PARADIGM pathway analysis of mRNASeq expression and copy number data
Prostate Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1C24V6Q
Maintained by Dan DiCara (Broad Institute)
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/C1C24V6Q
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 52 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
Angiopoietin receptor Tie2-mediated signaling 66
Ephrin A reverse signaling 65
Signaling mediated by p38-alpha and p38-beta 64
Glypican 2 network 63
Endothelins 57
Nephrin/Neph1 signaling in the kidney podocyte 47
Glucocorticoid receptor regulatory network 47
Aurora B signaling 40
Integrins in angiogenesis 39
IL23-mediated signaling events 39
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 374 . 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 ( 374 ).

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
Angiopoietin receptor Tie2-mediated signaling 0.1765 66 5868 88 -0.29 0.062 1000 -1000 -0.054 -1000
Ephrin A reverse signaling 0.1738 65 460 7 -0.041 0 1000 -1000 -0.004 -1000
Signaling mediated by p38-alpha and p38-beta 0.1711 64 2844 44 -0.16 0.028 1000 -1000 -0.018 -1000
Glypican 2 network 0.1684 63 253 4 -0.023 -0.003 1000 -1000 0.013 -1000
Endothelins 0.1524 57 5565 96 -0.18 0.028 1000 -1000 -0.04 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1257 47 1619 34 -0.044 0.028 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 0.1257 47 5428 114 -0.42 0.24 1000 -1000 -0.046 -1000
Aurora B signaling 0.1070 40 2708 67 -0.11 0.047 1000 -1000 -0.027 -1000
Integrins in angiogenesis 0.1043 39 3309 84 -0.099 0.052 1000 -1000 -0.026 -1000
IL23-mediated signaling events 0.1043 39 2379 60 -0.34 0.04 1000 -1000 -0.089 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1043 39 3042 78 -0.13 0.089 1000 -1000 -0.035 -1000
Thromboxane A2 receptor signaling 0.0963 36 3876 105 -0.12 0.035 1000 -1000 -0.031 -1000
Reelin signaling pathway 0.0963 36 2044 56 -0.099 0.067 1000 -1000 -0.027 -1000
Aurora C signaling 0.0856 32 228 7 -0.049 0.025 1000 -1000 -0.005 -1000
S1P5 pathway 0.0829 31 532 17 -0.038 0.035 1000 -1000 -0.001 -1000
LPA receptor mediated events 0.0829 31 3230 102 -0.11 0.036 1000 -1000 -0.057 -1000
Signaling events mediated by the Hedgehog family 0.0802 30 1569 52 -0.028 0.036 1000 -1000 -0.023 -1000
Noncanonical Wnt signaling pathway 0.0802 30 801 26 -0.042 0.028 1000 -1000 -0.027 -1000
Ras signaling in the CD4+ TCR pathway 0.0802 30 523 17 -0.07 0.045 1000 -1000 -0.014 -1000
IL6-mediated signaling events 0.0775 29 2242 75 -0.18 0.036 1000 -1000 -0.04 -1000
p75(NTR)-mediated signaling 0.0749 28 3525 125 -0.075 0.075 1000 -1000 -0.047 -1000
Glypican 1 network 0.0749 28 1350 48 -0.069 0.048 1000 -1000 -0.015 -1000
amb2 Integrin signaling 0.0749 28 2351 82 -0.13 0.036 1000 -1000 -0.02 -1000
S1P1 pathway 0.0749 28 1028 36 -0.19 0.028 1000 -1000 -0.029 -1000
EPHB forward signaling 0.0749 28 2433 85 -0.064 0.093 1000 -1000 -0.043 -1000
Wnt signaling 0.0749 28 196 7 -0.04 0.023 1000 -1000 -0.005 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0749 28 1946 68 -0.18 0.059 1000 -1000 -0.059 -1000
EGFR-dependent Endothelin signaling events 0.0749 28 601 21 -0.029 0.045 1000 -1000 -0.028 -1000
Ephrin B reverse signaling 0.0722 27 1340 48 -0.063 0.032 1000 -1000 -0.024 -1000
Nongenotropic Androgen signaling 0.0722 27 1411 52 -0.1 0.051 1000 -1000 -0.022 -1000
FOXM1 transcription factor network 0.0722 27 1399 51 -0.18 0.028 1000 -1000 -0.1 -1000
Syndecan-1-mediated signaling events 0.0695 26 911 34 -0.11 0.028 1000 -1000 -0.022 -1000
Calcium signaling in the CD4+ TCR pathway 0.0695 26 815 31 -0.097 0.028 1000 -1000 -0.039 -1000
Osteopontin-mediated events 0.0642 24 921 38 -0.048 0.028 1000 -1000 -0.029 -1000
HIF-1-alpha transcription factor network 0.0642 24 1856 76 -0.095 0.059 1000 -1000 -0.074 -1000
IL4-mediated signaling events 0.0642 24 2206 91 -0.37 0.24 1000 -1000 -0.12 -1000
BMP receptor signaling 0.0642 24 2015 81 -0.08 0.066 1000 -1000 -0.025 -1000
S1P4 pathway 0.0642 24 601 25 -0.038 0.042 1000 -1000 -0.012 -1000
JNK signaling in the CD4+ TCR pathway 0.0615 23 398 17 -0.12 0.055 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 0.0615 23 1947 82 -0.034 0.038 1000 -1000 -0.039 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0615 23 2826 120 -0.085 0.073 1000 -1000 -0.044 -1000
Effects of Botulinum toxin 0.0588 22 592 26 -0.036 0.045 1000 -1000 -0.003 -1000
EPO signaling pathway 0.0561 21 1165 55 -0.023 0.05 1000 -1000 -0.023 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0561 21 1126 52 -0.051 0.073 1000 -1000 -0.03 -1000
Signaling events mediated by PRL 0.0561 21 729 34 -0.048 0.045 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 0.0535 20 778 38 -0.047 0.033 1000 -1000 -0.007 -1000
Arf6 signaling events 0.0535 20 1297 62 -0.043 0.045 1000 -1000 -0.037 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0508 19 1648 85 -0.12 0.037 1000 -1000 -0.04 -1000
TCGA08_p53 0.0508 19 138 7 -0.02 0.027 1000 -1000 -0.012 -1000
TCR signaling in naïve CD8+ T cells 0.0508 19 1822 93 -0.058 0.072 1000 -1000 -0.036 -1000
Plasma membrane estrogen receptor signaling 0.0508 19 1695 86 -0.12 0.056 1000 -1000 -0.036 -1000
Rapid glucocorticoid signaling 0.0508 19 386 20 -0.057 0.034 1000 -1000 -0.003 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0481 18 979 54 -0.099 0.067 1000 -1000 -0.019 -1000
Fc-epsilon receptor I signaling in mast cells 0.0481 18 1824 97 -0.074 0.044 1000 -1000 -0.042 -1000
PLK1 signaling events 0.0481 18 1610 85 -0.056 0.054 1000 -1000 -0.019 -1000
Presenilin action in Notch and Wnt signaling 0.0455 17 1096 61 -0.13 0.076 1000 -1000 -0.036 -1000
PDGFR-alpha signaling pathway 0.0455 17 783 44 -0.12 0.055 1000 -1000 -0.035 -1000
Canonical Wnt signaling pathway 0.0455 17 896 51 -0.13 0.098 1000 -1000 -0.026 -1000
Regulation of p38-alpha and p38-beta 0.0455 17 946 54 -0.099 0.063 1000 -1000 -0.035 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0455 17 2145 125 -0.052 0.053 1000 -1000 -0.028 -1000
ErbB2/ErbB3 signaling events 0.0428 16 1089 65 -0.079 0.039 1000 -1000 -0.065 -1000
BARD1 signaling events 0.0428 16 945 57 -0.029 0.047 1000 -1000 -0.039 -1000
a4b1 and a4b7 Integrin signaling 0.0428 16 83 5 0.01 0.027 1000 -1000 0.01 -1000
Signaling events mediated by PTP1B 0.0428 16 1234 76 -0.16 0.043 1000 -1000 -0.035 -1000
FAS signaling pathway (CD95) 0.0428 16 778 47 -0.24 0.045 1000 -1000 -0.036 -1000
IL27-mediated signaling events 0.0428 16 830 51 -0.34 0.069 1000 -1000 -0.05 -1000
IL12-mediated signaling events 0.0401 15 1311 87 -0.17 0.051 1000 -1000 -0.06 -1000
Syndecan-2-mediated signaling events 0.0401 15 1077 69 -0.01 0.043 1000 -1000 -0.036 -1000
BCR signaling pathway 0.0401 15 1487 99 -0.12 0.051 1000 -1000 -0.049 -1000
Visual signal transduction: Rods 0.0401 15 803 52 -0.047 0.052 1000 -1000 -0.023 -1000
Aurora A signaling 0.0374 14 885 60 -0.075 0.05 1000 -1000 -0.013 -1000
IGF1 pathway 0.0374 14 799 57 -0.011 0.062 1000 -1000 -0.029 -1000
Insulin Pathway 0.0374 14 1045 74 -0.13 0.072 1000 -1000 -0.035 -1000
S1P3 pathway 0.0374 14 619 42 -0.02 0.042 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 0.0348 13 511 39 -0.022 0.027 1000 -1000 -0.015 -1000
Nectin adhesion pathway 0.0348 13 832 63 -0.043 0.065 1000 -1000 -0.035 -1000
IL1-mediated signaling events 0.0348 13 844 62 -0.033 0.07 1000 -1000 -0.027 -1000
HIF-2-alpha transcription factor network 0.0348 13 589 43 -0.033 0.043 1000 -1000 -0.042 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0348 13 990 74 -0.13 0.054 1000 -1000 -0.044 -1000
TCGA08_retinoblastoma 0.0348 13 108 8 -0.02 0.032 1000 -1000 -0.002 -1000
Syndecan-4-mediated signaling events 0.0348 13 884 67 -0.1 0.032 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0348 13 451 33 -0.069 0.064 1000 -1000 -0.026 -1000
Caspase cascade in apoptosis 0.0321 12 902 74 -0.032 0.067 1000 -1000 -0.031 -1000
Regulation of nuclear SMAD2/3 signaling 0.0321 12 1716 136 -0.19 0.088 1000 -1000 -0.041 -1000
Coregulation of Androgen receptor activity 0.0321 12 950 76 -0.035 0.047 1000 -1000 -0.016 -1000
ErbB4 signaling events 0.0321 12 873 69 -0.083 0.061 1000 -1000 -0.033 -1000
FOXA2 and FOXA3 transcription factor networks 0.0321 12 578 46 -0.12 0.032 1000 -1000 -0.089 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0321 12 465 37 -0.016 0.059 1000 -1000 -0.026 -1000
LPA4-mediated signaling events 0.0294 11 140 12 -0.027 0.017 1000 -1000 -0.015 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0294 11 319 28 -0.025 0.054 1000 -1000 -0.008 -1000
mTOR signaling pathway 0.0294 11 627 53 -0.15 0.054 1000 -1000 -0.024 -1000
Ceramide signaling pathway 0.0294 11 891 76 -0.022 0.077 1000 -1000 -0.012 -1000
Regulation of Androgen receptor activity 0.0294 11 802 70 -0.076 0.047 1000 -1000 -0.04 -1000
Hedgehog signaling events mediated by Gli proteins 0.0267 10 662 65 -0.22 0.069 1000 -1000 -0.041 -1000
ceramide signaling pathway 0.0267 10 519 49 0 0.04 1000 -1000 -0.022 -1000
IL2 signaling events mediated by PI3K 0.0267 10 628 58 -0.047 0.056 1000 -1000 -0.022 -1000
Class I PI3K signaling events 0.0267 10 777 73 -0.043 0.064 1000 -1000 -0.025 -1000
Signaling mediated by p38-gamma and p38-delta 0.0241 9 135 15 -0.011 0.028 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 0.0241 9 575 58 -0.042 0.051 1000 -1000 -0.028 -1000
TCGA08_rtk_signaling 0.0241 9 259 26 -0.02 0.05 1000 -1000 -0.006 -1000
IL2 signaling events mediated by STAT5 0.0241 9 204 22 -0.019 0.028 1000 -1000 -0.023 -1000
VEGFR1 specific signals 0.0241 9 522 56 -0.052 0.043 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class III 0.0214 8 344 40 -0.06 0.052 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0214 8 390 45 -0.003 0.068 1000 -1000 -0.022 -1000
IFN-gamma pathway 0.0187 7 506 68 -0.03 0.075 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0187 7 476 68 -0.035 0.052 1000 -1000 -0.02 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0187 7 646 83 -0.045 0.052 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0187 7 259 36 -0.049 0.051 1000 -1000 -0.027 -1000
Syndecan-3-mediated signaling events 0.0187 7 276 35 -0.021 0.075 1000 -1000 -0.013 -1000
E-cadherin signaling in the nascent adherens junction 0.0187 7 600 76 -0.007 0.06 1000 -1000 -0.038 -1000
PDGFR-beta signaling pathway 0.0187 7 760 97 -0.11 0.071 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 0.0187 7 303 43 -0.014 0.047 1000 -1000 -0.02 -1000
Atypical NF-kappaB pathway 0.0160 6 215 31 -0.011 0.032 1000 -1000 -0.009 -1000
Regulation of Telomerase 0.0160 6 626 102 -0.08 0.055 1000 -1000 -0.049 -1000
p38 MAPK signaling pathway 0.0160 6 287 44 -0.031 0.057 1000 -1000 -0.013 -1000
Canonical NF-kappaB pathway 0.0134 5 221 39 0 0.061 1000 -1000 -0.016 -1000
FoxO family signaling 0.0134 5 378 64 -0.04 0.054 1000 -1000 -0.053 -1000
Class IB PI3K non-lipid kinase events 0.0134 5 15 3 -0.025 0.025 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class II 0.0107 4 339 75 -0.031 0.069 1000 -1000 -0.019 -1000
PLK2 and PLK4 events 0.0080 3 9 3 0.01 0.026 1000 -1000 -0.008 -1000
Circadian rhythm pathway 0.0080 3 84 22 -0.008 0.041 1000 -1000 -0.029 -1000
TRAIL signaling pathway 0.0080 3 156 48 0 0.053 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class I 0.0080 3 314 104 -0.054 0.067 1000 -1000 -0.022 -1000
Arf6 trafficking events 0.0080 3 265 71 -0.048 0.052 1000 -1000 -0.022 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0053 2 68 23 0.006 0.056 1000 -1000 -0.015 -1000
Insulin-mediated glucose transport 0.0053 2 87 32 -0.002 0.048 1000 -1000 -0.017 -1000
Arf6 downstream pathway 0.0027 1 60 43 -0.055 0.056 1000 -1000 -0.025 -1000
Arf1 pathway 0.0027 1 75 54 -0.001 0.047 1000 -1000 -0.008 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 0 0.062 1000 -1000 -0.022 -1000
E-cadherin signaling events 0.0000 0 0 5 0.024 0.048 1000 -1000 0.013 -1000
Alternative NF-kappaB pathway 0.0000 0 6 13 0 0.074 1000 -1000 0 -1000
Total NA 2414 140762 7203 -9.9 6.9 131000 -131000 -3.8 -131000
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.2 0.4 -10000 0 -0.82 105 105
NCK1/PAK1/Dok-R -0.11 0.17 -10000 0 -0.39 100 100
NCK1/Dok-R -0.23 0.46 -10000 0 -0.93 104 104
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
mol:beta2-estradiol 0.062 0.11 0.24 103 -10000 0 103
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.007 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -10000 0 -10000 0 0
F2 0.056 0.14 0.27 95 -0.22 18 113
TNIP2 0.028 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.21 0.45 -10000 0 -0.89 105 105
FN1 0.022 0.043 -10000 0 -0.32 6 6
PLD2 -0.26 0.47 -10000 0 -0.98 105 105
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
GRB14 -0.014 0.091 -10000 0 -0.21 63 63
ELK1 -0.23 0.43 -10000 0 -0.9 103 103
GRB7 0.028 0.004 -10000 0 -10000 0 0
PAK1 0.024 0.036 -10000 0 -0.32 4 4
Tie2/Ang1/alpha5/beta1 Integrin -0.22 0.47 -10000 0 -0.95 104 104
CDKN1A -0.14 0.28 -10000 0 -0.59 92 92
ITGA5 0.017 0.059 -10000 0 -0.31 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.23 0.46 -10000 0 -0.94 105 105
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:NO -0.14 0.3 0.33 2 -0.61 102 104
PLG -0.27 0.48 -10000 0 -0.99 105 105
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.19 0.38 -10000 0 -0.78 104 104
GRB2 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
ANGPT2 -0.14 0.26 -10000 0 -0.65 52 52
BMX -0.27 0.48 -10000 0 -1 105 105
ANGPT1 -0.29 0.5 -10000 0 -1.1 101 101
tube development -0.16 0.31 -10000 0 -0.64 103 103
ANGPT4 0.023 0.013 -10000 0 -10000 0 0
response to hypoxia -0.018 0.03 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.26 0.5 -10000 0 -1 105 105
alpha5/beta1 Integrin 0.032 0.045 -10000 0 -0.21 12 12
FGF2 0.005 0.084 -10000 0 -0.31 24 24
STAT5A (dimer) -0.17 0.36 -10000 0 -0.73 101 101
mol:L-citrulline -0.14 0.3 0.33 2 -0.61 102 104
AGTR1 -0.02 0.098 -10000 0 -0.22 70 70
MAPK14 -0.25 0.48 -10000 0 -0.99 105 105
Tie2/SHP2 -0.15 0.36 -10000 0 -0.98 54 54
TEK -0.16 0.4 -10000 0 -1 56 56
RPS6KB1 -0.2 0.38 -10000 0 -0.8 104 104
Angiotensin II/AT1 -0.011 0.066 -10000 0 -0.14 70 70
Tie2/Ang1/GRB2 -0.26 0.5 -10000 0 -1 105 105
MAPK3 -0.24 0.43 -10000 0 -0.91 104 104
MAPK1 -0.24 0.43 -10000 0 -0.92 103 103
Tie2/Ang1/GRB7 -0.26 0.5 -10000 0 -1 105 105
NFKB1 0.028 0.003 -10000 0 -10000 0 0
MAPK8 -0.26 0.48 -10000 0 -0.99 105 105
PI3K -0.24 0.46 -10000 0 -0.94 105 105
FES -0.25 0.48 -10000 0 -0.99 105 105
Crk/Dok-R -0.23 0.46 -10000 0 -0.94 105 105
Tie2/Ang1/ABIN2 -0.26 0.5 -10000 0 -1 105 105
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.18 0.36 -10000 0 -0.74 105 105
STAT5A 0.026 0.019 -10000 0 -0.32 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.18 0.38 -10000 0 -0.78 103 103
Tie2/Ang2 -0.22 0.42 -10000 0 -0.87 101 101
Tie2/Ang1 -0.28 0.52 -10000 0 -1.1 105 105
FOXO1 -0.18 0.36 -10000 0 -0.74 104 104
ELF1 0.01 0.05 -10000 0 -0.18 14 14
ELF2 -0.25 0.47 -10000 0 -0.96 105 105
mol:Choline -0.25 0.45 -10000 0 -0.94 105 105
cell migration -0.057 0.1 -10000 0 -0.22 102 102
FYN -0.18 0.35 -10000 0 -0.73 101 101
DOK2 0.019 0.024 -10000 0 -0.21 3 3
negative regulation of cell cycle -0.12 0.26 -10000 0 -0.53 98 98
ETS1 -0.043 0.13 -10000 0 -0.25 98 98
PXN -0.14 0.33 0.38 4 -0.64 101 105
ITGB1 0.028 0.004 -10000 0 -10000 0 0
NOS3 -0.16 0.34 0.35 1 -0.7 102 103
RAC1 0.026 0.008 -10000 0 -10000 0 0
TNF -0.07 0.15 -10000 0 -0.27 126 126
MAPKKK cascade -0.25 0.45 -10000 0 -0.94 105 105
RASA1 0.025 0.026 -10000 0 -0.32 2 2
Tie2/Ang1/Shc -0.25 0.49 -10000 0 -1 105 105
NCK1 0.026 0.008 -10000 0 -10000 0 0
vasculogenesis -0.12 0.27 0.31 3 -0.55 103 106
mol:Phosphatidic acid -0.25 0.45 -10000 0 -0.94 105 105
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.14 0.3 0.33 2 -0.61 102 104
Rac1/GTP -0.18 0.36 -10000 0 -0.74 104 104
MMP2 -0.26 0.48 -10000 0 -0.99 105 105
Ephrin A reverse signaling

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
MAPKKK cascade -0.022 0.1 -10000 0 -0.19 93 93
EFNA5 -0.005 0.098 -10000 0 -0.31 34 34
FYN -0.024 0.081 0.18 2 -0.18 71 73
neuron projection morphogenesis -0.022 0.1 -10000 0 -0.19 93 93
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.022 0.1 -10000 0 -0.19 93 93
EPHA5 -0.041 0.14 -10000 0 -0.31 74 74
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.16 0.37 -10000 0 -0.89 72 72
MKNK1 0.028 0.003 -10000 0 -10000 0 0
MAPK14 -0.04 0.14 -10000 0 -0.3 81 81
ATF2/c-Jun -0.056 0.15 -10000 0 -0.46 29 29
MAPK11 -0.044 0.15 -10000 0 -0.3 85 85
MITF -0.054 0.17 -10000 0 -0.37 77 77
MAPKAPK5 -0.051 0.16 -10000 0 -0.36 76 76
KRT8 -0.05 0.16 -10000 0 -0.35 76 76
MAPKAPK3 0.028 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.057 0.21 -10000 0 -0.44 81 81
CEBPB -0.05 0.16 -10000 0 -0.35 76 76
SLC9A1 -0.053 0.16 -10000 0 -0.35 80 80
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.075 0.2 -10000 0 -0.37 96 96
p38alpha-beta/MNK1 -0.029 0.18 -10000 0 -0.35 80 80
JUN -0.058 0.15 -10000 0 -0.45 29 29
PPARGC1A -0.13 0.24 -10000 0 -0.42 124 124
USF1 -0.054 0.16 -10000 0 -0.36 78 78
RAB5/GDP/GDI1 -0.026 0.12 -10000 0 -0.26 75 75
NOS2 -0.09 0.26 -10000 0 -0.73 37 37
DDIT3 -0.052 0.16 -10000 0 -0.35 79 79
RAB5A 0.028 0.005 -10000 0 -10000 0 0
HSPB1 -0.04 0.14 0.28 13 -0.31 66 79
p38alpha-beta/HBP1 -0.027 0.17 -10000 0 -0.35 73 73
CREB1 -0.058 0.18 -10000 0 -0.38 78 78
RAB5/GDP 0.02 0.004 -10000 0 -10000 0 0
EIF4E -0.053 0.14 -10000 0 -0.32 79 79
RPS6KA4 -0.051 0.16 -10000 0 -0.35 78 78
PLA2G4A -0.06 0.16 -10000 0 -0.34 81 81
GDI1 -0.052 0.16 -10000 0 -0.35 80 80
TP53 -0.077 0.19 -10000 0 -0.44 77 77
RPS6KA5 -0.064 0.18 -10000 0 -0.37 84 84
ESR1 -0.065 0.18 -10000 0 -0.38 85 85
HBP1 0.026 0.008 -10000 0 -10000 0 0
MEF2C -0.061 0.18 -10000 0 -0.38 81 81
MEF2A -0.056 0.17 -10000 0 -0.36 81 81
EIF4EBP1 -0.072 0.2 -10000 0 -0.44 77 77
KRT19 -0.074 0.2 -10000 0 -0.39 90 90
ELK4 -0.053 0.16 -10000 0 -0.35 79 79
ATF6 -0.054 0.16 -10000 0 -0.36 78 78
ATF1 -0.059 0.18 -10000 0 -0.38 78 78
p38alpha-beta/MAPKAPK2 -0.029 0.18 -10000 0 -0.35 78 78
p38alpha-beta/MAPKAPK3 -0.027 0.18 -10000 0 -0.36 77 77
Glypican 2 network

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
MDK 0.019 0.043 -10000 0 -0.21 13 13
GPC2 -0.023 0.095 -10000 0 -0.21 76 76
GPC2/Midkine -0.003 0.08 0.24 1 -0.15 81 82
neuron projection morphogenesis -0.003 0.079 0.24 1 -0.15 81 82
Endothelins

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 -0.034 0.15 0.26 18 -0.32 54 72
PTK2B 0.021 0.013 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.4 -10000 0 -0.93 72 72
EDN1 -0.008 0.12 0.21 20 -0.28 40 60
EDN3 -0.081 0.16 -10000 0 -0.31 117 117
EDN2 0.005 0.082 -10000 0 -0.28 28 28
HRAS/GDP -0.068 0.21 0.28 5 -0.44 66 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.038 0.16 0.18 15 -0.36 55 70
ADCY4 -0.063 0.17 0.2 21 -0.35 70 91
ADCY5 -0.078 0.19 0.19 18 -0.4 79 97
ADCY6 -0.062 0.16 0.2 21 -0.35 68 89
ADCY7 -0.06 0.16 0.2 19 -0.35 69 88
ADCY1 -0.069 0.16 0.2 19 -0.36 68 87
ADCY2 -0.064 0.17 0.2 20 -0.36 69 89
ADCY3 -0.061 0.16 0.2 21 -0.35 68 89
ADCY8 -0.059 0.15 0.19 14 -0.34 61 75
ADCY9 -0.059 0.16 0.2 22 -0.36 66 88
arachidonic acid secretion -0.12 0.29 0.3 5 -0.55 92 97
ETB receptor/Endothelin-1/Gq/GTP -0.042 0.14 0.15 1 -0.31 67 68
GNAO1 -0.021 0.12 -10000 0 -0.32 50 50
HRAS 0.024 0.027 -10000 0 -0.21 5 5
ETA receptor/Endothelin-1/G12/GTP 0.005 0.16 0.33 16 -0.31 48 64
ETA receptor/Endothelin-1/Gs/GTP -0.035 0.19 0.32 14 -0.34 80 94
mol:GTP -0.002 0.007 -10000 0 -10000 0 0
COL3A1 -0.031 0.15 0.26 18 -0.36 42 60
EDNRB -0.016 0.11 -10000 0 -0.32 45 45
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.056 0.19 0.26 14 -0.44 62 76
CYSLTR1 -0.049 0.19 0.26 18 -0.48 44 62
SLC9A1 -0.015 0.096 0.18 18 -0.23 37 55
mol:GDP -0.081 0.22 0.26 7 -0.46 69 76
SLC9A3 -0.18 0.41 -10000 0 -0.83 85 85
RAF1 -0.088 0.23 0.27 6 -0.46 78 84
JUN -0.1 0.3 -10000 0 -0.74 51 51
JAK2 -0.036 0.15 0.26 16 -0.34 49 65
mol:IP3 -0.042 0.16 0.23 1 -0.35 57 58
ETA receptor/Endothelin-1 -0.011 0.2 0.38 18 -0.32 82 100
PLCB1 0.023 0.036 -10000 0 -0.32 4 4
PLCB2 0.024 0.019 -10000 0 -0.2 2 2
ETA receptor/Endothelin-3 -0.068 0.16 0.17 11 -0.27 121 132
FOS -0.14 0.35 0.4 2 -0.9 59 61
Gai/GDP -0.16 0.36 -10000 0 -0.78 88 88
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.068 0.21 0.25 14 -0.45 63 77
BCAR1 0.023 0.011 -10000 0 -10000 0 0
PRKCB1 -0.047 0.16 0.21 2 -0.35 57 59
GNAQ 0.02 0.02 -10000 0 -10000 0 0
GNAZ 0.003 0.089 -10000 0 -0.32 27 27
GNAL -0.057 0.15 -10000 0 -0.32 90 90
Gs family/GDP -0.096 0.23 0.26 6 -0.47 80 86
ETA receptor/Endothelin-1/Gq/GTP -0.041 0.17 0.19 15 -0.36 60 75
MAPK14 -0.043 0.14 0.22 1 -0.31 57 58
TRPC6 -0.17 0.43 -10000 0 -1 72 72
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.019 -10000 0 -0.32 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.041 0.15 -10000 0 -0.32 59 59
ETB receptor/Endothelin-2 -0.009 0.099 -10000 0 -0.21 69 69
ETB receptor/Endothelin-3 -0.063 0.15 -10000 0 -0.25 128 128
ETB receptor/Endothelin-1 -0.015 0.13 0.18 14 -0.27 60 74
MAPK3 -0.14 0.33 0.41 2 -0.8 63 65
MAPK1 -0.14 0.33 0.4 2 -0.8 64 66
Rac1/GDP -0.066 0.2 0.27 5 -0.44 61 66
cAMP biosynthetic process -0.055 0.18 0.23 19 -0.38 68 87
MAPK8 -0.13 0.38 0.34 1 -0.78 75 76
SRC 0.027 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.056 0.16 0.17 1 -0.35 71 72
p130Cas/CRK/Src/PYK2 -0.13 0.29 0.28 6 -0.61 82 88
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.065 0.2 0.27 5 -0.45 60 65
COL1A2 -0.049 0.18 0.26 13 -0.47 42 55
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.01 0.12 0.17 17 -0.24 62 79
mol:DAG -0.043 0.16 0.23 1 -0.35 58 59
MAP2K2 -0.11 0.27 0.35 2 -0.61 68 70
MAP2K1 -0.11 0.27 0.37 3 -0.59 71 74
EDNRA -0.018 0.14 0.21 18 -0.31 53 71
positive regulation of muscle contraction -0.021 0.14 0.23 31 -0.3 45 76
Gq family/GDP -0.057 0.21 0.25 1 -0.43 67 68
HRAS/GTP -0.073 0.2 0.24 7 -0.42 68 75
PRKCH -0.045 0.16 0.22 3 -0.36 53 56
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA -0.049 0.16 0.22 3 -0.36 58 61
PRKCB -0.069 0.19 0.22 6 -0.43 62 68
PRKCE -0.041 0.15 0.23 4 -0.34 52 56
PRKCD -0.046 0.16 0.21 3 -0.36 52 55
PRKCG -0.052 0.16 0.22 3 -0.35 59 62
regulation of vascular smooth muscle contraction -0.18 0.41 0.42 2 -1.1 59 61
PRKCQ -0.052 0.17 0.26 2 -0.4 49 51
PLA2G4A -0.14 0.33 0.3 5 -0.62 92 97
GNA14 0.02 0.02 -10000 0 -10000 0 0
GNA15 0.007 0.071 -10000 0 -0.32 16 16
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA11 0.01 0.065 -10000 0 -0.32 13 13
Rac1/GTP 0.005 0.16 0.33 16 -0.26 69 85
MMP1 -0.024 0.19 0.31 12 -0.68 20 32
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.02 0.11 0.22 83 -10000 0 83
KIRREL -0.043 0.14 -10000 0 -0.32 76 76
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.02 0.11 -10000 0 -0.22 83 83
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.008 -10000 0 -10000 0 0
WASL 0.026 0.008 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.017 0.099 0.2 1 -0.17 76 77
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.017 0.081 -10000 0 -0.19 67 67
FYN -0.022 0.079 0.22 12 -0.17 63 75
mol:Ca2+ 0.016 0.096 -10000 0 -0.17 74 74
mol:DAG 0.017 0.097 -10000 0 -0.17 74 74
NPHS2 0.005 0.034 -10000 0 -0.22 2 2
mol:IP3 0.017 0.097 -10000 0 -0.17 74 74
regulation of endocytosis 0.003 0.082 -10000 0 -0.15 74 74
Nephrin/NEPH1/podocin/Cholesterol 0.005 0.091 0.18 1 -0.17 76 77
establishment of cell polarity -0.02 0.11 -10000 0 -0.22 83 83
Nephrin/NEPH1/podocin/NCK1-2 0.025 0.095 -10000 0 -0.16 71 71
Nephrin/NEPH1/beta Arrestin2 0.004 0.084 -10000 0 -0.15 74 74
NPHS1 0.006 0.045 -10000 0 -0.21 9 9
Nephrin/NEPH1/podocin 0.003 0.086 -10000 0 -0.16 76 76
TJP1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.008 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.018 0.098 -10000 0 -0.17 74 74
CD2AP 0.028 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.017 0.098 -10000 0 -0.17 74 74
GRB2 0.027 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.044 0.1 0.23 10 -0.2 95 105
cytoskeleton organization -0.024 0.082 0.21 3 -0.19 64 67
Nephrin/NEPH1 -0.004 0.077 -10000 0 -0.15 76 76
Nephrin/NEPH1/ZO-1 0.006 0.095 -10000 0 -0.18 74 74
Glucocorticoid receptor regulatory 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
PCK2 0.084 0.096 0.3 8 -10000 0 8
SMARCC2 0.012 0.042 -10000 0 -0.12 20 20
SMARCC1 0.012 0.043 -10000 0 -0.13 8 8
TBX21 -0.088 0.16 -10000 0 -0.37 64 64
SUMO2 0.029 0.019 -10000 0 -10000 0 0
STAT1 (dimer) 0.027 0.034 -10000 0 -0.22 6 6
FKBP4 0.026 0.007 -10000 0 -10000 0 0
FKBP5 0.027 0.018 -10000 0 -0.32 1 1
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.29 73 -10000 0 73
PRL -0.07 0.12 -10000 0 -0.56 1 1
cortisol/GR alpha (dimer)/TIF2 0.13 0.25 0.53 75 -10000 0 75
RELA -0.037 0.099 -10000 0 -0.21 59 59
FGG 0.17 0.22 0.46 107 -10000 0 107
GR beta/TIF2 0.06 0.15 0.29 63 -0.24 28 91
IFNG -0.23 0.28 -10000 0 -0.65 89 89
apoptosis 0.093 0.2 0.51 51 -0.45 1 52
CREB1 -0.014 0.1 -10000 0 -0.29 37 37
histone acetylation -0.058 0.16 0.31 12 -0.36 56 68
BGLAP -0.093 0.15 -10000 0 -0.44 24 24
GR/PKAc 0.12 0.1 0.3 61 -10000 0 61
NF kappa B1 p50/RelA -0.059 0.18 -10000 0 -0.33 91 91
SMARCD1 0.012 0.042 -10000 0 -0.12 8 8
MDM2 0.09 0.1 0.23 104 -10000 0 104
GATA3 -0.068 0.15 -10000 0 -0.32 101 101
AKT1 0.023 0.004 -10000 0 -10000 0 0
CSF2 -0.074 0.12 -10000 0 -0.44 8 8
GSK3B 0.029 0.019 -10000 0 -10000 0 0
NR1I3 0.096 0.21 0.49 50 -0.7 3 53
CSN2 0.14 0.18 0.38 106 -10000 0 106
BRG1/BAF155/BAF170/BAF60A 0.023 0.13 -10000 0 -0.28 52 52
NFATC1 0.026 0.009 -10000 0 -10000 0 0
POU2F1 0.026 0.019 -10000 0 -0.31 1 1
CDKN1A -0.022 0.15 -10000 0 -1.4 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.004 0.014 -10000 0 -10000 0 0
SFN 0.002 0.091 -10000 0 -0.32 28 28
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.11 0.3 59 -10000 0 59
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.051 0.27 0.48 44 -0.68 29 73
JUN -0.14 0.18 -10000 0 -0.4 83 83
IL4 -0.091 0.14 -10000 0 -0.43 25 25
CDK5R1 0.021 0.045 -10000 0 -0.2 14 14
PRKACA 0.028 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.067 0.12 0.19 19 -0.27 59 78
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.1 0.3 69 -10000 0 69
cortisol/GR alpha (monomer) 0.24 0.29 0.62 110 -10000 0 110
NCOA2 -0.02 0.11 -10000 0 -0.32 47 47
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.067 0.14 -10000 0 -0.32 65 65
AP-1/NFAT1-c-4 -0.22 0.27 -10000 0 -0.57 119 119
AFP -0.11 0.13 -10000 0 -0.49 3 3
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.16 0.4 66 -10000 0 66
TP53 0.034 0.017 -10000 0 -10000 0 0
PPP5C 0.028 0.003 -10000 0 -10000 0 0
KRT17 -0.32 0.43 -10000 0 -0.94 102 102
KRT14 -0.36 0.54 0.34 3 -1.2 108 111
TBP 0.03 0.021 -10000 0 -0.21 1 1
CREBBP 0.054 0.14 0.26 83 -0.25 31 114
HDAC1 0.028 0.004 -10000 0 -10000 0 0
HDAC2 0.024 0.01 -10000 0 -10000 0 0
AP-1 -0.22 0.27 -10000 0 -0.57 120 120
MAPK14 0.03 0.016 -10000 0 -10000 0 0
MAPK10 0.028 0.031 -10000 0 -0.32 2 2
MAPK11 0.025 0.038 -10000 0 -0.21 7 7
KRT5 -0.42 0.5 -10000 0 -1 139 139
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.03 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.034 -10000 0 -0.22 6 6
CGA -0.17 0.3 -10000 0 -0.74 66 66
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.077 0.17 0.36 71 -0.3 16 87
MAPK3 0.03 0.018 -10000 0 -10000 0 0
MAPK1 0.03 0.017 -10000 0 -10000 0 0
ICAM1 -0.16 0.23 -10000 0 -0.51 92 92
NFKB1 -0.04 0.1 -10000 0 -0.22 60 60
MAPK8 -0.12 0.17 -10000 0 -0.37 92 92
MAPK9 0.029 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.091 0.2 0.51 50 -0.43 2 52
BAX -0.012 0.074 -10000 0 -10000 0 0
POMC -0.25 0.47 -10000 0 -1.4 46 46
EP300 0.052 0.14 0.26 85 -0.27 34 119
cortisol/GR alpha (dimer)/p53 0.18 0.24 0.55 86 -10000 0 86
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.084 0.19 68 -10000 0 68
SGK1 -0.063 0.46 0.44 2 -1.1 53 55
IL13 -0.29 0.36 -10000 0 -0.79 106 106
IL6 -0.26 0.38 -10000 0 -0.83 101 101
PRKACG 0.02 0.006 -10000 0 -10000 0 0
IL5 -0.25 0.3 -10000 0 -0.75 76 76
IL2 -0.23 0.28 -10000 0 -0.65 93 93
CDK5 0.028 0.016 -10000 0 -0.21 1 1
PRKACB 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
IL8 -0.2 0.31 -10000 0 -0.67 84 84
CDK5R1/CDK5 0.038 0.036 0.16 1 -0.14 10 11
NF kappa B1 p50/RelA/PKAc -0.015 0.15 -10000 0 -0.29 54 54
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.19 0.23 0.52 96 -10000 0 96
SMARCA4 0.013 0.041 -10000 0 -0.12 13 13
chromatin remodeling 0.083 0.21 0.37 76 -0.35 28 104
NF kappa B1 p50/RelA/Cbp -0.018 0.21 0.34 26 -0.36 63 89
JUN (dimer) -0.14 0.18 -10000 0 -0.4 82 82
YWHAH 0.028 0.004 -10000 0 -10000 0 0
VIPR1 -0.077 0.14 0.41 1 -0.33 69 70
NR3C1 0.15 0.19 0.41 96 -10000 0 96
NR4A1 -0.034 0.16 -10000 0 -0.41 54 54
TIF2/SUV420H1 0.001 0.085 -10000 0 -0.22 47 47
MAPKKK cascade 0.093 0.2 0.51 51 -0.45 1 52
cortisol/GR alpha (dimer)/Src-1 0.21 0.25 0.53 112 -10000 0 112
PBX1 0.026 0.02 -10000 0 -0.32 1 1
POU1F1 0.02 0.015 -10000 0 -0.23 1 1
SELE -0.26 0.39 -10000 0 -0.84 101 101
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.083 0.21 0.37 75 -0.35 29 104
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.19 0.23 0.52 96 -10000 0 96
mol:cortisol 0.14 0.18 0.36 119 -10000 0 119
MMP1 -0.12 0.27 -10000 0 -1 30 30
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.007 0.063 -10000 0 -0.23 15 15
STMN1 -0.035 0.076 0.16 1 -0.15 111 112
Aurora B/RasGAP/Survivin -0.024 0.12 0.22 5 -0.2 112 117
Chromosomal passenger complex/Cul3 protein complex -0.008 0.068 0.16 2 -0.2 29 31
BIRC5 -0.048 0.11 -10000 0 -0.21 116 116
DES -0.11 0.3 -10000 0 -0.65 86 86
Aurora C/Aurora B/INCENP 0.047 0.06 -10000 0 -0.14 26 26
Aurora B/TACC1 -0.01 0.065 -10000 0 -0.11 100 100
Aurora B/PP2A -0.016 0.084 -10000 0 -0.14 111 111
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.003 0.025 0.093 4 -0.11 12 16
mitotic metaphase/anaphase transition -0.001 0.004 -10000 0 -10000 0 0
NDC80 -0.029 0.075 0.19 5 -0.14 104 109
Cul3 protein complex 0.045 0.051 -10000 0 -0.18 17 17
KIF2C 0.002 0.04 0.17 1 -0.22 5 6
PEBP1 0.026 0.007 -10000 0 -10000 0 0
KIF20A -0.055 0.11 -10000 0 -0.21 130 130
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.017 0.085 -10000 0 -0.14 110 110
SEPT1 0.022 0.036 -10000 0 -0.21 9 9
SMC2 0.027 0.006 -10000 0 -10000 0 0
SMC4 0.026 0.014 -10000 0 -0.21 1 1
NSUN2/NPM1/Nucleolin -0.026 0.17 0.27 4 -0.5 41 45
PSMA3 0.028 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B -0.006 0.047 -10000 0 -0.22 12 12
AURKB -0.048 0.11 -10000 0 -0.22 113 113
AURKC 0.025 0.031 -10000 0 -0.26 4 4
CDCA8 0.004 0.07 -10000 0 -0.21 36 36
cytokinesis -0.01 0.098 0.21 3 -0.35 21 24
Aurora B/Septin1 0.017 0.12 0.26 4 -0.31 27 31
AURKA 0.017 0.05 -10000 0 -0.21 17 17
INCENP 0.026 0.009 -10000 0 -10000 0 0
KLHL13 0.012 0.074 -10000 0 -0.32 18 18
BUB1 -0.019 0.095 -10000 0 -0.21 73 73
hSgo1/Aurora B/Survivin -0.022 0.14 0.26 8 -0.23 100 108
EVI5 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.013 0.086 -10000 0 -0.26 14 14
SGOL1 -0.014 0.09 -10000 0 -0.21 65 65
CENPA -0.009 0.073 0.19 2 -0.2 37 39
NCAPG -0.045 0.11 -10000 0 -0.21 114 114
Aurora B/HC8 Proteasome -0.016 0.084 -10000 0 -0.14 110 110
NCAPD2 0.026 0.008 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.015 0.082 -10000 0 -0.14 108 108
RHOA 0.028 0.004 -10000 0 -10000 0 0
NCAPH -0.027 0.1 -10000 0 -0.21 86 86
NPM1 -0.02 0.11 -10000 0 -0.32 41 41
RASA1 0.025 0.026 -10000 0 -0.32 2 2
KLHL9 0.027 0.005 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.084 -10000 0 -0.14 110 110
PPP1CC 0.027 0.006 -10000 0 -10000 0 0
Centraspindlin 0.005 0.092 0.23 3 -0.28 16 19
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
NSUN2 -0.019 0.1 -10000 0 -0.3 41 41
MYLK -0.055 0.12 -10000 0 -0.28 77 77
KIF23 0.012 0.059 -10000 0 -0.21 25 25
VIM -0.033 0.073 0.18 1 -0.14 110 111
RACGAP1 0.027 0.018 -10000 0 -0.21 2 2
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.019 0.1 -10000 0 -0.3 40 40
Chromosomal passenger complex -0.013 0.072 0.2 3 -0.25 18 21
Chromosomal passenger complex/EVI5 0.04 0.13 0.26 22 -0.21 66 88
TACC1 0.02 0.027 -10000 0 -0.32 2 2
PPP2R5D 0.028 0.003 -10000 0 -10000 0 0
CUL3 0.028 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.014 0.083 -10000 0 -0.23 37 37
alphaV beta3 Integrin -0.004 0.12 -10000 0 -0.22 77 77
PTK2 -0.084 0.18 0.25 9 -0.4 73 82
IGF1R 0.026 0.022 -10000 0 -0.26 2 2
PI4KB 0.027 0.006 -10000 0 -10000 0 0
MFGE8 0.027 0.018 -10000 0 -0.32 1 1
SRC 0.027 0.006 -10000 0 -10000 0 0
CDKN1B -0.051 0.15 -10000 0 -0.4 52 52
VEGFA 0.009 0.077 -10000 0 -0.3 21 21
ILK -0.036 0.13 -10000 0 -0.41 36 36
ROCK1 0.026 0.019 -10000 0 -0.32 1 1
AKT1 -0.04 0.12 -10000 0 -0.38 36 36
PTK2B -0.023 0.084 0.18 3 -0.2 56 59
alphaV/beta3 Integrin/JAM-A -0.011 0.13 0.21 2 -0.2 100 102
CBL 0.026 0.019 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.054 0.12 -10000 0 -0.16 176 176
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.047 0.08 -10000 0 -0.2 31 31
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.045 0.12 -10000 0 -0.29 48 48
alphaV/beta3 Integrin/Syndecan-1 0 0.1 -10000 0 -0.18 81 81
PI4KA 0.028 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.011 0.14 -10000 0 -0.36 32 32
PI4 Kinase 0.039 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
alphaV/beta3 Integrin/Osteopontin -0.018 0.1 -10000 0 -0.16 118 118
RPS6KB1 -0.051 0.12 0.21 13 -0.36 30 43
TLN1 0.028 0.005 -10000 0 -10000 0 0
MAPK3 -0.09 0.2 -10000 0 -0.43 83 83
GPR124 0.017 0.041 -10000 0 -0.32 5 5
MAPK1 -0.092 0.2 -10000 0 -0.42 85 85
PXN 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
alphaV/beta3 Integrin/Tumstatin -0.005 0.11 -10000 0 -0.21 82 82
cell adhesion -0.042 0.11 -10000 0 -0.23 75 75
ANGPTL3 -0.068 0.12 -10000 0 -0.21 149 149
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.076 -10000 0 -0.2 35 35
IGF-1R heterotetramer 0.026 0.022 -10000 0 -0.26 2 2
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
TGFBR2 0.018 0.056 -10000 0 -0.32 10 10
ITGB3 -0.043 0.14 -10000 0 -0.32 76 76
IGF1 -0.003 0.093 -10000 0 -0.28 37 37
RAC1 0.026 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.001 0.092 -10000 0 -0.18 73 73
apoptosis 0.027 0.006 -10000 0 -10000 0 0
CD47 0.028 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.006 0.093 -10000 0 -0.18 73 73
VCL 0.009 0.078 -10000 0 -0.32 20 20
alphaV/beta3 Integrin/Del1 -0.032 0.14 -10000 0 -0.25 102 102
CSF1 0.019 0.053 -10000 0 -0.32 9 9
PIK3C2A -0.036 0.13 -10000 0 -0.4 36 36
PI4 Kinase/Pyk2 -0.041 0.11 -10000 0 -0.28 43 43
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.003 0.12 -10000 0 -0.2 88 88
FAK1/Vinculin -0.062 0.17 0.24 12 -0.35 72 84
alphaV beta3/Integrin/ppsTEM5 -0.001 0.093 -10000 0 -0.18 73 73
RHOA 0.028 0.004 -10000 0 -10000 0 0
VTN -0.036 0.12 -10000 0 -0.26 82 82
BCAR1 0.023 0.011 -10000 0 -10000 0 0
FGF2 0.005 0.084 -10000 0 -0.32 24 24
F11R 0 0.053 -10000 0 -0.22 21 21
alphaV/beta3 Integrin/Lactadherin 0.006 0.094 -10000 0 -0.18 74 74
alphaV/beta3 Integrin/TGFBR2 0.003 0.1 -10000 0 -0.2 71 71
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.052 0.046 -10000 0 -0.17 9 9
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.008 0.085 -10000 0 -0.16 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.022 0.043 -10000 0 -0.32 6 6
alphaV/beta3 Integrin/Pyk2 -0.013 0.1 0.18 1 -0.2 57 58
SDC1 0.018 0.058 -10000 0 -0.32 11 11
VAV3 -0.004 0.064 0.22 4 -0.3 6 10
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
IRS1 0.017 0.061 -10000 0 -0.32 12 12
FAK1/Paxillin -0.059 0.16 0.24 10 -0.33 69 79
cell migration -0.06 0.15 0.23 10 -0.32 67 77
ITGAV 0.027 0.006 -10000 0 -10000 0 0
PI3K -0.002 0.12 0.2 2 -0.2 80 82
SPP1 -0.01 0.089 -10000 0 -0.22 58 58
KDR 0.01 0.076 -10000 0 -0.32 19 19
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.006 -10000 0 -10000 0 0
COL4A3 0.007 0.082 -10000 0 -0.31 23 23
angiogenesis -0.099 0.21 0.26 1 -0.46 82 83
Rac1/GTP 0.01 0.062 0.18 4 -0.29 5 9
EDIL3 -0.042 0.14 -10000 0 -0.32 74 74
cell proliferation 0.003 0.1 -10000 0 -0.2 71 71
IL23-mediated signaling events

