PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1GQ6VT1
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1GQ6VT1
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 36 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 239
Signaling events mediated by Stem cell factor receptor (c-Kit) 160
Signaling events regulated by Ret tyrosine kinase 144
Reelin signaling pathway 127
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 109
Wnt signaling 100
PDGFR-alpha signaling pathway 95
FOXA2 and FOXA3 transcription factor networks 89
Noncanonical Wnt signaling pathway 86
Nongenotropic Androgen signaling 84
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 486 . 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 ( 486 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Ephrin A reverse signaling 0.4918 239 1679 7 -0.42 0 1000 -1000 -0.012 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3292 160 12515 78 -0.74 0.23 1000 -1000 -0.049 -1000
Signaling events regulated by Ret tyrosine kinase 0.2963 144 11815 82 -0.37 0.027 1000 -1000 -0.063 -1000
Reelin signaling pathway 0.2613 127 7132 56 -0.46 0.062 1000 -1000 -0.041 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2243 109 7468 68 -0.73 0.35 1000 -1000 -0.058 -1000
Wnt signaling 0.2058 100 700 7 -0.33 0.014 1000 -1000 -0.021 -1000
PDGFR-alpha signaling pathway 0.1955 95 4181 44 -0.41 0.043 1000 -1000 -0.05 -1000
FOXA2 and FOXA3 transcription factor networks 0.1831 89 4132 46 -0.85 0.031 1000 -1000 -0.063 -1000
Noncanonical Wnt signaling pathway 0.1770 86 2246 26 -0.33 0.027 1000 -1000 -0.046 -1000
Nongenotropic Androgen signaling 0.1728 84 4412 52 -0.26 0.19 1000 -1000 -0.032 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1584 77 4188 54 -0.46 0.039 1000 -1000 -0.05 -1000
Signaling events mediated by the Hedgehog family 0.1584 77 4033 52 -0.29 0.14 1000 -1000 -0.044 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1358 66 2246 34 -0.11 0.027 1000 -1000 -0.033 -1000
Calcium signaling in the CD4+ TCR pathway 0.1317 64 2002 31 -0.35 0.027 1000 -1000 -0.047 -1000
Endothelins 0.1255 61 5920 96 -0.32 0.031 1000 -1000 -0.043 -1000
IL4-mediated signaling events 0.1235 60 5537 91 -1.2 0.56 1000 -1000 -0.072 -1000
Glypican 1 network 0.1235 60 2910 48 -0.3 0.052 1000 -1000 -0.025 -1000
IGF1 pathway 0.1132 55 3138 57 -0.14 0.064 1000 -1000 -0.059 -1000
HIF-1-alpha transcription factor network 0.1111 54 4159 76 -0.48 0.041 1000 -1000 -0.053 -1000
EPHB forward signaling 0.1111 54 4591 85 -0.24 0.11 1000 -1000 -0.063 -1000
Ephrin B reverse signaling 0.1091 53 2569 48 -0.24 0.12 1000 -1000 -0.029 -1000
TCR signaling in naïve CD8+ T cells 0.1008 49 4605 93 -0.16 0.047 1000 -1000 -0.053 -1000
IL23-mediated signaling events 0.1008 49 2998 60 -0.3 0.027 1000 -1000 -0.051 -1000
BMP receptor signaling 0.0988 48 3913 81 -0.45 0.052 1000 -1000 -0.048 -1000
Arf6 signaling events 0.0947 46 2877 62 -0.26 0.061 1000 -1000 -0.028 -1000
Coregulation of Androgen receptor activity 0.0926 45 3478 76 -0.67 0.075 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 0.0926 45 5199 114 -0.45 0.26 1000 -1000 -0.058 -1000
Signaling mediated by p38-alpha and p38-beta 0.0844 41 1811 44 -0.22 0.027 1000 -1000 -0.032 -1000
Hedgehog signaling events mediated by Gli proteins 0.0720 35 2326 65 -0.59 0.064 1000 -1000 -0.042 -1000
Thromboxane A2 receptor signaling 0.0700 34 3663 105 -0.16 0.052 1000 -1000 -0.047 -1000
Ras signaling in the CD4+ TCR pathway 0.0700 34 589 17 -0.11 0.041 1000 -1000 -0.025 -1000
IL12-mediated signaling events 0.0679 33 2872 87 -0.37 0.029 1000 -1000 -0.065 -1000
IL6-mediated signaling events 0.0638 31 2344 75 -0.16 0.053 1000 -1000 -0.052 -1000
EGFR-dependent Endothelin signaling events 0.0597 29 624 21 -0.073 0.038 1000 -1000 -0.043 -1000
Plasma membrane estrogen receptor signaling 0.0556 27 2356 86 -0.13 0.049 1000 -1000 -0.05 -1000
Osteopontin-mediated events 0.0535 26 995 38 -0.16 0.042 1000 -1000 -0.032 -1000
ErbB2/ErbB3 signaling events 0.0494 24 1572 65 -0.17 0.037 1000 -1000 -0.048 -1000
FAS signaling pathway (CD95) 0.0494 24 1135 47 -0.22 0.043 1000 -1000 -0.029 -1000
Regulation of p38-alpha and p38-beta 0.0494 24 1324 54 -0.36 0.065 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0473 23 1994 85 -0.22 0.13 1000 -1000 -0.051 -1000
Regulation of Androgen receptor activity 0.0473 23 1648 70 -0.44 0.035 1000 -1000 -0.05 -1000
LPA receptor mediated events 0.0453 22 2314 102 -0.16 0.035 1000 -1000 -0.07 -1000
Ceramide signaling pathway 0.0412 20 1552 76 -0.15 0.075 1000 -1000 -0.036 -1000
BCR signaling pathway 0.0412 20 2050 99 -0.1 0.049 1000 -1000 -0.063 -1000
Syndecan-4-mediated signaling events 0.0412 20 1405 67 -0.14 0.039 1000 -1000 -0.05 -1000
Syndecan-1-mediated signaling events 0.0391 19 678 34 -0.079 0.027 1000 -1000 -0.046 -1000
Fc-epsilon receptor I signaling in mast cells 0.0391 19 1855 97 -0.16 0.043 1000 -1000 -0.059 -1000
IFN-gamma pathway 0.0391 19 1347 68 -0.16 0.036 1000 -1000 -0.053 -1000
Integrins in angiogenesis 0.0370 18 1517 84 -0.14 0.055 1000 -1000 -0.041 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0370 18 1653 88 -0.26 0.039 1000 -1000 -0.061 -1000
amb2 Integrin signaling 0.0350 17 1411 82 -0.21 0.035 1000 -1000 -0.032 -1000
ceramide signaling pathway 0.0350 17 873 49 -0.059 0.039 1000 -1000 -0.041 -1000
VEGFR1 specific signals 0.0350 17 968 56 -0.045 0.058 1000 -1000 -0.044 -1000
Signaling events mediated by PTP1B 0.0329 16 1246 76 -0.19 0.041 1000 -1000 -0.037 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0329 16 860 52 -0.18 0.056 1000 -1000 -0.032 -1000
IL27-mediated signaling events 0.0329 16 832 51 -0.11 0.044 1000 -1000 -0.047 -1000
Visual signal transduction: Cones 0.0288 14 553 38 -0.044 0.043 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 0.0288 14 1793 125 -0.28 0.07 1000 -1000 -0.06 -1000
Aurora C signaling 0.0288 14 103 7 -0.005 0.045 1000 -1000 -0.012 -1000
IL1-mediated signaling events 0.0288 14 883 62 -0.082 0.061 1000 -1000 -0.05 -1000
FOXM1 transcription factor network 0.0288 14 741 51 -0.22 0.052 1000 -1000 -0.073 -1000
LPA4-mediated signaling events 0.0267 13 167 12 -0.054 0.005 1000 -1000 -0.025 -1000
Regulation of nuclear SMAD2/3 signaling 0.0267 13 1892 136 -0.26 0.052 1000 -1000 -0.042 -1000
JNK signaling in the CD4+ TCR pathway 0.0267 13 224 17 -0.081 0.03 1000 -1000 -0.037 -1000
mTOR signaling pathway 0.0267 13 695 53 -0.041 0.031 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class III 0.0267 13 534 40 -0.28 0.047 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0267 13 619 45 -0.059 0.076 1000 -1000 -0.044 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0267 13 1572 120 -0.24 0.074 1000 -1000 -0.05 -1000
Caspase cascade in apoptosis 0.0247 12 941 74 -0.059 0.045 1000 -1000 -0.041 -1000
Cellular roles of Anthrax toxin 0.0247 12 468 39 -0.059 0.027 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 0.0247 12 787 61 -0.16 0.07 1000 -1000 -0.042 -1000
Nectin adhesion pathway 0.0247 12 792 63 -0.11 0.073 1000 -1000 -0.04 -1000
Syndecan-3-mediated signaling events 0.0247 12 447 35 -0.11 0.069 1000 -1000 -0.024 -1000
Insulin Pathway 0.0247 12 909 74 -0.053 0.065 1000 -1000 -0.051 -1000
Rapid glucocorticoid signaling 0.0247 12 252 20 -0.06 0.034 1000 -1000 -0.009 -1000
ErbB4 signaling events 0.0226 11 809 69 -0.053 0.036 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 0.0226 11 689 58 -0.056 0.048 1000 -1000 -0.041 -1000
Visual signal transduction: Rods 0.0226 11 597 52 -0.071 0.048 1000 -1000 -0.031 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0206 10 284 28 -0.13 0.056 1000 -1000 -0.018 -1000
S1P1 pathway 0.0206 10 389 36 -0.062 0.027 1000 -1000 -0.034 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0206 10 762 74 -0.13 0.07 1000 -1000 -0.055 -1000
S1P3 pathway 0.0206 10 426 42 -0.13 0.048 1000 -1000 -0.028 -1000
Signaling events mediated by PRL 0.0206 10 343 34 -0.085 0.04 1000 -1000 -0.047 -1000
Syndecan-2-mediated signaling events 0.0185 9 687 69 -0.14 0.05 1000 -1000 -0.033 -1000
Retinoic acid receptors-mediated signaling 0.0185 9 550 58 -0.034 0.053 1000 -1000 -0.045 -1000
BARD1 signaling events 0.0165 8 463 57 -0.043 0.051 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 0.0165 8 223 26 -0.19 0.045 1000 -1000 -0.011 -1000
Class I PI3K signaling events 0.0165 8 610 73 -0.19 0.05 1000 -1000 -0.036 -1000
Regulation of Telomerase 0.0165 8 855 102 -0.19 0.071 1000 -1000 -0.04 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0144 7 625 83 -0.17 0.049 1000 -1000 -0.038 -1000
TCGA08_p53 0.0144 7 55 7 -0.025 0.025 1000 -1000 -0.009 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0144 7 263 33 -0.11 0.055 1000 -1000 -0.028 -1000
Class IB PI3K non-lipid kinase events 0.0144 7 21 3 -0.015 0.015 1000 -1000 -0.002 -1000
Aurora B signaling 0.0144 7 499 67 -0.33 0.1 1000 -1000 -0.029 -1000
PLK1 signaling events 0.0123 6 545 85 -0.006 0.048 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class I 0.0123 6 633 104 -0.059 0.062 1000 -1000 -0.03 -1000
TCGA08_retinoblastoma 0.0123 6 49 8 -0.033 0.031 1000 -1000 -0.001 -1000
a4b1 and a4b7 Integrin signaling 0.0103 5 26 5 0.007 0.035 1000 -1000 -0.003 -1000
IL2 signaling events mediated by STAT5 0.0103 5 131 22 -0.031 0.033 1000 -1000 -0.039 -1000
PDGFR-beta signaling pathway 0.0103 5 488 97 -0.14 0.079 1000 -1000 -0.06 -1000
S1P4 pathway 0.0103 5 137 25 -0.002 0.047 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 0.0082 4 163 39 -0.059 0.061 1000 -1000 -0.031 -1000
Insulin-mediated glucose transport 0.0082 4 141 32 -0.083 0.05 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0082 4 278 68 -0.083 0.05 1000 -1000 -0.041 -1000
S1P5 pathway 0.0082 4 84 17 -0.006 0.032 1000 -1000 -0.013 -1000
Signaling mediated by p38-gamma and p38-delta 0.0082 4 62 15 -0.001 0.027 1000 -1000 -0.034 -1000
Canonical Wnt signaling pathway 0.0082 4 231 51 -0.04 0.065 1000 -1000 -0.047 -1000
Effects of Botulinum toxin 0.0082 4 121 26 -0.066 0.048 1000 -1000 -0.008 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 4 561 125 -0.008 0.072 1000 -1000 -0.053 -1000
Circadian rhythm pathway 0.0062 3 86 22 -0.013 0.041 1000 -1000 -0.019 -1000
EPO signaling pathway 0.0062 3 172 55 -0.012 0.06 1000 -1000 -0.036 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0062 3 120 37 0 0.064 1000 -1000 -0.035 -1000
HIF-2-alpha transcription factor network 0.0062 3 156 43 -0.16 0.16 1000 -1000 -0.038 -1000
FoxO family signaling 0.0062 3 250 64 -0.083 0.1 1000 -1000 -0.04 -1000
Atypical NF-kappaB pathway 0.0062 3 119 31 -0.015 0.04 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 0.0062 3 135 43 -0.029 0.051 1000 -1000 -0.039 -1000
p38 MAPK signaling pathway 0.0062 3 159 44 -0.029 0.049 1000 -1000 -0.023 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0041 2 64 23 -0.016 0.049 1000 -1000 -0.034 -1000
Paxillin-dependent events mediated by a4b1 0.0041 2 83 36 -0.054 0.056 1000 -1000 -0.045 -1000
Signaling events mediated by HDAC Class II 0.0021 1 92 75 -0.036 0.074 1000 -1000 -0.023 -1000
Aurora A signaling 0.0021 1 113 60 -0.021 0.055 1000 -1000 -0.026 -1000
TRAIL signaling pathway 0.0021 1 85 48 -0.014 0.075 1000 -1000 -0.035 -1000
E-cadherin signaling in the nascent adherens junction 0.0021 1 148 76 -0.058 0.066 1000 -1000 -0.058 -1000
Arf6 trafficking events 0.0021 1 97 71 -0.048 0.05 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.016 0.027 1000 -1000 -0.018 -1000
Arf6 downstream pathway 0.0000 0 9 43 -0.059 0.046 1000 -1000 -0.034 -1000
Glypican 2 network 0.0000 0 0 4 -0.019 0.016 1000 -1000 0.002 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 15 27 0 0.066 1000 -1000 -0.031 -1000
E-cadherin signaling events 0.0000 0 0 5 0.026 0.051 1000 -1000 -0.001 -1000
Arf1 pathway 0.0000 0 26 54 -0.001 0.051 1000 -1000 -0.018 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.072 1000 -1000 -0.002 -1000
Total NA 3394 195558 7203 -22 8.1 131000 -131000 -4.9 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.32 0.26 -9999 0 -0.48 329 329
EFNA5 -0.073 0.24 -9999 0 -0.68 68 68
FYN -0.3 0.24 -9999 0 -0.45 322 322
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.48 329 329
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.26 -9999 0 -0.48 329 329
EPHA5 -0.42 0.33 -9999 0 -0.67 302 302
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.21 0.21 0.38 1 -0.39 267 268
CRKL -0.22 0.22 -10000 0 -0.41 273 273
HRAS -0.19 0.19 -10000 0 -0.4 98 98
mol:PIP3 -0.2 0.21 -10000 0 -0.39 245 245
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.025 0.032 -10000 0 -0.68 1 1
GAB1 -0.24 0.24 -10000 0 -0.44 273 273
FOXO3 -0.19 0.21 0.45 1 -0.37 236 237
AKT1 -0.2 0.22 0.3 1 -0.4 260 261
BAD -0.19 0.21 0.31 1 -0.37 233 234
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 283 283
GSK3B -0.19 0.21 0.36 1 -0.37 234 235
RAF1 -0.16 0.16 0.35 1 -0.35 65 66
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.23 0.23 -10000 0 -0.44 269 269
STAT1 -0.59 0.56 -10000 0 -1.1 276 276
HRAS/SPRED1 -0.16 0.16 -10000 0 -0.35 67 67
cell proliferation -0.24 0.24 -10000 0 -0.43 277 277
PIK3CA 0.022 0.055 -10000 0 -0.68 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.22 0.23 -10000 0 -0.42 274 274
HRAS/SPRED2 -0.16 0.16 -10000 0 -0.35 64 64
LYN/TEC/p62DOK -0.21 0.24 -10000 0 -0.41 272 272
MAPK3 -0.11 0.13 0.3 6 -0.29 18 24
STAP1 -0.24 0.24 -10000 0 -0.44 273 273
GRAP2 -0.017 0.15 -10000 0 -0.55 31 31
JAK2 -0.49 0.48 -10000 0 -0.89 275 275
STAT1 (dimer) -0.57 0.55 -10000 0 -1 276 276
mol:Gleevec 0.007 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.2 0.24 -10000 0 -0.42 259 259
actin filament polymerization -0.23 0.23 -10000 0 -0.43 272 272
LYN 0.027 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.32 0.35 1 -0.61 275 276
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 260 260
PI3K -0.2 0.24 -10000 0 -0.41 270 270
PTEN 0.026 0.018 -10000 0 -0.36 1 1
SCF/KIT/EPO/EPOR -0.69 0.66 -10000 0 -1.3 275 275
MAPK8 -0.24 0.24 -10000 0 -0.44 277 277
STAT3 (dimer) -0.23 0.23 -10000 0 -0.43 269 269
positive regulation of transcription -0.083 0.11 0.33 8 -0.24 18 26
mol:GDP -0.2 0.2 -10000 0 -0.38 230 230
PIK3C2B -0.23 0.23 -10000 0 -0.44 250 250
CBL/CRKL -0.2 0.22 -10000 0 -0.39 270 270
FER -0.24 0.24 -10000 0 -0.44 273 273
SH2B3 -0.24 0.23 -10000 0 -0.44 275 275
PDPK1 -0.18 0.2 0.32 2 -0.36 242 244
SNAI2 -0.24 0.24 -10000 0 -0.44 275 275
positive regulation of cell proliferation -0.41 0.4 -10000 0 -0.75 276 276
KITLG -0.016 0.09 -10000 0 -0.71 7 7
cell motility -0.41 0.4 -10000 0 -0.75 276 276
PTPN6 0.038 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.2 -10000 0 -0.98 7 7
STAT5A (dimer) -0.33 0.33 -10000 0 -0.61 275 275
SOCS1 0.024 0.035 -10000 0 -0.68 1 1
cell migration 0.23 0.23 0.43 269 -10000 0 269
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.007 0.031 -10000 0 -10000 0 0
VAV1 0.012 0.06 -10000 0 -0.57 3 3
GRB10 -0.24 0.23 -10000 0 -0.44 273 273
PTPN11 0.033 0.033 -10000 0 -0.66 1 1
SCF/KIT -0.25 0.25 -10000 0 -0.46 275 275
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.12 0.13 0.27 3 -0.33 16 19
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.74 0.69 -10000 0 -1.3 275 275
MAP2K2 -0.12 0.13 0.37 3 -0.33 16 19
SHC/Grb2/SOS1 -0.2 0.23 -10000 0 -0.41 239 239
STAT5A -0.34 0.34 -10000 0 -0.63 275 275
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.24 0.24 -10000 0 -0.43 275 275
SHC/GRAP2 0.001 0.11 -10000 0 -0.38 31 31
PTPRO -0.25 0.23 -10000 0 -0.44 283 283
SH2B2 -0.24 0.23 -10000 0 -0.44 272 272
DOK1 0.027 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.44 269 269
CREBBP -0.042 0.077 -10000 0 -10000 0 0
BCL2 -0.22 0.4 -10000 0 -1.5 38 38
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.064 0.1 -10000 0 -0.62 8 8
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 248 248
JUN -0.26 0.26 -10000 0 -0.58 151 151
HRAS 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.27 0.29 -10000 0 -0.49 285 285
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.27 0.29 -10000 0 -0.49 287 287
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.21 0.22 -10000 0 -0.41 266 266
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.26 -10000 0 -0.44 281 281
GRB7 0.001 0.055 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.27 0.29 -10000 0 -0.49 281 281
MAPKKK cascade -0.24 0.24 -10000 0 -0.42 279 279
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.27 -10000 0 -0.46 281 281
lamellipodium assembly -0.2 0.18 -10000 0 -0.35 254 254
RET51/GFRalpha1/GDNF/SHC -0.26 0.29 -10000 0 -0.49 273 273
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.39 268 268
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.22 -10000 0 -0.4 271 271
MAPK3 -0.24 0.23 -10000 0 -0.42 277 277
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.083 0.25 -10000 0 -0.68 75 75
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.25 -10000 0 -0.45 278 278
DOK5 -0.068 0.24 -10000 0 -0.68 65 65
GFRA1 -0.37 0.35 -10000 0 -0.67 276 276
MAPK8 -0.2 0.2 -10000 0 -0.34 289 289
HRAS/GTP -0.26 0.28 -10000 0 -0.47 284 284
tube development -0.19 0.2 -10000 0 -0.38 255 255
MAPK1 -0.24 0.23 0.32 3 -0.42 279 282
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 255 255
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.025 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.33 -10000 0 -0.53 297 297
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.27 0.29 -10000 0 -0.49 287 287
RET51/GFRalpha1/GDNF/Dok5 -0.32 0.34 -10000 0 -0.55 300 300
PRKCA -0.006 0.15 -10000 0 -0.68 22 22
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
CREB1 -0.2 0.21 -10000 0 -0.38 252 252
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.15 0.16 -10000 0 -0.3 238 238
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.29 -10000 0 -0.49 285 285
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.11 0.26 -10000 0 -0.66 84 84
DOK4 0.026 0.009 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.56 151 151
RET9/GFRalpha1/GDNF/FRS2 -0.21 0.22 -10000 0 -0.4 267 267
SHANK3 0.02 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 240 240
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.35 283 283
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.35 288 288
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.4 273 273
PI3K -0.31 0.29 -10000 0 -0.55 256 256
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.21 -10000 0 -0.38 255 255
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.32 264 264
RET51/GFRalpha1/GDNF/FRS2 -0.27 0.29 -10000 0 -0.49 287 287
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.053 0.22 -10000 0 -0.68 55 55
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.4 271 271
RET51/GFRalpha1/GDNF/PKC alpha -0.28 0.31 -10000 0 -0.51 286 286
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GDNF -0.007 0.023 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.31 0.32 -10000 0 -0.54 298 298
Rac1/GTP -0.23 0.22 -10000 0 -0.42 253 253
RET9/GFRalpha1/GDNF -0.24 0.23 -10000 0 -0.44 275 275
GFRalpha1/GDNF -0.28 0.27 -10000 0 -0.5 275 275
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.014 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.65 21 21
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.025 0.015 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.31 0.24 -10000 0 -0.45 340 340
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.062 -10000 0 -0.38 7 7
AKT1 -0.2 0.15 -10000 0 -0.3 326 326
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.022 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.28 0.22 -10000 0 -0.42 329 329
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 19 19
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 329 329
DAB1/alpha3/beta1 Integrin -0.25 0.22 -10000 0 -0.39 318 318
long-term memory -0.26 0.23 -10000 0 -0.41 328 328
DAB1/LIS1 -0.25 0.22 -10000 0 -0.4 323 323
DAB1/CRLK/C3G -0.25 0.21 -10000 0 -0.38 326 326
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
DAB1/NCK2 -0.26 0.23 -10000 0 -0.4 329 329
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0 0.13 -10000 0 -0.68 16 16
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.68 333 333
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.45 337 337
GRIN2A/RELN/LRP8/DAB1/Fyn -0.27 0.24 -10000 0 -0.42 328 328
MAPK8 0.016 0.086 -10000 0 -0.64 8 8
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.41 340 340
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.41 329 329
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 335 335
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.41 328 328
PI3K 0.036 0.044 -10000 0 -0.51 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.015 -10000 0 -10000 0 0
RAP1A -0.24 0.21 0.49 3 -0.37 280 283
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.019 -10000 0 -10000 0 0
GRIN2B -0.005 0.02 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.42 36 36
neuron adhesion -0.22 0.21 0.46 10 -0.61 29 39
LRP8 -0.001 0.14 -10000 0 -0.68 19 19
GSK3B -0.19 0.14 -10000 0 -0.44 31 31
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.4 330 330
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.32 329 329
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.05 0.16 0.82 18 -0.61 3 21
neuron migration -0.26 0.2 -10000 0 -0.39 311 311
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.43 36 36
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 342 342
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.009 0.1 -10000 0 -0.47 15 15
NFATC2 -0.22 0.33 -10000 0 -0.7 130 130
NFATC3 -0.083 0.14 -10000 0 -0.31 51 51
CD40LG -0.62 0.55 -10000 0 -1.1 262 262
ITCH 0.038 0.016 -10000 0 -10000 0 0
CBLB 0.038 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.44 0.51 -10000 0 -1.2 132 132
JUNB 0.02 0.058 -10000 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.042 0.018 -10000 0 -0.32 1 1
T cell anergy 0.008 0.077 0.4 6 -0.43 2 8
TLE4 -0.21 0.36 -10000 0 -0.73 129 129
Jun/NFAT1-c-4/p21SNFT -0.55 0.59 -10000 0 -1.1 228 228
AP-1/NFAT1-c-4 -0.71 0.74 -10000 0 -1.3 251 251
IKZF1 -0.16 0.27 -10000 0 -0.58 109 109
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.82 104 104
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.74 201 201
CALM1 0.038 0.012 -10000 0 -10000 0 0
EGR2 -0.73 0.78 -10000 0 -1.5 229 229
EGR3 -0.54 0.7 -10000 0 -1.5 140 140
NFAT1/FOXP3 -0.17 0.28 -10000 0 -0.57 126 126
EGR1 -0.12 0.28 -10000 0 -0.68 96 96
JUN -0.13 0.28 -10000 0 -0.68 103 103
EGR4 -0.014 0.14 -10000 0 -0.66 22 22
mol:Ca2+ 0.012 0.009 -10000 0 -10000 0 0
GBP3 -0.16 0.26 -10000 0 -0.6 92 92
FOSL1 0.007 0.06 -10000 0 -0.52 2 2
NFAT1-c-4/MAF/IRF4 -0.48 0.56 -10000 0 -1 232 232
DGKA -0.15 0.24 -10000 0 -0.55 102 102
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.49 0.55 -10000 0 -1 230 230
CTLA4 -0.18 0.29 -10000 0 -0.68 98 98
NFAT1-c-4 (dimer)/EGR1 -0.56 0.63 -10000 0 -1.2 226 226
NFAT1-c-4 (dimer)/EGR4 -0.51 0.56 -10000 0 -1 234 234
FOS -0.17 0.3 -10000 0 -0.68 126 126
IFNG -0.37 0.5 -10000 0 -1.1 126 126
T cell activation -0.39 0.39 0.46 1 -0.86 164 165
MAF 0.026 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.41 0.74 222 -10000 0 222
TNF -0.54 0.55 -10000 0 -1 248 248
FASLG -0.7 0.76 -10000 0 -1.4 239 239
TBX21 -0.02 0.15 -10000 0 -0.69 22 22
BATF3 0.018 0.043 -10000 0 -0.68 1 1
PRKCQ 0.018 0.068 -10000 0 -0.61 5 5
PTPN1 -0.15 0.25 -10000 0 -0.53 117 117
NFAT1-c-4/ICER1 -0.49 0.55 -10000 0 -1 228 228
GATA3 -0.006 0.15 -10000 0 -0.64 24 24
T-helper 1 cell differentiation -0.36 0.48 -10000 0 -1.1 126 126
IL2RA -0.41 0.46 -10000 0 -0.99 142 142
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.15 0.25 -10000 0 -0.55 106 106
E2F1 -0.013 0.068 -10000 0 -10000 0 0
PPARG 0.016 0.085 -10000 0 -0.68 7 7
SLC3A2 -0.15 0.25 -10000 0 -0.58 90 90
IRF4 -0.046 0.18 -10000 0 -0.67 33 33
PTGS2 -0.6 0.55 0.5 1 -1.1 248 249
CSF2 -0.61 0.53 -10000 0 -1.1 252 252
JunB/Fra1/NFAT1-c-4 -0.46 0.54 -10000 0 -0.98 225 225
IL4 -0.29 0.35 -10000 0 -0.88 97 97
IL5 -0.59 0.52 -10000 0 -1 249 249
IL2 -0.4 0.4 0.46 1 -0.89 163 164
IL3 -0.069 0.086 -10000 0 -1.1 1 1
RNF128 0.035 0.038 -10000 0 -0.75 1 1
NFATC1 -0.36 0.42 -10000 0 -0.75 222 222
CDK4 0.24 0.25 0.61 66 -10000 0 66
PTPRK -0.15 0.25 -10000 0 -0.55 104 104
IL8 -0.6 0.53 0.5 1 -1.1 253 254
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.4 295 295
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.021 0.024 -9999 0 -10000 0 0
WNT4 -0.19 0.32 -9999 0 -0.67 151 151
FZD3 0.027 0.004 -9999 0 -10000 0 0
WNT5A 0.014 0.095 -9999 0 -0.68 9 9
WNT11 -0.33 0.35 -9999 0 -0.67 245 245
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.21 0.32 -10000 0 -0.69 150 150
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 149 149
positive regulation of JUN kinase activity -0.077 0.2 -10000 0 -0.4 131 131
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.15 0.25 -10000 0 -0.52 148 148
AP1 -0.41 0.54 -10000 0 -1.2 136 136
mol:IP3 -0.16 0.24 -10000 0 -0.53 147 147
PLCG1 -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.51 150 150
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.53 147 147
CAV3 -0.011 0.018 -10000 0 -10000 0 0
CAV1 0.013 0.095 -10000 0 -0.68 9 9
SHC/Grb2/SOS1 -0.077 0.2 -10000 0 -0.4 131 131
PDGF/PDGFRA/Shf -0.14 0.25 -10000 0 -0.51 149 149
FOS -0.4 0.52 -10000 0 -1.2 136 136
JUN -0.15 0.22 -10000 0 -0.58 102 102
oligodendrocyte development -0.14 0.25 -10000 0 -0.51 150 150
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA -0.21 0.32 -10000 0 -0.69 150 150
actin cytoskeleton reorganization -0.14 0.24 -10000 0 -0.5 149 149
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K -0.1 0.22 -10000 0 -0.44 146 146
PDGF/PDGFRA/Crk/C3G -0.1 0.22 -10000 0 -0.43 141 141
JAK1 -0.15 0.24 -10000 0 -0.51 149 149
ELK1/SRF -0.12 0.19 0.32 1 -0.41 141 142
SHB 0.025 0.008 -10000 0 -10000 0 0
SHF 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.024 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.54 149 149
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.077 0.2 -10000 0 -0.4 131 131
PDGF/PDGFRA/SHB -0.14 0.25 -10000 0 -0.51 149 149
PDGF/PDGFRA/Caveolin-1 -0.15 0.26 -10000 0 -0.52 150 150
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
ELK1 -0.16 0.22 -10000 0 -0.49 146 146
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PDGF/PDGFRA/Crk -0.14 0.24 -10000 0 -0.5 147 147
JAK-STAT cascade -0.15 0.24 -10000 0 -0.51 149 149
cell proliferation -0.14 0.25 -10000 0 -0.51 149 149
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.47 0.49 -10000 0 -0.96 205 205
PCK1 -0.31 0.45 -10000 0 -1.4 55 55
HNF4A -0.62 0.61 -10000 0 -1.2 231 231
KCNJ11 -0.45 0.48 -10000 0 -1 168 168
AKT1 -0.064 0.14 -10000 0 -0.46 12 12
response to starvation -0.018 0.039 -10000 0 -0.38 2 2
DLK1 -0.45 0.48 -10000 0 -0.99 174 174
NKX2-1 -0.17 0.19 -10000 0 -0.5 1 1
ACADM -0.47 0.49 -10000 0 -0.99 191 191
TAT -0.18 0.2 -10000 0 -0.59 9 9
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.071 -10000 0 -0.68 5 5
TTR -0.14 0.23 0.65 7 -0.72 27 34
PKLR -0.46 0.48 -10000 0 -0.93 219 219
APOA1 -0.85 0.84 -10000 0 -1.7 234 234
CPT1C -0.47 0.49 -10000 0 -0.97 202 202
ALAS1 -0.16 0.2 -10000 0 -0.91 2 2
TFRC -0.23 0.27 -10000 0 -0.72 38 38
FOXF1 0.013 0.071 -10000 0 -0.68 5 5
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.007 -10000 0 -10000 0 0
CPT1A -0.47 0.49 -10000 0 -0.98 199 199
HMGCS1 -0.47 0.49 -10000 0 -0.92 225 225
NR3C1 0.032 0.011 -10000 0 -10000 0 0
CPT1B -0.47 0.48 -10000 0 -0.98 196 196
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
GCK -0.6 0.62 -10000 0 -1.2 232 232
CREB1 0.008 0.067 -10000 0 -0.4 2 2
IGFBP1 -0.16 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -0.64 1 1
UCP2 -0.48 0.49 -10000 0 -0.97 202 202
ALDOB -0.44 0.48 -10000 0 -1 170 170
AFP -0.02 0.085 -10000 0 -0.39 1 1
BDH1 -0.47 0.49 -10000 0 -0.98 198 198
HADH -0.44 0.48 -10000 0 -0.98 176 176
F2 -0.58 0.58 -10000 0 -1.2 200 200
HNF1A 0.028 0.007 -10000 0 -10000 0 0
G6PC -0.001 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.24 -10000 0 -1.2 1 1
INS -0.022 0.014 -10000 0 -10000 0 0
FOXA1 -0.016 0.095 -10000 0 -0.32 29 29
FOXA3 -0.028 0.12 -10000 0 -0.32 35 35
FOXA2 -0.5 0.54 -10000 0 -1.1 199 199
ABCC8 -0.7 0.66 -10000 0 -1.3 249 249
ALB -0.063 0.27 -10000 0 -1.1 30 30
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.089 0.26 -10000 0 -0.67 80 80
GNB1/GNG2 -0.2 0.23 -10000 0 -0.53 113 113
mol:DAG -0.19 0.2 -10000 0 -0.49 109 109
PLCG1 -0.19 0.21 -10000 0 -0.5 109 109
YES1 -0.22 0.22 -10000 0 -0.53 119 119
FZD3 0.027 0.004 -10000 0 -10000 0 0
FZD6 0.027 0.005 -10000 0 -10000 0 0
G protein -0.19 0.22 -10000 0 -0.51 108 108
MAP3K7 -0.16 0.17 0.31 1 -0.42 105 106
mol:Ca2+ -0.18 0.2 -10000 0 -0.47 109 109
mol:IP3 -0.19 0.2 -10000 0 -0.49 109 109
NLK -0.002 0.066 -10000 0 -0.82 3 3
GNB1 0.026 0.005 -10000 0 -10000 0 0
CAMK2A -0.17 0.19 0.32 1 -0.45 106 107
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.24 -10000 0 -0.4 295 295
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.22 0.22 -10000 0 -0.53 115 115
GO:0007205 -0.18 0.2 -10000 0 -0.48 109 109
WNT6 0.021 0.024 -10000 0 -10000 0 0
WNT4 -0.19 0.32 -10000 0 -0.67 151 151
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.55 137 137
GNG2 0.025 0.032 -10000 0 -0.68 1 1
WNT5A 0.014 0.095 -10000 0 -0.68 9 9
WNT11 -0.33 0.35 -10000 0 -0.67 245 245
CDC42 -0.2 0.21 -10000 0 -0.52 112 112
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.14 0.22 -10000 0 -0.4 194 194
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.29 194 194
GNAO1 0.003 0.12 -10000 0 -0.68 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.059 -10000 0 -0.44 8 8
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.2 0.47 4 -0.37 190 194
T-DHT/AR -0.2 0.26 -10000 0 -0.5 200 200
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.005 129 129
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.68 1 1
mol:GDP -0.21 0.26 -10000 0 -0.53 196 196
cell proliferation -0.2 0.27 0.48 11 -0.52 148 159
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
FOS -0.26 0.38 0.53 8 -0.84 131 139
mol:Ca2+ -0.026 0.029 -10000 0 -0.067 107 107
MAPK3 -0.16 0.24 0.53 12 -0.5 98 110
MAPK1 -0.18 0.22 0.34 5 -0.41 174 179
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 116 116
cAMP biosynthetic process 0.017 0.07 0.26 10 -0.41 8 18
GNG2 0.025 0.032 -10000 0 -0.68 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 116 116
HRAS/GTP -0.14 0.2 -10000 0 -0.38 190 190
actin cytoskeleton reorganization 0.037 0.034 -10000 0 -0.36 3 3
SRC 0.025 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 116 116
PI3K 0.033 0.038 -10000 0 -0.44 3 3
apoptosis 0.19 0.25 0.52 149 -0.47 7 156
T-DHT/AR/PELP1 -0.16 0.23 -10000 0 -0.44 199 199
HRAS/GDP -0.2 0.26 -10000 0 -0.5 197 197
CREB1 -0.21 0.28 0.47 7 -0.56 149 156
RAC1-CDC42/GTP 0.047 0.036 -10000 0 -0.37 3 3
AR -0.26 0.34 -10000 0 -0.67 200 200
GNB1 0.026 0.005 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.54 6 -0.38 190 196
RAC1-CDC42/GDP -0.18 0.26 -10000 0 -0.48 196 196
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.41 191 191
MAP2K2 -0.14 0.2 0.51 3 -0.37 186 189
T-DHT/AR/PELP1/Src/PI3K -0.11 0.16 -10000 0 -0.3 194 194
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.014 0.09 -10000 0 -0.68 8 8
Gi family/GNB1/GNG2/GDP -0.033 0.1 -10000 0 -0.45 17 17
mol:T-DHT 0 0.003 0.002 2 -0.005 67 69
RAC1 0.026 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.034 -10000 0 -0.51 2 2
Gi family/GTP -0.087 0.11 -10000 0 -0.3 48 48
CDC42 0.027 0.005 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.65 21 21
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 335 335
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.28 0.21 -10000 0 -0.42 325 325
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.022 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.067 0.24 -10000 0 -0.68 65 65
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 19 19
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.004 -10000 0 -10000 0 0
CDK5R2 0.001 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.3 0.23 -10000 0 -0.45 340 340
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.18 0.36 5 -0.45 37 42
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.24 0.19 -10000 0 -0.38 315 315
RELN -0.46 0.32 -10000 0 -0.68 333 333
PAFAH/LIS1 -0.031 0.16 -10000 0 -0.43 65 65
LIS1/CLIP170 0.031 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.48 15 15
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.21 0.17 -10000 0 -0.3 324 324
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.23 0.18 0.64 1 -0.36 314 315
LIS1/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.015 -10000 0 -10000 0 0
PAFAH1B2 0.016 0.086 -10000 0 -0.64 8 8
MAP1B/LIS1/Dynein heavy chain 0.031 0.013 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.18 0.3 2 -0.53 20 22
LRP8 -0.001 0.14 -10000 0 -0.68 19 19
NDEL1/Katanin 60 -0.22 0.18 0.29 4 -0.34 311 315
P39/CDK5 -0.25 0.19 -10000 0 -0.38 324 324
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.2 -10000 0 -0.39 325 325
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.21 -10000 0 -0.4 319 319
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 342 342
CDC42 0.017 0.006 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.089 0.21 -10000 0 -0.63 29 29
IHH -0.16 0.32 -10000 0 -0.7 119 119
SHH Np/Cholesterol/GAS1 -0.055 0.16 -10000 0 -0.4 83 83
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.055 0.16 0.39 83 -10000 0 83
SMO/beta Arrestin2 -0.076 0.21 -10000 0 -0.42 108 108
SMO -0.097 0.21 -10000 0 -0.44 113 113
AKT1 -0.017 0.11 -10000 0 -0.88 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.015 0.09 -10000 0 -0.68 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.095 0.21 -10000 0 -0.43 113 113
STIL -0.066 0.16 -10000 0 -0.49 14 14
DHH N/PTCH2 -0.052 0.21 -10000 0 -0.51 79 79
DHH N/PTCH1 -0.078 0.19 -10000 0 -0.38 117 117
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
DHH 0.021 0.064 -10000 0 -0.68 4 4
PTHLH -0.14 0.31 -10000 0 -1 31 31
determination of left/right symmetry -0.095 0.21 -10000 0 -0.43 113 113
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development -0.14 0.31 -10000 0 -1 31 31
IHH N/Hhip -0.29 0.33 -10000 0 -0.59 251 251
DHH N/Hhip -0.17 0.27 -10000 0 -0.51 183 183
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.095 0.21 -10000 0 -0.43 113 113
pancreas development -0.25 0.33 -10000 0 -0.67 182 182
HHAT 0.024 0.033 -10000 0 -0.68 1 1
PI3K 0.036 0.044 -10000 0 -0.51 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.1 0.26 -10000 0 -0.63 95 95
somite specification -0.095 0.21 -10000 0 -0.43 113 113
SHH Np/Cholesterol/PTCH1 -0.071 0.16 -10000 0 -0.5 13 13
SHH Np/Cholesterol/PTCH2 -0.044 0.15 -10000 0 -0.38 78 78
SHH Np/Cholesterol/Megalin -0.079 0.18 -10000 0 -0.38 120 120
SHH -0.005 0.029 -10000 0 -0.51 1 1
catabolic process -0.095 0.2 -10000 0 -0.42 124 124
SMO/Vitamin D3 -0.077 0.18 -10000 0 -0.4 73 73
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.39 181 181
LRP2 -0.15 0.3 -10000 0 -0.66 125 125
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.6 40 40
SHH Np/Cholesterol/BOC 0.013 0.057 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.093 0.18 -10000 0 -0.38 138 138
mesenchymal cell differentiation 0.14 0.2 0.39 181 -10000 0 181
mol:Vitamin D3 -0.066 0.17 -10000 0 -0.5 13 13
IHH N/PTCH2 -0.17 0.29 -10000 0 -0.54 174 174
CDON -0.18 0.32 -10000 0 -0.67 139 139
IHH N/PTCH1 -0.093 0.21 -10000 0 -0.42 124 124
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.5 125 125
PTCH2 -0.086 0.26 -10000 0 -0.67 78 78
SHH Np/Cholesterol 0.009 0.023 -10000 0 -0.4 1 1
PTCH1 -0.096 0.2 -10000 0 -0.42 124 124
HHIP -0.25 0.33 -10000 0 -0.67 182 182
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.1 0.24 0.53 112 -10000 0 112
KIRREL -0.043 0.19 -10000 0 -0.69 37 37
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.1 0.25 -10000 0 -0.53 112 112
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.056 0.2 -10000 0 -0.43 103 103
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.057 0.16 -10000 0 -0.35 101 101
FYN -0.064 0.2 0.27 24 -0.41 103 127
mol:Ca2+ -0.056 0.2 -10000 0 -0.43 102 102
mol:DAG -0.056 0.2 -10000 0 -0.43 102 102
NPHS2 -0.005 0.054 -10000 0 -0.74 1 1
mol:IP3 -0.056 0.2 -10000 0 -0.43 102 102
regulation of endocytosis -0.05 0.18 -10000 0 -0.39 100 100
Nephrin/NEPH1/podocin/Cholesterol -0.068 0.2 -10000 0 -0.43 105 105
establishment of cell polarity -0.1 0.24 -10000 0 -0.53 112 112
Nephrin/NEPH1/podocin/NCK1-2 -0.04 0.2 -10000 0 -0.4 102 102
Nephrin/NEPH1/beta Arrestin2 -0.049 0.18 -10000 0 -0.39 100 100
NPHS1 -0.11 0.26 -10000 0 -0.68 84 84
Nephrin/NEPH1/podocin -0.061 0.19 -10000 0 -0.41 103 103
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.055 0.2 -10000 0 -0.43 102 102
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.055 0.2 -10000 0 -0.43 100 100
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.077 0.19 0.28 21 -0.41 104 125
cytoskeleton organization -0.082 0.2 -10000 0 -0.45 100 100
Nephrin/NEPH1 -0.072 0.18 -10000 0 -0.4 108 108
Nephrin/NEPH1/ZO-1 -0.069 0.21 -10000 0 -0.45 106 106
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.01 0.068 -9999 0 -0.45 9 9
NFATC2 -0.077 0.17 -9999 0 -0.45 80 80
