PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C12F7KXZ
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C12F7KXZ
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 50 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 249
Signaling events mediated by Stem cell factor receptor (c-Kit) 164
Signaling events regulated by Ret tyrosine kinase 149
TCGA08_retinoblastoma 142
Reelin signaling pathway 125
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 115
IL4-mediated signaling events 111
Wnt signaling 105
PDGFR-alpha signaling pathway 98
Noncanonical Wnt signaling pathway 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 488 . 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 ( 488 ).

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
Ephrin A reverse signaling 0.5102 249 1749 7 -0.52 0 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3361 164 12800 78 -0.8 0.24 1000 -1000 -0.067 -1000
Signaling events regulated by Ret tyrosine kinase 0.3053 149 12241 82 -0.46 0.013 1000 -1000 -0.081 -1000
TCGA08_retinoblastoma 0.2910 142 1141 8 -0.13 0.073 1000 -1000 -0.016 -1000
Reelin signaling pathway 0.2561 125 7027 56 -0.6 0.033 1000 -1000 -0.083 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2357 115 7820 68 -0.89 0.37 1000 -1000 -0.12 -1000
IL4-mediated signaling events 0.2275 111 10139 91 -1.3 0.66 1000 -1000 -0.12 -1000
Wnt signaling 0.2152 105 740 7 -0.41 0.013 1000 -1000 -0.02 -1000
PDGFR-alpha signaling pathway 0.2008 98 4336 44 -0.5 0.033 1000 -1000 -0.052 -1000
Noncanonical Wnt signaling pathway 0.1906 93 2427 26 -0.41 0.013 1000 -1000 -0.082 -1000
FOXA2 and FOXA3 transcription factor networks 0.1783 87 4030 46 -0.92 0.021 1000 -1000 -0.057 -1000
Nongenotropic Androgen signaling 0.1762 86 4512 52 -0.34 0.16 1000 -1000 -0.058 -1000
Signaling events mediated by the Hedgehog family 0.1619 79 4115 52 -0.38 0.2 1000 -1000 -0.083 -1000
Calcium signaling in the CD4+ TCR pathway 0.1516 74 2309 31 -0.52 0.013 1000 -1000 -0.089 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1496 73 2497 34 -0.17 0.013 1000 -1000 -0.054 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1475 72 3902 54 -0.6 0.028 1000 -1000 -0.1 -1000
Glypican 1 network 0.1311 64 3095 48 -0.38 0.028 1000 -1000 -0.044 -1000
Ephrin B reverse signaling 0.1291 63 3042 48 -0.31 0.19 1000 -1000 -0.072 -1000
Endothelins 0.1250 61 5928 96 -0.39 0.013 1000 -1000 -0.077 -1000
HIF-1-alpha transcription factor network 0.1209 59 4502 76 -0.56 0.042 1000 -1000 -0.091 -1000
IGF1 pathway 0.1189 58 3332 57 -0.2 0.06 1000 -1000 -0.094 -1000
Glucocorticoid receptor regulatory network 0.1107 54 6217 114 -0.56 0.37 1000 -1000 -0.07 -1000
IL23-mediated signaling events 0.1107 54 3264 60 -0.33 0.019 1000 -1000 -0.14 -1000
TCR signaling in naïve CD8+ T cells 0.1086 53 5020 93 -0.19 0.087 1000 -1000 -0.073 -1000
Glypican 2 network 0.1086 53 213 4 -0.088 -0.01 1000 -1000 -0.038 -1000
Arf6 signaling events 0.1025 50 3148 62 -0.32 0.021 1000 -1000 -0.067 -1000
BMP receptor signaling 0.1025 50 4102 81 -0.57 0.026 1000 -1000 -0.09 -1000
EPHB forward signaling 0.1025 50 4306 85 -0.31 0.15 1000 -1000 -0.086 -1000
Coregulation of Androgen receptor activity 0.0984 48 3692 76 -0.77 0.061 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 0.0943 46 1578 34 -0.2 0.013 1000 -1000 -0.059 -1000
IL6-mediated signaling events 0.0820 40 3051 75 -0.2 0.059 1000 -1000 -0.074 -1000
IL12-mediated signaling events 0.0779 38 3311 87 -0.4 0.022 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 0.0779 38 2496 65 -0.66 0.061 1000 -1000 -0.066 -1000
Signaling mediated by p38-alpha and p38-beta 0.0779 38 1673 44 -0.23 0.013 1000 -1000 -0.046 -1000
Syndecan-4-mediated signaling events 0.0779 38 2611 67 -0.24 0.015 1000 -1000 -0.091 -1000
amb2 Integrin signaling 0.0738 36 2993 82 -0.24 0.013 1000 -1000 -0.073 -1000
Ras signaling in the CD4+ TCR pathway 0.0717 35 599 17 -0.093 0.013 1000 -1000 -0.032 -1000
Thromboxane A2 receptor signaling 0.0676 33 3498 105 -0.22 0.032 1000 -1000 -0.07 -1000
EGFR-dependent Endothelin signaling events 0.0676 33 697 21 -0.11 0.013 1000 -1000 -0.062 -1000
TCGA08_p53 0.0615 30 210 7 -0.085 0.054 1000 -1000 -0.015 -1000
Osteopontin-mediated events 0.0594 29 1124 38 -0.26 0.013 1000 -1000 -0.11 -1000
FAS signaling pathway (CD95) 0.0594 29 1385 47 -0.26 0.03 1000 -1000 -0.047 -1000
Regulation of Androgen receptor activity 0.0553 27 1947 70 -0.48 0.034 1000 -1000 -0.062 -1000
Syndecan-2-mediated signaling events 0.0533 26 1843 69 -0.22 0.038 1000 -1000 -0.051 -1000
Regulation of p38-alpha and p38-beta 0.0533 26 1442 54 -0.47 0.013 1000 -1000 -0.055 -1000
Plasma membrane estrogen receptor signaling 0.0533 26 2277 86 -0.18 0.02 1000 -1000 -0.08 -1000
Visual signal transduction: Rods 0.0533 26 1364 52 -0.2 0.016 1000 -1000 -0.077 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0512 25 2197 85 -0.28 0.013 1000 -1000 -0.071 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0512 25 1321 52 -0.28 0.054 1000 -1000 -0.069 -1000
IL27-mediated signaling events 0.0512 25 1277 51 -0.17 0.066 1000 -1000 -0.063 -1000
ErbB2/ErbB3 signaling events 0.0492 24 1609 65 -0.13 0.027 1000 -1000 -0.066 -1000
JNK signaling in the CD4+ TCR pathway 0.0492 24 411 17 -0.1 0.02 1000 -1000 -0.052 -1000
LPA receptor mediated events 0.0492 24 2502 102 -0.25 0.031 1000 -1000 -0.08 -1000
BCR signaling pathway 0.0492 24 2473 99 -0.19 0.023 1000 -1000 -0.083 -1000
Integrins in angiogenesis 0.0471 23 1993 84 -0.24 0.034 1000 -1000 -0.091 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0471 23 2107 88 -0.32 0.028 1000 -1000 -0.11 -1000
Signaling events mediated by PTP1B 0.0430 21 1660 76 -0.24 0.021 1000 -1000 -0.073 -1000
Fc-epsilon receptor I signaling in mast cells 0.0430 21 2054 97 -0.2 0.03 1000 -1000 -0.076 -1000
VEGFR1 specific signals 0.0430 21 1205 56 -0.069 0.041 1000 -1000 -0.068 -1000
Aurora C signaling 0.0410 20 140 7 -0.06 0 1000 -1000 -0.041 -1000
Regulation of nuclear SMAD2/3 signaling 0.0389 19 2689 136 -0.34 0.066 1000 -1000 -0.07 -1000
Nectin adhesion pathway 0.0389 19 1230 63 -0.26 0.032 1000 -1000 -0.078 -1000
Visual signal transduction: Cones 0.0369 18 704 38 -0.089 0.013 1000 -1000 -0.064 -1000
p75(NTR)-mediated signaling 0.0369 18 2273 125 -0.35 0.066 1000 -1000 -0.099 -1000
IL1-mediated signaling events 0.0369 18 1166 62 -0.12 0.066 1000 -1000 -0.092 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0369 18 2185 120 -0.31 0.042 1000 -1000 -0.083 -1000
FOXM1 transcription factor network 0.0369 18 939 51 -0.18 0.049 1000 -1000 -0.16 -1000
ErbB4 signaling events 0.0348 17 1179 69 -0.14 0.056 1000 -1000 -0.092 -1000
Syndecan-3-mediated signaling events 0.0348 17 629 35 -0.16 0.013 1000 -1000 -0.068 -1000
TCGA08_rtk_signaling 0.0348 17 452 26 -0.24 0.025 1000 -1000 -0.018 -1000
Rapid glucocorticoid signaling 0.0328 16 326 20 -0.09 0.014 1000 -1000 -0.04 -1000
Aurora B signaling 0.0328 16 1098 67 -0.38 0.014 1000 -1000 -0.073 -1000
LPA4-mediated signaling events 0.0307 15 189 12 -0.12 0.015 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 0.0307 15 934 61 -0.2 0.042 1000 -1000 -0.068 -1000
Effects of Botulinum toxin 0.0307 15 399 26 -0.16 0.019 1000 -1000 -0.059 -1000
IL2 signaling events mediated by STAT5 0.0307 15 332 22 -0.069 0.039 1000 -1000 -0.049 -1000
Insulin Pathway 0.0307 15 1127 74 -0.087 0.038 1000 -1000 -0.08 -1000
Insulin-mediated glucose transport 0.0287 14 478 32 -0.21 0.042 1000 -1000 -0.064 -1000
IFN-gamma pathway 0.0287 14 965 68 -0.1 0.042 1000 -1000 -0.084 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0287 14 467 33 -0.16 0.035 1000 -1000 -0.056 -1000
Signaling events mediated by PRL 0.0287 14 485 34 -0.11 0.013 1000 -1000 -0.038 -1000
Class IB PI3K non-lipid kinase events 0.0287 14 42 3 -0.003 -1000 1000 -1000 -0.013 -1000
Ceramide signaling pathway 0.0266 13 1006 76 -0.18 0.024 1000 -1000 -0.061 -1000
Signaling events mediated by HDAC Class III 0.0266 13 548 40 -0.35 0.024 1000 -1000 -0.046 -1000
IL2 signaling events mediated by PI3K 0.0266 13 783 58 -0.067 0.031 1000 -1000 -0.084 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0246 12 349 28 -0.18 0.031 1000 -1000 -0.061 -1000
a4b1 and a4b7 Integrin signaling 0.0246 12 62 5 -0.031 0.002 1000 -1000 -0.039 -1000
mTOR signaling pathway 0.0246 12 640 53 -0.047 0.02 1000 -1000 -0.056 -1000
BARD1 signaling events 0.0225 11 637 57 -0.035 0.052 1000 -1000 -0.068 -1000
Cellular roles of Anthrax toxin 0.0225 11 437 39 -0.09 0.019 1000 -1000 -0.033 -1000
Class I PI3K signaling events 0.0225 11 813 73 -0.24 0.023 1000 -1000 -0.054 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0205 10 870 83 -0.21 0.052 1000 -1000 -0.076 -1000
Retinoic acid receptors-mediated signaling 0.0205 10 584 58 -0.12 0.032 1000 -1000 -0.07 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0205 10 451 45 -0.09 0.039 1000 -1000 -0.085 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0205 10 806 74 -0.18 0.085 1000 -1000 -0.091 -1000
Caspase cascade in apoptosis 0.0184 9 703 74 -0.09 0.029 1000 -1000 -0.053 -1000
Regulation of Telomerase 0.0184 9 964 102 -0.28 0.053 1000 -1000 -0.099 -1000
Class I PI3K signaling events mediated by Akt 0.0164 8 566 68 -0.21 0.052 1000 -1000 -0.064 -1000
ceramide signaling pathway 0.0164 8 421 49 -0.09 0.031 1000 -1000 -0.043 -1000
S1P3 pathway 0.0164 8 367 42 -0.18 0.048 1000 -1000 -0.062 -1000
TRAIL signaling pathway 0.0143 7 371 48 -0.077 0.047 1000 -1000 -0.068 -1000
S1P1 pathway 0.0143 7 257 36 -0.037 0.031 1000 -1000 -0.062 -1000
Signaling events mediated by HDAC Class I 0.0143 7 734 104 -0.09 0.059 1000 -1000 -0.062 -1000
Canonical Wnt signaling pathway 0.0143 7 370 51 -0.049 0.067 1000 -1000 -0.068 -1000
Canonical NF-kappaB pathway 0.0123 6 248 39 -0.09 0.071 1000 -1000 -0.076 -1000
Circadian rhythm pathway 0.0123 6 149 22 -0.057 0.013 1000 -1000 -0.055 -1000
Arf6 downstream pathway 0.0123 6 285 43 -0.18 0.094 1000 -1000 -0.041 -1000
FoxO family signaling 0.0123 6 419 64 -0.21 0.16 1000 -1000 -0.057 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0102 5 216 37 -0.032 0.039 1000 -1000 -0.062 -1000
Atypical NF-kappaB pathway 0.0102 5 159 31 -0.043 0.047 1000 -1000 -0.05 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0102 5 668 125 -0.035 0.085 1000 -1000 -0.082 -1000
E-cadherin signaling in the nascent adherens junction 0.0102 5 382 76 -0.17 0.074 1000 -1000 -0.084 -1000
EPO signaling pathway 0.0082 4 242 55 -0.037 0.061 1000 -1000 -0.089 -1000
PLK1 signaling events 0.0061 3 285 85 -0.04 0.033 1000 -1000 -0.044 -1000
S1P5 pathway 0.0061 3 62 17 -0.017 0.022 1000 -1000 -0.059 -1000
HIF-2-alpha transcription factor network 0.0061 3 142 43 -0.2 0.2 1000 -1000 -0.065 -1000
Signaling mediated by p38-gamma and p38-delta 0.0061 3 52 15 0 0.031 1000 -1000 -0.029 -1000
Paxillin-dependent events mediated by a4b1 0.0061 3 140 36 -0.031 0.024 1000 -1000 -0.078 -1000
PDGFR-beta signaling pathway 0.0061 3 368 97 -0.18 0.064 1000 -1000 -0.078 -1000
p38 MAPK signaling pathway 0.0061 3 150 44 -0.04 0.026 1000 -1000 -0.062 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0041 2 65 23 -0.04 0.049 1000 -1000 -0.065 -1000
Signaling events mediated by HDAC Class II 0.0041 2 178 75 -0.047 0.036 1000 -1000 -0.057 -1000
PLK2 and PLK4 events 0.0041 2 6 3 0.009 0.022 1000 -1000 -0.011 -1000
Aurora A signaling 0.0041 2 165 60 -0.048 0.038 1000 -1000 -0.062 -1000
E-cadherin signaling in keratinocytes 0.0041 2 127 43 -0.004 0.053 1000 -1000 -0.066 -1000
S1P4 pathway 0.0041 2 67 25 -0.017 0.032 1000 -1000 -0.058 -1000
Arf6 trafficking events 0.0020 1 80 71 -0.023 0.046 1000 -1000 -0.078 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.056 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0.013 1000 -1000 -0.044 -1000
Arf1 pathway 0.0000 0 36 54 -0.005 0.035 1000 -1000 -0.053 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 -0.001 0.013 1000 -1000 -0.063 -1000
Total NA 4089 224414 7203 -30 -990 131000 -131000 -8.7 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.42 0.31 -9999 0 -0.61 341 341
EFNA5 -0.11 0.3 -9999 0 -0.81 75 75
FYN -0.38 0.3 -9999 0 -0.56 341 341
neuron projection morphogenesis -0.42 0.31 -9999 0 -0.61 341 341
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.43 0.31 -9999 0 -0.61 341 341
EPHA5 -0.52 0.4 -9999 0 -0.82 310 310
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.22 0.22 -10000 0 -0.4 285 285
CRKL -0.22 0.24 -10000 0 -0.42 278 278
HRAS -0.19 0.21 -10000 0 -0.5 46 46
mol:PIP3 -0.22 0.22 -10000 0 -0.41 278 278
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.012 0.038 -10000 0 -0.82 1 1
GAB1 -0.24 0.25 -10000 0 -0.45 278 278
FOXO3 -0.19 0.22 -10000 0 -0.38 278 278
AKT1 -0.22 0.23 -10000 0 -0.42 278 278
BAD -0.19 0.22 -10000 0 -0.38 278 278
megakaryocyte differentiation -0.25 0.25 -10000 0 -0.45 286 286
GSK3B -0.19 0.22 -10000 0 -0.38 278 278
RAF1 -0.15 0.18 -10000 0 -0.4 40 40
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.24 0.25 -10000 0 -0.45 278 278
STAT1 -0.6 0.59 -10000 0 -1.1 280 280
HRAS/SPRED1 -0.18 0.14 -10000 0 -0.39 45 45
cell proliferation -0.24 0.26 -10000 0 -0.45 281 281
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 -10000 0 -0.45 278 278
HRAS/SPRED2 -0.18 0.14 -10000 0 -0.4 46 46
LYN/TEC/p62DOK -0.24 0.21 -10000 0 -0.41 278 278
MAPK3 -0.095 0.13 -10000 0 -0.31 24 24
STAP1 -0.26 0.25 -10000 0 -0.47 278 278
GRAP2 -0.041 0.2 -10000 0 -0.77 34 34
JAK2 -0.52 0.45 -10000 0 -0.9 280 280
STAT1 (dimer) -0.58 0.57 -10000 0 -1.1 280 280
mol:Gleevec 0.008 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.25 0.21 -10000 0 -0.42 281 281
actin filament polymerization -0.23 0.24 -10000 0 -0.44 278 278
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.35 0.34 -10000 0 -0.64 278 278
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.19 -10000 0 -0.37 278 278
PI3K -0.22 0.24 -10000 0 -0.42 279 279
PTEN 0.012 0.038 -10000 0 -0.82 1 1
SCF/KIT/EPO/EPOR -0.74 0.72 -10000 0 -1.4 278 278
MAPK8 -0.25 0.26 -10000 0 -0.46 281 281
STAT3 (dimer) -0.23 0.24 -10000 0 -0.44 278 278
positive regulation of transcription -0.076 0.11 -10000 0 -0.25 22 22
mol:GDP -0.23 0.19 -10000 0 -0.48 72 72
PIK3C2B -0.24 0.25 -10000 0 -0.45 278 278
CBL/CRKL -0.2 0.22 -10000 0 -0.39 278 278
FER -0.24 0.25 -10000 0 -0.45 279 279
SH2B3 -0.24 0.25 -10000 0 -0.45 278 278
PDPK1 -0.2 0.21 -10000 0 -0.37 279 279
SNAI2 -0.24 0.26 -10000 0 -0.46 280 280
positive regulation of cell proliferation -0.42 0.42 -10000 0 -0.77 280 280
KITLG -0.006 0.11 -10000 0 -0.85 8 8
cell motility -0.42 0.42 -10000 0 -0.77 280 280
PTPN6 0.021 0.018 -10000 0 -10000 0 0
EPOR -0.14 0.18 -10000 0 -0.56 8 8
STAT5A (dimer) -0.34 0.35 -10000 0 -0.63 280 280
SOCS1 0.009 0.048 -10000 0 -0.82 1 1
cell migration 0.24 0.25 0.45 281 -10000 0 281
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.005 0.041 -10000 0 -0.33 7 7
VAV1 -0.013 0.1 -10000 0 -0.36 35 35
GRB10 -0.24 0.25 -10000 0 -0.45 278 278
PTPN11 0.02 0.038 -10000 0 -0.8 1 1
SCF/KIT -0.26 0.26 -10000 0 -0.48 278 278
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.11 0.14 -10000 0 -0.35 24 24
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.8 0.75 -10000 0 -1.4 278 278
MAP2K2 -0.11 0.14 -10000 0 -0.35 24 24
SHC/Grb2/SOS1 -0.24 0.21 -10000 0 -0.41 278 278
STAT5A -0.35 0.36 -10000 0 -0.65 280 280
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.24 0.25 -10000 0 -0.45 280 280
SHC/GRAP2 -0.041 0.15 -10000 0 -0.63 31 31
PTPRO -0.26 0.25 -10000 0 -0.46 286 286
SH2B2 -0.24 0.25 -10000 0 -0.45 278 278
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.25 0.25 -10000 0 -0.46 281 281
CREBBP 0.017 0.02 -10000 0 -10000 0 0
BCL2 -0.22 0.42 -10000 0 -1.6 36 36
Signaling events regulated by Ret tyrosine kinase

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.088 0.068 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -9999 0 -0.51 119 119
JUN -0.32 0.31 -9999 0 -0.68 171 171
HRAS 0.012 0.021 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.38 0.32 -9999 0 -0.6 302 302
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.38 0.32 -9999 0 -0.6 302 302
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.29 0.25 -9999 0 -0.51 278 278
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.34 0.29 -9999 0 -0.54 302 302
GRB7 -0.042 0.12 -9999 0 -0.31 82 82
RET51/GFRalpha1/GDNF -0.38 0.32 -9999 0 -0.6 302 302
MAPKKK cascade -0.3 0.26 -9999 0 -0.48 302 302
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.35 0.31 -9999 0 -0.58 291 291
lamellipodium assembly -0.24 0.18 -9999 0 -0.38 279 279
RET51/GFRalpha1/GDNF/SHC -0.38 0.32 -9999 0 -0.6 302 302
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
RET9/GFRalpha1/GDNF/SHC -0.29 0.25 -9999 0 -0.51 278 278
RET9/GFRalpha1/GDNF/Shank3 -0.29 0.25 -9999 0 -0.51 278 278
MAPK3 -0.31 0.29 -9999 0 -0.51 302 302
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.3 -9999 0 -0.82 77 77
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.3 0.29 -9999 0 -0.67 128 128
DOK5 -0.1 0.29 -9999 0 -0.82 67 67
GFRA1 -0.46 0.41 -9999 0 -0.81 279 279
MAPK8 -0.24 0.24 -9999 0 -0.59 91 91
HRAS/GTP -0.35 0.3 -9999 0 -0.56 302 302
tube development -0.27 0.23 -9999 0 -0.47 278 278
MAPK1 -0.31 0.29 -9999 0 -0.51 302 302
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.18 0.18 -9999 0 -0.34 278 278
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
PDLIM7 0.011 0.029 -9999 0 -0.31 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.43 0.38 -9999 0 -0.66 313 313
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.38 0.32 -9999 0 -0.6 302 302
RET51/GFRalpha1/GDNF/Dok5 -0.45 0.38 -9999 0 -0.68 314 314
PRKCA -0.026 0.18 -9999 0 -0.82 23 23
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
CREB1 -0.24 0.24 -9999 0 -0.43 278 278
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.18 -9999 0 -0.34 278 278
RET51/GFRalpha1/GDNF/Grb7 -0.41 0.33 -9999 0 -0.63 302 302
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.16 0.32 -9999 0 -0.64 133 133
DOK4 0.013 0.015 -9999 0 -0.31 1 1
JNK cascade -0.31 0.3 -9999 0 -0.66 171 171
RET9/GFRalpha1/GDNF/FRS2 -0.29 0.25 -9999 0 -0.51 278 278
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.18 -9999 0 -0.34 278 278
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.25 0.24 -9999 0 -0.41 302 302
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.25 0.23 -9999 0 -0.41 302 302
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.28 0.31 -9999 0 -0.47 302 302
PI3K -0.37 0.34 -9999 0 -0.62 280 280
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.27 0.23 -9999 0 -0.47 278 278
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.22 0.21 -9999 0 -0.38 278 278
RET51/GFRalpha1/GDNF/FRS2 -0.38 0.32 -9999 0 -0.6 302 302
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.087 0.27 -9999 0 -0.82 59 59
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.28 0.31 -9999 0 -0.47 302 302
RET51/GFRalpha1/GDNF/PKC alpha -0.41 0.35 -9999 0 -0.64 304 304
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.002 0.043 -9999 0 -0.31 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.44 0.37 -9999 0 -0.67 314 314
Rac1/GTP -0.29 0.23 -9999 0 -0.46 279 279
RET9/GFRalpha1/GDNF -0.32 0.27 -9999 0 -0.56 278 278
GFRalpha1/GDNF -0.36 0.31 -9999 0 -0.63 278 278
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.12 0.16 -10000 0 -0.31 203 203
CDKN2C 0.027 0.036 -10000 0 -0.31 3 3
CDKN2A -0.13 0.16 -10000 0 -0.32 210 210
CCND2 0.07 0.073 0.17 144 -10000 0 144
RB1 -0.069 0.072 -10000 0 -0.17 144 144
CDK4 0.07 0.072 0.17 146 -10000 0 146
CDK6 0.073 0.078 0.18 144 -0.18 2 146
G1/S progression 0.061 0.08 0.17 145 -10000 0 145
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.001 0.013 -9999 0 -10000 0 0
VLDLR -0.022 0.17 -9999 0 -0.82 21 21
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.01 0.033 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.42 0.26 -9999 0 -0.56 363 363
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.01 0.068 -9999 0 -0.46 11 11
AKT1 -0.24 0.17 -9999 0 -0.33 364 364
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
RELN/LRP8/DAB1 -0.39 0.24 -9999 0 -0.52 361 361
LRPAP1/LRP8 -0.026 0.12 -9999 0 -0.63 20 20
RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 361 361
DAB1/alpha3/beta1 Integrin -0.34 0.23 -9999 0 -0.86 32 32
long-term memory -0.36 0.24 -9999 0 -0.48 363 363
DAB1/LIS1 -0.35 0.23 -9999 0 -0.47 367 367
DAB1/CRLK/C3G -0.34 0.23 -9999 0 -0.49 198 198
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
DAB1/NCK2 -0.36 0.24 -9999 0 -0.48 367 367
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.022 0.16 -9999 0 -0.63 27 27
CDK5R1 0.012 0.021 -9999 0 -0.31 2 2
RELN -0.6 0.37 -9999 0 -0.82 357 357
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.42 0.26 -9999 0 -0.56 361 361
GRIN2A/RELN/LRP8/DAB1/Fyn -0.38 0.25 -9999 0 -0.5 363 363
MAPK8 -0.005 0.12 -9999 0 -0.82 11 11
RELN/VLDLR/DAB1 -0.39 0.24 -9999 0 -0.52 363 363
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.36 0.26 -9999 0 -0.5 367 367
RELN/LRP8 -0.42 0.26 -9999 0 -0.56 361 361
GRIN2B/RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 361 361
PI3K -0.004 0.049 -9999 0 -0.63 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.02 -9999 0 -10000 0 0
RAP1A -0.3 0.23 -9999 0 -0.82 28 28
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.015 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.14 -9999 0 -0.53 22 22
neuron adhesion -0.28 0.22 -9999 0 -0.73 32 32
LRP8 -0.021 0.16 -9999 0 -0.82 20 20
GSK3B -0.22 0.16 -9999 0 -0.61 17 17
RELN/VLDLR/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 363 363
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.36 364 364
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.033 0.088 -9999 0 -0.33 20 20
neuron migration -0.3 0.22 -9999 0 -0.42 358 358
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.14 -9999 0 -0.54 22 22
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 367 367
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.042 0.16 -10000 0 -0.57 30 30
NFATC2 -0.24 0.38 -10000 0 -0.81 125 125
NFATC3 -0.084 0.13 -10000 0 -10000 0 0
CD40LG -0.73 0.57 -10000 0 -1.2 262 262
ITCH 0.051 0.015 -10000 0 -10000 0 0
CBLB 0.051 0.015 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.53 0.52 -10000 0 -1.2 152 152
JUNB 0.003 0.091 -10000 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.015 -10000 0 -0.34 1 1
T cell anergy 0.025 0.065 -10000 0 -0.49 1 1
TLE4 -0.24 0.44 -10000 0 -0.86 137 137
Jun/NFAT1-c-4/p21SNFT -0.66 0.61 -10000 0 -1.2 241 241
AP-1/NFAT1-c-4 -0.89 0.78 -10000 0 -1.5 266 266
IKZF1 -0.18 0.34 -10000 0 -0.74 97 97
T-helper 2 cell differentiation -0.32 0.35 -10000 0 -0.81 129 129
AP-1/NFAT1 -0.42 0.48 -10000 0 -0.9 213 213
CALM1 0.029 0.009 -10000 0 -10000 0 0
EGR2 -0.8 0.85 -10000 0 -1.6 231 231
EGR3 -0.58 0.75 -10000 0 -1.5 151 151
NFAT1/FOXP3 -0.22 0.33 -10000 0 -0.69 128 128
EGR1 -0.16 0.34 -10000 0 -0.82 104 104
JUN -0.18 0.34 -10000 0 -0.82 110 110
EGR4 -0.034 0.18 -10000 0 -0.72 29 29
mol:Ca2+ 0.016 0.01 -10000 0 -10000 0 0
GBP3 -0.16 0.32 -10000 0 -0.74 85 85
FOSL1 -0.03 0.12 -10000 0 -0.33 62 62
NFAT1-c-4/MAF/IRF4 -0.56 0.56 -10000 0 -1.1 242 242
DGKA -0.16 0.29 -10000 0 -0.66 98 98
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.56 0.56 -10000 0 -1.1 243 243
CTLA4 -0.23 0.37 -10000 0 -0.8 113 113
NFAT1-c-4 (dimer)/EGR1 -0.64 0.67 -10000 0 -1.2 243 243
NFAT1-c-4 (dimer)/EGR4 -0.58 0.56 -10000 0 -1.1 246 246
FOS -0.22 0.36 -10000 0 -0.82 128 128
IFNG -0.43 0.54 -10000 0 -1.1 146 146
T cell activation -0.44 0.42 -10000 0 -1 146 146
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.37 0.42 0.76 229 -10000 0 229
TNF -0.6 0.58 -10000 0 -1.1 252 252
FASLG -0.74 0.78 -10000 0 -1.5 243 243
TBX21 -0.036 0.18 -10000 0 -0.71 29 29
BATF3 -0.006 0.082 -10000 0 -0.33 27 27
PRKCQ 0.005 0.084 -10000 0 -0.82 5 5
PTPN1 -0.16 0.29 -10000 0 -0.67 95 95
NFAT1-c-4/ICER1 -0.55 0.56 -10000 0 -1 242 242
GATA3 -0.03 0.18 -10000 0 -0.78 27 27
T-helper 1 cell differentiation -0.41 0.51 -10000 0 -1.1 147 147
IL2RA -0.48 0.46 -10000 0 -1 160 160
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.29 -10000 0 -0.73 72 72
E2F1 -0.078 0.15 -10000 0 -10000 0 0
PPARG -0.002 0.1 -10000 0 -0.82 7 7
SLC3A2 -0.16 0.29 -10000 0 -0.73 72 72
IRF4 -0.1 0.23 -10000 0 -0.45 119 119
PTGS2 -0.71 0.57 -10000 0 -1.2 253 253
CSF2 -0.77 0.53 -10000 0 -1.2 266 266
JunB/Fra1/NFAT1-c-4 -0.54 0.54 -10000 0 -1 237 237
IL4 -0.33 0.37 -10000 0 -0.87 125 125
IL5 -0.69 0.54 -10000 0 -1.1 260 260
IL2 -0.45 0.44 -10000 0 -1 143 143
IL3 -0.097 0.062 -10000 0 -10000 0 0
RNF128 0.049 0.042 -10000 0 -0.87 1 1
NFATC1 -0.37 0.43 -10000 0 -0.76 229 229
CDK4 0.22 0.25 0.6 63 -10000 0 63
PTPRK -0.16 0.29 -10000 0 -0.66 97 97
IL8 -0.72 0.54 -10000 0 -1.2 254 254
POU2F1 0.013 0.015 -10000 0 -0.31 1 1
IL4-mediated signaling events

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
BCL2L1 -0.59 0.44 -10000 0 -1 187 187
STAT6 (cleaved dimer) -0.64 0.44 -10000 0 -0.96 278 278
IGHG1 -0.2 0.14 -10000 0 -0.34 107 107
IGHG3 -0.58 0.42 -10000 0 -0.92 245 245
AKT1 -0.32 0.26 -10000 0 -0.63 120 120
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.25 0.25 -10000 0 -0.66 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.35 0.28 -10000 0 -0.66 149 149
THY1 -0.59 0.44 -10000 0 -1.1 176 176
MYB -0.008 0.12 -10000 0 -0.63 16 16
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.41 0.31 -10000 0 -0.67 223 223
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.63 115 115
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.003 0.072 -10000 0 -0.31 25 25
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.62 0.44 -10000 0 -0.97 255 255
SOCS1 -0.4 0.28 -10000 0 -0.72 137 137
SOCS3 -0.38 0.35 -10000 0 -0.96 81 81
FCER2 -0.58 0.42 -10000 0 -0.9 260 260
PARP14 0.013 0.004 -10000 0 -10000 0 0
CCL17 -0.66 0.47 -10000 0 -1.1 223 223
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.21 -10000 0 -0.61 64 64
T cell proliferation -0.6 0.46 -10000 0 -1 219 219
IL4R/JAK1 -0.59 0.44 -10000 0 -1 199 199
EGR2 -0.93 0.72 -10000 0 -1.6 257 257
JAK2 -0.019 0.058 -10000 0 -0.85 2 2
JAK3 -0.068 0.14 -10000 0 -0.31 124 124
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.008 -10000 0 -10000 0 0
COL1A2 -0.19 0.15 -10000 0 -0.57 3 3
CCL26 -0.61 0.45 -10000 0 -1.1 196 196
IL4R -0.63 0.46 -10000 0 -1.1 214 214
PTPN6 0.028 0.009 -10000 0 -10000 0 0
IL13RA2 -0.69 0.56 -10000 0 -1.3 192 192
IL13RA1 -0.016 0.024 -10000 0 -10000 0 0
IRF4 -0.33 0.47 -10000 0 -1.2 90 90
ARG1 -0.14 0.11 -10000 0 -10000 0 0
CBL -0.38 0.29 -10000 0 -0.65 198 198
GTF3A 0.017 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
IL13RA1/JAK2 -0.025 0.052 -10000 0 -0.66 2 2
IRF4/BCL6 -0.3 0.43 -10000 0 -1.1 85 85
CD40LG -0.11 0.3 -10000 0 -0.79 76 76
MAPK14 -0.39 0.31 -10000 0 -0.71 168 168
mitosis -0.3 0.24 -10000 0 -0.6 120 120
STAT6 -0.67 0.51 -10000 0 -1.1 240 240
SPI1 0.002 0.07 -10000 0 -0.31 23 23
RPS6KB1 -0.29 0.23 -10000 0 -0.62 88 88
STAT6 (dimer) -0.67 0.51 -10000 0 -1.1 240 240
STAT6 (dimer)/PARP14 -0.62 0.47 -10000 0 -1 239 239
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.27 -10000 0 -0.64 121 121
FRAP1 -0.32 0.26 -10000 0 -0.63 120 120
LTA -0.61 0.46 -10000 0 -1.1 198 198
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.66 0.49 1.1 240 -10000 0 240
CCL11 -0.58 0.43 -10000 0 -1 186 186
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.65 113 113
IL2RG -0.043 0.19 -10000 0 -0.54 53 53
IL10 -0.61 0.46 -10000 0 -1.1 191 191
IRS1 -0.087 0.27 -10000 0 -0.82 59 59
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.094 -10000 0 -10000 0 0
IL5 -0.6 0.44 -10000 0 -1 189 189
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.48 0.33 -10000 0 -0.79 214 214
COL1A1 -0.26 0.23 -10000 0 -0.6 93 93
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.59 0.45 -10000 0 -1.1 163 163
IL2R gamma/JAK3 -0.081 0.18 -10000 0 -0.51 53 53
TFF3 -1.3 0.61 -10000 0 -1.6 399 399
ALOX15 -0.59 0.44 -10000 0 -1 189 189
MYBL1 0.013 0.015 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.51 0.36 -10000 0 -0.81 238 238
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.018 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.3 0.25 -10000 0 -0.64 93 93
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.63 120 120
PI3K -0.33 0.28 -10000 0 -0.68 118 118
DOK2 0.001 0.076 -10000 0 -0.38 16 16
ETS1 0.03 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.24 0.21 -10000 0 -0.6 61 61
ITGB3 -0.61 0.47 -10000 0 -1.1 176 176
PIGR -0.64 0.5 -10000 0 -1.1 202 202
IGHE 0.051 0.034 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.59 61 61
BCL6 0.012 0.038 -10000 0 -0.82 1 1
OPRM1 -0.6 0.44 -10000 0 -1.1 173 173
RETNLB -0.6 0.44 -10000 0 -1 188 188
SELP -0.6 0.45 -10000 0 -1 195 195
AICDA -0.58 0.42 -10000 0 -1 198 198
Wnt signaling

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
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.46 304 304
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.005 0.051 -9999 0 -0.31 12 12
WNT4 -0.26 0.39 -9999 0 -0.81 162 162
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 251 251
PDGFR-alpha signaling pathway

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
PDGFRA -0.25 0.39 -9999 0 -0.83 151 151
PDGF/PDGFRA/CRKL -0.19 0.29 -9999 0 -0.62 151 151
positive regulation of JUN kinase activity -0.15 0.22 -9999 0 -0.48 151 151
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.2 0.29 -9999 0 -0.63 151 151
AP1 -0.5 0.63 -9999 0 -1.4 135 135
mol:IP3 -0.19 0.3 -9999 0 -0.65 151 151
PLCG1 -0.19 0.31 -9999 0 -0.65 151 151
PDGF/PDGFRA/alphaV Integrin -0.2 0.29 -9999 0 -0.63 152 152
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.3 -9999 0 -0.64 151 151
CAV3 -0.001 0.029 -9999 0 -0.31 4 4
CAV1 -0.009 0.13 -9999 0 -0.82 13 13
SHC/Grb2/SOS1 -0.15 0.22 -9999 0 -0.48 151 151
PDGF/PDGFRA/Shf -0.19 0.29 -9999 0 -0.62 151 151
FOS -0.45 0.61 -9999 0 -1.4 135 135
JUN -0.17 0.28 -9999 0 -0.7 110 110
oligodendrocyte development -0.2 0.29 -9999 0 -0.62 152 152
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.3 -9999 0 -0.65 151 151
PDGF/PDGFRA -0.25 0.39 -9999 0 -0.83 151 151
actin cytoskeleton reorganization -0.19 0.29 -9999 0 -0.62 151 151
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.17 0.25 -9999 0 -0.53 154 154
PDGF/PDGFRA/Crk/C3G -0.16 0.25 -9999 0 -0.53 151 151
JAK1 -0.18 0.3 -9999 0 -0.62 151 151
ELK1/SRF -0.12 0.24 -9999 0 -0.48 151 151
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0.015 -9999 0 -10000 0 0
CSNK2A1 0.027 0.027 -9999 0 -10000 0 0
GO:0007205 -0.2 0.31 -9999 0 -0.66 151 151
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.15 0.22 -9999 0 -0.48 151 151
PDGF/PDGFRA/SHB -0.19 0.29 -9999 0 -0.62 151 151
PDGF/PDGFRA/Caveolin-1 -0.21 0.31 -9999 0 -0.66 154 154
ITGAV 0.01 0.053 -9999 0 -0.82 2 2
ELK1 -0.18 0.28 -9999 0 -0.59 151 151
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
PDGF/PDGFRA/Crk -0.19 0.29 -9999 0 -0.62 151 151
JAK-STAT cascade -0.18 0.3 -9999 0 -0.62 151 151
cell proliferation -0.19 0.29 -9999 0 -0.62 151 151
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.13 0.32 -9999 0 -0.82 85 85
GNB1/GNG2 -0.26 0.24 -9999 0 -0.59 125 125
mol:DAG -0.21 0.24 -9999 0 -0.55 116 116
PLCG1 -0.22 0.24 -9999 0 -0.57 116 116
YES1 -0.25 0.26 -9999 0 -0.62 124 124
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.22 0.25 -9999 0 -0.57 118 118
MAP3K7 -0.17 0.2 -9999 0 -0.45 116 116
mol:Ca2+ -0.2 0.23 -9999 0 -0.53 118 118
mol:IP3 -0.21 0.24 -9999 0 -0.55 116 116
NLK -0.01 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.19 0.22 -9999 0 -0.48 129 129
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.46 304 304
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.25 0.26 -9999 0 -0.58 141 141
GO:0007205 -0.21 0.23 -9999 0 -0.54 116 116
WNT6 0.005 0.051 -9999 0 -0.31 12 12
WNT4 -0.26 0.39 -9999 0 -0.81 162 162
NFAT1/CK1 alpha -0.3 0.25 -9999 0 -0.62 148 148
GNG2 0.012 0.038 -9999 0 -0.82 1 1
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 251 251
CDC42 -0.23 0.25 -9999 0 -0.59 118 118
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.51 0.54 -9999 0 -1.1 185 185
PCK1 -0.34 0.49 -9999 0 -1.5 60 60
HNF4A -0.67 0.66 -9999 0 -1.3 238 238
KCNJ11 -0.48 0.54 -9999 0 -1.1 193 193
AKT1 -0.042 0.12 -9999 0 -0.41 2 2
response to starvation -0.018 0.034 -9999 0 -10000 0 0
DLK1 -0.49 0.54 -9999 0 -1.1 175 175
NKX2-1 -0.16 0.21 -9999 0 -10000 0 0
ACADM -0.51 0.54 -9999 0 -1.1 183 183
TAT -0.2 0.22 -9999 0 -0.69 11 11
CEBPB 0.013 0.005 -9999 0 -10000 0 0
CEBPA 0.005 0.084 -9999 0 -0.82 5 5
TTR -0.2 0.22 -9999 0 -0.78 26 26
PKLR -0.52 0.54 -9999 0 -1.1 186 186
APOA1 -0.92 0.89 -9999 0 -1.7 246 246
CPT1C -0.53 0.54 -9999 0 -1.1 189 189
ALAS1 -0.16 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.3 -9999 0 -0.86 25 25
FOXF1 -0.011 0.092 -9999 0 -0.75 7 7
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.007 -9999 0 -10000 0 0
CPT1A -0.51 0.54 -9999 0 -1.1 185 185
HMGCS1 -0.51 0.54 -9999 0 -1.1 183 183
NR3C1 0.019 0.017 -9999 0 -10000 0 0
CPT1B -0.51 0.54 -9999 0 -1.1 184 184
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.66 0.7 -9999 0 -1.4 211 211
CREB1 0.001 0.052 -9999 0 -10000 0 0
IGFBP1 -0.18 0.2 -9999 0 -0.6 4 4
PDX1 -0.18 0.21 -9999 0 -10000 0 0
UCP2 -0.51 0.54 -9999 0 -1.1 187 187
ALDOB -0.48 0.54 -9999 0 -1.1 173 173
AFP -0.049 0.11 -9999 0 -0.51 7 7
BDH1 -0.51 0.54 -9999 0 -1.1 192 192
HADH -0.48 0.54 -9999 0 -1.1 181 181
F2 -0.62 0.63 -9999 0 -1.3 202 202
HNF1A 0.015 0.007 -9999 0 -10000 0 0
G6PC -0.006 0.091 -9999 0 -10000 0 0
SLC2A2 -0.23 0.26 -9999 0 -0.82 1 1
INS -0.008 0.019 -9999 0 -10000 0 0
FOXA1 -0.061 0.15 -9999 0 -0.36 65 65
FOXA3 -0.074 0.17 -9999 0 -0.5 35 35
FOXA2 -0.55 0.61 -9999 0 -1.2 200 200
ABCC8 -0.78 0.75 -9999 0 -1.4 258 258
ALB -0.1 0.32 -9999 0 -1.3 31 31
Nongenotropic Androgen signaling

