PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1HX1BH8
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1HX1BH8
Overview
Introduction

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

Summary

There were 49 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 253
Signaling events mediated by Stem cell factor receptor (c-Kit) 165
Signaling events regulated by Ret tyrosine kinase 146
Reelin signaling pathway 141
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 116
TCGA08_retinoblastoma 112
Wnt signaling 107
IL4-mediated signaling events 101
FOXA2 and FOXA3 transcription factor networks 98
PDGFR-alpha signaling pathway 98
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 494 . 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 ( 494 ).

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 0.5121 253 1775 7 -0.52 0 1000 -1000 -0.03 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3340 165 12917 78 -0.8 0.24 1000 -1000 -0.071 -1000
Signaling events regulated by Ret tyrosine kinase 0.2955 146 12002 82 -0.46 0.013 1000 -1000 -0.084 -1000
Reelin signaling pathway 0.2854 141 7923 56 -0.59 0.033 1000 -1000 -0.065 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2348 116 7918 68 -0.9 0.37 1000 -1000 -0.12 -1000
TCGA08_retinoblastoma 0.2267 112 901 8 -0.12 0.071 1000 -1000 -0.024 -1000
Wnt signaling 0.2166 107 750 7 -0.41 0.013 1000 -1000 -0.025 -1000
IL4-mediated signaling events 0.2045 101 9270 91 -1.3 0.67 1000 -1000 -0.13 -1000
FOXA2 and FOXA3 transcription factor networks 0.1984 98 4534 46 -0.91 0.021 1000 -1000 -0.033 -1000
PDGFR-alpha signaling pathway 0.1984 98 4337 44 -0.49 0.033 1000 -1000 -0.06 -1000
Noncanonical Wnt signaling pathway 0.1883 93 2431 26 -0.41 0.013 1000 -1000 -0.075 -1000
Nongenotropic Androgen signaling 0.1700 84 4388 52 -0.34 0.16 1000 -1000 -0.057 -1000
Signaling events mediated by the Hedgehog family 0.1680 83 4356 52 -0.38 0.2 1000 -1000 -0.073 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1599 79 4286 54 -0.59 0.028 1000 -1000 -0.084 -1000
Calcium signaling in the CD4+ TCR pathway 0.1579 78 2441 31 -0.52 0.013 1000 -1000 -0.081 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1518 75 2561 34 -0.17 0.013 1000 -1000 -0.056 -1000
Glypican 1 network 0.1316 65 3122 48 -0.38 0.028 1000 -1000 -0.051 -1000
Ephrin B reverse signaling 0.1255 62 3003 48 -0.3 0.18 1000 -1000 -0.075 -1000
Endothelins 0.1255 62 6005 96 -0.39 0.013 1000 -1000 -0.08 -1000
IGF1 pathway 0.1174 58 3338 57 -0.19 0.058 1000 -1000 -0.096 -1000
Glucocorticoid receptor regulatory network 0.1154 57 6570 114 -0.55 0.36 1000 -1000 -0.06 -1000
IL23-mediated signaling events 0.1134 56 3375 60 -0.31 0.019 1000 -1000 -0.13 -1000
TCR signaling in naïve CD8+ T cells 0.1093 54 5071 93 -0.2 0.087 1000 -1000 -0.08 -1000
Glypican 2 network 0.1073 53 212 4 -0.087 -0.009 1000 -1000 -0.034 -1000
Syndecan-1-mediated signaling events 0.1012 50 1717 34 -0.2 0.013 1000 -1000 -0.057 -1000
BMP receptor signaling 0.1012 50 4105 81 -0.57 0.026 1000 -1000 -0.077 -1000
Arf6 signaling events 0.0992 49 3055 62 -0.32 0.02 1000 -1000 -0.068 -1000
HIF-1-alpha transcription factor network 0.0972 48 3685 76 -0.57 0.041 1000 -1000 -0.11 -1000
Coregulation of Androgen receptor activity 0.0951 47 3640 76 -0.77 0.062 1000 -1000 -0.041 -1000
EPHB forward signaling 0.0931 46 3993 85 -0.3 0.15 1000 -1000 -0.09 -1000
Syndecan-4-mediated signaling events 0.0830 41 2802 67 -0.25 0.022 1000 -1000 -0.088 -1000
IL6-mediated signaling events 0.0810 40 3056 75 -0.2 0.059 1000 -1000 -0.07 -1000
IL12-mediated signaling events 0.0789 39 3400 87 -0.4 0.025 1000 -1000 -0.12 -1000
amb2 Integrin signaling 0.0789 39 3198 82 -0.24 0.013 1000 -1000 -0.081 -1000
Signaling mediated by p38-alpha and p38-beta 0.0789 39 1717 44 -0.23 0.013 1000 -1000 -0.051 -1000
Hedgehog signaling events mediated by Gli proteins 0.0769 38 2514 65 -0.66 0.061 1000 -1000 -0.064 -1000
EGFR-dependent Endothelin signaling events 0.0688 34 724 21 -0.11 0.013 1000 -1000 -0.065 -1000
Osteopontin-mediated events 0.0648 32 1229 38 -0.26 0.013 1000 -1000 -0.099 -1000
Thromboxane A2 receptor signaling 0.0648 32 3421 105 -0.22 0.034 1000 -1000 -0.061 -1000
Ras signaling in the CD4+ TCR pathway 0.0648 32 558 17 -0.089 0.013 1000 -1000 -0.041 -1000
FAS signaling pathway (CD95) 0.0607 30 1425 47 -0.23 0.03 1000 -1000 -0.051 -1000
Regulation of Androgen receptor activity 0.0587 29 2051 70 -0.48 0.034 1000 -1000 -0.057 -1000
Syndecan-2-mediated signaling events 0.0547 27 1907 69 -0.22 0.038 1000 -1000 -0.05 -1000
Regulation of p38-alpha and p38-beta 0.0547 27 1489 54 -0.47 0.013 1000 -1000 -0.055 -1000
Plasma membrane estrogen receptor signaling 0.0547 27 2345 86 -0.18 0.021 1000 -1000 -0.084 -1000
ErbB2/ErbB3 signaling events 0.0526 26 1702 65 -0.12 0.027 1000 -1000 -0.062 -1000
JNK signaling in the CD4+ TCR pathway 0.0506 25 427 17 -0.1 0.018 1000 -1000 -0.058 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0506 25 1346 52 -0.28 0.053 1000 -1000 -0.055 -1000
BCR signaling pathway 0.0506 25 2478 99 -0.19 0.023 1000 -1000 -0.083 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0486 24 2043 85 -0.27 0.013 1000 -1000 -0.077 -1000
Integrins in angiogenesis 0.0466 23 1992 84 -0.23 0.033 1000 -1000 -0.097 -1000
Effects of Botulinum toxin 0.0466 23 615 26 -0.16 0.019 1000 -1000 -0.054 -1000
LPA receptor mediated events 0.0466 23 2419 102 -0.25 0.031 1000 -1000 -0.084 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0466 23 2073 88 -0.32 0.03 1000 -1000 -0.1 -1000
Signaling events mediated by PTP1B 0.0445 22 1698 76 -0.24 0.021 1000 -1000 -0.077 -1000
VEGFR1 specific signals 0.0445 22 1234 56 -0.07 0.041 1000 -1000 -0.071 -1000
Signaling events mediated by PRL 0.0445 22 769 34 -0.11 0.013 1000 -1000 -0.039 -1000
Nectin adhesion pathway 0.0425 21 1345 63 -0.26 0.029 1000 -1000 -0.074 -1000
IL27-mediated signaling events 0.0425 21 1107 51 -0.15 0.067 1000 -1000 -0.09 -1000
Regulation of nuclear SMAD2/3 signaling 0.0405 20 2741 136 -0.34 0.064 1000 -1000 -0.07 -1000
Aurora C signaling 0.0405 20 144 7 -0.061 0 1000 -1000 -0.036 -1000
Fc-epsilon receptor I signaling in mast cells 0.0405 20 1944 97 -0.2 0.03 1000 -1000 -0.078 -1000
ErbB4 signaling events 0.0364 18 1296 69 -0.14 0.057 1000 -1000 -0.08 -1000
Visual signal transduction: Cones 0.0364 18 712 38 -0.088 0.013 1000 -1000 -0.063 -1000
p75(NTR)-mediated signaling 0.0364 18 2369 125 -0.35 0.066 1000 -1000 -0.11 -1000
IL1-mediated signaling events 0.0364 18 1139 62 -0.12 0.066 1000 -1000 -0.093 -1000
Syndecan-3-mediated signaling events 0.0364 18 646 35 -0.16 0.013 1000 -1000 -0.063 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0364 18 2183 120 -0.31 0.042 1000 -1000 -0.074 -1000
TCGA08_rtk_signaling 0.0344 17 457 26 -0.24 0.025 1000 -1000 -0.022 -1000
Rapid glucocorticoid signaling 0.0324 16 338 20 -0.094 0.015 1000 -1000 -0.039 -1000
LPA4-mediated signaling events 0.0304 15 187 12 -0.12 0.015 1000 -1000 -0.014 -1000
Presenilin action in Notch and Wnt signaling 0.0304 15 949 61 -0.2 0.042 1000 -1000 -0.063 -1000
IL2 signaling events mediated by STAT5 0.0304 15 347 22 -0.068 0.039 1000 -1000 -0.035 -1000
Insulin Pathway 0.0304 15 1132 74 -0.085 0.035 1000 -1000 -0.09 -1000
FOXM1 transcription factor network 0.0304 15 772 51 -0.18 0.053 1000 -1000 -0.15 -1000
Insulin-mediated glucose transport 0.0283 14 475 32 -0.21 0.042 1000 -1000 -0.061 -1000
IFN-gamma pathway 0.0283 14 984 68 -0.1 0.042 1000 -1000 -0.09 -1000
IL2 signaling events mediated by PI3K 0.0283 14 851 58 -0.066 0.031 1000 -1000 -0.076 -1000
Visual signal transduction: Rods 0.0283 14 756 52 -0.2 0.015 1000 -1000 -0.076 -1000
Class IB PI3K non-lipid kinase events 0.0283 14 42 3 -0.003 -1000 1000 -1000 -0.01 -1000
a4b1 and a4b7 Integrin signaling 0.0263 13 68 5 -0.033 0.002 1000 -1000 -0.039 -1000
Ceramide signaling pathway 0.0263 13 1023 76 -0.18 0.024 1000 -1000 -0.058 -1000
Signaling events mediated by HDAC Class III 0.0263 13 556 40 -0.35 0.024 1000 -1000 -0.043 -1000
Aurora B signaling 0.0263 13 926 67 -0.38 0.014 1000 -1000 -0.069 -1000
mTOR signaling pathway 0.0243 12 651 53 -0.046 0.02 1000 -1000 -0.056 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0243 12 571 45 -0.087 0.039 1000 -1000 -0.08 -1000
BARD1 signaling events 0.0223 11 662 57 -0.036 0.051 1000 -1000 -0.062 -1000
Cellular roles of Anthrax toxin 0.0223 11 429 39 -0.087 0.019 1000 -1000 -0.027 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0223 11 818 74 -0.18 0.085 1000 -1000 -0.095 -1000
Class I PI3K signaling events 0.0223 11 839 73 -0.24 0.032 1000 -1000 -0.058 -1000
Regulation of Telomerase 0.0223 11 1138 102 -0.28 0.052 1000 -1000 -0.1 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0202 10 873 83 -0.21 0.052 1000 -1000 -0.071 -1000
S1P1 pathway 0.0202 10 371 36 -0.03 0.032 1000 -1000 -0.051 -1000
Caspase cascade in apoptosis 0.0182 9 727 74 -0.087 0.028 1000 -1000 -0.061 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0182 9 254 28 -0.18 0.03 1000 -1000 -0.052 -1000
Retinoic acid receptors-mediated signaling 0.0182 9 537 58 -0.11 0.034 1000 -1000 -0.069 -1000
S1P3 pathway 0.0182 9 394 42 -0.18 0.049 1000 -1000 -0.06 -1000
Class I PI3K signaling events mediated by Akt 0.0162 8 564 68 -0.21 0.052 1000 -1000 -0.066 -1000
TRAIL signaling pathway 0.0162 8 399 48 -0.074 0.047 1000 -1000 -0.063 -1000
ceramide signaling pathway 0.0162 8 422 49 -0.087 0.031 1000 -1000 -0.045 -1000
Canonical Wnt signaling pathway 0.0142 7 375 51 -0.048 0.067 1000 -1000 -0.053 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0142 7 262 33 -0.16 0.035 1000 -1000 -0.058 -1000
Arf6 downstream pathway 0.0121 6 284 43 -0.17 0.091 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0121 6 229 37 -0.035 0.039 1000 -1000 -0.057 -1000
Signaling events mediated by HDAC Class I 0.0121 6 666 104 -0.087 0.059 1000 -1000 -0.063 -1000
FoxO family signaling 0.0121 6 425 64 -0.21 0.16 1000 -1000 -0.061 -1000
Atypical NF-kappaB pathway 0.0101 5 160 31 -0.042 0.047 1000 -1000 -0.038 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0101 5 637 125 -0.036 0.085 1000 -1000 -0.088 -1000
E-cadherin signaling in the nascent adherens junction 0.0101 5 393 76 -0.17 0.073 1000 -1000 -0.085 -1000
S1P4 pathway 0.0101 5 134 25 -0.017 0.032 1000 -1000 -0.052 -1000
Canonical NF-kappaB pathway 0.0081 4 157 39 -0.087 0.073 1000 -1000 -0.083 -1000
Circadian rhythm pathway 0.0081 4 106 22 -0.055 0.013 1000 -1000 -0.064 -1000
EPO signaling pathway 0.0081 4 242 55 -0.026 0.061 1000 -1000 -0.088 -1000
Paxillin-dependent events mediated by a4b1 0.0081 4 145 36 -0.033 0.024 1000 -1000 -0.069 -1000
PLK1 signaling events 0.0061 3 293 85 -0.035 0.033 1000 -1000 -0.05 -1000
S1P5 pathway 0.0061 3 60 17 -0.017 0.022 1000 -1000 -0.055 -1000
HIF-2-alpha transcription factor network 0.0061 3 144 43 -0.2 0.2 1000 -1000 -0.076 -1000
Signaling mediated by p38-gamma and p38-delta 0.0061 3 53 15 0 0.031 1000 -1000 -0.026 -1000
PDGFR-beta signaling pathway 0.0061 3 371 97 -0.18 0.064 1000 -1000 -0.076 -1000
p38 MAPK signaling pathway 0.0061 3 153 44 -0.04 0.026 1000 -1000 -0.06 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 2 67 23 -0.04 0.049 1000 -1000 -0.065 -1000
Signaling events mediated by HDAC Class II 0.0040 2 177 75 -0.046 0.036 1000 -1000 -0.06 -1000
PLK2 and PLK4 events 0.0040 2 6 3 0.009 0.022 1000 -1000 -0.017 -1000
Aurora A signaling 0.0040 2 134 60 -0.05 0.038 1000 -1000 -0.053 -1000
E-cadherin signaling in keratinocytes 0.0040 2 125 43 -0.005 0.052 1000 -1000 -0.073 -1000
Arf6 trafficking events 0.0020 1 82 71 -0.023 0.046 1000 -1000 -0.079 -1000
TCGA08_p53 0.0000 0 0 7 -0.08 0.051 1000 -1000 -0.017 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.056 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0.013 1000 -1000 -0.051 -1000
Arf1 pathway 0.0000 0 37 54 -0.006 0.035 1000 -1000 -0.042 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 -0.001 0.013 1000 -1000 -0.06 -1000
Total NA 4077 225370 7203 -29 -990 131000 -131000 -8.6 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.42 0.31 -9999 0 -0.61 346 346
EFNA5 -0.11 0.3 -9999 0 -0.81 76 76
FYN -0.38 0.3 -9999 0 -0.55 346 346
neuron projection morphogenesis -0.42 0.31 -9999 0 -0.61 346 346
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.43 0.31 -9999 0 -0.61 346 346
EPHA5 -0.52 0.4 -9999 0 -0.81 315 315
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.22 0.22 -10000 0 -0.4 287 287
CRKL -0.22 0.24 -10000 0 -0.42 282 282
HRAS -0.19 0.21 -10000 0 -0.5 48 48
mol:PIP3 -0.22 0.22 -10000 0 -0.41 282 282
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.012 0.037 -10000 0 -0.81 1 1
GAB1 -0.24 0.25 -10000 0 -0.45 282 282
FOXO3 -0.2 0.22 -10000 0 -0.38 282 282
AKT1 -0.22 0.23 -10000 0 -0.42 282 282
BAD -0.2 0.22 -10000 0 -0.38 282 282
megakaryocyte differentiation -0.25 0.24 -10000 0 -0.45 290 290
GSK3B -0.2 0.22 -10000 0 -0.38 282 282
RAF1 -0.15 0.18 -10000 0 -0.46 25 25
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.24 0.25 -10000 0 -0.45 282 282
STAT1 -0.6 0.58 -10000 0 -1.1 284 284
HRAS/SPRED1 -0.18 0.14 -10000 0 -0.44 29 29
cell proliferation -0.24 0.26 -10000 0 -0.45 285 285
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 -10000 0 -0.45 282 282
HRAS/SPRED2 -0.18 0.14 -10000 0 -0.44 29 29
LYN/TEC/p62DOK -0.24 0.21 -10000 0 -0.41 282 282
MAPK3 -0.097 0.13 -10000 0 -0.31 22 22
STAP1 -0.26 0.25 -10000 0 -0.47 282 282
GRAP2 -0.045 0.21 -10000 0 -0.75 38 38
JAK2 -0.52 0.45 -10000 0 -0.9 282 282
STAT1 (dimer) -0.58 0.57 -10000 0 -1.1 284 284
mol:Gleevec 0.008 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.25 0.21 -10000 0 -0.42 285 285
actin filament polymerization -0.24 0.24 -10000 0 -0.44 282 282
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.35 0.34 -10000 0 -0.64 282 282
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.19 -10000 0 -0.37 270 270
PI3K -0.22 0.24 -10000 0 -0.42 283 283
PTEN 0.012 0.037 -10000 0 -0.81 1 1
SCF/KIT/EPO/EPOR -0.74 0.71 -10000 0 -1.4 282 282
MAPK8 -0.25 0.26 -10000 0 -0.46 285 285
STAT3 (dimer) -0.23 0.24 -10000 0 -0.44 282 282
positive regulation of transcription -0.077 0.11 -10000 0 -0.25 22 22
mol:GDP -0.23 0.19 -10000 0 -0.48 75 75
PIK3C2B -0.24 0.25 -10000 0 -0.45 282 282
CBL/CRKL -0.2 0.22 -10000 0 -0.39 281 281
FER -0.24 0.25 -10000 0 -0.45 283 283
SH2B3 -0.24 0.25 -10000 0 -0.45 282 282
PDPK1 -0.2 0.21 -10000 0 -0.37 283 283
SNAI2 -0.25 0.26 -10000 0 -0.46 284 284
positive regulation of cell proliferation -0.42 0.42 -10000 0 -0.77 284 284
KITLG -0.005 0.11 -10000 0 -0.85 8 8
cell motility -0.42 0.42 -10000 0 -0.77 284 284
PTPN6 0.021 0.018 -10000 0 -10000 0 0
EPOR -0.14 0.18 -10000 0 -0.6 4 4
STAT5A (dimer) -0.34 0.34 -10000 0 -0.63 282 282
SOCS1 0.008 0.049 -10000 0 -0.39 6 6
cell migration 0.24 0.25 0.45 285 -10000 0 285
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.005 0.041 -10000 0 -0.32 7 7
VAV1 -0.015 0.1 -10000 0 -0.35 39 39
GRB10 -0.24 0.25 -10000 0 -0.45 282 282
PTPN11 0.02 0.038 -10000 0 -0.8 1 1
SCF/KIT -0.26 0.26 -10000 0 -0.48 282 282
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.11 0.14 -10000 0 -0.35 22 22
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.8 0.74 -10000 0 -1.4 282 282
MAP2K2 -0.11 0.14 -10000 0 -0.35 22 22
SHC/Grb2/SOS1 -0.24 0.21 -10000 0 -0.41 282 282
STAT5A -0.35 0.36 -10000 0 -0.66 282 282
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.24 0.25 -10000 0 -0.45 284 284
SHC/GRAP2 -0.044 0.16 -10000 0 -0.62 33 33
PTPRO -0.26 0.25 -10000 0 -0.46 290 290
SH2B2 -0.24 0.25 -10000 0 -0.45 282 282
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.25 0.25 -10000 0 -0.46 285 285
CREBBP 0.017 0.02 -10000 0 -10000 0 0
BCL2 -0.22 0.42 -10000 0 -1.6 36 36
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.088 0.068 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.25 0.2 -9999 0 -0.5 121 121
JUN -0.32 0.31 -9999 0 -0.66 180 180
HRAS 0.012 0.021 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.38 0.32 -9999 0 -0.6 304 304
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.38 0.32 -9999 0 -0.6 304 304
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.29 0.25 -9999 0 -0.51 280 280
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.34 0.29 -9999 0 -0.54 304 304
GRB7 -0.04 0.12 -9999 0 -0.31 82 82
RET51/GFRalpha1/GDNF -0.38 0.32 -9999 0 -0.6 304 304
MAPKKK cascade -0.3 0.26 -9999 0 -0.52 226 226
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.34 0.31 -9999 0 -0.58 293 293
lamellipodium assembly -0.24 0.18 -9999 0 -0.38 281 281
RET51/GFRalpha1/GDNF/SHC -0.38 0.32 -9999 0 -0.6 304 304
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
RET9/GFRalpha1/GDNF/SHC -0.29 0.25 -9999 0 -0.5 280 280
RET9/GFRalpha1/GDNF/Shank3 -0.29 0.25 -9999 0 -0.5 280 280
MAPK3 -0.31 0.29 -9999 0 -0.51 304 304
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.3 -9999 0 -0.81 79 79
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.3 0.29 -9999 0 -0.66 131 131
DOK5 -0.099 0.28 -9999 0 -0.81 67 67
GFRA1 -0.46 0.41 -9999 0 -0.81 281 281
MAPK8 -0.23 0.24 -9999 0 -0.59 93 93
HRAS/GTP -0.35 0.3 -9999 0 -0.56 304 304
tube development -0.27 0.23 -9999 0 -0.47 280 280
MAPK1 -0.31 0.29 -9999 0 -0.51 304 304
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.18 0.18 -9999 0 -0.34 280 280
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
PDLIM7 0.011 0.029 -9999 0 -0.31 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.43 0.38 -9999 0 -0.66 315 315
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.38 0.32 -9999 0 -0.6 304 304
RET51/GFRalpha1/GDNF/Dok5 -0.44 0.38 -9999 0 -0.68 316 316
PRKCA -0.018 0.16 -9999 0 -0.81 19 19
HRAS/GDP -0.001 0.013 -9999 0 -10000 0 0
CREB1 -0.24 0.24 -9999 0 -0.43 280 280
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.18 -9999 0 -0.34 280 280
RET51/GFRalpha1/GDNF/Grb7 -0.4 0.32 -9999 0 -0.63 304 304
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.16 0.31 -9999 0 -0.63 135 135
DOK4 0.013 0.015 -9999 0 -0.31 1 1
JNK cascade -0.31 0.3 -9999 0 -0.64 180 180
RET9/GFRalpha1/GDNF/FRS2 -0.29 0.25 -9999 0 -0.5 280 280
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 -0.34 280 280
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.24 0.24 -9999 0 -0.43 248 248
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.24 0.23 -9999 0 -0.41 304 304
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.28 0.31 -9999 0 -0.47 304 304
PI3K -0.36 0.34 -9999 0 -0.62 281 281
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.27 0.23 -9999 0 -0.47 280 280
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.22 0.21 -9999 0 -0.52 85 85
RET51/GFRalpha1/GDNF/FRS2 -0.38 0.32 -9999 0 -0.6 304 304
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.085 0.27 -9999 0 -0.81 59 59
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.28 0.31 -9999 0 -0.47 304 304
RET51/GFRalpha1/GDNF/PKC alpha -0.4 0.34 -9999 0 -0.63 305 305
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.002 0.042 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.44 0.36 -9999 0 -0.67 316 316
Rac1/GTP -0.29 0.23 -9999 0 -0.46 281 281
RET9/GFRalpha1/GDNF -0.32 0.27 -9999 0 -0.56 280 280
GFRalpha1/GDNF -0.36 0.31 -9999 0 -0.63 280 280
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.001 0.015 -9999 0 -10000 0 0
VLDLR -0.02 0.16 -9999 0 -0.81 20 20
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 0.032 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.41 0.26 -9999 0 -0.56 366 366
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.01 0.067 -9999 0 -0.46 11 11
AKT1 -0.23 0.17 -9999 0 -0.33 367 367
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 -0.38 0.24 -9999 0 -0.52 364 364
LRPAP1/LRP8 -0.025 0.12 -9999 0 -0.62 20 20
RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 364 364
DAB1/alpha3/beta1 Integrin -0.34 0.23 -9999 0 -0.45 370 370
long-term memory -0.36 0.24 -9999 0 -0.48 366 366
DAB1/LIS1 -0.35 0.23 -9999 0 -0.47 370 370
DAB1/CRLK/C3G -0.34 0.22 -9999 0 -0.45 370 370
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
DAB1/NCK2 -0.35 0.24 -9999 0 -0.47 370 370
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.022 0.16 -9999 0 -0.63 27 27
CDK5R1 0.011 0.025 -9999 0 -0.31 3 3
RELN -0.59 0.37 -9999 0 -0.81 360 360
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.41 0.26 -9999 0 -0.56 364 364
GRIN2A/RELN/LRP8/DAB1/Fyn -0.37 0.25 -9999 0 -0.5 366 366
MAPK8 -0.005 0.12 -9999 0 -0.81 11 11
RELN/VLDLR/DAB1 -0.38 0.24 -9999 0 -0.52 366 366
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.36 0.26 -9999 0 -0.49 370 370
RELN/LRP8 -0.41 0.26 -9999 0 -0.56 364 364
GRIN2B/RELN/LRP8/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 364 364
PI3K -0.004 0.048 -9999 0 -0.62 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.02 -9999 0 -10000 0 0
RAP1A -0.3 0.23 -9999 0 -0.42 370 370
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.015 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.14 -9999 0 -0.52 23 23
neuron adhesion -0.28 0.22 -9999 0 -0.73 31 31
LRP8 -0.02 0.16 -9999 0 -0.81 20 20
GSK3B -0.21 0.16 -9999 0 -0.61 16 16
RELN/VLDLR/DAB1/Fyn -0.36 0.23 -9999 0 -0.49 366 366
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.35 367 367
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.033 0.087 -9999 0 -0.56 5 5
neuron migration -0.29 0.22 -9999 0 -0.41 366 366
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.14 -9999 0 -0.52 23 23
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 370 370
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.04 0.16 -10000 0 -0.59 26 26
NFATC2 -0.24 0.38 -10000 0 -0.84 119 119
NFATC3 -0.084 0.13 -10000 0 -0.26 117 117
CD40LG -0.74 0.57 -10000 0 -1.2 277 277
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 -0.54 0.53 -10000 0 -1.2 147 147
JUNB 0.003 0.091 -10000 0 -0.81 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.015 -10000 0 -0.34 1 1
T cell anergy 0.025 0.065 -10000 0 -0.49 1 1
TLE4 -0.24 0.44 -10000 0 -0.94 117 117
Jun/NFAT1-c-4/p21SNFT -0.66 0.6 -10000 0 -1.2 250 250
AP-1/NFAT1-c-4 -0.9 0.78 -10000 0 -1.5 276 276
IKZF1 -0.18 0.34 -10000 0 -0.8 85 85
T-helper 2 cell differentiation -0.32 0.35 -10000 0 -0.86 116 116
AP-1/NFAT1 -0.42 0.48 -10000 0 -0.9 217 217
CALM1 0.029 0.009 -10000 0 -10000 0 0
EGR2 -0.8 0.85 -10000 0 -1.6 236 236
EGR3 -0.56 0.73 -10000 0 -1.4 162 162
NFAT1/FOXP3 -0.22 0.34 -10000 0 -0.71 124 124
EGR1 -0.17 0.34 -10000 0 -0.82 107 107
JUN -0.19 0.34 -10000 0 -0.82 112 112
EGR4 -0.036 0.18 -10000 0 -0.72 31 31
mol:Ca2+ 0.016 0.01 -10000 0 -10000 0 0
GBP3 -0.17 0.32 -10000 0 -0.77 78 78
FOSL1 -0.032 0.12 -10000 0 -0.32 68 68
NFAT1-c-4/MAF/IRF4 -0.57 0.56 -10000 0 -1 248 248
DGKA -0.16 0.3 -10000 0 -0.74 72 72
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.56 0.56 -10000 0 -1 250 250
CTLA4 -0.24 0.39 -10000 0 -0.84 116 116
NFAT1-c-4 (dimer)/EGR1 -0.65 0.66 -10000 0 -1.2 249 249
NFAT1-c-4 (dimer)/EGR4 -0.58 0.56 -10000 0 -1.1 253 253
FOS -0.21 0.36 -10000 0 -0.82 127 127
IFNG -0.43 0.54 -10000 0 -1.1 152 152
T cell activation -0.44 0.42 -10000 0 -0.95 170 170
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.37 0.42 0.8 180 -10000 0 180
TNF -0.6 0.57 -10000 0 -1.1 265 265
FASLG -0.75 0.78 -10000 0 -1.4 251 251
TBX21 -0.039 0.18 -10000 0 -0.71 30 30
BATF3 -0.005 0.081 -10000 0 -0.33 27 27
PRKCQ 0.003 0.092 -10000 0 -0.81 6 6
PTPN1 -0.16 0.3 -10000 0 -0.7 86 86
NFAT1-c-4/ICER1 -0.55 0.55 -10000 0 -1 246 246
GATA3 -0.029 0.18 -10000 0 -0.78 27 27
T-helper 1 cell differentiation -0.41 0.52 -10000 0 -1.1 153 153
IL2RA -0.49 0.46 -10000 0 -1 166 166
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.3 -10000 0 -0.74 71 71
E2F1 -0.078 0.15 -10000 0 -10000 0 0
PPARG -0.002 0.1 -10000 0 -0.6 12 12
SLC3A2 -0.16 0.3 -10000 0 -0.74 71 71
IRF4 -0.1 0.24 -10000 0 -0.47 116 116
PTGS2 -0.71 0.56 -10000 0 -1.2 266 266
CSF2 -0.78 0.53 -10000 0 -1.2 277 277
JunB/Fra1/NFAT1-c-4 -0.54 0.53 -10000 0 -1 247 247
IL4 -0.33 0.37 -10000 0 -0.92 112 112
IL5 -0.7 0.54 -10000 0 -1.1 271 271
IL2 -0.45 0.44 -10000 0 -0.99 166 166
IL3 -0.097 0.062 -10000 0 -10000 0 0
RNF128 0.049 0.041 -10000 0 -0.87 1 1
NFATC1 -0.37 0.42 -10000 0 -0.81 178 178
CDK4 0.22 0.24 0.66 30 -10000 0 30
PTPRK -0.16 0.3 -10000 0 -0.7 84 84
IL8 -0.72 0.54 -10000 0 -1.2 268 268
POU2F1 0.013 0.015 -10000 0 -0.31 1 1
TCGA08_retinoblastoma

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
CDKN2B -0.12 0.16 -10000 0 -0.31 204 204
CDKN2C 0.026 0.036 -10000 0 -0.32 3 3
CDKN2A -0.12 0.16 -10000 0 -0.33 1 1
CCND2 0.068 0.071 0.17 138 -10000 0 138
RB1 -0.067 0.071 -10000 0 -0.17 138 138
CDK4 0.068 0.07 0.17 139 -10000 0 139
CDK6 0.071 0.076 0.18 138 -0.18 2 140
G1/S progression 0.059 0.078 0.17 138 -10000 0 138
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.27 0.28 -9999 0 -0.46 307 307
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.003 0.055 -9999 0 -0.31 15 15
WNT4 -0.26 0.39 -9999 0 -0.8 164 164
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 253 253
IL4-mediated signaling events

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
BCL2L1 -0.6 0.44 -10000 0 -1.1 175 175
STAT6 (cleaved dimer) -0.65 0.44 -10000 0 -1 264 264
IGHG1 -0.21 0.14 -10000 0 -0.35 69 69
IGHG3 -0.59 0.42 -10000 0 -0.94 241 241
AKT1 -0.32 0.26 -10000 0 -0.7 86 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.25 -10000 0 -0.7 67 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.36 0.28 -10000 0 -0.71 122 122
THY1 -0.6 0.44 -10000 0 -1.1 174 174
MYB -0.009 0.13 -10000 0 -0.64 17 17
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.42 0.31 -10000 0 -0.7 197 197
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.68 89 89
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.63 0.44 -10000 0 -1 247 247
SOCS1 -0.41 0.29 -10000 0 -0.73 134 134
SOCS3 -0.37 0.34 -10000 0 -0.98 72 72
FCER2 -0.63 0.47 -10000 0 -1.1 199 199
PARP14 0.013 0.004 -10000 0 -10000 0 0
CCL17 -0.67 0.47 -10000 0 -1.1 198 198
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.21 -10000 0 -0.63 60 60
T cell proliferation -0.61 0.46 -10000 0 -1.1 198 198
IL4R/JAK1 -0.6 0.44 -10000 0 -1 190 190
EGR2 -0.96 0.72 -10000 0 -1.6 256 256
JAK2 -0.02 0.058 -10000 0 -0.85 2 2
JAK3 -0.066 0.14 -10000 0 -0.31 125 125
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.008 -10000 0 -10000 0 0
COL1A2 -0.2 0.17 -10000 0 -0.58 28 28
CCL26 -0.62 0.45 -10000 0 -1.1 184 184
IL4R -0.64 0.46 -10000 0 -1.1 199 199
PTPN6 0.029 0.009 -10000 0 -10000 0 0
IL13RA2 -0.71 0.56 -10000 0 -1.3 203 203
IL13RA1 -0.016 0.024 -10000 0 -10000 0 0
IRF4 -0.36 0.5 -10000 0 -1.1 110 110
ARG1 -0.15 0.11 -10000 0 -10000 0 0
CBL -0.39 0.29 -10000 0 -0.69 165 165
GTF3A 0.016 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
IL13RA1/JAK2 -0.026 0.052 -10000 0 -0.66 2 2
IRF4/BCL6 -0.32 0.46 -10000 0 -1.1 101 101
CD40LG -0.13 0.31 -10000 0 -0.8 87 87
MAPK14 -0.39 0.31 -10000 0 -0.75 140 140
mitosis -0.31 0.24 -10000 0 -0.66 86 86
STAT6 -0.68 0.51 -10000 0 -1.1 235 235
SPI1 0 0.074 -10000 0 -0.31 27 27
RPS6KB1 -0.29 0.23 -10000 0 -0.66 68 68
STAT6 (dimer) -0.68 0.51 -10000 0 -1.1 235 235
STAT6 (dimer)/PARP14 -0.64 0.47 -10000 0 -1.1 220 220
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.27 -10000 0 -0.71 91 91
FRAP1 -0.32 0.26 -10000 0 -0.7 86 86
LTA -0.62 0.45 -10000 0 -1.1 191 191
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.67 0.49 1.1 235 -10000 0 235
CCL11 -0.59 0.43 -10000 0 -1.1 160 160
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.7 93 93
IL2RG -0.045 0.19 -10000 0 -0.52 57 57
IL10 -0.62 0.47 -10000 0 -1.2 147 147
IRS1 -0.085 0.27 -10000 0 -0.81 59 59
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.094 -10000 0 -10000 0 0
IL5 -0.61 0.44 -10000 0 -1.1 175 175
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.49 0.33 -10000 0 -0.81 195 195
COL1A1 -0.26 0.23 -10000 0 -0.64 64 64
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.6 0.45 -10000 0 -1.1 164 164
IL2R gamma/JAK3 -0.081 0.18 -10000 0 -0.5 57 57
TFF3 -1.3 0.61 -10000 0 -1.6 402 402
ALOX15 -0.6 0.44 -10000 0 -1.1 173 173
MYBL1 0.013 0.015 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.52 0.36 -10000 0 -0.84 218 218
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 -0.31 0.25 -10000 0 -0.69 74 74
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.7 86 86
PI3K -0.34 0.28 -10000 0 -0.75 84 84
DOK2 -0.001 0.078 -10000 0 -0.36 19 19
ETS1 0.03 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.25 0.21 -10000 0 -0.63 56 56
ITGB3 -0.62 0.47 -10000 0 -1.1 165 165
PIGR -0.65 0.5 -10000 0 -1.2 176 176
IGHE 0.052 0.035 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.61 57 57
BCL6 0.012 0.037 -10000 0 -0.81 1 1
OPRM1 -0.61 0.44 -10000 0 -1.1 181 181
RETNLB -0.61 0.44 -10000 0 -1.1 141 141
SELP -0.61 0.45 -10000 0 -1.1 182 182
AICDA -0.59 0.42 -10000 0 -1 180 180
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 -0.51 0.54 -9999 0 -1 220 220
PCK1 -0.34 0.49 -9999 0 -1.4 66 66
HNF4A -0.66 0.65 -9999 0 -1.3 246 246
KCNJ11 -0.48 0.54 -9999 0 -1 203 203
AKT1 -0.042 0.12 -9999 0 -0.38 11 11
response to starvation -0.017 0.033 -9999 0 -10000 0 0
DLK1 -0.49 0.53 -9999 0 -1.1 182 182
NKX2-1 -0.16 0.21 -9999 0 -10000 0 0
ACADM -0.51 0.54 -9999 0 -1.1 205 205
TAT -0.2 0.22 -9999 0 -0.63 20 20
CEBPB 0.013 0.005 -9999 0 -10000 0 0
CEBPA 0.005 0.083 -9999 0 -0.81 5 5
TTR -0.19 0.22 -9999 0 -0.72 37 37
PKLR -0.52 0.54 -9999 0 -1.1 214 214
APOA1 -0.91 0.89 -9999 0 -1.7 249 249
CPT1C -0.53 0.54 -9999 0 -1.1 219 219
ALAS1 -0.16 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.3 -9999 0 -0.71 57 57
FOXF1 -0.007 0.075 -9999 0 -0.72 5 5
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.007 -9999 0 -10000 0 0
CPT1A -0.51 0.54 -9999 0 -1 214 214
HMGCS1 -0.51 0.54 -9999 0 -1 220 220
NR3C1 0.019 0.017 -9999 0 -10000 0 0
CPT1B -0.51 0.54 -9999 0 -1 220 220
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.66 0.7 -9999 0 -1.3 232 232
CREB1 0 0.053 -9999 0 -10000 0 0
IGFBP1 -0.18 0.2 -9999 0 -0.59 6 6
PDX1 -0.18 0.21 -9999 0 -0.6 1 1
UCP2 -0.51 0.54 -9999 0 -1 215 215
ALDOB -0.48 0.54 -9999 0 -1 201 201
AFP -0.045 0.11 -9999 0 -0.5 7 7
BDH1 -0.51 0.54 -9999 0 -1 214 214
HADH -0.48 0.53 -9999 0 -1 200 200
F2 -0.62 0.63 -9999 0 -1.3 211 211
HNF1A 0.015 0.007 -9999 0 -10000 0 0
G6PC -0.006 0.09 -9999 0 -10000 0 0
SLC2A2 -0.23 0.26 -9999 0 -0.82 1 1
INS -0.013 0.066 -9999 0 -0.82 3 3
FOXA1 -0.053 0.14 -9999 0 -0.33 88 88
FOXA3 -0.072 0.17 -9999 0 -0.5 35 35
FOXA2 -0.55 0.6 -9999 0 -1.1 223 223
ABCC8 -0.78 0.74 -9999 0 -1.4 274 274
ALB -0.094 0.31 -9999 0 -1.3 30 30
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 -0.25 0.38 -9999 0 -0.83 151 151
PDGF/PDGFRA/CRKL -0.19 0.29 -9999 0 -0.62 151 151
positive regulation of JUN kinase activity -0.15 0.22 -9999 0 -0.48 151 151
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.2 0.29 -9999 0 -0.63 151 151
AP1 -0.49 0.62 -9999 0 -1.4 134 134
mol:IP3 -0.19 0.3 -9999 0 -0.64 151 151
PLCG1 -0.19 0.3 -9999 0 -0.65 151 151
PDGF/PDGFRA/alphaV Integrin -0.19 0.29 -9999 0 -0.62 152 152
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.3 -9999 0 -0.64 151 151
CAV3 -0.001 0.028 -9999 0 -0.31 4 4
CAV1 -0.008 0.13 -9999 0 -0.81 13 13
SHC/Grb2/SOS1 -0.15 0.22 -9999 0 -0.48 151 151
PDGF/PDGFRA/Shf -0.19 0.29 -9999 0 -0.62 151 151
FOS -0.44 0.6 -9999 0 -1.4 134 134
JUN -0.17 0.28 -9999 0 -0.7 112 112
oligodendrocyte development -0.19 0.29 -9999 0 -0.62 152 152
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.3 -9999 0 -0.64 151 151
PDGF/PDGFRA -0.25 0.38 -9999 0 -0.83 151 151
actin cytoskeleton reorganization -0.19 0.29 -9999 0 -0.62 151 151
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.17 0.25 -9999 0 -0.53 154 154
PDGF/PDGFRA/Crk/C3G -0.16 0.24 -9999 0 -0.53 151 151
JAK1 -0.18 0.3 -9999 0 -0.62 151 151
ELK1/SRF -0.12 0.24 -9999 0 -0.48 151 151
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0.015 -9999 0 -0.31 1 1
CSNK2A1 0.027 0.027 -9999 0 -10000 0 0
GO:0007205 -0.2 0.31 -9999 0 -0.66 151 151
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.15 0.22 -9999 0 -0.48 151 151
PDGF/PDGFRA/SHB -0.19 0.29 -9999 0 -0.62 151 151
PDGF/PDGFRA/Caveolin-1 -0.2 0.31 -9999 0 -0.66 154 154
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
ELK1 -0.18 0.28 -9999 0 -0.59 151 151
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
PDGF/PDGFRA/Crk -0.19 0.29 -9999 0 -0.62 151 151
JAK-STAT cascade -0.18 0.29 -9999 0 -0.62 151 151
cell proliferation -0.19 0.29 -9999 0 -0.62 151 151
Noncanonical Wnt signaling pathway

