PARADIGM pathway analysis of mRNASeq expression and copy number data
Liver Hepatocellular Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1445KCJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1445KCJ
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 65 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
Glypican 2 network 119
FOXM1 transcription factor network 104
Plasma membrane estrogen receptor signaling 72
Signaling events regulated by Ret tyrosine kinase 65
PDGFR-alpha signaling pathway 60
FOXA2 and FOXA3 transcription factor networks 56
Signaling mediated by p38-alpha and p38-beta 55
Nongenotropic Androgen signaling 55
IL4-mediated signaling events 52
EPO signaling pathway 52
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 268 . 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 ( 268 ).

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
Glypican 2 network 0.4440 119 477 4 0.072 0.18 1000 -1000 0.01 -1000
FOXM1 transcription factor network 0.3881 104 5344 51 0.004 0.92 1000 -1000 -0.015 -1000
Plasma membrane estrogen receptor signaling 0.2687 72 6221 86 -0.52 0.48 1000 -1000 -0.058 -1000
Signaling events regulated by Ret tyrosine kinase 0.2425 65 5359 82 -0.33 0.03 1000 -1000 -0.055 -1000
PDGFR-alpha signaling pathway 0.2239 60 2647 44 -0.59 0.045 1000 -1000 -0.03 -1000
FOXA2 and FOXA3 transcription factor networks 0.2090 56 2606 46 -0.74 0.037 1000 -1000 -0.019 -1000
Signaling mediated by p38-alpha and p38-beta 0.2052 55 2456 44 -0.32 0.022 1000 -1000 -0.018 -1000
Nongenotropic Androgen signaling 0.2052 55 2861 52 -0.4 0.23 1000 -1000 -0.027 -1000
IL4-mediated signaling events 0.1940 52 4740 91 -0.94 0.5 1000 -1000 -0.086 -1000
EPO signaling pathway 0.1940 52 2908 55 -0.22 0.022 1000 -1000 -0.029 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1828 49 3350 68 -0.57 0.22 1000 -1000 -0.034 -1000
TCGA08_retinoblastoma 0.1791 48 390 8 -0.1 0.23 1000 -1000 -0.005 -1000
Aurora B signaling 0.1791 48 3242 67 -0.009 0.31 1000 -1000 -0.039 -1000
HIF-1-alpha transcription factor network 0.1716 46 3532 76 -0.53 0.038 1000 -1000 -0.034 -1000
p75(NTR)-mediated signaling 0.1716 46 5825 125 -0.41 0.21 1000 -1000 -0.059 -1000
PLK1 signaling events 0.1679 45 3858 85 -0.067 0.29 1000 -1000 -0.033 -1000
Reelin signaling pathway 0.1679 45 2534 56 -0.22 0.11 1000 -1000 -0.028 -1000
IGF1 pathway 0.1679 45 2618 57 -0.29 0.091 1000 -1000 -0.046 -1000
IL6-mediated signaling events 0.1604 43 3277 75 -0.47 0.056 1000 -1000 -0.03 -1000
Ephrin B reverse signaling 0.1530 41 1985 48 -0.26 0.083 1000 -1000 -0.029 -1000
Ephrin A reverse signaling 0.1493 40 284 7 -0.086 0.025 1000 -1000 -0.009 -1000
Wnt signaling 0.1381 37 264 7 -0.16 0.036 1000 -1000 -0.015 -1000
Endothelins 0.1343 36 3521 96 -0.51 0.17 1000 -1000 -0.031 -1000
IL23-mediated signaling events 0.1306 35 2116 60 -0.28 0.036 1000 -1000 -0.003 -1000
Calcium signaling in the CD4+ TCR pathway 0.1269 34 1084 31 -0.31 0.021 1000 -1000 -0.032 -1000
Signaling events mediated by the Hedgehog family 0.1231 33 1718 52 -0.31 0.18 1000 -1000 -0.025 -1000
Glypican 1 network 0.1231 33 1586 48 -0.24 0.028 1000 -1000 -0.016 -1000
EPHB forward signaling 0.1231 33 2861 85 -0.15 0.15 1000 -1000 -0.066 -1000
Syndecan-1-mediated signaling events 0.1194 32 1111 34 -0.32 0.1 1000 -1000 -0.032 -1000
Noncanonical Wnt signaling pathway 0.1194 32 833 26 -0.16 0.036 1000 -1000 -0.037 -1000
LPA receptor mediated events 0.1157 31 3247 102 -0.29 0.058 1000 -1000 -0.057 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1119 30 2632 85 -0.4 0.027 1000 -1000 -0.034 -1000
ErbB2/ErbB3 signaling events 0.1082 29 1901 65 -0.24 0.091 1000 -1000 -0.04 -1000
Thromboxane A2 receptor signaling 0.1082 29 3055 105 -0.14 0.099 1000 -1000 -0.043 -1000
IL12-mediated signaling events 0.1045 28 2451 87 -0.61 0.031 1000 -1000 -0.069 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1045 28 2497 88 -0.22 0.031 1000 -1000 -0.057 -1000
S1P5 pathway 0.0970 26 454 17 -0.28 0.17 1000 -1000 -0.012 -1000
S1P1 pathway 0.0970 26 950 36 -0.37 0.16 1000 -1000 -0.026 -1000
Syndecan-4-mediated signaling events 0.0933 25 1695 67 -0.27 0.19 1000 -1000 -0.04 -1000
Glucocorticoid receptor regulatory network 0.0896 24 2773 114 -0.68 0.2 1000 -1000 -0.049 -1000
TCGA08_p53 0.0896 24 169 7 -0.085 0.033 1000 -1000 -0.005 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0858 23 1244 54 -0.22 0.057 1000 -1000 -0.04 -1000
amb2 Integrin signaling 0.0858 23 1955 82 -0.31 0.1 1000 -1000 -0.026 -1000
BCR signaling pathway 0.0858 23 2319 99 -0.24 0.022 1000 -1000 -0.056 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0784 21 2586 120 -0.43 0.11 1000 -1000 -0.048 -1000
TCR signaling in naïve CD8+ T cells 0.0746 20 1877 93 -0.19 0.084 1000 -1000 -0.039 -1000
Osteopontin-mediated events 0.0709 19 729 38 -0.29 0.095 1000 -1000 -0.022 -1000
FoxO family signaling 0.0672 18 1187 64 -0.22 0.35 1000 -1000 -0.018 -1000
S1P4 pathway 0.0672 18 465 25 -0.28 0.17 1000 -1000 -0.023 -1000
Arf6 signaling events 0.0634 17 1076 62 -0.32 0.099 1000 -1000 -0.028 -1000
BMP receptor signaling 0.0634 17 1386 81 -0.13 0.085 1000 -1000 -0.053 -1000
Coregulation of Androgen receptor activity 0.0597 16 1259 76 -0.18 0.23 1000 -1000 -0.011 -1000
Aurora C signaling 0.0597 16 117 7 0 0.16 1000 -1000 -0.012 -1000
Fc-epsilon receptor I signaling in mast cells 0.0597 16 1595 97 -0.29 0.032 1000 -1000 -0.05 -1000
Integrins in angiogenesis 0.0597 16 1344 84 -0.29 0.11 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 0.0597 16 278 17 -0.16 0.021 1000 -1000 -0.015 -1000
ErbB4 signaling events 0.0560 15 1065 69 -0.18 0.093 1000 -1000 -0.03 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0560 15 436 28 -0.28 0.17 1000 -1000 -0.015 -1000
PLK2 and PLK4 events 0.0560 15 45 3 0.022 0.077 1000 -1000 -0.01 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0560 15 1149 74 -0.32 0.099 1000 -1000 -0.064 -1000
S1P3 pathway 0.0560 15 667 42 -0.28 0.17 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 0.0560 15 540 34 -0.23 0.046 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 0.0560 15 701 44 -0.32 0.039 1000 -1000 -0.02 -1000
Nectin adhesion pathway 0.0522 14 905 63 -0.075 0.037 1000 -1000 -0.043 -1000
IL1-mediated signaling events 0.0522 14 901 62 -0.08 0.035 1000 -1000 -0.036 -1000
LPA4-mediated signaling events 0.0485 13 161 12 -0.15 0.02 1000 -1000 -0.018 -1000
FAS signaling pathway (CD95) 0.0485 13 641 47 -0.32 0.029 1000 -1000 -0.027 -1000
IL27-mediated signaling events 0.0485 13 673 51 -0.15 0.11 1000 -1000 -0.034 -1000
Regulation of Telomerase 0.0485 13 1345 102 -0.34 0.23 1000 -1000 -0.031 -1000
Visual signal transduction: Rods 0.0485 13 696 52 -0.15 0.054 1000 -1000 -0.028 -1000
Presenilin action in Notch and Wnt signaling 0.0448 12 773 61 -0.29 0.12 1000 -1000 -0.049 -1000
Regulation of nuclear SMAD2/3 signaling 0.0410 11 1555 136 -0.38 0.37 1000 -1000 -0.029 -1000
JNK signaling in the CD4+ TCR pathway 0.0410 11 189 17 -0.078 0.038 1000 -1000 -0.022 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0410 11 410 37 -0.22 0.048 1000 -1000 -0.022 -1000
Canonical Wnt signaling pathway 0.0410 11 596 51 -0.054 0.15 1000 -1000 -0.041 -1000
IL2 signaling events mediated by STAT5 0.0410 11 242 22 -0.03 0.18 1000 -1000 -0.022 -1000
Regulation of Androgen receptor activity 0.0410 11 807 70 -0.2 0.087 1000 -1000 -0.024 -1000
Syndecan-2-mediated signaling events 0.0373 10 709 69 -0.11 0.1 1000 -1000 -0.035 -1000
IL2 signaling events mediated by PI3K 0.0373 10 599 58 -0.038 0.16 1000 -1000 -0.019 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0336 9 325 34 -0.013 0.042 1000 -1000 -0.018 -1000
Aurora A signaling 0.0336 9 589 60 -0.009 0.22 1000 -1000 -0.007 -1000
Signaling events mediated by HDAC Class III 0.0336 9 371 40 -0.26 0.039 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 0.0336 9 393 43 -0.2 0.034 1000 -1000 -0.056 -1000
Syndecan-3-mediated signaling events 0.0336 9 338 35 -0.11 0.047 1000 -1000 -0.021 -1000
Effects of Botulinum toxin 0.0336 9 244 26 -0.071 0.034 1000 -1000 -0.013 -1000
Class IB PI3K non-lipid kinase events 0.0336 9 27 3 -0.003 -1000 1000 -1000 -0.01 -1000
Signaling events mediated by PTP1B 0.0299 8 661 76 -0.16 0.15 1000 -1000 -0.035 -1000
Ceramide signaling pathway 0.0299 8 681 76 -0.29 0.099 1000 -1000 -0.036 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0299 8 272 33 0 0.23 1000 -1000 -0.018 -1000
E-cadherin signaling events 0.0299 8 42 5 -0.017 0.022 1000 -1000 0.011 -1000
Caspase cascade in apoptosis 0.0261 7 538 74 -0.065 0.058 1000 -1000 -0.028 -1000
Insulin-mediated glucose transport 0.0261 7 233 32 -0.013 0.2 1000 -1000 -0.018 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0261 7 374 52 -0.071 0.053 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0261 7 325 45 -0.043 0.052 1000 -1000 -0.036 -1000
E-cadherin signaling in the nascent adherens junction 0.0261 7 554 76 -0.049 0.037 1000 -1000 -0.051 -1000
BARD1 signaling events 0.0224 6 387 57 -0.053 0.13 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 0.0224 6 242 39 -0.056 0.022 1000 -1000 -0.017 -1000
Hedgehog signaling events mediated by Gli proteins 0.0224 6 411 65 -0.28 0.17 1000 -1000 -0.036 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0224 6 503 83 -0.089 0.2 1000 -1000 -0.019 -1000
Regulation of p38-alpha and p38-beta 0.0224 6 340 54 -0.1 0.054 1000 -1000 -0.043 -1000
TCGA08_rtk_signaling 0.0224 6 160 26 -0.23 0.034 1000 -1000 -0.017 -1000
E-cadherin signaling in keratinocytes 0.0224 6 269 43 -0.061 0.023 1000 -1000 -0.027 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0224 6 535 78 -0.22 0.033 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class II 0.0187 5 381 75 -0.34 0.06 1000 -1000 -0.026 -1000
Signaling mediated by p38-gamma and p38-delta 0.0187 5 87 15 -0.004 0.074 1000 -1000 -0.018 -1000
EGFR-dependent Endothelin signaling events 0.0187 5 114 21 0 0.099 1000 -1000 -0.036 -1000
Rapid glucocorticoid signaling 0.0187 5 111 20 -0.009 0.075 1000 -1000 -0.003 -1000
Visual signal transduction: Cones 0.0149 4 159 38 -0.013 0.055 1000 -1000 -0.016 -1000
Arf6 downstream pathway 0.0149 4 214 43 -0.025 0.038 1000 -1000 -0.022 -1000
mTOR signaling pathway 0.0149 4 240 53 -0.14 0.034 1000 -1000 -0.036 -1000
Class I PI3K signaling events mediated by Akt 0.0149 4 301 68 -0.061 0.2 1000 -1000 -0.029 -1000
Retinoic acid receptors-mediated signaling 0.0149 4 280 58 -0.1 0.043 1000 -1000 -0.023 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0149 4 569 125 -0.019 0.048 1000 -1000 -0.045 -1000
Class I PI3K signaling events 0.0149 4 308 73 -0.1 0.042 1000 -1000 -0.026 -1000
PDGFR-beta signaling pathway 0.0149 4 466 97 -0.14 0.075 1000 -1000 -0.052 -1000
a4b1 and a4b7 Integrin signaling 0.0112 3 18 5 0.011 0.025 1000 -1000 0.004 -1000
IFN-gamma pathway 0.0112 3 255 68 -0.32 0.063 1000 -1000 -0.047 -1000
TRAIL signaling pathway 0.0112 3 166 48 -0.002 0.036 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0075 2 108 49 -0.007 0.031 1000 -1000 -0.036 -1000
Paxillin-dependent events mediated by a4b1 0.0075 2 97 36 -0.041 0.043 1000 -1000 -0.034 -1000
Arf6 trafficking events 0.0075 2 195 71 -0.038 0.039 1000 -1000 -0.02 -1000
Insulin Pathway 0.0075 2 162 74 -0.051 0.056 1000 -1000 -0.042 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0037 1 27 23 -0.01 0.041 1000 -1000 -0.012 -1000
Canonical NF-kappaB pathway 0.0037 1 60 39 -0.007 0.046 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class I 0.0037 1 163 104 -0.034 0.051 1000 -1000 -0.025 -1000
Atypical NF-kappaB pathway 0.0037 1 58 31 0 0.028 1000 -1000 -0.017 -1000
VEGFR1 specific signals 0.0037 1 85 56 -0.021 0.052 1000 -1000 -0.042 -1000
Arf1 pathway 0.0037 1 60 54 -0.032 0.031 1000 -1000 -0.013 -1000
Circadian rhythm pathway 0.0000 0 14 22 -0.007 0.047 1000 -1000 -0.026 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 0 0.053 1000 -1000 -0.032 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.059 1000 -1000 0 -1000
Total NA 2619 152175 7203 -25 -990 131000 -131000 -3.8 -131000
Glypican 2 network

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
MDK 0.19 0.16 0.35 138 -9999 0 138
GPC2 0.072 0.12 0.35 41 -9999 0 41
GPC2/Midkine 0.18 0.14 0.29 149 -9999 0 149
neuron projection morphogenesis 0.18 0.14 0.29 149 -9999 0 149
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.68 0.61 1.2 125 -0.84 3 128
PLK1 0.5 0.4 0.84 138 -0.71 2 140
BIRC5 0.52 0.38 0.85 135 -10000 0 135
HSPA1B 0.71 0.64 1.3 124 -0.91 1 125
MAP2K1 0.23 0.2 0.42 119 -10000 0 119
BRCA2 0.68 0.65 1.2 125 -1 6 131
FOXM1 0.92 0.87 1.7 134 -0.98 3 137
XRCC1 0.68 0.62 1.2 127 -0.84 3 130
FOXM1B/p19 0.12 0.39 0.99 24 -0.88 4 28
Cyclin D1/CDK4 0.43 0.55 1 93 -0.88 5 98
CDC2 0.79 0.72 1.4 132 -0.88 3 135
TGFA 0.41 0.66 1.1 105 -0.98 20 125
SKP2 0.69 0.62 1.2 125 -0.84 3 128
CCNE1 0.17 0.17 0.4 86 -10000 0 86
CKS1B 0.68 0.61 1.2 132 -0.81 4 136
RB1 0.3 0.44 0.85 90 -0.64 4 94
FOXM1C/SP1 0.52 0.56 1.1 108 -0.88 4 112
AURKB 0.4 0.45 0.84 111 -0.85 7 118
CENPF 0.86 0.75 1.5 140 -0.86 2 142
CDK4 0.089 0.073 0.27 1 -10000 0 1
MYC 0.32 0.55 1 81 -0.84 8 89
CHEK2 0.23 0.2 0.42 120 -10000 0 120
ONECUT1 0.47 0.6 1.1 105 -0.91 6 111
CDKN2A 0.021 0.21 0.32 60 -0.36 21 81
LAMA4 0.68 0.62 1.2 126 -0.84 3 129
FOXM1B/HNF6 0.48 0.62 1.1 100 -1 6 106
FOS 0.16 0.86 1.3 78 -1.2 38 116
SP1 0.004 0.071 -10000 0 -0.3 12 12
CDC25B 0.68 0.62 1.2 125 -0.91 1 126
response to radiation 0.14 0.12 0.26 112 -10000 0 112
CENPB 0.68 0.62 1.2 125 -0.84 3 128
CENPA 0.82 0.73 1.4 135 -0.91 1 136
NEK2 0.88 0.74 1.5 144 -0.8 2 146
HIST1H2BA 0.7 0.63 1.3 123 -0.91 1 124
CCNA2 0.21 0.19 0.41 125 -10000 0 125
EP300 0.021 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.76 0.7 1.4 127 -0.94 3 130
CCNB2 0.84 0.73 1.4 140 -0.86 2 142
CCNB1 0.85 0.78 1.5 134 -0.88 3 137
ETV5 0.68 0.61 1.2 122 -0.91 1 123
ESR1 0.023 0.7 1.2 46 -1.1 25 71
CCND1 0.53 0.61 1.1 109 -0.9 5 114
GSK3A 0.16 0.13 0.3 85 -10000 0 85
Cyclin A-E1/CDK1-2 0.3 0.25 0.54 131 -10000 0 131
CDK2 0.069 0.046 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.22 0.19 0.38 136 -10000 0 136
FOXM1B/Cbp/p300 0.035 0.26 -10000 0 -0.86 4 4
GAS1 0.5 0.77 1.2 116 -1.2 16 132
MMP2 0.66 0.66 1.2 123 -1.1 5 128
RB1/FOXM1C 0.45 0.57 1.1 98 -0.89 4 102
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.18 0.22 -10000 0 -0.39 129 129
ER alpha/Gai/GDP/Gbeta gamma -0.42 0.42 -10000 0 -0.82 119 119
AKT1 -0.5 0.47 -10000 0 -0.91 148 148
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.52 0.49 -10000 0 -0.93 148 148
mol:Ca2+ -0.16 0.25 -10000 0 -0.63 51 51
IGF1R 0.019 0.071 0.35 3 -0.69 2 5
E2/ER alpha (dimer)/Striatin -0.23 0.24 -10000 0 -0.45 142 142
SHC1 0.017 0.009 -10000 0 -10000 0 0
apoptosis 0.48 0.44 0.86 148 -10000 0 148
RhoA/GTP -0.16 0.18 -10000 0 -0.35 122 122
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.36 0.35 -10000 0 -0.65 142 142
regulation of stress fiber formation 0.14 0.15 0.29 120 -10000 0 120
E2/ERA-ERB (dimer) -0.21 0.24 0.22 2 -0.44 137 139
KRAS 0.021 0.003 -10000 0 -10000 0 0
G13/GTP -0.19 0.21 -10000 0 -0.4 136 136
pseudopodium formation -0.14 0.15 -10000 0 -0.29 120 120
E2/ER alpha (dimer)/PELP1 -0.22 0.23 -10000 0 -0.44 137 137
GRB2 0.021 0.005 -10000 0 -10000 0 0
GNG2 0.019 0.044 -10000 0 -0.69 1 1
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
HRAS 0.023 0.02 0.35 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.39 0.38 -10000 0 -0.69 147 147
E2/ER beta (dimer) 0.017 0.019 0.23 2 -10000 0 2
mol:GDP -0.25 0.25 -10000 0 -0.48 136 136
mol:NADP -0.39 0.38 -10000 0 -0.69 147 147
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
mol:IP3 -0.17 0.26 -10000 0 -0.66 51 51
IGF-1R heterotetramer 0.019 0.071 0.35 3 -0.69 2 5
PLCB1 -0.16 0.27 -10000 0 -0.7 48 48
PLCB2 -0.17 0.27 -10000 0 -0.69 51 51
IGF1 -0.29 0.35 -10000 0 -0.69 114 114
mol:L-citrulline -0.39 0.38 -10000 0 -0.69 147 147
RHOA 0.022 0.001 -10000 0 -10000 0 0
Gai/GDP -0.38 0.47 -10000 0 -0.86 122 122
JNK cascade 0.017 0.019 0.23 2 -10000 0 2
BCAR1 0.02 0.005 -10000 0 -10000 0 0
ESR2 0.023 0.029 0.35 2 -10000 0 2
GNAQ 0.02 0.025 -10000 0 -0.38 1 1
ESR1 -0.34 0.35 -10000 0 -0.67 137 137
Gq family/GDP/Gbeta gamma -0.093 0.22 -10000 0 -0.69 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.16 0.18 -10000 0 -0.4 41 41
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.34 0.33 -10000 0 -0.63 135 135
GNAZ 0.17 0.16 0.35 117 -10000 0 117
E2/ER alpha (dimer) -0.26 0.26 -10000 0 -0.5 137 137
STRN 0 0.12 -10000 0 -0.69 8 8
GNAL 0.075 0.12 0.35 43 -10000 0 43
PELP1 0.019 0.007 -10000 0 -10000 0 0
MAPK11 0.019 0.035 0.2 8 -10000 0 8
GNAI2 0.021 0.002 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.016 0.062 -10000 0 -0.69 2 2
HBEGF -0.35 0.35 0.38 1 -0.7 115 116
cAMP biosynthetic process -0.16 0.2 -10000 0 -0.35 129 129
SRC -0.39 0.39 -10000 0 -0.78 117 117
PI3K 0.028 0.06 -10000 0 -0.93 1 1
GNB1 0.02 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.21 0.24 -10000 0 -0.43 134 134
SOS1 0.022 0.001 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.36 0.29 -10000 0 -0.59 151 151
Gs family/GTP -0.16 0.21 -10000 0 -0.36 129 129
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.04 0.015 -10000 0 -10000 0 0
vasodilation -0.36 0.35 -10000 0 -0.64 147 147
mol:DAG -0.17 0.26 -10000 0 -0.66 51 51
Gs family/GDP/Gbeta gamma -0.19 0.22 -10000 0 -0.4 127 127
MSN -0.15 0.16 -10000 0 -0.31 120 120
Gq family/GTP -0.18 0.28 -10000 0 -0.74 48 48
mol:PI-3-4-5-P3 -0.49 0.46 -10000 0 -0.88 148 148
NRAS 0.021 0.003 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.36 0.35 0.64 147 -10000 0 147
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP -0.23 0.24 -10000 0 -0.46 136 136
NOS3 -0.42 0.41 -10000 0 -0.74 147 147
GNA11 0.008 0.097 -10000 0 -0.69 5 5
MAPKKK cascade -0.39 0.37 -10000 0 -0.7 150 150
E2/ER alpha (dimer)/PELP1/Src -0.38 0.37 -10000 0 -0.69 142 142
ruffle organization -0.14 0.15 -10000 0 -0.29 120 120
ROCK2 -0.16 0.18 -10000 0 -0.34 126 126
GNA14 -0.098 0.26 -10000 0 -0.67 45 45
GNA15 0.024 0.029 0.35 2 -10000 0 2
GNA13 0.021 0.004 -10000 0 -10000 0 0
MMP9 -0.36 0.36 -10000 0 -0.72 114 114
MMP2 -0.37 0.36 -10000 0 -0.72 119 119
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.067 0.071 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.21 0.18 -10000 0 -0.37 126 126
JUN -0.23 0.23 -10000 0 -0.54 62 62
HRAS 0.023 0.02 0.35 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 -0.3 0.31 -10000 0 -0.5 166 166
RAP1A 0.021 0.004 -10000 0 -10000 0 0
FRS2 0.021 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.3 0.31 -10000 0 -0.51 166 166
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.093 0.21 -10000 0 -0.4 79 79
RHOA 0.022 0.001 -10000 0 -10000 0 0
RAP1A/GTP -0.27 0.28 -10000 0 -0.46 162 162
GRB7 0.019 0.088 0.35 5 -0.69 3 8
RET51/GFRalpha1/GDNF -0.3 0.3 -10000 0 -0.51 166 166
MAPKKK cascade -0.26 0.26 -10000 0 -0.46 151 151
BCAR1 0.02 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.096 0.21 -10000 0 -0.4 82 82
lamellipodium assembly -0.18 0.17 -10000 0 -0.38 82 82
RET51/GFRalpha1/GDNF/SHC -0.28 0.3 -10000 0 -0.48 161 161
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
RET9/GFRalpha1/GDNF/SHC -0.094 0.2 -10000 0 -0.38 79 79
RET9/GFRalpha1/GDNF/Shank3 -0.096 0.21 -10000 0 -0.41 76 76
MAPK3 -0.27 0.25 -10000 0 -0.45 157 157
DOK1 0.022 0 -10000 0 -10000 0 0
DOK6 -0.075 0.25 0.35 3 -0.69 37 40
PXN 0.021 0.002 -10000 0 -10000 0 0
neurite development -0.28 0.25 -10000 0 -0.45 152 152
DOK5 0.023 0.095 0.35 8 -0.69 3 11
GFRA1 -0.2 0.32 -10000 0 -0.67 83 83
MAPK8 -0.24 0.23 -10000 0 -0.38 163 163
HRAS/GTP -0.3 0.3 -10000 0 -0.5 164 164
tube development -0.084 0.2 -10000 0 -0.39 71 71
MAPK1 -0.27 0.25 -10000 0 -0.44 160 160
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.073 0.15 -10000 0 -0.3 68 68
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
SRC 0.023 0.02 0.35 1 -10000 0 1
PDLIM7 0.024 0.029 0.35 2 -10000 0 2
RET51/GFRalpha1/GDNF/Dok6 -0.33 0.34 -10000 0 -0.54 172 172
SHC1 0.017 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.3 0.31 -10000 0 -0.51 166 166
RET51/GFRalpha1/GDNF/Dok5 -0.3 0.31 -10000 0 -0.5 168 168
PRKCA 0.021 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.017 0.013 0.23 1 -10000 0 1
CREB1 -0.16 0.21 -10000 0 -0.46 77 77
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.075 0.15 -10000 0 -0.32 58 58
RET51/GFRalpha1/GDNF/Grb7 -0.3 0.31 -10000 0 -0.5 168 168
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.33 0.36 0.35 2 -0.68 130 132
DOK4 0.021 0.005 -10000 0 -10000 0 0
JNK cascade -0.23 0.22 -10000 0 -0.53 60 60
RET9/GFRalpha1/GDNF/FRS2 -0.095 0.21 -10000 0 -0.41 79 79
SHANK3 0.022 0.021 0.35 1 -10000 0 1
RASA1 0.016 0.062 -10000 0 -0.69 2 2
NCK1 0.019 0.044 -10000 0 -0.69 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.074 0.14 -10000 0 -0.31 58 58
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.22 0.22 -10000 0 -0.38 154 154
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.23 0.23 -10000 0 -0.39 161 161
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.25 0.29 -10000 0 -0.48 129 129
PI3K -0.27 0.28 -10000 0 -0.6 83 83
SOS1 0.022 0.001 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.081 0.2 -10000 0 -0.39 71 71
GRB10 0.021 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.17 0.18 -10000 0 -0.4 78 78
RET51/GFRalpha1/GDNF/FRS2 -0.3 0.31 -10000 0 -0.5 166 166
GAB1 0.021 0.005 -10000 0 -10000 0 0
IRS1 0.021 0.002 -10000 0 -10000 0 0
IRS2 0.007 0.097 -10000 0 -0.69 5 5
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.26 0.29 -10000 0 -0.48 133 133
RET51/GFRalpha1/GDNF/PKC alpha -0.29 0.3 -10000 0 -0.5 166 166
GRB2 0.021 0.005 -10000 0 -10000 0 0
PRKACA 0.021 0.003 -10000 0 -10000 0 0
GDNF 0.03 0.063 0.35 10 -10000 0 10
RAC1 0.021 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.3 0.31 -10000 0 -0.51 166 166
Rac1/GTP -0.21 0.22 -10000 0 -0.47 77 77
RET9/GFRalpha1/GDNF -0.12 0.22 0.22 6 -0.44 82 88
GFRalpha1/GDNF -0.13 0.26 0.25 6 -0.5 82 88
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.26 0.34 -9999 0 -0.7 96 96
PDGF/PDGFRA/CRKL -0.18 0.26 -9999 0 -0.52 94 94
positive regulation of JUN kinase activity -0.1 0.19 -9999 0 -0.42 60 60
CRKL 0.021 0.003 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.19 0.26 -9999 0 -0.52 96 96
AP1 -0.59 0.59 -9999 0 -1.2 118 118
mol:IP3 -0.21 0.26 -9999 0 -0.54 96 96
PLCG1 -0.21 0.26 -9999 0 -0.54 96 96
PDGF/PDGFRA/alphaV Integrin -0.18 0.26 -9999 0 -0.51 96 96
RAPGEF1 0.021 0.003 -9999 0 -10000 0 0
CRK 0.019 0.007 -9999 0 -10000 0 0
mol:Ca2+ -0.2 0.26 -9999 0 -0.54 96 96
CAV3 0.015 0.003 -9999 0 -10000 0 0
CAV1 0.021 0.005 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.1 0.2 -9999 0 -0.42 60 60
PDGF/PDGFRA/Shf -0.21 0.28 -9999 0 -0.54 107 107
FOS -0.58 0.57 -9999 0 -1.2 118 118
JUN -0.056 0.077 -9999 0 -0.55 5 5
oligodendrocyte development -0.18 0.26 -9999 0 -0.51 96 96
GRB2 0.021 0.005 -9999 0 -10000 0 0
PIK3R1 0.019 0.044 -9999 0 -0.69 1 1
mol:DAG -0.21 0.26 -9999 0 -0.54 96 96
PDGF/PDGFRA -0.26 0.34 -9999 0 -0.7 96 96
actin cytoskeleton reorganization -0.18 0.26 -9999 0 -0.52 97 97
SRF 0.023 0.013 -9999 0 -10000 0 0
SHC1 0.017 0.009 -9999 0 -10000 0 0
PI3K -0.14 0.24 -9999 0 -0.46 90 90
PDGF/PDGFRA/Crk/C3G -0.14 0.23 -9999 0 -0.45 90 90
JAK1 -0.19 0.25 -9999 0 -0.52 95 95
ELK1/SRF -0.15 0.2 -9999 0 -0.42 87 87
SHB 0.019 0.044 -9999 0 -0.69 1 1
SHF -0.026 0.18 -9999 0 -0.67 18 18
CSNK2A1 0.045 0.023 -9999 0 -10000 0 0
GO:0007205 -0.22 0.27 -9999 0 -0.56 96 96
SOS1 0.022 0.001 -9999 0 -10000 0 0
Ras protein signal transduction -0.1 0.19 -9999 0 -0.42 60 60
PDGF/PDGFRA/SHB -0.18 0.26 -9999 0 -0.52 97 97
PDGF/PDGFRA/Caveolin-1 -0.18 0.25 -9999 0 -0.5 96 96
ITGAV 0.021 0.003 -9999 0 -10000 0 0
ELK1 -0.21 0.24 -9999 0 -0.52 94 94
PIK3CA 0.019 0.044 -9999 0 -0.69 1 1
PDGF/PDGFRA/Crk -0.18 0.26 -9999 0 -0.51 96 96
JAK-STAT cascade -0.19 0.25 -9999 0 -0.51 95 95
cell proliferation -0.21 0.28 -9999 0 -0.54 107 107
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.41 0.58 -10000 0 -1.1 86 86
PCK1 -0.74 0.81 -10000 0 -1.6 121 121
HNF4A -0.48 0.71 -10000 0 -1.4 78 78
KCNJ11 -0.4 0.61 0.69 1 -1.2 76 77
AKT1 -0.16 0.22 -10000 0 -0.42 75 75
response to starvation -0.006 0.022 -10000 0 -10000 0 0
DLK1 -0.38 0.63 0.78 3 -1.2 76 79
NKX2-1 -0.12 0.23 0.5 4 -0.43 56 60
ACADM -0.42 0.6 -10000 0 -1.1 86 86
TAT -0.73 0.82 -10000 0 -1.6 115 115
CEBPB -0.001 0.038 -10000 0 -10000 0 0
CEBPA -0.007 0.088 0.35 1 -0.72 3 4
TTR -0.48 0.67 -10000 0 -1.4 85 85
PKLR -0.42 0.64 -10000 0 -1.2 79 79
APOA1 -0.56 0.79 -10000 0 -1.6 82 82
CPT1C -0.4 0.59 0.66 1 -1.1 83 84
ALAS1 -0.18 0.34 -10000 0 -1.6 7 7
TFRC -0.32 0.49 -10000 0 -1.1 45 45
FOXF1 -0.04 0.19 -10000 0 -0.66 23 23
NF1 0.02 0.034 -10000 0 -0.38 1 1
HNF1A (dimer) -0.002 0.13 -10000 0 -0.48 9 9
CPT1A -0.4 0.59 -10000 0 -1.1 87 87
HMGCS1 -0.4 0.59 -10000 0 -1.1 89 89
NR3C1 -0.072 0.11 -10000 0 -0.25 43 43
CPT1B -0.41 0.59 -10000 0 -1.1 85 85
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.032 0.073 -10000 0 -0.27 2 2
GCK -0.61 0.74 0.64 1 -1.3 132 133
CREB1 -0.055 0.1 -10000 0 -0.26 28 28
IGFBP1 -0.48 0.67 -10000 0 -1.5 68 68
PDX1 -0.2 0.48 0.62 1 -1.4 25 26
UCP2 -0.4 0.59 -10000 0 -1.1 88 88
ALDOB -0.54 0.75 -10000 0 -1.4 98 98
AFP -0.09 0.34 -10000 0 -0.96 24 24
BDH1 -0.43 0.64 -10000 0 -1.2 90 90
HADH -0.4 0.6 -10000 0 -1.1 83 83
F2 -0.49 0.72 -10000 0 -1.5 73 73
HNF1A -0.002 0.13 -10000 0 -0.48 9 9
G6PC -0.32 0.58 -10000 0 -1.5 48 48
SLC2A2 -0.34 0.63 -10000 0 -1.5 46 46
INS 0.037 0.099 0.32 14 -10000 0 14
FOXA1 0 0.18 -10000 0 -0.66 9 9
FOXA3 -0.16 0.27 -10000 0 -0.62 47 47
FOXA2 -0.47 0.73 0.86 1 -1.3 92 93
ABCC8 -0.39 0.62 0.75 4 -1.2 76 80
ALB -0.23 0.49 -10000 0 -1.2 47 47
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.29 0.53 -10000 0 -1.1 79 79
MKNK1 0.021 0.004 -10000 0 -10000 0 0
MAPK14 -0.066 0.19 -10000 0 -0.38 62 62
ATF2/c-Jun -0.077 0.22 -10000 0 -0.56 23 23
MAPK11 -0.062 0.21 0.37 6 -0.38 69 75
MITF -0.075 0.22 0.35 1 -0.44 65 66
MAPKAPK5 -0.076 0.22 0.35 1 -0.43 65 66
KRT8 -0.082 0.22 0.35 1 -0.43 68 69
MAPKAPK3 0.022 0.001 -10000 0 -10000 0 0
MAPKAPK2 0.018 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.11 0.32 0.44 1 -0.62 63 64
CEBPB -0.078 0.22 0.35 1 -0.44 65 66
SLC9A1 -0.081 0.23 0.35 1 -0.44 66 67
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.079 0.24 0.36 2 -0.44 65 67
p38alpha-beta/MNK1 -0.083 0.27 0.37 1 -0.52 62 63
JUN -0.074 0.21 -10000 0 -0.55 23 23
PPARGC1A -0.14 0.31 0.35 1 -0.53 84 85
USF1 -0.071 0.21 0.36 3 -0.42 63 66
RAB5/GDP/GDI1 -0.062 0.16 -10000 0 -0.33 63 63
NOS2 -0.053 0.24 0.54 2 -0.56 21 23
DDIT3 -0.076 0.22 0.35 1 -0.43 65 66
RAB5A 0.022 0 -10000 0 -10000 0 0
HSPB1 -0.057 0.18 0.28 2 -0.36 58 60
p38alpha-beta/HBP1 -0.077 0.27 0.37 1 -0.52 58 59
CREB1 -0.097 0.25 0.34 1 -0.48 66 67
RAB5/GDP 0.016 0 -10000 0 -10000 0 0
EIF4E -0.092 0.23 0.34 1 -0.47 61 62
RPS6KA4 -0.078 0.22 0.35 1 -0.43 66 67
PLA2G4A -0.098 0.23 0.36 1 -0.47 65 66
GDI1 -0.076 0.22 0.35 2 -0.43 65 67
TP53 -0.11 0.29 0.36 1 -0.6 61 62
RPS6KA5 -0.089 0.25 0.35 1 -0.48 65 66
ESR1 -0.32 0.37 0.35 1 -0.56 150 151
HBP1 0.021 0.004 -10000 0 -10000 0 0
MEF2C -0.077 0.22 0.35 1 -0.43 65 66
MEF2A -0.077 0.22 0.35 1 -0.44 64 65
EIF4EBP1 -0.1 0.27 0.34 1 -0.52 66 67
KRT19 -0.22 0.37 0.36 3 -0.58 112 115
ELK4 -0.074 0.22 0.38 2 -0.42 64 66
ATF6 -0.072 0.21 0.36 3 -0.41 64 67
ATF1 -0.097 0.24 0.34 1 -0.48 66 67
p38alpha-beta/MAPKAPK2 -0.07 0.23 -10000 0 -0.46 60 60
p38alpha-beta/MAPKAPK3 -0.08 0.27 0.37 1 -0.52 62 63
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.005 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.09 0.2 -10000 0 -0.42 73 73
regulation of S phase of mitotic cell cycle -0.075 0.15 -10000 0 -0.31 73 73
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
HRAS 0.021 0.02 0.34 1 -10000 0 1
SHBG/T-DHT -0.16 0.22 -10000 0 -0.41 107 107
PELP1 0.018 0.007 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.18 -10000 0 -0.4 72 72
T-DHT/AR -0.14 0.24 -10000 0 -0.52 72 72
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.003 -10000 0 -0.007 80 80
GNAI2 0.021 0.002 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.015 0.062 -10000 0 -0.69 2 2
mol:GDP -0.15 0.24 -10000 0 -0.54 73 73
cell proliferation -0.25 0.26 -10000 0 -0.48 123 123
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
FOS -0.4 0.42 -10000 0 -0.86 118 118
mol:Ca2+ -0.039 0.052 -10000 0 -0.094 104 104
MAPK3 -0.2 0.22 -10000 0 -0.49 68 68
MAPK1 -0.12 0.14 -10000 0 -0.33 45 45
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
mol:IP3 -0.002 0.002 -10000 0 -0.004 112 112
cAMP biosynthetic process -0.14 0.2 -10000 0 -0.37 105 105
GNG2 0.019 0.044 -10000 0 -0.69 1 1
potassium channel inhibitor activity -0.002 0.002 -10000 0 -0.004 112 112
HRAS/GTP -0.11 0.19 -10000 0 -0.4 72 72
actin cytoskeleton reorganization 0.027 0.047 -10000 0 -0.71 1 1
SRC 0.021 0.02 0.34 1 -10000 0 1
voltage-gated calcium channel activity -0.002 0.002 -10000 0 -0.004 112 112
PI3K 0.026 0.054 -10000 0 -0.84 1 1
apoptosis 0.23 0.25 0.48 117 -10000 0 117
T-DHT/AR/PELP1 -0.11 0.21 -10000 0 -0.46 72 72
HRAS/GDP -0.14 0.24 -10000 0 -0.52 73 73
CREB1 -0.25 0.27 -10000 0 -0.52 117 117
RAC1-CDC42/GTP 0.035 0.049 -10000 0 -0.73 1 1
AR -0.18 0.32 -10000 0 -0.69 72 72
GNB1 0.02 0.006 -10000 0 -10000 0 0
RAF1 -0.13 0.18 -10000 0 -0.4 72 72
RAC1-CDC42/GDP -0.12 0.24 -10000 0 -0.5 73 73
T-DHT/AR/PELP1/Src -0.1 0.2 -10000 0 -0.42 72 72
MAP2K2 -0.14 0.17 -10000 0 -0.4 71 71
T-DHT/AR/PELP1/Src/PI3K -0.076 0.15 -10000 0 -0.31 73 73
GNAZ 0.17 0.16 0.35 117 -10000 0 117
SHBG -0.25 0.33 -10000 0 -0.64 107 107
Gi family/GNB1/GNG2/GDP -0.19 0.27 -10000 0 -0.52 88 88
mol:T-DHT 0 0.001 -10000 0 -0.005 7 7
RAC1 0.021 0.003 -10000 0 -10000 0 0
GNRH1 0.006 0.012 0.2 1 -10000 0 1
Gi family/GTP -0.14 0.22 -10000 0 -0.42 81 81
CDC42 0.021 0.004 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.44 0.7 0.89 3 -1.2 90 93
STAT6 (cleaved dimer) -0.54 0.68 -10000 0 -1.2 115 115
IGHG1 -0.12 0.28 0.58 6 -0.46 49 55
IGHG3 -0.43 0.66 0.76 2 -1.1 110 112
AKT1 -0.2 0.4 0.72 2 -0.76 58 60
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.35 0.68 2 -0.66 49 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.19 0.41 0.76 2 -0.78 45 47
THY1 -0.4 0.74 1 10 -1.2 88 98
MYB 0.054 0.1 0.35 27 -10000 0 27
HMGA1 0.036 0.071 0.35 13 -10000 0 13
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.29 0.56 0.82 5 -0.9 86 91
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.19 0.41 0.76 2 -0.78 46 48
SP1 0.035 0.04 -10000 0 -10000 0 0
INPP5D 0.019 0.044 -10000 0 -0.69 1 1
SOCS5 0.024 0.043 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.72 0.84 1 -1.3 99 100
SOCS1 -0.27 0.45 0.75 1 -0.77 87 88
SOCS3 -0.29 0.55 0.82 1 -1.1 57 58
FCER2 -0.38 0.64 1.1 3 -1.2 78 81
PARP14 0.021 0.045 -10000 0 -0.69 1 1
CCL17 -0.43 0.7 1.1 3 -1.3 88 91
GRB2 0.021 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.12 0.32 0.75 2 -0.64 28 30
T cell proliferation -0.47 0.72 0.96 1 -1.3 93 94
IL4R/JAK1 -0.45 0.69 0.78 1 -1.2 94 95
EGR2 -0.6 0.86 1.1 2 -1.6 103 105
JAK2 -0.004 0.075 -10000 0 -0.41 1 1
JAK3 0.015 0.058 0.39 2 -0.67 1 3
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
JAK1 0.01 0.038 -10000 0 -10000 0 0
COL1A2 -0.076 0.28 0.66 4 -1.2 3 7
CCL26 -0.42 0.71 1.1 6 -1.3 85 91
IL4R -0.47 0.77 1.1 4 -1.3 90 94
PTPN6 0.021 0.029 -10000 0 -10000 0 0
IL13RA2 -0.94 0.79 0.89 1 -1.4 178 179
IL13RA1 -0.003 0.071 -10000 0 -10000 0 0
IRF4 -0.31 0.67 0.83 3 -1.5 57 60
ARG1 -0.36 0.64 -10000 0 -1.5 59 59
CBL -0.27 0.5 0.75 3 -0.84 85 88
GTF3A 0.042 0.057 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
IL13RA1/JAK2 0.004 0.1 0.35 1 -0.27 1 2
IRF4/BCL6 -0.3 0.6 -10000 0 -1.4 57 57
CD40LG -0.018 0.16 0.44 2 -0.7 11 13
MAPK14 -0.29 0.55 0.82 2 -0.95 77 79
mitosis -0.19 0.38 0.71 2 -0.71 58 60
STAT6 -0.55 0.94 1.1 8 -1.5 99 107
SPI1 -0.018 0.1 -10000 0 -0.4 9 9
RPS6KB1 -0.18 0.36 0.68 2 -0.68 52 54
STAT6 (dimer) -0.55 0.96 1.1 8 -1.5 102 110
STAT6 (dimer)/PARP14 -0.5 0.77 0.85 2 -1.3 109 111
mast cell activation 0.005 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.42 0.76 2 -0.73 67 69
FRAP1 -0.2 0.4 0.72 2 -0.76 58 60
LTA -0.43 0.7 1.1 2 -1.3 84 86
FES 0.016 0.062 -10000 0 -0.69 2 2
T-helper 1 cell differentiation 0.5 0.85 1.4 103 -1.1 8 111
CCL11 -0.42 0.67 0.89 3 -1.2 89 92
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.19 0.4 0.76 2 -0.71 57 59
IL2RG 0.011 0.1 0.36 5 -0.68 4 9
IL10 -0.47 0.76 1.2 2 -1.3 94 96
IRS1 0.021 0.002 -10000 0 -10000 0 0
IRS2 0.007 0.097 -10000 0 -0.69 5 5
IL4 -0.051 0.24 0.74 4 -1.3 1 5
IL5 -0.44 0.7 0.9 2 -1.3 86 88
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.3 0.56 0.92 8 -0.92 89 97
COL1A1 -0.091 0.4 0.83 11 -1.2 13 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.72 -10000 0 -1.3 87 87
IL2R gamma/JAK3 0.017 0.1 0.32 5 -0.62 4 9
TFF3 -0.44 0.71 0.91 2 -1.3 91 93
ALOX15 -0.43 0.7 1.1 2 -1.3 86 88
MYBL1 0.022 0.036 0.35 3 -10000 0 3
T-helper 2 cell differentiation -0.35 0.58 0.87 3 -0.99 91 94
SHC1 0.017 0.009 -10000 0 -10000 0 0
CEBPB -0.014 0.081 -10000 0 -0.3 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.4 0.74 2 -0.76 45 47
mol:PI-3-4-5-P3 -0.2 0.4 0.72 2 -0.76 58 60
PI3K -0.22 0.43 0.85 1 -0.82 58 59
DOK2 0.012 0.056 -10000 0 -0.49 3 3
ETS1 0.017 0.039 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.11 0.3 0.72 2 -0.62 23 25
ITGB3 -0.47 0.73 0.91 2 -1.3 91 93
PIGR -0.56 0.78 1.6 1 -1.4 105 106
IGHE -0.004 0.088 0.21 6 -0.31 4 10
MAPKKK cascade -0.11 0.3 0.72 2 -0.6 23 25
BCL6 0.02 0.01 -10000 0 -10000 0 0
OPRM1 -0.44 0.69 0.9 2 -1.3 89 91
RETNLB -0.44 0.69 0.9 2 -1.3 88 90
SELP -0.6 0.84 1.2 2 -1.4 113 115
AICDA -0.43 0.66 0.93 1 -1.2 89 90
EPO 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
BCL2L1 -0.083 0.21 -10000 0 -0.47 1 1
CRKL -0.1 0.18 -10000 0 -0.35 88 88
mol:DAG -0.12 0.2 -10000 0 -0.4 82 82
HRAS -0.057 0.16 0.3 2 -10000 0 2
MAPK8 -0.13 0.2 -10000 0 -0.4 90 90
RAP1A -0.1 0.18 -10000 0 -0.34 87 87
GAB1 -0.1 0.18 -10000 0 -0.34 88 88
MAPK14 -0.12 0.19 -10000 0 -0.39 79 79
EPO -0.22 0.35 0.34 8 -0.69 91 99
PLCG1 -0.12 0.21 -10000 0 -0.41 82 82
EPOR/TRPC2/IP3 Receptors 0.001 0.033 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.16 0.27 -10000 0 -0.47 106 106
GAB1/SHC/GRB2/SOS1 -0.069 0.16 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.15 0.27 0.26 1 -0.52 91 92
IRS2 -0.11 0.18 -10000 0 -0.35 88 88
STAT1 -0.11 0.21 -10000 0 -0.41 82 82
STAT5B -0.12 0.21 -10000 0 -0.41 81 81
cell proliferation -0.11 0.2 0.35 2 -0.38 85 87
GAB1/SHIP/PIK3R1/SHP2/SHC -0.074 0.15 -10000 0 -10000 0 0
TEC -0.11 0.19 -10000 0 -0.36 91 91
SOCS3 -0.05 0.21 -10000 0 -0.69 26 26
STAT1 (dimer) -0.11 0.21 -10000 0 -0.4 82 82
JAK2 -0.001 0.039 -10000 0 -0.36 1 1
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
EPO/EPOR (dimer)/JAK2 -0.08 0.21 -10000 0 -0.36 88 88
EPO/EPOR -0.15 0.27 0.26 1 -0.52 91 92
LYN 0.019 0.008 -10000 0 -10000 0 0
TEC/VAV2 -0.097 0.19 -10000 0 -0.34 90 90
elevation of cytosolic calcium ion concentration 0.001 0.033 -10000 0 -10000 0 0
SHC1 0.017 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.12 0.23 -10000 0 -0.43 84 84
mol:IP3 -0.12 0.2 -10000 0 -0.4 82 82
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.087 0.18 -10000 0 -0.33 88 88
SH2B3 0 0.033 -10000 0 -10000 0 0
NFKB1 -0.12 0.19 -10000 0 -0.39 84 84
EPO/EPOR (dimer)/JAK2/SOCS3 -0.13 0.19 0.21 1 -0.35 106 107
PTPN6 -0.1 0.18 -10000 0 -0.36 88 88
TEC/VAV2/GRB2 -0.088 0.18 -10000 0 -0.34 86 86
EPOR 0.001 0.033 -10000 0 -10000 0 0
INPP5D 0.019 0.044 -10000 0 -0.69 1 1
mol:GDP -0.071 0.16 -10000 0 -10000 0 0
SOS1 0.022 0.001 -10000 0 -10000 0 0
PLCG2 0.007 0.097 -10000 0 -0.69 5 5
CRKL/CBL/C3G -0.08 0.18 -10000 0 -0.33 76 76
VAV2 -0.1 0.18 -10000 0 -0.34 88 88
CBL -0.1 0.18 -10000 0 -0.34 88 88
SHC/Grb2/SOS1 -0.078 0.16 -10000 0 -0.33 67 67
STAT5A -0.12 0.21 -10000 0 -0.41 81 81
GRB2 0.021 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.092 0.2 -10000 0 -0.37 81 81
LYN/PLCgamma2 0.016 0.076 -10000 0 -0.52 5 5
PTPN11 0.021 0.002 -10000 0 -10000 0 0
BTK -0.11 0.19 -10000 0 -0.35 90 90
BCL2 -0.083 0.21 -10000 0 -0.5 2 2
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.041 0.14 0.33 21 -0.68 5 26
NFATC2 -0.12 0.34 0.55 4 -0.69 57 61
NFATC3 -0.036 0.12 -10000 0 -0.31 16 16
CD40LG -0.46 0.6 0.69 5 -1.2 90 95
ITCH 0.022 0.043 -10000 0 -10000 0 0
CBLB 0.023 0.042 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.26 0.52 0.88 7 -1.1 56 63
JUNB -0.006 0.14 -10000 0 -0.69 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.05 -10000 0 -0.33 5 5
T cell anergy -0.002 0.086 -10000 0 -0.46 5 5
TLE4 -0.09 0.25 -10000 0 -0.56 45 45
Jun/NFAT1-c-4/p21SNFT -0.28 0.55 0.69 4 -1.1 77 81
AP-1/NFAT1-c-4 -0.57 0.82 0.89 5 -1.6 91 96
IKZF1 -0.096 0.28 0.72 1 -0.59 51 52
T-helper 2 cell differentiation -0.22 0.38 0.6 1 -0.88 51 52
AP-1/NFAT1 -0.26 0.38 0.54 5 -0.6 128 133
CALM1 0.025 0.031 -10000 0 -10000 0 0
EGR2 -0.46 0.79 -10000 0 -1.7 75 75
EGR3 -0.37 0.71 0.64 2 -1.5 66 68
NFAT1/FOXP3 -0.058 0.3 0.57 8 -0.56 52 60
EGR1 -0.2 0.33 -10000 0 -0.69 81 81
JUN 0.003 0.095 -10000 0 -0.63 5 5
EGR4 0.02 0.031 0.34 2 -10000 0 2
mol:Ca2+ 0.004 0.027 -10000 0 -10000 0 0
GBP3 -0.12 0.31 -10000 0 -0.65 54 54
FOSL1 -0.002 0.14 0.35 3 -0.69 10 13
NFAT1-c-4/MAF/IRF4 -0.32 0.57 0.74 2 -1.1 85 87
DGKA -0.083 0.25 0.58 2 -0.52 51 53
CREM 0.021 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.29 0.56 0.59 1 -1.1 77 78
CTLA4 -0.046 0.29 0.51 23 -0.6 34 57
NFAT1-c-4 (dimer)/EGR1 -0.41 0.64 -10000 0 -1.3 83 83
NFAT1-c-4 (dimer)/EGR4 -0.29 0.56 -10000 0 -1.1 77 77
FOS -0.29 0.35 -10000 0 -0.68 117 117
IFNG -0.15 0.33 0.58 6 -0.75 39 45
T cell activation -0.27 0.39 0.56 1 -0.86 67 68
MAF 0.018 0.044 -10000 0 -0.69 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.2 0.4 0.76 75 -10000 0 75
TNF -0.36 0.54 -10000 0 -1.1 86 86
FASLG -0.46 0.78 0.75 2 -1.5 82 84
TBX21 0.008 0.13 -10000 0 -0.69 8 8
BATF3 0.016 0.049 0.35 1 -0.69 1 2
PRKCQ 0.007 0.11 0.35 2 -0.65 7 9
PTPN1 -0.086 0.24 -10000 0 -0.54 44 44
NFAT1-c-4/ICER1 -0.29 0.55 -10000 0 -1.1 77 77
GATA3 -0.026 0.18 0.35 1 -0.69 18 19
T-helper 1 cell differentiation -0.14 0.32 0.58 6 -0.71 43 49
IL2RA -0.25 0.48 0.75 9 -0.92 65 74
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.086 0.24 -10000 0 -0.53 47 47
E2F1 0.22 0.16 0.35 153 -10000 0 153
PPARG 0.023 0.02 0.35 1 -10000 0 1
SLC3A2 -0.085 0.24 0.44 1 -0.57 36 37
IRF4 -0.085 0.27 0.35 7 -0.69 42 49
PTGS2 -0.51 0.64 0.63 4 -1.3 96 100
CSF2 -0.45 0.59 0.63 4 -1.2 91 95
JunB/Fra1/NFAT1-c-4 -0.29 0.57 0.72 1 -1.1 79 80
IL4 -0.23 0.4 0.6 1 -0.98 46 47
IL5 -0.46 0.58 0.63 4 -1.2 91 95
IL2 -0.28 0.4 -10000 0 -0.88 67 67
IL3 -0.064 0.1 -10000 0 -0.79 2 2
RNF128 0.013 0.11 -10000 0 -0.77 5 5
NFATC1 -0.2 0.4 -10000 0 -0.77 75 75
CDK4 0.21 0.29 0.68 50 -10000 0 50
PTPRK -0.083 0.24 -10000 0 -0.53 48 48
IL8 -0.5 0.63 0.68 4 -1.2 104 108
POU2F1 0.018 0.009 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.04 0.077 0.36 14 -10000 0 14
CDKN2C 0.011 0.095 0.34 19 -10000 0 19
CDKN2A 0.23 0.16 0.35 169 -10000 0 169
CCND2 -0.091 0.09 -10000 0 -0.24 42 42
RB1 0.1 0.097 0.28 39 -10000 0 39
CDK4 -0.099 0.094 -10000 0 -0.3 29 29
CDK6 -0.1 0.11 -10000 0 -0.31 39 39
G1/S progression -0.099 0.099 -10000 0 -0.28 39 39
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.16 0.14 0.31 104 -10000 0 104
STMN1 0.093 0.11 0.42 9 -10000 0 9
Aurora B/RasGAP/Survivin 0.21 0.18 0.42 107 -0.28 2 109
Chromosomal passenger complex/Cul3 protein complex 0.13 0.13 0.28 88 -0.24 5 93
BIRC5 0.23 0.16 0.36 161 -10000 0 161
DES 0.034 0.28 0.48 2 -0.58 31 33
Aurora C/Aurora B/INCENP 0.11 0.097 0.4 2 -10000 0 2
Aurora B/TACC1 0.089 0.094 0.23 4 -10000 0 4
Aurora B/PP2A 0.11 0.11 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.039 0.038 0.16 1 -10000 0 1
mitotic metaphase/anaphase transition -0.009 0.008 -10000 0 -10000 0 0
NDC80 0.21 0.19 0.41 110 -10000 0 110
Cul3 protein complex 0.031 0.072 -10000 0 -0.45 5 5
KIF2C 0.22 0.16 0.33 164 -10000 0 164
PEBP1 0.013 0.098 -10000 0 -0.69 5 5
KIF20A 0.24 0.15 0.34 180 -10000 0 180
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.12 0.26 2 -0.43 2 4
SEPT1 0.023 0.02 0.35 1 -10000 0 1
SMC2 0.023 0.02 0.35 1 -10000 0 1
SMC4 0.025 0.035 0.35 3 -10000 0 3
NSUN2/NPM1/Nucleolin 0.13 0.21 0.34 83 -0.43 15 98
PSMA3 0.021 0.003 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.007 -10000 0 -10000 0 0
H3F3B 0.08 0.083 0.29 4 -10000 0 4
AURKB 0.15 0.16 0.33 113 -10000 0 113
AURKC 0.021 0.004 -10000 0 -10000 0 0
CDCA8 0.18 0.17 0.36 121 -10000 0 121
cytokinesis 0.23 0.22 0.48 109 -10000 0 109
Aurora B/Septin1 0.24 0.24 0.5 107 -10000 0 107
AURKA 0.092 0.14 0.34 60 -10000 0 60
INCENP 0.033 0.03 0.36 2 -10000 0 2
KLHL13 0.008 0.097 -10000 0 -0.69 5 5
BUB1 0.24 0.15 0.34 177 -10000 0 177
hSgo1/Aurora B/Survivin 0.27 0.24 0.51 120 -10000 0 120
EVI5 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.28 0.22 0.49 120 -10000 0 120
SGOL1 0.16 0.16 0.35 108 -10000 0 108
CENPA 0.23 0.18 0.38 137 -10000 0 137
NCAPG 0.22 0.16 0.35 164 -10000 0 164
Aurora B/HC8 Proteasome 0.11 0.11 0.25 12 -10000 0 12
NCAPD2 0.026 0.04 0.35 4 -10000 0 4
Aurora B/PP1-gamma 0.11 0.11 0.26 1 -10000 0 1
RHOA 0.022 0.001 -10000 0 -10000 0 0
NCAPH 0.18 0.16 0.35 126 -10000 0 126
NPM1 0.1 0.13 0.28 22 -10000 0 22
RASA1 0.016 0.062 -10000 0 -0.69 2 2
KLHL9 0.018 0.036 -10000 0 -0.38 2 2
mitotic prometaphase 0.005 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.11 0.25 12 -10000 0 12
PPP1CC 0.021 0.002 -10000 0 -10000 0 0
Centraspindlin 0.31 0.24 0.53 133 -10000 0 133
RhoA/GDP 0.016 0.001 -10000 0 -10000 0 0
NSUN2 0.097 0.15 0.28 27 -0.81 1 28
MYLK 0.07 0.096 0.18 11 -0.31 5 16
KIF23 0.18 0.17 0.36 123 -10000 0 123
VIM 0.094 0.1 0.44 4 -10000 0 4
RACGAP1 0.078 0.12 0.36 36 -10000 0 36
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.094 0.15 0.28 24 -0.85 1 25
Chromosomal passenger complex 0.24 0.19 0.39 148 -10000 0 148
Chromosomal passenger complex/EVI5 0.25 0.22 0.49 114 -10000 0 114
TACC1 0.018 0.008 -10000 0 -10000 0 0
PPP2R5D 0.02 0.006 -10000 0 -10000 0 0
CUL3 0.021 0.002 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.21 0.44 0.82 1 -0.89 53 54
HDAC7 0.025 0.021 0.35 1 -10000 0 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.46 0.84 2 -0.86 80 82
SMAD4 0.022 0.003 -10000 0 -10000 0 0
ID2 -0.19 0.47 0.84 1 -0.95 47 48
AP1 -0.22 0.28 -10000 0 -0.52 117 117
ABCG2 -0.23 0.48 -10000 0 -0.96 57 57
HIF1A -0.014 0.1 0.4 1 -10000 0 1
TFF3 -0.17 0.49 0.95 3 -0.93 50 53
GATA2 0.019 0.069 0.35 2 -0.69 2 4
AKT1 -0.037 0.14 0.38 3 -0.25 28 31
response to hypoxia -0.049 0.14 0.35 3 -0.22 58 61
MCL1 -0.18 0.44 0.84 1 -0.92 46 47
NDRG1 -0.18 0.44 0.84 1 -0.89 50 51
SERPINE1 -0.28 0.53 0.84 1 -0.98 71 72
FECH -0.18 0.46 0.84 1 -0.92 48 49
FURIN -0.19 0.47 0.84 1 -0.94 49 50
NCOA2 -0.047 0.18 -10000 0 -0.69 19 19
EP300 -0.08 0.24 0.58 4 -0.35 85 89
HMOX1 -0.19 0.48 0.84 1 -0.94 52 53
BHLHE40 -0.19 0.47 0.84 1 -0.93 49 50
BHLHE41 -0.18 0.48 0.91 2 -0.94 50 52
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.014 0.11 -10000 0 -10000 0 0
ENG 0.038 0.12 -10000 0 -10000 0 0
JUN 0.009 0.09 -10000 0 -0.63 5 5
RORA -0.19 0.46 0.84 1 -0.9 53 54
ABCB1 -0.21 0.42 -10000 0 -1.2 37 37
TFRC -0.18 0.46 0.84 1 -0.92 48 49
CXCR4 -0.18 0.47 0.84 1 -0.93 49 50
TF -0.22 0.49 0.84 1 -0.95 57 58
CITED2 -0.19 0.46 0.84 1 -0.94 48 49
HIF1A/ARNT -0.24 0.5 0.9 3 -1.1 44 47
LDHA -0.051 0.084 -10000 0 -0.65 3 3
ETS1 -0.18 0.46 0.84 1 -0.92 48 49
PGK1 -0.18 0.46 0.84 1 -0.92 49 50
NOS2 -0.16 0.48 0.88 3 -0.93 47 50
ITGB2 -0.18 0.47 0.84 1 -0.93 49 50
ALDOA -0.18 0.47 0.84 1 -0.92 49 50
Cbp/p300/CITED2 -0.32 0.56 0.98 1 -1 73 74
FOS -0.29 0.35 -10000 0 -0.67 117 117
HK2 -0.16 0.49 0.92 3 -0.93 49 52
SP1 0.007 0.052 -10000 0 -10000 0 0
GCK -0.53 0.79 0.89 3 -1.4 111 114
HK1 -0.18 0.46 0.84 1 -0.92 48 49
NPM1 -0.18 0.46 0.84 1 -0.92 48 49
EGLN1 -0.18 0.44 0.84 1 -0.9 47 48
CREB1 0.026 0.003 -10000 0 -10000 0 0
PGM1 -0.18 0.47 0.84 1 -0.94 48 49
SMAD3 0.022 0.004 -10000 0 -10000 0 0
EDN1 -0.23 0.34 -10000 0 -0.76 43 43
IGFBP1 -0.27 0.51 0.84 1 -1 64 65
VEGFA -0.2 0.41 0.94 1 -0.73 68 69
HIF1A/JAB1 -0.004 0.082 0.39 1 -10000 0 1
CP -0.23 0.52 0.84 1 -1 62 63
CXCL12 -0.33 0.52 -10000 0 -0.98 79 79
COPS5 0.004 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 0.032 0.008 -10000 0 -10000 0 0
BNIP3 -0.18 0.46 0.84 1 -0.92 48 49
EGLN3 -0.16 0.51 0.92 5 -0.95 50 55
CA9 -0.24 0.56 0.85 6 -0.98 68 74
TERT -0.11 0.51 0.89 7 -0.92 46 53
ENO1 -0.18 0.46 0.84 1 -0.92 49 50
PFKL -0.18 0.46 0.84 1 -0.92 49 50
NCOA1 0.016 0.018 -10000 0 -10000 0 0
ADM -0.18 0.46 0.84 1 -0.91 50 51
ARNT -0.001 0.082 -10000 0 -10000 0 0
HNF4A -0.033 0.13 -10000 0 -0.66 7 7
ADFP -0.21 0.44 0.82 1 -0.89 53 54
SLC2A1 -0.2 0.43 0.97 2 -0.75 65 67
LEP -0.18 0.47 0.92 5 -0.92 49 54
HIF1A/ARNT/Cbp/p300 -0.3 0.47 0.8 1 -0.87 78 79
EPO -0.46 0.61 0.93 4 -1.1 108 112
CREBBP -0.083 0.24 0.58 4 -0.36 84 88
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.46 0.77 1 -0.86 71 72
PFKFB3 -0.18 0.46 0.84 1 -0.92 49 50
NT5E -0.19 0.48 0.84 1 -0.94 52 53
p75(NTR)-mediated signaling