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
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.25 -10000 0 -0.5 206 206
regulation of S phase of mitotic cell cycle -0.12 0.18 -10000 0 -0.34 207 207
GNAO1 -0.017 0.15 -10000 0 -0.82 16 16
HRAS 0.011 0.021 -10000 0 -0.32 2 2
SHBG/T-DHT -0.008 0.071 -10000 0 -0.56 8 8
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.16 0.23 -10000 0 -0.43 205 205
T-DHT/AR -0.27 0.32 -10000 0 -0.64 205 205
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 128 128
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.038 -10000 0 -0.82 1 1
mol:GDP -0.26 0.3 -10000 0 -0.61 207 207
cell proliferation -0.2 0.28 -10000 0 -0.54 138 138
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
FOS -0.24 0.4 -10000 0 -0.89 128 128
mol:Ca2+ -0.027 0.03 -10000 0 -0.071 93 93
MAPK3 -0.18 0.26 -10000 0 -0.45 207 207
MAPK1 -0.083 0.13 -10000 0 -0.3 78 78
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 128 128
cAMP biosynthetic process 0.016 0.075 -10000 0 -0.52 8 8
GNG2 0.012 0.038 -10000 0 -0.82 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 128 128
HRAS/GTP -0.2 0.23 -10000 0 -0.47 205 205
actin cytoskeleton reorganization -0.003 0.034 -10000 0 -0.44 3 3
SRC 0.012 0.015 -10000 0 -0.32 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 128 128
PI3K -0.003 0.043 -10000 0 -0.55 3 3
apoptosis 0.16 0.25 0.52 129 -10000 0 129
T-DHT/AR/PELP1 -0.23 0.27 -10000 0 -0.55 205 205
HRAS/GDP -0.24 0.29 -10000 0 -0.58 206 206
CREB1 -0.18 0.27 -10000 0 -0.57 129 129
RAC1-CDC42/GTP -0.003 0.035 -10000 0 -0.45 3 3
AR -0.34 0.41 -10000 0 -0.82 205 205
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.17 0.24 -10000 0 -0.45 205 205
RAC1-CDC42/GDP -0.23 0.27 -10000 0 -0.55 205 205
T-DHT/AR/PELP1/Src -0.21 0.25 -10000 0 -0.51 205 205
MAP2K2 -0.16 0.23 -10000 0 -0.43 205 205
T-DHT/AR/PELP1/Src/PI3K -0.13 0.18 -10000 0 -0.34 207 207
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG 0 0.1 -10000 0 -0.82 8 8
Gi family/GNB1/GNG2/GDP -0.02 0.12 -10000 0 -0.54 16 16
mol:T-DHT 0 0.001 0.002 76 -0.003 50 126
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.009 0.043 -10000 0 -0.5 3 3
Gi family/GTP -0.095 0.12 -10000 0 -0.47 18 18
CDC42 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.11 0.26 -10000 0 -0.68 35 35
IHH -0.2 0.37 -10000 0 -0.84 121 121
SHH Np/Cholesterol/GAS1 -0.1 0.2 -10000 0 -0.51 97 97
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.1 0.2 0.51 97 -10000 0 97
SMO/beta Arrestin2 -0.095 0.24 -10000 0 -0.68 16 16
SMO -0.11 0.25 -10000 0 -0.51 124 124
AKT1 -0.027 0.12 -10000 0 -0.66 2 2
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC 0 0.1 -10000 0 -0.82 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.1 0.25 -10000 0 -0.5 124 124
STIL -0.077 0.2 -10000 0 -0.59 18 18
DHH N/PTCH2 -0.11 0.24 -10000 0 -0.64 82 82
DHH N/PTCH1 -0.099 0.22 -10000 0 -0.45 128 128
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
DHH 0.006 0.075 -10000 0 -0.82 4 4
PTHLH -0.16 0.37 -10000 0 -1.2 35 35
determination of left/right symmetry -0.1 0.25 -10000 0 -0.5 124 124
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.15 0.36 -10000 0 -1.1 35 35
IHH N/Hhip -0.38 0.4 -10000 0 -0.73 258 258
DHH N/Hhip -0.25 0.31 -10000 0 -0.63 191 191
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.1 0.25 -10000 0 -0.5 124 124
pancreas development -0.31 0.4 -10000 0 -0.81 191 191
HHAT 0.012 0.038 -10000 0 -0.82 1 1
PI3K -0.004 0.049 -10000 0 -0.63 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.15 0.33 -10000 0 -0.82 96 96
somite specification -0.1 0.25 -10000 0 -0.5 124 124
SHH Np/Cholesterol/PTCH1 -0.087 0.2 -10000 0 -0.62 17 17
SHH Np/Cholesterol/PTCH2 -0.088 0.19 -10000 0 -0.51 81 81
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.51 132 132
SHH 0.007 0.049 -10000 0 -0.63 1 1
catabolic process -0.11 0.25 -10000 0 -0.51 124 124
SMO/Vitamin D3 -0.091 0.22 -10000 0 -0.65 17 17
SHH Np/Cholesterol/Hhip -0.2 0.24 -10000 0 -0.51 190 190
LRP2 -0.21 0.37 -10000 0 -0.82 131 131
receptor-mediated endocytosis -0.2 0.23 -10000 0 -0.72 47 47
SHH Np/Cholesterol/BOC -0.014 0.074 -10000 0 -0.52 9 9
SHH Np/Cholesterol/CDO -0.15 0.23 -10000 0 -0.51 144 144
mesenchymal cell differentiation 0.2 0.24 0.5 190 -10000 0 190
mol:Vitamin D3 -0.086 0.21 -10000 0 -0.62 17 17
IHH N/PTCH2 -0.23 0.34 -10000 0 -0.66 180 180
CDON -0.23 0.38 -10000 0 -0.82 143 143
IHH N/PTCH1 -0.12 0.25 -10000 0 -0.51 124 124
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.63 131 131
PTCH2 -0.12 0.31 -10000 0 -0.82 80 80
SHH Np/Cholesterol -0.006 0.035 -10000 0 -0.51 1 1
PTCH1 -0.11 0.25 -10000 0 -0.51 124 124
HHIP -0.31 0.4 -10000 0 -0.81 191 191
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.08 -9999 0 -0.56 9 9
NFATC2 -0.1 0.22 -9999 0 -0.57 85 85
NFATC3 0 0.027 -9999 0 -10000 0 0
CD40LG -0.43 0.41 -9999 0 -0.88 192 192
PTGS2 -0.41 0.4 -9999 0 -0.86 178 178
JUNB 0.003 0.091 -9999 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.82 110 110
mol:Ca2+ -0.01 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.03 0.12 -9999 0 -0.33 62 62
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.59 167 167
FOS -0.21 0.36 -9999 0 -0.82 128 128
IFNG -0.43 0.4 -9999 0 -0.86 196 196
AP-1/NFAT1-c-4 -0.52 0.5 -9999 0 -1.1 183 183
FASLG -0.41 0.39 -9999 0 -0.83 185 185
NFAT1-c-4/ICER1 -0.11 0.2 -9999 0 -0.5 93 93
IL2RA -0.4 0.38 -9999 0 -0.83 179 179
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.47 0.36 -9999 0 -0.79 237 237
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.5 94 94
IL4 -0.39 0.36 -9999 0 -0.8 177 177
IL2 -0.012 0.026 -9999 0 -10000 0 0
IL3 -0.032 0.03 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.006 0.082 -9999 0 -0.33 27 27
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.015 -9999 0 -0.31 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.17 0.3 0.69 118 -10000 0 118
KIRREL -0.071 0.24 -10000 0 -0.84 42 42
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.17 0.3 -10000 0 -0.69 118 118
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.13 0.24 -10000 0 -0.54 118 118
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.076 0.2 -10000 0 -0.41 118 118
FYN -0.11 0.24 -10000 0 -0.51 118 118
mol:Ca2+ -0.13 0.24 -10000 0 -0.53 118 118
mol:DAG -0.13 0.24 -10000 0 -0.53 118 118
NPHS2 -0.017 0.052 -10000 0 -0.89 1 1
mol:IP3 -0.13 0.24 -10000 0 -0.53 118 118
regulation of endocytosis -0.12 0.21 -10000 0 -0.48 118 118
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.55 118 118
establishment of cell polarity -0.17 0.3 -10000 0 -0.69 118 118
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.49 118 118
Nephrin/NEPH1/beta Arrestin2 -0.1 0.23 -10000 0 -0.48 118 118
NPHS1 -0.15 0.32 -10000 0 -0.82 90 90
Nephrin/NEPH1/podocin -0.12 0.23 -10000 0 -0.51 118 118
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.13 0.24 -10000 0 -0.54 118 118
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 118 118
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.25 -10000 0 -0.51 122 122
cytoskeleton organization -0.1 0.26 -10000 0 -0.53 118 118
Nephrin/NEPH1 -0.13 0.24 -10000 0 -0.53 118 118
Nephrin/NEPH1/ZO-1 -0.14 0.26 -10000 0 -0.57 118 118
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.022 0.17 -9999 0 -0.82 21 21
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.42 0.26 -9999 0 -0.56 361 361
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.37 0.25 -9999 0 -0.51 361 361
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.095 0.28 -9999 0 -0.82 64 64
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.026 0.12 -9999 0 -0.63 20 20
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.012 0.021 -9999 0 -0.31 2 2
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.021 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.42 0.26 -9999 0 -0.56 363 363
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.27 0.2 -9999 0 -0.72 16 16
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.32 0.23 -9999 0 -0.44 361 361
RELN -0.6 0.37 -9999 0 -0.82 357 357
PAFAH/LIS1 -0.047 0.19 -9999 0 -0.54 64 64
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.22 0.14 -9999 0 -0.54 16 16
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.25 0.18 -9999 0 -0.34 364 364
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.3 0.22 -9999 0 -0.79 16 16
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.029 -9999 0 -10000 0 0
PAFAH1B2 -0.002 0.11 -9999 0 -0.82 9 9
MAP1B/LIS1/Dynein heavy chain 0.027 0.003 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.27 0.17 -9999 0 -0.69 16 16
LRP8 -0.021 0.16 -9999 0 -0.82 20 20
NDEL1/Katanin 60 -0.27 0.2 -9999 0 -0.72 16 16
P39/CDK5 -0.32 0.23 -9999 0 -0.45 361 361
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.34 0.24 -9999 0 -0.47 361 361
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.36 0.22 -9999 0 -0.48 363 363
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 367 367
CDC42 0 0 -9999 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.001 0.025 -10000 0 -0.54 1 1
fibroblast growth factor receptor signaling pathway -0.001 0.025 -10000 0 -0.54 1 1
LAMA1 -0.049 0.22 -10000 0 -0.8 37 37
PRNP 0.012 0.038 -10000 0 -0.82 1 1
GPC1/SLIT2 -0.095 0.22 -10000 0 -0.63 73 73
SMAD2 0.028 0.048 -10000 0 -0.49 3 3
GPC1/PrPc/Cu2+ -0.001 0.026 -10000 0 -0.55 1 1
GPC1/Laminin alpha1 -0.047 0.16 -10000 0 -0.63 36 36
TDGF1 -0.34 0.41 -10000 0 -0.82 207 207
CRIPTO/GPC1 -0.27 0.31 -10000 0 -0.63 207 207
APP/GPC1 0 0.009 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.21 0.28 -10000 0 -0.54 207 207
FLT1 0.012 0.038 -10000 0 -0.82 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.048 -10000 0 -0.54 3 3
SERPINC1 0.006 0.044 -10000 0 -0.31 9 9
FYN -0.21 0.28 -10000 0 -0.54 207 207
FGR -0.21 0.28 -10000 0 -0.54 207 207
positive regulation of MAPKKK cascade -0.28 0.31 -10000 0 -0.61 209 209
SLIT2 -0.11 0.3 -10000 0 -0.8 76 76
GPC1/NRG -0.059 0.18 -10000 0 -0.63 45 45
NRG1 -0.064 0.24 -10000 0 -0.8 47 47
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.058 -10000 0 -0.7 3 3
LYN -0.21 0.28 -10000 0 -0.54 207 207
mol:Spermine 0.012 0.01 -10000 0 -10000 0 0
cell growth -0.001 0.025 -10000 0 -0.54 1 1
BMP signaling pathway -0.013 0.015 0.31 1 -10000 0 1
SRC -0.21 0.28 -10000 0 -0.54 207 207
TGFBR1 0.006 0.048 -10000 0 -0.31 11 11
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.36 -10000 0 -0.68 184 184
GPC1 0.013 0.015 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.006 0.048 -10000 0 -0.31 11 11
VEGFA 0.008 0.065 -10000 0 -0.82 3 3
BLK -0.38 0.37 -10000 0 -0.66 281 281
HCK -0.22 0.28 -10000 0 -0.55 207 207
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.012 0.038 -10000 0 -0.82 1 1
VEGFR1 homodimer 0.012 0.037 -10000 0 -0.82 1 1
TGFBR2 0.008 0.065 -10000 0 -0.82 3 3
cell death 0 0.009 -10000 0 -10000 0 0
ATIII/GPC1 -0.004 0.029 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.19 0.27 -10000 0 -0.63 134 134
LCK -0.23 0.28 -10000 0 -0.55 212 212
neuron differentiation -0.059 0.18 -10000 0 -0.62 45 45
PrPc/Cu2+ -0.001 0.029 -10000 0 -0.64 1 1
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.008 0.065 -10000 0 -0.82 3 3
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.065 -10000 0 -0.82 3 3
EFNB1 0 0.12 -10000 0 -0.63 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.25 0.24 -10000 0 -0.52 205 205
Ephrin B2/EPHB1-2 -0.2 0.24 -10000 0 -0.5 192 192
neuron projection morphogenesis -0.24 0.23 -10000 0 -0.5 205 205
Ephrin B1/EPHB1-2/Tiam1 -0.27 0.26 -10000 0 -0.56 205 205
DNM1 -0.015 0.15 -10000 0 -0.79 17 17
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.005 0.089 -10000 0 -0.78 6 6
YES1 -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/NCK2 -0.19 0.24 -10000 0 -0.47 205 205
PI3K 0.003 0.12 -10000 0 -1 6 6
mol:GDP -0.26 0.26 -10000 0 -0.55 205 205
ITGA2B -0.072 0.25 -10000 0 -0.82 50 50
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.01 0.11 -10000 0 -1 6 6
MAP3K7 -0.012 0.092 -10000 0 -0.83 6 6
FGR -0.012 0.11 -10000 0 -1 6 6
TIAM1 -0.17 0.16 -10000 0 -0.32 277 277
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.041 0.2 -10000 0 -0.53 63 63
LYN -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.014 0.1 -10000 0 -0.96 6 6
Ephrin B1/EPHB1-2 -0.02 0.098 -10000 0 -0.89 6 6
SRC -0.012 0.11 -10000 0 -1 6 6
ITGB3 -0.01 0.14 -10000 0 -0.82 14 14
EPHB1 -0.31 0.4 -10000 0 -0.82 190 190
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.081 0.22 -10000 0 -0.67 59 59
BLK -0.066 0.14 -10000 0 -1.1 6 6
HCK -0.013 0.11 -10000 0 -1 6 6
regulation of stress fiber formation 0.19 0.24 0.46 205 -10000 0 205
MAPK8 0.003 0.13 -10000 0 -0.78 12 12
Ephrin B1/EPHB1-2/RGS3 -0.19 0.24 -10000 0 -0.47 205 205
endothelial cell migration -0.006 0.081 -10000 0 -0.72 6 6
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.004 0.1 -10000 0 -0.93 6 6
regulation of focal adhesion formation 0.19 0.24 0.46 205 -10000 0 205
chemotaxis 0.19 0.24 0.46 205 -10000 0 205
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
Rac1/GTP -0.24 0.24 -10000 0 -0.51 205 205
angiogenesis -0.02 0.098 -10000 0 -0.89 6 6
LCK -0.015 0.12 -10000 0 -1 6 6
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.051 0.14 -9999 0 -0.51 12 12
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.7 60 60
EDN1 -0.042 0.12 -9999 0 -0.79 6 6
EDN3 -0.39 0.41 -9999 0 -0.81 240 240
EDN2 -0.014 0.12 -9999 0 -0.41 32 32
HRAS/GDP -0.1 0.24 -9999 0 -0.54 81 81
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.084 0.18 -9999 0 -0.39 90 90
ADCY4 -0.095 0.19 -9999 0 -0.5 70 70
ADCY5 -0.16 0.25 -9999 0 -0.55 117 117
ADCY6 -0.095 0.19 -9999 0 -0.5 69 69
ADCY7 -0.095 0.19 -9999 0 -0.5 69 69
ADCY1 -0.1 0.21 -9999 0 -0.52 72 72
ADCY2 -0.14 0.24 -9999 0 -0.55 103 103
ADCY3 -0.095 0.19 -9999 0 -0.5 69 69
ADCY8 -0.2 0.2 -9999 0 -0.54 96 96
ADCY9 -0.095 0.19 -9999 0 -0.5 69 69
arachidonic acid secretion -0.17 0.32 -9999 0 -0.65 132 132
ETB receptor/Endothelin-1/Gq/GTP -0.096 0.22 -9999 0 -0.43 117 117
GNAO1 -0.017 0.15 -9999 0 -0.82 16 16
HRAS 0.01 0.021 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.013 0.16 -9999 0 -0.49 11 11
ETA receptor/Endothelin-1/Gs/GTP -0.08 0.22 -9999 0 -0.52 71 71
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.068 0.17 -9999 0 -0.5 39 39
EDNRB 0.003 0.093 -9999 0 -0.83 6 6
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.15 0.24 -9999 0 -0.63 55 55
CYSLTR1 -0.062 0.18 -9999 0 -0.75 17 17
SLC9A1 -0.021 0.076 -9999 0 -0.3 6 6
mol:GDP -0.12 0.26 -9999 0 -0.55 94 94
SLC9A3 -0.048 0.19 -9999 0 -0.8 21 21
RAF1 -0.15 0.3 -9999 0 -0.57 135 135
JUN -0.28 0.51 -9999 0 -1.2 119 119
JAK2 -0.053 0.15 -9999 0 -0.54 13 13
mol:IP3 -0.11 0.23 -9999 0 -0.5 101 101
ETA receptor/Endothelin-1 -0.034 0.2 -9999 0 -0.47 38 38
PLCB1 0.009 0.038 -9999 0 -0.82 1 1
PLCB2 0.005 0.043 -9999 0 -0.32 8 8
ETA receptor/Endothelin-3 -0.32 0.33 -9999 0 -0.66 240 240
FOS -0.26 0.48 -9999 0 -1 130 130
Gai/GDP -0.003 0.13 -9999 0 -0.66 16 16
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.23 -9999 0 -0.57 63 63
BCAR1 0.013 0.002 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.48 102 102
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.09 0.27 -9999 0 -0.82 61 61
Gs family/GDP -0.18 0.25 -9999 0 -0.56 119 119
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.46 102 102
MAPK14 -0.063 0.18 -9999 0 -0.48 34 34
TRPC6 -0.14 0.3 -9999 0 -0.76 59 59
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.18 -9999 0 -0.4 83 83
ETB receptor/Endothelin-2 -0.026 0.11 -9999 0 -0.63 12 12
ETB receptor/Endothelin-3 -0.31 0.32 -9999 0 -0.63 242 242
ETB receptor/Endothelin-1 -0.019 0.12 -9999 0 -0.63 12 12
MAPK3 -0.23 0.43 -9999 0 -0.89 136 136
MAPK1 -0.23 0.43 -9999 0 -0.89 136 136
Rac1/GDP -0.1 0.24 -9999 0 -0.53 79 79
cAMP biosynthetic process -0.14 0.21 -9999 0 -0.54 79 79
MAPK8 -0.17 0.35 -9999 0 -0.72 99 99
SRC 0.012 0.015 -9999 0 -0.32 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.009 0.078 -9999 0 -0.36 7 7
p130Cas/CRK/Src/PYK2 -0.13 0.29 -9999 0 -0.61 98 98
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.24 -9999 0 -0.53 79 79
COL1A2 -0.037 0.16 -9999 0 -0.6 10 10
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.57 10 10
mol:DAG -0.11 0.23 -9999 0 -0.5 101 101
MAP2K2 -0.18 0.35 -9999 0 -0.69 139 139
MAP2K1 -0.18 0.35 -9999 0 -0.69 139 139
EDNRA -0.038 0.1 -9999 0 -0.54 5 5
positive regulation of muscle contraction -0.036 0.12 -9999 0 -0.48 9 9
Gq family/GDP -0.19 0.29 -9999 0 -0.67 112 112
HRAS/GTP -0.13 0.26 -9999 0 -0.57 94 94
PRKCH -0.1 0.22 -9999 0 -0.52 79 79
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.12 0.26 -9999 0 -0.54 106 106
PRKCB -0.12 0.23 -9999 0 -0.52 92 92
PRKCE -0.1 0.24 -9999 0 -0.53 85 85
PRKCD -0.1 0.22 -9999 0 -0.51 83 83
PRKCG -0.11 0.22 -9999 0 -0.51 89 89
regulation of vascular smooth muscle contraction -0.3 0.55 -9999 0 -1.2 130 130
PRKCQ -0.11 0.23 -9999 0 -0.51 92 92
PLA2G4A -0.19 0.36 -9999 0 -0.72 132 132
GNA14 -0.18 0.35 -9999 0 -0.82 114 114
GNA15 -0.016 0.094 -9999 0 -0.33 39 39
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 -0.006 0.12 -9999 0 -0.82 10 10
Rac1/GTP -0.013 0.16 -9999 0 -0.49 11 11
MMP1 -0.096 0.16 -9999 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.18 0.42 -9999 0 -0.91 64 64
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.34 -9999 0 -0.82 106 106
SMAD4 0.015 0.003 -9999 0 -10000 0 0
ID2 -0.18 0.42 -9999 0 -0.92 64 64
AP1 -0.28 0.45 -9999 0 -0.92 151 151
ABCG2 -0.19 0.42 -9999 0 -0.96 56 56
HIF1A -0.008 0.067 -9999 0 -10000 0 0
TFF3 -0.56 0.51 -9999 0 -1 198 198
GATA2 0.014 0.015 -9999 0 -0.31 1 1
AKT1 -0.038 0.1 -9999 0 -10000 0 0
response to hypoxia -0.059 0.11 -9999 0 -0.24 41 41
MCL1 -0.18 0.42 -9999 0 -0.94 56 56
NDRG1 -0.18 0.42 -9999 0 -0.91 64 64
SERPINE1 -0.19 0.42 -9999 0 -0.93 66 66
FECH -0.18 0.42 -9999 0 -0.92 61 61
FURIN -0.18 0.42 -9999 0 -0.91 65 65
NCOA2 -0.066 0.24 -9999 0 -0.82 47 47
EP300 -0.062 0.18 -9999 0 -0.33 108 108
HMOX1 -0.19 0.42 -9999 0 -0.92 65 65
BHLHE40 -0.19 0.42 -9999 0 -0.95 60 60
BHLHE41 -0.18 0.42 -9999 0 -0.92 66 66
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.016 0.036 -9999 0 -10000 0 0
ENG 0.042 0.092 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.82 110 110
RORA -0.18 0.42 -9999 0 -0.93 64 64
ABCB1 -0.075 0.18 -9999 0 -1.4 8 8
TFRC -0.18 0.42 -9999 0 -0.95 58 58
CXCR4 -0.18 0.42 -9999 0 -0.9 68 68
TF -0.23 0.48 -9999 0 -1 90 90
CITED2 -0.21 0.47 -9999 0 -1 79 79
HIF1A/ARNT -0.29 0.38 -9999 0 -1 68 68
LDHA -0.038 0.05 -9999 0 -10000 0 0
ETS1 -0.18 0.42 -9999 0 -0.92 60 60
PGK1 -0.18 0.42 -9999 0 -0.9 68 68
NOS2 -0.2 0.43 -9999 0 -0.91 75 75
ITGB2 -0.19 0.42 -9999 0 -0.93 64 64
ALDOA -0.18 0.42 -9999 0 -0.92 61 61
Cbp/p300/CITED2 -0.32 0.5 -9999 0 -1.1 106 106
FOS -0.2 0.36 -9999 0 -0.82 128 128
HK2 -0.18 0.42 -9999 0 -0.91 66 66
SP1 0.022 0.01 -9999 0 -10000 0 0
GCK -0.39 0.71 -9999 0 -1.5 136 136
HK1 -0.18 0.42 -9999 0 -0.93 58 58
NPM1 -0.18 0.42 -9999 0 -0.9 68 68
EGLN1 -0.18 0.42 -9999 0 -0.92 66 66
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.18 0.42 -9999 0 -0.91 65 65
SMAD3 0.015 0.003 -9999 0 -10000 0 0
EDN1 -0.16 0.31 -9999 0 -0.73 65 65
IGFBP1 -0.2 0.42 -9999 0 -0.93 64 64
VEGFA -0.15 0.38 -9999 0 -0.76 74 74
HIF1A/JAB1 -0.011 0.02 -9999 0 -10000 0 0
CP -0.34 0.55 -9999 0 -1 147 147
CXCL12 -0.23 0.48 -9999 0 -1 81 81
COPS5 0.014 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.18 0.42 -9999 0 -0.9 68 68
EGLN3 -0.2 0.43 -9999 0 -0.94 70 70
CA9 -0.2 0.42 -9999 0 -0.92 69 69
TERT -0.19 0.41 -9999 0 -0.91 68 68
ENO1 -0.18 0.42 -9999 0 -0.9 68 68
PFKL -0.18 0.42 -9999 0 -0.93 58 58
NCOA1 0.014 0 -9999 0 -10000 0 0
ADM -0.22 0.44 -9999 0 -0.92 78 78
ARNT -0.009 0.067 -9999 0 -10000 0 0
HNF4A -0.026 0.065 -9999 0 -0.35 10 10
ADFP -0.2 0.41 -9999 0 -0.91 68 68
SLC2A1 -0.15 0.38 -9999 0 -0.75 73 73
LEP -0.2 0.42 -9999 0 -0.92 65 65
HIF1A/ARNT/Cbp/p300 -0.29 0.36 -9999 0 -0.86 105 105
EPO -0.14 0.33 -9999 0 -0.95 27 27
CREBBP -0.062 0.18 -9999 0 -0.34 107 107
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.34 -9999 0 -0.82 105 105
PFKFB3 -0.18 0.42 -9999 0 -0.9 69 69
NT5E -0.19 0.42 -9999 0 -0.96 58 58
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.13 0.24 -10000 0 -0.45 159 159
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.021 -10000 0 -0.31 2 2
IRS1/Crk -0.13 0.24 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.22 -10000 0 -0.52 113 113
AKT1 -0.092 0.22 -10000 0 -0.77 16 16
BAD -0.078 0.2 -10000 0 -0.7 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.13 0.24 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.24 -10000 0 -0.46 159 159
RAF1 -0.068 0.19 -10000 0 -0.65 16 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.21 -10000 0 -0.42 159 159
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.24 -10000 0 -0.49 159 159
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
RPS6KB1 -0.092 0.22 -10000 0 -0.77 16 16
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.06 0.16 -10000 0 -0.53 16 16
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.41 114 114
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.18 -10000 0 -0.42 113 113
IGF-1R heterotetramer -0.019 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.45 159 159
Crk/p130 Cas/Paxillin -0.13 0.2 -10000 0 -0.79 13 13
IGF1R -0.019 0.048 -10000 0 -10000 0 0
IGF1 -0.2 0.36 -10000 0 -0.84 113 113
IRS2/Crk -0.12 0.23 -10000 0 -0.46 113 113
PI3K -0.14 0.22 -10000 0 -0.43 159 159
apoptosis 0.06 0.18 0.57 16 -10000 0 16
HRAS/GDP -0.001 0.014 -10000 0 -10000 0 0
PRKCD -0.11 0.24 -10000 0 -0.53 113 113
RAF1/14-3-3 E -0.051 0.17 -10000 0 -0.53 16 16
BAD/14-3-3 -0.064 0.19 -10000 0 -0.62 16 16
PRKCZ -0.092 0.22 -10000 0 -0.77 16 16
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.16 -10000 0 -0.63 16 16
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.25 -10000 0 -0.56 113 113
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.19 -10000 0 -0.46 113 113
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.24 -10000 0 -0.45 159 159
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.45 159 159
IRS1 -0.15 0.25 -10000 0 -0.49 159 159
IRS2 -0.13 0.24 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1 -0.16 0.27 -10000 0 -0.66 113 113
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.11 0.23 -10000 0 -0.45 114 114
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.24 -10000 0 -0.53 114 114
SHC1 0.013 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.045 0.094 -10000 0 -10000 0 0
SMARCC2 0.014 0.014 -10000 0 -10000 0 0
SMARCC1 0.013 0.014 -10000 0 -10000 0 0
TBX21 -0.15 0.28 -10000 0 -0.65 77 77
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.05 -10000 0 -0.31 11 11
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.003 0.091 -10000 0 -0.82 6 6
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.33 52 -0.49 6 58
PRL -0.088 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.25 0.31 0.58 156 -0.48 24 180
RELA -0.036 0.088 -10000 0 -10000 0 0
FGG 0.24 0.19 0.52 106 -10000 0 106
GR beta/TIF2 0.081 0.24 0.34 77 -0.55 47 124
IFNG -0.5 0.51 -10000 0 -1.1 150 150
apoptosis 0.035 0.24 0.52 53 -0.56 2 55
CREB1 0.011 0.023 -10000 0 -10000 0 0
histone acetylation -0.07 0.16 -10000 0 -0.42 54 54
BGLAP -0.099 0.15 -10000 0 -0.55 8 8
GR/PKAc 0.13 0.1 0.34 32 -0.41 1 33
NF kappa B1 p50/RelA -0.074 0.16 -10000 0 -0.47 27 27
SMARCD1 0.013 0.014 -10000 0 -10000 0 0
MDM2 0.12 0.094 0.27 103 -10000 0 103
GATA3 -0.027 0.18 -10000 0 -0.78 27 27
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.58 33 33
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.062 0.23 0.51 42 -0.74 5 47
CSN2 0.2 0.14 0.42 81 -10000 0 81
BRG1/BAF155/BAF170/BAF60A 0.018 0.049 -10000 0 -10000 0 0
NFATC1 0 0.11 -10000 0 -0.82 9 9
POU2F1 0.013 0.015 -10000 0 -0.3 1 1
CDKN1A 0.023 0.055 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.012 -10000 0 -10000 0 0
SFN -0.21 0.18 -10000 0 -0.33 314 314
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.047 0.16 0.35 14 -0.48 13 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.075 0.44 0.5 37 -0.88 104 141
JUN -0.33 0.3 -10000 0 -0.72 156 156
IL4 -0.13 0.18 -10000 0 -0.62 28 28
CDK5R1 0.012 0.022 -10000 0 -0.32 2 2
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.37 0.41 -10000 0 -0.83 181 181
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.34 35 -0.47 5 40
cortisol/GR alpha (monomer) 0.37 0.3 0.69 179 -10000 0 179
NCOA2 -0.067 0.24 -10000 0 -0.82 47 47
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.25 0.36 -10000 0 -0.84 128 128
AP-1/NFAT1-c-4 -0.56 0.48 -10000 0 -0.99 221 221
AFP -0.22 0.22 -10000 0 -0.71 30 30
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.14 0.48 53 -10000 0 53
TP53 0.032 0.025 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.48 0.37 -10000 0 -0.9 143 143
KRT14 -0.24 0.18 -10000 0 -0.63 17 17
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.066 -10000 0 -10000 0 0
HDAC1 0.011 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.013 -10000 0 -10000 0 0
AP-1 -0.56 0.48 -10000 0 -1 222 222
MAPK14 0.014 0.011 -10000 0 -10000 0 0
MAPK10 0.013 0.04 -10000 0 -0.82 1 1
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.54 0.52 -10000 0 -1.1 170 170
interleukin-1 receptor activity 0.017 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.015 0.05 -10000 0 -0.31 11 11
CGA -0.12 0.16 -10000 0 -0.55 20 20
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.38 180 -10000 0 180
MAPK3 0.014 0.012 -10000 0 -10000 0 0
MAPK1 0.014 0.011 -10000 0 -10000 0 0
ICAM1 -0.26 0.26 -10000 0 -0.7 85 85
NFKB1 -0.038 0.097 -10000 0 -0.94 1 1
MAPK8 -0.19 0.21 -10000 0 -0.53 92 92
MAPK9 0.014 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.029 0.24 0.53 50 -0.58 2 52
BAX 0.028 0.035 -10000 0 -10000 0 0
POMC -0.54 0.69 -10000 0 -1.6 120 120
EP300 0.065 0.067 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.33 0.24 0.6 166 -10000 0 166
proteasomal ubiquitin-dependent protein catabolic process 0.087 0.071 0.24 35 -10000 0 35
SGK1 0.1 0.24 -10000 0 -1.4 11 11
IL13 -0.3 0.25 -10000 0 -0.81 57 57
IL6 -0.4 0.53 -10000 0 -1.2 129 129
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.2 -10000 0 -0.71 45 45
IL2 -0.36 0.27 -10000 0 -0.8 84 84
CDK5 0.013 0.007 -10000 0 -10000 0 0
PRKACB 0.012 0.038 -10000 0 -0.82 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.27 0.32 -10000 0 -0.75 95 95
CDK5R1/CDK5 0.007 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.032 0.12 -10000 0 -0.63 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.56 162 -10000 0 162
SMARCA4 0.014 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.41 107 -0.39 1 108
NF kappa B1 p50/RelA/Cbp 0.018 0.16 -10000 0 -0.52 5 5
JUN (dimer) -0.33 0.3 -10000 0 -0.72 156 156
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.24 0.41 -10000 0 -1 92 92
NR3C1 0.22 0.19 0.48 124 -10000 0 124
NR4A1 -0.31 0.41 -10000 0 -0.75 205 205
TIF2/SUV420H1 -0.06 0.18 -10000 0 -0.63 47 47
MAPKKK cascade 0.035 0.24 0.52 53 -0.56 2 55
cortisol/GR alpha (dimer)/Src-1 0.32 0.23 0.59 169 -10000 0 169
PBX1 0.012 0.038 -10000 0 -0.82 1 1
POU1F1 0.007 0.008 -10000 0 -10000 0 0
SELE -0.35 0.5 -10000 0 -1.2 101 101
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.41 107 -0.4 1 108
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.56 162 -10000 0 162
mol:cortisol 0.21 0.19 0.4 189 -10000 0 189
MMP1 -0.22 0.15 -10000 0 -0.44 57 57
IL23-mediated signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.22 0.55 -10000 0 -1.3 77 77
IL23A -0.23 0.56 -10000 0 -1.3 88 88
NF kappa B1 p50/RelA/I kappa B alpha -0.3 0.47 -10000 0 -1.2 87 87
positive regulation of T cell mediated cytotoxicity -0.25 0.62 -10000 0 -1.4 87 87
ITGA3 -0.2 0.52 -10000 0 -1.2 79 79
IL17F -0.11 0.34 -10000 0 -0.75 72 72
IL12B -0.001 0.1 -10000 0 -0.56 11 11
STAT1 (dimer) -0.24 0.58 -10000 0 -1.3 89 89
CD4 -0.2 0.51 -10000 0 -1.2 81 81
IL23 -0.24 0.54 -10000 0 -1.2 87 87
IL23R -0.005 0.099 -10000 0 -10000 0 0
IL1B -0.24 0.59 -10000 0 -1.3 87 87
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.2 0.51 -10000 0 -1.1 84 84
TYK2 0.014 0.023 -10000 0 -10000 0 0
STAT4 -0.024 0.14 -10000 0 -0.46 39 39
STAT3 0.013 0 -10000 0 -10000 0 0
IL18RAP -0.023 0.16 -10000 0 -0.79 21 21
IL12RB1 -0.022 0.12 -10000 0 -0.43 24 24
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
IL12Rbeta1/TYK2 -0.009 0.093 -10000 0 -0.67 4 4
IL23R/JAK2 -0.003 0.13 -10000 0 -0.63 2 2
positive regulation of chronic inflammatory response -0.25 0.62 -10000 0 -1.4 87 87
natural killer cell activation 0.001 0.009 0.036 1 -10000 0 1
JAK2 0.019 0.061 -10000 0 -0.84 2 2
PIK3R1 0.013 0 -10000 0 -10000 0 0
NFKB1 0.011 0.038 -10000 0 -0.82 1 1
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.22 0.5 -10000 0 -1.1 87 87
ALOX12B -0.22 0.52 -10000 0 -1.2 86 86
CXCL1 -0.22 0.53 -10000 0 -1.2 83 83
T cell proliferation -0.25 0.62 -10000 0 -1.4 87 87
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.062 0.28 -10000 0 -0.59 57 57
PI3K -0.31 0.49 -10000 0 -1.2 87 87
IFNG -0.02 0.054 -10000 0 -0.14 67 67
STAT3 (dimer) -0.29 0.45 -10000 0 -1.2 85 85
IL18R1 -0.03 0.14 -10000 0 -0.43 47 47
IL23/IL23R/JAK2/TYK2/SOCS3 -0.1 0.33 -10000 0 -0.77 51 51
IL18/IL18R -0.065 0.18 -10000 0 -0.56 45 45
macrophage activation -0.015 0.018 -10000 0 -0.044 87 87
TNF -0.27 0.63 -10000 0 -1.4 101 101
STAT3/STAT4 -0.31 0.5 -10000 0 -1.3 90 90
STAT4 (dimer) -0.25 0.59 -10000 0 -1.3 90 90
IL18 -0.039 0.15 -10000 0 -0.41 58 58
IL19 -0.2 0.51 -10000 0 -1.2 70 70
STAT5A (dimer) -0.24 0.58 -10000 0 -1.3 87 87
STAT1 0.006 0.048 -10000 0 -0.31 11 11
SOCS3 -0.033 0.19 -10000 0 -0.8 28 28
CXCL9 -0.3 0.63 -10000 0 -1.4 108 108
MPO -0.2 0.51 -10000 0 -1.2 79 79
positive regulation of humoral immune response -0.25 0.62 -10000 0 -1.4 87 87
IL23/IL23R/JAK2/TYK2 -0.3 0.74 -10000 0 -1.6 87 87
IL6 -0.33 0.66 -10000 0 -1.4 123 123
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.001 0.017 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 0.036 1 -10000 0 1
CD3E -0.23 0.58 -10000 0 -1.3 87 87
keratinocyte proliferation -0.25 0.62 -10000 0 -1.4 87 87
NOS2 -0.21 0.51 -10000 0 -1.1 88 88
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.62 75 75
FYN -0.1 0.35 -10000 0 -0.83 77 77
LAT/GRAP2/SLP76 -0.12 0.27 -10000 0 -0.66 85 85
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.052 0.22 -10000 0 -0.47 87 87
B2M 0.013 0.006 -10000 0 -10000 0 0
IKBKG -0.03 0.049 -10000 0 -0.15 31 31
MAP3K8 0 0.1 -10000 0 -0.82 8 8
mol:Ca2+ -0.03 0.05 -10000 0 -0.12 106 106
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.32 -10000 0 -0.74 87 87
TRPV6 -0.17 0.34 -10000 0 -0.8 108 108
CD28 -0.042 0.19 -10000 0 -0.58 45 45
SHC1 -0.11 0.34 -10000 0 -0.8 83 83
receptor internalization -0.14 0.38 -10000 0 -0.84 90 90
PRF1 -0.11 0.35 -10000 0 -0.88 71 71
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.035 0.18 -10000 0 -0.38 85 85
LAT -0.11 0.35 -10000 0 -0.82 83 83
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.092 0.27 -10000 0 -0.72 71 71
CD3E -0.068 0.24 -10000 0 -0.76 52 52
CD3G -0.15 0.32 -10000 0 -0.78 98 98
RASGRP2 0 0.031 -10000 0 -0.19 6 6
RASGRP1 -0.048 0.22 -10000 0 -0.47 89 89
HLA-A 0.011 0.021 -10000 0 -0.31 2 2
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.068 -10000 0 -0.12 66 66
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.056 0.089 -10000 0 -0.25 59 59
PRKCA -0.061 0.13 -10000 0 -0.31 89 89
GRAP2 -0.041 0.2 -10000 0 -0.77 34 34
mol:IP3 -0.05 0.23 0.27 85 -0.47 83 168
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.42 -10000 0 -0.97 80 80
ORAI1 0.087 0.16 0.39 101 -10000 0 101
CSK -0.12 0.35 -10000 0 -0.82 83 83
B7 family/CD28 -0.19 0.34 -10000 0 -0.74 112 112
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.15 0.42 -10000 0 -1 83 83
PTPN6 -0.12 0.36 -10000 0 -0.84 82 82
VAV1 -0.12 0.34 -10000 0 -0.79 87 87
Monovalent TCR/CD3 -0.16 0.4 -10000 0 -0.73 118 118
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.88 78 78
PAG1 -0.12 0.35 -10000 0 -0.83 83 83
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.15 0.42 -10000 0 -0.99 83 83
CD80 -0.069 0.25 -10000 0 -0.8 49 49
CD86 -0.008 0.1 -10000 0 -0.42 24 24
PDK1/CARD11/BCL10/MALT1 -0.068 0.11 -10000 0 -0.3 69 69
HRAS 0.012 0.021 -10000 0 -0.31 2 2
GO:0035030 -0.1 0.29 -10000 0 -0.58 112 112
CD8A -0.047 0.22 -10000 0 -0.82 35 35
CD8B -0.087 0.27 -10000 0 -0.73 67 67
PTPRC -0.033 0.17 -10000 0 -0.6 36 36
PDK1/PKC theta -0.066 0.27 -10000 0 -0.6 85 85
CSK/PAG1 -0.1 0.34 -10000 0 -0.84 76 76
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.015 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.15 0.32 -10000 0 -0.78 87 87
STIM1 0.046 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.009 0.091 -10000 0 -0.18 60 60
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.94 90 90
mol:DAG -0.07 0.18 -10000 0 -0.41 86 86
RAP1A/GDP 0.006 0.029 -10000 0 -0.063 12 12
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.02 0.16 -10000 0 -0.63 26 26
cytotoxic T cell degranulation -0.1 0.33 -10000 0 -0.83 71 71
RAP1A/GTP -0.003 0.009 -10000 0 -0.07 5 5
mol:PI-3-4-5-P3 -0.071 0.26 -10000 0 -0.58 87 87
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.078 0.29 0.3 76 -0.62 86 162
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.022 0.16 -10000 0 -0.6 28 28
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.25 -10000 0 -0.63 86 86
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.01 0.053 -10000 0 -0.82 2 2
CD8 heterodimer -0.1 0.29 -10000 0 -0.76 71 71
CARD11 -0.073 0.17 -10000 0 -0.35 116 116
PRKCB -0.058 0.13 -10000 0 -0.3 87 87
PRKCE -0.051 0.12 -10000 0 -0.3 73 73
PRKCQ -0.088 0.31 -10000 0 -0.69 86 86
LCP2 0.009 0.039 -10000 0 -0.31 7 7
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.039 0.18 -10000 0 -0.4 87 87
IKK complex 0.013 0.069 -10000 0 -0.12 55 55
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.016 0.14 -10000 0 -0.3 69 69
PDPK1 -0.045 0.21 -10000 0 -0.45 85 85
TCR/CD3/MHC I/CD8/Fyn -0.16 0.45 -10000 0 -1.1 82 82
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.088 0.15 -9999 0 -0.31 152 152
GPC2 -0.01 0.084 -9999 0 -0.31 35 35
GPC2/Midkine -0.077 0.11 -9999 0 -0.4 13 13
neuron projection morphogenesis -0.077 0.11 -9999 0 -0.4 13 13
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 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.042 0.11 -9999 0 -0.47 13 13
EGFR 0.006 0.075 -9999 0 -0.82 4 4
EPHA2 0.011 0.026 -9999 0 -0.31 3 3
USP6 0.011 0.026 -9999 0 -0.31 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.097 0.22 -9999 0 -0.63 74 74
ARRB2 -0.043 0.15 -9999 0 -0.45 59 59
mol:GTP 0.021 0.012 -9999 0 -10000 0 0
ARRB1 0.012 0.038 -9999 0 -0.82 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.01 0.053 -9999 0 -0.82 2 2
EGF -0.11 0.29 -9999 0 -0.78 76 76
somatostatin receptor activity 0 0 -9999 0 -0.001 141 141
ARAP2 0.01 0.053 -9999 0 -0.82 2 2
mol:GDP -0.12 0.15 -9999 0 -0.29 160 160
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 131 131
ITGA2B -0.072 0.25 -9999 0 -0.82 50 50
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.17 0.24 -9999 0 -0.68 74 74
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.31 141 141
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.084 0.19 -9999 0 -0.54 74 74
ADRB2 -0.009 0.13 -9999 0 -0.82 13 13
receptor agonist activity 0 0 -9999 0 0 153 153
actin filament binding 0 0 -9999 0 -0.001 141 141
SRC 0.013 0.015 -9999 0 -0.31 1 1
ITGB3 -0.01 0.14 -9999 0 -0.82 14 14
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 136 136
ARF6/GDP 0 0.068 -9999 0 -0.33 2 2
ARF6/GDP/GULP/ACAP1 -0.18 0.2 -9999 0 -0.5 110 110
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.064 0.18 -9999 0 -0.53 59 59
ACAP1 0.001 0.076 -9999 0 -0.38 16 16
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.08 0.22 -9999 0 -0.67 59 59
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.11 0.3 -9999 0 -0.82 74 74
CYTH3 0.009 0.041 -9999 0 -0.64 2 2
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 138 138
endosomal lumen acidification 0 0 -9999 0 -0.001 153 153
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.32 -9999 0 -0.82 88 88
GNAQ/ARNO 0.009 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 45 45
MET -0.11 0.16 -9999 0 -0.31 179 179
GNA14 -0.18 0.35 -9999 0 -0.82 114 114
GNA15 -0.014 0.095 -9999 0 -0.33 39 39
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 140 140
GNA11 -0.004 0.12 -9999 0 -0.82 10 10
LHCGR -0.097 0.27 -9999 0 -0.76 66 66
AGTR1 -0.32 0.41 -9999 0 -0.81 196 196
desensitization of G-protein coupled receptor protein signaling pathway -0.079 0.22 -9999 0 -0.67 59 59
IPCEF1/ARNO -0.056 0.16 -9999 0 -0.43 74 74
alphaIIb/beta3 Integrin -0.081 0.22 -9999 0 -0.67 59 59
BMP receptor signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.26 0.32 -9999 0 -0.59 216 216
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.046 0.21 -9999 0 -0.69 41 41
SMAD9 -0.22 0.28 -9999 0 -0.59 164 164
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.093 0.2 -9999 0 -0.56 27 27
BMP7/USAG1 -0.32 0.31 -9999 0 -0.63 252 252
SMAD5/SKI -0.081 0.19 -9999 0 -0.52 27 27
SMAD1 0.02 0.044 -9999 0 -10000 0 0
BMP2 -0.019 0.16 -9999 0 -0.82 19 19
SMAD1/SMAD1/SMAD4 -0.001 0.001 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.26 0.39 -9999 0 -0.82 160 160
BMPR1A-1B/BAMBI -0.18 0.26 -9999 0 -0.55 160 160
AHSG -0.019 0.087 -9999 0 -0.31 39 39
CER1 0 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.038 0.14 -9999 0 -0.55 32 32
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.075 0.19 -9999 0 -0.61 31 31
BMP2-4 (homodimer) -0.044 0.16 -9999 0 -0.63 32 32
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 160 160
RGMA -0.016 0.15 -9999 0 -0.82 17 17
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.086 0.18 -9999 0 -0.57 28 28
BMP2-4/USAG1 -0.32 0.3 -9999 0 -0.57 268 268
SMAD6/SMURF1/SMAD5 -0.081 0.19 -9999 0 -0.52 27 27
SOSTDC1 -0.42 0.41 -9999 0 -0.81 253 253
BMP7/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 160 160
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0.015 -9999 0 -0.31 1 1
HFE2 0.001 0.033 -9999 0 -0.31 5 5
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.049 0.16 -9999 0 -0.55 41 41
SMAD5/SMAD5/SMAD4 -0.081 0.19 -9999 0 -0.52 27 27
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.092 0.14 -9999 0 -0.48 28 28
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.017 0.057 -9999 0 -0.4 1 1
SMAD1/SKI 0.026 0.042 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.05 0.14 -9999 0 -0.56 32 32
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.35 -9999 0 -0.72 143 143
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.008 0.064 -9999 0 -0.54 7 7
BMPR1A-1B (homodimer) -0.2 0.29 -9999 0 -0.63 160 160
CHRDL1 -0.57 0.38 -9999 0 -0.82 346 346
ENDOFIN/SMAD1 0.026 0.042 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.006 0.008 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.081 -9999 0 -0.36 20 20
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.42 0.28 -9999 0 -0.58 352 352
BMP2-4/GREM1 -0.17 0.28 -9999 0 -0.6 134 134
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.19 0.28 -9999 0 -0.55 164 164
SMAD1/SMAD6 0.026 0.042 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.013 0.015 -9999 0 -0.31 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.065 0.16 -9999 0 -0.49 28 28
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.001 0.099 -9999 0 -0.82 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.19 0.31 -9999 0 -0.79 84 84
CHRD -0.004 0.12 -9999 0 -0.82 10 10
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.091 0.19 -9999 0 -0.6 28 28
BMP4 -0.013 0.14 -9999 0 -0.64 20 20
FST -0.19 0.35 -9999 0 -0.78 127 127
BMP2-4/NOG -0.075 0.18 -9999 0 -0.55 63 63
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.15 0.22 -9999 0 -0.46 160 160
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.087 0.2 -10000 0 -0.56 76 76
cell-cell adhesion 0.15 0.18 0.54 11 -10000 0 11
Ephrin B/EPHB2/RasGAP -0.014 0.068 -10000 0 -0.46 10 10
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.081 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.21 0.27 -10000 0 -0.55 190 190
HRAS/GDP -0.13 0.17 -10000 0 -0.49 13 13
Ephrin B/EPHB1/GRB7 -0.21 0.24 -10000 0 -0.5 195 195
Endophilin/SYNJ1 0.025 0.071 -10000 0 -0.43 10 10
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.19 0.23 -10000 0 -0.47 195 195
endothelial cell migration -0.003 0.036 -10000 0 -0.46 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.042 0.12 -10000 0 -0.31 82 82
PAK1 0.033 0.072 -10000 0 -0.43 10 10
HRAS 0.012 0.021 -10000 0 -0.31 2 2
RRAS 0.025 0.073 -10000 0 -0.44 10 10
DNM1 -0.015 0.15 -10000 0 -0.79 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.24 -10000 0 -0.45 195 195
lamellipodium assembly -0.15 0.18 -10000 0 -0.54 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.11 0.18 -10000 0 -0.33 190 190
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.065 -10000 0 -0.82 3 3
EPHB3 -0.19 0.16 -10000 0 -0.31 298 298
EPHB1 -0.31 0.4 -10000 0 -0.82 190 190
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.07 0.17 -10000 0 -0.46 11 11
Ephrin B/EPHB2 -0.014 0.069 -10000 0 -0.47 10 10
Ephrin B/EPHB3 -0.086 0.087 -10000 0 -0.57 7 7
JNK cascade -0.15 0.24 -10000 0 -0.45 192 192
Ephrin B/EPHB1 -0.19 0.23 -10000 0 -0.48 195 195
RAP1/GDP -0.054 0.15 -10000 0 -0.43 7 7
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.011 0.12 -10000 0 -0.45 25 25
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.2 0.25 -10000 0 -0.5 192 192
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.19 -10000 0 -0.51 18 18
Rap1/GTP -0.15 0.18 -10000 0 -0.55 11 11
axon guidance -0.086 0.2 -10000 0 -0.55 76 76
MAPK3 -0.08 0.16 -10000 0 -0.38 11 11
MAPK1 -0.08 0.16 -10000 0 -0.38 11 11
Rac1/GDP -0.046 0.17 -10000 0 -0.46 7 7
actin cytoskeleton reorganization -0.11 0.13 -10000 0 -0.45 6 6
CDC42/GDP -0.046 0.17 -10000 0 -0.46 7 7
PI3K -0.003 0.036 -10000 0 -0.47 3 3
EFNA5 -0.11 0.3 -10000 0 -0.81 75 75
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.055 -10000 0 -0.33 10 10
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.15 0.18 -10000 0 -0.53 12 12
PTK2 0.042 0.052 -10000 0 -10000 0 0
MAP4K4 -0.15 0.24 -10000 0 -0.46 192 192
SRC 0.013 0.015 -10000 0 -0.31 1 1
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.07 0.18 -10000 0 -0.54 3 3
MAP2K1 -0.092 0.17 -10000 0 -0.3 190 190
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.19 0.24 -10000 0 -0.49 192 192
cell migration -0.088 0.19 -10000 0 -0.35 60 60
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.025 0.072 -10000 0 -0.44 10 10
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.021 0.17 -10000 0 -0.44 61 61
HRAS/GTP -0.16 0.2 -10000 0 -0.4 197 197
Ephrin B1/EPHB1-2 -0.2 0.25 -10000 0 -0.5 192 192
cell adhesion mediated by integrin 0.013 0.075 0.5 7 -10000 0 7
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.18 0.21 -10000 0 -0.43 197 197
RAC1-CDC42/GTP -0.21 0.21 -10000 0 -0.49 147 147
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.054 0.15 -10000 0 -0.52 3 3
ruffle organization -0.11 0.22 -10000 0 -0.55 11 11
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.018 0.11 -10000 0 -0.45 24 24
Ephrin B/EPHB2/KALRN -0.014 0.068 -10000 0 -0.46 10 10
ROCK1 -0.074 0.081 -10000 0 -10000 0 0
RAS family/GDP -0.084 0.11 -10000 0 -0.52 3 3
Rac1/GTP -0.16 0.2 -10000 0 -0.58 11 11
Ephrin B/EPHB1/Src/Paxillin -0.11 0.18 -10000 0 -0.33 195 195
Coregulation of Androgen receptor activity