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
NFATC2 -0.13 0.31 -9999 0 -0.81 86 86
GNB1/GNG2 -0.26 0.24 -9999 0 -0.59 127 127
mol:DAG -0.21 0.24 -9999 0 -0.55 117 117
PLCG1 -0.22 0.24 -9999 0 -0.57 117 117
YES1 -0.25 0.26 -9999 0 -0.62 126 126
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.22 0.24 -9999 0 -0.57 117 117
MAP3K7 -0.17 0.2 -9999 0 -0.45 117 117
mol:Ca2+ -0.2 0.23 -9999 0 -0.53 117 117
mol:IP3 -0.21 0.24 -9999 0 -0.55 117 117
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 -0.49 118 118
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.27 0.28 -9999 0 -0.46 307 307
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.25 0.26 -9999 0 -0.62 126 126
GO:0007205 -0.2 0.23 -9999 0 -0.54 117 117
WNT6 0.003 0.055 -9999 0 -0.31 15 15
WNT4 -0.26 0.39 -9999 0 -0.8 164 164
NFAT1/CK1 alpha -0.3 0.25 -9999 0 -0.62 152 152
GNG2 0.012 0.037 -9999 0 -0.81 1 1
WNT5A -0.004 0.12 -9999 0 -0.77 11 11
WNT11 -0.41 0.41 -9999 0 -0.81 253 253
CDC42 -0.23 0.25 -9999 0 -0.58 126 126
Nongenotropic Androgen signaling

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.25 -10000 0 -0.5 210 210
regulation of S phase of mitotic cell cycle -0.13 0.18 -10000 0 -0.34 211 211
GNAO1 -0.017 0.15 -10000 0 -0.69 21 21
HRAS 0.012 0.021 -10000 0 -0.31 2 2
SHBG/T-DHT -0.008 0.07 -10000 0 -0.56 8 8
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.16 0.23 -10000 0 -0.43 209 209
T-DHT/AR -0.27 0.31 -10000 0 -0.64 209 209
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 127 127
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.82 1 1
mol:GDP -0.26 0.3 -10000 0 -0.61 211 211
cell proliferation -0.2 0.28 -10000 0 -0.65 86 86
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
FOS -0.24 0.39 -10000 0 -0.89 127 127
mol:Ca2+ -0.027 0.03 -10000 0 -0.071 92 92
MAPK3 -0.18 0.26 -10000 0 -0.59 86 86
MAPK1 -0.082 0.13 -10000 0 -0.3 77 77
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 127 127
cAMP biosynthetic process 0.016 0.074 -10000 0 -0.52 8 8
GNG2 0.012 0.037 -10000 0 -0.81 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 127 127
HRAS/GTP -0.2 0.23 -10000 0 -0.46 209 209
actin cytoskeleton reorganization -0.003 0.034 -10000 0 -0.44 3 3
SRC 0.012 0.015 -10000 0 -0.32 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 127 127
PI3K -0.003 0.042 -10000 0 -0.55 3 3
apoptosis 0.16 0.25 0.52 127 -10000 0 127
T-DHT/AR/PELP1 -0.23 0.27 -10000 0 -0.55 209 209
HRAS/GDP -0.25 0.29 -10000 0 -0.58 210 210
CREB1 -0.17 0.27 -10000 0 -0.57 127 127
RAC1-CDC42/GTP -0.003 0.035 -10000 0 -0.45 3 3
AR -0.34 0.41 -10000 0 -0.82 209 209
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.17 0.24 -10000 0 -0.45 209 209
RAC1-CDC42/GDP -0.23 0.27 -10000 0 -0.55 209 209
T-DHT/AR/PELP1/Src -0.21 0.25 -10000 0 -0.5 209 209
MAP2K2 -0.16 0.23 -10000 0 -0.43 209 209
T-DHT/AR/PELP1/Src/PI3K -0.13 0.18 -10000 0 -0.34 211 211
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG 0 0.1 -10000 0 -0.81 8 8
Gi family/GNB1/GNG2/GDP -0.02 0.12 -10000 0 -0.54 16 16
mol:T-DHT 0 0.001 0.001 75 -0.003 50 125
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.009 0.042 -10000 0 -0.49 3 3
Gi family/GTP -0.095 0.12 -10000 0 -0.46 18 18
CDC42 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.11 0.26 -10000 0 -0.68 35 35
IHH -0.2 0.37 -10000 0 -0.83 123 123
SHH Np/Cholesterol/GAS1 -0.1 0.2 -10000 0 -0.51 96 96
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.1 0.2 0.51 96 -10000 0 96
SMO/beta Arrestin2 -0.095 0.24 -10000 0 -0.48 126 126
SMO -0.11 0.25 -10000 0 -0.51 127 127
AKT1 -0.027 0.12 -10000 0 -0.66 2 2
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC 0 0.1 -10000 0 -0.81 8 8
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.1 0.25 -10000 0 -0.5 127 127
STIL -0.077 0.2 -10000 0 -0.59 18 18
DHH N/PTCH2 -0.11 0.24 -10000 0 -0.64 82 82
DHH N/PTCH1 -0.099 0.22 -10000 0 -0.45 130 130
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
DHH 0.007 0.074 -10000 0 -0.81 4 4
PTHLH -0.16 0.36 -10000 0 -1.2 35 35
determination of left/right symmetry -0.1 0.25 -10000 0 -0.5 127 127
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.15 0.36 -10000 0 -1.1 35 35
IHH N/Hhip -0.38 0.4 -10000 0 -0.73 263 263
DHH N/Hhip -0.25 0.31 -10000 0 -0.63 195 195
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.1 0.25 -10000 0 -0.5 127 127
pancreas development -0.31 0.4 -10000 0 -0.81 195 195
HHAT 0.012 0.037 -10000 0 -0.81 1 1
PI3K -0.004 0.048 -10000 0 -0.62 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.15 0.33 -10000 0 -0.81 95 95
somite specification -0.1 0.25 -10000 0 -0.5 127 127
SHH Np/Cholesterol/PTCH1 -0.087 0.2 -10000 0 -0.61 17 17
SHH Np/Cholesterol/PTCH2 -0.087 0.19 -10000 0 -0.51 81 81
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.51 134 134
SHH 0.007 0.049 -10000 0 -0.62 1 1
catabolic process -0.11 0.25 -10000 0 -0.5 126 126
SMO/Vitamin D3 -0.091 0.22 -10000 0 -0.65 17 17
SHH Np/Cholesterol/Hhip -0.2 0.24 -10000 0 -0.5 195 195
LRP2 -0.21 0.37 -10000 0 -0.81 133 133
receptor-mediated endocytosis -0.2 0.23 -10000 0 -0.71 49 49
SHH Np/Cholesterol/BOC -0.014 0.073 -10000 0 -0.52 9 9
SHH Np/Cholesterol/CDO -0.15 0.23 -10000 0 -0.51 146 146
mesenchymal cell differentiation 0.2 0.24 0.5 195 -10000 0 195
mol:Vitamin D3 -0.086 0.2 -10000 0 -0.42 86 86
IHH N/PTCH2 -0.23 0.34 -10000 0 -0.66 181 181
CDON -0.23 0.38 -10000 0 -0.81 145 145
IHH N/PTCH1 -0.12 0.25 -10000 0 -0.51 126 126
Megalin/LRPAP1 -0.17 0.28 -10000 0 -0.62 133 133
PTCH2 -0.12 0.3 -10000 0 -0.81 80 80
SHH Np/Cholesterol -0.006 0.035 -10000 0 -0.5 1 1
PTCH1 -0.11 0.25 -10000 0 -0.51 126 126
HHIP -0.31 0.4 -10000 0 -0.81 195 195
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 -0.02 0.16 -9999 0 -0.81 20 20
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.41 0.26 -9999 0 -0.56 364 364
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 -0.36 0.25 -9999 0 -0.51 364 364
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 -0.092 0.28 -9999 0 -0.81 63 63
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 -0.025 0.12 -9999 0 -0.62 20 20
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.011 0.025 -9999 0 -0.31 3 3
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.021 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.42 0.26 -9999 0 -0.56 366 366
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.27 0.2 -9999 0 -0.72 16 16
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.31 0.22 -9999 0 -0.44 364 364
RELN -0.59 0.37 -9999 0 -0.81 360 360
PAFAH/LIS1 -0.044 0.19 -9999 0 -0.54 63 63
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.22 0.14 -9999 0 -0.54 16 16
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.24 0.18 -9999 0 -0.34 371 371
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.29 0.22 -9999 0 -0.42 364 364
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.029 -9999 0 -0.31 4 4
PAFAH1B2 -0.002 0.11 -9999 0 -0.81 9 9
MAP1B/LIS1/Dynein heavy chain 0.027 0.003 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.27 0.17 -9999 0 -0.69 16 16
LRP8 -0.02 0.16 -9999 0 -0.81 20 20
NDEL1/Katanin 60 -0.27 0.2 -9999 0 -0.72 16 16
P39/CDK5 -0.32 0.23 -9999 0 -0.44 364 364
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.34 0.24 -9999 0 -0.47 364 364
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.36 0.22 -9999 0 -0.48 366 366
RELN/VLDLR -0.4 0.26 -9999 0 -0.53 370 370
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 0.079 -9999 0 -0.56 9 9
NFATC2 -0.1 0.22 -9999 0 -0.57 86 86
NFATC3 0 0.027 -9999 0 -10000 0 0
CD40LG -0.44 0.42 -9999 0 -0.88 203 203
PTGS2 -0.41 0.4 -9999 0 -0.84 188 188
JUNB 0.003 0.091 -9999 0 -0.81 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.82 112 112
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 -0.032 0.12 -9999 0 -0.32 68 68
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 -0.21 0.36 -9999 0 -0.82 127 127
IFNG -0.44 0.41 -9999 0 -0.86 203 203
AP-1/NFAT1-c-4 -0.52 0.52 -9999 0 -0.98 226 226
FASLG -0.42 0.39 -9999 0 -0.84 191 191
NFAT1-c-4/ICER1 -0.12 0.2 -9999 0 -0.5 94 94
IL2RA -0.41 0.39 -9999 0 -0.83 188 188
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.47 0.36 -9999 0 -0.77 261 261
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.5 99 99
IL4 -0.39 0.36 -9999 0 -0.8 183 183
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 -0.005 0.081 -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 0.17 0.3 0.68 121 -10000 0 121
KIRREL -0.073 0.24 -10000 0 -0.84 44 44
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.17 0.3 -10000 0 -0.69 121 121
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 -0.54 121 121
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.077 0.2 -10000 0 -0.41 121 121
FYN -0.11 0.24 -10000 0 -0.51 121 121
mol:Ca2+ -0.13 0.24 -10000 0 -0.53 121 121
mol:DAG -0.13 0.24 -10000 0 -0.53 121 121
NPHS2 -0.017 0.052 -10000 0 -0.89 1 1
mol:IP3 -0.13 0.24 -10000 0 -0.53 121 121
regulation of endocytosis -0.12 0.21 -10000 0 -0.47 121 121
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.54 121 121
establishment of cell polarity -0.17 0.3 -10000 0 -0.68 121 121
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.49 121 121
Nephrin/NEPH1/beta Arrestin2 -0.1 0.23 -10000 0 -0.48 121 121
NPHS1 -0.15 0.32 -10000 0 -0.82 92 92
Nephrin/NEPH1/podocin -0.12 0.23 -10000 0 -0.51 121 121
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 -0.54 121 121
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 121 121
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.25 -10000 0 -0.51 125 125
cytoskeleton organization -0.1 0.26 -10000 0 -0.53 121 121
Nephrin/NEPH1 -0.13 0.24 -10000 0 -0.52 121 121
Nephrin/NEPH1/ZO-1 -0.14 0.26 -10000 0 -0.57 121 121
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.001 0.025 -9999 0 -0.54 1 1
fibroblast growth factor receptor signaling pathway -0.001 0.025 -9999 0 -0.54 1 1
LAMA1 -0.048 0.22 -9999 0 -0.8 37 37
PRNP 0.012 0.037 -9999 0 -0.81 1 1
GPC1/SLIT2 -0.095 0.22 -9999 0 -0.62 74 74
SMAD2 0.028 0.048 -9999 0 -0.49 3 3
GPC1/PrPc/Cu2+ -0.001 0.026 -9999 0 -0.55 1 1
GPC1/Laminin alpha1 -0.046 0.16 -9999 0 -0.62 36 36
TDGF1 -0.34 0.41 -9999 0 -0.81 209 209
CRIPTO/GPC1 -0.26 0.31 -9999 0 -0.62 209 209
APP/GPC1 0 0.009 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.21 0.28 -9999 0 -0.54 209 209
FLT1 0.012 0.037 -9999 0 -0.81 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.048 -9999 0 -0.54 3 3
SERPINC1 0.006 0.046 -9999 0 -0.31 10 10
FYN -0.21 0.28 -9999 0 -0.54 209 209
FGR -0.21 0.28 -9999 0 -0.54 209 209
positive regulation of MAPKKK cascade -0.28 0.31 -9999 0 -0.61 211 211
SLIT2 -0.11 0.3 -9999 0 -0.79 77 77
GPC1/NRG -0.058 0.18 -9999 0 -0.62 45 45
NRG1 -0.063 0.24 -9999 0 -0.79 47 47
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.058 -9999 0 -0.7 3 3
LYN -0.21 0.28 -9999 0 -0.54 209 209
mol:Spermine 0.012 0.01 -9999 0 -10000 0 0
cell growth -0.001 0.025 -9999 0 -0.54 1 1
BMP signaling pathway -0.013 0.015 -9999 0 -10000 0 0
SRC -0.21 0.28 -9999 0 -0.54 209 209
TGFBR1 0.006 0.05 -9999 0 -0.31 12 12
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.24 0.36 -9999 0 -0.68 185 185
GPC1 0.013 0.015 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.006 0.05 -9999 0 -0.31 12 12
VEGFA 0.008 0.064 -9999 0 -0.81 3 3
BLK -0.38 0.37 -9999 0 -0.66 284 284
HCK -0.22 0.28 -9999 0 -0.55 209 209
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.012 0.037 -9999 0 -0.81 1 1
VEGFR1 homodimer 0.012 0.037 -9999 0 -0.81 1 1
TGFBR2 0.008 0.064 -9999 0 -0.81 3 3
cell death 0 0.009 -9999 0 -10000 0 0
ATIII/GPC1 -0.004 0.029 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.19 0.27 -9999 0 -0.62 134 134
LCK -0.22 0.28 -9999 0 -0.54 214 214
neuron differentiation -0.058 0.18 -9999 0 -0.62 45 45
PrPc/Cu2+ -0.001 0.028 -9999 0 -0.63 1 1
APP 0.013 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.008 0.064 -9999 0 -0.81 3 3
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.064 -10000 0 -0.82 3 3
EFNB1 0.001 0.12 -10000 0 -0.63 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.24 0.24 -10000 0 -0.52 201 201
Ephrin B2/EPHB1-2 -0.19 0.24 -10000 0 -0.5 188 188
neuron projection morphogenesis -0.23 0.23 -10000 0 -0.49 201 201
Ephrin B1/EPHB1-2/Tiam1 -0.26 0.26 -10000 0 -0.56 201 201
DNM1 -0.015 0.15 -10000 0 -0.79 17 17
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.005 0.088 -10000 0 -0.78 6 6
YES1 -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/NCK2 -0.18 0.24 -10000 0 -0.46 201 201
PI3K 0.003 0.12 -10000 0 -1 6 6
mol:GDP -0.25 0.26 -10000 0 -0.55 201 201
ITGA2B -0.075 0.26 -10000 0 -0.81 53 53
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.01 0.11 -10000 0 -1 6 6
MAP3K7 -0.012 0.091 -10000 0 -0.83 6 6
FGR -0.012 0.11 -10000 0 -1 6 6
TIAM1 -0.17 0.16 -10000 0 -0.31 276 276
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.044 0.2 -10000 0 -0.53 66 66
LYN -0.01 0.11 -10000 0 -1 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.014 0.1 -10000 0 -0.96 6 6
Ephrin B1/EPHB1-2 -0.019 0.098 -10000 0 -0.89 6 6
SRC -0.012 0.11 -10000 0 -1 6 6
ITGB3 -0.012 0.14 -10000 0 -0.81 15 15
EPHB1 -0.3 0.4 -10000 0 -0.82 186 186
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 -0.084 0.23 -10000 0 -0.67 62 62
BLK -0.066 0.14 -10000 0 -1.1 6 6
HCK -0.013 0.11 -10000 0 -1 6 6
regulation of stress fiber formation 0.18 0.24 0.46 201 -10000 0 201
MAPK8 0.003 0.13 -10000 0 -0.77 12 12
Ephrin B1/EPHB1-2/RGS3 -0.18 0.24 -10000 0 -0.46 201 201
endothelial cell migration -0.006 0.08 -10000 0 -0.72 6 6
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.005 0.1 -10000 0 -0.93 6 6
regulation of focal adhesion formation 0.18 0.24 0.46 201 -10000 0 201
chemotaxis 0.18 0.24 0.46 201 -10000 0 201
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
Rac1/GTP -0.24 0.24 -10000 0 -0.51 201 201
angiogenesis -0.019 0.097 -10000 0 -0.88 6 6
LCK -0.015 0.12 -10000 0 -1 6 6
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.052 0.14 -9999 0 -0.58 10 10
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.7 63 63
EDN1 -0.044 0.12 -9999 0 -0.76 7 7
EDN3 -0.39 0.41 -9999 0 -0.81 244 244
EDN2 -0.014 0.11 -9999 0 -0.4 32 32
HRAS/GDP -0.1 0.24 -9999 0 -0.54 82 82
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.086 0.18 -9999 0 -0.39 90 90
ADCY4 -0.097 0.19 -9999 0 -0.5 72 72
ADCY5 -0.16 0.25 -9999 0 -0.55 118 118
ADCY6 -0.097 0.19 -9999 0 -0.5 72 72
ADCY7 -0.097 0.19 -9999 0 -0.5 72 72
ADCY1 -0.1 0.21 -9999 0 -0.53 74 74
ADCY2 -0.14 0.24 -9999 0 -0.55 105 105
ADCY3 -0.097 0.19 -9999 0 -0.5 72 72
ADCY8 -0.2 0.21 -9999 0 -0.55 97 97
ADCY9 -0.097 0.19 -9999 0 -0.5 72 72
arachidonic acid secretion -0.17 0.32 -9999 0 -0.63 139 139
ETB receptor/Endothelin-1/Gq/GTP -0.097 0.22 -9999 0 -0.43 121 121
GNAO1 -0.017 0.15 -9999 0 -0.69 21 21
HRAS 0.01 0.021 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.018 0.16 -9999 0 -0.56 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.086 0.22 -9999 0 -0.53 72 72
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.069 0.17 -9999 0 -0.51 36 36
EDNRB 0.003 0.094 -9999 0 -0.75 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.15 0.24 -9999 0 -0.63 54 54
CYSLTR1 -0.063 0.18 -9999 0 -0.77 17 17
SLC9A1 -0.022 0.075 -9999 0 -0.31 7 7
mol:GDP -0.12 0.26 -9999 0 -0.56 92 92
SLC9A3 -0.049 0.19 -9999 0 -0.8 21 21
RAF1 -0.15 0.3 -9999 0 -0.59 125 125
JUN -0.28 0.52 -9999 0 -1.2 121 121
JAK2 -0.054 0.15 -9999 0 -0.59 12 12
mol:IP3 -0.11 0.23 -9999 0 -0.49 107 107
ETA receptor/Endothelin-1 -0.039 0.2 -9999 0 -0.63 12 12
PLCB1 0.009 0.038 -9999 0 -0.82 1 1
PLCB2 0.004 0.047 -9999 0 -0.32 10 10
ETA receptor/Endothelin-3 -0.32 0.33 -9999 0 -0.66 243 243
FOS -0.25 0.47 -9999 0 -1 129 129
Gai/GDP -0.002 0.13 -9999 0 -0.64 17 17
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.24 -9999 0 -0.62 50 50
BCAR1 0.013 0.001 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.48 107 107
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.094 0.28 -9999 0 -0.81 64 64
Gs family/GDP -0.19 0.25 -9999 0 -0.57 120 120
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.45 106 106
MAPK14 -0.065 0.18 -9999 0 -0.44 45 45
TRPC6 -0.14 0.3 -9999 0 -0.74 62 62
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.012 0.037 -9999 0 -0.81 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.077 0.19 -9999 0 -0.4 85 85
ETB receptor/Endothelin-2 -0.026 0.1 -9999 0 -0.63 12 12
ETB receptor/Endothelin-3 -0.31 0.32 -9999 0 -0.63 245 245
ETB receptor/Endothelin-1 -0.021 0.12 -9999 0 -0.65 12 12
MAPK3 -0.23 0.43 -9999 0 -0.9 134 134
MAPK1 -0.23 0.43 -9999 0 -0.9 134 134
Rac1/GDP -0.1 0.24 -9999 0 -0.54 76 76
cAMP biosynthetic process -0.14 0.21 -9999 0 -0.55 77 77
MAPK8 -0.18 0.35 -9999 0 -0.67 123 123
SRC 0.013 0.015 -9999 0 -0.31 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.008 0.078 -9999 0 -0.35 10 10
p130Cas/CRK/Src/PYK2 -0.13 0.3 -9999 0 -0.6 102 102
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.24 -9999 0 -0.54 79 79
COL1A2 -0.039 0.17 -9999 0 -0.69 10 10
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.49 14 14
mol:DAG -0.11 0.23 -9999 0 -0.49 107 107
MAP2K2 -0.18 0.35 -9999 0 -0.7 136 136
MAP2K1 -0.18 0.35 -9999 0 -0.7 137 137
EDNRA -0.038 0.098 -9999 0 -0.52 5 5
positive regulation of muscle contraction -0.036 0.12 -9999 0 -0.52 9 9
Gq family/GDP -0.19 0.29 -9999 0 -0.66 118 118
HRAS/GTP -0.13 0.26 -9999 0 -0.57 96 96
PRKCH -0.1 0.22 -9999 0 -0.51 85 85
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.12 0.25 -9999 0 -0.55 96 96
PRKCB -0.12 0.23 -9999 0 -0.52 91 91
PRKCE -0.11 0.24 -9999 0 -0.5 99 99
PRKCD -0.1 0.22 -9999 0 -0.51 85 85
PRKCG -0.11 0.23 -9999 0 -0.52 85 85
regulation of vascular smooth muscle contraction -0.3 0.55 -9999 0 -1.2 129 129
PRKCQ -0.11 0.23 -9999 0 -0.52 89 89
PLA2G4A -0.19 0.36 -9999 0 -0.7 139 139
GNA14 -0.19 0.36 -9999 0 -0.82 118 118
GNA15 -0.014 0.09 -9999 0 -0.32 36 36
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 -0.006 0.12 -9999 0 -0.82 10 10
Rac1/GTP -0.018 0.16 -9999 0 -0.56 9 9
MMP1 -0.09 0.15 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.13 0.23 -10000 0 -0.45 159 159
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.021 -10000 0 -0.31 2 2
IRS1/Crk -0.13 0.24 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.22 -10000 0 -0.52 113 113
AKT1 -0.09 0.21 -10000 0 -0.77 16 16
BAD -0.076 0.2 -10000 0 -0.7 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.13 0.23 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.24 -10000 0 -0.45 159 159
RAF1 -0.067 0.19 -10000 0 -0.65 16 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.21 -10000 0 -0.42 159 159
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.25 -10000 0 -0.49 159 159
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
RPS6KB1 -0.09 0.21 -10000 0 -0.77 16 16
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.16 -10000 0 -0.53 16 16
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.72 14 14
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.099 0.17 -10000 0 -0.42 113 113
IGF-1R heterotetramer -0.019 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.45 159 159
Crk/p130 Cas/Paxillin -0.13 0.2 -10000 0 -0.43 113 113
IGF1R -0.019 0.048 -10000 0 -10000 0 0
IGF1 -0.19 0.35 -10000 0 -0.81 119 119
IRS2/Crk -0.11 0.22 -10000 0 -0.46 113 113
PI3K -0.14 0.22 -10000 0 -0.43 159 159
apoptosis 0.058 0.18 0.57 16 -10000 0 16
HRAS/GDP -0.001 0.013 -10000 0 -10000 0 0
PRKCD -0.1 0.24 -10000 0 -0.53 113 113
RAF1/14-3-3 E -0.049 0.17 -10000 0 -0.53 16 16
BAD/14-3-3 -0.063 0.19 -10000 0 -0.62 16 16
PRKCZ -0.09 0.21 -10000 0 -0.77 16 16
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.16 -10000 0 -0.63 16 16
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.25 -10000 0 -0.56 113 113
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.19 -10000 0 -0.46 113 113
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.23 -10000 0 -0.45 159 159
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.45 159 159
IRS1 -0.14 0.25 -10000 0 -0.49 159 159
IRS2 -0.13 0.23 -10000 0 -0.45 159 159
IGF-1R heterotetramer/IGF1 -0.16 0.27 -10000 0 -0.65 113 113
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.1 0.23 -10000 0 -0.44 114 114
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.24 -10000 0 -0.53 114 114
SHC1 0.013 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

Figure 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
PCK2 0.045 0.093 -10000 0 -10000 0 0
SMARCC2 0.014 0.014 -10000 0 -10000 0 0
SMARCC1 0.014 0.014 -10000 0 -10000 0 0
TBX21 -0.15 0.28 -10000 0 -0.91 41 41
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.05 -10000 0 -0.3 12 12
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.003 0.091 -10000 0 -0.81 6 6
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.33 52 -0.49 6 58
PRL -0.086 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.24 0.31 0.59 151 -0.5 22 173
RELA -0.029 0.087 -10000 0 -10000 0 0
FGG 0.24 0.19 0.5 120 -10000 0 120
GR beta/TIF2 0.078 0.24 0.35 64 -0.56 48 112
IFNG -0.49 0.51 -10000 0 -1 175 175
apoptosis 0.034 0.24 0.52 58 -0.52 4 62
CREB1 0.012 0.023 -10000 0 -10000 0 0
histone acetylation -0.068 0.17 -10000 0 -0.44 49 49
BGLAP -0.096 0.15 -10000 0 -0.49 22 22
GR/PKAc 0.13 0.1 0.33 40 -0.4 1 41
NF kappa B1 p50/RelA -0.061 0.16 -10000 0 -0.44 30 30
SMARCD1 0.014 0.014 -10000 0 -10000 0 0
MDM2 0.12 0.095 0.28 92 -10000 0 92
GATA3 -0.026 0.18 -10000 0 -0.78 27 27
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.58 33 33
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.061 0.24 0.51 48 -0.73 5 53
CSN2 0.2 0.14 0.42 88 -10000 0 88
BRG1/BAF155/BAF170/BAF60A 0.022 0.048 -10000 0 -10000 0 0
NFATC1 0.001 0.11 -10000 0 -0.81 9 9
POU2F1 0.013 0.015 -10000 0 -0.3 1 1
CDKN1A 0.025 0.052 -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 -0.33 312 312
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.044 0.16 0.34 15 -0.46 17 32
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.078 0.45 0.48 51 -0.88 107 158
JUN -0.33 0.3 -10000 0 -0.7 170 170
IL4 -0.12 0.18 -10000 0 -0.67 22 22
CDK5R1 0.011 0.027 -10000 0 -0.32 3 3
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.36 0.41 -10000 0 -0.81 187 187
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.34 34 -0.47 5 39
cortisol/GR alpha (monomer) 0.36 0.3 0.69 183 -10000 0 183
NCOA2 -0.067 0.24 -10000 0 -0.81 48 48
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.24 0.35 -10000 0 -0.84 127 127
AP-1/NFAT1-c-4 -0.55 0.48 -10000 0 -0.96 236 236
AFP -0.22 0.22 -10000 0 -0.65 53 53
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.45 75 -10000 0 75
TP53 0.033 0.023 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.47 0.37 -10000 0 -0.88 153 153
KRT14 -0.23 0.17 -10000 0 -0.56 36 36
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.065 -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 -0.55 0.48 -10000 0 -0.96 238 238
MAPK14 0.014 0.012 -10000 0 -10000 0 0
MAPK10 0.013 0.04 -10000 0 -0.82 1 1
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.53 0.52 -10000 0 -1.1 178 178
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 -0.3 12 12
CGA -0.12 0.16 -10000 0 -0.48 38 38
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.38 166 -10000 0 166
MAPK3 0.015 0.013 -10000 0 -10000 0 0
MAPK1 0.014 0.012 -10000 0 -10000 0 0
ICAM1 -0.24 0.26 -10000 0 -0.64 108 108
NFKB1 -0.031 0.096 -10000 0 -0.94 1 1
MAPK8 -0.19 0.21 -10000 0 -0.5 110 110
MAPK9 0.014 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.029 0.25 0.52 58 -0.55 4 62
BAX 0.029 0.034 -10000 0 -10000 0 0
POMC -0.54 0.69 -10000 0 -1.6 128 128
EP300 0.065 0.065 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.32 0.24 0.59 176 -10000 0 176
proteasomal ubiquitin-dependent protein catabolic process 0.085 0.072 0.25 27 -10000 0 27
SGK1 0.1 0.22 -10000 0 -1.4 10 10
IL13 -0.29 0.25 -10000 0 -0.72 83 83
IL6 -0.37 0.52 -10000 0 -1.1 136 136
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.2 -10000 0 -0.7 47 47
IL2 -0.36 0.27 -10000 0 -0.72 125 125
CDK5 0.013 0.007 -10000 0 -10000 0 0
PRKACB 0.012 0.037 -10000 0 -0.81 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.26 0.32 -10000 0 -0.73 104 104
CDK5R1/CDK5 0.007 0.025 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.023 0.12 -10000 0 -0.51 4 4
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.3 0.22 0.56 162 -10000 0 162
SMARCA4 0.014 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.41 109 -0.39 1 110
NF kappa B1 p50/RelA/Cbp 0.028 0.16 -10000 0 -0.52 5 5
JUN (dimer) -0.33 0.3 -10000 0 -0.69 170 170
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.24 0.41 -10000 0 -1.1 89 89
NR3C1 0.21 0.19 0.47 135 -10000 0 135
NR4A1 -0.31 0.41 -10000 0 -0.74 218 218
TIF2/SUV420H1 -0.061 0.18 -10000 0 -0.62 48 48
MAPKKK cascade 0.034 0.24 0.52 58 -0.52 4 62
cortisol/GR alpha (dimer)/Src-1 0.32 0.24 0.58 178 -10000 0 178
PBX1 0.014 0.004 -10000 0 -10000 0 0
POU1F1 0.007 0.008 -10000 0 -10000 0 0
SELE -0.33 0.5 -10000 0 -1.2 104 104
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.41 109 -0.4 1 110
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.3 0.22 0.56 162 -10000 0 162
mol:cortisol 0.2 0.19 0.4 190 -10000 0 190
MMP1 -0.21 0.15 -10000 0 -0.44 34 34
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 -0.21 0.55 -10000 0 -1.3 83 83
IL23A -0.22 0.56 -10000 0 -1.3 83 83
NF kappa B1 p50/RelA/I kappa B alpha -0.29 0.46 -10000 0 -1.2 87 87
positive regulation of T cell mediated cytotoxicity -0.24 0.61 -10000 0 -1.3 90 90
ITGA3 -0.19 0.51 -10000 0 -1.2 75 75
IL17F -0.1 0.34 -10000 0 -0.74 74 74
IL12B -0.003 0.11 -10000 0 -0.56 13 13
STAT1 (dimer) -0.23 0.58 -10000 0 -1.3 88 88
CD4 -0.19 0.5 -10000 0 -1.1 84 84
IL23 -0.22 0.53 -10000 0 -1.2 83 83
IL23R -0.003 0.099 -10000 0 -10000 0 0
IL1B -0.23 0.58 -10000 0 -1.3 82 82
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.19 0.5 -10000 0 -1.1 82 82
TYK2 0.014 0.023 -10000 0 -10000 0 0
STAT4 -0.025 0.14 -10000 0 -0.44 41 41
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.028 0.18 -10000 0 -0.78 25 25
IL12RB1 -0.024 0.13 -10000 0 -0.39 47 47
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
IL12Rbeta1/TYK2 -0.011 0.1 -10000 0 -0.67 6 6
IL23R/JAK2 0 0.13 -10000 0 -0.63 2 2
positive regulation of chronic inflammatory response -0.24 0.61 -10000 0 -1.3 90 90
natural killer cell activation 0.001 0.009 0.036 1 -10000 0 1
JAK2 0.019 0.061 -10000 0 -0.84 2 2
PIK3R1 0.014 0 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.21 0.5 -10000 0 -1.1 83 83
ALOX12B -0.21 0.51 -10000 0 -1.2 84 84
CXCL1 -0.22 0.53 -10000 0 -1.2 89 89
T cell proliferation -0.24 0.61 -10000 0 -1.3 90 90
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.058 0.28 -10000 0 -0.57 64 64
PI3K -0.3 0.48 -10000 0 -1.2 90 90
IFNG -0.02 0.055 -10000 0 -0.12 89 89
STAT3 (dimer) -0.28 0.44 -10000 0 -1.1 87 87
IL18R1 -0.03 0.14 -10000 0 -0.42 47 47
IL23/IL23R/JAK2/TYK2/SOCS3 -0.095 0.33 -10000 0 -0.73 62 62
IL18/IL18R -0.067 0.18 -10000 0 -0.57 47 47
macrophage activation -0.014 0.018 -10000 0 -0.044 84 84
TNF -0.26 0.62 -10000 0 -1.4 100 100
STAT3/STAT4 -0.31 0.49 -10000 0 -1.2 91 91
STAT4 (dimer) -0.24 0.58 -10000 0 -1.3 91 91
IL18 -0.039 0.15 -10000 0 -0.41 60 60
IL19 -0.19 0.5 -10000 0 -1.1 86 86
STAT5A (dimer) -0.23 0.57 -10000 0 -1.3 90 90
STAT1 0.006 0.05 -10000 0 -0.31 12 12
SOCS3 -0.026 0.18 -10000 0 -0.79 24 24
CXCL9 -0.3 0.64 -10000 0 -1.4 112 112
MPO -0.2 0.51 -10000 0 -1.1 88 88
positive regulation of humoral immune response -0.24 0.61 -10000 0 -1.3 90 90
IL23/IL23R/JAK2/TYK2 -0.28 0.74 -10000 0 -1.6 90 90
IL6 -0.31 0.64 -10000 0 -1.3 122 122
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.001 0.017 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 0.036 1 -10000 0 1
CD3E -0.23 0.57 -10000 0 -1.3 89 89
keratinocyte proliferation -0.24 0.61 -10000 0 -1.3 90 90
NOS2 -0.2 0.5 -10000 0 -1.2 81 81
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 -0.61 79 79
FYN -0.11 0.35 -10000 0 -0.82 81 81
LAT/GRAP2/SLP76 -0.12 0.27 -10000 0 -0.66 89 89
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.056 0.22 -10000 0 -0.47 89 89
B2M 0.013 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.051 -10000 0 -0.18 15 15
MAP3K8 0.002 0.098 -10000 0 -0.81 7 7
mol:Ca2+ -0.031 0.05 -10000 0 -0.12 106 106
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.33 -10000 0 -0.74 89 89
TRPV6 -0.17 0.34 -10000 0 -0.82 103 103
CD28 -0.045 0.19 -10000 0 -0.59 48 48
SHC1 -0.12 0.34 -10000 0 -0.8 85 85
receptor internalization -0.14 0.38 -10000 0 -0.84 93 93
PRF1 -0.12 0.35 -10000 0 -0.9 70 70
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.038 0.18 -10000 0 -0.38 89 89
LAT -0.12 0.35 -10000 0 -0.82 85 85
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.093 0.27 -10000 0 -0.69 75 75
CD3E -0.068 0.24 -10000 0 -0.74 54 54
CD3G -0.14 0.32 -10000 0 -0.78 99 99
RASGRP2 0 0.031 -10000 0 -0.19 6 6
RASGRP1 -0.053 0.22 -10000 0 -0.47 93 93
HLA-A 0.011 0.021 -10000 0 -0.31 2 2
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.068 -10000 0 -0.12 64 64
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.057 0.091 -10000 0 -0.26 61 61
PRKCA -0.06 0.13 -10000 0 -0.31 84 84
GRAP2 -0.045 0.21 -10000 0 -0.75 38 38
mol:IP3 -0.053 0.23 0.27 85 -0.47 84 169
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.42 -10000 0 -0.97 82 82
ORAI1 0.087 0.16 0.39 103 -10000 0 103
CSK -0.12 0.35 -10000 0 -0.83 85 85
B7 family/CD28 -0.2 0.35 -10000 0 -0.82 97 97
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.42 -10000 0 -0.99 86 86
PTPN6 -0.12 0.36 -10000 0 -0.85 83 83
VAV1 -0.13 0.35 -10000 0 -0.79 90 90
Monovalent TCR/CD3 -0.16 0.4 -10000 0 -0.72 124 124
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.86 83 83
PAG1 -0.12 0.35 -10000 0 -0.83 85 85
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.42 -10000 0 -0.98 87 87
CD80 -0.071 0.25 -10000 0 -0.8 51 51
CD86 -0.009 0.1 -10000 0 -0.41 26 26
PDK1/CARD11/BCL10/MALT1 -0.07 0.11 -10000 0 -0.3 71 71
HRAS 0.012 0.021 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.29 -10000 0 -0.64 97 97
CD8A -0.052 0.22 -10000 0 -0.82 38 38
CD8B -0.091 0.27 -10000 0 -0.72 71 71
PTPRC -0.035 0.18 -10000 0 -0.59 39 39
PDK1/PKC theta -0.071 0.27 -10000 0 -0.6 88 88
CSK/PAG1 -0.11 0.34 -10000 0 -0.82 81 81
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 90 90
STIM1 0.047 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.007 0.091 -10000 0 -0.18 58 58
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.94 93 93
mol:DAG -0.072 0.18 -10000 0 -0.41 89 89
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.024 0.16 -10000 0 -0.62 30 30
cytotoxic T cell degranulation -0.11 0.33 -10000 0 -0.85 70 70
RAP1A/GTP -0.003 0.009 -10000 0 -0.07 5 5
mol:PI-3-4-5-P3 -0.076 0.26 -10000 0 -0.58 89 89
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.083 0.29 0.3 75 -0.62 88 163
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.026 0.17 -10000 0 -0.62 31 31
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.26 -10000 0 -0.62 90 90
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.01 0.053 -10000 0 -0.81 2 2
CD8 heterodimer -0.11 0.29 -10000 0 -0.75 77 77
CARD11 -0.07 0.17 -10000 0 -0.36 109 109
PRKCB -0.059 0.13 -10000 0 -0.32 77 77
PRKCE -0.053 0.12 -10000 0 -0.29 83 83
PRKCQ -0.094 0.31 -10000 0 -0.69 89 89
LCP2 0.008 0.043 -10000 0 -0.31 9 9
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.042 0.18 -10000 0 -0.4 87 87
IKK complex 0.013 0.068 -10000 0 -0.12 53 53
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.018 0.14 -10000 0 -0.3 65 65
PDPK1 -0.049 0.21 -10000 0 -0.45 86 86
TCR/CD3/MHC I/CD8/Fyn -0.17 0.45 -10000 0 -1.1 84 84
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.087 0.15 -9999 0 -0.31 152 152
GPC2 -0.009 0.082 -9999 0 -0.31 34 34
GPC2/Midkine -0.076 0.11 -9999 0 -0.41 13 13
neuron projection morphogenesis -0.076 0.11 -9999 0 -0.41 13 13
Syndecan-1-mediated signaling events