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
CCL2 -0.26 0.5 -9999 0 -1.2 61 61
IL23A -0.28 0.52 -9999 0 -1.3 60 60
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.52 -9999 0 -1.2 62 62
positive regulation of T cell mediated cytotoxicity -0.29 0.58 -9999 0 -1.4 62 62
ITGA3 -0.25 0.49 -9999 0 -1.2 59 59
IL17F -0.16 0.31 -9999 0 -0.73 61 61
IL12B -0.01 0.067 -9999 0 -0.22 19 19
STAT1 (dimer) -0.27 0.55 -9999 0 -1.3 62 62
CD4 -0.24 0.47 -9999 0 -1.2 59 59
IL23 -0.26 0.5 -9999 0 -1.2 61 61
IL23R -0.035 0.15 -9999 0 -0.77 10 10
IL1B -0.29 0.56 -9999 0 -1.4 64 64
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.24 0.47 -9999 0 -1.2 58 58
TYK2 0.003 0.038 -9999 0 -10000 0 0
STAT4 0.019 0.049 -9999 0 -0.23 13 13
STAT3 0.027 0.006 -9999 0 -10000 0 0
IL18RAP 0.011 0.071 -9999 0 -0.26 23 23
IL12RB1 -0.007 0.066 -9999 0 -0.26 16 16
PIK3CA 0.023 0.034 -9999 0 -0.29 4 4
IL12Rbeta1/TYK2 0.001 0.063 -9999 0 -0.19 14 14
IL23R/JAK2 -0.032 0.16 -9999 0 -0.94 5 5
positive regulation of chronic inflammatory response -0.29 0.58 -9999 0 -1.4 62 62
natural killer cell activation 0.003 0.007 -9999 0 -10000 0 0
JAK2 0.002 0.049 -9999 0 -0.32 1 1
PIK3R1 0.023 0.032 -9999 0 -0.32 3 3
NFKB1 0.027 0.005 -9999 0 -10000 0 0
RELA 0.027 0.006 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.25 0.47 -9999 0 -1.1 61 61
ALOX12B -0.26 0.49 -9999 0 -1.2 66 66
CXCL1 -0.34 0.58 -9999 0 -1.3 92 92
T cell proliferation -0.29 0.58 -9999 0 -1.4 62 62
NFKBIA 0.027 0.005 -9999 0 -10000 0 0
IL17A -0.12 0.25 -9999 0 -0.56 58 58
PI3K -0.25 0.52 -9999 0 -1.3 61 61
IFNG -0.004 0.026 -9999 0 -0.096 7 7
STAT3 (dimer) -0.24 0.49 -9999 0 -1.2 60 60
IL18R1 0.024 0.039 -9999 0 -0.31 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.15 0.32 -9999 0 -0.76 57 57
IL18/IL18R 0.04 0.068 -9999 0 -0.17 30 30
macrophage activation -0.013 0.02 -9999 0 -0.045 58 58
TNF -0.28 0.54 -9999 0 -1.3 63 63
STAT3/STAT4 -0.26 0.52 -9999 0 -1.3 61 61
STAT4 (dimer) -0.27 0.55 -9999 0 -1.3 62 62
IL18 0.02 0.053 -9999 0 -0.31 9 9
IL19 -0.24 0.47 -9999 0 -1.2 58 58
STAT5A (dimer) -0.27 0.55 -9999 0 -1.3 62 62
STAT1 0.024 0.03 -9999 0 -0.21 6 6
SOCS3 -0.02 0.12 -9999 0 -0.3 53 53
CXCL9 -0.25 0.48 -9999 0 -1.2 60 60
MPO -0.28 0.52 -9999 0 -1.2 74 74
positive regulation of humoral immune response -0.29 0.58 -9999 0 -1.4 62 62
IL23/IL23R/JAK2/TYK2 -0.32 0.66 -9999 0 -1.6 62 62
IL6 -0.34 0.59 -9999 0 -1.2 100 100
STAT5A 0.026 0.019 -9999 0 -0.32 1 1
IL2 0.02 0.017 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.007 -9999 0 -10000 0 0
CD3E -0.24 0.48 -9999 0 -1.2 59 59
keratinocyte proliferation -0.29 0.58 -9999 0 -1.4 62 62
NOS2 -0.27 0.51 -9999 0 -1.2 69 69
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.049 0.16 0.26 3 -0.43 48 51
CRKL -0.05 0.16 -10000 0 -0.43 52 52
HRAS -0.023 0.16 0.22 3 -0.39 51 54
mol:PIP3 -0.018 0.16 0.23 6 -0.38 49 55
SPRED1 0.024 0.036 -10000 0 -0.32 4 4
SPRED2 0.022 0.043 -10000 0 -0.32 6 6
GAB1 -0.051 0.17 -10000 0 -0.44 55 55
FOXO3 -0.02 0.16 0.25 6 -0.38 48 54
AKT1 -0.021 0.17 0.26 6 -0.41 50 56
BAD -0.018 0.16 0.25 9 -0.38 48 57
megakaryocyte differentiation -0.053 0.17 -10000 0 -0.44 54 54
GSK3B -0.014 0.16 0.28 9 -0.38 49 58
RAF1 -0.017 0.13 0.22 5 -0.32 49 54
SHC1 0.027 0.007 -10000 0 -10000 0 0
STAT3 -0.052 0.17 -10000 0 -0.44 55 55
STAT1 -0.12 0.37 -10000 0 -0.98 55 55
HRAS/SPRED1 -0.005 0.14 0.21 3 -0.33 47 50
cell proliferation -0.054 0.17 -10000 0 -0.44 54 54
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
TEC 0.028 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.035 0.18 -10000 0 -0.46 49 49
HRAS/SPRED2 -0.006 0.14 0.21 3 -0.33 49 52
LYN/TEC/p62DOK -0.009 0.17 -10000 0 -0.4 49 49
MAPK3 -0.004 0.1 0.25 10 -0.24 41 51
STAP1 -0.076 0.18 0.2 1 -0.47 57 58
GRAP2 0.015 0.063 -10000 0 -0.3 14 14
JAK2 -0.1 0.32 -10000 0 -0.85 54 54
STAT1 (dimer) -0.12 0.36 -10000 0 -0.96 55 55
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.015 0.18 -10000 0 -0.44 52 52
actin filament polymerization -0.051 0.16 0.22 1 -0.42 52 53
LYN 0.024 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.099 0.25 0.25 1 -0.67 54 55
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
CBL/CRKL/GRB2 -0.017 0.16 -10000 0 -0.41 47 47
PI3K -0.016 0.18 -10000 0 -0.45 48 48
PTEN 0.023 0.011 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.43 -10000 0 -1.2 48 48
MAPK8 -0.055 0.18 -10000 0 -0.45 54 54
STAT3 (dimer) -0.051 0.17 -10000 0 -0.43 55 55
positive regulation of transcription 0 0.089 0.22 11 -0.2 41 52
mol:GDP -0.022 0.16 0.21 1 -0.41 49 50
PIK3C2B -0.05 0.17 -10000 0 -0.44 53 53
CBL/CRKL -0.03 0.16 0.21 1 -0.42 48 49
FER -0.054 0.17 -10000 0 -0.45 55 55
SH2B3 -0.049 0.17 -10000 0 -0.44 53 53
PDPK1 -0.013 0.15 0.26 11 -0.36 45 56
SNAI2 -0.073 0.19 -10000 0 -0.49 55 55
positive regulation of cell proliferation -0.086 0.29 -10000 0 -0.76 54 54
KITLG 0.004 0.081 -10000 0 -0.34 18 18
cell motility -0.086 0.29 -10000 0 -0.76 54 54
PTPN6 0.027 0.012 -10000 0 -10000 0 0
EPOR -0.008 0.13 -10000 0 -0.79 2 2
STAT5A (dimer) -0.071 0.25 -10000 0 -0.64 53 53
SOCS1 0.024 0.03 -10000 0 -0.23 5 5
cell migration 0.089 0.18 0.47 59 -0.19 1 60
SOS1 0.027 0.006 -10000 0 -10000 0 0
EPO -0.019 0.1 -10000 0 -0.28 49 49
VAV1 0.015 0.064 -10000 0 -0.31 14 14
GRB10 -0.05 0.16 -10000 0 -0.42 53 53
PTPN11 0.027 0.019 -10000 0 -0.3 1 1
SCF/KIT -0.051 0.18 -10000 0 -0.46 55 55
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.009 0.11 0.25 10 -0.26 47 57
CBL 0.026 0.019 -10000 0 -0.32 1 1
KIT -0.13 0.43 -10000 0 -1.2 48 48
MAP2K2 -0.009 0.11 0.24 10 -0.26 46 56
SHC/Grb2/SOS1 -0.009 0.17 -10000 0 -0.42 51 51
STAT5A -0.076 0.25 -10000 0 -0.67 53 53
GRB2 0.027 0.006 -10000 0 -10000 0 0
response to radiation -0.071 0.18 -10000 0 -0.48 55 55
SHC/GRAP2 0.03 0.047 -10000 0 -0.2 13 13
PTPRO -0.053 0.17 -10000 0 -0.45 54 54
SH2B2 -0.052 0.16 0.22 1 -0.43 52 53
DOK1 0.028 0.004 -10000 0 -10000 0 0
MATK -0.091 0.18 0.19 1 -0.48 59 60
CREBBP 0.019 0.055 -10000 0 -0.12 47 47
BCL2 -0.098 0.36 -10000 0 -1.2 28 28
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.021 0.037 -10000 0 -0.22 8 8
GNB1/GNG2 -0.049 0.076 -10000 0 -0.18 83 83
AKT1 -0.025 0.11 0.31 3 -0.22 26 29
EGF 0 0.082 -10000 0 -0.23 40 40
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0 0.071 0.28 9 -0.23 5 14
mol:Ca2+ -0.052 0.15 0.34 4 -0.29 87 91
LYN -0.002 0.055 0.27 4 -0.23 4 8
RhoA/GTP -0.02 0.061 -10000 0 -0.13 72 72
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.059 0.16 0.33 7 -0.34 82 89
GNG2 0.023 0.04 -10000 0 -0.32 5 5
ARRB2 0.026 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.019 0.14 0.27 1 -0.38 39 40
G beta5/gamma2 -0.055 0.1 -10000 0 -0.24 82 82
PRKCH -0.062 0.16 0.31 6 -0.34 84 90
DNM1 0.025 0.022 -10000 0 -0.26 2 2
TXA2/TP beta/beta Arrestin3 0.012 0.017 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.004 0.088 -10000 0 -0.32 26 26
G12 family/GTP -0.057 0.13 -10000 0 -0.3 78 78
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.028 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.035 0.015 -10000 0 -0.18 1 1
mol:GDP 0.028 0.11 0.3 22 -0.25 4 26
mol:NADP 0.022 0.03 -10000 0 -0.21 6 6
RAB11A 0.028 0.003 -10000 0 -10000 0 0
PRKG1 -0.068 0.15 -10000 0 -0.32 102 102
mol:IP3 -0.068 0.18 0.36 4 -0.37 87 91
cell morphogenesis 0.034 0.015 -10000 0 -0.18 1 1
PLCB2 -0.098 0.24 0.38 4 -0.5 86 90
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.01 0.067 0.28 6 -0.23 8 14
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.069 0.3 6 -0.25 5 11
RHOA 0.028 0.004 -10000 0 -10000 0 0
PTGIR 0.003 0.075 -10000 0 -0.22 38 38
PRKCB1 -0.068 0.18 0.34 4 -0.36 86 90
GNAQ 0.027 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.022 0.03 -10000 0 -0.21 6 6
TXA2/TXA2-R family -0.1 0.24 0.39 4 -0.51 86 90
LCK -0.002 0.064 0.24 8 -0.23 4 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.009 0.062 0.2 1 -0.17 23 24
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.06 -10000 0 -0.43 5 5
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.011 0.06 -10000 0 -0.17 20 20
MAPK14 -0.036 0.12 0.26 9 -0.22 79 88
TGM2/GTP -0.081 0.19 0.4 1 -0.41 87 88
MAPK11 -0.038 0.12 0.27 8 -0.23 80 88
ARHGEF1 -0.032 0.082 0.21 1 -0.18 76 77
GNAI2 0.028 0.004 -10000 0 -10000 0 0
JNK cascade -0.071 0.18 0.36 4 -0.38 86 90
RAB11/GDP 0.028 0.004 -10000 0 -10000 0 0
ICAM1 -0.048 0.13 0.3 4 -0.28 85 89
cAMP biosynthetic process -0.067 0.17 0.36 4 -0.34 87 91
Gq family/GTP/EBP50 0.01 0.063 0.24 8 -0.18 28 36
actin cytoskeleton reorganization 0.034 0.015 -10000 0 -0.18 1 1
SRC -0.002 0.061 0.26 6 -0.23 4 10
GNB5 0.028 0.005 -10000 0 -10000 0 0
GNB1 0.028 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.018 0.091 0.29 10 -0.23 12 22
VCAM1 -0.052 0.14 0.3 4 -0.29 84 88
TP beta/Gq family/GDP/G beta5/gamma2 -0.019 0.14 0.27 1 -0.38 39 40
platelet activation -0.049 0.15 0.33 8 -0.29 84 92
PGI2/IP 0.004 0.05 -10000 0 -0.14 38 38
PRKACA -0.002 0.056 -10000 0 -0.18 30 30
Gq family/GDP/G beta5/gamma2 -0.014 0.12 0.23 2 -0.33 39 41
TXA2/TP beta/beta Arrestin2 0.005 0.046 -10000 0 -0.4 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.056 -10000 0 -0.18 32 32
mol:DAG -0.077 0.2 0.36 4 -0.41 85 89
EGFR -0.007 0.1 -10000 0 -0.32 36 36
TXA2/TP alpha -0.094 0.22 0.41 4 -0.47 87 91
Gq family/GTP -0.005 0.055 -10000 0 -0.16 40 40
YES1 0.001 0.067 0.27 8 -0.23 4 12
GNAI2/GTP 0.005 0.056 -10000 0 -0.2 9 9
PGD2/DP 0.004 0.06 -10000 0 -0.22 26 26
SLC9A3R1 0.027 0.005 -10000 0 -10000 0 0
FYN -0.001 0.06 0.27 6 -0.23 4 10
mol:NO 0.022 0.03 -10000 0 -0.21 6 6
GNA15 0.013 0.07 -10000 0 -0.32 16 16
PGK/cGMP -0.022 0.093 -10000 0 -0.18 97 97
RhoA/GDP 0.028 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.025 0.073 -10000 0 -0.29 5 5
NOS3 0.022 0.03 -10000 0 -0.21 6 6
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA -0.063 0.17 0.35 4 -0.34 86 90
PRKCB -0.08 0.18 0.31 3 -0.38 87 90
PRKCE -0.06 0.16 0.33 4 -0.34 82 86
PRKCD -0.069 0.18 0.33 4 -0.37 83 87
PRKCG -0.071 0.18 0.37 4 -0.38 86 90
muscle contraction -0.095 0.22 0.4 4 -0.47 87 91
PRKCZ -0.062 0.16 0.38 4 -0.34 86 90
ARR3 0.019 0.017 -10000 0 -0.21 2 2
TXA2/TP beta 0.012 0.064 -10000 0 -0.24 6 6
PRKCQ -0.067 0.17 0.36 4 -0.36 85 89
MAPKKK cascade -0.089 0.21 0.37 4 -0.45 86 90
SELE -0.07 0.17 0.3 4 -0.37 84 88
TP beta/GNAI2/GDP/G beta/gamma 0.025 0.072 -10000 0 -0.29 5 5
ROCK1 0.026 0.019 -10000 0 -0.32 1 1
GNA14 0.027 0.005 -10000 0 -10000 0 0
chemotaxis -0.12 0.27 0.39 4 -0.6 84 88
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.063 -10000 0 -0.32 13 13
Rac1/GTP 0.019 0.006 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.033 0.033 -10000 0 -0.14 12 12
VLDLR 0.027 0.006 -10000 0 -10000 0 0
CRKL 0.028 0.005 -10000 0 -10000 0 0
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
FYN 0.024 0.01 -10000 0 -10000 0 0
ITGA3 0.021 0.047 -10000 0 -0.32 7 7
RELN/VLDLR/Fyn 0.025 0.058 -10000 0 -0.17 3 3
MAPK8IP1/MKK7/MAP3K11/JNK1 0.067 0.048 -10000 0 -0.16 11 11
AKT1 -0.052 0.099 0.14 3 -0.19 117 120
MAP2K7 0.028 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.007 -10000 0 -10000 0 0
DAB1 -0.099 0.16 -10000 0 -0.31 136 136
RELN/LRP8/DAB1 -0.038 0.11 -10000 0 -0.18 121 121
LRPAP1/LRP8 0.039 0.018 -10000 0 -0.14 2 2
RELN/LRP8/DAB1/Fyn -0.016 0.11 0.18 3 -0.16 121 124
DAB1/alpha3/beta1 Integrin -0.025 0.1 -10000 0 -0.25 17 17
long-term memory -0.045 0.13 -10000 0 -0.21 104 104
DAB1/LIS1 -0.007 0.11 -10000 0 -0.17 106 106
DAB1/CRLK/C3G -0.024 0.1 -10000 0 -0.23 17 17
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
DAB1/NCK2 -0.005 0.12 -10000 0 -0.17 112 112
ARHGEF2 0.027 0.006 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.042 0.14 -10000 0 -0.31 75 75
CDK5R1 0.019 0.045 -10000 0 -0.21 14 14
RELN -0.005 0.081 -10000 0 -0.21 48 48
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
RELN/LRP8/Fyn 0.025 0.059 -10000 0 -0.17 4 4
GRIN2A/RELN/LRP8/DAB1/Fyn -0.041 0.14 -10000 0 -0.19 153 153
MAPK8 0.017 0.058 -10000 0 -0.32 11 11
RELN/VLDLR/DAB1 -0.038 0.11 -10000 0 -0.18 122 122
ITGB1 0.028 0.004 -10000 0 -10000 0 0
MAP1B -0.054 0.11 0.16 9 -0.2 113 122
RELN/LRP8 0.029 0.059 -10000 0 -0.12 44 44
GRIN2B/RELN/LRP8/DAB1/Fyn -0.013 0.11 -10000 0 -0.17 111 111
PI3K 0.032 0.038 -10000 0 -0.23 6 6
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.036 0.034 -10000 0 -0.22 6 6
RAP1A -0.042 0.11 0.37 10 -0.23 17 27
PAFAH1B1 0.026 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.013 -10000 0 -0.21 1 1
CRLK/C3G 0.039 0.011 -10000 0 -10000 0 0
GRIN2B 0.018 0.014 -10000 0 -0.21 1 1
NCK2 0.028 0.003 -10000 0 -10000 0 0
neuron differentiation -0.04 0.098 0.19 1 -0.26 28 29
neuron adhesion -0.043 0.1 0.33 11 -0.33 3 14
LRP8 0.026 0.022 -10000 0 -0.21 3 3
GSK3B -0.052 0.092 0.14 4 -0.23 30 34
RELN/VLDLR/DAB1/Fyn -0.017 0.11 0.18 3 -0.16 121 124
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.051 0.11 0.15 3 -0.2 119 122
CDK5 0.026 0.014 -10000 0 -0.21 1 1
MAPT 0.009 0.086 0.8 4 -0.26 1 5
neuron migration -0.055 0.12 0.26 10 -0.25 19 29
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.04 0.099 0.19 1 -0.26 28 29
RELN/VLDLR 0.067 0.044 0.2 6 -0.16 4 10
Aurora C signaling

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
INCENP 0.028 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.001 0.074 -9999 0 -0.11 108 108
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.001 0.039 -9999 0 -0.38 3 3
AURKB -0.049 0.11 -9999 0 -0.22 113 113
AURKC 0.025 0.031 -9999 0 -0.26 4 4
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.035 0.13 0.24 88 -10000 0 88
GNAI2 0.028 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0.075 -10000 0 -0.18 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.021 0.12 -10000 0 -0.32 50 50
RhoA/GTP -0.036 0.14 -10000 0 -0.24 88 88
negative regulation of cAMP metabolic process -0.038 0.14 0.14 1 -0.26 84 85
GNAZ 0.003 0.089 -10000 0 -0.32 27 27
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.008 -10000 0 -10000 0 0
S1PR5 -0.025 0.12 -10000 0 -0.32 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.038 0.14 -10000 0 -0.26 84 84
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
GNAI1 0.025 0.019 -10000 0 -0.32 1 1
LPA receptor mediated events

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.034 0.072 -10000 0 -0.19 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.1 0.26 5 -0.25 25 30
AP1 -0.017 0.11 -10000 0 -0.19 82 82
mol:PIP3 -0.025 0.084 -10000 0 -0.28 24 24
AKT1 0.028 0.078 0.26 13 -0.24 6 19
PTK2B -0.047 0.12 0.16 2 -0.23 90 92
RHOA 0.011 0.042 0.19 7 -0.25 2 9
PIK3CB 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.082 0.2 16 -0.26 17 33
MAGI3 0.028 0.004 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.019 0.089 -10000 0 -0.21 59 59
HRAS/GDP 0.019 0.018 -10000 0 -0.14 5 5
positive regulation of microtubule depolymerization -0.038 0.11 0.22 6 -0.26 44 50
NF kappa B1 p50/RelA -0.007 0.093 -10000 0 -0.26 24 24
endothelial cell migration 0 0.073 -10000 0 -0.24 25 25
ADCY4 -0.031 0.14 -10000 0 -0.41 38 38
ADCY5 -0.049 0.18 -10000 0 -0.48 47 47
ADCY6 -0.029 0.14 -10000 0 -0.4 38 38
ADCY7 -0.027 0.14 -10000 0 -0.4 36 36
ADCY1 -0.031 0.13 -10000 0 -0.4 35 35
ADCY2 -0.037 0.15 -10000 0 -0.42 42 42
ADCY3 -0.03 0.14 -10000 0 -0.4 38 38
ADCY8 -0.026 0.13 -10000 0 -0.39 33 33
ADCY9 -0.029 0.14 0.14 3 -0.4 37 40
GSK3B -0.041 0.12 0.2 7 -0.27 48 55
arachidonic acid secretion -0.034 0.14 -10000 0 -0.39 41 41
GNG2 0.023 0.04 -10000 0 -0.31 5 5
TRIP6 0.018 0.03 -10000 0 -0.29 3 3
GNAO1 -0.02 0.099 -10000 0 -0.25 50 50
HRAS 0.025 0.027 -10000 0 -0.21 5 5
NFKBIA -0.014 0.1 0.24 13 -0.25 39 52
GAB1 0.027 0.018 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.18 -10000 0 -0.82 15 15
JUN 0.024 0.033 -10000 0 -0.29 4 4
LPA/LPA2/NHERF2 0.033 0.029 -10000 0 -0.13 7 7
TIAM1 -0.006 0.2 -10000 0 -0.95 15 15
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
mol:IP3 -0.011 0.081 0.2 16 -0.21 33 49
PLCB3 0.02 0.036 0.18 13 -10000 0 13
FOS -0.023 0.12 -10000 0 -0.31 55 55
positive regulation of mitosis -0.034 0.14 -10000 0 -0.39 41 41
LPA/LPA1-2-3 0.015 0.093 -10000 0 -0.18 60 60
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.023 0.011 -10000 0 -10000 0 0
stress fiber formation -0.021 0.1 0.22 8 -0.28 31 39
GNAZ -0.01 0.085 -10000 0 -0.23 42 42
EGFR/PI3K-beta/Gab1 -0.017 0.092 -10000 0 -0.29 24 24
positive regulation of dendritic cell cytokine production 0.013 0.091 -10000 0 -0.18 60 60
LPA/LPA2/MAGI-3 0.036 0.023 -10000 0 -0.19 2 2
ARHGEF1 0.022 0.073 0.2 33 -0.25 3 36
GNAI2 0.001 0.06 -10000 0 -0.2 30 30
GNAI3 0.001 0.06 -10000 0 -0.2 29 29
GNAI1 0.003 0.059 0.2 2 -0.2 26 28
LPA/LPA3 -0.009 0.077 -10000 0 -0.2 52 52
LPA/LPA2 0.02 0.023 -10000 0 -0.14 5 5
LPA/LPA1 0.003 0.073 -10000 0 -0.23 31 31
HB-EGF/EGFR -0.068 0.093 0.16 3 -0.24 43 46
HBEGF -0.072 0.084 0.19 5 -0.14 205 210
mol:DAG -0.011 0.081 0.2 16 -0.21 33 49
cAMP biosynthetic process -0.029 0.15 0.23 12 -0.38 45 57
NFKB1 0.028 0.003 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
GNB1 0.028 0.005 -10000 0 -10000 0 0
LYN -0.004 0.11 0.26 18 -0.26 34 52
GNAQ -0.006 0.064 -10000 0 -0.19 39 39
LPAR2 0.027 0.018 -10000 0 -0.31 1 1
LPAR3 -0.015 0.11 -10000 0 -0.3 48 48
LPAR1 0 0.095 -10000 0 -0.31 31 31
IL8 -0.072 0.18 0.41 4 -0.43 59 63
PTK2 -0.01 0.067 0.18 5 -0.16 45 50
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
CASP3 -0.019 0.089 -10000 0 -0.21 59 59
EGFR -0.007 0.1 -10000 0 -0.32 36 36
PLCG1 -0.012 0.074 0.16 2 -0.21 37 39
PLD2 -0.009 0.079 0.18 12 -0.18 53 65
G12/G13 0.035 0.061 -10000 0 -0.17 25 25
PI3K-beta 0.009 0.052 -10000 0 -0.26 6 6
cell migration 0.002 0.064 -10000 0 -0.25 14 14
SLC9A3R2 0.024 0.027 -10000 0 -0.21 5 5
PXN -0.021 0.11 0.22 8 -0.29 31 39
HRAS/GTP -0.036 0.14 -10000 0 -0.41 40 40
RAC1 0.026 0.008 -10000 0 -10000 0 0
MMP9 -0.11 0.12 -10000 0 -0.21 209 209
PRKCE 0.027 0.006 -10000 0 -10000 0 0
PRKCD -0.013 0.085 0.2 17 -0.26 15 32
Gi(beta/gamma) -0.027 0.14 0.15 4 -0.38 39 43
mol:LPA -0.001 0.02 -10000 0 -0.16 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.003 0.09 -10000 0 -0.28 14 14
MAPKKK cascade -0.034 0.14 -10000 0 -0.39 41 41
contractile ring contraction involved in cytokinesis 0.012 0.043 0.2 6 -0.25 2 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.006 0.063 -10000 0 -0.19 39 39
GNA15 -0.012 0.078 -10000 0 -0.2 47 47
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
MAPT -0.039 0.11 0.22 6 -0.27 44 50
GNA11 -0.012 0.076 -10000 0 -0.2 46 46
Rac1/GTP 0.011 0.18 -10000 0 -0.87 15 15
MMP2 0 0.073 -10000 0 -0.24 25 25
Signaling events mediated by the Hedgehog family

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
TGFB2 0.009 0.12 -10000 0 -0.48 16 16
IHH 0.015 0.079 0.22 4 -0.19 39 43
SHH Np/Cholesterol/GAS1 -0.022 0.081 0.18 1 -0.15 95 96
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.022 0.08 0.15 95 -0.18 1 96
SMO/beta Arrestin2 0.015 0.091 -10000 0 -0.33 13 13
SMO 0.003 0.086 -10000 0 -0.33 18 18
AKT1 0.004 0.097 -10000 0 -0.41 10 10
ARRB2 0.026 0.008 -10000 0 -10000 0 0
BOC 0.018 0.056 -10000 0 -0.32 10 10
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping 0.004 0.086 -10000 0 -0.32 18 18
STIL -0.015 0.093 0.2 15 -0.26 19 34
DHH N/PTCH2 0.035 0.04 -10000 0 -0.2 10 10
DHH N/PTCH1 0.02 0.081 -10000 0 -0.26 19 19
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
DHH 0.021 0.047 -10000 0 -0.29 8 8
PTHLH -0.004 0.15 -10000 0 -0.62 17 17
determination of left/right symmetry 0.004 0.086 -10000 0 -0.32 18 18
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
skeletal system development -0.003 0.15 -10000 0 -0.62 17 17
IHH N/Hhip 0.016 0.11 0.17 3 -0.27 41 44
DHH N/Hhip 0.013 0.08 -10000 0 -0.21 41 41
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.004 0.086 -10000 0 -0.32 18 18
pancreas development -0.002 0.097 -10000 0 -0.31 33 33
HHAT 0.024 0.031 -10000 0 -0.32 3 3
PI3K 0.032 0.038 -10000 0 -0.23 6 6
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.005 0.1 -10000 0 -0.32 35 35
somite specification 0.004 0.086 -10000 0 -0.32 18 18
SHH Np/Cholesterol/PTCH1 -0.015 0.085 0.18 1 -0.27 18 19
SHH Np/Cholesterol/PTCH2 -0.009 0.072 0.16 3 -0.14 78 81
SHH Np/Cholesterol/Megalin -0.024 0.085 0.16 3 -0.17 73 76
SHH -0.028 0.086 0.23 3 -0.19 77 80
catabolic process 0.005 0.084 -10000 0 -0.31 17 17
SMO/Vitamin D3 -0.009 0.096 0.45 1 -0.32 15 16
SHH Np/Cholesterol/Hhip -0.021 0.088 0.16 3 -0.16 94 97
LRP2 -0.005 0.097 -10000 0 -0.3 36 36
receptor-mediated endocytosis -0.024 0.1 -10000 0 -0.34 18 18
SHH Np/Cholesterol/BOC -0.012 0.073 0.15 2 -0.17 53 55
SHH Np/Cholesterol/CDO -0.01 0.07 0.16 3 -0.14 80 83
mesenchymal cell differentiation 0.021 0.087 0.16 94 -0.16 3 97
mol:Vitamin D3 -0.004 0.098 0.21 16 -0.27 18 34
IHH N/PTCH2 0.036 0.067 0.17 3 -0.21 20 23
CDON 0.025 0.025 -10000 0 -0.24 3 3
IHH N/PTCH1 0.024 0.092 0.23 2 -0.31 17 19
Megalin/LRPAP1 0.015 0.073 -10000 0 -0.2 36 36
PTCH2 0.026 0.025 -10000 0 -0.32 2 2
SHH Np/Cholesterol -0.018 0.064 -10000 0 -0.14 79 79
PTCH1 0.005 0.084 -10000 0 -0.31 17 17
HHIP -0.002 0.097 -10000 0 -0.31 33 33
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.036 0.13 -10000 0 -0.32 68 68
GNB1/GNG2 -0.009 0.12 -10000 0 -0.3 29 29
mol:DAG -0.021 0.11 0.19 7 -0.28 29 36
PLCG1 -0.022 0.11 0.19 7 -0.28 29 36
YES1 -0.026 0.098 -10000 0 -0.22 62 62
FZD3 0.021 0.012 -10000 0 -10000 0 0
FZD6 0.023 0.011 -10000 0 -10000 0 0
G protein -0.005 0.12 0.21 11 -0.29 29 40
MAP3K7 -0.036 0.1 0.18 9 -0.27 32 41
mol:Ca2+ -0.021 0.1 0.18 7 -0.27 29 36
mol:IP3 -0.021 0.11 0.19 7 -0.28 29 36
NLK 0.005 0.072 -10000 0 -0.78 3 3
GNB1 0.028 0.004 -10000 0 -10000 0 0
CAMK2A -0.042 0.11 0.19 10 -0.27 43 53
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.023 0.11 -10000 0 -0.23 66 66
CSNK1A1 0.028 0.004 -10000 0 -10000 0 0
GNAS -0.028 0.099 -10000 0 -0.22 65 65
GO:0007205 -0.025 0.1 0.21 8 -0.27 30 38
WNT6 -0.04 0.14 -10000 0 -0.31 75 75
WNT4 0.023 0.04 -10000 0 -0.32 5 5
NFAT1/CK1 alpha -0.036 0.12 -10000 0 -0.3 32 32
GNG2 0.023 0.04 -10000 0 -0.32 5 5
WNT5A 0.004 0.084 -10000 0 -0.29 28 28
WNT11 0.012 0.064 -10000 0 -0.24 22 22
CDC42 -0.027 0.097 0.14 1 -0.29 24 25
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.037 0.18 0.26 1 -0.38 62 63
MAP3K8 0.018 0.053 -10000 0 -0.3 10 10
FOS -0.032 0.14 0.24 2 -0.36 39 41
PRKCA 0.011 0.064 -10000 0 -0.32 13 13
PTPN7 0.012 0.046 -10000 0 -0.2 13 13
HRAS 0.024 0.027 -10000 0 -0.21 5 5
PRKCB -0.049 0.14 -10000 0 -0.32 78 78
NRAS 0.027 0.018 -10000 0 -0.32 1 1
RAS family/GTP 0.045 0.025 -10000 0 -0.15 2 2
MAPK3 -0.007 0.094 0.24 1 -0.39 7 8
MAP2K1 -0.07 0.2 -10000 0 -0.41 77 77
ELK1 0.02 0.02 -10000 0 -10000 0 0
BRAF -0.056 0.17 -10000 0 -0.39 66 66
mol:GTP -0.001 0.002 -10000 0 -0.004 58 58
MAPK1 -0.011 0.11 0.24 1 -0.43 11 12
RAF1 -0.064 0.18 -10000 0 -0.38 76 76
KRAS 0.026 0.008 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.028 0.16 -10000 0 -0.75 4 4
CRP -0.029 0.17 0.5 3 -0.71 5 8
cell cycle arrest -0.035 0.18 0.39 1 -0.68 10 11
TIMP1 -0.018 0.18 -10000 0 -0.82 8 8
IL6ST -0.039 0.13 -10000 0 -0.32 67 67
Rac1/GDP -0.066 0.18 -10000 0 -0.38 67 67
AP1 0.017 0.14 -10000 0 -0.52 13 13
GAB2 0.028 0.005 -10000 0 -10000 0 0
TNFSF11 -0.036 0.18 -10000 0 -0.77 11 11
HSP90B1 0.022 0.078 -10000 0 -0.54 4 4
GAB1 0.028 0.018 -10000 0 -0.31 1 1
MAPK14 -0.12 0.26 0.21 2 -0.59 72 74
AKT1 0.027 0.069 0.26 1 -0.52 3 4
FOXO1 0.021 0.064 -10000 0 -0.49 3 3
MAP2K6 -0.1 0.21 -10000 0 -0.46 81 81
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.059 0.17 0.31 3 -0.38 55 58
MITF -0.079 0.17 -10000 0 -0.38 75 75
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.028 0.004 -10000 0 -10000 0 0
A2M -0.072 0.33 -10000 0 -1.2 31 31
CEBPB 0.032 0.007 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.004 0.11 -10000 0 -0.46 12 12
STAT3 -0.041 0.18 -10000 0 -0.72 10 10
STAT1 0.01 0.084 -10000 0 -0.88 3 3
CEBPD -0.014 0.17 0.54 1 -0.76 4 5
PIK3CA 0.024 0.034 -10000 0 -0.29 4 4
PI3K 0.033 0.039 -10000 0 -0.23 6 6
JUN 0.024 0.033 -10000 0 -0.29 4 4
PIAS3/MITF -0.067 0.18 0.21 1 -0.37 75 76
MAPK11 -0.12 0.26 0.22 1 -0.59 73 74
STAT3 (dimer)/FOXO1 -0.012 0.14 0.39 1 -0.59 5 6
GRB2/SOS1/GAB family -0.034 0.17 -10000 0 -0.33 67 67
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.071 0.17 0.17 2 -0.33 88 90
GRB2 0.028 0.006 -10000 0 -10000 0 0
JAK2 0.026 0.019 -10000 0 -0.32 1 1
LBP -0.016 0.15 0.37 1 -0.6 6 7
PIK3R1 0.024 0.032 -10000 0 -0.31 3 3
JAK1 0.023 0.02 -10000 0 -10000 0 0
MYC -0.003 0.18 0.47 5 -0.62 8 13
FGG -0.035 0.16 -10000 0 -0.64 7 7
macrophage differentiation -0.035 0.18 0.39 1 -0.68 10 11
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.021 0.15 -10000 0 -0.26 83 83
JUNB -0.045 0.21 0.53 1 -0.97 12 13
FOS -0.023 0.12 -10000 0 -0.31 55 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.08 0.18 -10000 0 -0.39 80 80
STAT1/PIAS1 -0.042 0.16 0.23 1 -0.33 54 55
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.073 -10000 0 -0.55 3 3
STAT3 (dimer) -0.038 0.18 -10000 0 -0.71 10 10
PRKCD -0.043 0.18 0.32 11 -0.53 20 31
IL6R -0.005 0.094 -10000 0 -0.32 30 30
SOCS3 -0.18 0.39 -10000 0 -1.1 49 49
gp130 (dimer)/JAK1/JAK1/LMO4 0.001 0.099 -10000 0 -0.19 70 70
Rac1/GTP -0.064 0.18 -10000 0 -0.38 66 66
HCK 0.024 0.033 -10000 0 -0.29 4 4
MAPKKK cascade 0.009 0.12 -10000 0 -0.55 11 11
bone resorption -0.031 0.18 -10000 0 -0.72 11 11
IRF1 -0.029 0.16 0.44 1 -0.76 4 5
mol:GDP -0.081 0.18 0.16 1 -0.38 79 80
SOS1 0.028 0.006 -10000 0 -10000 0 0
VAV1 -0.083 0.18 0.16 2 -0.38 79 81
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.13 0.29 -10000 0 -0.61 77 77
PTPN11 0.007 0.082 -10000 0 -0.66 5 5
IL6/IL6RA -0.046 0.12 -10000 0 -0.21 124 124
gp130 (dimer)/TYK2/TYK2/LMO4 0.003 0.095 -10000 0 -0.18 69 69
gp130 (dimer)/JAK2/JAK2/LMO4 0.003 0.096 -10000 0 -0.18 69 69
IL6 -0.062 0.14 -10000 0 -0.28 107 107
PIAS3 0.027 0.006 -10000 0 -10000 0 0
PTPRE 0.024 0.03 -10000 0 -0.28 3 3
PIAS1 0.027 0.018 -10000 0 -0.32 1 1
RAC1 0.026 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.072 0.16 0.16 2 -0.29 113 115
LMO4 0.022 0.031 -10000 0 -0.39 1 1
STAT3 (dimer)/PIAS3 -0.035 0.18 -10000 0 -0.66 11 11
MCL1 0.036 0.079 0.4 3 -0.81 1 4
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.04 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.031 0.045 -10000 0 -0.16 16 16
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.044 0.082 -10000 0 -0.16 48 48
NGF (dimer)/p75(NTR)/BEX1 -0.04 0.14 -10000 0 -0.21 130 130
NT-4/5 (dimer)/p75(NTR) -0.031 0.14 -10000 0 -0.27 84 84
IKBKB 0.022 0.012 -10000 0 -10000 0 0
AKT1 0 0.072 0.18 19 -0.29 3 22
IKBKG 0.028 0.001 -10000 0 -10000 0 0
BDNF -0.042 0.14 -10000 0 -0.32 75 75
MGDIs/NGR/p75(NTR)/LINGO1 0.017 0.081 -10000 0 -0.19 32 32
FURIN 0.028 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.01 0.12 -10000 0 -0.21 89 89
LINGO1 0.002 0.074 -10000 0 -0.21 41 41
Sortilin/TRAF6/NRIF 0.034 0.014 -10000 0 -10000 0 0
proBDNF (dimer) -0.042 0.14 -10000 0 -0.31 75 75
NTRK1 0.002 0.085 -10000 0 -0.29 28 28
RTN4R 0.027 0.013 -10000 0 -0.21 1 1
neuron apoptosis -0.042 0.12 0.3 1 -0.33 33 34
IRAK1 0.028 0.001 -10000 0 -10000 0 0
SHC1 -0.008 0.065 -10000 0 -0.18 43 43
ARHGDIA 0.028 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.021 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.075 0.027 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.038 0.084 -10000 0 -0.17 48 48
MAGEH1 0.024 0.034 -10000 0 -0.22 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.035 0.084 -10000 0 -0.17 48 48
Mammalian IAPs/DIABLO 0.067 0.023 -10000 0 -0.16 1 1
proNGF (dimer) 0.011 0.073 -10000 0 -0.31 18 18
MAGED1 0.028 0.012 -10000 0 -0.21 1 1
APP 0.026 0.026 -10000 0 -0.32 2 2
NT-4/5 (dimer) -0.046 0.14 -10000 0 -0.31 80 80
ZNF274 0.028 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.013 0.066 -10000 0 -0.16 45 45
NGF 0.011 0.073 -10000 0 -0.31 18 18
cell cycle arrest 0.004 0.081 0.24 17 -0.26 1 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.005 0.066 0.15 2 -0.18 38 40
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.008 0.12 -10000 0 -0.22 83 83
NCSTN 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0.021 0.081 -10000 0 -0.18 48 48
PSENEN 0.028 0.003 -10000 0 -10000 0 0
mol:ceramide -0.003 0.061 0.18 6 -0.17 36 42
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.006 0.055 0.14 2 -0.28 2 4
p75(NTR)/beta APP 0.017 0.075 -10000 0 -0.22 32 32
BEX1 -0.075 0.16 -10000 0 -0.31 113 113
mol:GDP -0.028 0.06 -10000 0 -0.18 48 48
NGF (dimer) 0.043 0.085 -10000 0 -0.18 40 40
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.052 0.073 0.2 1 -0.17 32 33
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
RAC1/GTP 0.019 0.067 -10000 0 -0.15 44 44
MYD88 0.028 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.021 0.082 -10000 0 -0.18 48 48
RHOB 0.022 0.043 -10000 0 -0.32 6 6
RHOA 0.028 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.036 -10000 0 -0.14 14 14
NT3 (dimer) -0.006 0.1 -10000 0 -0.31 35 35
TP53 -0.036 0.077 0.18 11 -0.27 13 24
PRDM4 -0.005 0.064 0.18 5 -0.17 44 49
BDNF (dimer) -0.017 0.14 -10000 0 -0.2 120 120
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
SORT1 0.028 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.039 0.079 -10000 0 -0.16 48 48
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.038 0.08 -10000 0 -0.17 46 46
RHOC 0.028 0.005 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
MAPK10 -0.033 0.1 0.32 3 -0.28 35 38
DIABLO 0.027 0.006 -10000 0 -10000 0 0
SMPD2 -0.003 0.062 0.18 6 -0.17 36 42
APH1B 0.028 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.022 0.082 -10000 0 -0.18 48 48
PSEN1 0.028 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.005 0.11 -10000 0 -0.25 54 54
MAPK8 -0.039 0.11 0.36 2 -0.31 29 31
MAPK9 -0.033 0.1 0.32 3 -0.28 33 36
APAF1 0.027 0.006 -10000 0 -10000 0 0
NTF3 -0.006 0.1 -10000 0 -0.32 35 35
NTF4 -0.047 0.14 -10000 0 -0.32 80 80
NDN 0.025 0.031 -10000 0 -0.32 3 3
RAC1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.037 0.079 -10000 0 -0.16 47 47
p75 CTF/Sortilin/TRAF6/NRIF 0.065 0.033 -10000 0 -0.16 5 5
RhoA-B-C/GTP 0.02 0.081 -10000 0 -0.18 48 48
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.016 0.11 -10000 0 -0.18 88 88
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.005 0.11 -10000 0 -0.19 89 89
PRKACB 0.027 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.013 0.11 -10000 0 -0.22 75 75
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.025 0.025 -10000 0 -0.24 3 3
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0 0.081 0.23 6 -0.19 24 30
BAD -0.034 0.12 0.25 11 -0.3 34 45
RIPK2 0.023 0.011 -10000 0 -10000 0 0
NGFR -0.002 0.096 -10000 0 -0.32 32 32
CYCS -0.005 0.06 0.18 6 -0.27 2 8
ADAM17 0.023 0.04 -10000 0 -0.32 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.032 0.076 0.2 2 -0.17 39 41
BCL2L11 -0.035 0.11 0.24 10 -0.3 34 44
BDNF (dimer)/p75(NTR) -0.029 0.13 -10000 0 -0.24 89 89
PI3K 0.03 0.082 -10000 0 -0.17 46 46
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.036 0.081 -10000 0 -0.17 47 47
NDNL2 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKCI 0.026 0.008 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.005 0.089 -10000 0 -0.22 49 49
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.037 0.082 -10000 0 -0.17 48 48
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCZ 0.028 0.004 -10000 0 -10000 0 0
PLG 0.01 0.053 -10000 0 -0.21 20 20
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.038 0.11 -10000 0 -0.21 95 95
SQSTM1 0.028 0.005 -10000 0 -10000 0 0
NGFRAP1 0.028 0.001 -10000 0 -10000 0 0
CASP3 -0.03 0.11 0.24 9 -0.3 26 35
E2F1 0.018 0.046 -10000 0 -0.21 15 15
CASP9 0.028 0.003 -10000 0 -10000 0 0
IKK complex 0.029 0.091 -10000 0 -0.28 8 8
NGF (dimer)/TRKA 0.009 0.083 -10000 0 -0.21 44 44
MMP7 -0.022 0.11 -10000 0 -0.25 66 66
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.081 -10000 0 -0.16 45 45
MMP3 -0.022 0.11 -10000 0 -0.27 60 60
APAF-1/Caspase 9 0 0.053 -10000 0 -0.24 3 3
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.031 0.057 -10000 0 -0.17 22 22
fibroblast growth factor receptor signaling pathway 0.031 0.056 -10000 0 -0.17 22 22
LAMA1 0.002 0.081 -10000 0 -0.26 32 32
PRNP 0.028 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 0.006 0.088 -10000 0 -0.22 48 48
SMAD2 0.015 0.038 0.18 10 -0.16 8 18
GPC1/PrPc/Cu2+ 0.036 0.013 -10000 0 -0.18 1 1
GPC1/Laminin alpha1 0.021 0.062 -10000 0 -0.17 32 32
TDGF1 -0.014 0.11 -10000 0 -0.31 45 45
CRIPTO/GPC1 0.01 0.082 -10000 0 -0.21 44 44
APP/GPC1 0.039 0.021 -10000 0 -0.22 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.006 0.062 0.1 1 -0.18 42 43
FLT1 0.023 0.038 -10000 0 -0.29 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.048 0.037 -10000 0 -0.18 8 8
SERPINC1 0.012 0.054 -10000 0 -0.21 21 21
FYN -0.006 0.06 -10000 0 -0.18 38 38
FGR -0.007 0.065 0.1 1 -0.18 46 47
positive regulation of MAPKKK cascade -0.029 0.1 0.37 3 -0.27 40 43
SLIT2 -0.017 0.12 -10000 0 -0.32 48 48
GPC1/NRG -0.001 0.084 -10000 0 -0.22 47 47
NRG1 -0.022 0.11 -10000 0 -0.32 47 47
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.038 0.062 -10000 0 -0.19 23 23
LYN -0.004 0.057 -10000 0 -0.18 36 36
mol:Spermine 0.007 0.012 -10000 0 -0.21 1 1
cell growth 0.031 0.056 -10000 0 -0.17 22 22
BMP signaling pathway -0.027 0.018 0.31 1 -10000 0 1
SRC -0.006 0.063 0.1 1 -0.18 43 44
TGFBR1 0.027 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.069 0.12 -10000 0 -0.22 146 146
GPC1 0.027 0.018 -10000 0 -0.32 1 1
TGFBR1 (dimer) 0.027 0.006 -10000 0 -10000 0 0
VEGFA 0.009 0.077 -10000 0 -0.3 21 21
BLK -0.031 0.083 -10000 0 -0.18 79 79
HCK -0.008 0.064 0.1 1 -0.18 46 47
FGF2 0.005 0.084 -10000 0 -0.32 24 24
FGFR1 0.02 0.021 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.023 0.038 -10000 0 -0.29 5 5
TGFBR2 0.018 0.056 -10000 0 -0.32 10 10
cell death 0.039 0.021 -10000 0 -0.22 2 2
ATIII/GPC1 0.028 0.044 -10000 0 -0.14 22 22
PLA2G2A/GPC1 -0.032 0.093 -10000 0 -0.15 145 145
LCK -0.007 0.064 0.1 1 -0.17 47 48
neuron differentiation -0.001 0.084 -10000 0 -0.22 47 47
PrPc/Cu2+ 0.021 0.003 -10000 0 -10000 0 0
APP 0.026 0.026 -10000 0 -0.32 2 2
TGFBR2 (dimer) 0.018 0.056 -10000 0 -0.31 10 10
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.018 0.066 -10000 0 -0.2 13 13
alphaM/beta2 Integrin/GPIbA 0.016 0.067 -10000 0 -0.19 15 15
alphaM/beta2 Integrin/proMMP-9 -0.063 0.087 -10000 0 -0.16 75 75
PLAUR 0.023 0.034 -10000 0 -0.21 8 8
HMGB1 0.007 0.034 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.022 0.059 -10000 0 -0.18 7 7
AGER -0.003 0.061 -10000 0 -0.24 15 15
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
SELPLG 0.024 0.028 -10000 0 -0.21 5 5
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.001 0.12 -10000 0 -0.2 86 86
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.11 0.12 -10000 0 -0.21 209 209
CYR61 0.017 0.055 -10000 0 -0.28 12 12
TLN1 0.028 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.02 0.1 -10000 0 -0.25 38 38
RHOA 0.028 0.004 -10000 0 -10000 0 0
P-selectin oligomer 0.021 0.044 -10000 0 -0.31 6 6
MYH2 -0.066 0.12 0.16 2 -0.32 47 49
MST1R 0.017 0.059 -10000 0 -0.29 13 13
leukocyte activation during inflammatory response -0.031 0.11 -10000 0 -0.19 104 104
APOB -0.049 0.14 -10000 0 -0.31 83 83
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.05 -10000 0 -0.32 8 8
JAM3 0.018 0.058 -10000 0 -0.32 11 11
GP1BA 0.018 0.048 -10000 0 -0.28 9 9
alphaM/beta2 Integrin/CTGF 0.013 0.076 -10000 0 -0.2 24 24
alphaM/beta2 Integrin -0.035 0.1 -10000 0 -0.27 41 41
JAM3 homodimer 0.018 0.058 -10000 0 -0.31 11 11
ICAM2 0.025 0.028 -10000 0 -0.28 3 3
ICAM1 0.022 0.036 -10000 0 -0.21 9 9
phagocytosis triggered by activation of immune response cell surface activating receptor -0.034 0.1 -10000 0 -0.27 41 41
cell adhesion 0.016 0.066 -10000 0 -0.19 15 15
NFKB1 -0.076 0.16 -10000 0 -0.34 91 91
THY1 0.025 0.025 -10000 0 -0.21 4 4
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.034 0.11 -10000 0 -0.2 111 111
alphaM/beta2 Integrin/LRP/tPA 0.024 0.068 -10000 0 -0.17 16 16
IL6 -0.13 0.24 -10000 0 -0.55 84 84
ITGB2 0.004 0.045 -10000 0 -0.21 6 6
elevation of cytosolic calcium ion concentration 0.023 0.073 0.19 1 -0.18 17 18
alphaM/beta2 Integrin/JAM2/JAM3 0.027 0.079 -10000 0 -0.2 19 19
JAM2 0.024 0.036 -10000 0 -0.32 4 4
alphaM/beta2 Integrin/ICAM1 0.036 0.088 0.2 1 -0.17 34 35
alphaM/beta2 Integrin/uPA/Plg 0.025 0.077 0.19 1 -0.17 25 26
RhoA/GTP -0.046 0.12 -10000 0 -0.3 46 46
positive regulation of phagocytosis -0.02 0.092 0.17 1 -0.26 21 22
Ron/MSP 0.012 0.071 -10000 0 -0.15 54 54
alphaM/beta2 Integrin/uPAR/uPA 0.025 0.075 0.2 1 -0.18 17 18
alphaM/beta2 Integrin/uPAR 0.018 0.064 -10000 0 -0.16 15 15
PLAU 0.019 0.053 -10000 0 -0.32 9 9
PLAT 0.012 0.052 -10000 0 -0.24 14 14
actin filament polymerization -0.063 0.12 -10000 0 -0.31 46 46
MST1 0.001 0.074 -10000 0 -0.21 42 42
alphaM/beta2 Integrin/lipoprotein(a) -0.027 0.12 0.18 1 -0.19 104 105
TNF -0.092 0.19 0.21 1 -0.39 86 87
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.016 0.069 -10000 0 -0.2 16 16
fibrinolysis 0.023 0.075 0.19 1 -0.17 25 26
HCK 0.024 0.033 -10000 0 -0.29 4 4
dendritic cell antigen processing and presentation -0.034 0.1 -10000 0 -0.27 41 41
VTN -0.036 0.12 -10000 0 -0.26 82 82
alphaM/beta2 Integrin/CYR61 0.017 0.071 -10000 0 -0.2 17 17
LPA -0.014 0.11 -10000 0 -0.3 46 46
LRP1 0.026 0.022 -10000 0 -0.26 2 2
cell migration -0.061 0.082 0.19 3 -0.18 49 52
FN1 0.022 0.043 -10000 0 -0.32 6 6
alphaM/beta2 Integrin/Thy1 0.02 0.061 -10000 0 -0.16 10 10
MPO -0.002 0.095 -10000 0 -0.32 31 31
KNG1 -0.004 0.07 -10000 0 -0.21 39 39
RAP1/GDP 0.035 0.015 -10000 0 -0.18 1 1
ROCK1 -0.044 0.11 0.16 2 -0.32 35 37
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.01 0.053 -10000 0 -0.21 20 20
CTGF 0.012 0.071 -10000 0 -0.31 17 17
alphaM/beta2 Integrin/Hck 0.02 0.064 -10000 0 -0.19 12 12
ITGAM 0.004 0.045 -10000 0 -0.26 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.029 0.071 0.2 1 -0.2 13 14
HP -0.019 0.099 -10000 0 -0.24 60 60
leukocyte adhesion -0.012 0.11 -10000 0 -0.28 25 25
SELP 0.021 0.044 -10000 0 -0.32 6 6
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.008 0.084 -10000 0 -0.23 37 37
PDGFRB 0.026 0.013 -10000 0 -0.21 1 1
SPHK1 -0.01 0.099 -10000 0 -0.63 8 8
mol:S1P -0.012 0.091 0.25 1 -0.52 8 9
S1P1/S1P/Gi -0.093 0.2 0.22 1 -0.41 86 87
GNAO1 -0.026 0.12 -10000 0 -0.32 50 50
PDGFB-D/PDGFRB/PLCgamma1 -0.07 0.18 0.24 3 -0.38 80 83
PLCG1 -0.088 0.18 0.21 1 -0.39 83 84
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.026 0.013 -10000 0 -0.21 1 1
GNAI2 0.021 0.019 -10000 0 -10000 0 0
GNAI3 0.02 0.019 -10000 0 -10000 0 0
GNAI1 0.018 0.026 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.019 0.061 -10000 0 -0.19 37 37
S1P1/S1P -0.026 0.097 0.18 5 -0.32 19 24
negative regulation of cAMP metabolic process -0.09 0.19 0.22 1 -0.4 86 87
MAPK3 -0.12 0.25 0.25 2 -0.55 84 86
calcium-dependent phospholipase C activity -0.002 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
KDR 0.009 0.076 -10000 0 -0.32 19 19
PLCB2 -0.018 0.092 0.2 8 -0.29 18 26
RAC1 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.083 -10000 0 -0.28 19 19
receptor internalization -0.025 0.091 0.17 4 -0.29 20 24
PTGS2 -0.19 0.39 0.38 1 -0.95 72 73
Rac1/GTP -0.021 0.081 -10000 0 -0.28 18 18
RHOA 0.028 0.004 -10000 0 -10000 0 0
VEGFA 0.008 0.078 -10000 0 -0.31 21 21
negative regulation of T cell proliferation -0.09 0.19 0.22 1 -0.4 86 87
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.004 0.091 -10000 0 -0.32 27 27
MAPK1 -0.12 0.26 0.23 2 -0.56 84 86
S1P1/S1P/PDGFB-D/PDGFRB -0.021 0.11 0.2 5 -0.27 28 33
ABCC1 0.027 0.006 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 0.013 0.069 -10000 0 -0.19 36 36
cell-cell adhesion 0.05 0.071 0.26 18 -10000 0 18
Ephrin B/EPHB2/RasGAP 0.038 0.09 -10000 0 -0.18 44 44
ITSN1 0.028 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
SHC1 0.027 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.034 0.023 -10000 0 -0.16 4 4
Ephrin B1/EPHB1 -0.022 0.095 -10000 0 -0.18 96 96
HRAS/GDP -0.026 0.099 -10000 0 -0.26 28 28
Ephrin B/EPHB1/GRB7 -0.008 0.12 -10000 0 -0.18 110 110
Endophilin/SYNJ1 -0.008 0.068 0.18 5 -0.32 5 10
KRAS 0.026 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.008 0.12 -10000 0 -0.17 110 110
endothelial cell migration 0.046 0.036 -10000 0 -0.2 3 3
GRB2 0.027 0.006 -10000 0 -10000 0 0
GRB7 0.028 0.004 -10000 0 -10000 0 0
PAK1 -0.014 0.074 0.2 17 -0.35 4 21
HRAS 0.025 0.027 -10000 0 -0.21 5 5
RRAS -0.01 0.072 0.18 4 -0.32 7 11
DNM1 0.025 0.022 -10000 0 -0.26 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.032 0.099 0.19 16 -0.27 22 38
lamellipodium assembly -0.05 0.071 -10000 0 -0.26 18 18
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.048 0.12 -10000 0 -0.29 48 48
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
EPHB2 0.023 0.037 -10000 0 -0.26 6 6
EPHB3 0.026 0.014 -10000 0 -0.21 1 1
EPHB1 -0.063 0.15 -10000 0 -0.32 96 96
EPHB4 0.026 0.008 -10000 0 -10000 0 0
mol:GDP -0.034 0.087 0.18 7 -0.23 41 48
Ephrin B/EPHB2 0.029 0.083 -10000 0 -0.17 44 44
Ephrin B/EPHB3 0.03 0.075 -10000 0 -0.16 40 40
JNK cascade -0.019 0.1 0.33 14 -0.32 3 17
Ephrin B/EPHB1 -0.016 0.11 -10000 0 -0.17 114 114
RAP1/GDP -0.015 0.1 0.26 9 -0.26 23 32
EFNB2 0.019 0.042 -10000 0 -0.21 12 12
EFNB3 -0.015 0.11 -10000 0 -0.32 42 42
EFNB1 0.025 0.035 -10000 0 -0.32 4 4
Ephrin B2/EPHB1-2 -0.011 0.096 -10000 0 -0.16 103 103
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
CDC42/GTP -0.02 0.11 -10000 0 -0.25 38 38
Rap1/GTP -0.031 0.091 -10000 0 -0.27 20 20
axon guidance 0.013 0.068 -10000 0 -0.19 36 36
MAPK3 -0.05 0.1 0.19 2 -0.26 49 51
MAPK1 -0.053 0.11 0.19 1 -0.26 51 52
Rac1/GDP -0.028 0.096 0.24 4 -0.25 27 31
actin cytoskeleton reorganization -0.034 0.072 -10000 0 -0.24 17 17
CDC42/GDP -0.024 0.1 0.25 9 -0.25 27 36
PI3K 0.05 0.038 -10000 0 -0.2 3 3
EFNA5 -0.005 0.098 -10000 0 -0.31 34 34
Ephrin B2/EPHB4 0.029 0.027 -10000 0 -0.11 10 10
Ephrin B/EPHB2/Intersectin/N-WASP -0.001 0.081 -10000 0 -0.21 39 39
CDC42 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.034 0.086 -10000 0 -0.25 23 23
PTK2 0.093 0.21 0.59 56 -10000 0 56
MAP4K4 -0.019 0.1 0.33 14 -0.32 3 17
SRC 0.027 0.006 -10000 0 -10000 0 0
KALRN 0.026 0.014 -10000 0 -0.21 1 1
Intersectin/N-WASP 0.038 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis -0.023 0.11 0.32 14 -0.28 16 30
MAP2K1 -0.05 0.11 -10000 0 -0.28 48 48
WASL 0.026 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.004 0.11 -10000 0 -0.17 95 95
cell migration -0.064 0.14 0.25 9 -0.31 55 64
NRAS 0.027 0.018 -10000 0 -0.32 1 1
SYNJ1 -0.008 0.068 0.18 5 -0.33 5 10
PXN 0.027 0.006 -10000 0 -10000 0 0
TF -0.041 0.082 0.18 3 -0.27 27 30
HRAS/GTP -0.017 0.1 -10000 0 -0.26 24 24
Ephrin B1/EPHB1-2 -0.009 0.098 -10000 0 -0.17 98 98
cell adhesion mediated by integrin 0.017 0.063 0.19 24 -0.19 2 26
RAC1 0.026 0.008 -10000 0 -10000 0 0
mol:GTP -0.017 0.11 -10000 0 -0.18 83 83
RAC1-CDC42/GTP -0.037 0.084 -10000 0 -0.26 20 20
RASA1 0.025 0.026 -10000 0 -0.32 2 2
RAC1-CDC42/GDP -0.021 0.097 0.29 1 -0.25 25 26
ruffle organization -0.025 0.12 0.34 16 -0.3 13 29
NCK1 0.026 0.008 -10000 0 -10000 0 0
receptor internalization -0.025 0.059 0.17 4 -0.28 6 10
Ephrin B/EPHB2/KALRN 0.042 0.082 -10000 0 -0.17 37 37
ROCK1 0.021 0.037 0.18 16 -0.16 2 18
RAS family/GDP -0.045 0.063 -10000 0 -0.24 17 17
Rac1/GTP -0.033 0.086 -10000 0 -0.28 18 18
Ephrin B/EPHB1/Src/Paxillin -0.054 0.13 -10000 0 -0.23 114 114
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.023 0.11 -9999 0 -0.23 66 66
FZD6 0.023 0.011 -9999 0 -10000 0 0
WNT6 -0.04 0.14 -9999 0 -0.31 75 75
WNT4 0.023 0.04 -9999 0 -0.32 5 5
FZD3 0.021 0.012 -9999 0 -10000 0 0
WNT5A 0.004 0.084 -9999 0 -0.29 28 28
WNT11 0.012 0.064 -9999 0 -0.24 22 22
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.007 0.068 -10000 0 -0.28 15 15
NFATC2 -0.008 0.16 -10000 0 -0.43 28 28
NFATC3 0.01 0.063 -10000 0 -0.21 8 8
CD40LG -0.12 0.26 -10000 0 -0.76 38 38
ITCH -0.013 0.082 -10000 0 -0.21 1 1
CBLB -0.011 0.081 -10000 0 -0.21 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.27 -10000 0 -0.7 44 44
JUNB 0.011 0.07 -10000 0 -0.26 22 22
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.1 -10000 0 -0.22 70 70
T cell anergy -0.051 0.14 0.25 1 -0.33 70 71
TLE4 -0.011 0.12 -10000 0 -0.42 11 11
Jun/NFAT1-c-4/p21SNFT -0.049 0.24 -10000 0 -0.74 24 24
AP-1/NFAT1-c-4 -0.093 0.31 -10000 0 -0.84 36 36
IKZF1 -0.012 0.11 -10000 0 -0.39 12 12
T-helper 2 cell differentiation -0.17 0.27 -10000 0 -0.68 45 45
AP-1/NFAT1 -0.029 0.16 -10000 0 -0.4 32 32
CALM1 0.002 0.068 -10000 0 -0.16 1 1
EGR2 -0.091 0.29 -10000 0 -0.94 27 27
EGR3 -0.1 0.31 -10000 0 -0.99 32 32
NFAT1/FOXP3 -0.016 0.15 -10000 0 -0.34 32 32
EGR1 -0.019 0.11 -10000 0 -0.27 54 54
JUN 0.01 0.043 -10000 0 -0.29 4 4
EGR4 -0.04 0.1 -10000 0 -0.21 101 101
mol:Ca2+ -0.021 0.056 -10000 0 -0.13 72 72
GBP3 -0.047 0.19 -10000 0 -0.56 38 38
FOSL1 -0.047 0.13 -10000 0 -0.28 90 90
NFAT1-c-4/MAF/IRF4 -0.04 0.23 -10000 0 -0.75 21 21
DGKA -0.012 0.11 -10000 0 -0.37 11 11
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.049 0.23 -10000 0 -0.75 24 24
CTLA4 -0.039 0.13 0.28 1 -0.35 27 28
NFAT1-c-4 (dimer)/EGR1 -0.058 0.26 -10000 0 -0.8 26 26
NFAT1-c-4 (dimer)/EGR4 -0.054 0.24 -10000 0 -0.73 24 24
FOS -0.036 0.12 -10000 0 -0.32 55 55
IFNG -0.069 0.19 -10000 0 -0.62 20 20
T cell activation -0.049 0.16 -10000 0 -0.6 12 12
MAF 0.021 0.027 -10000 0 -0.32 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.046 0.17 0.62 22 -10000 0 22
TNF -0.11 0.24 -10000 0 -0.72 33 33
FASLG -0.16 0.41 -10000 0 -1.3 39 39
TBX21 0.017 0.057 -10000 0 -0.24 16 16
BATF3 0.015 0.052 -10000 0 -0.21 19 19
PRKCQ 0.005 0.083 -10000 0 -0.28 26 26
PTPN1 -0.012 0.11 -10000 0 -0.34 14 14
NFAT1-c-4/ICER1 -0.044 0.23 -10000 0 -0.72 24 24
GATA3 -0.066 0.15 -10000 0 -0.32 101 101
T-helper 1 cell differentiation -0.068 0.19 -10000 0 -0.6 21 21
IL2RA -0.11 0.27 -10000 0 -0.66 49 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.011 0.11 -10000 0 -0.36 11 11
E2F1 0.022 0.046 -10000 0 -0.2 15 15
PPARG 0.01 0.075 -10000 0 -0.3 20 20
SLC3A2 -0.01 0.11 -10000 0 -0.37 10 10
IRF4 0.002 0.083 -10000 0 -0.25 34 34
PTGS2 -0.14 0.28 -10000 0 -0.78 42 42
CSF2 -0.12 0.25 -10000 0 -0.74 36 36
JunB/Fra1/NFAT1-c-4 -0.07 0.24 -10000 0 -0.76 25 25
IL4 -0.18 0.28 -10000 0 -0.71 45 45
IL5 -0.12 0.25 -10000 0 -0.74 36 36
IL2 -0.05 0.16 -10000 0 -0.61 12 12
IL3 -0.018 0.11 -10000 0 -0.64 8 8
RNF128 -0.058 0.17 -10000 0 -0.41 73 73
NFATC1 -0.045 0.17 -10000 0 -0.62 21 21
CDK4 0.059 0.14 0.55 12 -10000 0 12
PTPRK -0.013 0.11 -10000 0 -0.38 9 9
IL8 -0.13 0.26 -10000 0 -0.75 40 40
POU2F1 0.026 0.019 -10000 0 -0.31 1 1
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.027 -10000 0 -0.21 5 5
EGFR -0.007 0.1 -10000 0 -0.32 36 36
EGF/EGFR 0.003 0.11 -10000 0 -0.19 74 74
EGF/EGFR dimer/SHC/GRB2/SOS1 0.045 0.083 -10000 0 -0.17 40 40
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.005 0.1 -10000 0 -0.32 36 36
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0 0.082 -10000 0 -0.23 40 40
EGF/EGFR dimer/SHC 0.011 0.086 -10000 0 -0.16 65 65
mol:GDP 0.039 0.079 -10000 0 -0.16 40 40
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.005 0.084 -10000 0 -0.29 27 27
GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.012 0.073 -10000 0 -0.16 38 38
SHC1 0.027 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.038 0.078 -10000 0 -0.17 38 38
FRAP1 -0.029 0.052 0.079 4 -0.16 38 42
EGF/EGFR dimer -0.005 0.094 -10000 0 -0.2 67 67
SOS1 0.027 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0 0.1 -10000 0 -0.24 53 53
Ephrin B reverse signaling

