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.002 0.027 0.48 2 -10000 0 2
IL1B 0.003 0.07 -10000 0 -0.66 9 9
EBI3 -0.004 0.075 -10000 0 -0.56 12 12
TNF -0.002 0.08 -10000 0 -0.37 28 28
Coregulation of Androgen receptor activity

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
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 -0.14 72 72
T-DHT/AR/Ubc9 -0.075 0.18 -10000 0 -0.58 92 92
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.003 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 0.019 -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 0.012 0.1 0.21 4 -0.54 16 20
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 -0.28 1 1
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 0.11 -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 0.22 -10000 0 -0.63 105 105
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 -0.15 122 122
CDK6 -0.006 0.078 -10000 0 -0.71 9 9
TGFB1I1 -0.009 0.052 -10000 0 -0.84 3 3
T-DHT/AR/CyclinD1 -0.087 0.19 -10000 0 -0.59 95 95
XRCC6 0.006 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.063 0.21 -10000 0 -0.56 106 106
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 0.007 0.071 -10000 0 -0.83 5 5
CDKN2A -0.035 0.1 -10000 0 -0.28 114 114
SRF 0.023 0.02 -10000 0 -10000 0 0
NKX3-1 -0.084 0.2 -10000 0 -1.3 17 17
KLK3 -0.18 0.52 -10000 0 -1.6 103 103
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 -0.072 103 103
APPL1 0.034 0.033 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.067 0.19 -10000 0 -0.58 92 92
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 -10000 0 0
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 -0.54 92 92
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 -10000 0 -0.53 92 92
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 -0.55 97 97
TMPRSS2 -0.18 0.41 -10000 0 -1.2 109 109
CCND1 -0.016 0.074 -10000 0 -0.33 37 37
PIAS1 -0.006 0.031 -10000 0 -10000 0 0
mol:T-DHT -0.01 0.035 -10000 0 -0.08 158 158
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.013 0.05 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.077 0.19 -10000 0 -0.58 99 99
CMTM2 0.003 0.013 -10000 0 -0.28 1 1
SNURF -0.023 0.14 -10000 0 -0.84 23 23
ZMIZ1 0.002 0.032 -10000 0 -0.34 1 1
CCND3 0.001 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
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.003 0.13 -10000 0 -0.37 67 67
TBX21 -0.013 0.36 -10000 0 -1.4 42 42
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 -0.32 25 25
GADD45B 0.036 0.21 -10000 0 -0.82 24 24
IL12RB2 -0.059 0.2 -10000 0 -0.44 141 141
GADD45G 0.032 0.21 -10000 0 -0.77 29 29
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 0.046 -10000 0 -10000 0 0
IL2RA -0.028 0.11 -10000 0 -0.36 66 66
IFNG -0.041 0.098 -10000 0 -10000 0 0
STAT3 (dimer) 0.031 0.21 -10000 0 -0.65 41 41
HLA-DRB5 -0.022 0.093 -10000 0 -0.42 23 23
FASLG 0.012 0.27 -10000 0 -1.1 27 27
NF kappa B2 p52/RelB -0.077 0.19 -10000 0 -0.73 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 -0.024 0.15 -10000 0 -0.53 51 51
CD3E -0.023 0.14 -10000 0 -0.55 46 46
CD3G -0.031 0.16 -10000 0 -0.54 61 61
IL12Rbeta2/JAK2 -0.028 0.16 -10000 0 -0.65 42 42
CCL3 0.016 0.26 -10000 0 -1 27 27
CCL4 0.019 0.25 -10000 0 -1 24 24
HLA-A 0.009 0.015 -10000 0 -0.28 2 2
IL18/IL18R 0.024 0.15 -10000 0 -0.58 43 43
NOS2 0.022 0.25 -10000 0 -1 26 26
IL12/IL12R/TYK2/JAK2/SPHK2 -0.002 0.13 -10000 0 -0.42 41 41
IL1R1 0.01 0.28 -10000 0 -1.1 30 30
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 -0.033 0.26 -10000 0 -1.1 37 37
RAB7A 0.053 0.19 -10000 0 -0.7 21 21
lysosomal transport 0.054 0.18 -10000 0 -0.66 22 22
FOS -0.39 0.69 -10000 0 -1.3 282 282
STAT4 (dimer) 0.026 0.26 -10000 0 -0.88 40 40
STAT5A (dimer) -0.081 0.21 -10000 0 -0.8 41 41
GZMA 0.007 0.28 -10000 0 -1.1 30 30
GZMB -0.005 0.31 -10000 0 -1.2 34 34
HLX 0 0.01 -10000 0 -10000 0 0
LCK 0.01 0.28 -10000 0 -0.85 52 52
TCR/CD3/MHC II/CD4 -0.069 0.2 -10000 0 -0.6 62 62
IL2/IL2R -0.028 0.098 -10000 0 -0.47 31 31
MAPK14 0.042 0.22 -10000 0 -0.77 31 31
CCR5 0.03 0.22 -10000 0 -0.82 27 27
IL1B 0.007 0.092 -10000 0 -0.79 10 10
STAT6 0.027 0.086 -10000 0 -0.26 4 4
STAT4 -0.033 0.16 -10000 0 -0.84 33 33
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 -0.28 87 87
CD8A -0.002 0.08 -10000 0 -0.84 5 5
CD8B -0.027 0.16 -10000 0 -0.6 52 52
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.002 0.13 0.37 67 -10000 0 67
IL2RB -0.012 0.055 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.24 -10000 0 -0.79 40 40
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 -0.015 0.13 -10000 0 -0.77 22 22
IL2 -0.003 0.027 -10000 0 -0.28 8 8
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 0.013 0.28 -10000 0 -0.82 55 55
MAP2K3 0.038 0.22 -10000 0 -0.79 29 29
RIPK2 -0.001 0.019 -10000 0 -0.28 4 4
MAP2K6 0.034 0.22 -10000 0 -0.78 32 32
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 -0.78 37 37
IL12Rbeta1/TYK2 0.016 0.049 -10000 0 -0.7 1 1
EOMES -0.023 0.18 -10000 0 -1.5 12 12
STAT1 (dimer) 0.035 0.21 -10000 0 -0.72 28 28
T cell proliferation 0.037 0.2 -10000 0 -0.63 40 40
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 -0.06 0.17 -10000 0 -0.73 37 37
ATF2 0.05 0.21 -10000 0 -0.73 28 28
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.008 -10000 0 -10000 0 0
SMAD4 0 0 -10000 0 -10000 0 0
DKK2 -0.018 0.12 -10000 0 -0.84 17 17
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 -0.82 451 451
beta catenin/RanBP3 0.013 0.075 0.38 31 -10000 0 31
KREMEN2 -0.13 0.14 -10000 0 -10000 0 0
DKK1 -0.08 0.2 -10000 0 -0.43 157 157
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 0.002 0.027 -10000 0 -10000 0 0
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 -0.073 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 0.014 0.094 0.44 34 -0.44 1 35
LEF1 -0.037 0.1 -10000 0 -0.28 118 118
DVL1 0.072 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 0.013 -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 0.009 -10000 0 -10000 0 0
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 0.27 13 -10000 0 13
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
BCR 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
JUN 0.004 0.12 -10000 0 -0.46 30 30
IKBKB 0.016 0.055 -10000 0 -0.26 2 2
AKT1 0.006 0.082 0.25 2 -0.25 28 30
IKBKG 0.018 0.057 -10000 0 -0.28 1 1
CALM1 -0.013 0.098 -10000 0 -0.46 26 26
PIK3CA 0 0.01 -10000 0 -10000 0 0
MAP3K1 -0.01 0.16 -10000 0 -0.66 29 29
MAP3K7 0 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.1 -10000 0 -0.5 26 26
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.049 0.12 -10000 0 -0.27 64 64
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 -0.083 0.23 -10000 0 -0.7 88 88
CD22 -0.063 0.19 -10000 0 -0.56 82 82
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 -0.051 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 0.14 -10000 0 -0.56 29 29
B-cell antigen/BCR complex -0.083 0.23 -10000 0 -0.7 88 88
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 -0.062 0.18 -10000 0 -0.56 81 81
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 -0.69 35 35
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 79 79
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 -0.47 290 290
CHUK 0.018 0.057 -10000 0 -0.28 1 1
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.025 0.083 -10000 0 -0.48 16 16
PTPN6 -0.059 0.17 -10000 0 -0.52 82 82
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.13 1 1
VAV2 -0.071 0.18 -10000 0 -0.55 79 79
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 79 79
MAP4K1 -0.01 0.062 -10000 0 -0.84 2 2
CD72 -0.006 0.048 -10000 0 -0.31 17 17
PAG1 -0.002 0.021 -10000 0 -10000 0 0
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 68 68
RAF1 -0.002 0.1 -10000 0 -0.45 26 26
RasGAP/p62DOK/SHIP -0.058 0.17 -10000 0 -0.53 81 81
CD79A -0.085 0.23 -10000 0 -0.58 122 122
re-entry into mitotic cell cycle -0.048 0.12 -10000 0 -0.26 68 68
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.015 0.088 -10000 0 -0.44 14 14
MAPK1 0.015 0.088 -10000 0 -0.44 14 14
CD72/SHP1 -0.055 0.16 -10000 0 -0.69 35 35
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 -0.46 79 79
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 -0.056 0.18 -10000 0 -0.85 31 31
DAPP1 -0.056 0.21 -10000 0 -1 30 30
cytokine secretion -0.014 0.13 -10000 0 -0.51 29 29
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 -0.41 26 26
B-cell antigen/BCR complex/FcgammaRIIB -0.073 0.2 -10000 0 -0.65 81 81
mol:PI-3-4-5-P3 -0.04 0.093 0.35 2 -0.37 31 33
ETS1 0.004 0.09 -10000 0 -0.48 15 15
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.06 0.17 -10000 0 -0.56 79 79
B-cell antigen/BCR complex/LYN -0.061 0.2 -10000 0 -0.59 82 82
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
RAC1 -0.029 0.17 -10000 0 -0.57 51 51
B-cell antigen/BCR complex/LYN/SYK -0.06 0.19 -10000 0 -0.58 81 81
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 -0.28 1 1
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 -10000 0 -10000 0 0
PTPRC -0.008 0.066 -10000 0 -0.84 4 4
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 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
CBL/APS/CAP -0.12 0.22 -9999 0 -0.5 204 204
TC10/GTP -0.1 0.18 -9999 0 -0.44 192 192
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.1 -9999 0 -0.53 31 31
HRAS 0 0.01 -9999 0 -0.28 1 1
APS homodimer -0.01 0.051 -9999 0 -0.28 29 29
GRB14 -0.1 0.23 -9999 0 -0.84 65 65
FOXO3 -0.013 0.065 -9999 0 -0.73 6 6
AKT1 -0.054 0.13 -9999 0 -0.41 72 72
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 -0.84 192 192
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 -0.54 189 189
CBL/APS/CAP/Crk-II/C3G -0.11 0.2 -9999 0 -0.48 192 192
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 0.14 -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 0.12 -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 -0.06 0.14 -9999 0 -0.44 95 95
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 0.039 -9999 0 -0.63 1 1
SH2B2 -0.01 0.051 -9999 0 -0.28 29 29
SHC/SHIP -0.017 0.087 -9999 0 -0.46 31 31
F2RL2 -0.061 0.15 -9999 0 -0.84 15 15
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 -0.52 192 192
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 0.094 -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 -0.026 0.074 -9999 0 -0.49 15 15
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.26 1 -0.6 117 118
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 0.094 -10000 0 -0.37 1 1
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 -0.56 342 342
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 -0.46 251 251
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 0.039 -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 -0.008 0.065 -10000 0 -0.62 8 8
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 -0.28 12 12
RUNX3 -0.005 0.059 -10000 0 -0.65 6 6
RUNX1 -0.001 0.029 -10000 0 -0.84 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.007 0.082 -10000 0 -0.84 8 8
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 -0.42 4 4
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 -0.28 3 3
Cbp/p300/PIAS3 0.006 0.024 -10000 0 -10000 0 0
JUN -0.099 0.25 -10000 0 -0.47 148 148
SMAD3/SMAD4/IRF7 -0.011 0.057 -10000 0 -10000 0 0
TFE3 0.011 0.01 -10000 0 -10000 0 0
COL1A2 0.029 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 -0.31 137 137
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 -0.3 48 48
ESR1 -0.15 0.29 -10000 0 -0.57 229 229
HNF4A -0.004 0.034 -10000 0 -0.28 13 13
MEF2C 0.001 0.086 -10000 0 -0.94 1 1
SMAD2-3/SMAD4 -0.002 0.03 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.003 0.025 -10000 0 -0.56 1 1
IGHV3OR16-13 -0.001 0.009 -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 -0.28 11 11
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 -0.65 342 342
SMAD2 0.014 0.022 -10000 0 -10000 0 0
SMAD3 0.012 0.029 -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 0.082 -10000 0 -10000 0 0
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 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.007 0.051 -10000 0 -0.5 4 4
RUNX1-3/PEBPB2 -0.004 0.05 -10000 0 -0.68 4 4
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 -0.55 32 32
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 0.07 -10000 0 -0.28 58 58
FOXO3 0.025 0.033 -10000 0 -0.64 2 2
FOXO1 0.021 0.061 -10000 0 -0.64 7 7
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 -0.026 0.082 -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 0.031 -10000 0 -0.28 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.001 0.051 -10000 0 -0.64 4 4
SMAD3/SMAD4/SP1-3 0.004 0.024 -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 -0.007 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 -0.066 0.19 -10000 0 -0.61 92 92
AR -0.092 0.26 -10000 0 -0.84 92 92
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 -10000 0 0
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 0.041 -10000 0 -0.34 4 4
TFDP1 -0.001 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.14 0.23 -10000 0 -0.55 71 71
SMAD3/SMAD4/RUNX2 -0.003 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
Regulation of p38-alpha and p38-beta