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
TGFB1 0.008 0.041 -9999 0 -0.31 8 8
CCL5 -0.047 0.21 -9999 0 -0.69 42 42
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -9999 0 -0.44 61 61
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 -0.09 0.16 -9999 0 -0.54 32 32
Syndecan-1/Syntenin -0.09 0.16 -9999 0 -0.59 26 26
MAPK3 -0.067 0.14 -9999 0 -0.55 23 23
HGF/MET -0.16 0.24 -9999 0 -0.68 74 74
TGFB1/TGF beta receptor Type II 0.008 0.041 -9999 0 -0.31 8 8
BSG 0.013 0.015 -9999 0 -0.31 1 1
keratinocyte migration -0.088 0.15 -9999 0 -0.53 32 32
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.58 68 68
Syndecan-1/CD147 -0.079 0.15 -9999 0 -0.58 24 24
Syndecan-1/Syntenin/PIP2 -0.097 0.14 -9999 0 -0.57 26 26
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.096 0.14 -9999 0 -0.55 26 26
MMP7 -0.17 0.22 -9999 0 -0.37 243 243
HGF -0.11 0.3 -9999 0 -0.81 74 74
Syndecan-1/CASK -0.098 0.15 -9999 0 -0.42 61 61
Syndecan-1/HGF/MET -0.2 0.24 -9999 0 -0.63 89 89
regulation of cell adhesion -0.057 0.14 -9999 0 -0.57 19 19
HPSE -0.016 0.13 -9999 0 -0.51 28 28
positive regulation of cell migration -0.1 0.16 -9999 0 -0.44 61 61
SDC1 -0.1 0.16 -9999 0 -0.44 61 61
Syndecan-1/Collagen -0.1 0.16 -9999 0 -0.44 61 61
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.1 0.16 -9999 0 -0.31 179 179
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.58 80 80
MAPK1 -0.067 0.14 -9999 0 -0.55 23 23
homophilic cell adhesion -0.1 0.16 -9999 0 -0.44 61 61
MMP1 -0.14 0.16 -9999 0 -0.31 226 226
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.26 0.32 -9999 0 -0.59 217 217
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.047 0.21 -9999 0 -0.69 42 42
SMAD9 -0.22 0.28 -9999 0 -0.59 162 162
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.092 0.2 -9999 0 -0.55 29 29
BMP7/USAG1 -0.32 0.31 -9999 0 -0.62 254 254
SMAD5/SKI -0.081 0.19 -9999 0 -0.52 28 28
SMAD1 0.019 0.044 -9999 0 -10000 0 0
BMP2 -0.017 0.16 -9999 0 -0.81 18 18
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 -0.81 161 161
BMPR1A-1B/BAMBI -0.18 0.26 -9999 0 -0.55 161 161
AHSG -0.018 0.086 -9999 0 -0.31 39 39
CER1 0 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.037 0.13 -9999 0 -0.55 31 31
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.073 0.19 -9999 0 -0.62 31 31
BMP2-4 (homodimer) -0.042 0.15 -9999 0 -0.62 31 31
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 161 161
RGMA -0.017 0.16 -9999 0 -0.81 18 18
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.085 0.18 -9999 0 -0.56 29 29
BMP2-4/USAG1 -0.31 0.3 -9999 0 -0.57 270 270
SMAD6/SMURF1/SMAD5 -0.081 0.19 -9999 0 -0.52 28 28
SOSTDC1 -0.41 0.41 -9999 0 -0.81 255 255
BMP7/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.49 161 161
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.011 0.029 -9999 0 -0.31 4 4
HFE2 0.001 0.032 -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 -0.047 0.15 -9999 0 -0.55 40 40
SMAD5/SMAD5/SMAD4 -0.081 0.19 -9999 0 -0.52 28 28
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.091 0.14 -9999 0 -0.48 29 29
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.017 0.058 -9999 0 -0.39 1 1
SMAD1/SKI 0.026 0.042 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.048 0.14 -9999 0 -0.56 31 31
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.2 0.35 -9999 0 -0.72 140 140
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.007 0.059 -9999 0 -0.54 6 6
BMPR1A-1B (homodimer) -0.2 0.29 -9999 0 -0.62 161 161
CHRDL1 -0.57 0.38 -9999 0 -0.81 350 350
ENDOFIN/SMAD1 0.026 0.042 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.006 0.008 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.08 -9999 0 -0.81 2 2
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.42 0.28 -9999 0 -0.57 356 356
BMP2-4/GREM1 -0.17 0.27 -9999 0 -0.59 132 132
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.18 0.27 -9999 0 -0.55 162 162
SMAD1/SMAD6 0.026 0.042 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.011 0.029 -9999 0 -0.31 4 4
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.064 0.16 -9999 0 -0.49 29 29
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.003 0.091 -9999 0 -0.81 6 6
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.19 0.31 -9999 0 -0.79 84 84
CHRD -0.003 0.12 -9999 0 -0.81 10 10
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.09 0.19 -9999 0 -0.6 29 29
BMP4 -0.013 0.14 -9999 0 -0.64 20 20
FST -0.19 0.35 -9999 0 -0.78 127 127
BMP2-4/NOG -0.074 0.18 -9999 0 -0.55 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.15 0.21 -9999 0 -0.46 161 161
Arf6 signaling events

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
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.042 0.11 -9999 0 -0.47 12 12
EGFR 0.005 0.083 -9999 0 -0.81 5 5
EPHA2 0.011 0.025 -9999 0 -0.31 3 3
USP6 0.011 0.025 -9999 0 -0.31 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.1 0.23 -9999 0 -0.62 77 77
ARRB2 -0.044 0.15 -9999 0 -0.44 61 61
mol:GTP 0.02 0.012 -9999 0 -10000 0 0
ARRB1 0.012 0.037 -9999 0 -0.81 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.01 0.053 -9999 0 -0.82 2 2
EGF -0.11 0.29 -9999 0 -0.78 78 78
somatostatin receptor activity 0 0 -9999 0 -0.001 138 138
ARAP2 0.01 0.053 -9999 0 -0.81 2 2
mol:GDP -0.12 0.14 -9999 0 -0.31 130 130
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 127 127
ITGA2B -0.075 0.26 -9999 0 -0.81 53 53
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 -0.16 0.24 -9999 0 -0.68 74 74
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.31 141 141
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.086 0.2 -9999 0 -0.54 77 77
ADRB2 -0.007 0.13 -9999 0 -0.81 12 12
receptor agonist activity 0 0 -9999 0 0 144 144
actin filament binding 0 0 -9999 0 -0.001 135 135
SRC 0.013 0.015 -9999 0 -0.31 1 1
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 122 122
ARF6/GDP 0 0.068 -9999 0 -0.33 2 2
ARF6/GDP/GULP/ACAP1 -0.18 0.2 -9999 0 -0.5 112 112
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.067 0.18 -9999 0 -0.54 62 62
ACAP1 -0.001 0.078 -9999 0 -0.36 19 19
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.079 0.22 -9999 0 -0.67 61 61
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.11 0.3 -9999 0 -0.81 74 74
CYTH3 0.009 0.041 -9999 0 -0.64 2 2
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 112 112
endosomal lumen acidification 0 0 -9999 0 -0.001 144 144
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.32 -9999 0 -0.81 89 89
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 21 21
MET -0.1 0.16 -9999 0 -0.31 179 179
GNA14 -0.18 0.35 -9999 0 -0.81 118 118
GNA15 -0.011 0.09 -9999 0 -0.32 36 36
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 133 133
GNA11 -0.004 0.12 -9999 0 -0.81 10 10
LHCGR -0.098 0.27 -9999 0 -0.76 68 68
AGTR1 -0.32 0.4 -9999 0 -0.81 200 200
desensitization of G-protein coupled receptor protein signaling pathway -0.078 0.22 -9999 0 -0.67 61 61
IPCEF1/ARNO -0.057 0.16 -9999 0 -0.43 77 77
alphaIIb/beta3 Integrin -0.084 0.23 -9999 0 -0.67 62 62
HIF-1-alpha transcription factor network

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
PKM2 -0.19 0.42 -9999 0 -0.98 47 47
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.34 -9999 0 -0.84 100 100
SMAD4 0.015 0.003 -9999 0 -10000 0 0
ID2 -0.19 0.42 -9999 0 -1 44 44
AP1 -0.28 0.45 -9999 0 -0.92 151 151
ABCG2 -0.19 0.43 -9999 0 -1 46 46
HIF1A -0.009 0.068 -9999 0 -10000 0 0
TFF3 -0.57 0.51 -9999 0 -1.1 165 165
GATA2 0.014 0.015 -9999 0 -0.31 1 1
AKT1 -0.038 0.1 -9999 0 -10000 0 0
response to hypoxia -0.059 0.11 -9999 0 -0.24 41 41
MCL1 -0.19 0.42 -9999 0 -0.99 44 44
NDRG1 -0.19 0.42 -9999 0 -0.98 46 46
SERPINE1 -0.2 0.43 -9999 0 -0.99 49 49
FECH -0.19 0.42 -9999 0 -0.99 45 45
FURIN -0.19 0.42 -9999 0 -0.99 45 45
NCOA2 -0.066 0.24 -9999 0 -0.81 48 48
EP300 -0.062 0.18 -9999 0 -0.34 105 105
HMOX1 -0.19 0.42 -9999 0 -1 45 45
BHLHE40 -0.2 0.42 -9999 0 -1 48 48
BHLHE41 -0.19 0.42 -9999 0 -0.99 48 48
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.037 -9999 0 -10000 0 0
ENG 0.041 0.092 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.81 112 112
RORA -0.19 0.42 -9999 0 -1 46 46
ABCB1 -0.076 0.19 -9999 0 -1.4 8 8
TFRC -0.19 0.42 -9999 0 -1 47 47
CXCR4 -0.19 0.42 -9999 0 -0.99 45 45
TF -0.24 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 70 70
LDHA -0.039 0.05 -9999 0 -10000 0 0
ETS1 -0.19 0.42 -9999 0 -1 43 43
PGK1 -0.19 0.42 -9999 0 -0.99 44 44
NOS2 -0.2 0.43 -9999 0 -1 48 48
ITGB2 -0.2 0.42 -9999 0 -1 49 49
ALDOA -0.19 0.42 -9999 0 -1 43 43
Cbp/p300/CITED2 -0.32 0.51 -9999 0 -1.1 105 105
FOS -0.2 0.36 -9999 0 -0.81 127 127
HK2 -0.19 0.42 -9999 0 -0.98 49 49
SP1 0.022 0.007 -9999 0 -10000 0 0
GCK -0.38 0.71 -9999 0 -1.5 136 136
HK1 -0.19 0.42 -9999 0 -0.99 45 45
NPM1 -0.19 0.42 -9999 0 -0.98 46 46
EGLN1 -0.19 0.42 -9999 0 -0.99 46 46
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.19 0.42 -9999 0 -0.99 45 45
SMAD3 0.015 0.003 -9999 0 -10000 0 0
EDN1 -0.16 0.31 -9999 0 -0.76 53 53
IGFBP1 -0.2 0.42 -9999 0 -1 45 45
VEGFA -0.16 0.38 -9999 0 -0.76 69 69
HIF1A/JAB1 -0.011 0.021 -9999 0 -10000 0 0
CP -0.35 0.55 -9999 0 -1.1 125 125
CXCL12 -0.23 0.48 -9999 0 -1.1 68 68
COPS5 0.014 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.002 -9999 0 -10000 0 0
BNIP3 -0.19 0.42 -9999 0 -1 41 41
EGLN3 -0.2 0.44 -9999 0 -1 50 50
CA9 -0.2 0.42 -9999 0 -0.98 51 51
TERT -0.2 0.42 -9999 0 -1 46 46
ENO1 -0.19 0.42 -9999 0 -0.98 47 47
PFKL -0.19 0.42 -9999 0 -0.99 45 45
NCOA1 0.014 0 -9999 0 -10000 0 0
ADM -0.22 0.44 -9999 0 -1 49 49
ARNT -0.01 0.067 -9999 0 -10000 0 0
HNF4A -0.025 0.064 -9999 0 -0.35 10 10
ADFP -0.2 0.41 -9999 0 -0.92 65 65
SLC2A1 -0.15 0.38 -9999 0 -0.77 58 58
LEP -0.2 0.42 -9999 0 -0.98 51 51
HIF1A/ARNT/Cbp/p300 -0.29 0.36 -9999 0 -0.86 103 103
EPO -0.14 0.33 -9999 0 -0.96 26 26
CREBBP -0.062 0.18 -9999 0 -0.34 107 107
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.34 -9999 0 -0.86 86 86
PFKFB3 -0.19 0.42 -9999 0 -0.99 47 47
NT5E -0.2 0.43 -9999 0 -1 42 42
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 -0.015 0.064 -10000 0 -0.35 14 14
SVIL -0.007 0.031 -10000 0 -10000 0 0
ZNF318 0.062 0.092 -10000 0 -0.81 1 1
JMJD2C -0.064 0.069 -10000 0 -0.12 281 281
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.61 211 211
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 0.024 -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 -0.79 7 7
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.06 -10000 0 -0.81 2 2
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.069 0.24 -10000 0 -0.82 48 48
NCOA6 -0.007 0.047 -10000 0 -0.81 1 1
DNA-PK 0.059 0.084 0.26 1 -10000 0 1
NCOA4 0.012 0.003 -10000 0 -10000 0 0
PIAS3 -0.002 0.024 -10000 0 -10000 0 0
cell proliferation -0.011 0.15 -10000 0 -1 7 7
XRCC5 0.025 0.018 -10000 0 -10000 0 0
UBE3A -0.016 0.047 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.31 0.33 -10000 0 -0.66 219 219
FHL2 -0.15 0.36 -10000 0 -1.3 38 38
RANBP9 -0.005 0.029 -10000 0 -10000 0 0
JMJD1A 0.002 0.037 -10000 0 -0.12 37 37
CDK6 0.01 0.064 -10000 0 -0.81 3 3
TGFB1I1 -0.007 0.031 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.29 0.3 -10000 0 -0.62 217 217
XRCC6 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.31 -10000 0 -0.63 236 236
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 -0.1 0.16 -10000 0 -10000 0 0
SRF 0.028 0.039 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -0.63 15 15
KLK3 -0.44 0.71 -10000 0 -1.6 142 142
TMF1 0.006 0.053 -10000 0 -0.81 2 2
HNRNPA1 0.032 0.028 -10000 0 -10000 0 0
AOF2 -0.022 0.034 -10000 0 -0.075 142 142
APPL1 0.052 0.043 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.27 0.29 -10000 0 -0.6 209 209
AR -0.38 0.42 -10000 0 -0.86 209 209
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.032 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 0.037 0.036 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.25 0.28 -10000 0 -0.56 210 210
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.29 -10000 0 -0.61 211 211
LATS2 0.03 0.047 -10000 0 -0.81 1 1
T-DHT/AR/PRX1 -0.24 0.28 -10000 0 -0.56 209 209
Cyclin D3/CDK11 p58 0.001 0.004 -10000 0 -10000 0 0
VAV3 -0.012 0.093 -10000 0 -0.82 6 6
KLK2 -0.77 0.62 -10000 0 -1.3 281 281
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.66 216 216
TMPRSS2 -0.18 0.31 -10000 0 -1.2 36 36
CCND1 0.001 0.05 -10000 0 -0.31 12 12
PIAS1 -0.016 0.047 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.041 -10000 0 -0.081 168 168
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.036 0.077 -10000 0 -0.2 1 1
T-DHT/AR/CDK6 -0.28 0.3 -10000 0 -0.61 213 213
CMTM2 0.014 0.026 -10000 0 -0.31 3 3
SNURF -0.038 0.2 -10000 0 -0.81 30 30
ZMIZ1 -0.013 0.051 -10000 0 -0.8 1 1
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.032 0.028 -10000 0 -10000 0 0
FKBP4 -0.005 0.029 -10000 0 -10000 0 0
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 -0.087 0.2 -10000 0 -0.55 77 77
cell-cell adhesion 0.15 0.18 0.54 11 -10000 0 11
Ephrin B/EPHB2/RasGAP -0.013 0.067 -10000 0 -0.46 10 10
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.08 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.21 0.26 -10000 0 -0.55 186 186
HRAS/GDP -0.13 0.17 -10000 0 -0.49 13 13
Ephrin B/EPHB1/GRB7 -0.2 0.24 -10000 0 -0.5 191 191
Endophilin/SYNJ1 0.025 0.07 -10000 0 -0.43 10 10
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.18 0.23 -10000 0 -0.47 191 191
endothelial cell migration -0.003 0.036 -10000 0 -0.46 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.04 0.12 -10000 0 -0.31 82 82
PAK1 0.033 0.072 -10000 0 -0.43 10 10
HRAS 0.012 0.021 -10000 0 -0.31 2 2
RRAS 0.025 0.072 -10000 0 -0.44 10 10
DNM1 -0.014 0.15 -10000 0 -0.78 17 17
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.15 0.24 -10000 0 -0.44 191 191
lamellipodium assembly -0.15 0.18 -10000 0 -0.54 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.18 -10000 0 -0.33 186 186
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.064 -10000 0 -0.81 3 3
EPHB3 -0.18 0.16 -10000 0 -0.31 302 302
EPHB1 -0.3 0.4 -10000 0 -0.81 186 186
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.066 0.17 -10000 0 -0.51 7 7
Ephrin B/EPHB2 -0.014 0.069 -10000 0 -0.46 10 10
Ephrin B/EPHB3 -0.085 0.085 -10000 0 -0.56 7 7
JNK cascade -0.14 0.24 -10000 0 -0.45 188 188
Ephrin B/EPHB1 -0.19 0.23 -10000 0 -0.48 191 191
RAP1/GDP -0.05 0.15 -10000 0 -0.52 3 3
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.01 0.11 -10000 0 -0.45 25 25
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.19 0.24 -10000 0 -0.5 188 188
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.19 -10000 0 -0.51 18 18
Rap1/GTP -0.15 0.18 -10000 0 -0.55 11 11
axon guidance -0.086 0.2 -10000 0 -0.55 77 77
MAPK3 -0.075 0.16 -10000 0 -0.53 2 2
MAPK1 -0.075 0.16 -10000 0 -0.53 2 2
Rac1/GDP -0.041 0.17 -10000 0 -0.56 3 3
actin cytoskeleton reorganization -0.1 0.13 -10000 0 -0.45 6 6
CDC42/GDP -0.041 0.17 -10000 0 -0.46 7 7
PI3K -0.003 0.036 -10000 0 -0.46 3 3
EFNA5 -0.11 0.3 -10000 0 -0.81 76 76
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.054 -10000 0 -0.33 10 10
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.14 0.18 -10000 0 -0.52 12 12
PTK2 0.04 0.051 -10000 0 -10000 0 0
MAP4K4 -0.15 0.24 -10000 0 -0.46 188 188
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 -0.065 0.18 -10000 0 -0.54 3 3
MAP2K1 -0.087 0.17 -10000 0 -0.4 11 11
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.19 0.24 -10000 0 -0.49 188 188
cell migration -0.083 0.19 -10000 0 -0.43 11 11
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.072 -10000 0 -0.44 10 10
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.022 0.17 -10000 0 -0.44 62 62
HRAS/GTP -0.16 0.2 -10000 0 -0.4 193 193
Ephrin B1/EPHB1-2 -0.19 0.24 -10000 0 -0.5 188 188
cell adhesion mediated by integrin 0.014 0.074 0.5 7 -10000 0 7
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.17 0.21 -10000 0 -0.43 193 193
RAC1-CDC42/GTP -0.2 0.21 -10000 0 -0.49 144 144
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.05 0.15 -10000 0 -0.52 3 3
ruffle organization -0.11 0.22 -10000 0 -0.55 11 11
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.018 0.11 -10000 0 -0.45 24 24
Ephrin B/EPHB2/KALRN -0.013 0.067 -10000 0 -0.46 10 10
ROCK1 -0.073 0.08 -10000 0 -10000 0 0
RAS family/GDP -0.081 0.11 -10000 0 -0.52 3 3
Rac1/GTP -0.16 0.2 -10000 0 -0.58 11 11
Ephrin B/EPHB1/Src/Paxillin -0.11 0.18 -10000 0 -0.33 191 191
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.082 0.062 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.14 0.18 -9999 0 -0.65 43 43
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.6 72 72
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.64 45 45
CCL5 -0.047 0.21 -9999 0 -0.69 42 42
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 -0.002 0.038 -9999 0 -0.3 6 6
ADAM12 -0.067 0.14 -9999 0 -0.31 123 123
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 -0.063 0.043 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.17 0.21 -9999 0 -0.61 69 69
Syndecan-4/CXCL12/CXCR4 -0.17 0.23 -9999 0 -0.65 72 72
Syndecan-4/Laminin alpha3 -0.16 0.2 -9999 0 -0.63 54 54
MDK -0.087 0.15 -9999 0 -0.31 152 152
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.64 45 45
Syndecan-4/Midkine -0.18 0.2 -9999 0 -0.66 45 45
FZD7 0.007 0.074 -9999 0 -0.81 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 44 44
THBS1 -0.017 0.095 -9999 0 -0.31 47 47
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.64 46 46
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.6 72 72
Syndecan-4/TACI -0.25 0.26 -9999 0 -0.6 159 159
CXCR4 0.011 0.025 -9999 0 -0.31 3 3
cell adhesion -0.063 0.09 -9999 0 -0.44 19 19
Syndecan-4/Dynamin -0.14 0.18 -9999 0 -0.65 43 43
Syndecan-4/TSP1 -0.15 0.18 -9999 0 -0.65 44 44
Syndecan-4/GIPC -0.14 0.18 -9999 0 -0.65 43 43
Syndecan-4/RANTES -0.17 0.22 -9999 0 -0.71 56 56
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.048 0.22 -9999 0 -0.8 37 37
LAMA3 -0.025 0.16 -9999 0 -0.58 32 32
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.022 0.15 -9999 0 -0.73 19 19
Syndecan-4/alpha-Actinin -0.14 0.18 -9999 0 -0.65 43 43
TFPI -0.034 0.19 -9999 0 -0.81 28 28
F2 -0.007 0.052 -9999 0 -0.31 14 14
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.17 0.21 -9999 0 -0.66 58 58
ACTN1 0.013 0.015 -9999 0 -10000 0 0
TNC -0.11 0.17 -9999 0 -0.32 181 181
Syndecan-4/CXCL12 -0.18 0.24 -9999 0 -0.68 72 72
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.074 0.25 -9999 0 -0.81 52 52
TNFRSF13B -0.2 0.36 -9999 0 -0.79 131 131
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.012 0.037 -9999 0 -0.81 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.66 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 359 359
cell migration -0.021 0.016 -9999 0 -10000 0 0
PRKCD 0.008 0.014 -9999 0 -10000 0 0
vasculogenesis -0.14 0.18 -9999 0 -0.62 44 44
SDC4 -0.15 0.19 -9999 0 -0.7 43 43
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.69 44 44
Syndecan-4/PI-4-5-P2/PKC alpha -0.05 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.18 -9999 0 -0.65 43 43
MMP9 -0.085 0.24 -9999 0 -0.58 80 80
Rac1/GTP -0.07 0.087 -9999 0 -0.46 19 19
cytoskeleton organization -0.13 0.17 -9999 0 -0.62 43 43
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.21 -9999 0 -0.62 68 68
IL6-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
BCL2L1 -0.049 0.21 -10000 0 -0.62 29 29
CRP -0.054 0.21 -10000 0 -0.64 27 27
cell cycle arrest -0.07 0.23 -10000 0 -0.65 40 40
TIMP1 -0.15 0.21 -10000 0 -0.57 47 47
IL6ST -0.11 0.29 -10000 0 -0.81 72 72
Rac1/GDP -0.078 0.24 -10000 0 -0.61 57 57
AP1 -0.19 0.32 -10000 0 -0.66 139 139
GAB2 0.014 0.001 -10000 0 -10000 0 0
TNFSF11 -0.09 0.22 -10000 0 -0.62 35 35
HSP90B1 0.024 0.042 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
MAPK14 -0.085 0.29 -10000 0 -0.77 56 56
AKT1 0.053 0.056 -10000 0 -1.1 1 1
FOXO1 0.059 0.053 -10000 0 -0.98 1 1
MAP2K6 -0.091 0.28 -10000 0 -0.65 71 71
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.067 0.23 -10000 0 -0.63 44 44
MITF -0.079 0.25 -10000 0 -0.58 66 66
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 0.024 0.006 -10000 0 -10000 0 0
CEBPB 0.022 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.019 0.085 -10000 0 -0.49 1 1
STAT3 -0.082 0.24 -10000 0 -0.7 40 40
STAT1 -0.01 0.022 -10000 0 -10000 0 0
CEBPD -0.049 0.21 -10000 0 -0.62 29 29
PIK3CA 0.01 0.064 -10000 0 -0.81 3 3
PI3K 0.019 0.05 -10000 0 -0.62 3 3
JUN -0.18 0.35 -10000 0 -0.81 112 112
PIAS3/MITF -0.067 0.24 -10000 0 -0.62 51 51
MAPK11 -0.085 0.29 -10000 0 -0.78 55 55
STAT3 (dimer)/FOXO1 -0.001 0.2 -10000 0 -0.56 24 24
GRB2/SOS1/GAB family -0.11 0.19 -10000 0 -0.68 31 31
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.11 0.25 -10000 0 -0.44 147 147
GRB2 0.014 0 -10000 0 -10000 0 0
JAK2 0.01 0.053 -10000 0 -0.81 2 2
LBP -0.055 0.19 -10000 0 -0.54 27 27
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
MYC -0.063 0.26 -10000 0 -0.81 32 32
FGG -0.058 0.21 -10000 0 -0.62 33 33
macrophage differentiation -0.07 0.23 -10000 0 -0.65 40 40
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.17 0.28 -10000 0 -0.56 147 147
JUNB -0.055 0.23 -10000 0 -0.7 31 31
FOS -0.2 0.36 -10000 0 -0.81 127 127
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.089 0.27 -10000 0 -0.46 133 133
STAT1/PIAS1 -0.072 0.23 -10000 0 -0.54 64 64
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.06 -10000 0 -0.59 3 3
STAT3 (dimer) -0.079 0.24 -10000 0 -0.7 38 38
PRKCD -0.055 0.22 -10000 0 -0.62 38 38
IL6R -0.014 0.15 -10000 0 -0.81 17 17
SOCS3 -0.097 0.35 -10000 0 -1 49 49
gp130 (dimer)/JAK1/JAK1/LMO4 -0.058 0.2 -10000 0 -0.54 72 72
Rac1/GTP -0.088 0.24 -10000 0 -0.61 56 56
HCK -0.011 0.084 -10000 0 -0.31 36 36
MAPKKK cascade 0.012 0.076 -10000 0 -0.98 1 1
bone resorption -0.085 0.21 -10000 0 -0.58 36 36
IRF1 -0.049 0.21 -10000 0 -0.61 30 30
mol:GDP -0.09 0.25 -10000 0 -0.6 67 67
SOS1 0.013 0.001 -10000 0 -10000 0 0
VAV1 -0.092 0.26 -10000 0 -0.61 67 67
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.097 0.29 -10000 0 -0.8 53 53
PTPN11 -0.01 0.058 -10000 0 -1.2 1 1
IL6/IL6RA -0.13 0.27 -10000 0 -0.65 99 99
gp130 (dimer)/TYK2/TYK2/LMO4 -0.064 0.2 -10000 0 -0.54 72 72
gp130 (dimer)/JAK2/JAK2/LMO4 -0.066 0.2 -10000 0 -0.55 72 72
IL6 -0.15 0.32 -10000 0 -0.69 116 116
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE -0.087 0.15 -10000 0 -0.31 148 148
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 -0.093 0.26 -10000 0 -0.46 130 130
LMO4 0.013 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.097 0.23 0.38 1 -0.72 36 37
MCL1 0.059 0.048 -10000 0 -0.88 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.026 0.16 -10000 0 -0.45 28 28
TBX21 -0.12 0.44 -10000 0 -1.1 56 56
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 -0.022 0.13 -10000 0 -0.4 43 43
GADD45B -0.092 0.38 -10000 0 -1 51 51
IL12RB2 -0.015 0.16 -10000 0 -0.72 21 21
GADD45G -0.075 0.34 -10000 0 -0.93 43 43
natural killer cell activation 0.002 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.035 0.15 -10000 0 -0.4 60 60
IL2RA -0.047 0.2 -10000 0 -0.6 49 49
IFNG -0.11 0.28 -10000 0 -0.72 79 79
STAT3 (dimer) -0.073 0.32 -10000 0 -0.75 65 65
HLA-DRB5 -0.04 0.13 -10000 0 -0.34 71 71
FASLG -0.14 0.48 -10000 0 -1.2 69 69
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.91 62 62
CD4 -0.002 0.063 -10000 0 -0.31 19 19
SOCS1 0.008 0.049 -10000 0 -0.39 6 6
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.097 0.27 -10000 0 -0.7 75 75
CD3E -0.072 0.24 -10000 0 -0.74 54 54
CD3G -0.15 0.32 -10000 0 -0.78 99 99
IL12Rbeta2/JAK2 -0.002 0.13 -10000 0 -0.63 19 19
CCL3 -0.11 0.43 -10000 0 -1.2 46 46
CCL4 -0.15 0.51 -10000 0 -1.4 62 62
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
IL18/IL18R -0.032 0.2 -10000 0 -0.57 47 47
NOS2 -0.089 0.34 -10000 0 -0.9 47 47
IL12/IL12R/TYK2/JAK2/SPHK2 -0.024 0.15 -10000 0 -0.42 29 29
IL1R1 -0.088 0.37 -10000 0 -0.97 52 52
IL4 0.002 0.023 -10000 0 -10000 0 0
JAK2 0.012 0.057 -10000 0 -0.82 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.25 0.56 -10000 0 -1.2 106 106
RAB7A -0.042 0.29 -10000 0 -0.78 27 27
lysosomal transport -0.037 0.28 -10000 0 -0.73 29 29
FOS -0.4 0.65 -10000 0 -1.3 159 159
STAT4 (dimer) -0.08 0.35 -10000 0 -0.83 60 60
STAT5A (dimer) -0.22 0.36 -10000 0 -0.89 90 90
GZMA -0.11 0.41 -10000 0 -1.1 48 48
GZMB -0.1 0.39 -10000 0 -0.96 61 61
HLX 0.004 0.054 -10000 0 -0.31 14 14
LCK -0.11 0.43 -10000 0 -1 67 67
TCR/CD3/MHC II/CD4 -0.19 0.35 -10000 0 -0.59 146 146
IL2/IL2R -0.081 0.22 -10000 0 -0.67 48 48
MAPK14 -0.07 0.35 -10000 0 -0.83 58 58
CCR5 -0.1 0.41 -10000 0 -1.1 46 46
IL1B -0.044 0.22 -10000 0 -0.76 39 39
STAT6 -0.005 0.11 0.23 4 -0.25 23 27
STAT4 -0.025 0.14 -10000 0 -0.44 41 41
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.31 12 12
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.003 0.1 -10000 0 -0.55 13 13
CD8A -0.052 0.22 -10000 0 -0.82 38 38
CD8B -0.092 0.27 -10000 0 -0.71 71 71
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.025 0.16 0.45 28 -10000 0 28
IL2RB -0.014 0.13 -10000 0 -0.5 27 27
proteasomal ubiquitin-dependent protein catabolic process -0.068 0.32 -10000 0 -0.75 60 60
IL2RG -0.048 0.19 -10000 0 -0.52 57 57
IL12 -0.057 0.21 -10000 0 -0.63 57 57
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.028 0.16 -10000 0 -0.62 30 30
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 -0.073 0.26 -10000 0 -0.79 54 54
IL12/IL12R/TYK2/JAK2 -0.13 0.48 -10000 0 -1.1 69 69
MAP2K3 -0.072 0.34 -10000 0 -0.82 59 59
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.079 0.36 -10000 0 -0.82 64 64
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.029 0.13 -10000 0 -0.4 48 48
IL18RAP -0.025 0.18 -10000 0 -0.78 25 25
IL12Rbeta1/TYK2 -0.006 0.1 -10000 0 -0.65 6 6
EOMES -0.15 0.43 -10000 0 -1.5 45 45
STAT1 (dimer) -0.13 0.37 -10000 0 -0.78 93 93
T cell proliferation -0.05 0.27 -10000 0 -0.62 54 54
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.026 0.14 -10000 0 -0.42 47 47
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.24 -10000 0 -0.69 61 61
ATF2 -0.075 0.33 -10000 0 -0.76 59 59
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.042 0.12 -9999 0 -0.45 29 29
alphaM/beta2 Integrin/GPIbA -0.053 0.14 -9999 0 -0.49 38 38
alphaM/beta2 Integrin/proMMP-9 -0.092 0.2 -9999 0 -0.55 65 65
PLAUR -0.089 0.15 -9999 0 -0.31 156 156
HMGB1 0.003 0.023 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.033 0.098 -9999 0 -0.51 11 11
AGER -0.057 0.22 -9999 0 -0.78 38 38
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.01 0.083 -9999 0 -0.31 35 35
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.11 0.19 -9999 0 -0.65 38 38
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.58 80 80
CYR61 -0.24 0.38 -9999 0 -0.81 150 150
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.068 0.088 -9999 0 -0.38 13 13
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.002 0.1 -9999 0 -0.58 13 13
MYH2 -0.099 0.11 -9999 0 -0.38 42 42
MST1R 0.001 0.095 -9999 0 -0.61 10 10
leukocyte activation during inflammatory response -0.039 0.092 -9999 0 -0.5 8 8
APOB -0.011 0.079 -9999 0 -0.31 32 32
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.019 0.15 -9999 0 -0.61 25 25
alphaM/beta2 Integrin/CTGF -0.12 0.22 -9999 0 -0.56 93 93
alphaM/beta2 Integrin -0.091 0.11 -9999 0 -0.32 57 57
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.064 0.14 -9999 0 -0.31 119 119
phagocytosis triggered by activation of immune response cell surface activating receptor -0.09 0.11 -9999 0 -0.32 57 57
cell adhesion -0.053 0.14 -9999 0 -0.48 38 38
NFKB1 -0.12 0.29 -9999 0 -0.74 58 58
THY1 0.011 0.029 -9999 0 -0.31 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.014 0.049 -9999 0 -0.33 2 2
alphaM/beta2 Integrin/LRP/tPA -0.033 0.1 -9999 0 -0.58 9 9
IL6 -0.21 0.44 -9999 0 -1.1 94 94
ITGB2 -0.018 0.086 -9999 0 -0.33 30 30
elevation of cytosolic calcium ion concentration -0.14 0.16 -9999 0 -0.51 38 38
alphaM/beta2 Integrin/JAM2/JAM3 -0.031 0.099 -9999 0 -0.59 9 9
JAM2 0.006 0.076 -9999 0 -0.71 5 5
alphaM/beta2 Integrin/ICAM1 -0.059 0.12 -9999 0 -0.5 21 21
alphaM/beta2 Integrin/uPA/Plg -0.097 0.12 -9999 0 -0.51 20 20
RhoA/GTP -0.1 0.12 -9999 0 -0.38 53 53
positive regulation of phagocytosis -0.067 0.12 -9999 0 -0.48 17 17
Ron/MSP -0.011 0.076 -9999 0 -0.62 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.16 -9999 0 -0.51 38 38
alphaM/beta2 Integrin/uPAR -0.083 0.13 -9999 0 -0.45 35 35
PLAU -0.14 0.16 -9999 0 -0.31 230 230
PLAT 0.003 0.076 -9999 0 -0.45 11 11
actin filament polymerization -0.095 0.11 -9999 0 -0.36 42 42
MST1 0.011 0.04 -9999 0 -0.56 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.039 0.093 -9999 0 -0.5 8 8
TNF -0.17 0.39 -9999 0 -0.98 78 78
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.13 -9999 0 -0.53 21 21
fibrinolysis -0.097 0.12 -9999 0 -0.5 20 20
HCK -0.01 0.084 -9999 0 -0.31 36 36
dendritic cell antigen processing and presentation -0.09 0.11 -9999 0 -0.32 57 57
VTN -0.067 0.24 -9999 0 -0.75 52 52
alphaM/beta2 Integrin/CYR61 -0.2 0.27 -9999 0 -0.57 164 164
LPA -0.002 0.042 -9999 0 -0.31 9 9
LRP1 0.012 0.037 -9999 0 -0.81 1 1
cell migration -0.089 0.2 -9999 0 -0.57 59 59
FN1 -0.22 0.14 -9999 0 -0.31 359 359
alphaM/beta2 Integrin/Thy1 -0.034 0.099 -9999 0 -0.41 22 22
MPO 0 0.094 -9999 0 -0.65 9 9
KNG1 -0.014 0.078 -9999 0 -0.31 32 32
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.09 0.11 -9999 0 -0.38 38 38
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.004 0.039 -9999 0 -0.31 8 8
CTGF -0.11 0.3 -9999 0 -0.81 76 76
alphaM/beta2 Integrin/Hck -0.045 0.12 -9999 0 -0.45 35 35
ITGAM -0.022 0.11 -9999 0 -0.38 32 32
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.046 0.13 -9999 0 -0.52 26 26
HP -0.082 0.16 -9999 0 -0.33 135 135
leukocyte adhesion -0.087 0.16 -9999 0 -0.6 25 25
SELP -0.002 0.1 -9999 0 -0.58 13 13
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.38 -9999 0 -1.3 40 40
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.033 0.11 -9999 0 -0.39 20 20
ATF2/c-Jun -0.22 0.42 -9999 0 -0.97 113 113
MAPK11 -0.033 0.11 -9999 0 -0.39 20 20
MITF -0.026 0.13 -9999 0 -0.41 40 40
MAPKAPK5 -0.026 0.13 -9999 0 -0.41 40 40
KRT8 -0.026 0.13 -9999 0 -0.41 40 40
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.044 0.16 -9999 0 -0.52 40 40
CEBPB -0.026 0.13 -9999 0 -0.41 40 40
SLC9A1 -0.026 0.13 -9999 0 -0.41 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.071 0.19 -9999 0 -0.56 40 40
p38alpha-beta/MNK1 -0.022 0.13 -9999 0 -0.49 20 20
JUN -0.22 0.42 -9999 0 -0.96 113 113
PPARGC1A -0.23 0.25 -9999 0 -0.45 258 258
USF1 -0.026 0.13 -9999 0 -0.41 40 40
RAB5/GDP/GDI1 -0.036 0.082 -9999 0 -0.35 20 20
NOS2 -0.045 0.16 -9999 0 -0.66 8 8
DDIT3 -0.028 0.13 -9999 0 -0.41 40 40
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.01 0.11 -9999 0 -0.39 20 20
p38alpha-beta/HBP1 -0.022 0.13 -9999 0 -0.49 20 20
CREB1 -0.046 0.15 -9999 0 -0.46 40 40
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.012 0.12 -9999 0 -0.44 19 19
RPS6KA4 -0.026 0.13 -9999 0 -0.41 40 40
PLA2G4A -0.045 0.19 -9999 0 -0.58 45 45
GDI1 -0.026 0.13 -9999 0 -0.41 40 40
TP53 -0.034 0.16 -9999 0 -0.51 40 40
RPS6KA5 -0.075 0.2 -9999 0 -0.46 87 87
ESR1 -0.06 0.2 -9999 0 -0.54 55 55
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.027 0.13 -9999 0 -0.41 41 41
MEF2A -0.027 0.13 -9999 0 -0.41 41 41
EIF4EBP1 -0.046 0.15 -9999 0 -0.46 40 40
KRT19 -0.1 0.2 -9999 0 -0.53 56 56
ELK4 -0.026 0.13 -9999 0 -0.41 40 40
ATF6 -0.026 0.13 -9999 0 -0.41 40 40
ATF1 -0.047 0.16 -9999 0 -0.47 41 41
p38alpha-beta/MAPKAPK2 -0.022 0.13 -9999 0 -0.49 20 20
p38alpha-beta/MAPKAPK3 -0.022 0.13 -9999 0 -0.49 20 20
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.002 0.046 -9999 0 -1 1 1
forebrain development -0.31 0.28 -9999 0 -0.55 255 255
GNAO1 -0.02 0.15 -9999 0 -0.7 21 21
SMO/beta Arrestin2 0.011 0.031 -9999 0 -0.62 1 1
SMO 0.006 0.038 -9999 0 -0.81 1 1
ARRB2 0.008 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.056 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.029 -9999 0 -0.49 1 1
GNAI1 0.008 0.038 -9999 0 -0.82 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.24 0.19 -9999 0 -0.51 135 135
SAP30 0.013 0.037 -9999 0 -0.81 1 1
mol:GDP 0.006 0.038 -9999 0 -0.81 1 1
MIM/GLI2A -0.007 0.043 -9999 0 -0.3 1 1
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GLI2 0.033 0.061 -9999 0 -10000 0 0
GLI3 0.039 0.058 -9999 0 -0.3 3 3
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 0.037 -9999 0 -0.81 1 1
Gi family/GTP 0.008 0.07 -9999 0 -0.33 18 18
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.029 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.058 -9999 0 -10000 0 0
FOXA2 -0.66 0.66 -9999 0 -1.3 239 239
neural tube patterning -0.31 0.28 -9999 0 -0.55 255 255
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 -0.3 1 1
embryonic limb morphogenesis -0.31 0.28 -9999 0 -0.55 255 255
SUFU 0.016 0.021 -9999 0 -10000 0 0
LGALS3 -0.09 0.15 -9999 0 -0.31 157 157
catabolic process 0.061 0.068 -9999 0 -0.39 2 2
GLI3A/CBP -0.19 0.2 -9999 0 -0.38 255 255
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.32 0.29 -9999 0 -0.57 255 255
RAB23 0.007 0.074 -9999 0 -0.81 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 -0.029 0.079 -9999 0 -0.44 2 2
GNAZ 0.01 0.006 -9999 0 -10000 0 0
RBBP4 0.009 0.064 -9999 0 -0.81 3 3
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.057 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.013 0.062 -9999 0 -0.42 2 2
PTCH1 -0.28 0.27 -9999 0 -0.62 135 135
MIM/GLI1 -0.45 0.39 -9999 0 -0.75 253 253
CREBBP -0.19 0.2 -9999 0 -0.38 255 255
Su(fu)/SIN3/HDAC complex 0.055 0.026 -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 0.005 0.083 -9999 0 -0.81 5 5
EGF/EGFR -0.078 0.17 -9999 0 -0.45 83 83
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.073 0.17 -9999 0 -0.46 77 77
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.009 0.047 -9999 0 -0.41 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
EGF/EGFR dimer/SHC -0.086 0.2 -9999 0 -0.54 77 77
mol:GDP -0.072 0.16 -9999 0 -0.45 77 77
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.003 0.086 -9999 0 -0.81 5 5
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.066 0.15 -9999 0 -0.42 77 77
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.067 0.15 -9999 0 -0.42 77 77
FRAP1 -0.036 0.17 -9999 0 -0.44 77 77
EGF/EGFR dimer -0.1 0.23 -9999 0 -0.62 77 77
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 -0.59 7 7
Osteopontin-mediated events

