PARADIGM pathway analysis of mRNASeq expression and copy number data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1S46QXN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1S46QXN
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 57 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
Aurora B signaling 178
Endothelins 123
Aurora C signaling 120
Signaling events regulated by Ret tyrosine kinase 107
Angiopoietin receptor Tie2-mediated signaling 103
p75(NTR)-mediated signaling 99
FOXM1 transcription factor network 94
PDGFR-alpha signaling pathway 86
HIF-1-alpha transcription factor network 81
Integrins in angiogenesis 77
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 538 . 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 ( 538 ).

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
Aurora B signaling 0.3309 178 11934 67 -0.29 0.37 1000 -1000 -0.027 -1000
Endothelins 0.2286 123 11861 96 -0.4 0.16 1000 -1000 -0.033 -1000
Aurora C signaling 0.2230 120 843 7 0 0.23 1000 -1000 -0.009 -1000
Signaling events regulated by Ret tyrosine kinase 0.1989 107 8807 82 -0.14 0.037 1000 -1000 -0.038 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1914 103 9142 88 -0.3 0.11 1000 -1000 -0.052 -1000
p75(NTR)-mediated signaling 0.1840 99 12398 125 -0.16 0.074 1000 -1000 -0.042 -1000
FOXM1 transcription factor network 0.1747 94 4814 51 -0.29 0.27 1000 -1000 -0.08 -1000
PDGFR-alpha signaling pathway 0.1599 86 3822 44 -0.28 0.037 1000 -1000 -0.027 -1000
HIF-1-alpha transcription factor network 0.1506 81 6161 76 -0.25 0.044 1000 -1000 -0.029 -1000
Integrins in angiogenesis 0.1431 77 6550 84 -0.26 0.096 1000 -1000 -0.027 -1000
PLK1 signaling events 0.1413 76 6491 85 -0.056 0.25 1000 -1000 -0.031 -1000
Reelin signaling pathway 0.1413 76 4257 56 -0.12 0.045 1000 -1000 -0.018 -1000
Signaling events mediated by the Hedgehog family 0.1375 74 3875 52 -0.2 0.11 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 0.1283 69 2724 39 -0.093 0.053 1000 -1000 -0.016 -1000
S1P3 pathway 0.1190 64 2698 42 -0.39 0.031 1000 -1000 -0.022 -1000
Nongenotropic Androgen signaling 0.1115 60 3158 52 -0.23 0.14 1000 -1000 -0.024 -1000
Aurora A signaling 0.1078 58 3502 60 -0.14 0.22 1000 -1000 -0.014 -1000
Fc-epsilon receptor I signaling in mast cells 0.1078 58 5658 97 -0.096 0.024 1000 -1000 -0.036 -1000
Effects of Botulinum toxin 0.1059 57 1497 26 -0.1 0.11 1000 -1000 -0.009 -1000
Wnt signaling 0.1041 56 392 7 -0.066 0.037 1000 -1000 -0.003 -1000
IGF1 pathway 0.1004 54 3133 57 -0.076 0.035 1000 -1000 -0.019 -1000
Signaling mediated by p38-alpha and p38-beta 0.0948 51 2260 44 -0.075 0.023 1000 -1000 -0.014 -1000
TCGA08_p53 0.0929 50 354 7 -0.033 0.019 1000 -1000 -0.01 -1000
Ephrin B reverse signaling 0.0911 49 2365 48 -0.092 0.028 1000 -1000 -0.024 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0911 49 5937 120 -0.15 0.12 1000 -1000 -0.031 -1000
FOXA2 and FOXA3 transcription factor networks 0.0892 48 2234 46 -0.2 0.19 1000 -1000 -0.066 -1000
Noncanonical Wnt signaling pathway 0.0874 47 1241 26 -0.12 0.037 1000 -1000 -0.024 -1000
Glypican 1 network 0.0874 47 2294 48 -0.17 0.1 1000 -1000 -0.021 -1000
LPA4-mediated signaling events 0.0836 45 546 12 -0.11 0 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 0.0836 45 4747 105 -0.13 0.047 1000 -1000 -0.03 -1000
TCGA08_retinoblastoma 0.0836 45 364 8 -0.04 0.13 1000 -1000 -0.002 -1000
Syndecan-1-mediated signaling events 0.0799 43 1485 34 -0.049 0.16 1000 -1000 -0.017 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0799 43 2990 68 -0.15 0.074 1000 -1000 -0.05 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0762 41 1400 34 -0.017 0.029 1000 -1000 -0.027 -1000
BMP receptor signaling 0.0743 40 3285 81 -0.23 0.043 1000 -1000 -0.02 -1000
Plasma membrane estrogen receptor signaling 0.0725 39 3395 86 -0.19 0.08 1000 -1000 -0.035 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0725 39 3058 78 -0.13 0.055 1000 -1000 -0.048 -1000
amb2 Integrin signaling 0.0706 38 3152 82 -0.1 0.13 1000 -1000 -0.022 -1000
Ephrin A reverse signaling 0.0669 36 257 7 -0.027 0.012 1000 -1000 -0.008 -1000
LPA receptor mediated events 0.0669 36 3714 102 -0.13 0.13 1000 -1000 -0.056 -1000
Osteopontin-mediated events 0.0632 34 1309 38 -0.089 0.097 1000 -1000 -0.02 -1000
S1P4 pathway 0.0632 34 858 25 -0.065 0.038 1000 -1000 -0.013 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0613 33 2813 85 -0.21 0.031 1000 -1000 -0.039 -1000
Ras signaling in the CD4+ TCR pathway 0.0613 33 566 17 -0.091 0.023 1000 -1000 -0.016 -1000
S1P1 pathway 0.0595 32 1164 36 -0.15 0.022 1000 -1000 -0.02 -1000
EPHB forward signaling 0.0595 32 2800 85 -0.055 0.048 1000 -1000 -0.043 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0558 30 1620 54 -0.1 0.048 1000 -1000 -0.024 -1000
Arf6 signaling events 0.0558 30 1874 62 -0.063 0.043 1000 -1000 -0.022 -1000
IL4-mediated signaling events 0.0558 30 2793 91 -0.3 0.091 1000 -1000 -0.097 -1000
Visual signal transduction: Rods 0.0558 30 1569 52 -0.057 0.11 1000 -1000 -0.016 -1000
HIF-2-alpha transcription factor network 0.0539 29 1255 43 -0.16 0.075 1000 -1000 -0.038 -1000
Syndecan-4-mediated signaling events 0.0539 29 1993 67 -0.2 0.13 1000 -1000 -0.026 -1000
FAS signaling pathway (CD95) 0.0520 28 1338 47 -0.049 0.038 1000 -1000 -0.029 -1000
EGFR-dependent Endothelin signaling events 0.0520 28 603 21 -0.081 0.047 1000 -1000 -0.025 -1000
Glucocorticoid receptor regulatory network 0.0502 27 3152 114 -0.15 0.2 1000 -1000 -0.039 -1000
S1P5 pathway 0.0502 27 464 17 -0.065 0.036 1000 -1000 -0.005 -1000
Calcium signaling in the CD4+ TCR pathway 0.0502 27 858 31 -0.09 0.042 1000 -1000 -0.04 -1000
Glypican 2 network 0.0483 26 105 4 0.023 0.043 1000 -1000 0.018 -1000
Visual signal transduction: Cones 0.0465 25 956 38 -0.057 0.033 1000 -1000 -0.015 -1000
Syndecan-2-mediated signaling events 0.0465 25 1735 69 -0.01 0.1 1000 -1000 -0.029 -1000
Signaling events mediated by PTP1B 0.0465 25 1926 76 -0.088 0.037 1000 -1000 -0.032 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0465 25 1334 52 -0.056 0.047 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 0.0465 25 664 26 -0.096 0.032 1000 -1000 -0.008 -1000
Insulin Pathway 0.0465 25 1906 74 -0.095 0.11 1000 -1000 -0.031 -1000
Coregulation of Androgen receptor activity 0.0446 24 1888 76 -0.091 0.12 1000 -1000 -0.02 -1000
IL12-mediated signaling events 0.0446 24 2151 87 -0.3 0.06 1000 -1000 -0.053 -1000
Presenilin action in Notch and Wnt signaling 0.0446 24 1522 61 -0.088 0.083 1000 -1000 -0.032 -1000
TCR signaling in naïve CD8+ T cells 0.0446 24 2252 93 -0.014 0.053 1000 -1000 -0.044 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0446 24 3106 125 -0.055 0.044 1000 -1000 -0.02 -1000
Canonical Wnt signaling pathway 0.0409 22 1128 51 -0.046 0.083 1000 -1000 -0.03 -1000
IL2 signaling events mediated by STAT5 0.0409 22 498 22 -0.095 0.076 1000 -1000 -0.022 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0409 22 757 33 -0.12 0.13 1000 -1000 -0.02 -1000
Regulation of Androgen receptor activity 0.0409 22 1608 70 -0.037 0.19 1000 -1000 -0.039 -1000
EPO signaling pathway 0.0390 21 1192 55 -0.041 0.038 1000 -1000 -0.021 -1000
BARD1 signaling events 0.0372 20 1183 57 -0.045 0.13 1000 -1000 -0.036 -1000
Regulation of p38-alpha and p38-beta 0.0372 20 1101 54 -0.13 0.054 1000 -1000 -0.04 -1000
IL6-mediated signaling events 0.0372 20 1565 75 -0.088 0.09 1000 -1000 -0.036 -1000
BCR signaling pathway 0.0372 20 2076 99 -0.037 0.058 1000 -1000 -0.044 -1000
mTOR signaling pathway 0.0353 19 1021 53 -0.029 0.024 1000 -1000 -0.026 -1000
Class I PI3K signaling events mediated by Akt 0.0353 19 1342 68 -0.082 0.2 1000 -1000 -0.02 -1000
Hedgehog signaling events mediated by Gli proteins 0.0335 18 1202 65 -0.095 0.052 1000 -1000 -0.031 -1000
Nectin adhesion pathway 0.0335 18 1160 63 -0.039 0.054 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 0.0335 18 1044 58 -0.018 0.05 1000 -1000 -0.027 -1000
Rapid glucocorticoid signaling 0.0335 18 361 20 -0.031 0.026 1000 -1000 -0.009 -1000
Regulation of nuclear SMAD2/3 signaling 0.0316 17 2371 136 -0.088 0.14 1000 -1000 -0.037 -1000
IFN-gamma pathway 0.0316 17 1219 68 -0.18 0.073 1000 -1000 -0.033 -1000
Syndecan-3-mediated signaling events 0.0316 17 611 35 -0.059 0.095 1000 -1000 -0.009 -1000
Insulin-mediated glucose transport 0.0297 16 513 32 -0.084 0.2 1000 -1000 -0.018 -1000
Regulation of Telomerase 0.0297 16 1643 102 -0.24 0.086 1000 -1000 -0.032 -1000
ErbB2/ErbB3 signaling events 0.0279 15 1010 65 -0.076 0.047 1000 -1000 -0.045 -1000
Ceramide signaling pathway 0.0279 15 1160 76 -0.047 0.06 1000 -1000 -0.023 -1000
FoxO family signaling 0.0279 15 973 64 -0.016 0.2 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 0.0279 15 922 58 -0.031 0.12 1000 -1000 -0.026 -1000
IL23-mediated signaling events 0.0279 15 901 60 -0.007 0.23 1000 -1000 -0.069 -1000
PDGFR-beta signaling pathway 0.0279 15 1532 97 -0.021 0.049 1000 -1000 -0.029 -1000
E-cadherin signaling in keratinocytes 0.0279 15 646 43 -0.009 0.038 1000 -1000 -0.013 -1000
JNK signaling in the CD4+ TCR pathway 0.0260 14 240 17 -0.045 0.056 1000 -1000 -0.03 -1000
IL1-mediated signaling events 0.0260 14 884 62 -0.014 0.067 1000 -1000 -0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0260 14 647 45 -0.005 0.058 1000 -1000 -0.034 -1000
ErbB4 signaling events 0.0242 13 915 69 -0.047 0.054 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0242 13 660 49 -0.009 0.054 1000 -1000 -0.018 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0242 13 1157 83 -0.023 0.2 1000 -1000 -0.017 -1000
Signaling events mediated by PRL 0.0242 13 472 34 -0.036 0.091 1000 -1000 -0.027 -1000
Caspase cascade in apoptosis 0.0223 12 915 74 -0.028 0.15 1000 -1000 -0.032 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0223 12 359 28 -0.065 0.041 1000 -1000 -0.016 -1000
IL27-mediated signaling events 0.0223 12 615 51 -0.031 0.038 1000 -1000 -0.034 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0204 11 843 74 -0.049 0.077 1000 -1000 -0.045 -1000
E-cadherin signaling in the nascent adherens junction 0.0204 11 859 76 -0.03 0.056 1000 -1000 -0.035 -1000
Canonical NF-kappaB pathway 0.0186 10 393 39 -0.007 0.053 1000 -1000 -0.014 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0186 10 376 37 -0.021 0.063 1000 -1000 -0.018 -1000
Class IB PI3K non-lipid kinase events 0.0186 10 30 3 -0.022 0.022 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class III 0.0167 9 398 40 -0.054 0.04 1000 -1000 -0.032 -1000
p38 MAPK signaling pathway 0.0149 8 379 44 -0.002 0.064 1000 -1000 -0.013 -1000
Signaling events mediated by HDAC Class II 0.0130 7 570 75 -0.031 0.045 1000 -1000 -0.019 -1000
Class I PI3K signaling events 0.0130 7 520 73 -0.023 0.042 1000 -1000 -0.024 -1000
Arf6 trafficking events 0.0130 7 506 71 -0.16 0.04 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class I 0.0093 5 526 104 -0.035 0.057 1000 -1000 -0.033 -1000
TRAIL signaling pathway 0.0074 4 237 48 -0.01 0.049 1000 -1000 -0.02 -1000
Signaling mediated by p38-gamma and p38-delta 0.0074 4 66 15 -0.011 0.022 1000 -1000 -0.02 -1000
Paxillin-dependent events mediated by a4b1 0.0074 4 177 36 -0.041 0.042 1000 -1000 -0.025 -1000
VEGFR1 specific signals 0.0074 4 265 56 -0.04 0.047 1000 -1000 -0.024 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0056 3 74 23 0.002 0.046 1000 -1000 -0.02 -1000
PLK2 and PLK4 events 0.0056 3 11 3 -0.01 0.025 1000 -1000 -0.012 -1000
Arf6 downstream pathway 0.0056 3 164 43 -0.037 0.041 1000 -1000 -0.025 -1000
Arf1 pathway 0.0056 3 181 54 -0.005 0.041 1000 -1000 -0.011 -1000
a4b1 and a4b7 Integrin signaling 0.0037 2 10 5 0.022 0.033 1000 -1000 0.015 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0037 2 62 27 -0.013 0.054 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 0.0019 1 53 31 -0.011 0.026 1000 -1000 -0.016 -1000
E-cadherin signaling events 0.0019 1 7 5 0.019 0.038 1000 -1000 0.017 -1000
Circadian rhythm pathway 0.0000 0 19 22 -0.006 0.048 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.059 1000 -1000 0 -1000
Total NA 4156 249700 7203 -12 10 131000 -131000 -3.4 -131000
Aurora B 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
Condensin I complex 0.13 0.093 0.19 280 -0.3 6 286
STMN1 0.088 0.045 0.11 304 -10000 0 304
Aurora B/RasGAP/Survivin 0.26 0.15 0.33 420 -0.16 7 427
Chromosomal passenger complex/Cul3 protein complex 0.077 0.099 0.17 194 -0.25 7 201
BIRC5 0.23 0.11 0.29 403 -10000 0 403
DES -0.29 0.25 -10000 0 -0.55 119 119
Aurora C/Aurora B/INCENP 0.16 0.084 0.2 409 -10000 0 409
Aurora B/TACC1 0.081 0.14 0.19 317 -0.2 84 401
Aurora B/PP2A 0.17 0.079 0.21 413 -10000 0 413
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.041 0.025 0.12 21 -10000 0 21
mitotic metaphase/anaphase transition -0.008 0.005 -10000 0 -10000 0 0
NDC80 0.097 0.075 0.12 421 -10000 0 421
Cul3 protein complex -0.003 0.099 -10000 0 -0.21 98 98
KIF2C 0.15 0.076 0.21 296 -10000 0 296
PEBP1 0.024 0.003 -10000 0 -10000 0 0
KIF20A 0.25 0.083 0.28 469 -10000 0 469
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.16 0.088 0.21 407 -0.23 5 412
SEPT1 0.021 0.017 -10000 0 -0.35 1 1
SMC2 0.022 0.012 0.28 1 -10000 0 1
SMC4 0.022 0.005 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.11 0.17 0.29 23 -0.42 41 64
PSMA3 0.022 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.005 -10000 0 -10000 0 0
H3F3B 0.09 0.048 0.22 16 -10000 0 16
AURKB 0.23 0.11 0.29 425 -10000 0 425
AURKC 0.024 0.02 0.28 3 -10000 0 3
CDCA8 0.18 0.13 0.29 306 -10000 0 306
cytokinesis 0.14 0.092 0.22 260 -0.3 1 261
Aurora B/Septin1 0.2 0.14 0.29 346 -0.27 7 353
AURKA 0.094 0.12 0.28 158 -10000 0 158
INCENP 0.03 0.006 -10000 0 -10000 0 0
KLHL13 -0.048 0.15 -10000 0 -0.35 101 101
BUB1 0.21 0.11 0.28 411 -10000 0 411
hSgo1/Aurora B/Survivin 0.36 0.19 0.43 443 -0.16 2 445
EVI5 0.03 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.16 0.088 0.23 219 -0.25 2 221
SGOL1 0.22 0.11 0.28 402 -10000 0 402
CENPA 0.18 0.11 0.24 370 -0.26 5 375
NCAPG 0.19 0.12 0.28 343 -10000 0 343
Aurora B/HC8 Proteasome 0.17 0.078 0.21 418 -10000 0 418
NCAPD2 0.022 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.17 0.076 0.21 421 -10000 0 421
RHOA 0.022 0.005 -10000 0 -10000 0 0
NCAPH 0.22 0.11 0.28 409 -10000 0 409
NPM1 0.087 0.12 0.24 4 -0.33 32 36
RASA1 0.019 0.036 -10000 0 -0.35 5 5
KLHL9 0.021 0.017 -10000 0 -0.35 1 1
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.17 0.077 0.21 418 -10000 0 418
PPP1CC 0.023 0.002 -10000 0 -10000 0 0
Centraspindlin 0.18 0.097 0.24 299 -0.27 2 301
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
NSUN2 0.098 0.1 0.26 19 -0.28 26 45
MYLK -0.079 0.16 0.22 7 -0.22 292 299
KIF23 0.041 0.054 0.29 23 -10000 0 23
VIM 0.092 0.073 0.19 50 -0.23 6 56
RACGAP1 0.031 0.018 0.3 2 -10000 0 2
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.089 0.12 0.23 1 -0.34 29 30
Chromosomal passenger complex 0.18 0.093 0.23 400 -0.28 3 403
Chromosomal passenger complex/EVI5 0.37 0.19 0.45 417 -10000 0 417
TACC1 -0.038 0.14 -10000 0 -0.35 84 84
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
CUL3 0.023 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.14 0.15 -10000 0 -0.3 195 195
PTK2B 0.02 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.2 0.31 -10000 0 -0.76 103 103
EDN1 -0.053 0.079 -10000 0 -0.21 65 65
EDN3 0.03 0.16 0.28 97 -0.35 55 152
EDN2 0.063 0.094 0.28 82 -10000 0 82
HRAS/GDP -0.19 0.22 -10000 0 -0.48 146 146
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.13 0.18 -10000 0 -0.39 131 131
ADCY4 -0.14 0.16 0.22 3 -0.31 186 189
ADCY5 -0.16 0.16 0.3 1 -0.32 210 211
ADCY6 -0.13 0.15 0.24 2 -0.31 175 177
ADCY7 -0.13 0.15 0.3 1 -0.31 174 175
ADCY1 -0.14 0.16 0.3 1 -0.32 174 175
ADCY2 -0.21 0.18 -10000 0 -0.35 271 271
ADCY3 -0.13 0.15 0.22 3 -0.31 176 179
ADCY8 -0.12 0.14 -10000 0 -0.31 154 154
ADCY9 -0.15 0.17 0.22 3 -0.34 195 198
arachidonic acid secretion -0.24 0.27 -10000 0 -0.5 225 225
ETB receptor/Endothelin-1/Gq/GTP -0.086 0.15 -10000 0 -0.29 146 146
GNAO1 -0.065 0.16 -10000 0 -0.35 123 123
HRAS 0.021 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.12 0.14 -10000 0 -0.29 170 170
ETA receptor/Endothelin-1/Gs/GTP -0.14 0.16 -10000 0 -0.3 203 203
mol:GTP -0.003 0.005 -10000 0 -10000 0 0
COL3A1 -0.14 0.17 -10000 0 -0.37 140 140
EDNRB -0.056 0.15 -10000 0 -0.35 110 110
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.16 0.19 -10000 0 -0.43 152 152
CYSLTR1 -0.14 0.16 -10000 0 -0.35 147 147
SLC9A1 -0.085 0.097 -10000 0 -0.22 140 140
mol:GDP -0.2 0.24 -10000 0 -0.51 149 149
SLC9A3 -0.19 0.32 -10000 0 -0.7 128 128
RAF1 -0.22 0.25 -10000 0 -0.48 207 207
JUN -0.18 0.28 -10000 0 -0.71 97 97
JAK2 -0.14 0.15 -10000 0 -0.31 191 191
mol:IP3 -0.13 0.19 -10000 0 -0.46 103 103
ETA receptor/Endothelin-1 -0.16 0.18 -10000 0 -0.35 201 201
PLCB1 0.013 0.031 -10000 0 -0.35 3 3
PLCB2 0.011 0.019 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.093 0.18 0.2 53 -0.29 202 255
FOS -0.33 0.39 -10000 0 -0.82 193 193
Gai/GDP -0.26 0.39 -10000 0 -0.78 180 180
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.19 0.22 -10000 0 -0.44 171 171
BCAR1 0.021 0.008 -10000 0 -10000 0 0
PRKCB1 -0.14 0.19 -10000 0 -0.43 113 113
GNAQ 0.008 0.026 -10000 0 -0.35 1 1
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
GNAL -0.031 0.13 -10000 0 -0.35 76 76
Gs family/GDP -0.2 0.22 -10000 0 -0.47 165 165
ETA receptor/Endothelin-1/Gq/GTP -0.14 0.19 -10000 0 -0.37 167 167
MAPK14 -0.084 0.14 0.2 2 -0.34 88 90
TRPC6 -0.21 0.34 -10000 0 -0.82 102 102
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.085 0.15 -10000 0 -0.35 91 91
ETB receptor/Endothelin-2 -0.006 0.13 0.21 55 -0.24 106 161
ETB receptor/Endothelin-3 -0.02 0.17 0.21 87 -0.28 135 222
ETB receptor/Endothelin-1 -0.077 0.12 -10000 0 -0.28 120 120
MAPK3 -0.32 0.37 -10000 0 -0.76 198 198
MAPK1 -0.32 0.37 -10000 0 -0.77 197 197
Rac1/GDP -0.19 0.22 -10000 0 -0.48 143 143
cAMP biosynthetic process -0.21 0.2 0.3 4 -0.41 216 220
MAPK8 -0.22 0.35 -10000 0 -0.81 110 110
SRC 0.022 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.1 0.15 -10000 0 -0.3 150 150
p130Cas/CRK/Src/PYK2 -0.2 0.26 -10000 0 -0.59 128 128
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.18 0.22 -10000 0 -0.48 142 142
COL1A2 -0.17 0.19 -10000 0 -0.4 173 173
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.08 0.16 0.2 37 -0.3 149 186
mol:DAG -0.14 0.2 -10000 0 -0.46 103 103
MAP2K2 -0.26 0.29 -10000 0 -0.59 209 209
MAP2K1 -0.26 0.29 -10000 0 -0.59 205 205
EDNRA -0.15 0.18 -10000 0 -0.39 176 176
positive regulation of muscle contraction -0.12 0.13 0.2 2 -0.27 168 170
Gq family/GDP -0.16 0.22 -10000 0 -0.48 134 134
HRAS/GTP -0.19 0.23 -10000 0 -0.5 146 146
PRKCH -0.14 0.19 0.21 2 -0.46 103 105
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.13 0.19 0.21 1 -0.45 103 104
PRKCB -0.14 0.19 -10000 0 -0.45 111 111
PRKCE -0.14 0.18 -10000 0 -0.45 102 102
PRKCD -0.13 0.19 0.21 1 -0.44 106 107
PRKCG -0.14 0.19 -10000 0 -0.44 110 110
regulation of vascular smooth muscle contraction -0.4 0.46 -10000 0 -0.97 193 193
PRKCQ -0.15 0.2 -10000 0 -0.44 122 122
PLA2G4A -0.26 0.3 -10000 0 -0.55 225 225
GNA14 -0.023 0.1 -10000 0 -0.35 46 46
GNA15 0.018 0.033 0.27 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.008 0.052 -10000 0 -0.35 10 10
Rac1/GTP -0.12 0.14 -10000 0 -0.29 174 174
MMP1 0.16 0.13 0.26 287 -10000 0 287
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.023 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.15 0.083 0.19 409 -10000 0 409
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.012 0.039 -10000 0 -0.34 6 6
AURKB 0.23 0.11 0.28 425 -10000 0 425
AURKC 0.024 0.02 0.28 3 -10000 0 3
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.019 0.06 -10000 0 -0.39 9 9
Crk/p130 Cas/Paxillin -0.12 0.13 -10000 0 -0.27 194 194
JUN -0.086 0.12 -10000 0 -0.38 32 32
HRAS 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.061 0.14 0.51 1 -0.2 236 237
RAP1A 0.023 0.002 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.017 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.06 0.14 0.51 1 -0.2 235 236
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.06 0.11 0.27 2 -0.19 228 230
RHOA 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.056 0.12 0.43 1 -0.18 236 237
GRB7 0.037 0.073 0.32 30 -0.35 2 32
RET51/GFRalpha1/GDNF -0.06 0.14 0.24 8 -0.2 230 238
MAPKKK cascade -0.079 0.13 0.32 1 -0.22 209 210
BCAR1 0.02 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.076 0.13 0.27 2 -0.21 247 249
lamellipodium assembly -0.11 0.13 -10000 0 -0.25 202 202
RET51/GFRalpha1/GDNF/SHC -0.048 0.13 0.25 6 -0.2 191 197
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
RET9/GFRalpha1/GDNF/SHC -0.046 0.1 0.31 1 -0.19 182 183
RET9/GFRalpha1/GDNF/Shank3 -0.062 0.11 0.27 2 -0.19 230 232
MAPK3 -0.075 0.11 0.32 12 -0.31 21 33
DOK1 0.023 0.003 -10000 0 -10000 0 0
DOK6 -0.046 0.14 -10000 0 -0.35 97 97
PXN 0.023 0.003 -10000 0 -10000 0 0
neurite development -0.087 0.12 0.3 11 -0.26 81 92
DOK5 -0.011 0.11 0.28 1 -0.35 47 48
GFRA1 -0.14 0.19 0.28 2 -0.35 238 240
MAPK8 -0.087 0.12 0.17 1 -0.22 147 148
HRAS/GTP -0.076 0.15 0.44 1 -0.23 228 229
tube development -0.057 0.11 0.22 7 -0.18 225 232
MAPK1 -0.075 0.11 0.25 21 -0.31 21 42
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.075 0.1 0.15 1 -0.19 224 225
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
PDLIM7 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.081 0.16 0.5 1 -0.23 258 259
SHC1 0.019 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.063 0.14 0.51 1 -0.2 236 237
RET51/GFRalpha1/GDNF/Dok5 -0.076 0.15 0.51 1 -0.23 243 244
PRKCA 0 0.087 -10000 0 -0.35 31 31
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
CREB1 -0.076 0.13 0.26 1 -0.24 182 183
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.1 0.19 2 -0.2 182 184
RET51/GFRalpha1/GDNF/Grb7 -0.054 0.15 0.26 18 -0.21 230 248
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.013 0.099 0.28 21 -0.35 28 49
DOK4 0.021 0.007 -10000 0 -10000 0 0
JNK cascade -0.085 0.12 -10000 0 -0.38 32 32
RET9/GFRalpha1/GDNF/FRS2 -0.061 0.11 0.27 2 -0.19 230 232
SHANK3 0.021 0.007 -10000 0 -10000 0 0
RASA1 0.019 0.036 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.06 0.098 0.19 2 -0.19 180 182
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.08 0.12 0.22 1 -0.21 223 224
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.083 0.13 0.22 1 -0.22 225 226
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.068 0.12 0.29 1 -0.22 186 187
PI3K -0.14 0.19 0.3 1 -0.36 201 202
SOS1 0.023 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.053 0.11 0.34 1 -0.18 225 226
GRB10 0.022 0.017 -10000 0 -0.35 1 1
activation of MAPKK activity -0.072 0.11 0.18 1 -0.3 29 30
RET51/GFRalpha1/GDNF/FRS2 -0.06 0.14 0.51 1 -0.2 235 236
GAB1 0.019 0.032 -10000 0 -0.35 4 4
IRS1 -0.012 0.11 -10000 0 -0.35 50 50
IRS2 -0.024 0.12 -10000 0 -0.35 66 66
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.07 0.13 0.19 5 -0.22 185 190
RET51/GFRalpha1/GDNF/PKC alpha -0.072 0.15 0.51 1 -0.22 244 245
GRB2 0.022 0.006 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GDNF 0.02 0.02 0.28 3 -10000 0 3
RAC1 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.077 0.15 0.51 1 -0.22 251 252
Rac1/GTP -0.12 0.16 0.25 1 -0.29 200 201
RET9/GFRalpha1/GDNF -0.074 0.12 0.27 2 -0.2 231 233
GFRalpha1/GDNF -0.091 0.14 0.3 2 -0.25 231 233
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.22 0.41 0.45 2 -0.81 164 166
NCK1/PAK1/Dok-R -0.13 0.18 -10000 0 -0.4 162 162
NCK1/Dok-R -0.26 0.48 -10000 0 -0.95 160 160
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
mol:beta2-estradiol 0.046 0.092 0.23 107 -10000 0 107
RELA 0.022 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.009 -10000 0 -10000 0 0
Rac/GDP 0.016 0.004 -10000 0 -10000 0 0
F2 0.078 0.13 0.28 141 -10000 0 141
TNIP2 0.022 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.23 0.46 -10000 0 -0.89 161 161
FN1 0.019 0.036 -10000 0 -0.35 5 5
PLD2 -0.28 0.49 -10000 0 -0.99 159 159
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GRB14 0.11 0.13 0.28 189 -0.35 3 192
ELK1 -0.26 0.44 -10000 0 -0.9 161 161
GRB7 0.037 0.073 0.32 30 -0.35 2 32
PAK1 0.022 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.24 0.48 -10000 0 -0.94 161 161
CDKN1A -0.14 0.29 0.47 1 -0.6 113 114
ITGA5 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.26 0.48 -10000 0 -0.95 161 161
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:NO -0.16 0.31 0.4 3 -0.61 164 167
PLG -0.29 0.49 -10000 0 -1 159 159
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.22 0.38 -10000 0 -0.78 164 164
GRB2 0.022 0.006 -10000 0 -10000 0 0
PIK3R1 0.018 0.037 -10000 0 -0.35 5 5
ANGPT2 -0.11 0.22 -10000 0 -0.57 60 60
BMX -0.3 0.5 -10000 0 -1 161 161
ANGPT1 -0.22 0.45 -10000 0 -1.1 107 107
tube development -0.16 0.32 0.58 1 -0.61 162 163
ANGPT4 0.006 0.042 0.28 2 -0.35 5 7
response to hypoxia -0.019 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.24 0.54 -10000 0 -1 161 161
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
FGF2 -0.17 0.18 -10000 0 -0.35 272 272
STAT5A (dimer) -0.18 0.36 -10000 0 -0.72 141 141
mol:L-citrulline -0.16 0.31 0.4 3 -0.61 164 167
AGTR1 -0.057 0.15 0.29 2 -0.35 112 114
MAPK14 -0.29 0.51 -10000 0 -1 164 164
Tie2/SHP2 -0.18 0.4 -10000 0 -1 96 96
TEK -0.2 0.44 -10000 0 -1.1 94 94
RPS6KB1 -0.21 0.4 0.39 1 -0.78 163 164
Angiotensin II/AT1 -0.037 0.1 0.21 2 -0.24 112 114
Tie2/Ang1/GRB2 -0.28 0.51 -10000 0 -1 162 162
MAPK3 -0.26 0.45 -10000 0 -0.91 159 159
MAPK1 -0.26 0.45 -10000 0 -0.92 159 159
Tie2/Ang1/GRB7 -0.27 0.52 -10000 0 -1 162 162
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.28 0.49 -10000 0 -0.99 161 161
PI3K -0.26 0.47 -10000 0 -0.93 164 164
FES -0.29 0.51 -10000 0 -1 164 164
Crk/Dok-R -0.26 0.48 -10000 0 -0.94 161 161
Tie2/Ang1/ABIN2 -0.28 0.51 -10000 0 -1 162 162
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.19 0.37 0.45 2 -0.73 164 166
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.2 0.4 0.52 2 -0.78 161 163
Tie2/Ang2 -0.23 0.43 0.44 1 -0.83 159 160
Tie2/Ang1 -0.3 0.54 -10000 0 -1.1 161 161
FOXO1 -0.19 0.37 0.46 2 -0.73 164 166
ELF1 -0.006 0.061 -10000 0 -0.38 4 4
ELF2 -0.28 0.49 -10000 0 -0.99 159 159
mol:Choline -0.27 0.46 -10000 0 -0.95 159 159
cell migration -0.069 0.1 -10000 0 -0.22 163 163
FYN -0.19 0.36 0.59 1 -0.7 161 162
DOK2 0.021 0.021 0.28 3 -10000 0 3
negative regulation of cell cycle -0.13 0.26 0.46 1 -0.54 117 118
ETS1 -0.032 0.11 -10000 0 -0.24 102 102
PXN -0.16 0.34 0.43 5 -0.65 161 166
ITGB1 0.022 0.004 -10000 0 -10000 0 0
NOS3 -0.18 0.35 0.43 2 -0.69 164 166
RAC1 0.022 0.005 -10000 0 -10000 0 0
TNF -0.005 0.14 0.28 55 -0.24 106 161
MAPKKK cascade -0.27 0.46 -10000 0 -0.95 159 159
RASA1 0.019 0.036 -10000 0 -0.35 5 5
Tie2/Ang1/Shc -0.28 0.5 -10000 0 -0.99 162 162
NCK1 0.021 0.023 -10000 0 -0.35 2 2
vasculogenesis -0.14 0.28 0.4 3 -0.54 164 167
mol:Phosphatidic acid -0.27 0.46 -10000 0 -0.95 159 159
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.16 0.31 0.4 3 -0.61 164 167
Rac1/GTP -0.19 0.37 -10000 0 -0.73 164 164
MMP2 -0.29 0.5 -10000 0 -1 159 159
p75(NTR)-mediated 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
Sortilin/TRAF6 0.033 0.008 -10000 0 -10000 0 0
Necdin/E2F1 -0.076 0.15 0.21 37 -0.24 231 268
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.057 0.15 -10000 0 -0.22 219 219
NGF (dimer)/p75(NTR)/BEX1 -0.12 0.19 0.2 3 -0.29 264 267
NT-4/5 (dimer)/p75(NTR) -0.052 0.14 0.22 19 -0.25 170 189
IKBKB 0.021 0.007 -10000 0 -10000 0 0
AKT1 -0.084 0.12 0.17 31 -0.22 197 228
IKBKG 0.023 0.004 -10000 0 -10000 0 0
BDNF 0.061 0.092 0.28 80 -10000 0 80
MGDIs/NGR/p75(NTR)/LINGO1 -0.037 0.12 0.2 6 -0.21 170 176
FURIN 0.022 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.019 0.14 0.2 67 -0.21 170 237
LINGO1 0.024 0.03 0.28 5 -0.35 1 6
Sortilin/TRAF6/NRIF 0.019 0.026 -10000 0 -0.17 6 6
proBDNF (dimer) 0.061 0.092 0.28 80 -10000 0 80
NTRK1 0.019 0.045 0.28 7 -0.35 4 11
RTN4R 0.021 0.017 -10000 0 -0.35 1 1
neuron apoptosis -0.077 0.15 -10000 0 -0.36 62 62
IRAK1 0.023 0.003 -10000 0 -10000 0 0
SHC1 -0.095 0.12 -10000 0 -0.25 188 188
ARHGDIA 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.11 0.18 -10000 0 -0.26 273 273
MAGEH1 -0.067 0.16 -10000 0 -0.35 128 128
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.16 0.18 -10000 0 -0.28 337 337
Mammalian IAPs/DIABLO 0.054 0.033 -10000 0 -0.19 7 7
proNGF (dimer) -0.056 0.15 -10000 0 -0.35 112 112
MAGED1 0.021 0.023 -10000 0 -0.35 2 2
APP 0.023 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.032 0.055 0.28 23 -0.35 1 24
ZNF274 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.072 0.13 -10000 0 -0.22 215 215
NGF -0.056 0.15 -10000 0 -0.35 112 112
cell cycle arrest -0.078 0.11 0.24 4 -0.3 58 62
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.083 0.14 -10000 0 -0.25 201 201
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.034 0.12 0.21 17 -0.21 169 186
NCSTN 0.019 0.009 -10000 0 -10000 0 0
mol:GTP -0.082 0.16 0.2 1 -0.25 224 225
PSENEN 0.022 0.005 -10000 0 -10000 0 0
mol:ceramide -0.1 0.12 0.18 3 -0.23 214 217
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.073 0.12 -10000 0 -0.33 65 65
p75(NTR)/beta APP -0.057 0.13 0.21 1 -0.24 170 171
BEX1 -0.05 0.15 0.28 2 -0.35 106 108
mol:GDP -0.11 0.13 -10000 0 -0.25 221 221
NGF (dimer) -0.017 0.14 -10000 0 -0.21 163 163
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.025 0.12 0.21 6 -0.19 169 175
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RAC1/GTP -0.066 0.13 0.18 1 -0.21 217 218
MYD88 0.022 0.004 -10000 0 -10000 0 0
CHUK 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.082 0.16 0.2 1 -0.25 224 225
RHOB 0.022 0.017 -10000 0 -0.35 1 1
RHOA 0.022 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.062 0.068 0.21 90 -10000 0 90
NT3 (dimer) 0.003 0.091 0.28 5 -0.35 31 36
TP53 -0.054 0.087 0.17 17 -10000 0 17
PRDM4 -0.1 0.12 0.18 3 -0.23 217 220
BDNF (dimer) 0.074 0.15 0.24 165 -0.19 75 240
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
SORT1 0.023 0.003 -10000 0 -10000 0 0
activation of caspase activity -0.059 0.14 -10000 0 -0.22 219 219
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.064 0.15 -10000 0 -0.23 216 216
RHOC 0.023 0.001 -10000 0 -10000 0 0
XIAP 0.023 0.001 -10000 0 -10000 0 0
MAPK10 -0.13 0.17 0.22 4 -0.33 185 189
DIABLO 0.023 0.003 -10000 0 -10000 0 0
SMPD2 -0.1 0.12 0.18 3 -0.23 214 217
APH1B 0.018 0.04 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.079 0.16 0.2 1 -0.26 217 218
PSEN1 0.022 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.068 0.14 0.21 5 -0.26 182 187
MAPK8 -0.099 0.14 0.23 5 -0.28 165 170
MAPK9 -0.1 0.14 0.23 5 -0.28 164 169
APAF1 0.023 0.002 -10000 0 -10000 0 0
NTF3 0.003 0.091 0.28 5 -0.35 31 36
NTF4 0.032 0.055 0.28 23 -0.35 1 24
NDN -0.15 0.18 -10000 0 -0.35 243 243
RAC1/GDP 0.016 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.055 0.14 -10000 0 -0.21 218 218
p75 CTF/Sortilin/TRAF6/NRIF 0.053 0.019 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.082 0.15 0.2 1 -0.25 224 225
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.001 0.13 -10000 0 -0.18 168 168
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.007 0.14 0.21 67 -0.19 169 236
PRKACB 0.019 0.039 -10000 0 -0.35 6 6
proBDNF (dimer)/p75 ECD 0.058 0.064 0.21 79 -10000 0 79
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.018 0.046 0.28 2 -0.35 7 9
BIRC2 0.022 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.16 0.16 -10000 0 -0.32 239 239
BAD -0.12 0.15 0.22 4 -0.31 177 181
RIPK2 0.021 0.007 -10000 0 -10000 0 0
NGFR -0.098 0.17 0.28 1 -0.35 171 172
CYCS -0.094 0.11 0.2 7 -0.22 201 208
ADAM17 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.062 0.15 -10000 0 -0.23 206 206
BCL2L11 -0.12 0.15 0.22 3 -0.31 179 182
BDNF (dimer)/p75(NTR) -0.036 0.15 0.21 67 -0.24 171 238
PI3K -0.065 0.14 0.21 1 -0.23 212 213
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.064 0.15 -10000 0 -0.23 216 216
NDNL2 0.022 0.005 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.1 0.17 0.21 1 -0.3 221 222
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.063 0.15 -10000 0 -0.23 215 215
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
PLG -0.006 0.11 0.28 9 -0.35 45 54
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.089 0.14 0.18 1 -0.26 206 207
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
NGFRAP1 0.019 0.039 -10000 0 -0.35 6 6
CASP3 -0.11 0.15 0.22 3 -0.29 180 183
E2F1 0.071 0.1 0.28 99 -10000 0 99
CASP9 0.022 0.005 -10000 0 -10000 0 0
IKK complex -0.057 0.14 -10000 0 -0.32 82 82
NGF (dimer)/TRKA -0.023 0.11 0.21 5 -0.24 100 105
MMP7 0.027 0.13 0.28 60 -0.35 35 95
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.055 0.15 -10000 0 -0.22 211 211
MMP3 0.066 0.097 0.28 92 -10000 0 92
APAF-1/Caspase 9 -0.093 0.09 -10000 0 -0.29 54 54
FOXM1 transcription factor network

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
NFATC3 0.2 0.4 0.79 72 -0.89 8 80
PLK1 0.18 0.18 0.5 15 -0.68 9 24
BIRC5 0.2 0.16 0.5 15 -0.93 3 18
HSPA1B 0.2 0.4 0.78 82 -0.9 8 90
MAP2K1 0.062 0.083 0.23 57 -10000 0 57
BRCA2 0.19 0.4 0.77 78 -0.96 10 88
FOXM1 0.22 0.45 0.83 99 -0.97 12 111
XRCC1 0.2 0.4 0.78 80 -0.9 8 88
FOXM1B/p19 -0.002 0.34 0.69 38 -0.86 21 59
Cyclin D1/CDK4 0.19 0.37 0.7 92 -0.82 9 101
CDC2 0.2 0.42 0.77 100 -0.88 12 112
TGFA 0.18 0.37 0.68 102 -0.79 10 112
SKP2 0.2 0.4 0.77 86 -0.87 9 95
CCNE1 0.14 0.14 0.3 214 -10000 0 214
CKS1B 0.2 0.4 0.72 103 -0.83 12 115
RB1 0.16 0.25 0.51 118 -0.67 5 123
FOXM1C/SP1 0.18 0.39 0.73 76 -0.92 12 88
AURKB 0.17 0.24 0.48 18 -0.75 22 40
CENPF 0.25 0.42 0.8 117 -0.89 8 125
CDK4 0.038 0.038 0.16 3 -10000 0 3
MYC 0.14 0.35 0.66 85 -0.86 9 94
CHEK2 0.063 0.086 0.23 64 -10000 0 64
ONECUT1 0.19 0.38 0.72 88 -0.84 10 98
CDKN2A 0.06 0.14 0.24 192 -0.14 30 222
LAMA4 0.14 0.48 0.77 81 -0.94 42 123
FOXM1B/HNF6 0.19 0.4 0.74 83 -0.94 10 93
FOS -0.026 0.61 0.78 78 -0.98 97 175
SP1 0.022 0.012 -10000 0 -0.15 1 1
CDC25B 0.2 0.4 0.77 83 -0.87 9 92
response to radiation 0.037 0.058 0.16 58 -10000 0 58
CENPB 0.2 0.4 0.77 84 -0.87 9 93
CENPA 0.25 0.41 0.78 116 -0.85 9 125
NEK2 0.27 0.42 0.8 119 -0.9 7 126
HIST1H2BA 0.2 0.4 0.77 80 -0.89 9 89
CCNA2 0.082 0.11 0.3 111 -10000 0 111
EP300 0.021 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.19 0.42 0.81 75 -0.98 10 85
CCNB2 0.25 0.41 0.78 110 -0.9 7 117
CCNB1 0.21 0.42 0.81 89 -0.9 10 99
ETV5 0.21 0.41 0.78 91 -0.93 8 99
ESR1 0.12 0.5 0.78 84 -0.93 42 126
CCND1 0.19 0.38 0.71 99 -0.83 9 108
GSK3A 0.051 0.068 0.19 54 -10000 0 54
Cyclin A-E1/CDK1-2 0.16 0.15 0.31 214 -10000 0 214
CDK2 0.029 0.026 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.05 0.075 0.19 81 -10000 0 81
FOXM1B/Cbp/p300 0.13 0.36 0.66 56 -0.92 10 66
GAS1 -0.29 0.62 0.79 72 -0.92 169 241
MMP2 0.16 0.45 0.77 80 -1.1 24 104
RB1/FOXM1C 0.18 0.37 0.68 105 -0.88 8 113
CREBBP 0.022 0.005 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.093 0.16 -10000 0 -0.36 139 139
PDGF/PDGFRA/CRKL -0.053 0.12 -10000 0 -0.25 137 137
positive regulation of JUN kinase activity -0.002 0.088 -10000 0 -0.19 91 91
CRKL 0.022 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.056 0.12 0.19 1 -0.25 137 138
AP1 -0.28 0.36 -10000 0 -0.81 163 163
mol:IP3 -0.084 0.11 -10000 0 -0.27 128 128
PLCG1 -0.084 0.11 -10000 0 -0.27 128 128
PDGF/PDGFRA/alphaV Integrin -0.054 0.12 -10000 0 -0.25 138 138
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.084 0.11 -10000 0 -0.27 128 128
CAV3 0.018 0.012 0.28 1 -10000 0 1
CAV1 -0.04 0.14 -10000 0 -0.35 89 89
SHC/Grb2/SOS1 -0.001 0.089 -10000 0 -0.19 91 91
PDGF/PDGFRA/Shf -0.057 0.12 -10000 0 -0.25 141 141
FOS -0.28 0.36 0.31 2 -0.8 162 164
JUN -0.043 0.042 -10000 0 -0.3 7 7
oligodendrocyte development -0.053 0.12 -10000 0 -0.25 138 138
GRB2 0.022 0.006 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:DAG -0.084 0.11 -10000 0 -0.27 128 128
PDGF/PDGFRA -0.093 0.16 -10000 0 -0.36 139 139
actin cytoskeleton reorganization -0.053 0.12 -10000 0 -0.25 137 137
SRF 0.005 0.02 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
PI3K -0.028 0.1 -10000 0 -0.21 113 113
PDGF/PDGFRA/Crk/C3G -0.035 0.1 -10000 0 -0.2 137 137
JAK1 -0.076 0.1 -10000 0 -0.25 136 136
ELK1/SRF -0.067 0.09 0.16 11 -0.22 119 130
SHB 0.022 0.004 -10000 0 -10000 0 0
SHF 0.018 0.04 -10000 0 -0.35 6 6
CSNK2A1 0.037 0.022 -10000 0 -10000 0 0
GO:0007205 -0.089 0.12 -10000 0 -0.3 129 129
SOS1 0.023 0.003 -10000 0 -10000 0 0
Ras protein signal transduction -0.002 0.088 -10000 0 -0.19 91 91
PDGF/PDGFRA/SHB -0.053 0.12 -10000 0 -0.25 137 137
PDGF/PDGFRA/Caveolin-1 -0.09 0.16 -10000 0 -0.31 172 172
ITGAV 0.023 0.003 -10000 0 -10000 0 0
ELK1 -0.088 0.11 0.26 1 -0.27 125 126
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PDGF/PDGFRA/Crk -0.053 0.12 -10000 0 -0.24 137 137
JAK-STAT cascade -0.076 0.1 -10000 0 -0.25 136 136
cell proliferation -0.056 0.12 -10000 0 -0.25 141 141
HIF-1-alpha transcription factor network