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
NRIP1 -0.015 0.064 -10000 0 -0.36 13 13
SVIL -0.006 0.031 -10000 0 -10000 0 0
ZNF318 0.061 0.093 -10000 0 -0.82 1 1
JMJD2C -0.065 0.069 -10000 0 -0.12 279 279
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.62 205 205
CARM1 0.012 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.023 -10000 0 -10000 0 0
AKT1 0.026 0.019 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.025 0.019 -10000 0 -10000 0 0
MAK 0.05 0.13 0.22 5 -0.8 7 12
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.06 -10000 0 -0.82 2 2
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.068 0.24 -10000 0 -0.82 47 47
NCOA6 -0.007 0.047 -10000 0 -0.82 1 1
DNA-PK 0.058 0.084 -10000 0 -10000 0 0
NCOA4 0.011 0.004 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.012 0.15 -10000 0 -1 7 7
XRCC5 0.025 0.018 -10000 0 -10000 0 0
UBE3A -0.016 0.047 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.31 0.33 -10000 0 -0.66 213 213
FHL2 -0.16 0.36 -10000 0 -1.3 39 39
RANBP9 -0.005 0.029 -10000 0 -10000 0 0
JMJD1A 0.003 0.037 -10000 0 -0.12 36 36
CDK6 0.009 0.065 -10000 0 -0.82 3 3
TGFB1I1 -0.006 0.031 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.29 0.3 -10000 0 -0.63 208 208
XRCC6 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.32 -10000 0 -0.63 231 231
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.046 0.05 -10000 0 -10000 0 0
BRCA1 -0.006 0.031 -10000 0 -10000 0 0
TCF4 0.035 0.034 -10000 0 -10000 0 0
CDKN2A -0.11 0.16 -10000 0 -0.31 142 142
SRF 0.028 0.039 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -1.3 4 4
KLK3 -0.44 0.71 -10000 0 -1.6 138 138
TMF1 0.006 0.053 -10000 0 -0.82 2 2
HNRNPA1 0.031 0.028 -10000 0 -10000 0 0
AOF2 -0.022 0.034 -10000 0 -0.075 138 138
APPL1 0.052 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.27 0.29 -10000 0 -0.61 205 205
AR -0.38 0.42 -10000 0 -0.86 205 205
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.031 0.028 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.025 0.018 -10000 0 -10000 0 0
PA2G4 0.036 0.036 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.25 0.28 -10000 0 -0.56 205 205
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.29 -10000 0 -0.62 205 205
LATS2 0.029 0.047 -10000 0 -0.82 1 1
T-DHT/AR/PRX1 -0.24 0.28 -10000 0 -0.56 205 205
Cyclin D3/CDK11 p58 0 0.003 -10000 0 -10000 0 0
VAV3 -0.012 0.093 -10000 0 -0.82 6 6
KLK2 -0.77 0.62 -10000 0 -1.3 278 278
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.67 212 212
TMPRSS2 -0.19 0.31 -10000 0 -1.3 33 33
CCND1 0.001 0.051 -10000 0 -0.31 12 12
PIAS1 -0.016 0.047 -10000 0 -10000 0 0
mol:T-DHT -0.032 0.041 -10000 0 -0.082 164 164
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.036 0.077 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.28 0.3 -10000 0 -0.62 207 207
CMTM2 0.014 0.026 -10000 0 -0.31 3 3
SNURF -0.037 0.2 -10000 0 -0.82 29 29
ZMIZ1 -0.013 0.051 -10000 0 -0.8 1 1
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.031 0.028 -10000 0 -10000 0 0
FKBP4 -0.005 0.029 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.007 0.044 -9999 0 -0.31 9 9
CCL5 -0.043 0.2 -9999 0 -0.71 38 38
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -9999 0 -0.49 47 47
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.092 0.15 -9999 0 -0.63 22 22
Syndecan-1/Syntenin -0.092 0.15 -9999 0 -0.63 22 22
MAPK3 -0.069 0.14 -9999 0 -0.6 19 19
HGF/MET -0.17 0.24 -9999 0 -0.68 74 74
TGFB1/TGF beta receptor Type II 0.007 0.044 -9999 0 -0.31 9 9
BSG 0.013 0.015 -9999 0 -0.31 1 1
keratinocyte migration -0.09 0.15 -9999 0 -0.62 22 22
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.66 51 51
Syndecan-1/CD147 -0.081 0.15 -9999 0 -0.6 22 22
Syndecan-1/Syntenin/PIP2 -0.099 0.14 -9999 0 -0.61 22 22
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.097 0.14 -9999 0 -0.59 22 22
MMP7 -0.18 0.22 -9999 0 -0.37 246 246
HGF -0.11 0.3 -9999 0 -0.82 74 74
Syndecan-1/CASK -0.1 0.15 -9999 0 -0.47 47 47
Syndecan-1/HGF/MET -0.2 0.24 -9999 0 -0.64 87 87
regulation of cell adhesion -0.059 0.14 -9999 0 -0.57 19 19
HPSE -0.017 0.14 -9999 0 -0.51 28 28
positive regulation of cell migration -0.1 0.16 -9999 0 -0.49 47 47
SDC1 -0.11 0.16 -9999 0 -0.49 47 47
Syndecan-1/Collagen -0.1 0.16 -9999 0 -0.49 47 47
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.11 0.16 -9999 0 -0.31 179 179
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.081 0.24 -9999 0 -0.57 79 79
MAPK1 -0.069 0.14 -9999 0 -0.6 19 19
homophilic cell adhesion -0.1 0.16 -9999 0 -0.48 47 47
MMP1 -0.14 0.16 -9999 0 -0.31 232 232
IL6-mediated signaling events

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.06 0.21 -10000 0 -0.63 29 29
CRP -0.065 0.22 -10000 0 -0.63 32 32
cell cycle arrest -0.082 0.24 -10000 0 -0.71 35 35
TIMP1 -0.16 0.22 -10000 0 -0.59 45 45
IL6ST -0.11 0.29 -10000 0 -0.82 71 71
Rac1/GDP -0.09 0.25 -10000 0 -0.61 61 61
AP1 -0.19 0.32 -10000 0 -0.7 123 123
GAB2 0.014 0.001 -10000 0 -10000 0 0
TNFSF11 -0.1 0.23 -10000 0 -0.66 25 25
HSP90B1 0.022 0.043 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
MAPK14 -0.1 0.3 -10000 0 -0.8 57 57
AKT1 0.053 0.057 -10000 0 -1.1 1 1
FOXO1 0.059 0.053 -10000 0 -0.98 1 1
MAP2K6 -0.11 0.29 -10000 0 -0.63 82 82
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.078 0.24 -10000 0 -0.63 48 48
MITF -0.093 0.26 -10000 0 -0.58 72 72
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.013 0 -10000 0 -10000 0 0
A2M 0.025 0.006 -10000 0 -10000 0 0
CEBPB 0.022 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.023 0.086 -10000 0 -0.49 1 1
STAT3 -0.095 0.25 -10000 0 -0.76 36 36
STAT1 -0.011 0.023 -10000 0 -10000 0 0
CEBPD -0.06 0.21 -10000 0 -0.63 29 29
PIK3CA 0.01 0.065 -10000 0 -0.82 3 3
PI3K 0.019 0.051 -10000 0 -0.62 3 3
JUN -0.17 0.35 -10000 0 -0.82 110 110
PIAS3/MITF -0.08 0.25 -10000 0 -0.62 54 54
MAPK11 -0.1 0.3 -10000 0 -0.77 61 61
STAT3 (dimer)/FOXO1 -0.011 0.2 -10000 0 -0.57 23 23
GRB2/SOS1/GAB family -0.12 0.2 -10000 0 -0.68 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.26 -10000 0 -0.47 127 127
GRB2 0.014 0 -10000 0 -10000 0 0
JAK2 0.01 0.053 -10000 0 -0.82 2 2
LBP -0.063 0.2 -10000 0 -0.6 16 16
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.014 0.005 -10000 0 -10000 0 0
MYC -0.075 0.27 -10000 0 -0.89 28 28
FGG -0.069 0.22 -10000 0 -0.65 28 28
macrophage differentiation -0.082 0.24 -10000 0 -0.71 35 35
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.29 -10000 0 -0.56 155 155
JUNB -0.065 0.23 -10000 0 -0.71 30 30
FOS -0.2 0.36 -10000 0 -0.82 128 128
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.1 0.28 -10000 0 -0.5 122 122
STAT1/PIAS1 -0.085 0.24 -10000 0 -0.53 73 73
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.061 -10000 0 -0.59 3 3
STAT3 (dimer) -0.092 0.24 -10000 0 -0.74 35 35
PRKCD -0.066 0.23 -10000 0 -0.63 41 41
IL6R -0.017 0.16 -10000 0 -0.82 18 18
SOCS3 -0.12 0.37 -10000 0 -1 54 54
gp130 (dimer)/JAK1/JAK1/LMO4 -0.06 0.2 -10000 0 -0.54 71 71
Rac1/GTP -0.11 0.24 -10000 0 -0.62 61 61
HCK -0.008 0.08 -10000 0 -0.31 31 31
MAPKKK cascade 0.009 0.077 -10000 0 -0.98 1 1
bone resorption -0.097 0.22 -10000 0 -0.62 28 28
IRF1 -0.06 0.21 -10000 0 -0.63 28 28
mol:GDP -0.1 0.26 -10000 0 -0.58 78 78
SOS1 0.013 0.001 -10000 0 -10000 0 0
VAV1 -0.1 0.27 -10000 0 -0.6 77 77
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.3 -10000 0 -0.8 58 58
PTPN11 -0.011 0.059 -10000 0 -1.2 1 1
IL6/IL6RA -0.15 0.28 -10000 0 -0.66 109 109
gp130 (dimer)/TYK2/TYK2/LMO4 -0.065 0.2 -10000 0 -0.54 71 71
gp130 (dimer)/JAK2/JAK2/LMO4 -0.067 0.2 -10000 0 -0.56 71 71
IL6 -0.17 0.33 -10000 0 -0.71 124 124
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE -0.079 0.15 -10000 0 -0.32 133 133
PIAS1 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.11 0.26 -10000 0 -0.46 142 142
LMO4 0.012 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.11 0.23 0.38 1 -0.75 35 36
MCL1 0.059 0.048 -10000 0 -0.88 1 1
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.022 0.16 -10000 0 -0.45 27 27
TBX21 -0.11 0.43 -10000 0 -1 66 66
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 -0.019 0.12 -10000 0 -0.42 24 24
GADD45B -0.086 0.38 -10000 0 -0.97 55 55
IL12RB2 -0.015 0.16 -10000 0 -0.72 21 21
GADD45G -0.069 0.34 -10000 0 -0.92 44 44
natural killer cell activation 0.003 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.035 0.15 -10000 0 -0.41 58 58
IL2RA -0.045 0.19 -10000 0 -0.57 49 49
IFNG -0.11 0.28 -10000 0 -0.72 78 78
STAT3 (dimer) -0.068 0.32 -10000 0 -0.74 64 64
HLA-DRB5 -0.041 0.13 -10000 0 -0.35 70 70
FASLG -0.13 0.46 -10000 0 -1.2 65 65
NF kappa B2 p52/RelB -0.16 0.32 -10000 0 -0.86 66 66
CD4 0 0.059 -10000 0 -0.32 16 16
SOCS1 0.009 0.048 -10000 0 -0.82 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.096 0.27 -10000 0 -0.72 71 71
CD3E -0.072 0.24 -10000 0 -0.75 52 52
CD3G -0.15 0.32 -10000 0 -0.79 98 98
IL12Rbeta2/JAK2 -0.002 0.13 -10000 0 -0.63 19 19
CCL3 -0.1 0.42 -10000 0 -1.1 51 51
CCL4 -0.15 0.51 -10000 0 -1.3 66 66
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
IL18/IL18R -0.028 0.19 -10000 0 -0.56 45 45
NOS2 -0.083 0.34 -10000 0 -0.81 60 60
IL12/IL12R/TYK2/JAK2/SPHK2 -0.02 0.15 -10000 0 -0.42 29 29
IL1R1 -0.082 0.37 -10000 0 -0.96 51 51
IL4 0.001 0.022 -10000 0 -10000 0 0
JAK2 0.013 0.057 -10000 0 -0.83 2 2
EntrezGene:6957 -0.006 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.24 0.56 -10000 0 -1.2 103 103
RAB7A -0.037 0.29 -10000 0 -0.69 48 48
lysosomal transport -0.032 0.28 -10000 0 -0.65 50 50
FOS -0.4 0.65 -10000 0 -1.3 162 162
STAT4 (dimer) -0.072 0.35 -10000 0 -0.82 61 61
STAT5A (dimer) -0.21 0.36 -10000 0 -0.87 91 91
GZMA -0.1 0.41 -10000 0 -1 56 56
GZMB -0.097 0.39 -10000 0 -1 51 51
HLX 0.004 0.055 -10000 0 -0.31 14 14
LCK -0.1 0.42 -10000 0 -0.97 69 69
TCR/CD3/MHC II/CD4 -0.19 0.34 -10000 0 -0.74 99 99
IL2/IL2R -0.08 0.21 -10000 0 -0.65 47 47
MAPK14 -0.064 0.35 -10000 0 -0.8 64 64
CCR5 -0.093 0.4 -10000 0 -1.2 43 43
IL1B -0.053 0.23 -10000 0 -0.78 43 43
STAT6 -0.003 0.11 -10000 0 -10000 0 0
STAT4 -0.024 0.14 -10000 0 -0.46 39 39
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.048 -10000 0 -0.31 11 11
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B 0 0.095 -10000 0 -0.55 11 11
CD8A -0.047 0.22 -10000 0 -0.82 35 35
CD8B -0.088 0.26 -10000 0 -0.72 67 67
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.022 0.16 0.45 27 -10000 0 27
IL2RB -0.015 0.13 -10000 0 -0.5 27 27
proteasomal ubiquitin-dependent protein catabolic process -0.061 0.32 -10000 0 -0.74 61 61
IL2RG -0.047 0.19 -10000 0 -0.54 53 53
IL12 -0.056 0.21 -10000 0 -0.63 56 56
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.024 0.15 -10000 0 -0.63 26 26
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.074 0.26 -10000 0 -0.8 54 54
IL12/IL12R/TYK2/JAK2 -0.12 0.47 -10000 0 -1 71 71
MAP2K3 -0.066 0.34 -10000 0 -0.78 65 65
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.073 0.35 -10000 0 -0.82 64 64
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.027 0.13 -10000 0 -0.82 7 7
IL18RAP -0.019 0.17 -10000 0 -0.8 21 21
IL12Rbeta1/TYK2 -0.003 0.093 -10000 0 -0.64 4 4
EOMES -0.15 0.43 -10000 0 -1.5 44 44
STAT1 (dimer) -0.13 0.36 -10000 0 -0.77 93 93
T cell proliferation -0.045 0.27 -10000 0 -0.61 56 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.026 0.14 -10000 0 -0.42 47 47
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.24 -10000 0 -0.69 59 59
ATF2 -0.069 0.33 -10000 0 -0.75 61 61
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.002 0.046 -9999 0 -1 1 1
forebrain development -0.32 0.29 -9999 0 -0.56 253 253
GNAO1 -0.02 0.15 -9999 0 -0.82 16 16
SMO/beta Arrestin2 0.011 0.031 -9999 0 -0.62 1 1
SMO 0.006 0.038 -9999 0 -0.82 1 1
ARRB2 0.008 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.056 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.029 -9999 0 -0.49 1 1
GNAI1 0.008 0.038 -9999 0 -0.83 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.24 0.19 -9999 0 -0.51 135 135
SAP30 0.012 0.038 -9999 0 -0.82 1 1
mol:GDP 0.006 0.038 -9999 0 -0.81 1 1
MIM/GLI2A -0.007 0.043 -9999 0 -0.31 1 1
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GLI2 0.033 0.061 -9999 0 -10000 0 0
GLI3 0.039 0.059 -9999 0 -10000 0 0
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.012 0.038 -9999 0 -0.82 1 1
Gi family/GTP 0.007 0.07 -9999 0 -0.33 18 18
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.029 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.058 -9999 0 -10000 0 0
FOXA2 -0.66 0.66 -9999 0 -1.3 236 236
neural tube patterning -0.32 0.29 -9999 0 -0.56 253 253
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.022 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.007 0.043 -9999 0 -0.31 1 1
embryonic limb morphogenesis -0.32 0.29 -9999 0 -0.56 253 253
SUFU 0.016 0.021 -9999 0 -10000 0 0
LGALS3 -0.1 0.16 -9999 0 -0.31 171 171
catabolic process 0.061 0.068 -9999 0 -10000 0 0
GLI3A/CBP -0.19 0.2 -9999 0 -0.38 253 253
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.32 0.29 -9999 0 -0.57 253 253
RAB23 0.007 0.075 -9999 0 -0.82 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.034 0.079 -9999 0 -0.4 1 1
GNAZ 0.01 0.006 -9999 0 -10000 0 0
RBBP4 0.009 0.065 -9999 0 -0.82 3 3
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.057 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.013 0.063 -9999 0 -0.54 1 1
PTCH1 -0.28 0.27 -9999 0 -0.62 135 135
MIM/GLI1 -0.45 0.39 -9999 0 -0.76 248 248
CREBBP -0.19 0.2 -9999 0 -0.38 253 253
Su(fu)/SIN3/HDAC complex 0.056 0.027 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.11 0.39 -9999 0 -1.3 43 43
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.035 0.11 -9999 0 -0.39 19 19
ATF2/c-Jun -0.22 0.42 -9999 0 -0.97 111 111
MAPK11 -0.035 0.11 -9999 0 -0.39 19 19
MITF -0.029 0.13 -9999 0 -0.4 43 43
MAPKAPK5 -0.029 0.13 -9999 0 -0.47 19 19
KRT8 -0.029 0.13 -9999 0 -0.4 43 43
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.048 0.17 -9999 0 -0.51 43 43
CEBPB -0.029 0.13 -9999 0 -0.4 43 43
SLC9A1 -0.029 0.13 -9999 0 -0.4 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.072 0.19 -9999 0 -0.54 39 39
p38alpha-beta/MNK1 -0.024 0.14 -9999 0 -0.49 19 19
JUN -0.22 0.42 -9999 0 -0.96 111 111
PPARGC1A -0.23 0.25 -9999 0 -0.46 256 256
USF1 -0.029 0.13 -9999 0 -0.47 19 19
RAB5/GDP/GDI1 -0.038 0.083 -9999 0 -0.35 19 19
NOS2 -0.048 0.16 -9999 0 -0.54 19 19
DDIT3 -0.031 0.13 -9999 0 -0.4 43 43
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.012 0.11 -9999 0 -0.39 18 18
p38alpha-beta/HBP1 -0.024 0.14 -9999 0 -0.49 19 19
CREB1 -0.049 0.16 -9999 0 -0.46 43 43
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.015 0.12 -9999 0 -0.44 18 18
RPS6KA4 -0.029 0.13 -9999 0 -0.47 19 19
PLA2G4A -0.048 0.2 -9999 0 -0.6 44 44
GDI1 -0.029 0.13 -9999 0 -0.4 43 43
TP53 -0.037 0.16 -9999 0 -0.5 43 43
RPS6KA5 -0.079 0.2 -9999 0 -0.46 89 89
ESR1 -0.064 0.21 -9999 0 -0.55 55 55
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.029 0.13 -9999 0 -0.4 44 44
MEF2A -0.029 0.13 -9999 0 -0.4 44 44
EIF4EBP1 -0.049 0.16 -9999 0 -0.45 44 44
KRT19 -0.1 0.2 -9999 0 -0.54 55 55
ELK4 -0.029 0.13 -9999 0 -0.47 19 19
ATF6 -0.029 0.13 -9999 0 -0.4 43 43
ATF1 -0.05 0.16 -9999 0 -0.47 44 44
p38alpha-beta/MAPKAPK2 -0.024 0.14 -9999 0 -0.49 19 19
p38alpha-beta/MAPKAPK3 -0.024 0.14 -9999 0 -0.49 19 19
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.082 0.062 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.18 -9999 0 -0.64 40 40
positive regulation of JNK cascade -0.16 0.2 -9999 0 -0.6 68 68
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.64 42 42
CCL5 -0.043 0.2 -9999 0 -0.71 38 38
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG -0.001 0.039 -9999 0 -0.29 8 8
ADAM12 -0.068 0.14 -9999 0 -0.31 121 121
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.065 0.045 -9999 0 -0.23 4 4
Syndecan-4/Laminin alpha1 -0.17 0.21 -9999 0 -0.68 49 49
Syndecan-4/CXCL12/CXCR4 -0.17 0.22 -9999 0 -0.65 68 68
Syndecan-4/Laminin alpha3 -0.15 0.19 -9999 0 -0.66 45 45
MDK -0.088 0.15 -9999 0 -0.31 152 152
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.64 42 42
Syndecan-4/Midkine -0.18 0.19 -9999 0 -0.64 42 42
FZD7 0.007 0.075 -9999 0 -0.82 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.59 41 41
THBS1 -0.011 0.086 -9999 0 -0.31 37 37
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.66 41 41
positive regulation of MAPKKK cascade -0.16 0.2 -9999 0 -0.6 68 68
Syndecan-4/TACI -0.24 0.26 -9999 0 -0.63 120 120
CXCR4 0.012 0.021 -9999 0 -0.31 2 2
cell adhesion -0.068 0.096 -9999 0 -0.44 23 23
Syndecan-4/Dynamin -0.13 0.18 -9999 0 -0.64 40 40
Syndecan-4/TSP1 -0.14 0.18 -9999 0 -0.64 41 41
Syndecan-4/GIPC -0.13 0.18 -9999 0 -0.64 40 40
Syndecan-4/RANTES -0.16 0.22 -9999 0 -0.74 48 48
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.049 0.22 -9999 0 -0.8 37 37
LAMA3 -0.026 0.16 -9999 0 -0.58 32 32
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.015 0.17 -9999 0 -0.74 23 23
Syndecan-4/alpha-Actinin -0.13 0.18 -9999 0 -0.64 40 40
TFPI -0.033 0.19 -9999 0 -0.82 27 27
F2 -0.007 0.053 -9999 0 -0.31 14 14
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.17 0.21 -9999 0 -0.66 55 55
ACTN1 0.013 0.015 -9999 0 -0.31 1 1
TNC -0.11 0.17 -9999 0 -0.32 184 184
Syndecan-4/CXCL12 -0.18 0.23 -9999 0 -0.68 68 68
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.072 0.25 -9999 0 -0.82 50 50
TNFRSF13B -0.19 0.35 -9999 0 -0.79 120 120
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.012 0.038 -9999 0 -0.82 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.65 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.32 335 335
cell migration -0.022 0.017 -9999 0 -10000 0 0
PRKCD 0.008 0.015 -9999 0 -10000 0 0
vasculogenesis -0.14 0.17 -9999 0 -0.61 41 41
SDC4 -0.15 0.19 -9999 0 -0.69 40 40
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.69 41 41
Syndecan-4/PI-4-5-P2/PKC alpha -0.051 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.18 -9999 0 -0.64 40 40
MMP9 -0.083 0.24 -9999 0 -0.57 78 78
Rac1/GTP -0.074 0.094 -9999 0 -0.46 23 23
cytoskeleton organization -0.13 0.17 -9999 0 -0.62 40 40
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.2 -9999 0 -0.64 57 57
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.043 0.12 -9999 0 -0.46 28 28
alphaM/beta2 Integrin/GPIbA -0.053 0.14 -9999 0 -0.57 26 26
alphaM/beta2 Integrin/proMMP-9 -0.091 0.19 -9999 0 -0.58 54 54
PLAUR -0.09 0.15 -9999 0 -0.31 155 155
HMGB1 0.002 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.034 0.098 -9999 0 -0.43 20 20
AGER -0.059 0.22 -9999 0 -0.78 38 38
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.007 0.08 -9999 0 -0.31 31 31
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.12 0.19 -9999 0 -0.6 46 46
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.081 0.24 -9999 0 -0.57 79 79
CYR61 -0.24 0.38 -9999 0 -0.82 147 147
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.072 0.09 -9999 0 -0.39 14 14
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.003 0.1 -9999 0 -0.58 13 13
MYH2 -0.1 0.12 -9999 0 -0.46 16 16
MST1R 0.001 0.095 -9999 0 -0.65 9 9
leukocyte activation during inflammatory response -0.04 0.093 -9999 0 -0.42 14 14
APOB -0.011 0.08 -9999 0 -0.31 32 32
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.018 0.15 -9999 0 -0.64 23 23
alphaM/beta2 Integrin/CTGF -0.11 0.22 -9999 0 -0.56 89 89
alphaM/beta2 Integrin -0.095 0.11 -9999 0 -0.35 47 47
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.083 0.15 -9999 0 -0.31 144 144
phagocytosis triggered by activation of immune response cell surface activating receptor -0.094 0.11 -9999 0 -0.34 47 47
cell adhesion -0.053 0.14 -9999 0 -0.56 26 26
NFKB1 -0.13 0.29 -9999 0 -0.71 65 65
THY1 0.011 0.029 -9999 0 -0.31 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.014 0.05 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/LRP/tPA -0.034 0.1 -9999 0 -0.48 16 16
IL6 -0.23 0.46 -9999 0 -1 104 104
ITGB2 -0.018 0.086 -9999 0 -0.34 28 28
elevation of cytosolic calcium ion concentration -0.14 0.16 -9999 0 -0.5 42 42
alphaM/beta2 Integrin/JAM2/JAM3 -0.031 0.1 -9999 0 -0.49 15 15
JAM2 0.006 0.076 -9999 0 -0.72 5 5
alphaM/beta2 Integrin/ICAM1 -0.067 0.12 -9999 0 -0.5 22 22
alphaM/beta2 Integrin/uPA/Plg -0.099 0.12 -9999 0 -0.51 21 21
RhoA/GTP -0.11 0.12 -9999 0 -0.42 39 39
positive regulation of phagocytosis -0.07 0.12 -9999 0 -0.46 20 20
Ron/MSP -0.011 0.076 -9999 0 -0.63 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.16 -9999 0 -0.5 42 42
alphaM/beta2 Integrin/uPAR -0.085 0.13 -9999 0 -0.45 35 35
PLAU -0.14 0.16 -9999 0 -0.31 226 226
PLAT 0.001 0.085 -9999 0 -0.48 12 12
actin filament polymerization -0.1 0.11 -9999 0 -0.44 16 16
MST1 0.011 0.04 -9999 0 -0.56 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.04 0.094 -9999 0 -0.45 11 11
TNF -0.18 0.39 -9999 0 -0.97 81 81
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.13 -9999 0 -0.44 38 38
fibrinolysis -0.098 0.12 -9999 0 -0.5 21 21
HCK -0.007 0.08 -9999 0 -0.31 31 31
dendritic cell antigen processing and presentation -0.094 0.11 -9999 0 -0.34 47 47
VTN -0.068 0.24 -9999 0 -0.75 52 52
alphaM/beta2 Integrin/CYR61 -0.2 0.27 -9999 0 -0.57 161 161
LPA -0.002 0.043 -9999 0 -0.31 9 9
LRP1 0.012 0.038 -9999 0 -0.82 1 1
cell migration -0.088 0.19 -9999 0 -0.57 57 57
FN1 -0.22 0.15 -9999 0 -0.31 354 354
alphaM/beta2 Integrin/Thy1 -0.035 0.099 -9999 0 -0.42 21 21
MPO 0.001 0.087 -9999 0 -0.63 8 8
KNG1 -0.015 0.079 -9999 0 -0.31 32 32
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.094 0.12 -9999 0 -0.42 24 24
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.004 0.04 -9999 0 -0.31 8 8
CTGF -0.11 0.29 -9999 0 -0.82 72 72
alphaM/beta2 Integrin/Hck -0.044 0.12 -9999 0 -0.47 30 30
ITGAM -0.023 0.11 -9999 0 -0.39 31 31
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.046 0.13 -9999 0 -0.52 26 26
HP -0.082 0.16 -9999 0 -0.82 6 6
leukocyte adhesion -0.091 0.16 -9999 0 -0.6 27 27
SELP -0.003 0.1 -9999 0 -0.58 13 13
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.093 0.22 -9999 0 -0.41 145 145
MAP3K8 -0.003 0.11 -9999 0 -0.82 8 8
FOS -0.058 0.17 -9999 0 -0.45 44 44
PRKCA -0.028 0.18 -9999 0 -0.82 23 23
PTPN7 -0.044 0.17 -9999 0 -0.46 57 57
HRAS 0.011 0.021 -9999 0 -0.31 2 2
PRKCB -0.03 0.13 -9999 0 -0.36 53 53
NRAS 0.013 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.03 0.12 -9999 0 -0.41 28 28
MAP2K1 -0.025 0.15 -9999 0 -0.56 30 30
ELK1 0.008 0.01 -9999 0 -10000 0 0
BRAF -0.045 0.13 -9999 0 -0.57 27 27
mol:GTP -0.001 0.003 -9999 0 -0.006 127 127
MAPK1 -0.03 0.12 -9999 0 -0.41 28 28
RAF1 -0.045 0.13 -9999 0 -0.57 27 27
KRAS 0.013 0.002 -9999 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 -0.033 0.11 -10000 0 -0.31 67 67
GNB1/GNG2 -0.045 0.068 -10000 0 -0.2 48 48
AKT1 -0.013 0.1 -10000 0 -0.21 40 40
EGF -0.11 0.29 -10000 0 -0.78 76 76
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.031 0.076 -10000 0 -0.64 2 2
mol:Ca2+ -0.044 0.15 -10000 0 -0.31 75 75
LYN 0.032 0.075 -10000 0 -0.64 2 2
RhoA/GTP -0.031 0.045 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.044 0.16 -10000 0 -0.35 73 73
GNG2 0.012 0.038 -10000 0 -0.82 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.027 0.12 -10000 0 -0.55 12 12
G beta5/gamma2 -0.06 0.092 -10000 0 -0.27 49 49
PRKCH -0.052 0.16 -10000 0 -0.36 72 72
DNM1 -0.015 0.15 -10000 0 -0.79 17 17
TXA2/TP beta/beta Arrestin3 -0.013 0.055 -10000 0 -0.3 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.022 0.17 -10000 0 -0.82 21 21
G12 family/GTP -0.078 0.11 -10000 0 -0.31 73 73
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.1 0.35 16 -10000 0 16
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.22 0.37 -10000 0 -0.82 134 134
mol:IP3 -0.06 0.18 -10000 0 -0.39 75 75
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.088 0.23 -10000 0 -0.53 75 75
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.096 0.2 -10000 0 -0.39 143 143
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.024 0.08 -10000 0 -0.64 2 2
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.003 0.091 -10000 0 -0.82 6 6
PRKCB1 -0.06 0.17 -10000 0 -0.39 75 75
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.085 0.23 -10000 0 -0.54 76 76
LCK 0.022 0.096 -10000 0 -0.54 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.019 0.089 -10000 0 -0.96 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.031 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.019 0.088 -10000 0 -0.95 2 2
MAPK14 -0.019 0.11 -10000 0 -0.23 46 46
TGM2/GTP -0.073 0.2 -10000 0 -0.43 76 76
MAPK11 -0.019 0.11 -10000 0 -0.23 47 47
ARHGEF1 -0.015 0.089 -10000 0 -0.19 23 23
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.057 0.18 -10000 0 -0.39 77 77
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.052 0.15 -10000 0 -0.3 79 79
cAMP biosynthetic process -0.059 0.17 -10000 0 -0.36 74 74
Gq family/GTP/EBP50 -0.044 0.12 -10000 0 -0.25 121 121
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.032 0.075 -10000 0 -0.64 2 2
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.018 0.1 -10000 0 -0.31 16 16
VCAM1 -0.038 0.14 -10000 0 -0.3 75 75
TP beta/Gq family/GDP/G beta5/gamma2 -0.027 0.12 -10000 0 -0.55 12 12
platelet activation -0.026 0.15 -10000 0 -0.3 72 72
PGI2/IP -0.008 0.07 -10000 0 -0.64 6 6
PRKACA -0.001 0.11 -10000 0 -0.43 25 25
Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.5 12 12
TXA2/TP beta/beta Arrestin2 -0.023 0.12 -10000 0 -0.66 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.007 0.11 -10000 0 -0.41 25 25
mol:DAG -0.068 0.19 -10000 0 -0.44 75 75
EGFR 0.007 0.075 -10000 0 -0.82 4 4
TXA2/TP alpha -0.083 0.22 -10000 0 -0.5 74 74
Gq family/GTP -0.076 0.13 -10000 0 -0.3 121 121
YES1 0.032 0.075 -10000 0 -0.64 2 2
GNAI2/GTP -0.017 0.077 -10000 0 -0.8 2 2
PGD2/DP -0.027 0.13 -10000 0 -0.64 21 21
SLC9A3R1 0.012 0.021 -10000 0 -0.31 2 2
FYN 0.032 0.075 -10000 0 -0.64 2 2
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.014 0.095 -10000 0 -0.33 39 39
PGK/cGMP -0.15 0.24 -10000 0 -0.55 134 134
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.031 0.1 -10000 0 -0.66 6 6
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.064 0.18 -10000 0 -0.4 80 80
PRKCB -0.062 0.17 -10000 0 -0.38 76 76
PRKCE -0.055 0.17 -10000 0 -0.38 74 74
PRKCD -0.055 0.17 -10000 0 -0.39 73 73
PRKCG -0.059 0.18 -10000 0 -0.4 74 74
muscle contraction -0.075 0.22 -10000 0 -0.5 75 75
PRKCZ -0.044 0.16 -10000 0 -0.35 73 73
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.019 0.09 -10000 0 -0.98 2 2
PRKCQ -0.053 0.17 -10000 0 -0.36 76 76
MAPKKK cascade -0.075 0.2 -10000 0 -0.47 76 76
SELE -0.058 0.18 -10000 0 -0.43 74 74
TP beta/GNAI2/GDP/G beta/gamma -0.019 0.093 -10000 0 -1.1 2 2
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.35 -10000 0 -0.82 114 114
chemotaxis -0.098 0.26 -10000 0 -0.62 75 75
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.004 0.12 -10000 0 -0.82 10 10
Rac1/GTP 0.002 0.004 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0.021 -9999 0 -0.31 2 2
EGFR 0.007 0.075 -9999 0 -0.82 4 4
EGF/EGFR -0.076 0.17 -9999 0 -0.45 80 80
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.071 0.16 -9999 0 -0.46 74 74
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.009 0.048 -9999 0 -0.41 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 76 76
EGF/EGFR dimer/SHC -0.084 0.19 -9999 0 -0.54 74 74
mol:GDP -0.07 0.16 -9999 0 -0.45 74 74
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.004 0.085 -9999 0 -0.73 6 6
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.065 0.15 -9999 0 -0.42 74 74
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.066 0.15 -9999 0 -0.43 74 74
FRAP1 -0.035 0.17 -9999 0 -0.44 74 74
EGF/EGFR dimer -0.097 0.22 -9999 0 -0.63 74 74
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.072 -9999 0 -0.63 6 6
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.085 0.11 -9999 0 -0.21 210 210
TP53 -0.028 0.033 -9999 0 -10000 0 0
Senescence -0.028 0.033 -9999 0 -10000 0 0
Apoptosis -0.028 0.033 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.054 0.062 -9999 0 -10000 0 0
MDM4 0.013 0 -9999 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer -0.032 0.14 -9999 0 -0.46 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.054 0.11 -9999 0 -0.53 7 7
alphaV/beta3 Integrin/Osteopontin/Src -0.066 0.15 -9999 0 -0.61 24 24
AP1 -0.26 0.35 -9999 0 -0.85 108 108
ILK -0.032 0.15 -9999 0 -0.49 37 37
bone resorption -0.048 0.15 -9999 0 -0.64 12 12
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.051 0.12 -9999 0 -0.44 37 37
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.031 0.14 -9999 0 -0.63 24 24
alphaV/beta3 Integrin/Osteopontin -0.069 0.15 -9999 0 -0.55 37 37
MAP3K1 -0.032 0.15 -9999 0 -0.5 37 37
JUN -0.17 0.35 -9999 0 -0.82 110 110
MAPK3 -0.032 0.15 -9999 0 -0.46 37 37
MAPK1 -0.032 0.15 -9999 0 -0.46 37 37
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 -0.032 0.17 -9999 0 -0.5 44 44
ITGB3 -0.01 0.14 -9999 0 -0.81 14 14
NFKBIA -0.025 0.14 -9999 0 -0.58 7 7
FOS -0.2 0.36 -9999 0 -0.82 128 128
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.11 0.17 -9999 0 -0.69 4 4
NF kappa B1 p50/RelA -0.06 0.11 -9999 0 -0.57 4 4
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.02 0.12 -9999 0 -0.65 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.032 0.15 -9999 0 -0.5 37 37
VAV3 -0.026 0.15 -9999 0 -0.47 42 42
MAP3K14 -0.04 0.15 -9999 0 -0.5 37 37
ROCK2 -0.027 0.18 -9999 0 -0.82 24 24
SPP1 -0.082 0.2 -9999 0 -0.41 109 109
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.054 0.12 -9999 0 -0.52 12 12
MMP2 -0.18 0.29 -9999 0 -0.66 100 100
FAS signaling pathway (CD95)

