PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1G15Z7C
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1G15Z7C
Overview
Introduction

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

Summary

There were 48 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 246
Signaling events mediated by Stem cell factor receptor (c-Kit) 159
Signaling events regulated by Ret tyrosine kinase 144
TCGA08_retinoblastoma 139
Reelin signaling pathway 126
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 116
Noncanonical Wnt signaling pathway 108
Wnt signaling 104
FOXA2 and FOXA3 transcription factor networks 100
PDGFR-alpha signaling pathway 99
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 482 . 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 ( 482 ).

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 0.5104 246 1724 7 -0.52 0 1000 -1000 -0.027 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3299 159 12448 78 -0.8 0.24 1000 -1000 -0.076 -1000
Signaling events regulated by Ret tyrosine kinase 0.2988 144 11847 82 -0.46 0.013 1000 -1000 -0.084 -1000
TCGA08_retinoblastoma 0.2884 139 1114 8 -0.13 0.073 1000 -1000 -0.022 -1000
Reelin signaling pathway 0.2614 126 7111 56 -0.6 0.033 1000 -1000 -0.08 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2407 116 7901 68 -0.9 0.37 1000 -1000 -0.12 -1000
Noncanonical Wnt signaling pathway 0.2241 108 2818 26 -0.42 0.013 1000 -1000 -0.073 -1000
Wnt signaling 0.2158 104 730 7 -0.42 0.013 1000 -1000 -0.02 -1000
FOXA2 and FOXA3 transcription factor networks 0.2075 100 4637 46 -0.92 0.021 1000 -1000 -0.027 -1000
PDGFR-alpha signaling pathway 0.2054 99 4362 44 -0.51 0.033 1000 -1000 -0.057 -1000
IL4-mediated signaling events 0.1909 92 8446 91 -1.3 0.66 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 0.1763 85 4467 52 -0.38 0.2 1000 -1000 -0.077 -1000
Nongenotropic Androgen signaling 0.1701 82 4297 52 -0.34 0.16 1000 -1000 -0.06 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1598 77 4209 54 -0.6 0.028 1000 -1000 -0.093 -1000
Calcium signaling in the CD4+ TCR pathway 0.1577 76 2373 31 -0.53 0.013 1000 -1000 -0.081 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1473 71 2433 34 -0.17 0.013 1000 -1000 -0.065 -1000
Glypican 1 network 0.1307 63 3034 48 -0.38 0.028 1000 -1000 -0.049 -1000
Endothelins 0.1224 59 5754 96 -0.4 0.013 1000 -1000 -0.081 -1000
IGF1 pathway 0.1203 58 3311 57 -0.2 0.059 1000 -1000 -0.088 -1000
Glucocorticoid receptor regulatory network 0.1183 57 6511 114 -0.57 0.37 1000 -1000 -0.067 -1000
Ephrin B reverse signaling 0.1162 56 2711 48 -0.31 0.19 1000 -1000 -0.071 -1000
IL23-mediated signaling events 0.1162 56 3368 60 -0.34 0.02 1000 -1000 -0.15 -1000
TCR signaling in naïve CD8+ T cells 0.1120 54 5027 93 -0.2 0.087 1000 -1000 -0.076 -1000
BMP receptor signaling 0.1079 52 4225 81 -0.58 0.026 1000 -1000 -0.082 -1000
Glypican 2 network 0.1058 51 205 4 -0.086 -0.01 1000 -1000 -0.034 -1000
Arf6 signaling events 0.0996 48 2997 62 -0.32 0.021 1000 -1000 -0.064 -1000
Coregulation of Androgen receptor activity 0.0975 47 3632 76 -0.77 0.061 1000 -1000 -0.061 -1000
Syndecan-1-mediated signaling events 0.0975 47 1626 34 -0.2 0.013 1000 -1000 -0.054 -1000
HIF-1-alpha transcription factor network 0.0975 47 3616 76 -0.57 0.042 1000 -1000 -0.11 -1000
EPHB forward signaling 0.0913 44 3816 85 -0.31 0.15 1000 -1000 -0.088 -1000
Signaling mediated by p38-alpha and p38-beta 0.0809 39 1736 44 -0.23 0.013 1000 -1000 -0.051 -1000
IL12-mediated signaling events 0.0788 38 3322 87 -0.41 0.022 1000 -1000 -0.12 -1000
Hedgehog signaling events mediated by Gli proteins 0.0788 38 2508 65 -0.66 0.061 1000 -1000 -0.057 -1000
Syndecan-4-mediated signaling events 0.0788 38 2554 67 -0.24 0.016 1000 -1000 -0.091 -1000
IL6-mediated signaling events 0.0747 36 2769 75 -0.21 0.059 1000 -1000 -0.09 -1000
Ras signaling in the CD4+ TCR pathway 0.0685 33 574 17 -0.095 0.013 1000 -1000 -0.039 -1000
EGFR-dependent Endothelin signaling events 0.0664 32 679 21 -0.11 0.013 1000 -1000 -0.073 -1000
Thromboxane A2 receptor signaling 0.0643 31 3307 105 -0.21 0.032 1000 -1000 -0.072 -1000
Osteopontin-mediated events 0.0622 30 1162 38 -0.26 0.013 1000 -1000 -0.098 -1000
amb2 Integrin signaling 0.0602 29 2441 82 -0.24 0.013 1000 -1000 -0.082 -1000
TCGA08_p53 0.0602 29 206 7 -0.084 0.053 1000 -1000 -0.013 -1000
FAS signaling pathway (CD95) 0.0602 29 1407 47 -0.26 0.03 1000 -1000 -0.046 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0581 28 2384 85 -0.28 0.013 1000 -1000 -0.077 -1000
Plasma membrane estrogen receptor signaling 0.0560 27 2386 86 -0.18 0.02 1000 -1000 -0.08 -1000
Visual signal transduction: Rods 0.0560 27 1404 52 -0.2 0.016 1000 -1000 -0.074 -1000
Regulation of Androgen receptor activity 0.0560 27 1896 70 -0.48 0.034 1000 -1000 -0.074 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0539 26 1364 52 -0.28 0.054 1000 -1000 -0.062 -1000
Regulation of p38-alpha and p38-beta 0.0539 26 1412 54 -0.47 0.013 1000 -1000 -0.06 -1000
ErbB2/ErbB3 signaling events 0.0498 24 1568 65 -0.13 0.027 1000 -1000 -0.064 -1000
IL27-mediated signaling events 0.0498 24 1244 51 -0.17 0.064 1000 -1000 -0.091 -1000
LPA receptor mediated events 0.0498 24 2467 102 -0.26 0.031 1000 -1000 -0.089 -1000
JNK signaling in the CD4+ TCR pathway 0.0477 23 404 17 -0.1 0.02 1000 -1000 -0.065 -1000
BCR signaling pathway 0.0477 23 2313 99 -0.19 0.022 1000 -1000 -0.092 -1000
Syndecan-2-mediated signaling events 0.0436 21 1485 69 -0.22 0.038 1000 -1000 -0.056 -1000
Signaling events mediated by PTP1B 0.0436 21 1603 76 -0.25 0.021 1000 -1000 -0.079 -1000
p75(NTR)-mediated signaling 0.0436 21 2682 125 -0.36 0.065 1000 -1000 -0.091 -1000
Fc-epsilon receptor I signaling in mast cells 0.0394 19 1869 97 -0.21 0.031 1000 -1000 -0.081 -1000
Nectin adhesion pathway 0.0394 19 1198 63 -0.26 0.033 1000 -1000 -0.07 -1000
Integrins in angiogenesis 0.0394 19 1651 84 -0.24 0.034 1000 -1000 -0.094 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0394 19 1677 88 -0.32 0.028 1000 -1000 -0.11 -1000
FOXM1 transcription factor network 0.0394 19 969 51 -0.19 0.047 1000 -1000 -0.15 -1000
ErbB4 signaling events 0.0373 18 1248 69 -0.14 0.057 1000 -1000 -0.079 -1000
Visual signal transduction: Cones 0.0373 18 714 38 -0.092 0.013 1000 -1000 -0.057 -1000
Aurora C signaling 0.0373 18 130 7 -0.058 0 1000 -1000 -0.04 -1000
IL1-mediated signaling events 0.0373 18 1157 62 -0.12 0.067 1000 -1000 -0.091 -1000
Regulation of nuclear SMAD2/3 signaling 0.0353 17 2329 136 -0.34 0.066 1000 -1000 -0.072 -1000
Syndecan-3-mediated signaling events 0.0353 17 624 35 -0.16 0.013 1000 -1000 -0.062 -1000
TCGA08_rtk_signaling 0.0353 17 456 26 -0.25 0.024 1000 -1000 -0.022 -1000
Aurora B signaling 0.0353 17 1180 67 -0.38 0.014 1000 -1000 -0.068 -1000
Insulin-mediated glucose transport 0.0332 16 513 32 -0.21 0.042 1000 -1000 -0.065 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0332 16 1972 120 -0.31 0.042 1000 -1000 -0.078 -1000
Presenilin action in Notch and Wnt signaling 0.0311 15 923 61 -0.21 0.043 1000 -1000 -0.066 -1000
Effects of Botulinum toxin 0.0311 15 399 26 -0.16 0.019 1000 -1000 -0.055 -1000
Rapid glucocorticoid signaling 0.0311 15 318 20 -0.093 0.015 1000 -1000 -0.04 -1000
Signaling events mediated by PRL 0.0311 15 527 34 -0.11 0.013 1000 -1000 -0.039 -1000
LPA4-mediated signaling events 0.0290 14 178 12 -0.12 0.016 1000 -1000 -0.025 -1000
IFN-gamma pathway 0.0290 14 957 68 -0.11 0.041 1000 -1000 -0.089 -1000
IL2 signaling events mediated by STAT5 0.0290 14 328 22 -0.067 0.039 1000 -1000 -0.044 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0290 14 464 33 -0.16 0.035 1000 -1000 -0.066 -1000
Class IB PI3K non-lipid kinase events 0.0290 14 42 3 -0.004 -1000 1000 -1000 -0.011 -1000
Ceramide signaling pathway 0.0270 13 1004 76 -0.18 0.024 1000 -1000 -0.058 -1000
Signaling events mediated by HDAC Class III 0.0270 13 540 40 -0.35 0.024 1000 -1000 -0.043 -1000
IL2 signaling events mediated by PI3K 0.0270 13 759 58 -0.066 0.031 1000 -1000 -0.082 -1000
VEGFR1 specific signals 0.0270 13 775 56 -0.071 0.041 1000 -1000 -0.081 -1000
Insulin Pathway 0.0249 12 944 74 -0.082 0.038 1000 -1000 -0.096 -1000
a4b1 and a4b7 Integrin signaling 0.0228 11 59 5 -0.03 0.004 1000 -1000 -0.03 -1000
Cellular roles of Anthrax toxin 0.0228 11 429 39 -0.092 0.019 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0228 11 498 45 -0.092 0.039 1000 -1000 -0.083 -1000
Regulation of Telomerase 0.0228 11 1153 102 -0.29 0.053 1000 -1000 -0.1 -1000
mTOR signaling pathway 0.0207 10 543 53 -0.044 0.021 1000 -1000 -0.059 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0207 10 870 83 -0.21 0.052 1000 -1000 -0.072 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0207 10 802 74 -0.18 0.086 1000 -1000 -0.097 -1000
Caspase cascade in apoptosis 0.0187 9 682 74 -0.092 0.029 1000 -1000 -0.048 -1000
BARD1 signaling events 0.0187 9 548 57 -0.033 0.054 1000 -1000 -0.059 -1000
Retinoic acid receptors-mediated signaling 0.0187 9 560 58 -0.12 0.034 1000 -1000 -0.073 -1000
S1P3 pathway 0.0187 9 380 42 -0.18 0.049 1000 -1000 -0.062 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0166 8 249 28 -0.18 0.031 1000 -1000 -0.054 -1000
Class I PI3K signaling events mediated by Akt 0.0166 8 555 68 -0.21 0.052 1000 -1000 -0.061 -1000
ceramide signaling pathway 0.0166 8 410 49 -0.092 0.03 1000 -1000 -0.049 -1000
TRAIL signaling pathway 0.0145 7 375 48 -0.077 0.047 1000 -1000 -0.062 -1000
S1P1 pathway 0.0145 7 267 36 -0.038 0.032 1000 -1000 -0.063 -1000
Canonical Wnt signaling pathway 0.0145 7 361 51 -0.047 0.068 1000 -1000 -0.052 -1000
Class I PI3K signaling events 0.0145 7 512 73 -0.25 0.023 1000 -1000 -0.065 -1000
FoxO family signaling 0.0124 6 419 64 -0.21 0.16 1000 -1000 -0.061 -1000
Canonical NF-kappaB pathway 0.0104 5 216 39 -0.092 0.072 1000 -1000 -0.084 -1000
Circadian rhythm pathway 0.0104 5 127 22 -0.06 0.013 1000 -1000 -0.063 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0104 5 212 37 -0.031 0.04 1000 -1000 -0.055 -1000
S1P5 pathway 0.0104 5 98 17 -0.017 0.022 1000 -1000 -0.053 -1000
S1P4 pathway 0.0104 5 138 25 -0.017 0.032 1000 -1000 -0.048 -1000
EPO signaling pathway 0.0083 4 224 55 -0.037 0.062 1000 -1000 -0.1 -1000
Signaling events mediated by HDAC Class I 0.0083 4 498 104 -0.092 0.059 1000 -1000 -0.074 -1000
Atypical NF-kappaB pathway 0.0083 4 149 31 -0.039 0.047 1000 -1000 -0.055 -1000
PLK1 signaling events 0.0062 3 284 85 -0.042 0.033 1000 -1000 -0.047 -1000
HIF-2-alpha transcription factor network 0.0062 3 137 43 -0.2 0.21 1000 -1000 -0.08 -1000
Signaling mediated by p38-gamma and p38-delta 0.0062 3 48 15 0 0.032 1000 -1000 -0.031 -1000
Paxillin-dependent events mediated by a4b1 0.0062 3 126 36 -0.03 0.024 1000 -1000 -0.071 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0062 3 474 125 -0.034 0.087 1000 -1000 -0.11 -1000
PDGFR-beta signaling pathway 0.0062 3 347 97 -0.18 0.064 1000 -1000 -0.091 -1000
p38 MAPK signaling pathway 0.0062 3 144 44 -0.038 0.026 1000 -1000 -0.068 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0041 2 59 23 -0.037 0.049 1000 -1000 -0.067 -1000
Signaling events mediated by HDAC Class II 0.0041 2 177 75 -0.048 0.036 1000 -1000 -0.07 -1000
Aurora A signaling 0.0041 2 163 60 -0.048 0.038 1000 -1000 -0.057 -1000
Arf6 downstream pathway 0.0041 2 120 43 -0.18 0.094 1000 -1000 -0.042 -1000
E-cadherin signaling in keratinocytes 0.0041 2 121 43 -0.004 0.053 1000 -1000 -0.07 -1000
PLK2 and PLK4 events 0.0021 1 5 3 0.01 0.022 1000 -1000 -0.019 -1000
E-cadherin signaling in the nascent adherens junction 0.0021 1 104 76 -0.17 0.074 1000 -1000 -0.086 -1000
Arf6 trafficking events 0.0021 1 76 71 -0.021 0.046 1000 -1000 -0.072 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.058 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0.013 1000 -1000 -0.048 -1000
Arf1 pathway 0.0000 0 22 54 -0.005 0.036 1000 -1000 -0.05 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 -0.001 0.013 1000 -1000 -0.063 -1000
Total NA 4007 217615 7203 -30 -990 131000 -131000 -8.9 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.43 0.31 -9999 0 -0.62 336 336
EFNA5 -0.12 0.3 -9999 0 -0.82 75 75
FYN -0.38 0.3 -9999 0 -0.56 336 336
neuron projection morphogenesis -0.43 0.31 -9999 0 -0.62 336 336
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.43 0.32 -9999 0 -0.62 336 336
EPHA5 -0.52 0.4 -9999 0 -0.82 305 305
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.21 0.22 -10000 0 -0.4 280 280
CRKL -0.22 0.24 -10000 0 -0.42 273 273
HRAS -0.19 0.22 -10000 0 -0.51 42 42
mol:PIP3 -0.22 0.22 -10000 0 -0.41 273 273
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 -0.45 273 273
FOXO3 -0.19 0.22 -10000 0 -0.38 273 273
AKT1 -0.22 0.23 -10000 0 -0.42 273 273
BAD -0.19 0.22 -10000 0 -0.38 273 273
megakaryocyte differentiation -0.25 0.25 -10000 0 -0.45 281 281
GSK3B -0.19 0.22 -10000 0 -0.38 273 273
RAF1 -0.15 0.18 -10000 0 -0.46 23 23
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.24 0.25 -10000 0 -0.45 273 273
STAT1 -0.59 0.59 -10000 0 -1.1 273 273
HRAS/SPRED1 -0.17 0.14 -10000 0 -0.45 25 25
cell proliferation -0.24 0.25 -10000 0 -0.45 276 276
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 -10000 0 -0.45 273 273
HRAS/SPRED2 -0.17 0.15 -10000 0 -0.45 26 26
LYN/TEC/p62DOK -0.23 0.21 -10000 0 -0.41 273 273
MAPK3 -0.094 0.13 -10000 0 -0.32 21 21
STAP1 -0.26 0.25 -10000 0 -0.47 273 273
GRAP2 -0.042 0.21 -10000 0 -0.78 34 34
JAK2 -0.51 0.45 -10000 0 -0.9 273 273
STAT1 (dimer) -0.58 0.57 -10000 0 -1.1 273 273
mol:Gleevec 0.008 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.24 0.21 -10000 0 -0.42 276 276
actin filament polymerization -0.23 0.24 -10000 0 -0.44 273 273
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.35 0.34 -10000 0 -0.64 273 273
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.19 -10000 0 -0.37 263 263
PI3K -0.22 0.24 -10000 0 -0.42 274 274
PTEN 0.012 0.038 -10000 0 -0.82 1 1
SCF/KIT/EPO/EPOR -0.74 0.72 -10000 0 -1.4 273 273
MAPK8 -0.24 0.26 -10000 0 -0.46 276 276
STAT3 (dimer) -0.23 0.24 -10000 0 -0.44 273 273
positive regulation of transcription -0.075 0.11 -10000 0 -0.26 21 21
mol:GDP -0.23 0.19 -10000 0 -0.55 42 42
PIK3C2B -0.24 0.25 -10000 0 -0.45 273 273
CBL/CRKL -0.2 0.22 -10000 0 -0.39 273 273
FER -0.24 0.25 -10000 0 -0.45 274 274
SH2B3 -0.24 0.25 -10000 0 -0.45 273 273
PDPK1 -0.2 0.21 -10000 0 -0.37 274 274
SNAI2 -0.24 0.26 -10000 0 -0.46 274 274
positive regulation of cell proliferation -0.41 0.42 -10000 0 -0.77 273 273
KITLG -0.004 0.1 -10000 0 -0.86 7 7
cell motility -0.41 0.42 -10000 0 -0.77 273 273
PTPN6 0.021 0.018 -10000 0 -10000 0 0
EPOR -0.14 0.18 -10000 0 -0.67 2 2
STAT5A (dimer) -0.34 0.35 -10000 0 -0.63 273 273
SOCS1 0.009 0.048 -10000 0 -0.42 5 5
cell migration 0.24 0.25 0.45 276 -10000 0 276
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 34 34
GRB10 -0.24 0.25 -10000 0 -0.45 273 273
PTPN11 0.02 0.039 -10000 0 -0.81 1 1
SCF/KIT -0.26 0.26 -10000 0 -0.48 273 273
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.11 0.15 -10000 0 -0.35 21 21
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.8 0.75 -10000 0 -1.5 273 273
MAP2K2 -0.11 0.15 -10000 0 -0.35 21 21
SHC/Grb2/SOS1 -0.23 0.21 -10000 0 -0.41 273 273
STAT5A -0.35 0.36 -10000 0 -0.66 273 273
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.24 0.25 -10000 0 -0.45 274 274
SHC/GRAP2 -0.042 0.16 -10000 0 -0.63 31 31
PTPRO -0.25 0.25 -10000 0 -0.46 281 281
SH2B2 -0.24 0.25 -10000 0 -0.45 273 273
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.24 0.25 -10000 0 -0.46 276 276
CREBBP 0.018 0.021 -10000 0 -10000 0 0
BCL2 -0.22 0.42 -10000 0 -1.6 35 35
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 -0.09 0.069 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -9999 0 -0.51 118 118
JUN -0.32 0.32 -9999 0 -0.67 177 177
HRAS 0.012 0.021 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.39 0.32 -9999 0 -0.61 300 300
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 -0.39 0.32 -9999 0 -0.61 300 300
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 -0.3 0.25 -9999 0 -0.51 275 275
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.35 0.3 -9999 0 -0.55 300 300
GRB7 -0.042 0.12 -9999 0 -0.31 82 82
RET51/GFRalpha1/GDNF -0.39 0.32 -9999 0 -0.61 300 300
MAPKKK cascade -0.31 0.26 -9999 0 -0.52 222 222
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.35 0.31 -9999 0 -0.58 287 287
lamellipodium assembly -0.24 0.18 -9999 0 -0.38 276 276
RET51/GFRalpha1/GDNF/SHC -0.39 0.32 -9999 0 -0.61 300 300
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
RET9/GFRalpha1/GDNF/SHC -0.29 0.25 -9999 0 -0.51 275 275
RET9/GFRalpha1/GDNF/Shank3 -0.29 0.25 -9999 0 -0.51 275 275
MAPK3 -0.32 0.29 -9999 0 -0.52 300 300
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.3 -9999 0 -0.82 75 75
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.31 0.29 -9999 0 -0.67 128 128
DOK5 -0.1 0.29 -9999 0 -0.82 66 66
GFRA1 -0.46 0.41 -9999 0 -0.82 276 276
MAPK8 -0.24 0.23 -9999 0 -0.54 113 113
HRAS/GTP -0.36 0.31 -9999 0 -0.57 300 300
tube development -0.28 0.24 -9999 0 -0.48 275 275
MAPK1 -0.32 0.29 -9999 0 -0.52 300 300
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.18 0.18 -9999 0 -0.34 275 275
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
PDLIM7 0.01 0.033 -9999 0 -0.31 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.44 0.38 -9999 0 -0.67 311 311
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.39 0.32 -9999 0 -0.61 300 300
RET51/GFRalpha1/GDNF/Dok5 -0.46 0.39 -9999 0 -0.69 312 312
PRKCA -0.025 0.18 -9999 0 -0.82 22 22
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
CREB1 -0.25 0.24 -9999 0 -0.43 275 275
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.18 -9999 0 -0.34 275 275
RET51/GFRalpha1/GDNF/Grb7 -0.42 0.33 -9999 0 -0.64 300 300
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.17 0.32 -9999 0 -0.64 135 135
DOK4 0.013 0.015 -9999 0 -0.31 1 1
JNK cascade -0.31 0.3 -9999 0 -0.65 177 177
RET9/GFRalpha1/GDNF/FRS2 -0.29 0.25 -9999 0 -0.51 275 275
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 -0.34 275 275
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.25 0.24 -9999 0 -0.43 245 245
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.25 0.24 -9999 0 -0.41 300 300
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.29 0.31 -9999 0 -0.47 300 300
PI3K -0.37 0.34 -9999 0 -0.62 276 276
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.28 0.24 -9999 0 -0.48 275 275
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.22 0.21 -9999 0 -0.53 84 84
RET51/GFRalpha1/GDNF/FRS2 -0.39 0.32 -9999 0 -0.61 300 300
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.082 0.27 -9999 0 -0.82 55 55
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.29 0.31 -9999 0 -0.47 300 300
RET51/GFRalpha1/GDNF/PKC alpha -0.41 0.35 -9999 0 -0.64 302 302
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.002 0.041 -9999 0 -0.31 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.45 0.37 -9999 0 -0.68 311 311
Rac1/GTP -0.29 0.23 -9999 0 -0.47 276 276
RET9/GFRalpha1/GDNF -0.32 0.28 -9999 0 -0.56 275 275
GFRalpha1/GDNF -0.37 0.32 -9999 0 -0.64 275 275
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 -0.31 200 200
CDKN2C 0.026 0.036 -10000 0 -0.3 4 4
CDKN2A -0.13 0.16 -10000 0 -0.32 206 206
CCND2 0.07 0.073 0.17 140 -10000 0 140
RB1 -0.069 0.072 -10000 0 -0.17 140 140
CDK4 0.07 0.072 0.17 142 -10000 0 142
CDK6 0.073 0.077 0.18 140 -0.18 2 142
G1/S progression 0.061 0.08 0.17 140 -10000 0 140
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 -0.023 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 -0.57 358 358
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.009 0.063 -9999 0 -0.46 9 9
AKT1 -0.24 0.18 -9999 0 -0.33 359 359
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 0.25 -9999 0 -0.53 357 357
LRPAP1/LRP8 -0.026 0.13 -9999 0 -0.63 20 20
RELN/LRP8/DAB1/Fyn -0.37 0.23 -9999 0 -0.5 357 357
DAB1/alpha3/beta1 Integrin -0.35 0.23 -9999 0 -0.84 35 35
long-term memory -0.37 0.25 -9999 0 -0.49 359 359
DAB1/LIS1 -0.36 0.24 -9999 0 -0.48 362 362
DAB1/CRLK/C3G -0.35 0.23 -9999 0 -0.46 362 362
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
DAB1/NCK2 -0.36 0.24 -9999 0 -0.48 362 362
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.023 0.16 -9999 0 -0.64 27 27
CDK5R1 0.012 0.021 -9999 0 -0.31 2 2
RELN -0.6 0.37 -9999 0 -0.82 353 353
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.42 0.26 -9999 0 -0.57 357 357
GRIN2A/RELN/LRP8/DAB1/Fyn -0.38 0.26 -9999 0 -0.51 359 359
MAPK8 -0.002 0.11 -9999 0 -0.82 9 9
RELN/VLDLR/DAB1 -0.39 0.25 -9999 0 -0.53 358 358
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.37 0.26 -9999 0 -0.5 362 362
RELN/LRP8 -0.42 0.26 -9999 0 -0.57 357 357
GRIN2B/RELN/LRP8/DAB1/Fyn -0.37 0.23 -9999 0 -0.5 357 357
PI3K -0.004 0.05 -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 -0.31 0.23 -9999 0 -0.82 29 29
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 0.016 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.14 -9999 0 -0.52 22 22
neuron adhesion -0.28 0.23 -9999 0 -0.74 33 33
LRP8 -0.021 0.17 -9999 0 -0.82 20 20
GSK3B -0.22 0.17 -9999 0 -0.62 18 18
RELN/VLDLR/DAB1/Fyn -0.37 0.23 -9999 0 -0.5 358 358
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.36 359 359
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.033 0.089 -9999 0 -0.33 20 20
neuron migration -0.3 0.22 -9999 0 -0.42 354 354
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.14 -9999 0 -0.52 22 22
RELN/VLDLR -0.4 0.27 -9999 0 -0.54 362 362
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 -0.6 27 27
NFATC2 -0.24 0.38 -10000 0 -0.81 126 126
NFATC3 -0.083 0.13 -10000 0 -10000 0 0
CD40LG -0.74 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 -1.2 139 139
JUNB 0.003 0.093 -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 -0.25 0.44 -10000 0 -0.87 137 137
Jun/NFAT1-c-4/p21SNFT -0.67 0.61 -10000 0 -1.2 239 239
AP-1/NFAT1-c-4 -0.9 0.79 -10000 0 -1.5 263 263
IKZF1 -0.18 0.34 -10000 0 -0.72 107 107
T-helper 2 cell differentiation -0.32 0.35 -10000 0 -0.89 102 102
AP-1/NFAT1 -0.43 0.49 -10000 0 -0.9 214 214
CALM1 0.029 0.009 -10000 0 -10000 0 0
EGR2 -0.8 0.86 -10000 0 -1.7 221 221
EGR3 -0.58 0.75 -10000 0 -1.6 133 133
NFAT1/FOXP3 -0.22 0.34 -10000 0 -0.7 127 127
EGR1 -0.16 0.34 -10000 0 -0.82 102 102
JUN -0.19 0.35 -10000 0 -0.83 109 109
EGR4 -0.035 0.18 -10000 0 -0.72 29 29
mol:Ca2+ 0.016 0.01 -10000 0 -10000 0 0
GBP3 -0.17 0.32 -10000 0 -0.7 102 102
FOSL1 -0.029 0.12 -10000 0 -0.33 59 59
NFAT1-c-4/MAF/IRF4 -0.57 0.57 -10000 0 -1.1 238 238
DGKA -0.16 0.3 -10000 0 -0.66 100 100
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.56 0.56 -10000 0 -1.1 239 239
CTLA4 -0.24 0.38 -10000 0 -0.82 109 109
NFAT1-c-4 (dimer)/EGR1 -0.64 0.67 -10000 0 -1.3 235 235
NFAT1-c-4 (dimer)/EGR4 -0.58 0.57 -10000 0 -1.1 238 238
FOS -0.22 0.37 -10000 0 -0.83 128 128
IFNG -0.43 0.54 -10000 0 -1.2 143 143
T cell activation -0.44 0.43 -10000 0 -0.95 169 169
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 0.43 0.76 223 -10000 0 223
TNF -0.6 0.58 -10000 0 -1.1 234 234
FASLG -0.74 0.79 -10000 0 -1.5 239 239
TBX21 -0.037 0.18 -10000 0 -0.72 29 29
BATF3 -0.006 0.083 -10000 0 -0.33 27 27
PRKCQ 0.005 0.086 -10000 0 -0.82 5 5
PTPN1 -0.16 0.3 -10000 0 -0.68 92 92
NFAT1-c-4/ICER1 -0.55 0.56 -10000 0 -1.1 238 238
GATA3 -0.031 0.19 -10000 0 -0.79 27 27
T-helper 1 cell differentiation -0.41 0.52 -10000 0 -1.1 144 144
IL2RA -0.48 0.46 -10000 0 -1 154 154
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.3 -10000 0 -0.66 100 100
E2F1 -0.081 0.15 -10000 0 -0.3 150 150
PPARG -0.002 0.1 -10000 0 -0.61 12 12
SLC3A2 -0.16 0.3 -10000 0 -0.66 100 100
IRF4 -0.1 0.23 -10000 0 -0.46 119 119
PTGS2 -0.71 0.57 -10000 0 -1.2 252 252
CSF2 -0.78 0.54 -10000 0 -1.2 263 263
JunB/Fra1/NFAT1-c-4 -0.54 0.54 -10000 0 -1 233 233
IL4 -0.33 0.37 -10000 0 -0.95 99 99
IL5 -0.69 0.54 -10000 0 -1.2 248 248
IL2 -0.45 0.44 -10000 0 -0.98 169 169
IL3 -0.097 0.062 -10000 0 -10000 0 0
RNF128 0.049 0.042 -10000 0 -0.88 1 1
NFATC1 -0.37 0.43 -10000 0 -0.77 223 223
CDK4 0.22 0.25 0.6 63 -10000 0 63
PTPRK -0.16 0.3 -10000 0 -0.66 100 100
IL8 -0.72 0.55 -10000 0 -1.2 251 251
POU2F1 0.013 0.015 -10000 0 -0.31 1 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.13 0.32 -9999 0 -0.82 83 83
GNB1/GNG2 -0.26 0.24 -9999 0 -0.6 123 123
mol:DAG -0.21 0.24 -9999 0 -0.54 123 123
PLCG1 -0.22 0.25 -9999 0 -0.56 123 123
YES1 -0.25 0.27 -9999 0 -0.43 300 300
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.24 0.22 -9999 0 -0.57 118 118
MAP3K7 -0.17 0.2 -9999 0 -0.45 115 115
mol:Ca2+ -0.2 0.23 -9999 0 -0.52 123 123
mol:IP3 -0.21 0.24 -9999 0 -0.54 123 123
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 -0.48 128 128
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.47 300 300
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.25 0.27 -9999 0 -0.43 300 300
GO:0007205 -0.21 0.23 -9999 0 -0.53 123 123
WNT6 0.005 0.049 -9999 0 -0.31 11 11
WNT4 -0.26 0.39 -9999 0 -0.81 161 161
NFAT1/CK1 alpha -0.3 0.26 -9999 0 -0.58 183 183
GNG2 0.012 0.038 -9999 0 -0.82 1 1
WNT5A -0.005 0.12 -9999 0 -0.78 11 11
WNT11 -0.42 0.42 -9999 0 -0.82 247 247
CDC42 -0.23 0.25 -9999 0 -0.59 122 122
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 -0.47 300 300
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.005 0.049 -9999 0 -0.31 11 11
WNT4 -0.26 0.39 -9999 0 -0.81 161 161
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.005 0.12 -9999 0 -0.78 11 11
WNT11 -0.42 0.42 -9999 0 -0.82 247 247
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.52 0.54 -9999 0 -1 215 215
PCK1 -0.35 0.5 -9999 0 -1.4 72 72
HNF4A -0.67 0.66 -9999 0 -1.3 246 246
KCNJ11 -0.49 0.54 -9999 0 -1 199 199
AKT1 -0.041 0.12 -9999 0 -0.38 13 13
response to starvation -0.018 0.034 -9999 0 -10000 0 0
DLK1 -0.49 0.54 -9999 0 -1.1 198 198
NKX2-1 -0.16 0.21 -9999 0 -10000 0 0
ACADM -0.52 0.55 -9999 0 -1 220 220
TAT -0.2 0.22 -9999 0 -0.6 26 26
CEBPB 0.013 0.005 -9999 0 -10000 0 0
CEBPA 0.005 0.085 -9999 0 -0.82 5 5
TTR -0.2 0.22 -9999 0 -0.76 31 31
PKLR -0.52 0.55 -9999 0 -1.1 211 211
APOA1 -0.92 0.89 -9999 0 -1.7 261 261
CPT1C -0.53 0.55 -9999 0 -1 222 222
ALAS1 -0.16 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.3 -9999 0 -0.66 76 76
FOXF1 -0.011 0.093 -9999 0 -0.76 7 7
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.007 -9999 0 -10000 0 0
CPT1A -0.52 0.55 -9999 0 -1 217 217
HMGCS1 -0.52 0.54 -9999 0 -1 218 218
NR3C1 0.019 0.016 -9999 0 -10000 0 0
CPT1B -0.52 0.54 -9999 0 -1 216 216
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.67 0.7 -9999 0 -1.3 234 234
CREB1 0 0.053 -9999 0 -10000 0 0
IGFBP1 -0.18 0.2 -9999 0 -0.55 10 10
PDX1 -0.18 0.21 -9999 0 -10000 0 0
UCP2 -0.52 0.55 -9999 0 -1.1 211 211
ALDOB -0.49 0.54 -9999 0 -1 199 199
AFP -0.049 0.11 -9999 0 -0.51 6 6
BDH1 -0.52 0.54 -9999 0 -1.1 207 207
HADH -0.48 0.54 -9999 0 -1 199 199
F2 -0.63 0.64 -9999 0 -1.3 208 208
HNF1A 0.015 0.007 -9999 0 -10000 0 0
G6PC -0.007 0.09 -9999 0 -10000 0 0
SLC2A2 -0.23 0.26 -9999 0 -0.55 61 61
INS -0.008 0.018 -9999 0 -10000 0 0
FOXA1 -0.06 0.15 -9999 0 -0.52 14 14
FOXA3 -0.076 0.17 -9999 0 -0.35 114 114
FOXA2 -0.56 0.61 -9999 0 -1.1 223 223
ABCC8 -0.78 0.75 -9999 0 -1.4 267 267
ALB -0.1 0.32 -9999 0 -1.3 31 31
PDGFR-alpha 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
PDGFRA -0.26 0.39 -9999 0 -0.84 152 152
PDGF/PDGFRA/CRKL -0.2 0.29 -9999 0 -0.63 152 152
positive regulation of JUN kinase activity -0.15 0.22 -9999 0 -0.48 152 152
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.2 0.3 -9999 0 -0.64 152 152
AP1 -0.51 0.63 -9999 0 -1.5 135 135
mol:IP3 -0.2 0.31 -9999 0 -0.65 152 152
PLCG1 -0.2 0.31 -9999 0 -0.65 152 152
PDGF/PDGFRA/alphaV Integrin -0.2 0.3 -9999 0 -0.63 153 153
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.2 0.31 -9999 0 -0.65 152 152
CAV3 -0.001 0.029 -9999 0 -0.31 4 4
CAV1 -0.009 0.14 -9999 0 -0.82 13 13
SHC/Grb2/SOS1 -0.15 0.23 -9999 0 -0.49 152 152
PDGF/PDGFRA/Shf -0.2 0.29 -9999 0 -0.63 152 152
FOS -0.46 0.61 -9999 0 -1.4 135 135
JUN -0.17 0.29 -9999 0 -0.7 109 109
oligodendrocyte development -0.2 0.3 -9999 0 -0.63 153 153
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.2 0.31 -9999 0 -0.65 152 152
PDGF/PDGFRA -0.26 0.39 -9999 0 -0.84 152 152
actin cytoskeleton reorganization -0.2 0.29 -9999 0 -0.63 152 152
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 -0.54 155 155
PDGF/PDGFRA/Crk/C3G -0.17 0.25 -9999 0 -0.54 152 152
JAK1 -0.18 0.3 -9999 0 -0.63 152 152
ELK1/SRF -0.13 0.24 -9999 0 -0.49 152 152
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0.015 -9999 0 -0.31 1 1
CSNK2A1 0.028 0.028 -9999 0 -10000 0 0
GO:0007205 -0.2 0.32 -9999 0 -0.67 152 152
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.15 0.22 -9999 0 -0.48 152 152
PDGF/PDGFRA/SHB -0.2 0.29 -9999 0 -0.63 152 152
PDGF/PDGFRA/Caveolin-1 -0.21 0.32 -9999 0 -0.66 155 155
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
ELK1 -0.18 0.28 -9999 0 -0.6 152 152
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
PDGF/PDGFRA/Crk -0.2 0.29 -9999 0 -0.63 152 152
JAK-STAT cascade -0.18 0.3 -9999 0 -0.63 152 152
cell proliferation -0.2 0.29 -9999 0 -0.63 152 152
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.59 0.44 -10000 0 -1.1 157 157
STAT6 (cleaved dimer) -0.64 0.44 -10000 0 -1 250 250
IGHG1 -0.2 0.14 -10000 0 -0.36 56 56
IGHG3 -0.58 0.42 -10000 0 -0.95 224 224
AKT1 -0.32 0.26 -10000 0 -0.72 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.26 -10000 0 -0.76 54 54
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.35 0.28 -10000 0 -0.74 104 104
THY1 -0.59 0.44 -10000 0 -1.1 155 155
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 -0.73 173 173
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.74 66 66
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.003 0.071 -10000 0 -0.31 24 24
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.62 0.44 -10000 0 -0.99 238 238
SOCS1 -0.4 0.29 -10000 0 -0.73 127 127
SOCS3 -0.38 0.36 -10000 0 -0.97 80 80
FCER2 -0.58 0.42 -10000 0 -0.97 208 208
PARP14 0.013 0.004 -10000 0 -10000 0 0
CCL17 -0.66 0.48 -10000 0 -1.2 180 180
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.21 -10000 0 -0.7 41 41
T cell proliferation -0.6 0.46 -10000 0 -1.1 183 183
IL4R/JAK1 -0.59 0.44 -10000 0 -1.1 167 167
EGR2 -0.93 0.72 -10000 0 -1.6 236 236
JAK2 -0.017 0.045 -10000 0 -0.86 1 1
JAK3 -0.066 0.14 -10000 0 -0.31 120 120
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 -0.54 31 31
CCL26 -0.61 0.45 -10000 0 -1.1 168 168
IL4R -0.63 0.47 -10000 0 -1.1 170 170
PTPN6 0.028 0.009 -10000 0 -10000 0 0
IL13RA2 -0.7 0.57 -10000 0 -1.3 201 201
IL13RA1 -0.016 0.024 -10000 0 -10000 0 0
IRF4 -0.34 0.48 -10000 0 -1.2 91 91
ARG1 -0.14 0.11 -10000 0 -10000 0 0
CBL -0.38 0.3 -10000 0 -0.71 151 151
GTF3A 0.017 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
IL13RA1/JAK2 -0.024 0.045 -10000 0 -0.68 1 1
IRF4/BCL6 -0.31 0.44 -10000 0 -1.1 88 88
CD40LG -0.12 0.3 -10000 0 -0.8 77 77
MAPK14 -0.39 0.32 -10000 0 -0.76 136 136
mitosis -0.3 0.24 -10000 0 -0.67 75 75
STAT6 -0.67 0.51 -10000 0 -1.1 215 215
SPI1 0.001 0.071 -10000 0 -0.31 24 24
RPS6KB1 -0.29 0.24 -10000 0 -0.67 62 62
STAT6 (dimer) -0.67 0.51 -10000 0 -1.1 215 215
STAT6 (dimer)/PARP14 -0.62 0.47 -10000 0 -1.1 204 204
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.28 -10000 0 -0.71 89 89
FRAP1 -0.32 0.26 -10000 0 -0.72 75 75
LTA -0.61 0.46 -10000 0 -1.1 162 162
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.66 0.5 1.1 217 -10000 0 217
CCL11 -0.58 0.43 -10000 0 -1.1 143 143
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.7 89 89
IL2RG -0.044 0.19 -10000 0 -0.55 52 52
IL10 -0.61 0.47 -10000 0 -1.1 169 169
IRS1 -0.082 0.27 -10000 0 -0.82 55 55
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.095 -10000 0 -10000 0 0
IL5 -0.6 0.44 -10000 0 -1.1 157 157
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.48 0.33 -10000 0 -0.84 161 161
COL1A1 -0.26 0.24 -10000 0 -0.78 24 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.59 0.45 -10000 0 -1.2 122 122
IL2R gamma/JAK3 -0.081 0.18 -10000 0 -0.52 52 52
TFF3 -1.3 0.61 -10000 0 -1.6 391 391
ALOX15 -0.59 0.44 -10000 0 -1.1 157 157
MYBL1 0.013 0.015 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.51 0.36 -10000 0 -0.86 194 194
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 0.26 -10000 0 -0.68 76 76
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.72 75 75
PI3K -0.33 0.28 -10000 0 -0.77 75 75
DOK2 0 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 -0.7 38 38
ITGB3 -0.61 0.47 -10000 0 -1.1 162 162
PIGR -0.64 0.5 -10000 0 -1.2 168 168
IGHE 0.051 0.035 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.68 38 38
BCL6 0.012 0.038 -10000 0 -0.82 1 1
OPRM1 -0.6 0.44 -10000 0 -1.1 165 165
RETNLB -0.6 0.44 -10000 0 -1.1 165 165
SELP -0.6 0.46 -10000 0 -1.1 158 158
AICDA -0.58 0.42 -10000 0 -1.1 152 152
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.11 0.26 -10000 0 -0.69 35 35
IHH -0.21 0.37 -10000 0 -0.84 122 122
SHH Np/Cholesterol/GAS1 -0.11 0.21 -10000 0 -0.52 97 97
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.21 0.51 97 -10000 0 97
SMO/beta Arrestin2 -0.098 0.24 -10000 0 -0.48 124 124
SMO -0.11 0.26 -10000 0 -0.52 125 125
AKT1 -0.028 0.12 -10000 0 -0.66 2 2
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.001 0.11 -10000 0 -0.82 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.11 0.25 -10000 0 -0.51 125 125
STIL -0.08 0.2 -10000 0 -0.6 18 18
DHH N/PTCH2 -0.11 0.24 -10000 0 -0.64 80 80
DHH N/PTCH1 -0.1 0.23 -10000 0 -0.46 128 128
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
DHH 0.006 0.076 -10000 0 -0.82 4 4
PTHLH -0.16 0.37 -10000 0 -1.2 35 35
determination of left/right symmetry -0.11 0.25 -10000 0 -0.51 125 125
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.16 0.36 -10000 0 -1.1 35 35
IHH N/Hhip -0.38 0.4 -10000 0 -0.74 255 255
DHH N/Hhip -0.25 0.31 -10000 0 -0.64 188 188
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.11 0.25 -10000 0 -0.51 125 125
pancreas development -0.31 0.4 -10000 0 -0.82 188 188
HHAT 0.012 0.038 -10000 0 -0.82 1 1
PI3K -0.004 0.05 -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 -0.11 0.25 -10000 0 -0.51 125 125
SHH Np/Cholesterol/PTCH1 -0.09 0.2 -10000 0 -0.43 85 85
SHH Np/Cholesterol/PTCH2 -0.089 0.19 -10000 0 -0.52 79 79
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.52 127 127
SHH 0.007 0.05 -10000 0 -0.63 1 1
catabolic process -0.12 0.25 -10000 0 -0.51 125 125
SMO/Vitamin D3 -0.094 0.22 -10000 0 -0.44 125 125
SHH Np/Cholesterol/Hhip -0.2 0.25 -10000 0 -0.51 187 187
LRP2 -0.2 0.37 -10000 0 -0.82 126 126
receptor-mediated endocytosis -0.2 0.24 -10000 0 -0.72 47 47
SHH Np/Cholesterol/BOC -0.014 0.075 -10000 0 -0.53 9 9
SHH Np/Cholesterol/CDO -0.15 0.23 -10000 0 -0.52 140 140
mesenchymal cell differentiation 0.2 0.24 0.51 187 -10000 0 187
mol:Vitamin D3 -0.089 0.21 -10000 0 -0.41 125 125
IHH N/PTCH2 -0.23 0.35 -10000 0 -0.66 178 178
CDON -0.23 0.38 -10000 0 -0.82 139 139
IHH N/PTCH1 -0.12 0.25 -10000 0 -0.52 125 125
Megalin/LRPAP1 -0.16 0.28 -10000 0 -0.63 126 126
PTCH2 -0.12 0.31 -10000 0 -0.82 78 78
SHH Np/Cholesterol -0.006 0.036 -10000 0 -0.51 1 1
PTCH1 -0.12 0.25 -10000 0 -0.51 125 125
HHIP -0.31 0.4 -10000 0 -0.82 188 188
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.25 -10000 0 -0.51 203 203
regulation of S phase of mitotic cell cycle -0.13 0.18 -10000 0 -0.34 204 204
GNAO1 -0.017 0.15 -10000 0 -0.72 20 20
HRAS 0.011 0.021 -10000 0 -0.32 2 2
SHBG/T-DHT -0.009 0.072 -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 -0.17 0.24 -10000 0 -0.44 202 202
T-DHT/AR -0.27 0.32 -10000 0 -0.64 202 202
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 0.31 -10000 0 -0.62 204 204
cell proliferation -0.2 0.28 -10000 0 -0.65 87 87
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
FOS -0.25 0.4 -10000 0 -0.89 128 128
mol:Ca2+ -0.027 0.031 -10000 0 -0.071 92 92
MAPK3 -0.18 0.26 -10000 0 -0.6 86 86
MAPK1 -0.083 0.13 -10000 0 -0.31 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 0.076 -10000 0 -0.53 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 -0.47 202 202
actin cytoskeleton reorganization -0.003 0.035 -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 0.044 -10000 0 -0.56 3 3
apoptosis 0.16 0.25 0.53 128 -10000 0 128
T-DHT/AR/PELP1 -0.23 0.28 -10000 0 -0.56 202 202
HRAS/GDP -0.25 0.29 -10000 0 -0.59 203 203
CREB1 -0.18 0.27 -10000 0 -0.57 128 128
RAC1-CDC42/GTP -0.003 0.036 -10000 0 -0.45 3 3
AR -0.34 0.41 -10000 0 -0.83 202 202
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.18 0.24 -10000 0 -0.46 202 202
RAC1-CDC42/GDP -0.24 0.28 -10000 0 -0.56 202 202
T-DHT/AR/PELP1/Src -0.22 0.25 -10000 0 -0.51 202 202
MAP2K2 -0.17 0.24 -10000 0 -0.44 202 202
T-DHT/AR/PELP1/Src/PI3K -0.13 0.19 -10000 0 -0.34 204 204
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG -0.001 0.11 -10000 0 -0.82 8 8
Gi family/GNB1/GNG2/GDP -0.02 0.12 -10000 0 -0.55 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 -0.64 2 2
Gi family/GTP -0.095 0.12 -10000 0 -0.48 17 17
CDC42 0.013 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.023 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 -0.57 357 357
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 0.26 -9999 0 -0.52 357 357
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 -0.1 0.29 -9999 0 -0.82 65 65
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 0.13 -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 0.022 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.43 0.26 -9999 0 -0.57 358 358
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.28 0.2 -9999 0 -0.73 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 -0.45 357 357
RELN -0.6 0.37 -9999 0 -0.82 353 353
PAFAH/LIS1 -0.049 0.2 -9999 0 -0.55 65 65
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 -0.55 16 16
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.25 0.19 -9999 0 -0.34 363 363
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.3 0.22 -9999 0 -0.42 357 357
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 0.03 -9999 0 -0.31 4 4
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 -0.28 0.17 -9999 0 -0.7 16 16
LRP8 -0.021 0.17 -9999 0 -0.82 20 20
NDEL1/Katanin 60 -0.28 0.2 -9999 0 -0.73 16 16
P39/CDK5 -0.32 0.23 -9999 0 -0.45 357 357
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.34 0.24 -9999 0 -0.48 357 357
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 0.23 -9999 0 -0.49 358 358
RELN/VLDLR -0.4 0.27 -9999 0 -0.54 362 362
CDC42 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.011 0.081 -9999 0 -0.56 9 9
NFATC2 -0.1 0.22 -9999 0 -0.58 83 83
NFATC3 0 0.027 -9999 0 -10000 0 0
CD40LG -0.44 0.41 -9999 0 -0.87 197 197
PTGS2 -0.42 0.4 -9999 0 -0.86 183 183
JUNB 0.003 0.093 -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 -0.83 109 109
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 -0.029 0.12 -9999 0 -0.33 59 59
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.59 169 169
FOS -0.22 0.37 -9999 0 -0.83 128 128
IFNG -0.44 0.41 -9999 0 -0.86 197 197
AP-1/NFAT1-c-4 -0.53 0.51 -9999 0 -1 213 213
FASLG -0.42 0.39 -9999 0 -0.83 187 187
NFAT1-c-4/ICER1 -0.11 0.2 -9999 0 -0.5 91 91
IL2RA -0.41 0.38 -9999 0 -0.84 180 180
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.36 -9999 0 -0.77 259 259
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.5 97 97
IL4 -0.4 0.36 -9999 0 -0.8 178 178
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 0.083 -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 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
positive regulation of NF-kappaB transcription factor activity 0.16 0.3 0.69 115 -10000 0 115
KIRREL -0.067 0.23 -10000 0 -0.85 39 39
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.17 0.3 -10000 0 -0.69 115 115
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 -0.54 115 115
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.075 0.2 -10000 0 -0.41 115 115
FYN -0.11 0.24 -10000 0 -0.51 115 115
mol:Ca2+ -0.13 0.24 -10000 0 -0.54 115 115
mol:DAG -0.13 0.24 -10000 0 -0.54 115 115
NPHS2 -0.016 0.053 -10000 0 -0.9 1 1
mol:IP3 -0.13 0.24 -10000 0 -0.54 115 115
regulation of endocytosis -0.11 0.21 -10000 0 -0.48 115 115
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.55 115 115
establishment of cell polarity -0.16 0.3 -10000 0 -0.69 115 115
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.5 115 115
Nephrin/NEPH1/beta Arrestin2 -0.11 0.22 -10000 0 -0.48 115 115
NPHS1 -0.15 0.32 -10000 0 -0.83 89 89
Nephrin/NEPH1/podocin -0.12 0.23 -10000 0 -0.52 115 115
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 -0.54 115 115
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 115 115
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.24 -10000 0 -0.51 119 119
cytoskeleton organization -0.1 0.26 -10000 0 -0.54 115 115
Nephrin/NEPH1 -0.13 0.24 -10000 0 -0.53 115 115
Nephrin/NEPH1/ZO-1 -0.14 0.26 -10000 0 -0.57 115 115
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 0.026 -10000 0 -0.55 1 1
fibroblast growth factor receptor signaling pathway -0.001 0.026 -10000 0 -0.54 1 1
LAMA1 -0.05 0.22 -10000 0 -0.81 37 37
PRNP 0.012 0.038 -10000 0 -0.82 1 1
GPC1/SLIT2 -0.095 0.22 -10000 0 -0.63 71 71
SMAD2 0.028 0.049 -10000 0 -0.49 3 3
GPC1/PrPc/Cu2+ -0.001 0.026 -10000 0 -0.56 1 1
GPC1/Laminin alpha1 -0.048 0.17 -10000 0 -0.63 36 36
TDGF1 -0.34 0.41 -10000 0 -0.82 202 202
CRIPTO/GPC1 -0.26 0.31 -10000 0 -0.63 202 202
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 -0.54 202 202
FLT1 0.012 0.038 -10000 0 -0.82 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.008 0.05 -10000 0 -0.55 3 3
SERPINC1 0.007 0.042 -10000 0 -0.31 8 8
FYN -0.21 0.28 -10000 0 -0.54 202 202
FGR -0.21 0.28 -10000 0 -0.54 202 202
positive regulation of MAPKKK cascade -0.28 0.32 -10000 0 -0.62 204 204
SLIT2 -0.11 0.3 -10000 0 -0.8 74 74
GPC1/NRG -0.06 0.18 -10000 0 -0.63 45 45
NRG1 -0.066 0.24 -10000 0 -0.8 47 47
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.059 -10000 0 -0.71 3 3
LYN -0.21 0.28 -10000 0 -0.54 202 202
mol:Spermine 0.012 0.01 -10000 0 -10000 0 0
cell growth -0.001 0.026 -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 -0.55 202 202
TGFBR1 0.005 0.051 -10000 0 -0.31 12 12
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.37 -10000 0 -0.69 182 182
GPC1 0.013 0.015 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.005 0.051 -10000 0 -0.31 12 12
VEGFA 0.008 0.066 -10000 0 -0.82 3 3
BLK -0.38 0.38 -10000 0 -0.67 276 276
HCK -0.22 0.28 -10000 0 -0.55 202 202
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.012 0.038 -10000 0 -0.82 1 1
VEGFR1 homodimer 0.012 0.038 -10000 0 -0.82 1 1
TGFBR2 0.008 0.066 -10000 0 -0.82 3 3
cell death 0 0.009 -10000 0 -10000 0 0
ATIII/GPC1 -0.004 0.027 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.63 133 133
LCK -0.23 0.28 -10000 0 -0.55 207 207
neuron differentiation -0.06 0.18 -10000 0 -0.63 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 0.066 -10000 0 -0.82 3 3
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.051 0.14 -9999 0 -0.53 10 10
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.68 63 63
EDN1 -0.043 0.12 -9999 0 -0.74 7 7
EDN3 -0.4 0.42 -9999 0 -0.82 238 238
EDN2 -0.015 0.12 -9999 0 -0.41 33 33
HRAS/GDP -0.1 0.24 -9999 0 -0.54 77 77
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.083 0.18 -9999 0 -0.4 76 76
ADCY4 -0.096 0.19 -9999 0 -0.5 68 68
ADCY5 -0.16 0.25 -9999 0 -0.56 114 114
ADCY6 -0.096 0.19 -9999 0 -0.5 68 68
ADCY7 -0.096 0.19 -9999 0 -0.5 68 68
ADCY1 -0.1 0.2 -9999 0 -0.52 70 70
ADCY2 -0.14 0.24 -9999 0 -0.55 102 102
ADCY3 -0.096 0.19 -9999 0 -0.5 68 68
ADCY8 -0.2 0.2 -9999 0 -0.54 94 94
ADCY9 -0.096 0.19 -9999 0 -0.5 68 68
arachidonic acid secretion -0.17 0.32 -9999 0 -0.64 132 132
ETB receptor/Endothelin-1/Gq/GTP -0.094 0.21 -9999 0 -0.43 115 115
GNAO1 -0.017 0.15 -9999 0 -0.72 20 20
HRAS 0.01 0.021 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.014 0.16 -9999 0 -0.51 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.083 0.22 -9999 0 -0.53 69 69
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.067 0.17 -9999 0 -0.5 36 36
EDNRB 0.004 0.087 -9999 0 -0.84 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.16 0.24 -9999 0 -0.64 52 52
CYSLTR1 -0.059 0.17 -9999 0 -0.75 14 14
SLC9A1 -0.021 0.075 -9999 0 -0.31 5 5
mol:GDP -0.12 0.25 -9999 0 -0.56 87 87
SLC9A3 -0.046 0.19 -9999 0 -0.79 20 20
RAF1 -0.15 0.3 -9999 0 -0.58 124 124
JUN -0.28 0.52 -9999 0 -1.2 117 117
JAK2 -0.052 0.14 -9999 0 -0.54 10 10
mol:IP3 -0.11 0.22 -9999 0 -0.5 93 93
ETA receptor/Endothelin-1 -0.034 0.2 -9999 0 -0.51 22 22
PLCB1 0.009 0.039 -9999 0 -0.83 1 1
PLCB2 0.005 0.043 -9999 0 -0.32 8 8
ETA receptor/Endothelin-3 -0.33 0.34 -9999 0 -0.66 237 237
FOS -0.26 0.48 -9999 0 -1 130 130
Gai/GDP -0.003 0.13 -9999 0 -0.64 17 17
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.23 -9999 0 -0.6 51 51
BCAR1 0.013 0.002 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.5 93 93
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.093 0.28 -9999 0 -0.82 61 61
Gs family/GDP -0.18 0.25 -9999 0 -0.58 112 112
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.46 101 101
MAPK14 -0.062 0.17 -9999 0 -0.47 32 32
TRPC6 -0.14 0.3 -9999 0 -0.74 60 60
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 -0.074 0.18 -9999 0 -0.4 82 82
ETB receptor/Endothelin-2 -0.026 0.1 -9999 0 -0.64 11 11
ETB receptor/Endothelin-3 -0.32 0.32 -9999 0 -0.64 239 239
ETB receptor/Endothelin-1 -0.019 0.12 -9999 0 -0.63 11 11
MAPK3 -0.23 0.44 -9999 0 -0.89 135 135
MAPK1 -0.23 0.44 -9999 0 -0.9 134 134
Rac1/GDP -0.1 0.24 -9999 0 -0.55 68 68
cAMP biosynthetic process -0.14 0.21 -9999 0 -0.54 77 77
MAPK8 -0.17 0.34 -9999 0 -0.63 130 130
SRC 0.012 0.015 -9999 0 -0.32 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.009 0.078 -9999 0 -0.35 9 9
p130Cas/CRK/Src/PYK2 -0.13 0.29 -9999 0 -0.62 91 91
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.24 -9999 0 -0.54 75 75
COL1A2 -0.036 0.16 -9999 0 -0.51 19 19
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.63 8 8
mol:DAG -0.11 0.23 -9999 0 -0.51 93 93
MAP2K2 -0.18 0.35 -9999 0 -0.69 136 136
MAP2K1 -0.18 0.35 -9999 0 -0.69 138 138
EDNRA -0.037 0.098 -9999 0 -0.54 4 4
positive regulation of muscle contraction -0.036 0.12 -9999 0 -0.49 8 8
Gq family/GDP -0.19 0.29 -9999 0 -0.66 112 112
HRAS/GTP -0.13 0.26 -9999 0 -0.57 93 93
PRKCH -0.1 0.22 -9999 0 -0.51 79 79
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.12 0.26 -9999 0 -0.55 96 96
PRKCB -0.12 0.23 -9999 0 -0.52 89 89
PRKCE -0.1 0.23 -9999 0 -0.52 84 84
PRKCD -0.1 0.22 -9999 0 -0.51 83 83
PRKCG -0.11 0.22 -9999 0 -0.52 80 80
regulation of vascular smooth muscle contraction -0.31 0.56 -9999 0 -1.2 130 130
PRKCQ -0.11 0.23 -9999 0 -0.52 81 81
PLA2G4A -0.2 0.36 -9999 0 -0.72 132 132
GNA14 -0.18 0.36 -9999 0 -0.83 112 112
GNA15 -0.015 0.093 -9999 0 -0.33 37 37
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 -0.005 0.11 -9999 0 -0.82 9 9
Rac1/GTP -0.014 0.16 -9999 0 -0.53 8 8
MMP1 -0.096 0.16 -9999 0 -10000 0 0
IGF1 pathway