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
EFNB2 0.019 0.042 -10000 0 -0.21 12 12
EPHB2 0.023 0.037 -10000 0 -0.26 6 6
EFNB1 0.01 0.026 -10000 0 -0.2 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.095 -10000 0 -0.16 76 76
Ephrin B2/EPHB1-2 -0.01 0.095 -10000 0 -0.16 101 101
neuron projection morphogenesis -0.005 0.083 -10000 0 -0.15 76 76
Ephrin B1/EPHB1-2/Tiam1 0 0.097 -10000 0 -0.16 86 86
DNM1 0.025 0.023 -10000 0 -0.26 2 2
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.002 0.046 -10000 0 -0.44 4 4
YES1 0.007 0.073 -10000 0 -0.68 4 4
Ephrin B1/EPHB1-2/NCK2 0.001 0.095 -10000 0 -0.16 84 84
PI3K 0.032 0.065 -10000 0 -0.51 4 4
mol:GDP -0.001 0.096 -10000 0 -0.16 86 86
ITGA2B 0.016 0.056 -10000 0 -0.3 11 11
endothelial cell proliferation 0.029 0.027 -10000 0 -0.11 10 10
FYN 0.006 0.074 -10000 0 -0.67 4 4
MAP3K7 -0.001 0.05 -10000 0 -0.47 4 4
FGR 0.008 0.078 -10000 0 -0.64 5 5
TIAM1 0.025 0.028 -10000 0 -0.28 3 3
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
RGS3 0.026 0.007 -10000 0 -10000 0 0
cell adhesion -0.011 0.09 -10000 0 -0.38 9 9
LYN 0.008 0.07 -10000 0 -0.66 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.001 0.074 -10000 0 -0.63 5 5
Ephrin B1/EPHB1-2 0 0.054 -10000 0 -0.51 4 4
SRC 0.009 0.077 -10000 0 -0.64 5 5
ITGB3 -0.043 0.14 -10000 0 -0.32 76 76
EPHB1 -0.063 0.15 -10000 0 -0.31 96 96
EPHB4 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.027 -10000 0 -0.11 10 10
alphaIIb/beta3 Integrin -0.021 0.11 -10000 0 -0.22 84 84
BLK -0.012 0.091 -10000 0 -0.7 4 4
HCK 0.005 0.079 -10000 0 -0.64 5 5
regulation of stress fiber formation 0 0.094 0.16 84 -10000 0 84
MAPK8 -0.003 0.056 0.21 2 -0.46 4 6
Ephrin B1/EPHB1-2/RGS3 0 0.095 -10000 0 -0.16 86 86
endothelial cell migration 0.004 0.06 0.21 12 -0.38 4 16
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTPN13 0.027 0.025 -10000 0 -0.42 1 1
regulation of focal adhesion formation 0 0.094 0.16 84 -10000 0 84
chemotaxis 0.001 0.094 0.16 86 -10000 0 86
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
Rac1/GTP 0.002 0.089 -10000 0 -0.15 76 76
angiogenesis 0.001 0.054 -10000 0 -0.51 4 4
LCK 0.009 0.077 -10000 0 -0.64 5 5
Nongenotropic Androgen 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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.026 0.073 -10000 0 -0.17 45 45
regulation of S phase of mitotic cell cycle -0.005 0.079 -10000 0 -0.21 42 42
GNAO1 -0.021 0.12 -10000 0 -0.32 50 50
HRAS 0.024 0.027 -10000 0 -0.21 5 5
SHBG/T-DHT 0.013 0.024 -10000 0 -0.13 9 9
PELP1 0.025 0.009 -10000 0 -10000 0 0
AKT1 0.007 0.001 -10000 0 -10000 0 0
MAP2K1 -0.034 0.072 0.3 4 -0.24 10 14
T-DHT/AR -0.006 0.074 -10000 0 -0.22 41 41
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 58 58
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.019 -10000 0 -0.32 1 1
mol:GDP -0.034 0.11 -10000 0 -0.34 41 41
cell proliferation -0.06 0.16 0.39 5 -0.4 57 62
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
FOS -0.1 0.28 0.35 3 -0.74 58 61
mol:Ca2+ -0.01 0.027 -10000 0 -0.065 57 57
MAPK3 -0.043 0.12 0.34 6 -0.28 52 58
MAPK1 -0.025 0.097 0.25 4 -0.3 15 19
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
mol:IP3 -0.001 0.002 -10000 0 -0.005 58 58
cAMP biosynthetic process 0 0.025 0.089 2 -0.15 3 5
GNG2 0.023 0.04 -10000 0 -0.32 5 5
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 58 58
HRAS/GTP 0.013 0.074 -10000 0 -0.16 41 41
actin cytoskeleton reorganization 0.034 0.028 -10000 0 -0.19 3 3
SRC 0.027 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 58 58
PI3K 0.029 0.033 -10000 0 -0.2 6 6
apoptosis 0.051 0.16 0.4 59 -0.32 5 64
T-DHT/AR/PELP1 0.01 0.068 -10000 0 -0.18 41 41
HRAS/GDP -0.021 0.11 -10000 0 -0.33 41 41
CREB1 -0.055 0.18 0.32 5 -0.43 59 64
RAC1-CDC42/GTP 0.043 0.031 -10000 0 -0.19 3 3
AR -0.011 0.11 -10000 0 -0.32 41 41
GNB1 0.028 0.004 -10000 0 -10000 0 0
RAF1 -0.014 0.073 0.3 4 -0.22 10 14
RAC1-CDC42/GDP 0.003 0.11 -10000 0 -0.3 41 41
T-DHT/AR/PELP1/Src 0.022 0.069 -10000 0 -0.16 41 41
MAP2K2 -0.033 0.072 0.3 4 -0.24 11 15
T-DHT/AR/PELP1/Src/PI3K -0.005 0.079 -10000 0 -0.21 42 42
GNAZ 0.003 0.089 -10000 0 -0.32 27 27
SHBG 0.018 0.043 -10000 0 -0.24 9 9
Gi family/GNB1/GNG2/GDP -0.041 0.14 -10000 0 -0.33 56 56
mol:T-DHT 0 0.001 -10000 0 -0.003 43 43
RAC1 0.026 0.008 -10000 0 -10000 0 0
GNRH1 0.003 0.017 -10000 0 -0.14 5 5
Gi family/GTP -0.03 0.092 0.11 1 -0.22 59 60
CDC42 0.028 0.003 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.092 0.38 -9999 0 -1.1 32 32
PLK1 0.001 0.1 -9999 0 -1.2 2 2
BIRC5 -0.025 0.17 -9999 0 -0.93 11 11
HSPA1B -0.095 0.38 -9999 0 -1.1 32 32
MAP2K1 0.017 0.042 -9999 0 -10000 0 0
BRCA2 -0.12 0.43 -9999 0 -1.1 43 43
FOXM1 -0.14 0.53 -9999 0 -1.5 35 35
XRCC1 -0.094 0.38 -9999 0 -1.1 32 32
FOXM1B/p19 -0.1 0.45 -9999 0 -1.3 35 35
Cyclin D1/CDK4 -0.08 0.36 -9999 0 -1 31 31
CDC2 -0.1 0.41 -9999 0 -1.1 35 35
TGFA -0.093 0.37 -9999 0 -0.99 37 37
SKP2 -0.1 0.4 -9999 0 -1.1 35 35
CCNE1 0.023 0.027 -9999 0 -0.21 3 3
CKS1B -0.087 0.38 -9999 0 -1.1 32 32
RB1 -0.067 0.3 -9999 0 -0.83 34 34
FOXM1C/SP1 -0.11 0.45 -9999 0 -1.3 35 35
AURKB -0.1 0.32 -9999 0 -0.96 41 41
CENPF -0.1 0.39 -9999 0 -1.1 32 32
CDK4 0.021 0.023 -9999 0 -10000 0 0
MYC -0.073 0.33 -9999 0 -0.92 34 34
CHEK2 0.017 0.043 -9999 0 -0.27 1 1
ONECUT1 -0.093 0.38 -9999 0 -1.1 33 33
CDKN2A -0.019 0.094 -9999 0 -0.21 73 73
LAMA4 -0.097 0.4 -9999 0 -1.2 33 33
FOXM1B/HNF6 -0.12 0.46 -9999 0 -1.4 33 33
FOS -0.18 0.51 -9999 0 -1.2 66 66
SP1 0.028 0.005 -9999 0 -10000 0 0
CDC25B -0.095 0.38 -9999 0 -1.1 32 32
response to radiation 0.001 0.022 -9999 0 -10000 0 0
CENPB -0.094 0.38 -9999 0 -1.1 32 32
CENPA -0.11 0.39 -9999 0 -1.1 32 32
NEK2 -0.1 0.39 -9999 0 -1.1 33 33
HIST1H2BA -0.099 0.38 -9999 0 -1.1 32 32
CCNA2 -0.006 0.083 -9999 0 -0.21 49 49
EP300 0.025 0.031 -9999 0 -0.32 3 3
CCNB1/CDK1 -0.12 0.46 -9999 0 -1.4 32 32
CCNB2 -0.098 0.39 -9999 0 -1.1 32 32
CCNB1 -0.1 0.41 -9999 0 -1.2 32 32
ETV5 -0.11 0.44 -9999 0 -1.2 38 38
ESR1 -0.11 0.41 -9999 0 -1.1 37 37
CCND1 -0.087 0.36 -9999 0 -1 31 31
GSK3A 0.019 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.027 0.074 -9999 0 -0.15 26 26
CDK2 0.024 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.027 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.096 0.43 -9999 0 -1.2 35 35
GAS1 -0.13 0.47 -9999 0 -1.2 47 47
MMP2 -0.099 0.4 -9999 0 -1.2 33 33
RB1/FOXM1C -0.1 0.39 -9999 0 -1.1 33 33
CREBBP 0.027 0.005 -9999 0 -10000 0 0
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 0.028 0.003 -10000 0 -10000 0 0
CCL5 0.014 0.063 -10000 0 -0.27 17 17
SDCBP 0.024 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.037 0.085 -10000 0 -0.28 22 22
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 -0.033 0.087 0.2 3 -0.27 23 26
Syndecan-1/Syntenin -0.028 0.084 0.2 3 -0.27 20 23
MAPK3 -0.032 0.085 0.22 5 -0.29 15 20
HGF/MET 0.003 0.097 -10000 0 -0.24 45 45
TGFB1/TGF beta receptor Type II 0.028 0.003 -10000 0 -10000 0 0
BSG 0.028 0.012 -10000 0 -0.21 1 1
keratinocyte migration -0.032 0.086 0.2 3 -0.26 23 26
Syndecan-1/RANTES -0.035 0.095 0.23 4 -0.27 27 31
Syndecan-1/CD147 -0.012 0.099 0.24 5 -0.27 21 26
Syndecan-1/Syntenin/PIP2 -0.028 0.081 0.19 3 -0.27 19 22
LAMA5 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.027 0.08 0.19 3 -0.26 19 22
MMP7 -0.022 0.11 -10000 0 -0.25 66 66
HGF 0.004 0.08 -10000 0 -0.28 26 26
Syndecan-1/CASK -0.039 0.081 -10000 0 -0.26 25 25
Syndecan-1/HGF/MET -0.035 0.12 0.24 2 -0.31 36 38
regulation of cell adhesion -0.036 0.08 0.22 4 -0.29 14 18
HPSE 0.011 0.07 -10000 0 -0.28 20 20
positive regulation of cell migration -0.037 0.085 -10000 0 -0.28 22 22
SDC1 -0.037 0.085 -10000 0 -0.26 30 30
Syndecan-1/Collagen -0.037 0.085 -10000 0 -0.28 22 22
PPIB 0.026 0.021 -10000 0 -0.21 3 3
MET -0.002 0.093 -10000 0 -0.32 30 30
PRKACA 0.028 0.004 -10000 0 -10000 0 0
MMP9 -0.11 0.12 -10000 0 -0.21 209 209
MAPK1 -0.033 0.085 0.23 4 -0.26 21 25
homophilic cell adhesion -0.035 0.089 0.26 3 -0.28 23 26
MMP1 -0.024 0.11 -10000 0 -0.24 70 70
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.001 0.024 -10000 0 -10000 0 0
NFATC2 -0.033 0.077 -10000 0 -0.19 65 65
NFATC3 0.001 0.023 -10000 0 -10000 0 0
CD40LG -0.083 0.16 0.34 1 -0.4 51 52
PTGS2 -0.097 0.18 0.34 1 -0.42 70 71
JUNB 0.011 0.07 -10000 0 -0.26 22 22
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.021 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.021 -10000 0 -10000 0 0
CALM1 0.023 0.014 -10000 0 -10000 0 0
JUN 0.02 0.036 -10000 0 -0.29 4 4
mol:Ca2+ -0.004 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.006 -10000 0 -10000 0 0
FOSL1 -0.048 0.13 -10000 0 -0.28 90 90
CREM 0.028 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.028 0.11 -10000 0 -0.26 30 30
FOS -0.026 0.12 -10000 0 -0.32 55 55
IFNG -0.08 0.15 0.34 1 -0.38 44 45
AP-1/NFAT1-c-4 -0.066 0.18 -10000 0 -0.41 50 50
FASLG -0.08 0.16 0.34 1 -0.39 50 51
NFAT1-c-4/ICER1 -0.026 0.083 -10000 0 -0.2 32 32
IL2RA -0.086 0.16 0.34 1 -0.37 55 56
FKBP12/FK506 0.021 0.003 -10000 0 -10000 0 0
CSF2 -0.078 0.14 -10000 0 -0.38 45 45
JunB/Fra1/NFAT1-c-4 -0.046 0.11 0.21 1 -0.22 59 60
IL4 -0.078 0.14 -10000 0 -0.38 44 44
IL2 -0.003 0.14 -10000 0 -0.93 8 8
IL3 -0.01 0.14 -10000 0 -0.67 15 15
FKBP1A 0.028 0.004 -10000 0 -10000 0 0
BATF3 0.015 0.052 -10000 0 -0.21 19 19
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.019 -10000 0 -0.31 1 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.017 0.089 0.24 3 -0.23 14 17
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.1 0.27 5 -0.26 18 23
alphaV/beta3 Integrin/Osteopontin/Src 0.015 0.067 -10000 0 -0.14 54 54
AP1 -0.027 0.13 -10000 0 -0.33 30 30
ILK -0.027 0.087 0.22 5 -0.24 13 18
bone resorption -0.031 0.11 0.19 3 -0.28 37 40
PTK2B 0.021 0.013 -10000 0 -10000 0 0
PYK2/p130Cas 0.017 0.097 0.23 1 -0.24 10 11
ITGAV 0.028 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.009 0.088 -10000 0 -0.23 43 43
alphaV/beta3 Integrin/Osteopontin 0.013 0.11 -10000 0 -0.19 76 76
MAP3K1 -0.026 0.083 0.19 4 -0.18 63 67
JUN 0.024 0.034 -10000 0 -0.29 4 4
MAPK3 -0.033 0.084 0.24 4 -0.25 16 20
MAPK1 -0.034 0.083 0.25 3 -0.25 16 19
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.003 -10000 0 -10000 0 0
MAPK8 -0.032 0.084 0.19 6 -0.26 19 25
ITGB3 -0.042 0.14 -10000 0 -0.31 76 76
NFKBIA -0.033 0.087 0.25 3 -0.28 19 22
FOS -0.023 0.12 -10000 0 -0.31 55 55
CD44 0.021 0.047 -10000 0 -0.32 7 7
CHUK 0.027 0.007 -10000 0 -10000 0 0
PLAU -0.047 0.18 0.35 1 -1.1 9 10
NF kappa B1 p50/RelA -0.002 0.1 0.32 1 -0.35 10 11
BCAR1 0.023 0.011 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.01 0.1 -10000 0 -0.21 75 75
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.03 0.09 0.24 4 -0.24 19 23
VAV3 -0.048 0.1 0.23 5 -0.29 28 33
MAP3K14 -0.029 0.087 0.25 3 -0.23 17 20
ROCK2 -0.009 0.11 -10000 0 -0.32 40 40
SPP1 -0.009 0.089 -10000 0 -0.21 58 58
RAC1 0.026 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.033 0.096 0.21 5 -0.26 25 30
MMP2 -0.042 0.11 -10000 0 -0.39 14 14
HIF-1-alpha transcription factor network

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
PKM2 -0.048 0.28 0.38 2 -0.74 27 29
HDAC7 0.027 0.012 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.003 0.31 -10000 0 -0.77 29 29
SMAD4 0.026 0.009 -10000 0 -10000 0 0
ID2 -0.048 0.28 0.38 2 -0.75 27 29
AP1 -0.001 0.098 -10000 0 -0.23 56 56
ABCG2 -0.059 0.3 0.38 2 -0.73 37 39
HIF1A 0.006 0.068 -10000 0 -0.23 4 4
TFF3 -0.059 0.3 0.38 2 -0.74 33 35
GATA2 0.024 0.017 -10000 0 -10000 0 0
AKT1 0.004 0.081 -10000 0 -0.22 13 13
response to hypoxia -0.019 0.082 -10000 0 -0.2 31 31
MCL1 -0.049 0.27 0.38 2 -0.73 26 28
NDRG1 -0.044 0.25 -10000 0 -0.71 24 24
SERPINE1 -0.051 0.28 0.38 1 -0.71 32 33
FECH -0.05 0.27 0.38 2 -0.73 27 29
FURIN -0.047 0.27 0.38 2 -0.73 27 29
NCOA2 -0.024 0.11 -10000 0 -0.32 47 47
EP300 -0.007 0.12 -10000 0 -0.34 27 27
HMOX1 -0.048 0.28 0.38 2 -0.73 29 31
BHLHE40 -0.047 0.28 0.38 2 -0.76 26 28
BHLHE41 -0.051 0.28 0.38 2 -0.75 27 29
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.059 0.097 -10000 0 -10000 0 0
ENG 0.018 0.076 0.25 8 -10000 0 8
JUN 0.022 0.035 -10000 0 -0.29 4 4
RORA -0.049 0.27 0.37 1 -0.74 27 28
ABCB1 -0.012 0.17 -10000 0 -1 8 8
TFRC -0.049 0.27 0.38 2 -0.73 27 29
CXCR4 -0.05 0.28 0.38 1 -0.74 28 29
TF -0.069 0.29 0.38 2 -0.71 38 40
CITED2 -0.048 0.28 0.38 2 -0.74 27 29
HIF1A/ARNT 0.04 0.37 -10000 0 -0.83 25 25
LDHA 0.027 0.089 -10000 0 -0.79 2 2
ETS1 -0.051 0.28 0.38 2 -0.76 26 28
PGK1 -0.048 0.28 0.38 2 -0.73 28 30
NOS2 -0.059 0.29 0.38 2 -0.71 36 38
ITGB2 -0.049 0.28 0.38 2 -0.73 28 30
ALDOA -0.047 0.27 0.38 2 -0.74 27 29
Cbp/p300/CITED2 -0.052 0.33 -10000 0 -0.87 31 31
FOS -0.024 0.12 -10000 0 -0.31 55 55
HK2 -0.048 0.28 0.38 2 -0.74 27 29
SP1 0.031 0.017 -10000 0 -10000 0 0
GCK -0.045 0.31 -10000 0 -1.3 19 19
HK1 -0.048 0.27 0.38 2 -0.72 27 29
NPM1 -0.05 0.27 -10000 0 -0.73 27 27
EGLN1 -0.05 0.27 0.37 1 -0.74 26 27
CREB1 0.032 0.005 -10000 0 -10000 0 0
PGM1 -0.048 0.28 0.38 2 -0.74 27 29
SMAD3 0.029 0.003 -10000 0 -10000 0 0
EDN1 -0.063 0.31 -10000 0 -0.99 31 31
IGFBP1 -0.048 0.27 0.38 1 -0.72 27 28
VEGFA -0.036 0.26 0.36 2 -0.7 27 29
HIF1A/JAB1 0.019 0.054 -10000 0 -0.26 1 1
CP -0.063 0.29 0.38 2 -0.75 34 36
CXCL12 -0.052 0.28 0.38 2 -0.75 30 32
COPS5 0.019 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.013 -10000 0 -10000 0 0
BNIP3 -0.049 0.27 0.38 2 -0.73 27 29
EGLN3 -0.051 0.28 0.38 1 -0.74 30 31
CA9 -0.053 0.27 -10000 0 -0.72 28 28
TERT -0.058 0.29 0.36 1 -0.71 35 36
ENO1 -0.049 0.27 0.38 2 -0.74 27 29
PFKL -0.048 0.27 0.38 2 -0.73 27 29
NCOA1 0.026 0.011 -10000 0 -10000 0 0
ADM -0.049 0.28 0.38 2 -0.73 28 30
ARNT 0.009 0.063 -10000 0 -0.24 1 1
HNF4A 0.004 0.06 -10000 0 -0.18 30 30
ADFP -0.062 0.26 0.36 1 -0.69 33 34
SLC2A1 -0.03 0.25 0.36 2 -0.68 27 29
LEP -0.046 0.27 0.37 1 -0.74 25 26
HIF1A/ARNT/Cbp/p300 -0.006 0.32 -10000 0 -0.77 31 31
EPO -0.095 0.32 -10000 0 -0.82 46 46
CREBBP -0.003 0.11 -10000 0 -0.32 25 25
HIF1A/ARNT/Cbp/p300/HDAC7 0.005 0.32 -10000 0 -0.79 27 27
PFKFB3 -0.052 0.28 0.38 2 -0.74 29 31
NT5E -0.061 0.28 -10000 0 -0.73 34 34
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.22 0.39 -10000 0 -1.1 32 32
STAT6 (cleaved dimer) -0.24 0.42 -10000 0 -1.1 49 49
IGHG1 -0.071 0.16 -10000 0 -0.5 9 9
IGHG3 -0.21 0.38 -10000 0 -0.98 49 49
AKT1 -0.12 0.26 -10000 0 -0.7 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.088 0.22 -10000 0 -0.68 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.11 0.26 -10000 0 -0.8 20 20
THY1 -0.22 0.4 -10000 0 -1.1 33 33
MYB 0.017 0.049 -10000 0 -0.21 17 17
HMGA1 0.028 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.16 0.31 -10000 0 -0.81 44 44
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.27 -10000 0 -0.78 28 28
SP1 0.032 0.009 -10000 0 -10000 0 0
INPP5D 0.01 0.076 -10000 0 -0.32 19 19
SOCS5 0.035 0.019 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.23 0.42 -10000 0 -1.2 42 42
SOCS1 -0.15 0.28 -10000 0 -0.72 38 38
SOCS3 -0.22 0.44 -10000 0 -1.2 56 56
FCER2 -0.19 0.36 -10000 0 -1.1 34 34
PARP14 0.027 0.01 -10000 0 -10000 0 0
CCL17 -0.23 0.4 -10000 0 -1.2 32 32
GRB2 0.027 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.092 0.22 -10000 0 -0.65 25 25
T cell proliferation -0.22 0.41 -10000 0 -1.1 38 38
IL4R/JAK1 -0.22 0.4 -10000 0 -1.1 38 38
EGR2 -0.24 0.44 -10000 0 -1.3 36 36
JAK2 -0.003 0.047 -10000 0 -0.35 1 1
JAK3 0.015 0.046 -10000 0 -0.23 10 10
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
JAK1 0.009 0.027 -10000 0 -10000 0 0
COL1A2 -0.052 0.16 -10000 0 -1.1 2 2
CCL26 -0.21 0.4 -10000 0 -1.1 33 33
IL4R -0.24 0.42 -10000 0 -1.2 34 34
PTPN6 0.03 0.014 -10000 0 -10000 0 0
IL13RA2 -0.3 0.53 -10000 0 -1.3 65 65
IL13RA1 -0.002 0.045 -10000 0 -10000 0 0
IRF4 -0.096 0.33 -10000 0 -1.2 25 25
ARG1 -0.05 0.14 -10000 0 -0.64 4 4
CBL -0.15 0.29 -10000 0 -0.77 44 44
GTF3A 0.029 0.014 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
IL13RA1/JAK2 0.001 0.063 -10000 0 -0.25 1 1
IRF4/BCL6 -0.081 0.3 -10000 0 -1.1 25 25
CD40LG 0.002 0.086 -10000 0 -0.25 35 35
MAPK14 -0.18 0.34 -10000 0 -0.88 50 50
mitosis -0.11 0.24 -10000 0 -0.65 34 34
STAT6 -0.25 0.47 -10000 0 -1.2 45 45
SPI1 0.024 0.028 -10000 0 -0.2 4 4
RPS6KB1 -0.11 0.24 -10000 0 -0.63 32 32
STAT6 (dimer) -0.25 0.47 -10000 0 -1.2 45 45
STAT6 (dimer)/PARP14 -0.23 0.42 -10000 0 -1.1 41 41
mast cell activation 0.006 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.14 0.27 -10000 0 -0.72 35 35
FRAP1 -0.12 0.26 -10000 0 -0.7 33 33
LTA -0.23 0.4 -10000 0 -1.1 35 35
FES 0.025 0.031 -10000 0 -0.32 3 3
T-helper 1 cell differentiation 0.24 0.45 1.2 47 -10000 0 47
CCL11 -0.22 0.38 -10000 0 -1.2 30 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.25 -10000 0 -0.67 33 33
IL2RG 0.013 0.052 -10000 0 -0.22 14 14
IL10 -0.24 0.44 -10000 0 -1.2 41 41
IRS1 0.017 0.061 -10000 0 -0.32 12 12
IRS2 0.025 0.022 -10000 0 -0.21 3 3
IL4 -0.06 0.16 -10000 0 -0.93 7 7
IL5 -0.22 0.4 -10000 0 -1.2 29 29
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.18 0.33 -10000 0 -0.9 32 32
COL1A1 -0.059 0.15 -10000 0 -0.59 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.22 0.41 -10000 0 -1.2 31 31
IL2R gamma/JAK3 0.022 0.061 -10000 0 -0.22 16 16
TFF3 -0.23 0.4 -10000 0 -1.1 36 36
ALOX15 -0.27 0.45 -10000 0 -1.3 43 43
MYBL1 0.023 0.021 -10000 0 -0.32 1 1
T-helper 2 cell differentiation -0.2 0.36 -10000 0 -0.94 42 42
SHC1 0.027 0.007 -10000 0 -10000 0 0
CEBPB 0.026 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.11 0.24 -10000 0 -0.73 21 21
mol:PI-3-4-5-P3 -0.12 0.26 -10000 0 -0.7 33 33
PI3K -0.13 0.28 -10000 0 -0.76 32 32
DOK2 0.019 0.024 -10000 0 -0.21 3 3
ETS1 0.028 0.034 -10000 0 -0.26 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.082 0.19 -10000 0 -0.57 24 24
ITGB3 -0.37 0.6 -10000 0 -1.4 87 87
PIGR -0.34 0.57 -10000 0 -1.3 78 78
IGHE 0.011 0.053 0.17 13 -10000 0 13
MAPKKK cascade -0.081 0.19 -10000 0 -0.56 24 24
BCL6 0.027 0.008 -10000 0 -10000 0 0
OPRM1 -0.23 0.39 -10000 0 -1.2 32 32
RETNLB -0.22 0.4 -10000 0 -1.1 34 34
SELP -0.22 0.41 -10000 0 -1.2 34 34
AICDA -0.22 0.38 -10000 0 -1.1 32 32
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.022 0.11 -10000 0 -0.17 76 76
SMAD6-7/SMURF1 0.043 0.038 -10000 0 -0.18 7 7
NOG -0.013 0.11 -10000 0 -0.31 44 44
SMAD9 -0.074 0.19 -10000 0 -0.43 80 80
SMAD4 0.026 0.009 -10000 0 -10000 0 0
SMAD5 -0.002 0.067 0.25 1 -0.27 9 10
BMP7/USAG1 -0.069 0.15 -10000 0 -0.26 129 129
SMAD5/SKI 0.009 0.078 0.24 2 -0.26 9 11
SMAD1 0.025 0.028 -10000 0 -10000 0 0
BMP2 0.007 0.082 -10000 0 -0.31 23 23
SMAD1/SMAD1/SMAD4 0.035 0.035 -10000 0 -10000 0 0
BMPR1A 0.025 0.019 -10000 0 -0.32 1 1
BMPR1B 0.026 0.025 -10000 0 -0.24 3 3
BMPR1A-1B/BAMBI 0.041 0.043 -10000 0 -0.12 18 18
AHSG 0.005 0.055 -10000 0 -0.21 23 23
CER1 0.015 0.033 -10000 0 -0.21 8 8
BMP2-4/CER1 0.021 0.083 -10000 0 -0.2 41 41
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.001 0.09 -10000 0 -0.29 22 22
BMP2-4 (homodimer) 0.013 0.091 -10000 0 -0.26 34 34
RGMB 0.026 0.009 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.066 0.036 0.2 1 -0.15 2 3
RGMA 0.014 0.068 -10000 0 -0.32 15 15
SMURF1 0.026 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.006 0.087 -10000 0 -0.29 23 23
BMP2-4/USAG1 -0.038 0.14 -10000 0 -0.22 119 119
SMAD6/SMURF1/SMAD5 0.009 0.071 -10000 0 -0.26 7 7
SOSTDC1 -0.08 0.16 -10000 0 -0.32 114 114
BMP7/BMPR2/BMPR1A-1B 0.026 0.087 -10000 0 -0.16 61 61
SKI 0.028 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) 0.005 0.071 -10000 0 -0.21 35 35
HFE2 -0.001 0.069 -10000 0 -0.21 37 37
ZFYVE16 0.027 0.007 -10000 0 -10000 0 0
MAP3K7 0.023 0.011 -10000 0 -10000 0 0
BMP2-4/CHRD 0.011 0.093 -10000 0 -0.17 69 69
SMAD5/SMAD5/SMAD4 0.01 0.073 0.31 1 -0.29 6 7
MAPK1 0.028 0.004 -10000 0 -10000 0 0
TAK1/TAB family 0.008 0.079 -10000 0 -0.28 14 14
BMP7 (homodimer) -0.03 0.13 -10000 0 -0.31 62 62
NUP214 0.027 0.007 -10000 0 -10000 0 0
BMP6/FETUA 0.011 0.061 0.24 1 -0.14 49 50
SMAD1/SKI 0.042 0.042 0.32 2 -10000 0 2
SMAD6 0.022 0.047 -10000 0 -0.32 7 7
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.015 0.087 -10000 0 -0.18 51 51
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.011 0.1 -10000 0 -0.27 48 48
BMPR2 (homodimer) 0.028 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.051 0.022 -10000 0 -0.12 2 2
BMPR1A-1B (homodimer) 0.036 0.024 -10000 0 -0.18 3 3
CHRDL1 -0.057 0.15 -10000 0 -0.32 92 92
ENDOFIN/SMAD1 0.04 0.043 0.39 2 -10000 0 2
SMAD6-7/SMURF1/SMAD1 0.051 0.047 0.27 1 -10000 0 1
SMAD6/SMURF1 0.026 0.008 -10000 0 -10000 0 0
BAMBI 0.016 0.05 -10000 0 -0.21 18 18
SMURF2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.023 0.14 -10000 0 -0.23 100 100
BMP2-4/GREM1 0.006 0.11 -10000 0 -0.2 70 70
SMAD7 0.026 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.066 0.19 -10000 0 -0.4 87 87
SMAD1/SMAD6 0.036 0.036 0.27 1 -10000 0 1
TAK1/SMAD6 0.033 0.018 -10000 0 -10000 0 0
BMP7 -0.03 0.13 -10000 0 -0.31 62 62
BMP6 0.005 0.071 -10000 0 -0.21 35 35
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.002 0.089 -10000 0 -0.31 20 20
PPM1A 0.028 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.042 0.045 0.39 2 -10000 0 2
SMAD7/SMURF1 0.035 0.016 -10000 0 -10000 0 0
CTDSPL 0.028 0.005 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
CTDSP1 0.028 0.003 -10000 0 -10000 0 0
PPP1R15A 0.026 0.021 -10000 0 -0.21 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.027 0.14 -10000 0 -0.4 33 33
CHRD 0.001 0.075 -10000 0 -0.21 40 40
BMPR2 0.028 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.007 0.092 -10000 0 -0.3 26 26
BMP4 0.008 0.079 -10000 0 -0.32 21 21
FST -0.001 0.092 -10000 0 -0.3 31 31
BMP2-4/NOG 0.005 0.12 -10000 0 -0.24 63 63
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.037 0.082 -10000 0 -0.15 49 49
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.021 0.12 -10000 0 -0.32 50 50
CDC42/GTP -0.008 0.1 -10000 0 -0.23 50 50
PLCG1 -0.017 0.093 -10000 0 -0.24 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.014 -10000 0 -10000 0 0
cell migration -0.008 0.099 -10000 0 -0.22 50 50
S1PR5 -0.025 0.12 -10000 0 -0.32 57 57
S1PR4 0.017 0.049 -10000 0 -0.21 16 16
MAPK3 -0.016 0.093 -10000 0 -0.24 46 46
MAPK1 -0.015 0.089 -10000 0 -0.23 44 44
S1P/S1P5/Gi -0.038 0.14 -10000 0 -0.26 84 84
GNAI1 0.025 0.019 -10000 0 -0.32 1 1
CDC42/GDP 0.021 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.004 0.075 -10000 0 -0.18 52 52
RHOA 0.022 0.05 0.19 25 -10000 0 25
S1P/S1P4/Gi -0.013 0.1 -10000 0 -0.24 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.003 0.089 -10000 0 -0.32 27 27
S1P/S1P4/G12/G13 0.042 0.033 -10000 0 -10000 0 0
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.048 0.076 -10000 0 -0.21 25 25
MAP4K1 0.014 0.06 -10000 0 -0.23 20 20
MAP3K8 0.019 0.053 -10000 0 -0.29 10 10
PRKCB -0.045 0.14 -10000 0 -0.32 78 78
DBNL 0.026 0.008 -10000 0 -10000 0 0
CRKL 0.028 0.005 -10000 0 -10000 0 0
MAP3K1 0.011 0.059 -10000 0 -0.36 5 5
JUN -0.11 0.26 0.36 1 -0.54 92 93
MAP3K7 0.012 0.048 -10000 0 -0.33 3 3
GRAP2 0.015 0.063 -10000 0 -0.3 14 14
CRK 0.026 0.008 -10000 0 -10000 0 0
MAP2K4 0.006 0.075 0.27 4 -0.38 7 11
LAT 0.019 0.047 -10000 0 -0.23 12 12
LCP2 0.023 0.035 -10000 0 -0.24 6 6
MAPK8 -0.12 0.27 -10000 0 -0.56 93 93
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.017 0.065 -10000 0 -0.37 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55 0.055 0.075 -10000 0 -0.2 23 23
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.01 0.047 -10000 0 -0.34 5 5
Crk/p130 Cas/Paxillin -0.029 0.083 -10000 0 -0.24 33 33
JUN -0.022 0.08 -10000 0 -0.27 21 21
HRAS 0.025 0.027 -10000 0 -0.21 5 5
RET51/GFRalpha1/GDNF/GRB10 0.038 0.091 -10000 0 -0.2 41 41
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
FRS2 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.013 -10000 0 -0.21 1 1
RET51/GFRalpha1/GDNF/DOK1 0.038 0.096 -10000 0 -0.2 47 47
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.018 0.083 -10000 0 -0.18 51 51
RHOA 0.028 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.028 0.09 -10000 0 -0.18 49 49
GRB7 0.028 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.037 0.097 -10000 0 -0.19 49 49
MAPKKK cascade -0.004 0.081 -10000 0 -0.23 19 19
BCAR1 0.023 0.011 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.016 0.085 -10000 0 -0.19 51 51
lamellipodium assembly -0.015 0.085 -10000 0 -0.23 37 37
RET51/GFRalpha1/GDNF/SHC 0.036 0.095 -10000 0 -0.2 45 45
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
RET9/GFRalpha1/GDNF/SHC 0.021 0.073 -10000 0 -0.17 43 43
RET9/GFRalpha1/GDNF/Shank3 0.022 0.075 -10000 0 -0.17 46 46
MAPK3 -0.034 0.078 0.29 6 -0.27 11 17
DOK1 0.028 0.004 -10000 0 -10000 0 0
DOK6 0.005 0.075 -10000 0 -0.27 25 25
PXN 0.027 0.006 -10000 0 -10000 0 0
neurite development -0.025 0.073 0.28 3 -0.26 11 14
DOK5 0.011 0.07 -10000 0 -0.29 19 19
GFRA1 -0.002 0.095 -10000 0 -0.31 32 32
MAPK8 -0.015 0.078 -10000 0 -0.22 39 39
HRAS/GTP 0.031 0.096 -10000 0 -0.22 38 38
tube development 0.023 0.073 0.21 6 -0.16 42 48
MAPK1 -0.033 0.082 0.25 10 -0.26 12 22
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0 0.067 -10000 0 -0.18 41 41
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
PDLIM7 0.019 0.053 -10000 0 -0.29 10 10
RET51/GFRalpha1/GDNF/Dok6 0.034 0.11 -10000 0 -0.2 54 54
SHC1 0.027 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.032 0.099 -10000 0 -0.2 48 48
RET51/GFRalpha1/GDNF/Dok5 0.03 0.11 -10000 0 -0.2 56 56
PRKCA 0.016 0.063 -10000 0 -0.32 13 13
HRAS/GDP 0.019 0.018 -10000 0 -0.14 5 5
CREB1 -0.007 0.088 -10000 0 -0.23 41 41
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0 0.071 -10000 0 -0.2 39 39
RET51/GFRalpha1/GDNF/Grb7 0.038 0.097 -10000 0 -0.19 49 49
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.018 0.097 -10000 0 -0.22 69 69
DOK4 0.023 0.026 -10000 0 -0.32 2 2
JNK cascade -0.021 0.08 0.19 1 -0.28 18 19
RET9/GFRalpha1/GDNF/FRS2 0.022 0.073 -10000 0 -0.17 45 45
SHANK3 0.028 0.004 -10000 0 -10000 0 0
RASA1 0.025 0.026 -10000 0 -0.32 2 2
NCK1 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0 0.07 -10000 0 -0.19 39 39
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.004 0.08 -10000 0 -0.2 48 48
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.002 0.081 -10000 0 -0.22 40 40
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.004 0.083 -10000 0 -0.21 44 44
PI3K -0.023 0.12 0.24 2 -0.33 40 42
SOS1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.034 0.075 -10000 0 -0.16 42 42
GRB10 0.026 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.012 0.083 -10000 0 -0.25 27 27
RET51/GFRalpha1/GDNF/FRS2 0.037 0.095 -10000 0 -0.19 47 47
GAB1 0.027 0.018 -10000 0 -0.32 1 1
IRS1 0.017 0.061 -10000 0 -0.32 12 12
IRS2 0.025 0.022 -10000 0 -0.21 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.005 0.087 -10000 0 -0.22 45 45
RET51/GFRalpha1/GDNF/PKC alpha 0.03 0.11 -10000 0 -0.21 54 54
GRB2 0.027 0.006 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GDNF 0.009 0.074 -10000 0 -0.31 19 19
RAC1 0.026 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.031 0.11 -10000 0 -0.2 56 56
Rac1/GTP -0.014 0.1 -10000 0 -0.27 37 37
RET9/GFRalpha1/GDNF 0.007 0.075 -10000 0 -0.19 46 46
GFRalpha1/GDNF 0.005 0.089 -10000 0 -0.23 46 46
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.028 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.011 0.077 -10000 0 -0.22 30 30
NT3 (dimer)/TRKC -0.026 0.13 -10000 0 -0.27 78 78
NT3 (dimer)/TRKB -0.012 0.13 -10000 0 -0.23 81 81
SHC/Grb2/SOS1/GAB1/PI3K 0.022 0.034 -10000 0 -0.2 6 6
RAPGEF1 0.027 0.007 -10000 0 -10000 0 0
BDNF -0.042 0.14 -10000 0 -0.32 75 75
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
DYNLT1 0.028 0.005 -10000 0 -10000 0 0
NTRK1 0.002 0.085 -10000 0 -0.29 28 28
NTRK2 -0.016 0.11 -10000 0 -0.31 47 47
NTRK3 -0.036 0.13 -10000 0 -0.32 69 69
NT-4/5 (dimer)/TRKB -0.035 0.14 -10000 0 -0.24 110 110
neuron apoptosis 0.055 0.16 0.37 60 -10000 0 60
SHC 2-3/Grb2 -0.06 0.18 -10000 0 -0.4 60 60
SHC1 0.027 0.007 -10000 0 -10000 0 0
SHC2 -0.052 0.15 -10000 0 -0.41 42 42
SHC3 -0.079 0.2 -10000 0 -0.47 59 59
STAT3 (dimer) 0.032 0.009 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0 0.11 -10000 0 -0.22 69 69
RIN/GDP 0.009 0.093 0.28 10 -0.23 12 22
GIPC1 0.028 0.003 -10000 0 -10000 0 0
KRAS 0.026 0.008 -10000 0 -10000 0 0
DNAJA3 -0.029 0.098 -10000 0 -0.3 33 33
RIN/GTP 0.007 0.039 -10000 0 -0.14 23 23
CCND1 0.018 0.009 -10000 0 -10000 0 0
MAGED1 0.028 0.012 -10000 0 -0.21 1 1
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.046 0.14 -10000 0 -0.31 80 80
SHC/GRB2/SOS1 0.051 0.019 -10000 0 -10000 0 0
GRB2 0.027 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.047 0.11 -10000 0 -0.14 181 181
TRKA/NEDD4-2 0.014 0.069 -10000 0 -0.19 34 34
ELMO1 0.025 0.02 -10000 0 -0.32 1 1
RhoG/GTP/ELMO1/DOCK1 0.032 0.023 -10000 0 -0.18 3 3
NGF 0.011 0.073 -10000 0 -0.31 18 18
HRAS 0.025 0.027 -10000 0 -0.21 5 5
DOCK1 0.024 0.031 -10000 0 -0.32 3 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 0.007 0.058 -10000 0 -0.22 23 23
RIT1 0.027 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.025 0.022 -10000 0 -0.26 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.014 0.1 -10000 0 -0.28 34 34
mol:GDP -0.004 0.12 0.34 9 -0.32 16 25
NGF (dimer) 0.011 0.073 -10000 0 -0.31 18 18
RhoG/GDP 0.018 0.014 -10000 0 -0.21 1 1
RIT1/GDP 0.005 0.088 0.32 5 -0.22 13 18
TIAM1 0.025 0.028 -10000 0 -0.28 3 3
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
BDNF (dimer)/TRKB -0.016 0.13 -10000 0 -0.24 86 86
KIDINS220/CRKL/C3G 0.039 0.011 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.023 -10000 0 -0.22 2 2
FRS2 family/SHP2 0.053 0.019 -10000 0 -0.18 1 1
SHC/GRB2/SOS1/GAB1 0.064 0.027 -10000 0 -0.16 1 1
RIT1/GTP 0.02 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.006 0.1 -10000 0 -0.31 35 35
RAP1/GDP 0 0.068 -10000 0 -0.19 14 14
KIDINS220/CRKL 0.028 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.042 0.14 -10000 0 -0.31 75 75
ubiquitin-dependent protein catabolic process 0.017 0.08 -10000 0 -0.19 37 37
Schwann cell development -0.018 0.028 -10000 0 -10000 0 0
EHD4 0.027 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.029 0.03 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
CDC42/GTP -0.042 0.14 -10000 0 -0.33 53 53
ABL1 0.027 0.007 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
Rap1/GTP 0 0.088 -10000 0 -0.36 11 11
STAT3 0.032 0.009 -10000 0 -10000 0 0
axon guidance -0.049 0.13 -10000 0 -0.32 53 53
MAPK3 -0.052 0.086 0.22 3 -0.22 36 39
MAPK1 -0.054 0.085 0.23 2 -0.22 37 39
CDC42/GDP 0.007 0.092 0.29 8 -0.22 13 21
NTF3 -0.006 0.1 -10000 0 -0.32 35 35
NTF4 -0.047 0.14 -10000 0 -0.32 80 80
NGF (dimer)/TRKA/FAIM 0.022 0.075 -10000 0 -0.19 35 35
PI3K 0.032 0.038 -10000 0 -0.23 6 6
FRS3 0.028 0.004 -10000 0 -10000 0 0
FAIM 0.026 0.008 -10000 0 -10000 0 0
GAB1 0.027 0.018 -10000 0 -0.32 1 1
RASGRF1 -0.048 0.12 -10000 0 -0.34 42 42
SOS1 0.027 0.006 -10000 0 -10000 0 0
MCF2L -0.031 0.1 -10000 0 -0.23 71 71
RGS19 0.027 0.013 -10000 0 -0.21 1 1
CDC42 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.11 0.28 5 -0.42 13 18
Rac1/GDP 0.007 0.085 0.3 5 -0.23 11 16
NGF (dimer)/TRKA/GRIT 0.01 0.07 -10000 0 -0.18 44 44
neuron projection morphogenesis -0.038 0.18 0.38 1 -0.79 14 15
NGF (dimer)/TRKA/NEDD4-2 0.017 0.08 -10000 0 -0.19 37 37
MAP2K1 0.027 0.057 0.22 26 -10000 0 26
NGFR -0.002 0.096 -10000 0 -0.32 32 32
NGF (dimer)/TRKA/GIPC/GAIP 0.008 0.063 -10000 0 -0.18 33 33
RAS family/GTP/PI3K 0.017 0.035 -10000 0 -0.22 6 6
FRS2 family/SHP2/GRB2/SOS1 0.073 0.031 -10000 0 -0.16 1 1
NRAS 0.027 0.018 -10000 0 -0.32 1 1
GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
PRKCI 0.026 0.008 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCZ 0.028 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.072 0.22 -10000 0 -0.56 57 57
RASA1 0.025 0.026 -10000 0 -0.32 2 2
TRKA/c-Abl 0.021 0.061 -10000 0 -0.2 25 25
SQSTM1 0.028 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0 0.12 -10000 0 -0.22 87 87
NGF (dimer)/TRKA/p62/Atypical PKCs 0.047 0.076 -10000 0 -0.16 34 34
MATK -0.085 0.12 -10000 0 -0.21 175 175
NEDD4L 0.017 0.045 -10000 0 -0.21 13 13
RAS family/GDP -0.024 0.047 -10000 0 -0.16 21 21
NGF (dimer)/TRKA -0.026 0.1 -10000 0 -0.26 54 54
Rac1/GTP -0.039 0.092 -10000 0 -0.25 39 39
FRS2 family/SHP2/CRK family 0.072 0.032 -10000 0 -0.16 1 1
Effects of Botulinum toxin