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
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 -0.017 0.12 -9999 0 -0.81 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 0.034 -9999 0 -0.38 2 2
PRKG1 -0.033 0.16 -9999 0 -0.84 33 33
DUSP8 -0.003 0.051 -9999 0 -0.7 4 4
PGK/cGMP/p38 alpha -0.023 0.089 -9999 0 -0.43 35 35
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 -0.28 1 1
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 0.018 0.069 -9999 0 -0.36 14 14
BLK -0.036 0.1 -9999 0 -0.84 3 3
HCK -0.004 0.033 -9999 0 -0.28 12 12
MAP2K3 0 0.01 -9999 0 -0.28 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.014 -9999 0 -0.28 2 2
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 0.024 0.075 -9999 0 -0.38 14 14
LCK -0.019 0.1 -9999 0 -0.46 34 34
p38alpha-beta/MKP7 -0.011 0.055 -9999 0 -0.36 13 13
p38alpha-beta/MKP5 -0.011 0.055 -9999 0 -0.36 13 13
PGK/cGMP -0.026 0.13 -9999 0 -0.66 33 33
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.065 0.15 -9999 0 -0.4 127 127
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
Regulation of Telomerase

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
Telomerase catalytic core complex -0.05 0.11 -9999 0 -0.64 3 3
RAD9A 0 0.01 -9999 0 -0.28 1 1
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 -0.3 117 117
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.66 117 117
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 -0.063 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 -0.14 0.14 -9999 0 -0.28 453 453
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 -0.048 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 -0.043 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 0.078 -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 -0.28 3 3
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 0.061 -9999 0 -0.37 3 3
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.032 0.089 -9999 0 -10000 0 0
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 -0.56 230 230
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 0.01 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 -0.28 1 1
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.014 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.061 0.098 -9999 0 -0.67 3 3
NR2F2 -0.001 0.05 -9999 0 -0.84 3 3
MAPK3 0.014 0.02 -9999 0 -10000 0 0
MAPK1 0.014 0.02 -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 -0.84 293 293
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.35 0.37 -9999 0 -0.71 411 411
MYC -0.02 0.13 -9999 0 -0.84 20 20
IL2 0.003 0.028 -9999 0 -0.27 8 8
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -10000 0 0
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 -0.048 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 0.095 -9999 0 -10000 0 0
Telomerase/PinX1 -0.048 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 -0.048 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 -0.048 0.074 -9999 0 -0.54 3 3
E2F1 -0.088 0.14 -9999 0 -0.29 3 3
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
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.026 0.029 -9999 0 -10000 0 0
BIRC5 -0.2 0.12 -9999 0 -0.28 620 620
NFKBIA -0.025 0.031 -9999 0 -10000 0 0
CPEB1 -0.16 0.33 -9999 0 -0.84 164 164
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 -0.032 0.033 -9999 0 -10000 0 0
AURKAIP1 0 0.01 -9999 0 -10000 0 0
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 -0.025 0.025 -9999 0 -10000 0 0
AURKA -0.039 0.042 -9999 0 -10000 0 0
AURKB -0.002 0.008 -9999 0 -10000 0 0
CDC25B -0.018 0.024 -9999 0 -10000 0 0
G2/M transition checkpoint -0.027 0.042 -9999 0 -0.53 4 4
mRNA polyadenylation -0.13 0.21 -9999 0 -0.56 164 164
Aurora A/CPEB -0.13 0.22 -9999 0 -0.56 164 164
Aurora A/TACC1/TRAP/chTOG -0.026 0.078 -9999 0 -0.51 21 21
BRCA1 -0.001 0.014 -9999 0 -0.28 2 2
centrosome duplication -0.03 0.036 -9999 0 -10000 0 0
regulation of centrosome cycle -0.038 0.056 -9999 0 -10000 0 0
spindle assembly -0.026 0.077 -9999 0 -0.5 21 21
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 -0.026 0.029 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.026 -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 -0.021 0.13 -9999 0 -0.84 21 21
TACC3 -0.042 0.099 -9999 0 -0.28 126 126
Aurora A/Antizyme1 -0.02 0.02 -9999 0 -10000 0 0
Aurora A/RasGAP -0.026 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 -0.28 4 4
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
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.48 0.42 -10000 0 -0.84 477 477
CLTC 0.027 0.016 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.018 -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 0.017 -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 0.018 -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 0.013 -10000 0 -10000 0 0
TSHR -0.009 0.12 -10000 0 -0.57 37 37
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.009 0.087 -10000 0 -0.78 10 10
mol:Choline -0.001 0.018 -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 0.025 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -10000 0 0
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 -10000 0 0
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 -10000 0 0
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 0.018 -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 0.044 -10000 0 -0.34 10 10
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.24 0.21 -10000 0 -0.43 477 477
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.002 0.03 -10000 0 -0.35 6 6
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.013 -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 0.018 -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 -0.09 0.22 -10000 0 -0.46 213 213
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.029 -10000 0 -0.84 1 1
Dynamin 2/GDP -0.006 0.025 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.17 0.24 -10000 0 -0.46 350 350
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
TCGA08_retinoblastoma

