PARADIGM pathway analysis of mRNASeq expression and copy number data
Bladder Urothelial Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1DR2T6R
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/C1DR2T6R
Overview
Introduction

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

Summary

There were 65 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 72
Glypican 2 network 66
Aurora B signaling 57
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 54
IGF1 pathway 53
Endothelins 52
Signaling mediated by p38-alpha and p38-beta 52
Signaling events regulated by Ret tyrosine kinase 50
Signaling events mediated by the Hedgehog family 46
Signaling events mediated by Stem cell factor receptor (c-Kit) 44
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 267 . 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 ( 267 ).

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
FOXM1 transcription factor network 0.2697 72 3688 51 0.025 0.41 1000 -1000 -0.031 -1000
Glypican 2 network 0.2472 66 266 4 0.041 0.1 1000 -1000 0.017 -1000
Aurora B signaling 0.2135 57 3848 67 -0.27 0.27 1000 -1000 -0.034 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2022 54 3714 68 -0.62 0.32 1000 -1000 -0.034 -1000
IGF1 pathway 0.1985 53 3045 57 -0.18 0.055 1000 -1000 -0.022 -1000
Endothelins 0.1948 52 4995 96 -0.37 0.14 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 0.1948 52 2307 44 -0.2 0.026 1000 -1000 -0.012 -1000
Signaling events regulated by Ret tyrosine kinase 0.1873 50 4145 82 -0.19 0.032 1000 -1000 -0.037 -1000
Signaling events mediated by the Hedgehog family 0.1723 46 2405 52 -0.12 0.12 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1648 44 3450 78 -0.3 0.11 1000 -1000 -0.022 -1000
Nongenotropic Androgen signaling 0.1610 43 2254 52 -0.24 0.14 1000 -1000 -0.019 -1000
IL4-mediated signaling events 0.1498 40 3691 91 -0.69 0.48 1000 -1000 -0.05 -1000
Reelin signaling pathway 0.1498 40 2270 56 -0.12 0.068 1000 -1000 -0.023 -1000
Thromboxane A2 receptor signaling 0.1423 38 3990 105 -0.2 0.048 1000 -1000 -0.027 -1000
p75(NTR)-mediated signaling 0.1386 37 4712 125 -0.1 0.084 1000 -1000 -0.044 -1000
IL23-mediated signaling events 0.1348 36 2206 60 -0.42 0.054 1000 -1000 -0.033 -1000
TCGA08_retinoblastoma 0.1311 35 285 8 -0.04 0.13 1000 -1000 -0.002 -1000
Fc-epsilon receptor I signaling in mast cells 0.1273 34 3298 97 -0.12 0.031 1000 -1000 -0.054 -1000
Aurora C signaling 0.1236 33 232 7 0 0.13 1000 -1000 -0.008 -1000
TCR signaling in naïve CD8+ T cells 0.1199 32 3000 93 -0.12 0.052 1000 -1000 -0.031 -1000
Plasma membrane estrogen receptor signaling 0.1199 32 2758 86 -0.26 0.14 1000 -1000 -0.036 -1000
Ephrin A reverse signaling 0.1124 30 215 7 -0.048 0.014 1000 -1000 0 -1000
PLK1 signaling events 0.1124 30 2630 85 -0.045 0.2 1000 -1000 -0.028 -1000
Integrins in angiogenesis 0.1124 30 2548 84 -0.21 0.12 1000 -1000 -0.022 -1000
LPA receptor mediated events 0.1086 29 3003 102 -0.21 0.084 1000 -1000 -0.037 -1000
S1P4 pathway 0.1086 29 742 25 -0.11 0.045 1000 -1000 -0.013 -1000
Ras signaling in the CD4+ TCR pathway 0.1086 29 504 17 -0.11 0.03 1000 -1000 -0.014 -1000
BMP receptor signaling 0.1049 28 2333 81 -0.22 0.078 1000 -1000 -0.021 -1000
S1P5 pathway 0.1049 28 481 17 -0.11 0.075 1000 -1000 -0.005 -1000
amb2 Integrin signaling 0.1011 27 2254 82 -0.27 0.084 1000 -1000 -0.013 -1000
Rapid glucocorticoid signaling 0.1011 27 548 20 -0.14 0.067 1000 -1000 0 -1000
JNK signaling in the CD4+ TCR pathway 0.0974 26 447 17 -0.18 0.029 1000 -1000 -0.017 -1000
PDGFR-alpha signaling pathway 0.0974 26 1170 44 -0.28 0.037 1000 -1000 -0.024 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0974 26 1353 52 -0.21 0.038 1000 -1000 -0.015 -1000
S1P1 pathway 0.0974 26 945 36 -0.28 0.026 1000 -1000 -0.016 -1000
TCGA08_p53 0.0974 26 185 7 -0.015 0.026 1000 -1000 -0.004 -1000
IL6-mediated signaling events 0.0974 26 1970 75 -0.2 0.056 1000 -1000 -0.034 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0974 26 3139 120 -0.21 0.16 1000 -1000 -0.032 -1000
Calcium signaling in the CD4+ TCR pathway 0.0936 25 802 31 -0.15 0.025 1000 -1000 -0.03 -1000
Glypican 1 network 0.0899 24 1193 48 -0.18 0.047 1000 -1000 -0.015 -1000
Glucocorticoid receptor regulatory network 0.0899 24 2773 114 -0.49 0.096 1000 -1000 -0.044 -1000
Syndecan-1-mediated signaling events 0.0861 23 803 34 -0.069 0.16 1000 -1000 -0.012 -1000
LPA4-mediated signaling events 0.0824 22 271 12 -0.12 0.006 1000 -1000 -0.015 -1000
IL12-mediated signaling events 0.0824 22 1922 87 -0.38 0.061 1000 -1000 -0.039 -1000
Osteopontin-mediated events 0.0787 21 819 38 -0.1 0.13 1000 -1000 -0.026 -1000
BCR signaling pathway 0.0787 21 2170 99 -0.1 0.033 1000 -1000 -0.047 -1000
S1P3 pathway 0.0787 21 913 42 -0.11 0.039 1000 -1000 -0.024 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0749 20 1128 54 -0.12 0.068 1000 -1000 -0.023 -1000
Coregulation of Androgen receptor activity 0.0712 19 1494 76 -0.17 0.13 1000 -1000 -0.015 -1000
Visual signal transduction: Cones 0.0712 19 741 38 -0.066 0.089 1000 -1000 -0.001 -1000
HIF-1-alpha transcription factor network 0.0712 19 1478 76 -0.1 0.14 1000 -1000 -0.019 -1000
FAS signaling pathway (CD95) 0.0712 19 908 47 -0.52 0.043 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 0.0674 18 1249 69 -0.037 0.064 1000 -1000 -0.023 -1000
Wnt signaling 0.0674 18 126 7 -0.004 0.031 1000 -1000 -0.003 -1000
Arf6 signaling events 0.0637 17 1092 62 -0.16 0.06 1000 -1000 -0.01 -1000
Aurora A signaling 0.0637 17 1037 60 -0.19 0.2 1000 -1000 -0.007 -1000
ErbB2/ErbB3 signaling events 0.0599 16 1065 65 -0.16 0.038 1000 -1000 -0.051 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0599 16 577 34 -0.015 0.043 1000 -1000 -0.027 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0599 16 1376 85 -0.21 0.037 1000 -1000 -0.034 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0599 16 1467 88 -0.15 0.054 1000 -1000 -0.059 -1000
Noncanonical Wnt signaling pathway 0.0562 15 403 26 -0.06 0.031 1000 -1000 -0.022 -1000
Presenilin action in Notch and Wnt signaling 0.0524 14 859 61 -0.1 0.13 1000 -1000 -0.028 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0524 14 1096 74 -0.17 0.065 1000 -1000 -0.043 -1000
Syndecan-4-mediated signaling events 0.0524 14 958 67 -0.11 0.084 1000 -1000 -0.027 -1000
Class IB PI3K non-lipid kinase events 0.0524 14 42 3 -0.001 0.001 1000 -1000 -0.015 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0487 13 366 28 -0.11 0.057 1000 -1000 -0.006 -1000
Canonical Wnt signaling pathway 0.0487 13 696 51 -0.077 0.13 1000 -1000 -0.027 -1000
Effects of Botulinum toxin 0.0487 13 352 26 -0.01 0.065 1000 -1000 -0.003 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0487 13 456 33 -0.19 0.13 1000 -1000 -0.015 -1000
Visual signal transduction: Rods 0.0487 13 694 52 -0.066 0.13 1000 -1000 -0.017 -1000
Regulation of Androgen receptor activity 0.0487 13 942 70 -0.18 0.031 1000 -1000 -0.023 -1000
FOXA2 and FOXA3 transcription factor networks 0.0449 12 564 46 -0.14 0.24 1000 -1000 -0.022 -1000
Hedgehog signaling events mediated by Gli proteins 0.0412 11 723 65 -0.1 0.062 1000 -1000 -0.017 -1000
Nectin adhesion pathway 0.0412 11 745 63 -0.033 0.054 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0412 11 556 49 -0.002 0.049 1000 -1000 -0.022 -1000
Ephrin B reverse signaling 0.0412 11 543 48 -0.039 0.044 1000 -1000 -0.03 -1000
IL2 signaling events mediated by PI3K 0.0375 10 621 58 -0.062 0.12 1000 -1000 -0.021 -1000
EPHB forward signaling 0.0375 10 858 85 -0.029 0.069 1000 -1000 -0.043 -1000
IL27-mediated signaling events 0.0375 10 526 51 -0.16 0.063 1000 -1000 -0.019 -1000
Insulin Pathway 0.0375 10 769 74 -0.17 0.063 1000 -1000 -0.033 -1000
ErbB4 signaling events 0.0337 9 665 69 -0.16 0.045 1000 -1000 -0.023 -1000
Signaling events mediated by PTP1B 0.0337 9 741 76 -0.1 0.044 1000 -1000 -0.027 -1000
Ceramide signaling pathway 0.0337 9 757 76 -0.17 0.071 1000 -1000 -0.017 -1000
IL1-mediated signaling events 0.0337 9 595 62 -0.008 0.063 1000 -1000 -0.019 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0337 9 780 83 -0.22 0.046 1000 -1000 -0.011 -1000
IL2 signaling events mediated by STAT5 0.0337 9 206 22 -0.037 0.092 1000 -1000 -0.019 -1000
Caspase cascade in apoptosis 0.0300 8 636 74 -0.039 0.049 1000 -1000 -0.023 -1000
Regulation of nuclear SMAD2/3 signaling 0.0300 8 1117 136 -0.13 0.11 1000 -1000 -0.03 -1000
Cellular roles of Anthrax toxin 0.0300 8 344 39 -0.063 0.038 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 0.0300 8 475 54 -0.085 0.057 1000 -1000 -0.034 -1000
E-cadherin signaling in the nascent adherens junction 0.0300 8 610 76 -0.029 0.05 1000 -1000 -0.032 -1000
EGFR-dependent Endothelin signaling events 0.0300 8 174 21 -0.025 0.073 1000 -1000 -0.03 -1000
PDGFR-beta signaling pathway 0.0300 8 838 97 -0.075 0.058 1000 -1000 -0.037 -1000
a4b1 and a4b7 Integrin signaling 0.0262 7 38 5 0.012 0.026 1000 -1000 0.013 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0262 7 273 37 -0.019 0.054 1000 -1000 -0.015 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0262 7 315 45 -0.008 0.062 1000 -1000 -0.03 -1000
BARD1 signaling events 0.0225 6 357 57 -0.048 0.11 1000 -1000 -0.043 -1000
EPO signaling pathway 0.0225 6 357 55 -0.015 0.071 1000 -1000 -0.018 -1000
IFN-gamma pathway 0.0225 6 469 68 -0.11 0.079 1000 -1000 -0.036 -1000
Class I PI3K signaling events mediated by Akt 0.0225 6 450 68 -0.13 0.06 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class III 0.0225 6 259 40 -0.15 0.049 1000 -1000 -0.035 -1000
mTOR signaling pathway 0.0187 5 302 53 -0.038 0.034 1000 -1000 -0.019 -1000
HIF-2-alpha transcription factor network 0.0187 5 223 43 -0.1 0.11 1000 -1000 -0.039 -1000
Signaling mediated by p38-gamma and p38-delta 0.0187 5 82 15 -0.014 0.025 1000 -1000 -0.023 -1000
Syndecan-3-mediated signaling events 0.0187 5 191 35 -0.06 0.06 1000 -1000 -0.013 -1000
TCGA08_rtk_signaling 0.0187 5 139 26 -0.041 0.055 1000 -1000 -0.016 -1000
Class I PI3K signaling events 0.0187 5 376 73 -0.028 0.046 1000 -1000 -0.023 -1000
Arf6 trafficking events 0.0187 5 386 71 -0.26 0.048 1000 -1000 -0.031 -1000
Regulation of Telomerase 0.0187 5 603 102 -0.1 0.12 1000 -1000 -0.034 -1000
Signaling events mediated by PRL 0.0187 5 189 34 -0.051 0.046 1000 -1000 -0.025 -1000
E-cadherin signaling in keratinocytes 0.0187 5 230 43 -0.027 0.04 1000 -1000 -0.01 -1000
E-cadherin signaling events 0.0187 5 25 5 0.012 0.037 1000 -1000 0.015 -1000
Retinoic acid receptors-mediated signaling 0.0150 4 238 58 -0.058 0.058 1000 -1000 -0.017 -1000
Paxillin-dependent events mediated by a4b1 0.0150 4 160 36 -0.039 0.044 1000 -1000 -0.031 -1000
Insulin-mediated glucose transport 0.0112 3 110 32 -0.14 0.046 1000 -1000 -0.011 -1000
FoxO family signaling 0.0112 3 202 64 -0.015 0.16 1000 -1000 -0.034 -1000
p38 MAPK signaling pathway 0.0112 3 143 44 -0.003 0.062 1000 -1000 -0.012 -1000
Canonical NF-kappaB pathway 0.0075 2 98 39 0 0.063 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 0.0075 2 189 75 -0.045 0.064 1000 -1000 -0.022 -1000
TRAIL signaling pathway 0.0075 2 142 48 -0.017 0.055 1000 -1000 -0.019 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0075 2 54 27 -0.009 0.063 1000 -1000 -0.026 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0037 1 26 23 0.003 0.048 1000 -1000 -0.009 -1000
PLK2 and PLK4 events 0.0037 1 5 3 0.013 0.031 1000 -1000 -0.004 -1000
Arf6 downstream pathway 0.0037 1 45 43 -0.05 0.051 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class I 0.0037 1 143 104 -0.049 0.065 1000 -1000 -0.034 -1000
Atypical NF-kappaB pathway 0.0037 1 39 31 0 0.035 1000 -1000 -0.005 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0037 1 230 125 -0.043 0.069 1000 -1000 -0.018 -1000
VEGFR1 specific signals 0.0037 1 80 56 -0.055 0.067 1000 -1000 -0.031 -1000
Arf1 pathway 0.0037 1 69 54 -0.001 0.047 1000 -1000 -0.009 -1000
Circadian rhythm pathway 0.0000 0 19 22 -0.008 0.056 1000 -1000 -0.024 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.068 1000 -1000 0 -1000
Total NA 2342 138393 7203 -16 10 131000 -131000 -2.9 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.36 0.49 0.88 82 -0.87 6 88
PLK1 0.2 0.22 0.53 30 -0.92 3 33
BIRC5 0.26 0.2 0.56 22 -1.4 1 23
HSPA1B 0.36 0.49 0.88 77 -0.89 6 83
MAP2K1 0.11 0.11 0.26 70 -10000 0 70
BRCA2 0.36 0.5 0.9 81 -0.89 6 87
FOXM1 0.4 0.57 1 85 -1 6 91
XRCC1 0.36 0.5 0.89 77 -0.89 6 83
FOXM1B/p19 0.14 0.44 0.8 48 -0.95 7 55
Cyclin D1/CDK4 0.31 0.46 0.79 80 -0.84 8 88
CDC2 0.38 0.53 0.93 87 -0.93 6 93
TGFA 0.32 0.46 0.8 83 -0.78 8 91
SKP2 0.38 0.5 0.92 80 -0.85 6 86
CCNE1 0.079 0.097 0.3 41 -10000 0 41
CKS1B 0.37 0.5 0.92 77 -0.91 5 82
RB1 0.2 0.3 0.58 79 -0.69 2 81
FOXM1C/SP1 0.32 0.49 0.82 75 -0.96 8 83
AURKB 0.15 0.32 0.56 13 -0.9 14 27
CENPF 0.4 0.52 0.92 94 -0.89 5 99
CDK4 0.059 0.049 -10000 0 -10000 0 0
MYC 0.25 0.47 0.76 80 -0.85 12 92
CHEK2 0.11 0.11 0.26 64 -10000 0 64
ONECUT1 0.33 0.47 0.81 84 -0.85 8 92
CDKN2A 0.069 0.12 0.24 71 -0.16 1 72
LAMA4 0.35 0.51 0.88 76 -1.2 6 82
FOXM1B/HNF6 0.33 0.49 0.84 76 -0.95 8 84
FOS 0.087 0.69 0.9 71 -1 36 107
SP1 0.025 0.014 -10000 0 -10000 0 0
CDC25B 0.37 0.5 0.9 80 -0.89 6 86
response to radiation 0.071 0.08 0.18 71 -10000 0 71
CENPB 0.36 0.5 0.89 79 -0.89 6 85
CENPA 0.41 0.52 0.94 89 -0.89 5 94
NEK2 0.4 0.52 0.94 87 -0.89 5 92
HIST1H2BA 0.36 0.5 0.89 78 -0.89 6 84
CCNA2 0.11 0.12 0.3 71 -10000 0 71
EP300 0.026 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.36 0.53 0.96 69 -1 6 75
CCNB2 0.4 0.52 0.93 90 -0.9 5 95
CCNB1 0.39 0.53 0.96 81 -0.93 6 87
ETV5 0.36 0.5 0.91 75 -0.89 6 81
ESR1 0.22 0.66 0.88 77 -1.1 35 112
CCND1 0.3 0.48 0.82 83 -0.86 8 91
GSK3A 0.089 0.09 0.22 51 -10000 0 51
Cyclin A-E1/CDK1-2 0.16 0.15 0.35 81 -10000 0 81
CDK2 0.041 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.092 0.1 0.21 90 -10000 0 90
FOXM1B/Cbp/p300 0.2 0.42 0.74 42 -0.94 6 48
GAS1 0.18 0.73 0.89 75 -1.1 53 128
MMP2 0.28 0.6 0.88 74 -1 24 98
RB1/FOXM1C 0.28 0.46 0.77 83 -0.87 8 91
CREBBP 0.025 0.007 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.041 0.061 0.27 17 -9999 0 17
GPC2 0.1 0.11 0.27 83 -9999 0 83
GPC2/Midkine 0.095 0.092 0.22 83 -9999 0 83
neuron projection morphogenesis 0.094 0.092 0.22 83 -9999 0 83
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.09 0.098 0.2 80 -0.23 1 81
STMN1 0.062 0.06 0.19 15 -10000 0 15
Aurora B/RasGAP/Survivin 0.21 0.14 0.32 137 -0.25 1 138
Chromosomal passenger complex/Cul3 protein complex 0.029 0.12 0.19 29 -0.28 12 41
BIRC5 0.21 0.12 0.28 193 -0.43 1 194
DES -0.27 0.29 -10000 0 -0.57 84 84
Aurora C/Aurora B/INCENP 0.11 0.083 0.21 95 -10000 0 95
Aurora B/TACC1 0.08 0.079 0.19 90 -10000 0 90
Aurora B/PP2A 0.11 0.087 0.21 109 -10000 0 109
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.026 0.026 0.15 3 -10000 0 3
mitotic metaphase/anaphase transition -0.003 0.005 -10000 0 -10000 0 0
NDC80 0.096 0.12 0.25 71 -10000 0 71
Cul3 protein complex -0.017 0.12 -10000 0 -0.25 50 50
KIF2C 0.13 0.086 0.2 132 -10000 0 132
PEBP1 0.028 0.005 -10000 0 -10000 0 0
KIF20A 0.2 0.11 0.27 188 -10000 0 188
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.1 0.087 0.21 107 -10000 0 107
SEPT1 0.027 0.022 0.27 2 -10000 0 2
SMC2 0.025 0.017 0.27 1 -10000 0 1
SMC4 0.026 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.063 0.2 0.29 18 -0.52 24 42
PSMA3 0.026 0.003 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.005 -10000 0 -10000 0 0
H3F3B 0.055 0.049 0.23 1 -10000 0 1
AURKB 0.14 0.13 0.28 113 -10000 0 113
AURKC 0.033 0.042 0.27 8 -10000 0 8
CDCA8 0.1 0.11 0.28 77 -10000 0 77
cytokinesis 0.12 0.11 0.25 88 -0.24 1 89
Aurora B/Septin1 0.16 0.16 0.32 100 -0.26 5 105
AURKA 0.1 0.11 0.27 84 -10000 0 84
INCENP 0.033 0.017 0.28 1 -10000 0 1
KLHL13 -0.059 0.17 -10000 0 -0.42 50 50
BUB1 0.069 0.094 0.27 48 -10000 0 48
hSgo1/Aurora B/Survivin 0.26 0.17 0.37 167 -0.23 1 168
EVI5 0.03 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.14 0.32 113 -10000 0 113
SGOL1 0.14 0.12 0.27 117 -10000 0 117
CENPA 0.14 0.12 0.24 129 -0.2 2 131
NCAPG 0.13 0.12 0.27 116 -10000 0 116
Aurora B/HC8 Proteasome 0.11 0.086 0.21 111 -10000 0 111
NCAPD2 0.027 0.017 0.29 1 -10000 0 1
Aurora B/PP1-gamma 0.11 0.087 0.21 110 -10000 0 110
RHOA 0.025 0.006 -10000 0 -10000 0 0
NCAPH 0.18 0.12 0.27 160 -10000 0 160
NPM1 0.033 0.16 0.24 1 -0.43 20 21
RASA1 0.026 0.005 -10000 0 -10000 0 0
KLHL9 0.021 0.011 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.086 0.21 111 -10000 0 111
PPP1CC 0.026 0.004 -10000 0 -10000 0 0
Centraspindlin 0.2 0.15 0.34 118 -10000 0 118
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
NSUN2 0.063 0.11 0.25 20 -0.27 14 34
MYLK -0.053 0.17 0.22 3 -0.28 84 87
KIF23 0.15 0.12 0.28 128 -10000 0 128
VIM 0.058 0.078 0.34 8 -0.29 2 10
RACGAP1 0.035 0.023 0.28 2 -10000 0 2
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.024 0.18 0.24 1 -0.46 24 25
Chromosomal passenger complex 0.14 0.1 0.22 128 -0.19 1 129
Chromosomal passenger complex/EVI5 0.27 0.18 0.41 136 -0.22 1 137
TACC1 0.023 0.01 -10000 0 -10000 0 0
PPP2R5D 0.026 0.003 -10000 0 -10000 0 0
CUL3 0.025 0.007 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.035 0.053 0.35 6 -0.14 3 9
NFATC2 -0.1 0.25 -10000 0 -0.57 41 41
NFATC3 -0.084 0.14 -10000 0 -0.27 82 82
CD40LG -0.43 0.52 -10000 0 -0.95 118 118
ITCH 0.004 0.073 0.32 1 -0.22 24 25
CBLB 0.004 0.072 -10000 0 -0.22 25 25
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.27 0.46 0.48 3 -1.1 48 51
JUNB 0.021 0.047 -10000 0 -0.42 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.088 0.22 1 -0.26 25 26
T cell anergy -0.023 0.12 0.22 1 -0.35 24 25
TLE4 -0.068 0.19 -10000 0 -0.49 33 33
Jun/NFAT1-c-4/p21SNFT -0.36 0.54 -10000 0 -0.92 113 113
AP-1/NFAT1-c-4 -0.46 0.63 -10000 0 -1.1 118 118
IKZF1 -0.071 0.2 0.33 2 -0.48 35 37
T-helper 2 cell differentiation -0.2 0.34 -10000 0 -0.86 42 42
AP-1/NFAT1 -0.12 0.22 -10000 0 -0.4 74 74
CALM1 0.016 0.058 -10000 0 -0.16 25 25
EGR2 -0.44 0.66 -10000 0 -1.2 95 95
EGR3 -0.62 0.74 -10000 0 -1.4 121 121
NFAT1/FOXP3 -0.048 0.21 0.46 6 -0.42 40 46
EGR1 -0.069 0.18 -10000 0 -0.42 57 57
JUN 0.011 0.071 -10000 0 -0.42 6 6
EGR4 0.015 0.083 0.27 4 -0.42 8 12
mol:Ca2+ -0.006 0.047 -10000 0 -0.15 25 25
GBP3 -0.072 0.18 0.32 1 -0.42 40 41
FOSL1 -0.004 0.11 -10000 0 -0.42 18 18
NFAT1-c-4/MAF/IRF4 -0.36 0.54 -10000 0 -0.92 112 112
DGKA -0.067 0.17 -10000 0 -0.42 36 36
CREM 0.025 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.38 0.51 -10000 0 -0.92 110 110
CTLA4 -0.055 0.18 0.36 5 -0.4 39 44
NFAT1-c-4 (dimer)/EGR1 -0.4 0.57 -10000 0 -0.98 117 117
NFAT1-c-4 (dimer)/EGR4 -0.36 0.54 -10000 0 -0.92 114 114
FOS -0.11 0.2 -10000 0 -0.42 77 77
IFNG -0.12 0.3 -10000 0 -0.72 34 34
T cell activation -0.2 0.28 -10000 0 -0.66 43 43
MAF 0.014 0.072 -10000 0 -0.42 7 7
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.32 0.46 0.78 113 -10000 0 113
TNF -0.36 0.49 -10000 0 -0.87 117 117
FASLG -0.62 0.78 -10000 0 -1.4 126 126
TBX21 0.023 0.091 -10000 0 -0.42 10 10
BATF3 0.022 0.05 0.27 1 -0.42 3 4
PRKCQ -0.015 0.13 0.28 2 -0.42 23 25
PTPN1 -0.069 0.17 -10000 0 -0.42 37 37
NFAT1-c-4/ICER1 -0.37 0.53 -10000 0 -0.92 113 113
GATA3 -0.002 0.11 0.29 1 -0.42 16 17
T-helper 1 cell differentiation -0.12 0.29 -10000 0 -0.7 35 35
IL2RA -0.27 0.44 0.49 3 -0.99 53 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.066 0.17 -10000 0 -0.42 34 34
E2F1 0.087 0.11 0.28 62 -10000 0 62
PPARG -0.009 0.12 0.29 2 -0.42 20 22
SLC3A2 -0.069 0.17 -10000 0 -0.42 36 36
IRF4 -0.004 0.11 0.27 2 -0.42 18 20
PTGS2 -0.44 0.52 -10000 0 -0.95 122 122
CSF2 -0.39 0.52 0.53 1 -0.9 120 121
JunB/Fra1/NFAT1-c-4 -0.36 0.53 -10000 0 -0.91 115 115
IL4 -0.22 0.36 -10000 0 -0.93 40 40
IL5 -0.41 0.5 -10000 0 -0.91 119 119
IL2 -0.2 0.29 -10000 0 -0.68 41 41
IL3 -0.068 0.15 -10000 0 -0.88 6 6
RNF128 -0.022 0.16 0.23 1 -0.51 25 26
NFATC1 -0.33 0.47 -10000 0 -0.79 113 113
CDK4 0.21 0.28 0.59 65 -10000 0 65
PTPRK -0.066 0.17 -10000 0 -0.42 36 36
IL8 -0.43 0.52 -10000 0 -0.94 121 121
POU2F1 0.024 0.009 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.026 0.003 -10000 0 -10000 0 0
PTK2 0.024 0.009 -10000 0 -10000 0 0
CRKL -0.087 0.12 -10000 0 -0.22 112 112
GRB2/SOS1/SHC 0.047 0.019 -10000 0 -10000 0 0
HRAS 0.025 0.007 -10000 0 -10000 0 0
IRS1/Crk -0.084 0.12 -10000 0 -0.22 118 118
IGF-1R heterotetramer/IGF1/PTP1B -0.073 0.14 -10000 0 -0.24 106 106
AKT1 -0.08 0.1 0.19 7 -0.2 85 92
BAD -0.079 0.097 0.18 7 -0.19 84 91
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.077 0.11 -10000 0 -0.22 101 101
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.08 0.13 0.2 2 -0.22 117 119
RAF1 -0.058 0.1 0.29 1 -0.57 1 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.06 0.14 -10000 0 -0.21 112 112
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.088 0.14 -10000 0 -0.24 118 118
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.08 0.1 0.19 7 -0.2 86 93
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.045 0.095 0.27 1 -0.46 1 2
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
HRAS/GTP -0.06 0.11 -10000 0 -0.19 97 97
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.034 0.13 -10000 0 -0.2 97 97
IGF-1R heterotetramer -0.018 0.057 -10000 0 -0.48 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.073 0.13 -10000 0 -0.22 118 118
Crk/p130 Cas/Paxillin -0.059 0.13 -10000 0 -0.2 114 114
IGF1R -0.018 0.057 -10000 0 -0.48 1 1
IGF1 -0.18 0.23 -10000 0 -0.43 116 116
IRS2/Crk -0.082 0.12 -10000 0 -0.22 110 110
PI3K -0.057 0.13 -10000 0 -0.21 108 108
apoptosis 0.055 0.083 0.3 1 -0.22 1 2
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
PRKCD -0.13 0.16 -10000 0 -0.32 110 110
RAF1/14-3-3 E -0.04 0.1 0.29 1 -0.48 1 2
BAD/14-3-3 -0.058 0.087 0.23 1 -0.32 1 2
PRKCZ -0.082 0.1 0.19 7 -0.2 85 92
Crk/p130 Cas/Paxillin/FAK1 -0.049 0.1 -10000 0 -10000 0 0
PTPN1 0.025 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.14 0.18 -10000 0 -0.33 116 116
BCAR1 0.025 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.047 0.13 -10000 0 -0.21 97 97
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.081 0.13 -10000 0 -0.22 118 118
GRB10 0.024 0.028 -10000 0 -0.42 1 1
PTPN11 -0.09 0.12 -10000 0 -0.22 115 115
IRS1 -0.097 0.13 -10000 0 -0.24 118 118
IRS2 -0.093 0.13 -10000 0 -0.24 110 110
IGF-1R heterotetramer/IGF1 -0.12 0.18 -10000 0 -0.32 116 116
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDPK1 -0.085 0.1 0.19 6 -0.2 98 104
YWHAE 0.024 0.008 -10000 0 -10000 0 0
PRKD1 -0.14 0.18 -10000 0 -0.34 113 113
SHC1 0.025 0.018 0.29 1 -10000 0 1
Endothelins

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
AKT1 -0.078 0.13 -10000 0 -0.34 40 40
PTK2B 0.022 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.11 0.23 -10000 0 -0.65 29 29
EDN1 -0.031 0.083 0.26 4 -0.25 14 18
EDN3 0.003 0.043 0.27 5 -10000 0 5
EDN2 0.012 0.12 0.27 16 -0.42 16 32
HRAS/GDP -0.15 0.24 -10000 0 -0.47 72 72
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.082 0.18 -10000 0 -0.37 55 55
ADCY4 -0.12 0.18 0.28 7 -0.3 105 112
ADCY5 -0.21 0.23 0.19 4 -0.38 145 149
ADCY6 -0.12 0.18 0.28 7 -0.3 101 108
ADCY7 -0.12 0.18 0.32 5 -0.32 91 96
ADCY1 -0.12 0.18 0.3 6 -0.32 89 95
ADCY2 -0.17 0.21 0.23 2 -0.36 121 123
ADCY3 -0.12 0.18 0.3 6 -0.3 101 107
ADCY8 -0.12 0.18 0.29 4 -0.3 95 99
ADCY9 -0.12 0.19 0.28 7 -0.31 104 111
arachidonic acid secretion -0.18 0.27 0.3 2 -0.48 100 102
ETB receptor/Endothelin-1/Gq/GTP -0.059 0.16 -10000 0 -0.35 51 51
GNAO1 -0.11 0.2 -10000 0 -0.42 78 78
HRAS 0.024 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.057 0.13 0.26 1 -0.31 38 39
ETA receptor/Endothelin-1/Gs/GTP -0.14 0.18 -10000 0 -0.31 106 106
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.078 0.15 0.28 1 -0.37 38 39
EDNRB -0.026 0.14 -10000 0 -0.42 29 29
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.072 0.14 -10000 0 -0.37 31 31
CYSLTR1 -0.091 0.17 -10000 0 -0.49 31 31
SLC9A1 -0.042 0.081 -10000 0 -0.25 20 20
mol:GDP -0.16 0.25 -10000 0 -0.49 76 76
SLC9A3 -0.08 0.23 -10000 0 -0.62 33 33
RAF1 -0.18 0.28 0.32 3 -0.48 98 101
JUN -0.12 0.27 -10000 0 -0.81 28 28
JAK2 -0.072 0.13 -10000 0 -0.35 35 35
mol:IP3 -0.1 0.2 -10000 0 -0.45 55 55
ETA receptor/Endothelin-1 -0.085 0.16 0.28 1 -0.4 40 41
PLCB1 0.01 0.072 -10000 0 -0.42 7 7
PLCB2 0.015 0.033 -10000 0 -0.42 1 1
ETA receptor/Endothelin-3 -0.046 0.12 0.21 1 -0.34 28 29
FOS -0.3 0.43 0.34 1 -0.85 94 95
Gai/GDP -0.29 0.41 -10000 0 -0.82 93 93
CRK 0.024 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.13 0.22 -10000 0 -0.47 61 61
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.41 63 63
GNAQ 0.017 0.018 -10000 0 -10000 0 0
GNAZ -0.074 0.18 -10000 0 -0.42 59 59
GNAL -0.14 0.21 -10000 0 -0.42 100 100
Gs family/GDP -0.2 0.26 -10000 0 -0.49 97 97
ETA receptor/Endothelin-1/Gq/GTP -0.075 0.16 -10000 0 -0.34 52 52
MAPK14 -0.062 0.15 0.22 1 -0.41 33 34
TRPC6 -0.11 0.25 -10000 0 -0.7 28 28
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.025 0.028 -10000 0 -0.42 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.057 0.16 -10000 0 -0.41 34 34
ETB receptor/Endothelin-2 -0.009 0.14 0.21 12 -0.32 38 50
ETB receptor/Endothelin-3 -0.004 0.11 0.21 4 -0.3 28 32
ETB receptor/Endothelin-1 -0.043 0.12 -10000 0 -0.33 32 32
MAPK3 -0.28 0.4 0.34 2 -0.73 101 103
MAPK1 -0.28 0.39 0.34 2 -0.73 101 103
Rac1/GDP -0.14 0.24 -10000 0 -0.46 72 72
cAMP biosynthetic process -0.19 0.22 0.26 4 -0.42 105 109
MAPK8 -0.14 0.3 -10000 0 -0.77 38 38
SRC 0.025 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.12 0.18 -10000 0 -0.38 70 70
p130Cas/CRK/Src/PYK2 -0.14 0.25 -10000 0 -0.54 56 56
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.23 -10000 0 -0.46 71 71
COL1A2 -0.1 0.22 0.29 1 -0.69 24 25
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.057 0.14 0.21 3 -0.3 54 57
mol:DAG -0.11 0.2 -10000 0 -0.44 56 56
MAP2K2 -0.22 0.32 0.34 2 -0.57 104 106
MAP2K1 -0.22 0.32 0.34 2 -0.57 104 106
EDNRA -0.081 0.16 -10000 0 -0.41 40 40
positive regulation of muscle contraction -0.062 0.12 0.26 3 -0.3 38 41
Gq family/GDP -0.13 0.24 -10000 0 -0.46 72 72
HRAS/GTP -0.16 0.25 -10000 0 -0.48 81 81
PRKCH -0.11 0.2 0.22 1 -0.42 59 60
RAC1 0.026 0.005 -10000 0 -10000 0 0
PRKCA -0.11 0.2 0.22 4 -0.42 59 63
PRKCB -0.16 0.22 0.22 1 -0.42 91 92
PRKCE -0.11 0.2 -10000 0 -0.41 61 61
PRKCD -0.11 0.2 -10000 0 -0.42 59 59
PRKCG -0.11 0.2 0.33 1 -0.42 62 63
regulation of vascular smooth muscle contraction -0.37 0.51 -10000 0 -1 93 93
PRKCQ -0.12 0.22 0.24 4 -0.43 70 74
PLA2G4A -0.2 0.3 0.3 2 -0.53 100 102
GNA14 -0.039 0.15 -10000 0 -0.42 33 33
GNA15 0.02 0.04 -10000 0 -0.42 2 2
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA11 0.021 0.029 -10000 0 -0.42 1 1
Rac1/GTP -0.058 0.13 -10000 0 -0.31 39 39
MMP1 0.14 0.14 0.39 33 -10000 0 33
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.2 0.43 -10000 0 -0.92 66 66
MKNK1 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.038 0.15 -10000 0 -0.3 65 65
ATF2/c-Jun -0.05 0.16 -10000 0 -0.46 18 18
MAPK11 -0.036 0.15 -10000 0 -0.3 60 60
MITF -0.082 0.21 -10000 0 -0.39 74 74
MAPKAPK5 -0.052 0.17 0.26 2 -0.34 63 65
KRT8 -0.064 0.19 -10000 0 -0.38 64 64
MAPKAPK3 0.025 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.06 0.22 -10000 0 -0.43 65 65
CEBPB -0.049 0.16 -10000 0 -0.35 57 57
SLC9A1 -0.056 0.17 -10000 0 -0.35 64 64
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.055 0.18 -10000 0 -0.36 62 62
p38alpha-beta/MNK1 -0.033 0.19 -10000 0 -0.35 64 64
JUN -0.052 0.15 -10000 0 -0.45 18 18
PPARGC1A -0.18 0.24 -10000 0 -0.38 131 131
USF1 -0.046 0.15 -10000 0 -0.34 54 54
RAB5/GDP/GDI1 -0.032 0.12 -10000 0 -0.25 58 58
NOS2 -0.055 0.22 -10000 0 -0.6 18 18
DDIT3 -0.056 0.17 -10000 0 -0.35 64 64
RAB5A 0.025 0.006 -10000 0 -10000 0 0
HSPB1 -0.046 0.14 0.28 3 -0.29 61 64
p38alpha-beta/HBP1 -0.031 0.19 -10000 0 -0.35 62 62
CREB1 -0.067 0.19 -10000 0 -0.38 64 64
RAB5/GDP 0.019 0.005 -10000 0 -10000 0 0
EIF4E -0.054 0.15 0.24 2 -0.32 59 61
RPS6KA4 -0.058 0.17 -10000 0 -0.35 65 65
PLA2G4A -0.066 0.16 0.24 2 -0.33 66 68
GDI1 -0.055 0.17 -10000 0 -0.34 64 64
TP53 -0.085 0.2 -10000 0 -0.43 64 64
RPS6KA5 -0.065 0.18 -10000 0 -0.36 68 68
ESR1 -0.11 0.22 -10000 0 -0.39 89 89
HBP1 0.026 0.003 -10000 0 -10000 0 0
MEF2C -0.062 0.18 -10000 0 -0.36 66 66
MEF2A -0.058 0.17 -10000 0 -0.35 65 65
EIF4EBP1 -0.065 0.19 -10000 0 -0.38 62 62
KRT19 -0.068 0.19 -10000 0 -0.38 65 65
ELK4 -0.057 0.17 -10000 0 -0.34 65 65
ATF6 -0.048 0.16 -10000 0 -0.34 56 56
ATF1 -0.065 0.18 -10000 0 -0.38 64 64
p38alpha-beta/MAPKAPK2 -0.032 0.18 -10000 0 -0.34 65 65
p38alpha-beta/MAPKAPK3 -0.031 0.19 -10000 0 -0.35 63 63
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.016 0.059 -10000 0 -0.34 5 5
Crk/p130 Cas/Paxillin -0.11 0.12 -10000 0 -0.25 85 85
JUN -0.079 0.11 -10000 0 -0.34 10 10
HRAS 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.067 0.14 -10000 0 -0.24 99 99
RAP1A 0.027 0.002 -10000 0 -10000 0 0
FRS2 0.03 0.037 0.29 5 -10000 0 5
RAP1A/GDP 0.02 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.068 0.14 -10000 0 -0.24 102 102
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.076 0.13 -10000 0 -0.23 105 105
RHOA 0.025 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.061 0.13 -10000 0 -0.21 103 103
GRB7 0.032 0.064 0.29 10 -0.42 2 12
RET51/GFRalpha1/GDNF -0.07 0.14 -10000 0 -0.24 104 104
MAPKKK cascade -0.083 0.12 -10000 0 -0.23 92 92
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.079 0.13 -10000 0 -0.23 107 107
lamellipodium assembly -0.097 0.12 -10000 0 -0.24 90 90
RET51/GFRalpha1/GDNF/SHC -0.065 0.14 -10000 0 -0.24 98 98
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.07 0.12 -10000 0 -0.23 96 96
RET9/GFRalpha1/GDNF/Shank3 -0.075 0.13 -10000 0 -0.23 105 105
MAPK3 -0.076 0.11 0.18 2 -0.21 97 99
DOK1 0.027 0.016 0.27 1 -10000 0 1
DOK6 -0.12 0.21 -10000 0 -0.42 89 89
PXN 0.026 0.004 -10000 0 -10000 0 0
neurite development -0.097 0.12 -10000 0 -0.28 44 44
DOK5 -0.009 0.12 0.29 1 -0.42 20 21
GFRA1 -0.19 0.22 -10000 0 -0.42 127 127
MAPK8 -0.084 0.11 -10000 0 -0.22 55 55
HRAS/GTP -0.082 0.14 -10000 0 -0.25 96 96
tube development -0.068 0.12 0.2 5 -0.22 103 108
MAPK1 -0.077 0.11 0.19 1 -0.21 53 54
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.11 0.16 3 -0.21 99 102
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
PDLIM7 0.025 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.18 -10000 0 -0.29 133 133
SHC1 0.025 0.018 0.29 1 -10000 0 1
RET51/GFRalpha1/GDNF/Dok4 -0.068 0.14 -10000 0 -0.24 103 103
RET51/GFRalpha1/GDNF/Dok5 -0.081 0.16 -10000 0 -0.26 105 105
PRKCA 0.026 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
CREB1 -0.096 0.13 -10000 0 -0.25 94 94
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.076 0.11 -10000 0 -0.21 90 90
RET51/GFRalpha1/GDNF/Grb7 -0.066 0.14 -10000 0 -0.24 99 99
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.022 0.072 0.27 6 -0.42 5 11
DOK4 0.026 0.005 -10000 0 -10000 0 0
JNK cascade -0.078 0.11 -10000 0 -0.33 10 10
RET9/GFRalpha1/GDNF/FRS2 -0.073 0.13 0.2 4 -0.23 102 106
SHANK3 0.025 0.006 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.078 0.11 -10000 0 -0.21 92 92
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.082 0.12 0.24 1 -0.22 99 100
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.082 0.12 -10000 0 -0.22 96 96
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.078 0.12 -10000 0 -0.22 92 92
PI3K -0.13 0.18 -10000 0 -0.33 92 92
SOS1 0.026 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.066 0.12 -10000 0 -0.22 103 103
GRB10 0.024 0.028 -10000 0 -0.42 1 1
activation of MAPKK activity -0.059 0.12 0.19 1 -0.2 96 97
RET51/GFRalpha1/GDNF/FRS2 -0.068 0.14 0.36 1 -0.24 101 102
GAB1 0.026 0.006 -10000 0 -10000 0 0
IRS1 0.02 0.047 -10000 0 -0.42 3 3
IRS2 0.012 0.076 -10000 0 -0.42 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.077 0.12 -10000 0 -0.22 90 90
RET51/GFRalpha1/GDNF/PKC alpha -0.068 0.14 -10000 0 -0.24 101 101
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GDNF 0.007 0.036 0.28 3 -10000 0 3
RAC1 0.026 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.073 0.14 -10000 0 -0.24 106 106
Rac1/GTP -0.11 0.14 -10000 0 -0.28 83 83
RET9/GFRalpha1/GDNF -0.088 0.13 -10000 0 -0.25 105 105
GFRalpha1/GDNF -0.1 0.16 -10000 0 -0.3 105 105
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.018 0.2 -10000 0 -0.53 31 31
IHH 0.051 0.11 0.3 24 -0.24 9 33
SHH Np/Cholesterol/GAS1 -0.1 0.14 -10000 0 -0.25 118 118
LRPAP1 0.027 0.017 0.29 1 -10000 0 1
dorsoventral neural tube patterning 0.1 0.14 0.25 118 -10000 0 118
SMO/beta Arrestin2 -0.025 0.16 -10000 0 -0.39 26 26
SMO -0.038 0.16 -10000 0 -0.36 39 39
AKT1 -0.01 0.12 -10000 0 -0.45 12 12
ARRB2 0.024 0.008 -10000 0 -10000 0 0
BOC -0.009 0.12 -10000 0 -0.42 20 20
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
heart looping -0.036 0.15 -10000 0 -0.36 39 39
STIL -0.062 0.14 0.25 1 -0.29 36 37
DHH N/PTCH2 0.01 0.093 -10000 0 -0.3 22 22
DHH N/PTCH1 0.003 0.12 -10000 0 -0.26 38 38
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
DHH 0.006 0.085 -10000 0 -0.42 10 10
PTHLH -0.059 0.31 -10000 0 -0.84 32 32
determination of left/right symmetry -0.036 0.15 -10000 0 -0.36 39 39
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
skeletal system development -0.057 0.3 -10000 0 -0.83 32 32
IHH N/Hhip -0.039 0.18 0.2 18 -0.34 63 81
DHH N/Hhip -0.054 0.15 0.2 1 -0.3 69 70
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.036 0.15 -10000 0 -0.36 39 39
pancreas development -0.083 0.19 0.27 1 -0.42 62 63
HHAT 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.035 0.013 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.047 0.16 0.27 1 -0.42 43 44
somite specification -0.036 0.15 -10000 0 -0.36 39 39
SHH Np/Cholesterol/PTCH1 -0.072 0.14 -10000 0 -0.24 86 86
SHH Np/Cholesterol/PTCH2 -0.074 0.13 -10000 0 -0.24 96 96
SHH Np/Cholesterol/Megalin -0.048 0.13 0.17 24 -0.22 88 112
SHH -0.1 0.14 -10000 0 -0.3 90 90
catabolic process 0.002 0.12 -10000 0 -0.3 32 32
SMO/Vitamin D3 -0.075 0.16 -10000 0 -0.37 36 36
SHH Np/Cholesterol/Hhip -0.12 0.15 -10000 0 -0.26 126 126
LRP2 0.069 0.098 0.27 50 -10000 0 50
receptor-mediated endocytosis -0.074 0.16 -10000 0 -0.38 31 31
SHH Np/Cholesterol/BOC -0.075 0.13 -10000 0 -0.24 95 95
SHH Np/Cholesterol/CDO -0.092 0.14 -10000 0 -0.24 111 111
mesenchymal cell differentiation 0.12 0.15 0.26 126 -10000 0 126
mol:Vitamin D3 -0.068 0.14 -10000 0 -0.24 86 86
IHH N/PTCH2 0.032 0.1 0.2 22 -0.31 15 37
CDON -0.029 0.14 -10000 0 -0.42 32 32
IHH N/PTCH1 0.019 0.14 -10000 0 -0.3 33 33
Megalin/LRPAP1 0.065 0.065 0.2 46 -10000 0 46
PTCH2 0.006 0.093 -10000 0 -0.42 12 12
SHH Np/Cholesterol -0.069 0.11 -10000 0 -0.22 90 90
PTCH1 0.002 0.12 -10000 0 -0.3 32 32
HHIP -0.083 0.19 0.27 1 -0.42 62 63
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.081 0.19 -10000 0 -0.39 60 60
CRKL -0.092 0.18 -10000 0 -0.4 62 62
HRAS -0.088 0.19 -10000 0 -0.38 62 62
mol:PIP3 -0.082 0.18 -10000 0 -0.38 66 66
SPRED1 0.026 0.005 -10000 0 -10000 0 0
SPRED2 0.026 0.005 -10000 0 -10000 0 0
GAB1 -0.099 0.19 -10000 0 -0.42 65 65
FOXO3 -0.077 0.18 -10000 0 -0.37 61 61
AKT1 -0.082 0.19 -10000 0 -0.4 61 61
BAD -0.077 0.18 -10000 0 -0.37 60 60
megakaryocyte differentiation -0.097 0.19 -10000 0 -0.41 66 66
GSK3B -0.073 0.18 0.31 1 -0.37 59 60
RAF1 -0.064 0.15 0.25 4 -0.32 52 56
SHC1 0.025 0.018 0.29 1 -10000 0 1
STAT3 -0.1 0.19 -10000 0 -0.42 65 65
STAT1 -0.24 0.46 -10000 0 -1 67 67
HRAS/SPRED1 -0.063 0.16 -10000 0 -0.32 59 59
cell proliferation -0.098 0.19 -10000 0 -0.42 66 66
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
TEC 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.085 0.2 -10000 0 -0.41 65 65
HRAS/SPRED2 -0.062 0.16 -10000 0 -0.32 58 58
LYN/TEC/p62DOK -0.058 0.19 -10000 0 -0.4 57 57
MAPK3 -0.037 0.13 0.25 6 -0.27 21 27
STAP1 -0.11 0.2 -10000 0 -0.43 68 68
GRAP2 -0.028 0.14 -10000 0 -0.42 32 32
JAK2 -0.2 0.41 -10000 0 -0.87 67 67
STAT1 (dimer) -0.23 0.45 -10000 0 -0.98 67 67
mol:Gleevec 0.002 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.071 0.21 -10000 0 -0.42 63 63
actin filament polymerization -0.095 0.19 -10000 0 -0.41 64 64
LYN 0.024 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.15 0.28 -10000 0 -0.59 69 69
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.064 0.18 -10000 0 -0.38 60 60
PI3K -0.063 0.19 -10000 0 -0.4 59 59
PTEN 0.025 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.26 0.54 -10000 0 -1.2 64 64
MAPK8 -0.1 0.2 -10000 0 -0.42 66 66
STAT3 (dimer) -0.098 0.19 -10000 0 -0.41 65 65
positive regulation of transcription -0.027 0.11 0.23 7 -0.22 20 27
mol:GDP -0.086 0.19 -10000 0 -0.39 61 61
PIK3C2B -0.099 0.19 -10000 0 -0.42 65 65
CBL/CRKL -0.076 0.18 -10000 0 -0.38 62 62
FER -0.1 0.19 -10000 0 -0.42 65 65
SH2B3 -0.096 0.19 -10000 0 -0.42 65 65
PDPK1 -0.076 0.17 -10000 0 -0.35 65 65
SNAI2 -0.096 0.19 -10000 0 -0.42 60 60
positive regulation of cell proliferation -0.17 0.33 -10000 0 -0.72 68 68
KITLG 0.005 0.063 -10000 0 -0.44 4 4
cell motility -0.17 0.33 -10000 0 -0.72 68 68
PTPN6 0.029 0.014 -10000 0 -10000 0 0
EPOR -0.081 0.24 -10000 0 -0.77 17 17
STAT5A (dimer) -0.14 0.27 -10000 0 -0.58 69 69
SOCS1 0.026 0.016 0.27 1 -10000 0 1
cell migration 0.11 0.2 0.43 69 -10000 0 69
SOS1 0.026 0.004 -10000 0 -10000 0 0
EPO 0.036 0.076 0.26 24 -10000 0 24
VAV1 0.005 0.098 0.27 1 -0.42 13 14
GRB10 -0.098 0.19 -10000 0 -0.41 64 64
PTPN11 0.028 0.01 -10000 0 -10000 0 0
SCF/KIT -0.1 0.2 -10000 0 -0.44 66 66
GO:0007205 0.005 0.01 -10000 0 -10000 0 0
MAP2K1 -0.042 0.14 0.26 7 -0.26 49 56
CBL 0.025 0.007 -10000 0 -10000 0 0
KIT -0.3 0.56 -10000 0 -1.3 65 65
MAP2K2 -0.04 0.14 0.26 7 -0.26 49 56
SHC/Grb2/SOS1 -0.058 0.19 -10000 0 -0.4 55 55
STAT5A -0.14 0.28 -10000 0 -0.6 69 69
GRB2 0.026 0.005 -10000 0 -10000 0 0
response to radiation -0.094 0.19 -10000 0 -0.42 60 60
SHC/GRAP2 0.002 0.1 -10000 0 -0.3 26 26
PTPRO -0.098 0.19 -10000 0 -0.42 65 65
SH2B2 -0.097 0.19 -10000 0 -0.42 64 64
DOK1 0.027 0.016 0.27 1 -10000 0 1
MATK -0.11 0.2 -10000 0 -0.44 69 69
CREBBP 0.004 0.068 -10000 0 -0.18 7 7
BCL2 -0.15 0.38 -10000 0 -0.98 35 35
Nongenotropic Androgen signaling