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
STX1A 0.007 0.015 0.25 1 -0.14 1 2
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.036 -10000 0 -0.17 10 10
STXBP1 0.026 0.019 -10000 0 -0.32 1 1
ACh/CHRNA1 -0.01 0.064 0.13 8 -0.11 88 96
RAB3GAP2/RIMS1/UNC13B 0.045 0.035 -10000 0 -0.14 9 9
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 0.018 0.049 -10000 0 -0.26 11 11
mol:ACh -0.009 0.047 0.089 23 -0.11 44 67
RAB3GAP2 0.027 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.018 0.068 0.16 1 -0.21 12 13
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.01 0.064 0.13 8 -0.11 88 96
UNC13B 0.028 0.005 -10000 0 -10000 0 0
CHRNA1 -0.014 0.09 -10000 0 -0.21 63 63
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.026 0.096 0.1 2 -0.19 87 89
SNAP25 -0.025 0.077 -10000 0 -0.22 49 49
VAMP2 0.005 0.002 -10000 0 -10000 0 0
SYT1 -0.036 0.13 -10000 0 -0.31 70 70
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.018 0.19 1 -0.15 2 3
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.068 0.16 1 -0.21 12 13
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.028 0.11 0.43 3 -0.48 2 5
CRKL 0.011 0.077 0.27 9 -0.21 2 11
mol:DAG 0.009 0.075 -10000 0 -0.22 27 27
HRAS 0.015 0.085 0.28 15 -10000 0 15
MAPK8 0.01 0.082 0.18 38 -0.16 35 73
RAP1A 0.01 0.076 0.25 9 -0.24 3 12
GAB1 0.011 0.078 0.2 20 -0.21 3 23
MAPK14 0.016 0.078 0.18 41 -0.16 27 68
EPO -0.013 0.1 -10000 0 -0.27 49 49
PLCG1 0.008 0.076 -10000 0 -0.23 27 27
EPOR/TRPC2/IP3 Receptors 0.021 0.038 -10000 0 -0.2 8 8
RAPGEF1 0.027 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.007 0.1 -10000 0 -0.19 72 72
GAB1/SHC/GRB2/SOS1 0.034 0.073 0.28 1 -0.2 3 4
EPO/EPOR (dimer) 0.01 0.083 0.19 2 -0.18 51 53
IRS2 0.007 0.074 0.25 8 -0.22 3 11
STAT1 0.012 0.086 0.19 1 -0.23 31 32
STAT5B 0.008 0.08 -10000 0 -0.23 26 26
cell proliferation 0.006 0.1 0.23 49 -0.19 5 54
GAB1/SHIP/PIK3R1/SHP2/SHC 0.014 0.077 -10000 0 -0.26 12 12
TEC 0.01 0.076 0.28 8 -0.22 2 10
SOCS3 -0.02 0.12 -10000 0 -0.3 53 53
STAT1 (dimer) 0.012 0.085 0.19 1 -0.23 31 32
JAK2 0.024 0.026 -10000 0 -0.32 1 1
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
EPO/EPOR (dimer)/JAK2 0.05 0.076 -10000 0 -0.15 30 30
EPO/EPOR 0.01 0.083 0.19 2 -0.18 51 53
LYN 0.024 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.019 0.068 0.23 4 -0.21 2 6
elevation of cytosolic calcium ion concentration 0.021 0.038 -10000 0 -0.2 8 8
SHC1 0.027 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.034 0.069 -10000 0 -0.18 27 27
mol:IP3 0.009 0.075 -10000 0 -0.22 27 27
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.018 0.086 0.25 2 -0.24 13 15
SH2B3 0.024 0.019 -10000 0 -10000 0 0
NFKB1 0.017 0.078 0.18 42 -0.16 26 68
EPO/EPOR (dimer)/JAK2/SOCS3 -0.023 0.08 -10000 0 -0.19 63 63
PTPN6 0.01 0.071 0.17 30 -0.23 2 32
TEC/VAV2/GRB2 0.027 0.071 0.28 1 -0.21 2 3
EPOR 0.021 0.038 -10000 0 -0.2 8 8
INPP5D 0.01 0.076 -10000 0 -0.32 19 19
mol:GDP 0.033 0.073 0.28 1 -0.2 3 4
SOS1 0.027 0.006 -10000 0 -10000 0 0
PLCG2 0.02 0.032 -10000 0 -0.26 4 4
CRKL/CBL/C3G 0.026 0.071 0.28 1 -0.24 2 3
VAV2 0.007 0.068 0.18 15 -0.22 2 17
CBL 0.008 0.075 0.21 15 -0.24 3 18
SHC/Grb2/SOS1 0.025 0.059 -10000 0 -0.21 2 2
STAT5A 0.008 0.081 -10000 0 -0.23 27 27
GRB2 0.027 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.022 0.092 -10000 0 -0.31 9 9
LYN/PLCgamma2 0.028 0.029 -10000 0 -0.18 4 4
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
BTK 0.009 0.079 0.25 10 -0.22 4 14
BCL2 0.002 0.18 0.39 4 -0.68 18 22
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.033 0.32 4 -10000 0 4
VDR 0.023 0.041 -10000 0 -0.3 6 6
FAM120B 0.028 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.016 0.1 -10000 0 -0.29 22 22
RXRs/LXRs/DNA/Oxysterols -0.015 0.12 -10000 0 -0.42 21 21
MED1 0.028 0.004 -10000 0 -10000 0 0
mol:9cRA 0.001 0.012 -10000 0 -0.07 1 1
RARs/THRs/DNA/Src-1 0.026 0.032 -10000 0 -0.18 8 8
RXRs/NUR77 0.015 0.1 -10000 0 -0.18 73 73
RXRs/PPAR -0.021 0.097 -10000 0 -0.2 79 79
NCOR2 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.017 0.028 -10000 0 -0.2 6 6
RARs/VDR/DNA/Vit D3 0.056 0.047 -10000 0 -0.2 10 10
RARA 0.028 0.003 -10000 0 -10000 0 0
NCOA1 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.041 -10000 0 -0.3 6 6
RARs/RARs/DNA/9cRA 0.041 0.037 -10000 0 -0.16 9 9
RARG 0.024 0.036 -10000 0 -0.32 4 4
RPS6KB1 0.02 0.059 0.56 4 -10000 0 4
RARs/THRs/DNA/SMRT 0.025 0.034 -10000 0 -0.18 9 9
THRA 0.028 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.017 0.028 -10000 0 -0.2 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.006 0.095 -10000 0 -0.16 84 84
NR1H4 -0.041 0.13 -10000 0 -0.3 74 74
RXRs/LXRs/DNA 0.027 0.11 -10000 0 -0.22 21 21
NR1H2 0.027 0.019 -10000 0 -10000 0 0
NR1H3 0.026 0.02 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.014 0.094 -10000 0 -0.16 74 74
NR4A1 0.014 0.062 -10000 0 -0.25 18 18
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.047 0.1 -10000 0 -0.19 119 119
RXRG -0.051 0.14 -10000 0 -0.31 84 84
RXR alpha/CCPG 0.037 0.021 -10000 0 -10000 0 0
RXRA 0.025 0.02 -10000 0 -10000 0 0
RXRB 0.027 0.02 -10000 0 -10000 0 0
THRB 0.024 0.027 -10000 0 -0.21 5 5
PPARG 0.01 0.075 -10000 0 -0.3 20 20
PPARD 0.028 0.003 -10000 0 -10000 0 0
TNF -0.05 0.23 -10000 0 -0.95 21 21
mol:Oxysterols 0.001 0.011 -10000 0 -10000 0 0
cholesterol transport -0.015 0.12 -10000 0 -0.42 21 21
PPARA 0.028 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.04 -10000 0 -0.32 5 5
RXRs/NUR77/BCL2 -0.026 0.095 -10000 0 -0.2 77 77
SREBF1 -0.017 0.11 -10000 0 -0.5 8 8
RXRs/RXRs/DNA/9cRA 0.006 0.095 -10000 0 -0.16 84 84
ABCA1 -0.019 0.12 -10000 0 -0.55 8 8
RARs/THRs 0.073 0.044 -10000 0 -0.17 9 9
RXRs/FXR -0.019 0.12 -10000 0 -0.18 116 116
BCL2 0.016 0.056 -10000 0 -0.32 10 10
Signaling events mediated by PRL

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
CCNE1 0.026 0.021 -10000 0 -0.21 3 3
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.002 0.089 -10000 0 -0.32 27 27
CDKN1A 0.01 0.051 -10000 0 -0.42 4 4
PRL-3/alpha Tubulin 0.004 0.066 -10000 0 -0.14 63 63
mol:Ca2+ -0.048 0.068 0.25 4 -0.17 63 67
AGT -0.014 0.096 -10000 0 -0.23 58 58
CCNA2 -0.026 0.058 0.5 1 -0.23 6 7
TUBA1B 0.028 0.003 -10000 0 -10000 0 0
EGR1 -0.012 0.07 0.26 1 -0.17 54 55
CDK2/Cyclin E1 0.045 0.057 -10000 0 -0.37 4 4
MAPK3 0.001 0.085 0.26 22 -0.14 62 84
PRL-2 /Rab GGTase beta 0.04 0.009 -10000 0 -10000 0 0
MAPK1 0.001 0.085 0.26 22 -0.14 63 85
PTP4A1 -0.014 0.046 -10000 0 -10000 0 0
PTP4A3 -0.017 0.086 -10000 0 -0.21 63 63
PTP4A2 0.028 0.003 -10000 0 -10000 0 0
ITGB1 0.003 0.087 0.26 24 -0.14 61 85
SRC 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.017 0.047 -10000 0 -0.32 4 4
Rab GGTase beta/Rab GGTase alpha 0.04 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 0.006 0.061 -10000 0 -10000 0 0
RABGGTA 0.028 0.003 -10000 0 -10000 0 0
BCAR1 -0.029 0.034 -10000 0 -0.16 15 15
RHOC 0.016 0.056 -10000 0 -0.31 7 7
RHOA 0.018 0.051 -10000 0 -0.31 5 5
cell motility 0.029 0.071 0.33 4 -0.29 4 8
PRL-1/alpha Tubulin 0.008 0.06 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.011 0.087 -10000 0 -0.17 74 74
ROCK1 0.029 0.064 0.3 3 -0.31 3 6
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.028 0.005 -10000 0 -10000 0 0
mitosis -0.014 0.046 -10000 0 -10000 0 0
ATF5 0.025 0.027 -10000 0 -0.21 5 5
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.022 0.062 -10000 0 -0.15 39 39
RGS9BP 0.026 0.025 -10000 0 -0.24 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.016 0.027 -10000 0 -0.21 5 5
mol:Na + 0.018 0.03 -10000 0 -0.11 15 15
mol:ADP -0.011 0.018 -10000 0 -0.14 5 5
GNAT2 0.025 0.018 -10000 0 -0.21 2 2
RGS9-1/Gbeta5/R9AP 0.002 0.097 -10000 0 -0.18 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.02 -10000 0 -0.15 3 3
GRK7 0.022 0.008 -10000 0 -10000 0 0
CNGB3 0.011 0.037 -10000 0 -0.21 10 10
Cone Metarhodopsin II/X-Arrestin 0.015 0.012 -10000 0 -0.14 2 2
mol:Ca2+ 0.011 0.08 0.19 49 -10000 0 49
Cone PDE6 0.018 0.091 -10000 0 -0.16 72 72
Cone Metarhodopsin II 0.023 0.018 -10000 0 -0.1 5 5
Na + (4 Units) 0.017 0.048 0.22 1 -0.11 31 32
GNAT2/GDP 0.017 0.089 -10000 0 -0.15 77 77
GNB5 0.028 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.008 0.02 0.18 2 -0.17 1 3
Cone Transducin 0.024 0.066 -10000 0 -0.16 39 39
SLC24A2 0 0.07 -10000 0 -0.21 38 38
GNB3/GNGT2 0.011 0.078 -10000 0 -0.21 39 39
GNB3 -0.005 0.099 -10000 0 -0.32 34 34
GNAT2/GTP 0.018 0.012 -10000 0 -0.14 2 2
CNGA3 0.019 0.029 -10000 0 -0.21 6 6
ARR3 0.019 0.017 -10000 0 -0.21 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.018 0.03 -10000 0 -0.12 15 15
mol:Pi 0.002 0.097 -10000 0 -0.18 77 77
Cone CNG Channel 0.033 0.039 -10000 0 -0.16 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0 0.07 -10000 0 -0.21 38 38
RGS9 -0.047 0.14 -10000 0 -0.31 81 81
PDE6C 0.018 0.007 -10000 0 -10000 0 0
GNGT2 0.023 0.038 -10000 0 -0.29 5 5
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.018 -10000 0 -0.21 2 2
Arf6 signaling events

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.026 0.021 -10000 0 -0.13 2 2
ARNO/beta Arrestin1-2 0.032 0.088 -10000 0 -0.77 4 4
EGFR -0.007 0.1 -10000 0 -0.32 36 36
EPHA2 -0.004 0.099 -10000 0 -0.31 35 35
USP6 0.026 0.008 -10000 0 -10000 0 0
IQSEC1 0.028 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.005 0.094 -10000 0 -0.2 67 67
ARRB2 0.01 0.005 -10000 0 -10000 0 0
mol:GTP 0.009 0.038 0.12 15 -0.13 5 20
ARRB1 0.027 0.018 -10000 0 -0.32 1 1
FBXO8 0.027 0.005 -10000 0 -10000 0 0
TSHR 0.013 0.065 -10000 0 -0.28 17 17
EGF 0 0.082 -10000 0 -0.23 40 40
somatostatin receptor activity 0 0 0.001 23 -0.001 17 40
ARAP2 0.027 0.018 -10000 0 -0.32 1 1
mol:GDP 0.005 0.09 0.22 18 -0.23 20 38
mol:PI-3-4-5-P3 0 0 0.001 23 -0.001 5 28
ITGA2B 0.016 0.056 -10000 0 -0.3 11 11
ARF6 0.028 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.066 0.2 1 -0.16 28 29
ADAP1 0.024 0.023 -10000 0 -0.26 2 2
KIF13B 0.021 0.012 -10000 0 -10000 0 0
HGF/MET 0.003 0.097 -10000 0 -0.24 45 45
PXN 0.027 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.013 0.1 0.28 22 -0.23 15 37
EGFR/EGFR/EGF/EGF/ARFGEP100 0.012 0.087 -10000 0 -0.16 66 66
ADRB2 0.026 0.021 -10000 0 -0.21 3 3
receptor agonist activity 0 0 0 17 0 13 30
actin filament binding 0 0 0.001 22 0 16 38
SRC 0.027 0.006 -10000 0 -10000 0 0
ITGB3 -0.043 0.14 -10000 0 -0.32 76 76
GNAQ 0.027 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 37 -0.001 12 49
ARF6/GDP 0.004 0.11 0.24 13 -0.31 17 30
ARF6/GDP/GULP/ACAP1 0.031 0.095 0.22 14 -0.24 14 28
alphaIIb/beta3 Integrin/paxillin/GIT1 0.011 0.099 -10000 0 -0.17 82 82
ACAP1 0.014 0.048 -10000 0 -0.21 16 16
ACAP2 0.026 0.019 -10000 0 -0.32 1 1
LHCGR/beta Arrestin2 0.015 0.019 -10000 0 -10000 0 0
EFNA1 0.027 0.006 -10000 0 -10000 0 0
HGF 0.004 0.08 -10000 0 -0.28 26 26
CYTH3 0.007 0.021 0.25 2 -0.14 2 4
CYTH2 0.009 0.1 -10000 0 -1 4 4
NCK1 0.026 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 25 0 13 38
endosomal lumen acidification 0 0 0.001 20 0 22 42
microtubule-based process 0 0 -10000 0 0 4 4
GULP1 0.025 0.028 -10000 0 -0.23 4 4
GNAQ/ARNO 0.026 0.099 -10000 0 -0.91 4 4
mol:Phosphatidic acid 0 0 0 11 -10000 0 11
PIP3-E 0 0 0 19 0 6 25
MET -0.002 0.093 -10000 0 -0.32 30 30
GNA14 0.027 0.005 -10000 0 -10000 0 0
GNA15 0.013 0.07 -10000 0 -0.32 16 16
GIT1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 33 -0.001 12 45
GNA11 0.015 0.063 -10000 0 -0.32 13 13
LHCGR 0.019 0.013 -10000 0 -0.21 1 1
AGTR1 -0.021 0.098 -10000 0 -0.22 70 70
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.019 -10000 0 -10000 0 0
IPCEF1/ARNO 0.018 0.11 -10000 0 -0.83 4 4
alphaIIb/beta3 Integrin -0.021 0.11 -10000 0 -0.22 84 84
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.018 0.07 -10000 0 -0.22 29 29
CRKL 0.001 0.12 0.23 12 -0.45 12 24
mol:PIP3 -0.008 0.07 -10000 0 -0.76 3 3
AKT1 -0.004 0.075 0.25 1 -0.66 3 4
PTK2B 0.021 0.013 -10000 0 -10000 0 0
RAPGEF1 0.009 0.12 0.29 16 -0.41 12 28
RANBP10 0.025 0.01 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
HGF/MET/SHIP2 0.02 0.089 -10000 0 -0.22 36 36
MAP3K5 0.008 0.11 0.26 10 -0.37 16 26
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.086 -10000 0 -0.2 36 36
AP1 -0.003 0.09 -10000 0 -0.21 51 51
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.007 -10000 0 -10000 0 0
apoptosis -0.12 0.32 -10000 0 -0.76 70 70
STAT3 (dimer) -0.017 0.1 -10000 0 -0.35 22 22
GAB1/CRKL/SHP2/PI3K 0.029 0.12 0.28 2 -0.44 13 15
INPP5D 0.01 0.076 -10000 0 -0.32 19 19
CBL/CRK 0.017 0.12 0.27 7 -0.4 14 21
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.023 0.011 -10000 0 -10000 0 0
ELK1 0.002 0.097 0.32 26 -10000 0 26
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.002 0.064 -10000 0 -0.27 13 13
PAK1 -0.002 0.083 0.36 7 -0.58 3 10
HGF/MET/RANBP10 0.017 0.087 -10000 0 -0.22 36 36
HRAS -0.03 0.17 -10000 0 -0.55 35 35
DOCK1 0 0.11 0.22 11 -0.43 12 23
GAB1 -0.004 0.12 0.24 4 -0.44 14 18
CRK 0.001 0.12 0.25 11 -0.42 14 25
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.027 0.17 -10000 0 -0.51 38 38
JUN 0.024 0.033 -10000 0 -0.29 4 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.012 0.075 -10000 0 -0.22 38 38
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
cell morphogenesis -0.001 0.14 0.32 14 -0.4 23 37
GRB2/SHC 0.022 0.08 0.16 12 -0.22 26 38
FOS -0.023 0.12 -10000 0 -0.31 55 55
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.002 0.097 0.32 26 -10000 0 26
HGF/MET/MUC20 0.005 0.083 -10000 0 -0.2 45 45
cell migration 0.016 0.074 -10000 0 -0.22 26 26
GRB2 0.027 0.006 -10000 0 -10000 0 0
CBL 0.026 0.019 -10000 0 -0.32 1 1
MET/RANBP10 0.014 0.069 -10000 0 -0.21 30 30
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.004 0.086 -10000 0 -0.26 32 32
MET/MUC20 0 0.064 -10000 0 -0.21 30 30
RAP1B 0.014 0.12 0.28 23 -0.39 12 35
RAP1A 0.01 0.12 0.31 14 -0.39 12 26
HGF/MET/RANBP9 0.02 0.089 -10000 0 -0.22 36 36
RAF1 -0.02 0.17 0.33 1 -0.52 34 35
STAT3 -0.016 0.1 -10000 0 -0.36 20 20
cell proliferation -0.015 0.14 0.34 7 -0.38 34 41
RPS6KB1 0 0.048 -10000 0 -0.25 8 8
MAPK3 -0.008 0.099 0.46 7 -10000 0 7
MAPK1 -0.003 0.12 0.44 15 -10000 0 15
RANBP9 0.028 0.003 -10000 0 -10000 0 0
MAPK8 0.004 0.13 0.31 4 -0.44 18 22
SRC -0.009 0.079 -10000 0 -0.31 19 19
PI3K 0.019 0.086 0.16 11 -0.24 28 39
MET/Glomulin 0.003 0.058 -10000 0 -0.18 29 29
SOS1 0.027 0.006 -10000 0 -10000 0 0
MAP2K1 -0.015 0.16 0.34 3 -0.48 34 37
MET -0.002 0.093 -10000 0 -0.32 30 30
MAP4K1 0.009 0.12 0.26 9 -0.39 17 26
PTK2 0.023 0.011 -10000 0 -10000 0 0
MAP2K2 -0.017 0.16 0.35 2 -0.48 34 36
BAD -0.003 0.081 0.35 5 -0.63 3 8
MAP2K4 0.007 0.1 0.24 12 -0.35 15 27
SHP2/GRB2/SOS1/GAB1 0.014 0.11 -10000 0 -0.34 27 27
INPPL1 0.028 0.004 -10000 0 -10000 0 0
PXN 0.027 0.006 -10000 0 -10000 0 0
SH3KBP1 0.028 0.004 -10000 0 -10000 0 0
HGS -0.014 0.068 -10000 0 -0.21 36 36
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF 0.004 0.08 -10000 0 -0.28 26 26
RASA1 0.025 0.026 -10000 0 -0.32 2 2
NCK1 0.026 0.008 -10000 0 -10000 0 0
PTPRJ 0.028 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.017 0.08 0.17 1 -0.21 33 34
PDPK1 -0.005 0.077 0.23 4 -0.7 3 7
HGF/MET/SHIP 0.013 0.11 -10000 0 -0.26 42 42
TCGA08_p53

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
CDKN2A -0.02 0.061 0.25 2 -0.14 73 75
TP53 -0.008 0.048 -10000 0 -0.21 19 19
Senescence -0.008 0.047 -10000 0 -0.21 19 19
Apoptosis -0.008 0.047 -10000 0 -0.21 19 19
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.007 0.044 0.3 5 -0.17 1 6
MDM4 0.027 0.006 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.027 0.13 0.29 14 -0.46 14 28
FYN 0.006 0.16 0.31 13 -0.57 17 30
LAT/GRAP2/SLP76 0.011 0.13 0.25 6 -0.43 19 25
IKBKB 0.022 0.012 -10000 0 -10000 0 0
AKT1 0.012 0.13 0.31 17 -0.38 17 34
B2M 0.028 0.008 -10000 0 -10000 0 0
IKBKG 0.008 0.041 0.12 17 -0.13 8 25
MAP3K8 0.019 0.053 -10000 0 -0.29 10 10
mol:Ca2+ -0.011 0.009 -10000 0 -0.056 4 4
integrin-mediated signaling pathway 0.027 0.044 -10000 0 -0.18 16 16
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.002 0.16 0.35 11 -0.56 17 28
TRPV6 0.072 0.3 1.1 26 -10000 0 26
CD28 0.005 0.076 -10000 0 -0.23 34 34
SHC1 0.003 0.15 0.28 15 -0.51 19 34
receptor internalization -0.01 0.16 0.17 3 -0.43 31 34
PRF1 -0.009 0.2 -10000 0 -0.87 15 15
KRAS 0.026 0.008 -10000 0 -10000 0 0
GRB2 0.027 0.006 -10000 0 -10000 0 0
COT/AKT1 0.02 0.11 0.29 16 -0.33 14 30
LAT 0 0.15 0.26 12 -0.51 19 31
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.011 0.067 -10000 0 -0.24 23 23
CD3E 0.015 0.063 -10000 0 -0.27 16 16
CD3G -0.005 0.096 -10000 0 -0.28 38 38
RASGRP2 0 0.039 0.072 2 -0.17 17 19
RASGRP1 0.008 0.13 0.3 16 -0.39 19 35
HLA-A 0.023 0.042 -10000 0 -0.27 7 7
RASSF5 0.013 0.068 -10000 0 -0.32 15 15
RAP1A/GTP/RAPL 0.027 0.044 -10000 0 -0.18 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.066 0.19 26 -0.13 14 40
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.007 0.048 -10000 0 -0.18 16 16
PRKCA -0.001 0.073 0.17 12 -0.22 20 32
GRAP2 0.015 0.063 -10000 0 -0.3 14 14
mol:IP3 -0.01 0.094 0.15 1 -0.35 17 18
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.006 0.14 -10000 0 -0.53 17 17
ORAI1 -0.058 0.24 0.36 8 -0.94 25 33
CSK 0.002 0.15 0.24 9 -0.55 17 26
B7 family/CD28 0.03 0.15 0.29 4 -0.41 24 28
CHUK 0.027 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.006 0.16 0.21 4 -0.55 21 25
PTPN6 -0.003 0.14 0.24 7 -0.5 19 26
VAV1 -0.005 0.15 0.25 6 -0.54 19 25
Monovalent TCR/CD3 -0.006 0.092 0.14 1 -0.25 34 35
CBL 0.026 0.019 -10000 0 -0.32 1 1
LCK 0.008 0.16 0.3 12 -0.58 15 27
PAG1 0.014 0.15 0.22 32 -0.52 17 49
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
TCR/CD3/MHC I/CD8/LCK -0.005 0.16 0.21 6 -0.52 22 28
CD80 0.012 0.058 -10000 0 -0.22 22 22
CD86 0.022 0.035 -10000 0 -0.22 7 7
PDK1/CARD11/BCL10/MALT1 0.001 0.062 -10000 0 -0.22 16 16
HRAS 0.025 0.027 -10000 0 -0.21 5 5
GO:0035030 -0.007 0.12 0.23 6 -0.35 25 31
CD8A 0.02 0.051 -10000 0 -0.28 10 10
CD8B 0.02 0.05 -10000 0 -0.26 11 11
PTPRC 0.012 0.07 -10000 0 -0.28 19 19
PDK1/PKC theta 0.006 0.15 0.39 16 -0.48 16 32
CSK/PAG1 0.016 0.15 0.22 39 -0.5 17 56
SOS1 0.027 0.006 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.033 -10000 0 -0.18 7 7
GRAP2/SLP76 0.013 0.15 0.3 1 -0.5 19 20
STIM1 -0.01 0.11 0.98 3 -0.94 1 4
RAS family/GTP 0.022 0.083 0.24 18 -0.17 18 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.012 0.16 0.18 2 -0.45 31 33
mol:DAG -0.02 0.08 -10000 0 -0.31 18 18
RAP1A/GDP 0.014 0.032 0.1 19 -0.059 11 30
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 0.017 0.052 -10000 0 -0.23 15 15
cytotoxic T cell degranulation -0.007 0.19 -10000 0 -0.82 15 15
RAP1A/GTP 0 0.015 -10000 0 -0.062 18 18
mol:PI-3-4-5-P3 0.007 0.14 0.31 14 -0.46 17 31
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.006 0.12 -10000 0 -0.44 17 17
NRAS 0.027 0.018 -10000 0 -0.32 1 1
ZAP70 0.003 0.074 -10000 0 -0.21 39 39
GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.004 0.13 0.2 3 -0.43 19 22
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.031 0.059 -10000 0 -0.22 17 17
CARD11 0.017 0.051 -10000 0 -0.26 11 11
PRKCB -0.013 0.084 0.17 7 -0.23 34 41
PRKCE 0.003 0.069 0.17 12 -0.22 15 27
PRKCQ -0.001 0.16 0.34 13 -0.52 19 32
LCP2 0.023 0.035 -10000 0 -0.24 6 6
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.014 0.11 0.3 17 -0.33 16 33
IKK complex 0.006 0.075 0.23 21 -0.11 20 41
RAS family/GDP 0 0.01 -10000 0 -0.045 4 4
MAP3K14 0.012 0.086 0.25 15 -0.25 13 28
PDPK1 0.013 0.12 0.34 17 -0.38 14 31
TCR/CD3/MHC I/CD8/Fyn -0.011 0.19 -10000 0 -0.65 22 22
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.056 0.051 -10000 0 -0.16 16 16
ER alpha/Gai/GDP/Gbeta gamma -0.04 0.16 0.21 1 -0.38 43 44
AKT1 -0.023 0.19 -10000 0 -0.71 23 23
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.018 0.19 -10000 0 -0.72 23 23
mol:Ca2+ -0.001 0.056 0.18 2 -0.34 4 6
IGF1R 0.026 0.022 -10000 0 -0.26 2 2
E2/ER alpha (dimer)/Striatin 0.009 0.076 -10000 0 -0.19 43 43
SHC1 0.027 0.007 -10000 0 -10000 0 0
apoptosis 0.021 0.18 0.68 23 -10000 0 23
RhoA/GTP 0.017 0.034 -10000 0 -0.22 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.008 0.13 -10000 0 -0.35 29 29
regulation of stress fiber formation 0.017 0.06 0.22 8 -0.16 16 24
E2/ERA-ERB (dimer) 0.021 0.051 -10000 0 -0.14 33 33
KRAS 0.026 0.008 -10000 0 -10000 0 0
G13/GTP 0.028 0.036 -10000 0 -0.16 13 13
pseudopodium formation -0.017 0.06 0.16 16 -0.22 8 24
E2/ER alpha (dimer)/PELP1 0.027 0.041 -10000 0 -0.17 14 14
GRB2 0.027 0.006 -10000 0 -10000 0 0
GNG2 0.023 0.04 -10000 0 -0.32 5 5
GNAO1 -0.021 0.12 -10000 0 -0.32 50 50
HRAS 0.025 0.027 -10000 0 -0.21 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.021 0.14 0.22 1 -0.41 25 26
E2/ER beta (dimer) 0.012 0.035 -10000 0 -0.14 20 20
mol:GDP 0.007 0.06 -10000 0 -0.3 11 11
mol:NADP -0.021 0.14 0.22 1 -0.41 25 26
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
mol:IP3 -0.002 0.056 -10000 0 -0.35 4 4
IGF-1R heterotetramer 0.026 0.022 -10000 0 -0.26 2 2
PLCB1 0.002 0.059 -10000 0 -0.36 4 4
PLCB2 0.003 0.057 -10000 0 -0.32 4 4
IGF1 -0.003 0.093 -10000 0 -0.28 37 37
mol:L-citrulline -0.021 0.14 0.22 1 -0.41 25 26
RHOA 0.028 0.004 -10000 0 -10000 0 0
Gai/GDP -0.12 0.29 -10000 0 -0.62 89 89
JNK cascade 0.012 0.035 -10000 0 -0.13 20 20
BCAR1 0.023 0.011 -10000 0 -10000 0 0
ESR2 0.015 0.053 -10000 0 -0.21 20 20
GNAQ 0.027 0.005 -10000 0 -10000 0 0
ESR1 0.015 0.064 -10000 0 -0.31 14 14
Gq family/GDP/Gbeta gamma -0.019 0.17 -10000 0 -0.44 41 41
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.09 -10000 0 -0.56 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.009 0.13 -10000 0 -0.36 29 29
GNAZ 0.003 0.089 -10000 0 -0.32 27 27
E2/ER alpha (dimer) 0.012 0.044 -10000 0 -0.21 14 14
STRN -0.004 0.099 -10000 0 -0.32 34 34
GNAL -0.057 0.15 -10000 0 -0.32 90 90
PELP1 0.026 0.008 -10000 0 -10000 0 0
MAPK11 0.005 0.033 -10000 0 -0.11 27 27
GNAI2 0.028 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.019 -10000 0 -0.32 1 1
HBEGF -0.057 0.15 0.27 4 -0.38 41 45
cAMP biosynthetic process -0.023 0.082 -10000 0 -0.15 94 94
SRC -0.039 0.14 0.2 3 -0.38 39 42
PI3K 0.032 0.038 -10000 0 -0.23 6 6
GNB1 0.028 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.034 0.069 -10000 0 -0.28 11 11
SOS1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.032 0.11 -10000 0 -0.31 35 35
Gs family/GTP -0.019 0.087 -10000 0 -0.15 94 94
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.027 -10000 0 -0.11 6 6
vasodilation -0.019 0.13 0.22 1 -0.39 25 26
mol:DAG -0.002 0.056 -10000 0 -0.35 4 4
Gs family/GDP/Gbeta gamma -0.021 0.09 -10000 0 -0.29 19 19
MSN -0.018 0.063 0.16 16 -0.24 8 24
Gq family/GTP 0.008 0.062 -10000 0 -0.34 4 4
mol:PI-3-4-5-P3 -0.017 0.18 -10000 0 -0.69 23 23
NRAS 0.027 0.018 -10000 0 -0.32 1 1
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.019 0.13 0.39 25 -0.22 1 26
GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.065 -10000 0 -0.29 11 11
NOS3 -0.023 0.14 0.22 1 -0.43 25 26
GNA11 0.015 0.063 -10000 0 -0.32 13 13
MAPKKK cascade -0.035 0.16 0.33 1 -0.46 31 32
E2/ER alpha (dimer)/PELP1/Src -0.013 0.14 -10000 0 -0.36 32 32
ruffle organization -0.017 0.06 0.16 16 -0.22 8 24
ROCK2 -0.017 0.066 0.17 16 -0.24 8 24
GNA14 0.027 0.005 -10000 0 -10000 0 0
GNA15 0.013 0.07 -10000 0 -0.32 16 16
GNA13 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.076 0.15 0.27 6 -0.36 52 58
MMP2 -0.029 0.14 0.22 3 -0.37 39 42
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.003 0.089 -10000 0 -0.16 90 90
MAPK9 0.008 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.017 0.25 1 -0.14 2 3
GNB1/GNG2 0.034 0.026 -10000 0 -0.18 5 5
GNB1 0.028 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 0.008 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.026 0.075 -10000 0 -0.16 90 90
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.012 0.019 0.046 90 -10000 0 90
GNAL -0.057 0.15 -10000 0 -0.32 90 90
GNG2 0.023 0.04 -10000 0 -0.32 5 5
CRH 0.014 0.018 -10000 0 -0.21 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.043 -10000 0 -0.25 11 11
MAPK11 0.007 0.007 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.005 -10000 0 -10000 0 0
VLDLR 0.027 0.006 -10000 0 -10000 0 0
LRPAP1 0.028 0.004 -10000 0 -10000 0 0
NUDC 0.028 0.003 -10000 0 -10000 0 0
RELN/LRP8 0.029 0.059 -10000 0 -0.12 44 44
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.028 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.013 0.059 0.18 22 -0.18 3 25
IQGAP1/CaM 0.04 0.009 -10000 0 -10000 0 0
DAB1 -0.099 0.16 -10000 0 -0.31 136 136
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
PLA2G7 -0.039 0.11 -10000 0 -0.21 105 105
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.028 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.039 0.018 -10000 0 -0.14 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.006 -10000 0 -10000 0 0
CDK5R1 0.019 0.045 -10000 0 -0.21 14 14
LIS1/Poliovirus Protein 3A 0.01 0.003 -10000 0 -10000 0 0
CDK5R2 -0.002 0.077 -10000 0 -0.21 46 46
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.044 0.12 -10000 0 -0.2 122 122
YWHAE 0.026 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.024 0.082 0.29 22 -10000 0 22
MAP1B -0.009 0.057 -10000 0 -0.22 25 25
RAC1 0.013 0.006 -10000 0 -10000 0 0
p35/CDK5 0.009 0.056 0.26 7 -0.18 1 8
RELN -0.005 0.081 -10000 0 -0.21 48 48
PAFAH/LIS1 -0.01 0.065 0.21 1 -0.12 92 93
LIS1/CLIP170 0.028 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.012 0.051 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.05 0.11 -10000 0 -0.28 33 33
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.012 0.08 0.28 22 -0.19 3 25
LIS1/IQGAP1 0.029 0.01 -10000 0 -10000 0 0
RHOA 0.014 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.017 0.049 -10000 0 -0.21 17 17
PAFAH1B2 0.014 0.065 -10000 0 -0.32 14 14
MAP1B/LIS1/Dynein heavy chain 0.01 0.049 -10000 0 -0.15 21 21
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.079 0.31 12 -10000 0 12
LRP8 0.026 0.022 -10000 0 -0.21 3 3
NDEL1/Katanin 60 0.019 0.083 0.29 20 -10000 0 20
P39/CDK5 0.004 0.069 0.24 11 -0.18 7 18
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.029 0.01 -10000 0 -10000 0 0
CDK5 -0.016 0.037 0.18 4 -0.18 1 5
PPP2R5D 0.028 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.009 -10000 0 -10000 0 0
CSNK2A1 0.028 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.017 0.11 0.19 3 -0.17 108 111
RELN/VLDLR 0.067 0.044 0.2 6 -0.16 4 10
CDC42 0.014 0.005 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.023 0.025 -10000 0 -0.21 4 4
LAT2 -0.003 0.085 0.21 2 -0.3 21 23
AP1 0.006 0.15 0.27 1 -0.42 24 25
mol:PIP3 0.015 0.14 0.35 26 -0.37 17 43
IKBKB 0.009 0.12 0.29 31 -0.22 21 52
AKT1 0.004 0.11 0.29 28 -0.25 12 40
IKBKG 0 0.11 0.27 23 -0.22 24 47
MS4A2 0.012 0.07 -10000 0 -0.29 18 18
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
MAP3K1 0.015 0.11 0.25 21 -0.35 14 35
mol:Ca2+ 0.017 0.12 0.32 27 -0.28 17 44
LYN 0.025 0.011 -10000 0 -10000 0 0
CBLB -0.003 0.082 -10000 0 -0.28 22 22
SHC1 0.027 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.044 0.039 -10000 0 -0.16 11 11
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.01 0.076 -10000 0 -0.32 19 19
PLD2 -0.005 0.087 0.3 16 -0.24 11 27
PTPN13 0.004 0.12 -10000 0 -0.58 6 6
PTPN11 0.025 0.024 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.019 0.12 0.34 23 -0.29 11 34
SYK 0.024 0.04 -10000 0 -0.3 5 5
GRB2 0.027 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.004 0.11 -10000 0 -0.35 20 20
LAT -0.007 0.086 -10000 0 -0.28 24 24
PAK2 0.014 0.12 0.26 20 -0.38 15 35
NFATC2 -0.074 0.17 -10000 0 -0.44 66 66
HRAS 0.007 0.12 0.25 11 -0.4 17 28
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.02 0.084 -10000 0 -0.85 3 3
Fc epsilon R1 0.02 0.091 -10000 0 -0.21 45 45
Antigen/IgE/Fc epsilon R1 0.022 0.082 -10000 0 -0.19 44 44
mol:GDP 0.002 0.11 0.27 2 -0.42 17 19
JUN 0.024 0.033 -10000 0 -0.29 4 4
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
FOS -0.023 0.12 -10000 0 -0.31 55 55
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.002 0.089 0.16 1 -0.32 20 21
CHUK 0.003 0.11 0.27 25 -0.22 23 48
KLRG1 0.001 0.077 0.16 4 -0.3 15 19
VAV1 -0.008 0.097 0.17 1 -0.32 23 24
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.004 0.086 0.15 1 -0.28 25 26
negative regulation of mast cell degranulation 0.004 0.1 0.17 2 -0.34 20 22
BTK 0.007 0.11 0.23 1 -0.43 13 14
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.13 0.23 1 -0.35 38 39
GAB2/PI3K/SHP2 -0.008 0.062 -10000 0 -0.23 19 19
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.004 0.095 -10000 0 -0.29 25 25
RAF1 0.019 0.089 -10000 0 -0.92 3 3
Fc epsilon R1/FcgammaRIIB/SHIP 0.034 0.12 -10000 0 -0.24 49 49
FCER1G 0.025 0.026 -10000 0 -0.25 3 3
FCER1A -0.009 0.11 -10000 0 -0.32 38 38
Antigen/IgE/Fc epsilon R1/Fyn 0.029 0.079 -10000 0 -0.18 39 39
MAPK3 0.018 0.083 -10000 0 -0.84 3 3
MAPK1 0.017 0.086 -10000 0 -0.88 3 3
NFKB1 0.028 0.003 -10000 0 -10000 0 0
MAPK8 -0.023 0.2 -10000 0 -0.62 28 28
DUSP1 0.018 0.056 -10000 0 -0.32 10 10
NF-kappa-B/RelA 0.001 0.051 0.12 4 -0.15 16 20
actin cytoskeleton reorganization 0.004 0.12 -10000 0 -0.55 8 8
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.014 0.11 0.22 1 -0.38 19 20
FER -0.004 0.087 0.15 1 -0.31 20 21
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.002 0.061 -10000 0 -0.31 11 11
SOS1 0.027 0.006 -10000 0 -10000 0 0
PLCG1 0.009 0.12 0.25 13 -0.43 15 28
cytokine secretion -0.002 0.035 -10000 0 -0.13 5 5
SPHK1 -0.006 0.087 0.17 2 -0.28 23 25
PTK2 0.003 0.13 -10000 0 -0.6 7 7
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.004 0.11 0.21 1 -0.37 19 20
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.009 0.14 0.33 22 -0.36 19 41
MAP2K2 0.012 0.082 -10000 0 -0.86 3 3
MAP2K1 0.015 0.085 -10000 0 -0.86 3 3
MAP2K7 0.028 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 0.008 0.078 0.16 3 -0.28 16 19
MAP2K4 -0.046 0.27 -10000 0 -0.86 36 36
Fc epsilon R1/FcgammaRIIB 0.032 0.1 -10000 0 -0.22 44 44
mol:Choline -0.005 0.086 0.3 16 -0.24 11 27
SHC/Grb2/SOS1 0.038 0.098 0.24 1 -0.32 15 16
FYN 0.024 0.01 -10000 0 -10000 0 0
DOK1 0.028 0.004 -10000 0 -10000 0 0
PXN 0.007 0.13 0.38 5 -0.56 7 12
HCLS1 -0.003 0.083 0.15 1 -0.28 22 23
PRKCB -0.004 0.13 0.31 23 -0.3 26 49
FCGR2B 0.015 0.059 -10000 0 -0.26 15 15
IGHE 0.001 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.004 0.1 0.17 2 -0.35 20 22
LCP2 0.023 0.035 -10000 0 -0.24 6 6
PLA2G4A -0.01 0.099 0.15 1 -0.31 28 29
RASA1 0.025 0.026 -10000 0 -0.32 2 2
mol:Phosphatidic acid -0.005 0.086 0.3 16 -0.24 11 27
IKK complex 0.014 0.1 0.28 30 -0.19 11 41
WIPF1 0.023 0.038 -10000 0 -0.29 5 5
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.004 0.029 0.14 3 -0.15 8 11
BUB1B 0 0.034 0.16 4 -0.13 4 8
PLK1 0.01 0.025 0.094 14 -0.091 5 19
PLK1S1 0.011 0.023 0.13 2 -0.17 3 5
KIF2A 0.007 0.027 0.15 6 -10000 0 6
regulation of mitotic centrosome separation 0.01 0.025 0.094 14 -0.091 5 19
GOLGA2 0.027 0.007 -10000 0 -10000 0 0
Hec1/SPC24 0.028 0.058 0.14 10 -0.12 15 25
WEE1 0.015 0.042 0.17 1 -0.37 3 4
cytokinesis -0.008 0.07 0.21 9 -0.21 7 16
PP2A-alpha B56 0.054 0.095 -10000 0 -0.5 10 10
AURKA 0.014 0.023 0.13 8 -0.14 1 9
PICH/PLK1 0.007 0.046 0.15 3 -0.17 12 15
CENPE -0.005 0.037 0.11 2 -0.13 12 14
RhoA/GTP 0.021 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.028 0.15 6 -10000 0 6
PPP2CA 0.027 0.006 -10000 0 -10000 0 0
FZR1 0.027 0.005 -10000 0 -10000 0 0
TPX2 0.015 0.025 0.16 7 -0.18 1 8
PAK1 0.023 0.037 -10000 0 -0.32 4 4
SPC24 -0.029 0.1 -10000 0 -0.21 90 90
FBXW11 0.028 0.005 -10000 0 -10000 0 0
CLSPN 0.009 0.04 -10000 0 -0.26 7 7
GORASP1 0.028 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.014 10 -0.015 2 12
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.014 0.05 16 -0.051 5 21
G2 phase of mitotic cell cycle -0.001 0.001 0.01 2 -10000 0 2
STAG2 0.028 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.021 0.035 -10000 0 -0.43 2 2
spindle elongation 0.01 0.025 0.094 14 -0.091 5 19
ODF2 0.027 0.007 -10000 0 -10000 0 0
BUB1 0.028 0.097 -10000 0 -0.56 9 9
TPT1 -0.028 0.078 0.11 1 -0.18 75 76
CDC25C 0.018 0.044 0.16 8 -0.26 6 14
CDC25B 0.024 0.027 -10000 0 -0.24 3 3
SGOL1 0.004 0.029 0.15 8 -0.14 3 11
RHOA 0.028 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.038 0.036 -10000 0 -0.19 4 4
CDC14B 0.004 0.023 -10000 0 -0.22 4 4
CDC20 -0.048 0.11 -10000 0 -0.21 121 121
PLK1/PBIP1 0.001 0.031 0.078 3 -0.1 22 25
mitosis -0.003 0.003 0.017 3 -0.015 8 11
FBXO5 0.006 0.023 0.11 6 -10000 0 6
CDC2 0.001 0.002 -10000 0 -0.01 9 9
NDC80 0.025 0.026 -10000 0 -0.32 2 2
metaphase plate congression 0.013 0.024 -10000 0 -0.24 2 2
ERCC6L 0.009 0.048 -10000 0 -0.19 8 8
NLP/gamma Tubulin 0.004 0.021 0.07 7 -0.071 14 21
microtubule cytoskeleton organization -0.028 0.078 0.11 1 -0.18 75 76
G2/M transition DNA damage checkpoint -0.001 0.002 0.015 2 -10000 0 2
PPP1R12A 0.028 0.005 -10000 0 -10000 0 0
interphase -0.001 0.002 0.015 2 -10000 0 2
PLK1/PRC1-2 0.027 0.084 0.18 23 -0.18 22 45
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.024 -10000 0 -10000 0 0
RAB1A 0.028 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.022 0.08 20 -0.081 2 22
mitotic prometaphase -0.001 0.002 0.015 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.049 0.16 8 -0.28 5 13
microtubule-based process -0.003 0.066 0.12 24 -0.098 107 131
Golgi organization 0.01 0.025 0.094 14 -0.091 5 19
Cohesin/SA2 0.023 0.022 0.11 5 -0.093 2 7
PPP1CB/MYPT1 0.04 0.009 -10000 0 -10000 0 0
KIF20A -0.056 0.11 -10000 0 -0.21 130 130
APC/C/CDC20 0.002 0.067 0.12 27 -0.099 96 123
PPP2R1A 0.028 0.003 -10000 0 -10000 0 0
chromosome segregation 0.001 0.03 0.077 3 -0.1 22 25
PRC1 0.014 0.055 -10000 0 -0.21 22 22
ECT2 0.02 0.062 0.21 31 -0.11 4 35
C13orf34 0.009 0.022 0.081 16 -0.079 4 20
NUDC 0.013 0.024 -10000 0 -0.24 2 2
regulation of attachment of spindle microtubules to kinetochore 0 0.034 0.16 4 -0.13 4 8
spindle assembly 0.008 0.02 0.081 10 -0.078 5 15
spindle stabilization 0.011 0.023 0.13 2 -0.17 3 5
APC/C/HCDH1 0.022 0.022 -10000 0 -0.17 4 4
MKLP2/PLK1 -0.004 0.067 0.12 24 -0.098 107 131
CCNB1 0.017 0.05 -10000 0 -0.22 15 15
PPP1CB 0.028 0.004 -10000 0 -10000 0 0
BTRC 0.027 0.006 -10000 0 -10000 0 0
ROCK2 -0.02 0.12 0.19 2 -0.35 42 44
TUBG1 0.003 0.04 -10000 0 -0.17 16 16
G2/M transition of mitotic cell cycle 0.003 0.03 -10000 0 -0.19 4 4
MLF1IP -0.003 0.049 0.25 5 -0.14 29 34
INCENP 0.028 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.011 0.13 -10000 0 -0.48 24 24
HDAC1 0.026 0.003 -10000 0 -10000 0 0
AES 0.027 0.005 -10000 0 -10000 0 0
FBXW11 0.028 0.005 -10000 0 -10000 0 0
DTX1 0.016 0.051 -10000 0 -0.21 17 17
LRP6/FZD1 0.033 0.021 -10000 0 -0.22 1 1
TLE1 0.027 0.006 -10000 0 -10000 0 0
AP1 -0.02 0.1 -10000 0 -0.25 52 52
NCSTN 0.027 0.007 -10000 0 -10000 0 0
ADAM10 0.012 0.072 -10000 0 -0.32 17 17
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.041 -10000 0 -0.48 1 1
NICD/RBPSUH 0.013 0.13 -10000 0 -0.47 24 24
WIF1 -0.13 0.17 -10000 0 -0.31 170 170
NOTCH1 -0.005 0.13 -10000 0 -0.49 24 24
PSENEN 0.028 0.003 -10000 0 -10000 0 0
KREMEN2 0.008 0.072 -10000 0 -0.25 26 26
DKK1 -0.045 0.14 -10000 0 -0.3 81 81
beta catenin/beta TrCP1 0.04 0.055 0.27 4 -0.23 1 5
APH1B 0.028 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.006 -10000 0 -10000 0 0
AXIN1 0.004 0.065 0.25 3 -0.3 3 6
CtBP/CBP/TCF1/TLE1/AES 0.018 0.023 -10000 0 -10000 0 0
PSEN1 0.028 0.005 -10000 0 -10000 0 0
FOS -0.023 0.12 -10000 0 -0.31 55 55
JUN 0.024 0.033 -10000 0 -0.29 4 4
MAP3K7 0.023 0.011 -10000 0 -10000 0 0
CTNNB1 0.027 0.058 0.27 4 -0.24 1 5
MAPK3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.021 0.073 -10000 0 -0.16 45 45
HNF1A 0.003 0.071 -10000 0 -0.21 38 38
CTBP1 0.027 0.004 -10000 0 -10000 0 0
MYC 0.016 0.035 -10000 0 -10000 0 0
NKD1 0.002 0.084 -10000 0 -0.31 25 25
FZD1 0.025 0.019 -10000 0 -0.32 1 1
NOTCH1 precursor/Deltex homolog 1 0.014 0.13 -10000 0 -0.48 23 23
apoptosis -0.021 0.1 -10000 0 -0.24 55 55
Delta 1/NOTCHprecursor 0.012 0.13 -10000 0 -0.47 24 24
DLL1 0.024 0.036 -10000 0 -0.32 4 4
PPARD 0.027 0.045 -10000 0 -0.79 1 1
Gamma Secretase 0.076 0.027 -10000 0 -10000 0 0
APC -0.013 0.11 0.25 2 -0.39 17 19
DVL1 0.002 0.032 -10000 0 -0.23 4 4
CSNK2A1 0.028 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.009 0.1 -10000 0 -0.17 92 92
LRP6 0.025 0.009 -10000 0 -10000 0 0
CSNK1A1 0.028 0.004 -10000 0 -10000 0 0
NLK 0.011 0.005 -10000 0 -10000 0 0
CCND1 0.028 0.016 -10000 0 -10000 0 0
WNT1 0.02 0.036 -10000 0 -0.21 9 9
Axin1/APC/beta catenin 0.024 0.09 0.34 6 -0.37 6 12
DKK2 0.007 0.079 -10000 0 -0.28 26 26
NOTCH1 precursor/DVL1 0.001 0.12 -10000 0 -0.46 19 19
GSK3B 0.027 0.007 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.013 0.13 -10000 0 -0.49 23 23
PPP2R5D 0.021 0.055 0.2 10 -0.36 3 13
MAPK1 0.028 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.033 0.11 -10000 0 -0.16 151 151
RBPJ 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.029 0.005 -10000 0 -10000 0 0
PDGFR-alpha signaling 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
PDGFRA 0.003 0.079 -10000 0 -0.34 17 17
PDGF/PDGFRA/CRKL 0.022 0.058 -10000 0 -0.23 16 16
positive regulation of JUN kinase activity 0.053 0.047 -10000 0 -0.17 12 12
CRKL 0.028 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.038 0.12 -10000 0 -0.22 102 102
AP1 -0.12 0.27 -10000 0 -0.77 55 55
mol:IP3 -0.007 0.06 -10000 0 -0.26 17 17
PLCG1 -0.007 0.061 -10000 0 -0.26 17 17
PDGF/PDGFRA/alphaV Integrin 0.022 0.056 -10000 0 -0.22 16 16
RAPGEF1 0.027 0.007 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.06 -10000 0 -0.26 17 17
CAV3 -0.054 0.14 -10000 0 -0.3 91 91
CAV1 -0.013 0.11 -10000 0 -0.32 42 42
SHC/Grb2/SOS1 0.055 0.048 -10000 0 -0.17 12 12
PDGF/PDGFRA/Shf 0.021 0.059 -10000 0 -0.23 16 16
FOS -0.12 0.27 0.31 1 -0.76 55 56
JUN -0.029 0.03 -10000 0 -0.24 3 3
oligodendrocyte development 0.022 0.056 -10000 0 -0.22 16 16
GRB2 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
mol:DAG -0.007 0.06 -10000 0 -0.26 17 17
PDGF/PDGFRA 0.003 0.079 -10000 0 -0.34 17 17
actin cytoskeleton reorganization 0.023 0.055 -10000 0 -0.23 14 14
SRF 0.017 0.01 -10000 0 -10000 0 0
SHC1 0.027 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.06 -10000 0 -0.21 17 17
PDGF/PDGFRA/Crk/C3G 0.04 0.048 -10000 0 -0.18 13 13
JAK1 -0.002 0.051 -10000 0 -0.23 16 16
ELK1/SRF -0.003 0.051 0.16 6 -0.21 14 20
SHB 0.026 0.019 -10000 0 -0.32 1 1
SHF 0.026 0.022 -10000 0 -0.26 2 2
CSNK2A1 0.033 0.017 -10000 0 -10000 0 0
GO:0007205 -0.015 0.065 -10000 0 -0.29 17 17
SOS1 0.027 0.006 -10000 0 -10000 0 0
Ras protein signal transduction 0.053 0.047 -10000 0 -0.17 12 12
PDGF/PDGFRA/SHB 0.023 0.055 -10000 0 -0.23 14 14
PDGF/PDGFRA/Caveolin-1 -0.004 0.1 -10000 0 -0.27 44 44
ITGAV 0.027 0.006 -10000 0 -10000 0 0
ELK1 -0.025 0.064 0.23 1 -0.27 17 18
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
PDGF/PDGFRA/Crk 0.02 0.057 -10000 0 -0.22 17 17
JAK-STAT cascade -0.002 0.05 -10000 0 -0.23 16 16
cell proliferation 0.021 0.059 -10000 0 -0.23 16 16
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.01 -10000 0 -10000 0 0
AES 0.026 0.01 -10000 0 -10000 0 0
FBXW11 0.028 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.034 0.021 -10000 0 -0.22 1 1
SMAD4 0.026 0.009 -10000 0 -10000 0 0
DKK2 0.007 0.079 -10000 0 -0.28 26 26
TLE1 0.026 0.009 -10000 0 -10000 0 0
MACF1 0.029 0.001 -10000 0 -10000 0 0
CTNNB1 0.07 0.095 0.29 25 -0.41 1 26
WIF1 -0.13 0.17 -10000 0 -0.31 170 170
beta catenin/RanBP3 0.025 0.076 0.5 5 -0.33 1 6
KREMEN2 0.008 0.072 -10000 0 -0.25 26 26
DKK1 -0.044 0.14 -10000 0 -0.3 81 81
beta catenin/beta TrCP1 0.077 0.089 0.29 19 -0.38 1 20
FZD1 0.026 0.019 -10000 0 -0.32 1 1
AXIN2 -0.007 0.17 0.55 7 -1.3 5 12
AXIN1 0.028 0.006 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.031 0.088 -10000 0 -0.48 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.11 0.28 8 -0.43 9 17
Axin1/APC/GSK3 0.049 0.058 0.23 8 -0.42 1 9
Axin1/APC/GSK3/beta catenin/Macf1 0.041 0.087 0.3 10 -0.35 6 16
HNF1A 0.003 0.071 0.19 1 -0.21 37 38
CTBP1 0.026 0.008 -10000 0 -10000 0 0
MYC 0.098 0.21 0.53 70 -10000 0 70
RANBP3 0.028 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.021 0.073 -10000 0 -0.16 44 44
NKD1 0.002 0.084 -10000 0 -0.31 25 25
TCF4 0.022 0.027 -10000 0 -0.32 2 2
TCF3 0.026 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.058 0.034 -10000 0 -0.16 1 1
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.003 0.066 0.46 3 -0.29 1 4
LEF1 0.015 0.052 -10000 0 -0.22 17 17
DVL1 0.039 0.037 0.2 1 -10000 0 1
CSNK2A1 0.028 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.061 0.085 0.29 6 -0.35 3 9
DKK1/LRP6/Kremen 2 -0.009 0.1 -10000 0 -0.18 84 84
LRP6 0.025 0.01 -10000 0 -10000 0 0
CSNK1A1 0.027 0.011 -10000 0 -10000 0 0
NLK 0.028 0.006 -10000 0 -10000 0 0
CCND1 0.015 0.094 0.54 9 -10000 0 9
WNT1 0.021 0.036 -10000 0 -0.2 9 9
GSK3A 0.028 0.006 -10000 0 -10000 0 0
GSK3B 0.027 0.007 -10000 0 -10000 0 0
FRAT1 0.027 0.007 -10000 0 -10000 0 0
PPP2R5D 0.043 0.064 0.23 21 -0.3 3 24
APC 0.022 0.058 0.2 27 -10000 0 27
WNT1/LRP6/FZD1 0.061 0.079 0.18 112 -10000 0 112
CREBBP 0.026 0.008 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.037 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.028 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.051 -10000 0 -0.23 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.045 0.086 -10000 0 -0.16 127 127
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.006 -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 0.027 0.005 -10000 0 -10000 0 0
FYN 0.024 0.01 -10000 0 -10000 0 0
MAP3K12 0.022 0.043 -10000 0 -0.32 6 6
FGR 0.026 0.028 -10000 0 -0.28 3 3
p38 alpha/TAB1 -0.044 0.081 -10000 0 -0.25 36 36
PRKG1 -0.068 0.15 -10000 0 -0.32 102 102
DUSP8 0.026 0.021 -10000 0 -0.21 3 3
PGK/cGMP/p38 alpha -0.045 0.12 0.16 1 -0.27 60 61
apoptosis -0.043 0.078 -10000 0 -0.24 36 36
RAL/GTP 0.034 0.013 -10000 0 -10000 0 0
LYN 0.024 0.01 -10000 0 -10000 0 0
DUSP1 0.018 0.056 -10000 0 -0.32 10 10
PAK1 0.024 0.036 -10000 0 -0.32 4 4
SRC 0.027 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.063 0.025 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.011 -10000 0 -10000 0 0
MAPK11 -0.024 0.12 0.23 11 -0.3 32 43
BLK -0.027 0.11 -10000 0 -0.28 58 58
HCK 0.024 0.033 -10000 0 -0.29 4 4
MAP2K3 0.027 0.005 -10000 0 -10000 0 0
DUSP16 0.025 0.01 -10000 0 -10000 0 0
DUSP10 0.027 0.006 -10000 0 -10000 0 0
TRAF6/MEKK3 0.035 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.015 0.11 0.22 10 -0.28 32 42
positive regulation of innate immune response -0.025 0.14 0.26 12 -0.34 33 45
LCK 0.024 0.03 -10000 0 -0.21 6 6
p38alpha-beta/MKP7 -0.011 0.13 0.3 7 -0.33 30 37
p38alpha-beta/MKP5 -0.015 0.14 0.36 4 -0.33 29 33
PGK/cGMP -0.045 0.1 -10000 0 -0.21 102 102
PAK2 0.027 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.02 0.14 0.27 6 -0.34 31 37
CDC42 0.028 0.003 -10000 0 -10000 0 0
RALB 0.027 0.006 -10000 0 -10000 0 0
RALA 0.026 0.008 -10000 0 -10000 0 0
PAK3 -0.099 0.16 -10000 0 -0.32 136 136
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.013 0.1 -10000 0 -0.22 75 75
AKT1 -0.008 0.15 0.31 4 -0.43 32 36
PTK2B -0.031 0.13 0.18 4 -0.49 21 25
VEGFR2 homodimer/Frs2 0.008 0.12 -10000 0 -0.5 18 18
CAV1 -0.013 0.11 -10000 0 -0.32 42 42
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.015 0.12 -10000 0 -0.48 18 18
endothelial cell proliferation -0.012 0.16 0.26 14 -0.47 25 39
mol:Ca2+ -0.01 0.12 0.19 5 -0.47 19 24
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.026 0.12 -10000 0 -0.46 18 18
RP11-342D11.1 -0.02 0.11 0.18 5 -0.47 19 24
CDH5 0.025 0.009 -10000 0 -10000 0 0
VEGFA homodimer 0.053 0.056 -10000 0 -0.16 20 20
SHC1 0.027 0.007 -10000 0 -10000 0 0
SHC2 0.02 0.045 -10000 0 -0.21 13 13
HRAS/GDP 0.014 0.11 -10000 0 -0.42 19 19
SH2D2A 0.014 0.056 -10000 0 -0.22 20 20
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.025 0.13 0.32 1 -0.42 20 21
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.015 0.13 0.19 1 -0.48 19 20
VEGFR1 homodimer 0.023 0.038 -10000 0 -0.29 5 5
SHC/GRB2/SOS1 0.037 0.13 -10000 0 -0.45 19 19
GRB10 -0.01 0.11 0.19 2 -0.47 18 20
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
GRB2 0.027 0.006 -10000 0 -10000 0 0
PAK1 0.024 0.036 -10000 0 -0.32 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.036 0.12 -10000 0 -0.45 18 18
HRAS 0.025 0.027 -10000 0 -0.21 5 5
VEGF/Rho/ROCK1/Integrin Complex -0.035 0.14 -10000 0 -0.43 27 27
HIF1A 0.027 0.018 -10000 0 -0.32 1 1
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.025 0.12 -10000 0 -0.45 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.027 0.018 -10000 0 -0.32 1 1
Nck/Pak 0.035 0.029 -10000 0 -0.22 4 4
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.011 0.12 -10000 0 -0.49 18 18
mol:GDP 0.025 0.12 -10000 0 -0.43 19 19
mol:NADP 0.011 0.11 0.36 6 -0.37 20 26
eNOS/Hsp90 0.02 0.11 0.29 3 -0.35 20 23
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
mol:IP3 -0.01 0.12 0.19 5 -0.48 19 24
HIF1A/ARNT 0.038 0.017 -10000 0 -0.22 1 1
SHB 0.026 0.019 -10000 0 -0.32 1 1
VEGFA 0.01 0.077 -10000 0 -0.3 21 21
VEGFC 0.027 0.013 -10000 0 -0.21 1 1
FAK1/Vinculin -0.046 0.2 0.26 2 -0.55 35 37
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.009 0.16 -10000 0 -0.51 22 22
PTPN6 0.026 0.008 -10000 0 -10000 0 0
EPAS1 0.016 0.078 -10000 0 -0.31 19 19
mol:L-citrulline 0.011 0.11 0.36 6 -0.37 20 26
ITGAV 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.029 0.12 -10000 0 -0.45 18 18
VEGFR2 homodimer/VEGFA homodimer 0.016 0.13 -10000 0 -0.51 19 19
VEGFR2/3 heterodimer 0.008 0.12 -10000 0 -0.51 18 18
VEGFB 0.028 0.004 -10000 0 -10000 0 0
MAPK11 -0.025 0.12 0.19 6 -0.47 21 27
VEGFR2 homodimer -0.008 0.13 -10000 0 -0.58 18 18
FLT1 0.023 0.038 -10000 0 -0.29 5 5
NEDD4 0.021 0.05 -10000 0 -0.31 8 8
MAPK3 -0.038 0.12 0.19 6 -0.47 20 26
MAPK1 -0.037 0.12 0.21 5 -0.47 20 25
VEGFA145/NRP2 0.012 0.084 -10000 0 -0.22 42 42
VEGFR1/2 heterodimer 0.006 0.12 -10000 0 -0.54 18 18
KDR -0.008 0.13 -10000 0 -0.58 18 18
VEGFA165/NRP1/VEGFR2 homodimer 0.009 0.14 -10000 0 -0.52 20 20
SRC 0.027 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.034 0.13 0.22 8 -0.47 21 29
PI3K -0.007 0.15 -10000 0 -0.58 19 19
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.013 0.12 0.19 1 -0.33 33 34
FES -0.011 0.12 0.19 5 -0.49 19 24
GAB1 -0.006 0.15 -10000 0 -0.44 31 31
VEGFR2 homodimer/VEGFA homodimer/Src 0.015 0.12 -10000 0 -0.49 18 18
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
SOS1 0.027 0.006 -10000 0 -10000 0 0
ARNT 0.027 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.007 0.11 0.3 1 -0.41 19 20
VEGFR2 homodimer/VEGFA homodimer/Yes 0.014 0.12 -10000 0 -0.49 18 18
PI3K/GAB1 0 0.16 0.24 1 -0.45 33 34
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.034 0.12 -10000 0 -0.46 17 17
PRKACA 0.028 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.023 0.11 -10000 0 -0.48 18 18
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
CDC42 -0.01 0.12 0.19 5 -0.48 19 24
actin cytoskeleton reorganization 0.015 0.12 0.18 1 -0.48 19 20
PTK2 -0.052 0.18 -10000 0 -0.62 27 27
EDG1 -0.02 0.11 0.18 5 -0.47 19 24
mol:DAG -0.01 0.12 0.19 5 -0.48 19 24
CaM/Ca2+ 0.004 0.11 0.18 4 -0.44 19 23
MAP2K3 -0.023 0.12 0.18 6 -0.46 20 26
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.027 0.13 0.23 20 -0.48 18 38
PLCG1 -0.01 0.12 0.19 5 -0.48 19 24
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.028 0.12 -10000 0 -0.45 18 18
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
YES1 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.014 0.12 -10000 0 -0.5 18 18
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.013 0.12 -10000 0 -0.49 18 18
cell migration -0.036 0.18 0.25 4 -0.52 32 36
mol:PI-3-4-5-P3 -0.005 0.14 -10000 0 -0.54 19 19
FYN 0.024 0.01 -10000 0 -10000 0 0
VEGFB/NRP1 -0.003 0.11 0.18 4 -0.45 19 23
mol:NO 0.011 0.11 0.36 6 -0.37 20 26
PXN 0.027 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.003 0.1 -10000 0 -0.42 19 19
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.008 0.12 -10000 0 -0.48 18 18
VHL 0.026 0.019 -10000 0 -0.32 1 1
ITGB3 -0.043 0.14 -10000 0 -0.32 76 76
NOS3 0.009 0.12 0.37 6 -0.41 20 26
VEGFR2 homodimer/VEGFA homodimer/Sck 0.015 0.13 -10000 0 -0.5 19 19
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA -0.021 0.12 0.21 6 -0.48 18 24
PRKCB -0.046 0.13 0.18 4 -0.5 22 26
VCL 0.009 0.078 -10000 0 -0.32 20 20
VEGFA165/NRP1 -0.002 0.12 0.18 5 -0.47 19 24
VEGFR1/2 heterodimer/VEGFA homodimer 0.013 0.13 -10000 0 -0.52 18 18
VEGFA165/NRP2 0.012 0.084 -10000 0 -0.22 42 42
MAPKKK cascade 0.008 0.11 0.5 1 -0.42 17 18
NRP2 0.007 0.083 -10000 0 -0.32 23 23
VEGFC homodimer 0.027 0.013 -10000 0 -0.21 1 1
NCK1 0.026 0.008 -10000 0 -10000 0 0
ROCK1 0.026 0.019 -10000 0 -0.32 1 1
FAK1/Paxillin -0.041 0.18 0.26 2 -0.56 30 32
MAP3K13 -0.016 0.12 0.19 4 -0.47 21 25
PDPK1 -0.012 0.12 0.26 1 -0.46 19 20
ErbB2/ErbB3 signaling events