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
CDKN2B -0.002 0.057 -10000 0 -0.7 5 5
CDKN2C 0.006 0.032 -10000 0 -0.82 1 1
CDKN2A -0.045 0.11 -10000 0 -0.29 132 132
CCND2 0.005 0.028 0.26 5 -0.17 6 11
RB1 -0.006 0.028 0.17 2 -0.26 5 7
CDK4 0.008 0.026 0.26 5 -10000 0 5
CDK6 0.005 0.033 0.28 5 -0.21 7 12
G1/S progression -0.008 0.031 0.26 5 -0.17 2 7
Regulation of Androgen receptor activity

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
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 0.006 0.096 -9999 0 -0.65 17 17
FOXO1 -0.007 0.076 -9999 0 -0.84 7 7
T-DHT/AR -0.002 0.13 -9999 0 -0.53 17 17
MAP2K6 -0.017 0.12 -9999 0 -0.81 18 18
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 -1.2 51 51
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 -0.28 0.4 -9999 0 -0.84 285 285
RXRs/9cRA -0.13 0.22 -9999 0 -0.52 204 204
AR/RACK1/Src -0.001 0.1 -9999 0 -0.5 17 17
AR/GR -0.044 0.12 -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 -0.028 0.095 -9999 0 -0.51 22 22
SRC 0.024 0.086 -9999 0 -0.51 17 17
NR3C1 -0.008 0.081 -9999 0 -0.84 8 8
KLK3 -0.21 0.43 -9999 0 -1.2 116 116
APPBP2 -0.001 0.013 -9999 0 -10000 0 0
TRIM24 0 0.01 -9999 0 -0.28 1 1
T-DHT/AR/TIP60 -0.023 0.086 -9999 0 -0.53 17 17
TMPRSS2 -0.18 0.43 -9999 0 -1.3 111 111
RXRG -0.2 0.36 -9999 0 -0.84 205 205
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 -0.034 0.25 -9999 0 -0.82 71 71
AR -0.019 0.12 -9999 0 -0.34 101 101
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.01 -9999 0 -10000 0 0
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 -0.31 47 47
T-DHT/AR/RACK1/Src -0.024 0.085 -9999 0 -0.51 17 17
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 -0.71 61 61
T-DHT/AR/TIF2 0.026 0.066 -9999 0 -0.38 3 3
T-DHT/AR/Hsp90 -0.029 0.083 -9999 0 -0.53 17 17
GSK3B 0.001 0.004 -9999 0 -10000 0 0
NR2C1 0.002 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.018 0.091 -9999 0 -0.55 17 17
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 -0.03 0.088 -9999 0 -0.54 17 17
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 -0.001 0.013 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.005 0.037 -10000 0 -0.28 15 15
GNB1/GNG2 -0.013 0.045 -10000 0 -0.19 45 45
AKT1 0.053 0.068 -10000 0 -0.2 44 44
EGF -0.17 0.33 -10000 0 -0.84 167 167
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.009 0.046 -10000 0 -0.34 2 2
mol:Ca2+ 0.051 0.094 -10000 0 -0.3 44 44
LYN -0.009 0.046 -10000 0 -0.34 2 2
RhoA/GTP -0.008 0.028 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.057 0.1 -10000 0 -0.34 44 44
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 0.048 -10000 0 -0.6 3 3
G beta5/gamma2 -0.017 0.059 -10000 0 -0.28 24 24
PRKCH 0.053 0.1 -10000 0 -0.35 44 44
DNM1 -0.005 0.065 -10000 0 -0.84 5 5
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 -0.029 0.15 -10000 0 -0.74 33 33
G12 family/GTP -0.019 0.069 -10000 0 -0.3 44 44
ADRBK1 0 0.01 -10000 0 -10000 0 0
ADRBK2 -0.002 0.041 -10000 0 -0.84 2 2
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.04 0.074 0.36 14 -10000 0 14
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.014 -10000 0 -10000 0 0
PRKG1 -0.033 0.16 -10000 0 -0.84 33 33
mol:IP3 0.053 0.11 -10000 0 -0.38 44 44
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.052 0.14 -10000 0 -0.51 44 44
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.001 0.061 -10000 0 -0.4 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.008 0.047 -10000 0 -0.34 2 2
RHOA 0 0 -10000 0 -10000 0 0
PTGIR 0 0.01 -10000 0 -10000 0 0
PRKCB1 0.05 0.11 -10000 0 -0.37 44 44
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 0.054 0.15 -10000 0 -0.54 44 44
LCK -0.012 0.071 -10000 0 -0.46 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.056 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.025 0.029 -10000 0 -0.3 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.01 0.055 -10000 0 -10000 0 0
MAPK14 0.055 0.075 -10000 0 -0.22 44 44
TGM2/GTP 0.053 0.13 -10000 0 -0.42 44 44
MAPK11 0.054 0.077 -10000 0 -0.23 44 44
ARHGEF1 0.041 0.058 -10000 0 -0.18 22 22
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.055 0.12 -10000 0 -0.39 44 44
RAB11/GDP -0.001 0.013 -10000 0 -10000 0 0
ICAM1 0.05 0.088 -10000 0 -0.28 44 44
cAMP biosynthetic process 0.049 0.11 -10000 0 -0.36 44 44
Gq family/GTP/EBP50 -0.005 0.027 -10000 0 -0.25 9 9
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.009 0.046 -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 0.11 -10000 0 -0.31 33 33
VCAM1 0.049 0.096 -10000 0 -0.31 44 44
TP beta/Gq family/GDP/G beta5/gamma2 0.031 0.048 -10000 0 -0.6 3 3
platelet activation 0.071 0.1 -10000 0 -0.3 44 44
PGI2/IP 0 0.006 -10000 0 -10000 0 0
PRKACA -0.013 0.069 -10000 0 -0.39 27 27
Gq family/GDP/G beta5/gamma2 0.029 0.05 -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 -0.012 0.063 -10000 0 -0.36 27 27
mol:DAG 0.052 0.12 -10000 0 -0.42 44 44
EGFR -0.29 0.4 -10000 0 -0.84 293 293
TXA2/TP alpha 0.055 0.14 -10000 0 -0.49 44 44
Gq family/GTP -0.003 0.031 -10000 0 -0.29 9 9
YES1 -0.009 0.047 -10000 0 -0.36 3 3
GNAI2/GTP -0.01 0.052 -10000 0 -0.39 2 2
PGD2/DP -0.022 0.12 -10000 0 -0.66 27 27
SLC9A3R1 -0.027 0.082 -10000 0 -10000 0 0
FYN -0.009 0.047 -10000 0 -0.37 2 2
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 33 33
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.011 0.069 -10000 0 -0.52 6 6
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.046 0.12 -10000 0 -0.37 58 58
PRKCB 0.048 0.12 -10000 0 -0.36 55 55
PRKCE 0.055 0.1 -10000 0 -0.35 44 44
PRKCD 0.053 0.11 -10000 0 -0.38 44 44
PRKCG 0.05 0.11 -10000 0 -0.39 44 44
muscle contraction 0.057 0.14 -10000 0 -0.49 45 45
PRKCZ 0.057 0.11 -10000 0 -0.34 45 45
ARR3 -0.002 0.023 -10000 0 -10000 0 0
TXA2/TP beta -0.011 0.059 -10000 0 -0.44 2 2
PRKCQ 0.041 0.13 -10000 0 -0.37 68 68
MAPKKK cascade 0.051 0.14 -10000 0 -0.46 46 46
SELE 0.043 0.12 -10000 0 -0.42 44 44
TP beta/GNAI2/GDP/G beta/gamma -0.013 0.068 -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 0.053 0.17 -10000 0 -0.62 44 44
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
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.063 0.075 -9999 0 -0.42 6 6
EPHB2 -0.005 0.037 -9999 0 -0.28 15 15
Syndecan-2/TACI -0.017 0.083 -9999 0 -0.56 17 17
LAMA1 -0.095 0.26 -9999 0 -0.83 97 97
Syndecan-2/alpha2 ITGB1 -0.13 0.22 -9999 0 -0.49 214 214
HRAS 0 0.01 -9999 0 -0.28 1 1
Syndecan-2/CASK -0.003 0.035 -9999 0 -0.57 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 -0.84 202 202
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 -0.84 108 108
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 -0.65 16 16
dendrite morphogenesis -0.005 0.039 -9999 0 -0.56 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 -0.56 3 3
actin cytoskeleton reorganization -0.063 0.074 -9999 0 -0.42 6 6
Syndecan-2/Caveolin-2/Ras -0.068 0.18 -9999 0 -0.52 108 108
Syndecan-2/Laminin alpha3 -0.14 0.24 -9999 0 -0.56 205 205
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 -0.45 46 46
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.012 0.088 -9999 0 -0.65 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 -0.65 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 -0.51 4 4
angiogenesis -0.023 0.09 -9999 0 -0.56 20 20
MMP2 -0.008 0.081 -9999 0 -0.84 8 8
IL8 -0.035 0.13 -9999 0 -0.41 73 73
calcineurin-NFAT signaling pathway -0.017 0.083 -9999 0 -0.56 17 17
Effects of Botulinum toxin