NFATC3 -0.001 0.031 -9999 0 -10000 0 0
CD40LG -0.33 0.36 -9999 0 -0.75 174 174
PTGS2 -0.31 0.35 -9999 0 -0.74 160 160
JUNB 0.02 0.058 -9999 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.024 -9999 0 -10000 0 0
CaM/Ca2+ 0.007 0.024 -9999 0 -10000 0 0
CALM1 0.017 0.021 -9999 0 -10000 0 0
JUN -0.13 0.28 -9999 0 -0.68 103 103
mol:Ca2+ -0.008 0.02 -9999 0 -0.18 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -9999 0 -10000 0 0
FOSL1 0.007 0.06 -9999 0 -0.52 2 2
CREM 0.027 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.24 -9999 0 -0.46 160 160
FOS -0.17 0.3 -9999 0 -0.68 126 126
IFNG -0.33 0.36 -9999 0 -0.74 178 178
AP-1/NFAT1-c-4 -0.35 0.44 -9999 0 -0.84 172 172
FASLG -0.31 0.34 -9999 0 -0.72 164 164
NFAT1-c-4/ICER1 -0.077 0.17 -9999 0 -0.4 86 86
IL2RA -0.31 0.34 -9999 0 -0.72 164 164
FKBP12/FK506 0.02 0.004 -9999 0 -10000 0 0
CSF2 -0.33 0.31 -9999 0 -0.69 168 168
JunB/Fra1/NFAT1-c-4 -0.068 0.17 -9999 0 -0.4 85 85
IL4 -0.3 0.32 -9999 0 -0.69 158 158
IL2 0.001 0.08 -9999 0 -0.95 3 3
IL3 -0.009 0.052 -9999 0 -0.88 1 1
FKBP1A 0.027 0.005 -9999 0 -10000 0 0
BATF3 0.018 0.043 -9999 0 -0.68 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.025 0.01 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.029 0.092 -10000 0 -0.43 9 9
PTK2B 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.47 1 -0.68 68 69
EDN1 -0.002 0.097 -10000 0 -0.54 8 8
EDN3 -0.31 0.35 -10000 0 -0.68 229 229
EDN2 0.01 0.084 -10000 0 -0.68 6 6
HRAS/GDP -0.11 0.23 0.44 3 -0.49 89 92
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.073 0.15 -10000 0 -0.34 85 85
ADCY4 -0.069 0.14 0.35 1 -0.4 64 65
ADCY5 -0.12 0.2 0.35 1 -0.45 108 109
ADCY6 -0.067 0.14 0.35 1 -0.4 64 65
ADCY7 -0.066 0.14 0.35 1 -0.4 63 64
ADCY1 -0.07 0.15 0.35 1 -0.41 64 65
ADCY2 -0.1 0.18 -10000 0 -0.44 89 89
ADCY3 -0.068 0.15 0.35 1 -0.4 66 67
ADCY8 -0.097 0.15 0.35 1 -0.43 66 67
ADCY9 -0.067 0.14 0.35 1 -0.4 63 64
arachidonic acid secretion -0.19 0.32 0.37 9 -0.6 149 158
ETB receptor/Endothelin-1/Gq/GTP -0.081 0.18 -10000 0 -0.36 117 117
GNAO1 0.004 0.12 -10000 0 -0.68 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.031 0.1 -10000 0 -0.38 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.026 0.18 -10000 0 -0.42 68 68
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.033 0.099 -10000 0 -0.46 9 9
EDNRB 0.016 0.073 -10000 0 -0.68 5 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.067 0.15 -10000 0 -0.61 23 23
CYSLTR1 -0.034 0.12 -10000 0 -0.64 13 13
SLC9A1 0 0.056 -10000 0 -0.27 10 10
mol:GDP -0.12 0.24 0.42 5 -0.51 93 98
SLC9A3 -0.05 0.2 0.37 1 -0.68 34 35
RAF1 -0.16 0.28 0.44 3 -0.55 131 134
JUN -0.28 0.49 0.46 1 -1.1 121 122
JAK2 -0.028 0.094 -10000 0 -0.45 10 10
mol:IP3 -0.1 0.2 -10000 0 -0.42 113 113
ETA receptor/Endothelin-1 0.014 0.13 -10000 0 -0.45 17 17
PLCB1 0.023 0.033 -10000 0 -0.68 1 1
PLCB2 0.02 0.022 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.52 230 230
FOS -0.28 0.45 0.62 2 -0.99 130 132
Gai/GDP -0.013 0.15 -10000 0 -0.64 24 24
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.18 -10000 0 -0.47 57 57
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.1 0.2 -10000 0 -0.41 114 114
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.06 0.23 -10000 0 -0.66 61 61
Gs family/GDP -0.15 0.25 0.28 1 -0.52 114 115
ETA receptor/Endothelin-1/Gq/GTP -0.088 0.17 -10000 0 -0.37 109 109
MAPK14 -0.069 0.15 -10000 0 -0.37 56 56
TRPC6 -0.15 0.3 0.47 1 -0.73 66 67
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.68 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.07 0.16 -10000 0 -0.35 86 86
ETB receptor/Endothelin-2 0.021 0.085 -10000 0 -0.51 11 11
ETB receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.51 232 232
ETB receptor/Endothelin-1 0.016 0.094 -10000 0 -0.52 10 10
MAPK3 -0.24 0.41 0.38 7 -0.86 133 140
MAPK1 -0.29 0.45 0.63 2 -0.96 134 136
Rac1/GDP -0.11 0.22 0.37 1 -0.48 86 87
cAMP biosynthetic process -0.075 0.18 0.47 9 -0.45 59 68
MAPK8 -0.18 0.35 0.48 1 -0.73 99 100
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.002 0.075 -10000 0 -0.3 17 17
p130Cas/CRK/Src/PYK2 -0.15 0.28 0.44 8 -0.55 126 134
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.48 86 87
COL1A2 -0.004 0.095 -10000 0 -0.47 6 6
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.014 0.085 -10000 0 -0.53 7 7
mol:DAG -0.1 0.2 -10000 0 -0.42 113 113
MAP2K2 -0.19 0.34 0.39 10 -0.68 135 145
MAP2K1 -0.21 0.34 0.5 2 -0.69 139 141
EDNRA 0.002 0.072 -10000 0 -0.39 4 4
positive regulation of muscle contraction -0.023 0.076 -10000 0 -0.38 6 6
Gq family/GDP -0.14 0.28 0.38 3 -0.55 124 127
HRAS/GTP -0.14 0.24 0.34 5 -0.5 108 113
PRKCH -0.1 0.2 0.3 1 -0.44 91 92
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.22 0.3 1 -0.47 102 103
PRKCB -0.11 0.2 0.3 1 -0.45 93 94
PRKCE -0.11 0.2 -10000 0 -0.45 91 91
PRKCD -0.11 0.19 -10000 0 -0.44 92 92
PRKCG -0.1 0.19 -10000 0 -0.45 87 87
regulation of vascular smooth muscle contraction -0.32 0.53 0.65 2 -1.2 130 132
PRKCQ -0.11 0.2 -10000 0 -0.44 96 96
PLA2G4A -0.21 0.35 0.38 9 -0.67 149 158
GNA14 -0.14 0.29 -10000 0 -0.65 112 112
GNA15 0.007 0.051 -10000 0 -0.68 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA11 0.009 0.081 -10000 0 -0.63 7 7
Rac1/GTP 0.031 0.1 -10000 0 -0.38 8 8
MMP1 -0.035 0.079 0.63 2 -10000 0 2
IL4-mediated 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
BCL2L1 -0.51 0.4 -10000 0 -1.1 89 89
STAT6 (cleaved dimer) -0.52 0.41 -10000 0 -0.96 160 160
IGHG1 -0.18 0.13 -10000 0 -0.44 7 7
IGHG3 -0.49 0.38 -10000 0 -0.9 162 162
AKT1 -0.27 0.28 0.62 2 -0.81 62 64
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.93 54 54
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.31 0.3 -10000 0 -0.76 95 95
THY1 -0.51 0.4 -10000 0 -1.1 82 82
MYB 0.011 0.098 -10000 0 -0.64 10 10
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.31 -10000 0 -0.8 95 95
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.85 56 56
SP1 0.031 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.41 -10000 0 -1 130 130
SOCS1 -0.35 0.26 -10000 0 -0.72 73 73
SOCS3 -0.32 0.35 0.6 2 -1.1 59 61
FCER2 -0.51 0.42 -10000 0 -0.87 220 220
PARP14 0.027 0.006 -10000 0 -10000 0 0
CCL17 -0.54 0.42 -10000 0 -1.2 94 94
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.2 -10000 0 -0.67 42 42
T cell proliferation -0.5 0.41 -10000 0 -1.1 103 103
IL4R/JAK1 -0.5 0.4 -10000 0 -1.1 101 101
EGR2 -0.84 0.68 -10000 0 -1.5 221 221
JAK2 -0.031 0.038 -10000 0 -0.4 1 1
JAK3 -0.01 0.065 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.004 0.021 -10000 0 -10000 0 0
COL1A2 -0.16 0.13 -10000 0 -0.97 2 2
CCL26 -0.51 0.4 -10000 0 -1.1 81 81
IL4R -0.54 0.42 -10000 0 -1.1 96 96
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.6 0.54 -10000 0 -1.4 111 111
IL13RA1 -0.03 0.033 -10000 0 -10000 0 0
IRF4 -0.29 0.48 -10000 0 -1.1 99 99
ARG1 -0.13 0.14 -10000 0 -1 3 3
CBL -0.32 0.29 -10000 0 -0.8 79 79
GTF3A 0.025 0.017 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
IL13RA1/JAK2 -0.036 0.046 -10000 0 -10000 0 0
IRF4/BCL6 -0.26 0.44 -10000 0 -1 99 99
CD40LG -0.07 0.23 -10000 0 -0.64 67 67
MAPK14 -0.34 0.33 -10000 0 -0.92 76 76
mitosis -0.26 0.26 0.62 2 -0.75 63 65
STAT6 -0.57 0.48 -10000 0 -1.1 146 146
SPI1 0.023 0.032 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 0.78 2 -0.7 61 63
STAT6 (dimer) -0.57 0.48 -10000 0 -1.1 146 146
STAT6 (dimer)/PARP14 -0.53 0.44 -10000 0 -1 142 142
mast cell activation 0.014 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.31 -10000 0 -0.89 64 64
FRAP1 -0.27 0.28 0.62 2 -0.81 63 65
LTA -0.52 0.4 -10000 0 -1.1 101 101
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.56 0.46 1.1 147 -10000 0 147
CCL11 -0.49 0.38 -10000 0 -1 94 94
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.3 -10000 0 -0.89 65 65
IL2RG -0.01 0.14 -10000 0 -0.63 21 21
IL10 -0.52 0.42 -10000 0 -1.2 88 88
IRS1 -0.053 0.22 -10000 0 -0.68 55 55
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.091 -10000 0 -10000 0 0
IL5 -0.51 0.4 -10000 0 -1.1 101 101
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.44 0.36 -10000 0 -0.95 94 94
COL1A1 -0.21 0.24 -10000 0 -1 23 23
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.41 -10000 0 -1.2 72 72
IL2R gamma/JAK3 -0.02 0.12 -10000 0 -0.5 19 19
TFF3 -1.2 0.58 -10000 0 -1.4 392 392
ALOX15 -0.51 0.4 -10000 0 -1.1 82 82
MYBL1 0.027 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.44 0.35 -10000 0 -0.91 104 104
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.28 -10000 0 -0.84 55 55
mol:PI-3-4-5-P3 -0.27 0.28 0.62 2 -0.81 62 64
PI3K -0.29 0.3 0.67 1 -0.88 62 63
DOK2 0.02 0.051 -10000 0 -0.68 2 2
ETS1 0.039 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.65 37 37
ITGB3 -0.52 0.43 -10000 0 -1.2 89 89
PIGR -0.53 0.45 -10000 0 -1.3 82 82
IGHE 0.046 0.045 0.27 6 -10000 0 6
MAPKKK cascade -0.2 0.19 0.58 1 -0.64 37 38
BCL6 0.026 0.032 -10000 0 -0.67 1 1
OPRM1 -0.52 0.4 -10000 0 -1.2 77 77
RETNLB -0.52 0.4 -10000 0 -1.1 83 83
SELP -0.51 0.41 -10000 0 -1.2 75 75
AICDA -0.49 0.38 -10000 0 -1.1 80 80
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.026 -9999 0 -0.44 1 1
fibroblast growth factor receptor signaling pathway 0.052 0.025 -9999 0 -0.44 1 1
LAMA1 -0.021 0.18 -9999 0 -0.67 33 33
PRNP 0.025 0.032 -9999 0 -0.68 1 1
GPC1/SLIT2 -0.042 0.19 -9999 0 -0.5 72 72
SMAD2 0.016 0.039 -9999 0 -0.4 3 3
GPC1/PrPc/Cu2+ 0.034 0.024 -9999 0 -0.44 1 1
GPC1/Laminin alpha1 0.002 0.14 -9999 0 -0.5 33 33
TDGF1 -0.27 0.34 -9999 0 -0.67 203 203
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.51 203 203
APP/GPC1 0.038 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.22 -9999 0 -0.44 201 201
FLT1 0.024 0.033 -9999 0 -0.68 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.047 0.042 -9999 0 -0.44 3 3
SERPINC1 0.02 0.022 -9999 0 -10000 0 0
FYN -0.17 0.23 -9999 0 -0.44 201 201
FGR -0.17 0.22 -9999 0 -0.43 201 201
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.52 196 196
SLIT2 -0.078 0.25 -9999 0 -0.67 72 72
GPC1/NRG -0.012 0.16 -9999 0 -0.51 44 44
NRG1 -0.038 0.2 -9999 0 -0.67 45 45
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.053 -9999 0 -0.57 3 3
LYN -0.17 0.22 -9999 0 -0.44 200 200
mol:Spermine 0.009 0.004 -9999 0 -10000 0 0
cell growth 0.052 0.025 -9999 0 -0.44 1 1
BMP signaling pathway -0.026 0.008 -9999 0 -10000 0 0
SRC -0.17 0.22 -9999 0 -0.44 200 200
TGFBR1 0.021 0.024 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.18 0.3 -9999 0 -0.68 128 128
GPC1 0.026 0.008 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.021 0.024 -9999 0 -10000 0 0
VEGFA 0.023 0.055 -9999 0 -0.68 3 3
BLK -0.3 0.3 -9999 0 -0.54 272 272
HCK -0.18 0.22 -9999 0 -0.44 201 201
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.026 0.032 -9999 0 -0.68 1 1
VEGFR1 homodimer 0.024 0.033 -9999 0 -0.68 1 1
TGFBR2 0.023 0.055 -9999 0 -0.68 3 3
cell death 0.038 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.034 0.019 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.24 -9999 0 -0.51 128 128
LCK -0.18 0.23 -9999 0 -0.44 206 206
neuron differentiation -0.012 0.16 -9999 0 -0.51 44 44
PrPc/Cu2+ 0.019 0.024 -9999 0 -0.51 1 1
APP 0.026 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.023 0.055 -9999 0 -0.68 3 3
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 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.1 0.18 -10000 0 -0.36 149 149
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.092 0.19 -10000 0 -0.36 145 145
IGF-1R heterotetramer/IGF1/PTP1B -0.066 0.2 -10000 0 -0.43 106 106
AKT1 -0.09 0.17 -10000 0 -0.64 14 14
BAD -0.088 0.16 -10000 0 -0.6 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.098 0.18 -10000 0 -0.36 145 145
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.09 0.19 -10000 0 -0.37 149 149
RAF1 -0.069 0.15 0.39 1 -0.55 15 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.063 0.19 -10000 0 -0.35 143 143
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.097 0.21 -10000 0 -0.39 150 150
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
RPS6KB1 -0.089 0.17 -10000 0 -0.63 14 14
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.14 0.32 5 -0.47 13 18
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.071 0.16 -10000 0 -0.35 98 98
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.03 0.17 -10000 0 -0.35 97 97
IGF-1R heterotetramer -0.009 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.078 0.2 -10000 0 -0.36 149 149
Crk/p130 Cas/Paxillin -0.058 0.19 -10000 0 -0.37 103 103
IGF1R -0.009 0.058 -10000 0 -10000 0 0
IGF1 -0.14 0.3 -10000 0 -0.7 107 107
IRS2/Crk -0.086 0.18 -10000 0 -0.38 103 103
PI3K -0.066 0.2 -10000 0 -0.39 107 107
apoptosis 0.064 0.15 0.5 14 -0.4 1 15
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.091 0.2 -10000 0 -0.45 105 105
RAF1/14-3-3 E -0.045 0.14 0.33 3 -0.46 15 18
BAD/14-3-3 -0.068 0.16 0.4 2 -0.54 14 16
PRKCZ -0.088 0.17 0.25 1 -0.63 14 15
Crk/p130 Cas/Paxillin/FAK1 -0.059 0.16 -10000 0 -0.54 14 14
PTPN1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.095 0.21 -10000 0 -0.47 107 107
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.044 0.18 -10000 0 -0.38 103 103
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.088 0.19 -10000 0 -0.36 149 149
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.099 0.19 -10000 0 -0.36 149 149
IRS1 -0.11 0.2 -10000 0 -0.39 150 150
IRS2 -0.1 0.18 -10000 0 -0.36 149 149
IGF-1R heterotetramer/IGF1 -0.1 0.24 -10000 0 -0.54 107 107
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.09 0.18 -10000 0 -0.38 106 106
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKD1 -0.091 0.2 -10000 0 -0.45 105 105
SHC1 0.025 0.007 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.35 0.61 4 -0.83 50 54
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.4 -10000 0 -0.81 108 108
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.19 0.35 0.62 3 -0.83 50 53
AP1 -0.19 0.37 -10000 0 -0.72 149 149
ABCG2 -0.19 0.35 0.61 1 -0.84 52 53
HIF1A -0.018 0.072 -10000 0 -10000 0 0
TFF3 -0.48 0.43 0.62 3 -0.88 186 189
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.053 0.11 -10000 0 -0.29 6 6
response to hypoxia -0.068 0.11 -10000 0 -0.23 93 93
MCL1 -0.18 0.34 0.61 3 -0.84 46 49
NDRG1 -0.19 0.35 0.6 2 -0.83 49 51
SERPINE1 -0.19 0.35 0.61 1 -0.84 50 51
FECH -0.18 0.35 0.62 3 -0.83 49 52
FURIN -0.18 0.35 0.61 4 -0.84 49 53
NCOA2 -0.034 0.2 -10000 0 -0.68 42 42
EP300 -0.1 0.18 -10000 0 -0.35 151 151
HMOX1 -0.2 0.33 0.62 2 -0.83 50 52
BHLHE40 -0.19 0.35 0.62 2 -0.84 49 51
BHLHE41 -0.19 0.35 0.61 1 -0.84 50 51
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.031 0.1 -10000 0 -10000 0 0
ENG 0.014 0.094 0.47 4 -10000 0 4
JUN -0.12 0.29 -10000 0 -0.67 103 103
RORA -0.19 0.36 0.61 4 -0.84 50 54
ABCB1 -0.051 0.16 -10000 0 -1.2 8 8
TFRC -0.19 0.35 0.62 2 -0.84 51 53
CXCR4 -0.19 0.35 0.62 3 -0.83 50 53
TF -0.22 0.4 0.62 2 -0.92 76 78
CITED2 -0.21 0.39 0.62 2 -0.92 65 67
HIF1A/ARNT -0.21 0.38 -10000 0 -0.92 50 50
LDHA -0.032 0.11 -10000 0 -0.68 9 9
ETS1 -0.19 0.35 0.62 3 -0.83 50 53
PGK1 -0.19 0.34 0.61 1 -0.84 47 48
NOS2 -0.19 0.35 0.62 2 -0.82 54 56
ITGB2 -0.19 0.35 0.62 3 -0.84 49 52
ALDOA -0.19 0.34 0.61 1 -0.83 49 50
Cbp/p300/CITED2 -0.29 0.46 -10000 0 -0.97 110 110
FOS -0.16 0.31 -10000 0 -0.67 126 126
HK2 -0.19 0.35 0.62 3 -0.83 52 55
SP1 0.032 0.018 -10000 0 -10000 0 0
GCK -0.4 0.64 -10000 0 -1.4 134 134
HK1 -0.19 0.35 0.62 3 -0.83 50 53
NPM1 -0.19 0.34 0.61 1 -0.84 47 48
EGLN1 -0.18 0.34 0.61 3 -0.85 46 49
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.18 0.35 0.61 3 -0.83 50 53
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.29 0.5 1 -0.69 76 77
IGFBP1 -0.19 0.34 0.61 1 -0.84 47 48
VEGFA -0.2 0.35 -10000 0 -0.73 88 88
HIF1A/JAB1 0.005 0.058 -10000 0 -10000 0 0
CP -0.31 0.46 0.62 2 -0.92 134 136
CXCL12 -0.23 0.4 0.62 3 -0.93 73 76
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.008 -10000 0 -10000 0 0
BNIP3 -0.19 0.35 0.62 3 -0.83 50 53
EGLN3 -0.2 0.35 -10000 0 -0.85 55 55
CA9 -0.19 0.35 0.6 2 -0.82 56 58
TERT -0.19 0.34 0.6 1 -0.84 48 49
ENO1 -0.18 0.35 0.61 3 -0.84 49 52
PFKL -0.19 0.35 0.62 3 -0.83 49 52
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.2 0.36 0.62 3 -0.8 63 66
ARNT -0.014 0.072 -10000 0 -0.31 2 2
HNF4A -0.016 0.058 -10000 0 -0.22 4 4
ADFP -0.2 0.34 -10000 0 -0.77 66 66
SLC2A1 -0.19 0.35 -10000 0 -0.73 84 84
LEP -0.19 0.34 0.61 1 -0.84 48 49
HIF1A/ARNT/Cbp/p300 -0.25 0.41 -10000 0 -0.82 113 113
EPO -0.13 0.28 -10000 0 -0.84 24 24
CREBBP -0.081 0.17 -10000 0 -0.33 131 131
HIF1A/ARNT/Cbp/p300/HDAC7 -0.22 0.4 -10000 0 -0.83 96 96
PFKFB3 -0.19 0.35 0.62 3 -0.84 49 52
NT5E -0.19 0.36 0.61 3 -0.85 51 54
EPHB forward 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
Ephrin A5/EPHB2 -0.035 0.17 -10000 0 -0.44 70 70
cell-cell adhesion 0.11 0.16 0.32 173 -10000 0 173
Ephrin B/EPHB2/RasGAP 0.065 0.061 -10000 0 -0.38 7 7
ITSN1 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.025 0.047 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.23 -10000 0 -0.43 186 186
HRAS/GDP -0.083 0.16 -10000 0 -0.35 17 17
Ephrin B/EPHB1/GRB7 -0.1 0.23 -10000 0 -0.4 178 178
Endophilin/SYNJ1 0.023 0.073 0.46 5 -0.35 7 12
KRAS 0.027 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.22 -10000 0 -0.38 178 178
endothelial cell migration 0.051 0.038 -10000 0 -0.37 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.055 -10000 0 -10000 0 0
PAK1 0.025 0.075 0.46 5 -0.36 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.02 0.067 0.44 4 -0.36 6 10
DNM1 0.004 0.12 -10000 0 -0.62 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.13 0.19 -10000 0 -0.37 178 178
lamellipodium assembly -0.11 0.16 -10000 0 -0.32 173 173
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.088 0.16 -10000 0 -0.3 162 162
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.055 -10000 0 -0.68 3 3
EPHB3 -0.065 0.073 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.67 187 187
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.074 0.13 0.25 1 -0.38 12 13
Ephrin B/EPHB2 0.051 0.057 -10000 0 -0.38 7 7
Ephrin B/EPHB3 0.058 0.055 -10000 0 -0.43 4 4
JNK cascade -0.13 0.19 -10000 0 -0.38 176 176
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.38 180 180
RAP1/GDP -0.049 0.14 -10000 0 -0.35 8 8
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EFNB3 0.015 0.069 -10000 0 -0.68 4 4
EFNB1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.4 187 187
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.089 0.19 -10000 0 -0.33 173 173
Rap1/GTP -0.1 0.17 -10000 0 -0.33 163 163
axon guidance -0.035 0.17 -10000 0 -0.44 70 70
MAPK3 -0.084 0.14 -10000 0 -0.44 10 10
MAPK1 -0.081 0.14 -10000 0 -0.43 10 10
Rac1/GDP -0.061 0.14 -10000 0 -0.35 11 11
actin cytoskeleton reorganization -0.081 0.13 -10000 0 -0.33 5 5
CDC42/GDP -0.059 0.14 0.37 1 -0.35 12 13
PI3K 0.057 0.039 -10000 0 -0.38 3 3
EFNA5 -0.073 0.24 -10000 0 -0.68 68 68
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.045 -10000 0 -0.32 7 7
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.16 -10000 0 -0.32 168 168
PTK2 0.041 0.087 0.64 8 -10000 0 8
MAP4K4 -0.13 0.2 -10000 0 -0.38 176 176
SRC 0.026 0.008 -10000 0 -10000 0 0
KALRN 0.027 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.079 0.14 0.32 5 -0.32 2 7
MAP2K1 -0.084 0.15 -10000 0 -0.28 160 160
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.12 0.23 -10000 0 -0.4 187 187
cell migration -0.087 0.18 0.52 5 -0.41 20 25
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.074 0.46 5 -0.36 7 12
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.023 0.13 0.47 3 -0.38 49 52
HRAS/GTP -0.095 0.19 -10000 0 -0.34 172 172
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.4 187 187
cell adhesion mediated by integrin -0.008 0.073 0.39 4 -0.35 9 13
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.36 176 176
RAC1-CDC42/GTP -0.14 0.17 -10000 0 -0.36 171 171
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.051 0.14 -10000 0 -0.37 4 4
ruffle organization -0.11 0.18 0.58 4 -0.39 5 9
NCK1 0.027 0.004 -10000 0 -10000 0 0
receptor internalization 0.002 0.086 0.41 3 -0.37 17 20
Ephrin B/EPHB2/KALRN 0.065 0.061 -10000 0 -0.38 7 7
ROCK1 -0.023 0.044 -10000 0 -10000 0 0
RAS family/GDP -0.075 0.1 -10000 0 -0.33 4 4
Rac1/GTP -0.12 0.17 -10000 0 -0.34 173 173
Ephrin B/EPHB1/Src/Paxillin -0.094 0.16 -10000 0 -0.3 180 180
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.021 0.056 -10000 0 -0.68 3 3
EFNB1 -0.002 0.087 -10000 0 -0.48 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.22 -10000 0 -0.39 185 185
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.4 187 187
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.38 185 185
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.24 -10000 0 -0.42 191 191
DNM1 0.004 0.12 -10000 0 -0.64 15 15
cell-cell signaling -0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.001 0.091 0.41 1 -0.65 7 8
YES1 0.005 0.1 -10000 0 -0.9 6 6
Ephrin B1/EPHB1-2/NCK2 -0.12 0.22 -10000 0 -0.39 186 186
PI3K 0.025 0.1 -10000 0 -0.87 6 6
mol:GDP -0.13 0.23 -10000 0 -0.41 191 191
ITGA2B -0.042 0.21 -10000 0 -0.67 47 47
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN 0.005 0.11 -10000 0 -0.86 7 7
MAP3K7 -0.01 0.084 -10000 0 -0.68 7 7
FGR 0.003 0.1 -10000 0 -0.85 7 7
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.027 0.17 -10000 0 -0.44 55 55
LYN 0.005 0.11 -10000 0 -0.86 7 7
Ephrin B1/EPHB1-2/Src Family Kinases -0.005 0.1 -10000 0 -0.81 7 7
Ephrin B1/EPHB1-2 -0.009 0.088 -10000 0 -0.78 6 6
SRC 0.003 0.1 -10000 0 -0.85 7 7
ITGB3 0.009 0.11 -10000 0 -0.65 12 12
EPHB1 -0.24 0.34 -10000 0 -0.67 187 187
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.027 0.18 -10000 0 -0.53 55 55
BLK -0.047 0.14 -10000 0 -0.93 7 7
HCK 0.004 0.1 -10000 0 -0.85 7 7
regulation of stress fiber formation 0.12 0.21 0.38 186 -10000 0 186
MAPK8 -0.003 0.12 0.34 6 -0.67 10 16
Ephrin B1/EPHB1-2/RGS3 -0.12 0.22 -10000 0 -0.39 185 185
endothelial cell migration -0.006 0.078 0.41 1 -0.63 6 7
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.025 0.085 -10000 0 -0.8 5 5
regulation of focal adhesion formation 0.12 0.21 0.38 186 -10000 0 186
chemotaxis 0.12 0.21 0.38 185 -10000 0 185
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
Rac1/GTP -0.12 0.22 -10000 0 -0.39 185 185
angiogenesis -0.01 0.09 -10000 0 -0.73 7 7
LCK 0.001 0.11 -10000 0 -0.9 7 7
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.057 0.25 0.29 19 -0.59 73 92
FYN -0.1 0.32 0.9 1 -0.78 77 78
LAT/GRAP2/SLP76 -0.083 0.26 -10000 0 -0.61 79 79
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.062 0.21 0.54 8 -0.47 78 86
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.016 0.056 0.12 2 -0.15 34 36
MAP3K8 0.016 0.086 -10000 0 -0.64 8 8
mol:Ca2+ -0.03 0.043 0.092 5 -0.11 101 106
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.31 0.63 5 -0.72 82 87
TRPV6 -0.1 0.36 1 19 -0.68 101 120
CD28 -0.013 0.15 -10000 0 -0.65 23 23
SHC1 -0.1 0.32 0.31 21 -0.8 74 95
receptor internalization -0.13 0.35 -10000 0 -0.69 110 110
PRF1 -0.11 0.34 -10000 0 -0.82 74 74
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.043 0.18 0.58 5 -0.37 80 85
LAT -0.11 0.32 0.3 3 -0.78 77 80
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.052 0.21 -10000 0 -0.64 54 54
CD3E -0.034 0.19 -10000 0 -0.64 43 43
CD3G -0.1 0.26 -10000 0 -0.65 88 88
RASGRP2 -0.004 0.034 0.095 3 -0.18 12 15
RASGRP1 -0.049 0.22 0.6 10 -0.47 77 87
HLA-A 0.027 0.012 -10000 0 -10000 0 0
RASSF5 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.14 0.34 29 -0.13 43 72
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.048 0.085 -10000 0 -0.24 62 62
PRKCA -0.036 0.13 -10000 0 -0.3 75 75
GRAP2 -0.017 0.15 -10000 0 -0.55 31 31
mol:IP3 -0.032 0.21 0.26 71 -0.44 73 144
EntrezGene:6957 0 0.005 0.059 1 -10000 0 1
TCR/CD3/MHC I/CD8 -0.13 0.36 -10000 0 -0.87 76 76
ORAI1 0.047 0.21 0.7 2 -0.8 15 17
CSK -0.11 0.33 -10000 0 -0.78 81 81
B7 family/CD28 -0.11 0.35 -10000 0 -0.8 81 81
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.39 -10000 0 -0.9 84 84
PTPN6 -0.12 0.33 0.25 1 -0.81 77 78
VAV1 -0.11 0.32 -10000 0 -0.78 77 77
Monovalent TCR/CD3 -0.12 0.32 -10000 0 -0.62 108 108
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.11 0.34 0.88 1 -0.81 77 78
PAG1 -0.11 0.33 -10000 0 -0.8 78 78
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.39 -10000 0 -0.91 82 82
CD80 -0.041 0.21 -10000 0 -0.68 46 46
CD86 0.014 0.077 -10000 0 -0.68 5 5
PDK1/CARD11/BCL10/MALT1 -0.04 0.11 -10000 0 -0.29 63 63
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.6 89 89
CD8A -0.024 0.18 -10000 0 -0.66 36 36
CD8B -0.054 0.22 -10000 0 -0.66 55 55
PTPRC -0.008 0.14 -10000 0 -0.68 19 19
PDK1/PKC theta -0.074 0.27 0.64 11 -0.58 78 89
CSK/PAG1 -0.11 0.32 -10000 0 -0.77 77 77
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.31 -10000 0 -0.74 80 80
STIM1 0.019 0.16 1.2 2 -0.9 9 11
RAS family/GTP 0.012 0.11 0.26 26 -0.19 43 69
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.39 -10000 0 -0.76 110 110
mol:DAG -0.06 0.16 0.14 6 -0.39 76 82
RAP1A/GDP 0.011 0.083 0.25 17 -10000 0 17
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.002 0.13 -10000 0 -0.68 17 17
cytotoxic T cell degranulation -0.1 0.32 0.45 1 -0.77 75 76
RAP1A/GTP -0.001 0.013 -10000 0 -0.068 10 10
mol:PI-3-4-5-P3 -0.083 0.25 0.58 6 -0.57 82 88
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.26 0.28 67 -0.59 73 140
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0.001 0.12 -10000 0 -0.66 16 16
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.082 0.24 -10000 0 -0.59 77 77
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
CD8 heterodimer -0.057 0.24 -10000 0 -0.59 73 73
CARD11 -0.018 0.1 -10000 0 -0.68 8 8
PRKCB -0.03 0.12 -10000 0 -0.3 66 66
PRKCE -0.029 0.12 -10000 0 -0.29 67 67
PRKCQ -0.094 0.3 0.64 8 -0.68 79 87
LCP2 0.024 0.019 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.047 0.19 0.54 9 -0.39 78 87
IKK complex 0.019 0.14 0.43 22 -0.13 13 35
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.034 0.12 0.26 3 -0.29 62 65
PDPK1 -0.057 0.21 0.56 10 -0.44 78 88
TCR/CD3/MHC I/CD8/Fyn -0.16 0.42 -10000 0 -1 84 84
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.19 0.54 -10000 0 -1.3 79 79
IL23A -0.21 0.56 -10000 0 -1.3 88 88
NF kappa B1 p50/RelA/I kappa B alpha -0.18 0.55 -10000 0 -1.3 80 80
positive regulation of T cell mediated cytotoxicity -0.24 0.62 -10000 0 -1.5 80 80
ITGA3 -0.18 0.51 -10000 0 -1.2 78 78
IL17F -0.1 0.34 0.64 3 -0.74 77 80
IL12B 0.004 0.088 -10000 0 -0.7 5 5
STAT1 (dimer) -0.22 0.59 -10000 0 -1.4 79 79
CD4 -0.18 0.5 -10000 0 -1.2 76 76
IL23 -0.2 0.54 -10000 0 -1.2 90 90
IL23R 0.003 0.11 -10000 0 -0.96 2 2
IL1B -0.23 0.58 -10000 0 -1.4 80 80
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.51 -10000 0 -1.2 75 75
TYK2 0.015 0.035 -10000 0 -10000 0 0
STAT4 0.004 0.1 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.01 0.14 -10000 0 -0.68 21 21
IL12RB1 -0.001 0.077 -10000 0 -0.63 4 4
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
IL12Rbeta1/TYK2 0.014 0.069 -10000 0 -0.49 4 4
IL23R/JAK2 0.01 0.13 -10000 0 -0.87 2 2
positive regulation of chronic inflammatory response -0.24 0.62 -10000 0 -1.5 80 80
natural killer cell activation 0.001 0.008 -10000 0 -0.055 1 1
JAK2 0.015 0.049 -10000 0 -0.4 1 1
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.18 0.5 -10000 0 -1.1 91 91
ALOX12B -0.18 0.5 -10000 0 -1.2 77 77
CXCL1 -0.2 0.53 -10000 0 -1.3 79 79
T cell proliferation -0.24 0.62 -10000 0 -1.5 80 80
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.058 0.27 -10000 0 -0.57 70 70
PI3K -0.2 0.56 -10000 0 -1.3 78 78
IFNG -0.015 0.054 0.16 2 -0.13 64 66
STAT3 (dimer) -0.18 0.52 -10000 0 -1.2 77 77
IL18R1 -0.003 0.098 -10000 0 -0.59 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.098 0.34 -10000 0 -0.79 65 65
IL18/IL18R -0.002 0.15 -10000 0 -0.48 35 35
macrophage activation -0.009 0.021 -10000 0 -0.044 99 99
TNF -0.25 0.61 -10000 0 -1.4 97 97
STAT3/STAT4 -0.2 0.56 -10000 0 -1.3 79 79
STAT4 (dimer) -0.22 0.6 -10000 0 -1.4 80 80
IL18 -0.009 0.11 -10000 0 -0.65 11 11
IL19 -0.17 0.51 -10000 0 -1.2 75 75
STAT5A (dimer) -0.22 0.58 -10000 0 -1.4 79 79
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.008 0.15 -10000 0 -0.68 23 23
CXCL9 -0.27 0.62 -10000 0 -1.4 104 104
MPO -0.18 0.51 -10000 0 -1.2 79 79
positive regulation of humoral immune response -0.24 0.62 -10000 0 -1.5 80 80
IL23/IL23R/JAK2/TYK2 -0.28 0.75 -10000 0 -1.7 79 79
IL6 -0.3 0.64 -10000 0 -1.3 121 121
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.003 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.008 -10000 0 -0.055 1 1
CD3E -0.22 0.56 -10000 0 -1.3 86 86
keratinocyte proliferation -0.24 0.62 -10000 0 -1.5 80 80
NOS2 -0.18 0.5 -10000 0 -1.2 78 78
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.17 0.3 -10000 0 -0.49 206 206
SMAD6-7/SMURF1 0.052 0.014 -10000 0 -10000 0 0
NOG -0.021 0.17 -10000 0 -0.68 30 30
SMAD9 -0.19 0.27 -10000 0 -0.54 173 173
SMAD4 0.027 0.004 -10000 0 -10000 0 0
SMAD5 -0.084 0.17 -10000 0 -0.45 30 30
BMP7/USAG1 -0.24 0.27 -10000 0 -0.51 246 246
SMAD5/SKI -0.07 0.17 0.33 2 -0.45 27 29
SMAD1 -0.036 0.096 -10000 0 -0.45 3 3
BMP2 -0.001 0.14 -10000 0 -0.68 19 19
SMAD1/SMAD1/SMAD4 -0.021 0.086 -10000 0 -0.53 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.21 0.33 -10000 0 -0.68 159 159
BMPR1A-1B/BAMBI -0.11 0.24 -10000 0 -0.45 159 159
AHSG -0.004 0.04 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.012 0.12 -10000 0 -0.44 30 30
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.068 0.17 -10000 0 -0.55 28 28
BMP2-4 (homodimer) 0.003 0.13 -10000 0 -0.51 30 30
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.089 0.22 -10000 0 -0.4 159 159
RGMA 0.001 0.13 -10000 0 -0.66 18 18
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.08 0.16 -10000 0 -0.47 34 34
BMP2-4/USAG1 -0.23 0.26 -10000 0 -0.46 259 259
SMAD6/SMURF1/SMAD5 -0.068 0.17 0.32 1 -0.43 29 30
SOSTDC1 -0.34 0.35 -10000 0 -0.67 246 246
BMP7/BMPR2/BMPR1A-1B -0.088 0.22 -10000 0 -0.4 156 156
SKI 0.026 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.007 -10000 0 -10000 0 0
HFE2 -0.003 0.022 -10000 0 -10000 0 0
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.013 0.14 -10000 0 -0.45 39 39
SMAD5/SMAD5/SMAD4 -0.068 0.17 0.33 2 -0.43 31 33
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.055 0.15 -10000 0 -0.43 29 29
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.028 0.031 -10000 0 -10000 0 0
SMAD1/SKI -0.026 0.1 0.34 1 -0.62 1 2
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.02 0.12 -10000 0 -0.45 30 30
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.66 115 115
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.045 0.053 -10000 0 -0.44 5 5
BMPR1A-1B (homodimer) -0.14 0.26 -10000 0 -0.51 159 159
CHRDL1 -0.45 0.32 -10000 0 -0.66 331 331
ENDOFIN/SMAD1 -0.029 0.099 -10000 0 -0.44 3 3
SMAD6-7/SMURF1/SMAD1 -0.012 0.1 -10000 0 -0.47 2 2
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.053 -10000 0 -0.68 2 2
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.25 -10000 0 -0.47 322 322
BMP2-4/GREM1 -0.085 0.24 -10000 0 -0.48 125 125
SMAD7 0.027 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.18 0.26 -10000 0 -0.51 166 166
SMAD1/SMAD6 -0.027 0.098 -10000 0 -0.5 2 2
TAK1/SMAD6 0.039 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.059 0.14 -10000 0 -0.41 30 30
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.026 0.099 0.31 1 -0.44 3 4
SMAD7/SMURF1 0.038 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.004 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.018 0.071 -10000 0 -0.68 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -10000 0 -0.64 87 87
CHRD 0.013 0.1 -10000 0 -0.68 10 10
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.081 0.16 -10000 0 -0.5 31 31
BMP4 0.008 0.11 -10000 0 -0.65 12 12
FST -0.14 0.3 -10000 0 -0.68 112 112
BMP2-4/NOG -0.009 0.16 -10000 0 -0.44 59 59
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.073 0.21 -10000 0 -0.38 153 153
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.036 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.02 0.15 -10000 0 -0.72 13 13
EGFR 0.02 0.064 -10000 0 -0.68 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
USP6 0.025 0.014 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.042 0.19 -10000 0 -0.5 71 71
ARRB2 -0.036 0.13 -10000 0 -0.39 59 59
mol:GTP 0.024 0.037 0.17 19 -0.13 2 21
ARRB1 0.025 0.032 -10000 0 -0.68 1 1
FBXO8 0.027 0.004 -10000 0 -10000 0 0
TSHR 0.024 0.045 -10000 0 -0.68 2 2
EGF -0.073 0.24 -10000 0 -0.67 68 68
somatostatin receptor activity 0 0.001 0.002 15 -0.001 144 159
ARAP2 0.024 0.045 -10000 0 -0.68 2 2
mol:GDP -0.11 0.15 0.27 5 -0.28 149 154
mol:PI-3-4-5-P3 0 0.001 0.002 11 -0.001 75 86
ITGA2B -0.042 0.21 -10000 0 -0.67 47 47
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.024 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.004 -10000 0 -10000 0 0
HGF/MET -0.079 0.19 -10000 0 -0.52 69 69
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.16 0.51 9 -0.29 152 161
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.02 0.17 -10000 0 -0.44 71 71
ADRB2 0.009 0.11 -10000 0 -0.68 12 12
receptor agonist activity 0 0 0.001 18 0 153 171
actin filament binding 0 0 0.002 16 -0.001 146 162
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.009 0.11 -10000 0 -0.65 12 12
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.005 16 -0.001 92 108
ARF6/GDP -0.006 0.093 0.24 2 -0.44 10 12
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.42 111 111
alphaIIb/beta3 Integrin/paxillin/GIT1 0.009 0.16 -10000 0 -0.42 55 55
ACAP1 0.019 0.044 -10000 0 -0.52 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.051 0.19 -10000 0 -0.56 59 59
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF -0.075 0.25 -10000 0 -0.68 69 69
CYTH3 0.006 0.033 -10000 0 -0.51 2 2
CYTH2 -0.011 0.16 -10000 0 -0.93 14 14
NCK1 0.027 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 21 0 125 146
endosomal lumen acidification 0 0 0.002 7 0 145 152
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 -0.095 0.26 -10000 0 -0.66 86 86
GNAQ/ARNO 0.003 0.15 -10000 0 -0.85 14 14
mol:Phosphatidic acid 0 0 0.001 13 -10000 0 13
PIP3-E 0 0 0.001 10 0 24 34
MET -0.03 0.072 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.64 112 112
GNA15 0.013 0.05 -10000 0 -0.68 1 1
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 15 -0.001 130 145
GNA11 0.016 0.08 -10000 0 -0.63 7 7
LHCGR -0.074 0.23 -10000 0 -0.68 59 59
AGTR1 -0.26 0.34 -10000 0 -0.67 195 195
desensitization of G-protein coupled receptor protein signaling pathway -0.051 0.19 -10000 0 -0.56 59 59
IPCEF1/ARNO -0.036 0.18 -10000 0 -0.76 14 14
alphaIIb/beta3 Integrin -0.027 0.18 -10000 0 -0.53 55 55
Coregulation of Androgen receptor activity

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
NRIP1 -0.005 0.052 -10000 0 -0.21 1 1
SVIL -0.002 0.048 -10000 0 -10000 0 0
ZNF318 0.075 0.087 0.24 9 -0.68 1 10
JMJD2C -0.065 0.067 -10000 0 -0.12 272 272
T-DHT/AR/Ubc9 -0.22 0.24 -10000 0 -0.49 203 203
CARM1 0.023 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.013 -10000 0 -10000 0 0
CTNNB1 0.003 0.04 -10000 0 -10000 0 0
AKT1 0.038 0.02 -10000 0 -10000 0 0
PTK2B 0.008 0.032 -10000 0 -10000 0 0
MED1 0.037 0.021 -10000 0 -10000 0 0
MAK 0.068 0.11 0.24 9 -0.65 6 15
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.064 -10000 0 -0.68 2 2
GSN 0 0.044 -10000 0 -10000 0 0
NCOA2 -0.037 0.2 -10000 0 -0.68 42 42
NCOA6 -0.003 0.054 -10000 0 -0.68 1 1
DNA-PK 0.074 0.078 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.038 -10000 0 -10000 0 0
cell proliferation 0.001 0.14 -10000 0 -0.89 7 7
XRCC5 0.037 0.018 -10000 0 -10000 0 0
UBE3A -0.012 0.063 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.24 0.26 -10000 0 -0.52 207 207
FHL2 -0.14 0.33 -10000 0 -1.1 44 44
RANBP9 -0.001 0.046 -10000 0 -10000 0 0
JMJD1A -0.001 0.035 -10000 0 -0.12 34 34
CDK6 0.023 0.056 -10000 0 -0.68 3 3
TGFB1I1 -0.003 0.047 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.5 204 204
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.53 226 226
CTDSP1 0.012 0.023 -10000 0 -10000 0 0
CTDSP2 0.058 0.052 0.2 1 -10000 0 1
BRCA1 -0.003 0.047 -10000 0 -10000 0 0
TCF4 0.048 0.035 -10000 0 -10000 0 0
CDKN2A 0.002 0.083 -10000 0 -10000 0 0
SRF 0.034 0.051 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.7 11 11
KLK3 -0.39 0.65 -10000 0 -1.4 136 136
TMF1 0.018 0.047 -10000 0 -0.68 2 2
HNRNPA1 0.044 0.029 -10000 0 -10000 0 0
AOF2 -0.02 0.033 -10000 0 -0.072 136 136
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.49 198 198
AR -0.31 0.34 -10000 0 -0.71 200 200
UBA3 0.013 0.023 -10000 0 -10000 0 0
PATZ1 0.033 0.03 -10000 0 -10000 0 0
PAWR 0.02 0.015 -10000 0 -10000 0 0
PRKDC 0.037 0.017 -10000 0 -10000 0 0
PA2G4 0.048 0.037 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.22 -10000 0 -0.45 198 198
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.5 200 200
LATS2 0.04 0.043 -10000 0 -0.68 1 1
T-DHT/AR/PRX1 -0.19 0.22 -10000 0 -0.44 195 195
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.005 0.085 -10000 0 -0.68 6 6
KLK2 -0.67 0.56 -10000 0 -1.1 275 275
CASP8 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.53 203 203
TMPRSS2 -0.16 0.28 -10000 0 -1.1 34 34
CCND1 0.014 0.03 -10000 0 -10000 0 0
PIAS1 -0.012 0.063 -10000 0 -10000 0 0