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
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 -0.46 155 155
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 -0.46 155 155
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.22 -10000 0 -0.53 112 112
AKT1 -0.092 0.22 -10000 0 -0.78 15 15
BAD -0.078 0.2 -10000 0 -0.71 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.13 0.24 -10000 0 -0.46 155 155
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.24 -10000 0 -0.46 155 155
RAF1 -0.068 0.19 -10000 0 -0.66 15 15
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.21 -10000 0 -0.43 155 155
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.24 -10000 0 -0.5 155 155
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
RPS6KB1 -0.092 0.22 -10000 0 -0.78 15 15
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.059 0.17 -10000 0 -0.54 15 15
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 -0.73 13 13
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.18 -10000 0 -0.42 112 112
IGF-1R heterotetramer -0.019 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.46 155 155
Crk/p130 Cas/Paxillin -0.13 0.2 -10000 0 -0.44 112 112
IGF1R -0.019 0.048 -10000 0 -10000 0 0
IGF1 -0.2 0.36 -10000 0 -0.82 118 118
IRS2/Crk -0.11 0.23 -10000 0 -0.43 155 155
PI3K -0.14 0.22 -10000 0 -0.44 155 155
apoptosis 0.059 0.18 0.58 15 -10000 0 15
HRAS/GDP -0.001 0.014 -10000 0 -10000 0 0
PRKCD -0.11 0.24 -10000 0 -0.53 112 112
RAF1/14-3-3 E -0.05 0.17 -10000 0 -0.54 15 15
BAD/14-3-3 -0.064 0.19 -10000 0 -0.63 15 15
PRKCZ -0.092 0.22 -10000 0 -0.78 15 15
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.16 -10000 0 -0.64 15 15
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.26 -10000 0 -0.57 112 112
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.19 -10000 0 -0.46 112 112
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 -0.45 155 155
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.46 155 155
IRS1 -0.15 0.25 -10000 0 -0.5 155 155
IRS2 -0.13 0.24 -10000 0 -0.46 155 155
IGF-1R heterotetramer/IGF1 -0.17 0.28 -10000 0 -0.66 112 112
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.1 0.23 -10000 0 -0.45 113 113
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.24 -10000 0 -0.53 113 113
SHC1 0.013 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory 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
PCK2 0.045 0.094 0.34 4 -10000 0 4
SMARCC2 0.014 0.014 -10000 0 -10000 0 0
SMARCC1 0.013 0.014 -10000 0 -10000 0 0
TBX21 -0.16 0.28 -10000 0 -0.83 48 48
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 0.093 -10000 0 -0.82 6 6
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.33 59 -0.5 6 65
PRL -0.089 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.25 0.31 0.58 154 -0.5 19 173
RELA -0.036 0.089 -10000 0 -0.27 1 1
FGG 0.24 0.19 0.52 106 -10000 0 106
GR beta/TIF2 0.084 0.23 0.35 66 -0.56 44 110
IFNG -0.5 0.51 -10000 0 -1.1 155 155
apoptosis 0.037 0.24 0.51 57 -0.56 2 59
CREB1 0.011 0.023 -10000 0 -10000 0 0
histone acetylation -0.072 0.17 -10000 0 -0.44 46 46
BGLAP -0.099 0.15 -10000 0 -0.52 15 15
GR/PKAc 0.13 0.1 0.34 32 -0.41 1 33
NF kappa B1 p50/RelA -0.073 0.16 -10000 0 -0.45 32 32
SMARCD1 0.013 0.014 -10000 0 -10000 0 0
MDM2 0.12 0.095 0.27 95 -10000 0 95
GATA3 -0.027 0.19 -10000 0 -0.78 27 27
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.58 34 34
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.064 0.23 0.51 46 -0.74 5 51
CSN2 0.2 0.14 0.42 81 -10000 0 81
BRG1/BAF155/BAF170/BAF60A 0.017 0.05 -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 0.056 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 310 310
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.047 0.16 0.34 17 -0.47 15 32
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.073 0.44 0.49 46 -0.88 102 148
JUN -0.34 0.3 -10000 0 -0.68 176 176
IL4 -0.13 0.18 -10000 0 -0.7 19 19
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 -0.81 188 188
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.34 38 -0.48 5 43
cortisol/GR alpha (monomer) 0.37 0.3 0.69 181 -10000 0 181
NCOA2 -0.063 0.24 -10000 0 -0.82 44 44
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.26 0.36 -10000 0 -0.85 128 128
AP-1/NFAT1-c-4 -0.56 0.48 -10000 0 -0.96 237 237
AFP -0.22 0.22 -10000 0 -0.68 36 36
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.52 33 -10000 0 33
TP53 0.032 0.023 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.48 0.37 -10000 0 -0.82 188 188
KRT14 -0.24 0.18 -10000 0 -0.57 37 37
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.067 -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 -0.57 0.49 -10000 0 -0.97 238 238
MAPK14 0.014 0.012 -10000 0 -10000 0 0
MAPK10 0.013 0.04 -10000 0 -0.83 1 1
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.55 0.53 -10000 0 -1 204 204
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 -0.13 0.16 -10000 0 -0.53 25 25
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.38 173 -10000 0 173
MAPK3 0.014 0.013 -10000 0 -10000 0 0
MAPK1 0.014 0.012 -10000 0 -10000 0 0
ICAM1 -0.26 0.27 -10000 0 -0.64 117 117
NFKB1 -0.038 0.098 -10000 0 -0.95 1 1
MAPK8 -0.19 0.2 -10000 0 -0.48 115 115
MAPK9 0.014 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.031 0.24 0.52 55 -0.55 3 58
BAX 0.028 0.032 -10000 0 -10000 0 0
POMC -0.55 0.69 -10000 0 -1.6 122 122
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 0.088 0.071 0.25 28 -10000 0 28
SGK1 0.1 0.24 -10000 0 -1.4 11 11
IL13 -0.3 0.25 -10000 0 -0.78 66 66
IL6 -0.41 0.54 -10000 0 -1.1 143 143
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.2 -10000 0 -0.74 37 37
IL2 -0.36 0.27 -10000 0 -0.71 138 138
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 -0.71 110 110
CDK5R1/CDK5 0.007 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.032 0.12 -10000 0 -0.56 3 3
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.55 167 -10000 0 167
SMARCA4 0.014 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.41 104 -0.39 1 105
NF kappa B1 p50/RelA/Cbp 0.018 0.16 -10000 0 -0.52 5 5
JUN (dimer) -0.33 0.3 -10000 0 -0.68 176 176
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.24 0.41 -10000 0 -0.94 105 105
NR3C1 0.22 0.19 0.5 115 -10000 0 115
NR4A1 -0.31 0.41 -10000 0 -0.76 202 202
TIF2/SUV420H1 -0.058 0.18 -10000 0 -0.63 44 44
MAPKKK cascade 0.037 0.24 0.51 57 -0.56 2 59
cortisol/GR alpha (dimer)/Src-1 0.32 0.24 0.58 178 -10000 0 178
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 96 96
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.42 104 -10000 0 104
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.55 167 -10000 0 167
mol:cortisol 0.21 0.19 0.4 192 -10000 0 192
MMP1 -0.22 0.15 -10000 0 -0.44 63 63
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.066 -10000 0 -0.83 3 3
EFNB1 0 0.12 -10000 0 -0.64 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.25 0.24 -10000 0 -0.52 202 202
Ephrin B2/EPHB1-2 -0.2 0.25 -10000 0 -0.5 189 189
neuron projection morphogenesis -0.24 0.23 -10000 0 -0.5 202 202
Ephrin B1/EPHB1-2/Tiam1 -0.27 0.27 -10000 0 -0.57 202 202
DNM1 -0.016 0.15 -10000 0 -0.8 17 17
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.006 0.084 -10000 0 -0.8 5 5
YES1 -0.008 0.1 -10000 0 -1 5 5
Ephrin B1/EPHB1-2/NCK2 -0.19 0.24 -10000 0 -0.47 202 202
PI3K 0.004 0.11 -10000 0 -1.1 5 5
mol:GDP -0.27 0.26 -10000 0 -0.56 202 202
ITGA2B -0.073 0.26 -10000 0 -0.82 50 50
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.008 0.1 -10000 0 -1 5 5
MAP3K7 -0.011 0.087 -10000 0 -0.85 5 5
FGR -0.01 0.1 -10000 0 -1 5 5
TIAM1 -0.17 0.16 -10000 0 -0.82 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.042 0.2 -10000 0 -0.53 62 62
LYN -0.008 0.1 -10000 0 -1 5 5
Ephrin B1/EPHB1-2/Src Family Kinases -0.013 0.099 -10000 0 -0.98 5 5
Ephrin B1/EPHB1-2 -0.018 0.093 -10000 0 -0.92 5 5
SRC -0.01 0.1 -10000 0 -1 5 5
ITGB3 -0.011 0.14 -10000 0 -0.82 14 14
EPHB1 -0.31 0.41 -10000 0 -0.82 187 187
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 -0.083 0.23 -10000 0 -0.68 59 59
BLK -0.065 0.14 -10000 0 -1.1 5 5
HCK -0.012 0.1 -10000 0 -1 5 5
regulation of stress fiber formation 0.19 0.24 0.47 202 -10000 0 202
MAPK8 0.006 0.12 -10000 0 -0.78 10 10
Ephrin B1/EPHB1-2/RGS3 -0.19 0.24 -10000 0 -0.47 202 202
endothelial cell migration -0.005 0.076 -10000 0 -0.74 5 5
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.006 0.098 -10000 0 -0.94 5 5
regulation of focal adhesion formation 0.19 0.24 0.47 202 -10000 0 202
chemotaxis 0.19 0.24 0.47 202 -10000 0 202
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
Rac1/GTP -0.24 0.24 -10000 0 -0.52 202 202
angiogenesis -0.018 0.092 -10000 0 -0.91 5 5
LCK -0.014 0.11 -10000 0 -1.1 5 5
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.22 0.56 -10000 0 -1.2 86 86
IL23A -0.23 0.57 -10000 0 -1.3 89 89
NF kappa B1 p50/RelA/I kappa B alpha -0.3 0.48 -10000 0 -1.2 87 87
positive regulation of T cell mediated cytotoxicity -0.26 0.63 -10000 0 -1.4 90 90
ITGA3 -0.2 0.52 -10000 0 -1.2 79 79
IL17F -0.11 0.35 -10000 0 -0.74 77 77
IL12B -0.001 0.1 -10000 0 -0.57 11 11
STAT1 (dimer) -0.24 0.59 -10000 0 -1.3 89 89
CD4 -0.2 0.51 -10000 0 -1.2 79 79
IL23 -0.24 0.54 -10000 0 -1.2 88 88
IL23R -0.005 0.099 -10000 0 -10000 0 0
IL1B -0.24 0.6 -10000 0 -1.4 82 82
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.2 0.51 -10000 0 -1.2 82 82
TYK2 0.014 0.023 -10000 0 -10000 0 0
STAT4 -0.025 0.14 -10000 0 -0.45 40 40
STAT3 0.013 0 -10000 0 -10000 0 0
IL18RAP -0.026 0.17 -10000 0 -0.8 22 22
IL12RB1 -0.021 0.12 -10000 0 -0.37 44 44
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
IL12Rbeta1/TYK2 -0.009 0.093 -10000 0 -0.68 4 4
IL23R/JAK2 -0.002 0.13 -10000 0 -0.68 1 1
positive regulation of chronic inflammatory response -0.26 0.63 -10000 0 -1.4 90 90
natural killer cell activation 0.001 0.009 0.036 1 -10000 0 1
JAK2 0.02 0.048 -10000 0 -0.86 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
NFKB1 0.011 0.039 -10000 0 -0.83 1 1
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.22 0.51 -10000 0 -1.1 88 88
ALOX12B -0.22 0.52 -10000 0 -1.2 84 84
CXCL1 -0.23 0.54 -10000 0 -1.3 79 79
T cell proliferation -0.26 0.63 -10000 0 -1.4 90 90
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.063 0.28 -10000 0 -0.57 67 67
PI3K -0.31 0.49 -10000 0 -1.2 90 90
IFNG -0.02 0.055 -10000 0 -0.13 72 72
STAT3 (dimer) -0.29 0.45 -10000 0 -1.2 87 87
IL18R1 -0.031 0.15 -10000 0 -0.43 47 47
IL23/IL23R/JAK2/TYK2/SOCS3 -0.1 0.33 -10000 0 -0.72 64 64
IL18/IL18R -0.068 0.18 -10000 0 -0.56 46 46
macrophage activation -0.015 0.018 -10000 0 -0.044 90 90
TNF -0.28 0.63 -10000 0 -1.4 99 99
STAT3/STAT4 -0.32 0.5 -10000 0 -1.3 90 90
STAT4 (dimer) -0.26 0.6 -10000 0 -1.3 90 90
IL18 -0.04 0.16 -10000 0 -0.41 58 58
IL19 -0.2 0.51 -10000 0 -1.1 85 85
STAT5A (dimer) -0.24 0.59 -10000 0 -1.3 87 87
STAT1 0.006 0.049 -10000 0 -0.31 11 11
SOCS3 -0.034 0.19 -10000 0 -0.8 28 28
CXCL9 -0.3 0.64 -10000 0 -1.4 109 109
MPO -0.2 0.52 -10000 0 -1.1 87 87
positive regulation of humoral immune response -0.26 0.63 -10000 0 -1.4 90 90
IL23/IL23R/JAK2/TYK2 -0.3 0.75 -10000 0 -1.6 88 88
IL6 -0.34 0.66 -10000 0 -1.3 129 129
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 -0.24 0.58 -10000 0 -1.3 91 91
keratinocyte proliferation -0.26 0.63 -10000 0 -1.4 90 90
NOS2 -0.21 0.51 -10000 0 -1.2 85 85
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.62 75 75
FYN -0.11 0.35 -10000 0 -0.8 83 83
LAT/GRAP2/SLP76 -0.12 0.27 -10000 0 -0.66 86 86
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.054 0.22 -10000 0 -0.47 88 88
B2M 0.013 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.05 -10000 0 -0.18 11 11
MAP3K8 -0.001 0.11 -10000 0 -0.82 8 8
mol:Ca2+ -0.031 0.05 -10000 0 -0.12 104 104
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.33 -10000 0 -0.73 90 90
TRPV6 -0.18 0.34 -10000 0 -0.8 107 107
CD28 -0.043 0.19 -10000 0 -0.59 45 45
SHC1 -0.11 0.35 -10000 0 -0.8 85 85
receptor internalization -0.14 0.38 -10000 0 -0.83 94 94
PRF1 -0.12 0.36 -10000 0 -0.9 69 69
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.037 0.18 -10000 0 -0.38 87 87
LAT -0.12 0.35 -10000 0 -0.81 85 85
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.095 0.27 -10000 0 -0.72 72 72
CD3E -0.071 0.25 -10000 0 -0.76 53 53
CD3G -0.15 0.33 -10000 0 -0.79 96 96
RASGRP2 0 0.031 -10000 0 -0.19 6 6
RASGRP1 -0.05 0.22 -10000 0 -0.47 90 90
HLA-A 0.011 0.022 -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 62 62
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.056 0.09 -10000 0 -0.25 61 61
PRKCA -0.061 0.13 -10000 0 -0.3 95 95
GRAP2 -0.042 0.21 -10000 0 -0.78 34 34
mol:IP3 -0.052 0.23 0.28 83 -0.47 84 167
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.42 -10000 0 -0.98 81 81
ORAI1 0.087 0.16 0.39 100 -10000 0 100
CSK -0.12 0.36 -10000 0 -0.82 85 85
B7 family/CD28 -0.2 0.35 -10000 0 -0.75 112 112
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.43 -10000 0 -0.96 90 90
PTPN6 -0.12 0.36 -10000 0 -0.84 84 84
VAV1 -0.12 0.35 -10000 0 -0.79 89 89
Monovalent TCR/CD3 -0.16 0.41 -10000 0 -0.73 120 120
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.86 81 81
PAG1 -0.12 0.36 -10000 0 -0.82 85 85
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.43 -10000 0 -0.96 89 89
CD80 -0.07 0.25 -10000 0 -0.81 49 49
CD86 -0.009 0.11 -10000 0 -0.42 24 24
PDK1/CARD11/BCL10/MALT1 -0.069 0.11 -10000 0 -0.3 69 69
HRAS 0.012 0.021 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.3 -10000 0 -0.63 96 96
CD8A -0.05 0.22 -10000 0 -0.83 36 36
CD8B -0.091 0.27 -10000 0 -0.73 68 68
PTPRC -0.034 0.18 -10000 0 -0.59 37 37
PDK1/PKC theta -0.068 0.27 -10000 0 -0.6 86 86
CSK/PAG1 -0.11 0.34 -10000 0 -0.82 79 79
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 89 89
STIM1 0.047 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.092 -10000 0 -0.18 55 55
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.93 94 94
mol:DAG -0.071 0.18 -10000 0 -0.41 87 87
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.023 0.16 -10000 0 -0.64 27 27
cytotoxic T cell degranulation -0.11 0.34 -10000 0 -0.85 69 69
RAP1A/GTP -0.003 0.009 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.074 0.26 -10000 0 -0.57 90 90
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.081 0.29 0.3 75 -0.62 87 162
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.022 0.16 -10000 0 -0.62 27 27
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.26 -10000 0 -0.63 87 87
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.01 0.054 -10000 0 -0.82 2 2
CD8 heterodimer -0.11 0.3 -10000 0 -0.77 73 73
CARD11 -0.073 0.17 -10000 0 -0.35 115 115
PRKCB -0.059 0.13 -10000 0 -0.3 88 88
PRKCE -0.052 0.12 -10000 0 -0.3 73 73
PRKCQ -0.091 0.31 -10000 0 -0.69 87 87
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 -0.04 0.19 -10000 0 -0.4 88 88
IKK complex 0.013 0.069 -10000 0 -0.12 52 52
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.017 0.14 -10000 0 -0.3 70 70
PDPK1 -0.047 0.21 -10000 0 -0.46 84 84
TCR/CD3/MHC I/CD8/Fyn -0.17 0.46 -10000 0 -1.1 84 84
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.27 0.33 -9999 0 -0.6 215 215
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.047 0.21 -9999 0 -0.7 41 41
SMAD9 -0.22 0.28 -9999 0 -0.6 164 164
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.096 0.2 -9999 0 -0.37 159 159
BMP7/USAG1 -0.33 0.32 -9999 0 -0.63 251 251
SMAD5/SKI -0.084 0.2 -9999 0 -0.53 28 28
SMAD1 0.019 0.045 -9999 0 -10000 0 0
BMP2 -0.021 0.17 -9999 0 -0.82 20 20
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 -0.82 159 159
BMPR1A-1B/BAMBI -0.19 0.26 -9999 0 -0.56 159 159
AHSG -0.018 0.085 -9999 0 -0.31 37 37
CER1 0 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.04 0.14 -9999 0 -0.55 33 33
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.078 0.2 -9999 0 -0.63 32 32
BMP2-4 (homodimer) -0.046 0.16 -9999 0 -0.63 33 33
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.5 159 159
RGMA -0.018 0.16 -9999 0 -0.82 18 18
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.089 0.19 -9999 0 -0.58 29 29
BMP2-4/USAG1 -0.32 0.3 -9999 0 -0.58 267 267
SMAD6/SMURF1/SMAD5 -0.084 0.2 -9999 0 -0.53 28 28
SOSTDC1 -0.42 0.42 -9999 0 -0.82 252 252
BMP7/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.5 159 159
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 -0.051 0.16 -9999 0 -0.56 42 42
SMAD5/SMAD5/SMAD4 -0.084 0.2 -9999 0 -0.53 28 28
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.094 0.14 -9999 0 -0.49 29 29
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.016 0.056 -9999 0 -0.4 1 1
SMAD1/SKI 0.026 0.043 -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 -0.052 0.15 -9999 0 -0.57 33 33
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.36 -9999 0 -0.73 141 141
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.008 0.065 -9999 0 -0.55 7 7
BMPR1A-1B (homodimer) -0.21 0.3 -9999 0 -0.63 159 159
CHRDL1 -0.58 0.38 -9999 0 -0.82 342 342
ENDOFIN/SMAD1 0.026 0.043 -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 0.08 -9999 0 -0.37 19 19
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.42 0.28 -9999 0 -0.59 348 348
BMP2-4/GREM1 -0.18 0.28 -9999 0 -0.61 133 133
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 0.043 -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 -0.067 0.16 -9999 0 -0.5 29 29
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.043 -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 0.1 -9999 0 -0.82 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.2 0.32 -9999 0 -0.79 86 86
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 -0.095 0.2 -9999 0 -0.62 29 29
BMP4 -0.014 0.14 -9999 0 -0.64 20 20
FST -0.2 0.36 -9999 0 -0.79 126 126
BMP2-4/NOG -0.078 0.19 -9999 0 -0.56 63 63
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.15 0.22 -9999 0 -0.46 159 159
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 -0.086 0.15 -9999 0 -0.31 147 147
GPC2 -0.01 0.084 -9999 0 -0.31 34 34
GPC2/Midkine -0.076 0.11 -9999 0 -0.4 12 12
neuron projection morphogenesis -0.075 0.11 -9999 0 -0.4 12 12
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 -0.043 0.11 -9999 0 -0.47 13 13
EGFR 0.006 0.076 -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 0.23 -9999 0 -0.63 72 72
ARRB2 -0.044 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 0.054 -9999 0 -0.82 2 2
EGF -0.11 0.29 -9999 0 -0.78 74 74
somatostatin receptor activity 0 0 -9999 0 -0.001 135 135
ARAP2 0.01 0.054 -9999 0 -0.82 2 2
mol:GDP -0.12 0.15 -9999 0 -0.31 135 135
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 95 95
ITGA2B -0.074 0.26 -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 -0.69 73 73
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.31 138 138
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.084 0.2 -9999 0 -0.55 72 72
ADRB2 -0.009 0.14 -9999 0 -0.82 13 13
receptor agonist activity 0 0 -9999 0 0 143 143
actin filament binding 0 0 -9999 0 -0.001 134 134
SRC 0.013 0.015 -9999 0 -0.31 1 1
ITGB3 -0.011 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 -0.001 131 131
ARF6/GDP 0.001 0.069 -9999 0 -0.34 2 2
ARF6/GDP/GULP/ACAP1 -0.19 0.2 -9999 0 -0.5 114 114
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.066 0.18 -9999 0 -0.54 59 59
ACAP1 0.001 0.075 -9999 0 -0.38 15 15
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.082 0.22 -9999 0 -0.68 59 59
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.11 0.3 -9999 0 -0.82 73 73
CYTH3 0.009 0.042 -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 0 121 121
endosomal lumen acidification 0 0 -9999 0 -0.001 139 139
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 39 39
MET -0.11 0.16 -9999 0 -0.31 179 179
GNA14 -0.18 0.35 -9999 0 -0.82 112 112
GNA15 -0.013 0.094 -9999 0 -0.33 37 37
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 132 132
GNA11 -0.002 0.11 -9999 0 -0.82 9 9
LHCGR -0.099 0.27 -9999 0 -0.77 66 66
AGTR1 -0.32 0.41 -9999 0 -0.82 194 194
desensitization of G-protein coupled receptor protein signaling pathway -0.082 0.22 -9999 0 -0.68 59 59
IPCEF1/ARNO -0.056 0.16 -9999 0 -0.43 72 72
alphaIIb/beta3 Integrin -0.083 0.23 -9999 0 -0.68 59 59
Coregulation of Androgen receptor activity