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
STX1A 0.003 0.039 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.048 0.14 -9999 0 -0.65 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 -0.039 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 0.13 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.058 0.12 -9999 0 -0.48 45 45
SNAP25 -0.017 0.072 -9999 0 -0.39 30 30
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.085 0.18 -9999 0 -0.36 198 198
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
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.021 0.023 -10000 0 -0.65 1 1
MAP4K4 -0.006 0.042 -10000 0 -0.72 1 1
BAG4 -0.003 0.03 -10000 0 -10000 0 0
PKC zeta/ceramide -0.025 0.05 -10000 0 -0.62 1 1
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.011 0.086 -10000 0 -0.53 18 18
BAX -0.009 0.023 -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 0.035 -10000 0 -0.26 11 11
RB1 -0.023 0.047 0.21 1 -10000 0 1
FADD/Caspase 8 -0.006 0.042 -10000 0 -0.68 1 1
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 -0.31 3 3
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 -0.65 1 1
ASAH1 -0.001 0.017 -10000 0 -10000 0 0
negative regulation of cell cycle -0.023 0.047 0.21 1 -10000 0 1
cell proliferation -0.1 0.17 -10000 0 -0.41 187 187
BID 0.022 0.037 -10000 0 -0.41 1 1
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 0.045 -10000 0 -0.48 3 3
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 -0.19 0.35 -10000 0 -0.84 187 187
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 -0.28 31 31
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 -0.44 187 187
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 -0.65 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 -0.006 0.046 -10000 0 -0.76 1 1
TNFR1A/BAG4/TNF-alpha -0.012 0.067 -10000 0 -0.56 11 11
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 -0.01 0.066 -10000 0 -0.56 11 11
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.023 -10000 0 -0.34 1 1
MAP2K2 -0.007 0.046 -10000 0 -0.45 1 1
SMPD3 0.026 0.041 -10000 0 -0.28 13 13
TNF -0.017 0.1 -10000 0 -0.5 28 28
PKC zeta/PAR4 -0.001 0.022 -10000 0 -0.65 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
Osteopontin-mediated events