mol:T-DHT -0.033 0.039 -10000 0 -0.077 178 178
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.03 0.09 -10000 0 -0.2 5 5
T-DHT/AR/CDK6 -0.22 0.24 -10000 0 -0.49 202 202
CMTM2 0.028 0.012 -10000 0 -10000 0 0
SNURF -0.009 0.15 -10000 0 -0.64 25 25
ZMIZ1 -0.024 0.057 -10000 0 -0.67 1 1
CCND3 0.028 0.003 -10000 0 -10000 0 0
TGIF1 0.044 0.029 -10000 0 -10000 0 0
FKBP4 -0.002 0.045 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory 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
PCK2 0.085 0.086 -10000 0 -10000 0 0
SMARCC2 0.025 0.019 -10000 0 -10000 0 0
SMARCC1 0.026 0.018 -10000 0 -10000 0 0
TBX21 -0.12 0.24 0.33 1 -0.7 51 52
SUMO2 0.024 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.023 -10000 0 -10000 0 0
FKBP4 0.027 0.005 -10000 0 -10000 0 0
FKBP5 0.019 0.078 -10000 0 -0.68 6 6
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.34 47 -0.42 4 51
PRL -0.063 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.19 0.29 0.55 133 -0.46 18 151
RELA -0.03 0.1 -10000 0 -0.29 20 20
FGG 0.17 0.2 0.47 106 -10000 0 106
GR beta/TIF2 0.076 0.2 0.33 67 -0.45 42 109
IFNG -0.36 0.48 -10000 0 -1.1 117 117
apoptosis -0.012 0.23 0.5 33 -0.54 20 53
CREB1 0.026 0.014 -10000 0 -10000 0 0
histone acetylation -0.077 0.16 -10000 0 -0.43 58 58
BGLAP -0.077 0.13 -10000 0 -0.49 14 14
GR/PKAc 0.11 0.1 0.35 27 -0.34 1 28
NF kappa B1 p50/RelA -0.053 0.18 -10000 0 -0.46 40 40
SMARCD1 0.025 0.019 -10000 0 -10000 0 0
MDM2 0.085 0.097 0.26 80 -10000 0 80
GATA3 -0.004 0.15 -10000 0 -0.64 24 24
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.12 0.14 -10000 0 -0.56 18 18
GSK3B 0.025 0.018 -10000 0 -10000 0 0
NR1I3 0.007 0.23 0.51 29 -0.61 8 37
CSN2 0.14 0.16 0.39 88 -10000 0 88
BRG1/BAF155/BAF170/BAF60A 0.063 0.055 -10000 0 -0.32 6 6
NFATC1 0.015 0.095 -10000 0 -0.68 9 9
POU2F1 0.026 0.01 -10000 0 -10000 0 0
CDKN1A 0.026 0.035 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.083 0.12 -10000 0 -0.68 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.36 35 -0.39 10 45
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.39 0.49 24 -0.83 98 122
JUN -0.24 0.27 -10000 0 -0.57 162 162
IL4 -0.1 0.16 -10000 0 -0.63 21 21
CDK5R1 0.026 0.014 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.31 -10000 0 -0.66 152 152
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.36 32 -0.39 4 36
cortisol/GR alpha (monomer) 0.26 0.3 0.65 139 -10000 0 139
NCOA2 -0.034 0.2 -10000 0 -0.68 42 42
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.19 0.3 -10000 0 -0.69 127 127
AP-1/NFAT1-c-4 -0.38 0.41 -10000 0 -0.76 218 218
AFP -0.17 0.2 0.47 1 -0.61 39 40
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.48 32 -10000 0 32
TP53 0.04 0.015 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
KRT17 -0.3 0.34 -10000 0 -0.78 113 113
KRT14 -0.084 0.12 -10000 0 -0.5 6 6
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.034 0.048 -10000 0 -0.26 10 10
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.005 -10000 0 -10000 0 0
AP-1 -0.38 0.41 -10000 0 -0.77 217 217
MAPK14 0.027 0.016 -10000 0 -10000 0 0
MAPK10 0.025 0.036 -10000 0 -0.68 1 1
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.39 0.5 -10000 0 -1.1 138 138
interleukin-1 receptor activity 0.003 0.003 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.023 -10000 0 -10000 0 0
CGA -0.095 0.14 -10000 0 -0.52 15 15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.089 0.12 0.36 27 -10000 0 27
MAPK3 0.025 0.016 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.17 0.24 -10000 0 -0.66 69 69
NFKB1 -0.029 0.099 -10000 0 -0.27 27 27
MAPK8 -0.14 0.18 -10000 0 -0.44 89 89
MAPK9 0.027 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.017 0.23 0.5 32 -0.56 20 52
BAX 0.038 0.086 0.84 4 -10000 0 4
POMC -0.45 0.63 -10000 0 -1.4 122 122
EP300 0.026 0.045 -10000 0 -0.26 9 9
cortisol/GR alpha (dimer)/p53 0.23 0.24 0.56 134 -10000 0 134
proteasomal ubiquitin-dependent protein catabolic process 0.081 0.13 0.34 77 -10000 0 77
SGK1 0.009 0.22 0.51 1 -1.3 11 12
IL13 -0.21 0.25 -10000 0 -0.74 51 51
IL6 -0.31 0.5 -10000 0 -1.2 111 111
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.21 -10000 0 -0.65 44 44
IL2 -0.26 0.28 -10000 0 -0.66 109 109
CDK5 0.027 0.008 -10000 0 -10000 0 0
PRKACB 0.025 0.032 -10000 0 -0.68 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.29 -10000 0 -0.75 66 66
CDK5R1/CDK5 0.038 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.004 0.14 -10000 0 -0.4 20 20
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.54 127 -10000 0 127
SMARCA4 0.024 0.019 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.4 74 -0.43 2 76
NF kappa B1 p50/RelA/Cbp -0.014 0.16 -10000 0 -0.43 24 24
JUN (dimer) -0.24 0.27 -10000 0 -0.57 162 162
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.21 0.36 -10000 0 -0.92 87 87
NR3C1 0.16 0.19 0.45 103 -10000 0 103
NR4A1 -0.26 0.36 -10000 0 -0.67 203 203
TIF2/SUV420H1 -0.009 0.16 -10000 0 -0.51 42 42
MAPKKK cascade -0.012 0.23 0.5 33 -0.54 20 53
cortisol/GR alpha (dimer)/Src-1 0.23 0.24 0.56 136 -10000 0 136
PBX1 0.025 0.033 -10000 0 -0.68 1 1
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.26 0.46 -10000 0 -1.1 90 90
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.4 74 -0.44 2 76
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.54 127 -10000 0 127
mol:cortisol 0.14 0.19 0.38 142 -10000 0 142
MMP1 -0.1 0.15 -10000 0 -0.9 10 10
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.094 0.33 -10000 0 -1.1 43 43
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.019 0.11 -10000 0 -0.34 35 35
ATF2/c-Jun -0.2 0.35 -10000 0 -0.8 115 115
MAPK11 -0.013 0.097 -10000 0 -0.35 29 29
MITF -0.025 0.12 -10000 0 -0.41 39 39
MAPKAPK5 -0.021 0.12 -10000 0 -0.4 35 35
KRT8 -0.021 0.12 -10000 0 -0.4 35 35
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.027 0.15 -10000 0 -0.5 34 34
CEBPB -0.022 0.12 -10000 0 -0.4 37 37
SLC9A1 -0.025 0.12 -10000 0 -0.4 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.074 0.18 -10000 0 -0.42 79 79
p38alpha-beta/MNK1 -0.011 0.13 -10000 0 -0.4 34 34
JUN -0.2 0.35 -10000 0 -0.8 115 115
PPARGC1A -0.22 0.25 -10000 0 -0.45 244 244
USF1 -0.026 0.12 -10000 0 -0.4 40 40
RAB5/GDP/GDI1 -0.036 0.1 -10000 0 -0.31 37 37
NOS2 -0.03 0.12 -10000 0 -0.45 20 20
DDIT3 -0.021 0.12 -10000 0 -0.4 35 35
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.017 0.095 0.38 2 -0.33 33 35
p38alpha-beta/HBP1 -0.008 0.12 -10000 0 -0.41 28 28
CREB1 -0.056 0.16 -10000 0 -0.47 41 41
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.026 0.1 -10000 0 -0.37 30 30
RPS6KA4 -0.023 0.12 -10000 0 -0.41 37 37
PLA2G4A -0.053 0.16 -10000 0 -0.49 49 49
GDI1 -0.021 0.12 -10000 0 -0.42 34 34
TP53 -0.033 0.14 -10000 0 -0.5 30 30
RPS6KA5 -0.062 0.18 -10000 0 -0.45 76 76
ESR1 -0.054 0.2 -10000 0 -0.55 53 53
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.021 0.12 -10000 0 -0.4 36 36
MEF2A -0.027 0.13 -10000 0 -0.42 41 41
EIF4EBP1 -0.055 0.16 -10000 0 -0.46 42 42
KRT19 -0.054 0.17 -10000 0 -0.5 45 45
ELK4 -0.026 0.12 -10000 0 -0.4 40 40
ATF6 -0.026 0.12 -10000 0 -0.4 40 40
ATF1 -0.054 0.16 -10000 0 -0.47 40 40
p38alpha-beta/MAPKAPK2 -0.012 0.13 -10000 0 -0.4 34 34
p38alpha-beta/MAPKAPK3 -0.012 0.13 -10000 0 -0.41 34 34
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.043 -10000 0 -0.82 1 1
forebrain development -0.3 0.28 0.37 3 -0.54 240 243
GNAO1 0.002 0.12 -10000 0 -0.68 15 15
SMO/beta Arrestin2 0.015 0.036 -10000 0 -0.51 1 1
SMO 0.016 0.035 -10000 0 -0.68 1 1
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.037 0.073 -10000 0 -0.34 5 5
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
GNAI2 0.025 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.033 -10000 0 -0.4 1 1
GNAI1 0.023 0.033 -10000 0 -0.69 1 1
XPO1 0.016 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.21 0.22 -10000 0 -0.49 134 134
SAP30 0.026 0.032 -10000 0 -0.68 1 1
mol:GDP 0.016 0.035 -10000 0 -0.67 1 1
MIM/GLI2A -0.031 0.066 -10000 0 -10000 0 0
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.007 -10000 0 -10000 0 0
GLI2 0 0.08 0.28 2 -0.38 7 9
GLI3 0.027 0.077 0.28 3 -0.35 5 8
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.68 1 1
Gi family/GTP -0.016 0.07 -10000 0 -0.3 17 17
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.065 -10000 0 -0.45 2 2
GLI2/Su(fu) 0.009 0.077 -10000 0 -0.49 3 3
FOXA2 -0.59 0.62 -10000 0 -1.2 236 236
neural tube patterning -0.3 0.28 0.37 3 -0.54 240 243
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.034 0.029 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 -0.031 0.066 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.37 3 -0.54 240 243
SUFU 0.019 0.016 -10000 0 -0.24 1 1
LGALS3 -0.026 0.072 -10000 0 -10000 0 0
catabolic process 0.032 0.1 0.29 1 -0.44 8 9
GLI3A/CBP -0.18 0.2 -10000 0 -0.38 241 241
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.31 0.29 0.37 3 -0.55 240 243
RAB23 0.021 0.064 -10000 0 -0.68 4 4
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.018 0.05 -10000 0 -0.26 1 1
GNAZ 0.019 0.012 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.68 2 2
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GLI2/SPOP 0.011 0.082 -10000 0 -0.36 7 7
STK36 0.016 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.056 -10000 0 -0.31 6 6
PTCH1 -0.27 0.26 0.52 2 -0.59 133 135
MIM/GLI1 -0.43 0.38 0.34 1 -0.7 265 266
CREBBP -0.18 0.2 -10000 0 -0.38 241 241
Su(fu)/SIN3/HDAC complex 0.037 0.064 -10000 0 -0.53 4 4
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.006 0.052 -10000 0 -10000 0 0
GNB1/GNG2 -0.034 0.067 -10000 0 -0.19 67 67
AKT1 0.009 0.13 0.41 19 -0.26 1 20
EGF -0.073 0.24 -10000 0 -0.67 68 68
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.018 0.089 0.36 13 -0.51 3 16
mol:Ca2+ -0.021 0.15 0.4 12 -0.3 69 81
LYN 0.018 0.088 0.36 12 -0.51 3 15
RhoA/GTP -0.01 0.055 -10000 0 -0.15 3 3
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.021 0.16 0.41 16 -0.35 68 84
GNG2 0.025 0.032 -10000 0 -0.68 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.61 12 13
G beta5/gamma2 -0.044 0.091 -10000 0 -0.26 65 65
PRKCH -0.027 0.17 0.46 11 -0.36 68 79
DNM1 0.004 0.12 -10000 0 -0.62 16 16
TXA2/TP beta/beta Arrestin3 -0.011 0.12 -10000 0 -0.45 29 29
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.006 0.15 -10000 0 -0.68 22 22
G12 family/GTP -0.036 0.12 -10000 0 -0.31 67 67
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP 0.052 0.14 0.44 31 -0.35 6 37
mol:NADP 0.026 0.006 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.67 130 130
mol:IP3 -0.031 0.17 0.46 10 -0.38 69 79
cell morphogenesis 0.035 0.007 -10000 0 -10000 0 0
PLCB2 -0.054 0.22 0.45 8 -0.52 69 77
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.078 0.18 0.36 9 -0.34 120 129
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.012 0.082 0.34 9 -0.51 3 12
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.018 0.071 -10000 0 -0.68 5 5
PRKCB1 -0.032 0.17 0.44 10 -0.38 70 80
GNAQ 0.025 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.05 0.23 0.51 10 -0.54 70 80
LCK 0.013 0.1 0.36 13 -0.53 6 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.024 0.089 -10000 0 -0.68 3 3
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.029 -10000 0 -0.33 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.029 0.089 -10000 0 -0.68 3 3
MAPK14 -0.007 0.12 0.33 19 -0.24 34 53
TGM2/GTP -0.048 0.18 0.34 3 -0.43 65 68
MAPK11 -0.012 0.12 0.35 18 -0.24 32 50
ARHGEF1 -0.016 0.074 0.17 1 -0.19 33 34
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.028 0.18 0.42 15 -0.39 70 85
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.019 0.14 0.37 15 -0.29 70 85
cAMP biosynthetic process -0.033 0.17 0.43 12 -0.36 65 77
Gq family/GTP/EBP50 -0.043 0.11 0.24 2 -0.23 113 115
actin cytoskeleton reorganization 0.035 0.007 -10000 0 -10000 0 0
SRC 0.014 0.081 0.34 9 -0.51 3 12
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.021 0.13 0.44 15 -0.34 10 25
VCAM1 -0.016 0.14 0.36 15 -0.3 70 85
TP beta/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.61 12 13
platelet activation -0.008 0.16 0.44 20 -0.3 65 85
PGI2/IP 0.013 0.054 -10000 0 -0.51 5 5
PRKACA 0.002 0.089 -10000 0 -0.37 23 23
Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.28 1 -0.57 12 13
TXA2/TP beta/beta Arrestin2 0.005 0.11 -10000 0 -0.54 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.002 0.089 -10000 0 -0.37 21 21
mol:DAG -0.037 0.19 0.48 9 -0.43 70 79
EGFR 0.021 0.064 -10000 0 -0.68 4 4
TXA2/TP alpha -0.049 0.21 0.53 9 -0.49 65 74
Gq family/GTP -0.063 0.13 0.22 2 -0.27 129 131
YES1 0.019 0.09 0.37 13 -0.51 3 16
GNAI2/GTP 0.006 0.076 -10000 0 -0.6 3 3
PGD2/DP -0.004 0.11 -10000 0 -0.51 22 22
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.02 0.092 0.36 14 -0.51 3 17
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.013 0.05 -10000 0 -0.68 1 1
PGK/cGMP -0.09 0.21 -10000 0 -0.44 128 128
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.038 0.1 -10000 0 -0.51 7 7
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.034 0.18 0.45 12 -0.38 72 84
PRKCB -0.03 0.17 0.45 12 -0.37 69 81
PRKCE -0.034 0.16 0.37 8 -0.37 70 78
PRKCD -0.032 0.17 0.45 9 -0.39 69 78
PRKCG -0.032 0.17 0.41 13 -0.39 68 81
muscle contraction -0.042 0.22 0.5 11 -0.49 70 81
PRKCZ -0.021 0.16 0.42 15 -0.35 65 80
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.013 0.088 -10000 0 -0.7 3 3
PRKCQ -0.031 0.16 0.42 10 -0.36 71 81
MAPKKK cascade -0.041 0.2 0.46 12 -0.46 70 82
SELE -0.033 0.18 0.36 15 -0.42 70 85
TP beta/GNAI2/GDP/G beta/gamma 0.037 0.098 -10000 0 -0.76 3 3
ROCK1 0.027 0.004 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.64 112 112
chemotaxis -0.058 0.26 0.55 9 -0.62 70 79
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.016 0.08 -10000 0 -0.63 7 7
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.22 -10000 0 -0.43 132 132
MAP3K8 0.013 0.086 -10000 0 -0.64 8 8
FOS -0.079 0.18 0.29 3 -0.45 58 61
PRKCA -0.017 0.15 -10000 0 -0.68 22 22
PTPN7 -0.02 0.13 -10000 0 -0.68 16 16
HRAS 0.025 0.011 -10000 0 -10000 0 0
PRKCB -0.006 0.083 -10000 0 -0.68 5 5
NRAS 0.025 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.022 -10000 0 -10000 0 0
MAPK3 -0.016 0.12 -10000 0 -0.49 21 21
MAP2K1 -0.024 0.14 -10000 0 -0.54 27 27
ELK1 0.012 0.025 -10000 0 -10000 0 0
BRAF -0.018 0.13 -10000 0 -0.53 26 26
mol:GTP -0.002 0.004 -10000 0 -0.006 129 129
MAPK1 -0.1 0.2 -10000 0 -0.41 116 116
RAF1 -0.017 0.12 -10000 0 -0.52 26 26
KRAS 0.026 0.005 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.027 0.14 -10000 0 -0.38 38 38
TBX21 -0.12 0.43 -10000 0 -1.1 61 61
B2M 0.023 0.017 -10000 0 -10000 0 0
TYK2 0.02 0.03 -10000 0 -10000 0 0
IL12RB1 0.004 0.075 -10000 0 -0.61 4 4
GADD45B -0.098 0.39 -10000 0 -1 58 58
IL12RB2 -0.006 0.14 -10000 0 -0.68 18 18
GADD45G -0.093 0.36 -10000 0 -0.96 50 50
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 -0.003 0.11 -10000 0 -0.66 11 11
IL2RA -0.016 0.15 -10000 0 -0.64 26 26
IFNG -0.071 0.23 -10000 0 -0.68 59 59
STAT3 (dimer) -0.08 0.31 -10000 0 -0.8 59 59
HLA-DRB5 -0.009 0.082 -10000 0 -0.68 4 4
FASLG -0.13 0.45 -10000 0 -1.2 61 61
NF kappa B2 p52/RelB -0.1 0.38 -10000 0 -0.94 63 63
CD4 0.011 0.033 -10000 0 -10000 0 0
SOCS1 0.024 0.035 -10000 0 -0.68 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.066 0.21 -10000 0 -0.64 54 54
CD3E -0.047 0.19 -10000 0 -0.63 43 43
CD3G -0.11 0.26 -10000 0 -0.66 88 88
IL12Rbeta2/JAK2 0.01 0.11 -10000 0 -0.5 19 19
CCL3 -0.11 0.42 -10000 0 -1.2 47 47
CCL4 -0.15 0.49 -10000 0 -1.4 58 58
HLA-A 0.023 0.019 -10000 0 -10000 0 0
IL18/IL18R 0.029 0.16 -10000 0 -0.49 34 34
NOS2 -0.087 0.35 -10000 0 -0.9 56 56
IL12/IL12R/TYK2/JAK2/SPHK2 -0.027 0.14 -10000 0 -0.38 41 41
IL1R1 -0.1 0.37 -10000 0 -1 53 53
IL4 0 0.034 -10000 0 -10000 0 0
JAK2 0.019 0.036 -10000 0 -0.4 1 1
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1.1 97 97
RAB7A -0.057 0.3 -10000 0 -0.74 54 54
lysosomal transport -0.052 0.29 -10000 0 -0.69 56 56
FOS -0.37 0.61 -10000 0 -1.2 160 160
STAT4 (dimer) -0.083 0.36 -10000 0 -0.84 66 66
STAT5A (dimer) -0.14 0.4 -10000 0 -0.95 73 73
GZMA -0.12 0.4 -10000 0 -1.1 51 51
GZMB -0.11 0.39 -10000 0 -1.1 49 49
HLX 0.021 0.025 -10000 0 -10000 0 0
LCK -0.12 0.43 -10000 0 -1.1 62 62
TCR/CD3/MHC II/CD4 -0.15 0.29 -10000 0 -0.67 83 83
IL2/IL2R -0.007 0.17 -10000 0 -0.54 36 36
MAPK14 -0.084 0.37 -10000 0 -0.88 65 65
CCR5 -0.094 0.4 -10000 0 -1.1 47 47
IL1B -0.034 0.2 -10000 0 -0.7 38 38
STAT6 -0.007 0.11 -10000 0 -0.46 5 5
STAT4 0.004 0.1 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B 0.007 0.08 -10000 0 -0.69 5 5
CD8A -0.026 0.18 -10000 0 -0.66 36 36
CD8B -0.057 0.22 -10000 0 -0.64 56 56
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.027 0.14 0.38 38 -10000 0 38
IL2RB 0.003 0.092 -10000 0 -0.58 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.071 0.32 -10000 0 -0.76 66 66
IL2RG -0.012 0.14 -10000 0 -0.63 21 21
IL12 -0.034 0.18 -10000 0 -0.52 55 55
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.014 0.13 -10000 0 -0.68 17 17
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.054 0.22 -10000 0 -0.68 51 51
IL12/IL12R/TYK2/JAK2 -0.14 0.5 -10000 0 -1.2 65 65
MAP2K3 -0.086 0.37 -10000 0 -0.92 59 59
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.093 0.38 -10000 0 -0.91 65 65
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.093 -10000 0 -0.68 7 7
IL18RAP -0.004 0.14 -10000 0 -0.68 21 21
IL12Rbeta1/TYK2 0.024 0.065 -10000 0 -0.46 4 4
EOMES -0.12 0.4 -10000 0 -1.3 47 47
STAT1 (dimer) -0.12 0.36 -10000 0 -0.79 84 84
T cell proliferation -0.051 0.26 -10000 0 -0.61 64 64
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.004 0.097 -10000 0 -0.58 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.064 0.28 -10000 0 -0.67 67 67
ATF2 -0.086 0.34 -10000 0 -0.81 64 64
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.003 0.2 0.6 5 -0.63 14 19
CRP 0.001 0.21 0.6 8 -0.68 11 19
cell cycle arrest -0.018 0.21 0.75 1 -0.66 27 28
TIMP1 -0.041 0.22 0.6 3 -0.68 26 29
IL6ST -0.062 0.24 -10000 0 -0.67 62 62
Rac1/GDP -0.05 0.21 -10000 0 -0.55 46 46
AP1 -0.11 0.27 -10000 0 -0.61 89 89
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.014 0.2 0.62 4 -0.66 13 17
HSP90B1 0.04 0.069 -10000 0 -0.92 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.094 0.25 -10000 0 -0.71 51 51
AKT1 0.039 0.063 -10000 0 -0.98 1 1
FOXO1 0.038 0.06 -10000 0 -0.91 1 1
MAP2K6 -0.085 0.23 0.25 1 -0.59 59 60
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.035 0.2 0.35 3 -0.56 36 39
MITF -0.072 0.21 -10000 0 -0.57 50 50
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.008 -10000 0 -10000 0 0
A2M 0.026 0.071 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.005 0.1 -10000 0 -0.52 8 8
STAT3 -0.028 0.22 0.76 1 -0.71 27 28
STAT1 0.009 0.1 -10000 0 -0.94 5 5
CEBPD -0.006 0.2 0.64 2 -0.66 12 14
PIK3CA 0.024 0.055 -10000 0 -0.68 3 3
PI3K 0.038 0.044 -10000 0 -0.51 3 3
JUN -0.12 0.29 -10000 0 -0.67 103 103
PIAS3/MITF -0.057 0.21 -10000 0 -0.56 45 45
MAPK11 -0.095 0.24 -10000 0 -0.71 48 48
STAT3 (dimer)/FOXO1 0.012 0.17 -10000 0 -0.54 16 16
GRB2/SOS1/GAB family -0.033 0.2 -10000 0 -0.53 38 38
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.076 0.21 -10000 0 -0.38 133 133
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.025 0.019 -10000 0 -0.36 1 1
LBP 0.003 0.19 0.6 8 -0.6 8 16
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.026 0.015 -10000 0 -10000 0 0
MYC -0.019 0.25 0.63 3 -0.99 17 20
FGG -0.012 0.2 0.63 4 -0.67 13 17
macrophage differentiation -0.018 0.21 0.75 1 -0.66 27 28
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.074 0.26 -10000 0 -0.46 132 132
JUNB -0.007 0.21 0.6 3 -0.75 16 19
FOS -0.16 0.31 -10000 0 -0.67 126 126
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.071 0.23 -10000 0 -0.51 70 70
STAT1/PIAS1 -0.042 0.21 -10000 0 -0.53 44 44
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.065 -10000 0 -0.55 3 3
STAT3 (dimer) -0.023 0.22 0.76 1 -0.69 27 28
PRKCD -0.023 0.19 0.42 6 -0.57 29 35
IL6R 0.002 0.13 -10000 0 -0.68 16 16
SOCS3 -0.11 0.33 0.43 2 -0.94 50 52
gp130 (dimer)/JAK1/JAK1/LMO4 -0.005 0.17 -10000 0 -0.44 60 60
Rac1/GTP -0.047 0.2 -10000 0 -0.55 45 45
HCK 0.018 0.035 -10000 0 -10000 0 0
MAPKKK cascade 0.023 0.11 0.34 1 -0.59 8 9
bone resorption -0.012 0.19 0.62 4 -0.62 13 17
IRF1 -0.002 0.2 0.64 6 -0.66 10 16
mol:GDP -0.07 0.21 0.25 1 -0.55 52 53
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.071 0.21 0.25 1 -0.56 52 53
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.089 0.25 -10000 0 -0.69 53 53
PTPN11 0.014 0.075 -10000 0 -0.87 3 3
IL6/IL6RA -0.082 0.23 -10000 0 -0.53 100 100
gp130 (dimer)/TYK2/TYK2/LMO4 -0.008 0.16 -10000 0 -0.41 62 62
gp130 (dimer)/JAK2/JAK2/LMO4 -0.01 0.16 -10000 0 -0.44 60 60
IL6 -0.11 0.27 -10000 0 -0.68 90 90
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.021 0.076 -10000 0 -0.68 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.078 0.21 -10000 0 -0.38 131 131
LMO4 0.028 0.018 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.025 0.21 -10000 0 -0.71 25 25
MCL1 0.053 0.073 -10000 0 -0.82 1 1
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.011 -9999 0 -10000 0 0
EGFR 0.021 0.064 -9999 0 -0.68 4 4
EGF/EGFR -0.014 0.15 -9999 0 -0.37 73 73
EGF/EGFR dimer/SHC/GRB2/SOS1 0.006 0.16 -9999 0 -0.38 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.025 0.034 -9999 0 -0.68 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.073 0.24 -9999 0 -0.67 68 68
EGF/EGFR dimer/SHC -0.022 0.17 -9999 0 -0.43 71 71
mol:GDP 0.001 0.15 -9999 0 -0.38 65 65
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.019 0.072 -9999 0 -0.68 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.012 0.14 -9999 0 -0.36 65 65
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP 0.001 0.15 -9999 0 -0.36 65 65
FRAP1 -0.049 0.13 -9999 0 -0.36 65 65
EGF/EGFR dimer -0.042 0.19 -9999 0 -0.5 71 71
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.062 -9999 0 -0.51 6 6
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.038 0.11 -10000 0 -0.41 24 24
ER alpha/Gai/GDP/Gbeta gamma -0.006 0.14 -10000 0 -0.47 32 32
AKT1 -0.017 0.2 -10000 0 -0.77 31 31
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.013 0.21 -10000 0 -0.78 31 31
mol:Ca2+ -0.095 0.19 -10000 0 -0.42 115 115
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.02 0.15 -10000 0 -0.44 51 51
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.014 0.19 0.73 31 -10000 0 31
RhoA/GTP 0.004 0.075 -10000 0 -0.35 19 19
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.004 0.13 -10000 0 -0.53 22 22
regulation of stress fiber formation 0.008 0.087 0.31 15 -0.28 1 16
E2/ERA-ERB (dimer) 0.004 0.11 -10000 0 -0.44 26 26
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.008 0.089 -10000 0 -0.37 23 23
pseudopodium formation -0.008 0.087 0.28 1 -0.31 15 16
E2/ER alpha (dimer)/PELP1 0.008 0.097 -10000 0 -0.4 23 23
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.68 1 1
GNAO1 0.004 0.12 -10000 0 -0.68 15 15
HRAS 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.008 0.16 0.48 8 -0.57 25 33
E2/ER beta (dimer) 0.015 0.048 -10000 0 -0.51 4 4
mol:GDP 0 0.11 -10000 0 -0.47 25 25
mol:NADP 0.008 0.16 0.48 8 -0.57 25 33
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.099 0.2 -10000 0 -0.44 115 115
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.098 0.2 -10000 0 -0.45 115 115
PLCB2 -0.099 0.2 -10000 0 -0.45 115 115
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
mol:L-citrulline 0.008 0.16 0.48 8 -0.57 25 33
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP 0.002 0.15 -10000 0 -0.67 21 21
JNK cascade 0.015 0.048 -10000 0 -0.51 4 4
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.021 0.064 -10000 0 -0.68 4 4
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.016 0.15 -10000 0 -0.65 24 24
Gq family/GDP/Gbeta gamma -0.057 0.19 -10000 0 -0.65 28 28
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.017 0.1 -10000 0 -0.57 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.002 0.13 -10000 0 -0.54 21 21
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.011 0.11 -10000 0 -0.49 24 24
STRN -0.015 0.16 -10000 0 -0.66 29 29
GNAL -0.06 0.23 -10000 0 -0.66 61 61
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.041 -10000 0 -0.44 4 4
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.68 1 1
HBEGF -0.018 0.14 0.38 4 -0.49 27 31
cAMP biosynthetic process -0.042 0.16 -10000 0 -0.38 78 78
SRC -0.005 0.13 -10000 0 -0.49 24 24
PI3K 0.036 0.044 -10000 0 -0.51 3 3
GNB1 0.026 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.029 0.11 -10000 0 -0.43 25 25
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.071 0.16 -10000 0 -0.43 52 52
Gs family/GTP -0.031 0.16 -10000 0 -0.39 78 78
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.015 -10000 0 -10000 0 0
vasodilation 0.009 0.15 0.48 8 -0.54 25 33
mol:DAG -0.099 0.2 -10000 0 -0.44 115 115
Gs family/GDP/Gbeta gamma -0.027 0.14 -10000 0 -0.36 71 71
MSN -0.009 0.093 0.29 1 -0.34 15 16
Gq family/GTP -0.1 0.22 -10000 0 -0.47 120 120
mol:PI-3-4-5-P3 -0.011 0.2 -10000 0 -0.74 31 31
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.009 0.15 0.54 25 -0.48 8 33
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.11 -10000 0 -0.45 25 25
NOS3 0.001 0.16 0.42 3 -0.6 25 28
GNA11 0.016 0.08 -10000 0 -0.63 7 7
MAPKKK cascade -0.016 0.18 0.37 1 -0.5 51 52
E2/ER alpha (dimer)/PELP1/Src -0.001 0.14 -10000 0 -0.55 23 23
ruffle organization -0.008 0.087 0.28 1 -0.31 15 16
ROCK2 -0.003 0.11 0.36 5 -0.34 33 38
GNA14 -0.13 0.28 -10000 0 -0.64 112 112
GNA15 0.013 0.05 -10000 0 -0.68 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.032 0.16 -10000 0 -0.52 31 31
MMP2 -0.004 0.13 0.34 1 -0.48 24 25
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0.11 -10000 0 -0.39 30 30
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.11 0.32 7 -0.4 11 18
alphaV/beta3 Integrin/Osteopontin/Src -0.003 0.12 -10000 0 -0.5 24 24
AP1 -0.14 0.3 -10000 0 -0.67 96 96
ILK -0.007 0.12 -10000 0 -0.41 29 29
bone resorption -0.007 0.13 -10000 0 -0.38 36 36
PTK2B 0.027 0.004 -10000 0 -10000 0 0
PYK2/p130Cas 0.042 0.12 -10000 0 -0.38 30 30
ITGAV 0.026 0.045 -10000 0 -0.67 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.017 0.11 -10000 0 -0.51 19 19
alphaV/beta3 Integrin/Osteopontin 0.027 0.13 -10000 0 -0.43 34 34
MAP3K1 -0.008 0.12 -10000 0 -0.42 30 30
JUN -0.12 0.29 -10000 0 -0.67 103 103
MAPK3 -0.022 0.1 -10000 0 -0.39 30 30
MAPK1 -0.023 0.1 -10000 0 -0.38 30 30
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.018 0.12 -10000 0 -0.42 34 34
ITGB3 0.011 0.11 -10000 0 -0.64 12 12
NFKBIA -0.018 0.099 -10000 0 -0.38 30 30
FOS -0.16 0.31 -10000 0 -0.67 126 126
CD44 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.039 0.11 0.52 3 -0.64 2 5
NF kappa B1 p50/RelA 0.021 0.1 -10000 0 -0.47 5 5
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.027 0.096 -10000 0 -0.55 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.008 0.12 -10000 0 -0.42 30 30
VAV3 -0.016 0.12 0.4 1 -0.4 34 35
MAP3K14 -0.013 0.11 -10000 0 -0.42 30 30
ROCK2 -0.002 0.14 -10000 0 -0.66 20 20
SPP1 -0.029 0.15 -10000 0 -0.67 22 22
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.11 -10000 0 -0.37 34 34
MMP2 -0.13 0.24 0.3 1 -0.56 88 89
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.005 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.12 -10000 0 -0.37 19 19
NFATC4 -0.021 0.089 0.3 3 -0.31 1 4
ERBB2IP 0.027 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.017 0.11 -10000 0 -0.35 42 42
JUN -0.005 0.097 0.37 10 -0.25 3 13
HRAS 0.025 0.011 -10000 0 -10000 0 0
DOCK7 -0.027 0.11 -10000 0 -0.34 43 43
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.001 0.13 -10000 0 -0.4 43 43
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.005 -10000 0 -10000 0 0
MAPK10 -0.01 0.066 0.28 3 -0.39 1 4
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.018 0.12 -10000 0 -0.38 42 42
RAF1 -0.011 0.13 0.45 5 -0.39 19 24
ErbB2/ErbB3/neuregulin 2 -0.027 0.15 -10000 0 -0.42 59 59
STAT3 0.024 0.09 -10000 0 -0.85 5 5
cell migration 0.008 0.12 0.41 21 -0.28 4 25
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.16 0.32 0.48 1 -0.68 114 115
FOS -0.13 0.27 0.37 7 -0.5 151 158
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.11 -10000 0 -0.35 42 42
MAPK3 -0.081 0.24 0.44 3 -0.52 82 85
MAPK1 -0.17 0.31 0.44 2 -0.63 118 120
JAK2 -0.026 0.1 -10000 0 -0.34 40 40
NF2 -0.011 0.11 -10000 0 -0.62 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.013 0.11 -10000 0 -0.34 43 43
NRG1 -0.039 0.2 -10000 0 -0.67 45 45
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
MAPK8 -0.02 0.11 -10000 0 -0.33 47 47
MAPK9 -0.011 0.063 0.26 2 -10000 0 2
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.016 0.08 -10000 0 -0.63 7 7
SHC1 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.089 -10000 0 -0.83 5 5
RNF41 0 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.018 0.078 -10000 0 -0.26 19 19
ErbB2/ErbB2/HSP90 (dimer) 0.014 0.013 -10000 0 -10000 0 0
CHRNA1 -0.077 0.19 0.4 2 -0.39 105 107
myelination -0.01 0.14 0.57 16 -0.3 1 17
PPP3CB -0.024 0.098 -10000 0 -0.32 42 42
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.02 0.11 -10000 0 -0.34 15 15
NRG2 -0.053 0.22 -10000 0 -0.68 53 53
mol:GDP -0.013 0.11 -10000 0 -0.34 43 43
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.026 0.13 0.38 6 -0.39 19 25
SRC 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.025 0.11 0.25 1 -0.34 42 43
MAP2K1 -0.077 0.23 -10000 0 -0.61 31 31
heart morphogenesis -0.017 0.11 -10000 0 -0.35 42 42
RAS family/GDP 0.015 0.12 -10000 0 -0.37 15 15
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.012 0.13 -10000 0 -0.65 18 18
CHRNE 0.007 0.038 0.19 11 -0.23 1 12
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.006 -10000 0 -10000 0 0
nervous system development -0.017 0.11 -10000 0 -0.35 42 42
CDC42 0.027 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.013 0.061 0.24 31 -10000 0 31
RFC1 0.014 0.062 0.24 32 -10000 0 32
PRKDC 0.015 0.066 0.25 33 -10000 0 33
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.004 0.098 -10000 0 -0.76 6 6
FASLG/FAS/FADD/FAF1 -0.015 0.094 0.24 4 -0.34 31 35
MAP2K4 -0.031 0.17 0.32 2 -0.5 27 29
mol:ceramide -0.022 0.13 -10000 0 -0.43 32 32
GSN 0.013 0.061 0.24 31 -10000 0 31
FASLG/FAS/FADD/FAF1/Caspase 8 -0.021 0.12 -10000 0 -0.43 31 31
FAS 0.019 0.019 -10000 0 -10000 0 0
BID -0.018 0.035 0.28 3 -10000 0 3
MAP3K1 -0.011 0.12 0.26 4 -0.4 20 24
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
RB1 0.013 0.065 0.25 30 -0.21 1 31
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET -0.02 0.19 -10000 0 -0.47 71 71
ARHGDIB 0.015 0.068 0.25 35 -10000 0 35
FADD 0.019 0.019 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.061 -10000 0 -0.24 31 31
NFKB1 -0.02 0.1 -10000 0 -0.57 3 3
MAPK8 -0.07 0.23 0.4 2 -0.47 102 104
DFFA 0.014 0.062 0.24 32 -10000 0 32
DNA fragmentation during apoptosis 0.014 0.062 0.24 33 -10000 0 33
FAS/FADD/MET 0.042 0.042 -10000 0 -10000 0 0
CFLAR/RIP1 0.043 0.01 -10000 0 -10000 0 0
FAIM3 0.017 0.061 -10000 0 -0.67 3 3
FAF1 0.018 0.021 -10000 0 -10000 0 0
PARP1 0.018 0.079 0.29 33 -10000 0 33
DFFB 0.014 0.062 0.24 33 -10000 0 33
CHUK -0.018 0.092 -10000 0 -0.52 3 3
FASLG -0.032 0.17 -10000 0 -0.68 30 30
FAS/FADD 0.028 0.028 -10000 0 -10000 0 0
HGF -0.075 0.25 -10000 0 -0.68 69 69
LMNA 0.013 0.068 0.25 30 -10000 0 30
CASP6 0.014 0.062 0.24 32 -10000 0 32
CASP10 0.019 0.019 -10000 0 -10000 0 0
CASP3 0.018 0.078 0.3 34 -10000 0 34
PTPN13 0.02 0.071 -10000 0 -0.68 5 5
CASP8 -0.013 0.034 0.4 3 -10000 0 3
IL6 -0.22 0.53 -10000 0 -1.3 99 99
MET -0.029 0.072 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.056 0.22 31 -10000 0 31
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.14 -10000 0 -0.44 32 32
activation of caspase activity by cytochrome c -0.018 0.035 0.28 3 -10000 0 3
PAK2 0.014 0.063 0.24 33 -10000 0 33
BCL2 -0.023 0.18 -10000 0 -0.67 35 35
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.1 -10000 0 -0.68 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 247 247
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.044 0.073 -10000 0 -0.31 11 11
PRKG1 -0.16 0.31 -10000 0 -0.67 130 130
DUSP8 0.019 0.066 -10000 0 -0.68 4 4
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 127 127
apoptosis -0.043 0.07 -10000 0 -0.3 11 11
RAL/GTP 0.035 0.008 -10000 0 -10000 0 0
LYN 0.027 0.004 -10000 0 -10000 0 0
DUSP1 -0.083 0.25 -10000 0 -0.68 75 75
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.065 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
RAC1 0.026 0.006 -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 0.026 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.01 -10000 0 -10000 0 0
MAPK11 -0.054 0.16 0.48 14 -0.4 14 28
BLK -0.19 0.31 -10000 0 -0.67 143 143
HCK 0.018 0.035 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.023 0.034 -10000 0 -0.68 1 1
TRAF6/MEKK3 0.031 0.03 -10000 0 -0.4 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.011 0.12 0.4 15 -0.39 7 22
positive regulation of innate immune response -0.043 0.17 0.49 17 -0.48 9 26
LCK 0.012 0.083 -10000 0 -0.68 6 6
p38alpha-beta/MKP7 -0.046 0.14 0.35 6 -0.47 8 14
p38alpha-beta/MKP5 -0.035 0.16 0.51 12 -0.48 8 20
PGK/cGMP -0.12 0.23 -10000 0 -0.5 130 130
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.097 0.18 0.29 2 -0.47 45 47
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.004 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.34 -10000 0 -0.66 268 268
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.005 0.057 -10000 0 -10000 0 0
CRKL -0.015 0.091 0.36 1 -0.42 1 2
mol:PIP3 -0.002 0.017 -10000 0 -10000 0 0
AKT1 0.003 0.056 0.37 2 -0.45 3 5
PTK2B 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.002 0.11 0.46 8 -0.4 1 9
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
HGF/MET/SHIP2 -0.015 0.18 -10000 0 -0.46 67 67
MAP3K5 0.013 0.13 0.5 14 -0.43 4 18
HGF/MET/CIN85/CBL/ENDOPHILINS 0.001 0.17 -10000 0 -0.42 65 65
AP1 -0.18 0.33 -10000 0 -0.65 148 148
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis -0.22 0.4 0.38 1 -0.81 150 151
STAT3 (dimer) -0.02 0.11 -10000 0 -0.28 64 64
GAB1/CRKL/SHP2/PI3K 0.024 0.11 -10000 0 -0.56 2 2
INPP5D 0.019 0.033 -10000 0 -10000 0 0
CBL/CRK 0.015 0.12 0.5 7 -0.41 1 8
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
ELK1 0.035 0.14 0.43 29 -0.23 4 33
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.069 -10000 0 -0.24 5 5
PAK1 0.007 0.061 0.37 6 -0.4 2 8
HGF/MET/RANBP10 -0.016 0.18 -10000 0 -0.46 67 67
HRAS -0.02 0.13 -10000 0 -0.55 3 3
DOCK1 0 0.12 0.48 9 -0.48 2 11
GAB1 -0.012 0.097 -10000 0 -0.45 1 1
CRK -0.007 0.099 0.37 2 -0.43 1 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.044 0.19 -10000 0 -0.51 69 69
JUN -0.12 0.29 -10000 0 -0.67 103 103
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.031 0.086 -10000 0 -0.24 67 67
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.01 0.12 0.45 5 -0.51 3 8
GRB2/SHC 0.003 0.086 -10000 0 -0.28 1 1
FOS -0.16 0.31 -10000 0 -0.67 126 126
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.034 0.14 0.43 29 -0.23 4 33
HGF/MET/MUC20 -0.066 0.16 -10000 0 -0.46 69 69
cell migration 0.003 0.085 -10000 0 -0.27 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.005 0.056 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.017 0.11 -10000 0 -0.3 64 64
MET/MUC20 -0.017 0.047 -10000 0 -10000 0 0
RAP1B 0.011 0.13 0.57 13 -0.37 1 14
RAP1A 0.008 0.11 0.42 12 -0.37 1 13
HGF/MET/RANBP9 -0.015 0.18 -10000 0 -0.45 69 69
RAF1 -0.018 0.13 -10000 0 -0.49 2 2
STAT3 -0.02 0.11 -10000 0 -0.28 64 64
cell proliferation -0.025 0.15 -10000 0 -0.39 61 61
RPS6KB1 0 0.034 -10000 0 -0.22 2 2
MAPK3 -0.02 0.11 0.53 14 -10000 0 14
MAPK1 0.13 0.29 0.6 130 -10000 0 130
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.024 0.17 0.63 16 -0.65 7 23
SRC -0.021 0.1 -10000 0 -0.28 64 64
PI3K 0.003 0.095 -10000 0 -0.39 4 4
MET/Glomulin -0.007 0.044 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.011 0.12 0.34 1 -0.46 2 3
MET -0.029 0.072 -10000 0 -10000 0 0
MAP4K1 0.007 0.12 0.56 7 -0.46 4 11
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.008 0.12 0.32 2 -0.44 1 3
BAD 0.007 0.061 0.37 6 -0.4 2 8
MAP2K4 0.021 0.15 0.54 19 -0.42 3 22
SHP2/GRB2/SOS1/GAB1 0.017 0.1 -10000 0 -0.36 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.025 0.008 -10000 0 -10000 0 0
HGS -0.029 0.078 -10000 0 -0.22 65 65
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.075 0.25 -10000 0 -0.68 69 69
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.003 0.1 -10000 0 -0.24 66 66
PDPK1 -0.001 0.048 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.019 0.18 -10000 0 -0.46 67 67
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.013 -10000 0 -10000 0 0
REL -0.01 0.16 -10000 0 -0.66 29 29
HDAC7 -0.069 0.11 -10000 0 -0.48 18 18
JUN -0.12 0.29 -10000 0 -0.67 103 103
EP300 0.02 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.015 0.077 -10000 0 -0.52 10 10
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.068 0.13 -10000 0 -0.5 19 19
MAP2K6 0.004 0.1 -10000 0 -0.69 10 10
BRM/BAF57 0.018 0.032 -10000 0 -10000 0 0
MAP2K4 0.019 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.012 0.075 -10000 0 -0.58 2 2
NCOA2 -0.04 0.2 -10000 0 -0.68 42 42