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
PTK2 0.004 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.048 0.13 -10000 0 -0.23 90 90
regulation of S phase of mitotic cell cycle -0.052 0.11 -10000 0 -0.22 74 74
GNAO1 -0.11 0.2 -10000 0 -0.42 78 78
HRAS 0.024 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.016 0.006 -10000 0 -10000 0 0
PELP1 0.023 0.008 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 -0.081 0.11 0.17 6 -0.3 26 32
T-DHT/AR -0.09 0.15 -10000 0 -0.3 89 89
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 79 79
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.024 0.028 -10000 0 -0.42 1 1
mol:GDP -0.12 0.17 -10000 0 -0.36 86 86
cell proliferation -0.15 0.2 -10000 0 -0.43 79 79
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
FOS -0.24 0.36 -10000 0 -0.77 82 82
mol:Ca2+ -0.037 0.041 -10000 0 -0.079 110 110
MAPK3 -0.12 0.16 0.22 1 -0.34 69 70
MAPK1 -0.072 0.12 -10000 0 -0.29 29 29
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 78 78
cAMP biosynthetic process 0.025 0.038 0.19 4 -10000 0 4
GNG2 0.021 0.047 -10000 0 -0.42 3 3
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 78 78
HRAS/GTP -0.057 0.12 -10000 0 -0.22 79 79
actin cytoskeleton reorganization 0.035 0.015 -10000 0 -10000 0 0
SRC 0.024 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 78 78
PI3K 0.032 0.012 -10000 0 -10000 0 0
apoptosis 0.14 0.21 0.43 84 -10000 0 84
T-DHT/AR/PELP1 -0.067 0.13 -10000 0 -0.25 87 87
HRAS/GDP -0.11 0.17 -10000 0 -0.34 86 86
CREB1 -0.15 0.22 -10000 0 -0.46 84 84
RAC1-CDC42/GTP 0.043 0.019 -10000 0 -10000 0 0
AR -0.13 0.21 -10000 0 -0.42 89 89
GNB1 0.027 0.002 -10000 0 -10000 0 0
RAF1 -0.068 0.11 0.2 2 -0.23 61 63
RAC1-CDC42/GDP -0.082 0.18 -10000 0 -0.33 82 82
T-DHT/AR/PELP1/Src -0.049 0.12 -10000 0 -0.23 79 79
MAP2K2 -0.081 0.11 0.17 6 -0.3 26 32
T-DHT/AR/PELP1/Src/PI3K -0.052 0.11 -10000 0 -0.22 74 74
GNAZ -0.075 0.18 -10000 0 -0.42 59 59
SHBG 0.023 0.011 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.15 0.21 -10000 0 -0.43 81 81
mol:T-DHT 0 0.001 -10000 0 -0.003 40 40
RAC1 0.026 0.005 -10000 0 -10000 0 0
GNRH1 0.004 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.13 0.17 -10000 0 -0.32 95 95
CDC42 0.027 0.002 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.4 0.59 0.74 1 -1.2 72 73
STAT6 (cleaved dimer) -0.46 0.61 -10000 0 -1.2 82 82
IGHG1 -0.11 0.22 -10000 0 -0.72 3 3
IGHG3 -0.41 0.56 -10000 0 -1.1 79 79
AKT1 -0.2 0.34 -10000 0 -0.82 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.33 0.45 1 -0.81 30 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.36 -10000 0 -0.8 39 39
THY1 -0.42 0.58 -10000 0 -1.2 73 73
MYB 0.054 0.086 0.27 32 -0.42 1 33
HMGA1 0.028 0.021 0.27 2 -10000 0 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.43 0.51 1 -0.78 73 74
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.37 -10000 0 -0.82 39 39
SP1 0.026 0.026 -10000 0 -10000 0 0
INPP5D 0.016 0.061 -10000 0 -0.42 5 5
SOCS5 0.028 0.036 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.44 0.61 -10000 0 -1.2 78 78
SOCS1 -0.26 0.37 -10000 0 -0.74 73 73
SOCS3 -0.28 0.46 -10000 0 -1.2 40 40
FCER2 -0.65 0.74 -10000 0 -1.4 122 122
PARP14 0.014 0.028 -10000 0 -10000 0 0
CCL17 -0.42 0.59 -10000 0 -1.2 72 72
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.3 -10000 0 -0.69 31 31
T cell proliferation -0.44 0.61 -10000 0 -1.2 77 77
IL4R/JAK1 -0.43 0.59 -10000 0 -1.2 75 75
EGR2 -0.59 0.73 -10000 0 -1.5 93 93
JAK2 -0.012 0.056 -10000 0 -10000 0 0
JAK3 0.025 0.031 0.3 2 -10000 0 2
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
JAK1 0.006 0.032 -10000 0 -10000 0 0
COL1A2 -0.15 0.34 -10000 0 -1.4 13 13
CCL26 -0.44 0.6 -10000 0 -1.2 75 75
IL4R -0.45 0.64 -10000 0 -1.3 72 72
PTPN6 0.028 0.027 -10000 0 -10000 0 0
IL13RA2 -0.44 0.6 -10000 0 -1.2 73 73
IL13RA1 -0.013 0.059 -10000 0 -10000 0 0
IRF4 -0.23 0.49 0.48 1 -1.2 45 46
ARG1 -0.087 0.21 -10000 0 -0.66 13 13
CBL -0.25 0.39 -10000 0 -0.74 73 73
GTF3A 0.03 0.016 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.01 0.08 -10000 0 -10000 0 0
IRF4/BCL6 -0.19 0.44 -10000 0 -1.1 45 45
CD40LG -0.036 0.14 0.36 1 -0.42 29 30
MAPK14 -0.28 0.45 -10000 0 -0.87 65 65
mitosis -0.19 0.32 -10000 0 -0.76 35 35
STAT6 -0.5 0.74 -10000 0 -1.4 78 78
SPI1 0.026 0.062 0.27 3 -0.41 4 7
RPS6KB1 -0.18 0.31 -10000 0 -0.73 34 34
STAT6 (dimer) -0.5 0.74 -10000 0 -1.4 78 78
STAT6 (dimer)/PARP14 -0.5 0.66 -10000 0 -1.3 79 79
mast cell activation 0.008 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.38 -10000 0 -0.84 44 44
FRAP1 -0.2 0.34 -10000 0 -0.82 35 35
LTA -0.44 0.61 -10000 0 -1.3 74 74
FES 0.026 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.48 0.69 1.4 78 -10000 0 78
CCL11 -0.45 0.62 -10000 0 -1.3 77 77
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.36 0.48 1 -0.86 34 35
IL2RG 0.015 0.082 0.28 5 -0.42 7 12
IL10 -0.45 0.62 -10000 0 -1.3 76 76
IRS1 0.02 0.047 -10000 0 -0.42 3 3
IRS2 0.012 0.076 -10000 0 -0.42 8 8
IL4 -0.092 0.23 -10000 0 -1.1 8 8
IL5 -0.43 0.59 -10000 0 -1.2 72 72
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.34 0.48 -10000 0 -0.94 75 75
COL1A1 -0.12 0.27 -10000 0 -1.6 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.61 -10000 0 -1.3 71 71
IL2R gamma/JAK3 0.027 0.072 0.3 5 -0.3 7 12
TFF3 -0.56 0.71 -10000 0 -1.4 99 99
ALOX15 -0.41 0.6 -10000 0 -1.2 73 73
MYBL1 0.026 0.027 0.27 3 -10000 0 3
T-helper 2 cell differentiation -0.37 0.51 -10000 0 -1 81 81
SHC1 0.025 0.018 0.29 1 -10000 0 1
CEBPB 0.028 0.032 -10000 0 -0.42 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.34 -10000 0 -0.78 35 35
mol:PI-3-4-5-P3 -0.2 0.34 -10000 0 -0.82 35 35
PI3K -0.21 0.37 -10000 0 -0.9 35 35
DOK2 0.012 0.068 0.27 1 -0.42 6 7
ETS1 0.022 0.034 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.27 -10000 0 -0.65 26 26
ITGB3 -0.48 0.65 -10000 0 -1.3 80 80
PIGR -0.69 0.72 -10000 0 -1.3 134 134
IGHE 0.029 0.07 0.18 14 -0.28 1 15
MAPKKK cascade -0.14 0.26 -10000 0 -0.64 26 26
BCL6 0.029 0.014 -10000 0 -10000 0 0
OPRM1 -0.43 0.58 -10000 0 -1.2 73 73
RETNLB -0.42 0.59 -10000 0 -1.2 71 71
SELP -0.52 0.7 -10000 0 -1.4 92 92
AICDA -0.41 0.56 -10000 0 -1.2 73 73
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 0.045 0.038 0.2 13 -10000 0 13
VLDLR 0.01 0.076 -10000 0 -0.42 8 8
CRKL 0.027 0.022 0.27 2 -10000 0 2
LRPAP1 0.027 0.017 0.29 1 -10000 0 1
FYN 0.02 0.047 -10000 0 -0.42 3 3
ITGA3 0.029 0.027 0.28 3 -10000 0 3
RELN/VLDLR/Fyn -0.055 0.15 -10000 0 -0.26 89 89
MAPK8IP1/MKK7/MAP3K11/JNK1 0.059 0.048 -10000 0 -0.22 4 4
AKT1 -0.076 0.13 0.16 2 -0.24 86 88
MAP2K7 0.026 0.005 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
DAB1 -0.013 0.14 0.27 15 -0.42 23 38
RELN/LRP8/DAB1 -0.046 0.16 0.33 2 -0.24 100 102
LRPAP1/LRP8 0.062 0.06 0.2 39 -10000 0 39
RELN/LRP8/DAB1/Fyn -0.041 0.16 0.33 2 -0.22 102 104
DAB1/alpha3/beta1 Integrin -0.044 0.14 0.24 2 -0.24 61 63
long-term memory -0.07 0.19 0.34 2 -0.26 112 114
DAB1/LIS1 -0.037 0.16 0.31 1 -0.23 92 93
DAB1/CRLK/C3G -0.043 0.14 0.24 2 -0.24 58 60
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
DAB1/NCK2 -0.034 0.16 0.32 1 -0.23 95 96
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.055 0.16 0.27 2 -0.42 44 46
CDK5R1 0.041 0.059 0.27 16 -10000 0 16
RELN -0.12 0.21 0.27 3 -0.42 87 90
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.036 0.16 0.35 2 -0.25 88 90
GRIN2A/RELN/LRP8/DAB1/Fyn -0.073 0.19 0.48 1 -0.27 116 117
MAPK8 0.02 0.047 -10000 0 -0.42 3 3
RELN/VLDLR/DAB1 -0.064 0.15 -10000 0 -0.25 100 100
ITGB1 0.025 0.006 -10000 0 -10000 0 0
MAP1B -0.099 0.14 0.33 1 -0.26 101 102
RELN/LRP8 -0.032 0.16 0.35 2 -0.25 85 87
GRIN2B/RELN/LRP8/DAB1/Fyn -0.032 0.17 0.34 2 -0.23 100 102
PI3K 0.035 0.013 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.019 0.2 2 -10000 0 2
RAP1A -0.072 0.12 0.33 4 -0.37 10 14
PAFAH1B1 0.024 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.032 0.27 1 -0.42 1 2
CRLK/C3G 0.036 0.02 0.2 2 -10000 0 2
GRIN2B 0.007 0.051 0.27 8 -10000 0 8
NCK2 0.026 0.003 -10000 0 -10000 0 0
neuron differentiation -0.048 0.12 0.2 2 -0.31 21 23
neuron adhesion -0.063 0.13 0.32 5 -0.36 9 14
LRP8 0.068 0.092 0.27 45 -10000 0 45
GSK3B -0.074 0.12 -10000 0 -0.23 85 85
RELN/VLDLR/DAB1/Fyn -0.056 0.15 -10000 0 -0.23 102 102
MAP3K11 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.075 0.14 -10000 0 -0.25 89 89
CDK5 0.026 0.004 -10000 0 -10000 0 0
MAPT -0.003 0.16 0.73 7 -0.37 19 26
neuron migration -0.089 0.16 0.28 6 -0.3 69 75
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.048 0.12 0.2 2 -0.31 21 23
RELN/VLDLR -0.024 0.15 0.35 2 -0.23 85 87
Thromboxane A2 receptor 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
TGM2 0.018 0.081 0.27 6 -0.42 7 13
GNB1/GNG2 -0.076 0.089 -10000 0 -0.19 99 99
AKT1 -0.053 0.13 0.34 4 -0.21 46 50
EGF 0.035 0.057 0.27 14 -10000 0 14
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.002 0.064 0.23 2 -0.24 2 4
mol:Ca2+ -0.09 0.18 0.35 5 -0.3 103 108
LYN 0.003 0.057 0.28 1 -0.3 1 2
RhoA/GTP -0.039 0.074 0.14 3 -0.13 85 88
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.11 0.2 0.43 3 -0.34 98 101
GNG2 0.021 0.047 -10000 0 -0.42 3 3
ARRB2 0.024 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.035 0.14 -10000 0 -0.46 18 18
G beta5/gamma2 -0.092 0.12 -10000 0 -0.24 98 98
PRKCH -0.11 0.2 0.41 3 -0.34 99 102
DNM1 0.021 0.039 -10000 0 -0.42 2 2
TXA2/TP beta/beta Arrestin3 0.003 0.072 -10000 0 -0.55 4 4
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.001 0.093 -10000 0 -0.42 12 12
G12 family/GTP -0.1 0.16 -10000 0 -0.3 97 97
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
ADRBK2 0.024 0.032 0.29 1 -0.42 1 2
RhoA/GTP/ROCK1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.048 0.12 0.34 15 -0.29 3 18
mol:NADP 0.027 0.015 0.27 1 -10000 0 1
RAB11A 0.026 0.004 -10000 0 -10000 0 0
PRKG1 -0.068 0.18 -10000 0 -0.42 54 54
mol:IP3 -0.12 0.22 0.44 3 -0.37 103 106
cell morphogenesis 0.032 0.01 -10000 0 -10000 0 0
PLCB2 -0.17 0.28 0.53 2 -0.5 103 105
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.006 0.078 0.23 2 -0.2 16 18
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.001 0.064 0.21 3 -0.24 6 9
RHOA 0.025 0.006 -10000 0 -10000 0 0
PTGIR 0.024 0.028 -10000 0 -0.42 1 1
PRKCB1 -0.12 0.21 0.43 3 -0.37 102 105
GNAQ 0.025 0.007 -10000 0 -10000 0 0
mol:L-citrulline 0.027 0.015 0.27 1 -10000 0 1
TXA2/TXA2-R family -0.17 0.29 0.49 3 -0.52 100 103
LCK 0.001 0.068 0.28 1 -0.29 3 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.017 0.051 -10000 0 -0.19 12 12
TXA2-R family/G12 family/GDP/G beta/gamma 0.024 0.046 -10000 0 -0.38 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.02 0.051 -10000 0 -0.19 11 11
MAPK14 -0.068 0.14 0.32 4 -0.23 98 102
TGM2/GTP -0.14 0.24 0.5 3 -0.42 96 99
MAPK11 -0.068 0.14 0.32 4 -0.23 97 101
ARHGEF1 -0.054 0.1 0.25 4 -0.18 87 91
GNAI2 0.025 0.006 -10000 0 -10000 0 0
JNK cascade -0.12 0.22 0.46 3 -0.38 100 103
RAB11/GDP 0.026 0.005 -10000 0 -10000 0 0
ICAM1 -0.082 0.17 0.34 5 -0.28 99 104
cAMP biosynthetic process -0.11 0.2 0.43 3 -0.35 100 103
Gq family/GTP/EBP50 -0.024 0.084 -10000 0 -0.18 53 53
actin cytoskeleton reorganization 0.032 0.01 -10000 0 -10000 0 0
SRC 0.002 0.061 0.23 2 -0.3 1 3
GNB5 0.026 0.004 -10000 0 -10000 0 0
GNB1 0.027 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.011 0.085 0.23 12 -0.26 4 16
VCAM1 -0.091 0.18 0.41 3 -0.3 99 102
TP beta/Gq family/GDP/G beta5/gamma2 -0.035 0.14 -10000 0 -0.46 18 18
platelet activation -0.09 0.18 0.39 4 -0.3 99 103
PGI2/IP 0.018 0.02 -10000 0 -0.3 1 1
PRKACA 0.005 0.051 -10000 0 -0.22 13 13
Gq family/GDP/G beta5/gamma2 -0.031 0.13 -10000 0 -0.41 18 18
TXA2/TP beta/beta Arrestin2 -0.018 0.1 -10000 0 -0.36 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.003 0.047 -10000 0 -0.21 13 13
mol:DAG -0.13 0.24 0.45 3 -0.41 102 105
EGFR 0.023 0.073 0.29 6 -0.42 5 11
TXA2/TP alpha -0.16 0.27 0.48 3 -0.48 99 102
Gq family/GTP -0.027 0.085 -10000 0 -0.21 44 44
YES1 0.004 0.06 0.23 2 -0.3 1 3
GNAI2/GTP 0 0.052 -10000 0 -0.2 11 11
PGD2/DP 0.003 0.065 -10000 0 -0.29 12 12
SLC9A3R1 0.034 0.044 0.27 9 -10000 0 9
FYN 0.002 0.066 0.23 2 -0.26 4 6
mol:NO 0.027 0.015 0.27 1 -10000 0 1
GNA15 0.022 0.039 -10000 0 -0.42 2 2
PGK/cGMP -0.024 0.12 0.18 1 -0.25 53 54
RhoA/GDP 0.026 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.03 0.081 -10000 0 -0.22 18 18
NOS3 0.027 0.015 0.27 1 -10000 0 1
RAC1 0.026 0.005 -10000 0 -10000 0 0
PRKCA -0.1 0.2 0.38 4 -0.34 96 100
PRKCB -0.14 0.22 0.48 2 -0.4 100 102
PRKCE -0.11 0.2 0.45 3 -0.35 96 99
PRKCD -0.12 0.22 0.44 3 -0.38 99 102
PRKCG -0.12 0.22 0.41 4 -0.38 98 102
muscle contraction -0.16 0.27 0.5 3 -0.48 101 104
PRKCZ -0.11 0.2 0.43 3 -0.34 100 103
ARR3 -0.009 0.017 -10000 0 -10000 0 0
TXA2/TP beta 0.021 0.058 -10000 0 -0.21 12 12
PRKCQ -0.11 0.22 0.42 5 -0.37 97 102
MAPKKK cascade -0.15 0.26 0.45 3 -0.45 102 105
SELE -0.12 0.22 0.42 3 -0.39 99 102
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.061 -10000 0 -0.2 12 12
ROCK1 0.026 0.005 -10000 0 -10000 0 0
GNA14 -0.031 0.15 -10000 0 -0.42 33 33
chemotaxis -0.2 0.33 0.52 3 -0.61 99 102
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.024 0.028 -10000 0 -0.42 1 1
Rac1/GTP 0.018 0.004 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.037 0.011 -10000 0 -10000 0 0
Necdin/E2F1 0.02 0.13 0.2 36 -0.29 29 65
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.022 0.15 -10000 0 -0.25 76 76
NGF (dimer)/p75(NTR)/BEX1 -0.064 0.18 -10000 0 -0.31 86 86
NT-4/5 (dimer)/p75(NTR) -0.056 0.16 0.2 3 -0.32 70 73
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.063 0.12 0.18 15 -0.25 68 83
IKBKG 0.026 0.004 -10000 0 -10000 0 0
BDNF -0.046 0.16 -10000 0 -0.42 42 42
MGDIs/NGR/p75(NTR)/LINGO1 0.009 0.15 0.22 37 -0.25 56 93
FURIN 0.027 0.015 0.27 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.057 0.16 -10000 0 -0.28 84 84
LINGO1 0.036 0.049 0.27 11 -10000 0 11
Sortilin/TRAF6/NRIF 0.025 0.018 -10000 0 -10000 0 0
proBDNF (dimer) -0.046 0.16 -10000 0 -0.42 42 42
NTRK1 0.024 0.034 0.27 4 -10000 0 4
RTN4R 0.058 0.083 0.27 35 -10000 0 35
neuron apoptosis -0.07 0.18 0.34 3 -0.42 32 35
IRAK1 0.026 0.004 -10000 0 -10000 0 0
SHC1 -0.062 0.14 -10000 0 -0.28 66 66
ARHGDIA 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.06 0.035 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.031 0.16 -10000 0 -0.26 78 78
MAGEH1 0.023 0.039 -10000 0 -0.42 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.062 0.18 -10000 0 -0.3 92 92
Mammalian IAPs/DIABLO 0.049 0.065 0.22 1 -0.23 12 13
proNGF (dimer) -0.034 0.15 -10000 0 -0.42 35 35
MAGED1 0.026 0.003 -10000 0 -10000 0 0
APP 0.024 0.028 -10000 0 -0.42 1 1
NT-4/5 (dimer) -0.012 0.12 -10000 0 -0.42 22 22
ZNF274 0.026 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.046 0.13 -10000 0 -0.24 76 76
NGF -0.034 0.15 -10000 0 -0.42 35 35
cell cycle arrest -0.065 0.12 0.23 7 -0.22 77 84
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.046 0.13 -10000 0 -0.26 60 60
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.034 0.15 -10000 0 -0.27 68 68
NCSTN 0.023 0.009 -10000 0 -10000 0 0
mol:GTP -0.049 0.16 0.2 4 -0.28 79 83
PSENEN 0.025 0.006 -10000 0 -10000 0 0
mol:ceramide -0.063 0.13 0.18 6 -0.26 77 83
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.043 0.12 -10000 0 -0.37 18 18
p75(NTR)/beta APP -0.032 0.14 0.2 4 -0.3 56 60
BEX1 -0.01 0.12 0.27 4 -0.42 20 24
mol:GDP -0.088 0.13 -10000 0 -0.28 78 78
NGF (dimer) 0.028 0.14 0.22 1 -0.24 46 47
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.024 0.14 0.36 5 -0.23 55 60
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
RAC1/GTP -0.038 0.14 -10000 0 -0.24 76 76
MYD88 0.025 0.006 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.049 0.16 0.2 4 -0.28 79 83
RHOB 0.026 0.005 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.059 0.064 0.2 41 -10000 0 41
NT3 (dimer) -0.054 0.17 0.27 1 -0.42 47 48
TP53 -0.073 0.12 0.35 2 -0.24 74 76
PRDM4 -0.064 0.14 0.18 6 -0.26 77 83
BDNF (dimer) -0.01 0.18 0.35 5 -0.27 75 80
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
SORT1 0.027 0.002 -10000 0 -10000 0 0
activation of caspase activity -0.025 0.15 -10000 0 -0.25 76 76
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.03 0.16 -10000 0 -0.26 76 76
RHOC 0.027 0.002 -10000 0 -10000 0 0
XIAP 0.028 0.016 0.29 1 -10000 0 1
MAPK10 -0.1 0.17 0.38 1 -0.34 68 69
DIABLO 0.026 0.004 -10000 0 -10000 0 0
SMPD2 -0.063 0.13 0.18 6 -0.26 77 83
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.024 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.046 0.16 -10000 0 -0.29 77 77
PSEN1 0.026 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.006 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.086 0.18 0.2 3 -0.33 89 92
MAPK8 -0.091 0.16 0.35 3 -0.33 63 66
MAPK9 -0.09 0.16 0.41 2 -0.33 65 67
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 -0.054 0.17 0.27 1 -0.42 47 48
NTF4 -0.012 0.12 -10000 0 -0.42 22 22
NDN -0.028 0.14 -10000 0 -0.42 32 32
RAC1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.023 0.14 -10000 0 -0.23 75 75
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.024 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.049 0.16 0.2 4 -0.28 79 83
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.03 0.15 -10000 0 -0.24 82 82
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.04 0.16 -10000 0 -0.26 84 84
PRKACB 0.023 0.039 -10000 0 -0.42 2 2
proBDNF (dimer)/p75 ECD -0.018 0.12 -10000 0 -0.3 42 42
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.007 0.096 0.29 2 -0.42 12 14
BIRC2 0.027 0.024 0.29 2 -10000 0 2
neuron projection morphogenesis -0.095 0.15 -10000 0 -0.29 80 80
BAD -0.099 0.17 0.36 2 -0.34 65 67
RIPK2 0.022 0.01 -10000 0 -10000 0 0
NGFR -0.067 0.19 0.27 4 -0.42 57 61
CYCS -0.073 0.12 0.2 7 -0.24 75 82
ADAM17 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.025 0.14 -10000 0 -0.26 63 63
BCL2L11 -0.099 0.17 0.36 2 -0.34 64 66
BDNF (dimer)/p75(NTR) -0.081 0.18 0.2 4 -0.33 85 89
PI3K -0.028 0.15 -10000 0 -0.26 70 70
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.031 0.16 -10000 0 -0.26 77 77
NDNL2 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
PRKCI 0.025 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.07 0.18 0.2 4 -0.33 78 82
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.03 0.16 -10000 0 -0.26 77 77
TRAF6 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.005 -10000 0 -10000 0 0
PRKCZ 0.025 0.027 -10000 0 -0.42 1 1
PLG -0.006 0.03 0.27 2 -10000 0 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.1 0.17 -10000 0 -0.3 102 102
SQSTM1 0.025 0.006 -10000 0 -10000 0 0
NGFRAP1 0.023 0.039 -10000 0 -0.42 2 2
CASP3 -0.093 0.16 0.35 2 -0.33 63 65
E2F1 0.084 0.11 0.27 62 -10000 0 62
CASP9 0.026 0.003 -10000 0 -10000 0 0
IKK complex -0.015 0.14 -10000 0 -0.35 25 25
NGF (dimer)/TRKA -0.001 0.11 0.2 4 -0.3 31 35
MMP7 0.044 0.15 0.27 47 -0.42 15 62
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.02 0.15 -10000 0 -0.25 74 74
MMP3 -0.011 0.17 0.27 23 -0.42 33 56
APAF-1/Caspase 9 -0.08 0.098 -10000 0 -0.33 17 17
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.17 0.64 0.75 6 -1.2 54 60
IL23A -0.12 0.56 0.8 6 -1.1 42 48
NF kappa B1 p50/RelA/I kappa B alpha -0.14 0.54 0.62 1 -1 55 56
positive regulation of T cell mediated cytotoxicity -0.15 0.63 0.79 10 -1.2 54 64
ITGA3 -0.12 0.54 0.74 5 -1.1 46 51
IL17F -0.069 0.38 0.56 11 -0.67 51 62
IL12B 0.033 0.092 0.29 12 -10000 0 12
STAT1 (dimer) -0.15 0.59 0.7 5 -1.1 54 59
CD4 -0.12 0.55 0.74 6 -1 49 55
IL23 -0.12 0.53 0.78 3 -1.1 41 44
IL23R 0.041 0.14 0.53 2 -10000 0 2
IL1B -0.14 0.59 0.78 9 -1.2 46 55
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.11 0.55 0.77 9 -1.1 46 55
TYK2 0.021 0.058 0.2 1 -10000 0 1
STAT4 0.004 0.096 -10000 0 -0.42 13 13
STAT3 0.026 0.004 -10000 0 -10000 0 0
IL18RAP 0.006 0.096 -10000 0 -0.42 13 13
IL12RB1 0.026 0.11 0.29 17 -0.45 5 22
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.034 0.095 0.24 17 -0.34 4 21
IL23R/JAK2 0.054 0.17 0.53 2 -10000 0 2
positive regulation of chronic inflammatory response -0.15 0.63 0.79 10 -1.2 54 64
natural killer cell activation -0.002 0.013 -10000 0 -0.046 2 2
JAK2 0.03 0.075 0.24 4 -10000 0 4
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.007 -10000 0 -10000 0 0
RELA 0.028 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.1 0.51 0.73 5 -1 41 46
ALOX12B -0.12 0.54 0.77 6 -1 48 54
CXCL1 -0.16 0.62 0.77 9 -1.2 55 64
T cell proliferation -0.15 0.63 0.79 10 -1.2 54 64
NFKBIA 0.028 0.008 -10000 0 -10000 0 0
IL17A -0.025 0.33 0.51 18 -0.54 43 61
PI3K -0.14 0.55 0.67 5 -1.1 54 59
IFNG 0.02 0.055 0.13 27 -0.1 5 32
STAT3 (dimer) -0.14 0.53 0.64 4 -1 53 57
IL18R1 0.025 0.039 -10000 0 -0.42 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.055 0.41 0.57 16 -0.73 43 59
IL18/IL18R 0.04 0.091 -10000 0 -0.26 19 19
macrophage activation -0.003 0.029 0.051 26 -0.044 38 64
TNF -0.12 0.56 0.77 8 -1.1 45 53
STAT3/STAT4 -0.15 0.57 0.66 5 -1.1 55 60
STAT4 (dimer) -0.16 0.6 0.68 6 -1.1 55 61
IL18 0.019 0.061 -10000 0 -0.42 5 5
IL19 -0.12 0.54 0.73 7 -1.1 44 51
STAT5A (dimer) -0.15 0.59 0.7 5 -1.1 54 59
STAT1 0.029 0.026 0.27 3 -10000 0 3
SOCS3 -0.015 0.13 -10000 0 -0.42 24 24
CXCL9 -0.11 0.58 0.79 6 -1.1 48 54
MPO -0.12 0.54 0.75 5 -1 48 53
positive regulation of humoral immune response -0.15 0.63 0.79 10 -1.2 54 64
IL23/IL23R/JAK2/TYK2 -0.16 0.66 0.79 10 -1.2 54 64
IL6 -0.42 0.76 0.74 5 -1.2 124 129
STAT5A 0.024 0.028 -10000 0 -0.42 1 1
IL2 0.018 0.027 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.002 0.013 -10000 0 -0.046 2 2
CD3E -0.17 0.62 0.75 5 -1.2 51 56
keratinocyte proliferation -0.15 0.63 0.79 10 -1.2 54 64
NOS2 -0.12 0.56 0.74 8 -1.1 49 57
TCGA08_retinoblastoma

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
CDKN2B 0.032 0.071 0.27 17 -0.39 1 18
CDKN2C 0.02 0.025 0.29 1 -10000 0 1
CDKN2A 0.13 0.13 0.27 117 -10000 0 117
CCND2 -0.037 0.072 0.19 1 -0.27 12 13
RB1 0.038 0.072 0.29 10 -0.19 1 11
CDK4 -0.038 0.068 0.19 1 -0.2 20 21
CDK6 -0.04 0.077 0.2 1 -0.21 23 24
G1/S progression 0.009 0.12 0.18 70 -0.29 10 80
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.023 0.028 -10000 0 -0.42 1 1
LAT2 -0.067 0.14 0.18 1 -0.31 52 53
AP1 -0.12 0.22 -10000 0 -0.46 54 54
mol:PIP3 -0.068 0.19 0.28 11 -0.37 51 62
IKBKB -0.046 0.13 0.25 11 -0.25 39 50
AKT1 -0.017 0.16 0.32 22 -0.32 15 37
IKBKG -0.054 0.12 0.23 8 -0.24 46 54
MS4A2 -0.087 0.19 -10000 0 -0.41 66 66
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
MAP3K1 -0.058 0.16 0.25 7 -0.36 37 44
mol:Ca2+ -0.049 0.15 0.25 11 -0.28 51 62
LYN 0.025 0.013 -10000 0 -10000 0 0
CBLB -0.067 0.14 -10000 0 -0.32 48 48
SHC1 0.025 0.018 0.29 1 -10000 0 1
RasGAP/p62DOK -0.017 0.12 -10000 0 -0.23 59 59
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.016 0.061 -10000 0 -0.42 5 5
PLD2 -0.038 0.16 0.24 28 -0.25 66 94
PTPN13 -0.062 0.17 0.34 2 -0.45 23 25
PTPN11 0.018 0.023 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.026 0.14 0.31 10 -0.29 19 29
SYK 0.022 0.041 -10000 0 -0.43 2 2
GRB2 0.026 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.082 0.17 -10000 0 -0.37 53 53
LAT -0.063 0.14 0.18 1 -0.31 47 48
PAK2 -0.067 0.18 0.26 7 -0.4 38 45
NFATC2 -0.095 0.19 -10000 0 -0.49 43 43
HRAS -0.077 0.19 0.25 2 -0.37 58 60
GAB2 0.025 0.007 -10000 0 -10000 0 0
PLA2G1B 0.014 0.066 -10000 0 -0.88 1 1
Fc epsilon R1 -0.056 0.16 0.2 5 -0.3 74 79
Antigen/IgE/Fc epsilon R1 -0.049 0.15 0.19 5 -0.27 74 79
mol:GDP -0.083 0.2 0.23 1 -0.46 41 42
JUN 0.016 0.066 -10000 0 -0.42 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
FOS -0.1 0.2 -10000 0 -0.42 77 77
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.066 0.15 0.17 1 -0.29 67 68
CHUK -0.056 0.12 0.23 7 -0.25 44 51
KLRG1 -0.058 0.13 -10000 0 -0.25 65 65
VAV1 -0.075 0.15 -10000 0 -0.32 56 56
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.066 0.14 -10000 0 -0.31 50 50
negative regulation of mast cell degranulation -0.044 0.14 -10000 0 -0.28 50 50
BTK -0.089 0.21 -10000 0 -0.5 39 39
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.09 0.19 -10000 0 -0.33 78 78
GAB2/PI3K/SHP2 -0.069 0.1 -10000 0 -0.25 47 47
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.065 0.15 -10000 0 -0.27 72 72
RAF1 0.016 0.074 -10000 0 -0.98 1 1
Fc epsilon R1/FcgammaRIIB/SHIP -0.051 0.17 -10000 0 -0.28 82 82
FCER1G 0.031 0.056 0.27 9 -0.42 1 10
FCER1A -0.061 0.18 0.27 1 -0.43 49 50
Antigen/IgE/Fc epsilon R1/Fyn -0.041 0.15 -10000 0 -0.26 75 75
MAPK3 0.013 0.067 -10000 0 -0.89 1 1
MAPK1 0.012 0.067 -10000 0 -0.89 1 1
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.071 0.23 -10000 0 -0.62 33 33
DUSP1 -0.085 0.19 -10000 0 -0.42 65 65
NF-kappa-B/RelA -0.03 0.077 -10000 0 -0.17 29 29
actin cytoskeleton reorganization -0.064 0.17 -10000 0 -0.46 21 21
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.062 0.17 -10000 0 -0.39 37 37
FER -0.066 0.14 -10000 0 -0.32 47 47
RELA 0.026 0.004 -10000 0 -10000 0 0
ITK -0.053 0.13 -10000 0 -0.39 31 31
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG1 -0.074 0.2 0.3 3 -0.39 55 58
cytokine secretion -0.026 0.053 -10000 0 -0.15 5 5
SPHK1 -0.062 0.14 0.17 2 -0.31 49 51
PTK2 -0.067 0.18 -10000 0 -0.49 20 20
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.084 0.18 -10000 0 -0.38 55 55
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.069 0.18 0.3 6 -0.36 53 59
MAP2K2 0.009 0.066 -10000 0 -0.9 1 1
MAP2K1 0.009 0.067 -10000 0 -0.92 1 1
MAP2K7 0.026 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.048 0.12 0.18 2 -0.25 48 50
MAP2K4 -0.086 0.32 -10000 0 -0.9 33 33
Fc epsilon R1/FcgammaRIIB -0.056 0.17 -10000 0 -0.29 82 82
mol:Choline -0.037 0.16 0.23 28 -0.25 66 94
SHC/Grb2/SOS1 -0.033 0.15 -10000 0 -0.31 41 41
FYN 0.02 0.047 -10000 0 -0.42 3 3
DOK1 0.027 0.016 0.27 1 -10000 0 1
PXN -0.061 0.17 0.35 1 -0.46 20 21
HCLS1 -0.066 0.14 -10000 0 -0.32 47 47
PRKCB -0.079 0.16 0.27 6 -0.3 66 72
FCGR2B -0.004 0.11 0.28 2 -0.42 17 19
IGHE 0 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.045 0.14 -10000 0 -0.28 50 50
LCP2 0.023 0.028 -10000 0 -0.42 1 1
PLA2G4A -0.073 0.15 -10000 0 -0.33 52 52
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.037 0.16 0.23 28 -0.25 66 94
IKK complex -0.032 0.11 0.25 11 -0.2 31 42
WIPF1 0.013 0.076 -10000 0 -0.42 8 8
Aurora C signaling

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
INCENP 0.027 0.015 0.27 1 -9999 0 1
Aurora C/Aurora B/INCENP 0.1 0.08 0.2 110 -9999 0 110
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.016 0.009 -10000 0 -9999 0 0
AURKB 0.13 0.12 0.27 113 -9999 0 113
AURKC 0.033 0.042 0.27 8 -9999 0 8
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.028 0.22 0.29 10 -0.47 42 52
FYN -0.079 0.3 0.3 8 -0.64 47 55
LAT/GRAP2/SLP76 -0.053 0.24 0.24 3 -0.5 50 53
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.048 0.2 0.26 7 -0.4 51 58
B2M 0.025 0.011 -10000 0 -10000 0 0
IKBKG -0.008 0.06 0.12 6 -0.13 32 38
MAP3K8 0.022 0.039 -10000 0 -0.42 2 2
mol:Ca2+ -0.019 0.02 0.088 1 -0.056 30 31
integrin-mediated signaling pathway 0.033 0.025 -10000 0 -0.25 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.08 0.28 0.3 6 -0.59 51 57
TRPV6 -0.035 0.18 1.1 3 -0.41 29 32
CD28 0.006 0.095 0.27 1 -0.42 12 13
SHC1 -0.065 0.27 0.27 13 -0.55 51 64
receptor internalization -0.085 0.28 0.24 1 -0.58 52 53
PRF1 -0.089 0.33 -10000 0 -0.85 32 32
KRAS 0.027 0.017 0.29 1 -10000 0 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.028 0.16 0.25 6 -0.33 46 52
LAT -0.07 0.27 0.26 6 -0.54 53 59
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.01 0.13 0.28 2 -0.42 22 24
CD3E -0.017 0.13 -10000 0 -0.43 25 25
CD3G -0.021 0.14 -10000 0 -0.42 27 27
RASGRP2 -0.041 0.081 0.078 1 -0.17 73 74
RASGRP1 -0.04 0.2 0.27 7 -0.42 47 54
HLA-A 0.023 0.03 -10000 0 -0.43 1 1
RASSF5 0.023 0.039 -10000 0 -0.42 2 2
RAP1A/GTP/RAPL 0.033 0.025 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.076 0.16 12 -0.13 32 44
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.036 0.081 -10000 0 -0.2 44 44
PRKCA -0.02 0.12 0.18 6 -0.25 42 48
GRAP2 -0.028 0.14 -10000 0 -0.42 32 32
mol:IP3 -0.044 0.18 0.22 26 -0.38 49 75
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.066 0.26 0.2 4 -0.62 37 41
ORAI1 0.015 0.13 0.37 4 -0.94 3 7
CSK -0.074 0.28 0.26 7 -0.56 53 60
B7 family/CD28 -0.032 0.28 0.35 12 -0.59 42 54
CHUK 0.026 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.098 0.31 0.23 2 -0.63 54 56
PTPN6 -0.076 0.28 0.26 7 -0.56 51 58
VAV1 -0.08 0.28 0.26 7 -0.57 53 60
Monovalent TCR/CD3 -0.053 0.19 -10000 0 -0.43 42 42
CBL 0.025 0.007 -10000 0 -10000 0 0
LCK -0.078 0.3 0.29 7 -0.66 44 51
PAG1 -0.069 0.28 0.26 9 -0.55 53 62
RAP1A 0.027 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.093 0.31 0.24 5 -0.61 54 59
CD80 0.052 0.079 0.27 30 -10000 0 30
CD86 0.021 0.048 -10000 0 -0.42 3 3
PDK1/CARD11/BCL10/MALT1 -0.034 0.1 -10000 0 -0.24 43 43
HRAS 0.025 0.007 -10000 0 -10000 0 0
GO:0035030 -0.054 0.22 0.24 9 -0.48 43 52
CD8A -0.017 0.14 0.29 1 -0.42 26 27
CD8B -0.004 0.12 0.28 3 -0.43 19 22
PTPRC -0.028 0.15 0.27 1 -0.42 32 33
PDK1/PKC theta -0.057 0.24 0.29 7 -0.49 51 58
CSK/PAG1 -0.058 0.27 0.3 14 -0.57 45 59
SOS1 0.026 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.036 0.027 -10000 0 -0.29 1 1
GRAP2/SLP76 -0.068 0.28 0.26 3 -0.56 54 57
STIM1 0.003 0.044 -10000 0 -10000 0 0
RAS family/GTP 0.012 0.095 0.2 11 -0.17 30 41
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.094 0.3 -10000 0 -0.62 52 52
mol:DAG -0.059 0.15 0.11 5 -0.33 52 57
RAP1A/GDP 0.004 0.037 0.099 5 -0.064 22 27
PLCG1 0.025 0.007 -10000 0 -10000 0 0
CD247 0.016 0.064 0.27 1 -0.42 5 6
cytotoxic T cell degranulation -0.082 0.31 -10000 0 -0.8 32 32
RAP1A/GTP -0.017 0.03 -10000 0 -0.064 73 73
mol:PI-3-4-5-P3 -0.059 0.23 0.28 7 -0.48 51 58
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.053 0.24 0.24 24 -0.49 49 73
NRAS 0.027 0.002 -10000 0 -10000 0 0
ZAP70 0.009 0.085 -10000 0 -0.42 10 10
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.063 0.23 0.22 2 -0.49 50 52
MALT1 0.025 0.006 -10000 0 -10000 0 0
TRAF6 0.025 0.007 -10000 0 -10000 0 0
CD8 heterodimer -0.011 0.16 0.29 3 -0.4 32 35
CARD11 0.021 0.059 0.28 2 -0.42 4 6
PRKCB -0.052 0.14 0.17 3 -0.29 54 57
PRKCE -0.019 0.12 0.17 8 -0.26 41 49
PRKCQ -0.069 0.28 0.3 7 -0.55 53 60
LCP2 0.024 0.028 -10000 0 -0.42 1 1
BCL10 0.026 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.036 0.17 0.23 9 -0.34 51 60
IKK complex -0.001 0.068 0.16 13 -0.12 30 43
RAS family/GDP -0.006 0.014 -10000 0 -0.041 6 6
MAP3K14 -0.021 0.12 0.2 9 -0.25 44 53
PDPK1 -0.044 0.19 0.26 6 -0.38 49 55
TCR/CD3/MHC I/CD8/Fyn -0.12 0.35 -10000 0 -0.71 53 53
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.014 0.11 -10000 0 -0.22 42 42
ER alpha/Gai/GDP/Gbeta gamma -0.18 0.3 -10000 0 -0.58 75 75
AKT1 -0.15 0.35 -10000 0 -0.86 51 51
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.15 0.36 -10000 0 -0.88 51 51
mol:Ca2+ -0.056 0.16 -10000 0 -0.38 43 43
IGF1R 0.024 0.028 -10000 0 -0.42 1 1
E2/ER alpha (dimer)/Striatin -0.011 0.1 -10000 0 -0.25 41 41
SHC1 0.025 0.018 0.29 1 -10000 0 1
apoptosis 0.14 0.33 0.81 51 -10000 0 51
RhoA/GTP -0.01 0.076 -10000 0 -0.2 37 37
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.13 0.25 -10000 0 -0.48 72 72
regulation of stress fiber formation 0.03 0.073 0.31 2 -0.16 1 3
E2/ERA-ERB (dimer) -0.011 0.1 0.18 1 -0.25 42 43
KRAS 0.027 0.017 0.29 1 -10000 0 1
G13/GTP -0.009 0.093 -10000 0 -0.22 41 41
pseudopodium formation -0.03 0.073 0.16 1 -0.31 2 3
E2/ER alpha (dimer)/PELP1 -0.012 0.1 -10000 0 -0.25 41 41
GRB2 0.026 0.005 -10000 0 -10000 0 0
GNG2 0.021 0.047 -10000 0 -0.42 3 3
GNAO1 -0.11 0.2 -10000 0 -0.42 78 78
HRAS 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.27 -10000 0 -0.64 52 52
E2/ER beta (dimer) 0.02 0.011 0.18 1 -10000 0 1
mol:GDP -0.041 0.13 -10000 0 -0.32 44 44
mol:NADP -0.14 0.27 -10000 0 -0.64 52 52
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:IP3 -0.063 0.15 -10000 0 -0.4 40 40
IGF-1R heterotetramer 0.024 0.028 -10000 0 -0.42 1 1
PLCB1 -0.059 0.16 -10000 0 -0.41 40 40
PLCB2 -0.058 0.15 -10000 0 -0.39 42 42
IGF1 -0.17 0.22 -10000 0 -0.42 116 116
mol:L-citrulline -0.14 0.27 -10000 0 -0.64 52 52
RHOA 0.025 0.006 -10000 0 -10000 0 0
Gai/GDP -0.26 0.39 -10000 0 -0.76 93 93
JNK cascade 0.02 0.011 0.18 1 -10000 0 1
BCAR1 0.025 0.006 -10000 0 -10000 0 0
ESR2 0.027 0.015 0.27 1 -10000 0 1
GNAQ 0.025 0.007 -10000 0 -10000 0 0
ESR1 -0.045 0.16 -10000 0 -0.42 42 42
Gq family/GDP/Gbeta gamma -0.033 0.17 -10000 0 -0.7 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.018 0.1 -10000 0 -0.38 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.25 -10000 0 -0.48 71 71
GNAZ -0.074 0.18 -10000 0 -0.42 59 59
E2/ER alpha (dimer) -0.031 0.12 -10000 0 -0.29 42 42
STRN 0.026 0.004 -10000 0 -10000 0 0
GNAL -0.14 0.21 -10000 0 -0.42 100 100
PELP1 0.024 0.008 -10000 0 -10000 0 0
MAPK11 0.013 0.005 -10000 0 -10000 0 0
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.025 0.028 -10000 0 -0.42 1 1
HBEGF -0.15 0.28 0.35 7 -0.56 67 74
cAMP biosynthetic process -0.092 0.14 -10000 0 -0.24 118 118
SRC -0.16 0.28 0.34 1 -0.55 73 74
PI3K 0.035 0.013 -10000 0 -10000 0 0
GNB1 0.027 0.002 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.013 0.13 -10000 0 -0.32 37 37
SOS1 0.026 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.17 0.22 -10000 0 -0.43 95 95
Gs family/GTP -0.09 0.14 -10000 0 -0.24 118 118
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.019 0.2 1 -10000 0 1
vasodilation -0.13 0.26 -10000 0 -0.6 52 52
mol:DAG -0.063 0.15 -10000 0 -0.4 40 40
Gs family/GDP/Gbeta gamma -0.098 0.16 -10000 0 -0.36 49 49
MSN -0.032 0.077 0.16 1 -0.33 2 3
Gq family/GTP -0.052 0.16 -10000 0 -0.41 41 41
mol:PI-3-4-5-P3 -0.14 0.35 -10000 0 -0.84 51 51
NRAS 0.027 0.002 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.13 0.26 0.6 52 -10000 0 52
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
RhoA/GDP -0.025 0.13 -10000 0 -0.32 39 39
NOS3 -0.15 0.29 -10000 0 -0.68 52 52
GNA11 0.024 0.028 -10000 0 -0.42 1 1
MAPKKK cascade -0.12 0.28 -10000 0 -0.66 50 50
E2/ER alpha (dimer)/PELP1/Src -0.14 0.26 0.26 1 -0.5 73 74
ruffle organization -0.03 0.073 0.16 1 -0.31 2 3
ROCK2 -0.03 0.083 -10000 0 -0.22 6 6
GNA14 -0.031 0.15 -10000 0 -0.42 33 33
GNA15 0.022 0.039 -10000 0 -0.42 2 2
GNA13 0.026 0.005 -10000 0 -10000 0 0
MMP9 -0.14 0.28 0.4 7 -0.54 66 73
MMP2 -0.16 0.27 0.31 2 -0.53 77 79
Ephrin A reverse signaling

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.012 0.1 0.18 2 -0.25 40 42
EFNA5 0.014 0.072 -10000 0 -0.42 7 7
FYN -0.035 0.091 0.18 3 -0.23 43 46
neuron projection morphogenesis -0.012 0.1 0.18 2 -0.25 40 42
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.011 0.1 0.18 2 -0.26 40 42
EPHA5 -0.048 0.15 0.27 2 -0.42 34 36
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.045 0.049 0.13 1 -0.11 62 63
BUB1B 0.046 0.058 0.13 37 -0.14 4 41
PLK1 0.027 0.032 0.092 22 -0.08 1 23
PLK1S1 0.019 0.03 0.12 3 -0.16 3 6
KIF2A 0.02 0.028 0.12 1 -10000 0 1
regulation of mitotic centrosome separation 0.027 0.032 0.092 22 -0.079 1 23
GOLGA2 0.024 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.15 0.14 0.29 114 -10000 0 114
WEE1 0.019 0.095 -10000 0 -0.32 17 17
cytokinesis 0.081 0.08 0.18 42 -0.2 5 47
PP2A-alpha B56 0.075 0.089 -10000 0 -0.49 4 4
AURKA 0.043 0.047 0.12 43 -0.18 1 44
PICH/PLK1 0.063 0.071 0.18 52 -10000 0 52
CENPE 0.026 0.033 0.12 6 -10000 0 6
RhoA/GTP 0.019 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.021 0.029 0.12 1 -10000 0 1
PPP2CA 0.026 0.005 -10000 0 -10000 0 0
FZR1 0.026 0.005 -10000 0 -10000 0 0
TPX2 0.069 0.055 0.13 68 -10000 0 68
PAK1 0.023 0.028 -10000 0 -0.42 1 1
SPC24 0.1 0.11 0.27 85 -10000 0 85
FBXW11 0.025 0.006 -10000 0 -10000 0 0
CLSPN 0.058 0.053 0.13 55 -0.2 1 56
GORASP1 0.025 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.013 10 -0.011 2 12
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.012 0.016 0.046 21 -0.039 1 22
G2 phase of mitotic cell cycle 0.002 0.005 0.013 27 -10000 0 27
STAG2 0.026 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.014 0.075 -10000 0 -0.58 4 4
spindle elongation 0.027 0.032 0.092 22 -0.079 1 23
ODF2 0.025 0.009 -10000 0 -10000 0 0
BUB1 0.055 0.098 -10000 0 -0.53 4 4
TPT1 0.008 0.047 -10000 0 -0.16 16 16
CDC25C 0.077 0.079 0.15 45 -0.26 7 52
CDC25B 0.033 0.039 0.28 6 -10000 0 6
SGOL1 0.045 0.049 0.11 62 -0.13 1 63
RHOA 0.025 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.085 0.09 0.2 86 -10000 0 86
CDC14B 0.003 0.019 -10000 0 -0.3 1 1
CDC20 0.17 0.12 0.27 156 -10000 0 156
PLK1/PBIP1 0.013 0.025 0.11 7 -10000 0 7
mitosis -0.004 0.008 0.033 1 -0.016 4 5
FBXO5 0.018 0.029 0.097 4 -10000 0 4
CDC2 0.004 0.005 0.011 64 -10000 0 64
NDC80 0.11 0.12 0.27 89 -10000 0 89
metaphase plate congression 0.024 0.031 -10000 0 -0.26 2 2
ERCC6L 0.064 0.078 0.2 41 -10000 0 41
NLP/gamma Tubulin 0.015 0.019 0.073 7 -0.066 1 8
microtubule cytoskeleton organization 0.008 0.047 -10000 0 -0.16 16 16
G2/M transition DNA damage checkpoint 0 0.003 0.014 3 -10000 0 3
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.014 3 -10000 0 3
PLK1/PRC1-2 0.18 0.12 0.25 182 -10000 0 182
GRASP65/GM130/RAB1/GTP/PLK1 0.055 0.032 -10000 0 -10000 0 0
RAB1A 0.026 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.024 0.029 0.084 28 -10000 0 28
mitotic prometaphase 0 0.002 0.019 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.057 -10000 0 -0.24 4 4
microtubule-based process 0.15 0.087 0.21 188 -10000 0 188
Golgi organization 0.027 0.032 0.092 22 -0.079 1 23
Cohesin/SA2 0.037 0.027 0.11 2 -10000 0 2
PPP1CB/MYPT1 0.04 0.01 -10000 0 -10000 0 0
KIF20A 0.2 0.11 0.27 188 -10000 0 188
APC/C/CDC20 0.14 0.092 0.21 156 -10000 0 156
PPP2R1A 0.026 0.005 -10000 0 -10000 0 0
chromosome segregation 0.013 0.025 0.1 7 -10000 0 7
PRC1 0.073 0.096 0.27 51 -10000 0 51
ECT2 0.034 0.06 0.2 21 -10000 0 21
C13orf34 0.023 0.028 0.077 28 -10000 0 28
NUDC 0.024 0.031 -10000 0 -0.26 2 2
regulation of attachment of spindle microtubules to kinetochore 0.046 0.058 0.13 47 -0.13 4 51
spindle assembly 0.021 0.027 0.085 17 -10000 0 17
spindle stabilization 0.019 0.03 0.12 3 -0.16 3 6
APC/C/HCDH1 0.021 0.018 -10000 0 -0.25 1 1
MKLP2/PLK1 0.15 0.087 0.21 188 -10000 0 188
CCNB1 0.11 0.12 0.27 94 -10000 0 94
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.026 0.006 -10000 0 -10000 0 0
ROCK2 0.019 0.077 0.18 2 -0.36 8 10
TUBG1 0.019 0.021 0.12 1 -0.18 1 2
G2/M transition of mitotic cell cycle 0.032 0.053 0.17 11 -10000 0 11
MLF1IP 0.009 0.019 0.11 1 -10000 0 1
INCENP 0.027 0.015 0.27 1 -10000 0 1
Integrins in angiogenesis