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
PKM2 -0.16 0.3 0.38 7 -0.63 98 105
HDAC7 0.023 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.15 0.34 0.56 5 -0.7 94 99
SMAD4 0.023 0.005 -10000 0 -10000 0 0
ID2 -0.15 0.31 0.42 3 -0.64 93 96
AP1 -0.053 0.13 -10000 0 -0.25 160 160
ABCG2 -0.23 0.36 0.42 2 -0.65 172 174
HIF1A -0.032 0.078 -10000 0 -0.2 15 15
TFF3 -0.12 0.36 0.43 48 -0.68 88 136
GATA2 -0.011 0.11 -10000 0 -0.35 48 48
AKT1 -0.047 0.098 -10000 0 -0.22 62 62
response to hypoxia -0.054 0.093 0.15 3 -0.2 93 96
MCL1 -0.15 0.29 0.42 2 -0.64 87 89
NDRG1 -0.14 0.3 0.42 3 -0.63 89 92
SERPINE1 -0.15 0.31 0.42 3 -0.65 92 95
FECH -0.15 0.31 0.42 3 -0.65 91 94
FURIN -0.15 0.31 0.42 3 -0.64 94 97
NCOA2 0.008 0.066 -10000 0 -0.35 17 17
EP300 -0.062 0.14 0.22 2 -0.32 94 96
HMOX1 -0.15 0.31 0.44 4 -0.64 93 97
BHLHE40 -0.15 0.31 0.42 3 -0.64 93 96
BHLHE41 -0.16 0.33 0.42 3 -0.66 109 112
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.009 0.11 0.3 2 -0.28 2 4
ENG -0.002 0.11 0.26 10 -0.26 2 12
JUN 0.018 0.043 -10000 0 -0.35 7 7
RORA -0.16 0.32 0.42 3 -0.65 100 103
ABCB1 -0.25 0.44 -10000 0 -0.96 137 137
TFRC -0.14 0.3 0.44 4 -0.64 87 91
CXCR4 -0.15 0.31 0.42 3 -0.64 93 96
TF -0.15 0.32 0.45 6 -0.66 93 99
CITED2 -0.15 0.32 0.42 3 -0.65 96 99
HIF1A/ARNT -0.14 0.39 0.65 20 -0.75 77 97
LDHA -0.029 0.12 -10000 0 -0.59 15 15
ETS1 -0.15 0.31 0.42 3 -0.65 92 95
PGK1 -0.15 0.31 0.42 3 -0.64 94 97
NOS2 -0.15 0.31 0.42 3 -0.64 93 96
ITGB2 -0.14 0.31 0.46 5 -0.64 92 97
ALDOA -0.15 0.31 0.42 3 -0.64 91 94
Cbp/p300/CITED2 -0.19 0.38 0.47 4 -0.76 113 117
FOS -0.088 0.17 -10000 0 -0.35 158 158
HK2 -0.14 0.31 0.47 4 -0.65 89 93
SP1 -0.007 0.058 -10000 0 -0.14 10 10
GCK -0.18 0.43 -10000 0 -1.2 75 75
HK1 -0.15 0.31 0.42 3 -0.64 92 95
NPM1 -0.15 0.31 0.42 3 -0.65 91 94
EGLN1 -0.15 0.3 0.42 2 -0.64 89 91
CREB1 0.026 0.003 -10000 0 -10000 0 0
PGM1 -0.15 0.31 0.42 3 -0.64 94 97
SMAD3 0.02 0.032 -10000 0 -0.35 4 4
EDN1 -0.13 0.24 -10000 0 -0.59 78 78
IGFBP1 -0.17 0.34 0.46 6 -0.67 104 110
VEGFA -0.13 0.29 0.42 3 -0.61 92 95
HIF1A/JAB1 -0.01 0.06 -10000 0 -0.19 1 1
CP -0.13 0.33 0.47 12 -0.66 88 100
CXCL12 -0.24 0.36 0.42 3 -0.65 172 175
COPS5 0.02 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.031 0.026 -10000 0 -0.24 4 4
BNIP3 -0.14 0.31 0.42 3 -0.65 90 93
EGLN3 -0.15 0.31 0.49 2 -0.64 94 96
CA9 -0.1 0.34 0.44 42 -0.64 90 132
TERT -0.12 0.33 0.45 28 -0.64 88 116
ENO1 -0.15 0.31 0.42 3 -0.64 93 96
PFKL -0.15 0.31 0.42 3 -0.64 93 96
NCOA1 0.021 0.018 -10000 0 -0.35 1 1
ADM -0.14 0.32 0.44 8 -0.65 88 96
ARNT -0.02 0.064 0.18 1 -10000 0 1
HNF4A 0.044 0.1 0.27 76 -0.12 6 82
ADFP -0.16 0.3 0.38 7 -0.63 98 105
SLC2A1 -0.13 0.29 0.44 3 -0.61 92 95
LEP -0.15 0.31 0.43 4 -0.64 91 95
HIF1A/ARNT/Cbp/p300 -0.16 0.34 0.58 5 -0.71 95 100
EPO -0.11 0.27 0.43 1 -0.7 46 47
CREBBP -0.062 0.14 0.2 1 -0.32 92 93
HIF1A/ARNT/Cbp/p300/HDAC7 -0.15 0.33 0.57 5 -0.69 92 97
PFKFB3 -0.15 0.31 0.42 3 -0.65 89 92
NT5E -0.17 0.34 0.42 3 -0.67 113 116
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.065 -10000 0 -0.24 30 30
alphaV beta3 Integrin -0.12 0.15 0.2 1 -0.24 293 294
PTK2 -0.1 0.18 0.27 14 -0.38 113 127
IGF1R 0.009 0.069 -10000 0 -0.35 19 19
PI4KB 0.018 0.01 -10000 0 -10000 0 0
MFGE8 0.021 0.023 -10000 0 -0.35 2 2
SRC 0.022 0.005 -10000 0 -10000 0 0
CDKN1B -0.12 0.19 -10000 0 -0.52 89 89
VEGFA 0.023 0.003 -10000 0 -10000 0 0
ILK -0.1 0.17 -10000 0 -0.49 73 73
ROCK1 0.023 0.004 -10000 0 -10000 0 0
AKT1 -0.097 0.16 -10000 0 -0.46 71 71
PTK2B -0.041 0.084 0.2 14 -0.2 87 101
alphaV/beta3 Integrin/JAM-A -0.098 0.14 0.2 3 -0.22 271 274
CBL 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.001 0.095 0.2 3 -0.21 88 91
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.016 0.13 -10000 0 -0.24 129 129
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.046 0.11 -10000 0 -0.33 35 35
alphaV/beta3 Integrin/Syndecan-1 0.043 0.13 0.2 132 -0.2 84 216
PI4KA 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.18 -10000 0 -0.26 313 313
PI4 Kinase 0.025 0.015 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
alphaV/beta3 Integrin/Osteopontin 0.04 0.13 0.2 127 -0.2 87 214
RPS6KB1 -0.16 0.14 0.32 1 -0.36 137 138
TLN1 0.022 0.005 -10000 0 -10000 0 0
MAPK3 -0.25 0.25 -10000 0 -0.48 267 267
GPR124 -0.058 0.15 -10000 0 -0.35 112 112
MAPK1 -0.26 0.25 -10000 0 -0.48 270 270
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Tumstatin -0.012 0.12 0.2 18 -0.23 118 136
cell adhesion -0.006 0.097 0.23 2 -0.22 84 86
ANGPTL3 0.021 0.016 0.28 2 -10000 0 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.058 -10000 0 -0.21 28 28
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.35 19 19
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
TGFBR2 0.015 0.051 -10000 0 -0.35 10 10
ITGB3 -0.039 0.14 0.28 2 -0.35 89 91
IGF1 -0.047 0.15 -10000 0 -0.35 100 100
RAC1 0.022 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.045 0.13 0.2 1 -0.24 159 160
apoptosis 0.023 0.003 -10000 0 -10000 0 0
CD47 0.022 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.002 0.093 0.2 1 -0.21 85 86
VCL 0.022 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.04 0.14 0.2 2 -0.25 150 152
CSF1 0.016 0.051 -10000 0 -0.35 10 10
PIK3C2A -0.1 0.17 -10000 0 -0.48 72 72
PI4 Kinase/Pyk2 -0.095 0.13 -10000 0 -0.3 88 88
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.003 0.11 0.21 1 -0.21 99 100
FAK1/Vinculin -0.082 0.14 0.25 13 -0.32 91 104
alphaV beta3/Integrin/ppsTEM5 -0.045 0.14 0.2 1 -0.24 159 160
RHOA 0.022 0.005 -10000 0 -10000 0 0
VTN -0.022 0.12 0.3 3 -0.35 63 66
BCAR1 0.02 0.008 -10000 0 -10000 0 0
FGF2 -0.17 0.18 -10000 0 -0.35 272 272
F11R -0.1 0.12 -10000 0 -0.24 217 217
alphaV/beta3 Integrin/Lactadherin 0.001 0.096 0.2 2 -0.21 87 89
alphaV/beta3 Integrin/TGFBR2 -0.001 0.1 0.2 2 -0.22 89 91
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.045 0.039 -10000 0 -0.19 10 10
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.003 0.085 0.19 2 -0.19 87 89
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.036 -10000 0 -0.35 5 5
alphaV/beta3 Integrin/Pyk2 -0.009 0.094 0.19 1 -0.2 95 96
SDC1 0.095 0.12 0.28 149 -10000 0 149
VAV3 0.027 0.086 0.24 20 -10000 0 20
PTPN11 0.023 0.003 -10000 0 -10000 0 0
IRS1 -0.012 0.11 -10000 0 -0.35 50 50
FAK1/Paxillin -0.083 0.15 0.26 15 -0.32 95 110
cell migration -0.078 0.13 0.23 14 -0.3 82 96
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PI3K -0.082 0.13 -10000 0 -0.22 201 201
SPP1 0.096 0.12 0.28 151 -10000 0 151
KDR 0.001 0.087 -10000 0 -0.35 31 31
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.003 -10000 0 -10000 0 0
COL4A3 0 0.12 0.28 19 -0.35 45 64
angiogenesis -0.26 0.26 -10000 0 -0.49 264 264
Rac1/GTP 0.022 0.079 0.23 15 -10000 0 15
EDIL3 -0.047 0.14 -10000 0 -0.35 98 98
cell proliferation -0.001 0.1 0.2 2 -0.22 89 91
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.056 0.046 0.14 14 -0.11 34 48
BUB1B 0.061 0.064 0.12 151 -0.15 20 171
PLK1 0.035 0.033 0.1 42 -0.11 6 48
PLK1S1 0.022 0.025 0.11 9 -0.18 3 12
KIF2A 0.027 0.031 0.14 10 -0.11 1 11
regulation of mitotic centrosome separation 0.035 0.033 0.1 42 -0.1 6 48
GOLGA2 0.022 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.16 0.11 0.24 316 -0.11 1 317
WEE1 0.024 0.072 -10000 0 -0.29 21 21
cytokinesis 0.093 0.069 0.18 55 -0.23 8 63
PP2A-alpha B56 0.14 0.1 -10000 0 -0.55 8 8
AURKA 0.045 0.05 0.12 134 -0.2 4 138
PICH/PLK1 0.077 0.077 0.17 193 -10000 0 193
CENPE 0.032 0.035 0.12 26 -0.14 3 29
RhoA/GTP 0.016 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.028 0.031 0.14 10 -0.11 1 11
PPP2CA 0.023 0.003 -10000 0 -10000 0 0
FZR1 0.021 0.006 -10000 0 -10000 0 0
TPX2 0.089 0.047 0.11 388 -0.24 1 389
PAK1 0.021 0.004 -10000 0 -10000 0 0
SPC24 0.18 0.13 0.28 319 -10000 0 319
FBXW11 0.022 0.004 -10000 0 -10000 0 0
CLSPN 0.075 0.064 0.12 291 -0.23 8 299
GORASP1 0.022 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.013 5 -0.011 11 16
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.016 0.016 0.054 34 -0.053 6 40
G2 phase of mitotic cell cycle 0 0.004 0.015 26 -10000 0 26
STAG2 0.023 0.001 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.006 0.083 -10000 0 -0.51 13 13
spindle elongation 0.035 0.033 0.1 42 -0.1 6 48
ODF2 0.022 0.006 -10000 0 -10000 0 0
BUB1 0.14 0.11 -10000 0 -0.6 8 8
TPT1 0.011 0.05 0.12 2 -0.19 28 30
CDC25C 0.12 0.067 0.15 153 -0.28 10 163
CDC25B 0.023 0.009 -10000 0 -10000 0 0
SGOL1 0.056 0.046 0.11 34 -0.14 14 48
RHOA 0.022 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.055 0.064 0.19 78 -0.17 2 80
CDC14B -0.005 0.005 -10000 0 -10000 0 0
CDC20 0.25 0.083 0.28 468 -10000 0 468
PLK1/PBIP1 0.007 0.026 0.097 31 -0.093 5 36
mitosis -0.005 0.007 0.021 4 -0.017 107 111
FBXO5 0.022 0.03 0.14 11 -0.13 3 14
CDC2 0.002 0.004 0.011 10 -0.01 4 14
NDC80 0.042 0.071 0.29 39 -10000 0 39
metaphase plate congression 0.021 0.05 0.15 1 -0.22 17 18
ERCC6L 0.067 0.075 0.19 84 -0.17 1 85
NLP/gamma Tubulin 0.015 0.026 0.076 10 -0.095 14 24
microtubule cytoskeleton organization 0.011 0.05 0.12 2 -0.19 28 30
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 5 -10000 0 5
PPP1R12A 0.023 0.017 -10000 0 -0.35 1 1
interphase -0.001 0.002 0.014 5 -10000 0 5
PLK1/PRC1-2 0.19 0.081 0.22 451 -0.17 1 452
GRASP65/GM130/RAB1/GTP/PLK1 0.056 0.03 -10000 0 -10000 0 0
RAB1A 0.023 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.027 0.029 0.091 47 -0.089 3 50
mitotic prometaphase 0.001 0.004 0.021 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.05 0.069 0.18 1 -0.36 9 10
microtubule-based process 0.19 0.068 0.22 466 -0.17 1 467
Golgi organization 0.035 0.033 0.1 42 -0.1 6 48
Cohesin/SA2 0.041 0.027 0.11 9 -0.1 3 12
PPP1CB/MYPT1 0.033 0.014 -10000 0 -0.25 1 1
KIF20A 0.25 0.083 0.28 469 -10000 0 469
APC/C/CDC20 0.19 0.07 0.22 465 -0.14 2 467
PPP2R1A 0.023 0.004 -10000 0 -10000 0 0
chromosome segregation 0.007 0.026 0.096 31 -0.092 5 36
PRC1 0.034 0.053 0.28 23 -10000 0 23
ECT2 0.052 0.079 0.25 64 -0.12 1 65
C13orf34 0.027 0.028 0.088 42 -0.089 4 46
NUDC 0.021 0.05 0.15 1 -0.22 17 18
regulation of attachment of spindle microtubules to kinetochore 0.061 0.063 0.12 151 -0.15 20 171
spindle assembly 0.024 0.027 0.086 29 -0.091 7 36
spindle stabilization 0.022 0.025 0.11 9 -0.18 3 12
APC/C/HCDH1 0.018 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.19 0.068 0.22 466 -0.17 1 467
CCNB1 0.068 0.098 0.28 92 -10000 0 92
PPP1CB 0.023 0.005 -10000 0 -10000 0 0
BTRC 0.022 0.005 -10000 0 -10000 0 0
ROCK2 0.023 0.069 0.19 3 -0.3 17 20
TUBG1 0.011 0.048 0.12 1 -0.17 29 30
G2/M transition of mitotic cell cycle 0.022 0.038 0.2 5 -0.18 1 6
MLF1IP 0.003 0.026 0.11 31 -10000 0 31
INCENP 0.023 0.004 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.031 0.013 0.21 1 -10000 0 1
VLDLR 0.021 0.023 -10000 0 -0.35 2 2
CRKL 0.022 0.005 -10000 0 -10000 0 0
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
ITGA3 0.021 0.017 -10000 0 -0.35 1 1
RELN/VLDLR/Fyn -0.039 0.12 0.2 6 -0.21 172 178
MAPK8IP1/MKK7/MAP3K11/JNK1 0.045 0.04 -10000 0 -0.18 5 5
AKT1 -0.055 0.093 0.15 3 -0.19 170 173
MAP2K7 0.021 0.006 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
DAB1 0.027 0.041 0.28 13 -10000 0 13
RELN/LRP8/DAB1 -0.03 0.12 0.21 20 -0.19 178 198
LRPAP1/LRP8 0.035 0.019 0.21 5 -10000 0 5
RELN/LRP8/DAB1/Fyn -0.02 0.12 0.35 2 -0.18 172 174
DAB1/alpha3/beta1 Integrin -0.025 0.1 -10000 0 -0.18 157 157
long-term memory -0.09 0.15 0.31 3 -0.22 277 280
DAB1/LIS1 -0.02 0.11 -10000 0 -0.18 168 168
DAB1/CRLK/C3G -0.028 0.1 -10000 0 -0.18 160 160
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DAB1/NCK2 -0.018 0.12 -10000 0 -0.18 171 171
ARHGEF2 0.018 0.01 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.12 0.18 0.28 1 -0.35 196 197
CDK5R1 0.022 0.013 0.28 1 -10000 0 1
RELN -0.1 0.18 0.28 7 -0.35 180 187
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RELN/LRP8/Fyn -0.036 0.12 0.22 9 -0.21 173 182
GRIN2A/RELN/LRP8/DAB1/Fyn -0.092 0.15 -10000 0 -0.22 280 280
MAPK8 0.019 0.036 -10000 0 -0.35 5 5
RELN/VLDLR/DAB1 -0.033 0.11 0.2 16 -0.19 176 192
ITGB1 0.022 0.004 -10000 0 -10000 0 0
MAP1B -0.072 0.099 0.17 11 -0.2 187 198
RELN/LRP8 -0.038 0.12 0.23 8 -0.21 177 185
GRIN2B/RELN/LRP8/DAB1/Fyn -0.01 0.13 0.36 6 -0.18 171 177
PI3K 0.026 0.029 -10000 0 -0.24 5 5
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.015 -10000 0 -0.24 1 1
RAP1A -0.058 0.092 0.3 4 -0.31 1 5
PAFAH1B1 0.021 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.02 0.28 1 -0.35 1 2
CRLK/C3G 0.031 0.01 -10000 0 -10000 0 0
GRIN2B 0.03 0.052 0.28 21 -10000 0 21
NCK2 0.023 0.003 -10000 0 -10000 0 0
neuron differentiation -0.028 0.092 -10000 0 -0.31 12 12
neuron adhesion -0.054 0.1 0.31 10 -0.3 2 12
LRP8 0.025 0.026 0.29 5 -10000 0 5
GSK3B -0.057 0.087 0.14 2 -0.18 164 166
RELN/VLDLR/DAB1/Fyn -0.023 0.11 0.28 2 -0.18 170 172
MAP3K11 0.022 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.053 0.1 0.16 4 -0.2 175 179
CDK5 0.022 0.005 -10000 0 -10000 0 0
MAPT -0.003 0.081 0.66 4 -0.31 16 20
neuron migration -0.072 0.13 0.26 11 -0.25 157 168
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.027 0.092 -10000 0 -0.31 12 12
RELN/VLDLR -0.027 0.12 0.21 7 -0.19 174 181
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.042 0.16 -10000 0 -0.54 31 31
IHH -0.041 0.21 0.31 57 -0.39 121 178
SHH Np/Cholesterol/GAS1 -0.083 0.1 0.23 1 -0.19 259 260
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.083 0.1 0.18 259 -0.23 1 260
SMO/beta Arrestin2 -0.039 0.16 -10000 0 -0.41 27 27
SMO -0.056 0.15 -10000 0 -0.32 110 110
AKT1 -0.019 0.12 -10000 0 -0.47 22 22
ARRB2 0.021 0.006 -10000 0 -10000 0 0
BOC 0.011 0.066 -10000 0 -0.35 17 17
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
heart looping -0.055 0.15 -10000 0 -0.32 109 109
STIL -0.011 0.12 0.22 13 -0.28 27 40
DHH N/PTCH2 -0.004 0.098 -10000 0 -0.26 67 67
DHH N/PTCH1 -0.043 0.13 -10000 0 -0.34 40 40
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DHH -0.007 0.1 -10000 0 -0.35 42 42
PTHLH -0.062 0.19 -10000 0 -0.59 31 31
determination of left/right symmetry -0.055 0.15 -10000 0 -0.32 109 109
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
skeletal system development -0.061 0.19 -10000 0 -0.59 31 31
IHH N/Hhip -0.004 0.14 0.22 72 -0.23 121 193
DHH N/Hhip 0.016 0.089 0.21 26 -0.24 47 73
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.055 0.15 -10000 0 -0.32 109 109
pancreas development 0.032 0.068 0.28 28 -0.35 5 33
HHAT 0.017 0.033 -10000 0 -0.35 4 4
PI3K 0.026 0.029 -10000 0 -0.24 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.2 0.18 -10000 0 -0.35 318 318
somite specification -0.055 0.15 -10000 0 -0.32 109 109
SHH Np/Cholesterol/PTCH1 -0.022 0.11 0.24 5 -0.28 29 34
SHH Np/Cholesterol/PTCH2 0.015 0.059 0.22 6 -0.2 28 34
SHH Np/Cholesterol/Megalin 0.079 0.095 0.2 172 -0.18 6 178
SHH 0.004 0.058 0.13 63 -0.24 6 69
catabolic process -0.037 0.13 -10000 0 -0.25 127 127
SMO/Vitamin D3 -0.015 0.15 0.3 8 -0.34 27 35
SHH Np/Cholesterol/Hhip 0.03 0.059 0.2 33 -0.18 11 44
LRP2 0.11 0.12 0.28 183 -10000 0 183
receptor-mediated endocytosis -0.009 0.14 0.23 11 -0.33 27 38
SHH Np/Cholesterol/BOC 0.017 0.054 0.22 6 -0.19 22 28
SHH Np/Cholesterol/CDO 0.006 0.069 0.22 6 -0.19 47 53
mesenchymal cell differentiation -0.03 0.059 0.18 11 -0.2 33 44
mol:Vitamin D3 -0.001 0.13 0.29 16 -0.29 28 44
IHH N/PTCH2 -0.022 0.15 0.2 56 -0.25 134 190
CDON -0.015 0.11 -10000 0 -0.35 52 52
IHH N/PTCH1 -0.026 0.15 -10000 0 -0.25 127 127
Megalin/LRPAP1 0.09 0.084 0.21 176 -10000 0 176
PTCH2 0.002 0.085 -10000 0 -0.35 29 29
SHH Np/Cholesterol 0.008 0.022 -10000 0 -0.18 6 6
PTCH1 -0.037 0.13 -10000 0 -0.25 127 127
HHIP 0.032 0.069 0.28 28 -0.35 5 33
Cellular roles of Anthrax toxin

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
ANTXR1 0.009 0.069 -10000 0 -0.35 19 19
ANTXR2 -0.093 0.17 -10000 0 -0.35 164 164
negative regulation of myeloid dendritic cell antigen processing and presentation -0.017 0.024 -10000 0 -0.051 164 164
monocyte activation -0.007 0.12 -10000 0 -0.37 43 43
MAP2K2 -0.045 0.17 -10000 0 -0.6 44 44
MAP2K1 -0.018 0.022 0.12 1 -0.077 13 14
MAP2K7 -0.017 0.022 0.12 1 -0.076 13 14
MAP2K6 -0.015 0.028 0.19 3 -0.079 11 14
CYAA -0.061 0.085 -10000 0 -0.18 164 164
MAP2K4 -0.017 0.023 -10000 0 -0.083 15 15
IL1B -0.017 0.046 0.17 11 -0.13 31 42
Channel -0.042 0.11 -10000 0 -0.2 164 164
NLRP1 -0.024 0.042 -10000 0 -0.16 34 34
CALM1 0.022 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.016 0.065 -10000 0 -0.46 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.017 0.024 0.051 164 -10000 0 164
MAPK3 -0.018 0.021 -10000 0 -0.075 14 14
MAPK1 -0.018 0.021 -10000 0 -0.077 11 11
PGR -0.062 0.08 -10000 0 -0.19 147 147
PA/Cellular Receptors -0.047 0.12 -10000 0 -0.22 164 164
apoptosis -0.017 0.024 -10000 0 -0.051 164 164
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.04 0.1 -10000 0 -0.19 164 164
macrophage activation -0.018 0.026 0.13 6 -10000 0 6
TNF 0.053 0.088 0.28 65 -0.35 2 67
VCAM1 -0.006 0.12 -10000 0 -0.38 42 42
platelet activation -0.016 0.065 -10000 0 -0.46 9 9
MAPKKK cascade 0.015 0.029 0.088 22 -0.075 12 34
IL18 -0.018 0.029 -10000 0 -0.12 22 22
negative regulation of macrophage activation -0.017 0.024 -10000 0 -0.051 164 164
LEF -0.017 0.024 -10000 0 -0.052 164 164
CASP1 -0.018 0.033 -10000 0 -0.062 147 147
mol:cAMP -0.016 0.065 -10000 0 -0.46 9 9
necrosis -0.017 0.024 -10000 0 -0.051 164 164
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.038 0.1 -10000 0 -0.18 164 164
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.069 -10000 0 -0.35 19 19
mol:S1P -0.009 0.013 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.082 0.12 -10000 0 -0.24 159 159
GNAO1 -0.081 0.16 -10000 0 -0.36 123 123
S1P/S1P3/G12/G13 0.007 0.053 -10000 0 -0.2 16 16
AKT1 -0.064 0.16 -10000 0 -0.67 30 30
AKT3 -0.39 0.5 -10000 0 -1 202 202
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.069 -10000 0 -0.35 19 19
GNAI2 0 0.031 -10000 0 -10000 0 0
GNAI3 0.002 0.029 -10000 0 -10000 0 0
GNAI1 -0.003 0.052 -10000 0 -0.36 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.011 0.071 -10000 0 -0.36 17 17
S1PR2 0.021 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.19 -10000 0 -0.33 232 232
MAPK3 -0.13 0.18 -10000 0 -0.34 185 185
MAPK1 -0.13 0.18 -10000 0 -0.34 186 186
JAK2 -0.14 0.19 -10000 0 -0.36 194 194
CXCR4 -0.14 0.18 -10000 0 -0.34 193 193
FLT1 -0.003 0.036 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
SRC -0.13 0.18 -10000 0 -0.34 186 186
S1P/S1P3/Gi -0.14 0.19 -10000 0 -0.33 232 232
RAC1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.13 0.18 -10000 0 -0.33 203 203
VEGFA -0.003 0.035 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.083 0.13 -10000 0 -0.26 149 149
VEGFR1 homodimer/VEGFA homodimer -0.002 0.053 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.025 0.094 -10000 0 -0.26 63 63
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
GNAZ -0.008 0.065 -10000 0 -0.35 15 15
G12/G13 0.031 0.01 -10000 0 -10000 0 0
GNA14 -0.011 0.1 -10000 0 -0.35 46 46
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.014 0.051 -10000 0 -0.35 10 10
Rac1/GTP -0.13 0.18 -10000 0 -0.33 203 203
Nongenotropic Androgen signaling

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
PTK2 -0.005 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.001 0.088 -10000 0 -0.19 93 93
regulation of S phase of mitotic cell cycle -0.013 0.072 -10000 0 -0.2 63 63
GNAO1 -0.066 0.16 -10000 0 -0.35 123 123
HRAS 0.021 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.019 -10000 0 -0.2 4 4
PELP1 0.02 0.008 -10000 0 -10000 0 0
AKT1 -0.005 0.002 -10000 0 -10000 0 0
MAP2K1 -0.06 0.086 0.19 14 -0.26 27 41
T-DHT/AR -0.031 0.094 -10000 0 -0.24 87 87
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 160 160
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
mol:GDP -0.053 0.11 -10000 0 -0.3 84 84
cell proliferation -0.15 0.2 0.25 3 -0.41 166 169
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
FOS -0.23 0.34 -10000 0 -0.74 164 164
mol:Ca2+ -0.02 0.029 -10000 0 -0.061 145 145
MAPK3 -0.11 0.15 0.26 3 -0.31 153 156
MAPK1 -0.082 0.14 0.2 1 -0.36 52 53
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.001 0.002 -10000 0 -0.004 162 162
cAMP biosynthetic process 0.004 0.025 -10000 0 -0.16 4 4
GNG2 0.017 0.049 0.28 1 -0.35 9 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 162 162
HRAS/GTP -0.018 0.082 -10000 0 -0.18 75 75
actin cytoskeleton reorganization 0.027 0.023 -10000 0 -0.16 5 5
SRC 0.021 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 162 162
PI3K 0.024 0.025 -10000 0 -0.2 5 5
apoptosis 0.14 0.2 0.42 163 -0.26 1 164
T-DHT/AR/PELP1 -0.018 0.085 -10000 0 -0.21 85 85
HRAS/GDP -0.042 0.11 -10000 0 -0.3 75 75
CREB1 -0.15 0.22 0.27 1 -0.45 163 164
RAC1-CDC42/GTP 0.034 0.026 -10000 0 -0.16 5 5
AR -0.04 0.14 -10000 0 -0.35 87 87
GNB1 0.022 0.004 -10000 0 -10000 0 0
RAF1 -0.049 0.08 0.2 17 -0.24 25 42
RAC1-CDC42/GDP -0.016 0.12 -10000 0 -0.29 69 69
T-DHT/AR/PELP1/Src -0.011 0.08 -10000 0 -0.19 75 75
MAP2K2 -0.061 0.082 0.18 11 -0.26 26 37
T-DHT/AR/PELP1/Src/PI3K -0.013 0.072 -10000 0 -0.2 63 63
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
SHBG 0.018 0.033 -10000 0 -0.35 4 4
Gi family/GNB1/GNG2/GDP -0.097 0.17 -10000 0 -0.35 135 135
mol:T-DHT -0.001 0.001 0.002 1 -0.002 100 101
RAC1 0.022 0.005 -10000 0 -10000 0 0
GNRH1 -0.007 0.02 -10000 0 -0.24 4 4
Gi family/GTP -0.059 0.1 -10000 0 -0.24 92 92
CDC42 0.022 0.004 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.002 0.053 0.21 1 -10000 0 1
BIRC5 0.22 0.11 0.28 403 -10000 0 403
NFKBIA -0.006 0.055 0.29 7 -10000 0 7
CPEB1 -0.14 0.18 -10000 0 -0.35 224 224
AKT1 -0.007 0.051 0.25 6 -10000 0 6
NDEL1 0.021 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0 0.045 -10000 0 -0.16 1 1
NDEL1/TACC3 0.037 0.091 0.22 67 -10000 0 67
GADD45A 0.023 0.002 -10000 0 -10000 0 0
GSK3B -0.022 0.024 -10000 0 -10000 0 0
PAK1/Aurora A 0.002 0.052 0.21 1 -10000 0 1
MDM2 0.023 0.002 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.097 0.075 0.12 423 -10000 0 423
TP53 0 0.051 -10000 0 -0.2 22 22
DLG7 -0.004 0.045 0.13 29 -10000 0 29
AURKAIP1 0.022 0.004 -10000 0 -10000 0 0
ARHGEF7 0.022 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.039 0.096 0.24 67 -10000 0 67
G2/M transition of mitotic cell cycle 0 0.044 -10000 0 -0.16 1 1
AURKA 0.001 0.061 0.17 28 -10000 0 28
AURKB 0.12 0.074 0.16 371 -0.29 3 374
CDC25B 0.004 0.044 0.21 1 -0.17 2 3
G2/M transition checkpoint -0.008 0.032 0.12 2 -0.16 1 3
mRNA polyadenylation -0.077 0.1 -10000 0 -0.19 206 206
Aurora A/CPEB -0.078 0.1 -10000 0 -0.2 206 206
Aurora A/TACC1/TRAP/chTOG -0.018 0.085 -10000 0 -0.21 39 39
BRCA1 0.022 0.006 -10000 0 -10000 0 0
centrosome duplication 0.002 0.052 0.21 1 -10000 0 1
regulation of centrosome cycle 0.036 0.089 0.22 67 -10000 0 67
spindle assembly -0.019 0.083 -10000 0 -0.21 39 39
TDRD7 0.022 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.13 0.095 0.23 145 -0.18 4 149
CENPA 0.13 0.072 0.17 366 -0.28 3 369
Aurora A/PP2A 0.002 0.053 0.21 1 -0.18 1 2
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.003 0.051 0.25 9 -10000 0 9
negative regulation of DNA binding 0 0.052 -10000 0 -0.2 23 23
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.01 -10000 0 -10000 0 0
RASA1 0.019 0.036 -10000 0 -0.35 5 5
Ajuba/Aurora A -0.008 0.032 0.12 2 -0.16 1 3
mitotic prometaphase -0.023 0.031 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.002 0.062 0.18 29 -10000 0 29
TACC1 -0.038 0.14 -10000 0 -0.35 84 84
TACC3 0.083 0.11 0.28 123 -10000 0 123
Aurora A/Antizyme1 0.005 0.052 -10000 0 -10000 0 0
Aurora A/RasGAP 0.001 0.056 0.21 1 -0.23 5 6
OAZ1 0.021 0.006 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.021 0.024 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.042 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.097 0.075 0.12 423 -10000 0 423
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.077 0.074 0.23 59 -10000 0 59
PAK1 0.022 0.004 -10000 0 -10000 0 0
CKAP5 0.022 0.005 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.023 -10000 0 -0.35 2 2
LAT2 -0.062 0.12 -10000 0 -0.25 116 116
AP1 -0.085 0.17 -10000 0 -0.38 76 76
mol:PIP3 -0.048 0.17 0.25 45 -0.29 115 160
IKBKB -0.018 0.12 0.24 32 -0.22 48 80
AKT1 -0.003 0.16 0.3 70 -0.28 25 95
IKBKG -0.029 0.11 0.19 47 -0.22 52 99
MS4A2 -0.096 0.16 -10000 0 -0.34 163 163
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.019 0.018 -10000 0 -0.35 1 1
MAP3K1 -0.026 0.14 0.25 30 -0.31 37 67
mol:Ca2+ -0.034 0.14 0.22 53 -0.23 112 165
LYN 0.022 0.01 -10000 0 -10000 0 0
CBLB -0.062 0.12 -10000 0 -0.25 118 118
SHC1 0.019 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.012 0.099 -10000 0 -0.19 121 121
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
PLD2 -0.015 0.16 0.28 90 -0.24 55 145
PTPN13 -0.076 0.16 0.32 1 -0.56 14 15
PTPN11 0.018 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.019 0.14 0.34 17 -0.28 27 44
SYK 0.024 0.014 0.28 1 -10000 0 1
GRB2 0.022 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.069 0.14 -10000 0 -0.28 120 120
LAT -0.061 0.12 -10000 0 -0.25 117 117
PAK2 -0.029 0.15 0.26 28 -0.33 39 67
NFATC2 -0.055 0.14 -10000 0 -0.48 44 44
HRAS -0.041 0.15 0.24 11 -0.34 44 55
GAB2 0.02 0.032 -10000 0 -0.35 4 4
PLA2G1B -0.009 0.14 -10000 0 -0.88 12 12
Fc epsilon R1 -0.05 0.13 0.2 1 -0.22 173 174
Antigen/IgE/Fc epsilon R1 -0.043 0.12 0.19 1 -0.2 172 173
mol:GDP -0.061 0.13 -10000 0 -0.36 41 41
JUN 0.018 0.042 -10000 0 -0.35 7 7
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
FOS -0.088 0.17 -10000 0 -0.35 158 158
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.061 0.12 -10000 0 -0.26 119 119
CHUK -0.028 0.12 0.31 14 -0.22 48 62
KLRG1 -0.051 0.1 0.15 1 -0.3 38 39
VAV1 -0.058 0.11 -10000 0 -0.25 107 107
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.06 0.11 -10000 0 -0.25 110 110
negative regulation of mast cell degranulation -0.034 0.11 0.23 1 -0.29 37 38
BTK -0.062 0.13 -10000 0 -0.38 37 37
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.066 0.13 -10000 0 -0.23 159 159
GAB2/PI3K/SHP2 -0.061 0.078 -10000 0 -0.23 60 60
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.052 0.11 -10000 0 -0.26 69 69
RAF1 -0.006 0.15 -10000 0 -0.95 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.03 0.12 -10000 0 -0.2 163 163
FCER1G 0.022 0.025 0.29 2 -10000 0 2
FCER1A -0.036 0.13 -10000 0 -0.36 71 71
Antigen/IgE/Fc epsilon R1/Fyn -0.033 0.11 0.2 1 -0.19 166 167
MAPK3 -0.01 0.14 -10000 0 -0.88 12 12
MAPK1 -0.012 0.14 -10000 0 -0.9 12 12
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.053 0.2 -10000 0 -0.59 55 55
DUSP1 -0.063 0.16 -10000 0 -0.35 122 122
NF-kappa-B/RelA -0.016 0.067 0.12 5 -0.14 40 45
actin cytoskeleton reorganization -0.059 0.16 -10000 0 -0.45 26 26
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.051 0.13 -10000 0 -0.33 40 40
FER -0.061 0.12 -10000 0 -0.25 117 117
RELA 0.022 0.004 -10000 0 -10000 0 0
ITK -0.02 0.059 -10000 0 -0.32 14 14
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG1 -0.05 0.15 0.26 7 -0.36 41 48
cytokine secretion -0.019 0.041 -10000 0 -0.12 2 2
SPHK1 -0.06 0.12 -10000 0 -0.25 114 114
PTK2 -0.062 0.16 -10000 0 -0.64 9 9
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.069 0.14 0.23 1 -0.29 120 121
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.049 0.17 0.24 51 -0.29 114 165
MAP2K2 -0.012 0.14 -10000 0 -0.88 12 12
MAP2K1 -0.011 0.14 -10000 0 -0.89 12 12
MAP2K7 0.021 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.038 0.094 0.2 3 -0.27 36 39
MAP2K4 -0.086 0.32 -10000 0 -0.91 66 66
Fc epsilon R1/FcgammaRIIB -0.038 0.12 -10000 0 -0.2 172 172
mol:Choline -0.015 0.16 0.27 90 -0.24 55 145
SHC/Grb2/SOS1 -0.041 0.12 -10000 0 -0.32 37 37
FYN 0.023 0.004 -10000 0 -10000 0 0
DOK1 0.023 0.003 -10000 0 -10000 0 0
PXN -0.058 0.15 -10000 0 -0.58 9 9
HCLS1 -0.061 0.11 -10000 0 -0.25 116 116
PRKCB -0.043 0.14 0.22 42 -0.29 57 99
FCGR2B 0.018 0.027 0.28 1 -0.35 2 3
IGHE 0 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.033 0.12 0.24 1 -0.29 37 38
LCP2 0.023 0.012 0.28 1 -10000 0 1
PLA2G4A -0.068 0.12 -10000 0 -0.26 124 124
RASA1 0.019 0.036 -10000 0 -0.35 5 5
mol:Phosphatidic acid -0.015 0.16 0.27 90 -0.24 55 145
IKK complex -0.008 0.11 0.24 38 -0.18 31 69
WIPF1 0.021 0.023 -10000 0 -0.35 2 2
Effects of Botulinum toxin

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
STX1A -0.005 0.013 0.29 1 -10000 0 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.019 0.21 5 -10000 0 5
STXBP1 -0.003 0.093 -10000 0 -0.35 36 36
ACh/CHRNA1 0.043 0.11 0.18 185 -0.13 13 198
RAB3GAP2/RIMS1/UNC13B 0.037 0.024 0.21 4 -10000 0 4
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 0.023 0.026 0.29 5 -10000 0 5
mol:ACh -0.046 0.058 0.088 20 -0.1 238 258
RAB3GAP2 0.02 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.044 0.094 0.17 1 -0.23 40 41
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.043 0.11 0.18 185 -0.13 13 198
UNC13B 0.022 0.005 -10000 0 -10000 0 0
CHRNA1 0.11 0.12 0.28 188 -10000 0 188
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.074 0.11 -10000 0 -0.25 127 127
SNAP25 -0.1 0.12 -10000 0 -0.23 241 241
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 -0.059 0.15 -10000 0 -0.35 117 117
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.004 0.057 0.22 1 -0.2 36 37
STX1A/SNAP25 fragment 1/VAMP2 -0.044 0.094 0.17 1 -0.23 40 41
Wnt 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
Noncanonical Wnts/FZD -0.046 0.14 0.17 1 -0.25 129 130
FZD6 0.02 0.018 -10000 0 -0.35 1 1
WNT6 0.01 0.11 0.28 22 -0.35 34 56
WNT4 -0.066 0.16 -10000 0 -0.35 126 126
FZD3 0.02 0.008 -10000 0 -10000 0 0
WNT5A 0.011 0.064 -10000 0 -0.35 16 16
WNT11 0.037 0.098 0.28 49 -0.35 14 63
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.023 0.003 -10000 0 -10000 0 0
PTK2 0.021 0.007 -10000 0 -10000 0 0
CRKL -0.055 0.095 0.16 1 -0.24 101 102
GRB2/SOS1/SHC 0.035 0.021 -10000 0 -10000 0 0
HRAS 0.022 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.036 0.11 -10000 0 -0.24 103 103
IGF-1R heterotetramer/IGF1/PTP1B -0.009 0.11 -10000 0 -0.23 97 97
AKT1 -0.039 0.099 0.16 33 -0.22 81 114
BAD -0.04 0.093 0.15 32 -0.22 81 113
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.054 0.095 0.16 1 -0.24 96 97
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.032 0.11 0.2 2 -0.23 108 110
RAF1 -0.027 0.1 0.28 2 -0.4 14 16
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.01 0.12 -10000 0 -0.23 102 102
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.033 0.12 -10000 0 -0.23 129 129
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
RPS6KB1 -0.04 0.097 0.16 30 -0.22 79 109
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.018 0.095 0.26 7 -0.33 9 16
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
HRAS/GTP -0.02 0.088 -10000 0 -0.21 76 76
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.013 0.091 -10000 0 -0.19 76 76
IGF-1R heterotetramer -0.01 0.084 -10000 0 -0.4 19 19
IGF-1R heterotetramer/IGF1/IRS/Nck -0.022 0.12 -10000 0 -0.23 108 108
Crk/p130 Cas/Paxillin -0.013 0.11 -10000 0 -0.22 97 97
IGF1R -0.01 0.084 -10000 0 -0.4 19 19
IGF1 -0.056 0.16 -10000 0 -0.38 99 99
IRS2/Crk -0.055 0.12 0.15 1 -0.23 146 147
PI3K -0.01 0.11 -10000 0 -0.22 97 97
apoptosis 0.034 0.084 0.26 30 -0.2 3 33
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
PRKCD -0.057 0.13 -10000 0 -0.32 102 102
RAF1/14-3-3 E -0.01 0.1 0.27 2 -0.34 16 18
BAD/14-3-3 -0.036 0.088 0.2 3 -0.28 30 33
PRKCZ -0.038 0.099 0.16 35 -0.31 32 67
Crk/p130 Cas/Paxillin/FAK1 -0.014 0.09 -10000 0 -0.29 30 30
PTPN1 0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.059 0.14 -10000 0 -0.33 106 106
BCAR1 0.02 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.006 0.093 -10000 0 -0.2 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.032 0.11 -10000 0 -0.23 108 108
GRB10 0.022 0.017 -10000 0 -0.35 1 1
PTPN11 -0.059 0.096 0.16 1 -0.23 108 109
IRS1 -0.041 0.11 0.12 7 -0.25 105 112
IRS2 -0.076 0.12 0.16 1 -0.24 148 149
IGF-1R heterotetramer/IGF1 -0.038 0.14 -10000 0 -0.3 107 107
GRB2 0.022 0.006 -10000 0 -10000 0 0
PDPK1 -0.04 0.1 0.17 33 -0.23 83 116
YWHAE 0.021 0.007 -10000 0 -10000 0 0
PRKD1 -0.069 0.15 -10000 0 -0.33 110 110
SHC1 0.019 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.075 0.28 0.35 4 -0.8 63 67
MKNK1 0.023 0.004 -10000 0 -10000 0 0
MAPK14 -0.003 0.1 -10000 0 -0.28 60 60
ATF2/c-Jun -0.024 0.1 -10000 0 -0.37 20 20
MAPK11 -0.004 0.1 -10000 0 -0.29 55 55
MITF -0.038 0.14 -10000 0 -0.34 88 88
MAPKAPK5 -0.017 0.11 -10000 0 -0.33 60 60
KRT8 -0.008 0.12 0.26 1 -0.33 60 61
MAPKAPK3 0.022 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.008 0.14 -10000 0 -0.39 61 61
CEBPB -0.014 0.11 0.25 1 -0.32 55 56
SLC9A1 -0.017 0.11 -10000 0 -0.33 59 59
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.018 0.12 -10000 0 -0.32 62 62
p38alpha-beta/MNK1 0.009 0.12 -10000 0 -0.33 54 54
JUN -0.025 0.1 -10000 0 -0.37 20 20
PPARGC1A -0.07 0.16 -10000 0 -0.32 140 140
USF1 -0.015 0.11 0.27 5 -0.32 55 60
RAB5/GDP/GDI1 -0.011 0.089 -10000 0 -0.24 57 57
NOS2 -0.017 0.14 -10000 0 -0.41 48 48
DDIT3 -0.018 0.12 -10000 0 -0.33 61 61
RAB5A 0.022 0.004 -10000 0 -10000 0 0
HSPB1 -0.017 0.094 0.28 6 -0.27 57 63
p38alpha-beta/HBP1 0.007 0.12 -10000 0 -0.31 60 60
CREB1 -0.02 0.12 -10000 0 -0.36 59 59
RAB5/GDP 0.017 0.003 -10000 0 -10000 0 0
EIF4E -0.016 0.098 0.19 2 -0.3 47 49
RPS6KA4 -0.017 0.11 -10000 0 -0.33 60 60
PLA2G4A -0.023 0.11 0.22 4 -0.32 54 58
GDI1 -0.017 0.11 -10000 0 -0.33 59 59
TP53 -0.028 0.13 -10000 0 -0.41 52 52
RPS6KA5 -0.018 0.12 -10000 0 -0.33 61 61
ESR1 -0.039 0.15 -10000 0 -0.35 86 86
HBP1 0.022 0.004 -10000 0 -10000 0 0
MEF2C -0.038 0.15 -10000 0 -0.35 86 86
MEF2A -0.02 0.12 -10000 0 -0.33 65 65
EIF4EBP1 -0.02 0.12 -10000 0 -0.36 57 57
KRT19 -0.015 0.11 -10000 0 -0.33 57 57
ELK4 -0.016 0.11 0.27 6 -0.32 58 64
ATF6 -0.015 0.11 0.27 5 -0.32 55 60
ATF1 -0.019 0.12 -10000 0 -0.35 59 59
p38alpha-beta/MAPKAPK2 0.002 0.12 -10000 0 -0.3 60 60
p38alpha-beta/MAPKAPK3 0.008 0.12 -10000 0 -0.32 56 56
TCGA08_p53

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
CDKN2A 0.042 0.062 0.11 213 -10000 0 213
TP53 0.003 0.047 -10000 0 -0.15 43 43
Senescence 0.003 0.047 -10000 0 -0.15 43 43
Apoptosis 0.003 0.047 -10000 0 -0.15 43 43
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.033 0.047 0.27 5 -0.2 7 12
MDM4 0.019 0.009 -10000 0 -10000 0 0
Ephrin B reverse 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
EFNB2 0.02 0.028 -10000 0 -0.35 3 3
EPHB2 0.025 0.02 0.28 3 -10000 0 3
EFNB1 -0.007 0.033 -10000 0 -0.27 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.078 -10000 0 -0.18 62 62
Ephrin B2/EPHB1-2 0.02 0.07 0.19 3 -0.18 54 57
neuron projection morphogenesis 0.011 0.069 -10000 0 -0.17 62 62
Ephrin B1/EPHB1-2/Tiam1 0.018 0.079 0.2 4 -0.18 65 69
DNM1 0.018 0.04 -10000 0 -0.35 6 6
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.07 0.18 0.24 2 -0.48 79 81
YES1 -0.092 0.26 -10000 0 -0.7 79 79
Ephrin B1/EPHB1-2/NCK2 0.024 0.073 0.2 4 -0.18 55 59
PI3K -0.044 0.19 -10000 0 -0.48 79 79
mol:GDP 0.017 0.078 0.2 4 -0.18 65 69
ITGA2B 0.019 0.038 0.28 1 -0.35 5 6
endothelial cell proliferation 0.027 0.019 -10000 0 -0.2 3 3
FYN -0.092 0.26 -10000 0 -0.7 79 79
MAP3K7 -0.073 0.18 0.23 1 -0.51 78 79
FGR -0.091 0.25 -10000 0 -0.7 78 78
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
RGS3 0.022 0.006 -10000 0 -10000 0 0
cell adhesion -0.075 0.19 0.25 1 -0.51 77 78
LYN -0.091 0.25 -10000 0 -0.69 79 79
Ephrin B1/EPHB1-2/Src Family Kinases -0.09 0.24 -10000 0 -0.64 81 81
Ephrin B1/EPHB1-2 -0.074 0.2 -10000 0 -0.56 75 75
SRC -0.09 0.25 -10000 0 -0.69 79 79
ITGB3 -0.039 0.14 0.28 2 -0.35 89 91
EPHB1 -0.012 0.11 0.28 1 -0.35 51 52
EPHB4 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.02 -10000 0 -0.2 3 3
alphaIIb/beta3 Integrin -0.016 0.11 0.21 3 -0.24 94 97
BLK -0.086 0.25 -10000 0 -0.69 78 78
HCK -0.088 0.25 -10000 0 -0.7 77 77
regulation of stress fiber formation -0.022 0.072 0.18 55 -0.2 4 59
MAPK8 -0.067 0.17 0.22 2 -0.47 77 79
Ephrin B1/EPHB1-2/RGS3 0.023 0.072 0.2 4 -0.18 55 59
endothelial cell migration -0.057 0.15 0.21 8 -0.43 72 80
NCK2 0.023 0.003 -10000 0 -10000 0 0
PTPN13 -0.036 0.16 -10000 0 -0.46 64 64
regulation of focal adhesion formation -0.022 0.072 0.18 55 -0.2 4 59
chemotaxis -0.022 0.071 0.18 55 -0.2 4 59
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
Rac1/GTP 0.018 0.073 -10000 0 -0.17 62 62
angiogenesis -0.074 0.2 -10000 0 -0.55 76 76
LCK -0.09 0.25 -10000 0 -0.69 79 79
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.057 0.082 -10000 0 -0.23 39 39
NT3 (dimer)/TRKC -0.11 0.15 0.21 3 -0.26 249 252
NT3 (dimer)/TRKB -0.067 0.15 0.2 7 -0.24 208 215
SHC/Grb2/SOS1/GAB1/PI3K 0.011 0.03 -10000 0 -0.17 12 12
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
BDNF 0.061 0.092 0.28 80 -10000 0 80
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
DYNLT1 0.022 0.004 -10000 0 -10000 0 0
NTRK1 0.019 0.045 0.28 7 -0.35 4 11
NTRK2 -0.011 0.12 0.28 8 -0.35 52 60
NTRK3 -0.15 0.18 -10000 0 -0.35 246 246
NT-4/5 (dimer)/TRKB -0.054 0.14 0.2 20 -0.23 199 219
neuron apoptosis 0.12 0.19 0.38 130 -10000 0 130
SHC 2-3/Grb2 -0.12 0.21 -10000 0 -0.42 130 130
SHC1 0.019 0.009 -10000 0 -10000 0 0
SHC2 -0.15 0.24 0.22 1 -0.49 141 142
SHC3 -0.092 0.18 0.22 1 -0.4 92 93
STAT3 (dimer) 0.026 0.014 0.22 2 -10000 0 2
NT3 (dimer)/TRKA -0.04 0.12 0.2 6 -0.22 153 159
RIN/GDP -0.042 0.1 0.24 3 -0.24 34 37
GIPC1 0.022 0.006 -10000 0 -10000 0 0
KRAS 0.023 0.014 0.33 1 -10000 0 1
DNAJA3 -0.098 0.15 0.22 2 -0.28 179 181
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.013 0.027 0.36 3 -10000 0 3
MAGED1 0.021 0.023 -10000 0 -0.35 2 2
PTPN11 0.023 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.032 0.055 0.28 23 -0.35 1 24
SHC/GRB2/SOS1 0.035 0.021 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.014 0.1 0.2 5 -0.21 107 112
TRKA/NEDD4-2 0.026 0.036 0.21 6 -0.24 5 11
ELMO1 0.019 0.032 -10000 0 -0.35 4 4
RhoG/GTP/ELMO1/DOCK1 0.024 0.036 -10000 0 -0.22 10 10
NGF -0.056 0.15 -10000 0 -0.35 112 112
HRAS 0.022 0.005 -10000 0 -10000 0 0
DOCK1 0.017 0.043 -10000 0 -0.35 7 7
GAB2 0.02 0.032 -10000 0 -0.35 4 4
RIT2 0.017 0.005 -10000 0 -10000 0 0
RIT1 0.018 0.01 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
DNM1 0.018 0.04 -10000 0 -0.35 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.086 0.15 0.18 1 -0.28 177 178
mol:GDP -0.066 0.14 0.29 3 -0.34 42 45
NGF (dimer) -0.056 0.15 -10000 0 -0.35 112 112
RhoG/GDP 0.015 0.022 -10000 0 -0.24 4 4
RIT1/GDP -0.047 0.085 0.22 2 -0.24 31 33
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
BDNF (dimer)/TRKB 0.041 0.1 0.2 79 -0.21 51 130
KIDINS220/CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.024 0.03 -10000 0 -0.24 5 5
FRS2 family/SHP2 0.045 0.01 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.042 0.032 -10000 0 -0.18 3 3
RIT1/GTP 0.013 0.007 -10000 0 -10000 0 0
NT3 (dimer) 0.003 0.091 0.28 5 -0.35 31 36
RAP1/GDP -0.041 0.083 -10000 0 -0.2 36 36
KIDINS220/CRKL 0.022 0.005 -10000 0 -10000 0 0
BDNF (dimer) 0.061 0.092 0.28 80 -10000 0 80
ubiquitin-dependent protein catabolic process -0.01 0.098 0.2 5 -0.21 99 104
Schwann cell development -0.035 0.028 -10000 0 -10000 0 0
EHD4 0.022 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.053 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.006 0.058 -10000 0 -0.3 9 9
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.071 0.14 0.18 2 -0.2 250 252
ABL1 0.02 0.023 -10000 0 -0.35 2 2
SH2B family/GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
Rap1/GTP 0.003 0.079 -10000 0 -0.28 15 15
STAT3 0.026 0.014 0.21 2 -10000 0 2
axon guidance -0.075 0.13 -10000 0 -0.19 252 252
MAPK3 -0.021 0.1 0.18 70 -0.19 99 169
MAPK1 -0.022 0.1 0.18 70 -0.19 101 171
CDC42/GDP -0.041 0.1 0.24 3 -0.24 32 35
NTF3 0.003 0.091 0.28 5 -0.35 31 36
NTF4 0.032 0.055 0.28 23 -0.35 1 24
NGF (dimer)/TRKA/FAIM -0.008 0.098 0.2 5 -0.21 97 102
PI3K 0.026 0.029 -10000 0 -0.24 5 5
FRS3 0.023 0.003 -10000 0 -10000 0 0
FAIM 0.022 0.017 -10000 0 -0.35 1 1
GAB1 0.019 0.032 -10000 0 -0.35 4 4
RASGRF1 -0.11 0.16 0.22 2 -0.3 184 186
SOS1 0.023 0.003 -10000 0 -10000 0 0
MCF2L -0.11 0.11 -10000 0 -0.22 238 238
RGS19 0.022 0.006 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.01 0.096 -10000 0 -0.38 11 11
Rac1/GDP -0.043 0.1 0.24 3 -0.24 33 36
NGF (dimer)/TRKA/GRIT -0.017 0.092 0.19 5 -0.2 100 105
neuron projection morphogenesis -0.12 0.24 -10000 0 -0.87 30 30
NGF (dimer)/TRKA/NEDD4-2 -0.009 0.099 0.2 5 -0.21 99 104
MAP2K1 0.026 0.086 0.18 115 -0.18 2 117
NGFR -0.098 0.17 0.28 1 -0.35 171 172
NGF (dimer)/TRKA/GIPC/GAIP -0.022 0.081 -10000 0 -0.2 88 88
RAS family/GTP/PI3K 0.013 0.027 0.17 1 -0.2 7 8
FRS2 family/SHP2/GRB2/SOS1 0.061 0.022 -10000 0 -10000 0 0
NRAS 0.023 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
MAPKKK cascade -0.13 0.25 -10000 0 -0.56 121 121
RASA1 0.019 0.036 -10000 0 -0.35 5 5
TRKA/c-Abl 0.025 0.037 0.21 6 -0.24 6 12
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.05 0.096 -10000 0 -0.19 47 47
NGF (dimer)/TRKA/p62/Atypical PKCs 0.007 0.091 -10000 0 -0.18 87 87
MATK 0.013 0.057 0.28 1 -0.35 12 13
NEDD4L 0.021 0.017 -10000 0 -0.35 1 1
RAS family/GDP -0.052 0.06 -10000 0 -0.17 48 48
NGF (dimer)/TRKA -0.1 0.15 0.19 1 -0.29 182 183
Rac1/GTP -0.1 0.11 -10000 0 -0.24 155 155
FRS2 family/SHP2/CRK family 0.059 0.024 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.089 0.26 0.47 7 -0.6 57 64
PCK1 -0.069 0.32 0.49 7 -1.1 36 43
HNF4A -0.099 0.34 0.66 13 -0.78 66 79
KCNJ11 -0.08 0.27 0.6 5 -0.68 34 39
AKT1 -0.031 0.17 0.38 11 -0.36 22 33
response to starvation -0.004 0.034 -10000 0 -0.17 4 4
DLK1 -0.12 0.34 0.61 8 -0.78 78 86
NKX2-1 -0.078 0.16 0.36 8 -0.37 52 60
ACADM -0.093 0.27 0.5 5 -0.66 42 47
TAT -0.079 0.23 0.45 6 -0.56 48 54
CEBPB 0.023 0.008 -10000 0 -10000 0 0
CEBPA 0.023 0.033 0.28 2 -0.35 3 5
TTR 0.071 0.18 0.51 16 -0.66 8 24
PKLR -0.051 0.27 0.51 21 -0.62 36 57
APOA1 -0.15 0.44 0.67 10 -1.1 71 81
CPT1C -0.093 0.27 0.48 6 -0.67 45 51
ALAS1 -0.044 0.17 0.46 3 -0.67 3 6
TFRC -0.01 0.21 0.63 6 -0.62 7 13
FOXF1 0.017 0.036 -10000 0 -0.35 5 5
NF1 0.024 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.04 0.043 0.31 8 -10000 0 8
CPT1A -0.088 0.26 0.48 7 -0.64 42 49
HMGCS1 -0.085 0.26 0.49 8 -0.64 41 49
NR3C1 -0.052 0.15 -10000 0 -0.28 136 136
CPT1B -0.086 0.26 0.54 6 -0.64 43 49
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.023 -10000 0 -10000 0 0
GCK -0.15 0.35 0.55 6 -0.75 95 101
CREB1 0.017 0.055 -10000 0 -0.18 34 34
IGFBP1 -0.2 0.43 0.44 7 -1.1 90 97
PDX1 -0.007 0.18 0.5 10 -0.53 4 14
UCP2 -0.087 0.27 0.52 8 -0.61 51 59
ALDOB -0.078 0.26 0.57 7 -0.66 35 42
AFP 0.068 0.073 0.32 7 -0.27 5 12
BDH1 -0.074 0.27 0.51 12 -0.63 42 54
HADH -0.078 0.26 0.54 5 -0.68 29 34
F2 -0.098 0.34 0.67 13 -0.81 37 50
HNF1A 0.04 0.043 0.31 8 -10000 0 8
G6PC 0.028 0.071 0.4 1 -10000 0 1
SLC2A2 -0.026 0.19 0.64 4 -10000 0 4
INS 0.006 0.069 0.2 38 -10000 0 38
FOXA1 0.19 0.14 0.29 340 -0.26 7 347
FOXA3 0.075 0.13 0.31 101 -0.24 16 117
FOXA2 -0.078 0.33 0.7 12 -0.71 46 58
ABCC8 -0.16 0.37 0.6 5 -0.8 105 110
ALB 0.061 0.12 0.38 3 -0.74 9 12
Noncanonical Wnt signaling pathway