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
IKK alpha homodimer -0.031 0.14 -9999 0 -0.45 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.054 0.11 -9999 0 -0.54 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.064 0.15 -9999 0 -0.61 25 25
AP1 -0.26 0.35 -9999 0 -0.83 115 115
ILK -0.031 0.15 -9999 0 -0.48 39 39
bone resorption -0.04 0.16 -9999 0 -0.64 11 11
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.051 0.12 -9999 0 -0.43 39 39
ITGAV 0.01 0.052 -9999 0 -0.81 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.032 0.14 -9999 0 -0.62 25 25
alphaV/beta3 Integrin/Osteopontin -0.068 0.15 -9999 0 -0.54 39 39
MAP3K1 -0.031 0.15 -9999 0 -0.49 39 39
JUN -0.17 0.35 -9999 0 -0.81 112 112
MAPK3 -0.031 0.14 -9999 0 -0.45 39 39
MAPK1 -0.031 0.14 -9999 0 -0.45 39 39
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 -0.031 0.17 -9999 0 -0.49 46 46
ITGB3 -0.011 0.14 -9999 0 -0.81 15 15
NFKBIA -0.025 0.14 -9999 0 -0.44 39 39
FOS -0.2 0.36 -9999 0 -0.81 127 127
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.11 0.17 -9999 0 -0.69 4 4
NF kappa B1 p50/RelA -0.059 0.11 -9999 0 -0.53 6 6
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.65 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.031 0.15 -9999 0 -0.49 39 39
VAV3 -0.026 0.15 -9999 0 -0.46 44 44
MAP3K14 -0.039 0.15 -9999 0 -0.49 39 39
ROCK2 -0.028 0.18 -9999 0 -0.81 25 25
SPP1 -0.078 0.2 -9999 0 -0.42 104 104
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.045 0.13 -9999 0 -0.42 44 44
MMP2 -0.17 0.29 -9999 0 -0.64 111 111
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.033 0.11 -10000 0 -0.31 69 69
GNB1/GNG2 -0.042 0.067 -10000 0 -0.19 70 70
AKT1 -0.007 0.1 -10000 0 -0.21 39 39
EGF -0.11 0.29 -10000 0 -0.78 78 78
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.033 0.07 -10000 0 -0.71 1 1
mol:Ca2+ -0.035 0.14 -10000 0 -0.31 73 73
LYN 0.034 0.07 -10000 0 -0.71 1 1
RhoA/GTP -0.029 0.045 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.034 0.16 -10000 0 -0.34 72 72
GNG2 0.012 0.037 -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 -0.55 12 12
G beta5/gamma2 -0.056 0.091 -10000 0 -0.27 46 46
PRKCH -0.042 0.16 -10000 0 -0.36 72 72
DNM1 -0.014 0.15 -10000 0 -0.78 17 17
TXA2/TP beta/beta Arrestin3 -0.012 0.054 -10000 0 -0.3 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.02 0.16 -10000 0 -0.81 20 20
G12 family/GTP -0.072 0.11 -10000 0 -0.31 70 70
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 0.012 0.1 0.34 14 -10000 0 14
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.22 0.37 -10000 0 -0.81 137 137
mol:IP3 -0.05 0.18 -10000 0 -0.38 73 73
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.075 0.23 -10000 0 -0.53 72 72
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.094 0.2 -10000 0 -0.38 145 145
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.025 0.076 -10000 0 -0.71 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.005 0.083 -10000 0 -0.81 5 5
PRKCB1 -0.05 0.17 -10000 0 -0.39 72 72
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.072 0.23 -10000 0 -0.54 73 73
LCK 0.024 0.091 -10000 0 -0.54 6 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.017 0.081 -10000 0 -1.1 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.029 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.017 0.08 -10000 0 -1.1 1 1
MAPK14 -0.012 0.11 -10000 0 -0.23 70 70
TGM2/GTP -0.062 0.2 -10000 0 -0.43 73 73
MAPK11 -0.012 0.11 -10000 0 -0.23 70 70
ARHGEF1 -0.01 0.088 -10000 0 -0.19 15 15
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.046 0.18 -10000 0 -0.39 73 73
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.04 0.15 -10000 0 -0.29 81 81
cAMP biosynthetic process -0.05 0.16 -10000 0 -0.36 73 73
Gq family/GTP/EBP50 -0.045 0.12 -10000 0 -0.35 23 23
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.034 0.07 -10000 0 -0.71 1 1
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 -0.3 15 15
VCAM1 -0.029 0.14 -10000 0 -0.3 74 74
TP beta/Gq family/GDP/G beta5/gamma2 -0.026 0.12 -10000 0 -0.55 12 12
platelet activation -0.017 0.15 -10000 0 -0.3 70 70
PGI2/IP -0.006 0.063 -10000 0 -0.63 5 5
PRKACA 0.002 0.095 -10000 0 -0.4 24 24
Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.5 12 12
TXA2/TP beta/beta Arrestin2 -0.023 0.12 -10000 0 -0.66 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.009 0.1 -10000 0 -0.39 24 24
mol:DAG -0.057 0.19 -10000 0 -0.44 72 72
EGFR 0.005 0.083 -10000 0 -0.81 5 5
TXA2/TP alpha -0.071 0.22 -10000 0 -0.49 73 73
Gq family/GTP -0.077 0.13 -10000 0 -0.3 125 125
YES1 0.034 0.07 -10000 0 -0.71 1 1
GNAI2/GTP -0.015 0.07 -10000 0 -0.9 1 1
PGD2/DP -0.026 0.12 -10000 0 -0.63 20 20
SLC9A3R1 0.012 0.021 -10000 0 -0.31 2 2
FYN 0.034 0.07 -10000 0 -0.71 1 1
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.011 0.09 -10000 0 -0.32 36 36
PGK/cGMP -0.15 0.24 -10000 0 -0.55 137 137
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.029 0.092 -10000 0 -0.6 5 5
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.052 0.18 -10000 0 -0.39 78 78
PRKCB -0.051 0.17 -10000 0 -0.38 75 75
PRKCE -0.045 0.17 -10000 0 -0.37 74 74
PRKCD -0.045 0.17 -10000 0 -0.38 72 72
PRKCG -0.049 0.17 -10000 0 -0.39 72 72
muscle contraction -0.062 0.22 -10000 0 -0.49 73 73
PRKCZ -0.034 0.16 -10000 0 -0.34 72 72
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.017 0.081 -10000 0 -0.37 13 13
PRKCQ -0.044 0.17 -10000 0 -0.36 78 78
MAPKKK cascade -0.063 0.2 -10000 0 -0.47 73 73
SELE -0.049 0.18 -10000 0 -0.43 72 72
TP beta/GNAI2/GDP/G beta/gamma -0.017 0.086 -10000 0 -1.3 1 1
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.35 -10000 0 -0.81 118 118
chemotaxis -0.083 0.26 -10000 0 -0.62 73 73
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.003 0.12 -10000 0 -0.81 10 10
Rac1/GTP 0.004 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.089 0.22 -9999 0 -0.41 146 146
MAP3K8 -0.001 0.098 -9999 0 -0.82 7 7
FOS -0.055 0.17 -9999 0 -0.5 35 35
PRKCA -0.021 0.16 -9999 0 -0.82 19 19
PTPN7 -0.047 0.18 -9999 0 -0.46 61 61
HRAS 0.011 0.021 -9999 0 -0.31 2 2
PRKCB -0.024 0.12 -9999 0 -0.37 46 46
NRAS 0.013 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.029 0.12 -9999 0 -0.51 19 19
MAP2K1 -0.017 0.14 -9999 0 -0.59 23 23
ELK1 0.008 0.01 -9999 0 -10000 0 0
BRAF -0.039 0.12 -9999 0 -0.57 23 23
mol:GTP -0.001 0.003 -9999 0 -0.006 126 126
MAPK1 -0.029 0.12 -9999 0 -0.43 28 28
RAF1 -0.039 0.12 -9999 0 -0.57 23 23
KRAS 0.013 0.002 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.025 0.077 0.29 36 -10000 0 36
RFC1 0.025 0.077 0.29 36 -10000 0 36
PRKDC 0.025 0.077 0.29 36 -10000 0 36
RIPK1 0.014 0.004 -10000 0 -10000 0 0
CASP7 -0.012 0.045 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.029 0.1 0.26 5 -0.37 37 42
MAP2K4 -0.02 0.16 -10000 0 -0.5 18 18
mol:ceramide -0.022 0.15 -10000 0 -0.47 38 38
GSN 0.025 0.077 0.29 36 -10000 0 36
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.14 -10000 0 -0.46 37 37
FAS 0.011 0.006 -10000 0 -10000 0 0
BID -0.028 0.077 0.32 3 -10000 0 3
MAP3K1 0.006 0.097 -10000 0 -0.28 16 16
MAP3K7 0.011 0.005 -10000 0 -10000 0 0
RB1 0.024 0.078 0.29 35 -0.31 1 36
CFLAR 0.014 0.004 -10000 0 -10000 0 0
HGF/MET -0.14 0.22 -10000 0 -0.61 77 77
ARHGDIB 0.022 0.08 0.29 36 -10000 0 36
FADD 0.011 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.025 0.077 -10000 0 -0.29 36 36
NFKB1 -0.049 0.09 -10000 0 -0.32 17 17
MAPK8 -0.052 0.21 -10000 0 -0.45 93 93
DFFA 0.025 0.077 0.29 36 -10000 0 36
DNA fragmentation during apoptosis 0.025 0.077 0.29 36 -10000 0 36
FAS/FADD/MET -0.057 0.075 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.003 0.089 -10000 0 -0.38 22 22
FAF1 0.011 0.006 -10000 0 -10000 0 0
PARP1 0.025 0.077 0.29 36 -10000 0 36
DFFB 0.025 0.077 0.29 36 -10000 0 36
CHUK -0.042 0.08 -10000 0 -0.73 1 1
FASLG -0.064 0.23 -10000 0 -0.66 55 55
FAS/FADD -0.001 0.001 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.81 74 74
LMNA 0.023 0.07 0.26 36 -10000 0 36
CASP6 0.025 0.077 0.29 36 -10000 0 36
CASP10 0.011 0.006 -10000 0 -10000 0 0
CASP3 0.03 0.094 0.34 39 -10000 0 39
PTPN13 0.003 0.091 -10000 0 -0.81 6 6
CASP8 0.008 0.045 0.45 3 -10000 0 3
IL6 -0.23 0.54 -10000 0 -1.4 88 88
MET -0.1 0.16 -10000 0 -0.31 179 179
ICAD/CAD 0.023 0.072 0.27 36 -10000 0 36
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.15 -10000 0 -0.48 38 38
activation of caspase activity by cytochrome c -0.028 0.077 0.32 3 -10000 0 3
PAK2 0.025 0.077 0.29 36 -10000 0 36
BCL2 -0.047 0.22 -10000 0 -0.81 36 36
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.036 0.21 -9999 0 -0.81 33 33
HDAC7 -0.034 0.15 -9999 0 -0.64 17 17
JUN -0.18 0.34 -9999 0 -0.81 112 112
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 0.097 -9999 0 -0.64 11 11
FOXO1 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.047 0.16 -9999 0 -0.66 19 19
MAP2K6 -0.01 0.12 -9999 0 -0.78 12 12
BRM/BAF57 -0.002 0.003 -9999 0 -10000 0 0
MAP2K4 0.009 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.011 0.058 -9999 0 -10000 0 0
NCOA2 -0.074 0.24 -9999 0 -0.82 48 48
CEBPA 0.006 0.083 -9999 0 -0.81 5 5
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.07 0.15 -9999 0 -0.54 18 18
NR0B1 -0.002 0.04 -9999 0 -0.31 8 8
EGR1 -0.17 0.34 -9999 0 -0.82 107 107
RXRs/9cRA -0.13 0.058 -9999 0 -0.5 4 4
AR/RACK1/Src -0.12 0.16 -9999 0 -0.67 19 19
AR/GR -0.13 0.2 -9999 0 -0.34 210 210
GNB2L1 0.007 0.007 -9999 0 -10000 0 0
PKN1 0.013 0.001 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 -0.002 0.097 -9999 0 -0.63 11 11
T-DHT/AR/TIF2/CARM1 -0.13 0.24 -9999 0 -0.69 56 56
SRC -0.005 0.12 -9999 0 -0.55 19 19
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.4 0.57 -9999 0 -1.3 144 144
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.056 0.15 -9999 0 -0.67 19 19
TMPRSS2 -0.059 0.31 -9999 0 -1.2 32 32
RXRG -0.28 0.11 -9999 0 -0.32 437 437
mol:9cRA -0.002 0.003 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.007 0.007 -9999 0 -10000 0 0
NR2C2 -0.006 0.12 -9999 0 -0.81 11 11
KLK2 -0.48 0.42 -9999 0 -0.83 290 290
AR -0.15 0.22 -9999 0 -0.38 214 214
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 -0.013 0.05 -9999 0 -0.32 11 11
T-DHT/AR/RACK1/Src -0.079 0.15 -9999 0 -0.66 19 19
positive regulation of transcription 0.013 0.015 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.005 -9999 0 -10000 0 0
NCOA1 0.013 0.009 -9999 0 -10000 0 0
SPDEF -0.027 0.1 -9999 0 -0.32 54 54
T-DHT/AR/TIF2 -0.057 0.16 -9999 0 -0.46 50 50
T-DHT/AR/Hsp90 -0.058 0.15 -9999 0 -0.67 19 19
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.008 0.12 -9999 0 -0.59 19 19
SIRT1 0.011 0.037 -9999 0 -0.81 1 1
ZMIZ2 0.023 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.019 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.076 0.14 -9999 0 -0.68 19 19
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure 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
Syndecan-2/Fibronectin -0.11 0.1 -9999 0 -0.64 7 7
EPHB2 0.008 0.064 -9999 0 -0.81 3 3
Syndecan-2/TACI -0.13 0.25 -9999 0 -0.56 128 128
LAMA1 -0.048 0.22 -9999 0 -0.8 37 37
Syndecan-2/alpha2 ITGB1 -0.071 0.11 -9999 0 -0.46 24 24
HRAS 0.012 0.021 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.064 -9999 0 -0.54 7 7
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.023 0.1 -9999 0 -0.5 18 18
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.007 0.058 -9999 0 -0.49 7 7
LAMA3 -0.025 0.16 -9999 0 -0.58 32 32
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.064 -9999 0 -0.81 3 3
Syndecan-2/MMP2 0.008 0.1 -9999 0 -0.57 13 13
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.078 0.097 -9999 0 -10000 0 0
dendrite morphogenesis 0.014 0.079 -9999 0 -0.54 10 10
Syndecan-2/GM-CSF -0.11 0.097 -9999 0 -0.56 7 7
determination of left/right symmetry 0.012 0.076 -9999 0 -0.62 7 7
Syndecan-2/PKC delta 0.018 0.066 -9999 0 -0.54 7 7
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.086 0.09 -9999 0 -0.51 7 7
MAPK1 -0.086 0.09 -9999 0 -0.51 7 7
Syndecan-2/RACK1 -0.007 0.055 -9999 0 -0.46 7 7
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.076 -9999 0 -0.62 7 7
ITGA2 -0.11 0.16 -9999 0 -0.31 193 193
MAPK8 0.015 0.11 -9999 0 -0.55 18 18
Syndecan-2/alpha2/beta1 Integrin -0.084 0.14 -9999 0 -0.51 40 40
Syndecan-2/Kininogen -0.007 0.077 -9999 0 -0.54 7 7
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.057 -9999 0 -0.43 7 7
Syndecan-2/CASK/Protein 4.1 -0.007 0.058 -9999 0 -0.5 7 7
extracellular matrix organization 0.015 0.07 -9999 0 -0.53 7 7
actin cytoskeleton reorganization -0.11 0.1 -9999 0 -0.64 7 7
Syndecan-2/Caveolin-2/Ras -0.01 0.075 -9999 0 -0.54 9 9
Syndecan-2/Laminin alpha3 -0.007 0.12 -9999 0 -0.54 24 24
Syndecan-2/RasGAP -0.007 0.052 -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 0.079 -9999 0 -0.54 10 10
GO:0007205 0.004 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.056 -9999 0 -0.42 7 7
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.2 0.36 -9999 0 -0.79 131 131
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.078 0.097 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.018 0.066 -9999 0 -0.54 7 7
TGFB1 0.008 0.041 -9999 0 -0.31 8 8
CASP3 0.027 0.061 -9999 0 -0.48 7 7
FN1 -0.22 0.14 -9999 0 -0.31 359 359
Syndecan-2/IL8 -0.038 0.12 -9999 0 -0.54 18 18
SDC2 0.012 0.076 -9999 0 -0.62 7 7
KNG1 -0.014 0.078 -9999 0 -0.31 32 32
Syndecan-2/Neurofibromin 0.018 0.066 -9999 0 -0.54 7 7
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 335 335
Syndecan-2/TGFB1 0.015 0.07 -9999 0 -0.54 7 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.007 0.058 -9999 0 -0.5 7 7
Syndecan-2/Ezrin -0.007 0.058 -9999 0 -0.49 7 7
PRKACA 0.027 0.061 -9999 0 -0.48 7 7
angiogenesis -0.038 0.12 -9999 0 -0.54 18 18
MMP2 -0.001 0.1 -9999 0 -0.63 11 11
IL8 -0.082 0.18 -9999 0 -0.35 128 128
calcineurin-NFAT signaling pathway -0.13 0.25 -9999 0 -0.55 128 128
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.006 0.12 -9999 0 -0.77 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.15 -9999 0 -0.28 286 286
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.011 0.029 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.048 0.068 -9999 0 -0.31 5 5
PRKG1 -0.22 0.37 -9999 0 -0.81 137 137
DUSP8 0.003 0.082 -9999 0 -0.51 10 10
PGK/cGMP/p38 alpha -0.16 0.2 -9999 0 -0.46 140 140
apoptosis -0.046 0.066 -9999 0 -0.3 5 5
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.3 -9999 0 -0.81 80 80
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1/OSM/MEKK3/MKK3 -0.001 0.008 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.012 0.021 -9999 0 -0.31 2 2
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.061 0.13 -9999 0 -0.36 17 17
BLK -0.24 0.37 -9999 0 -0.74 168 168
HCK -0.01 0.084 -9999 0 -0.31 36 36
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.01 0.042 -9999 0 -0.48 3 3
TRAF6/MEKK3 -0.002 0.032 -9999 0 -0.5 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.028 0.092 -9999 0 -0.32 6 6
positive regulation of innate immune response -0.059 0.14 -9999 0 -0.39 16 16
LCK -0.01 0.11 -9999 0 -0.42 27 27
p38alpha-beta/MKP7 -0.05 0.13 -9999 0 -0.44 6 6
p38alpha-beta/MKP5 -0.051 0.13 -9999 0 -0.41 13 13
PGK/cGMP -0.18 0.28 -9999 0 -0.63 137 137
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.2 -9999 0 -0.46 88 88
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 -0.81 286 286
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.033 0.12 -10000 0 -0.5 25 25
ER alpha/Gai/GDP/Gbeta gamma 0.007 0.15 -10000 0 -0.54 24 24
AKT1 -0.014 0.2 -10000 0 -0.86 25 25
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.013 0.2 -10000 0 -0.87 25 25
mol:Ca2+ -0.1 0.23 -10000 0 -0.49 120 120
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.071 0.18 -10000 0 -0.58 53 53
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.19 0.81 25 -10000 0 25
RhoA/GTP -0.025 0.087 -10000 0 -0.4 23 23
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.036 0.13 -10000 0 -0.58 23 23
regulation of stress fiber formation -0.011 0.12 0.46 5 -10000 0 5
E2/ERA-ERB (dimer) -0.039 0.13 -10000 0 -0.57 25 25
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.033 0.11 -10000 0 -0.5 23 23
pseudopodium formation 0.011 0.12 -10000 0 -0.46 5 5
E2/ER alpha (dimer)/PELP1 -0.036 0.12 -10000 0 -0.55 23 23
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.012 0.037 -10000 0 -0.81 1 1
GNAO1 -0.017 0.15 -10000 0 -0.69 21 21
HRAS 0.012 0.021 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.013 0.15 -10000 0 -0.59 24 24
E2/ER beta (dimer) -0.004 0.049 -10000 0 -0.63 3 3
mol:GDP -0.034 0.12 -10000 0 -0.56 25 25
mol:NADP 0.013 0.15 -10000 0 -0.59 24 24
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.11 0.24 -10000 0 -0.52 120 120
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.25 -10000 0 -0.53 120 120
PLCB2 -0.12 0.25 -10000 0 -0.54 119 119
IGF1 -0.18 0.35 -10000 0 -0.79 119 119
mol:L-citrulline 0.013 0.15 -10000 0 -0.59 24 24
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.026 0.14 -10000 0 -0.78 16 16
JNK cascade -0.004 0.049 -10000 0 -0.63 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.008 0.064 -10000 0 -0.81 3 3
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.046 0.19 -10000 0 -0.52 55 55
Gq family/GDP/Gbeta gamma -0.057 0.18 -10000 0 -0.68 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.021 0.08 -10000 0 -0.36 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.036 0.13 -10000 0 -0.58 23 23
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.043 0.14 -10000 0 -0.63 23 23
STRN -0.04 0.2 -10000 0 -0.81 32 32
GNAL -0.094 0.28 -10000 0 -0.81 64 64
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.016 0.044 -10000 0 -0.55 3 3
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.81 1 1
HBEGF -0.004 0.16 -10000 0 -0.65 16 16
cAMP biosynthetic process -0.089 0.18 -10000 0 -0.48 85 85
SRC 0.015 0.14 -10000 0 -0.5 24 24
PI3K -0.004 0.048 -10000 0 -0.62 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.029 0.11 -10000 0 -0.5 25 25
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -10000 0 -0.53 36 36
Gs family/GTP -0.091 0.19 -10000 0 -0.48 85 85
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.009 -10000 0 -10000 0 0
vasodilation 0.014 0.14 -10000 0 -0.56 24 24
mol:DAG -0.11 0.24 -10000 0 -0.52 120 120
Gs family/GDP/Gbeta gamma -0.072 0.16 -10000 0 -0.4 85 85
MSN 0.01 0.12 -10000 0 -0.5 5 5
Gq family/GTP -0.15 0.24 -10000 0 -0.57 119 119
mol:PI-3-4-5-P3 -0.011 0.19 -10000 0 -0.83 25 25
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.014 0.14 0.56 24 -10000 0 24
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.031 0.12 -10000 0 -0.52 25 25
NOS3 0.012 0.16 -10000 0 -0.63 24 24
GNA11 -0.003 0.12 -10000 0 -0.81 10 10
MAPKKK cascade -0.008 0.19 -10000 0 -0.54 53 53
E2/ER alpha (dimer)/PELP1/Src -0.038 0.14 -10000 0 -0.62 23 23
ruffle organization 0.011 0.12 -10000 0 -0.46 5 5
ROCK2 0.001 0.14 -10000 0 -0.4 47 47
GNA14 -0.18 0.35 -10000 0 -0.81 118 118
GNA15 -0.011 0.09 -10000 0 -0.32 36 36
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.027 0.19 -10000 0 -0.51 49 49
MMP2 0.015 0.15 -10000 0 -0.67 11 11
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.01 0.12 -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 -0.044 0.13 -9999 0 -0.4 54 54
JUN 0.004 0.097 -9999 0 -0.27 13 13
HRAS 0.012 0.021 -9999 0 -0.31 2 2
DOCK7 -0.013 0.14 -9999 0 -0.38 57 57
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.054 0.15 -9999 0 -0.48 54 54
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.022 0.062 -9999 0 -0.36 2 2
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.15 -9999 0 -0.44 54 54
RAF1 -0.001 0.12 -9999 0 -0.39 21 21
ErbB2/ErbB3/neuregulin 2 -0.067 0.17 -9999 0 -0.51 64 64
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.022 0.082 -9999 0 -0.3 5 5
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.12 0.33 -9999 0 -0.68 118 118
FOS -0.1 0.28 -9999 0 -0.51 151 151
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.044 0.13 -9999 0 -0.4 54 54
MAPK3 -0.08 0.26 -9999 0 -0.5 116 116
MAPK1 -0.08 0.26 -9999 0 -0.5 116 116
JAK2 -0.012 0.13 -9999 0 -0.38 56 56
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.014 0.13 -9999 0 -0.37 54 54
NRG1 -0.065 0.24 -9999 0 -0.79 47 47
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.012 0.13 -9999 0 -0.35 64 64
MAPK9 -0.022 0.06 -9999 0 -0.26 2 2
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.007 0.12 -9999 0 -0.73 12 12
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.01 -9999 0 -10000 0 0
STAT3 (dimer) 0.002 0.006 -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 -0.031 0.086 -9999 0 -0.38 2 2
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.053 0.2 -9999 0 -0.38 117 117
myelination 0.01 0.11 -9999 0 -0.46 3 3
PPP3CB -0.009 0.12 -9999 0 -0.37 25 25
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.024 0.11 -9999 0 -0.64 2 2
NRG2 -0.079 0.26 -9999 0 -0.79 57 57
mol:GDP -0.014 0.13 -9999 0 -0.37 54 54
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.004 0.13 -9999 0 -0.41 21 21
SRC 0.013 0.015 -9999 0 -0.31 1 1
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.012 0.13 -9999 0 -0.38 55 55
MAP2K1 -0.072 0.23 -9999 0 -0.45 97 97
heart morphogenesis -0.044 0.13 -9999 0 -0.4 54 54
RAS family/GDP -0.005 0.11 -9999 0 -0.63 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.008 -9999 0 -10000 0 0
CHRNE 0.01 0.035 -9999 0 -0.13 18 18
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.044 0.13 -9999 0 -0.4 54 54
CDC42 0.013 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure 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
LAT/GRAP2/SLP76/HPK1 -0.057 0.16 -9999 0 -0.55 43 43
MAP4K1 -0.021 0.13 -9999 0 -0.39 42 42
MAP3K8 0.002 0.098 -9999 0 -0.81 7 7
PRKCB -0.022 0.12 -9999 0 -0.36 46 46
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.012 0.11 -9999 0 -0.55 6 6
JUN -0.1 0.25 -9999 0 -0.51 123 123
MAP3K7 0.012 0.11 -9999 0 -0.55 6 6
GRAP2 -0.045 0.21 -9999 0 -0.75 38 38
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.11 -9999 0 -0.52 7 7
LAT 0.005 0.077 -9999 0 -0.65 6 6
LCP2 0.007 0.043 -9999 0 -0.31 9 9
MAPK8 -0.003 0.14 -9999 0 -0.75 15 15
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.003 0.12 -9999 0 -0.36 36 36
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.053 0.15 -9999 0 -0.52 43 43
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.037 -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 -0.057 0.11 -9999 0 -0.35 47 47
RXRs/LXRs/DNA/Oxysterols -0.047 0.15 -9999 0 -0.46 57 57
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.083 -9999 0 -0.34 24 24
RXRs/NUR77 -0.26 0.25 -9999 0 -0.62 149 149
RXRs/PPAR -0.054 0.064 -9999 0 -0.4 11 11
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0.009 -9999 0 -0.21 1 1
RARs/VDR/DNA/Vit D3 -0.013 0.079 -9999 0 -0.47 14 14
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -9999 0 -0.31 1 1
RARs/RARs/DNA/9cRA -0.013 0.078 -9999 0 -0.47 14 14
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.053 0.031 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.021 0.083 -9999 0 -0.34 24 24
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0.009 -9999 0 -0.21 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.082 -9999 0 -0.58 4 4
NR1H4 0.001 0.032 -9999 0 -0.31 5 5
RXRs/LXRs/DNA -0.096 0.091 -9999 0 -0.57 4 4
NR1H2 0.016 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.1 0.067 -9999 0 -0.52 4 4
NR4A1 -0.23 0.38 -9999 0 -0.81 147 147
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.047 0.048 -9999 0 -0.32 4 4
RXRG -0.28 0.12 -9999 0 -0.31 437 437
RXR alpha/CCPG 0.021 0.009 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.015 0.014 -9999 0 -10000 0 0
THRB -0.005 0.12 -9999 0 -0.81 11 11
PPARG -0.002 0.1 -9999 0 -0.6 12 12
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.41 -9999 0 -1.3 57 57
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.046 0.15 -9999 0 -0.45 57 57
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.14 -9999 0 -0.81 14 14
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.44 172 172
SREBF1 -0.036 0.14 -9999 0 -0.62 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.082 -9999 0 -0.58 4 4
ABCA1 -0.036 0.14 -9999 0 -0.62 3 3
RARs/THRs -0.023 0.1 -9999 0 -0.48 24 24
RXRs/FXR -0.12 0.071 -9999 0 -0.55 4 4
BCL2 -0.047 0.22 -9999 0 -0.81 36 36
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.11 0.18 -9999 0 -0.46 65 65
IKBKB -0.018 0.073 -9999 0 -0.33 4 4
AKT1 -0.042 0.1 -9999 0 -0.26 25 25
IKBKG -0.017 0.077 -9999 0 -0.35 4 4
CALM1 -0.036 0.087 -9999 0 -0.35 3 3
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
MAP3K1 -0.076 0.18 -9999 0 -0.65 18 18
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.046 0.091 -9999 0 -0.37 3 3
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.081 0.13 -9999 0 -0.28 113 113
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 -0.52 145 145
CD22 -0.15 0.23 -9999 0 -0.64 56 56
CAMK2G -0.026 0.082 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
SHC/GRB2/SOS1 -0.098 0.15 -9999 0 -10000 0 0
GO:0007205 -0.046 0.092 -9999 0 -0.38 3 3
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.037 0.088 -9999 0 -0.35 3 3
NFATC1 -0.071 0.16 -9999 0 -0.55 22 22
B-cell antigen/BCR complex -0.17 0.24 -9999 0 -0.52 145 145
PAG1/CSK -0.002 0.029 -9999 0 -0.62 1 1
NFKBIB 0.003 0.028 -9999 0 -0.11 3 3
HRAS -0.039 0.1 -9999 0 -0.34 4 4
NFKBIA 0.003 0.028 -9999 0 -0.11 3 3
NF-kappa-B/RelA/I kappa B beta 0.009 0.025 -9999 0 -0.19 1 1
RasGAP/Csk -0.14 0.2 -9999 0 -0.49 100 100
mol:GDP -0.042 0.084 -9999 0 -0.35 3 3
PTEN 0.012 0.037 -9999 0 -0.81 1 1
CD79B -0.03 0.11 -9999 0 -0.31 67 67
NF-kappa-B/RelA/I kappa B alpha 0.009 0.025 -9999 0 -0.2 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.089 0.18 -9999 0 -0.43 79 79
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.052 0.089 -9999 0 -0.38 3 3
CSK 0.013 0.015 -9999 0 -0.31 1 1
FOS -0.14 0.21 -9999 0 -0.47 130 130
CHUK -0.017 0.077 -9999 0 -0.32 6 6
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.068 0.1 -9999 0 -0.5 12 12
PTPN6 -0.14 0.21 -9999 0 -0.61 53 53
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.005 0.035 -9999 0 -0.13 19 19
VAV2 -0.14 0.19 -9999 0 -0.85 13 13
ubiquitin-dependent protein catabolic process 0.008 0.027 -9999 0 -0.11 3 3
BTK -0.018 0.16 -9999 0 -1.2 8 8
CD19 -0.15 0.2 -9999 0 -0.46 102 102
MAP4K1 -0.021 0.13 -9999 0 -0.39 42 42
CD72 0.011 0.029 -9999 0 -0.31 4 4
PAG1 0.012 0.037 -9999 0 -0.81 1 1
MAPK14 -0.057 0.16 -9999 0 -0.53 18 18
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.036 0.09 -9999 0 -0.32 3 3
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.064 0.17 -9999 0 -0.43 76 76
RAF1 -0.029 0.096 -9999 0 -10000 0 0
RasGAP/p62DOK/SHIP -0.14 0.2 -9999 0 -0.47 97 97
CD79A -0.19 0.3 -9999 0 -0.52 190 190
re-entry into mitotic cell cycle -0.08 0.13 -9999 0 -0.28 111 111
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.01 0.085 -9999 0 -10000 0 0
MAPK1 -0.01 0.085 -9999 0 -10000 0 0
CD72/SHP1 -0.1 0.21 -9999 0 -0.66 35 35
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 -0.065 0.17 -9999 0 -0.56 24 24
actin cytoskeleton organization -0.089 0.18 -9999 0 -0.68 13 13
NF-kappa-B/RelA 0.023 0.045 -9999 0 -0.2 1 1
Calcineurin -0.036 0.06 -9999 0 -10000 0 0
PI3K -0.13 0.16 -9999 0 -0.52 35 35
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.056 0.087 -9999 0 -0.34 3 3
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.24 -9999 0 -0.98 23 23
DAPP1 -0.14 0.26 -9999 0 -1.2 20 20
cytokine secretion -0.066 0.15 -9999 0 -0.5 22 22
mol:DAG -0.052 0.089 -9999 0 -0.38 3 3
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.019 0.091 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.17 0.24 -9999 0 -0.57 99 99
mol:PI-3-4-5-P3 -0.097 0.12 -9999 0 -0.36 32 32
ETS1 -0.017 0.077 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.17 -9999 0 -0.46 79 79
B-cell antigen/BCR complex/LYN -0.12 0.2 -9999 0 -0.49 85 85
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
RAC1 -0.095 0.19 -9999 0 -0.75 13 13
B-cell antigen/BCR complex/LYN/SYK -0.15 0.22 -9999 0 -0.55 85 85
CARD11 -0.075 0.14 -9999 0 -0.55 16 16
FCGR2B -0.03 0.18 -9999 0 -0.73 29 29
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0 0.036 -9999 0 -0.14 2 2
PTPRC -0.034 0.18 -9999 0 -0.58 39 39
PDPK1 -0.044 0.1 -9999 0 -0.27 25 25
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.025 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.072 0.096 -10000 0 -10000 0 0
CRKL -0.03 0.11 -10000 0 -0.33 25 25
mol:PIP3 -0.019 0.032 0.68 1 -10000 0 1
AKT1 0.001 0.039 0.45 1 -0.53 2 3
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.021 0.11 -10000 0 -10000 0 0
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
HGF/MET/SHIP2 -0.14 0.2 -10000 0 -0.59 74 74
MAP3K5 -0.018 0.11 -10000 0 -0.47 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.54 74 74
AP1 -0.27 0.42 -10000 0 -0.87 151 151
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.26 0.4 -10000 0 -0.86 151 151
STAT3 (dimer) -0.038 0.13 -10000 0 -0.33 74 74
GAB1/CRKL/SHP2/PI3K -0.042 0.093 -10000 0 -0.69 2 2
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
CBL/CRK -0.021 0.11 -10000 0 -10000 0 0
PTPN11 0.012 0.037 -10000 0 -0.81 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.037 -10000 0 -0.81 1 1
ELK1 -0.047 0.061 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.039 0.071 -10000 0 -0.24 26 26
PAK1 0.009 0.037 0.42 1 -0.49 2 3
HGF/MET/RANBP10 -0.14 0.2 -10000 0 -0.59 74 74
HRAS -0.057 0.16 -10000 0 -0.48 26 26
DOCK1 -0.025 0.12 -10000 0 -0.55 4 4
GAB1 -0.04 0.12 -10000 0 -0.35 25 25
CRK -0.03 0.11 -10000 0 -10000 0 0
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.21 -10000 0 -0.6 74 74
JUN -0.17 0.35 -10000 0 -0.81 112 112
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.07 0.1 -10000 0 -0.29 74 74
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.011 0.14 -10000 0 -0.64 2 2
GRB2/SHC -0.037 0.096 -10000 0 -0.3 25 25
FOS -0.2 0.36 -10000 0 -0.81 127 127
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.047 0.061 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.6 74 74
cell migration -0.037 0.094 -10000 0 -0.29 25 25
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.072 0.096 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.05 0.14 -10000 0 -0.36 74 74
MET/MUC20 -0.076 0.1 -10000 0 -10000 0 0
RAP1B -0.012 0.1 -10000 0 -10000 0 0
RAP1A -0.012 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.14 0.2 -10000 0 -0.59 74 74
RAF1 -0.047 0.15 -10000 0 -0.45 26 26
STAT3 -0.039 0.13 -10000 0 -0.34 74 74
cell proliferation -0.046 0.17 -10000 0 -0.45 74 74
RPS6KB1 -0.015 0.039 -10000 0 -10000 0 0
MAPK3 -0.049 0.056 -10000 0 -10000 0 0
MAPK1 -0.049 0.056 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.008 0.14 -10000 0 -0.57 15 15
SRC -0.039 0.13 -10000 0 -0.38 25 25
PI3K -0.04 0.1 -10000 0 -0.32 28 28
MET/Glomulin -0.056 0.092 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.036 0.14 -10000 0 -10000 0 0
MET -0.1 0.16 -10000 0 -0.31 179 179
MAP4K1 -0.027 0.12 -10000 0 -0.54 4 4
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.036 0.14 -10000 0 -10000 0 0
BAD 0.009 0.037 0.42 1 -0.49 2 3
MAP2K4 -0.009 0.1 -10000 0 -0.42 5 5
SHP2/GRB2/SOS1/GAB1 -0.056 0.09 -10000 0 -10000 0 0
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 -0.048 0.1 -10000 0 -0.32 25 25
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.81 74 74
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.04 0.11 -10000 0 -0.33 25 25
PDPK1 -0.009 0.043 0.51 1 -0.57 2 3
HGF/MET/SHIP -0.14 0.2 -10000 0 -0.59 74 74
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.009 0.08 -9999 0 -0.71 6 6
alphaV beta3 Integrin -0.018 0.1 -9999 0 -0.57 16 16
PTK2 0.015 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 59 59
SRC 0.013 0.015 -9999 0 -0.31 1 1
CDKN1B -0.063 0.18 -9999 0 -0.61 45 45
VEGFA 0.008 0.064 -9999 0 -0.81 3 3
ILK -0.063 0.18 -9999 0 -0.61 45 45
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.024 0.18 -9999 0 -0.56 45 45
PTK2B 0.018 0.11 -9999 0 -0.49 22 22
alphaV/beta3 Integrin/JAM-A -0.059 0.16 -9999 0 -0.47 60 60
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.02 0.1 -9999 0 -0.57 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.17 0.26 -9999 0 -0.53 159 159
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.003 0.11 -9999 0 -0.54 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.1 -9999 0 -0.57 16 16
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.23 0.25 -9999 0 -0.61 119 119
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
alphaV/beta3 Integrin/Osteopontin -0.069 0.16 -9999 0 -0.56 39 39
RPS6KB1 -0.2 0.24 -9999 0 -0.56 119 119
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.094 0.15 -9999 0 -0.74 16 16
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.094 0.15 -9999 0 -0.74 16 16
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.034 0.15 -9999 0 -0.61 28 28
cell adhesion -0.029 0.099 -9999 0 -0.53 16 16
ANGPTL3 0.005 0.026 -9999 0 -0.31 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.071 -9999 0 -0.62 6 6
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.064 -9999 0 -0.81 3 3
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
IGF1 -0.18 0.35 -9999 0 -0.79 119 119
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.1 -9999 0 -0.57 16 16
apoptosis 0.01 0.052 -9999 0 -0.81 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.018 0.1 -9999 0 -0.57 16 16
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.039 0.14 -9999 0 -0.6 24 24
CSF1 0 0.1 -9999 0 -0.81 8 8
PIK3C2A -0.064 0.18 -9999 0 -0.61 46 46
PI4 Kinase/Pyk2 -0.054 0.14 -9999 0 -0.77 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.024 0.11 -9999 0 -0.53 22 22
FAK1/Vinculin 0.023 0.12 -9999 0 -0.48 8 8
alphaV beta3/Integrin/ppsTEM5 -0.018 0.1 -9999 0 -0.57 16 16
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.067 0.24 -9999 0 -0.75 52 52
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.037 0.11 -9999 0 -0.57 16 16
alphaV/beta3 Integrin/TGFBR2 -0.022 0.12 -9999 0 -0.59 18 18
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.01 0.075 -9999 0 -0.54 9 9
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.017 0.095 -9999 0 -0.53 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.14 -9999 0 -0.31 359 359
alphaV/beta3 Integrin/Pyk2 -0.022 0.11 -9999 0 -0.5 22 22
SDC1 0.01 0.032 -9999 0 -0.31 5 5
VAV3 0.026 0.097 -9999 0 -0.52 14 14
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
IRS1 -0.085 0.27 -9999 0 -0.81 59 59
FAK1/Paxillin 0.023 0.12 -9999 0 -0.48 8 8
cell migration 0.033 0.12 -9999 0 -0.42 8 8
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
PI3K -0.055 0.15 -9999 0 -0.84 4 4
SPP1 -0.078 0.2 -9999 0 -0.42 104 104
KDR 0.007 0.074 -9999 0 -0.81 4 4
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.052 -9999 0 -0.81 2 2
COL4A3 -0.012 0.14 -9999 0 -0.81 15 15
angiogenesis -0.083 0.18 -9999 0 -0.65 25 25
Rac1/GTP -0.013 0.082 -9999 0 -0.47 14 14
EDIL3 -0.024 0.14 -9999 0 -0.43 42 42
cell proliferation -0.021 0.11 -9999 0 -0.59 18 18
Effects of Botulinum toxin

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
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 -0.013 0.065 -9999 0 -0.2 39 39
RAB3GAP2/RIMS1/UNC13B -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.01 0.021 -9999 0 -0.31 2 2
mol:ACh -0.007 0.04 -9999 0 -0.15 29 29
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.013 0.065 -9999 0 -0.2 39 39
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.015 0.093 -9999 0 -0.32 39 39
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.1 0.16 -9999 0 -0.24 219 219
SNAP25 -0.031 0.095 -9999 0 -0.38 29 29
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.16 0.22 -9999 0 -0.38 219 219
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.044 0.15 -9999 0 -0.54 39 39
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.051 -9999 0 -0.59 1 1
AP1 -0.25 0.36 -9999 0 -0.68 176 176
mol:PIP3 -0.041 0.12 -9999 0 -0.64 8 8
AKT1 -0.002 0.11 -9999 0 -0.58 5 5
PTK2B 0 0.085 -9999 0 -0.27 40 40
RHOA 0.031 0.046 -9999 0 -0.26 1 1
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.003 0.074 -9999 0 -0.32 1 1
MAGI3 0.012 0.037 -9999 0 -0.81 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.014 0.13 -9999 0 -0.44 39 39
HRAS/GDP -0.001 0.013 -9999 0 -0.21 2 2
positive regulation of microtubule depolymerization 0.009 0.087 -9999 0 -0.42 5 5
NF kappa B1 p50/RelA -0.044 0.12 -9999 0 -0.54 13 13
endothelial cell migration -0.027 0.2 -9999 0 -0.64 41 41
ADCY4 -0.014 0.19 -9999 0 -0.61 40 40
ADCY5 -0.044 0.21 -9999 0 -0.64 43 43
ADCY6 -0.014 0.19 -9999 0 -0.61 40 40
ADCY7 -0.014 0.19 -9999 0 -0.61 40 40
ADCY1 -0.017 0.19 -9999 0 -0.62 40 40
ADCY2 -0.036 0.21 -9999 0 -0.66 40 40
ADCY3 -0.014 0.19 -9999 0 -0.61 40 40
ADCY8 -0.055 0.19 -9999 0 -0.63 43 43
ADCY9 -0.014 0.19 -9999 0 -0.61 40 40
GSK3B 0.009 0.081 -9999 0 -0.3 13 13
arachidonic acid secretion -0.007 0.18 -9999 0 -0.57 40 40
GNG2 0.012 0.037 -9999 0 -0.81 1 1
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.039 0.2 -9999 0 -0.59 54 54
HRAS 0.012 0.021 -9999 0 -0.31 2 2
NFKBIA 0.01 0.079 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.035 0.11 -9999 0 -0.97 6 6
JUN -0.17 0.35 -9999 0 -0.81 112 112
LPA/LPA2/NHERF2 -0.001 0.007 -9999 0 -10000 0 0
TIAM1 -0.045 0.13 -9999 0 -1.2 6 6
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.003 0.075 -9999 0 -0.32 1 1
PLCB3 0.03 0.009 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.81 127 127
positive regulation of mitosis -0.007 0.18 -9999 0 -0.57 40 40
LPA/LPA1-2-3 -0.049 0.15 -9999 0 -0.54 39 39
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.004 0.11 -9999 0 -0.35 39 39
GNAZ -0.02 0.17 -9999 0 -0.56 41 41
EGFR/PI3K-beta/Gab1 -0.043 0.13 -9999 0 -0.67 8 8
positive regulation of dendritic cell cytokine production -0.049 0.15 -9999 0 -0.53 39 39
LPA/LPA2/MAGI-3 -0.002 0.027 -9999 0 -0.59 1 1
ARHGEF1 0 0.15 -9999 0 -0.49 39 39
GNAI2 -0.02 0.17 -9999 0 -0.56 41 41
GNAI3 -0.02 0.17 -9999 0 -0.56 41 41
GNAI1 -0.021 0.17 -9999 0 -0.56 42 42
LPA/LPA3 -0.01 0.044 -9999 0 -0.27 2 2
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.055 0.18 -9999 0 -0.65 41 41
HB-EGF/EGFR -0.054 0.17 -9999 0 -0.53 50 50
HBEGF -0.061 0.19 -9999 0 -0.61 45 45
mol:DAG 0.003 0.075 -9999 0 -0.32 1 1
cAMP biosynthetic process -0.026 0.2 -9999 0 -0.56 53 53
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN 0.01 0.079 -9999 0 -10000 0 0
GNAQ 0.019 0.029 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.065 -9999 0 -0.31 21 21
LPAR1 -0.05 0.23 -9999 0 -0.83 39 39
IL8 -0.13 0.2 -9999 0 -0.47 61 61
PTK2 -0.009 0.15 -9999 0 -0.5 39 39
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.014 0.13 -9999 0 -0.44 39 39
EGFR 0.005 0.083 -9999 0 -0.81 5 5
PLCG1 -0.016 0.085 -9999 0 -0.29 14 14
PLD2 -0.009 0.15 -9999 0 -0.5 39 39
G12/G13 -0.043 0.15 -9999 0 -0.53 39 39
PI3K-beta -0.031 0.11 -9999 0 -0.7 5 5
cell migration -0.016 0.059 -9999 0 -0.25 11 11
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.004 0.11 -9999 0 -0.36 39 39
HRAS/GTP -0.009 0.19 -9999 0 -0.59 40 40
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.083 0.24 -9999 0 -0.58 80 80
PRKCE 0.005 0.083 -9999 0 -0.82 5 5
PRKCD 0.011 0.072 -9999 0 -10000 0 0
Gi(beta/gamma) -0.008 0.18 -9999 0 -0.58 40 40
mol:LPA 0.003 0.019 -9999 0 -0.22 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.029 0.13 -9999 0 -0.53 14 14
MAPKKK cascade -0.007 0.18 -9999 0 -0.57 40 40
contractile ring contraction involved in cytokinesis 0.031 0.045 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.088 0.2 -9999 0 -0.43 118 118
GNA15 0.009 0.054 -9999 0 -0.35 2 2
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.009 0.089 -9999 0 -0.43 5 5
GNA11 0.01 0.069 -9999 0 -0.42 10 10
Rac1/GTP -0.036 0.11 -9999 0 -1 6 6
MMP2 -0.028 0.2 -9999 0 -0.64 41 41
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.011 0.22 -10000 0 -0.97 21 21
NCK1/PAK1/Dok-R -0.028 0.09 -10000 0 -0.43 21 21
NCK1/Dok-R -0.068 0.25 -10000 0 -1.2 21 21
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
mol:beta2-estradiol -0.003 0.047 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 0.25 13 -0.33 12 25
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.06 0.23 -10000 0 -1.1 21 21
FN1 -0.22 0.14 -10000 0 -0.31 359 359
PLD2 0 0.28 -10000 0 -1.3 21 21
PTPN11 0.012 0.037 -10000 0 -0.81 1 1
GRB14 -0.01 0.14 -10000 0 -0.81 14 14
ELK1 0.016 0.24 -10000 0 -1.1 21 21
GRB7 -0.04 0.12 -10000 0 -0.31 82 82
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.1 0.25 -10000 0 -1.2 21 21
CDKN1A -0.009 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 -0.068 0.25 -10000 0 -1.2 21 21
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.027 0.17 -10000 0 -0.69 21 21
PLG -0.009 0.28 -10000 0 -1.3 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.01 0.21 -10000 0 -0.93 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 -0.78 19 19
BMX -0.014 0.29 -10000 0 -1.3 21 21
ANGPT1 -0.037 0.29 -10000 0 -1.5 18 18
tube development -0.016 0.18 -10000 0 -0.73 21 21
ANGPT4 -0.061 0.23 -10000 0 -0.74 49 49
response to hypoxia 0 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.018 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) -0.019 0.21 -10000 0 -0.84 21 21
mol:L-citrulline 0.027 0.17 -10000 0 -0.69 21 21
AGTR1 -0.32 0.4 -10000 0 -0.81 200 200
MAPK14 -0.011 0.27 -10000 0 -1.2 21 21
Tie2/SHP2 -0.027 0.16 -10000 0 -1.4 6 6
TEK 0.014 0.19 -10000 0 -1.5 6 6
RPS6KB1 0.011 0.21 -10000 0 -0.93 21 21
Angiotensin II/AT1 -0.25 0.32 -10000 0 -0.63 200 200
Tie2/Ang1/GRB2 -0.005 0.29 -10000 0 -1.3 21 21
MAPK3 0.011 0.25 -10000 0 -1.1 21 21
MAPK1 0.011 0.25 -10000 0 -1.1 21 21
Tie2/Ang1/GRB7 -0.028 0.29 -10000 0 -1.3 21 21
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
MAPK8 -0.008 0.29 -10000 0 -1.3 21 21
PI3K -0.004 0.26 -10000 0 -1.1 21 21
FES -0.011 0.27 -10000 0 -1.2 21 21
Crk/Dok-R -0.068 0.25 -10000 0 -1.2 21 21
Tie2/Ang1/ABIN2 -0.005 0.29 -10000 0 -1.3 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.016 0.2 -10000 0 -0.85 21 21
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.011 0.21 -10000 0 -0.93 21 21
Tie2/Ang2 -0.039 0.24 -10000 0 -1 21 21
Tie2/Ang1 -0.012 0.31 -10000 0 -1.4 21 21
FOXO1 0.022 0.2 -10000 0 -0.86 21 21
ELF1 0.015 0.078 -10000 0 -0.84 4 4
ELF2 -0.003 0.27 -10000 0 -1.2 21 21
mol:Choline 0.003 0.26 -10000 0 -1.2 21 21
cell migration -0.023 0.055 -10000 0 -0.24 21 21
FYN -0.022 0.21 -10000 0 -0.85 21 21
DOK2 -0.001 0.078 -10000 0 -0.36 19 19
negative regulation of cell cycle -0.006 0.16 -10000 0 -0.58 21 21
ETS1 0.016 0.045 -10000 0 -10000 0 0
PXN 0.024 0.18 -10000 0 -0.75 21 21
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.024 0.19 -10000 0 -0.8 21 21
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.085 0.27 -10000 0 -0.76 65 65
MAPKKK cascade 0.003 0.26 -10000 0 -1.2 21 21
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.008 0.29 -10000 0 -1.3 21 21
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.03 0.15 -10000 0 -0.61 21 21
mol:Phosphatidic acid 0.003 0.26 -10000 0 -1.2 21 21
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.027 0.17 -10000 0 -0.69 21 21
Rac1/GTP -0.049 0.18 -10000 0 -0.86 21 21
MMP2 -0.007 0.29 -10000 0 -1.3 21 21
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 0.037 -10000 0 -0.81 1 1
Jak2/Leptin Receptor -0.025 0.097 0.21 4 -0.43 13 17
PTP1B/AKT1 -0.004 0.064 -10000 0 -0.34 2 2
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.013 0.07 -10000 0 -0.34 4 4
EGFR 0.003 0.084 -10000 0 -0.82 5 5
EGF/EGFR -0.085 0.18 -10000 0 -0.5 77 77
CSF1 0 0.1 -10000 0 -0.81 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 -0.097 0.12 -10000 0 -0.44 20 20
Insulin Receptor/Insulin -0.016 0.054 -10000 0 -0.48 3 3
HCK -0.01 0.084 -10000 0 -0.31 36 36
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.004 0.067 -10000 0 -0.34 3 3
EGF -0.11 0.29 -10000 0 -0.78 78 78
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.019 0.1 -10000 0 -0.37 7 7
TXN 0.011 0.015 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.055 0.17 -10000 0 -0.49 60 60
cell migration 0.013 0.07 0.34 4 -10000 0 4
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.044 0.19 -10000 0 -0.59 47 47
ITGA2B -0.076 0.26 -10000 0 -0.82 53 53
CSF1R 0.008 0.049 -10000 0 -0.39 6 6
Prolactin Receptor/Prolactin -0.039 0.15 -10000 0 -0.63 26 26
FGR 0.011 0.029 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.005 0.066 -10000 0 -0.36 2 2
Crk/p130 Cas 0 0.061 -10000 0 -0.38 1 1
DOK1 0.005 0.064 -10000 0 -0.36 1 1
JAK2 -0.013 0.092 -10000 0 -0.4 14 14
Jak2/Leptin Receptor/Leptin -0.051 0.13 -10000 0 -0.57 24 24
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.013 0.071 -10000 0 -0.34 4 4
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.18 0.19 -10000 0 -0.34 279 279
SRC 0.011 0.03 -10000 0 -10000 0 0
ITGB3 -0.013 0.14 -10000 0 -0.82 15 15
CAT1/PTP1B -0.09 0.15 -10000 0 -0.38 62 62
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.013 0.015 -10000 0 -0.31 1 1
PI3K -0.018 0.061 -10000 0 -0.5 6 6
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.049 0.13 -10000 0 -0.6 24 24
negative regulation of transcription -0.013 0.091 -10000 0 -0.39 14 14
FCGR2A -0.007 0.084 -10000 0 -0.33 30 30
FER 0.007 0.065 -10000 0 -0.82 3 3
alphaIIb/beta3 Integrin -0.083 0.23 -10000 0 -0.68 62 62
BLK -0.24 0.37 -10000 0 -0.74 168 168
Insulin Receptor/Insulin/Shc -0.003 0.042 -10000 0 -0.54 3 3
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.004 0.085 -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 -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.44 69 69
PRL 0.001 0.015 -10000 0 -10000 0 0
SOCS3 -0.056 0.32 -10000 0 -1.5 23 23
SPRY2 0.009 0.055 -10000 0 -0.65 3 3
Insulin Receptor/Insulin/IRS1 -0.069 0.18 -10000 0 -0.55 62 62
CSF1/CSF1R -0.009 0.094 -10000 0 -0.51 10 10
Ras protein signal transduction 0.021 0.023 -10000 0 -10000 0 0
IRS1 -0.085 0.27 -10000 0 -0.81 59 59
INS -0.004 0.063 -10000 0 -0.82 3 3
LEP -0.008 0.067 -10000 0 -0.31 23 23
STAT5B -0.009 0.071 -10000 0 -0.3 6 6
STAT5A -0.009 0.071 -10000 0 -0.3 6 6
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.069 -10000 0 -0.36 4 4
CSN2 -0.007 0.054 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
LAT 0.001 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 -0.42 27 27
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 214 214
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.043 -9999 0 -0.92 1 1
VEGFR1 homodimer/NRP1 -0.002 0.042 -9999 0 -0.93 1 1
mol:DAG -0.012 0.16 -9999 0 -0.48 51 51
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.067 -9999 0 -0.76 3 3
CaM/Ca2+ -0.004 0.15 -9999 0 -0.45 51 51
HIF1A 0.021 0.018 -9999 0 -0.38 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.009 0.16 -9999 0 -0.9 3 3
PLCG1 -0.012 0.16 -9999 0 -0.49 51 51
NOS3 0.017 0.15 -9999 0 -0.42 51 51
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.018 0.15 -9999 0 -0.41 51 51
FLT1 0.031 0.048 -9999 0 -1 1 1
PGF -0.07 0.25 -9999 0 -0.81 50 50
VEGFR1 homodimer/NRP2/VEGFR121 -0.015 0.073 -9999 0 -0.76 3 3
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
eNOS/Hsp90 0.024 0.14 -9999 0 -0.8 1 1
endothelial cell proliferation -0.024 0.19 -9999 0 -0.51 52 52
mol:Ca2+ -0.012 0.16 -9999 0 -0.48 51 51
MAPK3 -0.012 0.17 -9999 0 -0.43 68 68
MAPK1 -0.012 0.17 -9999 0 -0.43 68 68
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.07 0.25 -9999 0 -0.81 50 50
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.008 0.13 -9999 0 -0.81 13 13
VEGFA homodimer 0.008 0.064 -9999 0 -0.81 3 3
VEGFR1 homodimer/VEGFA homodimer 0.029 0.073 -9999 0 -0.82 3 3
platelet activating factor biosynthetic process -0.004 0.17 -9999 0 -0.95 2 2
PI3K -0.05 0.15 -9999 0 -0.46 53 53
PRKCA -0.021 0.18 -9999 0 -0.46 68 68
PRKCB -0.02 0.16 -9999 0 -0.46 55 55
VEGFR1 homodimer/PLGF homodimer -0.025 0.18 -9999 0 -0.54 51 51
VEGFA 0.008 0.064 -9999 0 -0.81 3 3
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.012 0.16 -9999 0 -0.48 51 51
RASA1 0.041 0.04 -9999 0 -0.85 1 1
NRP2 -0.013 0.088 -9999 0 -0.31 40 40
VEGFR1 homodimer 0.03 0.047 -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 0.013 0.16 -9999 0 -0.79 4 4
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
mol:PI-3-4-5-P3 -0.049 0.15 -9999 0 -0.46 53 53
mol:L-citrulline 0.018 0.15 -9999 0 -0.41 51 51
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.004 0.063 -9999 0 -0.72 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.005 0.066 -9999 0 -0.76 3 3
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.047 0.14 -9999 0 -0.44 53 53
PDPK1 0 0.16 -9999 0 -0.44 53 53
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.005 0.083 -9999 0 -0.89 3 3
mol:NADP 0.018 0.15 -9999 0 -0.41 51 51
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.004 0.061 -9999 0 -0.7 3 3
VEGFR1 homodimer/NRP2 0.018 0.065 -9999 0 -0.92 1 1
Signaling events mediated by PRL

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
CCNE1 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.002 0.098 -9999 0 -0.81 7 7
CDKN1A -0.013 0.088 -9999 0 -0.25 2 2
PRL-3/alpha Tubulin -0.018 0.057 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.11 -9999 0 -0.64 10 10
AGT -0.02 0.14 -9999 0 -0.45 36 36
CCNA2 -0.063 0.2 -9999 0 -0.45 107 107
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.11 0.26 -9999 0 -0.62 107 107
CDK2/Cyclin E1 0.004 0.077 -9999 0 -10000 0 0
MAPK3 0.004 0.064 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.004 0.064 -9999 0 -10000 0 0
PTP4A1 -0.072 0.21 -9999 0 -0.48 107 107
PTP4A3 -0.015 0.092 -9999 0 -0.31 44 44
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.004 0.064 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1 -0.017 0.093 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.068 0.2 -9999 0 -0.45 107 107
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.013 0.042 -9999 0 -10000 0 0
RHOC -0.017 0.093 -9999 0 -10000 0 0
RHOA -0.017 0.093 -9999 0 -10000 0 0
cell motility -0.016 0.099 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.062 0.2 -9999 0 -0.44 107 107
PRL-3/alpha1 Integrin -0.026 0.095 -9999 0 -0.67 7 7
ROCK1 -0.016 0.1 -9999 0 -10000 0 0
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.072 0.21 -9999 0 -0.47 107 107
ATF5 0 0.064 -9999 0 -0.31 20 20
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 0.037 -9999 0 -0.81 1 1
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.66 16 16
PTK2 -0.043 0.16 -9999 0 -0.6 32 32
positive regulation of JNK cascade -0.023 0.085 -9999 0 -0.34 32 32
CDC42/GDP 0.027 0.13 -9999 0 -0.47 32 32
Rac1/GDP 0.029 0.13 -9999 0 -0.46 32 32
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 -0.028 0.1 -9999 0 -0.42 32 32
nectin-3/I-afadin -0.04 0.15 -9999 0 -0.62 32 32
RAPGEF1 0.02 0.15 -9999 0 -0.53 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.009 0.17 -9999 0 -0.62 32 32
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
TLN1 0.017 0.077 -9999 0 -0.93 1 1
Rap1/GTP -0.024 0.09 -9999 0 -0.36 32 32
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 -0.04 0.15 -9999 0 -0.62 32 32
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.02 0.16 -9999 0 -0.59 32 32
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
PI3K -0.033 0.13 -9999 0 -0.5 33 33
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.032 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.024 0.089 -9999 0 -0.36 32 32
PVRL1 0.005 0.052 -9999 0 -0.31 13 13
PVRL3 -0.04 0.2 -9999 0 -0.81 32 32
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 -0.32 402 402
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.56 42 42
SRC -0.047 0.18 -9999 0 -0.71 32 32
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.032 -9999 0 -10000 0 0
FARP2 0.015 0.16 -9999 0 -0.57 32 32
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) -0.035 0.13 -9999 0 -0.54 32 32
nectin-1/I-afadin -0.005 0.032 -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 -0.039 0.14 -9999 0 -0.54 32 32
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 -0.023 0.085 -9999 0 -0.34 32 32
alphaV/beta3 Integrin/Talin 0.016 0.13 -9999 0 -0.59 16 16
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 0.009 0.082 -9999 0 -0.28 32 32
VAV2 0.013 0.16 -9999 0 -0.59 32 32
RAP1/GDP -0.028 0.11 -9999 0 -0.43 32 32
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.035 0.13 -9999 0 -0.54 32 32
nectin-3(dimer)/I-afadin/I-afadin -0.04 0.15 -9999 0 -0.62 32 32
Rac1/GTP -0.029 0.11 -9999 0 -0.44 32 32
PTPRM -0.02 0.084 -9999 0 -0.31 32 32
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
IL27-mediated signaling events

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.041 -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 0.067 0.15 0.52 13 -10000 0 13
IL27/IL27R/JAK1 -0.12 0.19 -10000 0 -0.57 52 52
TBX21 -0.093 0.22 -10000 0 -0.66 31 31
IL12B -0.006 0.098 -10000 0 -0.54 13 13
IL12A -0.058 0.2 -10000 0 -0.64 51 51
IL6ST -0.11 0.29 -10000 0 -0.82 72 72
IL27RA/JAK1 0.012 0.026 -10000 0 -10000 0 0
IL27 0.001 0.039 -10000 0 -0.32 7 7
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.054 0.15 -10000 0 -0.51 1 1
T-helper 2 cell differentiation 0.067 0.15 0.52 13 -10000 0 13
T cell proliferation during immune response 0.067 0.15 0.52 13 -10000 0 13
MAPKKK cascade -0.067 0.15 -10000 0 -0.52 13 13
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.05 -10000 0 -0.31 12 12
IL12RB1 -0.026 0.13 -10000 0 -0.37 48 48
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.091 0.21 -10000 0 -0.64 28 28
IL27/IL27R/JAK2/TYK2 -0.068 0.15 -10000 0 -0.53 13 13
positive regulation of T cell mediated cytotoxicity -0.067 0.15 -10000 0 -0.52 13 13
STAT1 (dimer) -0.12 0.24 0.52 16 -0.74 19 35
JAK2 0.011 0.054 -10000 0 -0.82 2 2
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.056 0.14 -10000 0 -0.52 11 11
T cell proliferation -0.15 0.23 -10000 0 -0.53 99 99
IL12/IL12R/TYK2/JAK2 -0.058 0.17 -10000 0 -0.72 15 15
IL17A -0.054 0.15 -10000 0 -0.51 1 1
mast cell activation 0.067 0.15 0.52 13 -10000 0 13
IFNG -0.021 0.048 -10000 0 -0.13 68 68
T cell differentiation -0.005 0.008 -10000 0 -0.022 63 63
STAT3 (dimer) -0.056 0.14 -10000 0 -0.52 11 11
STAT5A (dimer) -0.056 0.14 -10000 0 -0.52 11 11
STAT4 (dimer) -0.076 0.16 -10000 0 -0.52 25 25
STAT4 -0.025 0.14 -10000 0 -0.44 41 41
T cell activation -0.012 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.063 0.19 -10000 0 -0.62 14 14
GATA3 -0.042 0.33 -10000 0 -1.5 25 25
IL18 -0.025 0.11 -10000 0 -0.64 11 11
positive regulation of mast cell cytokine production -0.055 0.14 -10000 0 -0.51 11 11
IL27/EBI3 -0.099 0.12 -10000 0 -0.43 7 7
IL27RA 0.003 0.027 -10000 0 -10000 0 0
IL6 -0.15 0.32 -10000 0 -0.69 116 116
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.014 -10000 0 -10000 0 0
IL1B -0.034 0.16 -10000 0 -0.64 33 33
EBI3 -0.15 0.16 -10000 0 -0.34 30 30
TNF -0.067 0.21 -10000 0 -0.59 64 64
Regulation of nuclear SMAD2/3 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
EP300 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.005 0.074 -10000 0 -0.81 4 4
SMAD3/SMAD4/ER alpha -0.051 0.14 -10000 0 -0.59 23 23
AKT1 0.008 0.011 -10000 0 -10000 0 0
GSC -0.2 0.54 -10000 0 -1.5 68 68
NKX2-5 0.002 0.028 -10000 0 -0.3 4 4
muscle cell differentiation 0.025 0.05 0.44 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.08 -10000 0 -10000 0 0
SMAD4 -0.011 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 0.076 -10000 0 -0.54 5 5
SMAD3/SMAD4/VDR 0.009 0.044 -10000 0 -10000 0 0
MYC 0.003 0.13 -10000 0 -0.82 12 12
CDKN2B -0.075 0.14 -10000 0 -10000 0 0
AP1 -0.25 0.5 -10000 0 -0.95 151 151
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.055 -10000 0 -0.7 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.061 -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 -0.011 0.075 -10000 0 -0.31 23 23
SMAD3/SMAD4/GR -0.017 0.046 -10000 0 -10000 0 0
GATA3 -0.031 0.18 -10000 0 -0.77 27 27
SKI/SIN3/HDAC complex/NCoR1 0.041 0.029 -10000 0 -10000 0 0
MEF2C/TIF2 -0.039 0.17 -10000 0 -0.56 27 27
endothelial cell migration -0.007 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 0.064 -10000 0 -0.81 3 3
RUNX2 -0.072 0.15 -10000 0 -0.32 128 128
RUNX3 -0.012 0.13 -10000 0 -0.81 12 12
RUNX1 -0.13 0.16 -10000 0 -0.31 215 215
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -0.31 1 1
CDKN1A 0.025 0.069 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.035 0.094 -10000 0 -0.44 3 3
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.004 -10000 0 -10000 0 0
SERPINE1 0.007 0.1 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.043 0.13 -10000 0 -0.59 22 22
SMAD3/SMAD4/ATF3 -0.16 0.26 -10000 0 -0.62 118 118
SAP30 0.01 0.037 -10000 0 -0.82 1 1
Cbp/p300/PIAS3 0.032 0.044 -10000 0 -10000 0 0
JUN -0.24 0.5 -10000 0 -0.96 145 145
SMAD3/SMAD4/IRF7 -0.017 0.046 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.004 0.1 -10000 0 -1.2 1 1
mesenchymal cell differentiation 0.064 0.094 0.5 3 -10000 0 3
DLX1 -0.03 0.18 -10000 0 -0.81 26 26
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.22 0.39 -10000 0 -0.88 127 127
SMAD3/SMAD4/Max -0.017 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.04 -10000 0 -0.54 2 2
ZBTB17 0.021 0.011 -10000 0 -10000 0 0
LAMC1 0.025 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.018 0.045 -10000 0 -10000 0 0
IRF7 0.014 0.015 -10000 0 -0.31 1 1
ESR1 -0.047 0.19 -10000 0 -0.52 55 55
HNF4A -0.003 0.044 -10000 0 -0.31 10 10
MEF2C 0.005 0.097 -10000 0 -1 1 1
SMAD2-3/SMAD4 -0.032 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.024 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.016 0.025 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.017 0.01 -10000 0 -10000 0 0
SKIL 0.012 0.037 -10000 0 -0.81 1 1
HDAC1 0.012 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.004 -10000 0 -10000 0 0
SNIP1 0.008 0.053 -10000 0 -0.81 2 2
GCN5L2 0.005 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.01 0.048 -10000 0 -10000 0 0
MSG1/HSC70 -0.17 0.1 -10000 0 -0.68 9 9
SMAD2 -0.002 0.039 -10000 0 -10000 0 0
SMAD3 -0.005 0.048 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.074 -10000 0 -0.41 7 7
SMAD2/SMAD2/SMAD4 0.014 0.028 -10000 0 -10000 0 0
NCOR1 0.012 0.004 -10000 0 -10000 0 0
NCOA2 -0.067 0.24 -10000 0 -0.81 48 48
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.014 0.076 -10000 0 -10000 0 0
IFNB1 0.014 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.098 -10000 0 -1 1 1
CITED1 -0.26 0.14 -10000 0 -0.32 407 407
SMAD2-3/SMAD4/ARC105 -0.022 0.046 -10000 0 -10000 0 0
RBL1 -0.007 0.13 -10000 0 -0.81 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.08 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.083 0.11 -10000 0 -0.56 12 12
SMAD7 -0.1 0.28 -10000 0 -0.59 104 104
MYC/MIZ-1 0.014 0.11 -10000 0 -0.62 12 12
SMAD3/SMAD4 0.061 0.1 0.31 43 -0.35 1 44
IL10 -0.028 0.19 -10000 0 -0.71 24 24
PIASy/HDAC complex 0.007 0.01 -10000 0 -10000 0 0
PIAS3 0.016 0.005 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.016 0.14 -10000 0 -0.5 25 25
CDK4 0.018 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.01 -10000 0 -10000 0 0
ATF3 -0.19 0.35 -10000 0 -0.79 125 125
SMAD3/SMAD4/SP1 -0.016 0.055 -10000 0 -10000 0 0
FOXG1 -0.001 0.06 -10000 0 -0.35 12 12
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 0.005 0.096 -10000 0 -0.99 1 1
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.048 0.14 -10000 0 -0.59 26 26
MYOD1 -0.001 0.028 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.053 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.052 0.14 -10000 0 -0.54 29 29
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.037 -10000 0 -0.81 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.076 0.11 -10000 0 -0.53 15 15
SMAD3/SMAD4/SP1-3 0.008 0.059 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.015 0.021 -10000 0 -10000 0 0
SIN3B 0.012 0.004 -10000 0 -10000 0 0
SIN3A 0.012 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.013 0.095 -10000 0 -0.52 2 2
ITGB5 0.036 0.06 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.26 0.29 -10000 0 -0.59 209 209
AR -0.34 0.41 -10000 0 -0.81 209 209
negative regulation of cell growth -0.04 0.13 -10000 0 -0.55 4 4
SMAD3/SMAD4/MYOD -0.023 0.05 -10000 0 -10000 0 0
E2F5 0.012 0.037 -10000 0 -0.81 1 1
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.01 0.067 -10000 0 -0.36 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.066 -10000 0 -10000 0 0
TFDP1 0.012 0.037 -10000 0 -0.81 1 1
SMAD3/SMAD4/AP1 -0.26 0.51 -10000 0 -0.99 145 145
SMAD3/SMAD4/RUNX2 -0.064 0.094 -10000 0 -0.5 3 3
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.023 0.17 -10000 0 -0.81 22 22
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.01 0.053 -9999 0 -0.81 2 2
Aurora C/Aurora B/INCENP -0.04 0.076 -9999 0 -0.38 8 8
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.011 0.02 -9999 0 -10000 0 0
AURKB -0.061 0.14 -9999 0 -0.31 113 113
AURKC 0 0.065 -9999 0 -0.31 21 21
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.015 -9999 0 -0.31 1 1
LAT2 -0.018 0.1 -9999 0 -0.33 10 10
AP1 -0.2 0.28 -9999 0 -0.57 162 162
mol:PIP3 -0.016 0.15 -9999 0 -0.5 15 15
IKBKB 0.004 0.092 -9999 0 -0.28 13 13
AKT1 -0.015 0.14 -9999 0 -0.58 6 6
IKBKG 0.004 0.092 -9999 0 -0.28 14 14
MS4A2 -0.065 0.14 -9999 0 -0.31 114 114
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.065 -9999 0 -0.82 3 3
MAP3K1 0.01 0.1 -9999 0 -0.44 8 8
mol:Ca2+ -0.008 0.12 -9999 0 -0.37 15 15
LYN 0.012 0.005 -9999 0 -10000 0 0
CBLB -0.009 0.087 -9999 0 -0.35 4 4
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.081 0.18 -9999 0 -0.5 80 80
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
PLD2 -0.046 0.14 -9999 0 -0.44 39 39
PTPN13 -0.001 0.099 -9999 0 -0.55 6 6
PTPN11 0.011 0.039 -9999 0 -0.85 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.019 0.1 -9999 0 -0.37 4 4
SYK 0.012 0.005 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.45 27 27
LAT -0.014 0.098 -9999 0 -0.42 8 8
PAK2 0.002 0.11 -9999 0 -0.5 8 8
NFATC2 -0.15 0.28 -9999 0 -0.75 86 86
HRAS -0.007 0.12 -9999 0 -0.5 11 11
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.096 0.16 -9999 0 -0.46 66 66
Antigen/IgE/Fc epsilon R1 -0.087 0.15 -9999 0 -0.42 66 66
mol:GDP -0.016 0.13 -9999 0 -0.5 15 15
JUN -0.17 0.35 -9999 0 -0.81 112 112
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.81 127 127
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.043 0.077 -9999 0 -0.27 24 24
CHUK 0.004 0.092 -9999 0 -0.28 14 14
KLRG1 -0.021 0.1 -9999 0 -0.39 16 16
VAV1 -0.022 0.11 -9999 0 -0.48 9 9
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.009 0.087 -9999 0 -0.35 4 4
negative regulation of mast cell degranulation -0.019 0.1 -9999 0 -0.37 15 15
BTK -0.021 0.12 -9999 0 -0.58 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.048 0.19 -9999 0 -0.52 46 46
GAB2/PI3K/SHP2 -0.063 0.12 -9999 0 -0.56 10 10
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.017 0.092 -9999 0 -0.28 35 35
RAF1 0.018 0.02 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.2 -9999 0 -0.58 56 56
FCER1G -0.008 0.081 -9999 0 -0.32 32 32
FCER1A -0.073 0.22 -9999 0 -0.54 75 75
Antigen/IgE/Fc epsilon R1/Fyn -0.078 0.14 -9999 0 -0.47 39 39
MAPK3 0.029 0.017 -9999 0 -10000 0 0
MAPK1 0.029 0.017 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 0.005 0.11 -9999 0 -0.66 11 11
DUSP1 -0.12 0.3 -9999 0 -0.81 80 80
NF-kappa-B/RelA -0.019 0.044 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.004 0.082 -9999 0 -0.37 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.042 0.1 -9999 0 -0.55 10 10
FER -0.012 0.096 -9999 0 -0.43 7 7
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.073 0.17 -9999 0 -0.52 62 62
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.012 0.13 -9999 0 -0.55 11 11
cytokine secretion -0.014 0.032 -9999 0 -10000 0 0
SPHK1 -0.013 0.091 -9999 0 -0.36 6 6
PTK2 -0.004 0.084 -9999 0 -0.39 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.065 0.13 -9999 0 -0.43 40 40
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.01 0.14 -9999 0 -0.49 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 -0.046 0.092 -9999 0 -0.42 14 14
MAP2K4 0.021 0.007 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.2 -9999 0 -0.62 52 52
mol:Choline -0.045 0.14 -9999 0 -0.44 39 39
SHC/Grb2/SOS1 -0.03 0.064 -9999 0 -0.39 1 1
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.004 0.08 -9999 0 -10000 0 0
HCLS1 -0.012 0.092 -9999 0 -0.38 5 5
PRKCB -0.009 0.12 -9999 0 -0.37 24 24
FCGR2B -0.03 0.18 -9999 0 -0.73 29 29
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.019 0.1 -9999 0 -0.38 15 15
LCP2 0.007 0.043 -9999 0 -0.31 9 9
PLA2G4A -0.039 0.15 -9999 0 -0.51 35 35
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.045 0.14 -9999 0 -0.44 39 39
IKK complex 0.019 0.075 -9999 0 -0.22 5 5
WIPF1 0.013 0 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.014 0.094 -10000 0 -0.34 7 7
epithelial cell differentiation -0.047 0.1 -10000 0 -0.47 12 12
ITCH 0.024 0.02 -10000 0 -10000 0 0
WWP1 -0.001 0.08 -10000 0 -0.43 1 1
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.005 0.083 -10000 0 -0.81 5 5
PRL 0.001 0.015 -10000 0 -0.31 1 1
neuron projection morphogenesis 0.004 0.14 -10000 0 -0.5 11 11
PTPRZ1 -0.017 0.14 -10000 0 -0.56 24 24
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.13 -10000 0 -0.44 46 46
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.043 0.17 -10000 0 -0.52 47 47
ADAM17 0.021 0.057 -10000 0 -0.81 2 2
ErbB4/ErbB4 -0.012 0.1 -10000 0 -0.51 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.045 0.17 -10000 0 -0.55 37 37
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.066 0.14 -10000 0 -0.49 46 46
GRIN2B -0.028 0.15 -10000 0 -0.46 46 46
ErbB4/ErbB2/betacellulin -0.04 0.12 -10000 0 -0.58 18 18
STAT1 0.006 0.05 -10000 0 -0.31 12 12
HBEGF -0.004 0.072 -10000 0 -0.31 26 26
PRLR -0.044 0.19 -10000 0 -0.59 47 47
E4ICDs/ETO2 -0.007 0.091 -10000 0 -0.48 3 3
axon guidance -0.001 0.086 -10000 0 -0.37 6 6
NEDD4 0.021 0.056 -10000 0 -0.8 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.043 0.15 -10000 0 -0.63 26 26
CBFA2T3 0.01 0.042 -10000 0 -0.48 3 3
ErbB4/ErbB2/HBEGF -0.03 0.061 -10000 0 -0.49 3 3
MAPK3 -0.005 0.14 -10000 0 -0.52 11 11
STAT1 (dimer) -0.009 0.091 -10000 0 -0.34 6 6
MAPK1 -0.005 0.14 -10000 0 -0.52 11 11
JAK2 0.01 0.053 -10000 0 -0.81 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.033 0.16 -10000 0 -0.49 47 47
NRG1 -0.032 0.2 -10000 0 -0.64 46 46
NRG3 -0.047 0.22 -10000 0 -0.81 36 36
NRG2 -0.079 0.26 -10000 0 -0.79 57 57
NRG4 0.008 0.035 -10000 0 -0.31 6 6
heart development -0.001 0.086 -10000 0 -0.37 6 6
neural crest cell migration -0.032 0.16 -10000 0 -0.48 47 47
ERBB2 0.028 0.042 -10000 0 -0.61 2 2
WWOX/E4ICDs -0.006 0.093 -10000 0 -0.94 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.038 0.086 -10000 0 -0.61 5 5
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 -0.079 0.087 -10000 0 -0.54 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.023 0.14 -10000 0 -0.63 18 18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.061 0.12 -10000 0 -0.48 28 28
MDM2 -0.001 0.088 -10000 0 -0.45 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.14 -10000 0 -0.5 46 46
STAT5A 0.007 0.081 -10000 0 -0.4 3 3
ErbB4/EGFR/neuregulin 1 beta -0.071 0.16 -10000 0 -0.51 50 50
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.033 0.064 -10000 0 -0.42 1 1
STAT5A (dimer) -0.05 0.11 -10000 0 -0.51 12 12
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.08 -10000 0 -0.4 3 3
LRIG1 0 0.1 -10000 0 -0.81 8 8
EREG -0.14 0.16 -10000 0 -0.31 230 230
BTC -0.015 0.15 -10000 0 -0.81 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.087 -10000 0 -0.37 6 6
ERBB4 -0.012 0.1 -10000 0 -0.52 1 1
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.011 0.02 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.026 0.057 -10000 0 -0.45 3 3
glial cell differentiation 0.033 0.063 0.42 1 -10000 0 1
WWOX 0.012 0.037 -10000 0 -0.81 1 1
cell proliferation -0.025 0.17 -10000 0 -0.45 56 56
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.085 -9999 0 -0.47 16 16
RGS9BP -0.037 0.2 -9999 0 -0.81 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.066 0.24 -9999 0 -0.8 48 48
mol:Na + -0.021 0.056 -9999 0 -10000 0 0
mol:ADP -0.044 0.19 -9999 0 -0.63 47 47
GNAT2 0.009 0.021 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.088 0.2 -9999 0 -0.55 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.062 -9999 0 -10000 0 0
Cone PDE6 -0.076 0.18 -9999 0 -0.48 78 78
Cone Metarhodopsin II -0.049 0.15 -9999 0 -0.51 47 47
Na + (4 Units) -0.025 0.057 -9999 0 -10000 0 0
GNAT2/GDP -0.076 0.18 -9999 0 -0.48 78 78
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.015 -9999 0 -10000 0 0
Cone Transducin -0.018 0.089 -9999 0 -0.5 16 16
SLC24A2 -0.009 0.064 -9999 0 -0.31 21 21
GNB3/GNGT2 -0.022 0.11 -9999 0 -0.62 16 16
GNB3 -0.012 0.14 -9999 0 -0.78 16 16
GNAT2/GTP -0.001 0.013 -9999 0 -10000 0 0
CNGA3 -0.027 0.11 -9999 0 -0.31 61 61
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 0.056 -9999 0 -10000 0 0
mol:Pi -0.087 0.2 -9999 0 -0.55 78 78
Cone CNG Channel -0.016 0.042 -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 21 21
RGS9 -0.072 0.25 -9999 0 -0.79 53 53
PDE6C 0.003 0.015 -9999 0 -0.31 1 1
GNGT2 0.009 0.047 -9999 0 -0.41 5 5
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

Figure 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
Sortilin/TRAF6 -0.003 0.04 -9999 0 -0.62 2 2
Necdin/E2F1 -0.067 0.11 -9999 0 -0.75 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.035 0.1 -9999 0 -0.48 20 20
NGF (dimer)/p75(NTR)/BEX1 -0.28 0.28 -9999 0 -0.56 234 234
NT-4/5 (dimer)/p75(NTR) -0.074 0.18 -9999 0 -0.66 37 37
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.003 0.12 -9999 0 -0.48 23 23
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.014 0.14 -9999 0 -0.61 22 22
MGDIs/NGR/p75(NTR)/LINGO1 -0.048 0.12 -9999 0 -0.56 18 18
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.057 0.14 -9999 0 -0.56 30 30
LINGO1 -0.003 0.071 -9999 0 -0.31 25 25
Sortilin/TRAF6/NRIF -0.002 0.025 -9999 0 -10000 0 0
proBDNF (dimer) -0.014 0.14 -9999 0 -0.61 22 22
NTRK1 -0.002 0.062 -9999 0 -0.31 19 19
RTN4R 0.013 0 -9999 0 -10000 0 0
neuron apoptosis -0.01 0.13 -9999 0 -0.48 26 26
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.02 0.13 -9999 0 -0.56 20 20
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.039 0.11 -9999 0 -0.51 20 20
MAGEH1 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.044 0.12 -9999 0 -0.51 25 25
Mammalian IAPs/DIABLO -0.028 0.11 -9999 0 -0.49 25 25
proNGF (dimer) 0.006 0.069 -9999 0 -0.56 6 6
MAGED1 0.013 0 -9999 0 -10000 0 0
APP 0.013 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -9999 0 -0.66 26 26
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.036 0.1 -9999 0 -0.48 20 20
NGF 0.006 0.069 -9999 0 -0.56 6 6
cell cycle arrest 0.043 0.16 -9999 0 -0.46 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.085 -9999 0 -0.35 22 22
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.064 0.16 -9999 0 -0.58 38 38
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.045 0.12 -9999 0 -0.56 21 21
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide -0.009 0.12 -9999 0 -0.51 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.07 -9999 0 -0.43 2 2
p75(NTR)/beta APP -0.049 0.13 -9999 0 -0.62 18 18
BEX1 -0.35 0.41 -9999 0 -0.81 219 219
mol:GDP -0.03 0.13 -9999 0 -0.57 20 20
NGF (dimer) -0.093 0.12 -9999 0 -0.5 30 30
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.042 0.11 -9999 0 -0.51 18 18
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.038 0.1 -9999 0 -0.49 20 20
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.045 0.12 -9999 0 -0.56 21 21
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.061 0.092 -9999 0 -10000 0 0
NT3 (dimer) -0.048 0.2 -9999 0 -0.6 49 49
TP53 -0.005 0.13 -9999 0 -0.44 32 32
PRDM4 -0.009 0.12 -9999 0 -0.51 20 20
BDNF (dimer) -0.13 0.16 -9999 0 -0.53 41 41
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.035 0.1 -9999 0 -0.47 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.11 -9999 0 -0.52 22 22
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 0.023 0.12 -9999 0 -0.6 4 4
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.009 0.12 -9999 0 -0.51 20 20
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.044 0.12 -9999 0 -0.56 20 20
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.028 -9999 0 -0.62 1 1
NT3 (dimer)/p75(NTR) -0.092 0.2 -9999 0 -0.66 45 45
MAPK8 0.017 0.13 -9999 0 -0.66 4 4
MAPK9 0.024 0.12 -9999 0 -0.6 3 3
APAF1 0.012 0.037 -9999 0 -0.81 1 1
NTF3 -0.048 0.2 -9999 0 -0.6 49 49
NTF4 -0.022 0.16 -9999 0 -0.66 26 26
NDN 0.005 0.083 -9999 0 -0.81 5 5
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.032 0.094 -9999 0 -0.44 21 21
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.053 -9999 0 -0.65 3 3
RhoA-B-C/GTP -0.045 0.12 -9999 0 -0.56 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.048 0.12 -9999 0 -0.48 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.052 0.13 -9999 0 -0.51 32 32
PRKACB 0.012 0.037 -9999 0 -0.81 1 1
proBDNF (dimer)/p75 ECD -0.023 0.11 -9999 0 -0.62 15 15
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.036 0.19 -9999 0 -0.65 37 37
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.066 0.17 -9999 0 -0.5 15 15
BAD 0.028 0.12 -9999 0 -0.59 4 4
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.06 0.18 -9999 0 -0.81 18 18
CYCS 0 0.11 -9999 0 -0.48 20 20
ADAM17 0.01 0.053 -9999 0 -0.81 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.041 0.11 -9999 0 -0.52 22 22
BCL2L11 0.028 0.12 -9999 0 -0.59 4 4
BDNF (dimer)/p75(NTR) -0.069 0.16 -9999 0 -0.62 32 32
PI3K -0.042 0.12 -9999 0 -0.52 23 23
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.039 0.11 -9999 0 -0.51 20 20
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.054 0.14 -9999 0 -0.65 20 20
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.039 0.11 -9999 0 -0.51 20 20
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG -0.004 0.039 -9999 0 -0.31 8 8
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.017 0.14 -9999 0 -0.48 32 32
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.013 0 -9999 0 -10000 0 0
CASP3 0.03 0.11 -9999 0 -0.53 4 4
E2F1 -0.085 0.15 -9999 0 -0.31 151 151
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.013 0.058 -9999 0 -0.53 3 3
NGF (dimer)/TRKA -0.013 0.063 -9999 0 -0.63 3 3
MMP7 -0.17 0.22 -9999 0 -0.37 243 243
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.037 0.11 -9999 0 -0.48 22 22
MMP3 -0.039 0.11 -9999 0 -0.31 69 69
APAF-1/Caspase 9 -0.04 0.11 -9999 0 -0.67 5 5
IL1-mediated signaling events

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
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 -0.027 0.064 -9999 0 -0.32 7 7
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.24 -9999 0 -0.66 75 75
IL1A -0.053 0.22 -9999 0 -0.78 41 41
IL1B -0.026 0.17 -9999 0 -0.63 36 36
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -0.42 2 2
IL1R2 -0.082 0.24 -9999 0 -0.58 79 79
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.067 -9999 0 -0.3 1 1
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.005 0.083 -9999 0 -0.81 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.066 0.027 -9999 0 -10000 0 0
JUN -0.073 0.22 -9999 0 -0.43 122 122
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.061 0.13 -9999 0 -0.47 37 37
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.072 0.14 -9999 0 -0.5 38 38
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.065 0.13 -9999 0 -0.47 38 38
IL1 beta fragment/IL1R1/IL1RAP -0.071 0.14 -9999 0 -0.52 35 35
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
MAPK8 0.019 0.11 -9999 0 -0.52 19 19
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.043 0.11 -9999 0 -0.62 11 11
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
PI3K -0.004 0.048 -9999 0 -0.62 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.001 0.082 -9999 0 -0.34 7 7
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.071 0.14 -9999 0 -0.52 35 35
IL1 beta/IL1R2 -0.098 0.22 -9999 0 -0.6 71 71
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.028 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA -0.053 0.11 -9999 0 -0.55 7 7
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.063 0.13 -9999 0 -0.48 39 39
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.014 0.1 -9999 0 -0.34 38 38
IL1 alpha/IL1R1/IL1RAP -0.082 0.15 -9999 0 -0.54 40 40
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 -0.46 2 2
IL1RAP -0.069 0.14 -9999 0 -0.31 126 126
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.049 0.11 -9999 0 -0.49 11 11
CASP1 0.007 0.062 -9999 0 -0.45 7 7
IL1RN/IL1R2 -0.11 0.21 -9999 0 -0.61 62 62
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.064 0.13 -9999 0 -0.49 35 35
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.08 -9999 0 -0.33 4 4
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
IL1RN -0.052 0.16 -9999 0 -0.38 83 83
TRAF6/TAK1/TAB1/TAB2 -0.002 0.029 -9999 0 -0.46 2 2
MAP2K6 0.021 0.075 -9999 0 -0.43 13 13
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 -0.04 0.12 -9999 0 -0.42 46 46
Syndecan-3/Neurocan -0.033 0.12 -9999 0 -0.46 34 34
POMC -0.16 0.34 -9999 0 -0.8 106 106
EGFR 0.005 0.083 -9999 0 -0.81 5 5
Syndecan-3/EGFR -0.005 0.046 -9999 0 -0.46 5 5
AGRP -0.006 0.064 -9999 0 -0.31 21 21
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 -0.048 0.21 -9999 0 -0.75 39 39
long-term memory 0 0.005 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.039 0.081 -9999 0 -0.46 11 11
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 0.045 -9999 0 -0.31 10 10
SRC 0.013 0.015 -9999 0 -0.31 1 1
PTN -0.064 0.24 -9999 0 -0.8 47 47
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis -0.066 0.15 -9999 0 -0.4 79 79
Syndecan-3/AgRP -0.006 0.025 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.008 0.029 -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 -0.039 0.08 -9999 0 -0.45 11 11
IL8 -0.082 0.18 -9999 0 -0.35 128 128
Syndecan-3/Fyn/Cortactin 0 0.005 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.14 0.26 -9999 0 -0.63 103 103
Gamma Secretase 0 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.063 0.08 -10000 0 -0.34 22 22
NT3 (dimer)/TRKC -0.087 0.19 -10000 0 -0.67 39 39
NT3 (dimer)/TRKB -0.083 0.18 -10000 0 -0.57 49 49
SHC/Grb2/SOS1/GAB1/PI3K 0.037 0.028 -10000 0 -0.33 3 3
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.014 0.14 -10000 0 -0.61 22 22
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.002 0.062 -10000 0 -0.31 19 19
NTRK2 0.005 0.083 -10000 0 -0.81 5 5
NTRK3 -0.054 0.16 -10000 0 -0.38 84 84
NT-4/5 (dimer)/TRKB -0.068 0.16 -10000 0 -0.57 41 41
neuron apoptosis 0.04 0.091 0.42 15 -10000 0 15
SHC 2-3/Grb2 -0.042 0.099 -10000 0 -0.46 15 15
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.029 0.092 -10000 0 -0.63 6 6
SHC3 -0.047 0.1 -10000 0 -0.55 12 12
STAT3 (dimer) 0.018 0.025 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.084 0.17 -10000 0 -0.58 44 44
RIN/GDP -0.008 0.061 -10000 0 -0.27 3 3
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.032 0.091 -10000 0 -0.44 19 19
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.026 0.045 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.012 0.037 -10000 0 -0.81 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.022 0.16 -10000 0 -0.66 26 26
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.019 0.079 -10000 0 -0.54 8 8
TRKA/NEDD4-2 -0.008 0.038 -10000 0 -10000 0 0
ELMO1 -0.31 0.4 -10000 0 -0.81 192 192
RhoG/GTP/ELMO1/DOCK1 -0.22 0.27 -10000 0 -0.55 193 193
NGF 0.006 0.069 -10000 0 -0.56 6 6
HRAS 0.012 0.021 -10000 0 -0.31 2 2
DOCK1 0.007 0.074 -10000 0 -0.81 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 -0.014 0.15 -10000 0 -0.78 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.2 0.23 -10000 0 -0.46 209 209
mol:GDP -0.014 0.088 -10000 0 -0.39 4 4
NGF (dimer) 0.006 0.069 -10000 0 -0.56 6 6
RhoG/GDP -0.25 0.31 -10000 0 -0.63 192 192
RIT1/GDP -0.003 0.062 -10000 0 -0.28 2 2
TIAM1 -0.17 0.16 -10000 0 -0.31 276 276
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.022 0.11 -10000 0 -0.57 17 17
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.024 -10000 0 -0.54 1 1
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.048 0.2 -10000 0 -0.6 49 49
RAP1/GDP -0.017 0.041 -10000 0 -0.25 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.014 0.14 -10000 0 -0.61 22 22
ubiquitin-dependent protein catabolic process -0.01 0.052 -10000 0 -0.54 3 3
Schwann cell development -0.042 0.032 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.016 -10000 0 -0.32 1 1
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.065 0.14 -10000 0 -0.58 14 14
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.036 -10000 0 -10000 0 0
STAT3 0.018 0.025 -10000 0 -10000 0 0
axon guidance -0.063 0.14 -10000 0 -0.43 54 54
MAPK3 0.014 0.078 -10000 0 -0.49 8 8
MAPK1 0.014 0.078 -10000 0 -0.49 8 8
CDC42/GDP -0.003 0.062 -10000 0 -0.28 2 2
NTF3 -0.048 0.2 -10000 0 -0.6 49 49
NTF4 -0.022 0.16 -10000 0 -0.66 26 26
NGF (dimer)/TRKA/FAIM -0.01 0.052 -10000 0 -0.54 3 3
PI3K -0.004 0.048 -10000 0 -0.62 3 3
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.11 -10000 0 -0.47 25 25
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.05 0.17 -10000 0 -0.58 38 38
RGS19 0.013 0.015 -10000 0 -0.31 1 1
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.046 -10000 0 -0.42 1 1
Rac1/GDP -0.003 0.062 -10000 0 -0.28 2 2
NGF (dimer)/TRKA/GRIT -0.011 0.054 -10000 0 -0.55 3 3
neuron projection morphogenesis 0 0.093 -10000 0 -0.43 10 10
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.052 -10000 0 -0.54 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.06 0.18 -10000 0 -0.81 18 18
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.076 -10000 0 -0.35 18 18
RAS family/GTP/PI3K 0.03 0.031 -10000 0 -0.36 3 3
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.021 -10000 0 -0.46 1 1
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.056 -10000 0 -0.61 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.038 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.02 0.098 -10000 0 -0.52 17 17
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.042 -10000 0 -0.46 3 3
MATK -0.003 0.096 -10000 0 -0.46 17 17
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.014 0.041 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.035 0.097 -10000 0 -0.44 23 23
Rac1/GTP -0.19 0.14 -10000 0 -0.35 196 196
FRS2 family/SHP2/CRK family -0.001 0.021 -10000 0 -0.46 1 1
TCGA08_rtk_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
PDGFRA -0.24 0.38 -10000 0 -0.81 151 151
HRAS 0.012 0.021 -10000 0 -0.31 2 2
EGFR 0.005 0.083 -10000 0 -0.81 5 5
AKT 0.019 0.025 0.2 1 -10000 0 1
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 -0.1 0.16 -10000 0 -0.31 179 179
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.014 0.14 -10000 0 -0.73 18 18
PIK3R3 0.012 0.037 -10000 0 -0.81 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.058 0.098 -10000 0 -0.26 42 42
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.024 0.19 1 -0.17 1 2
PI3K -0.039 0.095 0.22 1 -0.22 50 51
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.025 0.027 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.037 -10000 0 -0.81 1 1
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.062 0.16 -10000 0 -0.47 65 65
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.055 -10000 0 -0.21 34 34
GNB1/GNG2 -0.001 0.025 -10000 0 -0.55 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.067 0.17 -10000 0 -0.51 64 64
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 64 -10000 0 64
GNAL -0.094 0.28 -10000 0 -0.81 64 64
GNG2 0.012 0.037 -10000 0 -0.81 1 1
CRH -0.014 0.081 -10000 0 -0.31 34 34
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.069 -10000 0 -0.46 11 11
MAPK11 0.009 0 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.015 0.057 -9999 0 -0.55 5 5
ADCY5 -0.057 0.19 -9999 0 -0.55 66 66
ADCY6 0.015 0.057 -9999 0 -0.55 5 5
ADCY7 0.015 0.057 -9999 0 -0.55 5 5
ADCY1 0.008 0.09 -9999 0 -0.62 9 9
ADCY2 -0.039 0.17 -9999 0 -0.56 46 46
ADCY3 0.015 0.057 -9999 0 -0.55 5 5
ADCY8 -0.12 0.1 -9999 0 -0.7 5 5
PRKCE 0.006 0.065 -9999 0 -0.63 5 5
ADCY9 0.015 0.057 -9999 0 -0.55 5 5
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.055 0.1 -9999 0 -0.37 31 31
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) -0.019 0.12 -10000 0 -0.78 12 12
HDAC1 0.002 0.008 -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 0.002 0.098 -10000 0 -0.81 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.008 0.064 -10000 0 -0.81 3 3
AP1 -0.14 0.26 -10000 0 -0.52 139 139
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.007 0.13 -10000 0 -0.81 12 12
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.052 -10000 0 -0.34 1 1
NICD/RBPSUH -0.018 0.11 -10000 0 -0.73 12 12
WIF1 -0.033 0.1 -10000 0 -0.31 60 60
NOTCH1 -0.019 0.12 -10000 0 -0.76 12 12
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.01 0.083 -10000 0 -0.31 35 35
DKK1 -0.041 0.13 -10000 0 -0.32 80 80
beta catenin/beta TrCP1 0.036 0.037 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0 0.037 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.024 0.036 -10000 0 -0.34 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.2 0.36 -10000 0 -0.81 127 127
JUN -0.17 0.35 -10000 0 -0.81 112 112
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 -0.034 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 -0.011 0.24 -10000 0 -1.5 12 12
NKD1 -0.013 0.14 -10000 0 -0.7 18 18
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.024 0.12 -10000 0 -0.62 19 19
apoptosis -0.14 0.26 -10000 0 -0.52 139 139
Delta 1/NOTCHprecursor -0.019 0.12 -10000 0 -0.75 12 12
DLL1 0.011 0.04 -10000 0 -0.56 2 2
PPARD 0.024 0.016 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.002 0.06 -10000 0 -0.29 12 12
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 -0.038 0.08 -10000 0 -0.39 9 9
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.015 0.007 -10000 0 -10000 0 0
CCND1 0.018 0.044 -10000 0 -10000 0 0
WNT1 0.008 0.033 -10000 0 -0.31 5 5
Axin1/APC/beta catenin 0.042 0.052 -10000 0 -0.67 1 1
DKK2 -0.024 0.16 -10000 0 -0.65 28 28
NOTCH1 precursor/DVL1 -0.012 0.1 -10000 0 -0.64 12 12
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.024 0.12 -10000 0 -0.64 19 19
PPP2R5D 0.011 0.063 0.37 14 -10000 0 14
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.017 0.044 -10000 0 -10000 0 0
RBPJ 0.013 0.015 -10000 0 -0.31 1 1
CREBBP 0.017 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.014 0.12 -9999 0 -0.44 32 32
CCNA2 0.007 0.046 -9999 0 -0.31 10 10
PIK3CA 0.009 0.064 -9999 0 -0.81 3 3
JAK3 -0.068 0.14 -9999 0 -0.31 125 125
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 -0.57 19 19
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.022 0 -9999 0 -10000 0 0
IL2RA -0.044 0.25 -9999 0 -0.97 32 32
IL2RB -0.014 0.13 -9999 0 -0.5 27 27
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.048 0.19 -9999 0 -0.52 57 57
G1/S transition of mitotic cell cycle 0.039 0.054 -9999 0 -0.59 3 3
PTPN11 0.013 0.037 -9999 0 -0.81 1 1
CCND2 0.033 0 -9999 0 -10000 0 0
LCK -0.01 0.11 -9999 0 -0.42 27 27
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.008 0.064 -9999 0 -0.81 3 3
CCND3 0.027 0.13 -9999 0 -0.62 8 8
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.057 0.15 -9999 0 -0.44 61 61
TC10/GTP -0.004 0.037 -9999 0 -0.42 4 4
Insulin Receptor/Insulin/IRS1/Shp2 -0.064 0.17 -9999 0 -0.51 62 62
HRAS 0.012 0.021 -9999 0 -0.31 2 2
APS homodimer 0.013 0.015 -9999 0 -0.31 1 1
GRB14 -0.01 0.14 -9999 0 -0.81 14 14
FOXO3 -0.023 0.1 -9999 0 -0.69 10 10
AKT1 -0.015 0.16 -9999 0 -0.88 2 2
INSR 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.035 0.036 -9999 0 -0.42 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.007 0.074 -9999 0 -0.81 4 4
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.035 0.035 -9999 0 -0.41 3 3
CAV1 -0.047 0.18 -9999 0 -0.47 75 75
CBL/APS/CAP/Crk-II/C3G -0.004 0.041 -9999 0 -0.46 4 4
Insulin Receptor/Insulin/IRS1/NCK2 -0.063 0.17 -9999 0 -0.5 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.058 0.15 -9999 0 -0.45 64 64
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.001 0.11 -9999 0 -0.38 3 3
RPS6KB1 -0.004 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 0.003 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.057 0.13 -9999 0 -0.78 2 2
HRAS/GTP -0.052 0.13 -9999 0 -0.49 4 4
Insulin Receptor 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.059 0.16 -9999 0 -0.47 62 62
PRKCI -0.015 0.034 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.066 0.16 -9999 0 -0.42 73 73
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.004 -9999 0 -10000 0 0
PI3K -0.059 0.15 -9999 0 -0.45 64 64
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.013 -9999 0 -10000 0 0
AKT2 -0.015 0.16 -9999 0 -0.88 2 2
PRKCZ -0.015 0.034 -9999 0 -10000 0 0
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
SHC/SHIP -0.031 0.16 -9999 0 -0.45 62 62
F2RL2 -0.079 0.16 -9999 0 -0.32 137 137
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.003 0.036 -9999 0 -0.47 3 3
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.003 0.033 -9999 0 -0.42 3 3
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.004 0.044 -9999 0 -0.49 4 4
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.003 0.036 -9999 0 -0.46 3 3
INPP5D -0.042 0.17 -9999 0 -0.48 62 62
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.025 0.14 -9999 0 -1 10 10
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
IRS1 -0.085 0.27 -9999 0 -0.81 59 59
p62DOK/RasGAP 0 0.004 -9999 0 -10000 0 0
INS -0.001 0.063 -9999 0 -0.81 3 3
mol:PI-3-4-P2 -0.041 0.17 -9999 0 -0.47 62 62
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.005 0.15 -9999 0 -0.63 4 4
PTPRA 0.015 0.003 -9999 0 -10000 0 0
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0.053 -9999 0 -0.81 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.01 0.12 -9999 0 -0.33 62 62
Insulin Receptor/Insulin/IRS1 -0.064 0.17 -9999 0 -0.51 62 62
Insulin Receptor/Insulin/IRS3 -0.004 0.048 -9999 0 -0.62 3 3
Par3/Par6 -0.035 0.063 -9999 0 -0.46 3 3
FOXM1 transcription factor network

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
NFATC3 0.053 0.35 -9999 0 -0.89 15 15
PLK1 0.044 0.069 -9999 0 -10000 0 0
BIRC5 0.029 0.12 -9999 0 -1.5 1 1
HSPA1B 0.053 0.35 -9999 0 -0.89 15 15
MAP2K1 0.032 0.037 -9999 0 -10000 0 0
BRCA2 0.048 0.36 -9999 0 -0.97 17 17
FOXM1 0.043 0.39 -9999 0 -0.99 21 21
XRCC1 0.053 0.35 -9999 0 -0.9 14 14
FOXM1B/p19 -0.092 0.3 -9999 0 -0.89 26 26
Cyclin D1/CDK4 0.04 0.33 -9999 0 -0.85 14 14
CDC2 0.047 0.36 -9999 0 -0.88 21 21
TGFA 0.025 0.34 -9999 0 -0.84 16 16
SKP2 0.046 0.36 -9999 0 -0.95 18 18
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.053 0.35 -9999 0 -0.91 13 13
RB1 -0.052 0.11 -9999 0 -1.2 1 1
FOXM1C/SP1 0.039 0.36 -9999 0 -0.97 20 20
AURKB -0.005 0.12 -9999 0 -10000 0 0
CENPF 0.048 0.36 -9999 0 -0.92 15 15
CDK4 0.019 0.015 -9999 0 -10000 0 0
MYC 0.047 0.35 -9999 0 -0.92 21 21
CHEK2 0.032 0.037 -9999 0 -10000 0 0
ONECUT1 0.037 0.34 -9999 0 -0.89 15 15
CDKN2A -0.12 0.16 -9999 0 -10000 0 0
LAMA4 0.053 0.35 -9999 0 -0.9 14 14
FOXM1B/HNF6 0.031 0.37 -9999 0 -1 15 15
FOS -0.18 0.65 -9999 0 -1.2 128 128
SP1 0.014 0.005 -9999 0 -10000 0 0
CDC25B 0.053 0.35 -9999 0 -0.9 15 15
response to radiation 0.016 0.034 -9999 0 -10000 0 0
CENPB 0.053 0.35 -9999 0 -0.9 14 14
CENPA 0.039 0.37 -9999 0 -0.96 20 20
NEK2 0.044 0.36 -9999 0 -0.92 17 17
HIST1H2BA 0.045 0.35 -9999 0 -0.91 14 14
CCNA2 0.01 0.049 -9999 0 -0.32 10 10
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.042 0.37 -9999 0 -1 15 15
CCNB2 0.05 0.35 -9999 0 -0.93 15 15
CCNB1 0.049 0.36 -9999 0 -0.94 15 15
ETV5 0.053 0.35 -9999 0 -0.91 14 14
ESR1 0.006 0.43 -9999 0 -1.1 34 34
CCND1 0.043 0.34 -9999 0 -0.87 14 14
GSK3A 0.03 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.037 0.051 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.12 0.22 -9999 0 -0.88 21 21
GAS1 -0.12 0.6 -9999 0 -1.2 103 103
MMP2 0.044 0.38 -9999 0 -1.1 17 17
RB1/FOXM1C 0.051 0.34 -9999 0 -0.91 14 14
CREBBP 0.013 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.003 0.077 -10000 0 -0.36 8 8
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.012 0.037 -10000 0 -0.81 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.041 0.077 0.25 2 -10000 0 2
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.066 0.22 -10000 0 -0.62 69 69
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.024 -10000 0 -0.54 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.03 0.11 -10000 0 -0.31 64 64
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 0.082 0.26 2 -10000 0 2
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.027 0 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.33 312 312
LNPEP -0.013 0.15 -10000 0 -0.81 16 16
YWHAE 0.013 0 -10000 0 -10000 0 0
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 -0.43 66 66
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 -0.048 0.12 -9999 0 -0.74 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.011 0.043 -9999 0 -0.59 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -0.3 2 2
CaM/Ca2+ -0.056 0.14 -9999 0 -0.4 65 65
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.02 0.16 -9999 0 -0.4 66 66
AKT1 -0.003 0.15 -9999 0 -0.61 3 3
MAP2K1 -0.006 0.15 -9999 0 -0.5 6 6
MAP3K11 -0.017 0.16 -9999 0 -0.4 65 65
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.066 -9999 0 -0.63 1 1
Rap1/GTP -0.041 0.1 -9999 0 -0.6 1 1
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.063 0.15 -9999 0 -0.45 65 65
CEBPB 0.018 0.17 -9999 0 -0.8 6 6
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.059 0.15 -9999 0 -1.1 2 2
STAT1 -0.019 0.16 -9999 0 -0.4 66 66
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.28 -9999 0 -0.71 79 79
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
STAT1 (dimer)/PIAS1 -0.01 0.15 -9999 0 -0.46 6 6
CEBPB/PTGES2/Cbp/p300 -0.035 0.082 -9999 0 -0.44 6 6
mol:Ca2+ -0.06 0.15 -9999 0 -0.43 66 66
MAPK3 0.01 0.14 -9999 0 -0.52 6 6
STAT1 (dimer) -0.031 0.08 -9999 0 -0.42 2 2
MAPK1 0.01 0.14 -9999 0 -0.52 6 6
JAK2 0.006 0.056 -9999 0 -0.84 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.017 0.18 -9999 0 -0.66 23 23
SMAD7 0.04 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.05 0.12 -9999 0 -0.75 1 1
PI3K -0.056 0.14 -9999 0 -0.5 9 9
IFNG -0.1 0.28 -9999 0 -0.72 79 79
apoptosis 0.014 0.13 -9999 0 -0.45 23 23
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.004 0.068 -9999 0 -0.31 23 23
CAMK2B 0.005 0.083 -9999 0 -0.81 5 5
FRAP1 -0.001 0.14 -9999 0 -0.56 3 3
PRKCD -0.002 0.15 -9999 0 -0.73 2 2
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 0.028 0.12 -9999 0 -0.53 1 1
STAT1 (dimer)/PIASy -0.054 0.13 -9999 0 -0.46 6 6
SOCS1 0.001 0.074 -9999 0 -1.5 1 1
mol:GDP -0.048 0.12 -9999 0 -0.7 1 1
CASP1 0.038 0.063 -9999 0 -0.35 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.042 0.057 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.054 0.13 -9999 0 -0.48 9 9
RAP1/GDP -0.041 0.1 -9999 0 -0.6 1 1
CBL -0.017 0.16 -9999 0 -0.4 66 66
MAP3K1 -0.016 0.16 -9999 0 -0.4 66 66
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 66 66
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.12 -10000 0 -0.57 9 9
UGCG -0.03 0.18 -10000 0 -0.8 25 25
AKT1/mTOR/p70S6K/Hsp90/TERT 0.019 0.13 -10000 0 -0.4 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.024 0.18 -10000 0 -0.78 25 25
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.059 0.14 -10000 0 -0.45 37 37
FRAP1 0.002 0.2 -10000 0 -0.48 53 53
FOXO3 0.019 0.16 -10000 0 -0.59 19 19
AKT1 0.01 0.18 -10000 0 -0.56 28 28
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 0.009 0.031 -10000 0 -10000 0 0
SGMS1 0.009 0.031 -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 0.045 -10000 0 -0.56 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.003 0.16 -10000 0 -0.46 34 34
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.051 -10000 0 -0.63 3 3
RPS6KB1 0.016 0.042 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 4 4
JAK3 -0.066 0.14 -10000 0 -0.31 125 125
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
MYC 0.009 0.21 -10000 0 -0.91 18 18
MYB -0.018 0.2 -10000 0 -1.3 11 11
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 0.03 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 0.042 -10000 0 -0.5 3 3
T cell proliferation 0.017 0.15 -10000 0 -0.51 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 -0.052 17 17
PRKCZ 0.016 0.15 -10000 0 -0.53 22 22
NF kappa B1 p50/RelA -0.057 0.14 -10000 0 -0.45 37 37
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.13 -10000 0 -0.59 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.047 0.2 -10000 0 -0.6 49 49
IL2RB -0.013 0.13 -10000 0 -0.5 27 27
TERT -0.002 0.042 -10000 0 -0.31 9 9
E2F1 -0.005 0.078 -10000 0 -0.45 11 11
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 0.025 17 -10000 0 17
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
IL2RG -0.046 0.19 -10000 0 -0.52 57 57
actin cytoskeleton organization 0.017 0.15 -10000 0 -0.51 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 0.065 -10000 0 -0.82 3 3
Rac1/GTP 0.031 0.042 -10000 0 -0.48 3 3
LCK -0.008 0.11 -10000 0 -0.42 27 27
BCL2 -0.026 0.28 -10000 0 -0.81 49 49
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.016 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.011 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.018 0.07 -9999 0 -0.55 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.025 -9999 0 -0.31 3 3
GRK1 -0.066 0.24 -9999 0 -0.8 48 48
CNG Channel -0.029 0.083 -9999 0 -0.51 9 9
mol:Na + -0.023 0.081 -9999 0 -0.45 13 13
mol:ADP -0.066 0.24 -9999 0 -0.8 48 48
RGS9-1/Gbeta5/R9AP -0.088 0.2 -9999 0 -0.55 78 78
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.024 0.083 -9999 0 -0.46 13 13
CNGB1 -0.002 0.067 -9999 0 -0.31 22 22
RDH5 -0.2 0.16 -9999 0 -10000 0 0
SAG 0.002 0.015 -9999 0 -0.31 1 1
mol:Ca2+ 0.015 0.088 -9999 0 -0.6 2 2
Na + (4 Units) -0.021 0.074 -9999 0 -0.58 2 2
RGS9 -0.072 0.25 -9999 0 -0.79 53 53
GNB1/GNGT1 -0.003 0.024 -9999 0 -10000 0 0
GNAT1/GDP -0.077 0.18 -9999 0 -0.48 78 78
GUCY2D -0.01 0.11 -9999 0 -0.43 26 26
GNGT1 -0.004 0.037 -9999 0 -0.31 7 7
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.072 -9999 0 -0.47 5 5
mol:11-cis-retinal -0.2 0.15 -9999 0 -10000 0 0
mol:cGMP -0.016 0.07 -9999 0 -0.48 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.097 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0.001 0.09 -9999 0 -0.54 11 11
Metarhodopsin II -0.049 0.15 -9999 0 -0.51 47 47
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.074 -9999 0 -0.5 9 9
RGS9BP -0.037 0.2 -9999 0 -0.81 30 30
Metarhodopsin II/Transducin 0.011 0.015 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.043 -9999 0 -0.51 3 3
PDE6A/B -0.012 0.047 -9999 0 -10000 0 0
mol:Pi -0.087 0.2 -9999 0 -0.55 78 78
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.022 -9999 0 -10000 0 0
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.008 0.076 -9999 0 -0.31 29 29
PDE6G -0.017 0.11 -9999 0 -0.38 38 38
RHO 0.006 0.016 -9999 0 -0.31 1 1
PDE6 -0.089 0.18 -9999 0 -0.48 81 81
GUCA1A 0.004 0.032 -9999 0 -10000 0 0
GC2/GCAP Family -0.005 0.043 -9999 0 -0.51 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.066 -9999 0 -0.69 4 4
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 0.003 0.1 0.56 14 -10000 0 14
PI3K Class IB/PDE3B -0.003 0.1 -10000 0 -0.56 14 14
PDE3B -0.003 0.1 -10000 0 -0.56 14 14
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.51 35 35
ITGA4 0.002 0.077 -9999 0 -0.44 12 12
alpha4/beta7 Integrin -0.033 0.12 -9999 0 -0.62 18 18
alpha4/beta1 Integrin -0.007 0.055 -9999 0 -0.62 3 3
Ceramide signaling pathway

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
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.002 0.14 -10000 0 -0.7 11 11
BAG4 0.012 0.037 -10000 0 -0.81 1 1
PKC zeta/ceramide -0.018 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.65 37 37
BAX -0.006 0.02 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.008 -10000 0 -10000 0 0
BAD -0.018 0.041 -10000 0 -10000 0 0
SMPD1 -0.005 0.094 -10000 0 -0.26 57 57
RB1 -0.019 0.046 -10000 0 -0.49 1 1
FADD/Caspase 8 0.01 0.13 -10000 0 -0.66 11 11
MAP2K4 -0.009 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.05 -10000 0 -0.51 2 2
EGF -0.11 0.29 -10000 0 -0.78 78 78
mol:ceramide -0.029 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.029 -10000 0 -0.62 1 1
ASAH1 0.012 0.037 -10000 0 -0.81 1 1
negative regulation of cell cycle -0.019 0.045 -10000 0 -0.49 1 1
cell proliferation -0.097 0.16 -10000 0 -0.39 114 114
BID -0.015 0.091 -10000 0 -0.4 11 11
MAP3K1 -0.018 0.041 -10000 0 -10000 0 0
EIF2A -0.001 0.037 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.002 0.047 -10000 0 -0.47 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.047 -10000 0 -0.47 2 2
Cathepsin D/ceramide -0.018 0.041 -10000 0 -10000 0 0
FADD -0.002 0.14 -10000 0 -0.7 11 11
KSR1 -0.019 0.052 -10000 0 -0.54 2 2
MAPK8 -0.01 0.06 -10000 0 -0.32 11 11
PRKRA -0.018 0.041 -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 -0.79 119 119
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.043 -10000 0 -10000 0 0
CTSD 0.013 0.015 -10000 0 -0.31 1 1
regulation of nitric oxide biosynthetic process -0.001 0.028 -10000 0 -0.62 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.084 0.19 -10000 0 -0.42 114 114
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.029 -10000 0 -0.62 1 1
RelA/NF kappa B1 -0.001 0.028 -10000 0 -0.62 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 -0.011 0.15 -10000 0 -0.74 11 11
TNFR1A/BAG4/TNF-alpha -0.065 0.17 -10000 0 -0.54 58 58
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.003 0.048 -10000 0 -0.48 2 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.003 0.052 0.18 27 -10000 0 27
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.037 -10000 0 -0.81 1 1
TNFR1A/BAG4 -0.001 0.028 -10000 0 -0.62 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.064 0.17 -10000 0 -0.54 57 57
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.079 -10000 0 -0.33 11 11
MAP2K2 -0.003 0.048 -10000 0 -0.48 2 2
SMPD3 -0.011 0.12 -10000 0 -0.3 62 62
TNF -0.087 0.26 -10000 0 -0.76 64 64
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.024 0.11 0.28 72 -10000 0 72
NF kappa B1/RelA/I kappa B alpha -0.001 0.021 -10000 0 -0.46 1 1
AIFM1 0.003 0.052 0.18 27 -10000 0 27
BCL2 -0.047 0.22 -10000 0 -0.81 36 36
Signaling events mediated by HDAC Class III