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
NRIP1 -0.015 0.064 -10000 0 -0.36 13 13
SVIL -0.007 0.031 -10000 0 -10000 0 0
ZNF318 0.061 0.093 -10000 0 -0.82 1 1
JMJD2C -0.064 0.069 -10000 0 -0.12 273 273
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.62 202 202
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 0.02 -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 0.052 0.13 -10000 0 -0.8 6 6
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.061 -10000 0 -0.82 2 2
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.065 0.24 -10000 0 -0.82 44 44
NCOA6 -0.007 0.047 -10000 0 -0.82 1 1
DNA-PK 0.059 0.084 0.26 1 -10000 0 1
NCOA4 0.011 0.004 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.01 0.15 -10000 0 -1.1 6 6
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 -0.67 209 209
FHL2 -0.16 0.37 -10000 0 -1.3 39 39
RANBP9 -0.005 0.029 -10000 0 -10000 0 0
JMJD1A 0.002 0.037 -10000 0 -0.12 37 37
CDK6 0.009 0.066 -10000 0 -0.82 3 3
TGFB1I1 -0.007 0.031 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.3 0.3 -10000 0 -0.63 205 205
XRCC6 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.32 -10000 0 -0.64 228 228
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.046 0.051 -10000 0 -10000 0 0
BRCA1 -0.007 0.031 -10000 0 -10000 0 0
TCF4 0.036 0.034 -10000 0 -10000 0 0
CDKN2A -0.11 0.16 -10000 0 -0.31 140 140
SRF 0.028 0.04 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -1 6 6
KLK3 -0.44 0.71 -10000 0 -1.6 137 137
TMF1 0.006 0.054 -10000 0 -0.82 2 2
HNRNPA1 0.031 0.028 -10000 0 -10000 0 0
AOF2 -0.022 0.034 -10000 0 -0.075 137 137
APPL1 0.052 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.28 0.29 -10000 0 -0.61 202 202
AR -0.38 0.42 -10000 0 -0.87 202 202
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 -0.57 202 202
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.3 -10000 0 -0.62 202 202
LATS2 0.03 0.048 -10000 0 -0.82 1 1
T-DHT/AR/PRX1 -0.24 0.28 -10000 0 -0.56 202 202
Cyclin D3/CDK11 p58 0 0.003 -10000 0 -10000 0 0
VAV3 -0.012 0.095 -10000 0 -0.83 6 6
KLK2 -0.77 0.63 -10000 0 -1.3 273 273
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.67 208 208
TMPRSS2 -0.19 0.32 -10000 0 -1.2 35 35
CCND1 0.001 0.049 -10000 0 -0.31 11 11
PIAS1 -0.016 0.047 -10000 0 -10000 0 0
mol:T-DHT -0.032 0.041 -10000 0 -0.082 162 162
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 -0.62 204 204
CMTM2 0.014 0.027 -10000 0 -0.31 3 3
SNURF -0.032 0.19 -10000 0 -0.82 26 26
ZMIZ1 -0.013 0.051 -10000 0 -0.81 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 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
TGFB1 0.008 0.042 -9999 0 -0.31 8 8
CCL5 -0.044 0.2 -9999 0 -0.72 38 38
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -9999 0 -0.48 50 50
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 0.16 -9999 0 -0.54 31 31
Syndecan-1/Syntenin -0.092 0.16 -9999 0 -0.54 31 31
MAPK3 -0.069 0.14 -9999 0 -0.6 19 19
HGF/MET -0.17 0.24 -9999 0 -0.69 73 73
TGFB1/TGF beta receptor Type II 0.008 0.042 -9999 0 -0.31 8 8
BSG 0.013 0.015 -9999 0 -0.31 1 1
keratinocyte migration -0.091 0.15 -9999 0 -0.53 31 31
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.65 54 54
Syndecan-1/CD147 -0.081 0.15 -9999 0 -0.62 21 21
Syndecan-1/Syntenin/PIP2 -0.099 0.14 -9999 0 -0.55 28 28
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.097 0.14 -9999 0 -0.51 31 31
MMP7 -0.18 0.22 -9999 0 -0.37 240 240
HGF -0.11 0.3 -9999 0 -0.82 73 73
Syndecan-1/CASK -0.1 0.16 -9999 0 -0.46 50 50
Syndecan-1/HGF/MET -0.2 0.24 -9999 0 -0.65 86 86
regulation of cell adhesion -0.059 0.14 -9999 0 -0.58 19 19
HPSE -0.017 0.14 -9999 0 -0.51 28 28
positive regulation of cell migration -0.1 0.16 -9999 0 -0.48 50 50
SDC1 -0.11 0.16 -9999 0 -0.48 50 50
Syndecan-1/Collagen -0.1 0.16 -9999 0 -0.48 50 50
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 -0.083 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 -0.47 50 50
MMP1 -0.14 0.16 -9999 0 -0.31 229 229
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.42 -9999 0 -0.99 45 45
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.34 -9999 0 -0.83 103 103
SMAD4 0.015 0.003 -9999 0 -10000 0 0
ID2 -0.18 0.42 -9999 0 -1 43 43
AP1 -0.29 0.45 -9999 0 -0.92 151 151
ABCG2 -0.19 0.42 -9999 0 -1 43 43
HIF1A -0.008 0.067 -9999 0 -10000 0 0
TFF3 -0.57 0.51 -9999 0 -1.1 159 159
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 20 20
MCL1 -0.18 0.42 -9999 0 -0.99 44 44
NDRG1 -0.18 0.42 -9999 0 -0.99 44 44
SERPINE1 -0.2 0.43 -9999 0 -1 47 47
FECH -0.18 0.42 -9999 0 -1 37 37
FURIN -0.18 0.42 -9999 0 -1 43 43
NCOA2 -0.062 0.24 -9999 0 -0.82 44 44
EP300 -0.063 0.18 -9999 0 -0.34 105 105
HMOX1 -0.19 0.42 -9999 0 -1 45 45
BHLHE40 -0.19 0.42 -9999 0 -1 48 48
BHLHE41 -0.18 0.42 -9999 0 -0.98 50 50
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.036 -9999 0 -10000 0 0
ENG 0.042 0.092 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.82 109 109
RORA -0.18 0.42 -9999 0 -1 44 44
ABCB1 -0.076 0.19 -9999 0 -1.4 8 8
TFRC -0.18 0.42 -9999 0 -0.99 48 48
CXCR4 -0.18 0.42 -9999 0 -0.99 44 44
TF -0.23 0.49 -9999 0 -1.1 70 70
CITED2 -0.22 0.47 -9999 0 -1.1 59 59
HIF1A/ARNT -0.29 0.38 -9999 0 -1 66 66
LDHA -0.039 0.05 -9999 0 -10000 0 0
ETS1 -0.18 0.42 -9999 0 -0.99 44 44
PGK1 -0.18 0.42 -9999 0 -1 40 40
NOS2 -0.2 0.43 -9999 0 -1 49 49
ITGB2 -0.19 0.42 -9999 0 -1 46 46
ALDOA -0.18 0.42 -9999 0 -0.99 44 44
Cbp/p300/CITED2 -0.32 0.51 -9999 0 -1.1 101 101
FOS -0.21 0.37 -9999 0 -0.82 128 128
HK2 -0.19 0.42 -9999 0 -1 40 40
SP1 0.022 0.008 -9999 0 -10000 0 0
GCK -0.39 0.72 -9999 0 -1.5 135 135
HK1 -0.18 0.42 -9999 0 -0.99 44 44
NPM1 -0.18 0.42 -9999 0 -0.99 44 44
EGLN1 -0.18 0.42 -9999 0 -1 45 45
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.18 0.42 -9999 0 -0.98 47 47
SMAD3 0.015 0.003 -9999 0 -10000 0 0
EDN1 -0.16 0.32 -9999 0 -0.73 66 66
IGFBP1 -0.2 0.42 -9999 0 -1 46 46
VEGFA -0.16 0.38 -9999 0 -0.77 68 68
HIF1A/JAB1 -0.011 0.02 -9999 0 -10000 0 0
CP -0.35 0.55 -9999 0 -1.1 119 119
CXCL12 -0.23 0.48 -9999 0 -1.1 64 64
COPS5 0.014 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 -0.18 0.42 -9999 0 -1 37 37
EGLN3 -0.2 0.44 -9999 0 -1 49 49
CA9 -0.2 0.42 -9999 0 -1 45 45
TERT -0.2 0.42 -9999 0 -1 44 44
ENO1 -0.18 0.42 -9999 0 -0.97 48 48
PFKL -0.18 0.42 -9999 0 -1 43 43
NCOA1 0.014 0 -9999 0 -10000 0 0
ADM -0.22 0.44 -9999 0 -1 48 48
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 -0.93 61 61
SLC2A1 -0.15 0.38 -9999 0 -0.75 71 71
LEP -0.2 0.42 -9999 0 -0.98 50 50
HIF1A/ARNT/Cbp/p300 -0.29 0.36 -9999 0 -0.86 104 104
EPO -0.14 0.33 -9999 0 -0.95 25 25
CREBBP -0.063 0.18 -9999 0 -0.34 107 107
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.34 -9999 0 -0.82 101 101
PFKFB3 -0.18 0.42 -9999 0 -1 43 43
NT5E -0.19 0.43 -9999 0 -1.1 40 40
EPHB forward signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.089 0.21 -10000 0 -0.56 76 76
cell-cell adhesion 0.15 0.19 0.55 10 -10000 0 10
Ephrin B/EPHB2/RasGAP -0.014 0.069 -10000 0 -0.46 10 10
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -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 -0.22 0.27 -10000 0 -0.56 187 187
HRAS/GDP -0.14 0.17 -10000 0 -0.5 12 12
Ephrin B/EPHB1/GRB7 -0.21 0.25 -10000 0 -0.51 192 192
Endophilin/SYNJ1 0.025 0.072 -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 -0.48 192 192
endothelial cell migration -0.003 0.037 -10000 0 -0.47 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.042 0.12 -10000 0 -0.31 82 82
PAK1 0.034 0.073 -10000 0 -0.43 10 10
HRAS 0.012 0.021 -10000 0 -0.31 2 2
RRAS 0.025 0.074 -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 -0.45 192 192
lamellipodium assembly -0.15 0.19 -10000 0 -0.55 10 10
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.11 0.18 -10000 0 -0.44 10 10
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.066 -10000 0 -0.82 3 3
EPHB3 -0.19 0.16 -10000 0 -0.31 294 294
EPHB1 -0.31 0.41 -10000 0 -0.82 187 187
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.071 0.18 -10000 0 -0.46 11 11
Ephrin B/EPHB2 -0.014 0.07 -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 -0.46 189 189
Ephrin B/EPHB1 -0.19 0.24 -10000 0 -0.48 192 192
RAP1/GDP -0.055 0.16 -10000 0 -0.53 3 3
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.01 0.12 -10000 0 -0.46 24 24
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.2 0.25 -10000 0 -0.51 189 189
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 -0.52 17 17
Rap1/GTP -0.15 0.19 -10000 0 -0.56 10 10
axon guidance -0.088 0.2 -10000 0 -0.56 76 76
MAPK3 -0.08 0.16 -10000 0 -0.53 2 2
MAPK1 -0.08 0.16 -10000 0 -0.53 2 2
Rac1/GDP -0.046 0.17 -10000 0 -0.46 7 7
actin cytoskeleton reorganization -0.11 0.13 -10000 0 -0.46 6 6
CDC42/GDP -0.046 0.17 -10000 0 -0.46 7 7
PI3K -0.003 0.037 -10000 0 -0.47 3 3
EFNA5 -0.12 0.3 -10000 0 -0.82 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 -0.54 11 11
PTK2 0.042 0.052 -10000 0 -10000 0 0
MAP4K4 -0.16 0.25 -10000 0 -0.46 189 189
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 -0.071 0.18 -10000 0 -0.55 3 3
MAP2K1 -0.092 0.17 -10000 0 -0.41 10 10
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.2 0.24 -10000 0 -0.5 189 189
cell migration -0.089 0.19 -10000 0 -0.44 10 10
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.073 -10000 0 -0.44 10 10
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.021 0.17 -10000 0 -0.45 60 60
HRAS/GTP -0.17 0.2 -10000 0 -0.41 194 194
Ephrin B1/EPHB1-2 -0.2 0.25 -10000 0 -0.51 189 189
cell adhesion mediated by integrin 0.013 0.076 0.5 7 -10000 0 7
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.18 0.22 -10000 0 -0.44 194 194
RAC1-CDC42/GTP -0.21 0.21 -10000 0 -0.49 145 145
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.055 0.16 -10000 0 -0.53 3 3
ruffle organization -0.12 0.22 -10000 0 -0.57 10 10
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.017 0.12 -10000 0 -0.46 24 24
Ephrin B/EPHB2/KALRN -0.014 0.069 -10000 0 -0.46 10 10
ROCK1 -0.074 0.081 -10000 0 -10000 0 0
RAS family/GDP -0.085 0.11 -10000 0 -0.52 3 3
Rac1/GTP -0.16 0.2 -10000 0 -0.6 10 10
Ephrin B/EPHB1/Src/Paxillin -0.11 0.18 -10000 0 -0.34 192 192
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.11 0.39 -9999 0 -1.3 43 43
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.036 0.11 -9999 0 -0.39 19 19
ATF2/c-Jun -0.22 0.42 -9999 0 -0.97 110 110
MAPK11 -0.036 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 -0.48 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 -0.049 0.17 -9999 0 -0.52 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 -0.071 0.19 -9999 0 -0.44 67 67
p38alpha-beta/MNK1 -0.025 0.14 -9999 0 -0.5 19 19
JUN -0.22 0.42 -9999 0 -0.95 112 112
PPARGC1A -0.23 0.25 -9999 0 -0.46 252 252
USF1 -0.029 0.13 -9999 0 -0.48 19 19
RAB5/GDP/GDI1 -0.038 0.084 -9999 0 -0.35 19 19
NOS2 -0.049 0.16 -9999 0 -0.66 8 8
DDIT3 -0.031 0.14 -9999 0 -0.41 43 43
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.013 0.11 -9999 0 -0.39 18 18
p38alpha-beta/HBP1 -0.025 0.14 -9999 0 -0.5 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 -0.4 43 43
PLA2G4A -0.049 0.2 -9999 0 -0.61 44 44
GDI1 -0.029 0.13 -9999 0 -0.4 43 43
TP53 -0.038 0.16 -9999 0 -0.5 43 43
RPS6KA5 -0.077 0.2 -9999 0 -0.47 86 86
ESR1 -0.065 0.21 -9999 0 -0.54 57 57
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.03 0.14 -9999 0 -0.4 44 44
MEF2A -0.03 0.14 -9999 0 -0.4 44 44
EIF4EBP1 -0.049 0.16 -9999 0 -0.45 44 44
KRT19 -0.1 0.21 -9999 0 -0.54 58 58
ELK4 -0.029 0.13 -9999 0 -0.4 43 43
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 -0.025 0.14 -9999 0 -0.5 19 19
p38alpha-beta/MAPKAPK3 -0.025 0.14 -9999 0 -0.5 19 19
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 -0.43 32 32
TBX21 -0.11 0.44 -10000 0 -1.1 59 59
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 -0.018 0.12 -10000 0 -0.37 44 44
GADD45B -0.089 0.38 -10000 0 -0.96 56 56
IL12RB2 -0.016 0.16 -10000 0 -0.73 21 21
GADD45G -0.072 0.34 -10000 0 -0.92 45 45
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 0.16 -10000 0 -0.41 58 58
IL2RA -0.047 0.2 -10000 0 -0.58 49 49
IFNG -0.11 0.28 -10000 0 -0.72 78 78
STAT3 (dimer) -0.07 0.32 -10000 0 -0.76 61 61
HLA-DRB5 -0.041 0.13 -10000 0 -0.35 69 69
FASLG -0.13 0.47 -10000 0 -1.2 61 61
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.89 63 63
CD4 0.001 0.057 -10000 0 -0.33 5 5
SOCS1 0.009 0.048 -10000 0 -0.42 5 5
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.099 0.27 -10000 0 -0.72 72 72
CD3E -0.074 0.25 -10000 0 -0.75 53 53
CD3G -0.15 0.33 -10000 0 -0.8 96 96
IL12Rbeta2/JAK2 -0.001 0.13 -10000 0 -0.64 18 18
CCL3 -0.1 0.43 -10000 0 -1.2 49 49
CCL4 -0.15 0.52 -10000 0 -1.3 64 64
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
IL18/IL18R -0.031 0.2 -10000 0 -0.57 45 45
NOS2 -0.085 0.34 -10000 0 -0.89 48 48
IL12/IL12R/TYK2/JAK2/SPHK2 -0.02 0.15 -10000 0 -0.4 34 34
IL1R1 -0.084 0.37 -10000 0 -0.98 49 49
IL4 0.001 0.022 -10000 0 -10000 0 0
JAK2 0.014 0.044 -10000 0 -0.86 1 1
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 -0.038 0.29 -10000 0 -0.73 37 37
lysosomal transport -0.034 0.28 -10000 0 -0.68 39 39
FOS -0.41 0.65 -10000 0 -1.3 161 161
STAT4 (dimer) -0.075 0.35 -10000 0 -0.84 58 58
STAT5A (dimer) -0.22 0.36 -10000 0 -0.92 81 81
GZMA -0.1 0.41 -10000 0 -1.1 52 52
GZMB -0.098 0.39 -10000 0 -1.1 45 45
HLX 0.004 0.055 -10000 0 -0.31 14 14
LCK -0.11 0.43 -10000 0 -1 65 65
TCR/CD3/MHC II/CD4 -0.19 0.35 -10000 0 -0.62 134 134
IL2/IL2R -0.081 0.22 -10000 0 -0.67 47 47
MAPK14 -0.067 0.35 -10000 0 -0.82 60 60
CCR5 -0.095 0.4 -10000 0 -1.1 44 44
IL1B -0.054 0.24 -10000 0 -0.79 43 43
STAT6 -0.003 0.11 -10000 0 -0.25 23 23
STAT4 -0.025 0.14 -10000 0 -0.45 40 40
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.049 -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 -0.001 0.096 -10000 0 -0.56 11 11
CD8A -0.05 0.22 -10000 0 -0.83 36 36
CD8B -0.092 0.27 -10000 0 -0.73 68 68
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.022 0.16 0.43 32 -10000 0 32
IL2RB -0.015 0.13 -10000 0 -0.51 26 26
proteasomal ubiquitin-dependent protein catabolic process -0.063 0.32 -10000 0 -0.76 58 58
IL2RG -0.047 0.19 -10000 0 -0.55 52 52
IL12 -0.056 0.22 -10000 0 -0.64 55 55
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.027 0.16 -10000 0 -0.64 27 27
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 53 53
IL12/IL12R/TYK2/JAK2 -0.12 0.48 -10000 0 -1.1 66 66
MAP2K3 -0.068 0.35 -10000 0 -0.81 60 60
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.075 0.36 -10000 0 -0.83 62 62
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.027 0.13 -10000 0 -0.4 44 44
IL18RAP -0.022 0.17 -10000 0 -0.8 22 22
IL12Rbeta1/TYK2 -0.003 0.093 -10000 0 -0.64 4 4
EOMES -0.15 0.43 -10000 0 -1.5 43 43
STAT1 (dimer) -0.13 0.37 -10000 0 -0.79 88 88
T cell proliferation -0.047 0.27 -10000 0 -0.62 53 53
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.027 0.15 -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 0.047 -9999 0 -1 1 1
forebrain development -0.32 0.29 -9999 0 -0.56 254 254
GNAO1 -0.02 0.15 -9999 0 -0.72 20 20
SMO/beta Arrestin2 0.011 0.032 -9999 0 -0.63 1 1
SMO 0.006 0.039 -9999 0 -0.82 1 1
ARRB2 0.008 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.057 -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 0.03 -9999 0 -0.5 1 1
GNAI1 0.008 0.039 -9999 0 -0.84 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.24 0.19 -9999 0 -0.51 134 134
SAP30 0.012 0.038 -9999 0 -0.82 1 1
mol:GDP 0.006 0.039 -9999 0 -0.82 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 0.062 -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 0.071 -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) 0.022 0.059 -9999 0 -10000 0 0
FOXA2 -0.66 0.66 -9999 0 -1.3 234 234
neural tube patterning -0.32 0.29 -9999 0 -0.56 254 254
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 -0.56 254 254
SUFU 0.016 0.021 -9999 0 -0.28 1 1
LGALS3 -0.1 0.16 -9999 0 -0.31 171 171
catabolic process 0.061 0.069 -9999 0 -0.39 2 2
GLI3A/CBP -0.2 0.2 -9999 0 -0.38 253 253
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.33 0.29 -9999 0 -0.57 254 254
RAB23 0.006 0.076 -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 -0.035 0.079 -9999 0 -0.4 1 1
GNAZ 0.01 0.006 -9999 0 -10000 0 0
RBBP4 0.009 0.066 -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 0.058 -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 -0.42 2 2
PTCH1 -0.28 0.27 -9999 0 -0.62 134 134
MIM/GLI1 -0.45 0.39 -9999 0 -0.75 252 252
CREBBP -0.2 0.2 -9999 0 -0.38 253 253
Su(fu)/SIN3/HDAC complex 0.056 0.027 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.082 0.063 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.18 -9999 0 -0.65 40 40
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.61 69 69
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.65 41 41
CCL5 -0.044 0.2 -9999 0 -0.72 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 0.034 -9999 0 -0.31 4 4
ADAM12 -0.067 0.14 -9999 0 -0.31 119 119
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 -0.064 0.044 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.17 0.21 -9999 0 -0.68 49 49
Syndecan-4/CXCL12/CXCR4 -0.17 0.23 -9999 0 -0.66 69 69
Syndecan-4/Laminin alpha3 -0.15 0.19 -9999 0 -0.66 45 45
MDK -0.086 0.15 -9999 0 -0.31 147 147
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.64 42 42
Syndecan-4/Midkine -0.18 0.19 -9999 0 -0.65 41 41
FZD7 0.006 0.076 -9999 0 -0.82 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 41 41
THBS1 -0.011 0.086 -9999 0 -0.31 36 36
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.66 40 40
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.61 69 69
Syndecan-4/TACI -0.24 0.26 -9999 0 -0.64 119 119
CXCR4 0.012 0.021 -9999 0 -0.31 2 2
cell adhesion -0.072 0.091 -9999 0 -0.45 22 22
Syndecan-4/Dynamin -0.13 0.18 -9999 0 -0.65 40 40
Syndecan-4/TSP1 -0.14 0.18 -9999 0 -0.65 40 40
Syndecan-4/GIPC -0.13 0.18 -9999 0 -0.65 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 -0.05 0.22 -9999 0 -0.81 37 37
LAMA3 -0.026 0.16 -9999 0 -0.59 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.016 0.17 -9999 0 -0.75 22 22
Syndecan-4/alpha-Actinin -0.13 0.18 -9999 0 -0.65 40 40
TFPI -0.035 0.2 -9999 0 -0.82 28 28
F2 -0.006 0.05 -9999 0 -0.31 12 12
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.17 0.21 -9999 0 -0.67 54 54
ACTN1 0.013 0.015 -9999 0 -0.31 1 1
TNC -0.11 0.17 -9999 0 -0.32 182 182
Syndecan-4/CXCL12 -0.18 0.24 -9999 0 -0.68 69 69
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.075 0.26 -9999 0 -0.82 51 51
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 -0.66 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.32 302 302
cell migration -0.021 0.017 -9999 0 -10000 0 0
PRKCD 0.008 0.015 -9999 0 -10000 0 0
vasculogenesis -0.14 0.17 -9999 0 -0.62 40 40
SDC4 -0.15 0.19 -9999 0 -0.7 40 40
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.7 40 40
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 -0.65 40 40
MMP9 -0.085 0.24 -9999 0 -0.57 79 79
Rac1/GTP -0.073 0.094 -9999 0 -0.46 22 22
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 0.21 -9999 0 -0.65 58 58
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.057 0.21 -10000 0 -0.69 17 17
CRP -0.063 0.22 -10000 0 -0.71 17 17
cell cycle arrest -0.08 0.24 -10000 0 -0.73 32 32
TIMP1 -0.16 0.22 -10000 0 -0.59 42 42
IL6ST -0.11 0.29 -10000 0 -0.82 68 68
Rac1/GDP -0.088 0.25 -10000 0 -0.62 59 59
AP1 -0.19 0.32 -10000 0 -0.71 118 118
GAB2 0.014 0.001 -10000 0 -10000 0 0
TNFSF11 -0.099 0.23 -10000 0 -0.68 21 21
HSP90B1 0.022 0.043 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
MAPK14 -0.099 0.3 -10000 0 -0.81 55 55
AKT1 0.053 0.057 -10000 0 -1.1 1 1
FOXO1 0.059 0.053 -10000 0 -0.98 1 1
MAP2K6 -0.1 0.29 -10000 0 -0.72 62 62
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.076 0.24 -10000 0 -0.66 43 43
MITF -0.09 0.26 -10000 0 -0.63 59 59
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 -0.093 0.25 -10000 0 -0.79 32 32
STAT1 -0.011 0.023 -10000 0 -10000 0 0
CEBPD -0.057 0.21 -10000 0 -0.69 17 17
PIK3CA 0.01 0.066 -10000 0 -0.82 3 3
PI3K 0.019 0.051 -10000 0 -0.63 3 3
JUN -0.18 0.35 -10000 0 -0.82 109 109
PIAS3/MITF -0.078 0.25 -10000 0 -0.63 52 52
MAPK11 -0.099 0.3 -10000 0 -0.81 55 55
STAT3 (dimer)/FOXO1 -0.008 0.2 -10000 0 -0.6 18 18
GRB2/SOS1/GAB family -0.11 0.2 -10000 0 -0.7 31 31
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.26 -10000 0 -0.56 81 81
GRB2 0.014 0 -10000 0 -10000 0 0
JAK2 0.012 0.038 -10000 0 -0.82 1 1
LBP -0.061 0.2 -10000 0 -0.63 12 12
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.014 0.005 -10000 0 -10000 0 0
MYC -0.073 0.27 -10000 0 -0.94 24 24
FGG -0.067 0.22 -10000 0 -0.7 19 19
macrophage differentiation -0.08 0.24 -10000 0 -0.73 32 32
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.29 -10000 0 -0.56 152 152
JUNB -0.063 0.23 -10000 0 -0.71 30 30
FOS -0.21 0.37 -10000 0 -0.82 128 128
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.1 0.28 -10000 0 -0.52 105 105
STAT1/PIAS1 -0.083 0.24 -10000 0 -0.54 67 67
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.062 -10000 0 -1.2 1 1
STAT3 (dimer) -0.09 0.24 -10000 0 -0.76 32 32
PRKCD -0.064 0.23 -10000 0 -0.66 35 35
IL6R -0.014 0.15 -10000 0 -0.82 16 16
SOCS3 -0.12 0.37 -10000 0 -1.1 52 52
gp130 (dimer)/JAK1/JAK1/LMO4 -0.058 0.2 -10000 0 -0.55 68 68
Rac1/GTP -0.11 0.24 -10000 0 -0.62 58 58
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 -0.095 0.22 -10000 0 -0.65 21 21
IRF1 -0.057 0.21 -10000 0 -0.7 16 16
mol:GDP -0.1 0.26 -10000 0 -0.6 71 71
SOS1 0.013 0.001 -10000 0 -10000 0 0
VAV1 -0.1 0.27 -10000 0 -0.62 71 71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.3 -10000 0 -0.8 56 56
PTPN11 -0.011 0.059 -10000 0 -1.2 1 1
IL6/IL6RA -0.15 0.29 -10000 0 -0.66 107 107
gp130 (dimer)/TYK2/TYK2/LMO4 -0.064 0.2 -10000 0 -0.55 68 68
gp130 (dimer)/JAK2/JAK2/LMO4 -0.065 0.2 -10000 0 -0.55 68 68
IL6 -0.17 0.34 -10000 0 -0.72 123 123
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE -0.083 0.15 -10000 0 -0.32 137 137
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 -0.1 0.26 -10000 0 -0.46 136 136
LMO4 0.012 0.01 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.11 0.23 0.38 1 -0.79 31 32
MCL1 0.059 0.049 -10000 0 -0.88 1 1
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.095 0.22 -9999 0 -0.41 145 145
MAP3K8 -0.003 0.11 -9999 0 -0.83 8 8
FOS -0.058 0.17 -9999 0 -0.5 35 35
PRKCA -0.027 0.18 -9999 0 -0.83 22 22
PTPN7 -0.045 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 52 52
NRAS 0.013 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.031 0.12 -9999 0 -0.52 17 17
MAP2K1 -0.025 0.15 -9999 0 -0.56 29 29
ELK1 0.008 0.011 -9999 0 -10000 0 0
BRAF -0.045 0.13 -9999 0 -0.58 26 26
mol:GTP -0.001 0.003 -9999 0 -0.006 127 127
MAPK1 -0.031 0.12 -9999 0 -0.42 28 28
RAF1 -0.045 0.13 -9999 0 -0.58 26 26
KRAS 0.013 0.002 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.021 -9999 0 -0.31 2 2
EGFR 0.006 0.076 -9999 0 -0.82 4 4
EGF/EGFR -0.076 0.17 -9999 0 -0.46 78 78
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.071 0.16 -9999 0 -0.46 72 72
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.01 0.046 -9999 0 -0.44 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 74 74
EGF/EGFR dimer/SHC -0.084 0.2 -9999 0 -0.55 72 72
mol:GDP -0.07 0.16 -9999 0 -0.46 72 72
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.003 0.087 -9999 0 -0.68 7 7
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.065 0.15 -9999 0 -0.42 72 72
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.066 0.15 -9999 0 -0.43 72 72
FRAP1 -0.034 0.17 -9999 0 -0.44 72 72
EGF/EGFR dimer -0.097 0.22 -9999 0 -0.63 72 72
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.073 -9999 0 -0.63 6 6
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 -0.034 0.11 -10000 0 -0.31 67 67
GNB1/GNG2 -0.044 0.068 -10000 0 -0.2 46 46
AKT1 -0.013 0.1 -10000 0 -0.21 38 38
EGF -0.11 0.29 -10000 0 -0.78 74 74
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.031 0.077 -10000 0 -0.65 2 2
mol:Ca2+ -0.043 0.15 -10000 0 -0.31 73 73
LYN 0.032 0.076 -10000 0 -0.65 2 2
RhoA/GTP -0.031 0.045 -10000 0 -0.14 2 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.043 0.16 -10000 0 -0.35 71 71
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 -0.026 0.12 -10000 0 -0.54 11 11
G beta5/gamma2 -0.06 0.092 -10000 0 -0.27 46 46
PRKCH -0.051 0.16 -10000 0 -0.36 70 70
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 -0.023 0.17 -10000 0 -0.82 21 21
G12 family/GTP -0.077 0.11 -10000 0 -0.31 71 71
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 0.36 15 -10000 0 15
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.21 0.37 -10000 0 -0.82 131 131
mol:IP3 -0.059 0.18 -10000 0 -0.39 73 73
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.087 0.23 -10000 0 -0.53 71 71
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.098 0.2 -10000 0 -0.4 142 142
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.024 0.081 -10000 0 -0.65 2 2
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.003 0.093 -10000 0 -0.82 6 6
PRKCB1 -0.059 0.17 -10000 0 -0.39 73 73
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.084 0.23 -10000 0 -0.54 75 75
LCK 0.022 0.097 -10000 0 -0.55 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.019 0.09 -10000 0 -0.97 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 0.089 -10000 0 -0.96 2 2
MAPK14 -0.019 0.11 -10000 0 -0.24 38 38
TGM2/GTP -0.072 0.2 -10000 0 -0.44 72 72
MAPK11 -0.019 0.11 -10000 0 -0.23 44 44
ARHGEF1 -0.015 0.089 -10000 0 -0.19 23 23
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.056 0.18 -10000 0 -0.39 75 75
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.051 0.15 -10000 0 -0.3 80 80
cAMP biosynthetic process -0.058 0.17 -10000 0 -0.36 72 72
Gq family/GTP/EBP50 -0.043 0.12 -10000 0 -0.35 21 21
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.032 0.076 -10000 0 -0.65 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 -0.037 0.14 -10000 0 -0.3 74 74
TP beta/Gq family/GDP/G beta5/gamma2 -0.026 0.12 -10000 0 -0.54 11 11
platelet activation -0.025 0.15 -10000 0 -0.3 70 70
PGI2/IP -0.008 0.071 -10000 0 -0.64 6 6
PRKACA -0.001 0.11 -10000 0 -0.43 25 25
Gq family/GDP/G beta5/gamma2 -0.027 0.12 -10000 0 -0.5 11 11
TXA2/TP beta/beta Arrestin2 -0.024 0.12 -10000 0 -0.66 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.006 0.11 -10000 0 -0.42 25 25
mol:DAG -0.067 0.19 -10000 0 -0.44 73 73
EGFR 0.006 0.076 -10000 0 -0.82 4 4
TXA2/TP alpha -0.081 0.22 -10000 0 -0.5 72 72
Gq family/GTP -0.076 0.13 -10000 0 -0.3 119 119
YES1 0.032 0.076 -10000 0 -0.65 2 2
GNAI2/GTP -0.017 0.078 -10000 0 -0.8 2 2
PGD2/DP -0.028 0.13 -10000 0 -0.64 21 21
SLC9A3R1 0.012 0.021 -10000 0 -0.31 2 2
FYN 0.032 0.076 -10000 0 -0.65 2 2
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.013 0.094 -10000 0 -0.33 37 37
PGK/cGMP -0.15 0.25 -10000 0 -0.56 131 131
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.032 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 -0.063 0.18 -10000 0 -0.4 77 77
PRKCB -0.061 0.17 -10000 0 -0.38 75 75
PRKCE -0.053 0.17 -10000 0 -0.38 71 71
PRKCD -0.054 0.17 -10000 0 -0.39 71 71
PRKCG -0.058 0.18 -10000 0 -0.4 70 70
muscle contraction -0.073 0.22 -10000 0 -0.5 73 73
PRKCZ -0.043 0.16 -10000 0 -0.35 71 71
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.019 0.091 -10000 0 -0.98 2 2
PRKCQ -0.052 0.17 -10000 0 -0.37 74 74
MAPKKK cascade -0.074 0.2 -10000 0 -0.47 74 74
SELE -0.057 0.18 -10000 0 -0.43 72 72
TP beta/GNAI2/GDP/G beta/gamma -0.019 0.094 -10000 0 -1.1 2 2
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.35 -10000 0 -0.82 112 112
chemotaxis -0.096 0.26 -10000 0 -0.62 74 74
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.002 0.11 -10000 0 -0.82 9 9
Rac1/GTP 0 0 -10000 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer -0.033 0.14 -9999 0 -0.46 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.055 0.11 -9999 0 -0.54 7 7
alphaV/beta3 Integrin/Osteopontin/Src -0.067 0.15 -9999 0 -0.62 24 24
AP1 -0.26 0.35 -9999 0 -0.84 112 112
ILK -0.032 0.15 -9999 0 -0.49 37 37
bone resorption -0.047 0.15 -9999 0 -0.56 18 18
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.052 0.12 -9999 0 -0.45 37 37
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.028 0.13 -9999 0 -0.63 21 21
alphaV/beta3 Integrin/Osteopontin -0.07 0.15 -9999 0 -0.56 37 37
MAP3K1 -0.033 0.15 -9999 0 -0.5 37 37
JUN -0.18 0.35 -9999 0 -0.82 109 109
MAPK3 -0.033 0.15 -9999 0 -0.46 37 37
MAPK1 -0.033 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 -0.031 0.17 -9999 0 -0.51 42 42
ITGB3 -0.01 0.14 -9999 0 -0.82 14 14
NFKBIA -0.026 0.15 -9999 0 -0.45 37 37
FOS -0.21 0.37 -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 -0.7 4 4
NF kappa B1 p50/RelA -0.061 0.11 -9999 0 -0.55 5 5
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 -0.66 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.033 0.15 -9999 0 -0.5 37 37
VAV3 -0.027 0.16 -9999 0 -0.48 42 42
MAP3K14 -0.04 0.15 -9999 0 -0.5 37 37
ROCK2 -0.023 0.17 -9999 0 -0.82 21 21
SPP1 -0.083 0.2 -9999 0 -0.42 108 108
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.055 0.13 -9999 0 -0.53 11 11
MMP2 -0.18 0.29 -9999 0 -0.65 108 108
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.043 0.12 -9999 0 -0.54 18 18
alphaM/beta2 Integrin/GPIbA -0.054 0.14 -9999 0 -0.51 35 35
alphaM/beta2 Integrin/proMMP-9 -0.093 0.2 -9999 0 -0.58 56 56
PLAUR -0.088 0.15 -9999 0 -0.31 150 150
HMGB1 0.002 0.024 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.034 0.099 -9999 0 -0.52 11 11
AGER -0.06 0.22 -9999 0 -0.8 37 37
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.007 0.079 -9999 0 -0.31 30 30
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.12 0.19 -9999 0 -0.62 44 44
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.57 79 79
CYR61 -0.24 0.38 -9999 0 -0.82 146 146
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.072 0.091 -9999 0 -0.44 9 9
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.003 0.11 -9999 0 -0.59 13 13
MYH2 -0.1 0.12 -9999 0 -0.4 36 36
MST1R 0.001 0.096 -9999 0 -0.65 9 9
leukocyte activation during inflammatory response -0.039 0.093 -9999 0 -0.46 10 10
APOB -0.01 0.078 -9999 0 -0.31 30 30
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 -0.82 7 7
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.019 0.15 -9999 0 -0.63 24 24
alphaM/beta2 Integrin/CTGF -0.12 0.22 -9999 0 -0.57 88 88
alphaM/beta2 Integrin -0.095 0.11 -9999 0 -0.35 46 46
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.082 0.15 -9999 0 -0.31 141 141
phagocytosis triggered by activation of immune response cell surface activating receptor -0.094 0.11 -9999 0 -0.35 46 46
cell adhesion -0.054 0.14 -9999 0 -0.51 35 35
NFKB1 -0.13 0.3 -9999 0 -0.74 59 59
THY1 0.011 0.03 -9999 0 -0.31 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.014 0.049 -9999 0 -0.34 2 2
alphaM/beta2 Integrin/LRP/tPA -0.035 0.1 -9999 0 -0.58 10 10
IL6 -0.24 0.46 -9999 0 -1.1 104 104
ITGB2 -0.018 0.086 -9999 0 -0.34 28 28
elevation of cytosolic calcium ion concentration -0.14 0.16 -9999 0 -0.53 34 34
alphaM/beta2 Integrin/JAM2/JAM3 -0.032 0.1 -9999 0 -0.6 9 9
JAM2 0.006 0.077 -9999 0 -0.72 5 5
alphaM/beta2 Integrin/ICAM1 -0.068 0.13 -9999 0 -0.5 22 22
alphaM/beta2 Integrin/uPA/Plg -0.098 0.12 -9999 0 -0.52 19 19
RhoA/GTP -0.11 0.12 -9999 0 -0.42 39 39
positive regulation of phagocytosis -0.07 0.12 -9999 0 -0.48 17 17
Ron/MSP -0.011 0.078 -9999 0 -0.63 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.16 -9999 0 -0.54 34 34
alphaM/beta2 Integrin/uPAR -0.084 0.13 -9999 0 -0.45 35 35
PLAU -0.14 0.16 -9999 0 -10000 0 0
PLAT 0.001 0.086 -9999 0 -0.48 12 12
actin filament polymerization -0.099 0.11 -9999 0 -0.38 36 36
MST1 0.011 0.041 -9999 0 -0.57 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.04 0.094 -9999 0 -0.51 8 8
TNF -0.18 0.4 -9999 0 -1 75 75
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.13 -9999 0 -0.54 21 21
fibrinolysis -0.098 0.12 -9999 0 -0.51 19 19
HCK -0.008 0.08 -9999 0 -0.31 31 31
dendritic cell antigen processing and presentation -0.094 0.11 -9999 0 -0.35 46 46
VTN -0.07 0.24 -9999 0 -0.76 52 52
alphaM/beta2 Integrin/CYR61 -0.2 0.28 -9999 0 -0.58 160 160
LPA -0.002 0.043 -9999 0 -0.31 9 9
LRP1 0.012 0.038 -9999 0 -0.82 1 1
cell migration -0.089 0.2 -9999 0 -0.57 57 57
FN1 -0.22 0.15 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.035 0.1 -9999 0 -0.52 11 11
MPO 0.001 0.088 -9999 0 -0.63 8 8
KNG1 -0.014 0.077 -9999 0 -0.31 30 30
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.094 0.12 -9999 0 -0.46 15 15
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.003 0.035 -9999 0 -0.31 6 6
CTGF -0.11 0.3 -9999 0 -0.82 71 71
alphaM/beta2 Integrin/Hck -0.045 0.12 -9999 0 -0.56 19 19
ITGAM -0.023 0.11 -9999 0 -0.39 30 30
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.046 0.13 -9999 0 -0.52 26 26
HP -0.081 0.16 -9999 0 -0.34 129 129
leukocyte adhesion -0.092 0.16 -9999 0 -0.61 26 26
SELP -0.003 0.11 -9999 0 -0.59 13 13
TCGA08_p53