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 0.038 0.009 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.066 0.18 -10000 0 -0.31 83 83
PTK2 -0.073 0.19 0.28 8 -0.47 32 40
IGF1R 0.024 0.028 -10000 0 -0.42 1 1
PI4KB 0.023 0.009 -10000 0 -10000 0 0
MFGE8 0.024 0.028 -10000 0 -0.42 1 1
SRC 0.025 0.007 -10000 0 -10000 0 0
CDKN1B -0.1 0.22 -10000 0 -0.59 41 41
VEGFA 0.026 0.005 -10000 0 -10000 0 0
ILK -0.11 0.23 -10000 0 -0.58 46 46
ROCK1 0.026 0.005 -10000 0 -10000 0 0
AKT1 -0.11 0.21 -10000 0 -0.54 46 46
PTK2B -0.024 0.076 0.2 10 -0.22 26 36
alphaV/beta3 Integrin/JAM-A -0.076 0.18 -10000 0 -0.32 84 84
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.016 0.095 -10000 0 -0.26 28 28
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.069 0.15 -10000 0 -0.23 117 117
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.029 0.1 -10000 0 -0.33 16 16
alphaV/beta3 Integrin/Syndecan-1 0.018 0.093 -10000 0 -0.25 27 27
PI4KA 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.23 -10000 0 -0.34 128 128
PI4 Kinase 0.033 0.015 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.072 0.14 0.2 98 -0.25 28 126
RPS6KB1 -0.16 0.19 -10000 0 -0.42 76 76
TLN1 0.024 0.009 -10000 0 -10000 0 0
MAPK3 -0.21 0.31 -10000 0 -0.6 91 91
GPR124 -0.005 0.1 -10000 0 -0.42 16 16
MAPK1 -0.21 0.31 -10000 0 -0.6 93 93
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.059 0.16 0.2 3 -0.28 85 88
cell adhesion 0.01 0.092 -10000 0 -0.26 26 26
ANGPTL3 0.015 0.025 0.27 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.048 0.018 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.024 0.028 -10000 0 -0.42 1 1
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 0.024 0.028 -10000 0 -0.42 1 1
ITGB3 -0.022 0.14 -10000 0 -0.42 28 28
IGF1 -0.17 0.22 -10000 0 -0.42 116 116
RAC1 0.026 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.002 0.12 -10000 0 -0.31 30 30
apoptosis 0.026 0.005 -10000 0 -10000 0 0
CD47 0.025 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.018 0.091 -10000 0 -0.25 26 26
VCL 0.025 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.016 0.15 -10000 0 -0.34 44 44
CSF1 0.006 0.093 -10000 0 -0.42 12 12
PIK3C2A -0.11 0.23 -10000 0 -0.58 46 46
PI4 Kinase/Pyk2 -0.071 0.15 -10000 0 -0.3 70 70
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.031 0.09 -10000 0 -0.23 26 26
FAK1/Vinculin -0.047 0.17 0.27 10 -0.38 30 40
alphaV beta3/Integrin/ppsTEM5 -0.002 0.12 -10000 0 -0.31 30 30
RHOA 0.025 0.006 -10000 0 -10000 0 0
VTN -0.042 0.16 0.27 1 -0.42 40 41
BCAR1 0.025 0.006 -10000 0 -10000 0 0
FGF2 -0.11 0.2 -10000 0 -0.42 79 79
F11R -0.067 0.13 -10000 0 -0.3 65 65
alphaV/beta3 Integrin/Lactadherin 0.017 0.095 -10000 0 -0.25 28 28
alphaV/beta3 Integrin/TGFBR2 0.018 0.095 -10000 0 -0.26 26 26
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.045 0.065 -10000 0 -0.23 12 12
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.015 0.084 -10000 0 -0.23 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.027 0.098 0.27 16 -0.42 8 24
alphaV/beta3 Integrin/Pyk2 0.012 0.081 -10000 0 -0.22 26 26
SDC1 0.022 0.039 -10000 0 -0.42 2 2
VAV3 -0.013 0.068 0.21 10 -0.21 14 24
PTPN11 0.026 0.005 -10000 0 -10000 0 0
IRS1 0.02 0.047 -10000 0 -0.42 3 3
FAK1/Paxillin -0.047 0.17 0.27 11 -0.38 31 42
cell migration -0.044 0.15 0.25 13 -0.35 30 43
ITGAV 0.026 0.005 -10000 0 -10000 0 0
PI3K -0.046 0.18 -10000 0 -0.29 79 79
SPP1 0.12 0.12 0.27 105 -10000 0 105
KDR 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.005 -10000 0 -10000 0 0
COL4A3 -0.093 0.2 0.27 3 -0.42 69 72
angiogenesis -0.2 0.32 0.27 3 -0.6 92 95
Rac1/GTP 0.019 0.063 0.3 1 -0.2 14 15
EDIL3 -0.03 0.15 -10000 0 -0.42 33 33
cell proliferation 0.017 0.094 -10000 0 -0.26 26 26
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.014 0.1 -10000 0 -0.24 31 31
NF kappa B1 p50/RelA/I kappa B alpha -0.022 0.11 0.29 1 -0.27 23 24
AP1 -0.079 0.16 -10000 0 -0.26 98 98
mol:PIP3 -0.031 0.09 -10000 0 -0.23 34 34
AKT1 -0.002 0.083 0.27 2 -0.27 6 8
PTK2B -0.056 0.12 0.19 2 -0.3 36 38
RHOA -0.004 0.063 0.22 2 -0.27 7 9
PIK3CB 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.083 0.22 4 -0.23 22 26
MAGI3 0.027 0.002 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
apoptosis -0.033 0.11 0.18 1 -0.26 47 48
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.059 0.13 0.22 6 -0.34 27 33
NF kappa B1 p50/RelA -0.037 0.12 -10000 0 -0.27 38 38
endothelial cell migration -0.036 0.15 -10000 0 -0.44 30 30
ADCY4 -0.11 0.17 -10000 0 -0.37 66 66
ADCY5 -0.21 0.25 -10000 0 -0.48 102 102
ADCY6 -0.11 0.17 -10000 0 -0.37 66 66
ADCY7 -0.11 0.17 -10000 0 -0.37 65 65
ADCY1 -0.11 0.17 -10000 0 -0.37 66 66
ADCY2 -0.17 0.23 -10000 0 -0.44 90 90
ADCY3 -0.11 0.17 -10000 0 -0.37 65 65
ADCY8 -0.1 0.17 -10000 0 -0.37 63 63
ADCY9 -0.11 0.18 -10000 0 -0.38 65 65
GSK3B -0.051 0.12 0.2 6 -0.32 28 34
arachidonic acid secretion -0.12 0.19 -10000 0 -0.38 72 72
GNG2 0.021 0.047 -10000 0 -0.42 3 3
TRIP6 0.017 0.017 -10000 0 -10000 0 0
GNAO1 -0.078 0.15 -10000 0 -0.28 84 84
HRAS 0.025 0.007 -10000 0 -10000 0 0
NFKBIA -0.04 0.11 0.29 1 -0.29 23 24
GAB1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.016 0.16 -10000 0 -0.84 9 9
JUN 0.016 0.066 -10000 0 -0.42 6 6
LPA/LPA2/NHERF2 0.027 0.033 0.18 1 -10000 0 1
TIAM1 -0.001 0.18 -10000 0 -0.97 9 9
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:IP3 -0.026 0.084 0.22 4 -0.23 22 26
PLCB3 0.011 0.032 0.19 3 -10000 0 3
FOS -0.1 0.2 -10000 0 -0.42 77 77
positive regulation of mitosis -0.12 0.19 -10000 0 -0.38 72 72
LPA/LPA1-2-3 -0.005 0.12 -10000 0 -0.24 48 48
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.006 -10000 0 -10000 0 0
stress fiber formation -0.035 0.11 0.29 1 -0.34 16 17
GNAZ -0.066 0.14 -10000 0 -0.28 73 73
EGFR/PI3K-beta/Gab1 -0.022 0.098 -10000 0 -0.24 34 34
positive regulation of dendritic cell cytokine production -0.007 0.12 -10000 0 -0.24 48 48
LPA/LPA2/MAGI-3 0.028 0.035 0.18 1 -10000 0 1
ARHGEF1 -0.001 0.092 0.18 20 -0.23 25 45
GNAI2 -0.015 0.087 -10000 0 -0.25 30 30
GNAI3 -0.016 0.09 -10000 0 -0.25 31 31
GNAI1 -0.016 0.089 -10000 0 -0.25 30 30
LPA/LPA3 -0.015 0.094 0.19 2 -0.21 40 42
LPA/LPA2 0.012 0.034 0.18 1 -0.1 16 17
LPA/LPA1 -0.016 0.11 -10000 0 -0.29 32 32
HB-EGF/EGFR 0.032 0.085 0.24 9 -0.27 13 22
HBEGF 0.029 0.087 0.29 6 -0.33 8 14
mol:DAG -0.026 0.084 0.22 4 -0.23 22 26
cAMP biosynthetic process -0.14 0.2 0.28 1 -0.4 82 83
NFKB1 0.026 0.003 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
GNB1 0.027 0.002 -10000 0 -10000 0 0
LYN -0.033 0.11 0.26 3 -0.28 23 26
GNAQ -0.012 0.075 0.18 1 -0.24 23 24
LPAR2 0.029 0.027 0.28 3 -10000 0 3
LPAR3 -0.01 0.13 0.27 4 -0.42 23 27
LPAR1 -0.007 0.11 -10000 0 -0.45 12 12
IL8 -0.09 0.21 0.37 1 -0.48 51 52
PTK2 -0.025 0.1 0.21 7 -0.24 39 46
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.033 0.11 0.18 1 -0.26 47 48
EGFR 0.022 0.073 0.29 6 -0.42 5 11
PLCG1 -0.024 0.092 0.21 5 -0.25 29 34
PLD2 -0.027 0.11 0.21 7 -0.24 44 51
G12/G13 0.014 0.093 -10000 0 -0.23 29 29
PI3K-beta -0.014 0.079 -10000 0 -0.29 8 8
cell migration -0.001 0.072 0.19 2 -0.26 9 11
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN -0.035 0.11 0.29 1 -0.35 16 17
HRAS/GTP -0.13 0.19 -10000 0 -0.4 72 72
RAC1 0.026 0.005 -10000 0 -10000 0 0
MMP9 0.084 0.13 0.27 71 -0.42 4 75
PRKCE 0.026 0.005 -10000 0 -10000 0 0
PRKCD -0.029 0.084 0.3 1 -0.23 22 23
Gi(beta/gamma) -0.1 0.17 -10000 0 -0.36 68 68
mol:LPA -0.01 0.042 -10000 0 -0.15 19 19
TRIP6/p130 Cas/FAK1/Paxillin -0.016 0.12 0.3 1 -0.38 11 12
MAPKKK cascade -0.12 0.19 -10000 0 -0.38 72 72
contractile ring contraction involved in cytokinesis -0.004 0.066 0.22 2 -0.25 9 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.042 0.11 0.18 1 -0.25 53 54
GNA15 -0.012 0.077 0.18 1 -0.24 25 26
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
MAPT -0.061 0.13 0.24 4 -0.34 27 31
GNA11 -0.011 0.079 0.18 1 -0.25 23 24
Rac1/GTP 0.016 0.17 -10000 0 -0.88 9 9
MMP2 -0.036 0.15 -10000 0 -0.44 30 30
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.11 0.2 -10000 0 -0.42 78 78
CDC42/GTP -0.081 0.16 -10000 0 -0.29 78 78
PLCG1 -0.086 0.15 -10000 0 -0.3 71 71
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.003 -10000 0 -10000 0 0
G12/G13 0.036 0.011 -10000 0 -10000 0 0
cell migration -0.08 0.16 -10000 0 -0.29 78 78
S1PR5 0.031 0.06 0.27 9 -0.42 2 11
S1PR4 0.024 0.054 0.27 3 -0.42 3 6
MAPK3 -0.086 0.15 -10000 0 -0.31 72 72
MAPK1 -0.09 0.16 -10000 0 -0.31 74 74
S1P/S1P5/Gi -0.086 0.16 -10000 0 -0.3 89 89
GNAI1 0.025 0.028 -10000 0 -0.42 1 1
CDC42/GDP 0.02 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.035 0.035 0.18 6 -0.25 2 8
RHOA 0.003 0.057 0.19 19 -0.22 2 21
S1P/S1P4/Gi -0.089 0.17 -10000 0 -0.3 91 91
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.074 0.18 -10000 0 -0.42 59 59
S1P/S1P4/G12/G13 0.045 0.033 0.19 3 -0.23 2 5
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.002 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.21 -10000 0 -0.4 69 69
MAP3K8 0.018 0.04 -10000 0 -0.42 2 2
FOS -0.084 0.16 -10000 0 -0.38 42 42
PRKCA 0.012 0.022 -10000 0 -10000 0 0
PTPN7 0.007 0.065 0.27 3 -0.42 4 7
HRAS 0.024 0.007 -10000 0 -10000 0 0
PRKCB -0.1 0.19 -10000 0 -0.42 71 71
NRAS 0.026 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.032 -10000 0 -10000 0 0
MAPK3 -0.043 0.13 -10000 0 -0.53 10 10
MAP2K1 -0.098 0.19 -10000 0 -0.39 73 73
ELK1 0.009 0.028 -10000 0 -10000 0 0
BRAF -0.091 0.17 -10000 0 -0.37 70 70
mol:GTP -0.001 0.002 -10000 0 -0.005 79 79
MAPK1 -0.048 0.14 -10000 0 -0.53 12 12
RAF1 -0.087 0.17 0.21 1 -0.37 67 68
KRAS 0.026 0.017 0.29 1 -10000 0 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.035 0.15 0.34 1 -0.22 99 100
SMAD6-7/SMURF1 0.049 0.028 0.2 2 -0.25 1 3
NOG 0.039 0.072 0.27 22 -10000 0 22
SMAD9 -0.14 0.26 -10000 0 -0.51 75 75
SMAD4 0.025 0.007 -10000 0 -10000 0 0
SMAD5 -0.028 0.12 -10000 0 -0.38 16 16
BMP7/USAG1 -0.16 0.2 0.2 2 -0.34 134 136
SMAD5/SKI -0.021 0.13 -10000 0 -0.37 17 17
SMAD1 0.024 0.037 -10000 0 -10000 0 0
BMP2 -0.024 0.14 -10000 0 -0.42 29 29
SMAD1/SMAD1/SMAD4 0.028 0.061 -10000 0 -0.4 1 1
BMPR1A 0.025 0.006 -10000 0 -10000 0 0
BMPR1B 0.054 0.11 0.27 41 -0.42 4 45
BMPR1A-1B/BAMBI 0.042 0.099 0.2 31 -0.24 21 52
AHSG 0.02 0.078 0.27 22 -10000 0 22
CER1 -0.006 0.018 -10000 0 -10000 0 0
BMP2-4/CER1 0.001 0.1 0.2 2 -0.25 35 37
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.05 0.14 -10000 0 -0.35 25 25
BMP2-4 (homodimer) -0.008 0.12 0.2 2 -0.3 36 38
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.078 0.066 0.21 38 -0.23 3 41
RGMA -0.099 0.2 -10000 0 -0.42 74 74
SMURF1 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.045 0.13 -10000 0 -0.34 24 24
BMP2-4/USAG1 -0.073 0.16 0.2 4 -0.28 95 99
SMAD6/SMURF1/SMAD5 -0.021 0.13 -10000 0 -0.37 17 17
SOSTDC1 -0.12 0.2 0.27 4 -0.42 82 86
BMP7/BMPR2/BMPR1A-1B -0.032 0.15 0.21 18 -0.23 91 109
SKI 0.027 0.002 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.016 0.27 1 -10000 0 1
HFE2 0.001 0.026 0.27 1 -10000 0 1
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.014 0.14 0.2 3 -0.28 49 52
SMAD5/SMAD5/SMAD4 -0.019 0.12 -10000 0 -0.37 17 17
MAPK1 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.03 0.12 -10000 0 -0.31 21 21
BMP7 (homodimer) -0.12 0.21 -10000 0 -0.42 88 88
NUP214 0.024 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.045 0.047 0.2 20 -10000 0 20
SMAD1/SKI 0.031 0.073 -10000 0 -0.34 3 3
SMAD6 0.027 0.035 0.27 2 -0.42 1 3
CTDSP2 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.011 0.11 0.2 15 -0.25 36 51
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.008 0.2 0.27 39 -0.42 41 80
BMPR2 (homodimer) 0.026 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.049 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.056 0.075 0.2 39 -0.3 4 43
CHRDL1 -0.22 0.21 -10000 0 -0.42 144 144
ENDOFIN/SMAD1 0.031 0.071 -10000 0 -0.33 3 3
SMAD6-7/SMURF1/SMAD1 0.051 0.076 -10000 0 -0.46 1 1
SMAD6/SMURF1 0.026 0.004 -10000 0 -10000 0 0
BAMBI -0.001 0.11 0.27 3 -0.42 17 20
SMURF2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.15 0.17 -10000 0 -0.28 155 155
BMP2-4/GREM1 -0.017 0.16 0.2 38 -0.26 74 112
SMAD7 0.025 0.006 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.13 0.25 -10000 0 -0.48 76 76
SMAD1/SMAD6 0.031 0.073 -10000 0 -0.34 3 3
TAK1/SMAD6 0.037 0.01 -10000 0 -10000 0 0
BMP7 -0.12 0.21 -10000 0 -0.42 88 88
BMP6 0.027 0.016 0.27 1 -10000 0 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.046 0.14 -10000 0 -0.33 29 29
PPM1A 0.026 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.031 0.072 -10000 0 -0.34 3 3
SMAD7/SMURF1 0.037 0.011 -10000 0 -10000 0 0
CTDSPL 0.025 0.006 -10000 0 -10000 0 0
PPP1CA 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.016 0.29 1 -10000 0 1
CTDSP1 0.025 0.006 -10000 0 -10000 0 0
PPP1R15A 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.06 0.15 -10000 0 -0.37 31 31
CHRD -0.011 0.12 0.27 1 -0.42 22 23
BMPR2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.06 0.13 -10000 0 -0.37 24 24
BMP4 0.014 0.085 0.27 3 -0.42 9 12
FST 0.011 0.11 0.27 8 -0.42 13 21
BMP2-4/NOG 0.014 0.11 0.21 13 -0.25 36 49
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.023 0.14 -10000 0 -0.21 89 89
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.075 0.15 0.29 73 -10000 0 73
GNAI2 0.025 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.035 0.035 0.18 6 -0.25 2 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.11 0.2 -10000 0 -0.42 78 78
RhoA/GTP -0.076 0.16 -10000 0 -0.29 73 73
negative regulation of cAMP metabolic process -0.085 0.16 -10000 0 -0.29 89 89
GNAZ -0.074 0.18 -10000 0 -0.42 59 59
GNAI3 0.026 0.003 -10000 0 -10000 0 0
GNA12 0.025 0.006 -10000 0 -10000 0 0
S1PR5 0.031 0.06 0.27 9 -0.42 2 11
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.086 0.16 -10000 0 -0.3 89 89
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
GNAI1 0.025 0.028 -10000 0 -0.42 1 1
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.031 0.13 0.36 1 -0.33 31 32
alphaM/beta2 Integrin/GPIbA -0.009 0.11 0.23 11 -0.31 15 26
alphaM/beta2 Integrin/proMMP-9 0.027 0.15 0.3 14 -0.38 13 27
PLAUR 0.026 0.005 -10000 0 -10000 0 0
HMGB1 -0.008 0.041 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.011 0.1 0.36 1 -0.31 14 15
AGER -0.003 0.055 0.25 5 -10000 0 5
RAP1A 0.027 0.002 -10000 0 -10000 0 0
SELPLG 0.021 0.059 0.27 2 -0.42 4 6
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.05 0.16 0.36 1 -0.22 111 112
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.084 0.13 0.27 71 -0.42 4 75
CYR61 -0.099 0.2 -10000 0 -0.42 74 74
TLN1 0.024 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.006 0.13 -10000 0 -0.36 20 20
RHOA 0.025 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.055 0.17 -10000 0 -0.42 46 46
MYH2 -0.026 0.12 0.26 1 -0.34 21 22
MST1R 0.019 0.081 0.27 6 -0.42 7 13
leukocyte activation during inflammatory response -0.058 0.14 0.29 2 -0.25 70 72
APOB -0.045 0.16 0.28 3 -0.42 38 41
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.01 0.12 -10000 0 -0.42 21 21
JAM3 0.006 0.089 -10000 0 -0.42 11 11
GP1BA 0.024 0.048 0.27 6 -0.42 1 7
alphaM/beta2 Integrin/CTGF -0.054 0.16 0.36 1 -0.33 52 53
alphaM/beta2 Integrin -0.027 0.14 -10000 0 -0.39 22 22
JAM3 homodimer 0.006 0.089 -10000 0 -0.42 11 11
ICAM2 0.024 0.028 -10000 0 -0.42 1 1
ICAM1 0.031 0.037 0.27 6 -10000 0 6
phagocytosis triggered by activation of immune response cell surface activating receptor -0.024 0.14 -10000 0 -0.4 21 21
cell adhesion -0.009 0.11 0.23 11 -0.31 15 26
NFKB1 -0.13 0.21 0.38 4 -0.35 112 116
THY1 0.027 0.022 0.27 2 -10000 0 2
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.035 0.13 0.18 5 -0.27 59 64
alphaM/beta2 Integrin/LRP/tPA -0.011 0.12 0.36 2 -0.32 24 26
IL6 -0.27 0.35 0.35 4 -0.65 117 121
ITGB2 -0.009 0.081 0.27 7 -0.44 4 11
elevation of cytosolic calcium ion concentration 0.018 0.12 0.31 3 -0.29 13 16
alphaM/beta2 Integrin/JAM2/JAM3 -0.065 0.17 0.36 1 -0.3 72 73
JAM2 -0.082 0.19 -10000 0 -0.42 64 64
alphaM/beta2 Integrin/ICAM1 0.009 0.11 0.35 1 -0.25 20 21
alphaM/beta2 Integrin/uPA/Plg 0.017 0.12 0.35 2 -0.3 14 16
RhoA/GTP -0.021 0.12 -10000 0 -0.35 21 21
positive regulation of phagocytosis -0.022 0.14 0.27 4 -0.4 21 25
Ron/MSP 0.036 0.072 0.22 13 -0.3 8 21
alphaM/beta2 Integrin/uPAR/uPA 0.019 0.12 0.32 3 -0.29 13 16
alphaM/beta2 Integrin/uPAR -0.011 0.1 0.23 7 -0.32 13 20
PLAU 0.058 0.083 0.27 35 -10000 0 35
PLAT 0.005 0.095 0.28 2 -0.42 12 14
actin filament polymerization -0.025 0.12 0.26 1 -0.33 21 22
MST1 0.034 0.057 0.27 11 -0.42 1 12
alphaM/beta2 Integrin/lipoprotein(a) -0.056 0.14 0.31 2 -0.26 70 72
TNF -0.12 0.19 0.42 4 -0.33 110 114
RAP1B 0.025 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.01 0.12 0.27 6 -0.32 14 20
fibrinolysis 0.016 0.12 0.34 2 -0.29 14 16
HCK 0.014 0.077 0.27 3 -0.42 7 10
dendritic cell antigen processing and presentation -0.024 0.14 -10000 0 -0.4 21 21
VTN -0.042 0.16 0.27 1 -0.42 40 41
alphaM/beta2 Integrin/CYR61 -0.078 0.18 0.36 1 -0.34 72 73
LPA -0.029 0.14 0.27 4 -0.42 27 31
LRP1 0.021 0.047 -10000 0 -0.42 3 3
cell migration -0.01 0.14 0.26 10 -0.33 28 38
FN1 0.027 0.098 0.27 16 -0.42 8 24
alphaM/beta2 Integrin/Thy1 -0.009 0.1 0.36 1 -0.32 14 15
MPO 0.02 0.022 0.27 1 -10000 0 1
KNG1 -0.016 0.004 -10000 0 -10000 0 0
RAP1/GDP 0.033 0.01 -10000 0 -10000 0 0
ROCK1 -0.018 0.12 -10000 0 -0.34 21 21
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.006 0.03 0.27 2 -10000 0 2
CTGF -0.055 0.17 -10000 0 -0.42 48 48
alphaM/beta2 Integrin/Hck -0.011 0.12 0.36 4 -0.34 17 21
ITGAM -0.027 0.11 0.27 2 -0.44 13 15
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.043 0.14 0.36 2 -0.28 54 56
HP 0.039 0.087 0.27 26 -0.42 2 28
leukocyte adhesion -0.1 0.19 0.35 1 -0.39 56 57
SELP -0.055 0.17 -10000 0 -0.42 46 46
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.057 0.13 -10000 0 -0.22 99 99
MAPK9 0.007 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.028 0.076 0.13 66 -0.29 4 70
GNB1/GNG2 0.032 0.031 -10000 0 -0.25 3 3
GNB1 0.027 0.002 -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 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.076 0.12 -10000 0 -0.22 100 100
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 0.024 0.029 0.062 100 -10000 0 100
GNAL -0.14 0.21 -10000 0 -0.42 100 100
GNG2 0.021 0.047 -10000 0 -0.42 3 3
CRH 0.067 0.13 0.27 66 -0.42 4 70
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.031 -10000 0 -0.29 3 3
MAPK11 0.007 0.002 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.02 0.11 -10000 0 -0.25 32 32
MAP4K1 0.016 0.068 0.27 1 -0.42 6 7
MAP3K8 0.022 0.039 -10000 0 -0.42 2 2
PRKCB -0.095 0.2 -10000 0 -0.42 71 71
DBNL 0.026 0.004 -10000 0 -10000 0 0
CRKL 0.027 0.022 0.27 2 -10000 0 2
MAP3K1 -0.012 0.1 -10000 0 -0.27 26 26
JUN -0.17 0.3 -10000 0 -0.58 85 85
MAP3K7 -0.011 0.1 -10000 0 -0.27 27 27
GRAP2 -0.028 0.14 -10000 0 -0.42 32 32
CRK 0.024 0.008 -10000 0 -10000 0 0
MAP2K4 -0.014 0.12 -10000 0 -0.4 14 14
LAT 0.026 0.016 0.27 1 -10000 0 1
LCP2 0.024 0.028 -10000 0 -0.42 1 1
MAPK8 -0.18 0.31 -10000 0 -0.61 86 86
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.007 0.11 -10000 0 -0.28 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 0.029 0.11 -10000 0 -0.24 31 31
PDGFR-alpha signaling 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
PDGFRA -0.061 0.16 -10000 0 -0.44 40 40
PDGF/PDGFRA/CRKL -0.028 0.12 -10000 0 -0.3 39 39
positive regulation of JUN kinase activity 0.02 0.094 -10000 0 -0.23 30 30
CRKL 0.027 0.022 0.27 2 -10000 0 2
PDGF/PDGFRA/Caveolin-3 -0.031 0.12 -10000 0 -0.31 37 37
AP1 -0.28 0.4 -10000 0 -0.86 79 79
mol:IP3 -0.053 0.12 -10000 0 -0.33 37 37
PLCG1 -0.053 0.12 -10000 0 -0.33 37 37
PDGF/PDGFRA/alphaV Integrin -0.03 0.12 -10000 0 -0.3 40 40
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.12 -10000 0 -0.33 37 37
CAV3 -0.004 0.026 0.29 1 -10000 0 1
CAV1 0.008 0.089 -10000 0 -0.42 11 11
SHC/Grb2/SOS1 0.021 0.095 -10000 0 -0.23 30 30
PDGF/PDGFRA/Shf -0.034 0.13 -10000 0 -0.32 41 41
FOS -0.27 0.39 -10000 0 -0.85 79 79
JUN -0.043 0.057 -10000 0 -0.36 6 6
oligodendrocyte development -0.03 0.12 -10000 0 -0.3 40 40
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:DAG -0.053 0.12 -10000 0 -0.33 37 37
PDGF/PDGFRA -0.061 0.16 -10000 0 -0.44 40 40
actin cytoskeleton reorganization -0.028 0.12 -10000 0 -0.3 38 38
SRF 0.017 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.018 0.29 1 -10000 0 1
PI3K 0.005 0.1 -10000 0 -0.25 34 34
PDGF/PDGFRA/Crk/C3G 0 0.1 -10000 0 -0.25 39 39
JAK1 -0.046 0.11 -10000 0 -0.3 40 40
ELK1/SRF -0.048 0.096 0.15 8 -0.26 37 45
SHB 0.023 0.009 -10000 0 -10000 0 0
SHF 0.019 0.054 -10000 0 -0.42 4 4
CSNK2A1 0.037 0.024 -10000 0 -10000 0 0
GO:0007205 -0.065 0.12 -10000 0 -0.36 37 37
SOS1 0.026 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.02 0.094 -10000 0 -0.23 30 30
PDGF/PDGFRA/SHB -0.028 0.12 -10000 0 -0.3 38 38
PDGF/PDGFRA/Caveolin-1 -0.039 0.14 -10000 0 -0.33 44 44
ITGAV 0.026 0.005 -10000 0 -10000 0 0
ELK1 -0.069 0.11 -10000 0 -0.32 37 37
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.029 0.12 -10000 0 -0.3 39 39
JAK-STAT cascade -0.046 0.11 -10000 0 -0.3 40 40
cell proliferation -0.034 0.13 -10000 0 -0.32 41 41
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.018 0.069 0.35 4 -10000 0 4
VDR 0.026 0.032 0.29 1 -0.42 1 2
FAM120B 0.026 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.029 0.12 -10000 0 -0.34 12 12
RXRs/LXRs/DNA/Oxysterols -0.009 0.12 -10000 0 -0.32 11 11
MED1 0.025 0.006 -10000 0 -10000 0 0
mol:9cRA 0.005 0.005 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.003 0.086 -10000 0 -0.24 27 27
RXRs/NUR77 -0.14 0.17 -10000 0 -0.28 149 149
RXRs/PPAR -0.057 0.12 -10000 0 -0.24 73 73
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.019 -10000 0 -0.29 1 1
RARs/VDR/DNA/Vit D3 0.035 0.077 -10000 0 -0.22 21 21
RARA 0.026 0.005 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.032 0.29 1 -0.42 1 2
RARs/RARs/DNA/9cRA 0.025 0.07 -10000 0 -0.21 20 20
RARG 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.031 0.095 0.63 6 -10000 0 6
RARs/THRs/DNA/SMRT -0.004 0.088 -10000 0 -0.24 28 28
THRA 0.026 0.006 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.019 -10000 0 -0.29 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.02 0.12 -10000 0 -0.22 69 69
NR1H4 -0.062 0.18 0.27 13 -0.42 51 64
RXRs/LXRs/DNA 0.001 0.13 -10000 0 -0.21 56 56
NR1H2 0.031 0.006 -10000 0 -10000 0 0
NR1H3 0.03 0.009 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.012 0.12 0.27 1 -0.21 66 67
NR4A1 -0.21 0.22 -10000 0 -0.42 142 142
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.068 0.15 0.18 3 -0.24 89 92
RXRG -0.095 0.19 -10000 0 -0.42 70 70
RXR alpha/CCPG 0.038 0.015 -10000 0 -10000 0 0
RXRA 0.028 0.01 -10000 0 -10000 0 0
RXRB 0.031 0.006 -10000 0 -10000 0 0
THRB 0.002 0.1 -10000 0 -0.42 14 14
PPARG -0.009 0.12 0.29 2 -0.42 20 22
PPARD 0.027 0.002 -10000 0 -10000 0 0
TNF -0.006 0.11 -10000 0 -10000 0 0
mol:Oxysterols 0.005 0.005 -10000 0 -10000 0 0
cholesterol transport -0.008 0.12 -10000 0 -0.32 11 11
PPARA 0.022 0.039 -10000 0 -0.42 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.01 0.12 -10000 0 -0.42 21 21
RXRs/NUR77/BCL2 -0.17 0.17 -10000 0 -0.29 156 156
SREBF1 -0.009 0.1 -10000 0 -0.34 3 3
RXRs/RXRs/DNA/9cRA -0.02 0.12 -10000 0 -0.22 69 69
ABCA1 -0.009 0.1 -10000 0 -0.34 1 1
RARs/THRs 0.036 0.1 -10000 0 -0.25 28 28
RXRs/FXR -0.059 0.16 0.28 1 -0.26 96 97
BCL2 0.005 0.093 -10000 0 -0.42 12 12
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.024 -10000 0 -10000 0 0
PDGFRB 0.016 0.055 -10000 0 -0.42 4 4
SPHK1 0.005 0.088 -10000 0 -0.97 1 1
mol:S1P -0.005 0.09 0.33 1 -0.89 1 2
S1P1/S1P/Gi -0.18 0.24 -10000 0 -0.45 94 94
GNAO1 -0.12 0.2 -10000 0 -0.42 78 78
PDGFB-D/PDGFRB/PLCgamma1 -0.14 0.22 -10000 0 -0.41 88 88
PLCG1 -0.16 0.22 -10000 0 -0.43 90 90
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.055 -10000 0 -0.42 4 4
GNAI2 0.015 0.021 -10000 0 -10000 0 0
GNAI3 0.015 0.021 -10000 0 -10000 0 0
GNAI1 0.013 0.034 -10000 0 -0.42 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.007 0.015 -10000 0 -10000 0 0
S1P1/S1P -0.018 0.09 0.26 1 -0.66 1 2
negative regulation of cAMP metabolic process -0.17 0.23 -10000 0 -0.41 110 110
MAPK3 -0.21 0.29 0.3 2 -0.55 94 96
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
KDR 0.021 0.016 -10000 0 -10000 0 0
PLCB2 -0.007 0.093 0.26 1 -0.4 2 3
RAC1 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.024 0.067 -10000 0 -0.54 1 1
receptor internalization -0.02 0.081 -10000 0 -0.6 1 1
PTGS2 -0.28 0.42 -10000 0 -0.81 90 90
Rac1/GTP -0.024 0.067 -10000 0 -0.54 1 1
RHOA 0.025 0.006 -10000 0 -10000 0 0
VEGFA 0.02 0.016 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.17 0.23 -10000 0 -0.41 110 110
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.083 0.18 -10000 0 -0.42 59 59
MAPK1 -0.21 0.29 -10000 0 -0.55 95 95
S1P1/S1P/PDGFB-D/PDGFRB -0.021 0.11 0.24 3 -0.3 10 13
ABCC1 0.023 0.025 0.28 2 -10000 0 2
TCGA08_p53

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
CDKN2A 0.052 0.058 0.11 118 -10000 0 118
TP53 0.008 0.046 -10000 0 -0.15 16 16
Senescence 0.008 0.046 -10000 0 -0.15 16 16
Apoptosis 0.008 0.046 -10000 0 -0.15 16 16
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.015 0.088 0.29 16 -0.19 3 19
MDM4 0.026 0.004 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.001 0.22 -10000 0 -0.7 8 8
CRP -0.004 0.23 0.54 8 -0.59 13 21
cell cycle arrest -0.028 0.24 0.46 1 -0.61 23 24
TIMP1 -0.004 0.21 0.49 1 -0.64 8 9
IL6ST -0.038 0.16 -10000 0 -0.42 39 39
Rac1/GDP -0.094 0.23 0.28 2 -0.46 56 58
AP1 0 0.15 -10000 0 -0.48 5 5
GAB2 0.027 0.009 -10000 0 -10000 0 0
TNFSF11 -0.02 0.23 0.49 1 -0.66 12 13
HSP90B1 0.034 0.077 -10000 0 -0.51 3 3
GAB1 0.027 0.007 -10000 0 -10000 0 0
MAPK14 -0.15 0.27 -10000 0 -0.61 52 52
AKT1 0.034 0.05 -10000 0 -0.32 2 2
FOXO1 0.034 0.052 -10000 0 -0.3 2 2
MAP2K6 -0.13 0.24 0.22 1 -0.51 58 59
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.07 0.23 0.32 5 -0.47 48 53
MITF -0.12 0.23 -10000 0 -0.48 59 59
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.004 -10000 0 -10000 0 0
A2M -0.095 0.39 -10000 0 -1.3 24 24
CEBPB 0.029 0.029 -10000 0 -0.42 1 1
GRB2/SOS1/GAB family/SHP2 0 0.11 0.3 4 -0.48 3 7
STAT3 -0.035 0.25 0.46 1 -0.65 23 24
STAT1 -0.001 0.14 -10000 0 -0.86 6 6
CEBPD -0.011 0.24 0.57 1 -0.72 10 11
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.037 0.013 -10000 0 -10000 0 0
JUN 0.017 0.066 -10000 0 -0.42 6 6
PIAS3/MITF -0.1 0.22 -10000 0 -0.46 53 53
MAPK11 -0.15 0.27 -10000 0 -0.59 55 55
STAT3 (dimer)/FOXO1 -0.023 0.22 0.46 2 -0.52 22 24
GRB2/SOS1/GAB family -0.069 0.21 0.29 2 -0.44 42 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.11 0.22 -10000 0 -0.36 87 87
GRB2 0.028 0.006 -10000 0 -10000 0 0
JAK2 0.023 0.009 -10000 0 -10000 0 0
LBP 0.026 0.21 0.47 4 -0.51 10 14
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
JAK1 0.025 0.018 -10000 0 -10000 0 0
MYC -0.025 0.3 0.57 1 -1 15 16
FGG -0.017 0.22 0.49 1 -0.67 9 10
macrophage differentiation -0.028 0.24 0.46 1 -0.61 23 24
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.09 0.19 -10000 0 -0.29 105 105
JUNB -0.026 0.23 -10000 0 -0.77 9 9
FOS -0.1 0.2 -10000 0 -0.42 77 77
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.11 0.23 0.27 1 -0.48 55 56
STAT1/PIAS1 -0.069 0.21 0.29 2 -0.43 48 50
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.045 -10000 0 -0.34 1 1
STAT3 (dimer) -0.033 0.25 0.46 1 -0.63 23 24
PRKCD -0.045 0.23 0.36 6 -0.51 35 41
IL6R -0.006 0.11 -10000 0 -0.42 18 18
SOCS3 -0.2 0.38 0.38 1 -0.96 42 43
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.12 -10000 0 -0.26 40 40
Rac1/GTP -0.088 0.23 0.3 2 -0.47 54 56
HCK 0.015 0.077 0.27 3 -0.42 7 10
MAPKKK cascade 0.028 0.11 -10000 0 -0.54 3 3
bone resorption -0.017 0.22 0.46 3 -0.59 14 17
IRF1 -0.021 0.22 -10000 0 -0.7 8 8
mol:GDP -0.11 0.23 0.25 2 -0.48 57 59
SOS1 0.028 0.007 -10000 0 -10000 0 0
VAV1 -0.11 0.23 0.25 2 -0.49 57 59
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.3 0.46 1 -0.68 51 52
PTPN11 0.014 0.053 -10000 0 -0.72 1 1
IL6/IL6RA -0.1 0.19 -10000 0 -0.33 103 103
gp130 (dimer)/TYK2/TYK2/LMO4 0.009 0.11 -10000 0 -0.25 39 39
gp130 (dimer)/JAK2/JAK2/LMO4 0.002 0.11 -10000 0 -0.25 40 40
IL6 -0.16 0.22 -10000 0 -0.42 112 112
PIAS3 0.023 0.009 -10000 0 -10000 0 0
PTPRE 0.01 0.04 0.31 1 -0.41 1 2
PIAS1 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.21 -10000 0 -0.32 105 105
LMO4 0.026 0.036 -10000 0 -0.43 1 1
STAT3 (dimer)/PIAS3 -0.037 0.24 -10000 0 -0.61 23 23
MCL1 0.056 0.085 0.39 3 -10000 0 3
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.027 0.022 0.27 2 -10000 0 2
RAS family/GTP/Tiam1 -0.078 0.097 -10000 0 -0.23 44 44
NT3 (dimer)/TRKC -0.17 0.2 0.2 1 -0.35 142 143
NT3 (dimer)/TRKB -0.15 0.22 0.22 5 -0.36 128 133
SHC/Grb2/SOS1/GAB1/PI3K 0.021 0.023 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
BDNF -0.046 0.16 -10000 0 -0.42 42 42
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
NTRK1 0.024 0.034 0.27 4 -10000 0 4
NTRK2 -0.12 0.21 0.27 5 -0.42 88 93
NTRK3 -0.19 0.22 -10000 0 -0.42 127 127
NT-4/5 (dimer)/TRKB -0.13 0.21 0.23 6 -0.33 121 127
neuron apoptosis 0.16 0.22 0.46 78 -10000 0 78
SHC 2-3/Grb2 -0.18 0.25 -10000 0 -0.5 78 78
SHC1 0.025 0.018 0.29 1 -10000 0 1
SHC2 -0.17 0.25 -10000 0 -0.54 67 67
SHC3 -0.18 0.26 -10000 0 -0.52 82 82
STAT3 (dimer) 0.032 0.054 0.22 7 -0.32 4 11
NT3 (dimer)/TRKA -0.052 0.16 0.35 1 -0.28 81 82
RIN/GDP -0.051 0.11 0.24 3 -0.24 22 25
GIPC1 0.026 0.003 -10000 0 -10000 0 0
KRAS 0.027 0.017 0.29 1 -10000 0 1
DNAJA3 -0.068 0.14 -10000 0 -0.29 64 64
RIN/GTP 0.013 0.011 0.18 1 -10000 0 1
CCND1 0.016 0.11 0.4 8 -0.68 4 12
MAGED1 0.026 0.003 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.012 0.12 -10000 0 -0.42 22 22
SHC/GRB2/SOS1 0.047 0.019 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.003 0.12 -10000 0 -0.27 41 41
TRKA/NEDD4-2 0.036 0.022 0.2 3 -10000 0 3
ELMO1 0.022 0.039 -10000 0 -0.42 2 2
RhoG/GTP/ELMO1/DOCK1 0.03 0.037 -10000 0 -0.36 2 2
NGF -0.034 0.15 -10000 0 -0.42 35 35
HRAS 0.025 0.007 -10000 0 -10000 0 0
DOCK1 0.024 0.028 -10000 0 -0.42 1 1
GAB2 0.025 0.007 -10000 0 -10000 0 0
RIT2 -0.012 0.021 0.27 1 -10000 0 1
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.03 0.037 0.29 5 -10000 0 5
DNM1 0.021 0.039 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.05 0.14 -10000 0 -0.28 66 66
mol:GDP -0.08 0.15 0.32 2 -0.32 33 35
NGF (dimer) -0.034 0.15 -10000 0 -0.42 35 35
RhoG/GDP 0.017 0.027 -10000 0 -0.29 2 2
RIT1/GDP -0.05 0.11 0.27 2 -0.23 23 25
TIAM1 0.024 0.028 -10000 0 -0.42 1 1
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.094 0.18 0.2 5 -0.29 110 115
KIDINS220/CRKL/C3G 0.036 0.02 0.2 2 -10000 0 2
SHC/RasGAP 0.035 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.049 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.058 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.018 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.054 0.17 0.27 1 -0.42 47 48
RAP1/GDP -0.051 0.085 -10000 0 -0.2 23 23
KIDINS220/CRKL 0.027 0.022 0.27 2 -10000 0 2
BDNF (dimer) -0.046 0.16 -10000 0 -0.42 42 42
ubiquitin-dependent protein catabolic process 0.014 0.097 -10000 0 -0.25 29 29
Schwann cell development -0.044 0.033 -10000 0 -10000 0 0
EHD4 0.026 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.063 0.032 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.016 0.062 -10000 0 -0.26 3 3
RAP1B 0.025 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.21 0.22 0.36 1 -0.34 172 173
ABL1 0.024 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.042 0.1 -10000 0 -0.34 11 11
STAT3 0.032 0.054 0.22 7 -0.32 4 11
axon guidance -0.21 0.2 -10000 0 -0.33 172 172
MAPK3 -0.022 0.099 0.18 9 -0.24 39 48
MAPK1 -0.023 0.1 0.18 9 -0.25 40 49
CDC42/GDP -0.051 0.11 0.27 2 -0.23 24 26
NTF3 -0.054 0.17 0.27 1 -0.42 47 48
NTF4 -0.012 0.12 -10000 0 -0.42 22 22
NGF (dimer)/TRKA/FAIM 0.014 0.1 -10000 0 -0.25 31 31
PI3K 0.035 0.013 -10000 0 -10000 0 0
FRS3 0.026 0.003 -10000 0 -10000 0 0
FAIM 0.026 0.005 -10000 0 -10000 0 0
GAB1 0.026 0.006 -10000 0 -10000 0 0
RASGRF1 -0.065 0.14 -10000 0 -0.29 65 65
SOS1 0.026 0.004 -10000 0 -10000 0 0
MCF2L -0.16 0.18 -10000 0 -0.32 139 139
RGS19 0.025 0.007 -10000 0 -10000 0 0
CDC42 0.027 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.092 0.28 1 -0.4 4 5
Rac1/GDP -0.048 0.11 0.27 2 -0.23 23 25
NGF (dimer)/TRKA/GRIT 0.002 0.094 0.18 4 -0.25 31 35
neuron projection morphogenesis -0.058 0.16 -10000 0 -0.56 4 4
NGF (dimer)/TRKA/NEDD4-2 0.015 0.097 -10000 0 -0.25 29 29
MAP2K1 0.015 0.073 0.19 38 -10000 0 38
NGFR -0.067 0.19 0.27 4 -0.42 57 61
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.095 -10000 0 -0.27 27 27
RAS family/GTP/PI3K 0.02 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.071 0.033 -10000 0 -10000 0 0
NRAS 0.027 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
PRKCI 0.025 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.005 -10000 0 -10000 0 0
PRKCZ 0.025 0.027 -10000 0 -0.42 1 1
MAPKKK cascade -0.091 0.24 -10000 0 -0.66 36 36
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.035 0.023 0.2 3 -10000 0 3
SQSTM1 0.025 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.077 0.17 -10000 0 -0.26 110 110
NGF (dimer)/TRKA/p62/Atypical PKCs 0.035 0.098 -10000 0 -0.22 29 29
MATK 0 0.11 0.27 3 -0.42 17 20
NEDD4L 0.025 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.062 0.064 -10000 0 -0.18 31 31
NGF (dimer)/TRKA -0.07 0.15 -10000 0 -0.29 71 71
Rac1/GTP -0.082 0.11 -10000 0 -0.24 60 60
FRS2 family/SHP2/CRK family 0.065 0.041 -10000 0 -10000 0 0
Calcium 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
NFATC1 -0.01 0.068 -10000 0 -0.28 13 13
NFATC2 -0.039 0.1 -10000 0 -0.26 42 42
NFATC3 0.001 0.03 -10000 0 -10000 0 0
CD40LG -0.14 0.25 -10000 0 -0.5 63 63
PTGS2 -0.15 0.26 0.28 1 -0.49 82 83
JUNB 0.021 0.047 -10000 0 -0.42 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.025 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.025 -10000 0 -10000 0 0
CALM1 0.017 0.021 -10000 0 -10000 0 0
JUN 0.008 0.07 -10000 0 -0.43 6 6
mol:Ca2+ -0.003 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.009 -10000 0 -10000 0 0
FOSL1 -0.004 0.11 -10000 0 -0.42 18 18
CREM 0.025 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.027 0.17 -10000 0 -0.37 31 31
FOS -0.11 0.2 -10000 0 -0.42 77 77
IFNG -0.096 0.23 0.35 5 -0.45 55 60
AP-1/NFAT1-c-4 -0.1 0.28 0.45 3 -0.52 59 62
FASLG -0.12 0.22 -10000 0 -0.46 58 58
NFAT1-c-4/ICER1 -0.037 0.12 -10000 0 -0.27 40 40
IL2RA -0.12 0.24 0.33 2 -0.49 56 58
FKBP12/FK506 0.019 0.005 -10000 0 -10000 0 0
CSF2 -0.1 0.23 0.33 8 -0.45 57 65
JunB/Fra1/NFAT1-c-4 -0.034 0.15 -10000 0 -0.28 48 48
IL4 -0.12 0.22 -10000 0 -0.45 58 58
IL2 -0.008 0.14 -10000 0 -0.98 5 5
IL3 -0.013 0.13 -10000 0 -0.73 8 8
FKBP1A 0.025 0.006 -10000 0 -10000 0 0
BATF3 0.022 0.05 0.27 1 -0.42 3 4
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.024 0.009 -10000 0 -10000 0 0
Glypican 1 network

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.082 0.19 -10000 0 -0.34 84 84
fibroblast growth factor receptor signaling pathway -0.082 0.19 -10000 0 -0.34 84 84
LAMA1 0.047 0.13 0.27 41 -0.42 9 50
PRNP 0.017 0.061 -10000 0 -0.42 5 5
GPC1/SLIT2 -0.1 0.16 -10000 0 -0.29 112 112
SMAD2 0.014 0.032 0.18 7 -0.23 1 8
GPC1/PrPc/Cu2+ 0.026 0.04 -10000 0 -0.24 5 5
GPC1/Laminin alpha1 0.044 0.087 0.2 35 -0.29 9 44
TDGF1 0.008 0.027 0.27 1 -10000 0 1
CRIPTO/GPC1 0.033 0.016 0.2 1 -10000 0 1
APP/GPC1 0.034 0.023 -10000 0 -0.28 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.001 0.014 -10000 0 -10000 0 0
FLT1 0.026 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.043 0.028 -10000 0 -0.25 1 1
SERPINC1 0.032 0.061 0.27 15 -10000 0 15
FYN 0 0.027 -10000 0 -0.26 2 2
FGR 0 0.022 -10000 0 -0.25 1 1
positive regulation of MAPKKK cascade 0.002 0.097 0.29 4 -0.3 9 13
SLIT2 -0.17 0.22 -10000 0 -0.42 112 112
GPC1/NRG -0.006 0.12 0.2 13 -0.3 35 48
NRG1 -0.024 0.16 0.27 15 -0.42 35 50
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.019 -10000 0 -10000 0 0
LYN 0.002 0.014 -10000 0 -10000 0 0
mol:Spermine 0.006 0.002 -10000 0 -10000 0 0
cell growth -0.082 0.19 -10000 0 -0.34 84 84
BMP signaling pathway -0.024 0.008 -10000 0 -10000 0 0
SRC 0.002 0.014 -10000 0 -10000 0 0
TGFBR1 0.024 0.008 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.18 0.22 0.27 1 -0.42 121 122
GPC1 0.024 0.008 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.024 0.008 -10000 0 -10000 0 0
VEGFA 0.026 0.005 -10000 0 -10000 0 0
BLK -0.01 0.064 0.14 9 -0.26 14 23
HCK -0.003 0.043 -10000 0 -0.26 6 6
FGF2 -0.11 0.2 -10000 0 -0.42 79 79
FGFR1 -0.062 0.17 -10000 0 -0.42 50 50
VEGFR1 homodimer 0.026 0.005 -10000 0 -10000 0 0
TGFBR2 0.024 0.028 -10000 0 -0.42 1 1
cell death 0.034 0.023 -10000 0 -0.28 1 1
ATIII/GPC1 0.039 0.036 0.2 10 -10000 0 10
PLA2G2A/GPC1 -0.12 0.17 0.2 1 -0.3 121 122
LCK -0.001 0.032 -10000 0 -0.25 3 3
neuron differentiation -0.006 0.12 0.2 13 -0.29 35 48
PrPc/Cu2+ 0.013 0.043 -10000 0 -0.29 5 5
APP 0.024 0.028 -10000 0 -0.42 1 1
TGFBR2 (dimer) 0.024 0.028 -10000 0 -0.42 1 1
Glucocorticoid receptor regulatory network

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
PCK2 0.037 0.085 -10000 0 -10000 0 0
SMARCC2 0.023 0.021 -10000 0 -10000 0 0
SMARCC1 0.023 0.02 -10000 0 -10000 0 0
TBX21 -0.019 0.14 0.41 1 -0.56 11 12
SUMO2 0.017 0.019 -10000 0 -10000 0 0
STAT1 (dimer) 0.034 0.027 0.27 3 -10000 0 3
FKBP4 0.026 0.006 -10000 0 -10000 0 0
FKBP5 0.003 0.1 -10000 0 -0.42 14 14
GR alpha/HSP90/FKBP51/HSP90 0.046 0.11 0.26 7 -0.24 3 10
PRL -0.022 0.092 0.43 1 -10000 0 1
cortisol/GR alpha (dimer)/TIF2 0.072 0.22 0.44 34 -0.36 5 39
RELA -0.12 0.13 -10000 0 -0.24 118 118
FGG 0.086 0.2 0.38 47 -0.35 5 52
GR beta/TIF2 0.034 0.12 0.25 14 -0.29 7 21
IFNG -0.079 0.25 0.47 5 -0.55 22 27
apoptosis -0.049 0.18 -10000 0 -0.5 9 9
CREB1 0.032 0.021 -10000 0 -10000 0 0
histone acetylation -0.087 0.12 -10000 0 -0.37 23 23
BGLAP -0.024 0.11 -10000 0 -10000 0 0
GR/PKAc 0.057 0.1 0.27 4 -0.21 1 5
NF kappa B1 p50/RelA -0.21 0.25 -10000 0 -0.41 152 152
SMARCD1 0.023 0.022 -10000 0 -10000 0 0
MDM2 0.052 0.086 0.19 41 -10000 0 41
GATA3 0.001 0.11 0.3 1 -0.41 16 17
AKT1 0.022 0.008 -10000 0 -10000 0 0
CSF2 -0.048 0.11 -10000 0 -0.49 2 2
GSK3B 0.017 0.019 -10000 0 -10000 0 0
NR1I3 -0.012 0.18 0.46 2 -0.5 4 6
CSN2 0.058 0.17 0.32 42 -0.32 5 47
BRG1/BAF155/BAF170/BAF60A 0.058 0.059 -10000 0 -0.26 7 7
NFATC1 0.003 0.096 -10000 0 -0.42 13 13
POU2F1 0.026 0.013 -10000 0 -10000 0 0
CDKN1A 0.007 0.11 0.74 1 -1.3 1 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.006 -10000 0 -10000 0 0
SFN 0.046 0.082 0.27 25 -0.42 2 27
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.067 0.11 0.29 8 -0.23 2 10
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.15 0.34 0.42 2 -0.75 61 63
JUN -0.017 0.18 0.36 10 -0.37 19 29
IL4 -0.049 0.13 -10000 0 -0.48 10 10
CDK5R1 0.039 0.06 0.27 16 -10000 0 16
PRKACA 0.026 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.099 0.13 -10000 0 -0.32 48 48
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.055 0.11 0.28 4 -0.23 2 6
cortisol/GR alpha (monomer) 0.096 0.24 0.48 42 -0.41 5 47
NCOA2 0.003 0.092 -10000 0 -0.42 12 12
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.1 0.23 0.22 6 -0.41 81 87
AP-1/NFAT1-c-4 -0.089 0.32 0.45 14 -0.57 52 66
AFP -0.02 0.15 0.56 2 -10000 0 2
SUV420H1 0.025 0.006 -10000 0 -10000 0 0
IRF1 0.065 0.13 0.36 5 -10000 0 5
TP53 0.033 0.035 -10000 0 -0.5 1 1
PPP5C 0.026 0.004 -10000 0 -10000 0 0
KRT17 -0.13 0.36 0.47 4 -0.94 28 32
KRT14 0.052 0.2 0.5 8 -1.3 2 10
TBP 0.032 0.01 -10000 0 -10000 0 0
CREBBP -0.036 0.079 0.27 2 -0.31 10 12
HDAC1 0.025 0.009 -10000 0 -10000 0 0
HDAC2 0.016 0.019 -10000 0 -10000 0 0
AP-1 -0.09 0.32 0.45 14 -0.56 55 69
MAPK14 0.018 0.018 -10000 0 -10000 0 0
MAPK10 -0.023 0.13 -10000 0 -0.42 24 24
MAPK11 0.016 0.019 -10000 0 -10000 0 0
KRT5 -0.28 0.54 0.43 9 -1.1 78 87
interleukin-1 receptor activity -0.004 0.006 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.034 0.027 0.28 3 -10000 0 3
CGA -0.026 0.11 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.078 0.14 -10000 0 -0.35 23 23
MAPK3 0.017 0.018 -10000 0 -10000 0 0
MAPK1 0.018 0.018 -10000 0 -10000 0 0
ICAM1 -0.18 0.24 -10000 0 -0.5 61 61
NFKB1 -0.11 0.13 -10000 0 -0.23 137 137
MAPK8 -0.012 0.15 0.34 7 -0.29 30 37
MAPK9 0.018 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.052 0.18 -10000 0 -0.52 10 10
BAX 0.01 0.061 -10000 0 -10000 0 0
POMC -0.2 0.3 0.53 1 -0.71 29 30
EP300 -0.035 0.077 0.27 2 -0.3 9 11
cortisol/GR alpha (dimer)/p53 0.084 0.21 0.43 35 -0.37 2 37
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.069 0.19 11 -10000 0 11
SGK1 -0.065 0.28 -10000 0 -1.3 11 11
IL13 -0.087 0.21 -10000 0 -0.66 10 10
IL6 -0.49 0.54 -10000 0 -1 125 125
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.079 0.18 -10000 0 -0.64 5 5
IL2 -0.11 0.24 -10000 0 -0.53 32 32
CDK5 0.024 0.008 -10000 0 -10000 0 0
PRKACB 0.023 0.039 -10000 0 -0.42 2 2
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
IL8 -0.27 0.41 -10000 0 -0.72 90 90
CDK5R1/CDK5 0.041 0.04 0.2 13 -10000 0 13
NF kappa B1 p50/RelA/PKAc -0.14 0.21 -10000 0 -0.34 124 124
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.096 0.21 0.42 38 -0.34 2 40
SMARCA4 0.023 0.021 -10000 0 -10000 0 0
chromatin remodeling 0.056 0.15 0.32 17 -0.38 5 22
NF kappa B1 p50/RelA/Cbp -0.22 0.21 -10000 0 -0.42 113 113
JUN (dimer) -0.017 0.18 0.36 10 -0.37 19 29
YWHAH 0.025 0.006 -10000 0 -10000 0 0
VIPR1 -0.026 0.17 0.42 1 -0.65 13 14
NR3C1 0.061 0.15 0.31 32 -10000 0 32
NR4A1 -0.22 0.23 -10000 0 -0.42 142 142
TIF2/SUV420H1 0.018 0.07 -10000 0 -0.3 12 12
MAPKKK cascade -0.049 0.18 -10000 0 -0.5 9 9
cortisol/GR alpha (dimer)/Src-1 0.093 0.22 0.43 39 -0.36 4 43
PBX1 0.004 0.097 -10000 0 -0.42 13 13
POU1F1 0.007 0.028 0.27 1 -10000 0 1
SELE -0.43 0.52 -10000 0 -0.94 120 120
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.056 0.15 0.32 17 -0.38 5 22
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.096 0.21 0.42 38 -0.34 2 40
mol:cortisol 0.047 0.14 0.26 45 -0.22 5 50
MMP1 0.067 0.2 0.4 7 -0.7 8 15
Syndecan-1-mediated signaling events