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.036 0.053 -10000 0 -0.52 1 1
Necdin/E2F1 0.15 0.13 0.49 5 -0.45 3 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.13 0.26 -10000 0 -0.44 97 97
NGF (dimer)/p75(NTR)/BEX1 -0.29 0.35 -10000 0 -0.57 147 147
NT-4/5 (dimer)/p75(NTR) -0.17 0.27 -10000 0 -0.52 96 96
IKBKB 0.019 0.007 -10000 0 -10000 0 0
AKT1 -0.15 0.22 -10000 0 -0.42 96 96
IKBKG 0.021 0.003 -10000 0 -10000 0 0
BDNF 0.034 0.063 0.35 10 -10000 0 10
MGDIs/NGR/p75(NTR)/LINGO1 -0.11 0.26 -10000 0 -0.45 96 96
FURIN 0.011 0.079 -10000 0 -0.61 4 4
proBDNF (dimer)/p75(NTR)/Sortilin -0.13 0.24 0.44 1 -0.44 96 97
LINGO1 0.072 0.12 0.35 41 -10000 0 41
Sortilin/TRAF6/NRIF 0.022 0.023 -10000 0 -10000 0 0
proBDNF (dimer) 0.034 0.063 0.35 10 -10000 0 10
NTRK1 0.018 0.03 0.35 2 -10000 0 2
RTN4R 0.016 0.062 -10000 0 -0.69 2 2
neuron apoptosis -0.092 0.24 0.47 1 -0.5 43 44
IRAK1 0.021 0.003 -10000 0 -10000 0 0
SHC1 -0.16 0.23 -10000 0 -0.44 96 96
ARHGDIA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.001 -10000 0 -10000 0 0
Gamma Secretase 0.047 0.029 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.13 0.26 -10000 0 -0.45 97 97
MAGEH1 0.016 0.062 -10000 0 -0.69 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.13 0.26 0.42 1 -0.45 96 97
Mammalian IAPs/DIABLO 0.058 0.046 -10000 0 -0.42 1 1
proNGF (dimer) -0.009 0.14 -10000 0 -0.69 11 11
MAGED1 0.019 0.044 -10000 0 -0.69 1 1
APP 0.013 0.075 -10000 0 -0.69 3 3
NT-4/5 (dimer) 0.019 0.036 0.35 3 -10000 0 3
ZNF274 0.021 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.13 0.22 -10000 0 -0.42 92 92
NGF -0.009 0.14 -10000 0 -0.69 11 11
cell cycle arrest -0.12 0.23 0.37 2 -0.4 96 98
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.1 0.17 -10000 0 -0.34 77 77
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.14 0.24 -10000 0 -0.46 96 96
NCSTN 0.017 0.009 -10000 0 -10000 0 0
mol:GTP -0.16 0.26 -10000 0 -0.48 98 98
PSENEN 0.021 0.003 -10000 0 -10000 0 0
mol:ceramide -0.15 0.23 -10000 0 -0.44 96 96
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.098 0.17 -10000 0 -0.5 23 23
p75(NTR)/beta APP -0.18 0.27 -10000 0 -0.52 98 98
BEX1 -0.19 0.36 0.35 19 -0.69 86 105
mol:GDP -0.18 0.24 -10000 0 -0.48 99 99
NGF (dimer) -0.14 0.26 -10000 0 -0.44 101 101
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.092 0.25 -10000 0 -0.41 91 91
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
RAC1/GTP -0.13 0.23 -10000 0 -0.41 99 99
MYD88 0.022 0 -10000 0 -10000 0 0
CHUK 0.021 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.16 0.26 -10000 0 -0.48 98 98
RHOB -0.017 0.16 -10000 0 -0.69 14 14
RHOA 0.022 0.001 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.16 0.11 -10000 0 -10000 0 0
NT3 (dimer) -0.34 0.35 -10000 0 -0.67 138 138
TP53 -0.12 0.19 0.45 1 -0.37 88 89
PRDM4 -0.15 0.23 -10000 0 -0.44 96 96
BDNF (dimer) -0.1 0.25 0.47 4 -0.41 92 96
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
SORT1 0.032 0.06 0.35 9 -10000 0 9
activation of caspase activity -0.13 0.26 -10000 0 -0.44 97 97
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.13 0.26 -10000 0 -0.45 96 96
RHOC 0.021 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.002 -10000 0 -10000 0 0
MAPK10 -0.15 0.23 0.39 1 -0.45 85 86
DIABLO 0.021 0.002 -10000 0 -10000 0 0
SMPD2 -0.15 0.23 -10000 0 -0.44 96 96
APH1B 0.021 0.003 -10000 0 -10000 0 0
APH1A 0.017 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.15 0.27 -10000 0 -0.48 97 97
PSEN1 0.021 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.41 0.4 -10000 0 -0.71 157 157
MAPK8 -0.14 0.22 0.39 1 -0.42 87 88
MAPK9 -0.13 0.22 0.39 1 -0.41 85 86
APAF1 0.021 0.002 -10000 0 -10000 0 0
NTF3 -0.34 0.35 -10000 0 -0.67 138 138
NTF4 0.019 0.036 0.35 3 -10000 0 3
NDN 0.022 0.093 0.35 7 -0.69 3 10
RAC1/GDP 0.016 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.13 0.25 -10000 0 -0.43 99 99
p75 CTF/Sortilin/TRAF6/NRIF 0.055 0.048 -10000 0 -0.42 1 1
RhoA-B-C/GTP -0.15 0.26 -10000 0 -0.48 98 98
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.095 0.22 0.41 1 -0.39 92 93
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.11 0.24 0.38 2 -0.41 94 96
PRKACB 0.019 0.025 -10000 0 -0.38 1 1
proBDNF (dimer)/p75 ECD 0.039 0.04 0.25 9 -10000 0 9
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.029 0.074 0.35 9 -0.69 1 10
BIRC2 0.021 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.11 0.25 0.28 2 -0.41 94 96
BAD -0.14 0.22 0.39 1 -0.42 87 88
RIPK2 0.017 0.009 -10000 0 -10000 0 0
NGFR -0.24 0.34 -10000 0 -0.69 96 96
CYCS -0.14 0.22 -10000 0 -0.42 94 94
ADAM17 0.021 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.13 0.23 -10000 0 -0.45 78 78
BCL2L11 -0.14 0.22 0.39 1 -0.42 87 88
BDNF (dimer)/p75(NTR) -0.16 0.27 0.25 7 -0.52 96 103
PI3K -0.14 0.25 -10000 0 -0.45 97 97
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.13 0.25 -10000 0 -0.44 96 96
NDNL2 0.021 0.003 -10000 0 -10000 0 0
YWHAE 0.019 0.007 -10000 0 -10000 0 0
PRKCI 0.021 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.19 0.29 -10000 0 -0.55 99 99
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.13 0.25 -10000 0 -0.44 97 97
TRAF6 0.019 0.044 -10000 0 -0.69 1 1
RAC1 0.021 0.003 -10000 0 -10000 0 0
PRKCZ -0.009 0.14 -10000 0 -0.66 11 11
PLG -0.1 0.27 -10000 0 -0.66 48 48
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.15 0.24 0.29 1 -0.45 96 97
SQSTM1 0.022 0.021 0.35 1 -10000 0 1
NGFRAP1 -0.005 0.14 -10000 0 -0.69 10 10
CASP3 -0.14 0.21 0.38 1 -0.4 88 89
E2F1 0.21 0.16 0.35 153 -10000 0 153
CASP9 0.021 0.004 -10000 0 -10000 0 0
IKK complex -0.059 0.17 -10000 0 -0.49 20 20
NGF (dimer)/TRKA 0.005 0.1 -10000 0 -0.46 11 11
MMP7 -0.099 0.32 0.35 26 -0.67 58 84
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.12 0.25 -10000 0 -0.43 94 94
MMP3 0.039 0.082 0.35 17 -10000 0 17
APAF-1/Caspase 9 -0.11 0.17 -10000 0 -0.57 8 8
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.067 0.07 -10000 0 -0.15 107 107
BUB1B 0.12 0.092 0.2 133 -10000 0 133
PLK1 0.059 0.043 0.12 55 -10000 0 55
PLK1S1 0.035 0.03 0.15 3 -0.16 2 5
KIF2A 0.051 0.037 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.059 0.043 0.12 55 -10000 0 55
GOLGA2 0.021 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.28 0.19 0.39 178 -10000 0 178
WEE1 0.067 0.061 -10000 0 -0.54 1 1
cytokinesis 0.18 0.12 0.27 151 -10000 0 151
PP2A-alpha B56 0.15 0.12 -10000 0 -0.48 2 2
AURKA 0.062 0.061 0.16 61 -0.2 1 62
PICH/PLK1 0.14 0.13 0.33 75 -10000 0 75
CENPE 0.097 0.083 0.19 93 -10000 0 93
RhoA/GTP 0.016 0.001 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.051 0.037 -10000 0 -10000 0 0
PPP2CA 0.021 0.003 -10000 0 -10000 0 0
FZR1 0.021 0.003 -10000 0 -10000 0 0
TPX2 0.05 0.051 0.17 33 -10000 0 33
PAK1 0.02 0.003 -10000 0 -10000 0 0
SPC24 0.16 0.16 0.35 114 -10000 0 114
FBXW11 0.021 0.003 -10000 0 -10000 0 0
CLSPN 0.075 0.094 0.19 90 -0.21 8 98
GORASP1 0.022 0 -10000 0 -10000 0 0
metaphase 0 0.002 0.024 1 -0.012 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.029 0.021 0.055 55 -10000 0 55
G2 phase of mitotic cell cycle 0 0.003 0.015 3 -10000 0 3
STAG2 0.021 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.031 0.016 -10000 0 -10000 0 0
spindle elongation 0.059 0.043 0.12 55 -10000 0 55
ODF2 0.022 0.004 -10000 0 -10000 0 0
BUB1 0.16 0.12 0.46 1 -0.52 2 3
TPT1 0.021 0.051 -10000 0 -0.14 20 20
CDC25C 0.15 0.083 0.2 190 -10000 0 190
CDC25B 0.029 0.022 0.36 1 -10000 0 1
SGOL1 0.067 0.07 0.15 107 -10000 0 107
RHOA 0.022 0.001 -10000 0 -10000 0 0
CCNB1/CDK1 0.12 0.1 0.42 1 -0.3 1 2
CDC14B -0.01 0.092 -10000 0 -0.53 8 8
CDC20 0.24 0.16 0.35 176 -10000 0 176
PLK1/PBIP1 0.026 0.06 0.2 28 -10000 0 28
mitosis -0.001 0.004 0.026 2 -10000 0 2
FBXO5 0.045 0.039 -10000 0 -10000 0 0
CDC2 0.007 0.006 0.014 115 -10000 0 115
NDC80 0.24 0.16 0.35 172 -10000 0 172
metaphase plate congression 0.036 0.053 -10000 0 -0.23 6 6
ERCC6L 0.14 0.13 0.32 70 -0.29 1 71
NLP/gamma Tubulin 0.033 0.024 0.079 8 -10000 0 8
microtubule cytoskeleton organization 0.021 0.051 -10000 0 -0.14 20 20
G2/M transition DNA damage checkpoint -0.002 0.002 0.012 2 -10000 0 2
PPP1R12A 0.022 0.002 -10000 0 -10000 0 0
interphase -0.002 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 0.29 0.2 0.42 174 -10000 0 174
GRASP65/GM130/RAB1/GTP/PLK1 0.073 0.03 -10000 0 -10000 0 0
RAB1A 0.021 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.044 0.037 0.1 54 -10000 0 54
mitotic prometaphase 0.002 0.004 0.022 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.079 0.06 -10000 0 -10000 0 0
microtubule-based process 0.21 0.12 0.29 180 -10000 0 180
Golgi organization 0.059 0.043 0.12 55 -10000 0 55
Cohesin/SA2 0.059 0.033 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.032 0.005 -10000 0 -10000 0 0
KIF20A 0.25 0.15 0.35 180 -10000 0 180
APC/C/CDC20 0.2 0.13 0.29 176 -10000 0 176
PPP2R1A 0.021 0.004 -10000 0 -10000 0 0
chromosome segregation 0.026 0.059 0.19 28 -10000 0 28
PRC1 0.18 0.16 0.35 127 -10000 0 127
ECT2 0.079 0.073 0.19 65 -10000 0 65
C13orf34 0.046 0.035 0.098 55 -10000 0 55
NUDC 0.036 0.053 -10000 0 -0.23 6 6
regulation of attachment of spindle microtubules to kinetochore 0.12 0.092 0.2 133 -10000 0 133
spindle assembly 0.046 0.033 0.09 51 -10000 0 51
spindle stabilization 0.035 0.03 0.15 3 -0.16 2 5
APC/C/HCDH1 0.006 0.082 -10000 0 -0.45 8 8
MKLP2/PLK1 0.21 0.12 0.29 180 -10000 0 180
CCNB1 0.17 0.16 0.35 118 -10000 0 118
PPP1CB 0.022 0.002 -10000 0 -10000 0 0
BTRC 0.021 0.004 -10000 0 -10000 0 0
ROCK2 0.039 0.082 -10000 0 -0.42 7 7
TUBG1 0.034 0.026 -10000 0 -0.14 2 2
G2/M transition of mitotic cell cycle 0.083 0.076 0.29 1 -0.3 1 2
MLF1IP 0.029 0.064 0.21 29 -10000 0 29
INCENP 0.024 0.028 0.34 2 -10000 0 2
Reelin signaling pathway

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
CDK5R1/CDK5 0.031 0.016 0.25 1 -10000 0 1
VLDLR 0.009 0.21 0.35 30 -0.66 19 49
CRKL 0.021 0.003 -10000 0 -10000 0 0
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
FYN 0.021 0.005 -10000 0 -10000 0 0
ITGA3 0.051 0.094 0.35 24 -10000 0 24
RELN/VLDLR/Fyn -0.13 0.28 -10000 0 -0.47 97 97
MAPK8IP1/MKK7/MAP3K11/JNK1 0.033 0.086 -10000 0 -0.39 8 8
AKT1 -0.15 0.2 -10000 0 -0.35 111 111
MAP2K7 0.021 0.002 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
DAB1 -0.093 0.26 -10000 0 -0.68 42 42
RELN/LRP8/DAB1 -0.17 0.25 -10000 0 -0.43 117 117
LRPAP1/LRP8 0.054 0.069 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.15 0.24 -10000 0 -0.41 114 114
DAB1/alpha3/beta1 Integrin -0.14 0.25 0.42 2 -0.44 90 92
long-term memory -0.13 0.24 0.34 2 -0.4 103 105
DAB1/LIS1 -0.15 0.27 0.36 3 -0.45 95 98
DAB1/CRLK/C3G -0.16 0.26 -10000 0 -0.44 95 95
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
DAB1/NCK2 -0.15 0.27 0.37 4 -0.45 95 99
ARHGEF2 0.018 0.022 0.35 1 -10000 0 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.07 0.12 0.35 40 -10000 0 40
CDK5R1 0.022 0.02 0.35 1 -10000 0 1
RELN -0.22 0.34 0.35 2 -0.68 89 91
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
RELN/LRP8/Fyn -0.11 0.24 -10000 0 -0.43 88 88
GRIN2A/RELN/LRP8/DAB1/Fyn -0.13 0.25 0.41 2 -0.41 105 107
MAPK8 -0.006 0.14 -10000 0 -0.69 10 10
RELN/VLDLR/DAB1 -0.19 0.28 -10000 0 -0.46 125 125
ITGB1 0.021 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.25 -10000 0 -0.44 114 114
RELN/LRP8 -0.11 0.24 -10000 0 -0.43 87 87
GRIN2B/RELN/LRP8/DAB1/Fyn -0.15 0.25 -10000 0 -0.41 113 113
PI3K 0.028 0.06 -10000 0 -0.93 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.051 0.063 -10000 0 -10000 0 0
RAP1A -0.16 0.23 0.34 1 -0.64 21 22
PAFAH1B1 0.019 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.016 0.062 -10000 0 -0.69 2 2
CRLK/C3G 0.031 0.006 -10000 0 -10000 0 0
GRIN2B 0.017 0.005 -10000 0 -10000 0 0
NCK2 0.023 0.02 0.35 1 -10000 0 1
neuron differentiation -0.086 0.16 -10000 0 -0.34 42 42
neuron adhesion -0.14 0.22 0.41 1 -0.59 21 22
LRP8 0.057 0.1 0.35 29 -10000 0 29
GSK3B -0.14 0.19 -10000 0 -0.36 81 81
RELN/VLDLR/DAB1/Fyn -0.18 0.27 -10000 0 -0.44 120 120
MAP3K11 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.15 0.22 -10000 0 -0.37 111 111
CDK5 0.021 0.005 -10000 0 -10000 0 0
MAPT 0.11 0.15 0.36 41 -10000 0 41
neuron migration -0.17 0.23 0.37 1 -0.42 94 95
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.086 0.16 -10000 0 -0.35 42 42
RELN/VLDLR -0.097 0.27 0.41 7 -0.44 87 94
IGF1 pathway

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
NCK2 0.023 0.02 0.35 1 -10000 0 1
PTK2 0.016 0.009 -10000 0 -10000 0 0
CRKL -0.15 0.2 -10000 0 -0.38 112 112
GRB2/SOS1/SHC 0.033 0.019 -10000 0 -10000 0 0
HRAS 0.023 0.02 0.35 1 -10000 0 1
IRS1/Crk -0.15 0.2 -10000 0 -0.38 111 111
IGF-1R heterotetramer/IGF1/PTP1B -0.16 0.24 -10000 0 -0.43 110 110
AKT1 -0.14 0.18 -10000 0 -0.72 3 3
BAD -0.13 0.16 -10000 0 -0.66 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.15 0.2 -10000 0 -0.38 111 111
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.15 0.2 -10000 0 -0.38 112 112
RAF1 -0.12 0.15 -10000 0 -0.57 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.12 0.2 -10000 0 -0.36 109 109
YWHAZ 0.016 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.22 -10000 0 -0.4 114 114
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
RPS6KB1 -0.13 0.17 -10000 0 -0.62 3 3
GNB2L1 0.021 0.003 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.089 0.14 -10000 0 -0.49 2 2
PXN 0.021 0.002 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.16 -10000 0 -0.33 75 75
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.098 0.18 -10000 0 -0.35 75 75
IGF-1R heterotetramer -0.03 0.095 0.3 3 -0.78 2 5
IGF-1R heterotetramer/IGF1/IRS/Nck -0.14 0.21 -10000 0 -0.38 112 112
Crk/p130 Cas/Paxillin -0.12 0.2 -10000 0 -0.35 109 109
IGF1R -0.03 0.095 0.3 3 -0.79 2 5
IGF1 -0.29 0.36 -10000 0 -0.7 114 114
IRS2/Crk -0.14 0.19 -10000 0 -0.36 110 110
PI3K -0.13 0.21 -10000 0 -0.37 110 110
apoptosis 0.091 0.13 0.47 3 -10000 0 3
HRAS/GDP 0.017 0.013 0.23 1 -10000 0 1
PRKCD -0.18 0.22 -10000 0 -0.43 111 111
RAF1/14-3-3 E -0.092 0.14 -10000 0 -0.44 3 3
BAD/14-3-3 -0.096 0.14 -10000 0 -0.51 3 3
PRKCZ -0.15 0.19 -10000 0 -0.58 14 14
Crk/p130 Cas/Paxillin/FAK1 -0.093 0.14 -10000 0 -0.5 2 2
PTPN1 0.021 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.18 0.23 -10000 0 -0.45 114 114
BCAR1 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.12 0.19 -10000 0 -0.38 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.022 0.001 -10000 0 -10000 0 0
IRS1/NCK2 -0.14 0.2 -10000 0 -0.38 112 112
GRB10 0.021 0.003 -10000 0 -10000 0 0
PTPN11 -0.15 0.2 -10000 0 -0.38 112 112
IRS1 -0.17 0.21 -10000 0 -0.4 114 114
IRS2 -0.16 0.2 -10000 0 -0.38 110 110
IGF-1R heterotetramer/IGF1 -0.22 0.29 -10000 0 -0.54 114 114
GRB2 0.021 0.005 -10000 0 -10000 0 0
PDPK1 -0.14 0.19 -10000 0 -0.35 102 102
YWHAE 0.019 0.007 -10000 0 -10000 0 0
PRKD1 -0.18 0.22 -10000 0 -0.43 111 111
SHC1 0.017 0.009 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.34 0.39 -10000 0 -0.8 89 89
CRP -0.47 0.55 -10000 0 -1.1 108 108
cell cycle arrest -0.41 0.49 -10000 0 -0.96 97 97
TIMP1 -0.28 0.35 -10000 0 -0.7 85 85
IL6ST -0.15 0.29 -10000 0 -0.7 57 57
Rac1/GDP -0.18 0.26 -10000 0 -0.53 71 71
AP1 -0.14 0.22 -10000 0 -0.49 35 35
GAB2 0.025 0.008 -10000 0 -10000 0 0
TNFSF11 -0.46 0.51 -10000 0 -0.99 112 112
HSP90B1 -0.021 0.099 -10000 0 -0.89 2 2
GAB1 0.023 0.007 -10000 0 -10000 0 0
MAPK14 -0.16 0.29 -10000 0 -0.77 36 36
AKT1 0.024 0.047 -10000 0 -0.45 1 1
FOXO1 0.02 0.053 -10000 0 -0.39 2 2
MAP2K6 -0.17 0.27 -10000 0 -0.55 64 64
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.21 0.29 -10000 0 -0.59 72 72
MITF -0.16 0.24 -10000 0 -0.49 67 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.021 0.003 -10000 0 -10000 0 0
A2M -0.21 0.55 -10000 0 -1.5 42 42
CEBPB 0.025 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.023 0.11 -10000 0 -0.43 8 8
STAT3 -0.45 0.56 -10000 0 -1.1 96 96
STAT1 -0.006 0.08 -10000 0 -1.1 1 1
CEBPD -0.32 0.41 -10000 0 -0.87 74 74
PIK3CA 0.02 0.044 -10000 0 -0.69 1 1
PI3K 0.029 0.06 -10000 0 -0.93 1 1
JUN 0.008 0.09 -10000 0 -0.63 5 5
PIAS3/MITF -0.13 0.22 -10000 0 -0.5 52 52
MAPK11 -0.17 0.32 -10000 0 -0.78 43 43
STAT3 (dimer)/FOXO1 -0.31 0.38 -10000 0 -0.77 86 86
GRB2/SOS1/GAB family -0.077 0.21 -10000 0 -0.52 28 28
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.23 -10000 0 -0.44 76 76
GRB2 0.023 0.007 -10000 0 -10000 0 0
JAK2 0.019 0.025 -10000 0 -0.38 1 1
LBP -0.29 0.37 -10000 0 -0.78 71 71
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
JAK1 0.008 0.024 -10000 0 -10000 0 0
MYC -0.35 0.47 -10000 0 -0.94 85 85
FGG -0.38 0.45 -10000 0 -0.94 87 87
macrophage differentiation -0.41 0.49 -10000 0 -0.96 97 97
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.12 0.23 -10000 0 -0.46 70 70
JUNB -0.34 0.4 -10000 0 -0.85 77 77
FOS -0.29 0.35 -10000 0 -0.67 117 117
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.17 0.25 -10000 0 -0.5 72 72
STAT1/PIAS1 -0.16 0.24 -10000 0 -0.49 65 65
GRB2/SOS1/GAB family/SHP2/PI3K 0.025 0.053 -10000 0 -0.48 1 1
STAT3 (dimer) -0.45 0.55 -10000 0 -1.1 96 96
PRKCD -0.26 0.33 -10000 0 -0.66 83 83
IL6R -0.002 0.089 -10000 0 -0.7 4 4
SOCS3 -0.18 0.41 -10000 0 -1.2 35 35
gp130 (dimer)/JAK1/JAK1/LMO4 -0.1 0.2 -10000 0 -0.48 57 57
Rac1/GTP -0.19 0.28 -10000 0 -0.56 72 72
HCK -0.002 0.13 -10000 0 -0.69 9 9
MAPKKK cascade 0.007 0.11 -10000 0 -0.59 3 3
bone resorption -0.42 0.46 -10000 0 -0.9 112 112
IRF1 -0.33 0.39 -10000 0 -0.8 89 89
mol:GDP -0.18 0.26 -10000 0 -0.52 75 75
SOS1 0.025 0.008 -10000 0 -10000 0 0
VAV1 -0.19 0.27 -10000 0 -0.53 75 75
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.14 0.29 -10000 0 -0.72 37 37
PTPN11 -0.005 0.069 -10000 0 -1 1 1
IL6/IL6RA -0.066 0.19 0.26 4 -0.5 40 44
gp130 (dimer)/TYK2/TYK2/LMO4 -0.088 0.2 -10000 0 -0.47 57 57
gp130 (dimer)/JAK2/JAK2/LMO4 -0.087 0.2 -10000 0 -0.47 56 56
IL6 -0.089 0.25 0.35 6 -0.71 36 42
PIAS3 0.017 0.009 -10000 0 -10000 0 0
PTPRE 0.026 0.069 0.34 1 -0.68 2 3
PIAS1 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.02 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.2 -10000 0 -0.38 80 80
LMO4 -0.001 0.027 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.39 0.46 -10000 0 -0.93 92 92
MCL1 0.056 0.08 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.021 0.004 -10000 0 -10000 0 0
EPHB2 0.083 0.13 0.35 50 -10000 0 50
EFNB1 0.013 0.095 0.21 4 -0.52 6 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.026 0.21 0.32 5 -0.4 46 51
Ephrin B2/EPHB1-2 -0.025 0.19 -10000 0 -0.38 53 53
neuron projection morphogenesis -0.041 0.19 -10000 0 -0.38 47 47
Ephrin B1/EPHB1-2/Tiam1 -0.036 0.23 0.35 6 -0.41 55 61
DNM1 0.029 0.13 0.35 17 -0.69 5 22
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.17 0.31 -10000 0 -0.69 66 66
YES1 -0.23 0.42 -10000 0 -0.93 67 67
Ephrin B1/EPHB1-2/NCK2 -0.019 0.21 0.38 6 -0.4 47 53
PI3K -0.16 0.33 -10000 0 -0.71 67 67
mol:GDP -0.036 0.22 0.34 6 -0.41 55 61
ITGA2B 0.029 0.053 0.35 7 -10000 0 7
endothelial cell proliferation 0.027 0.008 -10000 0 -10000 0 0
FYN -0.23 0.42 -10000 0 -0.93 67 67
MAP3K7 -0.18 0.33 -10000 0 -0.73 67 67
FGR -0.23 0.42 -10000 0 -0.93 67 67
TIAM1 -0.006 0.14 -10000 0 -0.69 10 10
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
RGS3 0.021 0.003 -10000 0 -10000 0 0
cell adhesion -0.16 0.33 -10000 0 -0.68 68 68
LYN -0.22 0.41 -10000 0 -0.92 67 67
Ephrin B1/EPHB1-2/Src Family Kinases -0.22 0.39 -10000 0 -0.87 67 67
Ephrin B1/EPHB1-2 -0.2 0.35 -10000 0 -0.78 67 67
SRC -0.22 0.42 -10000 0 -0.92 67 67
ITGB3 -0.019 0.16 -10000 0 -0.69 15 15
EPHB1 -0.13 0.29 -10000 0 -0.69 56 56
EPHB4 0.022 0.021 0.35 1 -10000 0 1
RAC1 0.021 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.005 0.13 0.25 7 -0.52 15 22
BLK -0.26 0.43 -10000 0 -0.97 67 67
HCK -0.23 0.42 -10000 0 -0.94 67 67
regulation of stress fiber formation 0.02 0.21 0.39 48 -0.37 6 54
MAPK8 -0.18 0.3 -10000 0 -0.65 71 71
Ephrin B1/EPHB1-2/RGS3 -0.019 0.21 0.35 6 -0.4 46 52
endothelial cell migration -0.15 0.28 -10000 0 -0.62 66 66
NCK2 0.023 0.02 0.35 1 -10000 0 1
PTPN13 -0.15 0.33 0.34 2 -0.75 60 62
regulation of focal adhesion formation 0.02 0.21 0.39 48 -0.37 6 54
chemotaxis 0.02 0.21 0.39 46 -0.34 6 52
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
Rac1/GTP -0.033 0.2 -10000 0 -0.39 47 47
angiogenesis -0.2 0.35 -10000 0 -0.78 67 67
LCK -0.23 0.43 -10000 0 -0.94 67 67
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.045 0.21 0.42 3 -0.45 49 52
EFNA5 -0.086 0.3 0.35 20 -0.69 49 69
FYN -0.058 0.18 0.24 3 -0.42 49 52
neuron projection morphogenesis -0.045 0.21 0.42 3 -0.45 49 52
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.045 0.21 0.42 3 -0.45 49 52
EPHA5 0.025 0.054 0.35 7 -10000 0 7
Wnt signaling

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
Noncanonical Wnts/FZD -0.14 0.27 0.26 1 -0.47 81 82
FZD6 0.016 0.009 -10000 0 -10000 0 0
WNT6 0.036 0.068 0.35 12 -10000 0 12
WNT4 -0.038 0.27 0.35 29 -0.67 36 65
FZD3 0.005 0.086 -10000 0 -0.54 6 6
WNT5A -0.039 0.21 0.35 5 -0.68 25 30
WNT11 -0.16 0.31 -10000 0 -0.69 69 69
Endothelins

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
AKT1 -0.011 0.12 0.38 4 -0.46 8 12
PTK2B 0.018 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.045 0.27 0.5 14 -0.62 24 38
EDN1 -0.006 0.12 0.35 2 -0.63 6 8
EDN3 0.024 0.05 0.35 6 -10000 0 6
EDN2 -0.037 0.2 0.35 4 -0.66 24 28
HRAS/GDP -0.12 0.26 0.4 2 -0.54 53 55
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.065 0.2 0.38 2 -0.43 46 48
ADCY4 0.019 0.11 0.36 2 -0.4 6 8
ADCY5 -0.046 0.19 0.36 2 -0.42 40 42
ADCY6 0.02 0.11 0.36 2 -0.4 5 7
ADCY7 0.017 0.11 0.36 2 -0.4 6 8
ADCY1 -0.11 0.22 0.36 2 -0.42 74 76
ADCY2 0.021 0.12 0.41 4 -0.41 5 9
ADCY3 0.021 0.11 0.36 2 -0.4 6 8
ADCY8 0.019 0.11 0.37 2 -0.42 3 5
ADCY9 0.018 0.11 0.36 2 -0.4 6 8
arachidonic acid secretion -0.21 0.34 0.47 3 -0.55 106 109
ETB receptor/Endothelin-1/Gq/GTP -0.077 0.23 0.3 3 -0.47 53 56
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
HRAS 0.021 0.02 0.35 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP 0.004 0.12 0.46 4 -0.42 7 11
ETA receptor/Endothelin-1/Gs/GTP 0.023 0.13 0.46 3 -0.42 6 9
mol:GTP 0 0.009 -10000 0 -10000 0 0
COL3A1 -0.016 0.17 0.56 6 -0.63 10 16
EDNRB -0.017 0.17 -10000 0 -0.65 17 17
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.019 0.16 0.42 2 -0.57 13 15
CYSLTR1 -0.022 0.16 0.47 1 -0.6 14 15
SLC9A1 -0.006 0.086 0.27 4 -0.33 7 11
mol:GDP -0.14 0.28 0.42 2 -0.58 54 56
SLC9A3 -0.033 0.29 0.53 5 -0.73 30 35
RAF1 -0.2 0.31 0.36 2 -0.62 67 69
JUN -0.066 0.29 0.53 3 -0.73 26 29
JAK2 -0.013 0.12 0.38 4 -0.45 8 12
mol:IP3 -0.096 0.25 0.34 3 -0.52 54 57
ETA receptor/Endothelin-1 -0.01 0.15 0.54 4 -0.53 8 12
PLCB1 0.03 0.06 0.35 9 -10000 0 9
PLCB2 0 0.091 -10000 0 -0.63 5 5
ETA receptor/Endothelin-3 0.011 0.081 0.36 1 -0.37 3 4
FOS -0.44 0.52 -10000 0 -0.99 118 118
Gai/GDP -0.31 0.42 -10000 0 -0.75 117 117
CRK 0.019 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.091 0.26 0.45 3 -0.65 32 35
BCAR1 0.021 0.005 -10000 0 -10000 0 0
PRKCB1 -0.096 0.24 0.34 3 -0.5 54 57
GNAQ 0.015 0.031 -10000 0 -0.39 1 1
GNAZ 0.17 0.16 0.35 117 -10000 0 117
GNAL 0.075 0.12 0.35 43 -10000 0 43
Gs family/GDP -0.095 0.26 0.38 5 -0.53 47 52
ETA receptor/Endothelin-1/Gq/GTP -0.06 0.21 0.4 3 -0.45 44 47
MAPK14 -0.066 0.2 0.29 4 -0.49 34 38
TRPC6 -0.049 0.28 0.51 12 -0.66 23 35
GNAI2 0.021 0.002 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.016 0.062 -10000 0 -0.69 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.074 0.22 0.29 2 -0.45 49 51
ETB receptor/Endothelin-2 -0.045 0.2 0.25 3 -0.5 40 43
ETB receptor/Endothelin-3 0.002 0.14 -10000 0 -0.49 17 17
ETB receptor/Endothelin-1 -0.014 0.18 0.37 4 -0.56 19 23
MAPK3 -0.37 0.46 -10000 0 -0.83 121 121
MAPK1 -0.37 0.46 -10000 0 -0.84 121 121
Rac1/GDP -0.12 0.26 0.4 2 -0.55 51 53
cAMP biosynthetic process -0.052 0.17 0.4 2 -0.42 24 26
MAPK8 -0.079 0.32 0.48 6 -0.74 32 38
SRC 0.023 0.02 0.35 1 -10000 0 1
ETB receptor/Endothelin-1/Gi/GTP -0.087 0.19 0.3 1 -0.47 31 32
p130Cas/CRK/Src/PYK2 -0.11 0.29 0.43 7 -0.61 48 55
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.12 0.26 0.4 2 -0.55 51 53
COL1A2 -0.016 0.2 0.53 10 -0.6 13 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.035 0.17 0.36 1 -0.49 27 28
mol:DAG -0.096 0.25 0.34 3 -0.52 54 57
MAP2K2 -0.28 0.37 -10000 0 -0.64 117 117
MAP2K1 -0.28 0.36 -10000 0 -0.63 117 117
EDNRA -0.003 0.1 0.44 2 -0.41 6 8
positive regulation of muscle contraction -0.006 0.11 0.36 2 -0.4 7 9
Gq family/GDP -0.14 0.28 -10000 0 -0.6 57 57
HRAS/GTP -0.14 0.28 0.37 2 -0.57 58 60
PRKCH -0.097 0.24 0.36 2 -0.52 50 52
RAC1 0.021 0.003 -10000 0 -10000 0 0
PRKCA -0.092 0.23 0.34 3 -0.51 49 52
PRKCB -0.13 0.28 0.37 3 -0.56 62 65
PRKCE -0.098 0.24 0.36 2 -0.52 50 52
PRKCD -0.098 0.24 0.36 2 -0.52 50 52
PRKCG -0.097 0.24 0.36 2 -0.53 48 50
regulation of vascular smooth muscle contraction -0.51 0.6 -10000 0 -1.2 118 118
PRKCQ -0.1 0.25 0.36 2 -0.54 50 52
PLA2G4A -0.23 0.37 0.47 3 -0.6 107 110
GNA14 -0.1 0.26 -10000 0 -0.68 45 45
GNA15 0.024 0.03 0.35 2 -10000 0 2
GNA12 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.008 0.098 -10000 0 -0.69 5 5
Rac1/GTP 0.004 0.12 0.46 4 -0.42 7 11
MMP1 0.081 0.16 0.38 51 -0.33 1 52
IL23-mediated signaling events

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
CCL2 -0.16 0.64 0.95 9 -1.3 49 58
IL23A -0.15 0.62 0.99 9 -1.3 44 53
NF kappa B1 p50/RelA/I kappa B alpha -0.18 0.54 -10000 0 -1.1 51 51
positive regulation of T cell mediated cytotoxicity -0.15 0.69 1.1 11 -1.3 52 63
ITGA3 -0.11 0.59 1 10 -1.2 40 50
IL17F -0.062 0.39 0.68 11 -0.74 40 51
IL12B 0.033 0.097 0.43 6 -10000 0 6
STAT1 (dimer) -0.15 0.63 0.83 9 -1.2 52 61
CD4 -0.14 0.62 0.93 9 -1.3 44 53
IL23 -0.15 0.59 0.94 5 -1.2 44 49
IL23R 0.028 0.25 0.66 8 -1 7 15
IL1B -0.19 0.7 0.99 9 -1.4 50 59
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.084 0.58 0.99 10 -1.2 38 48
TYK2 0.024 0.06 0.26 2 -10000 0 2
STAT4 -0.004 0.14 0.35 1 -0.69 10 11
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP -0.02 0.17 -10000 0 -0.67 16 16
IL12RB1 0.003 0.14 -10000 0 -0.72 8 8
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
IL12Rbeta1/TYK2 0.014 0.12 0.29 2 -0.56 8 10
IL23R/JAK2 0.036 0.25 0.68 5 -0.91 7 12
positive regulation of chronic inflammatory response -0.15 0.69 1.1 11 -1.3 52 63
natural killer cell activation -0.003 0.016 -10000 0 -0.06 8 8
JAK2 0.033 0.087 0.35 5 -0.42 1 6
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
NFKB1 0.022 0.01 -10000 0 -10000 0 0
RELA 0.023 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.13 0.56 0.93 5 -1.1 45 50
ALOX12B -0.12 0.57 0.92 11 -1.2 40 51
CXCL1 -0.28 0.75 1 10 -1.3 83 93
T cell proliferation -0.15 0.69 1.1 11 -1.3 52 63
NFKBIA 0.023 0.008 -10000 0 -10000 0 0
IL17A -0.02 0.33 0.66 12 -0.6 28 40
PI3K -0.17 0.57 -10000 0 -1.2 52 52
IFNG 0.002 0.067 0.24 9 -0.12 8 17
STAT3 (dimer) -0.17 0.53 -10000 0 -1.1 52 52
IL18R1 -0.076 0.24 -10000 0 -0.68 37 37
IL23/IL23R/JAK2/TYK2/SOCS3 -0.059 0.45 0.8 12 -0.89 36 48
IL18/IL18R -0.054 0.23 -10000 0 -0.52 47 47
macrophage activation -0.004 0.032 0.079 18 -0.046 14 32
TNF -0.15 0.64 1 9 -1.4 40 49
STAT3/STAT4 -0.18 0.58 -10000 0 -1.2 52 52
STAT4 (dimer) -0.16 0.64 0.83 9 -1.2 52 61
IL18 0.012 0.095 0.34 2 -0.62 5 7
IL19 -0.089 0.57 0.96 9 -1.2 39 48
STAT5A (dimer) -0.15 0.63 0.83 9 -1.2 52 61
STAT1 0.024 0.028 0.35 2 -10000 0 2
SOCS3 -0.05 0.21 -10000 0 -0.69 26 26
CXCL9 -0.11 0.59 1 12 -1.2 41 53
MPO -0.14 0.6 0.92 10 -1.2 46 56
positive regulation of humoral immune response -0.15 0.69 1.1 11 -1.3 52 63
IL23/IL23R/JAK2/TYK2 -0.18 0.8 1.1 11 -1.5 52 63
IL6 -0.21 0.68 0.92 9 -1.3 60 69
STAT5A 0.021 0.003 -10000 0 -10000 0 0
IL2 0.009 0.029 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.003 0.016 -10000 0 -0.06 8 8
CD3E -0.12 0.59 0.96 9 -1.2 40 49
keratinocyte proliferation -0.15 0.69 1.1 11 -1.3 52 63
NOS2 -0.1 0.57 0.95 9 -1.2 40 49
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.005 0.058 0.26 3 -0.46 2 5
NFATC2 -0.066 0.18 0.26 3 -0.47 42 45
NFATC3 0.009 0.04 0.26 3 -10000 0 3
CD40LG -0.26 0.37 0.7 5 -0.71 83 88
PTGS2 -0.31 0.42 0.63 5 -0.82 89 94
JUNB -0.006 0.14 -10000 0 -0.69 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.027 0.17 3 -10000 0 3
CaM/Ca2+ 0.011 0.027 0.17 3 -10000 0 3
CALM1 0.019 0.017 -10000 0 -10000 0 0
JUN 0.007 0.093 -10000 0 -0.63 5 5
mol:Ca2+ -0.002 0.013 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.01 -10000 0 -10000 0 0
FOSL1 -0.002 0.14 0.35 3 -0.69 10 13
CREM 0.021 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.042 0.21 0.57 5 -0.44 38 43
FOS -0.29 0.35 -10000 0 -0.68 117 117
IFNG -0.24 0.36 0.72 6 -0.68 82 88
AP-1/NFAT1-c-4 -0.29 0.45 0.84 5 -0.83 85 90
FASLG -0.24 0.35 0.7 5 -0.67 83 88
NFAT1-c-4/ICER1 -0.051 0.19 0.4 5 -0.43 41 46
IL2RA -0.25 0.37 0.65 9 -0.68 84 93
FKBP12/FK506 0.016 0.002 -10000 0 -10000 0 0
CSF2 -0.25 0.35 0.63 5 -0.68 83 88
JunB/Fra1/NFAT1-c-4 -0.067 0.23 0.52 3 -0.44 56 59
IL4 -0.25 0.35 0.62 5 -0.68 82 87
IL2 -0.047 0.23 -10000 0 -1.1 12 12
IL3 -0.021 0.079 -10000 0 -0.8 2 2
FKBP1A 0.021 0.003 -10000 0 -10000 0 0
BATF3 0.016 0.049 0.35 1 -0.69 1 2
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.018 0.009 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.12 0.25 0.6 29 -0.63 7 36
IHH 0.058 0.16 0.38 13 -0.63 8 21
SHH Np/Cholesterol/GAS1 -0.058 0.17 -10000 0 -0.39 49 49
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.057 0.17 0.39 49 -10000 0 49
SMO/beta Arrestin2 0.063 0.2 0.38 9 -0.63 14 23
SMO 0.052 0.21 0.42 10 -0.66 14 24
AKT1 0.047 0.16 -10000 0 -0.77 4 4
ARRB2 0.019 0.007 -10000 0 -10000 0 0
BOC 0.033 0.059 0.35 9 -10000 0 9
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
heart looping 0.052 0.21 0.41 10 -0.65 14 24
STIL 0.088 0.19 0.41 29 -0.49 12 41
DHH N/PTCH2 0.03 0.042 -10000 0 -0.52 1 1
DHH N/PTCH1 0.075 0.19 0.42 14 -0.54 13 27
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
DHH 0.022 0.02 0.35 1 -10000 0 1
PTHLH 0.13 0.28 0.68 24 -0.71 7 31
determination of left/right symmetry 0.052 0.21 0.41 10 -0.65 14 24
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
skeletal system development 0.13 0.28 0.68 24 -0.7 7 31
IHH N/Hhip -0.24 0.31 0.29 2 -0.55 128 130
DHH N/Hhip -0.23 0.27 0.25 2 -0.52 124 126
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.052 0.21 0.41 10 -0.65 14 24
pancreas development -0.31 0.35 0.35 1 -0.68 124 125
HHAT 0.015 0.044 -10000 0 -0.69 1 1
PI3K 0.028 0.06 -10000 0 -0.93 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.091 0.26 0.35 1 -0.69 42 43
somite specification 0.052 0.21 0.41 10 -0.65 14 24
SHH Np/Cholesterol/PTCH1 0.034 0.17 0.37 9 -0.46 19 28
SHH Np/Cholesterol/PTCH2 0.001 0.093 -10000 0 -0.41 11 11
SHH Np/Cholesterol/Megalin -0.034 0.17 0.23 18 -0.38 44 62
SHH -0.009 0.11 0.26 2 -0.54 10 12
catabolic process 0.083 0.22 0.46 23 -0.59 13 36
SMO/Vitamin D3 0.079 0.22 0.43 21 -0.56 16 37
SHH Np/Cholesterol/Hhip -0.18 0.21 0.22 1 -0.39 128 129
LRP2 -0.05 0.26 0.35 18 -0.69 34 52
receptor-mediated endocytosis 0.006 0.22 0.38 17 -0.57 19 36
SHH Np/Cholesterol/BOC 0.008 0.097 0.32 1 -0.42 10 11
SHH Np/Cholesterol/CDO 0.001 0.09 -10000 0 -0.43 10 10
mesenchymal cell differentiation 0.18 0.21 0.38 128 -0.21 1 129
mol:Vitamin D3 0.087 0.21 0.44 22 -0.47 19 41
IHH N/PTCH2 0.048 0.11 0.31 1 -0.44 8 9
CDON 0.021 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.1 0.23 0.5 23 -0.6 13 36
Megalin/LRPAP1 -0.027 0.2 -10000 0 -0.52 34 34
PTCH2 0.02 0.052 0.35 2 -0.69 1 3
SHH Np/Cholesterol -0.006 0.089 -10000 0 -0.43 10 10
PTCH1 0.084 0.22 0.46 23 -0.6 13 36
HHIP -0.31 0.35 0.35 1 -0.68 124 125
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.017 0.17 0.44 1 -0.47 30 31
fibroblast growth factor receptor signaling pathway -0.017 0.17 0.43 1 -0.46 30 31
LAMA1 -0.036 0.24 0.35 17 -0.68 29 46
PRNP -0.027 0.18 -10000 0 -0.69 18 18
GPC1/SLIT2 -0.027 0.19 0.49 1 -0.51 33 34
SMAD2 -0.005 0.093 -10000 0 -0.41 13 13
GPC1/PrPc/Cu2+ -0.026 0.17 0.22 1 -0.52 26 27
GPC1/Laminin alpha1 -0.041 0.22 0.26 16 -0.53 40 56
TDGF1 0.028 0.24 0.35 49 -0.69 20 69
CRIPTO/GPC1 0.001 0.21 -10000 0 -0.52 32 32
APP/GPC1 -0.002 0.13 0.25 1 -0.52 16 17
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.019 0.17 -10000 0 -0.45 32 32
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.019 0.11 -10000 0 -0.45 13 13
SERPINC1 -0.093 0.26 -10000 0 -0.69 41 41
FYN -0.021 0.17 -10000 0 -0.45 32 32
FGR -0.022 0.17 -10000 0 -0.45 33 33
positive regulation of MAPKKK cascade -0.07 0.22 -10000 0 -0.54 35 35
SLIT2 -0.017 0.2 0.35 12 -0.67 20 32
GPC1/NRG -0.2 0.28 0.25 1 -0.49 113 114
NRG1 -0.24 0.32 -10000 0 -0.62 107 107
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.016 0.097 -10000 0 -0.45 9 9
LYN -0.021 0.16 -10000 0 -0.45 28 28
mol:Spermine -0.019 0.12 0.2 1 -0.52 13 14
cell growth -0.017 0.17 0.43 1 -0.46 30 31
BMP signaling pathway 0.013 0.16 0.69 13 -0.35 1 14
SRC -0.018 0.17 0.34 1 -0.45 31 32
TGFBR1 0.021 0.003 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.23 0.38 0.35 23 -0.67 105 128
GPC1 -0.013 0.16 0.35 1 -0.69 13 14
TGFBR1 (dimer) 0.021 0.003 -10000 0 -10000 0 0
VEGFA 0.019 0.007 -10000 0 -10000 0 0
BLK -0.097 0.24 -10000 0 -0.49 60 60
HCK -0.033 0.18 -10000 0 -0.46 38 38
FGF2 -0.018 0.18 0.35 4 -0.69 16 20
FGFR1 0.014 0.073 0.35 2 -0.59 3 5
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.022 0 -10000 0 -10000 0 0
cell death -0.002 0.13 0.25 1 -0.52 16 17
ATIII/GPC1 -0.085 0.22 -10000 0 -0.51 54 54
PLA2G2A/GPC1 -0.19 0.3 0.25 22 -0.52 113 135
LCK -0.033 0.19 -10000 0 -0.46 39 39
neuron differentiation -0.2 0.27 0.25 1 -0.49 113 114
PrPc/Cu2+ -0.021 0.14 -10000 0 -0.52 18 18
APP 0.013 0.075 -10000 0 -0.69 3 3
TGFBR2 (dimer) 0.022 0 -10000 0 -10000 0 0
EPHB forward signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.015 0.22 0.42 2 -0.43 49 51
cell-cell adhesion 0.13 0.19 0.42 63 -10000 0 63
Ephrin B/EPHB2/RasGAP -0.023 0.2 0.41 1 -0.38 50 51
ITSN1 0.021 0.003 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
SHC1 0.017 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.011 0.15 0.22 8 -0.45 25 33
Ephrin B1/EPHB1 -0.075 0.2 -10000 0 -0.46 56 56
HRAS/GDP -0.13 0.21 -10000 0 -0.47 53 53
Ephrin B/EPHB1/GRB7 -0.13 0.27 -10000 0 -0.48 89 89
Endophilin/SYNJ1 -0.054 0.16 -10000 0 -0.35 48 48
KRAS 0.021 0.003 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.13 0.26 -10000 0 -0.48 85 85
endothelial cell migration 0.04 0.041 -10000 0 -0.59 1 1
GRB2 0.021 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.088 0.35 5 -0.69 3 8
PAK1 -0.054 0.16 -10000 0 -0.38 35 35
HRAS 0.023 0.02 0.35 1 -10000 0 1
RRAS -0.052 0.16 -10000 0 -0.37 35 35
DNM1 0.029 0.13 0.35 17 -0.69 5 22
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.15 0.23 -10000 0 -0.46 85 85
lamellipodium assembly -0.13 0.19 -10000 0 -0.42 63 63
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.18 -10000 0 -0.4 50 50
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
EPHB2 0.083 0.13 0.35 50 -10000 0 50
EPHB3 -0.034 0.22 0.35 8 -0.69 24 32
EPHB1 -0.13 0.29 -10000 0 -0.69 56 56
EPHB4 0.022 0.021 0.35 1 -10000 0 1
mol:GDP -0.12 0.21 -10000 0 -0.46 53 53
Ephrin B/EPHB2 -0.027 0.19 0.4 1 -0.37 49 50
Ephrin B/EPHB3 -0.084 0.23 0.4 1 -0.46 62 63
JNK cascade -0.056 0.17 0.35 1 -0.39 41 42
Ephrin B/EPHB1 -0.14 0.26 -10000 0 -0.48 86 86
RAP1/GDP -0.099 0.19 -10000 0 -0.42 46 46
EFNB2 0.021 0.004 -10000 0 -10000 0 0
EFNB3 -0.14 0.29 0.35 1 -0.62 67 68
EFNB1 0.019 0.044 -10000 0 -0.69 1 1
Ephrin B2/EPHB1-2 -0.027 0.2 -10000 0 -0.39 53 53
RAP1B 0.021 0.002 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.24 -10000 0 -0.51 49 49
Rap1/GTP -0.12 0.2 -10000 0 -0.57 26 26
axon guidance -0.016 0.22 0.42 2 -0.43 49 51
MAPK3 -0.093 0.16 -10000 0 -0.44 28 28
MAPK1 -0.092 0.16 -10000 0 -0.44 28 28
Rac1/GDP -0.11 0.19 -10000 0 -0.44 46 46
actin cytoskeleton reorganization -0.11 0.16 -10000 0 -0.43 28 28
CDC42/GDP -0.11 0.2 -10000 0 -0.44 46 46
PI3K 0.044 0.042 -10000 0 -0.6 1 1
EFNA5 -0.086 0.3 0.35 20 -0.69 49 69
Ephrin B2/EPHB4 0.027 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.036 0.14 0.26 1 -0.31 40 41
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.12 0.2 -10000 0 -0.56 26 26
PTK2 0.15 0.25 0.59 62 -10000 0 62
MAP4K4 -0.056 0.17 0.36 1 -0.4 41 42
SRC 0.023 0.02 0.35 1 -10000 0 1
KALRN 0.019 0.044 -10000 0 -0.69 1 1
Intersectin/N-WASP 0.03 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.093 0.18 -10000 0 -0.46 25 25
MAP2K1 -0.095 0.16 -10000 0 -0.46 28 28
WASL 0.021 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.021 0.21 -10000 0 -0.4 57 57
cell migration -0.1 0.2 -10000 0 -0.51 29 29
NRAS 0.021 0.003 -10000 0 -10000 0 0
SYNJ1 -0.054 0.16 -10000 0 -0.35 48 48
PXN 0.021 0.002 -10000 0 -10000 0 0
TF -0.091 0.17 -10000 0 -0.38 49 49
HRAS/GTP -0.11 0.23 -10000 0 -0.44 69 69
Ephrin B1/EPHB1-2 -0.03 0.2 -10000 0 -0.4 56 56
cell adhesion mediated by integrin 0.086 0.17 0.39 53 -0.25 1 54
RAC1 0.021 0.003 -10000 0 -10000 0 0
mol:GTP -0.12 0.25 0.34 1 -0.47 69 70
RAC1-CDC42/GTP -0.15 0.23 -10000 0 -0.6 38 38
RASA1 0.016 0.062 -10000 0 -0.69 2 2
RAC1-CDC42/GDP -0.099 0.19 -10000 0 -0.43 44 44
ruffle organization -0.11 0.21 0.33 1 -0.56 26 27
NCK1 0.019 0.044 -10000 0 -0.69 1 1
receptor internalization -0.056 0.16 0.3 1 -0.38 36 37
Ephrin B/EPHB2/KALRN -0.02 0.2 0.41 1 -0.38 49 50
ROCK1 -0.023 0.13 -10000 0 -0.41 25 25
RAS family/GDP -0.11 0.15 -10000 0 -0.43 26 26
Rac1/GTP -0.13 0.21 -10000 0 -0.45 63 63
Ephrin B/EPHB1/Src/Paxillin -0.12 0.21 -10000 0 -0.38 86 86
Syndecan-1-mediated signaling events