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
CDKN2A -0.084 0.11 -9999 0 -0.21 206 206
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 0.053 0.062 -9999 0 -10000 0 0
MDM4 0.013 0 -9999 0 -10000 0 0
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 0.077 0.29 35 -10000 0 35
RFC1 0.025 0.077 0.29 35 -10000 0 35
PRKDC 0.025 0.077 0.29 35 -10000 0 35
RIPK1 0.014 0.004 -10000 0 -10000 0 0
CASP7 -0.013 0.045 0.2 3 -10000 0 3
FASLG/FAS/FADD/FAF1 -0.028 0.1 0.26 4 -0.37 31 35
MAP2K4 -0.023 0.16 -10000 0 -0.4 34 34
mol:ceramide -0.021 0.14 -10000 0 -0.48 32 32
GSN 0.025 0.077 0.29 35 -10000 0 35
FASLG/FAS/FADD/FAF1/Caspase 8 -0.019 0.13 -10000 0 -0.47 31 31
FAS 0.011 0.006 -10000 0 -10000 0 0
BID -0.033 0.081 0.32 3 -10000 0 3
MAP3K1 0.004 0.097 -10000 0 -0.28 15 15
MAP3K7 0.01 0.006 -10000 0 -10000 0 0
RB1 0.023 0.078 0.29 34 -0.32 1 35
CFLAR 0.014 0.004 -10000 0 -10000 0 0
HGF/MET -0.15 0.22 -10000 0 -0.62 75 75
ARHGDIB 0.022 0.081 0.29 35 -10000 0 35
FADD 0.011 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.025 0.077 -10000 0 -0.29 35 35
NFKB1 -0.053 0.093 -10000 0 -0.32 16 16
MAPK8 -0.058 0.22 -10000 0 -0.45 102 102
DFFA 0.025 0.077 0.29 35 -10000 0 35
DNA fragmentation during apoptosis 0.025 0.077 0.29 35 -10000 0 35
FAS/FADD/MET -0.059 0.077 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.002 0.089 -10000 0 -0.39 20 20
FAF1 0.011 0.007 -10000 0 -10000 0 0
PARP1 0.025 0.077 0.29 35 -10000 0 35
DFFB 0.025 0.077 0.29 35 -10000 0 35
CHUK -0.045 0.083 -10000 0 -0.73 1 1
FASLG -0.057 0.22 -10000 0 -0.65 49 49
FAS/FADD 0 0.001 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 73 73
LMNA 0.023 0.07 0.26 35 -10000 0 35
CASP6 0.025 0.077 0.29 35 -10000 0 35
CASP10 0.011 0.006 -10000 0 -10000 0 0
CASP3 0.03 0.094 0.35 38 -10000 0 38
PTPN13 0.005 0.085 -10000 0 -0.82 5 5
CASP8 0.008 0.045 0.46 3 -10000 0 3
IL6 -0.26 0.57 -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 35 -10000 0 35
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.14 -10000 0 -0.49 32 32
activation of caspase activity by cytochrome c -0.033 0.08 0.32 3 -10000 0 3
PAK2 0.025 0.077 0.29 35 -10000 0 35
BCL2 -0.047 0.22 -10000 0 -0.82 35 35
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.075 0.097 -10000 0 -10000 0 0
CRKL -0.032 0.11 -10000 0 -0.33 26 26
mol:PIP3 -0.019 0.033 0.69 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 0.066 -10000 0 -0.82 3 3
HGF/MET/SHIP2 -0.14 0.21 -10000 0 -0.6 73 73
MAP3K5 -0.019 0.11 -10000 0 -0.48 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.55 73 73
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 -0.27 0.4 -10000 0 -0.85 151 151
STAT3 (dimer) -0.04 0.13 -10000 0 -0.34 73 73
GAB1/CRKL/SHP2/PI3K -0.043 0.095 -10000 0 -0.59 3 3
INPP5D -0.003 0.071 -10000 0 -0.31 24 24
CBL/CRK -0.023 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 0.073 -10000 0 -10000 0 0
PAK1 0.009 0.038 0.42 1 -0.5 2 3
HGF/MET/RANBP10 -0.14 0.21 -10000 0 -0.6 73 73
HRAS -0.06 0.16 -10000 0 -0.43 73 73
DOCK1 -0.026 0.12 -10000 0 -0.55 4 4
GAB1 -0.042 0.12 -10000 0 -0.3 73 73
CRK -0.032 0.11 -10000 0 -0.33 26 26
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.21 -10000 0 -0.6 73 73
JUN -0.18 0.35 -10000 0 -0.82 109 109
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.071 0.1 -10000 0 -0.29 73 73
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 0.097 -10000 0 -10000 0 0
FOS -0.21 0.37 -10000 0 -0.82 128 128
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.049 0.062 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.61 73 73
cell migration -0.055 0.085 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.075 0.097 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.052 0.14 -10000 0 -0.36 73 73
MET/MUC20 -0.079 0.1 -10000 0 -0.21 179 179
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 0.21 -10000 0 -0.6 73 73
RAF1 -0.048 0.15 -10000 0 -0.45 27 27
STAT3 -0.041 0.13 -10000 0 -0.34 73 73
cell proliferation -0.048 0.18 -10000 0 -0.45 73 73
RPS6KB1 -0.015 0.04 -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 -0.007 0.13 -10000 0 -0.59 13 13
SRC -0.041 0.13 -10000 0 -0.33 73 73
PI3K -0.042 0.1 -10000 0 -0.32 29 29
MET/Glomulin -0.059 0.093 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.037 0.14 -10000 0 -0.42 27 27
MET -0.11 0.16 -10000 0 -0.31 179 179
MAP4K1 -0.028 0.12 -10000 0 -0.34 30 30
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.037 0.14 -10000 0 -0.42 27 27
BAD 0.009 0.038 0.42 1 -0.5 2 3
MAP2K4 -0.009 0.1 -10000 0 -0.43 5 5
SHP2/GRB2/SOS1/GAB1 -0.058 0.091 -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 26 26
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 73 73
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 26 26
PDPK1 -0.009 0.044 0.52 1 -0.58 2 3
HGF/MET/SHIP -0.15 0.21 -10000 0 -0.6 73 73
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.035 0.12 -10000 0 -0.51 26 26
ER alpha/Gai/GDP/Gbeta gamma 0.006 0.15 -10000 0 -0.48 35 35
AKT1 -0.015 0.2 -10000 0 -0.86 25 25
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.014 0.2 -10000 0 -0.87 25 25
mol:Ca2+ -0.099 0.23 -10000 0 -0.5 114 114
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.071 0.18 -10000 0 -0.58 51 51
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.012 0.19 0.82 25 -10000 0 25
RhoA/GTP -0.026 0.089 -10000 0 -0.41 23 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.037 0.13 -10000 0 -0.59 23 23
regulation of stress fiber formation -0.013 0.11 0.36 21 -10000 0 21
E2/ERA-ERB (dimer) -0.042 0.14 -10000 0 -0.57 26 26
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.034 0.11 -10000 0 -0.51 23 23
pseudopodium formation 0.013 0.11 -10000 0 -0.36 21 21
E2/ER alpha (dimer)/PELP1 -0.037 0.12 -10000 0 -0.56 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 -0.72 20 20
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 -0.6 24 24
E2/ER beta (dimer) -0.005 0.058 -10000 0 -0.64 4 4
mol:GDP -0.036 0.13 -10000 0 -0.56 26 26
mol:NADP 0.012 0.15 -10000 0 -0.6 24 24
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.1 0.24 -10000 0 -0.52 114 114
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.24 -10000 0 -0.54 114 114
PLCB2 -0.12 0.25 -10000 0 -0.54 113 113
IGF1 -0.18 0.35 -10000 0 -0.8 118 118
mol:L-citrulline 0.012 0.15 -10000 0 -0.6 24 24
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.027 0.14 -10000 0 -0.78 16 16
JNK cascade -0.005 0.058 -10000 0 -0.64 4 4
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.006 0.076 -10000 0 -0.82 4 4
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.048 0.19 -10000 0 -0.53 54 54
Gq family/GDP/Gbeta gamma -0.056 0.17 -10000 0 -0.53 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.081 -10000 0 -0.36 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.037 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 30 30
GNAL -0.093 0.28 -10000 0 -0.82 61 61
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.015 0.052 -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 -0.52 28 28
cAMP biosynthetic process -0.09 0.19 -10000 0 -0.48 83 83
SRC 0.014 0.14 -10000 0 -0.5 24 24
PI3K -0.004 0.05 -10000 0 -0.63 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.031 0.12 -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 -0.53 38 38
Gs family/GTP -0.092 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 -0.52 114 114
Gs family/GDP/Gbeta gamma -0.074 0.16 -10000 0 -0.41 83 83
MSN 0.012 0.12 -10000 0 -0.39 21 21
Gq family/GTP -0.15 0.24 -10000 0 -0.57 113 113
mol:PI-3-4-5-P3 -0.012 0.2 -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 -0.033 0.12 -10000 0 -0.52 26 26
NOS3 0.01 0.16 -10000 0 -0.64 24 24
GNA11 -0.002 0.11 -10000 0 -0.82 9 9
MAPKKK cascade -0.008 0.19 -10000 0 -0.54 51 51
E2/ER alpha (dimer)/PELP1/Src -0.039 0.14 -10000 0 -0.63 23 23
ruffle organization 0.013 0.11 -10000 0 -0.36 21 21
ROCK2 0.003 0.13 -10000 0 -0.41 43 43
GNA14 -0.18 0.35 -10000 0 -0.82 112 112
GNA15 -0.013 0.094 -10000 0 -0.33 37 37
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.027 0.19 -10000 0 -0.52 46 46
MMP2 0.015 0.15 -10000 0 -0.68 11 11
Visual signal transduction: Rods

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
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 0.071 -9999 0 -0.56 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 -0.067 0.25 -9999 0 -0.81 47 47
CNG Channel -0.028 0.085 -9999 0 -0.52 9 9
mol:Na + -0.023 0.082 -9999 0 -0.46 13 13
mol:ADP -0.067 0.25 -9999 0 -0.81 47 47
RGS9-1/Gbeta5/R9AP -0.092 0.21 -9999 0 -0.56 79 79
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.024 0.084 -9999 0 -0.47 13 13
CNGB1 0 0.062 -9999 0 -0.31 18 18
RDH5 -0.2 0.16 -9999 0 -0.31 314 314
SAG 0.002 0.015 -9999 0 -0.31 1 1
mol:Ca2+ 0.016 0.088 -9999 0 -0.44 13 13
Na + (4 Units) -0.021 0.075 -9999 0 -0.42 13 13
RGS9 -0.078 0.26 -9999 0 -0.8 54 54
GNB1/GNGT1 -0.003 0.024 -9999 0 -10000 0 0
GNAT1/GDP -0.081 0.18 -9999 0 -0.49 79 79
GUCY2D -0.011 0.11 -9999 0 -0.43 26 26
GNGT1 -0.004 0.038 -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 0.074 -9999 0 -0.48 5 5
mol:11-cis-retinal -0.2 0.16 -9999 0 -0.31 314 314
mol:cGMP -0.016 0.071 -9999 0 -0.48 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.14 0.098 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0.001 0.091 -9999 0 -0.57 10 10
Metarhodopsin II -0.05 0.15 -9999 0 -0.52 46 46
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.076 -9999 0 -0.51 9 9
RGS9BP -0.037 0.2 -9999 0 -0.82 29 29
Metarhodopsin II/Transducin 0.011 0.015 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.043 -9999 0 -0.52 3 3
PDE6A/B -0.012 0.047 -9999 0 -10000 0 0
mol:Pi -0.092 0.21 -9999 0 -0.56 79 79
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 0.076 -9999 0 -0.31 28 28
PDE6G -0.017 0.12 -9999 0 -0.38 37 37
RHO 0.006 0.016 -9999 0 -0.31 1 1
PDE6 -0.093 0.18 -9999 0 -0.48 82 82
GUCA1A 0.004 0.03 -9999 0 -0.31 4 4
GC2/GCAP Family -0.005 0.043 -9999 0 -0.52 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.007 0.067 -9999 0 -0.7 4 4
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.033 0.2 -9999 0 -0.82 30 30
HDAC7 -0.031 0.14 -9999 0 -0.63 15 15
JUN -0.18 0.35 -9999 0 -0.82 109 109
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 -0.002 0.095 -9999 0 -0.65 10 10
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.044 0.15 -9999 0 -0.65 17 17
MAP2K6 -0.01 0.12 -9999 0 -0.78 11 11
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 0.056 -9999 0 -10000 0 0
NCOA2 -0.07 0.24 -9999 0 -0.83 44 44
CEBPA 0.006 0.085 -9999 0 -0.82 5 5
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.067 0.15 -9999 0 -0.54 15 15
NR0B1 -0.002 0.041 -9999 0 -0.31 8 8
EGR1 -0.17 0.34 -9999 0 -0.83 102 102
RXRs/9cRA -0.13 0.059 -9999 0 -0.5 4 4
AR/RACK1/Src -0.11 0.16 -9999 0 -0.66 17 17
AR/GR -0.13 0.2 -9999 0 -0.36 141 141
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 0.09 -9999 0 -0.64 9 9
T-DHT/AR/TIF2/CARM1 -0.12 0.23 -9999 0 -0.69 52 52
SRC -0.003 0.11 -9999 0 -0.54 17 17
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.4 0.57 -9999 0 -1.3 137 137
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.054 0.14 -9999 0 -0.66 17 17
TMPRSS2 -0.061 0.32 -9999 0 -1.2 32 32
RXRG -0.28 0.12 -9999 0 -0.32 427 427
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 -0.003 0.11 -9999 0 -0.82 9 9
KLK2 -0.48 0.43 -9999 0 -0.83 279 279
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 0.023 0.015 -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 -0.076 0.15 -9999 0 -0.66 17 17
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 -0.026 0.1 -9999 0 -0.32 52 52
T-DHT/AR/TIF2 -0.053 0.16 -9999 0 -0.45 46 46
T-DHT/AR/Hsp90 -0.055 0.14 -9999 0 -0.67 17 17
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.005 0.12 -9999 0 -0.57 17 17
SIRT1 0.011 0.038 -9999 0 -0.82 1 1
ZMIZ2 0.023 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.02 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.074 0.14 -9999 0 -0.67 17 17
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.038 -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 49 49
RXRs/LXRs/DNA/Oxysterols -0.049 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 0.022 0.083 -9999 0 -0.34 23 23
RXRs/NUR77 -0.26 0.25 -9999 0 -0.63 144 144
RXRs/PPAR -0.055 0.065 -9999 0 -0.4 11 11
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -9999 0 -0.21 1 1
RARs/VDR/DNA/Vit D3 -0.013 0.078 -9999 0 -0.48 13 13
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 -0.012 0.078 -9999 0 -0.48 13 13
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.054 0.031 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.022 0.083 -9999 0 -0.34 23 23
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 -0.21 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.083 -9999 0 -0.53 5 5
NR1H4 0.001 0.033 -9999 0 -0.31 5 5
RXRs/LXRs/DNA -0.099 0.093 -9999 0 -0.58 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 0.068 -9999 0 -0.52 4 4
NR4A1 -0.23 0.38 -9999 0 -0.82 142 142
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.048 0.049 -9999 0 -0.33 4 4
RXRG -0.28 0.12 -9999 0 -0.32 427 427
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 -0.006 0.12 -9999 0 -0.82 11 11
PPARG -0.002 0.1 -9999 0 -0.61 12 12
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.42 -9999 0 -1.3 58 58
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.048 0.16 -9999 0 -0.46 58 58
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.009 0.14 -9999 0 -0.82 13 13
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.45 166 166
SREBF1 -0.038 0.14 -9999 0 -0.62 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.083 -9999 0 -0.53 5 5
ABCA1 -0.038 0.14 -9999 0 -0.43 47 47
RARs/THRs -0.023 0.1 -9999 0 -0.48 23 23
RXRs/FXR -0.12 0.072 -9999 0 -0.56 4 4
BCL2 -0.047 0.22 -9999 0 -0.82 35 35
Regulation of p38-alpha and p38-beta

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
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 -0.005 0.12 -9999 0 -0.78 11 11
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 -0.28 278 278
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 0.03 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.047 0.068 -9999 0 -0.3 6 6
PRKG1 -0.21 0.37 -9999 0 -0.82 131 131
DUSP8 0.002 0.084 -9999 0 -0.52 10 10
PGK/cGMP/p38 alpha -0.16 0.2 -9999 0 -0.47 134 134
apoptosis -0.046 0.066 -9999 0 -0.29 6 6
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 78 78
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 0.006 -9999 0 -10000 0 0
TRAF6 0.01 0.054 -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 0.013 0.015 -9999 0 -0.31 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.06 0.13 -9999 0 -0.38 14 14
BLK -0.25 0.38 -9999 0 -0.76 163 163
HCK -0.008 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 0.033 -9999 0 -0.51 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.027 0.092 -9999 0 -0.34 5 5
positive regulation of innate immune response -0.059 0.14 -9999 0 -0.41 12 12
LCK -0.01 0.11 -9999 0 -0.44 25 25
p38alpha-beta/MKP7 -0.049 0.13 -9999 0 -0.45 6 6
p38alpha-beta/MKP5 -0.051 0.13 -9999 0 -0.48 7 7
PGK/cGMP -0.17 0.28 -9999 0 -0.64 131 131
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.49 73 73
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 -0.82 278 278
ErbB2/ErbB3 signaling events