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
USP8 -0.006 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.003 0.09 -10000 0 -0.22 13 13
NFATC4 -0.029 0.064 0.23 7 -0.22 3 10
ERBB2IP 0.027 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.028 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.006 0.069 -10000 0 -0.18 42 42
JUN -0.006 0.072 0.25 5 -0.3 1 6
HRAS 0.025 0.027 -10000 0 -0.21 5 5
DOCK7 -0.034 0.06 0.18 4 -0.19 17 21
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.012 0.07 -10000 0 -0.17 41 41
AKT1 0.004 0.007 -10000 0 -10000 0 0
BAD -0.006 0.008 -10000 0 -0.11 1 1
MAPK10 -0.015 0.055 0.22 6 -0.18 2 8
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.008 0.074 -10000 0 -0.19 42 42
RAF1 -0.013 0.088 0.3 5 -0.24 14 19
ErbB2/ErbB3/neuregulin 2 -0.026 0.095 -10000 0 -0.18 99 99
STAT3 -0.014 0.21 -10000 0 -0.9 19 19
cell migration -0.003 0.081 0.26 18 -0.17 2 20
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.037 0.17 0.44 2 -0.5 21 23
FOS -0.052 0.19 0.34 4 -0.45 59 63
NRAS 0.027 0.019 -10000 0 -0.32 1 1
mol:Ca2+ -0.006 0.069 -10000 0 -0.18 42 42
MAPK3 -0.022 0.14 0.41 3 -0.45 10 13
MAPK1 -0.024 0.14 0.4 3 -0.45 14 17
JAK2 -0.033 0.059 0.18 4 -0.2 11 15
NF2 0.006 0.049 -10000 0 -0.66 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.009 0.07 -10000 0 -0.2 39 39
NRG1 -0.022 0.11 -10000 0 -0.32 46 46
GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
MAPK8 -0.04 0.098 -10000 0 -0.23 50 50
MAPK9 -0.016 0.049 0.18 5 -0.16 1 6
ERBB2 -0.021 0.017 -10000 0 -0.23 2 2
ERBB3 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
apoptosis 0.006 0.011 -10000 0 -10000 0 0
STAT3 (dimer) -0.014 0.2 -10000 0 -0.86 20 20
RNF41 -0.009 0.006 -10000 0 -10000 0 0
FRAP1 -0.003 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.018 0.05 -10000 0 -0.15 12 12
ErbB2/ErbB2/HSP90 (dimer) 0.005 0.024 -10000 0 -0.2 2 2
CHRNA1 -0.016 0.12 0.37 3 -0.36 9 12
myelination -0.014 0.096 0.34 14 -0.24 2 16
PPP3CB -0.033 0.056 0.18 4 -0.18 11 15
KRAS 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.001 0.084 -10000 0 -0.18 38 38
NRG2 -0.079 0.16 -10000 0 -0.32 114 114
mol:GDP -0.009 0.07 -10000 0 -0.2 39 39
SOS1 0.027 0.006 -10000 0 -10000 0 0
MAP2K2 -0.02 0.087 0.26 7 -0.26 12 19
SRC 0.027 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.034 0.058 0.18 4 -0.19 18 22
MAP2K1 -0.041 0.15 -10000 0 -0.5 12 12
heart morphogenesis -0.006 0.069 -10000 0 -0.18 42 42
RAS family/GDP 0.009 0.092 -10000 0 -0.22 12 12
GRB2 0.027 0.006 -10000 0 -10000 0 0
PRKACA 0.01 0.052 -10000 0 -0.69 2 2
CHRNE 0.005 0.022 0.12 4 -0.16 1 5
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.007 -10000 0 -10000 0 0
nervous system development -0.006 0.069 -10000 0 -0.18 42 42
CDC42 0.028 0.003 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.011 0.082 -10000 0 -0.22 42 42
ATM 0.026 0.019 -10000 0 -0.32 1 1
UBE2D3 0.028 0.003 -10000 0 -10000 0 0
PRKDC 0.023 0.016 -10000 0 -0.21 1 1
ATR 0.026 0.008 -10000 0 -10000 0 0
UBE2L3 0.028 0.005 -10000 0 -10000 0 0
FANCD2 0.02 0.013 0.2 1 -10000 0 1
protein ubiquitination 0.04 0.076 -10000 0 -0.16 42 42
XRCC5 0.028 0.004 -10000 0 -10000 0 0
XRCC6 0.028 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.044 0.024 -10000 0 -10000 0 0
MRE11A 0.027 0.005 -10000 0 -10000 0 0
DNA-PK 0.047 0.024 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.018 0.047 -10000 0 -10000 0 0
FANCF 0.028 0.003 -10000 0 -10000 0 0
BRCA1 0.027 0.006 -10000 0 -10000 0 0
CCNE1 0.026 0.021 -10000 0 -0.21 3 3
CDK2/Cyclin E1 0.039 0.018 -10000 0 -0.14 3 3
FANCG 0.028 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.01 0.082 -10000 0 -0.22 43 43
FANCE 0.028 0.003 -10000 0 -10000 0 0
FANCC 0.027 0.006 -10000 0 -10000 0 0
NBN 0.023 0.011 -10000 0 -10000 0 0
FANCA 0.007 0.065 -10000 0 -0.24 23 23
DNA repair -0.005 0.068 0.23 1 -0.25 1 2
BRCA1/BARD1/ubiquitin 0.01 0.082 -10000 0 -0.22 43 43
BARD1/DNA-PK 0.034 0.075 -10000 0 -0.16 41 41
FANCL 0.028 0.004 -10000 0 -10000 0 0
mRNA polyadenylation -0.011 0.082 0.22 42 -10000 0 42
BRCA1/BARD1/CTIP/M/R/N Complex 0.005 0.068 -10000 0 -0.19 4 4
BRCA1/BACH1/BARD1/TopBP1 0.024 0.075 -10000 0 -0.18 41 41
BRCA1/BARD1/P53 0.03 0.074 -10000 0 -0.16 41 41
BARD1/CSTF1/BRCA1 0.026 0.075 -10000 0 -0.18 41 41
BRCA1/BACH1 0.027 0.006 -10000 0 -10000 0 0
BARD1 -0.013 0.11 -10000 0 -0.32 44 44
PCNA 0.028 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.026 0.076 -10000 0 -0.18 43 43
BRCA1/BARD1/UbcH7 0.026 0.076 -10000 0 -0.18 43 43
BRCA1/BARD1/RAD51/PCNA 0.04 0.08 -10000 0 -0.18 41 41
BARD1/DNA-PK/P53 0.037 0.076 -10000 0 -0.15 41 41
BRCA1/BARD1/Ubiquitin 0.01 0.082 -10000 0 -0.22 43 43
BRCA1/BARD1/CTIP 0.016 0.069 -10000 0 -0.17 39 39
FA complex 0.026 0.037 -10000 0 -10000 0 0
BARD1/EWS 0.01 0.083 -10000 0 -0.22 44 44
RBBP8 0.012 0.017 -10000 0 -0.22 2 2
TP53 0.024 0.01 -10000 0 -10000 0 0
TOPBP1 0.026 0.008 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.029 0.073 0.16 41 -10000 0 41
BRCA1/BARD1 0.046 0.079 -10000 0 -0.16 42 42
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.007 0.076 -10000 0 -0.21 44 44
CDK2 0.028 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.014 0.054 -10000 0 -0.21 21 21
RAD50 0.027 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.01 0.082 -10000 0 -0.22 43 43
EWSR1 0.028 0.005 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.028 0.004 -9999 0 -10000 0 0
ITGB7 0.016 0.059 -9999 0 -0.29 13 13
ITGA4 0.01 0.07 -9999 0 -0.27 21 21
alpha4/beta7 Integrin 0.021 0.068 -9999 0 -0.21 28 28
alpha4/beta1 Integrin 0.027 0.053 -9999 0 -0.18 21 21
Signaling events mediated by PTP1B

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.027 0.013 -10000 0 -0.21 1 1
Jak2/Leptin Receptor 0.018 0.11 0.3 2 -0.39 13 15
PTP1B/AKT1 0.002 0.072 0.22 1 -0.23 6 7
FYN 0.024 0.01 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.01 0.072 0.21 2 -0.24 9 11
EGFR -0.008 0.1 -10000 0 -0.32 36 36
EGF/EGFR -0.007 0.1 -10000 0 -0.26 31 31
CSF1 0.019 0.053 -10000 0 -0.32 9 9
AKT1 0.028 0.005 -10000 0 -10000 0 0
INSR 0.028 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.021 0.098 0.23 1 -0.27 29 30
Insulin Receptor/Insulin 0.022 0.074 -10000 0 -0.22 2 2
HCK 0.024 0.033 -10000 0 -0.29 4 4
CRK 0.026 0.008 -10000 0 -10000 0 0
TYK2 -0.011 0.07 0.23 3 -0.24 7 10
EGF -0.003 0.082 -10000 0 -0.23 40 40
YES1 0.027 0.006 -10000 0 -10000 0 0
CAV1 -0.018 0.11 0.19 9 -0.3 25 34
TXN 0.026 0.014 -10000 0 -0.21 1 1
PTP1B/IRS1/GRB2 0.006 0.087 0.23 1 -0.31 9 10
cell migration 0.01 0.072 0.24 9 -0.21 2 11
STAT3 0.027 0.006 -10000 0 -10000 0 0
PRLR 0.004 0.083 -10000 0 -0.25 33 33
ITGA2B 0.016 0.056 -10000 0 -0.3 11 11
CSF1R 0.026 0.022 -10000 0 -0.26 2 2
Prolactin Receptor/Prolactin 0.019 0.066 -10000 0 -0.18 33 33
FGR 0.026 0.028 -10000 0 -0.28 3 3
PTP1B/p130 Cas 0.003 0.065 -10000 0 -0.22 8 8
Crk/p130 Cas 0.009 0.072 -10000 0 -0.23 5 5
DOK1 -0.001 0.07 0.21 5 -0.24 4 9
JAK2 0.004 0.1 0.34 1 -0.4 12 13
Jak2/Leptin Receptor/Leptin -0.021 0.11 -10000 0 -0.32 20 20
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
PTPN1 -0.01 0.072 0.21 2 -0.24 9 11
LYN 0.024 0.01 -10000 0 -10000 0 0
CDH2 -0.061 0.15 -10000 0 -0.31 95 95
SRC 0.011 0.077 -10000 0 -0.4 10 10
ITGB3 -0.043 0.14 -10000 0 -0.32 76 76
CAT1/PTP1B -0.013 0.11 0.25 12 -0.31 13 25
CAPN1 0.028 0.006 -10000 0 -10000 0 0
CSK 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.028 0.078 -10000 0 -0.35 3 3
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.023 0.11 -10000 0 -0.33 23 23
negative regulation of transcription 0.005 0.1 0.34 1 -0.39 12 13
FCGR2A 0.025 0.023 -10000 0 -0.26 2 2
FER 0.016 0.06 -10000 0 -0.32 11 11
alphaIIb/beta3 Integrin -0.021 0.11 -10000 0 -0.22 84 84
BLK -0.027 0.11 -10000 0 -0.28 58 58
Insulin Receptor/Insulin/Shc 0.043 0.032 -10000 0 -0.12 11 11
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.016 0.064 -10000 0 -0.31 14 14
BCAR1 0.023 0.011 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.027 0.006 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.032 0.13 0.24 5 -0.31 39 44
PRL 0.019 0.021 -10000 0 -0.2 3 3
SOCS3 -0.16 0.43 -10000 0 -1.2 58 58
SPRY2 0.023 0.032 -10000 0 -0.32 3 3
Insulin Receptor/Insulin/IRS1 0.038 0.052 -10000 0 -0.19 13 13
CSF1/CSF1R 0.007 0.088 -10000 0 -0.3 11 11
Ras protein signal transduction 0.011 0.082 0.5 9 -10000 0 9
IRS1 0.017 0.061 -10000 0 -0.32 12 12
INS 0.009 0.043 -10000 0 -0.21 13 13
LEP 0.013 0.037 -10000 0 -0.21 9 9
STAT5B -0.002 0.079 0.27 2 -0.3 6 8
STAT5A -0.002 0.079 0.27 2 -0.28 7 9
GRB2 0.027 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0 0.073 0.18 1 -0.23 9 10
CSN2 0 0.047 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
LAT 0.004 0.097 -10000 0 -0.42 16 16
YBX1 0.035 0.004 -10000 0 -10000 0 0
LCK 0.024 0.03 -10000 0 -0.21 6 6
SHC1 0.027 0.007 -10000 0 -10000 0 0
NOX4 -0.083 0.12 -10000 0 -0.2 178 178
FAS signaling pathway (CD95)

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
SPTAN1 0.004 0.047 0.2 18 -10000 0 18
RFC1 -0.002 0.026 0.16 9 -10000 0 9
PRKDC 0.017 0.066 0.2 41 -10000 0 41
RIPK1 0.03 0.006 -10000 0 -10000 0 0
CASP7 -0.011 0.089 -10000 0 -0.55 8 8
FASLG/FAS/FADD/FAF1 -0.012 0.059 0.17 1 -0.22 18 19
MAP2K4 -0.067 0.16 0.2 1 -0.32 86 87
mol:ceramide -0.02 0.097 -10000 0 -0.25 32 32
GSN 0.002 0.042 0.19 16 -0.17 1 17
FASLG/FAS/FADD/FAF1/Caspase 8 -0.018 0.074 -10000 0 -0.27 16 16
FAS 0.013 0.037 -10000 0 -0.32 3 3
BID -0.02 0.01 -10000 0 -10000 0 0
MAP3K1 -0.021 0.095 0.26 2 -0.3 12 14
MAP3K7 0.022 0.011 -10000 0 -10000 0 0
RB1 -0.002 0.026 0.16 8 -0.16 1 9
CFLAR 0.03 0.005 -10000 0 -10000 0 0
HGF/MET 0.021 0.088 -10000 0 -0.22 35 35
ARHGDIB -0.002 0.031 0.18 9 -10000 0 9
FADD 0.017 0.022 -10000 0 -10000 0 0
actin filament polymerization -0.001 0.044 0.18 3 -0.19 16 19
NFKB1 -0.022 0.095 -10000 0 -0.58 2 2
MAPK8 -0.1 0.21 -10000 0 -0.47 84 84
DFFA -0.001 0.029 0.16 10 -10000 0 10
DNA fragmentation during apoptosis -0.001 0.035 0.17 12 -0.18 2 14
FAS/FADD/MET 0.016 0.069 -10000 0 -0.19 28 28
CFLAR/RIP1 0.045 0.01 -10000 0 -10000 0 0
FAIM3 0.024 0.032 -10000 0 -0.2 7 7
FAF1 0.016 0.024 -10000 0 -10000 0 0
PARP1 -0.002 0.027 0.16 9 -10000 0 9
DFFB 0 0.033 0.17 12 -10000 0 12
CHUK -0.023 0.085 -10000 0 -0.55 2 2
FASLG -0.001 0.071 -10000 0 -0.27 21 21
FAS/FADD 0.021 0.037 -10000 0 -0.23 3 3
HGF 0.004 0.08 -10000 0 -0.28 26 26
LMNA -0.002 0.032 0.16 12 -10000 0 12
CASP6 -0.002 0.026 0.16 9 -10000 0 9
CASP10 0.012 0.046 -10000 0 -0.3 6 6
CASP3 0 0.031 0.19 9 -10000 0 9
PTPN13 0.027 0.018 -10000 0 -0.32 1 1
CASP8 -0.023 0.011 -10000 0 -0.16 1 1
IL6 -0.24 0.49 -10000 0 -1.2 81 81
MET -0.002 0.093 -10000 0 -0.32 30 30
ICAD/CAD -0.002 0.035 0.17 11 -10000 0 11
FASLG/FAS/FADD/FAF1/Caspase 10 -0.02 0.098 -10000 0 -0.25 32 32
activation of caspase activity by cytochrome c -0.02 0.01 -10000 0 -10000 0 0
PAK2 0.004 0.048 0.19 21 -0.19 1 22
BCL2 0.016 0.056 -10000 0 -0.32 10 10
IL27-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
TGFB1 0.026 0.015 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.011 0.14 0.6 11 -10000 0 11
IL27/IL27R/JAK1 0.041 0.19 0.38 5 -0.8 8 13
TBX21 0.021 0.17 0.36 12 -0.42 14 26
IL12B 0.014 0.052 -10000 0 -0.21 19 19
IL12A 0.001 0.032 -10000 0 -0.2 9 9
IL6ST -0.035 0.13 -10000 0 -0.32 67 67
IL27RA/JAK1 0.01 0.16 -10000 0 -1.1 7 7
IL27 0.017 0.044 -10000 0 -0.2 13 13
TYK2 0.029 0.01 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.026 0.1 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.011 0.14 0.6 11 -10000 0 11
T cell proliferation during immune response 0.011 0.14 0.6 11 -10000 0 11
MAPKKK cascade -0.011 0.14 -10000 0 -0.6 11 11
STAT3 0.027 0.006 -10000 0 -10000 0 0
STAT2 0.028 0.004 -10000 0 -10000 0 0
STAT1 0.027 0.031 -10000 0 -0.21 6 6
IL12RB1 0.017 0.054 -10000 0 -0.23 16 16
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.016 0.17 0.38 10 -0.46 14 24
IL27/IL27R/JAK2/TYK2 -0.012 0.14 -10000 0 -0.61 11 11
positive regulation of T cell mediated cytotoxicity -0.011 0.14 -10000 0 -0.6 11 11
STAT1 (dimer) 0.069 0.24 0.51 59 -0.55 12 71
JAK2 0.027 0.02 -10000 0 -0.32 1 1
JAK1 0.03 0.007 -10000 0 -10000 0 0
STAT2 (dimer) -0.006 0.14 -10000 0 -0.6 10 10
T cell proliferation -0.037 0.14 0.29 3 -0.53 14 17
IL12/IL12R/TYK2/JAK2 0.033 0.089 -10000 0 -0.59 4 4
IL17A -0.026 0.11 -10000 0 -10000 0 0
mast cell activation 0.011 0.14 0.6 11 -10000 0 11
IFNG 0.004 0.027 0.097 1 -0.094 6 7
T cell differentiation -0.002 0.005 0.014 3 -0.018 14 17
STAT3 (dimer) -0.005 0.14 0.3 1 -0.61 10 11
STAT5A (dimer) -0.006 0.14 0.3 1 -0.6 11 12
STAT4 (dimer) -0.007 0.14 0.3 1 -0.55 12 13
STAT4 0.019 0.049 -10000 0 -0.23 13 13
T cell activation -0.006 0.012 0.12 3 -10000 0 3
IL27R/JAK2/TYK2 0.002 0.16 -10000 0 -0.95 7 7
GATA3 -0.34 0.55 0.62 2 -1.2 106 108
IL18 0.002 0.034 -10000 0 -0.21 9 9
positive regulation of mast cell cytokine production -0.005 0.14 0.3 1 -0.57 11 12
IL27/EBI3 0.034 0.047 -10000 0 -0.15 18 18
IL27RA -0.009 0.16 -10000 0 -1.2 7 7
IL6 -0.064 0.14 -10000 0 -0.28 107 107
STAT5A 0.026 0.019 -10000 0 -0.32 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.004 0.074 0.5 7 -10000 0 7
IL1B -0.023 0.072 -10000 0 -0.19 57 57
EBI3 0.024 0.045 -10000 0 -0.25 9 9
TNF -0.01 0.056 -10000 0 -0.19 32 32
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.083 0.2 1 -0.28 9 10
TBX21 -0.046 0.29 -10000 0 -0.97 22 22
B2M 0.026 0.013 -10000 0 -10000 0 0
TYK2 0.022 0.029 -10000 0 -10000 0 0
IL12RB1 0.011 0.062 -10000 0 -0.24 16 16
GADD45B -0.025 0.25 -10000 0 -0.79 21 21
IL12RB2 0.004 0.076 -10000 0 -0.28 21 21
GADD45G -0.024 0.25 -10000 0 -0.91 14 14
natural killer cell activation 0.002 0.015 -10000 0 -10000 0 0
RELB 0.028 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 0.018 0.055 -10000 0 -0.32 9 9
IL2RA -0.009 0.086 -10000 0 -0.21 56 56
IFNG 0.012 0.053 -10000 0 -0.21 20 20
STAT3 (dimer) -0.028 0.24 -10000 0 -0.69 25 25
HLA-DRB5 0.011 0.052 -10000 0 -0.22 15 15
FASLG -0.052 0.32 -10000 0 -0.99 26 26
NF kappa B2 p52/RelB -0.03 0.27 -10000 0 -0.81 26 26
CD4 0.016 0.036 -10000 0 -0.22 6 6
SOCS1 0.024 0.03 -10000 0 -0.23 5 5
EntrezGene:6955 -0.003 0.011 -10000 0 -10000 0 0
CD3D 0.002 0.069 -10000 0 -0.24 23 23
CD3E 0.007 0.064 -10000 0 -0.27 16 16
CD3G -0.013 0.098 -10000 0 -0.29 38 38
IL12Rbeta2/JAK2 0.021 0.069 -10000 0 -0.2 20 20
CCL3 -0.056 0.31 -10000 0 -1 25 25
CCL4 -0.047 0.29 -10000 0 -0.95 22 22
HLA-A 0.021 0.043 -10000 0 -0.27 7 7
IL18/IL18R 0.043 0.082 -10000 0 -0.19 27 27
NOS2 -0.072 0.36 -10000 0 -1.1 33 33
IL12/IL12R/TYK2/JAK2/SPHK2 0.013 0.079 0.2 1 -0.25 10 11
IL1R1 -0.04 0.27 -10000 0 -0.93 18 18
IL4 -0.003 0.03 -10000 0 -10000 0 0
JAK2 0.021 0.034 -10000 0 -0.33 1 1
EntrezGene:6957 -0.003 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.035 0.2 -10000 0 -0.64 27 27
RAB7A 0.004 0.22 0.48 1 -0.76 12 13
lysosomal transport 0.007 0.21 0.45 2 -0.71 12 14
FOS -0.17 0.48 -10000 0 -1.2 60 60
STAT4 (dimer) -0.004 0.24 -10000 0 -0.81 17 17
STAT5A (dimer) -0.033 0.27 -10000 0 -0.79 28 28
GZMA -0.046 0.28 -10000 0 -1 18 18
GZMB -0.059 0.31 -10000 0 -1.1 22 22
HLX 0.02 0.04 -10000 0 -0.22 10 10
LCK -0.049 0.29 -10000 0 -0.87 27 27
TCR/CD3/MHC II/CD4 -0.036 0.14 -10000 0 -0.31 51 51
IL2/IL2R 0.051 0.079 -10000 0 -0.23 23 23
MAPK14 -0.017 0.26 -10000 0 -0.84 19 19
CCR5 -0.026 0.26 -10000 0 -1.1 11 11
IL1B -0.023 0.12 -10000 0 -0.29 57 57
STAT6 0.008 0.09 -10000 0 -0.47 2 2
STAT4 0.019 0.049 -10000 0 -0.23 13 13
STAT3 0.027 0.006 -10000 0 -10000 0 0
STAT1 0.024 0.03 -10000 0 -0.21 6 6
NFKB1 0.028 0.003 -10000 0 -10000 0 0
NFKB2 0.026 0.018 -10000 0 -0.21 2 2
IL12B 0.008 0.058 -10000 0 -0.21 19 19
CD8A 0.018 0.051 -10000 0 -0.28 10 10
CD8B 0.017 0.051 -10000 0 -0.26 11 11
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.011 0.082 0.28 9 -0.2 1 10
IL2RB 0.012 0.07 -10000 0 -0.29 19 19
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.23 -10000 0 -0.73 17 17
IL2RG 0.019 0.048 -10000 0 -0.22 14 14
IL12 0.017 0.066 -10000 0 -0.18 18 18
STAT5A 0.026 0.019 -10000 0 -0.32 1 1
CD247 0.009 0.055 -10000 0 -0.23 15 15
IL2 0.022 0.007 -10000 0 -10000 0 0
SPHK2 0.028 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.012 0.057 -10000 0 -0.3 9 9
IL12/IL12R/TYK2/JAK2 -0.048 0.31 -10000 0 -0.94 27 27
MAP2K3 -0.023 0.26 -10000 0 -0.82 21 21
RIPK2 0.023 0.011 -10000 0 -10000 0 0
MAP2K6 -0.022 0.26 -10000 0 -0.83 21 21
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.017 0.038 -10000 0 -0.25 5 5
IL18RAP 0.009 0.073 -10000 0 -0.26 23 23
IL12Rbeta1/TYK2 0.027 0.057 -10000 0 -0.18 13 13
EOMES -0.027 0.21 -10000 0 -1.1 13 13
STAT1 (dimer) -0.013 0.23 -10000 0 -0.67 26 26
T cell proliferation -0.003 0.2 -10000 0 -0.58 19 19
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.022 0.043 -10000 0 -0.32 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.008 0.21 -10000 0 -0.61 20 20
ATF2 -0.022 0.24 0.4 1 -0.76 21 22
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.019 0.037 -10000 0 -0.22 7 7
EPHB2 0.023 0.037 -10000 0 -0.26 6 6
Syndecan-2/TACI 0.015 0.052 0.2 9 -0.13 28 37
LAMA1 0.002 0.081 -10000 0 -0.26 32 32
Syndecan-2/alpha2 ITGB1 0.022 0.079 0.21 1 -0.19 34 35
HRAS 0.025 0.027 -10000 0 -0.21 5 5
Syndecan-2/CASK 0.005 0.019 -10000 0 -0.17 4 4
ITGA5 0.017 0.059 -10000 0 -0.31 12 12
BAX -0.001 0.03 -10000 0 -10000 0 0
EPB41 0.028 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.02 0.022 -10000 0 -0.16 4 4
LAMA3 0 0.09 -10000 0 -0.31 29 29
EZR 0.028 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.004 0.096 -10000 0 -0.32 32 32
Syndecan-2/MMP2 0.019 0.033 -10000 0 -0.2 7 7
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.015 0.074 -10000 0 -0.22 34 34
dendrite morphogenesis 0.02 0.031 -10000 0 -0.17 7 7
Syndecan-2/GM-CSF 0.016 0.027 -10000 0 -0.14 8 8
determination of left/right symmetry 0.008 0.023 -10000 0 -0.21 4 4
Syndecan-2/PKC delta 0.022 0.024 -10000 0 -0.18 4 4
GNB2L1 0.026 0.021 -10000 0 -0.21 3 3
MAPK3 0.033 0.066 0.19 52 -0.16 4 56
MAPK1 0.035 0.068 0.19 56 -0.16 4 60
Syndecan-2/RACK1 0.031 0.033 0.19 1 -0.17 4 5
NF1 0.028 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.008 0.023 -10000 0 -0.21 4 4
ITGA2 -0.006 0.1 -10000 0 -0.32 35 35
MAPK8 0.002 0.034 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.028 0.074 0.21 3 -0.18 31 34
Syndecan-2/Kininogen 0.009 0.049 0.2 7 -0.18 4 11
ITGB1 0.028 0.004 -10000 0 -10000 0 0
SRC 0.042 0.076 0.2 61 -0.22 1 62
Syndecan-2/CASK/Protein 4.1 0.02 0.022 -10000 0 -0.16 4 4
extracellular matrix organization 0.022 0.024 -10000 0 -0.17 4 4
actin cytoskeleton reorganization 0.019 0.037 -10000 0 -0.22 7 7
Syndecan-2/Caveolin-2/Ras 0.022 0.058 -10000 0 -0.19 21 21
Syndecan-2/Laminin alpha3 0.011 0.053 0.2 2 -0.18 23 25
Syndecan-2/RasGAP 0.042 0.037 0.19 1 -0.18 5 6
alpha5/beta1 Integrin 0.032 0.045 -10000 0 -0.21 12 12
PRKCD 0.028 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.031 -10000 0 -0.17 7 7
GO:0007205 0.002 0.002 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.035 0.18 3 -0.22 2 5
RHOA 0.028 0.004 -10000 0 -10000 0 0
SDCBP 0.024 0.01 -10000 0 -10000 0 0
TNFRSF13B 0.002 0.074 -10000 0 -0.22 34 34
RASA1 0.025 0.026 -10000 0 -0.32 2 2
alpha2/beta1 Integrin 0.015 0.074 -10000 0 -0.22 34 34
Syndecan-2/Synbindin 0.022 0.024 -10000 0 -0.18 4 4
TGFB1 0.028 0.003 -10000 0 -10000 0 0
CASP3 0.041 0.068 0.19 59 -0.16 4 63
FN1 0.022 0.043 -10000 0 -0.32 6 6
Syndecan-2/IL8 0.009 0.059 0.2 5 -0.15 37 42
SDC2 0.008 0.023 -10000 0 -0.21 4 4
KNG1 -0.004 0.07 -10000 0 -0.21 39 39
Syndecan-2/Neurofibromin 0.022 0.024 -10000 0 -0.18 4 4
TRAPPC4 0.027 0.006 -10000 0 -10000 0 0
CSF2 0.018 0.024 -10000 0 -0.21 4 4
Syndecan-2/TGFB1 0.022 0.024 -10000 0 -0.18 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.02 0.022 -10000 0 -0.16 4 4
Syndecan-2/Ezrin 0.034 0.028 -10000 0 -0.16 4 4
PRKACA 0.043 0.069 0.19 62 -0.16 4 66
angiogenesis 0.009 0.059 0.2 5 -0.15 37 42
MMP2 0.018 0.05 -10000 0 -0.32 8 8
IL8 -0.01 0.1 -10000 0 -0.26 48 48
calcineurin-NFAT signaling pathway 0.015 0.052 0.2 9 -0.13 28 37
BCR signaling pathway

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
JUN -0.028 0.13 0.27 9 -0.36 28 37
IKBKB -0.01 0.11 0.3 9 -0.27 30 39
AKT1 0.019 0.098 0.25 32 -0.19 6 38
IKBKG 0.031 0.068 0.27 11 -0.23 2 13
CALM1 0.01 0.076 0.26 8 -0.33 4 12
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
MAP3K1 -0.054 0.17 0.31 7 -0.44 41 48
MAP3K7 0.023 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0.009 0.076 0.24 7 -0.34 5 12
DOK1 0.028 0.004 -10000 0 -10000 0 0
AP-1 -0.01 0.076 0.23 6 -0.23 13 19
LYN 0.024 0.01 -10000 0 -10000 0 0
BLNK 0.026 0.007 -10000 0 -10000 0 0
SHC1 0.027 0.007 -10000 0 -10000 0 0
BCR complex 0.005 0.087 -10000 0 -0.19 56 56
CD22 -0.017 0.096 -10000 0 -0.41 14 14
CAMK2G 0.01 0.07 0.34 3 -0.37 2 5
CSNK2A1 0.028 0.004 -10000 0 -10000 0 0
INPP5D 0.01 0.076 -10000 0 -0.32 19 19
SHC/GRB2/SOS1 0.01 0.057 -10000 0 -0.2 10 10
GO:0007205 0.01 0.078 0.23 8 -0.35 5 13
SYK 0.023 0.038 -10000 0 -0.29 5 5
ELK1 0.008 0.077 0.22 7 -0.33 5 12
NFATC1 0.001 0.096 0.26 11 -0.3 11 22
B-cell antigen/BCR complex 0.005 0.087 -10000 0 -0.19 56 56
PAG1/CSK 0.034 0.017 -10000 0 -10000 0 0
NFKBIB 0.016 0.045 0.17 8 -0.12 4 12
HRAS 0.018 0.073 0.27 8 -0.25 2 10
NFKBIA 0.016 0.045 0.17 8 -0.12 4 12
NF-kappa-B/RelA/I kappa B beta 0.021 0.04 0.15 11 -10000 0 11
RasGAP/Csk 0.046 0.089 0.2 1 -0.19 40 41
mol:GDP 0.012 0.078 0.23 8 -0.31 6 14
PTEN 0.023 0.011 -10000 0 -10000 0 0
CD79B 0.014 0.059 -10000 0 -0.24 18 18
NF-kappa-B/RelA/I kappa B alpha 0.021 0.04 0.15 11 -10000 0 11
GRB2 0.027 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.021 0.12 0.32 4 -0.42 16 20
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
mol:IP3 0.01 0.071 0.22 8 -0.33 6 14
CSK 0.028 0.004 -10000 0 -10000 0 0
FOS -0.011 0.086 0.39 2 -0.29 10 12
CHUK 0.018 0.095 0.29 10 -0.28 18 28
IBTK 0.024 0.01 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.025 0.07 0.24 3 -0.32 2 5
PTPN6 -0.022 0.091 -10000 0 -0.4 14 14
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.016 0.029 0.14 5 -10000 0 5
VAV2 -0.022 0.09 -10000 0 -0.45 8 8
ubiquitin-dependent protein catabolic process 0.019 0.045 0.16 9 -0.12 4 13
BTK 0.019 0.11 -10000 0 -0.92 4 4
CD19 -0.031 0.096 -10000 0 -0.4 13 13
MAP4K1 0.014 0.06 -10000 0 -0.23 20 20
CD72 0.017 0.049 -10000 0 -0.21 16 16
PAG1 0.023 0.011 -10000 0 -10000 0 0
MAPK14 -0.045 0.15 0.28 8 -0.4 36 44
SH3BP5 0.028 0.004 -10000 0 -10000 0 0
PIK3AP1 0.012 0.071 0.21 1 -0.35 6 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.016 0.084 -10000 0 -0.43 7 7
RAF1 0.018 0.072 0.28 9 -0.27 1 10
RasGAP/p62DOK/SHIP 0.036 0.099 -10000 0 -0.19 52 52
CD79A -0.01 0.094 -10000 0 -0.24 53 53
re-entry into mitotic cell cycle -0.009 0.075 0.23 6 -0.23 13 19
RASA1 0.025 0.026 -10000 0 -0.32 2 2
MAPK3 0.019 0.074 0.28 12 -10000 0 12
MAPK1 0.017 0.073 0.31 9 -0.23 1 10
CD72/SHP1 -0.008 0.1 0.26 3 -0.36 16 19
NFKB1 0.028 0.003 -10000 0 -10000 0 0
MAPK8 -0.048 0.15 0.28 9 -0.4 37 46
actin cytoskeleton organization -0.012 0.089 0.3 4 -0.38 8 12
NF-kappa-B/RelA 0.044 0.076 0.27 11 -0.18 3 14
Calcineurin 0.024 0.065 0.28 1 -0.3 3 4
PI3K -0.023 0.085 -10000 0 -0.31 15 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.007 0.072 -10000 0 -0.36 9 9
SOS1 0.027 0.006 -10000 0 -10000 0 0
Bam32/HPK1 -0.089 0.3 -10000 0 -0.74 60 60
DAPP1 -0.12 0.33 -10000 0 -0.83 60 60
cytokine secretion 0.001 0.093 0.25 11 -0.3 9 20
mol:DAG 0.01 0.071 0.22 8 -0.33 6 14
PLCG2 0.02 0.032 -10000 0 -0.26 4 4
MAP2K1 0.017 0.07 0.28 8 -0.25 1 9
B-cell antigen/BCR complex/FcgammaRIIB 0.014 0.09 -10000 0 -0.18 60 60
mol:PI-3-4-5-P3 -0.023 0.06 0.16 2 -0.23 11 13
ETS1 0.01 0.072 0.28 8 -0.27 2 10
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.051 0.073 -10000 0 -0.18 25 25
B-cell antigen/BCR complex/LYN -0.005 0.091 -10000 0 -0.42 11 11
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 -0.016 0.087 0.25 2 -0.4 8 10
B-cell antigen/BCR complex/LYN/SYK 0.019 0.1 -10000 0 -0.37 13 13
CARD11 0.018 0.092 0.27 21 -0.36 3 24
FCGR2B 0.015 0.059 -10000 0 -0.26 15 15
PPP3CA 0.025 0.025 -10000 0 -0.21 4 4
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.012 0.054 0.18 18 -0.11 3 21
PTPRC 0.012 0.069 -10000 0 -0.28 19 19
PDPK1 -0.009 0.067 0.23 13 -0.19 4 17
PPP3CB 0.028 0.005 -10000 0 -10000 0 0
PPP3CC 0.02 0.013 -10000 0 -10000 0 0
POU2F2 0.016 0.031 0.15 5 -10000 0 5
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.028 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.009 -10000 0 -0.14 1 1
Metarhodopsin II/Arrestin 0.025 0.012 -10000 0 -0.11 1 1
PDE6G/GNAT1/GTP 0.02 0.04 -10000 0 -0.12 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.019 0.013 -10000 0 -0.21 1 1
GRK1 0.016 0.027 -10000 0 -0.21 5 5
CNG Channel 0.009 0.075 -10000 0 -0.2 17 17
mol:Na + 0.018 0.055 -10000 0 -0.18 2 2
mol:ADP 0.016 0.027 -10000 0 -0.21 5 5
RGS9-1/Gbeta5/R9AP 0.002 0.097 -10000 0 -0.18 77 77
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.029 0.059 -10000 0 -0.17 4 4
CNGB1 0.017 0.034 -10000 0 -0.21 8 8
RDH5 0.01 0.074 -10000 0 -0.3 20 20
SAG 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.068 0.27 10 -10000 0 10
Na + (4 Units) 0.013 0.051 -10000 0 -0.17 1 1
RGS9 -0.047 0.14 -10000 0 -0.31 81 81
GNB1/GNGT1 0.031 0.014 -10000 0 -0.14 1 1
GNAT1/GDP 0.015 0.087 -10000 0 -0.16 74 74
GUCY2D -0.001 0.075 -10000 0 -0.22 38 38
GNGT1 0.016 0.013 -10000 0 -0.21 1 1
GUCY2F 0.018 0.012 -10000 0 -0.21 1 1
GNB5 0.028 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.005 0.068 -10000 0 -0.18 35 35
mol:11-cis-retinal 0.01 0.074 -10000 0 -0.3 20 20
mol:cGMP 0.021 0.054 -10000 0 -0.17 7 7
GNB1 0.028 0.004 -10000 0 -10000 0 0
Rhodopsin 0.021 0.053 -10000 0 -0.2 18 18
SLC24A1 0.028 0.003 -10000 0 -10000 0 0
CNGA1 0.026 0.025 -10000 0 -0.24 3 3
Metarhodopsin II 0.021 0.019 -10000 0 -0.1 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.043 0.053 -10000 0 -0.13 21 21
RGS9BP 0.026 0.025 -10000 0 -0.24 3 3
Metarhodopsin II/Transducin 0.011 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.04 0.024 -10000 0 -0.12 6 6
PDE6A/B 0.007 0.093 -10000 0 -0.24 43 43
mol:Pi 0.002 0.097 -10000 0 -0.18 77 77
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.017 -10000 0 -0.1 2 2
PDE6B -0.005 0.1 -10000 0 -0.31 36 36
PDE6A 0.014 0.066 -10000 0 -0.29 16 16
PDE6G 0.01 0.062 -10000 0 -0.21 28 28
RHO 0.019 0.014 -10000 0 -0.21 1 1
PDE6 0.01 0.12 -10000 0 -0.19 89 89
GUCA1A 0.023 0.013 -10000 0 -0.21 1 1
GC2/GCAP Family 0.052 0.026 -10000 0 -0.12 6 6
GUCA1C 0.017 0.012 -10000 0 -0.21 1 1
GUCA1B 0.023 0.035 -10000 0 -0.22 7 7
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.025 0.038 -10000 0 -0.2 4 4
BIRC5 -0.048 0.11 -10000 0 -0.21 116 116
NFKBIA 0.002 0.031 0.18 6 -0.18 2 8
CPEB1 -0.075 0.16 -10000 0 -0.31 112 112
AKT1 0.002 0.027 0.18 5 -0.18 1 6
NDEL1 0.025 0.009 -10000 0 -10000 0 0
Aurora A/BRCA1 0.02 0.028 -10000 0 -0.16 2 2
NDEL1/TACC3 0.033 0.047 0.19 1 -0.19 4 5
GADD45A 0.026 0.025 -10000 0 -0.32 2 2
GSK3B 0.023 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.023 0.039 -10000 0 -0.18 6 6
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.02 0.074 0.23 7 -0.14 89 96
TP53 0 0.062 -10000 0 -0.2 32 32
DLG7 0.002 0.023 0.14 3 -0.18 2 5
AURKAIP1 0.022 0.038 -10000 0 -0.21 10 10
ARHGEF7 0.027 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.034 0.05 0.2 1 -0.21 4 5
G2/M transition of mitotic cell cycle 0.019 0.027 -10000 0 -0.16 2 2
AURKA 0.006 0.03 0.18 3 -0.22 2 5
AURKB 0.01 0.045 0.1 1 -0.14 27 28
CDC25B 0.012 0.026 -10000 0 -0.21 3 3
G2/M transition checkpoint 0 0.022 -10000 0 -0.16 2 2
mRNA polyadenylation -0.032 0.085 -10000 0 -0.16 104 104
Aurora A/CPEB -0.032 0.085 -10000 0 -0.16 104 104
Aurora A/TACC1/TRAP/chTOG 0.044 0.041 0.22 1 -0.17 2 3
BRCA1 0.027 0.006 -10000 0 -10000 0 0
centrosome duplication 0.023 0.039 -10000 0 -0.18 6 6
regulation of centrosome cycle 0.031 0.046 0.19 1 -0.19 4 5
spindle assembly 0.043 0.04 0.21 1 -0.17 2 3
TDRD7 0.027 0.007 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.03 0.08 0.2 3 -0.2 9 12
CENPA 0.024 0.034 0.16 3 -0.21 3 6
Aurora A/PP2A 0.027 0.032 -10000 0 -0.18 1 1
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.011 0.027 0.21 2 -0.2 1 3
negative regulation of DNA binding -0.003 0.066 -10000 0 -0.19 38 38
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.039 0.011 -10000 0 -10000 0 0
RASA1 0.025 0.026 -10000 0 -0.32 2 2
Ajuba/Aurora A 0 0.022 -10000 0 -0.16 2 2
mitotic prometaphase 0 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.03 0.18 3 -0.22 2 5
TACC1 0.02 0.027 -10000 0 -0.32 2 2
TACC3 0.013 0.057 -10000 0 -0.21 23 23
Aurora A/Antizyme1 0.041 0.037 -10000 0 -0.16 2 2
Aurora A/RasGAP 0.025 0.036 -10000 0 -0.18 4 4
OAZ1 0.028 0.005 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.008 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.029 -10000 0 -0.18 4 4
Importin alpha/Importin beta/TPX2 -0.02 0.074 0.23 7 -0.14 89 96
PPP2R5D 0.028 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 -0.008 0.063 0.23 3 -0.21 4 7
PAK1 0.024 0.036 -10000 0 -0.32 4 4
CKAP5 0.028 0.004 -10000 0 -10000 0 0
IGF1 pathway