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.005 -10000 0 -10000 0 0
CCL5 0.014 0.092 0.27 5 -0.42 10 15
SDCBP 0.024 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.069 0.11 0.27 22 -0.36 3 25
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.062 0.1 0.26 11 -0.31 5 16
Syndecan-1/Syntenin 0.065 0.11 0.29 10 -0.31 5 15
MAPK3 0.059 0.1 0.26 12 -0.34 3 15
HGF/MET -0.033 0.14 0.2 6 -0.3 59 65
TGFB1/TGF beta receptor Type II 0.026 0.005 -10000 0 -10000 0 0
BSG 0.026 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.061 0.1 0.26 11 -0.31 5 16
Syndecan-1/RANTES 0.064 0.13 0.29 17 -0.34 8 25
Syndecan-1/CD147 0.081 0.11 0.28 12 -0.36 3 15
Syndecan-1/Syntenin/PIP2 0.059 0.1 0.25 9 -0.3 5 14
LAMA5 0.025 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.057 0.098 0.25 9 -0.3 5 14
MMP7 0.044 0.15 0.27 47 -0.42 15 62
HGF -0.069 0.19 0.27 6 -0.42 59 65
Syndecan-1/CASK 0.053 0.1 0.21 21 -0.31 5 26
Syndecan-1/HGF/MET 0.033 0.16 0.29 13 -0.36 15 28
regulation of cell adhesion 0.051 0.095 0.25 12 -0.34 3 15
HPSE 0.045 0.081 0.27 24 -0.42 2 26
positive regulation of cell migration 0.069 0.11 0.27 22 -0.36 3 25
SDC1 0.073 0.11 0.27 22 -0.23 10 32
Syndecan-1/Collagen 0.069 0.11 0.27 22 -0.36 3 25
PPIB 0.026 0.004 -10000 0 -10000 0 0
MET 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
MMP9 0.084 0.13 0.27 71 -0.42 4 75
MAPK1 0.061 0.099 0.26 12 -0.34 3 15
homophilic cell adhesion 0.067 0.12 0.27 22 -0.32 5 27
MMP1 0.16 0.12 0.27 147 -10000 0 147
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.008 0.015 -10000 0 -0.25 1 1
ADCY5 -0.12 0.12 -10000 0 -0.25 123 123
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.007 0.002 -10000 0 -10000 0 0
ADCY1 -0.007 0.017 -10000 0 -0.25 1 1
ADCY2 -0.079 0.11 -10000 0 -0.25 79 79
ADCY3 -0.007 0.001 -10000 0 -10000 0 0
ADCY8 -0.009 0.006 -10000 0 -10000 0 0
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.01 0.026 -10000 0 -0.25 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.029 0.11 0.23 15 -0.17 49 64
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.011 0.12 0.26 8 -0.29 16 24
TBX21 -0.12 0.46 0.51 1 -1.1 40 41
B2M 0.024 0.016 -10000 0 -10000 0 0
TYK2 0.012 0.04 -10000 0 -10000 0 0
IL12RB1 0.017 0.099 0.3 13 -0.46 5 18
GADD45B -0.087 0.39 -10000 0 -0.99 31 31
IL12RB2 0.044 0.13 0.28 43 -0.43 6 49
GADD45G -0.097 0.39 -10000 0 -0.94 35 35
natural killer cell activation -0.002 0.024 -10000 0 -10000 0 0
RELB 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL18 0.016 0.064 -10000 0 -0.43 5 5
IL2RA 0.013 0.12 0.27 14 -0.42 14 28
IFNG 0.061 0.1 0.27 48 -10000 0 48
STAT3 (dimer) -0.084 0.35 0.45 2 -0.76 45 47
HLA-DRB5 -0.002 0.1 0.26 7 -0.42 12 19
FASLG -0.12 0.47 0.58 1 -1.1 42 43
NF kappa B2 p52/RelB -0.11 0.44 0.44 2 -0.96 44 46
CD4 0.008 0.045 -10000 0 -0.42 2 2
SOCS1 0.026 0.016 0.27 1 -10000 0 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.027 0.12 0.26 2 -0.42 22 24
CD3E -0.032 0.13 -10000 0 -0.42 25 25
CD3G -0.037 0.13 -10000 0 -0.42 27 27
IL12Rbeta2/JAK2 0.04 0.1 0.24 28 -0.31 6 34
CCL3 -0.13 0.48 0.58 1 -1.1 39 40
CCL4 -0.15 0.52 0.51 1 -1.2 43 44
HLA-A 0.023 0.031 -10000 0 -0.42 1 1
IL18/IL18R 0.04 0.1 -10000 0 -0.28 19 19
NOS2 -0.095 0.42 0.54 1 -0.97 38 39
IL12/IL12R/TYK2/JAK2/SPHK2 0.012 0.12 0.25 8 -0.29 16 24
IL1R1 -0.11 0.43 -10000 0 -1.1 34 34
IL4 -0.001 0.038 -10000 0 -10000 0 0
JAK2 0.011 0.038 -10000 0 -10000 0 0
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.32 -10000 0 -0.74 42 42
RAB7A -0.06 0.32 0.5 1 -0.77 32 33
lysosomal transport -0.054 0.31 0.5 1 -0.73 32 33
FOS -0.38 0.6 -10000 0 -1.1 95 95
STAT4 (dimer) -0.079 0.39 0.46 2 -0.83 45 47
STAT5A (dimer) -0.086 0.45 0.48 10 -0.97 43 53
GZMA -0.15 0.5 0.52 1 -1.2 42 43
GZMB -0.12 0.47 0.54 2 -1.1 40 42
HLX 0.026 0.004 -10000 0 -10000 0 0
LCK -0.13 0.49 0.5 2 -1.1 44 46
TCR/CD3/MHC II/CD4 -0.11 0.24 -10000 0 -0.4 74 74
IL2/IL2R 0.036 0.11 0.35 2 -0.3 20 22
MAPK14 -0.092 0.4 -10000 0 -0.94 37 37
CCR5 -0.098 0.42 -10000 0 -1.1 31 31
IL1B 0.006 0.12 0.28 13 -0.44 12 25
STAT6 -0.008 0.15 0.31 2 -0.41 12 14
STAT4 0.004 0.096 -10000 0 -0.42 13 13
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.029 0.026 0.27 3 -10000 0 3
NFKB1 0.026 0.003 -10000 0 -10000 0 0
NFKB2 0.026 0.005 -10000 0 -10000 0 0
IL12B 0.015 0.057 0.28 6 -10000 0 6
CD8A -0.018 0.14 0.29 1 -0.42 26 27
CD8B -0.006 0.12 0.28 3 -0.42 19 22
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.011 0.12 0.29 16 -0.26 8 24
IL2RB 0.017 0.061 -10000 0 -0.42 5 5
proteasomal ubiquitin-dependent protein catabolic process -0.064 0.35 0.46 2 -0.74 45 47
IL2RG 0.019 0.08 0.27 5 -0.42 7 12
IL12 0.027 0.066 0.24 7 -10000 0 7
STAT5A 0.024 0.028 -10000 0 -0.42 1 1
CD247 0.001 0.066 0.27 1 -0.42 5 6
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.027 0.015 0.27 1 -10000 0 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.016 0.051 0.28 4 -10000 0 4
IL12/IL12R/TYK2/JAK2 -0.15 0.56 0.56 2 -1.2 44 46
MAP2K3 -0.11 0.43 0.46 2 -0.95 42 44
RIPK2 0.022 0.01 -10000 0 -10000 0 0
MAP2K6 -0.09 0.4 -10000 0 -0.91 38 38
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.086 -10000 0 -0.42 10 10
IL18RAP 0.002 0.099 -10000 0 -0.42 13 13
IL12Rbeta1/TYK2 0.025 0.085 0.24 13 -0.35 4 17
EOMES -0.061 0.28 -10000 0 -1.1 15 15
STAT1 (dimer) -0.051 0.36 0.47 11 -0.76 41 52
T cell proliferation -0.054 0.28 0.39 2 -0.62 41 43
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.043 -10000 0 -0.43 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.081 0.29 -10000 0 -0.65 42 42
ATF2 -0.082 0.36 -10000 0 -0.85 37 37
Osteopontin-mediated events

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.032 0.093 -10000 0 -0.21 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.099 0.31 6 -10000 0 6
alphaV/beta3 Integrin/Osteopontin/Src 0.11 0.086 0.22 103 -10000 0 103
AP1 -0.036 0.18 0.32 1 -0.46 23 24
ILK 0.017 0.093 0.22 1 -0.22 27 28
bone resorption 0.013 0.1 0.22 7 -0.33 4 11
PTK2B 0.022 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.073 0.13 0.32 3 -0.2 21 24
ITGAV 0.029 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.019 0.073 -10000 0 -0.3 13 13
alphaV/beta3 Integrin/Osteopontin 0.084 0.14 0.25 23 -0.25 28 51
MAP3K1 0.018 0.094 0.2 10 -0.23 28 38
JUN 0.016 0.067 -10000 0 -0.42 6 6
MAPK3 0.013 0.086 0.19 6 -0.22 4 10
MAPK1 0.014 0.088 0.19 6 -0.21 23 29
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 0.001 0.088 0.2 9 -0.22 29 38
ITGB3 -0.018 0.14 -10000 0 -0.42 28 28
NFKBIA 0.014 0.087 0.36 1 -10000 0 1
FOS -0.1 0.2 -10000 0 -0.42 77 77
CD44 0.012 0.078 0.29 1 -0.42 8 9
CHUK 0.026 0.006 -10000 0 -10000 0 0
PLAU 0.034 0.11 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.063 0.1 0.33 2 -10000 0 2
BCAR1 0.025 0.006 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.008 0.11 -10000 0 -0.3 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.015 0.093 0.21 3 -0.22 29 32
VAV3 0.003 0.086 0.19 12 -0.21 25 37
MAP3K14 0.021 0.094 -10000 0 -0.22 28 28
ROCK2 0.016 0.066 -10000 0 -0.42 6 6
SPP1 0.13 0.12 0.28 105 -10000 0 105
RAC1 0.026 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.082 0.2 2 -0.2 24 26
MMP2 -0.066 0.17 -10000 0 -0.45 31 31
BCR signaling pathway

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
JUN -0.052 0.15 0.25 1 -0.36 31 32
IKBKB -0.023 0.1 -10000 0 -0.31 14 14
AKT1 -0.041 0.11 0.22 8 -0.21 41 49
IKBKG -0.017 0.095 -10000 0 -0.3 13 13
CALM1 -0.037 0.13 -10000 0 -0.4 17 17
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
MAP3K1 -0.08 0.22 0.26 1 -0.47 45 46
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.035 0.13 -10000 0 -0.39 20 20
DOK1 0.027 0.016 0.27 1 -10000 0 1
AP-1 -0.044 0.1 0.2 1 -0.26 13 14
LYN 0.024 0.008 -10000 0 -10000 0 0
BLNK 0.012 0.076 -10000 0 -0.42 8 8
SHC1 0.025 0.018 0.29 1 -10000 0 1
BCR complex -0.027 0.16 0.32 8 -0.33 51 59
CD22 -0.096 0.23 0.22 5 -0.48 56 61
CAMK2G -0.031 0.12 -10000 0 -0.38 16 16
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
INPP5D 0.016 0.061 -10000 0 -0.42 5 5
SHC/GRB2/SOS1 -0.017 0.1 -10000 0 -0.23 42 42
GO:0007205 -0.037 0.14 -10000 0 -0.39 21 21
SYK 0.021 0.039 -10000 0 -0.42 2 2
ELK1 -0.037 0.13 -10000 0 -0.4 17 17
NFATC1 -0.094 0.21 0.21 3 -0.44 53 56
B-cell antigen/BCR complex -0.027 0.16 0.32 8 -0.33 51 59
PAG1/CSK 0.033 0.015 -10000 0 -10000 0 0
NFKBIB 0.009 0.042 -10000 0 -0.13 5 5
HRAS -0.036 0.13 -10000 0 -0.36 19 19
NFKBIA 0.01 0.042 -10000 0 -0.12 5 5
NF-kappa-B/RelA/I kappa B beta 0.014 0.037 -10000 0 -10000 0 0
RasGAP/Csk -0.001 0.15 0.34 5 -0.28 49 54
mol:GDP -0.037 0.13 -10000 0 -0.4 19 19
PTEN 0.025 0.007 -10000 0 -10000 0 0
CD79B 0.012 0.096 0.27 5 -0.42 11 16
NF-kappa-B/RelA/I kappa B alpha 0.014 0.037 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.098 0.22 0.3 1 -0.48 47 48
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:IP3 -0.037 0.14 -10000 0 -0.4 20 20
CSK 0.026 0.004 -10000 0 -10000 0 0
FOS -0.088 0.15 -10000 0 -0.36 37 37
CHUK -0.025 0.11 -10000 0 -0.31 22 22
IBTK 0.026 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.012 0.13 -10000 0 -0.37 16 16
PTPN6 -0.093 0.22 0.22 1 -0.5 46 47
RELA 0.026 0.004 -10000 0 -10000 0 0
BCL2A1 0.009 0.032 -10000 0 -10000 0 0
VAV2 -0.1 0.24 -10000 0 -0.51 50 50
ubiquitin-dependent protein catabolic process 0.012 0.042 -10000 0 -0.12 5 5
BTK -0.037 0.25 -10000 0 -1.1 15 15
CD19 -0.093 0.22 0.22 5 -0.49 47 52
MAP4K1 0.016 0.068 0.27 1 -0.42 6 7
CD72 0.032 0.045 0.27 9 -10000 0 9
PAG1 0.023 0.01 -10000 0 -10000 0 0
MAPK14 -0.067 0.19 0.24 2 -0.41 42 44
SH3BP5 0.023 0.028 -10000 0 -0.42 1 1
PIK3AP1 -0.044 0.16 0.22 1 -0.42 24 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.069 0.23 0.27 1 -0.47 48 49
RAF1 -0.016 0.13 0.27 5 -0.38 12 17
RasGAP/p62DOK/SHIP -0.004 0.16 0.31 5 -0.29 48 53
CD79A -0.051 0.18 0.27 8 -0.42 50 58
re-entry into mitotic cell cycle -0.044 0.1 0.2 1 -0.26 12 13
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.007 0.11 0.26 4 -0.39 7 11
MAPK1 -0.012 0.12 0.27 7 -0.37 8 15
CD72/SHP1 -0.067 0.22 0.3 11 -0.47 45 56
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.066 0.19 0.27 5 -0.4 45 50
actin cytoskeleton organization -0.088 0.2 0.27 3 -0.45 47 50
NF-kappa-B/RelA 0.031 0.071 -10000 0 -0.19 3 3
Calcineurin -0.017 0.12 -10000 0 -0.36 15 15
PI3K -0.097 0.17 -10000 0 -0.38 54 54
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.04 0.15 0.22 1 -0.4 26 27
SOS1 0.026 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.08 0.26 0.41 1 -0.7 32 33
DAPP1 -0.096 0.28 -10000 0 -0.76 33 33
cytokine secretion -0.086 0.19 0.21 3 -0.41 53 56
mol:DAG -0.037 0.14 -10000 0 -0.4 20 20
PLCG2 0.025 0.032 0.27 1 -0.42 1 2
MAP2K1 -0.015 0.12 0.27 4 -0.38 10 14
B-cell antigen/BCR complex/FcgammaRIIB -0.021 0.16 0.3 8 -0.33 49 57
mol:PI-3-4-5-P3 -0.072 0.12 0.21 3 -0.29 48 51
ETS1 -0.028 0.11 0.25 1 -0.36 15 16
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.002 0.14 0.35 5 -0.25 52 57
B-cell antigen/BCR complex/LYN -0.065 0.21 0.24 5 -0.45 48 53
MALT1 0.025 0.006 -10000 0 -10000 0 0
TRAF6 0.025 0.007 -10000 0 -10000 0 0
RAC1 -0.095 0.22 0.29 2 -0.48 47 49
B-cell antigen/BCR complex/LYN/SYK -0.063 0.22 0.34 5 -0.47 45 50
CARD11 -0.034 0.14 -10000 0 -0.4 19 19
FCGR2B -0.004 0.11 0.28 2 -0.42 17 19
PPP3CA 0.026 0.004 -10000 0 -10000 0 0
BCL10 0.026 0.004 -10000 0 -10000 0 0
IKK complex -0.001 0.051 0.16 3 -0.12 10 13
PTPRC -0.027 0.15 0.27 1 -0.42 32 33
PDPK1 -0.045 0.098 0.2 9 -0.2 44 53
PPP3CB 0.025 0.006 -10000 0 -10000 0 0
PPP3CC 0.021 0.011 -10000 0 -10000 0 0
POU2F2 0.011 0.03 0.13 2 -10000 0 2
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.019 0.054 -10000 0 -0.42 4 4
mol:S1P 0 0.005 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.092 0.16 -10000 0 -0.29 93 93
GNAO1 -0.11 0.2 -10000 0 -0.42 78 78
S1P/S1P3/G12/G13 0.039 0.039 0.2 1 -0.23 3 4
AKT1 -0.042 0.16 -10000 0 -0.57 16 16
AKT3 -0.066 0.24 -10000 0 -1.2 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.019 0.054 -10000 0 -0.42 4 4
GNAI2 0.024 0.013 -10000 0 -10000 0 0
GNAI3 0.025 0.012 -10000 0 -10000 0 0
GNAI1 0.023 0.029 -10000 0 -0.42 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.019 0.051 0.29 1 -0.42 3 4
S1PR2 0.026 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.096 0.18 -10000 0 -0.41 55 55
MAPK3 -0.095 0.17 -10000 0 -0.4 53 53
MAPK1 -0.097 0.17 -10000 0 -0.4 54 54
JAK2 -0.1 0.2 0.22 1 -0.43 57 58
CXCR4 -0.1 0.18 -10000 0 -0.4 54 54
FLT1 0.025 0.014 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC -0.091 0.17 -10000 0 -0.4 51 51
S1P/S1P3/Gi -0.097 0.18 -10000 0 -0.41 55 55
RAC1 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.088 0.18 -10000 0 -0.38 56 56
VEGFA 0.025 0.015 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.086 0.16 -10000 0 -0.32 75 75
VEGFR1 homodimer/VEGFA homodimer 0.038 0.023 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.013 0.088 0.16 1 -0.22 38 39
GNAQ 0.025 0.007 -10000 0 -10000 0 0
GNAZ -0.075 0.18 -10000 0 -0.42 59 59
G12/G13 0.036 0.011 -10000 0 -10000 0 0
GNA14 -0.031 0.15 -10000 0 -0.42 33 33
GNA15 0.022 0.039 -10000 0 -0.42 2 2
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.024 0.028 -10000 0 -0.42 1 1
Rac1/GTP -0.087 0.17 -10000 0 -0.38 54 54
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.005 -10000 0 -10000 0 0
VLDLR 0.01 0.076 -10000 0 -0.42 8 8
LRPAP1 0.027 0.017 0.29 1 -10000 0 1
NUDC 0.026 0.003 -10000 0 -10000 0 0
RELN/LRP8 -0.032 0.16 0.35 2 -0.25 85 87
CaM/Ca2+ 0.019 0.003 -10000 0 -10000 0 0
KATNA1 0.026 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.06 0.12 0.19 5 -0.22 84 89
IQGAP1/CaM 0.038 0.008 -10000 0 -10000 0 0
DAB1 -0.013 0.14 0.27 15 -0.42 23 38
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
PLA2G7 0.063 0.088 0.27 40 -10000 0 40
CALM1 0.026 0.004 -10000 0 -10000 0 0
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.062 0.06 0.2 39 -10000 0 39
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.004 -10000 0 -10000 0 0
CDK5R1 0.041 0.059 0.27 16 -10000 0 16
LIS1/Poliovirus Protein 3A 0.008 0.003 -10000 0 -10000 0 0
CDK5R2 0.026 0.059 0.27 13 -10000 0 13
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.072 0.17 -10000 0 -0.27 100 100
YWHAE 0.024 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.041 0.11 0.24 1 -0.24 13 14
MAP1B -0.018 0.073 -10000 0 -0.26 23 23
RAC1 0.011 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.043 0.11 0.19 9 -0.21 55 64
RELN -0.12 0.21 0.27 3 -0.42 87 90
PAFAH/LIS1 0.05 0.062 0.19 40 -10000 0 40
LIS1/CLIP170 0.024 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.03 0.094 -10000 0 -0.22 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.077 0.16 0.21 2 -0.37 36 38
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.052 0.1 0.23 1 -0.26 12 13
LIS1/IQGAP1 0.024 0.011 -10000 0 -10000 0 0
RHOA 0.011 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.043 0.062 0.27 18 -10000 0 18
PAFAH1B2 0.025 0.006 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.002 0.057 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.033 0.11 0.24 1 -0.24 9 10
LRP8 0.068 0.092 0.27 45 -10000 0 45
NDEL1/Katanin 60 -0.043 0.11 0.24 1 -0.24 12 13
P39/CDK5 -0.051 0.11 0.2 10 -0.21 52 62
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.011 -10000 0 -10000 0 0
CDK5 -0.069 0.1 0.18 4 -0.21 82 86
PPP2R5D 0.026 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.009 -10000 0 -10000 0 0
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.055 0.14 -10000 0 -0.24 93 93
RELN/VLDLR -0.024 0.15 0.35 2 -0.23 85 87
CDC42 0.011 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.021 0.025 -10000 0 -10000 0 0
SVIL 0.018 0.045 -10000 0 -0.41 2 2
ZNF318 0.03 0.042 0.19 14 -10000 0 14
JMJD2C 0.015 0.028 0.083 35 -10000 0 35
T-DHT/AR/Ubc9 -0.068 0.15 -10000 0 -0.26 89 89
CARM1 0.024 0.01 -10000 0 -10000 0 0
PRDX1 0.027 0.004 -10000 0 -10000 0 0
PELP1 0.025 0.01 -10000 0 -10000 0 0
CTNNB1 0.022 0.021 -10000 0 -10000 0 0
AKT1 0.028 0.011 -10000 0 -10000 0 0
PTK2B 0.018 0.019 -10000 0 -10000 0 0
MED1 0.027 0.014 -10000 0 -10000 0 0
MAK 0.034 0.053 0.24 11 -10000 0 11
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.02 0.036 -10000 0 -0.42 1 1
GSN 0.017 0.045 -10000 0 -0.42 2 2
NCOA2 0.002 0.092 -10000 0 -0.42 12 12
NCOA6 0.022 0.029 0.29 1 -10000 0 1
DNA-PK 0.048 0.043 0.22 3 -10000 0 3
NCOA4 0.025 0.008 -10000 0 -10000 0 0
PIAS3 0.02 0.021 -10000 0 -10000 0 0
cell proliferation 0.003 0.072 0.28 2 -0.4 3 5
XRCC5 0.026 0.01 -10000 0 -10000 0 0
UBE3A 0.02 0.032 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.085 0.17 -10000 0 -0.29 94 94
FHL2 -0.017 0.095 -10000 0 -0.73 2 2
RANBP9 0.02 0.024 -10000 0 -10000 0 0
JMJD1A -0.013 0.055 0.1 9 -0.12 50 59
CDK6 0.011 0.081 -10000 0 -0.42 9 9
TGFB1I1 0.01 0.076 -10000 0 -0.42 7 7
T-DHT/AR/CyclinD1 -0.062 0.14 0.18 1 -0.26 78 79
XRCC6 0.027 0.01 -10000 0 -10000 0 0
T-DHT/AR -0.066 0.17 0.28 3 -0.25 106 109
CTDSP1 0.023 0.014 -10000 0 -10000 0 0
CTDSP2 0.027 0.027 -10000 0 -10000 0 0
BRCA1 0.022 0.029 0.28 1 -10000 0 1
TCF4 0.021 0.052 -10000 0 -0.42 3 3
CDKN2A 0.13 0.13 0.27 118 -10000 0 118
SRF 0.032 0.016 -10000 0 -0.13 1 1
NKX3-1 -0.084 0.17 0.31 1 -0.38 47 48
KLK3 -0.057 0.32 -10000 0 -1.4 14 14
TMF1 0.023 0.013 -10000 0 -10000 0 0
HNRNPA1 0.026 0.017 -10000 0 -10000 0 0
AOF2 -0.003 0.018 -10000 0 -0.074 14 14
APPL1 0.013 0.023 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.066 0.15 -10000 0 -0.26 89 89
AR -0.13 0.21 -10000 0 -0.43 89 89
UBA3 0.022 0.015 -10000 0 -10000 0 0
PATZ1 0.026 0.017 -10000 0 -10000 0 0
PAWR 0.022 0.029 -10000 0 -0.42 1 1
PRKDC 0.025 0.012 -10000 0 -10000 0 0
PA2G4 0.026 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.058 0.13 -10000 0 -0.24 88 88
RPS6KA3 0.022 0.024 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.068 0.14 0.17 1 -0.26 88 89
LATS2 0.025 0.032 -10000 0 -0.42 1 1
T-DHT/AR/PRX1 -0.056 0.14 -10000 0 -0.24 88 88
Cyclin D3/CDK11 p58 0.02 0.003 -10000 0 -10000 0 0
VAV3 0.024 0.053 0.26 5 -0.41 2 7
KLK2 -0.008 0.094 0.27 2 -0.4 1 3
CASP8 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.061 0.14 -10000 0 -0.25 85 85
TMPRSS2 -0.17 0.36 0.29 2 -0.86 52 54
CCND1 0.022 0.073 0.29 8 -0.41 4 12
PIAS1 0.021 0.032 -10000 0 -10000 0 0
mol:T-DHT -0.004 0.022 0.049 3 -0.057 25 28
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.019 0.043 -10000 0 -0.17 12 12
T-DHT/AR/CDK6 -0.075 0.16 -10000 0 -0.27 94 94
CMTM2 0.027 0.023 0.27 2 -10000 0 2
SNURF -0.013 0.11 -10000 0 -0.42 19 19
ZMIZ1 0.016 0.034 -10000 0 -10000 0 0
CCND3 0.027 0.004 -10000 0 -10000 0 0
TGIF1 0.024 0.018 -10000 0 -10000 0 0
FKBP4 0.021 0.024 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.039 0.04 0.18 2 -0.22 5 7
RGS9BP 0.009 0.088 0.29 2 -0.42 10 12
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.013 0.013 -10000 0 -10000 0 0
mol:Na + 0.032 0.098 0.18 45 -0.24 20 65
mol:ADP -0.012 0.02 0.28 1 -10000 0 1
GNAT2 0.021 0.028 0.28 2 -10000 0 2
RGS9-1/Gbeta5/R9AP -0.024 0.13 -10000 0 -0.26 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.03 0.015 0.18 2 -10000 0 2
GRK7 0.018 0.024 0.29 1 -10000 0 1
CNGB3 0.089 0.11 0.27 71 -10000 0 71
Cone Metarhodopsin II/X-Arrestin 0.013 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.017 0.097 0.19 42 -0.22 19 61
Cone PDE6 -0.007 0.12 -10000 0 -0.23 58 58
Cone Metarhodopsin II 0.024 0.009 -10000 0 -10000 0 0
Na + (4 Units) 0.042 0.1 0.21 42 -0.22 20 62
GNAT2/GDP -0.008 0.12 -10000 0 -0.22 60 60
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.01 0.03 0.18 6 -10000 0 6
Cone Transducin 0.043 0.042 0.2 2 -0.23 5 7
SLC24A2 0.026 0.063 0.27 15 -10000 0 15
GNB3/GNGT2 0.031 0.047 -10000 0 -0.3 5 5
GNB3 0.021 0.047 -10000 0 -0.42 3 3
GNAT2/GTP 0.019 0.011 0.18 1 -10000 0 1
CNGA3 -0.028 0.12 -10000 0 -0.42 24 24
ARR3 -0.009 0.017 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.033 0.098 0.18 45 -0.24 20 65
mol:Pi -0.024 0.13 -10000 0 -0.26 60 60
Cone CNG Channel 0.052 0.095 -10000 0 -0.21 20 20
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.026 0.063 0.27 15 -10000 0 15
RGS9 -0.066 0.18 -10000 0 -0.42 54 54
PDE6C -0.009 0.016 -10000 0 -10000 0 0
GNGT2 0.02 0.047 -10000 0 -0.42 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.008 0.024 0.27 1 -10000 0 1
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.052 0.28 -10000 0 -0.58 20 20
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.089 0.33 0.6 9 -0.64 19 28
SMAD4 0.026 0.007 -10000 0 -10000 0 0
ID2 0.051 0.28 -10000 0 -0.59 20 20
AP1 -0.061 0.16 -10000 0 -0.32 74 74
ABCG2 0.044 0.29 0.53 1 -0.59 22 23
HIF1A 0.029 0.087 -10000 0 -0.21 4 4
TFF3 0.018 0.33 0.54 4 -0.63 28 32
GATA2 0.027 0.068 0.27 7 -0.42 4 11
AKT1 0.022 0.097 -10000 0 -0.19 17 17
response to hypoxia 0.008 0.084 -10000 0 -0.18 18 18
MCL1 0.045 0.27 -10000 0 -0.58 18 18
NDRG1 0.051 0.28 -10000 0 -0.58 18 18
SERPINE1 0.054 0.29 0.48 1 -0.58 20 21
FECH 0.05 0.28 -10000 0 -0.58 20 20
FURIN 0.053 0.28 -10000 0 -0.58 20 20
NCOA2 0.006 0.093 -10000 0 -0.42 12 12
EP300 0.025 0.13 -10000 0 -0.29 21 21
HMOX1 0.056 0.29 0.59 6 -0.58 20 26
BHLHE40 0.046 0.28 -10000 0 -0.59 19 19
BHLHE41 0.049 0.29 -10000 0 -0.6 20 20
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.073 0.13 -10000 0 -0.32 1 1
ENG 0.046 0.095 0.34 1 -0.28 1 2
JUN 0.017 0.066 -10000 0 -0.42 6 6
RORA 0.047 0.29 -10000 0 -0.6 21 21
ABCB1 -0.097 0.31 -10000 0 -0.9 32 32
TFRC 0.056 0.28 -10000 0 -0.59 17 17
CXCR4 0.051 0.29 -10000 0 -0.6 21 21
TF 0.063 0.3 0.56 10 -0.59 21 31
CITED2 0.054 0.28 -10000 0 -0.58 20 20
HIF1A/ARNT 0.14 0.4 0.75 22 -0.69 14 36
LDHA -0.002 0.16 -10000 0 -0.59 12 12
ETS1 0.048 0.28 -10000 0 -0.59 19 19
PGK1 0.051 0.28 -10000 0 -0.59 19 19
NOS2 0.06 0.3 0.54 6 -0.62 20 26
ITGB2 0.051 0.29 0.54 4 -0.61 18 22
ALDOA 0.055 0.28 -10000 0 -0.59 18 18
Cbp/p300/CITED2 0.047 0.33 -10000 0 -0.69 24 24
FOS -0.1 0.2 -10000 0 -0.42 77 77
HK2 0.059 0.28 -10000 0 -0.58 20 20
SP1 0.014 0.051 -10000 0 -0.16 5 5
GCK -0.005 0.34 -10000 0 -1.3 16 16
HK1 0.051 0.28 -10000 0 -0.59 19 19
NPM1 0.051 0.28 -10000 0 -0.58 20 20
EGLN1 0.053 0.28 -10000 0 -0.59 19 19
CREB1 0.03 0.006 -10000 0 -10000 0 0
PGM1 0.05 0.28 -10000 0 -0.58 20 20
SMAD3 0.027 0.004 -10000 0 -10000 0 0
EDN1 -0.016 0.2 -10000 0 -0.68 9 9
IGFBP1 0.065 0.29 0.55 6 -0.59 18 24
VEGFA 0.054 0.26 0.47 1 -0.56 19 20
HIF1A/JAB1 0.041 0.067 -10000 0 -10000 0 0
CP 0.02 0.33 0.53 5 -0.62 27 32
CXCL12 -0.014 0.35 -10000 0 -0.65 39 39
COPS5 0.026 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.011 -10000 0 -10000 0 0
BNIP3 0.048 0.28 -10000 0 -0.58 20 20
EGLN3 0.047 0.29 -10000 0 -0.59 20 20
CA9 0.13 0.32 0.55 25 -0.6 17 42
TERT 0.099 0.3 0.56 17 -0.6 16 33
ENO1 0.054 0.29 -10000 0 -0.58 20 20
PFKL 0.05 0.28 -10000 0 -0.59 19 19
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM 0.049 0.28 -10000 0 -0.58 20 20
ARNT 0.03 0.074 -10000 0 -0.21 1 1
HNF4A 0.04 0.081 0.27 24 -10000 0 24
ADFP 0.032 0.27 -10000 0 -0.58 20 20
SLC2A1 0.054 0.26 0.47 1 -0.55 20 21
LEP 0.039 0.31 0.56 2 -0.61 24 26
HIF1A/ARNT/Cbp/p300 0.08 0.33 0.64 5 -0.65 20 25
EPO 0.075 0.24 0.51 6 -0.63 3 9
CREBBP 0.025 0.12 -10000 0 -0.28 22 22
HIF1A/ARNT/Cbp/p300/HDAC7 0.085 0.33 0.62 5 -0.63 19 24
PFKFB3 0.042 0.28 -10000 0 -0.58 20 20
NT5E 0.036 0.31 -10000 0 -0.62 23 23
FAS signaling pathway (CD95)