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
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.042 0.1 -9999 0 -0.38 21 21
NFATC4 -0.001 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 -0.046 0.13 -9999 0 -0.41 54 54
JUN 0.002 0.097 -9999 0 -0.28 11 11
HRAS 0.011 0.021 -9999 0 -0.32 2 2
DOCK7 -0.016 0.14 -9999 0 -0.38 57 57
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.056 0.16 -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 0.064 -9999 0 -0.37 2 2
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.026 0.15 -9999 0 -0.44 54 54
RAF1 -0.004 0.13 -9999 0 -0.4 21 21
ErbB2/ErbB3/neuregulin 2 -0.07 0.18 -9999 0 -0.52 64 64
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.022 0.083 -9999 0 -0.31 5 5
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.13 0.33 -9999 0 -0.68 114 114
FOS -0.11 0.28 -9999 0 -0.52 151 151
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.046 0.13 -9999 0 -0.41 54 54
MAPK3 -0.085 0.26 -9999 0 -0.5 110 110
MAPK1 -0.085 0.26 -9999 0 -0.5 110 110
JAK2 -0.014 0.14 -9999 0 -0.38 55 55
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.016 0.13 -9999 0 -0.38 54 54
NRG1 -0.068 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 62 62
MAPK9 -0.023 0.061 -9999 0 -0.29 1 1
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.008 0.12 -9999 0 -0.74 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 0.088 -9999 0 -0.38 2 2
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.057 0.2 -9999 0 -0.43 41 41
myelination 0.009 0.11 -9999 0 -0.46 3 3
PPP3CB -0.011 0.13 -9999 0 -0.36 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 -0.083 0.26 -9999 0 -0.8 57 57
mol:GDP -0.016 0.13 -9999 0 -0.37 54 54
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.006 0.14 -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 -0.014 0.14 -9999 0 -0.38 55 55
MAP2K1 -0.077 0.23 -9999 0 -0.58 33 33
heart morphogenesis -0.046 0.13 -9999 0 -0.41 54 54
RAS family/GDP -0.036 0.1 -9999 0 -0.64 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.009 -9999 0 -10000 0 0
CHRNE 0.01 0.034 -9999 0 -0.13 17 17
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 -0.046 0.13 -9999 0 -0.41 54 54
CDC42 0.013 0 -9999 0 -10000 0 0
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 0.042 -10000 0 -0.31 8 8
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.064 0.15 0.54 9 -10000 0 9
IL27/IL27R/JAK1 -0.12 0.19 -10000 0 -0.66 8 8
TBX21 -0.089 0.22 -10000 0 -0.66 30 30
IL12B -0.005 0.092 -10000 0 -0.55 11 11
IL12A -0.059 0.2 -10000 0 -0.62 53 53
IL6ST -0.11 0.29 -10000 0 -0.83 68 68
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 -0.063 0.16 -10000 0 -0.51 1 1
T-helper 2 cell differentiation 0.064 0.15 0.54 9 -10000 0 9
T cell proliferation during immune response 0.064 0.15 0.54 9 -10000 0 9
MAPKKK cascade -0.064 0.15 -10000 0 -0.54 9 9
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 -0.36 44 44
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.089 0.21 -10000 0 -0.64 28 28
IL27/IL27R/JAK2/TYK2 -0.065 0.15 -10000 0 -0.55 9 9
positive regulation of T cell mediated cytotoxicity -0.064 0.15 -10000 0 -0.54 9 9
STAT1 (dimer) -0.12 0.24 0.52 16 -0.77 15 31
JAK2 0.012 0.039 -10000 0 -0.84 1 1
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.054 0.14 -10000 0 -0.52 9 9
T cell proliferation -0.16 0.24 -10000 0 -0.54 100 100
IL12/IL12R/TYK2/JAK2 -0.055 0.17 -10000 0 -0.68 14 14
IL17A -0.064 0.16 -10000 0 -0.51 1 1
mast cell activation 0.064 0.15 0.54 9 -10000 0 9
IFNG -0.02 0.049 -10000 0 -0.13 65 65
T cell differentiation -0.005 0.008 -10000 0 -0.022 58 58
STAT3 (dimer) -0.054 0.14 -10000 0 -0.52 9 9
STAT5A (dimer) -0.054 0.14 -10000 0 -0.52 9 9
STAT4 (dimer) -0.074 0.16 -10000 0 -0.52 23 23
STAT4 -0.025 0.14 -10000 0 -0.45 40 40
T cell activation -0.012 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.062 0.18 -10000 0 -0.69 5 5
GATA3 -0.045 0.34 -10000 0 -1.5 25 25
IL18 -0.025 0.12 -10000 0 -0.3 58 58
positive regulation of mast cell cytokine production -0.053 0.14 -10000 0 -0.51 9 9
IL27/EBI3 -0.098 0.12 -10000 0 -0.44 6 6
IL27RA 0.004 0.027 -10000 0 -10000 0 0
IL6 -0.17 0.34 -10000 0 -0.71 123 123
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.013 -10000 0 -10000 0 0
IL1B -0.042 0.18 -10000 0 -0.64 38 38
EBI3 -0.15 0.17 -10000 0 -0.32 231 231
TNF -0.07 0.21 -10000 0 -0.64 58 58
LPA receptor mediated 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
GNB1/GNG2 -0.047 0.16 -9999 0 -0.54 40 40
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.051 -9999 0 -0.6 1 1
AP1 -0.26 0.36 -9999 0 -0.69 176 176
mol:PIP3 -0.042 0.13 -9999 0 -0.52 16 16
AKT1 -0.029 0.097 -9999 0 -0.58 5 5
PTK2B 0 0.087 -9999 0 -0.27 40 40
RHOA 0.031 0.047 -9999 0 -0.26 1 1
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.004 0.073 -9999 0 -10000 0 0
MAGI3 0.012 0.038 -9999 0 -0.82 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.016 0.14 -9999 0 -0.45 40 40
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.089 -9999 0 -0.36 9 9
NF kappa B1 p50/RelA -0.047 0.12 -9999 0 -0.55 13 13
endothelial cell migration -0.03 0.21 -9999 0 -0.64 42 42
ADCY4 -0.017 0.19 -9999 0 -0.62 41 41
ADCY5 -0.048 0.21 -9999 0 -0.65 44 44
ADCY6 -0.017 0.19 -9999 0 -0.62 41 41
ADCY7 -0.017 0.19 -9999 0 -0.62 41 41
ADCY1 -0.019 0.2 -9999 0 -0.62 41 41
ADCY2 -0.041 0.22 -9999 0 -0.66 42 42
ADCY3 -0.017 0.19 -9999 0 -0.62 41 41
ADCY8 -0.058 0.2 -9999 0 -0.63 44 44
ADCY9 -0.017 0.19 -9999 0 -0.62 41 41
GSK3B 0.008 0.083 -9999 0 -0.3 13 13
arachidonic acid secretion -0.01 0.19 -9999 0 -0.57 41 41
GNG2 0.012 0.038 -9999 0 -0.82 1 1
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.042 0.21 -9999 0 -0.6 55 55
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 -0.033 0.099 -9999 0 -0.97 5 5
JUN -0.18 0.35 -9999 0 -0.82 109 109
LPA/LPA2/NHERF2 -0.001 0.007 -9999 0 -10000 0 0
TIAM1 -0.043 0.12 -9999 0 -1.2 5 5
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.004 0.074 -9999 0 -10000 0 0
PLCB3 0.03 0.008 -9999 0 -10000 0 0
FOS -0.21 0.37 -9999 0 -0.82 128 128
positive regulation of mitosis -0.01 0.19 -9999 0 -0.57 41 41
LPA/LPA1-2-3 -0.052 0.16 -9999 0 -0.54 40 40
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 0.003 0.11 -9999 0 -0.36 40 40
GNAZ -0.022 0.17 -9999 0 -0.57 42 42
EGFR/PI3K-beta/Gab1 -0.044 0.13 -9999 0 -0.54 16 16
positive regulation of dendritic cell cytokine production -0.052 0.15 -9999 0 -0.54 40 40
LPA/LPA2/MAGI-3 -0.002 0.028 -9999 0 -0.6 1 1
ARHGEF1 -0.002 0.15 -9999 0 -0.5 40 40
GNAI2 -0.022 0.17 -9999 0 -0.57 42 42
GNAI3 -0.022 0.17 -9999 0 -0.57 42 42
GNAI1 -0.024 0.18 -9999 0 -0.57 43 43
LPA/LPA3 -0.01 0.043 -9999 0 -0.27 1 1
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.058 0.19 -9999 0 -0.66 42 42
HB-EGF/EGFR -0.053 0.17 -9999 0 -0.54 46 46
HBEGF -0.06 0.19 -9999 0 -0.62 42 42
mol:DAG 0.004 0.074 -9999 0 -10000 0 0
cAMP biosynthetic process -0.029 0.2 -9999 0 -0.56 54 54
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 0.028 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.065 -9999 0 -0.31 20 20
LPAR1 -0.054 0.24 -9999 0 -0.84 40 40
IL8 -0.13 0.2 -9999 0 -0.47 64 64
PTK2 -0.011 0.16 -9999 0 -0.5 40 40
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.016 0.14 -9999 0 -0.45 40 40
EGFR 0.006 0.076 -9999 0 -0.82 4 4
PLCG1 -0.015 0.085 -9999 0 -0.31 9 9
PLD2 -0.011 0.16 -9999 0 -0.5 40 40
G12/G13 -0.046 0.15 -9999 0 -0.53 40 40
PI3K-beta -0.033 0.12 -9999 0 -0.71 5 5
cell migration -0.016 0.059 -9999 0 -0.27 5 5
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.002 0.12 -9999 0 -0.36 40 40
HRAS/GTP -0.011 0.19 -9999 0 -0.59 41 41
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.57 79 79
PRKCE 0.007 0.076 -9999 0 -0.82 4 4
PRKCD 0.012 0.071 -9999 0 -10000 0 0
Gi(beta/gamma) -0.01 0.19 -9999 0 -0.59 41 41
mol:LPA 0.003 0.018 -9999 0 -0.22 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.031 0.13 -9999 0 -0.45 40 40
MAPKKK cascade -0.01 0.19 -9999 0 -0.57 41 41
contractile ring contraction involved in cytokinesis 0.031 0.046 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.086 0.2 -9999 0 -0.44 112 112
GNA15 0.009 0.055 -9999 0 -0.43 1 1
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.008 0.091 -9999 0 -0.37 9 9
GNA11 0.011 0.067 -9999 0 -0.43 9 9
Rac1/GTP -0.035 0.11 -9999 0 -1 5 5
MMP2 -0.03 0.21 -9999 0 -0.65 42 42
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 -0.055 0.16 -9999 0 -0.55 40 40
MAP4K1 -0.019 0.13 -9999 0 -0.41 37 37
MAP3K8 -0.001 0.11 -9999 0 -0.82 8 8
PRKCB -0.027 0.13 -9999 0 -0.36 52 52
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.014 0.11 -9999 0 -0.56 5 5
JUN -0.1 0.24 -9999 0 -0.51 119 119
MAP3K7 0.014 0.11 -9999 0 -0.56 5 5
GRAP2 -0.042 0.21 -9999 0 -0.78 34 34
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.02 0.11 -9999 0 -0.52 7 7
LAT 0.006 0.077 -9999 0 -0.72 5 5
LCP2 0.009 0.039 -9999 0 -0.31 7 7
MAPK8 -0.001 0.14 -9999 0 -0.76 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.11 -9999 0 -0.37 32 32
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.051 0.15 -9999 0 -0.52 40 40
BCR signaling pathway

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
JUN -0.11 0.18 -9999 0 -0.45 62 62
IKBKB -0.018 0.071 -9999 0 -0.33 4 4
AKT1 -0.041 0.1 -9999 0 -0.27 21 21
IKBKG -0.017 0.074 -9999 0 -0.33 5 5
CALM1 -0.035 0.085 -9999 0 -0.35 2 2
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
MAP3K1 -0.073 0.18 -9999 0 -0.65 16 16
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.045 0.089 -9999 0 -0.38 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.082 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 -0.17 0.24 -9999 0 -0.52 135 135
CD22 -0.15 0.22 -9999 0 -0.51 104 104
CAMK2G -0.025 0.081 -9999 0 -0.32 2 2
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 24 24
SHC/GRB2/SOS1 -0.096 0.15 -9999 0 -10000 0 0
GO:0007205 -0.045 0.09 -9999 0 -0.38 2 2
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.035 0.086 -9999 0 -0.36 2 2
NFATC1 -0.069 0.16 -9999 0 -0.54 20 20
B-cell antigen/BCR complex -0.17 0.24 -9999 0 -0.52 135 135
PAG1/CSK -0.001 0.029 -9999 0 -0.63 1 1
NFKBIB 0.002 0.028 -9999 0 -0.11 3 3
HRAS -0.037 0.099 -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 0.008 0.024 -9999 0 -0.2 1 1
RasGAP/Csk -0.14 0.2 -9999 0 -0.49 94 94
mol:GDP -0.041 0.083 -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 62 62
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 -0.086 0.18 -9999 0 -0.43 74 74
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.051 0.087 -9999 0 -0.38 2 2
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.14 0.21 -9999 0 -0.47 129 129
CHUK -0.017 0.074 -9999 0 -0.35 4 4
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.066 0.094 -9999 0 -0.49 8 8
PTPN6 -0.14 0.21 -9999 0 -0.6 51 51
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.005 0.035 -9999 0 -0.13 18 18
VAV2 -0.13 0.19 -9999 0 -0.51 41 41
ubiquitin-dependent protein catabolic process 0.007 0.027 -9999 0 -0.11 3 3
BTK -0.019 0.16 -9999 0 -1.2 8 8
CD19 -0.15 0.2 -9999 0 -0.45 98 98
MAP4K1 -0.019 0.13 -9999 0 -0.41 37 37
CD72 0.012 0.021 -9999 0 -0.31 2 2
PAG1 0.012 0.038 -9999 0 -0.82 1 1
MAPK14 -0.055 0.16 -9999 0 -0.52 16 16
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.034 0.088 -9999 0 -0.32 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.061 0.17 -9999 0 -0.43 71 71
RAF1 -0.027 0.094 -9999 0 -0.34 1 1
RasGAP/p62DOK/SHIP -0.14 0.19 -9999 0 -0.47 93 93
CD79A -0.19 0.3 -9999 0 -0.82 74 74
re-entry into mitotic cell cycle -0.081 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 -0.1 0.21 -9999 0 -0.56 51 51
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 -0.062 0.17 -9999 0 -0.53 24 24
actin cytoskeleton organization -0.086 0.18 -9999 0 -0.68 11 11
NF-kappa-B/RelA 0.022 0.045 -9999 0 -0.2 1 1
Calcineurin -0.035 0.059 -9999 0 -10000 0 0
PI3K -0.13 0.16 -9999 0 -0.54 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.055 0.085 -9999 0 -0.34 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.24 -9999 0 -0.9 25 25
DAPP1 -0.13 0.26 -9999 0 -1.2 18 18
cytokine secretion -0.064 0.15 -9999 0 -0.5 20 20
mol:DAG -0.051 0.087 -9999 0 -0.38 2 2
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.018 0.089 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.17 0.23 -9999 0 -0.58 94 94
mol:PI-3-4-5-P3 -0.096 0.12 -9999 0 -0.38 26 26
ETS1 -0.016 0.076 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.17 -9999 0 -0.46 74 74
B-cell antigen/BCR complex/LYN -0.12 0.2 -9999 0 -0.49 81 81
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.054 -9999 0 -0.82 2 2
RAC1 -0.092 0.19 -9999 0 -0.75 11 11
B-cell antigen/BCR complex/LYN/SYK -0.15 0.22 -9999 0 -0.55 81 81
CARD11 -0.074 0.12 -9999 0 -0.51 12 12
FCGR2B -0.029 0.18 -9999 0 -0.75 27 27
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0 0.035 -9999 0 -0.14 2 2
PTPRC -0.033 0.18 -9999 0 -0.59 37 37
PDPK1 -0.043 0.1 -9999 0 -0.27 21 21
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 -0.089 1 1
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.12 0.1 -9999 0 -0.65 7 7
EPHB2 0.008 0.066 -9999 0 -0.82 3 3
Syndecan-2/TACI -0.13 0.25 -9999 0 -0.56 117 117
LAMA1 -0.05 0.22 -9999 0 -0.81 37 37
Syndecan-2/alpha2 ITGB1 -0.073 0.11 -9999 0 -0.47 24 24
HRAS 0.012 0.021 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.066 -9999 0 -0.55 7 7
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.025 0.097 -9999 0 -0.5 16 16
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.007 0.06 -9999 0 -0.5 7 7
LAMA3 -0.026 0.16 -9999 0 -0.59 31 31
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.066 -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 -0.079 0.099 -9999 0 -10000 0 0
dendrite morphogenesis 0.014 0.081 -9999 0 -0.54 10 10
Syndecan-2/GM-CSF -0.11 0.099 -9999 0 -0.57 7 7
determination of left/right symmetry 0.012 0.078 -9999 0 -0.63 7 7
Syndecan-2/PKC delta 0.018 0.068 -9999 0 -0.54 7 7
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.087 0.092 -9999 0 -0.52 7 7
MAPK1 -0.087 0.092 -9999 0 -0.52 7 7
Syndecan-2/RACK1 -0.007 0.057 -9999 0 -0.47 7 7
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.078 -9999 0 -0.63 7 7
ITGA2 -0.12 0.16 -9999 0 -0.31 190 190
MAPK8 0.017 0.1 -9999 0 -0.55 16 16
Syndecan-2/alpha2/beta1 Integrin -0.087 0.14 -9999 0 -0.52 40 40
Syndecan-2/Kininogen -0.007 0.079 -9999 0 -0.55 7 7
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.058 -9999 0 -0.44 7 7
Syndecan-2/CASK/Protein 4.1 -0.007 0.06 -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 -0.65 7 7
Syndecan-2/Caveolin-2/Ras -0.011 0.077 -9999 0 -0.55 9 9
Syndecan-2/Laminin alpha3 -0.008 0.13 -9999 0 -0.55 24 24
Syndecan-2/RasGAP -0.007 0.054 -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 0.081 -9999 0 -0.55 10 10
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.057 -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 -0.079 0.099 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.018 0.068 -9999 0 -0.54 7 7
TGFB1 0.008 0.042 -9999 0 -0.31 8 8
CASP3 0.027 0.063 -9999 0 -0.49 7 7
FN1 -0.22 0.15 -9999 0 -10000 0 0
Syndecan-2/IL8 -0.038 0.12 -9999 0 -0.55 17 17
SDC2 0.012 0.078 -9999 0 -0.63 7 7
KNG1 -0.014 0.077 -9999 0 -0.31 30 30
Syndecan-2/Neurofibromin 0.018 0.068 -9999 0 -0.54 7 7
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 326 326
Syndecan-2/TGFB1 0.015 0.072 -9999 0 -0.54 7 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.007 0.06 -9999 0 -0.5 7 7
Syndecan-2/Ezrin -0.007 0.059 -9999 0 -0.49 7 7
PRKACA 0.027 0.063 -9999 0 -0.49 7 7
angiogenesis -0.037 0.12 -9999 0 -0.54 17 17
MMP2 -0.001 0.1 -9999 0 -0.82 7 7
IL8 -0.081 0.18 -9999 0 -0.36 123 123
calcineurin-NFAT signaling pathway -0.12 0.25 -9999 0 -0.56 117 117
Signaling events mediated by PTP1B

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
PDGFRB 0.012 0.038 -10000 0 -0.82 1 1
Jak2/Leptin Receptor -0.023 0.094 -10000 0 -0.41 12 12
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 0.07 -10000 0 -0.34 4 4
EGFR 0.005 0.077 -10000 0 -0.83 4 4
EGF/EGFR -0.083 0.18 -10000 0 -0.5 72 72
CSF1 -0.001 0.11 -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 -0.099 0.12 -10000 0 -0.45 20 20
Insulin Receptor/Insulin -0.013 0.04 -10000 0 -10000 0 0
HCK -0.008 0.08 -10000 0 -0.31 31 31
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.002 0.066 -10000 0 -0.34 3 3
EGF -0.11 0.29 -10000 0 -0.79 74 74
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 -0.053 0.17 -10000 0 -0.5 56 56
cell migration 0.011 0.07 0.34 4 -10000 0 4
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.045 0.2 -10000 0 -0.6 46 46
ITGA2B -0.074 0.26 -10000 0 -0.82 50 50
CSF1R 0.008 0.05 -10000 0 -0.4 6 6
Prolactin Receptor/Prolactin -0.04 0.15 -10000 0 -0.64 26 26
FGR 0.011 0.03 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.003 0.066 -10000 0 -0.34 3 3
Crk/p130 Cas 0.001 0.06 -10000 0 -0.35 2 2
DOK1 0.007 0.062 -10000 0 -0.32 2 2
JAK2 -0.011 0.088 -10000 0 -0.38 12 12
Jak2/Leptin Receptor/Leptin -0.056 0.14 -10000 0 -0.58 28 28
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 -0.83 14 14
CAT1/PTP1B -0.089 0.15 -10000 0 -0.39 52 52
CAPN1 0.013 0.003 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.015 0.053 -10000 0 -0.58 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.055 0.15 -10000 0 -0.63 27 27
negative regulation of transcription -0.01 0.088 -10000 0 -0.38 12 12
FCGR2A -0.007 0.084 -10000 0 -0.33 28 28
FER 0.007 0.067 -10000 0 -0.83 3 3
alphaIIb/beta3 Integrin -0.082 0.23 -10000 0 -0.68 59 59
BLK -0.25 0.38 -10000 0 -0.76 163 163
Insulin Receptor/Insulin/Shc 0 0.001 -10000 0 -10000 0 0
RHOA 0.013 0.003 -10000 0 -10000 0 0
LEPR 0.003 0.087 -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 49 49
PRL 0.001 0.016 -10000 0 -0.31 1 1
SOCS3 -0.071 0.35 -10000 0 -1.5 27 27
SPRY2 0.009 0.057 -10000 0 -0.83 2 2
Insulin Receptor/Insulin/IRS1 -0.064 0.18 -10000 0 -0.56 55 55
CSF1/CSF1R -0.009 0.095 -10000 0 -0.51 10 10
Ras protein signal transduction 0.02 0.023 -10000 0 -10000 0 0
IRS1 -0.082 0.27 -10000 0 -0.82 55 55
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.007 0.066 -10000 0 -0.31 21 21
STAT5B -0.007 0.069 -10000 0 -0.3 5 5
STAT5A -0.007 0.069 -10000 0 -0.3 5 5
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.069 -10000 0 -0.36 4 4
CSN2 -0.007 0.055 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
LAT 0.002 0.066 -10000 0 -0.54 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.01 0.11 -10000 0 -0.44 25 25
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 211 211
p75(NTR)-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
Sortilin/TRAF6 -0.003 0.041 -10000 0 -0.63 2 2
Necdin/E2F1 -0.069 0.12 -10000 0 -0.76 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.036 0.1 -10000 0 -0.49 20 20
NGF (dimer)/p75(NTR)/BEX1 -0.29 0.28 -10000 0 -0.57 228 228
NT-4/5 (dimer)/p75(NTR) -0.075 0.18 -10000 0 -0.67 35 35
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.005 0.12 -10000 0 -0.49 23 23
IKBKG 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.6 21 21
MGDIs/NGR/p75(NTR)/LINGO1 -0.05 0.12 -10000 0 -0.54 21 21
FURIN 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.058 0.14 -10000 0 -0.55 31 31
LINGO1 -0.004 0.072 -10000 0 -0.31 25 25
Sortilin/TRAF6/NRIF -0.002 0.026 -10000 0 -10000 0 0
proBDNF (dimer) -0.014 0.14 -10000 0 -0.6 21 21
NTRK1 -0.002 0.062 -10000 0 -0.31 18 18
RTN4R 0.013 0 -10000 0 -10000 0 0
neuron apoptosis -0.011 0.13 -10000 0 -0.49 24 24
IRAK1 0.013 0 -10000 0 -10000 0 0
SHC1 -0.022 0.13 -10000 0 -0.57 20 20
ARHGDIA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.04 0.11 -10000 0 -0.52 20 20
MAGEH1 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.045 0.12 -10000 0 -0.52 25 25
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.5 25 25
proNGF (dimer) 0.006 0.07 -10000 0 -0.57 6 6
MAGED1 0.013 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.021 0.16 -10000 0 -0.64 25 25
ZNF274 0.013 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.038 0.1 -10000 0 -0.49 20 20
NGF 0.006 0.071 -10000 0 -0.57 6 6
cell cycle arrest 0.042 0.16 -10000 0 -0.47 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.087 -10000 0 -0.35 22 22
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.065 0.16 -10000 0 -0.59 36 36
NCSTN 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.047 0.12 -10000 0 -0.57 21 21
PSENEN 0.013 0 -10000 0 -10000 0 0
mol:ceramide -0.011 0.12 -10000 0 -0.51 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.071 -10000 0 -0.44 2 2
p75(NTR)/beta APP -0.051 0.13 -10000 0 -0.63 18 18
BEX1 -0.36 0.42 -10000 0 -0.82 213 213
mol:GDP -0.032 0.13 -10000 0 -0.58 20 20
NGF (dimer) -0.095 0.13 -10000 0 -0.51 30 30
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.043 0.11 -10000 0 -0.52 18 18
PIK3R1 0.013 0 -10000 0 -10000 0 0
RAC1/GTP -0.039 0.11 -10000 0 -0.5 20 20
MYD88 0.013 0 -10000 0 -10000 0 0
CHUK 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.047 0.13 -10000 0 -0.57 21 21
RHOB 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.063 0.093 -10000 0 -10000 0 0
NT3 (dimer) -0.05 0.2 -10000 0 -0.62 48 48
TP53 -0.006 0.13 -10000 0 -0.45 31 31
PRDM4 -0.011 0.12 -10000 0 -0.52 20 20
BDNF (dimer) -0.13 0.16 -10000 0 -0.54 39 39
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
SORT1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.036 0.1 -10000 0 -0.48 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.042 0.12 -10000 0 -0.52 22 22
RHOC 0.013 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
MAPK10 0.022 0.12 -10000 0 -0.45 20 20
DIABLO 0.013 0 -10000 0 -10000 0 0
SMPD2 -0.011 0.12 -10000 0 -0.52 20 20
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.046 0.12 -10000 0 -0.57 20 20
PSEN1 0.013 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.029 -10000 0 -0.63 1 1
NT3 (dimer)/p75(NTR) -0.096 0.2 -10000 0 -0.66 46 46
MAPK8 0.017 0.13 -10000 0 -0.46 20 20
MAPK9 0.023 0.12 -10000 0 -0.44 19 19
APAF1 0.012 0.038 -10000 0 -0.82 1 1
NTF3 -0.05 0.21 -10000 0 -0.62 48 48
NTF4 -0.021 0.16 -10000 0 -0.64 25 25
NDN 0.005 0.085 -10000 0 -0.82 5 5
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.033 0.097 -10000 0 -0.45 21 21
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.055 -10000 0 -0.66 3 3
RhoA-B-C/GTP -0.047 0.12 -10000 0 -0.56 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.049 0.12 -10000 0 -0.48 31 31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.13 -10000 0 -0.52 31 31
PRKACB 0.012 0.038 -10000 0 -0.82 1 1
proBDNF (dimer)/p75 ECD -0.022 0.11 -10000 0 -0.63 14 14
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.037 0.19 -10000 0 -0.68 35 35
BIRC2 0.013 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.065 0.17 0.24 183 -0.47 20 203
BAD 0.029 0.12 -10000 0 -0.44 20 20
RIPK2 0.013 0 -10000 0 -10000 0 0
NGFR -0.063 0.19 -10000 0 -0.42 84 84
CYCS -0.002 0.12 -10000 0 -0.48 20 20
ADAM17 0.01 0.054 -10000 0 -0.82 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.042 0.12 -10000 0 -0.52 22 22
BCL2L11 0.029 0.12 -10000 0 -0.44 20 20
BDNF (dimer)/p75(NTR) -0.07 0.17 -10000 0 -0.63 31 31
PI3K -0.043 0.12 -10000 0 -0.53 23 23
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.04 0.11 -10000 0 -0.52 20 20
NDNL2 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.056 0.14 -10000 0 -0.66 20 20
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.04 0.11 -10000 0 -0.52 20 20
TRAF6 0.01 0.054 -10000 0 -0.82 2 2
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
PLG -0.003 0.035 -10000 0 -0.31 6 6
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.018 0.14 -10000 0 -0.49 31 31
SQSTM1 0.013 0 -10000 0 -10000 0 0
NGFRAP1 0.013 0 -10000 0 -10000 0 0
CASP3 0.03 0.11 -10000 0 -0.4 20 20
E2F1 -0.088 0.15 -10000 0 -0.31 150 150
CASP9 0.013 0 -10000 0 -10000 0 0
IKK complex -0.014 0.059 -10000 0 -0.54 3 3
NGF (dimer)/TRKA -0.013 0.064 -10000 0 -0.64 3 3
MMP7 -0.18 0.22 -10000 0 -0.37 240 240
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.11 -10000 0 -0.49 22 22
MMP3 -0.038 0.11 -10000 0 -0.31 66 66
APAF-1/Caspase 9 -0.041 0.11 -10000 0 -0.61 7 7
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.015 -9999 0 -0.31 1 1
LAT2 -0.019 0.1 -9999 0 -0.4 4 4
AP1 -0.21 0.28 -9999 0 -0.57 162 162
mol:PIP3 -0.018 0.15 -9999 0 -0.52 14 14
IKBKB 0.002 0.094 -9999 0 -0.28 15 15
AKT1 -0.019 0.14 -9999 0 -0.59 6 6
IKBKG 0.002 0.094 -9999 0 -0.28 15 15
MS4A2 -0.067 0.14 -9999 0 -0.31 113 113
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.83 3 3
MAP3K1 0.009 0.1 -9999 0 -0.47 7 7
mol:Ca2+ -0.009 0.12 -9999 0 -0.38 14 14
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.011 0.09 -9999 0 -0.36 3 3
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.082 0.19 -9999 0 -0.5 78 78
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 24 24
PLD2 -0.05 0.15 -9999 0 -0.45 42 42
PTPN13 -0.002 0.1 -9999 0 -0.59 5 5
PTPN11 0.011 0.04 -9999 0 -0.86 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.017 0.1 -9999 0 -0.36 5 5
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.064 0.13 -9999 0 -0.54 14 14
LAT -0.016 0.1 -9999 0 -0.43 8 8
PAK2 0 0.11 -9999 0 -0.51 8 8
NFATC2 -0.15 0.28 -9999 0 -0.76 83 83
HRAS -0.009 0.12 -9999 0 -0.54 9 9
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.031 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.17 -9999 0 -0.47 71 71
Antigen/IgE/Fc epsilon R1 -0.093 0.16 -9999 0 -0.43 71 71
mol:GDP -0.017 0.13 -9999 0 -0.5 15 15
JUN -0.18 0.35 -9999 0 -0.82 109 109
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.21 0.37 -9999 0 -0.82 128 128
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.045 0.08 -9999 0 -0.38 4 4
CHUK 0.002 0.094 -9999 0 -0.29 13 13
KLRG1 -0.023 0.11 -9999 0 -0.41 14 14
VAV1 -0.024 0.12 -9999 0 -0.49 9 9
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.011 0.09 -9999 0 -0.35 4 4
negative regulation of mast cell degranulation -0.021 0.11 -9999 0 -0.39 12 12
BTK -0.048 0.11 -9999 0 -0.59 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.05 0.19 -9999 0 -0.5 49 49
GAB2/PI3K/SHP2 -0.067 0.13 -9999 0 -0.63 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.02 0.096 -9999 0 -0.29 36 36
RAF1 0.018 0.021 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.2 -9999 0 -0.58 57 57
FCER1G -0.009 0.083 -9999 0 -0.32 32 32
FCER1A -0.079 0.23 -9999 0 -0.56 76 76
Antigen/IgE/Fc epsilon R1/Fyn -0.083 0.14 -9999 0 -0.48 43 43
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 0.006 0.1 -9999 0 -0.69 9 9
DUSP1 -0.12 0.31 -9999 0 -0.82 78 78
NF-kappa-B/RelA -0.02 0.044 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.006 0.085 -9999 0 -0.38 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.043 0.1 -9999 0 -0.55 10 10
FER -0.014 0.099 -9999 0 -0.43 7 7
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.074 0.18 -9999 0 -0.53 60 60
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.013 0.13 -9999 0 -0.57 10 10
cytokine secretion -0.014 0.032 -9999 0 -0.22 1 1
SPHK1 -0.015 0.094 -9999 0 -0.45 2 2
PTK2 -0.006 0.087 -9999 0 -0.39 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.067 0.14 -9999 0 -0.56 12 12
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.012 0.15 -9999 0 -0.5 13 13
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 -0.049 0.095 -9999 0 -0.42 14 14
MAP2K4 0.021 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.21 -9999 0 -0.62 54 54
mol:Choline -0.05 0.15 -9999 0 -0.44 42 42
SHC/Grb2/SOS1 -0.032 0.067 -9999 0 -0.4 1 1
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.002 0.082 -9999 0 -0.36 1 1
HCLS1 -0.013 0.094 -9999 0 -0.38 5 5
PRKCB -0.012 0.12 -9999 0 -0.38 22 22
FCGR2B -0.029 0.18 -9999 0 -0.75 27 27
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.022 0.11 -9999 0 -0.4 12 12
LCP2 0.008 0.039 -9999 0 -0.32 7 7
PLA2G4A -0.043 0.16 -9999 0 -0.52 35 35
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.05 0.15 -9999 0 -0.44 42 42
IKK complex 0.017 0.076 -9999 0 -0.22 5 5
WIPF1 0.013 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.67 15 15
PTK2 -0.039 0.15 -9999 0 -0.6 28 28
positive regulation of JNK cascade -0.02 0.081 -9999 0 -0.34 28 28
CDC42/GDP 0.031 0.13 -9999 0 -0.47 28 28
Rac1/GDP 0.033 0.12 -9999 0 -0.46 28 28
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 -0.025 0.1 -9999 0 -0.43 28 28
nectin-3/I-afadin -0.037 0.15 -9999 0 -0.63 28 28
RAPGEF1 0.024 0.14 -9999 0 -0.54 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0.16 -9999 0 -0.63 28 28
PDGFB-D/PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
TLN1 0.019 0.075 -9999 0 -0.94 1 1
Rap1/GTP -0.022 0.086 -9999 0 -0.37 28 28
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 28 28
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.025 0.16 -9999 0 -0.59 28 28
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
PI3K -0.031 0.13 -9999 0 -0.51 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.033 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.021 0.085 -9999 0 -0.36 28 28
PVRL1 0.005 0.053 -9999 0 -0.31 13 13
PVRL3 -0.035 0.2 -9999 0 -0.82 28 28
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 -0.33 393 393
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.58 38 38
SRC -0.043 0.17 -9999 0 -0.72 28 28
ITGB3 -0.011 0.14 -9999 0 -0.82 14 14
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.033 -9999 0 -10000 0 0
FARP2 0.019 0.15 -9999 0 -0.58 28 28
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 -0.55 28 28
nectin-1/I-afadin -0.005 0.033 -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 -0.036 0.13 -9999 0 -0.55 28 28
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 -0.02 0.081 -9999 0 -0.34 28 28
alphaV/beta3 Integrin/Talin 0.018 0.13 -9999 0 -0.6 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 -1 1 1
VAV2 0.018 0.15 -9999 0 -0.59 28 28
RAP1/GDP -0.026 0.1 -9999 0 -0.43 28 28
ITGAV 0.01 0.054 -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 -0.55 28 28
nectin-3(dimer)/I-afadin/I-afadin -0.037 0.15 -9999 0 -0.63 28 28
Rac1/GTP -0.026 0.1 -9999 0 -0.44 28 28
PTPRM -0.019 0.082 -9999 0 -0.32 28 28
E-cadherin/beta catenin/alpha catenin -0.003 0.016 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.008 0.077 -9999 0 -0.74 5 5
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.58 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 56 56
SRC 0.013 0.015 -9999 0 -0.31 1 1
CDKN1B -0.064 0.18 -9999 0 -0.61 46 46
VEGFA 0.008 0.066 -9999 0 -0.82 3 3
ILK -0.064 0.18 -9999 0 -0.61 45 45
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.059 0.17 -9999 0 -0.57 45 45
PTK2B 0.02 0.11 -9999 0 -0.51 20 20
alphaV/beta3 Integrin/JAM-A -0.06 0.16 -9999 0 -0.48 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 -0.17 0.26 -9999 0 -0.54 155 155
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 -0.58 15 15
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.24 0.25 -9999 0 -0.62 114 114
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
alphaV/beta3 Integrin/Osteopontin -0.071 0.16 -9999 0 -0.57 37 37
RPS6KB1 -0.21 0.24 -9999 0 -0.57 114 114
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.095 0.15 -9999 0 -0.75 15 15
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.095 0.15 -9999 0 -0.75 15 15
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.035 0.15 -9999 0 -0.62 27 27
cell adhesion -0.029 0.099 -9999 0 -0.54 15 15
ANGPTL3 0.005 0.026 -9999 0 -0.31 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.069 -9999 0 -0.64 5 5
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.066 -9999 0 -0.82 3 3
ITGB3 -0.011 0.14 -9999 0 -0.82 14 14
IGF1 -0.18 0.35 -9999 0 -0.8 118 118
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.1 -9999 0 -0.58 15 15
apoptosis 0.01 0.054 -9999 0 -0.82 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.018 0.1 -9999 0 -0.58 15 15
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.038 0.14 -9999 0 -0.61 22 22
CSF1 -0.001 0.11 -9999 0 -0.82 8 8
PIK3C2A -0.066 0.18 -9999 0 -0.61 46 46
PI4 Kinase/Pyk2 -0.054 0.14 -9999 0 -0.78 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.023 0.11 -9999 0 -0.55 20 20
FAK1/Vinculin 0.024 0.13 -9999 0 -0.48 8 8
alphaV beta3/Integrin/ppsTEM5 -0.018 0.1 -9999 0 -0.58 15 15
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.07 0.24 -9999 0 -0.76 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 -0.58 15 15
alphaV/beta3 Integrin/TGFBR2 -0.021 0.12 -9999 0 -0.6 17 17
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.01 0.077 -9999 0 -0.55 9 9
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.017 0.096 -9999 0 -0.54 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.021 0.1 -9999 0 -0.51 20 20
SDC1 0.011 0.03 -9999 0 -0.31 4 4
VAV3 0.026 0.1 -9999 0 -0.53 14 14
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
IRS1 -0.082 0.27 -9999 0 -0.82 55 55
FAK1/Paxillin 0.024 0.13 -9999 0 -0.48 8 8
cell migration 0.034 0.12 -9999 0 -0.43 8 8
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
PI3K -0.056 0.15 -9999 0 -0.44 60 60
SPP1 -0.083 0.2 -9999 0 -0.42 108 108
KDR 0.008 0.066 -9999 0 -0.82 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.054 -9999 0 -0.82 2 2
COL4A3 -0.013 0.14 -9999 0 -0.82 15 15
angiogenesis -0.084 0.18 -9999 0 -0.59 36 36
Rac1/GTP -0.014 0.084 -9999 0 -0.48 14 14
EDIL3 -0.023 0.14 -9999 0 -0.43 40 40
cell proliferation -0.021 0.12 -9999 0 -0.6 17 17
Angiopoietin receptor Tie2-mediated 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
AKT1 0.009 0.22 -10000 0 -0.96 21 21
NCK1/PAK1/Dok-R -0.029 0.091 -10000 0 -0.43 21 21
NCK1/Dok-R -0.069 0.24 -10000 0 -1.2 21 21
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
mol:beta2-estradiol -0.003 0.048 0.25 15 -10000 0 15
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 0.069 -10000 0 -0.33 11 11
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.061 0.23 -10000 0 -1.1 21 21
FN1 -0.22 0.15 -10000 0 -10000 0 0
PLD2 -0.001 0.28 -10000 0 -1.2 21 21
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
GRB14 -0.009 0.14 -10000 0 -0.82 13 13
ELK1 0.015 0.24 -10000 0 -1.1 21 21
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 21 21
CDKN1A -0.012 0.17 -10000 0 -0.64 21 21
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.069 0.24 -10000 0 -1.2 21 21
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.026 0.17 -10000 0 -0.69 21 21
PLG -0.01 0.28 -10000 0 -1.2 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.008 0.21 -10000 0 -0.92 21 21
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 -0.76 22 22
BMX -0.015 0.29 -10000 0 -1.3 21 21
ANGPT1 -0.04 0.3 -10000 0 -1.5 18 18
tube development -0.018 0.19 -10000 0 -0.73 21 21
ANGPT4 -0.06 0.23 -10000 0 -0.75 47 47
response to hypoxia 0 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.019 0.3 -10000 0 -1.3 21 21
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 -0.84 21 21
mol:L-citrulline 0.026 0.17 -10000 0 -0.69 21 21
AGTR1 -0.32 0.41 -10000 0 -0.82 194 194
MAPK14 -0.012 0.27 -10000 0 -1.2 21 21
Tie2/SHP2 -0.025 0.15 -10000 0 -1.4 5 5
TEK 0.015 0.17 -10000 0 -1.5 5 5
RPS6KB1 0.009 0.21 -10000 0 -0.92 21 21
Angiotensin II/AT1 -0.25 0.32 -10000 0 -0.64 194 194
Tie2/Ang1/GRB2 -0.006 0.28 -10000 0 -1.3 21 21
MAPK3 0.01 0.25 -10000 0 -1.1 21 21
MAPK1 0.01 0.25 -10000 0 -1.1 21 21
Tie2/Ang1/GRB7 -0.03 0.29 -10000 0 -1.3 21 21
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
MAPK8 -0.009 0.29 -10000 0 -1.2 22 22
PI3K -0.006 0.26 -10000 0 -1.1 21 21
FES -0.012 0.27 -10000 0 -1.2 21 21
Crk/Dok-R -0.069 0.24 -10000 0 -1.2 21 21
Tie2/Ang1/ABIN2 -0.006 0.28 -10000 0 -1.3 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.014 0.2 -10000 0 -0.84 21 21
STAT5A 0.014 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.009 0.21 -10000 0 -0.92 21 21
Tie2/Ang2 -0.041 0.24 -10000 0 -1 21 21
Tie2/Ang1 -0.013 0.3 -10000 0 -1.4 21 21
FOXO1 0.021 0.2 -10000 0 -0.85 21 21
ELF1 0.015 0.079 -10000 0 -0.85 4 4
ELF2 -0.004 0.27 -10000 0 -1.2 21 21
mol:Choline 0.002 0.26 -10000 0 -1.2 21 21
cell migration -0.024 0.056 -10000 0 -0.24 21 21
FYN -0.024 0.21 -10000 0 -0.84 21 21
DOK2 0 0.076 -10000 0 -0.38 16 16
negative regulation of cell cycle -0.008 0.16 -10000 0 -0.58 21 21
ETS1 0.015 0.045 -10000 0 -10000 0 0
PXN 0.022 0.18 -10000 0 -0.74 21 21
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.022 0.19 -10000 0 -0.79 21 21
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.09 0.28 -10000 0 -0.83 58 58
MAPKKK cascade 0.002 0.26 -10000 0 -1.2 21 21
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.01 0.28 -10000 0 -1.3 21 21
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.028 0.15 -10000 0 -0.61 21 21
mol:Phosphatidic acid 0.002 0.26 -10000 0 -1.2 21 21
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.026 0.17 -10000 0 -0.69 21 21
Rac1/GTP -0.052 0.18 -10000 0 -0.85 21 21
MMP2 -0.008 0.28 -10000 0 -1.3 21 21
FOXM1 transcription factor network