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
NFATC2 -0.011 0.1 -10000 0 -0.35 46 46
GNB1/GNG2 -0.035 0.14 -10000 0 -0.38 39 39
mol:DAG -0.044 0.12 0.2 8 -0.36 37 45
PLCG1 -0.046 0.13 0.21 8 -0.37 37 45
YES1 -0.052 0.12 0.2 2 -0.24 125 127
FZD3 0.02 0.008 -10000 0 -10000 0 0
FZD6 0.02 0.018 -10000 0 -0.35 1 1
G protein -0.031 0.14 0.25 3 -0.37 36 39
MAP3K7 -0.12 0.13 0.2 4 -0.31 110 114
mol:Ca2+ -0.043 0.12 0.2 8 -0.34 37 45
mol:IP3 -0.044 0.12 0.2 8 -0.36 37 45
NLK -0.027 0.15 -10000 0 -0.81 19 19
GNB1 0.022 0.004 -10000 0 -10000 0 0
CAMK2A -0.12 0.14 0.23 4 -0.33 110 114
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.046 0.14 0.17 1 -0.25 129 130
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
GNAS -0.051 0.12 0.21 3 -0.41 31 34
GO:0007205 -0.048 0.12 0.21 9 -0.35 38 47
WNT6 0.01 0.11 0.28 22 -0.35 34 56
WNT4 -0.066 0.16 -10000 0 -0.35 126 126
NFAT1/CK1 alpha -0.047 0.14 0.26 2 -0.36 44 46
GNG2 0.017 0.049 0.28 1 -0.35 9 10
WNT5A 0.011 0.064 -10000 0 -0.35 16 16
WNT11 0.037 0.098 0.28 49 -0.35 14 63
CDC42 -0.05 0.12 0.2 3 -0.39 31 34
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.08 0.12 -10000 0 -0.21 254 254
fibroblast growth factor receptor signaling pathway -0.08 0.12 -10000 0 -0.21 254 254
LAMA1 0.1 0.13 0.28 173 -0.35 4 177
PRNP -0.03 0.13 -10000 0 -0.35 74 74
GPC1/SLIT2 -0.002 0.09 -10000 0 -0.24 64 64
SMAD2 -0.015 0.032 0.18 6 -0.19 10 16
GPC1/PrPc/Cu2+ -0.003 0.081 -10000 0 -0.2 74 74
GPC1/Laminin alpha1 0.086 0.088 0.21 169 -0.24 4 173
TDGF1 0.013 0.091 0.28 17 -0.35 24 41
CRIPTO/GPC1 0.025 0.067 0.21 17 -0.24 24 41
APP/GPC1 0.033 0.007 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.042 -10000 0 -0.21 23 23
FLT1 0.022 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.038 0.036 -10000 0 -0.2 10 10
SERPINC1 0.022 0.032 0.29 7 -10000 0 7
FYN -0.018 0.042 -10000 0 -0.21 22 22
FGR -0.023 0.051 -10000 0 -0.21 33 33
positive regulation of MAPKKK cascade 0.01 0.09 0.24 31 -0.28 20 51
SLIT2 -0.023 0.12 -10000 0 -0.35 64 64
GPC1/NRG 0.025 0.038 0.21 1 -0.24 9 10
NRG1 0.014 0.05 0.28 1 -0.35 9 10
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.043 0.013 -10000 0 -10000 0 0
LYN -0.017 0.04 -10000 0 -0.21 20 20
mol:Spermine -0.006 0.001 -10000 0 -10000 0 0
cell growth -0.08 0.12 -10000 0 -0.21 254 254
BMP signaling pathway -0.023 0.003 -10000 0 -10000 0 0
SRC -0.018 0.042 -10000 0 -0.21 23 23
TGFBR1 0.022 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.004 0.11 0.28 10 -0.35 43 53
GPC1 0.023 0.003 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.022 0.006 -10000 0 -10000 0 0
VEGFA 0.023 0.003 -10000 0 -10000 0 0
BLK -0.006 0.059 0.15 36 -0.2 19 55
HCK -0.016 0.045 0.13 7 -0.21 22 29
FGF2 -0.17 0.18 -10000 0 -0.35 272 272
FGFR1 0.02 0.018 -10000 0 -0.35 1 1
VEGFR1 homodimer 0.022 0.005 -10000 0 -10000 0 0
TGFBR2 0.015 0.051 -10000 0 -0.35 10 10
cell death 0.033 0.007 -10000 0 -10000 0 0
ATIII/GPC1 0.03 0.025 0.22 7 -10000 0 7
PLA2G2A/GPC1 0.012 0.08 0.21 10 -0.24 43 53
LCK -0.017 0.043 0.13 3 -0.2 22 25
neuron differentiation 0.025 0.038 0.21 1 -0.24 9 10
PrPc/Cu2+ -0.019 0.089 -10000 0 -0.24 74 74
APP 0.023 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.015 0.051 -10000 0 -0.35 10 10
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.016 0.037 -10000 0 -0.2 20 20
ADCY5 -0.044 0.075 -10000 0 -0.2 97 97
ADCY6 -0.009 0.002 -10000 0 -10000 0 0
ADCY7 -0.008 0.003 -10000 0 -10000 0 0
ADCY1 -0.014 0.038 0.24 1 -0.2 18 19
ADCY2 -0.11 0.098 -10000 0 -0.2 274 274
ADCY3 -0.01 0.012 -10000 0 -0.2 2 2
ADCY8 -0.009 0.017 0.24 2 -10000 0 2
PRKCE -0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.035 0.067 -10000 0 -0.2 72 72
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.052 0.094 0.22 19 -0.21 41 60
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 -0.012 0.11 -10000 0 -0.35 48 48
GNB1/GNG2 -0.044 0.074 -10000 0 -0.19 97 97
AKT1 -0.036 0.098 0.21 2 -0.23 41 43
EGF 0.031 0.052 0.28 20 -0.35 1 21
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.012 0.063 0.26 5 -0.26 2 7
mol:Ca2+ -0.066 0.14 0.25 2 -0.31 109 111
LYN -0.01 0.054 0.27 4 -10000 0 4
RhoA/GTP -0.027 0.057 -10000 0 -0.13 87 87
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.15 -10000 0 -0.35 97 97
GNG2 0.017 0.05 0.28 1 -0.35 9 10
ARRB2 0.021 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.052 0.18 -10000 0 -0.56 51 51
G beta5/gamma2 -0.054 0.098 -10000 0 -0.25 95 95
PRKCH -0.076 0.16 -10000 0 -0.37 95 95
DNM1 0.018 0.04 -10000 0 -0.35 6 6
TXA2/TP beta/beta Arrestin3 0.012 0.026 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.01 0.1 -10000 0 -0.35 45 45
G12 family/GTP -0.068 0.13 -10000 0 -0.3 101 101
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
ADRBK2 0.021 0.017 -10000 0 -0.35 1 1
RhoA/GTP/ROCK1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.047 0.13 0.42 35 -10000 0 35
mol:NADP 0.022 0.02 0.28 1 -0.35 1 2
RAB11A 0.022 0.005 -10000 0 -10000 0 0
PRKG1 -0.13 0.18 -10000 0 -0.35 222 222
mol:IP3 -0.085 0.18 -10000 0 -0.39 110 110
cell morphogenesis 0.029 0.008 -10000 0 -10000 0 0
PLCB2 -0.12 0.24 -10000 0 -0.54 110 110
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.002 0.07 0.3 9 -0.2 1 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.009 0.056 0.24 4 -0.22 1 5
RHOA 0.022 0.005 -10000 0 -10000 0 0
PTGIR 0.022 0.017 -10000 0 -0.35 1 1
PRKCB1 -0.081 0.17 -10000 0 -0.39 100 100
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
mol:L-citrulline 0.022 0.02 0.28 1 -0.35 1 2
TXA2/TXA2-R family -0.11 0.22 -10000 0 -0.54 97 97
LCK -0.008 0.062 0.26 6 -0.22 1 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.011 0.056 -10000 0 -0.17 34 34
TXA2-R family/G12 family/GDP/G beta/gamma -0.002 0.093 -10000 0 -0.42 22 22
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.013 0.053 -10000 0 -0.17 30 30
MAPK14 -0.046 0.1 0.19 4 -0.23 92 96
TGM2/GTP -0.1 0.2 0.32 2 -0.44 117 119
MAPK11 -0.047 0.1 0.18 2 -0.23 96 98
ARHGEF1 -0.039 0.077 -10000 0 -0.18 92 92
GNAI2 0.022 0.005 -10000 0 -10000 0 0
JNK cascade -0.08 0.17 -10000 0 -0.39 97 97
RAB11/GDP 0.022 0.005 -10000 0 -10000 0 0
ICAM1 -0.054 0.12 -10000 0 -0.28 95 95
cAMP biosynthetic process -0.083 0.16 0.26 1 -0.36 119 120
Gq family/GTP/EBP50 -0.014 0.081 -10000 0 -0.21 65 65
actin cytoskeleton reorganization 0.029 0.008 -10000 0 -10000 0 0
SRC -0.01 0.058 0.25 5 -0.22 1 6
GNB5 0.022 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
EGF/EGFR 0.013 0.074 0.24 22 -0.24 3 25
VCAM1 -0.062 0.14 -10000 0 -0.32 97 97
TP beta/Gq family/GDP/G beta5/gamma2 -0.052 0.18 -10000 0 -0.56 51 51
platelet activation -0.063 0.14 0.24 3 -0.31 97 100
PGI2/IP 0.016 0.011 -10000 0 -0.24 1 1
PRKACA -0.003 0.055 -10000 0 -0.19 40 40
Gq family/GDP/G beta5/gamma2 -0.041 0.16 -10000 0 -0.48 48 48
TXA2/TP beta/beta Arrestin2 -0.003 0.071 -10000 0 -0.37 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.046 -10000 0 -0.18 35 35
mol:DAG -0.092 0.19 -10000 0 -0.45 100 100
EGFR 0.014 0.059 0.33 1 -0.35 13 14
TXA2/TP alpha -0.12 0.22 -10000 0 -0.5 119 119
Gq family/GTP -0.028 0.093 -10000 0 -0.23 78 78
YES1 -0.008 0.059 0.26 6 -10000 0 6
GNAI2/GTP 0 0.05 -10000 0 -0.16 33 33
PGD2/DP -0.006 0.072 -10000 0 -0.24 45 45
SLC9A3R1 0.024 0.023 0.28 4 -10000 0 4
FYN -0.011 0.058 0.26 5 -0.22 1 6
mol:NO 0.022 0.02 0.28 1 -0.35 1 2
GNA15 0.025 0.03 0.28 7 -10000 0 7
PGK/cGMP -0.069 0.11 -10000 0 -0.2 221 221
RhoA/GDP 0.022 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.006 0.086 -10000 0 -0.29 13 13
NOS3 0.022 0.02 0.28 1 -0.35 1 2
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.078 0.16 -10000 0 -0.37 99 99
PRKCB -0.081 0.16 -10000 0 -0.38 100 100
PRKCE -0.073 0.16 0.28 1 -0.37 95 96
PRKCD -0.078 0.17 -10000 0 -0.4 96 96
PRKCG -0.082 0.17 0.28 1 -0.4 100 101
muscle contraction -0.11 0.21 -10000 0 -0.5 103 103
PRKCZ -0.072 0.15 0.25 1 -0.35 97 98
ARR3 0.019 0.012 0.28 1 -10000 0 1
TXA2/TP beta 0.011 0.057 -10000 0 -0.18 31 31
PRKCQ -0.081 0.17 0.31 3 -0.38 103 106
MAPKKK cascade -0.1 0.21 -10000 0 -0.48 105 105
SELE -0.066 0.15 -10000 0 -0.34 97 97
TP beta/GNAI2/GDP/G beta/gamma 0.022 0.065 -10000 0 -0.27 3 3
ROCK1 0.023 0.004 -10000 0 -10000 0 0
GNA14 -0.011 0.1 -10000 0 -0.35 46 46
chemotaxis -0.12 0.24 -10000 0 -0.6 97 97
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.014 0.051 -10000 0 -0.35 10 10
Rac1/GTP 0.016 0.004 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.018 0.045 0.28 9 -10000 0 9
CDKN2C 0.021 0.049 -10000 0 -0.34 9 9
CDKN2A 0.13 0.13 0.28 213 -10000 0 213
CCND2 -0.037 0.06 0.14 1 -0.16 54 55
RB1 0.035 0.067 0.31 14 -0.14 2 16
CDK4 -0.035 0.068 0.13 2 -0.32 14 16
CDK6 -0.04 0.073 0.16 1 -0.27 25 26
G1/S progression -0.035 0.072 0.16 5 -0.32 15 20
Syndecan-1-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
TGFB1 0.022 0.017 -10000 0 -0.35 1 1
CCL5 0.021 0.046 0.28 6 -0.35 5 11
SDCBP 0.021 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.071 0.089 0.24 37 -0.24 4 41
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 0.064 0.089 0.25 18 -0.28 4 22
Syndecan-1/Syntenin 0.065 0.088 0.23 25 -0.26 5 30
MAPK3 0.053 0.08 0.22 18 -0.26 4 22
HGF/MET -0.021 0.12 0.21 4 -0.25 103 107
TGFB1/TGF beta receptor Type II 0.022 0.017 -10000 0 -0.35 1 1
BSG 0.021 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.064 0.088 0.24 18 -0.27 4 22
Syndecan-1/RANTES 0.07 0.091 0.25 24 -0.29 6 30
Syndecan-1/CD147 0.071 0.09 0.26 12 -0.26 5 17
Syndecan-1/Syntenin/PIP2 0.061 0.083 0.22 22 -0.25 5 27
LAMA5 0.022 0.015 0.33 1 -10000 0 1
positive regulation of cell-cell adhesion 0.059 0.081 0.21 21 -0.25 5 26
MMP7 0.027 0.13 0.28 60 -0.35 35 95
HGF -0.049 0.15 -10000 0 -0.35 102 102
Syndecan-1/CASK 0.055 0.086 0.16 89 -0.23 10 99
Syndecan-1/HGF/MET 0.044 0.12 0.27 17 -0.29 28 45
regulation of cell adhesion 0.045 0.074 0.24 10 -0.25 3 13
HPSE 0.017 0.051 0.28 2 -0.35 9 11
positive regulation of cell migration 0.071 0.089 0.24 37 -0.24 4 41
SDC1 0.072 0.086 0.19 89 -0.18 16 105
Syndecan-1/Collagen 0.071 0.089 0.24 37 -0.24 4 41
PPIB 0.023 0.012 0.28 1 -10000 0 1
MET 0.021 0.039 0.28 4 -0.35 4 8
PRKACA 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 218 -10000 0 218
MAPK1 0.054 0.078 0.2 20 -0.24 5 25
homophilic cell adhesion 0.07 0.092 0.25 35 -0.22 7 42
MMP1 0.16 0.13 0.28 281 -10000 0 281
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.061 0.095 0.32 62 -10000 0 62
NFATC2 0 0.18 -10000 0 -0.47 37 37
NFATC3 0 0.091 -10000 0 -0.27 37 37
CD40LG -0.11 0.3 -10000 0 -0.79 67 67
ITCH 0.021 0.02 -10000 0 -0.2 1 1
CBLB 0.022 0.02 -10000 0 -0.2 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.045 0.25 0.44 13 -0.64 45 58
JUNB 0.018 0.036 -10000 0 -0.35 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.035 -10000 0 -0.24 1 1
T cell anergy 0.018 0.053 0.27 8 -0.33 1 9
TLE4 -0.029 0.18 -10000 0 -0.55 49 49
Jun/NFAT1-c-4/p21SNFT -0.042 0.31 -10000 0 -0.76 66 66
AP-1/NFAT1-c-4 -0.073 0.38 0.56 5 -0.88 66 71
IKZF1 -0.004 0.12 0.34 1 -0.34 33 34
T-helper 2 cell differentiation -0.064 0.22 -10000 0 -0.68 34 34
AP-1/NFAT1 -0.034 0.18 0.31 3 -0.34 74 77
CALM1 0.031 0.016 -10000 0 -0.15 1 1
EGR2 -0.11 0.37 -10000 0 -0.98 66 66
EGR3 -0.14 0.42 -10000 0 -1.1 74 74
NFAT1/FOXP3 0.045 0.17 0.42 34 -0.34 32 66
EGR1 -0.023 0.12 -10000 0 -0.35 67 67
JUN 0.018 0.047 -10000 0 -0.35 7 7
EGR4 0.03 0.044 0.28 15 -10000 0 15
mol:Ca2+ 0.009 0.014 -10000 0 -0.14 1 1
GBP3 -0.006 0.13 -10000 0 -0.39 30 30
FOSL1 0.042 0.068 0.28 40 -10000 0 40
NFAT1-c-4/MAF/IRF4 -0.065 0.33 0.47 1 -0.8 70 71
DGKA -0.002 0.11 -10000 0 -0.35 25 25
CREM 0.021 0.009 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.06 0.32 -10000 0 -0.78 74 74
CTLA4 0.023 0.13 0.3 51 -0.29 27 78
NFAT1-c-4 (dimer)/EGR1 -0.067 0.34 -10000 0 -0.81 74 74
NFAT1-c-4 (dimer)/EGR4 -0.041 0.32 0.5 1 -0.77 72 73
FOS -0.087 0.17 -10000 0 -0.35 158 158
IFNG -0.031 0.2 0.37 1 -0.62 29 30
T cell activation -0.07 0.2 -10000 0 -0.6 40 40
MAF -0.033 0.13 -10000 0 -0.35 76 76
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.068 0.28 0.7 70 -10000 0 70
TNF -0.073 0.3 0.47 1 -0.75 70 71
FASLG -0.15 0.46 -10000 0 -1.1 85 85
TBX21 0.026 0.059 0.35 3 -0.35 9 12
BATF3 0.02 0.014 0.28 1 -10000 0 1
PRKCQ -0.006 0.1 0.32 1 -0.35 43 44
PTPN1 -0.004 0.12 -10000 0 -0.34 30 30
NFAT1-c-4/ICER1 -0.053 0.32 -10000 0 -0.76 73 73
GATA3 0.025 0.057 0.28 13 -0.35 6 19
T-helper 1 cell differentiation -0.03 0.2 0.37 1 -0.61 29 30
IL2RA -0.042 0.26 0.44 16 -0.63 50 66
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.004 0.11 -10000 0 -0.34 32 32
E2F1 0.074 0.1 0.29 99 -10000 0 99
PPARG 0.004 0.084 0.33 1 -0.35 28 29
SLC3A2 -0.003 0.11 -10000 0 -0.36 24 24
IRF4 0.02 0.061 0.28 9 -0.35 10 19
PTGS2 -0.12 0.31 0.41 1 -0.79 70 71
CSF2 -0.11 0.3 -10000 0 -0.77 67 67
JunB/Fra1/NFAT1-c-4 -0.033 0.31 0.46 2 -0.76 65 67
IL4 -0.067 0.22 -10000 0 -0.72 32 32
IL5 -0.11 0.3 -10000 0 -0.77 68 68
IL2 -0.071 0.2 -10000 0 -0.62 38 38
IL3 -0.021 0.11 -10000 0 -0.66 12 12
RNF128 0.032 0.059 0.22 42 -0.47 1 43
NFATC1 -0.068 0.28 -10000 0 -0.71 70 70
CDK4 0.063 0.19 0.55 46 -10000 0 46
PTPRK -0.003 0.12 0.34 1 -0.36 28 29
IL8 -0.073 0.32 0.42 3 -0.78 65 68
POU2F1 0.019 0.009 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.003 0.089 0.25 51 -0.21 11 62
KIRREL -0.017 0.11 -10000 0 -0.36 53 53
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.003 0.09 0.22 11 -0.26 51 62
PLCG1 0.022 0.005 -10000 0 -10000 0 0
ARRB2 0.021 0.006 -10000 0 -10000 0 0
WASL 0.022 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.023 0.078 0.31 2 -0.19 50 52
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.006 0.07 0.21 2 -0.21 49 51
FYN 0.016 0.12 0.23 97 -0.18 50 147
mol:Ca2+ 0.02 0.075 0.34 1 -0.19 50 51
mol:DAG 0.021 0.075 0.34 1 -0.19 50 51
NPHS2 -0.008 0.033 0.3 3 -10000 0 3
mol:IP3 0.021 0.075 0.34 1 -0.19 50 51
regulation of endocytosis 0.015 0.067 0.19 7 -0.17 50 57
Nephrin/NEPH1/podocin/Cholesterol 0.013 0.073 0.2 12 -0.18 51 63
establishment of cell polarity 0.003 0.089 0.21 11 -0.25 51 62
Nephrin/NEPH1/podocin/NCK1-2 0.029 0.08 0.31 2 -0.18 50 52
Nephrin/NEPH1/beta Arrestin2 0.016 0.069 0.2 8 -0.18 50 58
NPHS1 0.02 0.053 0.29 13 -10000 0 13
Nephrin/NEPH1/podocin 0.014 0.072 0.2 11 -0.18 50 61
TJP1 0.022 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.023 -10000 0 -0.35 2 2
NCK2 0.023 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.021 0.076 0.35 1 -0.19 50 51
CD2AP 0.023 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.021 0.076 0.35 1 -0.19 50 51
GRB2 0.022 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.006 0.12 0.23 91 -0.2 66 157
cytoskeleton organization -0.016 0.079 0.22 18 -0.22 48 66
Nephrin/NEPH1 0.007 0.063 0.18 11 -0.17 51 62
Nephrin/NEPH1/ZO-1 0.014 0.077 0.2 11 -0.2 51 62
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS 0.018 0.11 0.32 3 -0.19 94 97
SMAD6-7/SMURF1 0.041 0.023 -10000 0 -0.21 3 3
NOG 0.041 0.074 0.28 43 -0.35 2 45
SMAD9 -0.07 0.19 -10000 0 -0.49 84 84
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD5 -0.026 0.097 -10000 0 -0.34 23 23
BMP7/USAG1 0.021 0.11 0.22 54 -0.25 56 110
SMAD5/SKI -0.021 0.11 -10000 0 -0.35 28 28
SMAD1 0.004 0.064 0.24 2 -0.42 6 8
BMP2 -0.009 0.1 -10000 0 -0.35 45 45
SMAD1/SMAD1/SMAD4 0.016 0.06 -10000 0 -0.32 6 6
BMPR1A 0.022 0.006 -10000 0 -10000 0 0
BMPR1B 0.002 0.087 0.28 1 -0.35 30 31
BMPR1A-1B/BAMBI 0.025 0.074 0.21 7 -0.22 39 46
AHSG 0.024 0.038 0.28 11 -10000 0 11
CER1 0.018 0.005 -10000 0 -10000 0 0
BMP2-4/CER1 0.015 0.085 0.2 8 -0.22 56 64
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.044 0.11 -10000 0 -0.33 40 40
BMP2-4 (homodimer) 0.002 0.098 0.21 8 -0.26 60 68
RGMB 0.022 0.017 -10000 0 -0.35 1 1
BMP6/BMPR2/BMPR1A-1B 0.035 0.066 0.21 1 -0.2 36 37
RGMA -0.057 0.15 -10000 0 -0.35 113 113
SMURF1 0.022 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.1 -10000 0 -0.3 43 43
BMP2-4/USAG1 0.012 0.12 0.2 41 -0.23 84 125
SMAD6/SMURF1/SMAD5 -0.023 0.11 -10000 0 -0.36 27 27
SOSTDC1 0.018 0.11 0.28 38 -0.35 32 70
BMP7/BMPR2/BMPR1A-1B 0.035 0.082 0.23 3 -0.2 47 50
SKI 0.022 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.015 0.053 -10000 0 -0.35 11 11
HFE2 0.016 0.018 0.28 2 -10000 0 2
ZFYVE16 0.022 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD -0.016 0.12 0.2 8 -0.23 112 120
SMAD5/SMAD5/SMAD4 -0.021 0.11 -10000 0 -0.36 26 26
MAPK1 0.022 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.025 0.11 -10000 0 -0.28 41 41
BMP7 (homodimer) 0.018 0.11 0.29 30 -0.35 28 58
NUP214 0.022 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.027 0.048 0.21 11 -0.25 11 22
SMAD1/SKI 0.013 0.071 -10000 0 -0.39 7 7
SMAD6 0.021 0.017 -10000 0 -0.35 1 1
CTDSP2 0.023 0.001 -10000 0 -10000 0 0
BMP2-4/FETUA 0.021 0.082 0.2 16 -0.22 48 64
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.067 0.16 -10000 0 -0.35 126 126
BMPR2 (homodimer) 0.023 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.043 0.014 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.017 0.063 0.21 1 -0.24 28 29
CHRDL1 -0.23 0.17 -10000 0 -0.35 362 362
ENDOFIN/SMAD1 0.012 0.07 0.24 2 -0.38 7 9
SMAD6-7/SMURF1/SMAD1 0.029 0.074 -10000 0 -0.38 6 6
SMAD6/SMURF1 0.022 0.004 -10000 0 -10000 0 0
BAMBI 0.015 0.072 0.28 8 -0.35 16 24
SMURF2 0.022 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.15 0.14 0.2 2 -0.23 369 371
BMP2-4/GREM1 -0.041 0.14 0.2 7 -0.23 162 169
SMAD7 0.021 0.023 -10000 0 -0.35 2 2
SMAD8A/SMAD8A/SMAD4 -0.065 0.19 -10000 0 -0.46 90 90
SMAD1/SMAD6 0.011 0.072 -10000 0 -0.39 7 7
TAK1/SMAD6 0.033 0.007 -10000 0 -10000 0 0
BMP7 0.018 0.11 0.29 30 -0.35 28 58
BMP6 0.015 0.053 -10000 0 -0.35 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.037 0.11 -10000 0 -0.3 51 51
PPM1A 0.022 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.014 0.069 -10000 0 -0.39 7 7
SMAD7/SMURF1 0.031 0.019 -10000 0 -0.24 2 2
CTDSPL 0.022 0.004 -10000 0 -10000 0 0
PPP1CA 0.022 0.004 -10000 0 -10000 0 0
XIAP 0.023 0.001 -10000 0 -10000 0 0
CTDSP1 0.023 0.004 -10000 0 -10000 0 0
PPP1R15A 0.023 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.062 0.14 -10000 0 -0.38 63 63
CHRD -0.036 0.13 -10000 0 -0.35 81 81
BMPR2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.049 0.11 -10000 0 -0.33 41 41
BMP4 0.011 0.084 0.28 9 -0.35 23 32
FST -0.016 0.12 0.28 6 -0.35 58 64
BMP2-4/NOG 0.025 0.1 0.21 42 -0.22 62 104
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.042 0.081 0.23 2 -0.19 47 49
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.024 0.074 -10000 0 -0.18 60 60
ER alpha/Gai/GDP/Gbeta gamma -0.11 0.21 -10000 0 -0.48 89 89
AKT1 -0.081 0.25 -10000 0 -0.72 69 69
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.08 0.26 -10000 0 -0.73 69 69
mol:Ca2+ -0.033 0.11 0.18 1 -0.35 50 51
IGF1R 0.009 0.069 -10000 0 -0.35 19 19
E2/ER alpha (dimer)/Striatin 0.005 0.072 -10000 0 -0.2 56 56
SHC1 0.019 0.009 -10000 0 -10000 0 0
apoptosis 0.077 0.24 0.68 69 -10000 0 69
RhoA/GTP 0.003 0.053 -10000 0 -0.16 47 47
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.075 0.18 -10000 0 -0.44 69 69
regulation of stress fiber formation 0.021 0.067 0.26 2 -0.26 10 12
E2/ERA-ERB (dimer) 0.005 0.072 0.19 1 -0.2 55 56
KRAS 0.023 0.014 0.33 1 -10000 0 1
G13/GTP 0.005 0.064 -10000 0 -0.18 54 54
pseudopodium formation -0.021 0.067 0.26 10 -0.26 2 12
E2/ER alpha (dimer)/PELP1 0.004 0.069 -10000 0 -0.2 53 53
GRB2 0.022 0.006 -10000 0 -10000 0 0
GNG2 0.017 0.049 0.28 1 -0.35 9 10
GNAO1 -0.065 0.16 -10000 0 -0.35 123 123
HRAS 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.084 0.2 -10000 0 -0.5 75 75
E2/ER beta (dimer) 0.017 0.008 0.19 1 -10000 0 1
mol:GDP -0.02 0.097 -10000 0 -0.28 58 58
mol:NADP -0.084 0.2 -10000 0 -0.5 75 75
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.036 0.11 -10000 0 -0.36 51 51
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.35 19 19
PLCB1 -0.034 0.12 -10000 0 -0.37 54 54
PLCB2 -0.032 0.12 -10000 0 -0.37 51 51
IGF1 -0.047 0.15 -10000 0 -0.35 100 100
mol:L-citrulline -0.084 0.2 -10000 0 -0.5 75 75
RHOA 0.022 0.005 -10000 0 -10000 0 0
Gai/GDP -0.19 0.31 -10000 0 -0.62 177 177
JNK cascade 0.017 0.008 0.19 1 -10000 0 1
BCAR1 0.02 0.008 -10000 0 -10000 0 0
ESR2 0.023 0.012 0.28 1 -10000 0 1
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
ESR1 -0.017 0.11 -10000 0 -0.35 55 55
Gq family/GDP/Gbeta gamma -0.067 0.23 -10000 0 -0.65 61 61
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.019 0.12 -10000 0 -0.63 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.071 0.17 -10000 0 -0.44 63 63
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
E2/ER alpha (dimer) -0.01 0.078 -10000 0 -0.24 55 55
STRN 0.021 0.023 -10000 0 -0.35 2 2
GNAL -0.031 0.13 -10000 0 -0.35 76 76
PELP1 0.021 0.006 -10000 0 -10000 0 0
MAPK11 0.008 0.013 -10000 0 -0.2 2 2
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
HBEGF -0.091 0.19 0.28 3 -0.51 61 64
cAMP biosynthetic process -0.019 0.087 0.12 1 -0.18 111 112
SRC -0.1 0.2 0.26 1 -0.48 77 78
PI3K 0.026 0.029 -10000 0 -0.24 5 5
GNB1 0.022 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.004 0.097 -10000 0 -0.28 47 47
SOS1 0.023 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.09 0.16 -10000 0 -0.38 87 87
Gs family/GTP -0.015 0.09 0.15 1 -0.18 111 112
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.014 0.22 1 -10000 0 1
vasodilation -0.08 0.18 -10000 0 -0.47 76 76
mol:DAG -0.036 0.11 -10000 0 -0.36 51 51
Gs family/GDP/Gbeta gamma -0.032 0.11 -10000 0 -0.3 53 53
MSN -0.022 0.07 0.26 10 -0.28 2 12
Gq family/GTP -0.027 0.12 -10000 0 -0.4 49 49
mol:PI-3-4-5-P3 -0.076 0.25 -10000 0 -0.7 69 69
NRAS 0.023 0.001 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.08 0.18 0.47 76 -10000 0 76
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
RhoA/GDP -0.007 0.098 -10000 0 -0.3 48 48
NOS3 -0.089 0.21 -10000 0 -0.53 74 74
GNA11 0.014 0.051 -10000 0 -0.35 10 10
MAPKKK cascade -0.069 0.2 -10000 0 -0.53 72 72
E2/ER alpha (dimer)/PELP1/Src -0.081 0.18 0.25 1 -0.45 74 75
ruffle organization -0.021 0.067 0.26 10 -0.26 2 12
ROCK2 -0.019 0.075 0.28 10 -0.3 2 12
GNA14 -0.011 0.1 -10000 0 -0.35 46 46
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA13 0.022 0.005 -10000 0 -10000 0 0
MMP9 -0.089 0.19 0.3 6 -0.51 58 64
MMP2 -0.1 0.19 0.25 2 -0.5 67 69
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.047 0.13 -10000 0 -0.4 48 48
CRKL -0.052 0.14 -10000 0 -0.42 51 51
HRAS -0.035 0.12 -10000 0 -0.36 42 42
mol:PIP3 -0.021 0.15 0.26 4 -0.38 45 49
SPRED1 0.022 0.005 -10000 0 -10000 0 0
SPRED2 0.022 0.016 -10000 0 -0.35 1 1
GAB1 -0.054 0.15 -10000 0 -0.43 54 54
FOXO3 -0.034 0.14 0.34 2 -0.4 46 48
AKT1 -0.036 0.15 -10000 0 -0.43 47 47
BAD -0.033 0.14 -10000 0 -0.39 45 45
megakaryocyte differentiation -0.054 0.14 -10000 0 -0.41 55 55
GSK3B -0.032 0.14 0.27 2 -0.4 46 48
RAF1 -0.017 0.11 0.24 5 -0.3 39 44
SHC1 0.019 0.009 -10000 0 -10000 0 0
STAT3 -0.052 0.14 -10000 0 -0.43 51 51
STAT1 -0.12 0.33 -10000 0 -0.82 82 82
HRAS/SPRED1 -0.011 0.12 -10000 0 -0.31 39 39
cell proliferation -0.054 0.14 -10000 0 -0.43 53 53
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
TEC 0.023 0.012 0.28 1 -10000 0 1
RPS6KB1 -0.048 0.16 -10000 0 -0.44 59 59
HRAS/SPRED2 -0.011 0.12 -10000 0 -0.31 38 38
LYN/TEC/p62DOK -0.02 0.15 -10000 0 -0.4 47 47
MAPK3 -0.012 0.095 0.21 8 -0.25 32 40
STAP1 -0.053 0.14 -10000 0 -0.43 51 51
GRAP2 0.011 0.062 -10000 0 -0.35 15 15
JAK2 -0.1 0.29 -10000 0 -0.71 82 82
STAT1 (dimer) -0.12 0.32 -10000 0 -0.8 82 82
mol:Gleevec 0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.02 0.15 -10000 0 -0.41 46 46
actin filament polymerization -0.051 0.14 0.3 1 -0.41 52 53
LYN 0.021 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.083 0.22 -10000 0 -0.54 78 78
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
CBL/CRKL/GRB2 -0.03 0.14 -10000 0 -0.4 43 43
PI3K -0.024 0.16 -10000 0 -0.43 49 49
PTEN 0.021 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.36 -10000 0 -1.1 51 51
MAPK8 -0.055 0.15 -10000 0 -0.44 53 53
STAT3 (dimer) -0.051 0.14 0.26 1 -0.42 51 52
positive regulation of transcription -0.008 0.082 0.2 8 -0.21 29 37
mol:GDP -0.033 0.12 -10000 0 -0.38 40 40
PIK3C2B -0.051 0.14 -10000 0 -0.43 47 47
CBL/CRKL -0.041 0.14 -10000 0 -0.41 47 47
FER -0.054 0.14 -10000 0 -0.42 54 54
SH2B3 -0.054 0.15 -10000 0 -0.43 53 53
PDPK1 -0.018 0.14 0.27 6 -0.36 43 49
SNAI2 -0.066 0.16 -10000 0 -0.45 61 61
positive regulation of cell proliferation -0.095 0.26 -10000 0 -0.63 84 84
KITLG -0.019 0.11 -10000 0 -0.37 48 48
cell motility -0.095 0.26 -10000 0 -0.63 84 84
PTPN6 0.024 0.017 0.33 1 -10000 0 1
EPOR -0.042 0.19 -10000 0 -0.73 21 21
STAT5A (dimer) -0.081 0.22 0.28 1 -0.54 81 82
SOCS1 0.021 0.017 -10000 0 -0.35 1 1
cell migration 0.055 0.14 0.42 54 -10000 0 54
SOS1 0.023 0.003 -10000 0 -10000 0 0
EPO 0.002 0.068 0.28 1 -0.36 16 17
VAV1 0.023 0.03 0.28 5 -0.35 1 6
GRB10 -0.055 0.14 -10000 0 -0.42 54 54
PTPN11 0.024 0.009 -10000 0 -10000 0 0
SCF/KIT -0.052 0.15 -10000 0 -0.44 54 54
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.013 0.096 0.22 7 -0.24 38 45
CBL 0.022 0.005 -10000 0 -10000 0 0
KIT -0.1 0.34 -10000 0 -1.1 48 48
MAP2K2 -0.011 0.093 0.23 6 -0.25 34 40
SHC/Grb2/SOS1 -0.022 0.14 -10000 0 -0.41 43 43
STAT5A -0.083 0.23 -10000 0 -0.56 81 81
GRB2 0.022 0.006 -10000 0 -10000 0 0
response to radiation -0.064 0.16 0.29 2 -0.44 61 63
SHC/GRAP2 0.021 0.04 -10000 0 -0.24 10 10
PTPRO -0.055 0.15 -10000 0 -0.42 55 55
SH2B2 -0.053 0.14 -10000 0 -0.42 52 52
DOK1 0.023 0.003 -10000 0 -10000 0 0
MATK -0.056 0.15 -10000 0 -0.43 54 54
CREBBP 0.012 0.052 -10000 0 -0.18 9 9
BCL2 -0.13 0.39 -10000 0 -1.2 61 61
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.033 0.06 0.21 5 -0.21 22 27
alphaM/beta2 Integrin/GPIbA 0.042 0.043 0.26 6 -0.2 4 10
alphaM/beta2 Integrin/proMMP-9 0.11 0.093 0.22 207 -0.2 2 209
PLAUR 0.023 0.016 0.28 2 -10000 0 2
HMGB1 0.022 0.015 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.044 0.038 0.23 6 -0.2 3 9
AGER 0.022 0.022 -10000 0 -0.35 1 1
RAP1A 0.023 0.002 -10000 0 -10000 0 0
SELPLG 0.024 0.016 0.28 2 -10000 0 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.06 0.065 0.33 2 -0.19 16 18
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 218 -10000 0 218
CYR61 -0.009 0.1 -10000 0 -0.35 46 46
TLN1 0.022 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.002 0.1 0.21 1 -0.3 30 31
RHOA 0.022 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.096 0.17 -10000 0 -0.35 165 165
MYH2 -0.017 0.12 0.23 11 -0.44 21 32
MST1R 0.046 0.077 0.28 50 -0.35 1 51
leukocyte activation during inflammatory response 0.047 0.055 0.2 21 -0.17 10 31
APOB 0.016 0.046 0.3 2 -0.35 7 9
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.007 0.071 -10000 0 -0.35 20 20
JAM3 -0.073 0.16 -10000 0 -0.35 135 135
GP1BA 0.02 0.021 0.28 1 -0.35 1 2
alphaM/beta2 Integrin/CTGF 0.039 0.052 0.24 5 -0.2 15 20
alphaM/beta2 Integrin -0.008 0.1 0.22 8 -0.34 21 29
JAM3 homodimer -0.073 0.16 -10000 0 -0.35 135 135
ICAM2 0.022 0.005 -10000 0 -10000 0 0
ICAM1 0.024 0.025 0.3 4 -10000 0 4
phagocytosis triggered by activation of immune response cell surface activating receptor -0.008 0.1 0.22 8 -0.34 23 31
cell adhesion 0.041 0.042 0.26 6 -0.2 4 10
NFKB1 0.024 0.088 0.3 10 -0.32 16 26
THY1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.033 0.048 0.19 30 -0.2 7 37
alphaM/beta2 Integrin/LRP/tPA 0.028 0.078 0.21 5 -0.19 49 54
IL6 -0.005 0.12 0.29 10 -0.58 16 26
ITGB2 0.025 0.029 0.28 5 -10000 0 5
elevation of cytosolic calcium ion concentration 0.053 0.041 0.22 11 -0.19 2 13
alphaM/beta2 Integrin/JAM2/JAM3 -0.074 0.16 0.28 2 -0.24 229 231
JAM2 -0.1 0.18 -10000 0 -0.35 180 180
alphaM/beta2 Integrin/ICAM1 0.074 0.065 0.37 3 -0.17 3 6
alphaM/beta2 Integrin/uPA/Plg 0.04 0.076 0.28 5 -0.18 38 43
RhoA/GTP -0.022 0.13 0.24 8 -0.43 28 36
positive regulation of phagocytosis 0.006 0.083 0.25 7 -0.26 15 22
Ron/MSP 0.05 0.056 0.21 55 -0.24 1 56
alphaM/beta2 Integrin/uPAR/uPA 0.055 0.042 0.23 11 -0.19 2 13
alphaM/beta2 Integrin/uPAR 0.045 0.039 0.23 8 -0.2 3 11
PLAU 0.023 0.02 0.28 3 -10000 0 3
PLAT -0.014 0.11 -10000 0 -0.35 49 49
actin filament polymerization -0.017 0.12 0.25 9 -0.41 23 32
MST1 0.025 0.028 0.28 6 -10000 0 6
alphaM/beta2 Integrin/lipoprotein(a) 0.052 0.058 0.21 28 -0.17 10 38
TNF 0.008 0.1 0.33 10 -0.36 12 22
RAP1B 0.023 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.045 0.039 0.23 9 -0.2 2 11
fibrinolysis 0.038 0.075 0.28 5 -0.18 38 43
HCK 0.025 0.03 0.28 7 -10000 0 7
dendritic cell antigen processing and presentation -0.008 0.1 0.22 8 -0.34 23 31
VTN -0.022 0.12 0.3 3 -0.35 63 66
alphaM/beta2 Integrin/CYR61 0.023 0.079 0.21 5 -0.21 47 52
LPA 0.035 0.06 0.28 30 -10000 0 30
LRP1 0.022 0.023 -10000 0 -0.35 2 2
cell migration 0.052 0.065 0.24 10 -0.18 18 28
FN1 0.019 0.036 -10000 0 -0.35 5 5
alphaM/beta2 Integrin/Thy1 0.044 0.038 0.23 6 -0.2 3 9
MPO 0.025 0.03 0.28 7 -10000 0 7
KNG1 0.03 0.057 0.29 24 -10000 0 24
RAP1/GDP 0.031 0.004 -10000 0 -10000 0 0
ROCK1 -0.02 0.13 0.24 11 -0.4 29 40
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.006 0.11 0.28 9 -0.35 45 54
CTGF 0.013 0.058 -10000 0 -0.35 13 13
alphaM/beta2 Integrin/Hck 0.045 0.044 0.26 10 -0.2 2 12
ITGAM 0.021 0.035 0.28 2 -0.35 3 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.022 0.11 0.3 5 -0.19 156 161
HP 0.047 0.15 0.28 108 -0.35 36 144
leukocyte adhesion -0.063 0.14 0.28 2 -0.3 85 87
SELP -0.096 0.17 -10000 0 -0.35 165 165
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.005 0.069 0.18 1 -0.21 50 51
EFNA5 0.012 0.066 0.28 2 -0.35 16 18
FYN -0.027 0.054 0.18 4 -0.19 47 51
neuron projection morphogenesis 0.005 0.069 0.18 1 -0.21 50 51
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.006 0.07 0.19 1 -0.21 50 51
EPHA5 -0.006 0.091 -10000 0 -0.35 35 35
LPA receptor mediated events