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
SPTAN1 -0.007 0.04 0.18 6 -0.19 6 12
RFC1 -0.004 0.051 0.18 12 -0.19 5 17
PRKDC 0.011 0.077 0.21 29 -0.19 7 36
RIPK1 0.029 0.009 -10000 0 -10000 0 0
CASP7 -0.035 0.14 -10000 0 -0.67 10 10
FASLG/FAS/FADD/FAF1 -0.022 0.072 0.18 3 -0.27 10 13
MAP2K4 -0.12 0.19 -10000 0 -0.33 92 92
mol:ceramide -0.053 0.12 -10000 0 -0.32 20 20
GSN -0.008 0.042 0.18 6 -0.2 7 13
FASLG/FAS/FADD/FAF1/Caspase 8 -0.031 0.093 0.21 1 -0.29 16 17
FAS -0.002 0.053 -10000 0 -0.43 3 3
BID -0.017 0.035 0.25 4 -0.15 1 5
MAP3K1 -0.065 0.14 0.24 1 -0.37 25 26
MAP3K7 0.017 0.016 -10000 0 -10000 0 0
RB1 -0.004 0.042 0.18 9 -0.19 4 13
CFLAR 0.03 0.008 -10000 0 -10000 0 0
HGF/MET -0.019 0.13 0.2 6 -0.26 62 68
ARHGDIB -0.003 0.056 0.2 12 -0.19 7 19
FADD 0.005 0.04 0.29 3 -10000 0 3
actin filament polymerization 0.008 0.042 0.19 7 -0.18 6 13
NFKB1 -0.069 0.14 -10000 0 -0.54 8 8
MAPK8 -0.2 0.27 -10000 0 -0.47 119 119
DFFA -0.005 0.053 0.2 10 -0.19 7 17
DNA fragmentation during apoptosis -0.005 0.052 0.2 10 -0.19 5 15
FAS/FADD/MET 0.012 0.05 -10000 0 -0.27 3 3
CFLAR/RIP1 0.043 0.016 -10000 0 -10000 0 0
FAIM3 0.024 0.05 0.27 1 -0.42 3 4
FAF1 0 0.031 -10000 0 -10000 0 0
PARP1 -0.006 0.047 0.18 10 -0.19 7 17
DFFB -0.005 0.053 0.2 10 -0.19 7 17
CHUK -0.062 0.12 -10000 0 -0.48 7 7
FASLG -0.011 0.095 0.26 5 -0.43 10 15
FAS/FADD 0.003 0.049 -10000 0 -0.32 3 3
HGF -0.069 0.19 0.27 6 -0.42 59 65
LMNA 0.005 0.063 0.19 21 -10000 0 21
CASP6 -0.006 0.047 0.18 10 -0.19 7 17
CASP10 0.002 0.028 -10000 0 -10000 0 0
CASP3 0.002 0.044 0.22 10 -10000 0 10
PTPN13 0.017 0.061 -10000 0 -0.42 5 5
CASP8 -0.019 0.039 0.33 3 -0.18 1 4
IL6 -0.52 0.62 -10000 0 -1.2 119 119
MET 0.026 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.005 0.055 0.61 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.054 0.12 -10000 0 -0.33 20 20
activation of caspase activity by cytochrome c -0.017 0.035 0.25 4 -0.15 1 5
PAK2 0.003 0.064 0.21 19 -0.19 5 24
BCL2 0.006 0.093 -10000 0 -0.42 12 12
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.015 0.086 0.21 16 -0.26 17 33
EPHB2 0.041 0.058 0.27 16 -10000 0 16
Syndecan-2/TACI -0.007 0.088 0.19 4 -0.25 27 31
LAMA1 0.047 0.13 0.27 41 -0.42 9 50
Syndecan-2/alpha2 ITGB1 0.028 0.1 0.31 3 -0.24 24 27
HRAS 0.025 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK -0.005 0.054 -10000 0 -0.24 13 13
ITGA5 0.013 0.076 -10000 0 -0.42 8 8
BAX -0.009 0.049 -10000 0 -10000 0 0
EPB41 0.027 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.008 0.053 -10000 0 -0.22 13 13
LAMA3 0.009 0.15 0.27 24 -0.42 23 47
EZR 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.047 -10000 0 -0.42 3 3
Syndecan-2/MMP2 -0.008 0.098 -10000 0 -0.3 24 24
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.035 0.026 0.2 1 -0.3 1 2
dendrite morphogenesis 0.021 0.077 0.22 15 -0.24 13 28
Syndecan-2/GM-CSF 0.042 0.1 0.21 47 -0.24 13 60
determination of left/right symmetry -0.006 0.065 -10000 0 -0.29 13 13
Syndecan-2/PKC delta 0.01 0.056 -10000 0 -0.24 12 12
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 0.041 0.09 0.2 43 -0.22 11 54
MAPK1 0.041 0.094 0.2 45 -0.22 13 58
Syndecan-2/RACK1 0.019 0.054 -10000 0 -0.2 13 13
NF1 0.026 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.006 0.065 -10000 0 -0.29 13 13
ITGA2 0.027 0.039 0.28 3 -0.42 1 4
MAPK8 -0.007 0.058 -10000 0 -0.24 15 15
Syndecan-2/alpha2/beta1 Integrin 0.041 0.095 0.31 1 -0.22 17 18
Syndecan-2/Kininogen 0.004 0.056 -10000 0 -0.25 12 12
ITGB1 0.025 0.006 -10000 0 -10000 0 0
SRC 0.025 0.078 0.18 36 -0.2 13 49
Syndecan-2/CASK/Protein 4.1 0.009 0.053 -10000 0 -0.22 13 13
extracellular matrix organization 0.009 0.059 -10000 0 -0.24 13 13
actin cytoskeleton reorganization 0.015 0.086 0.21 16 -0.25 17 33
Syndecan-2/Caveolin-2/Ras 0.018 0.064 -10000 0 -0.24 14 14
Syndecan-2/Laminin alpha3 0.011 0.11 0.21 23 -0.26 25 48
Syndecan-2/RasGAP 0.028 0.056 -10000 0 -0.2 13 13
alpha5/beta1 Integrin 0.026 0.058 -10000 0 -0.3 8 8
PRKCD 0.025 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.077 0.22 15 -0.24 13 28
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.015 0.05 -10000 0 -0.2 12 12
RHOA 0.025 0.006 -10000 0 -10000 0 0
SDCBP 0.024 0.008 -10000 0 -10000 0 0
TNFRSF13B -0.009 0.11 0.27 4 -0.42 17 21
RASA1 0.026 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.035 0.026 0.2 1 -0.3 1 2
Syndecan-2/Synbindin 0.008 0.058 -10000 0 -0.24 13 13
TGFB1 0.026 0.005 -10000 0 -10000 0 0
CASP3 0.033 0.085 0.19 44 -0.22 11 55
FN1 0.027 0.098 0.27 16 -0.42 8 24
Syndecan-2/IL8 -0.019 0.1 0.19 1 -0.27 37 38
SDC2 -0.006 0.065 -10000 0 -0.29 13 13
KNG1 -0.016 0.004 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.009 0.059 -10000 0 -0.24 13 13
TRAPPC4 0.025 0.007 -10000 0 -10000 0 0
CSF2 0.064 0.097 0.27 47 -10000 0 47
Syndecan-2/TGFB1 0.009 0.059 -10000 0 -0.24 13 13
Syndecan-2/Syntenin/PI-4-5-P2 0.009 0.053 -10000 0 -0.22 13 13
Syndecan-2/Ezrin 0.022 0.056 -10000 0 -0.22 12 12
PRKACA 0.032 0.089 0.19 45 -0.22 13 58
angiogenesis -0.019 0.1 0.19 1 -0.27 37 38
MMP2 -0.01 0.12 -10000 0 -0.42 21 21
IL8 -0.037 0.16 0.27 1 -0.42 38 39
calcineurin-NFAT signaling pathway -0.007 0.087 0.19 4 -0.25 27 31
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.004 0.12 0.33 2 -0.27 29 31
FZD6 0.022 0.01 -10000 0 -10000 0 0
WNT6 0.031 0.11 0.27 24 -0.42 9 33
WNT4 -0.001 0.12 0.27 3 -0.42 18 21
FZD3 0.02 0.029 -10000 0 -0.42 1 1
WNT5A 0.024 0.073 0.27 7 -0.42 5 12
WNT11 0.027 0.1 0.27 19 -0.42 9 28
Arf6 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
CENTA1/KIF3B 0.025 0.032 -10000 0 -0.24 3 3
ARNO/beta Arrestin1-2 0.018 0.06 -10000 0 -10000 0 0
EGFR 0.023 0.073 0.29 6 -0.42 5 11
EPHA2 0.023 0.039 -10000 0 -0.42 2 2
USP6 0.024 0.008 -10000 0 -10000 0 0
IQSEC1 0.025 0.018 0.29 1 -10000 0 1
EGFR/EGFR/EGF/EGF 0.037 0.06 0.2 13 -0.3 5 18
ARRB2 0.009 0.009 -10000 0 -10000 0 0
mol:GTP 0.015 0.05 0.13 21 -0.17 4 25
ARRB1 0.021 0.039 -10000 0 -0.42 2 2
FBXO8 0.025 0.006 -10000 0 -10000 0 0
TSHR 0.02 0.04 0.27 5 -10000 0 5
EGF 0.035 0.057 0.27 14 -10000 0 14
somatostatin receptor activity 0 0 0 1 -0.001 45 46
ARAP2 0.023 0.039 -10000 0 -0.42 2 2
mol:GDP -0.063 0.13 -10000 0 -0.26 54 54
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 32 32
ITGA2B 0.044 0.067 0.27 21 -10000 0 21
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.038 -10000 0 -0.23 1 1
ADAP1 0.02 0.047 -10000 0 -0.42 3 3
KIF13B 0.022 0.01 -10000 0 -10000 0 0
HGF/MET -0.033 0.14 0.2 6 -0.3 59 65
PXN 0.026 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.057 0.12 0.18 1 -0.27 45 46
EGFR/EGFR/EGF/EGF/ARFGEP100 0.046 0.055 0.2 13 -0.25 4 17
ADRB2 -0.01 0.12 -10000 0 -0.42 21 21
receptor agonist activity 0 0 0 1 0 42 43
actin filament binding 0 0 -10000 0 -0.001 47 47
SRC 0.025 0.007 -10000 0 -10000 0 0
ITGB3 -0.022 0.14 -10000 0 -0.42 28 28
GNAQ 0.024 0.007 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 0.001 5 -0.001 30 35
ARF6/GDP -0.018 0.15 0.28 5 -0.41 23 28
ARF6/GDP/GULP/ACAP1 -0.067 0.17 -10000 0 -0.35 53 53
alphaIIb/beta3 Integrin/paxillin/GIT1 0.04 0.099 -10000 0 -0.23 27 27
ACAP1 0.016 0.072 0.27 3 -0.42 6 9
ACAP2 0.025 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.027 0.22 2 -10000 0 2
EFNA1 0.031 0.04 0.28 6 -10000 0 6
HGF -0.069 0.19 0.27 6 -0.42 59 65
CYTH3 0.006 0.001 -10000 0 -10000 0 0
CYTH2 0.018 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0 6 0 37 43
endosomal lumen acidification 0 0 0 4 0 42 46
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.038 0.16 -10000 0 -0.42 38 38
GNAQ/ARNO 0.031 0.012 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 2 2
MET 0.026 0.004 -10000 0 -10000 0 0
GNA14 -0.031 0.15 -10000 0 -0.42 33 33
GNA15 0.022 0.039 -10000 0 -0.42 2 2
GIT1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 4 -0.001 35 39
GNA11 0.024 0.028 -10000 0 -0.42 1 1
LHCGR -0.004 0.03 0.27 2 -10000 0 2
AGTR1 -0.16 0.22 -10000 0 -0.42 107 107
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.027 0.22 2 -10000 0 2
IPCEF1/ARNO 0.046 0.048 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.013 0.11 0.2 17 -0.29 28 45
Aurora A 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
Aurora A/GADD45A 0.014 0.054 -10000 0 -0.17 1 1
BIRC5 0.2 0.11 0.27 193 -0.42 1 194
NFKBIA 0.003 0.043 0.22 2 -10000 0 2
CPEB1 -0.19 0.21 -10000 0 -0.42 125 125
AKT1 0.004 0.044 0.22 2 -10000 0 2
NDEL1 0.024 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.013 0.048 0.2 1 -0.15 1 2
NDEL1/TACC3 0.03 0.062 0.21 8 -10000 0 8
GADD45A 0.027 0.002 -10000 0 -10000 0 0
GSK3B -0.013 0.028 -10000 0 -10000 0 0
PAK1/Aurora A 0.012 0.054 -10000 0 -0.2 2 2
MDM2 0.033 0.046 0.29 8 -10000 0 8
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.085 0.085 0.29 29 -10000 0 29
TP53 0.016 0.058 0.22 7 -0.22 5 12
DLG7 0.005 0.041 0.14 11 -10000 0 11
AURKAIP1 0.027 0.015 0.27 1 -10000 0 1
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.031 0.066 0.23 8 -10000 0 8
G2/M transition of mitotic cell cycle 0.013 0.048 0.2 1 -0.15 1 2
AURKA 0.013 0.055 0.18 11 -10000 0 11
AURKB 0.083 0.073 0.16 106 -0.28 2 108
CDC25B 0.015 0.041 0.16 2 -10000 0 2
G2/M transition checkpoint 0 0.035 0.12 2 -0.15 1 3
mRNA polyadenylation -0.1 0.11 -10000 0 -0.22 117 117
Aurora A/CPEB -0.1 0.11 -10000 0 -0.22 117 117
Aurora A/TACC1/TRAP/chTOG 0.024 0.057 -10000 0 -10000 0 0
BRCA1 0.027 0.016 0.27 1 -10000 0 1
centrosome duplication 0.012 0.053 -10000 0 -0.2 2 2
regulation of centrosome cycle 0.029 0.06 0.21 8 -10000 0 8
spindle assembly 0.023 0.055 -10000 0 -10000 0 0
TDRD7 0.024 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.09 0.26 20 -0.2 1 21
CENPA 0.1 0.079 0.17 122 -0.26 3 125
Aurora A/PP2A 0.014 0.053 -10000 0 -0.17 1 1
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.013 0.043 0.22 2 -10000 0 2
negative regulation of DNA binding 0.01 0.067 0.22 7 -0.2 13 20
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.036 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0 0.035 0.12 2 -0.15 1 3
mitotic prometaphase -0.009 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.055 0.18 11 -10000 0 11
TACC1 0.023 0.01 -10000 0 -10000 0 0
TACC3 0.044 0.065 0.28 19 -10000 0 19
Aurora A/Antizyme1 0.027 0.057 -10000 0 -10000 0 0
Aurora A/RasGAP 0.016 0.051 -10000 0 -10000 0 0
OAZ1 0.026 0.005 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.014 0.028 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.045 0.027 -10000 0 -0.25 1 1
Importin alpha/Importin beta/TPX2 0.084 0.085 0.29 29 -10000 0 29
PPP2R5D 0.026 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.062 0.085 0.24 28 -10000 0 28
PAK1 0.023 0.028 -10000 0 -0.42 1 1
CKAP5 0.025 0.006 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.11 0.24 1 -0.32 4 5
NFATC4 -0.031 0.087 0.23 7 -0.25 5 12
ERBB2IP 0.026 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.021 0.1 0.3 3 -0.23 36 39
JUN -0.007 0.085 0.26 3 -0.32 1 4
HRAS 0.025 0.007 -10000 0 -10000 0 0
DOCK7 -0.037 0.095 0.26 4 -0.23 35 39
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.009 0.11 0.25 3 -0.24 32 35
AKT1 0.001 0.008 -10000 0 -10000 0 0
BAD -0.007 0.005 -10000 0 -10000 0 0
MAPK10 -0.027 0.079 0.18 8 -0.18 21 29
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.018 0.11 0.32 3 -0.25 36 39
RAF1 -0.006 0.095 0.28 2 -0.33 4 6
ErbB2/ErbB3/neuregulin 2 -0.077 0.13 0.2 3 -0.24 97 100
STAT3 0.021 0.074 -10000 0 -0.8 2 2
cell migration -0.022 0.081 0.2 9 -0.2 11 20
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.052 0.21 0.37 1 -0.62 12 13
FOS -0.11 0.25 0.32 3 -0.46 82 85
NRAS 0.027 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.1 0.3 3 -0.23 36 39
MAPK3 -0.021 0.17 0.35 2 -0.57 8 10
MAPK1 -0.025 0.18 0.35 2 -0.58 10 12
JAK2 -0.038 0.089 0.32 1 -0.23 33 34
NF2 0 0.066 -10000 0 -0.6 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.009 0.095 0.18 4 -0.24 30 34
NRG1 -0.024 0.17 0.27 15 -0.42 35 50
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
MAPK8 -0.038 0.12 0.26 3 -0.26 37 40
MAPK9 -0.017 0.066 0.18 7 -0.21 1 8
ERBB2 -0.01 0.053 0.27 9 -10000 0 9
ERBB3 0.018 0.063 0.29 1 -0.42 5 6
SHC1 0.025 0.018 0.29 1 -10000 0 1
RAC1 0.026 0.005 -10000 0 -10000 0 0
apoptosis 0.013 0.013 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.072 -10000 0 -0.79 2 2
RNF41 -0.011 0.008 -10000 0 -10000 0 0
FRAP1 -0.004 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.04 0.058 -10000 0 -0.18 34 34
ErbB2/ErbB2/HSP90 (dimer) -0.007 0.04 0.2 8 -10000 0 8
CHRNA1 -0.002 0.14 0.36 3 -0.4 9 12
myelination -0.024 0.092 0.24 8 -0.42 1 9
PPP3CB -0.033 0.09 0.26 4 -0.22 33 37
KRAS 0.027 0.017 0.29 1 -10000 0 1
RAC1-CDC42/GDP 0.008 0.1 0.24 1 -0.27 6 7
NRG2 -0.16 0.22 -10000 0 -0.42 107 107
mol:GDP -0.009 0.095 0.18 3 -0.24 30 33
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K2 -0.012 0.096 0.28 2 -0.33 5 7
SRC 0.025 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.037 0.094 0.25 3 -0.23 35 38
MAP2K1 -0.046 0.18 -10000 0 -0.62 8 8
heart morphogenesis -0.021 0.1 0.3 3 -0.23 36 39
RAS family/GDP 0.014 0.11 -10000 0 -0.4 2 2
GRB2 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0 0.079 -10000 0 -0.63 4 4
CHRNE 0.004 0.026 0.12 3 -0.18 1 4
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.001 0.008 -10000 0 -10000 0 0
nervous system development -0.021 0.1 0.3 3 -0.23 36 39
CDC42 0.027 0.002 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.005 0.1 0.31 24 -0.21 6 30
KIRREL -0.015 0.13 -10000 0 -0.43 24 24
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.005 0.11 0.21 6 -0.31 24 30
PLCG1 0.025 0.007 -10000 0 -10000 0 0
ARRB2 0.024 0.008 -10000 0 -10000 0 0
WASL 0.026 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.034 0.095 0.27 1 -0.23 24 25
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.003 0.071 -10000 0 -0.22 19 19
FYN -0.004 0.099 0.27 10 -0.23 25 35
mol:Ca2+ 0.032 0.089 0.26 1 -0.23 21 22
mol:DAG 0.033 0.09 0.26 1 -0.23 21 22
NPHS2 0.012 0.064 0.27 12 -10000 0 12
mol:IP3 0.033 0.09 0.26 1 -0.23 21 22
regulation of endocytosis 0.021 0.083 -10000 0 -0.21 24 24
Nephrin/NEPH1/podocin/Cholesterol 0.021 0.089 0.19 13 -0.23 24 37
establishment of cell polarity 0.005 0.1 0.21 6 -0.31 24 30
Nephrin/NEPH1/podocin/NCK1-2 0.043 0.093 0.27 1 -0.21 23 24
Nephrin/NEPH1/beta Arrestin2 0.022 0.085 -10000 0 -0.22 24 24
NPHS1 0.006 0.052 0.28 6 -10000 0 6
Nephrin/NEPH1/podocin 0.02 0.091 0.19 4 -0.23 25 29
TJP1 0.026 0.006 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
NCK2 0.026 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.034 0.091 0.27 1 -0.23 21 22
CD2AP 0.026 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.035 0.093 0.27 1 -0.23 23 24
GRB2 0.026 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.002 0.098 0.26 12 -0.22 24 36
cytoskeleton organization -0.01 0.078 0.2 4 -0.24 22 26
Nephrin/NEPH1 0.009 0.075 0.17 6 -0.21 24 30
Nephrin/NEPH1/ZO-1 0.02 0.09 -10000 0 -0.25 24 24
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.012 -10000 0 -10000 0 0
CRKL -0.027 0.14 0.31 3 -0.5 10 13
mol:PIP3 -0.001 0.077 -10000 0 -0.87 2 2
AKT1 -0.005 0.071 -10000 0 -0.77 2 2
PTK2B 0.022 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.027 0.13 0.29 3 -0.47 10 13
RANBP10 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.009 0.12 0.2 6 -0.25 53 59
MAP3K5 -0.022 0.13 0.36 1 -0.45 11 12
HGF/MET/CIN85/CBL/ENDOPHILINS 0 0.13 -10000 0 -0.23 59 59
AP1 -0.059 0.14 0.18 1 -0.27 73 74
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.018 0.29 1 -10000 0 1
apoptosis -0.21 0.36 -10000 0 -0.74 81 81
STAT3 (dimer) -0.035 0.11 -10000 0 -0.3 17 17
GAB1/CRKL/SHP2/PI3K 0.003 0.13 0.39 1 -0.49 8 9
INPP5D 0.016 0.061 -10000 0 -0.42 5 5
CBL/CRK -0.018 0.13 0.27 2 -0.47 10 12
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
ELK1 0.006 0.096 0.39 10 -10000 0 10
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.022 0.079 -10000 0 -0.23 17 17
PAK1 0 0.078 -10000 0 -0.73 2 2
HGF/MET/RANBP10 -0.013 0.13 0.2 6 -0.25 57 63
HRAS -0.038 0.14 -10000 0 -0.52 10 10
DOCK1 -0.028 0.13 0.29 3 -0.48 10 13
GAB1 -0.031 0.14 0.25 1 -0.47 13 14
CRK -0.029 0.13 0.26 3 -0.5 10 13
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.069 0.19 -10000 0 -0.44 54 54
JUN 0.016 0.066 -10000 0 -0.42 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.033 0.083 -10000 0 -0.18 59 59
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
cell morphogenesis -0.022 0.14 0.33 10 -0.34 14 24
GRB2/SHC -0.007 0.087 0.2 1 -0.23 8 9
FOS -0.1 0.2 -10000 0 -0.42 77 77
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.006 0.096 0.39 10 -10000 0 10
HGF/MET/MUC20 -0.025 0.12 0.18 6 -0.25 59 65
cell migration -0.008 0.085 0.2 1 -0.23 8 9
GRB2 0.026 0.005 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
MET/RANBP10 0.037 0.011 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.027 0.1 -10000 0 -0.23 51 51
MET/MUC20 0.019 0.003 -10000 0 -10000 0 0
RAP1B -0.016 0.13 0.29 6 -0.49 8 14
RAP1A -0.028 0.12 0.31 2 -0.49 8 10
HGF/MET/RANBP9 -0.007 0.12 0.2 6 -0.25 51 57
RAF1 -0.016 0.15 0.3 1 -0.48 10 11
STAT3 -0.034 0.11 -10000 0 -0.31 17 17
cell proliferation -0.037 0.16 0.27 6 -0.32 45 51
RPS6KB1 -0.003 0.033 -10000 0 -10000 0 0
MAPK3 -0.001 0.1 0.67 5 -10000 0 5
MAPK1 0.004 0.12 0.7 7 -10000 0 7
RANBP9 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.015 0.13 0.3 3 -0.44 12 15
SRC -0.036 0.095 -10000 0 -0.28 15 15
PI3K -0.006 0.088 -10000 0 -0.22 10 10
MET/Glomulin 0.018 0.024 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
MAP2K1 -0.012 0.14 0.29 2 -0.45 10 12
MET 0.026 0.004 -10000 0 -10000 0 0
MAP4K1 -0.026 0.14 0.38 1 -0.48 11 12
PTK2 0.024 0.009 -10000 0 -10000 0 0
MAP2K2 -0.011 0.14 0.29 2 -0.45 10 12
BAD -0.006 0.072 0.38 1 -0.73 2 3
MAP2K4 -0.017 0.12 0.3 3 -0.46 8 11
SHP2/GRB2/SOS1/GAB1 -0.008 0.13 -10000 0 -0.49 8 8
INPPL1 0.025 0.007 -10000 0 -10000 0 0
PXN 0.026 0.004 -10000 0 -10000 0 0
SH3KBP1 0.026 0.003 -10000 0 -10000 0 0
HGS -0.033 0.075 -10000 0 -0.17 57 57
PLCgamma1/PKC 0.018 0.005 -10000 0 -10000 0 0
HGF -0.069 0.19 0.27 6 -0.42 59 65
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
PTPRJ 0.025 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.006 0.093 -10000 0 -0.18 50 50
PDPK1 -0.005 0.071 -10000 0 -0.81 2 2
HGF/MET/SHIP -0.02 0.14 0.2 6 -0.26 61 67
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.027 0.24 -10000 0 -0.81 20 20
NCK1/PAK1/Dok-R -0.041 0.11 -10000 0 -0.4 20 20
NCK1/Dok-R -0.029 0.27 -10000 0 -0.94 20 20
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol 0.008 0.058 0.23 16 -10000 0 16
RELA 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.026 0.018 0.29 1 -10000 0 1
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
F2 0.029 0.098 0.27 35 -10000 0 35
TNIP2 0.026 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.005 0.26 -10000 0 -0.88 20 20
FN1 0.027 0.098 0.27 16 -0.42 8 24
PLD2 -0.044 0.27 -10000 0 -0.96 20 20
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GRB14 0.054 0.079 0.27 31 -10000 0 31
ELK1 -0.03 0.25 -10000 0 -0.88 20 20
GRB7 0.032 0.064 0.29 10 -0.42 2 12
PAK1 0.023 0.028 -10000 0 -0.42 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.013 0.29 -10000 0 -0.96 20 20
CDKN1A -0.037 0.18 -10000 0 -0.59 18 18
ITGA5 0.013 0.076 -10000 0 -0.42 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.028 0.27 -10000 0 -0.95 20 20
CRK 0.024 0.008 -10000 0 -10000 0 0
mol:NO -0.013 0.18 -10000 0 -0.6 20 20
PLG -0.046 0.27 -10000 0 -0.96 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.029 0.22 -10000 0 -0.78 20 20
GRB2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.21 -10000 0 -0.68 18 18
BMX -0.085 0.29 -10000 0 -1.1 20 20
ANGPT1 -0.055 0.29 -10000 0 -1.2 16 16
tube development -0.046 0.19 -10000 0 -0.64 19 19
ANGPT4 0.02 0.036 0.27 4 -10000 0 4
response to hypoxia -0.003 0.018 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.014 0.29 -10000 0 -0.99 20 20
alpha5/beta1 Integrin 0.026 0.058 -10000 0 -0.3 8 8
FGF2 -0.11 0.2 -10000 0 -0.42 79 79
STAT5A (dimer) -0.045 0.22 -10000 0 -0.71 20 20
mol:L-citrulline -0.013 0.18 -10000 0 -0.6 20 20
AGTR1 -0.15 0.22 -10000 0 -0.42 107 107
MAPK14 -0.044 0.28 -10000 0 -0.99 20 20
Tie2/SHP2 -0.024 0.2 -10000 0 -0.96 8 8
TEK -0.012 0.2 -10000 0 -1 8 8
RPS6KB1 -0.027 0.23 -10000 0 -0.78 20 20
Angiotensin II/AT1 -0.11 0.15 -10000 0 -0.29 107 107
Tie2/Ang1/GRB2 -0.03 0.28 -10000 0 -0.98 20 20
MAPK3 -0.037 0.25 -10000 0 -0.88 20 20
MAPK1 -0.04 0.25 -10000 0 -0.9 20 20
Tie2/Ang1/GRB7 -0.027 0.28 -10000 0 -0.98 20 20
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.046 0.27 -10000 0 -0.96 20 20
PI3K -0.041 0.26 -10000 0 -0.92 20 20
FES -0.049 0.28 -10000 0 -0.98 20 20
Crk/Dok-R -0.028 0.27 -10000 0 -0.95 20 20
Tie2/Ang1/ABIN2 -0.031 0.28 -10000 0 -0.99 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.021 0.21 -10000 0 -0.72 20 20
STAT5A 0.025 0.028 -10000 0 -0.42 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.015 0.23 -10000 0 -0.76 20 20
Tie2/Ang2 -0.066 0.24 -10000 0 -0.84 19 19
Tie2/Ang1 -0.043 0.29 -10000 0 -1 20 20
FOXO1 -0.016 0.21 -10000 0 -0.73 20 20
ELF1 0.028 0.025 -10000 0 -10000 0 0
ELF2 -0.039 0.27 -10000 0 -0.94 20 20
mol:Choline -0.041 0.26 -10000 0 -0.93 20 20
cell migration -0.017 0.067 -10000 0 -0.23 20 20
FYN -0.054 0.21 -10000 0 -0.72 19 19
DOK2 0.012 0.068 0.27 1 -0.42 6 7
negative regulation of cell cycle -0.032 0.16 -10000 0 -0.53 18 18
ETS1 0.016 0.064 -10000 0 -0.25 14 14
PXN -0.007 0.2 0.42 1 -0.64 20 21
ITGB1 0.025 0.006 -10000 0 -10000 0 0
NOS3 -0.019 0.2 -10000 0 -0.68 20 20
RAC1 0.026 0.005 -10000 0 -10000 0 0
TNF 0.027 0.087 0.28 12 -0.24 16 28
MAPKKK cascade -0.041 0.26 -10000 0 -0.93 20 20
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.031 0.28 -10000 0 -0.96 20 20
NCK1 0.026 0.006 -10000 0 -10000 0 0
vasculogenesis -0.009 0.16 -10000 0 -0.54 20 20
mol:Phosphatidic acid -0.041 0.26 -10000 0 -0.93 20 20
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.013 0.18 -10000 0 -0.6 20 20
Rac1/GTP -0.023 0.22 -10000 0 -0.73 20 20
MMP2 -0.056 0.28 -10000 0 -1 20 20
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.048 0.16 -10000 0 -0.42 42 42
GNB1/GNG2 0.01 0.13 0.37 1 -0.38 10 11
mol:DAG -0.007 0.11 0.19 4 -0.37 9 13
PLCG1 -0.007 0.11 0.19 4 -0.38 9 13
YES1 -0.011 0.1 0.3 2 -0.41 8 10
FZD3 0.02 0.029 -10000 0 -0.42 1 1
FZD6 0.022 0.01 -10000 0 -10000 0 0
G protein 0.016 0.13 0.3 5 -0.38 9 14
MAP3K7 -0.057 0.12 0.19 2 -0.3 28 30
mol:Ca2+ -0.006 0.11 0.19 4 -0.35 9 13
mol:IP3 -0.007 0.11 0.19 4 -0.37 9 13
NLK 0.006 0.055 -10000 0 -0.86 1 1
GNB1 0.027 0.002 -10000 0 -10000 0 0
CAMK2A -0.06 0.13 0.2 2 -0.31 34 36
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.004 0.12 0.33 2 -0.27 29 31
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.017 0.1 0.18 2 -0.26 27 29
GO:0007205 -0.012 0.1 0.18 4 -0.36 9 13
WNT6 0.031 0.11 0.27 24 -0.42 9 33
WNT4 -0.001 0.12 0.27 3 -0.42 18 21
NFAT1/CK1 alpha -0.02 0.14 0.27 3 -0.39 13 16
GNG2 0.021 0.047 -10000 0 -0.42 3 3
WNT5A 0.024 0.073 0.27 7 -0.42 5 12
WNT11 0.027 0.1 0.27 19 -0.42 9 28
CDC42 -0.003 0.11 0.21 11 -0.37 9 20
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0 0.13 -10000 0 -0.39 26 26
HDAC1 0.025 0.013 -10000 0 -10000 0 0
AES 0.026 0.007 -10000 0 -10000 0 0
FBXW11 0.025 0.006 -10000 0 -10000 0 0
DTX1 0.017 0.076 0.27 3 -0.42 7 10
LRP6/FZD1 0.038 0.009 -10000 0 -10000 0 0
TLE1 0.023 0.029 -10000 0 -0.42 1 1
AP1 -0.058 0.13 -10000 0 -0.26 63 63
NCSTN 0.023 0.009 -10000 0 -10000 0 0
ADAM10 0.026 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.024 0.2 -10000 0 -0.69 18 18
NICD/RBPSUH 0.008 0.13 -10000 0 -0.38 26 26
WIF1 -0.079 0.18 0.27 6 -0.42 54 60
NOTCH1 -0.017 0.12 -10000 0 -0.4 24 24
PSENEN 0.025 0.006 -10000 0 -10000 0 0
KREMEN2 0.12 0.12 0.27 100 -10000 0 100
DKK1 -0.019 0.15 0.27 8 -0.42 31 39
beta catenin/beta TrCP1 0.038 0.061 0.25 2 -10000 0 2
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.024 0.009 -10000 0 -10000 0 0
AXIN1 -0.007 0.087 -10000 0 -0.37 7 7
CtBP/CBP/TCF1/TLE1/AES 0.009 0.053 0.28 1 -0.28 2 3
PSEN1 0.026 0.005 -10000 0 -10000 0 0
FOS -0.1 0.2 -10000 0 -0.42 77 77
JUN 0.016 0.066 -10000 0 -0.42 6 6
MAP3K7 0.025 0.007 -10000 0 -10000 0 0
CTNNB1 0.026 0.064 0.26 3 -10000 0 3
MAPK3 0.025 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.13 0.11 0.35 23 -0.25 1 24
HNF1A 0.03 0.03 0.27 4 -10000 0 4
CTBP1 0.027 0.018 0.29 1 -10000 0 1
MYC -0.049 0.3 -10000 0 -1.3 14 14
NKD1 0.013 0.085 0.27 3 -0.42 9 12
FZD1 0.026 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.005 0.14 -10000 0 -0.41 25 25
apoptosis -0.058 0.13 -10000 0 -0.26 63 63
Delta 1/NOTCHprecursor 0.006 0.14 -10000 0 -0.39 26 26
DLL1 0.024 0.044 0.27 2 -0.42 2 4
PPARD 0.018 0.056 -10000 0 -0.76 1 1
Gamma Secretase 0.06 0.035 -10000 0 -10000 0 0
APC -0.009 0.11 -10000 0 -0.53 7 7
DVL1 0.005 0.032 -10000 0 -0.26 2 2
CSNK2A1 0.025 0.007 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.065 0.14 0.35 3 -0.24 31 34
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.025 0.006 -10000 0 -10000 0 0
NLK 0.011 0.009 -10000 0 -10000 0 0
CCND1 -0.009 0.2 -10000 0 -1.2 7 7
WNT1 0.017 0.025 0.27 1 -10000 0 1
Axin1/APC/beta catenin 0.021 0.11 0.28 3 -0.4 6 9
DKK2 0.077 0.11 0.27 59 -0.42 1 60
NOTCH1 precursor/DVL1 -0.006 0.13 -10000 0 -0.45 13 13
GSK3B 0.025 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.001 0.14 -10000 0 -0.41 25 25
PPP2R5D 0.019 0.052 0.24 8 -0.3 2 10
MAPK1 0.026 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.003 0.12 -10000 0 -0.23 52 52
RBPJ 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.009 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.041 -10000 0 -0.21 8 8
epithelial cell differentiation 0.041 0.05 -10000 0 -0.21 8 8
CYFIP2 0.014 0.072 -10000 0 -0.42 7 7
ENAH 0.013 0.093 0.31 14 -0.27 1 15
EGFR 0.023 0.073 0.29 6 -0.42 5 11
EPHA2 0.023 0.039 -10000 0 -0.42 2 2
MYO6 -0.003 0.065 0.18 20 -0.21 8 28
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.04 0.051 -10000 0 -0.25 7 7
AQP5 0.015 0.057 -10000 0 -10000 0 0
CTNND1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.004 0.06 0.18 19 -0.2 8 27
regulation of calcium-dependent cell-cell adhesion 0.001 0.074 0.19 18 -0.2 11 29
EGF 0.035 0.057 0.27 14 -10000 0 14
NCKAP1 0.026 0.004 -10000 0 -10000 0 0
AQP3 -0.077 0.18 -10000 0 -0.42 53 53
cortical microtubule organization 0.041 0.05 -10000 0 -0.21 8 8
GO:0000145 -0.005 0.057 0.16 19 -0.2 8 27
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.052 -10000 0 -0.22 8 8
MLLT4 0.025 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.022 0.035 -10000 0 -0.36 1 1
ARF6 0.026 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.038 -10000 0 -0.23 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.005 0.054 0.26 2 -0.21 2 4
PVRL2 0.026 0.005 -10000 0 -10000 0 0
ZYX -0.004 0.066 0.18 20 -0.21 9 29
ARF6/GTP 0.065 0.039 -10000 0 -0.22 1 1
CDH1 0.012 0.076 -10000 0 -0.42 8 8
EGFR/EGFR/EGF/EGF 0.032 0.063 -10000 0 -0.22 12 12
RhoA/GDP 0.041 0.049 -10000 0 -0.21 8 8
actin cytoskeleton organization -0.005 0.061 0.17 19 -0.21 8 27
IGF-1R heterotetramer 0.024 0.028 -10000 0 -0.42 1 1
GIT1 0.025 0.006 -10000 0 -10000 0 0
IGF1R 0.024 0.028 -10000 0 -0.42 1 1
IGF1 -0.17 0.22 -10000 0 -0.42 116 116
DIAPH1 0.004 0.16 -10000 0 -0.55 14 14
Wnt receptor signaling pathway -0.041 0.05 0.21 8 -10000 0 8
RHOA 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.022 0.035 -10000 0 -0.22 6 6
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
VCL -0.005 0.062 0.17 19 -0.21 8 27
EFNA1 0.031 0.04 0.28 6 -10000 0 6
LPP -0.008 0.057 0.18 14 -0.2 7 21
Ephrin A1/EPHA2 0.033 0.05 -10000 0 -0.23 7 7
SEC6/SEC8 -0.019 0.029 -10000 0 -0.2 6 6
MGAT3 0.001 0.075 0.19 18 -0.21 11 29
HGF/MET -0.014 0.11 -10000 0 -0.2 62 62
HGF -0.069 0.19 0.27 6 -0.42 59 65
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.042 -10000 0 -0.21 8 8
actin cable formation 0.034 0.098 0.32 15 -0.23 1 16
KIAA1543 -0.004 0.064 0.17 20 -0.22 8 28
KIFC3 -0.004 0.063 0.19 18 -0.21 8 26
NCK1 0.026 0.006 -10000 0 -10000 0 0
EXOC3 0.022 0.01 -10000 0 -10000 0 0
ACTN1 -0.004 0.064 0.19 19 -0.21 8 27
NCK1/GIT1 0.036 0.012 -10000 0 -10000 0 0
mol:GDP 0.041 0.05 -10000 0 -0.21 8 8
EXOC4 0.026 0.005 -10000 0 -10000 0 0
STX4 -0.003 0.062 0.19 18 -0.21 7 25
PIP5K1C -0.004 0.061 0.18 19 -0.21 8 27
LIMA1 0.026 0.004 -10000 0 -10000 0 0
ABI1 0.025 0.006 -10000 0 -10000 0 0
ROCK1 0.017 0.1 0.32 15 -0.31 1 16
adherens junction assembly -0.002 0.075 0.27 1 -0.31 3 4
IGF-1R heterotetramer/IGF1 -0.068 0.12 -10000 0 -0.21 114 114
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
MET 0.026 0.004 -10000 0 -10000 0 0
PLEKHA7 -0.004 0.068 0.18 20 -0.23 8 28
mol:GTP 0.057 0.037 -10000 0 -0.23 1 1
establishment of epithelial cell apical/basal polarity 0.027 0.1 0.34 13 -10000 0 13
cortical actin cytoskeleton stabilization 0.013 0.041 -10000 0 -0.21 8 8
regulation of cell-cell adhesion -0.005 0.061 0.17 19 -0.21 8 27
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.042 -10000 0 -0.21 8 8
Syndecan-4-mediated signaling events

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
PTK2 0.009 0.13 0.25 1 -0.48 13 14
Syndecan-4/Syndesmos 0.047 0.15 0.36 3 -0.62 6 9
positive regulation of JNK cascade -0.01 0.18 0.34 3 -0.49 14 17
Syndecan-4/ADAM12 0.062 0.16 0.35 9 -0.62 6 15
CCL5 0.014 0.092 0.27 5 -0.42 10 15
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.026 0.004 -10000 0 -10000 0 0
ITGA5 0.013 0.076 -10000 0 -0.42 8 8
SDCBP 0.024 0.008 -10000 0 -10000 0 0
PLG -0.008 0.034 0.27 2 -10000 0 2
ADAM12 0.051 0.075 0.27 28 -10000 0 28
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.034 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.059 0.18 0.35 8 -0.63 7 15
Syndecan-4/CXCL12/CXCR4 -0.01 0.19 0.36 3 -0.53 14 17
Syndecan-4/Laminin alpha3 0.043 0.17 0.37 4 -0.65 6 10
MDK 0.041 0.061 0.27 17 -10000 0 17
Syndecan-4/FZD7 0.042 0.15 0.36 3 -0.6 7 10
Syndecan-4/Midkine 0.058 0.16 0.36 4 -0.62 6 10
FZD7 0.007 0.089 -10000 0 -0.42 11 11
Syndecan-4/FGFR1/FGF -0.042 0.21 0.32 2 -0.45 32 34
THBS1 0.01 0.081 -10000 0 -0.42 9 9
integrin-mediated signaling pathway 0.038 0.16 0.34 5 -0.6 8 13
positive regulation of MAPKKK cascade -0.01 0.18 0.34 3 -0.49 14 17
Syndecan-4/TACI 0.031 0.16 0.37 2 -0.56 8 10
CXCR4 0.02 0.054 -10000 0 -0.42 4 4
cell adhesion 0.013 0.078 0.19 9 -0.35 8 17
Syndecan-4/Dynamin 0.048 0.15 0.36 3 -0.67 5 8
Syndecan-4/TSP1 0.043 0.16 0.36 3 -0.64 7 10
Syndecan-4/GIPC 0.048 0.15 0.36 3 -0.62 6 9
Syndecan-4/RANTES 0.042 0.17 0.37 4 -0.66 7 11
ITGB1 0.025 0.006 -10000 0 -10000 0 0
LAMA1 0.047 0.13 0.27 41 -0.42 9 50
LAMA3 0.009 0.15 0.27 24 -0.42 23 47
RAC1 0.026 0.005 -10000 0 -10000 0 0
PRKCA 0.013 0.14 0.72 10 -10000 0 10
Syndecan-4/alpha-Actinin 0.048 0.15 0.36 3 -0.62 6 9
TFPI 0.016 0.066 -10000 0 -0.42 6 6
F2 0.045 0.069 0.28 20 -10000 0 20
alpha5/beta1 Integrin 0.026 0.058 -10000 0 -0.3 8 8
positive regulation of cell adhesion 0.032 0.17 0.34 3 -0.62 7 10
ACTN1 0.026 0.005 -10000 0 -10000 0 0
TNC 0 0.12 0.27 6 -0.42 18 24
Syndecan-4/CXCL12 -0.01 0.19 0.36 3 -0.54 14 17
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
CXCL12 -0.11 0.2 -10000 0 -0.42 81 81
TNFRSF13B -0.009 0.11 0.27 4 -0.42 17 21
FGF2 -0.11 0.2 -10000 0 -0.42 79 79
FGFR1 -0.062 0.17 -10000 0 -0.42 50 50
Syndecan-4/PI-4-5-P2 0.022 0.14 0.3 4 -0.62 6 10
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.097 0.26 16 -0.4 8 24
cell migration -0.02 0.015 -10000 0 -10000 0 0
PRKCD 0.018 0.022 -10000 0 -10000 0 0
vasculogenesis 0.043 0.15 0.35 3 -0.61 7 10
SDC4 0.033 0.14 0.33 4 -0.67 6 10
Syndecan-4/Tenascin C 0.037 0.17 0.34 5 -0.63 8 13
Syndecan-4/PI-4-5-P2/PKC alpha -0.027 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.043 0.15 0.36 3 -0.67 5 8
MMP9 0.084 0.13 0.27 71 -0.42 4 75
Rac1/GTP 0.012 0.08 0.19 9 -0.36 8 17
cytoskeleton organization 0.047 0.14 0.35 3 -0.59 6 9
GIPC1 0.026 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.044 0.16 0.36 3 -0.61 7 10
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.001 0.099 0.42 14 -10000 0 14
PI3K Class IB/PDE3B 0.001 0.099 -10000 0 -0.42 14 14
PDE3B 0.001 0.099 -10000 0 -0.42 14 14
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.027 0.015 0.27 1 -10000 0 1
SPHK1 0.055 0.086 0.27 33 -0.42 1 34
GNAI2 0.025 0.006 -10000 0 -10000 0 0
mol:S1P 0.023 0.034 0.2 2 -0.24 1 3
GNAO1 -0.11 0.2 -10000 0 -0.42 78 78
mol:Sphinganine-1-P 0.023 0.038 -10000 0 -0.3 1 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.057 0.042 -10000 0 -0.19 1 1
GNAI3 0.026 0.003 -10000 0 -10000 0 0
G12/G13 0.036 0.011 -10000 0 -10000 0 0
S1PR3 0.02 0.05 0.29 1 -0.42 3 4
S1PR2 0.026 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.013 0.029 0.14 1 -0.21 1 2
S1PR5 0.031 0.06 0.27 9 -0.42 2 11
S1PR4 0.024 0.054 0.27 3 -0.42 3 6
GNAI1 0.025 0.028 -10000 0 -0.42 1 1
S1P/S1P5/G12 0.05 0.052 0.23 3 -0.21 3 6
S1P/S1P3/Gq -0.029 0.13 -10000 0 -0.28 50 50
S1P/S1P4/Gi -0.077 0.17 -10000 0 -0.32 71 71
GNAQ 0.025 0.007 -10000 0 -10000 0 0
GNAZ -0.074 0.18 -10000 0 -0.42 59 59
GNA14 -0.031 0.15 -10000 0 -0.42 33 33
GNA15 0.022 0.039 -10000 0 -0.42 2 2
GNA12 0.025 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.005 -10000 0 -10000 0 0
GNA11 0.024 0.028 -10000 0 -0.42 1 1
ABCC1 0.027 0.023 0.28 2 -10000 0 2
Canonical Wnt signaling pathway

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
HDAC1 0.03 0.027 0.2 1 -10000 0 1
AES 0.029 0.024 -10000 0 -10000 0 0
FBXW11 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.009 -10000 0 -10000 0 0
SMAD4 0.025 0.007 -10000 0 -10000 0 0
DKK2 0.077 0.11 0.27 59 -0.42 1 60
TLE1 0.025 0.036 0.17 1 -0.42 1 2
MACF1 0.026 0.006 -10000 0 -10000 0 0
CTNNB1 0.058 0.094 0.26 12 -0.38 2 14
WIF1 -0.077 0.18 0.27 6 -0.42 54 60
beta catenin/RanBP3 0.048 0.14 0.4 28 -0.32 2 30
KREMEN2 0.12 0.12 0.27 100 -10000 0 100
DKK1 -0.019 0.15 0.27 8 -0.42 31 39
beta catenin/beta TrCP1 0.07 0.088 0.26 8 -0.34 2 10
FZD1 0.026 0.004 -10000 0 -10000 0 0
AXIN2 -0.055 0.33 0.58 10 -1.3 15 25
AXIN1 0.026 0.005 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.11 -10000 0 -0.48 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.16 -10000 0 -0.57 12 12
Axin1/APC/GSK3 0.034 0.058 0.22 5 -0.27 1 6
Axin1/APC/GSK3/beta catenin/Macf1 0.028 0.066 0.37 1 -0.34 1 2
HNF1A 0.032 0.039 0.24 6 -10000 0 6
CTBP1 0.029 0.027 0.2 2 -10000 0 2
MYC 0.008 0.37 0.57 35 -1.4 13 48
RANBP3 0.026 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.13 0.11 0.36 23 -0.25 1 24
NKD1 0.013 0.085 0.27 3 -0.42 9 12
TCF4 0.023 0.052 0.18 1 -0.4 3 4
TCF3 0.029 0.027 0.2 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.062 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.017 0.16 0.44 23 -0.45 6 29
LEF1 0.034 0.04 0.23 7 -10000 0 7
DVL1 0.033 0.052 0.22 1 -0.2 2 3
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.013 0.14 -10000 0 -0.47 14 14
DKK1/LRP6/Kremen 2 0.066 0.14 0.22 36 -0.24 31 67
LRP6 0.026 0.005 -10000 0 -10000 0 0
CSNK1A1 0.029 0.027 0.18 2 -10000 0 2
NLK 0.022 0.013 -10000 0 -10000 0 0
CCND1 0.043 0.28 0.62 31 -1.4 4 35
WNT1 0.02 0.022 0.27 1 -10000 0 1
GSK3A 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.006 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
PPP2R5D 0.037 0.061 0.27 8 -0.25 2 10
APC 0.001 0.052 0.24 9 -10000 0 9
WNT1/LRP6/FZD1 0.051 0.079 0.2 50 -10000 0 50
CREBBP 0.026 0.023 0.18 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.008 0.02 0.15 4 -10000 0 4
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.02 0.064 0.2 1 -0.29 10 11
STXBP1 0.014 0.066 -10000 0 -0.42 6 6
ACh/CHRNA1 0.043 0.083 0.21 45 -0.13 4 49
RAB3GAP2/RIMS1/UNC13B 0.033 0.06 0.2 1 -0.25 10 11
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 -0.006 0.086 0.27 1 -0.42 10 11
mol:ACh -0.005 0.042 0.076 17 -0.12 20 37
RAB3GAP2 0.026 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.013 0.083 0.22 1 -0.23 17 18
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.043 0.083 0.21 45 -0.13 4 49
UNC13B 0.024 0.009 -10000 0 -10000 0 0
CHRNA1 0.065 0.094 0.27 45 -10000 0 45
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.008 0.096 0.22 5 -0.26 26 31
SNAP25 -0.01 0.069 0.09 10 -0.26 18 28
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.008 0.13 0.27 5 -0.42 23 28
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.018 0.041 0.21 1 -0.25 5 6
STX1A/SNAP25 fragment 1/VAMP2 0.013 0.083 0.22 1 -0.23 17 18
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.19 0.22 -10000 0 -0.42 127 127
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.016 0.27 1 -10000 0 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.063 -10000 0 -0.27 11 11
HIF1A 0.003 0.055 -10000 0 -0.27 9 9
COPS5 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.038 -10000 0 -10000 0 0
FIH (dimer) 0.026 0.005 -10000 0 -10000 0 0
CDKN2A 0.13 0.13 0.27 118 -10000 0 118
ARNT/IPAS -0.11 0.16 -10000 0 -0.3 112 112
HIF1AN 0.026 0.005 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.013 0.057 -10000 0 -0.27 8 8
CUL2 0.025 0.006 -10000 0 -10000 0 0
OS9 0.026 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.044 0.024 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.015 0.064 -10000 0 -0.27 11 11
PHD1-3/OS9 0.055 0.049 -10000 0 -0.23 6 6
HIF1A/RACK1/Elongin B/Elongin C 0.031 0.066 -10000 0 -0.26 10 10
VHL 0.024 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.013 0.062 -10000 0 -0.27 10 10
EGLN3 0.016 0.066 -10000 0 -0.42 6 6
EGLN2 0.026 0.005 -10000 0 -10000 0 0
EGLN1 0.026 0.004 -10000 0 -10000 0 0
TP53 0.024 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.058 -10000 0 -0.49 3 3
ARNT 0.023 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.005 -10000 0 -10000 0 0
HIF1A/p19ARF 0.07 0.11 0.24 13 -0.25 10 23
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 + 0.026 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.012 0.18 1 -10000 0 1
Metarhodopsin II/Arrestin 0.022 0.008 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.036 0.029 0.18 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.012 0.026 0.27 1 -10000 0 1
GRK1 -0.013 0.013 -10000 0 -10000 0 0
CNG Channel 0.062 0.098 0.23 17 -0.2 21 38
mol:Na + 0.074 0.096 0.26 14 -0.2 13 27
mol:ADP -0.013 0.013 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.024 0.13 -10000 0 -0.26 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.093 0.11 0.31 14 -0.21 13 27
CNGB1 0.13 0.12 0.27 114 -10000 0 114
RDH5 0.024 0.028 -10000 0 -0.42 1 1
SAG -0.016 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.072 0.31 4 -10000 0 4
Na + (4 Units) 0.054 0.078 0.21 4 -0.2 12 16
RGS9 -0.066 0.18 -10000 0 -0.42 54 54
GNB1/GNGT1 0.045 0.034 0.2 11 -10000 0 11
GNAT1/GDP -0.009 0.12 -10000 0 -0.22 58 58
GUCY2D 0.039 0.075 0.27 24 -10000 0 24
GNGT1 0.034 0.058 0.27 14 -10000 0 14
GUCY2F -0.012 0.014 -10000 0 -10000 0 0
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.017 0.047 0.2 1 -0.22 8 9
mol:11-cis-retinal 0.024 0.028 -10000 0 -0.42 1 1
mol:cGMP 0.048 0.045 0.25 1 -0.21 1 2
GNB1 0.027 0.002 -10000 0 -10000 0 0
Rhodopsin 0.031 0.022 -10000 0 -0.3 1 1
SLC24A1 0.026 0.004 -10000 0 -10000 0 0
CNGA1 0.023 0.12 0.27 20 -0.42 13 33
Metarhodopsin II 0.021 0.007 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.067 0.061 0.35 1 -0.22 1 2
RGS9BP 0.009 0.088 0.29 2 -0.42 10 12
Metarhodopsin II/Transducin 0.018 0.019 0.16 2 -10000 0 2
GCAP Family/Ca ++ 0.047 0.037 0.19 1 -0.24 1 2
PDE6A/B 0.028 0.061 0.2 3 -0.3 8 11
mol:Pi -0.024 0.13 -10000 0 -0.26 60 60
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.052 0.034 0.2 2 -10000 0 2
PDE6B 0.012 0.076 -10000 0 -0.42 8 8
PDE6A 0.025 0.029 0.27 3 -10000 0 3
PDE6G 0.034 0.045 0.27 9 -10000 0 9
RHO -0.006 0.019 -10000 0 -10000 0 0
PDE6 -0.003 0.14 -10000 0 -0.23 64 64
GUCA1A 0.026 0.054 0.27 11 -10000 0 11
GC2/GCAP Family 0.057 0.039 -10000 0 -0.24 1 1
GUCA1C -0.013 0.021 0.27 1 -10000 0 1
GUCA1B 0.024 0.028 -10000 0 -0.42 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.007 -10000 0 -10000 0 0
SMARCC1 0.006 0.046 -10000 0 -0.72 1 1
REL 0.023 0.034 0.28 1 -0.42 1 2
HDAC7 -0.059 0.12 -10000 0 -0.3 40 40
JUN 0.016 0.066 -10000 0 -0.42 6 6
EP300 0.026 0.006 -10000 0 -10000 0 0
KAT2B 0.025 0.006 -10000 0 -10000 0 0
KAT5 0.026 0.004 -10000 0 -10000 0 0
MAPK14 -0.002 0.041 -10000 0 -0.3 3 3
FOXO1 0.025 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.046 0.14 -10000 0 -0.31 42 42
MAP2K6 0.011 0.054 0.27 1 -0.42 3 4
BRM/BAF57 0.031 0.023 -10000 0 -10000 0 0
MAP2K4 0.013 0.023 -10000 0 -10000 0 0
SMARCA2 0.021 0.015 -10000 0 -10000 0 0
PDE9A -0.15 0.38 -10000 0 -0.96 43 43
NCOA2 0.004 0.093 -10000 0 -0.42 12 12
CEBPA 0.031 0.049 0.27 7 -0.42 1 8
EHMT2 0.025 0.008 -10000 0 -10000 0 0
cell proliferation -0.021 0.17 0.4 12 -0.38 19 31
NR0B1 0.017 0.073 0.27 19 -10000 0 19
EGR1 -0.072 0.18 -10000 0 -0.42 57 57
RXRs/9cRA -0.034 0.12 -10000 0 -0.23 69 69
AR/RACK1/Src -0.009 0.1 0.31 5 -0.26 8 13
AR/GR -0.073 0.14 -10000 0 -0.26 75 75
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
PKN1 0.025 0.028 -10000 0 -0.42 1 1
RCHY1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.002 -10000 0 -10000 0 0
MAPK8 -0.003 0.039 -10000 0 -0.3 3 3
T-DHT/AR/TIF2/CARM1 -0.021 0.11 0.27 5 -0.31 11 16
SRC -0.017 0.057 0.19 8 -0.21 7 15
NR3C1 0.016 0.066 -10000 0 -0.42 6 6
KLK3 -0.093 0.27 -10000 0 -1.1 15 15
APPBP2 0.014 0.024 -10000 0 -10000 0 0
TRIM24 0.026 0.024 0.26 2 -10000 0 2
T-DHT/AR/TIP60 -0.032 0.091 0.26 1 -0.28 8 9
TMPRSS2 -0.18 0.43 0.4 1 -0.98 55 56
RXRG -0.11 0.19 -10000 0 -0.42 70 70
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.003 -10000 0 -10000 0 0
CARM1 0.027 0.005 -10000 0 -10000 0 0
NR2C2 0.024 0.033 0.29 1 -0.42 1 2
KLK2 -0.001 0.12 0.33 8 -0.45 2 10
AR -0.078 0.13 -10000 0 -0.27 80 80
SENP1 0.026 0.004 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
MDM2 0.031 0.048 0.29 8 -10000 0 8
SRY 0 0.008 0.029 14 -0.016 15 29
GATA2 0.026 0.068 0.27 7 -0.42 4 11
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.027 0.16 0.28 7 -0.42 33 40
T-DHT/AR/RACK1/Src -0.016 0.1 0.4 3 -0.28 7 10
positive regulation of transcription 0.025 0.068 0.27 7 -0.42 4 11
DNAJA1 0.014 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.029 0.19 7 -10000 0 7
NCOA1 0.03 0.018 -10000 0 -10000 0 0
SPDEF -0.003 0.16 0.27 22 -0.42 29 51
T-DHT/AR/TIF2 -0.028 0.1 0.23 3 -0.3 14 17
T-DHT/AR/Hsp90 -0.031 0.09 0.26 1 -0.28 8 9
GSK3B 0.023 0.013 -10000 0 -10000 0 0
NR2C1 0.026 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.021 0.054 0.22 3 -0.23 7 10
SIRT1 0.026 0.005 -10000 0 -10000 0 0
ZMIZ2 0.024 0.015 -10000 0 -10000 0 0
POU2F1 0.001 0.068 -10000 0 -0.18 17 17
T-DHT/AR/DAX-1 -0.026 0.1 0.32 3 -0.28 9 12
CREBBP 0.025 0.007 -10000 0 -10000 0 0
SMARCE1 0.024 0.014 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.14 0.16 0.55 7 -10000 0 7
PCK1 0.15 0.14 0.53 11 -10000 0 11
HNF4A 0.19 0.2 0.72 13 -10000 0 13
KCNJ11 0.13 0.26 0.58 3 -0.78 12 15
AKT1 0.12 0.13 0.39 10 -10000 0 10
response to starvation 0.01 0.018 -10000 0 -10000 0 0
DLK1 0.12 0.3 0.6 6 -0.8 17 23
NKX2-1 0.23 0.2 0.57 36 -10000 0 36
ACADM 0.15 0.17 0.53 7 -0.68 1 8
TAT 0.14 0.14 0.55 7 -10000 0 7
CEBPB 0.03 0.031 -10000 0 -0.4 1 1
CEBPA 0.041 0.054 0.3 7 -0.42 1 8
TTR 0.14 0.21 0.59 20 -0.47 1 21
PKLR 0.17 0.19 0.58 15 -10000 0 15
APOA1 0.2 0.22 0.75 11 -10000 0 11
CPT1C 0.15 0.16 0.54 8 -10000 0 8
ALAS1 0.14 0.12 -10000 0 -10000 0 0
TFRC 0.2 0.18 0.6 14 -10000 0 14
FOXF1 -0.14 0.21 -10000 0 -0.43 90 90
NF1 0.03 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.065 0.05 0.25 9 -10000 0 9
CPT1A 0.16 0.18 0.57 10 -0.76 1 11
HMGCS1 0.18 0.19 0.58 15 -10000 0 15
NR3C1 0.03 0.071 -10000 0 -0.4 6 6
CPT1B 0.14 0.16 0.55 6 -10000 0 6
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.055 0.033 -10000 0 -10000 0 0
GCK 0.11 0.26 0.53 8 -0.75 16 24
CREB1 0.035 0.02 -10000 0 -10000 0 0
IGFBP1 0.12 0.12 0.57 1 -10000 0 1
PDX1 0.2 0.17 0.57 11 -10000 0 11
UCP2 0.16 0.17 0.58 8 -10000 0 8
ALDOB 0.17 0.19 0.64 11 -10000 0 11
AFP 0.025 0.1 0.34 2 -10000 0 2
BDH1 0.16 0.17 0.56 9 -10000 0 9
HADH 0.17 0.18 0.57 5 -10000 0 5
F2 0.2 0.22 0.77 10 -10000 0 10
HNF1A 0.065 0.05 0.25 9 -10000 0 9
G6PC 0.084 0.092 0.4 2 -10000 0 2
SLC2A2 0.17 0.16 0.57 12 -10000 0 12
INS -0.03 0.02 -10000 0 -10000 0 0
FOXA1 -0.017 0.15 -10000 0 -0.41 31 31
FOXA3 0.12 0.12 0.33 57 -10000 0 57
FOXA2 0.24 0.25 0.75 19 -10000 0 19
ABCC8 0.16 0.18 0.59 4 -10000 0 4
ALB 0.032 0.11 0.31 4 -10000 0 4
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.026 0.002 -10000 0 -10000 0 0
HDAC2 0.025 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.067 -10000 0 -0.25 13 13
forebrain development -0.079 0.23 -10000 0 -0.54 42 42
GNAO1 -0.1 0.2 -10000 0 -0.42 78 78
SMO/beta Arrestin2 0.026 0.064 -10000 0 -0.29 10 10
SMO 0.011 0.085 -10000 0 -0.42 10 10
ARRB2 0.025 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.028 0.091 0.24 1 -0.38 5 6
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
GSK3B 0.026 0.006 -10000 0 -10000 0 0
GNAI2 0.026 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.062 0.02 -10000 0 -10000 0 0
GNAI1 0.025 0.028 -10000 0 -0.42 1 1
XPO1 0.028 0.007 -10000 0 -10000 0 0
GLI1/Su(fu) -0.06 0.21 -10000 0 -0.64 23 23
SAP30 0.025 0.006 -10000 0 -10000 0 0
mol:GDP 0.011 0.085 -10000 0 -0.42 10 10
MIM/GLI2A 0.034 0.031 -10000 0 -10000 0 0
IFT88 0.026 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.003 -10000 0 -10000 0 0
GLI2 -0.007 0.095 0.21 1 -0.31 13 14
GLI3 0.017 0.091 0.25 1 -0.4 5 6
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.026 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.005 -10000 0 -10000 0 0
GNG2 0.021 0.047 -10000 0 -0.42 3 3
Gi family/GTP -0.091 0.17 -10000 0 -0.32 77 77
SIN3B 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.016 0.11 -10000 0 -0.44 10 10
GLI2/Su(fu) -0.006 0.12 -10000 0 -0.34 21 21
FOXA2 0.036 0.11 -10000 0 -0.66 3 3
neural tube patterning -0.079 0.23 -10000 0 -0.54 42 42
SPOP 0.026 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.017 0.065 -10000 0 -0.35 2 2
GNB1 0.027 0.002 -10000 0 -10000 0 0
CSNK1G2 0.026 0.005 -10000 0 -10000 0 0
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
MTSS1 0.034 0.031 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.079 0.23 -10000 0 -0.54 42 42
SUFU 0.014 0.041 -10000 0 -0.18 9 9
LGALS3 0.025 0.028 -10000 0 -0.42 1 1
catabolic process 0.015 0.13 -10000 0 -0.39 16 16
GLI3A/CBP -0.01 0.12 -10000 0 -0.33 30 30
KIF3A 0.026 0.005 -10000 0 -10000 0 0
GLI1 -0.082 0.24 -10000 0 -0.55 42 42
RAB23 0.024 0.028 -10000 0 -0.42 1 1
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.002 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.015 0.068 -10000 0 -0.3 3 3
GNAZ -0.074 0.18 -10000 0 -0.42 59 59
RBBP4 0.026 0.002 -10000 0 -10000 0 0
CSNK1G1 0.026 0.004 -10000 0 -10000 0 0
PIAS1 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.002 0.1 -10000 0 -0.32 13 13
STK36 0.028 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.089 0.16 -10000 0 -0.39 47 47
PTCH1 -0.07 0.2 -10000 0 -0.59 23 23
MIM/GLI1 -0.051 0.22 -10000 0 -0.57 32 32
CREBBP -0.01 0.12 -10000 0 -0.33 30 30
Su(fu)/SIN3/HDAC complex 0.019 0.061 -10000 0 -0.38 4 4
Nectin adhesion 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 0.019 0.054 -10000 0 -0.42 4 4
alphaV beta3 Integrin 0.001 0.1 -10000 0 -0.3 28 28
PTK2 -0.013 0.12 -10000 0 -0.42 15 15
positive regulation of JNK cascade -0.015 0.12 -10000 0 -0.32 27 27
CDC42/GDP -0.006 0.16 -10000 0 -0.4 29 29
Rac1/GDP -0.008 0.16 -10000 0 -0.4 29 29
RAP1B 0.025 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.002 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.15 -10000 0 -0.39 26 26
nectin-3/I-afadin 0.017 0.082 0.2 2 -0.3 16 18
RAPGEF1 -0.006 0.14 0.34 1 -0.41 22 23
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.017 0.15 -10000 0 -0.45 24 24
PDGFB-D/PDGFRB 0.019 0.054 -10000 0 -0.42 4 4
TLN1 -0.008 0.038 -10000 0 -0.31 2 2
Rap1/GTP -0.006 0.099 -10000 0 -0.3 21 21
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.045 0.018 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.017 0.082 0.2 2 -0.3 16 18
PVR 0.026 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.025 0.19 -10000 0 -0.48 30 30
MLLT4 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.046 0.078 -10000 0 -0.22 18 18
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.012 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.016 0.12 -10000 0 -0.31 29 29
PVRL1 0.025 0.006 -10000 0 -10000 0 0
PVRL3 0 0.11 0.27 2 -0.42 16 18
PVRL2 0.026 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
CDH1 0.012 0.076 -10000 0 -0.42 8 8
CLDN1 0.013 0.092 0.27 5 -0.42 10 15
JAM-A/CLDN1 0.026 0.09 -10000 0 -0.24 23 23
SRC -0.021 0.16 -10000 0 -0.5 24 24
ITGB3 -0.022 0.14 -10000 0 -0.42 28 28
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.012 -10000 0 -10000 0 0
FARP2 -0.03 0.21 -10000 0 -0.54 30 30
RAC1 0.026 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.03 0.075 0.2 2 -0.25 16 18
nectin-1/I-afadin 0.036 0.012 -10000 0 -10000 0 0
nectin-2/I-afadin 0.036 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.034 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.029 0.075 0.2 2 -0.25 16 18
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.006 -10000 0 -10000 0 0
F11R 0.02 0.029 -10000 0 -0.42 1 1
positive regulation of filopodium formation -0.015 0.12 -10000 0 -0.32 27 27
alphaV/beta3 Integrin/Talin 0.004 0.1 0.25 2 -0.25 27 29
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.011 -10000 0 -10000 0 0
PIP5K1C -0.006 0.048 -10000 0 -0.19 15 15
VAV2 -0.033 0.21 -10000 0 -0.49 34 34
RAP1/GDP 0 0.14 -10000 0 -0.36 26 26
ITGAV 0.026 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.031 0.073 -10000 0 -0.25 15 15
nectin-3(dimer)/I-afadin/I-afadin 0.017 0.082 0.2 2 -0.3 16 18
Rac1/GTP -0.014 0.16 -10000 0 -0.39 27 27
PTPRM -0.005 0.065 -10000 0 -0.22 19 19
E-cadherin/beta catenin/alpha catenin 0.054 0.056 -10000 0 -0.21 7 7
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.002 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.002 0.11 0.23 3 -0.45 6 9
BAG4 0.022 0.01 -10000 0 -10000 0 0
BAD 0.008 0.047 0.16 3 -0.16 3 6
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.007 0.096 0.29 2 -0.42 12 14
BAX 0.009 0.049 0.18 3 -0.17 3 6
EnzymeConsortium:3.1.4.12 0.006 0.03 0.08 5 -0.09 6 11
IKBKB 0.012 0.12 0.33 5 -0.43 6 11
MAP2K2 0.029 0.081 0.2 33 -0.17 2 35
MAP2K1 0.028 0.081 0.2 34 -0.17 2 36
SMPD1 0.004 0.04 0.11 1 -0.14 11 12
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.018 0.12 0.27 5 -0.38 7 12
MAP2K4 0.011 0.047 0.24 4 -0.16 2 6
protein ubiquitination 0.007 0.12 0.38 2 -0.44 6 8
EnzymeConsortium:2.7.1.37 0.03 0.084 0.21 34 -0.17 2 36
response to UV 0 0.001 0.002 36 -10000 0 36
RAF1 0.03 0.084 0.21 34 -0.18 2 36
CRADD 0.026 0.004 -10000 0 -10000 0 0
mol:ceramide 0.009 0.047 0.12 4 -0.13 11 15
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.007 -10000 0 -10000 0 0
MADD 0.025 0.007 -10000 0 -10000 0 0
MAP3K1 0.01 0.046 0.15 4 -0.15 4 8
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.031 0.082 0.2 34 -10000 0 34
MAPK1 0.03 0.081 0.2 34 -10000 0 34
p50/RELA/I-kappa-B-alpha 0.038 0.008 -10000 0 -10000 0 0
FADD 0.014 0.11 0.26 6 -0.43 6 12
KSR1 0.016 0.061 0.2 13 -0.17 3 16
MAPK8 0.011 0.059 0.22 9 -0.18 3 12
TRAF2 0.024 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.002 9 -10000 0 9
CHUK 0.002 0.11 0.34 2 -0.43 6 8
TNF R/SODD 0.032 0.016 -10000 0 -10000 0 0
TNF 0.038 0.053 0.27 13 -10000 0 13
CYCS 0.016 0.053 0.16 11 -0.16 2 13
IKBKG 0.003 0.11 0.34 2 -0.43 6 8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.002 0.11 -10000 0 -0.45 7 7
RELA 0.026 0.004 -10000 0 -10000 0 0
RIPK1 0.025 0.006 -10000 0 -10000 0 0
AIFM1 0.014 0.051 0.16 9 -0.16 2 11
TNF/TNF R/SODD 0.049 0.039 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.002 9 -10000 0 9
CASP8 0 0.13 -10000 0 -0.53 14 14
NSMAF 0.008 0.11 0.24 5 -0.44 6 11
response to hydrogen peroxide 0 0.001 0.002 36 -10000 0 36
BCL2 0.005 0.093 -10000 0 -0.42 12 12
Ephrin B reverse signaling