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
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 0.029 0.62 1 -10000 0 1
CDKN1A -0.006 0.035 -10000 0 -10000 0 0
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
FOXO3 0 0.007 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.024 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.006 0.033 -10000 0 -0.31 5 5
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.019 -10000 0 -10000 0 0
PPARGC1A -0.35 0.41 -10000 0 -0.81 219 219
FHL2 -0.05 0.22 -10000 0 -0.81 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.03 -10000 0 -0.62 1 1
HIST2H4A 0.021 0.029 -10000 0 -0.62 1 1
SIRT1/FOXO3a 0 0.026 -10000 0 -0.55 1 1
SIRT1 0 0.039 -10000 0 -0.82 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.027 -10000 0 -0.54 1 1
SIRT1/Histone H1b -0.006 0.049 -10000 0 -0.33 10 10
apoptosis 0 0.028 0.54 1 -10000 0 1
SIRT1/PGC1A -0.24 0.28 -10000 0 -0.55 219 219
p53/SIRT1 0.004 0.042 -10000 0 -0.62 1 1
SIRT1/FOXO4 0.001 0.027 -10000 0 -0.52 1 1
FOXO1/FHL2/SIRT1 -0.038 0.14 -10000 0 -0.5 39 39
HIST1H1E 0.015 0.053 -10000 0 -0.36 9 9
SIRT1/p300 0.001 0.03 -10000 0 -0.62 1 1
muscle cell differentiation 0.001 0.03 0.55 1 -10000 0 1
TP53 0.002 0.012 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.028 -10000 0 -0.54 1 1
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.002 0.036 -10000 0 -0.62 1 1
ACSS2 0.021 0.029 -10000 0 -0.62 1 1
SIRT1/PCAF/MYOD -0.001 0.03 -10000 0 -0.55 1 1
Aurora B signaling

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
Condensin I complex -0.001 0.079 -9999 0 -10000 0 0
STMN1 -0.022 0.094 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.024 0.11 -9999 0 -0.43 2 2
Chromosomal passenger complex/Cul3 protein complex 0.007 0.069 -9999 0 -0.28 14 14
BIRC5 -0.011 0.091 -9999 0 -0.41 6 6
DES -0.38 0.3 -9999 0 -0.61 300 300
Aurora C/Aurora B/INCENP -0.016 0.087 -9999 0 -0.38 8 8
Aurora B/TACC1 -0.022 0.08 -9999 0 -0.7 1 1
Aurora B/PP2A -0.027 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.026 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.046 0.14 -9999 0 -0.39 56 56
Cul3 protein complex -0.018 0.086 -9999 0 -0.54 12 12
KIF2C 0 0.042 -9999 0 -0.18 2 2
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.035 0.12 -9999 0 -0.31 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.027 0.091 -9999 0 -10000 0 0
SEPT1 0.007 0.043 -9999 0 -0.31 9 9
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.007 0.044 -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 -0.008 0.055 -9999 0 -10000 0 0
AURKB -0.052 0.14 -9999 0 -0.31 113 113
AURKC 0 0.065 -9999 0 -0.31 21 21
CDCA8 0.01 0.03 -9999 0 -0.32 4 4
cytokinesis -0.064 0.081 -9999 0 -0.43 5 5
Aurora B/Septin1 -0.025 0.1 -9999 0 -0.44 7 7
AURKA 0.013 0.002 -9999 0 -10000 0 0
INCENP 0.009 0.054 -9999 0 -0.83 2 2
KLHL13 -0.017 0.14 -9999 0 -0.53 27 27
BUB1 -0.1 0.16 -9999 0 -0.82 1 1
hSgo1/Aurora B/Survivin -0.024 0.11 -9999 0 -0.44 16 16
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.029 0.071 -9999 0 -0.36 4 4
SGOL1 0.001 0.062 -9999 0 -0.31 19 19
CENPA -0.008 0.07 -9999 0 -0.21 27 27
NCAPG -0.019 0.097 -9999 0 -0.31 49 49
Aurora B/HC8 Proteasome -0.027 0.091 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.027 0.091 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.036 0.12 -9999 0 -0.31 75 75
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.09 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.034 0.079 -9999 0 -0.35 18 18
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.008 0.06 -9999 0 -0.55 1 1
KIF23 -0.003 0.072 -9999 0 -0.32 25 25
VIM -0.022 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 -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.012 0.081 -9999 0 -0.26 19 19
Chromosomal passenger complex/EVI5 0.011 0.12 -9999 0 -0.47 7 7
TACC1 0.012 0.037 -9999 0 -0.81 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
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.043 0.12 0.33 1 -0.36 61 62
FRAP1 0.008 0.027 -10000 0 -10000 0 0
AKT1 -0.009 0.11 0.24 1 -0.3 61 62
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.042 -10000 0 -0.55 3 3
mol:GTP -0.028 0.077 -10000 0 -0.5 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.008 0.022 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.066 -10000 0 -0.45 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.035 0.14 -10000 0 -0.42 59 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.009 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.06 0.2 1 -0.35 3 4
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 58 59
EIF4B 0.017 0.055 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.014 0.039 -10000 0 -0.31 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.025 0.14 -10000 0 -0.39 61 61
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.04 0.18 1 -0.25 3 4
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.023 0.065 -10000 0 -0.44 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 58 59
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.041 0.12 0.26 1 -0.33 61 62
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.034 -10000 0 -0.62 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.029 0.083 -10000 0 -0.56 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 58 -0.001 1 59
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 -0.046 0.15 -10000 0 -0.46 59 59
INS -0.005 0.063 -10000 0 -0.81 3 3
PTEN 0.011 0.037 -10000 0 -0.81 1 1
PDK2 -0.039 0.11 0.26 1 -0.32 61 62
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.064 -10000 0 -0.82 3 3
PPP2R5D 0.015 0.025 -10000 0 -10000 0 0
peptide biosynthetic process 0.015 0.04 -10000 0 -0.49 3 3
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 0.015 0.04 -10000 0 -0.5 3 3
eIF4E/4E-BP1 0.019 0.008 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0.037 -9999 0 -0.81 1 1
Caspase 8 (4 units) -0.022 0.063 -9999 0 -10000 0 0
NEF -0.013 0.056 -9999 0 -0.22 29 29
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.005 0.2 -9999 0 -0.8 26 26
CYCS -0.004 0.1 -9999 0 -0.39 7 7
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.039 0.19 -9999 0 -0.7 30 30
MAP2K7 0.023 0.081 -9999 0 -0.31 2 2
protein ubiquitination 0.039 0.086 -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 0.11 -9999 0 -0.42 7 7
NF-kappa-B/RelA/I kappa B alpha -0.022 0.08 -9999 0 -0.34 26 26
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.037 -9999 0 -0.81 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 0.08 -9999 0 -0.35 26 26
MAPK8 0.02 0.1 -9999 0 -0.41 11 11
APAF1 0.012 0.037 -9999 0 -0.81 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 0.008 0.098 -9999 0 -0.3 39 39
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 0.091 -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 -0.062 0.18 -9999 0 -0.52 54 54
TNF -0.087 0.26 -9999 0 -0.76 64 64
FASLG -0.074 0.29 -9999 0 -0.85 54 54
NFKB1 0.007 0.047 -9999 0 -0.81 1 1
TNFR1A/BAG4/TNF-alpha -0.065 0.17 -9999 0 -0.54 58 58
CASP6 -0.006 0.045 -9999 0 -10000 0 0
CASP7 0.028 0.16 -9999 0 -0.62 25 25
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.028 0.16 -9999 0 -0.62 25 25
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.028 -9999 0 -0.62 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.098 -9999 0 -0.37 2 2
APAF-1/Caspase 9 -0.047 0.12 -9999 0 -0.52 25 25
BCL2 -0.004 0.15 -9999 0 -0.4 44 44
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.035 0.14 -10000 0 -0.62 28 28
ATM 0.012 0.037 -10000 0 -0.81 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.012 0.037 -10000 0 -0.81 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.029 -10000 0 -0.44 2 2
protein ubiquitination -0.027 0.11 -10000 0 -0.45 29 29
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.042 -10000 0 -0.54 3 3
MRE11A 0.008 0.064 -10000 0 -0.81 3 3
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.035 0.14 -10000 0 -0.62 28 28
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA 0 0.065 -10000 0 -0.31 21 21
DNA repair 0.051 0.1 -10000 0 -0.46 2 2
BRCA1/BARD1/ubiquitin -0.035 0.14 -10000 0 -0.62 28 28
BARD1/DNA-PK -0.028 0.11 -10000 0 -0.49 28 28
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.035 0.14 0.62 28 -10000 0 28
BRCA1/BARD1/CTIP/M/R/N Complex 0.019 0.092 -10000 0 -0.33 32 32
BRCA1/BACH1/BARD1/TopBP1 -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/P53 -0.029 0.12 -10000 0 -0.49 29 29
BARD1/CSTF1/BRCA1 -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.034 0.19 -10000 0 -0.81 28 28
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/UbcH7 -0.031 0.12 -10000 0 -0.54 28 28
BRCA1/BARD1/RAD51/PCNA -0.029 0.12 -10000 0 -0.49 28 28
BARD1/DNA-PK/P53 -0.026 0.11 -10000 0 -0.46 28 28
BRCA1/BARD1/Ubiquitin -0.035 0.14 -10000 0 -0.62 28 28
BRCA1/BARD1/CTIP -0.029 0.12 -10000 0 -0.49 29 29
FA complex 0.038 0.024 -10000 0 -10000 0 0
BARD1/EWS -0.035 0.14 -10000 0 -0.62 28 28
RBBP8 0.023 0.029 -10000 0 -0.62 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 0.029 0.11 0.49 29 -10000 0 29
BRCA1/BARD1 -0.027 0.11 -10000 0 -0.46 29 29
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.036 0.15 -10000 0 -0.63 28 28
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.011 0.025 -10000 0 -0.31 3 3
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.035 0.14 -10000 0 -0.62 28 28
EWSR1 0.013 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 -0.003 0.12 -10000 0 -0.81 10 10
ANTXR2 0.008 0.064 -10000 0 -0.81 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.1 13 13
monocyte activation -0.046 0.17 -10000 0 -0.48 60 60
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 0.074 -10000 0 -0.49 11 11
CYAA 0.003 0.079 -10000 0 -0.48 13 13
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.019 0.12 -10000 0 -0.46 35 35
Channel -0.013 0.081 -10000 0 -0.5 13 13
NLRP1 -0.004 0.034 -10000 0 -0.49 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.1 13 -10000 0 13
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.022 0.083 -10000 0 -0.46 14 14
PA/Cellular Receptors -0.014 0.088 -10000 0 -0.55 13 13
apoptosis -0.003 0.016 -10000 0 -0.1 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.078 -10000 0 -0.47 13 13
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.087 0.26 -10000 0 -0.76 64 64
VCAM1 -0.046 0.17 -10000 0 -0.48 60 60
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.012 0.024 0.1 11 -10000 0 11
IL18 -0.01 0.085 -10000 0 -0.41 14 14
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.1 13 13
LEF -0.003 0.016 -10000 0 -0.1 13 13
CASP1 -0.003 0.02 -10000 0 -0.22 2 2
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.1 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.013 0.077 -10000 0 -0.48 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.033 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.07 0.009 -9999 0 -10000 0 0
EGFR 0.005 0.083 -9999 0 -0.81 5 5
EPHA2 0.011 0.025 -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 26 26
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 -0.037 0.073 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.072 0.19 -9999 0 -0.59 60 60
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.005 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.048 0.034 -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 -0.067 0.15 -9999 0 -0.42 77 77
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 -0.79 119 119
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.005 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.047 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.04 0.06 -9999 0 -0.42 8 8
Ephrin A1/EPHA2 -0.001 0.007 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.037 0.074 -9999 0 -10000 0 0
HGF/MET -0.099 0.16 -9999 0 -0.46 74 74
HGF -0.11 0.3 -9999 0 -0.81 74 74
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.085 0.021 -9999 0 -10000 0 0
KIAA1543 0.047 0.021 -9999 0 -0.41 1 1
KIFC3 0.041 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.04 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.041 0 -9999 0 -10000 0 0
PIP5K1C 0.041 0 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.064 0.019 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.097 0.18 -9999 0 -0.42 113 113
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.1 0.16 -9999 0 -0.31 179 179
PLEKHA7 0.04 0.022 -9999 0 -0.44 1 1
mol:GTP -0.001 0.01 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.066 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
Class I PI3K signaling events

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
ARF5/GTP -0.001 0.033 0.3 1 -0.46 2 3
DAPP1 -0.054 0.14 -10000 0 -0.44 16 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.059 0.18 -10000 0 -0.48 35 35
mol:DAG -0.006 0.097 -10000 0 -0.27 16 16
HRAS 0.013 0.02 -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 0.013 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 0.037 -10000 0 -0.81 1 1
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.011 0.029 -10000 0 -0.31 4 4
mol:Ca2+ 0.006 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.31 276 276
ZAP70 -0.026 0.16 -10000 0 -0.62 31 31
mol:IP3 0.004 0.072 -10000 0 -0.21 3 3
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 -0.002 0.035 -10000 0 -0.54 2 2
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.038 0.037 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
PLEKHA2 0.022 0.041 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.036 -10000 0 -0.79 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.014 0.3 1 -10000 0 1
RhoA/GTP 0 0.013 0.26 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.051 0.16 -10000 0 -0.59 14 14
BLK -0.24 0.37 -10000 0 -0.74 168 168
PDPK1 0.01 0.053 -10000 0 -0.81 2 2
CYTH1 0 0.013 0.26 1 -10000 0 1
HCK -0.01 0.084 -10000 0 -0.31 36 36
CYTH3 -0.002 0.033 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 -0.012 0.086 0.22 1 -0.59 10 11
SGK1 -0.013 0.096 0.24 1 -0.66 10 11
INPP5D -0.003 0.071 -10000 0 -0.31 25 25
mol:GDP 0.015 0.037 -10000 0 -0.49 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.019 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.017 0.36 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.013 0.26 1 -10000 0 1
VAV1 -0.015 0.1 -10000 0 -0.35 39 39
mol:PI-3-4-P2 0.013 0.049 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.032 0.009 -10000 0 -10000 0 0
PLEKHA1 0.022 0.041 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.035 -10000 0 -0.46 1 1
LAT 0.005 0.077 -10000 0 -0.65 6 6
Rac1/GTP -0.006 0.054 -10000 0 -0.47 2 2
ITK -0.056 0.14 -10000 0 -0.43 61 61
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.015 0.13 -10000 0 -0.39 17 17
LCK -0.01 0.11 -10000 0 -0.42 27 27
BTK -0.013 0.06 0.26 1 -0.43 8 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.024 0.095 -9999 0 -0.51 1 1
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.28 0.45 -9999 0 -0.92 151 151
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.069 -9999 0 -0.29 18 18
ER alpha/Oestrogen -0.041 0.14 -9999 0 -0.63 23 23
NFX1/SIN3/HDAC complex 0.047 0.026 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 78 78
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 0.072 -9999 0 -10000 0 0
SAP18 0.014 0 -9999 0 -10000 0 0
MRN complex -0.003 0.042 -9999 0 -0.54 3 3
WT1 -0.025 0.1 -9999 0 -0.31 54 54
WRN 0.012 0.037 -9999 0 -0.81 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 -0.03 0.056 -9999 0 -10000 0 0
Mad/Max 0.006 0.01 -9999 0 -10000 0 0
TERT -0.024 0.096 -9999 0 -10000 0 0
CCND1 -0.016 0.095 -9999 0 -0.56 1 1
MAX 0.014 0.002 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
RBBP4 0.009 0.064 -9999 0 -0.81 3 3
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
Telomerase/911 0.036 0.019 -9999 0 -10000 0 0
CDKN1B -0.039 0.19 -9999 0 -0.52 64 64
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 0.037 -9999 0 -0.81 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.001 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.81 112 112
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.006 -9999 0 -10000 0 0
FOS -0.2 0.36 -9999 0 -0.81 127 127
IFN-gamma/IRF1 -0.085 0.2 -9999 0 -0.6 65 65
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.013 0.015 -9999 0 -0.31 1 1
Telomerase 0.013 0.074 -9999 0 -0.48 6 6
IRF1 0.018 0.015 -9999 0 -0.3 1 1
ESR1 -0.046 0.19 -9999 0 -0.52 55 55
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.025 -9999 0 -0.55 1 1
ubiquitin-dependent protein catabolic process 0.052 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.052 0.027 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC2 0.014 0.003 -9999 0 -10000 0 0
ATM -0.001 0.025 -9999 0 -0.56 1 1
SMAD3 0.02 0.028 -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 0.064 -9999 0 -0.81 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 -0.032 0.067 -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 0.041 -9999 0 -0.31 8 8
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.025 -9999 0 -0.56 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.005 0.083 -9999 0 -0.82 5 5
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.1 0.23 -9999 0 -0.62 77 77
MYC -0.006 0.13 -9999 0 -0.81 12 12
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 0.041 -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 -0.015 0.084 -9999 0 -10000 0 0
SP1/HDAC2 0.023 0.005 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.03 0.056 -9999 0 -10000 0 0
Smad3/Myc 0.011 0.091 -9999 0 -0.55 12 12
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.099 0.28 -9999 0 -0.71 79 79
Telomerase/PinX1 -0.03 0.056 -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 -0.03 0.056 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.003 0.035 -9999 0 -0.45 3 3
TRF2/WRN -0.001 0.027 -9999 0 -0.59 1 1
Telomerase/hnRNP C1/C2 -0.03 0.056 -9999 0 -10000 0 0
E2F1 -0.085 0.15 -9999 0 -0.31 151 151
ZNFX1 0.014 0 -9999 0 -10000 0 0
PIF1 0.001 0.095 -9999 0 -0.61 10 10
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
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.046 0.059 -10000 0 -0.38 8 8
NFATC2 -0.02 0.097 -10000 0 -0.3 29 29
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 0.014 0.088 -10000 0 -0.32 22 22
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 -0.024 0.089 -10000 0 -0.53 9 9
BCL2/BAX -0.046 0.16 -10000 0 -0.62 36 36
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.01 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.018 0.084 -10000 0 -0.56 4 4
Calcineurin A alpha-beta B1/BCL2 -0.047 0.22 -10000 0 -0.81 36 36
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.082 0.55 4 -10000 0 4
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.33 312 312
MAP3K8 -0.002 0.098 -10000 0 -0.82 7 7
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.12 0.16 -10000 0 -0.49 24 24
CABIN1 0.014 0.089 -10000 0 -0.32 22 22
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.004 0.11 -10000 0 -0.53 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 -0.009 0.12 -10000 0 -0.82 11 11
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.007 0.05 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.014 0.05 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.049 -10000 0 -10000 0 0
PRKCB -0.022 0.12 -10000 0 -0.36 46 46
PRKCE 0.005 0.083 -10000 0 -0.81 5 5
JNK2/NFAT4 0.022 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.018 0.16 -10000 0 -0.81 19 19
PRKCG 0.005 0.025 -10000 0 -0.31 3 3
PRKCQ 0.003 0.091 -10000 0 -0.81 6 6
FKBP38/BCL2 -0.045 0.16 -10000 0 -0.62 36 36
EP300 0.01 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.031 0.089 -10000 0 -0.39 11 11
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.011 0.07 -10000 0 -0.56 7 7
NFATc/ERK1 0.052 0.056 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.023 0.088 -10000 0 -0.52 9 9
NR4A1 -0.19 0.36 -10000 0 -0.73 148 148
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 0.064 -10000 0 -0.39 5 5
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.01 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.041 0.061 -10000 0 -10000 0 0
CREBBP 0.01 0.007 -10000 0 -10000 0 0
BCL2 -0.047 0.22 -10000 0 -0.81 36 36
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.008 0.081 -9999 0 -0.71 6 6
PDGFRB 0.012 0.037 -9999 0 -0.82 1 1
SPHK1 -0.008 0.021 -9999 0 -10000 0 0
mol:S1P -0.009 0.025 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.015 0.14 -9999 0 -0.38 50 50
GNAO1 -0.017 0.15 -9999 0 -0.7 21 21
PDGFB-D/PDGFRB/PLCgamma1 0.025 0.13 -9999 0 -0.56 9 9
PLCG1 0.022 0.14 -9999 0 -0.6 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
GNAI2 0.014 0.004 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.073 -9999 0 -0.62 6 6
S1P1/S1P -0.016 0.066 -9999 0 -0.5 6 6
negative regulation of cAMP metabolic process 0.016 0.14 -9999 0 -0.37 50 50
MAPK3 0.009 0.19 -9999 0 -0.57 41 41
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.006 0.074 -9999 0 -0.82 4 4
PLCB2 0.03 0.072 -9999 0 -0.43 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.054 -9999 0 -0.41 6 6
receptor internalization -0.015 0.061 -9999 0 -0.46 6 6
PTGS2 -0.03 0.33 -9999 0 -1.1 41 41
Rac1/GTP -0.013 0.054 -9999 0 -0.41 6 6
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.064 -9999 0 -0.81 3 3
negative regulation of T cell proliferation 0.016 0.14 -9999 0 -0.37 50 50
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.005 -9999 0 -10000 0 0
MAPK1 0.009 0.19 -9999 0 -0.57 41 41
S1P1/S1P/PDGFB-D/PDGFRB 0.032 0.086 -9999 0 -0.49 7 7
ABCC1 0.014 0.002 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.017 0.093 -10000 0 -0.46 13 13
ACTA1 0.008 0.12 -10000 0 -0.57 13 13
NUMA1 0.017 0.093 -10000 0 -0.46 13 13
SPTAN1 0.013 0.12 -10000 0 -0.62 11 11
LIMK1 0.013 0.12 -10000 0 -0.62 11 11
BIRC3 -0.036 0.19 -10000 0 -0.65 37 37
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0.021 -10000 0 -0.31 2 2
CASP10 -0.003 0.12 -10000 0 -0.59 16 16
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.017 0.093 -10000 0 -0.46 13 13
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.013 0.12 -10000 0 -0.6 11 11
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.013 0.12 -10000 0 -0.62 11 11
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.055 0.22 -10000 0 -0.65 59 59
BID -0.01 0.069 -10000 0 -0.31 13 13
MAP3K1 0.013 0.043 -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 0.029 -10000 0 -0.62 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.01 0.12 -10000 0 -0.6 12 12
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.015 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 0.019 0.11 -10000 0 -0.59 11 11
APAF1 0.012 0.037 -10000 0 -0.81 1 1
CASP6 0.021 0.064 -10000 0 -0.42 4 4
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.02 0.11 -10000 0 -0.59 11 11
CASP7 0.01 0.08 0.34 25 -10000 0 25
KRT18 0.016 0.018 -10000 0 -10000 0 0
apoptosis 0.024 0.11 -10000 0 -0.55 13 13
DFFA 0.013 0.12 -10000 0 -0.62 11 11
DFFB 0.013 0.12 -10000 0 -0.62 11 11
PARP1 0.015 0.052 0.23 22 -0.17 2 24
actin filament polymerization -0.02 0.11 0.56 11 -10000 0 11
TNF -0.087 0.26 -10000 0 -0.76 64 64
CYCS 0.004 0.047 -10000 0 -0.22 13 13
SATB1 0.028 0.061 -10000 0 -0.42 3 3
SLK 0.01 0.13 -10000 0 -0.65 13 13
p15 BID/BAX -0.002 0.062 -10000 0 -0.34 5 5
CASP2 0.007 0.11 -10000 0 -0.46 11 11
JNK cascade -0.013 0.042 0.23 3 -10000 0 3
CASP3 0.005 0.12 -10000 0 -0.61 13 13
LMNB2 0.021 0.075 -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 -0.028 0.11 -10000 0 -0.49 25 25
negative regulation of DNA binding -0.054 0.22 -10000 0 -0.64 59 59
stress fiber formation 0.01 0.13 -10000 0 -0.63 13 13
GZMB -0.017 0.14 -10000 0 -0.68 16 16
CASP1 0.015 0.032 -10000 0 -0.45 2 2
LMNB1 0.02 0.075 -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 0.02 0.1 -10000 0 -0.5 11 11
LMNA 0.021 0.075 -10000 0 -0.32 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.002 0.12 -10000 0 -0.49 11 11
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.012 0.12 -10000 0 -0.62 11 11
APAF-1/Caspase 9 0.004 0.041 -10000 0 -0.39 1 1
nuclear fragmentation during apoptosis 0.017 0.092 -10000 0 -0.45 13 13
CFL2 0.02 0.11 -10000 0 -0.58 11 11
GAS2 0.007 0.13 -10000 0 -0.58 17 17
positive regulation of apoptosis 0.023 0.078 -10000 0 -0.31 4 4
PRF1 -0.004 0.11 -10000 0 -0.69 12 12
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.006 0.05 -9999 0 -0.31 12 12
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.017 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.69 21 21
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 0.032 -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 0.053 -9999 0 -0.81 1 1
S1PR4 0.009 0.038 -9999 0 -0.31 7 7
GNAI1 0.012 0.037 -9999 0 -0.81 1 1
S1P/S1P5/G12 -0.004 0.028 -9999 0 -0.48 1 1
S1P/S1P3/Gq -0.051 0.16 -9999 0 -0.41 25 25
S1P/S1P4/Gi 0.03 0.067 -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 -0.81 118 118
GNA15 -0.011 0.09 -9999 0 -0.32 36 36
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.81 10 10
ABCC1 0.013 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
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 0.061 -10000 0 -0.34 7 7
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.012 0.086 0.24 6 -0.41 15 21
RAR alpha/9cRA/Cyclin H -0.021 0.087 -10000 0 -0.41 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.03 0.068 -10000 0 -0.32 14 14
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.015 0.12 -10000 0 -0.7 11 11
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0.009 -10000 0 -0.21 1 1
RXRs/RARs/NRIP1/9cRA -0.016 0.15 -10000 0 -0.62 24 24
NCOA2 -0.067 0.24 -10000 0 -0.81 48 48
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -10000 0 -0.31 1 1
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.12 -10000 0 -0.81 11 11
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.033 0.13 -10000 0 -0.66 19 19
RARA 0.008 0.088 -10000 0 -0.33 28 28
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.14 -10000 0 -0.57 17 17
PRKCA -0.015 0.16 -10000 0 -0.81 19 19
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.027 0.15 -10000 0 -0.64 24 24
RXRG -0.11 0.1 -10000 0 -0.52 23 23
RXRA 0.014 0.088 -10000 0 -0.33 28 28
RXRB 0.008 0.091 -10000 0 -0.44 19 19
VDR/Vit D3/DNA 0 0.009 -10000 0 -0.21 1 1
RBP1 -0.003 0.11 -10000 0 -0.65 12 12
CRBP1/9-cic-RA -0.012 0.082 -10000 0 -0.49 12 12
RARB -0.008 0.14 -10000 0 -0.81 14 14
PRKCG 0.008 0.026 -10000 0 -0.31 3 3
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.022 0.16 -10000 0 -0.66 24 24
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.005 0.13 -10000 0 -0.54 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.087 -10000 0 -0.48 8 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.027 0.15 -10000 0 -0.64 24 24
positive regulation of DNA binding -0.02 0.082 -10000 0 -0.39 19 19
NRIP1 -0.023 0.14 -10000 0 -0.64 16 16
RXRs/RARs -0.034 0.15 -10000 0 -0.63 24 24
RXRs/RXRs/DNA/9cRA -0.044 0.13 -10000 0 -0.68 19 19
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 0.052 -10000 0 -0.52 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 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
PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.057 -9999 0 -0.27 17 17
GNAO1 -0.015 0.15 -9999 0 -0.69 21 21
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.028 -9999 0 -0.47 1 1
AKT3 0.049 0.049 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.037 -9999 0 -0.81 1 1
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.013 0.037 -9999 0 -0.81 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.01 0.032 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.036 0.066 -9999 0 -0.31 16 16
MAPK3 0.042 0.063 -9999 0 -10000 0 0
MAPK1 0.042 0.063 -9999 0 -10000 0 0
JAK2 0.045 0.065 -9999 0 -0.42 1 1
CXCR4 0.041 0.064 -9999 0 -10000 0 0
FLT1 0.015 0.037 -9999 0 -0.81 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.042 0.063 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.036 0.067 -9999 0 -0.32 16 16
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.051 -9999 0 -10000 0 0
VEGFA 0.012 0.064 -9999 0 -0.81 3 3
S1P/S1P2/Gi 0.03 0.067 -9999 0 -0.32 17 17
VEGFR1 homodimer/VEGFA homodimer 0.024 0.066 -9999 0 -0.79 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.068 0.17 -9999 0 -0.35 125 125
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 -0.81 118 118
GNA15 -0.011 0.09 -9999 0 -0.32 36 36
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.003 0.12 -9999 0 -0.81 10 10
Rac1/GTP -0.01 0.051 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.016 -10000 0 -10000 0 0
CDKN1A 0.034 0.029 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.016 -10000 0 -10000 0 0
AKT1 -0.001 0.014 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.016 0.029 -10000 0 -0.44 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.016 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.023 -10000 0 -0.42 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.012 0.037 -10000 0 -0.81 1 1
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.022 0.41 1 -10000 0 1
TSC1 0.039 0.016 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.016 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.016 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.054 0.2 -10000 0 -0.54 69 69
MAP3K5 0.012 0.037 -10000 0 -0.81 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.036 -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 -0.002 0.035 -10000 0 -0.54 2 2
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
AKT2/p21CIP1 -0.004 0.028 -10000 0 -0.41 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.006 -10000 0 -10000 0 0
CHUK 0.039 0.016 -10000 0 -10000 0 0
BAD/BCL-XL 0.052 0.015 -10000 0 -10000 0 0
mTORC2 -0.001 0.023 -10000 0 -0.5 1 1
AKT2 0.016 0.029 -10000 0 -0.44 2 2
FOXO1-3a-4/14-3-3 family 0.025 0.042 -10000 0 -10000 0 0
PDPK1 0.01 0.053 -10000 0 -0.81 2 2
MDM2 0.039 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.038 0.015 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.015 -10000 0 -10000 0 0
TSC1/TSC2 0.045 0.015 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.011 -10000 0 -10000 0 0
glucose import -0.062 0.21 -10000 0 -0.52 84 84
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.033 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.063 0.22 -10000 0 -0.52 84 84
GSK3A 0.039 0.016 -10000 0 -10000 0 0
FOXO1 0.039 0.016 -10000 0 -10000 0 0
GSK3B 0.039 0.016 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.33 312 312
G1/S transition of mitotic cell cycle 0.046 0.015 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.001 0.053 -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
TRAIL 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
TNFSF10 0.006 0.076 -9999 0 -0.71 5 5
positive regulation of NF-kappaB transcription factor activity -0.005 0.056 -9999 0 -0.62 4 4
MAP2K4 0.047 0.034 -9999 0 -0.3 4 4
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.008 0.064 -9999 0 -0.81 3 3
SMPD1 -0.002 0.026 -9999 0 -0.29 4 4
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 -0.005 0.057 -9999 0 -0.62 4 4
TRAIL/TRAILR3 -0.059 0.1 -9999 0 -0.66 4 4
TRAIL/TRAILR1 -0.009 0.074 -9999 0 -0.62 7 7
TRAIL/TRAILR4 -0.005 0.057 -9999 0 -0.62 4 4
TRAIL/TRAILR1/DAP3/GTP -0.007 0.059 -9999 0 -0.5 7 7
IKK complex -0.002 0.019 -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 0.019 0.059 -9999 0 -0.62 4 4
MAP3K1 -0.004 0.031 -9999 0 -0.32 4 4
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.064 -9999 0 -0.81 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.034 0.043 -9999 0 -0.33 7 7
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.019 0.059 -9999 0 -0.62 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP -0.007 0.054 -9999 0 -0.46 7 7
mol:ceramide 0.018 0.028 -9999 0 -0.29 4 4
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.042 0.082 -9999 0 -0.46 11 11
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.074 0.14 -9999 0 -0.31 133 133
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.008 0.064 -9999 0 -0.54 7 7
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.006 0.051 -9999 0 -0.51 4 4
JNK cascade -0.005 0.056 -9999 0 -0.62 4 4
TRAIL (trimer) 0.006 0.075 -9999 0 -0.71 5 5
TNFRSF10C -0.074 0.14 -9999 0 -0.31 133 133
TRAIL/TRAILR1/DAP3/GTP/FADD -0.007 0.055 -9999 0 -0.46 7 7
TRAIL/TRAILR2/FADD -0.005 0.049 -9999 0 -0.54 4 4
cell death 0.018 0.028 -9999 0 -0.29 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.036 0.033 -9999 0 -0.33 4 4
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.015 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.004 0.041 -9999 0 -0.46 4 4
ceramide 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
MAP4K4 0.006 0.13 -10000 0 -0.56 11 11
BAG4 0.012 0.037 -10000 0 -0.81 1 1
BAD 0.018 0.045 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.65 37 37
BAX 0.017 0.047 -10000 0 -0.22 1 1
EnzymeConsortium:3.1.4.12 0.004 0.033 -10000 0 -0.12 11 11
IKBKB 0.014 0.12 -10000 0 -0.52 11 11
MAP2K2 0.027 0.056 -10000 0 -0.36 2 2
MAP2K1 0.027 0.056 -10000 0 -0.36 2 2
SMPD1 0.01 0.033 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.014 0.12 -10000 0 -0.53 11 11
MAP2K4 0.024 0.046 -10000 0 -10000 0 0
protein ubiquitination 0.015 0.12 -10000 0 -0.52 11 11
EnzymeConsortium:2.7.1.37 0.031 0.061 -10000 0 -0.37 2 2
response to UV 0 0.001 -10000 0 -0.003 2 2
RAF1 0.022 0.056 -10000 0 -0.39 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.047 -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 0.018 0.047 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.03 0.055 -10000 0 -0.35 2 2
MAPK1 0.03 0.055 -10000 0 -0.35 2 2
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.006 0.13 -10000 0 -0.56 11 11
KSR1 0.016 0.056 -10000 0 -0.42 2 2
MAPK8 0.021 0.08 -10000 0 -0.42 11 11
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.014 0.12 -10000 0 -0.52 11 11
TNF R/SODD -0.001 0.028 -10000 0 -0.62 1 1
TNF -0.087 0.27 -10000 0 -0.76 64 64
CYCS 0.027 0.056 0.16 30 -10000 0 30
IKBKG 0.014 0.12 -10000 0 -0.52 11 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.13 -10000 0 -0.44 25 25
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.027 0.056 0.16 30 -10000 0 30
TNF/TNF R/SODD -0.065 0.17 -10000 0 -0.54 58 58
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.033 -10000 0 -10000 0 0
NSMAF 0.006 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 -0.81 36 36
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.023 -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 -0.024 0.16 -10000 0 -0.65 28 28
TLE1 0 0.065 -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 60 60
beta catenin/RanBP3 0.021 0.09 0.37 26 -10000 0 26
KREMEN2 -0.01 0.083 -10000 0 -0.31 35 35
DKK1 -0.041 0.13 -10000 0 -0.32 80 80
beta catenin/beta TrCP1 0.052 0.037 -10000 0 -10000 0 0
FZD1 0.014 0.001 -10000 0 -10000 0 0
AXIN2 -0.048 0.31 -10000 0 -1.6 19 19
AXIN1 0.014 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.044 0.29 1 -0.4 1 2
Axin1/APC/GSK3 0.007 0.031 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.021 -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 -0.028 0.25 -10000 0 -1.6 12 12
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.034 0.11 -10000 0 -0.55 19 19
NKD1 -0.013 0.14 -10000 0 -0.7 18 18
TCF4 0.006 0.021 -10000 0 -10000 0 0
TCF3 0.006 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.001 0.013 -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 -0.003 0.066 -10000 0 -0.4 10 10
DVL1 0.019 0.027 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.074 -10000 0 -0.46 5 5
DKK1/LRP6/Kremen 2 -0.038 0.08 -10000 0 -0.39 9 9
LRP6 0.014 0 -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 -0.64 2 2
WNT1 0.008 0.032 -10000 0 -0.31 5 5
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 0.059 0.36 14 -10000 0 14
APC 0.038 0.028 -10000 0 -0.46 1 1
WNT1/LRP6/FZD1 0.034 0.037 -10000 0 -10000 0 0
CREBBP 0.006 0.021 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.34 -9999 0 -0.81 103 103
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.025 -9999 0 -0.31 3 3
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.023 -9999 0 -10000 0 0
HIF1A 0.022 0.024 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.004 0.04 -9999 0 -0.5 3 3
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.12 0.16 -9999 0 -10000 0 0
ARNT/IPAS -0.13 0.25 -9999 0 -0.62 103 103
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.023 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.087 -9999 0 -0.53 12 12
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.017 -9999 0 -10000 0 0
VHL 0.008 0.064 -9999 0 -0.81 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 -0.5 30 30
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.01 0.053 -9999 0 -0.81 2 2
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.05 -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 -0.029 0.072 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.06 0.12 -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 -0.027 0.039 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.091 0.11 0.51 1 -10000 0 1
ARF1/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GM1 -0.011 0.034 -10000 0 -10000 0 0
mol:Choline 0.012 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.003 0.064 -10000 0 -10000 0 0
MAPK3 -0.017 0.065 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.091 0.11 -10000 0 -0.52 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.023 0.053 -10000 0 -10000 0 0
ARF1/GDP 0.004 0.059 -10000 0 -10000 0 0
ARF6 -0.002 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.32 276 276
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 -0.006 0.051 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.025 0.038 -10000 0 -10000 0 0
NME1 0.01 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.025 0.038 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.026 0.039 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.003 0.064 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.026 0.039 -10000 0 -10000 0 0
ARF6/GTP -0.027 0.039 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GDP -0.011 0.065 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.01 0.014 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0 0.033 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.003 0.064 -10000 0 -10000 0 0
ruffle organization 0.01 0.037 -10000 0 -0.32 2 2
regulation of epithelial cell migration -0.026 0.039 -10000 0 -10000 0 0
PLD2 0 0.033 -10000 0 -10000 0 0
PIP5K1A 0.01 0.037 -10000 0 -0.32 2 2
mol:Phosphatidic acid 0.012 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.064 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.094 -9999 0 -0.45 17 17
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.007 0.074 -9999 0 -0.81 4 4
ITGA4 0.002 0.077 -9999 0 -0.44 12 12
alpha4/beta7 Integrin/MAdCAM1 -0.035 0.11 -9999 0 -0.5 20 20
EPO 0.002 0.038 -9999 0 -0.31 7 7
alpha4/beta7 Integrin -0.033 0.12 -9999 0 -0.62 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.007 0.055 -9999 0 -0.62 3 3
EPO/EPOR (dimer) -0.007 0.036 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.037 -9999 0 -0.46 3 3
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
PI3K -0.004 0.048 -9999 0 -0.62 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.022 0.067 -9999 0 -0.62 4 4
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.012 0.096 -9999 0 -0.36 30 30
cell adhesion -0.035 0.1 -9999 0 -0.49 20 20
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.022 0.078 -9999 0 -0.55 7 7
ITGB7 -0.024 0.15 -9999 0 -0.51 35 35
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.013 0.08 -9999 0 -0.55 9 9
p130Cas/Crk/Dock1 0.039 0.079 -9999 0 -0.81 1 1
VCAM1 0.002 0.089 -9999 0 -0.56 10 10
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.042 -9999 0 -0.49 3 3
BCAR1 0.031 0.074 -9999 0 -0.51 7 7
EPOR 0.007 0.046 -9999 0 -0.31 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.038 -9999 0 -0.48 3 3
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.059 0.16 -9999 0 -0.5 58 58
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.15 -9999 0 -0.41 58 58
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 -0.024 0.065 -9999 0 -10000 0 0
YY1/LSF 0.028 0.049 -9999 0 -0.52 4 4
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.012 0.13 -9999 0 -0.36 57 57
I kappa B alpha/HDAC1 0.001 0.089 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.002 0.11 -9999 0 -0.32 57 57
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 0.001 0.089 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.049 0.02 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.003 0.11 -9999 0 -0.47 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
GATA1 0.008 0.016 -9999 0 -0.31 1 1
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.059 0.022 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.008 0.064 -9999 0 -0.81 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 -0.007 0.099 -9999 0 -0.28 57 57
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.044 0.027 -9999 0 -10000 0 0
SIN3 complex -0.001 0.022 -9999 0 -0.49 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.037 -9999 0 -0.81 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 0.016 0.083 -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 -0.059 0.15 -9999 0 -0.45 62 62
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 0.089 -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 0.021 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.007 0.099 -9999 0 -0.28 57 57
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.027 0 -9999 0 -10000 0 0
NFKB1 0.012 0.037 -9999 0 -0.81 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.004 0.043 -9999 0 -0.48 4 4
YY1/SAP30/HDAC1 -0.001 0.021 -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 -0.007 0.099 -9999 0 -0.28 57 57
histone deacetylation 0.049 0.02 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.083 -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 0.089 -9999 0 -10000 0 0
GATA1/HDAC1 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC3 -0.009 0.088 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.075 0.2 -9999 0 -0.62 57 57
SIN3/HDAC complex/Mad/Max 0.049 0.023 -9999 0 -10000 0 0
NuRD Complex 0.058 0.021 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.024 0.064 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.003 0.038 -9999 0 -0.49 3 3
GATA1/Fog1 0 0.009 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.087 0.26 -9999 0 -0.76 64 64
negative regulation of cell growth 0.049 0.023 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.049 0.02 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.051 0.14 -9999 0 -0.43 57 57
SIN3/HDAC complex/NCoR1 0.046 0.026 -9999 0 -10000 0 0
TFCP2 0.007 0.074 -9999 0 -0.81 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
FoxO family signaling

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
G6PC 0.038 0.025 -9999 0 -10000 0 0
PLK1 0.1 0.11 -9999 0 -0.73 1 1
CDKN1B 0.15 0.047 -9999 0 -0.39 1 1
FOXO3 0.1 0.11 -9999 0 -0.58 4 4
KAT2B 0.025 0.01 -9999 0 -10000 0 0
FOXO1/SIRT1 0.01 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 0.016 -9999 0 -10000 0 0
MAPK10 0.043 0.025 -9999 0 -0.5 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.065 -9999 0 -0.48 4 4
response to oxidative stress 0.015 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.013 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 0.04 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 0.039 0.05 -9999 0 -0.49 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 0.061 -9999 0 -0.72 1 1
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.042 -9999 0 -10000 0 0
MST1 0.023 0.042 -9999 0 -0.57 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 0.008 0.066 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.033 0.077 -9999 0 -0.48 11 11
MAPK9 0.044 0.007 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.006 0.042 -9999 0 -0.81 1 1
SOD2 0.16 0.073 -9999 0 -0.79 1 1
RBL2 0.11 0.15 -9999 0 -1.4 4 4
RAL/GDP 0.033 0.013 -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 0.042 0.01 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.082 0.42 -9999 0 -1.5 38 38
SKP2 0.007 0.074 -9999 0 -0.81 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 0.049 -9999 0 -0.42 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.05 -9999 0 -0.49 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.008 0.12 -9999 0 -0.81 10 10
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.003 -9999 0 -10000 0 0
ZFAND5 0.11 0.055 -9999 0 -0.47 1 1
SFN -0.21 0.19 -9999 0 -0.33 312 312
CDK2 0.014 0.003 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.016 0.065 -9999 0 -0.32 5 5
CREBBP 0.014 0.003 -9999 0 -10000 0 0
FBXO32 0.1 0.11 -9999 0 -0.73 1 1
BCL6 0.11 0.11 -9999 0 -0.94 2 2
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
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0.009 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.011 0.15 -9999 0 -0.55 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.039 -9999 0 -0.41 1 1
NFKBIA 0.024 0.037 -9999 0 -0.27 6 6
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.025 -9999 0 -0.54 1 1
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.042 0.21 -9999 0 -0.81 33 33
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.027 -9999 0 -0.54 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.025 -9999 0 -0.54 1 1
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
NF kappa B1 p50 dimer 0.02 0.029 -9999 0 -0.62 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.023 0.029 -9999 0 -0.62 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.038 -9999 0 -0.27 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.047 0.038 -9999 0 -0.4 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
PI3K -0.004 0.048 -9999 0 -0.62 3 3
NF kappa B1 p50/RelA 0.031 0.038 -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 0.045 0.036 -9999 0 -0.38 1 1
NF kappa B1 p105/c-Rel -0.011 0.15 -9999 0 -0.55 33 33
LCK -0.01 0.11 -9999 0 -0.42 27 27
BCL3 0.013 0.015 -9999 0 -0.31 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.021 0.12 -9999 0 -0.66 16 16
AKT1 0.083 0.089 -9999 0 -0.68 5 5
PTK2B 0.036 0.13 -9999 0 -0.91 5 5
VEGFR2 homodimer/Frs2 0.03 0.096 -9999 0 -1 4 4
CAV1 -0.008 0.13 -9999 0 -0.81 13 13
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.01 0.1 -9999 0 -0.86 6 6
endothelial cell proliferation 0.079 0.099 -9999 0 -0.61 5 5
mol:Ca2+ 0.05 0.1 -9999 0 -0.72 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.01 0.098 -9999 0 -0.81 6 6
RP11-342D11.1 0.041 0.1 -9999 0 -0.73 7 7
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.006 0.061 -9999 0 -0.58 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.064 -9999 0 -0.81 3 3
HRAS/GDP -0.009 0.082 -9999 0 -0.74 5 5
SH2D2A -0.036 0.18 -9999 0 -0.61 39 39
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.008 0.069 -9999 0 -0.69 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.036 0.15 -9999 0 -0.56 29 29
VEGFR1 homodimer 0.012 0.037 -9999 0 -0.81 1 1
SHC/GRB2/SOS1 -0.01 0.094 -9999 0 -0.93 4 4
GRB10 0.05 0.1 -9999 0 -0.95 4 4
PTPN11 0.012 0.037 -9999 0 -0.81 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 -0.009 0.094 -9999 0 -0.78 6 6
HRAS 0.012 0.021 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.077 -9999 0 -0.48 5 5
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.01 0.095 -9999 0 -0.79 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.003 0.091 -9999 0 -0.81 6 6
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.01 0.1 -9999 0 -0.86 6 6
mol:GDP -0.009 0.087 -9999 0 -0.87 4 4
mol:NADP 0.076 0.066 -9999 0 -0.56 4 4
eNOS/Hsp90 0.079 0.062 -9999 0 -0.52 4 4
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.05 0.11 -9999 0 -0.75 7 7
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.064 -9999 0 -0.81 3 3
VEGFC 0.012 0.037 -9999 0 -0.81 1 1
FAK1/Vinculin 0.058 0.11 -9999 0 -0.71 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.13 -9999 0 -0.57 22 22
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.019 0.063 -9999 0 -0.58 4 4
mol:L-citrulline 0.076 0.066 -9999 0 -0.56 4 4
ITGAV 0.01 0.053 -9999 0 -0.81 2 2
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.01 0.098 -9999 0 -0.81 6 6
VEGFR2 homodimer/VEGFA homodimer -0.012 0.12 -9999 0 -0.84 7 7
VEGFR2/3 heterodimer 0.024 0.13 -9999 0 -1 7 7
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.051 0.11 -9999 0 -0.77 7 7
VEGFR2 homodimer 0.029 0.1 -9999 0 -1.1 4 4
FLT1 0.012 0.037 -9999 0 -0.81 1 1
NEDD4 0.013 0.053 -9999 0 -0.81 2 2
MAPK3 0.045 0.1 -9999 0 -0.8 5 5
MAPK1 0.045 0.1 -9999 0 -0.8 5 5
VEGFA145/NRP2 -0.02 0.071 -9999 0 -0.62 3 3
VEGFR1/2 heterodimer 0.029 0.11 -9999 0 -1.1 4 4
KDR 0.029 0.11 -9999 0 -1.1 4 4
VEGFA165/NRP1/VEGFR2 homodimer -0.018 0.11 -9999 0 -0.78 7 7
SRC 0.013 0.015 -9999 0 -0.31 1 1
platelet activating factor biosynthetic process 0.047 0.11 -9999 0 -0.93 4 4
PI3K -0.011 0.094 -9999 0 -0.9 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.01 0.1 -9999 0 -0.86 6 6
FES 0.05 0.11 -9999 0 -0.77 7 7
GAB1 -0.01 0.093 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.011 0.1 -9999 0 -0.86 6 6
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.068 0.092 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer/Yes -0.01 0.1 -9999 0 -0.86 6 6
PI3K/GAB1 0.085 0.084 -9999 0 -0.7 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.009 0.094 -9999 0 -0.96 4 4
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.014 0.12 -9999 0 -0.88 8 8
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.05 0.11 -9999 0 -0.77 7 7
actin cytoskeleton reorganization -0.036 0.14 -9999 0 -0.55 29 29
PTK2 0.052 0.12 -9999 0 -0.79 7 7
EDG1 0.041 0.1 -9999 0 -0.73 7 7
mol:DAG 0.05 0.11 -9999 0 -0.75 7 7
CaM/Ca2+ -0.009 0.088 -9999 0 -0.88 4 4
MAP2K3 0.048 0.12 -9999 0 -0.98 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.011 0.11 -9999 0 -1.1 4 4
PLCG1 0.05 0.11 -9999 0 -0.77 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.01 0.099 -9999 0 -0.81 6 6
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.011 0.12 -9999 0 -0.91 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.01 0.1 -9999 0 -0.86 6 6
cell migration 0.082 0.096 -9999 0 -0.69 4 4
mol:PI-3-4-5-P3 -0.01 0.081 -9999 0 -0.78 4 4
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.047 0.095 -9999 0 -0.68 7 7
mol:NO 0.076 0.066 -9999 0 -0.56 4 4
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.009 0.081 -9999 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.049 0.12 -9999 0 -1.1 4 4
VHL 0.008 0.064 -9999 0 -0.81 3 3
ITGB3 -0.012 0.14 -9999 0 -0.81 15 15
NOS3 0.078 0.076 -9999 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/Sck -0.013 0.11 -9999 0 -0.73 9 9
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.039 0.14 -9999 0 -1.1 4 4
PRKCB 0.04 0.11 -9999 0 -0.88 4 4
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.04 0.11 -9999 0 -0.77 7 7
VEGFR1/2 heterodimer/VEGFA homodimer -0.011 0.12 -9999 0 -0.91 6 6
VEGFA165/NRP2 -0.02 0.071 -9999 0 -0.62 3 3
MAPKKK cascade -0.009 0.08 -9999 0 -0.79 4 4
NRP2 -0.013 0.088 -9999 0 -0.31 40 40
VEGFC homodimer 0.012 0.037 -9999 0 -0.81 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.058 0.11 -9999 0 -0.71 7 7
MAP3K13 0.04 0.14 -9999 0 -0.6 16 16
PDPK1 0.076 0.09 -9999 0 -0.71 5 5
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.045 0.002 -9999 0 -10000 0 0
KLHL20 -0.009 0.021 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.073 0.009 -9999 0 -10000 0 0
ENAH 0.045 0.002 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.001 0.014 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.019 0.084 -9999 0 -0.49 14 14
RAPGEF1 0.057 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 -0.026 0.11 -9999 0 -0.62 14 14
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 -0.078 0.071 -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 -0.31 276 276
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.011 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.073 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.073 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.027 0 -9999 0 -10000 0 0
ITGB7 -0.024 0.15 -9999 0 -0.51 35 35
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.072 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.032 -9999 0 -0.15 11 11
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.045 0.002 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.008 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.078 -9999 0 -0.46 14 14
CCND1 0.015 0.039 -9999 0 -0.18 11 11
VAV2 0.056 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.045 0.001 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.016 0.074 -9999 0 -0.43 14 14
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 0.064 -9999 0 -0.81 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
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.69 21 21
CDC42/GTP -0.011 0.054 -9999 0 -0.29 17 17
PLCG1 0.03 0.064 -9999 0 -0.33 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.011 0.053 -9999 0 -0.29 17 17
S1PR5 0.007 0.053 -9999 0 -0.81 1 1
S1PR4 0.009 0.038 -9999 0 -0.31 7 7
MAPK3 0.03 0.064 -9999 0 -0.3 17 17
MAPK1 0.03 0.064 -9999 0 -0.3 17 17
S1P/S1P5/Gi 0.022 0.07 -9999 0 -0.33 17 17
GNAI1 0.012 0.037 -9999 0 -0.81 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.031 -9999 0 -0.55 1 1
RHOA 0.032 0.018 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.022 0.068 -9999 0 -0.33 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.002 0.016 -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
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.073 0.051 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.029 0.078 -9999 0 -0.62 2 2
NFKBIA 0.048 0.023 -9999 0 -0.47 1 1
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.005 0.02 -9999 0 -10000 0 0
IKK complex/A20 -0.048 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 0.038 -9999 0 -0.42 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.002 0.014 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.034 -9999 0 -0.54 2 2
NOD2 -0.033 0.12 -9999 0 -0.81 2 2
NFKB1 0.015 0.037 -9999 0 -0.81 1 1
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.012 0.037 -9999 0 -0.81 1 1
TNF/TNFR1A -0.075 0.2 -9999 0 -0.62 57 57
TRAF6 0.01 0.053 -9999 0 -0.81 2 2
PRKCA -0.018 0.16 -9999 0 -0.81 19 19
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.087 0.26 -9999 0 -0.76 64 64
NF kappa B1 p50/RelA -0.001 0.023 -9999 0 -0.52 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.023 -9999 0 -0.46 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 -0.016 0.076 -9999 0 -0.53 1 1
Circadian rhythm 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
chromatin modification -0.025 0.047 -9999 0 -0.62 1 1
CLOCK -0.044 0.21 -9999 0 -0.82 33 33
TIMELESS/CRY2 -0.004 0.065 -9999 0 -10000 0 0
DEC1/BMAL1 -0.024 0.067 -9999 0 -10000 0 0
ATR 0.012 0.037 -9999 0 -0.81 1 1
NR1D1 -0.054 0.13 -9999 0 -10000 0 0
ARNTL -0.025 0.1 -9999 0 -0.33 17 17
TIMELESS -0.012 0.073 -9999 0 -10000 0 0
NPAS2 0.009 0.04 -9999 0 -0.56 2 2
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.006 0.03 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.006 0.03 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.035 0.16 -9999 0 -0.56 34 34
BMAL1/CLOCK -0.055 0.16 -9999 0 -0.62 15 15
S phase of mitotic cell cycle -0.025 0.047 -9999 0 -0.62 1 1
TIMELESS/CHEK1/ATR -0.025 0.048 -9999 0 -0.64 1 1
mol:NADPH -0.006 0.03 -9999 0 -10000 0 0
PER1/TIMELESS -0.004 0.065 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.014 -9999 0 -0.31 1 1
EPO signaling pathway

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.051 0.1 -9999 0 -10000 0 0
CRKL 0.037 0.049 -9999 0 -0.46 2 2
mol:DAG 0.041 0.051 -9999 0 -0.37 1 1
HRAS 0.061 0.044 -9999 0 -0.42 1 1
MAPK8 0.018 0.091 -9999 0 -0.55 11 11
RAP1A 0.037 0.049 -9999 0 -0.46 2 2
GAB1 0.037 0.049 -9999 0 -0.46 2 2
MAPK14 0.03 0.03 -9999 0 -10000 0 0
EPO 0.005 0.038 -9999 0 -0.3 7 7
PLCG1 0.041 0.052 -9999 0 -0.38 1 1
EPOR/TRPC2/IP3 Receptors 0.009 0.046 -9999 0 -0.31 10 10
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.021 0.12 -9999 0 -0.57 23 23
GAB1/SHC/GRB2/SOS1 -0.006 0.029 -9999 0 -0.45 1 1
EPO/EPOR (dimer) 0.013 0.041 -9999 0 -10000 0 0
IRS2 0.037 0.049 -9999 0 -0.46 2 2
STAT1 0.041 0.078 -9999 0 -10000 0 0
STAT5B 0.042 0.066 -9999 0 -0.38 1 1
cell proliferation 0.026 0.086 -9999 0 -0.51 11 11
GAB1/SHIP/PIK3R1/SHP2/SHC -0.009 0.036 -9999 0 -0.44 2 2
TEC 0.037 0.049 -9999 0 -0.46 2 2
SOCS3 -0.026 0.18 -9999 0 -0.79 24 24
STAT1 (dimer) 0.041 0.077 -9999 0 -10000 0 0
JAK2 0.011 0.053 -9999 0 -0.82 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.042 0.055 -9999 0 -0.49 2 2
EPO/EPOR 0.013 0.041 -9999 0 -10000 0 0
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.045 0.048 -9999 0 -0.44 2 2
elevation of cytosolic calcium ion concentration 0.009 0.046 -9999 0 -0.31 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.028 0.035 -9999 0 -10000 0 0
mol:IP3 0.041 0.051 -9999 0 -0.37 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.011 0.036 -9999 0 -0.47 1 1
SH2B3 0.014 0.005 -9999 0 -10000 0 0
NFKB1 0.029 0.038 -9999 0 -0.5 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.017 0.066 -9999 0 -0.29 25 25
PTPN6 0.03 0.051 -9999 0 -0.49 2 2
TEC/VAV2/GRB2 0.05 0.046 -9999 0 -0.48 1 1
EPOR 0.009 0.046 -9999 0 -0.31 10 10
INPP5D -0.003 0.071 -9999 0 -0.31 25 25
mol:GDP -0.006 0.029 -9999 0 -0.46 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.05 0.046 -9999 0 -0.48 1 1
VAV2 0.037 0.049 -9999 0 -0.46 2 2
CBL 0.037 0.049 -9999 0 -0.46 2 2
SHC/Grb2/SOS1 -0.007 0.031 -9999 0 -0.48 1 1
STAT5A 0.042 0.066 -9999 0 -0.38 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.052 0.098 -9999 0 -0.4 3 3
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
BTK 0.021 0.087 -9999 0 -0.48 9 9
BCL2 0.002 0.28 -9999 0 -0.98 36 36
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.007 -10000 0 -10000 0 0
DOCK1 0.007 0.074 -10000 0 -0.81 4 4
ITGA4 0.002 0.077 -10000 0 -0.44 12 12
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.033 0.12 -10000 0 -0.62 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.046 -10000 0 -0.54 3 3
alpha4/beta7 Integrin/Paxillin -0.025 0.095 -10000 0 -0.5 17 17
lamellipodium assembly -0.004 0.057 -10000 0 -0.54 5 5
PIK3CA 0.008 0.064 -10000 0 -0.81 3 3
PI3K -0.004 0.048 -10000 0 -0.62 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 0.034 -10000 0 -0.42 3 3
cell adhesion -0.005 0.038 -10000 0 -0.45 3 3
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.005 0.042 -10000 0 -0.49 3 3
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.024 0.15 -10000 0 -0.51 35 35
ARF6/GDP 0.001 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.011 0.068 -10000 0 -0.52 7 7
p130Cas/Crk/Dock1 -0.004 0.048 -10000 0 -0.54 4 4
VCAM1 0.002 0.089 -10000 0 -0.56 10 10
alpha4/beta1 Integrin/Paxillin/Talin -0.005 0.038 -10000 0 -0.46 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 -0.005 0.038 -10000 0 -0.46 3 3
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.038 0.45 3 -10000 0 3
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.005 0.038 -10000 0 -0.46 3 3
Rac1/GTP -0.005 0.067 -10000 0 -0.76 3 3
PLK1 signaling events

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.009 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 0.029 -9999 0 -0.58 1 1
regulation of mitotic centrosome separation 0.017 0.012 -9999 0 -10000 0 0
GOLGA2 0.013 0 -9999 0 -10000 0 0
Hec1/SPC24 0.001 0.073 -9999 0 -0.28 16 16
WEE1 0.022 0.011 -9999 0 -10000 0 0
cytokinesis 0.002 0.072 -9999 0 -0.3 6 6
PP2A-alpha B56 0.006 0.068 -9999 0 -0.72 3 3
AURKA 0.016 0.009 -9999 0 -10000 0 0
PICH/PLK1 0.033 0.018 -9999 0 -10000 0 0
CENPE 0.019 0.048 -9999 0 -0.3 8 8
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 0.022 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
SPC24 -0.008 0.08 -9999 0 -0.31 32 32
FBXW11 0.013 0 -9999 0 -10000 0 0
CLSPN 0.005 0.034 -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 -0.065 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 0.067 -9999 0 -0.8 3 3
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.012 0.022 -9999 0 -10000 0 0
CDC25B 0.012 0.025 -9999 0 -0.31 3 3
SGOL1 0.009 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 0.004 0.072 -9999 0 -0.64 6 6
CDC20 0.008 0.041 -9999 0 -0.31 8 8
PLK1/PBIP1 0.002 0.022 -9999 0 -10000 0 0
mitosis 0 0.002 -9999 0 -0.022 3 3
FBXO5 0.021 0.021 -9999 0 -0.39 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.027 0.11 -9999 0 -0.31 61 61
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 0.008 0.057 -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 0.038 -9999 0 -0.47 3 3
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.035 -9999 0 -0.3 3 3
microtubule-based process -0.001 0.06 -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 -0.035 0.12 -9999 0 -0.31 74 74
APC/C/CDC20 0.02 0.025 -9999 0 -10000 0 0
PPP2R1A 0.013 0 -9999 0 -10000 0 0
chromosome segregation 0.002 0.022 -9999 0 -10000 0 0
PRC1 0.013 0 -9999 0 -10000 0 0
ECT2 0.022 0.038 -9999 0 -0.55 2 2
C13orf34 0.018 0.039 -9999 0 -0.47 3 3
NUDC 0.015 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 0.012 0.062 -9999 0 -0.55 6 6
MKLP2/PLK1 -0.001 0.061 -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 -0.003 0.12 -9999 0 -0.52 25 25
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 0.032 -9999 0 -0.22 10 10
INCENP 0.009 0.053 -9999 0 -0.82 2 2
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.011 0.054 0.38 1 -10000 0 1
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.003 0.031 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.017 0.15 -10000 0 -0.69 21 21
RhoA/GTP -0.012 0.055 -10000 0 -0.39 1 1
negative regulation of cAMP metabolic process 0.022 0.07 -10000 0 -0.33 17 17
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 0.007 0.053 -10000 0 -0.81 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.07 -10000 0 -0.33 17 17
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.037 -10000 0 -0.81 1 1
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.001 0.025 -10000 0 -10000 0 0
oxygen homeostasis 0.015 0.011 -10000 0 -10000 0 0
TCEB2 0.011 0.025 -10000 0 -0.31 3 3
TCEB1 0.013 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.011 0.072 -10000 0 -0.69 4 4
EPO 0.18 0.14 -10000 0 -0.8 2 2
FIH (dimer) 0.028 0.011 -10000 0 -10000 0 0
APEX1 0.027 0.011 -10000 0 -10000 0 0
SERPINE1 0.17 0.17 -10000 0 -0.8 3 3
FLT1 -0.002 0.072 -10000 0 -1.6 1 1
ADORA2A 0.18 0.14 -10000 0 -0.85 2 2
germ cell development 0.19 0.14 -10000 0 -0.84 2 2
SLC11A2 0.19 0.15 -10000 0 -0.89 2 2
BHLHE40 0.18 0.16 -10000 0 -0.89 2 2
HIF1AN 0.028 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.003 0.076 -10000 0 -0.96 2 2
ETS1 0.03 0.003 -10000 0 -10000 0 0
CITED2 -0.093 0.32 -10000 0 -1.2 39 39
KDR -0.009 0.13 -10000 0 -1.4 4 4
PGK1 0.19 0.15 -10000 0 -0.89 2 2
SIRT1 0.012 0.037 -10000 0 -0.81 1 1
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.2 0.17 -10000 0 -1.2 2 2
EPAS1 0.1 0.1 -10000 0 -0.63 3 3
SP1 0.022 0.002 -10000 0 -10000 0 0
ABCG2 0.18 0.17 -10000 0 -0.88 5 5
EFNA1 0.19 0.15 -10000 0 -0.89 2 2
FXN 0.18 0.14 -10000 0 -0.85 2 2
POU5F1 0.19 0.15 -10000 0 -0.9 2 2
neuron apoptosis -0.2 0.16 0.91 3 -10000 0 3
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.002 0.14 -10000 0 -0.48 30 30
EGLN2 0.028 0.011 -10000 0 -10000 0 0
EGLN1 0.025 0.055 -10000 0 -0.82 2 2
VHL/Elongin B/Elongin C -0.004 0.047 -10000 0 -0.59 3 3
VHL 0.008 0.064 -10000 0 -0.81 3 3
ARNT 0.027 0.011 -10000 0 -10000 0 0
SLC2A1 0.18 0.14 -10000 0 -0.85 2 2
TWIST1 0.17 0.18 -10000 0 -0.65 10 10
ELK1 0.015 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.002 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 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
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.031 0.008 -9999 0 -10000 0 0
MAPK12 0.019 0.079 -9999 0 -0.47 12 12
CCND1 0.017 0.034 -9999 0 -0.25 1 1
p38 gamma/SNTA1 0.025 0.075 -9999 0 -0.44 12 12
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.019 0.079 -9999 0 -0.47 12 12
MAP2K6 0.012 0.085 -9999 0 -0.52 12 12
MAPT 0.024 0.045 -9999 0 -0.4 3 3
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.021 -9999 0 -0.45 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.001 0.04 -9999 0 -0.73 1 1
PDGFB-D/PDGFRB/SLAP 0.004 0.031 -9999 0 -0.63 1 1
PDGFB-D/PDGFRB/APS/CBL -0.001 0.025 -9999 0 -0.54 1 1
AKT1 0.059 0.043 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.024 0.05 -9999 0 -0.78 1 1
PIK3CA 0.008 0.064 -9999 0 -0.81 3 3
FGR 0.002 0.028 -9999 0 -0.56 1 1
mol:Ca2+ 0.02 0.048 -9999 0 -0.82 1 1
MYC 0.02 0.15 -9999 0 -0.84 13 13
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.028 -9999 0 -0.45 1 1
LRP1/PDGFRB/PDGFB -0.002 0.034 -9999 0 -0.54 2 2
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.037 -9999 0 -0.81 1 1
GO:0007205 0.02 0.049 -9999 0 -0.84 1 1
PTEN 0.012 0.037 -9999 0 -0.81 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.04 0.12 -9999 0 -0.31 82 82
PDGFB-D/PDGFRB/SHP2 0.003 0.041 -9999 0 -0.63 2 2
PDGFB-D/PDGFRB/GRB10 0.005 0.03 -9999 0 -0.63 1 1
cell cycle arrest -0.001 0.03 -9999 0 -0.62 1 1
HRAS 0.012 0.021 -9999 0 -0.31 2 2
HIF1A 0.064 0.039 -9999 0 -10000 0 0
GAB1 0.013 0.063 -9999 0 -0.86 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.059 -9999 0 -0.78 1 1
PDGFB-D/PDGFRB 0.012 0.031 -9999 0 -0.56 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.005 0.03 -9999 0 -0.63 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.047 -9999 0 -0.74 1 1
positive regulation of MAPKKK cascade -0.002 0.04 -9999 0 -0.63 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.049 -9999 0 -0.85 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.015 -9999 0 -0.31 1 1
PDGFB-D/PDGFRB/GRB7 -0.029 0.084 -9999 0 -0.78 1 1
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.18 0.28 -9999 0 -0.62 145 145
PTPN2 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.005 0.03 -9999 0 -0.63 1 1
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.017 0.07 -9999 0 -0.86 1 1
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.005 0.03 -9999 0 -0.63 1 1
LCK -0.008 0.087 -9999 0 -0.73 6 6
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.005 0.035 -9999 0 -0.54 1 1
ABL1 0.009 0.061 -9999 0 -0.83 1 1
PDGFB-D/PDGFRB/CBL 0.01 0.067 -9999 0 -0.94 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 0.05 -9999 0 -0.31 12 12
cell proliferation 0.022 0.13 -9999 0 -0.73 13 13
SLA 0.013 0.015 -9999 0 -0.31 1 1
actin cytoskeleton reorganization 0.052 0.024 -9999 0 -0.42 1 1
SRC 0.006 0.028 -9999 0 -0.55 1 1
PI3K -0.004 0.04 -9999 0 -0.4 2 2
PDGFB-D/PDGFRB/GRB7/SHC -0.027 0.065 -9999 0 -0.69 1 1
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
PLCgamma1/SPHK1 0.024 0.052 -9999 0 -0.82 1 1
LYN 0.006 0.029 -9999 0 -0.55 1 1
LRP1 0.012 0.037 -9999 0 -0.81 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.021 -9999 0 -0.44 1 1
SPHK1 0.006 0.05 -9999 0 -0.31 12 12
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.02 0.049 -9999 0 -0.85 1 1
PLCG1 0.02 0.051 -9999 0 -0.89 1 1
NHERF/PDGFRB -0.002 0.026 -9999 0 -0.54 1 1
YES1 0.004 0.027 -9999 0 -0.55 1 1
cell migration -0.002 0.026 -9999 0 -0.54 1 1
SHC/Grb2/SOS1 0 0.021 -9999 0 -0.44 1 1
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0.021 -9999 0 -0.31 2 2
NHERF1-2/PDGFRB/PTEN -0.003 0.032 -9999 0 -0.49 2 2
FYN 0.006 0.028 -9999 0 -0.55 1 1
DOK1 0.034 0.025 -9999 0 -0.5 1 1
HRAS/GTP -0.001 0.013 -9999 0 -0.21 2 2
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.028 0.087 -9999 0 -0.44 13 13
PRKCD 0.034 0.025 -9999 0 -0.5 1 1
FER 0.031 0.049 -9999 0 -0.5 4 4
MAPKKK cascade -0.001 0.02 -9999 0 -0.43 1 1
RASA1 0.034 0.025 -9999 0 -0.5 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.017 0.03 -9999 0 -0.45 1 1
PDGFB-D/PDGFRB/SHB 0.005 0.03 -9999 0 -0.63 1 1
chemotaxis 0.01 0.059 -9999 0 -0.79 1 1
STAT1-3-5/STAT1-3-5 -0.003 0.023 -9999 0 -0.42 1 1
Bovine Papilomavirus E5/PDGFRB 0.001 0.029 -9999 0 -0.64 1 1
PTPRJ 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.03 -9999 0 -0.39 3 3
TRAF2/ASK1 -0.001 0.025 -9999 0 -0.55 1 1
ATM 0.012 0.037 -9999 0 -0.81 1 1
MAP2K3 0.026 0.057 -9999 0 -0.52 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.023 0.079 -9999 0 -0.39 9 9
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0 0.1 -9999 0 -0.66 10 10
TXN 0.009 0.006 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.013 0.15 -9999 0 -0.81 16 16
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.028 -9999 0 -0.62 1 1
TAK1/TAB family -0.001 0.014 -9999 0 -0.21 2 2
RAC1/OSM/MEKK3 -0.001 0.009 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.009 0.033 -9999 0 -0.38 2 2
TRAF6 0.007 0.03 -9999 0 -0.46 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.005 0.083 -9999 0 -0.81 5 5
CCM2 0.012 0.021 -9999 0 -0.31 2 2
CaM/Ca2+/CAMKIIB -0.006 0.055 -9999 0 -0.55 5 5
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.006 0.062 -9999 0 -0.59 5 5
OSM/MEKK3 -0.001 0.013 -9999 0 -10000 0 0
TAOK1 -0.04 0.16 -9999 0 -0.46 61 61
TAOK2 0.017 0.021 -9999 0 -0.44 1 1
TAOK3 0.017 0.021 -9999 0 -0.44 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 0.037 -9999 0 -0.81 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.025 -9999 0 -0.54 1 1
GADD45/MTK1/MTK1 -0.022 0.1 -9999 0 -0.48 22 22
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0.02 -9999 0 -0.39 1 1
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.019 -9999 0 -0.42 1 1
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.04 0.15 -9999 0 -0.62 32 32
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 -0.04 0.2 -9999 0 -0.81 32 32
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.037 -9999 0 -0.81 1 1
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.001 0.022 -9999 0 -0.49 1 1
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0.009 -9999 0 -10000 0 0
GATA1/HDAC5 0 0.009 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.009 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.024 -9999 0 -0.54 1 1
HDAC9 -0.015 0.092 -9999 0 -0.31 44 44
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
HDAC4/RFXANK -0.001 0.013 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.028 -9999 0 -0.62 1 1
Histones 0.036 0.023 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.013 -9999 0 -10000 0 0
CAMK4 -0.004 0.11 -9999 0 -0.53 16 16
Tubulin/HDAC6 -0.005 0.054 -9999 0 -0.54 5 5
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.008 0.016 -9999 0 -0.31 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.006 0.062 -9999 0 -0.62 5 5
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.028 -9999 0 -0.62 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.01 0.067 -9999 0 -0.54 7 7
HDAC4/ER alpha -0.042 0.14 -9999 0 -0.62 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.036 0.022 -9999 0 -10000 0 0
cell motility -0.005 0.054 -9999 0 -0.54 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.012 0.037 -9999 0 -0.81 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 -0.046 0.19 -9999 0 -0.52 55 55
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.012 0.037 -9999 0 -0.81 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 0.037 -9999 0 -0.81 1 1
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.005 0.083 -9999 0 -0.81 5 5
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.012 0.021 -9999 0 -0.31 2 2
nuclear import 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.009 0.035 -9999 0 -0.31 6 6
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.022 0.024 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.008 -9999 0 -10000 0 0
BIRC5 -0.011 0.089 -9999 0 -0.81 1 1
NFKBIA 0.032 0.009 -9999 0 -10000 0 0
CPEB1 -0.05 0.22 -9999 0 -0.81 38 38
AKT1 0.032 0.009 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.012 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.015 -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 0.008 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.012 0.037 -9999 0 -0.81 1 1
TPX2 0.001 0.068 -9999 0 -10000 0 0
TP53 0.031 0.007 -9999 0 -10000 0 0
DLG7 0.021 0.009 -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 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.011 -9999 0 -10000 0 0
AURKA 0.026 0.012 -9999 0 -10000 0 0
AURKB -0.014 0.028 -9999 0 -0.14 4 4
CDC25B 0.007 0.019 -9999 0 -10000 0 0
G2/M transition checkpoint 0.002 0.025 -9999 0 -0.49 1 1
mRNA polyadenylation -0.036 0.13 -9999 0 -0.49 38 38
Aurora A/CPEB -0.036 0.13 -9999 0 -0.5 38 38
Aurora A/TACC1/TRAP/chTOG 0.003 0.026 -9999 0 -0.46 1 1
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.028 0.008 -9999 0 -10000 0 0
regulation of centrosome cycle 0.002 0.012 -9999 0 -10000 0 0
spindle assembly 0.002 0.023 -9999 0 -0.45 1 1
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.007 0.033 -9999 0 -0.44 1 1
CENPA -0.01 0.028 -9999 0 -0.26 4 4
Aurora A/PP2A 0.028 0.008 -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 0.007 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.002 0.025 -9999 0 -0.5 1 1
mitotic prometaphase 0.006 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.012 -9999 0 -10000 0 0
TACC1 0.012 0.037 -9999 0 -0.81 1 1
TACC3 0.012 0.021 -9999 0 -0.31 2 2
Aurora A/Antizyme1 0.003 0.016 -9999 0 -10000 0 0
Aurora A/RasGAP 0.028 0.008 -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 0.001 0.068 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.019 0.05 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.05 0.038 -10000 0 -0.43 3 3
adherens junction organization 0.04 0.038 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.052 0.059 -10000 0 -0.74 1 1
FMN1 0.019 0.11 -10000 0 -0.43 28 28
mol:IP3 -0.002 0.031 -10000 0 -0.4 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0 -10000 0 -10000 0 0
AKT1 0.049 0.035 -10000 0 -0.39 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.035 -10000 0 -0.48 2 2
VASP 0.046 0.011 -10000 0 -10000 0 0
ZYX 0.046 0.011 -10000 0 -10000 0 0
JUB 0.045 0.024 -10000 0 -0.43 1 1
EGFR(dimer) 0.041 0.051 -10000 0 -0.45 5 5
E-cadherin/beta catenin-gamma catenin 0 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.033 -10000 0 -0.42 3 3
PIK3CA 0.009 0.064 -10000 0 -0.81 3 3
PI3K -0.003 0.033 -10000 0 -0.43 3 3
FYN 0.051 0.034 -10000 0 -10000 0 0
mol:Ca2+ 0.042 0.034 -10000 0 -0.39 3 3
JUP 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.002 0.031 -10000 0 -0.4 3 3
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.052 0.059 -10000 0 -0.74 1 1
establishment of polarity of embryonic epithelium 0.046 0.011 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.005 0.083 -10000 0 -0.81 5 5
CASR 0.042 0.037 -10000 0 -0.38 3 3
RhoA/GTP -0.002 0.028 -10000 0 -0.36 3 3
AKT2 0.049 0.035 -10000 0 -0.39 3 3
actin cable formation 0.027 0.11 -10000 0 -0.41 28 28
apoptosis 0.002 0.032 0.41 3 -10000 0 3
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.046 0.063 -10000 0 -0.46 7 7
PIP5K1A 0.044 0.036 -10000 0 -0.5 2 2
PLCG1 -0.003 0.032 -10000 0 -0.41 3 3
Rac1/GTP -0.005 0.042 -10000 0 -0.41 5 5
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.023 0.16 -10000 0 -0.73 24 24
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.012 0.067 -10000 0 -0.55 7 7
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.028 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.018 0.036 -10000 0 -0.55 2 2
INS 0.009 0.045 -10000 0 -0.56 3 3
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 0.022 -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 0.007 -10000 0 -10000 0 0
ACAP1 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.002 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.01 0.071 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.017 0.08 -10000 0 -0.4 20 20
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.028 0 -10000 0 -10000 0 0
endocytosis 0.001 0.022 0.49 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.029 0.073 -10000 0 -0.43 12 12
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.012 0.037 -10000 0 -0.81 1 1
Dynamin 2/GDP 0.026 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.031 0.067 -10000 0 -0.43 10 10
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.08 0.11 -9999 0 -9999 0 0
TP53 -0.027 0.032 -9999 0 -9999 0 0
Senescence -0.027 0.032 -9999 0 -9999 0 0
Apoptosis -0.027 0.032 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.051 0.061 -9999 0 -9999 0 0
MDM4 0.013 0 -9999 0 -9999 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 0.03 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
E-cadherin signaling events

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

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

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

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.015 -9999 0 -0.21 2 2
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.003 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.001 0.062 -9999 0 -0.31 19 19
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.027 -9999 0 -0.42 2 2
ARF1/GTP -0.001 0.016 -9999 0 -0.25 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline -0.002 0.027 -9999 0 -0.42 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.002 -9999 0 -10000 0 0
ARFIP2 0 0.005 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0.008 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin -0.001 0.009 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin -0.001 0.009 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.004 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.035 0.016 -9999 0 -10000 0 0
PLD2 -0.002 0.027 -9999 0 -0.42 2 2
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.015 -9999 0 -0.23 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 -10000 0 0
USO1 -0.001 0.011 -9999 0 -10000 0 0
GBF1 -0.001 0.011 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.006 0.03 -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 0.037 -9999 0 -0.81 1 1
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.028 -9999 0 -0.62 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 494 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 -0.81 -0.81 -0.81 0.013
105_BMP4 0.013 -0.31 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR -0.49 -0.49 -0.49 -0.49
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.016
84_STAT5B 0.047 -0.096 0 -0.097
84_STAT5A 0.047 -0.096 0 -0.097
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/9830962/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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