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
NFATC3 0.047 0.35 -9999 0 -0.92 14 14
PLK1 0.044 0.07 -9999 0 -10000 0 0
BIRC5 0.024 0.12 -9999 0 -1.6 1 1
HSPA1B 0.047 0.35 -9999 0 -0.92 14 14
MAP2K1 0.032 0.038 -9999 0 -10000 0 0
BRCA2 0.042 0.36 -9999 0 -0.98 17 17
FOXM1 0.035 0.39 -9999 0 -1 19 19
XRCC1 0.047 0.35 -9999 0 -0.92 14 14
FOXM1B/p19 -0.097 0.31 -9999 0 -0.9 26 26
Cyclin D1/CDK4 0.034 0.34 -9999 0 -0.86 14 14
CDC2 0.04 0.37 -9999 0 -0.91 19 19
TGFA 0.017 0.35 -9999 0 -0.85 17 17
SKP2 0.04 0.37 -9999 0 -0.98 17 17
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.047 0.35 -9999 0 -0.92 14 14
RB1 -0.054 0.11 -9999 0 -1.2 1 1
FOXM1C/SP1 0.031 0.37 -9999 0 -1 18 18
AURKB -0.003 0.12 -9999 0 -10000 0 0
CENPF 0.042 0.36 -9999 0 -0.95 14 14
CDK4 0.019 0.015 -9999 0 -10000 0 0
MYC 0.039 0.36 -9999 0 -0.92 21 21
CHEK2 0.032 0.038 -9999 0 -10000 0 0
ONECUT1 0.031 0.35 -9999 0 -0.89 16 16
CDKN2A -0.13 0.16 -9999 0 -0.31 206 206
LAMA4 0.047 0.35 -9999 0 -0.92 14 14
FOXM1B/HNF6 0.023 0.37 -9999 0 -1 16 16
FOS -0.19 0.66 -9999 0 -1.2 129 129
SP1 0.014 0.005 -9999 0 -10000 0 0
CDC25B 0.046 0.35 -9999 0 -0.92 14 14
response to radiation 0.015 0.035 -9999 0 -10000 0 0
CENPB 0.047 0.35 -9999 0 -0.92 14 14
CENPA 0.034 0.37 -9999 0 -0.96 19 19
NEK2 0.037 0.36 -9999 0 -0.95 16 16
HIST1H2BA 0.038 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 0.035 0.38 -9999 0 -1 14 14
CCNB2 0.044 0.36 -9999 0 -0.95 14 14
CCNB1 0.042 0.37 -9999 0 -0.96 14 14
ETV5 0.046 0.35 -9999 0 -0.92 15 15
ESR1 -0.002 0.44 -9999 0 -1.1 35 35
CCND1 0.037 0.34 -9999 0 -0.88 14 14
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 0.017 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.13 0.23 -9999 0 -0.88 22 22
GAS1 -0.13 0.61 -9999 0 -1.2 104 104
MMP2 0.037 0.38 -9999 0 -1.2 16 16
RB1/FOXM1C 0.045 0.34 -9999 0 -0.93 14 14
CREBBP 0.013 0 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.012 0.093 -10000 0 -0.35 6 6
epithelial cell differentiation -0.047 0.1 -10000 0 -0.47 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 0.006 0.076 -10000 0 -0.82 4 4
PRL 0.001 0.015 -10000 0 -0.31 1 1
neuron projection morphogenesis 0.004 0.14 -10000 0 -0.51 10 10
PTPRZ1 -0.016 0.13 -10000 0 -0.56 23 23
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.13 -10000 0 -0.45 46 46
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.043 0.17 -10000 0 -0.53 47 47
ADAM17 0.02 0.058 -10000 0 -0.82 2 2
ErbB4/ErbB4 -0.01 0.1 -10000 0 -0.52 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.045 0.17 -10000 0 -0.56 37 37
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.067 0.15 -10000 0 -0.5 46 46
GRIN2B -0.029 0.16 -10000 0 -0.47 46 46
ErbB4/ErbB2/betacellulin -0.036 0.11 -10000 0 -0.63 13 13
STAT1 0.006 0.049 -10000 0 -0.31 11 11
HBEGF -0.004 0.072 -10000 0 -0.31 25 25
PRLR -0.046 0.2 -10000 0 -0.6 46 46
E4ICDs/ETO2 -0.005 0.091 -10000 0 -0.49 3 3
axon guidance -0.001 0.087 -10000 0 -0.39 5 5
NEDD4 0.02 0.057 -10000 0 -0.81 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.044 0.15 -10000 0 -0.64 26 26
CBFA2T3 0.011 0.041 -10000 0 -0.57 2 2
ErbB4/ErbB2/HBEGF -0.029 0.061 -10000 0 -0.58 2 2
MAPK3 -0.005 0.15 -10000 0 -0.54 10 10
STAT1 (dimer) -0.007 0.09 -10000 0 -0.35 5 5
MAPK1 -0.005 0.15 -10000 0 -0.53 11 11
JAK2 0.012 0.038 -10000 0 -0.82 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.067 0.15 -10000 0 -0.5 46 46
NRG1 -0.035 0.2 -10000 0 -0.65 46 46
NRG3 -0.049 0.22 -10000 0 -0.82 36 36
NRG2 -0.083 0.26 -10000 0 -0.8 57 57
NRG4 0.008 0.036 -10000 0 -0.31 6 6
heart development -0.001 0.087 -10000 0 -0.39 5 5
neural crest cell migration -0.033 0.16 -10000 0 -0.49 46 46
ERBB2 0.028 0.043 -10000 0 -0.62 2 2
WWOX/E4ICDs -0.005 0.093 -10000 0 -0.95 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.036 0.084 -10000 0 -0.66 4 4
apoptosis 0.057 0.14 0.46 37 -10000 0 37
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.066 0.19 -10000 0 -0.55 56 56
ErbB4/ErbB2/epiregulin -0.078 0.088 -10000 0 -0.55 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.018 0.14 -10000 0 -0.65 14 14
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.06 0.12 -10000 0 -0.47 27 27
MDM2 0.001 0.087 -10000 0 -0.46 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.062 0.15 -10000 0 -0.5 46 46
STAT5A 0.008 0.082 -10000 0 -0.41 3 3
ErbB4/EGFR/neuregulin 1 beta -0.071 0.16 -10000 0 -0.52 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 -0.43 1 1
STAT5A (dimer) -0.05 0.11 -10000 0 -0.51 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.08 -10000 0 -0.41 3 3
LRIG1 -0.001 0.11 -10000 0 -0.82 8 8
EREG -0.14 0.16 -10000 0 -0.31 224 224
BTC -0.009 0.14 -10000 0 -0.82 13 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.087 -10000 0 -0.4 5 5
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 -0.51 2 2
glial cell differentiation 0.032 0.063 0.42 1 -10000 0 1
WWOX 0.012 0.038 -10000 0 -0.82 1 1
cell proliferation -0.023 0.17 -10000 0 -0.46 53 53
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 -0.018 0.087 -9999 0 -0.48 16 16
RGS9BP -0.037 0.2 -9999 0 -0.82 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.067 0.25 -9999 0 -0.81 47 47
mol:Na + -0.021 0.057 -9999 0 -10000 0 0
mol:ADP -0.045 0.19 -9999 0 -0.64 46 46
GNAT2 0.009 0.022 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.092 0.21 -9999 0 -0.56 79 79
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 0.062 -9999 0 -0.3 2 2
Cone PDE6 -0.08 0.18 -9999 0 -0.49 79 79
Cone Metarhodopsin II -0.05 0.15 -9999 0 -0.52 46 46
Na + (4 Units) -0.025 0.057 -9999 0 -0.3 2 2
GNAT2/GDP -0.08 0.18 -9999 0 -0.48 79 79
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.015 -9999 0 -10000 0 0
Cone Transducin -0.019 0.092 -9999 0 -0.5 16 16
SLC24A2 -0.009 0.064 -9999 0 -0.31 20 20
GNB3/GNGT2 -0.023 0.11 -9999 0 -0.63 16 16
GNB3 -0.013 0.15 -9999 0 -0.79 16 16
GNAT2/GTP -0.001 0.014 -9999 0 -0.21 2 2
CNGA3 -0.027 0.11 -9999 0 -0.31 59 59
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 -0.092 0.21 -9999 0 -0.56 79 79
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 + -0.009 0.064 -9999 0 -0.31 20 20
RGS9 -0.078 0.26 -9999 0 -0.8 54 54
PDE6C 0.003 0.016 -9999 0 -0.31 1 1
GNGT2 0.01 0.046 -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
Aurora C 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
INCENP 0.01 0.054 -9999 0 -0.82 2 2
Aurora C/Aurora B/INCENP -0.039 0.077 -9999 0 -0.65 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.01 0.02 -9999 0 -10000 0 0
AURKB -0.058 0.14 -9999 0 -0.31 105 105
AURKC -0.001 0.067 -9999 0 -0.31 21 21
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 0.25 -9999 0 -0.67 74 74
IL1A -0.056 0.23 -9999 0 -0.79 41 41
IL1B -0.034 0.19 -9999 0 -0.64 40 40
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -0.43 2 2
IL1R2 -0.082 0.24 -9999 0 -0.59 76 76
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.069 -9999 0 -0.3 1 1
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.004 0.085 -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 0.067 0.028 -9999 0 -10000 0 0
JUN -0.073 0.22 -9999 0 -0.43 120 120
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.068 0.14 -9999 0 -0.47 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.074 0.14 -9999 0 -0.51 38 38
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.067 0.13 -9999 0 -0.48 38 38
IL1 beta fragment/IL1R1/IL1RAP -0.078 0.15 -9999 0 -0.53 39 39
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 0.021 0.11 -9999 0 -0.52 17 17
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.045 0.12 -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 0.054 -9999 0 -0.82 2 2
PI3K -0.004 0.05 -9999 0 -0.63 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.088 -9999 0 -0.34 8 8
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.078 0.15 -9999 0 -0.53 39 39
IL1 beta/IL1R2 -0.1 0.23 -9999 0 -0.61 73 73
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.028 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA -0.058 0.12 -9999 0 -0.55 8 8
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.07 0.14 -9999 0 -0.48 44 44
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.016 0.1 -9999 0 -0.34 38 38
IL1 alpha/IL1R1/IL1RAP -0.085 0.16 -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 -0.072 0.14 -9999 0 -0.31 126 126
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.054 0.12 -9999 0 -0.5 12 12
CASP1 0.008 0.06 -9999 0 -0.52 5 5
IL1RN/IL1R2 -0.11 0.22 -9999 0 -0.63 60 60
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.07 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 0.003 0.082 -9999 0 -0.34 4 4
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
IL1RN -0.055 0.17 -9999 0 -0.38 84 84
TRAF6/TAK1/TAB1/TAB2 -0.002 0.03 -9999 0 -0.46 2 2
MAP2K6 0.022 0.074 -9999 0 -0.44 12 12
Regulation of nuclear SMAD2/3 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
EP300 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.004 0.076 -10000 0 -0.82 4 4
SMAD3/SMAD4/ER alpha -0.052 0.14 -10000 0 -0.58 24 24
AKT1 0.008 0.011 -10000 0 -10000 0 0
GSC -0.21 0.56 -10000 0 -1.6 71 71
NKX2-5 0.002 0.029 -10000 0 -0.31 4 4
muscle cell differentiation 0.026 0.051 0.44 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.005 0.08 -10000 0 -10000 0 0
SMAD4 -0.012 0.06 -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 -0.55 5 5
SMAD3/SMAD4/VDR 0.01 0.044 -10000 0 -10000 0 0
MYC 0 0.14 -10000 0 -0.82 13 13
CDKN2B -0.076 0.14 -10000 0 -10000 0 0
AP1 -0.26 0.51 -10000 0 -0.94 151 151
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.056 -10000 0 -0.71 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.063 -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 21 21
SMAD3/SMAD4/GR -0.017 0.045 -10000 0 -10000 0 0
GATA3 -0.032 0.19 -10000 0 -0.78 27 27
SKI/SIN3/HDAC complex/NCoR1 0.04 0.03 -10000 0 -10000 0 0
MEF2C/TIF2 -0.046 0.17 -10000 0 -0.59 22 22
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 0.066 -10000 0 -0.82 3 3
RUNX2 -0.076 0.15 -10000 0 -0.32 128 128
RUNX3 -0.007 0.12 -10000 0 -0.6 16 16
RUNX1 -0.13 0.16 -10000 0 -0.31 211 211
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 0.023 0.073 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.039 0.094 -10000 0 -0.48 2 2
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.004 -10000 0 -10000 0 0
SERPINE1 0.008 0.1 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.039 0.12 -10000 0 -0.59 18 18
SMAD3/SMAD4/ATF3 -0.16 0.26 -10000 0 -0.63 113 113
SAP30 0.01 0.038 -10000 0 -0.83 1 1
Cbp/p300/PIAS3 0.033 0.045 -10000 0 -10000 0 0
JUN -0.25 0.5 -10000 0 -0.93 151 151
SMAD3/SMAD4/IRF7 -0.017 0.045 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.002 0.092 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.066 0.095 0.46 4 -10000 0 4
DLX1 -0.032 0.19 -10000 0 -0.82 26 26
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.23 0.4 -10000 0 -0.89 128 128
SMAD3/SMAD4/Max -0.017 0.045 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.042 -10000 0 -0.55 2 2
ZBTB17 0.021 0.012 -10000 0 -10000 0 0
LAMC1 0.026 0.053 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.017 0.044 -10000 0 -10000 0 0
IRF7 0.014 0.016 -10000 0 -10000 0 0
ESR1 -0.048 0.19 -10000 0 -0.53 54 54
HNF4A -0.004 0.045 -10000 0 -0.31 10 10
MEF2C 0.003 0.099 -10000 0 -1 1 1
SMAD2-3/SMAD4 -0.032 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.025 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 0.018 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 0.054 -10000 0 -0.82 2 2
GCN5L2 0.006 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.012 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.18 0.1 -10000 0 -0.68 9 9
SMAD2 -0.003 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 -0.36 13 13
SMAD2/SMAD2/SMAD4 0.014 0.028 -10000 0 -10000 0 0
NCOR1 0.012 0.004 -10000 0 -10000 0 0
NCOA2 -0.063 0.24 -10000 0 -0.82 44 44
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 0.013 0.077 -10000 0 -10000 0 0
IFNB1 0.014 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.1 -10000 0 -1 1 1
CITED1 -0.26 0.14 -10000 0 -0.82 5 5
SMAD2-3/SMAD4/ARC105 -0.022 0.046 -10000 0 -10000 0 0
RBL1 -0.008 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 -0.59 101 101
MYC/MIZ-1 0.013 0.11 -10000 0 -0.63 13 13
SMAD3/SMAD4 0.064 0.1 0.32 39 -0.35 1 40
IL10 -0.027 0.19 -10000 0 -0.62 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 -0.51 25 25
CDK4 0.019 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.01 -10000 0 -10000 0 0
ATF3 -0.19 0.35 -10000 0 -0.79 120 120
SMAD3/SMAD4/SP1 -0.016 0.054 -10000 0 -10000 0 0
FOXG1 -0.003 0.072 -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 0.003 0.098 -10000 0 -1 1 1
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.049 0.14 -10000 0 -0.6 26 26
MYOD1 -0.002 0.029 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.052 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.052 0.14 -10000 0 -0.54 30 30
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.038 -10000 0 -0.82 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.075 0.11 -10000 0 -0.55 11 11
SMAD3/SMAD4/SP1-3 0.007 0.057 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.015 0.022 -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 -0.6 202 202
AR -0.34 0.41 -10000 0 -0.82 202 202
negative regulation of cell growth -0.04 0.13 -10000 0 -0.46 8 8
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 -0.013 0.067 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.067 -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 -0.96 151 151
SMAD3/SMAD4/RUNX2 -0.066 0.096 -10000 0 -0.47 4 4
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.018 0.16 -10000 0 -0.82 18 18
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.041 0.12 -9999 0 -0.42 46 46
Syndecan-3/Neurocan -0.035 0.12 -9999 0 -0.47 35 35
POMC -0.16 0.34 -9999 0 -0.81 102 102
EGFR 0.006 0.076 -9999 0 -0.82 4 4
Syndecan-3/EGFR -0.004 0.043 -9999 0 -0.46 4 4
AGRP -0.004 0.06 -9999 0 -0.31 17 17
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 -0.051 0.22 -9999 0 -0.77 39 39
long-term memory 0 0.005 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.039 0.081 -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 0.039 -9999 0 -0.31 7 7
SRC 0.013 0.015 -9999 0 -0.31 1 1
PTN -0.067 0.25 -9999 0 -0.81 47 47
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis -0.069 0.15 -9999 0 -0.41 80 80
Syndecan-3/AgRP -0.005 0.023 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.006 0.025 -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 0.08 -9999 0 -0.46 10 10
IL8 -0.081 0.18 -9999 0 -0.36 123 123
Syndecan-3/Fyn/Cortactin -0.001 0.006 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.14 0.26 -9999 0 -0.64 99 99
Gamma Secretase 0 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.25 0.39 -10000 0 -0.82 152 152
HRAS 0.012 0.021 -10000 0 -0.31 2 2
EGFR 0.006 0.076 -10000 0 -0.82 4 4
AKT 0.018 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 0.066 -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 -0.011 0.13 -10000 0 -0.67 17 17
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 -0.061 0.099 -10000 0 -0.26 43 43
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.024 0.19 1 -0.17 1 2
PI3K -0.041 0.096 0.23 1 -0.22 50 51
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.024 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
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.001 0.078 -9999 0 -10000 0 0
STMN1 -0.02 0.093 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.025 0.11 -9999 0 -0.32 41 41
Chromosomal passenger complex/Cul3 protein complex 0.007 0.071 -9999 0 -0.29 14 14
BIRC5 -0.017 0.1 -9999 0 -0.33 42 42
DES -0.38 0.3 -9999 0 -0.61 295 295
Aurora C/Aurora B/INCENP -0.015 0.088 -9999 0 -0.65 2 2
Aurora B/TACC1 -0.02 0.08 -9999 0 -0.71 1 1
Aurora B/PP2A -0.025 0.09 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.025 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.049 0.15 -9999 0 -0.39 59 59
Cul3 protein complex -0.018 0.088 -9999 0 -0.55 12 12
KIF2C 0 0.042 -9999 0 -0.14 4 4
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.041 0.12 -9999 0 -0.31 81 81
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.025 0.09 -9999 0 -10000 0 0
SEPT1 0.008 0.042 -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 -0.006 0.054 -9999 0 -10000 0 0
AURKB -0.049 0.14 -9999 0 -0.31 105 105
AURKC -0.001 0.067 -9999 0 -0.31 21 21
CDCA8 0.01 0.027 -9999 0 -0.33 3 3
cytokinesis -0.066 0.082 -9999 0 -0.42 6 6
Aurora B/Septin1 -0.026 0.1 -9999 0 -0.44 7 7
AURKA 0.012 0.002 -9999 0 -10000 0 0
INCENP 0.009 0.055 -9999 0 -0.84 2 2
KLHL13 -0.017 0.14 -9999 0 -0.55 26 26
BUB1 -0.1 0.16 -9999 0 -0.32 167 167
hSgo1/Aurora B/Survivin -0.026 0.12 -9999 0 -0.35 42 42
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.03 0.072 -9999 0 -0.35 4 4
SGOL1 0.001 0.062 -9999 0 -0.31 18 18
CENPA -0.007 0.069 -9999 0 -0.21 26 26
NCAPG -0.018 0.097 -9999 0 -0.31 47 47
Aurora B/HC8 Proteasome -0.025 0.09 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.025 0.09 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.034 0.12 -9999 0 -0.31 70 70
NPM1 -0.011 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 -0.025 0.09 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.035 0.08 -9999 0 -0.35 18 18
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.011 0.048 -9999 0 -10000 0 0
MYLK -0.006 0.054 -9999 0 -10000 0 0
KIF23 -0.004 0.074 -9999 0 -0.32 25 25
VIM -0.02 0.092 -9999 0 -10000 0 0
RACGAP1 0.013 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.011 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.013 0.083 -9999 0 -0.25 26 26
Chromosomal passenger complex/EVI5 0.011 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
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.004 0.076 -10000 0 -0.36 7 7
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 0.042 0.077 0.23 15 -0.28 10 25
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 -0.066 0.23 -10000 0 -0.63 66 66
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 0.025 -10000 0 -0.55 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.03 0.11 -10000 0 -0.31 62 62
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 -0.038 0.1 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.042 0.081 0.24 15 -0.3 10 25
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.028 0 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 310 310
LNPEP -0.014 0.15 -10000 0 -0.82 16 16
YWHAE 0.013 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.065 0.082 -10000 0 -0.34 22 22
NT3 (dimer)/TRKC -0.09 0.2 -10000 0 -0.68 40 40
NT3 (dimer)/TRKB -0.086 0.18 -10000 0 -0.58 50 50
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.029 -10000 0 -0.33 3 3
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.6 21 21
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.002 0.062 -10000 0 -0.31 18 18
NTRK2 0.005 0.085 -10000 0 -0.82 5 5
NTRK3 -0.056 0.17 -10000 0 -0.39 83 83
NT-4/5 (dimer)/TRKB -0.068 0.16 -10000 0 -0.58 39 39
neuron apoptosis 0.04 0.092 0.42 15 -10000 0 15
SHC 2-3/Grb2 -0.043 0.1 -10000 0 -0.48 13 13
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.03 0.093 -10000 0 -0.64 6 6
SHC3 -0.047 0.1 -10000 0 -0.55 12 12
STAT3 (dimer) 0.018 0.024 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.087 0.18 -10000 0 -0.57 48 48
RIN/GDP -0.01 0.063 -10000 0 -0.28 2 2
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.033 0.093 -10000 0 -0.42 23 23
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.026 0.044 -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 0.16 -10000 0 -0.64 25 25
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.018 0.079 -10000 0 -0.52 9 9
TRKA/NEDD4-2 -0.008 0.038 -10000 0 -10000 0 0
ELMO1 -0.31 0.41 -10000 0 -0.82 188 188
RhoG/GTP/ELMO1/DOCK1 -0.22 0.28 -10000 0 -0.56 189 189
NGF 0.006 0.071 -10000 0 -0.57 6 6
HRAS 0.012 0.021 -10000 0 -0.31 2 2
DOCK1 0.006 0.076 -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 -0.21 0.23 -10000 0 -0.47 205 205
mol:GDP -0.016 0.09 -10000 0 -0.42 3 3
NGF (dimer) 0.006 0.07 -10000 0 -0.57 6 6
RhoG/GDP -0.25 0.31 -10000 0 -0.64 188 188
RIT1/GDP -0.004 0.063 -10000 0 -0.3 1 1
TIAM1 -0.17 0.16 -10000 0 -0.82 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.022 0.11 -10000 0 -0.61 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 0.025 -10000 0 -0.55 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 -0.62 48 48
RAP1/GDP -0.018 0.043 -10000 0 -10000 0 0
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.014 0.14 -10000 0 -0.6 21 21
ubiquitin-dependent protein catabolic process -0.01 0.053 -10000 0 -0.55 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 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.067 0.15 -10000 0 -0.47 52 52
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.037 -10000 0 -10000 0 0
STAT3 0.018 0.024 -10000 0 -10000 0 0
axon guidance -0.065 0.15 -10000 0 -0.45 52 52
MAPK3 0.015 0.078 -10000 0 -0.5 8 8
MAPK1 0.015 0.078 -10000 0 -0.5 8 8
CDC42/GDP -0.004 0.063 -10000 0 -0.28 2 2
NTF3 -0.05 0.21 -10000 0 -0.62 48 48
NTF4 -0.021 0.16 -10000 0 -0.64 25 25
NGF (dimer)/TRKA/FAIM -0.01 0.053 -10000 0 -0.55 3 3
PI3K -0.004 0.05 -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 -0.46 29 29
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.053 0.18 -10000 0 -0.59 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 -0.3 1 1
NGF (dimer)/TRKA/GRIT -0.011 0.055 -10000 0 -0.56 3 3
neuron projection morphogenesis 0 0.095 -10000 0 -0.52 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.053 -10000 0 -0.55 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.063 0.19 -10000 0 -0.42 84 84
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.077 -10000 0 -0.35 18 18
RAS family/GTP/PI3K 0.03 0.032 -10000 0 -0.37 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 0.057 -10000 0 -0.61 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.038 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.02 0.1 -10000 0 -0.56 15 15
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.043 -10000 0 -0.47 3 3
MATK 0 0.093 -10000 0 -0.53 12 12
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.015 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.036 0.099 -10000 0 -0.45 23 23
Rac1/GTP -0.19 0.15 -10000 0 -0.36 192 192
FRS2 family/SHP2/CRK family -0.001 0.021 -10000 0 -0.46 1 1
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.018 0.12 -10000 0 -0.79 11 11
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 0.1 -10000 0 -0.82 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.007 0.066 -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 -0.006 0.12 -10000 0 -0.82 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.054 -10000 0 -0.34 1 1
NICD/RBPSUH -0.017 0.11 -10000 0 -0.74 11 11
WIF1 -0.033 0.1 -10000 0 -0.31 58 58
NOTCH1 -0.018 0.12 -10000 0 -0.77 11 11
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.009 0.082 -10000 0 -0.31 33 33
DKK1 -0.042 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 0.036 -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 -0.21 0.37 -10000 0 -0.82 128 128
JUN -0.18 0.35 -10000 0 -0.82 109 109
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 -0.013 0.14 -10000 0 -0.73 17 17
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.023 0.12 -10000 0 -0.62 18 18
apoptosis -0.14 0.26 -10000 0 -0.52 140 140
Delta 1/NOTCHprecursor -0.018 0.12 -10000 0 -0.76 11 11
DLL1 0.011 0.041 -10000 0 -0.57 2 2
PPARD 0.024 0.017 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.001 0.06 -10000 0 -0.51 3 3
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 0.019 0.043 -10000 0 -10000 0 0
WNT1 0.01 0.021 -10000 0 -0.31 2 2
Axin1/APC/beta catenin 0.043 0.052 -10000 0 -0.67 1 1
DKK2 -0.026 0.17 -10000 0 -0.66 28 28
NOTCH1 precursor/DVL1 -0.012 0.098 -10000 0 -0.65 11 11
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.024 0.12 -10000 0 -0.64 18 18
PPP2R5D 0.011 0.064 0.37 14 -10000 0 14
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.016 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 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
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 0.064 -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 0.041 -9999 0 -0.15 29 29
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.045 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.015 0.064 -9999 0 -0.23 9 9
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.018 0.094 -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 -0.032 0.097 -9999 0 -0.38 29 29
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.16 0.23 -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 0.045 -9999 0 -10000 0 0
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma -0.062 0.16 -10000 0 -0.48 62 62
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.054 -10000 0 -0.21 31 31
GNB1/GNG2 -0.001 0.025 -10000 0 -0.56 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 -0.066 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 0.015 0.039 0.12 61 -10000 0 61
GNAL -0.093 0.28 -10000 0 -0.82 61 61
GNG2 0.012 0.038 -10000 0 -0.82 1 1
CRH -0.013 0.079 -10000 0 -0.31 31 31
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.063 -10000 0 -0.46 9 9
MAPK11 0.009 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.003 0.093 -9999 0 -0.82 6 6
CDKN1A -0.013 0.088 -9999 0 -10000 0 0
PRL-3/alpha Tubulin -0.016 0.054 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.11 -9999 0 -0.65 9 9
AGT -0.019 0.13 -9999 0 -0.82 9 9
CCNA2 -0.062 0.2 -9999 0 -0.59 4 4
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.11 0.27 -9999 0 -0.63 102 102
CDK2/Cyclin E1 0.004 0.077 -9999 0 -10000 0 0
MAPK3 0.007 0.061 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.007 0.061 -9999 0 -10000 0 0
PTP4A1 -0.071 0.21 -9999 0 -0.48 102 102
PTP4A3 -0.012 0.088 -9999 0 -0.31 38 38
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.007 0.061 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1 -0.016 0.092 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.067 0.2 -9999 0 -0.45 102 102
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.012 0.04 -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 -0.014 0.098 -9999 0 -0.26 13 13
PRL-1/alpha Tubulin -0.061 0.2 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.024 0.089 -9999 0 -0.66 6 6
ROCK1 -0.014 0.099 -9999 0 -0.27 13 13
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.071 0.21 -9999 0 -0.48 102 102
ATF5 0 0.065 -9999 0 -0.31 20 20
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.016 0.052 -9999 0 -0.55 4 4
ADCY5 -0.058 0.2 -9999 0 -0.56 65 65
ADCY6 0.016 0.052 -9999 0 -0.55 4 4
ADCY7 0.016 0.052 -9999 0 -0.55 4 4
ADCY1 0.009 0.078 -9999 0 -0.57 8 8
ADCY2 -0.041 0.18 -9999 0 -0.57 46 46
ADCY3 0.016 0.052 -9999 0 -0.55 4 4
ADCY8 -0.12 0.099 -9999 0 -0.7 4 4
PRKCE 0.007 0.059 -9999 0 -0.64 4 4
ADCY9 0.016 0.052 -9999 0 -0.55 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.056 0.1 -9999 0 -0.37 31 31
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.027 0.16 -9999 0 -0.44 64 64
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 -0.05 0.12 -9999 0 -0.75 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.01 0.037 -9999 0 -0.65 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -0.3 2 2
CaM/Ca2+ -0.056 0.14 -9999 0 -0.4 64 64
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.02 0.16 -9999 0 -0.41 64 64
AKT1 -0.003 0.15 -9999 0 -0.56 4 4
MAP2K1 -0.006 0.15 -9999 0 -0.52 5 5
MAP3K11 -0.017 0.16 -9999 0 -0.41 64 64
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.067 -9999 0 -0.64 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 0.16 -9999 0 -0.46 63 63
CEBPB 0.016 0.18 -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 -0.02 0.16 -9999 0 -0.41 64 64
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.11 0.28 -9999 0 -0.72 78 78
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
STAT1 (dimer)/PIAS1 -0.011 0.15 -9999 0 -0.48 5 5
CEBPB/PTGES2/Cbp/p300 -0.035 0.083 -9999 0 -0.44 5 5
mol:Ca2+ -0.06 0.15 -9999 0 -0.43 64 64
MAPK3 0.009 0.14 -9999 0 -0.53 5 5
STAT1 (dimer) -0.031 0.081 -9999 0 -0.42 2 2
MAPK1 0.009 0.14 -9999 0 -0.53 5 5
JAK2 0.008 0.043 -9999 0 -0.88 1 1
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 0.015 0.18 -9999 0 -0.66 24 24
SMAD7 0.041 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.05 0.12 -9999 0 -0.76 1 1
PI3K -0.057 0.14 -9999 0 -0.52 8 8
IFNG -0.11 0.28 -9999 0 -0.72 78 78
apoptosis 0.012 0.13 -9999 0 -0.45 24 24
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.004 0.068 -9999 0 -0.31 22 22
CAMK2B 0.005 0.085 -9999 0 -0.82 5 5
FRAP1 -0.001 0.14 -9999 0 -0.52 4 4
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 -0.024 0.061 -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 -0.055 0.13 -9999 0 -0.48 5 5
SOCS1 0.001 0.075 -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 0.041 0.058 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.055 0.14 -9999 0 -0.5 8 8
RAP1/GDP -0.042 0.1 -9999 0 -0.61 1 1
CBL -0.018 0.16 -9999 0 -0.41 64 64
MAP3K1 -0.017 0.16 -9999 0 -0.41 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 -0.024 0.061 -9999 0 -0.3 2 2
PTPN11 -0.027 0.16 -9999 0 -0.43 64 64
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.014 0.12 -9999 0 -0.44 30 30
CCNA2 0.007 0.044 -9999 0 -0.31 9 9
PIK3CA 0.009 0.066 -9999 0 -0.82 3 3
JAK3 -0.067 0.14 -9999 0 -0.31 120 120
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 0.017 0.15 -9999 0 -0.56 19 19
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.022 0 -9999 0 -10000 0 0
IL2RA -0.043 0.25 -9999 0 -0.98 30 30
IL2RB -0.014 0.13 -9999 0 -0.51 26 26
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.046 0.19 -9999 0 -0.55 52 52
G1/S transition of mitotic cell cycle 0.039 0.055 -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 -0.44 25 25
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.008 0.066 -9999 0 -0.82 3 3
CCND3 0.028 0.13 -9999 0 -0.64 7 7
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.34 -9999 0 -0.82 102 102
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 0.041 -9999 0 -0.51 3 3
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.13 0.16 -9999 0 -0.31 206 206
ARNT/IPAS -0.13 0.26 -9999 0 -0.63 102 102
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 0.089 -9999 0 -0.54 12 12
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.017 -9999 0 -10000 0 0
VHL 0.008 0.066 -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 0.054 -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 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.004 0.11 0.57 14 -10000 0 14
PI3K Class IB/PDE3B -0.004 0.11 -10000 0 -0.57 14 14
PDE3B -0.004 0.11 -10000 0 -0.57 14 14
Ceramide signaling pathway