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
TGFB1 0.024 0.029 0.35 2 -10000 0 2
CCL5 0.003 0.12 0.35 1 -0.69 7 8
SDCBP 0.018 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.023 0.21 0.32 12 -0.5 23 35
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.013 0.2 0.3 15 -0.47 23 38
Syndecan-1/Syntenin -0.023 0.19 0.28 12 -0.51 19 31
MAPK3 -0.015 0.19 0.26 11 -0.49 17 28
HGF/MET -0.24 0.28 -10000 0 -0.52 127 127
TGFB1/TGF beta receptor Type II 0.024 0.029 0.35 2 -10000 0 2
BSG 0.022 0.02 0.35 1 -10000 0 1
keratinocyte migration -0.012 0.2 0.3 15 -0.46 23 38
Syndecan-1/RANTES -0.026 0.22 0.3 11 -0.54 24 35
Syndecan-1/CD147 -0.009 0.2 -10000 0 -0.5 18 18
Syndecan-1/Syntenin/PIP2 -0.025 0.19 0.26 10 -0.49 19 29
LAMA5 0.027 0.045 0.35 5 -10000 0 5
positive regulation of cell-cell adhesion -0.025 0.18 0.26 11 -0.48 19 30
MMP7 -0.099 0.32 0.35 26 -0.67 58 84
HGF -0.32 0.35 -10000 0 -0.69 127 127
Syndecan-1/CASK -0.033 0.19 0.27 11 -0.48 23 34
Syndecan-1/HGF/MET -0.2 0.31 0.28 1 -0.51 108 109
regulation of cell adhesion -0.018 0.18 0.26 11 -0.48 16 27
HPSE -0.019 0.16 0.35 1 -0.65 16 17
positive regulation of cell migration -0.023 0.21 0.32 12 -0.5 23 35
SDC1 -0.02 0.21 0.32 12 -0.52 20 32
Syndecan-1/Collagen -0.023 0.21 0.32 12 -0.5 23 35
PPIB 0.021 0.003 -10000 0 -10000 0 0
MET 0.018 0.044 -10000 0 -0.69 1 1
PRKACA 0.021 0.003 -10000 0 -10000 0 0
MMP9 0.058 0.18 0.35 47 -0.69 8 55
MAPK1 -0.016 0.19 0.26 11 -0.48 18 29
homophilic cell adhesion -0.023 0.21 0.32 12 -0.49 23 35
MMP1 0.1 0.14 0.35 64 -10000 0 64
Noncanonical Wnt signaling pathway

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
NFATC2 -0.093 0.26 -10000 0 -0.69 42 42
GNB1/GNG2 -0.12 0.26 -10000 0 -0.57 42 42
mol:DAG -0.11 0.23 0.26 1 -0.53 40 41
PLCG1 -0.11 0.24 -10000 0 -0.55 40 40
YES1 -0.14 0.25 -10000 0 -0.59 42 42
FZD3 0.005 0.086 -10000 0 -0.54 6 6
FZD6 0.016 0.009 -10000 0 -10000 0 0
G protein -0.1 0.24 -10000 0 -0.57 36 36
MAP3K7 -0.088 0.19 -10000 0 -0.46 34 34
mol:Ca2+ -0.1 0.22 0.26 1 -0.51 40 41
mol:IP3 -0.11 0.23 0.26 1 -0.53 40 41
NLK 0.007 0.017 -10000 0 -10000 0 0
GNB1 0.02 0.006 -10000 0 -10000 0 0
CAMK2A -0.091 0.21 -10000 0 -0.5 34 34
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.14 0.27 0.26 1 -0.47 81 82
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
GNAS -0.13 0.25 -10000 0 -0.59 41 41
GO:0007205 -0.11 0.22 0.26 1 -0.54 36 37
WNT6 0.036 0.068 0.35 12 -10000 0 12
WNT4 -0.038 0.27 0.35 29 -0.67 36 65
NFAT1/CK1 alpha -0.16 0.28 0.35 1 -0.59 55 56
GNG2 0.019 0.044 -10000 0 -0.69 1 1
WNT5A -0.039 0.21 0.35 5 -0.68 25 30
WNT11 -0.16 0.31 -10000 0 -0.69 69 69
CDC42 -0.13 0.23 -10000 0 -0.57 41 41
LPA receptor mediated 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
GNB1/GNG2 -0.052 0.2 0.38 2 -0.42 55 57
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.11 -10000 0 -0.42 4 4
AP1 -0.21 0.29 0.3 1 -0.47 129 130
mol:PIP3 -0.07 0.15 -10000 0 -0.36 46 46
AKT1 -0.033 0.13 -10000 0 -0.43 6 6
PTK2B -0.076 0.18 0.25 2 -0.36 53 55
RHOA -0.003 0.06 -10000 0 -0.34 1 1
PIK3CB 0.022 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.084 -10000 0 -0.41 3 3
MAGI3 0.021 0.004 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
apoptosis -0.059 0.18 0.31 4 -0.39 53 57
HRAS/GDP 0.017 0.013 0.23 1 -10000 0 1
positive regulation of microtubule depolymerization -0.041 0.16 0.3 1 -0.41 22 23
NF kappa B1 p50/RelA -0.056 0.18 0.26 4 -0.43 28 32
endothelial cell migration -0.085 0.24 0.46 5 -0.49 57 62
ADCY4 -0.17 0.25 -10000 0 -0.57 59 59
ADCY5 -0.23 0.33 -10000 0 -0.69 74 74
ADCY6 -0.17 0.25 -10000 0 -0.58 59 59
ADCY7 -0.17 0.26 -10000 0 -0.59 58 58
ADCY1 -0.28 0.34 0.25 1 -0.66 99 100
ADCY2 -0.17 0.26 0.33 2 -0.58 59 61
ADCY3 -0.17 0.25 -10000 0 -0.57 59 59
ADCY8 -0.16 0.25 -10000 0 -0.56 60 60
ADCY9 -0.17 0.26 0.25 2 -0.58 60 62
GSK3B -0.073 0.17 0.24 1 -0.41 34 35
arachidonic acid secretion -0.19 0.25 -10000 0 -0.56 60 60
GNG2 0.019 0.044 -10000 0 -0.68 1 1
TRIP6 0.018 0.05 -10000 0 -0.38 3 3
GNAO1 -0.27 0.29 -10000 0 -0.52 141 141
HRAS 0.023 0.02 0.35 1 -10000 0 1
NFKBIA -0.023 0.12 -10000 0 -0.48 4 4
GAB1 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.029 0.25 -10000 0 -0.91 19 19
JUN 0.008 0.09 -10000 0 -0.63 5 5
LPA/LPA2/NHERF2 0.033 0.066 0.22 13 -0.37 3 16
TIAM1 -0.052 0.3 -10000 0 -1.1 19 19
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
mol:IP3 -0.002 0.085 -10000 0 -0.42 3 3
PLCB3 0.017 0.051 -10000 0 -0.41 2 2
FOS -0.29 0.35 -10000 0 -0.67 117 117
positive regulation of mitosis -0.19 0.25 -10000 0 -0.56 60 60
LPA/LPA1-2-3 -0.029 0.22 0.43 6 -0.42 55 61
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.02 0.005 -10000 0 -10000 0 0
stress fiber formation -0.055 0.18 0.3 1 -0.39 44 45
GNAZ -0.004 0.23 0.4 4 -0.41 56 60
EGFR/PI3K-beta/Gab1 -0.063 0.16 -10000 0 -0.38 46 46
positive regulation of dendritic cell cytokine production -0.03 0.22 0.42 6 -0.42 55 61
LPA/LPA2/MAGI-3 0.036 0.055 0.22 12 -0.45 1 13
ARHGEF1 -0.055 0.17 -10000 0 -0.4 44 44
GNAI2 -0.079 0.2 0.31 2 -0.45 57 59
GNAI3 -0.078 0.2 0.31 2 -0.44 57 59
GNAI1 -0.081 0.2 0.31 2 -0.45 58 60
LPA/LPA3 0.035 0.071 0.24 25 -10000 0 25
LPA/LPA2 0.025 0.062 0.23 13 -0.52 1 14
LPA/LPA1 -0.09 0.23 0.29 7 -0.51 58 65
HB-EGF/EGFR 0.024 0.12 -10000 0 -0.44 13 13
HBEGF 0.029 0.13 -10000 0 -0.52 9 9
mol:DAG -0.002 0.085 -10000 0 -0.42 3 3
cAMP biosynthetic process -0.23 0.29 -10000 0 -0.5 119 119
NFKB1 0.02 0.006 -10000 0 -10000 0 0
SRC 0.023 0.02 0.35 1 -10000 0 1
GNB1 0.02 0.006 -10000 0 -10000 0 0
LYN -0.016 0.14 -10000 0 -0.58 5 5
GNAQ 0.027 0.059 0.23 6 -0.32 2 8
LPAR2 0.035 0.084 0.35 13 -0.69 1 14
LPAR3 0.047 0.1 0.35 26 -10000 0 26
LPAR1 -0.12 0.3 0.4 4 -0.69 54 58
IL8 -0.16 0.28 0.47 6 -0.52 83 89
PTK2 -0.054 0.17 0.33 1 -0.41 40 41
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
CASP3 -0.059 0.18 0.31 4 -0.4 53 57
EGFR 0.01 0.087 -10000 0 -0.69 4 4
PLCG1 0.005 0.084 0.22 5 -0.26 6 11
PLD2 -0.054 0.18 0.33 1 -0.4 52 53
G12/G13 -0.041 0.19 0.38 2 -0.42 46 48
PI3K-beta -0.052 0.14 -10000 0 -0.4 14 14
cell migration -0.02 0.1 0.23 1 -0.28 18 19
SLC9A3R2 0.017 0.05 -10000 0 -0.54 2 2
PXN -0.057 0.18 0.3 1 -0.4 44 45
HRAS/GTP -0.2 0.26 -10000 0 -0.58 60 60
RAC1 0.021 0.003 -10000 0 -10000 0 0
MMP9 0.058 0.18 0.35 47 -0.69 8 55
PRKCE 0.02 0.048 0.35 1 -0.69 1 2
PRKCD -0.004 0.083 -10000 0 -0.4 3 3
Gi(beta/gamma) -0.17 0.26 -10000 0 -0.58 60 60
mol:LPA 0.001 0.031 -10000 0 -0.2 4 4
TRIP6/p130 Cas/FAK1/Paxillin -0.054 0.19 0.35 1 -0.49 20 21
MAPKKK cascade -0.19 0.25 -10000 0 -0.56 60 60
contractile ring contraction involved in cytokinesis -0.002 0.061 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.036 0.16 0.22 5 -0.36 44 49
GNA15 0.03 0.059 0.24 8 -0.37 1 9
GNA12 0.021 0.004 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
MAPT -0.043 0.16 0.31 1 -0.42 22 23
GNA11 0.021 0.078 0.23 6 -0.37 6 12
Rac1/GTP -0.032 0.26 -10000 0 -0.97 19 19
MMP2 -0.085 0.24 0.46 5 -0.49 57 62
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.026 0.035 -10000 0 -0.52 1 1
CRKL -0.12 0.2 -10000 0 -0.7 15 15
mol:PIP3 0.009 0.033 0.36 2 -10000 0 2
AKT1 0.006 0.028 -10000 0 -10000 0 0
PTK2B 0.017 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.12 0.19 -10000 0 -0.65 15 15
RANBP10 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
HGF/MET/SHIP2 -0.2 0.25 -10000 0 -0.45 127 127
MAP3K5 -0.14 0.23 -10000 0 -0.6 36 36
HGF/MET/CIN85/CBL/ENDOPHILINS -0.18 0.23 -10000 0 -0.42 126 126
AP1 -0.2 0.24 -10000 0 -0.46 116 116
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.017 0.009 -10000 0 -10000 0 0
apoptosis -0.4 0.46 -10000 0 -0.87 123 123
STAT3 (dimer) -0.14 0.17 -10000 0 -0.33 96 96
GAB1/CRKL/SHP2/PI3K -0.098 0.2 -10000 0 -0.67 14 14
INPP5D 0.019 0.044 -10000 0 -0.69 1 1
CBL/CRK -0.11 0.19 -10000 0 -0.65 15 15
PTPN11 0.021 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.021 0.003 -10000 0 -10000 0 0
PTEN 0.018 0.036 -10000 0 -0.38 2 2
ELK1 0.009 0.11 0.37 16 -0.25 1 17
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.077 0.11 -10000 0 -0.3 15 15
PAK1 0.008 0.034 -10000 0 -10000 0 0
HGF/MET/RANBP10 -0.2 0.25 -10000 0 -0.45 127 127
HRAS -0.16 0.2 -10000 0 -0.52 16 16
DOCK1 -0.12 0.2 -10000 0 -0.64 19 19
GAB1 -0.13 0.21 -10000 0 -0.71 16 16
CRK -0.12 0.2 -10000 0 -0.67 16 16
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.24 0.28 -10000 0 -0.53 126 126
JUN 0.009 0.09 -10000 0 -0.63 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.13 -10000 0 -0.24 126 126
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
cell morphogenesis -0.14 0.2 -10000 0 -0.56 18 18
GRB2/SHC -0.062 0.11 -10000 0 -0.35 3 3
FOS -0.29 0.35 -10000 0 -0.67 117 117
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.009 0.11 0.37 16 -0.25 1 17
HGF/MET/MUC20 -0.2 0.24 -10000 0 -0.45 127 127
cell migration -0.062 0.11 -10000 0 -0.35 3 3
GRB2 0.021 0.005 -10000 0 -10000 0 0
CBL 0.021 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.027 0.035 -10000 0 -0.52 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.14 0.17 -10000 0 -0.34 98 98
MET/MUC20 0.013 0.033 -10000 0 -0.52 1 1
RAP1B -0.11 0.18 -10000 0 -0.62 14 14
RAP1A -0.11 0.17 -10000 0 -0.64 13 13
HGF/MET/RANBP9 -0.19 0.24 -10000 0 -0.43 127 127
RAF1 -0.15 0.2 -10000 0 -0.52 13 13
STAT3 -0.14 0.17 -10000 0 -0.33 96 96
cell proliferation -0.14 0.23 0.33 2 -0.43 71 73
RPS6KB1 -0.032 0.051 -10000 0 -10000 0 0
MAPK3 0.006 0.13 0.77 5 -10000 0 5
MAPK1 0.008 0.14 0.7 7 -10000 0 7
RANBP9 0.02 0.006 -10000 0 -10000 0 0
MAPK8 -0.12 0.2 -10000 0 -0.51 39 39
SRC -0.13 0.16 -10000 0 -0.32 91 91
PI3K -0.086 0.13 -10000 0 -0.36 6 6
MET/Glomulin 0.013 0.035 -10000 0 -0.46 1 1
SOS1 0.022 0.001 -10000 0 -10000 0 0
MAP2K1 -0.13 0.18 -10000 0 -0.48 13 13
MET 0.018 0.044 -10000 0 -0.69 1 1
MAP4K1 -0.12 0.21 -10000 0 -0.7 17 17
PTK2 0.016 0.009 -10000 0 -10000 0 0
MAP2K2 -0.13 0.19 -10000 0 -0.48 13 13
BAD 0.005 0.026 -10000 0 -10000 0 0
MAP2K4 -0.12 0.2 -10000 0 -0.56 33 33
SHP2/GRB2/SOS1/GAB1 -0.1 0.18 -10000 0 -0.63 14 14
INPPL1 0.021 0.003 -10000 0 -10000 0 0
PXN 0.021 0.002 -10000 0 -10000 0 0
SH3KBP1 0.021 0.003 -10000 0 -10000 0 0
HGS -0.096 0.12 -10000 0 -0.22 118 118
PLCgamma1/PKC 0.016 0.002 -10000 0 -10000 0 0
HGF -0.32 0.35 -10000 0 -0.69 127 127
RASA1 0.016 0.062 -10000 0 -0.69 2 2
NCK1 0.019 0.044 -10000 0 -0.69 1 1
PTPRJ 0.022 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.094 0.14 -10000 0 -0.24 121 121
PDPK1 0.006 0.027 0.3 1 -10000 0 1
HGF/MET/SHIP -0.2 0.25 -10000 0 -0.46 127 127
ErbB2/ErbB3 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
USP8 -0.005 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.09 0.14 -10000 0 -0.32 23 23
NFATC4 -0.11 0.14 0.36 1 -0.29 79 80
ERBB2IP 0.024 0.003 -10000 0 -10000 0 0
HSP90 (dimer) 0.021 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.14 0.18 -10000 0 -0.37 85 85
JUN -0.059 0.083 -10000 0 -0.46 4 4
HRAS 0.022 0.02 0.35 1 -10000 0 1
DOCK7 -0.14 0.16 -10000 0 -0.36 85 85
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.12 0.2 -10000 0 -0.42 70 70
AKT1 0 0.008 -10000 0 -10000 0 0
BAD -0.001 0.006 -10000 0 -10000 0 0
MAPK10 -0.079 0.11 0.19 1 -0.31 16 17
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.15 0.19 -10000 0 -0.4 85 85
RAF1 -0.09 0.14 -10000 0 -0.37 7 7
ErbB2/ErbB3/neuregulin 2 0.04 0.11 -10000 0 -0.37 6 6
STAT3 0.017 0.081 -10000 0 -0.88 2 2
cell migration -0.08 0.096 -10000 0 -0.26 18 18
mol:PI-3-4-5-P3 -0.003 0.003 -10000 0 -10000 0 0
cell proliferation -0.18 0.22 -10000 0 -0.51 45 45
FOS -0.24 0.27 0.38 1 -0.52 118 119
NRAS 0.021 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.18 -10000 0 -0.37 85 85
MAPK3 -0.13 0.18 -10000 0 -0.56 9 9
MAPK1 -0.13 0.18 -10000 0 -0.56 11 11
JAK2 -0.14 0.16 -10000 0 -0.36 84 84
NF2 -0.004 0.043 -10000 0 -0.65 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.11 0.16 -10000 0 -0.32 83 83
NRG1 -0.24 0.32 -10000 0 -0.62 107 107
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
MAPK8 -0.15 0.16 -10000 0 -0.33 92 92
MAPK9 -0.072 0.09 -10000 0 -0.26 4 4
ERBB2 -0.023 0.056 -10000 0 -0.54 3 3
ERBB3 0.01 0.075 -10000 0 -0.69 3 3
SHC1 0.016 0.009 -10000 0 -10000 0 0
RAC1 0.021 0.003 -10000 0 -10000 0 0
apoptosis -0.001 0.01 -10000 0 -10000 0 0
STAT3 (dimer) 0.017 0.079 -10000 0 -0.86 2 2
RNF41 -0.01 0.01 -10000 0 -10000 0 0
FRAP1 -0.003 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.1 0.12 -10000 0 -0.26 78 78
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.052 -10000 0 -0.46 3 3
CHRNA1 -0.092 0.15 0.45 1 -0.41 6 7
myelination -0.11 0.13 0.37 1 -0.28 78 79
PPP3CB -0.13 0.15 -10000 0 -0.33 85 85
KRAS 0.021 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.081 0.15 -10000 0 -0.3 59 59
NRG2 0.091 0.13 0.35 56 -10000 0 56
mol:GDP -0.1 0.16 -10000 0 -0.31 83 83
SOS1 0.021 0.002 -10000 0 -10000 0 0
MAP2K2 -0.089 0.14 0.33 1 -0.4 4 5
SRC 0.023 0.02 0.35 1 -10000 0 1
mol:cAMP -0.002 0.002 -10000 0 -10000 0 0
PTPN11 -0.14 0.16 -10000 0 -0.36 85 85
MAP2K1 -0.16 0.2 -10000 0 -0.49 32 32
heart morphogenesis -0.14 0.18 -10000 0 -0.37 85 85
RAS family/GDP -0.079 0.15 -10000 0 -0.32 22 22
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA -0.003 0.045 -10000 0 -0.69 1 1
CHRNE -0.009 0.032 -10000 0 -0.23 4 4
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
activation of caspase activity 0 0.008 -10000 0 -10000 0 0
nervous system development -0.14 0.18 -10000 0 -0.37 85 85
CDC42 0.021 0.004 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.01 0.087 -10000 0 -0.69 4 4
GNB1/GNG2 -0.064 0.088 -10000 0 -0.19 77 77
AKT1 -0.042 0.13 0.3 4 -0.31 13 17
EGF 0.099 0.14 0.35 65 -10000 0 65
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.028 0.12 -10000 0 -0.48 8 8
mol:Ca2+ -0.06 0.17 0.36 4 -0.31 71 75
LYN -0.028 0.12 -10000 0 -0.45 9 9
RhoA/GTP -0.025 0.07 -10000 0 -0.14 9 9
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.073 0.19 0.37 4 -0.35 76 80
GNG2 0.018 0.044 -10000 0 -0.69 1 1
ARRB2 0.019 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.045 0.15 -10000 0 -0.52 14 14
G beta5/gamma2 -0.084 0.12 -10000 0 -0.26 74 74
PRKCH -0.075 0.19 0.37 4 -0.36 73 77
DNM1 0.029 0.13 0.35 17 -0.69 5 22
TXA2/TP beta/beta Arrestin3 0.011 0.058 -10000 0 -0.3 2 2
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.02 0.16 -10000 0 -0.65 16 16
G12 family/GTP -0.075 0.15 -10000 0 -0.31 74 74
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
ADRBK2 0.031 0.077 0.35 10 -0.69 1 11
RhoA/GTP/ROCK1 0.029 0.003 -10000 0 -10000 0 0
mol:GDP 0.048 0.15 0.38 28 -0.27 1 29
mol:NADP 0.015 0.062 -10000 0 -0.69 2 2
RAB11A 0.021 0.003 -10000 0 -10000 0 0
PRKG1 -0.003 0.13 0.35 1 -0.69 9 10
mol:IP3 -0.081 0.21 0.38 4 -0.39 73 77
cell morphogenesis 0.028 0.003 -10000 0 -10000 0 0
PLCB2 -0.12 0.28 0.44 1 -0.53 76 77
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.081 0.18 -10000 0 -0.4 50 50
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.036 0.14 -10000 0 -0.42 18 18
RHOA 0.022 0.001 -10000 0 -10000 0 0
PTGIR -0.026 0.18 -10000 0 -0.67 18 18
PRKCB1 -0.081 0.2 0.37 4 -0.39 74 78
GNAQ 0.02 0.025 -10000 0 -0.38 1 1
mol:L-citrulline 0.015 0.062 -10000 0 -0.69 2 2
TXA2/TXA2-R family -0.12 0.28 0.45 1 -0.54 77 78
LCK -0.036 0.14 -10000 0 -0.42 17 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.032 0.15 -10000 0 -0.36 35 35
TXA2-R family/G12 family/GDP/G beta/gamma -0.023 0.13 -10000 0 -0.44 21 21
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.031 0.15 -10000 0 -0.36 34 34
MAPK14 -0.036 0.13 0.34 4 -0.26 6 10
TGM2/GTP -0.096 0.23 0.41 4 -0.44 69 73
MAPK11 -0.041 0.13 0.33 4 -0.25 18 22
ARHGEF1 -0.033 0.1 0.24 4 -0.2 9 13
GNAI2 0.021 0.002 -10000 0 -10000 0 0
JNK cascade -0.083 0.21 0.39 4 -0.4 77 81
RAB11/GDP 0.021 0.004 -10000 0 -10000 0 0
ICAM1 -0.054 0.16 0.34 4 -0.29 66 70
cAMP biosynthetic process -0.077 0.19 0.35 4 -0.36 70 74
Gq family/GTP/EBP50 -0.032 0.11 -10000 0 -0.44 7 7
actin cytoskeleton reorganization 0.028 0.003 -10000 0 -10000 0 0
SRC -0.026 0.12 -10000 0 -0.42 11 11
GNB5 0.021 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.03 0.13 -10000 0 -0.33 22 22
VCAM1 -0.064 0.18 0.37 4 -0.32 74 78
TP beta/Gq family/GDP/G beta5/gamma2 -0.045 0.15 -10000 0 -0.52 14 14
platelet activation -0.053 0.18 0.41 4 -0.32 38 42
PGI2/IP -0.02 0.13 -10000 0 -0.51 18 18
PRKACA -0.03 0.14 -10000 0 -0.37 31 31
Gq family/GDP/G beta5/gamma2 -0.041 0.13 -10000 0 -0.42 18 18
TXA2/TP beta/beta Arrestin2 -0.005 0.12 0.24 7 -0.56 7 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.05 0.16 -10000 0 -0.4 37 37
mol:DAG -0.094 0.23 0.39 4 -0.44 74 78
EGFR 0.01 0.087 -10000 0 -0.69 4 4
TXA2/TP alpha -0.11 0.26 0.44 1 -0.5 75 76
Gq family/GTP -0.045 0.12 -10000 0 -0.28 50 50
YES1 -0.027 0.12 -10000 0 -0.42 11 11
GNAI2/GTP -0.028 0.14 -10000 0 -0.47 13 13
PGD2/DP -0.015 0.12 -10000 0 -0.49 16 16
SLC9A3R1 0.018 0.044 -10000 0 -0.69 1 1
FYN -0.028 0.12 -10000 0 -0.4 13 13
mol:NO 0.015 0.062 -10000 0 -0.69 2 2
GNA15 0.024 0.029 0.35 2 -10000 0 2
PGK/cGMP 0.008 0.097 0.22 1 -0.45 11 12
RhoA/GDP 0.022 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.022 0.17 -10000 0 -0.52 16 16
NOS3 0.015 0.062 -10000 0 -0.69 2 2
RAC1 0.021 0.003 -10000 0 -10000 0 0
PRKCA -0.07 0.19 0.37 4 -0.36 68 72
PRKCB -0.092 0.22 0.36 4 -0.4 76 80
PRKCE -0.075 0.2 0.37 4 -0.37 67 71
PRKCD -0.084 0.21 0.38 4 -0.39 76 80
PRKCG -0.084 0.21 0.38 4 -0.4 75 79
muscle contraction -0.11 0.26 0.41 4 -0.5 77 81
PRKCZ -0.08 0.19 0.37 4 -0.36 77 81
ARR3 0.017 0.021 0.35 1 -10000 0 1
TXA2/TP beta -0.024 0.16 -10000 0 -0.43 23 23
PRKCQ -0.078 0.2 0.37 4 -0.38 70 74
MAPKKK cascade -0.1 0.25 0.39 3 -0.47 76 79
SELE -0.089 0.21 0.36 4 -0.41 75 79
TP beta/GNAI2/GDP/G beta/gamma -0.017 0.16 -10000 0 -0.51 14 14
ROCK1 0.021 0.002 -10000 0 -10000 0 0
GNA14 -0.098 0.26 -10000 0 -0.67 45 45
chemotaxis -0.14 0.32 0.47 1 -0.62 77 78
GNA12 0.021 0.004 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.008 0.097 -10000 0 -0.69 5 5
Rac1/GTP 0.015 0.003 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.018 0.14 0.45 1 -0.43 13 14
TBX21 -0.19 0.44 0.86 1 -1.1 37 38
B2M 0.015 0.022 -10000 0 -10000 0 0
TYK2 0.004 0.037 -10000 0 -10000 0 0
IL12RB1 -0.018 0.13 -10000 0 -0.72 8 8
GADD45B -0.3 0.56 0.75 1 -1.2 69 70
IL12RB2 -0.011 0.15 0.34 8 -0.66 10 18
GADD45G -0.31 0.56 0.75 1 -1.1 72 73
natural killer cell activation -0.006 0.025 0.19 1 -0.05 6 7
RELB 0.021 0.003 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL18 0.004 0.098 0.35 2 -0.64 5 7
IL2RA 0.02 0.12 0.35 10 -0.69 5 15
IFNG 0.031 0.06 0.35 9 -10000 0 9
STAT3 (dimer) -0.17 0.36 0.71 1 -0.73 57 58
HLA-DRB5 -0.008 0.011 -10000 0 -0.028 13 13
FASLG -0.17 0.45 1.1 1 -1.1 32 33
NF kappa B2 p52/RelB -0.18 0.41 -10000 0 -0.89 48 48
CD4 -0.048 0.18 -10000 0 -0.68 20 20
SOCS1 0.017 0.065 0.35 1 -0.69 2 3
EntrezGene:6955 -0.013 0.019 -10000 0 -0.034 82 82
CD3D -0.015 0.13 0.34 7 -0.63 9 16
CD3E -0.027 0.14 0.35 1 -0.68 11 12
CD3G -0.022 0.15 0.34 6 -0.65 11 17
IL12Rbeta2/JAK2 -0.004 0.12 0.31 1 -0.49 11 12
CCL3 -0.24 0.52 0.86 1 -1.3 40 41
CCL4 -0.21 0.49 0.86 1 -1.3 31 32
HLA-A -0.004 0.014 -10000 0 -0.048 22 22
IL18/IL18R -0.057 0.25 -10000 0 -0.54 47 47
NOS2 -0.16 0.4 0.86 1 -0.96 32 33
IL12/IL12R/TYK2/JAK2/SPHK2 -0.016 0.12 0.45 1 -0.38 12 13
IL1R1 -0.18 0.42 0.86 1 -1.1 30 31
IL4 0.008 0.037 -10000 0 -10000 0 0
JAK2 0.002 0.045 -10000 0 -0.42 1 1
EntrezGene:6957 -0.012 0.018 -10000 0 -0.047 34 34
TCR/CD3/MHC I/CD8 -0.17 0.47 0.41 3 -1.2 39 42
RAB7A -0.22 0.4 0.69 1 -0.77 71 72
lysosomal transport -0.21 0.38 0.68 1 -0.72 72 73
FOS -0.61 0.73 0.65 1 -1.4 121 122
STAT4 (dimer) -0.19 0.42 0.71 1 -0.82 60 61
STAT5A (dimer) -0.17 0.42 0.67 2 -0.88 49 51
GZMA -0.19 0.44 0.98 1 -1.1 39 40
GZMB -0.2 0.44 0.98 1 -1.1 34 35
HLX 0.018 0.008 -10000 0 -10000 0 0
LCK -0.2 0.48 0.86 1 -0.99 50 51
TCR/CD3/MHC II/CD4 -0.12 0.24 0.25 4 -0.5 47 51
IL2/IL2R 0.012 0.16 0.42 2 -0.46 24 26
MAPK14 -0.29 0.52 0.74 1 -0.93 86 87
CCR5 -0.17 0.4 0.75 1 -0.93 38 39
IL1B -0.1 0.26 -10000 0 -0.7 40 40
STAT6 -0.035 0.14 0.59 1 -0.58 4 5
STAT4 -0.004 0.14 0.35 1 -0.69 10 11
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.024 0.028 0.35 2 -10000 0 2
NFKB1 0.02 0.006 -10000 0 -10000 0 0
NFKB2 0.021 0.003 -10000 0 -10000 0 0
IL12B 0.002 0.048 0.35 2 -10000 0 2
CD8A -0.029 0.19 0.35 3 -0.7 18 21
CD8B -0.011 0.17 0.35 7 -0.7 13 20
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.018 0.14 0.42 13 -0.45 1 14
IL2RB -0.03 0.18 -10000 0 -0.66 20 20
proteasomal ubiquitin-dependent protein catabolic process -0.17 0.38 0.7 1 -0.74 60 61
IL2RG 0.017 0.098 0.35 5 -0.69 4 9
IL12 0.014 0.071 0.31 1 -10000 0 1
STAT5A 0.021 0.003 -10000 0 -10000 0 0
CD247 -0.004 0.069 0.35 1 -0.7 2 3
IL2 0.016 0.005 -10000 0 -10000 0 0
SPHK2 0.021 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.012 0.07 0.34 8 -10000 0 8
IL12/IL12R/TYK2/JAK2 -0.22 0.53 1 1 -1.1 50 51
MAP2K3 -0.3 0.53 0.74 1 -0.94 88 89
RIPK2 0.017 0.009 -10000 0 -10000 0 0
MAP2K6 -0.29 0.52 0.74 1 -0.93 85 86
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.009 0.012 -10000 0 -0.027 64 64
IL18RAP -0.028 0.17 -10000 0 -0.68 16 16
IL12Rbeta1/TYK2 -0.008 0.11 -10000 0 -0.57 8 8
EOMES -0.15 0.47 -10000 0 -1.4 32 32
STAT1 (dimer) -0.15 0.36 0.88 1 -0.75 48 49
T cell proliferation -0.15 0.33 0.63 1 -0.62 64 65
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.084 0.25 -10000 0 -0.69 37 37
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.24 0.33 -10000 0 -0.7 74 74
ATF2 -0.26 0.46 0.7 1 -0.85 85 86
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.1 0.41 -10000 0 -0.96 47 47
NCK1/PAK1/Dok-R -0.083 0.17 -10000 0 -0.44 47 47
NCK1/Dok-R -0.13 0.44 -10000 0 -1 47 47
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
mol:beta2-estradiol 0 0.032 0.29 2 -10000 0 2
RELA 0.021 0.003 -10000 0 -10000 0 0
SHC1 0.017 0.009 -10000 0 -10000 0 0
Rac/GDP 0.016 0.003 -10000 0 -10000 0 0
F2 -0.052 0.2 0.32 2 -0.68 24 26
TNIP2 0.021 0.003 -10000 0 -10000 0 0
NF kappa B/RelA -0.11 0.41 -10000 0 -0.97 47 47
FN1 0.019 0.044 -10000 0 -0.69 1 1
PLD2 -0.15 0.44 -10000 0 -1.1 46 46
PTPN11 0.021 0.002 -10000 0 -10000 0 0
GRB14 0.002 0.11 -10000 0 -0.69 7 7
ELK1 -0.14 0.41 -10000 0 -1 47 47
GRB7 0.019 0.088 0.35 5 -0.69 3 8
PAK1 0.021 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.43 -10000 0 -1 46 46
CDKN1A -0.068 0.3 -10000 0 -0.68 48 48
ITGA5 0.021 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.44 -10000 0 -1.1 47 47
CRK 0.019 0.007 -10000 0 -10000 0 0
mol:NO -0.057 0.31 -10000 0 -0.7 47 47
PLG -0.22 0.46 -10000 0 -1.2 47 47
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.11 0.37 -10000 0 -0.89 47 47
GRB2 0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
ANGPT2 -0.042 0.22 0.43 7 -0.53 29 36
BMX -0.18 0.49 -10000 0 -1.2 47 47
ANGPT1 0.005 0.16 0.47 1 -1.4 2 3
tube development -0.086 0.33 -10000 0 -0.75 47 47
ANGPT4 0.023 0.056 0.35 7 -10000 0 7
response to hypoxia -0.01 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.46 -10000 0 -1.1 47 47
alpha5/beta1 Integrin 0.031 0.006 -10000 0 -10000 0 0
FGF2 -0.019 0.18 0.35 4 -0.69 16 20
STAT5A (dimer) -0.095 0.38 -10000 0 -0.87 48 48
mol:L-citrulline -0.057 0.31 -10000 0 -0.7 47 47
AGTR1 -0.057 0.23 -10000 0 -0.68 30 30
MAPK14 -0.17 0.5 -10000 0 -1.2 47 47
Tie2/SHP2 -0.17 0.46 -10000 0 -1.1 47 47
TEK -0.19 0.51 -10000 0 -1.3 47 47
RPS6KB1 -0.094 0.39 -10000 0 -0.9 47 47
Angiotensin II/AT1 -0.039 0.17 -10000 0 -0.52 30 30
Tie2/Ang1/GRB2 -0.14 0.45 -10000 0 -1.1 47 47
MAPK3 -0.14 0.41 -10000 0 -1 47 47
MAPK1 -0.14 0.41 -10000 0 -1 47 47
Tie2/Ang1/GRB7 -0.14 0.46 -10000 0 -1.1 47 47
NFKB1 0.02 0.006 -10000 0 -10000 0 0
MAPK8 -0.16 0.45 -10000 0 -1.1 47 47
PI3K -0.14 0.47 -10000 0 -1.1 47 47
FES -0.17 0.51 -10000 0 -1.2 47 47
Crk/Dok-R -0.13 0.43 -10000 0 -1 47 47
Tie2/Ang1/ABIN2 -0.15 0.46 -10000 0 -1.1 47 47
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.083 0.36 -10000 0 -0.84 47 47
STAT5A 0.021 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.066 0.4 -10000 0 -0.89 47 47
Tie2/Ang2 -0.14 0.45 -10000 0 -1.1 47 47
Tie2/Ang1 -0.16 0.48 -10000 0 -1.2 47 47
FOXO1 -0.083 0.37 -10000 0 -0.85 47 47
ELF1 0.004 0.066 -10000 0 -0.73 1 1
ELF2 -0.15 0.45 -10000 0 -1.1 46 46
mol:Choline -0.14 0.42 -10000 0 -1 47 47
cell migration -0.045 0.091 -10000 0 -0.24 47 47
FYN -0.11 0.37 -10000 0 -0.87 47 47
DOK2 0.012 0.056 -10000 0 -0.49 3 3
negative regulation of cell cycle -0.055 0.28 -10000 0 -0.61 48 48
ETS1 0.016 0.037 -10000 0 -0.29 2 2
PXN -0.04 0.34 -10000 0 -0.72 47 47
ITGB1 0.021 0.004 -10000 0 -10000 0 0
NOS3 -0.076 0.35 -10000 0 -0.8 47 47
RAC1 0.021 0.003 -10000 0 -10000 0 0
TNF -0.011 0.15 0.35 2 -0.63 13 15
MAPKKK cascade -0.14 0.42 -10000 0 -1 47 47
RASA1 0.016 0.062 -10000 0 -0.69 2 2
Tie2/Ang1/Shc -0.15 0.44 -10000 0 -1.1 46 46
NCK1 0.019 0.044 -10000 0 -0.69 1 1
vasculogenesis -0.044 0.28 -10000 0 -0.62 47 47
mol:Phosphatidic acid -0.14 0.42 -10000 0 -1 47 47
mol:Angiotensin II 0.002 0.008 -10000 0 -10000 0 0
mol:NADP -0.057 0.31 -10000 0 -0.7 47 47
Rac1/GTP -0.095 0.36 -10000 0 -0.85 47 47
MMP2 -0.15 0.46 -10000 0 -1.1 46 46
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.076 0.16 0.29 52 -10000 0 52
GNAI2 0.021 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.022 0.06 0.22 1 -0.45 4 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
RhoA/GTP -0.077 0.16 -10000 0 -0.3 52 52
negative regulation of cAMP metabolic process -0.088 0.17 -10000 0 -0.32 52 52
GNAZ 0.17 0.16 0.35 117 -10000 0 117
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNA12 0.021 0.004 -10000 0 -10000 0 0
S1PR5 0.012 0.089 0.35 1 -0.69 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.089 0.17 -10000 0 -0.32 52 52
RhoA/GDP 0.016 0.001 -10000 0 -10000 0 0
RHOA 0.022 0.001 -10000 0 -10000 0 0
GNAI1 0.016 0.062 -10000 0 -0.69 2 2
S1P1 pathway

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.011 0.075 -10000 0 -0.45 6 6
PDGFRB 0.027 0.049 0.34 6 -10000 0 6
SPHK1 0.007 0.13 0.24 1 -0.9 3 4
mol:S1P 0.003 0.13 0.26 8 -0.8 3 11
S1P1/S1P/Gi -0.18 0.26 -10000 0 -0.49 82 82
GNAO1 -0.29 0.34 -10000 0 -0.67 117 117
PDGFB-D/PDGFRB/PLCgamma1 -0.14 0.23 0.31 2 -0.52 46 48
PLCG1 -0.16 0.24 -10000 0 -0.49 64 64
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.049 0.34 6 -10000 0 6
GNAI2 0.012 0.018 -10000 0 -10000 0 0
GNAI3 0.01 0.017 -10000 0 -10000 0 0
GNAI1 0.006 0.064 -10000 0 -0.7 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.008 0.062 -10000 0 -0.39 6 6
S1P1/S1P -0.007 0.13 0.24 2 -0.49 8 10
negative regulation of cAMP metabolic process -0.17 0.25 -10000 0 -0.47 82 82
MAPK3 -0.23 0.32 -10000 0 -0.65 81 81
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.001 -10000 0 -10000 0 0
KDR 0.001 0.1 -10000 0 -0.64 6 6
PLCB2 0.003 0.14 0.29 3 -0.42 12 15
RAC1 0.021 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.025 0.09 -10000 0 -0.41 8 8
receptor internalization -0.009 0.12 0.22 2 -0.45 8 10
PTGS2 -0.37 0.51 -10000 0 -1.1 81 81
Rac1/GTP -0.024 0.088 -10000 0 -0.4 8 8
RHOA 0.022 0.001 -10000 0 -10000 0 0
VEGFA 0.015 0.013 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.17 0.25 -10000 0 -0.47 82 82
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.16 0.17 0.34 117 -10000 0 117
MAPK1 -0.23 0.32 -10000 0 -0.65 82 82
S1P1/S1P/PDGFB-D/PDGFRB -0.004 0.14 -10000 0 -0.49 8 8
ABCC1 0.029 0.057 0.35 8 -10000 0 8
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.021 0.079 -10000 0 -0.71 1 1
Syndecan-4/Syndesmos -0.075 0.29 -10000 0 -0.72 36 36
positive regulation of JNK cascade -0.2 0.29 -10000 0 -0.66 50 50
Syndecan-4/ADAM12 -0.061 0.29 0.37 6 -0.7 36 42
CCL5 0.003 0.12 0.35 1 -0.69 7 8
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
DNM2 0.021 0.002 -10000 0 -10000 0 0
ITGA5 0.021 0.002 -10000 0 -10000 0 0
SDCBP 0.018 0.008 -10000 0 -10000 0 0
PLG -0.1 0.26 -10000 0 -0.64 48 48
ADAM12 0.057 0.12 0.35 31 -0.69 1 32
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.033 0.03 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.11 0.3 -10000 0 -0.67 44 44
Syndecan-4/CXCL12/CXCR4 -0.21 0.32 -10000 0 -0.72 50 50
Syndecan-4/Laminin alpha3 -0.052 0.3 0.37 4 -0.72 36 40
MDK 0.19 0.16 0.35 138 -10000 0 138
Syndecan-4/FZD7 -0.077 0.29 -10000 0 -0.72 36 36
Syndecan-4/Midkine 0.011 0.32 0.37 23 -0.7 35 58
FZD7 0.018 0.086 0.35 4 -0.69 3 7
Syndecan-4/FGFR1/FGF -0.088 0.28 -10000 0 -0.65 42 42
THBS1 -0.072 0.24 -10000 0 -0.68 35 35
integrin-mediated signaling pathway -0.086 0.28 0.37 2 -0.7 36 38
positive regulation of MAPKKK cascade -0.2 0.29 -10000 0 -0.66 50 50
Syndecan-4/TACI -0.077 0.29 0.37 1 -0.72 36 37
CXCR4 0.016 0.062 -10000 0 -0.69 2 2
cell adhesion 0.024 0.04 -10000 0 -0.34 1 1
Syndecan-4/Dynamin -0.075 0.29 -10000 0 -0.72 36 36
Syndecan-4/TSP1 -0.12 0.31 -10000 0 -0.71 44 44
Syndecan-4/GIPC -0.073 0.29 -10000 0 -0.73 35 35
Syndecan-4/RANTES -0.084 0.3 -10000 0 -0.74 36 36
ITGB1 0.021 0.004 -10000 0 -10000 0 0
LAMA1 -0.036 0.24 0.35 17 -0.68 29 46
LAMA3 0.065 0.14 0.35 41 -0.69 3 44
RAC1 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.043 0.16 0.78 11 -10000 0 11
Syndecan-4/alpha-Actinin -0.075 0.29 -10000 0 -0.72 36 36
TFPI -0.014 0.15 -10000 0 -0.69 13 13
F2 -0.041 0.2 -10000 0 -0.67 24 24
alpha5/beta1 Integrin 0.031 0.006 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.097 0.29 -10000 0 -0.68 39 39
ACTN1 0.021 0.004 -10000 0 -10000 0 0
TNC -0.012 0.17 0.35 5 -0.67 15 20
Syndecan-4/CXCL12 -0.22 0.32 -10000 0 -0.68 61 61
FGF6 0.014 0.003 -10000 0 -10000 0 0
RHOA 0.022 0.001 -10000 0 -10000 0 0
CXCL12 -0.27 0.35 -10000 0 -0.68 108 108
TNFRSF13B 0.018 0.053 0.35 2 -0.69 1 3
FGF2 -0.018 0.18 0.35 4 -0.69 16 20
FGFR1 0.014 0.073 0.35 2 -0.59 3 5
Syndecan-4/PI-4-5-P2 -0.088 0.28 -10000 0 -0.72 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.044 -10000 0 -0.64 1 1
cell migration -0.014 0.01 -10000 0 -10000 0 0
PRKCD 0.021 0.015 -10000 0 -10000 0 0
vasculogenesis -0.12 0.29 -10000 0 -0.67 44 44
SDC4 -0.091 0.31 -10000 0 -0.78 36 36
Syndecan-4/Tenascin C -0.092 0.3 0.37 2 -0.74 36 38
Syndecan-4/PI-4-5-P2/PKC alpha -0.027 0.024 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.082 0.28 -10000 0 -0.73 35 35
MMP9 0.058 0.18 0.35 47 -0.69 8 55
Rac1/GTP 0.025 0.041 -10000 0 -0.35 1 1
cytoskeleton organization -0.069 0.27 -10000 0 -0.68 36 36
GIPC1 0.021 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.09 0.31 -10000 0 -0.77 37 37
Glucocorticoid receptor regulatory network