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTK2 0.023 0.011 -10000 0 -10000 0 0
CRKL 0.001 0.053 0.13 2 -0.2 20 22
GRB2/SOS1/SHC 0.051 0.019 -10000 0 -10000 0 0
HRAS 0.025 0.027 -10000 0 -0.21 5 5
IRS1/Crk 0.008 0.057 -10000 0 -0.18 25 25
IGF-1R heterotetramer/IGF1/PTP1B 0.038 0.061 0.18 1 -0.18 23 24
AKT1 -0.008 0.07 0.18 20 -0.28 7 27
BAD -0.011 0.068 0.17 20 -0.27 7 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.001 0.052 -10000 0 -0.19 22 22
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.063 0.16 1 -0.19 25 26
RAF1 0.008 0.075 0.28 2 -0.4 5 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.045 0.068 -10000 0 -0.18 25 25
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.02 0.065 0.17 1 -0.2 25 26
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
RPS6KB1 -0.009 0.071 0.18 21 -0.28 7 28
GNB2L1 0.026 0.021 -10000 0 -0.21 3 3
positive regulation of MAPKKK cascade 0.016 0.082 0.28 12 -0.36 3 15
PXN 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.016 0.055 -10000 0 -0.18 19 19
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.062 0.06 -10000 0 -0.15 21 21
IGF-1R heterotetramer 0.021 0.028 -10000 0 -0.11 6 6
IGF-1R heterotetramer/IGF1/IRS/Nck 0.036 0.064 0.18 1 -0.18 24 25
Crk/p130 Cas/Paxillin 0.036 0.063 -10000 0 -0.18 17 17
IGF1R 0.021 0.028 -10000 0 -0.11 6 6
IGF1 0.014 0.063 -10000 0 -0.25 18 18
IRS2/Crk 0.009 0.056 0.18 1 -0.18 21 22
PI3K 0.039 0.076 -10000 0 -0.19 26 26
apoptosis -0.008 0.054 0.22 4 -0.16 18 22
HRAS/GDP 0.019 0.018 -10000 0 -0.14 5 5
PRKCD 0 0.081 0.18 2 -0.3 21 23
RAF1/14-3-3 E 0.027 0.074 0.27 4 -0.34 5 9
BAD/14-3-3 0.008 0.057 0.16 18 -0.22 5 23
PRKCZ -0.009 0.072 0.18 21 -0.28 7 28
Crk/p130 Cas/Paxillin/FAK1 0.019 0.056 -10000 0 -0.27 4 4
PTPN1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0 0.085 -10000 0 -0.32 22 22
BCAR1 0.023 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.05 0.056 0.19 1 -0.16 19 20
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.006 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.061 0.15 2 -0.18 24 26
GRB10 0.026 0.008 -10000 0 -10000 0 0
PTPN11 -0.002 0.057 -10000 0 -0.19 25 25
IRS1 0.004 0.062 0.12 13 -0.2 25 38
IRS2 0 0.055 0.15 3 -0.19 23 26
IGF-1R heterotetramer/IGF1 0.014 0.076 -10000 0 -0.21 36 36
GRB2 0.027 0.006 -10000 0 -10000 0 0
PDPK1 0.004 0.067 0.17 12 -0.3 7 19
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKD1 -0.001 0.082 0.18 2 -0.3 22 24
SHC1 0.027 0.007 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.017 0.082 -10000 0 -0.18 41 41
TC10/GTP 0.019 0.065 -10000 0 -0.15 34 34
Insulin Receptor/Insulin/IRS1/Shp2 0.057 0.052 -10000 0 -0.18 13 13
HRAS 0.025 0.027 -10000 0 -0.21 5 5
APS homodimer 0.018 0.042 -10000 0 -0.22 11 11
GRB14 -0.014 0.091 -10000 0 -0.21 63 63
FOXO3 -0.13 0.26 -10000 0 -0.55 98 98
AKT1 -0.014 0.081 0.22 17 -0.26 7 24
INSR 0.03 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.059 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.008 -10000 0 -10000 0 0
SORBS1 -0.022 0.12 -10000 0 -0.32 52 52
CRK 0.026 0.008 -10000 0 -10000 0 0
PTPN1 0.004 0.023 0.16 5 -10000 0 5
CAV1 -0.012 0.071 0.25 2 -0.19 41 43
CBL/APS/CAP/Crk-II/C3G 0.041 0.08 -10000 0 -0.16 38 38
Insulin Receptor/Insulin/IRS1/NCK2 0.06 0.047 -10000 0 -0.17 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.04 0.054 -10000 0 -0.22 11 11
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.058 -10000 0 -0.31 5 5
RPS6KB1 -0.015 0.076 0.19 25 -0.26 6 31
PARD6A 0.021 0.031 -10000 0 -0.23 5 5
CBL 0.026 0.019 -10000 0 -0.32 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.012 0.074 -10000 0 -0.56 6 6
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.017 0.072 -10000 0 -0.25 7 7
HRAS/GTP 0.002 0.051 -10000 0 -0.26 5 5
Insulin Receptor 0.03 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.066 0.051 -10000 0 -0.17 12 12
PRKCI 0.022 0.055 -10000 0 -0.33 5 5
Insulin Receptor/Insulin/GRB14/PDK1 0.001 0.065 -10000 0 -0.25 9 9
SHC1 0.027 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.036 0.066 -10000 0 -0.42 6 6
PI3K 0.05 0.058 -10000 0 -0.22 11 11
NCK2 0.028 0.003 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.018 -10000 0 -0.14 5 5
AKT2 -0.013 0.082 0.24 14 -0.26 7 21
PRKCZ 0.024 0.051 -10000 0 -0.36 3 3
SH2B2 0.018 0.042 -10000 0 -0.22 11 11
SHC/SHIP 0.012 0.057 0.17 2 -0.18 23 25
F2RL2 -0.071 0.12 -10000 0 -0.22 149 149
TRIP10 0.028 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.048 0.021 -10000 0 -0.12 1 1
TC10/GTP/CIP4/Exocyst 0.037 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.072 0.031 -10000 0 -10000 0 0
RAPGEF1 0.027 0.007 -10000 0 -10000 0 0
RASA1 0.025 0.026 -10000 0 -0.32 2 2
NCK1 0.026 0.008 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.033 0.081 0.2 3 -0.17 43 46
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.06 0.03 -10000 0 -0.12 1 1
INPP5D -0.001 0.056 0.22 3 -0.19 23 26
SOS1 0.027 0.006 -10000 0 -10000 0 0
SGK1 -0.11 0.29 -10000 0 -0.78 58 58
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
IRS1 0.017 0.061 -10000 0 -0.32 12 12
p62DOK/RasGAP 0.037 0.067 -10000 0 -0.43 6 6
INS 0.013 0.04 -10000 0 -0.2 12 12
mol:PI-3-4-P2 0 0.056 0.22 3 -0.18 23 26
GRB2 0.027 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.022 0.077 0.2 15 -0.28 9 24
PTPRA 0.03 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
TC10/GTP/CIP4 0.037 0.008 -10000 0 -10000 0 0
PDPK1 0.027 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.019 0.041 -10000 0 -0.19 12 12
Insulin Receptor/Insulin/IRS1 0.043 0.044 -10000 0 -0.17 13 13
Insulin Receptor/Insulin/IRS3 0.03 0.034 -10000 0 -0.14 13 13
Par3/Par6 0.057 0.064 -10000 0 -0.15 18 18
S1P3 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
PDGFRB 0.027 0.013 -10000 0 -0.21 1 1
mol:S1P 0.001 0 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.017 0.095 0.15 1 -0.23 50 51
GNAO1 -0.02 0.12 -10000 0 -0.31 50 50
S1P/S1P3/G12/G13 0.042 0.041 -10000 0 -0.16 11 11
AKT1 0.013 0.07 -10000 0 -0.5 4 4
AKT3 -0.005 0.098 -10000 0 -0.44 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.027 0.013 -10000 0 -0.21 1 1
GNAI2 0.029 0.004 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.019 -10000 0 -0.31 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.016 0.064 -10000 0 -0.31 14 14
S1PR2 0.028 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.12 -10000 0 -0.27 51 51
MAPK3 -0.017 0.11 -10000 0 -0.34 28 28
MAPK1 -0.014 0.1 -10000 0 -0.34 25 25
JAK2 -0.015 0.11 0.19 1 -0.36 28 29
CXCR4 -0.014 0.1 -10000 0 -0.35 25 25
FLT1 0.025 0.038 -10000 0 -0.29 5 5
RhoA/GDP 0.021 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC -0.016 0.11 -10000 0 -0.34 27 27
S1P/S1P3/Gi -0.013 0.12 -10000 0 -0.27 51 51
RAC1 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.008 0.11 -10000 0 -0.31 32 32
VEGFA 0.011 0.078 -10000 0 -0.3 21 21
S1P/S1P2/Gi -0.008 0.1 -10000 0 -0.24 48 48
VEGFR1 homodimer/VEGFA homodimer 0.028 0.066 -10000 0 -0.21 25 25
RHOA 0.028 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.005 0.077 -10000 0 -0.22 33 33
GNAQ 0.027 0.005 -10000 0 -10000 0 0
GNAZ 0.004 0.089 -10000 0 -0.31 27 27
G12/G13 0.037 0.014 -10000 0 -10000 0 0
GNA14 0.027 0.005 -10000 0 -10000 0 0
GNA15 0.013 0.07 -10000 0 -0.32 16 16
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.063 -10000 0 -0.32 13 13
Rac1/GTP -0.008 0.11 -10000 0 -0.34 26 26
Cellular roles of Anthrax toxin

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
ANTXR1 0.019 0.056 -10000 0 -0.32 10 10
ANTXR2 0.02 0.053 -10000 0 -0.32 9 9
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.01 -10000 0 -0.048 16 16
monocyte activation -0.015 0.11 -10000 0 -0.34 38 38
MAP2K2 0.002 0.09 -10000 0 -0.57 9 9
MAP2K1 -0.005 0.009 -10000 0 -0.07 2 2
MAP2K7 -0.004 0.009 -10000 0 -0.07 2 2
MAP2K6 -0.008 0.022 0.14 1 -0.096 15 16
CYAA -0.011 0.034 -10000 0 -0.17 16 16
MAP2K4 -0.004 0.009 -10000 0 -0.07 2 2
IL1B -0.022 0.058 0.23 1 -0.14 55 56
Channel 0.026 0.045 -10000 0 -0.18 16 16
NLRP1 -0.007 0.025 -10000 0 -0.16 9 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.001 0.066 -10000 0 -0.41 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.01 0.048 16 -10000 0 16
MAPK3 -0.004 0.009 -10000 0 -0.07 2 2
MAPK1 -0.004 0.009 -10000 0 -0.07 2 2
PGR -0.021 0.05 -10000 0 -0.16 42 42
PA/Cellular Receptors 0.027 0.05 -10000 0 -0.2 16 16
apoptosis -0.003 0.01 -10000 0 -0.048 16 16
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.044 -10000 0 -0.17 16 16
macrophage activation -0.005 0.013 0.14 2 -10000 0 2
TNF 0.001 0.087 -10000 0 -0.28 32 32
VCAM1 -0.015 0.11 -10000 0 -0.34 38 38
platelet activation 0.001 0.066 -10000 0 -0.41 9 9
MAPKKK cascade 0.002 0.019 0.075 4 -0.084 8 12
IL18 -0.008 0.043 0.19 1 -0.19 14 15
negative regulation of macrophage activation -0.003 0.01 -10000 0 -0.048 16 16
LEF -0.003 0.01 -10000 0 -0.048 16 16
CASP1 -0.003 0.025 -10000 0 -0.14 10 10
mol:cAMP 0.001 0.067 -10000 0 -0.41 9 9
necrosis -0.003 0.01 -10000 0 -0.048 16 16
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.043 -10000 0 -0.17 16 16
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.027 0.013 -10000 0 -0.21 1 1
alphaV beta3 Integrin -0.013 0.1 -10000 0 -0.22 75 75
PTK2 -0.006 0.099 -10000 0 -0.39 17 17
positive regulation of JNK cascade 0.011 0.088 -10000 0 -0.31 15 15
CDC42/GDP 0.033 0.12 0.32 3 -0.41 16 19
Rac1/GDP 0.032 0.12 0.36 2 -0.39 16 18
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.02 0.11 -10000 0 -0.38 15 15
nectin-3/I-afadin 0.022 0.059 -10000 0 -0.17 31 31
RAPGEF1 0.006 0.12 0.29 5 -0.43 18 23
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.12 -10000 0 -0.45 22 22
PDGFB-D/PDGFRB 0.027 0.013 -10000 0 -0.21 1 1
TLN1 -0.004 0.031 0.11 1 -0.19 4 5
Rap1/GTP 0.007 0.087 -10000 0 -0.32 18 18
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.02 -10000 0 -0.16 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.022 0.059 -10000 0 -0.17 31 31
PVR 0.028 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.028 0.003 -10000 0 -10000 0 0
mol:GDP 0.021 0.14 0.35 3 -0.47 19 22
MLLT4 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
PI3K 0.058 0.065 -10000 0 -0.19 15 15
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.039 0.011 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.014 0.088 -10000 0 -0.31 17 17
PVRL1 0.027 0.006 -10000 0 -10000 0 0
PVRL3 0.004 0.078 -10000 0 -0.25 31 31
PVRL2 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
CDH1 0.024 0.01 -10000 0 -10000 0 0
CLDN1 -0.011 0.11 -10000 0 -0.31 41 41
JAM-A/CLDN1 0.031 0.084 0.2 1 -0.17 48 49
SRC -0.001 0.14 -10000 0 -0.48 24 24
ITGB3 -0.043 0.14 -10000 0 -0.32 76 76
nectin-1(dimer)/I-afadin/I-afadin 0.039 0.011 -10000 0 -10000 0 0
FARP2 0.017 0.14 0.33 1 -0.48 17 18
RAC1 0.026 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.056 -10000 0 -0.14 30 30
nectin-1/I-afadin 0.039 0.011 -10000 0 -10000 0 0
nectin-2/I-afadin 0.04 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.036 0.055 -10000 0 -0.14 26 26
CDC42/GTP/IQGAP1/filamentous actin 0.038 0.006 -10000 0 -10000 0 0
F11R 0.027 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.011 0.088 -10000 0 -0.31 15 15
alphaV/beta3 Integrin/Talin -0.003 0.086 0.22 7 -0.21 18 25
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.04 0.009 -10000 0 -10000 0 0
PIP5K1C -0.001 0.033 0.12 1 -0.14 16 17
VAV2 0.016 0.14 -10000 0 -0.49 16 16
RAP1/GDP 0.032 0.12 -10000 0 -0.38 16 16
ITGAV 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.056 -10000 0 -0.14 30 30
nectin-3(dimer)/I-afadin/I-afadin 0.022 0.059 -10000 0 -0.17 31 31
Rac1/GTP 0.02 0.11 -10000 0 -0.38 16 16
PTPRM 0.004 0.038 0.13 1 -0.16 16 17
E-cadherin/beta catenin/alpha catenin 0.065 0.036 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.003 -10000 0 -10000 0 0
IL1-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
UBC13/UEV1A 0.034 0.011 -10000 0 -10000 0 0
PRKCZ 0.028 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.004 0.057 -10000 0 -0.2 12 12
IRAK/TOLLIP 0.03 0.01 -10000 0 -10000 0 0
IKBKB 0.022 0.012 -10000 0 -10000 0 0
IKBKG 0.028 0.001 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.01 0.1 -10000 0 -0.22 70 70
IL1A 0.021 0.031 -10000 0 -0.26 4 4
IL1B -0.021 0.084 -10000 0 -0.21 57 57
IRAK/TRAF6/p62/Atypical PKCs 0.067 0.034 -10000 0 -10000 0 0
IL1R2 -0.033 0.13 -10000 0 -0.32 66 66
IL1R1 0.028 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.045 -10000 0 -0.2 3 3
TOLLIP 0.028 0.004 -10000 0 -10000 0 0
TICAM2 0.02 0.047 -10000 0 -0.32 7 7
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.013 0.086 0.27 5 -0.3 8 13
JUN -0.004 0.062 0.18 26 -0.26 1 27
MAP3K7 0.023 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.028 0.086 -10000 0 -0.18 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88 0.06 0.035 -10000 0 -0.17 5 5
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.07 0.038 -10000 0 -0.16 5 5
IL1 beta fragment/IL1R1/IL1RAP 0.01 0.076 -10000 0 -0.18 41 41
NFKB1 0.028 0.003 -10000 0 -10000 0 0
MAPK8 0.002 0.063 0.2 27 -10000 0 27
IRAK1 0.014 0.005 -10000 0 -10000 0 0
IL1RN/IL1R1 0.027 0.056 -10000 0 -0.19 22 22
IRAK4 0.028 0.004 -10000 0 -10000 0 0
PRKCI 0.026 0.008 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.032 0.038 -10000 0 -0.23 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.06 -10000 0 -0.22 11 11
CHUK 0.027 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.01 0.076 -10000 0 -0.18 41 41
IL1 beta/IL1R2 -0.031 0.11 -10000 0 -0.2 107 107
IRAK/TRAF6/TAK1/TAB1/TAB2 0.031 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.016 0.077 -10000 0 -0.28 6 6
IRAK3 0.013 0.068 -10000 0 -0.32 15 15
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.028 0.085 -10000 0 -0.16 39 39
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.025 0.026 -10000 0 -0.17 5 5
IL1 alpha/IL1R1/IL1RAP 0.046 0.034 -10000 0 -0.16 7 7
RELA 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.005 -10000 0 -10000 0 0
MYD88 0.028 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.054 0.032 0.18 20 -10000 0 20
IL1RAP 0.023 0.036 -10000 0 -0.32 4 4
UBE2N 0.027 0.006 -10000 0 -10000 0 0
IRAK/TRAF6 0.005 0.065 -10000 0 -0.26 4 4
CASP1 0.021 0.047 -10000 0 -0.32 7 7
IL1RN/IL1R2 -0.017 0.11 -10000 0 -0.22 82 82
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.023 0.079 -10000 0 -0.17 38 38
TMEM189-UBE2V1 0.021 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.029 0.044 -10000 0 -0.26 2 2
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
IL1RN 0.009 0.074 -10000 0 -0.28 22 22
TRAF6/TAK1/TAB1/TAB2 0.04 0.023 -10000 0 -10000 0 0
MAP2K6 0.013 0.057 0.2 26 -10000 0 26
HIF-2-alpha transcription factor network

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
MMP14 0.018 0.15 -10000 0 -0.9 8 8
oxygen homeostasis -0.002 0.013 -10000 0 -0.14 1 1
TCEB2 0.023 0.032 -10000 0 -0.21 7 7
TCEB1 0.023 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.025 0.084 0.29 1 -0.29 5 6
EPO -0.028 0.2 0.34 1 -0.48 42 43
FIH (dimer) 0.02 0.024 -10000 0 -0.16 1 1
APEX1 0.02 0.027 -10000 0 -10000 0 0
SERPINE1 -0.015 0.18 0.34 2 -0.5 25 27
FLT1 -0.007 0.2 -10000 0 -0.85 16 16
ADORA2A -0.022 0.17 0.36 3 -0.48 23 26
germ cell development -0.019 0.18 0.33 2 -0.48 32 34
SLC11A2 -0.013 0.17 -10000 0 -0.49 23 23
BHLHE40 -0.012 0.18 0.34 2 -0.52 21 23
HIF1AN 0.02 0.024 -10000 0 -0.16 1 1
HIF2A/ARNT/SIRT1 0.009 0.13 0.31 1 -0.31 18 19
ETS1 0.026 0.046 -10000 0 -0.23 8 8
CITED2 0.02 0.088 -10000 0 -0.56 6 6
KDR -0.03 0.28 -10000 0 -0.93 28 28
PGK1 -0.01 0.17 0.34 2 -0.49 22 24
SIRT1 0.027 0.006 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.031 0.21 0.39 1 -0.55 23 24
EPAS1 -0.001 0.073 -10000 0 -0.23 14 14
SP1 0.03 0.016 -10000 0 -10000 0 0
ABCG2 -0.025 0.2 0.34 2 -0.57 30 32
EFNA1 -0.014 0.17 -10000 0 -0.49 22 22
FXN -0.023 0.17 0.32 2 -0.48 23 25
POU5F1 -0.021 0.19 0.34 2 -0.49 32 34
neuron apoptosis -0.03 0.21 0.54 23 -0.38 1 24
EP300 0.025 0.031 -10000 0 -0.32 3 3
EGLN3 0.014 0.054 -10000 0 -0.32 8 8
EGLN2 0.021 0.024 -10000 0 -0.14 1 1
EGLN1 0.02 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.043 0.033 -10000 0 -0.28 1 1
VHL 0.026 0.019 -10000 0 -0.32 1 1
ARNT 0.019 0.027 -10000 0 -10000 0 0
SLC2A1 -0.022 0.17 0.36 3 -0.48 23 26
TWIST1 -0.033 0.18 0.34 4 -0.5 25 29
ELK1 0.032 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.023 0.13 0.32 1 -0.32 14 15
VEGFA -0.02 0.19 0.34 2 -0.5 27 29
CREBBP 0.027 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.022 0.011 -10000 0 -10000 0 0
epithelial cell differentiation 0.049 0.025 -10000 0 -10000 0 0
CYFIP2 0.028 0.005 -10000 0 -10000 0 0
ENAH 0.002 0.073 0.18 39 -10000 0 39
EGFR -0.007 0.1 -10000 0 -0.32 36 36
EPHA2 -0.004 0.099 -10000 0 -0.31 35 35
MYO6 0.014 0.057 0.2 20 -10000 0 20
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.015 -10000 0 -10000 0 0
AQP5 -0.13 0.19 -10000 0 -0.38 137 137
CTNND1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.042 0.19 21 -10000 0 21
regulation of calcium-dependent cell-cell adhesion 0.019 0.05 0.19 20 -10000 0 20
EGF 0 0.082 -10000 0 -0.23 40 40
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 0.012 0.062 0.25 3 -0.36 8 11
cortical microtubule organization 0.049 0.025 -10000 0 -10000 0 0
GO:0000145 0.004 0.045 0.18 21 -10000 0 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.054 0.027 -10000 0 -10000 0 0
MLLT4 0.027 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.021 0.032 -10000 0 -10000 0 0
ARF6 0.028 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.066 0.2 1 -0.16 28 29
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.034 0.18 6 -10000 0 6
PVRL2 0.028 0.003 -10000 0 -10000 0 0
ZYX 0.017 0.028 0.18 10 -10000 0 10
ARF6/GTP 0.051 0.066 -10000 0 -0.16 28 28
CDH1 0.024 0.01 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.013 0.07 -10000 0 -0.16 30 30
RhoA/GDP 0.051 0.025 -10000 0 -10000 0 0
actin cytoskeleton organization -0.013 0.053 0.17 17 -0.21 2 19
IGF-1R heterotetramer 0.026 0.022 -10000 0 -0.26 2 2
GIT1 0.028 0.003 -10000 0 -10000 0 0
IGF1R 0.026 0.022 -10000 0 -0.26 2 2
IGF1 -0.003 0.093 -10000 0 -0.28 37 37
DIAPH1 0.035 0.11 -10000 0 -0.58 3 3
Wnt receptor signaling pathway -0.049 0.025 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.032 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
VCL -0.013 0.054 0.17 17 -0.21 2 19
EFNA1 0.027 0.006 -10000 0 -10000 0 0
LPP -0.006 0.049 0.19 13 -10000 0 13
Ephrin A1/EPHA2 0.028 0.056 -10000 0 -0.15 21 21
SEC6/SEC8 0.012 0.008 -10000 0 -10000 0 0
MGAT3 0.019 0.05 0.19 20 -10000 0 20
HGF/MET 0.02 0.071 -10000 0 -0.27 10 10
HGF 0.004 0.08 -10000 0 -0.28 26 26
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.022 0.011 -10000 0 -10000 0 0
actin cable formation 0.029 0.1 0.28 35 -0.22 5 40
KIAA1543 0.002 0.043 0.18 17 -10000 0 17
KIFC3 0.018 0.034 0.18 15 -10000 0 15
NCK1 0.026 0.008 -10000 0 -10000 0 0
EXOC3 0.028 0.005 -10000 0 -10000 0 0
ACTN1 0.021 0.04 0.2 16 -10000 0 16
NCK1/GIT1 0.038 0.013 -10000 0 -10000 0 0
mol:GDP 0.049 0.025 -10000 0 -10000 0 0
EXOC4 0.026 0.008 -10000 0 -10000 0 0
STX4 0.022 0.04 0.19 18 -10000 0 18
PIP5K1C 0.024 0.043 0.19 21 -10000 0 21
LIMA1 0.028 0.003 -10000 0 -10000 0 0
ABI1 0.028 0.004 -10000 0 -10000 0 0
ROCK1 0.005 0.081 0.19 45 -10000 0 45
adherens junction assembly -0.002 0.097 0.24 14 -0.54 6 20
IGF-1R heterotetramer/IGF1 0.03 0.052 -10000 0 -0.15 16 16
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.009 -10000 0 -10000 0 0
MET -0.002 0.093 -10000 0 -0.32 30 30
PLEKHA7 0.022 0.04 0.19 17 -10000 0 17
mol:GTP 0.043 0.065 0.19 1 -0.16 28 29
establishment of epithelial cell apical/basal polarity 0.014 0.086 0.26 32 -10000 0 32
cortical actin cytoskeleton stabilization 0.022 0.011 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.013 0.053 0.17 17 -0.21 2 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.022 0.011 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.024 0.021 -10000 0 -10000 0 0
CDKN2C 0.032 0.029 0.29 1 -0.19 3 4
CDKN2A -0.02 0.098 -10000 0 -0.22 73 73
CCND2 -0.003 0.023 0.22 1 -0.089 10 11
RB1 0.001 0.023 0.13 3 -0.25 1 4
CDK4 0.001 0.022 0.15 3 -10000 0 3
CDK6 -0.003 0.031 0.26 1 -0.15 8 9
G1/S progression 0 0.028 0.26 2 -0.14 2 4
Syndecan-4-mediated signaling events

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
PTK2 0.026 0.068 -10000 0 -0.37 6 6
Syndecan-4/Syndesmos 0.011 0.13 0.44 1 -0.71 9 10
positive regulation of JNK cascade 0.016 0.12 -10000 0 -0.62 10 10
Syndecan-4/ADAM12 0.012 0.13 -10000 0 -0.67 10 10
CCL5 0.014 0.063 -10000 0 -0.27 17 17
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DNM2 0.028 0.004 -10000 0 -10000 0 0
ITGA5 0.017 0.059 -10000 0 -0.31 12 12
SDCBP 0.024 0.01 -10000 0 -10000 0 0
PLG 0.008 0.055 -10000 0 -0.21 20 20
ADAM12 0.014 0.059 -10000 0 -0.24 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.056 0.03 -10000 0 -0.12 6 6
Syndecan-4/Laminin alpha1 0.008 0.14 0.32 1 -0.73 9 10
Syndecan-4/CXCL12/CXCR4 0.017 0.13 -10000 0 -0.67 10 10
Syndecan-4/Laminin alpha3 0.006 0.14 -10000 0 -0.68 10 10
MDK 0.019 0.043 -10000 0 -0.21 13 13
Syndecan-4/FZD7 0.01 0.14 0.44 1 -0.69 10 11
Syndecan-4/Midkine 0.012 0.14 0.44 1 -0.72 9 10
FZD7 0.018 0.058 -10000 0 -0.32 11 11
Syndecan-4/FGFR1/FGF 0.012 0.13 -10000 0 -0.6 11 11
THBS1 0.012 0.068 -10000 0 -0.28 18 18
integrin-mediated signaling pathway 0.009 0.12 0.35 2 -0.62 10 12
positive regulation of MAPKKK cascade 0.016 0.12 -10000 0 -0.62 10 10
Syndecan-4/TACI 0.013 0.14 0.38 2 -0.71 9 11
CXCR4 0.022 0.033 -10000 0 -0.25 5 5
cell adhesion 0.011 0.053 0.2 6 -0.24 9 15
Syndecan-4/Dynamin 0.013 0.13 0.44 1 -0.71 9 10
Syndecan-4/TSP1 0.01 0.13 0.44 1 -0.64 10 11
Syndecan-4/GIPC 0.011 0.13 0.44 1 -0.71 9 10
Syndecan-4/RANTES 0.012 0.14 0.44 1 -0.7 10 11
ITGB1 0.028 0.004 -10000 0 -10000 0 0
LAMA1 0.002 0.081 -10000 0 -0.26 32 32
LAMA3 0 0.09 -10000 0 -0.31 29 29
RAC1 0.026 0.008 -10000 0 -10000 0 0
PRKCA 0.001 0.12 0.75 7 -0.29 12 19
Syndecan-4/alpha-Actinin 0.011 0.14 0.44 1 -0.72 9 10
TFPI 0.013 0.063 -10000 0 -0.24 20 20
F2 0.007 0.059 -10000 0 -0.21 24 24
alpha5/beta1 Integrin 0.032 0.045 -10000 0 -0.21 12 12
positive regulation of cell adhesion -0.011 0.14 0.26 2 -0.66 11 13
ACTN1 0.024 0.031 -10000 0 -0.32 3 3
TNC 0.007 0.079 -10000 0 -0.32 21 21
Syndecan-4/CXCL12 0.008 0.13 -10000 0 -0.71 9 9
FGF6 0.016 0.017 -10000 0 -0.21 2 2
RHOA 0.028 0.004 -10000 0 -10000 0 0
CXCL12 0.013 0.068 -10000 0 -0.32 15 15
TNFRSF13B 0.002 0.074 -10000 0 -0.22 34 34
FGF2 0.005 0.084 -10000 0 -0.32 24 24
FGFR1 0.02 0.021 -10000 0 -0.32 1 1
Syndecan-4/PI-4-5-P2 -0.007 0.13 0.31 3 -0.71 9 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.022 0.043 -10000 0 -0.29 6 6
cell migration -0.029 0.015 -10000 0 -10000 0 0
PRKCD 0.027 0.018 -10000 0 -0.17 1 1
vasculogenesis 0.011 0.12 0.35 2 -0.61 10 12
SDC4 -0.005 0.14 0.34 3 -0.76 9 12
Syndecan-4/Tenascin C 0.008 0.13 0.44 1 -0.65 10 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.045 0.024 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.007 0.12 -10000 0 -0.67 9 9
MMP9 -0.1 0.12 0.27 1 -0.21 209 210
Rac1/GTP 0.011 0.054 0.2 6 -0.25 9 15
cytoskeleton organization 0.012 0.13 0.44 1 -0.68 9 10
GIPC1 0.028 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.01 0.14 0.44 1 -0.72 9 10
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.069 0.15 -10000 0 -0.31 105 105
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.023 0.032 -10000 0 -0.21 7 7
TCEB1 0.023 0.011 -10000 0 -10000 0 0
HIF1A/p53 0.016 0.064 0.23 5 -0.24 17 22
HIF1A 0 0.058 -10000 0 -0.25 17 17
COPS5 0.023 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.064 0.04 -10000 0 -0.24 1 1
FIH (dimer) 0.027 0.007 -10000 0 -10000 0 0
CDKN2A -0.02 0.094 -10000 0 -0.21 73 73
ARNT/IPAS -0.028 0.11 -10000 0 -0.22 97 97
HIF1AN 0.027 0.007 -10000 0 -10000 0 0
GNB2L1 0.026 0.021 -10000 0 -0.21 3 3
HIF1A/ARNT 0.015 0.06 0.17 2 -0.24 16 18
CUL2 0.028 0.004 -10000 0 -10000 0 0
OS9 0.028 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.043 0.034 -10000 0 -0.15 6 6
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.016 0.061 0.17 1 -0.24 17 18
PHD1-3/OS9 0.062 0.037 -10000 0 -0.16 7 7
HIF1A/RACK1/Elongin B/Elongin C 0.031 0.066 -10000 0 -0.24 16 16
VHL 0.026 0.019 -10000 0 -0.32 1 1
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.012 0.061 0.22 2 -0.24 17 19
EGLN3 0.021 0.05 -10000 0 -0.32 8 8
EGLN2 0.028 0.003 -10000 0 -10000 0 0
EGLN1 0.027 0.007 -10000 0 -10000 0 0
TP53 0.024 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.022 0.093 -10000 0 -0.47 12 12
ARNT 0.027 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.028 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.023 0.079 0.26 4 -0.27 17 21
Caspase cascade in apoptosis

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
TOP1 0.01 0.076 0.22 3 -0.35 9 12
ACTA1 -0.032 0.093 0.21 8 -0.36 14 22
NUMA1 0.013 0.07 0.22 3 -0.34 8 11
SPTAN1 0.001 0.088 0.22 20 -0.35 11 31
LIMK1 0.005 0.092 0.21 27 -0.34 12 39
BIRC3 0.025 0.025 -10000 0 -0.24 3 3
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.026 0.018 -10000 0 -0.21 2 2
CASP10 -0.021 0.055 0.18 2 -0.24 16 18
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
PTK2 0.006 0.072 0.21 3 -0.35 7 10
DIABLO 0.027 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes 0 0.087 0.22 20 -0.34 11 31
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.006 -10000 0 -10000 0 0
GSN 0 0.089 0.22 19 -0.37 10 29
MADD 0.028 0.005 -10000 0 -10000 0 0
TFAP2A -0.004 0.16 -10000 0 -0.55 27 27
BID 0.001 0.032 0.14 1 -0.17 9 10
MAP3K1 -0.026 0.11 -10000 0 -0.36 36 36
TRADD 0.025 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.008 0.081 0.24 6 -0.35 12 18
CASP9 0.028 0.003 -10000 0 -10000 0 0
DNA repair -0.001 0.046 0.22 10 -0.13 1 11
neuron apoptosis 0.011 0.1 -10000 0 -0.58 10 10
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.006 0.078 0.23 7 -0.41 7 14
APAF1 0.027 0.006 -10000 0 -10000 0 0
CASP6 0.016 0.093 -10000 0 -0.82 3 3
TRAF2 0.027 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.008 0.078 0.24 7 -0.34 11 18
CASP7 -0.004 0.048 0.21 1 -0.21 11 12
KRT18 0.021 0.034 -10000 0 -0.48 1 1
apoptosis 0.002 0.074 0.28 4 -0.34 10 14
DFFA -0.009 0.077 0.2 5 -0.35 12 17
DFFB -0.007 0.079 0.23 7 -0.34 12 19
PARP1 0.001 0.046 0.13 1 -0.22 10 11
actin filament polymerization -0.005 0.097 0.33 12 -0.23 26 38
TNF 0.001 0.087 -10000 0 -0.28 32 32
CYCS 0.006 0.035 0.15 3 -0.17 4 7
SATB1 0.015 0.096 0.38 3 -0.77 3 6
SLK -0.007 0.077 0.25 6 -0.34 12 18
p15 BID/BAX 0.015 0.042 -10000 0 -0.24 4 4
CASP2 0.009 0.063 0.21 11 -0.28 4 15
JNK cascade 0.026 0.11 0.36 36 -10000 0 36
CASP3 -0.007 0.081 0.21 5 -0.37 12 17
LMNB2 0.02 0.086 0.26 8 -0.28 12 20
RIPK1 0.028 0.004 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.067 0.023 -10000 0 -0.17 1 1
negative regulation of DNA binding -0.003 0.16 -10000 0 -0.55 27 27
stress fiber formation -0.007 0.077 0.25 6 -0.33 12 18
GZMB -0.002 0.062 0.26 1 -0.19 30 31
CASP1 0.01 0.035 -10000 0 -0.24 7 7
LMNB1 0.022 0.088 0.26 8 -0.29 13 21
APP 0.011 0.1 -10000 0 -0.59 10 10
TNFRSF1A 0.026 0.008 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM 0.003 0.073 0.2 3 -0.34 11 14
LMNA 0.023 0.077 0.25 9 -0.27 7 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.012 0.048 -10000 0 -0.16 19 19
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.009 0.077 0.19 4 -0.35 12 16
APAF-1/Caspase 9 0.012 0.068 -10000 0 -0.61 4 4
nuclear fragmentation during apoptosis 0.013 0.069 0.22 3 -0.33 8 11
CFL2 0.005 0.098 0.23 27 -0.34 12 39
GAS2 -0.012 0.075 0.21 3 -0.34 12 15
positive regulation of apoptosis 0.026 0.082 0.23 17 -0.27 6 23
PRF1 0.021 0.043 -10000 0 -0.26 8 8
Regulation of nuclear SMAD2/3 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
EP300 0.023 0.033 -10000 0 -0.31 3 3
HSPA8 0.028 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.038 0.063 -10000 0 -0.2 13 13
AKT1 0.029 0.008 -10000 0 -10000 0 0
GSC -0.007 0.12 -10000 0 -1 3 3
NKX2-5 0.004 0.058 -10000 0 -0.2 26 26
muscle cell differentiation -0.021 0.08 0.27 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.077 0.057 -10000 0 -0.29 2 2
SMAD4 0.022 0.036 -10000 0 -0.16 2 2
CBFB 0.025 0.009 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.006 0.095 -10000 0 -0.18 74 74
SMAD3/SMAD4/VDR 0.069 0.059 -10000 0 -0.18 2 2
MYC 0.007 0.056 -10000 0 -0.21 23 23
CDKN2B -0.022 0.15 -10000 0 -1 4 4
AP1 0.016 0.083 -10000 0 -0.31 8 8
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.016 0.073 -10000 0 -0.28 8 8
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.008 0.053 -10000 0 -0.26 3 3
SP3 0.028 0.006 -10000 0 -10000 0 0
CREB1 0.028 0.003 -10000 0 -10000 0 0
FOXH1 -0.004 0.077 -10000 0 -0.22 41 41
SMAD3/SMAD4/GR 0.047 0.062 -10000 0 -0.21 9 9
GATA3 -0.071 0.15 -10000 0 -0.31 102 102
SKI/SIN3/HDAC complex/NCoR1 0.024 0.038 -10000 0 -0.17 1 1
MEF2C/TIF2 -0.011 0.095 0.26 3 -0.26 22 25
endothelial cell migration 0.031 0.23 1 17 -10000 0 17
MAX 0.029 0.011 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
RBBP4 0.026 0.025 -10000 0 -0.32 2 2
RUNX2 0.026 0.028 -10000 0 -0.28 3 3
RUNX3 0.022 0.041 -10000 0 -0.23 9 9
RUNX1 0.026 0.022 -10000 0 -0.26 2 2
CTBP1 0.028 0.004 -10000 0 -10000 0 0
NR3C1 0.02 0.054 -10000 0 -0.32 9 9
VDR 0.023 0.041 -10000 0 -0.3 6 6
CDKN1A 0.017 0.12 -10000 0 -1.2 3 3
KAT2B 0.026 0.01 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.032 0.067 -10000 0 -0.25 4 4
DCP1A 0.028 0.004 -10000 0 -10000 0 0
SKI 0.028 0.004 -10000 0 -10000 0 0
SERPINE1 -0.032 0.23 -10000 0 -1 17 17
SMAD3/SMAD4/ATF2 0.033 0.075 -10000 0 -0.19 26 26
SMAD3/SMAD4/ATF3 0.023 0.095 -10000 0 -0.21 38 38
SAP30 0.028 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.048 0.035 0.19 1 -0.18 3 4
JUN 0.001 0.076 -10000 0 -0.32 7 7
SMAD3/SMAD4/IRF7 0.05 0.054 -10000 0 -0.18 1 1
TFE3 0.028 0.017 -10000 0 -10000 0 0
COL1A2 0.022 0.049 -10000 0 -0.85 1 1
mesenchymal cell differentiation -0.05 0.047 0.24 1 -10000 0 1
DLX1 -0.19 0.073 -10000 0 -0.21 332 332
TCF3 0.028 0.005 -10000 0 -10000 0 0
FOS -0.017 0.12 -10000 0 -0.32 51 51
SMAD3/SMAD4/Max 0.052 0.048 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.05 0.03 -10000 0 -0.18 3 3
ZBTB17 0.027 0.005 -10000 0 -10000 0 0
LAMC1 0.017 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.052 0.043 -10000 0 -10000 0 0
IRF7 0.014 0.056 -10000 0 -0.2 23 23
ESR1 0.014 0.064 -10000 0 -0.31 14 14
HNF4A 0.007 0.054 -10000 0 -0.21 22 22
MEF2C 0.014 0.096 0.24 25 -0.34 5 30
SMAD2-3/SMAD4 0.054 0.048 -10000 0 -0.25 1 1
Cbp/p300/Src-1 0.049 0.031 -10000 0 -0.18 3 3
IGHV3OR16-13 0.013 0.009 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.012 -10000 0 -10000 0 0
SKIL 0.019 0.047 -10000 0 -0.29 8 8
HDAC1 0.028 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.01 -10000 0 -10000 0 0
SNIP1 0.028 0.002 -10000 0 -10000 0 0
GCN5L2 0 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.057 0.046 -10000 0 -0.18 1 1
MSG1/HSC70 -0.012 0.1 -10000 0 -0.21 80 80
SMAD2 0.026 0.019 -10000 0 -0.2 1 1
SMAD3 0.024 0.034 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.052 0.17 4 -0.25 1 5
SMAD2/SMAD2/SMAD4 -0.001 0.054 0.18 3 -0.17 11 14
NCOR1 0.027 0.007 -10000 0 -10000 0 0
NCOA2 -0.02 0.11 -10000 0 -0.32 47 47
NCOA1 0.028 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.027 0.037 -10000 0 -0.16 13 13
SMAD2-3/SMAD4/SP1/MIZ-1 0.088 0.06 -10000 0 -0.27 2 2
IFNB1 0.005 0.042 0.22 2 -10000 0 2
SMAD3/SMAD4/MEF2C 0.041 0.099 0.33 6 -0.36 4 10
CITED1 -0.045 0.14 -10000 0 -0.3 82 82
SMAD2-3/SMAD4/ARC105 0.068 0.048 -10000 0 -0.22 1 1
RBL1 0.004 0.086 -10000 0 -0.32 25 25
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.014 0.054 -10000 0 -0.34 3 3
RUNX1-3/PEBPB2 0.044 0.036 -10000 0 -0.14 8 8
SMAD7 0.024 0.089 -10000 0 -0.43 5 5
MYC/MIZ-1 0.02 0.044 -10000 0 -0.14 23 23
SMAD3/SMAD4 -0.002 0.095 0.29 2 -0.4 13 15
IL10 -0.038 0.11 0.2 1 -0.35 16 17
PIASy/HDAC complex 0.028 0.009 -10000 0 -10000 0 0
PIAS3 0.026 0.011 -10000 0 -10000 0 0
CDK2 0.026 0.012 -10000 0 -10000 0 0
IL5 -0.035 0.092 0.19 1 -0.3 8 9
CDK4 0.026 0.012 -10000 0 -10000 0 0
PIAS4 0.028 0.009 -10000 0 -10000 0 0
ATF3 -0.024 0.12 -10000 0 -0.28 61 61
SMAD3/SMAD4/SP1 0.061 0.052 -10000 0 -0.29 2 2
FOXG1 0.009 0.049 -10000 0 -0.2 18 18
FOXO3 0.014 0.007 -10000 0 -10000 0 0
FOXO1 0.013 0.009 -10000 0 -10000 0 0
FOXO4 0.016 0.007 -10000 0 -10000 0 0
heart looping 0.014 0.095 0.24 25 -0.33 5 30
CEBPB 0.028 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.044 0.12 -10000 0 -0.2 26 26
MYOD1 0.01 0.049 -10000 0 -0.24 13 13
SMAD3/SMAD4/HNF4 0.044 0.054 -10000 0 -0.18 2 2
SMAD3/SMAD4/GATA3 -0.015 0.12 -10000 0 -0.23 42 42
SnoN/SIN3/HDAC complex/NCoR1 0.019 0.047 -10000 0 -0.29 8 8
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.068 0.055 -10000 0 -0.17 2 2
SMAD3/SMAD4/SP1-3 0.075 0.055 -10000 0 -0.3 1 1
MED15 0.028 0.005 -10000 0 -10000 0 0
SP1 0.032 0.016 -10000 0 -0.18 1 1
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.046 0.081 0.25 2 -0.26 7 9
ITGB5 0.024 0.046 0.22 8 -0.28 1 9
TGIF/SIN3/HDAC complex/CtBP 0.028 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4/AR 0.025 0.086 -10000 0 -0.19 38 38
AR -0.01 0.11 -10000 0 -0.32 41 41
negative regulation of cell growth 0.003 0.071 -10000 0 -0.28 6 6
SMAD3/SMAD4/MYOD 0.042 0.053 -10000 0 -0.18 4 4
E2F5 0.022 0.016 -10000 0 -0.21 1 1
E2F4 0.025 0.009 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.067 0.073 0.23 1 -0.21 7 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.019 0.041 -10000 0 -0.33 3 3
TFDP1 0.027 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.036 0.092 -10000 0 -0.31 8 8
SMAD3/SMAD4/RUNX2 0.051 0.047 -10000 0 -0.24 1 1
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.007 -10000 0 -10000 0 0
ATF2 0.002 0.089 -10000 0 -0.32 27 27
Coregulation of Androgen receptor activity

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
NRIP1 0.027 0.02 -10000 0 -0.2 2 2
SVIL 0.015 0.066 -10000 0 -0.31 14 14
ZNF318 0.027 0.015 0.19 3 -10000 0 3
JMJD2C 0.004 0.007 -10000 0 -0.13 1 1
T-DHT/AR/Ubc9 0.016 0.072 -10000 0 -0.17 41 41
CARM1 0.028 0.006 -10000 0 -10000 0 0
PRDX1 0.028 0.003 -10000 0 -10000 0 0
PELP1 0.026 0.008 -10000 0 -10000 0 0
CTNNB1 0.027 0.009 -10000 0 -10000 0 0
AKT1 0.028 0.007 -10000 0 -10000 0 0
PTK2B 0.021 0.014 -10000 0 -10000 0 0
MED1 0.028 0.006 -10000 0 -10000 0 0
MAK -0.035 0.11 0.22 3 -0.21 99 102
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.015 0.062 -10000 0 -0.31 12 12
GSN 0.025 0.027 -10000 0 -0.31 2 2
NCOA2 -0.021 0.11 -10000 0 -0.32 47 47
NCOA6 0.028 0.01 -10000 0 -10000 0 0
DNA-PK 0.047 0.026 0.23 2 -10000 0 2
NCOA4 0.027 0.005 -10000 0 -10000 0 0
PIAS3 0.027 0.01 -10000 0 -10000 0 0
cell proliferation 0.019 0.044 0.22 1 -0.37 3 4
XRCC5 0.028 0.005 -10000 0 -10000 0 0
UBE3A 0.028 0.014 -10000 0 -0.13 1 1
T-DHT/AR/SNURF 0.01 0.086 -10000 0 -0.2 49 49
FHL2 -0.006 0.15 -10000 0 -0.75 14 14
RANBP9 0.028 0.011 -10000 0 -0.11 1 1
JMJD1A 0.008 0.01 -10000 0 -0.094 2 2
CDK6 0.017 0.054 -10000 0 -0.3 10 10
TGFB1I1 0.002 0.091 -10000 0 -0.32 28 28
T-DHT/AR/CyclinD1 0.017 0.072 -10000 0 -0.17 41 41
XRCC6 0.028 0.005 -10000 0 -10000 0 0
T-DHT/AR 0.025 0.083 -10000 0 -0.17 52 52
CTDSP1 0.028 0.006 -10000 0 -10000 0 0
CTDSP2 0.027 0.011 0.15 1 -10000 0 1
BRCA1 0.027 0.01 -10000 0 -10000 0 0
TCF4 0.023 0.027 -10000 0 -0.32 2 2
CDKN2A -0.018 0.093 0.18 1 -0.21 71 72
SRF 0.026 0.035 -10000 0 -0.15 12 12
NKX3-1 -0.008 0.085 -10000 0 -0.35 19 19
KLK3 0.002 0.12 -10000 0 -1.2 3 3
TMF1 0.027 0.007 -10000 0 -10000 0 0
HNRNPA1 0.028 0.008 -10000 0 -10000 0 0
AOF2 0 0.007 -10000 0 -0.08 3 3
APPL1 0.014 0.011 0.13 3 -10000 0 3
T-DHT/AR/Caspase 8 0.018 0.072 -10000 0 -0.17 41 41
AR -0.009 0.11 -10000 0 -0.31 41 41
UBA3 0.027 0.008 -10000 0 -10000 0 0
PATZ1 0.028 0.006 -10000 0 -10000 0 0
PAWR 0.027 0.006 -10000 0 -10000 0 0
PRKDC 0.023 0.014 -10000 0 -0.15 1 1
PA2G4 0.027 0.007 -10000 0 -10000 0 0
UBE2I 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.018 0.066 -10000 0 -0.16 41 41
RPS6KA3 0.027 0.021 -10000 0 -0.31 1 1
T-DHT/AR/ARA70 0.017 0.072 -10000 0 -0.17 41 41
LATS2 0.027 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.018 0.066 0.15 2 -0.16 41 43
Cyclin D3/CDK11 p58 0.021 0.003 -10000 0 -10000 0 0
VAV3 -0.009 0.11 -10000 0 -0.31 40 40
KLK2 0.009 0.036 -10000 0 -10000 0 0
CASP8 0.028 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.006 0.11 -10000 0 -0.26 48 48
TMPRSS2 -0.007 0.095 -10000 0 -0.4 17 17
CCND1 0.026 0.015 -10000 0 -0.21 1 1
PIAS1 0.027 0.022 -10000 0 -0.22 2 2
mol:T-DHT 0.001 0.019 -10000 0 -0.069 19 19
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.028 0.018 -10000 0 -0.17 3 3
T-DHT/AR/CDK6 0.013 0.078 -10000 0 -0.18 45 45
CMTM2 0.023 0.019 -10000 0 -0.21 2 2
SNURF 0.013 0.068 -10000 0 -0.32 15 15
ZMIZ1 0.025 0.032 -10000 0 -0.2 4 4
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.027 0.009 0.14 1 -10000 0 1
FKBP4 0.026 0.013 -10000 0 -0.11 1 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.032 0.063 -10000 0 -0.38 2 2
epithelial cell differentiation 0.041 0.067 -10000 0 -0.36 1 1
ITCH 0.032 0.016 -10000 0 -10000 0 0
WWP1 0.028 0.074 -10000 0 -10000 0 0
FYN 0.024 0.01 -10000 0 -10000 0 0
EGFR -0.007 0.1 -10000 0 -0.32 36 36
PRL 0.017 0.02 -10000 0 -0.21 3 3
neuron projection morphogenesis 0.011 0.089 0.27 16 -0.35 2 18
PTPRZ1 -0.083 0.16 -10000 0 -0.31 119 119
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.017 0.08 -10000 0 -0.32 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.006 0.07 -10000 0 -0.37 2 2
ADAM17 0.029 0.034 -10000 0 -0.32 3 3
ErbB4/ErbB4 0.007 0.048 -10000 0 -0.42 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.023 0.067 -10000 0 -0.35 4 4
NCOR1 0.027 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.004 0.069 -10000 0 -0.35 2 2
GRIN2B -0.003 0.065 0.24 4 -0.41 1 5
ErbB4/ErbB2/betacellulin 0.022 0.081 -10000 0 -0.37 7 7
STAT1 0.024 0.03 -10000 0 -0.21 6 6
HBEGF 0.022 0.039 -10000 0 -0.23 8 8
PRLR 0.002 0.082 -10000 0 -0.26 33 33
E4ICDs/ETO2 0.026 0.056 -10000 0 -0.45 1 1
axon guidance 0.029 0.064 -10000 0 -0.37 1 1
NEDD4 0.026 0.04 -10000 0 -0.3 5 5
Prolactin receptor/Prolactin receptor/Prolactin 0.013 0.063 -10000 0 -0.18 36 36
CBFA2T3 0.021 0.032 -10000 0 -0.32 3 3
ErbB4/ErbB2/HBEGF 0.031 0.059 -10000 0 -0.37 2 2
MAPK3 0.01 0.084 0.26 12 -0.36 2 14
STAT1 (dimer) 0.034 0.062 -10000 0 -0.48 1 1
MAPK1 0.009 0.081 0.25 10 -0.36 2 12
JAK2 0.026 0.019 -10000 0 -0.32 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.008 0.07 -10000 0 -0.42 2 2
NRG1 -0.02 0.078 -10000 0 -0.22 50 50
NRG3 -0.011 0.096 -10000 0 -0.28 41 41
NRG2 -0.079 0.16 -10000 0 -0.32 114 114
NRG4 -0.081 0.16 -10000 0 -0.31 119 119
heart development 0.029 0.064 -10000 0 -0.37 1 1
neural crest cell migration -0.007 0.07 -10000 0 -0.42 2 2
ERBB2 0.012 0.033 -10000 0 -0.2 8 8
WWOX/E4ICDs 0.027 0.054 -10000 0 -0.48 1 1
SHC1 0.027 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.025 0.12 -10000 0 -0.36 17 17
apoptosis 0.005 0.11 0.34 25 -10000 0 25
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.004 0.091 -10000 0 -0.3 17 17
ErbB4/ErbB2/epiregulin 0.023 0.071 -10000 0 -0.37 2 2
ErbB4/ErbB4/betacellulin/betacellulin 0.025 0.082 -10000 0 -0.32 11 11
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.052 0.083 -10000 0 -0.32 3 3
MDM2 0.019 0.067 0.33 7 -0.48 1 8
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.001 0.068 -10000 0 -0.35 1 1
STAT5A 0.033 0.069 0.31 1 -0.35 1 2
ErbB4/EGFR/neuregulin 1 beta -0.014 0.095 -10000 0 -0.34 14 14
DLG4 0.019 0.044 -10000 0 -0.32 6 6
GRB2/SHC 0.039 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.027 0.055 -10000 0 -0.45 1 1
STAT5A (dimer) 0.061 0.081 -10000 0 -0.38 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.059 0.078 0.32 2 -0.35 1 3
LRIG1 0.028 0.005 -10000 0 -10000 0 0
EREG -0.007 0.095 -10000 0 -0.27 41 41
BTC 0.004 0.088 -10000 0 -0.32 26 26
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.018 0.057 -10000 0 -0.37 1 1
ERBB4 0.007 0.048 -10000 0 -0.42 2 2
STAT5B 0.027 0.006 -10000 0 -10000 0 0
YAP1 0.018 0.065 -10000 0 -0.45 5 5
GRB2 0.027 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.013 0.097 -10000 0 -0.36 6 6
glial cell differentiation -0.026 0.055 0.44 1 -10000 0 1
WWOX 0.023 0.011 -10000 0 -10000 0 0
cell proliferation -0.024 0.12 0.27 1 -0.48 10 11
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.064 0.2 0.45 1 -0.62 17 18
PCK1 -0.047 0.16 -10000 0 -0.82 4 4
HNF4A -0.093 0.24 -10000 0 -0.79 24 24
KCNJ11 -0.055 0.21 0.93 1 -0.67 10 11
AKT1 0.011 0.12 -10000 0 -0.37 3 3
response to starvation -0.005 0.021 -10000 0 -0.13 3 3
DLK1 -0.092 0.27 0.83 1 -0.79 30 31
NKX2-1 -0.032 0.12 -10000 0 -10000 0 0
ACADM -0.07 0.2 0.45 1 -0.65 17 18
TAT -0.064 0.19 -10000 0 -0.68 16 16
CEBPB 0.024 0.017 -10000 0 -10000 0 0
CEBPA 0.024 0.016 -10000 0 -10000 0 0
TTR -0.065 0.24 -10000 0 -1.2 13 13
PKLR -0.066 0.21 0.44 1 -0.68 14 15
APOA1 -0.12 0.34 -10000 0 -1.1 27 27
CPT1C -0.072 0.21 0.45 1 -0.68 17 18
ALAS1 -0.017 0.12 -10000 0 -0.47 1 1
TFRC -0.053 0.2 -10000 0 -0.74 12 12
FOXF1 0.013 0.069 -10000 0 -0.31 15 15
NF1 0.032 0.003 -10000 0 -10000 0 0
HNF1A (dimer) 0.001 0.073 -10000 0 -0.2 39 39
CPT1A -0.063 0.2 -10000 0 -0.64 15 15
HMGCS1 -0.062 0.2 0.45 1 -0.63 13 14
NR3C1 0.019 0.055 -10000 0 -0.31 9 9
CPT1B -0.072 0.2 0.45 1 -0.65 16 17
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.026 0.018 -10000 0 -0.15 2 2
GCK -0.075 0.24 -10000 0 -0.76 24 24
CREB1 0.025 0.022 -10000 0 -0.2 1 1
IGFBP1 -0.029 0.12 -10000 0 -0.55 4 4
PDX1 -0.023 0.16 0.36 1 -1.1 3 4
UCP2 -0.065 0.2 -10000 0 -0.67 16 16
ALDOB -0.053 0.21 0.5 1 -0.65 12 13
AFP -0.012 0.07 -10000 0 -0.33 3 3
BDH1 -0.06 0.2 0.45 1 -0.62 16 17
HADH -0.059 0.2 0.5 1 -0.67 10 11
F2 -0.094 0.25 -10000 0 -0.87 10 10
HNF1A 0.001 0.073 -10000 0 -0.2 39 39
G6PC -0.004 0.069 -10000 0 -10000 0 0
SLC2A2 -0.027 0.14 -10000 0 -0.64 3 3
INS -0.023 0.04 -10000 0 -0.22 13 13
FOXA1 0.015 0.05 -10000 0 -0.23 4 4
FOXA3 -0.019 0.11 -10000 0 -0.31 37 37
FOXA2 -0.062 0.24 -10000 0 -0.73 13 13
ABCC8 -0.097 0.29 0.83 1 -0.79 38 39
ALB -0.021 0.094 -10000 0 -0.82 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.058 -10000 0 -0.24 17 17
CRKL 0.028 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DOCK1 0.024 0.031 -10000 0 -0.32 3 3
ITGA4 0.01 0.07 -10000 0 -0.27 21 21
alpha4/beta7 Integrin/MAdCAM1 0.055 0.075 -10000 0 -0.19 25 25
EPO -0.014 0.1 -10000 0 -0.27 49 49
alpha4/beta7 Integrin 0.021 0.068 -10000 0 -0.21 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.027 0.053 -10000 0 -0.18 21 21
EPO/EPOR (dimer) 0.005 0.081 0.24 1 -0.18 56 57
lamellipodium assembly 0.017 0.054 -10000 0 -0.52 2 2
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
PI3K 0.032 0.038 -10000 0 -0.23 6 6
ARF6 0.028 0.004 -10000 0 -10000 0 0
JAK2 -0.005 0.072 -10000 0 -0.19 41 41
PXN 0.027 0.006 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
MADCAM1 -0.016 0.091 -10000 0 -0.21 67 67
cell adhesion 0.052 0.074 -10000 0 -0.19 25 25
CRKL/CBL 0.039 0.017 -10000 0 -0.22 1 1
ITGB1 0.028 0.004 -10000 0 -10000 0 0
SRC 0.005 0.049 0.18 5 -0.18 17 22
ITGB7 0.016 0.059 -10000 0 -0.29 13 13
RAC1 0.026 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.037 0.06 -10000 0 -0.2 17 17
p130Cas/Crk/Dock1 0.019 0.051 0.19 2 -0.28 3 5
VCAM1 0.021 0.043 -10000 0 -0.24 9 9
RHOA 0.028 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.059 0.047 -10000 0 -0.16 12 12
BCAR1 -0.015 0.039 0.18 3 -0.22 3 6
EPOR 0.023 0.034 -10000 0 -0.21 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.019 -10000 0 -0.32 1 1
GIT1 0.028 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.055 -10000 0 -0.54 2 2
LPA4-mediated signaling events