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
SPTAN1 0.025 0.078 0.29 36 -10000 0 36
RFC1 0.025 0.078 0.29 36 -10000 0 36
PRKDC 0.025 0.078 0.29 36 -10000 0 36
RIPK1 0.014 0.004 -10000 0 -10000 0 0
CASP7 -0.013 0.044 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.027 0.099 0.26 5 -0.37 31 36
MAP2K4 -0.022 0.16 -10000 0 -0.53 15 15
mol:ceramide -0.02 0.14 -10000 0 -0.48 32 32
GSN 0.025 0.078 0.29 36 -10000 0 36
FASLG/FAS/FADD/FAF1/Caspase 8 -0.017 0.13 -10000 0 -0.47 31 31
FAS 0.011 0.006 -10000 0 -10000 0 0
BID -0.032 0.08 0.32 3 -10000 0 3
MAP3K1 0.005 0.097 -10000 0 -10000 0 0
MAP3K7 0.01 0.006 -10000 0 -10000 0 0
RB1 0.024 0.078 0.29 35 -0.31 1 36
CFLAR 0.014 0.004 -10000 0 -10000 0 0
HGF/MET -0.14 0.22 -10000 0 -0.61 77 77
ARHGDIB 0.022 0.081 0.29 36 -10000 0 36
FADD 0.011 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.025 0.077 -10000 0 -0.29 36 36
NFKB1 -0.052 0.093 -10000 0 -0.32 16 16
MAPK8 -0.058 0.22 -10000 0 -0.45 96 96
DFFA 0.025 0.078 0.29 36 -10000 0 36
DNA fragmentation during apoptosis 0.025 0.077 0.29 36 -10000 0 36
FAS/FADD/MET -0.058 0.077 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.002 0.088 -10000 0 -0.39 20 20
FAF1 0.011 0.007 -10000 0 -10000 0 0
PARP1 0.025 0.078 0.29 36 -10000 0 36
DFFB 0.025 0.078 0.29 36 -10000 0 36
CHUK -0.045 0.082 -10000 0 -0.73 1 1
FASLG -0.055 0.21 -10000 0 -0.66 48 48
FAS/FADD 0 0.001 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 74 74
LMNA 0.023 0.071 0.26 36 -10000 0 36
CASP6 0.025 0.078 0.29 36 -10000 0 36
CASP10 0.011 0.006 -10000 0 -10000 0 0
CASP3 0.03 0.094 0.34 39 -10000 0 39
PTPN13 0.003 0.091 -10000 0 -0.82 6 6
CASP8 0.008 0.044 0.45 3 -10000 0 3
IL6 -0.26 0.56 -10000 0 -1.4 98 98
MET -0.11 0.16 -10000 0 -0.31 179 179
ICAD/CAD 0.023 0.072 0.27 36 -10000 0 36
FASLG/FAS/FADD/FAF1/Caspase 10 -0.021 0.14 -10000 0 -0.49 32 32
activation of caspase activity by cytochrome c -0.032 0.079 0.32 3 -10000 0 3
PAK2 0.025 0.077 0.29 36 -10000 0 36
BCL2 -0.047 0.22 -10000 0 -0.82 36 36
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.037 0.21 -9999 0 -0.81 33 33
HDAC7 -0.034 0.15 -9999 0 -0.64 17 17
JUN -0.18 0.34 -9999 0 -0.82 110 110
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B 0.013 0.001 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.003 0.098 -9999 0 -0.64 11 11
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.046 0.16 -9999 0 -0.67 18 18
MAP2K6 -0.011 0.12 -9999 0 -0.78 12 12
BRM/BAF57 -0.002 0.003 -9999 0 -10000 0 0
MAP2K4 0.009 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.011 0.058 -9999 0 -10000 0 0
NCOA2 -0.074 0.24 -9999 0 -0.82 47 47
CEBPA 0.006 0.084 -9999 0 -0.82 5 5
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.069 0.15 -9999 0 -0.52 21 21
NR0B1 -0.002 0.041 -9999 0 -0.31 8 8
EGR1 -0.17 0.34 -9999 0 -0.82 104 104
RXRs/9cRA -0.13 0.058 -9999 0 -0.5 4 4
AR/RACK1/Src -0.12 0.16 -9999 0 -0.67 19 19
AR/GR -0.13 0.2 -9999 0 -0.38 128 128
GNB2L1 0.007 0.007 -9999 0 -10000 0 0
PKN1 0.013 0.001 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 -0.002 0.097 -9999 0 -0.64 11 11
T-DHT/AR/TIF2/CARM1 -0.13 0.24 -9999 0 -0.7 55 55
SRC -0.005 0.12 -9999 0 -0.55 19 19
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.4 0.57 -9999 0 -1.3 139 139
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.056 0.15 -9999 0 -0.68 19 19
TMPRSS2 -0.059 0.32 -9999 0 -1.2 32 32
RXRG -0.28 0.12 -9999 0 -0.32 433 433
mol:9cRA -0.002 0.002 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.007 0.007 -9999 0 -10000 0 0
NR2C2 -0.006 0.12 -9999 0 -0.82 11 11
KLK2 -0.48 0.43 -9999 0 -0.83 288 288
AR -0.15 0.22 -9999 0 -0.38 206 206
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.022 0.014 -9999 0 -10000 0 0
SRY 0.01 0.015 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.015 0.054 -9999 0 -0.32 13 13
T-DHT/AR/RACK1/Src -0.079 0.15 -9999 0 -0.67 19 19
positive regulation of transcription 0.013 0.015 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.005 -9999 0 -10000 0 0
NCOA1 0.013 0.009 -9999 0 -10000 0 0
SPDEF -0.028 0.1 -9999 0 -0.32 55 55
T-DHT/AR/TIF2 -0.056 0.16 -9999 0 -0.46 49 49
T-DHT/AR/Hsp90 -0.058 0.15 -9999 0 -0.68 19 19
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.008 0.12 -9999 0 -0.59 19 19
SIRT1 0.011 0.038 -9999 0 -0.82 1 1
ZMIZ2 0.023 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.019 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.077 0.14 -9999 0 -0.68 19 19
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.12 0.1 -9999 0 -0.65 7 7
EPHB2 0.008 0.065 -9999 0 -0.82 3 3
Syndecan-2/TACI -0.12 0.25 -9999 0 -0.56 118 118
LAMA1 -0.049 0.22 -9999 0 -0.8 37 37
Syndecan-2/alpha2 ITGB1 -0.071 0.11 -9999 0 -0.46 24 24
HRAS 0.012 0.021 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.065 -9999 0 -0.55 7 7
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.023 0.1 -9999 0 -0.75 2 2
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.007 0.059 -9999 0 -0.49 7 7
LAMA3 -0.026 0.16 -9999 0 -0.58 32 32
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.065 -9999 0 -0.82 3 3
Syndecan-2/MMP2 0.008 0.1 -9999 0 -0.58 13 13
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.078 0.098 -9999 0 -10000 0 0
dendrite morphogenesis 0.014 0.08 -9999 0 -0.54 10 10
Syndecan-2/GM-CSF -0.11 0.098 -9999 0 -0.56 7 7
determination of left/right symmetry 0.012 0.077 -9999 0 -0.62 7 7
Syndecan-2/PKC delta 0.018 0.067 -9999 0 -0.54 7 7
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.087 0.091 -9999 0 -0.51 7 7
MAPK1 -0.087 0.091 -9999 0 -0.51 7 7
Syndecan-2/RACK1 -0.007 0.056 -9999 0 -0.46 7 7
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.077 -9999 0 -0.62 7 7
ITGA2 -0.11 0.16 -9999 0 -0.31 188 188
MAPK8 0.015 0.11 -9999 0 -0.55 18 18
Syndecan-2/alpha2/beta1 Integrin -0.085 0.14 -9999 0 -0.51 40 40
Syndecan-2/Kininogen -0.008 0.078 -9999 0 -0.55 7 7
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.057 -9999 0 -0.43 7 7
Syndecan-2/CASK/Protein 4.1 -0.007 0.059 -9999 0 -0.5 7 7
extracellular matrix organization 0.014 0.071 -9999 0 -0.54 7 7
actin cytoskeleton reorganization -0.12 0.1 -9999 0 -0.64 7 7
Syndecan-2/Caveolin-2/Ras -0.011 0.076 -9999 0 -0.54 9 9
Syndecan-2/Laminin alpha3 -0.008 0.12 -9999 0 -0.54 24 24
Syndecan-2/RasGAP -0.007 0.053 -9999 0 -0.44 7 7
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.014 0.08 -9999 0 -0.54 10 10
GO:0007205 0.004 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.056 -9999 0 -0.42 7 7
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.19 0.35 -9999 0 -0.79 120 120
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.078 0.098 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.018 0.067 -9999 0 -0.54 7 7
TGFB1 0.007 0.044 -9999 0 -0.31 9 9
CASP3 0.027 0.062 -9999 0 -0.49 7 7
FN1 -0.22 0.15 -9999 0 -0.31 354 354
Syndecan-2/IL8 -0.037 0.12 -9999 0 -0.54 17 17
SDC2 0.012 0.077 -9999 0 -0.62 7 7
KNG1 -0.015 0.079 -9999 0 -0.31 32 32
Syndecan-2/Neurofibromin 0.018 0.067 -9999 0 -0.54 7 7
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 332 332
Syndecan-2/TGFB1 0.014 0.071 -9999 0 -0.54 7 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.007 0.059 -9999 0 -0.5 7 7
Syndecan-2/Ezrin -0.007 0.058 -9999 0 -0.49 7 7
PRKACA 0.027 0.062 -9999 0 -0.49 7 7
angiogenesis -0.037 0.12 -9999 0 -0.54 17 17
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
IL8 -0.081 0.17 -9999 0 -0.35 125 125
calcineurin-NFAT signaling pathway -0.12 0.25 -9999 0 -0.55 118 118
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.006 0.12 -9999 0 -0.77 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.15 -9999 0 -0.28 283 283
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.011 0.029 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.047 0.067 -9999 0 -0.31 4 4
PRKG1 -0.22 0.37 -9999 0 -0.82 134 134
DUSP8 0.004 0.074 -9999 0 -0.48 9 9
PGK/cGMP/p38 alpha -0.16 0.2 -9999 0 -0.46 136 136
apoptosis -0.046 0.065 -9999 0 -0.3 4 4
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.31 -9999 0 -0.82 79 79
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1/OSM/MEKK3/MKK3 -0.001 0.008 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.82 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.012 0.021 -9999 0 -0.31 2 2
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.06 0.13 -9999 0 -0.36 16 16
BLK -0.24 0.37 -9999 0 -0.75 165 165
HCK -0.007 0.08 -9999 0 -0.31 31 31
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.01 0.043 -9999 0 -0.48 3 3
TRAF6/MEKK3 -0.002 0.032 -9999 0 -0.51 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.027 0.091 -9999 0 -0.32 5 5
positive regulation of innate immune response -0.058 0.14 -9999 0 -0.39 13 13
LCK -0.01 0.11 -9999 0 -0.43 26 26
p38alpha-beta/MKP7 -0.049 0.13 -9999 0 -0.44 5 5
p38alpha-beta/MKP5 -0.05 0.13 -9999 0 -0.48 6 6
PGK/cGMP -0.17 0.28 -9999 0 -0.64 134 134
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.11 0.2 -9999 0 -0.47 83 83
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.47 0.41 -9999 0 -0.82 283 283
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.035 0.12 -10000 0 -0.5 26 26
ER alpha/Gai/GDP/Gbeta gamma 0.006 0.15 -10000 0 -0.54 24 24
AKT1 -0.014 0.2 -10000 0 -0.86 25 25
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.013 0.2 -10000 0 -0.87 25 25
mol:Ca2+ -0.1 0.23 -10000 0 -0.49 116 116
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.071 0.18 -10000 0 -0.58 52 52
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.012 0.19 0.81 25 -10000 0 25
RhoA/GTP -0.026 0.088 -10000 0 -0.41 23 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.036 0.13 -10000 0 -0.59 23 23
regulation of stress fiber formation -0.012 0.12 0.46 5 -10000 0 5
E2/ERA-ERB (dimer) -0.041 0.13 -10000 0 -0.57 26 26
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.034 0.11 -10000 0 -0.5 23 23
pseudopodium formation 0.012 0.12 -10000 0 -0.46 5 5
E2/ER alpha (dimer)/PELP1 -0.037 0.12 -10000 0 -0.55 23 23
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.012 0.038 -10000 0 -0.82 1 1
GNAO1 -0.017 0.15 -10000 0 -0.82 16 16
HRAS 0.012 0.021 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.012 0.15 -10000 0 -0.59 24 24
E2/ER beta (dimer) -0.005 0.057 -10000 0 -0.64 4 4
mol:GDP -0.035 0.13 -10000 0 -0.56 26 26
mol:NADP 0.012 0.15 -10000 0 -0.59 24 24
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.1 0.24 -10000 0 -0.52 116 116
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.24 -10000 0 -0.54 116 116
PLCB2 -0.12 0.25 -10000 0 -0.54 115 115
IGF1 -0.18 0.35 -10000 0 -0.82 113 113
mol:L-citrulline 0.012 0.15 -10000 0 -0.59 24 24
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.026 0.14 -10000 0 -0.78 16 16
JNK cascade -0.005 0.057 -10000 0 -0.63 4 4
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.007 0.075 -10000 0 -0.82 4 4
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.047 0.19 -10000 0 -0.52 55 55
Gq family/GDP/Gbeta gamma -0.057 0.18 -10000 0 -0.54 23 23
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.08 -10000 0 -0.33 23 23
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.036 0.13 -10000 0 -0.59 23 23
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.044 0.14 -10000 0 -0.64 23 23
STRN -0.039 0.2 -10000 0 -0.82 31 31
GNAL -0.09 0.27 -10000 0 -0.82 61 61
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.015 0.051 -10000 0 -0.55 4 4
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.038 -10000 0 -0.82 1 1
HBEGF -0.004 0.16 -10000 0 -0.66 15 15
cAMP biosynthetic process -0.088 0.18 -10000 0 -0.48 83 83
SRC 0.014 0.14 -10000 0 -0.5 24 24
PI3K -0.004 0.049 -10000 0 -0.63 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.031 0.11 -10000 0 -0.5 26 26
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -10000 0 -0.52 38 38
Gs family/GTP -0.09 0.19 -10000 0 -0.49 83 83
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.009 -10000 0 -10000 0 0
vasodilation 0.013 0.14 -10000 0 -0.56 24 24
mol:DAG -0.1 0.24 -10000 0 -0.52 116 116
Gs family/GDP/Gbeta gamma -0.072 0.16 -10000 0 -0.51 27 27
MSN 0.01 0.12 -10000 0 -0.5 5 5
Gq family/GTP -0.15 0.24 -10000 0 -0.57 115 115
mol:PI-3-4-5-P3 -0.011 0.19 -10000 0 -0.83 25 25
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.013 0.14 0.56 24 -10000 0 24
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.032 0.12 -10000 0 -0.52 26 26
NOS3 0.011 0.16 -10000 0 -0.63 24 24
GNA11 -0.004 0.12 -10000 0 -0.82 10 10
MAPKKK cascade -0.008 0.19 -10000 0 -0.54 52 52
E2/ER alpha (dimer)/PELP1/Src -0.039 0.14 -10000 0 -0.62 23 23
ruffle organization 0.012 0.12 -10000 0 -0.46 5 5
ROCK2 0.001 0.14 -10000 0 -0.4 46 46
GNA14 -0.18 0.35 -10000 0 -0.82 114 114
GNA15 -0.014 0.095 -10000 0 -0.33 39 39
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.026 0.19 -10000 0 -0.51 46 46
MMP2 0.015 0.15 -10000 0 -0.68 11 11
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.017 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.011 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.018 0.07 -9999 0 -0.55 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.026 -9999 0 -0.31 3 3
GRK1 -0.066 0.24 -9999 0 -0.81 47 47
CNG Channel -0.028 0.084 -9999 0 -0.51 9 9
mol:Na + -0.023 0.081 -9999 0 -0.45 13 13
mol:ADP -0.066 0.24 -9999 0 -0.8 47 47
RGS9-1/Gbeta5/R9AP -0.089 0.2 -9999 0 -0.55 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.023 0.083 -9999 0 -0.46 13 13
CNGB1 -0.001 0.063 -9999 0 -0.31 19 19
RDH5 -0.2 0.16 -9999 0 -0.31 315 315
SAG 0.002 0.015 -9999 0 -0.31 1 1
mol:Ca2+ 0.016 0.088 -9999 0 -0.54 3 3
Na + (4 Units) -0.021 0.075 -9999 0 -0.47 5 5
RGS9 -0.076 0.26 -9999 0 -0.82 52 52
GNB1/GNGT1 -0.003 0.024 -9999 0 -10000 0 0
GNAT1/GDP -0.078 0.18 -9999 0 -0.48 78 78
GUCY2D -0.01 0.11 -9999 0 -0.82 6 6
GNGT1 -0.004 0.037 -9999 0 -0.31 7 7
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.073 -9999 0 -0.47 5 5
mol:11-cis-retinal -0.2 0.16 -9999 0 -0.31 315 315
mol:cGMP -0.016 0.071 -9999 0 -0.48 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.099 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0.001 0.089 -9999 0 -0.56 10 10
Metarhodopsin II -0.049 0.15 -9999 0 -0.51 46 46
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.075 -9999 0 -0.5 9 9
RGS9BP -0.034 0.19 -9999 0 -0.82 28 28
Metarhodopsin II/Transducin 0.011 0.015 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.043 -9999 0 -0.51 3 3
PDE6A/B -0.012 0.048 -9999 0 -10000 0 0
mol:Pi -0.089 0.2 -9999 0 -0.55 78 78
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.023 -9999 0 -10000 0 0
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.008 0.077 -9999 0 -0.31 29 29
PDE6G -0.017 0.12 -9999 0 -0.38 37 37
RHO 0.006 0.016 -9999 0 -0.31 1 1
PDE6 -0.09 0.18 -9999 0 -0.48 81 81
GUCA1A 0.004 0.033 -9999 0 -0.31 5 5
GC2/GCAP Family -0.005 0.043 -9999 0 -0.51 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.066 -9999 0 -0.69 4 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.074 0.097 -10000 0 -10000 0 0
CRKL -0.031 0.11 -10000 0 -0.33 25 25
mol:PIP3 -0.019 0.032 0.68 1 -10000 0 1
AKT1 0.001 0.04 0.45 1 -0.53 2 3
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.022 0.11 -10000 0 -10000 0 0
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
HGF/MET/SHIP2 -0.14 0.2 -10000 0 -0.59 74 74
MAP3K5 -0.018 0.11 -10000 0 -0.47 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.54 74 74
AP1 -0.28 0.42 -10000 0 -0.87 151 151
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.26 0.4 -10000 0 -0.86 151 151
STAT3 (dimer) -0.04 0.13 -10000 0 -0.33 74 74
GAB1/CRKL/SHP2/PI3K -0.043 0.094 -10000 0 -0.59 3 3
INPP5D -0.003 0.072 -10000 0 -0.31 25 25
CBL/CRK -0.022 0.11 -10000 0 -10000 0 0
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.038 -10000 0 -0.82 1 1
ELK1 -0.049 0.062 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.04 0.072 -10000 0 -0.24 26 26
PAK1 0.009 0.037 0.42 1 -0.5 2 3
HGF/MET/RANBP10 -0.14 0.2 -10000 0 -0.59 74 74
HRAS -0.059 0.16 -10000 0 -0.48 26 26
DOCK1 -0.026 0.12 -10000 0 -0.55 4 4
GAB1 -0.041 0.12 -10000 0 -0.3 74 74
CRK -0.031 0.11 -10000 0 -0.33 25 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.21 -10000 0 -0.6 74 74
JUN -0.17 0.35 -10000 0 -0.82 110 110
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.071 0.1 -10000 0 -0.29 74 74
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.012 0.14 -10000 0 -0.65 2 2
GRB2/SHC -0.039 0.096 -10000 0 -0.3 25 25
FOS -0.2 0.36 -10000 0 -0.82 128 128
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.048 0.062 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.6 74 74
cell migration -0.038 0.095 -10000 0 -0.3 25 25
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.074 0.097 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.051 0.14 -10000 0 -0.36 74 74
MET/MUC20 -0.078 0.1 -10000 0 -10000 0 0
RAP1B -0.013 0.1 -10000 0 -10000 0 0
RAP1A -0.013 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.14 0.2 -10000 0 -0.59 74 74
RAF1 -0.048 0.15 -10000 0 -0.45 26 26
STAT3 -0.04 0.13 -10000 0 -0.34 74 74
cell proliferation -0.048 0.18 -10000 0 -0.45 74 74
RPS6KB1 -0.015 0.039 -10000 0 -10000 0 0
MAPK3 -0.05 0.057 -10000 0 -10000 0 0
MAPK1 -0.05 0.057 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.008 0.14 -10000 0 -0.57 15 15
SRC -0.04 0.13 -10000 0 -0.39 25 25
PI3K -0.042 0.1 -10000 0 -0.32 28 28
MET/Glomulin -0.058 0.093 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.037 0.14 -10000 0 -0.41 26 26
MET -0.11 0.16 -10000 0 -0.31 179 179
MAP4K1 -0.027 0.12 -10000 0 -0.33 31 31
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.037 0.14 -10000 0 -0.41 26 26
BAD 0.009 0.037 0.42 1 -0.5 2 3
MAP2K4 -0.009 0.1 -10000 0 -0.42 5 5
SHP2/GRB2/SOS1/GAB1 -0.057 0.09 -10000 0 -0.38 1 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.049 0.1 -10000 0 -0.32 25 25
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 74 74
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.041 0.11 -10000 0 -0.33 25 25
PDPK1 -0.009 0.043 0.51 1 -0.57 2 3
HGF/MET/SHIP -0.15 0.21 -10000 0 -0.6 74 74
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.037 0.039 -9999 0 -10000 0 0
VDR 0.013 0.015 -9999 0 -0.31 1 1
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.059 0.11 -9999 0 -0.35 48 48
RXRs/LXRs/DNA/Oxysterols -0.048 0.16 -9999 0 -0.46 58 58
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.084 -9999 0 -0.34 24 24
RXRs/NUR77 -0.26 0.25 -9999 0 -0.63 145 145
RXRs/PPAR -0.055 0.064 -9999 0 -0.4 11 11
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.014 0.08 -9999 0 -0.48 14 14
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -9999 0 -0.31 1 1
RARs/RARs/DNA/9cRA -0.013 0.079 -9999 0 -0.47 14 14
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.054 0.032 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.021 0.084 -9999 0 -0.34 24 24
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0.01 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.082 -9999 0 -0.58 4 4
NR1H4 0.001 0.033 -9999 0 -10000 0 0
RXRs/LXRs/DNA -0.099 0.092 -9999 0 -0.57 4 4
NR1H2 0.016 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.067 -9999 0 -0.52 4 4
NR4A1 -0.23 0.38 -9999 0 -0.81 143 143
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.047 0.049 -9999 0 -0.34 3 3
RXRG -0.28 0.12 -9999 0 -0.32 433 433
RXR alpha/CCPG 0.021 0.01 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.015 0.014 -9999 0 -10000 0 0
THRB -0.005 0.12 -9999 0 -0.82 11 11
PPARG -0.002 0.1 -9999 0 -0.82 7 7
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.41 -9999 0 -1.3 58 58
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.048 0.15 -9999 0 -0.45 58 58
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.14 -9999 0 -0.82 14 14
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.45 168 168
SREBF1 -0.038 0.14 -9999 0 -0.62 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.082 -9999 0 -0.58 4 4
ABCA1 -0.037 0.14 -9999 0 -0.62 3 3
RARs/THRs -0.023 0.1 -9999 0 -0.48 24 24
RXRs/FXR -0.12 0.071 -9999 0 -0.55 4 4
BCL2 -0.048 0.22 -9999 0 -0.82 36 36
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.044 -10000 0 -0.31 9 9
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.066 0.15 0.55 10 -10000 0 10
IL27/IL27R/JAK1 -0.12 0.19 -10000 0 -0.57 51 51
TBX21 -0.09 0.22 -10000 0 -0.63 35 35
IL12B -0.004 0.09 -10000 0 -0.54 11 11
IL12A -0.059 0.2 -10000 0 -0.61 54 54
IL6ST -0.11 0.29 -10000 0 -0.82 71 71
IL27RA/JAK1 0.013 0.026 -10000 0 -10000 0 0
IL27 0.002 0.037 -10000 0 -0.32 6 6
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.062 0.15 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.066 0.15 0.55 10 -10000 0 10
T cell proliferation during immune response 0.066 0.15 0.55 10 -10000 0 10
MAPKKK cascade -0.066 0.15 -10000 0 -0.55 10 10
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.049 -10000 0 -0.32 11 11
IL12RB1 -0.022 0.12 -10000 0 -0.82 4 4
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.09 0.21 -10000 0 -0.61 33 33
IL27/IL27R/JAK2/TYK2 -0.067 0.15 -10000 0 -0.56 10 10
positive regulation of T cell mediated cytotoxicity -0.066 0.15 -10000 0 -0.55 10 10
STAT1 (dimer) -0.12 0.24 0.52 16 -0.74 18 34
JAK2 0.011 0.054 -10000 0 -0.83 2 2
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.055 0.14 -10000 0 -0.53 10 10
T cell proliferation -0.16 0.24 -10000 0 -0.53 105 105
IL12/IL12R/TYK2/JAK2 -0.055 0.16 -10000 0 -0.68 14 14
IL17A -0.063 0.15 -10000 0 -10000 0 0
mast cell activation 0.066 0.15 0.55 10 -10000 0 10
IFNG -0.02 0.048 -10000 0 -0.13 66 66
T cell differentiation -0.005 0.008 -10000 0 -0.022 60 60
STAT3 (dimer) -0.055 0.14 -10000 0 -0.53 10 10
STAT5A (dimer) -0.055 0.14 -10000 0 -0.53 10 10
STAT4 (dimer) -0.075 0.16 -10000 0 -0.52 24 24
STAT4 -0.024 0.14 -10000 0 -0.46 39 39
T cell activation -0.012 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.063 0.19 -10000 0 -0.68 8 8
GATA3 -0.043 0.34 -10000 0 -1.5 25 25
IL18 -0.025 0.11 -10000 0 -0.29 58 58
positive regulation of mast cell cytokine production -0.055 0.14 -10000 0 -0.52 10 10
IL27/EBI3 -0.099 0.12 -10000 0 -0.44 6 6
IL27RA 0.004 0.027 -10000 0 -10000 0 0
IL6 -0.17 0.33 -10000 0 -0.82 97 97
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.014 -10000 0 -10000 0 0
IL1B -0.041 0.18 -10000 0 -0.59 43 43
EBI3 -0.15 0.17 -10000 0 -0.32 237 237
TNF -0.069 0.21 -10000 0 -0.6 64 64
ErbB2/ErbB3 signaling events