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
IKK alpha homodimer -0.03 0.069 -9999 0 -0.47 15 15
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.055 -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 -0.56 101 101
ILK -0.011 0.09 -9999 0 -0.5 15 15
bone resorption -0.022 0.064 -9999 0 -0.71 2 2
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.014 0.078 -9999 0 -0.45 15 15
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 -0.65 2 2
alphaV/beta3 Integrin/Osteopontin -0.043 0.087 -9999 0 -0.56 15 15
MAP3K1 -0.035 0.077 -9999 0 -0.51 15 15
JUN -0.009 0.086 -9999 0 -0.84 9 9
MAPK3 0.015 0.091 -9999 0 -0.46 15 15
MAPK1 0.015 0.091 -9999 0 -0.46 15 15
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.012 0.09 -9999 0 -0.47 15 15
ITGB3 -0.016 0.11 -9999 0 -0.71 19 19
NFKBIA 0.028 0.087 -9999 0 -0.45 15 15
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 0.088 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.016 0.053 -9999 0 -0.47 2 2
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.012 0.085 -9999 0 -0.63 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.036 0.077 -9999 0 -0.51 15 15
VAV3 0.005 0.096 -9999 0 -0.48 18 18
MAP3K14 0.002 0.095 -9999 0 -0.5 15 15
ROCK2 -0.002 0.041 -9999 0 -0.84 2 2
SPP1 -0.076 0.12 -9999 0 -0.28 17 17
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.029 0.068 -9999 0 -0.43 18 18
MMP2 -0.13 0.18 -9999 0 -0.7 24 24
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.001 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 -0.27 339 339
WEE1 -0.002 0.021 -9999 0 -10000 0 0
cytokinesis -0.044 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 -0.077 0.092 -9999 0 -0.32 10 10
CENPE -0.055 0.083 -9999 0 -0.2 2 2
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 -10000 0 0
SPC24 -0.17 0.14 -9999 0 -0.28 518 518
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.002 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 0.001 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 0.04 -9999 0 -10000 0 0
CDC14B -0.01 0.12 -9999 0 -0.66 25 25
CDC20 -0.15 0.14 -9999 0 -10000 0 0
PLK1/PBIP1 -0.03 0.054 -9999 0 -0.17 2 2
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 0.001 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 -0.27 214 214
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 -10000 0 0
microtubule-based process -0.12 0.059 -9999 0 -10000 0 0
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 -10000 0 0
APC/C/CDC20 -0.084 0.075 -9999 0 -10000 0 0
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.03 0.053 -9999 0 -0.17 2 2
PRC1 -0.078 0.12 -9999 0 -0.28 238 238
ECT2 -0.004 0.039 -9999 0 -10000 0 0
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 -0.038 0.045 -9999 0 -10000 0 0
spindle assembly -0.003 0.018 -9999 0 -10000 0 0
spindle stabilization 0.001 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 -10000 0 0
CCNB1 -0.065 0.12 -9999 0 -0.28 10 10
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 0.001 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 0.076 -9999 0 -10000 0 0
INCENP 0 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.004 0.099 -10000 0 -0.47 30 30
ACTA1 -0.019 0.14 -10000 0 -0.65 31 31
NUMA1 0.004 0.099 -10000 0 -0.47 30 30
SPTAN1 -0.006 0.13 -10000 0 -0.66 27 27
LIMK1 -0.006 0.13 -10000 0 -0.62 30 30
BIRC3 -0.011 0.086 -10000 0 -0.53 18 18
BIRC2 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.017 0.15 -10000 0 -0.7 31 31
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.004 0.099 -10000 0 -0.47 30 30
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.005 0.13 -10000 0 -0.64 27 27
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.013 0.15 -10000 0 -0.66 36 36
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.012 0.088 -10000 0 -0.7 12 12
BID 0.004 0.065 -10000 0 -0.3 30 30
MAP3K1 0.004 0.04 -10000 0 -0.24 7 7
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 -0.006 0.13 -10000 0 -0.62 30 30
CASP9 0 0.002 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.18 6 -0.22 3 9
neuron apoptosis 0.021 0.014 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.13 -10000 0 -0.63 27 27
APAF1 0 0 -10000 0 -10000 0 0
CASP6 0.022 0.06 -10000 0 -0.42 4 4
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD 0.002 0.13 -10000 0 -0.63 27 27
CASP7 -0.007 0.04 0.37 8 -10000 0 8
KRT18 0.015 0.017 -10000 0 -10000 0 0
apoptosis 0.008 0.11 -10000 0 -0.56 27 27
DFFA -0.006 0.13 -10000 0 -0.62 30 30
DFFB -0.006 0.13 -10000 0 -0.62 30 30
PARP1 0.002 0.031 0.22 3 -0.18 6 9
actin filament polymerization -0.003 0.12 0.61 27 -10000 0 27
TNF -0.017 0.1 -10000 0 -0.5 28 28
CYCS 0.007 0.052 -10000 0 -0.22 30 30
SATB1 0.018 0.1 -10000 0 -0.54 19 19
SLK -0.006 0.13 -10000 0 -0.62 30 30
p15 BID/BAX -0.014 0.051 -10000 0 -0.35 7 7
CASP2 0.043 0.043 -10000 0 -0.47 1 1
JNK cascade -0.004 0.04 0.24 7 -10000 0 7
CASP3 -0.015 0.14 -10000 0 -0.66 31 31
LMNB2 0.039 0.04 -10000 0 -0.4 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 0.051 -10000 0 -0.51 8 8
negative regulation of DNA binding 0.013 0.087 -10000 0 -0.69 12 12
stress fiber formation -0.005 0.13 -10000 0 -0.61 30 30
GZMB -0.03 0.16 -10000 0 -0.67 39 39
CASP1 -0.002 0.031 -10000 0 -0.46 4 4
LMNB1 0.045 0.041 -10000 0 -0.4 2 2
APP 0.021 0.014 -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 0.002 0.11 0.26 3 -0.53 28 31
LMNA 0.039 0.04 -10000 0 -0.4 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.039 -10000 0 -0.5 1 1
LRDD 0 0.01 -10000 0 -10000 0 0
SREBF1 -0.008 0.13 -10000 0 -0.66 27 27
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.004 0.098 -10000 0 -0.46 30 30
CFL2 0.002 0.13 -10000 0 -0.63 27 27
GAS2 -0.055 0.2 -10000 0 -0.54 107 107
positive regulation of apoptosis 0.045 0.04 -10000 0 -0.39 2 2
PRF1 -0.021 0.12 -10000 0 -0.65 27 27
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.008 0.061 -9999 0 -0.49 13 13
RGS9BP -0.017 0.066 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -10000 0 0
mol:Na + -0.021 0.051 -9999 0 -10000 0 0
mol:ADP 0.007 0.027 -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 93 93
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 -10000 0 0
mol:Ca2+ -0.099 0.076 -9999 0 -10000 0 0
Cone PDE6 -0.062 0.16 -9999 0 -0.49 93 93
Cone Metarhodopsin II -0.002 0.018 -9999 0 -10000 0 0
Na + (4 Units) -0.099 0.075 -9999 0 -10000 0 0
GNAT2/GDP -0.061 0.16 -9999 0 -0.49 93 93
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 -10000 0 0
GNB3/GNGT2 -0.01 0.08 -9999 0 -0.65 13 13
GNB3 -0.013 0.1 -9999 0 -0.76 14 14
GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
CNGA3 -0.029 0.085 -9999 0 -10000 0 0
ARR3 -0.002 0.023 -9999 0 -10000 0 0
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 93 93
Cone CNG Channel -0.016 0.038 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.18 0.13 -9999 0 -10000 0 0
RGS9 -0.096 0.26 -9999 0 -0.78 103 103
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 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.001 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 -0.53 102 102
GNAO1 -0.033 0.14 -9999 0 -0.48 58 58
SMO/beta Arrestin2 -0.006 0.059 -9999 0 -0.65 7 7
SMO -0.005 0.077 -9999 0 -0.77 8 8
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 -0.042 0.18 -9999 0 -0.84 42 42
XPO1 0.011 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.053 0.16 -9999 0 -0.68 28 28
SAP30 0 0.017 -9999 0 -0.28 3 3
mol:GDP -0.005 0.077 -9999 0 -0.77 8 8
MIM/GLI2A 0.001 0.03 -9999 0 -0.31 2 2
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 9 9
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 0.071 -9999 0 -0.84 6 6
Gi family/GTP -0.031 0.095 -9999 0 -0.38 38 38
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 -0.53 102 102
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 -0.31 2 2
embryonic limb morphogenesis -0.026 0.2 -9999 0 -0.53 102 102
SUFU -0.002 0.027 -9999 0 -0.31 1 1
LGALS3 -0.01 0.091 -9999 0 -0.84 10 10
catabolic process -0.004 0.029 -9999 0 -10000 0 0
GLI3A/CBP -0.028 0.099 -9999 0 -0.39 60 60
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.028 0.21 -9999 0 -0.54 102 102
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 0.065 -9999 0 -0.57 10 10
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 -0.45 17 17
PTCH1 -0.063 0.34 -9999 0 -1.2 57 57
MIM/GLI1 -0.053 0.19 -9999 0 -0.59 60 60
CREBBP -0.027 0.099 -9999 0 -0.39 60 60
Su(fu)/SIN3/HDAC complex 0.006 0.019 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.022 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 -10000 0 0
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 -0.007 0.054 -10000 0 -0.46 12 12
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 -10000 0 0
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 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -0.28 1 1
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 -0.51 477 477
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 -0.51 477 477
GSK3A 0.037 0.002 -10000 0 -10000 0 0
FOXO1 0.033 0.045 -10000 0 -0.46 7 7
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 -10000 0 0
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 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
TNFSF10 -0.007 0.077 -10000 0 -0.77 8 8
positive regulation of NF-kappaB transcription factor activity -0.066 0.2 -10000 0 -0.64 86 86
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 -0.079 0.24 -10000 0 -0.83 80 80
TRAIL/TRAILR2 -0.006 0.059 -10000 0 -0.65 7 7
TRAIL/TRAILR3 -0.009 0.076 -10000 0 -0.7 9 9
TRAIL/TRAILR1 -0.009 0.074 -10000 0 -0.65 11 11
TRAIL/TRAILR4 -0.066 0.2 -10000 0 -0.65 86 86
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) -0.079 0.24 -10000 0 -0.83 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 -10000 0 0
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 -10000 0 0
CASP10 0.02 0.11 0.31 75 -0.53 10 85
JNK cascade -0.066 0.2 -10000 0 -0.64 86 86
TRAIL (trimer) -0.007 0.077 -10000 0 -0.77 8 8
TNFRSF10C -0.006 0.057 -10000 0 -0.84 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD -0.009 0.058 -10000 0 -0.5 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
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.65 24 24
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.002 0.032 -9999 0 -0.84 1 1
CDH1 -0.024 0.14 -9999 0 -0.84 24 24
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0 0.01 -10000 0 -10000 0 0
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 0.005 0.069 -10000 0 -0.46 18 18
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 -0.011 0.072 -10000 0 -0.51 17 17
CYAA -0.005 0.051 -10000 0 -0.5 9 9
MAP2K4 -0.002 0.02 -10000 0 -0.51 1 1
IL1B 0.009 0.061 -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 -0.51 230 230
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 -0.017 0.1 -10000 0 -0.5 28 28
VCAM1 -0.01 0.067 -10000 0 -0.46 18 18
platelet activation -0.001 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.014 0.022 0.12 17 -10000 0 17
IL18 0.011 0.036 -10000 0 -0.3 2 2
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 0.03 -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 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
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 0.018 0.085 -9999 0 -0.51 20 20
CCND1 0.015 0.042 -9999 0 -0.23 19 19
p38 gamma/SNTA1 -0.012 0.074 -9999 0 -0.47 20 20
MAP2K3 0 0.01 -9999 0 -0.28 1 1
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.018 0.084 -9999 0 -0.5 20 20
MAP2K6 0.011 0.085 -9999 0 -0.53 20 20
MAPT -0.016 0.13 -9999 0 -0.41 83 83
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
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.033 0.14 -9999 0 -0.48 58 58
CDC42/GTP -0.025 0.079 -9999 0 -0.32 32 32
PLCG1 -0.026 0.082 -9999 0 -0.33 32 32
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 -0.024 0.078 -9999 0 -0.31 32 32
S1PR5 -0.008 0.061 -9999 0 -0.38 17 17
S1PR4 -0.011 0.08 -9999 0 -0.43 22 22
MAPK3 -0.026 0.082 -9999 0 -0.5 3 3
MAPK1 -0.026 0.082 -9999 0 -0.5 3 3
S1P/S1P5/Gi -0.027 0.09 -9999 0 -0.38 30 30
GNAI1 -0.042 0.18 -9999 0 -0.84 42 42
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 -0.028 0.089 -9999 0 -0.36 32 32
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.006 0.071 -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
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.023 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 -0.48 58 58
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 0.071 -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 -0.027 0.09 -10000 0 -0.38 30 30
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.042 0.18 -10000 0 -0.84 42 42
S1P3 pathway

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
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 -0.028 0.096 -9999 0 -0.35 67 67
GNAO1 -0.033 0.14 -9999 0 -0.48 58 58
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 0.017 0.18 -9999 0 -1.4 12 12
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 -0.042 0.18 -9999 0 -0.84 42 42
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 0.11 -9999 0 -0.4 32 32
MAPK3 0.018 0.1 -9999 0 -0.52 10 10
MAPK1 0.018 0.1 -9999 0 -0.52 10 10
JAK2 0.02 0.1 -9999 0 -0.38 30 30
CXCR4 0.014 0.1 -9999 0 -0.48 15 15
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 -0.52 10 10
S1P/S1P3/Gi 0.01 0.11 -9999 0 -0.4 32 32
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.024 0.085 -9999 0 -0.51 10 10
VEGFA 0.01 0.03 -9999 0 -0.28 9 9
S1P/S1P2/Gi -0.027 0.089 -9999 0 -0.38 31 31
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 0.085 -9999 0 -0.51 10 10
Retinoic acid receptors-mediated signaling

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
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 -0.41 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.035 0.046 -10000 0 -0.45 4 4
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 -10000 0 0
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 -0.6 22 22
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 0.017 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 -0.35 3 3
PRKCA -0.008 0.13 -10000 0 -0.84 21 21
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.004 0.13 -10000 0 -0.63 22 22
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 -0.021 0.094 -10000 0 -0.84 6 6
CRBP1/9-cic-RA -0.015 0.069 -10000 0 -0.66 6 6
RARB 0.004 0.083 -10000 0 -0.84 8 8
PRKCG -0.002 0.056 -10000 0 -0.27 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 -0.51 22 22
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 -0.63 22 22
positive regulation of DNA binding -0.009 0.057 -10000 0 -0.38 2 2
NRIP1 -0.003 0.12 -10000 0 -0.9 6 6
RXRs/RARs -0.011 0.13 -10000 0 -0.6 24 24
RXRs/RXRs/DNA/9cRA -0.045 0.12 -10000 0 -0.66 21 21
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
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.018 0.099 -9999 0 -0.6 24 24
KLHL20 -0.008 0.033 -9999 0 -0.25 2 2
CYFIP2 -0.01 0.061 -9999 0 -0.32 25 25
Rac1/GDP 0.048 0.07 -9999 0 -0.35 24 24
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 -0.62 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 -0.65 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 -0.65 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 -0.35 24 24
actin cytoskeleton organization -0.006 0.024 -9999 0 -0.18 2 2
CDC42/GDP 0.048 0.07 -9999 0 -0.35 24 24
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 -0.84 1 1
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 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.018 0.1 -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 0.036 -9999 0 -0.26 6 6
VAV2 0.034 0.096 -9999 0 -0.52 24 24
RAP1/GDP -0.01 0.058 -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
Sphingosine 1-phosphate (S1P) 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
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.004 0.048 -9999 0 -0.4 9 9
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 -0.48 58 58
mol:Sphinganine-1-P 0.019 0.037 -9999 0 -0.65 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 -0.43 22 22
GNAI1 -0.042 0.18 -9999 0 -0.84 42 42
S1P/S1P5/G12 -0.004 0.036 -9999 0 -0.5 3 3
S1P/S1P3/Gq -0.003 0.032 -9999 0 -0.29 9 9
S1P/S1P4/Gi -0.027 0.086 -9999 0 -0.35 33 33
GNAQ -0.002 0.041 -9999 0 -0.84 2 2
GNAZ -0.006 0.071 -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
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.016 0.087 -9999 0 -0.55 19 19
MAP4K1 -0.01 0.062 -9999 0 -0.84 2 2
MAP3K8 -0.005 0.065 -9999 0 -0.84 5 5
PRKCB -0.019 0.12 -9999 0 -0.58 28 28
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 -0.007 0.048 -9999 0 -0.58 2 2
JUN 0.019 0.11 -9999 0 -0.59 24 24
MAP3K7 -0.007 0.048 -9999 0 -0.58 2 2
GRAP2 -0.015 0.11 -9999 0 -0.74 17 17
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.044 0.059 -9999 0 -0.52 4 4
LAT -0.004 0.048 -9999 0 -0.84 2 2
LCP2 0 0.01 -9999 0 -10000 0 0
MAPK8 0.017 0.098 -9999 0 -0.69 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.052 -9999 0 -0.37 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.015 0.082 -9999 0 -0.53 17 17
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.049 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 -0.39 45 45
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 0.04 0.056 -10000 0 -0.25 22 22
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 0.009 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 -10000 0 0
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 -0.28 11 11
TERT -0.034 0.091 -10000 0 -0.28 102 102
E2F1 0.026 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 0.028 -10000 0 -0.27 8 8
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
Glypican 2 network

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
MDK -0.01 0.051 -9999 0 -10000 0 0
GPC2 -0.033 0.099 -9999 0 -0.84 3 3
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
Paxillin-independent events mediated by a4b1 and a4b7

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
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 -0.28 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.009 0.042 -9999 0 -0.45 4 4
EPO -0.048 0.1 -9999 0 -0.28 147 147
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 -0.28 31 31
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 0.048 -9999 0 -0.51 7 7
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 0.054 -9999 0 -0.56 7 7
p130Cas/Crk/Dock1 -0.005 0.039 -9999 0 -0.42 7 7
VCAM1 -0.009 0.079 -9999 0 -0.84 7 7
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.034 0.05 -9999 0 -0.47 7 7
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 -0.28 4 4
Rac1/GTP 0.001 0.006 -9999 0 -10000 0 0
IL1-mediated signaling events

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
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 0.035 -10000 0 -0.57 1 1
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 -0.032 0.13 -10000 0 -0.63 34 34
IL1A -0.005 0.038 -10000 0 -10000 0 0
IL1B 0.012 0.084 -10000 0 -0.7 11 11
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.016 -10000 0 -10000 0 0
IL1R2 -0.038 0.16 -10000 0 -0.64 50 50
IL1R1 -0.011 0.095 -10000 0 -0.84 11 11
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.058 0.24 23 -0.33 10 33
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 0.033 0.08 -10000 0 -0.46 9 9
MAP3K7 0 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.013 0.082 -10000 0 -0.49 21 21
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.009 0.06 -10000 0 -0.51 11 11
PIK3R1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.055 -10000 0 -0.48 11 11
IL1 beta fragment/IL1R1/IL1RAP -0.014 0.092 -10000 0 -0.55 21 21
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.031 0.065 -10000 0 -0.42 17 17
IRAK1 0.021 0.012 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.016 0.085 -10000 0 -0.65 13 13
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 -0.008 0.052 -10000 0 -0.36 11 11
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.014 0.092 -10000 0 -0.55 21 21
IL1 beta/IL1R2 -0.032 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 -0.011 0.073 -10000 0 -1.1 1 1
IRAK3 -0.026 0.14 -10000 0 -0.84 26 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.013 0.082 -10000 0 -0.49 21 21
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.038 -10000 0 -0.34 11 11
IL1 alpha/IL1R1/IL1RAP -0.01 0.066 -10000 0 -0.56 11 11
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 -0.01 0.066 -10000 0 -0.98 1 1
CASP1 -0.003 0.05 -10000 0 -0.84 3 3
IL1RN/IL1R2 -0.036 0.13 -10000 0 -0.63 36 36
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.013 0.087 -10000 0 -0.52 21 21
TMEM189-UBE2V1 -0.001 0.014 -10000 0 -0.28 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.044 -10000 0 -0.38 11 11
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 0.064 -10000 0 -0.45 17 17
Signaling events mediated by HDAC Class II

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
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 -0.65 1 1
GATA1/HDAC5 -0.002 0.019 -10000 0 -10000 0 0
GATA2/HDAC5 -0.017 0.098 -10000 0 -0.65 19 19
HDAC5/BCL6/BCoR -0.002 0.033 -10000 0 -0.56 3 3
HDAC9 -0.01 0.078 -10000 0 -0.46 18 18
Glucocorticoid receptor/Hsp90/HDAC6 -0.005 0.054 -10000 0 -0.56 8 8
HDAC4/ANKRA2 -0.001 0.022 -10000 0 -0.65 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 -0.65 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 -0.65 6 6
Histones -0.002 0.024 -10000 0 -10000 0 0
ADRBK1 0 0.01 -10000 0 -10000 0 0
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 -0.65 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 -10000 0 0
Tubulin/HDAC6 0 0.006 -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 -0.008 0.081 -10000 0 -0.84 8 8
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 -0.65 1 1
Tubulin 0 0.009 -10000 0 -10000 0 0
HDAC4/14-3-3 E -0.001 0.022 -10000 0 -0.65 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 -0.65 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 -0.65 118 118
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 -0.56 230 230
HDAC6/HDAC11 -0.001 0.01 -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 0.071 -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 0.017 -10000 0 -10000 0 0
HSP90AA1 0 0.01 -10000 0 -10000 0 0
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
a4b1 and a4b7 Integrin signaling

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
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 -0.28 10 10
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
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.29 30 31
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 -0.18 1 2
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
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.052 -10000 0 -0.44 2 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.015 0.064 -10000 0 -0.28 47 47
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 0 -10000 0 -10000 0 0
MAP3K7 0 0.01 -10000 0 -10000 0 0
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.002 0.031 -10000 0 -0.65 2 2
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 -0.64 100 100
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.049 0.15 -10000 0 -0.57 64 64
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 66 66
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 -0.006 0.023 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.27 147 147
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 0.056 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 -0.45 38 38
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) 0.059 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
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.048 0.025 -10000 0 -0.36 1 1
NFATC2 0.022 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 0.098 -10000 0 -0.42 25 25
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 -0.018 0.077 -10000 0 -0.53 11 11
BCL2/BAX -0.018 0.11 -10000 0 -0.65 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 -0.02 0.084 -10000 0 -0.59 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 0.02 0.083 0.58 11 -10000 0 11
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.034 0.091 -10000 0 -10000 0 0
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 -0.84 5 5
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 0.011 0.099 -10000 0 -0.43 25 25
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 -10000 0 0
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 -0.019 0.12 -10000 0 -0.58 28 28
PRKCE 0 0 -10000 0 -10000 0 0
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 -0.84 21 21
PRKCG -0.011 0.055 -10000 0 -0.28 34 34
PRKCQ -0.038 0.17 -10000 0 -0.68 47 47
FKBP38/BCL2 -0.018 0.11 -10000 0 -0.65 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 -0.018 0.076 -10000 0 -0.52 11 11
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 0.064 -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 -10000 0 0
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
IL2 signaling events mediated by STAT5

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
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 -10000 0 0
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 -0.015 0.083 -9999 0 -0.84 5 5
G1/S transition of mitotic cell cycle 0.012 0.11 -9999 0 -0.82 11 11
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 -0.002 0.027 -9999 0 -0.28 8 8
CDK6 -0.008 0.077 -9999 0 -0.71 9 9
CCND3 0.067 0.059 -9999 0 -0.63 2 2
VEGFR1 specific signals

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
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 -0.69 2 2
NOS3 0.063 0.032 -9999 0 -0.74 1 1
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 -1.2 1 1
MAPK1 0.039 0.088 -9999 0 -1.2 1 1
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 -0.84 175 175
VEGFA homodimer -0.003 0.028 -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 0.034 0.083 -9999 0 -0.52 16 16
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 -0.084 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 -0.84 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 -10000 0 0
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
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.003 0.03 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.007 0.047 -9999 0 -1 1 1
NEF -0.005 0.023 -9999 0 -10000 0 0
NFKBIA -0.002 0.012 -9999 0 -10000 0 0
BIRC3 -0.011 0.085 -9999 0 -0.84 8 8
CYCS 0.042 0.057 -9999 0 -0.98 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.027 0.13 -9999 0 -0.72 26 26
MAP2K7 0.042 0.047 -9999 0 -0.82 1 1
protein ubiquitination 0.066 0.035 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.003 0.05 -9999 0 -0.84 3 3
BID -0.009 0.051 -9999 0 -1.1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.005 0.036 -9999 0 -0.34 8 8
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 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.005 0.036 -9999 0 -0.34 8 8
MAPK8 0.049 0.044 -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 -0.01 0.056 -9999 0 -0.42 8 8
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.033 -9999 0 -0.38 2 2
CHUK 0.067 0.037 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.005 0.048 -9999 0 -0.62 4 4
TCRz/NEF -0.025 0.11 -9999 0 -0.56 30 30
TNF -0.017 0.1 -9999 0 -0.5 28 28
FASLG -0.004 0.13 -9999 0 -0.61 30 30
NFKB1 -0.002 0.012 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.012 0.067 -9999 0 -0.56 11 11
CASP6 -0.004 0.032 -9999 0 -0.72 1 1
CASP7 0.073 0.079 -9999 0 -0.64 8 8
RELA -0.002 0.012 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.073 0.079 -9999 0 -0.64 8 8
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 0.039 -9999 0 -0.36 1 1
APAF-1/Caspase 9 -0.009 0.057 -9999 0 -0.54 8 8
BCL2 0.042 0.089 -9999 0 -0.43 25 25
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.012 0.086 -9999 0 -0.65 15 15
AKT1 0.085 0.044 -9999 0 -0.69 2 2
PTK2B -0.011 0.074 -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 -0.84 175 175
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 0.072 -9999 0 -0.65 3 3
mol:Ca2+ -0.003 0.039 -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 -0.79 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 -0.64 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 -0.28 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.005 0.041 -9999 0 -0.52 2 2
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.03 -9999 0 -10000 0 0
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 -0.56 2 2
VEGFA -0.003 0.028 -9999 0 -0.27 9 9
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin -0.007 0.056 -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 -0.009 0.08 -9999 0 -0.54 16 16
PTPN6 -0.001 0.014 -9999 0 -10000 0 0
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 0.043 -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 -0.65 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 -0.28 1 1
platelet activating factor biosynthetic process 0.057 0.064 -9999 0 -0.81 3 3
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 -0.6 5 5
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 -0.01 0.17 -9999 0 -0.55 5 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.004 0.047 -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 -10000 0 0
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 0.071 -9999 0 -1 2 2
EDG1 0.046 0.043 -9999 0 -0.79 2 2
mol:DAG -0.003 0.039 -9999 0 -0.79 2 2
CaM/Ca2+ -0.002 0.036 -9999 0 -0.73 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 -0.7 3 3
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 0.085 0.06 -9999 0 -0.79 2 2
mol:PI-3-4-5-P3 -0.002 0.044 -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 -0.016 0.11 -9999 0 -0.72 19 19
NOS3 0.079 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 0.088 -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 -0.65 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 -0.007 0.056 -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
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.045 0.05 -10000 0 -0.57 1 1
BAG4 -0.003 0.03 -10000 0 -10000 0 0
BAD 0.032 0.018 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.011 0.086 -10000 0 -0.53 18 18
BAX 0.032 0.018 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.013 -10000 0 -0.11 2 2
IKBKB 0.051 0.048 -10000 0 -0.53 1 1
MAP2K2 0.044 0.026 -10000 0 -0.49 1 1
MAP2K1 0.044 0.026 -10000 0 -0.49 1 1
SMPD1 0.02 0.013 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.049 0.053 -10000 0 -0.46 3 3
MAP2K4 0.038 0.024 -10000 0 -0.42 1 1
protein ubiquitination 0.053 0.048 -10000 0 -0.54 1 1
EnzymeConsortium:2.7.1.37 0.049 0.029 -10000 0 -0.52 1 1
response to UV 0 0 -10000 0 -0.003 2 2
RAF1 0.039 0.027 -10000 0 -0.53 1 1
CRADD 0 0 -10000 0 -10000 0 0
mol:ceramide 0.025 0.019 -10000 0 -0.15 2 2
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 0.018 -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 0.026 -10000 0 -0.48 1 1
MAPK1 0.046 0.026 -10000 0 -0.48 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.042 0.054 -10000 0 -0.48 3 3
KSR1 0.032 0.028 -10000 0 -0.56 1 1
MAPK8 0.044 0.023 -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 0.051 0.047 -10000 0 -0.53 1 1
TNF R/SODD -0.002 0.019 -10000 0 -10000 0 0
TNF -0.017 0.1 -10000 0 -0.5 28 28
CYCS 0.037 0.025 0.15 22 -10000 0 22
IKBKG 0.051 0.047 -10000 0 -0.53 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.038 0.052 -10000 0 -0.37 8 8
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.025 0.15 22 -10000 0 22
TNF/TNF R/SODD -0.012 0.067 -10000 0 -0.56 11 11
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 0.049 -10000 0 -0.56 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 2 2
BCL2 -0.024 0.14 -10000 0 -0.84 24 24
HIF-2-alpha transcription factor network

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
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 -10000 0 0
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 -0.54 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 0.065 -10000 0 -0.39 1 1
ETS1 0.024 0.044 -10000 0 -0.87 2 2
CITED2 0.001 0.01 -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 0.14 -10000 0 -0.69 1 1
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 0.17 0.13 -10000 0 -0.57 1 1
POU5F1 0.17 0.14 -10000 0 -0.69 1 1
neuron apoptosis -0.057 0.13 0.67 1 -10000 0 1
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.08 -10000 0 -0.28 28 28
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 -0.54 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 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
NF kappa B/RelA -0.005 0.06 -9999 0 -0.52 11 11
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.048 -9999 0 -0.43 11 11
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.001 0.014 -9999 0 -0.28 2 2
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.024 -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 -0.006 0.043 -9999 0 -0.38 11 11
I kappa B alpha/HDAC1 -0.004 0.029 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.005 0.037 -9999 0 -0.33 11 11
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.029 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.033 -9999 0 -0.29 11 11
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 -0.005 0.033 -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 -0.28 3 3
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.029 -9999 0 -0.84 1 1
YY1/HDAC3 -0.003 0.025 -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 -0.097 0.18 -9999 0 -0.4 205 205
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 0.029 -9999 0 -10000 0 0
MBD3L2 -0.001 0.014 -9999 0 -0.28 2 2
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 -0.005 0.033 -9999 0 -10000 0 0
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 -0.28 1 1
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 -0.005 0.033 -9999 0 -10000 0 0
histone deacetylation 0.046 0.003 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.026 -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 0.032 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.012 0.077 -9999 0 -0.65 11 11
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 0.024 -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 -0.017 0.1 -9999 0 -0.5 28 28
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 0.051 -9999 0 -0.45 11 11
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 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
G6PC 0.03 0.035 -9999 0 -10000 0 0
PLK1 0.012 0.11 -9999 0 -0.6 1 1
CDKN1B 0.082 0.067 -9999 0 -0.55 3 3
FOXO3 0.044 0.096 -9999 0 -0.56 3 3
KAT2B 0.008 0.012 -9999 0 -10000 0 0
FOXO1/SIRT1 0.008 0.037 -9999 0 -0.34 3 3
CAT 0.047 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 0.032 0.038 -9999 0 -0.37 7 7
MAPK10 -0.047 0.19 -9999 0 -0.48 135 135
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.063 0.087 -9999 0 -10000 0 0
response to oxidative stress 0.005 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.012 0.059 -9999 0 -0.53 3 3
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 -0.003 0.031 -9999 0 -0.34 7 7
mol:GDP 0.005 0.011 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
GADD45A 0.069 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 2 2
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 -10000 0 0
SIRT1 0.002 0.007 -9999 0 -10000 0 0
SOD2 0.093 0.068 -9999 0 -10000 0 0
RBL2 0.063 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 0.036 0.1 -9999 0 -0.6 1 1
FOXO1-3a-4/beta catenin -0.006 0.032 -9999 0 -0.41 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.03 -9999 0 -0.33 7 7
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 0.068 0.077 -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 0.046 0.12 -9999 0 -1.4 3 3
BCL6 0.06 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
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 -0.39 1 3
DAPP1 0.036 0.052 -10000 0 -0.54 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.047 0.079 -10000 0 -0.52 9 9
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 0.017 -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 -0.28 1 1
mol:GTP 0 0.02 0.27 2 -0.42 1 3
ARF1/GTP 0 0.02 0.28 2 -0.4 1 3
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.029 -10000 0 -0.84 1 1
RAP1A/GTP 0 0.02 0.26 2 -0.42 1 3
ADAP1 -0.002 0.033 0.26 2 -0.43 4 6
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 -0.28 31 31
ARHGEF6 -0.006 0.071 -10000 0 -0.84 6 6
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.27 2 2
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 -0.026 0.13 -10000 0 -0.51 44 44
mol:IP3 0.049 0.038 -10000 0 -0.22 1 1
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.002 0.017 -10000 0 -10000 0 0
RhoA/GDP 0 0.019 0.28 2 -10000 0 2
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.064 0.025 -10000 0 -10000 0 0
SRC 0 0.01 -10000 0 -0.28 1 1
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 -10000 0 0
ARF6/GTP 0 0.02 0.3 2 -10000 0 2
RhoA/GTP 0 0.019 -10000 0 -0.4 1 1
Src family/SYK family/BLNK-LAT -0.01 0.057 -10000 0 -0.55 4 4
BLK -0.036 0.1 -10000 0 -0.84 3 3
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 0 0.019 0.26 2 -0.39 1 3
HCK -0.004 0.033 -10000 0 -0.28 12 12
CYTH3 0 0.019 0.26 2 -0.39 1 3
CYTH2 0 0.019 0.26 2 -0.39 1 3
KRAS 0 0.009 -10000 0 -0.27 1 1
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 0.023 -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 -0.36 1 3
mol:PI-3-4-5-P3 0 0.024 0.37 2 -0.42 1 3
ARAP3/RAP1A/GTP 0 0.02 0.26 2 -0.42 1 3
VAV1 -0.002 0.032 -10000 0 -0.84 1 1
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 -0.002 0.017 -10000 0 -10000 0 0
LAT -0.004 0.048 -10000 0 -0.84 2 2
Rac1/GTP -0.002 0.03 -10000 0 -0.34 6 6
ITK -0.018 0.083 0.26 1 -0.46 26 27
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.061 0.064 0.24 1 -0.39 5 6
LCK -0.019 0.1 -10000 0 -0.46 34 34
BTK 0 0.02 0.26 2 -0.39 1 3
PDGFR-beta signaling 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
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 0.036 -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 0.035 -9999 0 -0.64 2 2
HRAS 0 0.01 -9999 0 -0.28 1 1
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 -0.57 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 0.034 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 -0.56 2 2
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 -0.57 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 -0.43 3 3
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 0.051 -9999 0 -0.28 29 29
PLCgamma1/SPHK1 -0.004 0.043 -9999 0 -0.6 4 4
LYN -0.002 0.029 -9999 0 -0.54 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 -0.4 9 9
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.034 0.041 -9999 0 -0.7 2 2
PLCG1 0.034 0.042 -9999 0 -0.72 2 2
NHERF/PDGFRB -0.014 0.047 -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 -0.66 2 2
PTPRJ 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.032 -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 -0.004 0.048 -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 -0.28 24 24
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 -0.012 0.077 -9999 0 -0.65 11 11
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.022 0.13 -9999 0 -0.84 21 21
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.017 0.1 -9999 0 -0.5 28 28
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 0.006 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.01 0.063 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.42 10 10
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 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.13 0.15 -9999 0 -0.34 15 15
YWHAZ -0.001 0.017 -9999 0 -10000 0 0
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 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.001 0.017 -9999 0 -10000 0 0
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 -0.38 14 14
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
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.006 -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 -0.28 1 1
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 -10000 0 0
Circadian rhythm 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
chromatin modification 0.001 0.019 -9999 0 -10000 0 0
CLOCK 0 0.001 -9999 0 -10000 0 0
TIMELESS/CRY2 -0.001 0.007 -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 0.01 -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 -0.83 4 4
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 -10000 0 0
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 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.001 0.017 -9999 0 -0.28 3 3
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 0.028 0.33 6 -10000 0 6
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 0.021 0.05 -10000 0 -0.55 6 6
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 -0.006 0.02 -10000 0 -10000 0 0
ARF6 0.007 0.007 -10000 0 -10000 0 0
RAB11A -0.001 0.014 -10000 0 -10000 0 0
TIAM1 -0.001 0.019 -10000 0 -0.27 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 0.006 0.02 -10000 0 -10000 0 0
KALRN -0.01 0.069 -10000 0 -0.51 15 15
RAB11FIP3/RAB11A 0 0.009 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.02 -10000 0 -10000 0 0
NME1 -0.013 0.059 -10000 0 -10000 0 0
Rac1/GDP -0.006 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 0.028 -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 0.012 0.055 -10000 0 -0.62 6 6
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.03 -10000 0 -10000 0 0
ruffle organization -0.003 0.028 -10000 0 -0.33 6 6
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 0.028 -10000 0 -0.33 6 6
mol:Phosphatidic acid 0.021 0.05 -10000 0 -0.55 6 6
Rac1/GTP -0.004 0.03 -10000 0 -10000 0 0
IFN-gamma 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
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 0.032 -9999 0 -10000 0 0
CaM/Ca2+ 0.011 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 -0.005 0.013 -9999 0 -10000 0 0
MAP2K1 0.041 0.037 -9999 0 -10000 0 0
MAP3K11 -0.002 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 -0.026 0.1 -9999 0 -0.43 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 0.095 -9999 0 -10000 0 0
PIK3CA 0 0.01 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.008 0.027 -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) -0.003 0.047 -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 -10000 0 0
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 -0.64 100 100
FRAP1 0.043 0.033 -9999 0 -10000 0 0
PRKCD -0.005 0.014 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.008 0.032 -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 0.042 -9999 0 -0.36 3 3
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 0.037 -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 0.032 -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
Paxillin-dependent events mediated by a4b1

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
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 -0.28 10 10
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 0.014 -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 -0.006 0.045 -9999 0 -0.48 7 7
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.009 0.079 -9999 0 -0.84 7 7
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 -0.28 4 4
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
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
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 -0.65 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 -10000 0 0
PIAS4 0 0 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -10000 0 0
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 -0.053 0.11 -9999 0 -10000 0 0
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 0.014 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 0.008 -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 0.013 -9999 0 -0.28 2 2
BARD1 0 0.01 -9999 0 -10000 0 0
PCNA -0.001 0.017 -9999 0 -0.28 3 3
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 -0.045 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 -0.018 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 -10000 0 0
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
PLK2 and PLK4 events

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
PLK2 0 0 -9999 0 -9999 0 0
PLK4 -0.014 0.06 -9999 0 -9999 0 0
regulation of centriole replication 0.013 0.042 -9999 0 -9999 0 0
Aurora C signaling

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
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 -0.018 0.017 -9999 0 -10000 0 0
AURKB -0.16 0.14 -9999 0 -10000 0 0
AURKC -0.005 0.045 -9999 0 -0.84 1 1
TCGA08_p53

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
CDKN2A -0.02 0.072 -9999 0 -10000 0 0
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 -0.19 2 2
MDM4 0 0 -9999 0 -10000 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 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0 0.01 -9999 0 -0.28 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -10000 0 0
CD4 0 0 -9999 0 -10000 0 0
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0.012 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0.005 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0.006 -9999 0 -10000 0 0
AP2M1 0 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.007 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.001 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.003 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0 0 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0.012 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.012 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -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 842 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 -0.012 -0.076 -0.16 0.019
84_STAT5A -0.012 -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/3025930/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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