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
GNB1/GNG2 0.027 0.068 -10000 0 -0.22 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.088 0.31 4 -0.25 10 14
AP1 -0.033 0.12 -10000 0 -0.19 181 181
mol:PIP3 -0.024 0.062 -10000 0 -0.19 52 52
AKT1 -0.01 0.07 0.26 7 -0.28 10 17
PTK2B -0.024 0.096 0.19 1 -0.28 45 46
RHOA -0.001 0.057 0.19 6 -0.29 12 18
PIK3CB 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.062 0.22 8 -0.23 8 16
MAGI3 0.023 0.002 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
apoptosis -0.007 0.07 -10000 0 -0.21 50 50
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.028 0.092 0.22 7 -0.29 32 39
NF kappa B1 p50/RelA 0.009 0.091 0.2 3 -0.23 35 38
endothelial cell migration -0.009 0.094 -10000 0 -0.38 28 28
ADCY4 -0.053 0.12 -10000 0 -0.34 55 55
ADCY5 -0.079 0.14 -10000 0 -0.35 76 76
ADCY6 -0.046 0.11 -10000 0 -0.32 47 47
ADCY7 -0.044 0.11 -10000 0 -0.34 41 41
ADCY1 -0.051 0.12 -10000 0 -0.34 52 52
ADCY2 -0.13 0.16 -10000 0 -0.38 124 124
ADCY3 -0.047 0.11 -10000 0 -0.32 51 51
ADCY8 -0.043 0.1 -10000 0 -0.32 42 42
ADCY9 -0.072 0.14 -10000 0 -0.35 83 83
GSK3B -0.024 0.095 0.23 8 -0.28 38 46
arachidonic acid secretion -0.062 0.13 -10000 0 -0.35 56 56
GNG2 0.017 0.049 0.28 1 -0.35 9 10
TRIP6 0.011 0.035 0.15 1 -0.33 5 6
GNAO1 -0.047 0.11 -10000 0 -0.23 130 130
HRAS 0.022 0.005 -10000 0 -10000 0 0
NFKBIA -0.017 0.086 0.26 6 -0.24 32 38
GAB1 0.019 0.032 -10000 0 -0.35 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.001 0.18 -10000 0 -0.82 24 24
JUN 0.018 0.043 -10000 0 -0.35 7 7
LPA/LPA2/NHERF2 0.027 0.024 0.19 2 -10000 0 2
TIAM1 -0.015 0.21 -10000 0 -0.96 24 24
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.009 0.06 0.22 8 -0.19 22 30
PLCB3 0.013 0.034 0.18 16 -10000 0 16
FOS -0.088 0.17 -10000 0 -0.35 158 158
positive regulation of mitosis -0.062 0.13 -10000 0 -0.35 56 56
LPA/LPA1-2-3 0.028 0.084 0.2 23 -0.2 49 72
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.008 -10000 0 -10000 0 0
stress fiber formation -0.01 0.081 0.2 2 -0.29 20 22
GNAZ -0.006 0.066 -10000 0 -0.23 38 38
EGFR/PI3K-beta/Gab1 0 0.072 -10000 0 -0.2 53 53
positive regulation of dendritic cell cytokine production 0.026 0.083 0.19 23 -0.2 49 72
LPA/LPA2/MAGI-3 0.028 0.024 0.19 2 -10000 0 2
ARHGEF1 -0.006 0.056 0.18 20 -0.2 23 43
GNAI2 -0.001 0.055 -10000 0 -0.23 27 27
GNAI3 -0.001 0.056 -10000 0 -0.23 28 28
GNAI1 -0.003 0.061 -10000 0 -0.23 33 33
LPA/LPA3 0.01 0.069 0.19 23 -0.19 39 62
LPA/LPA2 0.015 0.023 0.19 2 -0.095 13 15
LPA/LPA1 0.004 0.067 -10000 0 -0.25 32 32
HB-EGF/EGFR 0.046 0.055 0.22 5 -0.2 12 17
HBEGF 0.042 0.066 0.12 215 -10000 0 215
mol:DAG -0.009 0.06 0.22 8 -0.19 22 30
cAMP biosynthetic process -0.082 0.13 0.21 2 -0.28 117 119
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
SRC 0.022 0.005 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
LYN -0.008 0.088 0.27 10 -0.24 24 34
GNAQ 0.001 0.05 -10000 0 -0.2 26 26
LPAR2 0.024 0.021 0.3 3 -10000 0 3
LPAR3 0.017 0.097 0.28 24 -0.35 25 49
LPAR1 0.009 0.068 -10000 0 -0.26 26 26
IL8 0.033 0.14 0.32 10 -0.35 23 33
PTK2 -0.015 0.061 0.18 8 -0.19 43 51
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
CASP3 -0.007 0.071 -10000 0 -0.21 50 50
EGFR 0.014 0.059 0.33 1 -0.35 13 14
PLCG1 -0.007 0.061 0.16 6 -0.21 32 38
PLD2 -0.017 0.063 0.18 7 -0.19 48 55
G12/G13 0.029 0.059 -10000 0 -0.21 25 25
PI3K-beta 0.001 0.064 -10000 0 -0.28 14 14
cell migration 0.001 0.064 -10000 0 -0.26 22 22
SLC9A3R2 0.022 0.005 -10000 0 -10000 0 0
PXN -0.01 0.082 0.2 2 -0.3 20 22
HRAS/GTP -0.063 0.13 -10000 0 -0.36 56 56
RAC1 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.13 0.13 0.28 218 -10000 0 218
PRKCE 0.023 0.003 -10000 0 -10000 0 0
PRKCD -0.015 0.068 0.21 12 -0.25 7 19
Gi(beta/gamma) -0.045 0.11 -10000 0 -0.33 45 45
mol:LPA -0.004 0.026 -10000 0 -0.14 16 16
TRIP6/p130 Cas/FAK1/Paxillin 0.006 0.081 -10000 0 -0.34 11 11
MAPKKK cascade -0.062 0.13 -10000 0 -0.35 56 56
contractile ring contraction involved in cytokinesis -0.001 0.059 0.19 6 -0.27 14 20
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.015 0.078 -10000 0 -0.21 66 66
GNA15 0.003 0.05 -10000 0 -0.2 25 25
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
MAPT -0.028 0.094 0.22 7 -0.3 32 39
GNA11 -0.002 0.056 -10000 0 -0.2 35 35
Rac1/GTP 0.001 0.19 -10000 0 -0.87 24 24
MMP2 -0.009 0.094 -10000 0 -0.39 28 28
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.003 0.08 0.2 1 -0.17 68 69
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.093 0.34 5 -0.24 8 13
alphaV/beta3 Integrin/Osteopontin/Src 0.083 0.08 0.21 146 -10000 0 146
AP1 -0.046 0.14 -10000 0 -0.32 55 55
ILK -0.006 0.082 0.29 4 -0.21 2 6
bone resorption -0.019 0.082 0.24 5 -0.31 6 11
PTK2B 0.02 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.042 0.11 0.26 1 -0.19 2 3
ITGAV 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.047 -10000 0 -0.24 15 15
alphaV/beta3 Integrin/Osteopontin 0.045 0.13 0.27 5 -0.2 87 92
MAP3K1 -0.008 0.083 0.21 9 -0.18 74 83
JUN 0.017 0.043 -10000 0 -0.35 7 7
MAPK3 -0.022 0.07 0.21 8 -0.19 2 10
MAPK1 -0.023 0.072 0.21 9 -0.19 2 11
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.026 0.074 0.21 9 -0.23 9 18
ITGB3 -0.038 0.14 0.28 2 -0.35 89 91
NFKBIA -0.016 0.072 0.23 8 -0.22 2 10
FOS -0.089 0.17 -10000 0 -0.35 158 158
CD44 0.018 0.04 -10000 0 -0.35 6 6
CHUK 0.022 0.005 -10000 0 -10000 0 0
PLAU -0.025 0.1 0.61 1 -0.49 4 5
NF kappa B1 p50/RelA 0.019 0.083 0.31 3 -10000 0 3
BCAR1 0.02 0.008 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.01 0.1 0.21 2 -0.24 88 90
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.006 0.084 0.23 11 -0.18 72 83
VAV3 -0.011 0.083 0.25 11 -0.18 2 13
MAP3K14 -0.007 0.083 0.21 9 -0.18 74 83
ROCK2 0.015 0.051 -10000 0 -0.35 10 10
SPP1 0.097 0.12 0.28 151 -10000 0 151
RAC1 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0 0.079 0.23 11 -10000 0 11
MMP2 -0.071 0.12 0.29 1 -0.33 54 55
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 123 123
CDC42/GTP -0.042 0.11 -10000 0 -0.29 35 35
PLCG1 -0.043 0.096 -10000 0 -0.21 115 115
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.002 -10000 0 -10000 0 0
G12/G13 0.031 0.01 -10000 0 -10000 0 0
cell migration -0.042 0.1 -10000 0 -0.28 35 35
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
S1PR4 0.02 0.026 0.28 1 -0.35 2 3
MAPK3 -0.045 0.099 -10000 0 -0.21 117 117
MAPK1 -0.041 0.097 -10000 0 -0.21 113 113
S1P/S1P5/Gi -0.038 0.1 0.17 2 -0.22 112 114
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
CDC42/GDP 0.017 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.029 0.19 10 -0.2 3 13
RHOA -0.008 0.034 0.18 16 -0.17 2 18
S1P/S1P4/Gi -0.039 0.1 -10000 0 -0.21 129 129
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
S1P/S1P4/G12/G13 0.038 0.022 0.19 1 -0.18 2 3
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.031 0.029 0.21 3 -0.24 4 7
CRKL -0.032 0.14 0.31 3 -0.53 23 26
mol:PIP3 -0.011 0.12 -10000 0 -0.78 12 12
AKT1 -0.01 0.11 0.35 2 -0.69 12 14
PTK2B 0.02 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.033 0.13 0.29 4 -0.51 22 26
RANBP10 0.02 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
HGF/MET/SHIP2 -0.004 0.1 0.2 4 -0.21 103 107
MAP3K5 -0.025 0.13 0.29 5 -0.48 25 30
HGF/MET/CIN85/CBL/ENDOPHILINS 0.007 0.1 -10000 0 -0.19 102 102
AP1 -0.049 0.11 0.17 2 -0.22 151 153
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
apoptosis -0.21 0.35 -10000 0 -0.71 170 170
STAT3 (dimer) -0.027 0.092 -10000 0 -0.33 17 17
GAB1/CRKL/SHP2/PI3K -0.008 0.13 0.28 1 -0.46 23 24
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
CBL/CRK -0.021 0.13 0.3 3 -0.52 22 25
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
ELK1 0.011 0.1 0.36 29 -10000 0 29
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.02 0.074 -10000 0 -0.26 26 26
PAK1 -0.009 0.11 0.36 6 -0.66 12 18
HGF/MET/RANBP10 -0.006 0.1 0.2 4 -0.21 103 107
HRAS -0.038 0.14 -10000 0 -0.54 22 22
DOCK1 -0.032 0.14 0.32 8 -0.49 25 33
GAB1 -0.032 0.14 -10000 0 -0.54 25 25
CRK -0.031 0.13 0.3 3 -0.54 23 26
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.068 0.18 -10000 0 -0.42 108 108
JUN 0.018 0.042 -10000 0 -0.35 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.025 0.072 -10000 0 -0.17 101 101
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
cell morphogenesis -0.023 0.13 0.3 15 -0.4 23 38
GRB2/SHC -0.002 0.07 -10000 0 -0.22 17 17
FOS -0.088 0.17 -10000 0 -0.35 158 158
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.01 0.1 0.35 29 -10000 0 29
HGF/MET/MUC20 -0.015 0.097 0.19 4 -0.21 103 107
cell migration -0.002 0.069 -10000 0 -0.21 17 17
GRB2 0.022 0.006 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.029 0.031 0.21 4 -0.24 4 8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.088 0.17 1 -0.21 88 89
MET/MUC20 0.016 0.027 0.19 4 -0.24 4 8
RAP1B -0.034 0.12 0.27 4 -0.48 22 26
RAP1A -0.035 0.12 0.27 4 -0.48 22 26
HGF/MET/RANBP9 -0.003 0.1 0.2 3 -0.21 99 102
RAF1 -0.035 0.13 -10000 0 -0.51 23 23
STAT3 -0.026 0.091 -10000 0 -0.33 16 16
cell proliferation -0.017 0.14 0.3 13 -0.31 69 82
RPS6KB1 -0.008 0.053 -10000 0 -0.28 13 13
MAPK3 0.006 0.14 0.62 21 -10000 0 21
MAPK1 0.018 0.16 0.68 26 -10000 0 26
RANBP9 0.022 0.004 -10000 0 -10000 0 0
MAPK8 -0.019 0.13 0.29 4 -0.46 27 31
SRC -0.028 0.08 0.15 1 -0.2 83 84
PI3K -0.003 0.078 -10000 0 -0.16 89 89
MET/Glomulin 0.016 0.03 0.21 4 -0.21 4 8
SOS1 0.023 0.003 -10000 0 -10000 0 0
MAP2K1 -0.032 0.13 -10000 0 -0.47 23 23
MET 0.021 0.039 0.28 4 -0.35 4 8
MAP4K1 -0.026 0.14 0.3 4 -0.52 24 28
PTK2 0.021 0.007 -10000 0 -10000 0 0
MAP2K2 -0.033 0.12 -10000 0 -0.47 23 23
BAD -0.009 0.11 0.4 4 -0.66 12 16
MAP2K4 -0.023 0.12 0.27 5 -0.44 24 29
SHP2/GRB2/SOS1/GAB1 -0.013 0.13 -10000 0 -0.46 24 24
INPPL1 0.023 0.003 -10000 0 -10000 0 0
PXN 0.023 0.003 -10000 0 -10000 0 0
SH3KBP1 0.023 0.003 -10000 0 -10000 0 0
HGS -0.026 0.064 -10000 0 -0.16 95 95
PLCgamma1/PKC 0.016 0.004 -10000 0 -10000 0 0
HGF -0.049 0.15 -10000 0 -0.35 102 102
RASA1 0.019 0.036 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
PTPRJ 0.022 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.005 0.084 -10000 0 -0.17 99 99
PDPK1 -0.011 0.11 -10000 0 -0.73 12 12
HGF/MET/SHIP -0.005 0.1 0.2 4 -0.21 103 107
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.091 0.2 -10000 0 -0.52 51 51
MAP3K8 0.01 0.033 -10000 0 -0.35 3 3
FOS -0.062 0.16 -10000 0 -0.46 47 47
PRKCA -0.012 0.087 -10000 0 -0.35 31 31
PTPN7 0.009 0.036 0.26 6 -10000 0 6
HRAS 0.021 0.005 -10000 0 -10000 0 0
PRKCB -0.012 0.087 -10000 0 -0.35 31 31
NRAS 0.022 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.034 0.22 1 -10000 0 1
MAPK3 -0.029 0.14 -10000 0 -0.68 16 16
MAP2K1 -0.06 0.15 -10000 0 -0.4 70 70
ELK1 0.006 0.027 -10000 0 -10000 0 0
BRAF -0.041 0.13 -10000 0 -0.36 62 62
mol:GTP -0.001 0.002 -10000 0 -0.005 163 163
MAPK1 -0.035 0.14 -10000 0 -0.58 24 24
RAF1 -0.041 0.13 -10000 0 -0.38 60 60
KRAS 0.022 0.014 0.33 1 -10000 0 1
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.014 0.066 -10000 0 -0.25 30 30
PDGFRB 0.007 0.07 -10000 0 -0.36 19 19
SPHK1 -0.018 0.12 -10000 0 -0.78 12 12
mol:S1P -0.021 0.11 -10000 0 -0.68 12 12
S1P1/S1P/Gi -0.1 0.19 0.24 1 -0.43 97 98
GNAO1 -0.069 0.16 -10000 0 -0.35 123 123
PDGFB-D/PDGFRB/PLCgamma1 -0.084 0.18 0.28 4 -0.4 95 99
PLCG1 -0.096 0.18 0.27 3 -0.42 91 94
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.07 -10000 0 -0.35 19 19
GNAI2 0.018 0.015 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.012 0.048 -10000 0 -0.36 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.047 -10000 0 -0.2 30 30
S1P1/S1P -0.026 0.095 0.22 2 -0.42 16 18
negative regulation of cAMP metabolic process -0.1 0.19 0.24 1 -0.42 97 98
MAPK3 -0.12 0.22 0.25 4 -0.54 89 93
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
KDR -0.001 0.088 -10000 0 -0.35 31 31
PLCB2 -0.019 0.089 0.22 5 -0.38 14 19
RAC1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.081 -10000 0 -0.33 19 19
receptor internalization -0.026 0.087 -10000 0 -0.36 19 19
PTGS2 -0.15 0.31 0.37 1 -0.9 67 68
Rac1/GTP -0.022 0.081 -10000 0 -0.33 19 19
RHOA 0.022 0.005 -10000 0 -10000 0 0
VEGFA 0.021 0.011 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.1 0.19 0.24 1 -0.42 97 98
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.007 0.063 -10000 0 -0.36 15 15
MAPK1 -0.12 0.23 0.23 1 -0.55 90 91
S1P1/S1P/PDGFB-D/PDGFRB -0.023 0.11 0.25 5 -0.35 27 32
ABCC1 0.018 0.014 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.024 0.043 0.19 4 -0.2 16 20
cell-cell adhesion 0.048 0.062 0.17 94 -10000 0 94
Ephrin B/EPHB2/RasGAP 0.032 0.081 -10000 0 -0.18 59 59
ITSN1 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
SHC1 0.019 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.04 0.19 14 -0.23 6 20
Ephrin B1/EPHB1 0.008 0.07 0.19 1 -0.2 52 53
HRAS/GDP -0.028 0.099 -10000 0 -0.23 59 59
Ephrin B/EPHB1/GRB7 0.016 0.11 0.23 17 -0.2 94 111
Endophilin/SYNJ1 -0.026 0.056 0.17 11 -0.17 50 61
KRAS 0.023 0.014 0.33 1 -10000 0 1
Ephrin B/EPHB1/Src 0.01 0.1 -10000 0 -0.19 94 94
endothelial cell migration 0.037 0.033 -10000 0 -0.18 8 8
GRB2 0.022 0.006 -10000 0 -10000 0 0
GRB7 0.037 0.073 0.32 30 -0.35 2 32
PAK1 -0.025 0.073 0.34 4 -0.32 3 7
HRAS 0.022 0.005 -10000 0 -10000 0 0
RRAS -0.026 0.057 0.17 11 -0.32 1 12
DNM1 0.018 0.04 -10000 0 -0.35 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.038 0.08 0.18 19 -0.32 8 27
lamellipodium assembly -0.048 0.062 -10000 0 -0.17 94 94
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.015 0.082 -10000 0 -0.3 12 12
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
EPHB2 0.024 0.02 0.28 3 -10000 0 3
EPHB3 0.024 0.059 0.28 15 -0.35 6 21
EPHB1 -0.013 0.11 0.28 1 -0.35 51 52
EPHB4 0.022 0.004 -10000 0 -10000 0 0
mol:GDP -0.04 0.085 0.37 1 -0.24 52 53
Ephrin B/EPHB2 0.025 0.072 0.19 3 -0.18 54 57
Ephrin B/EPHB3 0.024 0.075 0.2 7 -0.19 50 57
JNK cascade -0.021 0.082 0.28 21 -0.18 51 72
Ephrin B/EPHB1 0.003 0.094 -10000 0 -0.19 96 96
RAP1/GDP -0.028 0.099 0.24 6 -0.28 24 30
EFNB2 0.02 0.028 -10000 0 -0.35 3 3
EFNB3 -0.014 0.11 -10000 0 -0.35 51 51
EFNB1 0.022 0.016 -10000 0 -0.35 1 1
Ephrin B2/EPHB1-2 0.018 0.07 0.19 3 -0.18 54 57
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.098 -10000 0 -0.23 54 54
Rap1/GTP -0.052 0.063 -10000 0 -0.3 9 9
axon guidance 0.024 0.043 0.18 4 -0.2 16 20
MAPK3 -0.021 0.074 0.18 5 -0.3 9 14
MAPK1 -0.021 0.069 0.18 1 -0.32 6 7
Rac1/GDP -0.038 0.093 0.36 1 -0.27 31 32
actin cytoskeleton reorganization -0.054 0.06 -10000 0 -0.2 52 52
CDC42/GDP -0.035 0.096 0.24 6 -0.26 31 37
PI3K 0.041 0.035 -10000 0 -0.18 8 8
EFNA5 0.012 0.066 0.28 2 -0.35 16 18
Ephrin B2/EPHB4 0.027 0.019 -10000 0 -0.2 3 3
Ephrin B/EPHB2/Intersectin/N-WASP -0.007 0.073 -10000 0 -0.19 69 69
CDC42 0.022 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.051 0.062 -10000 0 -0.29 9 9
PTK2 0.044 0.16 0.55 47 -10000 0 47
MAP4K4 -0.022 0.083 0.28 21 -0.18 51 72
SRC 0.022 0.005 -10000 0 -10000 0 0
KALRN 0.019 0.036 -10000 0 -0.35 5 5
Intersectin/N-WASP 0.032 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.034 0.099 0.3 21 -0.29 11 32
MAP2K1 -0.018 0.075 -10000 0 -0.28 12 12
WASL 0.022 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.032 0.078 -10000 0 -0.19 53 53
cell migration -0.018 0.11 0.29 6 -0.33 16 22
NRAS 0.023 0.001 -10000 0 -10000 0 0
SYNJ1 -0.027 0.057 0.17 11 -0.18 50 61
PXN 0.023 0.003 -10000 0 -10000 0 0
TF -0.031 0.06 0.17 9 -0.19 15 24
HRAS/GTP -0.003 0.088 -10000 0 -0.18 96 96
Ephrin B1/EPHB1-2 0.021 0.07 0.19 4 -0.19 52 56
cell adhesion mediated by integrin 0.016 0.063 0.18 47 -0.21 8 55
RAC1 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.091 -10000 0 -0.18 97 97
RAC1-CDC42/GTP -0.048 0.065 -10000 0 -0.18 83 83
RASA1 0.019 0.036 -10000 0 -0.35 5 5
RAC1-CDC42/GDP -0.03 0.095 0.35 1 -0.26 30 31
ruffle organization -0.037 0.092 0.34 11 -0.3 9 20
NCK1 0.021 0.023 -10000 0 -0.35 2 2
receptor internalization -0.03 0.06 0.16 11 -0.27 7 18
Ephrin B/EPHB2/KALRN 0.032 0.082 -10000 0 -0.19 57 57
ROCK1 0.003 0.058 0.18 43 -0.21 6 49
RAS family/GDP -0.055 0.062 -10000 0 -0.2 52 52
Rac1/GTP -0.049 0.065 -10000 0 -0.18 94 94
Ephrin B/EPHB1/Src/Paxillin -0.024 0.093 -10000 0 -0.21 96 96
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.022 0.004 -10000 0 -10000 0 0
VLDLR 0.021 0.023 -10000 0 -0.35 2 2
LRPAP1 0.022 0.004 -10000 0 -10000 0 0
NUDC 0.022 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.038 0.12 0.23 8 -0.21 177 185
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.065 0.09 0.18 12 -0.19 168 180
IQGAP1/CaM 0.032 0.008 -10000 0 -10000 0 0
DAB1 0.027 0.041 0.28 13 -10000 0 13
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
PLA2G7 0.02 0.038 0.28 1 -0.35 5 6
CALM1 0.022 0.004 -10000 0 -10000 0 0
DYNLT1 0.022 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.035 0.019 0.21 5 -10000 0 5
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.003 -10000 0 -10000 0 0
CDK5R1 0.022 0.013 0.28 1 -10000 0 1
LIS1/Poliovirus Protein 3A -0.008 0.003 -10000 0 -10000 0 0
CDK5R2 0.048 0.08 0.28 56 -10000 0 56
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.038 0.12 0.21 16 -0.21 176 192
YWHAE 0.021 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.041 0.096 0.3 10 -0.22 3 13
MAP1B -0.006 0.048 -10000 0 -0.23 23 23
RAC1 0.008 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.064 0.08 0.18 9 -10000 0 9
RELN -0.1 0.18 0.28 7 -0.35 180 187
PAFAH/LIS1 0.019 0.025 0.2 1 -0.21 5 6
LIS1/CLIP170 0.021 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.036 0.08 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.05 0.11 0.25 2 -0.2 81 83
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.049 0.084 0.22 9 -0.22 4 13
LIS1/IQGAP1 0.021 0.008 -10000 0 -10000 0 0
RHOA 0.008 0.003 -10000 0 -10000 0 0
PAFAH1B1 -0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.034 0.28 9 -10000 0 9
PAFAH1B2 0.022 0.017 -10000 0 -0.35 1 1
MAP1B/LIS1/Dynein heavy chain 0.009 0.041 -10000 0 -0.16 21 21
NDEL1/Katanin 60/Dynein heavy chain -0.032 0.1 0.3 9 -0.22 4 13
LRP8 0.025 0.026 0.29 5 -10000 0 5
NDEL1/Katanin 60 -0.044 0.095 0.29 10 -0.22 7 17
P39/CDK5 -0.051 0.1 0.18 44 -10000 0 44
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.008 -10000 0 -10000 0 0
CDK5 -0.063 0.083 0.18 10 -0.18 164 174
PPP2R5D 0.023 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.007 -10000 0 -10000 0 0
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.03 0.11 0.22 10 -0.18 171 181
RELN/VLDLR -0.027 0.12 0.21 7 -0.19 174 181
CDC42 0.008 0.003 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.026 0.012 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.01 0.13 -10000 0 -0.78 10 10
EGFR 0.014 0.059 0.33 1 -0.35 13 14
EPHA2 0.022 0.005 -10000 0 -10000 0 0
USP6 0.021 0.006 -10000 0 -10000 0 0
IQSEC1 0.022 0.017 -10000 0 -0.35 1 1
EGFR/EGFR/EGF/EGF 0.032 0.056 0.21 20 -0.24 13 33
ARRB2 0.007 0.002 -10000 0 -10000 0 0
mol:GTP 0.012 0.05 0.13 26 -0.14 18 44
ARRB1 0.021 0.023 -10000 0 -0.35 2 2
FBXO8 0.022 0.004 -10000 0 -10000 0 0
TSHR 0.025 0.057 0.28 19 -0.35 3 22
EGF 0.03 0.052 0.28 20 -0.35 1 21
somatostatin receptor activity 0 0 0.001 6 -0.001 71 77
ARAP2 0.02 0.028 -10000 0 -0.35 3 3
mol:GDP -0.063 0.12 0.18 5 -0.29 80 85
mol:PI-3-4-5-P3 0 0 0.001 4 -0.001 42 46
ITGA2B 0.019 0.038 0.28 1 -0.35 5 6
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.031 0.21 1 -0.19 2 3
ADAP1 0.022 0.006 -10000 0 -10000 0 0
KIF13B 0.02 0.008 -10000 0 -10000 0 0
HGF/MET -0.021 0.12 0.21 4 -0.25 103 107
PXN 0.023 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.059 0.11 0.22 6 -0.27 73 79
EGFR/EGFR/EGF/EGF/ARFGEP100 0.041 0.053 0.2 19 -0.21 14 33
ADRB2 -0.043 0.14 -10000 0 -0.35 92 92
receptor agonist activity 0 0 0 3 0 65 68
actin filament binding 0 0 0 5 0 78 83
SRC 0.022 0.005 -10000 0 -10000 0 0
ITGB3 -0.039 0.14 0.28 2 -0.35 89 91
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
EFA6/PI-4-5-P2 0 0 0.001 11 -0.001 46 57
ARF6/GDP -0.015 0.14 0.26 8 -0.43 40 48
ARF6/GDP/GULP/ACAP1 -0.058 0.14 -10000 0 -0.34 68 68
alphaIIb/beta3 Integrin/paxillin/GIT1 0.013 0.094 -10000 0 -0.19 90 90
ACAP1 0.022 0.026 0.28 3 -0.35 1 4
ACAP2 0.02 0.018 -10000 0 -0.35 1 1
LHCGR/beta Arrestin2 0.011 0.018 -10000 0 -10000 0 0
EFNA1 0.02 0.02 0.3 2 -10000 0 2
HGF -0.049 0.15 -10000 0 -0.35 102 102
CYTH3 -0.006 0.001 -10000 0 -10000 0 0
CYTH2 -0.003 0.14 -10000 0 -0.99 10 10
NCK1 0.021 0.023 -10000 0 -0.35 2 2
fibronectin binding 0 0 0.001 7 0 60 67
endosomal lumen acidification 0 0 0.001 10 0 50 60
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.018 0.12 -10000 0 -0.35 58 58
GNAQ/ARNO 0.009 0.13 -10000 0 -0.92 10 10
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 6 0 10 16
MET 0.021 0.039 0.28 4 -0.35 4 8
GNA14 -0.011 0.1 -10000 0 -0.35 46 46
GNA15 0.025 0.03 0.28 7 -10000 0 7
GIT1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 55 65
GNA11 0.014 0.051 -10000 0 -0.35 10 10
LHCGR 0.004 0.017 -10000 0 -10000 0 0
AGTR1 -0.061 0.15 0.28 2 -0.35 112 114
desensitization of G-protein coupled receptor protein signaling pathway 0.011 0.018 -10000 0 -10000 0 0
IPCEF1/ARNO 0.02 0.12 -10000 0 -0.83 10 10
alphaIIb/beta3 Integrin -0.016 0.11 0.21 3 -0.24 94 97
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.081 0.45 0.66 1 -1.1 45 46
STAT6 (cleaved dimer) -0.1 0.44 0.56 2 -1.1 53 55
IGHG1 0.006 0.22 0.4 10 -0.7 7 17
IGHG3 -0.094 0.44 0.59 1 -1 54 55
AKT1 -0.022 0.26 0.5 3 -0.8 13 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.01 0.22 0.52 2 -0.91 7 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.026 0.28 0.53 2 -0.74 23 25
THY1 -0.092 0.46 0.66 1 -1.1 48 49
MYB 0.047 0.075 0.28 50 -10000 0 50
HMGA1 0.06 0.091 0.28 75 -10000 0 75
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.016 0.3 0.58 4 -0.7 26 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.008 0.26 0.51 3 -0.82 12 15
SP1 0.025 0.012 -10000 0 -10000 0 0
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
SOCS5 0.004 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.096 0.44 0.6 1 -1.1 52 53
SOCS1 -0.044 0.32 0.51 2 -0.7 45 47
SOCS3 -0.014 0.27 0.52 2 -0.79 12 14
FCER2 -0.071 0.4 0.72 2 -0.95 41 43
PARP14 0.024 0.006 -10000 0 -10000 0 0
CCL17 -0.088 0.46 0.74 2 -1.1 48 50
GRB2 0.022 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.015 0.22 0.42 11 -0.63 11 22
T cell proliferation -0.11 0.45 0.64 1 -1.1 55 56
IL4R/JAK1 -0.1 0.45 -10000 0 -1.1 51 51
EGR2 -0.12 0.52 0.69 2 -1.3 59 61
JAK2 0.011 0.08 0.17 2 -0.36 9 11
JAK3 0.023 0.028 0.3 4 -10000 0 4
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
JAK1 0.017 0.037 -10000 0 -0.34 1 1
COL1A2 0.002 0.23 -10000 0 -1.3 6 6
CCL26 -0.092 0.46 0.66 1 -1.1 46 47
IL4R -0.093 0.49 0.71 3 -1.2 51 54
PTPN6 0.008 0.035 0.34 1 -10000 0 1
IL13RA2 -0.086 0.46 0.65 2 -1.1 51 53
IL13RA1 0.018 0.066 0.18 1 -10000 0 1
IRF4 0.001 0.25 0.51 2 -1 19 21
ARG1 0.017 0.18 0.46 1 -0.65 3 4
CBL -0.021 0.28 0.51 4 -0.68 23 27
GTF3A 0.025 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL13RA1/JAK2 0.03 0.1 0.21 15 -0.24 8 23
IRF4/BCL6 0 0.22 -10000 0 -0.95 19 19
CD40LG 0.017 0.06 -10000 0 -0.31 15 15
MAPK14 -0.019 0.28 0.52 4 -0.7 22 26
mitosis -0.018 0.26 0.49 3 -0.75 13 16
STAT6 -0.095 0.53 0.76 4 -1.2 53 57
SPI1 0.025 0.02 0.28 3 -10000 0 3
RPS6KB1 -0.015 0.25 0.47 3 -0.72 13 16
STAT6 (dimer) -0.096 0.53 0.76 4 -1.2 53 57
STAT6 (dimer)/PARP14 -0.11 0.47 0.63 1 -1.1 53 54
mast cell activation -0.002 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.014 0.27 0.57 3 -0.77 16 19
FRAP1 -0.022 0.27 0.5 3 -0.8 13 16
LTA -0.089 0.46 0.69 2 -1.1 43 45
FES 0.022 0.017 -10000 0 -0.35 1 1
T-helper 1 cell differentiation 0.091 0.52 1.2 53 -0.76 4 57
CCL11 -0.11 0.46 -10000 0 -1.1 59 59
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.006 0.26 0.53 3 -0.9 9 12
IL2RG 0.023 0.042 0.29 6 -0.34 3 9
IL10 -0.062 0.47 0.76 10 -1.1 44 54
IRS1 -0.012 0.11 -10000 0 -0.35 50 50
IRS2 -0.024 0.12 -10000 0 -0.35 66 66
IL4 0.015 0.21 0.47 2 -0.95 9 11
IL5 -0.096 0.46 0.66 1 -1.1 48 49
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.054 0.41 0.66 4 -0.89 50 54
COL1A1 -0.016 0.28 0.48 2 -0.89 24 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.11 0.46 -10000 0 -1.1 49 49
IL2R gamma/JAK3 0.036 0.045 0.31 7 -0.25 3 10
TFF3 -0.092 0.52 0.72 2 -1.2 63 65
ALOX15 -0.075 0.46 0.72 2 -1.1 46 48
MYBL1 0.021 0.007 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.093 0.42 0.63 2 -0.94 57 59
SHC1 0.019 0.009 -10000 0 -10000 0 0
CEBPB 0.023 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.028 0.27 0.49 3 -0.8 15 18
mol:PI-3-4-5-P3 -0.021 0.27 0.5 3 -0.8 13 16
PI3K -0.026 0.28 0.52 2 -0.88 13 15
DOK2 0.021 0.021 0.28 3 -10000 0 3
ETS1 0.001 0.04 -10000 0 -0.33 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.019 0.21 0.4 11 -0.56 12 23
ITGB3 -0.22 0.61 0.66 1 -1.2 113 114
PIGR -0.095 0.56 0.77 10 -1.2 71 81
IGHE 0 0.07 0.18 25 -0.17 6 31
MAPKKK cascade 0.02 0.21 0.4 11 -0.55 12 23
BCL6 0.019 0.019 -10000 0 -0.35 1 1
OPRM1 -0.094 0.46 0.68 2 -1.1 47 49
RETNLB -0.093 0.46 0.68 2 -1.1 50 52
SELP -0.3 0.69 0.75 10 -1.2 185 195
AICDA -0.096 0.44 0.64 2 -1.1 48 50
Visual signal transduction: Rods

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
mol:K + 0.022 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.017 0.19 5 -10000 0 5
Metarhodopsin II/Arrestin 0.026 0.014 0.19 3 -10000 0 3
PDE6G/GNAT1/GTP 0.037 0.043 0.18 38 -0.2 1 39
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.022 0.026 0.28 5 -10000 0 5
GRK1 0.018 0.013 0.28 1 -10000 0 1
CNG Channel 0.038 0.059 0.23 8 -0.17 22 30
mol:Na + 0.04 0.046 0.27 3 -0.18 7 10
mol:ADP 0.018 0.012 0.28 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.007 0.11 0.21 14 -0.21 110 124
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.05 0.053 0.32 3 -0.18 7 10
CNGB1 0.031 0.053 0.28 23 -10000 0 23
RDH5 0.024 0.019 0.28 3 -10000 0 3
SAG 0.019 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.065 0.34 13 -10000 0 13
Na + (4 Units) 0.031 0.039 0.2 3 -0.17 7 10
RGS9 -0.057 0.15 -10000 0 -0.35 112 112
GNB1/GNGT1 0.091 0.084 0.21 176 -10000 0 176
GNAT1/GDP 0.001 0.097 0.21 5 -0.18 110 115
GUCY2D 0.025 0.037 0.28 11 -10000 0 11
GNGT1 0.11 0.12 0.28 185 -10000 0 185
GUCY2F 0.019 0.003 -10000 0 -10000 0 0
GNB5 0.022 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.016 0.048 0.18 10 -0.18 22 32
mol:11-cis-retinal 0.024 0.019 0.28 3 -10000 0 3
mol:cGMP 0.038 0.04 0.25 1 -0.18 7 8
GNB1 0.022 0.004 -10000 0 -10000 0 0
Rhodopsin 0.032 0.019 0.21 5 -10000 0 5
SLC24A1 0.022 0.005 -10000 0 -10000 0 0
CNGA1 0.029 0.041 0.28 14 -10000 0 14
Metarhodopsin II 0.023 0.015 0.18 4 -10000 0 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.05 0.048 0.35 1 -0.19 7 8
RGS9BP 0.033 0.056 0.29 23 -10000 0 23
Metarhodopsin II/Transducin 0.036 0.043 0.16 27 -10000 0 27
GCAP Family/Ca ++ 0.038 0.037 0.19 15 -0.19 7 22
PDE6A/B 0.023 0.057 0.21 4 -0.24 21 25
mol:Pi -0.008 0.11 0.21 14 -0.21 110 124
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.086 0.075 0.19 164 -10000 0 164
PDE6B 0.008 0.074 0.28 2 -0.35 21 23
PDE6A 0.024 0.022 0.28 4 -10000 0 4
PDE6G 0.043 0.075 0.28 44 -0.35 1 45
RHO 0.02 0.02 0.28 3 -10000 0 3
PDE6 0.01 0.12 0.33 5 -0.18 123 128
GUCA1A 0.028 0.046 0.28 17 -10000 0 17
GC2/GCAP Family 0.05 0.04 -10000 0 -0.19 7 7
GUCA1C 0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.018 0.043 -10000 0 -0.35 7 7
HIF-2-alpha transcription factor network

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
MMP14 -0.003 0.089 -10000 0 -0.65 7 7
oxygen homeostasis -0.008 0.013 -10000 0 -10000 0 0
TCEB2 0.023 0.012 0.28 1 -10000 0 1
TCEB1 0.021 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.002 0.092 0.24 1 -0.26 6 7
EPO -0.084 0.17 -10000 0 -0.45 38 38
FIH (dimer) -0.003 0.028 -10000 0 -10000 0 0
APEX1 -0.008 0.031 -10000 0 -10000 0 0
SERPINE1 -0.081 0.16 -10000 0 -0.41 52 52
FLT1 -0.042 0.18 -10000 0 -0.67 38 38
ADORA2A -0.065 0.17 0.3 28 -0.39 51 79
germ cell development -0.08 0.17 -10000 0 -0.41 54 54
SLC11A2 -0.079 0.16 -10000 0 -0.4 50 50
BHLHE40 -0.079 0.16 -10000 0 -0.4 51 51
HIF1AN -0.003 0.028 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.037 0.11 -10000 0 -0.31 14 14
ETS1 0.021 0.032 -10000 0 -0.36 1 1
CITED2 -0.031 0.19 -10000 0 -0.88 24 24
KDR -0.071 0.27 -10000 0 -0.87 51 51
PGK1 -0.079 0.16 -10000 0 -0.4 51 51
SIRT1 0.02 0.024 -10000 0 -0.35 2 2
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.076 0.19 -10000 0 -0.44 51 51
EPAS1 -0.031 0.07 -10000 0 -0.28 10 10
SP1 0.025 0.007 -10000 0 -10000 0 0
ABCG2 -0.16 0.24 -10000 0 -0.44 205 205
EFNA1 -0.076 0.16 0.35 1 -0.4 51 52
FXN -0.064 0.17 0.3 29 -0.39 49 78
POU5F1 -0.082 0.17 -10000 0 -0.43 54 54
neuron apoptosis 0.075 0.18 0.44 51 -10000 0 51
EP300 0.021 0.006 -10000 0 -10000 0 0
EGLN3 -0.003 0.038 0.28 3 -0.37 1 4
EGLN2 -0.004 0.028 -10000 0 -10000 0 0
EGLN1 -0.002 0.025 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.04 0.021 0.2 1 -0.21 1 2
VHL 0.022 0.017 -10000 0 -0.35 1 1
ARNT -0.005 0.027 -10000 0 -10000 0 0
SLC2A1 -0.063 0.18 0.3 30 -0.39 49 79
TWIST1 -0.083 0.21 0.3 29 -0.49 62 91
ELK1 0.022 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.033 0.11 -10000 0 -0.32 7 7
VEGFA -0.079 0.16 -10000 0 -0.4 50 50
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.026 0.074 0.23 1 -0.42 8 9
Syndecan-4/Syndesmos 0.057 0.11 0.33 10 -0.51 4 14
positive regulation of JNK cascade -0.034 0.13 0.36 2 -0.34 28 30
Syndecan-4/ADAM12 0.06 0.11 0.3 16 -0.51 4 20
CCL5 0.021 0.046 0.28 6 -0.35 5 11
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
DNM2 0.021 0.006 -10000 0 -10000 0 0
ITGA5 0.023 0.003 -10000 0 -10000 0 0
SDCBP 0.021 0.007 -10000 0 -10000 0 0
PLG -0.008 0.11 0.27 9 -0.34 45 54
ADAM12 0.027 0.035 0.28 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.04 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.1 0.14 0.3 80 -0.52 4 84
Syndecan-4/CXCL12/CXCR4 -0.035 0.14 0.38 2 -0.36 28 30
Syndecan-4/Laminin alpha3 0.053 0.11 0.32 11 -0.46 5 16
MDK 0.023 0.014 0.33 1 -10000 0 1
Syndecan-4/FZD7 0.04 0.12 0.31 11 -0.45 6 17
Syndecan-4/Midkine 0.057 0.11 0.32 11 -0.51 4 15
FZD7 -0.037 0.14 -10000 0 -0.35 85 85
Syndecan-4/FGFR1/FGF -0.029 0.13 0.29 1 -0.36 20 21
THBS1 -0.022 0.12 -10000 0 -0.35 63 63
integrin-mediated signaling pathway 0.052 0.11 0.31 9 -0.45 5 14
positive regulation of MAPKKK cascade -0.034 0.13 0.36 2 -0.34 28 30
Syndecan-4/TACI 0.058 0.11 0.31 21 -0.51 4 25
CXCR4 0.023 0.002 -10000 0 -10000 0 0
cell adhesion 0.008 0.047 0.18 12 -0.21 6 18
Syndecan-4/Dynamin 0.053 0.1 0.33 9 -0.59 3 12
Syndecan-4/TSP1 0.042 0.12 0.33 7 -0.45 8 15
Syndecan-4/GIPC 0.053 0.1 0.33 8 -0.59 3 11
Syndecan-4/RANTES 0.057 0.11 0.31 14 -0.47 5 19
ITGB1 0.022 0.004 -10000 0 -10000 0 0
LAMA1 0.1 0.13 0.28 173 -0.35 4 177
LAMA3 0.013 0.058 -10000 0 -0.35 13 13
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.013 0.14 0.72 14 -0.33 26 40
Syndecan-4/alpha-Actinin 0.057 0.11 0.32 11 -0.52 4 15
TFPI -0.021 0.12 -10000 0 -0.35 62 62
F2 0.049 0.076 0.29 47 -10000 0 47
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.064 0.12 0.32 19 -0.5 4 23
ACTN1 0.022 0.004 -10000 0 -10000 0 0
TNC 0.015 0.054 0.28 1 -0.35 11 12
Syndecan-4/CXCL12 -0.018 0.13 0.38 2 -0.36 28 30
FGF6 0.016 0.003 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
CXCL12 -0.2 0.18 -10000 0 -0.35 323 323
TNFRSF13B 0.027 0.045 0.28 16 -10000 0 16
FGF2 -0.17 0.18 -10000 0 -0.35 272 272
FGFR1 0.02 0.018 -10000 0 -0.35 1 1
Syndecan-4/PI-4-5-P2 0.038 0.1 0.28 7 -0.51 4 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.015 0.04 -10000 0 -0.33 5 5
cell migration -0.022 0.016 -10000 0 -10000 0 0
PRKCD 0.019 0.019 -10000 0 -10000 0 0
vasculogenesis 0.042 0.11 0.33 7 -0.44 8 15
SDC4 0.048 0.095 0.3 7 -0.59 2 9
Syndecan-4/Tenascin C 0.053 0.11 0.31 9 -0.47 5 14
Syndecan-4/PI-4-5-P2/PKC alpha -0.033 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.054 0.1 0.33 10 -0.59 3 13
MMP9 0.13 0.13 0.28 218 -10000 0 218
Rac1/GTP 0.008 0.047 0.19 12 -0.22 6 18
cytoskeleton organization 0.056 0.1 0.32 10 -0.49 4 14
GIPC1 0.022 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.043 0.12 0.31 9 -0.39 12 21
FAS signaling pathway (CD95)

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
SPTAN1 0.006 0.044 0.16 36 -0.18 2 38
RFC1 0.006 0.046 0.16 38 -0.18 3 41
PRKDC 0.019 0.07 0.2 67 -0.18 2 69
RIPK1 0.022 0.007 -10000 0 -10000 0 0
CASP7 -0.001 0.093 -10000 0 -0.55 14 14
FASLG/FAS/FADD/FAF1 0.02 0.051 0.17 39 -0.2 3 42
MAP2K4 0.018 0.093 0.28 7 -0.32 19 26
mol:ceramide 0.012 0.049 0.19 1 -0.22 4 5
GSN 0.005 0.046 0.16 36 -0.18 5 41
FASLG/FAS/FADD/FAF1/Caspase 8 0.021 0.055 0.24 4 -10000 0 4
FAS 0.018 0.033 -10000 0 -0.35 4 4
BID -0.015 0.019 0.24 2 -0.16 1 3
MAP3K1 0.016 0.09 0.25 8 -0.38 14 22
MAP3K7 0.022 0.007 -10000 0 -10000 0 0
RB1 0.006 0.044 0.16 36 -0.18 2 38
CFLAR 0.022 0.006 -10000 0 -10000 0 0
HGF/MET -0.032 0.13 0.2 3 -0.23 148 151
ARHGDIB 0.006 0.047 0.17 38 -0.18 3 41
FADD 0.022 0.01 -10000 0 -10000 0 0
actin filament polymerization -0.001 0.053 0.18 16 -0.16 36 52
NFKB1 -0.003 0.11 -10000 0 -0.58 17 17
MAPK8 0.013 0.11 0.32 9 -0.44 20 29
DFFA 0.008 0.05 0.17 40 -0.18 2 42
DNA fragmentation during apoptosis 0.002 0.055 0.17 39 -0.18 15 54
FAS/FADD/MET 0.038 0.039 0.2 4 -0.21 8 12
CFLAR/RIP1 0.032 0.01 -10000 0 -10000 0 0
FAIM3 0.019 0.027 0.28 1 -0.35 2 3
FAF1 0.022 0.01 -10000 0 -10000 0 0
PARP1 0.007 0.049 0.17 41 -0.18 3 44
DFFB 0.007 0.046 0.17 39 -0.18 2 41
CHUK -0.007 0.1 0.31 1 -0.55 16 17
FASLG 0.021 0.042 0.28 8 -0.35 2 10
FAS/FADD 0.028 0.028 -10000 0 -0.24 4 4
HGF -0.049 0.15 -10000 0 -0.35 102 102
LMNA 0.012 0.069 0.22 29 -10000 0 29
CASP6 0.006 0.049 0.17 38 -0.18 3 41
CASP10 0.021 0.025 -10000 0 -0.35 2 2
CASP3 0.012 0.052 0.2 37 -10000 0 37
PTPN13 -0.023 0.12 -10000 0 -0.35 65 65
CASP8 -0.016 0.022 0.3 2 -0.19 1 3
IL6 -0.012 0.22 -10000 0 -0.95 23 23
MET 0.021 0.039 0.28 4 -0.35 4 8
ICAD/CAD 0.005 0.047 0.16 41 -10000 0 41
FASLG/FAS/FADD/FAF1/Caspase 10 0.012 0.049 0.19 1 -0.22 4 5
activation of caspase activity by cytochrome c -0.015 0.019 0.24 2 -0.16 1 3
PAK2 0.022 0.076 0.21 69 -0.18 2 71
BCL2 -0.009 0.1 -10000 0 -0.35 44 44
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
EGF/EGFR -0.018 0.1 0.18 1 -0.18 147 148
EGF/EGFR dimer/SHC/GRB2/SOS1 0.047 0.052 0.23 1 -0.18 10 11
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.081 0.17 -10000 0 -0.35 147 147
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.031 0.052 0.28 20 -0.35 1 21
EGF/EGFR dimer/SHC 0.036 0.049 0.2 17 -0.21 10 27
mol:GDP 0.043 0.048 0.21 1 -0.18 10 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.018 0.043 -10000 0 -0.35 7 7
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.028 0.037 -10000 0 -0.17 10 10
SHC1 0.019 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.04 0.046 -10000 0 -0.17 10 10
FRAP1 -0.013 0.029 0.17 5 -0.17 10 15
EGF/EGFR dimer 0.032 0.056 0.21 20 -0.24 13 33
SOS1 0.023 0.003 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.047 0.13 -10000 0 -0.25 149 149
Glucocorticoid receptor regulatory network

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
PCK2 -0.047 0.068 -10000 0 -0.34 8 8
SMARCC2 0.023 0.006 -10000 0 -10000 0 0
SMARCC1 0.022 0.007 -10000 0 -10000 0 0
TBX21 0.055 0.12 0.41 5 -0.65 10 15
SUMO2 0.018 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.012 0.28 1 -10000 0 1
FKBP4 0.022 0.004 -10000 0 -10000 0 0
FKBP5 0.018 0.043 -10000 0 -0.35 7 7
GR alpha/HSP90/FKBP51/HSP90 -0.063 0.1 0.26 2 -0.26 62 64
PRL 0.018 0.24 0.44 11 -1.1 19 30
cortisol/GR alpha (dimer)/TIF2 -0.12 0.16 0.44 5 -0.4 39 44
RELA 0.014 0.078 -10000 0 -0.18 63 63
FGG -0.12 0.15 0.42 4 -0.36 47 51
GR beta/TIF2 -0.082 0.11 0.27 2 -0.31 70 72
IFNG 0.089 0.15 0.4 14 -0.46 4 18
apoptosis -0.12 0.2 0.51 6 -0.51 68 74
CREB1 0.03 0.023 -10000 0 -10000 0 0
histone acetylation 0.036 0.07 0.22 1 -0.25 3 4
BGLAP 0.086 0.095 0.34 8 -10000 0 8
GR/PKAc -0.054 0.097 0.27 1 -0.24 60 61
NF kappa B1 p50/RelA 0.028 0.14 -10000 0 -0.31 66 66
SMARCD1 0.023 0.005 -10000 0 -10000 0 0
MDM2 -0.024 0.047 0.18 4 -0.13 1 5
GATA3 0.027 0.057 0.28 13 -0.35 6 19
AKT1 0.02 0.003 -10000 0 -10000 0 0
CSF2 0.023 0.054 -10000 0 -10000 0 0
GSK3B 0.019 0.014 -10000 0 -10000 0 0
NR1I3 -0.078 0.19 0.49 8 -0.49 40 48
CSN2 -0.12 0.13 0.32 4 -0.33 50 54
BRG1/BAF155/BAF170/BAF60A 0.054 0.025 -10000 0 -0.14 2 2
NFATC1 0.014 0.058 -10000 0 -0.35 13 13
POU2F1 0.012 0.052 -10000 0 -0.26 17 17
CDKN1A 0.014 0.071 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN 0.2 0.12 0.28 379 -10000 0 379
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.061 0.15 0.29 21 -0.24 56 77
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.15 0.27 0.46 7 -0.75 76 83
JUN 0.096 0.11 0.3 50 -0.38 3 53
IL4 0.055 0.079 0.33 1 -0.33 1 2
CDK5R1 0.021 0.015 0.28 1 -10000 0 1
PRKACA 0.022 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.11 0.1 -10000 0 -0.26 127 127
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.052 0.1 0.28 1 -0.24 60 61
cortisol/GR alpha (monomer) -0.14 0.18 0.49 7 -0.42 51 58
NCOA2 0.009 0.065 -10000 0 -0.35 17 17
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.04 0.19 0.21 6 -0.33 156 162
AP-1/NFAT1-c-4 0.1 0.19 0.39 58 -0.48 11 69
AFP 0.072 0.091 0.34 5 -0.4 2 7
SUV420H1 0.022 0.004 -10000 0 -10000 0 0
IRF1 -0.062 0.09 0.34 1 -0.35 1 2
TP53 0.028 0.038 -10000 0 -0.83 1 1
PPP5C 0.023 0.004 -10000 0 -10000 0 0
KRT17 0.094 0.2 0.4 48 -0.85 10 58
KRT14 0.098 0.12 0.45 7 -10000 0 7
TBP 0.026 0.005 -10000 0 -10000 0 0
CREBBP -0.009 0.048 -10000 0 -0.25 1 1
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC2 0.022 0.007 -10000 0 -10000 0 0
AP-1 0.1 0.19 0.4 58 -0.47 12 70
MAPK14 0.018 0.014 -10000 0 -10000 0 0
MAPK10 -0.058 0.15 -10000 0 -0.35 110 110
MAPK11 0.016 0.026 -10000 0 -0.35 2 2
KRT5 0.1 0.22 0.41 51 -0.92 12 63
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.022 0.016 -10000 0 -0.35 1 1
STAT1 0.026 0.012 0.28 1 -10000 0 1
CGA 0.075 0.088 0.46 3 -10000 0 3
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.087 0.11 0.29 1 -0.35 32 33
MAPK3 0.018 0.015 -10000 0 -10000 0 0
MAPK1 0.018 0.014 -10000 0 -10000 0 0
ICAM1 0.062 0.13 0.4 3 -0.42 5 8
NFKB1 0.011 0.083 -10000 0 -0.22 29 29
MAPK8 0.1 0.1 0.29 51 -0.3 3 54
MAPK9 0.018 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.12 0.2 0.51 6 -0.53 69 75
BAX 0.011 0.06 -10000 0 -0.46 1 1
POMC 0.057 0.21 0.55 9 -1.1 11 20
EP300 -0.009 0.047 -10000 0 -0.25 1 1
cortisol/GR alpha (dimer)/p53 -0.12 0.15 0.46 6 -0.42 21 27
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.043 0.26 3 -10000 0 3
SGK1 -0.036 0.12 -10000 0 -1.1 3 3
IL13 0.065 0.13 0.42 2 -0.6 1 3
IL6 0.043 0.2 0.36 5 -0.86 16 21
PRKACG 0.017 0.005 -10000 0 -10000 0 0
IL5 0.056 0.11 -10000 0 -0.54 2 2
IL2 0.071 0.15 0.38 3 -0.46 8 11
CDK5 0.021 0.008 -10000 0 -10000 0 0
PRKACB 0.019 0.039 -10000 0 -0.35 6 6
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
IL8 0.094 0.15 0.34 23 -0.38 6 29
CDK5R1/CDK5 0.027 0.02 0.21 1 -10000 0 1
NF kappa B1 p50/RelA/PKAc 0.049 0.12 -10000 0 -0.26 40 40
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.11 0.15 0.42 7 -0.37 26 33
SMARCA4 0.022 0.008 -10000 0 -10000 0 0
chromatin remodeling -0.067 0.1 0.3 4 -0.34 14 18
NF kappa B1 p50/RelA/Cbp 0.012 0.13 -10000 0 -0.31 32 32
JUN (dimer) 0.096 0.11 0.29 50 -0.38 3 53
YWHAH 0.022 0.006 -10000 0 -10000 0 0
VIPR1 0.066 0.092 0.33 10 -0.57 3 13
NR3C1 -0.12 0.15 0.33 4 -0.4 70 74
NR4A1 -0.008 0.12 -10000 0 -0.4 44 44
TIF2/SUV420H1 0.021 0.05 -10000 0 -0.24 17 17
MAPKKK cascade -0.12 0.2 0.51 6 -0.51 68 74
cortisol/GR alpha (dimer)/Src-1 -0.12 0.16 0.45 6 -0.4 27 33
PBX1 0.001 0.085 -10000 0 -0.33 31 31
POU1F1 0.01 0.061 0.28 2 -0.29 19 21
SELE -0.011 0.31 0.38 4 -0.82 63 67
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.068 0.11 0.3 4 -0.35 14 18
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.11 0.15 0.42 7 -0.37 26 33
mol:cortisol -0.066 0.09 0.28 6 -0.21 27 33
MMP1 0.11 0.16 0.35 19 -0.48 12 31
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.036 0.1 0.28 30 -10000 0 30
GNAI2 0.022 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.029 0.19 10 -0.2 3 13
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 123 123
RhoA/GTP -0.036 0.1 -10000 0 -0.28 30 30
negative regulation of cAMP metabolic process -0.038 0.1 0.17 2 -0.21 112 114
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
GNAI3 0.023 0.002 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.038 0.1 0.17 2 -0.22 112 114
RhoA/GDP 0.016 0.004 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.003 0.037 -10000 0 -0.2 13 13
NFATC2 -0.009 0.061 -10000 0 -0.21 43 43
NFATC3 0.007 0.018 -10000 0 -0.11 1 1
CD40LG -0.051 0.14 0.32 1 -0.34 55 56
PTGS2 -0.056 0.16 -10000 0 -0.38 74 74
JUNB 0.018 0.036 -10000 0 -0.35 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.015 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.015 -10000 0 -10000 0 0
CALM1 0.02 0.014 -10000 0 -10000 0 0
JUN 0.016 0.044 -10000 0 -0.35 7 7
mol:Ca2+ 0 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.007 -10000 0 -10000 0 0
FOSL1 0.042 0.068 0.28 40 -10000 0 40
CREM 0.021 0.008 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.008 0.087 0.24 1 -0.28 16 17
FOS -0.09 0.17 -10000 0 -0.35 158 158
IFNG -0.038 0.14 0.27 5 -0.32 50 55
AP-1/NFAT1-c-4 -0.026 0.17 0.35 11 -0.36 51 62
FASLG -0.042 0.13 0.26 5 -0.32 49 54
NFAT1-c-4/ICER1 -0.001 0.073 -10000 0 -0.2 40 40
IL2RA -0.041 0.13 0.27 8 -0.32 49 57
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSF2 -0.045 0.13 0.27 4 -0.32 50 54
JunB/Fra1/NFAT1-c-4 0.018 0.089 0.21 24 -0.23 16 40
IL4 -0.048 0.13 0.32 1 -0.32 50 51
IL2 -0.01 0.16 -10000 0 -0.86 18 18
IL3 -0.003 0.1 -10000 0 -0.66 12 12
FKBP1A 0.022 0.004 -10000 0 -10000 0 0
BATF3 0.02 0.014 0.28 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.009 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.023 0.014 0.33 1 -9999 0 1
GPC2 0.041 0.068 0.28 38 -9999 0 38
GPC2/Midkine 0.043 0.045 0.21 33 -9999 0 33
neuron projection morphogenesis 0.043 0.045 0.21 33 -9999 0 33
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.023 0.055 0.18 2 -0.18 34 36
RGS9BP 0.033 0.056 0.29 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.018 0.013 0.28 1 -10000 0 1
mol:Na + 0.016 0.047 0.18 3 -0.2 21 24
mol:ADP -0.014 0.009 0.11 2 -10000 0 2
GNAT2 0.023 0.02 0.28 3 -10000 0 3
RGS9-1/Gbeta5/R9AP -0.007 0.11 0.21 14 -0.21 110 124
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.013 0.18 3 -10000 0 3
GRK7 0.02 0.012 0.28 1 -10000 0 1
CNGB3 0.003 0.072 -10000 0 -0.35 21 21
Cone Metarhodopsin II/X-Arrestin 0.014 0.008 0.19 1 -10000 0 1
mol:Ca2+ -0.008 0.063 0.18 37 -0.19 20 57
Cone PDE6 0.005 0.1 0.22 5 -0.18 108 113
Cone Metarhodopsin II 0.023 0.012 0.18 2 -10000 0 2
Na + (4 Units) 0.025 0.046 0.19 3 -0.19 21 24
GNAT2/GDP 0.003 0.097 0.21 5 -0.18 110 115
GNB5 0.022 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.012 0.025 0.18 8 -10000 0 8
Cone Transducin 0.026 0.059 0.19 2 -0.19 34 36
SLC24A2 0.019 0.014 0.33 1 -10000 0 1
GNB3/GNGT2 0.013 0.07 -10000 0 -0.25 34 34
GNB3 -0.001 0.09 -10000 0 -0.35 33 33
GNAT2/GTP 0.017 0.013 0.19 3 -10000 0 3
CNGA3 0.022 0.023 0.28 4 -10000 0 4
ARR3 0.019 0.012 0.28 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.016 0.047 0.19 3 -0.2 21 24
mol:Pi -0.008 0.11 0.21 14 -0.21 110 124
Cone CNG Channel 0.033 0.049 -10000 0 -0.18 21 21
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.019 0.014 0.33 1 -10000 0 1
RGS9 -0.057 0.15 -10000 0 -0.35 112 112
PDE6C 0.018 0.014 0.33 1 -10000 0 1
GNGT2 0.02 0.028 -10000 0 -0.35 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.004 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin 0.015 0.036 -10000 0 -0.2 14 14
EPHB2 0.024 0.02 0.28 3 -10000 0 3
Syndecan-2/TACI 0.019 0.044 0.2 15 -0.19 11 26
LAMA1 0.1 0.13 0.28 173 -0.35 4 177
Syndecan-2/alpha2 ITGB1 0.028 0.056 -10000 0 -0.19 28 28
HRAS 0.022 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.001 0.029 -10000 0 -0.2 11 11
ITGA5 0.023 0.003 -10000 0 -10000 0 0
BAX -0.01 0.028 -10000 0 -10000 0 0
EPB41 0.022 0.017 -10000 0 -0.35 1 1
positive regulation of cell-cell adhesion 0.014 0.029 -10000 0 -0.18 11 11
LAMA3 0.013 0.058 -10000 0 -0.35 13 13
EZR 0.022 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.009 0.1 -10000 0 -0.35 44 44
Syndecan-2/MMP2 0.008 0.05 -10000 0 -0.21 24 24
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.026 0.04 -10000 0 -0.24 11 11
dendrite morphogenesis 0.017 0.038 0.28 3 -0.2 11 14
Syndecan-2/GM-CSF 0.016 0.038 0.2 7 -0.2 11 18
determination of left/right symmetry 0.002 0.035 -10000 0 -0.24 11 11
Syndecan-2/PKC delta 0.015 0.032 -10000 0 -0.2 11 11
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
MAPK3 0.005 0.061 0.19 45 -0.18 10 55
MAPK1 0.003 0.06 0.19 42 -0.18 11 53
Syndecan-2/RACK1 0.025 0.031 -10000 0 -0.17 11 11
NF1 0.021 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.002 0.035 -10000 0 -0.24 11 11
ITGA2 0.014 0.053 -10000 0 -0.35 11 11
MAPK8 -0.002 0.032 -10000 0 -0.2 14 14
Syndecan-2/alpha2/beta1 Integrin 0.078 0.095 0.21 149 -0.17 23 172
Syndecan-2/Kininogen 0.022 0.05 0.21 23 -0.2 8 31
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.002 0.058 0.18 44 -0.17 11 55
Syndecan-2/CASK/Protein 4.1 0.014 0.03 -10000 0 -0.18 12 12
extracellular matrix organization 0.015 0.034 -10000 0 -0.2 12 12
actin cytoskeleton reorganization 0.014 0.036 -10000 0 -0.2 14 14
Syndecan-2/Caveolin-2/Ras 0.013 0.061 -10000 0 -0.19 41 41
Syndecan-2/Laminin alpha3 0.01 0.047 -10000 0 -0.21 22 22
Syndecan-2/RasGAP 0.032 0.039 -10000 0 -0.17 16 16
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
PRKCD 0.022 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.017 0.038 0.28 3 -0.2 11 14
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.018 0.037 0.17 4 -0.16 16 20
RHOA 0.022 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.027 0.045 0.28 16 -10000 0 16
RASA1 0.019 0.036 -10000 0 -0.35 5 5
alpha2/beta1 Integrin 0.026 0.04 -10000 0 -0.24 11 11
Syndecan-2/Synbindin 0.016 0.031 -10000 0 -0.2 10 10
TGFB1 0.022 0.017 -10000 0 -0.35 1 1
CASP3 0.004 0.061 0.19 44 -0.18 11 55
FN1 0.019 0.036 -10000 0 -0.35 5 5
Syndecan-2/IL8 0.067 0.093 0.2 149 -0.2 11 160
SDC2 0.002 0.035 -10000 0 -0.24 11 11
KNG1 0.03 0.057 0.29 24 -10000 0 24
Syndecan-2/Neurofibromin 0.015 0.032 -10000 0 -0.2 11 11
TRAPPC4 0.022 0.005 -10000 0 -10000 0 0
CSF2 0.024 0.032 0.28 8 -10000 0 8
Syndecan-2/TGFB1 0.015 0.034 -10000 0 -0.2 12 12
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.029 -10000 0 -0.18 11 11
Syndecan-2/Ezrin 0.027 0.033 -10000 0 -0.18 11 11
PRKACA 0.002 0.056 0.19 36 -0.18 10 46
angiogenesis 0.066 0.092 0.2 149 -0.2 11 160
MMP2 0.007 0.071 -10000 0 -0.35 20 20
IL8 0.095 0.12 0.28 151 -10000 0 151
calcineurin-NFAT signaling pathway 0.019 0.043 0.2 15 -0.19 11 26
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.009 0.069 -10000 0 -0.35 19 19
Jak2/Leptin Receptor -0.072 0.17 -10000 0 -0.36 96 96
PTP1B/AKT1 -0.003 0.084 0.26 1 -0.28 27 28
FYN 0.023 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.013 0.088 0.3 1 -0.3 29 30
EGFR 0.013 0.061 0.32 1 -0.36 13 14
EGF/EGFR 0.007 0.091 0.24 3 -0.25 33 36
CSF1 0.016 0.051 -10000 0 -0.35 10 10
AKT1 0.022 0.007 -10000 0 -10000 0 0
INSR 0.021 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.022 0.1 -10000 0 -0.29 45 45
Insulin Receptor/Insulin 0.01 0.082 0.24 1 -0.28 18 19
HCK 0.025 0.03 0.28 7 -10000 0 7
CRK 0.021 0.006 -10000 0 -10000 0 0
TYK2 -0.005 0.092 0.23 20 -0.28 27 47
EGF 0.03 0.053 0.28 20 -0.34 1 21
YES1 0.022 0.005 -10000 0 -10000 0 0
CAV1 -0.028 0.11 0.25 5 -0.32 38 43
TXN 0.022 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.009 0.1 -10000 0 -0.28 43 43
cell migration 0.013 0.088 0.3 29 -0.3 1 30
STAT3 0.022 0.006 -10000 0 -10000 0 0
PRLR -0.047 0.14 -10000 0 -0.35 99 99
ITGA2B 0.018 0.038 0.28 1 -0.35 5 6
CSF1R 0.021 0.03 0.28 1 -0.35 3 4
Prolactin Receptor/Prolactin -0.026 0.12 0.21 4 -0.25 109 113
FGR 0.015 0.053 -10000 0 -0.35 11 11
PTP1B/p130 Cas -0.002 0.085 0.27 1 -0.28 28 29
Crk/p130 Cas 0.006 0.086 0.27 1 -0.3 21 22
DOK1 -0.017 0.097 0.22 4 -0.33 29 33
JAK2 -0.053 0.15 0.26 1 -0.36 67 68
Jak2/Leptin Receptor/Leptin -0.01 0.094 -10000 0 -0.32 23 23
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
PTPN1 -0.013 0.089 0.3 1 -0.3 29 30
LYN 0.021 0.007 -10000 0 -10000 0 0
CDH2 -0.028 0.13 -10000 0 -0.35 72 72
SRC 0 0.11 -10000 0 -0.52 20 20
ITGB3 -0.04 0.14 0.28 2 -0.35 89 91
CAT1/PTP1B -0.002 0.12 0.29 13 -0.38 22 35
CAPN1 0.022 0.005 -10000 0 -10000 0 0
CSK 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.014 0.078 -10000 0 -0.27 16 16
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.008 0.086 -10000 0 -0.29 23 23
negative regulation of transcription -0.053 0.15 0.26 1 -0.36 67 68
FCGR2A 0.02 0.014 0.28 1 -10000 0 1
FER 0.023 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.017 0.11 0.21 3 -0.25 94 97
BLK 0.037 0.067 0.28 37 -10000 0 37
Insulin Receptor/Insulin/Shc 0.032 0.019 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
LEPR -0.088 0.17 -10000 0 -0.35 159 159
BCAR1 0.02 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.022 0.006 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 0.008 0.12 0.28 9 -0.41 17 26
PRL 0.006 0.071 0.28 5 -0.35 17 22
SOCS3 0 0.16 -10000 0 -1.1 11 11
SPRY2 0.019 0.033 -10000 0 -0.36 4 4
Insulin Receptor/Insulin/IRS1 0.015 0.074 -10000 0 -0.21 50 50
CSF1/CSF1R 0.002 0.095 -10000 0 -0.28 32 32
Ras protein signal transduction 0.02 0.12 0.56 24 -10000 0 24
IRS1 -0.012 0.11 -10000 0 -0.35 50 50
INS 0.009 0.015 -10000 0 -10000 0 0
LEP 0.016 0.021 0.28 2 -10000 0 2
STAT5B -0.031 0.12 0.29 1 -0.35 46 47
STAT5A -0.031 0.12 0.29 1 -0.35 45 46
GRB2 0.022 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.009 0.094 -10000 0 -0.29 35 35
CSN2 -0.021 0.078 -10000 0 -0.48 3 3
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
LAT 0.008 0.092 -10000 0 -0.54 12 12
YBX1 0.026 0.017 -10000 0 -0.35 1 1
LCK 0.024 0.028 0.28 4 -0.35 1 5
SHC1 0.019 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.035 0.28 1 -0.35 4 5
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.006 0.074 0.66 2 -0.62 1 3
VDR 0.029 0.042 0.29 13 -10000 0 13
FAM120B 0.022 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.014 0.076 0.22 9 -0.3 5 14
RXRs/LXRs/DNA/Oxysterols 0.03 0.085 0.29 2 -0.44 3 5
MED1 0.021 0.006 -10000 0 -10000 0 0
mol:9cRA 0.005 0.008 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.038 0.1 -10000 0 -0.2 122 122
RXRs/NUR77 0.017 0.1 0.25 5 -0.2 80 85
RXRs/PPAR -0.014 0.087 0.18 5 -0.2 82 87
NCOR2 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.023 0.19 9 -10000 0 9
RARs/VDR/DNA/Vit D3 0.047 0.039 0.22 2 -0.18 8 10
RARA 0.022 0.006 -10000 0 -10000 0 0
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
VDR/VDR/DNA 0.029 0.042 0.29 13 -10000 0 13
RARs/RARs/DNA/9cRA 0.036 0.031 -10000 0 -0.17 9 9
RARG 0.023 0.003 -10000 0 -10000 0 0
RPS6KB1 0.013 0.086 0.57 12 -10000 0 12
RARs/THRs/DNA/SMRT -0.037 0.099 -10000 0 -0.2 125 125
THRA 0.016 0.046 -10000 0 -0.35 8 8
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.023 0.19 9 -10000 0 9
RXRs/PPAR/9cRA/PGJ2/DNA 0.025 0.08 0.28 5 -0.18 39 44
NR1H4 0.027 0.049 0.28 19 -10000 0 19
RXRs/LXRs/DNA 0.042 0.087 0.34 1 -0.26 2 3
NR1H2 0.027 0.009 -10000 0 -10000 0 0
NR1H3 0.028 0.015 0.28 1 -10000 0 1
RXRs/VDR/DNA/Vit D3 0.03 0.078 0.23 8 -0.16 53 61
NR4A1 -0.002 0.092 -10000 0 -0.35 35 35
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0 0.072 0.2 6 -0.18 44 50
RXRG -0.013 0.12 0.31 9 -0.34 58 67
RXR alpha/CCPG 0.034 0.013 -10000 0 -10000 0 0
RXRA 0.026 0.011 -10000 0 -10000 0 0
RXRB 0.028 0.01 -10000 0 -10000 0 0
THRB -0.056 0.15 -10000 0 -0.35 111 111
PPARG 0.003 0.084 0.33 1 -0.35 28 29
PPARD 0.023 0.003 -10000 0 -10000 0 0
TNF 0.03 0.11 0.39 3 -0.96 2 5
mol:Oxysterols 0.005 0.007 -10000 0 -10000 0 0
cholesterol transport 0.03 0.084 0.29 2 -0.43 3 5
PPARA 0.021 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.016 0.048 -10000 0 -0.35 9 9
RXRs/NUR77/BCL2 -0.033 0.11 0.17 2 -0.25 96 98
SREBF1 0.023 0.077 -10000 0 -0.5 1 1
RXRs/RXRs/DNA/9cRA 0.025 0.08 0.28 5 -0.18 39 44
ABCA1 0.026 0.072 -10000 0 -0.5 1 1
RARs/THRs 0.002 0.11 -10000 0 -0.19 122 122
RXRs/FXR 0.031 0.085 0.25 6 -0.18 54 60
BCL2 -0.009 0.1 -10000 0 -0.35 44 44
TCGA08_rtk_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
PDGFRA -0.075 0.16 -10000 0 -0.35 139 139
HRAS 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
AKT -0.042 0.13 0.29 4 -0.25 124 128
FOXO3 0.023 0.003 -10000 0 -10000 0 0
AKT1 0.023 0.004 -10000 0 -10000 0 0
FOXO1 0.021 0.023 -10000 0 -0.35 2 2
AKT3 -0.096 0.17 -10000 0 -0.35 164 164
FOXO4 0.022 0.023 -10000 0 -0.35 2 2
MET 0.021 0.039 0.28 4 -0.35 4 8
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PIK3CB 0.022 0.005 -10000 0 -10000 0 0
NRAS 0.023 0.001 -10000 0 -10000 0 0
PIK3CG 0.013 0.062 0.28 2 -0.35 14 16
PIK3R3 0.023 0.012 0.28 1 -10000 0 1
PIK3R2 0.022 0.005 -10000 0 -10000 0 0
NF1 0.021 0.006 -10000 0 -10000 0 0
RAS -0.011 0.066 0.16 9 -0.13 104 113
ERBB2 0.029 0.049 0.33 14 -10000 0 14
proliferation/survival/translation 0.004 0.089 0.28 13 -0.28 5 18
PI3K 0.003 0.07 0.21 20 -0.22 9 29
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
KRAS 0.023 0.014 0.33 1 -10000 0 1
FOXO 0.032 0.048 0.23 9 -10000 0 9
AKT2 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP -0.041 0.12 -10000 0 -0.2 168 168
TC10/GTP -0.025 0.094 -10000 0 -0.17 152 152
Insulin Receptor/Insulin/IRS1/Shp2 0.029 0.074 -10000 0 -0.19 50 50
HRAS 0.022 0.005 -10000 0 -10000 0 0
APS homodimer 0.022 0.005 -10000 0 -10000 0 0
GRB14 0.11 0.13 0.28 189 -0.35 3 192
FOXO3 0.016 0.066 -10000 0 -0.57 6 6
AKT1 -0.006 0.08 0.23 18 -0.3 2 20
INSR 0.024 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.046 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.017 -10000 0 -0.35 1 1
SORBS1 -0.095 0.17 -10000 0 -0.35 167 167
CRK 0.021 0.006 -10000 0 -10000 0 0
PTPN1 -0.004 0.026 0.15 15 -10000 0 15
CAV1 -0.05 0.088 0.16 5 -0.21 106 111
CBL/APS/CAP/Crk-II/C3G -0.016 0.11 -10000 0 -0.18 155 155
Insulin Receptor/Insulin/IRS1/NCK2 0.028 0.074 -10000 0 -0.19 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.019 0.063 -10000 0 -0.18 43 43
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.008 0.089 -10000 0 -0.33 26 26
RPS6KB1 -0.011 0.072 0.2 25 -0.28 2 27
PARD6A 0.02 0.008 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.027 -10000 0 -0.57 1 1
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.007 0.064 0.17 2 -0.29 2 4
HRAS/GTP -0.025 0.038 -10000 0 -0.17 28 28
Insulin Receptor 0.023 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.032 0.064 -10000 0 -0.18 33 33
PRKCI 0.005 0.07 -10000 0 -0.38 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.021 0.065 -10000 0 -0.17 40 40
SHC1 0.019 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.033 0.042 -10000 0 -0.35 4 4
PI3K 0.026 0.067 -10000 0 -0.18 43 43
NCK2 0.023 0.003 -10000 0 -10000 0 0
RHOQ 0.023 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.016 0.004 -10000 0 -10000 0 0
AKT2 -0.008 0.077 0.24 14 -0.3 2 16
PRKCZ 0.002 0.078 -10000 0 -0.33 3 3
SH2B2 0.022 0.005 -10000 0 -10000 0 0
SHC/SHIP 0.006 0.05 -10000 0 -0.17 33 33
F2RL2 0.002 0.088 0.28 3 -0.35 30 33
TRIP10 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.047 0.032 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
RASA1 0.019 0.036 -10000 0 -0.35 5 5
NCK1 0.021 0.023 -10000 0 -0.35 2 2
CBL/APS/CAP/Crk-II -0.024 0.11 -10000 0 -0.19 160 160
TC10/GDP 0.017 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.042 0.029 -10000 0 -0.2 1 1
INPP5D -0.026 0.052 0.15 4 -0.18 49 53
SOS1 0.023 0.003 -10000 0 -10000 0 0
SGK1 0.005 0.069 -10000 0 -0.69 5 5
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.003 -10000 0 -10000 0 0
IRS1 -0.012 0.11 -10000 0 -0.35 50 50
p62DOK/RasGAP 0.034 0.042 -10000 0 -0.35 4 4
INS 0.018 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.026 0.052 0.15 4 -0.18 49 53
GRB2 0.022 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.01 0.075 0.22 27 -0.27 2 29
PTPRA 0.024 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
TC10/GTP/CIP4 0.029 0.009 -10000 0 -10000 0 0
PDPK1 0.022 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.056 -10000 0 -0.19 38 38
Insulin Receptor/Insulin/IRS1 0.017 0.068 -10000 0 -0.19 50 50
Insulin Receptor/Insulin/IRS3 0.03 0.013 -10000 0 -10000 0 0
Par3/Par6 0.034 0.055 -10000 0 -0.18 28 28
Coregulation of Androgen receptor activity

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
NRIP1 0.021 0.028 -10000 0 -0.35 3 3
SVIL -0.016 0.11 -10000 0 -0.35 55 55
ZNF318 0.02 0.01 -10000 0 -10000 0 0
JMJD2C -0.004 0.03 0.083 7 -0.12 28 35
T-DHT/AR/Ubc9 -0.009 0.093 -10000 0 -0.21 88 88
CARM1 0.021 0.006 -10000 0 -10000 0 0
PRDX1 0.023 0.003 -10000 0 -10000 0 0
PELP1 0.021 0.006 -10000 0 -10000 0 0
CTNNB1 0.023 0.005 -10000 0 -10000 0 0
AKT1 0.021 0.008 -10000 0 -10000 0 0
PTK2B 0.02 0.008 -10000 0 -10000 0 0
MED1 0.02 0.009 -10000 0 -10000 0 0
MAK 0.037 0.067 0.28 37 -10000 0 37
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.02 0.032 -10000 0 -0.35 4 4
GSN 0.019 0.036 -10000 0 -0.35 5 5
NCOA2 0.009 0.066 -10000 0 -0.35 17 17
NCOA6 0.023 0.005 -10000 0 -10000 0 0
DNA-PK 0.036 0.022 -10000 0 -10000 0 0
NCOA4 0.022 0.005 -10000 0 -10000 0 0
PIAS3 0.019 0.009 -10000 0 -10000 0 0
cell proliferation 0.016 0.066 0.22 3 -0.52 2 5
XRCC5 0.021 0.008 -10000 0 -10000 0 0
UBE3A 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.027 0.11 0.19 1 -0.21 122 123
FHL2 -0.004 0.09 -10000 0 -0.81 5 5
RANBP9 0.023 0.005 -10000 0 -10000 0 0
JMJD1A 0.005 0.022 0.087 22 -0.11 8 30
CDK6 0.014 0.055 -10000 0 -0.35 12 12
TGFB1I1 -0.091 0.17 -10000 0 -0.35 162 162
T-DHT/AR/CyclinD1 -0.008 0.093 0.19 1 -0.21 86 87
XRCC6 0.02 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.007 0.11 -10000 0 -0.21 103 103
CTDSP1 0.023 0.004 -10000 0 -10000 0 0
CTDSP2 0.021 0.009 -10000 0 -10000 0 0
BRCA1 0.023 0.006 -10000 0 -10000 0 0
TCF4 0.007 0.069 -10000 0 -0.35 19 19
CDKN2A 0.12 0.13 0.28 213 -10000 0 213
SRF 0.024 0.017 -10000 0 -0.14 5 5
NKX3-1 -0.015 0.053 0.1 1 -0.2 19 20
KLK3 -0.014 0.058 -10000 0 -10000 0 0
TMF1 0.022 0.005 -10000 0 -10000 0 0
HNRNPA1 0.021 0.008 -10000 0 -10000 0 0
AOF2 0.001 0.003 -10000 0 -10000 0 0
APPL1 -0.012 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.009 0.093 -10000 0 -0.21 86 86
AR -0.041 0.14 -10000 0 -0.36 87 87
UBA3 0.022 0.005 -10000 0 -10000 0 0
PATZ1 0.02 0.009 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
PRKDC 0.019 0.01 -10000 0 -10000 0 0
PA2G4 0.02 0.009 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.006 0.084 -10000 0 -0.19 85 85
RPS6KA3 0.023 0.017 -10000 0 -0.35 1 1
T-DHT/AR/ARA70 -0.009 0.093 -10000 0 -0.21 86 86
LATS2 0.019 0.024 -10000 0 -0.35 2 2
T-DHT/AR/PRX1 -0.007 0.084 -10000 0 -0.19 86 86
Cyclin D3/CDK11 p58 0.017 0.003 -10000 0 -10000 0 0
VAV3 0.084 0.11 0.28 125 -10000 0 125
KLK2 -0.043 0.18 -10000 0 -0.74 31 31
CASP8 0.023 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.002 0.093 -10000 0 -0.2 80 80
TMPRSS2 -0.011 0.12 0.3 1 -0.73 11 12
CCND1 0.024 0.022 0.31 3 -10000 0 3
PIAS1 0.023 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.001 0.015 -10000 0 -0.051 37 37
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.023 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.012 0.097 -10000 0 -0.21 94 94
CMTM2 0.021 0.021 0.28 3 -10000 0 3
SNURF -0.006 0.096 0.28 1 -0.35 38 39
ZMIZ1 0.017 0.036 -10000 0 -0.36 3 3
CCND3 0.023 0.004 -10000 0 -10000 0 0
TGIF1 0.02 0.009 -10000 0 -10000 0 0
FKBP4 0.023 0.005 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.017 0.084 0.3 12 -0.3 9 21
TBX21 -0.02 0.25 0.67 6 -1.1 15 21
B2M 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.012 0.031 0.17 2 -10000 0 2
IL12RB1 0.017 0.069 0.34 13 -0.38 4 17
GADD45B -0.008 0.2 0.58 6 -0.7 16 22
IL12RB2 0.028 0.07 0.28 32 -10000 0 32
GADD45G -0.021 0.26 0.58 6 -0.9 27 33
natural killer cell activation 0.001 0.02 0.093 9 -0.047 14 23
RELB 0.022 0.005 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
IL18 0.027 0.037 0.28 9 -10000 0 9
IL2RA 0.031 0.052 0.28 20 -0.35 1 21
IFNG 0.05 0.081 0.28 59 -10000 0 59
STAT3 (dimer) -0.014 0.2 0.53 7 -0.63 23 30
HLA-DRB5 -0.006 0.01 -10000 0 -0.023 145 145
FASLG 0.011 0.24 0.71 7 -0.88 15 22
NF kappa B2 p52/RelB -0.011 0.2 0.45 1 -0.81 16 17
CD4 0.007 0.027 0.23 1 -10000 0 1
SOCS1 0.021 0.017 -10000 0 -0.35 1 1
EntrezGene:6955 -0.007 0.013 -10000 0 -0.027 152 152
CD3D 0.008 0.065 0.26 14 -0.35 7 21
CD3E 0.003 0.06 0.28 5 -0.36 9 14
CD3G 0.007 0.047 0.28 7 -0.35 2 9
IL12Rbeta2/JAK2 0.027 0.073 0.22 31 -0.25 9 40
CCL3 -0.008 0.22 0.72 6 -0.98 10 16
CCL4 -0.013 0.23 0.71 6 -1.1 11 17
HLA-A 0 0.005 -10000 0 -0.044 7 7
IL18/IL18R 0.056 0.058 0.29 8 -0.22 8 16
NOS2 -0.013 0.24 0.66 6 -0.9 20 26
IL12/IL12R/TYK2/JAK2/SPHK2 0.018 0.082 0.3 12 -0.27 9 21
IL1R1 -0.022 0.25 0.64 6 -1 18 24
IL4 -0.001 0.033 -10000 0 -0.16 3 3
JAK2 0.006 0.058 0.17 2 -0.36 9 11
EntrezGene:6957 -0.006 0.012 -10000 0 -0.024 145 145
TCR/CD3/MHC I/CD8 -0.017 0.12 0.31 2 -0.59 17 19
RAB7A 0 0.2 0.58 4 -0.64 18 22
lysosomal transport 0.001 0.19 0.52 7 -0.6 19 26
FOS -0.3 0.54 0.53 4 -1.1 170 174
STAT4 (dimer) 0.016 0.2 0.55 7 -0.64 19 26
STAT5A (dimer) 0.008 0.23 0.62 9 -0.8 17 26
GZMA -0.024 0.26 0.66 6 -1.1 17 23
GZMB -0.007 0.23 0.64 8 -1.1 10 18
HLX 0.02 0.008 -10000 0 -10000 0 0
LCK -0.013 0.22 0.62 7 -0.89 16 23
TCR/CD3/MHC II/CD4 -0.043 0.12 0.18 5 -0.22 126 131
IL2/IL2R 0.06 0.057 0.26 31 -0.18 3 34
MAPK14 -0.009 0.22 0.56 7 -0.71 26 33
CCR5 -0.001 0.21 0.58 7 -0.79 17 24
IL1B 0.01 0.046 0.17 2 -0.38 4 6
STAT6 0.015 0.084 0.41 6 -0.51 1 7
STAT4 0.022 0.016 -10000 0 -0.35 1 1
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT1 0.023 0.012 0.28 1 -10000 0 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
NFKB2 0.022 0.005 -10000 0 -10000 0 0
IL12B 0.011 0.035 0.22 3 -10000 0 3
CD8A 0.018 0.054 0.29 4 -0.35 9 13
CD8B 0.03 0.07 0.28 25 -0.35 7 32
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.017 0.083 0.3 9 -0.3 12 21
IL2RB 0.021 0.017 -10000 0 -0.35 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.19 0.55 7 -0.59 19 26
IL2RG 0.024 0.039 0.28 6 -0.35 3 9
IL12 0.022 0.059 0.22 15 -0.26 4 19
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
CD247 0.004 0.035 0.28 1 -0.35 2 3
IL2 0.027 0.046 0.28 17 -10000 0 17
SPHK2 0.023 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.06 0.28 12 -0.37 4 16
IL12/IL12R/TYK2/JAK2 -0.014 0.25 0.7 7 -0.94 17 24
MAP2K3 -0.019 0.23 0.56 7 -0.68 31 38
RIPK2 0.021 0.007 -10000 0 -10000 0 0
MAP2K6 -0.004 0.22 0.56 7 -0.68 28 35
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.012 -10000 0 -0.026 147 147
IL18RAP 0.021 0.041 0.3 3 -0.35 4 7
IL12Rbeta1/TYK2 0.021 0.062 0.29 12 -0.29 4 16
EOMES -0.016 0.16 -10000 0 -0.86 15 15
STAT1 (dimer) 0.018 0.2 0.6 10 -0.62 19 29
T cell proliferation 0.014 0.17 0.47 7 -0.5 21 28
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.035 -10000 0 -0.35 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.16 0.5 2 -0.56 19 21
ATF2 -0.009 0.21 0.53 7 -0.66 26 33
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.008 0.12 -10000 0 -0.41 38 38
HDAC1 0.021 0.007 -10000 0 -10000 0 0
AES 0.021 0.006 -10000 0 -10000 0 0
FBXW11 0.022 0.004 -10000 0 -10000 0 0
DTX1 0.018 0.039 -10000 0 -0.35 6 6
LRP6/FZD1 0.032 0.018 -10000 0 -0.24 2 2
TLE1 0.022 0.005 -10000 0 -10000 0 0
AP1 -0.048 0.11 -10000 0 -0.22 134 134
NCSTN 0.019 0.009 -10000 0 -10000 0 0
ADAM10 0.02 0.028 -10000 0 -0.35 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.006 0.15 -10000 0 -0.67 24 24
NICD/RBPSUH -0.005 0.12 -10000 0 -0.4 38 38
WIF1 0.059 0.15 0.28 125 -0.35 33 158
NOTCH1 -0.007 0.099 -10000 0 -0.42 29 29
PSENEN 0.022 0.005 -10000 0 -10000 0 0
KREMEN2 0.045 0.074 0.28 47 -10000 0 47
DKK1 0.068 0.11 0.28 106 -0.35 7 113
beta catenin/beta TrCP1 0.029 0.069 0.22 2 -0.41 4 6
APH1B 0.018 0.04 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
AXIN1 -0.012 0.11 -10000 0 -0.45 21 21
CtBP/CBP/TCF1/TLE1/AES 0.01 0.039 -10000 0 -0.2 1 1
PSEN1 0.022 0.004 -10000 0 -10000 0 0
FOS -0.088 0.17 -10000 0 -0.35 158 158
JUN 0.018 0.042 -10000 0 -0.35 7 7
MAP3K7 0.022 0.004 -10000 0 -10000 0 0
CTNNB1 0.018 0.07 0.23 2 -0.37 6 8
MAPK3 0.022 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.042 0.077 0.21 43 -0.2 30 73
HNF1A 0.026 0.031 0.28 8 -10000 0 8
CTBP1 0.022 0.005 -10000 0 -10000 0 0
MYC -0.006 0.17 -10000 0 -1.2 11 11
NKD1 0.033 0.08 0.28 36 -0.35 8 44
FZD1 0.021 0.023 -10000 0 -0.35 2 2
NOTCH1 precursor/Deltex homolog 1 -0.007 0.12 -10000 0 -0.4 36 36
apoptosis -0.048 0.11 -10000 0 -0.22 134 134
Delta 1/NOTCHprecursor -0.009 0.12 -10000 0 -0.41 38 38
DLL1 0.011 0.066 -10000 0 -0.35 17 17
PPARD 0.017 0.058 -10000 0 -0.88 2 2
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
APC -0.011 0.11 -10000 0 -0.53 17 17
DVL1 0.012 0.032 -10000 0 -0.43 2 2
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.083 0.083 0.21 141 -0.2 7 148
LRP6 0.023 0.003 -10000 0 -10000 0 0
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
NLK 0.009 0.005 -10000 0 -10000 0 0
CCND1 0.008 0.11 -10000 0 -0.85 8 8
WNT1 0.025 0.03 0.28 7 -10000 0 7
Axin1/APC/beta catenin 0.016 0.12 -10000 0 -0.43 21 21
DKK2 0.002 0.087 0.28 2 -0.35 30 32
NOTCH1 precursor/DVL1 -0.012 0.13 -10000 0 -0.45 38 38
GSK3B 0.022 0.004 -10000 0 -10000 0 0
FRAT1 0.022 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.005 0.12 -10000 0 -0.4 36 36
PPP2R5D 0.014 0.033 0.22 4 -0.27 3 7
MAPK1 0.022 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.076 0.096 0.36 3 -0.19 33 36
RBPJ 0.022 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.058 0.13 0.28 84 -0.34 20 104
FYN 0.027 0.12 0.26 27 -0.38 23 50
LAT/GRAP2/SLP76 0.031 0.11 0.29 11 -0.38 21 32
IKBKB 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.019 0.11 0.25 19 -0.32 27 46
B2M 0.023 0.008 -10000 0 -10000 0 0
IKBKG 0.009 0.036 0.12 12 -0.11 11 23
MAP3K8 0.02 0.028 -10000 0 -0.35 3 3
mol:Ca2+ -0.012 0.012 0.086 1 -0.078 4 5
integrin-mediated signaling pathway 0.026 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.016 0.14 0.31 14 -0.43 29 43
TRPV6 -0.014 0.18 1.2 9 -10000 0 9
CD28 0.024 0.017 0.28 2 -10000 0 2
SHC1 0.044 0.15 0.29 86 -0.38 24 110
receptor internalization 0.016 0.12 0.31 6 -0.4 29 35
PRF1 0.009 0.17 0.45 1 -0.84 14 15
KRAS 0.023 0.014 0.33 1 -10000 0 1
GRB2 0.022 0.006 -10000 0 -10000 0 0
COT/AKT1 0.027 0.09 0.26 14 -0.26 23 37
LAT 0.02 0.12 0.29 13 -0.4 25 38
EntrezGene:6955 0 0.003 -10000 0 -0.034 1 1
CD3D 0.025 0.061 0.29 14 -0.36 7 21
CD3E 0.02 0.056 0.3 5 -0.36 9 14
CD3G 0.024 0.039 0.29 7 -0.35 2 9
RASGRP2 -0.014 0.058 0.092 1 -0.16 73 74
RASGRP1 0.012 0.12 0.3 15 -0.41 19 34
HLA-A 0.001 0.003 -10000 0 -10000 0 0
RASSF5 0.02 0.008 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.027 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.026 0.067 0.15 71 -0.13 15 86
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.005 0.04 -10000 0 -0.16 22 22
PRKCA 0.003 0.066 0.18 15 -0.22 14 29
GRAP2 0.011 0.062 -10000 0 -0.35 15 15
mol:IP3 0.013 0.085 0.2 36 -0.29 19 55
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.007 0.082 0.27 6 -0.42 13 19
ORAI1 0 0.15 0.4 3 -0.98 9 12
CSK 0.02 0.12 0.26 13 -0.39 26 39
B7 family/CD28 0.053 0.12 0.4 11 -0.41 15 26
CHUK 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.016 0.13 0.28 10 -0.42 27 37
PTPN6 0.016 0.12 0.26 14 -0.38 26 40
VAV1 0.019 0.12 0.28 11 -0.39 26 37
Monovalent TCR/CD3 0.011 0.053 0.23 8 -0.26 13 21
CBL 0.022 0.005 -10000 0 -10000 0 0
LCK 0.025 0.13 0.26 26 -0.42 20 46
PAG1 0.024 0.12 0.29 13 -0.39 24 37
RAP1A 0.023 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.017 0.13 0.25 14 -0.41 27 41
CD80 0.037 0.059 0.28 29 -10000 0 29
CD86 0.024 0.017 0.29 2 -10000 0 2
PDK1/CARD11/BCL10/MALT1 0.004 0.052 0.16 2 -0.2 22 24
HRAS 0.022 0.005 -10000 0 -10000 0 0
GO:0035030 0.017 0.095 0.28 10 -0.34 17 27
CD8A 0.019 0.055 0.3 4 -0.35 9 13
CD8B 0.031 0.071 0.28 25 -0.36 7 32
PTPRC 0.015 0.047 0.28 1 -0.35 8 9
PDK1/PKC theta 0.014 0.12 0.29 20 -0.38 24 44
CSK/PAG1 0.024 0.12 0.29 16 -0.38 23 39
SOS1 0.023 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.008 -10000 0 -10000 0 0
GRAP2/SLP76 0.033 0.12 0.35 6 -0.4 26 32
STIM1 0.002 0.062 1.2 1 -10000 0 1
RAS family/GTP 0.036 0.072 0.2 29 -0.17 12 41
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.015 0.12 0.31 6 -0.42 29 35
mol:DAG -0.005 0.062 0.095 6 -0.24 24 30
RAP1A/GDP 0.015 0.032 0.086 31 -0.065 6 37
PLCG1 0.022 0.005 -10000 0 -10000 0 0
CD247 0.019 0.027 0.3 1 -0.35 2 3
cytotoxic T cell degranulation 0.01 0.16 0.42 3 -0.8 14 17
RAP1A/GTP -0.006 0.022 -10000 0 -0.059 75 75
mol:PI-3-4-5-P3 0.019 0.12 0.28 17 -0.36 29 46
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.027 0.11 0.26 17 -0.36 19 36
NRAS 0.023 0.001 -10000 0 -10000 0 0
ZAP70 0.03 0.05 0.28 16 -0.35 2 18
GRB2/SOS1 0.032 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.021 0.1 0.32 5 -0.36 21 26
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.037 0.07 0.24 26 -0.26 15 41
CARD11 0.027 0.041 0.28 11 -0.35 1 12
PRKCB 0.003 0.072 0.19 13 -0.26 17 30
PRKCE 0.009 0.063 0.17 18 -0.2 15 33
PRKCQ 0.013 0.13 0.31 17 -0.41 28 45
LCP2 0.023 0.012 0.28 1 -10000 0 1
BCL10 0.023 0.002 -10000 0 -10000 0 0
regulation of survival gene product expression 0.02 0.095 0.24 20 -0.27 27 47
IKK complex 0.015 0.058 0.19 27 -0.11 8 35
RAS family/GDP -0.001 0.009 -10000 0 -0.04 5 5
MAP3K14 0.019 0.07 0.2 16 -0.21 21 37
PDPK1 0.019 0.1 0.26 19 -0.3 27 46
TCR/CD3/MHC I/CD8/Fyn -0.007 0.15 0.38 4 -0.5 32 36
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.013 0.1 0.21 2 -0.24 88 90
AKT1 -0.014 0.15 0.32 7 -0.48 37 44
PTK2B -0.055 0.13 -10000 0 -0.5 30 30
VEGFR2 homodimer/Frs2 -0.005 0.13 -10000 0 -0.53 30 30
CAV1 -0.04 0.14 -10000 0 -0.35 89 89
CALM1 0.022 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.009 0.12 -10000 0 -0.48 30 30
endothelial cell proliferation -0.02 0.15 0.34 15 -0.43 44 59
mol:Ca2+ -0.043 0.12 0.18 3 -0.49 31 34
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.02 0.12 -10000 0 -0.46 30 30
RP11-342D11.1 -0.041 0.12 0.17 6 -0.48 31 37
CDH5 0.016 0.04 -10000 0 -0.35 6 6
VEGFA homodimer 0.044 0.028 -10000 0 -0.19 1 1
SHC1 0.019 0.009 -10000 0 -10000 0 0
SHC2 -0.026 0.12 -10000 0 -0.35 67 67
HRAS/GDP -0.002 0.11 -10000 0 -0.42 29 29
SH2D2A 0.03 0.053 0.28 21 -10000 0 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.003 0.14 -10000 0 -0.43 37 37
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.01 0.12 0.22 3 -0.47 30 33
VEGFR1 homodimer 0.022 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.01 0.13 -10000 0 -0.46 29 29
GRB10 -0.043 0.12 -10000 0 -0.5 30 30
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
PAK1 0.022 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.026 0.13 -10000 0 -0.48 29 29
HRAS 0.022 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.03 0.11 -10000 0 -0.34 37 37
HIF1A 0.022 0.004 -10000 0 -10000 0 0
FRS2 0.023 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.019 0.12 -10000 0 -0.46 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.009 0.069 -10000 0 -0.35 19 19
Nck/Pak 0.031 0.019 -10000 0 -0.24 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.009 0.12 -10000 0 -0.48 30 30
mol:GDP 0.003 0.12 -10000 0 -0.45 29 29
mol:NADP -0.008 0.12 0.33 8 -0.38 37 45
eNOS/Hsp90 0.001 0.12 0.35 6 -0.36 37 43
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 -0.044 0.12 0.18 3 -0.49 31 34
HIF1A/ARNT 0.026 0.015 -10000 0 -10000 0 0
SHB 0.022 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.004 -10000 0 -10000 0 0
VEGFC 0.017 0.045 -10000 0 -0.35 8 8
FAK1/Vinculin -0.028 0.16 0.26 3 -0.56 32 35
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.014 0.15 -10000 0 -0.5 32 32
PTPN6 0.023 0.014 0.33 1 -10000 0 1
EPAS1 0.008 0.077 -10000 0 -0.31 30 30
mol:L-citrulline -0.008 0.12 0.33 8 -0.38 37 45
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.021 0.12 -10000 0 -0.44 30 30
VEGFR2 homodimer/VEGFA homodimer -0.003 0.14 -10000 0 -0.53 31 31
VEGFR2/3 heterodimer -0.013 0.14 -10000 0 -0.42 46 46
VEGFB 0.022 0.004 -10000 0 -10000 0 0
MAPK11 -0.041 0.13 0.34 2 -0.5 34 36
VEGFR2 homodimer -0.021 0.14 -10000 0 -0.61 29 29
FLT1 0.022 0.005 -10000 0 -10000 0 0
NEDD4 -0.002 0.092 -10000 0 -0.35 35 35
MAPK3 -0.039 0.13 0.29 11 -0.44 36 47
MAPK1 -0.04 0.13 0.29 10 -0.44 36 46
VEGFA145/NRP2 0.021 0.058 -10000 0 -0.24 24 24
VEGFR1/2 heterodimer -0.006 0.13 -10000 0 -0.52 30 30
KDR -0.021 0.14 -10000 0 -0.61 29 29
VEGFA165/NRP1/VEGFR2 homodimer -0.008 0.14 -10000 0 -0.48 34 34
SRC 0.022 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.04 0.14 0.29 11 -0.44 38 49
PI3K -0.016 0.14 -10000 0 -0.54 30 30
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.009 0.12 -10000 0 -0.47 31 31
FES -0.045 0.12 -10000 0 -0.5 32 32
GAB1 -0.021 0.14 -10000 0 -0.52 33 33
VEGFR2 homodimer/VEGFA homodimer/Src 0.009 0.12 -10000 0 -0.48 30 30
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
SOS1 0.023 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.019 0.14 0.31 4 -0.41 38 42
VEGFR2 homodimer/VEGFA homodimer/Yes 0.009 0.12 -10000 0 -0.48 30 30
PI3K/GAB1 -0.001 0.14 -10000 0 -0.5 31 31
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.031 0.12 -10000 0 -0.43 30 30
PRKACA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.14 -10000 0 -0.38 51 51
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
CDC42 -0.044 0.12 -10000 0 -0.5 31 31
actin cytoskeleton reorganization 0.009 0.12 0.22 3 -0.47 30 33
PTK2 -0.042 0.15 0.25 3 -0.61 30 33
EDG1 -0.041 0.12 0.17 6 -0.48 31 37
mol:DAG -0.044 0.12 0.18 3 -0.49 31 34
CaM/Ca2+ -0.013 0.12 -10000 0 -0.46 31 31
MAP2K3 -0.04 0.11 -10000 0 -0.47 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.001 0.14 -10000 0 -0.51 31 31
PLCG1 -0.044 0.12 0.18 3 -0.5 31 34
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.02 0.12 -10000 0 -0.46 30 30
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.009 0.12 -10000 0 -0.48 30 30
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.009 0.12 0.22 1 -0.48 30 31
cell migration -0.026 0.14 0.26 2 -0.5 33 35
mol:PI-3-4-5-P3 -0.014 0.13 -10000 0 -0.5 30 30
FYN 0.023 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 -0.019 0.12 -10000 0 -0.46 31 31
mol:NO -0.008 0.12 0.33 8 -0.38 37 45
PXN 0.023 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.013 0.11 -10000 0 -0.42 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.009 0.14 -10000 0 -0.51 31 31
VHL 0.022 0.017 -10000 0 -0.35 1 1
ITGB3 -0.039 0.14 0.28 2 -0.35 89 91
NOS3 -0.011 0.14 0.36 6 -0.43 37 43
VEGFR2 homodimer/VEGFA homodimer/Sck -0.02 0.14 -10000 0 -0.29 91 91
RAC1 0.022 0.005 -10000 0 -10000 0 0
PRKCA -0.05 0.12 -10000 0 -0.47 33 33
PRKCB -0.051 0.12 -10000 0 -0.47 33 33
VCL 0.022 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.017 0.13 -10000 0 -0.49 31 31
VEGFR1/2 heterodimer/VEGFA homodimer 0.009 0.12 -10000 0 -0.48 30 30
VEGFA165/NRP2 0.021 0.058 -10000 0 -0.24 24 24
MAPKKK cascade -0.012 0.13 0.33 2 -0.44 27 29
NRP2 0.006 0.077 -10000 0 -0.35 24 24
VEGFC homodimer 0.017 0.045 -10000 0 -0.35 8 8
NCK1 0.021 0.023 -10000 0 -0.35 2 2
ROCK1 0.023 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.03 0.16 0.26 3 -0.56 32 35
MAP3K13 -0.042 0.12 -10000 0 -0.49 29 29
PDPK1 -0.023 0.11 0.25 1 -0.45 30 31
Canonical Wnt signaling pathway

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
HDAC1 0.026 0.024 0.22 4 -10000 0 4
AES 0.024 0.021 0.19 4 -10000 0 4
FBXW11 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.019 -10000 0 -0.25 2 2
SMAD4 0.022 0.005 -10000 0 -10000 0 0
DKK2 0.002 0.087 0.28 2 -0.35 30 32
TLE1 0.024 0.021 0.2 4 -10000 0 4
MACF1 0.022 0.004 -10000 0 -10000 0 0
CTNNB1 0.009 0.082 0.31 7 -0.34 8 15
WIF1 0.059 0.15 0.28 125 -0.35 33 158
beta catenin/RanBP3 0.016 0.12 0.41 31 -0.38 2 33
KREMEN2 0.045 0.074 0.28 47 -10000 0 47
DKK1 0.068 0.11 0.28 106 -0.35 7 113
beta catenin/beta TrCP1 0.017 0.078 0.29 6 -0.31 8 14
FZD1 0.021 0.023 -10000 0 -0.35 2 2
AXIN2 -0.046 0.28 0.65 10 -1.2 27 37
AXIN1 0.022 0.005 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.007 0.11 -10000 0 -0.56 17 17
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.025 0.17 0.3 2 -0.56 39 41
Axin1/APC/GSK3 0.006 0.056 0.24 3 -0.29 5 8
Axin1/APC/GSK3/beta catenin/Macf1 0.011 0.065 0.29 4 -0.33 9 13
HNF1A 0.029 0.037 0.26 11 -10000 0 11
CTBP1 0.024 0.02 0.2 3 -10000 0 3
MYC 0.064 0.27 0.59 77 -1.1 10 87
RANBP3 0.022 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.042 0.077 0.21 43 -0.2 30 73
NKD1 0.033 0.08 0.28 36 -0.35 8 44
TCF4 0.012 0.07 0.2 4 -0.34 18 22
TCF3 0.024 0.022 0.2 4 -10000 0 4
WNT1/LRP6/FZD1/Axin1 0.055 0.027 0.21 5 -0.19 2 7
Ran/GTP 0.017 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.003 0.14 0.47 22 -0.43 13 35
LEF1 0.022 0.039 0.22 5 -0.33 4 9
DVL1 0.009 0.061 0.24 2 -0.39 7 9
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.036 0.19 -10000 0 -0.59 40 40
DKK1/LRP6/Kremen 2 0.083 0.083 0.21 141 -0.2 7 148
LRP6 0.023 0.003 -10000 0 -10000 0 0
CSNK1A1 0.025 0.022 0.22 3 -10000 0 3
NLK 0.02 0.011 -10000 0 -10000 0 0
CCND1 0.002 0.1 0.58 9 -0.6 3 12
WNT1 0.024 0.031 0.28 7 -10000 0 7
GSK3A 0.023 0.004 -10000 0 -10000 0 0
GSK3B 0.022 0.004 -10000 0 -10000 0 0
FRAT1 0.022 0.006 -10000 0 -10000 0 0
PPP2R5D 0.015 0.046 0.25 7 -0.27 3 10
APC -0.01 0.041 0.18 21 -0.18 2 23
WNT1/LRP6/FZD1 0.003 0.06 0.18 28 -0.2 6 34
CREBBP 0.024 0.021 0.2 3 -10000 0 3
IL2 signaling events mediated by STAT5

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
GAB2 0.02 0.032 -10000 0 -0.35 4 4
ELF1 0.026 0.042 -10000 0 -0.34 5 5
CCNA2 0.076 0.1 0.28 111 -10000 0 111
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
JAK3 0.024 0.023 0.28 4 -10000 0 4
PIK3R1 0.019 0.036 -10000 0 -0.35 5 5
JAK1 0.022 0.016 -10000 0 -0.35 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.077 -10000 0 -0.38 6 6
SHC1 0.019 0.009 -10000 0 -10000 0 0
SP1 -0.035 0.13 -10000 0 -0.31 97 97
IL2RA 0.016 0.052 0.21 20 -0.31 5 25
IL2RB 0.021 0.017 -10000 0 -0.35 1 1
SOS1 0.023 0.003 -10000 0 -10000 0 0
IL2RG 0.024 0.039 0.28 6 -0.35 3 9
G1/S transition of mitotic cell cycle -0.089 0.27 0.3 2 -0.61 98 100
PTPN11 0.023 0.003 -10000 0 -10000 0 0
CCND2 -0.095 0.23 -10000 0 -0.61 91 91
LCK 0.024 0.028 0.28 4 -0.35 1 5
GRB2 0.022 0.006 -10000 0 -10000 0 0
IL2 0.027 0.046 0.28 17 -10000 0 17
CDK6 0.014 0.055 -10000 0 -0.35 12 12
CCND3 0.039 0.081 0.35 2 -0.46 2 4
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.12 0.18 0.28 2 -0.35 207 209
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.023 0.012 0.28 1 -10000 0 1
TCEB1 0.021 0.007 -10000 0 -10000 0 0
HIF1A/p53 0.024 0.061 0.25 1 -0.26 16 17
HIF1A 0.007 0.055 -10000 0 -0.27 16 16
COPS5 0.021 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.03 -10000 0 -0.18 1 1
FIH (dimer) 0.022 0.005 -10000 0 -10000 0 0
CDKN2A 0.13 0.13 0.28 213 -10000 0 213
ARNT/IPAS -0.059 0.12 0.21 2 -0.24 163 165
HIF1AN 0.022 0.005 -10000 0 -10000 0 0
GNB2L1 0.023 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.011 0.051 -10000 0 -0.26 13 13
CUL2 0.022 0.004 -10000 0 -10000 0 0
OS9 0.023 0.001 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.018 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.023 0.061 -10000 0 -0.26 17 17
PHD1-3/OS9 0.047 0.03 -10000 0 -0.19 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.039 0.059 0.23 1 -0.25 14 15
VHL 0.022 0.017 -10000 0 -0.35 1 1
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.022 0.057 -10000 0 -0.26 13 13
EGLN3 0.023 0.025 0.28 3 -0.35 1 4
EGLN2 0.022 0.004 -10000 0 -10000 0 0
EGLN1 0.02 0.008 -10000 0 -10000 0 0
TP53 0.021 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.018 0.096 -10000 0 -0.53 15 15
ARNT 0.018 0.01 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.022 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.083 0.1 0.25 39 -0.26 16 55
Regulation of Androgen receptor activity

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
HDAC1 -0.01 0.005 -10000 0 -10000 0 0
SMARCC1 0.009 0.015 -10000 0 -10000 0 0
REL 0.021 0.008 -10000 0 -10000 0 0
HDAC7 -0.012 0.062 0.22 4 -0.26 8 12
JUN 0.018 0.043 -10000 0 -0.35 7 7
EP300 0.022 0.006 -10000 0 -10000 0 0
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
KAT5 0.022 0.004 -10000 0 -10000 0 0
MAPK14 0.007 0.045 0.12 59 -10000 0 59
FOXO1 0.021 0.023 -10000 0 -0.35 2 2
T-DHT/AR 0.021 0.075 0.28 4 -0.26 8 12
MAP2K6 0.052 0.088 0.28 66 -10000 0 66
BRM/BAF57 0.025 0.043 -10000 0 -0.24 13 13
MAP2K4 0.018 0.02 -10000 0 -0.34 1 1
SMARCA2 0.013 0.06 -10000 0 -0.35 14 14
PDE9A -0.003 0.1 -10000 0 -0.66 8 8
NCOA2 0.008 0.066 -10000 0 -0.35 17 17
CEBPA 0.021 0.032 0.28 2 -0.35 3 5
EHMT2 0.023 0.004 -10000 0 -10000 0 0
cell proliferation 0.004 0.14 0.35 19 -0.37 23 42
NR0B1 0.033 0.06 0.28 29 -10000 0 29
EGR1 -0.024 0.12 -10000 0 -0.35 67 67
RXRs/9cRA 0.013 0.074 0.21 8 -0.18 57 65
AR/RACK1/Src 0.002 0.074 0.23 8 -0.25 8 16
AR/GR -0.037 0.12 0.21 3 -0.24 82 85
GNB2L1 0.021 0.008 -10000 0 -10000 0 0
PKN1 0.022 0.006 -10000 0 -10000 0 0
RCHY1 0.023 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.013 6 6
MAPK8 -0.008 0.024 -10000 0 -0.25 4 4
T-DHT/AR/TIF2/CARM1 0.009 0.073 0.24 1 -0.29 9 10
SRC -0.003 0.05 0.18 29 -0.18 3 32
NR3C1 -0.031 0.13 -10000 0 -0.35 77 77
KLK3 0.023 0.11 0.38 3 -0.46 2 5
APPBP2 0.022 0.009 -10000 0 -10000 0 0
TRIM24 0.023 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.001 0.064 0.22 10 -0.3 2 12
TMPRSS2 -0.006 0.14 0.39 1 -0.86 11 12
RXRG -0.017 0.12 0.31 9 -0.35 58 67
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.022 0.006 -10000 0 -10000 0 0
RXRB 0.023 0.003 -10000 0 -10000 0 0
CARM1 0.02 0.01 -10000 0 -10000 0 0
NR2C2 0.015 0.051 -10000 0 -0.35 10 10
KLK2 -0.016 0.13 0.22 1 -0.49 28 29
AR -0.02 0.085 0.17 10 -0.22 72 82
SENP1 0.023 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
MDM2 0.021 0.009 -10000 0 -10000 0 0
SRY -0.001 0.003 -10000 0 -0.016 18 18
GATA2 -0.011 0.11 -10000 0 -0.35 48 48
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.19 0.12 0.28 346 -10000 0 346
T-DHT/AR/RACK1/Src -0.003 0.072 0.24 11 -0.3 2 13
positive regulation of transcription -0.011 0.11 -10000 0 -0.35 48 48
DNAJA1 0.022 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.004 -10000 0 -10000 0 0
NCOA1 0.026 0.022 -10000 0 -0.38 1 1
SPDEF 0.082 0.15 0.28 156 -0.35 24 180
T-DHT/AR/TIF2 -0.001 0.092 0.23 13 -0.32 22 35
T-DHT/AR/Hsp90 0.003 0.065 0.22 11 -0.24 4 15
GSK3B 0.023 0.006 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.035 0.21 8 -0.19 3 11
SIRT1 0.021 0.023 -10000 0 -0.35 2 2
ZMIZ2 0.02 0.01 -10000 0 -10000 0 0
POU2F1 0.024 0.025 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 0.003 0.075 0.25 14 -0.26 3 17
CREBBP 0.022 0.005 -10000 0 -10000 0 0
SMARCE1 0.022 0.006 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0 0.11 -10000 0 -0.41 8 8
CRKL -0.009 0.068 0.21 13 -0.24 5 18
mol:DAG 0.003 0.067 0.19 1 -0.25 18 19
HRAS 0.013 0.094 0.28 21 -0.23 5 26
MAPK8 0 0.073 0.18 60 -0.19 19 79
RAP1A -0.01 0.07 0.2 15 -0.24 5 20
GAB1 -0.011 0.07 0.2 14 -0.23 9 23
MAPK14 0.002 0.07 0.18 59 -0.18 14 73
EPO 0.008 0.067 0.29 1 -0.35 16 17
PLCG1 0.003 0.068 0.19 1 -0.25 18 19
EPOR/TRPC2/IP3 Receptors 0.021 0.037 0.29 7 -10000 0 7
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.031 0.055 0.2 8 -0.2 18 26
GAB1/SHC/GRB2/SOS1 0.019 0.06 0.26 1 -0.23 5 6
EPO/EPOR (dimer) 0.021 0.058 0.22 7 -0.25 16 23
IRS2 -0.031 0.083 0.19 13 -0.19 63 76
STAT1 -0.002 0.088 -10000 0 -0.25 47 47
STAT5B -0.001 0.079 -10000 0 -0.26 23 23
cell proliferation 0.003 0.081 0.2 64 -0.18 17 81
GAB1/SHIP/PIK3R1/SHP2/SHC 0.012 0.06 -10000 0 -0.24 9 9
TEC -0.01 0.068 0.2 15 -0.24 5 20
SOCS3 0.021 0.023 -10000 0 -0.35 2 2
STAT1 (dimer) -0.002 0.087 -10000 0 -0.24 47 47
JAK2 0.013 0.05 -10000 0 -0.35 9 9
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
EPO/EPOR (dimer)/JAK2 0.038 0.071 -10000 0 -0.18 24 24
EPO/EPOR 0.021 0.058 0.22 7 -0.25 16 23
LYN 0.017 0.015 -10000 0 -10000 0 0
TEC/VAV2 0.015 0.064 0.27 3 -0.24 5 8
elevation of cytosolic calcium ion concentration 0.021 0.037 0.29 7 -10000 0 7
SHC1 0.019 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.029 0.054 0.21 6 -0.2 15 21
mol:IP3 0.003 0.067 0.19 1 -0.25 18 19
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.001 0.095 0.28 4 -0.27 18 22
SH2B3 0.019 0.024 -10000 0 -0.35 1 1
NFKB1 0.001 0.071 0.18 59 -0.18 16 75
EPO/EPOR (dimer)/JAK2/SOCS3 0.001 0.053 0.2 1 -0.2 28 29
PTPN6 -0.008 0.066 0.16 42 -0.18 23 65
TEC/VAV2/GRB2 0.022 0.064 0.27 2 -0.23 5 7
EPOR 0.021 0.037 0.29 7 -10000 0 7
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
mol:GDP 0.018 0.061 0.26 1 -0.24 5 6
SOS1 0.023 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
CRKL/CBL/C3G 0.024 0.066 0.27 3 -0.23 5 8
VAV2 -0.01 0.067 0.2 14 -0.24 5 19
CBL -0.009 0.068 0.2 14 -0.24 5 19
SHC/Grb2/SOS1 0.013 0.052 -10000 0 -0.18 17 17
STAT5A 0 0.079 -10000 0 -0.26 22 22
GRB2 0.022 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.003 0.11 -10000 0 -0.32 35 35
LYN/PLCgamma2 0.024 0.023 0.21 1 -0.24 1 2
PTPN11 0.023 0.003 -10000 0 -10000 0 0
BTK -0.01 0.072 0.2 15 -0.27 5 20
BCL2 -0.041 0.24 -10000 0 -0.74 50 50
BARD1 signaling events

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
BARD1/CSTF1 0.026 0.04 -10000 0 -0.24 11 11
ATM 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.007 -10000 0 -10000 0 0
ATR 0.022 0.004 -10000 0 -10000 0 0
UBE2L3 0.022 0.005 -10000 0 -10000 0 0
FANCD2 0.015 0.011 0.24 1 -10000 0 1
protein ubiquitination 0.093 0.079 0.21 34 -0.17 10 44
XRCC5 0.023 0.003 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.016 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
DNA-PK 0.04 0.017 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.01 0.095 -10000 0 -0.43 15 15
FANCF 0.021 0.023 -10000 0 -0.35 2 2
BRCA1 0.022 0.006 -10000 0 -10000 0 0
CCNE1 0.13 0.13 0.29 214 -10000 0 214
CDK2/Cyclin E1 0.1 0.089 0.22 204 -10000 0 204
FANCG 0.022 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.026 0.04 -10000 0 -0.24 11 11
FANCE 0.023 0.004 -10000 0 -10000 0 0
FANCC 0.022 0.006 -10000 0 -10000 0 0
NBN 0.021 0.007 -10000 0 -10000 0 0
FANCA 0.078 0.11 0.28 119 -10000 0 119
DNA repair 0.011 0.077 0.26 6 -0.35 9 15
BRCA1/BARD1/ubiquitin 0.026 0.04 -10000 0 -0.24 11 11
BARD1/DNA-PK 0.045 0.041 -10000 0 -0.19 11 11
FANCL 0.023 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.026 0.04 0.24 11 -10000 0 11
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.049 -10000 0 -0.2 21 21
BRCA1/BACH1/BARD1/TopBP1 0.038 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/P53 0.046 0.04 -10000 0 -0.19 11 11
BARD1/CSTF1/BRCA1 0.037 0.038 -10000 0 -0.21 11 11
BRCA1/BACH1 0.022 0.006 -10000 0 -10000 0 0
BARD1 0.015 0.053 -10000 0 -0.35 11 11
PCNA 0.022 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.038 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/UbcH7 0.037 0.038 -10000 0 -0.21 11 11
BRCA1/BARD1/RAD51/PCNA 0.084 0.081 0.21 129 -0.18 11 140
BARD1/DNA-PK/P53 0.051 0.043 -10000 0 -0.18 11 11
BRCA1/BARD1/Ubiquitin 0.026 0.04 -10000 0 -0.24 11 11
BRCA1/BARD1/CTIP 0.028 0.034 -10000 0 -0.19 11 11
FA complex 0.025 0.058 0.24 2 -0.22 7 9
BARD1/EWS 0.026 0.04 -10000 0 -0.24 11 11
RBBP8 -0.011 0.003 -10000 0 -10000 0 0
TP53 0.021 0.006 -10000 0 -10000 0 0
TOPBP1 0.023 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.045 0.039 0.19 11 -10000 0 11
BRCA1/BARD1 0.1 0.084 0.23 35 -0.18 10 45
CSTF1 0.022 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.012 0.037 -10000 0 -0.24 11 11
CDK2 0.023 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.097 0.12 0.28 156 -10000 0 156
RAD50 0.023 0.003 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.026 0.04 -10000 0 -0.24 11 11
EWSR1 0.022 0.006 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.028 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.054 0.086 0.28 66 -10000 0 66
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.018 -10000 0 -0.35 1 1
RAC1-CDC42/GTP/PAK family -0.013 0.061 -10000 0 -0.17 67 67
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 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 0.022 0.006 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
MAP3K12 0.02 0.032 -10000 0 -0.35 4 4
FGR 0.015 0.053 -10000 0 -0.35 11 11
p38 alpha/TAB1 -0.022 0.073 -10000 0 -0.31 22 22
PRKG1 -0.13 0.18 -10000 0 -0.35 222 222
DUSP8 0.018 0.036 -10000 0 -0.35 5 5
PGK/cGMP/p38 alpha -0.046 0.11 -10000 0 -0.3 42 42
apoptosis -0.021 0.07 -10000 0 -0.3 22 22
RAL/GTP 0.03 0.006 -10000 0 -10000 0 0
LYN 0.021 0.007 -10000 0 -10000 0 0
DUSP1 -0.063 0.16 -10000 0 -0.35 122 122
PAK1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.051 0.021 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -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 0.023 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.008 -10000 0 -10000 0 0
MAPK11 0.021 0.098 0.25 14 -0.38 13 27
BLK 0.037 0.067 0.28 37 -10000 0 37
HCK 0.025 0.03 0.28 7 -10000 0 7
MAP2K3 0.021 0.006 -10000 0 -10000 0 0
DUSP16 0.023 0.003 -10000 0 -10000 0 0
DUSP10 0.02 0.008 -10000 0 -10000 0 0
TRAF6/MEKK3 0.027 0.009 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.019 0.1 0.23 12 -0.36 18 30
positive regulation of innate immune response 0.024 0.11 0.27 15 -0.45 14 29
LCK 0.024 0.028 0.28 4 -0.35 1 5
p38alpha-beta/MKP7 0.031 0.11 0.28 13 -0.43 14 27
p38alpha-beta/MKP5 0.023 0.11 0.29 10 -0.43 14 24
PGK/cGMP -0.091 0.13 -10000 0 -0.24 222 222
PAK2 0.021 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.009 0.12 0.28 10 -0.4 23 33
CDC42 0.022 0.004 -10000 0 -10000 0 0
RALB 0.023 0.002 -10000 0 -10000 0 0
RALA 0.022 0.004 -10000 0 -10000 0 0
PAK3 -0.032 0.13 -10000 0 -0.35 76 76
IL6-mediated signaling events

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 0.073 0.15 0.5 2 -0.87 2 4
CRP 0.09 0.18 0.5 24 -0.76 3 27
cell cycle arrest 0.066 0.16 0.48 5 -0.76 5 10
TIMP1 0.064 0.15 0.45 3 -0.62 7 10
IL6ST -0.025 0.13 -10000 0 -0.34 75 75
Rac1/GDP 0.021 0.12 0.28 5 -0.34 29 34
AP1 0.014 0.14 -10000 0 -0.55 11 11
GAB2 0.02 0.032 -10000 0 -0.35 4 4
TNFSF11 0.078 0.16 0.48 2 -0.76 3 5
HSP90B1 0.044 0.093 -10000 0 -0.73 4 4
GAB1 0.02 0.032 -10000 0 -0.35 4 4
MAPK14 -0.004 0.12 0.22 3 -0.38 27 30
AKT1 0.026 0.061 0.25 2 -0.39 6 8
FOXO1 0.026 0.06 0.32 1 -0.38 5 6
MAP2K6 -0.007 0.11 0.22 6 -0.37 29 35
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.034 0.13 0.31 9 -0.36 21 30
MITF -0.015 0.13 0.22 7 -0.36 45 52
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.021 0.007 -10000 0 -10000 0 0
A2M 0.001 0.15 -10000 0 -1.1 9 9
CEBPB 0.026 0.008 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.022 0.11 -10000 0 -0.52 11 11
STAT3 0.062 0.17 0.48 5 -0.82 5 10
STAT1 0.024 0.058 0.3 1 -0.82 2 3
CEBPD 0.074 0.16 0.5 3 -0.84 3 6
PIK3CA 0.021 0.018 -10000 0 -0.35 1 1
PI3K 0.028 0.03 -10000 0 -0.24 5 5
JUN 0.018 0.043 -10000 0 -0.35 7 7
PIAS3/MITF -0.014 0.13 0.27 1 -0.35 43 44
MAPK11 -0.004 0.11 0.24 1 -0.37 25 26
STAT3 (dimer)/FOXO1 0.066 0.15 0.43 7 -0.55 7 14
GRB2/SOS1/GAB family 0.025 0.12 -10000 0 -0.34 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.009 0.11 0.2 6 -0.35 30 36
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.016 0.048 -10000 0 -0.35 9 9
LBP 0.084 0.17 0.49 14 -0.66 5 19
PIK3R1 0.019 0.036 -10000 0 -0.35 5 5
JAK1 0.024 0.018 -10000 0 -0.34 1 1
MYC 0.079 0.2 0.51 5 -0.9 10 15
FGG 0.063 0.15 0.5 4 -0.76 3 7
macrophage differentiation 0.066 0.16 0.48 5 -0.76 5 10
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.12 0.23 5 -0.24 68 73
JUNB 0.062 0.17 0.48 1 -0.83 8 9
FOS -0.088 0.17 -10000 0 -0.35 158 158
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.001 0.12 0.26 4 -0.37 31 35
STAT1/PIAS1 0.034 0.12 0.3 5 -0.33 22 27
GRB2/SOS1/GAB family/SHP2/PI3K 0.029 0.06 -10000 0 -0.38 7 7
STAT3 (dimer) 0.064 0.17 0.48 5 -0.8 5 10
PRKCD 0.049 0.14 0.37 14 -0.49 7 21
IL6R -0.006 0.096 -10000 0 -0.34 39 39
SOCS3 -0.011 0.13 0.33 1 -0.6 9 10
gp130 (dimer)/JAK1/JAK1/LMO4 0.021 0.092 -10000 0 -0.19 76 76
Rac1/GTP 0.026 0.12 0.28 6 -0.36 24 30
HCK 0.025 0.03 0.28 7 -10000 0 7
MAPKKK cascade 0.037 0.11 -10000 0 -0.55 11 11
bone resorption 0.078 0.16 0.47 3 -0.71 3 6
IRF1 0.062 0.15 0.56 2 -0.76 3 5
mol:GDP 0.004 0.11 0.24 7 -0.35 29 36
SOS1 0.023 0.004 -10000 0 -10000 0 0
VAV1 0.001 0.11 0.24 7 -0.36 29 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.02 0.15 -10000 0 -0.45 43 43
PTPN11 0.022 0.064 -10000 0 -0.66 4 4
IL6/IL6RA 0.008 0.09 0.22 6 -0.26 49 55
gp130 (dimer)/TYK2/TYK2/LMO4 0.016 0.087 -10000 0 -0.2 70 70
gp130 (dimer)/JAK2/JAK2/LMO4 0.012 0.094 -10000 0 -0.2 81 81
IL6 0.022 0.071 0.29 9 -0.35 14 23
PIAS3 0.019 0.009 -10000 0 -10000 0 0
PTPRE 0 0.03 0.26 1 -0.35 1 2
PIAS1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.11 0.2 2 -0.28 63 65
LMO4 0.029 0.012 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.036 0.15 -10000 0 -0.76 5 5
MCL1 0.06 0.1 0.38 5 -0.47 2 7
BCR signaling pathway

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
JUN 0.009 0.12 0.31 11 -0.33 30 41
IKBKB 0.021 0.087 0.27 12 -0.3 9 21
AKT1 0.014 0.098 0.26 34 -0.21 18 52
IKBKG 0.018 0.081 0.24 5 -0.29 10 15
CALM1 0.012 0.096 0.23 8 -0.33 12 20
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
MAP3K1 0.002 0.16 0.33 10 -0.46 39 49
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.099 0.23 5 -0.35 12 17
DOK1 0.023 0.003 -10000 0 -10000 0 0
AP-1 -0.006 0.09 0.26 9 -0.24 14 23
LYN 0.021 0.007 -10000 0 -10000 0 0
BLNK 0.021 0.026 0.28 1 -0.35 2 3
SHC1 0.019 0.009 -10000 0 -10000 0 0
BCR complex 0.034 0.085 0.21 50 -0.26 25 75
CD22 -0.025 0.12 0.23 4 -0.44 29 33
CAMK2G 0.017 0.098 0.26 16 -0.33 9 25
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
SHC/GRB2/SOS1 0.018 0.041 -10000 0 -0.18 12 12
GO:0007205 0.013 0.1 0.23 5 -0.36 12 17
SYK 0.022 0.012 0.28 1 -10000 0 1
ELK1 0.012 0.1 0.25 7 -0.34 13 20
NFATC1 0.003 0.13 0.26 15 -0.37 29 44
B-cell antigen/BCR complex 0.034 0.085 0.21 50 -0.26 25 75
PAG1/CSK 0.029 0.02 -10000 0 -0.24 2 2
NFKBIB 0.022 0.046 0.15 11 -0.12 23 34
HRAS 0.016 0.094 0.24 11 -0.33 13 24
NFKBIA 0.022 0.045 0.15 11 -0.12 22 33
NF-kappa-B/RelA/I kappa B beta 0.025 0.04 0.15 11 -0.13 1 12
RasGAP/Csk 0.05 0.077 0.35 1 -0.19 25 26
mol:GDP 0.011 0.099 0.22 5 -0.35 12 17
PTEN 0.021 0.006 -10000 0 -10000 0 0
CD79B 0.005 0.077 -10000 0 -0.35 24 24
NF-kappa-B/RelA/I kappa B alpha 0.025 0.039 0.15 11 -0.13 1 12
GRB2 0.022 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.01 0.16 0.37 7 -0.42 43 50
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 0.017 0.096 0.23 5 -0.39 9 14
CSK 0.022 0.005 -10000 0 -10000 0 0
FOS -0.032 0.12 0.28 6 -0.32 28 34
CHUK 0.013 0.097 0.25 6 -0.36 19 25
IBTK 0.023 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.029 0.092 0.26 2 -0.31 10 12
PTPN6 -0.027 0.11 0.22 4 -0.44 25 29
RELA 0.022 0.004 -10000 0 -10000 0 0
BCL2A1 0.02 0.027 0.12 4 -10000 0 4
VAV2 0.008 0.12 0.46 1 -0.43 24 25
ubiquitin-dependent protein catabolic process 0.023 0.045 0.15 11 -0.12 23 34
BTK 0.007 0.12 -10000 0 -0.94 8 8
CD19 -0.003 0.094 0.2 4 -0.39 23 27
MAP4K1 0.028 0.04 0.29 12 -10000 0 12
CD72 0.024 0.02 0.28 3 -10000 0 3
PAG1 0.02 0.024 -10000 0 -0.35 2 2
MAPK14 0.006 0.14 0.3 13 -0.4 37 50
SH3BP5 -0.03 0.13 -10000 0 -0.35 74 74
PIK3AP1 0.019 0.099 0.26 9 -0.31 16 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.015 0.089 0.24 1 -0.46 9 10
RAF1 0.014 0.091 0.24 12 -0.31 13 25
RasGAP/p62DOK/SHIP 0.048 0.074 0.31 1 -0.18 26 27
CD79A 0.045 0.084 0.28 52 -0.35 4 56
re-entry into mitotic cell cycle -0.006 0.089 0.25 9 -0.23 15 24
RASA1 0.019 0.036 -10000 0 -0.35 5 5
MAPK3 0.013 0.082 0.24 13 -0.28 8 21
MAPK1 0.011 0.079 0.23 10 -0.28 8 18
CD72/SHP1 0.002 0.13 0.3 8 -0.42 26 34
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 0.004 0.15 0.36 11 -0.4 37 48
actin cytoskeleton organization 0.009 0.12 0.32 9 -0.38 26 35
NF-kappa-B/RelA 0.051 0.078 0.27 10 -0.2 8 18
Calcineurin 0.025 0.088 0.24 1 -0.33 7 8
PI3K -0.021 0.095 0.15 1 -0.36 23 24
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.023 0.1 0.25 8 -0.32 17 25
SOS1 0.023 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.014 0.23 -10000 0 -0.62 55 55
DAPP1 -0.037 0.24 -10000 0 -0.7 54 54
cytokine secretion 0.005 0.12 0.26 15 -0.35 29 44
mol:DAG 0.017 0.096 0.23 5 -0.39 9 14
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
MAP2K1 0.012 0.084 0.23 12 -0.29 11 23
B-cell antigen/BCR complex/FcgammaRIIB 0.039 0.075 0.21 46 -0.22 20 66
mol:PI-3-4-5-P3 -0.014 0.083 0.2 7 -0.26 21 28
ETS1 0.014 0.094 0.26 16 -0.34 6 22
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.058 0.072 0.35 1 -0.2 18 19
B-cell antigen/BCR complex/LYN 0.001 0.097 0.22 2 -0.4 24 26
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.008 0.12 0.35 4 -0.41 23 27
B-cell antigen/BCR complex/LYN/SYK 0.007 0.13 0.34 3 -0.42 25 28
CARD11 0.013 0.1 0.26 10 -0.34 14 24
FCGR2B 0.018 0.027 0.28 1 -0.35 2 3
PPP3CA 0.022 0.005 -10000 0 -10000 0 0
BCL10 0.023 0.002 -10000 0 -10000 0 0
IKK complex 0.021 0.055 0.17 29 -0.12 12 41
PTPRC 0.015 0.047 0.28 1 -0.35 8 9
PDPK1 0.001 0.083 0.24 24 -0.21 14 38
PPP3CB 0.022 0.005 -10000 0 -10000 0 0
PPP3CC 0.017 0.033 -10000 0 -0.35 4 4
POU2F2 0.019 0.031 0.14 8 -10000 0 8
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.023 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.029 0.069 -10000 0 -0.25 45 45
FRAP1 0.008 0.057 0.28 2 -0.37 6 8
AKT1 -0.01 0.077 0.16 38 -0.22 41 79
INSR 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.008 -10000 0 -10000 0 0
mol:GTP 0.011 0.072 0.27 2 -0.19 37 39
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.036 -10000 0 -0.17 9 9
TSC2 0.022 0.005 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.051 -10000 0 -0.17 34 34
TSC1 0.021 0.017 -10000 0 -0.35 1 1
Insulin Receptor/IRS1 -0.011 0.092 -10000 0 -0.28 57 57
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.006 0.045 -10000 0 -0.2 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.005 -10000 0 -10000 0 0
RPS6KB1 0.007 0.08 0.25 10 -0.29 13 23
MAP3K5 0.004 0.032 0.2 7 -0.21 6 13
PIK3R1 0.019 0.036 -10000 0 -0.35 5 5
apoptosis 0.004 0.032 0.2 7 -0.21 6 13
mol:LY294002 0 0 -10000 0 -0.001 57 57
EIF4B 0.008 0.077 0.25 11 -0.27 11 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.069 0.24 8 -0.26 8 16
eIF4E/eIF4G1/eIF4A1 0.007 0.032 -10000 0 -0.26 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.002 0.086 -10000 0 -0.26 49 49
mTOR/RHEB/GTP/Raptor/GBL 0.001 0.052 0.2 14 -0.15 7 21
FKBP1A 0.023 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.015 0.062 -10000 0 -0.25 3 3
mol:Amino Acids 0 0 -10000 0 -0.001 57 57
FKBP12/Rapamycin 0.017 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.077 0.15 34 -0.23 45 79
EIF4E 0.022 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.024 0.085 -10000 0 -0.49 11 11
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.004 0.079 -10000 0 -0.67 4 4
TSC1/TSC2 0.013 0.079 0.3 3 -0.2 37 40
tumor necrosis factor receptor activity 0 0 0.001 57 -10000 0 57
RPS6 0.022 0.005 -10000 0 -10000 0 0
PPP5C 0.023 0.004 -10000 0 -10000 0 0
EIF4G1 0.021 0.007 -10000 0 -10000 0 0
IRS1 -0.025 0.093 -10000 0 -0.29 57 57
INS 0.016 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
PDK2 -0.019 0.077 0.15 35 -0.23 44 79
EIF4EBP1 -0.024 0.23 -10000 0 -1 26 26
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PPP2R5D 0.01 0.063 0.27 9 -0.36 5 14
peptide biosynthetic process -0.012 0.017 0.18 4 -10000 0 4
RHEB 0.022 0.005 -10000 0 -10000 0 0
EIF4A1 0.021 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 55 -0.002 1 56
EEF2 -0.012 0.017 0.18 4 -10000 0 4
eIF4E/4E-BP1 -0.013 0.21 -10000 0 -0.94 26 26
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.01 0.014 0.3 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.03 0.017 0.21 1 -10000 0 1
CDKN1B 0.002 0.048 -10000 0 -0.29 7 7
CDKN1A 0.009 0.046 0.19 8 -0.29 8 16
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.007 -10000 0 -10000 0 0
FOXO3 0.008 0.037 -10000 0 -0.28 6 6
AKT1 0.007 0.036 -10000 0 -0.3 7 7
BAD 0.022 0.004 -10000 0 -10000 0 0
AKT3 -0.068 0.12 -10000 0 -0.26 153 153
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.042 -10000 0 -0.29 8 8
AKT1/ASK1 0.029 0.051 0.23 3 -0.28 8 11
BAD/YWHAZ 0.039 0.018 -10000 0 -10000 0 0
RICTOR 0.021 0.023 -10000 0 -0.35 2 2
RAF1 0.022 0.004 -10000 0 -10000 0 0
JNK cascade -0.026 0.046 0.27 8 -10000 0 8
TSC1 0.009 0.024 -10000 0 -0.27 2 2
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.032 0.051 0.24 2 -0.28 7 9
EP300 0.021 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.04 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.008 0.038 -10000 0 -0.29 7 7
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
TBC1D4 0.002 0.012 -10000 0 -0.19 2 2
MAP3K5 0.022 0.016 -10000 0 -0.35 1 1
MAPKAP1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.046 0.079 0.39 7 -0.24 14 21
YWHAH 0.022 0.006 -10000 0 -10000 0 0
AKT1S1 0.007 0.042 -10000 0 -0.29 8 8
CASP9 0.009 0.035 -10000 0 -0.28 5 5
YWHAB 0.022 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.023 0.067 0.28 7 -0.28 8 15
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.014 0.048 0.2 11 -0.26 7 18
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.048 -10000 0 -0.28 12 12
CHUK 0.009 0.04 -10000 0 -0.28 6 6
BAD/BCL-XL 0.03 0.043 0.26 1 -0.28 5 6
mTORC2 0.026 0.016 -10000 0 -0.18 2 2
AKT2 0.01 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.091 0.26 18 -0.4 8 26
PDPK1 0.022 0.005 -10000 0 -10000 0 0
MDM2 0.008 0.04 -10000 0 -0.29 7 7
MAPKKK cascade -0.032 0.051 0.28 7 -0.24 2 9
MDM2/Cbp/p300 0.039 0.055 0.26 4 -0.27 7 11
TSC1/TSC2 0.007 0.039 0.26 4 -0.26 5 9
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.053 0.25 4 -0.25 8 12
glucose import -0.08 0.091 0.2 5 -0.18 239 244
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.038 0.18 3 -0.18 8 11
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.082 0.089 0.2 2 -0.18 239 241
GSK3A 0.008 0.043 -10000 0 -0.29 8 8
FOXO1 0.007 0.036 -10000 0 -0.29 6 6
GSK3B 0.008 0.043 -10000 0 -0.29 8 8
SFN 0.2 0.12 0.28 379 -10000 0 379
G1/S transition of mitotic cell cycle 0.015 0.058 0.24 11 -0.28 8 19
p27Kip1/14-3-3 family 0.054 0.084 0.28 4 -0.51 6 10
PRKACA 0.022 0.005 -10000 0 -10000 0 0
KPNA1 0.022 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
RHEB 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.039 0.2 1 -0.2 11 12
forebrain development -0.093 0.21 -10000 0 -0.52 77 77
GNAO1 -0.066 0.16 -10000 0 -0.35 123 123
SMO/beta Arrestin2 0.026 0.03 -10000 0 -0.24 4 4
SMO 0.017 0.034 -10000 0 -0.35 4 4
ARRB2 0.02 0.01 -10000 0 -10000 0 0
GLI3/SPOP -0.037 0.13 -10000 0 -0.42 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.022 0.004 -10000 0 -10000 0 0
GNAI2 0.022 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.052 0.021 -10000 0 -10000 0 0
GNAI1 0.017 0.046 -10000 0 -0.35 8 8
XPO1 0.021 0.012 -10000 0 -10000 0 0
GLI1/Su(fu) -0.064 0.18 -10000 0 -0.54 43 43
SAP30 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.034 -10000 0 -0.35 4 4
MIM/GLI2A 0.015 0.032 -10000 0 -10000 0 0
IFT88 0.022 0.005 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GLI2 -0.037 0.099 -10000 0 -0.34 22 22
GLI3 -0.045 0.13 0.19 1 -0.42 18 19
CSNK1D 0.022 0.006 -10000 0 -10000 0 0
CSNK1E 0.022 0.006 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.022 0.005 -10000 0 -10000 0 0
GNG2 0.017 0.049 0.28 1 -0.35 9 10
Gi family/GTP -0.042 0.11 -10000 0 -0.22 122 122
SIN3B 0.022 0.006 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) -0.027 0.11 -10000 0 -0.4 18 18
GLI2/Su(fu) -0.029 0.1 -10000 0 -0.33 30 30
FOXA2 -0.074 0.29 -10000 0 -0.92 52 52
neural tube patterning -0.093 0.21 -10000 0 -0.52 77 77
SPOP 0.022 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.036 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
CSNK1G2 0.021 0.006 -10000 0 -10000 0 0
CSNK1G3 0.022 0.004 -10000 0 -10000 0 0
MTSS1 0.015 0.032 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.093 0.21 -10000 0 -0.52 77 77
SUFU 0.013 0.016 -10000 0 -10000 0 0
LGALS3 0.021 0.023 -10000 0 -0.35 2 2
catabolic process -0.06 0.15 -10000 0 -0.48 22 22
GLI3A/CBP -0.03 0.12 -10000 0 -0.31 87 87
KIF3A 0.022 0.016 -10000 0 -0.35 1 1
GLI1 -0.095 0.21 -10000 0 -0.54 77 77
RAB23 0.019 0.036 -10000 0 -0.35 5 5
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
IFT172 0.022 0.004 -10000 0 -10000 0 0
RBBP7 0.023 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.041 -10000 0 -0.17 2 2
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
RBBP4 0.02 0.028 -10000 0 -0.35 3 3
CSNK1G1 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GLI2/SPOP -0.027 0.11 -10000 0 -0.34 24 24
STK36 0.021 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.043 0.1 -10000 0 -0.34 27 27
PTCH1 -0.085 0.19 -10000 0 -0.58 38 38
MIM/GLI1 -0.087 0.22 -10000 0 -0.54 80 80
CREBBP -0.03 0.12 -10000 0 -0.31 87 87
Su(fu)/SIN3/HDAC complex 0.007 0.083 0.19 1 -0.42 13 14
Nectin adhesion 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 0.009 0.069 -10000 0 -0.35 19 19
alphaV beta3 Integrin -0.013 0.1 0.21 2 -0.24 88 90
PTK2 -0.018 0.097 -10000 0 -0.37 24 24
positive regulation of JNK cascade 0.001 0.081 -10000 0 -0.29 23 23
CDC42/GDP 0.009 0.12 -10000 0 -0.39 28 28
Rac1/GDP 0.007 0.12 0.32 1 -0.38 30 31
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.007 0.1 -10000 0 -0.36 22 22
nectin-3/I-afadin 0.021 0.056 -10000 0 -0.24 22 22
RAPGEF1 -0.002 0.1 0.31 4 -0.4 27 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.007 0.11 -10000 0 -0.45 27 27
PDGFB-D/PDGFRB 0.009 0.069 -10000 0 -0.35 19 19
TLN1 -0.02 0.058 -10000 0 -0.21 41 41
Rap1/GTP -0.003 0.078 -10000 0 -0.3 27 27
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.042 0.011 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.021 0.056 -10000 0 -0.24 22 22
PVR 0.022 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.005 -10000 0 -10000 0 0
mol:GDP -0.004 0.14 0.33 1 -0.47 30 31
MLLT4 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.042 0.066 -10000 0 -0.2 31 31
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.032 0.014 0.21 2 -10000 0 2
positive regulation of lamellipodium assembly -0.005 0.097 -10000 0 -0.31 32 32
PVRL1 0.023 0.016 0.28 2 -10000 0 2
PVRL3 0.007 0.074 -10000 0 -0.35 22 22
PVRL2 0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
CDH1 0.019 0.024 -10000 0 -0.35 2 2
CLDN1 -0.021 0.12 -10000 0 -0.35 59 59
JAM-A/CLDN1 0.013 0.082 -10000 0 -0.2 61 61
SRC -0.01 0.12 -10000 0 -0.49 29 29
ITGB3 -0.039 0.14 0.28 2 -0.35 89 91
nectin-1(dimer)/I-afadin/I-afadin 0.032 0.014 0.21 2 -10000 0 2
FARP2 0.002 0.13 -10000 0 -0.45 29 29
RAC1 0.022 0.005 -10000 0 -10000 0 0
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.032 0.051 -10000 0 -0.21 21 21
nectin-1/I-afadin 0.032 0.014 0.21 2 -10000 0 2
nectin-2/I-afadin 0.031 0.01 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.029 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.032 0.051 -10000 0 -0.21 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.029 0.008 -10000 0 -10000 0 0
F11R 0.018 0.018 -10000 0 -0.35 1 1
positive regulation of filopodium formation 0.001 0.081 -10000 0 -0.29 23 23
alphaV/beta3 Integrin/Talin -0.02 0.11 0.31 4 -0.3 34 38
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
PIP5K1C -0.015 0.064 -10000 0 -0.22 43 43
VAV2 -0.014 0.16 0.34 1 -0.51 35 36
RAP1/GDP 0.013 0.11 0.3 1 -0.36 26 27
ITGAV 0.023 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.032 0.051 -10000 0 -0.21 21 21
nectin-3(dimer)/I-afadin/I-afadin 0.021 0.056 -10000 0 -0.24 22 22
Rac1/GTP -0.002 0.12 -10000 0 -0.39 30 30
PTPRM -0.012 0.074 -10000 0 -0.24 47 47
E-cadherin/beta catenin/alpha catenin 0.054 0.033 -10000 0 -0.17 2 2
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.023 0.003 -10000 0 -10000 0 0
VDR 0.029 0.042 0.29 13 -10000 0 13
Cbp/p300/PCAF 0.038 0.033 -10000 0 -0.2 8 8
EP300 0.021 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.076 0.16 2 -0.3 21 23
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
MAPK14 0.023 0.004 -10000 0 -10000 0 0
AKT1 0.004 0.07 0.26 4 -0.25 11 15
RAR alpha/9cRA/Cyclin H 0.016 0.095 0.22 1 -0.26 38 39
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.004 0.088 0.16 1 -0.35 21 22
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.004 0.079 -10000 0 -0.22 49 49
NCOR2 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.023 0.19 9 -10000 0 9
RXRs/RARs/NRIP1/9cRA -0.011 0.15 0.32 1 -0.45 40 41
NCOA2 0.009 0.065 -10000 0 -0.35 17 17
NCOA3 0.022 0.015 0.33 1 -10000 0 1
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
VDR/VDR/DNA 0.029 0.042 0.29 13 -10000 0 13
RARG 0.023 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.029 0.008 -10000 0 -10000 0 0
MAPK3 0.022 0.006 -10000 0 -10000 0 0
MAPK1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.036 -10000 0 -0.35 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.13 0.26 4 -0.38 38 42
RARA 0.006 0.064 0.18 5 -0.22 32 37
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.009 0.089 0.16 1 -0.33 25 26
PRKCA 0.001 0.088 -10000 0 -0.35 31 31
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.011 0.16 -10000 0 -0.46 36 36
RXRG -0.015 0.12 0.23 11 -0.27 77 88
RXRA 0.004 0.061 0.18 7 -0.2 34 41
RXRB 0.009 0.081 0.22 5 -0.26 35 40
VDR/Vit D3/DNA 0.019 0.023 0.19 9 -10000 0 9
RBP1 0.008 0.071 -10000 0 -0.35 20 20
CRBP1/9-cic-RA 0.007 0.049 -10000 0 -0.24 20 20
RARB 0.017 0.048 -10000 0 -0.35 9 9
PRKCG 0.05 0.095 0.28 65 -0.35 6 71
MNAT1 0.022 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.013 0.14 0.27 3 -0.44 37 40
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.004 0.13 0.26 3 -0.38 42 45
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.11 0.21 7 -0.35 31 38
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.011 0.16 -10000 0 -0.46 38 38
positive regulation of DNA binding 0.007 0.086 -10000 0 -0.25 38 38
NRIP1 -0.012 0.16 -10000 0 -0.67 16 16
RXRs/RARs -0.009 0.16 -10000 0 -0.45 39 39
RXRs/RXRs/DNA/9cRA -0.018 0.12 -10000 0 -0.38 41 41
PRKACA 0.022 0.005 -10000 0 -10000 0 0
CDK7 0.022 0.005 -10000 0 -10000 0 0
TFIIH 0.044 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.028 0.075 -10000 0 -0.26 15 15
CCNH 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.04 0.017 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.004 0.08 0.18 1 -0.18 81 82
MAPK9 0.005 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.021 0.12 12 -10000 0 12
GNB1/GNG2 0.026 0.031 0.19 1 -0.2 9 10
GNB1 0.022 0.004 -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 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.013 0.068 -10000 0 -0.18 76 76
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 0.008 0.017 0.051 76 -10000 0 76
GNAL -0.031 0.13 -10000 0 -0.35 76 76
GNG2 0.017 0.049 0.28 1 -0.35 9 10
CRH 0.022 0.04 0.28 12 -10000 0 12
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.025 -10000 0 -0.26 5 5
MAPK11 0.004 0.016 -10000 0 -0.26 2 2
Regulation of nuclear SMAD2/3 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
EP300 0.012 0.018 -10000 0 -10000 0 0
HSPA8 0.023 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.002 0.092 -10000 0 -0.23 56 56
AKT1 0.024 0.005 -10000 0 -10000 0 0
GSC 0.053 0.099 0.39 3 -0.42 5 8
NKX2-5 -0.005 0.018 -10000 0 -10000 0 0
muscle cell differentiation -0.014 0.11 0.43 10 -10000 0 10
SMAD2-3/SMAD4/SP1 0.059 0.061 -10000 0 -0.25 4 4
SMAD4 0.013 0.038 -10000 0 -10000 0 0
CBFB 0.02 0.008 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.038 0.04 0.2 12 -0.21 3 15
SMAD3/SMAD4/VDR 0.051 0.052 0.24 2 -0.18 2 4
MYC 0.012 0.046 -10000 0 -0.35 8 8
CDKN2B -0.008 0.1 -10000 0 -0.53 10 10
AP1 -0.027 0.11 -10000 0 -0.3 21 21
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.018 0.073 -10000 0 -0.48 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.027 0.048 0.19 2 -0.24 4 6
SP3 0.024 0.003 -10000 0 -10000 0 0
CREB1 0.023 0.003 -10000 0 -10000 0 0
FOXH1 0.087 0.12 0.29 131 -10000 0 131
SMAD3/SMAD4/GR -0.008 0.1 -10000 0 -0.23 77 77
GATA3 0.028 0.057 0.28 13 -0.35 6 19
SKI/SIN3/HDAC complex/NCoR1 0.008 0.075 -10000 0 -0.38 13 13
MEF2C/TIF2 0.007 0.11 0.3 4 -0.36 38 42
endothelial cell migration -0.014 0.12 0.86 8 -10000 0 8
MAX 0.022 0.005 -10000 0 -10000 0 0
RBBP7 0.023 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.028 -10000 0 -0.35 3 3
RUNX2 0.029 0.044 0.28 14 -0.35 1 15
RUNX3 0.029 0.041 0.28 14 -10000 0 14
RUNX1 0.023 0.003 -10000 0 -10000 0 0
CTBP1 0.022 0.005 -10000 0 -10000 0 0
NR3C1 -0.032 0.13 -10000 0 -0.35 77 77
VDR 0.029 0.042 0.29 13 -10000 0 13
CDKN1A 0.008 0.064 -10000 0 -0.84 2 2
KAT2B 0.016 0.046 -10000 0 -0.35 8 8
SMAD2/SMAD2/SMAD4/FOXH1 0.086 0.099 0.25 84 -10000 0 84
DCP1A 0.022 0.005 -10000 0 -10000 0 0
SKI 0.023 0.004 -10000 0 -10000 0 0
SERPINE1 0.013 0.12 -10000 0 -0.87 8 8
SMAD3/SMAD4/ATF2 0.028 0.058 -10000 0 -0.29 5 5
SMAD3/SMAD4/ATF3 0.007 0.083 -10000 0 -0.24 41 41
SAP30 0.023 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.022 0.03 -10000 0 -10000 0 0
JUN -0.037 0.1 -10000 0 -0.36 14 14
SMAD3/SMAD4/IRF7 0.033 0.061 0.28 7 -0.25 3 10
TFE3 0.024 0.01 -10000 0 -10000 0 0
COL1A2 0.02 0.074 -10000 0 -0.54 7 7
mesenchymal cell differentiation -0.032 0.06 0.24 4 -0.24 11 15
DLX1 0.049 0.081 0.28 58 -10000 0 58
TCF3 0.021 0.006 -10000 0 -10000 0 0
FOS -0.088 0.17 -10000 0 -0.36 158 158
SMAD3/SMAD4/Max 0.028 0.052 -10000 0 -0.25 3 3
Cbp/p300/SNIP1 0.039 0.016 -10000 0 -10000 0 0
ZBTB17 0.02 0.009 -10000 0 -10000 0 0
LAMC1 0.007 0.043 0.2 8 -0.22 3 11
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.052 -10000 0 -0.25 3 3
IRF7 0.028 0.037 0.29 10 -10000 0 10
ESR1 -0.017 0.11 -10000 0 -0.35 54 54
HNF4A 0.059 0.093 0.28 76 -10000 0 76
MEF2C 0.008 0.12 0.24 23 -0.36 40 63
SMAD2-3/SMAD4 0.033 0.062 -10000 0 -0.27 3 3
Cbp/p300/Src-1 0.037 0.02 -10000 0 -0.19 1 1
IGHV3OR16-13 0.005 0.035 -10000 0 -0.34 5 5
TGIF2/HDAC complex 0.022 0.005 -10000 0 -10000 0 0
CREBBP 0.014 0.016 -10000 0 -10000 0 0
SKIL 0.021 0.007 -10000 0 -10000 0 0
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.003 -10000 0 -10000 0 0
SNIP1 0.023 0.004 -10000 0 -10000 0 0
GCN5L2 -0.002 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.033 0.054 -10000 0 -0.24 3 3
MSG1/HSC70 0.037 0.038 0.21 16 -0.24 3 19
SMAD2 0.022 0.027 -10000 0 -10000 0 0
SMAD3 0.009 0.046 -10000 0 -0.37 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.031 -10000 0 -0.21 5 5
SMAD2/SMAD2/SMAD4 0 0.057 0.19 3 -0.24 14 17
NCOR1 0.021 0.007 -10000 0 -10000 0 0
NCOA2 0.009 0.065 -10000 0 -0.35 17 17
NCOA1 0.022 0.017 -10000 0 -0.35 1 1
MYOD/E2A 0.04 0.046 0.21 35 -10000 0 35
SMAD2-3/SMAD4/SP1/MIZ-1 0.067 0.062 -10000 0 -0.27 2 2
IFNB1 0.004 0.048 0.24 9 -0.23 2 11
SMAD3/SMAD4/MEF2C 0.025 0.12 0.25 2 -0.35 39 41
CITED1 0.029 0.053 0.28 17 -0.35 3 20
SMAD2-3/SMAD4/ARC105 0.043 0.062 -10000 0 -0.24 3 3
RBL1 0.022 0.005 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.048 0.22 1 -0.34 3 4
RUNX1-3/PEBPB2 0.044 0.028 0.2 11 -10000 0 11
SMAD7 -0.025 0.12 -10000 0 -0.45 13 13
MYC/MIZ-1 0.02 0.037 -10000 0 -0.25 8 8
SMAD3/SMAD4 -0.011 0.067 -10000 0 -0.36 9 9
IL10 0.015 0.069 0.23 26 -0.23 4 30
PIASy/HDAC complex 0.023 0.008 -10000 0 -10000 0 0
PIAS3 0.018 0.009 -10000 0 -10000 0 0
CDK2 0.018 0.012 -10000 0 -10000 0 0
IL5 0.005 0.05 0.2 5 -0.23 5 10
CDK4 0.014 0.017 -10000 0 -10000 0 0
PIAS4 0.023 0.008 -10000 0 -10000 0 0
ATF3 -0.008 0.098 -10000 0 -0.35 40 40
SMAD3/SMAD4/SP1 0.035 0.057 -10000 0 -0.24 5 5
FOXG1 0.14 0.13 0.28 251 -10000 0 251
FOXO3 0.009 0.007 -10000 0 -10000 0 0
FOXO1 0.008 0.017 -10000 0 -0.24 2 2
FOXO4 0.008 0.017 -10000 0 -0.24 2 2
heart looping 0.008 0.12 0.24 23 -0.35 40 63
CEBPB 0.022 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.043 0.073 0.23 33 -0.24 3 36
MYOD1 0.042 0.075 0.28 47 -10000 0 47
SMAD3/SMAD4/HNF4 0.05 0.079 0.22 48 -0.24 3 51
SMAD3/SMAD4/GATA3 0.037 0.07 0.25 4 -0.23 9 13
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.057 0.052 0.27 2 -0.21 3 5
SMAD3/SMAD4/SP1-3 0.058 0.049 -10000 0 -0.24 2 2
MED15 0.022 0.005 -10000 0 -10000 0 0
SP1 0.025 0.017 -10000 0 -0.16 1 1
SIN3B 0.022 0.006 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.077 0.11 0.26 50 -0.2 36 86
ITGB5 0.007 0.044 0.32 1 -0.22 2 3
TGIF/SIN3/HDAC complex/CtBP 0.016 0.054 -10000 0 -0.36 6 6
SMAD3/SMAD4/AR -0.012 0.1 -10000 0 -0.22 88 88
AR -0.038 0.14 -10000 0 -0.35 87 87
negative regulation of cell growth 0.006 0.069 -10000 0 -0.28 12 12
SMAD3/SMAD4/MYOD 0.038 0.071 0.23 29 -0.25 3 32
E2F5 0.021 0.007 -10000 0 -10000 0 0
E2F4 0.02 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.09 0.093 0.27 42 -10000 0 42
SMAD2-3/SMAD4/FOXO1-3a-4 0.014 0.04 -10000 0 -0.27 3 3
TFDP1 0.022 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.012 0.12 -10000 0 -0.38 13 13
SMAD3/SMAD4/RUNX2 0.032 0.061 0.25 11 -0.24 4 15
TGIF2 0.022 0.005 -10000 0 -10000 0 0
TGIF1 0.022 0.006 -10000 0 -10000 0 0
ATF2 0.021 0.028 -10000 0 -0.35 3 3
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.065 0.059 -10000 0 -0.17 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.037 0.039 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.038 -10000 0 -0.21 10 10
antigen processing and presentation of peptide antigen via MHC class I -0.032 0.055 -10000 0 -0.19 8 8
CaM/Ca2+ 0.062 0.053 -10000 0 -0.16 7 7
RAP1A 0.023 0.002 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.026 0.036 0.17 3 -0.16 10 13
AKT1 0.008 0.072 0.3 11 -0.28 1 12
MAP2K1 -0.01 0.04 0.21 6 -10000 0 6
MAP3K11 -0.005 0.043 0.23 5 -0.17 2 7
IFNGR1 0.023 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.15 0.18 0.26 1 -0.32 261 262
Rap1/GTP -0.019 0.024 -10000 0 -10000 0 0
CRKL/C3G 0.031 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.073 0.061 -10000 0 -0.18 10 10
CEBPB -0.006 0.13 0.34 4 -0.57 18 22
STAT3 0.022 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.05 0.15 -10000 0 -0.68 19 19
STAT1 -0.006 0.044 0.2 10 -0.17 8 18
CALM1 0.022 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.045 0.088 0.29 59 -10000 0 59
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
STAT1 (dimer)/PIAS1 0.017 0.044 0.27 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.011 0.081 -10000 0 -0.37 15 15
mol:Ca2+ 0.061 0.056 -10000 0 -0.17 10 10
MAPK3 -0.016 0.14 -10000 0 -0.64 22 22
STAT1 (dimer) -0.038 0.074 -10000 0 -0.27 7 7
MAPK1 -0.028 0.17 -10000 0 -0.68 31 31
JAK2 0.017 0.049 -10000 0 -0.35 9 9
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
JAK1 0.023 0.018 -10000 0 -0.35 1 1
CAMK2D 0.022 0.017 -10000 0 -0.35 1 1
DAPK1 0.001 0.087 0.3 4 -0.39 14 18
SMAD7 -0.011 0.05 0.17 13 -0.2 3 16
CBL/CRKL/C3G 0.032 0.041 0.27 3 -10000 0 3
PI3K 0.052 0.053 -10000 0 -0.18 11 11
IFNG 0.045 0.088 0.29 59 -10000 0 59
apoptosis 0.001 0.075 0.27 1 -0.34 9 10
CAMK2G 0.022 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.006 -10000 0 -10000 0 0
CAMK2A -0.18 0.18 -10000 0 -0.35 289 289
CAMK2B 0.064 0.097 0.28 86 -0.35 1 87
FRAP1 0.006 0.068 0.25 15 -0.26 1 16
PRKCD 0.008 0.074 0.28 14 -0.29 1 15
RAP1B 0.023 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.032 0.055 -10000 0 -0.19 8 8
PTPN2 0.022 0.004 -10000 0 -10000 0 0
EP300 0.022 0.006 -10000 0 -10000 0 0
IRF1 -0.004 0.046 0.28 5 -0.31 1 6
STAT1 (dimer)/PIASy 0.016 0.043 0.27 3 -10000 0 3
SOCS1 -0.015 0.19 -10000 0 -1 19 19
mol:GDP 0.03 0.038 0.25 3 -10000 0 3
CASP1 -0.01 0.05 0.17 13 -0.16 4 17
PTGES2 0.022 0.005 -10000 0 -10000 0 0
IRF9 0.01 0.04 0.17 6 -0.15 11 17
mol:PI-3-4-5-P3 0.037 0.044 -10000 0 -0.17 11 11
RAP1/GDP 0.029 0.031 -10000 0 -10000 0 0
CBL -0.005 0.043 0.2 8 -10000 0 8
MAP3K1 -0.006 0.042 0.2 9 -0.17 2 11
PIAS1 0.022 0.005 -10000 0 -10000 0 0
PIAS4 0.021 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.032 0.055 -10000 0 -0.19 8 8
PTPN11 -0.004 0.045 0.24 5 -0.17 9 14
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.022 0.006 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.023 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.011 0.098 -10000 0 -0.34 10 10
Syndecan-3/Neurocan 0.018 0.06 0.25 6 -0.35 9 15
POMC 0.027 0.074 0.28 23 -0.35 10 33
EGFR 0.014 0.059 0.33 1 -0.35 13 14
Syndecan-3/EGFR 0.011 0.062 0.3 1 -0.35 11 12
AGRP 0.019 0.013 0.28 1 -10000 0 1
NCSTN 0.019 0.009 -10000 0 -10000 0 0
PSENEN 0.022 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.018 0.04 -10000 0 -0.35 6 6
APH1A 0.019 0.009 -10000 0 -10000 0 0
NCAN 0.027 0.047 0.29 16 -10000 0 16
long-term memory 0.043 0.064 -10000 0 -0.33 11 11
Syndecan-3/IL8 0.064 0.1 0.26 30 -0.35 11 41
PSEN1 0.022 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.032 0.009 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
limb bud formation 0 0.051 -10000 0 -0.39 9 9
MC4R 0.026 0.042 0.28 14 -10000 0 14
SRC 0.022 0.005 -10000 0 -10000 0 0
PTN -0.059 0.15 -10000 0 -0.35 115 115
FGFR/FGF/Syndecan-3 0 0.052 -10000 0 -0.39 9 9
neuron projection morphogenesis -0.015 0.084 0.3 4 -0.34 8 12
Syndecan-3/AgRP 0.011 0.054 -10000 0 -0.34 11 11
Syndecan-3/AgRP/MC4R 0.041 0.068 0.27 1 -0.32 11 12
Fyn/Cortactin 0.033 0.007 -10000 0 -10000 0 0
SDC3 0 0.052 -10000 0 -0.39 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.064 0.1 0.26 30 -0.34 11 41
IL8 0.095 0.12 0.28 151 -10000 0 151
Syndecan-3/Fyn/Cortactin 0.045 0.066 -10000 0 -0.33 11 11
Syndecan-3/CASK -0.001 0.051 -10000 0 -0.35 11 11
alpha-MSH/MC4R 0.036 0.061 0.22 31 -0.25 10 41
Gamma Secretase 0.045 0.04 -10000 0 -0.18 6 6
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.068 0.13 -10000 0 -0.37 35 35
CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
AKT1 0.023 0.004 -10000 0 -10000 0 0
AKT2 0.022 0.005 -10000 0 -10000 0 0
STXBP4 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.076 0.14 0.3 1 -0.39 39 40
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
TBC1D4 -0.012 0.015 -10000 0 -0.24 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
YWHAB 0.022 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.04 0.017 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
ASIP 0.02 0.013 0.28 1 -10000 0 1
PRKCI 0.021 0.007 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.017 0.003 -10000 0 -10000 0 0
RHOQ 0.023 0.003 -10000 0 -10000 0 0
GYS1 0.006 0.014 0.24 2 -10000 0 2
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
TRIP10 0.021 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.052 0.055 0.24 6 -0.25 6 12
VAMP2 0.021 0.007 -10000 0 -10000 0 0
SLC2A4 -0.084 0.15 0.31 1 -0.44 39 40
STX4 0.022 0.005 -10000 0 -10000 0 0
GSK3B 0.014 0.005 -10000 0 -10000 0 0
SFN 0.2 0.12 0.28 379 -10000 0 379
LNPEP 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
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 0.003 0.12 0.4 2 -0.49 2 4
RAD9A 0.022 0.004 -10000 0 -10000 0 0
AP1 -0.047 0.13 -10000 0 -0.25 160 160
IFNAR2 0.027 0.018 -10000 0 -0.34 1 1
AKT1 0.01 0.06 0.18 6 -0.16 37 43
ER alpha/Oestrogen -0.007 0.079 -10000 0 -0.24 55 55
NFX1/SIN3/HDAC complex 0.018 0.059 -10000 0 -0.35 9 9
EGF 0.033 0.052 0.28 20 -0.34 1 21
SMG5 0.019 0.009 -10000 0 -10000 0 0
SMG6 0.021 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.042 0.013 -10000 0 -10000 0 0
TERT/c-Abl 0.002 0.12 0.36 2 -0.57 1 3
SAP18 0.023 0.005 -10000 0 -10000 0 0
MRN complex 0.041 0.016 -10000 0 -10000 0 0
WT1 -0.24 0.17 -10000 0 -0.35 379 379
WRN 0.02 0.008 -10000 0 -10000 0 0
SP1 0.03 0.01 -10000 0 -10000 0 0
SP3 0.025 0.004 -10000 0 -10000 0 0
TERF2IP 0.02 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.001 0.11 -10000 0 -0.51 1 1
Mad/Max 0.039 0.012 -10000 0 -10000 0 0
TERT 0.003 0.13 0.41 2 -0.5 2 4
CCND1 0.005 0.12 0.41 2 -0.5 1 3
MAX 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.024 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.028 -10000 0 -0.35 3 3
TERF2 0.018 0.01 -10000 0 -10000 0 0
PTGES3 0.023 0.003 -10000 0 -10000 0 0
SIN3A 0.023 0.005 -10000 0 -10000 0 0
Telomerase/911 0.025 0.043 -10000 0 -0.36 1 1
CDKN1B -0.001 0.1 -10000 0 -0.46 23 23
RAD1 0.022 0.004 -10000 0 -10000 0 0
XRCC5 0.023 0.003 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
SAP30 0.023 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.029 0.013 -10000 0 -10000 0 0
UBE3A 0.024 0.006 -10000 0 -10000 0 0
JUN 0.02 0.043 -10000 0 -0.35 7 7
E6 0.002 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.008 -10000 0 -10000 0 0
FOS -0.086 0.17 -10000 0 -0.35 158 158
IFN-gamma/IRF1 0.05 0.084 0.22 59 -0.25 23 82
PARP2 0.022 0.004 -10000 0 -10000 0 0
BLM 0.051 0.082 0.28 59 -10000 0 59
Telomerase 0.027 0.085 0.22 4 -0.5 5 9
IRF1 0.02 0.036 -10000 0 -0.15 23 23
ESR1 -0.015 0.11 -10000 0 -0.35 55 55
KU/TER 0.032 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.029 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.058 -10000 0 -0.3 11 11
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.021 0.059 -10000 0 -0.31 11 11
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.029 0.008 -10000 0 -10000 0 0
ATM 0.015 0.019 -10000 0 -10000 0 0
SMAD3 -0.015 0.021 -10000 0 -0.25 4 4
ABL1 0.02 0.023 -10000 0 -0.35 2 2
MXD1 0.025 0.005 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
HUS1 0.022 0.004 -10000 0 -10000 0 0
RPS6KB1 0.022 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.022 0.12 0.38 1 -0.48 2 3
NR2F2 -0.011 0.078 -10000 0 -0.35 25 25
MAPK3 0.002 0.025 0.11 17 -10000 0 17
MAPK1 0.002 0.024 0.12 4 -10000 0 4
TGFB1/TGF beta receptor Type II 0.02 0.017 -10000 0 -0.35 1 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
HNRNPC 0.022 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.015 0.019 -10000 0 -10000 0 0
NBN 0.021 0.007 -10000 0 -10000 0 0
EGFR 0.016 0.059 0.33 1 -0.34 13 14
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.036 0.056 0.21 20 -0.24 13 33
MYC 0.016 0.046 -10000 0 -0.34 8 8
IL2 0.034 0.047 0.29 17 -10000 0 17
KU 0.032 0.009 -10000 0 -10000 0 0
RAD50 0.023 0.003 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
TGFB1 0.02 0.017 -10000 0 -0.35 1 1
TRF2/BLM 0.044 0.051 0.2 48 -10000 0 48
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.01 0.12 0.41 1 -0.53 1 2
SP1/HDAC2 0.048 0.02 -10000 0 -10000 0 0
PINX1 0.02 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.002 0.11 -10000 0 -0.51 1 1
Smad3/Myc 0.003 0.036 -10000 0 -0.23 9 9
911 complex 0.043 0.013 -10000 0 -10000 0 0
IFNG 0.047 0.091 0.28 59 -0.15 23 82
Telomerase/PinX1 -0.004 0.11 -10000 0 -0.51 1 1
Telomerase/AKT1/mTOR/p70S6K 0.018 0.076 0.26 3 -0.38 8 11
SIN3B 0.023 0.006 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.001 0.1 -10000 0 -0.51 1 1
response to DNA damage stimulus 0.004 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.051 0.028 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0 0.11 -10000 0 -0.51 1 1
E2F1 0.077 0.1 0.29 99 -10000 0 99
ZNFX1 0.023 0.005 -10000 0 -10000 0 0
PIF1 0.086 0.11 0.28 133 -10000 0 133
NCL 0.023 0.003 -10000 0 -10000 0 0
DKC1 0.023 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.074 0.24 2 -0.22 7 9
NFATC4 -0.004 0.077 0.34 15 -0.18 5 20
ERBB2IP 0.02 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.022 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0.004 0.051 0.19 1 -0.2 10 11
JUN 0.006 0.085 0.22 7 -0.33 4 11
HRAS 0.022 0.005 -10000 0 -10000 0 0
DOCK7 -0.016 0.054 0.29 3 -0.2 10 13
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.045 0.21 11 -0.2 8 19
AKT1 -0.003 0.008 -10000 0 -10000 0 0
BAD -0.008 0.005 -10000 0 -10000 0 0
MAPK10 -0.022 0.076 0.21 20 -0.16 38 58
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.007 0.058 0.34 2 -0.22 10 12
RAF1 0.035 0.088 0.27 14 -0.25 6 20
ErbB2/ErbB3/neuregulin 2 -0.002 0.081 0.2 10 -0.2 66 76
STAT3 -0.012 0.17 -10000 0 -0.78 25 25
cell migration -0.012 0.083 0.22 28 -0.2 10 38
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.025 0.23 0.37 4 -0.56 33 37
FOS -0.076 0.26 0.31 6 -0.44 167 173
NRAS 0.023 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.051 0.19 1 -0.2 10 11
MAPK3 0 0.19 0.36 5 -0.57 24 29
MAPK1 -0.005 0.2 0.35 3 -0.6 23 26
JAK2 -0.017 0.054 0.29 3 -0.2 11 14
NF2 0.005 0.028 -10000 0 -0.64 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.009 0.041 0.18 5 -0.22 9 14
NRG1 0.014 0.05 0.28 1 -0.35 9 10
GRB2/SOS1 0.032 0.01 -10000 0 -10000 0 0
MAPK8 -0.001 0.067 0.26 5 -0.25 13 18
MAPK9 0 0.063 0.22 24 -10000 0 24
ERBB2 -0.008 0.057 0.32 14 -10000 0 14
ERBB3 0.02 0.029 -10000 0 -0.35 3 3
SHC1 0.019 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis 0.007 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.011 0.17 -10000 0 -0.76 26 26
RNF41 -0.01 0.008 -10000 0 -10000 0 0
FRAP1 -0.003 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.017 0.031 -10000 0 -0.16 9 9
ErbB2/ErbB2/HSP90 (dimer) -0.008 0.036 0.21 12 -10000 0 12
CHRNA1 0.025 0.16 0.34 7 -0.37 20 27
myelination 0.013 0.1 0.31 38 -10000 0 38
PPP3CB -0.016 0.049 0.29 2 -0.19 10 12
KRAS 0.023 0.014 0.33 1 -10000 0 1
RAC1-CDC42/GDP 0.043 0.057 0.22 4 -0.2 8 12
NRG2 -0.028 0.13 -10000 0 -0.35 72 72
mol:GDP 0.009 0.041 0.18 5 -0.22 9 14
SOS1 0.023 0.004 -10000 0 -10000 0 0
MAP2K2 0.028 0.092 0.25 14 -0.28 5 19
SRC 0.022 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.016 0.053 0.29 3 -0.2 10 13
MAP2K1 -0.009 0.19 0.44 1 -0.56 25 26
heart morphogenesis 0.004 0.051 0.19 1 -0.2 10 11
RAS family/GDP 0.047 0.069 0.24 4 -0.21 7 11
GRB2 0.022 0.006 -10000 0 -10000 0 0
PRKACA 0.008 0.039 -10000 0 -0.61 2 2
CHRNE 0.006 0.025 0.08 4 -0.16 4 8
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.003 0.008 -10000 0 -10000 0 0
nervous system development 0.004 0.051 0.19 1 -0.2 10 11
CDC42 0.022 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.011 0.011 -10000 0 -0.24 1 1
MAP4K4 0.006 0.057 0.21 4 -0.28 7 11
BAG4 0.019 0.024 -10000 0 -0.35 2 2
PKC zeta/ceramide 0.013 0.041 0.2 1 -0.19 18 19
NFKBIA 0.022 0.004 -10000 0 -10000 0 0
BIRC3 0.018 0.046 0.28 2 -0.35 7 9
BAX 0.004 0.047 -10000 0 -0.33 9 9
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0 0.082 0.65 8 -10000 0 8
BAD -0.001 0.045 0.2 10 -0.18 19 29
SMPD1 0.012 0.059 0.16 23 -0.23 13 36
RB1 -0.005 0.036 0.2 1 -0.18 20 21
FADD/Caspase 8 0.01 0.065 0.23 4 -0.31 10 14
MAP2K4 -0.006 0.039 0.18 6 -0.17 20 26
NSMAF 0.021 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.047 0.2 12 -0.17 21 33
EGF 0.031 0.052 0.28 20 -0.35 1 21
mol:ceramide -0.001 0.038 0.12 1 -0.19 19 20
MADD 0.022 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.01 0.011 -10000 0 -0.24 1 1
ASAH1 0.02 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.005 0.036 0.2 1 -0.18 20 21
cell proliferation -0.013 0.075 0.18 3 -0.22 17 20
BID -0.012 0.16 -10000 0 -0.62 32 32
MAP3K1 -0.004 0.038 0.18 4 -0.18 19 23
EIF2A 0.002 0.055 0.18 33 -0.17 14 47
TRADD 0.02 0.008 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
MAPK3 -0.004 0.048 0.2 11 -0.17 19 30
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.007 0.051 0.19 13 -0.18 17 30
Cathepsin D/ceramide 0.014 0.039 0.18 1 -0.18 18 19
FADD 0.007 0.06 0.21 6 -0.28 8 14
KSR1 -0.003 0.043 0.2 7 -0.18 21 28
MAPK8 -0.003 0.051 -10000 0 -0.22 8 8
PRKRA -0.002 0.04 0.19 6 -0.18 18 24
PDGFA 0.021 0.017 -10000 0 -0.35 1 1
TRAF2 0.022 0.006 -10000 0 -10000 0 0
IGF1 -0.047 0.15 -10000 0 -0.35 100 100
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.038 0.12 1 -0.19 19 20
CTSD 0.022 0.012 0.28 1 -10000 0 1
regulation of nitric oxide biosynthetic process 0.032 0.015 -10000 0 -0.24 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.013 0.079 0.19 3 -0.23 17 20
PRKCD 0.022 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.01 0.011 -10000 0 -0.24 1 1
RelA/NF kappa B1 0.032 0.015 -10000 0 -0.24 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.011 0.052 0.23 1 -0.38 2 3
TNFR1A/BAG4/TNF-alpha 0.054 0.053 0.2 50 -0.21 2 52
mol:Sphingosine-1-phosphate -0.011 0.011 -10000 0 -0.24 1 1
MAP2K1 -0.006 0.046 0.19 13 -0.17 21 34
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
CYCS 0.016 0.051 0.16 16 -0.17 5 21
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
TNFR1A/BAG4 0.029 0.021 -10000 0 -0.24 2 2
EIF2AK2 -0.003 0.044 0.2 11 -0.18 17 28
TNF-alpha/TNFR1A/FAN 0.055 0.052 0.2 51 -0.21 1 52
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.059 -10000 0 -0.36 7 7
MAP2K2 -0.006 0.046 0.19 12 -0.17 21 33
SMPD3 0.003 0.089 0.2 8 -0.27 39 47
TNF 0.053 0.088 0.28 65 -0.35 2 67
PKC zeta/PAR4 0.033 0.016 0.21 1 -0.24 1 2
mol:PHOSPHOCHOLINE -0.002 0.035 0.13 3 -0.14 10 13
NF kappa B1/RelA/I kappa B alpha 0.06 0.026 -10000 0 -0.18 2 2
AIFM1 0.015 0.052 0.14 41 -0.16 7 48
BCL2 -0.009 0.1 -10000 0 -0.35 44 44
FoxO family signaling