CEBPA 0.019 0.071 -10000 0 -0.68 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.083 0.2 0.56 20 -0.47 20 40
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.12 0.28 -10000 0 -0.68 96 96
RXRs/9cRA 0.019 0.072 -10000 0 -0.4 4 4
AR/RACK1/Src -0.13 0.14 0.33 2 -0.54 17 19
AR/GR -0.12 0.18 0.28 2 -0.32 172 174
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.007 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.006 -10000 0 -0.014 64 64
MAPK8 -0.012 0.064 -10000 0 -0.52 7 7
T-DHT/AR/TIF2/CARM1 -0.13 0.18 0.34 3 -0.56 45 48
SRC -0.042 0.082 0.23 1 -0.45 14 15
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.35 0.55 0.38 2 -1.2 137 139
APPBP2 0.024 0.012 -10000 0 -10000 0 0
TRIM24 0.014 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.069 0.12 0.32 7 -0.54 15 22
TMPRSS2 -0.048 0.28 -10000 0 -1.1 31 31
RXRG -0.1 0.076 -10000 0 -0.68 4 4
mol:9cRA -0.002 0.003 -10000 0 -0.012 7 7
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.015 0.09 -10000 0 -0.68 8 8
KLK2 -0.44 0.38 0.34 2 -0.77 273 275
AR -0.14 0.18 -10000 0 -0.35 193 193
SENP1 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.035 0.016 -10000 0 -10000 0 0
SRY 0.009 0.015 0.032 136 -10000 0 136
GATA2 0.027 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.011 0.034 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.098 0.13 0.33 4 -0.56 14 18
positive regulation of transcription 0.027 0.008 -10000 0 -10000 0 0
DNAJA1 0.024 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.018 0.022 -10000 0 -10000 0 0
SPDEF -0.003 0.048 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.091 0.14 0.28 2 -0.43 48 50
T-DHT/AR/Hsp90 -0.07 0.13 0.33 7 -0.53 15 22
GSK3B 0.025 0.006 -10000 0 -10000 0 0
NR2C1 0.028 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.036 0.086 0.26 1 -0.46 15 16
SIRT1 0.025 0.032 -10000 0 -0.68 1 1
ZMIZ2 0.035 0.017 -10000 0 -10000 0 0
POU2F1 0.032 0.036 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.074 0.12 0.32 6 -0.55 15 21
CREBBP 0.026 0.006 -10000 0 -10000 0 0
SMARCE1 0.013 0.022 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.016 0.13 -10000 0 -0.42 35 35
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.087 0.34 2 -0.46 1 3
AP1 -0.16 0.3 -10000 0 -0.55 158 158
mol:PIP3 -0.013 0.095 -10000 0 -0.36 31 31
AKT1 0.03 0.1 0.32 5 -0.57 2 7
PTK2B -0.011 0.089 0.24 2 -0.34 15 17
RHOA 0.013 0.042 -10000 0 -10000 0 0
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.072 0.28 8 -0.26 1 9
MAGI3 0.025 0.032 -10000 0 -0.68 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.011 0.1 -10000 0 -0.35 39 39
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.002 0.1 0.38 9 -0.38 9 18
NF kappa B1 p50/RelA -0.02 0.1 -10000 0 -0.43 11 11
endothelial cell migration -0.018 0.15 -10000 0 -0.52 35 35
ADCY4 -0.032 0.15 -10000 0 -0.52 37 37
ADCY5 -0.059 0.17 -10000 0 -0.54 43 43
ADCY6 -0.032 0.15 -10000 0 -0.52 37 37
ADCY7 -0.033 0.15 -10000 0 -0.52 37 37
ADCY1 -0.034 0.15 -10000 0 -0.51 39 39
ADCY2 -0.054 0.17 -10000 0 -0.54 41 41
ADCY3 -0.032 0.15 -10000 0 -0.53 36 36
ADCY8 -0.041 0.15 -10000 0 -0.52 38 38
ADCY9 -0.033 0.15 -10000 0 -0.52 37 37
GSK3B -0.01 0.087 0.37 2 -0.34 12 14
arachidonic acid secretion -0.032 0.15 -10000 0 -0.44 49 49
GNG2 0.025 0.032 -10000 0 -0.67 1 1
TRIP6 0.024 0.01 -10000 0 -10000 0 0
GNAO1 -0.028 0.15 -10000 0 -0.47 48 48
HRAS 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.005 0.097 0.4 8 -0.52 1 9
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.18 -10000 0 -0.78 22 22
JUN -0.12 0.29 -10000 0 -0.67 103 103
LPA/LPA2/NHERF2 0.035 0.017 -10000 0 -10000 0 0
TIAM1 0 0.21 -10000 0 -0.92 23 23
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.01 0.066 0.36 2 -0.27 1 3
PLCB3 0.027 0.033 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 126 126
positive regulation of mitosis -0.032 0.15 -10000 0 -0.44 49 49
LPA/LPA1-2-3 0.016 0.12 -10000 0 -0.41 32 32
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation 0 0.1 0.38 3 -0.32 30 33
GNAZ -0.017 0.12 -10000 0 -0.44 35 35
EGFR/PI3K-beta/Gab1 -0.003 0.1 -10000 0 -0.37 31 31
positive regulation of dendritic cell cytokine production 0.015 0.12 -10000 0 -0.4 32 32
LPA/LPA2/MAGI-3 0.034 0.028 -10000 0 -0.45 1 1
ARHGEF1 0.003 0.11 0.36 3 -0.39 26 29
GNAI2 -0.015 0.13 -10000 0 -0.45 35 35
GNAI3 -0.014 0.13 -10000 0 -0.44 36 36
GNAI1 -0.014 0.12 -10000 0 -0.44 36 36
LPA/LPA3 0.015 0.024 -10000 0 -10000 0 0
LPA/LPA2 0.02 0.013 -10000 0 -10000 0 0
LPA/LPA1 -0.018 0.15 -10000 0 -0.47 42 42
HB-EGF/EGFR -0.018 0.13 -10000 0 -0.44 39 39
HBEGF -0.034 0.14 -10000 0 -0.49 38 38
mol:DAG -0.01 0.066 0.36 2 -0.27 1 3
cAMP biosynthetic process -0.038 0.17 0.41 11 -0.47 51 62
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
LYN -0.007 0.093 0.37 7 -0.42 2 9
GNAQ 0.016 0.015 -10000 0 -10000 0 0
LPAR2 0.025 0.007 -10000 0 -10000 0 0
LPAR3 0.013 0.033 -10000 0 -10000 0 0
LPAR1 -0.026 0.18 -10000 0 -0.62 40 40
IL8 -0.082 0.17 0.36 1 -0.47 36 37
PTK2 -0.004 0.11 -10000 0 -0.39 29 29
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.011 0.1 -10000 0 -0.35 39 39
EGFR 0.02 0.064 -10000 0 -0.68 4 4
PLCG1 -0.011 0.063 -10000 0 -0.3 2 2
PLD2 -0.004 0.11 -10000 0 -0.39 27 27
G12/G13 0.019 0.12 -10000 0 -0.4 34 34
PI3K-beta 0.003 0.092 -10000 0 -0.68 2 2
cell migration 0.018 0.074 -10000 0 -0.25 16 16
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN -0.002 0.1 0.26 2 -0.33 30 32
HRAS/GTP -0.03 0.15 -10000 0 -0.45 49 49
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 38 38
PRKCE 0.021 0.064 -10000 0 -0.68 4 4
PRKCD -0.006 0.085 0.33 12 -10000 0 12
Gi(beta/gamma) -0.026 0.15 -10000 0 -0.5 36 36
mol:LPA 0.002 0.017 -10000 0 -0.2 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.017 0.12 -10000 0 -0.38 29 29
MAPKKK cascade -0.032 0.15 -10000 0 -0.44 49 49
contractile ring contraction involved in cytokinesis 0.015 0.048 0.28 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.065 0.15 -10000 0 -0.35 102 102
GNA15 0.013 0.027 -10000 0 -0.36 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.005 0.097 0.35 7 -0.39 9 16
GNA11 0.012 0.044 -10000 0 -0.32 7 7
Rac1/GTP 0.014 0.19 -10000 0 -0.84 21 21
MMP2 -0.018 0.15 -10000 0 -0.52 35 35
Ceramide signaling pathway

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
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.015 0.12 -10000 0 -0.48 17 17
BAG4 0.026 0.032 -10000 0 -0.68 1 1
PKC zeta/ceramide -0.019 0.097 -10000 0 -0.37 19 19
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX -0.014 0.078 -10000 0 -0.35 21 21
RIPK1 0.027 0.002 -10000 0 -10000 0 0
AKT1 0.027 0.14 0.79 15 -10000 0 15
BAD -0.032 0.088 0.18 1 -0.29 31 32
SMPD1 -0.012 0.093 0.29 7 -0.23 62 69
RB1 -0.032 0.09 0.19 1 -0.32 27 28
FADD/Caspase 8 -0.006 0.12 -10000 0 -0.5 15 15
MAP2K4 -0.018 0.072 0.21 3 -0.39 7 10
NSMAF 0.027 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.023 0.082 -10000 0 -0.42 11 11
EGF -0.073 0.24 -10000 0 -0.67 68 68
mol:ceramide -0.036 0.097 -10000 0 -0.3 36 36
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.016 0.024 -10000 0 -0.51 1 1
ASAH1 0.025 0.032 -10000 0 -0.68 1 1
negative regulation of cell cycle -0.032 0.089 0.19 1 -0.31 27 28
cell proliferation -0.06 0.15 -10000 0 -0.33 103 103
BID -0.15 0.28 -10000 0 -0.6 122 122
MAP3K1 -0.027 0.078 0.19 1 -0.3 21 22
EIF2A -0.028 0.078 -10000 0 -0.45 10 10
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.07 -10000 0 -0.37 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.042 0.085 -10000 0 -0.38 12 12
Cathepsin D/ceramide -0.018 0.093 -10000 0 -0.28 33 33
FADD -0.015 0.12 -10000 0 -0.49 16 16
KSR1 -0.026 0.087 0.18 9 -0.3 26 35
MAPK8 -0.017 0.089 -10000 0 -0.4 15 15
PRKRA -0.034 0.09 -10000 0 -0.29 32 32
PDGFA 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.036 0.096 -10000 0 -0.3 35 35
CTSD 0.026 0.009 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.064 0.16 -10000 0 -0.35 103 103
PRKCD 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.016 0.024 -10000 0 -0.51 1 1
RelA/NF kappa B1 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.015 0.13 -10000 0 -0.5 17 17
TNFR1A/BAG4/TNF-alpha -0.006 0.16 -10000 0 -0.44 58 58
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.022 0.078 -10000 0 -0.39 11 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.006 0.071 0.17 24 -0.24 18 42
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.51 1 1
EIF2AK2 -0.03 0.084 -10000 0 -0.46 11 11
TNF-alpha/TNFR1A/FAN -0.005 0.16 -10000 0 -0.44 57 57
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.088 -10000 0 -0.51 6 6
MAP2K2 -0.014 0.067 -10000 0 -0.38 7 7
SMPD3 -0.019 0.11 -10000 0 -0.26 66 66
TNF -0.059 0.23 -10000 0 -0.68 57 57
PKC zeta/PAR4 0.038 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.015 0.11 0.25 67 -0.26 15 82
NF kappa B1/RelA/I kappa B alpha 0.075 0.023 -10000 0 -10000 0 0
AIFM1 -0.011 0.086 0.17 24 -0.27 26 50
BCL2 -0.023 0.18 -10000 0 -0.67 35 35
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 -0.064 0.17 0.43 10 -0.45 31 41
IKBKB 0.01 0.12 0.48 15 -0.31 7 22
AKT1 0 0.16 0.53 25 -0.25 13 38
IKBKG -0.003 0.12 0.42 16 -0.34 16 32
CALM1 -0.021 0.094 0.41 3 -0.44 6 9
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
MAP3K1 -0.012 0.17 0.48 11 -0.56 16 27
MAP3K7 0.027 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.092 0.34 1 -0.42 8 9
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.058 0.16 0.56 11 -0.26 90 101
LYN 0.027 0.004 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex -0.066 0.18 -10000 0 -0.5 60 60
CD22 -0.066 0.17 -10000 0 -0.42 78 78
CAMK2G -0.018 0.091 0.36 4 -0.43 5 9
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.036 0.12 -10000 0 -0.34 51 51
GO:0007205 -0.024 0.095 0.34 1 -0.43 8 9
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.018 0.093 0.33 4 -0.42 7 11
NFATC1 -0.038 0.14 0.39 7 -0.43 22 29
B-cell antigen/BCR complex -0.066 0.18 -10000 0 -0.5 60 60
PAG1/CSK 0.038 0.026 -10000 0 -0.51 1 1
NFKBIB 0.02 0.046 0.22 12 -0.13 8 20
HRAS -0.017 0.095 0.31 4 -0.43 4 8
NFKBIA 0.019 0.046 0.22 12 -0.13 8 20
NF-kappa-B/RelA/I kappa B beta 0.024 0.043 0.22 12 -10000 0 12
RasGAP/Csk -0.001 0.18 -10000 0 -0.41 68 68
mol:GDP -0.023 0.092 0.29 1 -0.43 8 9
PTEN 0.026 0.018 -10000 0 -0.36 1 1
CD79B 0.008 0.049 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.043 0.22 12 -10000 0 12
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.034 0.16 0.45 5 -0.52 12 17
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.022 0.091 0.34 1 -0.42 7 8
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.1 0.18 0.46 7 -0.37 127 134
CHUK 0.007 0.11 0.42 15 -0.33 8 23
IBTK 0.027 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.012 0.1 -10000 0 -0.45 8 8
PTPN6 -0.062 0.16 -10000 0 -0.48 40 40
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.014 0.036 0.17 7 -0.12 10 17
VAV2 -0.052 0.15 -10000 0 -0.63 14 14
ubiquitin-dependent protein catabolic process 0.023 0.046 0.22 12 -0.12 7 19
BTK -0.039 0.24 -10000 0 -0.98 30 30
CD19 -0.058 0.15 -10000 0 -0.61 16 16
MAP4K1 0.009 0.079 -10000 0 -0.68 5 5
CD72 0.025 0.012 -10000 0 -10000 0 0
PAG1 0.025 0.032 -10000 0 -0.68 1 1
MAPK14 -0.005 0.15 0.45 13 -0.5 13 26
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.015 0.094 -10000 0 -0.6 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.047 0.18 -10000 0 -0.42 72 72
RAF1 -0.014 0.095 0.33 7 -0.5 2 9
RasGAP/p62DOK/SHIP -0.003 0.17 -10000 0 -0.39 68 68
CD79A -0.096 0.23 -10000 0 -0.66 62 62
re-entry into mitotic cell cycle -0.057 0.15 0.55 11 -0.26 91 102
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.003 0.1 0.4 13 -0.42 2 15
MAPK1 -0.01 0.086 0.38 7 -0.4 2 9
CD72/SHP1 -0.044 0.17 0.31 1 -0.52 27 28
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.01 0.16 0.49 12 -0.52 15 27
actin cytoskeleton organization -0.042 0.14 0.34 2 -0.55 12 14
NF-kappa-B/RelA 0.049 0.076 0.38 12 -0.2 2 14
Calcineurin 0.009 0.09 -10000 0 -0.41 4 4
PI3K -0.059 0.14 -10000 0 -0.51 15 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.018 0.097 -10000 0 -0.46 9 9
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.021 0.22 -10000 0 -0.94 19 19
DAPP1 -0.042 0.25 -10000 0 -1.1 18 18
cytokine secretion -0.035 0.13 0.38 7 -0.4 22 29
mol:DAG -0.022 0.091 0.34 1 -0.42 7 8
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.012 0.09 0.34 6 -0.46 2 8
B-cell antigen/BCR complex/FcgammaRIIB -0.051 0.19 -10000 0 -0.45 75 75
mol:PI-3-4-5-P3 -0.052 0.096 -10000 0 -0.36 14 14
ETS1 -0.014 0.088 0.39 5 -0.41 4 9
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.014 0.15 -10000 0 -0.38 58 58
B-cell antigen/BCR complex/LYN -0.046 0.16 -10000 0 -0.42 63 63
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
RAC1 -0.046 0.14 0.36 1 -0.59 12 13
B-cell antigen/BCR complex/LYN/SYK -0.036 0.19 -10000 0 -0.46 61 61
CARD11 -0.035 0.11 0.4 4 -0.45 13 17
FCGR2B -0.009 0.15 -10000 0 -0.68 23 23
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.018 0.096 0.43 18 -0.13 6 24
PTPRC -0.007 0.14 -10000 0 -0.68 19 19
PDPK1 -0.027 0.086 0.24 9 -0.26 16 25
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.004 -10000 0 -10000 0 0
POU2F2 0.02 0.034 0.17 15 -10000 0 15
Syndecan-4-mediated signaling events

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
PTK2 -0.008 0.11 -10000 0 -0.75 7 7
Syndecan-4/Syndesmos -0.035 0.16 -10000 0 -0.55 38 38
positive regulation of JNK cascade -0.051 0.19 -10000 0 -0.57 40 40
Syndecan-4/ADAM12 -0.044 0.16 -10000 0 -0.56 38 38
CCL5 -0.019 0.17 -10000 0 -0.68 29 29
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.025 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
PLG 0.009 0.03 -10000 0 -10000 0 0
ADAM12 -0.01 0.065 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.057 0.031 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.058 0.18 -10000 0 -0.6 37 37
Syndecan-4/CXCL12/CXCR4 -0.054 0.2 -10000 0 -0.61 40 40
Syndecan-4/Laminin alpha3 -0.046 0.17 -10000 0 -0.58 36 36
MDK -0.019 0.069 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.036 0.16 -10000 0 -0.56 38 38
Syndecan-4/Midkine -0.046 0.16 -10000 0 -0.56 37 37
FZD7 0.022 0.052 -10000 0 -0.52 4 4
Syndecan-4/FGFR1/FGF -0.011 0.16 -10000 0 -0.52 37 37
THBS1 0.016 0.04 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.051 0.16 -10000 0 -0.56 38 38
positive regulation of MAPKKK cascade -0.051 0.19 -10000 0 -0.57 40 40
Syndecan-4/TACI -0.12 0.21 -10000 0 -0.63 37 37
CXCR4 0.026 0.011 -10000 0 -10000 0 0
cell adhesion -0.006 0.074 0.2 5 -0.31 22 27
Syndecan-4/Dynamin -0.035 0.16 -10000 0 -0.56 37 37
Syndecan-4/TSP1 -0.037 0.16 -10000 0 -0.56 38 38
Syndecan-4/GIPC -0.035 0.16 -10000 0 -0.56 37 37
Syndecan-4/RANTES -0.057 0.2 -10000 0 -0.66 39 39
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 -0.021 0.18 -10000 0 -0.67 33 33
LAMA3 -0.001 0.13 -10000 0 -0.68 16 16
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.009 0.2 0.76 19 -0.62 22 41
Syndecan-4/alpha-Actinin -0.034 0.16 -10000 0 -0.56 37 37
TFPI -0.013 0.16 -10000 0 -0.66 28 28
F2 0.011 0.028 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.071 0.18 -10000 0 -0.6 37 37
ACTN1 0.026 0.008 -10000 0 -10000 0 0
TNC -0.032 0.091 -10000 0 -0.68 4 4
Syndecan-4/CXCL12 -0.072 0.2 -10000 0 -0.63 40 40
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.05 0.22 -10000 0 -0.68 53 53
TNFRSF13B -0.14 0.29 -10000 0 -0.67 109 109
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.026 0.032 -10000 0 -0.68 1 1
Syndecan-4/PI-4-5-P2 -0.047 0.15 -10000 0 -0.56 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.076 0.075 -10000 0 -0.2 1 1
cell migration -0.026 0.012 -10000 0 -10000 0 0
PRKCD 0.025 0.023 -10000 0 -10000 0 0
vasculogenesis -0.035 0.15 -10000 0 -0.54 38 38
SDC4 -0.047 0.16 -10000 0 -0.59 38 38
Syndecan-4/Tenascin C -0.053 0.17 -10000 0 -0.59 38 38
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.024 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.035 0.16 -10000 0 -0.56 38 38
MMP9 -0.038 0.19 -10000 0 -0.66 38 38
Rac1/GTP -0.006 0.075 0.2 4 -0.32 22 26
cytoskeleton organization -0.034 0.15 -10000 0 -0.53 38 38
GIPC1 0.025 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.054 0.18 -10000 0 -0.58 39 39
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CCL5 -0.019 0.17 -10000 0 -0.68 29 29
SDCBP 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.038 0.14 -10000 0 -0.51 25 25
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 -0.032 0.14 -10000 0 -0.56 20 20
Syndecan-1/Syntenin -0.031 0.14 -10000 0 -0.55 22 22
MAPK3 -0.029 0.12 -10000 0 -0.53 18 18
HGF/MET -0.079 0.19 -10000 0 -0.52 69 69
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
BSG 0.025 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.031 0.14 -10000 0 -0.55 20 20
Syndecan-1/RANTES -0.051 0.19 -10000 0 -0.6 41 41
Syndecan-1/CD147 -0.015 0.14 -10000 0 -0.55 20 20
Syndecan-1/Syntenin/PIP2 -0.031 0.14 -10000 0 -0.53 22 22
LAMA5 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.03 0.13 -10000 0 -0.52 22 22
MMP7 -0.078 0.16 -10000 0 -0.66 25 25
HGF -0.075 0.25 -10000 0 -0.68 69 69
Syndecan-1/CASK -0.045 0.13 -10000 0 -0.52 25 25
Syndecan-1/HGF/MET -0.076 0.21 -10000 0 -0.53 62 62
regulation of cell adhesion -0.031 0.12 -10000 0 -0.51 18 18
HPSE 0.008 0.1 -10000 0 -0.64 10 10
positive regulation of cell migration -0.038 0.14 -10000 0 -0.51 25 25
SDC1 -0.038 0.13 -10000 0 -0.5 28 28
Syndecan-1/Collagen -0.038 0.14 -10000 0 -0.51 25 25
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET -0.029 0.072 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 38 38
MAPK1 -0.031 0.12 -10000 0 -0.53 19 19
homophilic cell adhesion -0.036 0.14 0.43 2 -0.52 24 26
MMP1 -0.046 0.073 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.003 0.066 -10000 0 -0.27 4 4
AP1 -0.12 0.26 -10000 0 -0.55 101 101
mol:PIP3 0.027 0.18 0.64 19 -0.42 12 31
IKBKB 0.037 0.17 0.66 23 -0.26 8 31
AKT1 -0.006 0.13 0.32 25 -0.46 6 31
IKBKG 0.04 0.18 0.67 25 -0.26 7 32
MS4A2 -0.014 0.062 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.056 -10000 0 -0.68 3 3
MAP3K1 0.024 0.12 0.49 12 -0.41 6 18
mol:Ca2+ 0.032 0.16 0.57 24 -0.32 12 36
LYN 0.027 0.011 -10000 0 -10000 0 0
CBLB -0.001 0.064 -10000 0 -0.27 1 1
SHC1 0.025 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK -0.021 0.16 -10000 0 -0.4 75 75
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
PLD2 -0.009 0.13 0.32 33 -0.38 29 62
PTPN13 0.011 0.14 0.48 2 -0.63 14 16
PTPN11 0.022 0.036 -10000 0 -0.7 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.031 0.16 0.63 20 -0.36 7 27
SYK 0.025 0.013 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.001 0.11 -10000 0 -0.39 21 21
LAT -0.004 0.07 -10000 0 -0.31 5 5
PAK2 0.016 0.1 0.37 5 -0.43 8 13
NFATC2 -0.1 0.23 -10000 0 -0.61 80 80
HRAS 0.011 0.1 0.25 1 -0.43 10 11
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.005 0.1 -10000 0 -0.72 7 7
Fc epsilon R1 0.005 0.13 -10000 0 -0.45 32 32
Antigen/IgE/Fc epsilon R1 0.008 0.12 -10000 0 -0.41 32 32
mol:GDP 0.002 0.11 -10000 0 -0.48 13 13
JUN -0.12 0.29 -10000 0 -0.67 103 103
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 126 126
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.003 0.07 -10000 0 -0.25 9 9
CHUK 0.036 0.16 0.63 23 -0.26 8 31
KLRG1 -0.008 0.078 -10000 0 -0.3 15 15
VAV1 -0.004 0.074 0.21 1 -0.36 6 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.001 0.064 -10000 0 -10000 0 0
negative regulation of mast cell degranulation 0.005 0.081 -10000 0 -0.31 10 10
BTK -0.006 0.12 -10000 0 -0.56 16 16
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.15 -10000 0 -0.46 40 40
GAB2/PI3K/SHP2 -0.029 0.1 -10000 0 -0.38 28 28
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.073 -10000 0 -0.27 29 29
RAF1 0.012 0.095 -10000 0 -0.86 5 5
Fc epsilon R1/FcgammaRIIB/SHIP 0.021 0.17 -10000 0 -0.5 42 42
FCER1G 0.018 0.035 -10000 0 -10000 0 0
FCER1A -0.034 0.18 -10000 0 -0.68 33 33
Antigen/IgE/Fc epsilon R1/Fyn 0.023 0.12 -10000 0 -0.38 32 32
MAPK3 0.019 0.092 -10000 0 -0.78 5 5
MAPK1 -0.015 0.11 -10000 0 -0.74 7 7
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0 0.18 -10000 0 -0.64 29 29
DUSP1 -0.083 0.25 -10000 0 -0.68 75 75
NF-kappa-B/RelA 0.015 0.048 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.013 0.13 0.4 2 -0.69 11 13
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.098 -10000 0 -0.47 7 7
FER -0.004 0.072 -10000 0 -0.39 4 4
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.045 0.15 -10000 0 -0.47 55 55
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.01 0.12 0.4 8 -0.52 10 18
cytokine secretion 0.005 0.031 -10000 0 -10000 0 0
SPHK1 -0.001 0.067 0.27 1 -0.27 3 4
PTK2 0.012 0.14 0.41 2 -0.74 11 13
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.006 0.11 -10000 0 -0.39 28 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.034 0.18 0.73 17 -0.42 12 29
MAP2K2 0.017 0.099 -10000 0 -0.8 5 5
MAP2K1 0.009 0.088 -10000 0 -0.8 5 5
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 -0.002 0.083 -10000 0 -0.33 12 12
MAP2K4 -0.01 0.2 -10000 0 -0.83 26 26
Fc epsilon R1/FcgammaRIIB 0.005 0.18 -10000 0 -0.52 42 42
mol:Choline -0.009 0.13 0.32 33 -0.37 29 62
SHC/Grb2/SOS1 0.036 0.077 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.017 0.13 0.46 5 -0.67 10 15
HCLS1 -0.002 0.065 -10000 0 -0.28 2 2
PRKCB 0.035 0.18 0.67 23 -0.33 13 36
FCGR2B -0.009 0.15 -10000 0 -0.68 23 23
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.005 0.083 -10000 0 -0.31 10 10
LCP2 0.024 0.019 -10000 0 -10000 0 0
PLA2G4A -0.024 0.12 -10000 0 -0.42 31 31
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.13 0.32 33 -0.37 29 62
IKK complex 0.043 0.18 0.69 25 -0.21 3 28
WIPF1 0.027 0.004 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.14 -10000 0 -0.36 59 59
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.002 0.12 -10000 0 -0.44 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.052 -10000 0 -0.3 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.008 0.071 -10000 0 -0.26 2 2
CaM/Ca2+ 0.015 0.13 -10000 0 -0.34 59 59
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.13 -10000 0 -0.34 59 59
AKT1 -0.015 0.12 0.38 5 -0.47 2 7
MAP2K1 -0.024 0.12 0.29 2 -0.33 54 56
MAP3K11 -0.021 0.12 0.3 5 -0.34 59 64
IFNGR1 0.02 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.017 0.073 -10000 0 -0.44 2 2
Rap1/GTP -0.019 0.094 -10000 0 -0.36 1 1
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.018 0.15 -10000 0 -0.37 58 58
CEBPB -0.058 0.19 0.52 6 -0.58 26 32
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.017 0.16 -10000 0 -0.7 6 6
STAT1 -0.021 0.13 0.32 6 -0.34 59 65
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.065 0.23 -10000 0 -0.68 59 59
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
STAT1 (dimer)/PIAS1 -0.005 0.12 0.3 4 -0.33 55 59
CEBPB/PTGES2/Cbp/p300 -0.024 0.12 -10000 0 -0.4 13 13
mol:Ca2+ 0.007 0.14 -10000 0 -0.35 59 59
MAPK3 -0.009 0.13 -10000 0 -0.69 5 5
STAT1 (dimer) 0.018 0.097 -10000 0 -0.35 2 2
MAPK1 -0.16 0.3 0.44 1 -0.66 120 121
JAK2 0.018 0.032 -10000 0 -0.4 1 1
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
JAK1 0.02 0.025 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.04 0.18 0.5 9 -0.61 26 35
SMAD7 0.019 0.065 0.42 6 -10000 0 6
CBL/CRKL/C3G -0.008 0.12 0.3 2 -0.36 4 6
PI3K 0.012 0.13 -10000 0 -0.34 58 58
IFNG -0.065 0.23 -10000 0 -0.68 59 59
apoptosis -0.035 0.16 0.56 6 -0.46 35 41
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.016 0.032 -10000 0 -10000 0 0
CAMK2B 0.021 0.064 -10000 0 -0.68 4 4
FRAP1 -0.022 0.11 0.37 5 -0.44 2 7
PRKCD -0.011 0.13 0.43 10 -0.39 6 16
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.008 0.071 -10000 0 -0.26 2 2
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
IRF1 -0.014 0.086 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.011 0.12 0.3 1 -0.32 55 56
SOCS1 0.017 0.12 -10000 0 -1 6 6
mol:GDP -0.009 0.11 0.28 2 -0.35 4 6
CASP1 0.016 0.064 0.45 4 -0.32 2 6
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.058 0.35 1 -10000 0 1
mol:PI-3-4-5-P3 -0.001 0.12 -10000 0 -0.33 58 58
RAP1/GDP -0.005 0.1 -10000 0 -0.36 1 1
CBL -0.021 0.12 0.29 6 -0.34 59 65
MAP3K1 -0.022 0.12 0.3 2 -0.34 57 59
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.008 0.071 -10000 0 -0.26 2 2
PTPN11 -0.024 0.13 -10000 0 -0.36 59 59
CREBBP 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.066 -10000 0 -0.59 5 5
alphaV beta3 Integrin 0.038 0.089 -10000 0 -0.48 12 12
PTK2 0.01 0.14 0.41 11 -0.51 13 24
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.009 0.048 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
CDKN1B -0.029 0.17 -10000 0 -0.52 47 47
VEGFA 0.023 0.055 -10000 0 -0.68 3 3
ILK -0.029 0.17 -10000 0 -0.53 46 46
ROCK1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.03 0.16 -10000 0 -0.5 45 45
PTK2B 0.012 0.094 0.36 1 -0.45 15 16
alphaV/beta3 Integrin/JAM-A 0.004 0.15 -10000 0 -0.4 51 51
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.035 0.087 -10000 0 -0.47 12 12
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.089 0.24 -10000 0 -0.43 149 149
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.001 0.095 -10000 0 -0.42 6 6
alphaV/beta3 Integrin/Syndecan-1 0.039 0.089 -10000 0 -0.51 11 11
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.095 0.24 -10000 0 -0.43 149 149
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
alphaV/beta3 Integrin/Osteopontin 0.019 0.13 -10000 0 -0.44 34 34
RPS6KB1 -0.14 0.19 0.42 2 -0.41 148 150
TLN1 0.025 0.008 -10000 0 -10000 0 0
MAPK3 -0.052 0.14 -10000 0 -0.66 13 13
GPR124 0.027 0.004 -10000 0 -10000 0 0
MAPK1 -0.062 0.14 -10000 0 -0.61 20 20
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.026 0.12 -10000 0 -0.52 21 21
cell adhesion 0.029 0.084 -10000 0 -0.47 11 11
ANGPTL3 0.007 0.024 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.061 -10000 0 -0.52 5 5
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 0.023 0.055 -10000 0 -0.68 3 3
ITGB3 0.009 0.11 -10000 0 -0.65 12 12
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.038 0.088 -10000 0 -0.51 11 11
apoptosis 0.024 0.045 -10000 0 -0.67 2 2
CD47 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.038 0.089 -10000 0 -0.48 12 12
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.11 -10000 0 -0.49 18 18
CSF1 0.015 0.09 -10000 0 -0.68 8 8
PIK3C2A -0.03 0.17 -10000 0 -0.53 47 47
PI4 Kinase/Pyk2 -0.015 0.13 -10000 0 -0.37 44 44
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.1 -10000 0 -0.46 16 16
FAK1/Vinculin 0.022 0.12 0.38 9 -0.41 11 20
alphaV beta3/Integrin/ppsTEM5 0.038 0.089 -10000 0 -0.51 11 11
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN -0.04 0.2 -10000 0 -0.68 44 44
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.04 0.089 -10000 0 -0.51 11 11
alphaV/beta3 Integrin/TGFBR2 0.036 0.093 -10000 0 -0.45 15 15
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.073 -10000 0 -0.44 9 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.034 0.082 -10000 0 -0.47 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.081 0.067 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.033 0.093 -10000 0 -0.45 15 15
SDC1 0.025 0.014 -10000 0 -10000 0 0
VAV3 0.009 0.083 0.36 1 -0.43 14 15
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
IRS1 -0.053 0.22 -10000 0 -0.68 55 55
FAK1/Paxillin 0.021 0.12 0.35 8 -0.41 11 19
cell migration 0.017 0.11 0.34 6 -0.4 8 14
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
PI3K 0.014 0.15 -10000 0 -0.39 52 52
SPP1 -0.031 0.15 -10000 0 -0.68 22 22
KDR 0.023 0.055 -10000 0 -0.68 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.045 -10000 0 -0.68 2 2
COL4A3 0.007 0.12 -10000 0 -0.65 14 14
angiogenesis -0.056 0.16 -10000 0 -0.53 33 33
Rac1/GTP 0.021 0.076 -10000 0 -0.4 14 14
EDIL3 0.007 0.09 -10000 0 -0.68 7 7
cell proliferation 0.036 0.093 -10000 0 -0.45 15 15
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.015 0.2 -10000 0 -0.93 20 20
NCK1/PAK1/Dok-R -0.029 0.089 -10000 0 -0.42 21 21
NCK1/Dok-R -0.005 0.25 -10000 0 -1.1 21 21
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
mol:beta2-estradiol 0 0.046 0.23 18 -10000 0 18
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
F2 -0.011 0.055 0.27 13 -10000 0 13
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.009 0.23 -10000 0 -1 20 20
FN1 -0.081 0.067 -10000 0 -10000 0 0
PLD2 -0.026 0.24 -10000 0 -1.1 20 20
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GRB14 0.007 0.12 -10000 0 -0.65 14 14
ELK1 -0.026 0.22 0.44 1 -1 20 21
GRB7 0.001 0.055 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.007 0.25 -10000 0 -1.1 20 20
CDKN1A -0.024 0.16 0.49 4 -0.63 20 24
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.005 0.24 -10000 0 -1.1 21 21
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.009 0.17 0.5 12 -0.67 20 32
PLG -0.032 0.24 -10000 0 -1.2 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.013 0.19 -10000 0 -0.88 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 0.42 1 -0.78 18 19
BMX -0.035 0.25 -10000 0 -1.2 20 20
ANGPT1 -0.046 0.27 -10000 0 -1.3 18 18
tube development -0.038 0.17 0.44 4 -0.72 20 24
ANGPT4 -0.032 0.19 -10000 0 -0.68 39 39
response to hypoxia -0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.027 0.27 -10000 0 -1.2 20 20
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.039 0.19 -10000 0 -0.82 20 20
mol:L-citrulline 0.009 0.17 0.5 12 -0.67 20 32
AGTR1 -0.26 0.34 -10000 0 -0.67 195 195
MAPK14 -0.027 0.25 -10000 0 -1.1 20 20
Tie2/SHP2 -0.002 0.18 -10000 0 -1.2 7 7
TEK 0.006 0.18 -10000 0 -1.4 7 7
RPS6KB1 -0.01 0.2 0.5 2 -0.88 20 22
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.5 195 195
Tie2/Ang1/GRB2 -0.018 0.26 -10000 0 -1.2 20 20
MAPK3 -0.022 0.22 -10000 0 -1 20 20
MAPK1 -0.031 0.22 -10000 0 -1 20 20
Tie2/Ang1/GRB7 -0.018 0.26 -10000 0 -1.2 20 20
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.032 0.25 -10000 0 -1.1 21 21
PI3K -0.022 0.23 -10000 0 -1.1 20 20
FES -0.03 0.25 -10000 0 -1.2 20 20
Crk/Dok-R -0.005 0.24 -10000 0 -1.1 21 21
Tie2/Ang1/ABIN2 -0.017 0.26 -10000 0 -1.2 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.006 0.19 0.48 5 -0.82 20 25
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.013 0.2 0.48 1 -0.89 20 21
Tie2/Ang2 -0.057 0.22 -10000 0 -1 20 20
Tie2/Ang1 -0.028 0.27 -10000 0 -1.2 20 20
FOXO1 -0.002 0.19 0.56 4 -0.83 20 24
ELF1 0.028 0.053 -10000 0 -0.59 3 3
ELF2 -0.024 0.24 -10000 0 -1.1 20 20
mol:Choline -0.023 0.23 -10000 0 -1.1 20 20
cell migration -0.01 0.057 -10000 0 -0.24 20 20
FYN -0.047 0.19 0.53 1 -0.83 20 21
DOK2 0.02 0.051 -10000 0 -0.68 2 2
negative regulation of cell cycle -0.02 0.15 0.48 4 -0.57 20 24
ETS1 0.026 0.047 -10000 0 -0.24 13 13
PXN 0.001 0.18 0.54 7 -0.72 20 27
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.003 0.19 0.55 8 -0.77 20 28
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.06 0.24 -10000 0 -0.6 72 72
MAPKKK cascade -0.023 0.23 -10000 0 -1.1 20 20
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.019 0.26 -10000 0 -1.2 20 20
NCK1 0.027 0.004 -10000 0 -10000 0 0
vasculogenesis 0.012 0.16 0.5 12 -0.6 20 32
mol:Phosphatidic acid -0.023 0.23 -10000 0 -1.1 20 20
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.009 0.17 0.5 12 -0.67 20 32
Rac1/GTP -0.007 0.18 -10000 0 -0.82 20 20
MMP2 -0.031 0.25 -10000 0 -1.2 20 20
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.007 0.1 -10000 0 -0.52 11 11
alphaM/beta2 Integrin/GPIbA -0.002 0.12 -10000 0 -0.5 18 18
alphaM/beta2 Integrin/proMMP-9 -0.022 0.16 -10000 0 -0.49 41 41
PLAUR -0.021 0.069 -10000 0 -10000 0 0
HMGB1 0.007 0.037 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.012 0.087 -10000 0 -0.57 5 5
AGER -0.04 0.18 -10000 0 -0.7 32 32
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.018 0.036 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.04 0.2 -10000 0 -0.48 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.039 0.19 -10000 0 -0.67 38 38
CYR61 -0.18 0.32 -10000 0 -0.67 139 139
TLN1 0.025 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.089 -10000 0 -0.36 10 10
RHOA 0.027 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.015 0.079 -10000 0 -0.68 6 6
MYH2 -0.033 0.1 -10000 0 -0.36 18 18
MST1R 0.02 0.065 -10000 0 -0.68 4 4
leukocyte activation during inflammatory response 0.011 0.082 -10000 0 -0.55 4 4
APOB 0.007 0.038 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.016 0.08 -10000 0 -0.63 7 7
JAM3 0.027 0.005 -10000 0 -10000 0 0
GP1BA 0.002 0.12 -10000 0 -0.63 15 15
alphaM/beta2 Integrin/CTGF -0.05 0.19 -10000 0 -0.47 71 71
alphaM/beta2 Integrin -0.025 0.092 -10000 0 -0.3 27 27
JAM3 homodimer 0.027 0.005 -10000 0 -10000 0 0
ICAM2 0.026 0.007 -10000 0 -10000 0 0
ICAM1 -0.019 0.067 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.026 0.092 -10000 0 -0.31 26 26
cell adhesion -0.002 0.12 -10000 0 -0.49 18 18
NFKB1 -0.12 0.26 0.39 1 -0.5 137 138
THY1 0.026 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.021 0.027 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.02 0.099 -10000 0 -0.47 10 10
IL6 -0.21 0.39 -10000 0 -0.95 97 97
ITGB2 -0.004 0.058 -10000 0 -0.46 2 2
elevation of cytosolic calcium ion concentration -0.021 0.1 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.022 0.096 -10000 0 -0.48 9 9
JAM2 0.02 0.064 -10000 0 -0.68 4 4
alphaM/beta2 Integrin/ICAM1 0.029 0.11 -10000 0 -0.52 8 8
alphaM/beta2 Integrin/uPA/Plg 0.011 0.099 -10000 0 -0.53 5 5
RhoA/GTP -0.028 0.11 -10000 0 -0.31 47 47
positive regulation of phagocytosis -0.009 0.098 -10000 0 -0.49 7 7
Ron/MSP 0.034 0.057 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/uPAR/uPA -0.02 0.11 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/uPAR 0.004 0.095 -10000 0 -0.63 4 4
PLAU -0.042 0.074 -10000 0 -10000 0 0
PLAT 0.019 0.066 -10000 0 -0.68 4 4
actin filament polymerization -0.031 0.097 -10000 0 -0.36 16 16
MST1 0.026 0.032 -10000 0 -0.68 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.016 0.084 -10000 0 -0.56 4 4
TNF -0.17 0.35 0.38 1 -0.92 74 75
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.002 0.1 -10000 0 -0.51 6 6
fibrinolysis 0.009 0.097 -10000 0 -0.52 5 5
HCK 0.018 0.035 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.026 0.092 -10000 0 -0.31 26 26
VTN -0.04 0.2 -10000 0 -0.68 44 44
alphaM/beta2 Integrin/CYR61 -0.12 0.23 -10000 0 -0.47 141 141
LPA -0.005 0.026 -10000 0 -10000 0 0
LRP1 0.025 0.032 -10000 0 -0.68 1 1
cell migration -0.031 0.16 -10000 0 -0.49 41 41
FN1 -0.081 0.067 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.013 0.088 -10000 0 -0.56 5 5
MPO 0.013 0.072 -10000 0 -0.68 5 5
KNG1 -0.004 0.037 -10000 0 -10000 0 0
RAP1/GDP 0.035 0.009 -10000 0 -10000 0 0
ROCK1 -0.026 0.1 -10000 0 -0.34 20 20
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.013 0.018 -10000 0 -10000 0 0
CTGF -0.073 0.24 -10000 0 -0.66 70 70
alphaM/beta2 Integrin/Hck 0.008 0.092 -10000 0 -0.51 6 6
ITGAM -0.007 0.081 -10000 0 -0.73 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.016 0.1 -10000 0 -0.53 10 10
HP -0.022 0.097 -10000 0 -0.68 6 6
leukocyte adhesion -0.032 0.17 -10000 0 -0.52 26 26
SELP 0.015 0.08 -10000 0 -0.68 6 6
ceramide signaling pathway

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.017 0.12 -10000 0 -0.44 21 21
BAG4 0.026 0.032 -10000 0 -0.68 1 1
BAD 0.007 0.068 0.36 9 -10000 0 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX 0.012 0.072 0.25 23 -10000 0 23
EnzymeConsortium:3.1.4.12 0.002 0.042 0.16 11 -0.1 19 30
IKBKB -0.016 0.12 0.29 1 -0.43 19 20
MAP2K2 0.016 0.096 0.34 23 -0.3 2 25
MAP2K1 0.01 0.086 0.32 19 -0.3 2 21
SMPD1 0.005 0.048 0.24 8 -0.15 3 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.012 0.13 -10000 0 -0.47 18 18
MAP2K4 0.017 0.099 0.35 26 -10000 0 26
protein ubiquitination -0.012 0.13 0.41 5 -0.43 19 24
EnzymeConsortium:2.7.1.37 0.017 0.11 0.38 25 -0.31 2 27
response to UV 0 0.002 0.006 27 -0.002 4 31
RAF1 0.011 0.088 0.32 21 -0.32 2 23
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.004 0.062 0.24 12 -0.15 18 30
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.008 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.08 0.33 17 -10000 0 17
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.09 0.34 19 -0.28 3 22
MAPK1 -0.005 0.093 0.34 16 -0.27 5 21
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.017 0.12 -10000 0 -0.44 20 20
KSR1 0.01 0.083 0.28 23 -0.33 2 25
MAPK8 0.012 0.11 0.39 22 -0.36 7 29
TRAF2 0.025 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 13 -10000 0 13
CHUK -0.016 0.12 0.33 1 -0.43 19 20
TNF R/SODD 0.038 0.026 -10000 0 -0.51 1 1
TNF -0.059 0.23 -10000 0 -0.68 57 57
CYCS 0.019 0.083 0.25 28 -0.18 1 29
IKBKG -0.014 0.12 0.32 2 -0.45 14 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.018 0.13 -10000 0 -0.46 21 21
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.028 0.002 -10000 0 -10000 0 0
AIFM1 0.017 0.081 0.2 44 -0.18 2 46
TNF/TNF R/SODD -0.006 0.16 -10000 0 -0.44 58 58
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.008 0.13 -10000 0 -0.75 13 13
NSMAF -0.017 0.12 -10000 0 -0.44 21 21
response to hydrogen peroxide 0 0.002 0.006 27 -0.002 4 31
BCL2 -0.023 0.18 -10000 0 -0.67 35 35
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.04 -10000 0 -0.82 1 1
VEGFR1 homodimer/NRP1 0.015 0.038 -10000 0 -0.82 1 1
mol:DAG -0.021 0.13 -10000 0 -0.4 48 48
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.06 -10000 0 -0.64 3 3