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
ADCY4 -0.007 0.016 -10000 0 -0.18 3 3
ADCY5 -0.027 0.058 -10000 0 -0.18 47 47
ADCY6 -0.005 0.001 -10000 0 -10000 0 0
ADCY7 -0.005 0.006 -10000 0 -0.11 1 1
ADCY1 -0.014 0.041 0.22 4 -0.11 37 41
ADCY2 -0.011 0.031 -10000 0 -0.16 14 14
ADCY3 -0.005 0.001 -10000 0 -10000 0 0
ADCY8 -0.008 0.013 -10000 0 -0.11 5 5
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.009 -10000 0 -0.18 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.017 0.073 0.21 27 -0.14 1 28
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.028 0.004 -10000 0 -10000 0 0
SPHK1 0.017 0.049 -10000 0 -0.21 16 16
GNAI2 0.028 0.004 -10000 0 -10000 0 0
mol:S1P 0.014 0.017 0.18 1 -0.2 1 2
GNAO1 -0.021 0.12 -10000 0 -0.32 50 50
mol:Sphinganine-1-P 0.007 0.035 0.26 1 -0.14 16 17
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.054 0.033 -10000 0 -10000 0 0
GNAI3 0.028 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.014 -10000 0 -10000 0 0
S1PR3 0.015 0.064 -10000 0 -0.31 14 14
S1PR2 0.028 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.007 0.02 -10000 0 -0.17 1 1
S1PR5 -0.025 0.12 -10000 0 -0.32 57 57
S1PR4 0.017 0.049 -10000 0 -0.21 16 16
GNAI1 0.025 0.019 -10000 0 -0.32 1 1
S1P/S1P5/G12 0.015 0.073 0.17 2 -0.15 51 53
S1P/S1P3/Gq 0.012 0.078 -10000 0 -0.4 7 7
S1P/S1P4/Gi -0.009 0.1 0.2 1 -0.3 28 29
GNAQ 0.027 0.005 -10000 0 -10000 0 0
GNAZ 0.003 0.089 -10000 0 -0.32 27 27
GNA14 0.027 0.005 -10000 0 -10000 0 0
GNA15 0.013 0.07 -10000 0 -0.32 16 16
GNA12 0.026 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.063 -10000 0 -0.32 13 13
ABCC1 0.027 0.005 -10000 0 -10000 0 0
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.028 0.003 -10000 0 -10000 0 0
mol:PIP3 0 0.048 -10000 0 -0.31 7 7
FRAP1 0.025 0.055 0.27 1 -0.34 3 4
AKT1 0.004 0.056 0.16 19 -0.27 7 26
INSR 0.028 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.028 -10000 0 -0.12 13 13
mol:GTP 0.049 0.071 0.19 25 -0.24 6 31
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.026 -10000 0 -0.16 3 3
TSC2 0.027 0.005 -10000 0 -10000 0 0
RHEB/GDP 0.014 0.036 -10000 0 -0.22 6 6
TSC1 0.027 0.006 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.056 -10000 0 -0.27 13 13
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.026 0.038 -10000 0 -0.18 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 0.034 0.07 0.24 9 -0.26 3 12
MAP3K5 0.002 0.03 0.18 1 -0.18 9 10
PIK3R1 0.024 0.032 -10000 0 -0.32 3 3
apoptosis 0.002 0.03 0.18 1 -0.18 9 10
mol:LY294002 0 0 -10000 0 -0.001 12 12
EIF4B 0.035 0.073 0.24 17 -0.23 3 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.05 0.061 0.23 9 -0.22 3 12
eIF4E/eIF4G1/eIF4A1 0.014 0.028 -10000 0 -0.24 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.029 0.066 -10000 0 -0.28 13 13
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.06 0.13 78 -0.14 3 81
FKBP1A 0.028 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.045 0.057 0.17 4 -0.28 3 7
mol:Amino Acids 0 0 -10000 0 -0.001 12 12
FKBP12/Rapamycin 0.022 0.004 -10000 0 -10000 0 0
PDPK1 -0.011 0.044 0.16 1 -0.29 7 8
EIF4E 0.028 0.003 -10000 0 -10000 0 0
ASK1/PP5C 0.031 0.11 -10000 0 -0.52 11 11
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.037 -10000 0 -0.22 5 5
TSC1/TSC2 0.054 0.076 0.21 25 -0.26 6 31
tumor necrosis factor receptor activity 0 0 0.001 12 -10000 0 12
RPS6 0.027 0.013 -10000 0 -0.21 1 1
PPP5C 0.028 0.003 -10000 0 -10000 0 0
EIF4G1 0.027 0.007 -10000 0 -10000 0 0
IRS1 0 0.056 -10000 0 -0.29 13 13
INS 0.01 0.043 -10000 0 -0.21 13 13
PTEN 0.022 0.012 -10000 0 -10000 0 0
PDK2 -0.01 0.046 0.18 2 -0.29 7 9
EIF4EBP1 -0.15 0.41 -10000 0 -1.1 63 63
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
PPP2R5D 0.025 0.056 0.26 4 -0.31 3 7
peptide biosynthetic process 0.01 0.03 0.18 5 -0.16 1 6
RHEB 0.026 0.008 -10000 0 -10000 0 0
EIF4A1 0.024 0.01 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.003 74 -0.002 1 75
EEF2 0.01 0.03 0.18 5 -0.16 1 6
eIF4E/4E-BP1 -0.13 0.38 -10000 0 -0.98 63 63
Ceramide signaling pathway

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
SPHK2 0.013 0.004 -10000 0 -10000 0 0
MAP4K4 0.004 0.053 -10000 0 -0.31 3 3
BAG4 0.005 0.073 -10000 0 -0.32 18 18
PKC zeta/ceramide 0.002 0.067 -10000 0 -0.2 30 30
NFKBIA 0.028 0.004 -10000 0 -10000 0 0
BIRC3 0.025 0.025 -10000 0 -0.24 3 3
BAX 0.001 0.052 -10000 0 -0.33 7 7
RIPK1 0.028 0.004 -10000 0 -10000 0 0
AKT1 0.004 0.088 0.75 5 -10000 0 5
BAD -0.013 0.063 0.18 3 -0.2 25 28
SMPD1 0.014 0.054 0.19 9 -0.15 3 12
RB1 -0.016 0.06 -10000 0 -0.19 28 28
FADD/Caspase 8 0.011 0.054 0.2 1 -0.29 4 5
MAP2K4 -0.016 0.057 -10000 0 -0.2 21 21
NSMAF 0.024 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.019 0.065 0.17 2 -0.21 24 26
EGF 0 0.082 -10000 0 -0.23 40 40
mol:ceramide -0.015 0.066 -10000 0 -0.21 30 30
MADD 0.028 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.007 -10000 0 -10000 0 0
ASAH1 0.021 0.013 -10000 0 -10000 0 0
negative regulation of cell cycle -0.016 0.059 -10000 0 -0.19 28 28
cell proliferation -0.002 0.079 0.18 1 -0.27 12 13
BID 0.008 0.11 -10000 0 -0.64 8 8
MAP3K1 -0.017 0.061 -10000 0 -0.19 31 31
EIF2A -0.001 0.071 0.19 24 -0.19 18 42
TRADD 0.025 0.009 -10000 0 -10000 0 0
CRADD 0.027 0.006 -10000 0 -10000 0 0
MAPK3 -0.016 0.063 0.16 2 -0.27 9 11
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.067 0.16 2 -0.28 9 11
Cathepsin D/ceramide 0.003 0.066 -10000 0 -0.2 27 27
FADD 0.005 0.054 0.21 2 -0.31 3 5
KSR1 -0.022 0.073 0.19 1 -0.21 37 38
MAPK8 -0.011 0.075 -10000 0 -0.29 11 11
PRKRA -0.014 0.057 0.19 1 -0.19 28 29
PDGFA 0.026 0.008 -10000 0 -10000 0 0
TRAF2 0.027 0.006 -10000 0 -10000 0 0
IGF1 -0.003 0.093 -10000 0 -0.28 37 37
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.015 0.066 -10000 0 -0.2 30 30
CTSD 0.028 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.04 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.001 0.086 0.19 1 -0.29 12 13
PRKCD 0.028 0.004 -10000 0 -10000 0 0
PRKCZ 0.028 0.004 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.007 -10000 0 -10000 0 0
RelA/NF kappa B1 0.04 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.012 0.049 -10000 0 -0.17 20 20
TNFR1A/BAG4/TNF-alpha 0.014 0.075 -10000 0 -0.17 46 46
mol:Sphingosine-1-phosphate 0.013 0.004 -10000 0 -10000 0 0
MAP2K1 -0.02 0.064 0.17 4 -0.24 13 17
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS 0.014 0.05 0.14 12 -0.2 6 18
TNFRSF1A 0.026 0.008 -10000 0 -10000 0 0
NFKB1 0.028 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.018 0.056 -10000 0 -0.22 18 18
EIF2AK2 -0.013 0.057 0.18 4 -0.19 25 29
TNF-alpha/TNFR1A/FAN 0.03 0.058 -10000 0 -0.16 27 27
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.034 -10000 0 -10000 0 0
MAP2K2 -0.021 0.063 0.16 2 -0.24 14 16
SMPD3 -0.006 0.087 0.14 1 -0.28 25 26
TNF 0.001 0.087 -10000 0 -0.28 32 32
PKC zeta/PAR4 0.04 0.009 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.007 0.051 0.16 8 -0.16 19 27
NF kappa B1/RelA/I kappa B alpha 0.077 0.025 -10000 0 -10000 0 0
AIFM1 0.008 0.055 0.14 9 -0.19 6 15
BCL2 0.016 0.056 -10000 0 -0.32 10 10
Regulation of Androgen receptor activity

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
HDAC1 0.014 0.004 -10000 0 -10000 0 0
SMARCC1 0.017 0.008 -10000 0 -10000 0 0
REL -0.012 0.11 -10000 0 -0.32 42 42
HDAC7 0.004 0.06 0.23 1 -0.23 10 11
JUN 0.024 0.033 -10000 0 -0.29 4 4
EP300 0.025 0.031 -10000 0 -0.32 3 3
KAT2B 0.028 0.005 -10000 0 -10000 0 0
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.008 0.036 0.23 1 -0.15 14 15
FOXO1 0.023 0.011 -10000 0 -10000 0 0
T-DHT/AR 0.029 0.071 0.25 1 -0.24 10 11
MAP2K6 0.017 0.051 -10000 0 -0.22 15 15
BRM/BAF57 0.041 0.011 -10000 0 -10000 0 0
MAP2K4 0.026 0.01 -10000 0 -10000 0 0
SMARCA2 0.027 0.007 -10000 0 -10000 0 0
PDE9A 0.013 0.11 -10000 0 -0.51 12 12
NCOA2 -0.02 0.11 -10000 0 -0.32 47 47
CEBPA 0.028 0.003 -10000 0 -10000 0 0
EHMT2 0.028 0.004 -10000 0 -10000 0 0
cell proliferation 0.047 0.11 0.32 28 -0.29 2 30
NR0B1 0.019 0.024 -10000 0 -0.21 4 4
EGR1 -0.016 0.11 -10000 0 -0.27 54 54
RXRs/9cRA 0.008 0.084 -10000 0 -0.16 70 70
AR/RACK1/Src 0.013 0.068 0.2 9 -0.25 11 20
AR/GR -0.002 0.094 0.19 3 -0.24 40 43
GNB2L1 0.026 0.022 -10000 0 -0.21 3 3
PKN1 0.023 0.034 -10000 0 -0.21 8 8
RCHY1 0.028 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.026 1 1
MAPK8 0.007 0.041 -10000 0 -0.22 11 11
T-DHT/AR/TIF2/CARM1 0.001 0.093 0.21 2 -0.32 12 14
SRC -0.009 0.043 0.19 8 -0.17 2 10
NR3C1 0.019 0.053 -10000 0 -0.32 9 9
KLK3 0.021 0.12 -10000 0 -1.1 3 3
APPBP2 0.028 0.008 -10000 0 -10000 0 0
TRIM24 0.026 0.01 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.007 0.062 0.19 6 -0.25 10 16
TMPRSS2 -0.076 0.22 -10000 0 -0.51 71 71
RXRG -0.05 0.14 -10000 0 -0.31 84 84
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.027 0.007 -10000 0 -10000 0 0
RXRB 0.028 0.003 -10000 0 -10000 0 0
CARM1 0.028 0.005 -10000 0 -10000 0 0
NR2C2 0.015 0.065 -10000 0 -0.32 14 14
KLK2 -0.008 0.089 -10000 0 -0.34 9 9
AR -0.012 0.085 0.15 8 -0.25 37 45
SENP1 0.028 0.003 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
SRY -0.001 0.003 0.035 3 -10000 0 3
GATA2 0.026 0.008 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.01 0.068 0.2 9 -0.25 11 20
positive regulation of transcription 0.026 0.008 -10000 0 -10000 0 0
DNAJA1 0.028 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.005 -10000 0 -10000 0 0
NCOA1 0.031 0.013 -10000 0 -10000 0 0
SPDEF 0.028 0.013 -10000 0 -0.2 1 1
T-DHT/AR/TIF2 0.002 0.11 0.22 15 -0.25 38 53
T-DHT/AR/Hsp90 0.008 0.064 0.19 8 -0.25 10 18
GSK3B 0.027 0.007 -10000 0 -10000 0 0
NR2C1 0.027 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.012 0.034 0.12 1 -0.17 12 13
SIRT1 0.027 0.005 -10000 0 -10000 0 0
ZMIZ2 0.025 0.008 -10000 0 -10000 0 0
POU2F1 0.032 0.022 -10000 0 -0.31 1 1
T-DHT/AR/DAX-1 0.003 0.065 0.2 4 -0.26 10 14
CREBBP 0.028 0.005 -10000 0 -10000 0 0
SMARCE1 0.028 0.006 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.01 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.032 -10000 0 -0.18 5 5
forebrain development -0.035 0.13 0.33 1 -0.45 11 12
GNAO1 -0.022 0.12 -10000 0 -0.32 50 50
SMO/beta Arrestin2 0.025 0.026 -10000 0 -10000 0 0
SMO 0.018 0.018 -10000 0 -10000 0 0
ARRB2 0.024 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.038 0.081 0.3 6 -0.38 4 10
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
GSK3B 0.027 0.007 -10000 0 -10000 0 0
GNAI2 0.026 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.069 0.021 -10000 0 -10000 0 0
GNAI1 0.024 0.019 -10000 0 -0.32 1 1
XPO1 0.016 0.023 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.13 -10000 0 -0.47 11 11
SAP30 0.028 0.005 -10000 0 -10000 0 0
mol:GDP 0.018 0.018 -10000 0 -10000 0 0
MIM/GLI2A -0.005 0.058 -10000 0 -0.11 77 77
IFT88 0.027 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GLI2 0.018 0.052 0.21 3 -0.24 3 6
GLI3 0.024 0.084 0.32 6 -0.4 4 10
CSNK1D 0.028 0.005 -10000 0 -10000 0 0
CSNK1E 0.028 0.003 -10000 0 -10000 0 0
SAP18 0.028 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.006 -10000 0 -10000 0 0
GNG2 0.023 0.04 -10000 0 -0.32 5 5
Gi family/GTP -0.021 0.098 -10000 0 -0.26 46 46
SIN3B 0.029 0.004 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.026 0.065 0.26 1 -0.33 4 5
GLI2/Su(fu) 0.024 0.048 -10000 0 -0.24 4 4
FOXA2 -0.22 0.42 -10000 0 -0.89 103 103
neural tube patterning -0.035 0.13 0.33 1 -0.45 11 12
SPOP 0.028 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.029 0.043 -10000 0 -10000 0 0
GNB1 0.028 0.004 -10000 0 -10000 0 0
CSNK1G2 0.028 0.005 -10000 0 -10000 0 0
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
MTSS1 -0.005 0.058 -10000 0 -0.11 77 77
embryonic limb morphogenesis -0.035 0.13 0.33 1 -0.45 11 12
SUFU 0.018 0.012 -10000 0 -10000 0 0
LGALS3 0.004 0.088 -10000 0 -0.32 26 26
catabolic process 0.046 0.094 0.37 4 -0.39 5 9
GLI3A/CBP 0.027 0.036 -10000 0 -0.34 3 3
KIF3A 0.027 0.006 -10000 0 -10000 0 0
GLI1 -0.036 0.13 0.33 1 -0.46 11 12
RAB23 0.027 0.018 -10000 0 -0.32 1 1
CSNK1A1 0.028 0.004 -10000 0 -10000 0 0
IFT172 0.028 0.004 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.018 0.06 -10000 0 -0.22 6 6
GNAZ 0.002 0.089 -10000 0 -0.32 27 27
RBBP4 0.027 0.025 -10000 0 -0.32 2 2
CSNK1G1 0.028 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.018 -10000 0 -0.32 1 1
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.031 0.054 0.25 1 -0.22 3 4
STK36 0.016 0.023 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.016 0.097 -10000 0 -0.28 34 34
PTCH1 -0.027 0.14 0.5 1 -0.61 5 6
MIM/GLI1 -0.064 0.2 -10000 0 -0.41 80 80
CREBBP 0.027 0.036 -10000 0 -0.34 3 3
Su(fu)/SIN3/HDAC complex 0.029 0.039 -10000 0 -0.25 2 2
ceramide 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
MAP4K4 0.007 0.068 0.23 2 -0.3 5 7
BAG4 0.005 0.073 -10000 0 -0.32 18 18
BAD 0.009 0.046 0.22 9 -0.12 4 13
NFKBIA 0.028 0.004 -10000 0 -10000 0 0
BIRC3 0.025 0.025 -10000 0 -0.24 3 3
BAX 0.008 0.04 0.17 10 -0.12 3 13
EnzymeConsortium:3.1.4.12 0.003 0.023 0.072 8 -0.075 7 15
IKBKB 0.018 0.078 0.25 14 -0.27 6 20
MAP2K2 0.002 0.05 0.21 6 -0.19 6 12
MAP2K1 0.002 0.053 0.2 9 -0.19 6 15
SMPD1 0.006 0.026 0.12 5 -0.092 2 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.017 0.077 0.28 7 -0.29 6 13
MAP2K4 0.007 0.033 0.15 5 -0.13 2 7
protein ubiquitination 0.011 0.079 0.36 3 -0.29 6 9
EnzymeConsortium:2.7.1.37 0.002 0.055 0.19 10 -0.21 5 15
response to UV 0 0.001 0.002 8 -0.002 5 13
RAF1 0.002 0.051 0.2 7 -0.19 6 13
CRADD 0.027 0.006 -10000 0 -10000 0 0
mol:ceramide 0.008 0.036 0.13 9 -0.11 6 15
I-kappa-B-alpha/RELA/p50/ubiquitin 0.037 0.008 -10000 0 -10000 0 0
MADD 0.028 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.034 0.14 7 -0.12 3 10
TRADD 0.025 0.009 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.005 0.052 0.2 8 -0.22 3 11
MAPK1 0.004 0.052 0.19 8 -0.22 3 11
p50/RELA/I-kappa-B-alpha 0.04 0.009 -10000 0 -10000 0 0
FADD 0.01 0.07 0.24 5 -0.32 4 9
KSR1 0.002 0.046 0.14 6 -0.15 16 22
MAPK8 0.003 0.044 0.18 6 -0.17 3 9
TRAF2 0.027 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -0.002 1 5
CHUK 0.012 0.072 0.29 5 -0.28 5 10
TNF R/SODD 0.018 0.056 -10000 0 -0.22 18 18
TNF 0.001 0.087 -10000 0 -0.28 32 32
CYCS 0.022 0.054 0.15 30 -0.11 2 32
IKBKG 0.008 0.072 0.28 3 -0.28 6 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.01 0.067 -10000 0 -0.26 7 7
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.028 0.004 -10000 0 -10000 0 0
AIFM1 0.017 0.048 0.14 25 -0.11 2 27
TNF/TNF R/SODD 0.014 0.075 -10000 0 -0.17 46 46
TNFRSF1A 0.026 0.008 -10000 0 -10000 0 0
response to heat 0 0 0.002 4 -0.002 1 5
CASP8 0.03 0.021 -10000 0 -10000 0 0
NSMAF 0.021 0.072 0.21 21 -0.28 4 25
response to hydrogen peroxide 0 0.001 0.002 8 -0.002 5 13
BCL2 0.016 0.056 -10000 0 -0.32 10 10
IL2 signaling events mediated by PI3K

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
BCL2L1 0.015 0.068 -10000 0 -0.48 1 1
UGCG -0.047 0.21 -10000 0 -0.63 40 40
AKT1/mTOR/p70S6K/Hsp90/TERT 0.032 0.1 0.39 2 -0.37 10 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.046 0.2 -10000 0 -0.62 40 40
mol:DAG -0.003 0.1 -10000 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.12 0.28 2 -0.4 19 21
FRAP1 0.02 0.13 0.31 2 -0.46 19 21
FOXO3 0.023 0.1 0.34 3 -0.38 10 13
AKT1 0.025 0.1 0.29 3 -0.36 14 17
GAB2 0.028 0.005 -10000 0 -10000 0 0
SMPD1 0.019 0.049 -10000 0 -0.57 2 2
SGMS1 0.013 0.078 -10000 0 -0.57 6 6
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 0.002 0.027 -10000 0 -0.19 6 6
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation 0.005 0.14 0.3 6 -0.34 41 47
EIF3A 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.034 0.039 -10000 0 -0.23 6 6
RPS6KB1 0.012 0.1 -10000 0 -0.74 7 7
mol:sphingomyelin -0.003 0.1 -10000 0 -0.82 6 6
natural killer cell activation 0 0.002 -10000 0 -0.01 1 1
JAK3 0.023 0.042 -10000 0 -0.23 10 10
PIK3R1 0.024 0.032 -10000 0 -0.32 3 3
JAK1 0.029 0.005 -10000 0 -10000 0 0
NFKB1 0.028 0.003 -10000 0 -10000 0 0
MYC 0.056 0.12 0.36 12 -0.39 6 18
MYB 0.02 0.037 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.022 0.088 0.21 1 -0.31 14 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.1 -10000 0 -0.68 7 7
mol:PI-3-4-5-P3 0.023 0.087 0.21 1 -0.31 13 14
Rac1/GDP 0.018 0.026 -10000 0 -0.21 3 3
T cell proliferation 0.022 0.085 0.23 4 -0.31 11 15
SHC1 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.002 -10000 0 -10000 0 0
PRKCZ 0.02 0.085 0.21 2 -0.32 11 13
NF kappa B1 p50/RelA 0.038 0.12 -10000 0 -0.4 19 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.017 0.064 -10000 0 -0.34 7 7
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.009 0.086 -10000 0 -0.21 56 56
IL2RB 0.013 0.071 -10000 0 -0.29 19 19
TERT -0.044 0.11 -10000 0 -0.21 112 112
E2F1 0.025 0.04 -10000 0 -0.37 2 2
SOS1 0.027 0.006 -10000 0 -10000 0 0
RPS6 0.027 0.013 -10000 0 -0.21 1 1
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.026 0.019 -10000 0 -0.31 1 1
IL2RG 0.02 0.048 -10000 0 -0.22 14 14
actin cytoskeleton organization 0.022 0.085 0.23 4 -0.31 11 15
GRB2 0.027 0.006 -10000 0 -10000 0 0
IL2 0.022 0.01 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.29 4 4
Rac1/GTP 0.041 0.034 -10000 0 -0.2 3 3
LCK 0.026 0.03 -10000 0 -0.2 6 6
BCL2 0.005 0.19 0.36 2 -0.8 17 19
Class I PI3K signaling events

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
ARF5/GTP -0.011 0.037 0.18 8 -10000 0 8
DAPP1 -0.043 0.14 0.21 5 -0.32 51 56
Src family/SYK family/BLNK-LAT/BTK-ITK -0.019 0.13 0.46 1 -0.46 14 15
mol:DAG 0.006 0.081 0.26 12 -0.21 9 21
HRAS 0.028 0.028 -10000 0 -0.2 5 5
RAP1A 0.029 0.02 -10000 0 -0.32 1 1
ARF5/GDP 0.032 0.066 0.24 5 -0.28 5 10
PLCG2 0.02 0.032 -10000 0 -0.26 4 4
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.008 -10000 0 -10000 0 0
mol:GTP -0.011 0.033 0.16 9 -10000 0 9
ARF1/GTP 0 0.036 0.17 8 -10000 0 8
RHOA 0.028 0.004 -10000 0 -10000 0 0
YES1 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.01 0.031 0.16 8 -10000 0 8
ADAP1 -0.009 0.046 0.22 8 -0.26 1 9
ARAP3 -0.011 0.033 0.16 9 -10000 0 9
INPPL1 0.028 0.004 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.027 0.018 -10000 0 -0.32 1 1
ARHGEF7 0.027 0.007 -10000 0 -10000 0 0
ARF1 0.027 0.007 -10000 0 -10000 0 0
NRAS 0.03 0.02 -10000 0 -0.32 1 1
FYN 0.024 0.01 -10000 0 -10000 0 0
ARF6 0.028 0.004 -10000 0 -10000 0 0
FGR 0.026 0.028 -10000 0 -0.28 3 3
mol:Ca2+ 0.012 0.06 0.15 43 -0.12 3 46
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.028 -10000 0 -0.28 3 3
ZAP70 0.003 0.074 -10000 0 -0.21 39 39
mol:IP3 0.008 0.071 0.19 34 -0.15 8 42
LYN 0.024 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.067 0.25 4 -0.23 9 13
RhoA/GDP 0.028 0.044 0.24 3 -10000 0 3
PDK1/Src/Hsp90 0.052 0.017 -10000 0 -10000 0 0
BLNK 0.026 0.007 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.04 0.082 0.3 15 -0.23 2 17
SRC 0.027 0.006 -10000 0 -10000 0 0
PLEKHA2 -0.013 0.039 -10000 0 -0.22 11 11
RAC1 0.026 0.008 -10000 0 -10000 0 0
PTEN 0.021 0.015 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.033 0.17 8 -10000 0 8
RhoA/GTP -0.011 0.032 0.17 7 -10000 0 7
Src family/SYK family/BLNK-LAT -0.014 0.095 -10000 0 -0.34 15 15
BLK -0.027 0.11 -10000 0 -0.28 58 58
PDPK1 0.027 0.005 -10000 0 -10000 0 0
CYTH1 -0.009 0.035 0.17 6 -10000 0 6
HCK 0.024 0.033 -10000 0 -0.29 4 4
CYTH3 -0.009 0.045 0.22 8 -10000 0 8
CYTH2 -0.008 0.044 0.2 8 -10000 0 8
KRAS 0.029 0.011 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.032 0.13 -10000 0 -0.38 44 44
SGK1 -0.028 0.14 -10000 0 -0.42 41 41
INPP5D 0.01 0.076 -10000 0 -0.32 19 19
mol:GDP 0.022 0.068 0.22 6 -0.24 9 15
SOS1 0.027 0.006 -10000 0 -10000 0 0
SYK 0.023 0.038 -10000 0 -0.29 5 5
ARF6/GDP 0.015 0.042 0.27 3 -10000 0 3
mol:PI-3-4-5-P3 -0.009 0.037 0.17 7 -10000 0 7
ARAP3/RAP1A/GTP -0.01 0.031 0.16 8 -10000 0 8
VAV1 0.015 0.064 -10000 0 -0.31 14 14
mol:PI-3-4-P2 0.002 0.05 -10000 0 -0.22 18 18
RAS family/GTP/PI3K Class I 0.064 0.066 0.2 67 -0.15 2 69
PLEKHA1 -0.016 0.037 -10000 0 -0.18 18 18
Rac1/GDP 0.031 0.065 0.25 3 -0.26 6 9
LAT 0.019 0.047 -10000 0 -0.23 12 12
Rac1/GTP 0.023 0.056 0.18 1 -0.29 6 7
ITK -0.019 0.042 0.24 1 -0.26 1 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.001 0.091 0.32 6 -0.28 10 16
LCK 0.024 0.03 -10000 0 -0.21 6 6
BTK -0.011 0.039 0.16 8 -10000 0 8
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.024 -10000 0 -0.18 7 7
SNTA1 0.028 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.028 0.13 1 -0.21 6 7
MAPK12 -0.009 0.059 0.18 6 -0.22 17 23
CCND1 0.007 0.026 -10000 0 -10000 0 0
p38 gamma/SNTA1 0.006 0.063 0.2 5 -0.24 13 18
MAP2K3 0.027 0.005 -10000 0 -10000 0 0
PKN1 0.023 0.034 -10000 0 -0.21 8 8
G2/M transition checkpoint -0.008 0.06 0.21 5 -0.24 14 19
MAP2K6 -0.005 0.049 -10000 0 -0.22 15 15
MAPT -0.003 0.051 0.16 8 -0.19 11 19
MAPK13 0.009 0.032 -10000 0 -0.22 7 7
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.048 -10000 0 -0.25 12 12
Retinoic acid receptors-mediated signaling

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
HDAC1 0.028 0.003 -10000 0 -10000 0 0
HDAC3 0.027 0.005 -10000 0 -10000 0 0
VDR 0.023 0.041 -10000 0 -0.3 6 6
Cbp/p300/PCAF 0.051 0.026 -10000 0 -0.18 3 3
EP300 0.025 0.031 -10000 0 -0.32 3 3
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.02 0.047 0.2 1 -0.23 5 6
KAT2B 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.028 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.067 0.19 25 -0.21 7 32
RAR alpha/9cRA/Cyclin H 0.038 0.074 0.22 4 -0.25 11 15
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.047 0.16 3 -0.18 9 12
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.015 0.07 -10000 0 -0.33 11 11
NCOR2 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.017 0.028 -10000 0 -0.2 6 6
RXRs/RARs/NRIP1/9cRA 0.012 0.097 0.37 3 -0.39 11 14
NCOA2 -0.02 0.11 -10000 0 -0.32 47 47
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.041 -10000 0 -0.3 6 6
RARG 0.024 0.036 -10000 0 -0.32 4 4
RAR gamma1/9cRA 0.035 0.024 -10000 0 -0.18 4 4
MAPK3 0.028 0.005 -10000 0 -10000 0 0
MAPK1 0.028 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.058 -10000 0 -0.31 11 11
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.014 0.092 0.23 1 -0.4 12 13
RARA 0.006 0.056 -10000 0 -0.21 22 22
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.004 0.076 -10000 0 -0.28 13 13
PRKCA 0.017 0.063 -10000 0 -0.31 13 13
RXRs/RARs/NRIP1/9cRA/HDAC1 0.007 0.097 0.32 2 -0.39 13 15
RXRG -0.042 0.12 0.2 1 -0.25 84 85
RXRA 0.011 0.054 -10000 0 -0.19 20 20
RXRB 0.013 0.05 0.2 1 -0.24 13 14
VDR/Vit D3/DNA 0.017 0.028 -10000 0 -0.2 6 6
RBP1 -0.003 0.094 -10000 0 -0.31 32 32
CRBP1/9-cic-RA -0.001 0.065 -10000 0 -0.21 32 32
RARB 0.024 0.04 -10000 0 -0.32 5 5
PRKCG 0.018 0.039 -10000 0 -0.2 11 11
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs 0.012 0.1 0.25 5 -0.44 10 15
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.014 0.088 0.31 4 -0.34 12 16
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.068 0.22 8 -0.25 9 17
RXRs/RARs/NRIP1/9cRA/HDAC3 0.008 0.098 0.35 2 -0.39 13 15
positive regulation of DNA binding 0.026 0.064 -10000 0 -0.24 11 11
NRIP1 0.007 0.091 -10000 0 -0.48 3 3
RXRs/RARs 0.006 0.097 0.3 2 -0.39 13 15
RXRs/RXRs/DNA/9cRA -0.003 0.082 -10000 0 -0.4 12 12
PRKACA 0.028 0.004 -10000 0 -10000 0 0
CDK7 0.026 0.008 -10000 0 -10000 0 0
TFIIH 0.049 0.024 -10000 0 -0.12 2 2
RAR alpha/9cRA 0.045 0.058 -10000 0 -0.29 2 2
CCNH 0.025 0.022 -10000 0 -0.21 3 3
CREBBP 0.027 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.03 -10000 0 -0.15 3 3
TCGA08_rtk_signaling

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
PDGFRA 0.013 0.071 -10000 0 -0.31 17 17
HRAS 0.025 0.027 -10000 0 -0.21 5 5
EGFR -0.007 0.1 -10000 0 -0.32 36 36
AKT 0.035 0.091 0.23 21 -0.23 12 33
FOXO3 0.024 0.01 -10000 0 -10000 0 0
AKT1 0.028 0.005 -10000 0 -10000 0 0
FOXO1 0.023 0.011 -10000 0 -10000 0 0
AKT3 0.027 0.006 -10000 0 -10000 0 0
FOXO4 0.027 0.018 -10000 0 -0.32 1 1
MET -0.002 0.093 -10000 0 -0.32 30 30
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
PIK3CB 0.026 0.008 -10000 0 -10000 0 0
NRAS 0.027 0.018 -10000 0 -0.32 1 1
PIK3CG -0.003 0.093 -10000 0 -0.3 33 33
PIK3R3 0.028 0.004 -10000 0 -10000 0 0
PIK3R2 0.028 0.003 -10000 0 -10000 0 0
NF1 0.028 0.003 -10000 0 -10000 0 0
RAS -0.005 0.07 0.14 1 -0.25 15 16
ERBB2 0.025 0.031 -10000 0 -0.32 3 3
proliferation/survival/translation -0.02 0.087 0.24 21 -0.2 6 27
PI3K 0.012 0.098 0.25 16 -0.26 22 38
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
KRAS 0.026 0.008 -10000 0 -10000 0 0
FOXO 0.05 0.054 0.2 12 -10000 0 12
AKT2 0.028 0.003 -10000 0 -10000 0 0
PTEN 0.023 0.011 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.028 0.005 -10000 0 -10000 0 0
ELF1 0.008 0.056 -10000 0 -0.3 7 7
CCNA2 -0.004 0.08 -10000 0 -0.21 49 49
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
JAK3 0.022 0.042 -10000 0 -0.23 10 10
PIK3R1 0.024 0.032 -10000 0 -0.31 3 3
JAK1 0.028 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.021 0.081 -10000 0 -0.35 8 8
SHC1 0.027 0.007 -10000 0 -10000 0 0
SP1 0.017 0.07 -10000 0 -0.28 19 19
IL2RA -0.013 0.078 -10000 0 -0.37 7 7
IL2RB 0.012 0.07 -10000 0 -0.29 19 19
SOS1 0.028 0.006 -10000 0 -10000 0 0
IL2RG 0.019 0.048 -10000 0 -0.22 14 14
G1/S transition of mitotic cell cycle -0.019 0.19 0.35 2 -0.66 24 26
PTPN11 0.027 0.019 -10000 0 -0.32 1 1
CCND2 -0.008 0.12 -10000 0 -0.59 16 16
LCK 0.025 0.03 -10000 0 -0.21 6 6
GRB2 0.028 0.006 -10000 0 -10000 0 0
IL2 0.022 0.007 -10000 0 -10000 0 0
CDK6 0.017 0.054 -10000 0 -0.3 10 10
CCND3 0.025 0.084 0.47 2 -0.39 3 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.026 0.059 -10000 0 -0.51 4 4
VEGFR1 homodimer/NRP1 0.007 0.056 -10000 0 -0.51 4 4
mol:DAG -0.01 0.077 -10000 0 -0.47 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.014 0.07 -10000 0 -0.51 4 4
CaM/Ca2+ 0.005 0.078 -10000 0 -0.44 4 4
HIF1A 0.028 0.039 -10000 0 -0.3 5 5
GAB1 0.027 0.018 -10000 0 -0.32 1 1
AKT1 -0.011 0.084 0.27 1 -0.38 7 8
PLCG1 -0.01 0.077 -10000 0 -0.47 4 4
NOS3 -0.002 0.078 0.24 2 -0.44 4 6
CBL 0.026 0.019 -10000 0 -0.32 1 1
mol:NO 0.002 0.089 0.34 5 -0.43 5 10
FLT1 0.011 0.064 -10000 0 -0.59 4 4
PGF -0.015 0.11 -10000 0 -0.31 46 46
VEGFR1 homodimer/NRP2/VEGFR121 0.019 0.09 -10000 0 -0.43 7 7
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
eNOS/Hsp90 0.015 0.088 0.28 4 -0.41 5 9
endothelial cell proliferation -0.047 0.14 0.34 2 -0.41 33 35
mol:Ca2+ -0.01 0.076 -10000 0 -0.47 4 4
MAPK3 -0.028 0.077 0.22 4 -0.38 9 13
MAPK1 -0.028 0.077 0.22 4 -0.38 9 13
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
PLGF homodimer -0.015 0.11 -10000 0 -0.31 46 46
PRKACA 0.028 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.013 0.11 -10000 0 -0.32 42 42
VEGFA homodimer 0.009 0.077 -10000 0 -0.3 21 21
VEGFR1 homodimer/VEGFA homodimer 0.015 0.076 -10000 0 -0.55 4 4
platelet activating factor biosynthetic process -0.028 0.074 0.21 4 -0.38 9 13
PI3K 0.023 0.09 -10000 0 -0.36 8 8
PRKCA -0.03 0.078 0.18 3 -0.4 9 12
PRKCB -0.052 0.1 0.18 3 -0.32 31 34
VEGFR1 homodimer/PLGF homodimer 0.001 0.088 -10000 0 -0.51 4 4
VEGFA 0.009 0.077 -10000 0 -0.3 21 21
VEGFB 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.01 0.077 -10000 0 -0.47 4 4
RASA1 0.009 0.057 0.19 2 -0.44 5 7
NRP2 0.007 0.083 -10000 0 -0.32 23 23
VEGFR1 homodimer 0.011 0.064 -10000 0 -0.59 4 4
VEGFB homodimer 0.028 0.004 -10000 0 -10000 0 0
NCK1 0.026 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.001 0.1 0.31 2 -0.33 16 18
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
mol:PI-3-4-5-P3 0.021 0.089 -10000 0 -0.36 8 8
mol:L-citrulline 0.002 0.089 0.34 5 -0.43 5 10
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.043 0.077 -10000 0 -0.45 5 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.074 -10000 0 -0.51 4 4
CD2AP 0.028 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.031 0.092 -10000 0 -0.34 8 8
PDPK1 -0.005 0.077 -10000 0 -0.36 7 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.03 0.076 -10000 0 -0.47 5 5
mol:NADP 0.002 0.089 0.34 5 -0.43 5 10
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.041 0.075 -10000 0 -0.44 5 5
VEGFR1 homodimer/NRP2 0.014 0.079 -10000 0 -0.51 5 5
Signaling events mediated by HDAC Class III

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
EP300 0.025 0.031 -10000 0 -0.32 3 3
HDAC4 0.028 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 -0.011 0.024 0.14 5 -0.26 1 6
CDKN1A -0.008 0.008 -10000 0 -10000 0 0
KAT2B 0.027 0.005 -10000 0 -10000 0 0
BAX 0.026 0.018 -10000 0 -0.21 2 2
FOXO3 -0.003 0.028 0.31 3 -10000 0 3
FOXO1 0.023 0.011 -10000 0 -10000 0 0
FOXO4 0.014 0.024 -10000 0 -0.21 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.028 0.004 -10000 0 -10000 0 0
TAT 0.009 0.055 -10000 0 -0.22 19 19
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.015 0.03 -10000 0 -0.16 13 13
PPARGC1A -0.06 0.15 -10000 0 -0.32 95 95
FHL2 0.016 0.063 -10000 0 -0.32 13 13
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.039 0.011 -10000 0 -10000 0 0
HIST2H4A 0.011 0.024 0.26 1 -0.14 5 6
SIRT1/FOXO3a 0.015 0.029 0.23 3 -0.18 1 4
SIRT1 0.026 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.051 0.018 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.015 0.041 -10000 0 -0.18 5 5
apoptosis -0.051 0.019 -10000 0 -10000 0 0
SIRT1/PGC1A -0.019 0.092 -10000 0 -0.18 93 93
p53/SIRT1 0.029 0.015 -10000 0 -10000 0 0
SIRT1/FOXO4 0.028 0.031 -10000 0 -0.18 4 4
FOXO1/FHL2/SIRT1 0.036 0.042 -10000 0 -0.15 12 12
HIST1H1E 0.004 0.036 0.18 2 -0.19 7 9
SIRT1/p300 0.037 0.026 -10000 0 -0.22 3 3
muscle cell differentiation -0.027 0.037 0.14 13 -0.22 3 16
TP53 0.022 0.009 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.052 0.019 -10000 0 -10000 0 0
CREBBP 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.027 0.006 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.022 0.04 -10000 0 -0.14 18 18
ACSS2 0.012 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.027 0.038 0.22 3 -0.14 13 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.005 0.073 -10000 0 -0.32 18 18
Caspase 8 (4 units) 0.031 0.059 -10000 0 -0.18 12 12
NEF -0.003 0.024 -10000 0 -0.14 9 9
NFKBIA 0.029 0.01 -10000 0 -10000 0 0
BIRC3 0.021 0.031 0.18 4 -0.24 3 7
CYCS 0.005 0.048 0.18 5 -0.21 12 17
RIPK1 0.028 0.004 -10000 0 -10000 0 0
CD247 0.012 0.065 -10000 0 -0.22 24 24
MAP2K7 0.015 0.11 0.28 1 -0.6 8 9
protein ubiquitination 0.018 0.08 0.31 11 -0.25 5 16
CRADD 0.027 0.006 -10000 0 -10000 0 0
DAXX 0.028 0.003 -10000 0 -10000 0 0
FAS 0.022 0.032 -10000 0 -0.32 3 3
BID 0.009 0.051 0.18 4 -0.21 14 18
NF-kappa-B/RelA/I kappa B alpha 0.059 0.025 -10000 0 -0.14 3 3
TRADD 0.025 0.009 -10000 0 -10000 0 0
MAP3K5 0.027 0.013 -10000 0 -0.21 1 1
CFLAR 0.028 0.003 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.059 0.025 -10000 0 -0.14 3 3
MAPK8 0.011 0.1 0.27 1 -0.58 7 8
APAF1 0.027 0.006 -10000 0 -10000 0 0
TRAF1 0.026 0.014 -10000 0 -0.21 1 1
TRAF2 0.027 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.015 0.055 0.19 5 -0.22 14 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.011 0.068 -10000 0 -0.3 6 6
CHUK 0.014 0.069 0.25 8 -0.27 5 13
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.068 0.039 -10000 0 -0.16 3 3
TCRz/NEF 0.009 0.063 -10000 0 -0.19 29 29
TNF 0.001 0.087 -10000 0 -0.28 32 32
FASLG -0.003 0.088 0.21 1 -0.32 22 23
NFKB1 0.029 0.009 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.014 0.075 -10000 0 -0.17 46 46
CASP6 0.037 0.06 -10000 0 -0.44 2 2
CASP7 0.031 0.083 0.33 12 -0.49 1 13
RELA 0.028 0.01 -10000 0 -10000 0 0
CASP2 0.022 0.036 -10000 0 -0.32 4 4
CASP3 0.033 0.073 0.31 12 -0.49 1 13
TNFRSF1A 0.026 0.008 -10000 0 -10000 0 0
TNFR1A/BAG4 0.018 0.056 -10000 0 -0.22 18 18
CASP8 0.028 0.003 -10000 0 -10000 0 0
CASP9 0.028 0.003 -10000 0 -10000 0 0
MAP3K14 0.012 0.067 0.22 4 -0.3 5 9
APAF-1/Caspase 9 0.022 0.059 -10000 0 -0.26 3 3
BCL2 0.006 0.099 0.26 1 -0.52 7 8
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.063 0.038 0.2 1 -0.28 1 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.028 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.046 0.066 0.32 7 -0.23 4 11
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.054 0.025 -10000 0 -0.22 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.005 0.049 -10000 0 -0.2 6 6
CaM/Ca2+ 0.063 0.038 -10000 0 -0.26 1 1
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
STAT1 (dimer)/SHP2 0.024 0.043 -10000 0 -0.22 3 3
AKT1 0.017 0.071 0.21 25 -0.48 1 26
MAP2K1 -0.005 0.046 0.24 8 -0.38 1 9
MAP3K11 0.016 0.052 0.24 12 -0.26 1 13
IFNGR1 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.013 0.12 -10000 0 -0.31 47 47
Rap1/GTP 0.015 0.032 -10000 0 -0.43 1 1
CRKL/C3G 0.039 0.011 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.075 0.038 -10000 0 -0.2 1 1
CEBPB 0.029 0.071 0.32 7 -0.37 2 9
STAT3 0.027 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.07 0.081 -10000 0 -0.88 2 2
STAT1 0.014 0.057 0.29 8 -0.22 3 11
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.013 0.053 -10000 0 -0.21 20 20
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
STAT1 (dimer)/PIAS1 0.03 0.058 0.31 7 -0.21 3 10
CEBPB/PTGES2/Cbp/p300 0.036 0.044 -10000 0 -0.28 1 1
mol:Ca2+ 0.06 0.036 0.19 1 -0.27 1 2
MAPK3 0.014 0.08 -10000 0 -0.58 4 4
STAT1 (dimer) 0.015 0.067 -10000 0 -0.27 6 6
MAPK1 0.011 0.098 -10000 0 -0.65 6 6
JAK2 0.028 0.021 -10000 0 -0.34 1 1
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
JAK1 0.029 0.009 -10000 0 -10000 0 0
CAMK2D 0.028 0.004 -10000 0 -10000 0 0
DAPK1 0.028 0.075 0.32 7 -0.51 2 9
SMAD7 0.013 0.047 0.18 12 -0.12 1 13
CBL/CRKL/C3G 0.039 0.049 0.29 5 -0.37 1 6
PI3K 0.05 0.052 -10000 0 -0.28 3 3
IFNG 0.013 0.053 -10000 0 -0.21 20 20
apoptosis 0.027 0.068 0.3 6 -0.41 3 9
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.006 -10000 0 -10000 0 0
CAMK2A -0.03 0.12 -10000 0 -0.3 65 65
CAMK2B 0.014 0.052 -10000 0 -0.21 18 18
FRAP1 0.005 0.068 0.19 27 -0.44 1 28
PRKCD 0.016 0.067 0.2 24 -0.48 1 25
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.005 0.049 -10000 0 -0.2 6 6
PTPN2 0.027 0.006 -10000 0 -10000 0 0
EP300 0.025 0.031 -10000 0 -0.31 3 3
IRF1 0.008 0.07 0.28 10 -0.27 4 14
STAT1 (dimer)/PIASy 0.029 0.058 0.3 7 -0.21 3 10
SOCS1 0.02 0.087 -10000 0 -1.2 2 2
mol:GDP 0.036 0.047 0.27 5 -0.36 1 6
CASP1 0.011 0.054 0.18 13 -0.18 8 21
PTGES2 0.027 0.007 -10000 0 -10000 0 0
IRF9 0.028 0.036 0.18 9 -10000 0 9
mol:PI-3-4-5-P3 0.036 0.046 -10000 0 -0.33 2 2
RAP1/GDP 0.033 0.039 -10000 0 -0.44 1 1
CBL 0.014 0.054 0.24 12 -0.4 1 13
MAP3K1 0.012 0.048 0.24 8 -0.4 1 9
PIAS1 0.027 0.018 -10000 0 -0.32 1 1
PIAS4 0.028 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.005 0.049 -10000 0 -0.2 6 6
PTPN11 0.01 0.034 0.16 5 -0.28 1 6
CREBBP 0.028 0.005 -10000 0 -10000 0 0
RAPGEF1 0.027 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.014 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.038 0.021 -10000 0 -10000 0 0
CDKN1B 0.008 0.053 -10000 0 -0.29 9 9
CDKN1A 0.008 0.057 0.2 1 -0.28 11 12
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.023 0.016 -10000 0 -0.21 1 1
FOXO3 0.009 0.044 -10000 0 -0.25 9 9
AKT1 0.012 0.04 -10000 0 -0.25 8 8
BAD 0.027 0.013 -10000 0 -0.21 1 1
AKT3 0.014 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.058 -10000 0 -0.28 12 12
AKT1/ASK1 0.033 0.069 0.3 1 -0.27 11 12
BAD/YWHAZ 0.045 0.025 -10000 0 -0.12 1 1
RICTOR 0.027 0.005 -10000 0 -10000 0 0
RAF1 0.028 0.004 -10000 0 -10000 0 0
JNK cascade -0.029 0.064 0.26 12 -10000 0 12
TSC1 0.009 0.047 -10000 0 -0.25 11 11
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.071 0.32 1 -0.28 12 13
EP300 0.025 0.031 -10000 0 -0.32 3 3
mol:GDP 0.011 0.059 -10000 0 -0.29 12 12
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.056 -10000 0 -0.28 12 12
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
TBC1D4 0.006 0.008 -10000 0 -10000 0 0
MAP3K5 0.027 0.013 -10000 0 -0.21 1 1
MAPKAP1 0.027 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.071 0.26 7 -0.21 15 22
YWHAH 0.028 0.004 -10000 0 -10000 0 0
AKT1S1 0.008 0.058 -10000 0 -0.28 12 12
CASP9 0.008 0.057 -10000 0 -0.28 12 12
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.068 0.27 4 -0.29 8 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.052 0.017 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
AKT2/p21CIP1 0.014 0.056 0.22 2 -0.32 4 6
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.046 -10000 0 -0.34 5 5
CHUK 0.012 0.043 0.2 1 -0.25 8 9
BAD/BCL-XL 0.041 0.068 0.24 1 -0.27 12 13
mTORC2 0.034 0.01 -10000 0 -10000 0 0
AKT2 0.015 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.039 0.086 0.29 10 -0.31 7 17
PDPK1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.01 0.061 0.2 5 -0.28 12 17
MAPKKK cascade -0.035 0.07 0.27 12 -0.32 1 13
MDM2/Cbp/p300 0.049 0.08 0.3 8 -0.27 11 19
TSC1/TSC2 0.015 0.066 0.27 12 -0.24 11 23
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.076 0.29 8 -0.26 11 19
glucose import -0.011 0.043 -10000 0 -0.15 30 30
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.043 -10000 0 -0.26 4 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.043 -10000 0 -0.15 30 30
GSK3A 0.008 0.057 -10000 0 -0.28 12 12
FOXO1 0.012 0.029 -10000 0 -0.24 4 4
GSK3B 0.014 0.06 0.2 9 -0.29 9 18
SFN 0.002 0.091 -10000 0 -0.32 28 28
G1/S transition of mitotic cell cycle 0.017 0.069 0.23 11 -0.29 9 20
p27Kip1/14-3-3 family 0.022 0.051 -10000 0 -0.43 2 2
PRKACA 0.028 0.004 -10000 0 -10000 0 0
KPNA1 0.027 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.008 -10000 0 -10000 0 0
RHEB 0.026 0.008 -10000 0 -10000 0 0
CREBBP 0.027 0.005 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.028 0.005 -10000 0 -10000 0 0
NFATC1 0.025 0.073 0.26 6 -0.29 2 8
NFATC2 -0.001 0.067 0.15 6 -0.2 18 24
NFATC3 0.02 0.009 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.023 0.11 0.21 3 -0.3 36 39
Exportin 1/Ran/NUP214 0.052 0.018 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.003 0.12 0.22 1 -0.29 35 36
BCL2/BAX 0.029 0.045 -10000 0 -0.2 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.008 -10000 0 -10000 0 0
BAX 0.026 0.018 -10000 0 -0.21 2 2
MAPK14 0.028 0.003 -10000 0 -10000 0 0
BAD 0.027 0.013 -10000 0 -0.21 1 1
CABIN1/MEF2D -0.01 0.11 0.22 2 -0.28 35 37
Calcineurin A alpha-beta B1/BCL2 0.016 0.056 -10000 0 -0.31 10 10
FKBP8 0.028 0.002 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.01 0.11 0.28 35 -0.22 2 37
KPNB1 0.028 0.005 -10000 0 -10000 0 0
KPNA2 0.026 0.018 -10000 0 -0.21 2 2
XPO1 0.028 0.004 -10000 0 -10000 0 0
SFN 0.002 0.091 -10000 0 -0.32 28 28
MAP3K8 0.019 0.053 -10000 0 -0.29 10 10
NFAT4/CK1 alpha 0.027 0.021 -10000 0 -0.14 1 1
MEF2D/NFAT1/Cbp/p300 0.03 0.09 0.21 1 -0.23 16 17
CABIN1 -0.023 0.11 0.21 3 -0.3 36 39
CALM1 0.027 0.005 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
MAP3K1 0.025 0.02 -10000 0 -0.32 1 1
CAMK4 0.002 0.087 -10000 0 -0.31 26 26
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.027 0.005 -10000 0 -10000 0 0
YWHAH 0.028 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.029 -10000 0 -0.15 8 8
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.017 0.058 -10000 0 -0.32 11 11
MAPK9 0.028 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.008 -10000 0 -10000 0 0
FKBP1A 0.028 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.028 0.075 0.26 3 -0.29 3 6
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.037 0.026 -10000 0 -0.22 3 3
CASP3 0.028 0.004 -10000 0 -10000 0 0
PIM1 0.025 0.027 -10000 0 -0.21 5 5
Calcineurin A alpha-beta B1/FKBP12/FK506 0.019 0.004 -10000 0 -10000 0 0
apoptosis 0.017 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.022 0.042 -10000 0 -0.22 2 2
PRKCB -0.045 0.14 -10000 0 -0.32 78 78
PRKCE 0.027 0.005 -10000 0 -10000 0 0
JNK2/NFAT4 0.018 0.054 -10000 0 -10000 0 0
BAD/BCL-XL 0.04 0.013 -10000 0 -0.14 1 1
PRKCD 0.028 0.004 -10000 0 -10000 0 0
NUP214 0.027 0.007 -10000 0 -10000 0 0
PRKCZ 0.028 0.004 -10000 0 -10000 0 0
PRKCA 0.016 0.063 -10000 0 -0.32 13 13
PRKCG 0.017 0.039 -10000 0 -0.21 11 11
PRKCQ 0.006 0.08 -10000 0 -0.28 26 26
FKBP38/BCL2 0.03 0.043 -10000 0 -0.22 10 10
EP300 0.024 0.032 -10000 0 -0.31 3 3
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.028 0.004 -10000 0 -10000 0 0
NFATc/JNK1 0.036 0.073 0.27 5 -0.31 1 6
CaM/Ca2+/FKBP38 0.037 0.009 -10000 0 -10000 0 0
FKBP12/FK506 0.021 0.003 -10000 0 -10000 0 0
CSNK1A1 0.014 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.02 0.054 -10000 0 -0.17 25 25
NFATc/ERK1 0.037 0.073 0.27 5 -0.28 2 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.003 0.12 -10000 0 -0.28 37 37
NR4A1 0.005 0.089 0.19 12 -0.31 13 25
GSK3B 0.027 0.007 -10000 0 -10000 0 0
positive T cell selection 0.019 0.009 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0 0.051 -10000 0 -0.17 12 12
RCH1/ KPNB1 0.04 0.015 -10000 0 -0.14 2 2
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
AKAP5 0.022 0.037 -10000 0 -0.22 8 8
MEF2D 0.026 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.038 0.074 0.27 5 -0.28 2 7
CREBBP 0.027 0.008 -10000 0 -10000 0 0
BCL2 0.016 0.056 -10000 0 -0.32 10 10
Paxillin-dependent events mediated by a4b1