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
PCK2 -0.092 0.39 -10000 0 -1.1 30 30
SMARCC2 0.02 0.015 -10000 0 -10000 0 0
SMARCC1 0.02 0.018 -10000 0 -10000 0 0
TBX21 -0.075 0.23 -10000 0 -0.83 13 13
SUMO2 0.009 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.029 0.028 0.35 2 -10000 0 2
FKBP4 0.021 0.004 -10000 0 -10000 0 0
FKBP5 0.02 0.006 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.057 0.12 0.31 3 -10000 0 3
PRL -0.015 0.15 0.77 1 -0.75 1 2
cortisol/GR alpha (dimer)/TIF2 0.054 0.32 0.54 41 -0.56 22 63
RELA -0.066 0.13 -10000 0 -0.3 19 19
FGG -0.007 0.34 0.46 18 -0.71 36 54
GR beta/TIF2 0.007 0.2 0.31 16 -0.52 19 35
IFNG -0.066 0.28 0.61 11 -0.55 18 29
apoptosis -0.19 0.36 0.59 2 -0.84 39 41
CREB1 0.036 0.044 -10000 0 -10000 0 0
histone acetylation -0.061 0.13 -10000 0 -0.37 16 16
BGLAP -0.006 0.14 0.48 1 -0.46 3 4
GR/PKAc 0.065 0.12 0.32 4 -10000 0 4
NF kappa B1 p50/RelA -0.12 0.24 0.4 1 -0.46 59 60
SMARCD1 0.02 0.015 -10000 0 -10000 0 0
MDM2 0.04 0.096 0.23 19 -10000 0 19
GATA3 -0.019 0.18 0.36 1 -0.68 18 19
AKT1 0.033 0.047 0.23 1 -10000 0 1
CSF2 -0.049 0.1 -10000 0 -10000 0 0
GSK3B 0.009 0.02 -10000 0 -10000 0 0
NR1I3 -0.24 0.45 0.61 3 -0.94 64 67
CSN2 0.026 0.21 0.39 9 -0.47 14 23
BRG1/BAF155/BAF170/BAF60A 0.052 0.045 -10000 0 -0.27 2 2
NFATC1 0.016 0.062 -10000 0 -0.69 2 2
POU2F1 0.019 0.014 -10000 0 -10000 0 0
CDKN1A -0.005 0.21 -10000 0 -1.5 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.004 0.01 -10000 0 -10000 0 0
SFN 0.2 0.16 0.35 148 -10000 0 148
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.16 0.15 0.37 51 -10000 0 51
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.31 0.45 0.62 1 -0.87 94 95
JUN 0.041 0.25 0.51 28 -0.45 18 46
IL4 -0.046 0.15 -10000 0 -0.78 2 2
CDK5R1 0.018 0.022 0.34 1 -10000 0 1
PRKACA 0.021 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.17 0.2 -10000 0 -0.41 86 86
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.063 0.11 -10000 0 -10000 0 0
cortisol/GR alpha (monomer) 0.14 0.36 0.59 61 -0.54 21 82
NCOA2 -0.034 0.18 -10000 0 -0.69 19 19
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.24 0.37 0.34 5 -0.63 117 122
AP-1/NFAT1-c-4 -0.1 0.37 0.58 21 -0.56 67 88
AFP 0.019 0.37 0.6 15 -1.4 10 25
SUV420H1 0.021 0.003 -10000 0 -10000 0 0
IRF1 0.069 0.16 0.41 7 -10000 0 7
TP53 0.023 0.058 -10000 0 -0.5 3 3
PPP5C 0.021 0.003 -10000 0 -10000 0 0
KRT17 -0.056 0.4 0.62 25 -0.99 17 42
KRT14 0.003 0.2 0.52 14 -10000 0 14
TBP 0.026 0.017 -10000 0 -10000 0 0
CREBBP -0.003 0.069 -10000 0 -0.27 7 7
HDAC1 0.02 0.004 -10000 0 -10000 0 0
HDAC2 0.02 0.004 -10000 0 -10000 0 0
AP-1 -0.1 0.37 0.58 21 -0.56 66 87
MAPK14 0.009 0.019 -10000 0 -10000 0 0
MAPK10 -0.014 0.15 0.34 7 -0.62 13 20
MAPK11 0.019 0.06 0.34 8 -10000 0 8
KRT5 -0.041 0.32 0.62 22 -0.61 16 38
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.012 0.034 -10000 0 -10000 0 0
STAT1 0.029 0.029 0.35 2 -10000 0 2
CGA -0.016 0.17 0.56 2 -10000 0 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.018 0.16 0.34 1 -0.43 13 14
MAPK3 0.008 0.02 -10000 0 -10000 0 0
MAPK1 0.008 0.02 -10000 0 -10000 0 0
ICAM1 -0.13 0.25 -10000 0 -0.64 26 26
NFKB1 -0.061 0.12 -10000 0 -0.28 35 35
MAPK8 -0.008 0.24 0.45 23 -0.43 31 54
MAPK9 0.008 0.019 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.21 0.4 0.59 2 -0.93 39 41
BAX 0.003 0.077 -10000 0 -10000 0 0
POMC -0.086 0.24 -10000 0 -1.3 3 3
EP300 -0.002 0.068 -10000 0 -0.27 4 4
cortisol/GR alpha (dimer)/p53 0.089 0.29 0.52 33 -0.52 13 46
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.092 0.36 7 -10000 0 7
SGK1 -0.031 0.27 -10000 0 -1.5 8 8
IL13 -0.086 0.29 0.61 3 -0.78 19 22
IL6 -0.26 0.5 0.52 4 -1.2 49 53
PRKACG 0.015 0.003 -10000 0 -10000 0 0
IL5 -0.077 0.24 -10000 0 -0.74 14 14
IL2 -0.093 0.28 0.54 8 -0.67 16 24
CDK5 0.016 0.011 -10000 0 -10000 0 0
PRKACB 0.019 0.025 -10000 0 -0.38 1 1
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
IL8 -0.33 0.57 0.56 7 -1.2 67 74
CDK5R1/CDK5 0.021 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.069 0.19 -10000 0 -0.42 30 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.12 0.29 0.52 42 -0.47 13 55
SMARCA4 0.019 0.018 -10000 0 -10000 0 0
chromatin remodeling 0.064 0.18 0.37 17 -0.44 4 21
NF kappa B1 p50/RelA/Cbp -0.11 0.21 -10000 0 -0.46 37 37
JUN (dimer) 0.041 0.25 0.51 28 -0.45 18 46
YWHAH 0.021 0.003 -10000 0 -10000 0 0
VIPR1 -0.68 0.51 -10000 0 -1 175 175
NR3C1 0.071 0.2 0.4 35 -0.32 3 38
NR4A1 -0.069 0.24 -10000 0 -0.67 36 36
TIF2/SUV420H1 -0.015 0.14 -10000 0 -0.52 19 19
MAPKKK cascade -0.19 0.36 0.59 2 -0.84 39 41
cortisol/GR alpha (dimer)/Src-1 0.11 0.32 0.54 47 -0.52 19 66
PBX1 -0.011 0.14 -10000 0 -0.69 11 11
POU1F1 0.019 0.024 0.35 1 -10000 0 1
SELE -0.34 0.57 -10000 0 -1.2 69 69
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.064 0.18 0.37 17 -0.44 4 21
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.12 0.29 0.52 42 -0.47 13 55
mol:cortisol 0.062 0.19 0.34 48 -0.28 18 66
MMP1 0.073 0.26 0.47 48 -0.82 5 53
TCGA08_p53

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.13 0.094 0.2 169 -9999 0 169
TP53 0.033 0.035 -10000 0 -9999 0 0
Senescence 0.033 0.035 -10000 0 -9999 0 0
Apoptosis 0.033 0.035 -10000 0 -9999 0 0
Activated_Oncogenes 0 0 -10000 0 -9999 0 0
MDM2 -0.085 0.062 -10000 0 -9999 0 0
MDM4 0.018 0.008 -10000 0 -9999 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.021 0.004 -10000 0 -10000 0 0
VLDLR 0.009 0.21 0.35 30 -0.66 19 49
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
NUDC 0.021 0.004 -10000 0 -10000 0 0
RELN/LRP8 -0.11 0.24 -10000 0 -0.43 87 87
CaM/Ca2+ 0.016 0.003 -10000 0 -10000 0 0
KATNA1 0.02 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.12 0.2 -10000 0 -0.4 85 85
IQGAP1/CaM 0.03 0.008 -10000 0 -10000 0 0
DAB1 -0.093 0.26 -10000 0 -0.68 42 42
IQGAP1 0.021 0.004 -10000 0 -10000 0 0
PLA2G7 0.031 0.06 0.35 9 -10000 0 9
CALM1 0.021 0.004 -10000 0 -10000 0 0
DYNLT1 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.054 0.069 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.002 -10000 0 -10000 0 0
CDK5R1 0.022 0.02 0.35 1 -10000 0 1
LIS1/Poliovirus Protein 3A 0.009 0.003 -10000 0 -10000 0 0
CDK5R2 0.026 0.057 0.35 8 -10000 0 8
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.21 0.31 -10000 0 -0.5 125 125
YWHAE 0.019 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.078 0.18 0.34 3 -0.38 16 19
MAP1B 0.008 0.021 -10000 0 -10000 0 0
RAC1 0.012 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.095 0.18 -10000 0 -0.37 69 69
RELN -0.22 0.34 0.35 2 -0.68 89 91
PAFAH/LIS1 0.029 0.041 -10000 0 -10000 0 0
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.072 0.14 -10000 0 -0.34 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.24 -10000 0 -0.4 100 100
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.095 0.18 -10000 0 -0.36 71 71
LIS1/IQGAP1 0.022 0.009 -10000 0 -10000 0 0
RHOA 0.012 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.012 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.049 0.091 0.35 22 -10000 0 22
PAFAH1B2 0.021 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.026 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.074 0.18 0.39 1 -0.38 16 17
LRP8 0.057 0.1 0.35 29 -10000 0 29
NDEL1/Katanin 60 -0.081 0.18 0.36 2 -0.35 48 50
P39/CDK5 -0.095 0.19 0.3 3 -0.37 70 73
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.009 -10000 0 -10000 0 0
CDK5 -0.11 0.19 -10000 0 -0.37 84 84
PPP2R5D 0.02 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.008 -10000 0 -10000 0 0
CSNK2A1 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.18 0.27 -10000 0 -0.45 118 118
RELN/VLDLR -0.097 0.27 0.41 7 -0.44 87 94
CDC42 0.012 0.005 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.009 0.13 -10000 0 -0.59 9 9
alphaM/beta2 Integrin/GPIbA 0.012 0.1 -10000 0 -0.48 8 8
alphaM/beta2 Integrin/proMMP-9 0.04 0.16 0.35 3 -0.52 12 15
PLAUR 0.02 0.071 0.35 3 -0.69 2 5
HMGB1 0.011 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.019 0.09 -10000 0 -0.5 5 5
AGER 0.016 0.052 0.36 4 -10000 0 4
RAP1A 0.021 0.004 -10000 0 -10000 0 0
SELPLG 0.019 0.044 -10000 0 -0.69 1 1
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.016 0.14 0.43 1 -0.44 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.058 0.18 0.35 47 -0.69 8 55
CYR61 -0.039 0.19 -10000 0 -0.64 24 24
TLN1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP -0.077 0.18 -10000 0 -0.46 34 34
RHOA 0.022 0.001 -10000 0 -10000 0 0
P-selectin oligomer -0.14 0.29 -10000 0 -0.68 59 59
MYH2 -0.14 0.27 -10000 0 -0.67 41 41
MST1R 0.063 0.15 0.35 42 -0.69 4 46
leukocyte activation during inflammatory response -0.19 0.23 -10000 0 -0.42 123 123
APOB -0.019 0.16 -10000 0 -0.69 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.009 0.12 0.35 5 -0.64 7 12
JAM3 0.022 0.021 0.35 1 -10000 0 1
GP1BA 0.013 0.087 0.35 3 -0.61 4 7
alphaM/beta2 Integrin/CTGF 0.012 0.11 -10000 0 -0.55 7 7
alphaM/beta2 Integrin -0.1 0.2 -10000 0 -0.5 38 38
JAM3 homodimer 0.022 0.02 0.35 1 -10000 0 1
ICAM2 0.022 0.021 0.35 1 -10000 0 1
ICAM1 0.021 0.003 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.1 0.2 -10000 0 -0.51 37 37
cell adhesion 0.011 0.1 -10000 0 -0.48 8 8
NFKB1 -0.036 0.21 0.4 3 -0.46 39 42
THY1 0.1 0.14 0.35 64 -10000 0 64
RhoA/GDP 0.016 0.001 -10000 0 -10000 0 0
Lipoprotein(a) -0.22 0.25 -10000 0 -0.45 133 133
alphaM/beta2 Integrin/LRP/tPA 0.023 0.1 -10000 0 -0.51 6 6
IL6 -0.099 0.34 0.43 8 -0.88 37 45
ITGB2 0.006 0.074 0.35 1 -0.71 2 3
elevation of cytosolic calcium ion concentration 0.028 0.1 0.38 2 -0.45 7 9
alphaM/beta2 Integrin/JAM2/JAM3 0.014 0.12 0.43 1 -0.43 14 15
JAM2 -0.005 0.14 0.35 1 -0.63 11 12
alphaM/beta2 Integrin/ICAM1 0.014 0.17 -10000 0 -0.37 32 32
alphaM/beta2 Integrin/uPA/Plg -0.05 0.18 -10000 0 -0.42 45 45
RhoA/GTP -0.14 0.29 -10000 0 -0.61 51 51
positive regulation of phagocytosis -0.074 0.18 -10000 0 -0.51 28 28
Ron/MSP 0.002 0.18 -10000 0 -0.48 28 28
alphaM/beta2 Integrin/uPAR/uPA 0.03 0.1 0.39 2 -0.45 7 9
alphaM/beta2 Integrin/uPAR 0.017 0.1 0.3 1 -0.49 7 8
PLAU 0.027 0.045 0.35 5 -10000 0 5
PLAT 0.019 0.074 0.35 4 -0.69 2 6
actin filament polymerization -0.13 0.25 -10000 0 -0.62 41 41
MST1 -0.043 0.2 -10000 0 -0.69 24 24
alphaM/beta2 Integrin/lipoprotein(a) -0.19 0.24 -10000 0 -0.42 123 123
TNF -0.059 0.25 0.47 2 -0.86 16 18
RAP1B 0.021 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.021 0.094 -10000 0 -0.5 5 5
fibrinolysis -0.05 0.18 -10000 0 -0.42 45 45
HCK -0.003 0.13 -10000 0 -0.69 9 9
dendritic cell antigen processing and presentation -0.1 0.2 -10000 0 -0.51 37 37
VTN -0.011 0.15 -10000 0 -0.69 12 12
alphaM/beta2 Integrin/CYR61 -0.021 0.16 -10000 0 -0.49 25 25
LPA -0.31 0.34 -10000 0 -0.66 127 127
LRP1 0.019 0.044 -10000 0 -0.69 1 1
cell migration 0.016 0.16 0.36 1 -0.51 16 17
FN1 0.019 0.044 -10000 0 -0.69 1 1
alphaM/beta2 Integrin/Thy1 0.066 0.13 0.36 5 -0.5 5 10
MPO -0.001 0.12 0.35 1 -0.69 8 9
KNG1 -0.052 0.22 -10000 0 -0.69 27 27
RAP1/GDP 0.028 0.006 -10000 0 -10000 0 0
ROCK1 -0.13 0.26 -10000 0 -0.66 37 37
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.1 0.27 -10000 0 -0.66 48 48
CTGF 0.011 0.079 -10000 0 -0.61 4 4
alphaM/beta2 Integrin/Hck 0.004 0.14 -10000 0 -0.62 11 11
ITGAM 0.004 0.09 0.34 2 -0.73 3 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.074 0.21 -10000 0 -0.44 61 61
HP -0.2 0.32 -10000 0 -0.66 84 84
leukocyte adhesion 0.031 0.16 0.35 5 -0.5 5 10
SELP -0.14 0.29 -10000 0 -0.68 59 59
BCR signaling pathway

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
JUN -0.059 0.16 0.45 1 -0.39 24 25
IKBKB -0.039 0.12 0.27 3 -0.31 20 23
AKT1 -0.042 0.12 0.29 5 -0.26 15 20
IKBKG -0.011 0.089 0.26 3 -0.36 1 4
CALM1 -0.04 0.13 -10000 0 -0.43 12 12
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
MAP3K1 -0.088 0.22 0.55 1 -0.51 32 33
MAP3K7 0.021 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.043 0.13 -10000 0 -0.42 16 16
DOK1 0.022 0 -10000 0 -10000 0 0
AP-1 -0.088 0.12 0.31 1 -0.26 41 42
LYN 0.018 0.008 -10000 0 -10000 0 0
BLNK 0.005 0.11 -10000 0 -0.69 6 6
SHC1 0.017 0.009 -10000 0 -10000 0 0
BCR complex -0.1 0.24 0.49 1 -0.51 67 68
CD22 -0.15 0.24 0.48 1 -0.52 61 62
CAMK2G -0.036 0.12 -10000 0 -0.4 12 12
CSNK2A1 0.021 0.003 -10000 0 -10000 0 0
INPP5D 0.019 0.044 -10000 0 -0.69 1 1
SHC/GRB2/SOS1 -0.065 0.16 -10000 0 -0.38 45 45
GO:0007205 -0.044 0.14 -10000 0 -0.43 16 16
SYK 0.019 0.044 -10000 0 -0.69 1 1
ELK1 -0.043 0.13 -10000 0 -0.42 14 14
NFATC1 -0.065 0.18 -10000 0 -0.43 24 24
B-cell antigen/BCR complex -0.1 0.24 0.49 1 -0.51 67 68
PAG1/CSK 0.021 0.051 -10000 0 -0.52 2 2
NFKBIB -0.003 0.052 0.15 3 -0.13 13 16
HRAS -0.028 0.14 0.26 1 -0.4 15 16
NFKBIA -0.002 0.052 0.15 3 -0.13 17 20
NF-kappa-B/RelA/I kappa B beta 0.004 0.044 0.15 3 -10000 0 3
RasGAP/Csk -0.2 0.29 0.41 1 -0.49 114 115
mol:GDP -0.036 0.13 -10000 0 -0.4 16 16
PTEN 0.018 0.036 -10000 0 -0.38 2 2
CD79B 0.022 0.02 0.35 1 -10000 0 1
NF-kappa-B/RelA/I kappa B alpha 0.004 0.043 0.15 3 -10000 0 3
GRB2 0.021 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.096 0.22 0.45 1 -0.48 40 41
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
mol:IP3 -0.044 0.14 -10000 0 -0.43 16 16
CSK 0.021 0.003 -10000 0 -10000 0 0
FOS -0.19 0.22 -10000 0 -0.44 96 96
CHUK -0.016 0.1 0.26 3 -0.34 7 10
IBTK 0.021 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.025 0.14 -10000 0 -0.44 15 15
PTPN6 -0.14 0.23 0.44 1 -0.53 51 52
RELA 0.021 0.003 -10000 0 -10000 0 0
BCL2A1 0 0.042 -10000 0 -0.13 7 7
VAV2 -0.12 0.21 0.44 1 -0.51 40 41
ubiquitin-dependent protein catabolic process 0 0.052 0.15 3 -0.12 20 23
BTK -0.004 0.14 -10000 0 -1.1 4 4
CD19 -0.12 0.21 0.48 1 -0.46 54 55
MAP4K1 0.008 0.11 0.35 2 -0.69 6 8
CD72 0.013 0.092 0.35 2 -0.69 4 6
PAG1 0.013 0.065 0.35 1 -0.69 2 3
MAPK14 -0.064 0.18 0.53 1 -0.45 23 24
SH3BP5 0.016 0.062 -10000 0 -0.69 2 2
PIK3AP1 -0.042 0.14 -10000 0 -0.49 14 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.089 0.23 0.32 1 -0.46 58 59
RAF1 -0.026 0.13 0.28 1 -0.39 13 14
RasGAP/p62DOK/SHIP -0.2 0.28 0.37 1 -0.47 115 116
CD79A -0.15 0.32 0.35 6 -0.69 67 73
re-entry into mitotic cell cycle -0.087 0.12 0.31 1 -0.26 41 42
RASA1 0.016 0.062 -10000 0 -0.69 2 2
MAPK3 -0.02 0.12 -10000 0 -0.35 10 10
MAPK1 -0.02 0.12 -10000 0 -0.35 10 10
CD72/SHP1 -0.12 0.24 0.62 1 -0.51 53 54
NFKB1 0.02 0.006 -10000 0 -10000 0 0
MAPK8 -0.086 0.19 0.53 1 -0.45 32 33
actin cytoskeleton organization -0.084 0.2 0.36 2 -0.44 37 39
NF-kappa-B/RelA 0.011 0.086 0.27 3 -0.2 2 5
Calcineurin -0.02 0.12 -10000 0 -0.38 10 10
PI3K -0.12 0.18 -10000 0 -0.45 46 46
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.041 0.14 -10000 0 -0.45 16 16
SOS1 0.022 0.001 -10000 0 -10000 0 0
Bam32/HPK1 -0.14 0.3 0.76 1 -0.81 31 32
DAPP1 -0.16 0.33 0.59 1 -0.92 30 31
cytokine secretion -0.06 0.17 -10000 0 -0.4 24 24
mol:DAG -0.044 0.14 -10000 0 -0.43 16 16
PLCG2 0.007 0.097 -10000 0 -0.69 5 5
MAP2K1 -0.023 0.12 -10000 0 -0.38 11 11
B-cell antigen/BCR complex/FcgammaRIIB -0.24 0.31 0.44 1 -0.52 131 132
mol:PI-3-4-5-P3 -0.084 0.13 -10000 0 -0.32 39 39
ETS1 -0.034 0.11 -10000 0 -0.38 10 10
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.062 0.21 0.41 1 -0.41 60 61
B-cell antigen/BCR complex/LYN -0.13 0.21 0.43 1 -0.47 59 60
MALT1 0.021 0.003 -10000 0 -10000 0 0
TRAF6 0.019 0.044 -10000 0 -0.69 1 1
RAC1 -0.098 0.2 0.41 1 -0.47 37 38
B-cell antigen/BCR complex/LYN/SYK -0.14 0.25 0.47 1 -0.55 56 57
CARD11 -0.048 0.16 0.32 2 -0.47 19 21
FCGR2B -0.24 0.34 0.35 2 -0.69 97 99
PPP3CA 0.02 0.005 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
IKK complex -0.004 0.049 0.18 3 -0.14 1 4
PTPRC -0.022 0.16 0.35 1 -0.69 15 16
PDPK1 -0.041 0.11 0.28 5 -0.25 14 19
PPP3CB 0.021 0.003 -10000 0 -10000 0 0
PPP3CC 0.017 0.009 -10000 0 -10000 0 0
POU2F2 0.003 0.039 0.17 2 -0.14 7 9
Neurotrophic factor-mediated Trk 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
CRKL 0.021 0.003 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.12 0.15 -10000 0 -0.39 28 28
NT3 (dimer)/TRKC -0.28 0.29 -10000 0 -0.53 144 144
NT3 (dimer)/TRKB -0.43 0.43 -10000 0 -0.73 161 161
SHC/Grb2/SOS1/GAB1/PI3K 0.018 0.035 -10000 0 -0.51 1 1
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
BDNF 0.034 0.063 0.35 10 -10000 0 10
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
DYNLT1 0.02 0.005 -10000 0 -10000 0 0
NTRK1 0.018 0.03 0.35 2 -10000 0 2
NTRK2 -0.1 0.29 0.35 8 -0.69 50 58
NTRK3 -0.015 0.17 0.35 4 -0.69 15 19
NT-4/5 (dimer)/TRKB -0.21 0.33 -10000 0 -0.56 113 113
neuron apoptosis 0.11 0.22 0.49 46 -0.37 1 47
SHC 2-3/Grb2 -0.12 0.24 0.38 1 -0.54 46 47
SHC1 0.017 0.009 -10000 0 -10000 0 0
SHC2 -0.15 0.24 -10000 0 -0.58 49 49
SHC3 -0.12 0.22 0.36 2 -0.54 43 45
STAT3 (dimer) 0.011 0.076 -10000 0 -0.37 10 10
NT3 (dimer)/TRKA -0.34 0.35 -10000 0 -0.63 143 143
RIN/GDP -0.064 0.12 0.22 1 -0.26 13 14
GIPC1 0.021 0.003 -10000 0 -10000 0 0
KRAS 0.021 0.003 -10000 0 -10000 0 0
DNAJA3 -0.14 0.2 0.33 1 -0.39 96 97
RIN/GTP 0.011 0.002 -10000 0 -10000 0 0
CCND1 -0.019 0.18 -10000 0 -0.91 10 10
MAGED1 0.019 0.044 -10000 0 -0.69 1 1
PTPN11 0.021 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.036 0.35 3 -10000 0 3
SHC/GRB2/SOS1 0.033 0.019 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.018 0.094 -10000 0 -0.4 11 11
TRKA/NEDD4-2 0.026 0.023 -10000 0 -10000 0 0
ELMO1 0.018 0.044 -10000 0 -0.69 1 1
RhoG/GTP/ELMO1/DOCK1 0.016 0.079 -10000 0 -0.53 5 5
NGF -0.009 0.14 -10000 0 -0.69 11 11
HRAS 0.023 0.02 0.35 1 -10000 0 1
DOCK1 0.007 0.097 -10000 0 -0.69 5 5
GAB2 0.021 0.003 -10000 0 -10000 0 0
RIT2 0.015 0.003 -10000 0 -10000 0 0
RIT1 0.017 0.009 -10000 0 -10000 0 0
FRS2 0.021 0.003 -10000 0 -10000 0 0
DNM1 0.029 0.13 0.35 17 -0.69 5 22
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.13 0.2 0.31 1 -0.39 93 94
mol:GDP -0.1 0.17 -10000 0 -0.37 23 23
NGF (dimer) -0.009 0.14 -10000 0 -0.69 11 11
RhoG/GDP 0.014 0.033 -10000 0 -0.52 1 1
RIT1/GDP -0.063 0.11 -10000 0 -0.26 12 12
TIAM1 -0.006 0.14 -10000 0 -0.69 10 10
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
BDNF (dimer)/TRKB -0.04 0.21 0.44 2 -0.45 50 52
KIDINS220/CRKL/C3G 0.031 0.006 -10000 0 -10000 0 0
SHC/RasGAP 0.021 0.042 -10000 0 -0.41 2 2
FRS2 family/SHP2 0.04 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.04 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.013 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.34 0.35 -10000 0 -0.67 138 138
RAP1/GDP -0.066 0.09 -10000 0 -0.22 13 13
KIDINS220/CRKL 0.021 0.003 -10000 0 -10000 0 0
BDNF (dimer) 0.034 0.063 0.35 10 -10000 0 10
ubiquitin-dependent protein catabolic process 0.016 0.092 -10000 0 -0.4 11 11
Schwann cell development -0.049 0.042 -10000 0 -10000 0 0
EHD4 0.021 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.049 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.015 0.034 -10000 0 -10000 0 0
RAP1B 0.021 0.002 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.23 0.28 0.31 2 -0.46 135 137
ABL1 0.021 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.012 0.11 -10000 0 -0.47 5 5
STAT3 0.011 0.076 -10000 0 -0.37 10 10
axon guidance -0.23 0.26 -10000 0 -0.44 140 140
MAPK3 -0.002 0.079 -10000 0 -0.41 8 8
MAPK1 -0.003 0.079 -10000 0 -0.41 8 8
CDC42/GDP -0.063 0.12 0.22 1 -0.26 12 13
NTF3 -0.34 0.35 -10000 0 -0.67 138 138
NTF4 0.019 0.036 0.35 3 -10000 0 3
NGF (dimer)/TRKA/FAIM 0.017 0.091 -10000 0 -0.44 8 8
PI3K 0.028 0.06 -10000 0 -0.93 1 1
FRS3 0.02 0.006 -10000 0 -10000 0 0
FAIM 0.023 0.02 0.35 1 -10000 0 1
GAB1 0.021 0.005 -10000 0 -10000 0 0
RASGRF1 -0.12 0.21 0.33 1 -0.38 93 94
SOS1 0.022 0.001 -10000 0 -10000 0 0
MCF2L -0.24 0.25 -10000 0 -0.47 130 130
RGS19 0.021 0.003 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.007 0.1 -10000 0 -0.43 3 3
Rac1/GDP -0.062 0.12 0.22 1 -0.26 14 15
NGF (dimer)/TRKA/GRIT 0.006 0.089 -10000 0 -0.4 11 11
neuron projection morphogenesis -0.13 0.23 -10000 0 -0.68 16 16
NGF (dimer)/TRKA/NEDD4-2 0.016 0.092 -10000 0 -0.4 11 11
MAP2K1 0.057 0.08 0.36 5 -10000 0 5
NGFR -0.24 0.34 -10000 0 -0.69 96 96
NGF (dimer)/TRKA/GIPC/GAIP 0.008 0.089 0.24 1 -0.35 11 12
RAS family/GTP/PI3K 0.02 0.031 -10000 0 -0.47 1 1
FRS2 family/SHP2/GRB2/SOS1 0.057 0.021 -10000 0 -10000 0 0
NRAS 0.021 0.003 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
PRKCI 0.021 0.002 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.021 0.003 -10000 0 -10000 0 0
PRKCZ -0.009 0.14 -10000 0 -0.66 11 11
MAPKKK cascade -0.047 0.16 -10000 0 -0.65 15 15
RASA1 0.016 0.062 -10000 0 -0.69 2 2
TRKA/c-Abl 0.026 0.024 -10000 0 -10000 0 0
SQSTM1 0.022 0.021 0.35 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.027 0.2 0.42 2 -0.41 50 52
NGF (dimer)/TRKA/p62/Atypical PKCs 0.014 0.12 -10000 0 -0.39 16 16
MATK 0.024 0.029 0.35 2 -10000 0 2
NEDD4L 0.021 0.003 -10000 0 -10000 0 0
RAS family/GDP -0.074 0.071 -10000 0 -0.22 1 1
NGF (dimer)/TRKA -0.14 0.21 0.34 1 -0.41 98 99
Rac1/GTP -0.14 0.15 -10000 0 -0.33 84 84
FRS2 family/SHP2/CRK family 0.052 0.026 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.035 0.2 0.29 31 -0.54 21 52
FYN -0.013 0.26 0.4 5 -0.68 28 33
LAT/GRAP2/SLP76 0.003 0.22 0.52 3 -0.58 24 27
IKBKB 0.019 0.007 -10000 0 -10000 0 0
AKT1 -0.001 0.17 0.47 3 -0.45 26 29
B2M 0.022 0.006 -10000 0 -10000 0 0
IKBKG 0.006 0.053 0.15 2 -0.17 10 12
MAP3K8 0.016 0.062 -10000 0 -0.69 2 2
mol:Ca2+ -0.036 0.05 0.066 1 -0.11 78 79
integrin-mediated signaling pathway 0.02 0.043 -10000 0 -0.45 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.016 0.25 0.52 3 -0.63 29 32
TRPV6 -0.19 0.37 1 5 -0.69 81 86
CD28 0.02 0.048 0.35 1 -0.68 1 2
SHC1 0.013 0.26 0.32 33 -0.64 26 59
receptor internalization -0.022 0.25 0.48 3 -0.64 29 32
PRF1 -0.025 0.26 0.48 1 -0.93 15 16
KRAS 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
COT/AKT1 0.012 0.15 0.43 3 -0.37 24 27
LAT -0.018 0.25 0.5 3 -0.66 27 30
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D 0.008 0.13 0.35 7 -0.63 9 16
CD3E -0.005 0.14 0.36 1 -0.67 11 12
CD3G 0 0.14 0.35 6 -0.64 11 17
RASGRP2 0.007 0.039 0.19 4 -0.17 4 8
RASGRP1 0.005 0.18 0.57 3 -0.47 24 27
HLA-A 0.001 0.004 -10000 0 -10000 0 0
RASSF5 0.012 0.062 -10000 0 -0.69 2 2
RAP1A/GTP/RAPL 0.02 0.043 -10000 0 -0.45 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.08 0.17 32 -0.13 13 45
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.029 0.073 -10000 0 -0.25 21 21
PRKCA 0.009 0.1 0.36 3 -0.26 22 25
GRAP2 0.008 0.12 0.35 4 -0.64 7 11
mol:IP3 0.03 0.2 0.28 64 -0.44 23 87
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.038 0.22 0.42 3 -0.68 23 26
ORAI1 0.084 0.21 -10000 0 -0.87 5 5
CSK -0.018 0.25 0.41 4 -0.67 27 31
B7 family/CD28 -0.014 0.26 0.64 1 -0.64 30 31
CHUK 0.021 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.03 0.29 0.44 4 -0.76 28 32
PTPN6 -0.027 0.25 0.45 3 -0.68 27 30
VAV1 -0.029 0.27 0.47 3 -0.69 30 33
Monovalent TCR/CD3 -0.017 0.16 0.29 5 -0.47 22 27
CBL 0.021 0.004 -10000 0 -10000 0 0
LCK -0.021 0.28 0.43 4 -0.73 28 32
PAG1 -0.019 0.26 0.33 13 -0.69 26 39
RAP1A 0.021 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.031 0.29 0.42 4 -0.76 28 32
CD80 -0.002 0.13 0.35 1 -0.69 9 10
CD86 0 0.12 -10000 0 -0.69 8 8
PDK1/CARD11/BCL10/MALT1 -0.02 0.096 0.15 1 -0.3 21 22
HRAS 0.023 0.02 0.35 1 -10000 0 1
GO:0035030 -0.021 0.21 0.4 3 -0.52 30 33
CD8A -0.023 0.19 0.36 3 -0.7 18 21
CD8B -0.004 0.17 0.35 7 -0.7 13 20
PTPRC -0.022 0.17 0.36 1 -0.69 15 16
PDK1/PKC theta -0.006 0.21 0.52 3 -0.57 25 28
CSK/PAG1 0.003 0.26 0.33 12 -0.7 24 36
SOS1 0.022 0.001 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.01 -10000 0 -10000 0 0
GRAP2/SLP76 -0.002 0.25 0.53 3 -0.65 27 30
STIM1 0.055 0.12 1.1 2 -10000 0 2
RAS family/GTP 0.037 0.094 0.24 12 -0.19 14 26
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.027 0.27 0.49 3 -0.69 29 32
mol:DAG -0.016 0.14 0.14 13 -0.38 25 38
RAP1A/GDP 0.021 0.039 0.13 8 -10000 0 8
PLCG1 0.021 0.003 -10000 0 -10000 0 0
CD247 0.013 0.066 0.35 1 -0.69 2 3
cytotoxic T cell degranulation -0.021 0.25 0.48 1 -0.85 16 17
RAP1A/GTP 0.001 0.01 -10000 0 -0.062 4 4
mol:PI-3-4-5-P3 -0.004 0.2 0.5 3 -0.51 28 31
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.03 0.24 0.31 60 -0.59 23 83
NRAS 0.021 0.003 -10000 0 -10000 0 0
ZAP70 0.021 0.074 0.35 4 -0.69 2 6
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.012 0.21 0.5 3 -0.57 26 29
MALT1 0.021 0.003 -10000 0 -10000 0 0
TRAF6 0.019 0.044 -10000 0 -0.69 1 1
CD8 heterodimer -0.019 0.22 0.5 3 -0.65 24 27
CARD11 0.006 0.13 0.35 5 -0.69 8 13
PRKCB -0.009 0.14 0.36 3 -0.36 29 32
PRKCE 0.006 0.11 0.31 4 -0.27 23 27
PRKCQ -0.013 0.24 0.53 3 -0.62 28 31
LCP2 0.01 0.087 -10000 0 -0.69 4 4
BCL10 0.021 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.005 0.15 0.45 3 -0.37 26 29
IKK complex 0.015 0.064 0.27 4 -0.13 14 18
RAS family/GDP -0.002 0.01 -10000 0 -10000 0 0
MAP3K14 0.012 0.11 0.38 3 -0.28 21 24
PDPK1 0.003 0.16 0.46 3 -0.44 23 26
TCR/CD3/MHC I/CD8/Fyn -0.057 0.31 0.51 3 -0.87 27 30
Osteopontin-mediated events

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
IKK alpha homodimer 0.026 0.15 0.32 1 -0.38 22 23
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.14 0.41 2 -0.48 1 3
alphaV/beta3 Integrin/Osteopontin/Src 0.079 0.18 0.3 6 -0.45 17 23
AP1 -0.14 0.29 0.54 4 -0.71 29 33
ILK 0.015 0.15 -10000 0 -0.41 21 21
bone resorption 0.01 0.16 0.39 1 -0.62 4 5
PTK2B 0.017 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.059 0.18 0.34 1 -0.39 21 22
ITGAV 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.019 0.1 -10000 0 -0.52 8 8
alphaV/beta3 Integrin/Osteopontin 0.06 0.2 0.35 4 -0.42 28 32
MAP3K1 0.014 0.15 0.29 1 -0.39 28 29
JUN 0.009 0.09 -10000 0 -0.63 5 5
MAPK3 0.015 0.15 0.36 5 -0.38 21 26
MAPK1 0.014 0.15 0.36 5 -0.38 22 27
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.02 0.006 -10000 0 -10000 0 0
MAPK8 -0.003 0.16 0.32 1 -0.4 31 32
ITGB3 -0.016 0.16 -10000 0 -0.68 15 15
NFKBIA 0.018 0.14 0.36 5 -0.37 20 25
FOS -0.29 0.35 -10000 0 -0.67 117 117
CD44 0.025 0.063 0.35 5 -0.69 1 6
CHUK 0.021 0.004 -10000 0 -10000 0 0
PLAU 0.012 0.16 0.58 3 -10000 0 3
NF kappa B1 p50/RelA 0.04 0.14 0.39 5 -0.47 1 6
BCAR1 0.02 0.005 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.006 0.13 -10000 0 -0.51 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.012 0.16 -10000 0 -0.4 28 28
VAV3 0.012 0.15 0.38 1 -0.4 20 21
MAP3K14 0.017 0.16 0.31 5 -0.39 28 33
ROCK2 0.002 0.11 -10000 0 -0.69 7 7
SPP1 0.095 0.24 0.35 91 -0.61 17 108
RAC1 0.021 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.14 -10000 0 -0.38 18 18
MMP2 -0.13 0.25 0.51 6 -0.58 32 38
FoxO family signaling

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
G6PC -0.22 0.54 -10000 0 -1.4 47 47
PLK1 0.37 0.34 0.76 86 -10000 0 86
CDKN1B 0.19 0.2 0.49 56 -0.37 2 58
FOXO3 0.31 0.33 0.7 86 -0.61 5 91
KAT2B 0.081 0.1 0.24 4 -0.67 3 7
FOXO1/SIRT1 -0.061 0.16 0.29 1 -0.4 47 48
CAT 0.24 0.41 0.62 70 -1.1 14 84
CTNNB1 0.021 0 -10000 0 -10000 0 0
AKT1 0.078 0.065 0.26 2 -10000 0 2
FOXO1 -0.048 0.18 -10000 0 -0.41 47 47
MAPK10 0.03 0.093 0.25 3 -0.37 10 13
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
FOXO4 0.058 0.12 -10000 0 -0.6 3 3
response to oxidative stress 0.064 0.062 0.2 8 -10000 0 8
FOXO3A/SIRT1 0.27 0.27 0.57 85 -0.65 5 90
XPO1 0.022 0.002 -10000 0 -10000 0 0
EP300 0.01 0.032 -10000 0 -10000 0 0
BCL2L11 0.098 0.1 -10000 0 -10000 0 0
FOXO1/SKP2 -0.035 0.16 -10000 0 -0.38 43 43
mol:GDP 0.064 0.062 0.2 8 -10000 0 8
RAN 0.022 0.003 -10000 0 -10000 0 0
GADD45A 0.19 0.25 0.61 5 -0.83 7 12
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.064 0.1 -10000 0 -0.4 2 2
MST1 0.026 0.21 0.25 2 -0.62 24 26
CSNK1D 0.02 0.005 -10000 0 -10000 0 0
CSNK1E 0.021 0.003 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.083 0.12 -10000 0 -0.49 4 4
YWHAB 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.03 0.088 -10000 0 -0.38 10 10
MAPK9 0.044 0.035 -10000 0 -10000 0 0
YWHAG 0.021 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.007 -10000 0 -10000 0 0
YWHAZ 0.016 0.009 -10000 0 -10000 0 0
SIRT1 0.009 0.057 0.45 1 -0.68 1 2
SOD2 0.18 0.24 0.57 11 -0.66 7 18
RBL2 0.19 0.35 0.65 8 -1.1 9 17
RAL/GDP 0.071 0.044 -10000 0 -10000 0 0
CHUK 0.089 0.063 0.26 1 -10000 0 1
Ran/GTP 0.017 0.006 -10000 0 -10000 0 0
CSNK1G2 0.021 0.003 -10000 0 -10000 0 0
RAL/GTP 0.071 0.043 -10000 0 -10000 0 0
CSNK1G1 0.021 0.003 -10000 0 -10000 0 0
FASLG 0.054 0.3 -10000 0 -1.4 10 10
SKP2 0.021 0.003 -10000 0 -10000 0 0
USP7 0.022 0.004 -10000 0 -10000 0 0
IKBKB 0.082 0.065 0.26 1 -10000 0 1
CCNB1 0.35 0.34 0.75 87 -0.6 1 88
FOXO1-3a-4/beta catenin 0.17 0.21 0.54 10 -0.42 5 15
proteasomal ubiquitin-dependent protein catabolic process -0.034 0.16 -10000 0 -0.38 43 43
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
SGK1 0.065 0.14 -10000 0 -0.61 8 8
CSNK1G3 0.021 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.009 -10000 0 -10000 0 0
ZFAND5 0.055 0.11 -10000 0 -0.73 2 2
SFN 0.2 0.16 0.35 148 -10000 0 148
CDK2 -0.001 0.046 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.16 0.13 0.33 49 -10000 0 49
CREBBP -0.002 0.046 -10000 0 -10000 0 0
FBXO32 0.34 0.34 0.71 85 -1.4 1 86
BCL6 0.25 0.24 0.65 8 -0.62 2 10
RALB 0.022 0.003 -10000 0 -10000 0 0
RALA 0.022 0.004 -10000 0 -10000 0 0
YWHAH 0.021 0.003 -10000 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
CDC42/GTP -0.073 0.15 -10000 0 -0.41 8 8
PLCG1 -0.082 0.15 -10000 0 -0.3 46 46
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.002 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
G12/G13 0.03 0.008 -10000 0 -10000 0 0
cell migration -0.072 0.15 -10000 0 -0.4 8 8
S1PR5 0.012 0.089 0.35 1 -0.69 4 5
S1PR4 0.022 0.02 0.35 1 -10000 0 1
MAPK3 -0.08 0.16 -10000 0 -0.42 8 8
MAPK1 -0.08 0.15 -10000 0 -0.3 46 46
S1P/S1P5/Gi -0.089 0.17 -10000 0 -0.32 52 52
GNAI1 0.016 0.062 -10000 0 -0.69 2 2
CDC42/GDP 0.015 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.022 0.06 0.22 1 -0.45 4 5
RHOA 0.024 0.042 0.36 1 -10000 0 1
S1P/S1P4/Gi -0.084 0.16 -10000 0 -0.32 49 49
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.17 0.16 0.35 117 -10000 0 117
S1P/S1P4/G12/G13 0.039 0.016 -10000 0 -10000 0 0
GNA12 0.021 0.004 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.017 0.078 -10000 0 -0.45 6 6
ARNO/beta Arrestin1-2 -0.041 0.17 -10000 0 -0.88 4 4
EGFR 0.01 0.087 -10000 0 -0.69 4 4
EPHA2 -0.005 0.13 -10000 0 -0.66 10 10
USP6 0.019 0.007 -10000 0 -10000 0 0
IQSEC1 0.022 0 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.071 0.12 -10000 0 -0.5 4 4
ARRB2 0.007 0.003 -10000 0 -10000 0 0
mol:GTP 0.003 0.052 0.16 2 -0.18 10 12
ARRB1 0.013 0.075 -10000 0 -0.69 3 3
FBXO8 0.02 0.005 -10000 0 -10000 0 0
TSHR 0.019 0.004 -10000 0 -10000 0 0
EGF 0.099 0.14 0.35 65 -10000 0 65
somatostatin receptor activity 0 0 0.001 2 -0.001 39 41
ARAP2 -0.003 0.13 -10000 0 -0.69 9 9
mol:GDP -0.064 0.13 0.19 1 -0.34 33 34
mol:PI-3-4-5-P3 0 0 0.001 1 -0.001 22 23
ITGA2B 0.029 0.053 0.35 7 -10000 0 7
ARF6 0.021 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.023 0.09 -10000 0 -0.42 8 8
ADAP1 0.016 0.12 0.35 9 -0.69 6 15
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET -0.24 0.28 -10000 0 -0.52 127 127
PXN 0.021 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.069 0.13 0.25 1 -0.3 41 42
EGFR/EGFR/EGF/EGF/ARFGEP100 0.077 0.11 -10000 0 -0.43 4 4
ADRB2 -0.082 0.25 -10000 0 -0.69 38 38
receptor agonist activity 0 0 -10000 0 0 34 34
actin filament binding 0 0 0.001 1 -0.001 42 43
SRC 0.023 0.02 0.35 1 -10000 0 1
ITGB3 -0.019 0.16 -10000 0 -0.69 15 15
GNAQ 0.02 0.025 -10000 0 -0.39 1 1
EFA6/PI-4-5-P2 0 0 0.001 3 -0.001 21 24
ARF6/GDP -0.046 0.16 -10000 0 -0.47 22 22
ARF6/GDP/GULP/ACAP1 -0.052 0.18 0.26 1 -0.4 37 38
alphaIIb/beta3 Integrin/paxillin/GIT1 0.032 0.11 -10000 0 -0.42 15 15
ACAP1 0.007 0.089 0.35 1 -0.54 6 7
ACAP2 0.021 0.002 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.007 0.023 -10000 0 -10000 0 0
EFNA1 0.009 0.075 -10000 0 -0.69 3 3
HGF -0.32 0.35 -10000 0 -0.69 127 127
CYTH3 0.008 0.017 0.2 2 -10000 0 2
CYTH2 -0.002 0.13 -10000 0 -1 4 4
NCK1 0.019 0.044 -10000 0 -0.69 1 1
fibronectin binding 0 0 0.001 1 0 41 42
endosomal lumen acidification 0 0 0 3 -0.001 30 33
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.021 0.24 0.35 44 -0.67 21 65
GNAQ/ARNO 0.01 0.12 -10000 0 -0.96 4 4
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 2 2
MET 0.018 0.044 -10000 0 -0.69 1 1
GNA14 -0.098 0.26 -10000 0 -0.67 45 45
GNA15 0.024 0.029 0.35 2 -10000 0 2
GIT1 0.021 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 2 -0.001 26 28
GNA11 0.008 0.097 -10000 0 -0.69 5 5
LHCGR 0.014 0.002 -10000 0 -10000 0 0
AGTR1 -0.06 0.23 -10000 0 -0.69 30 30
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.023 -10000 0 -10000 0 0
IPCEF1/ARNO 0.051 0.14 -10000 0 -0.86 4 4
alphaIIb/beta3 Integrin 0.005 0.13 0.25 7 -0.52 15 22
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.056 0.22 0.41 1 -0.4 69 70
SMAD6-7/SMURF1 0.022 0.092 -10000 0 -0.43 10 10
NOG 0.022 0.041 0.35 4 -10000 0 4
SMAD9 -0.053 0.18 -10000 0 -0.53 27 27
SMAD4 0.021 0.003 -10000 0 -10000 0 0
SMAD5 -0.05 0.15 -10000 0 -0.33 41 41
BMP7/USAG1 0.085 0.11 0.49 6 -10000 0 6
SMAD5/SKI -0.045 0.15 -10000 0 -0.42 12 12
SMAD1 -0.001 0.074 -10000 0 -0.45 4 4
BMP2 0.013 0.075 -10000 0 -0.69 3 3
SMAD1/SMAD1/SMAD4 -0.004 0.097 -10000 0 -0.5 4 4
BMPR1A 0.021 0.004 -10000 0 -10000 0 0
BMPR1B -0.13 0.29 0.35 3 -0.66 59 62
BMPR1A-1B/BAMBI -0.094 0.24 -10000 0 -0.47 70 70
AHSG -0.12 0.28 -10000 0 -0.69 51 51
CER1 0.018 0.036 0.35 3 -10000 0 3
BMP2-4/CER1 0.048 0.074 -10000 0 -0.42 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.049 0.14 -10000 0 -0.41 12 12
BMP2-4 (homodimer) 0.042 0.081 0.25 20 -0.49 3 23
RGMB 0.017 0.065 0.35 1 -0.69 2 3
BMP6/BMPR2/BMPR1A-1B -0.042 0.18 -10000 0 -0.41 48 48
RGMA 0.047 0.089 0.35 21 -10000 0 21
SMURF1 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.057 0.15 -10000 0 -0.43 12 12
BMP2-4/USAG1 0.078 0.1 0.44 4 -0.42 3 7
SMAD6/SMURF1/SMAD5 -0.044 0.15 -10000 0 -0.42 12 12
SOSTDC1 0.068 0.12 0.35 39 -10000 0 39
BMP7/BMPR2/BMPR1A-1B -0.026 0.2 0.42 1 -0.41 50 51
SKI 0.02 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.02 0.052 0.35 2 -0.69 1 3
HFE2 -0.064 0.22 -10000 0 -0.69 30 30
ZFYVE16 0.022 0.001 -10000 0 -10000 0 0
MAP3K7 0.021 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD 0.04 0.1 -10000 0 -0.43 9 9
SMAD5/SMAD5/SMAD4 -0.044 0.15 -10000 0 -0.42 12 12
MAPK1 0.021 0.003 -10000 0 -10000 0 0
TAK1/TAB family -0.042 0.13 -10000 0 -0.4 11 11
BMP7 (homodimer) 0.057 0.11 0.35 31 -10000 0 31
NUP214 0.021 0.003 -10000 0 -10000 0 0
BMP6/FETUA -0.078 0.22 -10000 0 -0.51 52 52
SMAD1/SKI 0.006 0.081 -10000 0 -0.46 4 4
SMAD6 -0.002 0.12 -10000 0 -0.65 9 9
CTDSP2 0.021 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.046 0.21 -10000 0 -0.44 54 54
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.03 0.25 0.35 23 -0.68 30 53
BMPR2 (homodimer) 0.021 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.043 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.086 0.22 0.25 3 -0.49 59 62
CHRDL1 -0.11 0.29 0.35 7 -0.69 52 59
ENDOFIN/SMAD1 0.007 0.083 -10000 0 -0.46 4 4
SMAD6-7/SMURF1/SMAD1 0.007 0.11 -10000 0 -0.52 5 5
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI -0.03 0.18 -10000 0 -0.69 19 19
SMURF2 0.021 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.042 0.21 -10000 0 -0.44 54 54
BMP2-4/GREM1 0.009 0.18 0.44 1 -0.44 32 33
SMAD7 0.016 0.062 -10000 0 -0.69 2 2
SMAD8A/SMAD8A/SMAD4 -0.046 0.18 -10000 0 -0.5 31 31
SMAD1/SMAD6 0.006 0.078 -10000 0 -0.42 4 4
TAK1/SMAD6 0.029 0.01 -10000 0 -10000 0 0
BMP7 0.057 0.11 0.35 31 -10000 0 31
BMP6 0.02 0.053 0.35 2 -0.69 1 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.044 0.13 -10000 0 -0.4 12 12
PPM1A 0.021 0.003 -10000 0 -10000 0 0
SMAD1/SMURF2 0.006 0.083 -10000 0 -0.46 4 4
SMAD7/SMURF1 0.027 0.041 -10000 0 -0.41 2 2
CTDSPL 0.022 0 -10000 0 -10000 0 0
PPP1CA 0.021 0.003 -10000 0 -10000 0 0
XIAP 0.021 0.002 -10000 0 -10000 0 0
CTDSP1 0.021 0.003 -10000 0 -10000 0 0
PPP1R15A 0.022 0.02 0.35 1 -10000 0 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.065 0.18 -10000 0 -0.44 25 25
CHRD 0.005 0.11 -10000 0 -0.69 6 6
BMPR2 0.021 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.055 0.15 -10000 0 -0.28 65 65
BMP4 0.047 0.089 0.35 21 -10000 0 21
FST -0.039 0.2 0.35 1 -0.69 23 24
BMP2-4/NOG 0.052 0.073 -10000 0 -0.36 3 3
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.02 0.2 0.41 1 -0.39 49 50
Coregulation of Androgen receptor activity