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
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.041 0.1 -9999 0 -0.38 21 21
NFATC4 0 0.11 -9999 0 -0.5 3 3
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.045 0.13 -9999 0 -0.4 54 54
JUN 0.002 0.097 -9999 0 -0.28 12 12
HRAS 0.011 0.021 -9999 0 -0.32 2 2
DOCK7 -0.014 0.14 -9999 0 -0.38 57 57
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.055 0.15 -9999 0 -0.49 54 54
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.023 0.063 -9999 0 -0.36 2 2
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.024 0.15 -9999 0 -0.44 54 54
RAF1 -0.003 0.12 -9999 0 -0.4 21 21
ErbB2/ErbB3/neuregulin 2 -0.068 0.17 -9999 0 -0.51 64 64
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.022 0.082 -9999 0 -0.3 5 5
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.13 0.33 -9999 0 -0.68 115 115
FOS -0.11 0.28 -9999 0 -0.52 151 151
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.045 0.13 -9999 0 -0.4 54 54
MAPK3 -0.083 0.25 -9999 0 -0.5 111 111
MAPK1 -0.083 0.25 -9999 0 -0.5 111 111
JAK2 -0.014 0.14 -9999 0 -0.39 35 35
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.015 0.13 -9999 0 -0.37 54 54
NRG1 -0.067 0.24 -9999 0 -0.8 47 47
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.014 0.13 -9999 0 -0.35 64 64
MAPK9 -0.022 0.061 -9999 0 -0.29 1 1
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.008 0.12 -9999 0 -0.73 12 12
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.01 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.003 -9999 0 -10000 0 0
RNF41 0.027 0.007 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.032 0.086 -9999 0 -0.38 2 2
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.056 0.2 -9999 0 -0.39 94 94
myelination 0.009 0.11 -9999 0 -0.46 3 3
PPP3CB -0.01 0.12 -9999 0 -0.35 54 54
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.024 0.11 -9999 0 -0.65 2 2
NRG2 -0.081 0.26 -9999 0 -0.79 57 57
mol:GDP -0.015 0.13 -9999 0 -0.37 54 54
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.005 0.13 -9999 0 -0.41 21 21
SRC 0.013 0.015 -9999 0 -0.31 1 1
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.013 0.13 -9999 0 -0.39 26 26
MAP2K1 -0.075 0.23 -9999 0 -0.53 44 44
heart morphogenesis -0.045 0.13 -9999 0 -0.4 54 54
RAS family/GDP -0.035 0.1 -9999 0 -0.36 21 21
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.009 -9999 0 -10000 0 0
CHRNE 0.01 0.035 -9999 0 -0.13 18 18
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.045 0.13 -9999 0 -0.4 54 54
CDC42 0.013 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.054 0.16 -9999 0 -0.54 40 40
MAP4K1 -0.019 0.12 -9999 0 -0.41 38 38
MAP3K8 0 0.1 -9999 0 -0.82 8 8
PRKCB -0.027 0.13 -9999 0 -0.36 53 53
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.014 0.1 -9999 0 -0.55 5 5
JUN -0.1 0.24 -9999 0 -0.51 121 121
MAP3K7 0.014 0.1 -9999 0 -0.55 5 5
GRAP2 -0.041 0.2 -9999 0 -0.77 34 34
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.02 0.11 -9999 0 -0.51 7 7
LAT 0.006 0.076 -9999 0 -0.72 5 5
LCP2 0.009 0.039 -9999 0 -0.31 7 7
MAPK8 -0.004 0.14 -9999 0 -0.74 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.11 -9999 0 -0.36 33 33
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.05 0.15 -9999 0 -0.51 40 40
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.045 0.15 -9999 0 -0.54 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.051 -9999 0 -0.6 1 1
AP1 -0.25 0.36 -9999 0 -0.68 175 175
mol:PIP3 -0.041 0.12 -9999 0 -0.42 42 42
AKT1 -0.027 0.095 -9999 0 -0.58 5 5
PTK2B 0 0.085 -9999 0 -0.27 40 40
RHOA 0.031 0.046 -9999 0 -10000 0 0
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.004 0.074 -9999 0 -0.32 1 1
MAGI3 0.012 0.037 -9999 0 -0.82 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.014 0.13 -9999 0 -0.44 39 39
HRAS/GDP -0.001 0.014 -9999 0 -0.21 2 2
positive regulation of microtubule depolymerization 0.009 0.088 -9999 0 -0.36 9 9
NF kappa B1 p50/RelA -0.044 0.12 -9999 0 -0.54 13 13
endothelial cell migration -0.028 0.2 -9999 0 -0.64 41 41
ADCY4 -0.015 0.19 -9999 0 -0.61 40 40
ADCY5 -0.046 0.21 -9999 0 -0.64 43 43
ADCY6 -0.015 0.19 -9999 0 -0.62 39 39
ADCY7 -0.015 0.19 -9999 0 -0.62 39 39
ADCY1 -0.018 0.19 -9999 0 -0.62 40 40
ADCY2 -0.038 0.21 -9999 0 -0.66 41 41
ADCY3 -0.015 0.19 -9999 0 -0.61 40 40
ADCY8 -0.056 0.19 -9999 0 -0.65 40 40
ADCY9 -0.015 0.19 -9999 0 -0.62 39 39
GSK3B 0.008 0.081 -9999 0 -0.3 12 12
arachidonic acid secretion -0.008 0.18 -9999 0 -0.57 39 39
GNG2 0.012 0.037 -9999 0 -0.81 1 1
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.04 0.2 -9999 0 -0.6 53 53
HRAS 0.012 0.021 -9999 0 -0.31 2 2
NFKBIA 0.01 0.079 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.035 0.11 -9999 0 -0.97 6 6
JUN -0.17 0.35 -9999 0 -0.82 110 110
LPA/LPA2/NHERF2 -0.001 0.007 -9999 0 -10000 0 0
TIAM1 -0.045 0.13 -9999 0 -1.2 6 6
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.003 0.075 -9999 0 -0.32 1 1
PLCB3 0.03 0.009 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.82 128 128
positive regulation of mitosis -0.008 0.18 -9999 0 -0.57 39 39
LPA/LPA1-2-3 -0.05 0.15 -9999 0 -0.54 39 39
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.004 0.11 -9999 0 -0.35 39 39
GNAZ -0.02 0.17 -9999 0 -0.57 41 41
EGFR/PI3K-beta/Gab1 -0.043 0.13 -9999 0 -0.44 42 42
positive regulation of dendritic cell cytokine production -0.05 0.15 -9999 0 -0.53 39 39
LPA/LPA2/MAGI-3 -0.002 0.027 -9999 0 -0.59 1 1
ARHGEF1 -0.001 0.15 -9999 0 -0.49 39 39
GNAI2 -0.02 0.17 -9999 0 -0.57 41 41
GNAI3 -0.02 0.17 -9999 0 -0.57 41 41
GNAI1 -0.022 0.17 -9999 0 -0.56 42 42
LPA/LPA3 -0.01 0.044 -9999 0 -0.21 21 21
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.056 0.19 -9999 0 -0.65 41 41
HB-EGF/EGFR -0.052 0.17 -9999 0 -0.54 44 44
HBEGF -0.059 0.19 -9999 0 -0.62 42 42
mol:DAG 0.003 0.075 -9999 0 -0.32 1 1
cAMP biosynthetic process -0.027 0.2 -9999 0 -0.56 53 53
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN 0.01 0.079 -9999 0 -10000 0 0
GNAQ 0.019 0.029 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.066 -9999 0 -0.31 21 21
LPAR1 -0.051 0.23 -9999 0 -0.83 39 39
IL8 -0.13 0.19 -9999 0 -0.48 58 58
PTK2 -0.01 0.15 -9999 0 -0.5 39 39
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.014 0.13 -9999 0 -0.45 39 39
EGFR 0.006 0.075 -9999 0 -0.82 4 4
PLCG1 -0.016 0.085 -9999 0 -0.29 14 14
PLD2 -0.01 0.15 -9999 0 -0.5 39 39
G12/G13 -0.044 0.15 -9999 0 -0.53 39 39
PI3K-beta -0.032 0.11 -9999 0 -0.71 5 5
cell migration -0.016 0.059 -9999 0 -0.25 11 11
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.003 0.11 -9999 0 -0.36 39 39
HRAS/GTP -0.009 0.19 -9999 0 -0.59 39 39
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.081 0.24 -9999 0 -0.57 79 79
PRKCE 0.005 0.084 -9999 0 -0.82 5 5
PRKCD 0.011 0.072 -9999 0 -10000 0 0
Gi(beta/gamma) -0.008 0.18 -9999 0 -0.59 39 39
mol:LPA 0.003 0.019 -9999 0 -0.22 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.03 0.13 -9999 0 -0.45 39 39
MAPKKK cascade -0.008 0.18 -9999 0 -0.57 39 39
contractile ring contraction involved in cytokinesis 0.031 0.046 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.086 0.19 -9999 0 -0.43 114 114
GNA15 0.008 0.056 -9999 0 -0.35 2 2
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.008 0.09 -9999 0 -0.41 6 6
GNA11 0.01 0.069 -9999 0 -0.42 10 10
Rac1/GTP -0.036 0.12 -9999 0 -1 6 6
MMP2 -0.028 0.2 -9999 0 -0.64 41 41
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.11 0.18 -9999 0 -0.46 60 60
IKBKB -0.018 0.071 -9999 0 -0.36 3 3
AKT1 -0.04 0.1 -9999 0 -0.26 23 23
IKBKG -0.016 0.074 -9999 0 -0.33 5 5
CALM1 -0.034 0.085 -9999 0 -0.35 2 2
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
MAP3K1 -0.071 0.18 -9999 0 -0.64 16 16
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.044 0.089 -9999 0 -0.38 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.081 0.13 -9999 0 -0.28 110 110
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.16 0.24 -9999 0 -0.52 136 136
CD22 -0.15 0.22 -9999 0 -0.51 103 103
CAMK2G -0.024 0.081 -9999 0 -0.32 2 2
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.003 0.072 -9999 0 -0.31 25 25
SHC/GRB2/SOS1 -0.094 0.14 -9999 0 -10000 0 0
GO:0007205 -0.044 0.09 -9999 0 -0.38 2 2
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.034 0.086 -9999 0 -0.35 2 2
NFATC1 -0.068 0.16 -9999 0 -0.53 20 20
B-cell antigen/BCR complex -0.16 0.24 -9999 0 -0.52 136 136
PAG1/CSK -0.001 0.028 -9999 0 -0.63 1 1
NFKBIB 0.003 0.028 -9999 0 -0.11 3 3
HRAS -0.036 0.098 -9999 0 -0.35 2 2
NFKBIA 0.003 0.027 -9999 0 -0.11 3 3
NF-kappa-B/RelA/I kappa B beta 0.009 0.024 -9999 0 -0.2 1 1
RasGAP/Csk -0.14 0.2 -9999 0 -0.48 94 94
mol:GDP -0.04 0.082 -9999 0 -0.36 2 2
PTEN 0.012 0.038 -9999 0 -0.82 1 1
CD79B -0.029 0.11 -9999 0 -0.31 63 63
NF-kappa-B/RelA/I kappa B alpha 0.009 0.024 -9999 0 -0.2 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.084 0.18 -9999 0 -0.43 74 74
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.05 0.087 -9999 0 -0.38 2 2
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.14 0.21 -9999 0 -0.47 130 130
CHUK -0.016 0.074 -9999 0 -0.33 5 5
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.066 0.093 -9999 0 -0.49 8 8
PTPN6 -0.14 0.2 -9999 0 -0.6 51 51
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.005 0.034 -9999 0 -0.13 18 18
VAV2 -0.13 0.18 -9999 0 -0.51 41 41
ubiquitin-dependent protein catabolic process 0.008 0.027 -9999 0 -0.11 3 3
BTK -0.018 0.16 -9999 0 -1.2 8 8
CD19 -0.14 0.2 -9999 0 -0.45 97 97
MAP4K1 -0.019 0.12 -9999 0 -0.41 38 38
CD72 0.012 0.021 -9999 0 -0.31 2 2
PAG1 0.012 0.038 -9999 0 -0.82 1 1
MAPK14 -0.053 0.16 -9999 0 -0.52 16 16
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.034 0.088 -9999 0 -10000 0 0
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.059 0.17 -9999 0 -0.43 71 71
RAF1 -0.027 0.094 -9999 0 -0.32 2 2
RasGAP/p62DOK/SHIP -0.14 0.19 -9999 0 -0.47 93 93
CD79A -0.19 0.3 -9999 0 -0.52 184 184
re-entry into mitotic cell cycle -0.08 0.13 -9999 0 -0.28 108 108
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.008 0.083 -9999 0 -10000 0 0
MAPK1 -0.008 0.083 -9999 0 -10000 0 0
CD72/SHP1 -0.099 0.21 -9999 0 -0.64 34 34
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 -0.062 0.17 -9999 0 -0.52 25 25
actin cytoskeleton organization -0.084 0.18 -9999 0 -0.68 11 11
NF-kappa-B/RelA 0.023 0.044 -9999 0 -0.2 1 1
Calcineurin -0.035 0.058 -9999 0 -10000 0 0
PI3K -0.13 0.16 -9999 0 -0.52 32 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.054 0.085 -9999 0 -0.34 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.1 0.24 -9999 0 -0.97 22 22
DAPP1 -0.13 0.26 -9999 0 -1.2 18 18
cytokine secretion -0.063 0.15 -9999 0 -0.49 20 20
mol:DAG -0.05 0.087 -9999 0 -0.38 2 2
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.017 0.089 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.16 0.23 -9999 0 -0.48 154 154
mol:PI-3-4-5-P3 -0.094 0.12 -9999 0 -0.36 29 29
ETS1 -0.015 0.076 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.11 0.17 -9999 0 -0.46 74 74
B-cell antigen/BCR complex/LYN -0.12 0.2 -9999 0 -0.48 81 81
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.82 2 2
RAC1 -0.09 0.19 -9999 0 -0.74 11 11
B-cell antigen/BCR complex/LYN/SYK -0.15 0.22 -9999 0 -0.55 81 81
CARD11 -0.073 0.12 -9999 0 -0.51 12 12
FCGR2B -0.028 0.18 -9999 0 -0.74 27 27
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0.001 0.035 -9999 0 -0.14 2 2
PTPRC -0.031 0.17 -9999 0 -0.59 36 36
PDPK1 -0.042 0.1 -9999 0 -0.27 23 23
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.024 -9999 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.009 0.081 -9999 0 -0.71 6 6
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.57 15 15
PTK2 0.016 0.15 -9999 0 -0.54 16 16
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.025 0.1 -9999 0 -0.31 57 57
SRC 0.013 0.015 -9999 0 -0.31 1 1
CDKN1B -0.063 0.18 -9999 0 -0.61 45 45
VEGFA 0.008 0.065 -9999 0 -0.82 3 3
ILK -0.063 0.18 -9999 0 -0.61 45 45
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.058 0.16 -9999 0 -0.56 45 45
PTK2B 0.019 0.11 -9999 0 -0.5 21 21
alphaV/beta3 Integrin/JAM-A -0.059 0.16 -9999 0 -0.47 59 59
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.019 0.1 -9999 0 -0.58 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.18 0.26 -9999 0 -0.53 159 159
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.003 0.11 -9999 0 -0.54 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.019 0.1 -9999 0 -0.57 15 15
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.24 0.25 -9999 0 -0.61 118 118
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
alphaV/beta3 Integrin/Osteopontin -0.07 0.16 -9999 0 -0.57 37 37
RPS6KB1 -0.21 0.24 -9999 0 -0.57 118 118
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.094 0.15 -9999 0 -0.74 15 15
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.094 0.15 -9999 0 -0.74 15 15
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.034 0.15 -9999 0 -0.61 27 27
cell adhesion -0.029 0.098 -9999 0 -0.53 15 15
ANGPTL3 0.005 0.026 -9999 0 -0.31 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.072 -9999 0 -0.62 6 6
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.065 -9999 0 -0.82 3 3
ITGB3 -0.01 0.14 -9999 0 -0.82 14 14
IGF1 -0.18 0.35 -9999 0 -0.82 113 113
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.1 -9999 0 -0.57 15 15
apoptosis 0.01 0.053 -9999 0 -0.81 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.018 0.1 -9999 0 -0.57 15 15
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.037 0.13 -9999 0 -0.61 22 22
CSF1 0 0.1 -9999 0 -0.82 8 8
PIK3C2A -0.064 0.18 -9999 0 -0.61 46 46
PI4 Kinase/Pyk2 -0.054 0.14 -9999 0 -0.77 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.023 0.11 -9999 0 -0.54 21 21
FAK1/Vinculin 0.024 0.12 -9999 0 -0.48 8 8
alphaV beta3/Integrin/ppsTEM5 -0.018 0.1 -9999 0 -0.57 15 15
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.068 0.24 -9999 0 -0.75 52 52
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.036 0.11 -9999 0 -0.57 15 15
alphaV/beta3 Integrin/TGFBR2 -0.021 0.11 -9999 0 -0.6 17 17
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.01 0.076 -9999 0 -0.54 9 9
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.016 0.094 -9999 0 -0.53 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 354 354
alphaV/beta3 Integrin/Pyk2 -0.022 0.1 -9999 0 -0.5 21 21
SDC1 0.01 0.033 -9999 0 -0.31 5 5
VAV3 0.026 0.098 -9999 0 -0.52 14 14
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
IRS1 -0.087 0.27 -9999 0 -0.82 59 59
FAK1/Paxillin 0.024 0.12 -9999 0 -0.48 8 8
cell migration 0.034 0.12 -9999 0 -0.42 8 8
ITGAV 0.01 0.053 -9999 0 -0.82 2 2
PI3K -0.055 0.15 -9999 0 -0.44 60 60
SPP1 -0.082 0.2 -9999 0 -0.42 109 109
KDR 0.007 0.075 -9999 0 -0.82 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.053 -9999 0 -0.82 2 2
COL4A3 -0.012 0.14 -9999 0 -0.82 15 15
angiogenesis -0.083 0.18 -9999 0 -0.59 36 36
Rac1/GTP -0.014 0.083 -9999 0 -0.47 14 14
EDIL3 -0.023 0.14 -9999 0 -0.82 9 9
cell proliferation -0.021 0.11 -9999 0 -0.59 17 17
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.009 0.23 -10000 0 -0.97 22 22
NCK1/PAK1/Dok-R -0.029 0.093 -10000 0 -0.43 23 23
NCK1/Dok-R -0.071 0.25 -10000 0 -1.2 22 22
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
mol:beta2-estradiol -0.003 0.049 0.25 16 -10000 0 16
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.014 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.01 0.071 0.25 14 -0.33 12 26
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.062 0.23 -10000 0 -1.1 22 22
FN1 -0.22 0.15 -10000 0 -0.31 354 354
PLD2 -0.003 0.28 -10000 0 -1.3 22 22
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
GRB14 -0.007 0.13 -10000 0 -0.82 12 12
ELK1 0.013 0.25 -10000 0 -1.1 22 22
GRB7 -0.042 0.12 -10000 0 -0.31 82 82
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.25 -10000 0 -1.2 22 22
CDKN1A -0.011 0.18 -10000 0 -0.65 21 21
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.071 0.25 -10000 0 -1.2 22 22
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.025 0.17 -10000 0 -0.69 22 22
PLG -0.013 0.28 -10000 0 -1.3 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.007 0.22 -10000 0 -0.93 22 22
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
ANGPT2 -0.11 0.22 -10000 0 -0.74 23 23
BMX -0.018 0.3 -10000 0 -1.3 23 23
ANGPT1 -0.041 0.3 -10000 0 -1.5 19 19
tube development -0.018 0.19 -10000 0 -0.74 22 22
ANGPT4 -0.058 0.23 -10000 0 -0.75 46 46
response to hypoxia 0 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.02 0.3 -10000 0 -1.3 22 22
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.001 -10000 0 -10000 0 0
STAT5A (dimer) -0.021 0.21 -10000 0 -0.85 22 22
mol:L-citrulline 0.025 0.17 -10000 0 -0.69 22 22
AGTR1 -0.32 0.41 -10000 0 -0.81 196 196
MAPK14 -0.014 0.28 -10000 0 -1.2 22 22
Tie2/SHP2 -0.028 0.16 -10000 0 -1.4 6 6
TEK 0.012 0.19 -10000 0 -1.5 6 6
RPS6KB1 0.008 0.22 -10000 0 -0.93 22 22
Angiotensin II/AT1 -0.24 0.32 -10000 0 -0.63 195 195
Tie2/Ang1/GRB2 -0.008 0.3 -10000 0 -1.3 22 22
MAPK3 0.008 0.26 -10000 0 -1.1 22 22
MAPK1 0.008 0.26 -10000 0 -1.1 22 22
Tie2/Ang1/GRB7 -0.032 0.3 -10000 0 -1.3 22 22
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
MAPK8 -0.012 0.3 -10000 0 -1.3 23 23
PI3K -0.007 0.26 -10000 0 -1.1 22 22
FES -0.014 0.28 -10000 0 -1.2 22 22
Crk/Dok-R -0.071 0.25 -10000 0 -1.2 22 22
Tie2/Ang1/ABIN2 -0.008 0.3 -10000 0 -1.3 22 22
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.014 0.2 -10000 0 -0.85 22 22
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.008 0.22 -10000 0 -0.93 22 22
Tie2/Ang2 -0.041 0.25 -10000 0 -1 22 22
Tie2/Ang1 -0.016 0.31 -10000 0 -1.4 22 22
FOXO1 0.02 0.2 -10000 0 -0.86 22 22
ELF1 0.015 0.078 -10000 0 -0.84 4 4
ELF2 -0.007 0.28 -10000 0 -1.2 22 22
mol:Choline 0 0.27 -10000 0 -1.2 22 22
cell migration -0.024 0.057 -10000 0 -0.24 22 22
FYN -0.024 0.21 -10000 0 -0.85 22 22
DOK2 0.001 0.076 -10000 0 -0.38 16 16
negative regulation of cell cycle -0.008 0.16 -10000 0 -0.58 22 22
ETS1 0.015 0.046 -10000 0 -10000 0 0
PXN 0.022 0.18 -10000 0 -0.75 22 22
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.022 0.19 -10000 0 -0.8 22 22
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.089 0.28 -10000 0 -0.77 65 65
MAPKKK cascade 0 0.27 -10000 0 -1.2 22 22
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.012 0.3 -10000 0 -1.3 22 22
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.028 0.16 -10000 0 -0.61 22 22
mol:Phosphatidic acid 0 0.27 -10000 0 -1.2 22 22
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.025 0.17 -10000 0 -0.69 22 22
Rac1/GTP -0.053 0.18 -10000 0 -0.86 22 22
MMP2 -0.01 0.29 -10000 0 -1.3 22 22
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.038 -10000 0 -0.82 1 1
Jak2/Leptin Receptor -0.023 0.097 0.21 4 -0.39 18 22
PTP1B/AKT1 -0.002 0.063 -10000 0 -0.32 3 3
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.011 0.069 -10000 0 -0.32 5 5
EGFR 0.005 0.076 -10000 0 -0.83 4 4
EGF/EGFR -0.083 0.18 -10000 0 -0.5 74 74
CSF1 0 0.1 -10000 0 -0.82 8 8
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.014 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.098 0.12 -10000 0 -0.45 20 20
Insulin Receptor/Insulin -0.012 0.04 -10000 0 -10000 0 0
HCK -0.007 0.08 -10000 0 -0.31 31 31
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.002 0.066 -10000 0 -0.31 4 4
EGF -0.11 0.29 -10000 0 -0.78 76 76
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.017 0.099 -10000 0 -0.39 5 5
TXN 0.011 0.016 -10000 0 -0.32 1 1
PTP1B/IRS1/GRB2 -0.055 0.17 -10000 0 -0.49 60 60
cell migration 0.011 0.069 0.32 5 -10000 0 5
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.044 0.19 -10000 0 -0.6 45 45
ITGA2B -0.072 0.25 -10000 0 -0.82 50 50
CSF1R 0.009 0.048 -10000 0 -0.41 5 5
Prolactin Receptor/Prolactin -0.039 0.15 -10000 0 -0.64 26 26
FGR 0.011 0.029 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.003 0.065 -10000 0 -0.34 3 3
Crk/p130 Cas 0.001 0.06 -10000 0 -0.38 1 1
DOK1 0.007 0.062 -10000 0 -0.32 2 2
JAK2 -0.012 0.092 -10000 0 -0.4 14 14
Jak2/Leptin Receptor/Leptin -0.055 0.14 -10000 0 -0.57 29 29
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.011 0.07 -10000 0 -0.32 5 5
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.19 0.2 -10000 0 -0.34 275 275
SRC 0.012 0.029 -10000 0 -10000 0 0
ITGB3 -0.012 0.14 -10000 0 -0.82 14 14
CAT1/PTP1B -0.088 0.15 -10000 0 -0.38 60 60
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.015 0.052 -10000 0 -0.57 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.054 0.14 -10000 0 -0.61 28 28
negative regulation of transcription -0.011 0.092 -10000 0 -0.39 14 14
FCGR2A -0.006 0.082 -10000 0 -0.33 27 27
FER 0.007 0.066 -10000 0 -0.82 3 3
alphaIIb/beta3 Integrin -0.08 0.22 -10000 0 -0.67 59 59
BLK -0.24 0.37 -10000 0 -0.75 165 165
Insulin Receptor/Insulin/Shc 0 0.001 -10000 0 -10000 0 0
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.004 0.086 -10000 0 -0.67 7 7
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.5 50 50
PRL 0.001 0.016 -10000 0 -0.31 1 1
SOCS3 -0.07 0.34 -10000 0 -1.5 27 27
SPRY2 0.009 0.056 -10000 0 -0.65 3 3
Insulin Receptor/Insulin/IRS1 -0.067 0.18 -10000 0 -0.55 59 59
CSF1/CSF1R -0.008 0.094 -10000 0 -0.51 10 10
Ras protein signal transduction 0.02 0.023 -10000 0 -10000 0 0
IRS1 -0.087 0.27 -10000 0 -0.82 59 59
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.008 0.067 -10000 0 -0.31 22 22
STAT5B -0.007 0.07 -10000 0 -0.27 10 10
STAT5A -0.007 0.07 -10000 0 -0.27 10 10
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.068 -10000 0 -0.36 4 4
CSN2 -0.007 0.055 -10000 0 -10000 0 0
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
LAT 0.002 0.065 -10000 0 -0.54 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.01 0.11 -10000 0 -0.43 26 26
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 213 213
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.015 -9999 0 -0.31 1 1
LAT2 -0.018 0.1 -9999 0 -0.37 6 6
AP1 -0.2 0.28 -9999 0 -0.61 135 135
mol:PIP3 -0.016 0.15 -9999 0 -0.42 39 39
IKBKB 0.003 0.092 -9999 0 -0.27 20 20
AKT1 -0.017 0.14 -9999 0 -0.58 6 6
IKBKG 0.003 0.092 -9999 0 -0.26 21 21
MS4A2 -0.066 0.14 -9999 0 -0.31 114 114
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
MAP3K1 0.01 0.1 -9999 0 -0.46 7 7
mol:Ca2+ -0.008 0.12 -9999 0 -0.31 39 39
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.01 0.089 -9999 0 -0.38 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.081 0.18 -9999 0 -0.5 79 79
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.072 -9999 0 -0.31 25 25
PLD2 -0.048 0.15 -9999 0 -0.44 42 42
PTPN13 -0.002 0.1 -9999 0 -0.55 6 6
PTPN11 0.011 0.039 -9999 0 -0.85 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.018 0.1 -9999 0 -0.37 4 4
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.42 39 39
LAT -0.014 0.1 -9999 0 -0.43 8 8
PAK2 0.002 0.11 -9999 0 -0.51 8 8
NFATC2 -0.15 0.28 -9999 0 -0.75 85 85
HRAS -0.008 0.12 -9999 0 -0.51 10 10
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.099 0.17 -9999 0 -0.46 69 69
Antigen/IgE/Fc epsilon R1 -0.09 0.15 -9999 0 -0.43 69 69
mol:GDP -0.016 0.13 -9999 0 -0.5 15 15
JUN -0.17 0.35 -9999 0 -0.82 110 110
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.82 128 128
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.044 0.079 -9999 0 -0.34 6 6
CHUK 0.003 0.092 -9999 0 -0.27 20 20
KLRG1 -0.022 0.11 -9999 0 -0.41 14 14
VAV1 -0.022 0.11 -9999 0 -0.48 9 9
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.01 0.089 -9999 0 -0.35 4 4
negative regulation of mast cell degranulation -0.02 0.1 -9999 0 -0.39 12 12
BTK -0.047 0.11 -9999 0 -0.58 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.048 0.18 -9999 0 -0.5 48 48
GAB2/PI3K/SHP2 -0.065 0.13 -9999 0 -0.44 37 37
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.019 0.094 -9999 0 -0.29 35 35
RAF1 0.018 0.02 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.2 -9999 0 -0.57 57 57
FCER1G -0.008 0.082 -9999 0 -0.32 31 31
FCER1A -0.076 0.23 -9999 0 -0.55 76 76
Antigen/IgE/Fc epsilon R1/Fyn -0.081 0.14 -9999 0 -0.47 42 42
MAPK3 0.029 0.017 -9999 0 -10000 0 0
MAPK1 0.029 0.017 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 0.005 0.11 -9999 0 -0.66 11 11
DUSP1 -0.12 0.31 -9999 0 -0.82 79 79
NF-kappa-B/RelA -0.019 0.044 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.004 0.083 -9999 0 -0.37 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.042 0.1 -9999 0 -0.55 10 10
FER -0.013 0.098 -9999 0 -0.43 7 7
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.072 0.17 -9999 0 -0.53 60 60
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.012 0.13 -9999 0 -0.55 11 11
cytokine secretion -0.014 0.032 -9999 0 -0.22 1 1
SPHK1 -0.014 0.092 -9999 0 -0.37 5 5
PTK2 -0.005 0.085 -9999 0 -0.39 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.065 0.13 -9999 0 -0.43 46 46
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.01 0.14 -9999 0 -0.4 39 39
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.047 0.093 -9999 0 -0.42 13 13
MAP2K4 0.021 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.2 -9999 0 -0.61 54 54
mol:Choline -0.048 0.14 -9999 0 -0.43 42 42
SHC/Grb2/SOS1 -0.031 0.066 -9999 0 -0.39 1 1
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.003 0.081 -9999 0 -10000 0 0
HCLS1 -0.012 0.093 -9999 0 -0.38 5 5
PRKCB -0.01 0.12 -9999 0 -0.33 41 41
FCGR2B -0.028 0.18 -9999 0 -0.74 27 27
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.02 0.11 -9999 0 -0.4 12 12
LCP2 0.009 0.039 -9999 0 -0.32 7 7
PLA2G4A -0.041 0.16 -9999 0 -0.51 35 35
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.048 0.14 -9999 0 -0.43 42 42
IKK complex 0.018 0.075 -9999 0 -0.22 8 8
WIPF1 0.013 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.043 -9999 0 -0.92 1 1
VEGFR1 homodimer/NRP1 -0.002 0.042 -9999 0 -0.93 1 1
mol:DAG -0.011 0.16 -9999 0 -0.49 49 49
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.067 -9999 0 -0.77 3 3
CaM/Ca2+ -0.003 0.15 -9999 0 -0.45 49 49
HIF1A 0.021 0.018 -9999 0 -0.38 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.01 0.16 -9999 0 -0.9 3 3
PLCG1 -0.011 0.16 -9999 0 -0.49 49 49
NOS3 0.018 0.15 -9999 0 -0.43 49 49
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.019 0.15 -9999 0 -0.41 49 49
FLT1 0.031 0.048 -9999 0 -1 1 1
PGF -0.069 0.25 -9999 0 -0.81 49 49
VEGFR1 homodimer/NRP2/VEGFR121 -0.015 0.074 -9999 0 -0.76 3 3
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
eNOS/Hsp90 0.025 0.14 -9999 0 -0.8 1 1
endothelial cell proliferation -0.028 0.19 -9999 0 -0.52 50 50
mol:Ca2+ -0.011 0.16 -9999 0 -0.48 49 49
MAPK3 -0.015 0.18 -9999 0 -0.43 70 70
MAPK1 -0.015 0.18 -9999 0 -0.43 70 70
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.069 0.25 -9999 0 -0.8 49 49
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.009 0.13 -9999 0 -0.82 13 13
VEGFA homodimer 0.008 0.065 -9999 0 -0.82 3 3
VEGFR1 homodimer/VEGFA homodimer 0.029 0.074 -9999 0 -0.82 3 3
platelet activating factor biosynthetic process -0.007 0.17 -9999 0 -0.95 2 2
PI3K -0.049 0.15 -9999 0 -0.47 51 51
PRKCA -0.024 0.18 -9999 0 -0.46 70 70
PRKCB -0.021 0.16 -9999 0 -0.47 53 53
VEGFR1 homodimer/PLGF homodimer -0.024 0.17 -9999 0 -0.54 49 49
VEGFA 0.008 0.065 -9999 0 -0.82 3 3
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.011 0.16 -9999 0 -0.49 49 49
RASA1 0.041 0.04 -9999 0 -0.85 1 1
NRP2 -0.013 0.089 -9999 0 -0.31 39 39
VEGFR1 homodimer 0.031 0.048 -9999 0 -1 1 1
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.014 0.16 -9999 0 -0.8 4 4
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
mol:PI-3-4-5-P3 -0.048 0.14 -9999 0 -0.46 51 51
mol:L-citrulline 0.019 0.15 -9999 0 -0.41 49 49
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.004 0.063 -9999 0 -0.72 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.005 0.067 -9999 0 -0.76 3 3
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.046 0.14 -9999 0 -0.44 51 51
PDPK1 0.001 0.16 -9999 0 -0.45 51 51
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.005 0.083 -9999 0 -0.89 3 3
mol:NADP 0.019 0.15 -9999 0 -0.41 49 49
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.004 0.062 -9999 0 -0.7 3 3
VEGFR1 homodimer/NRP2 0.018 0.066 -9999 0 -0.92 1 1
Aurora C signaling

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
INCENP 0.01 0.053 -9999 0 -0.82 2 2
Aurora C/Aurora B/INCENP -0.039 0.077 -9999 0 -0.38 8 8
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.011 0.02 -9999 0 -10000 0 0
AURKB -0.06 0.14 -9999 0 -0.31 109 109
AURKC -0.001 0.066 -9999 0 -0.31 21 21
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 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.004 0.075 -10000 0 -0.82 4 4
SMAD3/SMAD4/ER alpha -0.051 0.14 -10000 0 -0.59 23 23
AKT1 0.008 0.01 -10000 0 -10000 0 0
GSC -0.2 0.55 -10000 0 -1.5 70 70
NKX2-5 0.002 0.029 -10000 0 -0.31 4 4
muscle cell differentiation 0.025 0.05 0.44 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.005 0.079 -10000 0 -10000 0 0
SMAD4 -0.011 0.059 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.012 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.078 -10000 0 -0.54 5 5
SMAD3/SMAD4/VDR 0.01 0.044 -10000 0 -10000 0 0
MYC 0.001 0.14 -10000 0 -0.82 13 13
CDKN2B -0.075 0.14 -10000 0 -10000 0 0
AP1 -0.25 0.5 -10000 0 -1 132 132
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.055 -10000 0 -0.71 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.062 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.012 0.074 -10000 0 -0.31 22 22
SMAD3/SMAD4/GR -0.017 0.044 -10000 0 -10000 0 0
GATA3 -0.031 0.18 -10000 0 -0.77 27 27
SKI/SIN3/HDAC complex/NCoR1 0.041 0.029 -10000 0 -10000 0 0
MEF2C/TIF2 -0.047 0.17 -10000 0 -0.5 48 48
endothelial cell migration -0.009 0.1 1.4 1 -10000 0 1
MAX 0.013 0.006 -10000 0 -10000 0 0
RBBP7 0.012 0.004 -10000 0 -10000 0 0
RBBP4 0.007 0.065 -10000 0 -0.82 3 3
RUNX2 -0.076 0.15 -10000 0 -0.32 131 131
RUNX3 -0.007 0.12 -10000 0 -0.6 16 16
RUNX1 -0.13 0.16 -10000 0 -0.31 215 215
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -0.31 1 1
CDKN1A 0.024 0.071 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.037 0.094 -10000 0 -0.44 3 3
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.004 -10000 0 -10000 0 0
SERPINE1 0.009 0.1 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.041 0.12 -10000 0 -0.59 21 21
SMAD3/SMAD4/ATF3 -0.15 0.26 -10000 0 -0.62 113 113
SAP30 0.01 0.038 -10000 0 -0.82 1 1
Cbp/p300/PIAS3 0.033 0.045 -10000 0 -10000 0 0
JUN -0.25 0.5 -10000 0 -1 123 123
SMAD3/SMAD4/IRF7 -0.016 0.045 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.002 0.091 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.066 0.095 0.46 4 -10000 0 4
DLX1 -0.031 0.19 -10000 0 -0.82 26 26
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.22 0.39 -10000 0 -0.88 128 128
SMAD3/SMAD4/Max -0.017 0.044 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.041 -10000 0 -0.54 2 2
ZBTB17 0.021 0.011 -10000 0 -10000 0 0
LAMC1 0.026 0.053 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.017 0.043 -10000 0 -10000 0 0
IRF7 0.014 0.016 -10000 0 -0.31 1 1
ESR1 -0.048 0.19 -10000 0 -0.53 55 55
HNF4A -0.003 0.045 -10000 0 -0.31 10 10
MEF2C 0.004 0.098 -10000 0 -0.7 2 2
SMAD2-3/SMAD4 -0.031 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.024 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.016 0.024 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.017 0.01 -10000 0 -10000 0 0
SKIL 0.012 0.038 -10000 0 -0.82 1 1
HDAC1 0.012 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.004 -10000 0 -10000 0 0
SNIP1 0.008 0.053 -10000 0 -0.82 2 2
GCN5L2 0.006 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.011 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.18 0.1 -10000 0 -0.68 9 9
SMAD2 -0.002 0.04 -10000 0 -10000 0 0
SMAD3 -0.005 0.047 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.075 -10000 0 -0.44 5 5
SMAD2/SMAD2/SMAD4 0.014 0.027 -10000 0 -10000 0 0
NCOR1 0.012 0.004 -10000 0 -10000 0 0
NCOA2 -0.067 0.24 -10000 0 -0.82 47 47
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.014 0.076 -10000 0 -10000 0 0
IFNB1 0.014 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.099 -10000 0 -1 1 1
CITED1 -0.26 0.14 -10000 0 -0.32 404 404
SMAD2-3/SMAD4/ARC105 -0.022 0.046 -10000 0 -10000 0 0
RBL1 -0.007 0.13 -10000 0 -0.82 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.006 0.081 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.081 0.11 -10000 0 -0.49 14 14
SMAD7 -0.1 0.28 -10000 0 -0.6 92 92
MYC/MIZ-1 0.013 0.11 -10000 0 -0.63 13 13
SMAD3/SMAD4 0.063 0.1 0.31 44 -0.35 1 45
IL10 -0.026 0.19 -10000 0 -0.61 38 38
PIASy/HDAC complex 0.007 0.01 -10000 0 -10000 0 0
PIAS3 0.016 0.005 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.016 0.14 -10000 0 -0.5 25 25
CDK4 0.019 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.01 -10000 0 -10000 0 0
ATF3 -0.18 0.35 -10000 0 -0.79 120 120
SMAD3/SMAD4/SP1 -0.015 0.054 -10000 0 -10000 0 0
FOXG1 -0.003 0.071 -10000 0 -0.39 13 13
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.004 0.097 -10000 0 -0.68 2 2
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.048 0.14 -10000 0 -0.6 26 26
MYOD1 -0.002 0.029 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.023 0.052 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.051 0.14 -10000 0 -0.54 29 29
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.037 -10000 0 -0.82 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.075 0.11 -10000 0 -0.54 11 11
SMAD3/SMAD4/SP1-3 0.007 0.056 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.015 0.021 -10000 0 -10000 0 0
SIN3B 0.012 0.004 -10000 0 -10000 0 0
SIN3A 0.012 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.017 0.095 -10000 0 -0.52 2 2
ITGB5 0.036 0.059 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.26 0.29 -10000 0 -0.59 205 205
AR -0.34 0.41 -10000 0 -0.82 205 205
negative regulation of cell growth -0.039 0.13 -10000 0 -0.55 4 4
SMAD3/SMAD4/MYOD -0.023 0.049 -10000 0 -10000 0 0
E2F5 0.012 0.038 -10000 0 -0.82 1 1
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.011 0.067 -10000 0 -0.36 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.066 -10000 0 -10000 0 0
TFDP1 0.012 0.038 -10000 0 -0.82 1 1
SMAD3/SMAD4/AP1 -0.27 0.51 -10000 0 -1.1 123 123
SMAD3/SMAD4/RUNX2 -0.066 0.095 -10000 0 -0.46 4 4
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.022 0.17 -10000 0 -0.82 21 21
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
alphaV beta3 Integrin -0.02 0.12 -9999 0 -0.66 15 15
PTK2 -0.04 0.15 -9999 0 -0.6 29 29
positive regulation of JNK cascade -0.021 0.081 -9999 0 -0.34 29 29
CDC42/GDP 0.03 0.13 -9999 0 -0.47 29 29
Rac1/GDP 0.032 0.12 -9999 0 -0.46 29 29
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.026 0.1 -9999 0 -0.42 29 29
nectin-3/I-afadin -0.037 0.15 -9999 0 -0.63 29 29
RAPGEF1 0.023 0.14 -9999 0 -0.53 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0.16 -9999 0 -0.62 29 29
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
TLN1 0.019 0.075 -9999 0 -0.93 1 1
Rap1/GTP -0.022 0.087 -9999 0 -0.36 29 29
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.037 0.15 -9999 0 -0.63 29 29
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.024 0.16 -9999 0 -0.58 29 29
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
PI3K -0.031 0.12 -9999 0 -0.5 30 30
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.006 0.034 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.022 0.085 -9999 0 -0.36 29 29
PVRL1 0.004 0.055 -9999 0 -0.31 14 14
PVRL3 -0.036 0.2 -9999 0 -0.82 29 29
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.26 0.15 -9999 0 -0.33 398 398
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.57 39 39
SRC -0.043 0.17 -9999 0 -0.71 29 29
ITGB3 -0.01 0.14 -9999 0 -0.82 14 14
nectin-1(dimer)/I-afadin/I-afadin -0.006 0.034 -9999 0 -10000 0 0
FARP2 0.018 0.15 -9999 0 -0.57 29 29
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.032 0.13 -9999 0 -0.54 29 29
nectin-1/I-afadin -0.006 0.034 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.037 0.13 -9999 0 -0.55 29 29
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.021 0.081 -9999 0 -0.34 29 29
alphaV/beta3 Integrin/Talin 0.018 0.13 -9999 0 -0.59 15 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.011 0.08 -9999 0 -0.99 1 1
VAV2 0.017 0.15 -9999 0 -0.59 29 29
RAP1/GDP -0.026 0.1 -9999 0 -0.43 29 29
ITGAV 0.01 0.053 -9999 0 -0.82 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.032 0.13 -9999 0 -0.54 29 29
nectin-3(dimer)/I-afadin/I-afadin -0.037 0.15 -9999 0 -0.63 29 29
Rac1/GTP -0.027 0.1 -9999 0 -0.44 29 29
PTPRM -0.019 0.082 -9999 0 -0.32 29 29
E-cadherin/beta catenin/alpha catenin -0.003 0.017 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.017 0.085 -9999 0 -0.47 16 16
RGS9BP -0.034 0.19 -9999 0 -0.82 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.066 0.24 -9999 0 -0.81 47 47
mol:Na + -0.021 0.057 -9999 0 -10000 0 0
mol:ADP -0.044 0.19 -9999 0 -0.63 46 46
GNAT2 0.009 0.021 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.089 0.2 -9999 0 -0.55 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.063 -9999 0 -10000 0 0
Cone PDE6 -0.077 0.18 -9999 0 -0.48 78 78
Cone Metarhodopsin II -0.048 0.15 -9999 0 -0.51 46 46
Na + (4 Units) -0.025 0.057 -9999 0 -10000 0 0
GNAT2/GDP -0.077 0.18 -9999 0 -0.48 78 78
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.015 -9999 0 -10000 0 0
Cone Transducin -0.018 0.09 -9999 0 -0.5 16 16
SLC24A2 -0.01 0.065 -9999 0 -0.31 21 21
GNB3/GNGT2 -0.022 0.11 -9999 0 -0.63 16 16
GNB3 -0.013 0.14 -9999 0 -0.78 16 16
GNAT2/GTP -0.001 0.014 -9999 0 -10000 0 0
CNGA3 -0.027 0.11 -9999 0 -0.31 60 60
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.021 0.057 -9999 0 -10000 0 0
mol:Pi -0.089 0.2 -9999 0 -0.55 78 78
Cone CNG Channel -0.016 0.043 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.01 0.065 -9999 0 -0.31 21 21
RGS9 -0.076 0.26 -9999 0 -0.82 52 52
PDE6C 0.003 0.016 -9999 0 -0.31 1 1
GNGT2 0.01 0.045 -9999 0 -0.44 4 4
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.003 0.04 -9999 0 -0.63 2 2
Necdin/E2F1 -0.067 0.12 -9999 0 -0.75 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.036 0.1 -9999 0 -0.48 20 20
NGF (dimer)/p75(NTR)/BEX1 -0.28 0.28 -9999 0 -0.57 231 231
NT-4/5 (dimer)/p75(NTR) -0.074 0.18 -9999 0 -0.66 35 35
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.004 0.12 -9999 0 -0.48 23 23
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.013 0.14 -9999 0 -0.6 21 21
MGDIs/NGR/p75(NTR)/LINGO1 -0.049 0.12 -9999 0 -0.56 18 18
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.057 0.14 -9999 0 -0.56 29 29
LINGO1 -0.003 0.072 -9999 0 -0.31 25 25
Sortilin/TRAF6/NRIF -0.002 0.025 -9999 0 -10000 0 0
proBDNF (dimer) -0.013 0.14 -9999 0 -0.6 21 21
NTRK1 -0.003 0.063 -9999 0 -0.31 19 19
RTN4R 0.013 0 -9999 0 -10000 0 0
neuron apoptosis -0.01 0.13 -9999 0 -0.49 24 24
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.021 0.13 -9999 0 -0.56 20 20
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.04 0.11 -9999 0 -0.51 20 20
MAGEH1 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.045 0.12 -9999 0 -0.51 25 25
Mammalian IAPs/DIABLO -0.028 0.11 -9999 0 -0.49 25 25
proNGF (dimer) 0.006 0.069 -9999 0 -0.56 6 6
MAGED1 0.013 0 -9999 0 -10000 0 0
APP 0.013 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.021 0.15 -9999 0 -0.62 26 26
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.037 0.1 -9999 0 -0.48 20 20
NGF 0.006 0.07 -9999 0 -0.56 6 6
cell cycle arrest 0.042 0.16 -9999 0 -0.47 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.086 -9999 0 -0.35 22 22
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.064 0.16 -9999 0 -0.59 36 36
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.046 0.12 -9999 0 -0.56 21 21
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide -0.01 0.12 -9999 0 -0.51 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.07 -9999 0 -0.43 2 2
p75(NTR)/beta APP -0.05 0.13 -9999 0 -0.63 18 18
BEX1 -0.35 0.41 -9999 0 -0.82 216 216
mol:GDP -0.031 0.13 -9999 0 -0.57 20 20
NGF (dimer) -0.096 0.13 -9999 0 -0.5 30 30
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.043 0.11 -9999 0 -0.52 18 18
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.039 0.11 -9999 0 -0.5 20 20
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.046 0.12 -9999 0 -0.56 21 21
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.061 0.093 -9999 0 -10000 0 0
NT3 (dimer) -0.05 0.2 -9999 0 -0.6 50 50
TP53 -0.005 0.13 -9999 0 -0.45 31 31
PRDM4 -0.01 0.12 -9999 0 -0.51 20 20
BDNF (dimer) -0.13 0.16 -9999 0 -0.54 40 40
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.035 0.1 -9999 0 -0.48 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.042 0.12 -9999 0 -0.52 22 22
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 0.023 0.12 -9999 0 -0.6 4 4
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.01 0.12 -9999 0 -0.51 20 20
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.045 0.12 -9999 0 -0.56 20 20
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.028 -9999 0 -0.63 1 1
NT3 (dimer)/p75(NTR) -0.095 0.2 -9999 0 -0.66 46 46
MAPK8 0.017 0.13 -9999 0 -0.66 4 4
MAPK9 0.024 0.12 -9999 0 -0.6 3 3
APAF1 0.012 0.038 -9999 0 -0.82 1 1
NTF3 -0.05 0.2 -9999 0 -0.6 50 50
NTF4 -0.021 0.15 -9999 0 -0.62 26 26
NDN 0.005 0.084 -9999 0 -0.82 5 5
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.033 0.095 -9999 0 -0.44 21 21
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.054 -9999 0 -0.65 3 3
RhoA-B-C/GTP -0.046 0.12 -9999 0 -0.56 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.048 0.12 -9999 0 -0.48 31 31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.052 0.13 -9999 0 -0.51 31 31
PRKACB 0.012 0.038 -9999 0 -0.82 1 1
proBDNF (dimer)/p75 ECD -0.022 0.11 -9999 0 -0.63 14 14
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.036 0.19 -9999 0 -0.67 35 35
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.066 0.17 -9999 0 -0.47 20 20
BAD 0.029 0.12 -9999 0 -0.59 4 4
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.061 0.18 -9999 0 -0.42 84 84
CYCS -0.001 0.11 -9999 0 -0.48 20 20
ADAM17 0.01 0.053 -9999 0 -0.82 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.042 0.12 -9999 0 -0.52 22 22
BCL2L11 0.029 0.12 -9999 0 -0.59 4 4
BDNF (dimer)/p75(NTR) -0.069 0.16 -9999 0 -0.63 31 31
PI3K -0.042 0.12 -9999 0 -0.52 23 23
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.04 0.11 -9999 0 -0.51 20 20
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.055 0.14 -9999 0 -0.65 20 20
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.04 0.11 -9999 0 -0.51 20 20
TRAF6 0.01 0.053 -9999 0 -0.82 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG -0.004 0.04 -9999 0 -0.31 8 8
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.017 0.14 -9999 0 -0.49 31 31
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.013 0 -9999 0 -10000 0 0
CASP3 0.03 0.11 -9999 0 -0.53 4 4
E2F1 -0.086 0.15 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.013 0.059 -9999 0 -0.53 3 3
NGF (dimer)/TRKA -0.013 0.064 -9999 0 -0.63 3 3
MMP7 -0.18 0.22 -9999 0 -0.37 246 246
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.11 -9999 0 -0.49 22 22
MMP3 -0.04 0.11 -9999 0 -0.31 69 69
APAF-1/Caspase 9 -0.04 0.11 -9999 0 -0.6 7 7
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.03 0.068 -9999 0 -0.32 8 8
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.24 -9999 0 -0.67 74 74
IL1A -0.054 0.22 -9999 0 -0.78 41 41
IL1B -0.032 0.18 -9999 0 -0.63 40 40
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -0.42 2 2
IL1R2 -0.082 0.24 -9999 0 -0.58 78 78
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.071 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.005 0.084 -9999 0 -0.82 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.066 0.027 -9999 0 -10000 0 0
JUN -0.073 0.22 -9999 0 -0.43 122 122
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.066 0.13 -9999 0 -0.47 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.072 0.14 -9999 0 -0.51 38 38
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.066 0.13 -9999 0 -0.47 38 38
IL1 beta fragment/IL1R1/IL1RAP -0.076 0.15 -9999 0 -0.53 39 39
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 0.019 0.12 -9999 0 -0.52 19 19
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.045 0.11 -9999 0 -0.63 11 11
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.82 2 2
PI3K -0.004 0.049 -9999 0 -0.63 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.001 0.087 -9999 0 -0.34 8 8
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.076 0.15 -9999 0 -0.53 39 39
IL1 beta/IL1R2 -0.1 0.22 -9999 0 -0.6 75 75
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.028 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA -0.057 0.12 -9999 0 -0.55 8 8
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.068 0.14 -9999 0 -0.48 44 44
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.1 -9999 0 -0.34 38 38
IL1 alpha/IL1R1/IL1RAP -0.083 0.15 -9999 0 -0.56 38 38
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.022 0.035 -9999 0 -0.47 2 2
IL1RAP -0.07 0.14 -9999 0 -0.31 124 124
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.053 0.12 -9999 0 -0.49 12 12
CASP1 0.008 0.059 -9999 0 -0.52 5 5
IL1RN/IL1R2 -0.11 0.21 -9999 0 -0.62 61 61
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.069 0.14 -9999 0 -0.5 39 39
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.081 -9999 0 -0.34 4 4
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
IL1RN -0.056 0.16 -9999 0 -0.38 86 86
TRAF6/TAK1/TAB1/TAB2 -0.002 0.029 -9999 0 -0.46 2 2
MAP2K6 0.021 0.076 -9999 0 -0.44 13 13
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.065 0.082 -10000 0 -0.33 23 23
NT3 (dimer)/TRKC -0.09 0.19 -10000 0 -0.67 40 40
NT3 (dimer)/TRKB -0.085 0.18 -10000 0 -0.57 50 50
SHC/Grb2/SOS1/GAB1/PI3K 0.037 0.029 -10000 0 -0.33 3 3
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.013 0.14 -10000 0 -0.6 21 21
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.003 0.063 -10000 0 -0.31 19 19
NTRK2 0.005 0.084 -10000 0 -0.82 5 5
NTRK3 -0.055 0.17 -10000 0 -0.39 83 83
NT-4/5 (dimer)/TRKB -0.067 0.16 -10000 0 -0.58 39 39
neuron apoptosis 0.039 0.091 0.42 15 -10000 0 15
SHC 2-3/Grb2 -0.042 0.099 -10000 0 -0.46 15 15
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.029 0.092 -10000 0 -0.63 6 6
SHC3 -0.046 0.1 -10000 0 -0.55 12 12
STAT3 (dimer) 0.018 0.025 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.087 0.17 -10000 0 -0.58 45 45
RIN/GDP -0.009 0.062 -10000 0 -0.27 3 3
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.032 0.091 -10000 0 -0.44 18 18
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.025 0.045 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.021 0.15 -10000 0 -0.62 26 26
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.019 0.078 -10000 0 -0.54 8 8
TRKA/NEDD4-2 -0.008 0.039 -10000 0 -10000 0 0
ELMO1 -0.31 0.4 -10000 0 -0.82 190 190
RhoG/GTP/ELMO1/DOCK1 -0.22 0.27 -10000 0 -0.56 191 191
NGF 0.006 0.07 -10000 0 -0.56 6 6
HRAS 0.012 0.021 -10000 0 -0.31 2 2
DOCK1 0.007 0.075 -10000 0 -0.82 4 4
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.015 0.15 -10000 0 -0.79 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.2 0.23 -10000 0 -0.47 205 205
mol:GDP -0.016 0.089 -10000 0 -0.38 5 5
NGF (dimer) 0.006 0.069 -10000 0 -0.56 6 6
RhoG/GDP -0.25 0.31 -10000 0 -0.64 190 190
RIT1/GDP -0.004 0.063 -10000 0 -0.28 2 2
TIAM1 -0.17 0.16 -10000 0 -0.32 277 277
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.021 0.11 -10000 0 -0.6 15 15
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.024 -10000 0 -0.54 1 1
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.05 0.2 -10000 0 -0.6 50 50
RAP1/GDP -0.018 0.042 -10000 0 -0.25 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.013 0.14 -10000 0 -0.6 21 21
ubiquitin-dependent protein catabolic process -0.01 0.053 -10000 0 -0.54 3 3
Schwann cell development -0.042 0.032 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.017 -10000 0 -0.32 1 1
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.066 0.15 -10000 0 -0.66 13 13
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.036 -10000 0 -10000 0 0
STAT3 0.018 0.025 -10000 0 -10000 0 0
axon guidance -0.064 0.14 -10000 0 -0.62 13 13
MAPK3 0.015 0.077 -10000 0 -0.49 8 8
MAPK1 0.015 0.077 -10000 0 -0.49 8 8
CDC42/GDP -0.004 0.063 -10000 0 -0.28 2 2
NTF3 -0.05 0.2 -10000 0 -0.6 50 50
NTF4 -0.021 0.15 -10000 0 -0.62 26 26
NGF (dimer)/TRKA/FAIM -0.01 0.053 -10000 0 -0.54 3 3
PI3K -0.004 0.049 -10000 0 -0.63 3 3
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.11 -10000 0 -0.47 26 26
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.053 0.18 -10000 0 -0.58 40 40
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.047 -10000 0 -0.42 1 1
Rac1/GDP -0.004 0.063 -10000 0 -0.26 3 3
NGF (dimer)/TRKA/GRIT -0.011 0.055 -10000 0 -0.55 3 3
neuron projection morphogenesis 0 0.094 -10000 0 -0.52 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.053 -10000 0 -0.54 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.061 0.18 -10000 0 -0.42 84 84
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.076 -10000 0 -0.35 18 18
RAS family/GTP/PI3K 0.03 0.032 -10000 0 -0.36 3 3
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.021 -10000 0 -0.46 1 1
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.056 -10000 0 -0.61 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.039 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.019 0.1 -10000 0 -0.55 15 15
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.043 -10000 0 -0.46 3 3
MATK -0.001 0.093 -10000 0 -0.51 13 13
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.015 0.041 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.036 0.098 -10000 0 -0.44 23 23
Rac1/GTP -0.19 0.14 -10000 0 -0.35 194 194
FRS2 family/SHP2/CRK family -0.001 0.021 -10000 0 -0.46 1 1
FOXM1 transcription factor network

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
NFATC3 0.049 0.35 -9999 0 -0.92 14 14
PLK1 0.044 0.068 -9999 0 -10000 0 0
BIRC5 0.024 0.12 -9999 0 -1.5 1 1
HSPA1B 0.049 0.35 -9999 0 -0.92 14 14
MAP2K1 0.032 0.037 -9999 0 -10000 0 0
BRCA2 0.044 0.36 -9999 0 -0.98 17 17
FOXM1 0.038 0.39 -9999 0 -1 17 17
XRCC1 0.049 0.35 -9999 0 -0.92 14 14
FOXM1B/p19 -0.095 0.31 -9999 0 -0.91 25 25
Cyclin D1/CDK4 0.036 0.33 -9999 0 -0.88 11 11
CDC2 0.042 0.36 -9999 0 -0.94 16 16
TGFA 0.02 0.34 -9999 0 -0.92 9 9
SKP2 0.042 0.36 -9999 0 -0.98 17 17
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.049 0.35 -9999 0 -0.92 14 14
RB1 -0.053 0.11 -9999 0 -1.2 1 1
FOXM1C/SP1 0.034 0.36 -9999 0 -1 17 17
AURKB -0.005 0.12 -9999 0 -10000 0 0
CENPF 0.043 0.36 -9999 0 -0.95 14 14
CDK4 0.019 0.015 -9999 0 -10000 0 0
MYC 0.041 0.35 -9999 0 -0.92 21 21
CHEK2 0.032 0.037 -9999 0 -10000 0 0
ONECUT1 0.033 0.34 -9999 0 -0.91 14 14
CDKN2A -0.13 0.16 -9999 0 -0.31 205 205
LAMA4 0.049 0.35 -9999 0 -0.92 14 14
FOXM1B/HNF6 0.026 0.37 -9999 0 -1 14 14
FOS -0.18 0.66 -9999 0 -1.2 129 129
SP1 0.014 0.005 -9999 0 -10000 0 0
CDC25B 0.048 0.35 -9999 0 -0.92 14 14
response to radiation 0.015 0.034 -9999 0 -10000 0 0
CENPB 0.049 0.35 -9999 0 -0.92 14 14
CENPA 0.036 0.37 -9999 0 -0.97 18 18
NEK2 0.039 0.36 -9999 0 -0.96 14 14
HIST1H2BA 0.04 0.35 -9999 0 -0.92 14 14
CCNA2 0.01 0.047 -9999 0 -0.33 9 9
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.037 0.37 -9999 0 -1 14 14
CCNB2 0.046 0.35 -9999 0 -0.95 14 14
CCNB1 0.045 0.36 -9999 0 -0.96 14 14
ETV5 0.048 0.35 -9999 0 -0.92 14 14
ESR1 0 0.43 -9999 0 -1.1 34 34
CCND1 0.039 0.34 -9999 0 -0.89 13 13
GSK3A 0.03 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.037 0.05 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.12 0.23 -9999 0 -0.89 20 20
GAS1 -0.12 0.61 -9999 0 -1.2 104 104
MMP2 0.039 0.38 -9999 0 -1.1 17 17
RB1/FOXM1C 0.047 0.34 -9999 0 -0.92 14 14
CREBBP 0.013 0 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.012 0.093 -10000 0 -0.45 1 1
epithelial cell differentiation -0.047 0.1 -10000 0 -0.48 10 10
ITCH 0.024 0.02 -10000 0 -10000 0 0
WWP1 0 0.079 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.007 0.075 -10000 0 -0.82 4 4
PRL 0.001 0.015 -10000 0 -0.31 1 1
neuron projection morphogenesis 0.005 0.14 -10000 0 -0.51 10 10
PTPRZ1 -0.015 0.13 -10000 0 -0.55 23 23
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.13 -10000 0 -0.56 11 11
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.042 0.17 -10000 0 -0.53 46 46
ADAM17 0.02 0.057 -10000 0 -0.81 2 2
ErbB4/ErbB4 -0.01 0.1 -10000 0 -0.52 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.044 0.17 -10000 0 -0.55 37 37
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.066 0.15 -10000 0 -0.49 46 46
GRIN2B -0.028 0.15 -10000 0 -0.46 46 46
ErbB4/ErbB2/betacellulin -0.039 0.12 -10000 0 -0.61 16 16
STAT1 0.006 0.048 -10000 0 -0.31 11 11
HBEGF -0.004 0.073 -10000 0 -0.31 26 26
PRLR -0.044 0.19 -10000 0 -0.6 46 46
E4ICDs/ETO2 -0.005 0.09 -10000 0 -0.57 2 2
axon guidance 0 0.086 -10000 0 -0.43 3 3
NEDD4 0.02 0.056 -10000 0 -0.8 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.043 0.15 -10000 0 -0.64 26 26
CBFA2T3 0.011 0.04 -10000 0 -0.56 2 2
ErbB4/ErbB2/HBEGF -0.029 0.061 -10000 0 -0.57 2 2
MAPK3 -0.004 0.14 -10000 0 -0.52 11 11
STAT1 (dimer) -0.007 0.089 -10000 0 -0.35 5 5
MAPK1 -0.004 0.14 -10000 0 -0.52 11 11
JAK2 0.01 0.053 -10000 0 -0.82 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.066 0.15 -10000 0 -0.49 46 46
NRG1 -0.034 0.2 -10000 0 -0.64 46 46
NRG3 -0.048 0.22 -10000 0 -0.82 36 36
NRG2 -0.081 0.26 -10000 0 -0.79 57 57
NRG4 0.009 0.033 -10000 0 -0.31 5 5
heart development 0 0.086 -10000 0 -0.43 3 3
neural crest cell migration -0.032 0.16 -10000 0 -0.49 46 46
ERBB2 0.028 0.043 -10000 0 -0.61 2 2
WWOX/E4ICDs -0.004 0.092 -10000 0 -0.94 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.036 0.083 -10000 0 -0.65 4 4
apoptosis 0.056 0.14 0.46 37 -10000 0 37
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.065 0.19 -10000 0 -0.55 55 55
ErbB4/ErbB2/epiregulin -0.078 0.087 -10000 0 -0.55 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.021 0.14 -10000 0 -0.64 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.061 0.12 -10000 0 -0.47 28 28
MDM2 0.001 0.087 -10000 0 -0.45 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.15 -10000 0 -0.5 46 46
STAT5A 0.008 0.081 -10000 0 -0.51 1 1
ErbB4/EGFR/neuregulin 1 beta -0.07 0.16 -10000 0 -0.51 49 49
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.032 0.063 -10000 0 -0.42 1 1
STAT5A (dimer) -0.05 0.11 -10000 0 -0.52 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.079 -10000 0 -0.51 1 1
LRIG1 0 0.1 -10000 0 -0.82 8 8
EREG -0.14 0.16 -10000 0 -0.31 228 228
BTC -0.014 0.15 -10000 0 -0.82 16 16
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0 0.086 -10000 0 -0.44 3 3
ERBB4 -0.01 0.1 -10000 0 -0.52 1 1
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.01 0.02 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.025 0.056 -10000 0 -0.5 2 2
glial cell differentiation 0.032 0.062 0.42 1 -10000 0 1
WWOX 0.012 0.038 -10000 0 -0.82 1 1
cell proliferation -0.024 0.17 -10000 0 -0.54 21 21
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.04 0.12 -9999 0 -0.42 46 46
Syndecan-3/Neurocan -0.035 0.12 -9999 0 -0.46 35 35
POMC -0.16 0.33 -9999 0 -0.8 102 102
EGFR 0.007 0.075 -9999 0 -0.82 4 4
Syndecan-3/EGFR -0.004 0.042 -9999 0 -0.46 4 4
AGRP -0.005 0.064 -9999 0 -0.31 20 20
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.05 0.22 -9999 0 -0.76 39 39
long-term memory 0 0.005 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.039 0.08 -9999 0 -0.46 10 10
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0 0.009 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.008 -9999 0 -10000 0 0
MC4R 0.001 0.038 -9999 0 -0.31 7 7
SRC 0.013 0.015 -9999 0 -0.31 1 1
PTN -0.066 0.24 -9999 0 -0.81 47 47
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis -0.068 0.15 -9999 0 -0.41 80 80
Syndecan-3/AgRP -0.006 0.025 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.007 0.027 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.038 0.079 -9999 0 -0.45 10 10
IL8 -0.081 0.17 -9999 0 -0.35 125 125
Syndecan-3/Fyn/Cortactin 0 0.005 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.13 0.25 -9999 0 -0.63 99 99
Gamma Secretase 0 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.24 0.38 -10000 0 -0.82 151 151
HRAS 0.012 0.021 -10000 0 -0.31 2 2
EGFR 0.007 0.075 -10000 0 -0.82 4 4
AKT 0.019 0.025 -10000 0 -10000 0 0
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.11 0.16 -10000 0 -0.31 179 179
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.01 0.13 -10000 0 -0.69 16 16
PIK3R3 0.012 0.038 -10000 0 -0.82 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.059 0.098 -10000 0 -0.26 42 42
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.024 0.19 1 -0.17 1 2
PI3K -0.039 0.095 0.23 1 -0.22 49 50
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.025 0.027 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.038 -10000 0 -0.82 1 1
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.06 0.16 -10000 0 -0.47 62 62
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.056 -10000 0 -0.21 34 34
GNB1/GNG2 -0.001 0.025 -10000 0 -0.55 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.064 0.17 -10000 0 -0.52 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.014 0.038 0.12 61 -10000 0 61
GNAL -0.09 0.27 -10000 0 -0.82 61 61
GNG2 0.012 0.038 -10000 0 -0.82 1 1
CRH -0.015 0.082 -10000 0 -0.31 34 34
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.069 -10000 0 -0.46 11 11
MAPK11 0.009 0 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0 0.078 -9999 0 -10000 0 0
STMN1 -0.021 0.094 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.027 0.11 -9999 0 -0.33 27 27
Chromosomal passenger complex/Cul3 protein complex 0.006 0.071 -9999 0 -0.28 14 14
BIRC5 -0.018 0.1 -9999 0 -0.33 44 44
DES -0.38 0.3 -9999 0 -0.61 296 296
Aurora C/Aurora B/INCENP -0.016 0.088 -9999 0 -0.4 7 7
Aurora B/TACC1 -0.022 0.081 -9999 0 -0.71 1 1
Aurora B/PP2A -0.026 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.026 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.048 0.15 -9999 0 -0.39 58 58
Cul3 protein complex -0.018 0.087 -9999 0 -0.54 12 12
KIF2C 0 0.042 -9999 0 -10000 0 0
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.04 0.12 -9999 0 -0.31 80 80
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.026 0.091 -9999 0 -10000 0 0
SEPT1 0.008 0.041 -9999 0 -0.31 8 8
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.007 0.045 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
H3F3B -0.007 0.055 -9999 0 -10000 0 0
AURKB -0.051 0.14 -9999 0 -0.31 109 109
AURKC -0.001 0.066 -9999 0 -0.31 21 21
CDCA8 0.01 0.027 -9999 0 -0.33 3 3
cytokinesis -0.066 0.083 -9999 0 -0.43 5 5
Aurora B/Septin1 -0.027 0.1 -9999 0 -0.46 5 5
AURKA 0.012 0.002 -9999 0 -10000 0 0
INCENP 0.009 0.054 -9999 0 -0.83 2 2
KLHL13 -0.017 0.14 -9999 0 -0.54 27 27
BUB1 -0.1 0.16 -9999 0 -0.32 170 170
hSgo1/Aurora B/Survivin -0.028 0.12 -9999 0 -0.44 18 18
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.073 -9999 0 -10000 0 0
SGOL1 0.001 0.062 -9999 0 -0.31 18 18
CENPA -0.007 0.069 -9999 0 -0.26 3 3
NCAPG -0.018 0.096 -9999 0 -0.31 47 47
Aurora B/HC8 Proteasome -0.026 0.091 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.026 0.091 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.035 0.12 -9999 0 -0.31 72 72
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.026 0.091 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.035 0.081 -9999 0 -0.39 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.008 0.06 -9999 0 -0.55 1 1
KIF23 -0.005 0.075 -9999 0 -0.32 26 26
VIM -0.021 0.093 -9999 0 -10000 0 0
RACGAP1 0.013 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.013 0.083 -9999 0 -0.27 12 12
Chromosomal passenger complex/EVI5 0.009 0.12 -9999 0 -0.48 6 6
TACC1 0.012 0.038 -9999 0 -0.82 1 1
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.015 0.057 -9999 0 -0.55 5 5
ADCY5 -0.058 0.2 -9999 0 -0.55 66 66
ADCY6 0.015 0.057 -9999 0 -0.55 5 5
ADCY7 0.015 0.057 -9999 0 -0.55 5 5
ADCY1 0.007 0.091 -9999 0 -0.62 9 9
ADCY2 -0.041 0.17 -9999 0 -0.56 47 47
ADCY3 0.015 0.057 -9999 0 -0.55 5 5
ADCY8 -0.12 0.1 -9999 0 -0.7 5 5
PRKCE 0.005 0.065 -9999 0 -0.64 5 5
ADCY9 0.015 0.057 -9999 0 -0.55 5 5
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.057 0.11 -9999 0 -0.38 32 32
Presenilin action in Notch and Wnt signaling

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.019 0.12 -10000 0 -0.78 12 12
HDAC1 0.002 0.009 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 0.001 0.099 -10000 0 -0.82 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.008 0.065 -10000 0 -0.82 3 3
AP1 -0.14 0.26 -10000 0 -0.52 140 140
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.007 0.13 -10000 0 -0.82 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.054 -10000 0 -0.34 1 1
NICD/RBPSUH -0.018 0.11 -10000 0 -0.73 12 12
WIF1 -0.033 0.1 -10000 0 -0.31 59 59
NOTCH1 -0.019 0.12 -10000 0 -0.76 12 12
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.01 0.083 -10000 0 -0.31 34 34
DKK1 -0.041 0.12 -10000 0 -0.32 79 79
beta catenin/beta TrCP1 0.036 0.037 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0 0.037 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.024 0.037 -10000 0 -0.35 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.2 0.36 -10000 0 -0.82 128 128
JUN -0.17 0.35 -10000 0 -0.82 110 110
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.029 0.04 0.24 13 -10000 0 13
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.035 0.11 -10000 0 -0.55 19 19
HNF1A 0.012 0.002 -10000 0 -10000 0 0
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.015 0.25 -10000 0 -1.5 13 13
NKD1 -0.014 0.14 -10000 0 -0.7 18 18
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.024 0.12 -10000 0 -0.62 19 19
apoptosis -0.14 0.26 -10000 0 -0.52 140 140
Delta 1/NOTCHprecursor -0.019 0.12 -10000 0 -0.76 12 12
DLL1 0.011 0.04 -10000 0 -0.56 2 2
PPARD 0.024 0.017 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.002 0.061 -10000 0 -1.1 1 1
DVL1 0.003 0.01 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.037 0.078 -10000 0 -0.37 8 8
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.015 0.008 -10000 0 -10000 0 0
CCND1 0.018 0.044 -10000 0 -10000 0 0
WNT1 0.009 0.026 -10000 0 -0.31 3 3
Axin1/APC/beta catenin 0.042 0.052 -10000 0 -0.67 1 1
DKK2 -0.025 0.16 -10000 0 -0.66 28 28
NOTCH1 precursor/DVL1 -0.013 0.1 -10000 0 -0.64 12 12
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.025 0.13 -10000 0 -0.64 19 19
PPP2R5D 0.011 0.063 0.37 14 -10000 0 14
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.017 0.044 -10000 0 -10000 0 0
RBPJ 0.013 0.015 -10000 0 -0.31 1 1
CREBBP 0.017 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.012 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.013 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.015 0.063 -9999 0 -0.23 9 9
RAB3GAP2/RIMS1/UNC13B -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.01 0.021 -9999 0 -0.31 2 2
mol:ACh -0.007 0.04 -9999 0 -0.15 29 29
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.015 0.063 -9999 0 -0.23 9 9
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.018 0.093 -9999 0 -0.31 44 44
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.11 0.16 -9999 0 -0.4 61 61
SNAP25 -0.031 0.096 -9999 0 -0.38 29 29
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.16 0.22 -9999 0 -0.38 216 216
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.013 0.12 -9999 0 -0.44 29 29
CCNA2 0.007 0.044 -9999 0 -0.31 9 9
PIK3CA 0.009 0.065 -9999 0 -0.82 3 3
JAK3 -0.069 0.14 -9999 0 -0.31 124 124
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.018 0.14 -9999 0 -0.56 18 18
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.022 0 -9999 0 -10000 0 0
IL2RA -0.04 0.24 -9999 0 -0.97 29 29
IL2RB -0.014 0.13 -9999 0 -0.5 27 27
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.046 0.19 -9999 0 -0.54 53 53
G1/S transition of mitotic cell cycle 0.039 0.054 -9999 0 -0.59 3 3
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
CCND2 0.033 0 -9999 0 -10000 0 0
LCK -0.009 0.11 -9999 0 -0.43 26 26
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.008 0.065 -9999 0 -0.82 3 3
CCND3 0.028 0.13 -9999 0 -0.64 7 7
Insulin Pathway