CaM/Ca2+ -0.005 0.13 -10000 0 -0.38 48 48
HIF1A 0.032 0.019 -10000 0 -0.37 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.019 0.13 -10000 0 -0.7 4 4
PLCG1 -0.021 0.13 -10000 0 -0.41 48 48
NOS3 -0.012 0.12 -10000 0 -0.81 1 1
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:NO -0.008 0.12 0.47 3 -0.77 1 4
FLT1 0.02 0.043 -10000 0 -0.91 1 1
PGF -0.043 0.21 -10000 0 -0.67 48 48
VEGFR1 homodimer/NRP2/VEGFR121 0.045 0.063 -10000 0 -0.64 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
eNOS/Hsp90 0.005 0.12 -10000 0 -0.74 1 1
endothelial cell proliferation -0.041 0.15 0.36 2 -0.44 48 50
mol:Ca2+ -0.021 0.13 -10000 0 -0.4 48 48
MAPK3 -0.042 0.14 0.36 2 -0.37 64 66
MAPK1 -0.045 0.13 0.36 1 -0.37 65 66
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.043 0.21 -10000 0 -0.67 48 48
PRKACA 0.025 0.008 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.013 0.095 -10000 0 -0.68 9 9
VEGFA homodimer 0.023 0.055 -10000 0 -0.68 3 3
VEGFR1 homodimer/VEGFA homodimer 0.031 0.064 -10000 0 -0.68 3 3
platelet activating factor biosynthetic process -0.045 0.13 -10000 0 -0.4 17 17
PI3K 0.016 0.14 -10000 0 -0.39 49 49
PRKCA -0.043 0.14 -10000 0 -0.39 67 67
PRKCB -0.035 0.13 -10000 0 -0.39 52 52
VEGFR1 homodimer/PLGF homodimer -0.013 0.14 -10000 0 -0.44 48 48
VEGFA 0.023 0.055 -10000 0 -0.68 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.021 0.13 -10000 0 -0.4 48 48
RASA1 0.02 0.038 -10000 0 -0.76 1 1
NRP2 0.015 0.041 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.043 -10000 0 -0.91 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.002 0.14 0.55 4 -0.62 4 8
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
mol:PI-3-4-5-P3 0.014 0.14 -10000 0 -0.39 49 49
mol:L-citrulline -0.008 0.12 0.47 3 -0.77 1 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.062 -10000 0 -0.61 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.062 -10000 0 -0.64 3 3
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.026 0.14 -10000 0 -0.37 47 47
PDPK1 -0.016 0.13 0.34 3 -0.38 45 48
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.075 -10000 0 -0.75 3 3
mol:NADP -0.008 0.12 0.47 3 -0.77 1 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.061 -10000 0 -0.6 3 3
VEGFR1 homodimer/NRP2 0.026 0.047 -10000 0 -0.82 1 1
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
Jak2/Leptin Receptor -0.006 0.13 0.32 1 -0.38 28 29
PTP1B/AKT1 0.006 0.074 0.32 2 -0.32 6 8
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.001 0.088 0.34 11 -0.3 10 21
EGFR 0.015 0.066 -10000 0 -0.68 4 4
EGF/EGFR -0.034 0.16 -10000 0 -0.39 71 71
CSF1 0.015 0.09 -10000 0 -0.68 8 8
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.026 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.11 0.32 7 -0.36 19 26
Insulin Receptor/Insulin 0.016 0.069 -10000 0 -0.32 3 3
HCK 0.018 0.035 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.008 0.096 0.31 22 -0.32 5 27
EGF -0.073 0.24 -10000 0 -0.68 68 68
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.002 0.12 0.44 12 -0.32 11 23
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.028 0.14 0.27 1 -0.38 56 57
cell migration -0.001 0.088 0.3 10 -0.34 11 21
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.017 0.16 -10000 0 -0.68 26 26
ITGA2B -0.042 0.21 -10000 0 -0.67 47 47
CSF1R 0.023 0.036 -10000 0 -0.68 1 1
Prolactin Receptor/Prolactin 0 0.12 -10000 0 -0.51 26 26
FGR 0.025 0.014 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.005 0.075 0.28 3 -0.31 7 10
Crk/p130 Cas 0.012 0.074 -10000 0 -0.32 5 5
DOK1 0.013 0.095 0.41 12 -0.36 5 17
JAK2 -0.012 0.13 0.37 5 -0.39 30 35
Jak2/Leptin Receptor/Leptin -0.013 0.14 -10000 0 -0.5 25 25
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.001 0.089 0.34 11 -0.3 10 21
LYN 0.027 0.004 -10000 0 -10000 0 0
CDH2 -0.073 0.13 -10000 0 -0.63 15 15
SRC 0.022 0.062 0.32 1 -0.44 5 6
ITGB3 0.008 0.11 -10000 0 -0.65 12 12
CAT1/PTP1B -0.06 0.16 0.46 12 -0.36 43 55
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.022 0.08 -10000 0 -0.54 3 3
mol:H2O2 -0.001 0.006 -10000 0 -10000 0 0
STAT3 (dimer) -0.013 0.14 -10000 0 -0.52 25 25
negative regulation of transcription -0.01 0.13 0.37 5 -0.39 30 35
FCGR2A 0.017 0.044 -10000 0 -0.68 1 1
FER 0.021 0.056 -10000 0 -0.68 3 3
alphaIIb/beta3 Integrin -0.028 0.18 -10000 0 -0.53 55 55
BLK -0.19 0.31 -10000 0 -0.67 143 143
Insulin Receptor/Insulin/Shc 0.041 0.018 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.02 0.065 -10000 0 -0.6 5 5
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.09 0.18 0.41 4 -0.47 41 45
PRL -0.005 0.02 -10000 0 -10000 0 0
SOCS3 -0.053 0.32 -10000 0 -1.3 31 31
SPRY2 0.022 0.047 -10000 0 -0.68 2 2
Insulin Receptor/Insulin/IRS1 -0.012 0.16 -10000 0 -0.45 54 54
CSF1/CSF1R 0.007 0.099 0.28 1 -0.45 12 13
Ras protein signal transduction 0.024 0.1 0.46 22 -10000 0 22
IRS1 -0.053 0.22 -10000 0 -0.68 55 55
INS 0.011 0.014 -10000 0 -10000 0 0
LEP 0.009 0.032 -10000 0 -10000 0 0
STAT5B 0.002 0.097 0.32 11 -0.3 16 27
STAT5A 0.002 0.097 0.32 11 -0.3 16 27
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.076 0.28 1 -0.34 8 9
CSN2 0 0.064 0.81 1 -10000 0 1
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
LAT 0.019 0.081 0.29 3 -0.46 10 13
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.012 0.083 -10000 0 -0.68 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.039 0.074 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.039 0.12 0.88 6 -10000 0 6
VDR 0.026 0.008 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.007 0.11 -10000 0 -0.3 43 43
RXRs/LXRs/DNA/Oxysterols -0.012 0.15 -10000 0 -0.42 55 55
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.002 0.019 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.021 0.069 -10000 0 -0.3 20 20
RXRs/NUR77 -0.09 0.23 -10000 0 -0.45 130 130
RXRs/PPAR -0.019 0.081 -10000 0 -0.38 11 11
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.049 0.073 -10000 0 -0.39 12 12
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.032 0.07 -10000 0 -0.37 13 13
RARG 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 0.051 0.12 0.56 26 -10000 0 26
RARs/THRs/DNA/SMRT 0.021 0.069 -10000 0 -0.3 19 19
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.036 0.099 -10000 0 -0.44 5 5
NR1H4 -0.004 0.022 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.056 0.12 -10000 0 -0.5 4 4
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.023 0.027 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.047 0.081 -10000 0 -0.45 3 3
NR4A1 -0.18 0.32 -10000 0 -0.68 141 141
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.003 0.056 -10000 0 -0.31 3 3
RXRG -0.1 0.077 -10000 0 -0.6 5 5
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.02 0.026 -10000 0 -10000 0 0
RXRB 0.023 0.027 -10000 0 -10000 0 0
THRB 0.013 0.097 -10000 0 -0.64 10 10
PPARG 0.016 0.085 -10000 0 -0.68 7 7
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.1 0.38 -10000 0 -1.1 58 58
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.011 0.15 -10000 0 -0.41 55 55
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.008 0.11 -10000 0 -0.68 13 13
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 145 145
SREBF1 -0.012 0.14 -10000 0 -0.52 7 7
RXRs/RXRs/DNA/9cRA 0.036 0.099 -10000 0 -0.44 5 5
ABCA1 -0.012 0.14 -10000 0 -0.54 6 6
RARs/THRs 0.056 0.097 -10000 0 -0.4 19 19
RXRs/FXR 0.047 0.087 -10000 0 -0.48 3 3
BCL2 -0.023 0.18 -10000 0 -0.67 35 35
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.044 0.13 0.49 13 -10000 0 13
IL27/IL27R/JAK1 -0.012 0.17 -10000 0 -0.5 8 8
TBX21 -0.064 0.18 0.39 5 -0.58 27 32
IL12B 0.006 0.074 -10000 0 -0.68 5 5
IL12A -0.049 0.16 -10000 0 -0.51 51 51
IL6ST -0.069 0.24 -10000 0 -0.68 62 62
IL27RA/JAK1 0.019 0.053 0.55 1 -10000 0 1
IL27 0.011 0.027 -10000 0 -10000 0 0
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.047 0.14 -10000 0 -0.49 4 4
T-helper 2 cell differentiation 0.044 0.13 0.49 13 -10000 0 13
T cell proliferation during immune response 0.044 0.13 0.49 13 -10000 0 13
MAPKKK cascade -0.044 0.13 -10000 0 -0.49 13 13
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
IL12RB1 0.007 0.07 -10000 0 -0.6 4 4
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.059 0.19 0.5 10 -0.57 24 34
IL27/IL27R/JAK2/TYK2 -0.044 0.13 -10000 0 -0.51 12 12
positive regulation of T cell mediated cytotoxicity -0.044 0.13 -10000 0 -0.49 13 13
STAT1 (dimer) -0.026 0.21 0.53 10 -0.66 11 21
JAK2 0.02 0.026 -10000 0 -0.37 1 1
JAK1 0.027 0.008 -10000 0 -10000 0 0
STAT2 (dimer) -0.033 0.14 -10000 0 -0.49 12 12
T cell proliferation -0.11 0.2 -10000 0 -0.52 55 55
IL12/IL12R/TYK2/JAK2 -0.069 0.23 -10000 0 -0.79 29 29
IL17A -0.048 0.14 -10000 0 -0.49 4 4
mast cell activation 0.044 0.13 0.49 13 -10000 0 13
IFNG -0.016 0.051 0.099 2 -0.13 66 68
T cell differentiation -0.004 0.008 0.014 1 -0.023 57 58
STAT3 (dimer) -0.032 0.13 -10000 0 -0.47 12 12
STAT5A (dimer) -0.032 0.13 -10000 0 -0.47 12 12
STAT4 (dimer) -0.039 0.15 -10000 0 -0.48 18 18
STAT4 0.004 0.1 -10000 0 -0.59 11 11
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.023 0.15 -10000 0 -0.52 4 4
GATA3 -0.057 0.3 -10000 0 -1.3 24 24
IL18 -0.012 0.078 -10000 0 -0.49 11 11
positive regulation of mast cell cytokine production -0.031 0.13 -10000 0 -0.46 12 12
IL27/EBI3 -0.027 0.059 -10000 0 -0.26 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.11 0.27 -10000 0 -0.68 90 90
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.011 0.022 -10000 0 -10000 0 0
IL1B -0.034 0.14 -10000 0 -0.51 38 38
EBI3 -0.049 0.073 -10000 0 -0.37 1 1
TNF -0.055 0.17 -10000 0 -0.51 57 57
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.075 -9999 0 -0.38 15 15
RGS9BP -0.015 0.16 -9999 0 -0.66 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.04 0.2 -9999 0 -0.66 46 46
mol:Na + 0.018 0.032 -9999 0 -10000 0 0
mol:ADP -0.044 0.15 -9999 0 -0.5 45 45
GNAT2 0.016 0.021 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.025 0.18 -9999 0 -0.45 72 72
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.01 -9999 0 -10000 0 0
GRK7 0.005 0.022 -9999 0 -10000 0 0
CNGB3 -0.007 0.018 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.01 0.026 -9999 0 -10000 0 0
Cone PDE6 -0.006 0.17 -9999 0 -0.4 70 70
Cone Metarhodopsin II -0.011 0.12 -9999 0 -0.4 45 45
Na + (4 Units) 0.023 0.038 -9999 0 -10000 0 0
GNAT2/GDP -0.011 0.16 -9999 0 -0.39 68 68
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.002 0.023 -9999 0 -10000 0 0
Cone Transducin 0.032 0.08 -9999 0 -0.4 15 15
SLC24A2 -0.006 0.029 -9999 0 -10000 0 0
GNB3/GNGT2 0.02 0.096 -9999 0 -0.51 15 15
GNB3 0.006 0.12 -9999 0 -0.68 14 14
GNAT2/GTP 0.017 0.008 -9999 0 -10000 0 0
CNGA3 0.008 0.049 -9999 0 -10000 0 0
ARR3 -0.002 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.018 0.033 -9999 0 -10000 0 0
mol:Pi -0.025 0.18 -9999 0 -0.44 72 72
Cone CNG Channel 0.043 0.033 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.006 0.029 -9999 0 -10000 0 0
RGS9 -0.043 0.21 -9999 0 -0.68 47 47
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.023 0.035 -9999 0 -0.68 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.02 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.036 0.037 -10000 0 -0.51 2 2
Necdin/E2F1 -0.002 0.078 -10000 0 -0.55 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.056 0.093 -10000 0 -0.41 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.25 -10000 0 -0.45 218 218
NT-4/5 (dimer)/p75(NTR) -0.011 0.13 -10000 0 -0.52 28 28
IKBKB 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.004 0.098 0.36 1 -0.4 19 20
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.68 10 10
MGDIs/NGR/p75(NTR)/LINGO1 0.022 0.093 -10000 0 -0.45 16 16
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.027 0.11 -10000 0 -0.42 26 26
LINGO1 0.02 0.032 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.028 -10000 0 -0.35 2 2
proBDNF (dimer) 0.009 0.1 -10000 0 -0.68 10 10
NTRK1 0.011 0.03 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.022 0.13 0.4 16 -0.44 17 33
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.007 0.09 -10000 0 -0.46 15 15
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.046 0.094 -10000 0 -0.43 16 16
MAGEH1 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.045 0.1 -10000 0 -0.42 20 20
Mammalian IAPs/DIABLO 0.045 0.095 -10000 0 -0.4 20 20
proNGF (dimer) 0.021 0.057 -10000 0 -0.68 3 3
MAGED1 0.025 0.007 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.11 -10000 0 -0.65 13 13
ZNF274 0.025 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.011 0.086 -10000 0 -0.4 16 16
NGF 0.021 0.057 -10000 0 -0.68 3 3
cell cycle arrest 0.056 0.14 0.44 17 -0.38 16 33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.07 -10000 0 -0.32 18 18
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.019 0.12 -10000 0 -0.46 30 30
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.033 0.099 -10000 0 -0.45 18 18
PSENEN 0.026 0.007 -10000 0 -10000 0 0
mol:ceramide 0.003 0.093 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.059 -10000 0 -0.38 4 4
p75(NTR)/beta APP 0.004 0.1 -10000 0 -0.51 16 16
BEX1 -0.28 0.35 -10000 0 -0.67 209 209
mol:GDP -0.018 0.089 -10000 0 -0.44 18 18
NGF (dimer) 0.038 0.11 -10000 0 -0.41 26 26
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.034 0.091 -10000 0 -0.41 16 16
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.03 0.084 -10000 0 -0.4 16 16
MYD88 0.027 0.004 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.034 0.099 -10000 0 -0.45 18 18
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.004 0.054 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.16 -10000 0 -0.68 26 26
TP53 -0.002 0.099 0.35 1 -0.36 25 26
PRDM4 0 0.091 -10000 0 -0.43 16 16
BDNF (dimer) 0.007 0.14 -10000 0 -0.44 32 32
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.05 0.09 -10000 0 -0.4 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.047 0.098 -10000 0 -0.43 18 18
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
MAPK10 0.016 0.12 0.36 17 -0.4 15 32
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.003 0.094 -10000 0 -0.43 16 16
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.035 0.097 -10000 0 -0.45 17 17
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.027 -10000 0 -0.51 1 1
NT3 (dimer)/p75(NTR) -0.028 0.16 -10000 0 -0.52 41 41
MAPK8 0.012 0.12 0.38 14 -0.41 16 30
MAPK9 0.01 0.1 0.35 9 -0.39 14 23
APAF1 0.025 0.032 -10000 0 -0.68 1 1
NTF3 -0.018 0.16 -10000 0 -0.68 26 26
NTF4 0.004 0.11 -10000 0 -0.65 13 13
NDN 0.02 0.071 -10000 0 -0.68 5 5
RAC1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.087 -10000 0 -0.38 17 17
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.053 -10000 0 -0.52 3 3
RhoA-B-C/GTP 0.033 0.098 -10000 0 -0.45 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.11 -10000 0 -0.38 25 25
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.11 -10000 0 -0.4 26 26
PRKACB 0.025 0.032 -10000 0 -0.68 1 1
proBDNF (dimer)/p75 ECD 0.023 0.087 -10000 0 -0.51 12 12
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.07 0.15 0.52 11 -0.39 16 27
BAD 0.03 0.15 0.46 26 -0.4 16 42
RIPK2 0.027 0.005 -10000 0 -10000 0 0
NGFR -0.017 0.13 -10000 0 -0.68 16 16
CYCS 0.008 0.1 0.36 12 -0.4 16 28
ADAM17 0.024 0.045 -10000 0 -0.68 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.046 0.099 -10000 0 -0.43 18 18
BCL2L11 0.03 0.15 0.45 26 -0.4 16 42
BDNF (dimer)/p75(NTR) -0.009 0.13 -10000 0 -0.51 26 26
PI3K 0.045 0.1 -10000 0 -0.43 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.094 -10000 0 -0.43 16 16
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.001 0.11 -10000 0 -0.51 18 18
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.046 0.094 -10000 0 -0.43 16 16
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
PLG -0.013 0.018 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.006 0.099 -10000 0 -0.4 25 25
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.025 0.007 -10000 0 -10000 0 0
CASP3 0.032 0.14 0.45 26 -0.36 16 42
E2F1 -0.019 0.069 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.05 0.075 -10000 0 -0.47 3 3
NGF (dimer)/TRKA 0.028 0.049 -10000 0 -0.51 3 3
MMP7 -0.078 0.16 -10000 0 -0.66 25 25
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.054 0.097 -10000 0 -0.4 18 18
MMP3 -0.016 0.047 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.015 0.097 -10000 0 -0.54 6 6
Aurora C signaling

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
INCENP 0.024 0.045 -9999 0 -0.68 2 2
Aurora C/Aurora B/INCENP 0.045 0.043 -9999 0 -0.45 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.008 0.021 -9999 0 -0.34 1 1
AURKB -0.005 0.06 -9999 0 -0.12 98 98
AURKC 0.02 0.029 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.033 0.008 -9999 0 -10000 0 0
PRKCZ 0.026 0.005 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.013 0.066 -9999 0 -0.3 4 4
IRAK/TOLLIP 0.03 0.011 -9999 0 -10000 0 0
IKBKB 0.027 0.004 -9999 0 -10000 0 0
IKBKG 0.025 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.055 0.21 -9999 0 -0.53 72 72
IL1A -0.032 0.19 -9999 0 -0.67 38 38
IL1B -0.027 0.15 -9999 0 -0.52 39 39
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.038 -9999 0 -0.36 2 2
IL1R2 -0.042 0.19 -9999 0 -0.66 40 40
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.052 -9999 0 -0.28 1 1
TOLLIP 0.026 0.005 -9999 0 -10000 0 0
TICAM2 0.019 0.071 -9999 0 -0.68 5 5
MAP3K3 0.026 0.007 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.034 0.058 -9999 0 -10000 0 0
JUN -0.082 0.16 -9999 0 -0.37 107 107
MAP3K7 0.027 0.003 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.035 0.13 -9999 0 -0.38 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88 0.034 0.13 -9999 0 -0.41 37 37
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.046 0.13 -9999 0 -0.39 37 37
IL1 beta fragment/IL1R1/IL1RAP 0.012 0.13 -9999 0 -0.42 38 38
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAPK8 -0.012 0.082 -9999 0 -0.43 15 15
IRAK1 0.015 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 0.01 0.088 -9999 0 -0.48 11 11
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.004 -9999 0 -10000 0 0
TRAF6 0.024 0.045 -9999 0 -0.68 2 2
PI3K 0.036 0.044 -9999 0 -0.51 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.072 -9999 0 -0.35 4 4
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.012 0.13 -9999 0 -0.42 38 38
IL1 beta/IL1R2 -0.047 0.19 -9999 0 -0.49 69 69
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.029 -9999 0 -0.36 2 2
NF kappa B1 p50/RelA 0.024 0.12 -9999 0 -0.36 37 37
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.033 0.13 -9999 0 -0.39 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.086 -9999 0 -0.29 37 37
IL1 alpha/IL1R1/IL1RAP 0.017 0.14 -9999 0 -0.45 37 37
RELA 0.027 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.027 0.004 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.033 -9999 0 -0.39 2 2
IL1RAP -0.013 0.066 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.011 0.11 -9999 0 -0.39 11 11
CASP1 0.023 0.047 -9999 0 -0.68 2 2
IL1RN/IL1R2 -0.041 0.17 -9999 0 -0.52 48 48
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.13 -9999 0 -0.4 38 38
TMEM189-UBE2V1 -0.004 0.02 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.07 -9999 0 -0.36 1 1
PIK3CA 0.023 0.055 -9999 0 -0.68 3 3
IL1RN -0.012 0.11 -9999 0 -0.65 11 11
TRAF6/TAK1/TAB1/TAB2 0.045 0.03 -9999 0 -0.37 2 2
MAP2K6 0.007 0.062 -9999 0 -0.36 12 12
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.013 0.32 0.8 2 -0.93 11 13
PLK1 0.029 0.095 -10000 0 -0.81 5 5
BIRC5 0.024 0.11 -10000 0 -1 4 4
HSPA1B -0.019 0.31 -10000 0 -0.93 11 11
MAP2K1 0.025 0.045 -10000 0 -10000 0 0
BRCA2 -0.022 0.33 0.8 1 -0.99 14 15
FOXM1 -0.044 0.34 -10000 0 -0.93 25 25
XRCC1 -0.011 0.31 -10000 0 -0.92 11 11
FOXM1B/p19 -0.043 0.34 -10000 0 -0.88 26 26
Cyclin D1/CDK4 0.003 0.29 -10000 0 -0.83 11 11
CDC2 -0.022 0.32 -10000 0 -0.84 24 24
TGFA -0.011 0.29 -10000 0 -0.8 13 13
SKP2 -0.016 0.33 0.8 2 -0.97 15 17
CCNE1 0.027 0.01 -10000 0 -10000 0 0
CKS1B -0.008 0.31 0.79 1 -0.89 13 14
RB1 0.028 0.19 -10000 0 -0.69 9 9
FOXM1C/SP1 -0.026 0.33 -10000 0 -0.93 22 22
AURKB 0.008 0.14 -10000 0 -0.8 11 11
CENPF -0.008 0.31 0.79 1 -0.89 13 14
CDK4 0.027 0.019 -10000 0 -10000 0 0
MYC -0.025 0.31 -10000 0 -0.91 18 18
CHEK2 0.02 0.04 -10000 0 -10000 0 0
ONECUT1 -0.009 0.3 -10000 0 -0.86 13 13
CDKN2A -0.034 0.071 -10000 0 -10000 0 0
LAMA4 -0.019 0.31 -10000 0 -0.93 11 11
FOXM1B/HNF6 -0.016 0.33 -10000 0 -0.98 13 13
FOS -0.22 0.6 0.8 2 -1.2 129 131
SP1 0.026 0.009 -10000 0 -10000 0 0
CDC25B -0.014 0.32 0.8 1 -0.88 14 15
response to radiation 0.007 0.026 -10000 0 -10000 0 0
CENPB -0.014 0.32 0.8 1 -0.93 11 12
CENPA -0.026 0.32 -10000 0 -0.96 14 14
NEK2 -0.009 0.31 0.79 1 -0.92 11 12
HIST1H2BA -0.025 0.31 -10000 0 -0.94 11 11
CCNA2 0.026 0.021 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.029 0.33 -10000 0 -1 14 14
CCNB2 -0.02 0.31 -10000 0 -0.92 12 12
CCNB1 -0.02 0.32 0.68 2 -0.93 14 16
ETV5 -0.019 0.31 -10000 0 -0.92 12 12
ESR1 -0.057 0.39 -10000 0 -1.1 33 33
CCND1 -0.003 0.3 0.59 1 -0.85 11 12
GSK3A 0.022 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.052 0.043 -10000 0 -10000 0 0
CDK2 0.028 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.009 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.034 0.31 -10000 0 -0.86 21 21
GAS1 -0.17 0.55 0.8 1 -1.2 99 100
MMP2 -0.021 0.34 0.8 2 -1.2 12 14
RB1/FOXM1C -0.003 0.3 -10000 0 -0.88 12 12
CREBBP 0.026 0.006 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.003 0.041 -10000 0 -0.44 4 4
ADCY5 -0.054 0.15 -10000 0 -0.44 65 65
ADCY6 0.003 0.041 -10000 0 -0.44 4 4
ADCY7 0.003 0.041 -10000 0 -0.44 4 4
ADCY1 0 0.054 -10000 0 -0.45 7 7
ADCY2 -0.038 0.13 -10000 0 -0.45 44 44
ADCY3 0.003 0.041 -10000 0 -0.44 4 4
ADCY8 -0.047 0.05 -10000 0 -0.49 4 4
PRKCE 0.005 0.047 -10000 0 -0.51 4 4
ADCY9 0.003 0.041 -10000 0 -0.44 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.035 0.094 0.34 7 -0.34 16 23
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.026 0.025 0.37 1 -10000 0 1
HSPA8 0.02 0.058 -10000 0 -0.6 4 4
SMAD3/SMAD4/ER alpha -0.006 0.13 -10000 0 -0.45 25 25
AKT1 0.026 0.006 -10000 0 -10000 0 0
GSC -0.18 0.51 -10000 0 -1.4 70 70
NKX2-5 0.018 0.014 -10000 0 -10000 0 0
muscle cell differentiation -0.009 0.083 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.037 0.095 -10000 0 -10000 0 0
SMAD4 -0.008 0.071 -10000 0 -0.26 1 1
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.041 0.069 -10000 0 -0.44 3 3
SMAD3/SMAD4/VDR 0.049 0.073 -10000 0 -10000 0 0
MYC 0.011 0.11 -10000 0 -0.65 12 12
CDKN2B -0.021 0.11 -10000 0 -0.47 3 3
AP1 -0.19 0.41 -10000 0 -0.76 148 148
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.027 0.066 -10000 0 -0.55 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.034 -10000 0 -10000 0 0
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 0.005 0.053 -10000 0 -0.22 1 1
SMAD3/SMAD4/GR 0.02 0.078 -10000 0 -10000 0 0
GATA3 -0.009 0.15 -10000 0 -0.63 24 24
SKI/SIN3/HDAC complex/NCoR1 0.026 0.054 -10000 0 -0.71 2 2
MEF2C/TIF2 -0.032 0.14 -10000 0 -0.41 36 36
endothelial cell migration -0.023 0.079 0.76 3 -10000 0 3
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.007 -10000 0 -10000 0 0
RBBP4 0.023 0.045 -10000 0 -0.68 2 2
RUNX2 -0.015 0.079 -10000 0 -0.68 2 2
RUNX3 0.013 0.091 -10000 0 -0.68 8 8
RUNX1 -0.038 0.074 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
CDKN1A 0.02 0.043 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.012 0.12 -10000 0 -0.29 43 43
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 0.023 0.08 -10000 0 -0.76 3 3
SMAD3/SMAD4/ATF2 0.005 0.12 -10000 0 -0.48 16 16
SMAD3/SMAD4/ATF3 -0.077 0.24 -10000 0 -0.51 104 104
SAP30 0.025 0.032 -10000 0 -0.68 1 1
Cbp/p300/PIAS3 0.049 0.045 -10000 0 -10000 0 0
JUN -0.2 0.4 0.3 1 -0.75 148 149
SMAD3/SMAD4/IRF7 0.024 0.079 -10000 0 -10000 0 0
TFE3 0.03 0.009 -10000 0 -10000 0 0
COL1A2 0.028 0.041 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.014 0.096 0.4 3 -10000 0 3
DLX1 -0.011 0.16 -10000 0 -0.65 27 27
TCF3 0.025 0.008 -10000 0 -10000 0 0
FOS -0.17 0.33 -10000 0 -0.73 126 126
SMAD3/SMAD4/Max 0.019 0.079 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.042 0.036 -10000 0 -0.42 1 1
ZBTB17 0.027 0.006 -10000 0 -10000 0 0
LAMC1 0.011 0.06 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.021 0.079 -10000 0 -10000 0 0
IRF7 0.027 0.01 -10000 0 -10000 0 0
ESR1 -0.018 0.15 -10000 0 -0.65 24 24
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.014 0.1 0.39 3 -0.89 1 4
SMAD2-3/SMAD4 0.01 0.095 -10000 0 -0.29 2 2
Cbp/p300/Src-1 0.047 0.035 -10000 0 -10000 0 0
IGHV3OR16-13 0.002 0.029 -10000 0 -0.32 2 2
TGIF2/HDAC complex 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.03 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.032 -10000 0 -0.68 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
SNIP1 0.024 0.032 -10000 0 -0.68 1 1
GCN5L2 0.005 0.013 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.029 0.08 -10000 0 -10000 0 0
MSG1/HSC70 -0.064 0.07 -10000 0 -0.46 8 8
SMAD2 0.011 0.048 -10000 0 -10000 0 0
SMAD3 0.005 0.059 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.066 -10000 0 -0.37 7 7
SMAD2/SMAD2/SMAD4 0.003 0.036 0.23 3 -10000 0 3
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.034 0.2 -10000 0 -0.68 42 42
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.045 0.094 -10000 0 -10000 0 0
IFNB1 -0.001 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.003 0.11 -10000 0 -0.88 1 1
CITED1 -0.097 0.075 -10000 0 -0.6 4 4
SMAD2-3/SMAD4/ARC105 0.012 0.086 -10000 0 -10000 0 0
RBL1 0.013 0.095 -10000 0 -0.68 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.012 0.035 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.046 0.069 -10000 0 -0.46 7 7
SMAD7 -0.09 0.25 -10000 0 -0.54 91 91
MYC/MIZ-1 0.027 0.084 -10000 0 -0.49 12 12
SMAD3/SMAD4 0.025 0.11 0.29 36 -0.52 1 37
IL10 -0.029 0.15 -10000 0 -0.52 33 33
PIASy/HDAC complex 0.017 0.02 -10000 0 -10000 0 0
PIAS3 0.027 0.009 -10000 0 -10000 0 0
CDK2 0.03 0.011 -10000 0 -10000 0 0
IL5 -0.022 0.11 -10000 0 -0.4 22 22
CDK4 0.031 0.012 -10000 0 -10000 0 0
PIAS4 0.017 0.02 -10000 0 -10000 0 0
ATF3 -0.13 0.29 -10000 0 -0.67 104 104
SMAD3/SMAD4/SP1 0.032 0.081 -10000 0 -10000 0 0
FOXG1 0.008 0.042 -10000 0 -0.68 1 1
FOXO3 0.015 0.008 -10000 0 -10000 0 0
FOXO1 0.014 0.008 -10000 0 -10000 0 0
FOXO4 0.015 0.008 -10000 0 -10000 0 0
heart looping -0.014 0.1 0.39 3 -0.87 1 4
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.005 0.14 -10000 0 -0.48 26 26
MYOD1 -0.013 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.016 0.08 -10000 0 -0.27 3 3
SMAD3/SMAD4/GATA3 -0.001 0.14 -10000 0 -0.41 33 33
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.032 -10000 0 -0.68 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.03 0.11 -10000 0 -0.5 7 7
SMAD3/SMAD4/SP1-3 0.052 0.08 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.032 0.01 -10000 0 -10000 0 0
SIN3B 0.025 0.007 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.028 0.12 -10000 0 -0.41 3 3
ITGB5 0.015 0.059 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.029 0.046 -10000 0 -0.57 2 2
SMAD3/SMAD4/AR -0.18 0.26 -10000 0 -0.48 194 194
AR -0.26 0.34 -10000 0 -0.66 200 200
negative regulation of cell growth -0.023 0.12 -10000 0 -0.42 8 8
SMAD3/SMAD4/MYOD 0.015 0.08 -10000 0 -10000 0 0
E2F5 0.025 0.032 -10000 0 -0.68 1 1
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.026 0.098 -10000 0 -0.31 3 3
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.036 -10000 0 -10000 0 0
TFDP1 0.025 0.019 -10000 0 -0.36 1 1
SMAD3/SMAD4/AP1 -0.18 0.42 -10000 0 -0.77 148 148
SMAD3/SMAD4/RUNX2 0.015 0.097 -10000 0 -0.4 3 3
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.004 -10000 0 -10000 0 0
ATF2 0.003 0.13 -10000 0 -0.66 17 17
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.02 0.12 -10000 0 -0.45 22 22
MAP4K1 0.009 0.079 -10000 0 -0.68 5 5
MAP3K8 0.016 0.086 -10000 0 -0.64 8 8
PRKCB 0.005 0.082 -10000 0 -0.68 5 5
DBNL 0.026 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.003 0.079 -10000 0 -0.41 8 8
JUN -0.081 0.21 0.42 2 -0.51 50 52
MAP3K7 0.003 0.079 -10000 0 -0.41 8 8
GRAP2 -0.017 0.15 -10000 0 -0.55 31 31
CRK 0.026 0.007 -10000 0 -10000 0 0
MAP2K4 -0.003 0.097 0.38 2 -0.42 10 12
LAT 0.021 0.058 -10000 0 -0.6 4 4
LCP2 0.024 0.019 -10000 0 -10000 0 0
MAPK8 -0.005 0.14 -10000 0 -0.61 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.084 -10000 0 -0.33 24 24
LAT/GRAP2/SLP76/HPK1/HIP-55 0.03 0.12 -10000 0 -0.43 22 22
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.029 0.11 -10000 0 -0.33 55 55
FRAP1 0.01 0.051 0.36 3 -0.41 2 5
AKT1 -0.025 0.095 -10000 0 -0.52 3 3
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.004 0.088 -10000 0 -0.42 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.007 0.036 -10000 0 -0.24 1 1
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP 0 0.074 -10000 0 -0.39 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.023 0.13 -10000 0 -0.38 55 55
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.044 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.018 0.098 0.38 17 -0.35 4 21
MAP3K5 0.006 0.028 0.18 1 -0.22 6 7
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.03 0.17 2 -0.21 7 9
mol:LY294002 0 0.001 0.001 1 -0.002 68 69
EIF4B 0.023 0.11 0.45 21 -0.32 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.071 0.36 5 -0.33 2 7
eIF4E/eIF4G1/eIF4A1 0.015 0.027 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.006 0.13 -10000 0 -0.36 56 56
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.047 0.28 3 -0.24 2 5
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.013 0.08 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 68 69
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.031 0.11 -10000 0 -0.32 53 53
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.075 -10000 0 -0.47 9 9
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.006 0.095 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 68 -0.001 1 69
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.041 0.13 -10000 0 -0.39 60 60
INS -0.016 0.003 -10000 0 -10000 0 0
PTEN 0.025 0.019 -10000 0 -0.36 1 1
PDK2 -0.028 0.1 0.25 1 -0.31 52 53
EIF4EBP1 0.016 0.097 -10000 0 -0.93 5 5
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PPP2R5D 0.019 0.075 0.37 13 -0.37 2 15
peptide biosynthetic process 0.014 0.016 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.008 18 -0.003 2 20
EEF2 0.014 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.031 0.089 -10000 0 -0.83 5 5
Signaling events mediated by HDAC Class III

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.012 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.024 0.51 1 -10000 0 1
CDKN1A -0.007 0.013 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
BAX 0.025 0.007 -10000 0 -10000 0 0
FOXO3 -0.004 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
TAT 0.011 0.024 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.009 -10000 0 -10000 0 0
PPARGC1A -0.28 0.35 -10000 0 -0.67 209 209
FHL2 -0.03 0.19 -10000 0 -0.68 39 39
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.026 0.03 -10000 0 -0.51 1 1
HIST2H4A 0.013 0.024 -10000 0 -0.51 1 1
SIRT1/FOXO3a 0.038 0.052 -10000 0 -0.31 2 2
SIRT1 0.022 0.032 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.028 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.006 0.071 -10000 0 -0.32 10 10
apoptosis -0.037 0.033 0.44 1 -10000 0 1
SIRT1/PGC1A -0.17 0.24 -10000 0 -0.44 209 209
p53/SIRT1 0.028 0.028 -10000 0 -0.51 1 1
SIRT1/FOXO4 -0.004 0.064 -10000 0 -0.31 4 4
FOXO1/FHL2/SIRT1 0.008 0.12 -10000 0 -0.4 40 40
HIST1H1E 0.008 0.047 -10000 0 -0.34 8 8
SIRT1/p300 0.026 0.03 -10000 0 -0.51 1 1
muscle cell differentiation -0.03 0.029 0.45 1 -10000 0 1
TP53 0.022 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.033 -10000 0 -0.44 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.025 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.029 -10000 0 -0.51 1 1
ACSS2 0.014 0.024 -10000 0 -0.51 1 1
SIRT1/PCAF/MYOD 0.03 0.03 -10000 0 -0.45 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.032 -10000 0 -0.68 1 1
Caspase 8 (4 units) 0.025 0.089 -10000 0 -0.41 6 6
NEF -0.011 0.06 -10000 0 -0.23 26 26
NFKBIA 0.021 0.032 -10000 0 -10000 0 0
BIRC3 -0.004 0.15 -10000 0 -0.66 23 23
CYCS -0.007 0.09 0.22 1 -0.31 22 23
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CD247 -0.014 0.15 -10000 0 -0.43 40 40
MAP2K7 0 0.16 0.36 1 -0.61 24 25
protein ubiquitination 0.008 0.1 0.36 6 -0.4 3 9
CRADD 0.027 0.005 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.027 0.005 -10000 0 -10000 0 0
BID -0.008 0.096 0.22 1 -0.31 31 32
NF-kappa-B/RelA/I kappa B alpha 0.042 0.081 -10000 0 -0.32 20 20
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.68 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.042 0.081 -10000 0 -0.33 20 20
MAPK8 -0.003 0.16 0.35 2 -0.57 26 28
APAF1 0.025 0.032 -10000 0 -0.68 1 1
TRAF1 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.001 0.096 -10000 0 -0.32 31 31
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.41 10 10
CHUK 0.004 0.099 0.28 3 -0.44 3 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.076 0.03 -10000 0 -0.38 1 1
TCRz/NEF -0.021 0.15 -10000 0 -0.45 43 43
TNF -0.059 0.23 -10000 0 -0.68 57 57
FASLG -0.045 0.22 -10000 0 -0.74 40 40
NFKB1 0.021 0.034 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.006 0.16 -10000 0 -0.44 58 58
CASP6 0.04 0.094 -10000 0 -0.72 4 4
CASP7 0.012 0.16 0.36 4 -0.58 26 30
RELA 0.021 0.033 -10000 0 -10000 0 0
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.011 0.15 0.32 2 -0.57 26 28
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.51 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
MAP3K14 0.001 0.1 -10000 0 -0.41 7 7
APAF-1/Caspase 9 -0.001 0.12 -10000 0 -0.48 22 22
BCL2 -0.024 0.16 0.42 2 -0.55 24 26
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.003 0.066 -10000 0 -0.28 6 6
NT3 (dimer)/TRKC -0.022 0.14 -10000 0 -0.51 36 36
NT3 (dimer)/TRKB 0.002 0.15 -10000 0 -0.44 45 45
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.028 -10000 0 -0.29 3 3
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.68 10 10
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.011 0.03 -10000 0 -10000 0 0
NTRK2 0.019 0.066 -10000 0 -0.61 5 5
NTRK3 -0.011 0.11 -10000 0 -0.62 12 12
NT-4/5 (dimer)/TRKB 0.013 0.13 -10000 0 -0.45 32 32
neuron apoptosis -0.01 0.11 0.38 18 -10000 0 18
SHC 2-3/Grb2 0.01 0.12 -10000 0 -0.42 18 18
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.001 0.1 -10000 0 -0.55 10 10
SHC3 -0.006 0.12 -10000 0 -0.42 29 29
STAT3 (dimer) 0.03 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.001 0.14 -10000 0 -0.44 40 40
RIN/GDP -0.004 0.079 0.29 8 -0.26 4 12
GIPC1 0.025 0.008 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
DNAJA3 -0.006 0.072 -10000 0 -0.38 15 15
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.02 0.017 -10000 0 -10000 0 0
MAGED1 0.025 0.007 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.11 -10000 0 -0.65 13 13
SHC/GRB2/SOS1 0.048 0.02 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.037 0.068 -10000 0 -0.44 8 8
TRKA/NEDD4-2 0.032 0.022 -10000 0 -10000 0 0
ELMO1 -0.24 0.34 -10000 0 -0.68 184 184
RhoG/GTP/ELMO1/DOCK1 -0.15 0.24 -10000 0 -0.45 184 184
NGF 0.021 0.057 -10000 0 -0.68 3 3
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.055 -10000 0 -0.68 3 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 -0.009 0.016 -10000 0 -10000 0 0
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.004 0.12 -10000 0 -0.62 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.19 -10000 0 -0.35 185 185
mol:GDP -0.012 0.11 0.39 10 -0.36 7 17
NGF (dimer) 0.021 0.057 -10000 0 -0.68 3 3
RhoG/GDP -0.18 0.26 -10000 0 -0.51 184 184
RIT1/GDP -0.002 0.083 0.35 8 -0.26 4 12
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.036 0.089 -10000 0 -0.48 13 13
KIDINS220/CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.025 -10000 0 -0.44 1 1
SHC/GRB2/SOS1/GAB1 0.061 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.16 -10000 0 -0.68 26 26
RAP1/GDP -0.006 0.058 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.1 -10000 0 -0.68 10 10
ubiquitin-dependent protein catabolic process 0.045 0.043 -10000 0 -0.44 3 3
Schwann cell development -0.03 0.029 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.02 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.039 -10000 0 -0.28 1 1
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.12 -10000 0 -0.37 44 44
ABL1 0.025 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.008 0.1 -10000 0 -0.5 6 6
STAT3 0.03 0.015 -10000 0 -10000 0 0
axon guidance -0.016 0.12 -10000 0 -0.35 44 44
MAPK3 0.017 0.071 -10000 0 -0.4 8 8
MAPK1 0.009 0.065 -10000 0 -0.4 8 8
CDC42/GDP 0 0.085 0.35 8 -0.26 3 11
NTF3 -0.018 0.16 -10000 0 -0.68 26 26
NTF4 0.004 0.11 -10000 0 -0.65 13 13
NGF (dimer)/TRKA/FAIM 0.046 0.043 -10000 0 -0.44 3 3
PI3K 0.036 0.044 -10000 0 -0.51 3 3
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.004 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.042 0.084 -10000 0 -0.4 18 18
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.028 0.12 -10000 0 -0.44 35 35
RGS19 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.069 -10000 0 -0.48 2 2