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
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EPHB2 0.042 0.058 0.27 16 -10000 0 16
EFNB1 0.007 0.029 -10000 0 -0.3 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.043 0.083 -10000 0 -0.22 16 16
Ephrin B2/EPHB1-2 0.038 0.08 0.21 1 -0.23 17 18
neuron projection morphogenesis 0.026 0.071 -10000 0 -0.22 16 16
Ephrin B1/EPHB1-2/Tiam1 0.037 0.086 -10000 0 -0.23 17 17
DNM1 0.021 0.04 -10000 0 -0.42 2 2
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.013 0.095 0.24 2 -0.45 11 13
YES1 -0.017 0.14 -10000 0 -0.67 12 12
Ephrin B1/EPHB1-2/NCK2 0.04 0.087 -10000 0 -0.23 18 18
PI3K 0.02 0.1 -10000 0 -0.44 12 12
mol:GDP 0.036 0.085 -10000 0 -0.23 17 17
ITGA2B 0.044 0.067 0.27 21 -10000 0 21
endothelial cell proliferation 0.034 0.009 -10000 0 -10000 0 0
FYN -0.02 0.15 -10000 0 -0.7 12 12
MAP3K7 -0.017 0.099 -10000 0 -0.48 11 11
FGR -0.016 0.15 -10000 0 -0.67 13 13
TIAM1 0.024 0.028 -10000 0 -0.42 1 1
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
RGS3 0.024 0.008 -10000 0 -10000 0 0
cell adhesion -0.004 0.11 -10000 0 -0.41 10 10
LYN -0.017 0.15 -10000 0 -0.68 12 12
Ephrin B1/EPHB1-2/Src Family Kinases -0.022 0.14 -10000 0 -0.61 13 13
Ephrin B1/EPHB1-2 -0.016 0.11 -10000 0 -0.52 11 11
SRC -0.015 0.15 -10000 0 -0.66 13 13
ITGB3 -0.022 0.14 -10000 0 -0.42 28 28
EPHB1 -0.003 0.11 0.27 1 -0.42 18 19
EPHB4 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.009 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.013 0.11 0.2 17 -0.29 28 45
BLK -0.031 0.16 -10000 0 -0.67 13 13
HCK -0.022 0.15 -10000 0 -0.67 13 13
regulation of stress fiber formation -0.038 0.085 0.23 18 -10000 0 18
MAPK8 -0.014 0.11 0.26 4 -0.45 12 16
Ephrin B1/EPHB1-2/RGS3 0.041 0.085 -10000 0 -0.23 17 17
endothelial cell migration -0.008 0.091 0.23 6 -0.39 11 17
NCK2 0.026 0.003 -10000 0 -10000 0 0
PTPN13 0.014 0.076 -10000 0 -0.53 5 5
regulation of focal adhesion formation -0.038 0.085 0.23 18 -10000 0 18
chemotaxis -0.039 0.084 0.23 17 -10000 0 17
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.077 -10000 0 -0.22 16 16
angiogenesis -0.018 0.11 -10000 0 -0.51 12 12
LCK -0.017 0.15 -10000 0 -0.66 13 13
IL2 signaling events mediated by PI3K

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.032 0.093 0.4 1 -0.56 2 3
UGCG -0.062 0.23 -10000 0 -0.62 35 35
AKT1/mTOR/p70S6K/Hsp90/TERT 0.069 0.12 0.29 7 -0.29 9 16
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.058 0.23 -10000 0 -0.62 35 35
mol:DAG -0.001 0.13 -10000 0 -0.76 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.16 0.33 1 -0.42 21 22
FRAP1 0.022 0.17 0.36 1 -0.48 22 23
FOXO3 0.024 0.15 0.31 2 -0.43 19 21
AKT1 0.025 0.16 0.35 1 -0.44 21 22
GAB2 0.024 0.01 -10000 0 -10000 0 0
SMPD1 -0.013 0.15 -10000 0 -0.59 16 16
SGMS1 0.008 0.099 -10000 0 -0.55 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.009 -10000 0 -10000 0 0
CALM1 0.026 0.004 -10000 0 -10000 0 0
cell proliferation -0.014 0.2 0.28 3 -0.51 24 27
EIF3A 0.026 0.005 -10000 0 -10000 0 0
PI3K 0.036 0.018 -10000 0 -10000 0 0
RPS6KB1 0.035 0.035 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.13 -10000 0 -0.76 7 7
natural killer cell activation 0 0.003 -10000 0 -0.013 6 6
JAK3 0.029 0.023 0.27 2 -10000 0 2
PIK3R1 0.025 0.011 -10000 0 -10000 0 0
JAK1 0.027 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MYC 0.023 0.25 0.45 2 -0.89 15 17
MYB 0.072 0.12 0.46 3 -1.1 1 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.027 0.13 0.26 1 -0.42 12 13
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.053 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.13 0.26 1 -0.41 12 13
Rac1/GDP 0.018 0.016 -10000 0 -10000 0 0
T cell proliferation 0.028 0.12 0.31 3 -0.43 9 12
SHC1 0.025 0.019 0.29 1 -10000 0 1
RAC1 0.026 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.01 0.021 0.064 32 -0.081 1 33
PRKCZ 0.025 0.12 0.3 2 -0.43 10 12
NF kappa B1 p50/RelA 0.042 0.16 0.35 1 -0.42 20 21
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.017 0.084 -10000 0 -0.43 6 6
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL2RA 0.012 0.12 0.27 14 -0.42 14 28
IL2RB 0.018 0.061 -10000 0 -0.42 5 5
TERT 0.12 0.12 0.27 104 -10000 0 104
E2F1 0.075 0.085 0.3 18 -0.28 1 19
SOS1 0.025 0.009 -10000 0 -10000 0 0
RPS6 0.023 0.01 -10000 0 -10000 0 0
mol:cAMP -0.005 0.01 0.033 1 -0.031 32 33
PTPN11 0.024 0.011 -10000 0 -10000 0 0
IL2RG 0.02 0.08 0.27 5 -0.42 7 12
actin cytoskeleton organization 0.028 0.12 0.31 3 -0.43 9 12
GRB2 0.025 0.009 -10000 0 -10000 0 0
IL2 0.018 0.014 -10000 0 -10000 0 0
PIK3CA 0.025 0.011 -10000 0 -10000 0 0
Rac1/GTP 0.042 0.029 -10000 0 -10000 0 0
LCK 0.021 0.057 0.27 1 -0.42 4 5
BCL2 0.005 0.22 0.32 3 -0.69 19 22
EPHB forward signaling

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
Ephrin A5/EPHB2 0.036 0.059 0.18 15 -0.25 7 22
cell-cell adhesion 0.025 0.048 0.19 18 -10000 0 18
Ephrin B/EPHB2/RasGAP 0.069 0.061 -10000 0 -0.22 4 4
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
SHC1 0.025 0.018 0.29 1 -10000 0 1
Ephrin B1/EPHB3 0.039 0.036 0.18 11 -0.25 1 12
Ephrin B1/EPHB1 0.015 0.072 0.18 1 -0.25 18 19
HRAS/GDP 0.002 0.082 -10000 0 -0.25 10 10
Ephrin B/EPHB1/GRB7 0.044 0.091 -10000 0 -0.22 22 22
Endophilin/SYNJ1 0 0.054 0.19 14 -0.2 4 18
KRAS 0.027 0.017 0.29 1 -10000 0 1
Ephrin B/EPHB1/Src 0.039 0.085 -10000 0 -0.22 21 21
endothelial cell migration 0.048 0.022 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.032 0.064 0.29 10 -0.42 2 12
PAK1 0 0.064 0.27 2 -0.21 6 8
HRAS 0.025 0.007 -10000 0 -10000 0 0
RRAS -0.003 0.053 0.19 12 -0.2 5 17
DNM1 0.021 0.039 -10000 0 -0.42 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.013 0.074 0.18 18 -0.21 17 35
lamellipodium assembly -0.025 0.048 -10000 0 -0.19 18 18
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.004 0.075 -10000 0 -0.23 16 16
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
EPHB2 0.041 0.058 0.27 16 -10000 0 16
EPHB3 0.034 0.057 0.27 11 -0.42 1 12
EPHB1 -0.004 0.11 0.27 1 -0.42 18 19
EPHB4 0.026 0.004 -10000 0 -10000 0 0
mol:GDP -0.007 0.063 -10000 0 -0.27 7 7
Ephrin B/EPHB2 0.057 0.056 -10000 0 -0.22 4 4
Ephrin B/EPHB3 0.051 0.054 -10000 0 -0.21 5 5
JNK cascade -0.012 0.088 0.34 8 -0.23 17 25
Ephrin B/EPHB1 0.031 0.079 -10000 0 -0.21 21 21
RAP1/GDP 0.01 0.087 0.38 2 -0.25 8 10
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EFNB3 0.021 0.063 0.27 4 -0.42 4 8
EFNB1 0.026 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.038 0.08 0.19 17 -0.23 17 34
RAP1B 0.025 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.002 -10000 0 -10000 0 0
CDC42/GTP 0.029 0.08 -10000 0 -0.23 8 8
Rap1/GTP 0.009 0.057 -10000 0 -0.2 15 15
axon guidance 0.035 0.059 0.18 15 -0.25 7 22
MAPK3 -0.001 0.075 0.24 5 -0.29 4 9
MAPK1 -0.003 0.071 0.19 3 -0.29 4 7
Rac1/GDP -0.001 0.085 0.27 3 -0.25 10 13
actin cytoskeleton reorganization -0.028 0.049 -10000 0 -0.21 7 7
CDC42/GDP -0.001 0.088 0.3 4 -0.25 10 14
PI3K 0.053 0.024 -10000 0 -10000 0 0
EFNA5 0.014 0.072 -10000 0 -0.42 7 7
Ephrin B2/EPHB4 0.034 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.023 0.041 -10000 0 -0.21 4 4
CDC42 0.027 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.058 -10000 0 -0.19 15 15
PTK2 0.053 0.17 0.56 27 -10000 0 27
MAP4K4 -0.012 0.089 0.34 8 -0.23 17 25
SRC 0.025 0.007 -10000 0 -10000 0 0
KALRN 0.024 0.044 0.27 2 -0.42 2 4
Intersectin/N-WASP 0.038 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis -0.002 0.089 0.3 9 -0.28 2 11
MAP2K1 -0.002 0.071 -10000 0 -0.3 4 4
WASL 0.026 0.003 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.052 0.086 -10000 0 -0.23 18 18
cell migration 0.011 0.1 0.26 7 -0.36 4 11
NRAS 0.027 0.002 -10000 0 -10000 0 0
SYNJ1 0 0.054 0.19 14 -0.21 4 18
PXN 0.026 0.004 -10000 0 -10000 0 0
TF 0.002 0.065 0.18 16 -0.2 7 23
HRAS/GTP 0.028 0.072 -10000 0 -0.2 17 17
Ephrin B1/EPHB1-2 0.039 0.081 -10000 0 -0.23 18 18
cell adhesion mediated by integrin 0 0.048 0.21 4 -0.19 9 13
RAC1 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0.032 0.077 -10000 0 -0.2 21 21
RAC1-CDC42/GTP -0.025 0.049 -10000 0 -0.2 12 12
RASA1 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.009 0.086 0.38 1 -0.24 10 11
ruffle organization -0.009 0.078 0.33 2 -10000 0 2
NCK1 0.026 0.006 -10000 0 -10000 0 0
receptor internalization -0.005 0.053 0.18 13 -0.2 6 19
Ephrin B/EPHB2/KALRN 0.066 0.068 -10000 0 -0.22 6 6
ROCK1 0.023 0.042 0.18 14 -0.23 1 15
RAS family/GDP -0.029 0.047 -10000 0 -0.21 7 7
Rac1/GTP 0.003 0.058 -10000 0 -0.2 18 18
Ephrin B/EPHB1/Src/Paxillin 0.002 0.072 -10000 0 -0.23 20 20
IL27-mediated signaling events

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
TGFB1 0.028 0.006 -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 -0.001 0.12 0.36 3 -0.55 1 4
IL27/IL27R/JAK1 0.056 0.16 0.58 5 -10000 0 5
TBX21 0.007 0.16 0.44 8 -0.42 10 18
IL12B 0.027 0.042 0.28 6 -10000 0 6
IL12A 0.009 0.02 0.15 4 -10000 0 4
IL6ST -0.037 0.16 -10000 0 -0.42 39 39
IL27RA/JAK1 0.027 0.044 -10000 0 -10000 0 0
IL27 0.036 0.062 0.28 14 -10000 0 14
TYK2 0.032 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.091 0.14 -10000 0 -0.4 1 1
T-helper 2 cell differentiation -0.001 0.12 0.36 3 -0.55 1 4
T cell proliferation during immune response -0.001 0.12 0.36 3 -0.55 1 4
MAPKKK cascade 0.001 0.12 0.55 1 -0.36 3 4
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT2 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.03 0.028 0.27 3 -10000 0 3
IL12RB1 0.031 0.082 0.27 13 -0.42 5 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.023 0.17 0.44 11 -0.45 8 19
IL27/IL27R/JAK2/TYK2 0.001 0.12 0.55 1 -0.37 3 4
positive regulation of T cell mediated cytotoxicity 0.001 0.12 0.55 1 -0.36 3 4
STAT1 (dimer) 0.063 0.22 0.65 16 -0.47 6 22
JAK2 0.027 0.013 -10000 0 -10000 0 0
JAK1 0.028 0.008 -10000 0 -10000 0 0
STAT2 (dimer) 0.007 0.13 0.48 1 -0.35 3 4
T cell proliferation -0.078 0.17 0.49 1 -0.38 38 39
IL12/IL12R/TYK2/JAK2 0.023 0.2 -10000 0 -0.8 12 12
IL17A -0.091 0.14 -10000 0 -0.4 1 1
mast cell activation -0.001 0.12 0.36 3 -0.55 1 4
IFNG 0.014 0.042 0.11 15 -0.12 1 16
T cell differentiation -0.001 0.005 0.013 6 -0.015 6 12
STAT3 (dimer) 0.007 0.13 0.48 1 -0.35 3 4
STAT5A (dimer) 0.006 0.13 0.48 1 -0.35 3 4
STAT4 (dimer) -0.001 0.14 0.48 1 -0.36 9 10
STAT4 0.004 0.096 -10000 0 -0.42 13 13
T cell activation -0.007 0.007 -10000 0 -0.066 2 2
IL27R/JAK2/TYK2 0.022 0.11 0.43 1 -10000 0 1
GATA3 -0.029 0.39 0.59 27 -1.3 18 45
IL18 0.001 0.041 -10000 0 -0.29 5 5
positive regulation of mast cell cytokine production 0.007 0.13 0.47 1 -0.35 3 4
IL27/EBI3 0.053 0.063 0.25 18 -0.3 1 19
IL27RA 0.012 0.036 -10000 0 -10000 0 0
IL6 -0.16 0.22 -10000 0 -0.42 112 112
STAT5A 0.024 0.028 -10000 0 -0.42 1 1
monocyte differentiation 0.001 0.001 -10000 0 -10000 0 0
IL2 -0.015 0.034 -10000 0 -10000 0 0
IL1B -0.001 0.07 0.12 13 -0.29 12 25
EBI3 0.034 0.048 0.28 6 -0.42 1 7
TNF 0.012 0.022 0.11 13 -10000 0 13
Insulin Pathway

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.064 0.13 -10000 0 -0.21 110 110
TC10/GTP -0.062 0.12 -10000 0 -0.2 113 113
Insulin Receptor/Insulin/IRS1/Shp2 0.053 0.041 -10000 0 -0.22 3 3
HRAS 0.025 0.007 -10000 0 -10000 0 0
APS homodimer 0.029 0.026 0.27 3 -10000 0 3
GRB14 0.054 0.079 0.27 31 -10000 0 31
FOXO3 -0.031 0.18 -10000 0 -0.55 26 26
AKT1 0.005 0.059 0.33 3 -10000 0 3
INSR 0.029 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.051 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.028 -10000 0 -0.42 1 1
SORBS1 -0.17 0.22 -10000 0 -0.42 117 117
CRK 0.024 0.008 -10000 0 -10000 0 0
PTPN1 0 0.027 -10000 0 -10000 0 0
CAV1 -0.017 0.05 -10000 0 -0.22 13 13
CBL/APS/CAP/Crk-II/C3G -0.056 0.14 -10000 0 -0.21 115 115
Insulin Receptor/Insulin/IRS1/NCK2 0.054 0.041 -10000 0 -0.22 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.032 -10000 0 -0.19 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.027 0.062 -10000 0 -0.33 5 5
RPS6KB1 -0.001 0.056 0.32 3 -10000 0 3
PARD6A 0.024 0.028 -10000 0 -0.42 1 1
CBL 0.025 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.047 -10000 0 -0.48 2 2
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.035 0.035 -10000 0 -10000 0 0
HRAS/GTP -0.016 0.027 -10000 0 -0.19 2 2
Insulin Receptor 0.029 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.06 0.043 -10000 0 -0.2 2 2
PRKCI 0.026 0.053 -10000 0 -0.47 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.029 0.031 -10000 0 -0.18 2 2
SHC1 0.025 0.018 0.29 1 -10000 0 1
negative regulation of MAPKKK cascade 0.041 0.046 -10000 0 -0.41 2 2
PI3K 0.051 0.037 -10000 0 -0.19 2 2
NCK2 0.026 0.003 -10000 0 -10000 0 0
RHOQ 0.026 0.005 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.005 -10000 0 -10000 0 0
AKT2 0.005 0.058 0.33 3 -10000 0 3
PRKCZ 0.024 0.061 -10000 0 -0.42 2 2
SH2B2 0.029 0.026 0.27 3 -10000 0 3
SHC/SHIP 0.023 0.038 -10000 0 -0.2 5 5
F2RL2 0.014 0.095 0.27 7 -0.42 10 17
TRIP10 0.024 0.028 -10000 0 -0.42 1 1
Insulin Receptor/Insulin/Shc 0.042 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.033 0.018 -10000 0 -0.23 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.063 0.036 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.067 0.14 -10000 0 -0.23 115 115
TC10/GDP 0.019 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.055 0.032 -10000 0 -10000 0 0
INPP5D -0.011 0.04 0.17 1 -0.21 7 8
SOS1 0.026 0.004 -10000 0 -10000 0 0
SGK1 -0.038 0.19 -10000 0 -0.72 19 19
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.005 -10000 0 -10000 0 0
IRS1 0.02 0.047 -10000 0 -0.42 3 3
p62DOK/RasGAP 0.041 0.046 -10000 0 -0.41 2 2
INS 0.019 0.01 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.011 0.04 0.17 1 -0.21 7 8
GRB2 0.026 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.005 0.063 0.33 4 -10000 0 4
PTPRA 0.027 0.009 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.033 0.018 -10000 0 -0.23 1 1
PDPK1 0.025 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.02 0.03 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.04 0.036 -10000 0 -0.22 3 3
Insulin Receptor/Insulin/IRS3 0.036 0.017 -10000 0 -10000 0 0
Par3/Par6 0.046 0.062 -10000 0 -0.21 11 11
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.036 0.064 -10000 0 -0.33 3 3
epithelial cell differentiation 0.007 0.086 0.27 1 -0.37 3 4
ITCH 0.026 0.023 0.27 1 -10000 0 1
WWP1 0.03 0.057 -10000 0 -10000 0 0
FYN 0.02 0.047 -10000 0 -0.42 3 3
EGFR 0.023 0.073 0.29 6 -0.42 5 11
PRL 0.001 0.039 0.28 4 -10000 0 4
neuron projection morphogenesis 0.019 0.099 0.27 12 -0.33 1 13
PTPRZ1 -0.045 0.2 0.27 29 -0.42 53 82
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.022 0.089 -10000 0 -0.35 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.002 0.087 0.29 1 -0.31 3 4
ADAM17 0.024 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 0.029 0.037 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.042 0.057 0.31 1 -0.25 1 2
NCOR1 0.023 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.003 0.091 0.27 1 -0.33 3 4
GRIN2B -0.005 0.088 0.27 3 -0.35 2 5
ErbB4/ErbB2/betacellulin 0.016 0.089 0.28 3 -0.28 2 5
STAT1 0.029 0.026 0.27 3 -10000 0 3
HBEGF 0.014 0.072 -10000 0 -0.42 7 7
PRLR 0.023 0.11 0.28 18 -0.42 10 28
E4ICDs/ETO2 0.035 0.062 -10000 0 -10000 0 0
axon guidance 0.02 0.093 0.29 6 -10000 0 6
NEDD4 0.022 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.02 0.071 0.2 10 -0.3 9 19
CBFA2T3 0.012 0.076 -10000 0 -0.42 8 8
ErbB4/ErbB2/HBEGF 0.04 0.06 0.28 3 -0.32 2 5
MAPK3 0.017 0.092 0.28 4 -0.34 1 5
STAT1 (dimer) 0.045 0.05 -10000 0 -10000 0 0
MAPK1 0.02 0.093 0.29 3 -0.34 1 4
JAK2 0.023 0.009 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.001 0.088 0.27 3 -0.3 3 6
NRG1 -0.024 0.11 0.25 3 -0.3 33 36
NRG3 0.011 0.048 0.27 7 -10000 0 7
NRG2 -0.16 0.22 -10000 0 -0.42 107 107
NRG4 -0.014 0.12 -10000 0 -0.42 23 23
heart development 0.02 0.093 0.29 6 -10000 0 6
neural crest cell migration 0.001 0.087 0.27 3 -0.29 3 6
ERBB2 0.02 0.053 0.3 9 -10000 0 9
WWOX/E4ICDs 0.037 0.048 -10000 0 -0.25 1 1
SHC1 0.025 0.018 0.29 1 -10000 0 1
ErbB4/EGFR/neuregulin 4 0.03 0.096 0.28 2 -0.32 5 7
apoptosis -0.028 0.069 0.27 3 -0.3 1 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.053 0.13 -10000 0 -0.31 11 11
ErbB4/ErbB2/epiregulin 0.04 0.11 0.28 10 -0.25 1 11
ErbB4/ErbB4/betacellulin/betacellulin 0.015 0.094 -10000 0 -0.29 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.043 0.088 0.3 1 -0.3 4 5
MDM2 0.039 0.076 0.28 20 -10000 0 20
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0 0.082 -10000 0 -0.26 3 3
STAT5A 0.023 0.097 0.32 6 -10000 0 6
ErbB4/EGFR/neuregulin 1 beta 0.006 0.096 0.26 3 -0.31 4 7
DLG4 0.024 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.031 0.042 -10000 0 -10000 0 0
STAT5A (dimer) 0.024 0.11 0.32 1 -0.4 3 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.037 0.1 0.33 2 -10000 0 2
LRIG1 -0.003 0.11 -10000 0 -0.42 17 17
EREG -0.001 0.18 0.27 37 -0.42 35 72
BTC -0.028 0.14 -10000 0 -0.42 31 31
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.012 0.087 0.29 5 -10000 0 5
ERBB4 0.019 0.024 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
YAP1 0.009 0.086 0.32 1 -0.44 8 9
GRB2 0.026 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.026 0.072 0.27 1 -0.25 1 2
glial cell differentiation -0.031 0.042 -10000 0 -10000 0 0
WWOX 0.022 0.028 -10000 0 -0.42 1 1
cell proliferation -0.027 0.14 0.31 8 -0.48 7 15
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.019 0.054 -10000 0 -0.42 4 4
Jak2/Leptin Receptor 0.019 0.15 0.28 7 -0.36 22 29
PTP1B/AKT1 0.026 0.078 0.18 1 -0.28 6 7
FYN 0.02 0.047 -10000 0 -0.42 3 3
p210 bcr-abl/PTP1B 0.016 0.081 0.18 2 -0.3 6 8
EGFR 0.023 0.073 0.28 6 -0.42 5 11
EGF/EGFR 0.035 0.09 0.22 6 -0.29 6 12
CSF1 0.006 0.093 -10000 0 -0.42 12 12
AKT1 0.026 0.005 -10000 0 -10000 0 0
INSR 0.026 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.037 0.097 0.24 13 -0.31 5 18
Insulin Receptor/Insulin 0.037 0.076 -10000 0 -0.33 3 3
HCK 0.014 0.077 0.27 3 -0.42 7 10
CRK 0.024 0.008 -10000 0 -10000 0 0
TYK2 0.014 0.08 0.24 3 -0.33 4 7
EGF 0.038 0.056 0.27 14 -10000 0 14
YES1 0.024 0.008 -10000 0 -10000 0 0
CAV1 0.02 0.09 0.19 4 -0.3 8 12
TXN 0.026 0.017 0.27 1 -10000 0 1
PTP1B/IRS1/GRB2 0.033 0.084 -10000 0 -0.32 4 4
cell migration -0.016 0.081 0.3 6 -0.18 2 8
STAT3 0.026 0.004 -10000 0 -10000 0 0
PRLR 0.024 0.11 0.28 18 -0.42 10 28
ITGA2B 0.044 0.067 0.27 21 -10000 0 21
CSF1R 0.004 0.1 0.27 2 -0.42 14 16
Prolactin Receptor/Prolactin 0.023 0.073 0.22 7 -0.3 9 16
FGR 0.025 0.027 -10000 0 -0.42 1 1
PTP1B/p130 Cas 0.025 0.08 -10000 0 -0.31 5 5
Crk/p130 Cas 0.033 0.081 -10000 0 -0.32 4 4
DOK1 0.014 0.092 -10000 0 -0.3 11 11
JAK2 0.009 0.15 0.26 4 -0.37 24 28
Jak2/Leptin Receptor/Leptin -0.013 0.16 0.29 2 -0.36 26 28
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
PTPN1 0.016 0.082 0.18 2 -0.3 6 8
LYN 0.024 0.008 -10000 0 -10000 0 0
CDH2 0.044 0.082 0.27 24 -0.42 2 26
SRC 0.027 0.08 -10000 0 -0.55 4 4
ITGB3 -0.021 0.14 -10000 0 -0.42 28 28
CAT1/PTP1B 0.007 0.13 0.28 6 -0.38 8 14
CAPN1 0.027 0.004 -10000 0 -10000 0 0
CSK 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.075 -10000 0 -0.31 3 3
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.017 0.15 0.27 1 -0.36 29 30
negative regulation of transcription 0.01 0.15 0.26 4 -0.36 24 28
FCGR2A 0.029 0.054 0.27 9 -0.42 1 10
FER 0.025 0.028 -10000 0 -0.42 1 1
alphaIIb/beta3 Integrin 0.013 0.11 0.2 17 -0.3 28 45
BLK -0.003 0.12 0.27 9 -0.42 17 26
Insulin Receptor/Insulin/Shc 0.04 0.018 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
LEPR 0.014 0.075 -10000 0 -0.41 8 8
BCAR1 0.025 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.019 0.14 0.28 3 -0.34 22 25
PRL 0.008 0.039 0.28 4 -10000 0 4
SOCS3 -0.1 0.38 -10000 0 -1.2 27 27
SPRY2 0.016 0.067 -10000 0 -0.42 6 6
Insulin Receptor/Insulin/IRS1 0.038 0.037 -10000 0 -0.26 3 3
CSF1/CSF1R 0.018 0.12 0.22 1 -0.33 14 15
Ras protein signal transduction 0.003 0.09 0.48 8 -10000 0 8
IRS1 0.02 0.047 -10000 0 -0.42 3 3
INS 0.01 0.014 -10000 0 -10000 0 0
LEP -0.013 0.14 0.27 9 -0.42 23 32
STAT5B 0.023 0.1 0.21 7 -0.31 9 16
STAT5A 0.022 0.1 0.21 7 -0.32 9 16
GRB2 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.024 0.088 -10000 0 -0.29 9 9
CSN2 0.03 0.074 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
LAT 0.035 0.066 -10000 0 -0.42 3 3
YBX1 0.034 0.017 0.28 1 -10000 0 1
LCK 0.021 0.056 0.27 1 -0.42 4 5
SHC1 0.025 0.018 0.29 1 -10000 0 1
NOX4 0.04 0.057 0.27 15 -10000 0 15
Ceramide signaling pathway

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
SPHK2 0.012 0.007 -10000 0 -10000 0 0
MAP4K4 0.007 0.077 0.2 4 -0.31 4 8
BAG4 0.022 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide 0.009 0.048 -10000 0 -0.19 14 14
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.007 0.096 0.29 2 -0.42 12 14
BAX 0.008 0.029 -10000 0 -0.34 1 1
RIPK1 0.025 0.006 -10000 0 -10000 0 0
AKT1 -0.001 0.072 0.66 3 -10000 0 3
BAD -0.007 0.044 0.18 2 -0.19 13 15
SMPD1 0.009 0.062 0.15 5 -0.2 13 18
RB1 -0.008 0.039 -10000 0 -0.18 12 12
FADD/Caspase 8 0.019 0.094 0.27 6 -0.3 5 11
MAP2K4 -0.007 0.045 0.18 4 -0.18 12 16
NSMAF 0.024 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.022 0.084 0.2 37 -0.18 8 45
EGF 0.035 0.057 0.27 14 -10000 0 14
mol:ceramide -0.006 0.044 -10000 0 -0.2 13 13
MADD 0.025 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.005 -10000 0 -10000 0 0
ASAH1 0.021 0.011 -10000 0 -10000 0 0
negative regulation of cell cycle -0.008 0.038 -10000 0 -0.18 12 12
cell proliferation -0.044 0.12 0.33 3 -0.22 20 23
BID -0.002 0.14 -10000 0 -0.61 9 9
MAP3K1 -0.008 0.043 0.19 1 -0.19 13 14
EIF2A -0.002 0.06 0.2 13 -0.18 11 24
TRADD 0.025 0.006 -10000 0 -10000 0 0
CRADD 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.021 0.081 0.2 37 -0.18 2 39
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.08 0.2 36 -0.19 1 37
Cathepsin D/ceramide 0.011 0.045 -10000 0 -0.18 13 13
FADD 0.018 0.081 0.22 14 -0.28 3 17
KSR1 0.001 0.058 0.19 12 -0.19 12 24
MAPK8 -0.002 0.055 -10000 0 -0.21 5 5
PRKRA -0.008 0.043 0.2 1 -0.18 13 14
PDGFA 0.026 0.005 -10000 0 -10000 0 0
TRAF2 0.024 0.008 -10000 0 -10000 0 0
IGF1 -0.17 0.22 -10000 0 -0.42 116 116
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.006 0.044 -10000 0 -0.19 13 13
CTSD 0.025 0.007 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.038 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.046 0.13 0.35 3 -0.24 18 21
PRKCD 0.025 0.006 -10000 0 -10000 0 0
PRKCZ 0.025 0.027 -10000 0 -0.42 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.005 -10000 0 -10000 0 0
RelA/NF kappa B1 0.038 0.007 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.028 -10000 0 -0.42 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.007 0.068 0.2 1 -0.32 4 5
TNFR1A/BAG4/TNF-alpha 0.049 0.039 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.012 0.007 -10000 0 -10000 0 0
MAP2K1 0.018 0.08 0.2 36 -0.18 8 44
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
CYCS 0.012 0.045 0.15 11 -0.17 1 12
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.016 -10000 0 -10000 0 0
EIF2AK2 -0.007 0.045 0.19 4 -0.18 12 16
TNF-alpha/TNFR1A/FAN 0.053 0.038 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.093 -10000 0 -0.36 12 12
MAP2K2 0.017 0.08 0.2 35 -0.18 8 43
SMPD3 0.014 0.056 0.16 1 -0.24 6 7
TNF 0.038 0.053 0.27 13 -10000 0 13
PKC zeta/PAR4 0.036 0.03 -10000 0 -0.3 2 2
mol:PHOSPHOCHOLINE -0.005 0.035 -10000 0 -0.13 9 9
NF kappa B1/RelA/I kappa B alpha 0.071 0.034 -10000 0 -0.22 2 2
AIFM1 0.01 0.047 0.16 11 -0.17 2 13
BCL2 0.005 0.093 -10000 0 -0.42 12 12
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.033 0.011 -10000 0 -10000 0 0
PRKCZ 0.025 0.027 -10000 0 -0.42 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.015 0.048 -10000 0 -0.2 4 4
IRAK/TOLLIP 0.024 0.012 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.026 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.038 0.13 0.22 46 -0.3 25 71
IL1A 0.014 0.15 0.27 27 -0.42 22 49
IL1B -0.008 0.088 -10000 0 -0.31 19 19
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.044 -10000 0 -0.21 1 1
IL1R2 0.044 0.094 0.27 27 -0.42 4 31
IL1R1 0.026 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.066 0.24 2 -0.26 3 5
TOLLIP 0.025 0.007 -10000 0 -10000 0 0
TICAM2 0.023 0.028 -10000 0 -0.42 1 1
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.03 0.065 0.27 1 -10000 0 1
JUN -0.008 0.055 0.15 19 -0.19 8 27
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.048 0.079 0.26 1 -0.22 15 16
IL1 alpha/IL1R1/IL1RAP/MYD88 0.056 0.1 0.36 2 -0.23 20 22
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.1 0.35 2 -0.22 20 22
IL1 beta fragment/IL1R1/IL1RAP 0.028 0.079 0.26 2 -0.24 16 18
NFKB1 0.026 0.003 -10000 0 -10000 0 0
MAPK8 -0.001 0.059 0.17 22 -0.2 5 27
IRAK1 0 0.014 -10000 0 -10000 0 0
IL1RN/IL1R1 0.043 0.04 0.2 10 -0.3 1 11
IRAK4 0.026 0.004 -10000 0 -10000 0 0
PRKCI 0.025 0.006 -10000 0 -10000 0 0
TRAF6 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.013 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.017 0.061 0.28 1 -0.25 5 6
CHUK 0.026 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.028 0.079 0.26 2 -0.24 16 18
IL1 beta/IL1R2 0.023 0.1 0.2 26 -0.27 22 48
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.034 0.068 -10000 0 -0.22 13 13
IRAK3 0.015 0.066 -10000 0 -0.42 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.049 0.079 0.27 2 -0.21 16 18
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.076 0.22 1 -0.21 21 22
IL1 alpha/IL1R1/IL1RAP 0.045 0.1 0.36 2 -0.25 20 22
RELA 0.026 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.025 0.006 -10000 0 -10000 0 0
MYD88 0.025 0.006 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.05 0.04 -10000 0 -10000 0 0
IL1RAP 0.033 0.043 0.27 8 -10000 0 8
UBE2N 0.026 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.017 0.054 -10000 0 -10000 0 0
CASP1 0.012 0.076 -10000 0 -0.42 8 8
IL1RN/IL1R2 0.054 0.079 0.22 34 -0.3 5 39
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.04 0.078 0.27 2 -0.23 15 17
TMEM189-UBE2V1 0.005 0.021 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.077 -10000 0 -0.31 4 4
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
IL1RN 0.034 0.054 0.27 10 -0.42 1 11
TRAF6/TAK1/TAB1/TAB2 0.041 0.02 -10000 0 -10000 0 0
MAP2K6 0.006 0.063 0.18 26 -0.2 3 29
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.019 0.29 1 -10000 0 1
NFATC1 0.002 0.099 0.34 1 -0.33 12 13
NFATC2 -0.037 0.079 -10000 0 -0.19 36 36
NFATC3 0.01 0.024 -10000 0 -0.34 1 1
YWHAE 0.024 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.038 0.14 0.27 5 -0.34 27 32
Exportin 1/Ran/NUP214 0.043 0.018 -10000 0 -10000 0 0
mol:DAG -0.003 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.029 0.13 0.24 2 -0.33 23 25
BCL2/BAX 0.022 0.07 -10000 0 -0.3 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.021 -10000 0 -10000 0 0
CaM/Ca2+ -0.003 0.021 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0.023 0.004 -10000 0 -10000 0 0
BAD 0.026 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.027 0.13 0.25 4 -0.32 25 29
Calcineurin A alpha-beta B1/BCL2 0.005 0.092 -10000 0 -0.42 12 12
FKBP8 0.026 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.026 0.13 0.32 25 -0.24 4 29
KPNB1 0.026 0.005 -10000 0 -10000 0 0
KPNA2 0.028 0.022 0.28 2 -10000 0 2
XPO1 0.025 0.005 -10000 0 -10000 0 0
SFN 0.046 0.082 0.27 25 -0.42 2 27
MAP3K8 0.018 0.039 -10000 0 -0.42 2 2
NFAT4/CK1 alpha -0.003 0.033 -10000 0 -0.2 1 1
MEF2D/NFAT1/Cbp/p300 -0.12 0.16 -10000 0 -0.27 117 117
CABIN1 -0.037 0.14 0.27 5 -0.34 27 32
CALM1 0.02 0.011 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
CAMK4 0.016 0.068 0.27 1 -0.42 6 7
mol:Ca2+ -0.007 0.007 -10000 0 -10000 0 0
MAPK3 0.025 0.006 -10000 0 -10000 0 0
YWHAH 0.025 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.038 0.019 0.2 3 -10000 0 3
YWHAB 0.024 0.008 -10000 0 -10000 0 0
MAPK8 0.016 0.047 -10000 0 -0.42 3 3
MAPK9 0.025 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
FKBP1A 0.025 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.009 0.11 0.33 1 -0.34 11 12
PRKCH 0.026 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.036 -10000 0 -10000 0 0
CASP3 0.023 0.006 -10000 0 -10000 0 0
PIM1 0.026 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.013 -10000 0 -10000 0 0
apoptosis 0.014 0.025 0.18 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.05 0.21 1 -0.26 1 2
PRKCB -0.095 0.2 -10000 0 -0.42 71 71
PRKCE 0.026 0.005 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.035 -10000 0 -0.32 1 1
BAD/BCL-XL 0.034 0.014 -10000 0 -10000 0 0
PRKCD 0.025 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.02 0.028 -10000 0 -0.42 1 1
PRKCA 0.026 0.005 -10000 0 -10000 0 0
PRKCG 0.012 0.049 0.28 7 -10000 0 7
PRKCQ -0.013 0.13 0.28 2 -0.42 23 25
FKBP38/BCL2 0.022 0.07 -10000 0 -0.3 12 12
EP300 -0.001 0.025 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.007 0.1 0.33 1 -0.32 13 14
CaM/Ca2+/FKBP38 0.005 0.028 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.005 -10000 0 -10000 0 0
CSNK1A1 -0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.001 0.049 0.16 1 -0.26 6 7
NFATc/ERK1 0.015 0.096 0.34 1 -0.32 10 11
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.026 0.13 0.22 2 -0.32 28 30
NR4A1 -0.22 0.23 0.22 1 -0.43 141 142
GSK3B 0.021 0.008 -10000 0 -10000 0 0
positive T cell selection 0.01 0.024 -10000 0 -0.34 1 1
NFAT1/CK1 alpha -0.031 0.066 -10000 0 -0.17 30 30
RCH1/ KPNB1 0.039 0.013 0.2 1 -10000 0 1
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.004 -10000 0 -10000 0 0
AKAP5 0.029 0.026 0.27 3 -10000 0 3
MEF2D -0.001 0.025 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.012 0.1 0.33 1 -0.32 12 13
CREBBP -0.001 0.025 -10000 0 -10000 0 0
BCL2 0.005 0.093 -10000 0 -0.42 12 12
IL2 signaling events mediated by STAT5

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
GAB2 0.025 0.007 -10000 0 -10000 0 0
ELF1 0.017 0.089 -10000 0 -0.34 14 14
CCNA2 0.092 0.11 0.27 71 -10000 0 71
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
JAK3 0.029 0.021 0.27 2 -10000 0 2
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.003 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.035 0.11 -10000 0 -0.49 5 5
SHC1 0.026 0.018 0.29 1 -10000 0 1
SP1 0.005 0.095 -10000 0 -0.32 20 20
IL2RA -0.011 0.16 -10000 0 -0.66 14 14
IL2RB 0.018 0.061 -10000 0 -0.42 5 5
SOS1 0.027 0.004 -10000 0 -10000 0 0
IL2RG 0.02 0.08 0.27 5 -0.42 7 12
G1/S transition of mitotic cell cycle -0.018 0.23 0.35 3 -0.69 23 26
PTPN11 0.026 0.005 -10000 0 -10000 0 0
CCND2 -0.037 0.19 -10000 0 -0.68 20 20
LCK 0.021 0.057 0.27 1 -0.42 4 5
GRB2 0.026 0.005 -10000 0 -10000 0 0
IL2 0.016 0.013 -10000 0 -10000 0 0
CDK6 0.011 0.081 -10000 0 -0.42 9 9
CCND3 0.041 0.1 -10000 0 -0.59 2 2
Caspase cascade in apoptosis

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
TOP1 -0.001 0.11 -10000 0 -0.45 10 10
ACTA1 -0.02 0.13 -10000 0 -0.43 16 16
NUMA1 -0.006 0.12 -10000 0 -0.46 12 12
SPTAN1 -0.021 0.13 -10000 0 -0.44 15 15
LIMK1 -0.02 0.13 0.19 1 -0.46 14 15
BIRC3 0.007 0.096 0.29 2 -0.42 12 14
BIRC2 0.027 0.024 0.29 2 -10000 0 2
BAX 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.021 0.082 -10000 0 -0.33 15 15
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.016 0.29 1 -10000 0 1
PTK2 -0.004 0.12 -10000 0 -0.49 11 11
DIABLO 0.026 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.02 0.13 -10000 0 -0.43 15 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.004 -10000 0 -10000 0 0
GSN -0.023 0.13 -10000 0 -0.44 16 16
MADD 0.025 0.006 -10000 0 -10000 0 0
TFAP2A 0.039 0.098 0.31 2 -0.68 3 5
BID -0.003 0.055 0.18 1 -0.21 15 16
MAP3K1 -0.013 0.096 -10000 0 -0.35 16 16
TRADD 0.025 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.006 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.02 0.13 -10000 0 -0.44 15 15
CASP9 0.027 0.003 -10000 0 -10000 0 0
DNA repair -0.004 0.053 0.2 3 -0.16 6 9
neuron apoptosis -0.001 0.13 -10000 0 -0.68 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.016 0.13 -10000 0 -0.44 17 17
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 0.001 0.13 -10000 0 -0.93 4 4
TRAF2 0.024 0.008 -10000 0 -10000 0 0
ICAD/CAD -0.024 0.12 -10000 0 -0.47 13 13
CASP7 -0.001 0.093 0.26 12 -0.29 6 18
KRT18 0.018 0.059 -10000 0 -0.51 2 2
apoptosis -0.009 0.13 0.29 1 -0.51 11 12
DFFA -0.022 0.13 -10000 0 -0.46 14 14
DFFB -0.022 0.13 -10000 0 -0.46 14 14
PARP1 0.004 0.053 0.16 6 -0.2 3 9
actin filament polymerization 0.021 0.12 0.42 14 -10000 0 14
TNF 0.038 0.053 0.27 13 -10000 0 13
CYCS 0.001 0.047 -10000 0 -0.2 7 7
SATB1 0.002 0.14 -10000 0 -0.86 4 4
SLK -0.021 0.13 -10000 0 -0.44 15 15
p15 BID/BAX 0.006 0.067 -10000 0 -0.19 23 23
CASP2 0.003 0.069 0.21 2 -0.3 4 6
JNK cascade 0.013 0.096 0.35 16 -10000 0 16
CASP3 -0.021 0.14 -10000 0 -0.44 17 17
LMNB2 0.007 0.11 -10000 0 -0.42 11 11
RIPK1 0.025 0.006 -10000 0 -10000 0 0
CASP4 0.026 0.017 0.29 1 -10000 0 1
Mammalian IAPs/DIABLO 0.049 0.066 0.22 1 -0.23 12 13
negative regulation of DNA binding 0.039 0.096 0.31 2 -0.67 3 5
stress fiber formation -0.021 0.13 -10000 0 -0.43 15 15
GZMB -0.003 0.1 0.18 8 -0.37 16 24
CASP1 0.004 0.051 -10000 0 -0.28 8 8
LMNB1 0.011 0.12 -10000 0 -0.55 8 8
APP -0.002 0.13 -10000 0 -0.7 8 8
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM -0.006 0.13 0.3 1 -0.48 12 13
LMNA 0.016 0.074 -10000 0 -0.34 5 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.072 0.19 1 -0.3 5 6
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.018 0.13 0.22 5 -0.44 15 20
APAF-1/Caspase 9 0.019 0.048 -10000 0 -0.4 1 1
nuclear fragmentation during apoptosis -0.006 0.12 -10000 0 -0.45 12 12
CFL2 -0.022 0.12 -10000 0 -0.43 14 14
GAS2 -0.039 0.14 -10000 0 -0.43 17 17
positive regulation of apoptosis 0.014 0.11 -10000 0 -0.5 7 7
PRF1 0.017 0.097 0.27 9 -0.42 10 19
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.023 0.012 -10000 0 -10000 0 0
HSPA8 0.025 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.016 0.13 -10000 0 -0.29 41 41
AKT1 0.027 0.016 -10000 0 -10000 0 0
GSC 0.027 0.073 -10000 0 -10000 0 0
NKX2-5 0.058 0.092 0.27 41 -10000 0 41
muscle cell differentiation -0.012 0.095 0.44 4 -10000 0 4
SMAD2-3/SMAD4/SP1 0.061 0.093 -10000 0 -0.31 7 7
SMAD4 0.01 0.053 -10000 0 -0.2 4 4
CBFB 0.025 0.006 -10000 0 -10000 0 0
SAP18 0.026 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.048 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.054 0.067 -10000 0 -0.32 1 1
MYC -0.004 0.097 -10000 0 -0.42 13 13
CDKN2B -0.13 0.29 -10000 0 -0.88 16 16
AP1 -0.037 0.14 -10000 0 -0.43 13 13
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.014 0.074 -10000 0 -0.34 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.077 -10000 0 -0.34 7 7
SP3 0.027 0.004 -10000 0 -10000 0 0
CREB1 0.026 0.005 -10000 0 -10000 0 0
FOXH1 0.085 0.1 0.28 61 -10000 0 61
SMAD3/SMAD4/GR 0.018 0.085 -10000 0 -0.3 8 8
GATA3 -0.009 0.12 0.29 1 -0.4 18 19
SKI/SIN3/HDAC complex/NCoR1 0.011 0.064 -10000 0 -0.35 4 4
MEF2C/TIF2 0.027 0.087 0.32 2 -0.46 3 5
endothelial cell migration -0.018 0.12 1 3 -10000 0 3
MAX 0.025 0.008 -10000 0 -10000 0 0
RBBP7 0.027 0.002 -10000 0 -10000 0 0
RBBP4 0.027 0.002 -10000 0 -10000 0 0
RUNX2 0.028 0.038 0.27 3 -0.42 1 4
RUNX3 0.01 0.085 -10000 0 -0.42 10 10
RUNX1 0.025 0.006 -10000 0 -10000 0 0
CTBP1 0.027 0.017 0.29 1 -10000 0 1
NR3C1 0.014 0.067 -10000 0 -0.42 6 6
VDR 0.026 0.032 0.29 1 -0.42 1 2
CDKN1A 0 0.11 -10000 0 -0.88 2 2
KAT2B 0.025 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.076 0.075 0.3 2 -0.25 1 3
DCP1A 0.025 0.006 -10000 0 -10000 0 0
SKI 0.027 0.002 -10000 0 -10000 0 0
SERPINE1 0.017 0.12 -10000 0 -1 3 3
SMAD3/SMAD4/ATF2 0.026 0.069 -10000 0 -0.22 3 3
SMAD3/SMAD4/ATF3 -0.022 0.14 -10000 0 -0.3 47 47
SAP30 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.041 0.025 -10000 0 -10000 0 0
JUN -0.048 0.13 -10000 0 -0.42 13 13
SMAD3/SMAD4/IRF7 0.03 0.081 0.34 1 -0.27 3 4
TFE3 0.029 0.015 -10000 0 -0.19 1 1
COL1A2 -0.003 0.19 -10000 0 -0.86 12 12
mesenchymal cell differentiation -0.027 0.073 0.22 4 -10000 0 4
DLX1 0.047 0.078 0.27 28 -10000 0 28
TCF3 0.026 0.005 -10000 0 -10000 0 0
FOS -0.11 0.2 -10000 0 -0.42 77 77
SMAD3/SMAD4/Max 0.024 0.069 -10000 0 -0.22 3 3
Cbp/p300/SNIP1 0.047 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.017 -10000 0 -10000 0 0
LAMC1 0.005 0.054 -10000 0 -0.35 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.026 0.066 -10000 0 -0.22 3 3
IRF7 0.031 0.052 0.28 8 -0.42 1 9
ESR1 -0.044 0.16 -10000 0 -0.41 42 42
HNF4A 0.04 0.079 0.27 26 -10000 0 26
MEF2C 0.035 0.081 0.25 7 -0.42 3 10
SMAD2-3/SMAD4 0.034 0.075 -10000 0 -0.26 4 4
Cbp/p300/Src-1 0.046 0.021 -10000 0 -10000 0 0
IGHV3OR16-13 -0.004 0.067 -10000 0 -0.34 9 9
TGIF2/HDAC complex 0.025 0.007 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.017 0.29 1 -10000 0 1
HDAC1 0.027 0.002 -10000 0 -10000 0 0
HDAC2 0.025 0.006 -10000 0 -10000 0 0
SNIP1 0.026 0.004 -10000 0 -10000 0 0
GCN5L2 -0.001 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.038 0.071 -10000 0 -0.23 4 4
MSG1/HSC70 0.04 0.025 0.2 5 -10000 0 5
SMAD2 0.029 0.021 -10000 0 -0.12 1 1
SMAD3 0.006 0.053 -10000 0 -0.19 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.043 -10000 0 -0.22 1 1
SMAD2/SMAD2/SMAD4 0.007 0.059 0.22 3 -0.2 3 6
NCOR1 0.023 0.009 -10000 0 -10000 0 0
NCOA2 0.003 0.092 -10000 0 -0.42 12 12
NCOA1 0.026 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.009 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.072 0.096 -10000 0 -0.34 5 5
IFNB1 0.003 0.052 0.25 2 -0.27 2 4
SMAD3/SMAD4/MEF2C 0.053 0.097 -10000 0 -0.42 4 4
CITED1 0.031 0.034 0.27 5 -10000 0 5
SMAD2-3/SMAD4/ARC105 0.055 0.068 -10000 0 -0.24 3 3
RBL1 0.026 0.017 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.01 0.11 -10000 0 -0.54 7 7
RUNX1-3/PEBPB2 0.039 0.056 -10000 0 -0.25 9 9
SMAD7 -0.027 0.14 -10000 0 -0.46 12 12
MYC/MIZ-1 0.009 0.077 -10000 0 -0.3 13 13
SMAD3/SMAD4 -0.001 0.069 -10000 0 -0.36 4 4
IL10 -0.01 0.14 0.23 2 -0.38 26 28
PIASy/HDAC complex 0.026 0.008 -10000 0 -10000 0 0
PIAS3 0.023 0.009 -10000 0 -10000 0 0
CDK2 0.025 0.008 -10000 0 -10000 0 0
IL5 -0.004 0.11 -10000 0 -0.28 15 15
CDK4 0.025 0.008 -10000 0 -10000 0 0
PIAS4 0.026 0.008 -10000 0 -10000 0 0
ATF3 -0.052 0.17 -10000 0 -0.42 46 46
SMAD3/SMAD4/SP1 0.04 0.087 -10000 0 -0.29 10 10
FOXG1 0.03 0.095 0.27 35 -10000 0 35
FOXO3 0.013 0.018 -10000 0 -10000 0 0
FOXO1 0.013 0.017 -10000 0 -10000 0 0
FOXO4 0.015 0.018 -10000 0 -10000 0 0
heart looping 0.035 0.081 0.25 7 -0.42 3 10
CEBPB 0.023 0.031 -10000 0 -0.42 1 1
SMAD3/SMAD4/DLX1 0.04 0.086 0.24 1 -0.22 3 4
MYOD1 -0.016 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.038 0.083 0.27 1 -0.22 3 4
SMAD3/SMAD4/GATA3 0.002 0.12 -10000 0 -0.28 30 30
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.017 0.29 1 -10000 0 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.046 0.086 -10000 0 -0.27 10 10
SMAD3/SMAD4/SP1-3 0.057 0.085 -10000 0 -0.28 7 7
MED15 0.026 0.006 -10000 0 -10000 0 0
SP1 0.025 0.034 -10000 0 -10000 0 0
SIN3B 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.11 0.1 0.34 11 -0.3 2 13
ITGB5 0.004 0.061 -10000 0 -0.29 4 4
TGIF/SIN3/HDAC complex/CtBP 0.026 0.055 -10000 0 -0.46 2 2
SMAD3/SMAD4/AR -0.074 0.16 -10000 0 -0.28 89 89
AR -0.13 0.21 -10000 0 -0.42 89 89
negative regulation of cell growth -0.014 0.087 -10000 0 -0.29 9 9
SMAD3/SMAD4/MYOD 0.018 0.067 -10000 0 -0.2 4 4
E2F5 0.022 0.033 0.27 1 -0.42 1 2
E2F4 0.025 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.097 0.079 0.29 2 -0.2 1 3
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.072 -10000 0 -0.38 6 6
TFDP1 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.022 0.15 -10000 0 -0.45 12 12
SMAD3/SMAD4/RUNX2 0.027 0.073 -10000 0 -0.23 4 4
TGIF2 0.025 0.007 -10000 0 -10000 0 0
TGIF1 0.024 0.008 -10000 0 -10000 0 0
ATF2 0.026 0.004 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.026 0.005 -10000 0 -10000 0 0
ANTXR2 0.004 0.096 -10000 0 -0.42 13 13
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.012 -10000 0 -0.057 12 12
monocyte activation 0.007 0.087 -10000 0 -0.37 12 12
MAP2K2 -0.005 0.11 -10000 0 -0.57 9 9
MAP2K1 -0.006 0.011 -10000 0 -10000 0 0
MAP2K7 -0.005 0.014 0.14 1 -10000 0 1
MAP2K6 -0.008 0.026 0.14 1 -0.21 3 4
CYAA -0.015 0.042 -10000 0 -0.21 12 12
MAP2K4 -0.005 0.01 -10000 0 -10000 0 0
IL1B -0.013 0.056 0.16 4 -0.18 19 23
Channel 0.021 0.054 -10000 0 -0.22 12 12
NLRP1 -0.008 0.024 -10000 0 -0.21 3 3
CALM1 0.026 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.001 0.056 -10000 0 -0.38 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.012 0.057 12 -10000 0 12
MAPK3 -0.005 0.014 0.14 1 -10000 0 1
MAPK1 -0.004 0.018 0.14 3 -10000 0 3
PGR -0.063 0.094 -10000 0 -0.21 73 73
PA/Cellular Receptors 0.022 0.059 -10000 0 -0.25 12 12
apoptosis -0.004 0.012 -10000 0 -0.057 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.052 -10000 0 -0.21 12 12
macrophage activation -0.005 0.019 0.13 4 -10000 0 4
TNF 0.038 0.053 0.27 13 -10000 0 13
VCAM1 0.007 0.087 -10000 0 -0.37 12 12
platelet activation 0.001 0.056 -10000 0 -0.38 5 5
MAPKKK cascade 0 0.024 -10000 0 -0.092 5 5
IL18 -0.009 0.042 0.11 2 -0.19 10 12
negative regulation of macrophage activation -0.004 0.012 -10000 0 -0.057 12 12
LEF -0.004 0.012 -10000 0 -0.057 12 12
CASP1 -0.005 0.027 -10000 0 -0.13 9 9
mol:cAMP 0.001 0.056 -10000 0 -0.39 5 5
necrosis -0.004 0.012 -10000 0 -0.057 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.051 -10000 0 -0.21 12 12
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.021 0.05 0.27 1 -0.42 3 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.023 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.02 0.15 2 -0.18 1 3
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.024 0.008 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
FYN 0.02 0.047 -10000 0 -0.42 3 3
MAP3K12 0.025 0.028 -10000 0 -0.42 1 1
FGR 0.025 0.027 -10000 0 -0.42 1 1
p38 alpha/TAB1 -0.039 0.083 -10000 0 -0.28 21 21
PRKG1 -0.068 0.18 -10000 0 -0.42 54 54
DUSP8 0.003 0.096 -10000 0 -0.42 13 13
PGK/cGMP/p38 alpha -0.036 0.14 -10000 0 -0.31 35 35
apoptosis -0.038 0.08 -10000 0 -0.28 21 21
RAL/GTP 0.034 0.008 -10000 0 -10000 0 0
LYN 0.024 0.008 -10000 0 -10000 0 0
DUSP1 -0.085 0.19 -10000 0 -0.42 65 65
PAK1 0.023 0.028 -10000 0 -0.42 1 1
SRC 0.025 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.057 0.028 -10000 0 -10000 0 0
TRAF6 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.027 0.015 0.27 1 -10000 0 1
RAC1-CDC42/GTP 0.034 0.008 -10000 0 -10000 0 0
MAPK11 0.006 0.11 0.27 6 -0.3 12 18
BLK -0.003 0.12 0.27 9 -0.42 17 26
HCK 0.014 0.077 0.27 3 -0.42 7 10
MAP2K3 0.024 0.009 -10000 0 -10000 0 0
DUSP16 0.026 0.004 -10000 0 -10000 0 0
DUSP10 0.03 0.03 0.27 4 -10000 0 4
TRAF6/MEKK3 0.031 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.12 0.26 4 -0.31 20 24
positive regulation of innate immune response 0.002 0.13 0.3 5 -0.32 19 24
LCK 0.021 0.056 0.27 1 -0.42 4 5
p38alpha-beta/MKP7 0.011 0.13 0.32 4 -0.32 18 22
p38alpha-beta/MKP5 0.013 0.13 0.32 4 -0.32 18 22
PGK/cGMP -0.046 0.13 -10000 0 -0.29 54 54
PAK2 0.025 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.03 0.15 0.26 2 -0.34 33 35
CDC42 0.027 0.002 -10000 0 -10000 0 0
RALB 0.026 0.004 -10000 0 -10000 0 0
RALA 0.026 0.005 -10000 0 -10000 0 0
PAK3 0.015 0.05 0.27 8 -10000 0 8
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.002 0.097 -10000 0 -0.33 19 19
KLHL20 0.008 0.084 0.2 4 -0.2 21 25
CYFIP2 0.014 0.072 -10000 0 -0.42 7 7
Rac1/GDP 0.019 0.089 0.26 7 -0.25 9 16
ENAH -0.002 0.099 -10000 0 -0.33 20 20
AP1M1 0.026 0.004 -10000 0 -10000 0 0
RAP1B 0.025 0.007 -10000 0 -10000 0 0
RAP1A 0.027 0.002 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.043 -10000 0 -0.18 8 8
ABI1/Sra1/Nap1 -0.021 0.044 -10000 0 -0.14 23 23
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.043 0.067 -10000 0 -0.25 11 11
RAPGEF1 0.008 0.096 0.25 6 -0.36 10 16
CTNND1 0.026 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.1 -10000 0 -0.34 20 20
CRK 0.002 0.093 -10000 0 -0.33 16 16
E-cadherin/gamma catenin/alpha catenin 0.038 0.06 -10000 0 -0.28 8 8
alphaE/beta7 Integrin 0.03 0.042 -10000 0 -0.29 4 4
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
NCKAP1 0.026 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.045 0.018 -10000 0 -10000 0 0
DLG1 -0.002 0.096 -10000 0 -0.32 20 20
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.024 -10000 0 -0.14 7 7
MLLT4 0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.046 0.025 0.19 1 -0.23 1 2
PI3K 0.003 0.035 -10000 0 -0.18 7 7
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.025 0.065 -10000 0 -0.33 8 8
TIAM1 0.024 0.028 -10000 0 -0.42 1 1
E-cadherin(dimer)/Ca2+ 0.046 0.052 -10000 0 -0.22 8 8
AKT1 0.003 0.039 0.15 2 -10000 0 2
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
CDH1 0.012 0.076 -10000 0 -0.42 8 8
RhoA/GDP 0.02 0.087 0.27 6 -0.25 9 15
actin cytoskeleton organization 0.009 0.065 0.17 5 -0.15 21 26
CDC42/GDP 0.02 0.089 0.26 7 -0.25 9 16
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.009 0.047 -10000 0 -0.23 9 9
ITGB7 0.019 0.054 -10000 0 -0.42 4 4
RAC1 0.026 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.05 0.056 -10000 0 -0.23 8 8
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.047 -10000 0 -0.21 8 8
mol:GDP 0.006 0.094 0.27 7 -0.28 9 16
CDC42/GTP/IQGAP1 0.035 0.006 -10000 0 -10000 0 0
JUP 0.024 0.028 -10000 0 -0.42 1 1
p120 catenin/RhoA/GDP 0.024 0.087 0.27 5 -0.26 8 13
RAC1/GTP/IQGAP1 0.034 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.038 0.008 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
CDC42 0.027 0.002 -10000 0 -10000 0 0
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.054 0.16 10 -0.14 9 19
NME1 0.027 0.016 0.27 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.003 0.091 -10000 0 -0.35 15 15
regulation of cell-cell adhesion 0.008 0.036 -10000 0 -0.16 8 8
WASF2 0.004 0.036 0.087 2 -0.084 2 4
Rap1/GTP 0.021 0.057 0.27 2 -0.2 8 10
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.073 -10000 0 -0.25 11 11
CCND1 0.013 0.064 0.18 10 -0.16 10 20
VAV2 -0.029 0.2 -10000 0 -0.52 30 30
RAP1/GDP 0.024 0.073 0.28 3 -0.21 8 11
adherens junction assembly 0.003 0.089 -10000 0 -0.34 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.006 -10000 0 -10000 0 0
PIP5K1C 0.026 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.067 -10000 0 -0.24 11 11
E-cadherin/beta catenin 0.001 0.058 -10000 0 -0.3 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.002 0.097 -10000 0 -0.34 19 19
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.023 0.11 0.23 4 -0.31 23 27
E-cadherin/beta catenin/alpha catenin 0.038 0.055 -10000 0 -0.25 8 8
ITGAE 0.024 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.005 0.1 -10000 0 -0.34 20 20
EGFR-dependent Endothelin signaling events