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
CRKL 0.028 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.012 -10000 0 -10000 0 0
DOCK1 0.024 0.031 -10000 0 -0.32 3 3
ITGA4 0.01 0.07 -10000 0 -0.27 21 21
RAC1 0.026 0.008 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.021 0.068 -10000 0 -0.21 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.051 -10000 0 -0.18 12 12
alpha4/beta7 Integrin/Paxillin 0.028 0.057 -10000 0 -0.17 23 23
lamellipodium assembly -0.012 0.12 -10000 0 -0.41 23 23
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
PI3K 0.032 0.038 -10000 0 -0.23 6 6
ARF6 0.028 0.004 -10000 0 -10000 0 0
TLN1 0.028 0.005 -10000 0 -10000 0 0
PXN 0.014 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
ARF6/GTP 0.049 0.041 -10000 0 -10000 0 0
cell adhesion 0.049 0.042 -10000 0 -0.16 11 11
CRKL/CBL 0.039 0.017 -10000 0 -0.22 1 1
alpha4/beta1 Integrin/Paxillin 0.033 0.045 -10000 0 -0.16 12 12
ITGB1 0.028 0.004 -10000 0 -10000 0 0
ITGB7 0.016 0.059 -10000 0 -0.29 13 13
ARF6/GDP 0.027 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.046 0.054 -10000 0 -0.17 17 17
p130Cas/Crk/Dock1 0.042 0.032 -10000 0 -0.18 3 3
VCAM1 0.021 0.043 -10000 0 -0.24 9 9
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.043 -10000 0 -0.16 11 11
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.044 -10000 0 -0.16 12 12
BCAR1 0.023 0.011 -10000 0 -10000 0 0
mol:GDP -0.049 0.043 0.16 12 -10000 0 12
CBL 0.026 0.019 -10000 0 -0.32 1 1
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.043 -10000 0 -0.16 11 11
Rac1/GTP -0.014 0.13 -10000 0 -0.46 23 23
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.034 0.067 -10000 0 -0.36 1 1
Syndecan-3/Neurocan 0.034 0.028 -10000 0 -0.38 1 1
POMC -0.014 0.11 -10000 0 -0.3 46 46
EGFR -0.007 0.1 -10000 0 -0.32 36 36
Syndecan-3/EGFR 0.014 0.053 -10000 0 -0.38 1 1
AGRP 0.019 0.015 -10000 0 -0.21 1 1
NCSTN 0.027 0.007 -10000 0 -10000 0 0
PSENEN 0.028 0.003 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.028 0.004 -10000 0 -10000 0 0
APH1A 0.027 0.006 -10000 0 -10000 0 0
NCAN 0.007 0.062 -10000 0 -0.21 29 29
long-term memory 0.042 0.03 -10000 0 -0.33 1 1
Syndecan-3/IL8 0.023 0.049 -10000 0 -0.38 1 1
PSEN1 0.028 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.039 0.011 -10000 0 -10000 0 0
FYN 0.024 0.01 -10000 0 -10000 0 0
limb bud formation 0.013 0.021 -10000 0 -0.39 1 1
MC4R 0.018 0.014 -10000 0 -0.21 1 1
SRC 0.027 0.006 -10000 0 -10000 0 0
PTN -0.021 0.12 -10000 0 -0.31 51 51
FGFR/FGF/Syndecan-3 0.013 0.021 -10000 0 -0.39 1 1
neuron projection morphogenesis 0.007 0.072 0.28 4 -0.35 1 5
Syndecan-3/AgRP 0.025 0.024 -10000 0 -0.35 1 1
Syndecan-3/AgRP/MC4R 0.034 0.028 -10000 0 -0.32 1 1
Fyn/Cortactin 0.035 0.016 -10000 0 -10000 0 0
SDC3 0.013 0.022 -10000 0 -0.39 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.024 0.047 -10000 0 -0.37 1 1
IL8 -0.01 0.1 -10000 0 -0.26 48 48
Syndecan-3/Fyn/Cortactin 0.043 0.031 -10000 0 -0.34 1 1
Syndecan-3/CASK 0.012 0.02 -10000 0 -0.37 1 1
alpha-MSH/MC4R 0.002 0.08 -10000 0 -0.21 46 46
Gamma Secretase 0.075 0.027 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.006 0.088 -10000 0 -0.25 43 43
KLHL20 0.02 0.045 0.16 6 -0.18 1 7
CYFIP2 0.028 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.06 0.28 6 -10000 0 6
ENAH -0.004 0.085 -10000 0 -0.25 40 40
AP1M1 0.028 0.003 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.018 -10000 0 -0.32 1 1
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.024 0.025 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.019 -10000 0 -0.13 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.053 0.044 -10000 0 -0.15 9 9
RAPGEF1 -0.002 0.077 0.21 7 -0.22 23 30
CTNND1 0.028 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.093 -10000 0 -0.25 44 44
CRK -0.002 0.074 -10000 0 -0.24 31 31
E-cadherin/gamma catenin/alpha catenin 0.047 0.022 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.03 0.045 -10000 0 -0.19 13 13
IQGAP1 0.028 0.003 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.02 -10000 0 -0.16 1 1
DLG1 -0.004 0.084 -10000 0 -0.25 39 39
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.003 0.019 -10000 0 -0.22 1 1
MLLT4 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.046 0.032 -10000 0 -0.11 12 12
PI3K 0.007 0.025 -10000 0 -0.28 1 1
ARF6 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.036 0.015 -10000 0 -10000 0 0
TIAM1 0.025 0.028 -10000 0 -0.28 3 3
E-cadherin(dimer)/Ca2+ 0.054 0.027 -10000 0 -10000 0 0
AKT1 0.009 0.027 0.097 11 -0.16 1 12
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
CDH1 0.024 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.063 0.25 9 -10000 0 9
actin cytoskeleton organization 0.019 0.041 0.17 9 -0.14 1 10
CDC42/GDP 0.028 0.069 0.26 14 -10000 0 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.018 0.009 -10000 0 -10000 0 0
ITGB7 0.016 0.059 -10000 0 -0.29 13 13
RAC1 0.026 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.059 0.029 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.041 0.02 -10000 0 -10000 0 0
mol:GDP 0.015 0.073 0.26 15 -10000 0 15
CDC42/GTP/IQGAP1 0.038 0.006 -10000 0 -10000 0 0
JUP 0.028 0.004 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.031 0.061 0.33 3 -10000 0 3
RAC1/GTP/IQGAP1 0.035 0.011 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.04 0.009 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
CDC42 0.028 0.003 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.017 0.037 0.16 10 -10000 0 10
NME1 0.021 0.04 -10000 0 -0.21 11 11
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.003 0.085 -10000 0 -0.25 39 39
regulation of cell-cell adhesion 0.015 0.019 -10000 0 -10000 0 0
WASF2 0.01 0.021 0.084 4 -10000 0 4
Rap1/GTP 0.028 0.035 0.19 7 -10000 0 7
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.048 -10000 0 -0.15 7 7
CCND1 0.02 0.043 0.2 9 -10000 0 9
VAV2 0.014 0.091 0.33 1 -0.54 1 2
RAP1/GDP 0.036 0.048 0.22 10 -10000 0 10
adherens junction assembly -0.003 0.083 -10000 0 -0.24 39 39
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.028 0.004 -10000 0 -10000 0 0
PIP5K1C 0.027 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.047 0.042 0.19 4 -0.15 6 10
E-cadherin/beta catenin 0.012 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.005 0.087 -10000 0 -0.25 42 42
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
Rac1/GTP 0.003 0.046 -10000 0 -0.28 1 1
E-cadherin/beta catenin/alpha catenin 0.047 0.023 -10000 0 -10000 0 0
ITGAE 0.026 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.095 -10000 0 -0.26 44 44
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.026 0.049 0.21 4 -0.28 2 6
PDGFB-D/PDGFRB/SLAP 0.029 0.034 -10000 0 -0.15 9 9
PDGFB-D/PDGFRB/APS/CBL 0.044 0.038 -10000 0 -0.13 11 11
AKT1 0.021 0.088 0.24 31 -0.25 1 32
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.03 0.06 0.27 3 -0.3 3 6
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
FGR 0.015 0.053 0.3 1 -0.39 4 5
mol:Ca2+ 0.016 0.063 0.25 3 -0.37 3 6
MYC 0.057 0.12 0.34 36 -10000 0 36
SHC1 0.027 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.032 0.037 0.17 15 -0.19 2 17
LRP1/PDGFRB/PDGFB 0.053 0.022 -10000 0 -0.14 3 3
GRB10 0.026 0.008 -10000 0 -10000 0 0
PTPN11 0.026 0.019 -10000 0 -0.32 1 1
GO:0007205 0.015 0.063 0.28 2 -0.37 3 5
PTEN 0.023 0.011 -10000 0 -10000 0 0
GRB2 0.027 0.006 -10000 0 -10000 0 0
GRB7 0.028 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.039 0.019 -10000 0 -0.18 2 2
PDGFB-D/PDGFRB/GRB10 0.038 0.015 -10000 0 -0.13 1 1
cell cycle arrest 0.029 0.034 -10000 0 -0.15 9 9
HRAS 0.025 0.027 -10000 0 -0.21 5 5
HIF1A 0.016 0.083 0.22 32 -0.27 2 34
GAB1 0.014 0.072 0.31 2 -0.29 6 8
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.014 0.064 0.26 6 -0.26 3 9
PDGFB-D/PDGFRB 0.052 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.04 0.013 -10000 0 -0.13 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.032 0.036 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.038 0.019 -10000 0 -0.18 2 2
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
mol:IP3 0.016 0.063 0.28 2 -0.38 3 5
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.028 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.04 0.012 -10000 0 -0.13 1 1
SHB 0.026 0.019 -10000 0 -0.32 1 1
BLK -0.11 0.2 0.3 1 -0.41 112 113
PTPN2 0.027 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.04 0.013 -10000 0 -0.13 1 1
BCAR1 0.023 0.011 -10000 0 -10000 0 0
VAV2 0.019 0.077 0.28 5 -0.27 8 13
CBL 0.026 0.019 -10000 0 -0.32 1 1
PDGFB-D/PDGFRB/DEP1 0.04 0.013 -10000 0 -0.13 1 1
LCK 0.018 0.037 0.3 1 -0.35 1 2
PDGFRB 0.028 0.013 -10000 0 -0.2 1 1
ACP1 0.028 0.004 -10000 0 -10000 0 0
HCK 0.016 0.064 0.3 1 -0.47 5 6
ABL1 0.005 0.074 0.25 5 -0.26 10 15
PDGFB-D/PDGFRB/CBL 0.01 0.078 0.42 1 -0.32 8 9
PTPN1 0.028 0.006 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.027 0.006 -10000 0 -10000 0 0
STAT1 0.024 0.03 -10000 0 -0.21 6 6
cell proliferation 0.057 0.12 0.32 38 -10000 0 38
SLA 0.017 0.037 -10000 0 -0.21 9 9
actin cytoskeleton reorganization 0.047 0.06 0.21 36 -10000 0 36
SRC 0.01 0.069 0.3 1 -0.43 7 8
PI3K 0.003 0.028 -10000 0 -0.24 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.053 0.018 -10000 0 -0.11 1 1
SH2B2 0.018 0.042 -10000 0 -0.22 11 11
PLCgamma1/SPHK1 0.031 0.061 0.27 3 -0.31 3 6
LYN 0.009 0.059 0.3 1 -0.39 6 7
LRP1 0.026 0.022 -10000 0 -0.26 2 2
SOS1 0.027 0.006 -10000 0 -10000 0 0
STAT5B 0.027 0.006 -10000 0 -10000 0 0
STAT5A 0.026 0.019 -10000 0 -0.32 1 1
NCK1-2/p130 Cas 0.061 0.041 -10000 0 -10000 0 0
SPHK1 0.017 0.049 -10000 0 -0.21 16 16
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.016 0.063 0.28 2 -0.38 3 5
PLCG1 0.016 0.064 0.28 2 -0.38 3 5
NHERF/PDGFRB 0.05 0.027 -10000 0 -0.12 2 2
YES1 -0.004 0.12 0.3 1 -0.52 16 17
cell migration 0.049 0.027 -10000 0 -0.12 2 2
SHC/Grb2/SOS1 0.071 0.034 -10000 0 -10000 0 0
SLC9A3R2 0.024 0.027 -10000 0 -0.21 5 5
SLC9A3R1 0.027 0.005 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.055 0.034 -10000 0 -10000 0 0
FYN -0.031 0.13 0.3 1 -0.36 48 49
DOK1 0.022 0.035 0.18 17 -10000 0 17
HRAS/GTP 0.019 0.018 -10000 0 -0.14 5 5
PDGFB 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.03 0.089 0.3 13 -0.3 3 16
PRKCD 0.022 0.036 0.18 18 -10000 0 18
FER 0.014 0.044 0.18 13 -0.17 10 23
MAPKKK cascade 0.009 0.075 0.28 16 -10000 0 16
RASA1 0.02 0.038 0.18 17 -0.17 2 19
NCK1 0.026 0.008 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.038 0.031 0.17 16 -10000 0 16
PDGFB-D/PDGFRB/SHB 0.039 0.019 -10000 0 -0.18 2 2
chemotaxis 0.006 0.073 0.24 5 -0.25 10 15
STAT1-3-5/STAT1-3-5 0.061 0.029 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.02 0.009 -10000 0 -0.13 1 1
PTPRJ 0.028 0.005 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.014 0.049 0.15 13 -0.22 5 18
adherens junction organization 0 0.059 0.15 2 -0.23 8 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.01 0.069 0.24 1 -0.31 3 4
FMN1 -0.009 0.069 0.15 2 -0.23 15 17
mol:IP3 0.011 0.037 -10000 0 -0.21 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.009 0.058 0.16 1 -0.23 8 9
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
AKT1 0.012 0.045 0.18 1 -0.22 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.1 -10000 0 -0.62 4 4
CTNND1 0.029 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.005 0.053 0.15 1 -0.24 6 7
VASP 0.005 0.056 0.15 2 -0.23 7 9
ZYX 0.005 0.052 -10000 0 -0.24 6 6
JUB 0.006 0.055 0.15 2 -0.22 8 10
EGFR(dimer) 0.012 0.074 -10000 0 -0.24 17 17
E-cadherin/beta catenin-gamma catenin 0.047 0.021 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.031 0.052 0.21 2 -0.23 3 5
PIK3CA 0.024 0.034 -10000 0 -0.29 4 4
PI3K 0.031 0.053 0.22 2 -0.23 3 5
FYN 0.007 0.051 0.18 5 -0.26 3 8
mol:Ca2+ 0.011 0.036 -10000 0 -0.21 3 3
JUP 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.032 -10000 0 -0.32 3 3
mol:DAG 0.011 0.037 -10000 0 -0.21 3 3
CDH1 0.024 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.075 0.18 14 -0.28 4 18
establishment of polarity of embryonic epithelium 0.005 0.055 0.15 2 -0.23 7 9
SRC 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
EGFR -0.007 0.1 -10000 0 -0.32 36 36
CASR 0.007 0.039 0.16 8 -0.2 3 11
RhoA/GTP 0.026 0.046 -10000 0 -0.19 3 3
AKT2 0.012 0.045 0.18 1 -0.22 3 4
actin cable formation -0.011 0.068 0.17 4 -0.24 12 16
apoptosis -0.014 0.051 0.24 3 -0.15 13 16
CTNNA1 0.028 0.006 -10000 0 -10000 0 0
mol:GDP -0.003 0.063 0.16 10 -0.27 5 15
PIP5K1A 0.005 0.053 0.15 1 -0.24 6 7
PLCG1 0.011 0.037 -10000 0 -0.21 3 3
Rac1/GTP 0.014 0.081 -10000 0 -0.23 16 16
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.034 0.033 -10000 0 -0.14 12 12
FBXW11 0.028 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.002 0.065 0.2 1 -0.18 42 43
NF kappa B1 p50/RelA/I kappa B alpha 0.029 0.031 0.19 1 -10000 0 1
NFKBIA 0.015 0.024 0.12 9 -0.16 3 12
MAPK14 0.028 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0.016 0.2 1 -10000 0 1
ARRB2 0.014 0.005 -10000 0 -10000 0 0
REL -0.011 0.11 -10000 0 -0.32 42 42
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.03 0.2 2 -0.12 10 12
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0.016 0.2 1 -10000 0 1
PIK3CA 0.023 0.034 -10000 0 -0.29 4 4
NF kappa B1 p50 dimer 0.018 0.015 0.25 1 -10000 0 1
PIK3R1 0.023 0.032 -10000 0 -0.32 3 3
NFKB1 0.012 0.014 0.26 1 -10000 0 1
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.018 0.029 -10000 0 -0.16 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.03 0.031 -10000 0 -10000 0 0
SRC 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.032 0.038 -10000 0 -0.23 6 6
NF kappa B1 p50/RelA 0.018 0.029 -10000 0 -0.17 2 2
IKBKB 0.022 0.012 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 -10000 0 0
SYK 0.023 0.038 -10000 0 -0.29 5 5
I kappa B alpha/PIK3R1 0.031 0.033 0.19 3 -0.15 3 6
cell death 0.029 0.03 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.002 0.065 0.2 1 -0.18 42 43
LCK 0.024 0.03 -10000 0 -0.21 6 6
BCL3 0.02 0.042 -10000 0 -0.21 12 12
Regulation of Telomerase

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
Telomerase catalytic core complex 0 0.089 0.45 1 -0.48 1 2
RAD9A 0.027 0.013 -10000 0 -0.21 1 1
AP1 0 0.095 -10000 0 -0.22 56 56
IFNAR2 0.028 0.005 -10000 0 -10000 0 0
AKT1 0.013 0.032 -10000 0 -0.16 9 9
ER alpha/Oestrogen 0.012 0.044 -10000 0 -0.21 14 14
NFX1/SIN3/HDAC complex 0.026 0.028 -10000 0 -0.23 1 1
EGF 0 0.082 -10000 0 -0.23 40 40
SMG5 0.027 0.006 -10000 0 -10000 0 0
SMG6 0.026 0.008 -10000 0 -10000 0 0
SP3/HDAC2 0.035 0.016 -10000 0 -10000 0 0
TERT/c-Abl 0.009 0.083 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
MRN complex 0.044 0.024 -10000 0 -10000 0 0
WT1 -0.08 0.13 -10000 0 -0.22 156 156
WRN 0.022 0.012 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
SP3 0.027 0.006 -10000 0 -10000 0 0
TERF2IP 0.023 0.011 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.024 0.087 -10000 0 -0.43 1 1
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT 0 0.09 0.45 1 -0.49 1 2
CCND1 0.006 0.094 0.56 2 -10000 0 2
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
RBBP4 0.026 0.025 -10000 0 -0.32 2 2
TERF2 0.021 0.011 -10000 0 -10000 0 0
PTGES3 0.028 0.004 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
Telomerase/911 0.034 0.044 -10000 0 -10000 0 0
CDKN1B 0.009 0.037 -10000 0 -0.21 4 4
RAD1 0.027 0.006 -10000 0 -10000 0 0
XRCC5 0.028 0.004 -10000 0 -10000 0 0
XRCC6 0.028 0.004 -10000 0 -10000 0 0
SAP30 0.028 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.034 0.015 -10000 0 -10000 0 0
UBE3A 0.027 0.005 -10000 0 -10000 0 0
JUN 0.024 0.033 -10000 0 -0.29 4 4
E6 0 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.004 -10000 0 -10000 0 0
FOS -0.023 0.12 -10000 0 -0.31 55 55
IFN-gamma/IRF1 0.028 0.053 -10000 0 -0.18 9 9
PARP2 0.028 0.004 -10000 0 -10000 0 0
BLM 0.016 0.052 -10000 0 -0.21 19 19
Telomerase 0.016 0.036 -10000 0 -0.25 1 1
IRF1 0.022 0.041 -10000 0 -0.2 12 12
ESR1 0.015 0.064 -10000 0 -0.31 14 14
KU/TER 0.041 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.021 -10000 0 -0.22 1 1
ubiquitin-dependent protein catabolic process 0.03 0.034 -10000 0 -0.28 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.031 0.034 -10000 0 -0.28 1 1
HDAC1 0.028 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.01 -10000 0 -10000 0 0
ATM 0.016 0.025 -10000 0 -0.3 1 1
SMAD3 0.014 0.002 -10000 0 -10000 0 0
ABL1 0.027 0.007 -10000 0 -10000 0 0
MXD1 0.028 0.004 -10000 0 -10000 0 0
MRE11A 0.027 0.005 -10000 0 -10000 0 0
HUS1 0.026 0.008 -10000 0 -10000 0 0
RPS6KB1 0.027 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.022 0.093 -10000 0 -0.57 1 1
NR2F2 0.028 0.004 -10000 0 -10000 0 0
MAPK3 0 0.013 -10000 0 -10000 0 0
MAPK1 0 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.028 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.003 -10000 0 -10000 0 0
HNRNPC 0.028 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.016 0.025 -10000 0 -0.3 1 1
NBN 0.023 0.011 -10000 0 -10000 0 0
EGFR -0.007 0.1 -10000 0 -0.32 36 36
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.094 -10000 0 -0.2 67 67
MYC 0.008 0.056 -10000 0 -0.21 23 23
IL2 0.016 0.017 -10000 0 -10000 0 0
KU 0.041 0.008 -10000 0 -10000 0 0
RAD50 0.027 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
TGFB1 0.028 0.003 -10000 0 -10000 0 0
TRF2/BLM 0.03 0.03 0.15 1 -0.13 9 10
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.019 0.095 0.42 1 -0.46 1 2
SP1/HDAC2 0.035 0.016 -10000 0 -10000 0 0
PINX1 0.021 0.012 -10000 0 -10000 0 0
Telomerase/EST1A 0.023 0.086 -10000 0 -0.43 1 1
Smad3/Myc 0.016 0.036 -10000 0 -0.11 23 23
911 complex 0.05 0.021 -10000 0 -10000 0 0
IFNG 0.015 0.052 -10000 0 -0.2 20 20
Telomerase/PinX1 0.016 0.081 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.02 0.056 0.27 1 -0.31 2 3
SIN3B 0.028 0.003 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
Telomerase/EST1B 0.024 0.086 -10000 0 -0.43 1 1
response to DNA damage stimulus 0.006 0.02 0.13 1 -0.11 6 7
MRN complex/TRF2/Rap1 0.055 0.038 -10000 0 -10000 0 0
TRF2/WRN 0.029 0.019 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.024 0.088 -10000 0 -0.43 1 1
E2F1 0.018 0.046 -10000 0 -0.21 15 15
ZNFX1 0.027 0.006 -10000 0 -10000 0 0
PIF1 0.023 0.035 -10000 0 -0.22 7 7
NCL 0.028 0.003 -10000 0 -10000 0 0
DKC1 0.028 0.001 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.012 -10000 0 -0.087 1 1
TRAF2/ASK1 0.035 0.012 -10000 0 -0.11 1 1
ATM 0.026 0.019 -10000 0 -0.32 1 1
MAP2K3 -0.017 0.1 0.22 4 -0.3 31 35
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.01 0.087 0.27 2 -0.29 17 19
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.005 0.081 -10000 0 -0.21 50 50
TXN 0.007 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.026 0.025 -10000 0 -0.32 2 2
GADD45B 0.017 0.048 -10000 0 -0.21 16 16
MAP3K1 0.025 0.02 -10000 0 -0.32 1 1
MAP3K6 0.028 0.003 -10000 0 -10000 0 0
MAP3K7 0.023 0.011 -10000 0 -10000 0 0
MAP3K4 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.04 0.012 -10000 0 -0.14 1 1
TAK1/TAB family -0.002 0.013 -10000 0 -0.13 2 2
RAC1/OSM/MEKK3 0.048 0.018 -10000 0 -10000 0 0
TRAF2 0.027 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.002 0.085 -10000 0 -0.28 16 16
TRAF6 0.008 0.001 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.014 0.052 -10000 0 -0.21 18 18
CCM2 0.026 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.027 0.034 -10000 0 -0.12 16 16
MAPK11 0.023 0.032 -10000 0 -0.21 7 7
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.04 0.038 -10000 0 -0.11 17 17
OSM/MEKK3 0.037 0.013 -10000 0 -10000 0 0
TAOK1 -0.031 0.098 -10000 0 -0.24 66 66
TAOK2 0.014 0.014 -10000 0 -0.24 1 1
TAOK3 0.014 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.028 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.013 -10000 0 -0.21 1 1
MAP3K10 0.028 0.003 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.024 0.013 -10000 0 -0.1 1 1
GADD45/MTK1/MTK1 0.057 0.053 0.18 2 -0.17 13 15
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.083 0.23 11 -0.23 4 15
ERC1 0.027 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.04 -10000 0 -0.2 9 9
NFKBIA 0.015 0.025 0.21 6 -10000 0 6
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.022 0.012 -10000 0 -10000 0 0
RIPK2 0.023 0.011 -10000 0 -10000 0 0
IKBKG 0.021 0.028 -10000 0 -10000 0 0
IKK complex/A20 0.028 0.099 0.25 2 -0.28 18 20
NEMO/A20/RIP2 0.023 0.011 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.022 0.095 0.26 1 -0.29 19 20
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.024 0.084 -10000 0 -0.27 17 17
BCL10/MALT1/TRAF6 0.05 0.02 -10000 0 -10000 0 0
NOD2 0.016 0.056 -10000 0 -0.3 11 11
NFKB1 0.03 0.003 -10000 0 -10000 0 0
RELA 0.029 0.006 -10000 0 -10000 0 0
MALT1 0.025 0.009 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.04 0.009 -10000 0 -10000 0 0
ATM 0.026 0.019 -10000 0 -0.32 1 1
TNF/TNFR1A 0.018 0.066 -10000 0 -0.19 32 32
TRAF6 0.028 0.004 -10000 0 -10000 0 0
PRKCA 0.016 0.063 -10000 0 -0.32 13 13
CHUK 0.027 0.007 -10000 0 -10000 0 0
UBE2D3 0.028 0.003 -10000 0 -10000 0 0
TNF 0.001 0.087 -10000 0 -0.28 32 32
NF kappa B1 p50/RelA 0.061 0.015 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.025 0.21 6 -10000 0 6
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.008 -10000 0 -10000 0 0
IKK complex 0.028 0.09 0.25 2 -0.28 18 20
CYLD 0.025 0.009 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.031 0.096 -10000 0 -0.28 19 19
FoxO family signaling

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
G6PC 0 0.05 -10000 0 -10000 0 0
PLK1 -0.007 0.14 -10000 0 -0.92 2 2
CDKN1B 0.041 0.092 0.43 2 -0.35 3 5
FOXO3 0 0.14 -10000 0 -0.66 6 6
KAT2B 0.03 0.016 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.052 0.28 1 -0.19 1 2
CAT -0.001 0.13 -10000 0 -0.88 2 2
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
AKT1 0.031 0.016 -10000 0 -10000 0 0
FOXO1 0.006 0.054 0.26 2 -0.2 1 3
MAPK10 0.031 0.043 0.19 23 -0.16 1 24
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.053 0.076 0.29 11 -0.35 3 14
response to oxidative stress 0.005 0.008 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.009 0.13 -10000 0 -0.66 4 4
XPO1 0.028 0.004 -10000 0 -10000 0 0
EP300 0.026 0.031 -10000 0 -0.32 3 3
BCL2L11 0.007 0.14 -10000 0 -0.86 8 8
FOXO1/SKP2 0.015 0.055 -10000 0 -0.23 4 4
mol:GDP 0.005 0.008 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.036 0.13 -10000 0 -0.64 9 9
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.07 0.22 2 -0.5 1 3
MST1 0.004 0.077 -10000 0 -0.21 42 42
CSNK1D 0.028 0.005 -10000 0 -10000 0 0
CSNK1E 0.028 0.003 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.017 0.093 -10000 0 -0.42 8 8
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.046 0.19 22 -0.18 4 26
MAPK9 0.031 0.042 0.19 23 -10000 0 23
YWHAG 0.026 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
SIRT1 0.027 0.011 -10000 0 -10000 0 0
SOD2 0.036 0.098 0.43 1 -0.54 1 2
RBL2 -0.04 0.26 -10000 0 -0.73 36 36
RAL/GDP 0.039 0.018 -10000 0 -10000 0 0
CHUK 0.029 0.015 -10000 0 -10000 0 0
Ran/GTP 0.022 0.007 -10000 0 -10000 0 0
CSNK1G2 0.028 0.005 -10000 0 -10000 0 0
RAL/GTP 0.041 0.019 -10000 0 -10000 0 0
CSNK1G1 0.028 0.004 -10000 0 -10000 0 0
FASLG -0.025 0.24 -10000 0 -1.1 17 17
SKP2 0.021 0.047 -10000 0 -0.32 7 7
USP7 0.028 0.005 -10000 0 -10000 0 0
IKBKB 0.024 0.018 -10000 0 -10000 0 0
CCNB1 -0.004 0.13 -10000 0 -0.91 2 2
FOXO1-3a-4/beta catenin 0.053 0.1 0.34 5 -0.41 6 11
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.055 -10000 0 -0.23 4 4
CSNK1A1 0.028 0.004 -10000 0 -10000 0 0
SGK1 -0.021 0.12 -10000 0 -0.3 57 57
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.011 -10000 0 -10000 0 0
ZFAND5 0.054 0.079 0.43 4 -10000 0 4
SFN 0.002 0.091 -10000 0 -0.32 28 28
CDK2 0.027 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.014 0.1 -10000 0 -0.45 9 9
CREBBP 0.027 0.007 -10000 0 -10000 0 0
FBXO32 0.029 0.16 0.51 1 -1 3 4
BCL6 0.015 0.14 -10000 0 -0.66 9 9
RALB 0.028 0.006 -10000 0 -10000 0 0
RALA 0.027 0.008 -10000 0 -10000 0 0
YWHAH 0.028 0.004 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.025 0.027 0.2 5 -10000 0 5
PI3K Class IB/PDE3B 0.025 0.027 -10000 0 -0.21 5 5
PDE3B 0.025 0.027 -10000 0 -0.21 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.061 0.035 -10000 0 -0.16 5 5
HDAC3 0.027 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -10000 0 -10000 0 0
GATA1/HDAC4 0.039 0.018 -10000 0 -0.18 2 2
GATA1/HDAC5 0.037 0.019 -10000 0 -0.16 2 2
GATA2/HDAC5 0.035 0.016 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.02 -10000 0 -10000 0 0
HDAC9 0.002 0.082 -10000 0 -0.28 28 28
Glucocorticoid receptor/Hsp90/HDAC6 0.049 0.037 -10000 0 -0.18 8 8
HDAC4/ANKRA2 0.038 0.012 -10000 0 -10000 0 0
HDAC5/YWHAB 0.037 0.013 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.006 -10000 0 -10000 0 0
GATA2 0.026 0.008 -10000 0 -10000 0 0
HDAC4/RFXANK 0.038 0.024 -10000 0 -0.14 6 6
BCOR 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.025 0.027 -10000 0 -0.21 5 5
HDAC5 0.026 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.031 -10000 0 -0.22 5 5
Histones 0.02 0.054 0.22 1 -0.24 3 4
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
HDAC4 0.028 0.004 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.036 0.015 -10000 0 -10000 0 0
HDAC4/Ubc9 0.04 0.01 -10000 0 -10000 0 0
HDAC7 0.028 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.036 0.015 -10000 0 -10000 0 0
TUBA1B 0.028 0.003 -10000 0 -10000 0 0
HDAC6 0.028 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.036 0.025 -10000 0 -0.14 6 6
CAMK4 0.002 0.087 -10000 0 -0.31 26 26
Tubulin/HDAC6 0.038 0.053 -10000 0 -0.12 38 38
SUMO1 0.028 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
GATA1 0.025 0.022 -10000 0 -0.26 2 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
NR3C1 0.019 0.053 -10000 0 -0.32 9 9
SUMO1/HDAC4 0.045 0.023 -10000 0 -10000 0 0
SRF 0.028 0.003 -10000 0 -10000 0 0
HDAC4/YWHAB 0.04 0.01 -10000 0 -10000 0 0
Tubulin 0.022 0.055 -10000 0 -0.14 38 38
HDAC4/14-3-3 E 0.038 0.012 -10000 0 -10000 0 0
GNB1 0.028 0.004 -10000 0 -10000 0 0
RANGAP1 0.026 0.021 -10000 0 -0.21 3 3
BCL6/BCoR 0.039 0.011 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.017 -10000 0 -10000 0 0
HDAC4/SRF 0.035 0.061 -10000 0 -0.18 25 25
HDAC4/ER alpha 0.031 0.048 -10000 0 -0.21 14 14
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.02 0.054 0.21 1 -0.24 3 4
cell motility 0.037 0.052 -10000 0 -0.11 38 38
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.04 0.009 -10000 0 -10000 0 0
BCL6 0.026 0.007 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.028 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.041 0.007 -10000 0 -10000 0 0
ESR1 0.015 0.064 -10000 0 -0.31 14 14
HDAC6/HDAC11 0.041 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0.026 -10000 0 -10000 0 0
NPC 0.016 0.006 -10000 0 -10000 0 0
MEF2C 0.023 0.033 -10000 0 -0.29 4 4
RAN 0.027 0.006 -10000 0 -10000 0 0
HDAC4/MEF2C 0.069 0.037 -10000 0 -0.15 3 3
GNG2 0.023 0.04 -10000 0 -0.32 5 5
NCOR2 0.027 0.006 -10000 0 -10000 0 0
TUBB2A 0.004 0.071 -10000 0 -0.21 38 38
HDAC11 0.028 0.005 -10000 0 -10000 0 0
HSP90AA1 0.028 0.005 -10000 0 -10000 0 0
RANBP2 0.027 0.013 -10000 0 -0.21 1 1
ANKRA2 0.026 0.008 -10000 0 -10000 0 0
RFXANK 0.024 0.03 -10000 0 -0.21 6 6
nuclear import -0.031 0.015 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.023 0.032 -9999 0 -0.32 3 3
PLK4 0.026 0.018 -9999 0 -0.21 2 2
regulation of centriole replication 0.01 0.023 -9999 0 -0.2 4 4
Circadian rhythm pathway

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
chromatin modification 0.04 0.033 -9999 0 -10000 0 0
CLOCK -0.004 0.1 -9999 0 -0.31 37 37
TIMELESS/CRY2 0.032 0.026 -9999 0 -10000 0 0
DEC1/BMAL1 0.033 0.017 -9999 0 -0.22 1 1
ATR 0.026 0.008 -9999 0 -10000 0 0
NR1D1 0.016 0.018 -9999 0 -10000 0 0
ARNTL 0.029 0.018 -9999 0 -0.31 1 1
TIMELESS 0.016 0.018 -9999 0 -10000 0 0
NPAS2 0.03 0.003 -9999 0 -10000 0 0
CRY2 0.028 0.004 -9999 0 -10000 0 0
mol:CO -0.008 0.001 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.008 0.001 -9999 0 -10000 0 0
PER1 0.019 0.047 -9999 0 -0.32 7 7
BMAL/CLOCK/NPAS2 0.04 0.074 -9999 0 -0.18 37 37
BMAL1/CLOCK -0.006 0.1 -9999 0 -0.48 1 1
S phase of mitotic cell cycle 0.04 0.033 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.041 0.033 -9999 0 -10000 0 0
mol:NADPH 0.008 0.001 -9999 0 -10000 0 0
PER1/TIMELESS 0.028 0.028 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.018 0.006 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.025 0.023 -10000 0 -0.26 2 2
positive regulation of NF-kappaB transcription factor activity 0.023 0.039 -10000 0 -0.2 8 8
MAP2K4 0.015 0.023 -10000 0 -10000 0 0
IKBKB 0.022 0.012 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.013 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.028 -10000 0 -0.32 2 2
SMPD1 0.011 0.01 0.13 1 -10000 0 1
IKBKG 0.028 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.013 0.05 -10000 0 -0.32 8 8
TRAIL/TRAILR2 0.027 0.024 -10000 0 -0.16 2 2
TRAIL/TRAILR3 0.018 0.05 -10000 0 -0.2 15 15
TRAIL/TRAILR1 0.025 0.03 -10000 0 -0.19 4 4
TRAIL/TRAILR4 0.023 0.039 -10000 0 -0.2 8 8
TRAIL/TRAILR1/DAP3/GTP 0.033 0.032 -10000 0 -0.14 4 4
IKK complex 0.019 0.038 -10000 0 -0.26 1 1
RIPK1 0.028 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.013 0.023 0.26 2 -0.18 2 4
MAP3K1 0.019 0.027 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.013 0.05 -10000 0 -0.31 8 8
TRADD 0.025 0.009 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.028 -10000 0 -0.31 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.02 0.023 0.15 1 -0.17 2 3
CFLAR 0.028 0.003 -10000 0 -10000 0 0
MAPK1 0.014 0.02 0.26 2 -0.14 1 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.051 0.045 -10000 0 -0.16 2 2
mol:ceramide 0.011 0.01 0.13 1 -10000 0 1
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.012 0.038 -10000 0 -0.2 4 4
TRAF2 0.027 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.008 0.062 -10000 0 -0.31 13 13
CHUK 0.027 0.007 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.036 0.034 -10000 0 -0.16 4 4
DAP3 0.027 0.006 -10000 0 -10000 0 0
CASP10 0.016 0.055 0.19 24 -0.22 3 27
JNK cascade 0.023 0.039 -10000 0 -0.2 8 8
TRAIL (trimer) 0.025 0.023 -10000 0 -0.26 2 2
TNFRSF10C 0.008 0.062 -10000 0 -0.31 13 13
TRAIL/TRAILR1/DAP3/GTP/FADD 0.042 0.037 0.18 1 -0.14 3 4
TRAIL/TRAILR2/FADD 0.037 0.03 -10000 0 -0.15 1 1
cell death 0.011 0.01 0.13 1 -10000 0 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.021 0.018 0.15 1 -10000 0 1
TRAILR2 (trimer) 0.02 0.013 -10000 0 -10000 0 0
CASP8 0.015 0.014 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.053 0.042 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.047 0.073 -10000 0 -0.21 19 19
Ran/GTP/Exportin 1/HDAC1 0.007 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.074 -10000 0 -0.22 20 20
SUMO1 0.028 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.011 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.006 -10000 0 -10000 0 0
FKBP3 0.028 0.003 -10000 0 -10000 0 0
Histones 0.046 0.051 -10000 0 -10000 0 0
YY1/LSF 0.032 0.036 -10000 0 -0.18 4 4
SMG5 0.027 0.006 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.014 0.047 -10000 0 -0.17 20 20
I kappa B alpha/HDAC1 0.025 0.043 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
RELA 0.01 0.049 -10000 0 -0.16 22 22
HDAC1/Smad7 0.047 0.022 -10000 0 -10000 0 0
RANGAP1 0.026 0.021 -10000 0 -0.21 3 3
HDAC3/TR2 0.024 0.043 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.02 0.041 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.063 0.23 3 -0.19 3 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.026 0.008 -10000 0 -10000 0 0
GATA1 0.025 0.022 -10000 0 -0.26 2 2
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.003 0.07 -10000 0 -0.26 4 4
RBBP7 0.028 0.005 -10000 0 -10000 0 0
NPC 0.016 0.006 -10000 0 -0.09 1 1
RBBP4 0.026 0.025 -10000 0 -0.32 2 2
MAX 0.028 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.028 0.005 -10000 0 -10000 0 0
NFKBIA 0.013 0.036 -10000 0 -0.13 19 19
KAT2B 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.025 0.018 -10000 0 -10000 0 0
SIN3 complex 0.067 0.02 -10000 0 -10000 0 0
SMURF1 0.026 0.008 -10000 0 -10000 0 0
CHD3 0.024 0.01 -10000 0 -10000 0 0
SAP30 0.028 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.021 0.042 -10000 0 -10000 0 0
YY1/HDAC2 0.029 0.035 -10000 0 -0.18 4 4
YY1/HDAC1 0.033 0.036 -10000 0 -0.18 4 4
NuRD/MBD2 Complex (MeCP1) 0.021 0.037 -10000 0 -10000 0 0
PPARG -0.005 0.08 -10000 0 -0.24 35 35
HDAC8/hEST1B 0.054 0.014 -10000 0 -10000 0 0
UBE2I 0.027 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.008 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.024 0.042 -10000 0 -10000 0 0
MBD3L2 0.018 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.047 0.022 -10000 0 -10000 0 0
CREBBP 0.027 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.017 0.051 -10000 0 -0.21 1 1
HDAC1 0.028 0.003 -10000 0 -10000 0 0
HDAC3 0.013 0.036 -10000 0 -10000 0 0
HDAC2 0.025 0.01 -10000 0 -10000 0 0
YY1 0.018 0.021 -10000 0 -0.2 3 3
HDAC8 0.028 0.003 -10000 0 -10000 0 0
SMAD7 0.026 0.008 -10000 0 -10000 0 0
NCOR2 0.027 0.006 -10000 0 -10000 0 0
MXD1 0.028 0.004 -10000 0 -10000 0 0
STAT3 0.019 0.024 -10000 0 -0.24 3 3
NFKB1 0.028 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.013 -10000 0 -0.21 1 1
YY1/LSF/HDAC1 0.047 0.038 0.18 1 -0.17 4 5
YY1/SAP30/HDAC1 0.046 0.038 -10000 0 -0.17 4 4
EP300 0.025 0.031 -10000 0 -0.32 3 3
STAT3 (dimer non-phopshorylated) 0.019 0.024 -10000 0 -0.24 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.036 -10000 0 -0.13 19 19
histone deacetylation 0.012 0.046 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.036 -10000 0 -0.16 3 3
nuclear export -0.054 0.014 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
GATAD2B 0.027 0.007 -10000 0 -10000 0 0
GATAD2A 0.028 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.022 0.043 -10000 0 -10000 0 0
GATA1/HDAC1 0.039 0.017 -10000 0 -0.18 2 2
GATA1/HDAC3 0.023 0.045 -10000 0 -10000 0 0
CHD4 0.026 0.008 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.018 0.066 -10000 0 -0.19 32 32
SIN3/HDAC complex/Mad/Max 0.029 0.028 -10000 0 -10000 0 0
NuRD Complex 0.014 0.06 -10000 0 -0.22 8 8
positive regulation of chromatin silencing 0.044 0.05 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
MTA2 0.028 0.004 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.044 0.023 -10000 0 -10000 0 0
HDAC complex 0.061 0.031 -10000 0 -0.16 2 2
GATA1/Fog1 0.033 0.021 -10000 0 -0.18 1 1
FKBP25/HDAC1/HDAC2 0.05 0.02 -10000 0 -10000 0 0
TNF 0.001 0.087 -10000 0 -0.28 32 32
negative regulation of cell growth 0.022 0.042 -10000 0 -0.32 1 1
NuRD/MBD2/PRMT5 Complex 0.021 0.037 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0.026 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.007 0.069 -10000 0 -0.22 21 21
SIN3/HDAC complex/NCoR1 0.024 0.03 -10000 0 -0.23 1 1
TFCP2 0.028 0.005 -10000 0 -10000 0 0
NR2C1 0.027 0.005 -10000 0 -10000 0 0
MBD3 0.026 0.021 -10000 0 -0.21 3 3
MBD2 0.025 0.015 -10000 0 -0.21 1 1
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.018 0.11 -10000 0 -0.31 46 46
CLTC 0.023 0.034 0.21 1 -0.34 1 2
calcium ion-dependent exocytosis 0.014 0.033 0.2 1 -0.14 4 5
Dynamin 2/GTP 0.023 0.023 -10000 0 -10000 0 0
EXOC4 0.026 0.008 -10000 0 -10000 0 0
CD59 0.015 0.023 -10000 0 -0.28 1 1
CPE 0.013 0.019 -10000 0 -0.16 4 4
CTNNB1 0.028 0.005 -10000 0 -10000 0 0
membrane fusion 0.014 0.028 0.1 17 -0.11 8 25
CTNND1 0.014 0.037 0.2 10 -10000 0 10
DNM2 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.033 0.21 4 -0.16 1 5
TSHR 0.005 0.037 -10000 0 -0.16 17 17
INS 0.012 0.051 -10000 0 -0.45 4 4
BIN1 0.025 0.022 -10000 0 -0.21 3 3
mol:Choline 0.014 0.028 0.1 17 -0.11 8 25
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.022 -10000 0 -0.11 11 11
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.023 -10000 0 -10000 0 0
JUP 0.015 0.024 -10000 0 -0.28 1 1
ASAP2/amphiphysin II 0.049 0.02 -10000 0 -10000 0 0
ARF6/GTP 0.021 0.003 -10000 0 -10000 0 0
CDH1 0.014 0.028 -10000 0 -0.35 1 1
clathrin-independent pinocytosis 0.021 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.018 -10000 0 -0.21 2 2
positive regulation of endocytosis 0.021 0.003 -10000 0 -10000 0 0
EXOC2 0.028 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.024 0.026 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.028 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.044 0.037 0.26 1 -0.25 1 2
positive regulation of phagocytosis 0.015 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.014 -10000 0 -0.11 2 2
ACAP1 0.019 0.025 0.12 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.018 0.061 -10000 0 -0.28 1 1
clathrin heavy chain/ACAP1 0.022 0.037 0.2 4 -0.25 1 5
JIP4/KLC1 0.052 0.013 -10000 0 -10000 0 0
EXOC1 0.028 0.004 -10000 0 -10000 0 0
exocyst 0.024 0.026 -10000 0 -10000 0 0
RALA/GTP 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.037 0.008 -10000 0 -10000 0 0
receptor recycling 0.021 0.003 -10000 0 -10000 0 0
CTNNA1 0.012 0.033 0.18 9 -10000 0 9
NME1 0.011 0.022 -10000 0 -0.11 11 11
clathrin coat assembly 0.023 0.036 0.21 1 -0.34 1 2
IL2RA 0.009 0.03 -10000 0 -0.33 1 1
VAMP3 0.015 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.014 0.057 -10000 0 -0.22 2 2
EXOC6 0.026 0.008 -10000 0 -10000 0 0
PLD1 0.007 0.04 -10000 0 -0.22 11 11
PLD2 0.014 0.006 -10000 0 -10000 0 0
EXOC5 0.028 0.004 -10000 0 -10000 0 0
PIP5K1C 0.015 0.023 0.19 1 -0.16 1 2
SDC1 0.011 0.036 -10000 0 -0.28 1 1
ARF6/GDP 0.021 0.024 -10000 0 -0.11 11 11
EXOC7 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.047 0.039 0.26 1 -0.27 1 2
mol:Phosphatidic acid 0.014 0.028 0.1 17 -0.11 8 25
endocytosis -0.048 0.019 -10000 0 -10000 0 0
SCAMP2 0.028 0.004 -10000 0 -10000 0 0
ADRB2 0.023 0.046 0.24 6 -0.32 1 7
EXOC3 0.028 0.005 -10000 0 -10000 0 0
ASAP2 0.028 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.027 0.024 -10000 0 -10000 0 0
KLC1 0.028 0.004 -10000 0 -10000 0 0
AVPR2 0.019 0.041 0.2 1 -0.29 2 3
RALA 0.026 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.043 0.043 0.22 3 -0.26 1 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.026 0.009 -10000 0 -10000 0 0
SMAD2 0.013 0.043 0.2 6 -0.2 3 9
SMAD3 0.025 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.035 -10000 0 -0.31 2 2
SMAD4/Ubc9/PIASy 0.049 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.056 0.039 -10000 0 -10000 0 0
PPM1A 0.028 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.024 0.033 0.19 3 -0.18 2 5
MAP3K1 0.025 0.02 -10000 0 -0.32 1 1
TRAP-1/SMAD4 0.021 0.064 -10000 0 -0.22 24 24
MAPK3 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.028 0.004 -10000 0 -10000 0 0
NUP214 0.027 0.007 -10000 0 -10000 0 0
CTDSP1 0.028 0.003 -10000 0 -10000 0 0
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
CTDSPL 0.028 0.005 -10000 0 -10000 0 0
KPNB1 0.028 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.006 0.084 -10000 0 -0.32 24 24
UBE2I 0.027 0.006 -10000 0 -10000 0 0
NUP153 0.027 0.018 -10000 0 -0.32 1 1
KPNA2 0.026 0.018 -10000 0 -0.21 2 2
PIAS4 0.028 0.004 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.006 0.1 -10000 0 -0.41 5 5
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.028 0.005 -10000 0 -10000 0 0
AKT2 0.028 0.003 -10000 0 -10000 0 0
STXBP4 0.026 0.026 -10000 0 -0.32 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0 0.1 0.2 2 -0.44 5 7
YWHAZ 0.023 0.011 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.028 0.004 -10000 0 -10000 0 0
TBC1D4 0.011 0.012 -10000 0 -0.14 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.028 0.004 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.048 0.027 -10000 0 -0.18 2 2
YWHAG 0.026 0.008 -10000 0 -10000 0 0
ASIP 0.018 0.041 -10000 0 -0.27 7 7
PRKCI 0.026 0.008 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.013 0.017 0.24 2 -10000 0 2
PRKCZ 0.028 0.004 -10000 0 -10000 0 0
TRIP10 0.028 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.016 0.047 -10000 0 -0.2 2 2
VAMP2 0.025 0.009 -10000 0 -10000 0 0
SLC2A4 -0.002 0.11 0.21 1 -0.5 5 6
STX4 0.028 0.005 -10000 0 -10000 0 0
GSK3B 0.021 0.007 -10000 0 -10000 0 0
SFN 0.002 0.091 -10000 0 -0.32 28 28
LNPEP 0.004 0.084 -10000 0 -0.32 24 24
YWHAE 0.026 0.008 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.023 0.018 -10000 0 -10000 0 0
regulation of axonogenesis -0.009 0.023 0.24 1 -10000 0 1
myoblast fusion -0.028 0.025 -10000 0 -10000 0 0
mol:GTP 0.023 0.011 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.055 0.028 0.15 1 -10000 0 1
ARF1/GTP 0.037 0.014 -10000 0 -10000 0 0
mol:GM1 0.011 0.009 -10000 0 -0.11 1 1
mol:Choline 0.006 0.028 -10000 0 -0.16 9 9
lamellipodium assembly 0.017 0.026 -10000 0 -0.33 1 1
MAPK3 0.024 0.014 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.056 0.029 -10000 0 -0.15 1 1
ARF1 0.027 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.028 0.025 -10000 0 -10000 0 0
ARF1/GDP 0.033 0.027 -10000 0 -0.18 1 1
ARF6 0.036 0.008 -10000 0 -10000 0 0
RAB11A 0.028 0.003 -10000 0 -10000 0 0
TIAM1 0.026 0.028 -10000 0 -0.27 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.014 -10000 0 -10000 0 0
actin filament bundle formation -0.037 0.023 0.18 1 -10000 0 1
KALRN 0.015 0.015 0.18 1 -10000 0 1
RAB11FIP3/RAB11A 0.04 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.038 0.023 -10000 0 -0.18 1 1
NME1 0.021 0.04 -10000 0 -0.2 11 11
Rac1/GDP 0.035 0.023 -10000 0 -0.18 1 1
substrate adhesion-dependent cell spreading 0.023 0.011 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.017 0.026 -10000 0 -0.33 1 1
RAC1 0.026 0.008 -10000 0 -10000 0 0
liver development 0.023 0.011 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.011 -10000 0 -10000 0 0
RhoA/GTP 0.038 0.013 -10000 0 -10000 0 0
mol:GDP 0.015 0.016 -10000 0 -0.2 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.053 0.017 -10000 0 -10000 0 0
RHOA 0.028 0.004 -10000 0 -10000 0 0
PLD1 0.012 0.039 -10000 0 -0.19 12 12
RAB11FIP3 0.027 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.026 -10000 0 -0.33 1 1
ruffle organization 0.009 0.023 -10000 0 -0.24 1 1
regulation of epithelial cell migration 0.023 0.011 -10000 0 -10000 0 0
PLD2 0.02 0.012 -10000 0 -10000 0 0
PIP5K1A 0.009 0.023 -10000 0 -0.24 1 1
mol:Phosphatidic acid 0.006 0.028 -10000 0 -0.16 9 9
Rac1/GTP 0.017 0.026 -10000 0 -0.33 1 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.009 0.025 0.15 9 -0.16 1 10
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.01 0.037 0.13 5 -0.19 2 7
AP2 0.039 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.035 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.013 -10000 0 -0.21 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.019 0.008 -10000 0 -10000 0 0
CD4 0.022 0.033 -10000 0 -0.22 6 6
CLTA 0.028 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.011 -10000 0 -0.14 2 2
mol:PI-4-5-P2 0.006 0.008 -10000 0 -10000 0 0
ARF1/GTP 0.033 0.012 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.011 0.01 -10000 0 -0.14 1 1
mol:Choline 0.006 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.008 -10000 0 -10000 0 0
DDEF1 0.005 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.003 0.014 -10000 0 -0.088 4 4
AP2M1 0.027 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.007 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.018 -10000 0 -0.097 1 1
ARFIP2 0.021 0.017 -10000 0 -10000 0 0
COPA 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.012 0.025 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.018 0.007 -10000 0 -10000 0 0
GGA3 0.027 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.02 0.037 -10000 0 -0.22 8 8
AP2A1 0.028 0.003 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.016 0.01 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.019 0.043 -10000 0 -0.25 8 8
Arfaptin 2/Rac/GDP 0.034 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.036 0.013 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -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 0.018 0.023 -10000 0 -10000 0 0
PLD2 0.006 0.008 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.011 -10000 0 -0.14 2 2
PIP5K1A 0.006 0.008 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.017 0.021 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.008 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.011 -10000 0 -0.14 2 2
GOSR2 0.006 0.044 -10000 0 -0.31 7 7
USO1 0.012 0.007 -10000 0 -10000 0 0
GBF1 0.004 0.053 -10000 0 -0.31 10 10
ARF1/GTP/Arfaptin 2 0.037 0.013 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.047 0.03 -10000 0 -0.13 6 6
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.028 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.007 -10000 0 -10000 0 0
MDM2/SUMO1 0.043 0.023 -10000 0 -10000 0 0
HDAC4 0.028 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.007 -10000 0 -10000 0 0
SUMO1 0.028 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.012 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.011 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.027 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.013 -10000 0 -0.21 1 1
SUMO1/HDAC4 0.045 0.023 -10000 0 -10000 0 0
SUMO1/HDAC1 0.044 0.023 -10000 0 -10000 0 0
RANGAP1 0.026 0.021 -10000 0 -0.21 3 3
MDM2/SUMO1/SUMO1 0.062 0.028 -10000 0 -0.16 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.006 -10000 0 -10000 0 0
Ran/GTP 0.03 0.023 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
UBE2I 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.025 0.25 1 -10000 0 1
NPC 0.016 0.006 -10000 0 -0.09 1 1
PIAS2 0.026 0.008 -10000 0 -10000 0 0
PIAS1 0.027 0.018 -10000 0 -0.32 1 1
EntrezGene:9972 0 0 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.048 0.022 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.035 0.015 -9999 0 -9999 0 0
CTNNB1 0.028 0.005 -9999 0 -9999 0 0
JUP 0.028 0.004 -9999 0 -9999 0 0
CDH1 0.024 0.01 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.013 -9999 0 -10000 0 0
FBXW11 0.028 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.005 -9999 0 -10000 0 0
CHUK 0.027 0.007 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.074 0.029 -9999 0 -10000 0 0
NFKB1 0.028 0.003 -9999 0 -10000 0 0
MAP3K14 0.027 0.007 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.041 0.007 -9999 0 -10000 0 0
RELB 0.028 0.003 -9999 0 -10000 0 0
NFKB2 0.026 0.018 -9999 0 -0.21 2 2
NF kappa B2 p52/RelB 0.035 0.014 -9999 0 -0.11 2 2
regulation of B cell activation 0.035 0.014 -9999 0 -0.11 2 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 370 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.YL.A8HO TCGA.YL.A8HM TCGA.YL.A8HL TCGA.YL.A8HK
109_MAP3K5 0.27 0.084 -0.095 0.033
47_PPARGC1A 0.028 -0.31 -0.31 0.028
105_BMP4 0.028 0.028 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 -0.31 -0.31 0.028
105_BMP2 0.028 -0.31 0.028 0.028
131_RELN/VLDLR 0 0 -0.17 0.073
30_TGFB1/TGF beta receptor Type II 0.028 0.029 0.028 0.028
84_STAT5B 0.082 0.11 0.027 0.027
84_STAT5A 0.082 0.11 0.027 0.027
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/PRAD-TP/9830648/PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/PRAD-TP/10006152/GDAC_Gistic2Report_10008508/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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle