PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1TH8M3H
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1TH8M3H
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 40 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
Nephrin/Neph1 signaling in the kidney podocyte 248
HIF-1-alpha transcription factor network 178
TCGA08_retinoblastoma 171
TCGA08_p53 158
EGFR-dependent Endothelin signaling events 142
TCR signaling in naïve CD8+ T cells 140
PDGFR-alpha signaling pathway 115
FOXA2 and FOXA3 transcription factor networks 114
Syndecan-4-mediated signaling events 94
Aurora B signaling 93
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 533 . Pathway is significant if Significance.Ratio > 0.05 .

  • 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. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 533 ).

Pathway.Name Significance.Ratio 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
Nephrin/Neph1 signaling in the kidney podocyte 0.4653 248 8465 34 -0.51 0.03 1000 -1000 -0.052 -1000
HIF-1-alpha transcription factor network 0.3340 178 13558 76 -1.1 0.045 1000 -1000 -0.16 -1000
TCGA08_retinoblastoma 0.3208 171 1375 8 -0.58 0.16 1000 -1000 -0.007 -1000
TCGA08_p53 0.2964 158 1111 7 -0.42 0.22 1000 -1000 -0.015 -1000
EGFR-dependent Endothelin signaling events 0.2664 142 2989 21 -0.57 0.043 1000 -1000 -0.058 -1000
TCR signaling in naïve CD8+ T cells 0.2627 140 13059 93 -0.44 0.2 1000 -1000 -0.076 -1000
PDGFR-alpha signaling pathway 0.2158 115 5067 44 -0.22 0.037 1000 -1000 -0.056 -1000
FOXA2 and FOXA3 transcription factor networks 0.2139 114 5280 46 -1.1 0.036 1000 -1000 -0.13 -1000
Syndecan-4-mediated signaling events 0.1764 94 6336 67 -0.43 0.089 1000 -1000 -0.067 -1000
Aurora B signaling 0.1745 93 6262 67 -0.26 0.042 1000 -1000 -0.057 -1000
IL12-mediated signaling events 0.1689 90 7883 87 -0.44 0.11 1000 -1000 -0.13 -1000
Glypican 1 network 0.1595 85 4095 48 -0.4 0.046 1000 -1000 -0.039 -1000
FOXM1 transcription factor network 0.1482 79 4039 51 -0.56 0.031 1000 -1000 -0.13 -1000
amb2 Integrin signaling 0.1388 74 6085 82 -0.45 0.038 1000 -1000 -0.054 -1000
BMP receptor signaling 0.1332 71 5798 81 -0.52 0.054 1000 -1000 -0.084 -1000
Aurora C signaling 0.1295 69 486 7 -0.26 0.027 1000 -1000 -0.019 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1220 65 2158 33 -0.57 0.056 1000 -1000 -0.056 -1000
Glypican 2 network 0.1182 63 253 4 -0.041 -1000 1000 -1000 0.001 -1000
IL4-mediated signaling events 0.1144 61 5581 91 -0.79 0.49 1000 -1000 -0.12 -1000
Caspase cascade in apoptosis 0.1051 56 4189 74 -0.29 0.093 1000 -1000 -0.047 -1000
Syndecan-1-mediated signaling events 0.0994 53 1824 34 -0.25 0.03 1000 -1000 -0.063 -1000
JNK signaling in the CD4+ TCR pathway 0.0957 51 869 17 -0.22 0.03 1000 -1000 -0.052 -1000
Fc-epsilon receptor I signaling in mast cells 0.0901 48 4685 97 -0.23 0.04 1000 -1000 -0.088 -1000
HIF-2-alpha transcription factor network 0.0769 41 1799 43 -0.53 0.25 1000 -1000 -0.072 -1000
Effects of Botulinum toxin 0.0732 39 1021 26 -0.23 0.04 1000 -1000 -0.036 -1000
Arf6 signaling events 0.0713 38 2407 62 -0.57 0.065 1000 -1000 -0.05 -1000
Calcium signaling in the CD4+ TCR pathway 0.0694 37 1151 31 -0.37 0.029 1000 -1000 -0.071 -1000
Coregulation of Androgen receptor activity 0.0675 36 2788 76 -0.86 0.055 1000 -1000 -0.031 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0675 36 1953 54 -0.44 0.041 1000 -1000 -0.08 -1000
Signaling events mediated by the Hedgehog family 0.0657 35 1852 52 -0.28 0.068 1000 -1000 -0.064 -1000
Reelin signaling pathway 0.0657 35 1997 56 -0.17 0.079 1000 -1000 -0.066 -1000
IL27-mediated signaling events 0.0638 34 1742 51 -0.6 0.059 1000 -1000 -0.069 -1000
Ephrin A reverse signaling 0.0619 33 232 7 -0.026 0.012 1000 -1000 -0.019 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0619 33 2266 68 -0.33 0.059 1000 -1000 -0.11 -1000
PLK1 signaling events 0.0600 32 2770 85 -0.18 0.042 1000 -1000 -0.038 -1000
LPA4-mediated signaling events 0.0582 31 383 12 -0.1 0.011 1000 -1000 -0.028 -1000
IL2 signaling events mediated by STAT5 0.0582 31 702 22 -0.29 0.036 1000 -1000 -0.066 -1000
p75(NTR)-mediated signaling 0.0544 29 3674 125 -0.3 0.079 1000 -1000 -0.11 -1000
S1P1 pathway 0.0544 29 1052 36 -0.25 0.029 1000 -1000 -0.062 -1000
Integrins in angiogenesis 0.0507 27 2284 84 -0.27 0.067 1000 -1000 -0.068 -1000
IL23-mediated signaling events 0.0488 26 1560 60 -0.26 0.029 1000 -1000 -0.12 -1000
BCR signaling pathway 0.0469 25 2482 99 -0.22 0.057 1000 -1000 -0.096 -1000
IL2 signaling events mediated by PI3K 0.0450 24 1444 58 -0.29 0.047 1000 -1000 -0.055 -1000
VEGFR1 specific signals 0.0450 24 1370 56 -0.32 0.03 1000 -1000 -0.081 -1000
Signaling events mediated by PTP1B 0.0432 23 1764 76 -0.57 0.065 1000 -1000 -0.057 -1000
Glucocorticoid receptor regulatory network 0.0432 23 2706 114 -0.34 0.15 1000 -1000 -0.081 -1000
Wnt signaling 0.0432 23 162 7 -0.042 0.028 1000 -1000 -0.034 -1000
Ceramide signaling pathway 0.0413 22 1723 76 -0.57 0.21 1000 -1000 -0.059 -1000
Regulation of Telomerase 0.0413 22 2274 102 -0.57 0.062 1000 -1000 -0.086 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0413 22 1960 88 -0.2 0.046 1000 -1000 -0.086 -1000
FoxO family signaling 0.0394 21 1357 64 -0.56 0.095 1000 -1000 -0.057 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0394 21 983 45 -0.36 0.078 1000 -1000 -0.083 -1000
Visual signal transduction: Rods 0.0394 21 1142 52 -0.16 0.04 1000 -1000 -0.056 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0394 21 1654 78 -0.25 0.046 1000 -1000 -0.066 -1000
Noncanonical Wnt signaling pathway 0.0356 19 509 26 -0.098 0.029 1000 -1000 -0.071 -1000
Syndecan-2-mediated signaling events 0.0356 19 1320 69 -0.45 0.063 1000 -1000 -0.055 -1000
EPO signaling pathway 0.0338 18 1040 55 -0.17 0.036 1000 -1000 -0.078 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0338 18 2198 120 -0.11 0.081 1000 -1000 -0.076 -1000
Endothelins 0.0319 17 1653 96 -0.33 0.048 1000 -1000 -0.076 -1000
IL6-mediated signaling events 0.0319 17 1348 75 -0.22 0.06 1000 -1000 -0.058 -1000
Regulation of nuclear SMAD2/3 signaling 0.0300 16 2259 136 -0.3 0.1 1000 -1000 -0.06 -1000
Presenilin action in Notch and Wnt signaling 0.0300 16 1004 61 -0.14 0.084 1000 -1000 -0.063 -1000
LPA receptor mediated events 0.0300 16 1657 102 -0.25 0.052 1000 -1000 -0.079 -1000
Thromboxane A2 receptor signaling 0.0281 15 1630 105 -0.57 0.047 1000 -1000 -0.065 -1000
Aurora A signaling 0.0281 15 904 60 -0.15 0.063 1000 -1000 -0.041 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0281 15 1141 74 -0.57 0.11 1000 -1000 -0.093 -1000
Class I PI3K signaling events 0.0281 15 1128 73 -0.31 0.08 1000 -1000 -0.062 -1000
IFN-gamma pathway 0.0263 14 969 68 -0.24 0.043 1000 -1000 -0.091 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0263 14 518 37 -0.17 0.058 1000 -1000 -0.048 -1000
Canonical Wnt signaling pathway 0.0263 14 723 51 -0.14 0.098 1000 -1000 -0.071 -1000
S1P5 pathway 0.0244 13 223 17 -0.079 0.029 1000 -1000 -0.037 -1000
Nongenotropic Androgen signaling 0.0244 13 715 52 -0.12 0.045 1000 -1000 -0.049 -1000
Plasma membrane estrogen receptor signaling 0.0244 13 1135 86 -0.15 0.053 1000 -1000 -0.093 -1000
Regulation of Androgen receptor activity 0.0244 13 962 70 -0.91 0.054 1000 -1000 -0.059 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0225 12 348 28 -0.079 0.048 1000 -1000 -0.039 -1000
PLK2 and PLK4 events 0.0225 12 38 3 0.006 0.026 1000 -1000 -0.025 -1000
Signaling events regulated by Ret tyrosine kinase 0.0225 12 1030 82 -0.03 0.03 1000 -1000 -0.097 -1000
S1P3 pathway 0.0225 12 528 42 -0.24 0.051 1000 -1000 -0.058 -1000
ErbB4 signaling events 0.0206 11 826 69 -0.16 0.095 1000 -1000 -0.063 -1000
FAS signaling pathway (CD95) 0.0206 11 555 47 -0.28 0.049 1000 -1000 -0.055 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0206 11 1402 125 -0.24 0.044 1000 -1000 -0.079 -1000
TCGA08_rtk_signaling 0.0206 11 291 26 -0.22 0.057 1000 -1000 -0.029 -1000
S1P4 pathway 0.0206 11 294 25 -0.079 0.039 1000 -1000 -0.045 -1000
E-cadherin signaling events 0.0206 11 57 5 0.007 0.026 1000 -1000 -0.013 -1000
Syndecan-3-mediated signaling events 0.0188 10 363 35 -0.011 0.079 1000 -1000 -0.038 -1000
a4b1 and a4b7 Integrin signaling 0.0169 9 48 5 0.01 0.029 1000 -1000 -0.004 -1000
ceramide signaling pathway 0.0169 9 467 49 -0.064 0.045 1000 -1000 -0.061 -1000
Visual signal transduction: Cones 0.0150 8 318 38 -0.013 0.044 1000 -1000 -0.029 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0131 7 663 85 -0.038 0.082 1000 -1000 -0.069 -1000
Ephrin B reverse signaling 0.0131 7 375 48 -0.047 0.052 1000 -1000 -0.042 -1000
Signaling events mediated by PRL 0.0131 7 248 34 -0.044 0.063 1000 -1000 -0.059 -1000
Class IB PI3K non-lipid kinase events 0.0131 7 21 3 -0.021 0.021 1000 -1000 -0.005 -1000
Canonical NF-kappaB pathway 0.0113 6 267 39 -0.11 0.057 1000 -1000 -0.059 -1000
Insulin-mediated glucose transport 0.0113 6 192 32 -0.041 0.057 1000 -1000 -0.037 -1000
mTOR signaling pathway 0.0113 6 324 53 -0.064 0.054 1000 -1000 -0.059 -1000
IL1-mediated signaling events 0.0113 6 376 62 -0.041 0.065 1000 -1000 -0.075 -1000
E-cadherin signaling in the nascent adherens junction 0.0113 6 493 76 -0.031 0.05 1000 -1000 -0.091 -1000
Ras signaling in the CD4+ TCR pathway 0.0113 6 106 17 -0.01 0.054 1000 -1000 -0.038 -1000
ErbB2/ErbB3 signaling events 0.0094 5 339 65 -0.12 0.042 1000 -1000 -0.062 -1000
Cellular roles of Anthrax toxin 0.0094 5 220 39 -0.01 0.039 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class III 0.0094 5 232 40 -0.054 0.054 1000 -1000 -0.023 -1000
Signaling mediated by p38-gamma and p38-delta 0.0094 5 75 15 0 0.03 1000 -1000 -0.031 -1000
Signaling mediated by p38-alpha and p38-beta 0.0094 5 246 44 -0.042 0.053 1000 -1000 -0.051 -1000
EPHB forward signaling 0.0094 5 437 85 -0.054 0.073 1000 -1000 -0.1 -1000
PDGFR-beta signaling pathway 0.0094 5 511 97 -0.019 0.087 1000 -1000 -0.087 -1000
p38 MAPK signaling pathway 0.0094 5 253 44 -0.063 0.057 1000 -1000 -0.048 -1000
Regulation of p38-alpha and p38-beta 0.0075 4 263 54 -0.022 0.067 1000 -1000 -0.061 -1000
Insulin Pathway 0.0075 4 310 74 -0.032 0.08 1000 -1000 -0.085 -1000
E-cadherin signaling in keratinocytes 0.0075 4 212 43 -0.22 0.042 1000 -1000 -0.064 -1000
BARD1 signaling events 0.0056 3 207 57 -0.095 0.076 1000 -1000 -0.071 -1000
Osteopontin-mediated events 0.0056 3 120 38 0 0.085 1000 -1000 -0.062 -1000
Hedgehog signaling events mediated by Gli proteins 0.0056 3 227 65 -0.005 0.1 1000 -1000 -0.067 -1000
Class I PI3K signaling events mediated by Akt 0.0056 3 234 68 -0.041 0.055 1000 -1000 -0.05 -1000
Nectin adhesion pathway 0.0056 3 192 63 0 0.057 1000 -1000 -0.067 -1000
Arf6 trafficking events 0.0056 3 252 71 -0.12 0.063 1000 -1000 -0.064 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0038 2 127 52 -0.015 0.1 1000 -1000 -0.054 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0038 2 223 83 -0.041 0.074 1000 -1000 -0.063 -1000
Retinoic acid receptors-mediated signaling 0.0038 2 119 58 -0.015 0.053 1000 -1000 -0.063 -1000
Paxillin-dependent events mediated by a4b1 0.0038 2 75 36 -0.052 0.054 1000 -1000 -0.061 -1000
Atypical NF-kappaB pathway 0.0038 2 62 31 0 0.037 1000 -1000 -0.044 -1000
IGF1 pathway 0.0038 2 126 57 -0.048 0.078 1000 -1000 -0.09 -1000
Signaling events mediated by HDAC Class II 0.0019 1 116 75 -0.041 0.062 1000 -1000 -0.044 -1000
Circadian rhythm pathway 0.0019 1 25 22 -0.014 0.069 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 0.0019 1 183 104 -0.057 0.076 1000 -1000 -0.059 -1000
Arf1 pathway 0.0019 1 80 54 0 0.049 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 19 23 -0.027 0.056 1000 -1000 -0.042 -1000
Arf6 downstream pathway 0.0000 0 40 43 -0.047 0.048 1000 -1000 -0.045 -1000
TRAIL signaling pathway 0.0000 0 32 48 0 0.072 1000 -1000 -0.057 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 0 0.07 1000 -1000 -0.057 -1000
Rapid glucocorticoid signaling 0.0000 0 12 20 -0.008 0.036 1000 -1000 -0.012 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 0 0.062 1000 -1000 -0.015 -1000
Total NA 3822 202347 7203 -30 -990 131000 -131000 -7.9 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.4 0.23 0.52 392 -10000 0 392
KIRREL -0.06 0.087 -10000 0 -0.63 9 9
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.4 0.23 -10000 0 -0.52 392 392
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARRB2 0.028 0.032 -10000 0 -0.71 1 1
WASL 0.027 0.009 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.42 0.28 -10000 0 -0.54 413 413
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.34 0.24 -10000 0 -0.46 369 369
FYN -0.4 0.25 0.26 1 -0.5 417 418
mol:Ca2+ -0.41 0.28 -10000 0 -0.53 406 406
mol:DAG -0.41 0.28 -10000 0 -0.53 406 406
NPHS2 -0.34 0.33 -10000 0 -0.69 241 241
mol:IP3 -0.41 0.28 -10000 0 -0.53 406 406
regulation of endocytosis -0.37 0.25 -10000 0 -0.49 394 394
Nephrin/NEPH1/podocin/Cholesterol -0.42 0.28 -10000 0 -0.54 417 417
establishment of cell polarity -0.4 0.23 -10000 0 -0.52 392 392
Nephrin/NEPH1/podocin/NCK1-2 -0.38 0.27 -10000 0 -0.65 216 216
Nephrin/NEPH1/beta Arrestin2 -0.38 0.25 -10000 0 -0.49 394 394
NPHS1 -0.51 0.28 -10000 0 -0.67 404 404
Nephrin/NEPH1/podocin -0.4 0.26 -10000 0 -0.51 417 417
TJP1 0.03 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.03 -10000 0 -0.64 1 1
NCK2 0.029 0.006 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.41 0.28 -10000 0 -0.54 406 406
CD2AP 0.029 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.41 0.28 -10000 0 -0.54 411 411
GRB2 0.029 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.39 0.26 0.28 1 -0.5 408 409
cytoskeleton organization -0.43 0.28 -10000 0 -0.58 369 369
Nephrin/NEPH1 -0.29 0.17 -10000 0 -0.38 392 392
Nephrin/NEPH1/ZO-1 -0.32 0.2 -10000 0 -0.43 390 390
HIF-1-alpha transcription factor network

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
PKM2 -0.88 0.48 -10000 0 -1.2 302 302
HDAC7 0.027 0.01 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.63 0.31 -10000 0 -0.92 206 206
SMAD4 0.03 0.005 -10000 0 -10000 0 0
ID2 -0.87 0.48 -10000 0 -1.3 260 260
AP1 0.029 0.077 -10000 0 -0.46 12 12
ABCG2 -0.87 0.48 -10000 0 -1.3 273 273
HIF1A -0.11 0.074 -10000 0 -0.77 2 2
TFF3 -0.88 0.49 -10000 0 -1.3 273 273
GATA2 0.014 0.097 -10000 0 -0.61 12 12
AKT1 -0.1 0.061 -10000 0 -10000 0 0
response to hypoxia -0.12 0.061 -10000 0 -0.37 6 6
MCL1 -0.87 0.48 -10000 0 -1.2 275 275
NDRG1 -0.87 0.48 -10000 0 -1.3 272 272
SERPINE1 -0.89 0.51 -10000 0 -1.3 275 275
FECH -0.87 0.48 -10000 0 -1.3 274 274
FURIN -0.87 0.48 -10000 0 -1.3 271 271
NCOA2 0.012 0.091 -10000 0 -0.64 10 10
EP300 -0.11 0.077 -10000 0 -0.43 5 5
HMOX1 -0.88 0.49 -10000 0 -1.3 275 275
BHLHE40 -0.87 0.48 -10000 0 -1.3 265 265
BHLHE41 -0.93 0.52 -10000 0 -1.3 281 281
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.1 0.083 -10000 0 -0.54 2 2
ENG -0.085 0.087 0.43 1 -0.49 2 3
JUN 0.029 0.007 -10000 0 -10000 0 0
RORA -0.87 0.48 -10000 0 -1.3 263 263
ABCB1 -0.27 0.39 -10000 0 -1.3 66 66
TFRC -0.87 0.48 -10000 0 -1.3 273 273
CXCR4 -0.95 0.53 -10000 0 -1.3 298 298
TF -0.92 0.52 -10000 0 -1.3 279 279
CITED2 -0.87 0.48 -10000 0 -1.3 269 269
HIF1A/ARNT -1.1 0.72 -10000 0 -1.5 306 306
LDHA -0.082 0.12 -10000 0 -0.78 12 12
ETS1 -0.87 0.48 -10000 0 -1.3 272 272
PGK1 -0.87 0.48 -10000 0 -1.3 270 270
NOS2 -0.88 0.48 -10000 0 -1.3 266 266
ITGB2 -0.91 0.51 -10000 0 -1.3 288 288
ALDOA -0.87 0.48 -10000 0 -1.3 271 271
Cbp/p300/CITED2 -0.87 0.48 -10000 0 -1.3 263 263
FOS 0.013 0.099 -10000 0 -0.63 12 12
HK2 -1 0.52 -10000 0 -1.4 340 340
SP1 0.023 0.043 -10000 0 -10000 0 0
GCK -0.17 0.16 -10000 0 -0.95 9 9
HK1 -0.87 0.48 -10000 0 -1.3 265 265
NPM1 -0.84 0.49 -10000 0 -1.2 262 262
EGLN1 -0.87 0.48 -10000 0 -1.3 271 271
CREB1 0.036 0.01 -10000 0 -10000 0 0
PGM1 -0.87 0.48 -10000 0 -1.3 271 271
SMAD3 0.031 0.003 -10000 0 -10000 0 0
EDN1 -0.12 0.14 -10000 0 -0.62 16 16
IGFBP1 -0.91 0.52 -10000 0 -1.3 275 275
VEGFA -0.68 0.34 -10000 0 -1 218 218
HIF1A/JAB1 -0.063 0.056 -10000 0 -0.58 2 2
CP -1 0.53 -10000 0 -1.3 348 348
CXCL12 -0.88 0.48 -10000 0 -1.3 274 274
COPS5 0.025 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.045 0.009 -10000 0 -10000 0 0
BNIP3 -0.87 0.48 -10000 0 -1.3 271 271
EGLN3 -1.1 0.48 -10000 0 -1.3 370 370
CA9 -1.1 0.47 -10000 0 -1.3 383 383
TERT -0.89 0.5 -10000 0 -1.3 276 276
ENO1 -0.87 0.48 -10000 0 -1.3 261 261
PFKL -0.87 0.48 -10000 0 -1.2 279 279
NCOA1 0.029 0.005 -10000 0 -10000 0 0
ADM -0.93 0.51 -10000 0 -1.3 286 286
ARNT -0.11 0.055 -10000 0 -10000 0 0
HNF4A -0.017 0.17 -10000 0 -0.64 38 38
ADFP -0.88 0.48 -10000 0 -1.2 302 302
SLC2A1 -0.58 0.3 -10000 0 -0.91 153 153
LEP -0.88 0.5 -10000 0 -1.3 275 275
HIF1A/ARNT/Cbp/p300 -0.65 0.32 -10000 0 -0.94 213 213
EPO -0.54 0.32 -10000 0 -0.9 182 182
CREBBP -0.1 0.076 -10000 0 -0.4 5 5
HIF1A/ARNT/Cbp/p300/HDAC7 -0.67 0.35 -10000 0 -1 208 208
PFKFB3 -0.87 0.48 -10000 0 -1.3 272 272
NT5E -0.87 0.48 -10000 0 -1.3 271 271
TCGA08_retinoblastoma

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
CDKN2B 0.024 0.073 -10000 0 -0.6 7 7
CDKN2C 0.078 0.023 -10000 0 -10000 0 0
CDKN2A -0.58 0.13 -10000 0 -0.6 503 503
CCND2 0.14 0.055 0.22 92 -10000 0 92
RB1 -0.15 0.063 0.27 1 -0.24 93 94
CDK4 0.16 0.063 0.17 493 -10000 0 493
CDK6 0.15 0.066 0.25 89 -0.16 1 90
G1/S progression 0.15 0.064 0.24 95 -0.27 1 96
TCGA08_p53

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
CDKN2A -0.42 0.099 0.17 3 -0.44 503 506
TP53 -0.12 0.075 -10000 0 -0.37 34 34
Senescence -0.12 0.075 -10000 0 -0.37 34 34
Apoptosis -0.12 0.075 -10000 0 -0.37 34 34
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.22 0.096 0.23 503 -10000 0 503
MDM4 0.029 0.006 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.029 0.027 -9999 0 -0.59 1 1
EGFR 0.02 0.067 -9999 0 -0.6 6 6
EGF/EGFR -0.29 0.13 -9999 0 -0.35 425 425
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.28 0.14 -9999 0 -0.35 399 399
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.028 0.027 -9999 0 -0.59 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.57 0.2 -9999 0 -0.63 474 474
EGF/EGFR dimer/SHC -0.34 0.15 -9999 0 -0.41 411 411
mol:GDP -0.28 0.14 -9999 0 -0.34 399 399
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.008 0.11 -9999 0 -0.59 18 18
GRB2/SOS1 0.043 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.26 0.12 -9999 0 -0.6 6 6
SHC1 0.029 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.26 0.13 -9999 0 -0.61 6 6
FRAP1 -0.27 0.12 -9999 0 -0.33 399 399
EGF/EGFR dimer -0.4 0.16 -9999 0 -0.48 425 425
SOS1 0.029 0.005 -9999 0 -10000 0 0
GRB2 0.029 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.025 0.09 -9999 0 -0.43 19 19
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.24 0.3 0.29 5 -0.57 218 223
FYN -0.3 0.39 0.41 13 -0.69 232 245
LAT/GRAP2/SLP76 -0.29 0.33 0.34 4 -0.64 218 222
IKBKB 0.028 0.008 -10000 0 -10000 0 0
AKT1 -0.2 0.28 0.42 22 -0.48 229 251
B2M 0.026 0.007 -10000 0 -10000 0 0
IKBKG -0.055 0.085 0.16 11 -0.17 73 84
MAP3K8 0.027 0.038 -10000 0 -0.59 2 2
mol:Ca2+ -0.088 0.054 0.071 12 -0.13 285 297
integrin-mediated signaling pathway 0.024 0.073 -10000 0 -0.37 17 17
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.31 0.4 0.47 16 -0.72 233 249
TRPV6 -0.44 0.41 0.7 45 -0.64 406 451
CD28 -0.019 0.16 -10000 0 -0.6 39 39
SHC1 -0.33 0.39 0.42 6 -0.72 234 240
receptor internalization -0.36 0.4 0.46 1 -0.75 248 249
PRF1 -0.33 0.42 0.41 1 -0.82 201 202
KRAS 0.029 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.15 0.23 0.39 20 -0.38 207 227
LAT -0.38 0.43 0.39 5 -0.8 241 246
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.25 0.31 -10000 0 -0.6 235 235
CD3E -0.22 0.31 -10000 0 -0.6 211 211
CD3G -0.21 0.3 -10000 0 -0.6 203 203
RASGRP2 -0.014 0.029 0.1 3 -0.11 4 7
RASGRP1 -0.17 0.28 0.46 24 -0.46 208 232
HLA-A -0.004 0.008 0.062 1 -10000 0 1
RASSF5 0.009 0.11 -10000 0 -0.59 17 17
RAP1A/GTP/RAPL 0.025 0.073 -10000 0 -0.37 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.14 0.31 38 -0.13 4 42
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.12 0.12 -10000 0 -0.27 162 162
PRKCA -0.11 0.16 0.23 10 -0.3 162 172
GRAP2 -0.012 0.16 -10000 0 -0.59 35 35
mol:IP3 -0.13 0.3 0.24 149 -0.46 201 350
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.3 0.38 0.26 1 -0.7 226 227
ORAI1 0.2 0.26 0.67 6 -0.62 23 29
CSK -0.34 0.39 0.35 5 -0.73 237 242
B7 family/CD28 -0.36 0.45 0.32 2 -0.82 224 226
CHUK 0.029 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.39 0.45 -10000 0 -0.83 242 242
PTPN6 -0.32 0.39 0.26 2 -0.72 233 235
VAV1 -0.37 0.43 0.47 5 -0.8 240 245
Monovalent TCR/CD3 -0.26 0.32 -10000 0 -0.61 226 226
CBL 0.028 0.029 -10000 0 -0.64 1 1
LCK -0.31 0.4 0.44 10 -0.72 233 243
PAG1 -0.34 0.39 0.28 2 -0.74 235 237
RAP1A 0.029 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.37 0.44 -10000 0 -0.82 235 235
CD80 -0.11 0.26 -10000 0 -0.6 116 116
CD86 -0.071 0.23 -10000 0 -0.6 82 82
PDK1/CARD11/BCL10/MALT1 -0.14 0.16 0.16 1 -0.32 173 174
HRAS 0.029 0.027 -10000 0 -0.59 1 1
GO:0035030 -0.29 0.34 0.38 4 -0.64 228 232
CD8A -0.25 0.31 -10000 0 -0.6 232 232
CD8B -0.19 0.3 -10000 0 -0.6 185 185
PTPRC -0.036 0.19 -10000 0 -0.6 53 53
PDK1/PKC theta -0.24 0.35 0.54 22 -0.6 224 246
CSK/PAG1 -0.33 0.38 0.3 3 -0.73 226 229
SOS1 0.029 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.01 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.31 0.37 0.34 1 -0.72 217 218
STIM1 0.11 0.11 0.96 1 -0.6 3 4
RAS family/GTP -0.04 0.14 0.32 29 -0.18 7 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.38 0.44 0.46 1 -0.81 248 249
mol:DAG -0.18 0.22 0.15 1 -0.42 210 211
RAP1A/GDP 0.001 0.08 0.2 31 -10000 0 31
PLCG1 0.029 0.006 -10000 0 -10000 0 0
CD247 -0.17 0.29 -10000 0 -0.6 169 169
cytotoxic T cell degranulation -0.31 0.41 0.4 1 -0.77 204 205
RAP1A/GTP -0.005 0.01 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.24 0.33 0.43 18 -0.57 232 250
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.21 0.39 0.28 85 -0.63 206 291
NRAS 0.029 0.006 -10000 0 -10000 0 0
ZAP70 -0.32 0.31 -10000 0 -0.59 291 291
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.3 0.33 0.27 2 -0.65 221 223
MALT1 0.029 0.005 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
CD8 heterodimer -0.3 0.39 -10000 0 -0.71 238 238
CARD11 -0.089 0.24 -10000 0 -0.59 98 98
PRKCB -0.12 0.16 0.21 8 -0.3 180 188
PRKCE -0.12 0.16 0.18 30 -0.3 185 215
PRKCQ -0.3 0.39 0.46 21 -0.69 233 254
LCP2 -0.011 0.14 -10000 0 -0.59 29 29
BCL10 0.029 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.16 0.24 0.4 23 -0.4 226 249
IKK complex -0.006 0.14 0.27 63 -0.13 4 67
RAS family/GDP -0.012 0.013 -10000 0 -0.081 1 1
MAP3K14 -0.11 0.18 0.34 19 -0.3 184 203
PDPK1 -0.18 0.27 0.46 22 -0.45 223 245
TCR/CD3/MHC I/CD8/Fyn -0.36 0.44 0.42 1 -0.84 227 228
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.32 -10000 0 -0.63 202 202
PDGF/PDGFRA/CRKL -0.15 0.24 -10000 0 -0.46 196 196
positive regulation of JUN kinase activity -0.083 0.2 -10000 0 -0.35 177 177
CRKL 0.03 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.16 0.24 -10000 0 -0.46 202 202
AP1 -0.12 0.22 0.47 1 -1 12 13
mol:IP3 -0.16 0.24 -10000 0 -0.47 193 193
PLCG1 -0.16 0.24 -10000 0 -0.47 193 193
PDGF/PDGFRA/alphaV Integrin -0.14 0.24 -10000 0 -0.46 190 190
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.47 193 193
CAV3 0.012 0.05 -10000 0 -0.63 3 3
CAV1 -0.009 0.14 -10000 0 -0.59 30 30
SHC/Grb2/SOS1 -0.082 0.2 -10000 0 -0.35 177 177
PDGF/PDGFRA/Shf -0.15 0.24 -10000 0 -0.46 198 198
FOS -0.13 0.21 -10000 0 -1 12 12
JUN -0.024 0.022 -10000 0 -10000 0 0
oligodendrocyte development -0.14 0.24 -10000 0 -0.46 190 190
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
mol:DAG -0.16 0.24 -10000 0 -0.47 193 193
PDGF/PDGFRA -0.22 0.32 -10000 0 -0.63 202 202
actin cytoskeleton reorganization -0.15 0.24 -10000 0 -0.46 198 198
SRF 0.025 0.01 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
PI3K -0.1 0.21 -10000 0 -0.39 171 171
PDGF/PDGFRA/Crk/C3G -0.11 0.22 -10000 0 -0.39 196 196
JAK1 -0.16 0.23 -10000 0 -0.46 198 198
ELK1/SRF -0.11 0.18 -10000 0 -0.35 179 179
SHB 0.029 0.006 -10000 0 -10000 0 0
SHF 0.028 0.029 -10000 0 -0.64 1 1
CSNK2A1 0.037 0.017 -10000 0 -10000 0 0
GO:0007205 -0.17 0.24 -10000 0 -0.48 198 198
SOS1 0.029 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.083 0.2 -10000 0 -0.35 177 177
PDGF/PDGFRA/SHB -0.15 0.24 -10000 0 -0.46 198 198
PDGF/PDGFRA/Caveolin-1 -0.17 0.25 -10000 0 -0.47 201 201
ITGAV 0.029 0.007 -10000 0 -10000 0 0
ELK1 -0.15 0.21 -10000 0 -0.42 191 191
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PDGF/PDGFRA/Crk -0.15 0.24 -10000 0 -0.46 197 197
JAK-STAT cascade -0.16 0.23 -10000 0 -0.46 198 198
cell proliferation -0.15 0.24 -10000 0 -0.46 198 198
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.44 0.41 -10000 0 -1.1 111 111
PCK1 -0.9 0.67 -10000 0 -1.4 286 286
HNF4A -0.52 0.49 -10000 0 -1.2 122 122
KCNJ11 -0.44 0.45 -10000 0 -1.1 108 108
AKT1 -0.2 0.2 -10000 0 -0.84 13 13
response to starvation -0.015 0.027 -10000 0 -10000 0 0
DLK1 -0.53 0.51 -10000 0 -1.2 147 147
NKX2-1 -0.075 0.17 0.34 5 -0.44 13 18
ACADM -0.43 0.42 -10000 0 -1.1 97 97
TAT -0.48 0.31 -10000 0 -0.86 144 144
CEBPB -0.022 0.089 -10000 0 -0.65 8 8
CEBPA -0.022 0.093 -10000 0 -0.63 10 10
TTR -0.84 0.47 -10000 0 -1.1 327 327
PKLR -0.48 0.49 -10000 0 -1.2 122 122
APOA1 -0.53 0.49 -10000 0 -1.2 120 120
CPT1C -0.44 0.42 -10000 0 -1.1 94 94
ALAS1 -0.22 0.21 -10000 0 -0.72 14 14
TFRC -0.63 0.39 -10000 0 -0.95 251 251
FOXF1 0.019 0.076 -10000 0 -0.59 8 8
NF1 0.036 0.006 -10000 0 -10000 0 0
HNF1A (dimer) -0.012 0.082 -10000 0 -0.68 4 4
CPT1A -0.44 0.41 -10000 0 -1.1 110 110
HMGCS1 -0.42 0.41 -10000 0 -1.1 107 107
NR3C1 0.007 0.058 -10000 0 -0.67 1 1
CPT1B -0.45 0.43 -10000 0 -1.1 122 122
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.03 0.007 -10000 0 -10000 0 0
GCK -0.43 0.42 -10000 0 -1.1 105 105
CREB1 -0.038 0.08 -10000 0 -0.31 2 2
IGFBP1 -0.25 0.32 -10000 0 -0.8 95 95
PDX1 -0.19 0.2 -10000 0 -0.84 9 9
UCP2 -0.44 0.41 -10000 0 -1 113 113
ALDOB -0.88 0.56 -10000 0 -1.2 381 381
AFP -0.64 0.44 -10000 0 -0.86 328 328
BDH1 -0.56 0.5 -10000 0 -1.1 184 184
HADH -0.44 0.43 -10000 0 -1.1 109 109
F2 -0.58 0.5 -10000 0 -1.3 126 126
HNF1A -0.012 0.082 -10000 0 -0.68 4 4
G6PC -0.77 0.63 -10000 0 -1.4 247 247
SLC2A2 -0.31 0.43 -10000 0 -1.5 47 47
INS 0.001 0.062 -10000 0 -10000 0 0
FOXA1 -0.31 0.28 -10000 0 -0.68 152 152
FOXA3 -0.56 0.3 -10000 0 -0.73 356 356
FOXA2 -0.5 0.49 -10000 0 -1.2 125 125
ABCC8 -0.44 0.43 -10000 0 -1.1 99 99
ALB -1.1 0.43 -10000 0 -1.2 454 454
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.1 0.16 -10000 0 -0.7 16 16
Syndecan-4/Syndesmos -0.31 0.26 -10000 0 -0.6 179 179
positive regulation of JNK cascade -0.37 0.28 -10000 0 -0.67 201 201
Syndecan-4/ADAM12 -0.39 0.33 -10000 0 -0.7 228 228
CCL5 -0.23 0.3 -10000 0 -0.59 220 220
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DNM2 0.03 0.003 -10000 0 -10000 0 0
ITGA5 -0.012 0.15 -10000 0 -0.59 35 35
SDCBP 0.028 0.007 -10000 0 -10000 0 0
PLG -0.29 0.32 -10000 0 -0.59 270 270
ADAM12 -0.13 0.27 -10000 0 -0.59 138 138
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.029 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.085 0.064 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.32 0.27 -10000 0 -0.62 178 178
Syndecan-4/CXCL12/CXCR4 -0.4 0.31 -10000 0 -0.73 198 198
Syndecan-4/Laminin alpha3 -0.32 0.26 -10000 0 -0.6 184 184
MDK -0.015 0.16 -10000 0 -0.59 38 38
Syndecan-4/FZD7 -0.32 0.26 -10000 0 -0.66 128 128
Syndecan-4/Midkine -0.34 0.28 -10000 0 -0.62 196 196
FZD7 0.027 0.03 -10000 0 -0.64 1 1
Syndecan-4/FGFR1/FGF -0.29 0.25 -10000 0 -0.62 121 121
THBS1 0.026 0.05 -10000 0 -0.64 3 3
integrin-mediated signaling pathway -0.31 0.25 -10000 0 -0.58 186 186
positive regulation of MAPKKK cascade -0.37 0.28 -10000 0 -0.67 201 201
Syndecan-4/TACI -0.34 0.29 -10000 0 -0.64 197 197
CXCR4 -0.19 0.29 -10000 0 -0.59 182 182
cell adhesion 0.016 0.078 0.23 2 -0.31 10 12
Syndecan-4/Dynamin -0.32 0.26 -10000 0 -0.65 132 132
Syndecan-4/TSP1 -0.32 0.26 -10000 0 -0.6 182 182
Syndecan-4/GIPC -0.32 0.26 -10000 0 -0.6 177 177
Syndecan-4/RANTES -0.43 0.31 -10000 0 -0.69 261 261
ITGB1 0.029 0.004 -10000 0 -10000 0 0
LAMA1 0.013 0.098 -10000 0 -0.56 14 14
LAMA3 0.022 0.066 -10000 0 -0.59 6 6
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.089 0.13 1 9 -10000 0 9
Syndecan-4/alpha-Actinin -0.32 0.26 -10000 0 -0.6 181 181
TFPI 0.019 0.074 -10000 0 -0.57 8 8
F2 -0.2 0.3 -10000 0 -0.59 196 196
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 35 35
positive regulation of cell adhesion -0.31 0.26 -10000 0 -0.66 127 127
ACTN1 0.026 0.03 -10000 0 -0.64 1 1
TNC 0.014 0.099 -10000 0 -0.64 12 12
Syndecan-4/CXCL12 -0.32 0.27 -10000 0 -0.6 185 185
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
CXCL12 0.017 0.086 -10000 0 -0.55 11 11
TNFRSF13B -0.034 0.18 -10000 0 -0.59 52 52
FGF2 0.023 0.064 -10000 0 -0.63 5 5
FGFR1 0.027 0.009 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.32 0.26 -10000 0 -0.57 218 218
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.001 0.16 -10000 0 -0.57 38 38
cell migration -0.028 0.021 -10000 0 -10000 0 0
PRKCD 0.03 0.035 -10000 0 -0.57 1 1
vasculogenesis -0.31 0.25 -10000 0 -0.58 183 183
SDC4 -0.34 0.28 -10000 0 -0.61 218 218
Syndecan-4/Tenascin C -0.32 0.26 -10000 0 -0.6 186 186
Syndecan-4/PI-4-5-P2/PKC alpha -0.067 0.05 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.31 0.26 -10000 0 -0.6 177 177
MMP9 -0.24 0.31 -10000 0 -0.59 234 234
Rac1/GTP 0.016 0.079 0.24 2 -0.32 9 11
cytoskeleton organization -0.3 0.25 -10000 0 -0.57 182 182
GIPC1 0.029 0.029 -10000 0 -0.64 1 1
Syndecan-4/TFPI -0.32 0.26 -10000 0 -0.6 181 181
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.12 0.2 -10000 0 -0.4 149 149
STMN1 -0.18 0.22 -10000 0 -0.43 244 244
Aurora B/RasGAP/Survivin -0.22 0.31 -10000 0 -0.55 231 231
Chromosomal passenger complex/Cul3 protein complex -0.092 0.16 -10000 0 -0.31 144 144
BIRC5 -0.15 0.28 -10000 0 -0.6 149 149
DES -0.26 0.3 -10000 0 -0.66 160 160
Aurora C/Aurora B/INCENP -0.12 0.2 -10000 0 -0.33 239 239
Aurora B/TACC1 -0.15 0.2 -10000 0 -0.36 243 243
Aurora B/PP2A -0.17 0.24 -10000 0 -0.42 243 243
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.036 0.06 -10000 0 -0.22 3 3
mitotic metaphase/anaphase transition 0 0.006 -10000 0 -10000 0 0
NDC80 -0.26 0.32 -10000 0 -0.57 247 247
Cul3 protein complex 0.042 0.079 -10000 0 -0.4 15 15
KIF2C -0.082 0.15 -10000 0 -0.29 118 118
PEBP1 0.023 0.011 -10000 0 -10000 0 0
KIF20A -0.18 0.29 -10000 0 -0.59 176 176
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.17 0.23 -10000 0 -0.43 219 219
SEPT1 -0.052 0.21 -10000 0 -0.59 68 68
SMC2 0.029 0.006 -10000 0 -10000 0 0
SMC4 0.029 0.007 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.059 0.17 -10000 0 -0.72 11 11
PSMA3 0.028 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -10000 0 -10000 0 0
H3F3B -0.099 0.13 -10000 0 -0.24 239 239
AURKB -0.26 0.31 -10000 0 -0.59 244 244
AURKC 0.027 0.038 -10000 0 -0.59 2 2
CDCA8 -0.006 0.12 -10000 0 -0.62 20 20
cytokinesis -0.17 0.22 -10000 0 -0.49 135 135
Aurora B/Septin1 -0.18 0.28 -10000 0 -0.57 138 138
AURKA 0.024 0.061 -10000 0 -0.6 5 5
INCENP 0.017 0.02 -10000 0 -10000 0 0
KLHL13 0.01 0.11 -10000 0 -0.62 16 16
BUB1 -0.24 0.31 -10000 0 -0.59 225 225
hSgo1/Aurora B/Survivin -0.23 0.31 -10000 0 -0.52 246 246
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.14 0.22 -10000 0 -0.46 122 122
SGOL1 0 0.12 -10000 0 -0.61 18 18
CENPA -0.15 0.2 0.19 1 -0.39 191 192
NCAPG -0.18 0.29 -10000 0 -0.59 173 173
Aurora B/HC8 Proteasome -0.17 0.23 -10000 0 -0.42 243 243
NCAPD2 0.029 0.006 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.17 0.23 -10000 0 -0.43 235 235
RHOA 0.021 0.014 -10000 0 -10000 0 0
NCAPH -0.073 0.23 -10000 0 -0.59 86 86
NPM1 -0.098 0.14 -10000 0 -0.62 6 6
RASA1 0.025 0.03 -10000 0 -0.64 1 1
KLHL9 0.029 0.006 -10000 0 -10000 0 0
mitotic prometaphase -0.006 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.17 0.23 -10000 0 -0.42 243 243
PPP1CC 0.029 0.005 -10000 0 -10000 0 0
Centraspindlin -0.15 0.24 -10000 0 -0.47 150 150
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
NSUN2 -0.1 0.14 -10000 0 -0.61 6 6
MYLK -0.1 0.14 -10000 0 -0.25 242 242
KIF23 0.017 0.077 -10000 0 -0.6 8 8
VIM -0.22 0.27 -10000 0 -0.48 256 256
RACGAP1 0.025 0.028 -10000 0 -0.6 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.12 0.17 -10000 0 -0.65 17 17
Chromosomal passenger complex -0.17 0.24 -10000 0 -0.45 188 188
Chromosomal passenger complex/EVI5 -0.18 0.32 -10000 0 -0.64 146 146
TACC1 0.027 0.009 -10000 0 -10000 0 0
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
CUL3 0.029 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.11 0.18 -10000 0 -0.45 67 67
TBX21 -0.41 0.53 0.79 1 -1.1 154 155
B2M 0.023 0.014 -10000 0 -10000 0 0
TYK2 0.003 0.037 -10000 0 -10000 0 0
IL12RB1 -0.18 0.3 -10000 0 -0.63 159 159
GADD45B -0.22 0.34 0.61 1 -0.75 62 63
IL12RB2 -0.084 0.22 -10000 0 -0.6 76 76
GADD45G -0.23 0.34 0.61 1 -0.74 76 77
natural killer cell activation -0.011 0.026 0.051 3 -0.043 85 88
RELB 0.03 0.003 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
IL18 0.022 0.061 -10000 0 -0.58 5 5
IL2RA -0.09 0.24 -10000 0 -0.59 101 101
IFNG -0.24 0.31 -10000 0 -0.59 232 232
STAT3 (dimer) -0.29 0.38 -10000 0 -0.78 159 159
HLA-DRB5 0 0.003 -10000 0 -0.023 10 10
FASLG -0.44 0.54 0.79 1 -1.1 177 178
NF kappa B2 p52/RelB -0.34 0.46 -10000 0 -0.96 155 155
CD4 0.018 0.081 -10000 0 -0.59 9 9
SOCS1 0.022 0.066 -10000 0 -0.59 6 6
EntrezGene:6955 -0.003 0.009 -10000 0 -0.025 46 46
CD3D -0.25 0.31 -10000 0 -0.6 235 235
CD3E -0.23 0.31 -10000 0 -0.6 211 211
CD3G -0.22 0.31 -10000 0 -0.6 203 203
IL12Rbeta2/JAK2 -0.061 0.17 -10000 0 -0.46 76 76
CCL3 -0.37 0.5 0.79 1 -1 147 148
CCL4 -0.38 0.52 0.79 1 -1.1 146 147
HLA-A -0.004 0.008 -10000 0 -0.026 37 37
IL18/IL18R -0.066 0.21 -10000 0 -0.39 141 141
NOS2 -0.28 0.37 -10000 0 -0.84 99 99
IL12/IL12R/TYK2/JAK2/SPHK2 -0.11 0.18 -10000 0 -0.45 62 62
IL1R1 -0.34 0.47 0.79 1 -0.98 141 142
IL4 0.017 0.037 -10000 0 -10000 0 0
JAK2 0.003 0.037 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.009 -10000 0 -0.025 47 47
TCR/CD3/MHC I/CD8 -0.4 0.48 -10000 0 -0.9 232 232
RAB7A -0.18 0.31 0.56 4 -0.69 25 29
lysosomal transport -0.17 0.3 0.55 5 -0.66 25 30
FOS -0.29 0.38 -10000 0 -0.74 173 173
STAT4 (dimer) -0.3 0.43 0.58 5 -0.85 147 152
STAT5A (dimer) -0.44 0.54 -10000 0 -1 202 202
GZMA -0.41 0.54 0.52 1 -1 189 190
GZMB -0.4 0.52 -10000 0 -1.1 165 165
HLX -0.045 0.2 -10000 0 -0.59 62 62
LCK -0.39 0.52 0.56 1 -1.1 157 158
TCR/CD3/MHC II/CD4 -0.22 0.27 -10000 0 -0.51 226 226
IL2/IL2R -0.23 0.3 -10000 0 -0.45 299 299
MAPK14 -0.22 0.35 0.62 1 -0.75 79 80
CCR5 -0.4 0.45 0.61 1 -0.94 174 175
IL1B -0.005 0.075 -10000 0 -0.61 6 6
STAT6 -0.073 0.12 -10000 0 -10000 0 0
STAT4 -0.007 0.14 -10000 0 -0.59 30 30
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.028 -10000 0 -0.59 1 1
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
NFKB2 0.029 0.006 -10000 0 -10000 0 0
IL12B -0.061 0.19 -10000 0 -0.62 54 54
CD8A -0.25 0.31 -10000 0 -0.6 232 232
CD8B -0.2 0.3 -10000 0 -0.6 185 185
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.11 0.18 0.45 67 -10000 0 67
IL2RB -0.29 0.31 -10000 0 -0.59 272 272
proteasomal ubiquitin-dependent protein catabolic process -0.27 0.39 0.57 5 -0.77 146 151
IL2RG -0.01 0.15 -10000 0 -0.59 34 34
IL12 -0.044 0.15 -10000 0 -0.48 54 54
STAT5A 0.029 0.004 -10000 0 -10000 0 0
CD247 -0.18 0.29 -10000 0 -0.6 169 169
IL2 0.013 0.084 -10000 0 -0.59 10 10
SPHK2 0.027 0.041 -10000 0 -0.64 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.037 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.42 0.53 -10000 0 -1.1 158 158
MAP2K3 -0.22 0.35 0.61 1 -0.73 94 95
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
MAP2K6 -0.22 0.35 0.61 1 -0.75 81 82
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.004 -10000 0 -0.027 10 10
IL18RAP -0.13 0.27 -10000 0 -0.6 136 136
IL12Rbeta1/TYK2 -0.13 0.24 -10000 0 -0.48 159 159
EOMES -0.32 0.33 -10000 0 -0.64 159 159
STAT1 (dimer) -0.34 0.41 -10000 0 -0.82 183 183
T cell proliferation -0.21 0.31 0.48 5 -0.61 125 130
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.074 -10000 0 -0.61 7 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.28 0.3 -10000 0 -0.7 113 113
ATF2 -0.2 0.34 0.57 6 -0.71 69 75
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.052 -10000 0 -0.4 6 6
fibroblast growth factor receptor signaling pathway 0.046 0.052 -10000 0 -0.4 6 6
LAMA1 0.013 0.098 -10000 0 -0.56 14 14
PRNP 0.029 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.068 0.21 -10000 0 -0.47 108 108
SMAD2 0.022 0.027 -10000 0 -0.37 1 1
GPC1/PrPc/Cu2+ 0.036 0.022 -10000 0 -0.41 1 1
GPC1/Laminin alpha1 0.029 0.076 -10000 0 -0.46 11 11
TDGF1 -0.4 0.27 -10000 0 -0.54 394 394
CRIPTO/GPC1 -0.29 0.21 -10000 0 -0.47 272 272
APP/GPC1 0.04 0.026 -10000 0 -0.47 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.24 0.18 -10000 0 -0.4 269 269
FLT1 0.023 0.06 -10000 0 -0.59 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.041 0.034 -10000 0 -0.4 1 1
SERPINC1 -0.028 0.18 -10000 0 -0.63 44 44
FYN -0.24 0.18 -10000 0 -0.4 271 271
FGR -0.24 0.18 -10000 0 -0.41 272 272
positive regulation of MAPKKK cascade -0.28 0.2 0.38 3 -0.44 280 283
SLIT2 -0.11 0.27 -10000 0 -0.62 116 116
GPC1/NRG 0.023 0.085 -10000 0 -0.47 14 14
NRG1 0.008 0.11 -10000 0 -0.56 17 17
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.14 0.22 -10000 0 -0.38 229 229
LYN -0.24 0.18 -10000 0 -0.4 263 263
mol:Spermine 0.01 0.021 -10000 0 -0.47 1 1
cell growth 0.046 0.052 -10000 0 -0.4 6 6
BMP signaling pathway -0.027 0.03 0.63 1 -10000 0 1
SRC -0.24 0.18 -10000 0 -0.4 264 264
TGFBR1 0.029 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.025 0.17 -10000 0 -0.59 43 43
GPC1 0.027 0.03 -10000 0 -0.64 1 1
TGFBR1 (dimer) 0.029 0.006 -10000 0 -10000 0 0
VEGFA -0.25 0.31 -10000 0 -0.59 234 234
BLK -0.26 0.21 -10000 0 -0.44 276 276
HCK -0.26 0.19 -10000 0 -0.42 277 277
FGF2 0.023 0.064 -10000 0 -0.63 5 5
FGFR1 0.027 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer 0.023 0.06 -10000 0 -0.59 5 5
TGFBR2 0.022 0.014 -10000 0 -10000 0 0
cell death 0.04 0.025 -10000 0 -0.47 1 1
ATIII/GPC1 -0.004 0.14 -10000 0 -0.47 45 45
PLA2G2A/GPC1 -0.002 0.13 -10000 0 -0.43 44 44
LCK -0.26 0.19 -10000 0 -0.42 280 280
neuron differentiation 0.023 0.085 -10000 0 -0.46 14 14
PrPc/Cu2+ 0.021 0.004 -10000 0 -10000 0 0
APP 0.029 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.021 0.014 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.14 0.54 0.78 1 -1.1 86 87
PLK1 -0.051 0.26 -10000 0 -0.5 121 121
BIRC5 -0.078 0.28 -10000 0 -0.5 142 142
HSPA1B -0.15 0.54 0.78 2 -1.1 87 89
MAP2K1 0.026 0.053 -10000 0 -10000 0 0
BRCA2 -0.15 0.54 -10000 0 -1.1 79 79
FOXM1 -0.23 0.69 -10000 0 -1.4 101 101
XRCC1 -0.15 0.53 -10000 0 -1.1 92 92
FOXM1B/p19 -0.3 0.48 -10000 0 -1.1 91 91
Cyclin D1/CDK4 -0.14 0.49 -10000 0 -1 81 81
CDC2 -0.16 0.56 -10000 0 -1.1 100 100
TGFA -0.14 0.49 -10000 0 -0.98 82 82
SKP2 -0.14 0.54 0.72 4 -1.1 86 90
CCNE1 0.023 0.073 -10000 0 -0.6 7 7
CKS1B -0.15 0.54 -10000 0 -1.1 101 101
RB1 -0.035 0.3 -10000 0 -0.94 13 13
FOXM1C/SP1 -0.18 0.61 -10000 0 -1.3 96 96
AURKB -0.16 0.32 -10000 0 -1.3 8 8
CENPF -0.17 0.57 0.69 1 -1.2 86 87
CDK4 0.026 0.025 -10000 0 -10000 0 0
MYC -0.13 0.48 -10000 0 -0.96 88 88
CHEK2 0.024 0.067 -10000 0 -0.64 2 2
ONECUT1 -0.15 0.52 -10000 0 -1.1 91 91
CDKN2A -0.56 0.13 -10000 0 -0.59 503 503
LAMA4 -0.2 0.55 0.78 1 -1.1 97 98
FOXM1B/HNF6 -0.2 0.61 -10000 0 -1.3 93 93
FOS -0.16 0.55 -10000 0 -1.1 94 94
SP1 0.029 0.009 -10000 0 -10000 0 0
CDC25B -0.15 0.54 -10000 0 -1.1 85 85
response to radiation 0.005 0.036 -10000 0 -10000 0 0
CENPB -0.15 0.54 -10000 0 -1.1 87 87
CENPA -0.21 0.61 -10000 0 -1.2 112 112
NEK2 -0.19 0.59 0.69 1 -1.2 101 102
HIST1H2BA -0.16 0.54 0.78 1 -1.1 87 88
CCNA2 -0.09 0.25 -10000 0 -0.6 101 101
EP300 0.028 0.029 -10000 0 -0.64 1 1
CCNB1/CDK1 -0.19 0.62 -10000 0 -1.3 93 93
CCNB2 -0.19 0.6 0.78 1 -1.2 108 109
CCNB1 -0.16 0.57 -10000 0 -1.2 91 91
ETV5 -0.15 0.54 -10000 0 -1.1 88 88
ESR1 -0.15 0.54 0.78 1 -1.1 86 87
CCND1 -0.14 0.5 -10000 0 -1 84 84
GSK3A 0.027 0.046 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.024 0.2 -10000 0 -0.42 97 97
CDK2 0.031 0.01 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.006 0.043 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.17 0.57 -10000 0 -1.2 94 94
GAS1 -0.19 0.57 -10000 0 -1.1 108 108
MMP2 -0.15 0.54 0.78 1 -1.1 87 88
RB1/FOXM1C -0.16 0.54 -10000 0 -1.1 88 88
CREBBP 0.029 0.006 -10000 0 -10000 0 0
amb2 Integrin signaling

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.047 0.2 -10000 0 -0.43 103 103
alphaM/beta2 Integrin/GPIbA -0.045 0.2 -10000 0 -0.43 100 100
alphaM/beta2 Integrin/proMMP-9 -0.21 0.29 -10000 0 -0.48 256 256
PLAUR 0 0.13 -10000 0 -0.59 25 25
HMGB1 0.025 0.022 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.045 0.2 -10000 0 -0.43 99 99
AGER -0.088 0.24 -10000 0 -0.59 95 95
RAP1A 0.029 0.006 -10000 0 -10000 0 0
SELPLG -0.009 0.15 -10000 0 -0.59 32 32
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.1 0.25 -10000 0 -0.61 59 59
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 234 234
CYR61 0.023 0.057 -10000 0 -0.48 6 6
TLN1 0.029 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.19 0.16 -10000 0 -0.44 106 106
RHOA 0.021 0.014 -10000 0 -10000 0 0
P-selectin oligomer 0.001 0.13 -10000 0 -0.62 22 22
MYH2 -0.29 0.2 -10000 0 -0.51 180 180
MST1R 0.013 0.071 -10000 0 -0.58 7 7
leukocyte activation during inflammatory response -0.14 0.24 -10000 0 -0.55 83 83
APOB -0.17 0.29 -10000 0 -0.59 166 166
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.067 -10000 0 -0.6 6 6
JAM3 0.03 0.003 -10000 0 -10000 0 0
GP1BA 0.028 0.029 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/CTGF -0.051 0.2 -10000 0 -0.43 104 104
alphaM/beta2 Integrin -0.23 0.18 -10000 0 -0.41 216 216
JAM3 homodimer 0.03 0.003 -10000 0 -10000 0 0
ICAM2 0.029 0.005 -10000 0 -10000 0 0
ICAM1 0.017 0.089 -10000 0 -0.59 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.23 0.18 -10000 0 -0.4 216 216
cell adhesion -0.045 0.2 -10000 0 -0.42 100 100
NFKB1 -0.12 0.25 0.4 5 -0.63 63 68
THY1 0.028 0.029 -10000 0 -0.64 1 1
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
Lipoprotein(a) -0.099 0.2 -10000 0 -0.38 166 166
alphaM/beta2 Integrin/LRP/tPA -0.031 0.19 -10000 0 -0.52 37 37
IL6 -0.15 0.3 0.39 3 -0.72 78 81
ITGB2 -0.092 0.24 -10000 0 -0.59 98 98
elevation of cytosolic calcium ion concentration -0.046 0.21 -10000 0 -0.56 42 42
alphaM/beta2 Integrin/JAM2/JAM3 -0.022 0.19 -10000 0 -0.53 30 30
JAM2 0.029 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.042 0.19 -10000 0 -0.56 34 34
alphaM/beta2 Integrin/uPA/Plg -0.23 0.27 -10000 0 -0.46 252 252
RhoA/GTP -0.29 0.21 -10000 0 -0.52 190 190
positive regulation of phagocytosis -0.19 0.2 -10000 0 -0.55 81 81
Ron/MSP 0.018 0.081 -10000 0 -0.45 14 14
alphaM/beta2 Integrin/uPAR/uPA -0.045 0.21 -10000 0 -0.56 42 42
alphaM/beta2 Integrin/uPAR -0.06 0.22 -10000 0 -0.45 113 113
PLAU 0.02 0.074 -10000 0 -0.56 8 8
PLAT 0.016 0.088 -10000 0 -0.6 10 10
actin filament polymerization -0.27 0.19 -10000 0 -0.48 178 178
MST1 0.012 0.079 -10000 0 -0.61 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.14 0.25 -10000 0 -0.56 83 83
TNF -0.11 0.24 0.39 4 -0.6 64 68
RAP1B 0.029 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.05 0.2 -10000 0 -0.43 105 105
fibrinolysis -0.23 0.27 -10000 0 -0.46 252 252
HCK -0.003 0.14 -10000 0 -0.59 27 27
dendritic cell antigen processing and presentation -0.23 0.18 -10000 0 -0.4 216 216
VTN -0.069 0.24 -10000 0 -0.62 79 79
alphaM/beta2 Integrin/CYR61 -0.047 0.2 -10000 0 -0.43 102 102
LPA 0.018 0.05 -10000 0 -0.63 3 3
LRP1 0.029 0.005 -10000 0 -10000 0 0
cell migration -0.2 0.28 -10000 0 -0.6 111 111
FN1 -0.017 0.16 -10000 0 -0.6 38 38
alphaM/beta2 Integrin/Thy1 -0.044 0.2 -10000 0 -0.43 100 100
MPO 0.009 0.11 -10000 0 -0.59 17 17
KNG1 -0.45 0.29 -10000 0 -0.63 380 380
RAP1/GDP 0.038 0.01 -10000 0 -10000 0 0
ROCK1 -0.27 0.2 -10000 0 -0.5 173 173
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.3 0.32 -10000 0 -0.61 270 270
CTGF 0.019 0.076 -10000 0 -0.64 7 7
alphaM/beta2 Integrin/Hck -0.06 0.24 -10000 0 -0.5 101 101
ITGAM 0.001 0.12 -10000 0 -0.59 20 20
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.056 0.24 -10000 0 -0.58 62 62
HP -0.12 0.27 -10000 0 -0.59 128 128
leukocyte adhesion -0.075 0.2 -10000 0 -0.54 41 41
SELP 0.001 0.13 -10000 0 -0.62 22 22
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.46 0.28 -10000 0 -0.56 421 421
SMAD6-7/SMURF1 0.053 0.021 -10000 0 -10000 0 0
NOG -0.072 0.23 -10000 0 -0.6 84 84
SMAD9 -0.066 0.17 -10000 0 -0.64 38 38
SMAD4 0.029 0.005 -10000 0 -10000 0 0
SMAD5 -0.14 0.16 -10000 0 -0.49 30 30
BMP7/USAG1 -0.52 0.32 -10000 0 -0.64 434 434
SMAD5/SKI -0.15 0.16 0.33 2 -0.48 26 28
SMAD1 -0.023 0.054 -10000 0 -10000 0 0
BMP2 0.025 0.05 -10000 0 -0.64 3 3
SMAD1/SMAD1/SMAD4 0.012 0.054 -10000 0 -10000 0 0
BMPR1A 0.029 0.006 -10000 0 -10000 0 0
BMPR1B -0.43 0.31 -10000 0 -0.63 362 362
BMPR1A-1B/BAMBI -0.26 0.22 -10000 0 -0.41 358 358
AHSG 0.008 0.093 -10000 0 -0.6 12 12
CER1 0.02 0.006 -10000 0 -10000 0 0
BMP2-4/CER1 0.044 0.047 -10000 0 -0.41 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.12 -10000 0 -0.46 9 9
BMP2-4 (homodimer) 0.035 0.05 -10000 0 -0.4 6 6
RGMB 0.023 0.039 -10000 0 -0.59 2 2
BMP6/BMPR2/BMPR1A-1B -0.23 0.2 -10000 0 -0.37 346 346
RGMA 0.023 0.065 -10000 0 -0.64 5 5
SMURF1 0.027 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.12 0.14 -10000 0 -0.37 47 47
BMP2-4/USAG1 -0.21 0.22 -10000 0 -0.41 298 298
SMAD6/SMURF1/SMAD5 -0.14 0.16 0.31 1 -0.5 22 23
SOSTDC1 -0.35 0.32 -10000 0 -0.64 299 299
BMP7/BMPR2/BMPR1A-1B -0.46 0.27 -10000 0 -0.56 430 430
SKI 0.029 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.019 0.078 -10000 0 -0.6 8 8
HFE2 0.004 0.12 -10000 0 -0.6 19 19
ZFYVE16 0.027 0.009 -10000 0 -10000 0 0
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.043 0.072 -10000 0 -0.43 10 10
SMAD5/SMAD5/SMAD4 -0.15 0.16 0.31 1 -0.48 28 29
MAPK1 0.03 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.1 0.12 -10000 0 -0.39 17 17
BMP7 (homodimer) -0.4 0.31 -10000 0 -0.63 340 340
NUP214 0.029 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.02 0.087 -10000 0 -0.45 16 16
SMAD1/SKI -0.018 0.066 0.34 1 -0.42 1 2
SMAD6 0.03 0.003 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.036 0.076 -10000 0 -0.38 15 15
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.63 132 132
BMPR2 (homodimer) 0.029 0.007 -10000 0 -10000 0 0
GADD34/PP1CA 0.054 0.02 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.31 0.24 -10000 0 -0.47 356 356
CHRDL1 -0.31 0.33 -10000 0 -0.63 271 271
ENDOFIN/SMAD1 -0.015 0.064 0.34 1 -0.44 1 2
SMAD6-7/SMURF1/SMAD1 0.016 0.066 -10000 0 -10000 0 0
SMAD6/SMURF1 0.027 0.009 -10000 0 -10000 0 0
BAMBI 0.021 0.072 -10000 0 -0.59 7 7
SMURF2 0.028 0.029 -10000 0 -0.64 1 1
BMP2-4/CHRDL1 -0.18 0.23 -10000 0 -0.41 264 264
BMP2-4/GREM1 -0.062 0.2 -10000 0 -0.4 130 130
SMAD7 0.029 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.063 0.17 -10000 0 -0.58 44 44
SMAD1/SMAD6 -0.017 0.061 -10000 0 -0.44 1 1
TAK1/SMAD6 0.037 0.016 -10000 0 -10000 0 0
BMP7 -0.4 0.31 -10000 0 -0.64 340 340
BMP6 0.019 0.078 -10000 0 -0.6 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.099 0.11 -10000 0 -0.35 27 27
PPM1A 0.028 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.02 0.067 0.34 1 -0.44 1 2
SMAD7/SMURF1 0.039 0.015 -10000 0 -10000 0 0
CTDSPL 0.021 0.014 -10000 0 -10000 0 0
PPP1CA 0.03 0.003 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
CTDSP1 0.028 0.007 -10000 0 -10000 0 0
PPP1R15A 0.03 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.18 -10000 0 -0.47 77 77
CHRD 0.017 0.084 -10000 0 -0.62 9 9
BMPR2 0.029 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.14 0.13 -10000 0 -0.38 44 44
BMP4 0.024 0.051 -10000 0 -0.64 3 3
FST -0.04 0.2 -10000 0 -0.63 54 54
BMP2-4/NOG -0.017 0.16 -10000 0 -0.38 83 83
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.42 0.26 -10000 0 -0.66 248 248
Aurora C 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
INCENP 0.03 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.13 0.2 -9999 0 -0.34 239 239
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.03 0.059 -9999 0 -0.62 1 1
AURKB -0.26 0.31 -9999 0 -0.59 244 244
AURKC 0.027 0.038 -9999 0 -0.59 2 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.012 0.11 -10000 0 -0.62 14 14
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.048 -10000 0 -0.6 3 3
TCEB1 0.028 0.007 -10000 0 -10000 0 0
HIF1A/p53 -0.069 0.079 0.26 1 -0.47 14 15
HIF1A -0.076 0.08 -10000 0 -0.49 14 14
COPS5 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.052 -10000 0 -10000 0 0
FIH (dimer) 0.029 0.006 -10000 0 -10000 0 0
CDKN2A -0.57 0.13 -10000 0 -0.6 503 503
ARNT/IPAS 0.029 0.082 -10000 0 -0.46 14 14
HIF1AN 0.029 0.006 -10000 0 -10000 0 0
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
HIF1A/ARNT -0.067 0.081 0.26 1 -0.47 14 15
CUL2 0.029 0.004 -10000 0 -10000 0 0
OS9 0.029 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.042 -10000 0 -0.38 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.065 0.079 -10000 0 -0.47 14 14
PHD1-3/OS9 -0.28 0.13 -10000 0 -0.34 435 435
HIF1A/RACK1/Elongin B/Elongin C -0.045 0.081 -10000 0 -0.45 13 13
VHL 0.021 0.02 -10000 0 -0.32 1 1
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.066 0.08 -10000 0 -0.47 14 14
EGLN3 -0.52 0.2 -10000 0 -0.6 462 462
EGLN2 0.03 0.003 -10000 0 -10000 0 0
EGLN1 0.029 0.006 -10000 0 -10000 0 0
TP53 0.029 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.13 0.26 -10000 0 -0.53 142 142
ARNT 0.029 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.36 0.1 -10000 0 -0.37 496 496
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.015 0.16 -9999 0 -0.59 38 38
GPC2 -0.038 0.19 -9999 0 -0.59 55 55
GPC2/Midkine -0.041 0.19 -9999 0 -0.48 80 80
neuron projection morphogenesis -0.041 0.19 -9999 0 -0.48 80 80
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 -0.44 0.42 -10000 0 -1.1 84 84
STAT6 (cleaved dimer) -0.49 0.44 -10000 0 -1.1 132 132
IGHG1 -0.16 0.16 -10000 0 -0.48 11 11
IGHG3 -0.43 0.4 -10000 0 -1 116 116
AKT1 -0.24 0.26 -10000 0 -0.71 59 59
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.18 0.22 -10000 0 -0.66 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.26 -10000 0 -0.75 46 46
THY1 -0.45 0.42 -10000 0 -1.1 81 81
MYB -0.14 0.28 -10000 0 -0.6 139 139
HMGA1 0.028 0.028 -10000 0 -0.59 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.31 -10000 0 -0.78 110 110
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.26 -10000 0 -0.75 45 45
SP1 0.026 0.032 -10000 0 -10000 0 0
INPP5D 0.024 0.054 -10000 0 -0.59 4 4
SOCS5 0.04 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.47 0.44 -10000 0 -1.1 123 123
SOCS1 -0.32 0.3 -10000 0 -0.76 77 77
SOCS3 -0.27 0.27 -10000 0 -0.77 49 49
FCER2 -0.38 0.37 -10000 0 -0.99 76 76
PARP14 0.028 0.009 -10000 0 -10000 0 0
CCL17 -0.46 0.43 -10000 0 -1.1 87 87
GRB2 0.029 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.23 -10000 0 -0.69 38 38
T cell proliferation -0.45 0.44 -10000 0 -1.1 103 103
IL4R/JAK1 -0.44 0.42 -10000 0 -1.1 91 91
EGR2 -0.46 0.43 -10000 0 -1.2 87 87
JAK2 -0.02 0.038 -10000 0 -10000 0 0
JAK3 -0.094 0.25 -10000 0 -0.59 105 105
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
JAK1 0.01 0.019 -10000 0 -10000 0 0
COL1A2 -0.17 0.21 -10000 0 -0.68 35 35
CCL26 -0.44 0.43 -10000 0 -1.1 86 86
IL4R -0.47 0.44 -10000 0 -1.2 87 87
PTPN6 0.04 0.015 -10000 0 -10000 0 0
IL13RA2 -0.51 0.5 -10000 0 -1.3 114 114
IL13RA1 -0.02 0.04 -10000 0 -10000 0 0
IRF4 -0.2 0.28 -10000 0 -0.72 82 82
ARG1 -0.15 0.19 -10000 0 -0.74 14 14
CBL -0.3 0.3 -10000 0 -0.75 103 103
GTF3A -0.002 0.049 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
IL13RA1/JAK2 -0.025 0.054 -10000 0 -10000 0 0
IRF4/BCL6 -0.18 0.27 -10000 0 -0.68 72 72
CD40LG -0.047 0.2 -10000 0 -0.64 55 55
MAPK14 -0.3 0.3 -10000 0 -0.78 84 84
mitosis -0.23 0.25 -10000 0 -0.67 59 59
STAT6 -0.5 0.48 -10000 0 -1.2 109 109
SPI1 -0.054 0.22 -10000 0 -0.59 73 73
RPS6KB1 -0.22 0.25 -10000 0 -0.67 46 46
STAT6 (dimer) -0.5 0.47 -10000 0 -1.2 109 109
STAT6 (dimer)/PARP14 -0.46 0.44 -10000 0 -1.1 109 109
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.26 -10000 0 -0.71 68 68
FRAP1 -0.24 0.27 -10000 0 -0.71 59 59
LTA -0.52 0.45 -10000 0 -1.2 115 115
FES 0.027 0.041 -10000 0 -0.64 2 2
T-helper 1 cell differentiation 0.49 0.47 1.2 109 -10000 0 109
CCL11 -0.65 0.57 -10000 0 -1.3 208 208
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.23 0.25 -10000 0 -0.7 56 56
IL2RG -0.008 0.16 -10000 0 -0.59 34 34
IL10 -0.46 0.43 -10000 0 -1.1 108 108
IRS1 0.023 0.058 -10000 0 -0.64 4 4
IRS2 0.02 0.078 -10000 0 -0.6 8 8
IL4 -0.11 0.13 -10000 0 -1.1 3 3
IL5 -0.42 0.43 -10000 0 -1.1 81 81
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.37 0.34 -10000 0 -0.87 87 87
COL1A1 -0.3 0.31 -10000 0 -0.67 168 168
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.42 -10000 0 -1.2 77 77
IL2R gamma/JAK3 -0.081 0.25 -10000 0 -0.55 109 109
TFF3 -0.46 0.44 -10000 0 -1.2 87 87
ALOX15 -0.45 0.42 -10000 0 -1.1 85 85
MYBL1 -0.007 0.14 -10000 0 -0.59 30 30
T-helper 2 cell differentiation -0.39 0.37 -10000 0 -0.94 100 100
SHC1 0.029 0.007 -10000 0 -10000 0 0
CEBPB 0.022 0.079 -10000 0 -0.6 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.25 -10000 0 -0.7 52 52
mol:PI-3-4-5-P3 -0.24 0.27 -10000 0 -0.71 59 59
PI3K -0.25 0.28 -10000 0 -0.76 59 59
DOK2 -0.01 0.15 -10000 0 -0.59 31 31
ETS1 0.04 0.02 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.22 -10000 0 -0.66 42 42
ITGB3 -0.45 0.43 -10000 0 -1.1 94 94
PIGR -0.79 0.66 -10000 0 -1.4 256 256
IGHE 0.032 0.073 0.3 5 -0.39 1 6
MAPKKK cascade -0.19 0.22 -10000 0 -0.65 42 42
BCL6 0.028 0.007 -10000 0 -10000 0 0
OPRM1 -0.45 0.42 -10000 0 -1.1 83 83
RETNLB -0.45 0.42 -10000 0 -1.1 84 84
SELP -0.47 0.47 -10000 0 -1.2 87 87
AICDA -0.52 0.44 -10000 0 -1.1 135 135
Caspase cascade in apoptosis

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
TOP1 -0.078 0.18 -10000 0 -0.37 112 112
ACTA1 -0.12 0.22 -10000 0 -0.49 112 112
NUMA1 -0.078 0.18 0.25 1 -0.38 113 114
SPTAN1 -0.12 0.22 0.26 1 -0.49 108 109
LIMK1 -0.11 0.22 0.34 2 -0.48 109 111
BIRC3 -0.064 0.22 -10000 0 -0.59 79 79
BIRC2 0.029 0.004 -10000 0 -10000 0 0
BAX 0.03 0.003 -10000 0 -10000 0 0
CASP10 -0.19 0.29 -10000 0 -0.55 188 188
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
PTK2 -0.081 0.18 0.25 1 -0.38 113 114
DIABLO 0.029 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.12 0.21 0.26 1 -0.49 108 109
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 -10000 0 0
GSN -0.12 0.22 0.27 1 -0.49 108 109
MADD 0.03 0.003 -10000 0 -10000 0 0
TFAP2A -0.29 0.3 -10000 0 -0.54 278 278
BID -0.074 0.12 -10000 0 -0.28 109 109
MAP3K1 -0.03 0.078 -10000 0 -10000 0 0
TRADD 0.029 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.042 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.12 0.22 0.31 3 -0.49 108 111
CASP9 0.029 0.006 -10000 0 -10000 0 0
DNA repair 0.017 0.086 0.3 15 -0.19 3 18
neuron apoptosis 0.005 0.11 -10000 0 -0.61 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.1 0.21 -10000 0 -0.47 110 110
APAF1 0.029 0.006 -10000 0 -10000 0 0
CASP6 -0.029 0.15 0.36 2 -0.9 7 9
TRAF2 0.029 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.12 0.21 0.43 1 -0.48 108 109
CASP7 0.032 0.11 0.27 46 -0.3 11 57
KRT18 0.011 0.041 -10000 0 -0.32 1 1
apoptosis -0.12 0.21 0.41 2 -0.48 95 97
DFFA -0.12 0.22 -10000 0 -0.49 108 108
DFFB -0.12 0.22 -10000 0 -0.49 108 108
PARP1 -0.017 0.087 0.19 3 -0.3 15 18
actin filament polymerization 0.093 0.21 0.45 101 -0.41 2 103
TNF 0.019 0.079 -10000 0 -0.61 8 8
CYCS -0.047 0.11 0.19 5 -0.22 105 110
SATB1 -0.026 0.14 0.44 2 -0.83 7 9
SLK -0.12 0.22 0.34 1 -0.5 109 110
p15 BID/BAX -0.051 0.12 -10000 0 -0.28 2 2
CASP2 0.029 0.082 -10000 0 -0.47 2 2
JNK cascade 0.029 0.078 -10000 0 -10000 0 0
CASP3 -0.13 0.23 -10000 0 -0.52 110 110
LMNB2 0.025 0.11 0.36 11 -0.54 6 17
RIPK1 0.029 0.006 -10000 0 -10000 0 0
CASP4 0.03 0.003 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.013 0.14 -10000 0 -0.33 75 75
negative regulation of DNA binding -0.29 0.29 -10000 0 -0.53 279 279
stress fiber formation -0.12 0.22 0.34 1 -0.49 109 110
GZMB -0.21 0.33 -10000 0 -0.63 190 190
CASP1 0.021 0.003 -10000 0 -10000 0 0
LMNB1 0.018 0.1 0.39 8 -0.44 5 13
APP 0.005 0.11 -10000 0 -0.62 14 14
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.002 -10000 0 -10000 0 0
VIM -0.11 0.21 0.28 1 -0.47 94 95
LMNA 0.022 0.11 0.36 11 -0.38 10 21
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.015 0.065 -10000 0 -0.5 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.12 0.22 0.3 1 -0.49 108 109
APAF-1/Caspase 9 -0.014 0.13 -10000 0 -0.58 22 22
nuclear fragmentation during apoptosis -0.077 0.18 0.24 1 -0.37 113 114
CFL2 -0.098 0.22 0.41 2 -0.46 101 103
GAS2 -0.13 0.22 0.41 1 -0.49 117 118
positive regulation of apoptosis 0.027 0.11 0.36 11 -0.49 6 17
PRF1 -0.13 0.27 -10000 0 -0.59 132 132
Syndecan-1-mediated 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
TGFB1 0.025 0.054 -10000 0 -0.59 4 4
CCL5 -0.23 0.3 -10000 0 -0.59 220 220
SDCBP 0.028 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.14 0.17 0.27 2 -0.4 92 94
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.13 0.16 -10000 0 -0.45 51 51
Syndecan-1/Syntenin -0.12 0.16 0.33 2 -0.46 45 47
MAPK3 -0.11 0.15 -10000 0 -0.5 23 23
HGF/MET 0.019 0.1 -10000 0 -0.47 20 20
TGFB1/TGF beta receptor Type II 0.025 0.054 -10000 0 -0.59 4 4
BSG 0.028 0.027 -10000 0 -0.59 1 1
keratinocyte migration -0.12 0.16 -10000 0 -0.44 51 51
Syndecan-1/RANTES -0.25 0.22 0.4 2 -0.5 185 187
Syndecan-1/CD147 -0.11 0.17 -10000 0 -0.53 23 23
Syndecan-1/Syntenin/PIP2 -0.12 0.16 0.26 1 -0.44 45 46
LAMA5 0.027 0.04 -10000 0 -0.61 2 2
positive regulation of cell-cell adhesion -0.12 0.15 -10000 0 -0.44 45 45
MMP7 -0.09 0.26 -10000 0 -0.63 95 95
HGF 0.003 0.12 -10000 0 -0.6 20 20
Syndecan-1/CASK -0.13 0.15 -10000 0 -0.38 92 92
Syndecan-1/HGF/MET -0.12 0.18 -10000 0 -0.53 36 36
regulation of cell adhesion -0.1 0.15 0.51 1 -0.49 23 24
HPSE 0.027 0.041 -10000 0 -0.64 2 2
positive regulation of cell migration -0.14 0.17 0.27 2 -0.4 92 94
SDC1 -0.14 0.17 0.25 1 -0.4 92 93
Syndecan-1/Collagen -0.14 0.17 0.27 2 -0.4 92 94
PPIB 0.03 0.003 -10000 0 -10000 0 0
MET 0.024 0.039 -10000 0 -0.59 2 2
PRKACA 0.03 0.002 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 234 234
MAPK1 -0.11 0.15 0.28 1 -0.5 23 24
homophilic cell adhesion -0.13 0.17 0.27 2 -0.4 91 93
MMP1 -0.095 0.25 -10000 0 -0.6 103 103
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.22 0.36 -10000 0 -0.76 121 121
MAP4K1 -0.22 0.3 -10000 0 -0.59 214 214
MAP3K8 0.027 0.038 -10000 0 -0.59 2 2
PRKCB 0.022 0.062 -10000 0 -0.61 5 5
DBNL 0.027 0.009 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
MAP3K1 -0.078 0.16 -10000 0 -0.52 37 37
JUN 0.013 0.12 0.33 2 -0.57 14 16
MAP3K7 -0.081 0.16 -10000 0 -0.51 39 39
GRAP2 -0.012 0.16 -10000 0 -0.59 35 35
CRK 0.029 0.005 -10000 0 -10000 0 0
MAP2K4 -0.044 0.19 0.34 15 -0.49 37 52
LAT -0.14 0.28 -10000 0 -0.59 144 144
LCP2 -0.012 0.14 -10000 0 -0.59 29 29
MAPK8 0.009 0.12 0.3 1 -0.58 16 17
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.086 0.17 -10000 0 -0.54 39 39
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.2 0.34 -10000 0 -0.73 119 119
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.009 -10000 0 -10000 0 0
LAT2 -0.076 0.15 -10000 0 -0.45 47 47
AP1 -0.044 0.16 -10000 0 -0.51 12 12
mol:PIP3 -0.099 0.3 0.44 38 -0.6 85 123
IKBKB -0.017 0.19 0.34 62 -0.3 47 109
AKT1 -0.07 0.2 0.44 12 -0.52 20 32
IKBKG -0.018 0.19 0.33 61 -0.3 49 110
MS4A2 -0.1 0.26 -10000 0 -0.59 114 114
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
MAP3K1 -0.048 0.2 0.38 26 -0.41 40 66
mol:Ca2+ -0.063 0.24 0.38 45 -0.43 84 129
LYN 0.025 0.012 -10000 0 -10000 0 0
CBLB -0.051 0.11 -10000 0 -0.35 16 16
SHC1 0.029 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.04 0.036 -10000 0 -0.35 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.054 -10000 0 -0.59 4 4
PLD2 -0.1 0.2 0.34 17 -0.59 21 38
PTPN13 -0.025 0.14 0.39 3 -0.64 10 13
PTPN11 0.026 0.014 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.006 0.17 0.43 31 -0.37 1 32
SYK 0.024 0.035 -10000 0 -0.49 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.17 0.24 -10000 0 -0.59 108 108
LAT -0.13 0.19 -10000 0 -0.48 87 87
PAK2 -0.071 0.2 0.38 16 -0.44 68 84
NFATC2 -0.036 0.081 -10000 0 -0.53 5 5
HRAS -0.088 0.2 0.34 7 -0.47 74 81
GAB2 0.03 0.003 -10000 0 -10000 0 0
PLA2G1B -0.2 0.38 -10000 0 -0.8 150 150
Fc epsilon R1 -0.13 0.24 -10000 0 -0.41 206 206
Antigen/IgE/Fc epsilon R1 -0.12 0.22 -10000 0 -0.38 206 206
mol:GDP -0.11 0.21 0.26 1 -0.51 79 80
JUN 0.029 0.006 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.64 1 1
FOS 0.013 0.099 -10000 0 -0.63 12 12
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.054 0.12 -10000 0 -0.35 23 23
CHUK -0.019 0.19 0.33 60 -0.3 47 107
KLRG1 -0.055 0.11 -10000 0 -0.35 20 20
VAV1 -0.12 0.19 -10000 0 -0.47 92 92
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.05 0.11 -10000 0 -0.36 17 17
negative regulation of mast cell degranulation -0.043 0.12 -10000 0 -0.46 8 8
BTK -0.067 0.15 -10000 0 -0.44 16 16
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.07 0.16 -10000 0 -0.36 82 82
GAB2/PI3K/SHP2 -0.11 0.17 -10000 0 -0.57 21 21
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.052 0.12 -10000 0 -0.37 26 26
RAF1 -0.23 0.42 -10000 0 -0.89 150 150
Fc epsilon R1/FcgammaRIIB/SHIP -0.15 0.28 -10000 0 -0.66 83 83
FCER1G -0.082 0.24 -10000 0 -0.6 94 94
FCER1A 0.001 0.12 -10000 0 -0.63 19 19
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.21 -10000 0 -0.36 201 201
MAPK3 -0.2 0.38 -10000 0 -0.81 150 150
MAPK1 -0.2 0.39 -10000 0 -0.81 150 150
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
MAPK8 0.007 0.14 -10000 0 -0.68 15 15
DUSP1 0.021 0.03 -10000 0 -0.59 1 1
NF-kappa-B/RelA -0.03 0.083 -10000 0 -0.28 1 1
actin cytoskeleton reorganization -0.022 0.14 0.4 3 -0.67 9 12
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.1 0.21 -10000 0 -0.51 70 70
FER -0.049 0.11 -10000 0 -0.36 18 18
RELA 0.03 0.003 -10000 0 -10000 0 0
ITK -0.056 0.11 -10000 0 -0.26 84 84
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG1 -0.087 0.24 0.39 13 -0.52 82 95
cytokine secretion -0.029 0.053 -10000 0 -10000 0 0
SPHK1 -0.071 0.14 -10000 0 -0.45 35 35
PTK2 -0.024 0.15 0.4 3 -0.71 9 12
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.13 0.22 -10000 0 -0.56 80 80
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.059 0.28 0.4 56 -0.54 72 128
MAP2K2 -0.22 0.39 -10000 0 -0.83 150 150
MAP2K1 -0.21 0.39 -10000 0 -0.83 150 150
MAP2K7 0.03 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.05 0.12 0.29 2 -0.37 10 12
MAP2K4 0.018 0.13 -10000 0 -0.81 12 12
Fc epsilon R1/FcgammaRIIB -0.16 0.29 -10000 0 -0.47 224 224
mol:Choline -0.099 0.2 0.34 17 -0.58 21 38
SHC/Grb2/SOS1 -0.019 0.13 -10000 0 -0.38 3 3
FYN 0.028 0.008 -10000 0 -10000 0 0
DOK1 0.029 0.005 -10000 0 -10000 0 0
PXN -0.014 0.15 0.42 10 -0.67 8 18
HCLS1 -0.058 0.13 -10000 0 -0.45 25 25
PRKCB -0.043 0.23 0.37 59 -0.41 74 133
FCGR2B -0.078 0.23 -10000 0 -0.59 90 90
IGHE -0.003 0.011 -10000 0 -10000 0 0
KLRG1/SHIP -0.044 0.12 -10000 0 -0.47 8 8
LCP2 -0.012 0.14 -10000 0 -0.59 29 29
PLA2G4A -0.052 0.12 -10000 0 -0.42 9 9
RASA1 0.025 0.03 -10000 0 -0.64 1 1
mol:Phosphatidic acid -0.099 0.2 0.34 17 -0.58 21 38
IKK complex 0.002 0.16 0.33 61 -0.25 3 64
WIPF1 0.029 0.006 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.018 0.15 -10000 0 -0.79 14 14
oxygen homeostasis -0.003 0.014 -10000 0 -10000 0 0
TCEB2 0.025 0.048 -10000 0 -0.6 3 3
TCEB1 0.028 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.15 0.13 -10000 0 -0.45 8 8
EPO -0.29 0.3 -10000 0 -0.76 79 79
FIH (dimer) 0.022 0.023 -10000 0 -10000 0 0
APEX1 0.024 0.02 -10000 0 -10000 0 0
SERPINE1 -0.25 0.3 -10000 0 -0.81 65 65
FLT1 0.001 0.12 -10000 0 -0.82 7 7
ADORA2A -0.24 0.27 0.53 2 -0.74 43 45
germ cell development -0.3 0.34 -10000 0 -0.74 142 142
SLC11A2 -0.22 0.27 -10000 0 -0.74 41 41
BHLHE40 -0.23 0.26 -10000 0 -0.75 40 40
HIF1AN 0.022 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.21 0.2 -10000 0 -0.48 78 78
ETS1 0.045 0.012 -10000 0 -10000 0 0
CITED2 -0.035 0.17 -10000 0 -0.74 23 23
KDR 0.009 0.098 -10000 0 -0.86 5 5
PGK1 -0.23 0.27 -10000 0 -0.75 41 41
SIRT1 0.028 0.006 -10000 0 -10000 0 0
response to hypoxia -0.002 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.26 0.32 -10000 0 -0.89 44 44
EPAS1 -0.19 0.14 0.33 1 -0.36 108 109
SP1 0.035 0.015 -10000 0 -10000 0 0
ABCG2 -0.23 0.27 -10000 0 -0.75 43 43
EFNA1 -0.22 0.27 -10000 0 -0.74 42 42
FXN -0.24 0.27 0.56 1 -0.74 43 44
POU5F1 -0.32 0.35 -10000 0 -0.78 144 144
neuron apoptosis 0.25 0.31 0.86 44 -10000 0 44
EP300 0.028 0.029 -10000 0 -0.64 1 1
EGLN3 -0.53 0.21 -10000 0 -0.6 462 462
EGLN2 0.025 0.018 -10000 0 -10000 0 0
EGLN1 0.021 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.037 0.044 -10000 0 -0.38 3 3
VHL 0.021 0.02 -10000 0 -0.32 1 1
ARNT 0.02 0.023 -10000 0 -10000 0 0
SLC2A1 -0.25 0.29 0.5 1 -0.82 50 51
TWIST1 -0.23 0.26 0.56 1 -0.72 46 47
ELK1 0.037 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.17 0.18 -10000 0 -0.5 23 23
VEGFA -0.34 0.36 -10000 0 -0.78 150 150
CREBBP 0.029 0.006 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.008 0.041 0.17 2 -0.45 4 6
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.025 0.085 -10000 0 -0.46 15 15
STXBP1 0.028 0.029 -10000 0 -0.64 1 1
ACh/CHRNA1 -0.16 0.2 -10000 0 -0.39 220 220
RAB3GAP2/RIMS1/UNC13B 0.04 0.077 -10000 0 -0.39 15 15
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.007 0.11 -10000 0 -0.63 15 15
mol:ACh 0.002 0.046 0.1 43 -0.15 3 46
RAB3GAP2 0.029 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.019 0.087 -10000 0 -0.4 8 8
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.16 0.2 -10000 0 -0.39 220 220
UNC13B 0.029 0.006 -10000 0 -10000 0 0
CHRNA1 -0.23 0.3 -10000 0 -0.59 220 220
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.052 0.16 -10000 0 -0.43 82 82
SNAP25 -0.022 0.077 0.12 4 -0.21 74 78
VAMP2 0.007 0.001 -10000 0 -10000 0 0
SYT1 -0.074 0.24 -10000 0 -0.63 82 82
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.042 -10000 0 -0.38 5 5
STX1A/SNAP25 fragment 1/VAMP2 0.019 0.087 -10000 0 -0.4 8 8
Arf6 signaling events

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
CENTA1/KIF3B 0.03 0.041 -10000 0 -0.4 4 4
ARNO/beta Arrestin1-2 0.022 0.066 -10000 0 -0.78 1 1
EGFR 0.019 0.067 -10000 0 -0.6 6 6
EPHA2 0.027 0.03 -10000 0 -0.64 1 1
USP6 0.028 0.027 -10000 0 -0.59 1 1
IQSEC1 0.021 0.014 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.4 0.16 -10000 0 -0.48 425 425
ARRB2 -0.006 0.075 -10000 0 -0.26 40 40
mol:GTP 0.001 0.046 0.19 6 -0.18 4 10
ARRB1 0.03 0.003 -10000 0 -10000 0 0
FBXO8 0.029 0.004 -10000 0 -10000 0 0
TSHR -0.043 0.2 -10000 0 -0.59 60 60
EGF -0.57 0.2 -10000 0 -0.63 474 474
somatostatin receptor activity 0 0 0.001 16 -0.001 21 37
ARAP2 0.027 0.041 -10000 0 -0.64 2 2
mol:GDP -0.046 0.099 0.25 5 -0.33 24 29
mol:PI-3-4-5-P3 0 0 0.001 8 -0.001 10 18
ITGA2B 0.007 0.12 -10000 0 -0.59 19 19
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.065 0.041 -10000 0 -0.36 3 3
ADAP1 0.022 0.058 -10000 0 -0.64 4 4
KIF13B 0.027 0.009 -10000 0 -10000 0 0
HGF/MET 0.019 0.1 -10000 0 -0.47 20 20
PXN 0.029 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.065 0.11 0.29 11 -0.34 23 34
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.34 0.14 -10000 0 -0.4 422 422
ADRB2 0.02 0.043 -10000 0 -0.64 2 2
receptor agonist activity 0 0 0 19 0 15 34
actin filament binding 0 0 0.001 19 -0.001 23 42
SRC 0.029 0.006 -10000 0 -10000 0 0
ITGB3 0.023 0.065 -10000 0 -0.64 5 5
GNAQ 0.029 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 25 -0.001 13 38
ARF6/GDP -0.049 0.12 0.27 5 -0.42 15 20
ARF6/GDP/GULP/ACAP1 -0.14 0.19 0.27 1 -0.43 89 90
alphaIIb/beta3 Integrin/paxillin/GIT1 0.055 0.09 -10000 0 -0.42 6 6
ACAP1 -0.21 0.3 -10000 0 -0.59 203 203
ACAP2 0.028 0.007 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.007 0.1 -10000 0 -0.36 40 40
EFNA1 0.027 0.028 -10000 0 -0.59 1 1
HGF 0.003 0.12 -10000 0 -0.6 20 20
CYTH3 0.011 0.004 -10000 0 -10000 0 0
CYTH2 0.018 0.044 -10000 0 -0.99 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
fibronectin binding 0 0 0.001 31 -0.001 14 45
endosomal lumen acidification 0 0 0.001 3 -0.001 21 24
microtubule-based process 0 0 -10000 0 -0.001 1 1
GULP1 0.006 0.12 -10000 0 -0.62 18 18
GNAQ/ARNO 0.034 0.043 -10000 0 -0.92 1 1
mol:Phosphatidic acid 0 0 0 4 -10000 0 4
PIP3-E 0 0 0.001 2 0 1 3
MET 0.024 0.039 -10000 0 -0.59 2 2
GNA14 0.02 0.076 -10000 0 -0.64 7 7
GNA15 0.012 0.1 -10000 0 -0.59 15 15
GIT1 0.029 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 22 -0.001 16 38
GNA11 0.026 0.05 -10000 0 -0.64 3 3
LHCGR -0.04 0.16 -10000 0 -0.59 39 39
AGTR1 -0.002 0.14 -10000 0 -0.62 25 25
desensitization of G-protein coupled receptor protein signaling pathway -0.007 0.1 -10000 0 -0.36 40 40
IPCEF1/ARNO -0.25 0.12 -10000 0 -0.64 6 6
alphaIIb/beta3 Integrin 0.021 0.1 -10000 0 -0.46 23 23
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.024 0.046 -9999 0 -10000 0 0
NFATC2 -0.025 0.061 -9999 0 -0.45 5 5
NFATC3 -0.023 0.046 -9999 0 -10000 0 0
CD40LG -0.27 0.34 -9999 0 -0.79 103 103
PTGS2 -0.26 0.31 -9999 0 -0.74 93 93
JUNB 0.027 0.041 -9999 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.033 -9999 0 -10000 0 0
CaM/Ca2+ -0.013 0.033 -9999 0 -10000 0 0
CALM1 0.004 0.027 -9999 0 -10000 0 0
JUN 0.003 0.028 -9999 0 -10000 0 0
mol:Ca2+ -0.017 0.016 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.007 0.016 -9999 0 -10000 0 0
FOSL1 -0.001 0.13 -9999 0 -0.59 26 26
CREM 0.029 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.14 0.2 -9999 0 -0.6 28 28
FOS -0.011 0.1 -9999 0 -0.64 12 12
IFNG -0.36 0.4 -9999 0 -0.78 218 218
AP-1/NFAT1-c-4 -0.3 0.37 -9999 0 -0.87 98 98
FASLG -0.37 0.4 -9999 0 -0.77 221 221
NFAT1-c-4/ICER1 -0.063 0.11 -9999 0 -0.46 5 5
IL2RA -0.29 0.35 -9999 0 -0.82 109 109
FKBP12/FK506 0.021 0.004 -9999 0 -10000 0 0
CSF2 -0.25 0.3 -9999 0 -0.74 85 85
JunB/Fra1/NFAT1-c-4 -0.07 0.13 -9999 0 -0.48 11 11
IL4 -0.24 0.29 -9999 0 -0.72 82 82
IL2 -0.007 0.12 -9999 0 -0.86 7 7
IL3 -0.014 0.074 -9999 0 -0.69 1 1
FKBP1A 0.029 0.005 -9999 0 -10000 0 0
BATF3 -0.025 0.17 -9999 0 -0.59 45 45
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.029 0.007 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.028 0.011 -9999 0 -10000 0 0
SVIL 0.028 0.01 -9999 0 -10000 0 0
ZNF318 0.03 0.013 -9999 0 -10000 0 0
JMJD2C -0.001 0.017 -9999 0 -0.086 18 18
T-DHT/AR/Ubc9 -0.084 0.093 -9999 0 -0.47 23 23
CARM1 0.03 0.003 -9999 0 -10000 0 0
PRDX1 0.029 0.006 -9999 0 -10000 0 0
PELP1 0.029 0.005 -9999 0 -10000 0 0
CTNNB1 0.02 0.015 -9999 0 -10000 0 0
AKT1 0.028 0.009 -9999 0 -10000 0 0
PTK2B 0.026 0.011 -9999 0 -10000 0 0
MED1 0.03 0.005 -9999 0 -10000 0 0
MAK 0.029 0.03 -9999 0 -0.59 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.02 0.06 -9999 0 -0.65 4 4
GSN 0.027 0.012 -9999 0 -10000 0 0
NCOA2 0.015 0.091 -9999 0 -0.64 10 10
NCOA6 0.027 0.011 -9999 0 -10000 0 0
DNA-PK 0.055 0.022 -9999 0 -10000 0 0
NCOA4 0.029 0.005 -9999 0 -10000 0 0
PIAS3 0.028 0.009 -9999 0 -10000 0 0
cell proliferation -0.044 0.1 -9999 0 -0.54 19 19
XRCC5 0.029 0.007 -9999 0 -10000 0 0
UBE3A 0.027 0.015 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.099 0.12 -9999 0 -0.5 38 38
FHL2 -0.051 0.11 -9999 0 -0.74 9 9
RANBP9 0.028 0.011 -9999 0 -10000 0 0
JMJD1A -0.12 0.052 -9999 0 -0.14 453 453
CDK6 0.025 0.03 -9999 0 -0.63 1 1
TGFB1I1 0.026 0.029 -9999 0 -0.59 1 1
T-DHT/AR/CyclinD1 -0.099 0.11 -9999 0 -0.46 42 42
XRCC6 0.03 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.16 0.1 -9999 0 -0.44 34 34
CTDSP1 0.028 0.007 -9999 0 -10000 0 0
CTDSP2 0.031 0.012 -9999 0 -10000 0 0
BRCA1 0.028 0.01 -9999 0 -10000 0 0
TCF4 0.03 0.009 -9999 0 -10000 0 0
CDKN2A -0.57 0.13 -9999 0 -0.6 503 503
SRF 0.036 0.015 -9999 0 -10000 0 0
NKX3-1 -0.21 0.082 -9999 0 -0.24 465 465
KLK3 0.02 0.089 -9999 0 -0.45 12 12
TMF1 0.023 0.012 -9999 0 -10000 0 0
HNRNPA1 0.03 0.007 -9999 0 -10000 0 0
AOF2 -0.001 0.006 -9999 0 -0.049 1 1
APPL1 0.017 0.014 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.084 0.093 -9999 0 -0.46 24 24
AR -0.083 0.14 -9999 0 -0.66 26 26
UBA3 0.023 0.012 -9999 0 -10000 0 0
PATZ1 0.03 0.007 -9999 0 -10000 0 0
PAWR 0.028 0.029 -9999 0 -0.64 1 1
PRKDC 0.028 0.008 -9999 0 -10000 0 0
PA2G4 0.03 0.008 -9999 0 -10000 0 0
UBE2I 0.029 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.076 0.086 -9999 0 -0.42 25 25
RPS6KA3 0.027 0.032 -9999 0 -0.66 1 1
T-DHT/AR/ARA70 -0.086 0.093 -9999 0 -0.46 24 24
LATS2 0.03 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.077 0.085 -9999 0 -0.42 25 25
Cyclin D3/CDK11 p58 0.021 0.005 -9999 0 -10000 0 0
VAV3 0.011 0.11 -9999 0 -0.64 14 14
KLK2 -0.078 0.096 -9999 0 -0.53 19 19
CASP8 0.029 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.077 0.11 -9999 0 -0.49 26 26
TMPRSS2 -0.86 0.33 -9999 0 -0.98 457 457
CCND1 0.008 0.11 -9999 0 -0.59 18 18
PIAS1 0.028 0.015 -9999 0 -10000 0 0
mol:T-DHT -0.059 0.025 -9999 0 -0.069 444 444
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.027 0.02 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.079 0.096 -9999 0 -0.47 22 22
CMTM2 0.016 0.089 -9999 0 -0.59 11 11
SNURF 0.008 0.12 -9999 0 -0.64 17 17
ZMIZ1 -0.049 0.033 -9999 0 -10000 0 0
CCND3 0.029 0.006 -9999 0 -10000 0 0
TGIF1 0.03 0.007 -9999 0 -10000 0 0
FKBP4 0.027 0.011 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.008 -10000 0 -10000 0 0
VLDLR 0.029 0.006 -10000 0 -10000 0 0
LRPAP1 0.029 0.004 -10000 0 -10000 0 0
NUDC 0.029 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.087 0.21 -10000 0 -0.4 159 159
CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
KATNA1 0.027 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.08 0.19 -10000 0 -0.36 158 158
IQGAP1/CaM 0.041 0.012 -10000 0 -10000 0 0
DAB1 0.01 0.096 -10000 0 -0.59 13 13
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
PLA2G7 -0.44 0.27 -10000 0 -0.59 396 396
CALM1 0.028 0.008 -10000 0 -10000 0 0
DYNLT1 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.041 0.023 -10000 0 -0.43 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.005 -10000 0 -10000 0 0
CDK5R1 0.029 0.005 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.016 0.004 -10000 0 -10000 0 0
CDK5R2 -0.049 0.2 -10000 0 -0.6 63 63
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.099 0.21 -10000 0 -0.4 168 168
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.052 0.18 0.32 26 -0.46 13 39
MAP1B 0.008 0.007 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
p35/CDK5 -0.071 0.16 -10000 0 -10000 0 0
RELN -0.17 0.3 -10000 0 -0.63 158 158
PAFAH/LIS1 -0.27 0.18 -10000 0 -0.37 383 383
LIS1/CLIP170 0.037 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.052 0.13 -10000 0 -0.41 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.061 0.14 -10000 0 -0.43 14 14
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.085 0.16 -10000 0 -0.5 13 13
LIS1/IQGAP1 0.037 0.01 -10000 0 -10000 0 0
RHOA 0.016 0.011 -10000 0 -10000 0 0
PAFAH1B1 0.022 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.028 0.029 -10000 0 -0.64 1 1
PAFAH1B2 0.028 0.029 -10000 0 -0.64 1 1
MAP1B/LIS1/Dynein heavy chain 0.038 0.023 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.049 0.18 0.34 14 -0.46 10 24
LRP8 0.028 0.028 -10000 0 -0.59 1 1
NDEL1/Katanin 60 -0.055 0.18 0.32 24 -0.46 12 36
P39/CDK5 -0.1 0.19 -10000 0 -0.59 15 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.037 0.011 -10000 0 -10000 0 0
CDK5 -0.087 0.16 -10000 0 -10000 0 0
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.032 0.009 -10000 0 -10000 0 0
CSNK2A1 0.029 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.073 0.19 -10000 0 -0.35 149 149
RELN/VLDLR -0.068 0.2 -10000 0 -0.36 158 158
CDC42 0.022 0.007 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.18 0.19 -10000 0 -0.58 32 32
IHH -0.08 0.19 -10000 0 -0.69 44 44
SHH Np/Cholesterol/GAS1 0.004 0.098 -10000 0 -0.37 30 30
LRPAP1 0.029 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.004 0.097 0.37 30 -10000 0 30
SMO/beta Arrestin2 -0.085 0.15 -10000 0 -0.52 25 25
SMO -0.096 0.15 -10000 0 -0.54 25 25
AKT1 -0.034 0.11 -10000 0 -0.54 10 10
ARRB2 0.028 0.032 -10000 0 -0.71 1 1
BOC 0.028 0.008 -10000 0 -10000 0 0
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
heart looping -0.094 0.14 -10000 0 -0.53 25 25
STIL -0.069 0.13 -10000 0 -0.52 6 6
DHH N/PTCH2 0.008 0.12 -10000 0 -0.44 36 36
DHH N/PTCH1 -0.1 0.15 -10000 0 -0.5 32 32
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
DHH 0.014 0.099 -10000 0 -0.64 12 12
PTHLH -0.28 0.27 -10000 0 -0.81 37 37
determination of left/right symmetry -0.094 0.14 -10000 0 -0.53 25 25
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
skeletal system development -0.28 0.27 -10000 0 -0.8 37 37
IHH N/Hhip -0.16 0.25 -10000 0 -0.53 156 156
DHH N/Hhip -0.093 0.23 -10000 0 -0.48 133 133
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.094 0.14 -10000 0 -0.53 25 25
pancreas development -0.13 0.28 -10000 0 -0.62 130 130
HHAT 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.037 0.035 -10000 0 -0.47 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.15 -10000 0 -0.58 32 32
somite specification -0.094 0.14 -10000 0 -0.53 25 25
SHH Np/Cholesterol/PTCH1 -0.082 0.13 -10000 0 -0.44 26 26
SHH Np/Cholesterol/PTCH2 0.007 0.091 -10000 0 -0.34 31 31
SHH Np/Cholesterol/Megalin -0.004 0.12 -10000 0 -0.4 36 36
SHH 0.011 0.068 -10000 0 -0.47 10 10
catabolic process -0.12 0.16 -10000 0 -0.52 32 32
SMO/Vitamin D3 -0.084 0.14 -10000 0 -0.49 26 26
SHH Np/Cholesterol/Hhip -0.068 0.18 -10000 0 -0.38 116 116
LRP2 -0.022 0.17 -10000 0 -0.59 43 43
receptor-mediated endocytosis -0.096 0.16 -10000 0 -0.65 17 17
SHH Np/Cholesterol/BOC 0.022 0.056 -10000 0 -0.36 10 10
SHH Np/Cholesterol/CDO -0.015 0.12 -10000 0 -0.34 61 61
mesenchymal cell differentiation 0.068 0.17 0.38 116 -10000 0 116
mol:Vitamin D3 -0.076 0.14 -10000 0 -0.45 26 26
IHH N/PTCH2 -0.057 0.16 -10000 0 -0.46 67 67
CDON -0.04 0.2 -10000 0 -0.59 59 59
IHH N/PTCH1 -0.12 0.16 -10000 0 -0.53 32 32
Megalin/LRPAP1 0.004 0.13 -10000 0 -0.47 35 35
PTCH2 -0.001 0.13 -10000 0 -0.59 25 25
SHH Np/Cholesterol 0.011 0.053 -10000 0 -0.37 10 10
PTCH1 -0.12 0.16 -10000 0 -0.52 32 32
HHIP -0.13 0.28 -10000 0 -0.62 130 130
Reelin signaling pathway

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
CDK5R1/CDK5 0.039 0.015 -10000 0 -10000 0 0
VLDLR 0.029 0.006 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
LRPAP1 0.029 0.004 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ITGA3 0.028 0.027 -10000 0 -0.59 1 1
RELN/VLDLR/Fyn -0.087 0.21 -10000 0 -0.4 158 158
MAPK8IP1/MKK7/MAP3K11/JNK1 0.079 0.05 -10000 0 -0.68 1 1
AKT1 -0.065 0.13 -10000 0 -0.38 15 15
MAP2K7 0.03 0.003 -10000 0 -10000 0 0
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
DAB1 0.01 0.096 -10000 0 -0.59 13 13
RELN/LRP8/DAB1 -0.089 0.2 -10000 0 -0.37 169 169
LRPAP1/LRP8 0.041 0.023 -10000 0 -0.43 1 1
RELN/LRP8/DAB1/Fyn -0.075 0.19 -10000 0 -0.35 162 162
DAB1/alpha3/beta1 Integrin -0.064 0.18 -10000 0 -0.6 1 1
long-term memory -0.11 0.21 -10000 0 -0.62 19 19
DAB1/LIS1 -0.059 0.19 -10000 0 -0.62 1 1
DAB1/CRLK/C3G -0.065 0.18 -10000 0 -0.6 1 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
DAB1/NCK2 -0.059 0.19 -10000 0 -0.62 1 1
ARHGEF2 0.028 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.053 0.21 -10000 0 -0.6 68 68
CDK5R1 0.029 0.005 -10000 0 -10000 0 0
RELN -0.17 0.3 -10000 0 -0.63 158 158
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
RELN/LRP8/Fyn -0.087 0.21 -10000 0 -0.4 159 159
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.22 -10000 0 -0.64 20 20
MAPK8 0.027 0.041 -10000 0 -0.64 2 2
RELN/VLDLR/DAB1 -0.089 0.2 -10000 0 -0.37 168 168
ITGB1 0.029 0.004 -10000 0 -10000 0 0
MAP1B -0.087 0.18 -10000 0 -0.35 130 130
RELN/LRP8 -0.087 0.21 -10000 0 -0.4 159 159
GRIN2B/RELN/LRP8/DAB1/Fyn -0.066 0.2 -10000 0 -0.38 28 28
PI3K 0.037 0.035 -10000 0 -0.47 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.042 0.022 -10000 0 -0.43 1 1
RAP1A -0.056 0.18 0.44 5 -0.57 1 6
PAFAH1B1 0.029 0.005 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.041 -10000 0 -0.64 2 2
CRLK/C3G 0.043 0.009 -10000 0 -10000 0 0
GRIN2B 0.023 0.039 -10000 0 -0.59 2 2
NCK2 0.029 0.006 -10000 0 -10000 0 0
neuron differentiation -0.034 0.13 -10000 0 -0.4 24 24
neuron adhesion -0.048 0.17 0.4 8 -0.54 1 9
LRP8 0.028 0.028 -10000 0 -0.59 1 1
GSK3B -0.059 0.12 -10000 0 -0.52 2 2
RELN/VLDLR/DAB1/Fyn -0.075 0.19 -10000 0 -0.35 168 168
MAP3K11 0.029 0.029 -10000 0 -0.64 1 1
RELN/VLDLR/DAB1/P13K -0.069 0.14 -10000 0 -0.29 143 143
CDK5 0.027 0.009 -10000 0 -10000 0 0
MAPT 0.012 0.096 0.71 5 -0.59 6 11
neuron migration -0.066 0.18 0.46 4 -0.52 2 6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.034 0.13 -10000 0 -0.4 24 24
RELN/VLDLR -0.068 0.2 -10000 0 -0.36 158 158
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.054 -10000 0 -0.59 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.059 0.15 0.44 29 -0.35 1 30
IL27/IL27R/JAK1 -0.027 0.27 0.67 3 -0.69 31 34
TBX21 -0.14 0.34 0.57 9 -0.63 112 121
IL12B -0.046 0.19 -10000 0 -0.6 54 54
IL12A 0.007 0.01 -10000 0 -10000 0 0
IL6ST -0.005 0.12 -10000 0 -0.63 18 18
IL27RA/JAK1 0.013 0.063 -10000 0 -0.44 1 1
IL27 -0.022 0.15 -10000 0 -0.6 32 32
TYK2 0.011 0.026 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.011 0.11 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.059 0.15 0.44 29 -0.35 1 30
T cell proliferation during immune response 0.059 0.15 0.44 29 -0.35 1 30
MAPKKK cascade -0.059 0.15 0.35 1 -0.44 29 30
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT2 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.029 -10000 0 -0.59 1 1
IL12RB1 -0.16 0.29 -10000 0 -0.6 159 159
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.1 0.3 0.56 9 -0.59 78 87
IL27/IL27R/JAK2/TYK2 -0.059 0.15 0.36 1 -0.45 28 29
positive regulation of T cell mediated cytotoxicity -0.059 0.15 0.35 1 -0.44 29 30
STAT1 (dimer) 0.018 0.42 0.54 108 -0.74 59 167
JAK2 0.015 0.021 -10000 0 -10000 0 0
JAK1 0.03 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.039 0.15 0.39 2 -0.44 18 20
T cell proliferation -0.088 0.17 -10000 0 -0.53 31 31
IL12/IL12R/TYK2/JAK2 -0.099 0.17 -10000 0 -0.8 3 3
IL17A -0.011 0.11 -10000 0 -10000 0 0
mast cell activation 0.059 0.15 0.44 29 -0.35 1 30
IFNG -0.027 0.056 0.14 4 -0.1 50 54
T cell differentiation -0.008 0.01 0.02 4 -0.023 116 120
STAT3 (dimer) -0.04 0.16 0.39 2 -0.47 11 13
STAT5A (dimer) -0.04 0.16 0.39 2 -0.44 19 21
STAT4 (dimer) -0.058 0.18 0.39 2 -0.52 39 41
STAT4 -0.007 0.14 -10000 0 -0.59 30 30
T cell activation -0.009 0.006 0.07 1 -10000 0 1
IL27R/JAK2/TYK2 -0.012 0.11 -10000 0 -0.47 5 5
GATA3 -0.6 0.65 0.5 1 -1.3 258 259
IL18 0.007 0.044 -10000 0 -0.44 5 5
positive regulation of mast cell cytokine production -0.04 0.15 0.38 2 -0.46 11 13
IL27/EBI3 -0.066 0.22 -10000 0 -0.55 86 86
IL27RA -0.004 0.049 -10000 0 -0.47 1 1
IL6 -0.047 0.2 -10000 0 -0.61 62 62
STAT5A 0.029 0.004 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 -0.011 0.057 -10000 0 -10000 0 0
IL1B 0.005 0.048 -10000 0 -0.44 6 6
EBI3 -0.068 0.22 -10000 0 -0.61 76 76
TNF 0.003 0.057 -10000 0 -0.46 8 8
Ephrin A reverse signaling

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
MAPKKK cascade -0.012 0.13 -9999 0 -0.42 46 46
EFNA5 -0.026 0.18 -9999 0 -0.63 40 40
FYN 0.007 0.14 -9999 0 -0.38 46 46
neuron projection morphogenesis -0.012 0.13 -9999 0 -0.42 46 46
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.012 0.13 -9999 0 -0.42 46 46
EPHA5 0.012 0.077 -9999 0 -0.6 8 8
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.14 0.26 -10000 0 -0.7 76 76
NFATC2 -0.075 0.21 -10000 0 -0.73 14 14
NFATC3 -0.019 0.066 -10000 0 -0.34 1 1
CD40LG -0.19 0.35 -10000 0 -0.95 47 47
ITCH 0.041 0.046 -10000 0 -10000 0 0
CBLB 0.038 0.047 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.33 0.44 -10000 0 -0.98 120 120
JUNB 0.027 0.041 -10000 0 -0.64 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.038 0.055 -10000 0 -0.3 11 11
T cell anergy 0.025 0.073 -10000 0 -0.41 10 10
TLE4 -0.038 0.15 -10000 0 -0.57 11 11
Jun/NFAT1-c-4/p21SNFT -0.13 0.28 -10000 0 -0.93 15 15
AP-1/NFAT1-c-4 -0.18 0.35 -10000 0 -1.1 22 22
IKZF1 -0.094 0.25 -10000 0 -0.62 88 88
T-helper 2 cell differentiation -0.28 0.26 0.5 2 -0.68 67 69
AP-1/NFAT1 -0.052 0.17 -10000 0 -0.59 13 13
CALM1 0.037 0.034 -10000 0 -10000 0 0
EGR2 -0.091 0.24 -10000 0 -1.3 9 9
EGR3 -0.092 0.23 -10000 0 -1.3 9 9
NFAT1/FOXP3 -0.18 0.32 -10000 0 -0.71 110 110
EGR1 0.012 0.086 -10000 0 -0.63 9 9
JUN 0.011 0.032 -10000 0 -10000 0 0
EGR4 0.02 0.061 -10000 0 -0.59 5 5
mol:Ca2+ 0 0.039 -10000 0 -0.45 1 1
GBP3 -0.04 0.16 -10000 0 -0.63 11 11
FOSL1 -0.001 0.13 -10000 0 -0.59 26 26
NFAT1-c-4/MAF/IRF4 -0.14 0.31 -10000 0 -0.84 23 23
DGKA -0.039 0.16 -10000 0 -0.7 11 11
CREM 0.029 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.1 0.22 -10000 0 -1 7 7
CTLA4 -0.29 0.4 -10000 0 -0.71 232 232
NFAT1-c-4 (dimer)/EGR1 -0.084 0.24 -10000 0 -1.1 8 8
NFAT1-c-4 (dimer)/EGR4 -0.09 0.24 -10000 0 -1 8 8
FOS -0.005 0.1 -10000 0 -0.63 12 12
IFNG -0.28 0.36 -10000 0 -0.78 127 127
T cell activation -0.045 0.18 -10000 0 -0.72 7 7
MAF 0.029 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.059 0.16 0.79 5 -10000 0 5
TNF -0.066 0.23 -10000 0 -1.1 7 7
FASLG -0.21 0.34 -10000 0 -1.3 11 11
TBX21 -0.21 0.31 -10000 0 -0.64 172 172
BATF3 -0.024 0.17 -10000 0 -0.59 45 45
PRKCQ -0.026 0.1 -10000 0 -0.57 15 15
PTPN1 -0.037 0.15 -10000 0 -0.57 11 11
NFAT1-c-4/ICER1 -0.088 0.23 -10000 0 -0.97 8 8
GATA3 -0.3 0.33 -10000 0 -0.63 258 258
T-helper 1 cell differentiation -0.27 0.35 -10000 0 -0.75 134 134
IL2RA -0.23 0.36 -10000 0 -0.86 95 95
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.037 0.15 -10000 0 -0.57 11 11
E2F1 -0.028 0.19 -10000 0 -0.58 54 54
PPARG 0.021 0.014 -10000 0 -10000 0 0
SLC3A2 -0.037 0.15 -10000 0 -0.58 10 10
IRF4 -0.11 0.26 -10000 0 -0.59 118 118
PTGS2 -0.18 0.32 -10000 0 -1 22 22
CSF2 -0.17 0.3 -10000 0 -1 20 20
JunB/Fra1/NFAT1-c-4 -0.087 0.24 -10000 0 -0.96 8 8
IL4 -0.29 0.26 0.55 1 -0.72 63 64
IL5 -0.16 0.29 -10000 0 -0.97 17 17
IL2 -0.046 0.18 -10000 0 -0.73 7 7
IL3 -0.03 0.057 -10000 0 -0.9 1 1
RNF128 0.028 0.12 -10000 0 -0.63 16 16
NFATC1 -0.058 0.16 -10000 0 -0.84 4 4
CDK4 0.041 0.13 -10000 0 -10000 0 0
PTPRK -0.042 0.15 -10000 0 -0.62 10 10
IL8 -0.18 0.33 -10000 0 -1 29 29
POU2F1 0.029 0.007 -10000 0 -10000 0 0
PLK1 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
regulation of centriole-centriole cohesion 0.037 0.069 0.14 141 -0.14 2 143
BUB1B -0.006 0.085 0.2 8 -0.31 27 35
PLK1 -0.004 0.047 0.15 10 -0.15 10 20
PLK1S1 0.007 0.031 0.15 9 -0.2 1 10
KIF2A 0.014 0.086 0.25 42 -0.33 4 46
regulation of mitotic centrosome separation -0.004 0.047 0.15 10 -0.15 10 20
GOLGA2 0.029 0.006 -10000 0 -10000 0 0
Hec1/SPC24 -0.074 0.22 -10000 0 -0.45 122 122
WEE1 0.012 0.058 0.23 4 -0.85 1 5
cytokinesis -0.054 0.17 0.26 12 -0.31 105 117
PP2A-alpha B56 -0.024 0.12 -10000 0 -0.6 7 7
AURKA 0.005 0.033 0.14 6 -0.17 5 11
PICH/PLK1 -0.014 0.11 -10000 0 -0.52 18 18
CENPE -0.041 0.13 0.27 3 -0.39 62 65
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.014 0.085 0.25 42 -0.33 4 46
PPP2CA 0.023 0.013 -10000 0 -10000 0 0
FZR1 0.028 0.029 -10000 0 -0.64 1 1
TPX2 -0.018 0.074 0.15 13 -0.15 107 120
PAK1 0.03 0.003 -10000 0 -10000 0 0
SPC24 -0.033 0.19 -10000 0 -0.59 53 53
FBXW11 0.023 0.013 -10000 0 -10000 0 0
CLSPN -0.017 0.076 0.16 1 -0.2 59 60
GORASP1 0.021 0.014 -10000 0 -10000 0 0
metaphase -0.002 0.006 0.017 20 -0.012 100 120
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.003 0.026 0.085 11 -0.077 10 21
G2 phase of mitotic cell cycle 0 0.002 0.017 2 -0.011 1 3
STAG2 0.03 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.11 0.22 -10000 0 -0.45 145 145
spindle elongation -0.004 0.047 0.15 10 -0.15 10 20
ODF2 0.029 0.006 -10000 0 -10000 0 0
BUB1 -0.056 0.12 -10000 0 -0.66 7 7
TPT1 0.002 0.039 0.15 4 -0.19 11 15
CDC25C -0.03 0.11 0.17 7 -0.2 93 100
CDC25B 0.025 0.055 -10000 0 -0.6 4 4
SGOL1 -0.038 0.069 0.14 2 -0.14 141 143
RHOA 0.021 0.014 -10000 0 -10000 0 0
CCNB1/CDK1 0.017 0.071 -10000 0 -0.43 8 8
CDC14B 0.011 0.003 -10000 0 -10000 0 0
CDC20 -0.022 0.17 -10000 0 -0.6 43 43
PLK1/PBIP1 -0.013 0.079 0.14 2 -0.37 18 20
mitosis -0.002 0.003 0.025 2 -10000 0 2
FBXO5 -0.001 0.046 0.2 6 -0.21 3 9
CDC2 0 0.003 -10000 0 -0.017 8 8
NDC80 -0.099 0.25 -10000 0 -0.59 109 109
metaphase plate congression -0.004 0.061 0.14 3 -0.25 22 25
ERCC6L -0.001 0.1 -10000 0 -0.5 18 18
NLP/gamma Tubulin -0.001 0.031 0.12 7 -0.12 8 15
microtubule cytoskeleton organization 0.002 0.039 0.14 4 -0.19 11 15
G2/M transition DNA damage checkpoint 0 0.002 0.012 2 -10000 0 2
PPP1R12A 0.03 0.005 -10000 0 -10000 0 0
interphase 0 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 -0.088 0.2 -10000 0 -0.35 176 176
GRASP65/GM130/RAB1/GTP/PLK1 0.02 0.046 -10000 0 -10000 0 0
RAB1A 0.029 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.001 0.034 0.12 13 -0.13 8 21
mitotic prometaphase -0.002 0.005 0.017 17 -0.012 1 18
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.057 -10000 0 -0.49 3 3
microtubule-based process -0.11 0.18 0.21 1 -0.36 176 177
Golgi organization -0.004 0.047 0.15 10 -0.15 10 20
Cohesin/SA2 0.008 0.046 0.17 3 -10000 0 3
PPP1CB/MYPT1 0.042 0.011 -10000 0 -10000 0 0
KIF20A -0.18 0.29 -10000 0 -0.59 176 176
APC/C/CDC20 -0.016 0.12 0.18 4 -0.39 43 47
PPP2R1A 0.03 0.003 -10000 0 -10000 0 0
chromosome segregation -0.013 0.078 0.14 2 -0.37 18 20
PRC1 0.024 0.06 -10000 0 -0.59 5 5
ECT2 0.004 0.056 0.24 14 -10000 0 14
C13orf34 -0.001 0.036 0.12 11 -0.13 7 18
NUDC -0.004 0.061 0.14 3 -0.25 22 25
regulation of attachment of spindle microtubules to kinetochore -0.006 0.084 0.2 8 -0.3 27 35
spindle assembly -0.002 0.04 0.14 10 -0.13 7 17
spindle stabilization 0.007 0.031 0.15 9 -0.2 1 10
APC/C/HCDH1 0.029 0.02 -10000 0 -0.41 1 1
MKLP2/PLK1 -0.11 0.18 0.21 1 -0.36 176 177
CCNB1 0.018 0.077 -10000 0 -0.59 8 8
PPP1CB 0.03 0.005 -10000 0 -10000 0 0
BTRC 0.029 0.006 -10000 0 -10000 0 0
ROCK2 -0.022 0.077 0.2 1 -0.38 10 11
TUBG1 0.004 0.037 0.16 3 -0.23 6 9
G2/M transition of mitotic cell cycle -0.009 0.06 -10000 0 -0.42 8 8
MLF1IP -0.006 0.084 -10000 0 -0.45 18 18
INCENP 0.028 0.003 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.01 0.018 -10000 0 -0.41 1 1
ADCY5 -0.005 0.079 -10000 0 -0.41 19 19
ADCY6 0.01 0.034 -10000 0 -0.76 1 1
ADCY7 -0.001 0.066 -10000 0 -0.37 16 16
ADCY1 0.001 0.062 -10000 0 -0.4 12 12
ADCY2 -0.067 0.16 -10000 0 -0.37 114 114
ADCY3 0.011 0.018 -10000 0 -0.41 1 1
ADCY8 -0.1 0.18 -10000 0 -0.37 156 156
PRKCE 0.011 0.021 -10000 0 -0.48 1 1
ADCY9 0.01 0.018 -10000 0 -0.41 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.042 0.13 0.29 20 -0.32 41 61
IL2 signaling events mediated by STAT5

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
GAB2 0.03 0.003 -10000 0 -10000 0 0
ELF1 -0.023 0.12 -10000 0 -0.53 4 4
CCNA2 -0.09 0.24 -10000 0 -0.59 101 101
PIK3CA 0.028 0.03 -10000 0 -0.64 1 1
JAK3 -0.093 0.25 -10000 0 -0.59 105 105
PIK3R1 0.027 0.03 -10000 0 -0.64 1 1
JAK1 0.029 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.052 0.16 -10000 0 -0.48 34 34
SHC1 0.029 0.007 -10000 0 -10000 0 0
SP1 0.036 0.019 -10000 0 -10000 0 0
IL2RA -0.075 0.21 -10000 0 -0.51 102 102
IL2RB -0.29 0.31 -10000 0 -0.59 272 272
SOS1 0.03 0.005 -10000 0 -10000 0 0
IL2RG -0.01 0.15 -10000 0 -0.59 34 34
G1/S transition of mitotic cell cycle -0.001 0.13 0.43 7 -0.53 4 11
PTPN11 0.03 0.006 -10000 0 -10000 0 0
CCND2 0.028 0.034 -10000 0 -0.51 2 2
LCK 0.003 0.12 -10000 0 -0.59 22 22
GRB2 0.03 0.005 -10000 0 -10000 0 0
IL2 0.014 0.084 -10000 0 -0.59 10 10
CDK6 0.025 0.03 -10000 0 -0.64 1 1
CCND3 -0.036 0.14 0.5 1 -0.6 1 2
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.042 0.024 -10000 0 -0.47 1 1
Necdin/E2F1 -0.008 0.15 -10000 0 -0.43 56 56
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.023 0.15 -10000 0 -0.62 7 7
NGF (dimer)/p75(NTR)/BEX1 -0.17 0.25 -10000 0 -0.43 245 245
NT-4/5 (dimer)/p75(NTR) 0.002 0.13 -10000 0 -0.45 38 38
IKBKB 0.028 0.008 -10000 0 -10000 0 0
AKT1 -0.009 0.15 0.41 4 -0.62 8 12
IKBKG 0.03 0.004 -10000 0 -10000 0 0
BDNF -0.052 0.21 -10000 0 -0.59 69 69
MGDIs/NGR/p75(NTR)/LINGO1 0.009 0.14 -10000 0 -0.4 57 57
FURIN 0.03 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.025 0.18 -10000 0 -0.4 95 95
LINGO1 0.005 0.12 -10000 0 -0.59 21 21
Sortilin/TRAF6/NRIF 0.036 0.021 -10000 0 -10000 0 0
proBDNF (dimer) -0.052 0.21 -10000 0 -0.59 69 69
NTRK1 -0.017 0.16 -10000 0 -0.61 37 37
RTN4R 0.022 0.067 -10000 0 -0.6 6 6
neuron apoptosis -0.027 0.16 0.45 6 -0.55 12 18
IRAK1 0.03 0.003 -10000 0 -10000 0 0
SHC1 -0.033 0.15 -10000 0 -0.4 73 73
ARHGDIA 0.028 0.029 -10000 0 -0.64 1 1
RhoA/GTP 0.016 0.01 -10000 0 -10000 0 0
Gamma Secretase 0.079 0.029 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.011 0.16 -10000 0 -0.55 11 11
MAGEH1 0.03 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.009 0.16 -10000 0 -0.52 13 13
Mammalian IAPs/DIABLO 0.013 0.14 -10000 0 -0.33 75 75
proNGF (dimer) -0.026 0.18 -10000 0 -0.59 47 47
MAGED1 0.03 0.003 -10000 0 -10000 0 0
APP 0.029 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.056 -10000 0 -0.62 4 4
ZNF274 0.03 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.019 0.14 -10000 0 -0.53 10 10
NGF -0.027 0.18 -10000 0 -0.59 47 47
cell cycle arrest 0.012 0.17 0.36 10 -0.65 7 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.006 0.097 -10000 0 -0.4 16 16
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.022 0.11 -10000 0 -0.38 38 38
NCSTN 0.029 0.007 -10000 0 -10000 0 0
mol:GTP -0.007 0.16 -10000 0 -0.4 73 73
PSENEN 0.03 0.003 -10000 0 -10000 0 0
mol:ceramide -0.026 0.14 -10000 0 -0.54 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.009 0.068 -10000 0 -0.46 3 3
p75(NTR)/beta APP 0.011 0.12 -10000 0 -0.44 33 33
BEX1 -0.22 0.32 -10000 0 -0.63 193 193
mol:GDP -0.045 0.15 -10000 0 -0.4 73 73
NGF (dimer) -0.25 0.26 -10000 0 -0.44 300 300
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.026 0.14 -10000 0 -0.56 8 8
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
RAC1/GTP -0.007 0.14 -10000 0 -0.35 67 67
MYD88 0.021 0.014 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.006 0.16 -10000 0 -0.4 73 73
RHOB 0.029 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.007 0.14 -10000 0 -0.43 54 54
NT3 (dimer) 0.023 0.063 -10000 0 -0.62 5 5
TP53 -0.029 0.14 0.34 3 -0.59 7 10
PRDM4 -0.025 0.14 -10000 0 -0.57 10 10
BDNF (dimer) -0.29 0.29 -10000 0 -0.48 340 340
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
SORT1 0.028 0.029 -10000 0 -0.64 1 1
activation of caspase activity 0.017 0.15 -10000 0 -0.61 7 7
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.011 0.16 -10000 0 -0.55 11 11
RHOC 0.029 0.006 -10000 0 -10000 0 0
XIAP 0.03 0.003 -10000 0 -10000 0 0
MAPK10 -0.013 0.15 0.46 7 -0.5 5 12
DIABLO 0.029 0.005 -10000 0 -10000 0 0
SMPD2 -0.027 0.14 -10000 0 -0.54 11 11
APH1B 0.03 0.003 -10000 0 -10000 0 0
APH1A 0.029 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.007 0.16 -10000 0 -0.4 74 74
PSEN1 0.028 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.006 0.13 -10000 0 -0.45 38 38
MAPK8 -0.014 0.14 0.43 7 -0.47 4 11
MAPK9 -0.018 0.13 0.45 6 -0.52 2 8
APAF1 0.029 0.005 -10000 0 -10000 0 0
NTF3 0.023 0.063 -10000 0 -0.62 5 5
NTF4 0.017 0.056 -10000 0 -0.62 4 4
NDN 0.027 0.041 -10000 0 -0.64 2 2
RAC1/GDP 0.02 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.003 0.14 -10000 0 -0.57 7 7
p75 CTF/Sortilin/TRAF6/NRIF 0.071 0.028 -10000 0 -0.37 1 1
RhoA-B-C/GTP -0.007 0.16 -10000 0 -0.4 73 73
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.007 0.17 -10000 0 -0.55 10 10
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.006 0.17 -10000 0 -0.56 11 11
PRKACB 0.029 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.02 0.16 -10000 0 -0.43 68 68
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.064 0.22 -10000 0 -0.59 79 79
BIRC2 0.03 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.031 0.16 0.33 5 -0.53 7 12
BAD 0.004 0.15 0.48 10 -0.47 5 15
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
NGFR -0.011 0.16 -10000 0 -0.6 34 34
CYCS -0.021 0.14 0.43 2 -0.62 8 10
ADAM17 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.008 0.16 -10000 0 -0.57 10 10
BCL2L11 0.005 0.15 0.46 10 -0.48 5 15
BDNF (dimer)/p75(NTR) -0.049 0.2 -10000 0 -0.46 96 96
PI3K 0.005 0.16 -10000 0 -0.58 11 11
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.011 0.16 -10000 0 -0.55 11 11
NDNL2 0.03 0.003 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.028 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.029 0.18 -10000 0 -0.47 73 73
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.011 0.16 -10000 0 -0.55 11 11
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.05 -10000 0 -0.64 3 3
PLG -0.3 0.32 -10000 0 -0.61 270 270
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.048 0.16 -10000 0 -0.52 24 24
SQSTM1 0.022 0.013 -10000 0 -10000 0 0
NGFRAP1 0.03 0.003 -10000 0 -10000 0 0
CASP3 0.008 0.14 0.46 10 -0.44 5 15
E2F1 -0.035 0.19 -10000 0 -0.59 54 54
CASP9 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.021 0.13 -10000 0 -0.52 1 1
NGF (dimer)/TRKA -0.035 0.18 -10000 0 -0.45 80 80
MMP7 -0.09 0.26 -10000 0 -0.63 95 95
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.024 0.15 -10000 0 -0.62 7 7
MMP3 -0.03 0.17 -10000 0 -0.59 46 46
APAF-1/Caspase 9 -0.053 0.13 -10000 0 -0.48 9 9
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.17 0.24 -10000 0 -0.43 234 234
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
SPHK1 -0.01 0.082 -10000 0 -0.59 6 6
mol:S1P -0.005 0.076 -10000 0 -0.5 6 6
S1P1/S1P/Gi -0.054 0.13 0.32 1 -0.5 19 20
GNAO1 0.026 0.055 -10000 0 -0.6 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.029 0.11 0.33 1 -0.6 5 6
PLCG1 -0.043 0.12 0.32 2 -0.52 12 14
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.013 -10000 0 -10000 0 0
GNAI2 0.022 0.016 -10000 0 -10000 0 0
GNAI3 0.029 0.008 -10000 0 -10000 0 0
GNAI1 0.026 0.031 -10000 0 -0.65 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.16 0.19 -10000 0 -0.36 234 234
S1P1/S1P -0.097 0.15 0.25 1 -0.38 28 29
negative regulation of cAMP metabolic process -0.052 0.13 0.32 1 -0.49 19 20
MAPK3 -0.053 0.16 0.42 2 -0.62 23 25
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
KDR 0.029 0.029 -10000 0 -0.64 1 1
PLCB2 -0.11 0.18 0.32 9 -0.44 53 62
RAC1 0.027 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.092 0.12 -10000 0 -0.35 16 16
receptor internalization -0.094 0.14 -10000 0 -0.35 29 29
PTGS2 -0.053 0.24 0.49 6 -0.96 25 31
Rac1/GTP -0.085 0.12 -10000 0 -0.34 17 17
RHOA 0.021 0.014 -10000 0 -10000 0 0
VEGFA -0.25 0.31 -10000 0 -0.59 234 234
negative regulation of T cell proliferation -0.052 0.13 0.32 1 -0.49 19 20
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.051 -10000 0 -0.64 3 3
MAPK1 -0.056 0.16 0.32 1 -0.62 24 25
S1P1/S1P/PDGFB-D/PDGFRB -0.087 0.14 0.3 1 -0.42 14 15
ABCC1 0.029 0.007 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.17 0.24 -10000 0 -0.44 234 234
alphaV beta3 Integrin 0.048 0.068 -10000 0 -0.44 9 9
PTK2 -0.093 0.17 0.57 4 -0.52 9 13
IGF1R 0.03 0.003 -10000 0 -10000 0 0
PI4KB 0.029 0.007 -10000 0 -10000 0 0
MFGE8 0.028 0.027 -10000 0 -0.59 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
CDKN1B -0.042 0.18 -10000 0 -0.48 72 72
VEGFA -0.25 0.31 -10000 0 -0.59 234 234
ILK -0.043 0.18 -10000 0 -0.48 74 74
ROCK1 0.029 0.005 -10000 0 -10000 0 0
AKT1 -0.041 0.17 -10000 0 -0.46 68 68
PTK2B -0.12 0.17 0.36 2 -0.5 2 4
alphaV/beta3 Integrin/JAM-A 0.002 0.15 -10000 0 -0.68 1 1
CBL 0.028 0.029 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.15 0.22 -10000 0 -0.4 222 222
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.064 0.058 -10000 0 -0.37 4 4
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.096 0.16 -10000 0 -0.43 60 60
alphaV/beta3 Integrin/Syndecan-1 0.047 0.068 -10000 0 -0.4 11 11
PI4KA 0.03 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.026 0.12 -10000 0 -0.62 4 4
PI4 Kinase 0.042 0.011 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
alphaV/beta3 Integrin/Osteopontin 0.05 0.056 -10000 0 -0.4 7 7
RPS6KB1 0.018 0.13 0.47 13 -0.57 4 17
TLN1 0.029 0.006 -10000 0 -10000 0 0
MAPK3 0 0.11 -10000 0 -0.6 9 9
GPR124 0.025 0.039 -10000 0 -0.59 2 2
MAPK1 0.001 0.11 -10000 0 -0.6 9 9
PXN 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
alphaV/beta3 Integrin/Tumstatin 0.003 0.15 -10000 0 -0.42 57 57
cell adhesion -0.11 0.18 -10000 0 -0.38 25 25
ANGPTL3 -0.27 0.32 -10000 0 -0.61 241 241
VEGFR2 homodimer/VEGFA homodimer/Src -0.13 0.21 -10000 0 -0.37 231 231
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
TGFBR2 0.022 0.014 -10000 0 -10000 0 0
ITGB3 0.023 0.065 -10000 0 -0.64 5 5
IGF1 0.023 0.06 -10000 0 -0.59 5 5
RAC1 0.027 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.047 0.053 -10000 0 -0.4 6 6
apoptosis 0.028 0.006 -10000 0 -10000 0 0
CD47 0.027 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.048 0.049 -10000 0 -0.4 5 5
VCL 0.029 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.036 0.087 -10000 0 -0.41 17 17
CSF1 0.028 0.029 -10000 0 -0.64 1 1
PIK3C2A -0.045 0.19 -10000 0 -0.49 75 75
PI4 Kinase/Pyk2 -0.14 0.19 -10000 0 -0.56 43 43
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.2 -10000 0 -0.34 226 226
FAK1/Vinculin -0.069 0.15 0.59 3 -0.47 4 7
alphaV beta3/Integrin/ppsTEM5 0.047 0.053 -10000 0 -0.4 6 6
RHOA 0.021 0.014 -10000 0 -10000 0 0
VTN -0.069 0.24 -10000 0 -0.62 79 79
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
FGF2 0.023 0.064 -10000 0 -0.63 5 5
F11R 0.018 0.045 -10000 0 -0.47 4 4
alphaV/beta3 Integrin/Lactadherin 0.051 0.051 -10000 0 -0.4 6 6
alphaV/beta3 Integrin/TGFBR2 0.038 0.051 -10000 0 -0.4 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.067 0.046 -10000 0 -0.54 2 2
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.048 0.044 -10000 0 -0.37 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.017 0.16 -10000 0 -0.6 38 38
alphaV/beta3 Integrin/Pyk2 -0.11 0.18 -10000 0 -0.39 7 7
SDC1 0.021 0.071 -10000 0 -0.64 6 6
VAV3 0.03 0.084 0.36 7 -0.67 1 8
PTPN11 0.029 0.005 -10000 0 -10000 0 0
IRS1 0.023 0.058 -10000 0 -0.64 4 4
FAK1/Paxillin -0.07 0.14 0.53 2 -0.5 3 5
cell migration -0.063 0.13 0.52 2 -0.45 3 5
ITGAV 0.029 0.007 -10000 0 -10000 0 0
PI3K 0.012 0.14 -10000 0 -0.92 1 1
SPP1 0.026 0.05 -10000 0 -0.64 3 3
KDR 0.028 0.029 -10000 0 -0.64 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.007 -10000 0 -10000 0 0
COL4A3 -0.042 0.2 -10000 0 -0.61 58 58
angiogenesis -0.008 0.14 0.32 4 -0.62 9 13
Rac1/GTP 0.035 0.065 -10000 0 -0.62 1 1
EDIL3 0.01 0.1 -10000 0 -0.6 14 14
cell proliferation 0.037 0.051 -10000 0 -0.4 5 5
IL23-mediated signaling events

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
CCL2 -0.18 0.36 -10000 0 -1.1 17 17
IL23A -0.16 0.36 -10000 0 -1.2 10 10
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.36 -10000 0 -1 21 21
positive regulation of T cell mediated cytotoxicity -0.19 0.39 -10000 0 -1.1 30 30
ITGA3 -0.16 0.36 -10000 0 -1.1 11 11
IL17F -0.11 0.28 0.58 4 -0.73 12 16
IL12B -0.057 0.19 -10000 0 -0.61 54 54
STAT1 (dimer) -0.18 0.37 -10000 0 -1 28 28
CD4 -0.17 0.37 -10000 0 -1.1 16 16
IL23 -0.19 0.34 -10000 0 -1.1 15 15
IL23R -0.021 0.16 -10000 0 -0.71 14 14
IL1B -0.17 0.37 -10000 0 -1.1 14 14
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.36 -10000 0 -1 17 17
TYK2 0.014 0.035 -10000 0 -10000 0 0
STAT4 -0.007 0.14 -10000 0 -0.59 30 30
STAT3 0.029 0.005 -10000 0 -10000 0 0
IL18RAP -0.14 0.27 -10000 0 -0.6 136 136
IL12RB1 -0.17 0.3 -10000 0 -0.62 159 159
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
IL12Rbeta1/TYK2 -0.12 0.24 -10000 0 -0.47 159 159
IL23R/JAK2 -0.024 0.16 -10000 0 -0.76 8 8
positive regulation of chronic inflammatory response -0.19 0.39 -10000 0 -1.1 30 30
natural killer cell activation 0.002 0.01 0.049 10 -10000 0 10
JAK2 0.01 0.042 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
NFKB1 0.028 0.029 -10000 0 -0.63 1 1
RELA 0.029 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.33 -10000 0 -1.1 15 15
ALOX12B -0.21 0.38 -10000 0 -1.1 21 21
CXCL1 -0.2 0.41 -10000 0 -1.2 34 34
T cell proliferation -0.19 0.39 -10000 0 -1.1 30 30
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
IL17A -0.079 0.23 0.4 1 -0.6 4 5
PI3K -0.17 0.36 -10000 0 -1 26 26
IFNG -0.04 0.059 0.12 6 -0.12 23 29
STAT3 (dimer) -0.16 0.35 -10000 0 -1 21 21
IL18R1 0.012 0.074 -10000 0 -0.61 7 7
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.28 -10000 0 -0.74 20 20
IL18/IL18R -0.095 0.2 -10000 0 -0.4 144 144
macrophage activation -0.014 0.015 -10000 0 -10000 0 0
TNF -0.17 0.37 -10000 0 -1.2 15 15
STAT3/STAT4 -0.18 0.38 -10000 0 -1 34 34
STAT4 (dimer) -0.2 0.39 -10000 0 -1.1 35 35
IL18 0.015 0.061 -10000 0 -0.59 5 5
IL19 -0.17 0.36 -10000 0 -1.1 14 14
STAT5A (dimer) -0.18 0.38 -10000 0 -1 29 29
STAT1 0.027 0.028 -10000 0 -0.59 1 1
SOCS3 0.024 0.054 -10000 0 -0.59 4 4
CXCL9 -0.26 0.43 -10000 0 -1 46 46
MPO -0.18 0.36 -10000 0 -1.1 15 15
positive regulation of humoral immune response -0.19 0.39 -10000 0 -1.1 30 30
IL23/IL23R/JAK2/TYK2 -0.2 0.39 -10000 0 -1.1 29 29
IL6 -0.2 0.44 -10000 0 -1.2 41 41
STAT5A 0.029 0.004 -10000 0 -10000 0 0
IL2 -0.011 0.086 -10000 0 -0.59 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.01 0.049 10 -10000 0 10
CD3E -0.25 0.43 -10000 0 -1 46 46
keratinocyte proliferation -0.19 0.39 -10000 0 -1.1 30 30
NOS2 -0.17 0.36 -10000 0 -1.1 16 16
BCR signaling pathway

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
JUN -0.022 0.15 0.37 13 -0.44 11 24
IKBKB 0.006 0.12 0.33 19 -0.31 5 24
AKT1 0.001 0.14 0.41 24 -0.29 4 28
IKBKG 0.02 0.11 0.32 15 -0.3 1 16
CALM1 -0.003 0.09 0.36 1 -10000 0 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
MAP3K1 -0.045 0.19 0.41 16 -0.47 33 49
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.095 -10000 0 -0.32 7 7
DOK1 0.029 0.005 -10000 0 -10000 0 0
AP-1 0.013 0.11 0.29 24 -0.28 6 30
LYN 0.028 0.007 -10000 0 -10000 0 0
BLNK 0.028 0.03 -10000 0 -0.64 1 1
SHC1 0.029 0.007 -10000 0 -10000 0 0
BCR complex -0.075 0.21 -10000 0 -0.44 126 126
CD22 -0.064 0.16 -10000 0 -0.5 28 28
CAMK2G 0.003 0.088 0.35 1 -10000 0 1
CSNK2A1 0.029 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.054 -10000 0 -0.59 4 4
SHC/GRB2/SOS1 -0.041 0.14 -10000 0 -0.55 3 3
GO:0007205 -0.005 0.096 -10000 0 -0.33 7 7
SYK 0.027 0.033 -10000 0 -0.48 2 2
ELK1 0 0.095 0.3 1 -10000 0 1
NFATC1 -0.038 0.15 0.37 7 -0.39 28 35
B-cell antigen/BCR complex -0.075 0.21 -10000 0 -0.44 126 126
PAG1/CSK 0.041 0.011 -10000 0 -10000 0 0
NFKBIB 0.021 0.053 0.14 28 -0.13 5 33
HRAS -0.003 0.094 0.31 2 -0.33 2 4
NFKBIA 0.021 0.052 0.14 28 -0.13 4 32
NF-kappa-B/RelA/I kappa B beta 0.027 0.049 0.16 18 -0.17 1 19
RasGAP/Csk -0.079 0.23 -10000 0 -0.62 46 46
mol:GDP -0.003 0.092 0.26 1 -0.34 5 6
PTEN 0.029 0.006 -10000 0 -10000 0 0
CD79B 0.026 0.047 -10000 0 -0.59 3 3
NF-kappa-B/RelA/I kappa B alpha 0.027 0.048 0.16 18 -0.17 1 19
GRB2 0.029 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.014 0.18 0.4 14 -0.45 16 30
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
mol:IP3 -0.007 0.094 -10000 0 -0.33 7 7
CSK 0.03 0.003 -10000 0 -10000 0 0
FOS -0.005 0.1 0.32 3 -0.52 3 6
CHUK 0.012 0.12 0.32 15 -0.32 6 21
IBTK 0.028 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.027 0.16 0.39 1 -0.48 4 5
PTPN6 -0.058 0.15 -10000 0 -0.48 26 26
RELA 0.03 0.003 -10000 0 -10000 0 0
BCL2A1 0.004 0.06 0.15 12 -0.13 3 15
VAV2 -0.074 0.19 -10000 0 -0.51 62 62
ubiquitin-dependent protein catabolic process 0.025 0.052 0.14 30 -0.13 4 34
BTK -0.041 0.15 -10000 0 -0.88 11 11
CD19 -0.091 0.21 -10000 0 -0.57 67 67
MAP4K1 -0.22 0.3 -10000 0 -0.59 214 214
CD72 -0.12 0.26 -10000 0 -0.59 124 124
PAG1 0.028 0.007 -10000 0 -10000 0 0
MAPK14 -0.033 0.18 0.37 21 -0.42 19 40
SH3BP5 0.02 0.032 -10000 0 -0.64 1 1
PIK3AP1 0.001 0.095 0.3 1 -0.45 3 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.061 0.14 -10000 0 -0.46 12 12
RAF1 0.001 0.091 0.31 3 -10000 0 3
RasGAP/p62DOK/SHIP -0.077 0.23 -10000 0 -0.61 46 46
CD79A -0.12 0.27 -10000 0 -0.59 128 128
re-entry into mitotic cell cycle 0.013 0.11 0.29 23 -0.28 6 29
RASA1 0.025 0.03 -10000 0 -0.64 1 1
MAPK3 0.018 0.1 0.39 9 -10000 0 9
MAPK1 0.014 0.093 0.38 5 -10000 0 5
CD72/SHP1 -0.11 0.23 0.34 1 -0.54 85 86
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
MAPK8 -0.035 0.18 0.37 22 -0.42 18 40
actin cytoskeleton organization -0.048 0.18 0.36 5 -0.48 37 42
NF-kappa-B/RelA 0.057 0.088 0.27 26 -10000 0 26
Calcineurin 0.02 0.089 -10000 0 -10000 0 0
PI3K -0.074 0.16 -10000 0 -0.49 37 37
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.007 0.091 0.31 1 -0.38 6 7
SOS1 0.029 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.14 0.23 -10000 0 -0.58 43 43
DAPP1 -0.041 0.15 -10000 0 -0.69 11 11
cytokine secretion -0.035 0.14 0.37 7 -0.37 28 35
mol:DAG -0.007 0.094 -10000 0 -0.33 7 7
PLCG2 0.02 0.073 -10000 0 -0.61 7 7
MAP2K1 0.01 0.094 0.37 4 -10000 0 4
B-cell antigen/BCR complex/FcgammaRIIB -0.11 0.26 -10000 0 -0.46 166 166
mol:PI-3-4-5-P3 -0.057 0.12 -10000 0 -0.37 20 20
ETS1 0.007 0.088 0.43 2 -10000 0 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.021 0.17 -10000 0 -0.62 3 3
B-cell antigen/BCR complex/LYN -0.062 0.14 -10000 0 -0.4 34 34
MALT1 0.029 0.005 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 -0.054 0.19 0.33 2 -0.51 37 39
B-cell antigen/BCR complex/LYN/SYK -0.057 0.18 -10000 0 -0.53 27 27
CARD11 -0.042 0.18 0.36 8 -0.42 54 62
FCGR2B -0.078 0.23 -10000 0 -0.59 90 90
PPP3CA 0.03 0.003 -10000 0 -10000 0 0
BCL10 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.02 0.071 0.2 35 -10000 0 35
PTPRC -0.034 0.19 -10000 0 -0.59 53 53
PDPK1 -0.021 0.11 0.36 8 -0.29 7 15
PPP3CB 0.029 0.006 -10000 0 -10000 0 0
PPP3CC 0.027 0.009 -10000 0 -10000 0 0
POU2F2 0.012 0.054 0.15 12 -0.12 1 13
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.064 0.15 -10000 0 -0.53 17 17
UGCG -0.012 0.11 -10000 0 -0.57 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT -0.035 0.15 0.35 3 -0.43 23 26
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.011 0.11 -10000 0 -0.56 19 19
mol:DAG -0.013 0.13 -10000 0 -0.84 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.14 0.29 1 -0.44 17 18
FRAP1 -0.038 0.16 0.36 3 -0.48 24 27
FOXO3 -0.034 0.16 0.36 4 -0.46 22 26
AKT1 -0.043 0.16 0.31 1 -0.48 28 29
GAB2 0.03 0.003 -10000 0 -10000 0 0
SMPD1 0.007 0.046 -10000 0 -0.74 1 1
SGMS1 -0.007 0.11 -10000 0 -0.7 12 12
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 0.013 0.027 -10000 0 -0.4 2 2
CALM1 0.028 0.008 -10000 0 -10000 0 0
cell proliferation -0.014 0.12 0.3 4 -0.5 16 20
EIF3A 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.041 0.036 -10000 0 -0.47 2 2
RPS6KB1 -0.017 0.12 -10000 0 -0.91 6 6
mol:sphingomyelin -0.013 0.13 -10000 0 -0.84 12 12
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.092 0.25 -10000 0 -0.59 105 105
PIK3R1 0.028 0.03 -10000 0 -0.63 1 1
JAK1 0.031 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
MYC -0.031 0.16 0.43 4 -0.57 8 12
MYB -0.097 0.21 -10000 0 -0.58 24 24
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.054 0.16 0.26 1 -0.5 36 37
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.009 0.12 -10000 0 -0.86 6 6
mol:PI-3-4-5-P3 -0.053 0.16 0.26 1 -0.48 36 37
Rac1/GDP 0.027 0.028 -10000 0 -0.36 2 2
T cell proliferation -0.046 0.16 0.31 1 -0.46 33 34
SHC1 0.029 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.007 0.021 -10000 0 -0.041 137 137
PRKCZ -0.046 0.16 -10000 0 -0.48 32 32
NF kappa B1 p50/RelA -0.014 0.15 0.31 1 -0.45 15 16
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.081 0.16 -10000 0 -0.48 45 45
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
IL2RA -0.09 0.24 -10000 0 -0.59 101 101
IL2RB -0.29 0.31 -10000 0 -0.59 272 272
TERT -0.05 0.2 -10000 0 -0.59 61 61
E2F1 -0.048 0.14 -10000 0 -0.41 26 26
SOS1 0.029 0.005 -10000 0 -10000 0 0
RPS6 0.026 0.039 -10000 0 -0.59 2 2
mol:cAMP 0.003 0.01 0.02 137 -10000 0 137
PTPN11 0.029 0.006 -10000 0 -10000 0 0
IL2RG -0.008 0.15 -10000 0 -0.59 34 34
actin cytoskeleton organization -0.046 0.16 0.31 1 -0.46 33 34
GRB2 0.03 0.005 -10000 0 -10000 0 0
IL2 0.015 0.085 -10000 0 -0.59 10 10
PIK3CA 0.029 0.03 -10000 0 -0.63 1 1
Rac1/GTP 0.047 0.037 -10000 0 -0.34 2 2
LCK 0.005 0.12 -10000 0 -0.59 22 22
BCL2 -0.021 0.14 0.45 2 -0.47 3 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.035 0.055 -10000 0 -0.44 5 5
VEGFR1 homodimer/NRP1 0.015 0.052 -10000 0 -0.43 7 7
mol:DAG -0.17 0.18 -10000 0 -0.7 6 6
VEGFR1 homodimer/NRP1/VEGFR 121 -0.13 0.19 -10000 0 -0.58 7 7
CaM/Ca2+ -0.15 0.18 -10000 0 -0.66 6 6
HIF1A 0.03 0.049 -10000 0 -0.62 2 2
GAB1 0.03 0.004 -10000 0 -10000 0 0
AKT1 -0.12 0.16 -10000 0 -0.67 6 6
PLCG1 -0.17 0.19 -10000 0 -0.71 6 6
NOS3 -0.1 0.15 -10000 0 -0.54 10 10
CBL 0.028 0.029 -10000 0 -0.64 1 1
mol:NO -0.096 0.15 0.72 1 -0.52 10 11
FLT1 0.022 0.061 -10000 0 -0.5 7 7
PGF -0.32 0.31 -10000 0 -0.6 289 289
VEGFR1 homodimer/NRP2/VEGFR121 -0.12 0.2 -10000 0 -0.59 9 9
CALM1 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
eNOS/Hsp90 -0.083 0.16 0.56 1 -0.55 6 7
endothelial cell proliferation -0.12 0.16 0.59 1 -0.57 8 9
mol:Ca2+ -0.17 0.18 -10000 0 -0.69 6 6
MAPK3 -0.15 0.16 0.46 2 -0.6 6 8
MAPK1 -0.15 0.16 0.46 2 -0.62 6 8
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
PLGF homodimer -0.32 0.31 -10000 0 -0.59 289 289
PRKACA 0.03 0.002 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.009 0.14 -10000 0 -0.59 30 30
VEGFA homodimer -0.25 0.31 -10000 0 -0.59 234 234
VEGFR1 homodimer/VEGFA homodimer -0.14 0.21 -10000 0 -0.57 9 9
platelet activating factor biosynthetic process -0.14 0.16 0.44 2 -0.58 6 8
PI3K -0.14 0.19 -10000 0 -0.73 6 6
PRKCA -0.16 0.17 0.58 1 -0.65 6 7
PRKCB -0.16 0.17 0.58 1 -0.62 8 9
VEGFR1 homodimer/PLGF homodimer -0.19 0.21 -10000 0 -0.55 18 18
VEGFA -0.25 0.31 -10000 0 -0.59 234 234
VEGFB 0.03 0.003 -10000 0 -10000 0 0
mol:IP3 -0.17 0.18 -10000 0 -0.7 6 6
RASA1 0.022 0.055 -10000 0 -0.7 1 1
NRP2 0.02 0.071 -10000 0 -0.59 7 7
VEGFR1 homodimer 0.021 0.061 -10000 0 -0.5 7 7
VEGFB homodimer 0.03 0.003 -10000 0 -10000 0 0
NCK1 0.027 0.03 -10000 0 -0.64 1 1
eNOS/Caveolin-1 -0.1 0.16 -10000 0 -0.53 25 25
PTPN11 0.029 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.14 0.19 -10000 0 -0.72 6 6
mol:L-citrulline -0.096 0.15 0.72 1 -0.52 10 11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.1 0.2 -10000 0 -0.68 5 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.12 0.2 -10000 0 -0.66 6 6
CD2AP 0.029 0.006 -10000 0 -10000 0 0
PI3K/GAB1 -0.13 0.19 -10000 0 -0.69 6 6
PDPK1 -0.13 0.18 0.35 1 -0.7 6 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.12 0.2 -10000 0 -0.66 5 5
mol:NADP -0.096 0.15 0.72 1 -0.52 10 11
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.1 0.19 -10000 0 -0.67 5 5
VEGFR1 homodimer/NRP2 0.03 0.069 -10000 0 -0.44 5 5
Signaling events mediated by PTP1B

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
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.062 0.13 -10000 0 -0.44 25 25
PTP1B/AKT1 -0.051 0.072 -10000 0 -0.33 5 5
FYN 0.028 0.008 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.065 0.075 0.37 1 -0.31 10 11
EGFR -0.011 0.066 -10000 0 -0.61 6 6
EGF/EGFR -0.3 0.13 -10000 0 -0.36 393 393
CSF1 0.028 0.029 -10000 0 -0.64 1 1
AKT1 0.028 0.008 -10000 0 -10000 0 0
INSR 0.03 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.067 0.09 -10000 0 -0.4 16 16
Insulin Receptor/Insulin -0.02 0.084 0.3 1 -10000 0 1
HCK -0.003 0.14 -10000 0 -0.59 27 27
CRK 0.029 0.005 -10000 0 -10000 0 0
TYK2 -0.059 0.073 0.34 1 -0.35 5 6
EGF -0.57 0.2 -10000 0 -0.63 474 474
YES1 0.029 0.005 -10000 0 -10000 0 0
CAV1 -0.14 0.11 0.32 5 -0.32 47 52
TXN 0.023 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.053 0.079 0.34 1 -0.4 6 7
cell migration 0.065 0.075 0.31 10 -0.37 1 11
STAT3 0.029 0.005 -10000 0 -10000 0 0
PRLR -0.052 0.21 -10000 0 -0.64 62 62
ITGA2B 0.006 0.12 -10000 0 -0.59 19 19
CSF1R 0.017 0.061 -10000 0 -0.59 5 5
Prolactin Receptor/Prolactin -0.029 0.16 -10000 0 -0.48 62 62
FGR 0.025 0.047 -10000 0 -0.59 3 3
PTP1B/p130 Cas -0.058 0.072 -10000 0 -0.34 6 6
Crk/p130 Cas -0.052 0.072 -10000 0 -0.36 3 3
DOK1 -0.026 0.081 0.3 4 -0.34 2 6
JAK2 -0.069 0.14 0.32 1 -0.42 42 43
Jak2/Leptin Receptor/Leptin -0.04 0.12 -10000 0 -0.54 4 4
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
PTPN1 -0.066 0.076 0.37 1 -0.32 10 11
LYN 0.028 0.007 -10000 0 -10000 0 0
CDH2 0.01 0.11 -10000 0 -0.62 16 16
SRC 0.002 0.046 0.34 1 -0.52 2 3
ITGB3 0.022 0.065 -10000 0 -0.64 5 5
CAT1/PTP1B -0.22 0.16 0.4 5 -0.45 74 79
CAPN1 0.028 0.003 -10000 0 -10000 0 0
CSK 0.03 0.003 -10000 0 -10000 0 0
PI3K 0.002 0.084 -10000 0 -0.56 1 1
mol:H2O2 -0.006 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.033 0.11 -10000 0 -0.53 4 4
negative regulation of transcription -0.067 0.14 0.32 1 -0.42 42 43
FCGR2A 0.001 0.13 -10000 0 -0.59 23 23
FER 0.017 0.042 -10000 0 -0.65 2 2
alphaIIb/beta3 Integrin 0.019 0.1 -10000 0 -0.46 23 23
BLK -0.013 0.15 -10000 0 -0.59 34 34
Insulin Receptor/Insulin/Shc 0.05 0.013 -10000 0 -10000 0 0
RHOA 0.02 0.013 -10000 0 -10000 0 0
LEPR 0.029 0.006 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
p210 bcr-abl/Grb2 0.029 0.005 -10000 0 -10000 0 0
mol:NADPH -0.006 0.003 -10000 0 -10000 0 0
TRPV6 -0.19 0.16 0.36 4 -0.43 102 106
PRL 0.002 0.022 -10000 0 -10000 0 0
SOCS3 0.025 0.12 -10000 0 -0.98 6 6
SPRY2 0.025 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.046 0.043 -10000 0 -0.42 4 4
CSF1/CSF1R -0.047 0.075 0.34 1 -0.4 6 7
Ras protein signal transduction 0.034 0.069 0.5 10 -10000 0 10
IRS1 0.023 0.058 -10000 0 -0.64 4 4
INS 0.006 0.019 -10000 0 -10000 0 0
LEP -0.039 0.17 -10000 0 -0.59 47 47
STAT5B -0.059 0.093 0.37 1 -0.35 22 23
STAT5A -0.059 0.093 0.37 1 -0.35 22 23
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.047 0.068 0.34 1 -0.37 3 4
CSN2 0.003 0.072 -10000 0 -0.62 1 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
LAT -0.056 0.11 -10000 0 -0.48 8 8
YBX1 0.033 0.008 -10000 0 -10000 0 0
LCK 0.003 0.12 -10000 0 -0.59 22 22
SHC1 0.029 0.007 -10000 0 -10000 0 0
NOX4 0.021 0.053 -10000 0 -0.56 4 4
Glucocorticoid receptor regulatory network