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
HRAS 0.025 0.007 -10000 0 -10000 0 0
EGFR 0.023 0.073 0.29 6 -0.42 5 11
EGF/EGFR 0.024 0.092 -10000 0 -0.21 30 30
EGF/EGFR dimer/SHC/GRB2/SOS1 0.073 0.055 0.36 1 -0.22 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.025 0.14 -10000 0 -0.42 30 30
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.035 0.057 0.27 14 -10000 0 14
EGF/EGFR dimer/SHC 0.05 0.054 0.22 13 -0.25 3 16
mol:GDP 0.067 0.051 0.33 1 -0.22 1 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.027 0.053 0.28 5 -0.42 2 7
GRB2/SOS1 0.038 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.04 0.036 0.23 1 -0.2 1 2
SHC1 0.025 0.018 0.29 1 -10000 0 1
HRAS/GDP 0.059 0.048 0.29 1 -0.21 1 2
FRAP1 -0.007 0.032 0.17 7 -0.21 1 8
EGF/EGFR dimer 0.037 0.06 0.2 13 -0.3 5 18
SOS1 0.026 0.004 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.001 0.11 0.2 2 -0.3 29 31
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.033 0.12 0.33 2 -0.37 11 13
PDGFB-D/PDGFRB/SLAP 0.022 0.07 -10000 0 -0.33 9 9
PDGFB-D/PDGFRB/APS/CBL 0.046 0.044 0.2 3 -0.25 4 7
AKT1 0.025 0.09 0.34 7 -10000 0 7
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.043 0.13 0.29 4 -0.4 12 16
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
FGR 0.016 0.079 -10000 0 -0.37 4 4
mol:Ca2+ 0.02 0.12 0.26 10 -0.41 13 23
MYC 0.02 0.22 0.38 8 -0.7 16 24
SHC1 0.025 0.018 0.29 1 -10000 0 1
HRAS/GDP 0.039 0.06 -10000 0 -0.22 4 4
LRP1/PDGFRB/PDGFB 0.043 0.049 0.21 1 -0.25 6 7
GRB10 0.024 0.028 -10000 0 -0.42 1 1
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GO:0007205 0.019 0.13 0.26 10 -0.42 13 23
PTEN 0.025 0.007 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
GRB7 0.032 0.064 0.29 10 -0.42 2 12
PDGFB-D/PDGFRB/SHP2 0.032 0.043 -10000 0 -0.3 4 4
PDGFB-D/PDGFRB/GRB10 0.031 0.047 -10000 0 -0.3 5 5
cell cycle arrest 0.022 0.07 -10000 0 -0.33 9 9
HRAS 0.025 0.007 -10000 0 -10000 0 0
HIF1A 0.02 0.085 0.31 8 -10000 0 8
GAB1 0.019 0.12 0.36 3 -0.4 12 15
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.022 0.12 0.32 6 -0.38 10 16
PDGFB-D/PDGFRB 0.036 0.046 -10000 0 -0.26 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.033 0.038 -10000 0 -0.3 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.025 0.1 0.31 1 -0.42 6 7
positive regulation of MAPKKK cascade 0.032 0.043 -10000 0 -0.3 4 4
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:IP3 0.02 0.13 0.27 10 -0.42 13 23
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.053 0.21 1 -0.3 6 7
SHB 0.023 0.009 -10000 0 -10000 0 0
BLK -0.075 0.21 -10000 0 -0.43 59 59
PTPN2 0.024 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.042 -10000 0 -0.3 4 4
BCAR1 0.025 0.006 -10000 0 -10000 0 0
VAV2 0.019 0.14 0.35 5 -0.43 11 16
CBL 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.032 0.044 -10000 0 -0.3 4 4
LCK 0.009 0.11 -10000 0 -0.48 7 7
PDGFRB 0.019 0.056 -10000 0 -0.42 4 4
ACP1 0.026 0.005 -10000 0 -10000 0 0
HCK 0.003 0.14 -10000 0 -0.6 9 9
ABL1 0.016 0.12 0.26 10 -0.37 10 20
PDGFB-D/PDGFRB/CBL 0.012 0.14 0.33 3 -0.48 13 16
PTPN1 0.024 0.01 -10000 0 -10000 0 0
SNX15 0.026 0.004 -10000 0 -10000 0 0
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.029 0.026 0.27 3 -10000 0 3
cell proliferation 0.024 0.2 0.36 10 -0.6 17 27
SLA 0.014 0.066 -10000 0 -0.42 6 6
actin cytoskeleton reorganization 0.046 0.075 0.33 4 -10000 0 4
SRC 0.017 0.071 -10000 0 -0.34 3 3
PI3K -0.014 0.025 -10000 0 -0.21 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.04 0.047 0.2 1 -0.25 5 6
SH2B2 0.029 0.026 0.27 3 -10000 0 3
PLCgamma1/SPHK1 0.043 0.13 0.29 4 -0.41 12 16
LYN 0.016 0.083 -10000 0 -0.42 4 4
LRP1 0.021 0.047 -10000 0 -0.42 3 3
SOS1 0.026 0.004 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
STAT5A 0.024 0.028 -10000 0 -0.42 1 1
NCK1-2/p130 Cas 0.054 0.05 -10000 0 -0.22 3 3
SPHK1 0.056 0.086 0.27 33 -0.42 1 34
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.02 0.13 0.27 10 -0.42 13 23
PLCG1 0.019 0.13 0.29 6 -0.43 13 19
NHERF/PDGFRB 0.049 0.05 0.21 2 -0.25 4 6
YES1 0.006 0.09 -10000 0 -0.45 6 6
cell migration 0.048 0.049 0.2 2 -0.25 4 6
SHC/Grb2/SOS1 0.054 0.048 -10000 0 -0.22 2 2
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.044 0.27 9 -10000 0 9
NHERF1-2/PDGFRB/PTEN 0.058 0.051 -10000 0 -0.23 4 4
FYN -0.012 0.13 -10000 0 -0.42 20 20
DOK1 0.032 0.069 0.18 39 -0.24 3 42
HRAS/GTP 0.018 0.005 -10000 0 -10000 0 0
PDGFB 0.027 0.016 0.27 1 -10000 0 1
RAC1 0.017 0.16 0.34 7 -0.42 19 26
PRKCD 0.028 0.07 0.18 37 -0.24 4 41
FER 0.027 0.068 0.18 33 -0.24 4 37
MAPKKK cascade 0.029 0.096 0.4 7 -0.21 2 9
RASA1 0.028 0.069 0.18 35 -0.24 4 39
NCK1 0.026 0.006 -10000 0 -10000 0 0
NCK2 0.026 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.046 0.061 0.31 1 -0.22 3 4
PDGFB-D/PDGFRB/SHB 0.03 0.043 -10000 0 -0.29 4 4
chemotaxis 0.017 0.11 0.26 10 -0.36 10 20
STAT1-3-5/STAT1-3-5 0.044 0.05 -10000 0 -0.21 5 5
Bovine Papilomavirus E5/PDGFRB 0.014 0.04 -10000 0 -0.3 4 4
PTPRJ 0.025 0.006 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.025 0.006 -10000 0 -10000 0 0
ITGB7 0.019 0.054 -10000 0 -0.42 4 4
ITGA4 0.012 0.082 0.27 1 -0.42 9 10
alpha4/beta7 Integrin 0.022 0.074 0.2 1 -0.3 13 14
alpha4/beta1 Integrin 0.026 0.063 0.2 1 -0.3 9 10
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.005 0.065 -10000 0 -0.3 11 11
CRKL 0.027 0.022 0.27 2 -10000 0 2
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DOCK1 0.024 0.028 -10000 0 -0.42 1 1
ITGA4 0.012 0.082 0.27 1 -0.42 9 10
alpha4/beta7 Integrin/MAdCAM1 0.051 0.071 0.21 8 -0.23 13 21
EPO 0.04 0.075 0.27 24 -10000 0 24
alpha4/beta7 Integrin 0.022 0.074 0.2 1 -0.3 13 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.026 0.063 0.2 1 -0.3 9 10
EPO/EPOR (dimer) 0.054 0.052 0.2 27 -10000 0 27
lamellipodium assembly 0.016 0.067 -10000 0 -0.43 3 3
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.013 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
JAK2 0.017 0.054 -10000 0 -0.27 7 7
PXN 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
MADCAM1 0.03 0.05 0.27 10 -10000 0 10
cell adhesion 0.049 0.07 0.2 8 -0.22 13 21
CRKL/CBL 0.037 0.019 0.2 2 -10000 0 2
ITGB1 0.025 0.006 -10000 0 -10000 0 0
SRC 0.002 0.077 0.18 9 -0.27 15 24
ITGB7 0.019 0.054 -10000 0 -0.42 4 4
RAC1 0.026 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.028 0.09 0.2 1 -0.31 16 17
p130Cas/Crk/Dock1 0.027 0.08 -10000 0 -0.25 12 12
VCAM1 0.008 0.089 -10000 0 -0.42 11 11
RHOA 0.025 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.059 -10000 0 -0.23 9 9
BCAR1 -0.019 0.07 0.18 9 -0.26 14 23
EPOR 0.033 0.039 0.27 7 -10000 0 7
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.007 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.069 -10000 0 -0.44 3 3
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.03 0.077 -10000 0 -0.21 12 12
NEF -0.008 0.052 -10000 0 -0.21 15 15
NFKBIA 0.022 0.027 -10000 0 -0.14 1 1
BIRC3 0 0.1 0.25 2 -0.44 12 14
CYCS 0.019 0.085 0.19 21 -0.25 10 31
RIPK1 0.025 0.006 -10000 0 -10000 0 0
CD247 0.012 0.073 0.27 1 -0.25 15 16
MAP2K7 0.02 0.14 -10000 0 -0.69 6 6
protein ubiquitination 0.018 0.073 -10000 0 -0.32 1 1
CRADD 0.026 0.004 -10000 0 -10000 0 0
DAXX 0.026 0.003 -10000 0 -10000 0 0
FAS 0.02 0.047 -10000 0 -0.42 3 3
BID 0.016 0.08 0.18 15 -0.25 12 27
NF-kappa-B/RelA/I kappa B alpha 0.046 0.067 0.24 2 -0.25 11 13
TRADD 0.025 0.006 -10000 0 -10000 0 0
MAP3K5 0.025 0.006 -10000 0 -10000 0 0
CFLAR 0.026 0.006 -10000 0 -10000 0 0
FADD 0.029 0.037 0.29 5 -10000 0 5
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.046 0.067 0.24 2 -0.25 11 13
MAPK8 0.02 0.13 0.33 1 -0.64 6 7
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.024 0.008 -10000 0 -10000 0 0
TRAF2 0.024 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.021 0.084 0.19 15 -0.25 14 29
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.016 0.082 0.24 1 -0.33 3 4
CHUK 0.018 0.076 -10000 0 -0.35 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.062 0.05 -10000 0 -0.22 3 3
TCRz/NEF 0.008 0.073 0.18 1 -0.28 15 16
TNF 0.038 0.053 0.27 13 -10000 0 13
FASLG -0.006 0.12 0.25 5 -0.43 15 20
NFKB1 0.022 0.028 -10000 0 -0.14 1 1
TNFR1A/BAG4/TNF-alpha 0.049 0.039 -10000 0 -10000 0 0
CASP6 0.023 0.14 -10000 0 -0.51 13 13
CASP7 0.002 0.14 -10000 0 -0.42 16 16
RELA 0.022 0.026 -10000 0 -10000 0 0
CASP2 0.026 0.003 -10000 0 -10000 0 0
CASP3 0.002 0.14 -10000 0 -0.42 18 18
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.016 -10000 0 -10000 0 0
CASP8 0.025 0.006 -10000 0 -10000 0 0
CASP9 0.026 0.003 -10000 0 -10000 0 0
MAP3K14 0.018 0.082 -10000 0 -0.4 1 1
APAF-1/Caspase 9 0.013 0.094 -10000 0 -0.33 9 9
BCL2 0.01 0.13 0.32 1 -0.6 6 7
BARD1 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
BARD1/CSTF1 0.027 0.051 -10000 0 -0.3 6 6
ATM 0.025 0.007 -10000 0 -10000 0 0
UBE2D3 0.026 0.003 -10000 0 -10000 0 0
PRKDC 0.024 0.008 -10000 0 -10000 0 0
ATR 0.026 0.005 -10000 0 -10000 0 0
UBE2L3 0.026 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.02 0.23 2 -10000 0 2
protein ubiquitination 0.069 0.07 -10000 0 -0.22 6 6
XRCC5 0.025 0.006 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
M/R/N Complex 0.042 0.023 -10000 0 -10000 0 0
MRE11A 0.026 0.006 -10000 0 -10000 0 0
DNA-PK 0.046 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.004 0.14 -10000 0 -0.51 16 16
FANCF 0.024 0.032 0.27 1 -0.42 1 2
BRCA1 0.027 0.016 0.27 1 -10000 0 1
CCNE1 0.065 0.091 0.28 41 -10000 0 41
CDK2/Cyclin E1 0.052 0.052 0.2 26 -10000 0 26
FANCG 0.024 0.008 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.029 0.052 0.2 1 -0.3 6 7
FANCE 0.027 0.002 -10000 0 -10000 0 0
FANCC 0.025 0.017 0.27 1 -10000 0 1
NBN 0.022 0.01 -10000 0 -10000 0 0
FANCA 0.04 0.058 0.27 16 -10000 0 16
DNA repair 0.029 0.1 0.29 8 -0.35 6 14
BRCA1/BARD1/ubiquitin 0.029 0.052 0.2 1 -0.3 6 7
BARD1/DNA-PK 0.052 0.047 -10000 0 -0.23 5 5
FANCL 0.027 0.016 0.27 1 -10000 0 1
mRNA polyadenylation -0.027 0.051 0.3 6 -10000 0 6
BRCA1/BARD1/CTIP/M/R/N Complex 0.023 0.061 -10000 0 -0.22 9 9
BRCA1/BACH1/BARD1/TopBP1 0.042 0.049 0.2 1 -0.25 6 7
BRCA1/BARD1/P53 0.05 0.051 -10000 0 -0.23 6 6
BARD1/CSTF1/BRCA1 0.04 0.049 0.2 1 -0.25 6 7
BRCA1/BACH1 0.027 0.016 0.27 1 -10000 0 1
BARD1 0.014 0.066 -10000 0 -0.42 6 6
PCNA 0.026 0.016 0.27 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.043 0.049 -10000 0 -0.25 6 6
BRCA1/BARD1/UbcH7 0.042 0.049 -10000 0 -0.25 6 6
BRCA1/BARD1/RAD51/PCNA 0.094 0.089 -10000 0 -0.23 6 6
BARD1/DNA-PK/P53 0.056 0.051 -10000 0 -0.22 5 5
BRCA1/BARD1/Ubiquitin 0.029 0.052 0.2 1 -0.3 6 7
BRCA1/BARD1/CTIP 0.031 0.044 0.19 1 -0.23 6 7
FA complex 0.019 0.064 0.25 1 -0.26 7 8
BARD1/EWS 0.028 0.051 -10000 0 -0.3 6 6
RBBP8 0.011 0.004 -10000 0 -10000 0 0
TP53 0.024 0.008 -10000 0 -10000 0 0
TOPBP1 0.026 0.005 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.048 0.05 0.23 6 -10000 0 6
BRCA1/BARD1 0.076 0.074 -10000 0 -0.22 6 6
CSTF1 0.025 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.047 -10000 0 -0.29 6 6
CDK2 0.026 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.12 0.27 87 -10000 0 87
RAD50 0.026 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.029 0.052 0.2 1 -0.3 6 7
EWSR1 0.025 0.006 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.037 0.083 0.36 1 -10000 0 1
CRKL 0.022 0.047 0.26 2 -10000 0 2
mol:DAG 0.033 0.049 -10000 0 -10000 0 0
HRAS 0.023 0.081 0.31 9 -10000 0 9
MAPK8 0.025 0.068 0.22 18 -0.23 3 21
RAP1A 0.023 0.048 0.26 2 -10000 0 2
GAB1 0.022 0.047 0.26 2 -10000 0 2
MAPK14 0.03 0.064 0.22 20 -10000 0 20
EPO 0.048 0.074 0.28 24 -10000 0 24
PLCG1 0.034 0.049 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.034 0.042 0.28 7 -10000 0 7
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.039 0.099 0.21 20 -0.26 20 40
GAB1/SHC/GRB2/SOS1 0.048 0.046 0.26 2 -10000 0 2
EPO/EPOR (dimer) 0.056 0.055 0.21 25 -10000 0 25
IRS2 0.015 0.062 0.26 2 -0.22 7 9
STAT1 0.039 0.066 0.25 1 -10000 0 1
STAT5B 0.036 0.056 -10000 0 -10000 0 0
cell proliferation 0.009 0.075 0.23 21 -0.22 3 24
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.04 -10000 0 -0.22 1 1
TEC 0.022 0.047 0.26 2 -10000 0 2
SOCS3 -0.015 0.13 -10000 0 -0.42 24 24
STAT1 (dimer) 0.039 0.065 0.25 1 -10000 0 1
JAK2 0.024 0.013 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.071 0.061 -10000 0 -10000 0 0
EPO/EPOR 0.056 0.055 0.21 25 -10000 0 25
LYN 0.023 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.035 0.047 0.28 1 -0.2 1 2
elevation of cytosolic calcium ion concentration 0.034 0.042 0.28 7 -10000 0 7
SHC1 0.025 0.018 0.29 1 -10000 0 1
EPO/EPOR (dimer)/LYN 0.065 0.052 0.23 3 -10000 0 3
mol:IP3 0.033 0.049 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.033 0.072 0.28 3 -0.26 2 5
SH2B3 0.026 0.012 -10000 0 -10000 0 0
NFKB1 0.03 0.064 0.22 21 -10000 0 21
EPO/EPOR (dimer)/JAK2/SOCS3 0 0.067 0.22 1 -0.21 17 18
PTPN6 0.023 0.046 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.044 0.049 0.28 1 -10000 0 1
EPOR 0.034 0.042 0.28 7 -10000 0 7
INPP5D 0.016 0.061 -10000 0 -0.42 5 5
mol:GDP 0.045 0.043 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
PLCG2 0.025 0.032 0.27 1 -0.42 1 2
CRKL/CBL/C3G 0.044 0.047 0.28 1 -10000 0 1
VAV2 0.021 0.046 0.29 1 -0.2 1 2
CBL 0.021 0.045 0.29 1 -10000 0 1
SHC/Grb2/SOS1 0.037 0.039 -10000 0 -10000 0 0
STAT5A 0.035 0.059 -10000 0 -0.26 1 1
GRB2 0.026 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.049 0.083 -10000 0 -0.3 9 9
LYN/PLCgamma2 0.034 0.027 0.21 1 -0.3 1 2
PTPN11 0.026 0.005 -10000 0 -10000 0 0
BTK 0.012 0.069 0.29 1 -0.22 12 13
BCL2 0.022 0.18 0.36 2 -0.79 11 13
IFN-gamma pathway

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.075 0.067 0.34 1 -10000 0 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.027 0.022 0.27 2 -10000 0 2
STAT1 (dimer)/Cbp/p300 0.062 0.054 0.29 4 -10000 0 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.029 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.009 0.059 -10000 0 -0.22 5 5
CaM/Ca2+ 0.072 0.061 0.3 1 -10000 0 1
RAP1A 0.027 0.002 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.039 0.043 -10000 0 -10000 0 0
AKT1 0.025 0.079 0.31 11 -10000 0 11
MAP2K1 0.013 0.059 0.26 6 -10000 0 6
MAP3K11 0.026 0.057 0.27 6 -10000 0 6
IFNGR1 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.068 0.18 -10000 0 -0.34 69 69
Rap1/GTP 0.015 0.016 -10000 0 -10000 0 0
CRKL/C3G 0.036 0.02 0.2 2 -10000 0 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.079 0.068 0.31 1 -10000 0 1
CEBPB 0.038 0.11 0.32 3 -0.57 5 8
STAT3 0.026 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.068 0.13 -10000 0 -0.68 6 6
STAT1 0.028 0.058 0.27 6 -10000 0 6
CALM1 0.026 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.063 0.1 0.28 48 -10000 0 48
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.047 0.058 0.28 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.027 0.066 -10000 0 -0.35 5 5
mol:Ca2+ 0.071 0.064 0.33 1 -10000 0 1
MAPK3 0.023 0.11 -10000 0 -0.72 4 4
STAT1 (dimer) -0.003 0.084 -10000 0 -0.3 5 5
MAPK1 0.019 0.12 -10000 0 -0.75 5 5
JAK2 0.026 0.012 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
JAK1 0.03 0.007 -10000 0 -10000 0 0
CAMK2D 0.026 0.004 -10000 0 -10000 0 0
DAPK1 0.032 0.096 0.32 1 -0.51 5 6
SMAD7 0.007 0.048 0.18 5 -0.15 3 8
CBL/CRKL/C3G 0.052 0.052 0.28 4 -10000 0 4
PI3K 0.064 0.057 0.27 1 -10000 0 1
IFNG 0.063 0.1 0.28 48 -10000 0 48
apoptosis 0.023 0.098 0.26 1 -0.39 10 11
CAMK2G 0.025 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.004 -10000 0 -10000 0 0
CAMK2A -0.11 0.2 -10000 0 -0.42 79 79
CAMK2B 0.05 0.076 0.27 28 -10000 0 28
FRAP1 0.021 0.075 0.3 11 -10000 0 11
PRKCD 0.024 0.077 0.3 10 -10000 0 10
RAP1B 0.025 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.009 0.059 -10000 0 -0.22 5 5
PTPN2 0.024 0.008 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
IRF1 0.017 0.05 0.25 4 -10000 0 4
STAT1 (dimer)/PIASy 0.044 0.058 0.28 6 -10000 0 6
SOCS1 0.002 0.16 -10000 0 -1 6 6
mol:GDP 0.048 0.049 0.27 4 -10000 0 4
CASP1 0.004 0.059 0.18 5 -0.23 7 12
PTGES2 0.024 0.008 -10000 0 -10000 0 0
IRF9 0.025 0.036 0.14 2 -0.16 2 4
mol:PI-3-4-5-P3 0.046 0.044 0.21 1 -10000 0 1
RAP1/GDP 0.037 0.029 -10000 0 -10000 0 0
CBL 0.024 0.054 0.26 5 -10000 0 5
MAP3K1 0.025 0.056 0.27 6 -10000 0 6
PIAS1 0.026 0.004 -10000 0 -10000 0 0
PIAS4 0.026 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.009 0.059 -10000 0 -0.22 5 5
PTPN11 0.024 0.05 0.26 3 -10000 0 3
CREBBP 0.025 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.008 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.018 0.29 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.03 0.024 0.21 1 -10000 0 1
CDKN1B 0.015 0.042 -10000 0 -0.29 2 2
CDKN1A 0.013 0.048 -10000 0 -0.29 3 3
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.008 -10000 0 -10000 0 0
FOXO3 0.017 0.035 -10000 0 -0.29 2 2
AKT1 0.007 0.042 -10000 0 -0.29 5 5
BAD 0.026 0.003 -10000 0 -10000 0 0
AKT3 0.002 0.057 -10000 0 -0.28 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.015 0.048 -10000 0 -0.29 3 3
AKT1/ASK1 0.038 0.06 -10000 0 -0.28 3 3
BAD/YWHAZ 0.04 0.024 -10000 0 -10000 0 0
RICTOR 0.023 0.01 -10000 0 -10000 0 0
RAF1 0.024 0.019 0.29 1 -10000 0 1
JNK cascade -0.034 0.056 0.28 3 -10000 0 3
TSC1 0.016 0.04 -10000 0 -0.29 2 2
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.036 0.062 -10000 0 -0.28 4 4
EP300 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.017 0.048 -10000 0 -0.28 5 5
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.015 0.046 -10000 0 -0.29 3 3
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
TBC1D4 0.005 0.002 -10000 0 -10000 0 0
MAP3K5 0.025 0.006 -10000 0 -10000 0 0
MAPKAP1 0.024 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.048 0.069 0.33 2 -0.23 5 7
YWHAH 0.025 0.006 -10000 0 -10000 0 0
AKT1S1 0.016 0.044 -10000 0 -0.3 2 2
CASP9 0.016 0.049 -10000 0 -0.29 3 3
YWHAB 0.024 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.064 -10000 0 -0.28 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.046 0.019 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.019 0.049 0.25 2 -0.25 2 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.031 -10000 0 -0.27 2 2
CHUK 0.015 0.042 -10000 0 -0.28 3 3
BAD/BCL-XL 0.033 0.058 0.26 1 -0.28 3 4
mTORC2 0.026 0.015 -10000 0 -10000 0 0
AKT2 0.013 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.053 0.082 0.25 5 -0.4 2 7
PDPK1 0.025 0.006 -10000 0 -10000 0 0
MDM2 0.027 0.067 0.26 2 -0.29 3 5
MAPKKK cascade -0.036 0.061 0.28 4 -10000 0 4
MDM2/Cbp/p300 0.06 0.078 0.31 1 -0.28 3 4
TSC1/TSC2 0.014 0.038 -10000 0 -0.28 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.075 0.28 2 -0.27 3 5
glucose import -0.13 0.11 0.21 1 -0.22 155 156
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.018 0.037 0.23 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.12 0.11 0.21 1 -0.22 148 149
GSK3A 0.02 0.05 -10000 0 -0.3 2 2
FOXO1 0.014 0.042 -10000 0 -0.3 2 2
GSK3B 0.018 0.054 -10000 0 -0.28 4 4
SFN 0.046 0.082 0.27 25 -0.42 2 27
G1/S transition of mitotic cell cycle 0.026 0.066 0.25 3 -0.29 2 5
p27Kip1/14-3-3 family 0.029 0.048 -10000 0 -0.33 1 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
KPNA1 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
RHEB 0.026 0.004 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.026 0.006 -10000 0 -10000 0 0
HDAC4 0.025 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.005 0.053 -10000 0 -0.27 8 8
CDKN1A -0.01 0.04 -10000 0 -0.65 1 1
KAT2B 0.025 0.006 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.025 0.006 -10000 0 -10000 0 0
FOXO4 0.013 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
TAT 0.018 0.046 0.27 7 -10000 0 7
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.013 0.005 -10000 0 -10000 0 0
PPARGC1A -0.15 0.22 0.27 1 -0.42 102 103
FHL2 0.025 0.028 -10000 0 -0.42 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.012 -10000 0 -10000 0 0
HIST2H4A 0.005 0.053 0.27 8 -10000 0 8
SIRT1/FOXO3a 0.016 0.019 -10000 0 -10000 0 0
SIRT1 0.024 0.012 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.044 0.021 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.022 0.05 -10000 0 -0.2 5 5
apoptosis -0.048 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A -0.077 0.14 0.18 1 -0.25 102 103
p53/SIRT1 0.029 0.024 0.38 1 -10000 0 1
SIRT1/FOXO4 0.014 0.049 -10000 0 -0.2 7 7
FOXO1/FHL2/SIRT1 0.045 0.023 -10000 0 -0.23 1 1
HIST1H1E 0.02 0.024 0.2 1 -10000 0 1
SIRT1/p300 0.036 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.017 -10000 0 -0.22 1 1
TP53 0.022 0.013 0.2 1 -10000 0 1
KU70/SIRT1/BAX 0.049 0.016 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
MEF2D 0.025 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.038 0.03 0.2 7 -10000 0 7
ACSS2 -0.006 0.021 0.21 2 -10000 0 2
SIRT1/PCAF/MYOD 0.029 0.017 0.22 1 -10000 0 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.026 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.014 0.042 -10000 0 -0.2 9 9
FRAP1 0.015 0.05 -10000 0 -0.41 2 2
AKT1 0.003 0.054 0.16 14 -0.21 3 17
INSR 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.008 -10000 0 -10000 0 0
mol:GTP 0.028 0.054 0.26 2 -0.19 2 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.011 0.019 -10000 0 -10000 0 0
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.014 0.033 -10000 0 -0.17 2 2
TSC1 0.024 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.007 0.064 -10000 0 -0.21 20 20
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.024 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 0.023 0.049 0.23 2 -10000 0 2
MAP3K5 0.004 0.042 0.2 5 -0.18 8 13
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
apoptosis 0.004 0.042 0.2 5 -0.18 8 13
mol:LY294002 0 0 -10000 0 -0.001 19 19
EIF4B 0.022 0.05 0.25 4 -10000 0 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.043 0.23 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1 0.015 0.028 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.059 -10000 0 -0.19 15 15
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.043 0.18 6 -10000 0 6
FKBP1A 0.025 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.03 0.046 0.21 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 19 19
FKBP12/Rapamycin 0.019 0.005 -10000 0 -10000 0 0
PDPK1 -0.008 0.053 0.16 13 -0.22 4 17
EIF4E 0.026 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.024 0.11 -10000 0 -0.53 9 9
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.009 0.039 -10000 0 -0.22 6 6
TSC1/TSC2 0.031 0.058 0.28 2 -0.2 2 4
tumor necrosis factor receptor activity 0 0 0.001 19 -10000 0 19
RPS6 0.023 0.01 -10000 0 -10000 0 0
PPP5C 0.026 0.004 -10000 0 -10000 0 0
EIF4G1 0.025 0.006 -10000 0 -10000 0 0
IRS1 -0.009 0.064 -10000 0 -0.23 20 20
INS -0.016 0.004 -10000 0 -10000 0 0
PTEN 0.024 0.007 -10000 0 -10000 0 0
PDK2 -0.008 0.05 0.16 12 -0.24 3 15
EIF4EBP1 -0.038 0.27 -10000 0 -1 18 18
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PPP2R5D 0.016 0.05 -10000 0 -0.38 2 2
peptide biosynthetic process -0.011 0.017 0.18 2 -10000 0 2
RHEB 0.026 0.004 -10000 0 -10000 0 0
EIF4A1 0.024 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 21 -10000 0 21
EEF2 -0.011 0.017 0.18 2 -10000 0 2
eIF4E/4E-BP1 -0.026 0.25 -10000 0 -0.95 18 18
HIF-2-alpha transcription factor network

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
MMP14 0.027 0.095 -10000 0 -0.53 4 4
oxygen homeostasis 0.005 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.016 0.27 1 -10000 0 1
TCEB1 0.023 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.049 0.084 -10000 0 -0.25 2 2
EPO 0.092 0.16 0.43 9 -0.43 1 10
FIH (dimer) 0.026 0.022 -10000 0 -10000 0 0
APEX1 0.025 0.027 -10000 0 -10000 0 0
SERPINE1 0.077 0.15 0.38 7 -0.48 3 10
FLT1 0.018 0.12 -10000 0 -0.6 5 5
ADORA2A 0.077 0.14 0.37 5 -0.41 2 7
germ cell development 0.092 0.17 0.42 15 -0.4 4 19
SLC11A2 0.078 0.15 0.39 4 -0.46 1 5
BHLHE40 0.069 0.15 0.39 4 -0.4 4 8
HIF1AN 0.026 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.072 0.11 0.37 4 -0.29 2 6
ETS1 0.034 0.009 -10000 0 -10000 0 0
CITED2 0.025 0.097 -10000 0 -0.54 6 6
KDR 0.018 0.12 -10000 0 -0.63 4 4
PGK1 0.077 0.15 0.39 4 -0.42 2 6
SIRT1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0.001 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.11 0.18 0.51 2 -0.47 2 4
EPAS1 0.035 0.076 0.22 5 -0.25 3 8
SP1 0.031 0.006 -10000 0 -10000 0 0
ABCG2 0.07 0.16 0.41 6 -0.44 8 14
EFNA1 0.078 0.15 0.51 5 -0.42 2 7
FXN 0.083 0.14 0.37 6 -0.41 2 8
POU5F1 0.093 0.17 0.42 14 -0.42 4 18
neuron apoptosis -0.1 0.18 0.46 2 -0.5 2 4
EP300 0.026 0.006 -10000 0 -10000 0 0
EGLN3 0.016 0.069 -10000 0 -0.41 6 6
EGLN2 0.026 0.022 -10000 0 -10000 0 0
EGLN1 0.026 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.041 0.026 0.2 1 -10000 0 1
VHL 0.024 0.009 -10000 0 -10000 0 0
ARNT 0.023 0.026 -10000 0 -10000 0 0
SLC2A1 0.078 0.14 0.36 7 -0.41 2 9
TWIST1 0.038 0.21 0.37 5 -0.41 36 41
ELK1 0.031 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.067 0.11 0.34 2 -0.29 2 4
VEGFA 0.078 0.15 0.39 4 -0.42 2 6
CREBBP 0.025 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.009 0.004 -10000 0 -10000 0 0
SNTA1 0.024 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.003 0.025 0.28 1 -10000 0 1
MAPK12 0.005 0.048 0.21 10 -0.22 3 13
CCND1 0.008 0.068 0.17 6 -0.38 6 12
p38 gamma/SNTA1 0.017 0.046 0.2 8 -0.2 4 12
MAP2K3 0.024 0.009 -10000 0 -10000 0 0
PKN1 0.025 0.028 -10000 0 -0.42 1 1
G2/M transition checkpoint 0.005 0.048 0.21 10 -0.22 3 13
MAP2K6 0.002 0.031 0.16 1 -0.24 4 5
MAPT -0.014 0.089 0.26 4 -0.28 20 24
MAPK13 0.011 0.004 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.012 0.019 -10000 0 -0.28 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.024 0.019 0.29 1 -10000 0 1
Syndecan-3/Src/Cortactin 0.016 0.11 0.28 1 -0.38 1 2
Syndecan-3/Neurocan 0.033 0.053 0.27 1 -0.4 2 3
POMC 0.023 0.073 0.27 7 -0.42 5 12
EGFR 0.023 0.073 0.29 6 -0.42 5 11
Syndecan-3/EGFR 0.028 0.048 -10000 0 -0.31 2 2
AGRP 0.008 0.021 -10000 0 -10000 0 0
NCSTN 0.023 0.009 -10000 0 -10000 0 0
PSENEN 0.025 0.006 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.004 -10000 0 -10000 0 0
APH1A 0.024 0.009 -10000 0 -10000 0 0
NCAN 0.018 0.055 0.27 10 -10000 0 10
long-term memory 0.04 0.059 -10000 0 -0.46 2 2
Syndecan-3/IL8 0.001 0.088 -10000 0 -0.49 2 2
PSEN1 0.026 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.032 0.015 -10000 0 -10000 0 0
FYN 0.02 0.047 -10000 0 -0.42 3 3
limb bud formation 0.008 0.036 -10000 0 -0.57 1 1
MC4R 0.003 0.039 0.27 4 -10000 0 4
SRC 0.025 0.007 -10000 0 -10000 0 0
PTN -0.06 0.19 0.27 11 -0.42 57 68
FGFR/FGF/Syndecan-3 0.008 0.037 -10000 0 -0.58 1 1
neuron projection morphogenesis 0.003 0.11 0.4 2 -0.38 1 3
Syndecan-3/AgRP 0.025 0.043 -10000 0 -0.4 2 2
Syndecan-3/AgRP/MC4R 0.043 0.054 0.34 1 -0.55 1 2
Fyn/Cortactin 0.03 0.033 -10000 0 -0.3 2 2
SDC3 0.008 0.037 -10000 0 -0.58 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.001 0.087 -10000 0 -0.48 2 2
IL8 -0.037 0.16 0.27 1 -0.42 38 39
Syndecan-3/Fyn/Cortactin 0.041 0.061 -10000 0 -0.48 2 2
Syndecan-3/CASK 0.006 0.038 -10000 0 -0.39 2 2
alpha-MSH/MC4R 0.031 0.057 0.2 9 -0.3 5 14
Gamma Secretase 0.06 0.035 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.041 0.16 -10000 0 -0.42 40 40
HRAS 0.025 0.007 -10000 0 -10000 0 0
EGFR 0.023 0.073 0.29 6 -0.42 5 11
AKT 0.027 0.091 0.25 5 -0.27 9 14
FOXO3 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.025 0.006 -10000 0 -10000 0 0
AKT3 0.009 0.085 -10000 0 -0.42 10 10
FOXO4 0.027 0.015 0.27 1 -10000 0 1
MET 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PIK3CB 0.026 0.005 -10000 0 -10000 0 0
NRAS 0.027 0.002 -10000 0 -10000 0 0
PIK3CG 0.011 0.088 0.27 2 -0.42 10 12
PIK3R3 0.026 0.004 -10000 0 -10000 0 0
PIK3R2 0.026 0.003 -10000 0 -10000 0 0
NF1 0.026 0.005 -10000 0 -10000 0 0
RAS 0.008 0.07 0.19 4 -0.24 5 9
ERBB2 0.035 0.048 0.29 9 -10000 0 9
proliferation/survival/translation -0.032 0.07 0.26 6 -0.21 1 7
PI3K 0.022 0.072 0.2 14 -0.18 3 17
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
KRAS 0.027 0.017 0.29 1 -10000 0 1
FOXO 0.055 0.059 0.24 5 -0.1 3 8
AKT2 0.025 0.006 -10000 0 -10000 0 0
PTEN 0.025 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.009 0.047 0.29 1 -10000 0 1
DAPP1 0.005 0.1 0.33 2 -0.3 11 13
Src family/SYK family/BLNK-LAT/BTK-ITK -0.024 0.16 0.33 1 -0.44 20 21
mol:DAG 0.003 0.088 0.22 11 -0.21 11 22
HRAS 0.026 0.009 -10000 0 -10000 0 0
RAP1A 0.028 0.004 -10000 0 -10000 0 0
ARF5/GDP 0.029 0.073 -10000 0 -0.3 6 6
PLCG2 0.025 0.032 0.27 1 -0.42 1 2
PLCG1 0.025 0.007 -10000 0 -10000 0 0
ARF5 0.026 0.003 -10000 0 -10000 0 0
mol:GTP -0.011 0.037 0.2 3 -10000 0 3
ARF1/GTP 0 0.038 0.28 1 -10000 0 1
RHOA 0.025 0.006 -10000 0 -10000 0 0
YES1 0.024 0.008 -10000 0 -10000 0 0
RAP1A/GTP -0.012 0.034 0.16 10 -10000 0 10
ADAP1 -0.013 0.042 0.28 1 -0.21 2 3
ARAP3 -0.011 0.037 0.2 3 -10000 0 3
INPPL1 0.025 0.007 -10000 0 -10000 0 0
PREX1 0.025 0.007 -10000 0 -10000 0 0
ARHGEF6 0.023 0.039 -10000 0 -0.42 2 2
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
ARF1 0.026 0.004 -10000 0 -10000 0 0
NRAS 0.028 0.004 -10000 0 -10000 0 0
FYN 0.02 0.047 -10000 0 -0.42 3 3
ARF6 0.026 0.004 -10000 0 -10000 0 0
FGR 0.025 0.027 -10000 0 -0.42 1 1
mol:Ca2+ 0.006 0.06 0.18 13 -0.12 5 18
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.024 0.028 -10000 0 -0.42 1 1
ZAP70 0.009 0.085 -10000 0 -0.42 10 10
mol:IP3 0.003 0.075 0.21 13 -0.16 9 22
LYN 0.024 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.029 0.073 -10000 0 -0.3 6 6
RhoA/GDP 0.033 0.047 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.046 0.019 -10000 0 -10000 0 0
BLNK 0.012 0.076 -10000 0 -0.42 8 8
actin cytoskeleton reorganization 0.021 0.075 0.25 3 -0.26 4 7
SRC 0.025 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.011 0.026 -10000 0 -0.25 3 3
RAC1 0.026 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.013 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.012 0.042 0.29 1 -10000 0 1
RhoA/GTP -0.012 0.039 0.3 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.009 0.1 -10000 0 -0.29 21 21
BLK -0.003 0.12 0.27 9 -0.42 17 26
PDPK1 0.025 0.006 -10000 0 -10000 0 0
CYTH1 -0.012 0.036 0.28 1 -10000 0 1
HCK 0.014 0.077 0.27 3 -0.42 7 10
CYTH3 -0.012 0.037 0.28 1 -10000 0 1
CYTH2 -0.012 0.038 0.28 1 -10000 0 1
KRAS 0.027 0.016 0.26 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.004 0.091 -10000 0 -0.4 11 11
SGK1 -0.007 0.11 -10000 0 -0.39 16 16
INPP5D 0.016 0.061 -10000 0 -0.42 5 5
mol:GDP 0.016 0.072 -10000 0 -0.31 6 6
SOS1 0.026 0.004 -10000 0 -10000 0 0
SYK 0.021 0.039 -10000 0 -0.42 2 2
ARF6/GDP 0.02 0.047 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 -0.011 0.035 0.28 1 -10000 0 1
ARAP3/RAP1A/GTP -0.012 0.035 0.16 10 -10000 0 10
VAV1 0.005 0.098 0.27 1 -0.42 13 14
mol:PI-3-4-P2 0.007 0.033 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.043 0.039 -10000 0 -10000 0 0
PLEKHA1 -0.012 0.026 -10000 0 -0.25 3 3
Rac1/GDP 0.027 0.073 -10000 0 -0.3 6 6
LAT 0.026 0.016 0.27 1 -10000 0 1
Rac1/GTP 0.013 0.066 -10000 0 -0.3 5 5
ITK -0.028 0.065 0.28 1 -0.21 21 22
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.005 0.11 0.24 7 -0.27 16 23
LCK 0.021 0.056 0.27 1 -0.42 4 5
BTK -0.021 0.055 0.28 1 -0.21 12 13
Arf6 trafficking events

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
SLC2A4 -0.26 0.21 -10000 0 -0.42 168 168
CLTC 0.017 0.065 -10000 0 -0.45 4 4
calcium ion-dependent exocytosis 0.012 0.023 -10000 0 -0.15 3 3
Dynamin 2/GTP 0.025 0.008 -10000 0 -10000 0 0
EXOC4 0.026 0.005 -10000 0 -10000 0 0
CD59 0.013 0.033 -10000 0 -0.31 2 2
CPE 0.008 0.037 0.14 1 -0.25 5 6
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
membrane fusion 0.013 0.015 -10000 0 -10000 0 0
CTNND1 -0.005 0.033 0.18 8 -10000 0 8
DNM2 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.012 0.05 0.18 1 -0.3 4 5
TSHR 0.009 0.021 0.14 5 -10000 0 5
INS -0.014 0.12 -10000 0 -0.48 15 15
BIN1 -0.026 0.14 -10000 0 -0.42 31 31
mol:Choline 0.013 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.008 0.14 1 -10000 0 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.008 -10000 0 -10000 0 0
JUP 0.012 0.04 -10000 0 -0.31 3 3
ASAP2/amphiphysin II 0.017 0.086 -10000 0 -0.23 28 28
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 0.008 0.053 -10000 0 -0.34 3 3
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.027 0.038 0.27 3 -0.42 1 4
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.025 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.027 0.047 -10000 0 -0.22 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.036 0.063 0.33 4 -0.25 1 5
positive regulation of phagocytosis 0.013 0.002 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.025 0.18 3 -0.25 1 4
ACAP1 0.015 0.026 -10000 0 -0.16 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.05 0.093 -10000 0 -0.36 4 4
clathrin heavy chain/ACAP1 0.016 0.06 -10000 0 -0.39 4 4
JIP4/KLC1 0.048 0.014 -10000 0 -10000 0 0
EXOC1 0.026 0.003 -10000 0 -10000 0 0
exocyst 0.019 0.023 -10000 0 -0.22 1 1
RALA/GTP 0.019 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.008 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 -0.005 0.033 0.18 8 -10000 0 8
NME1 0.013 0.008 0.14 1 -10000 0 1
clathrin coat assembly 0.021 0.067 0.26 1 -0.44 4 5
IL2RA 0.014 0.06 -10000 0 -0.33 2 2
VAMP3 0.013 0.002 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.1 0.1 -10000 0 -0.37 6 6
EXOC6 0.025 0.006 -10000 0 -10000 0 0
PLD1 0.012 0.007 -10000 0 -10000 0 0
PLD2 0.012 0.006 -10000 0 -10000 0 0
EXOC5 0.026 0.003 -10000 0 -10000 0 0
PIP5K1C 0.011 0.028 -10000 0 -0.2 3 3
SDC1 0.012 0.043 -10000 0 -0.31 3 3
ARF6/GDP 0.023 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.038 0.065 0.26 1 -0.34 4 5
mol:Phosphatidic acid 0.013 0.015 -10000 0 -10000 0 0
endocytosis -0.016 0.085 0.23 28 -10000 0 28
SCAMP2 0.026 0.004 -10000 0 -10000 0 0
ADRB2 0.002 0.077 -10000 0 -0.42 4 4
EXOC3 0.022 0.01 -10000 0 -10000 0 0
ASAP2 0.026 0.005 -10000 0 -10000 0 0
Dynamin 2/GDP 0.028 0.01 -10000 0 -10000 0 0
KLC1 0.026 0.005 -10000 0 -10000 0 0
AVPR2 0.002 0.091 0.25 1 -0.36 6 7
RALA 0.026 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.035 0.068 0.28 3 -0.32 4 7
Regulation of Telomerase