Rac1/GDP -0.005 0.068 0.22 1 -0.26 2 3
NGF (dimer)/TRKA/GRIT 0.026 0.043 -10000 0 -0.44 3 3
neuron projection morphogenesis 0.022 0.096 -10000 0 -0.72 3 3
NGF (dimer)/TRKA/NEDD4-2 0.045 0.043 -10000 0 -0.44 3 3
MAP2K1 0.038 0.056 0.36 3 -10000 0 3
NGFR -0.017 0.13 -10000 0 -0.68 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.073 -10000 0 -0.36 15 15
RAS family/GTP/PI3K 0.026 0.027 -10000 0 -0.3 3 3
FRS2 family/SHP2/GRB2/SOS1 0.074 0.032 -10000 0 -0.38 1 1
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.076 -10000 0 -0.54 6 6
RASA1 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.023 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.048 0.085 -10000 0 -0.44 12 12
NGF (dimer)/TRKA/p62/Atypical PKCs 0.068 0.046 -10000 0 -0.38 3 3
MATK 0.015 0.075 -10000 0 -0.62 6 6
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.003 0.078 -10000 0 -0.39 16 16
Rac1/GTP -0.11 0.12 -10000 0 -0.28 92 92
FRS2 family/SHP2/CRK family 0.057 0.043 -10000 0 -0.38 1 1
Caspase cascade in apoptosis

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
TOP1 0.022 0.086 0.32 5 -0.42 10 15
ACTA1 0.011 0.1 0.34 6 -0.48 11 17
NUMA1 0.017 0.1 0.28 6 -0.52 12 18
SPTAN1 0.008 0.1 0.35 6 -0.5 10 16
LIMK1 0.014 0.11 0.44 8 -0.52 9 17
BIRC3 -0.01 0.15 -10000 0 -0.63 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.025 0.007 -10000 0 -10000 0 0
CASP10 -0.009 0.088 -10000 0 -0.55 11 11
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.007 -10000 0 -10000 0 0
PTK2 0.015 0.097 0.39 2 -0.43 15 17
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.008 0.099 0.35 6 -0.49 10 16
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN 0.008 0.1 0.34 6 -0.5 10 16
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.042 0.22 -10000 0 -0.6 61 61
BID -0.012 0.061 -10000 0 -0.22 29 29
MAP3K1 0.018 0.041 0.27 3 -10000 0 3
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.027 -10000 0 -0.51 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.011 0.11 0.44 8 -0.52 9 17
CASP9 0.027 0.005 -10000 0 -10000 0 0
DNA repair -0.018 0.056 0.42 2 -0.21 19 21
neuron apoptosis 0.007 0.11 -10000 0 -0.55 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.017 0.11 0.35 4 -0.53 12 16
APAF1 0.025 0.032 -10000 0 -0.68 1 1
CASP6 0.021 0.091 0.37 2 -0.64 4 6
TRAF2 0.025 0.009 -10000 0 -10000 0 0
ICAD/CAD 0.014 0.11 0.4 14 -0.51 9 23
CASP7 0.008 0.096 0.31 22 -0.45 7 29
KRT18 0.021 0.041 -10000 0 -0.44 2 2
apoptosis 0.018 0.098 0.48 4 -0.45 10 14
DFFA 0.01 0.1 0.34 7 -0.5 10 17
DFFB 0.01 0.1 0.32 9 -0.5 10 19
PARP1 0.018 0.056 0.21 19 -0.43 2 21
actin filament polymerization -0.019 0.12 0.48 9 -0.52 12 21
TNF -0.059 0.23 -10000 0 -0.68 57 57
CYCS 0 0.049 0.23 4 -0.22 10 14
SATB1 0.021 0.09 0.52 2 -0.6 4 6
SLK 0.006 0.1 0.41 4 -0.48 12 16
p15 BID/BAX -0.01 0.069 -10000 0 -0.3 11 11
CASP2 -0.016 0.11 0.21 3 -0.37 19 22
JNK cascade -0.019 0.041 -10000 0 -0.27 3 3
CASP3 0.007 0.1 0.32 7 -0.47 13 20
LMNB2 0.006 0.12 0.37 10 -0.41 12 22
RIPK1 0.027 0.002 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.045 0.095 -10000 0 -0.4 20 20
negative regulation of DNA binding -0.041 0.22 -10000 0 -0.6 61 61
stress fiber formation 0.006 0.1 0.41 4 -0.48 12 16
GZMB -0.005 0.1 -10000 0 -0.62 11 11
CASP1 0.015 0.026 -10000 0 -0.39 2 2
LMNB1 0.019 0.094 0.35 11 -0.44 2 13
APP 0.006 0.12 -10000 0 -0.57 16 16
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM 0.019 0.091 0.45 3 -0.46 8 11
LMNA 0.016 0.1 0.36 12 -0.42 5 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.015 0.11 -10000 0 -0.4 17 17
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.016 0.11 0.42 9 -0.55 8 17
APAF-1/Caspase 9 0.014 0.057 -10000 0 -0.53 3 3
nuclear fragmentation during apoptosis 0.017 0.1 0.28 6 -0.51 12 18
CFL2 0.019 0.12 0.53 12 -0.5 9 21
GAS2 0.005 0.1 0.32 6 -0.49 12 18
positive regulation of apoptosis 0.016 0.1 0.37 10 -0.41 6 16
PRF1 0.016 0.085 -10000 0 -0.68 7 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.093 -10000 0 -0.61 10 10
ANTXR2 0.023 0.055 -10000 0 -0.68 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.014 -10000 0 -0.082 13 13
monocyte activation -0.039 0.16 -10000 0 -0.44 64 64
MAP2K2 -0.009 0.12 -10000 0 -0.54 22 22
MAP2K1 -0.001 0.012 -10000 0 -10000 0 0
MAP2K7 -0.001 0.012 -10000 0 -10000 0 0
MAP2K6 -0.009 0.057 0.11 1 -0.39 10 11
CYAA -0.007 0.058 -10000 0 -0.35 13 13
MAP2K4 -0.001 0.013 0.11 1 -10000 0 1
IL1B -0.027 0.1 0.18 1 -0.36 40 41
Channel 0.023 0.067 -10000 0 -0.37 13 13
NLRP1 -0.002 0.028 -10000 0 -0.38 2 2
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.029 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.014 0.082 13 -10000 0 13
MAPK3 -0.001 0.012 -10000 0 -10000 0 0
MAPK1 -0.001 0.012 -10000 0 -10000 0 0
PGR -0.012 0.058 -10000 0 -0.32 14 14
PA/Cellular Receptors 0.024 0.073 -10000 0 -0.4 13 13
apoptosis -0.002 0.014 -10000 0 -0.082 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.063 -10000 0 -0.35 13 13
macrophage activation -0.001 0.011 -10000 0 -10000 0 0
TNF -0.059 0.23 -10000 0 -0.68 57 57
VCAM1 -0.039 0.16 -10000 0 -0.44 64 64
platelet activation 0.011 0.029 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.029 0.11 9 -0.13 8 17
IL18 -0.009 0.06 -10000 0 -0.33 13 13
negative regulation of macrophage activation -0.002 0.014 -10000 0 -0.082 13 13
LEF -0.002 0.014 -10000 0 -0.082 13 13
CASP1 0.001 0.018 -10000 0 -0.17 3 3
mol:cAMP 0.011 0.029 -10000 0 -0.52 1 1
necrosis -0.002 0.014 -10000 0 -0.082 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.023 0.064 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
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) 0.005 0.14 -10000 0 -0.69 10 10
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.025 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.045 -10000 0 -0.68 2 2
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.056 -10000 0 -0.68 3 3
AP1 -0.13 0.24 -10000 0 -0.48 142 142
NCSTN 0.026 0.007 -10000 0 -10000 0 0
ADAM10 0.012 0.1 -10000 0 -0.68 10 10
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.075 -10000 0 -0.55 4 4
NICD/RBPSUH 0.005 0.13 -10000 0 -0.64 10 10
WIF1 0 0.047 -10000 0 -10000 0 0
NOTCH1 -0.005 0.13 -10000 0 -0.46 33 33
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.037 -10000 0 -10000 0 0
DKK1 -0.001 0.07 -10000 0 -0.68 2 2
beta catenin/beta TrCP1 0.046 0.047 0.28 3 -10000 0 3
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.007 -10000 0 -10000 0 0
AXIN1 -0.006 0.084 0.38 1 -0.4 11 12
CtBP/CBP/TCF1/TLE1/AES 0.019 0.032 -10000 0 -0.3 3 3
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 126 126
JUN -0.12 0.29 -10000 0 -0.67 103 103
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.039 0.063 0.3 14 -10000 0 14
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.033 0.097 -10000 0 -0.44 19 19
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC -0.019 0.25 -10000 0 -1.2 19 19
NKD1 0.006 0.11 -10000 0 -0.68 13 13
FZD1 0.026 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.004 0.14 -10000 0 -0.64 12 12
apoptosis -0.13 0.24 -10000 0 -0.48 142 142
Delta 1/NOTCHprecursor 0.005 0.14 -10000 0 -0.67 10 10
DLL1 0.025 0.033 -10000 0 -0.68 1 1
PPARD 0.025 0.055 -10000 0 -0.77 2 2
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
APC 0 0.074 0.31 3 -0.55 3 6
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.048 0.045 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -10000 0 0
CCND1 0.009 0.13 -10000 0 -0.85 10 10
WNT1 0.023 0.014 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.046 0.098 0.41 14 -0.42 3 17
DKK2 -0.006 0.14 -10000 0 -0.68 20 20
NOTCH1 precursor/DVL1 0.012 0.12 -10000 0 -0.59 10 10
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.005 0.14 -10000 0 -0.65 12 12
PPP2R5D 0.029 0.057 0.33 13 -0.34 2 15
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.064 0.017 -10000 0 -10000 0 0
RBPJ 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
alphaV beta3 Integrin 0.023 0.097 -10000 0 -0.55 12 12
PTK2 0.01 0.14 -10000 0 -0.55 26 26
positive regulation of JNK cascade 0.015 0.095 -10000 0 -0.33 27 27
CDC42/GDP 0.032 0.14 0.44 1 -0.45 29 30
Rac1/GDP 0.03 0.13 -10000 0 -0.46 25 25
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.025 0.12 -10000 0 -0.4 27 27
nectin-3/I-afadin 0.01 0.12 -10000 0 -0.5 27 27
RAPGEF1 0.013 0.13 0.36 1 -0.51 26 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.15 -10000 0 -0.58 27 27
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
TLN1 -0.003 0.06 -10000 0 -0.79 1 1
Rap1/GTP 0.013 0.093 -10000 0 -0.36 25 25
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.12 -10000 0 -0.5 27 27
PVR 0.026 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.007 -10000 0 -10000 0 0
mol:GDP 0.017 0.17 0.47 1 -0.55 32 33
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PI3K 0.051 0.12 -10000 0 -0.42 25 25
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.009 0.11 -10000 0 -0.36 26 26
PVRL1 0.023 0.025 -10000 0 -10000 0 0
PVRL3 -0.012 0.16 -10000 0 -0.68 27 27
PVRL2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.095 -10000 0 -0.61 10 10
JAM-A/CLDN1 0.041 0.13 -10000 0 -0.41 32 32
SRC 0.007 0.17 -10000 0 -0.65 27 27
ITGB3 0.009 0.11 -10000 0 -0.65 12 12
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
FARP2 0.021 0.16 -10000 0 -0.54 30 30
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.024 0.11 -10000 0 -0.43 27 27
nectin-1/I-afadin 0.036 0.02 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.027 0.11 -10000 0 -0.44 26 26
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.025 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.015 0.095 -10000 0 -0.33 27 27
alphaV/beta3 Integrin/Talin 0.023 0.11 -10000 0 -0.57 11 11
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
PIP5K1C -0.001 0.064 -10000 0 -0.25 26 26
VAV2 0 0.18 0.37 1 -0.6 30 31
RAP1/GDP 0.035 0.12 0.28 1 -0.42 27 28
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.024 0.11 -10000 0 -0.43 27 27
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.12 -10000 0 -0.5 27 27
Rac1/GTP 0.015 0.13 -10000 0 -0.45 26 26
PTPRM 0.002 0.071 -10000 0 -0.27 26 26
E-cadherin/beta catenin/alpha catenin 0.073 0.027 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.025 0.12 -9999 0 -0.34 36 36
Syndecan-3/Neurocan 0.004 0.097 -9999 0 -0.36 29 29
POMC -0.11 0.28 -9999 0 -0.67 98 98
EGFR 0.021 0.064 -9999 0 -0.68 4 4
Syndecan-3/EGFR 0.028 0.041 -9999 0 -0.34 5 5
AGRP 0.004 0.032 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.026 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.027 0.18 -9999 0 -0.67 34 34
long-term memory 0.05 0.029 -9999 0 -0.27 1 1
Syndecan-3/IL8 0.03 0.065 -9999 0 -0.36 11 11
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.011 -9999 0 -10000 0 0
FYN 0.027 0.004 -9999 0 -10000 0 0
limb bud formation 0.015 0.006 -9999 0 -10000 0 0
MC4R 0 0.026 -9999 0 -10000 0 0
SRC 0.026 0.008 -9999 0 -10000 0 0
PTN -0.04 0.2 -9999 0 -0.68 45 45
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.024 0.13 -9999 0 -0.34 61 61
Syndecan-3/AgRP 0.03 0.023 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.045 0.029 -9999 0 -0.29 1 1
Fyn/Cortactin 0.039 0.008 -9999 0 -10000 0 0
SDC3 0.015 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.03 0.065 -9999 0 -0.35 11 11
IL8 -0.023 0.11 -9999 0 -0.68 10 10
Syndecan-3/Fyn/Cortactin 0.052 0.03 -9999 0 -0.28 1 1
Syndecan-3/CASK 0.012 0.022 -9999 0 -0.3 1 1
alpha-MSH/MC4R -0.077 0.22 -9999 0 -0.5 98 98
Gamma Secretase 0.069 0.03 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0 0.14 -10000 0 -0.37 56 56
TC10/GTP 0.042 0.038 -10000 0 -0.35 3 3
Insulin Receptor/Insulin/IRS1/Shp2 0.004 0.16 -10000 0 -0.42 54 54
HRAS 0.026 0.011 -10000 0 -10000 0 0
APS homodimer 0.026 0.009 -10000 0 -10000 0 0
GRB14 0.007 0.12 -10000 0 -0.65 14 14
FOXO3 0 0.12 -10000 0 -0.65 15 15
AKT1 -0.025 0.14 0.36 5 -0.75 2 7
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.006 -10000 0 -10000 0 0
SORBS1 0.021 0.064 -10000 0 -0.68 4 4
CRK 0.026 0.007 -10000 0 -10000 0 0
PTPN1 0.017 0.027 -10000 0 -10000 0 0
CAV1 -0.033 0.14 -10000 0 -0.39 60 60
CBL/APS/CAP/Crk-II/C3G 0.065 0.048 -10000 0 -0.38 3 3
Insulin Receptor/Insulin/IRS1/NCK2 0.005 0.15 -10000 0 -0.42 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.14 -10000 0 -0.38 56 56
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.005 0.098 -10000 0 -0.41 6 6
RPS6KB1 -0.03 0.12 0.32 2 -0.66 2 4
PARD6A 0.026 0.006 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.025 -10000 0 -0.5 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.009 0.13 -10000 0 -0.68 2 2
HRAS/GTP -0.021 0.1 -10000 0 -0.34 43 43
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.017 0.14 -10000 0 -0.39 43 43
PRKCI 0.014 0.072 -10000 0 -0.5 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.14 -10000 0 -0.36 65 65
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.046 0.041 -10000 0 -0.4 1 1
PI3K 0.007 0.14 -10000 0 -0.38 56 56
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
AKT2 -0.027 0.14 0.38 7 -0.75 2 9
PRKCZ 0.014 0.071 -10000 0 -0.52 4 4
SH2B2 0.026 0.009 -10000 0 -10000 0 0
SHC/SHIP -0.011 0.12 0.3 1 -0.37 45 46
F2RL2 -0.018 0.084 -10000 0 -0.68 3 3
TRIP10 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.041 0.019 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.064 0.031 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.06 0.045 -10000 0 -0.4 3 3
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.055 0.025 -10000 0 -10000 0 0
INPP5D -0.029 0.13 0.31 1 -0.39 54 55
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.015 0.16 -10000 0 -0.84 16 16
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
IRS1 -0.053 0.22 -10000 0 -0.68 55 55
p62DOK/RasGAP 0.046 0.042 -10000 0 -0.4 1 1
INS 0.019 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.029 0.13 0.31 1 -0.39 54 55
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.03 0.12 0.36 3 -0.57 3 6
PTPRA 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
TC10/GTP/CIP4 0.034 0.011 -10000 0 -10000 0 0
PDPK1 0.023 0.046 -10000 0 -0.68 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.006 0.096 -10000 0 -0.29 43 43
Insulin Receptor/Insulin/IRS1 -0.009 0.15 -10000 0 -0.42 54 54
Insulin Receptor/Insulin/IRS3 0.033 0.012 -10000 0 -10000 0 0
Par3/Par6 0.058 0.039 -10000 0 -0.38 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.006 0.14 -10000 0 -0.37 59 59
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.021 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.023 -10000 0 -0.44 1 1
GNB1 0.026 0.005 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.035 0.14 -10000 0 -0.39 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.012 0.032 0.096 61 -10000 0 61
GNAL -0.06 0.23 -10000 0 -0.66 61 61
GNG2 0.025 0.032 -10000 0 -0.68 1 1
CRH 0 0.038 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.05 -10000 0 -0.38 8 8
MAPK11 0.006 0.004 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.001 0.086 -10000 0 -0.43 2 2
epithelial cell differentiation -0.005 0.1 -10000 0 -0.43 8 8
ITCH 0.036 0.019 -10000 0 -10000 0 0
WWP1 -0.008 0.068 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.021 0.064 -10000 0 -0.68 4 4
PRL -0.012 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.02 0.11 0.34 3 -0.48 6 9
PTPRZ1 0.002 0.1 -10000 0 -0.68 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.001 0.13 -10000 0 -0.51 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.14 -10000 0 -0.42 46 46
ADAM17 0.033 0.049 -10000 0 -0.68 2 2
ErbB4/ErbB4 -0.013 0.087 -10000 0 -0.38 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.14 -10000 0 -0.45 34 34
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.026 0.14 -10000 0 -0.4 44 44
GRIN2B -0.036 0.13 -10000 0 -0.4 31 31
ErbB4/ErbB2/betacellulin 0.003 0.1 -10000 0 -0.5 12 12
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.019 0.034 -10000 0 -10000 0 0
PRLR -0.017 0.16 -10000 0 -0.68 26 26
E4ICDs/ETO2 -0.002 0.087 -10000 0 -0.47 3 3
axon guidance -0.007 0.079 -10000 0 -0.52 3 3
NEDD4 0.033 0.049 -10000 0 -0.66 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.001 0.12 -10000 0 -0.51 26 26
CBFA2T3 0.024 0.033 -10000 0 -0.68 1 1
ErbB4/ErbB2/HBEGF 0.012 0.073 -10000 0 -0.41 3 3
MAPK3 -0.014 0.12 -10000 0 -0.48 7 7
STAT1 (dimer) 0.001 0.086 -10000 0 -0.42 2 2
MAPK1 -0.019 0.11 -10000 0 -0.5 6 6
JAK2 0.025 0.019 -10000 0 -0.36 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.032 0.13 -10000 0 -0.4 41 41
NRG1 -0.029 0.16 -10000 0 -0.52 45 45
NRG3 -0.023 0.18 -10000 0 -0.65 35 35
NRG2 -0.053 0.22 -10000 0 -0.68 53 53
NRG4 0.021 0.021 -10000 0 -10000 0 0
heart development -0.007 0.079 -10000 0 -0.52 3 3
neural crest cell migration -0.032 0.13 -10000 0 -0.4 41 41
ERBB2 0.019 0.035 -10000 0 -0.5 2 2
WWOX/E4ICDs -0.002 0.089 -10000 0 -0.62 2 2
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.01 0.096 -10000 0 -0.5 5 5
apoptosis 0.022 0.13 0.41 36 -10000 0 36
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.048 0.16 -10000 0 -0.44 55 55
ErbB4/ErbB2/epiregulin 0.012 0.085 -10000 0 -0.4 4 4
ErbB4/ErbB4/betacellulin/betacellulin -0.012 0.12 -10000 0 -0.52 14 14
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.12 -10000 0 -0.37 28 28
MDM2 -0.011 0.077 -10000 0 -0.41 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.023 0.13 -10000 0 -0.4 44 44
STAT5A -0.002 0.078 -10000 0 -0.59 2 2
ErbB4/EGFR/neuregulin 1 beta -0.028 0.14 -10000 0 -0.42 46 46
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.001 0.076 -10000 0 -0.39 2 2
STAT5A (dimer) 0.003 0.12 -10000 0 -0.46 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.004 0.08 -10000 0 -0.59 2 2
LRIG1 0.015 0.09 -10000 0 -0.68 8 8
EREG -0.049 0.07 -10000 0 -10000 0 0
BTC 0.009 0.11 -10000 0 -0.68 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.008 0.079 -10000 0 -0.62 2 2
ERBB4 -0.013 0.087 -10000 0 -0.38 2 2
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.005 0.069 -10000 0 -0.46 9 9
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.011 0.072 -10000 0 -0.39 3 3
glial cell differentiation 0.001 0.076 0.39 2 -10000 0 2
WWOX 0.025 0.033 -10000 0 -0.68 1 1
cell proliferation -0.025 0.14 -10000 0 -0.59 10 10
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.62 8 8
UGCG -0.053 0.21 -10000 0 -0.63 53 53
AKT1/mTOR/p70S6K/Hsp90/TERT 0.014 0.14 0.42 5 -0.4 22 27
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.056 0.21 -10000 0 -0.61 57 57
mol:DAG -0.008 0.12 -10000 0 -0.77 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.17 -10000 0 -0.46 37 37
FRAP1 -0.014 0.19 0.44 2 -0.5 46 48
FOXO3 -0.001 0.16 0.44 2 -0.61 20 22
AKT1 -0.006 0.18 -10000 0 -0.66 21 21
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.009 0.086 -10000 0 -0.77 5 5
SGMS1 0.003 0.1 -10000 0 -0.61 11 11
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 0.007 0.037 -10000 0 -0.45 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.027 0.18 0.33 5 -0.5 38 43
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.045 -10000 0 -0.52 3 3
RPS6KB1 0.015 0.072 -10000 0 -0.74 3 3
mol:sphingomyelin -0.008 0.12 -10000 0 -0.77 11 11
natural killer cell activation 0 0.004 -10000 0 -0.023 4 4
JAK3 -0.009 0.064 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.006 0.21 0.47 4 -0.93 17 21
MYB 0.003 0.19 -10000 0 -1.3 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.005 0.15 -10000 0 -0.56 22 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.072 -10000 0 -0.67 3 3
mol:PI-3-4-5-P3 -0.004 0.14 -10000 0 -0.54 22 22
Rac1/GDP 0.023 0.036 -10000 0 -0.41 3 3
T cell proliferation -0.004 0.13 -10000 0 -0.52 19 19
SHC1 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.062 10 10
PRKCZ -0.005 0.14 -10000 0 -0.55 19 19
NF kappa B1 p50/RelA 0.012 0.17 -10000 0 -0.54 21 21
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.11 -10000 0 -0.57 12 12
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.016 0.15 -10000 0 -0.64 26 26
IL2RB 0.005 0.092 -10000 0 -0.58 10 10
TERT -0.005 0.022 -10000 0 -10000 0 0
E2F1 0.022 0.077 -10000 0 -0.47 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.031 10 -10000 0 10
PTPN11 0.025 0.033 -10000 0 -0.68 1 1
IL2RG -0.01 0.14 -10000 0 -0.63 21 21
actin cytoskeleton organization -0.004 0.13 -10000 0 -0.52 19 19
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.018 0.014 -10000 0 -10000 0 0
PIK3CA 0.024 0.056 -10000 0 -0.68 3 3
Rac1/GTP 0.048 0.042 -10000 0 -0.39 3 3
LCK 0.014 0.083 -10000 0 -0.68 6 6
BCL2 -0.039 0.27 0.47 4 -0.79 47 51
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.009 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.02 0.049 -10000 0 -0.44 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.001 0.023 -10000 0 -10000 0 0
GRK1 -0.04 0.2 -10000 0 -0.66 46 46
CNG Channel 0.037 0.059 -10000 0 -0.38 7 7
mol:Na + 0.029 0.07 -10000 0 -0.39 9 9
mol:ADP -0.04 0.2 -10000 0 -0.65 46 46
RGS9-1/Gbeta5/R9AP -0.025 0.18 -10000 0 -0.45 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.041 0.073 -10000 0 -0.4 9 9
CNGB1 0.018 0.029 -10000 0 -10000 0 0
RDH5 -0.071 0.071 -10000 0 -10000 0 0
SAG -0.008 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.1 0.49 11 -0.38 9 20
Na + (4 Units) 0.022 0.065 -10000 0 -0.37 9 9
RGS9 -0.043 0.21 -10000 0 -0.68 47 47
GNB1/GNGT1 0.029 0.014 -10000 0 -10000 0 0
GNAT1/GDP -0.013 0.16 -10000 0 -0.4 70 70
GUCY2D 0.012 0.078 -10000 0 -0.62 6 6
GNGT1 -0.015 0.013 -10000 0 -10000 0 0
GUCY2F -0.013 0.01 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.044 -10000 0 -0.38 3 3
mol:11-cis-retinal -0.07 0.071 -10000 0 -10000 0 0
mol:cGMP 0.032 0.058 -10000 0 -0.4 6 6
GNB1 0.026 0.005 -10000 0 -10000 0 0
Rhodopsin -0.041 0.055 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.018 0.073 -10000 0 -0.68 5 5
Metarhodopsin II -0.011 0.12 -10000 0 -0.39 46 46
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.048 0.063 -10000 0 -0.41 8 8
RGS9BP -0.015 0.16 -10000 0 -0.66 28 28
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.038 0.038 -10000 0 -0.42 3 3
PDE6A/B 0.031 0.028 -10000 0 -10000 0 0
mol:Pi -0.025 0.18 -10000 0 -0.44 72 72
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.015 -10000 0 -10000 0 0
PDE6B 0.027 0.005 -10000 0 -10000 0 0
PDE6A 0.012 0.036 -10000 0 -10000 0 0
PDE6G 0.01 0.073 -10000 0 -0.68 4 4
RHO 0.006 0.023 -10000 0 -10000 0 0
PDE6 0.001 0.17 -10000 0 -0.39 71 71
GUCA1A 0.006 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.037 -10000 0 -0.36 3 3
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.023 0.056 -10000 0 -0.68 3 3
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.025 0.007 -9999 0 -10000 0 0
SPHK1 0.023 0.022 -9999 0 -10000 0 0
GNAI2 0.027 0.004 -9999 0 -10000 0 0
mol:S1P 0.017 0.007 -9999 0 -10000 0 0
GNAO1 0.004 0.12 -9999 0 -0.68 15 15
mol:Sphinganine-1-P 0.014 0.014 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.056 0.028 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
S1PR3 0.025 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.018 -9999 0 -0.2 2 2
S1PR5 0.023 0.034 -9999 0 -0.68 1 1
S1PR4 0.024 0.017 -9999 0 -10000 0 0
GNAI1 0.025 0.032 -9999 0 -0.68 1 1
S1P/S1P5/G12 0.043 0.032 -9999 0 -0.39 1 1
S1P/S1P3/Gq -0.053 0.16 -9999 0 -0.3 127 127
S1P/S1P4/Gi 0.003 0.079 -9999 0 -0.32 17 17
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.64 112 112
GNA15 0.013 0.05 -9999 0 -0.68 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.016 0.08 -9999 0 -0.63 7 7
ABCC1 0.026 0.006 -9999 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.031 0.067 -10000 0 -0.59 5 5
PDGFRB 0.025 0.033 -10000 0 -0.68 1 1
SPHK1 0.008 0.064 -10000 0 -0.73 3 3
mol:S1P 0.007 0.061 -10000 0 -0.65 3 3
S1P1/S1P/Gi -0.01 0.13 -10000 0 -0.42 40 40
GNAO1 0.001 0.12 -10000 0 -0.68 15 15
PDGFB-D/PDGFRB/PLCgamma1 -0.008 0.12 -10000 0 -0.39 33 33
PLCG1 -0.01 0.12 -10000 0 -0.41 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.033 -10000 0 -0.68 1 1
GNAI2 0.025 0.013 -10000 0 -10000 0 0
GNAI3 0.024 0.013 -10000 0 -10000 0 0
GNAI1 0.023 0.034 -10000 0 -0.68 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.056 -10000 0 -0.51 5 5
S1P1/S1P 0.003 0.07 -10000 0 -0.48 6 6
negative regulation of cAMP metabolic process -0.009 0.13 -10000 0 -0.4 40 40
MAPK3 -0.023 0.17 -10000 0 -0.6 35 35
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.022 0.056 -10000 0 -0.68 3 3
PLCB2 0.013 0.077 0.4 5 -0.42 6 11
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.009 0.061 -10000 0 -0.4 6 6
receptor internalization 0.003 0.065 -10000 0 -0.44 6 6
PTGS2 -0.062 0.3 0.64 3 -0.99 44 47
Rac1/GTP 0.01 0.06 -10000 0 -0.4 6 6
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.022 0.055 -10000 0 -0.68 3 3
negative regulation of T cell proliferation -0.009 0.13 -10000 0 -0.4 40 40
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.015 -10000 0 -10000 0 0
MAPK1 -0.024 0.18 -10000 0 -0.61 37 37
S1P1/S1P/PDGFB-D/PDGFRB 0.011 0.08 -10000 0 -0.46 7 7
ABCC1 0.026 0.006 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.029 0.009 -10000 0 -10000 0 0
epithelial cell differentiation 0.055 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
ENAH 0.023 0.079 0.46 11 -10000 0 11
EGFR 0.021 0.064 -10000 0 -0.68 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
MYO6 0.033 0.069 0.43 12 -10000 0 12
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.013 -10000 0 -10000 0 0
AQP5 0.001 0.11 -10000 0 -0.54 19 19
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.052 0.4 8 -10000 0 8
regulation of calcium-dependent cell-cell adhesion -0.009 0.057 0.39 6 -10000 0 6
EGF -0.073 0.24 -10000 0 -0.67 68 68
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
AQP3 -0.043 0.17 -10000 0 -0.53 50 50
cortical microtubule organization 0.055 0.016 -10000 0 -10000 0 0
GO:0000145 0.014 0.052 0.39 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.061 0.018 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.014 0.028 -10000 0 -10000 0 0
PVRL2 0.026 0.007 -10000 0 -10000 0 0
ZYX 0.021 0.021 -10000 0 -10000 0 0
ARF6/GTP 0.067 0.027 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.009 0.14 -10000 0 -0.36 69 69
RhoA/GDP 0.057 0.017 -10000 0 -10000 0 0
actin cytoskeleton organization 0.022 0.056 0.4 9 -10000 0 9
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
DIAPH1 0.051 0.045 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.055 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL 0.022 0.056 0.4 9 -10000 0 9
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.012 0.054 0.35 3 -0.36 6 9
Ephrin A1/EPHA2 0.047 0.019 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 -0.01 0.058 0.4 6 -10000 0 6
HGF/MET -0.006 0.15 -10000 0 -0.38 63 63
HGF -0.075 0.25 -10000 0 -0.68 69 69
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.009 -10000 0 -10000 0 0
actin cable formation 0.07 0.14 0.39 50 -0.33 1 51
KIAA1543 0.014 0.053 0.37 8 -0.35 1 9
KIFC3 0.022 0.024 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ACTN1 0.025 0.038 0.36 4 -10000 0 4
NCK1/GIT1 0.038 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.022 0.024 -10000 0 -10000 0 0
PIP5K1C 0.026 0.053 0.4 8 -10000 0 8
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.045 0.1 0.43 23 -10000 0 23
adherens junction assembly 0.028 0.093 0.48 13 -0.56 1 14
IGF-1R heterotetramer/IGF1 -0.038 0.17 -10000 0 -0.36 101 101
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET -0.029 0.072 -10000 0 -10000 0 0
PLEKHA7 0.026 0.053 0.38 8 -0.37 1 9
mol:GTP 0.059 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.033 0.067 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.009 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.022 0.056 0.4 9 -10000 0 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.009 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -9999 0 -0.68 1 1
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.053 -9999 0 -0.26 16 16
GNAO1 0.005 0.12 -9999 0 -0.68 15 15
S1P/S1P3/G12/G13 0.048 0.02 -9999 0 -10000 0 0
AKT1 0.023 0.041 -9999 0 -0.35 3 3
AKT3 0.02 0.067 -9999 0 -0.48 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -9999 0 -0.68 1 1
GNAI2 0.029 0.004 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.033 -9999 0 -0.68 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.07 -9999 0 -0.29 17 17
MAPK3 0.003 0.066 -9999 0 -0.29 15 15
MAPK1 0.014 0.059 -9999 0 -0.28 15 15
JAK2 0.007 0.067 -9999 0 -0.4 3 3
CXCR4 0.003 0.065 -9999 0 -0.29 15 15
FLT1 0.027 0.033 -9999 0 -0.68 1 1
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
SRC 0.004 0.063 -9999 0 -0.28 15 15
S1P/S1P3/Gi 0.006 0.071 -9999 0 -0.3 17 17
RAC1 0.026 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.01 0.074 -9999 0 -0.28 15 15
VEGFA 0.025 0.055 -9999 0 -0.68 3 3
S1P/S1P2/Gi 0.004 0.075 -9999 0 -0.32 17 17
VEGFR1 homodimer/VEGFA homodimer 0.04 0.057 -9999 0 -0.64 3 3
RHOA 0.027 0.004 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.054 0.15 -9999 0 -0.31 115 115
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.013 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.64 112 112
GNA15 0.013 0.05 -9999 0 -0.68 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.016 0.08 -9999 0 -0.63 7 7
Rac1/GTP 0.01 0.073 -9999 0 -0.28 15 15
Signaling events mediated by PRL

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
CCNE1 0.025 0.008 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.018 0.078 -10000 0 -0.68 6 6
CDKN1A -0.005 0.066 -10000 0 -10000 0 0
PRL-3/alpha Tubulin 0.029 0.033 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.073 0.24 4 -0.5 9 13
AGT 0.005 0.099 -10000 0 -0.68 9 9
CCNA2 -0.065 0.15 -10000 0 -0.41 3 3
TUBA1B 0.027 0.005 -10000 0 -10000 0 0
EGR1 -0.085 0.21 -10000 0 -0.5 96 96
CDK2/Cyclin E1 0.019 0.076 -10000 0 -0.54 1 1
MAPK3 0.009 0.025 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.008 -10000 0 -10000 0 0
MAPK1 0.008 0.022 -10000 0 -10000 0 0
PTP4A1 -0.068 0.16 -10000 0 -0.39 95 95
PTP4A3 0.014 0.041 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.009 0.026 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.01 0.078 -10000 0 -0.62 1 1
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.05 0.16 -10000 0 -0.41 3 3
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.012 0.013 -10000 0 -10000 0 0
RHOC -0.01 0.077 -10000 0 -0.62 1 1
RHOA -0.01 0.081 -10000 0 -0.62 2 2
cell motility -0.005 0.097 0.31 4 -0.59 3 7
PRL-1/alpha Tubulin -0.048 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.022 0.069 -10000 0 -0.52 6 6
ROCK1 -0.005 0.095 0.33 2 -0.6 3 5
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.005 -10000 0 -10000 0 0
mitosis -0.067 0.16 -10000 0 -0.39 95 95
ATF5 0.02 0.028 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin -0.037 0.059 -10000 0 -0.4 6 6
EPHB2 0.022 0.055 -10000 0 -0.68 3 3
Syndecan-2/TACI -0.082 0.2 -10000 0 -0.44 111 111
LAMA1 -0.021 0.18 -10000 0 -0.67 33 33
Syndecan-2/alpha2 ITGB1 0.042 0.093 -10000 0 -0.38 19 19
HRAS 0.026 0.011 -10000 0 -10000 0 0
Syndecan-2/CASK 0.007 0.043 -10000 0 -0.33 7 7
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.004 0.06 -10000 0 -10000 0 0
EPB41 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.041 -10000 0 -0.4 4 4
LAMA3 -0.001 0.13 -10000 0 -0.68 16 16
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.045 -10000 0 -0.68 2 2
Syndecan-2/MMP2 0.02 0.072 -10000 0 -0.45 10 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.008 0.057 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.058 -10000 0 -0.36 10 10
Syndecan-2/GM-CSF -0.034 0.055 -10000 0 -0.37 6 6
determination of left/right symmetry 0.01 0.051 -10000 0 -0.39 7 7
Syndecan-2/PKC delta 0.026 0.046 -10000 0 -0.33 7 7
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.031 0.047 -10000 0 -0.41 4 4
MAPK1 -0.025 0.046 -10000 0 -0.41 4 4
Syndecan-2/RACK1 0.038 0.042 -10000 0 -0.38 4 4
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.051 -10000 0 -0.39 7 7
ITGA2 -0.033 0.073 -10000 0 -10000 0 0
MAPK8 0.006 0.069 -10000 0 -0.42 12 12
Syndecan-2/alpha2/beta1 Integrin 0.032 0.12 -10000 0 -0.42 31 31
Syndecan-2/Kininogen 0.016 0.05 -10000 0 -0.34 7 7
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.021 0.044 0.35 1 -0.36 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.042 -10000 0 -0.32 6 6
extracellular matrix organization 0.024 0.045 -10000 0 -0.43 4 4
actin cytoskeleton reorganization -0.037 0.059 -10000 0 -0.4 6 6
Syndecan-2/Caveolin-2/Ras 0.039 0.05 -10000 0 -0.4 6 6
Syndecan-2/Laminin alpha3 0.008 0.095 -10000 0 -0.44 20 20
Syndecan-2/RasGAP 0.05 0.043 -10000 0 -0.36 4 4
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.059 -10000 0 -0.36 10 10
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.042 -10000 0 -0.35 4 4
RHOA 0.027 0.004 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
TNFRSF13B -0.14 0.29 -10000 0 -0.67 109 109
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.008 0.057 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.045 -10000 0 -0.35 6 6
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CASP3 0.018 0.044 0.19 4 -0.4 4 8
FN1 -0.081 0.067 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.004 0.085 -10000 0 -0.39 17 17
SDC2 0.01 0.051 -10000 0 -0.39 7 7
KNG1 -0.004 0.037 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.044 -10000 0 -0.43 4 4
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 -0.079 0.064 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.045 -10000 0 -0.43 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.042 -10000 0 -0.4 4 4
Syndecan-2/Ezrin 0.042 0.044 -10000 0 -0.4 4 4
PRKACA 0.016 0.04 -10000 0 -0.4 4 4
angiogenesis -0.004 0.085 -10000 0 -0.39 17 17
MMP2 0.016 0.08 -10000 0 -0.63 7 7
IL8 -0.023 0.11 -10000 0 -0.68 10 10
calcineurin-NFAT signaling pathway -0.081 0.2 -10000 0 -0.44 111 111
Retinoic acid receptors-mediated signaling

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.026 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.069 -10000 0 -0.31 8 8
KAT2B 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.012 0.081 0.25 12 -0.35 13 25
RAR alpha/9cRA/Cyclin H 0.03 0.1 -10000 0 -0.38 21 21
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.066 0.24 1 -0.36 7 8
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.01 0.094 -10000 0 -0.54 9 9
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.007 0.14 -10000 0 -0.54 25 25
NCOA2 -0.034 0.2 -10000 0 -0.68 42 42
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARG 0.027 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.017 0.086 -10000 0 -0.64 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.004 0.13 -10000 0 -0.52 24 24
RARA 0.003 0.078 -10000 0 -0.3 27 27
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.015 0.12 -10000 0 -0.46 25 25
PRKCA -0.004 0.15 -10000 0 -0.68 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 0.005 0.15 0.42 3 -0.53 26 29
RXRG -0.031 0.086 -10000 0 -0.39 26 26
RXRA 0.004 0.081 -10000 0 -0.32 25 25
RXRB 0.005 0.083 -10000 0 -0.37 22 22
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RBP1 0.014 0.091 -10000 0 -0.68 8 8
CRBP1/9-cic-RA 0.011 0.068 -10000 0 -0.51 8 8
RARB 0.01 0.11 -10000 0 -0.68 13 13
PRKCG 0.021 0.014 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.011 0.14 -10000 0 -0.57 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.004 0.13 -10000 0 -0.48 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.091 0.41 2 -0.42 11 13
RXRs/RARs/NRIP1/9cRA/HDAC3 0.006 0.15 0.42 5 -0.53 26 31
positive regulation of DNA binding 0.019 0.094 -10000 0 -0.36 21 21
NRIP1 0.006 0.14 0.5 1 -0.69 6 7
RXRs/RARs -0.001 0.14 -10000 0 -0.52 27 27
RXRs/RXRs/DNA/9cRA -0.015 0.12 -10000 0 -0.53 24 24
PRKACA 0.025 0.008 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.053 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.046 0.07 -10000 0 -0.42 3 3
CCNH 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.05 0.018 -10000 0 -10000 0 0
BARD1 signaling 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
BARD1/CSTF1 0.014 0.11 -10000 0 -0.47 24 24
ATM 0.025 0.032 -10000 0 -0.68 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
ATR 0.026 0.032 -10000 0 -0.68 1 1
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.023 0.027 -10000 0 -0.38 2 2
protein ubiquitination 0.045 0.093 -10000 0 -0.38 19 19
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.05 0.035 -10000 0 -0.44 2 2
MRE11A 0.024 0.045 -10000 0 -0.68 2 2
DNA-PK 0.04 0.025 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.02 0.092 -10000 0 -0.58 10 10
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
CCNE1 0.025 0.008 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.012 -10000 0 -10000 0 0
FANCG 0.025 0.008 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.014 0.11 -10000 0 -0.48 21 21
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.008 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA 0.019 0.031 -10000 0 -10000 0 0
DNA repair 0.019 0.086 0.41 2 -0.48 4 6
BRCA1/BARD1/ubiquitin 0.014 0.11 -10000 0 -0.48 21 21
BARD1/DNA-PK 0.03 0.098 -10000 0 -0.4 21 21
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.014 0.11 0.47 24 -10000 0 24
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.073 -10000 0 -0.48 1 1
BRCA1/BACH1/BARD1/TopBP1 0.03 0.099 -10000 0 -0.44 18 18
BRCA1/BARD1/P53 0.045 0.096 -10000 0 -0.4 19 19
BARD1/CSTF1/BRCA1 0.031 0.098 -10000 0 -0.42 20 20