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
NRIP1 0.018 0.047 -10000 0 -0.69 1 1
SVIL 0.018 0.045 -10000 0 -0.66 1 1
ZNF318 0.02 0.03 0.23 1 -10000 0 1
JMJD2C 0.017 0.051 0.18 22 -10000 0 22
T-DHT/AR/Ubc9 -0.11 0.22 -10000 0 -0.45 72 72
CARM1 0.021 0.006 -10000 0 -10000 0 0
PRDX1 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.019 0.009 -10000 0 -10000 0 0
CTNNB1 0.021 0.014 -10000 0 -10000 0 0
AKT1 0.019 0.013 -10000 0 -10000 0 0
PTK2B 0.018 0.011 -10000 0 -10000 0 0
MED1 0.02 0.012 -10000 0 -10000 0 0
MAK 0.019 0.03 -10000 0 -10000 0 0
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.012 0.077 -10000 0 -0.69 3 3
GSN 0.021 0.017 -10000 0 -10000 0 0
NCOA2 -0.035 0.18 -10000 0 -0.69 19 19
NCOA6 0.021 0.015 -10000 0 -10000 0 0
DNA-PK 0.036 0.035 -10000 0 -10000 0 0
NCOA4 0.021 0.003 -10000 0 -10000 0 0
PIAS3 0.017 0.013 -10000 0 -10000 0 0
cell proliferation -0.008 0.044 -10000 0 -10000 0 0
XRCC5 0.02 0.012 -10000 0 -10000 0 0
UBE3A 0.02 0.021 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.23 -10000 0 -0.45 75 75
FHL2 -0.091 0.28 -10000 0 -1 19 19
RANBP9 0.019 0.015 -10000 0 -10000 0 0
JMJD1A -0.002 0.028 -10000 0 -0.12 13 13
CDK6 -0.024 0.17 -10000 0 -0.67 17 17
TGFB1I1 0.02 0.017 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.12 0.24 -10000 0 -0.46 79 79
XRCC6 0.02 0.012 -10000 0 -10000 0 0
T-DHT/AR -0.1 0.24 -10000 0 -0.45 76 76
CTDSP1 0.021 0.008 -10000 0 -10000 0 0
CTDSP2 0.02 0.02 -10000 0 -10000 0 0
BRCA1 0.02 0.017 -10000 0 -10000 0 0
TCF4 0.02 0.016 -10000 0 -10000 0 0
CDKN2A 0.23 0.16 0.35 169 -10000 0 169
SRF 0.015 0.038 -10000 0 -10000 0 0
NKX3-1 -0.057 0.1 -10000 0 -0.2 79 79
KLK3 -0.028 0.25 -10000 0 -1.5 6 6
TMF1 0.021 0.006 -10000 0 -10000 0 0
HNRNPA1 0.02 0.014 -10000 0 -10000 0 0
AOF2 0 0.013 0.051 1 -0.072 6 7
APPL1 0.012 0.018 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.1 0.22 -10000 0 -0.45 72 72
AR -0.18 0.32 -10000 0 -0.69 72 72
UBA3 0.021 0.008 -10000 0 -10000 0 0
PATZ1 0.02 0.014 -10000 0 -10000 0 0
PAWR 0.021 0.006 -10000 0 -10000 0 0
PRKDC 0.017 0.013 -10000 0 -10000 0 0
PA2G4 0.02 0.017 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.093 0.2 -10000 0 -0.41 71 71
RPS6KA3 0.018 0.047 -10000 0 -0.69 1 1
T-DHT/AR/ARA70 -0.1 0.22 -10000 0 -0.45 72 72
LATS2 0.02 0.014 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.096 0.2 -10000 0 -0.42 72 72
Cyclin D3/CDK11 p58 0.015 0.005 -10000 0 -10000 0 0
VAV3 0.025 0.042 0.35 4 -10000 0 4
KLK2 -0.013 0.15 0.42 15 -0.57 1 16
CASP8 0.021 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.11 0.24 -10000 0 -0.47 67 67
TMPRSS2 -0.089 0.27 -10000 0 -1.2 14 14
CCND1 -0.007 0.14 -10000 0 -0.69 10 10
PIAS1 0.02 0.021 -10000 0 -10000 0 0
mol:T-DHT -0.001 0.026 0.052 14 -0.078 19 33
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.019 0.034 -10000 0 -0.21 1 1
T-DHT/AR/CDK6 -0.13 0.24 -10000 0 -0.46 84 84
CMTM2 0.022 0.029 0.35 2 -10000 0 2
SNURF 0.017 0.092 0.35 5 -0.61 4 9
ZMIZ1 0.018 0.031 -10000 0 -10000 0 0
CCND3 0.02 0.006 -10000 0 -10000 0 0
TGIF1 0.02 0.014 -10000 0 -10000 0 0
FKBP4 0.021 0.016 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.029 0.35 2 -9999 0 2
Aurora C/Aurora B/INCENP 0.11 0.1 0.41 2 -9999 0 2
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.005 0.006 -10000 0 -9999 0 0
AURKB 0.16 0.16 0.35 113 -9999 0 113
AURKC 0.021 0.004 -10000 0 -9999 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.002 -10000 0 -10000 0 0
LAT2 -0.006 0.088 -10000 0 -0.35 4 4
AP1 -0.13 0.23 -10000 0 -0.53 40 40
mol:PIP3 0.022 0.17 0.35 4 -0.39 27 31
IKBKB 0.018 0.12 0.28 5 -0.31 14 19
AKT1 0.031 0.17 0.31 27 -0.35 20 47
IKBKG 0.021 0.13 0.28 7 -0.31 14 21
MS4A2 0.023 0.051 0.34 6 -10000 0 6
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
MAP3K1 0.022 0.13 -10000 0 -0.48 6 6
mol:Ca2+ 0.027 0.14 0.28 8 -0.3 27 35
LYN 0.02 0.012 -10000 0 -10000 0 0
CBLB -0.007 0.09 -10000 0 -0.35 5 5
SHC1 0.017 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0.001 0.13 -10000 0 -0.43 22 22
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.044 -10000 0 -0.69 1 1
PLD2 0.03 0.18 0.32 45 -0.37 27 72
PTPN13 -0.06 0.19 -10000 0 -0.56 15 15
PTPN11 0.02 0.017 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.023 0.12 0.38 1 -0.34 2 3
SYK 0.021 0.046 -10000 0 -0.7 1 1
GRB2 0.021 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.031 0.14 -10000 0 -0.4 28 28
LAT -0.006 0.09 -10000 0 -0.35 5 5
PAK2 0.022 0.14 -10000 0 -0.54 6 6
NFATC2 -0.096 0.22 -10000 0 -0.56 43 43
HRAS 0.02 0.15 -10000 0 -0.55 7 7
GAB2 0.021 0.003 -10000 0 -10000 0 0
PLA2G1B 0.032 0.049 -10000 0 -10000 0 0
Fc epsilon R1 -0.015 0.16 -10000 0 -0.46 27 27
Antigen/IgE/Fc epsilon R1 -0.012 0.14 -10000 0 -0.42 27 27
mol:GDP -0.013 0.14 -10000 0 -0.63 7 7
JUN 0.009 0.09 -10000 0 -0.63 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
FOS -0.29 0.35 -10000 0 -0.67 117 117
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.006 0.095 -10000 0 -0.35 6 6
CHUK 0.018 0.12 0.28 5 -0.31 14 19
KLRG1 -0.01 0.097 -10000 0 -0.35 8 8
VAV1 -0.021 0.12 -10000 0 -0.48 10 10
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.007 0.09 -10000 0 -0.35 5 5
negative regulation of mast cell degranulation -0.003 0.096 -10000 0 -0.35 6 6
BTK -0.008 0.14 -10000 0 -0.67 6 6
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.14 0.24 -10000 0 -0.4 97 97
GAB2/PI3K/SHP2 -0.032 0.12 -10000 0 -0.37 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.015 0.09 -10000 0 -0.27 25 25
RAF1 0.027 0.051 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.16 0.27 -10000 0 -0.47 102 102
FCER1G 0.006 0.078 0.34 1 -0.68 3 4
FCER1A -0.049 0.21 -10000 0 -0.7 24 24
Antigen/IgE/Fc epsilon R1/Fyn -0.004 0.14 -10000 0 -0.4 27 27
MAPK3 0.027 0.05 -10000 0 -10000 0 0
MAPK1 0.026 0.052 -10000 0 -10000 0 0
NFKB1 0.02 0.006 -10000 0 -10000 0 0
MAPK8 -0.036 0.2 -10000 0 -0.55 28 28
DUSP1 -0.036 0.19 -10000 0 -0.69 21 21
NF-kappa-B/RelA 0.01 0.07 -10000 0 -0.2 9 9
actin cytoskeleton reorganization 0.011 0.12 -10000 0 -0.62 2 2
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.003 0.13 -10000 0 -0.59 6 6
FER -0.006 0.089 -10000 0 -0.35 5 5
RELA 0.021 0.003 -10000 0 -10000 0 0
ITK -0.02 0.11 -10000 0 -0.51 12 12
SOS1 0.022 0.001 -10000 0 -10000 0 0
PLCG1 0.011 0.16 -10000 0 -0.58 8 8
cytokine secretion -0.006 0.042 -10000 0 -10000 0 0
SPHK1 0.014 0.11 0.25 12 -0.35 6 18
PTK2 0.01 0.12 -10000 0 -0.66 2 2
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.03 0.15 -10000 0 -0.41 28 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.026 0.17 0.35 4 -0.38 26 30
MAP2K2 0.025 0.05 -10000 0 -10000 0 0
MAP2K1 0.023 0.048 -10000 0 -10000 0 0
MAP2K7 0.021 0.002 -10000 0 -10000 0 0
KLRG1/SHP2 -0.006 0.098 -10000 0 -0.41 4 4
MAP2K4 -0.072 0.29 -10000 0 -0.86 31 31
Fc epsilon R1/FcgammaRIIB -0.17 0.28 -10000 0 -0.49 102 102
mol:Choline 0.03 0.18 0.32 45 -0.37 27 72
SHC/Grb2/SOS1 0.016 0.097 -10000 0 -0.35 4 4
FYN 0.021 0.005 -10000 0 -10000 0 0
DOK1 0.022 0 -10000 0 -10000 0 0
PXN 0.011 0.11 -10000 0 -0.6 2 2
HCLS1 -0.008 0.093 -10000 0 -0.36 6 6
PRKCB 0.013 0.16 0.32 5 -0.43 16 21
FCGR2B -0.24 0.34 0.35 2 -0.69 97 99
IGHE 0.002 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.003 0.098 -10000 0 -0.36 6 6
LCP2 0.011 0.087 -10000 0 -0.69 4 4
PLA2G4A -0.024 0.14 -10000 0 -0.46 16 16
RASA1 0.016 0.062 -10000 0 -0.69 2 2
mol:Phosphatidic acid 0.03 0.18 0.32 45 -0.37 27 72
IKK complex 0.026 0.1 0.26 7 -0.24 10 17
WIPF1 0.021 0.002 -10000 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.073 -10000 0 -0.44 6 6
alphaV beta3 Integrin -0.013 0.17 -10000 0 -0.48 28 28
PTK2 0.02 0.17 0.36 1 -0.6 8 9
IGF1R 0.019 0.071 0.35 3 -0.69 2 5
PI4KB 0.017 0.009 -10000 0 -10000 0 0
MFGE8 0.026 0.04 0.35 4 -10000 0 4
SRC 0.023 0.02 0.35 1 -10000 0 1
CDKN1B -0.026 0.14 -10000 0 -0.57 13 13
VEGFA 0.019 0.007 -10000 0 -10000 0 0
ILK -0.023 0.13 -10000 0 -0.55 12 12
ROCK1 0.021 0.002 -10000 0 -10000 0 0
AKT1 -0.025 0.12 -10000 0 -0.51 12 12
PTK2B -0.001 0.12 0.36 1 -0.44 14 15
alphaV/beta3 Integrin/JAM-A -0.021 0.16 -10000 0 -0.43 28 28
CBL 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.048 0.2 -10000 0 -0.48 44 44
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.15 0.24 -10000 0 -0.42 112 112
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.008 0.091 -10000 0 -0.37 4 4
alphaV/beta3 Integrin/Syndecan-1 0.006 0.13 -10000 0 -0.45 19 19
PI4KA 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.18 0.26 -10000 0 -0.43 117 117
PI4 Kinase 0.025 0.014 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
alphaV/beta3 Integrin/Osteopontin 0.049 0.2 -10000 0 -0.44 28 28
RPS6KB1 -0.18 0.22 -10000 0 -0.67 20 20
TLN1 0.021 0.003 -10000 0 -10000 0 0
MAPK3 -0.11 0.24 -10000 0 -0.68 32 32
GPR124 0.014 0.051 -10000 0 -0.54 2 2
MAPK1 -0.11 0.24 -10000 0 -0.67 33 33
PXN 0.021 0.002 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
alphaV/beta3 Integrin/Tumstatin 0.003 0.18 -10000 0 -0.52 24 24
cell adhesion -0.038 0.17 -10000 0 -0.41 41 41
ANGPTL3 -0.067 0.23 -10000 0 -0.68 33 33
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.067 -10000 0 -0.41 5 5
IGF-1R heterotetramer 0.019 0.071 0.35 3 -0.69 2 5
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
TGFBR2 0.022 0 -10000 0 -10000 0 0
ITGB3 -0.019 0.16 -10000 0 -0.69 15 15
IGF1 -0.29 0.35 -10000 0 -0.69 114 114
RAC1 0.021 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.007 0.12 -10000 0 -0.45 16 16
apoptosis 0.021 0.003 -10000 0 -10000 0 0
CD47 0.019 0.044 -10000 0 -0.69 1 1
alphaV/beta3 Integrin/CD47 0.012 0.12 -10000 0 -0.45 16 16
VCL 0.021 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.064 0.15 -10000 0 -0.45 15 15
CSF1 0.018 0.068 0.35 2 -0.69 2 4
PIK3C2A -0.023 0.13 -10000 0 -0.55 12 12
PI4 Kinase/Pyk2 -0.03 0.14 -10000 0 -0.4 24 24
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.016 0.13 -10000 0 -0.46 15 15
FAK1/Vinculin 0.036 0.15 0.34 1 -0.46 8 9
alphaV beta3/Integrin/ppsTEM5 0.007 0.12 -10000 0 -0.45 16 16
RHOA 0.022 0.001 -10000 0 -10000 0 0
VTN -0.011 0.15 -10000 0 -0.69 12 12
BCAR1 0.02 0.005 -10000 0 -10000 0 0
FGF2 -0.018 0.18 0.35 4 -0.69 16 20
F11R -0.015 0.12 0.46 1 -0.47 16 17
alphaV/beta3 Integrin/Lactadherin 0.017 0.12 -10000 0 -0.44 15 15
alphaV/beta3 Integrin/TGFBR2 0.014 0.12 -10000 0 -0.45 15 15
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.041 -10000 0 -0.42 1 1
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.014 0.11 -10000 0 -0.41 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.044 -10000 0 -0.69 1 1
alphaV/beta3 Integrin/Pyk2 0.002 0.11 -10000 0 -0.44 14 14
SDC1 0.011 0.087 -10000 0 -0.69 4 4
VAV3 0.015 0.038 -10000 0 -0.39 1 1
PTPN11 0.021 0.002 -10000 0 -10000 0 0
IRS1 0.021 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.036 0.15 0.34 1 -0.46 8 9
cell migration 0.035 0.14 0.3 4 -0.41 8 12
ITGAV 0.021 0.003 -10000 0 -10000 0 0
PI3K -0.015 0.16 -10000 0 -0.42 29 29
SPP1 0.092 0.24 0.35 91 -0.62 17 108
KDR 0.006 0.1 -10000 0 -0.64 6 6
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.003 -10000 0 -10000 0 0
COL4A3 0.004 0.18 0.35 17 -0.69 14 31
angiogenesis -0.093 0.25 -10000 0 -0.63 39 39
Rac1/GTP 0.027 0.027 -10000 0 -10000 0 0
EDIL3 0.11 0.14 0.35 69 -10000 0 69
cell proliferation 0.014 0.11 -10000 0 -0.45 15 15
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.16 0.25 -10000 0 -0.62 28 28
MAP3K8 0.01 0.062 -10000 0 -0.69 2 2
FOS -0.086 0.18 -10000 0 -0.5 24 24
PRKCA 0.005 0.02 -10000 0 -10000 0 0
PTPN7 0.002 0.061 0.35 3 -0.69 1 4
HRAS 0.021 0.02 0.34 1 -10000 0 1
PRKCB -0.053 0.19 -10000 0 -0.68 22 22
NRAS 0.02 0.003 -10000 0 -10000 0 0
RAS family/GTP 0.016 0.032 -10000 0 -10000 0 0
MAPK3 -0.045 0.13 -10000 0 -0.66 7 7
MAP2K1 -0.059 0.16 -10000 0 -0.54 23 23
ELK1 -0.001 0.027 -10000 0 -10000 0 0
BRAF -0.046 0.15 -10000 0 -0.52 22 22
mol:GTP -0.002 0.003 -10000 0 -0.006 115 115
MAPK1 -0.046 0.13 -10000 0 -0.63 8 8
RAF1 -0.044 0.14 -10000 0 -0.5 22 22
KRAS 0.02 0.004 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.044 0.045 -10000 0 -0.38 1 1
epithelial cell differentiation -0.015 0.098 -10000 0 -0.4 4 4
ITCH 0.022 0.009 -10000 0 -10000 0 0
WWP1 0.057 0.081 -10000 0 -10000 0 0
FYN 0.021 0.005 -10000 0 -10000 0 0
EGFR 0.01 0.087 -10000 0 -0.69 4 4
PRL 0.017 0.029 0.35 2 -10000 0 2
neuron projection morphogenesis -0.058 0.17 0.35 3 -10000 0 3
PTPRZ1 0.033 0.066 0.35 11 -10000 0 11
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.079 0.16 -10000 0 -0.39 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.12 0.19 -10000 0 -0.39 81 81
ADAM17 0.022 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4 0.018 0.024 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.024 0.17 0.36 2 -0.4 42 44
NCOR1 0.016 0.036 -10000 0 -0.38 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.11 0.18 -10000 0 -0.38 60 60
GRIN2B -0.11 0.17 -10000 0 -0.36 56 56
ErbB4/ErbB2/betacellulin 0.037 0.056 -10000 0 -0.38 3 3
STAT1 0.024 0.028 0.35 2 -10000 0 2
HBEGF 0.019 0.044 -10000 0 -0.69 1 1
PRLR -0.006 0.14 -10000 0 -0.69 10 10
E4ICDs/ETO2 -0.007 0.14 -10000 0 -0.4 29 29
axon guidance -0.022 0.085 -10000 0 -10000 0 0
NEDD4 0.016 0.062 -10000 0 -0.68 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.005 0.1 0.25 1 -0.51 10 11
CBFA2T3 -0.064 0.22 -10000 0 -0.63 34 34
ErbB4/ErbB2/HBEGF 0.038 0.056 -10000 0 -0.38 3 3
MAPK3 -0.072 0.16 -10000 0 -10000 0 0
STAT1 (dimer) 0.048 0.041 0.33 1 -10000 0 1
MAPK1 -0.071 0.16 -10000 0 -0.37 1 1
JAK2 0.019 0.025 -10000 0 -0.38 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.12 0.19 -10000 0 -0.4 61 61
NRG1 -0.18 0.24 -10000 0 -0.47 107 107
NRG3 -0.091 0.27 0.35 5 -0.67 44 49
NRG2 0.091 0.13 0.35 56 -10000 0 56
NRG4 -0.089 0.26 -10000 0 -0.68 41 41
heart development -0.022 0.085 -10000 0 -10000 0 0
neural crest cell migration -0.12 0.19 -10000 0 -0.39 61 61
ERBB2 0.008 0.058 -10000 0 -0.53 3 3
WWOX/E4ICDs 0.044 0.036 -10000 0 -10000 0 0
SHC1 0.017 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.018 0.16 -10000 0 -0.4 30 30
apoptosis 0.022 0.17 0.39 40 -0.32 2 42
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.093 0.1 0.33 15 -10000 0 15
ErbB4/ErbB2/epiregulin 0.055 0.082 -10000 0 -0.38 3 3
ErbB4/ErbB4/betacellulin/betacellulin 0.044 0.042 0.33 1 -10000 0 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.045 0.091 -10000 0 -0.36 8 8
MDM2 0.016 0.028 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.12 0.18 -10000 0 -0.38 80 80
STAT5A -0.021 0.08 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.11 0.19 -10000 0 -0.39 58 58
DLG4 0.019 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.024 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.036 0.037 -10000 0 -10000 0 0
STAT5A (dimer) -0.009 0.11 -10000 0 -0.43 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.013 0.086 -10000 0 -10000 0 0
LRIG1 0.021 0.003 -10000 0 -10000 0 0
EREG 0.05 0.097 0.35 25 -10000 0 25
BTC 0.02 0.021 0.35 1 -10000 0 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.021 0.085 -10000 0 -10000 0 0
ERBB4 0.018 0.024 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
YAP1 0.011 0.054 -10000 0 -0.44 2 2
GRB2 0.021 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.024 0.15 -10000 0 -0.38 31 31
glial cell differentiation -0.036 0.037 -10000 0 -10000 0 0
WWOX 0.02 0.005 -10000 0 -10000 0 0
cell proliferation -0.13 0.2 -10000 0 -0.53 20 20
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.021 0.003 -10000 0 -10000 0 0
SPHK1 0.075 0.14 0.35 48 -0.69 2 50
GNAI2 0.021 0.002 -10000 0 -10000 0 0
mol:S1P 0.04 0.079 0.29 9 -0.42 2 11
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
mol:Sphinganine-1-P 0.046 0.096 0.46 2 -0.52 2 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.057 0.064 -10000 0 -0.39 2 2
GNAI3 0.021 0.004 -10000 0 -10000 0 0
G12/G13 0.03 0.008 -10000 0 -10000 0 0
S1PR3 0.012 0.089 0.35 1 -0.69 4 5
S1PR2 0.019 0.044 -10000 0 -0.69 1 1
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.022 0.058 0.18 7 -0.37 2 9
S1PR5 0.012 0.089 0.35 1 -0.69 4 5
S1PR4 0.022 0.02 0.35 1 -10000 0 1
GNAI1 0.016 0.062 -10000 0 -0.69 2 2
S1P/S1P5/G12 0.045 0.086 -10000 0 -0.44 5 5
S1P/S1P3/Gq -0.024 0.14 -10000 0 -0.33 35 35
S1P/S1P4/Gi -0.068 0.16 0.28 1 -0.41 10 11
GNAQ 0.02 0.025 -10000 0 -0.38 1 1
GNAZ 0.17 0.16 0.35 117 -10000 0 117
GNA14 -0.098 0.26 -10000 0 -0.67 45 45
GNA15 0.024 0.029 0.35 2 -10000 0 2
GNA12 0.021 0.004 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.008 0.097 -10000 0 -0.69 5 5
ABCC1 0.031 0.056 0.35 8 -10000 0 8
PLK2 and PLK4 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
PLK2 0.022 0 -10000 0 -9999 0 0
PLK4 0.077 0.12 0.35 45 -9999 0 45
regulation of centriole replication 0.046 0.073 -10000 0 -9999 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.005 0.072 -10000 0 -0.3 14 14
epithelial cell differentiation 0.02 0.098 -10000 0 -0.39 14 14
CYFIP2 -0.016 0.16 -10000 0 -0.69 14 14
ENAH -0.001 0.087 -10000 0 -0.44 3 3
EGFR 0.01 0.087 -10000 0 -0.69 4 4
EPHA2 -0.005 0.13 -10000 0 -0.66 10 10
MYO6 -0.006 0.089 -10000 0 -0.37 14 14
CTNNB1 0.022 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.018 0.11 -10000 0 -0.45 12 12
AQP5 0.004 0.08 -10000 0 -10000 0 0
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.006 0.087 -10000 0 -0.37 14 14
regulation of calcium-dependent cell-cell adhesion 0.006 0.1 -10000 0 -0.37 15 15
EGF 0.099 0.14 0.35 65 -10000 0 65
NCKAP1 0.021 0.002 -10000 0 -10000 0 0
AQP3 -0.049 0.18 -10000 0 -0.6 22 22
cortical microtubule organization 0.02 0.098 -10000 0 -0.39 14 14
GO:0000145 -0.014 0.082 -10000 0 -0.35 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.1 -10000 0 -0.39 14 14
MLLT4 0.02 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.026 0.11 -10000 0 -0.41 15 15
ARF6 0.021 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.023 0.09 -10000 0 -0.42 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.007 0.082 -10000 0 -0.34 14 14
PVRL2 0.021 0.003 -10000 0 -10000 0 0
ZYX -0.006 0.089 -10000 0 -0.37 14 14
ARF6/GTP 0.028 0.086 -10000 0 -0.39 8 8
CDH1 -0.017 0.16 -10000 0 -0.69 14 14
EGFR/EGFR/EGF/EGF 0.035 0.12 -10000 0 -0.42 12 12
RhoA/GDP 0.022 0.094 -10000 0 -0.37 14 14
actin cytoskeleton organization -0.01 0.082 -10000 0 -0.36 13 13
IGF-1R heterotetramer 0.019 0.071 0.35 3 -0.69 2 5
GIT1 0.021 0.002 -10000 0 -10000 0 0
IGF1R 0.019 0.071 0.35 3 -0.69 2 5
IGF1 -0.29 0.35 -10000 0 -0.69 114 114
DIAPH1 -0.01 0.17 -10000 0 -0.65 16 16
Wnt receptor signaling pathway -0.02 0.098 0.39 14 -10000 0 14
RHOA 0.022 0.001 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.11 -10000 0 -0.58 5 5
CTNNA1 0.021 0.002 -10000 0 -10000 0 0
VCL -0.01 0.084 -10000 0 -0.37 13 13
EFNA1 0.009 0.075 -10000 0 -0.69 3 3
LPP -0.011 0.084 -10000 0 -0.36 14 14
Ephrin A1/EPHA2 -0.003 0.12 -10000 0 -0.45 16 16
SEC6/SEC8 -0.009 0.08 -10000 0 -0.34 14 14
MGAT3 0.006 0.11 -10000 0 -0.37 15 15
HGF/MET -0.18 0.23 -10000 0 -0.4 128 128
HGF -0.32 0.35 -10000 0 -0.69 127 127
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.005 0.073 -10000 0 -0.3 14 14
actin cable formation 0.031 0.11 0.33 4 -0.35 4 8
KIAA1543 -0.017 0.088 -10000 0 -0.36 16 16
KIFC3 -0.006 0.089 -10000 0 -0.37 14 14
NCK1 0.019 0.044 -10000 0 -0.69 1 1
EXOC3 0.021 0.005 -10000 0 -10000 0 0
ACTN1 -0.006 0.089 -10000 0 -0.37 14 14
NCK1/GIT1 0.03 0.034 -10000 0 -0.52 1 1
mol:GDP 0.02 0.098 -10000 0 -0.39 14 14
EXOC4 0.021 0.005 -10000 0 -10000 0 0
STX4 -0.006 0.089 -10000 0 -0.37 14 14
PIP5K1C -0.006 0.089 -10000 0 -0.37 14 14
LIMA1 0.021 0.002 -10000 0 -10000 0 0
ABI1 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0.015 0.12 -10000 0 -0.5 5 5
adherens junction assembly -0.016 0.09 -10000 0 -0.38 2 2
IGF-1R heterotetramer/IGF1 -0.16 0.21 -10000 0 -0.38 120 120
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.029 0.009 -10000 0 -10000 0 0
MET 0.018 0.044 -10000 0 -0.69 1 1
PLEKHA7 -0.009 0.094 -10000 0 -0.38 16 16
mol:GTP 0.021 0.089 -10000 0 -0.41 8 8
establishment of epithelial cell apical/basal polarity 0.009 0.095 0.33 2 -10000 0 2
cortical actin cytoskeleton stabilization 0.005 0.072 -10000 0 -0.3 14 14
regulation of cell-cell adhesion -0.01 0.082 -10000 0 -0.36 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.005 0.073 -10000 0 -0.3 14 14
S1P3 pathway

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
PDGFRB 0.029 0.049 0.35 6 -10000 0 6
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.057 0.14 -10000 0 -0.26 48 48
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
S1P/S1P3/G12/G13 0.035 0.054 -10000 0 -0.37 4 4
AKT1 -0.022 0.12 -10000 0 -0.51 9 9
AKT3 -0.03 0.12 -10000 0 -0.68 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.029 0.049 0.35 6 -10000 0 6
GNAI2 0.023 0.004 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.016 0.062 -10000 0 -0.69 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.013 0.09 0.35 1 -0.69 4 5
S1PR2 0.019 0.044 -10000 0 -0.69 1 1
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.082 0.18 -10000 0 -0.34 50 50
MAPK3 -0.077 0.17 -10000 0 -0.53 9 9
MAPK1 -0.077 0.17 -10000 0 -0.34 34 34
JAK2 -0.082 0.17 -10000 0 -0.49 13 13
CXCR4 -0.081 0.17 -10000 0 -0.5 11 11
FLT1 0.022 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
SRC -0.079 0.17 -10000 0 -0.53 9 9
S1P/S1P3/Gi -0.083 0.18 -10000 0 -0.34 50 50
RAC1 0.021 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.072 0.17 -10000 0 -0.51 9 9
VEGFA 0.021 0.009 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.082 0.17 -10000 0 -0.32 50 50
VEGFR1 homodimer/VEGFA homodimer 0.031 0.018 -10000 0 -10000 0 0
RHOA 0.022 0.001 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.046 0.15 -10000 0 -0.33 53 53
GNAQ 0.02 0.025 -10000 0 -0.38 1 1
GNAZ 0.17 0.16 0.35 117 -10000 0 117
G12/G13 0.03 0.008 -10000 0 -10000 0 0
GNA14 -0.098 0.26 -10000 0 -0.67 45 45
GNA15 0.024 0.029 0.35 2 -10000 0 2
GNA12 0.021 0.004 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.008 0.097 -10000 0 -0.69 5 5
Rac1/GTP -0.072 0.17 -10000 0 -0.51 9 9
Signaling events mediated by PRL

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
CCNE1 0.13 0.15 0.35 86 -10000 0 86
mol:Halofuginone 0.002 0.005 -10000 0 -10000 0 0
ITGA1 0.019 0.044 -10000 0 -0.69 1 1
CDKN1A -0.054 0.14 -10000 0 -0.52 13 13
PRL-3/alpha Tubulin 0.044 0.066 0.25 24 -10000 0 24
mol:Ca2+ -0.034 0.087 -10000 0 -0.29 24 24
AGT 0.007 0.087 -10000 0 -0.69 4 4
CCNA2 -0.062 0.2 -10000 0 -1.1 1 1
TUBA1B 0.021 0.002 -10000 0 -10000 0 0
EGR1 -0.15 0.25 -10000 0 -0.52 81 81
CDK2/Cyclin E1 0.034 0.16 0.33 2 -0.59 7 9
MAPK3 0.046 0.082 0.26 18 -10000 0 18
PRL-2 /Rab GGTase beta 0.031 0.007 -10000 0 -10000 0 0
MAPK1 0.046 0.082 0.23 42 -10000 0 42
PTP4A1 -0.12 0.2 -10000 0 -1.3 1 1
PTP4A3 0.046 0.096 0.35 24 -10000 0 24
PTP4A2 0.021 0.004 -10000 0 -10000 0 0
ITGB1 0.046 0.084 0.28 18 -10000 0 18
SRC 0.023 0.02 0.35 1 -10000 0 1
RAC1 -0.012 0.098 -10000 0 -0.3 2 2
Rab GGTase beta/Rab GGTase alpha 0.031 0.006 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.23 0.27 -10000 0 -0.75 30 30
RABGGTA 0.022 0 -10000 0 -10000 0 0
BCAR1 -0.031 0.067 -10000 0 -0.24 24 24
RHOC -0.022 0.12 -10000 0 -0.42 7 7
RHOA -0.014 0.1 0.23 1 -0.38 3 4
cell motility -0.011 0.12 0.27 1 -0.45 4 5
PRL-1/alpha Tubulin -0.099 0.2 -10000 0 -1.2 1 1
PRL-3/alpha1 Integrin 0.042 0.075 0.25 24 -0.52 1 25
ROCK1 -0.016 0.12 0.27 1 -0.45 4 5
RABGGTB 0.021 0.004 -10000 0 -10000 0 0
CDK2 0.021 0.002 -10000 0 -10000 0 0
mitosis -0.12 0.2 -10000 0 -1.3 1 1
ATF5 -0.22 0.33 -10000 0 -0.68 89 89
p38 MAPK signaling pathway

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
TRAF6/ASK1 -0.02 0.11 -10000 0 -0.36 26 26
TRAF2/ASK1 -0.016 0.13 -10000 0 -0.42 25 25
ATM 0.021 0.004 -10000 0 -10000 0 0
MAP2K3 -0.055 0.091 -10000 0 -0.37 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.07 0.14 -10000 0 -0.44 26 26
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.085 0.25 -10000 0 -0.66 41 41
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.021 0.004 -10000 0 -10000 0 0
GADD45A 0.012 0.071 -10000 0 -0.54 4 4
GADD45B -0.089 0.26 -10000 0 -0.68 41 41
MAP3K1 0.022 0 -10000 0 -10000 0 0
MAP3K6 0.022 0.021 0.35 1 -10000 0 1
MAP3K7 0.021 0.005 -10000 0 -10000 0 0
MAP3K4 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.019 0.16 -10000 0 -0.52 22 22
TAK1/TAB family -0.005 0.028 -10000 0 -0.18 2 2
RAC1/OSM/MEKK3 0.039 0.01 -10000 0 -10000 0 0
TRAF2 0.021 0.003 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.037 0.08 -10000 0 -0.32 1 1
TRAF6 0.005 0.025 -10000 0 -0.4 1 1
RAC1 0.021 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.32 0.35 -10000 0 -0.69 125 125
CCM2 0.021 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.2 0.24 -10000 0 -0.45 125 125
MAPK11 0.031 0.057 0.35 8 -10000 0 8
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.22 0.25 -10000 0 -0.44 137 137
OSM/MEKK3 0.03 0.008 -10000 0 -10000 0 0
TAOK1 0.011 0.025 -10000 0 -0.4 1 1
TAOK2 0.013 0.003 -10000 0 -10000 0 0
TAOK3 0.013 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.043 0.2 -10000 0 -0.65 25 25
MAP3K10 0.021 0.003 -10000 0 -10000 0 0
MAP3K3 0.021 0.004 -10000 0 -10000 0 0
TRX/ASK1 -0.023 0.13 -10000 0 -0.41 25 25
GADD45/MTK1/MTK1 -0.087 0.24 -10000 0 -0.48 63 63
Nectin adhesion pathway

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
PDGFRB 0.029 0.049 0.35 6 -10000 0 6
alphaV beta3 Integrin -0.001 0.13 -10000 0 -0.52 15 15
PTK2 -0.055 0.18 -10000 0 -0.55 24 24
positive regulation of JNK cascade -0.041 0.13 -10000 0 -0.33 31 31
CDC42/GDP -0.034 0.18 -10000 0 -0.45 31 31
Rac1/GDP -0.032 0.18 -10000 0 -0.45 31 31
RAP1B 0.021 0.002 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CTNNB1 0.022 0 -10000 0 -10000 0 0
CDC42/GTP -0.035 0.16 -10000 0 -0.41 30 30
nectin-3/I-afadin -0.034 0.18 -10000 0 -0.52 30 30
RAPGEF1 -0.047 0.19 -10000 0 -0.51 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.067 0.21 -10000 0 -0.58 30 30
PDGFB-D/PDGFRB 0.029 0.049 0.35 6 -10000 0 6
TLN1 -0.019 0.074 -10000 0 -0.41 1 1
Rap1/GTP -0.042 0.13 -10000 0 -0.36 29 29
IQGAP1 0.021 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.037 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.034 0.18 -10000 0 -0.52 30 30
PVR 0.021 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.021 0.003 -10000 0 -10000 0 0
mol:GDP -0.055 0.22 -10000 0 -0.55 32 32
MLLT4 0.02 0.006 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
PI3K 0.006 0.15 -10000 0 -0.4 30 30
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.03 0.017 0.25 1 -10000 0 1
positive regulation of lamellipodium assembly -0.034 0.14 -10000 0 -0.35 31 31
PVRL1 0.022 0.021 0.35 1 -10000 0 1
PVRL3 -0.06 0.23 -10000 0 -0.69 30 30
PVRL2 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
CDH1 -0.017 0.16 -10000 0 -0.69 14 14
CLDN1 0.008 0.097 -10000 0 -0.69 5 5
JAM-A/CLDN1 -0.017 0.15 -10000 0 -0.43 28 28
SRC -0.075 0.23 -10000 0 -0.64 31 31
ITGB3 -0.019 0.16 -10000 0 -0.69 15 15
nectin-1(dimer)/I-afadin/I-afadin 0.03 0.017 0.25 1 -10000 0 1
FARP2 -0.054 0.22 -10000 0 -0.55 31 31
RAC1 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 0.021 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.017 0.16 -10000 0 -0.45 30 30
nectin-1/I-afadin 0.03 0.017 0.25 1 -10000 0 1
nectin-2/I-afadin 0.029 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.028 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.016 0.16 -10000 0 -0.45 30 30
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.008 -10000 0 -10000 0 0
F11R 0.017 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.041 0.13 -10000 0 -0.33 31 31
alphaV/beta3 Integrin/Talin -0.019 0.14 0.34 1 -0.49 15 16
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.029 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.029 0.009 -10000 0 -10000 0 0
PIP5K1C -0.02 0.08 -10000 0 -0.24 29 29
VAV2 -0.059 0.22 -10000 0 -0.57 29 29
RAP1/GDP -0.029 0.17 -10000 0 -0.42 29 29
ITGAV 0.021 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.017 0.16 -10000 0 -0.45 30 30
nectin-3(dimer)/I-afadin/I-afadin -0.034 0.18 -10000 0 -0.52 30 30
Rac1/GTP -0.038 0.17 -10000 0 -0.43 31 31
PTPRM -0.02 0.089 -10000 0 -0.26 30 30
E-cadherin/beta catenin/alpha catenin 0.032 0.1 -10000 0 -0.38 14 14
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.016 0.002 -10000 0 -10000 0 0
PRKCZ -0.009 0.14 -10000 0 -0.66 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.021 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.045 0.14 -10000 0 -0.35 28 28
IRAK/TOLLIP 0.026 0.005 -10000 0 -10000 0 0
IKBKB 0.019 0.007 -10000 0 -10000 0 0
IKBKG 0.021 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.03 0.041 -10000 0 -0.52 1 1
IL1A 0.021 0.029 0.35 2 -10000 0 2
IL1B -0.067 0.19 -10000 0 -0.52 39 39
IRAK/TRAF6/p62/Atypical PKCs 0.03 0.087 -10000 0 -0.37 11 11
IL1R2 0.02 0.048 0.35 1 -0.69 1 2
IL1R1 0.013 0.075 -10000 0 -0.69 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.04 0.13 0.26 1 -0.51 8 9
TOLLIP 0.021 0.002 -10000 0 -10000 0 0
TICAM2 0.019 0.044 -10000 0 -0.69 1 1
MAP3K3 0.021 0.004 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.014 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.009 0.079 -10000 0 -0.48 1 1
JUN -0.02 0.1 -10000 0 -0.39 17 17
MAP3K7 0.021 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.058 0.22 -10000 0 -0.43 62 62
IL1 alpha/IL1R1/IL1RAP/MYD88 0.002 0.16 -10000 0 -0.46 27 27
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.15 -10000 0 -0.43 27 27
IL1 beta fragment/IL1R1/IL1RAP -0.08 0.22 -10000 0 -0.46 62 62
NFKB1 0.02 0.006 -10000 0 -10000 0 0
MAPK8 -0.012 0.093 -10000 0 -0.38 15 15
IRAK1 0.013 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.044 0.19 -10000 0 -0.52 36 36
IRAK4 0.021 0.002 -10000 0 -10000 0 0
PRKCI 0.021 0.002 -10000 0 -10000 0 0
TRAF6 0.019 0.044 -10000 0 -0.69 1 1
PI3K 0.028 0.06 -10000 0 -0.93 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.051 0.16 -10000 0 -0.38 30 30
CHUK 0.021 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.08 0.22 -10000 0 -0.46 62 62
IL1 beta/IL1R2 -0.044 0.18 -10000 0 -0.46 39 39
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.026 -10000 0 -0.37 1 1
NF kappa B1 p50/RelA -0.061 0.2 -10000 0 -0.39 62 62
IRAK3 0.005 0.11 -10000 0 -0.69 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.057 0.21 -10000 0 -0.42 62 62
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.01 0.11 -10000 0 -0.33 27 27
IL1 alpha/IL1R1/IL1RAP -0.013 0.17 -10000 0 -0.5 27 27
RELA 0.021 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.022 0.021 0.35 1 -10000 0 1
MYD88 0.022 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.035 0.028 -10000 0 -0.39 1 1
IL1RAP -0.052 0.22 -10000 0 -0.69 27 27
UBE2N 0.021 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 -0.063 0.18 -10000 0 -0.36 59 59
CASP1 0.021 0.003 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.039 0.19 -10000 0 -0.53 33 33
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.066 0.22 -10000 0 -0.43 62 62
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.1 -10000 0 -0.49 4 4
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
IL1RN -0.068 0.24 -10000 0 -0.69 33 33
TRAF6/TAK1/TAB1/TAB2 0.028 0.026 -10000 0 -0.38 1 1
MAP2K6 0.006 0.073 -10000 0 -0.42 6 6
LPA4-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
ADCY4 0.003 0.029 -10000 0 -0.45 1 1
ADCY5 -0.075 0.17 -10000 0 -0.45 46 46
ADCY6 0.004 0.018 -10000 0 -0.26 1 1
ADCY7 0.003 0.029 -10000 0 -0.45 1 1
ADCY1 -0.15 0.22 -10000 0 -0.45 90 90
ADCY2 0.001 0.029 -10000 0 -0.26 1 1
ADCY3 0.004 0.032 -10000 0 -0.45 1 1
ADCY8 0.02 0.066 0.24 15 -0.26 1 16
PRKCE 0.006 0.035 0.2 1 -0.52 1 2
ADCY9 0.003 0.029 -10000 0 -0.45 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.014 0.075 -10000 0 -0.23 1 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.004 0.019 -10000 0 -0.29 1 1
RFC1 -0.004 0.019 -10000 0 -0.29 1 1
PRKDC -0.001 0.016 0.23 1 -10000 0 1
RIPK1 0.02 0.01 -10000 0 -10000 0 0
CASP7 -0.013 0.13 -10000 0 -0.7 8 8
FASLG/FAS/FADD/FAF1 0.022 0.12 0.26 27 -0.35 11 38
MAP2K4 -0.03 0.18 0.31 2 -0.5 21 23
mol:ceramide -0.006 0.12 0.29 2 -0.46 9 11
GSN -0.004 0.019 -10000 0 -0.29 1 1
FASLG/FAS/FADD/FAF1/Caspase 8 0.023 0.1 0.27 3 -0.36 8 11
FAS -0.01 0.14 -10000 0 -0.69 10 10
BID -0.008 0.029 0.29 2 -10000 0 2
MAP3K1 -0.021 0.13 -10000 0 -0.48 13 13
MAP3K7 0.019 0.008 -10000 0 -10000 0 0
RB1 -0.004 0.019 -10000 0 -0.29 1 1
CFLAR 0.022 0.008 -10000 0 -10000 0 0
HGF/MET -0.28 0.32 -10000 0 -0.56 138 138
ARHGDIB -0.004 0.019 -10000 0 -0.29 1 1
FADD 0.016 0.016 -10000 0 -10000 0 0
actin filament polymerization 0.004 0.019 0.29 1 -10000 0 1
NFKB1 -0.05 0.21 -10000 0 -0.7 19 19
MAPK8 -0.065 0.23 0.37 2 -0.51 44 46
DFFA -0.004 0.019 -10000 0 -0.29 1 1
DNA fragmentation during apoptosis -0.005 0.032 -10000 0 -0.36 2 2
FAS/FADD/MET 0.015 0.096 -10000 0 -0.42 11 11
CFLAR/RIP1 0.029 0.015 -10000 0 -10000 0 0
FAIM3 0.014 0.065 0.35 1 -0.69 2 3
FAF1 0.017 0.018 -10000 0 -10000 0 0
PARP1 -0.004 0.019 -10000 0 -0.29 1 1
DFFB -0.005 0.032 -10000 0 -0.36 2 2
CHUK -0.046 0.19 -10000 0 -0.69 17 17
FASLG -0.003 0.12 0.35 2 -0.69 7 9
FAS/FADD 0.004 0.11 -10000 0 -0.52 10 10
HGF -0.32 0.35 -10000 0 -0.69 127 127
LMNA 0.003 0.05 -10000 0 -0.27 1 1
CASP6 -0.004 0.019 -10000 0 -0.29 1 1
CASP10 0.017 0.016 -10000 0 -10000 0 0
CASP3 -0.004 0.022 -10000 0 -0.32 1 1
PTPN13 -0.12 0.28 0.35 2 -0.63 60 62
CASP8 -0.009 0.04 0.41 2 -0.24 1 3
IL6 -0.19 0.51 0.45 4 -1.3 43 47
MET 0.018 0.044 -10000 0 -0.69 1 1
ICAD/CAD -0.005 0.03 -10000 0 -0.34 2 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.006 0.12 0.3 2 -0.46 9 11
activation of caspase activity by cytochrome c -0.008 0.029 0.29 2 -10000 0 2
PAK2 -0.004 0.02 -10000 0 -0.29 1 1
BCL2 0.021 0.003 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.025 0.031 0.35 2 -10000 0 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.11 0.21 0.73 14 -10000 0 14
IL27/IL27R/JAK1 -0.12 0.25 -10000 0 -0.68 16 16
TBX21 -0.12 0.22 -10000 0 -0.56 23 23
IL12B 0.023 0.032 0.38 2 -10000 0 2
IL12A 0.012 0.034 0.2 8 -10000 0 8
IL6ST -0.13 0.3 -10000 0 -0.69 57 57
IL27RA/JAK1 0.011 0.043 -10000 0 -10000 0 0
IL27 -0.12 0.28 -10000 0 -0.69 52 52
TYK2 0.023 0.014 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.012 0.14 0.62 1 -10000 0 1
T-helper 2 cell differentiation 0.11 0.21 0.73 14 -10000 0 14
T cell proliferation during immune response 0.11 0.21 0.73 14 -10000 0 14
MAPKKK cascade -0.11 0.21 -10000 0 -0.73 14 14
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT2 0.021 0.002 -10000 0 -10000 0 0
STAT1 0.024 0.029 0.35 2 -10000 0 2
IL12RB1 0 0.12 -10000 0 -0.69 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.11 0.22 -10000 0 -0.62 20 20
IL27/IL27R/JAK2/TYK2 -0.11 0.21 -10000 0 -0.74 14 14
positive regulation of T cell mediated cytotoxicity -0.11 0.21 -10000 0 -0.73 14 14
STAT1 (dimer) -0.12 0.29 0.55 10 -0.74 17 27
JAK2 0.021 0.028 -10000 0 -0.39 1 1
JAK1 0.021 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.1 0.21 -10000 0 -0.7 14 14
T cell proliferation -0.15 0.24 -10000 0 -0.68 26 26
IL12/IL12R/TYK2/JAK2 0.024 0.12 0.46 2 -0.83 3 5
IL17A -0.012 0.14 0.62 1 -10000 0 1
mast cell activation 0.11 0.21 0.73 14 -10000 0 14
IFNG -0.006 0.039 0.16 4 -0.11 4 8
T cell differentiation -0.004 0.007 0.017 3 -0.022 9 12
STAT3 (dimer) -0.099 0.21 -10000 0 -0.7 14 14
STAT5A (dimer) -0.099 0.21 -10000 0 -0.7 14 14
STAT4 (dimer) -0.11 0.22 -10000 0 -0.68 21 21
STAT4 -0.004 0.14 0.35 1 -0.69 10 11
T cell activation -0.011 0.013 -10000 0 -0.18 1 1
IL27R/JAK2/TYK2 -0.038 0.2 -10000 0 -0.47 11 11
GATA3 -0.064 0.38 0.72 4 -1.4 18 22
IL18 -0.001 0.069 0.2 2 -0.47 5 7
positive regulation of mast cell cytokine production -0.098 0.2 -10000 0 -0.69 14 14
IL27/EBI3 -0.1 0.24 -10000 0 -0.51 66 66
IL27RA 0.001 0.045 -10000 0 -10000 0 0
IL6 -0.067 0.25 0.35 6 -0.69 36 42
STAT5A 0.021 0.003 -10000 0 -10000 0 0
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.005 0.027 -10000 0 -10000 0 0
IL1B -0.073 0.19 -10000 0 -0.51 40 40
EBI3 -0.013 0.15 -10000 0 -0.64 14 14
TNF -0.014 0.11 0.2 2 -0.52 11 13
Regulation of Telomerase