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
PCK2 0.037 0.089 -10000 0 -1.2 1 1
SMARCC2 0.031 0.005 -10000 0 -10000 0 0
SMARCC1 0.023 0.014 -10000 0 -10000 0 0
TBX21 -0.18 0.27 0.57 1 -0.55 173 174
SUMO2 0.024 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.035 0.037 -10000 0 -0.8 1 1
FKBP4 0.029 0.006 -10000 0 -10000 0 0
FKBP5 0.02 0.072 -10000 0 -0.6 7 7
GR alpha/HSP90/FKBP51/HSP90 0.065 0.1 0.39 3 -0.43 2 5
PRL -0.029 0.11 -10000 0 -0.62 5 5
cortisol/GR alpha (dimer)/TIF2 0.12 0.22 0.54 52 -0.43 2 54
RELA 0.01 0.081 -10000 0 -0.31 1 1
FGG -0.047 0.29 0.54 9 -0.51 80 89
GR beta/TIF2 0.049 0.12 0.36 7 -0.42 8 15
IFNG -0.29 0.29 -10000 0 -0.71 108 108
apoptosis -0.079 0.21 -10000 0 -0.6 26 26
CREB1 -0.003 0.1 -10000 0 -0.35 41 41
histone acetylation -0.002 0.1 0.31 3 -0.42 5 8
BGLAP -0.02 0.098 -10000 0 -0.63 2 2
GR/PKAc 0.074 0.094 0.38 3 -0.37 1 4
NF kappa B1 p50/RelA 0.016 0.15 -10000 0 -0.5 16 16
SMARCD1 0.031 0.005 -10000 0 -10000 0 0
MDM2 0.04 0.08 0.28 10 -10000 0 10
GATA3 -0.29 0.33 -10000 0 -0.63 258 258
AKT1 0.021 0.008 -10000 0 -10000 0 0
CSF2 -0.023 0.11 -10000 0 -0.66 4 4
GSK3B 0.023 0.012 -10000 0 -10000 0 0
NR1I3 -0.044 0.22 -10000 0 -0.73 15 15
CSN2 0.064 0.16 0.42 12 -0.38 1 13
BRG1/BAF155/BAF170/BAF60A 0.06 0.04 -10000 0 -10000 0 0
NFATC1 0.031 0.007 -10000 0 -10000 0 0
POU2F1 0.032 0.008 -10000 0 -10000 0 0
CDKN1A 0.033 0.059 0.85 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.041 0.2 -10000 0 -0.59 59 59
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.032 0.15 0.37 2 -0.4 14 16
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.018 0.24 -10000 0 -0.77 14 14
JUN -0.19 0.21 -10000 0 -0.57 77 77
IL4 -0.029 0.092 -10000 0 -0.53 1 1
CDK5R1 0.027 0.006 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.22 0.26 9 -0.52 95 104
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.075 0.1 0.4 2 -0.42 1 3
cortisol/GR alpha (monomer) 0.14 0.26 0.62 58 -0.48 1 59
NCOA2 0.015 0.091 -10000 0 -0.64 10 10
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.045 0.12 -10000 0 -0.69 12 12
AP-1/NFAT1-c-4 -0.26 0.27 -10000 0 -0.72 76 76
AFP -0.34 0.53 -10000 0 -1.3 109 109
SUV420H1 0.03 0.003 -10000 0 -10000 0 0
IRF1 0.067 0.11 0.48 5 -10000 0 5
TP53 0.051 0.018 -10000 0 -10000 0 0
PPP5C 0.03 0.003 -10000 0 -10000 0 0
KRT17 -0.22 0.34 -10000 0 -1 59 59
KRT14 -0.12 0.2 -10000 0 -0.6 47 47
TBP 0.036 0.014 -10000 0 -10000 0 0
CREBBP 0.053 0.058 -10000 0 -10000 0 0
HDAC1 0.027 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.011 -10000 0 -10000 0 0
AP-1 -0.26 0.27 -10000 0 -0.72 78 78
MAPK14 0.025 0.01 -10000 0 -10000 0 0
MAPK10 0.019 0.066 -10000 0 -0.64 5 5
MAPK11 0.022 0.04 -10000 0 -0.6 2 2
KRT5 -0.21 0.27 -10000 0 -0.71 76 76
interleukin-1 receptor activity 0 0.008 -10000 0 -10000 0 0
NCOA1 0.032 0.007 -10000 0 -10000 0 0
STAT1 0.035 0.038 -10000 0 -0.8 1 1
CGA -0.13 0.33 -10000 0 -1.1 50 50
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.079 0.12 0.47 12 -10000 0 12
MAPK3 0.025 0.01 -10000 0 -10000 0 0
MAPK1 0.026 0.009 -10000 0 -10000 0 0
ICAM1 -0.054 0.18 -10000 0 -0.64 25 25
NFKB1 0.009 0.088 -10000 0 -0.8 1 1
MAPK8 -0.12 0.16 -10000 0 -0.47 37 37
MAPK9 0.02 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.084 0.22 -10000 0 -0.63 26 26
BAX 0.036 0.033 -10000 0 -10000 0 0
POMC -0.051 0.14 0.49 1 -0.76 6 7
EP300 0.055 0.064 -10000 0 -0.53 1 1
cortisol/GR alpha (dimer)/p53 0.15 0.22 0.56 56 -10000 0 56
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.062 0.24 3 -10000 0 3
SGK1 0.075 0.089 -10000 0 -10000 0 0
IL13 -0.29 0.25 -10000 0 -0.71 84 84
IL6 -0.11 0.3 -10000 0 -0.86 58 58
PRKACG 0.02 0.006 -10000 0 -10000 0 0
IL5 -0.24 0.2 -10000 0 -0.65 37 37
IL2 -0.16 0.21 -10000 0 -0.7 25 25
CDK5 0.025 0.009 -10000 0 -10000 0 0
PRKACB 0.029 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
IL8 -0.075 0.24 -10000 0 -0.74 42 42
CDK5R1/CDK5 0.035 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.05 0.13 -10000 0 -0.54 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.21 0.54 48 -10000 0 48
SMARCA4 0.032 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.07 0.12 0.39 18 -10000 0 18
NF kappa B1 p50/RelA/Cbp 0.073 0.14 -10000 0 -0.67 2 2
JUN (dimer) -0.19 0.21 -10000 0 -0.57 77 77
YWHAH 0.03 0.004 -10000 0 -10000 0 0
VIPR1 -0.052 0.16 -10000 0 -0.77 15 15
NR3C1 0.065 0.15 0.46 20 -0.62 1 21
NR4A1 0.018 0.11 -10000 0 -0.62 15 15
TIF2/SUV420H1 0.032 0.071 -10000 0 -0.47 10 10
MAPKKK cascade -0.079 0.21 -10000 0 -0.6 26 26
cortisol/GR alpha (dimer)/Src-1 0.14 0.22 0.56 51 -0.51 1 52
PBX1 0.011 0.12 -10000 0 -0.63 16 16
POU1F1 0.021 0.011 -10000 0 -10000 0 0
SELE -0.096 0.32 -10000 0 -1.2 36 36
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.07 0.12 0.4 18 -10000 0 18
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.21 0.54 48 -10000 0 48
mol:cortisol 0.047 0.17 0.34 55 -0.29 26 81
MMP1 -0.17 0.32 -10000 0 -0.79 86 86
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.039 0.15 -9999 0 -0.43 44 44
FZD6 0.028 0.007 -9999 0 -10000 0 0
WNT6 0.005 0.12 -9999 0 -0.6 20 20
WNT4 -0.042 0.2 -9999 0 -0.62 57 57
FZD3 0.027 0.009 -9999 0 -10000 0 0
WNT5A 0.019 0.038 -9999 0 -0.43 3 3
WNT11 -0.018 0.17 -9999 0 -0.63 38 38
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.018 0.038 -10000 0 -0.47 3 3
MAP4K4 0.013 0.066 -10000 0 -0.5 2 2
BAG4 0.026 0.03 -10000 0 -0.64 1 1
PKC zeta/ceramide -0.1 0.084 -10000 0 -0.31 52 52
NFKBIA 0.028 0.007 -10000 0 -10000 0 0
BIRC3 -0.064 0.22 -10000 0 -0.59 79 79
BAX -0.036 0.036 -10000 0 -0.3 4 4
RIPK1 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.028 0.068 0.89 3 -10000 0 3
BAD -0.1 0.079 -10000 0 -0.3 49 49
SMPD1 0.022 0.054 0.28 9 -10000 0 9
RB1 -0.1 0.078 -10000 0 -0.3 48 48
FADD/Caspase 8 0.023 0.077 -10000 0 -0.48 3 3
MAP2K4 -0.08 0.076 -10000 0 -0.43 5 5
NSMAF 0.028 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.077 0.087 -10000 0 -0.32 29 29
EGF -0.57 0.2 -10000 0 -0.63 474 474
mol:ceramide -0.11 0.083 0.18 1 -0.3 57 58
MADD 0.03 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.018 0.023 -10000 0 -0.47 1 1
ASAH1 0.027 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.1 0.077 -10000 0 -0.3 48 48
cell proliferation -0.058 0.073 -10000 0 -0.4 8 8
BID -0.004 0.071 -10000 0 -0.54 4 4
MAP3K1 -0.092 0.073 -10000 0 -0.29 38 38
EIF2A -0.076 0.083 0.3 5 -0.6 3 8
TRADD 0.029 0.006 -10000 0 -10000 0 0
CRADD 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.077 0.073 -10000 0 -0.46 7 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.077 0.073 -10000 0 -0.46 7 7
Cathepsin D/ceramide -0.1 0.08 -10000 0 -0.3 49 49
FADD 0.014 0.066 -10000 0 -0.5 2 2
KSR1 -0.1 0.083 0.19 1 -0.31 52 53
MAPK8 -0.082 0.086 -10000 0 -0.41 15 15
PRKRA -0.099 0.08 -10000 0 -0.3 47 47
PDGFA 0.025 0.03 -10000 0 -0.64 1 1
TRAF2 0.029 0.005 -10000 0 -10000 0 0
IGF1 0.023 0.06 -10000 0 -0.59 5 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.083 0.18 1 -0.3 57 58
CTSD 0.029 0.029 -10000 0 -0.64 1 1
regulation of nitric oxide biosynthetic process 0.043 0.023 -10000 0 -0.47 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.061 0.079 -10000 0 -0.44 8 8
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
PRKCZ 0.025 0.05 -10000 0 -0.64 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.018 0.023 -10000 0 -0.47 1 1
RelA/NF kappa B1 0.043 0.023 -10000 0 -0.47 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.029 -10000 0 -0.64 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.071 -10000 0 -0.53 2 2
TNFR1A/BAG4/TNF-alpha 0.045 0.061 -10000 0 -0.39 9 9
mol:Sphingosine-1-phosphate 0.018 0.038 -10000 0 -0.47 3 3
MAP2K1 -0.083 0.076 -10000 0 -0.48 7 7
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.03 0.003 -10000 0 -10000 0 0
CYCS -0.055 0.035 -10000 0 -0.31 4 4
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
TNFR1A/BAG4 0.039 0.026 -10000 0 -0.47 1 1
EIF2AK2 -0.087 0.088 0.27 6 -0.29 39 45
TNF-alpha/TNFR1A/FAN 0.047 0.057 -10000 0 -0.39 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.072 -10000 0 -0.42 6 6
MAP2K2 -0.084 0.074 -10000 0 -0.46 7 7
SMPD3 0.017 0.054 0.21 2 -0.41 2 4
TNF 0.019 0.079 -10000 0 -0.61 8 8
PKC zeta/PAR4 0.037 0.046 -10000 0 -0.47 4 4
mol:PHOSPHOCHOLINE 0.21 0.087 0.24 423 -10000 0 423
NF kappa B1/RelA/I kappa B alpha 0.075 0.046 -10000 0 -10000 0 0
AIFM1 -0.062 0.049 -10000 0 -0.35 4 4
BCL2 0.029 0.005 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.17 0.21 0.49 1 -0.67 47 48
RAD9A 0.03 0.003 -10000 0 -10000 0 0
AP1 0.027 0.077 -10000 0 -0.47 12 12
IFNAR2 0.028 0.009 -10000 0 -10000 0 0
AKT1 0.013 0.051 -10000 0 -0.53 1 1
ER alpha/Oestrogen 0.016 0.044 -10000 0 -0.42 5 5
NFX1/SIN3/HDAC complex 0.029 0.068 -10000 0 -0.38 6 6
EGF -0.57 0.2 -10000 0 -0.63 474 474
SMG5 0.029 0.007 -10000 0 -10000 0 0
SMG6 0.029 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.018 -10000 0 -10000 0 0
TERT/c-Abl -0.16 0.2 -10000 0 -0.64 44 44
SAP18 0.029 0.005 -10000 0 -10000 0 0
MRN complex 0.044 0.027 -10000 0 -10000 0 0
WT1 -0.28 0.33 -10000 0 -0.64 241 241
WRN 0.027 0.009 -10000 0 -10000 0 0
SP1 0.026 0.014 -10000 0 -10000 0 0
SP3 0.028 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.19 -10000 0 -0.62 28 28
Mad/Max 0.039 0.015 -10000 0 -10000 0 0
TERT -0.18 0.22 0.5 1 -0.7 45 46
CCND1 -0.16 0.21 0.65 1 -0.7 30 31
MAX 0.027 0.008 -10000 0 -10000 0 0
RBBP7 0.029 0.003 -10000 0 -10000 0 0
RBBP4 0.027 0.03 -10000 0 -0.64 1 1
TERF2 0.026 0.007 -10000 0 -10000 0 0
PTGES3 0.029 0.005 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
Telomerase/911 0.028 0.043 -10000 0 -10000 0 0
CDKN1B -0.12 0.18 -10000 0 -0.67 1 1
RAD1 0.027 0.009 -10000 0 -10000 0 0
XRCC5 0.028 0.007 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
SAP30 0.008 0.11 -10000 0 -0.59 18 18
TRF2/PARP2 0.039 0.013 -10000 0 -10000 0 0
UBE3A 0.029 0.004 -10000 0 -10000 0 0
JUN 0.028 0.007 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.009 -10000 0 -10000 0 0
FOS 0.012 0.099 -10000 0 -0.63 12 12
IFN-gamma/IRF1 -0.15 0.22 -10000 0 -0.42 190 190
PARP2 0.028 0.007 -10000 0 -10000 0 0
BLM 0.017 0.089 -10000 0 -0.59 11 11
Telomerase -0.021 0.12 -10000 0 -0.63 3 3
IRF1 0.025 0.03 -10000 0 -0.58 1 1
ESR1 0.022 0.059 -10000 0 -0.56 5 5
KU/TER 0.042 0.011 -10000 0 -10000 0 0
ATM/TRF2 0.042 0.023 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.04 0.056 -10000 0 -0.39 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.04 0.057 -10000 0 -0.4 2 2
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.025 0.014 -10000 0 -10000 0 0
ATM 0.01 0.022 -10000 0 -0.46 1 1
SMAD3 0.02 0.04 -10000 0 -0.43 4 4
ABL1 0.029 0.005 -10000 0 -10000 0 0
MXD1 0.029 0.006 -10000 0 -10000 0 0
MRE11A 0.03 0.004 -10000 0 -10000 0 0
HUS1 0.027 0.009 -10000 0 -10000 0 0
RPS6KB1 0.029 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.2 -10000 0 -0.69 24 24
NR2F2 0.031 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.063 -10000 0 -0.44 10 10
MAPK1 0.007 0.063 -10000 0 -0.44 10 10
TGFB1/TGF beta receptor Type II 0.025 0.054 -10000 0 -0.59 4 4
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
HNRNPC 0.028 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.022 -10000 0 -0.46 1 1
NBN 0.028 0.007 -10000 0 -10000 0 0
EGFR 0.02 0.067 -10000 0 -0.6 6 6
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.41 0.16 -10000 0 -0.48 425 425
MYC 0.006 0.12 -10000 0 -0.59 19 19
IL2 0.008 0.086 -10000 0 -0.59 10 10
KU 0.042 0.011 -10000 0 -10000 0 0
RAD50 0.023 0.013 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
TGFB1 0.025 0.054 -10000 0 -0.59 4 4
TRF2/BLM 0.032 0.065 -10000 0 -0.41 11 11
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.15 0.2 -10000 0 -0.66 38 38
SP1/HDAC2 0.035 0.025 -10000 0 -10000 0 0
PINX1 0.027 0.009 -10000 0 -10000 0 0
Telomerase/EST1A -0.14 0.19 -10000 0 -0.62 30 30
Smad3/Myc 0.02 0.086 -10000 0 -0.38 22 22
911 complex 0.051 0.023 -10000 0 -10000 0 0
IFNG -0.24 0.3 -10000 0 -0.58 232 232
Telomerase/PinX1 -0.14 0.19 -10000 0 -0.62 30 30
Telomerase/AKT1/mTOR/p70S6K -0.019 0.096 -10000 0 -0.48 4 4
SIN3B 0.03 0.003 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Telomerase/EST1B -0.14 0.19 -10000 0 -0.61 30 30
response to DNA damage stimulus 0.006 0.012 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.062 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.038 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.19 -10000 0 -0.62 28 28
E2F1 -0.036 0.19 -10000 0 -0.59 54 54
ZNFX1 0.029 0.006 -10000 0 -10000 0 0
PIF1 -0.08 0.24 -10000 0 -0.59 93 93
NCL 0.028 0.007 -10000 0 -10000 0 0
DKC1 0.03 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.07 0.26 -10000 0 -0.89 29 29
NCK1/PAK1/Dok-R -0.063 0.1 -10000 0 -0.41 27 27
NCK1/Dok-R 0.006 0.27 -10000 0 -1 30 30
PIK3CA 0.026 0.03 -10000 0 -0.63 1 1
mol:beta2-estradiol -0.003 0.035 0.27 8 -10000 0 8
RELA 0.03 0.003 -10000 0 -10000 0 0
SHC1 0.028 0.007 -10000 0 -10000 0 0
Rac/GDP 0.02 0.007 -10000 0 -10000 0 0
F2 -0.2 0.3 0.27 3 -0.58 195 198
TNIP2 0.03 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.046 0.26 -10000 0 -0.95 30 30
FN1 -0.017 0.16 -10000 0 -0.6 38 38
PLD2 0.004 0.28 -10000 0 -1.1 30 30
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GRB14 -0.005 0.15 -10000 0 -0.64 27 27
ELK1 0.02 0.25 -10000 0 -0.93 30 30
GRB7 0.02 0.076 -10000 0 -0.64 7 7
PAK1 0.03 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.002 0.29 -10000 0 -1 29 29
CDKN1A -0.077 0.24 -10000 0 -0.63 25 25
ITGA5 -0.012 0.15 -10000 0 -0.59 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.001 0.27 -10000 0 -1 30 30
CRK 0.029 0.005 -10000 0 -10000 0 0
mol:NO -0.028 0.22 0.44 5 -0.63 29 34
PLG -0.16 0.31 -10000 0 -1.2 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.045 0.23 -10000 0 -0.82 29 29
GRB2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.64 1 1
ANGPT2 -0.13 0.27 -10000 0 -0.65 31 31
BMX -0.042 0.29 -10000 0 -1.1 30 30
ANGPT1 0.045 0.17 -10000 0 -1.2 8 8
tube development -0.096 0.25 -10000 0 -0.7 28 28
ANGPT4 0.003 0.11 -10000 0 -0.6 16 16
response to hypoxia -0.005 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.004 0.3 -10000 0 -1.1 30 30
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 35 35
FGF2 0.028 0.065 -10000 0 -0.62 5 5
STAT5A (dimer) -0.097 0.28 -10000 0 -0.79 28 28
mol:L-citrulline -0.028 0.22 0.44 5 -0.63 29 34
AGTR1 -0.023 0.14 -10000 0 -0.63 25 25
MAPK14 -0.029 0.3 -10000 0 -1.1 32 32
Tie2/SHP2 -0.002 0.26 -10000 0 -1.1 28 28
TEK -0.007 0.29 -10000 0 -1.2 28 28
RPS6KB1 -0.042 0.25 -10000 0 -0.83 30 30
Angiotensin II/AT1 -0.026 0.1 -10000 0 -0.47 25 25
Tie2/Ang1/GRB2 0.015 0.29 -10000 0 -1.1 30 30
MAPK3 0.01 0.25 -10000 0 -0.95 30 30
MAPK1 0.008 0.25 -10000 0 -0.96 30 30
Tie2/Ang1/GRB7 0.011 0.29 -10000 0 -1.1 30 30
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
MAPK8 0.002 0.28 -10000 0 -1.1 30 30
PI3K -0.061 0.28 -10000 0 -1 30 30
FES -0.024 0.29 -10000 0 -1.1 31 31
Crk/Dok-R 0.009 0.28 -10000 0 -1 29 29
Tie2/Ang1/ABIN2 0.014 0.29 -10000 0 -1.1 30 30
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.059 0.24 0.44 1 -0.78 30 31
STAT5A 0.03 0.005 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.039 0.25 0.51 1 -0.84 29 30
Tie2/Ang2 -0.13 0.31 -10000 0 -0.98 28 28
Tie2/Ang1 0.001 0.3 -10000 0 -1.2 30 30
FOXO1 -0.079 0.25 -10000 0 -0.8 28 28
ELF1 0.031 0.042 -10000 0 -0.63 1 1
ELF2 0.003 0.28 -10000 0 -1.1 30 30
mol:Choline 0.007 0.26 -10000 0 -1 30 30
cell migration -0.043 0.064 -10000 0 -0.25 9 9
FYN -0.11 0.27 -10000 0 -0.81 28 28
DOK2 -0.01 0.15 -10000 0 -0.59 31 31
negative regulation of cell cycle -0.068 0.22 -10000 0 -0.56 30 30
ETS1 0.035 0.04 -10000 0 -0.29 5 5
PXN -0.022 0.22 0.5 7 -0.69 28 35
ITGB1 0.029 0.004 -10000 0 -10000 0 0
NOS3 -0.038 0.23 0.52 2 -0.72 29 31
RAC1 0.027 0.009 -10000 0 -10000 0 0
TNF 0.02 0.088 -10000 0 -0.58 9 9
MAPKKK cascade 0.007 0.26 -10000 0 -1 30 30
RASA1 0.025 0.03 -10000 0 -0.64 1 1
Tie2/Ang1/Shc 0.007 0.28 -10000 0 -1.1 30 30
NCK1 0.027 0.03 -10000 0 -0.64 1 1
vasculogenesis -0.022 0.2 0.41 8 -0.56 29 37
mol:Phosphatidic acid 0.007 0.26 -10000 0 -1 30 30
mol:Angiotensin II -0.011 0.015 -10000 0 -10000 0 0
mol:NADP -0.028 0.22 0.44 5 -0.63 29 34
Rac1/GTP -0.041 0.22 -10000 0 -0.78 29 29
MMP2 -0.001 0.28 -10000 0 -1.1 30 30
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.56 0.64 -10000 0 -1.2 245 245
PLK1 -0.13 0.24 0.48 1 -0.7 24 25
CDKN1B -0.01 0.15 0.54 1 -0.38 1 2
FOXO3 -0.068 0.18 -10000 0 -0.59 17 17
KAT2B 0.013 0.039 -10000 0 -0.67 1 1
FOXO1/SIRT1 -0.13 0.22 -10000 0 -0.38 215 215
CAT -0.082 0.19 0.48 1 -1 4 5
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
AKT1 -0.01 0.05 -10000 0 -10000 0 0
FOXO1 -0.17 0.23 0.3 1 -0.42 226 227
MAPK10 0.037 0.069 0.34 3 -0.36 4 7
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.094 0.086 0.38 14 -10000 0 14
response to oxidative stress -0.028 0.042 -10000 0 -0.29 1 1
FOXO3A/SIRT1 -0.022 0.19 -10000 0 -0.59 12 12
XPO1 0.03 0.005 -10000 0 -10000 0 0
EP300 -0.011 0.055 -10000 0 -0.48 2 2
BCL2L11 0.005 0.084 -10000 0 -0.72 6 6
FOXO1/SKP2 -0.14 0.21 -10000 0 -0.39 196 196
mol:GDP -0.028 0.042 -10000 0 -0.29 1 1
RAN 0.031 0.006 -10000 0 -10000 0 0
GADD45A 0.059 0.16 -10000 0 -0.63 14 14
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.031 0.11 -10000 0 -0.55 8 8
MST1 0.004 0.082 -10000 0 -0.62 8 8
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.03 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.027 0.11 -10000 0 -0.61 7 7
YWHAB 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.039 0.063 0.34 2 -0.37 2 4
MAPK9 0.025 0.048 0.35 2 -10000 0 2
YWHAG 0.027 0.009 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
SIRT1 0.044 0.018 -10000 0 -10000 0 0
SOD2 -0.05 0.18 0.47 1 -0.54 14 15
RBL2 -0.021 0.16 -10000 0 -0.91 7 7
RAL/GDP 0.018 0.034 -10000 0 -10000 0 0
CHUK 0.021 0.026 -10000 0 -10000 0 0
Ran/GTP 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.028 0.029 -10000 0 -0.64 1 1
RAL/GTP 0.028 0.032 -10000 0 -10000 0 0
CSNK1G1 0.03 0.003 -10000 0 -10000 0 0
FASLG -0.22 0.24 -10000 0 -0.67 9 9
SKP2 0.027 0.009 -10000 0 -10000 0 0
USP7 0.03 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.026 -10000 0 -10000 0 0
CCNB1 -0.069 0.19 -10000 0 -0.73 10 10
FOXO1-3a-4/beta catenin -0.039 0.14 0.4 4 -0.43 1 5
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -10000 0 -0.38 196 196
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
SGK1 0.02 0.026 -10000 0 -10000 0 0
CSNK1G3 0.023 0.012 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.012 -10000 0 -10000 0 0
ZFAND5 0.095 0.085 0.45 9 -10000 0 9
SFN -0.041 0.2 -10000 0 -0.59 59 59
CDK2 -0.02 0.059 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.007 0.11 -10000 0 -0.53 12 12
CREBBP -0.018 0.057 -10000 0 -10000 0 0
FBXO32 -0.076 0.18 0.48 1 -0.69 6 7
BCL6 -0.026 0.17 -10000 0 -0.8 8 8
RALB 0.031 0.005 -10000 0 -10000 0 0
RALA 0.028 0.01 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.03 -10000 0 -0.64 1 1
Caspase 8 (4 units) -0.062 0.11 -10000 0 -0.38 1 1
NEF -0.056 0.076 -10000 0 -0.46 5 5
NFKBIA 0.013 0.046 -10000 0 -10000 0 0
BIRC3 -0.05 0.21 -10000 0 -0.55 79 79
CYCS -0.073 0.11 -10000 0 -0.4 2 2
RIPK1 0.029 0.006 -10000 0 -10000 0 0
CD247 -0.25 0.34 -10000 0 -0.73 169 169
MAP2K7 -0.044 0.14 0.38 2 -0.6 14 16
protein ubiquitination 0.032 0.099 0.4 8 -0.55 3 11
CRADD 0.029 0.005 -10000 0 -10000 0 0
DAXX 0.029 0.006 -10000 0 -10000 0 0
FAS 0.029 0.006 -10000 0 -10000 0 0
BID -0.083 0.12 -10000 0 -0.36 2 2
NF-kappa-B/RelA/I kappa B alpha 0.014 0.12 -10000 0 -0.47 2 2
TRADD 0.029 0.006 -10000 0 -10000 0 0
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
CFLAR 0.029 0.006 -10000 0 -10000 0 0
FADD 0.03 0.003 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.014 0.12 -10000 0 -0.47 2 2
MAPK8 -0.038 0.13 0.43 3 -0.59 11 14
APAF1 0.029 0.005 -10000 0 -10000 0 0
TRAF1 0.028 0.028 -10000 0 -0.59 1 1
TRAF2 0.029 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.09 0.12 -10000 0 -0.32 8 8
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.096 -10000 0 -0.65 4 4
CHUK 0.031 0.093 0.3 6 -0.62 3 9
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.078 0.03 -10000 0 -10000 0 0
TCRz/NEF -0.26 0.31 -10000 0 -0.52 279 279
TNF 0.019 0.079 -10000 0 -0.61 8 8
FASLG -0.36 0.4 -10000 0 -0.72 276 276
NFKB1 0.012 0.055 -10000 0 -0.63 1 1
TNFR1A/BAG4/TNF-alpha 0.045 0.061 -10000 0 -0.39 9 9
CASP6 -0.022 0.12 -10000 0 -0.56 11 11
CASP7 -0.065 0.16 0.38 1 -0.48 3 4
RELA 0.013 0.048 -10000 0 -10000 0 0
CASP2 0.027 0.009 -10000 0 -10000 0 0
CASP3 -0.062 0.16 0.38 1 -0.48 4 5
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.026 -10000 0 -0.47 1 1
CASP8 0.029 0.006 -10000 0 -10000 0 0
CASP9 0.029 0.006 -10000 0 -10000 0 0
MAP3K14 0.022 0.096 -10000 0 -0.72 3 3
APAF-1/Caspase 9 -0.088 0.16 -10000 0 -0.45 47 47
BCL2 -0.031 0.13 0.47 3 -0.55 10 13
Visual signal transduction: Rods

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
mol:K + 0.03 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.005 0.06 -10000 0 -0.47 8 8
Metarhodopsin II/Arrestin 0.016 0.069 -10000 0 -0.38 15 15
PDE6G/GNAT1/GTP 0.014 0.069 -10000 0 -0.4 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.006 0.081 -10000 0 -0.63 8 8
GRK1 0.02 0.006 -10000 0 -10000 0 0
CNG Channel -0.046 0.16 -10000 0 -0.7 7 7
mol:Na + -0.047 0.18 -10000 0 -0.56 21 21
mol:ADP 0.02 0.006 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.028 0.11 -10000 0 -0.39 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.041 0.19 -10000 0 -0.58 21 21
CNGB1 0.014 0.08 -10000 0 -0.59 9 9
RDH5 0.021 0.073 -10000 0 -0.6 7 7
SAG 0.017 0.027 -10000 0 -0.59 1 1
mol:Ca2+ -0.068 0.16 0.38 3 -0.56 19 22
Na + (4 Units) -0.047 0.16 -10000 0 -0.54 19 19
RGS9 0.013 0.1 -10000 0 -0.58 14 14
GNB1/GNGT1 -0.1 0.21 -10000 0 -0.43 154 154
GNAT1/GDP 0.014 0.11 -10000 0 -0.36 34 34
GUCY2D -0.004 0.13 -10000 0 -0.59 26 26
GNGT1 -0.16 0.28 -10000 0 -0.59 154 154
GUCY2F 0.019 0.004 -10000 0 -10000 0 0
GNB5 0.03 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0.002 0.093 -10000 0 -0.48 10 10
mol:11-cis-retinal 0.021 0.073 -10000 0 -0.6 7 7
mol:cGMP 0.016 0.11 -10000 0 -0.38 14 14
GNB1 0.029 0.006 -10000 0 -10000 0 0
Rhodopsin 0.018 0.096 -10000 0 -0.44 22 22
SLC24A1 0.03 0.003 -10000 0 -10000 0 0
CNGA1 -0.093 0.26 -10000 0 -0.63 98 98
Metarhodopsin II 0.016 0.063 -10000 0 -0.35 15 15
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.025 0.11 -10000 0 -0.36 39 39
RGS9BP 0 0.14 -10000 0 -0.64 23 23
Metarhodopsin II/Transducin -0.063 0.13 -10000 0 -0.37 50 50
GCAP Family/Ca ++ 0.03 0.071 -10000 0 -0.37 15 15
PDE6A/B 0.016 0.092 -10000 0 -0.47 17 17
mol:Pi 0.027 0.11 -10000 0 -0.39 34 34
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.082 0.18 -10000 0 -0.34 157 157
PDE6B 0.023 0.065 -10000 0 -0.64 5 5
PDE6A 0.006 0.096 -10000 0 -0.59 13 13
PDE6G 0.023 0.064 -10000 0 -0.63 5 5
RHO 0.006 0.1 -10000 0 -0.59 15 15
PDE6 0.027 0.13 -10000 0 -0.64 5 5
GUCA1A 0.011 0.08 -10000 0 -0.59 9 9
GC2/GCAP Family 0.04 0.075 -10000 0 -0.37 15 15
GUCA1C 0.016 0.041 -10000 0 -0.64 2 2
GUCA1B 0.023 0.06 -10000 0 -0.59 5 5
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.11 0.18 -10000 0 -0.62 21 21
CRKL 0.006 0.11 -10000 0 -0.48 20 20
HRAS -0.013 0.14 -10000 0 -0.53 10 10
mol:PIP3 0.011 0.12 -10000 0 -0.45 20 20
SPRED1 0.03 0.003 -10000 0 -10000 0 0
SPRED2 0.028 0.029 -10000 0 -0.64 1 1
GAB1 0.004 0.12 -10000 0 -0.49 24 24
FOXO3 0.012 0.14 0.46 1 -0.62 12 13
AKT1 0.009 0.16 -10000 0 -0.55 22 22
BAD 0.013 0.15 0.46 1 -0.63 12 13
megakaryocyte differentiation -0.055 0.18 -10000 0 -0.46 57 57
GSK3B 0.015 0.15 0.42 1 -0.62 12 13
RAF1 -0.02 0.11 0.31 2 -0.43 8 10
SHC1 0.029 0.007 -10000 0 -10000 0 0
STAT3 0.003 0.12 -10000 0 -0.49 23 23
STAT1 -0.016 0.25 -10000 0 -1.1 24 24
HRAS/SPRED1 0.003 0.12 -10000 0 -0.42 10 10
cell proliferation 0.002 0.13 -10000 0 -0.5 25 25
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
TEC 0.029 0.004 -10000 0 -10000 0 0
RPS6KB1 0.01 0.14 -10000 0 -0.49 27 27
HRAS/SPRED2 0.002 0.12 -10000 0 -0.42 11 11
LYN/TEC/p62DOK 0.042 0.12 -10000 0 -0.52 12 12
MAPK3 0.012 0.099 0.31 9 -0.34 3 12
STAP1 -0.25 0.19 -10000 0 -0.41 157 157
GRAP2 -0.012 0.16 -10000 0 -0.59 35 35
JAK2 -0.016 0.23 -10000 0 -0.98 24 24
STAT1 (dimer) -0.013 0.24 -10000 0 -1 24 24
mol:Gleevec -0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.038 0.18 -10000 0 -0.55 21 21
actin filament polymerization -0.001 0.12 -10000 0 -0.5 21 21
LYN 0.028 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.22 0.21 -10000 0 -0.77 32 32
PIK3R1 0.026 0.03 -10000 0 -0.63 1 1
CBL/CRKL/GRB2 0.036 0.11 -10000 0 -0.54 7 7
PI3K 0.031 0.13 -10000 0 -0.51 18 18
PTEN 0.029 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.062 0.29 -10000 0 -1.2 24 24
MAPK8 0.001 0.13 -10000 0 -0.51 25 25
STAT3 (dimer) 0.003 0.12 -10000 0 -0.48 23 23
positive regulation of transcription 0.015 0.088 0.3 10 -0.27 3 13
mol:GDP -0.03 0.16 -10000 0 -0.51 18 18
PIK3C2B 0.003 0.12 -10000 0 -0.48 24 24
CBL/CRKL 0.022 0.11 -10000 0 -0.46 17 17
FER -0.003 0.12 -10000 0 -0.49 23 23
SH2B3 0.004 0.12 -10000 0 -0.49 23 23
PDPK1 0.02 0.12 0.34 6 -0.43 16 22
SNAI2 0.002 0.12 -10000 0 -0.5 23 23
positive regulation of cell proliferation 0.007 0.19 -10000 0 -0.79 24 24
KITLG 0.017 0.095 -10000 0 -0.65 10 10
cell motility 0.007 0.19 -10000 0 -0.79 24 24
PTPN6 0.027 0.008 -10000 0 -10000 0 0
EPOR 0.041 0.096 -10000 0 -1.1 2 2
STAT5A (dimer) 0.019 0.17 -10000 0 -0.62 27 27
SOCS1 0.022 0.066 -10000 0 -0.59 6 6
cell migration 0.028 0.16 0.51 30 -10000 0 30
SOS1 0.029 0.005 -10000 0 -10000 0 0
EPO -0.17 0.28 -10000 0 -0.58 168 168
VAV1 -0.12 0.26 -10000 0 -0.59 123 123
GRB10 0.001 0.12 -10000 0 -0.49 22 22
PTPN11 0.028 0.007 -10000 0 -10000 0 0
SCF/KIT 0.003 0.13 -10000 0 -0.51 26 26
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.012 0.093 0.31 3 -0.39 3 6
CBL 0.028 0.029 -10000 0 -0.64 1 1
KIT -0.01 0.29 -10000 0 -1.3 24 24
MAP2K2 -0.012 0.094 0.35 3 -0.39 3 6
SHC/Grb2/SOS1 0.043 0.12 -10000 0 -0.48 16 16
STAT5A 0.019 0.17 -10000 0 -0.65 27 27
GRB2 0.029 0.005 -10000 0 -10000 0 0
response to radiation 0.003 0.12 0.28 1 -0.49 23 24
SHC/GRAP2 0.01 0.12 -10000 0 -0.43 34 34
PTPRO -0.057 0.18 -10000 0 -0.47 57 57
SH2B2 -0.002 0.12 -10000 0 -0.52 21 21
DOK1 0.029 0.005 -10000 0 -10000 0 0
MATK -0.029 0.16 -10000 0 -0.53 30 30
CREBBP 0.046 0.032 -10000 0 -10000 0 0
BCL2 0.041 0.097 -10000 0 -0.88 2 2
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.023 0.063 -9999 0 -0.62 5 5
GNB1/GNG2 -0.025 0.15 -9999 0 -0.47 22 22
mol:DAG -0.032 0.13 -9999 0 -0.44 19 19
PLCG1 -0.033 0.13 -9999 0 -0.46 19 19
YES1 -0.037 0.14 -9999 0 -0.41 42 42
FZD3 0.027 0.009 -9999 0 -10000 0 0
FZD6 0.028 0.007 -9999 0 -10000 0 0
G protein -0.022 0.14 -9999 0 -0.46 19 19
MAP3K7 -0.089 0.17 -9999 0 -0.5 33 33
mol:Ca2+ -0.031 0.13 -9999 0 -0.43 19 19
mol:IP3 -0.032 0.13 -9999 0 -0.44 19 19
NLK -0.001 0.089 -9999 0 -0.81 6 6
GNB1 0.029 0.006 -9999 0 -10000 0 0
CAMK2A -0.098 0.18 -9999 0 -0.5 46 46
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.039 0.15 -9999 0 -0.43 44 44
CSNK1A1 0.023 0.013 -9999 0 -10000 0 0
GNAS -0.037 0.14 -9999 0 -0.41 43 43
GO:0007205 -0.036 0.12 -9999 0 -0.43 21 21
WNT6 0.005 0.12 -9999 0 -0.6 20 20
WNT4 -0.042 0.2 -9999 0 -0.62 57 57
NFAT1/CK1 alpha -0.015 0.13 -9999 0 -0.46 12 12
GNG2 0.028 0.008 -9999 0 -10000 0 0
WNT5A 0.019 0.038 -9999 0 -0.43 3 3
WNT11 -0.018 0.17 -9999 0 -0.63 38 38
CDC42 -0.033 0.13 -9999 0 -0.46 22 22
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.007 0.1 -10000 0 -0.37 34 34
EPHB2 0.019 0.076 -10000 0 -0.5 10 10
Syndecan-2/TACI -0.005 0.12 -10000 0 -0.36 51 51
LAMA1 0.013 0.098 -10000 0 -0.56 14 14
Syndecan-2/alpha2 ITGB1 0.054 0.055 -10000 0 -0.34 1 1
HRAS 0.029 0.027 -10000 0 -0.59 1 1
Syndecan-2/CASK 0.015 0.004 -10000 0 -10000 0 0
ITGA5 -0.012 0.15 -10000 0 -0.59 35 35
BAX 0.021 0.024 -10000 0 -10000 0 0
EPB41 0.029 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.032 0.009 -10000 0 -10000 0 0
LAMA3 0.022 0.066 -10000 0 -0.59 6 6
EZR 0.028 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.02 0.067 -10000 0 -0.6 6 6
Syndecan-2/MMP2 0.03 0.042 -10000 0 -0.37 5 5
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.036 0.048 -10000 0 -0.47 4 4
dendrite morphogenesis 0.029 0.044 -10000 0 -0.4 4 4
Syndecan-2/GM-CSF 0.014 0.063 -10000 0 -0.36 13 13
determination of left/right symmetry 0.02 0.005 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.025 0.024 -10000 0 -0.36 1 1
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
MAPK3 0.012 0.06 -10000 0 -0.33 13 13
MAPK1 0.013 0.061 -10000 0 -0.33 13 13
Syndecan-2/RACK1 0.037 0.028 -10000 0 -0.31 1 1
NF1 0.029 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.02 0.005 -10000 0 -10000 0 0
ITGA2 0.022 0.06 -10000 0 -0.57 5 5
MAPK8 0.023 0.027 -10000 0 -0.39 2 2
Syndecan-2/alpha2/beta1 Integrin 0.049 0.069 -10000 0 -10000 0 0
Syndecan-2/Kininogen -0.28 0.19 -10000 0 -0.4 361 361
ITGB1 0.029 0.004 -10000 0 -10000 0 0
SRC 0.063 0.066 0.35 1 -10000 0 1
Syndecan-2/CASK/Protein 4.1 0.031 0.01 -10000 0 -10000 0 0
extracellular matrix organization 0.032 0.036 -10000 0 -0.36 4 4
actin cytoskeleton reorganization 0.007 0.1 -10000 0 -0.37 34 34
Syndecan-2/Caveolin-2/Ras 0.042 0.046 -10000 0 -0.36 1 1
Syndecan-2/Laminin alpha3 0.031 0.041 -10000 0 -0.36 5 5
Syndecan-2/RasGAP 0.046 0.042 -10000 0 -0.62 1 1
alpha5/beta1 Integrin 0.011 0.12 -10000 0 -0.43 35 35
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
Syndecan-2 dimer 0.029 0.045 -10000 0 -0.4 4 4
GO:0007205 0.004 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.06 0.059 -10000 0 -0.6 1 1
RHOA 0.021 0.014 -10000 0 -10000 0 0
SDCBP 0.028 0.007 -10000 0 -10000 0 0
TNFRSF13B -0.034 0.18 -10000 0 -0.59 52 52
RASA1 0.025 0.03 -10000 0 -0.64 1 1
alpha2/beta1 Integrin 0.036 0.048 -10000 0 -0.47 4 4
Syndecan-2/Synbindin 0.035 0.009 -10000 0 -10000 0 0
TGFB1 0.025 0.054 -10000 0 -0.59 4 4
CASP3 0.025 0.034 -10000 0 -0.33 1 1
FN1 -0.017 0.16 -10000 0 -0.6 38 38
Syndecan-2/IL8 0.009 0.099 -10000 0 -0.38 32 32
SDC2 0.02 0.005 -10000 0 -10000 0 0
KNG1 -0.45 0.29 -10000 0 -0.63 380 380
Syndecan-2/Neurofibromin 0.035 0.01 -10000 0 -10000 0 0
TRAPPC4 0.03 0.003 -10000 0 -10000 0 0
CSF2 0.002 0.099 -10000 0 -0.59 14 14
Syndecan-2/TGFB1 0.032 0.036 -10000 0 -0.36 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.032 0.009 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.037 0.026 -10000 0 -10000 0 0
PRKACA 0.034 0.03 -10000 0 -10000 0 0
angiogenesis 0.009 0.099 -10000 0 -0.37 32 32
MMP2 0.022 0.067 -10000 0 -0.6 6 6
IL8 -0.011 0.16 -10000 0 -0.6 34 34
calcineurin-NFAT signaling pathway -0.005 0.12 -10000 0 -0.36 51 51
EPO signaling pathway

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
BCL2L1 0.02 0.11 0.46 3 -10000 0 3
CRKL -0.031 0.16 0.38 14 -10000 0 14
mol:DAG -0.025 0.12 -10000 0 -10000 0 0
HRAS -0.009 0.16 0.44 14 -0.46 1 15
MAPK8 -0.061 0.17 0.36 1 -0.52 2 3
RAP1A -0.032 0.16 0.38 15 -10000 0 15
GAB1 -0.032 0.16 0.36 13 -10000 0 13
MAPK14 -0.059 0.17 0.36 1 -10000 0 1
EPO -0.17 0.29 -10000 0 -0.58 168 168
PLCG1 -0.025 0.12 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.016 0.032 -10000 0 -10000 0 0
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.076 0.19 -10000 0 -0.35 167 167
GAB1/SHC/GRB2/SOS1 -0.013 0.15 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.11 0.22 -10000 0 -0.43 168 168
IRS2 -0.037 0.16 0.37 13 -0.47 2 15
STAT1 -0.017 0.13 -10000 0 -10000 0 0
STAT5B -0.022 0.12 -10000 0 -10000 0 0
cell proliferation -0.054 0.17 0.38 6 -0.62 1 7
GAB1/SHIP/PIK3R1/SHP2/SHC -0.034 0.12 -10000 0 -0.47 1 1
TEC -0.032 0.16 0.36 13 -10000 0 13
SOCS3 0.024 0.054 -10000 0 -0.59 4 4
STAT1 (dimer) -0.016 0.12 -10000 0 -10000 0 0
JAK2 0.014 0.031 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
EPO/EPOR (dimer)/JAK2 -0.026 0.17 -10000 0 -10000 0 0
EPO/EPOR -0.11 0.22 -10000 0 -0.43 168 168
LYN 0.03 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.026 0.15 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.016 0.032 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.069 0.19 -10000 0 -0.34 157 157
mol:IP3 -0.025 0.12 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.022 0.15 0.41 2 -0.5 2 4
SH2B3 0.013 0.03 -10000 0 -10000 0 0
NFKB1 -0.059 0.17 0.36 1 -0.66 1 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.048 0.1 -10000 0 -0.34 7 7
PTPN6 -0.044 0.15 0.3 3 -10000 0 3
TEC/VAV2/GRB2 -0.017 0.15 -10000 0 -10000 0 0
EPOR 0.016 0.032 -10000 0 -10000 0 0
INPP5D 0.024 0.054 -10000 0 -0.59 4 4
mol:GDP -0.014 0.15 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
PLCG2 0.02 0.073 -10000 0 -0.61 7 7
CRKL/CBL/C3G -0.016 0.15 -10000 0 -0.54 1 1
VAV2 -0.031 0.16 0.37 14 -10000 0 14
CBL -0.034 0.16 0.36 12 -0.58 1 13
SHC/Grb2/SOS1 -0.042 0.13 -10000 0 -10000 0 0
STAT5A -0.022 0.12 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.005 0.13 -10000 0 -10000 0 0
LYN/PLCgamma2 0.036 0.055 -10000 0 -0.44 6 6
PTPN11 0.029 0.005 -10000 0 -10000 0 0
BTK -0.097 0.2 0.38 13 -0.55 29 42
BCL2 0.022 0.12 0.42 4 -10000 0 4
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.03 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.025 0.052 -10000 0 -0.36 2 2
NT3 (dimer)/TRKC 0.013 0.12 -10000 0 -0.5 26 26
NT3 (dimer)/TRKB -0.048 0.2 -10000 0 -0.42 106 106
SHC/Grb2/SOS1/GAB1/PI3K 0.036 0.031 -10000 0 -0.45 1 1
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
BDNF -0.052 0.21 -10000 0 -0.59 69 69
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
DYNLT1 0.028 0.008 -10000 0 -10000 0 0
NTRK1 -0.017 0.16 -10000 0 -0.61 37 37
NTRK2 -0.089 0.25 -10000 0 -0.62 96 96
NTRK3 -0.006 0.15 -10000 0 -0.64 28 28
NT-4/5 (dimer)/TRKB -0.056 0.2 -10000 0 -0.43 112 112
neuron apoptosis 0.078 0.18 0.52 40 -10000 0 40
SHC 2-3/Grb2 -0.085 0.2 -10000 0 -0.58 40 40
SHC1 0.029 0.007 -10000 0 -10000 0 0
SHC2 -0.044 0.14 -10000 0 -0.5 24 24
SHC3 -0.11 0.23 -10000 0 -0.6 79 79
STAT3 (dimer) 0.027 0.053 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.007 0.16 -10000 0 -0.4 69 69
RIN/GDP 0.049 0.084 0.31 13 -0.32 4 17
GIPC1 0.029 0.029 -10000 0 -0.64 1 1
KRAS 0.029 0.006 -10000 0 -10000 0 0
DNAJA3 -0.03 0.11 -10000 0 -0.43 16 16
RIN/GTP 0.014 0.02 -10000 0 -0.44 1 1
CCND1 0.012 0.098 -10000 0 -0.51 18 18
MAGED1 0.03 0.003 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.056 -10000 0 -0.62 4 4
SHC/GRB2/SOS1 0.056 0.017 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.053 0.2 -10000 0 -0.41 122 122
TRKA/NEDD4-2 0.006 0.13 -10000 0 -0.47 34 34
ELMO1 0.026 0.028 -10000 0 -0.59 1 1
RhoG/GTP/ELMO1/DOCK1 0.034 0.03 -10000 0 -0.39 2 2
NGF -0.027 0.18 -10000 0 -0.59 47 47
HRAS 0.029 0.027 -10000 0 -0.59 1 1
DOCK1 0.028 0.03 -10000 0 -0.64 1 1
GAB2 0.03 0.003 -10000 0 -10000 0 0
RIT2 0.019 0.027 -10000 0 -0.59 1 1
RIT1 0.028 0.007 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
DNM1 0.015 0.094 -10000 0 -0.6 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.014 0.11 -10000 0 -0.42 16 16
mol:GDP 0.056 0.12 0.41 14 -0.46 7 21
NGF (dimer) -0.026 0.18 -10000 0 -0.59 47 47
RhoG/GDP 0.019 0.021 -10000 0 -0.44 1 1
RIT1/GDP 0.051 0.079 0.32 10 -0.31 4 14
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
BDNF (dimer)/TRKB -0.076 0.22 -10000 0 -0.41 146 146
KIDINS220/CRKL/C3G 0.043 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.028 -10000 0 -0.47 1 1
FRS2 family/SHP2 0.056 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.07 0.023 -10000 0 -10000 0 0
RIT1/GTP 0.021 0.005 -10000 0 -10000 0 0
NT3 (dimer) 0.023 0.063 -10000 0 -0.62 5 5
RAP1/GDP 0.034 0.056 -10000 0 -0.28 2 2
KIDINS220/CRKL 0.03 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.052 0.21 -10000 0 -0.59 69 69
ubiquitin-dependent protein catabolic process -0.014 0.16 -10000 0 -0.38 79 79
Schwann cell development -0.019 0.027 -10000 0 -10000 0 0
EHD4 0.03 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.07 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.024 -10000 0 -10000 0 0
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.062 0.2 -10000 0 -0.62 25 25
ABL1 0.029 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
Rap1/GTP 0 0.11 -10000 0 -0.49 7 7
STAT3 0.027 0.053 -10000 0 -10000 0 0
axon guidance -0.069 0.18 -10000 0 -0.59 25 25
MAPK3 -0.062 0.18 -10000 0 -0.43 44 44
MAPK1 -0.061 0.18 -10000 0 -0.45 38 38
CDC42/GDP 0.057 0.086 0.33 16 -0.31 4 20
NTF3 0.023 0.063 -10000 0 -0.62 5 5
NTF4 0.017 0.056 -10000 0 -0.62 4 4
NGF (dimer)/TRKA/FAIM -0.014 0.16 -10000 0 -0.39 79 79
PI3K 0.037 0.035 -10000 0 -0.47 2 2
FRS3 0.029 0.006 -10000 0 -10000 0 0
FAIM 0.028 0.007 -10000 0 -10000 0 0
GAB1 0.03 0.004 -10000 0 -10000 0 0
RASGRF1 -0.036 0.12 -10000 0 -0.45 19 19
SOS1 0.029 0.005 -10000 0 -10000 0 0
MCF2L 0.003 0.1 -10000 0 -0.43 26 26
RGS19 0.029 0.006 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.096 0.33 3 -0.57 6 9
Rac1/GDP 0.046 0.074 0.3 6 -0.32 4 10
NGF (dimer)/TRKA/GRIT -0.029 0.16 -10000 0 -0.39 80 80
neuron projection morphogenesis 0.001 0.16 0.41 1 -1.1 6 7
NGF (dimer)/TRKA/NEDD4-2 -0.014 0.16 -10000 0 -0.39 79 79
MAP2K1 0.041 0.047 0.43 3 -10000 0 3
NGFR -0.011 0.16 -10000 0 -0.6 34 34
NGF (dimer)/TRKA/GIPC/GAIP -0.007 0.11 -10000 0 -0.43 11 11
RAS family/GTP/PI3K 0.03 0.033 -10000 0 -0.45 2 2
FRS2 family/SHP2/GRB2/SOS1 0.08 0.028 -10000 0 -10000 0 0
NRAS 0.029 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
PRKCI 0.028 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.05 -10000 0 -0.64 3 3
MAPKKK cascade -0.064 0.2 -10000 0 -0.61 55 55
RASA1 0.025 0.03 -10000 0 -0.64 1 1
TRKA/c-Abl 0.006 0.13 -10000 0 -0.47 34 34
SQSTM1 0.022 0.013 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.058 0.2 -10000 0 -0.4 89 89
NGF (dimer)/TRKA/p62/Atypical PKCs 0.009 0.13 -10000 0 -0.65 1 1
MATK -0.033 0.19 -10000 0 -0.59 53 53
NEDD4L 0.028 0.029 -10000 0 -0.64 1 1
RAS family/GDP -0.008 0.034 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.032 0.12 -10000 0 -0.45 17 17
Rac1/GTP -0.03 0.068 -10000 0 -0.36 5 5
FRS2 family/SHP2/CRK family 0.081 0.027 -10000 0 -10000 0 0
Endothelins

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
AKT1 0 0.16 0.38 2 -0.52 5 7
PTK2B 0.027 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.047 0.15 0.48 2 -0.79 5 7
EDN1 0.001 0.16 0.42 1 -0.5 22 23
EDN3 0.011 0.088 -10000 0 -0.59 11 11
EDN2 -0.047 0.2 -10000 0 -0.57 66 66
HRAS/GDP 0.032 0.15 0.32 5 -0.59 11 16
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.017 0.12 0.27 1 -0.54 10 11
ADCY4 0.004 0.13 0.34 1 -0.42 5 6
ADCY5 -0.01 0.15 0.35 2 -0.52 15 17
ADCY6 0.003 0.13 0.34 1 -0.44 6 7
ADCY7 -0.007 0.14 0.34 1 -0.47 9 10
ADCY1 -0.005 0.14 0.34 1 -0.48 6 7
ADCY2 -0.068 0.18 0.36 1 -0.46 30 31
ADCY3 0.006 0.13 0.35 2 -0.44 6 8
ADCY8 -0.093 0.19 0.34 1 -0.49 36 37
ADCY9 0.004 0.13 0.35 2 -0.44 6 8
arachidonic acid secretion 0.043 0.15 0.38 7 -0.56 12 19
ETB receptor/Endothelin-1/Gq/GTP 0.027 0.088 -10000 0 -0.5 6 6
GNAO1 0.024 0.055 -10000 0 -0.6 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
ETA receptor/Endothelin-1/G12/GTP 0.037 0.18 0.4 20 -0.53 4 24
ETA receptor/Endothelin-1/Gs/GTP 0.039 0.17 0.38 23 -0.47 6 29
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.026 0.23 0.41 1 -0.66 49 50
EDNRB 0.018 0.056 -10000 0 -0.51 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.03 0.22 0.6 1 -0.54 46 47
CYSLTR1 0.002 0.17 0.41 1 -0.54 7 8
SLC9A1 0.013 0.097 0.28 2 -0.32 4 6
mol:GDP 0.023 0.16 0.32 8 -0.62 12 20
SLC9A3 -0.33 0.29 -10000 0 -0.67 132 132
RAF1 0.013 0.15 0.32 5 -0.62 12 17
JUN 0.048 0.14 -10000 0 -0.66 5 5
JAK2 0.001 0.17 0.38 2 -0.55 5 7
mol:IP3 0.012 0.13 0.26 1 -0.58 11 12
ETA receptor/Endothelin-1 0.026 0.23 0.47 24 -0.45 40 64
PLCB1 0.018 0.087 -10000 0 -0.64 9 9
PLCB2 -0.038 0.2 -10000 0 -0.59 58 58
ETA receptor/Endothelin-3 0.023 0.11 -10000 0 -0.44 11 11
FOS 0.029 0.18 0.39 4 -0.81 16 20
Gai/GDP -0.1 0.25 -10000 0 -0.62 46 46
CRK 0.03 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.001 0.18 0.33 1 -0.6 14 15
BCAR1 0.028 0.03 -10000 0 -0.63 1 1
PRKCB1 0.014 0.13 -10000 0 -0.55 11 11
GNAQ 0.032 0.007 -10000 0 -10000 0 0
GNAZ 0.026 0.05 -10000 0 -0.64 3 3
GNAL 0.029 0.005 -10000 0 -10000 0 0
Gs family/GDP 0.028 0.14 0.3 5 -0.58 10 15
ETA receptor/Endothelin-1/Gq/GTP 0.035 0.11 0.26 1 -0.49 5 6
MAPK14 0.014 0.1 0.35 1 -0.53 8 9
TRPC6 0.046 0.16 0.55 1 -0.91 4 5
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GNAI1 0.026 0.03 -10000 0 -0.64 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.012 0.11 -10000 0 -0.5 12 12
ETB receptor/Endothelin-2 -0.025 0.16 -10000 0 -0.44 61 61
ETB receptor/Endothelin-3 0.02 0.08 -10000 0 -0.44 13 13
ETB receptor/Endothelin-1 0.014 0.14 -10000 0 -0.42 17 17
MAPK3 0.032 0.17 0.39 5 -0.73 16 21
MAPK1 0.032 0.18 0.4 5 -0.71 17 22
Rac1/GDP 0.024 0.14 0.31 2 -0.59 10 12
cAMP biosynthetic process -0.024 0.15 0.42 6 -0.48 11 17
MAPK8 0.045 0.16 0.4 1 -0.68 11 12
SRC 0.029 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.012 0.073 -10000 0 -0.47 4 4
p130Cas/CRK/Src/PYK2 0.039 0.16 0.41 10 -0.62 11 21
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.024 0.14 0.31 2 -0.59 10 12
COL1A2 -0.025 0.24 0.64 1 -0.6 61 62
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.022 0.17 0.29 1 -0.44 60 61
mol:DAG 0.012 0.13 0.26 1 -0.58 11 12
MAP2K2 0.028 0.16 0.46 3 -0.62 15 18
MAP2K1 0.03 0.16 0.38 5 -0.64 13 18
EDNRA 0.022 0.12 0.41 1 -0.36 5 6
positive regulation of muscle contraction 0.021 0.15 0.42 7 -0.46 4 11
Gq family/GDP 0.036 0.15 -10000 0 -0.62 11 11
HRAS/GTP 0.018 0.15 0.32 5 -0.61 12 17
PRKCH 0.013 0.12 -10000 0 -0.58 8 8
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.019 0.13 -10000 0 -0.59 9 9
PRKCB 0.017 0.14 0.33 6 -0.61 12 18
PRKCE 0.016 0.13 -10000 0 -0.57 10 10
PRKCD -0.002 0.12 -10000 0 -0.59 9 9
PRKCG -0.001 0.15 -10000 0 -0.56 18 18
regulation of vascular smooth muscle contraction 0.028 0.21 0.42 5 -0.93 16 21
PRKCQ 0.007 0.14 0.29 1 -0.63 12 13
PLA2G4A 0.041 0.16 0.38 7 -0.61 12 19
GNA14 0.023 0.077 -10000 0 -0.63 7 7
GNA15 0.014 0.1 -10000 0 -0.59 15 15
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA11 0.028 0.05 -10000 0 -0.63 3 3
Rac1/GTP 0.038 0.18 0.41 19 -0.53 4 23
MMP1 -0.11 0.28 0.7 1 -0.63 103 104
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.094 0.24 0.57 3 -0.66 16 19
CRP -0.13 0.29 0.55 1 -0.7 59 60
cell cycle arrest -0.12 0.26 -10000 0 -0.68 41 41
TIMP1 -0.097 0.26 -10000 0 -0.68 33 33
IL6ST 0.003 0.12 -10000 0 -0.62 18 18
Rac1/GDP -0.085 0.18 -10000 0 -0.47 39 39
AP1 0.029 0.12 0.46 1 -0.75 4 5
GAB2 0.03 0.003 -10000 0 -10000 0 0
TNFSF11 -0.13 0.28 0.61 1 -0.73 39 40
HSP90B1 0.026 0.064 -10000 0 -10000 0 0
GAB1 0.03 0.004 -10000 0 -10000 0 0
MAPK14 0.005 0.1 -10000 0 -0.54 6 6
AKT1 0.045 0.04 -10000 0 -0.5 1 1
FOXO1 0.054 0.044 -10000 0 -0.48 1 1
MAP2K6 -0.017 0.1 -10000 0 -0.58 6 6
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.099 0.19 -10000 0 -0.5 40 40
MITF -0.027 0.1 -10000 0 -0.48 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.03 0.003 -10000 0 -10000 0 0
A2M 0.029 0.07 -10000 0 -1.1 2 2
CEBPB 0.024 0.077 -10000 0 -0.59 8 8
GRB2/SOS1/GAB family/SHP2 0.014 0.08 -10000 0 -0.66 4 4
STAT3 -0.14 0.26 -10000 0 -0.72 40 40
STAT1 0.001 0.1 -10000 0 -0.82 7 7
CEBPD -0.096 0.24 0.55 2 -0.64 18 20
PIK3CA 0.029 0.03 -10000 0 -0.64 1 1
PI3K 0.04 0.035 -10000 0 -0.47 2 2
JUN 0.028 0.006 -10000 0 -10000 0 0
PIAS3/MITF -0.012 0.11 -10000 0 -0.55 5 5
MAPK11 0.004 0.11 -10000 0 -0.58 7 7
STAT3 (dimer)/FOXO1 -0.063 0.21 0.43 1 -0.62 7 8
GRB2/SOS1/GAB family 0.028 0.12 -10000 0 -0.51 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.019 0.12 -10000 0 -0.43 16 16
GRB2 0.029 0.005 -10000 0 -10000 0 0
JAK2 0.028 0.007 -10000 0 -10000 0 0
LBP -0.22 0.4 0.57 3 -0.8 138 141
PIK3R1 0.027 0.03 -10000 0 -0.63 1 1
JAK1 0.028 0.011 -10000 0 -10000 0 0
MYC -0.1 0.25 0.54 3 -0.67 22 25
FGG -0.18 0.31 0.52 1 -0.71 70 71
macrophage differentiation -0.12 0.26 -10000 0 -0.68 41 41
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.005 0.15 -10000 0 -0.48 9 9
JUNB -0.099 0.24 -10000 0 -0.68 19 19
FOS 0.012 0.099 -10000 0 -0.63 12 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.12 -10000 0 -0.46 11 11
STAT1/PIAS1 -0.031 0.13 -10000 0 -0.53 7 7
GRB2/SOS1/GAB family/SHP2/PI3K 0.042 0.043 -10000 0 -0.54 1 1
STAT3 (dimer) -0.13 0.27 -10000 0 -0.71 41 41
PRKCD -0.11 0.21 0.42 7 -0.57 34 41
IL6R 0.028 0.01 -10000 0 -10000 0 0
SOCS3 0.032 0.12 0.45 1 -0.62 4 5
gp130 (dimer)/JAK1/JAK1/LMO4 0.032 0.086 -10000 0 -0.4 17 17
Rac1/GTP -0.093 0.18 -10000 0 -0.47 50 50
HCK -0.004 0.14 -10000 0 -0.59 27 27
MAPKKK cascade 0.033 0.096 -10000 0 -0.78 3 3
bone resorption -0.12 0.27 0.61 1 -0.69 39 40
IRF1 -0.066 0.26 0.56 6 -0.66 16 22
mol:GDP -0.1 0.17 -10000 0 -0.44 60 60
SOS1 0.029 0.005 -10000 0 -10000 0 0
VAV1 -0.1 0.17 -10000 0 -0.44 60 60
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.006 0.12 -10000 0 -0.55 8 8
PTPN11 0.012 0.038 -10000 0 -0.7 1 1
IL6/IL6RA -0.022 0.16 -10000 0 -0.45 61 61
gp130 (dimer)/TYK2/TYK2/LMO4 0.035 0.084 -10000 0 -0.4 17 17
gp130 (dimer)/JAK2/JAK2/LMO4 0.032 0.084 -10000 0 -0.4 17 17
IL6 -0.052 0.21 -10000 0 -0.61 62 62
PIAS3 0.029 0.006 -10000 0 -10000 0 0
PTPRE 0.029 0.031 -10000 0 -0.55 1 1
PIAS1 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.026 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.02 0.1 -10000 0 -0.46 8 8
LMO4 0.025 0.017 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.12 0.25 -10000 0 -0.71 28 28
MCL1 0.06 0.057 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.023 0.034 -10000 0 -0.62 1 1
HSPA8 0.03 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.076 0.074 0.36 1 -0.4 4 5
AKT1 0.03 0.012 -10000 0 -10000 0 0
GSC -0.028 0.16 -10000 0 -0.56 14 14
NKX2-5 0.003 0.001 -10000 0 -10000 0 0
muscle cell differentiation -0.044 0.08 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.094 0.09 -10000 0 -10000 0 0
SMAD4 0.041 0.036 -10000 0 -10000 0 0
CBFB 0.029 0.006 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.047 0.044 -10000 0 -0.37 3 3
SMAD3/SMAD4/VDR 0.091 0.061 -10000 0 -10000 0 0
MYC 0.004 0.12 -10000 0 -0.59 19 19
CDKN2B 0.022 0.11 -10000 0 -0.56 2 2
AP1 0.063 0.067 -10000 0 -0.39 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.054 0.065 -10000 0 -0.49 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.045 0.044 -10000 0 -10000 0 0
SP3 0.032 0.007 -10000 0 -10000 0 0
CREB1 0.029 0.006 -10000 0 -10000 0 0
FOXH1 -0.021 0.17 -10000 0 -0.6 40 40
SMAD3/SMAD4/GR 0.064 0.056 -10000 0 -0.39 1 1
GATA3 -0.3 0.33 -10000 0 -0.63 258 258
SKI/SIN3/HDAC complex/NCoR1 0.043 0.036 -10000 0 -0.36 1 1
MEF2C/TIF2 0.024 0.12 -10000 0 -0.65 3 3
endothelial cell migration 0.054 0.17 0.52 19 -10000 0 19
MAX 0.03 0.014 -10000 0 -10000 0 0
RBBP7 0.03 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
RUNX2 0.012 0.1 -10000 0 -0.59 14 14
RUNX3 -0.24 0.31 -10000 0 -0.59 229 229
RUNX1 -0.013 0.15 -10000 0 -0.59 35 35
CTBP1 0.029 0.004 -10000 0 -10000 0 0
NR3C1 0.024 0.032 -10000 0 -0.59 1 1
VDR 0.025 0.05 -10000 0 -0.64 3 3
CDKN1A 0.05 0.082 -10000 0 -10000 0 0
KAT2B 0.02 0.031 -10000 0 -0.63 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.038 0.14 -10000 0 -0.4 33 33
DCP1A 0.022 0.013 -10000 0 -10000 0 0
SKI 0.029 0.007 -10000 0 -10000 0 0
SERPINE1 -0.054 0.17 -10000 0 -0.52 19 19
SMAD3/SMAD4/ATF2 0.073 0.05 -10000 0 -0.41 1 1
SMAD3/SMAD4/ATF3 0.071 0.062 -10000 0 -0.42 4 4
SAP30 0.008 0.11 -10000 0 -0.59 18 18
Cbp/p300/PIAS3 0.047 0.041 -10000 0 -0.38 1 1
JUN 0.051 0.064 -10000 0 -0.38 1 1
SMAD3/SMAD4/IRF7 0.063 0.092 -10000 0 -0.39 6 6
TFE3 0.029 0.021 -10000 0 -10000 0 0
COL1A2 -0.029 0.16 -10000 0 -0.47 58 58
mesenchymal cell differentiation -0.063 0.085 0.39 11 -10000 0 11
DLX1 -0.29 0.31 -10000 0 -0.59 272 272
TCF3 0.03 0.003 -10000 0 -10000 0 0
FOS 0.02 0.099 -10000 0 -0.62 12 12
SMAD3/SMAD4/Max 0.079 0.049 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.053 0.028 -10000 0 -0.39 1 1
ZBTB17 0.024 0.04 -10000 0 -0.61 2 2
LAMC1 0.053 0.039 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.075 0.044 -10000 0 -10000 0 0
IRF7 0.009 0.12 -10000 0 -0.59 19 19
ESR1 0.024 0.06 -10000 0 -0.56 5 5
HNF4A -0.019 0.17 -10000 0 -0.64 38 38
MEF2C 0.022 0.11 0.38 5 -0.42 5 10
SMAD2-3/SMAD4 0.083 0.049 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.051 0.031 -10000 0 -0.39 1 1
IGHV3OR16-13 -0.024 0.066 -10000 0 -0.49 5 5
TGIF2/HDAC complex 0.029 0.006 -10000 0 -10000 0 0
CREBBP 0.027 0.011 -10000 0 -10000 0 0
SKIL 0.028 0.007 -10000 0 -10000 0 0
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
SNIP1 0.029 0.006 -10000 0 -10000 0 0
GCN5L2 -0.002 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.079 0.054 -10000 0 -10000 0 0
MSG1/HSC70 0.043 0.03 -10000 0 -0.44 2 2
SMAD2 0.031 0.024 -10000 0 -10000 0 0
SMAD3 0.042 0.034 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.052 0.033 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.015 0.068 -10000 0 -0.45 4 4
NCOR1 0.029 0.005 -10000 0 -10000 0 0
NCOA2 0.015 0.091 -10000 0 -0.64 10 10
NCOA1 0.029 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.012 0.11 -10000 0 -0.43 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.1 0.094 -10000 0 -10000 0 0
IFNB1 0.031 0.078 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.051 0.11 -10000 0 -10000 0 0
CITED1 0.027 0.038 -10000 0 -0.59 2 2
SMAD2-3/SMAD4/ARC105 0.097 0.047 -10000 0 -10000 0 0
RBL1 0.029 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.055 0.046 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.15 0.22 -10000 0 -0.39 241 241
SMAD7 0.08 0.068 -10000 0 -10000 0 0
MYC/MIZ-1 0.017 0.093 -10000 0 -0.43 21 21
SMAD3/SMAD4 0.015 0.094 -10000 0 -0.48 1 1
IL10 -0.16 0.24 -10000 0 -0.64 38 38
PIASy/HDAC complex 0.031 0.009 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.027 0.01 -10000 0 -10000 0 0
IL5 -0.13 0.19 -10000 0 -0.55 17 17
CDK4 0.025 0.014 -10000 0 -10000 0 0
PIAS4 0.031 0.009 -10000 0 -10000 0 0
ATF3 0.023 0.06 -10000 0 -0.57 5 5
SMAD3/SMAD4/SP1 0.07 0.087 -10000 0 -0.38 1 1
FOXG1 -0.01 0.11 -10000 0 -0.59 18 18
FOXO3 0.024 0.013 -10000 0 -10000 0 0
FOXO1 0.025 0.012 -10000 0 -10000 0 0
FOXO4 0.026 0.011 -10000 0 -10000 0 0
heart looping 0.022 0.11 0.38 5 -0.41 7 12
CEBPB 0.021 0.077 -10000 0 -0.59 8 8
SMAD3/SMAD4/DLX1 -0.16 0.22 -10000 0 -0.38 251 251
MYOD1 -0.012 0.14 -10000 0 -0.59 29 29
SMAD3/SMAD4/HNF4 0.04 0.14 -10000 0 -0.42 38 38
SMAD3/SMAD4/GATA3 -0.16 0.25 -10000 0 -0.41 218 218
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.1 0.21 -10000 0 -0.55 22 22
SMAD3/SMAD4/SP1-3 0.087 0.085 -10000 0 -10000 0 0
MED15 0.03 0.004 -10000 0 -10000 0 0
SP1 0.023 0.05 -10000 0 -10000 0 0
SIN3B 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.043 0.12 -10000 0 -0.43 14 14
ITGB5 0.058 0.077 0.43 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP 0.039 0.05 -10000 0 -0.47 3 3
SMAD3/SMAD4/AR 0.055 0.11 -10000 0 -0.42 25 25
AR -0.002 0.14 -10000 0 -0.62 26 26
negative regulation of cell growth 0.055 0.044 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.048 0.11 -10000 0 -0.38 27 27
E2F5 0.027 0.03 -10000 0 -0.64 1 1
E2F4 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.039 0.12 -10000 0 -0.43 12 12
SMAD2-3/SMAD4/FOXO1-3a-4 0.053 0.036 -10000 0 -10000 0 0
TFDP1 0.029 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.082 0.071 -10000 0 -0.39 1 1
SMAD3/SMAD4/RUNX2 0.063 0.085 -10000 0 -0.39 11 11
TGIF2 0.029 0.006 -10000 0 -10000 0 0
TGIF1 0.029 0.005 -10000 0 -10000 0 0
ATF2 0.027 0.03 -10000 0 -0.64 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.037 0.077 -10000 0 -0.63 1 1
HDAC1 0.026 0.008 -10000 0 -10000 0 0
AES 0.029 0.004 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
DTX1 -0.027 0.18 -10000 0 -0.63 45 45
LRP6/FZD1 0.039 0.015 -10000 0 -10000 0 0
TLE1 0.028 0.006 -10000 0 -10000 0 0
AP1 -0.065 0.16 -10000 0 -0.32 136 136
NCSTN 0.029 0.007 -10000 0 -10000 0 0
ADAM10 0.028 0.029 -10000 0 -0.64 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.046 0.062 -10000 0 -0.74 1 1
NICD/RBPSUH 0.04 0.077 -10000 0 -0.61 1 1
WIF1 0.016 0.064 -10000 0 -0.63 5 5
NOTCH1 0.025 0.075 -10000 0 -0.65 1 1
PSENEN 0.03 0.003 -10000 0 -10000 0 0
KREMEN2 -0.043 0.2 -10000 0 -0.59 60 60
DKK1 0.002 0.13 -10000 0 -0.61 22 22
beta catenin/beta TrCP1 0.036 0.091 0.3 4 -10000 0 4
APH1B 0.03 0.003 -10000 0 -10000 0 0
APH1A 0.029 0.007 -10000 0 -10000 0 0
AXIN1 0.011 0.066 0.28 3 -0.32 1 4
CtBP/CBP/TCF1/TLE1/AES 0.028 0.038 -10000 0 -0.36 2 2
PSEN1 0.028 0.008 -10000 0 -10000 0 0
FOS 0.013 0.099 -10000 0 -0.63 12 12
JUN 0.029 0.006 -10000 0 -10000 0 0
MAP3K7 0.027 0.008 -10000 0 -10000 0 0
CTNNB1 0.036 0.11 0.29 12 -0.33 4 16
MAPK3 0.029 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.009 0.15 -10000 0 -0.38 75 75
HNF1A 0.023 0.058 -10000 0 -0.64 4 4
CTBP1 0.029 0.004 -10000 0 -10000 0 0
MYC 0.007 0.14 -10000 0 -0.7 10 10
NKD1 -0.14 0.29 -10000 0 -0.63 134 134
FZD1 0.027 0.009 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.009 0.13 -10000 0 -0.6 4 4
apoptosis -0.065 0.16 -10000 0 -0.32 136 136
Delta 1/NOTCHprecursor 0.037 0.077 -10000 0 -0.61 1 1
DLL1 0.027 0.008 -10000 0 -10000 0 0
PPARD 0.009 0.15 -10000 0 -0.75 19 19
Gamma Secretase 0.079 0.029 -10000 0 -10000 0 0
APC 0.011 0.072 0.3 3 -0.4 3 6
DVL1 0.02 0.035 -10000 0 -0.43 2 2
CSNK2A1 0.029 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.008 0.16 -10000 0 -0.4 69 69
LRP6 0.029 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
NLK 0.017 0.009 -10000 0 -10000 0 0
CCND1 0.02 0.099 -10000 0 -0.57 5 5
WNT1 -0.001 0.13 -10000 0 -0.59 25 25
Axin1/APC/beta catenin 0.081 0.099 0.4 17 -10000 0 17
DKK2 0 0.13 -10000 0 -0.6 24 24
NOTCH1 precursor/DVL1 0.046 0.081 -10000 0 -0.55 1 1
GSK3B 0.028 0.008 -10000 0 -10000 0 0
FRAT1 0.028 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.01 0.13 -10000 0 -0.61 4 4
PPP2R5D 0.084 0.15 0.34 119 -0.37 9 128
MAPK1 0.03 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.041 0.096 -10000 0 -0.34 29 29
RBPJ 0.029 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.009 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 0.037 0.089 -10000 0 -0.36 22 22
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.078 -10000 0 -10000 0 0
AP1 0.019 0.097 -10000 0 -0.39 4 4
mol:PIP3 -0.003 0.067 -10000 0 -0.49 1 1
AKT1 0.01 0.11 0.38 2 -0.4 1 3
PTK2B 0.005 0.086 0.26 1 -0.39 8 9
RHOA -0.04 0.12 -10000 0 -0.38 22 22
PIK3CB 0.028 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.028 0.059 0.42 2 -0.39 2 4
MAGI3 0.025 0.05 -10000 0 -0.63 3 3
RELA 0.03 0.003 -10000 0 -10000 0 0
apoptosis 0.009 0.079 -10000 0 -0.33 23 23
HRAS/GDP 0.021 0.02 -10000 0 -0.44 1 1
positive regulation of microtubule depolymerization 0.01 0.087 0.28 4 -0.34 8 12
NF kappa B1 p50/RelA 0.026 0.079 -10000 0 -10000 0 0
endothelial cell migration 0.005 0.1 -10000 0 -0.42 28 28
ADCY4 0.004 0.1 -10000 0 -0.45 22 22
ADCY5 -0.001 0.11 -10000 0 -0.44 27 27
ADCY6 0.004 0.1 -10000 0 -0.45 22 22
ADCY7 0.001 0.1 -10000 0 -0.45 22 22
ADCY1 0.001 0.1 -10000 0 -0.44 22 22
ADCY2 -0.025 0.12 -10000 0 -0.44 27 27
ADCY3 0.004 0.1 -10000 0 -0.44 23 23
ADCY8 -0.032 0.12 -10000 0 -0.44 28 28
ADCY9 0.003 0.1 -10000 0 -0.45 22 22
GSK3B 0.008 0.083 0.28 4 -0.38 7 11
arachidonic acid secretion 0.006 0.1 -10000 0 -0.44 22 22
GNG2 0.028 0.008 -10000 0 -10000 0 0
TRIP6 0.029 0.012 -10000 0 -10000 0 0
GNAO1 0.006 0.095 -10000 0 -0.38 27 27
HRAS 0.029 0.027 -10000 0 -0.59 1 1
NFKBIA 0.032 0.076 0.36 4 -0.39 1 5
GAB1 0.03 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.016 0.17 -10000 0 -0.82 19 19
JUN 0.029 0.006 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.039 0.025 -10000 0 -0.4 1 1
TIAM1 -0.001 0.2 -10000 0 -0.98 20 20
PIK3R1 0.026 0.03 -10000 0 -0.63 1 1
mol:IP3 0.027 0.059 0.42 2 -0.4 2 4
PLCB3 0.035 0.039 -10000 0 -0.36 1 1
FOS 0.013 0.099 -10000 0 -0.63 12 12
positive regulation of mitosis 0.006 0.1 -10000 0 -0.44 22 22
LPA/LPA1-2-3 0.035 0.095 -10000 0 -0.36 25 25
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
stress fiber formation 0.018 0.087 0.38 1 -0.37 6 7
GNAZ 0.007 0.096 -10000 0 -0.4 25 25
EGFR/PI3K-beta/Gab1 0.009 0.074 -10000 0 -0.51 1 1
positive regulation of dendritic cell cytokine production 0.033 0.094 -10000 0 -0.36 25 25
LPA/LPA2/MAGI-3 0.037 0.037 -10000 0 -0.4 3 3
ARHGEF1 0.032 0.092 0.37 6 -0.33 15 21
GNAI2 0.003 0.085 -10000 0 -0.37 23 23
GNAI3 0.009 0.09 -10000 0 -0.39 22 22
GNAI1 0.009 0.084 -10000 0 -0.38 20 20
LPA/LPA3 0.017 0.038 -10000 0 -0.43 3 3
LPA/LPA2 0.024 0.016 -10000 0 -10000 0 0
LPA/LPA1 0.005 0.1 -10000 0 -0.42 28 28
HB-EGF/EGFR -0.13 0.19 -10000 0 -0.37 182 182
HBEGF -0.16 0.21 -10000 0 -0.43 187 187
mol:DAG 0.027 0.059 0.42 2 -0.4 2 4
cAMP biosynthetic process 0.011 0.12 0.36 10 -0.42 18 28
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
GNB1 0.028 0.006 -10000 0 -10000 0 0
LYN 0.034 0.08 0.36 5 -0.41 1 6
GNAQ 0.022 0.026 -10000 0 -10000 0 0
LPAR2 0.03 0.003 -10000 0 -10000 0 0
LPAR3 0.02 0.047 -10000 0 -0.59 3 3
LPAR1 0.003 0.13 -10000 0 -0.58 24 24
IL8 -0.033 0.15 0.3 1 -0.43 19 20
PTK2 0.013 0.083 -10000 0 -0.35 12 12
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
CASP3 0.009 0.079 -10000 0 -0.33 23 23
EGFR 0.02 0.067 -10000 0 -0.6 6 6
PLCG1 0.02 0.041 -10000 0 -0.37 2 2
PLD2 0.014 0.083 -10000 0 -0.34 20 20
G12/G13 0.038 0.081 -10000 0 -0.36 15 15
PI3K-beta -0.023 0.1 -10000 0 -0.43 11 11
cell migration 0.028 0.065 -10000 0 -0.26 10 10
SLC9A3R2 0.027 0.03 -10000 0 -0.64 1 1
PXN 0.018 0.088 0.38 1 -0.38 6 7
HRAS/GTP 0.003 0.1 -10000 0 -0.45 22 22
RAC1 0.027 0.009 -10000 0 -10000 0 0
MMP9 -0.25 0.31 -10000 0 -0.59 234 234
PRKCE 0.028 0.03 -10000 0 -0.64 1 1
PRKCD 0.024 0.063 0.36 4 -0.39 1 5
Gi(beta/gamma) 0.009 0.1 -10000 0 -0.42 22 22
mol:LPA 0.001 0.022 -10000 0 -0.28 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.035 0.089 -10000 0 -10000 0 0
MAPKKK cascade 0.006 0.1 -10000 0 -0.44 22 22
contractile ring contraction involved in cytokinesis -0.044 0.12 -10000 0 -0.37 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.017 0.051 -10000 0 -0.38 6 6
GNA15 0.015 0.054 -10000 0 -0.46 1 1
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
MAPT 0.01 0.089 0.28 4 -0.35 8 12
GNA11 0.021 0.037 -10000 0 -0.34 3 3
Rac1/GTP 0.016 0.18 -10000 0 -0.87 19 19
MMP2 0.005 0.1 -10000 0 -0.42 28 28
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.022 0.066 -10000 0 -0.59 6 6
GNB1/GNG2 -0.027 0.054 -10000 0 -0.2 18 18
AKT1 0.027 0.11 0.29 7 -0.35 12 19
EGF -0.57 0.2 -10000 0 -0.63 474 474
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.013 0.075 0.34 3 -0.4 2 5
mol:Ca2+ 0.038 0.12 0.33 6 -0.33 16 22
LYN 0.013 0.069 0.37 2 -10000 0 2
RhoA/GTP 0.008 0.047 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.035 0.13 0.34 6 -0.36 16 22
GNG2 0.028 0.008 -10000 0 -10000 0 0
ARRB2 0.028 0.032 -10000 0 -0.71 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.016 0.078 0.36 1 -0.48 5 6
G beta5/gamma2 -0.034 0.07 -10000 0 -0.27 19 19
PRKCH 0.032 0.13 0.38 3 -0.38 16 19
DNM1 0.015 0.094 -10000 0 -0.6 12 12
TXA2/TP beta/beta Arrestin3 0.003 0.036 -10000 0 -0.42 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.061 0.22 -10000 0 -0.59 75 75
G12 family/GTP 0.009 0.1 -10000 0 -0.32 13 13
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
ADRBK2 0.03 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.029 0.019 -10000 0 -10000 0 0
mol:GDP -0.032 0.091 0.42 4 -0.31 3 7
mol:NADP 0.027 0.009 -10000 0 -10000 0 0
RAB11A 0.03 0.003 -10000 0 -10000 0 0
PRKG1 0.011 0.11 -10000 0 -0.64 14 14
mol:IP3 0.036 0.14 0.39 4 -0.41 19 23
cell morphogenesis 0.028 0.019 -10000 0 -10000 0 0
PLCB2 0.03 0.18 0.5 2 -0.55 22 24
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.006 0.1 0.37 2 -0.4 15 17
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.095 0.39 1 -0.39 9 10
RHOA 0.021 0.014 -10000 0 -10000 0 0
PTGIR 0.027 0.04 -10000 0 -0.61 2 2
PRKCB1 0.033 0.14 0.37 4 -0.38 28 32
GNAQ 0.029 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.027 0.009 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.03 0.18 0.46 3 -0.52 37 40
LCK 0.004 0.097 0.34 3 -0.4 12 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.007 0.079 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.014 0.084 -10000 0 -0.46 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.011 0.081 -10000 0 -0.35 1 1
MAPK14 0.035 0.097 0.28 10 -0.26 1 11
TGM2/GTP 0.035 0.16 0.38 2 -0.46 13 15
MAPK11 0.037 0.097 0.28 10 -0.3 3 13
ARHGEF1 0.021 0.068 -10000 0 -0.23 1 1
GNAI2 0.021 0.014 -10000 0 -10000 0 0
JNK cascade 0.036 0.14 0.4 4 -0.38 34 38
RAB11/GDP 0.029 0.003 -10000 0 -10000 0 0
ICAM1 0.036 0.12 0.32 5 -0.32 19 24
cAMP biosynthetic process 0.032 0.14 0.35 6 -0.38 18 24
Gq family/GTP/EBP50 0.018 0.054 0.23 3 -0.28 4 7
actin cytoskeleton reorganization 0.028 0.019 -10000 0 -10000 0 0
SRC 0.012 0.067 0.39 1 -10000 0 1
GNB5 0.03 0.003 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.086 0.27 2 -0.32 18 20
VCAM1 0.034 0.12 0.31 6 -0.35 16 22
TP beta/Gq family/GDP/G beta5/gamma2 0.016 0.078 0.36 1 -0.48 5 6
platelet activation 0.047 0.13 0.34 12 -0.33 10 22
PGI2/IP 0.02 0.03 -10000 0 -0.46 2 2
PRKACA -0.008 0.084 -10000 0 -0.32 2 2
Gq family/GDP/G beta5/gamma2 0.013 0.075 0.26 1 -0.44 5 6
TXA2/TP beta/beta Arrestin2 0.001 0.051 -10000 0 -0.39 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.008 0.078 -10000 0 -0.3 2 2
mol:DAG 0.035 0.16 0.42 3 -0.43 29 32
EGFR 0.02 0.067 -10000 0 -0.6 6 6
TXA2/TP alpha 0.033 0.18 0.47 3 -0.51 20 23
Gq family/GTP 0.012 0.051 0.22 1 -0.31 7 8
YES1 0.015 0.071 0.37 2 -10000 0 2
GNAI2/GTP 0.001 0.067 -10000 0 -10000 0 0
PGD2/DP -0.045 0.16 -10000 0 -0.44 75 75
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
FYN 0.013 0.07 0.34 3 -10000 0 3
mol:NO 0.027 0.009 -10000 0 -10000 0 0
GNA15 0.012 0.1 -10000 0 -0.59 15 15
PGK/cGMP 0.024 0.069 -10000 0 -0.41 12 12
RhoA/GDP 0.021 0.013 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.024 0.092 -10000 0 -0.45 1 1
NOS3 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA 0.036 0.13 0.37 6 -0.39 12 18
PRKCB 0.037 0.14 0.35 12 -0.4 20 32
PRKCE 0.036 0.14 0.34 5 -0.39 16 21
PRKCD 0.011 0.13 0.41 3 -0.39 26 29
PRKCG 0.029 0.15 0.42 3 -0.43 25 28
muscle contraction 0.034 0.17 0.46 3 -0.48 33 36
PRKCZ 0.035 0.13 0.35 5 -0.36 15 20
ARR3 0.021 0.005 -10000 0 -10000 0 0
TXA2/TP beta 0.019 0.082 -10000 0 -10000 0 0
PRKCQ 0.03 0.14 0.37 5 -0.41 18 23
MAPKKK cascade 0.031 0.16 0.43 3 -0.47 25 28
SELE 0.028 0.14 0.33 5 -0.41 36 41
TP beta/GNAI2/GDP/G beta/gamma 0.015 0.082 -10000 0 -10000 0 0
ROCK1 0.029 0.005 -10000 0 -10000 0 0
GNA14 0.02 0.076 -10000 0 -0.64 7 7
chemotaxis 0.028 0.2 0.52 2 -0.6 37 39
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.05 -10000 0 -0.64 3 3
Rac1/GTP 0.02 0.007 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.037 0.04 -10000 0 -10000 0 0
BIRC5 -0.15 0.28 -10000 0 -0.59 149 149
NFKBIA 0.024 0.026 0.26 1 -10000 0 1
CPEB1 -0.1 0.26 -10000 0 -0.63 106 106
AKT1 0.023 0.024 -10000 0 -10000 0 0
NDEL1 0.029 0.005 -10000 0 -10000 0 0
Aurora A/BRCA1 0.031 0.035 -10000 0 -10000 0 0
NDEL1/TACC3 0.047 0.053 -10000 0 -0.46 3 3
GADD45A 0.029 0.006 -10000 0 -10000 0 0
GSK3B 0.031 0.013 -10000 0 -10000 0 0
PAK1/Aurora A 0.039 0.041 -10000 0 -10000 0 0
MDM2 0.029 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.072 0.19 -10000 0 -0.43 110 110
TP53 0.033 0.025 -10000 0 -0.34 1 1
DLG7 0.021 0.025 -10000 0 -10000 0 0
AURKAIP1 0.025 0.049 -10000 0 -0.62 3 3
ARHGEF7 0.029 0.004 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.05 0.056 -10000 0 -0.48 3 3
G2/M transition of mitotic cell cycle 0.031 0.034 -10000 0 -10000 0 0
AURKA 0.031 0.033 -10000 0 -10000 0 0
AURKB -0.066 0.093 -10000 0 -0.18 155 155
CDC25B 0.029 0.032 -10000 0 -0.34 1 1
G2/M transition checkpoint 0.013 0.03 -10000 0 -10000 0 0
mRNA polyadenylation -0.047 0.16 -10000 0 -0.36 103 103
Aurora A/CPEB -0.047 0.16 -10000 0 -0.36 103 103
Aurora A/TACC1/TRAP/chTOG 0.063 0.045 -10000 0 -10000 0 0
BRCA1 0.029 0.004 -10000 0 -10000 0 0
centrosome duplication 0.038 0.041 -10000 0 -10000 0 0
regulation of centrosome cycle 0.045 0.052 -10000 0 -0.45 3 3
spindle assembly 0.061 0.044 -10000 0 -10000 0 0
TDRD7 0.029 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.036 0.16 -10000 0 -0.41 13 13
CENPA -0.049 0.085 -10000 0 -0.26 14 14
Aurora A/PP2A 0.037 0.04 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.03 0.031 -10000 0 -10000 0 0
negative regulation of DNA binding 0.033 0.027 -10000 0 -0.34 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.043 0.008 -10000 0 -10000 0 0
RASA1 0.025 0.03 -10000 0 -0.64 1 1
Ajuba/Aurora A 0.013 0.03 -10000 0 -10000 0 0
mitotic prometaphase 0.023 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.033 -10000 0 -10000 0 0
TACC1 0.027 0.009 -10000 0 -10000 0 0
TACC3 0.025 0.054 -10000 0 -0.59 4 4
Aurora A/Antizyme1 0.049 0.052 -10000 0 -0.34 3 3
Aurora A/RasGAP 0.034 0.044 -10000 0 -0.4 1 1
OAZ1 0.028 0.027 -10000 0 -0.59 1 1
RAN 0.029 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.033 0.01 -10000 0 -10000 0 0
GIT1 0.029 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.059 0.012 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.071 0.19 -10000 0 -0.43 110 110
PPP2R5D 0.029 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 -0.045 0.15 -10000 0 -0.39 15 15
PAK1 0.03 0.003 -10000 0 -10000 0 0
CKAP5 0.03 0.003 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.058 -10000 0 -0.41 3 3
epithelial cell differentiation 0.027 0.071 -10000 0 -0.34 14 14
CYFIP2 0.014 0.077 -10000 0 -0.64 7 7
ENAH 0.062 0.1 0.39 17 -10000 0 17
EGFR 0.02 0.067 -10000 0 -0.6 6 6
EPHA2 0.027 0.03 -10000 0 -0.64 1 1
MYO6 0.058 0.11 0.38 13 -0.48 2 15
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.058 -10000 0 -0.4 7 7
AQP5 -0.1 0.24 -10000 0 -0.51 108 108
CTNND1 0.03 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.062 0.11 0.4 13 -10000 0 13
regulation of calcium-dependent cell-cell adhesion 0.052 0.12 0.4 11 -0.46 1 12
EGF -0.57 0.2 -10000 0 -0.63 474 474
NCKAP1 0.029 0.006 -10000 0 -10000 0 0
AQP3 0.007 0.16 -10000 0 -0.55 30 30
cortical microtubule organization 0.027 0.071 -10000 0 -0.34 14 14
GO:0000145 0.052 0.11 0.39 13 -10000 0 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.073 -10000 0 -0.34 14 14
MLLT4 0.027 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.046 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.065 0.041 -10000 0 -0.36 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.041 0.084 0.38 2 -10000 0 2
PVRL2 0.03 0.003 -10000 0 -10000 0 0
ZYX 0.048 0.094 0.36 5 -10000 0 5
ARF6/GTP 0.069 0.044 -10000 0 -0.34 2 2
CDH1 0.007 0.12 -10000 0 -0.62 18 18
EGFR/EGFR/EGF/EGF -0.24 0.14 -10000 0 -0.59 19 19
RhoA/GDP 0.029 0.068 -10000 0 -10000 0 0
actin cytoskeleton organization 0.051 0.1 0.35 12 -0.45 2 14
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
GIT1 0.029 0.004 -10000 0 -10000 0 0
IGF1R 0.03 0.003 -10000 0 -10000 0 0
IGF1 0.023 0.06 -10000 0 -0.59 5 5
DIAPH1 0.032 0.11 -10000 0 -0.67 7 7
Wnt receptor signaling pathway -0.027 0.071 0.34 14 -10000 0 14
RHOA 0.021 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.009 0.048 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
VCL 0.051 0.1 0.35 12 -0.46 2 14
EFNA1 0.027 0.028 -10000 0 -0.59 1 1
LPP 0.046 0.095 0.39 6 -10000 0 6
Ephrin A1/EPHA2 0.023 0.065 -10000 0 -10000 0 0
SEC6/SEC8 0.001 0.05 -10000 0 -10000 0 0
MGAT3 0.053 0.12 0.41 11 -0.47 1 12
HGF/MET 0.012 0.09 -10000 0 -0.6 3 3
HGF 0.003 0.12 -10000 0 -0.6 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.058 -10000 0 -0.41 3 3
actin cable formation 0.11 0.13 0.33 73 -10000 0 73
KIAA1543 0.048 0.11 0.36 10 -0.53 2 12
KIFC3 0.051 0.094 -10000 0 -10000 0 0
NCK1 0.027 0.03 -10000 0 -0.64 1 1
EXOC3 0.027 0.009 -10000 0 -10000 0 0
ACTN1 0.052 0.1 0.43 7 -10000 0 7
NCK1/GIT1 0.04 0.025 -10000 0 -0.47 1 1
mol:GDP 0.027 0.071 -10000 0 -0.34 14 14
EXOC4 0.027 0.009 -10000 0 -10000 0 0
STX4 0.051 0.092 -10000 0 -10000 0 0
PIP5K1C 0.062 0.11 0.4 13 -10000 0 13
LIMA1 0.029 0.005 -10000 0 -10000 0 0
ABI1 0.029 0.004 -10000 0 -10000 0 0
ROCK1 0.075 0.11 0.41 19 -10000 0 19
adherens junction assembly 0.071 0.14 0.51 16 -0.71 2 18
IGF-1R heterotetramer/IGF1 0.022 0.069 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
MET 0.024 0.039 -10000 0 -0.59 2 2
PLEKHA7 0.057 0.11 0.36 10 -0.56 2 12
mol:GTP 0.063 0.04 -10000 0 -0.35 3 3
establishment of epithelial cell apical/basal polarity 0.083 0.13 0.38 50 -10000 0 50
cortical actin cytoskeleton stabilization 0.013 0.058 -10000 0 -0.41 3 3
regulation of cell-cell adhesion 0.051 0.1 0.35 12 -0.45 2 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.058 -10000 0 -0.41 3 3
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.024 0.029 -10000 0 -10000 0 0
DAPP1 0.009 0.11 0.34 8 -0.41 13 21
Src family/SYK family/BLNK-LAT/BTK-ITK -0.08 0.19 0.29 1 -0.51 45 46
mol:DAG -0.021 0.15 0.29 55 -0.26 37 92
HRAS 0.033 0.028 -10000 0 -0.59 1 1
RAP1A 0.033 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.031 0.076 0.26 2 -0.38 4 6
PLCG2 0.02 0.073 -10000 0 -0.61 7 7
PLCG1 0.029 0.006 -10000 0 -10000 0 0
ARF5 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.01 0.03 0.3 2 -10000 0 2
ARF1/GTP 0.037 0.057 0.31 3 -10000 0 3
RHOA 0.021 0.014 -10000 0 -10000 0 0
YES1 0.029 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.028 0.3 1 -10000 0 1
ADAP1 0.034 0.07 0.29 3 -10000 0 3
ARAP3 0.01 0.03 0.3 2 -10000 0 2
INPPL1 0.03 0.003 -10000 0 -10000 0 0
PREX1 0.029 0.006 -10000 0 -10000 0 0
ARHGEF6 0.03 0.003 -10000 0 -10000 0 0
ARHGEF7 0.029 0.004 -10000 0 -10000 0 0
ARF1 0.029 0.006 -10000 0 -10000 0 0
NRAS 0.033 0.01 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
FGR 0.025 0.047 -10000 0 -0.59 3 3
mol:Ca2+ 0 0.097 0.32 19 -10000 0 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.029 0.006 -10000 0 -10000 0 0
ZAP70 -0.31 0.31 -10000 0 -0.59 291 291
mol:IP3 -0.009 0.12 0.33 22 -10000 0 22
LYN 0.028 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.042 0.081 0.26 6 -0.37 4 10
RhoA/GDP 0.018 0.046 0.38 1 -10000 0 1
PDK1/Src/Hsp90 0.052 0.029 -10000 0 -0.4 1 1
BLNK 0.028 0.03 -10000 0 -0.64 1 1
actin cytoskeleton reorganization 0.04 0.098 0.38 12 -10000 0 12
SRC 0.029 0.006 -10000 0 -10000 0 0
PLEKHA2 0.013 0.034 -10000 0 -0.37 4 4
RAC1 0.027 0.009 -10000 0 -10000 0 0
PTEN 0.021 0.013 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
ARF6/GTP 0.024 0.027 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.03 0.3 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.1 0.17 -10000 0 -0.43 63 63
BLK -0.013 0.15 -10000 0 -0.59 34 34
PDPK1 0.027 0.03 -10000 0 -0.64 1 1
CYTH1 0.048 0.073 0.29 11 -10000 0 11
HCK -0.003 0.14 -10000 0 -0.59 27 27
CYTH3 0.037 0.063 0.29 3 -10000 0 3
CYTH2 0.047 0.072 0.29 11 -10000 0 11
KRAS 0.033 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.043 0.056 -10000 0 -0.42 1 1
SGK1 0.038 0.072 -10000 0 -0.45 1 1
INPP5D 0.024 0.054 -10000 0 -0.59 4 4
mol:GDP 0.031 0.083 0.26 8 -0.4 4 12
SOS1 0.029 0.005 -10000 0 -10000 0 0
SYK 0.027 0.033 -10000 0 -0.48 2 2
ARF6/GDP 0.018 0.045 0.39 1 -10000 0 1
mol:PI-3-4-5-P3 0.039 0.062 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.021 0.028 0.3 1 -10000 0 1
VAV1 -0.12 0.26 -10000 0 -0.59 123 123
mol:PI-3-4-P2 0.019 0.04 -10000 0 -0.43 4 4
RAS family/GTP/PI3K Class I 0.08 0.066 0.34 1 -10000 0 1
PLEKHA1 0.013 0.034 -10000 0 -0.37 4 4
Rac1/GDP 0.031 0.075 0.24 1 -0.38 4 5
LAT -0.14 0.28 -10000 0 -0.59 144 144
Rac1/GTP 0.016 0.073 -10000 0 -0.4 1 1
ITK -0.056 0.15 0.33 3 -10000 0 3
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.047 0.18 0.3 48 -0.38 39 87
LCK 0.003 0.12 -10000 0 -0.59 22 22
BTK -0.015 0.15 0.29 12 -10000 0 12
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.081 0.17 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.05 0.15 -10000 0 -0.79 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.062 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.06 0.086 -10000 0 -0.34 1 1
CaM/Ca2+ -0.073 0.16 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.084 0.15 -10000 0 -0.66 1 1
AKT1 -0.057 0.16 0.4 8 -10000 0 8
MAP2K1 -0.077 0.14 0.31 5 -10000 0 5
MAP3K11 -0.086 0.16 0.31 7 -0.58 1 8
IFNGR1 0.005 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.17 0.25 -10000 0 -0.59 98 98
Rap1/GTP -0.073 0.11 -10000 0 -10000 0 0
CRKL/C3G 0.043 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.087 0.19 -10000 0 -10000 0 0
CEBPB -0.007 0.15 0.5 11 -10000 0 11
STAT3 0.029 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.063 0.17 -10000 0 -0.62 3 3
STAT1 -0.083 0.16 0.32 8 -0.66 1 9
CALM1 0.028 0.008 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.24 0.3 -10000 0 -0.58 232 232
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
STAT1 (dimer)/PIAS1 -0.069 0.16 0.32 3 -0.62 1 4
CEBPB/PTGES2/Cbp/p300 -0.01 0.085 -10000 0 -0.4 1 1
mol:Ca2+ -0.081 0.16 -10000 0 -10000 0 0
MAPK3 -0.038 0.13 0.42 3 -0.62 1 4
STAT1 (dimer) -0.075 0.12 -10000 0 -0.49 1 1
MAPK1 -0.037 0.13 0.45 4 -0.59 2 6
JAK2 0.005 0.031 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
JAK1 0.005 0.032 -10000 0 -10000 0 0
CAMK2D 0.03 0.004 -10000 0 -10000 0 0
DAPK1 0.008 0.13 0.4 18 -0.61 3 21
SMAD7 -0.011 0.077 0.24 20 -10000 0 20
CBL/CRKL/C3G -0.061 0.16 -10000 0 -10000 0 0
PI3K -0.07 0.15 -10000 0 -10000 0 0
IFNG -0.24 0.3 -10000 0 -0.58 232 232
apoptosis 0 0.12 0.4 14 -0.43 7 21
CAMK2G 0.029 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.004 -10000 0 -10000 0 0
CAMK2A -0.14 0.28 -10000 0 -0.64 127 127
CAMK2B -0.063 0.22 -10000 0 -0.63 71 71
FRAP1 -0.057 0.14 0.35 12 -10000 0 12
PRKCD -0.069 0.14 0.37 6 -10000 0 6
RAP1B 0.029 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.06 0.086 -10000 0 -0.34 1 1
PTPN2 0.029 0.005 -10000 0 -10000 0 0
EP300 0.029 0.029 -10000 0 -0.63 1 1
IRF1 -0.036 0.12 0.42 5 -0.75 1 6
STAT1 (dimer)/PIASy -0.071 0.16 0.37 2 -0.63 1 3
SOCS1 0.028 0.069 -10000 0 -0.98 1 1
mol:GDP -0.061 0.15 -10000 0 -10000 0 0
CASP1 -0.012 0.076 0.24 20 -10000 0 20
PTGES2 0.026 0.041 -10000 0 -0.64 2 2
IRF9 0.023 0.071 0.25 17 -10000 0 17
mol:PI-3-4-5-P3 -0.077 0.14 -10000 0 -10000 0 0
RAP1/GDP -0.061 0.12 -10000 0 -10000 0 0
CBL -0.087 0.15 0.3 7 -10000 0 7
MAP3K1 -0.084 0.15 0.33 5 -10000 0 5
PIAS1 0.03 0.003 -10000 0 -10000 0 0
PIAS4 0.029 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.06 0.086 -10000 0 -0.34 1 1
PTPN11 -0.096 0.15 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.06 -10000 0 -10000 0 0
CRKL 0.03 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
DOCK1 0.028 0.03 -10000 0 -0.64 1 1
ITGA4 0.01 0.11 -10000 0 -0.59 16 16
alpha4/beta7 Integrin/MAdCAM1 0.031 0.092 -10000 0 -0.34 25 25
EPO -0.17 0.29 -10000 0 -0.59 168 168
alpha4/beta7 Integrin 0.027 0.082 -10000 0 -0.43 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.027 0.082 -10000 0 -0.43 16 16
EPO/EPOR (dimer) -0.11 0.22 -10000 0 -0.43 168 168
lamellipodium assembly 0.024 0.089 0.31 1 -0.54 6 7
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PI3K 0.037 0.035 -10000 0 -0.47 2 2
ARF6 0.028 0.008 -10000 0 -10000 0 0
JAK2 -0.045 0.12 -10000 0 -0.39 10 10
PXN 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
MADCAM1 0.014 0.09 -10000 0 -0.6 11 11
cell adhesion 0.029 0.091 -10000 0 -0.34 25 25
CRKL/CBL 0.042 0.024 -10000 0 -0.47 1 1
ITGB1 0.029 0.004 -10000 0 -10000 0 0
SRC 0.014 0.084 -10000 0 -0.35 1 1
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.034 0.095 -10000 0 -0.37 26 26
p130Cas/Crk/Dock1 0.037 0.084 -10000 0 -0.59 1 1
VCAM1 0.015 0.089 -10000 0 -0.53 13 13
RHOA 0.021 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.073 -10000 0 -10000 0 0
BCAR1 0.008 0.082 -10000 0 -0.64 1 1
EPOR 0.03 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.028 0.029 -10000 0 -0.64 1 1
GIT1 0.029 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.091 0.32 1 -0.56 6 7
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.013 -10000 0 -10000 0 0
AES 0.027 0.011 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.04 0.015 -10000 0 -10000 0 0
SMAD4 0.029 0.005 -10000 0 -10000 0 0
DKK2 0.001 0.13 -10000 0 -0.6 24 24
TLE1 0.027 0.012 -10000 0 -10000 0 0
MACF1 0.03 0.007 -10000 0 -10000 0 0
CTNNB1 0.037 0.12 0.41 10 -0.41 1 11
WIF1 0.002 0.066 -10000 0 -0.63 5 5
beta catenin/RanBP3 -0.009 0.089 0.32 10 -10000 0 10
KREMEN2 -0.043 0.2 -10000 0 -0.59 60 60
DKK1 0.002 0.13 -10000 0 -0.61 22 22
beta catenin/beta TrCP1 0.02 0.087 0.35 2 -10000 0 2
FZD1 0.027 0.01 -10000 0 -10000 0 0
AXIN2 -0.001 0.12 0.54 9 -1.4 2 11
AXIN1 0.029 0.007 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.12 -10000 0 -0.54 13 13
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.062 0.087 0.34 1 -0.75 1 2
Axin1/APC/GSK3 0.074 0.087 0.36 12 -10000 0 12
Axin1/APC/GSK3/beta catenin/Macf1 0.05 0.1 0.42 6 -10000 0 6
HNF1A 0.022 0.059 -10000 0 -0.64 4 4
CTBP1 0.027 0.012 -10000 0 -10000 0 0
MYC -0.002 0.14 0.59 12 -0.53 3 15
RANBP3 0.03 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.009 0.15 -10000 0 -0.38 75 75
NKD1 -0.14 0.29 -10000 0 -0.63 134 134
TCF4 0.027 0.012 -10000 0 -10000 0 0
TCF3 0.027 0.011 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.088 -10000 0 -0.33 24 24
Ran/GTP 0.021 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.015 0.093 0.37 13 -0.52 2 15
LEF1 0.008 0.11 -10000 0 -0.6 16 16
DVL1 0.021 0.031 -10000 0 -0.3 2 2
CSNK2A1 0.03 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.07 0.088 0.35 1 -0.6 2 3
DKK1/LRP6/Kremen 2 -0.008 0.16 -10000 0 -0.4 69 69
LRP6 0.03 0.006 -10000 0 -10000 0 0
CSNK1A1 0.021 0.016 -10000 0 -10000 0 0
NLK 0.03 0.005 -10000 0 -10000 0 0
CCND1 -0.015 0.1 0.57 2 -0.48 17 19
WNT1 0 0.13 -10000 0 -0.59 25 25
GSK3A 0.031 0.004 -10000 0 -10000 0 0
GSK3B 0.028 0.008 -10000 0 -10000 0 0
FRAT1 0.028 0.006 -10000 0 -10000 0 0
PPP2R5D 0.098 0.14 0.34 124 -0.34 8 132
APC 0.027 0.096 0.38 9 -10000 0 9
WNT1/LRP6/FZD1 0.036 0.053 0.25 3 -10000 0 3
CREBBP 0.026 0.012 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.007 0.095 0.57 1 -10000 0 1
GNAI2 0.021 0.014 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.032 0.15 -10000 0 -0.37 83 83
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.024 0.055 -10000 0 -0.6 4 4
RhoA/GTP -0.006 0.097 -10000 0 -0.58 1 1
negative regulation of cAMP metabolic process -0.016 0.1 -10000 0 -0.36 19 19
GNAZ 0.026 0.05 -10000 0 -0.64 3 3
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GNA12 0.027 0.009 -10000 0 -10000 0 0
S1PR5 -0.079 0.24 -10000 0 -0.59 92 92
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.016 0.1 -10000 0 -0.36 19 19
RhoA/GDP 0.016 0.01 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
GNAI1 0.026 0.03 -10000 0 -0.64 1 1
Nongenotropic Androgen 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
PTK2 0.011 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.032 0.09 -10000 0 -0.36 25 25
regulation of S phase of mitotic cell cycle 0.019 0.07 -10000 0 -0.38 6 6
GNAO1 0.024 0.055 -10000 0 -0.6 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
SHBG/T-DHT -0.024 0.13 -10000 0 -0.4 54 54
PELP1 0.029 0.006 -10000 0 -10000 0 0
AKT1 0.011 0.003 -10000 0 -10000 0 0
MAP2K1 0.009 0.073 0.35 1 -0.4 3 4
T-DHT/AR -0.002 0.11 -10000 0 -0.46 26 26
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.009 13 13
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GNAI1 0.026 0.03 -10000 0 -0.64 1 1
mol:GDP -0.007 0.1 -10000 0 -0.46 24 24
cell proliferation 0.006 0.11 0.31 4 -0.56 6 10
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
FOS 0.01 0.14 -10000 0 -0.73 14 14
mol:Ca2+ 0.003 0.016 -10000 0 -0.083 9 9
MAPK3 0.011 0.091 0.31 5 -0.48 5 10
MAPK1 0.014 0.062 -10000 0 -0.43 4 4
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
mol:IP3 0 0.001 -10000 0 -0.005 12 12
cAMP biosynthetic process -0.039 0.12 0.24 2 -0.39 53 55
GNG2 0.028 0.008 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 12 12
HRAS/GTP 0.041 0.08 -10000 0 -0.33 21 21
actin cytoskeleton reorganization 0.036 0.029 -10000 0 -0.32 2 2
SRC 0.029 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 12 12
PI3K 0.034 0.03 -10000 0 -0.41 2 2
apoptosis -0.015 0.1 0.5 12 -0.26 3 15
T-DHT/AR/PELP1 0.019 0.094 -10000 0 -0.4 24 24
HRAS/GDP 0.01 0.1 -10000 0 -0.45 24 24
CREB1 0.016 0.11 0.27 2 -0.54 12 14
RAC1-CDC42/GTP 0.045 0.033 -10000 0 -0.32 2 2
AR -0.002 0.14 -10000 0 -0.62 26 26
GNB1 0.029 0.006 -10000 0 -10000 0 0
RAF1 0.011 0.076 0.35 1 -0.39 3 4
RAC1-CDC42/GDP 0.03 0.1 -10000 0 -0.45 18 18
T-DHT/AR/PELP1/Src 0.038 0.085 -10000 0 -0.37 20 20
MAP2K2 0.008 0.072 0.35 1 -0.4 3 4
T-DHT/AR/PELP1/Src/PI3K 0.019 0.07 -10000 0 -0.38 6 6
GNAZ 0.026 0.05 -10000 0 -0.64 3 3
SHBG -0.039 0.2 -10000 0 -0.63 54 54
Gi family/GNB1/GNG2/GDP -0.009 0.12 -10000 0 -0.5 15 15
mol:T-DHT 0 0.001 -10000 0 -0.007 9 9
RAC1 0.027 0.009 -10000 0 -10000 0 0
GNRH1 -0.12 0.2 -10000 0 -0.44 147 147
Gi family/GTP 0.007 0.059 -10000 0 -0.35 7 7
CDC42 0.029 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.053 0.06 -10000 0 -0.33 10 10
ER alpha/Gai/GDP/Gbeta gamma -0.031 0.17 -10000 0 -0.54 36 36
AKT1 -0.03 0.22 -10000 0 -0.73 45 45
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.03 0.23 -10000 0 -0.75 45 45
mol:Ca2+ -0.018 0.12 -10000 0 -0.47 17 17
IGF1R 0.03 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.03 0.059 -10000 0 -0.45 7 7
SHC1 0.029 0.007 -10000 0 -10000 0 0
apoptosis 0.027 0.22 0.7 45 -10000 0 45
RhoA/GTP 0.017 0.034 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.004 0.14 -10000 0 -0.58 13 13
regulation of stress fiber formation -0.034 0.058 0.48 1 -0.36 4 5
E2/ERA-ERB (dimer) 0.026 0.061 -10000 0 -0.39 10 10
KRAS 0.029 0.006 -10000 0 -10000 0 0
G13/GTP 0.031 0.037 -10000 0 -0.36 4 4
pseudopodium formation 0.034 0.058 0.36 4 -0.48 1 5
E2/ER alpha (dimer)/PELP1 0.033 0.04 -10000 0 -0.4 4 4
GRB2 0.029 0.005 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
GNAO1 0.024 0.055 -10000 0 -0.6 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.004 0.18 0.33 4 -0.54 40 44
E2/ER beta (dimer) 0.015 0.051 -10000 0 -0.41 7 7
mol:GDP 0.02 0.054 -10000 0 -0.42 4 4
mol:NADP -0.004 0.18 0.33 4 -0.54 40 44
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
mol:IP3 -0.019 0.13 -10000 0 -0.49 17 17
IGF-1R heterotetramer 0.03 0.003 -10000 0 -10000 0 0
PLCB1 0.015 0.09 -10000 0 -0.5 10 10
PLCB2 -0.014 0.12 -10000 0 -0.47 16 16
IGF1 0.023 0.06 -10000 0 -0.59 5 5
mol:L-citrulline -0.004 0.18 0.33 4 -0.54 40 44
RHOA 0.021 0.014 -10000 0 -10000 0 0
Gai/GDP -0.11 0.26 -10000 0 -0.53 119 119
JNK cascade 0.015 0.05 -10000 0 -0.41 7 7
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
ESR2 0.02 0.069 -10000 0 -0.56 7 7
GNAQ 0.029 0.006 -10000 0 -10000 0 0
ESR1 0.022 0.059 -10000 0 -0.56 5 5
Gq family/GDP/Gbeta gamma 0.021 0.12 -10000 0 -0.76 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.03 0.14 -10000 0 -0.91 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.005 0.14 -10000 0 -0.58 13 13
GNAZ 0.026 0.05 -10000 0 -0.64 3 3
E2/ER alpha (dimer) 0.016 0.044 -10000 0 -0.42 5 5
STRN 0.024 0.058 -10000 0 -0.64 4 4
GNAL 0.029 0.005 -10000 0 -10000 0 0
PELP1 0.029 0.005 -10000 0 -10000 0 0
MAPK11 0.014 0.05 -10000 0 -0.38 8 8
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GNAI1 0.026 0.03 -10000 0 -0.64 1 1
HBEGF -0.08 0.18 0.41 10 -0.54 31 41
cAMP biosynthetic process 0.023 0.049 -10000 0 -0.31 10 10
SRC -0.025 0.16 -10000 0 -0.62 21 21
PI3K 0.037 0.035 -10000 0 -0.47 2 2
GNB1 0.029 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.042 0.065 -10000 0 -0.4 2 2
SOS1 0.029 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.038 0.098 -10000 0 -0.48 13 13
Gs family/GTP 0.03 0.052 -10000 0 -0.32 10 10
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.023 -10000 0 -0.34 1 1
vasodilation -0.002 0.17 0.31 5 -0.51 40 45
mol:DAG -0.019 0.13 -10000 0 -0.49 17 17
Gs family/GDP/Gbeta gamma 0.021 0.056 -10000 0 -0.37 2 2
MSN 0.035 0.061 0.37 4 -0.52 1 5
Gq family/GTP 0.023 0.079 -10000 0 -0.48 9 9
mol:PI-3-4-5-P3 -0.028 0.22 -10000 0 -0.72 45 45
NRAS 0.029 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.002 0.17 0.51 40 -0.31 5 45
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.063 -10000 0 -0.41 3 3
NOS3 -0.006 0.19 0.36 3 -0.57 40 43
GNA11 0.026 0.05 -10000 0 -0.64 3 3
MAPKKK cascade 0.006 0.18 0.41 3 -0.55 44 47
E2/ER alpha (dimer)/PELP1/Src 0.002 0.15 -10000 0 -0.6 14 14
ruffle organization 0.034 0.058 0.36 4 -0.48 1 5
ROCK2 0.039 0.064 0.38 4 -0.58 1 5
GNA14 0.02 0.076 -10000 0 -0.64 7 7
GNA15 0.012 0.1 -10000 0 -0.59 15 15
GNA13 0.029 0.005 -10000 0 -10000 0 0
MMP9 -0.15 0.2 0.38 7 -0.5 63 70
MMP2 -0.019 0.16 0.33 2 -0.58 20 22
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.006 -10000 0 -10000 0 0
SMARCC1 0.009 0.046 -10000 0 -0.66 2 2
REL 0.025 0.053 -10000 0 -0.56 4 4
HDAC7 -0.13 0.096 -10000 0 -0.61 4 4
JUN 0.029 0.006 -10000 0 -10000 0 0
EP300 0.028 0.029 -10000 0 -0.64 1 1
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
KAT5 0.03 0.003 -10000 0 -10000 0 0
MAPK14 -0.016 0.041 -10000 0 -0.5 3 3
FOXO1 0.029 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.14 0.1 -10000 0 -0.6 5 5
MAP2K6 0.014 0.052 -10000 0 -0.66 3 3
BRM/BAF57 0.041 0.012 -10000 0 -10000 0 0
MAP2K4 0.018 0.011 -10000 0 -10000 0 0
SMARCA2 0.028 0.007 -10000 0 -10000 0 0
PDE9A -0.12 0.14 -10000 0 -0.82 14 14
NCOA2 0.015 0.091 -10000 0 -0.64 10 10
CEBPA 0.018 0.085 -10000 0 -0.59 10 10
EHMT2 0.029 0.006 -10000 0 -10000 0 0
cell proliferation -0.12 0.13 0.51 4 -0.47 16 20
NR0B1 -0.016 0.15 -10000 0 -0.59 32 32
EGR1 0.011 0.087 -10000 0 -0.64 9 9
RXRs/9cRA 0.048 0.037 -10000 0 -0.36 3 3
AR/RACK1/Src -0.037 0.067 -10000 0 -0.46 5 5
AR/GR -0.019 0.091 -10000 0 -0.5 11 11
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
PKN1 0.03 0.002 -10000 0 -10000 0 0
RCHY1 0.03 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.017 1 1
MAPK8 -0.016 0.034 -10000 0 -0.48 2 2
T-DHT/AR/TIF2/CARM1 -0.048 0.093 -10000 0 -0.59 8 8
SRC -0.037 0.042 -10000 0 -0.4 3 3
NR3C1 0.022 0.03 -10000 0 -0.59 1 1
KLK3 -0.027 0.14 0.35 1 -0.59 19 20
APPBP2 0 0.018 -10000 0 -10000 0 0
TRIM24 0.027 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.05 0.07 -10000 0 -0.49 6 6
TMPRSS2 -0.91 0.36 -10000 0 -1 460 460
RXRG 0.022 0.057 -10000 0 -0.62 4 4
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.029 0.005 -10000 0 -10000 0 0
RXRB 0.029 0.006 -10000 0 -10000 0 0
CARM1 0.03 0.003 -10000 0 -10000 0 0
NR2C2 0.02 0.032 -10000 0 -0.64 1 1
KLK2 -0.037 0.11 -10000 0 -0.54 16 16
AR -0.023 0.077 -10000 0 -0.4 16 16
SENP1 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
MDM2 0.029 0.007 -10000 0 -10000 0 0
SRY 0 0.004 0.02 18 -10000 0 18
GATA2 0.014 0.096 -10000 0 -0.61 12 12
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.095 0.24 -10000 0 -0.59 101 101
T-DHT/AR/RACK1/Src -0.037 0.067 -10000 0 -0.47 4 4
positive regulation of transcription 0.014 0.096 -10000 0 -0.61 12 12
DNAJA1 -0.001 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.009 -10000 0 -10000 0 0
NCOA1 0.054 0.032 -10000 0 -10000 0 0
SPDEF -0.1 0.26 -10000 0 -0.6 111 111
T-DHT/AR/TIF2 -0.03 0.095 -10000 0 -0.54 9 9
T-DHT/AR/Hsp90 -0.048 0.068 -10000 0 -0.51 4 4
GSK3B 0.024 0.008 -10000 0 -10000 0 0
NR2C1 0.029 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.044 0.047 -10000 0 -0.41 5 5
SIRT1 0.029 0.005 -10000 0 -10000 0 0
ZMIZ2 0.027 0.01 -10000 0 -10000 0 0
POU2F1 -0.071 0.047 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.11 -10000 0 -0.55 11 11
CREBBP 0.029 0.006 -10000 0 -10000 0 0
SMARCE1 0.029 0.005 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.041 -10000 0 -0.64 2 2
SPHK1 -0.02 0.17 -10000 0 -0.59 42 42
GNAI2 0.021 0.014 -10000 0 -10000 0 0
mol:S1P 0.006 0.062 -10000 0 -0.31 3 3
GNAO1 0.024 0.055 -10000 0 -0.6 4 4
mol:Sphinganine-1-P -0.015 0.13 -10000 0 -0.44 43 43
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.048 0.061 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
G12/G13 0.039 0.015 -10000 0 -10000 0 0
S1PR3 0.029 0.006 -10000 0 -10000 0 0
S1PR2 0.03 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.052 -10000 0 -0.27 3 3
S1PR5 -0.079 0.24 -10000 0 -0.59 92 92
S1PR4 -0.006 0.14 -10000 0 -0.59 30 30
GNAI1 0.026 0.03 -10000 0 -0.64 1 1
S1P/S1P5/G12 -0.025 0.15 -10000 0 -0.34 83 83
S1P/S1P3/Gq 0.022 0.09 -10000 0 -0.4 8 8
S1P/S1P4/Gi 0.013 0.076 0.29 1 -0.33 8 9
GNAQ 0.029 0.006 -10000 0 -10000 0 0
GNAZ 0.026 0.05 -10000 0 -0.64 3 3
GNA14 0.02 0.076 -10000 0 -0.64 7 7
GNA15 0.012 0.1 -10000 0 -0.59 15 15
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.026 0.05 -10000 0 -0.64 3 3
ABCC1 0.029 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.008 0.11 -9999 0 -0.59 16 16
PLK4 0.026 0.047 -9999 0 -0.59 3 3
regulation of centriole replication 0.006 0.086 -9999 0 -0.43 19 19
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.002 0.11 -10000 0 -0.55 17 17
Crk/p130 Cas/Paxillin -0.03 0.084 -10000 0 -0.42 5 5
JUN 0.006 0.095 -10000 0 -0.49 8 8
HRAS 0.029 0.027 -10000 0 -0.59 1 1
RET51/GFRalpha1/GDNF/GRB10 0.02 0.13 -10000 0 -0.39 38 38
RAP1A 0.029 0.006 -10000 0 -10000 0 0
FRS2 0.029 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.019 0.13 -10000 0 -0.4 38 38
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.01 0.1 -10000 0 -0.36 29 29
RHOA 0.021 0.014 -10000 0 -10000 0 0
RAP1A/GTP 0.02 0.12 -10000 0 -0.62 3 3
GRB7 0.02 0.076 -10000 0 -0.64 7 7
RET51/GFRalpha1/GDNF 0.02 0.14 -10000 0 -0.4 39 39
MAPKKK cascade 0.01 0.11 -10000 0 -0.53 4 4
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/IRS1 0.012 0.11 -10000 0 -0.38 38 38
lamellipodium assembly 0.003 0.091 -10000 0 -0.37 6 6
RET51/GFRalpha1/GDNF/SHC 0.02 0.13 -10000 0 -0.39 41 41
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC 0.016 0.1 -10000 0 -0.37 33 33
RET9/GFRalpha1/GDNF/Shank3 0.016 0.11 -10000 0 -0.37 35 35
MAPK3 0.005 0.12 0.52 1 -0.59 3 4
DOK1 0.029 0.005 -10000 0 -10000 0 0
DOK6 0.016 0.092 -10000 0 -0.61 11 11
PXN 0.029 0.005 -10000 0 -10000 0 0
neurite development 0.005 0.11 -10000 0 -0.48 6 6
DOK5 0.016 0.09 -10000 0 -0.63 10 10
GFRA1 -0.016 0.16 -10000 0 -0.58 39 39
MAPK8 0.002 0.099 -10000 0 -0.5 9 9
HRAS/GTP 0.018 0.13 -10000 0 -0.6 4 4
tube development 0.02 0.1 -10000 0 -0.35 29 29
MAPK1 0.011 0.13 0.43 6 -0.59 3 9
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.009 0.074 -10000 0 -0.35 1 1
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
PDLIM7 0.019 0.048 -10000 0 -0.59 3 3
RET51/GFRalpha1/GDNF/Dok6 0.024 0.14 -10000 0 -0.62 9 9
SHC1 0.029 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.019 0.13 -10000 0 -0.4 39 39
RET51/GFRalpha1/GDNF/Dok5 0.014 0.15 -10000 0 -0.43 43 43
PRKCA 0.029 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.02 -10000 0 -0.44 1 1
CREB1 0.007 0.097 -10000 0 -0.44 9 9
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.006 0.082 -10000 0 -0.3 25 25
RET51/GFRalpha1/GDNF/Grb7 0.015 0.15 -10000 0 -0.43 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.007 0.12 -10000 0 -0.61 18 18
DOK4 0.029 0.006 -10000 0 -10000 0 0
JNK cascade 0.006 0.093 -10000 0 -0.48 8 8
RET9/GFRalpha1/GDNF/FRS2 0.017 0.1 -10000 0 -0.37 31 31
SHANK3 0.03 0.003 -10000 0 -10000 0 0
RASA1 0.025 0.03 -10000 0 -0.64 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.006 0.085 -10000 0 -0.3 31 31
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.005 0.095 -10000 0 -0.38 9 9
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.002 0.11 -10000 0 -0.42 16 16
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.004 0.1 -10000 0 -0.45 11 11
PI3K 0.005 0.14 -10000 0 -0.51 12 12
SOS1 0.029 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.028 0.1 -10000 0 -0.35 29 29
GRB10 0.027 0.009 -10000 0 -10000 0 0
activation of MAPKK activity 0.005 0.085 -10000 0 -0.41 3 3
RET51/GFRalpha1/GDNF/FRS2 0.021 0.13 -10000 0 -0.4 35 35
GAB1 0.03 0.004 -10000 0 -10000 0 0
IRS1 0.023 0.058 -10000 0 -0.64 4 4
IRS2 0.02 0.078 -10000 0 -0.6 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.002 0.11 -10000 0 -0.42 15 15
RET51/GFRalpha1/GDNF/PKC alpha 0.019 0.13 -10000 0 -0.4 38 38
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GDNF 0.017 0.047 -10000 0 -0.59 3 3
RAC1 0.027 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.015 0.14 -10000 0 -0.4 42 42
Rac1/GTP 0.01 0.11 -10000 0 -0.45 6 6
RET9/GFRalpha1/GDNF -0.001 0.11 -10000 0 -0.41 35 35
GFRalpha1/GDNF -0.003 0.13 -10000 0 -0.47 35 35
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.013 -9999 0 -10000 0 0
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.011 0.049 -9999 0 -10000 0 0
GNAO1 0.026 0.055 -9999 0 -0.6 4 4
S1P/S1P3/G12/G13 0.051 0.022 -9999 0 -10000 0 0
AKT1 0.027 0.038 -9999 0 -0.37 1 1
AKT3 -0.017 0.097 -9999 0 -0.57 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.013 -9999 0 -10000 0 0
GNAI2 0.023 0.014 -9999 0 -10000 0 0
GNAI3 0.03 0.006 -9999 0 -10000 0 0
GNAI1 0.027 0.03 -9999 0 -0.63 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.031 0.006 -9999 0 -10000 0 0
S1PR2 0.03 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.04 -9999 0 -0.33 1 1
MAPK3 0.03 0.037 -9999 0 -10000 0 0
MAPK1 0.03 0.038 -9999 0 -10000 0 0
JAK2 -0.028 0.097 -9999 0 -0.46 4 4
CXCR4 -0.083 0.16 -9999 0 -0.41 7 7
FLT1 0.026 0.06 -9999 0 -0.59 5 5
RhoA/GDP 0.016 0.01 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.007 -9999 0 -10000 0 0
SRC 0.03 0.037 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.033 0.04 -9999 0 -0.34 1 1
RAC1 0.027 0.009 -9999 0 -10000 0 0
RhoA/GTP 0.038 0.047 -9999 0 -10000 0 0
VEGFA -0.24 0.31 -9999 0 -0.59 234 234
S1P/S1P2/Gi 0.03 0.041 -9999 0 -0.34 1 1
VEGFR1 homodimer/VEGFA homodimer -0.17 0.24 -9999 0 -0.44 234 234
RHOA 0.021 0.014 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.058 -9999 0 -0.4 3 3
GNAQ 0.029 0.006 -9999 0 -10000 0 0
GNAZ 0.027 0.05 -9999 0 -0.63 3 3
G12/G13 0.039 0.015 -9999 0 -10000 0 0
GNA14 0.02 0.076 -9999 0 -0.64 7 7
GNA15 0.012 0.1 -9999 0 -0.59 15 15
GNA12 0.027 0.009 -9999 0 -10000 0 0
GNA13 0.029 0.005 -9999 0 -10000 0 0
GNA11 0.026 0.05 -9999 0 -0.64 3 3
Rac1/GTP 0.028 0.053 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.077 0.082 -10000 0 -0.38 1 1
epithelial cell differentiation -0.049 0.1 -10000 0 -0.46 3 3
ITCH 0.063 0.02 -10000 0 -10000 0 0
WWP1 -0.092 0.064 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
EGFR 0.02 0.067 -10000 0 -0.6 6 6
PRL 0.021 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.047 0.08 0.38 2 -0.52 1 3
PTPRZ1 -0.049 0.2 -10000 0 -0.63 58 58
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.079 -10000 0 -0.44 5 5
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.08 0.083 -10000 0 -0.46 11 11
ADAM17 0.064 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.084 -10000 0 -0.33 3 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.092 -10000 0 -0.46 10 10
NCOR1 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.069 0.081 -10000 0 -0.45 9 9
GRIN2B -0.067 0.077 -10000 0 -0.43 10 10
ErbB4/ErbB2/betacellulin -0.12 0.14 -10000 0 -0.44 64 64
STAT1 0.027 0.028 -10000 0 -0.59 1 1
HBEGF 0.023 0.013 -10000 0 -10000 0 0
PRLR -0.051 0.21 -10000 0 -0.64 62 62
E4ICDs/ETO2 -0.1 0.079 -10000 0 -0.45 3 3
axon guidance -0.044 0.082 -10000 0 -10000 0 0
NEDD4 0.062 0.046 -10000 0 -0.62 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.027 0.16 -10000 0 -0.48 62 62
CBFA2T3 0.027 0.039 -10000 0 -0.59 2 2
ErbB4/ErbB2/HBEGF -0.047 0.064 -10000 0 -0.44 1 1
MAPK3 -0.052 0.079 0.45 1 -0.54 1 2
STAT1 (dimer) -0.1 0.076 -10000 0 -0.35 2 2
MAPK1 -0.051 0.081 0.38 2 -0.54 1 3
JAK2 0.028 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.076 0.079 -10000 0 -0.45 10 10
NRG1 0.026 0.082 -10000 0 -0.46 13 13
NRG3 0.016 0.09 -10000 0 -0.6 11 11
NRG2 0.012 0.081 -10000 0 -0.6 9 9
NRG4 -0.028 0.18 -10000 0 -0.63 45 45
heart development -0.044 0.082 -10000 0 -10000 0 0
neural crest cell migration -0.075 0.078 -10000 0 -0.45 10 10
ERBB2 0.042 0.034 -10000 0 -0.47 2 2
WWOX/E4ICDs -0.1 0.077 -10000 0 -0.41 2 2
SHC1 0.029 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.12 0.13 -10000 0 -0.46 40 40
apoptosis 0.089 0.078 0.35 11 -10000 0 11
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.084 0.089 -10000 0 -0.39 9 9
ErbB4/ErbB2/epiregulin -0.084 0.097 -10000 0 -0.41 22 22
ErbB4/ErbB4/betacellulin/betacellulin -0.16 0.15 -10000 0 -0.48 78 78
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.094 0.13 -10000 0 -0.45 35 35
MDM2 -0.1 0.071 -10000 0 -0.38 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.052 0.071 -10000 0 -0.43 10 10
STAT5A -0.038 0.077 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.072 0.086 -10000 0 -0.44 14 14
DLG4 0.029 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.042 0.011 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.096 0.068 -10000 0 -0.35 1 1
STAT5A (dimer) -0.048 0.12 -10000 0 -0.49 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.036 0.085 0.35 1 -10000 0 1
LRIG1 0.023 0.013 -10000 0 -10000 0 0
EREG -0.009 0.15 -10000 0 -0.59 32 32
BTC -0.069 0.24 -10000 0 -0.62 79 79
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.044 0.081 -10000 0 -10000 0 0
ERBB4 -0.12 0.084 -10000 0 -0.34 3 3
STAT5B 0.029 0.004 -10000 0 -10000 0 0
YAP1 -0.021 0.039 -10000 0 -0.53 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.095 0.12 -10000 0 -0.44 37 37
glial cell differentiation 0.095 0.068 0.35 1 -10000 0 1
WWOX 0.027 0.028 -10000 0 -0.59 1 1
cell proliferation -0.079 0.15 0.35 1 -0.54 20 21
FAS signaling pathway (CD95)

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
SPTAN1 0.008 0.026 -10000 0 -10000 0 0
RFC1 0.008 0.025 -10000 0 -10000 0 0
PRKDC 0.01 0.036 0.33 1 -10000 0 1
RIPK1 0.029 0.007 -10000 0 -10000 0 0
CASP7 -0.009 0.11 -10000 0 -0.64 11 11
FASLG/FAS/FADD/FAF1 -0.073 0.11 0.24 6 -0.31 2 8
MAP2K4 -0.053 0.15 0.31 5 -0.56 18 23
mol:ceramide -0.084 0.13 -10000 0 -0.39 10 10
GSN 0.008 0.026 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.085 0.12 -10000 0 -0.44 4 4
FAS 0.027 0.011 -10000 0 -10000 0 0
BID 0.002 0.041 -10000 0 -10000 0 0
MAP3K1 -0.017 0.12 0.32 5 -0.51 15 20
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
RB1 0.009 0.029 -10000 0 -10000 0 0
CFLAR 0.029 0.007 -10000 0 -10000 0 0
HGF/MET 0.03 0.1 -10000 0 -0.42 25 25
ARHGDIB 0.012 0.038 -10000 0 -10000 0 0
FADD 0.028 0.011 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.026 -10000 0 -10000 0 0
NFKB1 -0.027 0.088 -10000 0 -0.59 6 6
MAPK8 -0.061 0.17 0.41 3 -0.52 33 36
DFFA 0.008 0.025 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.008 0.025 -10000 0 -10000 0 0
FAS/FADD/MET 0.049 0.034 -10000 0 -0.37 2 2
CFLAR/RIP1 0.042 0.013 -10000 0 -10000 0 0
FAIM3 -0.013 0.16 -10000 0 -0.59 36 36
FAF1 0.026 0.014 -10000 0 -10000 0 0
PARP1 0.008 0.025 -10000 0 -10000 0 0
DFFB 0.008 0.025 -10000 0 -10000 0 0
CHUK -0.021 0.078 -10000 0 -0.6 4 4
FASLG -0.28 0.31 -10000 0 -0.59 258 258
FAS/FADD 0.04 0.017 -10000 0 -10000 0 0
HGF 0.003 0.12 -10000 0 -0.6 20 20
LMNA 0.007 0.033 0.29 1 -0.33 1 2
CASP6 0.008 0.025 -10000 0 -10000 0 0
CASP10 0.027 0.011 -10000 0 -10000 0 0
CASP3 0.006 0.032 -10000 0 -10000 0 0
PTPN13 0.018 0.086 -10000 0 -0.64 9 9
CASP8 0.005 0.07 0.26 36 -10000 0 36
IL6 -0.086 0.3 -10000 0 -1.1 32 32
MET 0.024 0.039 -10000 0 -0.59 2 2
ICAD/CAD 0.01 0.023 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.085 0.13 -10000 0 -0.39 10 10
activation of caspase activity by cytochrome c 0.002 0.041 -10000 0 -10000 0 0
PAK2 0.011 0.038 -10000 0 -10000 0 0
BCL2 0.029 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.037 0.051 -10000 0 -0.47 5 5
AKT1 -0.018 0.14 0.6 3 -0.63 2 5
PTK2B -0.099 0.17 0.36 2 -0.89 1 3
VEGFR2 homodimer/Frs2 0.043 0.042 -10000 0 -0.76 1 1
CAV1 -0.009 0.14 -10000 0 -0.59 30 30
CALM1 0.028 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.11 0.19 -10000 0 -0.7 2 2
endothelial cell proliferation 0.002 0.16 0.49 18 -0.5 1 19
mol:Ca2+ -0.1 0.17 -10000 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.085 0.18 -10000 0 -0.8 1 1
RP11-342D11.1 -0.11 0.16 -10000 0 -0.89 1 1
CDH5 0.028 0.028 -10000 0 -0.59 1 1
VEGFA homodimer -0.11 0.19 -10000 0 -0.33 146 146
SHC1 0.029 0.007 -10000 0 -10000 0 0
SHC2 0.022 0.068 -10000 0 -0.6 6 6
HRAS/GDP -0.078 0.15 -10000 0 -0.6 2 2
SH2D2A -0.16 0.29 -10000 0 -0.59 164 164
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.024 0.14 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.22 0.23 -10000 0 -0.63 64 64
VEGFR1 homodimer 0.023 0.06 -10000 0 -0.59 5 5
SHC/GRB2/SOS1 -0.07 0.18 -10000 0 -0.73 1 1
GRB10 -0.095 0.16 -10000 0 -0.75 1 1
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
PAK1 0.03 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.083 0.18 -10000 0 -0.75 2 2
HRAS 0.029 0.027 -10000 0 -0.59 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.05 0.11 -10000 0 -0.41 14 14
HIF1A 0.025 0.042 -10000 0 -0.64 2 2
FRS2 0.029 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.085 0.18 -10000 0 -0.79 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.013 -10000 0 -10000 0 0
Nck/Pak 0.041 0.025 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.11 0.19 -10000 0 -0.69 2 2
mol:GDP -0.077 0.16 -10000 0 -0.7 1 1
mol:NADP -0.02 0.13 0.47 5 -0.49 1 6
eNOS/Hsp90 -0.015 0.12 0.37 2 -0.45 1 3
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
mol:IP3 -0.1 0.17 -10000 0 -0.76 1 1
HIF1A/ARNT 0.038 0.035 -10000 0 -0.47 2 2
SHB 0.029 0.006 -10000 0 -10000 0 0
VEGFA -0.24 0.31 -10000 0 -0.59 234 234
VEGFC 0.028 0.027 -10000 0 -0.59 1 1
FAK1/Vinculin -0.066 0.15 0.45 2 -0.68 2 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.091 0.19 -10000 0 -0.96 1 1
PTPN6 0.029 0.006 -10000 0 -10000 0 0
EPAS1 0.037 0.034 -10000 0 -0.48 2 2
mol:L-citrulline -0.02 0.13 0.47 5 -0.49 1 6
ITGAV 0.029 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.09 0.19 -10000 0 -0.96 1 1
VEGFR2 homodimer/VEGFA homodimer -0.1 0.19 -10000 0 -0.99 1 1
VEGFR2/3 heterodimer 0.033 0.039 -10000 0 -0.49 2 2
VEGFB 0.03 0.003 -10000 0 -10000 0 0
MAPK11 -0.096 0.16 0.35 1 -0.66 2 3
VEGFR2 homodimer 0.032 0.045 -10000 0 -0.65 2 2
FLT1 0.023 0.06 -10000 0 -0.59 5 5
NEDD4 0.029 0.041 -10000 0 -0.63 2 2
MAPK3 -0.095 0.15 0.35 2 -0.72 1 3
MAPK1 -0.093 0.16 0.35 2 -0.66 1 3
VEGFA145/NRP2 -0.17 0.24 -10000 0 -0.43 231 231
VEGFR1/2 heterodimer 0.04 0.057 -10000 0 -0.74 1 1
KDR 0.032 0.045 -10000 0 -0.65 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.088 0.18 -10000 0 -0.88 2 2
SRC 0.029 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.084 0.17 0.46 4 -0.7 1 5
PI3K -0.052 0.14 -10000 0 -0.58 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.11 0.19 -10000 0 -0.62 2 2
FES -0.1 0.18 -10000 0 -0.78 2 2
GAB1 -0.059 0.14 -10000 0 -0.8 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.11 0.19 -10000 0 -0.62 2 2
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
ARNT 0.029 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.033 0.12 0.33 1 -0.44 3 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.1 0.19 -10000 0 -0.7 2 2
PI3K/GAB1 -0.017 0.12 -10000 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.079 0.18 -10000 0 -0.77 1 1
PRKACA 0.03 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.044 0.046 -10000 0 -0.55 1 1
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
CDC42 -0.1 0.17 -10000 0 -0.92 1 1
actin cytoskeleton reorganization -0.22 0.23 -10000 0 -0.62 65 65
PTK2 -0.078 0.14 -10000 0 -0.74 2 2
EDG1 -0.11 0.16 -10000 0 -0.89 1 1
mol:DAG -0.1 0.17 -10000 0 -0.76 1 1
CaM/Ca2+ -0.086 0.16 -10000 0 -0.69 1 1
MAP2K3 -0.098 0.16 0.39 1 -0.74 1 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.077 0.19 -10000 0 -0.79 1 1
PLCG1 -0.1 0.17 -10000 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.091 0.19 -10000 0 -0.8 1 1
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
YES1 0.029 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.11 0.19 -10000 0 -0.7 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.11 0.19 -10000 0 -0.7 2 2
cell migration -0.033 0.14 0.43 3 -0.53 3 6
mol:PI-3-4-5-P3 -0.049 0.13 -10000 0 -0.53 3 3
FYN 0.028 0.008 -10000 0 -10000 0 0
VEGFB/NRP1 -0.093 0.16 -10000 0 -0.85 1 1
mol:NO -0.02 0.13 0.47 5 -0.49 1 6
PXN 0.029 0.005 -10000 0 -10000 0 0
HRAS/GTP -0.089 0.14 -10000 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.091 0.17 -10000 0 -0.8 1 1
VHL 0.021 0.02 -10000 0 -0.32 1 1
ITGB3 0.023 0.065 -10000 0 -0.64 5 5
NOS3 -0.025 0.14 0.48 5 -0.56 1 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.11 0.2 -10000 0 -0.68 4 4
RAC1 0.027 0.009 -10000 0 -10000 0 0
PRKCA -0.097 0.16 -10000 0 -0.71 1 1
PRKCB -0.098 0.16 -10000 0 -0.64 2 2
VCL 0.029 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.1 0.18 -10000 0 -0.93 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.11 0.2 -10000 0 -0.65 6 6
VEGFA165/NRP2 -0.17 0.24 -10000 0 -0.43 231 231
MAPKKK cascade -0.064 0.16 0.4 1 -0.53 2 3
NRP2 0.02 0.071 -10000 0 -0.59 7 7
VEGFC homodimer 0.028 0.027 -10000 0 -0.59 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
ROCK1 0.029 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.065 0.15 0.45 2 -0.68 2 4
MAP3K13 -0.1 0.17 -10000 0 -0.78 1 1
PDPK1 -0.047 0.12 -10000 0 -0.63 2 2
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.32 -10000 0 -0.63 202 202
HRAS 0.029 0.027 -10000 0 -0.59 1 1
EGFR 0.02 0.067 -10000 0 -0.6 6 6
AKT 0.032 0.088 0.32 12 -10000 0 12
FOXO3 0.028 0.008 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
FOXO1 0.029 0.005 -10000 0 -10000 0 0
AKT3 0.028 0.007 -10000 0 -10000 0 0
FOXO4 0.03 0.001 -10000 0 -10000 0 0
MET 0.024 0.039 -10000 0 -0.59 2 2
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PIK3CB 0.028 0.007 -10000 0 -10000 0 0
NRAS 0.029 0.006 -10000 0 -10000 0 0
PIK3CG 0.023 0.047 -10000 0 -0.59 3 3
PIK3R3 0.029 0.006 -10000 0 -10000 0 0
PIK3R2 0.03 0.003 -10000 0 -10000 0 0
NF1 0.029 0.004 -10000 0 -10000 0 0
RAS -0.029 0.083 -10000 0 -0.26 4 4
ERBB2 0.027 0.041 -10000 0 -0.64 2 2
proliferation/survival/translation -0.044 0.06 0.27 5 -0.23 1 6
PI3K 0 0.1 0.3 24 -0.28 4 28
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
KRAS 0.029 0.006 -10000 0 -10000 0 0
FOXO 0.057 0.071 0.27 23 -10000 0 23
AKT2 0.03 0.003 -10000 0 -10000 0 0
PTEN 0.029 0.006 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.024 0.055 -10000 0 -0.6 4 4
CDC42/GTP 0.012 0.071 -10000 0 -0.33 5 5
PLCG1 0.012 0.06 -10000 0 -0.34 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.014 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
G12/G13 0.039 0.015 -10000 0 -10000 0 0
cell migration 0.011 0.069 -10000 0 -0.32 5 5
S1PR5 -0.079 0.24 -10000 0 -0.59 92 92
S1PR4 -0.006 0.14 -10000 0 -0.59 30 30
MAPK3 0.011 0.06 -10000 0 -0.34 5 5
MAPK1 0.012 0.061 -10000 0 -0.34 5 5
S1P/S1P5/Gi -0.016 0.1 -10000 0 -0.36 19 19
GNAI1 0.026 0.03 -10000 0 -0.64 1 1
CDC42/GDP 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.032 0.15 -10000 0 -0.37 83 83
RHOA 0.012 0.091 0.36 4 -10000 0 4
S1P/S1P4/Gi 0.013 0.065 -10000 0 -0.36 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.05 -10000 0 -0.64 3 3
S1P/S1P4/G12/G13 0.028 0.09 -10000 0 -0.34 28 28
GNA12 0.027 0.009 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.024 0.092 -9999 0 -0.42 19 19
E-cadherin/beta catenin 0.014 0.091 -9999 0 -0.47 17 17
CTNNB1 0.021 0.014 -9999 0 -10000 0 0
JUP 0.026 0.05 -9999 0 -0.64 3 3
CDH1 0.007 0.12 -9999 0 -0.62 18 18
Syndecan-3-mediated signaling events

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
CTTN 0.03 0.003 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.044 0.092 -9999 0 -0.63 1 1
Syndecan-3/Neurocan 0.014 0.09 -9999 0 -0.33 32 32
POMC 0.026 0.044 -9999 0 -0.67 2 2
EGFR 0.02 0.067 -9999 0 -0.6 6 6
Syndecan-3/EGFR 0.018 0.079 -9999 0 -0.34 21 21
AGRP 0.022 0.041 -9999 0 -0.64 2 2
NCSTN 0.029 0.007 -9999 0 -10000 0 0
PSENEN 0.03 0.003 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.03 0.003 -9999 0 -10000 0 0
APH1A 0.029 0.007 -9999 0 -10000 0 0
NCAN 0.011 0.096 -9999 0 -0.59 13 13
long-term memory 0.04 0.073 -9999 0 -0.32 12 12
Syndecan-3/IL8 0.003 0.11 -9999 0 -0.32 51 51
PSEN1 0.028 0.008 -9999 0 -10000 0 0
Src/Cortactin 0.043 0.009 -9999 0 -10000 0 0
FYN 0.028 0.008 -9999 0 -10000 0 0
limb bud formation 0.012 0.056 -9999 0 -0.36 11 11
MC4R 0.01 0.08 -9999 0 -0.59 9 9
SRC 0.029 0.006 -9999 0 -10000 0 0
PTN 0.011 0.1 -9999 0 -0.63 13 13
FGFR/FGF/Syndecan-3 0.012 0.056 -9999 0 -0.36 11 11
neuron projection morphogenesis 0.023 0.1 -9999 0 -0.6 2 2
Syndecan-3/AgRP 0.019 0.075 -9999 0 -0.33 22 22
Syndecan-3/AgRP/MC4R 0.026 0.088 -9999 0 -0.33 16 16
Fyn/Cortactin 0.041 0.012 -9999 0 -10000 0 0
SDC3 0.011 0.057 -9999 0 -0.37 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.11 -9999 0 -0.31 51 51
IL8 -0.011 0.16 -9999 0 -0.6 34 34
Syndecan-3/Fyn/Cortactin 0.042 0.074 -9999 0 -0.33 12 12
Syndecan-3/CASK 0.004 0.069 -9999 0 -0.34 20 20
alpha-MSH/MC4R 0.026 0.07 -9999 0 -0.45 11 11
Gamma Secretase 0.079 0.029 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.029 0.004 -9999 0 -10000 0 0
ITGB7 0.029 0.005 -9999 0 -10000 0 0
ITGA4 0.01 0.11 -9999 0 -0.59 16 16
alpha4/beta7 Integrin 0.027 0.082 -9999 0 -0.43 16 16
alpha4/beta1 Integrin 0.027 0.082 -9999 0 -0.43 16 16
ceramide signaling pathway

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
MAP4K4 0.018 0.087 -10000 0 -0.56 3 3
BAG4 0.026 0.03 -10000 0 -0.64 1 1
BAD 0.02 0.056 0.38 5 -0.3 2 7
NFKBIA 0.028 0.007 -10000 0 -10000 0 0
BIRC3 -0.064 0.22 -10000 0 -0.59 79 79
BAX 0.022 0.048 0.25 11 -10000 0 11
EnzymeConsortium:3.1.4.12 0.011 0.032 0.12 12 -0.12 3 15
IKBKB 0.025 0.086 0.33 3 -0.52 3 6
MAP2K2 0.029 0.06 0.29 11 -0.28 1 12
MAP2K1 0.031 0.062 0.31 11 -10000 0 11
SMPD1 0.016 0.035 0.21 6 -0.15 2 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.092 0.37 1 -0.53 4 5
MAP2K4 0.037 0.072 0.26 25 -10000 0 25
protein ubiquitination 0.03 0.1 0.4 8 -0.54 3 11
EnzymeConsortium:2.7.1.37 0.036 0.07 0.36 10 -10000 0 10
response to UV 0 0.001 0.004 20 -0.003 1 21
RAF1 0.018 0.058 0.29 11 -0.25 3 14
CRADD 0.029 0.005 -10000 0 -10000 0 0
mol:ceramide 0.019 0.046 0.22 9 -0.18 3 12
I-kappa-B-alpha/RELA/p50/ubiquitin 0.038 0.01 -10000 0 -10000 0 0
MADD 0.03 0.003 -10000 0 -10000 0 0
MAP3K1 0.034 0.07 0.22 44 -10000 0 44
TRADD 0.029 0.006 -10000 0 -10000 0 0
RELA/p50 0.03 0.003 -10000 0 -10000 0 0
MAPK3 0.033 0.06 0.29 12 -10000 0 12
MAPK1 0.033 0.061 0.29 12 -10000 0 12
p50/RELA/I-kappa-B-alpha 0.042 0.011 -10000 0 -10000 0 0
FADD 0.015 0.087 0.37 1 -0.55 3 4
KSR1 0.022 0.056 0.26 10 -0.26 5 15
MAPK8 0.037 0.076 0.32 14 -0.28 2 16
TRAF2 0.029 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.004 8 -10000 0 8
CHUK 0.025 0.088 0.3 2 -0.52 3 5
TNF R/SODD 0.039 0.026 -10000 0 -0.47 1 1
TNF 0.019 0.079 -10000 0 -0.61 8 8
CYCS 0.026 0.06 0.25 15 -10000 0 15
IKBKG 0.026 0.091 0.32 3 -0.52 3 6
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.014 0.091 -10000 0 -0.51 5 5
RELA 0.03 0.003 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
AIFM1 0.02 0.052 0.26 11 -10000 0 11
TNF/TNF R/SODD 0.045 0.061 -10000 0 -0.39 9 9
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 8 -10000 0 8
CASP8 0.024 0.097 -10000 0 -0.61 11 11
NSMAF 0.017 0.089 0.32 2 -0.55 3 5
response to hydrogen peroxide 0 0.001 0.004 20 -0.003 1 21
BCL2 0.029 0.005 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.029 0.082 -9999 0 -0.32 27 27
RGS9BP 0 0.14 -9999 0 -0.64 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.02 0.006 -9999 0 -10000 0 0
mol:Na + 0.021 0.052 -9999 0 -0.38 8 8
mol:ADP 0.004 0.031 -9999 0 -0.44 2 2
GNAT2 0.027 0.007 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.028 0.11 -9999 0 -0.39 34 34
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.031 0.01 -9999 0 -10000 0 0
GRK7 0.023 0.039 -9999 0 -0.59 2 2
CNGB3 0.014 0.068 -9999 0 -0.61 6 6
Cone Metarhodopsin II/X-Arrestin 0.016 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.077 -9999 0 -0.44 12 12
Cone PDE6 0.044 0.1 -9999 0 -0.36 6 6
Cone Metarhodopsin II 0.027 0.025 -9999 0 -0.35 2 2
Na + (4 Units) 0.025 0.075 -9999 0 -0.44 12 12
GNAT2/GDP 0.038 0.1 -9999 0 -0.35 25 25
GNB5 0.03 0.003 -9999 0 -10000 0 0
mol:GMP (4 units) 0.01 0.041 -9999 0 -0.33 2 2
Cone Transducin 0.032 0.088 -9999 0 -0.34 27 27
SLC24A2 0.011 0.074 -9999 0 -0.62 7 7
GNB3/GNGT2 0.017 0.1 -9999 0 -0.43 27 27
GNB3 -0.002 0.13 -9999 0 -0.59 26 26
GNAT2/GTP 0.02 0.005 -9999 0 -10000 0 0
CNGA3 0.017 0.046 -9999 0 -0.59 3 3
ARR3 0.021 0.005 -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 -0.38 8 8
mol:Pi 0.027 0.11 -9999 0 -0.39 34 34
Cone CNG Channel 0.044 0.054 -9999 0 -0.45 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.011 0.074 -9999 0 -0.62 7 7
RGS9 0.013 0.1 -9999 0 -0.58 14 14
PDE6C 0.02 0.038 -9999 0 -0.59 2 2
GNGT2 0.028 0.027 -9999 0 -0.59 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.021 0.007 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.033 -10000 0 -0.43 2 2
CRKL 0.049 0.097 0.39 8 -0.43 7 15
mol:PIP3 -0.011 0.044 -10000 0 -0.7 2 2
AKT1 0.001 0.056 -10000 0 -0.52 3 3
PTK2B 0.027 0.009 -10000 0 -10000 0 0
RAPGEF1 0.052 0.097 0.39 11 -0.48 3 14
RANBP10 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
HGF/MET/SHIP2 0.036 0.091 -10000 0 -0.4 20 20
MAP3K5 0.016 0.12 0.44 11 -0.49 3 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.05 0.092 -10000 0 -0.38 20 20
AP1 0.029 0.073 -10000 0 -0.4 12 12
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.029 0.007 -10000 0 -10000 0 0
apoptosis -0.038 0.24 -10000 0 -0.71 55 55
STAT3 (dimer) 0.03 0.066 -10000 0 -0.48 3 3
GAB1/CRKL/SHP2/PI3K 0.066 0.086 0.43 1 -0.5 3 4
INPP5D 0.024 0.054 -10000 0 -0.59 4 4
CBL/CRK 0.064 0.098 0.35 11 -0.51 4 15
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.029 0.006 -10000 0 -10000 0 0
PTEN 0.029 0.006 -10000 0 -10000 0 0
ELK1 0.023 0.11 0.33 54 -0.24 2 56
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.024 0.043 -10000 0 -0.27 4 4
PAK1 0.004 0.056 0.38 1 -0.57 2 3
HGF/MET/RANBP10 0.035 0.089 -10000 0 -0.4 19 19
HRAS 0.019 0.099 -10000 0 -0.56 6 6
DOCK1 0.052 0.1 0.4 12 -0.51 4 16
GAB1 0.034 0.084 0.25 3 -0.46 7 10
CRK 0.047 0.093 0.31 9 -0.43 7 16
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.1 -10000 0 -0.56 10 10
JUN 0.029 0.006 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.009 0.042 -10000 0 -0.22 10 10
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
cell morphogenesis 0.082 0.14 0.49 29 -0.55 3 32
GRB2/SHC 0.039 0.045 -10000 0 -0.29 1 1
FOS 0.013 0.099 -10000 0 -0.63 12 12
GLMN 0.005 0.001 -10000 0 -10000 0 0
cell motility 0.022 0.11 0.33 54 -0.24 2 56
HGF/MET/MUC20 0.019 0.087 -10000 0 -0.4 20 20
cell migration 0.038 0.045 -10000 0 -0.29 1 1
GRB2 0.029 0.005 -10000 0 -10000 0 0
CBL 0.028 0.029 -10000 0 -0.64 1 1
MET/RANBP10 0.037 0.033 -10000 0 -0.43 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.023 0.061 -10000 0 -0.46 3 3
MET/MUC20 0.018 0.029 -10000 0 -0.44 2 2
RAP1B 0.06 0.11 0.52 12 -0.49 2 14
RAP1A 0.055 0.096 0.44 9 -0.58 1 10
HGF/MET/RANBP9 0.034 0.09 -10000 0 -0.4 20 20
RAF1 0.019 0.096 -10000 0 -0.57 4 4
STAT3 0.03 0.067 -10000 0 -0.48 3 3
cell proliferation 0.044 0.084 0.35 3 -0.48 3 6
RPS6KB1 0.013 0.037 -10000 0 -0.42 3 3
MAPK3 0.011 0.1 0.44 9 -10000 0 9
MAPK1 0.011 0.11 0.52 8 -10000 0 8
RANBP9 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.038 0.13 0.48 13 -0.46 5 18
SRC 0.02 0.057 -10000 0 -0.44 3 3
PI3K 0.037 0.055 -10000 0 -0.44 3 3
MET/Glomulin 0.018 0.033 -10000 0 -0.38 2 2
SOS1 0.029 0.005 -10000 0 -10000 0 0
MAP2K1 0.044 0.1 -10000 0 -0.55 3 3
MET 0.024 0.039 -10000 0 -0.59 2 2
MAP4K1 0.014 0.12 0.44 11 -0.48 5 16
PTK2 0.029 0.007 -10000 0 -10000 0 0
MAP2K2 0.045 0.1 0.42 2 -0.55 3 5
BAD 0.002 0.062 0.38 1 -0.6 3 4
MAP2K4 0.021 0.11 0.44 12 -0.54 1 13
SHP2/GRB2/SOS1/GAB1 0.045 0.067 -10000 0 -0.62 1 1
INPPL1 0.03 0.003 -10000 0 -10000 0 0
PXN 0.029 0.005 -10000 0 -10000 0 0
SH3KBP1 0.03 0.003 -10000 0 -10000 0 0
HGS 0.009 0.038 -10000 0 -0.31 1 1
PLCgamma1/PKC 0.021 0.004 -10000 0 -10000 0 0
HGF 0.003 0.12 -10000 0 -0.6 20 20
RASA1 0.025 0.03 -10000 0 -0.64 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
PTPRJ 0.03 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.04 0.054 -10000 0 -0.42 2 2
PDPK1 -0.002 0.058 -10000 0 -0.56 3 3
HGF/MET/SHIP 0.031 0.099 -10000 0 -0.41 23 23
Ephrin B reverse signaling

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
EFNB2 0.029 0.004 -10000 0 -10000 0 0
EPHB2 0.019 0.076 -10000 0 -0.5 10 10
EFNB1 0.012 0.069 -10000 0 -0.44 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.052 0.082 -10000 0 -0.52 4 4
Ephrin B2/EPHB1-2 0.044 0.062 -10000 0 -0.42 7 7
neuron projection morphogenesis 0.033 0.073 -10000 0 -0.5 4 4
Ephrin B1/EPHB1-2/Tiam1 0.048 0.084 -10000 0 -0.56 4 4
DNM1 0.015 0.094 -10000 0 -0.6 12 12
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.003 0.087 -10000 0 -0.5 14 14
YES1 0.001 0.12 -10000 0 -0.74 14 14
Ephrin B1/EPHB1-2/NCK2 0.048 0.084 -10000 0 -0.56 4 4
PI3K 0.03 0.097 -10000 0 -0.53 13 13
mol:GDP 0.046 0.083 -10000 0 -0.55 4 4
ITGA2B 0.007 0.12 -10000 0 -0.59 19 19
endothelial cell proliferation 0.035 0.013 -10000 0 -10000 0 0
FYN -0.001 0.13 -10000 0 -0.75 14 14
MAP3K7 -0.002 0.091 -10000 0 -0.56 13 13
FGR 0 0.12 -10000 0 -0.74 14 14
TIAM1 0.029 0.006 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
RGS3 0.029 0.006 -10000 0 -10000 0 0
cell adhesion 0.014 0.12 -10000 0 -0.6 11 11
LYN 0.001 0.12 -10000 0 -0.74 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.12 -10000 0 -0.69 14 14
Ephrin B1/EPHB1-2 -0.006 0.1 -10000 0 -0.6 14 14
SRC 0.003 0.12 -10000 0 -0.72 14 14
ITGB3 0.023 0.065 -10000 0 -0.64 5 5
EPHB1 0.023 0.056 -10000 0 -0.62 4 4
EPHB4 0.027 0.009 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.036 0.013 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.021 0.1 -10000 0 -0.46 23 23
BLK -0.004 0.12 -10000 0 -0.74 14 14
HCK -0.002 0.12 -10000 0 -0.73 14 14
regulation of stress fiber formation -0.046 0.083 0.55 4 -10000 0 4
MAPK8 0.006 0.088 0.4 1 -0.5 12 13
Ephrin B1/EPHB1-2/RGS3 0.048 0.085 -10000 0 -0.56 4 4
endothelial cell migration 0.018 0.098 0.39 4 -0.5 10 14
NCK2 0.029 0.006 -10000 0 -10000 0 0
PTPN13 0.016 0.099 -10000 0 -0.73 9 9
regulation of focal adhesion formation -0.046 0.083 0.55 4 -10000 0 4
chemotaxis -0.047 0.083 0.55 4 -10000 0 4
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
Rac1/GTP 0.043 0.078 -10000 0 -0.52 4 4
angiogenesis -0.006 0.099 -10000 0 -0.59 14 14
LCK -0.002 0.13 -10000 0 -0.75 14 14
Signaling events mediated by PRL

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
CCNE1 0.022 0.071 -10000 0 -0.59 7 7
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 0.027 0.009 -10000 0 -10000 0 0
CDKN1A 0.018 0.049 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.026 0.085 -10000 0 -0.43 17 17
mol:Ca2+ -0.023 0.1 0.26 17 -0.44 21 38
AGT 0.001 0.13 -10000 0 -0.57 24 24
CCNA2 -0.044 0.13 -10000 0 -0.63 6 6
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
EGR1 0.011 0.063 -10000 0 -0.46 9 9
CDK2/Cyclin E1 0.059 0.11 -10000 0 -0.55 5 5
MAPK3 0.007 0.081 -10000 0 -0.43 17 17
PRL-2 /Rab GGTase beta 0.043 0.009 -10000 0 -10000 0 0
MAPK1 0.008 0.081 -10000 0 -0.43 17 17
PTP4A1 0.01 0.046 -10000 0 -10000 0 0
PTP4A3 0.008 0.11 -10000 0 -0.59 17 17
PTP4A2 0.029 0.006 -10000 0 -10000 0 0
ITGB1 0.008 0.081 -10000 0 -0.43 17 17
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.017 0.038 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.039 0.034 -10000 0 -0.47 2 2
PRL-1/ATF-5 0.062 0.087 -10000 0 -10000 0 0
RABGGTA 0.026 0.041 -10000 0 -0.64 2 2
BCAR1 -0.005 0.054 0.26 17 -0.49 1 18
RHOC 0.014 0.054 -10000 0 -0.58 1 1
RHOA -0.026 0.12 -10000 0 -0.57 4 4
cell motility 0.021 0.09 0.29 8 -0.33 8 16
PRL-1/alpha Tubulin 0.063 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.024 0.083 -10000 0 -0.43 16 16
ROCK1 0.021 0.085 0.27 6 -0.32 6 12
RABGGTB 0.029 0.006 -10000 0 -10000 0 0
CDK2 0.029 0.005 -10000 0 -10000 0 0
mitosis 0.01 0.046 -10000 0 -10000 0 0
ATF5 0.026 0.047 -10000 0 -0.59 3 3
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.021 0.073 0.61 7 -10000 0 7
PI3K Class IB/PDE3B 0.021 0.073 -10000 0 -0.61 7 7
PDE3B 0.021 0.073 -10000 0 -0.61 7 7
Canonical NF-kappaB pathway

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
FBXW11 0.025 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.074 0.31 9 -10000 0 9
ERC1 0.029 0.006 -10000 0 -10000 0 0
RIP2/NOD2 -0.067 0.2 -10000 0 -0.44 116 116
NFKBIA 0.025 0.023 -10000 0 -10000 0 0
BIRC2 0.03 0.004 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
RIPK2 0.027 0.028 -10000 0 -0.59 1 1
IKBKG 0.009 0.067 -10000 0 -10000 0 0
IKK complex/A20 0.034 0.098 -10000 0 -0.48 1 1
NEMO/A20/RIP2 0.027 0.028 -10000 0 -0.59 1 1
XPO1 0.029 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.023 0.086 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.038 0.01 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.077 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.057 0.015 -10000 0 -10000 0 0
NOD2 -0.11 0.26 -10000 0 -0.59 120 120
NFKB1 0.032 0.029 -10000 0 -0.63 1 1
RELA 0.034 0.003 -10000 0 -10000 0 0
MALT1 0.029 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.043 0.007 -10000 0 -10000 0 0
ATM 0.028 0.029 -10000 0 -0.64 1 1
TNF/TNFR1A 0.034 0.062 -10000 0 -0.45 8 8
TRAF6 0.03 0.003 -10000 0 -10000 0 0
PRKCA 0.029 0.005 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
UBE2D3 0.03 0.004 -10000 0 -10000 0 0
TNF 0.019 0.079 -10000 0 -0.61 8 8
NF kappa B1 p50/RelA 0.053 0.037 -10000 0 -0.39 1 1
BCL10 0.029 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.023 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.032 0.087 -10000 0 -10000 0 0
CYLD 0.029 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.04 0.089 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.047 0.11 0.3 1 -0.57 7 8
CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
AKT2 0.03 0.003 -10000 0 -10000 0 0
STXBP4 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.042 0.13 0.27 34 -0.5 14 48
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
YWHAB 0.029 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.057 0.016 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
ASIP -0.027 0.17 -10000 0 -0.59 45 45
PRKCI 0.028 0.007 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.021 0.006 -10000 0 -10000 0 0
RHOQ 0.029 0.005 -10000 0 -10000 0 0
GYS1 0.023 0.009 -10000 0 -10000 0 0
PRKCZ 0.025 0.05 -10000 0 -0.64 3 3
TRIP10 0.03 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.021 0.062 -10000 0 -0.34 3 3
VAMP2 0.029 0.005 -10000 0 -10000 0 0
SLC2A4 0.04 0.14 0.33 9 -0.56 15 24
STX4 0.029 0.006 -10000 0 -10000 0 0
GSK3B 0.028 0.011 -10000 0 -10000 0 0
SFN -0.041 0.2 -10000 0 -0.59 59 59
LNPEP 0.023 0.042 -10000 0 -0.64 2 2
YWHAE 0.029 0.005 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.029 0.006 -10000 0 -10000 0 0
mol:PIP3 0.007 0.046 -10000 0 -0.35 6 6
FRAP1 0.025 0.043 0.28 1 -10000 0 1
AKT1 0.023 0.065 0.28 2 -0.43 3 5
INSR 0.03 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0.045 0.062 0.3 1 -0.39 2 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.025 -10000 0 -0.26 1 1
TSC2 0.029 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.02 0.04 -10000 0 -0.36 2 2
TSC1 0.029 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.051 -10000 0 -0.37 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.029 0.033 -10000 0 -0.3 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.029 0.006 -10000 0 -10000 0 0
RPS6KB1 0.039 0.072 0.33 7 -0.55 1 8
MAP3K5 -0.004 0.051 0.17 1 -0.18 15 16
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
apoptosis -0.004 0.051 0.17 1 -0.18 15 16
mol:LY294002 0 0 -10000 0 -0.001 14 14
EIF4B 0.044 0.077 0.33 14 -0.46 1 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.054 0.064 0.29 5 -0.61 1 6
eIF4E/eIF4G1/eIF4A1 0.02 0.018 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.034 0.057 -10000 0 -0.36 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.047 0.24 7 -0.22 1 8
FKBP1A 0.029 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.041 0.053 -10000 0 -0.35 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 14 14
FKBP12/Rapamycin 0.022 0.005 -10000 0 -10000 0 0
PDPK1 0.007 0.05 -10000 0 -0.39 5 5
EIF4E 0.03 0.003 -10000 0 -10000 0 0
ASK1/PP5C 0.001 0.16 -10000 0 -0.54 41 41
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.031 -10000 0 -10000 0 0
TSC1/TSC2 0.05 0.067 0.32 1 -0.42 2 3
tumor necrosis factor receptor activity 0 0 0.001 14 -10000 0 14
RPS6 0.026 0.039 -10000 0 -0.59 2 2
PPP5C 0.03 0.003 -10000 0 -10000 0 0
EIF4G1 0.029 0.006 -10000 0 -10000 0 0
IRS1 0.004 0.052 -10000 0 -0.23 22 22
INS 0.018 0.002 -10000 0 -10000 0 0
PTEN 0.028 0.006 -10000 0 -10000 0 0
PDK2 0.01 0.048 -10000 0 -0.38 2 2
EIF4EBP1 -0.064 0.28 -10000 0 -1 41 41
PIK3CA 0.028 0.03 -10000 0 -0.64 1 1
PPP2R5D 0.029 0.05 0.33 5 -10000 0 5
peptide biosynthetic process 0.018 0.013 -10000 0 -10000 0 0
RHEB 0.027 0.009 -10000 0 -10000 0 0
EIF4A1 0.029 0.005 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.005 17 -0.003 1 18
EEF2 0.018 0.013 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.044 0.26 -10000 0 -0.92 41 41
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.022 0.004 -10000 0 -10000 0 0
PRKCZ 0.025 0.05 -10000 0 -0.64 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.02 0.095 -10000 0 -0.39 2 2
IRAK/TOLLIP 0.038 0.009 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
IKBKG 0.03 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.024 0.17 -10000 0 -0.46 68 68
IL1A 0.011 0.1 -10000 0 -0.59 14 14
IL1B 0.017 0.049 -10000 0 -0.44 6 6
IRAK/TRAF6/p62/Atypical PKCs 0.055 0.045 -10000 0 -10000 0 0
IL1R2 -0.041 0.2 -10000 0 -0.61 58 58
IL1R1 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.009 0.046 -10000 0 -10000 0 0
TOLLIP 0.03 0.003 -10000 0 -10000 0 0
TICAM2 0.024 0.012 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.058 0.06 -10000 0 -10000 0 0
JUN 0.02 0.044 0.33 2 -10000 0 2
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.065 0.064 -10000 0 -0.65 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 0.039 0.078 -10000 0 -0.36 2 2
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.046 0.078 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.045 0.054 -10000 0 -0.34 9 9
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
MAPK8 0.024 0.047 0.34 2 -10000 0 2
IRAK1 0.021 0.005 -10000 0 -10000 0 0
IL1RN/IL1R1 0.028 0.086 -10000 0 -0.44 17 17
IRAK4 0.029 0.005 -10000 0 -10000 0 0
PRKCI 0.028 0.007 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
PI3K 0.037 0.035 -10000 0 -0.47 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.077 -10000 0 -0.4 1 1
CHUK 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.045 0.054 -10000 0 -0.34 9 9
IL1 beta/IL1R2 -0.008 0.14 -10000 0 -0.39 61 61
IRAK/TRAF6/TAK1/TAB1/TAB2 0.043 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.049 0.063 -10000 0 -0.88 1 1
IRAK3 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.056 0.059 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.023 0.045 -10000 0 -0.35 1 1
IL1 alpha/IL1R1/IL1RAP 0.041 0.078 -10000 0 -0.37 17 17
RELA 0.03 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.022 0.013 -10000 0 -10000 0 0
MYD88 0.021 0.014 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.053 0.016 -10000 0 -10000 0 0
IL1RAP 0.024 0.055 -10000 0 -0.6 4 4
UBE2N 0.029 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 0.03 0.043 -10000 0 -10000 0 0
CASP1 0.03 0.004 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.026 0.18 -10000 0 -0.46 71 71
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.042 0.059 -10000 0 -10000 0 0
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.016 0.098 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
IL1RN 0.009 0.11 -10000 0 -0.6 17 17
TRAF6/TAK1/TAB1/TAB2 0.04 0.013 -10000 0 -10000 0 0
MAP2K6 0.029 0.043 0.35 2 -0.32 3 5
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.022 0.12 -10000 0 -0.48 17 17
KLHL20 0.022 0.075 0.21 2 -0.32 2 4
CYFIP2 0.014 0.077 -10000 0 -0.64 7 7
Rac1/GDP 0.024 0.087 0.3 4 -10000 0 4
ENAH -0.02 0.12 -10000 0 -0.48 18 18
AP1M1 0.03 0.003 -10000 0 -10000 0 0
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.053 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.034 -10000 0 -0.2 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.082 -10000 0 -0.37 14 14
RAPGEF1 -0.011 0.12 0.27 4 -0.43 12 16
CTNND1 0.03 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.023 0.13 -10000 0 -0.5 18 18
CRK -0.01 0.12 -10000 0 -0.45 15 15
E-cadherin/gamma catenin/alpha catenin 0.028 0.089 -10000 0 -0.42 16 16
alphaE/beta7 Integrin 0.042 0.01 -10000 0 -10000 0 0
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
NCKAP1 0.029 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.02 -10000 0 -10000 0 0
DLG1 -0.018 0.12 -10000 0 -0.48 16 16
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.029 -10000 0 -10000 0 0
MLLT4 0.027 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.05 0.025 -10000 0 -0.34 1 1
PI3K -0.007 0.037 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.022 0.1 -10000 0 -0.49 19 19
TIAM1 0.029 0.006 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.031 0.073 -10000 0 -0.34 14 14
AKT1 0.021 0.032 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
CDH1 0.007 0.12 -10000 0 -0.62 18 18
RhoA/GDP 0.041 0.085 0.34 9 -10000 0 9
actin cytoskeleton organization 0.023 0.062 0.17 15 -0.23 2 17
CDC42/GDP 0.032 0.11 0.37 15 -10000 0 15
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.063 -10000 0 -0.3 16 16
ITGB7 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.034 0.078 -10000 0 -0.36 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.02 0.068 -10000 0 -0.34 14 14
mol:GDP 0.021 0.12 0.44 10 -0.4 3 13
CDC42/GTP/IQGAP1 0.039 0.009 -10000 0 -10000 0 0
JUP 0.026 0.05 -10000 0 -0.64 3 3
p120 catenin/RhoA/GDP 0.019 0.081 0.31 3 -10000 0 3
RAC1/GTP/IQGAP1 0.036 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.044 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.02 0.062 0.17 15 -0.22 18 33
NME1 0.028 0.027 -10000 0 -0.59 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.022 0.12 -10000 0 -0.48 17 17
regulation of cell-cell adhesion 0.013 0.042 -10000 0 -10000 0 0
WASF2 0.014 0.03 -10000 0 -10000 0 0
Rap1/GTP 0.034 0.066 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.087 -10000 0 -0.66 1 1
CCND1 0.021 0.073 0.2 8 -0.27 18 26
VAV2 -0.017 0.16 -10000 0 -0.56 16 16
RAP1/GDP 0.043 0.077 0.29 2 -10000 0 2
adherens junction assembly -0.021 0.12 -10000 0 -0.47 17 17
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.029 0.004 -10000 0 -10000 0 0
PIP5K1C 0.03 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.048 0.091 -10000 0 -0.64 1 1
E-cadherin/beta catenin 0 0.078 -10000 0 -0.41 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.021 0.12 -10000 0 -0.48 17 17
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
Rac1/GTP -0.031 0.078 -10000 0 -0.4 5 5
E-cadherin/beta catenin/alpha catenin 0.023 0.079 -10000 0 -0.4 14 14
ITGAE 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.024 0.13 -10000 0 -0.51 18 18
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.045 0.12 0.38 2 -0.55 10 12
MAP3K8 0.027 0.038 -10000 0 -0.59 2 2
FOS 0.032 0.1 0.36 4 -0.53 8 12
PRKCA 0.03 0.008 -10000 0 -10000 0 0
PTPN7 -0.01 0.15 -10000 0 -0.59 34 34
HRAS 0.029 0.027 -10000 0 -0.59 1 1
PRKCB 0.023 0.063 -10000 0 -0.62 5 5
NRAS 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.024 -10000 0 -0.34 1 1
MAPK3 0.019 0.087 -10000 0 -0.49 9 9
MAP2K1 0.029 0.054 -10000 0 -0.49 2 2
ELK1 0.03 0.009 -10000 0 -10000 0 0
BRAF 0.029 0.039 -10000 0 -0.45 2 2
mol:GTP 0 0.002 -10000 0 -0.007 13 13
MAPK1 0.019 0.088 -10000 0 -0.45 11 11
RAF1 0.022 0.04 -10000 0 -0.45 2 2
KRAS 0.029 0.006 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.011 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.015 0.094 -10000 0 -0.53 6 6
NFATC4 0.009 0.065 0.28 7 -0.48 1 8
ERBB2IP 0.027 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.028 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis 0.014 0.073 -10000 0 -10000 0 0
JUN 0.019 0.065 0.27 3 -0.31 2 5
HRAS 0.028 0.027 -10000 0 -0.59 1 1
DOCK7 0.006 0.069 -10000 0 -0.57 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.083 -10000 0 -0.35 21 21
AKT1 0.011 0.005 -10000 0 -10000 0 0
BAD 0.01 0.025 -10000 0 -0.39 2 2
MAPK10 0.018 0.056 0.2 7 -0.31 2 9
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.015 0.078 -10000 0 -10000 0 0
RAF1 -0.006 0.087 -10000 0 -0.51 6 6
ErbB2/ErbB3/neuregulin 2 0.015 0.071 -10000 0 -0.36 16 16
STAT3 0.028 0.099 -10000 0 -0.89 6 6
cell migration 0.039 0.084 0.33 17 -0.26 2 19
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.11 0.19 -10000 0 -0.53 12 12
FOS -0.068 0.14 0.3 1 -0.49 12 13
NRAS 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.073 -10000 0 -10000 0 0
MAPK3 -0.09 0.16 0.35 1 -0.56 6 7
MAPK1 -0.09 0.16 0.38 1 -0.58 7 8
JAK2 0.007 0.065 -10000 0 -10000 0 0
NF2 0.018 0.037 -10000 0 -0.79 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.009 0.085 -10000 0 -0.39 18 18
NRG1 0.008 0.11 -10000 0 -0.56 17 17
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
MAPK8 0.01 0.078 -10000 0 -0.37 6 6
MAPK9 0.011 0.044 0.2 5 -0.27 1 6
ERBB2 -0.015 0.03 -10000 0 -0.49 2 2
ERBB3 0.018 0.081 -10000 0 -0.64 8 8
SHC1 0.028 0.006 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
apoptosis -0.006 0.022 0.28 2 -10000 0 2
STAT3 (dimer) 0.028 0.097 -10000 0 -0.87 6 6
RNF41 0.009 0.006 -10000 0 -10000 0 0
FRAP1 0.005 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.01 0.049 -10000 0 -0.39 1 1
ErbB2/ErbB2/HSP90 (dimer) 0.016 0.028 -10000 0 -0.42 2 2
CHRNA1 -0.12 0.19 0.34 1 -0.43 58 59
myelination 0.007 0.078 0.4 7 -0.43 1 8
PPP3CB 0.007 0.063 -10000 0 -10000 0 0
KRAS 0.028 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.034 0.085 -10000 0 -0.53 5 5
NRG2 0.012 0.081 -10000 0 -0.6 9 9
mol:GDP 0.009 0.085 -10000 0 -0.39 18 18
SOS1 0.029 0.005 -10000 0 -10000 0 0
MAP2K2 -0.015 0.091 0.29 1 -0.48 6 7
SRC 0.029 0.006 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.008 0.066 -10000 0 -10000 0 0
MAP2K1 -0.11 0.18 -10000 0 -0.56 14 14
heart morphogenesis 0.014 0.073 -10000 0 -10000 0 0
RAS family/GDP 0.041 0.091 -10000 0 -0.53 6 6
GRB2 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.016 0.038 -10000 0 -0.83 1 1
CHRNE 0.013 0.022 0.2 1 -0.19 2 3
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
activation of caspase activity -0.011 0.005 -10000 0 -10000 0 0
nervous system development 0.014 0.073 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.029 0.016 -10000 0 -0.32 1 1
ANTXR2 0.03 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0.002 0.002 -10000 0 -0.045 1 1
monocyte activation 0.004 0.092 -10000 0 -0.36 26 26
MAP2K2 0.014 0.06 -10000 0 -0.59 5 5
MAP2K1 0.004 0.002 -10000 0 -10000 0 0
MAP2K7 0.004 0.002 -10000 0 -10000 0 0
MAP2K6 0.002 0.026 -10000 0 -0.34 3 3
CYAA 0.006 0.007 -10000 0 -10000 0 0
MAP2K4 0.004 0.001 -10000 0 -10000 0 0
IL1B 0.006 0.045 0.24 6 -0.31 6 12
Channel 0.037 0.012 -10000 0 -10000 0 0
NLRP1 0.001 0.033 -10000 0 -0.34 5 5
CALM1 0.028 0.008 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.094 -10000 0 -0.37 33 33
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation -0.002 0.002 0.045 1 -10000 0 1
MAPK3 0.004 0.002 -10000 0 -10000 0 0
MAPK1 0.004 0.002 -10000 0 -10000 0 0
PGR -0.007 0.061 -10000 0 -0.35 16 16
PA/Cellular Receptors 0.039 0.012 -10000 0 -10000 0 0
apoptosis 0.002 0.002 -10000 0 -0.045 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.036 0.011 -10000 0 -10000 0 0
macrophage activation 0.006 0.002 -10000 0 -10000 0 0
TNF 0.019 0.079 -10000 0 -0.61 8 8
VCAM1 0.004 0.092 -10000 0 -0.36 25 25
platelet activation -0.007 0.094 -10000 0 -0.37 33 33
MAPKKK cascade -0.01 0.018 -10000 0 -0.14 4 4
IL18 0.004 0.035 -10000 0 -0.31 5 5
negative regulation of macrophage activation 0.002 0.002 -10000 0 -0.045 1 1
LEF 0.002 0.002 -10000 0 -0.045 1 1
CASP1 0.005 0.017 -10000 0 -0.16 5 5
mol:cAMP -0.007 0.095 -10000 0 -0.37 33 33
necrosis 0.002 0.002 -10000 0 -0.045 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.036 0.011 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.028 0.029 -10000 0 -0.64 1 1
HDAC4 0.028 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.018 0.027 0.41 2 -10000 0 2
CDKN1A -0.004 0.025 -10000 0 -0.4 2 2
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
BAX 0.03 0.003 -10000 0 -10000 0 0
FOXO3 -0.007 0.021 0.47 1 -10000 0 1
FOXO1 0.029 0.005 -10000 0 -10000 0 0
FOXO4 0.023 0.016 -10000 0 -0.3 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
TAT 0.015 0.085 -10000 0 -0.59 10 10
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.014 0.1 -10000 0 -0.43 30 30
PPARGC1A -0.034 0.2 -10000 0 -0.63 51 51
FHL2 0.024 0.057 -10000 0 -0.62 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.039 0.01 -10000 0 -10000 0 0
HIST2H4A 0.018 0.027 -10000 0 -0.41 2 2
SIRT1/FOXO3a 0.01 0.027 0.31 1 -10000 0 1
SIRT1 0.024 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.051 0.019 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.034 0.03 -10000 0 -10000 0 0
apoptosis -0.054 0.014 -10000 0 -10000 0 0
SIRT1/PGC1A -0.007 0.13 -10000 0 -0.41 50 50
p53/SIRT1 0.029 0.018 -10000 0 -10000 0 0
SIRT1/FOXO4 0.038 0.023 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.048 0.038 -10000 0 -0.36 4 4
HIST1H1E 0.022 0.019 -10000 0 -0.31 1 1
SIRT1/p300 0.038 0.025 -10000 0 -0.47 1 1
muscle cell differentiation -0.003 0.093 0.37 30 -10000 0 30
TP53 0.024 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.054 0.014 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
MEF2D 0.029 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.028 0.065 -10000 0 -0.43 10 10
ACSS2 0.02 0.006 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.003 0.093 -10000 0 -0.37 30 30
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.012 0.041 -10000 0 -0.4 5 5
SNTA1 0.028 0.03 -10000 0 -0.64 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.013 0.04 -10000 0 -0.39 5 5
MAPK12 0.004 0.05 -10000 0 -0.34 11 11
CCND1 0.008 0.045 -10000 0 -0.32 4 4
p38 gamma/SNTA1 0.026 0.062 -10000 0 -0.35 11 11
MAP2K3 0.029 0.005 -10000 0 -10000 0 0
PKN1 0.03 0.002 -10000 0 -10000 0 0
G2/M transition checkpoint 0.004 0.05 -10000 0 -0.34 11 11
MAP2K6 0.009 0.031 -10000 0 -0.4 3 3
MAPT 0.01 0.078 0.29 4 -0.39 15 19
MAPK13 0.018 0.048 -10000 0 -0.47 5 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.001 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0 0.23 -10000 0 -1.1 21 21
MKNK1 0.029 0.006 -10000 0 -10000 0 0
MAPK14 0.031 0.076 -10000 0 -0.42 2 2
ATF2/c-Jun 0.027 0.061 -10000 0 -0.43 1 1
MAPK11 0.029 0.086 -10000 0 -0.47 5 5
MITF 0.02 0.097 -10000 0 -0.54 6 6
MAPKAPK5 0.031 0.088 -10000 0 -0.5 3 3
KRT8 0.03 0.09 -10000 0 -0.49 4 4
MAPKAPK3 0.021 0.014 -10000 0 -10000 0 0
MAPKAPK2 0.029 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.038 0.12 -10000 0 -0.46 21 21
CEBPB 0.028 0.094 -10000 0 -0.5 3 3
SLC9A1 0.029 0.095 -10000 0 -0.58 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.034 0.091 -10000 0 -0.5 4 4
p38alpha-beta/MNK1 0.052 0.1 -10000 0 -0.55 3 3
JUN 0.029 0.062 -10000 0 -0.42 1 1
PPARGC1A -0.005 0.14 -10000 0 -0.54 8 8
USF1 0.031 0.085 -10000 0 -0.45 2 2
RAB5/GDP/GDI1 0.021 0.066 -10000 0 -0.37 3 3
NOS2 0.031 0.1 -10000 0 -0.79 1 1
DDIT3 0.029 0.093 -10000 0 -0.48 5 5
RAB5A 0.022 0.014 -10000 0 -10000 0 0
HSPB1 0.043 0.11 0.3 42 -0.44 6 48
p38alpha-beta/HBP1 0.048 0.099 -10000 0 -0.56 3 3
CREB1 0.03 0.097 -10000 0 -0.54 6 6
RAB5/GDP 0.016 0.01 -10000 0 -10000 0 0
EIF4E 0.027 0.082 -10000 0 -0.53 2 2
RPS6KA4 0.032 0.089 -10000 0 -0.54 3 3
PLA2G4A 0.02 0.096 -10000 0 -0.56 5 5
GDI1 0.031 0.089 -10000 0 -0.5 3 3
TP53 0.021 0.11 -10000 0 -0.46 21 21
RPS6KA5 0.028 0.097 -10000 0 -0.56 6 6
ESR1 0.025 0.1 -10000 0 -0.58 6 6
HBP1 0.027 0.009 -10000 0 -10000 0 0
MEF2C 0.028 0.085 -10000 0 -0.5 4 4
MEF2A 0.032 0.091 -10000 0 -0.61 3 3
EIF4EBP1 0.024 0.11 -10000 0 -0.58 8 8
KRT19 -0.042 0.18 -10000 0 -0.67 14 14
ELK4 0.031 0.087 -10000 0 -0.48 3 3
ATF6 0.031 0.085 -10000 0 -0.45 2 2
ATF1 0.031 0.097 -10000 0 -0.54 6 6
p38alpha-beta/MAPKAPK2 0.053 0.1 -10000 0 -0.5 3 3
p38alpha-beta/MAPKAPK3 0.036 0.1 -10000 0 -0.56 3 3
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.008 0.12 -10000 0 -0.4 45 45
cell-cell adhesion -0.003 0.052 0.55 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.064 0.069 -10000 0 -10000 0 0
ITSN1 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
SHC1 0.029 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.064 -10000 0 -0.41 11 11
Ephrin B1/EPHB1 0.035 0.038 -10000 0 -0.39 4 4
HRAS/GDP 0.034 0.059 -10000 0 -0.48 1 1
Ephrin B/EPHB1/GRB7 0.068 0.076 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.022 0.055 -10000 0 -10000 0 0
KRAS 0.029 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.071 0.064 -10000 0 -10000 0 0
endothelial cell migration 0.05 0.036 -10000 0 -0.34 2 2
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.02 0.076 -10000 0 -0.64 7 7
PAK1 0.028 0.055 -10000 0 -10000 0 0
HRAS 0.029 0.027 -10000 0 -0.59 1 1
RRAS 0.023 0.055 -10000 0 -10000 0 0
DNM1 0.015 0.094 -10000 0 -0.6 12 12
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.026 0.054 -10000 0 -10000 0 0
lamellipodium assembly 0.003 0.052 -10000 0 -0.55 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.038 0.046 -10000 0 -0.43 1 1
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
EPHB2 0.019 0.076 -10000 0 -0.5 10 10
EPHB3 0.015 0.095 -10000 0 -0.64 11 11
EPHB1 0.023 0.056 -10000 0 -0.61 4 4
EPHB4 0.027 0.009 -10000 0 -10000 0 0
mol:GDP 0.022 0.057 0.34 3 -0.47 1 4
Ephrin B/EPHB2 0.058 0.06 -10000 0 -10000 0 0
Ephrin B/EPHB3 0.052 0.078 -10000 0 -0.37 16 16
JNK cascade 0.025 0.066 0.36 5 -0.56 2 7
Ephrin B/EPHB1 0.057 0.059 -10000 0 -0.35 7 7
RAP1/GDP 0.064 0.078 0.35 5 -10000 0 5
EFNB2 0.029 0.004 -10000 0 -10000 0 0
EFNB3 0.021 0.072 -10000 0 -0.59 7 7
EFNB1 0.03 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.044 0.062 -10000 0 -0.42 7 7
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.045 0.073 -10000 0 -0.54 2 2
Rap1/GTP 0.022 0.058 -10000 0 -0.56 1 1
axon guidance -0.008 0.12 -10000 0 -0.4 45 45
MAPK3 0.032 0.043 -10000 0 -0.38 1 1
MAPK1 0.033 0.043 -10000 0 -0.38 1 1
Rac1/GDP 0.038 0.063 0.36 2 -0.43 1 3
actin cytoskeleton reorganization -0.008 0.044 -10000 0 -0.39 3 3
CDC42/GDP 0.057 0.081 0.35 6 -0.42 1 7
PI3K 0.056 0.038 -10000 0 -0.35 2 2
EFNA5 -0.026 0.18 -10000 0 -0.63 40 40
Ephrin B2/EPHB4 0.036 0.013 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.032 0.05 -10000 0 -0.37 1 1
CDC42 0.029 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.016 0.059 -10000 0 -0.54 2 2
PTK2 0.021 0.085 0.53 14 -10000 0 14
MAP4K4 0.025 0.066 0.36 5 -0.57 2 7
SRC 0.029 0.006 -10000 0 -10000 0 0
KALRN 0.028 0.008 -10000 0 -10000 0 0
Intersectin/N-WASP 0.039 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis 0.073 0.12 0.42 36 -0.45 1 37
MAP2K1 0.034 0.043 -10000 0 -0.4 1 1
WASL 0.027 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.06 0.069 -10000 0 -0.47 5 5
cell migration 0.047 0.079 0.46 5 -0.43 1 6
NRAS 0.029 0.006 -10000 0 -10000 0 0
SYNJ1 0.022 0.056 -10000 0 -10000 0 0
PXN 0.029 0.005 -10000 0 -10000 0 0
TF -0.054 0.14 -10000 0 -0.6 2 2
HRAS/GTP 0.044 0.072 -10000 0 -0.59 2 2
Ephrin B1/EPHB1-2 0.044 0.064 -10000 0 -0.41 8 8
cell adhesion mediated by integrin -0.005 0.058 0.37 6 -0.37 3 9
RAC1 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.048 0.073 -10000 0 -0.54 2 2
RAC1-CDC42/GTP 0.004 0.071 -10000 0 -0.68 2 2
RASA1 0.025 0.03 -10000 0 -0.64 1 1
RAC1-CDC42/GDP 0.05 0.063 0.36 2 -10000 0 2
ruffle organization 0.073 0.13 0.4 48 -0.56 1 49
NCK1 0.027 0.03 -10000 0 -0.64 1 1
receptor internalization 0.01 0.069 -10000 0 -0.42 1 1
Ephrin B/EPHB2/KALRN 0.069 0.066 -10000 0 -10000 0 0
ROCK1 0.02 0.061 -10000 0 -0.37 11 11
RAS family/GDP -0.008 0.044 -10000 0 -0.42 1 1
Rac1/GTP 0.011 0.057 -10000 0 -0.59 1 1
Ephrin B/EPHB1/Src/Paxillin 0.035 0.043 -10000 0 -0.34 1 1
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.012 0.083 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SLAP 0.009 0.1 -10000 0 -0.44 25 25
PDGFB-D/PDGFRB/APS/CBL 0.04 0.047 -10000 0 -0.38 4 4
AKT1 0.087 0.13 0.38 58 -10000 0 58
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.041 0.1 0.34 6 -10000 0 6
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
FGR 0.037 0.1 0.33 6 -0.62 2 8
mol:Ca2+ 0.049 0.065 0.33 8 -10000 0 8
MYC 0.062 0.14 0.47 17 -0.44 4 21
SHC1 0.029 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.051 0.055 -10000 0 -0.63 1 1
LRP1/PDGFRB/PDGFB 0.046 0.027 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
GO:0007205 0.049 0.065 0.34 7 -10000 0 7
PTEN 0.029 0.006 -10000 0 -10000 0 0
GRB2 0.029 0.005 -10000 0 -10000 0 0
GRB7 0.02 0.076 -10000 0 -0.64 7 7
PDGFB-D/PDGFRB/SHP2 0.033 0.02 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.032 0.02 -10000 0 -10000 0 0
cell cycle arrest 0.009 0.1 -10000 0 -0.44 25 25
HRAS 0.029 0.027 -10000 0 -0.59 1 1
HIF1A 0.079 0.13 0.37 57 -0.53 1 58
GAB1 0.046 0.083 0.35 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.046 0.087 0.38 8 -10000 0 8
PDGFB-D/PDGFRB 0.044 0.029 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.033 0.02 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.009 0.085 -10000 0 -0.4 1 1
positive regulation of MAPKKK cascade 0.033 0.02 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
mol:IP3 0.049 0.066 0.34 7 -10000 0 7
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.027 0.059 -10000 0 -0.48 6 6
SHB 0.029 0.006 -10000 0 -10000 0 0
BLK 0.013 0.12 0.32 4 -0.48 8 12
PTPN2 0.031 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.019 -10000 0 -10000 0 0
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
VAV2 0.048 0.092 0.38 8 -10000 0 8
CBL 0.028 0.029 -10000 0 -0.64 1 1
PDGFB-D/PDGFRB/DEP1 0.034 0.019 -10000 0 -10000 0 0
LCK 0.029 0.12 0.33 6 -0.57 4 10
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
ACP1 0.029 0.005 -10000 0 -10000 0 0
HCK 0.043 0.082 0.34 5 -10000 0 5
ABL1 0.048 0.089 0.34 11 -0.44 2 13
PDGFB-D/PDGFRB/CBL 0.041 0.076 0.38 2 -10000 0 2
PTPN1 0.03 0.007 -10000 0 -10000 0 0
SNX15 0.03 0.003 -10000 0 -10000 0 0
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.028 -10000 0 -0.59 1 1
cell proliferation 0.062 0.13 0.44 19 -0.4 4 23
SLA -0.002 0.13 -10000 0 -0.59 26 26
actin cytoskeleton reorganization 0.041 0.047 0.36 2 -10000 0 2
SRC 0.05 0.064 0.32 4 -10000 0 4
PI3K 0.011 0.025 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.039 0.054 -10000 0 -0.41 5 5
SH2B2 0.022 0.054 -10000 0 -0.59 4 4
PLCgamma1/SPHK1 0.042 0.1 0.34 6 -10000 0 6
LYN 0.041 0.09 0.32 3 -0.63 2 5
LRP1 0.029 0.005 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
STAT5B 0.029 0.004 -10000 0 -10000 0 0
STAT5A 0.029 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.061 0.05 -10000 0 -10000 0 0
SPHK1 -0.019 0.17 -10000 0 -0.59 42 42
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.049 0.066 0.34 7 -10000 0 7
PLCG1 0.05 0.066 0.34 7 -10000 0 7
NHERF/PDGFRB 0.044 0.034 -10000 0 -0.4 1 1
YES1 0.048 0.073 0.32 2 -0.55 2 4
cell migration 0.043 0.033 -10000 0 -0.4 1 1
SHC/Grb2/SOS1 0.063 0.043 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.03 -10000 0 -0.64 1 1
SLC9A3R1 0.029 0.005 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.054 0.04 -10000 0 -0.37 1 1
FYN 0.029 0.11 0.32 4 -0.45 6 10
DOK1 0.06 0.063 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.02 -10000 0 -0.44 1 1
PDGFB 0.03 0.004 -10000 0 -10000 0 0
RAC1 0.065 0.12 0.46 13 -0.48 1 14
PRKCD 0.039 0.057 -10000 0 -0.34 1 1
FER 0.035 0.051 -10000 0 -0.38 2 2
MAPKKK cascade 0.043 0.082 0.37 15 -10000 0 15
RASA1 0.045 0.057 -10000 0 -0.38 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
NCK2 0.029 0.006 -10000 0 -10000 0 0
p62DOK/Csk 0.075 0.059 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.033 0.02 -10000 0 -10000 0 0
chemotaxis 0.048 0.088 0.34 11 -0.43 2 13
STAT1-3-5/STAT1-3-5 0.052 0.038 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.017 0.01 -10000 0 -10000 0 0
PTPRJ 0.03 0.003 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.024 0.008 -10000 0 -10000 0 0
TRAF2/ASK1 0.036 0.012 -10000 0 -10000 0 0
ATM 0.028 0.029 -10000 0 -0.64 1 1
MAP2K3 0.034 0.069 0.47 3 -10000 0 3
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.071 0.41 3 -0.36 3 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.018 0.081 -10000 0 -0.6 9 9
TXN 0.01 0.002 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
GADD45A 0.029 0.006 -10000 0 -10000 0 0
GADD45B 0.03 0.003 -10000 0 -10000 0 0
MAP3K1 0.027 0.009 -10000 0 -10000 0 0
MAP3K6 0.028 0.03 -10000 0 -0.64 1 1
MAP3K7 0.028 0.007 -10000 0 -10000 0 0
MAP3K4 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.039 0.026 -10000 0 -0.47 1 1
TAK1/TAB family -0.003 0.015 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.05 0.019 -10000 0 -10000 0 0
TRAF2 0.029 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.039 0.051 -10000 0 -10000 0 0
TRAF6 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.063 0.22 -10000 0 -0.63 71 71
CCM2 0.027 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.025 0.15 -10000 0 -0.4 71 71
MAPK11 0.027 0.038 -10000 0 -0.59 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.009 0.14 -10000 0 -0.36 71 71
OSM/MEKK3 0.039 0.015 -10000 0 -10000 0 0
TAOK1 0.015 0.045 -10000 0 -0.34 8 8
TAOK2 0.02 0.018 -10000 0 -0.37 1 1
TAOK3 0.02 0.017 -10000 0 -0.37 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
MAP3K10 0.028 0.029 -10000 0 -0.64 1 1
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.018 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.057 0.052 -10000 0 -0.3 6 6
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.038 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.05 -10000 0 -0.64 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.021 0.029 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.029 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.029 0.005 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
MAP3K12 0.028 0.029 -10000 0 -0.64 1 1
FGR 0.025 0.047 -10000 0 -0.59 3 3
p38 alpha/TAB1 -0.022 0.08 -10000 0 -0.61 7 7
PRKG1 0.011 0.11 -10000 0 -0.64 14 14
DUSP8 0.029 0.029 -10000 0 -0.64 1 1
PGK/cGMP/p38 alpha 0.023 0.11 -10000 0 -0.5 11 11
apoptosis -0.021 0.076 -10000 0 -0.57 7 7
RAL/GTP 0.035 0.014 -10000 0 -10000 0 0
LYN 0.028 0.007 -10000 0 -10000 0 0
DUSP1 0.021 0.03 -10000 0 -0.59 1 1
PAK1 0.03 0.003 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.067 0.026 -10000 0 -10000 0 0
TRAF6 0.03 0.003 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.027 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.014 -10000 0 -10000 0 0
MAPK11 0.045 0.12 0.38 13 -0.43 8 21
BLK -0.013 0.15 -10000 0 -0.59 34 34
HCK -0.003 0.14 -10000 0 -0.59 27 27
MAP2K3 0.029 0.005 -10000 0 -10000 0 0
DUSP16 0.029 0.006 -10000 0 -10000 0 0
DUSP10 0.025 0.05 -10000 0 -0.63 3 3
TRAF6/MEKK3 0.037 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.04 0.12 0.31 13 -0.66 7 20
positive regulation of innate immune response 0.051 0.14 0.41 13 -0.59 8 21
LCK 0.003 0.12 -10000 0 -0.59 22 22
p38alpha-beta/MKP7 0.055 0.12 0.36 6 -0.62 6 12
p38alpha-beta/MKP5 0.058 0.14 0.45 9 -0.58 8 17
PGK/cGMP 0.008 0.08 -10000 0 -0.47 14 14
PAK2 0.028 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.035 0.12 0.43 4 -0.58 7 11
CDC42 0.029 0.006 -10000 0 -10000 0 0
RALB 0.029 0.005 -10000 0 -10000 0 0
RALA 0.027 0.009 -10000 0 -10000 0 0
PAK3 0.013 0.098 -10000 0 -0.6 13 13
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.044 0.056 -10000 0 -10000 0 0
TC10/GTP 0.044 0.043 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.064 0.045 -10000 0 -0.38 4 4
HRAS 0.029 0.027 -10000 0 -0.59 1 1
APS homodimer 0.022 0.054 -10000 0 -0.59 4 4
GRB14 -0.005 0.15 -10000 0 -0.64 27 27
FOXO3 -0.001 0.15 -10000 0 -0.6 28 28
AKT1 0.035 0.11 0.41 16 -0.57 2 18
INSR 0.033 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.065 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
SORBS1 0.028 0.03 -10000 0 -0.64 1 1
CRK 0.029 0.005 -10000 0 -10000 0 0
PTPN1 0.022 0.01 -10000 0 -10000 0 0
CAV1 0 0.089 -10000 0 -0.33 32 32
CBL/APS/CAP/Crk-II/C3G 0.07 0.054 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.065 0.045 -10000 0 -0.38 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.046 0.047 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.043 0.039 -10000 0 -10000 0 0
RPS6KB1 0.029 0.1 0.38 14 -0.52 2 16
PARD6A 0.025 0.05 -10000 0 -0.64 3 3
CBL 0.028 0.029 -10000 0 -0.64 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.056 -10000 0 -0.49 6 6
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.028 0.076 -10000 0 -0.53 2 2
HRAS/GTP 0.016 0.043 -10000 0 -0.55 1 1
Insulin Receptor 0.033 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.075 0.047 -10000 0 -10000 0 0
PRKCI 0.032 0.051 -10000 0 -0.48 2 2
Insulin Receptor/Insulin/GRB14/PDK1 0.013 0.083 -10000 0 -0.62 2 2
SHC1 0.029 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.039 0.062 -10000 0 -0.45 7 7
PI3K 0.057 0.051 -10000 0 -10000 0 0
NCK2 0.029 0.006 -10000 0 -10000 0 0
RHOQ 0.029 0.005 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.02 -10000 0 -0.44 1 1
AKT2 0.041 0.12 0.41 20 -0.57 2 22
PRKCZ 0.03 0.067 -10000 0 -0.59 5 5
SH2B2 0.022 0.054 -10000 0 -0.59 4 4
SHC/SHIP 0.034 0.051 -10000 0 -0.63 1 1
F2RL2 -0.005 0.14 -10000 0 -0.59 27 27
TRIP10 0.03 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.052 0.015 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.08 0.026 -10000 0 -10000 0 0
RAPGEF1 0.029 0.005 -10000 0 -10000 0 0
RASA1 0.025 0.03 -10000 0 -0.64 1 1
NCK1 0.027 0.03 -10000 0 -0.64 1 1
CBL/APS/CAP/Crk-II 0.062 0.052 -10000 0 -0.37 2 2
TC10/GDP 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.064 0.027 -10000 0 -10000 0 0
INPP5D 0.019 0.052 -10000 0 -0.43 4 4
SOS1 0.029 0.005 -10000 0 -10000 0 0
SGK1 -0.032 0.17 -10000 0 -0.62 40 40
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.005 -10000 0 -10000 0 0
IRS1 0.023 0.058 -10000 0 -0.64 4 4
p62DOK/RasGAP 0.039 0.063 -10000 0 -0.45 7 7
INS 0.023 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.019 0.051 -10000 0 -0.43 4 4
GRB2 0.029 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.011 0.12 0.38 13 -0.58 5 18
PTPRA 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
TC10/GTP/CIP4 0.039 0.008 -10000 0 -10000 0 0
PDPK1 0.027 0.03 -10000 0 -0.64 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.03 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.048 0.041 -10000 0 -0.38 4 4
Insulin Receptor/Insulin/IRS3 0.041 0.011 -10000 0 -10000 0 0
Par3/Par6 0.039 0.09 -10000 0 -0.35 3 3
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.039 0.069 0.37 1 -0.38 1 2
adherens junction organization 0.002 0.093 0.25 5 -0.43 5 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.042 0.078 0.34 2 -10000 0 2
FMN1 -0.016 0.1 -10000 0 -0.43 12 12
mol:IP3 0.024 0.053 -10000 0 -0.36 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.001 0.078 -10000 0 -0.49 3 3
CTNNB1 0.022 0.014 -10000 0 -10000 0 0
AKT1 0.026 0.06 0.26 1 -10000 0 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.051 0.14 -10000 0 -0.57 21 21
CTNND1 0.032 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.073 -10000 0 -0.41 4 4
VASP -0.001 0.075 -10000 0 -0.47 3 3
ZYX 0 0.073 -10000 0 -0.47 3 3
JUB -0.002 0.074 -10000 0 -0.47 3 3
EGFR(dimer) 0.007 0.085 -10000 0 -0.46 4 4
E-cadherin/beta catenin-gamma catenin 0.023 0.088 -10000 0 -0.4 19 19
mol:PI-3-4-5-P3 0.033 0.069 -10000 0 -0.4 2 2
PIK3CA 0.03 0.03 -10000 0 -0.64 1 1
PI3K 0.034 0.071 -10000 0 -0.41 2 2
FYN -0.2 0.14 -10000 0 -0.45 34 34
mol:Ca2+ 0.024 0.053 -10000 0 -0.35 2 2
JUP 0.028 0.051 -10000 0 -0.63 3 3
PIK3R1 0.028 0.031 -10000 0 -0.64 1 1
mol:DAG 0.024 0.053 -10000 0 -0.36 2 2
CDH1 0.008 0.12 -10000 0 -0.62 18 18
RhoA/GDP 0.041 0.078 0.35 3 -10000 0 3
establishment of polarity of embryonic epithelium 0 0.074 -10000 0 -0.46 3 3
SRC 0.029 0.006 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
EGFR 0.02 0.067 -10000 0 -0.6 6 6
CASR -0.22 0.15 -10000 0 -0.47 15 15
RhoA/GTP 0.029 0.051 -10000 0 -10000 0 0
AKT2 0.027 0.064 0.26 2 -0.4 1 3
actin cable formation -0.015 0.1 -10000 0 -0.43 11 11
apoptosis -0.028 0.07 0.36 2 -0.35 6 8
CTNNA1 0.024 0.013 -10000 0 -10000 0 0
mol:GDP 0.016 0.059 -10000 0 -10000 0 0
PIP5K1A 0 0.074 -10000 0 -0.42 4 4
PLCG1 0.024 0.054 -10000 0 -0.37 1 1
Rac1/GTP 0.018 0.085 -10000 0 -0.42 4 4
homophilic cell adhesion 0.001 0.003 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.038 0.036 -10000 0 -0.47 2 2
ATM 0.028 0.029 -10000 0 -0.64 1 1
UBE2D3 0.03 0.004 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
ATR 0.028 0.007 -10000 0 -10000 0 0
UBE2L3 0.03 0.004 -10000 0 -10000 0 0
FANCD2 0.021 0.022 -10000 0 -0.36 1 1
protein ubiquitination 0.067 0.06 -10000 0 -0.64 1 1
XRCC5 0.028 0.007 -10000 0 -10000 0 0
XRCC6 0.03 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.044 0.027 -10000 0 -10000 0 0
MRE11A 0.03 0.004 -10000 0 -10000 0 0
DNA-PK 0.054 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.003 0.11 -10000 0 -0.57 12 12
FANCF 0.03 0.004 -10000 0 -10000 0 0
BRCA1 0.029 0.004 -10000 0 -10000 0 0
CCNE1 0.022 0.071 -10000 0 -0.59 7 7
CDK2/Cyclin E1 0.037 0.055 -10000 0 -0.43 7 7
FANCG 0.029 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.039 0.037 -10000 0 -0.47 2 2
FANCE 0.028 0.028 -10000 0 -0.59 1 1
FANCC 0.029 0.006 -10000 0 -10000 0 0
NBN 0.028 0.007 -10000 0 -10000 0 0
FANCA -0.095 0.25 -10000 0 -0.59 105 105
DNA repair 0.015 0.11 0.37 6 -0.62 4 10
BRCA1/BARD1/ubiquitin 0.039 0.037 -10000 0 -0.47 2 2
BARD1/DNA-PK 0.066 0.039 -10000 0 -0.37 2 2
FANCL 0.029 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.038 0.036 0.47 2 -10000 0 2
BRCA1/BARD1/CTIP/M/R/N Complex 0.028 0.046 -10000 0 -0.69 1 1
BRCA1/BACH1/BARD1/TopBP1 0.052 0.037 -10000 0 -0.4 2 2
BRCA1/BARD1/P53 0.066 0.038 -10000 0 -0.37 2 2
BARD1/CSTF1/BRCA1 0.053 0.034 -10000 0 -0.4 2 2
BRCA1/BACH1 0.029 0.004 -10000 0 -10000 0 0
BARD1 0.025 0.047 -10000 0 -0.48 4 4
PCNA 0.029 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.035 -10000 0 -0.4 2 2
BRCA1/BARD1/UbcH7 0.054 0.035 -10000 0 -0.4 2 2
BRCA1/BARD1/RAD51/PCNA 0.057 0.074 -10000 0 -0.39 3 3
BARD1/DNA-PK/P53 0.076 0.041 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.039 0.037 -10000 0 -0.47 2 2
BRCA1/BARD1/CTIP 0.048 0.047 -10000 0 -0.48 3 3
FA complex -0.001 0.093 -10000 0 -0.45 5 5
BARD1/EWS 0.039 0.037 -10000 0 -0.47 2 2
RBBP8 0.021 0.038 -10000 0 -0.85 1 1
TP53 0.029 0.005 -10000 0 -10000 0 0
TOPBP1 0.028 0.007 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.064 0.038 0.36 2 -10000 0 2
BRCA1/BARD1 0.074 0.062 -10000 0 -0.65 1 1
CSTF1 0.029 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.018 0.034 -10000 0 -0.47 2 2
CDK2 0.029 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.013 0.1 -10000 0 -0.6 14 14
RAD50 0.023 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.039 0.037 -10000 0 -0.47 2 2
EWSR1 0.03 0.004 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.058 0.063 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.077 0.08 0.37 5 -0.58 1 6
alphaV/beta3 Integrin/Osteopontin/Src 0.047 0.043 -10000 0 -0.47 3 3
AP1 0.085 0.1 -10000 0 -0.6 3 3
ILK 0.047 0.058 -10000 0 -10000 0 0
bone resorption 0.043 0.092 -10000 0 -0.58 3 3
PTK2B 0.027 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.072 0.066 -10000 0 -10000 0 0
ITGAV 0.033 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.023 0.095 -10000 0 -0.44 21 21
alphaV/beta3 Integrin/Osteopontin 0.064 0.059 -10000 0 -0.38 7 7
MAP3K1 0.042 0.059 -10000 0 -10000 0 0
JUN 0.029 0.007 -10000 0 -10000 0 0
MAPK3 0.039 0.064 -10000 0 -10000 0 0
MAPK1 0.042 0.063 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
MAPK8 0.038 0.07 0.41 1 -0.65 2 3
ITGB3 0.027 0.065 -10000 0 -0.62 5 5
NFKBIA 0.04 0.062 -10000 0 -10000 0 0
FOS 0.013 0.099 -10000 0 -0.63 12 12
CD44 0.008 0.11 -10000 0 -0.59 18 18
CHUK 0.029 0.006 -10000 0 -10000 0 0
PLAU 0.05 0.16 0.52 4 -1.1 8 12
NF kappa B1 p50/RelA 0.083 0.077 0.38 1 -0.56 1 2
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
RELA 0.03 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.045 0.052 -10000 0 -0.46 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.045 0.061 -10000 0 -10000 0 0
VAV3 0.029 0.083 -10000 0 -0.66 1 1
MAP3K14 0.046 0.065 -10000 0 -10000 0 0
ROCK2 0.025 0.053 -10000 0 -0.56 4 4
SPP1 0.03 0.051 -10000 0 -0.63 3 3
RAC1 0.027 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.037 0.074 -10000 0 -0.61 1 1
MMP2 0.053 0.1 0.43 2 -0.51 7 9
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.049 0.031 -10000 0 -0.4 1 1
forebrain development 0.047 0.11 0.47 5 -0.48 5 10
GNAO1 0.024 0.055 -10000 0 -0.6 4 4
SMO/beta Arrestin2 0.039 0.037 -10000 0 -0.5 2 2
SMO 0.026 0.031 -10000 0 -0.63 1 1
ARRB2 0.029 0.033 -10000 0 -0.71 1 1
GLI3/SPOP 0.056 0.09 -10000 0 -0.5 8 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.028 0.008 -10000 0 -10000 0 0
GNAI2 0.022 0.014 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.076 -10000 0 -0.33 18 18
GNAI1 0.026 0.03 -10000 0 -0.63 1 1
XPO1 0.03 0.011 -10000 0 -10000 0 0
GLI1/Su(fu) 0.04 0.096 -10000 0 -0.58 5 5
SAP30 0.008 0.11 -10000 0 -0.59 18 18
mol:GDP 0.026 0.031 -10000 0 -0.63 1 1
MIM/GLI2A 0.027 0.03 -10000 0 -10000 0 0
IFT88 0.028 0.029 -10000 0 -0.64 1 1
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GLI2 0.071 0.077 0.31 12 -10000 0 12
GLI3 0.042 0.096 0.3 3 -0.56 8 11
CSNK1D 0.029 0.005 -10000 0 -10000 0 0
CSNK1E 0.03 0.004 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.028 0.029 -10000 0 -0.63 1 1
GNG2 0.028 0.008 -10000 0 -10000 0 0
Gi family/GTP 0.024 0.044 -10000 0 -0.39 3 3
SIN3B 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.046 0.1 -10000 0 -0.62 8 8
GLI2/Su(fu) 0.072 0.067 0.27 2 -0.57 1 3
FOXA2 -0.005 0.21 -10000 0 -1 14 14
neural tube patterning 0.047 0.11 0.47 5 -0.48 5 10
SPOP 0.029 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.046 0.048 -10000 0 -0.54 1 1
GNB1 0.029 0.006 -10000 0 -10000 0 0
CSNK1G2 0.028 0.029 -10000 0 -0.64 1 1
CSNK1G3 0.023 0.012 -10000 0 -10000 0 0
MTSS1 0.027 0.03 -10000 0 -10000 0 0
embryonic limb morphogenesis 0.047 0.11 0.47 5 -0.48 5 10
SUFU 0.03 0.032 -10000 0 -0.58 1 1
LGALS3 0.015 0.09 -10000 0 -0.6 11 11
catabolic process 0.1 0.12 0.38 10 -0.56 5 15
GLI3A/CBP 0.031 0.044 -10000 0 -0.36 2 2
KIF3A 0.023 0.013 -10000 0 -10000 0 0
GLI1 0.047 0.11 0.48 5 -0.49 5 10
RAB23 0.029 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.013 -10000 0 -10000 0 0
IFT172 0.029 0.005 -10000 0 -10000 0 0
RBBP7 0.03 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.036 0.079 -10000 0 -0.51 6 6
GNAZ 0.026 0.05 -10000 0 -0.64 3 3
RBBP4 0.027 0.03 -10000 0 -0.64 1 1
CSNK1G1 0.03 0.003 -10000 0 -10000 0 0
PIAS1 0.03 0.003 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GLI2/SPOP 0.084 0.065 0.29 6 -10000 0 6
STK36 0.03 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.029 0.038 -10000 0 -0.44 1 1
PTCH1 0.047 0.11 0.48 4 -0.97 1 5
MIM/GLI1 0.049 0.14 0.45 2 -0.55 5 7
CREBBP 0.031 0.044 -10000 0 -0.36 2 2
Su(fu)/SIN3/HDAC complex 0.03 0.1 0.26 1 -0.54 11 12
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.023 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.05 0.029 -10000 0 -0.37 1 1
CDKN1B 0.019 0.076 -10000 0 -0.57 1 1
CDKN1A 0.019 0.075 -10000 0 -0.58 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.008 -10000 0 -10000 0 0
FOXO3 0.019 0.071 -10000 0 -0.58 2 2
AKT1 0.025 0.031 -10000 0 -0.6 1 1
BAD 0.027 0.04 -10000 0 -0.61 2 2
AKT3 0.019 0.018 -10000 0 -0.37 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.016 0.08 -10000 0 -0.58 2 2
AKT1/ASK1 0.026 0.091 -10000 0 -0.5 4 4
BAD/YWHAZ 0.055 0.031 -10000 0 -0.39 2 2
RICTOR 0.027 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.014 -10000 0 -10000 0 0
JNK cascade -0.025 0.088 0.49 4 -10000 0 4
TSC1 0.021 0.067 -10000 0 -0.57 1 1
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.02 0.091 -10000 0 -0.51 4 4
EP300 0.028 0.029 -10000 0 -0.64 1 1
mol:GDP 0.012 0.072 -10000 0 -0.6 2 2
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0.079 -10000 0 -0.58 2 2
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
TBC1D4 0.017 0.015 -10000 0 -0.31 1 1
MAP3K5 0.028 0.008 -10000 0 -10000 0 0
MAPKAP1 0.029 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.082 0.32 9 -0.25 10 19
YWHAH 0.03 0.004 -10000 0 -10000 0 0
AKT1S1 0.017 0.079 -10000 0 -0.58 2 2
CASP9 0.02 0.07 -10000 0 -0.59 1 1
YWHAB 0.029 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.033 0.094 0.34 5 -0.45 4 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.052 0.029 -10000 0 -0.4 1 1
YWHAE 0.029 0.005 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0.016 0.078 -10000 0 -0.47 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.027 -10000 0 -10000 0 0
CHUK 0.018 0.076 -10000 0 -0.58 2 2
BAD/BCL-XL 0.039 0.093 -10000 0 -0.47 5 5
mTORC2 0.033 0.013 -10000 0 -10000 0 0
AKT2 0.02 0.018 -10000 0 -0.37 1 1
FOXO1-3a-4/14-3-3 family 0.036 0.11 0.3 9 -0.41 11 20
PDPK1 0.027 0.03 -10000 0 -0.64 1 1
MDM2 0.02 0.077 -10000 0 -0.57 1 1
MAPKKK cascade -0.019 0.089 0.5 4 -10000 0 4
MDM2/Cbp/p300 0.047 0.095 0.32 3 -0.44 5 8
TSC1/TSC2 0.026 0.074 0.28 11 -0.56 1 12
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.091 0.31 3 -0.42 5 8
glucose import 0.01 0.058 -10000 0 -0.35 11 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.053 0.24 3 -0.32 2 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.008 0.055 -10000 0 -0.36 11 11
GSK3A 0.017 0.079 -10000 0 -0.58 2 2
FOXO1 0.017 0.079 -10000 0 -0.58 2 2
GSK3B 0.018 0.073 -10000 0 -0.58 2 2
SFN -0.041 0.2 -10000 0 -0.59 59 59
G1/S transition of mitotic cell cycle 0.024 0.079 0.34 3 -0.52 3 6
p27Kip1/14-3-3 family 0.039 0.069 0.27 2 -0.38 3 5
PRKACA 0.03 0.002 -10000 0 -10000 0 0
KPNA1 0.028 0.008 -10000 0 -10000 0 0
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
RHEB 0.027 0.009 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.023 0.013 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.037 0.051 -10000 0 -0.47 5 5
PTK2 0.029 0.078 -10000 0 -0.7 1 1
positive regulation of JNK cascade 0.01 0.1 -10000 0 -0.34 14 14
CDC42/GDP 0.036 0.14 0.37 3 -0.46 9 12
Rac1/GDP 0.03 0.13 -10000 0 -0.5 5 5
RAP1B 0.029 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.021 0.13 -10000 0 -0.43 14 14
nectin-3/I-afadin 0.036 0.037 -10000 0 -0.47 2 2
RAPGEF1 0.019 0.12 0.3 2 -0.47 3 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0.13 -10000 0 -0.54 3 3
PDGFB-D/PDGFRB 0.023 0.013 -10000 0 -10000 0 0
TLN1 0.016 0.016 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.09 -10000 0 -0.39 1 1
IQGAP1 0.03 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.02 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.036 0.037 -10000 0 -0.47 2 2
PVR 0.03 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.03 0.003 -10000 0 -10000 0 0
mol:GDP 0.022 0.16 0.39 3 -0.54 13 16
MLLT4 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
PI3K 0.055 0.056 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.013 0.1 -10000 0 -0.37 10 10
PVRL1 0.03 0.003 -10000 0 -10000 0 0
PVRL3 0.024 0.044 -10000 0 -0.53 3 3
PVRL2 0.03 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
CDH1 0.007 0.12 -10000 0 -0.62 18 18
CLDN1 0.022 0.063 -10000 0 -0.62 5 5
JAM-A/CLDN1 0.057 0.055 -10000 0 -0.36 5 5
SRC 0.006 0.14 -10000 0 -0.6 3 3
ITGB3 0.023 0.065 -10000 0 -0.64 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
FARP2 0.015 0.17 -10000 0 -0.64 15 15
RAC1 0.027 0.009 -10000 0 -10000 0 0
CTNNA1 0.023 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.049 0.037 -10000 0 -0.4 2 2
nectin-1/I-afadin 0.04 0.013 -10000 0 -10000 0 0
nectin-2/I-afadin 0.04 0.013 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.036 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.05 0.037 -10000 0 -0.4 2 2
CDC42/GTP/IQGAP1/filamentous actin 0.039 0.009 -10000 0 -10000 0 0
F11R 0.029 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.01 0.1 -10000 0 -0.34 14 14
alphaV/beta3 Integrin/Talin 0.047 0.051 -10000 0 -0.49 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.04 0.013 -10000 0 -10000 0 0
PIP5K1C 0.017 0.017 -10000 0 -10000 0 0
VAV2 0.016 0.17 -10000 0 -0.63 12 12
RAP1/GDP 0.036 0.13 -10000 0 -0.44 2 2
ITGAV 0.029 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.049 0.037 -10000 0 -0.4 2 2
nectin-3(dimer)/I-afadin/I-afadin 0.036 0.037 -10000 0 -0.47 2 2
Rac1/GTP 0.021 0.13 -10000 0 -0.46 9 9
PTPRM 0.018 0.019 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.04 0.075 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.029 0.006 -10000 0 -10000 0 0
Arf6 trafficking 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
SLC2A4 0.015 0.097 -10000 0 -0.64 11 11
CLTC 0.019 0.085 -10000 0 -0.39 5 5
calcium ion-dependent exocytosis 0.027 0.028 0.2 1 -10000 0 1
Dynamin 2/GTP 0.032 0.019 -10000 0 -0.34 1 1
EXOC4 0.027 0.009 -10000 0 -10000 0 0
CD59 0.016 0.064 -10000 0 -0.3 4 4
CPE 0.005 0.077 -10000 0 -0.37 21 21
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
membrane fusion 0.02 0.015 -10000 0 -10000 0 0
CTNND1 0.026 0.025 -10000 0 -10000 0 0
DNM2 0.03 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.049 0.26 1 -0.44 1 2
TSHR -0.025 0.12 -10000 0 -0.37 60 60
INS 0.017 0.038 -10000 0 -0.77 1 1
BIN1 0.029 0.005 -10000 0 -10000 0 0
mol:Choline 0.02 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.018 -10000 0 -0.37 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.032 0.019 -10000 0 -0.33 1 1
JUP 0.014 0.068 -10000 0 -0.38 1 1
ASAP2/amphiphysin II 0.051 0.025 -10000 0 -0.37 1 1
ARF6/GTP 0.021 0.006 -10000 0 -10000 0 0
CDH1 0.009 0.078 -10000 0 -0.45 3 3
clathrin-independent pinocytosis 0.021 0.006 -10000 0 -10000 0 0
MAPK8IP3 -0.014 0.16 -10000 0 -0.59 36 36
positive regulation of endocytosis 0.021 0.006 -10000 0 -10000 0 0
EXOC2 0.029 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.036 0.022 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.077 0.51 1 -10000 0 1
positive regulation of phagocytosis 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.009 0.1 -10000 0 -0.37 36 36
ACAP1 0.012 0.036 -10000 0 -0.27 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.008 0.062 -10000 0 -0.32 5 5
clathrin heavy chain/ACAP1 0.022 0.069 -10000 0 -0.49 1 1
JIP4/KLC1 0.052 0.018 -10000 0 -10000 0 0
EXOC1 0.03 0.004 -10000 0 -10000 0 0
exocyst 0.036 0.022 -10000 0 -10000 0 0
RALA/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.037 0.012 -10000 0 -10000 0 0
receptor recycling 0.021 0.006 -10000 0 -10000 0 0
CTNNA1 0.021 0.027 -10000 0 -10000 0 0
NME1 0.019 0.018 -10000 0 -0.37 1 1
clathrin coat assembly 0.019 0.088 -10000 0 -0.38 5 5
IL2RA -0.018 0.093 -10000 0 -0.38 7 7
VAMP3 0.02 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.02 0.08 -10000 0 -0.44 4 4
EXOC6 0.029 0.006 -10000 0 -10000 0 0
PLD1 0.021 0.009 -10000 0 -10000 0 0
PLD2 0.021 0.009 -10000 0 -10000 0 0
EXOC5 0.028 0.008 -10000 0 -10000 0 0
PIP5K1C 0.024 0.046 -10000 0 -0.45 1 1
SDC1 0.013 0.074 -10000 0 -0.51 2 2
ARF6/GDP 0.028 0.02 -10000 0 -0.37 1 1
EXOC7 0.029 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.023 0.08 -10000 0 -0.52 1 1
mol:Phosphatidic acid 0.02 0.015 -10000 0 -10000 0 0
endocytosis -0.05 0.025 0.37 1 -10000 0 1
SCAMP2 0.03 0.003 -10000 0 -10000 0 0
ADRB2 0.063 0.1 0.33 6 -0.51 1 7
EXOC3 0.027 0.009 -10000 0 -10000 0 0
ASAP2 0.028 0.029 -10000 0 -0.64 1 1
Dynamin 2/GDP 0.035 0.02 -10000 0 -0.33 1 1
KLC1 0.028 0.008 -10000 0 -10000 0 0
AVPR2 -0.12 0.19 0.3 1 -0.58 25 26
RALA 0.027 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.039 0.08 -10000 0 -0.49 1 1
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.067 0.84 1 -10000 0 1
VDR 0.025 0.05 -10000 0 -0.64 3 3
FAM120B 0.027 0.008 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.057 0.046 -10000 0 -0.34 1 1
RXRs/LXRs/DNA/Oxysterols 0.062 0.056 -10000 0 -10000 0 0
MED1 0.029 0.004 -10000 0 -10000 0 0
mol:9cRA 0.006 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.012 0.074 -10000 0 -10000 0 0
RXRs/NUR77 0.065 0.085 -10000 0 -0.37 6 6
RXRs/PPAR 0.034 0.039 -10000 0 -0.55 1 1
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.038 -10000 0 -0.47 3 3
RARs/VDR/DNA/Vit D3 0.045 0.05 -10000 0 -0.35 2 2
RARA 0.029 0.004 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.05 -10000 0 -0.63 3 3
RARs/RARs/DNA/9cRA 0.037 0.036 -10000 0 -0.35 2 2
RARG 0.029 0.005 -10000 0 -10000 0 0
RPS6KB1 0.02 0.071 0.5 9 -0.44 1 10
RARs/THRs/DNA/SMRT 0.013 0.074 -10000 0 -10000 0 0
THRA 0.028 0.029 -10000 0 -0.64 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.038 -10000 0 -0.47 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.067 0.05 0.33 1 -0.39 1 2
NR1H4 0.011 0.11 -10000 0 -0.64 14 14
RXRs/LXRs/DNA 0.1 0.062 -10000 0 -10000 0 0
NR1H2 0.034 0.031 -10000 0 -0.63 1 1
NR1H3 0.036 0.01 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.069 0.054 -10000 0 -0.35 3 3
NR4A1 0.012 0.11 -10000 0 -0.63 14 14
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.027 0.073 -10000 0 -0.43 9 9
RXRG 0.027 0.057 -10000 0 -0.61 4 4
RXR alpha/CCPG 0.043 0.017 -10000 0 -10000 0 0
RXRA 0.034 0.011 -10000 0 -10000 0 0
RXRB 0.035 0.012 -10000 0 -10000 0 0
THRB -0.015 0.14 -10000 0 -0.57 32 32
PPARG 0.021 0.014 -10000 0 -10000 0 0
PPARD 0.029 0.006 -10000 0 -10000 0 0
TNF 0.056 0.11 -10000 0 -1 4 4
mol:Oxysterols 0.006 0.006 -10000 0 -10000 0 0
cholesterol transport 0.062 0.056 -10000 0 -10000 0 0
PPARA 0.03 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.043 -10000 0 -0.64 2 2
RXRs/NUR77/BCL2 0.027 0.059 -10000 0 -0.46 2 2
SREBF1 0.062 0.051 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.067 0.05 0.33 1 -0.39 1 2
ABCA1 0.061 0.058 -10000 0 -10000 0 0
RARs/THRs 0.037 0.1 -10000 0 -10000 0 0
RXRs/FXR 0.066 0.084 -10000 0 -0.42 2 2
BCL2 0.029 0.005 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.029 0.006 -10000 0 -10000 0 0
NFATC1 0.045 0.071 0.37 3 -0.44 1 4
NFATC2 0.037 0.068 0.23 7 -0.26 12 19
NFATC3 0.025 0.031 -10000 0 -0.35 3 3
YWHAE 0.029 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0 0.085 0.31 2 -0.37 9 11
Exportin 1/Ran/NUP214 0.056 0.018 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.025 0.078 -10000 0 -0.43 3 3
BCL2/BAX 0.043 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.021 0.01 -10000 0 -10000 0 0
BAX 0.03 0.003 -10000 0 -10000 0 0
MAPK14 0.029 0.006 -10000 0 -10000 0 0
BAD 0.027 0.04 -10000 0 -0.61 2 2
CABIN1/MEF2D 0.014 0.082 0.31 1 -0.39 5 6
Calcineurin A alpha-beta B1/BCL2 0.029 0.005 -10000 0 -10000 0 0
FKBP8 0.029 0.029 -10000 0 -0.64 1 1
activation-induced cell death of T cells -0.014 0.081 0.38 5 -0.31 1 6
KPNB1 0.029 0.005 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
SFN -0.041 0.2 -10000 0 -0.59 59 59
MAP3K8 0.027 0.038 -10000 0 -0.59 2 2
NFAT4/CK1 alpha 0.032 0.03 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.074 0.089 -10000 0 -0.44 3 3
CABIN1 0 0.084 0.31 2 -0.38 8 10
CALM1 0.028 0.009 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
MAP3K1 0.027 0.009 -10000 0 -10000 0 0
CAMK4 0.023 0.031 -10000 0 -0.64 1 1
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 -10000 0 0
YWHAH 0.03 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.039 0.034 -10000 0 -0.47 2 2
YWHAB 0.029 0.006 -10000 0 -10000 0 0
MAPK8 0.027 0.041 -10000 0 -0.64 2 2
MAPK9 0.022 0.013 -10000 0 -10000 0 0
YWHAG 0.027 0.009 -10000 0 -10000 0 0
FKBP1A 0.029 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.07 0.079 -10000 0 -0.45 1 1
PRKCH 0.028 0.008 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.041 0.027 -10000 0 -0.47 1 1
CASP3 0.03 0.004 -10000 0 -10000 0 0
PIM1 0.029 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
apoptosis 0.025 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.061 -10000 0 -0.36 5 5
PRKCB 0.022 0.062 -10000 0 -0.61 5 5
PRKCE 0.028 0.029 -10000 0 -0.64 1 1
JNK2/NFAT4 0.026 0.044 -10000 0 -0.4 1 1
BAD/BCL-XL 0.041 0.032 -10000 0 -0.45 2 2
PRKCD 0.02 0.03 -10000 0 -0.59 1 1
NUP214 0.029 0.005 -10000 0 -10000 0 0
PRKCZ 0.025 0.051 -10000 0 -0.64 3 3
PRKCA 0.029 0.005 -10000 0 -10000 0 0
PRKCG -0.001 0.12 -10000 0 -0.6 21 21
PRKCQ 0.012 0.1 -10000 0 -0.57 15 15
FKBP38/BCL2 0.042 0.024 -10000 0 -0.47 1 1
EP300 0.028 0.03 -10000 0 -0.63 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.029 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.057 0.075 0.35 2 -0.39 1 3
CaM/Ca2+/FKBP38 0.037 0.024 -10000 0 -0.42 1 1
FKBP12/FK506 0.021 0.004 -10000 0 -10000 0 0
CSNK1A1 0.017 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.031 0.026 -10000 0 -0.39 1 1
NFATc/ERK1 0.054 0.07 -10000 0 -0.41 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.025 0.079 -10000 0 -0.44 3 3
NR4A1 0.051 0.12 -10000 0 -0.58 13 13
GSK3B 0.028 0.008 -10000 0 -10000 0 0
positive T cell selection 0.025 0.031 -10000 0 -0.35 3 3
NFAT1/CK1 alpha 0.021 0.038 -10000 0 -10000 0 0
RCH1/ KPNB1 0.043 0.008 -10000 0 -10000 0 0
YWHAQ 0.029 0.005 -10000 0 -10000 0 0
PRKACA 0.03 0.003 -10000 0 -10000 0 0
AKAP5 0.025 0.042 -10000 0 -0.64 2 2
MEF2D 0.029 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.06 0.071 0.37 3 -0.39 1 4
CREBBP 0.029 0.008 -10000 0 -10000 0 0
BCL2 0.029 0.005 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.013 -10000 0 -10000 0 0
VDR 0.025 0.05 -10000 0 -0.64 3 3
Cbp/p300/PCAF 0.041 0.045 -10000 0 -0.76 1 1
EP300 0.028 0.029 -10000 0 -0.64 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.028 0.051 -10000 0 -0.33 4 4
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
MAPK14 0.029 0.006 -10000 0 -10000 0 0
AKT1 0 0.054 0.22 1 -10000 0 1
RAR alpha/9cRA/Cyclin H 0.05 0.057 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.027 0.053 -10000 0 -0.44 1 1
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.025 0.056 -10000 0 -0.37 6 6
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.038 -10000 0 -0.47 3 3
RXRs/RARs/NRIP1/9cRA 0.03 0.078 -10000 0 -0.53 1 1
NCOA2 0.015 0.091 -10000 0 -0.64 10 10
NCOA3 0.029 0.006 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.05 -10000 0 -0.63 3 3
RARG 0.03 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.04 0.008 -10000 0 -10000 0 0
MAPK3 0.03 0.006 -10000 0 -10000 0 0
MAPK1 0.03 0.004 -10000 0 -10000 0 0
MAPK8 0.028 0.041 -10000 0 -0.63 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.045 0.07 -10000 0 -0.54 1 1
RARA 0.022 0.04 -10000 0 -0.26 3 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.02 0.08 -10000 0 -0.47 9 9
PRKCA 0.032 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.004 0.1 0.36 1 -0.52 3 4
RXRG 0.017 0.062 -10000 0 -0.62 1 1
RXRA 0.028 0.044 -10000 0 -10000 0 0
RXRB 0.019 0.063 -10000 0 -0.5 3 3
VDR/Vit D3/DNA 0.019 0.038 -10000 0 -0.47 3 3
RBP1 0.024 0.055 -10000 0 -0.6 4 4
CRBP1/9-cic-RA 0.018 0.041 -10000 0 -0.44 4 4
RARB 0.021 0.043 -10000 0 -0.64 2 2
PRKCG 0.002 0.12 -10000 0 -0.59 21 21
MNAT1 0.028 0.008 -10000 0 -10000 0 0
RAR alpha/RXRs 0.024 0.076 -10000 0 -0.53 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.032 0.073 0.3 1 -0.43 2 3
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.11 0.28 8 -0.36 5 13
RXRs/RARs/NRIP1/9cRA/HDAC3 0.014 0.1 0.4 1 -0.51 2 3
positive regulation of DNA binding 0.037 0.049 -10000 0 -10000 0 0
NRIP1 -0.008 0.12 -10000 0 -10000 0 0
RXRs/RARs -0.015 0.12 -10000 0 -0.49 4 4
RXRs/RXRs/DNA/9cRA 0.028 0.062 -10000 0 -0.48 2 2
PRKACA 0.03 0.002 -10000 0 -10000 0 0
CDK7 0.027 0.009 -10000 0 -10000 0 0
TFIIH 0.051 0.023 -10000 0 -10000 0 0
RAR alpha/9cRA 0.053 0.054 -10000 0 -10000 0 0
CCNH 0.026 0.01 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.048 0.025 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.03 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.013 -9999 0 -10000 0 0
DOCK1 0.028 0.03 -9999 0 -0.64 1 1
ITGA4 0.01 0.11 -9999 0 -0.59 16 16
RAC1 0.027 0.009 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.027 0.082 -9999 0 -0.43 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.029 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.044 0.075 -9999 0 -0.37 16 16
alpha4/beta7 Integrin/Paxillin 0.04 0.068 -9999 0 -10000 0 0
lamellipodium assembly 0.038 0.058 -9999 0 -0.62 2 2
PIK3CA 0.027 0.03 -9999 0 -0.64 1 1
PI3K 0.037 0.035 -9999 0 -0.47 2 2
ARF6 0.028 0.008 -9999 0 -10000 0 0
TLN1 0.029 0.006 -9999 0 -10000 0 0
PXN 0.023 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.03 -9999 0 -0.64 1 1
ARF6/GTP 0.049 0.064 -9999 0 -10000 0 0
cell adhesion 0.051 0.068 -9999 0 -10000 0 0
CRKL/CBL 0.042 0.024 -9999 0 -0.47 1 1
alpha4/beta1 Integrin/Paxillin 0.04 0.068 -9999 0 -10000 0 0
ITGB1 0.029 0.004 -9999 0 -10000 0 0
ITGB7 0.029 0.005 -9999 0 -10000 0 0
ARF6/GDP 0.024 0.012 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.045 0.086 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 0.054 0.033 -9999 0 -0.4 2 2
VCAM1 0.015 0.089 -9999 0 -0.53 13 13
alpha4/beta1 Integrin/Paxillin/Talin 0.053 0.069 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.069 -9999 0 -10000 0 0
BCAR1 0.028 0.03 -9999 0 -0.64 1 1
mol:GDP -0.052 0.068 -9999 0 -10000 0 0
CBL 0.028 0.029 -9999 0 -0.64 1 1
PRKACA 0.03 0.002 -9999 0 -10000 0 0
GIT1 0.029 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.053 0.069 -9999 0 -10000 0 0
Rac1/GTP 0.04 0.065 -9999 0 -0.72 2 2
Atypical NF-kappaB 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
BCL3/RelA 0.042 0.03 -10000 0 -0.43 2 2
FBXW11 0.023 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.032 0.041 -10000 0 -0.41 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.035 0.06 -10000 0 -10000 0 0
NFKBIA 0.019 0.044 -10000 0 -0.33 2 2
MAPK14 0.029 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.026 -10000 0 -0.4 1 1
ARRB2 0.019 0.028 -10000 0 -0.62 1 1
REL 0.025 0.053 -10000 0 -0.56 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.034 0.033 -10000 0 -0.39 2 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.035 0.022 -10000 0 -0.4 1 1
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
NF kappa B1 p50 dimer 0.025 0.023 -10000 0 -0.47 1 1
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
NFKB1 0.02 0.023 -10000 0 -0.47 1 1
RELA 0.03 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.023 0.042 -10000 0 -0.28 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.037 0.068 -10000 0 -0.5 1 1
SRC 0.029 0.006 -10000 0 -10000 0 0
PI3K 0.037 0.035 -10000 0 -0.47 2 2
NF kappa B1 p50/RelA 0.024 0.043 -10000 0 -0.29 2 2
IKBKB 0.028 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -10000 0 -10000 0 0
SYK 0.027 0.033 -10000 0 -0.48 2 2
I kappa B alpha/PIK3R1 0.022 0.063 0.28 1 -0.41 2 3
cell death 0.035 0.065 -10000 0 -0.48 1 1
NF kappa B1 p105/c-Rel 0.032 0.041 -10000 0 -0.41 4 4
LCK 0.003 0.12 -10000 0 -0.59 22 22
BCL3 0.027 0.038 -10000 0 -0.59 2 2
IGF1 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
NCK2 0.029 0.006 -10000 0 -10000 0 0
PTK2 0.029 0.007 -10000 0 -10000 0 0
CRKL 0.025 0.038 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.056 0.017 -10000 0 -10000 0 0
HRAS 0.029 0.027 -10000 0 -0.59 1 1
IRS1/Crk 0.03 0.035 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/PTP1B 0.052 0.042 -10000 0 -0.33 2 2
AKT1 0.036 0.068 0.31 6 -0.61 1 7
BAD 0.032 0.073 0.3 6 -0.82 1 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.035 0.037 -10000 0 -10000 0 0
RAF1 -0.04 0.18 0.34 2 -0.59 2 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.064 0.042 -10000 0 -10000 0 0
YWHAZ 0.028 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.033 0.039 -10000 0 -0.27 6 6
PIK3CA 0.027 0.03 -10000 0 -0.64 1 1
RPS6KB1 0.04 0.072 0.32 7 -0.61 1 8
GNB2L1 0.023 0.013 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.038 0.16 0.33 8 -0.48 2 10
PXN 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.03 -10000 0 -0.64 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.031 0.034 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.078 0.041 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.05 0.041 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin 0.065 0.046 -10000 0 -10000 0 0
IGF1R 0.032 0.016 -10000 0 -10000 0 0
IGF1 0.026 0.06 -10000 0 -0.57 5 5
IRS2/Crk 0.032 0.054 -10000 0 -0.32 4 4
PI3K 0.058 0.052 -10000 0 -0.34 1 1
apoptosis -0.048 0.072 0.66 1 -0.31 9 10
HRAS/GDP 0.021 0.02 -10000 0 -0.44 1 1
PRKCD 0.029 0.05 -10000 0 -0.44 3 3
RAF1/14-3-3 E -0.037 0.18 0.34 4 -0.5 2 6
BAD/14-3-3 0.05 0.075 0.33 6 -0.73 1 7
PRKCZ 0.036 0.071 0.32 5 -0.61 1 6
Crk/p130 Cas/Paxillin/FAK1 0.041 0.045 -10000 0 -0.51 1 1
PTPN1 0.029 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.025 0.039 -10000 0 -0.36 3 3
BCAR1 0.028 0.03 -10000 0 -0.64 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.061 0.044 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.029 0.005 -10000 0 -10000 0 0
IRS1/NCK2 0.038 0.039 -10000 0 -10000 0 0
GRB10 0.027 0.009 -10000 0 -10000 0 0
PTPN11 0.026 0.039 -10000 0 -10000 0 0
IRS1 0.022 0.041 0.21 1 -0.27 6 7
IRS2 0.02 0.057 -10000 0 -0.33 7 7
IGF-1R heterotetramer/IGF1 0.039 0.048 -10000 0 -0.4 5 5
GRB2 0.029 0.005 -10000 0 -10000 0 0
PDPK1 0.043 0.071 0.32 7 -0.64 1 8
YWHAE 0.029 0.005 -10000 0 -10000 0 0
PRKD1 0.041 0.05 -10000 0 -0.37 4 4
SHC1 0.029 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.068 0.031 -10000 0 -0.37 1 1
HDAC3 0.023 0.013 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.008 0.002 -10000 0 -10000 0 0
GATA1/HDAC4 0.023 0.09 -10000 0 -0.43 19 19
GATA1/HDAC5 0.023 0.094 -10000 0 -0.44 21 21
GATA2/HDAC5 0.029 0.076 -10000 0 -0.47 11 11
HDAC5/BCL6/BCoR 0.055 0.026 -10000 0 -0.4 1 1
HDAC9 0.027 0.009 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.033 -10000 0 -0.37 1 1
HDAC4/ANKRA2 0.038 0.016 -10000 0 -10000 0 0
HDAC5/YWHAB 0.041 0.025 -10000 0 -0.47 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.022 0.008 -10000 0 -10000 0 0
GATA2 0.014 0.096 -10000 0 -0.61 12 12
HDAC4/RFXANK 0.041 0.023 -10000 0 -0.43 1 1
BCOR 0.03 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.028 0.029 -10000 0 -0.64 1 1
HDAC5 0.028 0.029 -10000 0 -0.64 1 1
GNB1/GNG2 0.04 0.014 -10000 0 -10000 0 0
Histones 0.032 0.045 -10000 0 -0.72 1 1
ADRBK1 0.03 0.003 -10000 0 -10000 0 0
HDAC4 0.028 0.007 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.027 -10000 0 -0.47 1 1
HDAC4/Ubc9 0.04 0.013 -10000 0 -10000 0 0
HDAC7 0.029 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.042 0.024 -10000 0 -0.47 1 1
TUBA1B 0.029 0.005 -10000 0 -10000 0 0
HDAC6 0.03 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.041 0.032 -10000 0 -0.45 2 2
CAMK4 0.023 0.031 -10000 0 -0.64 1 1
Tubulin/HDAC6 0.056 0.026 -10000 0 -0.4 1 1
SUMO1 0.029 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.029 0.006 -10000 0 -10000 0 0
GATA1 0.004 0.12 -10000 0 -0.59 20 20
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.029 0.005 -10000 0 -10000 0 0
NR3C1 0.022 0.03 -10000 0 -0.59 1 1
SUMO1/HDAC4 0.051 0.027 -10000 0 -10000 0 0
SRF 0.029 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.041 0.012 -10000 0 -10000 0 0
Tubulin 0.041 0.025 -10000 0 -0.47 1 1
HDAC4/14-3-3 E 0.041 0.011 -10000 0 -10000 0 0
GNB1 0.029 0.006 -10000 0 -10000 0 0
RANGAP1 0.03 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.042 0.011 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.043 0.028 -10000 0 -10000 0 0
HDAC4/SRF 0.045 0.033 -10000 0 -0.4 1 1
HDAC4/ER alpha 0.035 0.047 -10000 0 -0.46 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.044 -10000 0 -0.72 1 1
cell motility 0.055 0.026 -10000 0 -0.4 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.034 0.019 -10000 0 -10000 0 0
BCL6 0.029 0.007 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.041 0.012 -10000 0 -10000 0 0
ESR1 0.022 0.059 -10000 0 -0.56 5 5
HDAC6/HDAC11 0.03 0.03 -10000 0 -0.47 1 1
Ran/GTP/Exportin 1 0.052 0.029 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
MEF2C 0.026 0.01 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
HDAC4/MEF2C 0.062 0.041 -10000 0 -10000 0 0
GNG2 0.028 0.008 -10000 0 -10000 0 0
NCOR2 0.029 0.005 -10000 0 -10000 0 0
TUBB2A 0.028 0.03 -10000 0 -0.64 1 1
HDAC11 0.02 0.032 -10000 0 -0.64 1 1
HSP90AA1 0.028 0.008 -10000 0 -10000 0 0
RANBP2 0.029 0.005 -10000 0 -10000 0 0
ANKRA2 0.027 0.009 -10000 0 -10000 0 0
RFXANK 0.029 0.027 -10000 0 -0.59 1 1
nuclear import -0.041 0.022 0.35 1 -10000 0 1
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.066 0.03 -10000 0 -10000 0 0
CLOCK 0.032 0.03 -10000 0 -0.63 1 1
TIMELESS/CRY2 0.056 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.037 0.023 -10000 0 -0.43 1 1
ATR 0.028 0.007 -10000 0 -10000 0 0
NR1D1 0.035 0.064 -10000 0 -0.84 2 2
ARNTL 0.033 0.006 -10000 0 -10000 0 0
TIMELESS 0.038 0.024 -10000 0 -10000 0 0
NPAS2 0.024 0.071 -10000 0 -0.49 9 9
CRY2 0.03 0.003 -10000 0 -10000 0 0
mol:CO -0.014 0.008 0.11 2 -10000 0 2
CHEK1 0.03 0.003 -10000 0 -10000 0 0
mol:HEME 0.014 0.008 -10000 0 -0.11 2 2
PER1 0.029 0.005 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.069 0.051 -10000 0 -0.39 4 4
BMAL1/CLOCK 0.05 0.06 -10000 0 -0.8 1 1
S phase of mitotic cell cycle 0.066 0.03 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.067 0.03 -10000 0 -10000 0 0
mol:NADPH 0.014 0.008 -10000 0 -0.11 2 2
PER1/TIMELESS 0.055 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.027 -10000 0 -0.59 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.049 0.06 -10000 0 -0.41 3 3
Ran/GTP/Exportin 1/HDAC1 0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.055 -10000 0 -0.46 1 1
SUMO1 0.029 0.007 -10000 0 -10000 0 0
ZFPM1 0.025 0.05 -10000 0 -0.64 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.022 0.008 -10000 0 -10000 0 0
FKBP3 0.028 0.008 -10000 0 -10000 0 0
Histones 0.056 0.045 -10000 0 -10000 0 0
YY1/LSF 0.009 0.067 -10000 0 -0.64 1 1
SMG5 0.029 0.007 -10000 0 -10000 0 0
RAN 0.029 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.034 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.03 0.039 -10000 0 -10000 0 0
SAP18 0.029 0.005 -10000 0 -10000 0 0
RELA 0.027 0.037 -10000 0 -10000 0 0
HDAC1/Smad7 0.052 0.022 -10000 0 -10000 0 0
RANGAP1 0.03 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.033 0.032 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.044 0.027 -10000 0 -0.32 1 1
NF kappa B1 p50/RelA 0.076 0.069 0.28 8 -0.55 1 9
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.014 0.096 -10000 0 -0.61 12 12
GATA1 0.004 0.12 -10000 0 -0.59 20 20
Mad/Max 0.04 0.013 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.049 0.055 -10000 0 -0.42 2 2
RBBP7 0.03 0.003 -10000 0 -10000 0 0
NPC 0.017 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.03 -10000 0 -0.64 1 1
MAX 0.028 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.023 0.013 -10000 0 -10000 0 0
NFKBIA 0.021 0.029 -10000 0 -10000 0 0
KAT2B 0.02 0.032 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.035 0.045 -10000 0 -0.42 2 2
SIN3 complex 0.059 0.076 -10000 0 -0.33 18 18
SMURF1 0.027 0.009 -10000 0 -10000 0 0
CHD3 0.029 0.005 -10000 0 -10000 0 0
SAP30 0.008 0.11 -10000 0 -0.59 18 18
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.029 0.005 -10000 0 -10000 0 0
YY1/HDAC3 0.019 0.05 -10000 0 -0.56 1 1
YY1/HDAC2 0.012 0.064 -10000 0 -0.64 1 1
YY1/HDAC1 0.01 0.066 -10000 0 -0.64 1 1
NuRD/MBD2 Complex (MeCP1) 0.044 0.022 -10000 0 -10000 0 0
PPARG 0.021 0.041 -10000 0 -0.34 2 2
HDAC8/hEST1B 0.058 0.014 -10000 0 -10000 0 0
UBE2I 0.029 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -10000 0 -10000 0 0
TNFRSF1A 0.029 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.033 0.032 -10000 0 -10000 0 0
MBD3L2 0.018 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.022 -10000 0 -10000 0 0
CREBBP 0.029 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.046 0.062 -10000 0 -0.37 1 1
HDAC1 0.029 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.027 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
YY1 0.021 0.036 -10000 0 -0.71 1 1
HDAC8 0.03 0.001 -10000 0 -10000 0 0
SMAD7 0.029 0.005 -10000 0 -10000 0 0
NCOR2 0.029 0.005 -10000 0 -10000 0 0
MXD1 0.029 0.005 -10000 0 -10000 0 0
STAT3 0.029 0.019 -10000 0 -0.36 1 1
NFKB1 0.028 0.029 -10000 0 -0.64 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.029 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.067 -10000 0 -0.6 1 1
YY1/SAP30/HDAC1 0.01 0.094 -10000 0 -0.47 5 5
EP300 0.028 0.029 -10000 0 -0.64 1 1
STAT3 (dimer non-phopshorylated) 0.029 0.019 -10000 0 -0.36 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.029 -10000 0 -10000 0 0
histone deacetylation 0.05 0.025 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.032 -10000 0 -10000 0 0
nuclear export -0.057 0.014 -10000 0 -10000 0 0
PRKACA 0.03 0.002 -10000 0 -10000 0 0
GATAD2B 0.029 0.007 -10000 0 -10000 0 0
GATAD2A 0.03 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.026 0.06 -10000 0 -0.36 8 8
GATA1/HDAC1 0.023 0.091 -10000 0 -0.43 20 20
GATA1/HDAC3 0.022 0.066 -10000 0 -10000 0 0
CHD4 0.029 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.062 -10000 0 -0.45 8 8
SIN3/HDAC complex/Mad/Max 0.038 0.043 -10000 0 -0.41 2 2
NuRD Complex 0.051 0.06 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.053 0.043 -10000 0 -10000 0 0
SIN3B 0.03 0.003 -10000 0 -10000 0 0
MTA2 0.03 0.003 -10000 0 -10000 0 0
SIN3A 0.03 0.003 -10000 0 -10000 0 0
XPO1 0.029 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.051 0.027 -10000 0 -10000 0 0
HDAC complex 0.069 0.03 -10000 0 -10000 0 0
GATA1/Fog1 0.021 0.096 -10000 0 -0.44 21 21
FKBP25/HDAC1/HDAC2 0.052 0.021 -10000 0 -10000 0 0
TNF 0.019 0.079 -10000 0 -0.61 8 8
negative regulation of cell growth 0.04 0.043 -10000 0 -0.4 2 2
NuRD/MBD2/PRMT5 Complex 0.044 0.022 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.052 0.029 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.029 0.041 -10000 0 -0.34 2 2
SIN3/HDAC complex/NCoR1 0.038 0.041 -10000 0 -0.35 1 1
TFCP2 0.029 0.005 -10000 0 -10000 0 0
NR2C1 0.029 0.005 -10000 0 -10000 0 0
MBD3 0.027 0.04 -10000 0 -0.61 2 2
MBD2 0.029 0.005 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.052 0.074 0.31 9 -0.45 1 10
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.017 0.051 0.15 1 -0.28 9 10
AP2 0.042 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.037 0.014 -10000 0 -10000 0 0
CLTB 0.022 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.014 -10000 0 -10000 0 0
CD4 0.018 0.081 -10000 0 -0.59 9 9
CLTA 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
ARFGAP1 0.011 0.021 -10000 0 -0.48 1 1
mol:PI-4-5-P2 0.011 0.016 -10000 0 -0.35 1 1
ARF1/GTP 0.035 0.013 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0.021 -10000 0 -0.4 1 1
mol:Choline 0.011 0.016 -10000 0 -0.34 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.029 0.007 -10000 0 -10000 0 0
DDEF1 0.01 0.016 -10000 0 -0.35 1 1
ARF1/GDP 0.007 0.021 -10000 0 -0.39 1 1
AP2M1 0.029 0.006 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.017 0.007 -10000 0 -10000 0 0
Rac/GTP 0.021 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.042 0.022 -10000 0 -0.35 1 1
ARFIP2 0.027 0.008 -10000 0 -10000 0 0
COPA 0.029 0.007 -10000 0 -10000 0 0
RAC1 0.027 0.009 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.036 -10000 0 -0.29 4 4
ARF1/GTP/ARHGAP10 0.02 0.005 -10000 0 -10000 0 0
GGA3 0.029 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.028 0.029 -10000 0 -0.23 6 6
AP2A1 0.03 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.017 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.028 0.037 -10000 0 -0.3 6 6
Arfaptin 2/Rac/GDP 0.036 0.013 -10000 0 -10000 0 0
CYTH2 0.031 0.005 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.039 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.02 0.007 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.022 0.028 -10000 0 -10000 0 0
PLD2 0.011 0.016 -10000 0 -0.34 1 1
ARF-GAP1/v-SNARE 0.011 0.021 -10000 0 -0.47 1 1
PIP5K1A 0.011 0.016 -10000 0 -0.35 1 1
ARF1/GTP/Membrin/GBF1/p115 0.028 0.017 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.016 -10000 0 -0.34 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.011 0.021 -10000 0 -0.47 1 1
GOSR2 0.018 0.009 -10000 0 -10000 0 0
USO1 0.016 0.025 -10000 0 -0.3 3 3
GBF1 0.011 0.046 -10000 0 -0.3 11 11
ARF1/GTP/Arfaptin 2 0.041 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.049 0.058 -10000 0 -0.37 9 9
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.029 0.005 -10000 0 -10000 0 0
SMAD2 -0.027 0.066 0.23 1 -10000 0 1
SMAD3 0.027 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.034 0.091 -10000 0 -0.47 11 11
SMAD4/Ubc9/PIASy 0.056 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.022 0.082 -10000 0 -10000 0 0
PPM1A 0.028 0.008 -10000 0 -10000 0 0
CALM1 0.028 0.008 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.016 0.076 -10000 0 -0.3 6 6
MAP3K1 0.027 0.009 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.042 0.015 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 -10000 0 0
MAPK1 0.03 0.004 -10000 0 -10000 0 0
NUP214 0.029 0.005 -10000 0 -10000 0 0
CTDSP1 0.028 0.007 -10000 0 -10000 0 0
CTDSP2 0.029 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.014 -10000 0 -10000 0 0
KPNB1 0.029 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.028 0.016 -10000 0 -0.32 1 1
UBE2I 0.029 0.006 -10000 0 -10000 0 0
NUP153 0.029 0.006 -10000 0 -10000 0 0
KPNA2 0.029 0.005 -10000 0 -10000 0 0
PIAS4 0.03 0.003 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.015 0.1 -10000 0 -0.5 1 1
regulation of axonogenesis -0.011 0.052 -10000 0 -10000 0 0
myoblast fusion -0.018 0.061 0.35 3 -10000 0 3
mol:GTP 0.012 0.046 -10000 0 -0.39 1 1
regulation of calcium-dependent cell-cell adhesion -0.047 0.054 0.34 1 -10000 0 1
ARF1/GTP 0.025 0.047 -10000 0 -0.3 1 1
mol:GM1 0.002 0.039 -10000 0 -0.31 1 1
mol:Choline 0.014 0.032 -10000 0 -10000 0 0
lamellipodium assembly 0.007 0.077 -10000 0 -0.46 2 2
MAPK3 0.022 0.056 -10000 0 -0.48 1 1
ARF6/GTP/NME1/Tiam1 0.048 0.054 -10000 0 -0.34 1 1
ARF1 0.029 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.061 -10000 0 -0.35 3 3
ARF1/GDP 0.017 0.074 -10000 0 -0.36 2 2
ARF6 0.028 0.027 -10000 0 -10000 0 0
RAB11A 0.03 0.003 -10000 0 -10000 0 0
TIAM1 0.03 0.009 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.054 -10000 0 -0.3 1 1
actin filament bundle formation -0.01 0.073 0.36 2 -10000 0 2
KALRN 0.012 0.046 -10000 0 -0.35 1 1
RAB11FIP3/RAB11A 0.042 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.01 0.074 -10000 0 -0.36 2 2
NME1 0.029 0.028 -10000 0 -0.59 1 1
Rac1/GDP 0.023 0.069 -10000 0 -0.38 1 1
substrate adhesion-dependent cell spreading 0.012 0.046 -10000 0 -0.39 1 1
cortical actin cytoskeleton organization 0.006 0.077 -10000 0 -0.46 2 2
RAC1 0.027 0.009 -10000 0 -10000 0 0
liver development 0.012 0.046 -10000 0 -0.39 1 1
ARF6/GTP 0.012 0.046 -10000 0 -0.4 1 1
RhoA/GTP 0.017 0.044 -10000 0 -0.3 1 1
mol:GDP 0.003 0.069 -10000 0 -0.36 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.046 -10000 0 -10000 0 0
RHOA 0.021 0.014 -10000 0 -10000 0 0
PLD1 0.016 0.037 -10000 0 -10000 0 0
RAB11FIP3 0.029 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.077 -10000 0 -0.46 2 2
ruffle organization 0.011 0.052 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.012 0.046 -10000 0 -0.39 1 1
PLD2 0.015 0.042 -10000 0 -0.28 1 1
PIP5K1A 0.011 0.052 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.014 0.032 -10000 0 -10000 0 0
Rac1/GTP 0.006 0.077 -10000 0 -0.47 2 2
TRAIL signaling pathway