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.007 0.15 -10000 0 -0.62 25 25
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.03 0.099 -10000 0 -0.44 18 18
BRCA1/BARD1/UbcH7 0.019 0.097 -10000 0 -0.43 19 19
BRCA1/BARD1/RAD51/PCNA 0.045 0.094 -10000 0 -0.4 18 18
BARD1/DNA-PK/P53 0.039 0.095 -10000 0 -0.38 19 19
BRCA1/BARD1/Ubiquitin 0.014 0.11 -10000 0 -0.48 21 21
BRCA1/BARD1/CTIP 0.025 0.091 -10000 0 -0.4 19 19
FA complex 0.028 0.035 -10000 0 -0.24 4 4
BARD1/EWS 0.004 0.11 -10000 0 -0.48 23 23
RBBP8 0.016 0.024 -10000 0 -0.51 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.043 0.095 0.4 19 -10000 0 19
BRCA1/BARD1 0.051 0.095 -10000 0 -0.38 19 19
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.005 0.11 -10000 0 -0.47 25 25
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.011 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.014 0.11 -10000 0 -0.48 21 21
EWSR1 0.02 0.012 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.19 0.32 -10000 0 -0.67 151 151
HRAS 0.026 0.011 -10000 0 -10000 0 0
EGFR 0.021 0.064 -10000 0 -0.68 4 4
AKT 0.015 0.086 0.34 10 -10000 0 10
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.025 0.008 -10000 0 -10000 0 0
FOXO4 0.025 0.007 -10000 0 -10000 0 0
MET -0.029 0.072 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.009 0.11 -10000 0 -0.68 11 11
PIK3R3 0.027 0.005 -10000 0 -10000 0 0
PIK3R2 0.025 0.008 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.033 0.088 -10000 0 -0.31 6 6
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.036 0.068 0.36 8 -10000 0 8
PI3K -0.017 0.1 0.41 8 -0.24 13 21
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
FOXO 0.045 0.06 0.32 8 -10000 0 8
AKT2 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
Class I PI3K signaling events

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
ARF5/GTP 0.027 0.049 0.29 11 -0.36 1 12
DAPP1 -0.037 0.13 0.34 4 -0.5 12 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.052 0.17 0.29 5 -0.49 27 32
mol:DAG -0.016 0.096 0.34 11 -0.26 13 24
HRAS 0.027 0.012 -10000 0 -10000 0 0
RAP1A 0.028 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.034 0.068 0.28 2 -0.33 6 8
PLCG2 0.026 0.006 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0.001 0.05 0.3 11 -10000 0 11
ARF1/GTP 0.004 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
ADAP1 0.001 0.048 0.29 11 -10000 0 11
ARAP3 0.001 0.05 0.3 11 -10000 0 11
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.025 0.019 -10000 0 -0.36 1 1
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.025 0.008 -10000 0 -10000 0 0
NRAS 0.028 0.008 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.065 0.31 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
ZAP70 0.001 0.12 -10000 0 -0.66 16 16
mol:IP3 -0.012 0.069 0.24 11 -0.21 4 15
LYN 0.027 0.004 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.078 0.32 8 -0.33 8 16
RhoA/GDP 0.038 0.043 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.035 -10000 0 -0.44 2 2
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.078 0.41 10 -10000 0 10
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 0.005 0.016 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.021 -10000 0 -0.34 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.026 0.041 0.29 10 -10000 0 10
RhoA/GTP 0.025 0.042 0.3 9 -10000 0 9
Src family/SYK family/BLNK-LAT -0.044 0.14 -10000 0 -0.45 24 24
BLK -0.19 0.31 -10000 0 -0.67 143 143
PDPK1 0.023 0.046 -10000 0 -0.68 2 2
CYTH1 0.002 0.055 0.31 12 -10000 0 12
HCK 0.018 0.035 -10000 0 -10000 0 0
CYTH3 -0.001 0.052 0.29 11 -0.37 1 12
CYTH2 0.004 0.059 0.31 15 -10000 0 15
KRAS 0.028 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.017 0.097 -10000 0 -0.57 11 11
SGK1 0.017 0.11 -10000 0 -0.62 11 11
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.026 0.085 0.32 12 -0.32 10 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.029 0.052 0.29 9 -10000 0 9
mol:PI-3-4-5-P3 -0.007 0.015 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
VAV1 0.012 0.06 -10000 0 -0.57 3 3
mol:PI-3-4-P2 0.012 0.021 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.03 0.33 1 -10000 0 1
PLEKHA1 0.005 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.068 0.35 1 -0.32 7 8
LAT 0.021 0.058 -10000 0 -0.6 4 4
Rac1/GTP 0.018 0.063 0.28 2 -0.48 3 5
ITK -0.04 0.12 0.28 11 -0.37 50 61
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.37 9 -0.37 15 24
LCK 0.012 0.083 -10000 0 -0.68 6 6
BTK -0.004 0.069 0.29 14 -0.37 6 20
Regulation of Telomerase

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.002 0.1 0.54 5 -0.48 1 6
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.37 -10000 0 -0.72 149 149
IFNAR2 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.055 -10000 0 -0.24 21 21
ER alpha/Oestrogen -0.011 0.11 -10000 0 -0.49 24 24
NFX1/SIN3/HDAC complex 0.03 0.047 -10000 0 -0.56 2 2
EGF -0.073 0.24 -10000 0 -0.67 68 68
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.003 0.088 0.55 2 -0.44 1 3
SAP18 0.026 0.006 -10000 0 -10000 0 0
MRN complex 0.05 0.035 -10000 0 -0.44 2 2
WT1 0.008 0.046 -10000 0 -10000 0 0
WRN 0.026 0.032 -10000 0 -0.68 1 1
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.027 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.011 0.084 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT -0.002 0.11 0.54 5 -0.49 1 6
CCND1 0.001 0.11 0.57 6 -10000 0 6
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.68 2 2
TERF2 0.024 0.009 -10000 0 -10000 0 0
PTGES3 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
Telomerase/911 0.025 0.061 -10000 0 -0.3 3 3
CDKN1B -0.028 0.14 -10000 0 -0.43 54 54
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.026 0.032 -10000 0 -0.68 1 1
TRF2/PARP2 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.027 0.004 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.67 103 103
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.16 0.31 -10000 0 -0.67 126 126
IFN-gamma/IRF1 -0.018 0.17 -10000 0 -0.48 59 59
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.027 0.008 -10000 0 -10000 0 0
Telomerase 0.013 0.11 0.27 1 -0.51 12 13
IRF1 0.03 0.009 -10000 0 -10000 0 0
ESR1 -0.016 0.15 -10000 0 -0.65 24 24
KU/TER 0.029 0.018 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.025 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.037 0.042 -10000 0 -0.37 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.043 -10000 0 -0.38 3 3
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
ATM 0.01 0.024 -10000 0 -0.48 1 1
SMAD3 0.015 0.011 -10000 0 -10000 0 0
ABL1 0.025 0.008 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
MRE11A 0.024 0.045 -10000 0 -0.68 2 2
HUS1 0.026 0.006 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.016 0.084 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.013 -10000 0 -10000 0 0
MAPK1 0.002 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.024 -10000 0 -0.48 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.021 0.064 -10000 0 -0.68 4 4
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.041 0.19 -10000 0 -0.5 71 71
MYC 0.01 0.11 -10000 0 -0.65 12 12
IL2 0.02 0.009 -10000 0 -10000 0 0
KU 0.029 0.018 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.017 -10000 0 -10000 0 0
TRF2/BLM 0.037 0.013 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.002 0.088 0.51 2 -10000 0 2
SP1/HDAC2 0.042 0.01 -10000 0 -10000 0 0
PINX1 0.027 0.004 -10000 0 -10000 0 0
Telomerase/EST1A 0.01 0.082 -10000 0 -10000 0 0
Smad3/Myc 0.018 0.07 -10000 0 -0.42 11 11
911 complex 0.052 0.015 -10000 0 -10000 0 0
IFNG -0.061 0.23 -10000 0 -0.67 59 59
Telomerase/PinX1 0.01 0.084 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.013 0.066 0.37 1 -0.42 3 4
SIN3B 0.026 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.009 0.08 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.071 0.036 -10000 0 -0.38 2 2
TRF2/WRN 0.037 0.026 -10000 0 -0.48 1 1
Telomerase/hnRNP C1/C2 0.011 0.084 -10000 0 -10000 0 0
E2F1 -0.018 0.069 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.018 0.072 -10000 0 -0.68 5 5
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.025 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.036 0.098 0.45 10 -0.43 4 14
NFATC2 -0.021 0.096 0.29 9 -0.26 27 36
NFATC3 0.019 0.01 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.01 0.089 0.28 1 -0.4 10 11
Exportin 1/Ran/NUP214 0.047 0.018 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.003 0.1 -10000 0 -0.48 9 9
BCL2/BAX -0.001 0.14 -10000 0 -0.49 35 35
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.02 -10000 0 -10000 0 0
BAX 0.025 0.007 -10000 0 -10000 0 0
MAPK14 0.025 0.005 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.005 0.094 0.33 4 -0.4 9 13
Calcineurin A alpha-beta B1/BCL2 -0.023 0.18 -10000 0 -0.67 35 35
FKBP8 0.025 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.005 0.093 0.39 9 -0.33 4 13
KPNB1 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SFN -0.083 0.12 -10000 0 -0.68 13 13
MAP3K8 0.014 0.086 -10000 0 -0.64 8 8
NFAT4/CK1 alpha 0.02 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.071 0.17 -10000 0 -0.34 105 105
CABIN1 -0.01 0.087 0.28 1 -0.39 9 10
CALM1 0.023 0.01 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
CAMK4 0.013 0.086 -10000 0 -0.68 7 7
mol:Ca2+ -0.004 0.009 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.086 -10000 0 -0.64 8 8
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.087 0.46 1 -0.46 3 4
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
apoptosis 0.01 0.044 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.053 -10000 0 -0.32 5 5
PRKCB 0.005 0.082 -10000 0 -0.68 5 5
PRKCE 0.021 0.064 -10000 0 -0.68 4 4
JNK2/NFAT4 0.031 0.025 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.007 -10000 0 -10000 0 0
PRKCA -0.006 0.15 -10000 0 -0.68 22 22
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.02 0.066 -10000 0 -0.61 5 5
FKBP38/BCL2 -0.001 0.14 -10000 0 -0.49 35 35
EP300 0.01 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.039 0.1 0.43 7 -0.51 3 10
CaM/Ca2+/FKBP38 0.019 0.025 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.063 -10000 0 -0.45 7 7
NFATc/ERK1 0.042 0.082 0.44 3 -0.48 2 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.007 0.11 -10000 0 -0.5 9 9
NR4A1 -0.17 0.29 -10000 0 -0.61 143 143
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection 0.019 0.01 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.022 0.07 -10000 0 -0.32 7 7
RCH1/ KPNB1 0.038 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.008 -10000 0 -10000 0 0
AKAP5 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.014 0.021 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.049 0.097 0.44 10 -0.49 2 12
CREBBP 0.013 0.022 -10000 0 -10000 0 0
BCL2 -0.023 0.18 -10000 0 -0.67 35 35
TCGA08_p53

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
CDKN2A -0.025 0.042 -10000 0 -10000 0 0
TP53 -0.008 0.035 -10000 0 -0.18 18 18
Senescence -0.008 0.035 -10000 0 -0.18 18 18
Apoptosis -0.008 0.035 -10000 0 -0.18 18 18
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.011 0.025 0.35 1 -10000 0 1
MDM4 0.025 0.007 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.28 -10000 0 -0.67 97 97
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.004 -10000 0 -10000 0 0
HIF1A/p53 0.033 0.039 0.35 1 -0.24 2 3
HIF1A 0.009 0.024 -10000 0 -0.25 2 2
COPS5 0.027 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.052 -10000 0 -0.39 3 3
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.032 0.072 -10000 0 -10000 0 0
ARNT/IPAS -0.07 0.21 -10000 0 -0.48 97 97
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.033 0.049 0.3 8 -0.24 2 10
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.027 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.033 0.038 0.28 1 -0.24 2 3
PHD1-3/OS9 0.049 0.074 -10000 0 -0.4 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.055 0.039 -10000 0 -10000 0 0
VHL 0.023 0.055 -10000 0 -0.68 3 3
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.047 0.34 4 -0.24 2 6
EGLN3 0.007 0.1 -10000 0 -0.68 10 10
EGLN2 0.026 0.007 -10000 0 -10000 0 0
EGLN1 0.024 0.033 -10000 0 -0.68 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.025 0.078 -10000 0 -0.52 8 8
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.038 0.053 0.31 7 -0.24 2 9
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.015 0.081 0.63 7 -10000 0 7
PI3K Class IB/PDE3B 0.015 0.081 -10000 0 -0.63 7 7
PDE3B 0.015 0.082 -10000 0 -0.63 7 7
Aurora B signaling

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
Condensin I complex 0.017 0.043 -10000 0 -0.28 3 3
STMN1 0.002 0.041 0.19 3 -10000 0 3
Aurora B/RasGAP/Survivin 0.049 0.055 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.013 0.053 -10000 0 -0.25 12 12
BIRC5 0.014 0.051 -10000 0 -0.68 1 1
DES -0.33 0.3 -10000 0 -0.56 294 294
Aurora C/Aurora B/INCENP 0.054 0.045 -10000 0 -0.45 2 2
Aurora B/TACC1 0.031 0.042 -10000 0 -0.5 1 1
Aurora B/PP2A 0.021 0.049 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.006 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.01 0.059 0.18 1 -10000 0 1
Cul3 protein complex 0.038 0.071 -10000 0 -0.44 9 9
KIF2C 0.015 0.03 -10000 0 -0.52 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.001 0.056 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.021 0.048 -10000 0 -10000 0 0
SEPT1 0.024 0.02 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.015 0.084 0.27 3 -0.54 9 12
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.012 0.016 -10000 0 -10000 0 0
AURKB 0.003 0.063 -10000 0 -0.12 85 85
AURKC 0.02 0.029 -10000 0 -10000 0 0
CDCA8 0.028 0.014 -10000 0 -10000 0 0
cytokinesis -0.019 0.057 -10000 0 -0.37 5 5
Aurora B/Septin1 0.044 0.069 0.27 1 -0.35 5 6
AURKA 0.026 0.005 -10000 0 -10000 0 0
INCENP 0.026 0.046 -10000 0 -0.69 2 2
KLHL13 0.007 0.1 -10000 0 -0.62 11 11
BUB1 -0.027 0.077 -10000 0 -0.68 1 1
hSgo1/Aurora B/Survivin 0.047 0.056 -10000 0 -0.4 1 1
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.049 0.048 -10000 0 -0.28 1 1
SGOL1 0.021 0.029 -10000 0 -10000 0 0
CENPA 0.019 0.039 0.19 1 -0.22 6 7
NCAPG 0.013 0.044 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.021 0.049 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.021 0.049 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.006 0.052 -10000 0 -10000 0 0
NPM1 0.011 0.044 -10000 0 -0.3 9 9
RASA1 0.027 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.049 -10000 0 -10000 0 0
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin 0.042 0.049 -10000 0 -0.3 1 1
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 0.011 0.046 -10000 0 -0.29 9 9
MYLK 0.012 0.016 -10000 0 -10000 0 0
KIF23 0.021 0.033 -10000 0 -10000 0 0
VIM 0.001 0.038 -10000 0 -10000 0 0
RACGAP1 0.027 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.005 0.082 -10000 0 -0.43 12 12
Chromosomal passenger complex 0.016 0.036 -10000 0 -0.25 5 5
Chromosomal passenger complex/EVI5 0.1 0.066 -10000 0 -0.42 3 3
TACC1 0.026 0.032 -10000 0 -0.68 1 1
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.006 0.018 0.12 2 -0.14 3 5
BUB1B 0.014 0.031 0.18 9 -0.17 1 10
PLK1 0.012 0.031 0.16 13 -0.12 1 14
PLK1S1 0.015 0.027 0.18 10 -10000 0 10
KIF2A 0.018 0.069 0.32 20 -0.39 1 21
regulation of mitotic centrosome separation 0.012 0.032 0.16 13 -0.12 1 14
GOLGA2 0.025 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.033 0.037 -10000 0 -10000 0 0
WEE1 0.022 0.047 0.25 8 -0.25 6 14
cytokinesis 0.012 0.06 0.28 7 -0.27 2 9
PP2A-alpha B56 0.048 0.095 -10000 0 -0.58 7 7
AURKA 0.014 0.026 0.17 7 -0.26 1 8
PICH/PLK1 0.02 0.015 -10000 0 -10000 0 0
CENPE 0.01 0.053 0.25 11 -0.39 3 14
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.068 0.32 20 -0.39 1 21
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.015 0.03 0.18 11 -0.25 1 12
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.036 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.013 0.03 0.15 3 -0.28 3 6
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.023 26 -10000 0 26
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.019 0.097 14 -0.049 1 15
G2 phase of mitotic cell cycle 0 0.004 0.019 12 -10000 0 12
STAG2 0.025 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.023 0.037 -10000 0 -0.43 3 3
spindle elongation 0.012 0.032 0.16 13 -0.12 1 14
ODF2 0.025 0.008 -10000 0 -10000 0 0
BUB1 0.024 0.095 -10000 0 -0.57 11 11
TPT1 0.005 0.045 0.16 5 -0.18 23 28
CDC25C 0.019 0.026 0.18 8 -10000 0 8
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.018 0.14 3 -0.12 2 5
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.015 -10000 0 -10000 0 0
CDC14B 0.003 0.044 -10000 0 -0.41 5 5
CDC20 0.025 0.017 -10000 0 -10000 0 0
PLK1/PBIP1 0.011 0.022 0.15 4 -10000 0 4
mitosis -0.001 0.003 0.021 4 -10000 0 4
FBXO5 0.013 0.038 0.22 9 -0.34 1 10
CDC2 0.002 0.001 0.011 1 -10000 0 1
NDC80 0.006 0.052 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.027 0.17 2 -0.24 3 5
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.011 0.028 0.14 15 -10000 0 15
microtubule cytoskeleton organization 0.005 0.045 0.16 5 -0.18 23 28
G2/M transition DNA damage checkpoint 0 0.004 0.019 14 -10000 0 14
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.004 0.019 14 -10000 0 14
PLK1/PRC1-2 0.038 0.028 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.022 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.028 0.15 13 -0.11 1 14
mitotic prometaphase 0 0.003 0.026 6 -10000 0 6
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.026 -10000 0 -10000 0 0
microtubule-based process 0.015 0.031 -10000 0 -10000 0 0
Golgi organization 0.012 0.032 0.16 13 -0.12 1 14
Cohesin/SA2 0.021 0.017 0.17 1 -10000 0 1
PPP1CB/MYPT1 0.04 0.009 -10000 0 -10000 0 0
KIF20A 0.001 0.056 -10000 0 -10000 0 0
APC/C/CDC20 0.025 0.026 0.2 3 -10000 0 3
PPP2R1A 0.025 0.007 -10000 0 -10000 0 0
chromosome segregation 0.01 0.022 0.15 4 -10000 0 4
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.042 0.22 8 -0.41 2 10
C13orf34 0.01 0.027 0.14 13 -0.11 1 14
NUDC 0.014 0.027 0.17 2 -0.24 3 5
regulation of attachment of spindle microtubules to kinetochore 0.014 0.031 0.18 9 -0.17 1 10
spindle assembly 0.014 0.038 0.17 19 -0.086 1 20
spindle stabilization 0.015 0.027 0.18 10 -10000 0 10
APC/C/HCDH1 0.019 0.041 -10000 0 -0.35 5 5
MKLP2/PLK1 0.015 0.031 -10000 0 -10000 0 0
CCNB1 0.027 0.006 -10000 0 -10000 0 0
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.002 0.1 0.26 2 -0.41 26 28
TUBG1 0.015 0.03 0.18 9 -0.16 3 12
G2/M transition of mitotic cell cycle 0.013 0.01 -10000 0 -10000 0 0
MLF1IP 0.007 0.013 -10000 0 -10000 0 0
INCENP 0.024 0.046 -10000 0 -0.68 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.004 0.16 -10000 0 -0.44 57 57
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.14 -10000 0 -0.38 56 56
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.035 0.085 -10000 0 -10000 0 0
YY1/LSF 0.006 0.066 -10000 0 -0.43 4 4
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.008 0.11 -10000 0 -0.31 55 55
I kappa B alpha/HDAC1 0.01 0.082 -10000 0 -10000 0 0
SAP18 0.026 0.006 -10000 0 -10000 0 0
RELA -0.017 0.11 -10000 0 -0.32 57 57
HDAC1/Smad7 0.051 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.011 0.082 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.031 0.038 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.025 0.12 0.32 1 -0.43 15 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.008 -10000 0 -10000 0 0
GATA1 0.012 0.02 -10000 0 -10000 0 0
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.034 0.068 -10000 0 -0.49 5 5
RBBP7 0.025 0.008 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.68 2 2
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.004 0.085 -10000 0 -0.24 56 56
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.034 -10000 0 -0.55 1 1
SIN3 complex 0.061 0.032 -10000 0 -0.4 1 1
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.025 0.032 -10000 0 -0.68 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.009 0.08 -10000 0 -10000 0 0
YY1/HDAC2 0.009 0.055 -10000 0 -0.28 1 1
YY1/HDAC1 0.01 0.053 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.031 0.031 -10000 0 -0.4 1 1
PPARG -0.023 0.14 -10000 0 -0.39 61 61
HDAC8/hEST1B 0.046 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.011 0.082 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.016 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.035 0.062 -10000 0 -0.45 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 -0.004 0.085 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.019 0.012 -10000 0 -10000 0 0
HDAC8 0.025 0.007 -10000 0 -10000 0 0
SMAD7 0.027 0.004 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.018 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.019 0.066 -10000 0 -0.4 4 4
YY1/SAP30/HDAC1 0.021 0.057 -10000 0 -0.31 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.084 -10000 0 -0.24 56 56
histone deacetylation 0.038 0.034 -10000 0 -0.39 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.002 0.076 -10000 0 -0.3 1 1
nuclear export -0.046 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.011 0.082 -10000 0 -10000 0 0
GATA1/HDAC1 0.035 0.012 -10000 0 -10000 0 0
GATA1/HDAC3 0.008 0.081 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.027 0.18 -10000 0 -0.51 57 57
SIN3/HDAC complex/Mad/Max 0.031 0.046 -10000 0 -0.57 2 2
NuRD Complex 0.041 0.052 -10000 0 -0.42 3 3
positive regulation of chromatin silencing 0.032 0.083 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.014 0.057 -10000 0 -0.31 1 1
HDAC complex 0.062 0.036 -10000 0 -0.4 2 2
GATA1/Fog1 0.034 0.013 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.053 0.014 -10000 0 -10000 0 0
TNF -0.059 0.23 -10000 0 -0.68 57 57
negative regulation of cell growth 0.034 0.047 -10000 0 -0.57 2 2
NuRD/MBD2/PRMT5 Complex 0.031 0.031 -10000 0 -0.4 1 1
Ran/GTP/Exportin 1 0.017 0.052 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.032 0.14 -10000 0 -0.4 57 57
SIN3/HDAC complex/NCoR1 0.03 0.054 -10000 0 -0.5 3 3
TFCP2 0.021 0.064 -10000 0 -0.68 4 4
NR2C1 0.027 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.008 -10000 0 -10000 0 0
MBD2 0.027 0.004 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.033 0.075 -10000 0 -10000 0 0
CDKN2C 0.031 0.019 -10000 0 -10000 0 0
CDKN2A -0.033 0.076 -10000 0 -10000 0 0
CCND2 0.01 0.023 -10000 0 -10000 0 0
RB1 -0.014 0.046 0.32 2 -0.25 10 12
CDK4 0.014 0.042 0.25 10 -10000 0 10
CDK6 0.016 0.043 0.26 10 -0.16 1 11
G1/S progression 0.015 0.05 0.24 14 -0.32 2 16
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.007 0.1 -9999 0 -0.64 10 10
ITGA4 0.021 0.05 -9999 0 -0.68 2 2
alpha4/beta7 Integrin 0.019 0.087 -9999 0 -0.49 12 12
alpha4/beta1 Integrin 0.035 0.039 -9999 0 -0.51 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.005 -10000 0 -10000 0 0
ELF1 0.005 0.1 -10000 0 -0.39 27 27
CCNA2 0.024 0.02 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
JAK3 -0.01 0.064 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.003 0.13 -10000 0 -0.58 16 16
SHC1 0.026 0.008 -10000 0 -10000 0 0
SP1 0.033 0.006 -10000 0 -10000 0 0
IL2RA -0.031 0.2 -10000 0 -0.87 26 26
IL2RB 0.004 0.092 -10000 0 -0.58 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG -0.011 0.14 -10000 0 -0.63 21 21
G1/S transition of mitotic cell cycle 0.031 0.068 0.43 6 -0.5 3 9
PTPN11 0.026 0.032 -10000 0 -0.68 1 1
CCND2 0.023 0.005 -10000 0 -10000 0 0
LCK 0.013 0.083 -10000 0 -0.68 6 6
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.022 0.055 -10000 0 -0.68 3 3
CCND3 0.007 0.12 -10000 0 -0.6 9 9
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.025 0.057 0.35 2 -0.55 2 4
PDGFB-D/PDGFRB/SLAP 0.038 0.028 -10000 0 -0.51 1 1
PDGFB-D/PDGFRB/APS/CBL 0.052 0.026 -10000 0 -0.42 1 1
AKT1 0.03 0.087 0.5 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.06 0.35 2 -0.62 2 4
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
FGR 0.017 0.048 0.36 1 -0.59 2 3
mol:Ca2+ 0.033 0.086 0.42 11 -0.68 2 13
MYC 0.028 0.18 0.58 17 -0.77 14 31
SHC1 0.025 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.024 -10000 0 -0.38 1 1
LRP1/PDGFRB/PDGFB 0.038 0.04 -10000 0 -0.44 2 2
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GO:0007205 0.033 0.087 0.42 11 -0.69 2 13
PTEN 0.026 0.018 -10000 0 -0.36 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.055 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.037 0.037 -10000 0 -0.52 2 2
PDGFB-D/PDGFRB/GRB10 0.038 0.027 -10000 0 -0.51 1 1
cell cycle arrest 0.037 0.028 -10000 0 -0.51 1 1
HRAS 0.026 0.011 -10000 0 -10000 0 0
HIF1A 0.024 0.084 0.48 11 -10000 0 11
GAB1 0.028 0.094 0.43 11 -0.64 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.033 0.11 0.5 15 -0.56 2 17
PDGFB-D/PDGFRB 0.054 0.029 -10000 0 -0.46 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.027 -10000 0 -0.51 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.033 0.054 -10000 0 -0.67 1 1
positive regulation of MAPKKK cascade 0.037 0.037 -10000 0 -0.51 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.033 0.087 0.42 11 -0.7 2 13
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.018 0.052 -10000 0 -0.57 1 1
SHB 0.025 0.008 -10000 0 -10000 0 0
BLK -0.14 0.26 -10000 0 -0.56 139 139
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.038 0.026 -10000 0 -0.49 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.033 0.11 0.48 14 -0.6 3 17
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.027 -10000 0 -0.51 1 1
LCK 0.01 0.083 -10000 0 -0.67 6 6
PDGFRB 0.026 0.033 -10000 0 -0.69 1 1
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.022 0.046 0.29 1 -0.59 2 3
ABL1 0.026 0.098 0.42 13 -0.68 2 15
PDGFB-D/PDGFRB/CBL 0.023 0.085 0.45 4 -0.72 2 6
PTPN1 0.027 0.005 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
cell proliferation 0.03 0.17 0.55 19 -0.68 14 33
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.033 0.026 -10000 0 -0.37 1 1
SRC 0.017 0.048 0.29 1 -0.51 3 4
PI3K 0.012 0.034 -10000 0 -0.35 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.028 -10000 0 -0.3 1 1
SH2B2 0.026 0.009 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.029 0.062 0.36 2 -0.64 2 4
LYN 0.018 0.035 -10000 0 -0.44 2 2
LRP1 0.025 0.032 -10000 0 -0.68 1 1
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.079 0.032 -10000 0 -0.38 1 1
SPHK1 0.023 0.022 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.033 0.087 0.42 11 -0.7 2 13
PLCG1 0.033 0.088 0.42 11 -0.72 2 13
NHERF/PDGFRB 0.05 0.028 -10000 0 -0.44 1 1
YES1 0.015 0.06 0.37 1 -0.54 4 5
cell migration 0.049 0.028 -10000 0 -0.44 1 1
SHC/Grb2/SOS1 0.072 0.035 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.033 -10000 0 -0.41 1 1
FYN 0.016 0.053 -10000 0 -0.52 3 3
DOK1 0.023 0.029 -10000 0 -0.41 1 1
HRAS/GTP 0.019 0.008 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.038 0.14 0.54 19 -0.47 11 30
PRKCD 0.024 0.03 -10000 0 -0.42 1 1
FER 0.02 0.043 -10000 0 -0.42 4 4
MAPKKK cascade 0.016 0.055 0.37 1 -10000 0 1
RASA1 0.023 0.027 -10000 0 -0.42 1 1
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.029 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.028 -10000 0 -0.51 1 1
chemotaxis 0.026 0.096 0.41 14 -0.65 2 16
STAT1-3-5/STAT1-3-5 0.064 0.029 -10000 0 -0.37 1 1
Bovine Papilomavirus E5/PDGFRB 0.019 0.025 -10000 0 -0.52 1 1
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.68 15 15
CDC42/GTP 0.007 0.075 -10000 0 -0.31 14 14
PLCG1 -0.001 0.067 -10000 0 -0.31 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.011 -10000 0 -10000 0 0
cell migration 0.006 0.073 -10000 0 -0.3 14 14
S1PR5 0.023 0.034 -10000 0 -0.68 1 1
S1PR4 0.024 0.017 -10000 0 -10000 0 0
MAPK3 -0.002 0.069 -10000 0 -0.31 15 15
MAPK1 0.009 0.061 -10000 0 -0.31 15 15
S1P/S1P5/Gi -0.001 0.075 -10000 0 -0.32 18 18
GNAI1 0.025 0.032 -10000 0 -0.68 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.026 -10000 0 -0.44 1 1
RHOA 0.034 0.069 0.41 11 -10000 0 11
S1P/S1P4/Gi 0 0.074 -10000 0 -0.32 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.018 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.07 0.38 1 -0.36 1 2
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.022 0.052 -10000 0 -0.51 2 2
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.027 0.004 -10000 0 -10000 0 0
RIPK2 0.027 0.005 -10000 0 -10000 0 0
IKBKG 0.033 0.025 -10000 0 -10000 0 0
IKK complex/A20 0.012 0.15 0.33 1 -0.52 7 8
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.032 0.076 -10000 0 -0.44 2 2
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.072 -10000 0 -0.51 1 1
BCL10/MALT1/TRAF6 0.05 0.035 -10000 0 -0.44 2 2
NOD2 0.004 0.066 -10000 0 -0.68 2 2
NFKB1 0.03 0.004 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.008 -10000 0 -10000 0 0
ATM 0.025 0.032 -10000 0 -0.68 1 1
TNF/TNFR1A -0.027 0.18 -10000 0 -0.51 57 57
TRAF6 0.024 0.045 -10000 0 -0.68 2 2
PRKCA -0.006 0.15 -10000 0 -0.68 22 22
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.059 0.23 -10000 0 -0.68 57 57
NF kappa B1 p50/RelA 0.061 0.016 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.047 0.077 -10000 0 -0.55 1 1
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.037 0.11 -10000 0 -0.51 4 4
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.028 0.1 -10000 0 -0.54 5 5
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.026 0.007 -10000 0 -10000 0 0
STXBP4 0.024 0.033 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.024 0.11 0.39 6 -0.5 7 13
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.052 0.18 -10000 0 -0.49 65 65
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.028 -10000 0 -0.44 1 1
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.005 0.048 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.017 0.012 0.25 1 -10000 0 1
PRKCZ 0.026 0.005 -10000 0 -10000 0 0
TRIP10 0.025 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
AS160/14-3-3 -0.032 0.093 -10000 0 -0.35 14 14
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.023 0.12 0.41 5 -0.57 7 12
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.023 0.008 -10000 0 -10000 0 0
SFN -0.083 0.12 -10000 0 -0.68 13 13
LNPEP 0.003 0.13 -10000 0 -0.68 16 16
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.016 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.044 0.015 -10000 0 -10000 0 0
CDKN1B 0.022 0.024 -10000 0 -10000 0 0
CDKN1A 0.02 0.025 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.004 -10000 0 -10000 0 0
FOXO3 0.022 0.024 -10000 0 -10000 0 0
AKT1 0.022 0.023 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.013 0.027 -10000 0 -0.39 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.022 0.026 -10000 0 -10000 0 0
AKT1/ASK1 0.038 0.037 -10000 0 -0.33 1 1
BAD/YWHAZ 0.05 0.018 -10000 0 -10000 0 0
RICTOR 0.025 0.032 -10000 0 -0.68 1 1
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.035 0.32 1 -10000 0 1
TSC1 0.021 0.025 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.036 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.022 0.024 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.021 0.023 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.046 0.15 -10000 0 -0.43 61 61
MAP3K5 0.026 0.032 -10000 0 -0.68 1 1
MAPKAP1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.082 0.46 4 -0.36 8 12
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.026 0.037 -10000 0 -10000 0 0
CASP9 0.024 0.03 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.047 0.38 5 -10000 0 5
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.035 -10000 0 -0.44 2 2
YWHAE 0.026 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.021 0.029 -10000 0 -0.36 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.011 -10000 0 -10000 0 0
CHUK 0.022 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.034 -10000 0 -10000 0 0
mTORC2 0.03 0.023 -10000 0 -0.4 1 1
AKT2 0.014 0.026 -10000 0 -0.39 2 2
FOXO1-3a-4/14-3-3 family 0.021 0.088 0.45 7 -0.4 3 10
PDPK1 0.023 0.046 -10000 0 -0.68 2 2
MDM2 0.022 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.035 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.034 -10000 0 -10000 0 0
TSC1/TSC2 0.024 0.04 0.44 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.032 -10000 0 -10000 0 0
glucose import -0.055 0.16 0.21 4 -0.41 74 78
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.029 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.057 0.16 -10000 0 -0.42 74 74
GSK3A 0.026 0.036 -10000 0 -10000 0 0
FOXO1 0.021 0.024 -10000 0 -10000 0 0
GSK3B 0.022 0.024 -10000 0 -10000 0 0
SFN -0.083 0.12 -10000 0 -0.68 13 13
G1/S transition of mitotic cell cycle 0.028 0.044 0.32 2 -10000 0 2
p27Kip1/14-3-3 family 0.015 0.063 -10000 0 -0.41 6 6
PRKACA 0.025 0.008 -10000 0 -10000 0 0
KPNA1 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.006 0.075 0.3 15 -10000 0 15
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.026 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.68 15 15
RhoA/GTP 0.007 0.077 -10000 0 -0.3 15 15
negative regulation of cAMP metabolic process -0.001 0.075 -10000 0 -0.32 18 18
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
S1PR5 0.023 0.034 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.075 -10000 0 -0.32 18 18
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.68 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.009 0.003 -10000 0 -10000 0 0
SNTA1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.009 0.004 -10000 0 -10000 0 0
MAPK12 -0.001 0.053 -10000 0 -0.38 9 9
CCND1 0.007 0.046 -10000 0 -0.4 4 4
p38 gamma/SNTA1 0.02 0.066 -10000 0 -0.36 11 11
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
G2/M transition checkpoint 0.001 0.062 0.21 7 -0.38 10 17
MAP2K6 0.001 0.064 -10000 0 -0.42 11 11
MAPT 0.013 0.051 0.32 6 -0.36 3 9
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.019 -10000 0 -0.39 1 1
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.024 0.24 3 -10000 0 3
AES 0.026 0.02 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
SMAD4 0.027 0.004 -10000 0 -10000 0 0
DKK2 -0.006 0.14 -10000 0 -0.68 20 20
TLE1 0.021 0.058 0.22 2 -0.66 3 5
MACF1 0.027 0.006 -10000 0 -10000 0 0
CTNNB1 0.049 0.093 0.49 15 -10000 0 15
WIF1 -0.014 0.045 -10000 0 -10000 0 0
beta catenin/RanBP3 0.03 0.085 0.38 23 -10000 0 23
KREMEN2 0.016 0.037 -10000 0 -10000 0 0
DKK1 -0.001 0.07 -10000 0 -0.68 2 2
beta catenin/beta TrCP1 0.047 0.046 0.49 1 -10000 0 1
FZD1 0.026 0.006 -10000 0 -10000 0 0
AXIN2 -0.029 0.3 0.58 17 -1.4 18 35
AXIN1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.029 0.071 -10000 0 -0.5 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.038 0.098 0.3 1 -0.59 4 5
Axin1/APC/GSK3 0.034 0.045 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.035 0.043 0.51 2 -10000 0 2
HNF1A 0.027 0.02 0.23 1 -10000 0 1
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.04 0.24 0.6 2 -1.4 14 16
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.097 -10000 0 -0.44 19 19
NKD1 0.006 0.11 -10000 0 -0.68 13 13
TCF4 0.027 0.019 0.22 1 -10000 0 1
TCF3 0.026 0.023 0.25 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.065 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.024 0.13 0.53 22 -10000 0 22
LEF1 0.023 0.05 0.22 1 -0.63 2 3
DVL1 0.028 0.016 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.12 -10000 0 -0.54 9 9
DKK1/LRP6/Kremen 2 0.048 0.045 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 0.019 -10000 0 -10000 0 0
NLK 0.026 0.008 -10000 0 -10000 0 0
CCND1 -0.011 0.087 0.58 2 -0.68 3 5
WNT1 0.023 0.013 -10000 0 -10000 0 0
GSK3A 0.026 0.008 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
PPP2R5D 0.032 0.055 0.33 13 -0.33 1 14
APC 0.022 0.039 0.36 3 -0.39 1 4
WNT1/LRP6/FZD1 0.031 0.02 -10000 0 -10000 0 0
CREBBP 0.027 0.02 0.23 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.013 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.009 0.039 -10000 0 -0.17 3 3
RAB3GAP2/RIMS1/UNC13B 0.048 0.019 -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 0.021 0.017 -10000 0 -10000 0 0
mol:ACh 0.001 0.044 0.15 17 -0.14 24 41
RAB3GAP2 0.025 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.056 -10000 0 -0.26 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.009 0.039 -10000 0 -0.17 3 3
UNC13B 0.025 0.008 -10000 0 -10000 0 0
CHRNA1 0.009 0.043 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.04 0.11 -10000 0 -0.48 24 24
SNAP25 -0.016 0.076 -10000 0 -0.34 25 25
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 -0.066 0.15 -10000 0 -0.68 23 23
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.056 -10000 0 -0.26 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.023 0.097 -10000 0 -0.55 12 12
AKT1 0.04 0.087 0.39 2 -0.61 5 7
PTK2B 0.018 0.11 0.35 1 -0.5 15 16
VEGFR2 homodimer/Frs2 0.034 0.075 -10000 0 -0.9 3 3
CAV1 0.013 0.095 -10000 0 -0.68 9 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.048 0.089 -10000 0 -0.73 5 5
endothelial cell proliferation 0.053 0.15 0.62 17 -0.67 3 20
mol:Ca2+ 0.025 0.086 -10000 0 -0.64 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.062 0.086 -10000 0 -0.78 4 4
RP11-342D11.1 0.014 0.085 -10000 0 -0.64 6 6
CDH5 0.026 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.059 0.059 -10000 0 -0.5 4 4
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.021 0.056 -10000 0 -0.68 3 3
HRAS/GDP 0.041 0.074 -10000 0 -0.74 3 3