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
Telomerase catalytic core complex 0.16 0.24 0.51 53 -0.6 3 56
RAD9A 0.021 0.003 -10000 0 -10000 0 0
AP1 -0.2 0.28 -10000 0 -0.51 117 117
IFNAR2 0.036 0.022 -10000 0 -10000 0 0
AKT1 -0.1 0.16 -10000 0 -0.28 80 80
ER alpha/Oestrogen -0.25 0.26 -10000 0 -0.5 137 137
NFX1/SIN3/HDAC complex 0.041 0.06 -10000 0 -0.31 4 4
EGF 0.1 0.14 0.36 65 -10000 0 65
SMG5 0.017 0.009 -10000 0 -10000 0 0
SMG6 0.019 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.054 0.034 -10000 0 -10000 0 0
TERT/c-Abl 0.079 0.18 0.42 7 -0.57 3 10
SAP18 0.023 0.006 -10000 0 -10000 0 0
MRN complex 0.032 0.02 -10000 0 -10000 0 0
WT1 0.053 0.08 0.37 15 -10000 0 15
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.043 0.03 -10000 0 -10000 0 0
SP3 0.028 0.01 -10000 0 -10000 0 0
TERF2IP 0.02 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.01 0.096 -10000 0 -0.52 3 3
Mad/Max 0.051 0.031 0.3 1 -10000 0 1
TERT 0.16 0.24 0.51 50 -0.62 3 53
CCND1 0.12 0.33 0.57 25 -1.1 10 35
MAX 0.029 0.011 -10000 0 -10000 0 0
RBBP7 0.024 0.005 -10000 0 -10000 0 0
RBBP4 0.023 0.005 -10000 0 -10000 0 0
TERF2 0.018 0.006 -10000 0 -10000 0 0
PTGES3 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.024 0.005 -10000 0 -10000 0 0
Telomerase/911 0.074 0.066 -10000 0 -10000 0 0
CDKN1B 0.035 0.03 -10000 0 -10000 0 0
RAD1 0.021 0.003 -10000 0 -10000 0 0
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.021 0.003 -10000 0 -10000 0 0
SAP30 0.023 0.007 -10000 0 -10000 0 0
TRF2/PARP2 0.029 0.009 -10000 0 -10000 0 0
UBE3A 0.028 0.01 -10000 0 -10000 0 0
JUN 0.013 0.091 -10000 0 -0.62 5 5
E6 0.007 0.009 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.033 0.022 -10000 0 -10000 0 0
FOS -0.28 0.35 -10000 0 -0.66 117 117
IFN-gamma/IRF1 0.061 0.049 0.3 5 -10000 0 5
PARP2 0.022 0.001 -10000 0 -10000 0 0
BLM 0.13 0.15 0.35 86 -10000 0 86
Telomerase 0.076 0.099 -10000 0 -10000 0 0
IRF1 0.032 0.011 -10000 0 -10000 0 0
ESR1 -0.34 0.35 -10000 0 -0.66 137 137
KU/TER 0.031 0.006 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.072 -10000 0 -0.33 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.039 0.073 -10000 0 -0.33 4 4
HDAC1 0.023 0.005 -10000 0 -10000 0 0
HDAC2 0.038 0.025 -10000 0 -10000 0 0
ATM 0.011 0.014 -10000 0 -10000 0 0
SMAD3 0.002 0.03 0.26 1 -10000 0 1
ABL1 0.021 0.003 -10000 0 -10000 0 0
MXD1 0.031 0.023 0.37 1 -10000 0 1
MRE11A 0.021 0.003 -10000 0 -10000 0 0
HUS1 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.021 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.059 0.23 0.47 17 -0.59 7 24
NR2F2 -0.001 0.028 -10000 0 -10000 0 0
MAPK3 0.02 0.021 -10000 0 -10000 0 0
MAPK1 0.02 0.02 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.011 0.035 0.35 2 -10000 0 2
NFKB1 0.02 0.006 -10000 0 -10000 0 0
HNRNPC 0.021 0.002 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.014 -10000 0 -10000 0 0
NBN 0.017 0.009 -10000 0 -10000 0 0
EGFR 0.016 0.087 -10000 0 -0.68 4 4
mol:Oestrogen 0.002 0.004 -10000 0 -10000 0 0
EGF/EGFR 0.082 0.12 0.28 24 -0.49 4 28
MYC -0.048 0.21 -10000 0 -0.66 27 27
IL2 0.037 0.031 -10000 0 -10000 0 0
KU 0.031 0.006 -10000 0 -10000 0 0
RAD50 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
TGFB1 0.011 0.035 0.35 2 -10000 0 2
TRF2/BLM 0.089 0.096 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.15 0.22 0.47 39 -0.56 3 42
SP1/HDAC2 0.07 0.055 -10000 0 -10000 0 0
PINX1 0.018 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.01 0.094 -10000 0 -0.52 3 3
Smad3/Myc -0.036 0.13 -10000 0 -0.44 25 25
911 complex 0.041 0.011 -10000 0 -10000 0 0
IFNG 0.042 0.061 0.36 9 -10000 0 9
Telomerase/PinX1 0.008 0.093 -10000 0 -0.52 3 3
Telomerase/AKT1/mTOR/p70S6K 0.039 0.14 0.32 4 -0.4 7 11
SIN3B 0.024 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.008 0.087 -10000 0 -0.55 2 2
response to DNA damage stimulus 0.004 0.013 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.043 0.029 -10000 0 -10000 0 0
TRF2/WRN 0.024 0.013 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.01 0.096 -10000 0 -0.53 3 3
E2F1 0.23 0.17 0.36 153 -10000 0 153
ZNFX1 0.024 0.005 -10000 0 -10000 0 0
PIF1 0.11 0.14 0.35 71 -10000 0 71
NCL 0.021 0.002 -10000 0 -10000 0 0
DKC1 0.021 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.021 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.23 2 -10000 0 2
Metarhodopsin II/Arrestin 0.028 0.032 0.22 1 -10000 0 1
PDE6G/GNAT1/GTP 0.02 0.068 -10000 0 -0.45 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.029 0.35 2 -10000 0 2
GRK1 0.014 0.003 -10000 0 -10000 0 0
CNG Channel -0.061 0.18 -10000 0 -0.38 47 47
mol:Na + -0.059 0.18 -10000 0 -0.38 50 50
mol:ADP 0.014 0.003 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.039 0.097 0.44 1 -0.45 7 8
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.054 0.18 -10000 0 -0.39 50 50
CNGB1 0.03 0.064 0.35 10 -10000 0 10
RDH5 -0.084 0.25 -10000 0 -0.69 39 39
SAG 0.017 0.021 0.35 1 -10000 0 1
mol:Ca2+ -0.068 0.18 0.34 8 -0.39 28 36
Na + (4 Units) -0.06 0.16 -10000 0 -0.36 50 50
RGS9 0.017 0.14 0.35 12 -0.69 7 19
GNB1/GNGT1 0.049 0.071 0.25 29 -10000 0 29
GNAT1/GDP 0.048 0.089 0.36 2 -0.39 7 9
GUCY2D 0.05 0.099 0.35 26 -10000 0 26
GNGT1 0.053 0.11 0.35 30 -10000 0 30
GUCY2F 0.016 0.003 -10000 0 -10000 0 0
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.027 0.079 0.32 2 -0.36 6 8
mol:11-cis-retinal -0.084 0.25 -10000 0 -0.69 39 39
mol:cGMP 0.033 0.08 0.34 1 -0.4 6 7
GNB1 0.02 0.006 -10000 0 -10000 0 0
Rhodopsin -0.047 0.2 -10000 0 -0.52 39 39
SLC24A1 0.021 0.003 -10000 0 -10000 0 0
CNGA1 -0.15 0.3 -10000 0 -0.67 66 66
Metarhodopsin II 0.025 0.028 0.2 6 -10000 0 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.046 0.096 0.42 1 -0.42 6 7
RGS9BP 0.027 0.049 0.35 6 -10000 0 6
Metarhodopsin II/Transducin 0.029 0.042 0.23 2 -10000 0 2
GCAP Family/Ca ++ 0.022 0.07 -10000 0 -0.42 6 6
PDE6A/B 0.044 0.08 0.25 23 -0.52 2 25
mol:Pi 0.039 0.096 0.43 1 -0.45 7 8
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.055 0.062 -10000 0 -10000 0 0
PDE6B 0.032 0.095 0.35 13 -0.69 2 15
PDE6A 0.033 0.066 0.35 11 -10000 0 11
PDE6G 0.007 0.097 -10000 0 -0.69 5 5
RHO 0.027 0.049 0.35 6 -10000 0 6
PDE6 0.054 0.11 0.37 1 -0.38 11 12
GUCA1A 0.018 0.029 0.35 2 -10000 0 2
GC2/GCAP Family 0.032 0.073 -10000 0 -0.42 6 6
GUCA1C 0.014 0 -10000 0 -10000 0 0
GUCA1B 0.004 0.11 -10000 0 -0.69 6 6
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.008 0.11 -10000 0 -0.76 2 2
HDAC1 0.024 0.015 -10000 0 -10000 0 0
AES 0.022 0.007 -10000 0 -10000 0 0
FBXW11 0.021 0.003 -10000 0 -10000 0 0
DTX1 -0.18 0.32 -10000 0 -0.69 73 73
LRP6/FZD1 0.024 0.061 -10000 0 -0.52 3 3
TLE1 0.019 0.044 -10000 0 -0.69 1 1
AP1 -0.14 0.21 -10000 0 -0.38 93 93
NCSTN 0.017 0.009 -10000 0 -10000 0 0
ADAM10 0.018 0.044 -10000 0 -0.69 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.029 0.18 -10000 0 -0.67 12 12
NICD/RBPSUH 0.016 0.083 -10000 0 -0.49 2 2
WIF1 0.045 0.097 0.35 24 -10000 0 24
NOTCH1 0.006 0.077 -10000 0 -0.6 1 1
PSENEN 0.021 0.003 -10000 0 -10000 0 0
KREMEN2 0.056 0.1 0.35 29 -10000 0 29
DKK1 0.12 0.15 0.35 82 -10000 0 82
beta catenin/beta TrCP1 0.014 0.075 0.27 2 -10000 0 2
APH1B 0.021 0.003 -10000 0 -10000 0 0
APH1A 0.017 0.009 -10000 0 -10000 0 0
AXIN1 0.002 0.092 0.32 1 -0.44 6 7
CtBP/CBP/TCF1/TLE1/AES 0.025 0.069 0.29 2 -0.4 3 5
PSEN1 0.021 0.004 -10000 0 -10000 0 0
FOS -0.29 0.35 -10000 0 -0.67 117 117
JUN 0.009 0.09 -10000 0 -0.63 5 5
MAP3K7 0.022 0.008 -10000 0 -10000 0 0
CTNNB1 0.006 0.075 0.28 2 -10000 0 2
MAPK3 0.021 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.085 0.091 0.44 3 -10000 0 3
HNF1A 0.011 0.087 -10000 0 -0.68 4 4
CTBP1 0.022 0.007 -10000 0 -10000 0 0
MYC -0.15 0.48 -10000 0 -1.5 29 29
NKD1 0.058 0.21 0.35 55 -0.66 12 67
FZD1 0.014 0.078 0.35 1 -0.69 3 4
NOTCH1 precursor/Deltex homolog 1 -0.087 0.19 -10000 0 -0.64 7 7
apoptosis -0.14 0.21 -10000 0 -0.38 93 93
Delta 1/NOTCHprecursor 0.01 0.11 -10000 0 -0.76 2 2
DLL1 0.01 0.095 0.35 2 -0.63 5 7
PPARD 0 0.12 -10000 0 -1.1 3 3
Gamma Secretase 0.046 0.029 -10000 0 -10000 0 0
APC 0.012 0.061 0.32 1 -0.32 3 4
DVL1 0.018 0.016 -10000 0 -10000 0 0
CSNK2A1 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.11 0.12 0.44 13 -10000 0 13
LRP6 0.021 0.004 -10000 0 -10000 0 0
CSNK1A1 0.021 0.004 -10000 0 -10000 0 0
NLK 0.015 0.015 -10000 0 -10000 0 0
CCND1 -0.046 0.3 -10000 0 -1.5 11 11
WNT1 0.021 0.036 0.35 3 -10000 0 3
Axin1/APC/beta catenin 0.024 0.093 0.3 1 -0.43 2 3
DKK2 0.065 0.11 0.35 36 -10000 0 36
NOTCH1 precursor/DVL1 0.008 0.088 -10000 0 -0.5 3 3
GSK3B 0.022 0.002 -10000 0 -10000 0 0
FRAT1 0.019 0.044 -10000 0 -0.69 1 1
NOTCH/Deltex homolog 1 -0.089 0.19 -10000 0 -0.68 6 6
PPP2R5D -0.004 0.094 0.31 9 -0.35 1 10
MAPK1 0.021 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.057 0.077 -10000 0 -0.42 3 3
RBPJ 0.021 0.004 -10000 0 -10000 0 0
CREBBP 0.02 0.009 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.002 0.028 -10000 0 -10000 0 0
HSPA8 0.021 0.044 -10000 0 -0.68 1 1
SMAD3/SMAD4/ER alpha -0.25 0.25 -10000 0 -0.49 133 133
AKT1 0.025 0.014 -10000 0 -10000 0 0
GSC 0.049 0.12 0.56 3 -10000 0 3
NKX2-5 0.001 0 -10000 0 -10000 0 0
muscle cell differentiation -0.002 0.073 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.05 0.099 -10000 0 -0.46 1 1
SMAD4 0 0.062 -10000 0 -0.3 1 1
CBFB 0.02 0.005 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.021 0.055 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.006 0.11 0.37 1 -0.43 7 8
MYC -0.06 0.21 -10000 0 -0.67 27 27
CDKN2B 0.013 0.15 0.47 8 -0.44 3 11
AP1 -0.14 0.23 -10000 0 -0.39 106 106
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.082 -10000 0 -0.38 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.022 0.061 0.28 1 -0.32 1 2
SP3 0.023 0.003 -10000 0 -10000 0 0
CREB1 0.021 0.003 -10000 0 -10000 0 0
FOXH1 0.034 0.072 0.36 12 -10000 0 12
SMAD3/SMAD4/GR 0.034 0.087 -10000 0 -0.32 1 1
GATA3 -0.043 0.2 0.35 1 -0.62 23 24
SKI/SIN3/HDAC complex/NCoR1 0.018 0.064 -10000 0 -0.37 5 5
MEF2C/TIF2 0.012 0.11 -10000 0 -0.38 11 11
endothelial cell migration 0.37 0.64 1.4 72 -10000 0 72
MAX 0.033 0.023 -10000 0 -10000 0 0
RBBP7 0.022 0.003 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
RUNX2 0.019 0.062 0.35 3 -0.54 2 5
RUNX3 0.002 0.11 -10000 0 -0.69 7 7
RUNX1 0.019 0.044 -10000 0 -0.69 1 1
CTBP1 0.021 0.003 -10000 0 -10000 0 0
NR3C1 0.034 0.022 -10000 0 -10000 0 0
VDR 0.015 0.12 0.35 8 -0.69 6 14
CDKN1A -0.001 0.18 -10000 0 -1.4 4 4
KAT2B 0.002 0.077 -10000 0 -0.69 3 3
SMAD2/SMAD2/SMAD4/FOXH1 0.044 0.072 0.43 2 -10000 0 2
DCP1A 0.021 0.002 -10000 0 -10000 0 0
SKI 0.021 0.006 -10000 0 -10000 0 0
SERPINE1 -0.38 0.65 -10000 0 -1.4 72 72
SMAD3/SMAD4/ATF2 0.005 0.098 -10000 0 -0.45 5 5
SMAD3/SMAD4/ATF3 -0.009 0.13 -10000 0 -0.54 12 12
SAP30 0.021 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.008 0.042 -10000 0 -10000 0 0
JUN -0.14 0.22 -10000 0 -0.38 101 101
SMAD3/SMAD4/IRF7 0.007 0.096 -10000 0 -0.48 4 4
TFE3 0.003 0.039 -10000 0 -10000 0 0
COL1A2 0.11 0.15 0.52 14 -1.2 1 15
mesenchymal cell differentiation -0.012 0.089 0.44 2 -0.35 3 5
DLX1 0.046 0.089 0.35 21 -10000 0 21
TCF3 0.021 0.003 -10000 0 -10000 0 0
FOS -0.29 0.35 -10000 0 -0.67 117 117
SMAD3/SMAD4/Max 0.034 0.087 -10000 0 -0.32 1 1
Cbp/p300/SNIP1 0.021 0.033 -10000 0 -10000 0 0
ZBTB17 0.014 0.024 -10000 0 -10000 0 0
LAMC1 -0.002 0.064 0.44 1 -10000 0 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.012 0.077 -10000 0 -0.38 1 1
IRF7 0.014 0.075 -10000 0 -0.69 3 3
ESR1 -0.35 0.35 -10000 0 -0.68 137 137
HNF4A 0.005 0.11 -10000 0 -0.69 6 6
MEF2C 0.068 0.084 -10000 0 -10000 0 0
SMAD2-3/SMAD4 0.021 0.084 -10000 0 -0.38 1 1
Cbp/p300/Src-1 0.016 0.038 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.038 -10000 0 -0.34 2 2
TGIF2/HDAC complex 0.021 0.002 -10000 0 -10000 0 0
CREBBP 0.004 0.023 -10000 0 -10000 0 0
SKIL 0.021 0.002 -10000 0 -10000 0 0
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC2 0.022 0.005 -10000 0 -10000 0 0
SNIP1 0.023 0.005 -10000 0 -10000 0 0
GCN5L2 -0.009 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.002 0.087 -10000 0 -0.43 1 1
MSG1/HSC70 0.042 0.051 0.27 3 -0.41 1 4
SMAD2 0.03 0.016 -10000 0 -10000 0 0
SMAD3 -0.002 0.061 -10000 0 -0.3 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.058 -10000 0 -0.32 2 2
SMAD2/SMAD2/SMAD4 0.001 0.058 -10000 0 -0.38 3 3
NCOR1 0.017 0.036 -10000 0 -0.38 2 2
NCOA2 -0.034 0.18 -10000 0 -0.69 19 19
NCOA1 0.021 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.026 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.067 0.095 0.41 1 -0.44 1 2
IFNB1 -0.006 0.076 -10000 0 -0.46 3 3
SMAD3/SMAD4/MEF2C 0.048 0.093 -10000 0 -10000 0 0
CITED1 0.035 0.066 0.35 11 -10000 0 11
SMAD2-3/SMAD4/ARC105 0.031 0.081 -10000 0 -0.33 1 1
RBL1 0.035 0.066 0.35 11 -10000 0 11
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.028 0.066 0.31 3 -10000 0 3
RUNX1-3/PEBPB2 0.026 0.092 -10000 0 -0.5 7 7
SMAD7 -0.11 0.22 -10000 0 -0.78 8 8
MYC/MIZ-1 -0.04 0.16 -10000 0 -0.51 27 27
SMAD3/SMAD4 -0.13 0.22 -10000 0 -0.47 70 70
IL10 -0.07 0.23 0.46 1 -0.61 36 37
PIASy/HDAC complex 0.029 0.013 -10000 0 -10000 0 0
PIAS3 0.008 0.016 -10000 0 -10000 0 0
CDK2 0.006 0.022 -10000 0 -10000 0 0
IL5 -0.05 0.18 -10000 0 -0.5 27 27
CDK4 0.005 0.023 -10000 0 -10000 0 0
PIAS4 0.029 0.013 -10000 0 -10000 0 0
ATF3 -0.015 0.15 -10000 0 -0.69 12 12
SMAD3/SMAD4/SP1 0.027 0.097 -10000 0 -0.52 1 1
FOXG1 0.025 0.062 0.35 9 -10000 0 9
FOXO3 0.018 0.019 -10000 0 -10000 0 0
FOXO1 0.014 0.045 -10000 0 -0.35 3 3
FOXO4 0.019 0.018 -10000 0 -10000 0 0
heart looping 0.068 0.083 -10000 0 -10000 0 0
CEBPB 0.024 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.025 0.096 0.37 2 -0.38 1 3
MYOD1 0.014 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0 0.1 -10000 0 -0.46 7 7
SMAD3/SMAD4/GATA3 -0.042 0.2 -10000 0 -0.5 35 35
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.016 0.12 -10000 0 -0.53 7 7
SMAD3/SMAD4/SP1-3 0.041 0.092 -10000 0 -0.46 1 1
MED15 0.021 0.003 -10000 0 -10000 0 0
SP1 0.029 0.022 -10000 0 -10000 0 0
SIN3B 0.022 0.003 -10000 0 -10000 0 0
SIN3A 0.022 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.045 0.067 0.41 2 -10000 0 2
ITGB5 0.016 0.066 -10000 0 -0.43 1 1
TGIF/SIN3/HDAC complex/CtBP 0.025 0.034 -10000 0 -0.34 1 1
SMAD3/SMAD4/AR -0.12 0.24 -10000 0 -0.49 73 73
AR -0.17 0.32 -10000 0 -0.69 72 72
negative regulation of cell growth 0.006 0.074 -10000 0 -0.32 3 3
SMAD3/SMAD4/MYOD 0.007 0.078 -10000 0 -0.38 1 1
E2F5 0.017 0.053 0.35 2 -0.69 1 3
E2F4 0.02 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.049 0.069 0.39 2 -10000 0 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.025 0.057 0.27 1 -10000 0 1
TFDP1 0.018 0.044 -10000 0 -0.69 1 1
SMAD3/SMAD4/AP1 -0.13 0.24 -10000 0 -0.39 106 106
SMAD3/SMAD4/RUNX2 0.012 0.09 0.35 3 -0.44 2 5
TGIF2 0.021 0.002 -10000 0 -10000 0 0
TGIF1 0.021 0.003 -10000 0 -10000 0 0
ATF2 0.011 0.087 -10000 0 -0.69 4 4
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.031 0.14 0.62 1 -0.55 11 12
MAP4K1 0.008 0.11 0.35 2 -0.69 6 8
MAP3K8 0.016 0.062 -10000 0 -0.69 2 2
PRKCB -0.037 0.19 -10000 0 -0.67 22 22
DBNL 0.021 0.003 -10000 0 -10000 0 0
CRKL 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 -0.003 0.13 0.29 1 -0.54 10 11
JUN -0.078 0.26 -10000 0 -0.68 38 38
MAP3K7 -0.002 0.13 0.29 1 -0.61 8 9
GRAP2 0.008 0.12 0.35 4 -0.64 7 11
CRK 0.019 0.007 -10000 0 -10000 0 0
MAP2K4 -0.006 0.14 0.28 1 -0.63 9 10
LAT 0.022 0.02 0.35 1 -10000 0 1
LCP2 0.01 0.087 -10000 0 -0.69 4 4
MAPK8 -0.076 0.28 -10000 0 -0.7 38 38
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.004 0.14 0.33 1 -0.57 10 11
LAT/GRAP2/SLP76/HPK1/HIP-55 0.038 0.14 0.59 1 -0.52 11 12
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.005 0.075 -10000 0 -0.44 7 7
CRKL 0.021 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.003 -10000 0 -10000 0 0
DOCK1 0.007 0.097 -10000 0 -0.69 5 5
ITGA4 0.015 0.078 0.35 1 -0.69 3 4
alpha4/beta7 Integrin/MAdCAM1 0.044 0.081 0.42 1 -0.41 7 8
EPO -0.22 0.35 0.35 8 -0.69 91 99
alpha4/beta7 Integrin 0.018 0.09 -10000 0 -0.52 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.025 0.061 -10000 0 -0.52 3 3
EPO/EPOR (dimer) -0.15 0.27 -10000 0 -0.52 91 91
lamellipodium assembly 0.013 0.058 -10000 0 -0.67 1 1
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
PI3K 0.028 0.06 -10000 0 -0.93 1 1
ARF6 0.021 0.003 -10000 0 -10000 0 0
JAK2 -0.1 0.18 -10000 0 -0.34 86 86
PXN 0.021 0.002 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
MADCAM1 0.024 0.035 0.35 3 -10000 0 3
cell adhesion 0.042 0.08 0.42 1 -0.41 7 8
CRKL/CBL 0.03 0.007 -10000 0 -10000 0 0
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC -0.01 0.12 -10000 0 -0.47 14 14
ITGB7 0.011 0.087 -10000 0 -0.69 4 4
RAC1 0.021 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.011 0.14 -10000 0 -0.5 15 15
p130Cas/Crk/Dock1 0.006 0.13 -10000 0 -0.45 16 16
VCAM1 -0.016 0.17 0.35 3 -0.69 15 18
RHOA 0.022 0.001 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.053 -10000 0 -0.42 3 3
BCAR1 -0.01 0.11 -10000 0 -0.44 14 14
EPOR 0.021 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.021 0.004 -10000 0 -10000 0 0
GIT1 0.021 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.06 -10000 0 -0.7 1 1
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.049 0.25 2 -10000 0 2
AES 0.026 0.042 -10000 0 -10000 0 0
FBXW11 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.024 0.061 -10000 0 -0.52 3 3
SMAD4 0.021 0.003 -10000 0 -10000 0 0
DKK2 0.065 0.11 0.35 36 -10000 0 36
TLE1 0.022 0.061 0.22 1 -0.69 1 2
MACF1 0.021 0.004 -10000 0 -10000 0 0
CTNNB1 0.03 0.076 0.33 2 -10000 0 2
WIF1 0.046 0.096 0.35 24 -10000 0 24
beta catenin/RanBP3 0.038 0.17 0.44 32 -0.46 1 33
KREMEN2 0.056 0.1 0.35 29 -10000 0 29
DKK1 0.12 0.15 0.35 82 -10000 0 82
beta catenin/beta TrCP1 0.04 0.075 0.36 1 -10000 0 1
FZD1 0.014 0.078 0.35 1 -0.69 3 4
AXIN2 -0.02 0.35 0.66 7 -1.3 12 19
AXIN1 0.021 0.004 -10000 0 -10000 0 0
RAN 0.022 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.019 0.086 -10000 0 -0.43 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.052 0.12 -10000 0 -0.61 4 4
Axin1/APC/GSK3 0.008 0.058 0.27 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.03 0.064 0.4 1 -0.39 2 3
HNF1A 0.013 0.095 0.23 1 -0.68 4 5
CTBP1 0.025 0.044 0.22 3 -10000 0 3
MYC -0.037 0.57 0.6 33 -1.5 29 62
RANBP3 0.022 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.086 0.091 0.44 3 -10000 0 3
NKD1 0.058 0.21 0.35 55 -0.66 12 67
TCF4 0.024 0.041 -10000 0 -10000 0 0
TCF3 0.025 0.043 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.046 0.058 -10000 0 -0.42 3 3
Ran/GTP 0.016 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.052 0.24 0.56 31 -0.51 3 34
LEF1 0.15 0.16 0.34 100 -10000 0 100
DVL1 0.015 0.033 -10000 0 -10000 0 0
CSNK2A1 0.021 0.003 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.041 0.14 -10000 0 -0.48 5 5
DKK1/LRP6/Kremen 2 0.12 0.12 0.44 13 -10000 0 13
LRP6 0.021 0.004 -10000 0 -10000 0 0
CSNK1A1 0.027 0.048 -10000 0 -10000 0 0
NLK 0.018 0.013 -10000 0 -10000 0 0
CCND1 -0.054 0.35 0.57 12 -1.3 15 27
WNT1 0.022 0.036 0.35 3 -10000 0 3
GSK3A 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.022 0.001 -10000 0 -10000 0 0
FRAT1 0.018 0.044 -10000 0 -0.69 1 1
PPP2R5D -0.005 0.1 0.32 11 -0.26 2 13
APC 0.017 0.059 0.36 1 -0.39 3 4
WNT1/LRP6/FZD1 0.005 0.059 -10000 0 -0.31 3 3
CREBBP 0.024 0.043 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.022 0.003 -10000 0 -10000 0 0
ELF1 0.022 0.077 -10000 0 -0.4 6 6
CCNA2 0.18 0.16 0.35 125 -10000 0 125
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
JAK3 0.021 0.052 0.35 2 -0.69 1 3
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
JAK1 0.021 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.023 0.15 0.39 1 -0.58 12 13
SHC1 0.017 0.009 -10000 0 -10000 0 0
SP1 0.029 0.026 -10000 0 -10000 0 0
IL2RA 0.012 0.14 0.4 10 -0.78 6 16
IL2RB -0.03 0.18 -10000 0 -0.66 20 20
SOS1 0.022 0.001 -10000 0 -10000 0 0
IL2RG 0.017 0.098 0.35 5 -0.69 4 9
G1/S transition of mitotic cell cycle 0.052 0.19 0.39 3 -0.76 8 11
PTPN11 0.022 0.002 -10000 0 -10000 0 0
CCND2 0.024 0.053 0.4 5 -10000 0 5
LCK 0.001 0.12 0.35 1 -0.69 8 9
GRB2 0.021 0.005 -10000 0 -10000 0 0
IL2 0.016 0.005 -10000 0 -10000 0 0
CDK6 -0.024 0.17 -10000 0 -0.67 17 17
CCND3 0.034 0.14 -10000 0 -0.56 6 6
Regulation of Androgen receptor activity

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
HDAC1 0.013 0.005 -10000 0 -10000 0 0
SMARCC1 0.013 0.015 -10000 0 -10000 0 0
REL 0 0.12 -10000 0 -0.69 7 7
HDAC7 -0.045 0.15 -10000 0 -0.46 18 18
JUN 0.009 0.09 -10000 0 -0.63 5 5
EP300 0.021 0.003 -10000 0 -10000 0 0
KAT2B 0.014 0.075 -10000 0 -0.69 3 3
KAT5 0.021 0.003 -10000 0 -10000 0 0
MAPK14 0.002 0.089 0.45 1 -0.52 6 7
FOXO1 0.015 0.056 -10000 0 -0.49 3 3
T-DHT/AR -0.037 0.16 -10000 0 -0.48 18 18
MAP2K6 0.006 0.12 0.35 4 -0.69 6 10
BRM/BAF57 0.017 0.089 -10000 0 -0.46 8 8
MAP2K4 0.016 0.015 -10000 0 -10000 0 0
SMARCA2 0.002 0.11 -10000 0 -0.61 8 8
PDE9A -0.1 0.33 -10000 0 -1.1 25 25
NCOA2 -0.033 0.18 -10000 0 -0.69 19 19
CEBPA 0.014 0.078 0.35 1 -0.69 3 4
EHMT2 0.021 0.007 -10000 0 -10000 0 0
cell proliferation 0.004 0.16 0.42 3 -0.47 10 13
NR0B1 0.077 0.13 0.35 48 -10000 0 48
EGR1 -0.2 0.33 -10000 0 -0.69 81 81
RXRs/9cRA 0.038 0.085 0.26 2 -0.41 5 7
AR/RACK1/Src -0.013 0.15 0.43 4 -0.45 14 18
AR/GR -0.071 0.16 -10000 0 -0.32 67 67
GNB2L1 0.022 0.005 -10000 0 -10000 0 0
PKN1 0.021 0.003 -10000 0 -10000 0 0
RCHY1 0.02 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.004 0.022 3 -10000 0 3
MAPK8 -0.01 0.1 -10000 0 -0.53 10 10
T-DHT/AR/TIF2/CARM1 -0.037 0.18 0.43 2 -0.5 24 26
SRC -0.018 0.1 0.29 2 -0.4 15 17
NR3C1 0.021 0.002 -10000 0 -10000 0 0
KLK3 -0.006 0.23 0.52 8 -1.2 6 14
APPBP2 0.016 0.016 -10000 0 -10000 0 0
TRIM24 0.022 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.034 0.14 -10000 0 -0.47 16 16
TMPRSS2 -0.063 0.28 -10000 0 -1.2 13 13
RXRG 0.035 0.13 0.35 23 -0.69 4 27
mol:9cRA 0 0.002 -10000 0 -10000 0 0
RXRA 0.018 0.044 -10000 0 -0.69 1 1
RXRB 0.02 0.006 -10000 0 -10000 0 0
CARM1 0.023 0.005 -10000 0 -10000 0 0
NR2C2 0.014 0.075 -10000 0 -0.69 3 3
KLK2 -0.006 0.18 0.48 14 -0.47 9 23
AR -0.087 0.17 0.23 1 -0.34 74 75
SENP1 0.022 0.003 -10000 0 -10000 0 0
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
MDM2 0.018 0.017 -10000 0 -10000 0 0
SRY -0.002 0.012 0.032 6 -0.046 14 20
GATA2 0.019 0.068 0.35 2 -0.69 2 4
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.087 0.14 0.35 55 -10000 0 55
T-DHT/AR/RACK1/Src -0.024 0.14 0.33 3 -0.46 15 18
positive regulation of transcription 0.019 0.068 0.35 2 -0.69 2 4
DNAJA1 0.016 0.017 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.007 -10000 0 -10000 0 0
NCOA1 0.025 0.013 -10000 0 -10000 0 0
SPDEF 0.069 0.12 0.35 39 -10000 0 39
T-DHT/AR/TIF2 -0.028 0.16 0.26 2 -0.47 18 20
T-DHT/AR/Hsp90 -0.032 0.14 -10000 0 -0.47 16 16
GSK3B 0.021 0.008 -10000 0 -10000 0 0
NR2C1 0.02 0.009 -10000 0 -10000 0 0
mol:T-DHT -0.021 0.11 0.3 1 -0.43 15 16
SIRT1 0.019 0.044 -10000 0 -0.69 1 1
ZMIZ2 0.018 0.016 -10000 0 -10000 0 0
POU2F1 0.01 0.041 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 0.001 0.16 0.39 2 -0.47 15 17
CREBBP 0.021 0.004 -10000 0 -10000 0 0
SMARCE1 0.022 0.009 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.017 0.031 -10000 0 -0.45 1 1
EPHB2 0.083 0.13 0.35 50 -10000 0 50
Syndecan-2/TACI 0.016 0.036 0.24 2 -0.45 1 3
LAMA1 -0.036 0.24 0.35 17 -0.68 29 46
Syndecan-2/alpha2 ITGB1 0.1 0.14 0.4 30 -0.39 2 32
HRAS 0.023 0.02 0.35 1 -10000 0 1
Syndecan-2/CASK 0.007 0.004 -10000 0 -10000 0 0
ITGA5 0.021 0.002 -10000 0 -10000 0 0
BAX -0.005 0.06 -10000 0 -10000 0 0
EPB41 0.021 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.009 -10000 0 -10000 0 0
LAMA3 0.065 0.14 0.35 41 -0.69 3 44
EZR 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.004 0.11 -10000 0 -0.69 6 6
Syndecan-2/MMP2 0.011 0.075 0.24 5 -0.42 6 11
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.07 0.084 -10000 0 -10000 0 0
dendrite morphogenesis 0.067 0.1 0.27 50 -10000 0 50
Syndecan-2/GM-CSF 0.016 0.01 -10000 0 -10000 0 0
determination of left/right symmetry 0.009 0.005 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.019 0.011 -10000 0 -10000 0 0
GNB2L1 0.021 0.003 -10000 0 -10000 0 0
MAPK3 0.051 0.072 -10000 0 -10000 0 0
MAPK1 0.051 0.072 -10000 0 -10000 0 0
Syndecan-2/RACK1 0.028 0.023 0.32 1 -10000 0 1
NF1 0.02 0.025 -10000 0 -0.38 1 1
FGFR/FGF/Syndecan-2 0.009 0.005 -10000 0 -10000 0 0
ITGA2 0.081 0.13 0.35 48 -10000 0 48
MAPK8 -0.003 0.068 -10000 0 -0.44 4 4
Syndecan-2/alpha2/beta1 Integrin 0.044 0.16 0.37 11 -0.37 16 27
Syndecan-2/Kininogen -0.027 0.14 -10000 0 -0.42 27 27
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC 0.053 0.069 0.28 1 -10000 0 1
Syndecan-2/CASK/Protein 4.1 0.017 0.01 -10000 0 -10000 0 0
extracellular matrix organization 0.02 0.022 0.24 2 -10000 0 2
actin cytoskeleton reorganization 0.017 0.03 -10000 0 -0.44 1 1
Syndecan-2/Caveolin-2/Ras 0.019 0.06 -10000 0 -0.35 6 6
Syndecan-2/Laminin alpha3 0.054 0.1 0.27 41 -0.38 3 44
Syndecan-2/RasGAP 0.032 0.033 -10000 0 -0.38 1 1
alpha5/beta1 Integrin 0.031 0.006 -10000 0 -10000 0 0
PRKCD 0.021 0.002 -10000 0 -10000 0 0
Syndecan-2 dimer 0.067 0.1 0.27 50 -10000 0 50
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.033 -10000 0 -0.37 1 1
RHOA 0.022 0.001 -10000 0 -10000 0 0
SDCBP 0.018 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.018 0.053 0.35 2 -0.69 1 3
RASA1 0.016 0.062 -10000 0 -0.69 2 2
alpha2/beta1 Integrin 0.07 0.084 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.018 0.011 -10000 0 -10000 0 0
TGFB1 0.024 0.029 0.35 2 -10000 0 2
CASP3 0.052 0.075 -10000 0 -10000 0 0
FN1 0.019 0.044 -10000 0 -0.69 1 1
Syndecan-2/IL8 -0.063 0.18 0.27 9 -0.39 57 66
SDC2 0.009 0.005 -10000 0 -10000 0 0
KNG1 -0.052 0.22 -10000 0 -0.69 27 27
Syndecan-2/Neurofibromin 0.018 0.018 -10000 0 -0.22 1 1
TRAPPC4 0.021 0.004 -10000 0 -10000 0 0
CSF2 0.017 0.004 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.02 0.022 0.24 2 -10000 0 2
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.01 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.026 0.017 -10000 0 -10000 0 0
PRKACA 0.053 0.074 -10000 0 -10000 0 0
angiogenesis -0.062 0.18 0.27 9 -0.39 57 66
MMP2 0.009 0.12 0.35 5 -0.64 7 12
IL8 -0.11 0.29 0.35 9 -0.65 57 66
calcineurin-NFAT signaling pathway 0.016 0.036 0.24 2 -0.44 1 3
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.011 0.16 -10000 0 -0.66 11 11
UGCG -0.038 0.21 -10000 0 -0.74 20 20
AKT1/mTOR/p70S6K/Hsp90/TERT 0.057 0.15 0.35 4 -0.41 10 14
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.036 0.21 -10000 0 -0.73 20 20
mol:DAG -0.001 0.092 -10000 0 -0.84 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.18 -10000 0 -0.44 26 26
FRAP1 0 0.21 0.44 1 -0.52 25 26
FOXO3 -0.009 0.2 0.41 1 -0.52 26 27
AKT1 -0.011 0.22 0.42 1 -0.56 27 28
GAB2 0.02 0.009 -10000 0 -10000 0 0
SMPD1 0.017 0.046 -10000 0 -0.47 1 1
SGMS1 0.012 0.081 -10000 0 -0.65 3 3
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 0.003 0.052 -10000 0 -0.83 1 1
CALM1 0.021 0.004 -10000 0 -10000 0 0
cell proliferation -0.008 0.21 -10000 0 -0.53 20 20
EIF3A 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.028 0.061 -10000 0 -0.93 1 1
RPS6KB1 0.039 0.061 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.092 -10000 0 -0.84 3 3
natural killer cell activation 0 0.004 -10000 0 -0.025 1 1
JAK3 0.022 0.053 0.35 2 -0.69 1 3
PIK3R1 0.018 0.044 -10000 0 -0.68 1 1
JAK1 0.021 0.007 -10000 0 -10000 0 0
NFKB1 0.02 0.006 -10000 0 -10000 0 0
MYC -0.026 0.37 -10000 0 -0.97 31 31
MYB 0.14 0.14 0.53 24 -10000 0 24
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.18 0.42 1 -0.59 13 14
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.055 0.056 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.01 0.17 0.42 1 -0.57 13 14
Rac1/GDP 0.016 0.051 -10000 0 -0.77 1 1
T cell proliferation -0.002 0.17 0.39 1 -0.54 13 14
SHC1 0.016 0.011 -10000 0 -10000 0 0
RAC1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.021 0.051 0.17 27 -10000 0 27
PRKCZ -0.001 0.17 0.4 1 -0.56 13 14
NF kappa B1 p50/RelA 0.016 0.18 0.42 1 -0.52 15 16
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.013 0.17 0.34 1 -0.63 15 16
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL2RA 0.018 0.12 0.35 10 -0.69 5 15
IL2RB -0.03 0.18 -10000 0 -0.66 20 20
TERT 0.13 0.16 0.35 86 -10000 0 86
E2F1 0.16 0.14 0.49 27 -10000 0 27
SOS1 0.02 0.009 -10000 0 -10000 0 0
RPS6 0.021 0.003 -10000 0 -10000 0 0
mol:cAMP -0.009 0.023 -10000 0 -0.076 27 27
PTPN11 0.02 0.009 -10000 0 -10000 0 0
IL2RG 0.017 0.099 0.35 5 -0.69 4 9
actin cytoskeleton organization -0.002 0.17 0.39 1 -0.54 13 14
GRB2 0.019 0.009 -10000 0 -10000 0 0
IL2 0.014 0.011 -10000 0 -10000 0 0
PIK3CA 0.018 0.044 -10000 0 -0.68 1 1
Rac1/GTP 0.037 0.054 -10000 0 -0.74 1 1
LCK 0 0.12 0.36 1 -0.69 8 9
BCL2 0.01 0.16 0.42 1 -0.53 9 10
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.007 0.12 0.52 12 -0.27 2 14
KIRREL -0.013 0.15 -10000 0 -0.69 12 12
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.007 0.12 0.27 2 -0.52 12 14
PLCG1 0.021 0.003 -10000 0 -10000 0 0
ARRB2 0.019 0.007 -10000 0 -10000 0 0
WASL 0.021 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.027 0.099 -10000 0 -0.39 10 10
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.009 0.077 -10000 0 -0.32 10 10
FYN 0.042 0.13 0.27 41 -0.37 12 53
mol:Ca2+ 0.027 0.1 -10000 0 -0.39 12 12
mol:DAG 0.028 0.1 -10000 0 -0.39 12 12
NPHS2 0.018 0.049 0.34 5 -10000 0 5
mol:IP3 0.028 0.1 -10000 0 -0.39 12 12
regulation of endocytosis 0.016 0.087 -10000 0 -0.35 12 12
Nephrin/NEPH1/podocin/Cholesterol 0.018 0.1 0.27 2 -0.39 12 14
establishment of cell polarity 0.007 0.12 0.27 2 -0.52 12 14
Nephrin/NEPH1/podocin/NCK1-2 0.036 0.1 -10000 0 -0.37 13 13
Nephrin/NEPH1/beta Arrestin2 0.017 0.088 -10000 0 -0.35 12 12
NPHS1 0.039 0.077 0.34 14 -10000 0 14
Nephrin/NEPH1/podocin 0.018 0.095 -10000 0 -0.37 12 12
TJP1 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.019 0.044 -10000 0 -0.69 1 1
NCK2 0.023 0.02 0.35 1 -10000 0 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.1 -10000 0 -0.39 12 12
CD2AP 0.02 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.03 0.097 0.28 2 -0.4 9 11
GRB2 0.021 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.023 0.12 0.42 8 -0.36 12 20
cytoskeleton organization 0.007 0.09 -10000 0 -0.38 9 9
Nephrin/NEPH1 0.009 0.092 0.22 2 -0.38 12 14
Nephrin/NEPH1/ZO-1 0.018 0.1 -10000 0 -0.42 12 12
Aurora A 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
Aurora A/GADD45A 0.011 0.075 -10000 0 -0.4 4 4
BIRC5 0.22 0.16 0.35 161 -10000 0 161
NFKBIA 0.009 0.053 0.33 1 -10000 0 1
CPEB1 0.031 0.066 0.35 11 -10000 0 11
AKT1 0.008 0.049 -10000 0 -10000 0 0
NDEL1 0.019 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.013 0.047 -10000 0 -10000 0 0
NDEL1/TACC3 0.039 0.079 0.28 15 -10000 0 15
GADD45A 0.012 0.071 -10000 0 -0.54 4 4
GSK3B -0.009 0.026 -10000 0 -10000 0 0
PAK1/Aurora A 0.017 0.055 -10000 0 -10000 0 0
MDM2 0.021 0.003 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.037 0.064 0.21 32 -10000 0 32
TP53 0.017 0.036 -10000 0 -10000 0 0
DLG7 0.007 0.049 -10000 0 -10000 0 0
AURKAIP1 0.02 0.006 -10000 0 -10000 0 0
ARHGEF7 0.021 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.041 0.084 0.29 15 -10000 0 15
G2/M transition of mitotic cell cycle 0.013 0.047 -10000 0 -10000 0 0
AURKA 0.013 0.066 -10000 0 -10000 0 0
AURKB 0.1 0.098 0.22 105 -10000 0 105
CDC25B 0.015 0.048 0.23 1 -10000 0 1
G2/M transition checkpoint 0.004 0.041 -10000 0 -10000 0 0
mRNA polyadenylation 0.018 0.063 0.27 4 -10000 0 4
Aurora A/CPEB 0.019 0.063 0.28 4 -10000 0 4
Aurora A/TACC1/TRAP/chTOG 0.025 0.055 -10000 0 -10000 0 0
BRCA1 0.021 0.003 -10000 0 -10000 0 0
centrosome duplication 0.017 0.055 -10000 0 -10000 0 0
regulation of centrosome cycle 0.037 0.077 0.27 15 -10000 0 15
spindle assembly 0.024 0.054 -10000 0 -10000 0 0
TDRD7 0.021 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.1 0.32 4 -0.33 1 5
CENPA 0.12 0.1 0.21 131 -10000 0 131
Aurora A/PP2A 0.016 0.053 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.019 0.048 -10000 0 -10000 0 0
negative regulation of DNA binding 0.005 0.067 -10000 0 -0.23 14 14
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.03 0.007 -10000 0 -10000 0 0
RASA1 0.016 0.062 -10000 0 -0.69 2 2
Ajuba/Aurora A 0.005 0.041 -10000 0 -10000 0 0
mitotic prometaphase -0.008 0.033 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.066 -10000 0 -10000 0 0
TACC1 0.018 0.008 -10000 0 -10000 0 0
TACC3 0.058 0.1 0.35 30 -10000 0 30
Aurora A/Antizyme1 0.022 0.053 -10000 0 -10000 0 0
Aurora A/RasGAP 0.013 0.069 -10000 0 -0.44 2 2
OAZ1 0.021 0.004 -10000 0 -10000 0 0
RAN 0.021 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.009 0.026 -10000 0 -10000 0 0
GIT1 0.021 0.002 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.041 0.012 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.037 0.064 0.21 32 -10000 0 32
PPP2R5D 0.02 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.032 0.075 0.23 1 -10000 0 1
PAK1 0.021 0.003 -10000 0 -10000 0 0
CKAP5 0.022 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.021 0.003 -10000 0 -10000 0 0
HDAC4 0.022 0.02 0.35 1 -10000 0 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.024 0.059 0.3 1 -0.26 5 6
CDKN1A -0.016 0.1 -10000 0 -0.83 4 4
KAT2B 0.013 0.075 -10000 0 -0.69 3 3
BAX 0.021 0.003 -10000 0 -10000 0 0
FOXO3 -0.005 0.01 -10000 0 -10000 0 0
FOXO1 0.015 0.056 -10000 0 -0.49 3 3
FOXO4 0.014 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.021 0.003 -10000 0 -10000 0 0
TAT -0.26 0.34 -10000 0 -0.66 108 108
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.014 0.055 -10000 0 -0.52 3 3
PPARGC1A -0.072 0.24 -10000 0 -0.68 35 35
FHL2 -0.027 0.18 -10000 0 -0.69 18 18
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.037 -10000 0 -0.52 1 1
HIST2H4A 0.024 0.059 0.26 5 -0.3 1 6
SIRT1/FOXO3a 0.011 0.035 -10000 0 -0.44 1 1
SIRT1 0.019 0.049 -10000 0 -0.69 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.033 0.031 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.028 0.048 -10000 0 -0.32 2 2
apoptosis -0.039 0.033 0.45 1 -10000 0 1
SIRT1/PGC1A -0.037 0.16 -10000 0 -0.45 35 35
p53/SIRT1 0.023 0.055 0.43 3 -0.52 1 4
SIRT1/FOXO4 0.019 0.043 -10000 0 -0.43 1 1
FOXO1/FHL2/SIRT1 0.002 0.12 -10000 0 -0.41 20 20
HIST1H1E 0.019 0.028 -10000 0 -10000 0 0
SIRT1/p300 0.029 0.037 -10000 0 -0.52 1 1
muscle cell differentiation -0.019 0.069 0.58 3 -10000 0 3
TP53 0.018 0.022 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.039 0.034 -10000 0 -0.45 1 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
MEF2D 0.017 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.19 0.27 -10000 0 -0.5 108 108
ACSS2 0.012 0.04 0.34 1 -0.52 1 2
SIRT1/PCAF/MYOD 0.019 0.069 -10000 0 -0.59 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.02 0.081 0.46 3 -10000 0 3
oxygen homeostasis 0.001 0.023 -10000 0 -10000 0 0
TCEB2 0.022 0.021 0.35 1 -10000 0 1
TCEB1 0.017 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.031 0.12 0.39 3 -0.46 2 5
EPO -0.2 0.42 0.78 6 -0.73 79 85
FIH (dimer) 0.014 0.031 -10000 0 -10000 0 0
APEX1 0.011 0.036 -10000 0 -10000 0 0
SERPINE1 -0.12 0.37 0.72 4 -0.69 59 63
FLT1 -0.023 0.16 -10000 0 -0.8 6 6
ADORA2A -0.029 0.25 0.7 4 -0.73 4 8
germ cell development 0.016 0.26 0.77 8 -0.65 4 12
SLC11A2 -0.011 0.24 0.72 4 -0.7 4 8
BHLHE40 -0.015 0.25 0.72 4 -0.74 6 10
HIF1AN 0.014 0.031 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.02 0.2 0.65 5 -0.56 3 8
ETS1 0.026 0.023 -10000 0 -10000 0 0
CITED2 -0.034 0.19 -10000 0 -0.76 14 14
KDR -0.036 0.21 -10000 0 -0.92 12 12
PGK1 -0.011 0.24 0.72 4 -0.7 4 8
SIRT1 0.01 0.047 -10000 0 -0.69 1 1
response to hypoxia -0.004 0.009 -10000 0 -10000 0 0
HIF2A/ARNT -0.011 0.27 0.85 4 -0.75 6 10
EPAS1 0.016 0.14 0.5 6 -0.42 5 11
SP1 0.031 0.031 -10000 0 -10000 0 0
ABCG2 -0.062 0.28 0.74 3 -0.76 15 18
EFNA1 -0.015 0.24 0.72 4 -0.69 5 9
FXN -0.029 0.25 0.7 4 -0.73 4 8
POU5F1 0.013 0.26 0.77 8 -0.68 4 12
neuron apoptosis 0.01 0.27 0.73 6 -0.84 4 10
EP300 0.021 0.003 -10000 0 -10000 0 0
EGLN3 0.03 0.16 0.37 28 -0.7 7 35
EGLN2 0.014 0.031 -10000 0 -10000 0 0
EGLN1 0.013 0.027 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.034 0.019 -10000 0 -10000 0 0
VHL 0.022 0 -10000 0 -10000 0 0
ARNT 0.01 0.032 -10000 0 -10000 0 0
SLC2A1 -0.022 0.26 0.8 4 -0.73 5 9
TWIST1 -0.023 0.25 0.68 6 -0.61 7 13
ELK1 0.025 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.019 0.17 0.56 5 -0.53 2 7
VEGFA -0.017 0.22 0.74 3 -0.68 4 7
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.006 0.14 -10000 0 -0.36 30 30
Syndecan-3/Neurocan 0.016 0.064 -10000 0 -0.39 5 5
POMC 0.02 0.071 0.35 3 -0.69 2 5
EGFR 0.01 0.087 -10000 0 -0.69 4 4
Syndecan-3/EGFR 0.009 0.074 -10000 0 -0.38 8 8
AGRP 0.028 0.061 0.35 9 -10000 0 9
NCSTN 0.017 0.009 -10000 0 -10000 0 0
PSENEN 0.021 0.003 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.021 0.003 -10000 0 -10000 0 0
APH1A 0.017 0.009 -10000 0 -10000 0 0
NCAN 0.023 0.035 0.35 3 -10000 0 3
long-term memory 0.022 0.059 -10000 0 -0.36 5 5
Syndecan-3/IL8 -0.053 0.17 0.32 2 -0.38 45 47
PSEN1 0.021 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.032 0.015 0.25 1 -10000 0 1
FYN 0.021 0.005 -10000 0 -10000 0 0
limb bud formation 0.002 0.056 -10000 0 -0.4 5 5
MC4R 0.015 0.003 -10000 0 -10000 0 0
SRC 0.023 0.02 0.35 1 -10000 0 1
PTN -0.057 0.23 0.35 3 -0.69 30 33
FGFR/FGF/Syndecan-3 0.002 0.057 -10000 0 -0.4 5 5
neuron projection morphogenesis -0.023 0.13 0.34 1 -0.36 28 29
Syndecan-3/AgRP 0.022 0.073 0.32 4 -0.37 5 9
Syndecan-3/AgRP/MC4R 0.028 0.072 0.31 4 -0.36 5 9
Fyn/Cortactin 0.029 0.009 -10000 0 -10000 0 0
SDC3 0.002 0.057 -10000 0 -0.41 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.052 0.17 0.31 2 -0.38 45 47
IL8 -0.11 0.29 0.35 9 -0.65 57 66
Syndecan-3/Fyn/Cortactin 0.023 0.06 -10000 0 -0.37 5 5
Syndecan-3/CASK 0 0.055 -10000 0 -0.39 5 5
alpha-MSH/MC4R 0.025 0.054 -10000 0 -0.52 2 2
Gamma Secretase 0.047 0.029 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.013 0.036 0.2 9 -10000 0 9
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.028 -10000 0 -10000 0 0
STXBP1 0.021 0.003 -10000 0 -10000 0 0
ACh/CHRNA1 0.017 0.07 0.28 11 -0.17 3 14
RAB3GAP2/RIMS1/UNC13B 0.034 0.031 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.02 0.036 0.35 3 -10000 0 3
mol:ACh -0.004 0.053 0.097 9 -0.16 18 27
RAB3GAP2 0.018 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.017 0.066 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.017 0.07 0.28 11 -0.17 3 14
UNC13B 0.022 0.02 0.35 1 -10000 0 1
CHRNA1 0.033 0.066 0.35 11 -10000 0 11
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.053 0.2 0.26 15 -0.48 43 58
SNAP25 -0.007 0.1 0.14 28 -0.34 20 48
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.071 0.28 0.35 17 -0.69 42 59
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.025 0.026 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.017 0.066 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.003 0.13 0.68 9 -10000 0 9
PI3K Class IB/PDE3B -0.003 0.13 -10000 0 -0.69 9 9
PDE3B -0.003 0.13 -10000 0 -0.69 9 9
Signaling events mediated by PTP1B

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
PDGFRB 0.029 0.049 0.35 6 -10000 0 6
Jak2/Leptin Receptor -0.006 0.17 0.28 1 -0.39 24 25
PTP1B/AKT1 0.056 0.064 -10000 0 -0.3 1 1
FYN 0.021 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.054 0.07 0.26 1 -0.34 1 2
EGFR 0.013 0.088 -10000 0 -0.69 4 4
EGF/EGFR 0.084 0.11 0.34 1 -0.34 4 5
CSF1 0.018 0.068 0.35 2 -0.69 2 4
AKT1 0.021 0.005 -10000 0 -10000 0 0
INSR 0.022 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.047 0.098 -10000 0 -0.35 9 9
Insulin Receptor/Insulin 0.06 0.062 0.36 1 -10000 0 1
HCK -0.003 0.13 -10000 0 -0.69 9 9
CRK 0.019 0.007 -10000 0 -10000 0 0
TYK2 0.051 0.068 0.28 2 -0.32 1 3
EGF 0.1 0.14 0.35 65 -10000 0 65
YES1 0.021 0.003 -10000 0 -10000 0 0
CAV1 0.061 0.079 0.3 1 -0.33 1 2
TXN 0.023 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.065 0.067 -10000 0 -0.32 1 1
cell migration -0.054 0.07 0.34 1 -0.26 1 2
STAT3 0.021 0.003 -10000 0 -10000 0 0
PRLR -0.005 0.14 -10000 0 -0.69 10 10
ITGA2B 0.029 0.053 0.35 7 -10000 0 7
CSF1R 0.002 0.11 -10000 0 -0.69 7 7
Prolactin Receptor/Prolactin 0.007 0.11 -10000 0 -0.51 10 10
FGR 0.018 0.044 -10000 0 -0.69 1 1
PTP1B/p130 Cas 0.061 0.063 -10000 0 -0.31 1 1
Crk/p130 Cas 0.064 0.065 -10000 0 -0.29 1 1
DOK1 0.055 0.065 -10000 0 -0.31 1 1
JAK2 0.04 0.091 -10000 0 -0.38 4 4
Jak2/Leptin Receptor/Leptin -0.013 0.19 0.3 1 -0.53 26 27
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
PTPN1 0.054 0.07 0.27 1 -0.34 1 2
LYN 0.018 0.008 -10000 0 -10000 0 0
CDH2 -0.003 0.13 -10000 0 -0.69 9 9
SRC 0.039 0.068 -10000 0 -0.45 3 3
ITGB3 -0.019 0.16 -10000 0 -0.69 15 15
CAT1/PTP1B -0.059 0.19 -10000 0 -0.49 25 25
CAPN1 0.022 0.003 -10000 0 -10000 0 0
CSK 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.058 0.073 0.31 1 -0.68 1 2
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.019 0.2 0.28 1 -0.55 28 29
negative regulation of transcription 0.041 0.09 -10000 0 -0.38 4 4
FCGR2A 0.02 0.03 0.35 2 -10000 0 2
FER 0.023 0.003 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.005 0.14 0.25 1 -0.52 15 16
BLK -0.1 0.26 0.35 2 -0.59 52 54
Insulin Receptor/Insulin/Shc 0.033 0.028 -10000 0 -10000 0 0
RHOA 0.023 0.002 -10000 0 -10000 0 0
LEPR -0.096 0.26 -10000 0 -0.66 45 45
BCAR1 0.02 0.005 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.021 0.005 -10000 0 -10000 0 0
mol:NADPH 0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.14 0.23 -10000 0 -0.52 45 45
PRL 0.017 0.03 0.35 2 -10000 0 2
SOCS3 -0.16 0.46 -10000 0 -1.4 33 33
SPRY2 0.015 0.051 -10000 0 -0.54 2 2
Insulin Receptor/Insulin/IRS1 0.043 0.028 -10000 0 -10000 0 0
CSF1/CSF1R 0.055 0.1 0.31 2 -0.39 7 9
Ras protein signal transduction 0.004 0.12 0.5 13 -10000 0 13
IRS1 0.021 0.002 -10000 0 -10000 0 0
INS 0.019 0.047 0.35 5 -10000 0 5
LEP 0.024 0.059 0.35 8 -10000 0 8
STAT5B 0.054 0.07 0.23 1 -0.41 1 2
STAT5A 0.054 0.07 0.23 1 -0.41 1 2
GRB2 0.021 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.063 0.076 0.31 6 -0.32 1 7
CSN2 -0.016 0.067 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
LAT 0.041 0.066 -10000 0 -0.47 3 3
YBX1 0.026 0.006 -10000 0 -10000 0 0
LCK 0 0.12 0.35 1 -0.69 8 9
SHC1 0.017 0.009 -10000 0 -10000 0 0
NOX4 0.15 0.16 0.35 105 -10000 0 105
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.023 0.045 0.26 1 -10000 0 1
MAP4K4 0.008 0.061 -10000 0 -10000 0 0
BAG4 0 0.1 -10000 0 -0.57 8 8
PKC zeta/ceramide -0.002 0.088 -10000 0 -0.29 18 18
NFKBIA 0.021 0.002 -10000 0 -10000 0 0
BIRC3 0.029 0.074 0.35 9 -0.69 1 10
BAX 0.006 0.047 -10000 0 -0.34 4 4
RIPK1 0.02 0.006 -10000 0 -10000 0 0
AKT1 0.003 0.046 0.7 1 -10000 0 1
BAD 0.002 0.041 -10000 0 -10000 0 0
SMPD1 0.022 0.072 0.23 5 -0.24 9 14
RB1 0 0.041 -10000 0 -10000 0 0
FADD/Caspase 8 0.015 0.068 0.29 1 -10000 0 1
MAP2K4 0 0.039 -10000 0 -10000 0 0
NSMAF 0.018 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.044 0.22 1 -10000 0 1
EGF 0.099 0.14 0.35 65 -10000 0 65
mol:ceramide 0.003 0.045 -10000 0 -0.19 8 8
MADD 0.022 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.02 0.045 0.42 1 -10000 0 1
ASAH1 0.019 0.022 0.35 1 -10000 0 1
negative regulation of cell cycle 0.001 0.041 -10000 0 -10000 0 0
cell proliferation -0.12 0.17 -10000 0 -0.32 107 107
BID 0.009 0.12 -10000 0 -0.6 8 8
MAP3K1 0.002 0.042 -10000 0 -0.18 8 8
EIF2A 0.005 0.044 -10000 0 -10000 0 0
TRADD 0.019 0.026 -10000 0 -0.38 1 1
CRADD 0.019 0.044 -10000 0 -0.69 1 1
MAPK3 0.007 0.045 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.046 -10000 0 -10000 0 0
Cathepsin D/ceramide 0.015 0.045 -10000 0 -0.18 7 7
FADD 0.009 0.064 0.3 1 -10000 0 1
KSR1 0.004 0.045 0.21 2 -0.18 6 8
MAPK8 -0.025 0.11 -10000 0 -0.34 18 18
PRKRA 0.005 0.046 0.2 3 -0.18 8 11
PDGFA 0.037 0.071 0.35 13 -10000 0 13
TRAF2 0.021 0.003 -10000 0 -10000 0 0
IGF1 -0.29 0.35 -10000 0 -0.69 114 114
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.003 0.044 -10000 0 -0.19 8 8
CTSD 0.021 0.002 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.029 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.13 0.18 -10000 0 -0.34 107 107
PRKCD 0.021 0.002 -10000 0 -10000 0 0
PRKCZ -0.009 0.14 -10000 0 -0.66 11 11
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.02 0.045 0.42 1 -10000 0 1
RelA/NF kappa B1 0.029 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.012 0.063 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.005 0.12 -10000 0 -0.45 16 16
mol:Sphingosine-1-phosphate 0.023 0.045 0.26 1 -10000 0 1
MAP2K1 0.004 0.043 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
CYCS 0.008 0.032 -10000 0 -0.18 1 1
TNFRSF1A 0.021 0.004 -10000 0 -10000 0 0
NFKB1 0.02 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.014 0.08 -10000 0 -0.45 7 7
EIF2AK2 0.005 0.045 0.21 1 -10000 0 1
TNF-alpha/TNFR1A/FAN 0.016 0.095 -10000 0 -0.42 11 11
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.068 -10000 0 -0.33 2 2
MAP2K2 0.006 0.046 -10000 0 -10000 0 0
SMPD3 -0.021 0.15 0.22 4 -0.34 38 42
TNF -0.007 0.14 0.35 2 -0.69 11 13
PKC zeta/PAR4 0.007 0.11 -10000 0 -0.5 11 11
mol:PHOSPHOCHOLINE -0.042 0.07 -10000 0 -0.21 9 9
NF kappa B1/RelA/I kappa B alpha 0.037 0.089 -10000 0 -0.39 10 10
AIFM1 0.006 0.036 -10000 0 -10000 0 0
BCL2 0.021 0.003 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.001 0.15 0.35 6 -0.69 10 16
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.022 0.021 0.35 1 -10000 0 1
TCEB1 0.017 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.025 0.061 -10000 0 -0.52 1 1
HIF1A 0.004 0.052 -10000 0 -0.32 5 5
COPS5 0.018 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.046 0.029 -10000 0 -10000 0 0
FIH (dimer) 0.021 0.004 -10000 0 -10000 0 0
CDKN2A 0.23 0.16 0.35 169 -10000 0 169
ARNT/IPAS 0.01 0.1 -10000 0 -0.48 10 10
HIF1AN 0.021 0.004 -10000 0 -10000 0 0
GNB2L1 0.021 0.003 -10000 0 -10000 0 0
HIF1A/ARNT 0.018 0.053 -10000 0 -0.32 4 4
CUL2 0.021 0.004 -10000 0 -10000 0 0
OS9 0.021 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.033 0.019 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.029 0.062 -10000 0 -0.53 1 1
PHD1-3/OS9 0.052 0.09 -10000 0 -0.41 4 4
HIF1A/RACK1/Elongin B/Elongin C 0.033 0.063 -10000 0 -0.5 1 1
VHL 0.022 0 -10000 0 -10000 0 0
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.022 0.063 -10000 0 -0.53 1 1
EGLN3 0.038 0.16 0.35 28 -0.69 7 35
EGLN2 0.021 0.003 -10000 0 -10000 0 0
EGLN1 0.018 0.008 -10000 0 -10000 0 0
TP53 0.019 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.043 -10000 0 -0.6 1 1
ARNT 0.017 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.021 0.003 -10000 0 -10000 0 0
HIF1A/p19ARF 0.15 0.11 0.3 22 -0.46 1 23
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.014 0.11 -9999 0 -0.45 14 14
E-cadherin/beta catenin 0.001 0.12 -9999 0 -0.52 14 14
CTNNB1 0.022 0 -9999 0 -10000 0 0
JUP 0.021 0.003 -9999 0 -10000 0 0
CDH1 -0.017 0.16 -9999 0 -0.69 14 14
Caspase cascade in apoptosis