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
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.004 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 -0.037 0.19 -10000 0 -0.68 35 35
BAX -0.005 0.019 -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 -0.007 0.097 -10000 0 -0.26 58 58
RB1 -0.018 0.046 -10000 0 -0.5 1 1
FADD/Caspase 8 0.008 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 -0.52 2 2
EGF -0.11 0.29 -10000 0 -0.78 74 74
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 0.03 -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 -0.1 0.16 -10000 0 -0.39 113 113
BID -0.018 0.093 -10000 0 -0.4 11 11
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 -0.48 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.047 -10000 0 -0.48 2 2
Cathepsin D/ceramide -0.018 0.041 -10000 0 -0.16 1 1
FADD -0.004 0.14 -10000 0 -0.7 11 11
KSR1 -0.019 0.053 -10000 0 -0.55 2 2
MAPK8 -0.009 0.056 -10000 0 -0.31 9 9
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 -0.8 118 118
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 0.029 -10000 0 -0.63 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.087 0.19 -10000 0 -0.42 113 113
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 0.03 -10000 0 -0.63 1 1
RelA/NF kappa B1 -0.001 0.029 -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 -0.013 0.15 -10000 0 -0.75 11 11
TNFR1A/BAG4/TNF-alpha -0.069 0.18 -10000 0 -0.55 59 59
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.002 0.048 -10000 0 -0.49 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 26 -10000 0 26
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
TNFR1A/BAG4 -0.001 0.029 -10000 0 -0.63 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.068 0.18 -10000 0 -0.55 58 58
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.08 -10000 0 -0.33 11 11
MAP2K2 -0.002 0.048 -10000 0 -0.49 2 2
SMPD3 -0.012 0.12 -10000 0 -0.3 63 63
TNF -0.092 0.27 -10000 0 -0.82 58 58
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.023 0.11 0.28 68 -10000 0 68
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 26 -10000 0 26
BCL2 -0.047 0.22 -10000 0 -0.82 35 35
Signaling events mediated by HDAC Class III

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
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 0.63 1 -10000 0 1
CDKN1A -0.007 0.039 -10000 0 -10000 0 0
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
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 0.03 -10000 0 -0.31 4 4
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.02 -10000 0 -10000 0 0
PPARGC1A -0.35 0.42 -10000 0 -0.82 211 211
FHL2 -0.054 0.23 -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 0.001 0.027 -10000 0 -0.56 1 1
SIRT1 0.001 0.04 -10000 0 -0.82 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.028 -10000 0 -0.55 1 1
SIRT1/Histone H1b -0.005 0.051 -10000 0 -0.33 10 10
apoptosis -0.001 0.029 0.55 1 -10000 0 1
SIRT1/PGC1A -0.24 0.28 -10000 0 -0.56 211 211
p53/SIRT1 0.005 0.045 -10000 0 -0.63 1 1
SIRT1/FOXO4 0.001 0.028 -10000 0 -0.53 1 1
FOXO1/FHL2/SIRT1 -0.04 0.14 -10000 0 -0.51 40 40
HIST1H1E 0.015 0.054 -10000 0 -0.37 9 9
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 0.003 0.013 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.001 0.029 -10000 0 -0.55 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 0.036 -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 -0.56 1 1
IL2 signaling events mediated by PI3K

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
BCL2L1 0.011 0.12 -10000 0 -0.88 2 2
UGCG -0.04 0.17 -10000 0 -0.82 21 21
AKT1/mTOR/p70S6K/Hsp90/TERT 0.02 0.13 -10000 0 -0.41 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.019 0.18 -10000 0 -0.8 21 21
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.06 0.14 -10000 0 -0.46 35 35
FRAP1 0.001 0.2 -10000 0 -0.54 35 35
FOXO3 0.019 0.17 -10000 0 -0.6 18 18
AKT1 0.01 0.18 -10000 0 -0.61 22 22
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 -0.006 0.023 -10000 0 -10000 0 0
SGMS1 -0.006 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 0.047 -10000 0 -0.56 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.001 0.16 -10000 0 -0.51 26 26
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.053 -10000 0 -0.64 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 -0.066 0.14 -10000 0 -0.31 120 120
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 -0.016 0.2 -10000 0 -1.3 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.007 0.16 -10000 0 -0.55 25 25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.16 -10000 0 -0.53 25 25
Rac1/GDP 0.024 0.043 -10000 0 -0.51 3 3
T cell proliferation 0.017 0.15 -10000 0 -0.5 22 22
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 22 22
NF kappa B1 p50/RelA -0.058 0.14 -10000 0 -0.52 20 20
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.001 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 -0.048 0.2 -10000 0 -0.58 49 49
IL2RB -0.013 0.13 -10000 0 -0.51 26 26
TERT 0 0.033 -10000 0 -0.31 5 5
E2F1 -0.005 0.076 -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 0.039 -10000 0 -0.83 1 1
IL2RG -0.045 0.19 -10000 0 -0.55 52 52
actin cytoskeleton organization 0.017 0.15 -10000 0 -0.5 22 22
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.066 -10000 0 -0.83 3 3
Rac1/GTP 0.031 0.043 -10000 0 -0.49 3 3
LCK -0.008 0.11 -10000 0 -0.43 25 25
BCL2 -0.025 0.28 -10000 0 -0.84 45 45
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.044 -9999 0 -0.93 1 1
VEGFR1 homodimer/NRP1 -0.002 0.043 -9999 0 -0.94 1 1
mol:DAG -0.012 0.16 -9999 0 -0.49 49 49
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.068 -9999 0 -0.78 3 3
CaM/Ca2+ -0.004 0.15 -9999 0 -0.46 49 49
HIF1A 0.021 0.018 -9999 0 -0.38 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.009 0.17 -9999 0 -1.1 2 2
PLCG1 -0.012 0.16 -9999 0 -0.5 49 49
NOS3 0.017 0.15 -9999 0 -0.91 1 1
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.018 0.15 -9999 0 -0.85 1 1
FLT1 0.031 0.049 -9999 0 -1 1 1
PGF -0.071 0.25 -9999 0 -0.81 49 49
VEGFR1 homodimer/NRP2/VEGFR121 -0.015 0.075 -9999 0 -0.77 3 3
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
eNOS/Hsp90 0.025 0.14 -9999 0 -0.81 1 1
endothelial cell proliferation -0.028 0.19 -9999 0 -0.52 50 50
mol:Ca2+ -0.012 0.16 -9999 0 -0.49 49 49
MAPK3 -0.016 0.18 -9999 0 -1 2 2
MAPK1 -0.016 0.18 -9999 0 -1 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.071 0.25 -9999 0 -0.81 49 49
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.009 0.14 -9999 0 -0.82 13 13
VEGFA homodimer 0.008 0.066 -9999 0 -0.82 3 3
VEGFR1 homodimer/VEGFA homodimer 0.029 0.075 -9999 0 -0.82 3 3
platelet activating factor biosynthetic process -0.007 0.17 -9999 0 -0.96 2 2
PI3K -0.05 0.15 -9999 0 -0.47 51 51
PRKCA -0.025 0.19 -9999 0 -0.47 69 69
PRKCB -0.022 0.17 -9999 0 -0.47 53 53
VEGFR1 homodimer/PLGF homodimer -0.025 0.18 -9999 0 -0.55 49 49
VEGFA 0.008 0.066 -9999 0 -0.82 3 3
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.012 0.16 -9999 0 -0.49 49 49
RASA1 0.041 0.041 -9999 0 -0.86 1 1
NRP2 -0.012 0.088 -9999 0 -0.31 38 38
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 0.012 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 -0.05 0.15 -9999 0 -0.47 51 51
mol:L-citrulline 0.018 0.15 -9999 0 -0.85 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.005 0.064 -9999 0 -0.73 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.005 0.068 -9999 0 -0.77 3 3
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.047 0.14 -9999 0 -1.2 1 1
PDPK1 0 0.16 -9999 0 -1.2 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.006 0.084 -9999 0 -0.9 3 3
mol:NADP 0.018 0.15 -9999 0 -0.85 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.004 0.062 -9999 0 -0.71 3 3
VEGFR1 homodimer/NRP2 0.018 0.066 -9999 0 -0.93 1 1
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.052 0.14 -9999 0 -0.44 57 57
TC10/GTP -0.003 0.033 -9999 0 -0.42 3 3
Insulin Receptor/Insulin/IRS1/Shp2 -0.06 0.17 -9999 0 -0.52 55 55
HRAS 0.012 0.021 -9999 0 -0.31 2 2
APS homodimer 0.013 0.015 -9999 0 -0.31 1 1
GRB14 -0.009 0.14 -9999 0 -0.82 13 13
FOXO3 -0.025 0.11 -9999 0 -0.72 11 11
AKT1 -0.01 0.16 -9999 0 -0.89 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 0.008 0.066 -9999 0 -0.82 3 3
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.038 0 -9999 0 -10000 0 0
CAV1 -0.043 0.18 -9999 0 -0.48 68 68
CBL/APS/CAP/Crk-II/C3G -0.003 0.037 -9999 0 -0.46 3 3
Insulin Receptor/Insulin/IRS1/NCK2 -0.059 0.16 -9999 0 -0.51 55 55
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.054 0.15 -9999 0 -0.46 57 57
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.005 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 -0.053 0.13 -9999 0 -0.78 2 2
HRAS/GTP -0.048 0.12 -9999 0 -0.5 3 3
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.054 0.15 -9999 0 -0.48 55 55
PRKCI -0.014 0.034 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.062 0.16 -9999 0 -1 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.055 0.15 -9999 0 -0.46 57 57
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 -0.01 0.16 -9999 0 -0.89 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 -0.027 0.16 -9999 0 -0.45 55 55
F2RL2 -0.08 0.16 -9999 0 -0.32 133 133
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 -0.003 0.039 -9999 0 -0.5 3 3
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.037 0.16 -9999 0 -0.49 55 55
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.028 0.16 -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 -0.082 0.27 -9999 0 -0.82 55 55
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.037 0.16 -9999 0 -0.48 55 55
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.001 0.15 -9999 0 -0.64 4 4
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0.054 -9999 0 -0.82 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.006 0.12 -9999 0 -0.33 55 55
Insulin Receptor/Insulin/IRS1 -0.06 0.17 -9999 0 -0.52 55 55
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.036 0.064 -9999 0 -0.47 3 3
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
ITGA4 0.004 0.069 -9999 0 -0.41 11 11
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.62 15 15
alpha4/beta1 Integrin -0.006 0.049 -9999 0 -0.63 2 2
Cellular roles of Anthrax toxin

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
ANTXR1 -0.004 0.12 -10000 0 -0.82 10 10
ANTXR2 0.008 0.066 -10000 0 -0.82 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.017 -10000 0 -0.1 13 13
monocyte activation -0.048 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 -0.013 0.073 -10000 0 -0.5 10 10
CYAA 0.003 0.081 -10000 0 -0.48 13 13
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.025 0.14 -10000 0 -0.47 40 40
Channel -0.014 0.083 -10000 0 -0.51 13 13
NLRP1 -0.004 0.035 -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 0.017 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 -0.023 0.087 -10000 0 -0.47 15 15
PA/Cellular Receptors -0.015 0.09 -10000 0 -0.56 13 13
apoptosis -0.003 0.017 -10000 0 -0.1 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.003 0.081 -10000 0 -0.48 13 13
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.092 0.27 -10000 0 -0.82 58 58
VCAM1 -0.049 0.17 -10000 0 -0.49 61 61
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.024 0.11 10 -10000 0 10
IL18 -0.011 0.087 -10000 0 -0.42 14 14
negative regulation of macrophage activation -0.003 0.017 -10000 0 -0.1 13 13
LEF -0.003 0.017 -10000 0 -0.1 13 13
CASP1 -0.004 0.02 -10000 0 -0.22 2 2
mol:cAMP -0.003 0.02 -10000 0 -10000 0 0
necrosis -0.003 0.017 -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 0.079 -10000 0 -0.49 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0.038 -9999 0 -0.82 1 1
Caspase 8 (4 units) -0.02 0.06 -9999 0 -10000 0 0
NEF -0.011 0.053 -9999 0 -10000 0 0
NFKBIA 0.009 0.03 -9999 0 -10000 0 0
BIRC3 -0.005 0.2 -9999 0 -0.81 26 26
CYCS -0.005 0.1 -9999 0 -0.4 5 5
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.035 0.18 -9999 0 -0.71 27 27
MAP2K7 0.025 0.078 -9999 0 -10000 0 0
protein ubiquitination 0.039 0.088 -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 -0.013 0.1 -9999 0 -0.42 5 5
NF-kappa-B/RelA/I kappa B alpha -0.022 0.081 -9999 0 -0.35 26 26
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 -0.022 0.081 -9999 0 -0.35 26 26
MAPK8 0.024 0.096 -9999 0 -0.42 9 9
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 0.011 0.094 -9999 0 -0.31 26 26
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 0.093 -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 -0.057 0.17 -9999 0 -0.52 48 48
TNF -0.092 0.27 -9999 0 -0.82 58 58
FASLG -0.065 0.28 -9999 0 -0.84 48 48
NFKB1 0.007 0.048 -9999 0 -0.82 1 1
TNFR1A/BAG4/TNF-alpha -0.069 0.18 -9999 0 -0.55 59 59
CASP6 -0.003 0.045 -9999 0 -10000 0 0
CASP7 0.03 0.17 -9999 0 -0.62 25 25
RELA 0.009 0.03 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.03 0.17 -9999 0 -0.62 25 25
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.029 -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 -0.046 0.12 -9999 0 -0.52 25 25
BCL2 -0.001 0.15 -9999 0 -0.41 41 41
Regulation of Telomerase

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
Telomerase catalytic core complex -0.023 0.092 -9999 0 -10000 0 0
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.29 0.45 -9999 0 -0.92 151 151
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.07 -9999 0 -0.29 23 23
ER alpha/Oestrogen -0.044 0.14 -9999 0 -0.4 54 54
NFX1/SIN3/HDAC complex 0.047 0.026 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 74 74
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 -10000 0 0
SAP18 0.014 0 -9999 0 -10000 0 0
MRN complex -0.003 0.043 -9999 0 -0.55 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 -0.029 0.053 -9999 0 -10000 0 0
Mad/Max 0.006 0.01 -9999 0 -10000 0 0
TERT -0.024 0.093 -9999 0 -10000 0 0
CCND1 -0.015 0.092 -9999 0 -10000 0 0
MAX 0.014 0.002 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
RBBP4 0.008 0.066 -9999 0 -0.82 3 3
TERF2 0 0.005 -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 0.02 -9999 0 -10000 0 0
CDKN1B -0.04 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 -0.18 0.35 -9999 0 -0.82 109 109
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.006 -9999 0 -10000 0 0
FOS -0.21 0.37 -9999 0 -0.82 128 128
IFN-gamma/IRF1 -0.087 0.21 -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 0.072 -9999 0 -0.48 5 5
IRF1 0.018 0.015 -9999 0 -10000 0 0
ESR1 -0.047 0.19 -9999 0 -0.53 54 54
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.025 -9999 0 -0.56 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 0.026 -9999 0 -0.56 1 1
SMAD3 0.02 0.029 -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 0.066 -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 0.065 -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 0.008 0.042 -9999 0 -0.31 8 8
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 0.026 -9999 0 -0.56 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.007 0.076 -9999 0 -0.82 4 4
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.097 0.22 -9999 0 -0.63 72 72
MYC -0.009 0.14 -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 0.008 0.042 -9999 0 -0.31 8 8
TRF2/BLM 0 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.018 0.078 -9999 0 -10000 0 0
SP1/HDAC2 0.022 0.007 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.029 0.053 -9999 0 -10000 0 0
Smad3/Myc 0.009 0.097 -9999 0 -0.56 13 13
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.1 0.28 -9999 0 -0.71 78 78
Telomerase/PinX1 -0.029 0.053 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.021 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 -0.029 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 0.036 -9999 0 -0.46 3 3
TRF2/WRN -0.001 0.027 -9999 0 -0.59 1 1
Telomerase/hnRNP C1/C2 -0.029 0.053 -9999 0 -10000 0 0
E2F1 -0.087 0.15 -9999 0 -0.31 150 150
ZNFX1 0.014 0 -9999 0 -10000 0 0
PIF1 0.002 0.09 -9999 0 -0.6 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
mTOR signaling pathway

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.042 0.12 0.33 1 -0.36 57 58
FRAP1 0.008 0.027 -10000 0 -10000 0 0
AKT1 -0.035 0.1 0.25 1 -0.66 3 4
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.027 0.077 -10000 0 -0.51 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.022 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.065 -10000 0 -0.46 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.033 0.14 -10000 0 -0.42 55 55
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 0.01 0.06 -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 1 -0.002 54 55
EIF4B 0.017 0.054 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.013 0.039 -10000 0 -0.32 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.024 0.14 -10000 0 -0.39 57 57
mTOR/RHEB/GTP/Raptor/GBL 0.021 0.04 0.18 1 -0.28 2 3
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.022 0.064 -10000 0 -0.45 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 54 55
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.039 0.12 0.26 1 -0.34 57 58
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 -0.029 0.083 -10000 0 -0.56 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 54 -0.001 1 55
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 -0.044 0.15 -10000 0 -0.46 55 55
INS 0 0 -10000 0 -10000 0 0
PTEN 0.011 0.038 -10000 0 -0.82 1 1
PDK2 -0.038 0.11 0.26 1 -0.32 57 58
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -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
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.046 0.06 -10000 0 -0.38 8 8
NFATC2 -0.019 0.095 -10000 0 -0.29 26 26
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 0.012 0.091 -10000 0 -0.32 24 24
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 -0.025 0.097 -10000 0 -0.59 9 9
BCL2/BAX -0.046 0.16 -10000 0 -0.63 35 35
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 0.013 0.015 -10000 0 -0.31 1 1
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.016 0.086 -10000 0 -0.57 4 4
Calcineurin A alpha-beta B1/BCL2 -0.047 0.22 -10000 0 -0.82 35 35
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.016 0.085 0.56 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 0.19 -10000 0 -0.34 310 310
MAP3K8 -0.004 0.11 -10000 0 -0.83 8 8
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.12 0.16 -10000 0 -0.49 22 22
CABIN1 0.012 0.091 -10000 0 -0.32 24 24
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 -0.005 0.11 -10000 0 -0.54 16 16
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 -0.006 0.11 -10000 0 -0.82 9 9
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 -0.006 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 -0.014 0.051 -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 52 52
PRKCE 0.006 0.076 -10000 0 -0.82 4 4
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 -0.025 0.18 -10000 0 -0.82 22 22
PRKCG 0.005 0.022 -10000 0 -0.31 2 2
PRKCQ 0.005 0.085 -10000 0 -0.82 5 5
FKBP38/BCL2 -0.046 0.16 -10000 0 -0.63 35 35
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 0.032 0.086 -10000 0 -0.38 17 17
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 -0.012 0.071 -10000 0 -0.56 7 7
NFATc/ERK1 0.052 0.057 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.096 -10000 0 -0.58 9 9
NR4A1 -0.19 0.36 -10000 0 -0.73 143 143
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 -0.036 0.062 -10000 0 -0.41 4 4
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 -0.047 0.22 -10000 0 -0.82 35 35
Stabilization and expansion of the E-cadherin adherens junction

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
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 0.071 0.009 -9999 0 -10000 0 0
EGFR 0.006 0.076 -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 -0.039 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 74 74
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.074 0.2 -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 0.049 0.032 -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 -0.43 72 72
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 -0.8 118 118
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 0.048 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.041 0.057 -9999 0 -0.43 7 7
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 -0.48 73 73
HGF -0.11 0.3 -9999 0 -0.82 73 73
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.086 0.02 -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 0.02 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -9999 0 -0.43 112 112
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 -0.45 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 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
TOP1 0.018 0.093 -10000 0 -0.46 12 12
ACTA1 0.01 0.12 -10000 0 -0.64 10 10
NUMA1 0.018 0.093 -10000 0 -0.46 12 12
SPTAN1 0.015 0.12 -10000 0 -0.64 10 10
LIMK1 0.015 0.12 -10000 0 -0.64 10 10
BIRC3 -0.037 0.19 -10000 0 -0.68 35 35
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
CASP10 -0.001 0.12 -10000 0 -0.67 12 12
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.018 0.093 -10000 0 -0.46 12 12
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.015 0.11 -10000 0 -0.62 10 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.015 0.12 -10000 0 -0.64 10 10
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.058 0.22 -10000 0 -0.65 60 60
BID -0.011 0.068 -10000 0 -0.31 12 12
MAP3K1 0.014 0.042 -10000 0 -0.23 3 3
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 0.029 -10000 0 -0.63 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.012 0.12 -10000 0 -0.61 11 11
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.016 0.052 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 0.021 0.11 -10000 0 -0.61 10 10
APAF1 0.012 0.038 -10000 0 -0.82 1 1
CASP6 0.022 0.064 -10000 0 -0.43 4 4
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.022 0.11 -10000 0 -0.61 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 -0.56 12 12
DFFA 0.015 0.12 -10000 0 -0.64 10 10
DFFB 0.015 0.12 -10000 0 -0.64 10 10
PARP1 0.016 0.052 0.23 22 -0.18 1 23
actin filament polymerization -0.023 0.11 0.58 10 -10000 0 10
TNF -0.092 0.27 -10000 0 -0.82 58 58
CYCS 0.005 0.045 -10000 0 -0.22 12 12
SATB1 0.029 0.061 -10000 0 -0.4 4 4
SLK 0.012 0.13 -10000 0 -0.67 12 12
p15 BID/BAX -0.003 0.061 -10000 0 -0.35 4 4
CASP2 0.005 0.12 -10000 0 -0.46 11 11
JNK cascade -0.014 0.042 0.23 3 -10000 0 3
CASP3 0.007 0.12 -10000 0 -0.62 12 12
LMNB2 0.02 0.077 -10000 0 -0.32 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.029 0.11 -10000 0 -0.5 25 25
negative regulation of DNA binding -0.057 0.22 -10000 0 -0.64 60 60
stress fiber formation 0.012 0.13 -10000 0 -0.65 12 12
GZMB -0.013 0.14 -10000 0 -0.71 14 14
CASP1 0.016 0.032 -10000 0 -0.45 2 2
LMNB1 0.02 0.077 -10000 0 -0.32 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 0.022 0.1 -10000 0 -0.51 10 10
LMNA 0.02 0.077 -10000 0 -0.32 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 0.014 0.12 -10000 0 -0.64 10 10
APAF-1/Caspase 9 0.005 0.042 -10000 0 -0.4 1 1
nuclear fragmentation during apoptosis 0.019 0.091 -10000 0 -0.46 12 12
CFL2 0.022 0.11 -10000 0 -0.6 10 10
GAS2 0.01 0.13 -10000 0 -0.6 15 15
positive regulation of apoptosis 0.022 0.079 -10000 0 -0.33 3 3
PRF1 -0.002 0.11 -10000 0 -0.72 10 10
BARD1 signaling events