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
G6PC 0.004 0.048 -10000 0 -10000 0 0
PLK1 0.13 0.19 0.5 7 -0.63 4 11
CDKN1B 0.06 0.16 0.36 9 -0.4 34 43
FOXO3 0.1 0.19 0.41 19 -0.47 20 39
KAT2B 0.027 0.056 -10000 0 -0.34 8 8
FOXO1/SIRT1 0.013 0.045 0.25 1 -10000 0 1
CAT 0.092 0.18 0.5 5 -0.66 5 10
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.035 0.033 -10000 0 -10000 0 0
FOXO1 0.008 0.051 0.25 4 -10000 0 4
MAPK10 -0.016 0.081 0.2 11 -0.17 107 118
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.007 0.08 0.3 3 -0.35 2 5
response to oxidative stress 0.017 0.023 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.083 0.17 0.37 14 -0.45 19 33
XPO1 0.023 0.003 -10000 0 -10000 0 0
EP300 0.022 0.007 -10000 0 -10000 0 0
BCL2L11 0.038 0.086 -10000 0 -0.74 5 5
FOXO1/SKP2 0.018 0.047 0.28 1 -10000 0 1
mol:GDP 0.017 0.023 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
GADD45A 0.071 0.12 -10000 0 -0.58 3 3
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.033 0.14 0.24 3 -0.54 24 27
MST1 0.036 0.043 0.29 6 -10000 0 6
CSNK1D 0.022 0.006 -10000 0 -10000 0 0
CSNK1E 0.022 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.049 0.12 0.24 1 -0.44 22 23
YWHAB 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.036 0.21 10 -0.16 5 15
MAPK9 0.021 0.033 0.2 13 -10000 0 13
YWHAG 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
SIRT1 0.014 0.027 -10000 0 -0.34 2 2
SOD2 0.078 0.14 0.38 11 -0.46 6 17
RBL2 0.03 0.26 0.45 1 -0.66 47 48
RAL/GDP 0.04 0.025 -10000 0 -10000 0 0
CHUK 0.033 0.032 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CSNK1G2 0.021 0.006 -10000 0 -10000 0 0
RAL/GTP 0.041 0.024 -10000 0 -10000 0 0
CSNK1G1 0.022 0.005 -10000 0 -10000 0 0
FASLG 0.038 0.11 -10000 0 -1.2 4 4
SKP2 0.022 0.005 -10000 0 -10000 0 0
USP7 0.023 0.005 -10000 0 -10000 0 0
IKBKB 0.029 0.032 -10000 0 -10000 0 0
CCNB1 0.1 0.18 0.5 4 -0.62 5 9
FOXO1-3a-4/beta catenin 0.07 0.12 0.36 10 -0.37 5 15
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.047 0.28 1 -10000 0 1
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
SGK1 0.033 0.037 -10000 0 -0.37 1 1
CSNK1G3 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.033 0.007 -10000 0 -10000 0 0
ZFAND5 0.007 0.071 0.32 1 -10000 0 1
SFN 0.2 0.12 0.28 379 -10000 0 379
CDK2 0.022 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.068 0.12 0.25 5 -0.45 17 22
CREBBP 0.022 0.006 -10000 0 -10000 0 0
FBXO32 0.021 0.4 0.49 31 -0.96 68 99
BCL6 0.085 0.16 0.45 1 -0.58 9 10
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.023 0.004 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.019 0.055 -10000 0 -10000 0 0
UGCG -0.03 0.18 -10000 0 -0.64 41 41
AKT1/mTOR/p70S6K/Hsp90/TERT 0.043 0.14 0.28 8 -0.51 16 24
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.028 0.18 -10000 0 -0.62 42 42
mol:DAG 0.004 0.095 -10000 0 -0.77 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.15 0.26 2 -0.38 46 48
FRAP1 0.007 0.17 0.28 2 -0.44 50 52
FOXO3 0.02 0.14 0.32 7 -0.5 16 23
AKT1 0.02 0.15 0.29 2 -0.52 18 20
GAB2 0.018 0.034 -10000 0 -0.35 4 4
SMPD1 -0.008 0.14 -10000 0 -0.63 23 23
SGMS1 0.012 0.073 -10000 0 -0.58 7 7
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 -0.008 0.02 -10000 0 -0.21 5 5
CALM1 0.022 0.004 -10000 0 -10000 0 0
cell proliferation 0.01 0.14 0.25 3 -0.46 28 31
EIF3A 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.032 -10000 0 -0.25 5 5
RPS6KB1 0.004 0.14 -10000 0 -0.81 15 15
mol:sphingomyelin 0.004 0.095 -10000 0 -0.77 7 7
natural killer cell activation 0 0.003 -10000 0 -0.014 2 2
JAK3 0.023 0.024 0.28 4 -10000 0 4
PIK3R1 0.017 0.037 -10000 0 -0.35 5 5
JAK1 0.022 0.018 -10000 0 -0.35 1 1
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MYC 0.038 0.17 0.38 5 -0.84 11 16
MYB 0.052 0.082 0.48 2 -0.78 1 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.025 0.095 0.24 1 -0.43 9 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.13 -10000 0 -0.72 15 15
mol:PI-3-4-5-P3 0.029 0.096 0.24 1 -0.42 9 10
Rac1/GDP 0.011 0.023 -10000 0 -0.18 5 5
T cell proliferation 0.027 0.095 0.24 5 -0.4 9 14
SHC1 0.018 0.011 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.007 0.016 0.054 51 -10000 0 51
PRKCZ 0.026 0.096 0.24 3 -0.42 9 12
NF kappa B1 p50/RelA 0.025 0.16 -10000 0 -0.4 40 40
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.014 0.049 -10000 0 -0.41 3 3
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.053 0.28 20 -0.35 1 21
IL2RB 0.021 0.018 -10000 0 -0.35 1 1
TERT 0.12 0.13 0.28 192 -10000 0 192
E2F1 0.054 0.08 0.3 6 -0.9 1 7
SOS1 0.021 0.01 -10000 0 -10000 0 0
RPS6 0.022 0.005 -10000 0 -10000 0 0
mol:cAMP -0.004 0.008 -10000 0 -0.028 50 50
PTPN11 0.019 0.012 -10000 0 -10000 0 0
IL2RG 0.023 0.04 0.28 6 -0.35 3 9
actin cytoskeleton organization 0.027 0.095 0.24 5 -0.4 9 14
GRB2 0.02 0.01 -10000 0 -10000 0 0
IL2 0.024 0.048 0.28 17 -10000 0 17
PIK3CA 0.019 0.019 -10000 0 -0.35 1 1
Rac1/GTP 0.032 0.032 -10000 0 -0.17 5 5
LCK 0.023 0.029 0.28 4 -0.35 1 5
BCL2 -0.031 0.26 -10000 0 -0.76 54 54
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.18 0.26 0.66 8 -1.2 7 15
IL23A 0.2 0.24 0.72 9 -1.2 4 13
NF kappa B1 p50/RelA/I kappa B alpha 0.18 0.22 0.58 3 -1.1 5 8
positive regulation of T cell mediated cytotoxicity 0.21 0.26 0.66 20 -1.2 5 25
ITGA3 0.19 0.24 0.66 7 -1.2 4 11
IL17F 0.15 0.19 0.49 30 -0.68 5 35
IL12B 0.062 0.049 0.21 7 -10000 0 7
STAT1 (dimer) 0.19 0.24 0.61 7 -1.2 5 12
CD4 0.2 0.23 0.66 6 -1.1 4 10
IL23 0.19 0.24 0.67 8 -1.2 4 12
IL23R 0.1 0.097 0.44 2 -0.58 2 4
IL1B 0.2 0.25 0.69 10 -1.1 7 17
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.22 0.25 0.68 19 -1.1 4 23
TYK2 0.043 0.034 -10000 0 -10000 0 0
STAT4 0.022 0.016 -10000 0 -0.35 1 1
STAT3 0.022 0.006 -10000 0 -10000 0 0
IL18RAP 0.022 0.039 0.29 3 -0.35 4 7
IL12RB1 0.049 0.068 0.35 13 -0.37 4 17
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL12Rbeta1/TYK2 0.057 0.059 0.27 12 -0.27 4 16
IL23R/JAK2 0.13 0.12 0.45 2 -0.48 1 3
positive regulation of chronic inflammatory response 0.21 0.26 0.66 20 -1.2 5 25
natural killer cell activation -0.007 0.008 -10000 0 -0.042 2 2
JAK2 0.057 0.072 0.18 17 -0.35 9 26
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
NFKB1 0.026 0.018 -10000 0 -0.35 1 1
RELA 0.026 0.008 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.19 0.23 0.66 8 -1.1 4 12
ALOX12B 0.19 0.23 0.66 8 -1.1 4 12
CXCL1 0.2 0.28 0.68 14 -1.1 12 26
T cell proliferation 0.21 0.26 0.66 20 -1.2 5 25
NFKBIA 0.026 0.008 -10000 0 -10000 0 0
IL17A 0.15 0.17 0.44 38 -0.55 4 42
PI3K 0.16 0.23 0.57 3 -1.1 5 8
IFNG 0.027 0.038 0.11 51 -0.11 2 53
STAT3 (dimer) 0.16 0.22 0.56 3 -1 5 8
IL18R1 0.021 0.032 -10000 0 -0.35 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.17 0.2 0.52 30 -0.75 5 35
IL18/IL18R 0.048 0.049 0.26 10 -0.21 8 18
macrophage activation 0.012 0.017 0.04 72 -0.044 4 76
TNF 0.2 0.25 0.69 12 -1.3 4 16
STAT3/STAT4 0.18 0.23 0.6 5 -1.1 5 10
STAT4 (dimer) 0.19 0.24 0.61 7 -1.2 5 12
IL18 0.027 0.034 0.28 9 -10000 0 9
IL19 0.23 0.25 0.66 24 -1.1 4 28
STAT5A (dimer) 0.18 0.24 0.62 6 -1.2 5 11
STAT1 0.023 0.012 0.28 1 -10000 0 1
SOCS3 0.021 0.023 -10000 0 -0.35 2 2
CXCL9 0.2 0.27 0.68 13 -1.2 8 21
MPO 0.19 0.24 0.67 8 -1.1 4 12
positive regulation of humoral immune response 0.21 0.26 0.66 20 -1.2 5 25
IL23/IL23R/JAK2/TYK2 0.21 0.26 0.67 17 -1.2 5 22
IL6 0.18 0.29 0.65 11 -1.1 17 28
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
IL2 0.009 0.055 0.28 17 -10000 0 17
positive regulation of tyrosine phosphorylation of STAT protein -0.007 0.008 -10000 0 -0.042 2 2
CD3E 0.18 0.27 0.65 11 -1.1 12 23
keratinocyte proliferation 0.21 0.26 0.66 20 -1.2 5 25
NOS2 0.18 0.26 0.65 10 -1 11 21
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.014 0.092 0.26 8 -0.34 22 30
PDGFB-D/PDGFRB/SLAP 0.025 0.043 0.21 1 -0.24 12 13
PDGFB-D/PDGFRB/APS/CBL 0.036 0.043 -10000 0 -0.2 15 15
AKT1 0.015 0.098 0.31 33 -0.3 1 34
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.02 0.11 0.27 15 -0.36 25 40
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
FGR -0.014 0.12 0.33 1 -0.53 20 21
mol:Ca2+ 0.009 0.11 0.26 15 -0.39 28 43
MYC 0.035 0.15 0.38 18 -0.7 11 29
SHC1 0.019 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.048 0.18 1 -0.18 15 16
LRP1/PDGFRB/PDGFB 0.034 0.05 -10000 0 -0.21 19 19
GRB10 0.022 0.017 -10000 0 -0.35 1 1
PTPN11 0.023 0.003 -10000 0 -10000 0 0
GO:0007205 0.009 0.12 0.26 15 -0.4 28 43
PTEN 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.022 0.006 -10000 0 -10000 0 0
GRB7 0.037 0.073 0.32 30 -0.35 2 32
PDGFB-D/PDGFRB/SHP2 0.024 0.051 -10000 0 -0.24 18 18
PDGFB-D/PDGFRB/GRB10 0.023 0.052 -10000 0 -0.24 19 19
cell cycle arrest 0.024 0.043 0.21 1 -0.24 12 13
HRAS 0.022 0.005 -10000 0 -10000 0 0
HIF1A 0.011 0.092 0.29 35 -0.27 1 36
GAB1 0.015 0.11 0.29 10 -0.37 25 35
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.018 0.11 0.29 21 -0.35 19 40
PDGFB-D/PDGFRB 0.036 0.043 -10000 0 -0.21 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.024 0.049 -10000 0 -0.24 17 17
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.013 0.078 0.23 2 -0.33 15 17
positive regulation of MAPKKK cascade 0.024 0.05 -10000 0 -0.24 18 18
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
mol:IP3 0.009 0.12 0.26 15 -0.4 28 43
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.02 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.03 0.069 0.24 22 -0.24 21 43
SHB 0.022 0.004 -10000 0 -10000 0 0
BLK -0.017 0.14 0.38 2 -0.47 36 38
PTPN2 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.024 0.049 -10000 0 -0.24 17 17
BCAR1 0.02 0.008 -10000 0 -10000 0 0
VAV2 0.017 0.12 0.32 10 -0.38 24 34
CBL 0.022 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.023 0.051 -10000 0 -0.24 19 19
LCK -0.001 0.087 0.33 1 -0.5 9 10
PDGFRB 0.01 0.07 -10000 0 -0.35 19 19
ACP1 0.022 0.005 -10000 0 -10000 0 0
HCK 0.006 0.064 0.32 1 -0.91 1 2
ABL1 0.014 0.1 0.25 18 -0.33 25 43
PDGFB-D/PDGFRB/CBL 0.012 0.12 0.3 8 -0.42 29 37
PTPN1 0.021 0.009 -10000 0 -10000 0 0
SNX15 0.022 0.004 -10000 0 -10000 0 0
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT1 0.023 0.012 0.28 1 -10000 0 1
cell proliferation 0.036 0.14 0.37 19 -0.62 11 30
SLA 0.021 0.013 0.28 1 -10000 0 1
actin cytoskeleton reorganization -0.004 0.068 0.32 9 -0.32 1 10
SRC 0.003 0.07 0.33 1 -0.82 2 3
PI3K -0.021 0.025 -10000 0 -0.19 8 8
PDGFB-D/PDGFRB/GRB7/SHC 0.036 0.06 0.23 21 -0.2 16 37
SH2B2 0.022 0.005 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.02 0.11 0.27 15 -0.38 25 40
LYN 0.003 0.056 0.33 1 -0.44 2 3
LRP1 0.022 0.023 -10000 0 -0.35 2 2
SOS1 0.023 0.003 -10000 0 -10000 0 0
STAT5B 0.02 0.023 -10000 0 -0.35 2 2
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
NCK1-2/p130 Cas 0.049 0.049 -10000 0 -0.2 6 6
SPHK1 0.023 0.018 0.3 2 -10000 0 2
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.009 0.12 0.26 15 -0.4 28 43
PLCG1 0.009 0.12 0.26 15 -0.41 28 43
NHERF/PDGFRB 0.037 0.046 0.2 4 -0.2 16 20
YES1 -0.005 0.087 -10000 0 -0.46 13 13
cell migration 0.036 0.046 0.2 4 -0.2 16 20
SHC/Grb2/SOS1 0.044 0.045 -10000 0 -0.18 8 8
SLC9A3R2 0.022 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.024 0.023 0.28 4 -10000 0 4
NHERF1-2/PDGFRB/PTEN 0.045 0.046 0.21 4 -0.18 15 19
FYN 0.003 0.069 0.33 1 -0.61 3 4
DOK1 -0.007 0.049 0.17 25 -0.19 13 38
HRAS/GTP 0.016 0.004 -10000 0 -10000 0 0
PDGFB 0.022 0.006 -10000 0 -10000 0 0
RAC1 0.015 0.14 0.34 10 -0.46 23 33
PRKCD -0.005 0.051 0.18 28 -0.19 11 39
FER -0.006 0.051 0.18 27 -0.19 12 39
MAPKKK cascade 0.028 0.098 0.26 33 -10000 0 33
RASA1 -0.007 0.056 0.18 28 -0.2 16 44
NCK1 0.021 0.023 -10000 0 -0.35 2 2
NCK2 0.023 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.023 0.044 0.17 9 -0.18 12 21
PDGFB-D/PDGFRB/SHB 0.024 0.05 -10000 0 -0.24 18 18
chemotaxis 0.015 0.1 0.25 18 -0.32 25 43
STAT1-3-5/STAT1-3-5 0.042 0.044 -10000 0 -0.19 10 10
Bovine Papilomavirus E5/PDGFRB 0.008 0.048 -10000 0 -0.24 19 19
PTPRJ 0.022 0.004 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.004 0.061 0.2 2 -0.22 22 24
adherens junction organization -0.007 0.09 0.29 1 -0.35 24 25
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.012 0.062 0.21 2 -0.21 8 10
FMN1 -0.003 0.076 -10000 0 -0.31 22 22
mol:IP3 0 0.043 -10000 0 -0.19 13 13
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.003 0.086 -10000 0 -0.31 28 28
CTNNB1 0.023 0.006 -10000 0 -10000 0 0
AKT1 0 0.052 -10000 0 -0.2 20 20
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.12 -10000 0 -0.53 16 16
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.073 -10000 0 -0.3 23 23
VASP -0.007 0.08 -10000 0 -0.3 26 26
ZYX -0.007 0.079 -10000 0 -0.3 26 26
JUB -0.005 0.082 -10000 0 -0.29 28 28
EGFR(dimer) 0.001 0.095 0.26 1 -0.3 33 34
E-cadherin/beta catenin-gamma catenin 0.038 0.026 -10000 0 -0.28 2 2
mol:PI-3-4-5-P3 0.014 0.062 -10000 0 -0.21 20 20
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.015 0.063 -10000 0 -0.21 20 20
FYN 0.005 0.054 0.18 4 -0.29 4 8
mol:Ca2+ 0 0.042 -10000 0 -0.18 13 13
JUP 0.022 0.017 -10000 0 -0.34 1 1
PIK3R1 0.019 0.037 -10000 0 -0.35 5 5
mol:DAG 0 0.043 -10000 0 -0.19 13 13
CDH1 0.019 0.024 -10000 0 -0.35 2 2
RhoA/GDP 0.013 0.064 0.21 1 -0.24 7 8
establishment of polarity of embryonic epithelium -0.007 0.08 -10000 0 -0.3 27 27
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
CASR 0.001 0.054 0.16 20 -0.2 6 26
RhoA/GTP 0.017 0.052 -10000 0 -0.18 11 11
AKT2 -0.001 0.052 -10000 0 -0.22 14 14
actin cable formation -0.003 0.074 0.2 8 -0.31 18 26
apoptosis -0.009 0.073 0.22 26 -0.24 10 36
CTNNA1 0.023 0.006 -10000 0 -10000 0 0
mol:GDP -0.001 0.059 0.15 26 -0.23 10 36
PIP5K1A -0.007 0.072 -10000 0 -0.3 22 22
PLCG1 0 0.043 -10000 0 -0.19 13 13
Rac1/GTP 0.009 0.091 0.24 1 -0.28 32 33
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.048 0.051 0.23 10 -0.19 14 24
MAP4K1 0.028 0.04 0.29 12 -10000 0 12
MAP3K8 0.02 0.028 -10000 0 -0.35 3 3
PRKCB 0.001 0.087 -10000 0 -0.35 31 31
DBNL 0.023 0.004 -10000 0 -10000 0 0
CRKL 0.022 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.045 -10000 0 -0.26 3 3
JUN -0.045 0.19 -10000 0 -0.57 58 58
MAP3K7 0.006 0.047 -10000 0 -0.26 3 3
GRAP2 0.011 0.062 -10000 0 -0.35 15 15
CRK 0.021 0.006 -10000 0 -10000 0 0
MAP2K4 0.005 0.061 -10000 0 -0.28 8 8
LAT 0.022 0.005 -10000 0 -10000 0 0
LCP2 0.023 0.012 0.28 1 -10000 0 1
MAPK8 -0.041 0.2 -10000 0 -0.59 58 58
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.014 0.049 -10000 0 -0.2 10 10
LAT/GRAP2/SLP76/HPK1/HIP-55 0.056 0.049 0.27 3 -0.18 11 14
IL1-mediated signaling events

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
UBC13/UEV1A 0.017 0.002 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.022 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.041 -10000 0 -0.22 12 12
IRAK/TOLLIP 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.021 0.007 -10000 0 -10000 0 0
IKBKG 0.023 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.053 0.07 0.23 60 -0.25 4 64
IL1A 0.038 0.062 0.28 33 -10000 0 33
IL1B -0.014 0.028 -10000 0 -0.28 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.046 0.025 -10000 0 -0.17 1 1
IL1R2 0.036 0.07 0.28 33 -0.35 4 37
IL1R1 0.017 0.048 -10000 0 -0.35 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.059 0.22 2 -0.24 15 17
TOLLIP 0.022 0.005 -10000 0 -10000 0 0
TICAM2 0.017 0.045 -10000 0 -0.35 8 8
MAP3K3 0.022 0.006 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.017 0.049 0.23 1 -0.32 1 2
JUN -0.01 0.041 0.17 15 -0.18 9 24
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.042 0.053 -10000 0 -0.21 15 15
IL1 alpha/IL1R1/IL1RAP/MYD88 0.056 0.055 0.21 31 -0.21 9 40
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.055 -10000 0 -0.2 9 9
IL1 beta fragment/IL1R1/IL1RAP 0.025 0.042 -10000 0 -0.21 14 14
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
MAPK8 -0.002 0.042 0.19 14 -0.16 3 17
IRAK1 0.01 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 0.053 0.073 0.21 73 -0.24 9 82
IRAK4 0.023 0.003 -10000 0 -10000 0 0
PRKCI 0.021 0.007 -10000 0 -10000 0 0
TRAF6 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.029 -10000 0 -0.24 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.013 0.053 -10000 0 -0.27 9 9
CHUK 0.022 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.025 0.042 -10000 0 -0.21 14 14
IL1 beta/IL1R2 0.038 0.059 0.2 44 -0.23 9 53
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.048 -10000 0 -0.21 14 14
IRAK3 0.006 0.077 -10000 0 -0.35 24 24
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.055 -10000 0 -0.2 20 20
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.017 0.044 -10000 0 -0.23 8 8
IL1 alpha/IL1R1/IL1RAP 0.046 0.055 0.2 31 -0.23 9 40
RELA 0.022 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.022 0.004 -10000 0 -10000 0 0
MYD88 0.022 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.035 0.013 -10000 0 -10000 0 0
IL1RAP 0.019 0.029 -10000 0 -0.35 3 3
UBE2N 0.023 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 0.017 0.043 -10000 0 -0.19 18 18
CASP1 0.021 0.023 -10000 0 -0.35 2 2
IL1RN/IL1R2 0.067 0.082 0.23 98 -0.24 3 101
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.035 0.044 -10000 0 -0.2 14 14
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.057 -10000 0 -0.28 13 13
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
IL1RN 0.059 0.091 0.28 75 -10000 0 75
TRAF6/TAK1/TAB1/TAB2 0.032 0.008 -10000 0 -10000 0 0
MAP2K6 0.012 0.061 0.16 73 -10000 0 73
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.024 -10000 0 -0.35 2 2
Caspase 8 (4 units) 0.03 0.048 -10000 0 -0.59 1 1
NEF 0.001 0.019 -10000 0 -0.2 4 4
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC3 0.011 0.057 0.2 2 -0.38 8 10
CYCS 0.024 0.067 0.17 69 -0.62 1 70
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.02 0.03 0.33 1 -0.25 4 5
MAP2K7 0.004 0.19 0.28 1 -0.66 33 34
protein ubiquitination 0.01 0.076 0.28 7 -0.28 9 16
CRADD 0.023 0.002 -10000 0 -10000 0 0
DAXX 0.023 0.003 -10000 0 -10000 0 0
FAS 0.019 0.033 -10000 0 -0.35 4 4
BID 0.029 0.069 0.18 70 -0.25 6 76
NF-kappa-B/RelA/I kappa B alpha 0.044 0.037 -10000 0 -0.22 8 8
TRADD 0.02 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.016 -10000 0 -0.35 1 1
CFLAR 0.023 0.003 -10000 0 -10000 0 0
FADD 0.022 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.037 -10000 0 -0.23 8 8
MAPK8 0.006 0.18 0.38 6 -0.62 33 39
APAF1 0.023 0.002 -10000 0 -10000 0 0
TRAF1 0.022 0.005 -10000 0 -10000 0 0
TRAF2 0.022 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.037 0.071 0.19 70 -0.26 6 76
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.004 0.089 0.21 3 -0.33 17 20
CHUK 0.011 0.078 0.29 7 -0.31 8 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.058 0.033 -10000 0 -0.18 5 5
TCRz/NEF 0.018 0.03 0.16 7 -0.24 4 11
TNF 0.053 0.088 0.28 65 -0.35 2 67
FASLG 0.012 0.045 0.25 8 -0.33 4 12
NFKB1 0.021 0.021 -10000 0 -0.35 1 1
TNFR1A/BAG4/TNF-alpha 0.054 0.053 0.2 50 -0.21 2 52
CASP6 0.041 0.1 -10000 0 -0.47 12 12
CASP7 0.031 0.1 0.38 7 -0.43 9 16
RELA 0.022 0.014 -10000 0 -10000 0 0
CASP2 0.022 0.005 -10000 0 -10000 0 0
CASP3 0.03 0.11 0.37 9 -0.4 12 21
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.029 0.021 -10000 0 -0.24 2 2
CASP8 0.023 0.003 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
MAP3K14 0.009 0.082 0.2 2 -0.32 13 15
APAF-1/Caspase 9 0.029 0.058 -10000 0 -0.29 7 7
BCL2 -0.005 0.17 0.36 5 -0.57 32 37
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.027 0.053 -10000 0 -10000 0 0
epithelial cell differentiation -0.009 0.089 0.24 1 -0.32 5 6
ITCH 0.016 0.024 -10000 0 -10000 0 0
WWP1 0.019 0.055 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
EGFR 0.014 0.059 0.33 1 -0.35 13 14
PRL 0.011 0.07 0.28 5 -0.35 17 22
neuron projection morphogenesis 0.035 0.094 0.26 32 -10000 0 32
PTPRZ1 0.034 0.06 0.28 30 -10000 0 30
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.028 0.051 -10000 0 -0.24 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.008 0.042 -10000 0 -0.26 2 2
ADAM17 0.016 0.024 -10000 0 -10000 0 0
ErbB4/ErbB4 0.017 0.049 0.23 1 -10000 0 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.031 0.065 0.25 11 -10000 0 11
NCOR1 0.021 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.046 -10000 0 -0.25 2 2
GRIN2B 0.016 0.062 0.24 15 -0.24 2 17
ErbB4/ErbB2/betacellulin 0.022 0.06 0.25 7 -0.22 1 8
STAT1 0.023 0.012 0.28 1 -10000 0 1
HBEGF 0.023 0.004 -10000 0 -10000 0 0
PRLR -0.047 0.14 -10000 0 -0.35 99 99
E4ICDs/ETO2 0.006 0.076 -10000 0 -0.29 6 6
axon guidance 0.012 0.048 -10000 0 -10000 0 0
NEDD4 -0.012 0.092 -10000 0 -0.35 35 35
Prolactin receptor/Prolactin receptor/Prolactin -0.026 0.12 0.21 4 -0.25 109 113
CBFA2T3 -0.025 0.12 -10000 0 -0.35 64 64
ErbB4/ErbB2/HBEGF 0.029 0.05 0.25 7 -10000 0 7
MAPK3 0.03 0.083 0.25 16 -10000 0 16
STAT1 (dimer) 0.026 0.054 -10000 0 -10000 0 0
MAPK1 0.03 0.083 0.25 19 -10000 0 19
JAK2 0.016 0.048 -10000 0 -0.35 9 9
ErbB4/ErbB2/neuregulin 1 beta 0.01 0.05 0.22 10 -0.25 2 12
NRG1 -0.012 0.034 -10000 0 -0.25 9 9
NRG3 0.029 0.051 0.29 20 -10000 0 20
NRG2 -0.028 0.13 -10000 0 -0.35 72 72
NRG4 0.044 0.073 0.28 46 -10000 0 46
heart development 0.012 0.048 -10000 0 -10000 0 0
neural crest cell migration 0.011 0.051 0.23 11 -0.25 2 13
ERBB2 0.001 0.051 0.3 14 -10000 0 14
WWOX/E4ICDs 0.025 0.049 -10000 0 -10000 0 0
SHC1 0.019 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.043 0.077 0.3 2 -0.28 2 4
apoptosis -0.032 0.06 0.31 2 -0.26 3 5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.004 0.082 -10000 0 -0.29 9 9
ErbB4/ErbB2/epiregulin 0.05 0.082 0.31 16 -10000 0 16
ErbB4/ErbB4/betacellulin/betacellulin 0.02 0.065 -10000 0 -0.25 2 2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.006 0.11 0.27 2 -0.28 25 27
MDM2 0.013 0.047 0.26 3 -10000 0 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.015 0.036 -10000 0 -0.23 2 2
STAT5A 0.01 0.052 0.28 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta 0.014 0.056 0.27 1 -0.29 6 7
DLG4 0.02 0.023 -10000 0 -0.35 2 2
GRB2/SHC 0.026 0.015 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.022 0.047 -10000 0 -10000 0 0
STAT5A (dimer) -0.001 0.1 0.29 1 -0.34 5 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.024 0.058 -10000 0 -0.27 2 2
LRIG1 0.02 0.028 -10000 0 -0.35 3 3
EREG 0.054 0.086 0.28 67 -10000 0 67
BTC 0.01 0.066 -10000 0 -0.35 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.009 0.041 -10000 0 -10000 0 0
ERBB4 0.017 0.049 0.23 1 -10000 0 1
STAT5B 0.02 0.023 -10000 0 -0.35 2 2
YAP1 0.013 0.073 -10000 0 -0.47 10 10
GRB2 0.022 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.042 0.072 0.32 13 -10000 0 13
glial cell differentiation -0.022 0.047 -10000 0 -10000 0 0
WWOX 0.02 0.008 -10000 0 -10000 0 0
cell proliferation 0.014 0.089 0.28 10 -0.34 4 14
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.007 0.084 0.27 2 -0.39 12 14
BAG4 0.019 0.024 -10000 0 -0.35 2 2
BAD 0.005 0.043 0.16 13 -0.15 9 22
NFKBIA 0.022 0.004 -10000 0 -10000 0 0
BIRC3 0.018 0.045 0.28 2 -0.35 7 9
BAX 0.004 0.041 0.16 8 -0.15 9 17
EnzymeConsortium:3.1.4.12 0.003 0.024 0.072 8 -0.085 15 23
IKBKB 0.018 0.097 0.28 20 -0.38 9 29
MAP2K2 0.002 0.042 0.21 8 -0.16 3 11
MAP2K1 0.002 0.042 0.21 8 -0.17 4 12
SMPD1 0.001 0.033 -10000 0 -0.14 16 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.015 0.086 0.26 5 -0.36 14 19
MAP2K4 0.003 0.035 0.23 3 -0.16 3 6
protein ubiquitination 0.012 0.09 0.29 6 -0.37 11 17
EnzymeConsortium:2.7.1.37 0.001 0.047 0.2 11 -0.18 3 14
response to UV 0 0 0.002 9 -0.002 1 10
RAF1 0.003 0.045 0.21 9 -0.16 7 16
CRADD 0.023 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.038 0.11 9 -0.14 15 24
I-kappa-B-alpha/RELA/p50/ubiquitin 0.029 0.008 -10000 0 -10000 0 0
MADD 0.022 0.005 -10000 0 -10000 0 0
MAP3K1 0.004 0.039 0.18 6 -0.15 8 14
TRADD 0.02 0.008 -10000 0 -10000 0 0
RELA/p50 0.022 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.048 0.21 9 -0.18 5 14
MAPK1 0 0.052 0.2 9 -0.22 7 16
p50/RELA/I-kappa-B-alpha 0.032 0.008 -10000 0 -10000 0 0
FADD 0.009 0.082 0.23 2 -0.38 12 14
KSR1 0.004 0.041 0.17 7 -0.15 10 17
MAPK8 0.001 0.042 0.19 8 -0.18 1 9
TRAF2 0.022 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -10000 0 4
CHUK 0.007 0.084 0.27 5 -0.38 11 16
TNF R/SODD 0.029 0.021 -10000 0 -0.24 2 2
TNF 0.053 0.088 0.28 65 -0.35 2 67
CYCS 0.013 0.049 0.15 23 -0.15 7 30
IKBKG 0.006 0.085 0.3 5 -0.39 10 15
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.011 0.085 0.21 2 -0.42 11 13
RELA 0.022 0.004 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AIFM1 0.012 0.046 0.14 23 -0.15 6 29
TNF/TNF R/SODD 0.054 0.053 0.2 50 -0.21 2 52
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 4 -10000 0 4
CASP8 0.018 0.081 -10000 0 -0.59 8 8
NSMAF 0.018 0.09 0.25 12 -0.41 9 21
response to hydrogen peroxide 0 0 0.002 9 -0.002 1 10
BCL2 -0.009 0.1 -10000 0 -0.35 44 44
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.022 0.015 0.33 1 -10000 0 1
NFATC1 0.012 0.078 0.27 4 -0.4 4 8
NFATC2 -0.001 0.066 0.15 3 -0.24 15 18
NFATC3 0.012 0.016 -10000 0 -0.3 1 1
YWHAE 0.021 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.022 0.12 0.21 4 -0.36 33 37
Exportin 1/Ran/NUP214 0.043 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.001 0.1 -10000 0 -0.33 25 25
BCL2/BAX 0.009 0.077 -10000 0 -0.24 44 44
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.01 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
MAPK14 0.022 0.005 -10000 0 -10000 0 0
BAD 0.022 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.009 0.1 -10000 0 -0.35 25 25
Calcineurin A alpha-beta B1/BCL2 -0.009 0.1 -10000 0 -0.35 44 44
FKBP8 0.022 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.009 0.1 0.35 25 -0.19 1 26
KPNB1 0.022 0.005 -10000 0 -10000 0 0
KPNA2 0.035 0.058 0.3 24 -10000 0 24
XPO1 0.023 0.003 -10000 0 -10000 0 0
SFN 0.2 0.12 0.28 379 -10000 0 379
MAP3K8 0.02 0.028 -10000 0 -0.35 3 3
NFAT4/CK1 alpha 0.017 0.022 -10000 0 -0.16 1 1
MEF2D/NFAT1/Cbp/p300 0.013 0.088 -10000 0 -0.24 34 34
CABIN1 -0.023 0.12 0.24 2 -0.36 33 35
CALM1 0.02 0.01 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
CAMK4 0.023 0.038 0.28 5 -0.35 3 8
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.022 0.005 -10000 0 -10000 0 0
YWHAH 0.022 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.019 -10000 0 -0.24 2 2
YWHAB 0.022 0.005 -10000 0 -10000 0 0
MAPK8 0.018 0.036 -10000 0 -0.35 5 5
MAPK9 0.023 0.004 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
FKBP1A 0.022 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.013 0.085 0.26 3 -0.38 6 9
PRKCH 0.021 0.023 -10000 0 -0.35 2 2
CABIN1/Cbp/p300 0.027 0.019 -10000 0 -10000 0 0
CASP3 0.022 0.006 -10000 0 -10000 0 0
PIM1 0.023 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.007 -10000 0 -10000 0 0
apoptosis 0.007 0.031 0.19 1 -0.25 2 3
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.049 0.059 0.2 6 -0.29 6 12
PRKCB 0.001 0.087 -10000 0 -0.35 31 31
PRKCE 0.023 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.011 0.053 -10000 0 -0.27 1 1
BAD/BCL-XL 0.032 0.014 0.24 1 -10000 0 1
PRKCD 0.022 0.005 -10000 0 -10000 0 0
NUP214 0.022 0.006 -10000 0 -10000 0 0
PRKCZ 0.022 0.02 0.28 1 -0.35 1 2
PRKCA 0 0.087 -10000 0 -0.35 31 31
PRKCG 0.049 0.095 0.28 65 -0.35 6 71
PRKCQ -0.007 0.1 0.28 1 -0.35 43 44
FKBP38/BCL2 0.008 0.077 -10000 0 -0.24 44 44
EP300 0.019 0.012 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.004 -10000 0 -10000 0 0
NFATc/JNK1 0.023 0.078 0.27 4 -0.38 4 8
CaM/Ca2+/FKBP38 0.026 0.015 -10000 0 -10000 0 0
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSNK1A1 0.008 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.027 0.027 0.19 5 -0.2 3 8
NFATc/ERK1 0.023 0.077 0.28 3 -0.37 4 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.002 0.11 -10000 0 -0.33 30 30
NR4A1 0.01 0.13 0.23 14 -0.38 32 46
GSK3B 0.022 0.006 -10000 0 -10000 0 0
positive T cell selection 0.012 0.016 -10000 0 -0.3 1 1
NFAT1/CK1 alpha 0.002 0.048 0.12 1 -0.2 9 10
RCH1/ KPNB1 0.04 0.039 0.22 23 -10000 0 23
YWHAQ 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.021 0.006 -10000 0 -10000 0 0
AKAP5 0.021 0.023 -10000 0 -0.35 2 2
MEF2D 0.017 0.013 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.021 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.022 0.076 0.28 3 -0.38 4 7
CREBBP 0.019 0.013 -10000 0 -10000 0 0
BCL2 -0.009 0.1 -10000 0 -0.35 44 44
Signaling events mediated by PRL

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
CCNE1 0.13 0.13 0.29 214 -10000 0 214
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.021 0.023 -10000 0 -0.35 2 2
CDKN1A 0.002 0.042 -10000 0 -0.31 6 6
PRL-3/alpha Tubulin 0.031 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.076 0.28 2 -0.25 54 56
AGT -0.023 0.13 0.29 8 -0.35 66 74
CCNA2 -0.022 0.056 0.21 5 -10000 0 5
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
EGR1 -0.022 0.081 -10000 0 -0.24 67 67
CDK2/Cyclin E1 0.091 0.1 0.3 10 -10000 0 10
MAPK3 -0.01 0.004 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.033 0.006 -10000 0 -10000 0 0
MAPK1 -0.01 0.004 -10000 0 -10000 0 0
PTP4A1 -0.027 0.055 -10000 0 -10000 0 0
PTP4A3 0.021 0.007 -10000 0 -10000 0 0
PTP4A2 0.022 0.004 -10000 0 -10000 0 0
ITGB1 -0.01 0.004 -10000 0 -10000 0 0
SRC 0.022 0.005 -10000 0 -10000 0 0
RAC1 0 0.046 -10000 0 -0.33 7 7
Rab GGTase beta/Rab GGTase alpha 0.033 0.007 -10000 0 -10000 0 0
PRL-1/ATF-5 0 0.071 0.35 1 -10000 0 1
RABGGTA 0.022 0.004 -10000 0 -10000 0 0
BCAR1 -0.016 0.008 -10000 0 -10000 0 0
RHOC 0.002 0.04 -10000 0 -0.35 4 4
RHOA -0.001 0.052 -10000 0 -0.34 9 9
cell motility 0.012 0.061 0.34 1 -0.35 5 6
PRL-1/alpha Tubulin -0.001 0.07 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.03 0.017 -10000 0 -0.24 1 1
ROCK1 0.012 0.06 0.34 1 -0.35 5 6
RABGGTB 0.023 0.002 -10000 0 -10000 0 0
CDK2 0.023 0.004 -10000 0 -10000 0 0
mitosis -0.027 0.055 -10000 0 -10000 0 0
ATF5 0.024 0.022 0.28 4 -10000 0 4
Caspase cascade in apoptosis

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
TOP1 0.009 0.091 0.2 2 -0.39 18 20
ACTA1 0.011 0.067 0.21 8 -0.26 10 18
NUMA1 0.008 0.094 0.22 1 -0.41 17 18
SPTAN1 0.002 0.062 0.2 5 -0.27 10 15
LIMK1 0.004 0.07 0.26 9 -0.28 10 19
BIRC3 0.018 0.046 0.28 2 -0.35 7 9
BIRC2 0.022 0.004 -10000 0 -10000 0 0
BAX 0.023 0.004 -10000 0 -10000 0 0
CASP10 -0.008 0.04 0.26 3 -0.27 6 9
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.023 0.001 -10000 0 -10000 0 0
PTK2 0.008 0.091 0.21 2 -0.4 16 18
DIABLO 0.023 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes 0.002 0.062 0.2 5 -0.27 10 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
GSN 0 0.062 0.23 2 -0.28 9 11
MADD 0.022 0.005 -10000 0 -10000 0 0
TFAP2A 0.15 0.12 0.37 4 -0.66 5 9
BID 0.004 0.023 0.16 3 -0.17 5 8
MAP3K1 -0.007 0.1 -10000 0 -0.42 26 26
TRADD 0.02 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.002 0.067 0.24 7 -0.26 12 19
CASP9 0.022 0.005 -10000 0 -10000 0 0
DNA repair -0.015 0.044 0.26 4 -0.19 1 5
neuron apoptosis 0.008 0.11 -10000 0 -0.83 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.004 0.088 0.22 2 -0.38 16 18
APAF1 0.023 0.002 -10000 0 -10000 0 0
CASP6 -0.005 0.17 -10000 0 -0.89 17 17
TRAF2 0.022 0.006 -10000 0 -10000 0 0
ICAD/CAD 0 0.064 0.24 7 -0.3 7 14
CASP7 -0.002 0.057 0.32 2 -0.27 2 4
KRT18 0.017 0.056 -10000 0 -0.64 2 2
apoptosis 0.003 0.11 0.4 12 -0.42 18 30
DFFA 0.003 0.065 0.24 7 -0.27 10 17
DFFB 0.001 0.063 0.2 5 -0.27 11 16
PARP1 0.015 0.044 0.19 1 -0.27 4 5
actin filament polymerization -0.002 0.072 0.28 6 -0.28 13 19
TNF 0.053 0.088 0.28 65 -0.35 2 67
CYCS 0.007 0.042 0.17 9 -0.2 8 17
SATB1 -0.028 0.17 0.33 1 -0.86 17 18
SLK 0.004 0.073 0.31 10 -0.29 8 18
p15 BID/BAX 0.015 0.042 -10000 0 -0.17 8 8
CASP2 0.012 0.055 0.21 9 -0.29 6 15
JNK cascade 0.007 0.1 0.42 26 -10000 0 26
CASP3 0.004 0.067 0.21 5 -0.28 12 17
LMNB2 -0.014 0.16 0.23 6 -0.47 44 50
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CASP4 0.022 0.017 -10000 0 -0.35 1 1
Mammalian IAPs/DIABLO 0.054 0.033 -10000 0 -0.19 7 7
negative regulation of DNA binding 0.15 0.11 0.37 4 -0.65 5 9
stress fiber formation 0.004 0.072 0.31 10 -0.29 8 18
GZMB -0.001 0.05 0.12 50 -0.28 5 55
CASP1 0.009 0.02 -10000 0 -0.26 3 3
LMNB1 0.006 0.12 0.26 4 -0.5 20 24
APP 0.008 0.11 -10000 0 -0.85 8 8
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.001 -10000 0 -10000 0 0
VIM 0.002 0.1 0.31 10 -0.43 18 28
LMNA 0.01 0.086 0.27 2 -0.36 17 19
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.014 0.058 0.22 3 -0.27 9 12
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.004 0.064 0.2 10 -0.28 9 19
APAF-1/Caspase 9 0.007 0.097 -10000 0 -0.64 11 11
nuclear fragmentation during apoptosis 0.008 0.093 0.21 2 -0.4 17 19
CFL2 0.002 0.073 0.28 13 -0.28 6 19
GAS2 -0.01 0.075 0.2 4 -0.28 15 19
positive regulation of apoptosis 0 0.13 0.23 7 -0.49 25 32
PRF1 0.022 0.036 0.28 4 -0.35 3 7
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.023 0.004 -10000 0 -10000 0 0
SPHK1 0.023 0.018 0.3 2 -10000 0 2
GNAI2 0.022 0.005 -10000 0 -10000 0 0
mol:S1P 0.01 0.005 -10000 0 -10000 0 0
GNAO1 -0.065 0.16 -10000 0 -0.35 123 123
mol:Sphinganine-1-P -0.01 0.015 0.2 2 -10000 0 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.041 0.037 -10000 0 -0.19 5 5
GNAI3 0.023 0.002 -10000 0 -10000 0 0
G12/G13 0.031 0.01 -10000 0 -10000 0 0
S1PR3 0.01 0.066 -10000 0 -0.35 17 17
S1PR2 0.021 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.001 0.03 -10000 0 -0.22 5 5
S1PR5 0.025 0.053 0.29 13 -0.35 4 17
S1PR4 0.02 0.026 0.28 1 -0.35 2 3
GNAI1 0.017 0.045 -10000 0 -0.35 8 8
S1P/S1P5/G12 0.033 0.044 0.2 8 -0.19 8 16
S1P/S1P3/Gq -0.015 0.11 -10000 0 -0.31 54 54
S1P/S1P4/Gi -0.038 0.11 -10000 0 -0.35 28 28
GNAQ 0.021 0.017 -10000 0 -0.35 1 1
GNAZ 0.011 0.062 -10000 0 -0.35 15 15
GNA14 -0.011 0.1 -10000 0 -0.35 46 46
GNA15 0.025 0.03 0.28 7 -10000 0 7
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.014 0.051 -10000 0 -0.35 10 10
ABCC1 0.022 0.005 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.017 -10000 0 -0.35 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.012 0.11 0.4 12 -0.37 1 13
IL27/IL27R/JAK1 0.026 0.12 0.44 5 -0.95 2 7
TBX21 -0.015 0.11 0.34 4 -0.4 9 13
IL12B 0.023 0.013 0.28 1 -10000 0 1
IL12A -0.003 0.029 0.12 11 -0.24 4 15
IL6ST -0.031 0.13 -10000 0 -0.35 75 75
IL27RA/JAK1 0.017 0.084 -10000 0 -1 2 2
IL27 0.025 0.043 0.29 12 -10000 0 12
TYK2 0.022 0.014 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.007 0.065 0.44 2 -0.38 1 3
T-helper 2 cell differentiation 0.012 0.11 0.4 12 -0.37 1 13
T cell proliferation during immune response 0.012 0.11 0.4 12 -0.37 1 13
MAPKKK cascade -0.012 0.11 0.37 1 -0.4 12 13
STAT3 0.022 0.006 -10000 0 -10000 0 0
STAT2 0.023 0.003 -10000 0 -10000 0 0
STAT1 0.023 0.012 0.29 1 -10000 0 1
IL12RB1 0.026 0.053 0.29 13 -0.35 4 17
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.007 0.11 0.36 8 -0.51 3 11
IL27/IL27R/JAK2/TYK2 -0.011 0.1 0.37 1 -0.41 10 11
positive regulation of T cell mediated cytotoxicity -0.012 0.11 0.37 1 -0.4 12 13
STAT1 (dimer) 0.018 0.14 0.56 6 -0.72 3 9
JAK2 0.017 0.049 -10000 0 -0.35 9 9
JAK1 0.022 0.017 -10000 0 -0.35 1 1
STAT2 (dimer) -0.005 0.12 0.34 1 -0.35 19 20
T cell proliferation -0.018 0.11 0.35 1 -0.39 15 16
IL12/IL12R/TYK2/JAK2 0.005 0.17 -10000 0 -0.71 26 26
IL17A 0.006 0.063 0.44 2 -0.38 1 3
mast cell activation 0.012 0.11 0.4 12 -0.37 1 13
IFNG 0.007 0.034 0.1 13 -0.091 12 25
T cell differentiation -0.001 0.005 0.012 4 -0.018 12 16
STAT3 (dimer) -0.004 0.12 0.34 1 -0.37 16 17
STAT5A (dimer) -0.004 0.12 0.34 1 -0.37 16 17
STAT4 (dimer) -0.006 0.12 0.34 1 -0.36 20 21
STAT4 0.022 0.016 -10000 0 -0.35 1 1
T cell activation -0.005 0.01 0.12 2 -0.087 2 4
IL27R/JAK2/TYK2 0.008 0.11 -10000 0 -0.98 2 2
GATA3 0.001 0.16 0.58 14 -1.1 6 20
IL18 -0.002 0.015 0.11 9 -10000 0 9
positive regulation of mast cell cytokine production -0.004 0.12 0.33 1 -0.36 18 19
IL27/EBI3 0.038 0.048 0.25 20 -10000 0 20
IL27RA 0.005 0.084 0.37 1 -1.1 2 3
IL6 0.017 0.069 0.28 9 -0.35 14 23
STAT5A 0.021 0.017 -10000 0 -0.35 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.007 0.038 0.43 2 -10000 0 2
IL1B -0.006 0.021 -10000 0 -0.24 4 4
EBI3 0.027 0.044 0.29 13 -10000 0 13
TNF 0.009 0.043 0.11 65 -0.24 2 67
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.025 -10000 0 -0.18 8 8
epithelial cell differentiation 0.041 0.022 -10000 0 -0.17 2 2
CYFIP2 0.021 0.028 -10000 0 -0.35 3 3
ENAH -0.006 0.057 0.26 13 -10000 0 13
EGFR 0.014 0.059 0.33 1 -0.35 13 14
EPHA2 0.022 0.005 -10000 0 -10000 0 0
MYO6 -0.012 0.024 0.17 6 -0.17 1 7
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.043 0.017 -10000 0 -0.21 1 1
AQP5 0.077 0.088 0.26 3 -0.34 9 12
CTNND1 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.017 0.17 2 -0.17 1 3
regulation of calcium-dependent cell-cell adhesion -0.016 0.036 0.17 6 -0.18 14 20
EGF 0.031 0.052 0.28 20 -0.35 1 21
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
AQP3 -0.001 0.057 -10000 0 -0.3 15 15
cortical microtubule organization 0.041 0.022 -10000 0 -0.17 2 2
GO:0000145 -0.013 0.016 0.16 2 -0.16 1 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.024 -10000 0 -0.17 2 2
MLLT4 0.022 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.018 -10000 0 -0.16 3 3
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.031 0.21 1 -0.19 2 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.004 0.016 0.16 3 -10000 0 3
PVRL2 0.022 0.005 -10000 0 -10000 0 0
ZYX -0.012 0.023 0.17 5 -0.17 1 6
ARF6/GTP 0.047 0.033 -10000 0 -0.18 2 2
CDH1 0.019 0.024 -10000 0 -0.35 2 2
EGFR/EGFR/EGF/EGF 0.033 0.043 -10000 0 -0.18 13 13
RhoA/GDP 0.042 0.023 -10000 0 -0.16 2 2
actin cytoskeleton organization -0.014 0.02 0.16 5 -0.17 1 6
IGF-1R heterotetramer 0.009 0.069 -10000 0 -0.35 19 19
GIT1 0.022 0.005 -10000 0 -10000 0 0
IGF1R 0.009 0.069 -10000 0 -0.35 19 19
IGF1 -0.047 0.15 -10000 0 -0.35 100 100
DIAPH1 0.018 0.097 -10000 0 -0.53 7 7
Wnt receptor signaling pathway -0.041 0.022 0.17 2 -10000 0 2
RHOA 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.018 -10000 0 -0.16 3 3
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
VCL -0.014 0.021 0.16 5 -0.18 1 6
EFNA1 0.02 0.02 0.3 2 -10000 0 2
LPP -0.014 0.022 0.17 5 -10000 0 5
Ephrin A1/EPHA2 0.03 0.025 -10000 0 -0.16 2 2
SEC6/SEC8 -0.02 0.012 -10000 0 -0.15 1 1
MGAT3 -0.016 0.036 0.17 6 -0.18 14 20
HGF/MET -0.003 0.087 -10000 0 -0.17 102 102
HGF -0.049 0.15 -10000 0 -0.35 102 102
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.025 -10000 0 -0.18 8 8
actin cable formation 0.046 0.1 0.31 33 -0.24 2 35
KIAA1543 -0.013 0.022 0.16 5 -0.16 2 7
KIFC3 -0.013 0.022 0.17 5 -0.17 1 6
NCK1 0.021 0.023 -10000 0 -0.35 2 2
EXOC3 0.022 0.006 -10000 0 -10000 0 0
ACTN1 -0.012 0.024 0.17 6 -0.17 1 7
NCK1/GIT1 0.03 0.02 -10000 0 -0.24 2 2
mol:GDP 0.041 0.022 -10000 0 -0.17 2 2
EXOC4 0.022 0.005 -10000 0 -10000 0 0
STX4 -0.012 0.024 0.17 6 -0.17 1 7
PIP5K1C -0.014 0.017 0.17 2 -0.17 1 3
LIMA1 0.023 0.003 -10000 0 -10000 0 0
ABI1 0.022 0.005 -10000 0 -10000 0 0
ROCK1 0.018 0.086 0.3 19 -10000 0 19
adherens junction assembly -0.044 0.14 0.2 1 -0.56 30 31
IGF-1R heterotetramer/IGF1 -0.007 0.093 -10000 0 -0.18 107 107
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.01 -10000 0 -10000 0 0
MET 0.021 0.039 0.28 4 -0.35 4 8
PLEKHA7 -0.013 0.023 0.17 5 -0.17 2 7
mol:GTP 0.042 0.03 -10000 0 -0.19 2 2
establishment of epithelial cell apical/basal polarity 0.001 0.076 0.35 12 -10000 0 12
cortical actin cytoskeleton stabilization 0.013 0.025 -10000 0 -0.18 8 8
regulation of cell-cell adhesion -0.014 0.02 0.16 5 -0.17 1 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.025 -10000 0 -0.18 8 8
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.015 0.092 -10000 0 -0.27 58 58
KLHL20 -0.005 0.062 0.2 2 -0.2 29 31
CYFIP2 0.021 0.028 -10000 0 -0.35 3 3
Rac1/GDP 0.001 0.069 0.25 3 -0.25 9 12
ENAH -0.019 0.093 -10000 0 -0.28 59 59
AP1M1 0.022 0.005 -10000 0 -10000 0 0
RAP1B 0.023 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.002 -10000 0 -10000 0 0
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.014 0.028 -10000 0 -0.19 2 2
ABI1/Sra1/Nap1 -0.013 0.038 -10000 0 -0.14 30 30
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.048 0.028 0.21 1 -0.19 2 3
RAPGEF1 -0.012 0.08 0.22 2 -0.26 38 40
CTNND1 0.023 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.012 0.1 -10000 0 -0.28 64 64
CRK -0.009 0.083 -10000 0 -0.27 42 42
E-cadherin/gamma catenin/alpha catenin 0.039 0.027 -10000 0 -0.29 2 2
alphaE/beta7 Integrin 0.032 0.013 0.21 1 -10000 0 1
IQGAP1 0.022 0.004 -10000 0 -10000 0 0
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.042 0.011 -10000 0 -10000 0 0
DLG1 -0.013 0.087 -10000 0 -0.28 51 51
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.016 -10000 0 -0.14 2 2
MLLT4 0.022 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.036 -10000 0 -0.18 12 12
PI3K -0.019 0.02 -10000 0 -0.18 2 2
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.028 0.027 -10000 0 -0.34 2 2
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
E-cadherin(dimer)/Ca2+ 0.046 0.024 -10000 0 -0.17 2 2
AKT1 -0.012 0.021 -10000 0 -0.13 1 1
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
CDH1 0.019 0.024 -10000 0 -0.35 2 2
RhoA/GDP 0.001 0.068 0.23 1 -0.25 7 8
actin cytoskeleton organization -0.003 0.048 0.17 3 -0.15 28 31
CDC42/GDP 0.003 0.069 0.25 3 -0.25 9 12
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.022 -10000 0 -0.32 2 2
ITGB7 0.023 0.012 0.28 1 -10000 0 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.05 0.026 -10000 0 -0.18 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.019 -10000 0 -0.16 2 2
mol:GDP -0.011 0.074 0.25 3 -0.29 10 13
CDC42/GTP/IQGAP1 0.029 0.008 -10000 0 -10000 0 0
JUP 0.021 0.017 -10000 0 -0.35 1 1
p120 catenin/RhoA/GDP 0.008 0.07 0.24 1 -0.27 5 6
RAC1/GTP/IQGAP1 0.029 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.03 0.011 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.004 -10000 0 -10000 0 0
CTNNA1 0.023 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.004 0.037 0.16 6 -0.1 10 16
NME1 0.022 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.01 0.084 -10000 0 -0.27 48 48
regulation of cell-cell adhesion 0.008 0.023 -10000 0 -0.17 2 2
WASF2 -0.001 0.025 -10000 0 -10000 0 0
Rap1/GTP 0.017 0.039 -10000 0 -0.21 2 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.034 -10000 0 -0.25 2 2
CCND1 0.004 0.043 0.18 6 -0.12 12 18
VAV2 -0.03 0.16 -10000 0 -0.57 34 34
RAP1/GDP 0.018 0.06 0.25 4 -0.24 5 9
adherens junction assembly -0.011 0.084 -10000 0 -0.26 50 50
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.022 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.041 0.029 -10000 0 -0.24 2 2
E-cadherin/beta catenin 0.008 0.019 -10000 0 -0.29 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.016 0.093 -10000 0 -0.28 58 58
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
Rac1/GTP -0.018 0.086 0.18 1 -0.31 31 32
E-cadherin/beta catenin/alpha catenin 0.039 0.022 -10000 0 -0.2 2 2
ITGAE 0.021 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.013 0.1 -10000 0 -0.28 64 64
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.093 0.25 8 -0.29 22 30
ERC1 0.022 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.029 0.019 0.21 1 -0.24 1 2
NFKBIA -0.007 0.028 0.2 8 -0.18 1 9
BIRC2 0.022 0.004 -10000 0 -10000 0 0
IKBKB 0.021 0.007 -10000 0 -10000 0 0
RIPK2 0.021 0.007 -10000 0 -10000 0 0
IKBKG 0.016 0.02 -10000 0 -10000 0 0
IKK complex/A20 0.032 0.11 -10000 0 -0.33 34 34
NEMO/A20/RIP2 0.021 0.007 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.01 0.11 0.26 1 -0.35 38 39
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.031 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.012 0.098 -10000 0 -0.32 35 35
BCL10/MALT1/TRAF6 0.043 0.013 -10000 0 -10000 0 0
NOD2 0.021 0.021 0.28 1 -0.35 1 2
NFKB1 0.023 0.017 -10000 0 -0.35 1 1
RELA 0.023 0.005 -10000 0 -10000 0 0
MALT1 0.022 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.008 -10000 0 -10000 0 0
ATM 0.022 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.052 0.06 0.21 61 -0.24 2 63
TRAF6 0.022 0.005 -10000 0 -10000 0 0
PRKCA 0 0.087 -10000 0 -0.35 31 31
CHUK 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.004 -10000 0 -10000 0 0
TNF 0.053 0.088 0.28 65 -0.35 2 67
NF kappa B1 p50/RelA 0.047 0.018 -10000 0 -0.2 1 1
BCL10 0.023 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.028 0.2 8 -0.18 1 9
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
IKK complex 0.013 0.1 0.26 1 -0.34 35 36
CYLD 0.021 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.011 0.11 0.26 1 -0.35 33 34
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.014 0.015 -10000 0 -0.27 1 1
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.004 -10000 0 -10000 0 0
DOCK1 0.017 0.043 -10000 0 -0.35 7 7
ITGA4 0.022 0.026 0.28 1 -0.35 2 3
alpha4/beta7 Integrin/MAdCAM1 0.063 0.047 0.21 40 -0.19 1 41
EPO 0.01 0.065 0.28 1 -0.35 16 17
alpha4/beta7 Integrin 0.033 0.017 0.21 2 -0.24 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.032 0.02 0.21 1 -0.24 2 3
EPO/EPOR (dimer) 0.025 0.054 0.23 8 -0.24 16 24
lamellipodium assembly 0.013 0.074 -10000 0 -0.4 9 9
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.026 0.029 -10000 0 -0.24 5 5
ARF6 0.023 0.003 -10000 0 -10000 0 0
JAK2 0.009 0.05 0.17 4 -0.21 23 27
PXN 0.023 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
MADCAM1 0.04 0.069 0.28 40 -10000 0 40
cell adhesion 0.061 0.045 0.22 1 -0.19 1 2
CRKL/CBL 0.031 0.01 -10000 0 -10000 0 0
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC -0.021 0.056 0.18 14 -0.2 33 47
ITGB7 0.023 0.012 0.28 1 -10000 0 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.027 0.068 0.2 1 -0.22 36 37
p130Cas/Crk/Dock1 0.008 0.056 0.18 5 -0.38 2 7
VCAM1 -0.004 0.097 -10000 0 -0.35 39 39
RHOA 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.053 0.024 0.21 1 -0.19 2 3
BCAR1 -0.02 0.05 0.18 12 -0.19 26 38
EPOR 0.026 0.034 0.31 7 -10000 0 7
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.076 -10000 0 -0.41 9 9
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.022 0.043 0.35 4 -0.29 6 10
PI3K Class IB/PDE3B 0.022 0.043 0.29 6 -0.35 4 10
PDE3B 0.022 0.043 0.29 6 -0.35 4 10
Signaling events mediated by HDAC Class III

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
EP300 0.021 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.008 0.034 0.24 2 -0.23 7 9
CDKN1A -0.008 0.007 -10000 0 -10000 0 0
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
BAX 0.023 0.004 -10000 0 -10000 0 0
FOXO3 -0.003 0.006 -10000 0 -10000 0 0
FOXO1 0.021 0.023 -10000 0 -0.35 2 2
FOXO4 0.009 0.015 -10000 0 -0.22 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.006 -10000 0 -10000 0 0
TAT 0.019 0.014 0.28 1 -10000 0 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.005 0.05 0.12 45 -0.24 8 53
PPARGC1A -0.054 0.15 0.28 2 -0.35 109 111
FHL2 0.019 0.036 -10000 0 -0.35 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.019 -10000 0 -0.25 2 2
HIST2H4A -0.008 0.034 0.23 7 -0.25 2 9
SIRT1/FOXO3a 0.016 0.033 -10000 0 -0.2 7 7
SIRT1 0.019 0.023 -10000 0 -0.35 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.035 0.024 -10000 0 -0.21 2 2
SIRT1/Histone H1b 0.016 0.05 -10000 0 -0.22 12 12
apoptosis -0.039 0.021 0.21 2 -10000 0 2
SIRT1/PGC1A -0.02 0.096 0.19 2 -0.2 110 112
p53/SIRT1 0.025 0.019 -10000 0 -0.25 2 2
SIRT1/FOXO4 0.011 0.048 -10000 0 -0.2 15 15
FOXO1/FHL2/SIRT1 0.036 0.03 -10000 0 -0.19 8 8
HIST1H1E 0.014 0.022 0.21 2 -10000 0 2
SIRT1/p300 0.029 0.02 -10000 0 -0.25 2 2
muscle cell differentiation -0.022 0.037 0.22 9 -0.21 2 11
TP53 0.02 0.016 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.04 0.021 -10000 0 -0.21 2 2
CREBBP 0.022 0.005 -10000 0 -10000 0 0
MEF2D 0.019 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.026 0.022 0.21 1 -0.25 2 3
ACSS2 -0.013 0.015 -10000 0 -0.25 2 2
SIRT1/PCAF/MYOD 0.022 0.037 0.21 2 -0.22 9 11
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.021 -10000 0 -0.16 1 1
TRAF2/ASK1 0.028 0.013 -10000 0 -0.2 1 1
ATM 0.022 0.005 -10000 0 -10000 0 0
MAP2K3 -0.002 0.094 0.26 1 -0.34 25 26
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.006 0.088 0.28 3 -0.34 19 22
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.013 0.055 -10000 0 -0.35 12 12
TXN 0.005 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
GADD45A 0.023 0.002 -10000 0 -10000 0 0
GADD45B 0.021 0.006 -10000 0 -10000 0 0
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
MAP3K6 0.022 0.004 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
MAP3K4 0.022 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.014 -10000 0 -0.24 1 1
TAK1/TAB family 0.001 0.024 0.14 2 -0.15 4 6
RAC1/OSM/MEKK3 0.04 0.013 -10000 0 -10000 0 0
TRAF2 0.022 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.015 0.079 -10000 0 -0.31 17 17
TRAF6 0.005 0.001 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.064 0.097 0.28 86 -0.35 1 87
CCM2 0.023 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.052 0.057 0.19 77 -0.2 1 78
MAPK11 0.019 0.024 -10000 0 -0.35 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.063 0.057 0.19 79 -0.19 2 81
OSM/MEKK3 0.032 0.01 -10000 0 -10000 0 0
TAOK1 0.009 0.012 -10000 0 -0.26 1 1
TAOK2 0.01 0.003 -10000 0 -10000 0 0
TAOK3 0.01 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.016 -10000 0 -0.35 1 1
MAP3K10 0.022 0.005 -10000 0 -10000 0 0
MAP3K3 0.022 0.006 -10000 0 -10000 0 0
TRX/ASK1 0.013 0.029 -10000 0 -0.1 32 32
GADD45/MTK1/MTK1 0.043 0.037 -10000 0 -0.18 11 11
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.034 -10000 0 -0.19 7 7
HDAC3 0.023 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.012 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.031 0.007 -10000 0 -10000 0 0
GATA1/HDAC5 0.03 0.009 -10000 0 -10000 0 0
GATA2/HDAC5 0.007 0.079 -10000 0 -0.24 48 48
HDAC5/BCL6/BCoR 0.039 0.02 -10000 0 -0.21 1 1
HDAC9 0.016 0.048 -10000 0 -0.35 9 9
Glucocorticoid receptor/Hsp90/HDAC6 0.007 0.089 -10000 0 -0.21 77 77
HDAC4/ANKRA2 0.032 0.015 -10000 0 -0.24 1 1
HDAC5/YWHAB 0.031 0.011 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.003 -10000 0 -10000 0 0
GATA2 -0.011 0.11 -10000 0 -0.35 48 48
HDAC4/RFXANK 0.033 0.017 0.22 3 -10000 0 3
BCOR 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.021 0.007 -10000 0 -10000 0 0
HDAC5 0.022 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.037 0.21 1 -0.24 9 10
Histones 0.004 0.058 -10000 0 -0.29 6 6
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.023 0.004 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.015 -10000 0 -0.24 1 1
HDAC4/Ubc9 0.032 0.009 -10000 0 -10000 0 0
HDAC7 0.022 0.005 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.031 0.011 -10000 0 -10000 0 0
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
HDAC6 0.023 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.032 0.015 0.21 2 -10000 0 2
CAMK4 0.023 0.038 0.28 5 -0.35 3 8
Tubulin/HDAC6 0.045 0.02 0.2 3 -0.21 1 4
SUMO1 0.023 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.022 0.005 -10000 0 -10000 0 0
GATA1 0.019 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.021 0.007 -10000 0 -10000 0 0
NR3C1 -0.031 0.13 -10000 0 -0.35 77 77
SUMO1/HDAC4 0.024 0.044 -10000 0 -0.19 12 12
SRF 0.022 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.032 0.009 -10000 0 -10000 0 0
Tubulin 0.033 0.023 0.21 3 -0.24 2 5
HDAC4/14-3-3 E 0.031 0.01 -10000 0 -10000 0 0
GNB1 0.022 0.004 -10000 0 -10000 0 0
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.03 0.016 -10000 0 -0.24 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.044 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.044 0.024 0.2 4 -0.21 2 6
HDAC4/ER alpha 0.003 0.085 -10000 0 -0.24 55 55
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.005 0.058 -10000 0 -0.29 6 6
cell motility 0.044 0.02 0.2 3 -0.21 1 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
HDAC7/HDAC3 0.032 0.009 -10000 0 -10000 0 0
BCL6 0.02 0.017 -10000 0 -0.35 1 1
HDAC4/CaMK II delta B 0.023 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.032 0.008 -10000 0 -10000 0 0
ESR1 -0.017 0.11 -10000 0 -0.35 55 55
HDAC6/HDAC11 0.032 0.009 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.042 -10000 0 -0.17 11 11
NPC 0.014 0.001 -10000 0 -10000 0 0
MEF2C -0.011 0.11 -10000 0 -0.35 47 47
RAN 0.023 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.041 0.07 -10000 0 -0.18 45 45
GNG2 0.017 0.049 0.28 1 -0.35 9 10
NCOR2 0.023 0.004 -10000 0 -10000 0 0
TUBB2A 0.022 0.03 0.28 3 -0.35 2 5
HDAC11 0.023 0.014 0.33 1 -10000 0 1
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.017 -10000 0 -0.35 1 1
RFXANK 0.024 0.021 0.3 3 -10000 0 3
nuclear import -0.025 0.01 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.02 0.029 -10000 0 -10000 0 0
DAPP1 0.022 0.081 0.24 16 -0.36 7 23
Src family/SYK family/BLNK-LAT/BTK-ITK 0.016 0.11 0.31 4 -0.46 12 16
mol:DAG 0.013 0.06 0.22 21 -0.18 2 23
HRAS 0.023 0.007 -10000 0 -10000 0 0
RAP1A 0.024 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.011 0.072 -10000 0 -0.24 23 23
PLCG2 0.02 0.021 0.28 1 -0.35 1 2
PLCG1 0.022 0.005 -10000 0 -10000 0 0
ARF5 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.017 0.026 0.14 12 -10000 0 12
ARF1/GTP -0.007 0.027 0.23 1 -10000 0 1
RHOA 0.022 0.005 -10000 0 -10000 0 0
YES1 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.017 0.028 0.15 12 -10000 0 12
ADAP1 -0.018 0.025 0.14 3 -10000 0 3
ARAP3 -0.017 0.026 0.14 12 -10000 0 12
INPPL1 0.023 0.003 -10000 0 -10000 0 0
PREX1 0.022 0.005 -10000 0 -10000 0 0
ARHGEF6 0.015 0.055 -10000 0 -0.35 12 12
ARHGEF7 0.022 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.008 -10000 0 -10000 0 0
NRAS 0.024 0.005 -10000 0 -10000 0 0
FYN 0.023 0.004 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
FGR 0.015 0.053 -10000 0 -0.35 11 11
mol:Ca2+ 0.009 0.051 0.18 28 -10000 0 28
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
ZAP70 0.029 0.05 0.28 16 -0.35 2 18
mol:IP3 0.009 0.062 0.21 29 -0.15 1 30
LYN 0.021 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.008 0.07 0.2 1 -0.24 22 23
RhoA/GDP 0.018 0.046 0.23 4 -0.22 1 5
PDK1/Src/Hsp90 0.042 0.015 -10000 0 -10000 0 0
BLNK 0.021 0.026 0.28 1 -0.35 2 3
actin cytoskeleton reorganization 0.003 0.066 0.26 11 -0.28 6 17
SRC 0.022 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.012 0.01 -10000 0 -0.21 1 1
RAC1 0.022 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.01 -10000 0 -10000 0 0
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.02 0.03 -10000 0 -10000 0 0
RhoA/GTP -0.018 0.027 0.15 12 -10000 0 12
Src family/SYK family/BLNK-LAT 0.019 0.06 0.21 4 -0.29 7 11
BLK 0.037 0.067 0.28 37 -10000 0 37
PDPK1 0.022 0.005 -10000 0 -10000 0 0
CYTH1 -0.018 0.027 0.14 3 -10000 0 3
HCK 0.025 0.03 0.28 7 -10000 0 7
CYTH3 -0.019 0.025 0.14 3 -10000 0 3
CYTH2 -0.019 0.026 0.14 3 -10000 0 3
KRAS 0.023 0.014 0.3 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.006 0.035 -10000 0 -0.36 2 2
SGK1 0.011 0.037 -10000 0 -0.38 2 2
INPP5D 0.022 0.016 -10000 0 -0.35 1 1
mol:GDP -0.001 0.072 0.18 5 -0.24 25 30
SOS1 0.023 0.003 -10000 0 -10000 0 0
SYK 0.022 0.012 0.28 1 -10000 0 1
ARF6/GDP -0.012 0.043 0.22 4 -0.22 1 5
mol:PI-3-4-5-P3 -0.017 0.026 0.15 2 -10000 0 2
ARAP3/RAP1A/GTP -0.017 0.028 0.16 12 -10000 0 12
VAV1 0.023 0.03 0.28 5 -0.35 1 6
mol:PI-3-4-P2 -0.012 0.01 -10000 0 -0.24 1 1
RAS family/GTP/PI3K Class I 0.034 0.031 0.22 4 -0.15 1 5
PLEKHA1 -0.013 0.009 -10000 0 -0.21 1 1
Rac1/GDP 0.011 0.072 -10000 0 -0.25 20 20
LAT 0.022 0.005 -10000 0 -10000 0 0
Rac1/GTP 0 0.08 -10000 0 -0.29 30 30
ITK -0.023 0.033 0.14 1 -0.18 11 12
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.013 0.068 0.27 13 -0.25 2 15
LCK 0.024 0.028 0.28 4 -0.35 1 5
BTK -0.02 0.028 0.14 3 -0.18 2 5
Arf6 trafficking events

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
SLC2A4 -0.16 0.18 -10000 0 -0.35 252 252
CLTC 0.01 0.065 -10000 0 -0.47 8 8
calcium ion-dependent exocytosis 0.007 0.031 -10000 0 -0.26 4 4
Dynamin 2/GTP 0.019 0.007 -10000 0 -10000 0 0
EXOC4 0.022 0.005 -10000 0 -10000 0 0
CD59 0.005 0.046 -10000 0 -0.38 7 7
CPE -0.011 0.063 -10000 0 -0.2 52 52
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
membrane fusion 0.009 0.015 -10000 0 -10000 0 0
CTNND1 -0.009 0.028 0.18 11 -10000 0 11
DNM2 0.021 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.046 0.18 2 -0.38 4 6
TSHR 0.008 0.031 0.14 19 -0.2 3 22
INS -0.01 0.11 -10000 0 -0.48 24 24
BIN1 0.02 0.032 -10000 0 -0.35 4 4
mol:Choline 0.009 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.003 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.007 -10000 0 -10000 0 0
JUP 0.006 0.041 -10000 0 -0.39 5 5
ASAP2/amphiphysin II 0.04 0.021 -10000 0 -0.19 3 3
ARF6/GTP 0.017 0.003 -10000 0 -10000 0 0
CDH1 0.005 0.041 -10000 0 -0.39 5 5
clathrin-independent pinocytosis 0.017 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.005 -10000 0 -10000 0 0
positive regulation of endocytosis 0.017 0.003 -10000 0 -10000 0 0
EXOC2 0.022 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.01 0.038 -10000 0 -0.3 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.027 0.047 0.36 4 -10000 0 4
positive regulation of phagocytosis 0.01 0.002 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.029 0.008 -10000 0 -10000 0 0
ACAP1 0.01 0.031 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.006 0.04 -10000 0 -0.35 6 6
clathrin heavy chain/ACAP1 0.011 0.056 -10000 0 -0.38 7 7
JIP4/KLC1 0.04 0.013 -10000 0 -10000 0 0
EXOC1 0.023 0.003 -10000 0 -10000 0 0
exocyst 0.01 0.038 -10000 0 -0.3 3 3
RALA/GTP 0.017 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.008 -10000 0 -10000 0 0
receptor recycling 0.017 0.003 -10000 0 -10000 0 0
CTNNA1 -0.01 0.025 0.18 9 -10000 0 9
NME1 0.009 0.003 -10000 0 -10000 0 0
clathrin coat assembly 0.01 0.07 0.26 1 -0.47 8 9
IL2RA 0.008 0.048 -10000 0 -0.36 7 7
VAMP3 0.01 0.002 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.057 0.094 -10000 0 -0.38 9 9
EXOC6 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.008 0.007 -10000 0 -10000 0 0
PLD2 0.009 0.005 -10000 0 -10000 0 0
EXOC5 0.022 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.038 -10000 0 -0.5 2 2
SDC1 0.019 0.044 -10000 0 -0.35 5 5
ARF6/GDP 0.019 0.005 -10000 0 -10000 0 0
EXOC7 0.022 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.029 0.049 -10000 0 -0.37 4 4
mol:Phosphatidic acid 0.009 0.015 -10000 0 -10000 0 0
endocytosis -0.039 0.02 0.18 3 -10000 0 3
SCAMP2 0.022 0.005 -10000 0 -10000 0 0
ADRB2 -0.019 0.087 0.3 1 -0.44 9 10
EXOC3 0.022 0.006 -10000 0 -10000 0 0
ASAP2 0.022 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.022 0.008 -10000 0 -10000 0 0
KLC1 0.022 0.004 -10000 0 -10000 0 0
AVPR2 -0.038 0.1 0.24 3 -0.44 10 13
RALA 0.022 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.048 0.32 1 -0.35 4 5
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.057 0.071 0.23 2 -0.25 5 7
Ran/GTP/Exportin 1/HDAC1 -0.012 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.061 -10000 0 -0.28 7 7
SUMO1 0.023 0.003 -10000 0 -10000 0 0
ZFPM1 0.02 0.018 -10000 0 -0.35 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.003 -10000 0 -10000 0 0
FKBP3 0.023 0.004 -10000 0 -10000 0 0
Histones 0.055 0.038 -10000 0 -10000 0 0
YY1/LSF 0.007 0.069 -10000 0 -0.23 32 32
SMG5 0.019 0.009 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.029 0.17 7 -0.19 2 9
I kappa B alpha/HDAC1 0.032 0.034 -10000 0 -10000 0 0
SAP18 0.022 0.005 -10000 0 -10000 0 0
RELA 0.025 0.035 0.19 7 -0.17 2 9
HDAC1/Smad7 0.042 0.021 -10000 0 -0.21 2 2
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.033 0.036 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.026 0.042 -10000 0 -0.35 1 1
NF kappa B1 p50/RelA 0.022 0.071 0.23 1 -0.29 13 14
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.011 0.11 -10000 0 -0.35 48 48
GATA1 0.019 0.005 -10000 0 -10000 0 0
Mad/Max 0.033 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.072 -10000 0 -0.35 7 7
RBBP7 0.023 0.003 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
RBBP4 0.02 0.028 -10000 0 -0.35 3 3
MAX 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.022 0.004 -10000 0 -10000 0 0
NFKBIA 0.021 0.022 0.15 2 -10000 0 2
KAT2B 0.017 0.045 -10000 0 -0.35 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.012 0.028 -10000 0 -10000 0 0
SIN3 complex 0.052 0.021 -10000 0 -10000 0 0
SMURF1 0.022 0.004 -10000 0 -10000 0 0
CHD3 0.021 0.006 -10000 0 -10000 0 0
SAP30 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.021 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.014 0.058 -10000 0 -0.29 7 7
YY1/HDAC2 0.009 0.065 -10000 0 -0.22 28 28
YY1/HDAC1 0.012 0.061 -10000 0 -0.22 25 25
NuRD/MBD2 Complex (MeCP1) 0.027 0.044 -10000 0 -0.3 2 2
PPARG 0.011 0.071 0.19 5 -0.26 25 30
HDAC8/hEST1B 0.036 0.02 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.022 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.032 0.035 -10000 0 -10000 0 0
MBD3L2 0.016 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.041 0.02 -10000 0 -0.21 2 2
CREBBP 0.022 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.02 0.068 -10000 0 -0.29 13 13
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC3 0.022 0.022 -10000 0 -10000 0 0
HDAC2 0.023 0.003 -10000 0 -10000 0 0
YY1 0.01 0.025 -10000 0 -0.22 6 6
HDAC8 0.023 0.002 -10000 0 -10000 0 0
SMAD7 0.021 0.023 -10000 0 -0.35 2 2
NCOR2 0.023 0.004 -10000 0 -10000 0 0
MXD1 0.023 0.004 -10000 0 -10000 0 0
STAT3 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.017 -10000 0 -0.35 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.065 -10000 0 -0.21 24 24
YY1/SAP30/HDAC1 0.024 0.061 -10000 0 -0.2 23 23
EP300 0.021 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.014 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.022 0.15 2 -10000 0 2
histone deacetylation 0.027 0.043 -10000 0 -0.3 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.022 0.031 -10000 0 -0.24 1 1
nuclear export -0.035 0.02 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GATAD2B 0.019 0.009 -10000 0 -10000 0 0
GATAD2A 0.022 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.013 0.069 -10000 0 -0.29 5 5
GATA1/HDAC1 0.03 0.008 -10000 0 -10000 0 0
GATA1/HDAC3 0.029 0.036 -10000 0 -10000 0 0
CHD4 0.022 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.052 0.06 0.21 61 -0.24 2 63
SIN3/HDAC complex/Mad/Max 0.016 0.048 -10000 0 -0.32 5 5
NuRD Complex 0.023 0.064 -10000 0 -0.32 8 8
positive regulation of chromatin silencing 0.052 0.036 -10000 0 -10000 0 0
SIN3B 0.022 0.006 -10000 0 -10000 0 0
MTA2 0.023 0.003 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
XPO1 0.023 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.025 0.041 -10000 0 -0.19 10 10
HDAC complex 0.054 0.024 -10000 0 -0.19 3 3
GATA1/Fog1 0.027 0.017 -10000 0 -0.25 1 1
FKBP25/HDAC1/HDAC2 0.044 0.012 -10000 0 -10000 0 0
TNF 0.053 0.088 0.28 65 -0.35 2 67
negative regulation of cell growth 0.016 0.047 -10000 0 -0.32 5 5
NuRD/MBD2/PRMT5 Complex 0.027 0.044 -10000 0 -0.3 2 2
Ran/GTP/Exportin 1 0.026 0.042 -10000 0 -0.17 11 11
NF kappa B/RelA/I kappa B alpha 0.02 0.055 0.18 6 -0.28 8 14
SIN3/HDAC complex/NCoR1 0.006 0.065 -10000 0 -0.4 8 8
TFCP2 0.019 0.039 -10000 0 -0.35 6 6
NR2C1 0.023 0.002 -10000 0 -10000 0 0
MBD3 0.021 0.006 -10000 0 -10000 0 0
MBD2 0.022 0.004 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.037 0.33 3 -0.35 3 6
positive regulation of NF-kappaB transcription factor activity 0.022 0.046 0.24 3 -0.24 12 15
MAP2K4 0.006 0.04 0.24 1 -0.24 6 7
IKBKB 0.021 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.02 0.008 -10000 0 -10000 0 0
SMPD1 0.008 0.015 0.15 3 -0.15 2 5
IKBKG 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.012 0.053 -10000 0 -0.35 11 11
TRAIL/TRAILR2 0.027 0.027 0.24 3 -0.24 2 5
TRAIL/TRAILR3 0.027 0.029 0.24 3 -0.24 3 6
TRAIL/TRAILR1 0.027 0.027 0.24 3 -0.24 2 5
TRAIL/TRAILR4 0.022 0.046 0.24 3 -0.24 12 15
TRAIL/TRAILR1/DAP3/GTP 0.028 0.028 0.22 2 -0.19 2 4
IKK complex 0.012 0.032 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.007 -10000 0 -10000 0 0
MAPK3 -0.01 0.029 0.3 3 -0.24 3 6
MAP3K1 0.012 0.038 0.26 1 -0.21 6 7
TRAILR4 (trimer) 0.012 0.053 -10000 0 -0.35 11 11
TRADD 0.02 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.02 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.013 0.027 0.17 1 -0.17 9 10
CFLAR 0.023 0.003 -10000 0 -10000 0 0
MAPK1 -0.01 0.026 0.3 2 -0.24 3 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.049 0.036 0.23 2 -0.18 2 4
mol:ceramide 0.008 0.015 0.15 3 -0.15 2 5
FADD 0.022 0.004 -10000 0 -10000 0 0
MAPK8 0.009 0.052 0.22 1 -0.26 4 5
TRAF2 0.022 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.018 -10000 0 -0.35 1 1
CHUK 0.022 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.036 0.028 0.23 2 -0.21 2 4
DAP3 0.018 0.009 -10000 0 -10000 0 0
CASP10 0.009 0.057 0.17 48 -0.36 2 50
JNK cascade 0.022 0.046 0.24 3 -0.24 12 15
TRAIL (trimer) 0.02 0.037 0.33 3 -0.35 3 6
TNFRSF10C 0.019 0.018 -10000 0 -0.35 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.031 0.22 1 -0.18 2 3
TRAIL/TRAILR2/FADD 0.036 0.028 0.23 2 -0.21 2 4
cell death 0.008 0.015 0.15 3 -0.15 2 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.027 0.17 1 -0.17 9 10
TRAILR2 (trimer) 0.02 0.008 -10000 0 -10000 0 0
CASP8 0.012 0.039 -10000 0 -0.54 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.049 0.036 0.23 2 -0.18 2 4
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.016 0.24 2 -10000 0 2
SNTA1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.017 0.24 2 -10000 0 2
MAPK12 -0.003 0.014 0.2 1 -0.18 1 2
CCND1 0.007 0.03 0.18 1 -0.33 3 4
p38 gamma/SNTA1 0.019 0.035 0.21 13 -0.17 1 14
MAP2K3 0.021 0.006 -10000 0 -10000 0 0
PKN1 0.022 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint -0.003 0.014 0.2 1 -0.18 1 2
MAP2K6 0.001 0.015 0.24 1 -10000 0 1
MAPT -0.003 0.062 0.18 8 -0.24 25 33
MAPK13 -0.008 0.022 0.17 6 -10000 0 6
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.001 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.022 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.012 -10000 0 -10000 0 0
DOCK1 0.017 0.043 -10000 0 -0.35 7 7
ITGA4 0.022 0.026 0.28 1 -0.35 2 3
RAC1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.033 0.017 0.21 2 -0.24 1 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.022 0.2 1 -0.21 2 3
alpha4/beta7 Integrin/Paxillin 0.034 0.018 0.19 2 -0.19 1 3
lamellipodium assembly -0.007 0.093 -10000 0 -0.39 23 23
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
PI3K 0.026 0.029 -10000 0 -0.24 5 5
ARF6 0.023 0.003 -10000 0 -10000 0 0
TLN1 0.022 0.005 -10000 0 -10000 0 0
PXN -0.011 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
ARF6/GTP 0.041 0.023 -10000 0 -0.17 2 2
cell adhesion 0.041 0.023 0.19 1 -0.18 2 3
CRKL/CBL 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.032 0.019 0.19 1 -0.19 2 3
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.023 0.012 0.28 1 -10000 0 1
ARF6/GDP 0.021 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.03 0.06 0.2 1 -0.19 33 34
p130Cas/Crk/Dock1 0.035 0.033 -10000 0 -0.21 7 7
VCAM1 -0.004 0.097 -10000 0 -0.35 39 39
alpha4/beta1 Integrin/Paxillin/Talin 0.042 0.024 0.2 1 -0.18 2 3
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.023 0.2 1 -0.18 2 3
BCAR1 0.02 0.008 -10000 0 -10000 0 0
mol:GDP -0.041 0.023 0.18 2 -0.19 1 3
CBL 0.022 0.005 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.022 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.042 0.024 0.2 1 -0.18 2 3
Rac1/GTP -0.009 0.1 -10000 0 -0.44 23 23
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.008 0.002 -10000 0 -10000 0 0
mol:DAG -0.011 0.013 0.18 2 -10000 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.01 -10000 0 -10000 0 0
HIF1A 0.026 0.005 -10000 0 -10000 0 0
GAB1 0.019 0.032 -10000 0 -0.35 4 4
AKT1 0.002 0.054 0.48 1 -10000 0 1
PLCG1 -0.011 0.013 0.18 2 -10000 0 2
NOS3 0.014 0.049 0.43 2 -0.35 1 3
CBL 0.022 0.005 -10000 0 -10000 0 0
mol:NO 0.02 0.065 0.36 8 -0.34 1 9
FLT1 0.011 0.003 -10000 0 -10000 0 0
PGF 0.023 0.012 0.28 1 -10000 0 1
VEGFR1 homodimer/NRP2/VEGFR121 0.026 0.047 -10000 0 -0.19 20 20
CALM1 0.022 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
eNOS/Hsp90 0.027 0.057 0.28 4 -0.32 1 5
endothelial cell proliferation -0.009 0.065 0.32 4 -0.28 4 8
mol:Ca2+ -0.011 0.013 0.18 2 -10000 0 2
MAPK3 -0.02 0.047 0.31 5 -10000 0 5
MAPK1 -0.02 0.047 0.31 5 -10000 0 5
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
PLGF homodimer 0.023 0.012 0.28 1 -10000 0 1
PRKACA 0.022 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.04 0.14 -10000 0 -0.35 89 89
VEGFA homodimer 0.023 0.003 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.021 0.045 0.33 4 -10000 0 4
PI3K 0.04 0.03 -10000 0 -0.18 4 4
PRKCA -0.021 0.037 0.17 1 -10000 0 1
PRKCB -0.021 0.038 0.17 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer 0.024 0.011 -10000 0 -10000 0 0
VEGFA 0.023 0.003 -10000 0 -10000 0 0
VEGFB 0.022 0.004 -10000 0 -10000 0 0
mol:IP3 -0.011 0.013 0.18 2 -10000 0 2
RASA1 -0.012 0.025 0.18 4 -10000 0 4
NRP2 0.006 0.077 -10000 0 -0.35 24 24
VEGFR1 homodimer 0.011 0.003 -10000 0 -10000 0 0
VEGFB homodimer 0.022 0.004 -10000 0 -10000 0 0
NCK1 0.021 0.023 -10000 0 -0.35 2 2
eNOS/Caveolin-1 0.003 0.088 0.41 5 -0.28 5 10
PTPN11 0.023 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.03 -10000 0 -0.18 4 4
mol:L-citrulline 0.02 0.065 0.36 8 -0.34 1 9
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.046 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.034 0.019 -10000 0 -0.19 2 2
CD2AP 0.023 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.047 0.036 -10000 0 -10000 0 0
PDPK1 -0.002 0.054 0.33 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.036 0.012 -10000 0 -10000 0 0
mol:NADP 0.02 0.065 0.36 8 -0.34 1 9
HSP90AA1 0.022 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.014 0.047 -10000 0 -0.2 24 24
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD2 0.002 0.042 0.25 4 -0.27 3 7
SMAD3 0.013 0.025 -10000 0 -0.25 1 1
SMAD3/SMAD4 0.019 0.094 -10000 0 -0.48 16 16
SMAD4/Ubc9/PIASy 0.041 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.053 0.27 1 -0.28 1 2
PPM1A 0.022 0.004 -10000 0 -10000 0 0
CALM1 0.022 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.014 0.041 0.22 3 -0.24 4 7
MAP3K1 0.022 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.029 0.034 -10000 0 -0.24 8 8
MAPK3 0.022 0.005 -10000 0 -10000 0 0
MAPK1 0.022 0.005 -10000 0 -10000 0 0
NUP214 0.022 0.006 -10000 0 -10000 0 0
CTDSP1 0.023 0.004 -10000 0 -10000 0 0
CTDSP2 0.023 0.001 -10000 0 -10000 0 0
CTDSPL 0.022 0.004 -10000 0 -10000 0 0
KPNB1 0.022 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.017 0.045 -10000 0 -0.35 8 8
UBE2I 0.022 0.005 -10000 0 -10000 0 0
NUP153 0.022 0.017 -10000 0 -0.35 1 1
KPNA2 0.035 0.058 0.3 24 -10000 0 24
PIAS4 0.021 0.007 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.021 0.017 -10000 0 -0.35 1 1
PLK4 0.025 0.025 0.28 5 -10000 0 5
regulation of centriole replication -0.01 0.015 0.11 4 -0.24 1 5
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.015 0.019 -10000 0 -10000 0 0
regulation of axonogenesis -0.004 0.023 0.24 4 -10000 0 4
myoblast fusion -0.02 0.027 -10000 0 -10000 0 0
mol:GTP 0.016 0.023 -10000 0 -0.16 8 8
regulation of calcium-dependent cell-cell adhesion -0.037 0.042 0.19 12 -10000 0 12
ARF1/GTP 0.025 0.023 -10000 0 -10000 0 0
mol:GM1 0.007 0.016 -10000 0 -10000 0 0
mol:Choline 0.004 0.014 -10000 0 -0.19 1 1
lamellipodium assembly 0.007 0.05 -10000 0 -0.36 8 8
MAPK3 0.016 0.016 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.038 0.043 -10000 0 -0.19 12 12
ARF1 0.02 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.027 -10000 0 -10000 0 0
ARF1/GDP 0.018 0.039 -10000 0 -0.21 8 8
ARF6 0.029 0.009 -10000 0 -10000 0 0
RAB11A 0.022 0.005 -10000 0 -10000 0 0
TIAM1 0.013 0.058 -10000 0 -0.35 13 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.018 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.036 0.21 7 -10000 0 7
KALRN 0.009 0.022 -10000 0 -0.18 4 4
RAB11FIP3/RAB11A 0.032 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.036 -10000 0 -0.22 7 7
NME1 0.022 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.038 -10000 0 -0.22 8 8
substrate adhesion-dependent cell spreading 0.016 0.023 -10000 0 -0.16 8 8
cortical actin cytoskeleton organization 0.007 0.05 -10000 0 -0.36 8 8
RAC1 0.022 0.005 -10000 0 -10000 0 0
liver development 0.016 0.023 -10000 0 -0.16 8 8
ARF6/GTP 0.016 0.023 -10000 0 -0.16 8 8
RhoA/GTP 0.029 0.021 -10000 0 -10000 0 0
mol:GDP 0.009 0.028 -10000 0 -0.22 6 6
ARF6/GTP/RAB11FIP3/RAB11A 0.041 0.02 -10000 0 -10000 0 0
RHOA 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.013 0.017 -10000 0 -10000 0 0
RAB11FIP3 0.022 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.05 -10000 0 -0.36 8 8
ruffle organization 0.004 0.023 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.016 0.023 -10000 0 -0.16 8 8
PLD2 0.014 0.017 -10000 0 -0.21 1 1
PIP5K1A 0.004 0.023 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.004 0.014 -10000 0 -0.19 1 1
Rac1/GTP 0.007 0.051 -10000 0 -0.36 8 8
Arf1 pathway

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
coatomer protein complex 0.008 0.032 0.15 23 -10000 0 23
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.055 0.14 76 -0.18 6 82
AP2 0.03 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.026 0.014 -10000 0 -10000 0 0
CLTB 0.023 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.008 -10000 0 -10000 0 0
CD4 0.023 0.012 0.28 1 -10000 0 1
CLTA 0.022 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.01 -10000 0 -0.14 1 1
ARF1/GTP 0.021 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.005 0.004 -10000 0 -10000 0 0
mol:Choline 0.003 0.01 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.002 0.01 -10000 0 -0.15 1 1
ARF1/GDP 0.001 0.018 -10000 0 -0.092 11 11
AP2M1 0.021 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.004 0.011 -10000 0 -10000 0 0
Rac/GTP 0.019 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.025 0.016 -10000 0 -10000 0 0
ARFIP2 0.011 0.019 -10000 0 -10000 0 0
COPA 0.019 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.027 -10000 0 -0.24 1 1
ARF1/GTP/ARHGAP10 0.013 0.008 -10000 0 -10000 0 0
GGA3 0.022 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.008 0.046 -10000 0 -0.23 15 15
AP2A1 0.022 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.007 0.021 -10000 0 -0.22 3 3
ARF1/GDP/Membrin 0.009 0.055 -10000 0 -0.24 23 23
Arfaptin 2/Rac/GDP 0.021 0.018 -10000 0 -10000 0 0
CYTH2 0.027 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.025 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.016 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 0.011 0.019 -10000 0 -10000 0 0
PLD2 0.003 0.01 -10000 0 -0.14 1 1
ARF-GAP1/v-SNARE -0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.003 0.01 -10000 0 -0.14 1 1
ARF1/GTP/Membrin/GBF1/p115 0.011 0.021 -10000 0 -0.12 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.003 0.01 -10000 0 -0.14 1 1
KDEL Receptor/Ligand/ARF-GAP1 -0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.006 0.025 -10000 0 -0.32 3 3
USO1 0.005 0.029 -10000 0 -0.32 4 4
GBF1 0.004 0.034 -10000 0 -0.34 5 5
ARF1/GTP/Arfaptin 2 0.025 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.041 0.018 0.2 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.023 0.012 0.28 1 -10000 0 1
ITGA4 0.022 0.026 0.28 1 -0.35 2 3
alpha4/beta7 Integrin 0.033 0.017 0.21 2 -0.24 1 3
alpha4/beta1 Integrin 0.032 0.02 0.21 1 -0.24 2 3
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.013 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.024 0.045 -10000 0 -0.19 12 12
HDAC4 0.023 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.013 0.009 -10000 0 -10000 0 0
SUMO1 0.023 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.007 0.014 -10000 0 -0.26 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0 0.02 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.024 0.044 -10000 0 -0.19 12 12
SUMO1/HDAC1 0.025 0.041 -10000 0 -0.19 10 10
RANGAP1 0.021 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.054 0.018 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.003 -10000 0 -10000 0 0
Ran/GTP 0.014 0.039 -10000 0 -0.17 12 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.002 -10000 0 -10000 0 0
UBE2I 0.022 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.013 0.041 0.18 5 -0.18 10 15
NPC 0.014 0.001 -10000 0 -10000 0 0
PIAS2 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.032 0.012 0.21 1 -10000 0 1
FBXW11 0.022 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.02 0.013 -10000 0 -0.21 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.023 0.035 0.19 5 -0.24 1 6
NFKBIA 0.012 0.023 -10000 0 -10000 0 0
MAPK14 0.023 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.02 0.013 -10000 0 -0.21 1 1
ARRB2 0.01 0.003 -10000 0 -10000 0 0
REL 0.023 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.019 0.015 0.2 1 -0.21 1 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.019 0.013 -10000 0 -0.21 1 1
PIK3CA 0.02 0.018 -10000 0 -0.35 1 1
NF kappa B1 p50 dimer 0.014 0.016 0.24 1 -0.24 1 2
PIK3R1 0.018 0.036 -10000 0 -0.35 5 5
NFKB1 -0.011 0.011 -10000 0 -0.24 1 1
RELA 0.022 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.017 0.032 -10000 0 -0.25 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.022 0.035 -10000 0 -0.19 2 2
SRC 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.026 0.029 -10000 0 -0.24 5 5
NF kappa B1 p50/RelA 0.017 0.032 -10000 0 -0.25 2 2
IKBKB 0.021 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -10000 0 -10000 0 0
SYK 0.022 0.012 0.28 1 -10000 0 1
I kappa B alpha/PIK3R1 0.022 0.044 0.2 6 -0.2 5 11
cell death 0.021 0.034 -10000 0 -0.18 2 2
NF kappa B1 p105/c-Rel 0.02 0.013 -10000 0 -0.21 1 1
LCK 0.024 0.028 0.28 4 -0.35 1 5
BCL3 0.023 0.012 0.28 1 -10000 0 1
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 0.038 0.028 -9999 0 -0.3 2 2
E-cadherin/beta catenin 0.028 0.021 -9999 0 -0.24 2 2
CTNNB1 0.022 0.004 -9999 0 -10000 0 0
JUP 0.021 0.017 -9999 0 -0.35 1 1
CDH1 0.019 0.024 -9999 0 -0.35 2 2
Circadian rhythm 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
chromatin modification 0.039 0.019 -10000 0 -10000 0 0
CLOCK 0.024 0.003 -10000 0 -10000 0 0
TIMELESS/CRY2 0.029 0.019 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.015 -10000 0 -0.25 1 1
ATR 0.022 0.004 -10000 0 -10000 0 0
NR1D1 0.013 0.01 -10000 0 -10000 0 0
ARNTL 0.023 0.017 -10000 0 -0.35 1 1
TIMELESS 0.014 0.016 -10000 0 -10000 0 0
NPAS2 0.021 0.036 -10000 0 -0.35 5 5
CRY2 0.022 0.004 -10000 0 -10000 0 0
mol:CO -0.006 0.004 -10000 0 -0.069 2 2
CHEK1 0.022 0.005 -10000 0 -10000 0 0
mol:HEME 0.006 0.004 0.069 2 -10000 0 2
PER1 0.02 0.017 -10000 0 -0.35 1 1
BMAL/CLOCK/NPAS2 0.048 0.028 -10000 0 -0.2 5 5
BMAL1/CLOCK 0.013 0.051 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.039 0.019 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.039 0.02 -10000 0 -10000 0 0
mol:NADPH 0.006 0.004 0.069 2 -10000 0 2
PER1/TIMELESS 0.026 0.02 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.016 0.005 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.031 0.01 -9999 0 -10000 0 0
FBXW11 0.022 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.004 -9999 0 -10000 0 0
CHUK 0.022 0.005 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.059 0.025 -9999 0 -10000 0 0
NFKB1 0.022 0.017 -9999 0 -0.35 1 1
MAP3K14 0.022 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.031 0.015 -9999 0 -0.24 1 1
RELB 0.022 0.005 -9999 0 -10000 0 0
NFKB2 0.022 0.005 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.029 0.009 -9999 0 -10000 0 0
regulation of B cell activation 0.028 0.009 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 530 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.SL.A6JA TCGA.SL.A6J9 TCGA.SJ.A6ZJ TCGA.SJ.A6ZI
109_MAP3K5 -0.14 0.019 0.019 0.019
47_PPARGC1A -0.35 0.023 0.023 -0.35
105_BMP4 0.023 -0.35 0.023 0.023
105_BMP6 0.023 0.023 0.023 0.023
105_BMP7 0.023 0 0.023 0.023
105_BMP2 0.023 -0.35 0.023 0.023
131_RELN/VLDLR -0.19 0 0.06 -0.19
30_TGFB1/TGF beta receptor Type II 0.023 0.023 0.02 0.023
84_STAT5B -0.031 0.029 -0.031 0.024
84_STAT5A -0.031 0.029 -0.031 0.024
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/UCEC-TP/11493814/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/UCEC-TP/11541760/GDAC_Gistic2Report_11548410/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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