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
TOP1 -0.02 0.14 -10000 0 -0.44 18 18
ACTA1 -0.01 0.12 -10000 0 -0.5 10 10
NUMA1 -0.019 0.14 -10000 0 -0.43 18 18
SPTAN1 -0.023 0.11 -10000 0 -0.51 10 10
LIMK1 -0.017 0.12 -10000 0 -0.52 10 10
BIRC3 0.029 0.074 0.35 9 -0.69 1 10
BIRC2 0.021 0.004 -10000 0 -10000 0 0
BAX 0.021 0.003 -10000 0 -10000 0 0
CASP10 -0.012 0.098 -10000 0 -0.49 10 10
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.021 0.002 -10000 0 -10000 0 0
PTK2 -0.025 0.13 -10000 0 -0.41 17 17
DIABLO 0.021 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.022 0.11 -10000 0 -0.5 10 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.019 0.044 -10000 0 -0.69 1 1
GSN -0.023 0.11 -10000 0 -0.52 10 10
MADD 0.022 0 -10000 0 -10000 0 0
TFAP2A 0.014 0.19 0.41 2 -0.7 13 15
BID -0.001 0.051 -10000 0 -0.25 10 10
MAP3K1 0.003 0.038 -10000 0 -0.24 1 1
TRADD 0.019 0.026 -10000 0 -0.38 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.031 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.023 0.11 -10000 0 -0.52 10 10
CASP9 0.021 0.004 -10000 0 -10000 0 0
DNA repair 0.002 0.06 0.29 6 -0.2 1 7
neuron apoptosis -0.013 0.15 -10000 0 -0.74 10 10
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.024 0.13 -10000 0 -0.5 13 13
APAF1 0.021 0.002 -10000 0 -10000 0 0
CASP6 -0.039 0.23 -10000 0 -0.89 16 16
TRAF2 0.021 0.003 -10000 0 -10000 0 0
ICAD/CAD -0.023 0.11 -10000 0 -0.48 11 11
CASP7 -0.019 0.081 0.3 1 -0.62 2 3
KRT18 0.006 0.058 -10000 0 -0.67 1 1
apoptosis -0.03 0.14 -10000 0 -0.46 17 17
DFFA -0.022 0.11 -10000 0 -0.51 10 10
DFFB -0.024 0.12 -10000 0 -0.5 11 11
PARP1 -0.002 0.061 0.2 1 -0.29 6 7
actin filament polymerization 0.017 0.11 0.46 11 -10000 0 11
TNF -0.007 0.14 0.35 2 -0.69 11 13
CYCS 0.005 0.041 0.17 1 -0.18 8 9
SATB1 -0.065 0.24 -10000 0 -0.79 21 21
SLK -0.022 0.11 -10000 0 -0.51 10 10
p15 BID/BAX 0.01 0.054 -10000 0 -0.34 1 1
CASP2 0.007 0.063 -10000 0 -10000 0 0
JNK cascade -0.003 0.037 0.24 1 -10000 0 1
CASP3 -0.023 0.12 -10000 0 -0.54 10 10
LMNB2 0.005 0.11 -10000 0 -0.35 12 12
RIPK1 0.02 0.006 -10000 0 -10000 0 0
CASP4 0.018 0.044 -10000 0 -0.69 1 1
Mammalian IAPs/DIABLO 0.058 0.046 -10000 0 -0.42 1 1
negative regulation of DNA binding 0.015 0.19 0.41 2 -0.68 13 15
stress fiber formation -0.022 0.11 -10000 0 -0.5 10 10
GZMB -0.008 0.11 -10000 0 -0.56 10 10
CASP1 0.011 0.025 -10000 0 -0.4 1 1
LMNB1 0.005 0.1 -10000 0 -0.35 11 11
APP -0.014 0.16 -10000 0 -0.75 10 10
TNFRSF1A 0.021 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.03 0.14 -10000 0 -0.43 24 24
LMNA 0.001 0.1 -10000 0 -0.36 12 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.009 0.067 -10000 0 -10000 0 0
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.023 0.12 0.3 1 -0.5 11 12
APAF-1/Caspase 9 -0.013 0.12 -10000 0 -0.61 10 10
nuclear fragmentation during apoptosis -0.019 0.13 -10000 0 -0.42 18 18
CFL2 -0.018 0.11 -10000 0 -0.48 11 11
GAS2 -0.042 0.14 -10000 0 -0.44 22 22
positive regulation of apoptosis 0.005 0.11 -10000 0 -0.38 11 11
PRF1 0.01 0.087 -10000 0 -0.69 4 4
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.002 0.15 -10000 0 -0.39 17 17
CaM/Ca2+ 0.016 0.003 -10000 0 -10000 0 0
AKT1 0.021 0.005 -10000 0 -10000 0 0
AKT2 0.021 0.003 -10000 0 -10000 0 0
STXBP4 0.024 0.029 0.35 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.008 0.16 -10000 0 -0.4 25 25
YWHAZ 0.016 0.009 -10000 0 -10000 0 0
CALM1 0.021 0.004 -10000 0 -10000 0 0
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 0.008 0.047 -10000 0 -0.52 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.021 0.003 -10000 0 -10000 0 0
YWHAB 0.021 0.003 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.024 -10000 0 -10000 0 0
YWHAG 0.021 0.004 -10000 0 -10000 0 0
ASIP 0.02 0.004 -10000 0 -10000 0 0
PRKCI 0.021 0.002 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.016 0.003 -10000 0 -10000 0 0
RHOQ 0.021 0.002 -10000 0 -10000 0 0
GYS1 0.012 0.004 -10000 0 -10000 0 0
PRKCZ -0.009 0.14 -10000 0 -0.66 11 11
TRIP10 0.021 0.002 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.004 -10000 0 -10000 0 0
AS160/14-3-3 0.076 0.083 -10000 0 -0.34 2 2
VAMP2 0.019 0.007 -10000 0 -10000 0 0
SLC2A4 -0.013 0.17 -10000 0 -0.44 26 26
STX4 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.2 0.16 0.35 148 -10000 0 148
LNPEP 0.021 0.002 -10000 0 -10000 0 0
YWHAE 0.019 0.007 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.019 0.077 0.71 1 -10000 0 1
VDR 0.015 0.12 0.35 8 -0.69 6 14
FAM120B 0.02 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.021 0.097 -10000 0 -0.43 3 3
RXRs/LXRs/DNA/Oxysterols 0.01 0.14 0.35 1 -0.49 11 12
MED1 0.021 0.003 -10000 0 -10000 0 0
mol:9cRA 0 0.017 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.013 0.067 -10000 0 -0.3 11 11
RXRs/NUR77 -0.01 0.17 -10000 0 -0.41 35 35
RXRs/PPAR 0.027 0.068 -10000 0 -0.33 5 5
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.01 0.089 0.23 8 -0.52 6 14
RARs/VDR/DNA/Vit D3 0.031 0.1 -10000 0 -0.39 14 14
RARA 0.021 0.003 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.015 0.12 0.35 8 -0.69 6 14
RARs/RARs/DNA/9cRA 0.022 0.079 -10000 0 -0.39 9 9
RARG 0.021 0.002 -10000 0 -10000 0 0
RPS6KB1 0.028 0.096 0.49 10 -10000 0 10
RARs/THRs/DNA/SMRT 0.012 0.073 -10000 0 -0.5 1 1
THRA 0.021 0.003 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.01 0.089 0.23 8 -0.52 6 14
RXRs/PPAR/9cRA/PGJ2/DNA 0.039 0.092 -10000 0 -0.4 5 5
NR1H4 -0.006 0.14 -10000 0 -0.69 10 10
RXRs/LXRs/DNA 0.053 0.1 -10000 0 -0.38 5 5
NR1H2 0.02 0.02 -10000 0 -10000 0 0
NR1H3 0.02 0.022 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.044 0.11 0.35 4 -0.38 9 13
NR4A1 -0.071 0.24 -10000 0 -0.69 34 34
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.009 0.09 -10000 0 -0.31 14 14
RXRG 0.034 0.13 0.35 23 -0.68 4 27
RXR alpha/CCPG 0.026 0.038 -10000 0 -0.52 1 1
RXRA 0.017 0.048 -10000 0 -0.68 1 1
RXRB 0.019 0.02 -10000 0 -10000 0 0
THRB 0.014 0.075 -10000 0 -0.69 3 3
PPARG 0.023 0.02 0.35 1 -10000 0 1
PPARD 0.02 0.006 -10000 0 -10000 0 0
TNF -0.012 0.26 -10000 0 -1.1 13 13
mol:Oxysterols 0 0.014 -10000 0 -10000 0 0
cholesterol transport 0.01 0.13 0.35 1 -0.48 11 12
PPARA 0.021 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.003 0.13 -10000 0 -0.69 9 9
RXRs/NUR77/BCL2 -0.018 0.13 -10000 0 -0.32 31 31
SREBF1 0.014 0.14 -10000 0 -0.9 3 3
RXRs/RXRs/DNA/9cRA 0.039 0.092 -10000 0 -0.4 5 5
ABCA1 0.011 0.17 -10000 0 -0.96 5 5
RARs/THRs 0.042 0.096 -10000 0 -0.39 12 12
RXRs/FXR 0.031 0.13 -10000 0 -0.44 13 13
BCL2 0.021 0.003 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0 0.1 -10000 0 -0.57 8 8
Caspase 8 (4 units) -0.012 0.14 -10000 0 -0.55 10 10
NEF -0.007 0.066 -10000 0 -0.48 4 4
NFKBIA 0.025 0.016 -10000 0 -10000 0 0
BIRC3 0.031 0.089 0.43 9 -0.72 1 10
CYCS -0.005 0.14 0.26 1 -0.55 9 10
RIPK1 0.02 0.006 -10000 0 -10000 0 0
CD247 0.012 0.08 0.35 1 -0.78 2 3
MAP2K7 -0.002 0.18 -10000 0 -0.64 11 11
protein ubiquitination 0.003 0.11 0.31 2 -0.39 7 9
CRADD 0.019 0.044 -10000 0 -0.69 1 1
DAXX 0.02 0.005 -10000 0 -10000 0 0
FAS -0.006 0.14 -10000 0 -0.69 10 10
BID -0.004 0.15 0.28 1 -0.57 10 11
NF-kappa-B/RelA/I kappa B alpha 0.051 0.05 -10000 0 -0.34 1 1
TRADD 0.019 0.026 -10000 0 -0.38 1 1
MAP3K5 -0.043 0.2 -10000 0 -0.65 25 25
CFLAR 0.021 0.002 -10000 0 -10000 0 0
FADD 0.021 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.052 0.051 -10000 0 -0.34 1 1
MAPK8 -0.013 0.18 -10000 0 -0.59 13 13
APAF1 0.021 0.002 -10000 0 -10000 0 0
TRAF1 0.022 0.02 0.35 1 -10000 0 1
TRAF2 0.021 0.003 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.025 0.14 0.3 1 -0.41 25 26
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.01 0.12 -10000 0 -0.52 7 7
CHUK 0.002 0.11 0.32 2 -0.43 7 9
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.002 0.16 -10000 0 -0.44 25 25
TCRz/NEF 0.005 0.087 0.24 3 -0.37 10 13
TNF -0.007 0.14 0.35 2 -0.69 11 13
FASLG -0.005 0.14 0.41 2 -0.74 8 10
NFKB1 0.024 0.017 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.005 0.12 -10000 0 -0.45 16 16
CASP6 -0.005 0.17 -10000 0 -0.6 10 10
CASP7 0.022 0.14 0.42 3 -0.47 8 11
RELA 0.025 0.015 -10000 0 -10000 0 0
CASP2 0.021 0.004 -10000 0 -10000 0 0
CASP3 0.02 0.15 0.39 5 -0.5 9 14
TNFRSF1A 0.021 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.014 0.08 -10000 0 -0.45 7 7
CASP8 0.021 0.002 -10000 0 -10000 0 0
CASP9 0.021 0.004 -10000 0 -10000 0 0
MAP3K14 -0.005 0.12 -10000 0 -0.48 7 7
APAF-1/Caspase 9 0.001 0.11 0.3 7 -0.41 8 15
BCL2 -0.01 0.16 -10000 0 -0.53 13 13
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.019 0.14 -10000 0 -0.53 14 14
KLHL20 -0.003 0.075 -10000 0 -0.27 6 6
CYFIP2 -0.016 0.16 -10000 0 -0.69 14 14
Rac1/GDP 0.001 0.092 -10000 0 -0.34 13 13
ENAH -0.012 0.12 -10000 0 -0.49 14 14
AP1M1 0.021 0.003 -10000 0 -10000 0 0
RAP1B 0.021 0.002 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CTNNB1 0.022 0 -10000 0 -10000 0 0
CDC42/GTP 0.007 0.07 -10000 0 -0.29 1 1
ABI1/Sra1/Nap1 -0.028 0.056 -10000 0 -0.2 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.018 0.12 -10000 0 -0.41 18 18
RAPGEF1 -0.016 0.12 -10000 0 -0.47 14 14
CTNND1 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.019 0.14 -10000 0 -0.55 15 15
CRK -0.014 0.12 -10000 0 -0.51 14 14
E-cadherin/gamma catenin/alpha catenin 0.014 0.11 -10000 0 -0.45 14 14
alphaE/beta7 Integrin 0.023 0.071 -10000 0 -0.51 4 4
IQGAP1 0.021 0.004 -10000 0 -10000 0 0
NCKAP1 0.021 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.037 0.013 -10000 0 -10000 0 0
DLG1 -0.019 0.14 -10000 0 -0.55 14 14
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.051 -10000 0 -0.24 2 2
MLLT4 0.02 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.023 0.089 -10000 0 -0.41 10 10
PI3K -0.006 0.067 -10000 0 -0.32 2 2
ARF6 0.021 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0 0.12 -10000 0 -0.52 14 14
TIAM1 -0.006 0.14 -10000 0 -0.69 10 10
E-cadherin(dimer)/Ca2+ 0.024 0.1 -10000 0 -0.39 14 14
AKT1 0.001 0.041 -10000 0 -0.2 1 1
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
CDH1 -0.017 0.16 -10000 0 -0.69 14 14
RhoA/GDP 0.002 0.094 -10000 0 -0.34 14 14
actin cytoskeleton organization 0 0.057 -10000 0 -0.2 5 5
CDC42/GDP 0.002 0.093 -10000 0 -0.34 14 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0 0.073 -10000 0 -0.31 14 14
ITGB7 0.011 0.087 -10000 0 -0.69 4 4
RAC1 0.021 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.027 0.11 -10000 0 -0.41 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.013 0.097 -10000 0 -0.39 14 14
mol:GDP -0.012 0.1 -10000 0 -0.39 14 14
CDC42/GTP/IQGAP1 0.027 0.008 -10000 0 -10000 0 0
JUP 0.021 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.007 0.098 -10000 0 -0.34 14 14
RAC1/GTP/IQGAP1 0.028 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.031 0.006 -10000 0 -10000 0 0
RHOA 0.022 0.001 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.002 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.004 0.062 0.17 1 -0.26 10 11
NME1 0.024 0.029 0.35 2 -10000 0 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.02 0.14 -10000 0 -0.55 14 14
regulation of cell-cell adhesion 0.001 0.06 -10000 0 -0.25 1 1
WASF2 -0.004 0.036 -10000 0 -0.14 1 1
Rap1/GTP 0.009 0.081 -10000 0 -0.31 14 14
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.026 0.12 -10000 0 -0.39 18 18
CCND1 -0.006 0.075 -10000 0 -0.33 10 10
VAV2 -0.027 0.17 -10000 0 -0.52 23 23
RAP1/GDP 0.008 0.085 -10000 0 -0.31 14 14
adherens junction assembly -0.018 0.14 -10000 0 -0.52 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.021 0.003 -10000 0 -10000 0 0
PIP5K1C 0.021 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.017 0.11 -10000 0 -0.38 18 18
E-cadherin/beta catenin -0.012 0.1 -10000 0 -0.45 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.02 0.14 -10000 0 -0.55 14 14
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
Rac1/GTP -0.049 0.12 -10000 0 -0.4 15 15
E-cadherin/beta catenin/alpha catenin 0.015 0.11 -10000 0 -0.45 14 14
ITGAE 0.023 0.036 0.35 3 -10000 0 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.15 -10000 0 -0.56 15 15
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.042 0.049 0.25 14 -10000 0 14
ATM 0.021 0.004 -10000 0 -10000 0 0
UBE2D3 0.02 0.006 -10000 0 -10000 0 0
PRKDC 0.018 0.008 -10000 0 -10000 0 0
ATR 0.021 0.002 -10000 0 -10000 0 0
UBE2L3 0.021 0.003 -10000 0 -10000 0 0
FANCD2 0.062 0.073 0.3 2 -10000 0 2
protein ubiquitination 0.11 0.091 0.39 8 -10000 0 8
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.021 0.003 -10000 0 -10000 0 0
M/R/N Complex 0.032 0.02 -10000 0 -10000 0 0
MRE11A 0.021 0.003 -10000 0 -10000 0 0
DNA-PK 0.036 0.017 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.043 0.07 -10000 0 -0.49 2 2
FANCF 0.022 0.001 -10000 0 -10000 0 0
BRCA1 0.021 0.003 -10000 0 -10000 0 0
CCNE1 0.13 0.15 0.35 86 -10000 0 86
CDK2/Cyclin E1 0.1 0.1 0.25 85 -10000 0 85
FANCG 0.022 0.02 0.35 1 -10000 0 1
BRCA1/BACH1/BARD1 0.042 0.048 0.25 13 -10000 0 13
FANCE 0.028 0.049 0.35 6 -10000 0 6
FANCC 0.019 0.044 -10000 0 -0.69 1 1
NBN 0.017 0.009 -10000 0 -10000 0 0
FANCA 0.02 0.005 -10000 0 -10000 0 0
DNA repair 0.071 0.085 0.33 1 -10000 0 1
BRCA1/BARD1/ubiquitin 0.042 0.048 0.25 13 -10000 0 13
BARD1/DNA-PK 0.054 0.044 -10000 0 -10000 0 0
FANCL 0.021 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.042 0.049 -10000 0 -0.25 14 14
BRCA1/BARD1/CTIP/M/R/N Complex 0.019 0.042 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.052 0.043 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.055 0.043 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.051 0.044 -10000 0 -10000 0 0
BRCA1/BACH1 0.021 0.003 -10000 0 -10000 0 0
BARD1 0.038 0.074 0.35 14 -10000 0 14
PCNA 0.021 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.047 0.04 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.049 0.041 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.11 0.099 0.42 8 -10000 0 8
BARD1/DNA-PK/P53 0.054 0.047 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.042 0.048 0.25 13 -10000 0 13
BRCA1/BARD1/CTIP 0.045 0.043 -10000 0 -10000 0 0
FA complex 0.025 0.026 -10000 0 -10000 0 0
BARD1/EWS 0.04 0.044 -10000 0 -10000 0 0
RBBP8 0.013 0.002 -10000 0 -10000 0 0
TP53 0.019 0.007 -10000 0 -10000 0 0
TOPBP1 0.021 0.002 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.053 0.042 -10000 0 -10000 0 0
BRCA1/BARD1 0.12 0.097 0.41 8 -10000 0 8
CSTF1 0.021 0.004 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.027 0.048 0.23 14 -10000 0 14
CDK2 0.021 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.14 0.35 71 -10000 0 71
RAD50 0.021 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.042 0.048 0.25 13 -10000 0 13
EWSR1 0.021 0.004 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.048 0.35 1 -0.69 1 2
ANTXR2 0.013 0.067 -10000 0 -0.59 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.01 -10000 0 -0.08 4 4
monocyte activation -0.036 0.17 -10000 0 -0.49 29 29
MAP2K2 0.002 0.084 -10000 0 -0.59 5 5
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.007 0.061 -10000 0 -0.39 6 6
CYAA -0.004 0.043 -10000 0 -0.39 3 3
MAP2K4 -0.001 0.008 -10000 0 -10000 0 0
IL1B -0.056 0.14 -10000 0 -0.39 39 39
Channel 0.021 0.051 -10000 0 -0.36 4 4
NLRP1 -0.001 0.01 -10000 0 -10000 0 0
CALM1 0.021 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.07 -10000 0 -0.39 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.01 0.08 4 -10000 0 4
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.055 0.14 -10000 0 -0.39 37 37
PA/Cellular Receptors 0.022 0.055 -10000 0 -0.39 4 4
apoptosis -0.001 0.01 -10000 0 -0.08 4 4
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.048 0.2 1 -0.34 4 5
macrophage activation -0.002 0.009 -10000 0 -10000 0 0
TNF -0.007 0.14 0.35 2 -0.69 11 13
VCAM1 -0.036 0.18 -10000 0 -0.49 29 29
platelet activation -0.003 0.07 -10000 0 -0.39 8 8
MAPKKK cascade -0.001 0.022 0.096 5 -0.093 1 6
IL18 -0.004 0.05 -10000 0 -0.4 4 4
negative regulation of macrophage activation -0.001 0.01 -10000 0 -0.08 4 4
LEF -0.001 0.01 -10000 0 -0.08 4 4
CASP1 0.002 0.009 -10000 0 -10000 0 0
mol:cAMP -0.003 0.07 -10000 0 -0.39 8 8
necrosis -0.001 0.01 -10000 0 -0.08 4 4
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.048 0.21 1 -0.34 4 5
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.021 0.004 -10000 0 -10000 0 0
HDAC2 0.021 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.033 0.054 -10000 0 -0.45 3 3
forebrain development -0.013 0.13 -10000 0 -0.54 7 7
GNAO1 -0.28 0.34 -10000 0 -0.66 117 117
SMO/beta Arrestin2 0.024 0.05 -10000 0 -0.52 2 2
SMO 0.015 0.062 -10000 0 -0.69 2 2
ARRB2 0.019 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.039 0.046 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.022 0 -10000 0 -10000 0 0
GNAI2 0.021 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.049 0.018 -10000 0 -10000 0 0
GNAI1 0.016 0.062 -10000 0 -0.69 2 2
XPO1 0.022 0.01 -10000 0 -10000 0 0
GLI1/Su(fu) -0.008 0.13 -10000 0 -0.56 6 6
SAP30 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0.015 0.062 -10000 0 -0.69 2 2
MIM/GLI2A 0.018 0.016 -10000 0 -10000 0 0
IFT88 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GLI2 0.011 0.075 -10000 0 -0.31 2 2
GLI3 0.028 0.05 0.3 1 -10000 0 1
CSNK1D 0.02 0.005 -10000 0 -10000 0 0
CSNK1E 0.021 0.003 -10000 0 -10000 0 0
SAP18 0.021 0.004 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.004 -10000 0 -10000 0 0
GNG2 0.019 0.044 -10000 0 -0.69 1 1
Gi family/GTP -0.085 0.17 -10000 0 -0.32 56 56
SIN3B 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.031 0.054 -10000 0 -0.41 1 1
GLI2/Su(fu) 0.016 0.079 -10000 0 -0.38 3 3
FOXA2 0.007 0.12 -10000 0 -1.1 3 3
neural tube patterning -0.013 0.13 -10000 0 -0.54 7 7
SPOP 0.021 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.04 -10000 0 -10000 0 0
GNB1 0.02 0.006 -10000 0 -10000 0 0
CSNK1G2 0.021 0.003 -10000 0 -10000 0 0
CSNK1G3 0.021 0.002 -10000 0 -10000 0 0
MTSS1 0.018 0.016 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.013 0.13 -10000 0 -0.54 7 7
SUFU 0.017 0.026 -10000 0 -10000 0 0
LGALS3 0.046 0.087 0.35 20 -10000 0 20
catabolic process 0.042 0.076 -10000 0 -0.4 1 1
GLI3A/CBP 0.034 0.048 -10000 0 -0.29 1 1
KIF3A 0.021 0.003 -10000 0 -10000 0 0
GLI1 -0.014 0.13 -10000 0 -0.55 7 7
RAB23 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
IFT172 0.021 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.034 0.069 -10000 0 -10000 0 0
GNAZ 0.17 0.16 0.35 117 -10000 0 117
RBBP4 0.021 0.004 -10000 0 -10000 0 0
CSNK1G1 0.021 0.003 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.021 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.02 0.073 -10000 0 -0.32 1 1
STK36 0.021 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.071 0.16 -10000 0 -0.39 19 19
PTCH1 -0.034 0.23 -10000 0 -1.1 9 9
MIM/GLI1 -0.008 0.12 -10000 0 -0.52 4 4
CREBBP 0.034 0.048 -10000 0 -0.29 1 1
Su(fu)/SIN3/HDAC complex 0.007 0.088 -10000 0 -0.4 9 9
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.021 0.002 -10000 0 -10000 0 0
NFATC1 0.009 0.089 -10000 0 -0.5 1 1
NFATC2 -0.038 0.1 -10000 0 -0.3 20 20
NFATC3 -0.005 0.095 -10000 0 -0.45 11 11
YWHAE 0.019 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.005 0.098 -10000 0 -0.4 9 9
Exportin 1/Ran/NUP214 0.041 0.009 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.02 0.14 -10000 0 -0.39 22 22
BCL2/BAX 0.031 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.013 -10000 0 -10000 0 0
BAX 0.021 0.003 -10000 0 -10000 0 0
MAPK14 0.019 0.006 -10000 0 -10000 0 0
BAD 0.021 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D 0.003 0.091 -10000 0 -0.4 7 7
Calcineurin A alpha-beta B1/BCL2 0.021 0.003 -10000 0 -10000 0 0
FKBP8 0.021 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.003 0.09 0.4 7 -10000 0 7
KPNB1 0.021 0.003 -10000 0 -10000 0 0
KPNA2 0.022 0.021 0.35 1 -10000 0 1
XPO1 0.021 0.002 -10000 0 -10000 0 0
SFN 0.2 0.16 0.35 148 -10000 0 148
MAP3K8 0.015 0.062 -10000 0 -0.69 2 2
NFAT4/CK1 alpha 0.006 0.067 -10000 0 -0.31 10 10
MEF2D/NFAT1/Cbp/p300 -0.038 0.15 -10000 0 -0.36 30 30
CABIN1 -0.005 0.099 -10000 0 -0.41 9 9
CALM1 0.018 0.011 -10000 0 -10000 0 0
RAN 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 0.022 0 -10000 0 -10000 0 0
CAMK4 -0.043 0.21 0.35 1 -0.69 24 25
mol:Ca2+ -0.002 0.006 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
YWHAH 0.021 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.031 0.015 0.25 1 -10000 0 1
YWHAB 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.007 0.14 -10000 0 -0.69 10 10
MAPK9 0.021 0.004 -10000 0 -10000 0 0
YWHAG 0.021 0.004 -10000 0 -10000 0 0
FKBP1A 0.021 0.003 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.006 0.12 -10000 0 -0.41 11 11
PRKCH 0.021 0.003 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.024 0.022 -10000 0 -10000 0 0
CASP3 0.018 0.026 -10000 0 -0.39 1 1
PIM1 0.02 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.008 -10000 0 -10000 0 0
apoptosis 0.017 0.005 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.069 0.072 -10000 0 -0.36 1 1
PRKCB -0.037 0.19 -10000 0 -0.67 22 22
PRKCE 0.02 0.048 0.35 1 -0.69 1 2
JNK2/NFAT4 -0.008 0.1 -10000 0 -0.42 11 11
BAD/BCL-XL 0.032 0.004 -10000 0 -10000 0 0
PRKCD 0.021 0.002 -10000 0 -10000 0 0
NUP214 0.021 0.003 -10000 0 -10000 0 0
PRKCZ -0.01 0.14 -10000 0 -0.66 11 11
PRKCA 0.021 0.004 -10000 0 -10000 0 0
PRKCG 0.02 0.036 0.35 3 -10000 0 3
PRKCQ 0.006 0.11 0.35 2 -0.64 7 9
FKBP38/BCL2 0.031 0.006 -10000 0 -10000 0 0
EP300 0.016 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.021 0.003 -10000 0 -10000 0 0
NFATc/JNK1 0.005 0.12 -10000 0 -0.42 9 9
CaM/Ca2+/FKBP38 0.023 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.016 0.002 -10000 0 -10000 0 0
CSNK1A1 0.009 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.02 0.14 0.22 1 -0.45 24 25
NFATc/ERK1 0.02 0.088 -10000 0 -0.46 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.015 0.14 -10000 0 -0.38 26 26
NR4A1 -0.089 0.23 -10000 0 -0.66 34 34
GSK3B 0.02 0.005 -10000 0 -10000 0 0
positive T cell selection -0.005 0.094 -10000 0 -0.45 11 11
NFAT1/CK1 alpha -0.028 0.081 -10000 0 -0.29 10 10
RCH1/ KPNB1 0.031 0.015 0.25 1 -10000 0 1
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
PRKACA 0.02 0.004 -10000 0 -10000 0 0
AKAP5 0.022 0.021 0.35 1 -10000 0 1
MEF2D 0.013 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0.009 -10000 0 -10000 0 0
NFATc/p38 alpha 0.014 0.082 -10000 0 -0.46 1 1
CREBBP 0.016 0.015 -10000 0 -10000 0 0
BCL2 0.021 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.02 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.009 0.11 0.35 4 -0.69 6 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.019 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.025 0.03 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.021 0.003 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.021 0.004 -10000 0 -10000 0 0
FYN 0.021 0.005 -10000 0 -10000 0 0
MAP3K12 0.023 0.02 0.35 1 -10000 0 1
FGR 0.018 0.044 -10000 0 -0.69 1 1
p38 alpha/TAB1 -0.054 0.11 -10000 0 -0.33 23 23
PRKG1 -0.002 0.13 0.35 1 -0.69 9 10
DUSP8 0.019 0.044 -10000 0 -0.69 1 1
PGK/cGMP/p38 alpha -0.032 0.14 0.26 1 -0.35 28 29
apoptosis -0.052 0.1 -10000 0 -0.32 22 22
RAL/GTP 0.028 0.005 -10000 0 -10000 0 0
LYN 0.018 0.008 -10000 0 -10000 0 0
DUSP1 -0.036 0.19 -10000 0 -0.69 21 21
PAK1 0.021 0.003 -10000 0 -10000 0 0
SRC 0.023 0.02 0.35 1 -10000 0 1
RAC1/OSM/MEKK3/MKK3 0.05 0.018 -10000 0 -10000 0 0
TRAF6 0.019 0.044 -10000 0 -0.69 1 1
RAC1 0.021 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.021 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.027 0.007 -10000 0 -10000 0 0
MAPK11 -0.03 0.15 0.45 1 -0.47 13 14
BLK -0.1 0.26 0.35 2 -0.59 52 54
HCK -0.003 0.13 -10000 0 -0.69 9 9
MAP2K3 0.02 0.005 -10000 0 -10000 0 0
DUSP16 0.018 0.044 -10000 0 -0.69 1 1
DUSP10 0.007 0.087 -10000 0 -0.69 4 4
TRAF6/MEKK3 0.025 0.028 -10000 0 -0.41 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.023 0.14 0.35 1 -0.37 21 22
positive regulation of innate immune response -0.03 0.16 0.48 1 -0.5 15 16
LCK 0 0.12 0.35 1 -0.69 8 9
p38alpha-beta/MKP7 -0.023 0.16 0.46 1 -0.48 14 15
p38alpha-beta/MKP5 -0.023 0.15 -10000 0 -0.52 12 12
PGK/cGMP -0.002 0.099 0.23 1 -0.52 9 10
PAK2 0.021 0.002 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.048 0.19 0.46 1 -0.47 24 25
CDC42 0.021 0.004 -10000 0 -10000 0 0
RALB 0.021 0.002 -10000 0 -10000 0 0
RALA 0.021 0.003 -10000 0 -10000 0 0
PAK3 0.054 0.1 0.35 28 -10000 0 28
TCGA08_rtk_signaling