SH2D2A -0.008 0.14 -10000 0 -0.68 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.056 0.094 -10000 0 -0.63 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.026 0.13 -10000 0 -0.46 26 26
VEGFR1 homodimer 0.024 0.033 -10000 0 -0.68 1 1
SHC/GRB2/SOS1 0.067 0.09 -10000 0 -0.86 3 3
GRB10 0.026 0.084 -10000 0 -0.92 3 3
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.071 0.087 -10000 0 -0.68 5 5
HRAS 0.026 0.011 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.067 -10000 0 -0.44 6 6
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.06 0.083 -10000 0 -0.76 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.019 0.071 -10000 0 -0.68 5 5
Nck/Pak 0.039 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.049 0.089 -10000 0 -0.73 5 5
mol:GDP 0.053 0.081 -10000 0 -0.8 3 3
mol:NADP 0.041 0.1 0.48 7 -0.53 4 11
eNOS/Hsp90 0.044 0.08 -10000 0 -0.49 4 4
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.025 0.088 -10000 0 -0.66 6 6
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.025 0.008 -10000 0 -10000 0 0
VEGFA 0.025 0.055 -10000 0 -0.67 3 3
VEGFC 0.025 0.032 -10000 0 -0.68 1 1
FAK1/Vinculin 0.039 0.1 -10000 0 -0.65 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.12 -10000 0 -0.53 15 15
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.031 0.054 -10000 0 -0.58 3 3
mol:L-citrulline 0.041 0.1 0.48 7 -0.53 4 11
ITGAV 0.024 0.045 -10000 0 -0.68 2 2
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.06 0.087 -10000 0 -0.78 4 4
VEGFR2 homodimer/VEGFA homodimer 0.051 0.1 -10000 0 -0.72 6 6
VEGFR2/3 heterodimer 0.029 0.1 -10000 0 -0.79 6 6
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.008 0.094 0.38 1 -0.69 6 7
VEGFR2 homodimer 0.021 0.081 -10000 0 -1 3 3
FLT1 0.024 0.033 -10000 0 -0.68 1 1
NEDD4 0.026 0.045 -10000 0 -0.67 2 2
MAPK3 0.001 0.089 0.38 1 -0.76 4 5
MAPK1 -0.003 0.089 0.38 1 -0.76 4 5
VEGFA145/NRP2 0.028 0.053 -10000 0 -0.51 3 3
VEGFR1/2 heterodimer 0.032 0.087 -10000 0 -1 3 3
KDR 0.021 0.082 -10000 0 -1 3 3
VEGFA165/NRP1/VEGFR2 homodimer 0.055 0.095 -10000 0 -0.67 6 6
SRC 0.026 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.013 0.12 0.41 13 -0.93 3 16
PI3K 0.043 0.093 -10000 0 -0.92 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.049 0.089 -10000 0 -0.73 5 5
FES 0.026 0.092 -10000 0 -0.74 5 5
GAB1 0.031 0.088 -10000 0 -0.79 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.089 -10000 0 -0.73 5 5
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.04 0.091 0.4 1 -0.54 5 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.048 0.089 -10000 0 -0.73 5 5
PI3K/GAB1 0.052 0.079 -10000 0 -0.62 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.072 0.086 -10000 0 -0.89 3 3
PRKACA 0.025 0.008 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.1 -10000 0 -0.69 7 7
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.024 0.092 -10000 0 -0.74 5 5
actin cytoskeleton reorganization 0.026 0.12 -10000 0 -0.45 26 26
PTK2 0.026 0.1 -10000 0 -0.71 6 6
EDG1 0.014 0.085 -10000 0 -0.64 6 6
mol:DAG 0.025 0.088 -10000 0 -0.66 6 6
CaM/Ca2+ 0.038 0.081 -10000 0 -0.86 3 3
MAP2K3 0.012 0.099 0.37 1 -0.97 3 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.053 0.098 -10000 0 -1 3 3
PLCG1 0.025 0.092 -10000 0 -0.68 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.059 0.088 -10000 0 -0.7 5 5
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.047 0.099 -10000 0 -0.8 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.048 0.089 -10000 0 -0.73 5 5
cell migration 0.046 0.083 0.34 1 -0.56 5 6
mol:PI-3-4-5-P3 0.043 0.081 -10000 0 -0.79 3 3
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.03 0.081 -10000 0 -0.6 6 6
mol:NO 0.041 0.1 0.48 7 -0.53 4 11
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.07 -10000 0 -0.74 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.045 0.095 -10000 0 -1 3 3
VHL 0.023 0.055 -10000 0 -0.68 3 3
ITGB3 0.009 0.11 -10000 0 -0.65 12 12
NOS3 0.041 0.11 0.5 7 -0.61 4 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.043 0.094 -10000 0 -0.64 7 7
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0 0.12 0.36 1 -1.1 3 4
PRKCB 0.007 0.09 0.36 1 -0.86 3 4
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.031 0.091 -10000 0 -0.66 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.046 0.099 -10000 0 -0.79 5 5
VEGFA165/NRP2 0.028 0.053 -10000 0 -0.51 3 3
MAPKKK cascade 0.054 0.086 0.35 1 -0.75 3 4
NRP2 0.015 0.041 -10000 0 -10000 0 0
VEGFC homodimer 0.025 0.032 -10000 0 -0.68 1 1
NCK1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.027 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.1 -10000 0 -0.65 6 6
MAP3K13 0.019 0.11 -10000 0 -0.54 12 12
PDPK1 0.029 0.077 -10000 0 -0.69 4 4
Circadian rhythm 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
chromatin modification 0.04 0.042 -9999 0 -0.45 1 1
CLOCK -0.013 0.16 -9999 0 -0.68 28 28
TIMELESS/CRY2 0.027 0.034 -9999 0 -10000 0 0
DEC1/BMAL1 0.019 0.035 -9999 0 -10000 0 0
ATR 0.026 0.032 -9999 0 -0.68 1 1
NR1D1 0 0.04 -9999 0 -10000 0 0
ARNTL 0.013 0.044 -9999 0 -10000 0 0
TIMELESS 0.011 0.03 -9999 0 -10000 0 0
NPAS2 0.027 0.019 -9999 0 -0.36 1 1
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.004 0.009 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.004 0.009 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.026 0.12 -9999 0 -0.44 28 28
BMAL1/CLOCK -0.003 0.1 -9999 0 -0.41 25 25
S phase of mitotic cell cycle 0.04 0.042 -9999 0 -0.45 1 1
TIMELESS/CHEK1/ATR 0.041 0.042 -9999 0 -0.46 1 1
mol:NADPH 0.004 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.026 0.032 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.032 0.097 0.34 2 -10000 0 2
CRKL 0.014 0.047 0.46 3 -10000 0 3
mol:DAG 0.029 0.047 -10000 0 -10000 0 0
HRAS 0.034 0.062 0.36 5 -10000 0 5
MAPK8 0.014 0.063 -10000 0 -0.44 7 7
RAP1A 0.024 0.064 0.48 6 -10000 0 6
GAB1 0.022 0.055 0.45 4 -10000 0 4
MAPK14 0.021 0.032 -10000 0 -10000 0 0
EPO 0.019 0.023 -10000 0 -10000 0 0
PLCG1 0.029 0.047 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.024 0.022 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.023 0.1 -10000 0 -0.42 23 23
GAB1/SHC/GRB2/SOS1 0.048 0.043 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.03 0.027 -10000 0 -10000 0 0
IRS2 0.022 0.06 0.47 5 -10000 0 5
STAT1 0.03 0.071 -10000 0 -10000 0 0
STAT5B 0.028 0.06 -10000 0 -10000 0 0
cell proliferation 0.013 0.073 0.35 7 -0.41 7 14
GAB1/SHIP/PIK3R1/SHP2/SHC 0.037 0.041 -10000 0 -0.41 1 1
TEC 0.022 0.055 0.45 4 -10000 0 4
SOCS3 -0.008 0.15 -10000 0 -0.68 23 23
STAT1 (dimer) 0.03 0.07 -10000 0 -10000 0 0
JAK2 0.027 0.02 -10000 0 -0.33 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.052 -10000 0 -10000 0 0
EPO/EPOR 0.03 0.027 -10000 0 -10000 0 0
LYN 0.025 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.032 0.04 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.024 0.022 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.05 0.032 -10000 0 -10000 0 0
mol:IP3 0.029 0.047 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.044 0.045 -10000 0 -10000 0 0
SH2B3 0.028 0.007 -10000 0 -10000 0 0
NFKB1 0.02 0.031 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0 0.061 -10000 0 -0.26 20 20
PTPN6 0.023 0.046 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.042 0.043 -10000 0 -10000 0 0
EPOR 0.024 0.022 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.047 0.043 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.031 0.041 -10000 0 -10000 0 0
VAV2 0.024 0.061 0.46 6 -10000 0 6
CBL 0.022 0.055 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.036 0.038 -10000 0 -10000 0 0
STAT5A 0.028 0.06 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.04 0.096 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.01 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
BTK 0.011 0.058 0.26 1 -0.36 6 7
BCL2 -0.012 0.25 -10000 0 -0.91 34 34
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.015 0.062 -9999 0 -0.38 11 11
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
DOCK1 0.023 0.055 -9999 0 -0.68 3 3
ITGA4 0.021 0.05 -9999 0 -0.68 2 2
alpha4/beta7 Integrin/MAdCAM1 0.048 0.081 -9999 0 -0.4 13 13
EPO 0.004 0.026 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.087 -9999 0 -0.49 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.035 0.039 -9999 0 -0.51 2 2
EPO/EPOR (dimer) 0.03 0.021 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.037 -9999 0 -0.4 3 3
PIK3CA 0.023 0.055 -9999 0 -0.68 3 3
PI3K 0.036 0.044 -9999 0 -0.51 3 3
ARF6 0.027 0.005 -9999 0 -10000 0 0
JAK2 0.024 0.032 -9999 0 -0.42 2 2
PXN 0.027 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
MADCAM1 0.006 0.056 -9999 0 -0.68 2 2
cell adhesion 0.046 0.08 -9999 0 -0.4 13 13
CRKL/CBL 0.03 0.018 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.017 0.067 -9999 0 -0.46 7 7
ITGB7 0.007 0.1 -9999 0 -0.64 10 10
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.069 -9999 0 -0.5 7 7
p130Cas/Crk/Dock1 0.034 0.067 -9999 0 -0.37 10 10
VCAM1 0.016 0.079 -9999 0 -0.68 6 6
RHOA 0.027 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.064 0.032 -9999 0 -0.4 1 1
BCAR1 0.008 0.062 -9999 0 -0.43 7 7
EPOR 0.024 0.017 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.038 -9999 0 -0.41 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.014 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.087 -10000 0 -0.54 3 3
EPO 0.12 0.11 -10000 0 -0.91 1 1
FIH (dimer) 0.037 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.12 -10000 0 -0.75 2 2
FLT1 -0.002 0.12 -10000 0 -0.7 9 9
ADORA2A 0.1 0.11 0.4 10 -0.96 1 11
germ cell development 0.13 0.11 -10000 0 -0.94 1 1
SLC11A2 0.12 0.11 -10000 0 -1 1 1
BHLHE40 0.13 0.11 -10000 0 -1 1 1
HIF1AN 0.037 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.096 0.36 1 -0.66 2 3
ETS1 0.038 0.014 -10000 0 -10000 0 0
CITED2 -0.033 0.31 -10000 0 -1.1 37 37
KDR 0.005 0.11 -10000 0 -0.98 5 5
PGK1 0.12 0.11 -10000 0 -1 1 1
SIRT1 0.026 0.032 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.14 -10000 0 -1.3 1 1
EPAS1 0.061 0.069 -10000 0 -0.39 3 3
SP1 0.033 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.12 -10000 0 -0.76 3 3
EFNA1 0.13 0.11 -10000 0 -1 1 1
FXN 0.12 0.12 0.42 14 -0.96 1 15
POU5F1 0.13 0.11 -10000 0 -1 1 1
neuron apoptosis -0.16 0.13 1.2 1 -10000 0 1
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.016 0.1 -10000 0 -0.66 10 10
EGLN2 0.035 0.014 -10000 0 -10000 0 0
EGLN1 0.034 0.035 -10000 0 -0.68 1 1
VHL/Elongin B/Elongin C 0.049 0.042 -10000 0 -0.46 3 3
VHL 0.023 0.055 -10000 0 -0.68 3 3
ARNT 0.034 0.015 -10000 0 -10000 0 0
SLC2A1 0.14 0.12 0.48 7 -0.96 1 8
TWIST1 0.12 0.14 0.4 17 -0.58 8 25
ELK1 0.022 0.035 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.091 0.097 -10000 0 -0.49 2 2
VEGFA 0.12 0.12 -10000 0 -0.77 3 3
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.025 0.11 0.64 11 -10000 0 11
PLK1 0.071 0.11 0.58 3 -0.71 1 4
CDKN1B 0.074 0.094 0.53 4 -0.4 1 5
FOXO3 0.068 0.11 -10000 0 -0.63 4 4
KAT2B 0.033 0.018 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.055 0.42 2 -0.4 1 3
CAT 0.065 0.13 0.54 1 -0.97 4 5
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.034 0.019 -10000 0 -10000 0 0
FOXO1 0.018 0.082 0.44 12 -10000 0 12
MAPK10 0.033 0.033 0.2 3 -0.41 1 4
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.071 0.089 0.5 11 -0.51 3 14
response to oxidative stress 0.011 0.011 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.084 0.088 -10000 0 -0.66 3 3
XPO1 0.027 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.027 0.1 -10000 0 -0.67 8 8
FOXO1/SKP2 0.015 0.055 -10000 0 -0.44 3 3
mol:GDP 0.011 0.011 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.099 0.094 0.46 7 -0.55 4 11
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.11 -10000 0 -0.5 7 7
MST1 0.031 0.037 -10000 0 -0.67 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.007 0.12 -10000 0 -0.57 10 10
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.058 -10000 0 -0.39 7 7
MAPK9 0.031 0.017 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.025 0.037 -10000 0 -0.67 1 1
SOD2 0.1 0.11 0.61 9 -0.62 2 11
RBL2 0.077 0.16 0.57 1 -0.97 6 7
RAL/GDP 0.046 0.014 -10000 0 -10000 0 0
CHUK 0.032 0.018 -10000 0 -10000 0 0
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
RAL/GTP 0.05 0.015 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.059 0.36 -10000 0 -1.3 35 35
SKP2 0.022 0.055 -10000 0 -0.68 3 3
USP7 0.027 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.018 -10000 0 -10000 0 0
CCNB1 0.072 0.11 0.58 3 -0.63 2 5
FOXO1-3a-4/beta catenin 0.1 0.098 0.45 6 -0.42 4 10
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.055 -10000 0 -0.43 3 3
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.017 0.11 -10000 0 -0.67 11 11
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.01 -10000 0 -10000 0 0
ZFAND5 0.078 0.11 0.57 15 -0.44 2 17
SFN -0.083 0.12 -10000 0 -0.68 13 13
CDK2 0.027 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.009 0.11 -10000 0 -0.53 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.068 0.11 0.56 2 -0.6 3 5
BCL6 0.084 0.12 0.53 2 -0.78 5 7
RALB 0.028 0.005 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.037 0.013 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.005 0.11 -10000 0 -0.44 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.04 -10000 0 -10000 0 0
NFKBIA 0.014 0.029 -10000 0 -0.24 5 5
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.016 0.005 -10000 0 -10000 0 0
REL -0.015 0.16 -10000 0 -0.66 29 29
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.007 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
NF kappa B1 p50 dimer 0.025 0.023 0.25 5 -10000 0 5
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.02 0.041 -10000 0 -0.31 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.041 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.044 -10000 0 -0.51 3 3
NF kappa B1 p50/RelA 0.02 0.041 -10000 0 -0.31 6 6
IKBKB 0.027 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.039 -10000 0 -10000 0 0
cell death 0.038 0.039 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.005 0.11 -10000 0 -0.44 28 28
LCK 0.012 0.083 -10000 0 -0.68 6 6
BCL3 0.025 0.01 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.028 0.042 0.29 3 -0.38 3 6
adherens junction organization 0.02 0.043 0.25 4 -0.3 1 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.037 0.051 -10000 0 -0.41 3 3
FMN1 0.009 0.08 -10000 0 -0.34 22 22
mol:IP3 0.027 0.033 -10000 0 -0.33 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.026 -10000 0 -0.29 1 1
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.037 0.25 1 -0.33 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.035 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.033 -10000 0 -0.39 2 2
VASP 0.024 0.023 -10000 0 -0.28 1 1
ZYX 0.025 0.025 -10000 0 -0.28 1 1
JUB 0.024 0.025 -10000 0 -0.28 1 1
EGFR(dimer) 0.039 0.048 -10000 0 -0.35 5 5
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.04 -10000 0 -0.34 3 3
PIK3CA 0.024 0.056 -10000 0 -0.68 3 3
PI3K 0.049 0.041 -10000 0 -0.35 3 3
FYN 0.026 0.037 0.29 3 -10000 0 3
mol:Ca2+ 0.027 0.033 -10000 0 -0.32 3 3
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.027 0.033 -10000 0 -0.33 3 3
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.037 0.051 -10000 0 -0.36 6 6
establishment of polarity of embryonic epithelium 0.024 0.023 -10000 0 -0.28 1 1
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.021 0.064 -10000 0 -0.68 4 4
CASR 0.018 0.032 -10000 0 -0.32 3 3
RhoA/GTP 0.039 0.033 -10000 0 -0.3 3 3
AKT2 0.031 0.034 -10000 0 -0.32 3 3
actin cable formation 0.007 0.076 -10000 0 -0.34 21 21
apoptosis -0.029 0.044 0.36 3 -0.32 4 7
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.022 0.051 -10000 0 -0.39 6 6
PIP5K1A 0.023 0.034 -10000 0 -0.4 2 2
PLCG1 0.027 0.034 -10000 0 -0.34 3 3
Rac1/GTP 0.048 0.047 -10000 0 -0.34 4 4
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0.019 0.03 -10000 0 -0.32 3 3
TRAF2/ASK1 0.032 0.025 -10000 0 -0.44 1 1
ATM 0.025 0.032 -10000 0 -0.68 1 1
MAP2K3 0.036 0.095 0.42 15 -0.38 3 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.095 0.34 14 -0.41 6 20
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.085 -10000 0 -0.68 7 7
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.005 0.12 -10000 0 -0.63 15 15
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
MAP3K6 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.003 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.026 -10000 0 -0.51 1 1
TAK1/TAB family 0.011 0.032 -10000 0 -0.19 3 3
RAC1/OSM/MEKK3 0.049 0.015 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.037 0.056 -10000 0 -0.33 2 2
TRAF6 0.007 0.026 -10000 0 -0.4 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.021 0.064 -10000 0 -0.68 4 4
CCM2 0.026 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.031 0.044 -10000 0 -0.44 4 4
MAPK11 0.02 0.012 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.045 0.053 -10000 0 -0.5 4 4
OSM/MEKK3 0.037 0.012 -10000 0 -10000 0 0
TAOK1 -0.029 0.13 -10000 0 -0.4 52 52
TAOK2 0.015 0.019 -10000 0 -0.39 1 1
TAOK3 0.016 0.019 -10000 0 -0.39 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.68 1 1
MAP3K10 0.026 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.016 0.037 -10000 0 -0.43 1 1
GADD45/MTK1/MTK1 0.036 0.093 -10000 0 -0.4 18 18
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.027 0.004 -9999 0 -10000 0 0
SMAD2 -0.016 0.044 -9999 0 -0.24 1 1
SMAD3 0.021 0.016 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.052 -9999 0 -0.43 5 5
SMAD4/Ubc9/PIASy 0.049 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.063 -9999 0 -0.42 1 1
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.003 0.054 -9999 0 -0.34 2 2
MAP3K1 0.026 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.01 0.12 -9999 0 -0.49 27 27
MAPK3 0.026 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.025 0.008 -9999 0 -10000 0 0
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
CTDSPL 0.027 0.004 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.012 0.16 -9999 0 -0.66 27 27
UBE2I 0.026 0.007 -9999 0 -10000 0 0
NUP153 0.026 0.032 -9999 0 -0.68 1 1
KPNA2 0.026 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.008 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.055 -10000 0 -0.68 3 3
ITGA4 0.021 0.05 -10000 0 -0.68 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.087 -10000 0 -0.49 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.036 -10000 0 -0.44 2 2
alpha4/beta7 Integrin/Paxillin 0.034 0.069 -10000 0 -0.4 11 11
lamellipodium assembly 0.024 0.066 -10000 0 -0.53 5 5
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PI3K 0.036 0.044 -10000 0 -0.51 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.025 0.008 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.053 0.03 -10000 0 -0.35 1 1
cell adhesion 0.051 0.036 -10000 0 -0.37 2 2
CRKL/CBL 0.03 0.018 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.043 0.033 -10000 0 -0.4 2 2
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.007 0.1 -10000 0 -0.64 10 10
ARF6/GDP 0.024 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.064 -10000 0 -0.43 7 7
p130Cas/Crk/Dock1 0.048 0.042 -10000 0 -0.44 3 3
VCAM1 0.016 0.079 -10000 0 -0.68 6 6
alpha4/beta1 Integrin/Paxillin/Talin 0.053 0.036 -10000 0 -0.37 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.056 0.032 -10000 0 -0.38 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.054 0.031 0.38 1 -10000 0 1
CBL 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.053 0.036 -10000 0 -0.37 2 2
Rac1/GTP 0.025 0.075 -10000 0 -0.61 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.03 -9999 0 -0.39 1 1
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.012 -9999 0 -10000 0 0
GATA2/HDAC5 0.038 0.01 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.028 -9999 0 -0.44 1 1
HDAC9 0.012 0.044 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.017 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.039 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.038 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -9999 0 -10000 0 0
GATA2 0.027 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.037 0.014 -9999 0 -10000 0 0
BCOR 0.025 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.012 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.027 -9999 0 -0.51 1 1
Histones 0.008 0.048 -9999 0 -10000 0 0
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.027 0.005 -9999 0 -10000 0 0
HDAC6 0.025 0.007 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.015 -9999 0 -10000 0 0
CAMK4 0.013 0.086 -9999 0 -0.68 7 7
Tubulin/HDAC6 0.047 0.049 -9999 0 -0.4 5 5
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.005 -9999 0 -10000 0 0
GATA1 0.012 0.02 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.007 -9999 0 -10000 0 0
NR3C1 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.059 -9999 0 -0.3 2 2
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.034 0.056 -9999 0 -0.51 5 5
HDAC4/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.005 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.037 0.027 -9999 0 -0.51 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.046 0.061 -9999 0 -0.44 7 7
HDAC4/ER alpha 0.006 0.12 -9999 0 -0.49 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.048 -9999 0 -10000 0 0
cell motility 0.046 0.049 -9999 0 -0.4 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.026 0.032 -9999 0 -0.68 1 1
HDAC4/CaMK II delta B 0.027 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.012 -9999 0 -10000 0 0
ESR1 -0.016 0.15 -9999 0 -0.65 24 24
HDAC6/HDAC11 0.038 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.052 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
MEF2C 0.025 0.032 -9999 0 -0.68 1 1
RAN 0.027 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.074 0.031 -9999 0 -0.38 1 1
GNG2 0.025 0.032 -9999 0 -0.68 1 1
NCOR2 0.027 0.005 -9999 0 -10000 0 0
TUBB2A 0.02 0.071 -9999 0 -0.68 5 5
HDAC11 0.027 0.004 -9999 0 -10000 0 0
HSP90AA1 0.027 0.005 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
ANKRA2 0.026 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.012 -9999 0 -10000 0 0
nuclear import -0.036 0.012 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.029 0.024 -10000 0 -10000 0 0
BIRC5 0.013 0.05 -10000 0 -0.68 1 1
NFKBIA 0.014 0.021 0.25 3 -10000 0 3
CPEB1 -0.021 0.17 -10000 0 -0.65 34 34
AKT1 0.015 0.024 0.25 4 -10000 0 4
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.027 0.02 -10000 0 -10000 0 0
NDEL1/TACC3 0.043 0.023 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.029 0.025 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.027 -10000 0 -10000 0 0
TP53 0.025 0.011 -10000 0 -10000 0 0
DLG7 0.012 0.009 -10000 0 -10000 0 0
AURKAIP1 0.026 0.011 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.046 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.026 0.02 -10000 0 -10000 0 0
AURKA 0.02 0.013 -10000 0 -10000 0 0
AURKB 0.013 0.021 -10000 0 -0.16 3 3
CDC25B 0.021 0.01 -10000 0 -10000 0 0
G2/M transition checkpoint 0.009 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.001 0.11 -10000 0 -0.4 30 30
Aurora A/CPEB -0.001 0.11 -10000 0 -0.41 30 30
Aurora A/TACC1/TRAP/chTOG 0.054 0.039 -10000 0 -0.38 1 1
BRCA1 0.026 0.007 -10000 0 -10000 0 0
centrosome duplication 0.029 0.024 -10000 0 -10000 0 0
regulation of centrosome cycle 0.042 0.023 -10000 0 -10000 0 0
spindle assembly 0.052 0.038 -10000 0 -0.37 1 1
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.055 0.034 -10000 0 -0.36 1 1
CENPA 0.017 0.026 -10000 0 -0.25 4 4
Aurora A/PP2A 0.03 0.024 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.021 0.017 -10000 0 -10000 0 0
negative regulation of DNA binding 0.025 0.011 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.009 0.018 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.013 -10000 0 -10000 0 0
TACC1 0.026 0.032 -10000 0 -0.68 1 1
TACC3 0.026 0.008 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.046 0.02 -10000 0 -10000 0 0
Aurora A/RasGAP 0.029 0.024 -10000 0 -10000 0 0
OAZ1 0.025 0.008 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.01 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.017 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.027 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.017 0.029 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
TRAIL signaling 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
TNFSF10 0.024 0.046 -10000 0 -0.68 2 2
positive regulation of NF-kappaB transcription factor activity 0.037 0.036 -10000 0 -0.51 2 2
MAP2K4 0.027 0.047 -10000 0 -0.44 1 1
IKBKB 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.004 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.055 -10000 0 -0.68 3 3
SMPD1 0.015 0.028 -10000 0 -0.4 2 2
IKBKG 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.036 -10000 0 -0.51 2 2
TRAIL/TRAILR3 0.005 0.062 -10000 0 -0.51 2 2
TRAIL/TRAILR1 0.034 0.056 -10000 0 -0.51 5 5
TRAIL/TRAILR4 0.037 0.036 -10000 0 -0.51 2 2
TRAIL/TRAILR1/DAP3/GTP 0.043 0.049 -10000 0 -0.4 5 5
IKK complex 0.024 0.053 -10000 0 -0.4 2 2
RIPK1 0.027 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.006 -10000 0 -10000 0 0
MAPK3 0.014 0.034 -10000 0 -0.51 2 2
MAP3K1 0.027 0.049 -10000 0 -0.38 4 4
TRAILR4 (trimer) 0.027 0.004 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.055 -10000 0 -0.68 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.041 -10000 0 -0.34 5 5
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.011 0.034 -10000 0 -0.5 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.072 0.051 -10000 0 -0.38 5 5
mol:ceramide 0.015 0.028 -10000 0 -0.39 2 2
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.017 0.069 0.28 1 -0.37 8 9
TRAF2 0.025 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.067 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.048 0.051 -10000 0 -0.44 5 5
DAP3 0.025 0.007 -10000 0 -10000 0 0
CASP10 0.011 0.036 -10000 0 -0.43 2 2
JNK cascade 0.037 0.036 -10000 0 -0.51 2 2
TRAIL (trimer) 0.024 0.046 -10000 0 -0.68 2 2
TNFRSF10C -0.014 0.067 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.054 0.049 -10000 0 -0.38 5 5
TRAIL/TRAILR2/FADD 0.051 0.034 -10000 0 -0.43 2 2
cell death 0.015 0.028 -10000 0 -0.39 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.033 -10000 0 -0.42 2 2
TRAILR2 (trimer) 0.027 0.004 -10000 0 -10000 0 0
CASP8 0.012 0.03 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.075 0.036 -10000 0 -0.37 2 2
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.03 0.032 -10000 0 -10000 0 0
KLHL20 0.013 0.052 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.043 0.27 2 -10000 0 2
ENAH 0.027 0.03 -10000 0 -10000 0 0
AP1M1 0.025 0.008 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.016 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.067 -10000 0 -0.4 9 9
RAPGEF1 0.026 0.036 0.27 1 -10000 0 1
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.032 0.036 -10000 0 -0.3 1 1
CRK 0.026 0.029 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.017 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.023 0.077 -10000 0 -0.51 9 9
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
DLG1 0.029 0.035 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.054 0.031 -10000 0 -0.4 1 1
PI3K 0.016 0.022 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.037 0.012 -10000 0 -10000 0 0
TIAM1 -0.058 0.079 -10000 0 -0.68 1 1
E-cadherin(dimer)/Ca2+ 0.061 0.018 -10000 0 -10000 0 0
AKT1 0.018 0.021 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.047 0.074 0.45 9 -10000 0 9
actin cytoskeleton organization 0.012 0.042 0.19 3 -10000 0 3
CDC42/GDP 0.047 0.081 0.5 10 -10000 0 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.008 -10000 0 -10000 0 0
ITGB7 0.007 0.1 -10000 0 -0.64 10 10
RAC1 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.012 -10000 0 -10000 0 0
mol:GDP 0.038 0.087 0.51 11 -10000 0 11
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.045 0.045 0.28 1 -10000 0 1
RAC1/GTP/IQGAP1 0.035 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.037 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.036 0.21 4 -10000 0 4
NME1 0.026 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.029 0.035 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.025 0.012 -10000 0 -10000 0 0
WASF2 0.007 0.022 -10000 0 -10000 0 0
Rap1/GTP 0.042 0.027 0.24 2 -10000 0 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.065 0.067 -10000 0 -0.38 9 9
CCND1 0.012 0.039 0.2 3 -10000 0 3
VAV2 0.005 0.14 -10000 0 -0.51 32 32
RAP1/GDP 0.048 0.039 0.3 5 -10000 0 5
adherens junction assembly 0.029 0.035 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.063 -10000 0 -0.37 9 9
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.03 0.032 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
Rac1/GTP -0.006 0.077 -10000 0 -0.31 12 12
E-cadherin/beta catenin/alpha catenin 0.052 0.014 -10000 0 -10000 0 0
ITGAE 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.032 0.037 -10000 0 -0.31 1 1
Arf6 trafficking events

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
SLC2A4 -0.001 0.13 -10000 0 -0.66 18 18
CLTC 0.028 0.021 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.015 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.01 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
CD59 0.022 0.011 -10000 0 -10000 0 0
CPE 0.009 0.058 -10000 0 -0.44 8 8
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
membrane fusion 0.018 0.006 -10000 0 -10000 0 0
CTNND1 0.022 0.036 0.36 3 -10000 0 3
DNM2 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.03 0.24 1 -10000 0 1
TSHR 0.015 0.03 -10000 0 -0.44 2 2
INS 0.009 0.06 -10000 0 -0.43 8 8
BIN1 0.027 0.004 -10000 0 -10000 0 0
mol:Choline 0.018 0.006 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.01 -10000 0 -10000 0 0
JUP 0.021 0.009 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.05 0.023 -10000 0 -0.4 1 1
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.009 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.027 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0.013 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.046 0.024 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.01 -10000 0 -10000 0 0
ACAP1 0.023 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.01 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.029 0.024 -10000 0 -10000 0 0
JIP4/KLC1 0.049 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.013 -10000 0 -10000 0 0
RALA/GTP 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.02 0.028 0.36 1 -10000 0 1
NME1 0.016 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.036 0.34 3 -10000 0 3
IL2RA 0.008 0.055 -10000 0 -10000 0 0
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.025 0.068 -10000 0 -0.32 17 17
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.005 -10000 0 -10000 0 0
PLD2 0.018 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.049 0.026 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.018 0.006 -10000 0 -10000 0 0
endocytosis -0.048 0.023 0.4 1 -10000 0 1
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 0.028 0.085 0.44 8 -0.34 10 18
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ASAP2 0.025 0.032 -10000 0 -0.68 1 1
Dynamin 2/GDP 0.03 0.011 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.028 0.079 0.48 6 -0.34 9 15
RALA 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.025 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.025 0.016 -9999 0 -9999 0 0
PLK4 0.027 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.016 0.01 -9999 0 -9999 0 0
Arf6 downstream 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
PLAUR -0.002 0.04 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.021 0.27 2 -10000 0 2
myoblast fusion -0.011 0.028 -10000 0 -10000 0 0
mol:GTP 0.009 0.018 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.025 0.063 0.42 1 -10000 0 1
ARF1/GTP 0.03 0.013 -10000 0 -10000 0 0
mol:GM1 0.005 0.011 -10000 0 -10000 0 0
mol:Choline 0.009 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.027 -10000 0 -10000 0 0
MAPK3 0.009 0.026 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.026 0.063 -10000 0 -0.42 1 1
ARF1 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.028 -10000 0 -10000 0 0
ARF1/GDP 0.021 0.029 -10000 0 -10000 0 0
ARF6 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.059 0.08 -10000 0 -0.68 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.024 0.029 -10000 0 -10000 0 0
KALRN 0.009 0.02 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.03 -10000 0 -10000 0 0
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.026 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.018 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.015 0.027 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.009 0.018 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.018 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.009 0.02 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.013 0.017 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.015 0.027 -10000 0 -10000 0 0
ruffle organization 0.012 0.021 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.009 0.018 -10000 0 -10000 0 0
PLD2 0.012 0.017 -10000 0 -10000 0 0
PIP5K1A 0.012 0.021 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.009 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.027 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.019 0.069 -9999 0 -9999 0 0
GPC2 0.016 0.037 -9999 0 -9999 0 0
GPC2/Midkine -0.003 0.059 -9999 0 -9999 0 0
neuron projection morphogenesis -0.003 0.058 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.001 0.013 -9999 0 -10000 0 0
MDM2/SUMO1 0.015 0.055 -9999 0 -0.31 1 1
HDAC4 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.001 0.013 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.006 0.038 -9999 0 -0.24 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.012 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.059 -9999 0 -0.3 2 2
SUMO1/HDAC1 0.014 0.057 -9999 0 -0.31 1 1
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.006 0.047 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.045 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
PIAS2 0.027 0.004 -9999 0 -10000 0 0
PIAS1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.009 -9999 0 -9999 0 0
CTNNB1 0.027 0.004 -9999 0 -9999 0 0
JUP 0.026 0.007 -9999 0 -9999 0 0
CDH1 0.026 0.006 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.017 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0.035 0.2 1 -0.19 3 4
AP2 0.037 0.012 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.036 0.011 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.022 0.026 -10000 0 -10000 0 0
CLTA 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.025 -10000 0 -0.37 2 2
ARF1/GTP 0.028 0.02 -10000 0 -0.2 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.007 -10000 0 -10000 0 0
mol:Choline 0.006 0.024 -10000 0 -0.37 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.028 -10000 0 -0.37 2 2
ARF1/GDP 0.005 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.015 -10000 0 -10000 0 0
ARFIP2 0.022 0.013 -10000 0 -10000 0 0
COPA 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.034 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.017 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.023 -10000 0 -0.28 1 1
AP2A1 0.025 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.009 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.025 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.034 0.011 -10000 0 -10000 0 0
CYTH2 0.028 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -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 0.024 0.025 -10000 0 -10000 0 0
PLD2 0.006 0.024 -10000 0 -0.37 2 2
ARF-GAP1/v-SNARE 0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.006 0.025 -10000 0 -0.37 2 2
ARF1/GTP/Membrin/GBF1/p115 0.023 0.02 -10000 0 -0.2 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.024 -10000 0 -0.37 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.014 0.013 -10000 0 -10000 0 0
USO1 0.014 0.013 -10000 0 -10000 0 0
GBF1 0.013 0.024 -10000 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.035 0.014 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.051 0.017 -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 0.038 0.011 -9999 0 -9999 0 0
FBXW11 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.072 0.027 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.026 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 483 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N9 TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU
109_MAP3K5 -0.2 0.026 0.026 0.026
47_PPARGC1A -0.68 -0.68 -0.68 0.028
105_BMP4 0.028 -0.12 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR -0.4 -0.4 -0.4 -0.4
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.04 -0.05 0.032 -0.048
84_STAT5A 0.04 -0.05 0.032 -0.048
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/3353350/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/THCA-TP/3472009/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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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