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.033 0.14 -10000 0 -0.63 25 25
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 -0.025 0.1 -10000 0 -0.46 26 26
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.043 -10000 0 -0.55 3 3
MRE11A 0.008 0.066 -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 -0.033 0.14 -10000 0 -0.63 25 25
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 -0.001 0.067 -10000 0 -10000 0 0
DNA repair 0.054 0.099 -10000 0 -0.41 1 1
BRCA1/BARD1/ubiquitin -0.033 0.14 -10000 0 -0.63 25 25
BARD1/DNA-PK -0.026 0.11 -10000 0 -0.5 25 25
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.033 0.14 0.63 25 -10000 0 25
BRCA1/BARD1/CTIP/M/R/N Complex 0.021 0.09 -10000 0 -0.39 4 4
BRCA1/BACH1/BARD1/TopBP1 -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BARD1/P53 -0.027 0.11 -10000 0 -0.5 26 26
BARD1/CSTF1/BRCA1 -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.03 0.19 -10000 0 -0.82 25 25
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BARD1/UbcH7 -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BARD1/RAD51/PCNA -0.026 0.11 -10000 0 -0.5 25 25
BARD1/DNA-PK/P53 -0.024 0.1 -10000 0 -0.46 25 25
BRCA1/BARD1/Ubiquitin -0.033 0.14 -10000 0 -0.63 25 25
BRCA1/BARD1/CTIP -0.027 0.11 -10000 0 -0.5 26 26
FA complex 0.038 0.024 -10000 0 -10000 0 0
BARD1/EWS -0.033 0.14 -10000 0 -0.63 25 25
RBBP8 0.023 0.03 -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 0.027 0.11 0.49 26 -10000 0 26
BRCA1/BARD1 -0.025 0.1 -10000 0 -0.46 26 26
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.033 0.14 -10000 0 -0.64 25 25
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 -0.033 0.14 -10000 0 -0.63 25 25
EWSR1 0.013 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
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 0.034 0.06 -10000 0 -0.34 6 6
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.011 0.084 0.24 5 -0.41 14 19
RAR alpha/9cRA/Cyclin H -0.023 0.092 -10000 0 -0.41 22 22
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.03 0.067 -10000 0 -0.39 6 6
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.014 0.11 -10000 0 -0.39 29 29
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -10000 0 -0.21 1 1
RXRs/RARs/NRIP1/9cRA -0.019 0.16 -10000 0 -0.63 25 25
NCOA2 -0.063 0.24 -10000 0 -0.82 44 44
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 -0.001 0.11 -10000 0 -0.82 9 9
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.037 0.14 -10000 0 -0.66 22 22
RARA 0.007 0.091 -10000 0 -0.34 29 29
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.14 -10000 0 -0.55 16 16
PRKCA -0.022 0.18 -10000 0 -0.82 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.03 0.16 -10000 0 -0.65 25 25
RXRG -0.12 0.11 -10000 0 -0.53 26 26
RXRA 0.013 0.092 -10000 0 -0.34 29 29
RXRB 0.005 0.099 -10000 0 -0.44 22 22
VDR/Vit D3/DNA 0 0.01 -10000 0 -0.21 1 1
RBP1 -0.002 0.1 -10000 0 -0.64 11 11
CRBP1/9-cic-RA -0.011 0.079 -10000 0 -0.64 7 7
RARB -0.007 0.14 -10000 0 -0.82 13 13
PRKCG 0.008 0.022 -10000 0 -0.31 2 2
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.026 0.16 -10000 0 -0.68 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.008 0.14 -10000 0 -0.55 25 25
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.087 -10000 0 -0.49 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.03 0.16 -10000 0 -0.65 25 25
positive regulation of DNA binding -0.022 0.087 -10000 0 -0.38 22 22
NRIP1 -0.025 0.14 -10000 0 -0.63 19 19
RXRs/RARs -0.038 0.16 -10000 0 -0.65 25 25
RXRs/RXRs/DNA/9cRA -0.048 0.14 -10000 0 -0.69 22 22
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 -0.012 0.053 -10000 0 -0.53 2 2
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
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.28 17 17
GNAO1 -0.015 0.15 -9999 0 -0.72 20 20
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.029 -9999 0 -0.47 1 1
AKT3 0.049 0.05 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.038 -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 -0.32 16 16
MAPK3 0.042 0.064 -9999 0 -10000 0 0
MAPK1 0.042 0.064 -9999 0 -10000 0 0
JAK2 0.046 0.066 -9999 0 -0.43 1 1
CXCR4 0.042 0.065 -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 0.068 -9999 0 -0.32 16 16
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.052 -9999 0 -10000 0 0
VEGFA 0.011 0.066 -9999 0 -0.82 3 3
S1P/S1P2/Gi 0.03 0.069 -9999 0 -0.32 16 16
VEGFR1 homodimer/VEGFA homodimer 0.024 0.068 -9999 0 -0.8 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.066 0.17 -9999 0 -0.35 119 119
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 -0.82 112 112
GNA15 -0.013 0.094 -9999 0 -0.33 37 37
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.002 0.11 -9999 0 -0.82 9 9
Rac1/GTP -0.01 0.052 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.006 0.049 -9999 0 -0.31 11 11
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.016 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.72 20 20
mol:Sphinganine-1-P 0.019 0.034 -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 0.029 -9999 0 -0.49 1 1
S1P/S1P3/Gq -0.049 0.15 -9999 0 -0.4 23 23
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 -0.82 112 112
GNA15 -0.013 0.094 -9999 0 -0.33 37 37
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.002 0.11 -9999 0 -0.82 9 9
ABCC1 0.013 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 -0.26 1 1
CDKN1A 0.033 0.032 -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 0.015 -10000 0 -0.28 1 1
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 0.024 -10000 0 -0.43 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 0.023 0.42 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 0.017 -10000 0 -0.28 1 1
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 -0.053 0.2 -10000 0 -0.55 66 66
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 0.036 -10000 0 -0.55 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 0.03 -10000 0 -0.37 2 2
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 0.024 0.041 -10000 0 -10000 0 0
PDPK1 0.01 0.054 -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 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.011 -10000 0 -10000 0 0
glucose import -0.06 0.21 -10000 0 -0.52 80 80
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 -0.061 0.21 -10000 0 -0.53 80 80
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 0.19 -10000 0 -0.34 310 310
G1/S transition of mitotic cell cycle 0.046 0.016 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.001 0.052 -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 0.004 0.13 -10000 0 -0.56 11 11
BAG4 0.012 0.038 -10000 0 -0.82 1 1
BAD 0.017 0.046 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.037 0.19 -10000 0 -0.68 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 0.012 0.12 -10000 0 -0.52 11 11
MAP2K2 0.027 0.057 -10000 0 -0.37 2 2
MAP2K1 0.027 0.057 -10000 0 -0.37 2 2
SMPD1 0.01 0.034 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.012 0.13 -10000 0 -0.54 11 11
MAP2K4 0.024 0.047 -10000 0 -10000 0 0
protein ubiquitination 0.014 0.13 -10000 0 -0.53 11 11
EnzymeConsortium:2.7.1.37 0.03 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 -0.4 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 0.048 -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 -0.36 2 2
MAPK1 0.03 0.056 -10000 0 -0.36 2 2
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.004 0.13 -10000 0 -0.56 11 11
KSR1 0.015 0.057 -10000 0 -0.43 2 2
MAPK8 0.023 0.078 -10000 0 -0.44 9 9
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.012 0.12 -10000 0 -0.52 11 11
TNF R/SODD -0.001 0.029 -10000 0 -0.63 1 1
TNF -0.092 0.27 -10000 0 -0.82 58 58
CYCS 0.027 0.057 0.16 29 -10000 0 29
IKBKG 0.012 0.12 -10000 0 -0.52 11 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.004 0.14 -10000 0 -0.45 25 25
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.027 0.057 0.16 29 -10000 0 29
TNF/TNF R/SODD -0.069 0.18 -10000 0 -0.55 59 59
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.033 -10000 0 -10000 0 0
NSMAF 0.004 0.13 -10000 0 -0.55 11 11
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 2 2
BCL2 -0.047 0.22 -10000 0 -0.82 35 35
TRAIL signaling 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
TNFSF10 0.007 0.067 -9999 0 -0.7 4 4
positive regulation of NF-kappaB transcription factor activity -0.004 0.05 -9999 0 -0.63 3 3
MAP2K4 0.047 0.031 -9999 0 -0.3 3 3
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.008 0.066 -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 0.051 -9999 0 -0.63 3 3
TRAIL/TRAILR3 -0.06 0.1 -9999 0 -0.68 3 3
TRAIL/TRAILR1 -0.008 0.071 -9999 0 -0.63 6 6
TRAIL/TRAILR4 -0.004 0.051 -9999 0 -0.63 3 3
TRAIL/TRAILR1/DAP3/GTP -0.007 0.056 -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 -0.63 3 3
MAP3K1 -0.003 0.028 -9999 0 -0.32 3 3
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.066 -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 -0.63 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP -0.006 0.052 -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 0.045 0.077 -9999 0 -0.47 9 9
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.077 0.15 -9999 0 -0.31 134 134
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.007 0.061 -9999 0 -0.55 6 6
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.005 0.046 -9999 0 -0.52 3 3
JNK cascade -0.004 0.05 -9999 0 -0.63 3 3
TRAIL (trimer) 0.007 0.067 -9999 0 -0.7 4 4
TNFRSF10C -0.077 0.15 -9999 0 -0.31 134 134
TRAIL/TRAILR1/DAP3/GTP/FADD -0.006 0.053 -9999 0 -0.47 6 6
TRAIL/TRAILR2/FADD -0.004 0.044 -9999 0 -0.55 3 3
cell death 0.019 0.025 -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 0.037 -9999 0 -0.46 3 3
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.008 0.077 -9999 0 -0.74 5 5
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 0.013 0.15 -9999 0 -0.67 11 11
GNAO1 -0.017 0.15 -9999 0 -0.73 20 20
PDGFB-D/PDGFRB/PLCgamma1 0.022 0.14 -9999 0 -0.57 11 11
PLCG1 0.019 0.14 -9999 0 -0.61 11 11
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 0.039 -9999 0 -0.83 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.012 0.07 -9999 0 -0.64 5 5
S1P1/S1P -0.016 0.065 -9999 0 -0.51 5 5
negative regulation of cAMP metabolic process 0.013 0.15 -9999 0 -0.52 18 18
MAPK3 0.005 0.2 -9999 0 -0.59 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 0.008 0.066 -9999 0 -0.83 3 3
PLCB2 0.03 0.07 -9999 0 -0.51 3 3
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.052 -9999 0 -0.42 5 5
receptor internalization -0.015 0.06 -9999 0 -0.47 5 5
PTGS2 -0.038 0.34 -9999 0 -1.1 44 44
Rac1/GTP -0.013 0.052 -9999 0 -0.48 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.066 -9999 0 -0.82 3 3
negative regulation of T cell proliferation 0.013 0.15 -9999 0 -0.52 18 18
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 -0.59 44 44
S1P1/S1P/PDGFB-D/PDGFRB 0.032 0.086 -9999 0 -0.51 6 6
ABCC1 0.014 0.002 -9999 0 -10000 0 0
Canonical Wnt signaling 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
HDAC1 0.006 0.024 -10000 0 -10000 0 0
AES 0.005 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 -0.026 0.17 -10000 0 -0.66 28 28
TLE1 0 0.067 -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 58 58
beta catenin/RanBP3 0.022 0.091 0.37 25 -10000 0 25
KREMEN2 -0.009 0.082 -10000 0 -0.31 33 33
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 -0.047 0.31 -10000 0 -1.6 18 18
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 0.045 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 0.059 0.018 -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 -0.73 17 17
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 0.008 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.12 0.48 27 -10000 0 27
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 0.068 0.074 -10000 0 -0.48 4 4
DKK1/LRP6/Kremen 2 -0.037 0.078 -10000 0 -0.37 8 8
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.006 0.023 -10000 0 -10000 0 0
NLK 0.014 0.004 -10000 0 -10000 0 0
CCND1 0 0.075 -10000 0 -0.81 1 1
WNT1 0.01 0.021 -10000 0 -0.31 2 2
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 0.37 14 -10000 0 14
APC 0.039 0.026 -10000 0 -0.47 1 1
WNT1/LRP6/FZD1 0.035 0.036 -10000 0 -10000 0 0
CREBBP 0.006 0.021 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.034 0.3 1 -0.47 2 3
DAPP1 -0.054 0.14 -10000 0 -0.5 12 12
Src family/SYK family/BLNK-LAT/BTK-ITK -0.058 0.18 -10000 0 -0.57 19 19
mol:DAG -0.005 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 -10000 0 1
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 0.03 -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 -0.82 1 1
ZAP70 -0.022 0.16 -10000 0 -0.62 27 27
mol:IP3 0.005 0.072 -10000 0 -10000 0 0
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 0.036 -10000 0 -0.55 2 2
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.038 0.038 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
PLEKHA2 0.023 0.041 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.036 -10000 0 -0.8 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 -0.049 0.16 -10000 0 -0.61 13 13
BLK -0.25 0.38 -10000 0 -0.76 163 163
PDPK1 0.01 0.054 -10000 0 -0.82 2 2
CYTH1 0 0.013 0.26 1 -10000 0 1
HCK -0.008 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 0.096 -10000 0 -0.62 11 11
SGK1 -0.015 0.11 -10000 0 -0.69 11 11
INPP5D -0.003 0.071 -10000 0 -0.31 24 24
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 0.02 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.018 0.37 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 34 34
mol:PI-3-4-P2 0.013 0.049 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.006 -10000 0 -10000 0 0
PLEKHA1 0.023 0.041 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.035 -10000 0 -0.46 1 1
LAT 0.006 0.077 -10000 0 -0.72 5 5
Rac1/GTP -0.007 0.055 -10000 0 -0.47 2 2
ITK -0.056 0.14 -10000 0 -0.44 59 59
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.014 0.13 -10000 0 -0.4 15 15
LCK -0.01 0.11 -10000 0 -0.44 25 25
BTK -0.014 0.062 0.26 1 -0.44 8 9
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.039 0.022 -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 0.009 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 0.015 -9999 0 -10000 0 0
MAPK10 0.043 0.026 -9999 0 -0.51 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.064 -9999 0 -0.48 4 4
response to oxidative stress 0.015 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.01 0.087 -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 -0.5 3 3
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.041 -9999 0 -10000 0 0
MST1 0.023 0.042 -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 0.064 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.035 0.073 -9999 0 -0.49 9 9
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 0.043 -9999 0 -0.82 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 0.01 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.066 0.39 -9999 0 -1.5 32 32
SKP2 0.006 0.076 -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 0.051 -9999 0 -0.5 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.006 0.13 -9999 0 -0.82 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 0.053 -9999 0 -0.47 1 1
SFN -0.21 0.19 -9999 0 -0.34 310 310
CDK2 0.014 0.003 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.017 0.062 -9999 0 -0.32 4 4
CREBBP 0.014 0.003 -9999 0 -10000 0 0
FBXO32 0.11 0.11 -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
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 0.072 0.054 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.028 0.078 -9999 0 -0.63 2 2
NFKBIA 0.049 0.024 -9999 0 -0.48 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 0.021 -9999 0 -10000 0 0
IKK complex/A20 -0.05 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 -0.43 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 -0.55 2 2
NOD2 -0.032 0.12 -9999 0 -0.33 63 63
NFKB1 0.015 0.038 -9999 0 -0.82 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 -0.079 0.21 -9999 0 -0.63 58 58
TRAF6 0.01 0.054 -9999 0 -0.82 2 2
PRKCA -0.025 0.18 -9999 0 -0.82 22 22
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.092 0.27 -9999 0 -0.82 58 58
NF kappa B1 p50/RelA -0.001 0.024 -9999 0 -0.53 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.024 -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 -0.54 1 1
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 -0.027 0.048 -9999 0 -0.63 1 1
CLOCK -0.04 0.2 -9999 0 -0.83 29 29
TIMELESS/CRY2 -0.006 0.066 -9999 0 -10000 0 0
DEC1/BMAL1 -0.021 0.064 -9999 0 -10000 0 0
ATR 0.012 0.038 -9999 0 -0.82 1 1
NR1D1 -0.06 0.13 -9999 0 -10000 0 0
ARNTL -0.02 0.097 -9999 0 -0.32 46 46
TIMELESS -0.014 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 0.008 0.031 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.008 0.031 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.03 0.15 -9999 0 -0.56 30 30
BMAL1/CLOCK -0.056 0.15 -9999 0 -0.62 15 15
S phase of mitotic cell cycle -0.027 0.048 -9999 0 -0.63 1 1
TIMELESS/CHEK1/ATR -0.027 0.049 -9999 0 -0.64 1 1
mol:NADPH -0.008 0.031 -9999 0 -10000 0 0
PER1/TIMELESS -0.006 0.066 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.015 -9999 0 -0.31 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.011 0.086 -9999 0 -0.44 14 14
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.006 0.076 -9999 0 -0.82 4 4
ITGA4 0.004 0.069 -9999 0 -0.41 11 11
alpha4/beta7 Integrin/MAdCAM1 -0.031 0.098 -9999 0 -0.5 16 16
EPO 0.002 0.039 -9999 0 -0.31 7 7
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.62 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.049 -9999 0 -0.63 2 2
EPO/EPOR (dimer) -0.007 0.037 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.038 -9999 0 -0.47 3 3
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
PI3K -0.004 0.05 -9999 0 -0.63 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.024 0.049 -9999 0 -0.5 3 3
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.011 0.09 -9999 0 -0.35 28 28
cell adhesion -0.031 0.097 -9999 0 -0.49 16 16
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.023 0.077 -9999 0 -0.57 6 6
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.013 0.079 -9999 0 -0.55 8 8
p130Cas/Crk/Dock1 0.04 0.079 -9999 0 -0.45 10 10
VCAM1 0.001 0.092 -9999 0 -0.55 11 11
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.036 -9999 0 -0.5 2 2
BCAR1 0.031 0.073 -9999 0 -0.53 6 6
EPOR 0.007 0.047 -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 -0.002 0.039 -9999 0 -0.48 3 3
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.012 0.056 0.29 17 -10000 0 17
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.032 -10000 0 -0.56 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.017 0.15 -10000 0 -0.72 20 20
RhoA/GTP -0.012 0.057 -10000 0 -0.3 17 17
negative regulation of cAMP metabolic process 0.022 0.071 -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 -0.34 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
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.72 20 20
CDC42/GTP -0.011 0.055 -9999 0 -0.3 17 17
PLCG1 0.03 0.065 -9999 0 -0.31 17 17
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 0.054 -9999 0 -0.29 17 17
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 -0.33 1 1
MAPK1 0.03 0.065 -9999 0 -0.31 17 17
S1P/S1P5/Gi 0.022 0.071 -9999 0 -0.34 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 -0.56 1 1
RHOA 0.032 0.016 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.023 0.069 -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
EPO signaling 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
BCL2L1 0.052 0.1 -9999 0 -10000 0 0
CRKL 0.038 0.045 -9999 0 -0.53 1 1
mol:DAG 0.042 0.05 -9999 0 -10000 0 0
HRAS 0.062 0.042 -9999 0 -10000 0 0
MAPK8 0.02 0.086 -9999 0 -0.57 9 9
RAP1A 0.038 0.045 -9999 0 -0.53 1 1
GAB1 0.038 0.045 -9999 0 -0.53 1 1
MAPK14 0.03 0.031 -9999 0 -10000 0 0
EPO 0.005 0.039 -9999 0 -0.3 7 7
PLCG1 0.042 0.05 -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 -0.005 0.025 -9999 0 -0.46 1 1
EPO/EPOR (dimer) 0.013 0.042 -9999 0 -10000 0 0
IRS2 0.038 0.045 -9999 0 -0.53 1 1
STAT1 0.042 0.077 -9999 0 -10000 0 0
STAT5B 0.043 0.065 -9999 0 -10000 0 0
cell proliferation 0.028 0.082 -9999 0 -0.53 9 9
GAB1/SHIP/PIK3R1/SHP2/SHC -0.008 0.034 -9999 0 -10000 0 0
TEC 0.038 0.045 -9999 0 -0.53 1 1
SOCS3 -0.034 0.19 -9999 0 -0.8 28 28
STAT1 (dimer) 0.042 0.076 -9999 0 -10000 0 0
JAK2 0.013 0.039 -9999 0 -0.84 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.043 0.051 -9999 0 -0.57 1 1
EPO/EPOR 0.013 0.042 -9999 0 -10000 0 0
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.046 0.044 -9999 0 -0.51 1 1
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 0.042 0.05 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.01 0.033 -9999 0 -0.48 1 1
SH2B3 0.014 0.005 -9999 0 -10000 0 0
NFKB1 0.029 0.039 -9999 0 -0.51 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.019 0.069 -9999 0 -0.29 28 28
PTPN6 0.031 0.047 -9999 0 -0.56 1 1
TEC/VAV2/GRB2 0.051 0.043 -9999 0 -0.49 1 1
EPOR 0.009 0.047 -9999 0 -0.32 10 10
INPP5D -0.003 0.071 -9999 0 -0.31 24 24
mol:GDP -0.005 0.025 -9999 0 -0.47 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.051 0.043 -9999 0 -0.49 1 1
VAV2 0.038 0.045 -9999 0 -0.53 1 1
CBL 0.038 0.045 -9999 0 -0.53 1 1
SHC/Grb2/SOS1 -0.006 0.028 -9999 0 -0.49 1 1
STAT5A 0.043 0.065 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.053 0.097 -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 0.021 0.088 -9999 0 -0.5 8 8
BCL2 0.003 0.28 -9999 0 -0.98 35 35
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.063 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 -0.05 0.14 -9999 0 -0.42 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 0.067 -9999 0 -10000 0 0
YY1/LSF 0.028 0.051 -9999 0 -0.53 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 -0.014 0.13 -9999 0 -0.37 58 58
I kappa B alpha/HDAC1 -0.001 0.091 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.004 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 -0.001 0.091 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.049 0.02 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.001 0.11 -9999 0 -0.48 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
GATA1 0.009 0.006 -9999 0 -10000 0 0
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 0.066 -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 -10000 0 0
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.044 0.028 -9999 0 -10000 0 0
SIN3 complex -0.001 0.023 -9999 0 -0.5 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 0.014 0.085 -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 -0.061 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) -0.001 0.091 -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 -10000 0 0
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 0.028 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 0.044 -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 -10000 0 0
histone deacetylation 0.049 0.02 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.011 0.086 -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 -0.001 0.092 -9999 0 -10000 0 0
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 -0.01 0.091 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.079 0.21 -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 -0.025 0.066 -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 0.039 -9999 0 -0.5 3 3
GATA1/Fog1 0 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.092 0.27 -9999 0 -0.82 58 58
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 -0.054 0.14 -9999 0 -0.44 58 58
SIN3/HDAC complex/NCoR1 0.046 0.027 -9999 0 -0.26 3 3
TFCP2 0.006 0.076 -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
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.009 0.14 -9999 0 -0.56 30 30
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.039 -9999 0 -0.42 1 1
NFKBIA 0.024 0.037 -9999 0 -0.28 6 6
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.026 -9999 0 -0.55 1 1
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.039 0.2 -9999 0 -0.82 30 30
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.027 -9999 0 -0.55 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.026 -9999 0 -0.55 1 1
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
NF kappa B1 p50 dimer 0.02 0.03 -9999 0 -0.63 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.023 0.03 -9999 0 -0.63 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.039 -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 0.05 -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 0.029 -9999 0 -0.38 1 1
NF kappa B1 p105/c-Rel -0.009 0.14 -9999 0 -0.56 30 30
LCK -0.01 0.11 -9999 0 -0.44 25 25
BCL3 0.013 0.015 -9999 0 -0.31 1 1
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.01 0.018 -9999 0 -10000 0 0
BUB1B 0.017 0.027 -9999 0 -0.15 1 1
PLK1 0.017 0.012 -9999 0 -10000 0 0
PLK1S1 0.015 0.007 -9999 0 -10000 0 0
KIF2A 0.023 0.03 -9999 0 -0.59 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 0.002 0.07 -9999 0 -0.29 5 5
PP2A-alpha B56 -0.018 0.059 -9999 0 -0.73 3 3
AURKA 0.016 0.009 -9999 0 -10000 0 0
PICH/PLK1 0.033 0.019 -9999 0 -10000 0 0
CENPE 0.019 0.049 -9999 0 -0.53 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 -0.009 0.081 -9999 0 -0.31 32 32
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 -0.027 0.068 -9999 0 -0.8 3 3
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.011 0.023 -9999 0 -10000 0 0
CDC25B 0.012 0.026 -9999 0 -0.31 3 3
SGOL1 0.01 0.018 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.005 0.013 -9999 0 -10000 0 0
CDC14B 0.005 0.067 -9999 0 -0.65 5 5
CDC20 0.009 0.039 -9999 0 -0.31 7 7
PLK1/PBIP1 0.002 0.022 -9999 0 -10000 0 0
mitosis 0 0.002 -9999 0 -0.022 3 3
FBXO5 0.021 0.022 -9999 0 -0.4 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.033 0.11 -9999 0 -0.31 69 69
metaphase plate congression 0.015 0.007 -9999 0 -10000 0 0
ERCC6L 0.007 0.016 -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 0.018 0.039 -9999 0 -0.48 3 3
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.034 -9999 0 -0.32 2 2
microtubule-based process -0.004 0.064 -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 -0.042 0.12 -9999 0 -0.31 81 81
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 0.039 -9999 0 -0.56 2 2
C13orf34 0.018 0.04 -9999 0 -0.48 3 3
NUDC 0.016 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.027 -9999 0 -0.15 1 1
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 0.013 0.059 -9999 0 -0.56 5 5
MKLP2/PLK1 -0.004 0.064 -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 0.001 0.11 -9999 0 -0.52 21 21
TUBG1 0.015 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.009 -9999 0 -10000 0 0
MLF1IP 0.008 0.033 -9999 0 -10000 0 0
INCENP 0.009 0.054 -9999 0 -0.83 2 2
HIF-2-alpha transcription factor network

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
MMP14 -0.001 0.023 -10000 0 -10000 0 0
oxygen homeostasis 0.016 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 0.074 -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 0.19 0.14 -10000 0 -0.86 2 2
germ cell development 0.19 0.14 -10000 0 -0.85 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 -0.002 0.076 -10000 0 -0.97 2 2
ETS1 0.03 0.002 -10000 0 -10000 0 0
CITED2 -0.09 0.32 -10000 0 -1.2 37 37
KDR -0.007 0.11 -10000 0 -1.4 3 3
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 0.21 0.16 -10000 0 -1.2 2 2
EPAS1 0.11 0.1 -10000 0 -0.63 3 3
SP1 0.022 0.002 -10000 0 -10000 0 0
ABCG2 0.19 0.16 -10000 0 -0.88 4 4
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 1.1 2 -10000 0 2
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.002 0.14 -10000 0 -0.5 28 28
EGLN2 0.029 0.011 -10000 0 -10000 0 0
EGLN1 0.025 0.056 -10000 0 -0.82 2 2
VHL/Elongin B/Elongin C -0.004 0.048 -10000 0 -0.6 3 3
VHL 0.008 0.066 -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 0.17 -10000 0 -0.66 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 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
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 0.032 0.009 -9999 0 -10000 0 0
MAPK12 0.02 0.078 -9999 0 -0.48 11 11
CCND1 0.017 0.034 -9999 0 -0.25 1 1
p38 gamma/SNTA1 0.025 0.074 -9999 0 -0.46 10 10
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.02 0.077 -9999 0 -0.48 11 11
MAP2K6 0.013 0.083 -9999 0 -0.53 11 11
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 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
CRKL 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.006 -10000 0 -10000 0 0
DOCK1 0.006 0.076 -10000 0 -0.82 4 4
ITGA4 0.004 0.069 -10000 0 -0.41 11 11
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.12 -10000 0 -0.62 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.005 0.041 -10000 0 -0.55 2 2
alpha4/beta7 Integrin/Paxillin -0.022 0.088 -10000 0 -0.5 14 14
lamellipodium assembly -0.004 0.058 -10000 0 -0.54 5 5
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
PI3K -0.004 0.05 -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 0.03 -10000 0 -0.42 2 2
cell adhesion -0.004 0.033 -10000 0 -0.46 2 2
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.004 0.036 -10000 0 -0.5 2 2
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.02 0.14 -10000 0 -0.51 31 31
ARF6/GDP 0.001 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.01 0.067 -10000 0 -0.54 6 6
p130Cas/Crk/Dock1 -0.005 0.05 -10000 0 -0.55 4 4
VCAM1 0.001 0.092 -10000 0 -0.55 11 11
alpha4/beta1 Integrin/Paxillin/Talin -0.004 0.033 -10000 0 -0.46 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.033 -10000 0 -0.46 2 2
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.033 0.46 2 -10000 0 2
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 -0.004 0.033 -10000 0 -0.46 2 2
Rac1/GTP -0.005 0.068 -10000 0 -0.77 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.67 15 15
AKT1 0.085 0.085 -9999 0 -0.69 4 4
PTK2B 0.038 0.13 -9999 0 -0.96 4 4
VEGFR2 homodimer/Frs2 0.032 0.088 -9999 0 -1.1 3 3
CAV1 -0.009 0.14 -9999 0 -0.82 13 13
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.009 0.099 -9999 0 -0.87 5 5
endothelial cell proliferation 0.077 0.099 -9999 0 -0.63 4 4
mol:Ca2+ 0.052 0.097 -9999 0 -1 3 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.009 0.094 -9999 0 -1.1 3 3
RP11-342D11.1 0.043 0.097 -9999 0 -0.73 6 6
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.006 0.063 -9999 0 -0.59 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.066 -9999 0 -0.82 3 3
HRAS/GDP -0.008 0.078 -9999 0 -0.76 4 4
SH2D2A -0.033 0.18 -9999 0 -0.64 34 34
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.007 0.064 -9999 0 -0.72 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.034 0.14 -9999 0 -0.56 27 27
VEGFR1 homodimer 0.012 0.038 -9999 0 -0.82 1 1
SHC/GRB2/SOS1 -0.009 0.09 -9999 0 -1 3 3
GRB10 0.052 0.097 -9999 0 -1 3 3
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 -0.008 0.089 -9999 0 -1 3 3
HRAS 0.012 0.021 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.041 0.075 -9999 0 -0.51 4 4
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 -0.008 0.09 -9999 0 -1 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.005 0.085 -9999 0 -0.82 5 5
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.099 -9999 0 -0.87 5 5
mol:GDP -0.008 0.082 -9999 0 -0.93 3 3
mol:NADP 0.078 0.062 -9999 0 -0.58 3 3
eNOS/Hsp90 0.08 0.058 -9999 0 -0.54 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.052 0.1 -9999 0 -1.1 3 3
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.066 -9999 0 -0.82 3 3
VEGFC 0.012 0.038 -9999 0 -0.82 1 1
FAK1/Vinculin 0.06 0.11 -9999 0 -0.83 4 4
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 -0.024 0.13 -9999 0 -1 4 4
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.02 0.061 -9999 0 -0.65 3 3
mol:L-citrulline 0.078 0.062 -9999 0 -0.58 3 3
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.009 0.094 -9999 0 -1.1 3 3
VEGFR2 homodimer/VEGFA homodimer -0.011 0.11 -9999 0 -1.2 3 3
VEGFR2/3 heterodimer 0.026 0.12 -9999 0 -0.95 6 6
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.054 0.11 -9999 0 -1.1 3 3
VEGFR2 homodimer 0.031 0.096 -9999 0 -1.2 3 3
FLT1 0.012 0.038 -9999 0 -0.82 1 1
NEDD4 0.012 0.054 -9999 0 -0.82 2 2
MAPK3 0.044 0.1 -9999 0 -0.96 3 3
MAPK1 0.044 0.1 -9999 0 -0.96 3 3
VEGFA145/NRP2 -0.02 0.072 -9999 0 -0.63 3 3
VEGFR1/2 heterodimer 0.031 0.1 -9999 0 -1.2 3 3
KDR 0.031 0.097 -9999 0 -1.2 3 3
VEGFA165/NRP1/VEGFR2 homodimer -0.017 0.1 -9999 0 -1.2 3 3
SRC 0.013 0.015 -9999 0 -0.31 1 1
platelet activating factor biosynthetic process 0.046 0.1 -9999 0 -1 3 3
PI3K -0.01 0.089 -9999 0 -0.96 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.009 0.099 -9999 0 -0.87 5 5
FES 0.052 0.11 -9999 0 -1.1 3 3
GAB1 -0.009 0.088 -9999 0 -0.99 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.009 0.099 -9999 0 -0.87 5 5
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 0.069 0.09 -9999 0 -0.63 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.009 0.099 -9999 0 -0.87 5 5
PI3K/GAB1 0.087 0.079 -9999 0 -0.72 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.008 0.089 -9999 0 -1 3 3
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.012 0.11 -9999 0 -0.83 7 7
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.052 0.11 -9999 0 -1.1 3 3
actin cytoskeleton reorganization -0.034 0.14 -9999 0 -0.55 27 27
PTK2 0.054 0.12 -9999 0 -0.79 6 6
EDG1 0.043 0.097 -9999 0 -0.73 6 6
mol:DAG 0.052 0.1 -9999 0 -1.1 3 3
CaM/Ca2+ -0.008 0.084 -9999 0 -0.94 3 3
MAP2K3 0.052 0.12 -9999 0 -1.1 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.01 0.11 -9999 0 -1.2 3 3
PLCG1 0.052 0.11 -9999 0 -1.1 3 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.009 0.094 -9999 0 -1.1 3 3
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.01 0.11 -9999 0 -0.94 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.009 0.099 -9999 0 -0.87 5 5
cell migration 0.084 0.091 -9999 0 -0.72 3 3
mol:PI-3-4-5-P3 -0.009 0.077 -9999 0 -0.82 3 3
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.008 0.084 -9999 0 -0.95 3 3
mol:NO 0.078 0.062 -9999 0 -0.58 3 3
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.077 -9999 0 -0.76 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.051 0.11 -9999 0 -1.2 3 3
VHL 0.008 0.066 -9999 0 -0.82 3 3
ITGB3 -0.011 0.14 -9999 0 -0.82 14 14
NOS3 0.08 0.071 -9999 0 -0.69 3 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.012 0.11 -9999 0 -0.72 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.037 0.15 -9999 0 -1.2 3 3
PRKCB 0.039 0.11 -9999 0 -0.94 3 3
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.042 0.1 -9999 0 -0.77 6 6
VEGFR1/2 heterodimer/VEGFA homodimer -0.01 0.11 -9999 0 -0.94 5 5
VEGFA165/NRP2 -0.02 0.072 -9999 0 -0.63 3 3
MAPKKK cascade -0.008 0.076 -9999 0 -0.85 3 3
NRP2 -0.012 0.088 -9999 0 -0.31 38 38
VEGFC homodimer 0.012 0.038 -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 0.06 0.11 -9999 0 -0.83 4 4
MAP3K13 0.044 0.13 -9999 0 -1.2 3 3
PDPK1 0.077 0.087 -9999 0 -0.74 4 4
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.001 0.04 -9999 0 -0.74 1 1
PDGFB-D/PDGFRB/SLAP -0.002 0.03 -9999 0 -0.64 1 1
PDGFB-D/PDGFRB/APS/CBL -0.001 0.026 -9999 0 -0.55 1 1
AKT1 0.059 0.044 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.024 0.051 -9999 0 -0.79 1 1
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
FGR 0.002 0.029 -9999 0 -0.56 1 1
mol:Ca2+ 0.02 0.049 -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 -0.55 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 0.05 -9999 0 -0.85 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 -0.003 0.041 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/GRB10 -0.001 0.029 -9999 0 -0.64 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 -0.87 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.06 -9999 0 -0.78 1 1
PDGFB-D/PDGFRB 0.012 0.031 -9999 0 -0.57 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.029 -9999 0 -0.64 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.001 0.048 -9999 0 -0.75 1 1
positive regulation of MAPKKK cascade -0.003 0.041 -9999 0 -0.64 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.05 -9999 0 -0.86 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 -0.036 0.084 -9999 0 -0.8 1 1
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.18 0.28 -9999 0 -0.62 142 142
PTPN2 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.029 -9999 0 -0.64 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 0.029 -9999 0 -0.64 1 1
LCK -0.008 0.088 -9999 0 -0.73 6 6
PDGFRB 0.012 0.039 -9999 0 -0.83 1 1
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.005 0.035 -9999 0 -0.55 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 0.049 -9999 0 -0.31 11 11
cell proliferation 0.02 0.14 -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 0.029 -9999 0 -0.56 1 1
PI3K -0.005 0.041 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.028 0.066 -9999 0 -0.7 1 1
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
PLCgamma1/SPHK1 0.024 0.053 -9999 0 -0.83 1 1
LYN 0.006 0.029 -9999 0 -0.56 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 -0.45 1 1
SPHK1 0.007 0.049 -9999 0 -0.31 5 5
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.02 0.05 -9999 0 -0.86 1 1
PLCG1 0.02 0.052 -9999 0 -0.9 1 1
NHERF/PDGFRB -0.002 0.027 -9999 0 -0.55 1 1
YES1 0.003 0.028 -9999 0 -0.56 1 1
cell migration -0.002 0.027 -9999 0 -0.55 1 1
SHC/Grb2/SOS1 0 0.021 -9999 0 -0.45 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 -0.5 2 2
FYN 0.006 0.029 -9999 0 -0.56 1 1
DOK1 0.034 0.025 -9999 0 -0.5 1 1
HRAS/GTP -0.001 0.014 -9999 0 -10000 0 0
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.027 0.09 -9999 0 -0.54 4 4
PRKCD 0.034 0.026 -9999 0 -0.51 1 1
FER 0.031 0.05 -9999 0 -0.51 4 4
MAPKKK cascade -0.001 0.021 -9999 0 -0.44 1 1
RASA1 0.034 0.026 -9999 0 -0.51 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 -0.46 1 1
PDGFB-D/PDGFRB/SHB -0.001 0.029 -9999 0 -0.64 1 1
chemotaxis 0.009 0.06 -9999 0 -0.79 1 1
STAT1-3-5/STAT1-3-5 -0.003 0.023 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.001 0.03 -9999 0 -0.65 1 1
PTPRJ 0.013 0 -9999 0 -10000 0 0
p38 MAPK 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
TRAF6/ASK1 -0.002 0.031 -9999 0 -0.39 3 3
TRAF2/ASK1 -0.001 0.025 -9999 0 -0.56 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 0.025 0.078 -9999 0 -0.44 6 6
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 -0.67 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 0.029 -9999 0 -0.63 1 1
TAK1/TAB family -0.001 0.014 -9999 0 -0.22 2 2
RAC1/OSM/MEKK3 0 0.006 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.033 -9999 0 -0.47 1 1
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 0.085 -9999 0 -0.82 5 5
CCM2 0.013 0.015 -9999 0 -0.31 1 1
CaM/Ca2+/CAMKIIB -0.006 0.056 -9999 0 -0.56 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 0.064 -9999 0 -0.6 5 5
OSM/MEKK3 0 0.009 -9999 0 -10000 0 0
TAOK1 -0.038 0.16 -9999 0 -0.46 57 57
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 -0.55 1 1
GADD45/MTK1/MTK1 -0.023 0.1 -9999 0 -0.49 22 22
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.045 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 -0.037 0.15 -9999 0 -0.63 28 28
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 -0.035 0.2 -9999 0 -0.82 28 28
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 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
G beta1gamma2/HDAC5 -0.001 0.023 -9999 0 -0.5 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 -9999 0 -10000 0 0
GATA1/HDAC5 0 0 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.009 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.025 -9999 0 -0.55 1 1
HDAC9 -0.018 0.096 -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 0.029 -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 -0.005 0.11 -9999 0 -0.54 16 16
Tubulin/HDAC6 -0.006 0.055 -9999 0 -0.55 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 0.009 0.006 -9999 0 -10000 0 0
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 -0.007 0.064 -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 0.029 -9999 0 -0.63 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.011 0.068 -9999 0 -0.55 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 0.055 -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 -0.048 0.19 -9999 0 -0.53 54 54
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 0.085 -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
Aurora A signaling

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
Aurora A/GADD45A 0.028 0.007 -9999 0 -10000 0 0
BIRC5 -0.016 0.098 -9999 0 -0.33 42 42
NFKBIA 0.032 0.008 -9999 0 -10000 0 0
CPEB1 -0.048 0.22 -9999 0 -0.82 35 35
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 0.067 -9999 0 -10000 0 0
TP53 0.032 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 -0.14 3 3
CDC25B 0.007 0.018 -9999 0 -10000 0 0
G2/M transition checkpoint 0.002 0.025 -9999 0 -0.5 1 1
mRNA polyadenylation -0.034 0.13 -9999 0 -0.5 35 35
Aurora A/CPEB -0.034 0.13 -9999 0 -0.5 35 35
Aurora A/TACC1/TRAP/chTOG 0.003 0.026 -9999 0 -0.47 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 0.011 -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 0.036 -9999 0 -0.45 1 1
CENPA -0.009 0.026 -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 0.026 -9999 0 -0.5 1 1
mitotic prometaphase 0.005 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 0.016 -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 0.067 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.02 0.049 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.06 0.13 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.037 0.32 2 -10000 0 2
myoblast fusion 0.023 0.052 -10000 0 -10000 0 0
mol:GTP -0.026 0.039 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.094 0.11 0.52 1 -10000 0 1
ARF1/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GM1 -0.011 0.033 -10000 0 -10000 0 0
mol:Choline 0.012 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.002 0.064 -10000 0 -10000 0 0
MAPK3 -0.017 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 -0.023 0.052 -10000 0 -10000 0 0
ARF1/GDP 0.005 0.059 -10000 0 -10000 0 0
ARF6 -0.001 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.18 0.17 -10000 0 -0.33 112 112
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.065 -10000 0 -10000 0 0
actin filament bundle formation 0.025 0.038 -10000 0 -10000 0 0
KALRN -0.005 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 0.011 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.025 0.038 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.026 0.039 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.002 0.064 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.026 0.039 -10000 0 -10000 0 0
ARF6/GTP -0.026 0.039 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GDP -0.01 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 0.001 0.033 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.002 0.064 -10000 0 -10000 0 0
ruffle organization 0.01 0.037 -10000 0 -0.32 2 2
regulation of epithelial cell migration -0.026 0.039 -10000 0 -10000 0 0
PLD2 0.001 0.033 -10000 0 -10000 0 0
PIP5K1A 0.01 0.037 -10000 0 -0.33 2 2
mol:Phosphatidic acid 0.012 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.064 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.051 0.039 -10000 0 -0.44 3 3
adherens junction organization 0.041 0.037 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.053 0.057 -10000 0 -0.74 1 1
FMN1 0.022 0.11 -10000 0 -0.44 25 25
mol:IP3 -0.003 0.032 -10000 0 -0.41 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 0.036 -10000 0 -0.4 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 0.036 -10000 0 -0.49 2 2
VASP 0.047 0.012 -10000 0 -10000 0 0
ZYX 0.047 0.012 -10000 0 -10000 0 0
JUB 0.046 0.025 -10000 0 -0.44 1 1
EGFR(dimer) 0.042 0.048 -10000 0 -0.47 4 4
E-cadherin/beta catenin-gamma catenin 0 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.034 -10000 0 -0.43 3 3
PIK3CA 0.009 0.066 -10000 0 -0.82 3 3
PI3K -0.003 0.034 -10000 0 -0.44 3 3
FYN 0.051 0.035 -10000 0 -0.35 3 3
mol:Ca2+ -0.002 0.031 -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 -0.003 0.032 -10000 0 -0.41 3 3
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.053 0.057 -10000 0 -0.47 4 4
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 0.006 0.076 -10000 0 -0.82 4 4
CASR 0.042 0.037 -10000 0 -0.38 3 3
RhoA/GTP -0.002 0.029 -10000 0 -0.36 3 3
AKT2 0.049 0.036 -10000 0 -0.4 3 3
actin cable formation 0.029 0.11 -10000 0 -0.42 25 25
apoptosis 0.003 0.033 0.41 3 -10000 0 3
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.047 0.062 -10000 0 -0.48 6 6
PIP5K1A 0.045 0.037 -10000 0 -0.5 2 2
PLCG1 -0.003 0.033 -10000 0 -0.42 3 3
Rac1/GTP -0.004 0.039 -10000 0 -0.42 4 4
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.01 0.033 -9999 0 -0.31 5 5
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.022 0.023 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.044 0.007 -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 0.044 0.007 -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 0.014 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.081 -9999 0 -0.5 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 -0.024 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 -0.82 1 1
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 0.074 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.074 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 0.073 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 0.032 -9999 0 -0.15 10 10
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.044 0.007 -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 0.075 -9999 0 -0.46 12 12
CCND1 0.015 0.038 -9999 0 -0.18 10 10
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 0.071 -9999 0 -0.44 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 0.009 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
Rac1/GTP -0.017 0.033 -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
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 -0.021 0.16 -10000 0 -0.73 22 22
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 0.069 -10000 0 -0.56 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 0.037 -10000 0 -0.56 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 0.026 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 0.07 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.016 0.078 -10000 0 -0.41 18 18
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 0.008 -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 0.023 0.5 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.028 0.078 -10000 0 -0.44 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 0.027 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.031 0.069 -10000 0 -0.44 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 0.004 -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 0.057 -9999 0 -10000 0 0
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 0.028 -9999 0 -0.43 2 2
ARF1/GTP -0.001 0.016 -9999 0 -10000 0 0
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 0.028 -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 0.01 -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 0.036 0.014 -9999 0 -10000 0 0
PLD2 -0.002 0.027 -9999 0 -0.43 2 2
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.002 0.028 -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 -0.17 2 2
GBF1 -0.001 0.011 -9999 0 -0.17 2 2
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 0.027 -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 0.029 -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 482 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 -0.5 -0.5 -0.5 -0.5
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B 0.047 -0.097 0 -0.097
84_STAT5A 0.047 -0.097 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/4403501/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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