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
PDGFRA -0.23 0.34 -10000 0 -0.67 96 96
HRAS 0.023 0.02 0.35 1 -10000 0 1
EGFR 0.01 0.087 -10000 0 -0.69 4 4
AKT -0.004 0.075 -10000 0 -0.23 1 1
FOXO3 0.021 0.005 -10000 0 -10000 0 0
AKT1 0.021 0.005 -10000 0 -10000 0 0
FOXO1 0.015 0.056 -10000 0 -0.49 3 3
AKT3 0.019 0.022 0.35 1 -10000 0 1
FOXO4 0.022 0 -10000 0 -10000 0 0
MET 0.018 0.044 -10000 0 -0.69 1 1
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
PIK3CB 0.022 0.001 -10000 0 -10000 0 0
NRAS 0.021 0.003 -10000 0 -10000 0 0
PIK3CG -0.006 0.14 0.35 2 -0.69 11 13
PIK3R3 0.022 0.021 0.35 1 -10000 0 1
PIK3R2 0.021 0.004 -10000 0 -10000 0 0
NF1 0.02 0.025 -10000 0 -0.38 1 1
RAS -0.046 0.094 -10000 0 -0.29 9 9
ERBB2 0.013 0.075 -10000 0 -0.69 3 3
proliferation/survival/translation -0.017 0.065 0.24 9 -10000 0 9
PI3K -0.035 0.093 0.22 1 -0.27 10 11
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
KRAS 0.021 0.003 -10000 0 -10000 0 0
FOXO 0.034 0.04 0.22 1 -0.15 1 2
AKT2 0.021 0.003 -10000 0 -10000 0 0
PTEN 0.018 0.036 -10000 0 -0.38 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.007 0.063 -10000 0 -0.69 1 1
adherens junction organization -0.003 0.077 -10000 0 -0.29 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.01 0.08 -10000 0 -0.45 5 5
FMN1 0.001 0.078 -10000 0 -0.29 13 13
mol:IP3 0.007 0.062 -10000 0 -0.65 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.001 0.08 -10000 0 -0.3 14 14
CTNNB1 0.022 0.003 -10000 0 -10000 0 0
AKT1 0.008 0.068 -10000 0 -0.65 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.12 -10000 0 -0.47 14 14
CTNND1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.063 -10000 0 -0.28 10 10
VASP -0.003 0.076 -10000 0 -0.29 14 14
ZYX -0.002 0.075 -10000 0 -0.29 14 14
JUB -0.003 0.076 -10000 0 -0.29 14 14
EGFR(dimer) 0.003 0.099 -10000 0 -0.35 15 15
E-cadherin/beta catenin-gamma catenin 0.015 0.11 -10000 0 -0.44 14 14
mol:PI-3-4-5-P3 0.019 0.076 -10000 0 -0.69 1 1
PIK3CA 0.019 0.045 -10000 0 -0.7 1 1
PI3K 0.019 0.077 -10000 0 -0.71 1 1
FYN -0.051 0.14 -10000 0 -0.44 10 10
mol:Ca2+ 0.007 0.061 -10000 0 -0.63 1 1
JUP 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.045 -10000 0 -0.7 1 1
mol:DAG 0.007 0.062 -10000 0 -0.65 1 1
CDH1 -0.018 0.16 -10000 0 -0.69 14 14
RhoA/GDP 0.01 0.08 -10000 0 -0.45 5 5
establishment of polarity of embryonic epithelium -0.003 0.075 -10000 0 -0.28 14 14
SRC 0.023 0.02 0.35 1 -10000 0 1
RAC1 0.021 0.003 -10000 0 -10000 0 0
RHOA 0.022 0.001 -10000 0 -10000 0 0
EGFR 0.01 0.087 -10000 0 -0.69 4 4
CASR -0.061 0.15 0.26 1 -0.36 46 47
RhoA/GTP 0.016 0.059 -10000 0 -0.58 1 1
AKT2 0.007 0.069 -10000 0 -0.65 1 1
actin cable formation -0.001 0.075 -10000 0 -0.29 2 2
apoptosis -0.005 0.065 0.65 1 -10000 0 1
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
mol:GDP -0.001 0.081 -10000 0 -0.48 5 5
PIP5K1A 0 0.064 -10000 0 -0.29 10 10
PLCG1 0.006 0.063 -10000 0 -0.68 1 1
Rac1/GTP 0.012 0.094 -10000 0 -0.46 4 4
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.006 0.094 -10000 0 -0.41 8 8
CRKL -0.002 0.071 -10000 0 -0.41 4 4
HRAS -0.001 0.11 0.36 1 -0.45 7 8
mol:PIP3 0.024 0.087 -10000 0 -0.39 4 4
SPRED1 0.021 0.003 -10000 0 -10000 0 0
SPRED2 0.021 0.002 -10000 0 -10000 0 0
GAB1 -0.002 0.075 0.27 3 -0.43 4 7
FOXO3 0.006 0.098 -10000 0 -0.42 6 6
AKT1 0.006 0.1 -10000 0 -0.41 9 9
BAD 0.006 0.099 -10000 0 -0.4 7 7
megakaryocyte differentiation -0.021 0.11 0.27 3 -0.38 18 21
GSK3B 0.006 0.099 -10000 0 -0.4 7 7
RAF1 0.015 0.1 0.34 2 -0.38 6 8
SHC1 0.017 0.009 -10000 0 -10000 0 0
STAT3 -0.003 0.076 0.27 3 -0.43 4 7
STAT1 -0.034 0.17 -10000 0 -0.96 5 5
HRAS/SPRED1 0.007 0.093 0.33 1 -0.39 5 6
cell proliferation -0.017 0.098 0.27 3 -0.38 13 16
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
TEC 0.005 0.11 -10000 0 -0.69 6 6
RPS6KB1 0.009 0.082 -10000 0 -0.45 4 4
HRAS/SPRED2 0.006 0.092 0.33 1 -0.4 5 6
LYN/TEC/p62DOK 0.007 0.098 -10000 0 -0.39 9 9
MAPK3 0.025 0.086 0.28 4 -0.28 6 10
STAP1 -0.002 0.075 0.27 3 -0.43 4 7
GRAP2 0.008 0.12 0.35 4 -0.64 7 11
JAK2 -0.03 0.15 -10000 0 -0.74 7 7
STAT1 (dimer) -0.032 0.16 -10000 0 -0.94 5 5
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.003 0.12 -10000 0 -0.39 14 14
actin filament polymerization -0.003 0.075 -10000 0 -0.42 4 4
LYN 0.018 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.008 0.1 -10000 0 -0.57 5 5
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
CBL/CRKL/GRB2 0.014 0.073 -10000 0 -0.38 3 3
PI3K 0.023 0.094 -10000 0 -0.48 5 5
PTEN 0.018 0.036 -10000 0 -0.39 2 2
SCF/KIT/EPO/EPOR -0.12 0.28 -10000 0 -1.4 4 4
MAPK8 -0.017 0.1 0.27 2 -0.38 13 15
STAT3 (dimer) -0.003 0.075 0.27 3 -0.42 4 7
positive regulation of transcription 0.025 0.076 0.26 4 -0.23 6 10
mol:GDP -0.001 0.12 0.39 1 -0.49 7 8
PIK3C2B -0.002 0.074 -10000 0 -0.43 4 4
CBL/CRKL 0.01 0.074 -10000 0 -0.39 4 4
FER -0.004 0.075 0.27 3 -0.43 4 7
SH2B3 -0.003 0.076 -10000 0 -0.43 4 4
PDPK1 0.023 0.082 -10000 0 -0.36 4 4
SNAI2 -0.002 0.079 -10000 0 -0.43 4 4
positive regulation of cell proliferation -0.014 0.13 -10000 0 -0.7 5 5
KITLG 0.014 0.035 0.34 2 -10000 0 2
cell motility -0.014 0.13 -10000 0 -0.7 5 5
PTPN6 0.02 0.009 -10000 0 -10000 0 0
EPOR -0.001 0.13 -10000 0 -0.66 5 5
STAT5A (dimer) -0.009 0.11 -10000 0 -0.57 5 5
SOCS1 0.017 0.065 0.35 1 -0.69 2 3
cell migration 0.002 0.076 0.42 4 -0.27 3 7
SOS1 0.022 0.001 -10000 0 -10000 0 0
EPO -0.22 0.35 0.35 8 -0.69 91 99
VAV1 -0.011 0.15 -10000 0 -0.69 12 12
GRB10 -0.004 0.076 0.27 3 -0.4 5 8
PTPN11 0.021 0.006 -10000 0 -10000 0 0
SCF/KIT -0.003 0.081 0.29 3 -0.42 5 8
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.023 0.087 0.31 2 -0.32 4 6
CBL 0.021 0.004 -10000 0 -10000 0 0
KIT -0.017 0.22 -10000 0 -1.2 6 6
MAP2K2 0.023 0.089 0.31 4 -0.32 4 8
SHC/Grb2/SOS1 0.017 0.077 -10000 0 -0.41 3 3
STAT5A -0.009 0.11 -10000 0 -0.59 5 5
GRB2 0.021 0.005 -10000 0 -10000 0 0
response to radiation -0.002 0.078 0.27 2 -0.42 4 6
SHC/GRAP2 0.016 0.081 0.25 4 -0.42 7 11
PTPRO -0.021 0.11 0.27 3 -0.38 18 21
SH2B2 -0.003 0.076 -10000 0 -0.43 4 4
DOK1 0.022 0 -10000 0 -10000 0 0
MATK -0.002 0.077 -10000 0 -0.43 4 4
CREBBP 0.033 0.032 -10000 0 -10000 0 0
BCL2 0.001 0.14 -10000 0 -0.69 8 8
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.047 0.034 -10000 0 -0.42 1 1
HDAC3 0.021 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0.032 0.027 -10000 0 -10000 0 0
GATA1/HDAC5 0.031 0.024 0.25 3 -10000 0 3
GATA2/HDAC5 0.029 0.052 0.25 2 -0.52 2 4
HDAC5/BCL6/BCoR 0.042 0.009 -10000 0 -10000 0 0
HDAC9 -0.009 0.14 -10000 0 -0.69 11 11
Glucocorticoid receptor/Hsp90/HDAC6 0.042 0.009 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.037 -10000 0 -0.52 1 1
HDAC5/YWHAB 0.031 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.024 -10000 0 -0.37 1 1
GATA2 0.019 0.068 0.35 2 -0.69 2 4
HDAC4/RFXANK 0.033 0.024 -10000 0 -10000 0 0
BCOR 0.021 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.021 0.005 -10000 0 -10000 0 0
HDAC5 0.021 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.027 0.035 -10000 0 -0.52 1 1
Histones 0.013 0.065 -10000 0 -0.4 1 1
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
HDAC4 0.022 0.02 0.35 1 -10000 0 1
XPO1 0.021 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.029 0.034 -10000 0 -0.52 1 1
HDAC4/Ubc9 0.031 0.015 -10000 0 -10000 0 0
HDAC7 0.023 0.02 0.35 1 -10000 0 1
HDAC5/14-3-3 E 0.028 0.011 -10000 0 -10000 0 0
TUBA1B 0.021 0.002 -10000 0 -10000 0 0
HDAC6 0.022 0.001 -10000 0 -10000 0 0
HDAC5/RFXANK 0.032 0.015 0.25 1 -10000 0 1
CAMK4 -0.043 0.21 0.35 1 -0.69 24 25
Tubulin/HDAC6 0.04 0.012 -10000 0 -10000 0 0
SUMO1 0.021 0.002 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.021 0.003 -10000 0 -10000 0 0
GATA1 0.021 0.035 0.35 3 -10000 0 3
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.007 -10000 0 -10000 0 0
NR3C1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.029 0.036 -10000 0 -0.32 1 1
SRF 0.02 0.006 -10000 0 -10000 0 0
HDAC4/YWHAB 0.032 0.015 -10000 0 -10000 0 0
Tubulin 0.029 0.009 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.028 0.011 -10000 0 -10000 0 0
GNB1 0.02 0.006 -10000 0 -10000 0 0
RANGAP1 0.021 0.003 -10000 0 -10000 0 0
BCL6/BCoR 0.031 0.005 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.043 0.015 -10000 0 -10000 0 0
HDAC4/SRF 0 0.13 -10000 0 -0.41 24 24
HDAC4/ER alpha -0.25 0.27 0.25 1 -0.5 137 138
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.066 -10000 0 -0.4 1 1
cell motility 0.04 0.012 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.033 0.014 0.25 1 -10000 0 1
BCL6 0.021 0.002 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.022 0.02 0.35 1 -10000 0 1
Hsp90/HDAC6 0.031 0.006 -10000 0 -10000 0 0
ESR1 -0.34 0.35 -10000 0 -0.67 137 137
HDAC6/HDAC11 0.038 0.035 0.25 7 -10000 0 7
Ran/GTP/Exportin 1 0.03 0.036 -10000 0 -0.33 1 1
NPC 0.013 0.001 -10000 0 -10000 0 0
MEF2C 0.021 0.002 -10000 0 -10000 0 0
RAN 0.021 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.06 0.021 -10000 0 -10000 0 0
GNG2 0.019 0.044 -10000 0 -0.69 1 1
NCOR2 0.021 0.003 -10000 0 -10000 0 0
TUBB2A 0.02 0.006 -10000 0 -10000 0 0
HDAC11 0.03 0.053 0.35 7 -10000 0 7
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
ANKRA2 0.019 0.044 -10000 0 -0.69 1 1
RFXANK 0.024 0.029 0.35 2 -10000 0 2
nuclear import -0.026 0.011 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.024 0.076 0.31 2 -0.45 3 5
SNTA1 0.024 0.029 0.35 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.031 0.088 0.31 8 -0.45 3 11
MAPK12 0.011 0.073 0.27 2 -0.38 6 8
CCND1 -0.004 0.095 0.18 1 -0.42 11 12
p38 gamma/SNTA1 0.031 0.076 0.28 1 -0.35 6 7
MAP2K3 0.02 0.005 -10000 0 -10000 0 0
PKN1 0.021 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint 0.011 0.073 0.27 2 -0.37 6 8
MAP2K6 -0.004 0.068 -10000 0 -0.44 6 6
MAPT 0.074 0.091 0.26 20 -0.29 2 22
MAPK13 0.04 0.099 0.33 3 -0.52 3 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.006 0.001 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.023 0.02 0.35 1 -10000 0 1
EGFR 0.01 0.087 -10000 0 -0.69 4 4
EGF/EGFR 0.056 0.1 0.35 1 -0.37 8 9
EGF/EGFR dimer/SHC/GRB2/SOS1 0.064 0.092 -10000 0 -0.37 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.022 0.021 0.35 1 -10000 0 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.099 0.14 0.35 65 -10000 0 65
EGF/EGFR dimer/SHC 0.057 0.098 -10000 0 -0.38 4 4
mol:GDP 0.058 0.086 -10000 0 -0.36 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.008 0.099 0.35 1 -0.69 5 6
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP 0.038 0.064 -10000 0 -0.34 3 3
SHC1 0.017 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.053 0.077 -10000 0 -0.34 3 3
FRAP1 0.007 0.052 -10000 0 -0.35 3 3
EGF/EGFR dimer 0.071 0.12 -10000 0 -0.5 4 4
SOS1 0.022 0.001 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.02 0.078 -10000 0 -0.52 5 5
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.06 0.07 -10000 0 -0.39 1 1
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.002 0.019 0.2 2 -10000 0 2
GNB1/GNG2 0.025 0.031 -10000 0 -0.45 1 1
GNB1 0.02 0.006 -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 0.006 0.002 -10000 0 -10000 0 0
Gs family/GTP 0.044 0.068 0.2 43 -10000 0 43
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 0 -10000 0 -10000 0 0
GNAL 0.075 0.12 0.35 43 -10000 0 43
GNG2 0.019 0.044 -10000 0 -0.69 1 1
CRH 0.016 0.03 0.35 2 -10000 0 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.009 0.079 -10000 0 -0.4 10 10
MAPK11 0.011 0.028 0.17 8 -10000 0 8
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.034 0.053 -10000 0 -0.39 3 3
RGS9BP 0.027 0.049 0.35 6 -10000 0 6
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.014 0.003 -10000 0 -10000 0 0
mol:Na + 0.032 0.058 0.23 20 -10000 0 20
mol:ADP -0.013 0.004 -10000 0 -10000 0 0
GNAT2 0.02 0.005 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.039 0.097 0.44 1 -0.45 7 8
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.006 -10000 0 -10000 0 0
GRK7 0.017 0.004 -10000 0 -10000 0 0
CNGB3 0.04 0.091 0.35 21 -10000 0 21
Cone Metarhodopsin II/X-Arrestin 0.012 0.014 0.23 1 -10000 0 1
mol:Ca2+ 0.004 0.045 0.23 1 -10000 0 1
Cone PDE6 0.055 0.094 0.4 1 -0.4 7 8
Cone Metarhodopsin II 0.019 0.005 -10000 0 -10000 0 0
Na + (4 Units) 0.036 0.055 0.4 1 -10000 0 1
GNAT2/GDP 0.045 0.088 0.36 2 -0.39 7 9
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.008 0.039 -10000 0 -10000 0 0
Cone Transducin 0.036 0.057 -10000 0 -0.41 3 3
SLC24A2 0.014 0.002 -10000 0 -10000 0 0
GNB3/GNGT2 0.029 0.067 0.25 6 -0.52 3 9
GNB3 0.027 0.049 0.35 6 -10000 0 6
GNAT2/GTP 0.015 0.003 -10000 0 -10000 0 0
CNGA3 0.016 0.021 0.35 1 -10000 0 1
ARR3 0.017 0.021 0.35 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.033 0.058 0.23 20 -10000 0 20
mol:Pi 0.039 0.096 0.43 1 -0.45 7 8
Cone CNG Channel 0.046 0.055 0.35 1 -10000 0 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.014 0.002 -10000 0 -10000 0 0
RGS9 0.017 0.14 0.35 12 -0.69 7 19
PDE6C 0.03 0.063 0.35 10 -10000 0 10
GNGT2 0.013 0.075 -10000 0 -0.69 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.015 0.003 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.016 0.12 0.43 3 -1.2 2 5
regulation of axonogenesis 0.002 0.06 0.26 11 -10000 0 11
myoblast fusion -0.019 0.05 0.41 2 -0.25 3 5
mol:GTP 0.014 0.035 -10000 0 -0.18 6 6
regulation of calcium-dependent cell-cell adhesion -0.025 0.1 0.4 12 -10000 0 12
ARF1/GTP 0.023 0.029 -10000 0 -10000 0 0
mol:GM1 0.007 0.026 -10000 0 -0.18 2 2
mol:Choline -0.009 0.094 -10000 0 -0.42 12 12
lamellipodium assembly 0.014 0.06 0.25 3 -0.39 4 7
MAPK3 0.019 0.046 0.28 3 -0.35 2 5
ARF6/GTP/NME1/Tiam1 0.025 0.1 -10000 0 -0.4 12 12
ARF1 0.018 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.019 0.05 0.25 3 -0.42 2 5
ARF1/GDP 0.02 0.051 -10000 0 -0.38 2 2
ARF6 0.025 0.018 -10000 0 -10000 0 0
RAB11A 0.021 0.003 -10000 0 -10000 0 0
TIAM1 -0.006 0.14 -10000 0 -0.69 10 10
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.019 0.046 0.28 3 -0.35 2 5
actin filament bundle formation -0.024 0.051 0.38 2 -0.22 3 5
KALRN 0.012 0.042 -10000 0 -0.35 3 3
RAB11FIP3/RAB11A 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.052 0.22 3 -0.39 2 5
NME1 0.024 0.029 0.35 2 -10000 0 2
Rac1/GDP 0.026 0.048 -10000 0 -0.39 2 2
substrate adhesion-dependent cell spreading 0.014 0.035 -10000 0 -0.18 6 6
cortical actin cytoskeleton organization 0.014 0.06 0.25 3 -0.39 4 7
RAC1 0.021 0.003 -10000 0 -10000 0 0
liver development 0.014 0.035 -10000 0 -0.18 6 6
ARF6/GTP 0.014 0.035 -10000 0 -0.18 6 6
RhoA/GTP 0.027 0.029 -10000 0 -0.18 2 2
mol:GDP 0.013 0.057 0.28 3 -0.42 2 5
ARF6/GTP/RAB11FIP3/RAB11A 0.038 0.029 -10000 0 -10000 0 0
RHOA 0.022 0.001 -10000 0 -10000 0 0
PLD1 -0.007 0.11 -10000 0 -0.48 12 12
RAB11FIP3 0.021 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.014 0.06 0.25 3 -0.39 4 7
ruffle organization -0.002 0.06 -10000 0 -0.26 11 11
regulation of epithelial cell migration 0.014 0.035 -10000 0 -0.18 6 6
PLD2 0.015 0.026 -10000 0 -10000 0 0
PIP5K1A -0.002 0.061 -10000 0 -0.26 11 11
mol:Phosphatidic acid -0.009 0.094 -10000 0 -0.42 12 12
Rac1/GTP 0.014 0.06 0.25 3 -0.39 4 7
mTOR signaling pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.021 0.004 -10000 0 -10000 0 0
mol:PIP3 0.005 0.048 0.23 1 -0.7 1 2
FRAP1 0.007 0.056 -10000 0 -0.45 3 3
AKT1 0.003 0.048 -10000 0 -0.65 1 1
INSR 0.021 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.028 0.027 -10000 0 -10000 0 0
mol:GTP 0.022 0.053 -10000 0 -0.53 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.022 -10000 0 -10000 0 0
TSC2 0.018 0.035 -10000 0 -0.38 2 2
RHEB/GDP 0.012 0.042 -10000 0 -0.48 1 1
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.019 0.022 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.017 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.021 0.005 -10000 0 -10000 0 0
RPS6KB1 0.021 0.051 -10000 0 -0.36 1 1
MAP3K5 -0.041 0.12 -10000 0 -0.35 34 34
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
apoptosis -0.041 0.12 -10000 0 -0.35 34 34
mol:LY294002 0 0 0.001 1 -0.001 3 4
EIF4B 0.021 0.048 0.24 1 -0.31 1 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.044 -10000 0 -0.3 1 1
eIF4E/eIF4G1/eIF4A1 0.01 0.033 -10000 0 -0.27 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.052 -10000 0 -0.73 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.032 -10000 0 -0.27 1 1
FKBP1A 0.021 0.003 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.048 -10000 0 -0.48 1 1
mol:Amino Acids 0 0 0.001 1 -0.001 3 4
FKBP12/Rapamycin 0.016 0.003 -10000 0 -10000 0 0
PDPK1 0.001 0.044 -10000 0 -0.66 1 1
EIF4E 0.02 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.057 0.22 -10000 0 -0.6 37 37
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.007 0.083 -10000 0 -0.82 1 1
TSC1/TSC2 0.024 0.058 -10000 0 -0.58 1 1
tumor necrosis factor receptor activity 0 0 0.001 3 -0.001 1 4
RPS6 0.021 0.003 -10000 0 -10000 0 0
PPP5C 0.021 0.003 -10000 0 -10000 0 0
EIF4G1 0.021 0.002 -10000 0 -10000 0 0
IRS1 0.005 0.022 -10000 0 -0.2 3 3
INS 0.021 0.046 0.35 5 -10000 0 5
PTEN 0.018 0.035 -10000 0 -0.38 2 2
PDK2 0 0.051 0.21 1 -0.51 2 3
EIF4EBP1 -0.14 0.38 -10000 0 -1 39 39
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
PPP2R5D 0.02 0.069 -10000 0 -0.41 3 3
peptide biosynthetic process 0.013 0.015 -10000 0 -10000 0 0
RHEB 0.021 0.005 -10000 0 -10000 0 0
EIF4A1 0.019 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 3 -0.004 1 4
EEF2 0.013 0.015 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.12 0.35 -10000 0 -0.96 39 39
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.013 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.027 0.017 -10000 0 -10000 0 0
CDKN1B -0.003 0.077 -10000 0 -0.62 1 1
CDKN1A 0 0.087 -10000 0 -0.36 3 3
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.018 0.008 -10000 0 -10000 0 0
FOXO3 -0.002 0.075 -10000 0 -0.62 1 1
AKT1 -0.004 0.082 -10000 0 -0.34 9 9
BAD 0.021 0.002 -10000 0 -10000 0 0
AKT3 0.011 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.003 0.079 -10000 0 -0.62 1 1
AKT1/ASK1 -0.018 0.13 -10000 0 -0.4 17 17
BAD/YWHAZ 0.032 0.02 -10000 0 -10000 0 0
RICTOR 0.021 0.003 -10000 0 -10000 0 0
RAF1 0.022 0.001 -10000 0 -10000 0 0
JNK cascade 0.018 0.13 0.36 22 -10000 0 22
TSC1 -0.004 0.079 -10000 0 -0.62 1 1
YWHAZ 0.016 0.009 -10000 0 -10000 0 0
AKT1/RAF1 0.017 0.085 -10000 0 -0.62 1 1
EP300 0.021 0.003 -10000 0 -10000 0 0
mol:GDP -0.004 0.081 -10000 0 -0.34 9 9
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.005 0.082 -10000 0 -0.54 2 2
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 0.005 0.039 -10000 0 -0.44 2 2
MAP3K5 -0.043 0.2 -10000 0 -0.65 25 25
MAPKAP1 0.021 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.061 0.087 0.32 6 -0.22 2 8
YWHAH 0.021 0.003 -10000 0 -10000 0 0
AKT1S1 0 0.076 -10000 0 -0.62 1 1
CASP9 -0.001 0.075 -10000 0 -0.62 1 1
YWHAB 0.021 0.003 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.018 0.082 -10000 0 -0.58 1 1
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.017 -10000 0 -10000 0 0
YWHAE 0.019 0.007 -10000 0 -10000 0 0
SRC 0.023 0.02 0.35 1 -10000 0 1
AKT2/p21CIP1 0.007 0.087 -10000 0 -0.37 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL -0.001 0.068 -10000 0 -0.4 6 6
CHUK 0.003 0.061 -10000 0 -10000 0 0
BAD/BCL-XL 0.023 0.083 -10000 0 -0.58 1 1
mTORC2 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.062 0.12 0.28 1 -0.44 6 7
PDPK1 0.021 0.004 -10000 0 -10000 0 0
MDM2 -0.001 0.083 -10000 0 -0.62 1 1
MAPKKK cascade -0.017 0.084 0.6 1 -10000 0 1
MDM2/Cbp/p300 0.031 0.085 -10000 0 -0.57 1 1
TSC1/TSC2 -0.005 0.08 -10000 0 -0.52 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.081 -10000 0 -0.54 1 1
glucose import 0 0.064 -10000 0 -0.4 6 6
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.002 0.066 -10000 0 -0.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0 0.064 -10000 0 -0.4 6 6
GSK3A -0.002 0.081 -10000 0 -0.62 1 1
FOXO1 0.001 0.07 -10000 0 -0.36 6 6
GSK3B -0.003 0.079 -10000 0 -0.62 1 1
SFN 0.2 0.16 0.35 148 -10000 0 148
G1/S transition of mitotic cell cycle -0.002 0.08 -10000 0 -0.6 1 1
p27Kip1/14-3-3 family 0.079 0.081 -10000 0 -0.45 1 1
PRKACA 0.021 0.003 -10000 0 -10000 0 0
KPNA1 0.022 0 -10000 0 -10000 0 0
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
YWHAG 0.021 0.004 -10000 0 -10000 0 0
RHEB 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.004 -10000 0 -10000 0 0
HDAC3 0.021 0.002 -10000 0 -10000 0 0
VDR 0.015 0.12 0.35 8 -0.69 6 14
Cbp/p300/PCAF 0.036 0.053 -10000 0 -0.45 3 3
EP300 0.021 0.003 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.016 0.072 -10000 0 -0.48 2 2
KAT2B 0.013 0.075 -10000 0 -0.69 3 3
MAPK14 0.02 0.006 -10000 0 -10000 0 0
AKT1 0.034 0.098 0.28 4 -0.28 7 11
RAR alpha/9cRA/Cyclin H 0.032 0.07 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.073 -10000 0 -0.41 3 3
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.004 0.11 -10000 0 -0.55 10 10
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.01 0.089 0.23 8 -0.52 6 14
RXRs/RARs/NRIP1/9cRA 0.031 0.086 -10000 0 -0.52 2 2
NCOA2 -0.034 0.18 -10000 0 -0.69 19 19
NCOA3 0.021 0.003 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.015 0.12 0.35 8 -0.69 6 14
RARG 0.022 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.029 0.005 -10000 0 -10000 0 0
MAPK3 0.022 0.004 -10000 0 -10000 0 0
MAPK1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.005 0.14 -10000 0 -0.69 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.032 0.088 -10000 0 -0.34 3 3
RARA 0.007 0.056 -10000 0 -0.28 9 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.014 0.12 -10000 0 -0.5 8 8
PRKCA 0.022 0.007 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.033 0.082 -10000 0 -0.53 1 1
RXRG 0.031 0.08 0.29 2 -0.39 4 6
RXRA 0.005 0.057 0.22 1 -0.26 10 11
RXRB 0.018 0.02 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.01 0.089 0.23 8 -0.52 6 14
RBP1 -0.1 0.28 0.35 4 -0.69 48 52
CRBP1/9-cic-RA -0.079 0.21 0.23 4 -0.52 48 52
RARB -0.002 0.13 -10000 0 -0.69 9 9
PRKCG 0.021 0.036 0.35 3 -10000 0 3
MNAT1 0.021 0.003 -10000 0 -10000 0 0
RAR alpha/RXRs 0.028 0.089 0.42 1 -10000 0 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.032 0.079 -10000 0 -0.59 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.079 -10000 0 -0.47 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 0.034 0.082 -10000 0 -0.53 1 1
positive regulation of DNA binding 0.019 0.061 -10000 0 -10000 0 0
NRIP1 0.031 0.1 -10000 0 -1.2 1 1
RXRs/RARs 0.035 0.075 -10000 0 -0.36 1 1
RXRs/RXRs/DNA/9cRA 0.01 0.056 -10000 0 -10000 0 0
PRKACA 0.021 0.003 -10000 0 -10000 0 0
CDK7 0.021 0.002 -10000 0 -10000 0 0
TFIIH 0.043 0.007 -10000 0 -10000 0 0
RAR alpha/9cRA 0.041 0.051 -10000 0 -10000 0 0
CCNH 0.021 0.002 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.038 0.014 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.001 0.13 -10000 0 -0.52 15 15
AKT1 0.021 0.11 -10000 0 -0.61 6 6
PTK2B -0.006 0.14 -10000 0 -0.67 6 6
VEGFR2 homodimer/Frs2 0.012 0.12 -10000 0 -0.76 6 6
CAV1 0.021 0.005 -10000 0 -10000 0 0
CALM1 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.022 0.11 -10000 0 -0.68 6 6
endothelial cell proliferation 0.015 0.12 -10000 0 -0.58 6 6
mol:Ca2+ 0.004 0.12 -10000 0 -0.65 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.031 0.11 -10000 0 -0.65 6 6
RP11-342D11.1 -0.005 0.11 -10000 0 -0.65 7 7
CDH5 0.018 0.044 -10000 0 -0.69 1 1
VEGFA homodimer 0.039 0.026 -10000 0 -10000 0 0
SHC1 0.017 0.009 -10000 0 -10000 0 0
SHC2 0.006 0.1 -10000 0 -0.64 6 6
HRAS/GDP 0.015 0.083 -10000 0 -0.54 4 4
SH2D2A 0.005 0.099 0.35 1 -0.69 5 6
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.024 0.12 -10000 0 -0.65 6 6
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.01 0.12 -10000 0 -0.62 8 8
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.028 0.099 -10000 0 -0.7 3 3
GRB10 0.005 0.11 -10000 0 -0.67 6 6
PTPN11 0.021 0.002 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
PAK1 0.021 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.036 0.12 -10000 0 -0.72 6 6
HRAS 0.023 0.02 0.35 1 -10000 0 1
VEGF/Rho/ROCK1/Integrin Complex 0.002 0.089 -10000 0 -0.49 4 4
HIF1A 0.021 0.003 -10000 0 -10000 0 0
FRS2 0.021 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.03 0.11 -10000 0 -0.64 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.018 0.044 -10000 0 -0.69 1 1
Nck/Pak 0.029 0.034 -10000 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.021 0.11 -10000 0 -0.71 6 6
mol:GDP 0.021 0.093 -10000 0 -0.55 5 5
mol:NADP 0.026 0.11 -10000 0 -0.53 7 7
eNOS/Hsp90 0.036 0.11 -10000 0 -0.52 6 6
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
mol:IP3 0.004 0.12 -10000 0 -0.66 7 7
HIF1A/ARNT 0.025 0.013 -10000 0 -10000 0 0
SHB 0.019 0.044 -10000 0 -0.69 1 1
VEGFA 0.02 0.007 -10000 0 -10000 0 0
VEGFC 0.022 0.021 0.35 1 -10000 0 1
FAK1/Vinculin 0.017 0.15 -10000 0 -0.74 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.022 0.001 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.01 0.15 -10000 0 -0.5 18 18
PTPN6 0.021 0.004 -10000 0 -10000 0 0
EPAS1 0.018 0.06 -10000 0 -0.37 6 6
mol:L-citrulline 0.026 0.11 -10000 0 -0.53 7 7
ITGAV 0.021 0.003 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.033 0.1 -10000 0 -0.6 6 6
VEGFR2 homodimer/VEGFA homodimer 0.021 0.13 -10000 0 -0.72 7 7
VEGFR2/3 heterodimer 0.01 0.13 -10000 0 -0.83 6 6
VEGFB 0.002 0.13 0.35 2 -0.69 8 10
MAPK11 0.018 0.13 0.38 1 -0.68 7 8
VEGFR2 homodimer -0.001 0.14 -10000 0 -0.88 6 6
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.017 0.062 -10000 0 -0.69 2 2
MAPK3 0.008 0.13 0.37 1 -0.64 6 7
MAPK1 0.009 0.13 0.37 1 -0.64 6 7
VEGFA145/NRP2 0.025 0.05 -10000 0 -0.51 2 2
VEGFR1/2 heterodimer 0.01 0.12 -10000 0 -0.79 6 6
KDR -0.001 0.14 -10000 0 -0.89 6 6
VEGFA165/NRP1/VEGFR2 homodimer 0.022 0.13 -10000 0 -0.65 8 8
SRC 0.023 0.02 0.35 1 -10000 0 1
platelet activating factor biosynthetic process 0.01 0.13 0.37 1 -0.65 6 7
PI3K 0.014 0.13 -10000 0 -0.77 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.021 0.13 -10000 0 -0.77 6 6
FES 0.002 0.12 -10000 0 -0.64 8 8
GAB1 0.008 0.1 -10000 0 -0.65 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.022 0.12 -10000 0 -0.71 6 6
CTNNB1 0.022 0 -10000 0 -10000 0 0
SOS1 0.022 0.001 -10000 0 -10000 0 0
ARNT 0.017 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.033 0.11 -10000 0 -0.5 6 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.021 0.11 -10000 0 -0.71 6 6
PI3K/GAB1 0.033 0.11 -10000 0 -0.58 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.038 0.12 -10000 0 -0.69 6 6
PRKACA 0.021 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.021 0.12 -10000 0 -0.78 6 6
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.003 0.12 -10000 0 -0.68 7 7
actin cytoskeleton reorganization 0.01 0.12 -10000 0 -0.61 8 8
PTK2 -0.007 0.15 -10000 0 -0.81 6 6
EDG1 -0.005 0.11 -10000 0 -0.65 7 7
mol:DAG 0.004 0.12 -10000 0 -0.66 7 7
CaM/Ca2+ 0.013 0.11 -10000 0 -0.61 7 7
MAP2K3 0.012 0.12 0.36 1 -0.64 6 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.025 0.12 -10000 0 -0.71 6 6
PLCG1 0.004 0.12 -10000 0 -0.68 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.03 0.12 -10000 0 -0.64 7 7
IQGAP1 0.021 0.004 -10000 0 -10000 0 0
YES1 0.021 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.023 0.11 -10000 0 -0.68 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.022 0.11 -10000 0 -0.71 6 6
cell migration 0.023 0.13 -10000 0 -0.7 5 5
mol:PI-3-4-5-P3 0.015 0.12 -10000 0 -0.69 6 6
FYN 0.021 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 0 0.12 -10000 0 -0.55 10 10
mol:NO 0.026 0.11 -10000 0 -0.53 7 7
PXN 0.021 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.08 -10000 0 -0.51 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.017 0.12 -10000 0 -0.71 6 6
VHL 0.022 0 -10000 0 -10000 0 0
ITGB3 -0.019 0.16 -10000 0 -0.69 15 15
NOS3 0.024 0.13 -10000 0 -0.61 7 7
VEGFR2 homodimer/VEGFA homodimer/Sck 0.013 0.13 -10000 0 -0.59 10 10
RAC1 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.015 0.11 0.35 1 -0.61 6 7
PRKCB -0.014 0.15 0.35 1 -0.47 19 20
VCL 0.021 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.007 0.11 -10000 0 -0.65 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.02 0.11 -10000 0 -0.71 6 6
VEGFA165/NRP2 0.025 0.05 -10000 0 -0.51 2 2
MAPKKK cascade 0.048 0.11 -10000 0 -0.62 3 3
NRP2 0.017 0.065 0.35 1 -0.69 2 3
VEGFC homodimer 0.022 0.021 0.35 1 -10000 0 1
NCK1 0.019 0.044 -10000 0 -0.69 1 1
ROCK1 0.021 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.018 0.15 -10000 0 -0.79 5 5
MAP3K13 0.002 0.13 0.36 1 -0.61 9 10
PDPK1 0.008 0.1 -10000 0 -0.59 6 6
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.018 0.025 0.29 1 -10000 0 1
DAPP1 -0.055 0.17 0.28 1 -0.5 21 22
Src family/SYK family/BLNK-LAT/BTK-ITK -0.069 0.21 0.4 1 -0.61 23 24
mol:DAG -0.018 0.09 0.3 1 -0.27 12 13
HRAS 0.023 0.02 0.34 1 -10000 0 1
RAP1A 0.021 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.014 0.078 -10000 0 -0.33 5 5
PLCG2 0.007 0.097 -10000 0 -0.69 5 5
PLCG1 0.021 0.003 -10000 0 -10000 0 0
ARF5 0.021 0.004 -10000 0 -10000 0 0
mol:GTP -0.004 0.029 0.3 1 -10000 0 1
ARF1/GTP 0.005 0.023 0.28 1 -10000 0 1
RHOA 0.022 0.001 -10000 0 -10000 0 0
YES1 0.021 0.003 -10000 0 -10000 0 0
RAP1A/GTP 0.015 0.021 -10000 0 -10000 0 0
ADAP1 -0.007 0.069 0.29 2 -0.37 6 8
ARAP3 -0.004 0.029 0.3 1 -10000 0 1
INPPL1 0.021 0.003 -10000 0 -10000 0 0
PREX1 0.021 0.003 -10000 0 -10000 0 0
ARHGEF6 0.021 0.002 -10000 0 -10000 0 0
ARHGEF7 0.021 0.005 -10000 0 -10000 0 0
ARF1 0.018 0.008 -10000 0 -10000 0 0
NRAS 0.022 0.005 -10000 0 -10000 0 0
FYN 0.021 0.005 -10000 0 -10000 0 0
ARF6 0.021 0.003 -10000 0 -10000 0 0
FGR 0.018 0.044 -10000 0 -0.69 1 1
mol:Ca2+ -0.007 0.048 0.21 1 -10000 0 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.006 0.14 -10000 0 -0.69 10 10
ZAP70 0.021 0.074 0.35 4 -0.69 2 6
mol:IP3 -0.012 0.065 0.25 1 -0.2 7 8
LYN 0.018 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.014 0.072 -10000 0 -0.33 5 5
RhoA/GDP 0.028 0.045 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.017 -10000 0 -10000 0 0
BLNK 0.005 0.11 -10000 0 -0.69 6 6
actin cytoskeleton reorganization 0.014 0.07 0.32 1 -0.38 2 3
SRC 0.023 0.02 0.35 1 -10000 0 1
PLEKHA2 0.003 0.032 -10000 0 -0.45 1 1
RAC1 0.021 0.003 -10000 0 -10000 0 0
PTEN 0.017 0.034 -10000 0 -0.36 2 2
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.017 0.024 0.29 1 -10000 0 1
RhoA/GTP 0.016 0.027 0.3 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.06 0.17 0.36 1 -0.54 18 19
BLK -0.1 0.26 0.35 2 -0.59 52 54
PDPK1 0.021 0.004 -10000 0 -10000 0 0
CYTH1 -0.002 0.033 0.29 2 -10000 0 2
HCK -0.003 0.13 -10000 0 -0.69 9 9
CYTH3 -0.002 0.035 0.29 2 -10000 0 2
CYTH2 -0.003 0.032 0.29 2 -10000 0 2
KRAS 0.022 0.005 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.002 0.1 -10000 0 -0.51 8 8
SGK1 -0.011 0.12 -10000 0 -0.5 10 10
INPP5D 0.019 0.044 -10000 0 -0.69 1 1
mol:GDP 0.002 0.079 -10000 0 -0.35 5 5
SOS1 0.022 0.001 -10000 0 -10000 0 0
SYK 0.019 0.044 -10000 0 -0.69 1 1
ARF6/GDP 0.019 0.045 0.32 1 -10000 0 1
mol:PI-3-4-5-P3 -0.005 0.026 0.3 1 -10000 0 1
ARAP3/RAP1A/GTP 0.015 0.021 -10000 0 -10000 0 0
VAV1 -0.011 0.15 -10000 0 -0.69 12 12
mol:PI-3-4-P2 0.011 0.033 -10000 0 -0.52 1 1
RAS family/GTP/PI3K Class I 0.038 0.034 0.31 1 -10000 0 1
PLEKHA1 0.004 0.028 -10000 0 -0.45 1 1
Rac1/GDP 0.014 0.077 -10000 0 -0.33 5 5
LAT 0.022 0.02 0.35 1 -10000 0 1
Rac1/GTP 0.001 0.09 -10000 0 -0.37 7 7
ITK -0.019 0.076 0.29 1 -0.37 9 10
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.03 0.12 0.34 1 -0.39 12 13
LCK 0 0.12 0.35 1 -0.69 8 9
BTK -0.008 0.053 0.29 2 -0.37 3 5
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.039 0.11 0.35 3 -0.42 3 6
PDGFB-D/PDGFRB/SLAP 0.015 0.09 -10000 0 -0.53 6 6
PDGFB-D/PDGFRB/APS/CBL 0.047 0.04 0.44 1 -10000 0 1
AKT1 0.017 0.071 0.31 1 -0.59 1 2
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.045 0.11 0.36 3 -0.42 4 7
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
FGR -0.001 0.1 -10000 0 -0.58 6 6
mol:Ca2+ 0.011 0.078 -10000 0 -0.44 3 3
MYC -0.02 0.3 -10000 0 -0.84 28 28
SHC1 0.017 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.038 -10000 0 -0.33 2 2
LRP1/PDGFRB/PDGFB 0.045 0.045 -10000 0 -0.45 1 1
GRB10 0.021 0.003 -10000 0 -10000 0 0
PTPN11 0.021 0.002 -10000 0 -10000 0 0
GO:0007205 0.011 0.079 -10000 0 -0.45 3 3
PTEN 0.018 0.036 -10000 0 -0.38 2 2
GRB2 0.021 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.088 0.35 5 -0.69 3 8
PDGFB-D/PDGFRB/SHP2 0.036 0.033 0.25 6 -10000 0 6
PDGFB-D/PDGFRB/GRB10 0.036 0.033 0.25 6 -10000 0 6
cell cycle arrest 0.015 0.089 -10000 0 -0.53 6 6
HRAS 0.023 0.02 0.35 1 -10000 0 1
HIF1A 0.013 0.066 0.3 1 -0.52 1 2
GAB1 0.003 0.1 -10000 0 -0.45 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.006 0.097 -10000 0 -0.41 3 3
PDGFB-D/PDGFRB 0.043 0.038 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.036 0.033 0.25 6 -10000 0 6
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.037 0.13 0.37 3 -0.47 3 6
positive regulation of MAPKKK cascade 0.036 0.032 0.24 6 -10000 0 6
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
mol:IP3 0.011 0.079 -10000 0 -0.45 3 3
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.021 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.033 0.071 0.25 10 -0.49 3 13
SHB 0.019 0.044 -10000 0 -0.69 1 1
BLK -0.14 0.25 -10000 0 -0.52 76 76
PTPN2 0.021 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.036 0.033 0.25 6 -10000 0 6
BCAR1 0.02 0.005 -10000 0 -10000 0 0
VAV2 -0.004 0.14 -10000 0 -0.52 7 7
CBL 0.021 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.037 0.032 0.25 6 -10000 0 6
LCK -0.017 0.14 -10000 0 -0.62 12 12
PDGFRB 0.027 0.05 0.35 6 -10000 0 6
ACP1 0.021 0.002 -10000 0 -10000 0 0
HCK -0.001 0.12 -10000 0 -0.58 9 9
ABL1 -0.004 0.099 -10000 0 -0.4 6 6
PDGFB-D/PDGFRB/CBL 0 0.11 -10000 0 -0.47 4 4
PTPN1 0.021 0.006 -10000 0 -10000 0 0
SNX15 0.021 0.003 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.024 0.028 0.35 2 -10000 0 2
cell proliferation -0.009 0.27 -10000 0 -0.73 28 28
SLA 0 0.11 -10000 0 -0.69 6 6
actin cytoskeleton reorganization 0.031 0.054 0.33 1 -0.36 1 2
SRC 0.016 0.041 -10000 0 -10000 0 0
PI3K 0.001 0.056 -10000 0 -0.46 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.036 0.06 -10000 0 -0.36 3 3
SH2B2 0.023 0.029 0.35 2 -10000 0 2
PLCgamma1/SPHK1 0.045 0.12 0.36 3 -0.43 4 7
LYN 0.01 0.064 -10000 0 -0.51 2 2
LRP1 0.019 0.044 -10000 0 -0.69 1 1
SOS1 0.022 0.001 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
STAT5A 0.021 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.057 0.049 0.38 1 -0.37 1 2
SPHK1 0.075 0.14 0.35 48 -0.69 2 50
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.011 0.079 -10000 0 -0.45 3 3
PLCG1 0.011 0.081 -10000 0 -0.46 3 3
NHERF/PDGFRB 0.039 0.056 -10000 0 -0.46 2 2
YES1 0.012 0.07 -10000 0 -0.66 2 2
cell migration 0.039 0.056 -10000 0 -0.45 2 2
SHC/Grb2/SOS1 0.047 0.043 -10000 0 -10000 0 0
SLC9A3R2 0.017 0.05 -10000 0 -0.54 2 2
SLC9A3R1 0.018 0.044 -10000 0 -0.69 1 1
NHERF1-2/PDGFRB/PTEN 0.047 0.059 -10000 0 -0.41 2 2
FYN -0.004 0.1 -10000 0 -0.44 11 11
DOK1 0.017 0.022 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.013 0.23 1 -10000 0 1
PDGFB 0.022 0.02 0.35 1 -10000 0 1
RAC1 -0.018 0.18 -10000 0 -0.5 27 27
PRKCD 0.016 0.021 -10000 0 -10000 0 0
FER 0.016 0.021 -10000 0 -10000 0 0
MAPKKK cascade 0.053 0.097 0.39 8 -10000 0 8
RASA1 0.012 0.043 -10000 0 -0.42 2 2
NCK1 0.019 0.044 -10000 0 -0.69 1 1
NCK2 0.023 0.02 0.35 1 -10000 0 1
p62DOK/Csk 0.035 0.029 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.034 0.041 0.25 5 -0.42 1 6
chemotaxis -0.003 0.097 -10000 0 -0.39 6 6
STAT1-3-5/STAT1-3-5 0.051 0.029 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.019 0.033 0.23 6 -10000 0 6
PTPRJ 0.022 0 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.011 0.087 -10000 0 -0.69 4 4
ITGA4 0.015 0.078 0.35 1 -0.69 3 4
alpha4/beta7 Integrin 0.018 0.09 -10000 0 -0.52 7 7
alpha4/beta1 Integrin 0.025 0.061 -10000 0 -0.52 3 3
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.054 0.041 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.021 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.052 0.035 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.024 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.046 0.081 -10000 0 -0.44 2 2
CaM/Ca2+ 0.054 0.038 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.035 0.033 -10000 0 -10000 0 0
AKT1 0.019 0.059 -10000 0 -0.77 1 1
MAP2K1 0.018 0.037 0.28 2 -10000 0 2
MAP3K11 0.023 0.036 0.28 2 -10000 0 2
IFNGR1 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.2 -10000 0 -0.45 23 23
Rap1/GTP 0.016 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.031 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.063 0.042 -10000 0 -10000 0 0
CEBPB 0.028 0.086 0.39 1 -0.5 3 4
STAT3 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.039 0.16 -10000 0 -0.82 8 8
STAT1 0.023 0.032 -10000 0 -10000 0 0
CALM1 0.021 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.032 0.059 0.34 9 -10000 0 9
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
STAT1 (dimer)/PIAS1 0.035 0.036 -10000 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0.03 0.053 -10000 0 -0.4 1 1
mol:Ca2+ 0.051 0.039 -10000 0 -10000 0 0
MAPK3 0.018 0.1 -10000 0 -0.73 4 4
STAT1 (dimer) -0.054 0.12 -10000 0 -0.7 2 2
MAPK1 0.015 0.11 -10000 0 -0.71 5 5
JAK2 0.021 0.026 -10000 0 -0.39 1 1
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
JAK1 0.022 0.006 -10000 0 -10000 0 0
CAMK2D 0.02 0.005 -10000 0 -10000 0 0
DAPK1 0.024 0.079 0.34 1 -0.55 3 4
SMAD7 -0.017 0.059 0.27 1 -0.38 2 3
CBL/CRKL/C3G 0.043 0.035 -10000 0 -10000 0 0
PI3K 0.049 0.064 -10000 0 -0.86 1 1
IFNG 0.032 0.059 0.34 9 -10000 0 9
apoptosis 0.013 0.071 -10000 0 -0.43 4 4
CAMK2G 0.021 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.003 -10000 0 -10000 0 0
CAMK2A 0.044 0.085 0.35 19 -10000 0 19
CAMK2B -0.32 0.35 -10000 0 -0.69 125 125
FRAP1 0.011 0.055 -10000 0 -0.7 1 1
PRKCD 0.02 0.061 -10000 0 -0.79 1 1
RAP1B 0.021 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.046 0.081 -10000 0 -0.44 2 2
PTPN2 0.021 0.003 -10000 0 -10000 0 0
EP300 0.022 0.003 -10000 0 -10000 0 0
IRF1 0.021 0.049 0.41 1 -10000 0 1
STAT1 (dimer)/PIASy 0.033 0.038 -10000 0 -10000 0 0
SOCS1 -0.01 0.2 -10000 0 -1.1 8 8
mol:GDP 0.037 0.027 -10000 0 -10000 0 0
CASP1 -0.017 0.053 0.27 1 -0.23 1 2
PTGES2 0.023 0.02 0.35 1 -10000 0 1
IRF9 0.026 0.03 0.21 1 -10000 0 1
mol:PI-3-4-5-P3 0.035 0.058 -10000 0 -0.81 1 1
RAP1/GDP 0.034 0.019 -10000 0 -10000 0 0
CBL 0.021 0.032 0.29 1 -10000 0 1
MAP3K1 0.023 0.036 0.28 2 -10000 0 2
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PIAS4 0.021 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.046 0.081 -10000 0 -0.44 2 2
PTPN11 0.022 0.034 0.29 1 -10000 0 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.008 0.097 -10000 0 -0.69 5 5
positive regulation of NF-kappaB transcription factor activity 0.013 0.082 -10000 0 -0.52 6 6
MAP2K4 0.011 0.051 -10000 0 -10000 0 0
IKBKB 0.019 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.009 -10000 0 -10000 0 0
TNFRSF10A 0.008 0.079 -10000 0 -0.61 4 4
SMPD1 0.006 0.037 -10000 0 -0.25 5 5
IKBKG 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.015 0.044 -10000 0 -0.69 1 1
TRAIL/TRAILR2 0.015 0.076 -10000 0 -0.52 5 5
TRAIL/TRAILR3 0.016 0.082 -10000 0 -0.52 5 5
TRAIL/TRAILR1 0.008 0.096 -10000 0 -0.49 9 9
TRAIL/TRAILR4 0.013 0.083 -10000 0 -0.52 6 6
TRAIL/TRAILR1/DAP3/GTP 0.013 0.077 -10000 0 -0.39 8 8
IKK complex 0 0.063 -10000 0 -10000 0 0
RIPK1 0.02 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.013 0.007 -10000 0 -10000 0 0
MAPK3 0.003 0.073 -10000 0 -0.52 5 5
MAP3K1 0.011 0.057 -10000 0 -0.29 5 5
TRAILR4 (trimer) 0.015 0.044 -10000 0 -0.69 1 1
TRADD 0.019 0.026 -10000 0 -0.38 1 1
TRAILR1 (trimer) 0.008 0.079 -10000 0 -0.61 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.009 0.06 -10000 0 -0.3 8 8
CFLAR 0.021 0.002 -10000 0 -10000 0 0
MAPK1 0.003 0.073 -10000 0 -0.52 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.03 0.083 -10000 0 -0.39 8 8
mol:ceramide 0.006 0.037 -10000 0 -0.25 5 5
FADD 0.021 0.004 -10000 0 -10000 0 0
MAPK8 0 0.098 -10000 0 -0.42 10 10
TRAF2 0.021 0.003 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.02 0.044 0.35 3 -0.38 1 4
CHUK 0.021 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.018 0.087 -10000 0 -0.45 8 8
DAP3 0.017 0.009 -10000 0 -10000 0 0
CASP10 -0.002 0.07 0.26 1 -0.44 5 6
JNK cascade 0.013 0.082 -10000 0 -0.52 6 6
TRAIL (trimer) 0.008 0.097 -10000 0 -0.69 5 5
TNFRSF10C 0.02 0.044 0.35 3 -0.38 1 4
TRAIL/TRAILR1/DAP3/GTP/FADD 0.019 0.075 -10000 0 -0.39 7 7
TRAIL/TRAILR2/FADD 0.024 0.069 -10000 0 -0.45 5 5
cell death 0.006 0.036 -10000 0 -0.25 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.048 -10000 0 -0.3 5 5
TRAILR2 (trimer) 0.017 0.008 -10000 0 -10000 0 0
CASP8 0.011 0.019 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.036 0.068 -10000 0 -0.39 5 5
ceramide 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
MAP4K4 0.01 0.074 -10000 0 -10000 0 0
BAG4 0 0.1 -10000 0 -0.57 8 8
BAD 0.014 0.037 -10000 0 -10000 0 0
NFKBIA 0.021 0.002 -10000 0 -10000 0 0
BIRC3 0.029 0.074 0.35 9 -0.69 1 10
BAX 0.016 0.041 0.2 2 -10000 0 2
EnzymeConsortium:3.1.4.12 0.007 0.026 0.079 2 -10000 0 2
IKBKB 0.012 0.077 0.32 1 -10000 0 1
MAP2K2 0.017 0.05 0.24 4 -10000 0 4
MAP2K1 0.016 0.048 0.23 3 -10000 0 3
SMPD1 0.009 0.027 -10000 0 -0.14 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.022 0.087 0.32 1 -10000 0 1
MAP2K4 0.016 0.035 -10000 0 -10000 0 0
protein ubiquitination 0.017 0.082 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.018 0.052 0.25 3 -10000 0 3
response to UV 0 0.001 0.003 3 -10000 0 3
RAF1 0.016 0.047 0.24 3 -10000 0 3
CRADD 0.019 0.044 -10000 0 -0.69 1 1
mol:ceramide 0.015 0.039 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0.029 0.005 -10000 0 -10000 0 0
MADD 0.022 0.001 -10000 0 -10000 0 0
MAP3K1 0.014 0.039 -10000 0 -10000 0 0
TRADD 0.019 0.026 -10000 0 -0.39 1 1
RELA/p50 0.021 0.003 -10000 0 -10000 0 0
MAPK3 0.019 0.051 0.25 3 -10000 0 3
MAPK1 0.018 0.052 0.25 3 -10000 0 3
p50/RELA/I-kappa-B-alpha 0.031 0.005 -10000 0 -10000 0 0
FADD 0.013 0.081 0.32 1 -10000 0 1
KSR1 0.016 0.045 0.24 3 -10000 0 3
MAPK8 0.001 0.072 -10000 0 -0.32 10 10
TRAF2 0.021 0.003 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.016 0.074 -10000 0 -10000 0 0
TNF R/SODD 0.014 0.08 -10000 0 -0.45 7 7
TNF -0.007 0.14 0.35 2 -0.69 11 13
CYCS 0.017 0.038 0.15 1 -10000 0 1
IKBKG 0.017 0.082 0.31 1 -10000 0 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.01 0.079 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
RIPK1 0.02 0.006 -10000 0 -10000 0 0
AIFM1 0.016 0.039 -10000 0 -10000 0 0
TNF/TNF R/SODD 0.005 0.12 -10000 0 -0.45 16 16
TNFRSF1A 0.021 0.004 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.075 -10000 0 -0.61 3 3
NSMAF 0.011 0.075 0.31 1 -10000 0 1
response to hydrogen peroxide 0 0.001 0.003 3 -10000 0 3
BCL2 0.021 0.003 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.021 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.008 -10000 0 -10000 0 0
DOCK1 0.007 0.097 -10000 0 -0.69 5 5
ITGA4 0.015 0.078 0.35 1 -0.69 3 4
RAC1 0.021 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.018 0.09 -10000 0 -0.52 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.055 -10000 0 -0.45 3 3
alpha4/beta7 Integrin/Paxillin 0.026 0.074 -10000 0 -0.41 7 7
lamellipodium assembly 0.008 0.082 -10000 0 -0.54 3 3
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
PI3K 0.028 0.06 -10000 0 -0.93 1 1
ARF6 0.021 0.003 -10000 0 -10000 0 0
TLN1 0.021 0.003 -10000 0 -10000 0 0
PXN 0.013 0.002 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
ARF6/GTP 0.04 0.046 -10000 0 -0.36 3 3
cell adhesion 0.041 0.049 -10000 0 -0.39 3 3
CRKL/CBL 0.03 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.032 0.05 -10000 0 -0.42 3 3
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.011 0.087 -10000 0 -0.69 4 4
ARF6/GDP 0.02 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.02 0.12 -10000 0 -0.44 14 14
p130Cas/Crk/Dock1 0.029 0.064 -10000 0 -0.41 5 5
VCAM1 -0.016 0.17 0.35 3 -0.69 15 18
alpha4/beta1 Integrin/Paxillin/Talin 0.042 0.05 -10000 0 -0.39 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 0.043 0.05 -10000 0 -0.39 3 3
BCAR1 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.041 0.049 0.39 3 -10000 0 3
CBL 0.021 0.004 -10000 0 -10000 0 0
PRKACA 0.021 0.003 -10000 0 -10000 0 0
GIT1 0.021 0.002 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.042 0.05 -10000 0 -0.39 3 3
Rac1/GTP 0.007 0.093 -10000 0 -0.62 3 3
Arf6 trafficking events

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
SLC2A4 0.019 0.11 0.35 9 -0.69 4 13
CLTC 0.013 0.05 -10000 0 -0.35 4 4
calcium ion-dependent exocytosis 0.004 0.049 -10000 0 -0.2 10 10
Dynamin 2/GTP 0.023 0.012 -10000 0 -10000 0 0
EXOC4 0.021 0.005 -10000 0 -10000 0 0
CD59 0.01 0.038 -10000 0 -0.3 3 3
CPE 0.018 0.033 0.2 8 -10000 0 8
CTNNB1 0.022 0 -10000 0 -10000 0 0
membrane fusion 0.004 0.04 -10000 0 -0.19 10 10
CTNND1 0.018 0.03 -10000 0 -10000 0 0
DNM2 0.021 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.01 0.037 -10000 0 -0.21 1 1
TSHR 0.012 0.003 -10000 0 -10000 0 0
INS 0.01 0.049 -10000 0 -0.46 2 2
BIN1 0.019 0.044 -10000 0 -0.69 1 1
mol:Choline 0.004 0.04 -10000 0 -0.19 10 10
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.017 0.2 2 -10000 0 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.021 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.012 -10000 0 -10000 0 0
JUP 0.01 0.038 -10000 0 -0.3 3 3
ASAP2/amphiphysin II 0.039 0.031 -10000 0 -0.41 1 1
ARF6/GTP 0.016 0.002 -10000 0 -10000 0 0
CDH1 -0.004 0.07 -10000 0 -0.28 15 15
clathrin-independent pinocytosis 0.016 0.002 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.016 0.002 -10000 0 -10000 0 0
EXOC2 0.02 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.022 0.017 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.018 0.071 0.29 3 -10000 0 3
positive regulation of phagocytosis 0.012 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.027 0.007 -10000 0 -10000 0 0
ACAP1 0.01 0.038 -10000 0 -0.23 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.004 0.048 -10000 0 -0.29 6 6
clathrin heavy chain/ACAP1 0.013 0.052 0.25 2 -0.28 4 6
JIP4/KLC1 0.038 0.012 -10000 0 -10000 0 0
EXOC1 0.021 0.003 -10000 0 -10000 0 0
exocyst 0.022 0.018 -10000 0 -10000 0 0
RALA/GTP 0.016 0.002 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.028 0.006 -10000 0 -10000 0 0
receptor recycling 0.016 0.002 -10000 0 -10000 0 0
CTNNA1 0.018 0.03 -10000 0 -10000 0 0
NME1 0.014 0.017 0.2 2 -10000 0 2
clathrin coat assembly 0.015 0.051 -10000 0 -0.34 4 4
IL2RA 0.008 0.053 -10000 0 -0.28 7 7
VAMP3 0.012 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.073 -10000 0 -0.31 6 6
EXOC6 0.021 0.003 -10000 0 -10000 0 0
PLD1 -0.002 0.072 -10000 0 -0.33 12 12
PLD2 0.012 0.005 -10000 0 -10000 0 0
EXOC5 0.021 0.003 -10000 0 -10000 0 0
PIP5K1C 0.01 0.031 -10000 0 -0.21 1 1
SDC1 0.006 0.05 -10000 0 -0.27 7 7
ARF6/GDP 0.021 0.013 -10000 0 -10000 0 0
EXOC7 0.021 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.02 0.073 -10000 0 -0.32 1 1
mol:Phosphatidic acid 0.004 0.04 -10000 0 -0.19 10 10
endocytosis -0.038 0.031 0.41 1 -10000 0 1
SCAMP2 0.021 0.003 -10000 0 -10000 0 0
ADRB2 -0.037 0.15 -10000 0 -0.37 39 39
EXOC3 0.021 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.02 0.35 1 -10000 0 1
Dynamin 2/GDP 0.026 0.015 -10000 0 -10000 0 0
KLC1 0.021 0.004 -10000 0 -10000 0 0
AVPR2 0.022 0.061 0.36 1 -0.33 4 5
RALA 0.021 0.003 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.071 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.041 0.034 -10000 0 -0.37 1 1
TC10/GTP 0.034 0.031 -10000 0 -0.36 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.055 0.027 -10000 0 -10000 0 0
HRAS 0.023 0.02 0.35 1 -10000 0 1
APS homodimer 0.023 0.029 0.35 2 -10000 0 2
GRB14 0.002 0.11 -10000 0 -0.69 7 7
FOXO3 -0.035 0.19 -10000 0 -0.65 22 22
AKT1 0.001 0.072 -10000 0 -0.63 1 1
INSR 0.023 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.035 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.003 -10000 0 -10000 0 0
SORBS1 0.018 0.044 -10000 0 -0.69 1 1
CRK 0.019 0.007 -10000 0 -10000 0 0
PTPN1 0.01 0.015 -10000 0 -10000 0 0
CAV1 0.014 0.012 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G 0.053 0.04 -10000 0 -0.39 1 1
Insulin Receptor/Insulin/IRS1/NCK2 0.056 0.029 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.051 -10000 0 -0.73 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.022 0.038 -10000 0 -10000 0 0
RPS6KB1 -0.012 0.064 -10000 0 -0.57 1 1
PARD6A 0.022 0.021 0.35 1 -10000 0 1
CBL 0.021 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.013 0.008 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.023 0.068 -10000 0 -0.57 1 1
HRAS/GTP 0.012 0.008 -10000 0 -10000 0 0
Insulin Receptor 0.023 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.048 0.035 -10000 0 -10000 0 0
PRKCI 0.023 0.047 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.014 0.077 -10000 0 -0.4 8 8
SHC1 0.017 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.032 0.056 -10000 0 -0.56 2 2
PI3K 0.051 0.054 -10000 0 -0.74 1 1
NCK2 0.023 0.02 0.35 1 -10000 0 1
RHOQ 0.021 0.002 -10000 0 -10000 0 0
mol:H2O2 0 0.001 -10000 0 -10000 0 0
HRAS/GDP 0.017 0.013 0.23 1 -10000 0 1
AKT2 0.002 0.071 -10000 0 -0.63 1 1
PRKCZ -0.025 0.15 -10000 0 -0.61 11 11
SH2B2 0.023 0.029 0.35 2 -10000 0 2
SHC/SHIP 0.021 0.018 -10000 0 -10000 0 0
F2RL2 -0.038 0.22 0.35 7 -0.69 25 32
TRIP10 0.021 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.026 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.048 0.034 -10000 0 -10000 0 0
RAPGEF1 0.021 0.003 -10000 0 -10000 0 0
RASA1 0.016 0.062 -10000 0 -0.69 2 2
NCK1 0.019 0.044 -10000 0 -0.69 1 1
CBL/APS/CAP/Crk-II 0.046 0.039 -10000 0 -0.42 1 1
TC10/GDP 0.016 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.031 -10000 0 -10000 0 0
INPP5D 0.013 0.024 -10000 0 -0.32 1 1
SOS1 0.022 0.001 -10000 0 -10000 0 0
SGK1 -0.051 0.22 -10000 0 -0.79 21 21
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.002 -10000 0 -10000 0 0
IRS1 0.021 0.002 -10000 0 -10000 0 0
p62DOK/RasGAP 0.032 0.057 -10000 0 -0.57 2 2
INS 0.023 0.045 0.34 5 -10000 0 5
mol:PI-3-4-P2 0.013 0.024 -10000 0 -0.32 1 1
GRB2 0.021 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.011 0.064 -10000 0 -0.57 1 1
PTPRA 0.023 0.004 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
TC10/GTP/CIP4 0.029 0.004 -10000 0 -10000 0 0
PDPK1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.021 0.017 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.042 0.026 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.034 0.03 -10000 0 -10000 0 0
Par3/Par6 0.011 0.13 -10000 0 -0.39 25 25
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.021 0.003 -10000 0 -10000 0 0
SMAD2 0.001 0.027 -10000 0 -10000 0 0
SMAD3 0.021 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4 0.032 0.045 -10000 0 -0.39 2 2
SMAD4/Ubc9/PIASy 0.041 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.035 -10000 0 -10000 0 0
PPM1A 0.021 0.003 -10000 0 -10000 0 0
CALM1 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.013 0.027 -10000 0 -10000 0 0
MAP3K1 0.022 0 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.007 0.11 -10000 0 -0.5 12 12
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.021 0.003 -10000 0 -10000 0 0
NUP214 0.021 0.003 -10000 0 -10000 0 0
CTDSP1 0.021 0.003 -10000 0 -10000 0 0
CTDSP2 0.021 0.003 -10000 0 -10000 0 0
CTDSPL 0.022 0 -10000 0 -10000 0 0
KPNB1 0.021 0.003 -10000 0 -10000 0 0
TGFBRAP1 -0.01 0.14 -10000 0 -0.66 12 12
UBE2I 0.021 0.004 -10000 0 -10000 0 0
NUP153 0.02 0.006 -10000 0 -10000 0 0
KPNA2 0.022 0.021 0.35 1 -10000 0 1
PIAS4 0.021 0.003 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.028 0.092 -10000 0 -0.34 4 4
ERC1 0.021 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.016 0.068 -10000 0 -0.52 4 4
NFKBIA 0.017 0.013 -10000 0 -10000 0 0
BIRC2 0.021 0.004 -10000 0 -10000 0 0
IKBKB 0.019 0.007 -10000 0 -10000 0 0
RIPK2 0.017 0.009 -10000 0 -10000 0 0
IKBKG 0.015 0.04 -10000 0 -0.39 1 1
IKK complex/A20 0.026 0.12 -10000 0 -0.46 4 4
NEMO/A20/RIP2 0.017 0.009 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.029 0.097 -10000 0 -0.43 5 5
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.021 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.029 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.027 0.09 -10000 0 -0.42 4 4
BCL10/MALT1/TRAF6 0.04 0.032 -10000 0 -0.45 1 1
NOD2 0.01 0.087 -10000 0 -0.69 4 4
NFKB1 0.022 0.006 -10000 0 -10000 0 0
RELA 0.023 0.003 -10000 0 -10000 0 0
MALT1 0.021 0.003 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.029 0.009 -10000 0 -10000 0 0
ATM 0.021 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.007 0.11 -10000 0 -0.52 11 11
TRAF6 0.019 0.044 -10000 0 -0.69 1 1
PRKCA 0.021 0.004 -10000 0 -10000 0 0
CHUK 0.021 0.004 -10000 0 -10000 0 0
UBE2D3 0.02 0.006 -10000 0 -10000 0 0
TNF -0.007 0.14 0.35 2 -0.69 11 13
NF kappa B1 p50/RelA 0.046 0.015 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.013 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.034 0.098 -10000 0 -0.44 4 4
CYLD 0.021 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.041 0.094 -10000 0 -0.43 4 4
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.023 0.11 -10000 0 -0.44 11 11
Ran/GTP/Exportin 1/HDAC1 0.006 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.094 -10000 0 -0.39 11 11
SUMO1 0.021 0.002 -10000 0 -10000 0 0
ZFPM1 0.018 0.044 -10000 0 -0.69 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.024 -10000 0 -0.37 1 1
FKBP3 0.022 0.001 -10000 0 -10000 0 0
Histones 0.043 0.058 -10000 0 -10000 0 0
YY1/LSF 0.016 0.051 -10000 0 -0.28 3 3
SMG5 0.017 0.009 -10000 0 -10000 0 0
RAN 0.021 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.009 0.071 -10000 0 -0.32 11 11
I kappa B alpha/HDAC1 0.017 0.052 -10000 0 -10000 0 0
SAP18 0.021 0.004 -10000 0 -10000 0 0
RELA 0.014 0.073 -10000 0 -0.3 11 11
HDAC1/Smad7 0.037 0.038 -10000 0 -0.36 2 2
RANGAP1 0.021 0.003 -10000 0 -10000 0 0
HDAC3/TR2 0.017 0.053 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.019 0.032 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.019 0.079 -10000 0 -0.41 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.019 0.068 0.35 2 -0.69 2 4
GATA1 0.021 0.035 0.35 3 -10000 0 3
Mad/Max 0.032 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.01 0.064 -10000 0 -0.32 2 2
RBBP7 0.021 0.003 -10000 0 -10000 0 0
NPC 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.021 0.004 -10000 0 -10000 0 0
MAX 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.021 0.003 -10000 0 -10000 0 0
NFKBIA 0.009 0.054 -10000 0 -10000 0 0
KAT2B 0.013 0.075 -10000 0 -0.69 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.023 0.026 -10000 0 -0.36 1 1
SIN3 complex 0.05 0.018 -10000 0 -10000 0 0
SMURF1 0.02 0.005 -10000 0 -10000 0 0
CHD3 0.027 0.054 0.35 7 -10000 0 7
SAP30 0.02 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.016 0.036 -10000 0 -0.38 2 2
YY1/HDAC3 0.009 0.063 -10000 0 -10000 0 0
YY1/HDAC2 0.016 0.05 -10000 0 -0.28 3 3
YY1/HDAC1 0.018 0.048 -10000 0 -0.28 3 3
NuRD/MBD2 Complex (MeCP1) 0.018 0.037 -10000 0 -10000 0 0
PPARG 0.002 0.096 -10000 0 -0.45 10 10
HDAC8/hEST1B 0.034 0.018 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.003 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.019 0.051 -10000 0 -10000 0 0
MBD3L2 0.014 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.037 -10000 0 -0.35 2 2
CREBBP 0.021 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.025 0.066 -10000 0 -0.33 1 1
HDAC1 0.021 0.004 -10000 0 -10000 0 0
HDAC3 0.009 0.054 -10000 0 -10000 0 0
HDAC2 0.021 0.005 -10000 0 -10000 0 0
YY1 0.014 0.037 -10000 0 -0.32 3 3
HDAC8 0.022 0 -10000 0 -10000 0 0
SMAD7 0.016 0.062 -10000 0 -0.69 2 2
NCOR2 0.021 0.003 -10000 0 -10000 0 0
MXD1 0.023 0.02 0.35 1 -10000 0 1
STAT3 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.02 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.028 0.05 -10000 0 -10000 0 0
YY1/SAP30/HDAC1 0.028 0.048 -10000 0 -0.26 2 2
EP300 0.021 0.003 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.019 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.054 -10000 0 -10000 0 0
histone deacetylation 0.015 0.046 -10000 0 -0.25 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.017 0.05 -10000 0 -10000 0 0
nuclear export -0.034 0.018 -10000 0 -10000 0 0
PRKACA 0.021 0.003 -10000 0 -10000 0 0
GATAD2B 0.017 0.009 -10000 0 -10000 0 0
GATAD2A 0.021 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.016 0.068 -10000 0 -0.4 2 2
GATA1/HDAC1 0.031 0.024 0.25 3 -10000 0 3
GATA1/HDAC3 0.017 0.059 -10000 0 -10000 0 0
CHD4 0.021 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.007 0.11 -10000 0 -0.52 11 11
SIN3/HDAC complex/Mad/Max 0.024 0.032 -10000 0 -0.35 1 1
NuRD Complex 0.027 0.064 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.04 0.057 -10000 0 -10000 0 0
SIN3B 0.021 0.003 -10000 0 -10000 0 0
MTA2 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.033 -10000 0 -0.34 1 1
HDAC complex 0.051 0.016 -10000 0 -10000 0 0
GATA1/Fog1 0.028 0.042 0.25 3 -0.52 1 4
FKBP25/HDAC1/HDAC2 0.041 0.012 -10000 0 -10000 0 0
TNF -0.007 0.14 0.35 2 -0.69 11 13
negative regulation of cell growth 0.016 0.057 -10000 0 -0.35 1 1
NuRD/MBD2/PRMT5 Complex 0.018 0.037 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.036 -10000 0 -0.33 1 1
NF kappa B/RelA/I kappa B alpha 0 0.093 -10000 0 -0.4 12 12
SIN3/HDAC complex/NCoR1 0.006 0.068 -10000 0 -0.29 9 9
TFCP2 0.021 0.002 -10000 0 -10000 0 0
NR2C1 0.021 0.002 -10000 0 -10000 0 0
MBD3 0.021 0.003 -10000 0 -10000 0 0
MBD2 0.021 0.003 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.031 0.006 -10000 0 -10000 0 0
FBXW11 0.021 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.009 0.076 -10000 0 -0.44 7 7
NF kappa B1 p50/RelA/I kappa B alpha 0.019 0.061 -10000 0 -0.58 1 1
NFKBIA 0.005 0.058 -10000 0 -0.32 6 6
MAPK14 0.02 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.01 -10000 0 -10000 0 0
ARRB2 0.011 0.005 -10000 0 -10000 0 0
REL 0.003 0.11 -10000 0 -0.69 7 7
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.01 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
NF kappa B1 p50 dimer 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
NFKB1 0.011 0.005 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.007 0.058 -10000 0 -0.32 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.016 0.063 -10000 0 -0.6 1 1
SRC 0.023 0.02 0.35 1 -10000 0 1
PI3K 0.028 0.06 -10000 0 -0.93 1 1
NF kappa B1 p50/RelA 0.007 0.058 -10000 0 -0.32 6 6
IKBKB 0.019 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.003 -10000 0 -10000 0 0
SYK 0.019 0.044 -10000 0 -0.69 1 1
I kappa B alpha/PIK3R1 0.018 0.071 -10000 0 -0.5 2 2
cell death 0.016 0.061 -10000 0 -0.57 1 1
NF kappa B1 p105/c-Rel 0.009 0.076 -10000 0 -0.44 7 7
LCK 0 0.12 0.35 1 -0.69 8 9
BCL3 0.021 0.003 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.014 0.085 -10000 0 -0.45 8 8
VEGFR1 homodimer/NRP1 0.012 0.003 -10000 0 -10000 0 0
mol:DAG 0.017 0.019 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.028 0.018 -10000 0 -10000 0 0
HIF1A 0.026 0.004 -10000 0 -10000 0 0
GAB1 0.021 0.005 -10000 0 -10000 0 0
AKT1 0.015 0.049 -10000 0 -0.72 1 1
PLCG1 0.017 0.019 -10000 0 -10000 0 0
NOS3 0.017 0.048 -10000 0 -0.44 1 1
CBL 0.021 0.004 -10000 0 -10000 0 0
mol:NO 0.017 0.062 -10000 0 -0.43 2 2
FLT1 0.016 0.005 -10000 0 -10000 0 0
PGF 0.024 0.035 0.35 3 -10000 0 3
VEGFR1 homodimer/NRP2/VEGFR121 0.032 0.043 -10000 0 -0.4 2 2
CALM1 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.019 0.044 -10000 0 -0.69 1 1
eNOS/Hsp90 0.027 0.064 -10000 0 -10000 0 0
endothelial cell proliferation -0.006 0.089 -10000 0 -0.42 2 2
mol:Ca2+ 0.017 0.019 -10000 0 -10000 0 0
MAPK3 0.006 0.015 -10000 0 -10000 0 0
MAPK1 0.006 0.015 -10000 0 -10000 0 0
PIK3R1 0.019 0.044 -10000 0 -0.69 1 1
PLGF homodimer 0.024 0.035 0.35 3 -10000 0 3
PRKACA 0.021 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.021 0.005 -10000 0 -10000 0 0
VEGFA homodimer 0.019 0.007 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.011 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.004 0.014 -10000 0 -10000 0 0
PI3K 0.046 0.056 -10000 0 -0.76 1 1
PRKCA 0.01 0.016 -10000 0 -10000 0 0
PRKCB -0.021 0.11 -10000 0 -0.39 15 15
VEGFR1 homodimer/PLGF homodimer 0.029 0.025 -10000 0 -10000 0 0
VEGFA 0.019 0.007 -10000 0 -10000 0 0
VEGFB 0.002 0.13 0.35 2 -0.69 8 10
mol:IP3 0.017 0.019 -10000 0 -10000 0 0
RASA1 0.001 0.084 -10000 0 -0.41 10 10
NRP2 0.017 0.065 0.35 1 -0.69 2 3
VEGFR1 homodimer 0.016 0.005 -10000 0 -10000 0 0
VEGFB homodimer 0.002 0.12 0.35 2 -0.69 8 10
NCK1 0.019 0.044 -10000 0 -0.69 1 1
eNOS/Caveolin-1 0.022 0.065 -10000 0 -0.41 1 1
PTPN11 0.021 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.045 0.055 -10000 0 -0.74 1 1
mol:L-citrulline 0.017 0.062 -10000 0 -0.43 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.043 0.021 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.033 0.032 -10000 0 -0.41 1 1
CD2AP 0.02 0.005 -10000 0 -10000 0 0
PI3K/GAB1 0.052 0.056 -10000 0 -0.73 1 1
PDPK1 0.016 0.048 -10000 0 -0.71 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.034 0.016 -10000 0 -10000 0 0
mol:NADP 0.017 0.062 -10000 0 -0.43 2 2
HSP90AA1 0.021 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.042 0.02 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.024 0.044 -10000 0 -0.44 2 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0.019 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.053 0.2 1 -0.23 2 3
AP2 0.031 0.006 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.026 0.01 -10000 0 -10000 0 0
CLTB 0.021 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.015 0.009 -10000 0 -10000 0 0
CD4 -0.032 0.18 -10000 0 -0.67 20 20
CLTA 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
ARFGAP1 0.007 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.005 0.004 -10000 0 -10000 0 0
ARF1/GTP 0.02 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.01 0.006 -10000 0 -10000 0 0
mol:Choline 0.004 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.019 0.01 -10000 0 -10000 0 0
DDEF1 0.004 0.003 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.021 -10000 0 -10000 0 0
AP2M1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.007 -10000 0 -10000 0 0
Rac/GTP 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.015 -10000 0 -10000 0 0
ARFIP2 0.012 0.015 -10000 0 -10000 0 0
COPA 0.017 0.009 -10000 0 -10000 0 0
RAC1 0.021 0.003 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.011 0.019 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.012 0.007 -10000 0 -10000 0 0
GGA3 0.021 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.012 -10000 0 -10000 0 0
AP2A1 0.021 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.013 0.008 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.015 0.015 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.023 0.011 -10000 0 -10000 0 0
CYTH2 0.026 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.024 0.013 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.016 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.001 0.065 -10000 0 -0.26 13 13
PLD2 0.004 0.003 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.001 -10000 0 -10000 0 0
PIP5K1A 0.005 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.009 0.024 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.003 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.001 -10000 0 -10000 0 0
GOSR2 0.008 0.006 -10000 0 -10000 0 0
USO1 0.002 0.045 -10000 0 -0.32 5 5
GBF1 0.008 0.006 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.023 0.014 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.004 0.13 -10000 0 -0.45 19 19
Circadian rhythm pathway

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
chromatin modification 0.045 0.036 -10000 0 -10000 0 0
CLOCK 0.02 0.044 -10000 0 -0.68 1 1
TIMELESS/CRY2 0.032 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.027 0.006 -10000 0 -10000 0 0
ATR 0.021 0.002 -10000 0 -10000 0 0
NR1D1 0.015 0.088 -10000 0 -1.4 1 1
ARNTL 0.023 0.005 -10000 0 -10000 0 0
TIMELESS 0.019 0.027 -10000 0 -10000 0 0
NPAS2 0.02 0.044 -10000 0 -0.68 1 1
CRY2 0.022 0 -10000 0 -10000 0 0
mol:CO -0.007 0.009 0.14 1 -10000 0 1
CHEK1 0.027 0.045 0.35 5 -10000 0 5
mol:HEME 0.007 0.009 -10000 0 -0.14 1 1
PER1 0.019 0.007 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.047 0.046 -10000 0 -0.45 2 2
BMAL1/CLOCK 0.016 0.076 -10000 0 -0.88 1 1
S phase of mitotic cell cycle 0.045 0.036 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.046 0.037 -10000 0 -10000 0 0
mol:NADPH 0.007 0.009 -10000 0 -0.14 1 1
PER1/TIMELESS 0.028 0.029 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.014 0.002 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.004 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.029 0.037 -10000 0 -0.34 1 1
HDAC4 0.022 0.02 0.35 1 -10000 0 1
Ran/GTP/Exportin 1/HDAC1 0.004 0.009 -10000 0 -10000 0 0
SUMO1 0.021 0.002 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.018 -10000 0 -0.27 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.009 0.025 -10000 0 -0.35 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.029 0.036 -10000 0 -0.32 1 1
SUMO1/HDAC1 0.03 0.033 -10000 0 -0.34 1 1
RANGAP1 0.021 0.003 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.053 0.012 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.012 0.024 -10000 0 -0.37 1 1
Ran/GTP 0.019 0.035 -10000 0 -0.34 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.021 0.003 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.019 0.034 -10000 0 -0.33 1 1
NPC 0.013 0.001 -10000 0 -10000 0 0
PIAS2 0.021 0.003 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 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 0.031 0.007 -9999 0 -9999 0 0
FBXW11 0.021 0.003 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.003 -9999 0 -9999 0 0
CHUK 0.021 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.059 0.018 -9999 0 -9999 0 0
NFKB1 0.02 0.006 -9999 0 -9999 0 0
MAP3K14 0.021 0.003 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.029 0.009 -9999 0 -9999 0 0
RELB 0.021 0.003 -9999 0 -9999 0 0
NFKB2 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.028 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.027 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 262 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZS.A9CG TCGA.ZS.A9CF TCGA.ZS.A9CE TCGA.ZS.A9CD
109_MAP3K5 -0.18 -0.37 -0.23 0.063
47_PPARGC1A 0.022 0 0.022 0.022
105_BMP4 0.022 0.022 0.022 0.022
105_BMP6 0.022 0.022 0.022 0.022
105_BMP7 0.022 0.022 0.022 0.014
105_BMP2 0.022 0.022 0.022 0.022
131_RELN/VLDLR 0.056 -0.58 0.051 0.056
30_TGFB1/TGF beta receptor Type II 0.021 0.018 -0.016 0.021
84_STAT5B 0.097 0.12 0.031 0.03
84_STAT5A 0.097 0.12 0.031 0.03
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/LIHC-TP/11493539/LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LIHC-TP/11541427/GDAC_Gistic2Report_11548548/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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