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
TNFSF10 0.027 0.03 -10000 0 -0.64 1 1
positive regulation of NF-kappaB transcription factor activity 0.037 0.027 -10000 0 -0.47 1 1
MAP2K4 0.037 0.031 -10000 0 -10000 0 0
IKBKB 0.028 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.028 -10000 0 -0.59 1 1
TNFRSF10A 0.026 0.018 -10000 0 -0.32 1 1
SMPD1 0.019 0.014 -10000 0 -0.23 1 1
IKBKG 0.03 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.029 -10000 0 -0.47 1 1
TRAIL/TRAILR3 0.038 0.027 -10000 0 -0.47 1 1
TRAIL/TRAILR1 0.038 0.027 -10000 0 -0.47 1 1
TRAIL/TRAILR4 0.038 0.027 -10000 0 -0.47 1 1
TRAIL/TRAILR1/DAP3/GTP 0.047 0.029 -10000 0 -0.37 1 1
IKK complex 0.039 0.028 -10000 0 -10000 0 0
RIPK1 0.029 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.021 0.005 -10000 0 -10000 0 0
MAPK3 0.021 0.022 -10000 0 -0.47 1 1
MAP3K1 0.038 0.031 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.027 0.009 -10000 0 -10000 0 0
TRADD 0.029 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.026 0.018 -10000 0 -0.32 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.037 0.023 -10000 0 -10000 0 0
CFLAR 0.029 0.006 -10000 0 -10000 0 0
MAPK1 0.021 0.022 -10000 0 -0.47 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.072 0.039 -10000 0 -10000 0 0
mol:ceramide 0.019 0.014 -10000 0 -0.23 1 1
FADD 0.03 0.003 -10000 0 -10000 0 0
MAPK8 0.037 0.04 0.29 1 -10000 0 1
TRAF2 0.029 0.005 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.027 0.009 -10000 0 -10000 0 0
CHUK 0.029 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.052 0.029 -10000 0 -0.4 1 1
DAP3 0.028 0.007 -10000 0 -10000 0 0
CASP10 0.017 0.02 -10000 0 -0.4 1 1
JNK cascade 0.037 0.027 -10000 0 -0.47 1 1
TRAIL (trimer) 0.027 0.03 -10000 0 -0.63 1 1
TNFRSF10C 0.027 0.009 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.058 0.032 -10000 0 -0.35 1 1
TRAIL/TRAILR2/FADD 0.051 0.031 -10000 0 -0.4 1 1
cell death 0.019 0.014 -10000 0 -0.23 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.037 0.023 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.026 0.028 -10000 0 -0.59 1 1
CASP8 0.005 0.079 -10000 0 -0.58 9 9
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.072 0.04 -10000 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 0.029 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.001 -10000 0 -9999 0 0
MDM2/SUMO1 0.05 0.028 -10000 0 -9999 0 0
HDAC4 0.028 0.007 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.001 -10000 0 -9999 0 0
SUMO1 0.029 0.007 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.016 0.023 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0.022 0.007 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0.029 0.006 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0.029 0.005 -10000 0 -9999 0 0
SUMO1/HDAC4 0.051 0.027 -10000 0 -9999 0 0
SUMO1/HDAC1 0.051 0.027 -10000 0 -9999 0 0
RANGAP1 0.03 0.004 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.07 0.023 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.022 0.008 -10000 0 -9999 0 0
Ran/GTP 0.037 0.028 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0.029 0.005 -10000 0 -9999 0 0
UBE2I 0.029 0.006 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0.039 0.027 0.25 1 -9999 0 1
NPC 0.017 0.003 -10000 0 -9999 0 0
PIAS2 0.029 0.005 -10000 0 -9999 0 0
PIAS1 0.03 0.003 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.047 0.017 -9999 0 -10000 0 0
MAPK9 0.008 0.005 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.039 -9999 0 -0.44 4 4
GNB1/GNG2 0.036 0.012 -9999 0 -10000 0 0
GNB1 0.029 0.006 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.01 0.002 -9999 0 -10000 0 0
Gs family/GTP 0.019 0.003 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.029 0.005 -9999 0 -10000 0 0
GNG2 0.028 0.008 -9999 0 -10000 0 0
CRH 0.015 0.053 -9999 0 -0.59 4 4
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.009 0.024 -9999 0 -0.38 2 2
MAPK11 0.01 0.016 -9999 0 -0.26 2 2
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.039 0.042 -9999 0 -0.43 4 4
FBXW11 0.023 0.013 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.013 -9999 0 -10000 0 0
CHUK 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.062 0.048 -9999 0 -10000 0 0
NFKB1 0.028 0.029 -9999 0 -0.64 1 1
MAP3K14 0.025 0.054 -9999 0 -0.59 4 4
NF kappa B1 p50/RelB 0.042 0.024 -9999 0 -0.47 1 1
RELB 0.03 0.003 -9999 0 -10000 0 0
NFKB2 0.029 0.006 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.039 0.009 -9999 0 -10000 0 0
regulation of B cell activation 0.038 0.009 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 525 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.T7.A92I TCGA.MW.A4EC TCGA.MM.A84U TCGA.MM.A564
109_MAP3K5 0.054 0.1 -0.064 0.054
47_PPARGC1A 0.03 0.03 0.03 0.03
105_BMP4 0.03 0.03 0.03 0.03
105_BMP6 0.03 0.03 0.03 0.03
105_BMP7 0.03 0.018 -0.64 -0.64
105_BMP2 0.03 0.03 0.03 0.03
131_RELN/VLDLR -0.35 -0.37 0.077 -0.37
30_TGFB1/TGF beta receptor Type II 0.03 0.029 0.029 0.034
84_STAT5B -0.022 -0.052 -0.14 -0.14
84_STAT5A -0.022 -0.052 -0.14 -0.14
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/KIRC-TP/22312814/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/KIRC-TP/22506705/GDAC_Gistic2Report_22529582/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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