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
CBL/APS/CAP -0.055 0.15 -9999 0 -0.44 61 61
TC10/GTP -0.004 0.038 -9999 0 -0.42 4 4
Insulin Receptor/Insulin/IRS1/Shp2 -0.062 0.17 -9999 0 -0.52 59 59
HRAS 0.012 0.021 -9999 0 -0.31 2 2
APS homodimer 0.013 0.015 -9999 0 -0.31 1 1
GRB14 -0.007 0.13 -9999 0 -0.82 12 12
FOXO3 -0.025 0.11 -9999 0 -0.72 11 11
AKT1 -0.011 0.16 -9999 0 -0.88 2 2
INSR 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.007 0.075 -9999 0 -0.82 4 4
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.038 0 -9999 0 -10000 0 0
CAV1 -0.046 0.18 -9999 0 -0.48 72 72
CBL/APS/CAP/Crk-II/C3G -0.004 0.042 -9999 0 -0.46 4 4
Insulin Receptor/Insulin/IRS1/NCK2 -0.061 0.17 -9999 0 -0.51 59 59
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.056 0.15 -9999 0 -0.45 61 61
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.003 0.1 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.15 -9999 0 -0.76 2 2
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.054 0.13 -9999 0 -0.78 2 2
HRAS/GTP -0.05 0.13 -9999 0 -0.38 59 59
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.057 0.15 -9999 0 -0.47 59 59
PRKCI -0.014 0.034 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.063 0.16 -9999 0 -0.42 73 73
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.057 0.15 -9999 0 -0.46 61 61
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
AKT2 -0.011 0.16 -9999 0 -0.88 2 2
PRKCZ -0.014 0.034 -9999 0 -10000 0 0
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
SHC/SHIP -0.03 0.16 -9999 0 -0.45 59 59
F2RL2 -0.08 0.16 -9999 0 -0.32 134 134
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.004 0.045 -9999 0 -0.49 4 4
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.04 0.17 -9999 0 -0.48 59 59
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.027 0.15 -9999 0 -1 11 11
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
IRS1 -0.087 0.27 -9999 0 -0.82 59 59
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.04 0.16 -9999 0 -0.48 59 59
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.002 0.15 -9999 0 -0.63 4 4
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0.053 -9999 0 -0.82 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.008 0.12 -9999 0 -0.33 59 59
Insulin Receptor/Insulin/IRS1 -0.062 0.17 -9999 0 -0.52 59 59
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.036 0.064 -9999 0 -0.47 3 3
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.002 0.079 -10000 0 -0.36 8 8
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.012 0.038 -10000 0 -0.82 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.041 0.078 0.26 2 -10000 0 2
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.068 0.23 -10000 0 -0.63 69 69
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.024 -10000 0 -0.54 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.03 0.11 -10000 0 -0.31 63 63
PRKCI 0.013 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.039 0.1 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.042 0.082 0.26 2 -10000 0 2
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.027 0 -10000 0 -10000 0 0
SFN -0.21 0.18 -10000 0 -0.33 314 314
LNPEP -0.017 0.16 -10000 0 -0.82 18 18
YWHAE 0.013 0 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.027 0.16 -9999 0 -0.43 65 65
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.049 0.12 -9999 0 -0.74 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.011 0.043 -9999 0 -0.59 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.06 -9999 0 -0.3 2 2
CaM/Ca2+ -0.056 0.14 -9999 0 -0.4 65 65
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.02 0.16 -9999 0 -0.4 65 65
AKT1 -0.002 0.15 -9999 0 -0.62 3 3
MAP2K1 -0.005 0.15 -9999 0 -0.51 5 5
MAP3K11 -0.017 0.16 -9999 0 -0.4 65 65
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.024 0.066 -9999 0 -0.63 1 1
Rap1/GTP -0.041 0.1 -9999 0 -0.6 1 1
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.063 0.15 -9999 0 -0.45 64 64
CEBPB 0.018 0.17 -9999 0 -0.82 5 5
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.059 0.15 -9999 0 -1.1 2 2
STAT1 -0.019 0.16 -9999 0 -0.4 65 65
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.28 -9999 0 -0.71 78 78
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
STAT1 (dimer)/PIAS1 -0.01 0.15 -9999 0 -0.47 5 5
CEBPB/PTGES2/Cbp/p300 -0.035 0.081 -9999 0 -0.44 5 5
mol:Ca2+ -0.06 0.15 -9999 0 -0.43 65 65
MAPK3 0.01 0.14 -9999 0 -0.52 5 5
STAT1 (dimer) -0.03 0.08 -9999 0 -0.42 2 2
MAPK1 0.01 0.14 -9999 0 -0.52 5 5
JAK2 0.006 0.056 -9999 0 -0.84 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.017 0.18 -9999 0 -0.66 23 23
SMAD7 0.041 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.05 0.12 -9999 0 -0.76 1 1
PI3K -0.056 0.14 -9999 0 -0.51 8 8
IFNG -0.1 0.28 -9999 0 -0.72 78 78
apoptosis 0.013 0.13 -9999 0 -0.45 23 23
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.004 0.067 -9999 0 -0.31 22 22
CAMK2B 0.005 0.084 -9999 0 -0.82 5 5
FRAP1 0 0.14 -9999 0 -0.56 3 3
PRKCD -0.002 0.15 -9999 0 -0.63 3 3
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.023 0.06 -9999 0 -0.3 2 2
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.029 0.12 -9999 0 -0.53 1 1
STAT1 (dimer)/PIASy -0.054 0.13 -9999 0 -0.48 5 5
SOCS1 0.001 0.074 -9999 0 -1.5 1 1
mol:GDP -0.048 0.12 -9999 0 -0.71 1 1
CASP1 0.039 0.062 -9999 0 -0.35 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.042 0.057 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.055 0.13 -9999 0 -0.48 9 9
RAP1/GDP -0.041 0.1 -9999 0 -0.6 1 1
CBL -0.017 0.16 -9999 0 -0.4 65 65
MAP3K1 -0.016 0.16 -9999 0 -0.4 64 64
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.023 0.06 -9999 0 -0.3 2 2
PTPN11 -0.027 0.16 -9999 0 -0.43 65 65
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.16 0.34 -9999 0 -0.82 101 101
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.026 -9999 0 -0.31 3 3
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.023 -9999 0 -10000 0 0
HIF1A 0.022 0.024 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.004 0.04 -9999 0 -0.5 3 3
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.13 0.16 -9999 0 -0.31 210 210
ARNT/IPAS -0.13 0.25 -9999 0 -0.63 101 101
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.023 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.087 -9999 0 -0.53 12 12
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.017 -9999 0 -10000 0 0
VHL 0.008 0.065 -9999 0 -0.82 3 3
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.023 -9999 0 -10000 0 0
EGLN3 -0.017 0.14 -9999 0 -0.51 28 28
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.01 0.053 -9999 0 -0.82 2 2
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.051 -9999 0 -0.6 3 3
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.032 0.073 -9999 0 -0.29 1 1
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.001 0.099 -9999 0 -0.82 7 7
CDKN1A -0.012 0.088 -9999 0 -10000 0 0
PRL-3/alpha Tubulin -0.017 0.056 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.1 -9999 0 -0.64 9 9
AGT -0.019 0.13 -9999 0 -0.44 35 35
CCNA2 -0.061 0.2 -9999 0 -0.58 4 4
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.11 0.26 -9999 0 -0.62 104 104
CDK2/Cyclin E1 0.004 0.076 -9999 0 -10000 0 0
MAPK3 0.005 0.063 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.005 0.063 -9999 0 -10000 0 0
PTP4A1 -0.071 0.21 -9999 0 -0.48 104 104
PTP4A3 -0.014 0.091 -9999 0 -0.31 41 41
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.005 0.063 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1 -0.016 0.092 -9999 0 -0.25 15 15
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.067 0.2 -9999 0 -0.58 4 4
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.012 0.041 -9999 0 -10000 0 0
RHOC -0.016 0.092 -9999 0 -10000 0 0
RHOA -0.016 0.092 -9999 0 -10000 0 0
cell motility -0.015 0.098 -9999 0 -0.26 15 15
PRL-1/alpha Tubulin -0.06 0.2 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.026 0.096 -9999 0 -0.67 7 7
ROCK1 -0.015 0.099 -9999 0 -0.26 15 15
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.07 0.21 -9999 0 -0.48 104 104
ATF5 0 0.065 -9999 0 -0.31 20 20
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.003 0.1 0.56 14 -10000 0 14
PI3K Class IB/PDE3B -0.003 0.1 -10000 0 -0.56 14 14
PDE3B -0.003 0.1 -10000 0 -0.56 14 14
Ceramide signaling 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
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.003 0.14 -10000 0 -0.7 11 11
BAG4 0.012 0.038 -10000 0 -0.82 1 1
PKC zeta/ceramide -0.018 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.67 35 35
BAX -0.006 0.02 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.008 -10000 0 -10000 0 0
BAD -0.017 0.04 -10000 0 -10000 0 0
SMPD1 -0.006 0.096 -10000 0 -0.26 58 58
RB1 -0.018 0.046 -10000 0 -0.5 1 1
FADD/Caspase 8 0.009 0.14 -10000 0 -0.66 11 11
MAP2K4 -0.009 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.05 -10000 0 -0.51 2 2
EGF -0.11 0.29 -10000 0 -0.78 76 76
mol:ceramide -0.028 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.029 -10000 0 -0.63 1 1
ASAH1 0.012 0.038 -10000 0 -0.82 1 1
negative regulation of cell cycle -0.019 0.045 -10000 0 -0.49 1 1
cell proliferation -0.099 0.16 -10000 0 -0.39 114 114
BID -0.017 0.092 -10000 0 -0.38 13 13
MAP3K1 -0.017 0.04 -10000 0 -10000 0 0
EIF2A 0 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.002 0.047 -10000 0 -0.47 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.047 -10000 0 -0.47 2 2
Cathepsin D/ceramide -0.018 0.041 -10000 0 -10000 0 0
FADD -0.003 0.14 -10000 0 -0.7 11 11
KSR1 -0.019 0.053 -10000 0 -0.55 2 2
MAPK8 -0.01 0.06 -10000 0 -0.32 11 11
PRKRA -0.017 0.04 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.35 -10000 0 -0.82 113 113
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.042 -10000 0 -10000 0 0
CTSD 0.013 0.015 -10000 0 -0.31 1 1
regulation of nitric oxide biosynthetic process -0.001 0.028 -10000 0 -0.62 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.086 0.19 -10000 0 -0.42 114 114
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.029 -10000 0 -0.63 1 1
RelA/NF kappa B1 -0.001 0.028 -10000 0 -0.63 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.012 0.15 -10000 0 -0.74 11 11
TNFR1A/BAG4/TNF-alpha -0.067 0.18 -10000 0 -0.54 59 59
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.002 0.048 -10000 0 -0.48 2 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.004 0.052 0.18 27 -10000 0 27
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
TNFR1A/BAG4 -0.001 0.028 -10000 0 -0.63 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.066 0.18 -10000 0 -0.54 58 58
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.079 -10000 0 -10000 0 0
MAP2K2 -0.002 0.048 -10000 0 -0.48 2 2
SMPD3 -0.011 0.12 -10000 0 -0.3 63 63
TNF -0.09 0.27 -10000 0 -0.77 64 64
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.023 0.11 0.28 70 -10000 0 70
NF kappa B1/RelA/I kappa B alpha -0.001 0.021 -10000 0 -0.46 1 1
AIFM1 0.003 0.052 0.18 27 -10000 0 27
BCL2 -0.048 0.22 -10000 0 -0.82 36 36
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.03 0.62 1 -10000 0 1
CDKN1A -0.007 0.037 -10000 0 -10000 0 0
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
FOXO3 0 0.007 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.024 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.006 0.033 -10000 0 -0.31 5 5
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.02 -10000 0 -10000 0 0
PPARGC1A -0.35 0.41 -10000 0 -0.82 215 215
FHL2 -0.053 0.22 -10000 0 -0.82 39 39
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.031 -10000 0 -0.63 1 1
HIST2H4A 0.021 0.03 -10000 0 -0.63 1 1
SIRT1/FOXO3a 0 0.026 -10000 0 -0.55 1 1
SIRT1 0.001 0.039 -10000 0 -0.82 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.027 -10000 0 -0.54 1 1
SIRT1/Histone H1b -0.005 0.048 -10000 0 -0.33 9 9
apoptosis 0 0.029 0.54 1 -10000 0 1
SIRT1/PGC1A -0.24 0.28 -10000 0 -0.55 215 215
p53/SIRT1 0.005 0.044 -10000 0 -0.63 1 1
SIRT1/FOXO4 0.001 0.027 -10000 0 -0.53 1 1
FOXO1/FHL2/SIRT1 -0.039 0.14 -10000 0 -0.5 40 40
HIST1H1E 0.016 0.051 -10000 0 -0.36 8 8
SIRT1/p300 0.001 0.031 -10000 0 -0.63 1 1
muscle cell differentiation 0 0.031 0.55 1 -10000 0 1
TP53 0.002 0.013 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.029 -10000 0 -0.54 1 1
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.001 0.037 -10000 0 -0.63 1 1
ACSS2 0.021 0.03 -10000 0 -0.63 1 1
SIRT1/PCAF/MYOD 0 0.031 -10000 0 -0.55 1 1
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.01 0.12 -10000 0 -0.57 9 9
UGCG -0.044 0.18 -10000 0 -0.8 24 24
AKT1/mTOR/p70S6K/Hsp90/TERT 0.02 0.13 -10000 0 -0.41 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.023 0.18 -10000 0 -0.78 24 24
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.059 0.14 -10000 0 -0.46 35 35
FRAP1 0.001 0.2 -10000 0 -0.54 35 35
FOXO3 0.019 0.16 -10000 0 -0.61 17 17
AKT1 0.01 0.18 -10000 0 -0.62 21 21
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 -0.005 0.023 -10000 0 -10000 0 0
SGMS1 -0.005 0.023 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.046 -10000 0 -0.56 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.003 0.16 -10000 0 -0.44 36 36
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.052 -10000 0 -0.63 3 3
RPS6KB1 0.016 0.041 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.012 5 5
JAK3 -0.067 0.14 -10000 0 -0.31 124 124
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
MYC 0.007 0.22 -10000 0 -0.94 18 18
MYB -0.015 0.2 -10000 0 -1.3 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.16 -10000 0 -0.55 24 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.037 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.16 -10000 0 -0.53 24 24
Rac1/GDP 0.024 0.043 -10000 0 -0.5 3 3
T cell proliferation 0.017 0.15 -10000 0 -0.51 21 21
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.051 16 16
PRKCZ 0.016 0.15 -10000 0 -0.53 21 21
NF kappa B1 p50/RelA -0.058 0.14 -10000 0 -0.53 19 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.13 -10000 0 -0.6 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.045 0.19 -10000 0 -0.57 49 49
IL2RB -0.013 0.13 -10000 0 -0.5 27 27
TERT 0 0.032 -10000 0 -0.31 5 5
E2F1 -0.004 0.075 -10000 0 -0.45 10 10
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.024 16 -10000 0 16
PTPN11 0.011 0.038 -10000 0 -0.82 1 1
IL2RG -0.045 0.19 -10000 0 -0.54 53 53
actin cytoskeleton organization 0.017 0.15 -10000 0 -0.51 21 21
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.006 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.066 -10000 0 -0.82 3 3
Rac1/GTP 0.031 0.042 -10000 0 -0.48 3 3
LCK -0.008 0.11 -10000 0 -0.43 26 26
BCL2 -0.026 0.28 -10000 0 -0.82 48 48
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.005 0.051 -9999 0 -0.31 12 12
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.017 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.82 16 16
mol:Sphinganine-1-P 0.019 0.035 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.002 0.014 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.01 0.033 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.011 -9999 0 -10000 0 0
S1PR5 0.007 0.054 -9999 0 -0.38 8 8
S1PR4 0.01 0.033 -9999 0 -0.31 5 5
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
S1P/S1P5/G12 -0.004 0.028 -9999 0 -0.48 1 1
S1P/S1P3/Gq -0.05 0.15 -9999 0 -0.31 121 121
S1P/S1P4/Gi 0.031 0.068 -9999 0 -0.32 17 17
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.82 114 114
GNA15 -0.014 0.095 -9999 0 -0.33 39 39
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.004 0.12 -9999 0 -0.82 10 10
ABCC1 0.013 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
ITGA4 0.002 0.078 -9999 0 -0.44 12 12
alpha4/beta7 Integrin -0.031 0.12 -9999 0 -0.62 16 16
alpha4/beta1 Integrin -0.008 0.056 -9999 0 -0.63 3 3
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.044 0.12 0.33 1 -0.36 61 62
FRAP1 0.008 0.027 -10000 0 -10000 0 0
AKT1 -0.01 0.11 0.24 1 -0.3 61 62
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.028 0.078 -10000 0 -0.5 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.008 0.023 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.066 -10000 0 -0.45 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.036 0.14 -10000 0 -0.42 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.009 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.061 -10000 0 -0.35 3 3
MAP3K5 0.011 0.021 -10000 0 -0.45 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.021 -10000 0 -0.45 1 1
mol:LY294002 0 0.001 0.001 2 -0.002 58 60
EIF4B 0.016 0.055 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.014 0.039 -10000 0 -0.31 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.026 0.14 -10000 0 -0.39 61 61
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.041 0.18 1 -0.28 2 3
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.023 0.065 -10000 0 -0.44 3 3
mol:Amino Acids 0 0.001 0.001 2 -0.002 58 60
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.041 0.12 0.26 1 -0.33 61 62
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.034 -10000 0 -0.62 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.03 0.084 -10000 0 -0.56 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 58 -0.001 2 60
RPS6 0.013 0 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.047 0.15 -10000 0 -0.46 59 59
INS 0 0 -10000 0 -10000 0 0
PTEN 0.011 0.037 -10000 0 -0.82 1 1
PDK2 -0.04 0.11 0.26 1 -0.32 61 62
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
PPP2R5D 0.015 0.025 -10000 0 -10000 0 0
peptide biosynthetic process 0.018 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.004 3 4
EEF2 0.018 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.019 0.008 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.035 0.14 -10000 0 -0.63 27 27
ATM 0.012 0.038 -10000 0 -0.82 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.012 0.038 -10000 0 -0.82 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.03 -10000 0 -0.44 2 2
protein ubiquitination -0.026 0.1 -10000 0 -0.45 28 28
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.042 -10000 0 -0.54 3 3
MRE11A 0.008 0.065 -10000 0 -0.82 3 3
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.035 0.14 -10000 0 -0.63 27 27
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA 0 0.065 -10000 0 -0.31 20 20
DNA repair 0.052 0.1 -10000 0 -0.41 1 1
BRCA1/BARD1/ubiquitin -0.035 0.14 -10000 0 -0.63 27 27
BARD1/DNA-PK -0.027 0.11 -10000 0 -0.49 27 27
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.035 0.14 0.62 27 -10000 0 27
BRCA1/BARD1/CTIP/M/R/N Complex 0.02 0.091 -10000 0 -0.33 31 31
BRCA1/BACH1/BARD1/TopBP1 -0.03 0.12 -10000 0 -0.54 27 27
BRCA1/BARD1/P53 -0.028 0.11 -10000 0 -0.49 28 28
BARD1/CSTF1/BRCA1 -0.03 0.12 -10000 0 -0.54 27 27
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.033 0.19 -10000 0 -0.82 27 27
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.03 0.12 -10000 0 -0.54 27 27
BRCA1/BARD1/UbcH7 -0.03 0.12 -10000 0 -0.54 27 27
BRCA1/BARD1/RAD51/PCNA -0.028 0.11 -10000 0 -0.49 27 27
BARD1/DNA-PK/P53 -0.025 0.1 -10000 0 -0.46 27 27
BRCA1/BARD1/Ubiquitin -0.035 0.14 -10000 0 -0.63 27 27
BRCA1/BARD1/CTIP -0.028 0.11 -10000 0 -0.49 28 28
FA complex 0.038 0.024 -10000 0 -10000 0 0
BARD1/EWS -0.035 0.14 -10000 0 -0.63 27 27
RBBP8 0.023 0.029 -10000 0 -0.63 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.028 0.11 0.49 28 -10000 0 28
BRCA1/BARD1 -0.026 0.11 -10000 0 -0.46 28 28
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.035 0.14 -10000 0 -0.64 27 27
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0.021 -10000 0 -0.31 2 2
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.035 0.14 -10000 0 -0.63 27 27
EWSR1 0.013 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.004 0.12 -10000 0 -0.82 10 10
ANTXR2 0.008 0.065 -10000 0 -0.82 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.1 13 13
monocyte activation -0.047 0.17 -10000 0 -0.48 61 61
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.014 -10000 0 -10000 0 0
MAP2K7 -0.002 0.014 -10000 0 -10000 0 0
MAP2K6 -0.014 0.075 -10000 0 -0.5 11 11
CYAA 0.003 0.08 -10000 0 -0.48 13 13
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.024 0.13 -10000 0 -0.46 40 40
Channel -0.014 0.082 -10000 0 -0.51 13 13
NLRP1 -0.004 0.034 -10000 0 -0.49 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.1 13 -10000 0 13
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.022 0.086 -10000 0 -0.46 15 15
PA/Cellular Receptors -0.015 0.088 -10000 0 -0.55 13 13
apoptosis -0.003 0.016 -10000 0 -0.1 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.079 -10000 0 -0.48 13 13
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.09 0.27 -10000 0 -0.77 64 64
VCAM1 -0.048 0.17 -10000 0 -0.48 61 61
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.012 0.024 0.1 11 -10000 0 11
IL18 -0.01 0.085 -10000 0 -0.41 14 14
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.1 13 13
LEF -0.003 0.016 -10000 0 -0.1 13 13
CASP1 -0.003 0.02 -10000 0 -0.22 2 2
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.1 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.013 0.078 -10000 0 -0.48 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.033 0.3 1 -0.47 2 3
DAPP1 -0.053 0.14 -10000 0 -0.48 13 13
Src family/SYK family/BLNK-LAT/BTK-ITK -0.057 0.18 -10000 0 -0.49 31 31
mol:DAG -0.004 0.096 -10000 0 -0.28 15 15
HRAS 0.013 0.021 -10000 0 -0.31 2 2
RAP1A 0.014 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.023 0.035 -10000 0 -0.46 1 1
PLCG2 0.013 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.014 0.27 1 -10000 0 1
ARF1/GTP -0.001 0.022 0.28 1 -0.32 1 2
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0 0.013 0.26 1 -10000 0 1
ADAP1 0 0.013 0.26 1 -10000 0 1
ARAP3 0 0.014 0.27 1 -10000 0 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.012 0.038 -10000 0 -0.82 1 1
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.011 0.029 -10000 0 -0.31 4 4
mol:Ca2+ 0.007 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.32 277 277
ZAP70 -0.022 0.16 -10000 0 -0.6 28 28
mol:IP3 0.005 0.071 -10000 0 -0.21 4 4
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.035 -10000 0 -0.46 1 1
RhoA/GDP -0.001 0.019 0.28 1 -10000 0 1
PDK1/Src/Hsp90 -0.003 0.035 -10000 0 -0.54 2 2
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.038 0.037 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
PLEKHA2 0.022 0.041 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.036 -10000 0 -0.79 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.015 0.3 1 -10000 0 1
RhoA/GTP 0 0.013 0.26 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.048 0.16 -10000 0 -0.6 13 13
BLK -0.24 0.37 -10000 0 -0.75 165 165
PDPK1 0.01 0.053 -10000 0 -0.82 2 2
CYTH1 0 0.013 0.26 1 -10000 0 1
HCK -0.007 0.08 -10000 0 -0.31 31 31
CYTH3 -0.002 0.034 0.26 1 -0.49 2 3
CYTH2 0 0.013 0.26 1 -10000 0 1
KRAS 0.014 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.014 0.095 -10000 0 -0.62 11 11
SGK1 -0.015 0.11 -10000 0 -0.69 11 11
INPP5D -0.003 0.072 -10000 0 -0.31 25 25
mol:GDP 0.015 0.037 -10000 0 -0.49 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.019 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.018 0.36 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.013 0.26 1 -10000 0 1
VAV1 -0.013 0.1 -10000 0 -0.36 35 35
mol:PI-3-4-P2 0.013 0.05 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.006 -10000 0 -10000 0 0
PLEKHA1 0.022 0.041 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.035 -10000 0 -0.46 1 1
LAT 0.006 0.076 -10000 0 -0.72 5 5
Rac1/GTP -0.006 0.054 -10000 0 -0.47 2 2
ITK -0.055 0.14 -10000 0 -0.43 59 59
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.013 0.12 -10000 0 -0.39 16 16
LCK -0.01 0.11 -10000 0 -0.43 26 26
BTK -0.013 0.061 0.26 1 -0.43 8 9
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.046 0.059 -10000 0 -10000 0 0
NFATC2 -0.02 0.097 -10000 0 -0.3 28 28
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.091 -10000 0 -0.31 26 26
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.026 0.096 -10000 0 -0.59 9 9
BCL2/BAX -0.047 0.16 -10000 0 -0.63 36 36
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.01 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.015 0.087 -10000 0 -0.56 4 4
Calcineurin A alpha-beta B1/BCL2 -0.048 0.22 -10000 0 -0.82 36 36
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.015 0.086 0.55 4 -10000 0 4
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.18 -10000 0 -0.33 314 314
MAP3K8 -0.004 0.1 -10000 0 -0.82 8 8
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.12 0.16 -10000 0 -0.5 23 23
CABIN1 0.011 0.092 -10000 0 -0.32 26 26
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.11 -10000 0 -0.55 15 15
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.009 0.12 -10000 0 -0.82 11 11
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.007 0.05 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.015 0.05 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.047 -10000 0 -10000 0 0
PRKCB -0.027 0.13 -10000 0 -0.36 53 53
PRKCE 0.005 0.084 -10000 0 -0.82 5 5
JNK2/NFAT4 0.022 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.026 0.18 -10000 0 -0.82 23 23
PRKCG 0.005 0.022 -10000 0 -0.31 2 2
PRKCQ 0.005 0.084 -10000 0 -0.82 5 5
FKBP38/BCL2 -0.046 0.16 -10000 0 -0.63 36 36
EP300 0.01 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.031 0.089 -10000 0 -0.41 3 3
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.011 0.07 -10000 0 -0.56 7 7
NFATc/ERK1 0.052 0.056 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.095 -10000 0 -0.58 9 9
NR4A1 -0.18 0.36 -10000 0 -0.73 144 144
GSK3B 0.01 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.037 0.064 -10000 0 -0.4 5 5
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.01 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.041 0.062 -10000 0 -10000 0 0
CREBBP 0.01 0.007 -10000 0 -10000 0 0
BCL2 -0.048 0.22 -10000 0 -0.82 36 36
Retinoic acid receptors-mediated signaling

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -0.31 1 1
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.032 0.062 -10000 0 -0.34 7 7
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.01 0.087 0.24 5 -0.4 16 21
RAR alpha/9cRA/Cyclin H -0.024 0.097 -10000 0 -0.42 23 23
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.028 0.069 -10000 0 -0.37 8 8
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.017 0.12 -10000 0 -0.73 11 11
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.021 0.16 -10000 0 -0.63 27 27
NCOA2 -0.067 0.24 -10000 0 -0.82 47 47
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -10000 0 -0.31 1 1
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 -10000 0 -0.82 11 11
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.038 0.14 -10000 0 -0.67 23 23
RARA 0.005 0.097 -10000 0 -0.35 31 31
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.003 0.14 -10000 0 -0.56 18 18
PRKCA -0.023 0.18 -10000 0 -0.82 23 23
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.032 0.16 -10000 0 -0.65 27 27
RXRG -0.12 0.11 -10000 0 -0.53 27 27
RXRA 0.011 0.096 -10000 0 -0.34 31 31
RXRB 0.005 0.1 -10000 0 -0.44 23 23
VDR/Vit D3/DNA 0 0.01 -10000 0 -10000 0 0
RBP1 -0.001 0.1 -10000 0 -0.63 11 11
CRBP1/9-cic-RA -0.011 0.078 -10000 0 -0.48 11 11
RARB -0.008 0.14 -10000 0 -0.82 14 14
PRKCG 0.008 0.022 -10000 0 -0.31 2 2
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.028 0.17 -10000 0 -0.67 27 27
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.14 -10000 0 -0.55 27 27
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.093 -10000 0 -0.49 9 9
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.032 0.16 -10000 0 -0.65 27 27
positive regulation of DNA binding -0.023 0.091 -10000 0 -0.39 23 23
NRIP1 -0.027 0.15 -10000 0 -0.63 20 20
RXRs/RARs -0.04 0.16 -10000 0 -0.64 27 27
RXRs/RXRs/DNA/9cRA -0.05 0.15 -10000 0 -0.69 23 23
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.014 0.058 -10000 0 -0.52 3 3
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure 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
BAG4 0.012 0.038 -9999 0 -0.82 1 1
Caspase 8 (4 units) -0.02 0.059 -9999 0 -10000 0 0
NEF -0.01 0.053 -9999 0 -0.22 25 25
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.004 0.2 -9999 0 -0.81 26 26
CYCS -0.003 0.099 -9999 0 -0.39 5 5
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.033 0.18 -9999 0 -0.77 22 22
MAP2K7 0.026 0.078 -9999 0 -10000 0 0
protein ubiquitination 0.039 0.087 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID -0.011 0.1 -9999 0 -0.42 5 5
NF-kappa-B/RelA/I kappa B alpha -0.021 0.08 -9999 0 -0.52 1 1
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.038 -9999 0 -0.82 1 1
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.08 -9999 0 -0.52 1 1
MAPK8 0.023 0.099 -9999 0 -0.41 11 11
APAF1 0.012 0.038 -9999 0 -0.82 1 1
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.012 0.093 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.1 -9999 0 -0.36 11 11
CHUK 0.039 0.092 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.021 -9999 0 -0.46 1 1
TCRz/NEF -0.054 0.17 -9999 0 -0.52 47 47
TNF -0.09 0.27 -9999 0 -0.77 64 64
FASLG -0.061 0.27 -9999 0 -0.84 47 47
NFKB1 0.007 0.047 -9999 0 -0.81 1 1
TNFR1A/BAG4/TNF-alpha -0.067 0.18 -9999 0 -0.54 59 59
CASP6 -0.003 0.044 -9999 0 -10000 0 0
CASP7 0.031 0.16 -9999 0 -0.62 25 25
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.031 0.16 -9999 0 -0.62 25 25
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.028 -9999 0 -0.63 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.099 -9999 0 -0.37 2 2
APAF-1/Caspase 9 -0.045 0.12 -9999 0 -0.52 25 25
BCL2 -0.002 0.15 -9999 0 -0.4 44 44
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.033 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.07 0.009 -9999 0 -10000 0 0
EGFR 0.007 0.075 -9999 0 -0.82 4 4
EPHA2 0.011 0.026 -9999 0 -0.31 3 3
MYO6 0.041 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.038 0.13 -9999 0 -0.59 25 25
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.074 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 76 76
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.073 0.19 -9999 0 -0.59 60 60
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.005 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.048 0.036 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.041 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.009 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.065 0.15 -9999 0 -0.42 74 74
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.047 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.18 0.35 -9999 0 -0.82 113 113
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.005 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.047 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.039 0.064 -9999 0 -0.42 9 9
Ephrin A1/EPHA2 -0.001 0.008 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.038 0.074 -9999 0 -10000 0 0
HGF/MET -0.1 0.16 -9999 0 -0.47 74 74
HGF -0.11 0.3 -9999 0 -0.82 74 74
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.085 0.022 -9999 0 -10000 0 0
KIAA1543 0.047 0.021 -9999 0 -0.42 1 1
KIFC3 0.041 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.04 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.041 0 -9999 0 -10000 0 0
PIP5K1C 0.041 0 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.064 0.019 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.099 0.18 -9999 0 -0.42 113 113
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.11 0.16 -9999 0 -0.31 179 179
PLEKHA7 0.04 0.022 -9999 0 -0.44 1 1
mol:GTP -0.001 0.01 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.067 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.033 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.047 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.033 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.019 0.087 -10000 0 -0.43 12 12
ACTA1 0.011 0.11 -10000 0 -0.54 12 12
NUMA1 0.019 0.087 -10000 0 -0.43 12 12
SPTAN1 0.015 0.11 -10000 0 -0.58 10 10
LIMK1 0.015 0.11 -10000 0 -0.58 10 10
BIRC3 -0.036 0.19 -10000 0 -0.67 35 35
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
CASP10 0 0.12 -10000 0 -0.58 14 14
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.019 0.087 -10000 0 -0.43 12 12
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.016 0.11 -10000 0 -0.57 10 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.016 0.11 -10000 0 -0.58 10 10
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.057 0.22 -10000 0 -0.64 60 60
BID -0.01 0.066 -10000 0 -0.3 12 12
MAP3K1 0.014 0.041 -10000 0 -0.24 1 1
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.028 -10000 0 -0.62 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.013 0.11 -10000 0 -0.56 11 11
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.016 0.051 0.17 1 -0.23 22 23
neuron apoptosis 0.023 0.015 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.022 0.1 -10000 0 -0.56 10 10
APAF1 0.012 0.037 -10000 0 -0.82 1 1
CASP6 0.022 0.061 -10000 0 -0.37 5 5
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.023 0.1 -10000 0 -0.56 10 10
CASP7 0.009 0.08 0.34 25 -10000 0 25
KRT18 0.017 0.018 -10000 0 -10000 0 0
apoptosis 0.026 0.11 -10000 0 -0.52 12 12
DFFA 0.015 0.11 -10000 0 -0.56 11 11
DFFB 0.015 0.11 -10000 0 -0.58 10 10
PARP1 0.016 0.052 0.23 22 -0.18 1 23
actin filament polymerization -0.023 0.1 0.53 10 -10000 0 10
TNF -0.09 0.27 -10000 0 -0.77 64 64
CYCS 0.005 0.044 -10000 0 -0.22 12 12
SATB1 0.029 0.058 -10000 0 -0.36 4 4
SLK 0.013 0.12 -10000 0 -0.62 12 12
p15 BID/BAX -0.002 0.06 -10000 0 -0.34 3 3
CASP2 0.006 0.12 -10000 0 -0.46 11 11
JNK cascade -0.014 0.041 0.24 1 -10000 0 1
CASP3 0.008 0.12 -10000 0 -0.57 12 12
LMNB2 0.021 0.075 -10000 0 -0.3 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.49 25 25
negative regulation of DNA binding -0.056 0.22 -10000 0 -0.64 60 60
stress fiber formation 0.013 0.12 -10000 0 -0.6 12 12
GZMB -0.013 0.13 -10000 0 -0.67 14 14
CASP1 0.016 0.031 -10000 0 -0.45 2 2
LMNB1 0.021 0.076 -10000 0 -0.3 4 4
APP 0.023 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM 0.023 0.094 0.26 12 -0.47 10 22
LMNA 0.021 0.075 -10000 0 -0.3 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.003 0.12 -10000 0 -0.49 11 11
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.015 0.11 -10000 0 -0.58 10 10
APAF-1/Caspase 9 0.004 0.041 -10000 0 -0.39 1 1
nuclear fragmentation during apoptosis 0.019 0.086 -10000 0 -0.42 12 12
CFL2 0.023 0.1 -10000 0 -0.54 10 10
GAS2 0.01 0.12 -10000 0 -0.55 16 16
positive regulation of apoptosis 0.023 0.078 -10000 0 -0.3 4 4
PRF1 0 0.1 -10000 0 -0.7 9 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.022 0.092 -9999 0 -0.51 1 1
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.28 0.45 -9999 0 -0.92 151 151
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.069 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.043 0.14 -9999 0 -0.6 25 25
NFX1/SIN3/HDAC complex 0.047 0.026 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 76 76
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.007 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.035 0.068 -9999 0 -0.48 1 1
SAP18 0.014 0 -9999 0 -10000 0 0
MRN complex -0.003 0.042 -9999 0 -0.54 3 3
WT1 -0.025 0.1 -9999 0 -0.31 53 53
WRN 0.012 0.038 -9999 0 -0.82 1 1
SP1 0.015 0.003 -9999 0 -10000 0 0
SP3 0.014 0.002 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.028 0.053 -9999 0 -10000 0 0
Mad/Max 0.006 0.01 -9999 0 -10000 0 0
TERT -0.023 0.093 -9999 0 -0.52 1 1
CCND1 -0.014 0.093 -9999 0 -0.57 1 1
MAX 0.014 0.002 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
RBBP4 0.008 0.065 -9999 0 -0.82 3 3
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
Telomerase/911 0.036 0.019 -9999 0 -10000 0 0
CDKN1B -0.039 0.19 -9999 0 -0.52 63 63
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.038 -9999 0 -0.82 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.001 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.82 110 110
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.006 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.82 128 128
IFN-gamma/IRF1 -0.085 0.2 -9999 0 -0.61 64 64
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.013 0.015 -9999 0 -0.31 1 1
Telomerase 0.014 0.071 -9999 0 -0.48 5 5
IRF1 0.018 0.015 -9999 0 -0.3 1 1
ESR1 -0.047 0.19 -9999 0 -0.52 55 55
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.025 -9999 0 -0.55 1 1
ubiquitin-dependent protein catabolic process 0.052 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.053 0.027 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC2 0.015 0.003 -9999 0 -10000 0 0
ATM -0.001 0.025 -9999 0 -0.56 1 1
SMAD3 0.02 0.03 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.014 0.002 -9999 0 -10000 0 0
MRE11A 0.008 0.065 -9999 0 -0.82 3 3
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.031 0.064 -9999 0 -10000 0 0
NR2F2 0.012 0.002 -9999 0 -10000 0 0
MAPK3 0.017 0.006 -9999 0 -10000 0 0
MAPK1 0.017 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.007 0.044 -9999 0 -0.31 9 9
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.025 -9999 0 -0.56 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.007 0.075 -9999 0 -0.82 4 4
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.097 0.22 -9999 0 -0.62 74 74
MYC -0.008 0.13 -9999 0 -0.82 13 13
IL2 0.006 0.007 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.007 0.044 -9999 0 -0.31 9 9
TRF2/BLM 0 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.016 0.079 -9999 0 -10000 0 0
SP1/HDAC2 0.023 0.006 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.028 0.053 -9999 0 -10000 0 0
Smad3/Myc 0.009 0.096 -9999 0 -0.55 13 13
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.099 0.28 -9999 0 -0.71 78 78
Telomerase/PinX1 -0.028 0.053 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.022 0.037 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.028 0.053 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.003 0.035 -9999 0 -0.45 3 3
TRF2/WRN -0.001 0.027 -9999 0 -0.59 1 1
Telomerase/hnRNP C1/C2 -0.028 0.053 -9999 0 -10000 0 0
E2F1 -0.085 0.15 -9999 0 -10000 0 0
ZNFX1 0.014 0 -9999 0 -10000 0 0
PIF1 0.002 0.088 -9999 0 -0.59 9 9
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.016 -10000 0 -10000 0 0
CDKN1A 0.034 0.031 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.016 -10000 0 -10000 0 0
AKT1 -0.001 0.014 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.016 0.03 -10000 0 -0.45 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.016 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.023 -10000 0 -0.42 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.012 0.038 -10000 0 -0.82 1 1
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.022 0.41 1 -10000 0 1
TSC1 0.039 0.016 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.016 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.016 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.055 0.2 -10000 0 -0.55 69 69
MAP3K5 0.012 0.038 -10000 0 -0.82 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.035 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.039 0.016 -10000 0 -10000 0 0
CASP9 0.039 0.016 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.015 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.003 0.035 -10000 0 -0.54 2 2
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
AKT2/p21CIP1 -0.005 0.029 -10000 0 -0.41 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.006 -10000 0 -10000 0 0
CHUK 0.039 0.016 -10000 0 -10000 0 0
BAD/BCL-XL 0.052 0.015 -10000 0 -10000 0 0
mTORC2 -0.001 0.023 -10000 0 -0.51 1 1
AKT2 0.016 0.03 -10000 0 -0.45 2 2
FOXO1-3a-4/14-3-3 family 0.025 0.041 -10000 0 -10000 0 0
PDPK1 0.01 0.053 -10000 0 -0.82 2 2
MDM2 0.039 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.038 0.016 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.015 -10000 0 -10000 0 0
TSC1/TSC2 0.046 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.011 -10000 0 -10000 0 0
glucose import -0.064 0.21 -10000 0 -0.52 84 84
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.033 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.064 0.22 -10000 0 -0.52 84 84
GSK3A 0.039 0.016 -10000 0 -10000 0 0
FOXO1 0.039 0.016 -10000 0 -10000 0 0
GSK3B 0.039 0.016 -10000 0 -10000 0 0
SFN -0.21 0.18 -10000 0 -0.33 314 314
G1/S transition of mitotic cell cycle 0.046 0.015 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.001 0.051 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.005 0.13 -10000 0 -0.56 11 11
BAG4 0.012 0.038 -10000 0 -0.82 1 1
BAD 0.018 0.046 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.67 35 35
BAX 0.017 0.047 -10000 0 -0.22 1 1
EnzymeConsortium:3.1.4.12 0.004 0.034 -10000 0 -0.12 11 11
IKBKB 0.013 0.12 -10000 0 -0.52 11 11
MAP2K2 0.027 0.056 -10000 0 -0.36 2 2
MAP2K1 0.027 0.056 -10000 0 -0.36 2 2
SMPD1 0.01 0.034 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.013 0.13 -10000 0 -0.53 11 11
MAP2K4 0.024 0.047 -10000 0 -10000 0 0
protein ubiquitination 0.014 0.12 -10000 0 -0.52 11 11
EnzymeConsortium:2.7.1.37 0.031 0.062 -10000 0 -0.37 2 2
response to UV 0 0.001 -10000 0 -0.003 2 2
RAF1 0.022 0.057 -10000 0 -0.39 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.048 -10000 0 -0.17 11 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.017 0.047 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.03 0.056 -10000 0 -0.35 2 2
MAPK1 0.03 0.056 -10000 0 -0.35 2 2
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.005 0.13 -10000 0 -0.56 11 11
KSR1 0.016 0.056 -10000 0 -0.42 2 2
MAPK8 0.021 0.081 -10000 0 -0.43 11 11
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.013 0.12 -10000 0 -0.52 11 11
TNF R/SODD -0.001 0.028 -10000 0 -0.63 1 1
TNF -0.09 0.27 -10000 0 -0.77 64 64
CYCS 0.027 0.056 0.16 30 -10000 0 30
IKBKG 0.013 0.12 -10000 0 -0.52 11 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.004 0.14 -10000 0 -0.44 25 25
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.027 0.056 0.16 30 -10000 0 30
TNF/TNF R/SODD -0.067 0.18 -10000 0 -0.54 59 59
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.033 -10000 0 -10000 0 0
NSMAF 0.005 0.13 -10000 0 -0.55 11 11
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 2 2
BCL2 -0.048 0.22 -10000 0 -0.82 36 36
S1P3 pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.058 -9999 0 -0.33 1 1
GNAO1 -0.015 0.15 -9999 0 -0.82 16 16
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.029 -9999 0 -0.47 1 1
AKT3 0.048 0.05 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.013 0.038 -9999 0 -0.82 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.01 0.033 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.036 0.067 -9999 0 -0.31 16 16
MAPK3 0.042 0.063 -9999 0 -10000 0 0
MAPK1 0.042 0.063 -9999 0 -10000 0 0
JAK2 0.045 0.065 -9999 0 -0.42 1 1
CXCR4 0.041 0.064 -9999 0 -10000 0 0
FLT1 0.015 0.038 -9999 0 -0.82 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.042 0.064 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.036 0.067 -9999 0 -0.32 16 16
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.051 -9999 0 -10000 0 0
VEGFA 0.012 0.065 -9999 0 -0.82 3 3
S1P/S1P2/Gi 0.03 0.068 -9999 0 -0.32 16 16
VEGFR1 homodimer/VEGFA homodimer 0.024 0.067 -9999 0 -0.79 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.067 0.17 -9999 0 -0.35 121 121
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.82 114 114
GNA15 -0.014 0.095 -9999 0 -0.33 39 39
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.004 0.12 -9999 0 -0.82 10 10
Rac1/GTP -0.01 0.051 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.008 0.066 -9999 0 -0.82 3 3
positive regulation of NF-kappaB transcription factor activity -0.004 0.05 -9999 0 -0.62 3 3
MAP2K4 0.047 0.031 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.008 0.065 -9999 0 -0.82 3 3
SMPD1 -0.002 0.023 -9999 0 -0.29 3 3
IKBKG 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.004 0.05 -9999 0 -0.63 3 3
TRAIL/TRAILR3 -0.06 0.1 -9999 0 -0.68 3 3
TRAIL/TRAILR1 -0.008 0.069 -9999 0 -0.63 6 6
TRAIL/TRAILR4 -0.004 0.05 -9999 0 -0.63 3 3
TRAIL/TRAILR1/DAP3/GTP -0.006 0.055 -9999 0 -0.5 6 6
IKK complex -0.002 0.017 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.02 0.052 -9999 0 -0.62 3 3
MAP3K1 -0.003 0.027 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.065 -9999 0 -0.82 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.035 0.041 -9999 0 -0.33 6 6
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.02 0.052 -9999 0 -0.62 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP -0.006 0.051 -9999 0 -0.46 6 6
mol:ceramide -0.002 0.023 -9999 0 -0.29 3 3
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.043 0.081 -9999 0 -0.46 11 11
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.077 0.15 -9999 0 -0.31 135 135
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.007 0.06 -9999 0 -0.54 6 6
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.005 0.045 -9999 0 -0.52 3 3
JNK cascade -0.004 0.05 -9999 0 -0.62 3 3
TRAIL (trimer) 0.008 0.066 -9999 0 -0.82 3 3
TNFRSF10C -0.077 0.15 -9999 0 -0.31 135 135
TRAIL/TRAILR1/DAP3/GTP/FADD -0.006 0.052 -9999 0 -0.47 6 6
TRAIL/TRAILR2/FADD -0.004 0.043 -9999 0 -0.54 3 3
cell death 0.019 0.024 -9999 0 -0.29 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.037 0.029 -9999 0 -0.33 3 3
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.013 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.003 0.036 -9999 0 -0.46 3 3
S1P1 pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.009 0.081 -9999 0 -0.71 6 6
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
SPHK1 -0.008 0.022 -9999 0 -10000 0 0
mol:S1P -0.009 0.026 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.012 0.15 -9999 0 -0.7 10 10
GNAO1 -0.017 0.15 -9999 0 -0.82 16 16
PDGFB-D/PDGFRB/PLCgamma1 0.022 0.14 -9999 0 -0.57 11 11
PLCG1 0.019 0.14 -9999 0 -0.64 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
GNAI2 0.013 0.005 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.074 -9999 0 -0.62 6 6
S1P1/S1P -0.017 0.067 -9999 0 -0.5 6 6
negative regulation of cAMP metabolic process 0.013 0.15 -9999 0 -0.68 10 10
MAPK3 0.005 0.2 -9999 0 -0.58 44 44
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.006 0.075 -9999 0 -0.82 4 4
PLCB2 0.03 0.072 -9999 0 -0.43 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.054 -9999 0 -0.41 6 6
receptor internalization -0.016 0.062 -9999 0 -0.46 6 6
PTGS2 -0.037 0.34 -9999 0 -1.1 43 43
Rac1/GTP -0.014 0.054 -9999 0 -0.41 6 6
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.065 -9999 0 -0.82 3 3
negative regulation of T cell proliferation 0.013 0.15 -9999 0 -0.68 10 10
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.005 -9999 0 -10000 0 0
MAPK1 0.005 0.2 -9999 0 -0.58 44 44
S1P1/S1P/PDGFB-D/PDGFRB 0.031 0.088 -9999 0 -0.49 7 7
ABCC1 0.014 0.002 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.061 0.16 -9999 0 -0.5 59 59
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.15 -9999 0 -0.41 59 59
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.025 0.066 -9999 0 -10000 0 0
YY1/LSF 0.028 0.05 -9999 0 -0.52 4 4
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.013 0.13 -9999 0 -0.36 58 58
I kappa B alpha/HDAC1 0 0.09 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.003 0.12 -9999 0 -0.32 58 58
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 0 0.09 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.049 0.02 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.002 0.11 -9999 0 -0.29 59 59
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
GATA1 0.008 0.016 -9999 0 -0.31 1 1
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.059 0.022 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.008 0.065 -9999 0 -0.82 3 3
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.008 0.1 -9999 0 -0.28 58 58
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.044 0.027 -9999 0 -10000 0 0
SIN3 complex -0.001 0.022 -9999 0 -0.49 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.038 -9999 0 -0.82 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 0.015 0.084 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0 -9999 0 -10000 0 0
YY1/HDAC1 0.033 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.049 0.02 -9999 0 -10000 0 0
PPARG -0.06 0.16 -9999 0 -0.46 63 63
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0 0.09 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.022 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.008 0.1 -9999 0 -0.28 58 58
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.027 0 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.004 0.043 -9999 0 -0.48 4 4
YY1/SAP30/HDAC1 -0.001 0.022 -9999 0 -0.48 1 1
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.1 -9999 0 -0.28 58 58
histone deacetylation 0.049 0.02 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.085 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 0 0.09 -9999 0 -10000 0 0
GATA1/HDAC1 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC3 -0.01 0.09 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.077 0.2 -9999 0 -0.63 58 58
SIN3/HDAC complex/Mad/Max 0.049 0.023 -9999 0 -10000 0 0
NuRD Complex 0.058 0.022 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.024 0.065 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.003 0.038 -9999 0 -0.49 3 3
GATA1/Fog1 0 0.009 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.09 0.27 -9999 0 -0.77 64 64
negative regulation of cell growth 0.049 0.023 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.049 0.02 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.053 0.14 -9999 0 -0.44 58 58
SIN3/HDAC complex/NCoR1 0.046 0.026 -9999 0 -10000 0 0
TFCP2 0.007 0.075 -9999 0 -0.82 4 4
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0.024 -10000 0 -10000 0 0
AES 0.006 0.02 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.025 0.16 -10000 0 -0.65 28 28
TLE1 0 0.066 -10000 0 -0.8 3 3
MACF1 0.014 0 -10000 0 -10000 0 0
CTNNB1 0.047 0.039 -10000 0 -10000 0 0
WIF1 -0.034 0.1 -10000 0 -0.31 59 59
beta catenin/RanBP3 0.023 0.092 0.37 26 -10000 0 26
KREMEN2 -0.01 0.083 -10000 0 -0.31 34 34
DKK1 -0.041 0.12 -10000 0 -0.32 79 79
beta catenin/beta TrCP1 0.053 0.037 -10000 0 -10000 0 0
FZD1 0.014 0.001 -10000 0 -10000 0 0
AXIN2 -0.049 0.31 -10000 0 -1.6 19 19
AXIN1 0.014 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.063 0.044 0.29 1 -0.41 1 2
Axin1/APC/GSK3 0.007 0.031 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.019 -10000 0 -10000 0 0
HNF1A 0.006 0.021 -10000 0 -10000 0 0
CTBP1 0.006 0.021 -10000 0 -10000 0 0
MYC -0.032 0.26 -10000 0 -1.6 13 13
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.035 0.11 -10000 0 -0.55 19 19
NKD1 -0.013 0.14 -10000 0 -0.7 18 18
TCF4 0.006 0.021 -10000 0 -10000 0 0
TCF3 0.006 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.01 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.03 0.12 0.48 28 -10000 0 28
LEF1 -0.002 0.066 -10000 0 -0.42 9 9
DVL1 0.019 0.028 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.074 -10000 0 -0.46 5 5
DKK1/LRP6/Kremen 2 -0.037 0.077 -10000 0 -0.37 8 8
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.006 0.023 0.22 1 -10000 0 1
NLK 0.013 0.004 -10000 0 -10000 0 0
CCND1 -0.001 0.076 -10000 0 -0.8 1 1
WNT1 0.009 0.026 -10000 0 -0.31 3 3
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.03 0.06 0.36 14 -10000 0 14
APC 0.038 0.027 -10000 0 -0.46 1 1
WNT1/LRP6/FZD1 0.035 0.037 -10000 0 -10000 0 0
CREBBP 0.006 0.021 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.071 0.055 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.029 0.078 -9999 0 -0.63 2 2
NFKBIA 0.049 0.023 -9999 0 -0.47 1 1
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.005 0.02 -9999 0 -10000 0 0
IKK complex/A20 -0.049 0.13 -9999 0 -0.64 2 2
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.042 0.039 -9999 0 -0.42 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.002 0.014 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.035 -9999 0 -0.54 2 2
NOD2 -0.033 0.12 -9999 0 -0.33 66 66
NFKB1 0.015 0.037 -9999 0 -0.81 1 1
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.012 0.038 -9999 0 -0.82 1 1
TNF/TNFR1A -0.077 0.2 -9999 0 -0.63 58 58
TRAF6 0.01 0.053 -9999 0 -0.82 2 2
PRKCA -0.026 0.18 -9999 0 -0.82 23 23
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.09 0.27 -9999 0 -0.77 64 64
NF kappa B1 p50/RelA -0.001 0.024 -9999 0 -0.52 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.023 -9999 0 -0.47 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.003 0.016 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.02 0.084 -9999 0 -0.39 23 23
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.026 0.048 -9999 0 -0.63 1 1
CLOCK -0.043 0.21 -9999 0 -0.82 32 32
TIMELESS/CRY2 -0.005 0.065 -9999 0 -10000 0 0
DEC1/BMAL1 -0.021 0.063 -9999 0 -10000 0 0
ATR 0.012 0.038 -9999 0 -0.82 1 1
NR1D1 -0.057 0.13 -9999 0 -10000 0 0
ARNTL -0.02 0.096 -9999 0 -0.32 46 46
TIMELESS -0.013 0.074 -9999 0 -10000 0 0
NPAS2 0.009 0.041 -9999 0 -0.56 2 2
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.007 0.03 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.007 0.03 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.032 0.15 -9999 0 -0.56 33 33
BMAL1/CLOCK -0.056 0.16 -9999 0 -0.51 32 32
S phase of mitotic cell cycle -0.026 0.048 -9999 0 -0.63 1 1
TIMELESS/CHEK1/ATR -0.026 0.048 -9999 0 -0.64 1 1
mol:NADPH -0.007 0.03 -9999 0 -10000 0 0
PER1/TIMELESS -0.005 0.065 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.015 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.061 0.13 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.037 0.32 2 -10000 0 2
myoblast fusion 0.024 0.052 -10000 0 -10000 0 0
mol:GTP -0.027 0.039 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.094 0.11 0.51 1 -10000 0 1
ARF1/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GM1 -0.011 0.034 -10000 0 -10000 0 0
mol:Choline 0.012 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.064 -10000 0 -10000 0 0
MAPK3 -0.018 0.065 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.094 0.11 -10000 0 -0.52 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.024 0.052 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.059 -10000 0 -10000 0 0
ARF6 -0.002 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.18 0.17 -10000 0 -0.32 277 277
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.065 -10000 0 -10000 0 0
actin filament bundle formation 0.025 0.038 -10000 0 -10000 0 0
KALRN -0.006 0.051 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.025 0.038 -10000 0 -10000 0 0
NME1 0.01 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.025 0.038 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.027 0.039 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.003 0.064 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.027 0.039 -10000 0 -10000 0 0
ARF6/GTP -0.027 0.039 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GDP -0.011 0.065 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.01 0.014 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0 0.033 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.003 0.064 -10000 0 -10000 0 0
ruffle organization 0.01 0.037 -10000 0 -0.32 2 2
regulation of epithelial cell migration -0.027 0.039 -10000 0 -10000 0 0
PLD2 0 0.033 -10000 0 -10000 0 0
PIP5K1A 0.01 0.037 -10000 0 -0.32 2 2
mol:Phosphatidic acid 0.012 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.064 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.038 0.027 -9999 0 -10000 0 0
PLK1 0.11 0.11 -9999 0 -0.73 1 1
CDKN1B 0.15 0.048 -9999 0 -0.39 1 1
FOXO3 0.11 0.11 -9999 0 -0.58 4 4
KAT2B 0.025 0.01 -9999 0 -10000 0 0
FOXO1/SIRT1 0.008 0.038 -9999 0 -0.59 1 1
CAT 0.1 0.15 -9999 0 -1.4 3 3
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.028 0.011 -9999 0 -10000 0 0
FOXO1 0.042 0.018 -9999 0 -10000 0 0
MAPK10 0.043 0.026 -9999 0 -0.5 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.065 -9999 0 -0.48 4 4
response to oxidative stress 0.015 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.011 0.086 -9999 0 -0.72 3 3
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.002 -9999 0 -10000 0 0
BCL2L11 0.041 0.027 -9999 0 -10000 0 0
FOXO1/SKP2 0.039 0.051 -9999 0 -0.5 4 4
mol:GDP 0.015 0.013 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.13 0.062 -9999 0 -0.72 1 1
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.04 -9999 0 -10000 0 0
MST1 0.023 0.041 -9999 0 -0.55 2 2
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.063 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.033 0.078 -9999 0 -0.48 11 11
MAPK9 0.044 0.007 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.005 0.042 -9999 0 -0.81 1 1
SOD2 0.16 0.073 -9999 0 -0.79 1 1
RBL2 0.11 0.15 -9999 0 -1.4 4 4
RAL/GDP 0.034 0.012 -9999 0 -10000 0 0
CHUK 0.025 0.01 -9999 0 -10000 0 0
Ran/GTP 0.015 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.043 0.009 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.063 0.39 -9999 0 -1.5 32 32
SKP2 0.007 0.075 -9999 0 -0.82 4 4
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.025 0.01 -9999 0 -10000 0 0
CCNB1 0.11 0.1 -9999 0 -0.73 1 1
FOXO1-3a-4/beta catenin -0.003 0.05 -9999 0 -0.42 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.05 -9999 0 -0.49 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.007 0.12 -9999 0 -0.81 11 11
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.003 -9999 0 -10000 0 0
ZFAND5 0.11 0.055 -9999 0 -0.47 1 1
SFN -0.21 0.18 -9999 0 -0.33 314 314
CDK2 0.014 0.003 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.017 0.062 -9999 0 -10000 0 0
CREBBP 0.014 0.003 -9999 0 -10000 0 0
FBXO32 0.11 0.1 -9999 0 -0.73 1 1
BCL6 0.12 0.1 -9999 0 -0.69 4 4
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0.091 -9999 0 -0.46 15 15
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.007 0.075 -9999 0 -0.82 4 4
ITGA4 0.002 0.078 -9999 0 -0.44 12 12
alpha4/beta7 Integrin/MAdCAM1 -0.032 0.1 -9999 0 -0.5 17 17
EPO 0.002 0.039 -9999 0 -0.31 7 7
alpha4/beta7 Integrin -0.031 0.12 -9999 0 -0.62 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.008 0.056 -9999 0 -0.63 3 3
EPO/EPOR (dimer) -0.007 0.037 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.037 -9999 0 -0.46 3 3
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
PI3K -0.004 0.049 -9999 0 -0.63 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.022 0.067 -9999 0 -0.62 4 4
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.01 0.089 -9999 0 -0.35 28 28
cell adhesion -0.032 0.099 -9999 0 -0.5 17 17
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.022 0.079 -9999 0 -0.56 7 7
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.014 0.081 -9999 0 -0.61 7 7
p130Cas/Crk/Dock1 0.039 0.08 -9999 0 -0.49 5 5
VCAM1 0.001 0.091 -9999 0 -0.54 11 11
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.042 -9999 0 -0.49 3 3
BCAR1 0.03 0.075 -9999 0 -0.52 7 7
EPOR 0.007 0.046 -9999 0 -0.31 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.039 -9999 0 -0.48 3 3
Atypical NF-kappaB pathway

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
BCL3/RelA 0 0.009 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.011 0.15 -9999 0 -0.56 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.039 -9999 0 -0.41 1 1
NFKBIA 0.024 0.037 -9999 0 -0.27 6 6
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.026 -9999 0 -0.54 1 1
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.043 0.21 -9999 0 -0.82 33 33
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.027 -9999 0 -0.54 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.026 -9999 0 -0.54 1 1
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
NF kappa B1 p50 dimer 0.02 0.029 -9999 0 -0.63 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.023 0.029 -9999 0 -0.63 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.038 -9999 0 -0.27 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.047 0.038 -9999 0 -0.4 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
PI3K -0.004 0.049 -9999 0 -0.63 3 3
NF kappa B1 p50/RelA 0.031 0.039 -9999 0 -0.27 6 6
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.03 0.035 -9999 0 -10000 0 0
cell death -0.004 0.028 -9999 0 -0.38 1 1
NF kappa B1 p105/c-Rel -0.011 0.15 -9999 0 -0.56 33 33
LCK -0.01 0.11 -9999 0 -0.43 26 26
BCL3 0.013 0.015 -9999 0 -0.31 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.02 0.12 -9999 0 -0.66 15 15
AKT1 0.084 0.09 -9999 0 -0.6 7 7
PTK2B 0.036 0.13 -9999 0 -0.91 5 5
VEGFR2 homodimer/Frs2 0.03 0.097 -9999 0 -1 4 4
CAV1 -0.009 0.13 -9999 0 -0.82 13 13
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.011 0.1 -9999 0 -0.86 6 6
endothelial cell proliferation 0.075 0.1 -9999 0 -0.61 5 5
mol:Ca2+ 0.05 0.1 -9999 0 -0.73 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.01 0.099 -9999 0 -0.82 6 6
RP11-342D11.1 0.041 0.1 -9999 0 -0.73 7 7
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.006 0.062 -9999 0 -0.58 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.065 -9999 0 -0.82 3 3
HRAS/GDP -0.009 0.082 -9999 0 -0.74 5 5
SH2D2A -0.032 0.18 -9999 0 -0.64 34 34
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.008 0.069 -9999 0 -0.69 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.035 0.14 -9999 0 -0.56 28 28
VEGFR1 homodimer 0.012 0.037 -9999 0 -0.82 1 1
SHC/GRB2/SOS1 -0.01 0.095 -9999 0 -0.93 4 4
GRB10 0.05 0.1 -9999 0 -0.95 4 4
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.01 0.095 -9999 0 -0.96 4 4
HRAS 0.012 0.021 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.076 -9999 0 -0.48 5 5
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.01 0.095 -9999 0 -0.79 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.003 0.091 -9999 0 -0.82 6 6
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.011 0.1 -9999 0 -0.86 6 6
mol:GDP -0.009 0.087 -9999 0 -0.87 4 4
mol:NADP 0.076 0.067 -9999 0 -0.56 4 4
eNOS/Hsp90 0.079 0.063 -9999 0 -0.52 4 4
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.05 0.11 -9999 0 -0.75 7 7
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.065 -9999 0 -0.81 3 3
VEGFC 0.012 0.038 -9999 0 -0.82 1 1
FAK1/Vinculin 0.058 0.11 -9999 0 -0.71 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.13 -9999 0 -0.57 21 21
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.019 0.063 -9999 0 -0.58 4 4
mol:L-citrulline 0.076 0.067 -9999 0 -0.56 4 4
ITGAV 0.01 0.053 -9999 0 -0.82 2 2
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.01 0.099 -9999 0 -0.82 6 6
VEGFR2 homodimer/VEGFA homodimer -0.012 0.12 -9999 0 -0.85 7 7
VEGFR2/3 heterodimer 0.024 0.14 -9999 0 -1 7 7
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.052 0.11 -9999 0 -0.77 7 7
VEGFR2 homodimer 0.029 0.11 -9999 0 -1.1 4 4
FLT1 0.012 0.038 -9999 0 -0.82 1 1
NEDD4 0.012 0.053 -9999 0 -0.81 2 2
MAPK3 0.042 0.1 -9999 0 -0.64 8 8
MAPK1 0.042 0.1 -9999 0 -0.64 8 8
VEGFA145/NRP2 -0.02 0.072 -9999 0 -0.62 3 3
VEGFR1/2 heterodimer 0.029 0.11 -9999 0 -1.1 4 4
KDR 0.029 0.11 -9999 0 -1.1 4 4
VEGFA165/NRP1/VEGFR2 homodimer -0.018 0.11 -9999 0 -0.78 7 7
SRC 0.013 0.015 -9999 0 -0.31 1 1
platelet activating factor biosynthetic process 0.045 0.11 -9999 0 -0.67 8 8
PI3K -0.012 0.094 -9999 0 -0.9 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.011 0.1 -9999 0 -0.86 6 6
FES 0.05 0.11 -9999 0 -0.78 7 7
GAB1 -0.01 0.093 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.011 0.1 -9999 0 -0.86 6 6
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.068 0.092 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.011 0.1 -9999 0 -0.86 6 6
PI3K/GAB1 0.085 0.085 -9999 0 -0.61 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.01 0.095 -9999 0 -0.78 6 6
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.014 0.13 -9999 0 -0.88 8 8
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.05 0.11 -9999 0 -0.78 7 7
actin cytoskeleton reorganization -0.035 0.14 -9999 0 -0.56 28 28
PTK2 0.053 0.12 -9999 0 -0.79 7 7
EDG1 0.041 0.1 -9999 0 -0.73 7 7
mol:DAG 0.05 0.11 -9999 0 -0.75 7 7
CaM/Ca2+ -0.01 0.089 -9999 0 -0.88 4 4
MAP2K3 0.049 0.12 -9999 0 -0.98 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.011 0.11 -9999 0 -1.1 4 4
PLCG1 0.05 0.11 -9999 0 -0.78 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.01 0.099 -9999 0 -0.82 6 6
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.011 0.12 -9999 0 -0.92 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.011 0.1 -9999 0 -0.86 6 6
cell migration 0.083 0.096 -9999 0 -0.69 4 4
mol:PI-3-4-5-P3 -0.01 0.082 -9999 0 -0.66 6 6
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.047 0.096 -9999 0 -0.68 7 7
mol:NO 0.076 0.067 -9999 0 -0.56 4 4
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.009 0.082 -9999 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.049 0.12 -9999 0 -1.1 4 4
VHL 0.008 0.065 -9999 0 -0.82 3 3
ITGB3 -0.01 0.14 -9999 0 -0.82 14 14
NOS3 0.078 0.076 -9999 0 -0.66 4 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.014 0.11 -9999 0 -0.73 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.035 0.15 -9999 0 -0.52 25 25
PRKCB 0.037 0.12 -9999 0 -0.62 9 9
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.04 0.11 -9999 0 -0.77 7 7
VEGFR1/2 heterodimer/VEGFA homodimer -0.011 0.12 -9999 0 -0.92 6 6
VEGFA165/NRP2 -0.02 0.072 -9999 0 -0.62 3 3
MAPKKK cascade -0.009 0.081 -9999 0 -0.73 5 5
NRP2 -0.013 0.089 -9999 0 -0.31 39 39
VEGFC homodimer 0.012 0.037 -9999 0 -0.82 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.058 0.11 -9999 0 -0.71 7 7
MAP3K13 0.041 0.14 -9999 0 -0.61 15 15
PDPK1 0.076 0.091 -9999 0 -0.71 5 5
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.045 0.002 -9999 0 -10000 0 0
KLHL20 -0.009 0.021 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.074 0.009 -9999 0 -10000 0 0
ENAH 0.045 0.002 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.001 0.015 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.079 -9999 0 -0.49 12 12
RAPGEF1 0.058 0.006 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.052 0.006 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.023 0.1 -9999 0 -0.63 12 12
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.045 0.002 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.016 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.08 0.072 -9999 0 -0.5 1 1
PI3K -0.002 0.021 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.17 0.16 -9999 0 -0.32 277 277
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.012 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.073 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.073 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.027 0 -9999 0 -10000 0 0
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.072 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.033 -9999 0 -0.15 11 11
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.045 0.002 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.008 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.074 -9999 0 -0.46 12 12
CCND1 0.014 0.039 -9999 0 -0.18 11 11
VAV2 0.056 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.045 0.001 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.015 0.069 -9999 0 -0.43 12 12
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.044 0.01 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
Rac1/GTP -0.018 0.034 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
EPO signaling pathway

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 0.051 0.1 -9999 0 -10000 0 0
CRKL 0.037 0.049 -9999 0 -0.46 2 2
mol:DAG 0.041 0.052 -9999 0 -0.37 1 1
HRAS 0.061 0.045 -9999 0 -0.42 1 1
MAPK8 0.018 0.092 -9999 0 -0.56 11 11
RAP1A 0.037 0.049 -9999 0 -0.46 2 2
GAB1 0.037 0.049 -9999 0 -0.46 2 2
MAPK14 0.03 0.031 -9999 0 -10000 0 0
EPO 0.005 0.038 -9999 0 -10000 0 0
PLCG1 0.041 0.052 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.009 0.047 -9999 0 -0.32 10 10
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.037 0.13 -9999 0 -0.57 27 27
GAB1/SHC/GRB2/SOS1 -0.006 0.029 -9999 0 -0.45 1 1
EPO/EPOR (dimer) 0.013 0.042 -9999 0 -10000 0 0
IRS2 0.037 0.049 -9999 0 -0.46 2 2
STAT1 0.041 0.078 -9999 0 -10000 0 0
STAT5B 0.042 0.066 -9999 0 -10000 0 0
cell proliferation 0.026 0.087 -9999 0 -0.52 11 11
GAB1/SHIP/PIK3R1/SHP2/SHC -0.009 0.037 -9999 0 -0.44 2 2
TEC 0.037 0.049 -9999 0 -0.46 2 2
SOCS3 -0.033 0.19 -9999 0 -0.8 28 28
STAT1 (dimer) 0.041 0.077 -9999 0 -0.36 1 1
JAK2 0.011 0.054 -9999 0 -0.82 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.042 0.055 -9999 0 -0.49 2 2
EPO/EPOR 0.013 0.042 -9999 0 -10000 0 0
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.045 0.048 -9999 0 -0.44 2 2
elevation of cytosolic calcium ion concentration 0.009 0.047 -9999 0 -0.32 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.028 0.036 -9999 0 -10000 0 0
mol:IP3 0.041 0.052 -9999 0 -0.37 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.011 0.037 -9999 0 -0.47 1 1
SH2B3 0.014 0.005 -9999 0 -10000 0 0
NFKB1 0.029 0.039 -9999 0 -0.5 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.019 0.07 -9999 0 -0.29 29 29
PTPN6 0.03 0.051 -9999 0 -0.49 2 2
TEC/VAV2/GRB2 0.05 0.047 -9999 0 -0.48 1 1
EPOR 0.009 0.047 -9999 0 -0.32 10 10
INPP5D -0.003 0.072 -9999 0 -0.31 25 25
mol:GDP -0.006 0.029 -9999 0 -0.46 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.05 0.047 -9999 0 -0.48 1 1
VAV2 0.037 0.049 -9999 0 -0.46 2 2
CBL 0.037 0.049 -9999 0 -0.46 2 2
SHC/Grb2/SOS1 -0.007 0.032 -9999 0 -0.48 1 1
STAT5A 0.042 0.066 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.052 0.099 -9999 0 -10000 0 0
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
BTK 0.02 0.089 -9999 0 -0.48 9 9
BCL2 0.002 0.28 -9999 0 -0.98 36 36
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.01 0.018 -9999 0 -10000 0 0
BUB1B 0.018 0.027 -9999 0 -10000 0 0
PLK1 0.017 0.012 -9999 0 -10000 0 0
PLK1S1 0.015 0.007 -9999 0 -10000 0 0
KIF2A 0.023 0.029 -9999 0 -0.58 1 1
regulation of mitotic centrosome separation 0.017 0.012 -9999 0 -10000 0 0
GOLGA2 0.013 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.002 0.076 -9999 0 -0.28 16 16
WEE1 0.023 0.011 -9999 0 -10000 0 0
cytokinesis 0.001 0.071 -9999 0 -0.31 3 3
PP2A-alpha B56 -0.018 0.059 -9999 0 -0.72 3 3
AURKA 0.016 0.009 -9999 0 -10000 0 0
PICH/PLK1 0.033 0.017 -9999 0 -10000 0 0
CENPE 0.019 0.049 -9999 0 -0.52 3 3
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.029 -9999 0 -0.58 1 1
PPP2CA 0.013 0 -9999 0 -10000 0 0
FZR1 0.013 0 -9999 0 -10000 0 0
TPX2 0.009 0.021 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
SPC24 -0.01 0.083 -9999 0 -0.31 34 34
FBXW11 0.013 0 -9999 0 -10000 0 0
CLSPN 0.005 0.035 -9999 0 -0.35 2 2
GORASP1 0.013 0 -9999 0 -10000 0 0
metaphase 0.001 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.009 0.007 -9999 0 -0.066 3 3
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
STAG2 0.013 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.003 -9999 0 -10000 0 0
spindle elongation 0.017 0.012 -9999 0 -10000 0 0
ODF2 0.013 0.001 -9999 0 -10000 0 0
BUB1 -0.026 0.068 -9999 0 -0.8 3 3
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.012 0.022 -9999 0 -10000 0 0
CDC25B 0.012 0.021 -9999 0 -0.31 2 2
SGOL1 0.01 0.018 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.006 0.012 -9999 0 -10000 0 0
CDC14B 0.004 0.072 -9999 0 -0.64 6 6
CDC20 0.009 0.039 -9999 0 -10000 0 0
PLK1/PBIP1 0.002 0.022 -9999 0 -10000 0 0
mitosis 0 0.002 -9999 0 -0.022 3 3
FBXO5 0.021 0.021 -9999 0 -0.4 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.031 0.11 -9999 0 -0.31 66 66
metaphase plate congression 0.016 0.007 -9999 0 -10000 0 0
ERCC6L 0.007 0.015 -9999 0 -10000 0 0
NLP/gamma Tubulin 0.013 0.009 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.007 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -0.011 3 3
PPP1R12A 0.013 0 -9999 0 -10000 0 0
interphase 0 0.001 -9999 0 -0.011 3 3
PLK1/PRC1-2 0.005 0.06 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0 0.004 -9999 0 -10000 0 0
RAB1A 0.013 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.019 0.039 -9999 0 -0.47 3 3
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.036 -9999 0 -0.32 2 2
microtubule-based process -0.004 0.063 -9999 0 -10000 0 0
Golgi organization 0.017 0.012 -9999 0 -10000 0 0
Cohesin/SA2 -0.001 0.005 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.04 0.12 -9999 0 -0.31 80 80
APC/C/CDC20 0.021 0.024 -9999 0 -10000 0 0
PPP2R1A 0.013 0 -9999 0 -10000 0 0
chromosome segregation 0.002 0.022 -9999 0 -10000 0 0
PRC1 0.013 0 -9999 0 -10000 0 0
ECT2 0.022 0.038 -9999 0 -0.56 2 2
C13orf34 0.019 0.039 -9999 0 -0.48 3 3
NUDC 0.016 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.018 0.027 -9999 0 -10000 0 0
spindle assembly 0.017 0.011 -9999 0 -10000 0 0
spindle stabilization 0.015 0.007 -9999 0 -10000 0 0
APC/C/HCDH1 0.012 0.063 -9999 0 -0.55 6 6
MKLP2/PLK1 -0.004 0.063 -9999 0 -10000 0 0
CCNB1 0.014 0.001 -9999 0 -10000 0 0
PPP1CB 0.013 0 -9999 0 -10000 0 0
BTRC 0.013 0 -9999 0 -10000 0 0
ROCK2 -0.002 0.12 -9999 0 -0.52 24 24
TUBG1 0.015 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.008 -9999 0 -10000 0 0
MLF1IP 0.008 0.033 -9999 0 -0.22 10 10
INCENP 0.009 0.053 -9999 0 -0.82 2 2
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.012 0.055 0.38 1 -10000 0 1
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.032 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.017 0.15 -10000 0 -0.82 16 16
RhoA/GTP -0.012 0.056 -10000 0 -0.39 1 1
negative regulation of cAMP metabolic process 0.022 0.07 -10000 0 -0.33 17 17
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 0.007 0.054 -10000 0 -0.38 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.071 -10000 0 -0.33 17 17
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.038 -10000 0 -0.82 1 1
HIF-2-alpha transcription factor network

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.001 0.025 -10000 0 -10000 0 0
oxygen homeostasis 0.015 0.011 -10000 0 -10000 0 0
TCEB2 0.011 0.026 -10000 0 -0.31 3 3
TCEB1 0.013 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.011 0.073 -10000 0 -0.7 4 4
EPO 0.18 0.14 -10000 0 -0.8 2 2
FIH (dimer) 0.029 0.011 -10000 0 -10000 0 0
APEX1 0.027 0.011 -10000 0 -10000 0 0
SERPINE1 0.18 0.17 -10000 0 -0.8 3 3
FLT1 -0.002 0.072 -10000 0 -1.6 1 1
ADORA2A 0.18 0.14 -10000 0 -0.86 2 2
germ cell development 0.19 0.14 -10000 0 -0.84 2 2
SLC11A2 0.19 0.15 -10000 0 -0.89 2 2
BHLHE40 0.18 0.16 -10000 0 -0.89 2 2
HIF1AN 0.029 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.003 0.076 -10000 0 -0.96 2 2
ETS1 0.03 0.003 -10000 0 -10000 0 0
CITED2 -0.089 0.32 -10000 0 -1.2 37 37
KDR -0.009 0.13 -10000 0 -1.4 4 4
PGK1 0.19 0.15 -10000 0 -0.89 2 2
SIRT1 0.012 0.038 -10000 0 -0.82 1 1
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.2 0.17 -10000 0 -0.96 3 3
EPAS1 0.11 0.1 -10000 0 -0.55 4 4
SP1 0.022 0.002 -10000 0 -10000 0 0
ABCG2 0.19 0.17 -10000 0 -0.88 5 5
EFNA1 0.19 0.15 -10000 0 -0.89 2 2
FXN 0.19 0.14 -10000 0 -0.86 2 2
POU5F1 0.19 0.15 -10000 0 -0.9 2 2
neuron apoptosis -0.2 0.16 0.91 3 -10000 0 3
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.001 0.14 -10000 0 -0.5 28 28
EGLN2 0.029 0.011 -10000 0 -10000 0 0
EGLN1 0.025 0.055 -10000 0 -0.82 2 2
VHL/Elongin B/Elongin C -0.004 0.048 -10000 0 -0.59 3 3
VHL 0.008 0.065 -10000 0 -0.82 3 3
ARNT 0.027 0.011 -10000 0 -10000 0 0
SLC2A1 0.19 0.14 -10000 0 -0.86 2 2
TWIST1 0.18 0.18 -10000 0 -0.65 10 10
ELK1 0.015 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.001 0.067 -10000 0 -0.76 2 2
VEGFA 0.19 0.16 -10000 0 -0.84 4 4
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.031 0.009 -9999 0 -10000 0 0
MAPK12 0.019 0.08 -9999 0 -0.48 12 12
CCND1 0.017 0.035 -9999 0 -0.25 1 1
p38 gamma/SNTA1 0.025 0.075 -9999 0 -0.45 11 11
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.019 0.079 -9999 0 -0.47 12 12
MAP2K6 0.012 0.085 -9999 0 -0.52 12 12
MAPT 0.024 0.045 -9999 0 -0.4 3 3
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.021 -9999 0 -0.45 1 1
Paxillin-dependent events mediated by a4b1

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.007 -10000 0 -10000 0 0
DOCK1 0.007 0.075 -10000 0 -0.82 4 4
ITGA4 0.002 0.078 -10000 0 -0.44 12 12
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.031 0.12 -10000 0 -0.62 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.047 -10000 0 -0.54 3 3
alpha4/beta7 Integrin/Paxillin -0.023 0.091 -10000 0 -0.5 15 15
lamellipodium assembly -0.004 0.058 -10000 0 -0.54 5 5
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
PI3K -0.004 0.049 -10000 0 -0.63 3 3
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.024 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.035 -10000 0 -0.42 3 3
cell adhesion -0.005 0.038 -10000 0 -0.45 3 3
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.005 0.042 -10000 0 -0.49 3 3
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.02 0.14 -10000 0 -0.51 31 31
ARF6/GDP 0.001 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.011 0.069 -10000 0 -0.52 7 7
p130Cas/Crk/Dock1 -0.004 0.049 -10000 0 -0.54 4 4
VCAM1 0.001 0.091 -10000 0 -0.54 11 11
alpha4/beta1 Integrin/Paxillin/Talin -0.005 0.039 -10000 0 -0.46 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.039 -10000 0 -0.46 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.038 0.45 3 -10000 0 3
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.005 0.039 -10000 0 -0.46 3 3
Rac1/GTP -0.005 0.067 -10000 0 -0.62 5 5
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.001 0.04 -9999 0 -0.73 1 1
PDGFB-D/PDGFRB/SLAP -0.002 0.03 -9999 0 -0.63 1 1
PDGFB-D/PDGFRB/APS/CBL -0.001 0.025 -9999 0 -0.54 1 1
AKT1 0.059 0.043 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.023 0.051 -9999 0 -0.78 1 1
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
FGR 0.002 0.028 -9999 0 -0.56 1 1
mol:Ca2+ 0.02 0.048 -9999 0 -0.82 1 1
MYC 0.018 0.15 -9999 0 -0.84 14 14
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.029 -9999 0 -0.45 1 1
LRP1/PDGFRB/PDGFB -0.002 0.035 -9999 0 -0.54 2 2
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
GO:0007205 0.02 0.049 -9999 0 -0.84 1 1
PTEN 0.012 0.038 -9999 0 -0.82 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.042 0.12 -9999 0 -0.31 82 82
PDGFB-D/PDGFRB/SHP2 -0.002 0.04 -9999 0 -0.63 2 2
PDGFB-D/PDGFRB/GRB10 -0.001 0.028 -9999 0 -0.63 1 1
cell cycle arrest -0.002 0.03 -9999 0 -0.63 1 1
HRAS 0.012 0.021 -9999 0 -0.31 2 2
HIF1A 0.064 0.04 -9999 0 -10000 0 0
GAB1 0.013 0.064 -9999 0 -0.86 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.059 -9999 0 -0.78 1 1
PDGFB-D/PDGFRB 0.012 0.031 -9999 0 -0.56 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.028 -9999 0 -0.63 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.001 0.048 -9999 0 -0.75 1 1
positive regulation of MAPKKK cascade -0.002 0.04 -9999 0 -0.63 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.05 -9999 0 -0.85 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.013 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.035 0.083 -9999 0 -0.79 1 1
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.18 0.28 -9999 0 -0.62 143 143
PTPN2 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.028 -9999 0 -0.63 1 1
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.017 0.071 -9999 0 -0.87 1 1
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.001 0.028 -9999 0 -0.63 1 1
LCK -0.008 0.087 -9999 0 -0.73 6 6
PDGFRB 0.012 0.038 -9999 0 -0.83 1 1
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.005 0.035 -9999 0 -0.54 1 1
ABL1 0.009 0.061 -9999 0 -0.83 1 1
PDGFB-D/PDGFRB/CBL 0.009 0.068 -9999 0 -0.95 1 1
PTPN1 0.014 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.006 0.048 -9999 0 -0.31 11 11
cell proliferation 0.02 0.13 -9999 0 -0.73 14 14
SLA 0.013 0.015 -9999 0 -0.31 1 1
actin cytoskeleton reorganization 0.052 0.025 -9999 0 -0.43 1 1
SRC 0.005 0.028 -9999 0 -0.56 1 1
PI3K -0.004 0.04 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.028 0.066 -9999 0 -0.69 1 1
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
PLCgamma1/SPHK1 0.024 0.053 -9999 0 -0.82 1 1
LYN 0.006 0.029 -9999 0 -0.55 1 1
LRP1 0.012 0.038 -9999 0 -0.82 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.021 -9999 0 -0.44 1 1
SPHK1 0.006 0.05 -9999 0 -0.31 12 12
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.02 0.05 -9999 0 -0.85 1 1
PLCG1 0.02 0.051 -9999 0 -0.89 1 1
NHERF/PDGFRB -0.002 0.026 -9999 0 -0.54 1 1
YES1 0.004 0.027 -9999 0 -0.55 1 1
cell migration -0.002 0.026 -9999 0 -0.54 1 1
SHC/Grb2/SOS1 0 0.021 -9999 0 -0.44 1 1
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0.021 -9999 0 -0.31 2 2
NHERF1-2/PDGFRB/PTEN -0.003 0.033 -9999 0 -0.49 2 2
FYN 0.006 0.028 -9999 0 -0.55 1 1
DOK1 0.034 0.025 -9999 0 -0.5 1 1
HRAS/GTP -0.001 0.014 -9999 0 -0.21 2 2
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.027 0.09 -9999 0 -0.44 14 14
PRKCD 0.034 0.025 -9999 0 -0.5 1 1
FER 0.031 0.049 -9999 0 -0.5 4 4
MAPKKK cascade -0.001 0.02 -9999 0 -0.43 1 1
RASA1 0.034 0.025 -9999 0 -0.5 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.017 0.03 -9999 0 -0.45 1 1
PDGFB-D/PDGFRB/SHB -0.001 0.028 -9999 0 -0.63 1 1
chemotaxis 0.01 0.059 -9999 0 -0.79 1 1
STAT1-3-5/STAT1-3-5 -0.003 0.023 -9999 0 -0.42 1 1
Bovine Papilomavirus E5/PDGFRB 0.001 0.029 -9999 0 -0.64 1 1
PTPRJ 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.031 -9999 0 -0.39 3 3
TRAF2/ASK1 -0.001 0.025 -9999 0 -0.55 1 1
ATM 0.012 0.038 -9999 0 -0.82 1 1
MAP2K3 0.026 0.057 -9999 0 -0.53 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.023 0.08 -9999 0 -0.42 7 7
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.001 0.1 -9999 0 -0.66 10 10
TXN 0.009 0.006 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.014 0.15 -9999 0 -0.82 16 16
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.028 -9999 0 -0.63 1 1
TAK1/TAB family -0.001 0.014 -9999 0 -0.21 2 2
RAC1/OSM/MEKK3 -0.001 0.009 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.009 0.033 -9999 0 -0.38 2 2
TRAF6 0.007 0.03 -9999 0 -0.46 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.005 0.084 -9999 0 -0.82 5 5
CCM2 0.012 0.021 -9999 0 -0.31 2 2
CaM/Ca2+/CAMKIIB -0.006 0.055 -9999 0 -0.55 5 5
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.006 0.063 -9999 0 -0.59 5 5
OSM/MEKK3 -0.001 0.013 -9999 0 -10000 0 0
TAOK1 -0.04 0.16 -9999 0 -0.46 60 60
TAOK2 0.017 0.021 -9999 0 -0.45 1 1
TAOK3 0.017 0.021 -9999 0 -0.45 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.038 -9999 0 -0.82 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.026 -9999 0 -0.54 1 1
GADD45/MTK1/MTK1 -0.023 0.1 -9999 0 -0.49 22 22
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0.02 -9999 0 -0.39 1 1
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.019 -9999 0 -0.42 1 1
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.04 0.15 -9999 0 -0.63 31 31
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.039 0.2 -9999 0 -0.82 31 31
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.038 -9999 0 -0.82 1 1
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.001 0.022 -9999 0 -0.49 1 1
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC5 0 0.009 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.009 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.024 -9999 0 -0.54 1 1
HDAC9 -0.017 0.095 -9999 0 -0.31 46 46
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
HDAC4/RFXANK -0.001 0.013 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.028 -9999 0 -0.63 1 1
Histones 0.036 0.023 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.013 -9999 0 -10000 0 0
CAMK4 -0.004 0.11 -9999 0 -0.55 15 15
Tubulin/HDAC6 -0.006 0.054 -9999 0 -0.54 5 5
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.008 0.016 -9999 0 -0.31 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.006 0.063 -9999 0 -0.63 5 5
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.028 -9999 0 -0.63 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.01 0.067 -9999 0 -0.54 7 7
HDAC4/ER alpha -0.043 0.14 -9999 0 -0.63 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.023 -9999 0 -10000 0 0
cell motility -0.006 0.054 -9999 0 -0.54 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.012 0.038 -9999 0 -0.82 1 1
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.047 0.19 -9999 0 -0.52 55 55
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.012 0.038 -9999 0 -0.82 1 1
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.001 0.021 -9999 0 -0.46 1 1
GNG2 0.012 0.038 -9999 0 -0.82 1 1
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.005 0.084 -9999 0 -0.82 5 5
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.012 0.021 -9999 0 -0.31 2 2
nuclear import 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.009 0.036 -9999 0 -0.31 6 6
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.022 0.025 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.007 -9999 0 -10000 0 0
BIRC5 -0.017 0.099 -9999 0 -0.32 44 44
NFKBIA 0.032 0.008 -9999 0 -10000 0 0
CPEB1 -0.048 0.22 -9999 0 -0.82 36 36
AKT1 0.032 0.008 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.011 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.013 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.013 0.005 -9999 0 -10000 0 0
PAK1/Aurora A 0.028 0.007 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.012 0.038 -9999 0 -0.82 1 1
TPX2 0.002 0.068 -9999 0 -10000 0 0
TP53 0.031 0.006 -9999 0 -10000 0 0
DLG7 0.021 0.008 -9999 0 -10000 0 0
AURKAIP1 0.012 0.021 -9999 0 -0.31 2 2
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.003 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.011 -9999 0 -10000 0 0
AURKA 0.026 0.011 -9999 0 -10000 0 0
AURKB -0.014 0.027 -9999 0 -10000 0 0
CDC25B 0.007 0.018 -9999 0 -10000 0 0
G2/M transition checkpoint 0.001 0.025 -9999 0 -0.5 1 1
mRNA polyadenylation -0.034 0.13 -9999 0 -0.5 36 36
Aurora A/CPEB -0.035 0.13 -9999 0 -0.5 36 36
Aurora A/TACC1/TRAP/chTOG 0.003 0.025 -9999 0 -0.46 1 1
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.028 0.007 -9999 0 -10000 0 0
regulation of centrosome cycle 0.002 0.01 -9999 0 -10000 0 0
spindle assembly 0.002 0.024 -9999 0 -0.46 1 1
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.01 0.037 -9999 0 -0.44 1 1
CENPA -0.009 0.025 -9999 0 -0.26 3 3
Aurora A/PP2A 0.028 0.007 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.038 0.008 -9999 0 -10000 0 0
negative regulation of DNA binding 0.031 0.006 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.002 0.025 -9999 0 -0.5 1 1
mitotic prometaphase 0.006 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.011 -9999 0 -10000 0 0
TACC1 0.012 0.038 -9999 0 -0.82 1 1
TACC3 0.013 0.015 -9999 0 -0.31 1 1
Aurora A/Antizyme1 0.003 0.015 -9999 0 -10000 0 0
Aurora A/RasGAP 0.028 0.007 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.005 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.002 0.068 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.019 0.05 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.051 0.038 -10000 0 -0.44 3 3
adherens junction organization 0.04 0.038 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.053 0.056 -10000 0 -0.46 4 4
FMN1 0.019 0.11 -10000 0 -0.43 28 28
mol:IP3 -0.002 0.032 -10000 0 -0.4 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0 -10000 0 -10000 0 0
AKT1 0.049 0.035 -10000 0 -0.39 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.035 -10000 0 -0.48 2 2
VASP 0.047 0.011 -10000 0 -10000 0 0
ZYX 0.047 0.011 -10000 0 -10000 0 0
JUB 0.046 0.024 -10000 0 -0.43 1 1
EGFR(dimer) 0.042 0.047 -10000 0 -0.46 4 4
E-cadherin/beta catenin-gamma catenin 0 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.033 -10000 0 -0.42 3 3
PIK3CA 0.009 0.065 -10000 0 -0.82 3 3
PI3K -0.003 0.034 -10000 0 -0.43 3 3
FYN 0.051 0.034 -10000 0 -0.35 3 3
mol:Ca2+ 0.042 0.034 -10000 0 -0.4 3 3
JUP 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.002 0.032 -10000 0 -0.4 3 3
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.053 0.056 -10000 0 -0.74 1 1
establishment of polarity of embryonic epithelium 0.046 0.011 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.007 0.075 -10000 0 -0.82 4 4
CASR 0.042 0.037 -10000 0 -0.38 3 3
RhoA/GTP -0.002 0.028 -10000 0 -0.36 3 3
AKT2 0.049 0.035 -10000 0 -0.39 3 3
actin cable formation 0.027 0.11 -10000 0 -0.41 28 28
apoptosis 0.003 0.032 0.41 3 -10000 0 3
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.047 0.06 -10000 0 -0.47 6 6
PIP5K1A 0.045 0.036 -10000 0 -0.5 2 2
PLCG1 -0.003 0.032 -10000 0 -0.41 3 3
Rac1/GTP -0.004 0.038 -10000 0 -0.42 4 4
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.82 16 16
CDC42/GTP -0.011 0.054 -9999 0 -10000 0 0
PLCG1 0.03 0.065 -9999 0 -0.33 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.011 0.053 -9999 0 -10000 0 0
S1PR5 0.007 0.054 -9999 0 -0.38 8 8
S1PR4 0.01 0.033 -9999 0 -0.31 5 5
MAPK3 0.03 0.065 -9999 0 -10000 0 0
MAPK1 0.03 0.065 -9999 0 -0.33 1 1
S1P/S1P5/Gi 0.022 0.071 -9999 0 -0.33 17 17
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.032 -9999 0 -0.55 1 1
RHOA 0.032 0.016 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.023 0.068 -9999 0 -0.33 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.001 0.014 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.023 0.17 -10000 0 -0.73 24 24
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.012 0.068 -10000 0 -0.55 7 7
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.028 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.018 0.036 -10000 0 -0.55 2 2
INS 0.013 0 -10000 0 -10000 0 0
BIN1 0.013 0 -10000 0 -10000 0 0
mol:Choline 0.028 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.031 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.023 -10000 0 -0.5 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.031 0 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.015 -10000 0 -0.31 1 1
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.008 -10000 0 -10000 0 0
ACAP1 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.002 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.011 0.068 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.017 0.08 -10000 0 -0.4 20 20
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.028 0 -10000 0 -10000 0 0
endocytosis 0.001 0.022 0.5 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.028 0.076 -10000 0 -0.43 13 13
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.012 0.038 -10000 0 -0.82 1 1
Dynamin 2/GDP 0.026 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.031 0.068 -10000 0 -0.43 10 10
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0.013 0 -9999 0 -9999 0 0
JUP 0.013 0 -9999 0 -9999 0 0
CDH1 0.013 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.015 -9999 0 -0.21 2 2
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.003 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.003 0.058 -9999 0 -0.31 16 16
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.027 -9999 0 -0.42 2 2
ARF1/GTP -0.001 0.016 -9999 0 -0.25 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline -0.002 0.027 -9999 0 -0.42 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.002 -9999 0 -10000 0 0
ARFIP2 0 0.005 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0.008 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin -0.001 0.009 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin -0.001 0.009 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.004 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.035 0.014 -9999 0 -10000 0 0
PLD2 -0.002 0.027 -9999 0 -0.42 2 2
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.015 -9999 0 -0.24 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.027 -9999 0 -0.42 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 -0.001 0.011 -9999 0 -0.17 2 2
USO1 -0.001 0.011 -9999 0 -10000 0 0
GBF1 -0.001 0.011 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.028 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.028 -9999 0 -0.63 1 1
RELB 0.013 0 -9999 0 -10000 0 0
NFKB2 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 488 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N9 TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU
109_MAP3K5 -0.28 -0.017 -0.017 -0.017
47_PPARGC1A -0.82 -0.82 -0.82 0.013
105_BMP4 0.013 -0.31 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR -0.49 -0.49 -0.49 -0.49
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B 0.047 -0.096 0 -0.097
84_STAT5A 0.047 -0.096 0 -0.097
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/6044636/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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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