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
Telomerase catalytic core complex 0.12 0.14 -10000 0 -0.59 1 1
RAD9A 0.031 0.034 0.27 5 -10000 0 5
AP1 -0.055 0.16 -10000 0 -0.31 74 74
IFNAR2 0.033 0.012 -10000 0 -10000 0 0
AKT1 -0.002 0.077 -10000 0 -0.18 27 27
ER alpha/Oestrogen -0.027 0.12 -10000 0 -0.29 42 42
NFX1/SIN3/HDAC complex 0.041 0.038 -10000 0 -0.35 1 1
EGF 0.041 0.055 0.27 14 -10000 0 14
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.024 0.008 -10000 0 -10000 0 0
SP3/HDAC2 0.049 0.021 -10000 0 -10000 0 0
TERT/c-Abl 0.1 0.13 -10000 0 -0.54 1 1
SAP18 0.027 0.005 -10000 0 -10000 0 0
MRN complex 0.042 0.023 -10000 0 -10000 0 0
WT1 0.06 0.085 0.28 34 -10000 0 34
WRN 0.022 0.01 -10000 0 -10000 0 0
SP1 0.036 0.015 -10000 0 -10000 0 0
SP3 0.029 0.007 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.1 0.12 -10000 0 -0.51 1 1
Mad/Max 0.046 0.019 0.22 1 -10000 0 1
TERT 0.12 0.14 -10000 0 -0.6 1 1
CCND1 0.12 0.2 0.52 3 -1 4 7
MAX 0.03 0.007 -10000 0 -10000 0 0
RBBP7 0.028 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.002 -10000 0 -10000 0 0
TERF2 0.024 0.013 -10000 0 -10000 0 0
PTGES3 0.026 0.004 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
Telomerase/911 0.067 0.059 0.31 1 -10000 0 1
CDKN1B 0.035 0.036 0.24 4 -10000 0 4
RAD1 0.023 0.009 -10000 0 -10000 0 0
XRCC5 0.025 0.006 -10000 0 -10000 0 0
XRCC6 0.026 0.005 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.037 0.014 -10000 0 -10000 0 0
UBE3A 0.029 0.007 -10000 0 -10000 0 0
JUN 0.019 0.066 -10000 0 -0.41 6 6
E6 0.003 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.027 0.011 -10000 0 -10000 0 0
FOS -0.1 0.2 -10000 0 -0.41 77 77
IFN-gamma/IRF1 0.075 0.068 0.22 43 -10000 0 43
PARP2 0.026 0.005 -10000 0 -10000 0 0
BLM 0.034 0.042 0.27 8 -10000 0 8
Telomerase 0.033 0.063 0.24 1 -0.34 1 2
IRF1 0.033 0.008 -10000 0 -10000 0 0
ESR1 -0.043 0.16 -10000 0 -0.42 42 42
KU/TER 0.037 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.013 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.049 -10000 0 -0.25 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.04 0.049 -10000 0 -0.26 3 3
HDAC1 0.028 0.002 -10000 0 -10000 0 0
HDAC2 0.034 0.014 -10000 0 -10000 0 0
ATM 0.011 0.011 -10000 0 -10000 0 0
SMAD3 -0.001 0.015 -10000 0 -10000 0 0
ABL1 0.024 0.008 -10000 0 -10000 0 0
MXD1 0.03 0.017 0.28 1 -10000 0 1
MRE11A 0.026 0.006 -10000 0 -10000 0 0
HUS1 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 0.026 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.1 0.14 -10000 0 -0.51 1 1
NR2F2 0.004 0.035 -10000 0 -0.42 1 1
MAPK3 0.006 0.017 -10000 0 -10000 0 0
MAPK1 0.006 0.017 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.006 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
HNRNPC 0.026 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.011 -10000 0 -10000 0 0
NBN 0.022 0.01 -10000 0 -10000 0 0
EGFR 0.025 0.073 0.29 6 -0.41 5 11
mol:Oestrogen 0.002 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.043 0.062 0.21 13 -0.29 5 18
MYC 0.004 0.096 -10000 0 -0.42 13 13
IL2 0.029 0.015 -10000 0 -10000 0 0
KU 0.037 0.01 -10000 0 -10000 0 0
RAD50 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.006 -10000 0 -10000 0 0
TRF2/BLM 0.041 0.03 0.2 7 -10000 0 7
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.12 0.13 -10000 0 -0.53 1 1
SP1/HDAC2 0.057 0.028 -10000 0 -10000 0 0
PINX1 0.022 0.01 -10000 0 -10000 0 0
Telomerase/EST1A 0.099 0.12 -10000 0 -0.52 1 1
Smad3/Myc 0.006 0.06 -10000 0 -0.25 13 13
911 complex 0.046 0.029 0.2 4 -10000 0 4
IFNG 0.074 0.097 0.28 48 -10000 0 48
Telomerase/PinX1 0.086 0.12 -10000 0 -0.51 1 1
Telomerase/AKT1/mTOR/p70S6K 0.049 0.082 -10000 0 -0.28 2 2
SIN3B 0.028 0.004 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
Telomerase/EST1B 0.096 0.11 -10000 0 -0.52 1 1
response to DNA damage stimulus 0 0.025 -10000 0 -0.12 1 1
MRN complex/TRF2/Rap1 0.055 0.035 -10000 0 -10000 0 0
TRF2/WRN 0.032 0.018 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.1 0.11 -10000 0 -0.51 1 1
E2F1 0.089 0.11 0.28 61 -10000 0 61
ZNFX1 0.026 0.008 -10000 0 -10000 0 0
PIF1 0.041 0.068 0.27 18 -0.42 1 19
NCL 0.025 0.007 -10000 0 -10000 0 0
DKC1 0.026 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.065 0.091 0.28 41 -10000 0 41
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.026 0.005 -10000 0 -10000 0 0
CDKN1A -0.005 0.065 -10000 0 -0.42 4 4
PRL-3/alpha Tubulin 0.034 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.05 0.091 -10000 0 -0.31 29 29
AGT -0.025 0.14 0.27 1 -0.42 31 32
CCNA2 -0.029 0.09 0.26 5 -10000 0 5
TUBA1B 0.026 0.004 -10000 0 -10000 0 0
EGR1 -0.051 0.12 -10000 0 -0.29 57 57
CDK2/Cyclin E1 0.046 0.094 0.29 1 -0.39 4 5
MAPK3 0.01 0.004 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.039 0.006 -10000 0 -10000 0 0
MAPK1 0.01 0.004 -10000 0 -10000 0 0
PTP4A1 -0.042 0.084 -10000 0 -10000 0 0
PTP4A3 0.024 0.009 -10000 0 -10000 0 0
PTP4A2 0.027 0 -10000 0 -10000 0 0
ITGB1 0.01 0.005 -10000 0 -10000 0 0
SRC 0.025 0.007 -10000 0 -10000 0 0
RAC1 0 0.036 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.037 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.017 0.098 -10000 0 -10000 0 0
RABGGTA 0.026 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.008 -10000 0 -10000 0 0
RHOC 0.001 0.036 -10000 0 -10000 0 0
RHOA -0.006 0.063 -10000 0 -0.34 6 6
cell motility 0.009 0.072 0.28 2 -0.3 3 5
PRL-1/alpha Tubulin -0.017 0.098 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.034 0.014 -10000 0 -10000 0 0
ROCK1 0.012 0.066 0.28 2 -0.29 2 4
RABGGTB 0.026 0.004 -10000 0 -10000 0 0
CDK2 0.026 0.005 -10000 0 -10000 0 0
mitosis -0.042 0.083 -10000 0 -10000 0 0
ATF5 0.027 0.015 0.27 1 -10000 0 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.016 0.058 0.24 4 -0.31 1 5
adherens junction organization 0.018 0.069 0.22 2 -0.26 8 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.074 0.26 6 -0.3 2 8
FMN1 0.015 0.063 -10000 0 -0.25 9 9
mol:IP3 0.01 0.042 -10000 0 -0.32 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.017 0.068 -10000 0 -0.25 10 10
CTNNB1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.02 0.057 0.18 5 -0.36 1 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.019 0.091 0.26 1 -0.34 10 11
CTNND1 0.027 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.062 -10000 0 -0.24 10 10
VASP 0.012 0.063 -10000 0 -0.25 9 9
ZYX 0.011 0.067 -10000 0 -0.25 11 11
JUB 0.014 0.065 -10000 0 -0.24 10 10
EGFR(dimer) 0.027 0.083 0.24 2 -0.27 9 11
E-cadherin/beta catenin-gamma catenin 0.037 0.057 -10000 0 -0.26 8 8
mol:PI-3-4-5-P3 0.039 0.066 -10000 0 -0.38 1 1
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.04 0.067 -10000 0 -0.38 1 1
FYN 0.007 0.068 0.26 4 -0.25 8 12
mol:Ca2+ 0.009 0.041 -10000 0 -0.31 1 1
JUP 0.024 0.028 -10000 0 -0.41 1 1
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.01 0.042 -10000 0 -0.32 1 1
CDH1 0.012 0.076 -10000 0 -0.42 8 8
RhoA/GDP 0.032 0.073 0.26 5 -0.3 2 7
establishment of polarity of embryonic epithelium 0.013 0.063 -10000 0 -0.24 9 9
SRC 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.005 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
EGFR 0.023 0.073 0.29 6 -0.42 5 11
CASR 0.012 0.056 0.26 5 -0.3 1 6
RhoA/GTP 0.026 0.049 -10000 0 -0.29 1 1
AKT2 0.019 0.055 0.19 2 -0.36 1 3
actin cable formation 0.015 0.064 0.19 5 -0.26 7 12
apoptosis -0.027 0.067 0.34 1 -0.24 7 8
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.012 0.064 0.21 7 -0.32 2 9
PIP5K1A 0.008 0.063 -10000 0 -0.24 10 10
PLCG1 0.01 0.042 -10000 0 -0.32 1 1
Rac1/GTP 0.034 0.081 0.24 1 -0.26 8 9
homophilic cell adhesion 0.001 0.003 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.037 0.06 -9999 0 -0.28 8 8
E-cadherin/beta catenin 0.026 0.058 -9999 0 -0.3 8 8
CTNNB1 0.026 0.005 -9999 0 -10000 0 0
JUP 0.024 0.028 -9999 0 -0.42 1 1
CDH1 0.012 0.076 -9999 0 -0.42 8 8
Retinoic acid receptors-mediated signaling

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
HDAC1 0.027 0.002 -10000 0 -10000 0 0
HDAC3 0.026 0.005 -10000 0 -10000 0 0
VDR 0.026 0.032 0.29 1 -0.42 1 2
Cbp/p300/PCAF 0.047 0.019 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.009 0.066 -10000 0 -0.27 7 7
KAT2B 0.025 0.006 -10000 0 -10000 0 0
MAPK14 0.027 0.002 -10000 0 -10000 0 0
AKT1 0.01 0.082 0.21 11 -0.22 16 27
RAR alpha/9cRA/Cyclin H 0.046 0.06 -10000 0 -0.35 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.003 0.075 -10000 0 -0.28 7 7
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.028 0.051 -10000 0 -0.39 3 3
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.019 -10000 0 -0.29 1 1
RXRs/RARs/NRIP1/9cRA 0.008 0.093 0.34 2 -0.56 1 3
NCOA2 0.003 0.092 -10000 0 -0.42 12 12
NCOA3 0.025 0.007 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.032 0.29 1 -0.42 1 2
RARG 0.027 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.036 0.006 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
MAPK1 0.026 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.047 -10000 0 -0.42 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.013 0.072 -10000 0 -0.4 1 1
RARA 0.015 0.036 0.19 2 -0.26 3 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.006 0.087 -10000 0 -0.34 8 8
PRKCA 0.028 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.004 0.097 0.29 2 -0.45 2 4
RXRG -0.058 0.13 0.23 1 -0.28 66 67
RXRA 0.022 0.045 0.17 1 -0.23 3 4
RXRB 0.022 0.023 0.23 2 -10000 0 2
VDR/Vit D3/DNA 0.018 0.019 -10000 0 -0.29 1 1
RBP1 0.008 0.09 0.27 1 -0.42 11 12
CRBP1/9-cic-RA 0.007 0.064 0.18 1 -0.29 11 12
RARB -0.009 0.12 -10000 0 -0.42 21 21
PRKCG 0.03 0.041 0.28 7 -10000 0 7
MNAT1 0.026 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.002 0.084 0.3 1 -0.61 1 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.012 0.086 0.25 1 -0.41 2 3
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.081 0.25 4 -0.33 4 8
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.098 0.29 2 -0.46 2 4
positive regulation of DNA binding 0.034 0.052 -10000 0 -0.34 1 1
NRIP1 0.004 0.095 -10000 0 -0.47 1 1
RXRs/RARs -0.001 0.098 -10000 0 -0.39 5 5
RXRs/RXRs/DNA/9cRA -0.005 0.059 -10000 0 -0.41 1 1
PRKACA 0.026 0.003 -10000 0 -10000 0 0
CDK7 0.025 0.006 -10000 0 -10000 0 0
TFIIH 0.051 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.058 0.044 -10000 0 -0.27 1 1
CCNH 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.016 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.027 0.022 0.27 2 -10000 0 2
Rac1/GDP 0.024 0.013 -10000 0 -10000 0 0
DOCK1 0.024 0.028 -10000 0 -0.42 1 1
ITGA4 0.012 0.082 0.27 1 -0.42 9 10
RAC1 0.026 0.005 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.022 0.074 0.2 1 -0.3 13 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.04 0.058 -10000 0 -0.25 9 9
alpha4/beta7 Integrin/Paxillin 0.029 0.061 0.19 1 -0.23 13 14
lamellipodium assembly 0.004 0.079 -10000 0 -0.39 6 6
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.013 -10000 0 -10000 0 0
ARF6 0.026 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.009 -10000 0 -10000 0 0
PXN 0.012 0.002 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.039 0.051 -10000 0 -0.2 9 9
cell adhesion 0.038 0.053 -10000 0 -0.21 9 9
CRKL/CBL 0.037 0.019 0.2 2 -10000 0 2
alpha4/beta1 Integrin/Paxillin 0.031 0.052 0.19 1 -0.23 9 10
ITGB1 0.025 0.006 -10000 0 -10000 0 0
ITGB7 0.019 0.054 -10000 0 -0.42 4 4
ARF6/GDP 0.024 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.033 0.082 -10000 0 -0.27 16 16
p130Cas/Crk/Dock1 0.044 0.028 -10000 0 -0.25 1 1
VCAM1 0.008 0.089 -10000 0 -0.42 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.039 0.054 -10000 0 -0.21 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.041 0.054 -10000 0 -0.22 9 9
BCAR1 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.039 0.053 0.22 9 -10000 0 9
CBL 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GIT1 0.025 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.039 0.054 -10000 0 -0.21 9 9
Rac1/GTP 0.004 0.086 -10000 0 -0.43 6 6
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.12 0.12 -10000 0 -0.34 24 24
CaM/Ca2+ 0.019 0.003 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.025 0.006 -10000 0 -10000 0 0
STXBP4 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.13 0.12 0.23 1 -0.37 24 25
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
CALM1 0.026 0.004 -10000 0 -10000 0 0
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
TBC1D4 0.011 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.025 0.006 -10000 0 -10000 0 0
YWHAB 0.024 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.046 0.02 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
ASIP 0.013 0.035 0.28 3 -10000 0 3
PRKCI 0.025 0.006 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.003 -10000 0 -10000 0 0
RHOQ 0.026 0.005 -10000 0 -10000 0 0
GYS1 0.01 0.015 0.24 1 -10000 0 1
PRKCZ 0.025 0.027 -10000 0 -0.42 1 1
TRIP10 0.024 0.028 -10000 0 -0.42 1 1
TC10/GTP/CIP4/Exocyst 0.033 0.018 -10000 0 -0.23 1 1
AS160/14-3-3 0.029 0.059 0.25 1 -0.29 2 3
VAMP2 0.024 0.008 -10000 0 -10000 0 0
SLC2A4 -0.14 0.13 -10000 0 -0.41 24 24
STX4 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.018 0.007 -10000 0 -10000 0 0
SFN 0.046 0.082 0.27 25 -0.42 2 27
LNPEP 0.026 0.005 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.021 0.065 -10000 0 -10000 0 0
PLK1 0.16 0.17 0.57 4 -10000 0 4
CDKN1B 0.13 0.12 0.38 4 -0.33 4 8
FOXO3 0.14 0.15 0.43 10 -10000 0 10
KAT2B 0.044 0.028 -10000 0 -10000 0 0
FOXO1/SIRT1 0.025 0.047 -10000 0 -10000 0 0
CAT 0.13 0.14 0.5 1 -10000 0 1
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.048 0.028 -10000 0 -10000 0 0
FOXO1 0.019 0.054 -10000 0 -10000 0 0
MAPK10 0.014 0.072 0.2 9 -0.2 22 31
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.049 0.068 0.28 1 -10000 0 1
response to oxidative stress 0.025 0.022 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.14 0.12 0.39 9 -10000 0 9
XPO1 0.026 0.005 -10000 0 -10000 0 0
EP300 0.028 0.008 -10000 0 -10000 0 0
BCL2L11 0.05 0.066 -10000 0 -0.56 2 2
FOXO1/SKP2 0.03 0.056 0.3 1 -10000 0 1
mol:GDP 0.025 0.022 -10000 0 -10000 0 0
RAN 0.027 0.004 -10000 0 -10000 0 0
GADD45A 0.12 0.1 0.38 1 -10000 0 1
YWHAQ 0.026 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.11 -10000 0 -0.49 6 6
MST1 0.054 0.061 0.28 11 -0.37 1 12
CSNK1D 0.026 0.005 -10000 0 -10000 0 0
CSNK1E 0.026 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.035 0.092 -10000 0 -0.47 4 4
YWHAB 0.024 0.008 -10000 0 -10000 0 0
MAPK8 0.031 0.043 0.2 10 -0.2 3 13
MAPK9 0.033 0.035 0.2 10 -10000 0 10
YWHAG 0.026 0.004 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
YWHAZ 0.02 0.011 -10000 0 -10000 0 0
SIRT1 0.023 0.023 -10000 0 -10000 0 0
SOD2 0.12 0.12 0.45 2 -0.39 1 3
RBL2 0.11 0.17 -10000 0 -0.62 7 7
RAL/GDP 0.053 0.021 -10000 0 -10000 0 0
CHUK 0.045 0.029 -10000 0 -10000 0 0
Ran/GTP 0.022 0.003 -10000 0 -10000 0 0
CSNK1G2 0.026 0.005 -10000 0 -10000 0 0
RAL/GTP 0.055 0.02 -10000 0 -10000 0 0
CSNK1G1 0.026 0.004 -10000 0 -10000 0 0
FASLG -0.015 0.32 -10000 0 -1.3 15 15
SKP2 0.028 0.036 0.28 5 -10000 0 5
USP7 0.026 0.007 -10000 0 -10000 0 0
IKBKB 0.041 0.03 -10000 0 -10000 0 0
CCNB1 0.15 0.16 0.55 2 -10000 0 2
FOXO1-3a-4/beta catenin 0.13 0.11 0.38 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.056 0.3 1 -10000 0 1
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.026 0.09 -10000 0 -0.4 10 10
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0.01 -10000 0 -10000 0 0
ZFAND5 0.046 0.063 -10000 0 -10000 0 0
SFN 0.046 0.082 0.27 25 -0.42 2 27
CDK2 0.028 0.009 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.061 0.09 -10000 0 -0.42 3 3
CREBBP 0.026 0.011 -10000 0 -10000 0 0
FBXO32 0.16 0.16 0.53 12 -10000 0 12
BCL6 0.13 0.12 -10000 0 -10000 0 0
RALB 0.027 0.004 -10000 0 -10000 0 0
RALA 0.027 0.005 -10000 0 -10000 0 0
YWHAH 0.025 0.006 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.015 0.023 -10000 0 -10000 0 0
TRAF2/ASK1 0.031 0.013 -10000 0 -10000 0 0
ATM 0.025 0.007 -10000 0 -10000 0 0
MAP2K3 0 0.098 -10000 0 -0.33 14 14
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.07 0.21 2 -0.26 3 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.016 0.061 -10000 0 -0.42 5 5
TXN 0.007 0.006 0.099 1 -10000 0 1
CALM1 0.026 0.004 -10000 0 -10000 0 0
GADD45A 0.027 0.002 -10000 0 -10000 0 0
GADD45B 0.014 0.072 -10000 0 -0.42 7 7
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
MAP3K6 0.027 0 -10000 0 -10000 0 0
MAP3K7 0.025 0.006 -10000 0 -10000 0 0
MAP3K4 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.009 -10000 0 -10000 0 0
TAK1/TAB family -0.003 0.016 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.048 0.017 0.19 1 -10000 0 1
TRAF2 0.024 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.018 0.086 -10000 0 -0.26 13 13
TRAF6 0.006 0.002 -10000 0 -10000 0 0
RAC1 0.026 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.05 0.076 0.27 28 -10000 0 28
CCM2 0.027 0.015 0.27 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.05 0.046 0.18 27 -10000 0 27
MAPK11 0.025 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.062 0.046 0.19 27 -10000 0 27
OSM/MEKK3 0.038 0.014 0.2 1 -10000 0 1
TAOK1 0.011 0.019 -10000 0 -0.28 1 1
TAOK2 0.012 0.005 -10000 0 -10000 0 0
TAOK3 0.013 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.002 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.025 0.006 -10000 0 -10000 0 0
MAP3K10 0.027 0.017 0.29 1 -10000 0 1
MAP3K3 0.026 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.014 0.033 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.043 0.062 -10000 0 -0.23 11 11
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.056 0.082 0.28 5 -0.32 2 7
ERC1 0.026 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.043 0.047 0.2 18 -10000 0 18
NFKBIA 0.01 0.018 0.21 2 -10000 0 2
BIRC2 0.027 0.024 0.29 2 -10000 0 2
IKBKB 0.024 0.009 -10000 0 -10000 0 0
RIPK2 0.022 0.01 -10000 0 -10000 0 0
IKBKG 0.037 0.045 -10000 0 -10000 0 0
IKK complex/A20 0.063 0.089 0.3 4 -0.37 2 6
NEMO/A20/RIP2 0.022 0.01 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.049 0.079 0.27 1 -0.33 6 7
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.034 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.046 0.072 -10000 0 -0.35 2 2
BCL10/MALT1/TRAF6 0.047 0.019 -10000 0 -10000 0 0
NOD2 0.042 0.071 0.27 20 -0.42 1 21
NFKB1 0.028 0.003 -10000 0 -10000 0 0
RELA 0.028 0.004 -10000 0 -10000 0 0
MALT1 0.025 0.006 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.036 0.011 -10000 0 -10000 0 0
ATM 0.025 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.046 0.037 0.2 13 -10000 0 13
TRAF6 0.025 0.007 -10000 0 -10000 0 0
PRKCA 0.026 0.005 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
UBE2D3 0.026 0.003 -10000 0 -10000 0 0
TNF 0.038 0.053 0.27 13 -10000 0 13
NF kappa B1 p50/RelA 0.057 0.016 -10000 0 -10000 0 0
BCL10 0.026 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.018 0.21 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
IKK complex 0.053 0.079 -10000 0 -0.34 3 3
CYLD 0.026 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.06 0.079 -10000 0 -0.36 2 2
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 0.06 0.037 -10000 0 -0.23 3 3
HDAC3 0.026 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 0.034 0.011 -10000 0 -10000 0 0
GATA1/HDAC5 0.036 0.008 -10000 0 -10000 0 0
GATA2/HDAC5 0.035 0.048 0.2 5 -0.3 4 9
HDAC5/BCL6/BCoR 0.049 0.016 -10000 0 -10000 0 0
HDAC9 -0.002 0.11 -10000 0 -0.42 16 16
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.047 -10000 0 -0.25 6 6
HDAC4/ANKRA2 0.035 0.013 -10000 0 -10000 0 0
HDAC5/YWHAB 0.035 0.013 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.004 -10000 0 -10000 0 0
GATA2 0.026 0.068 0.27 7 -0.42 4 11
HDAC4/RFXANK 0.036 0.016 0.2 1 -10000 0 1
BCOR 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.025 0.006 -10000 0 -10000 0 0
HDAC5 0.026 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.035 0.036 -10000 0 -0.3 3 3
Histones 0.004 0.067 -10000 0 -0.27 4 4
ADRBK1 0.026 0.005 -10000 0 -10000 0 0
HDAC4 0.025 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.037 0.011 -10000 0 -10000 0 0
HDAC4/Ubc9 0.035 0.012 -10000 0 -10000 0 0
HDAC7 0.026 0.004 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.035 0.013 -10000 0 -10000 0 0
TUBA1B 0.026 0.004 -10000 0 -10000 0 0
HDAC6 0.026 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.038 0.014 0.2 1 -10000 0 1
CAMK4 0.016 0.068 0.27 1 -0.42 6 7
Tubulin/HDAC6 0.049 0.024 -10000 0 -0.25 1 1
SUMO1 0.026 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.024 0.008 -10000 0 -10000 0 0
GATA1 0.013 0.02 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.024 0.008 -10000 0 -10000 0 0
NR3C1 0.016 0.066 -10000 0 -0.42 6 6
SUMO1/HDAC4 0.031 0.047 -10000 0 -0.22 5 5
SRF 0.026 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.015 -10000 0 -10000 0 0
Tubulin 0.036 0.023 -10000 0 -0.3 1 1
HDAC4/14-3-3 E 0.033 0.015 -10000 0 -10000 0 0
GNB1 0.027 0.002 -10000 0 -10000 0 0
RANGAP1 0.026 0.005 -10000 0 -10000 0 0
BCL6/BCoR 0.037 0.01 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.048 0.018 -10000 0 -10000 0 0
HDAC4/SRF 0.04 0.049 -10000 0 -0.25 6 6
HDAC4/ER alpha -0.017 0.12 -10000 0 -0.3 42 42
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.004 0.067 -10000 0 -0.27 4 4
cell motility 0.049 0.023 -10000 0 -0.25 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.038 0.009 -10000 0 -10000 0 0
BCL6 0.025 0.006 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.024 0.007 -10000 0 -10000 0 0
Hsp90/HDAC6 0.038 0.008 -10000 0 -10000 0 0
ESR1 -0.045 0.16 -10000 0 -0.42 42 42
HDAC6/HDAC11 0.034 0.024 -10000 0 -0.3 1 1
Ran/GTP/Exportin 1 0.029 0.049 -10000 0 -0.2 6 6
NPC 0.016 0.002 -10000 0 -10000 0 0
MEF2C 0.021 0.047 -10000 0 -0.42 3 3
RAN 0.026 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.064 0.043 -10000 0 -0.22 3 3
GNG2 0.021 0.047 -10000 0 -0.42 3 3
NCOR2 0.026 0.004 -10000 0 -10000 0 0
TUBB2A 0.024 0.028 -10000 0 -0.42 1 1
HDAC11 0.023 0.033 0.29 1 -0.42 1 2
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
RANBP2 0.026 0.004 -10000 0 -10000 0 0
ANKRA2 0.025 0.006 -10000 0 -10000 0 0
RFXANK 0.027 0.015 0.27 1 -10000 0 1
nuclear import -0.026 0.018 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.036 0.05 0.27 11 -10000 0 11
positive regulation of NF-kappaB transcription factor activity 0.027 0.049 0.2 4 -0.3 4 8
MAP2K4 0.019 0.049 0.24 3 -10000 0 3
IKBKB 0.024 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.021 0.011 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.029 -10000 0 -0.42 1 1
SMPD1 0.011 0.012 0.15 1 -10000 0 1
IKBKG 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.014 0.055 -10000 0 -0.42 4 4
TRAIL/TRAILR2 0.032 0.028 0.2 4 -10000 0 4
TRAIL/TRAILR3 0.032 0.037 0.2 6 -0.3 1 7
TRAIL/TRAILR1 0.031 0.034 0.2 4 -0.3 1 5
TRAIL/TRAILR4 0.027 0.049 0.2 4 -0.3 4 8
TRAIL/TRAILR1/DAP3/GTP 0.039 0.032 0.19 5 -10000 0 5
IKK complex 0.013 0.046 -10000 0 -10000 0 0
RIPK1 0.025 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.018 0.005 -10000 0 -10000 0 0
MAPK3 0.016 0.03 0.29 2 -10000 0 2
MAP3K1 0.023 0.041 0.28 1 -0.22 1 2
TRAILR4 (trimer) 0.014 0.055 -10000 0 -0.42 4 4
TRADD 0.025 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.029 -10000 0 -0.42 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.017 0.035 -10000 0 -0.21 1 1
CFLAR 0.026 0.006 -10000 0 -10000 0 0
MAPK1 0.015 0.028 0.29 2 -10000 0 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.054 0.05 -10000 0 -0.22 1 1
mol:ceramide 0.011 0.012 0.15 1 -10000 0 1
FADD 0.029 0.037 0.29 5 -10000 0 5
MAPK8 0.015 0.06 0.25 3 -10000 0 3
TRAF2 0.024 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.021 0.036 0.27 2 -0.42 1 3
CHUK 0.026 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.038 0.037 0.2 4 -0.25 1 5
DAP3 0.025 0.007 -10000 0 -10000 0 0
CASP10 0.026 0.061 0.23 10 -10000 0 10
JNK cascade 0.027 0.049 0.2 4 -0.3 4 8
TRAIL (trimer) 0.036 0.05 0.27 11 -10000 0 11
TNFRSF10C 0.021 0.036 0.27 2 -0.42 1 3
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.042 0.2 5 -10000 0 5
TRAIL/TRAILR2/FADD 0.039 0.033 0.2 4 -10000 0 4
cell death 0.011 0.012 0.15 1 -10000 0 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.017 0.034 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.021 0.011 -10000 0 -10000 0 0
CASP8 -0.017 0.13 -10000 0 -0.58 13 13
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.055 0.048 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.027 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.009 -10000 0 -10000 0 0
MDM2/SUMO1 0.033 0.059 -10000 0 -0.21 6 6
HDAC4 0.025 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.009 0.01 -10000 0 -10000 0 0
SUMO1 0.026 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.024 -10000 0 -0.22 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.026 -10000 0 -0.22 3 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.031 0.047 -10000 0 -0.22 5 5
SUMO1/HDAC1 0.03 0.051 -10000 0 -0.21 6 6
RANGAP1 0.026 0.005 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.063 0.037 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.004 -10000 0 -10000 0 0
Ran/GTP 0.017 0.046 -10000 0 -0.19 9 9
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.046 0.29 8 -10000 0 8
UBE2I 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.02 0.056 0.2 9 -0.2 6 15
NPC 0.016 0.002 -10000 0 -10000 0 0
PIAS2 0.025 0.006 -10000 0 -10000 0 0
PIAS1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.025 0.007 -10000 0 -10000 0 0
SMAD2 0.003 0.053 0.21 3 -0.24 5 8
SMAD3 0.023 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.037 -10000 0 -0.36 1 1
SMAD4/Ubc9/PIASy 0.048 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.059 -10000 0 -0.29 1 1
PPM1A 0.026 0.004 -10000 0 -10000 0 0
CALM1 0.026 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.014 0.051 -10000 0 -0.22 6 6
MAP3K1 0.025 0.006 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.032 0.042 -10000 0 -0.29 4 4
MAPK3 0.025 0.006 -10000 0 -10000 0 0
MAPK1 0.026 0.005 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
CTDSP1 0.025 0.006 -10000 0 -10000 0 0
CTDSP2 0.026 0.004 -10000 0 -10000 0 0
CTDSPL 0.025 0.006 -10000 0 -10000 0 0
KPNB1 0.026 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.02 0.054 -10000 0 -0.42 4 4
UBE2I 0.026 0.006 -10000 0 -10000 0 0
NUP153 0.025 0.007 -10000 0 -10000 0 0
KPNA2 0.028 0.022 0.28 2 -10000 0 2
PIAS4 0.026 0.005 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.026 0.006 -10000 0 -9999 0 0
PLK4 0.031 0.033 0.27 5 -9999 0 5
regulation of centriole replication 0.013 0.014 -10000 0 -9999 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.022 0.016 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.007 -10000 0 -10000 0 0
myoblast fusion -0.023 0.025 -10000 0 -10000 0 0
mol:GTP 0.019 0.02 -10000 0 -0.15 3 3
regulation of calcium-dependent cell-cell adhesion -0.05 0.033 0.23 1 -10000 0 1
ARF1/GTP 0.034 0.02 -10000 0 -10000 0 0
mol:GM1 0.009 0.014 -10000 0 -10000 0 0
mol:Choline 0.008 0.008 -10000 0 -10000 0 0
lamellipodium assembly 0.012 0.045 -10000 0 -0.35 3 3
MAPK3 0.022 0.015 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.051 0.033 -10000 0 -0.23 1 1
ARF1 0.026 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.023 0.025 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.038 -10000 0 -0.2 3 3
ARF6 0.032 0.009 -10000 0 -10000 0 0
RAB11A 0.026 0.004 -10000 0 -10000 0 0
TIAM1 0.025 0.028 -10000 0 -0.42 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.013 -10000 0 -10000 0 0
actin filament bundle formation -0.033 0.033 0.2 2 -10000 0 2
KALRN 0.011 0.024 -10000 0 -0.22 2 2
RAB11FIP3/RAB11A 0.038 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.033 0.033 -10000 0 -0.21 2 2
NME1 0.028 0.016 0.27 1 -10000 0 1
Rac1/GDP 0.033 0.035 -10000 0 -0.21 3 3
substrate adhesion-dependent cell spreading 0.019 0.02 -10000 0 -0.15 3 3
cortical actin cytoskeleton organization 0.012 0.046 -10000 0 -0.35 3 3
RAC1 0.026 0.005 -10000 0 -10000 0 0
liver development 0.019 0.02 -10000 0 -0.15 3 3
ARF6/GTP 0.019 0.02 -10000 0 -0.15 3 3
RhoA/GTP 0.033 0.02 -10000 0 -10000 0 0
mol:GDP 0.011 0.022 -10000 0 -0.2 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.048 0.022 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
PLD1 0.017 0.018 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.012 0.045 -10000 0 -0.35 3 3
ruffle organization 0.01 0.007 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.019 0.02 -10000 0 -0.15 3 3
PLD2 0.018 0.011 -10000 0 -10000 0 0
PIP5K1A 0.01 0.007 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.012 0.046 -10000 0 -0.35 3 3
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.06 0.054 0.24 1 -10000 0 1
Ran/GTP/Exportin 1/HDAC1 -0.009 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.056 -10000 0 -10000 0 0
SUMO1 0.026 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.004 -10000 0 -10000 0 0
FKBP3 0.026 0.004 -10000 0 -10000 0 0
Histones 0.055 0.05 -10000 0 -10000 0 0
YY1/LSF 0.022 0.052 -10000 0 -0.21 6 6
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.026 0.016 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.029 0.046 -10000 0 -10000 0 0
SAP18 0.026 0.005 -10000 0 -10000 0 0
RELA 0.026 0.025 -10000 0 -10000 0 0
HDAC1/Smad7 0.05 0.016 -10000 0 -10000 0 0
RANGAP1 0.026 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.031 0.044 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.026 0.047 -10000 0 -0.25 2 2
NF kappa B1 p50/RelA 0.023 0.064 -10000 0 -0.22 6 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.026 0.068 0.27 7 -0.42 4 11
GATA1 0.013 0.02 -10000 0 -10000 0 0
Mad/Max 0.038 0.014 0.2 1 -10000 0 1
NuRD/MBD3 Complex/GATA1/Fog1 0.029 0.048 -10000 0 -10000 0 0
RBBP7 0.027 0.002 -10000 0 -10000 0 0
NPC 0.016 0.002 -10000 0 -10000 0 0
RBBP4 0.027 0.002 -10000 0 -10000 0 0
MAX 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.025 0.006 -10000 0 -10000 0 0
NFKBIA 0.022 0.012 -10000 0 -10000 0 0
KAT2B 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.036 -10000 0 -0.36 2 2
SIN3 complex 0.063 0.02 -10000 0 -10000 0 0
SMURF1 0.026 0.004 -10000 0 -10000 0 0
CHD3 0.024 0.008 -10000 0 -10000 0 0
SAP30 0.025 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.023 0.009 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.047 -10000 0 -10000 0 0
YY1/HDAC2 0.022 0.05 -10000 0 -0.2 6 6
YY1/HDAC1 0.022 0.052 -10000 0 -0.21 6 6
NuRD/MBD2 Complex (MeCP1) 0.02 0.054 -10000 0 -0.25 3 3
PPARG 0.001 0.076 -10000 0 -0.26 15 15
HDAC8/hEST1B 0.049 0.016 -10000 0 -10000 0 0
UBE2I 0.026 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.026 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.044 -10000 0 -10000 0 0
MBD3L2 -0.017 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.016 -10000 0 -10000 0 0
CREBBP 0.025 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.025 0.062 -10000 0 -0.3 4 4
HDAC1 0.027 0.002 -10000 0 -10000 0 0
HDAC3 0.023 0.012 -10000 0 -10000 0 0
HDAC2 0.025 0.006 -10000 0 -10000 0 0
YY1 0.016 0.007 -10000 0 -10000 0 0
HDAC8 0.026 0.003 -10000 0 -10000 0 0
SMAD7 0.025 0.006 -10000 0 -10000 0 0
NCOR2 0.026 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.016 0.27 1 -10000 0 1
STAT3 0.018 0.007 -10000 0 -10000 0 0
NFKB1 0.026 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.035 0.053 -10000 0 -0.19 6 6
YY1/SAP30/HDAC1 0.035 0.053 -10000 0 -0.19 5 5
EP300 0.026 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.012 -10000 0 -10000 0 0
histone deacetylation 0.02 0.054 -10000 0 -0.24 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.035 -10000 0 -0.2 3 3
nuclear export -0.049 0.016 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
GATAD2B 0.024 0.008 -10000 0 -10000 0 0
GATAD2A 0.026 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.028 0.061 0.2 5 -0.23 5 10
GATA1/HDAC1 0.037 0.006 -10000 0 -10000 0 0
GATA1/HDAC3 0.028 0.045 -10000 0 -10000 0 0
CHD4 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.046 0.037 0.2 13 -10000 0 13
SIN3/HDAC complex/Mad/Max 0.022 0.052 -10000 0 -0.35 3 3
NuRD Complex 0.025 0.054 -10000 0 -0.3 1 1
positive regulation of chromatin silencing 0.053 0.049 -10000 0 -10000 0 0
SIN3B 0.026 0.003 -10000 0 -10000 0 0
MTA2 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.051 -10000 0 -0.21 6 6
HDAC complex 0.065 0.017 -10000 0 -10000 0 0
GATA1/Fog1 0.036 0.009 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.05 0.014 -10000 0 -10000 0 0
TNF 0.038 0.053 0.27 13 -10000 0 13
negative regulation of cell growth 0.022 0.052 -10000 0 -0.35 3 3
NuRD/MBD2/PRMT5 Complex 0.02 0.054 -10000 0 -0.25 3 3
Ran/GTP/Exportin 1 0.029 0.049 -10000 0 -0.2 6 6
NF kappa B/RelA/I kappa B alpha 0.02 0.04 -10000 0 -0.22 1 1
SIN3/HDAC complex/NCoR1 0.01 0.053 -10000 0 -0.29 3 3
TFCP2 0.026 0.004 -10000 0 -10000 0 0
NR2C1 0.026 0.004 -10000 0 -10000 0 0
MBD3 0.026 0.005 -10000 0 -10000 0 0
MBD2 0.025 0.006 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.036 0.023 -10000 0 -0.3 1 1
FBXW11 0.025 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.023 0.19 1 -0.25 1 2
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.05 -10000 0 -10000 0 0
NFKBIA 0.013 0.043 -10000 0 -0.21 6 6
MAPK14 0.027 0.002 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.024 0.011 -10000 0 -10000 0 0
ARRB2 0.012 0.004 -10000 0 -10000 0 0
REL 0.025 0.032 0.27 1 -0.42 1 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.024 0.019 -10000 0 -0.23 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0.01 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
NFKB1 0.011 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.019 0.04 -10000 0 -0.18 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.021 0.054 -10000 0 -0.2 3 3
SRC 0.025 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.013 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.019 0.04 -10000 0 -0.19 5 5
IKBKB 0.024 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.006 -10000 0 -10000 0 0
SYK 0.021 0.039 -10000 0 -0.42 2 2
I kappa B alpha/PIK3R1 0.021 0.054 -10000 0 -0.28 1 1
cell death 0.02 0.052 -10000 0 -0.19 3 3
NF kappa B1 p105/c-Rel 0.024 0.023 0.19 1 -0.25 1 2
LCK 0.021 0.056 0.27 1 -0.42 4 5
BCL3 0.024 0.028 -10000 0 -0.42 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.001 0.1 -10000 0 -0.3 28 28
AKT1 0.041 0.072 0.28 1 -0.38 1 2
PTK2B -0.001 0.075 -10000 0 -0.28 1 1
VEGFR2 homodimer/Frs2 0.034 0.028 -10000 0 -10000 0 0
CAV1 0.008 0.089 -10000 0 -0.42 11 11
CALM1 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.047 0.031 -10000 0 -10000 0 0
endothelial cell proliferation 0.021 0.11 0.34 5 -0.34 2 7
mol:Ca2+ 0.023 0.038 -10000 0 -0.22 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.058 0.025 -10000 0 -10000 0 0
RP11-342D11.1 0.014 0.037 -10000 0 -0.22 1 1
CDH5 0.024 0.028 -10000 0 -0.42 1 1
VEGFA homodimer 0.053 0.03 -10000 0 -10000 0 0
SHC1 0.025 0.018 0.29 1 -10000 0 1
SHC2 0.003 0.1 0.27 1 -0.42 14 15
HRAS/GDP 0.038 0.026 -10000 0 -10000 0 0
SH2D2A 0.028 0.027 0.27 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.054 0.074 -10000 0 -0.45 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.046 0.026 -10000 0 -10000 0 0
VEGFR1 homodimer 0.026 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.069 0.039 -10000 0 -10000 0 0
GRB10 0.022 0.043 -10000 0 -0.45 1 1
PTPN11 0.026 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.005 -10000 0 -10000 0 0
PAK1 0.023 0.028 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.068 0.033 -10000 0 -10000 0 0
HRAS 0.025 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.07 -10000 0 -0.31 3 3
HIF1A 0.027 0.015 0.27 1 -10000 0 1
FRS2 0.03 0.037 0.29 5 -10000 0 5
oxygen and reactive oxygen species metabolic process 0.056 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.025 0.006 -10000 0 -10000 0 0
Nck/Pak 0.035 0.024 -10000 0 -0.3 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.041 0.035 -10000 0 -0.22 3 3
mol:GDP 0.052 0.031 -10000 0 -10000 0 0
mol:NADP 0.041 0.078 0.29 1 -0.43 2 3
eNOS/Hsp90 0.052 0.075 0.29 1 -0.41 2 3
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
mol:IP3 0.023 0.038 -10000 0 -10000 0 0
HIF1A/ARNT 0.034 0.014 -10000 0 -10000 0 0
SHB 0.023 0.009 -10000 0 -10000 0 0
VEGFA 0.027 0.008 -10000 0 -10000 0 0
VEGFC 0.024 0.028 -10000 0 -0.42 1 1
FAK1/Vinculin 0.022 0.086 0.28 1 -0.39 1 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.031 0.083 -10000 0 -0.28 2 2
PTPN6 0.026 0.005 -10000 0 -10000 0 0
EPAS1 0.033 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.041 0.078 0.29 1 -0.43 2 3
ITGAV 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.058 0.035 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.049 0.024 -10000 0 -0.24 1 1
VEGFR2/3 heterodimer 0.031 0.012 -10000 0 -10000 0 0
VEGFB 0.026 0.003 -10000 0 -10000 0 0
MAPK11 0.015 0.049 0.25 1 -0.25 1 2
VEGFR2 homodimer 0.019 0.005 -10000 0 -10000 0 0
FLT1 0.026 0.005 -10000 0 -10000 0 0
NEDD4 0.027 0.007 -10000 0 -10000 0 0
MAPK3 -0.002 0.075 0.24 5 -0.3 1 6
MAPK1 -0.001 0.075 0.24 6 -0.3 1 7
VEGFA145/NRP2 0.024 0.068 -10000 0 -0.3 11 11
VEGFR1/2 heterodimer 0.032 0.011 -10000 0 -10000 0 0
KDR 0.019 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.038 0.058 -10000 0 -0.4 1 1
SRC 0.025 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.005 0.078 0.24 6 -0.31 1 7
PI3K 0.039 0.037 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.045 0.02 -10000 0 -10000 0 0
FES 0.025 0.038 -10000 0 -10000 0 0
GAB1 0.04 0.04 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.021 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
SOS1 0.026 0.004 -10000 0 -10000 0 0
ARNT 0.023 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.044 0.08 0.29 1 -0.41 2 3
VEGFR2 homodimer/VEGFA homodimer/Yes 0.043 0.022 -10000 0 -10000 0 0
PI3K/GAB1 0.041 0.063 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.066 0.046 -10000 0 -10000 0 0
PRKACA 0.026 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.024 -10000 0 -0.21 1 1
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.038 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.046 0.026 -10000 0 -10000 0 0
PTK2 0.006 0.068 -10000 0 -0.41 1 1
EDG1 0.014 0.037 -10000 0 -0.22 1 1
mol:DAG 0.023 0.038 -10000 0 -10000 0 0
CaM/Ca2+ 0.038 0.041 -10000 0 -10000 0 0
MAP2K3 0.005 0.045 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.051 0.045 -10000 0 -0.46 1 1
PLCG1 0.023 0.038 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.049 0.031 -10000 0 -10000 0 0
IQGAP1 0.026 0.004 -10000 0 -10000 0 0
YES1 0.024 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.046 0.019 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.046 0.019 -10000 0 -10000 0 0
cell migration 0.025 0.082 0.29 1 -0.34 1 2
mol:PI-3-4-5-P3 0.038 0.036 -10000 0 -10000 0 0
FYN 0.02 0.047 -10000 0 -0.42 3 3
VEGFB/NRP1 0.029 0.035 -10000 0 -10000 0 0
mol:NO 0.041 0.078 0.29 1 -0.43 2 3
PXN 0.026 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.023 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.038 0.034 -10000 0 -0.45 1 1
VHL 0.024 0.009 -10000 0 -10000 0 0
ITGB3 -0.022 0.14 -10000 0 -0.42 28 28
NOS3 0.042 0.083 0.3 1 -0.48 2 3
VEGFR2 homodimer/VEGFA homodimer/Sck 0.034 0.06 -10000 0 -0.22 12 12
RAC1 0.026 0.005 -10000 0 -10000 0 0
PRKCA 0.005 0.047 -10000 0 -10000 0 0
PRKCB -0.043 0.095 -10000 0 -0.4 1 1
VCL 0.025 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 0.034 0.036 -10000 0 -0.22 1 1
VEGFR1/2 heterodimer/VEGFA homodimer 0.046 0.019 -10000 0 -10000 0 0
VEGFA165/NRP2 0.024 0.068 -10000 0 -0.3 11 11
MAPKKK cascade 0.042 0.056 0.34 1 -0.37 1 2
NRP2 0.007 0.089 -10000 0 -0.42 11 11
VEGFC homodimer 0.024 0.028 -10000 0 -0.42 1 1
NCK1 0.026 0.006 -10000 0 -10000 0 0
ROCK1 0.026 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.023 0.088 0.29 2 -0.39 1 3
MAP3K13 0.023 0.037 -10000 0 -10000 0 0
PDPK1 0.029 0.046 0.26 4 -10000 0 4
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.013 0.005 -10000 0 -10000 0 0
mol:DAG 0.017 0.029 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.009 -10000 0 -10000 0 0
CaM/Ca2+ 0.032 0.028 -10000 0 -10000 0 0
HIF1A 0.033 0.016 0.28 1 -10000 0 1
GAB1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.021 0.044 -10000 0 -10000 0 0
PLCG1 0.017 0.029 -10000 0 -10000 0 0
NOS3 0.028 0.053 0.28 1 -0.34 1 2
CBL 0.025 0.007 -10000 0 -10000 0 0
mol:NO 0.029 0.059 0.29 2 -0.33 1 3
FLT1 0.017 0.007 -10000 0 -10000 0 0
PGF 0.032 0.039 0.27 7 -10000 0 7
VEGFR1 homodimer/NRP2/VEGFR121 0.031 0.056 -10000 0 -0.23 11 11
CALM1 0.026 0.004 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
eNOS/Hsp90 0.042 0.056 0.28 1 -0.33 1 2
endothelial cell proliferation -0.018 0.1 0.32 4 -10000 0 4
mol:Ca2+ 0.017 0.029 -10000 0 -10000 0 0
MAPK3 -0.004 0.034 0.19 1 -10000 0 1
MAPK1 -0.004 0.034 0.19 1 -10000 0 1
PIK3R1 0.025 0.006 -10000 0 -10000 0 0
PLGF homodimer 0.032 0.039 0.27 7 -10000 0 7
PRKACA 0.026 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.008 0.089 -10000 0 -0.42 11 11
VEGFA homodimer 0.026 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.031 0.01 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.006 0.032 -10000 0 -10000 0 0
PI3K 0.056 0.034 -10000 0 -10000 0 0
PRKCA -0.004 0.03 -10000 0 -10000 0 0
PRKCB -0.055 0.096 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.036 0.028 -10000 0 -10000 0 0
VEGFA 0.026 0.005 -10000 0 -10000 0 0
VEGFB 0.026 0.003 -10000 0 -10000 0 0
mol:IP3 0.017 0.029 -10000 0 -10000 0 0
RASA1 0.017 0.03 -10000 0 -10000 0 0
NRP2 0.007 0.089 -10000 0 -0.42 11 11
VEGFR1 homodimer 0.017 0.007 -10000 0 -10000 0 0
VEGFB homodimer 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.034 0.068 0.3 1 -0.33 1 2
PTPN11 0.026 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.054 0.033 -10000 0 -10000 0 0
mol:L-citrulline 0.029 0.059 0.29 2 -0.33 1 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.054 0.023 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.043 0.017 -10000 0 -10000 0 0
CD2AP 0.026 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.067 0.041 -10000 0 -10000 0 0
PDPK1 0.007 0.054 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.043 0.016 -10000 0 -10000 0 0
mol:NADP 0.029 0.059 0.29 2 -0.33 1 3
HSP90AA1 0.026 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.052 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.019 0.057 -10000 0 -0.25 11 11
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 0.032 0.15 12 -10000 0 12
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.028 0.14 2 -10000 0 2
AP2 0.037 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.033 0.012 -10000 0 -10000 0 0
CLTB 0.025 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.015 0.01 -10000 0 -10000 0 0
CD4 0.022 0.039 -10000 0 -0.42 2 2
CLTA 0.024 0.009 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.006 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.028 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.006 -10000 0 -10000 0 0
mol:Choline 0.005 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.029 0.006 -10000 0 -10000 0 0
DDEF1 0.004 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.017 -10000 0 -0.091 4 4
AP2M1 0.025 0.006 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.007 -10000 0 -10000 0 0
Rac/GTP 0.021 0.005 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.014 -10000 0 -10000 0 0
ARFIP2 0.019 0.015 -10000 0 -10000 0 0
COPA 0.023 0.009 -10000 0 -10000 0 0
RAC1 0.026 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.024 0.05 0.14 19 -0.16 6 25
ARF1/GTP/ARHGAP10 0.017 0.008 -10000 0 -10000 0 0
GGA3 0.026 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.021 -10000 0 -0.22 1 1
AP2A1 0.026 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.004 0.039 -10000 0 -0.17 12 12
ARF1/GDP/Membrin 0.03 0.026 -10000 0 -0.25 1 1
Arfaptin 2/Rac/GDP 0.031 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.005 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.037 0.009 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.022 0.036 -10000 0 -0.17 2 2
PLD2 0.005 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.002 -10000 0 -10000 0 0
PIP5K1A 0.006 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.018 0.021 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.002 -10000 0 -10000 0 0
GOSR2 0.009 0.021 -10000 0 -0.31 1 1
USO1 0.009 0.021 -10000 0 -0.31 1 1
GBF1 0.005 0.04 -10000 0 -0.31 4 4
ARF1/GTP/Arfaptin 2 0.034 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.047 0.031 -10000 0 -0.25 2 2
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.048 0.03 -10000 0 -10000 0 0
CLOCK 0.028 0.004 -10000 0 -10000 0 0
TIMELESS/CRY2 0.037 0.022 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.022 0.21 3 -10000 0 3
ATR 0.026 0.005 -10000 0 -10000 0 0
NR1D1 0.019 0.012 -10000 0 -10000 0 0
ARNTL 0.027 0.007 -10000 0 -10000 0 0
TIMELESS 0.02 0.017 -10000 0 -10000 0 0
NPAS2 0.026 0.028 -10000 0 -0.42 1 1
CRY2 0.025 0.007 -10000 0 -10000 0 0
mol:CO -0.008 0.005 -10000 0 -10000 0 0
CHEK1 0.028 0.027 0.27 3 -10000 0 3
mol:HEME 0.008 0.005 -10000 0 -10000 0 0
PER1 0.012 0.071 -10000 0 -0.42 7 7
BMAL/CLOCK/NPAS2 0.056 0.028 -10000 0 -0.25 1 1
BMAL1/CLOCK 0.027 0.038 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.048 0.03 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.049 0.03 -10000 0 -10000 0 0
mol:NADPH 0.008 0.005 -10000 0 -10000 0 0
PER1/TIMELESS 0.028 0.046 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.005 0.038 0.27 4 -10000 0 4
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 0.037 0.01 -9999 0 -9999 0 0
FBXW11 0.025 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.006 -9999 0 -9999 0 0
CHUK 0.026 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.068 0.028 -9999 0 -9999 0 0
NFKB1 0.026 0.003 -9999 0 -9999 0 0
MAP3K14 0.026 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.009 -9999 0 -9999 0 0
RELB 0.026 0.005 -9999 0 -9999 0 0
NFKB2 0.026 0.005 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.033 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.033 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 263 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.YC.A89H TCGA.XF.A8HG TCGA.XF.A8HF TCGA.XF.A8HE
109_MAP3K5 0.025 -0.046 0.16 0.027
47_PPARGC1A -0.42 -0.42 -0.42 0.027
105_BMP4 0.027 0.027 0.027 0.027
105_BMP6 0.027 0.027 0.027 0.027
105_BMP7 0.027 -0.42 0 -0.42
105_BMP2 0.027 0.027 0 0.027
131_RELN/VLDLR -0.23 0 -0.23 0.21
30_TGFB1/TGF beta receptor Type II 0.022 0.026 0.026 0.023
84_STAT5B 0.03 0.14 0.15 0.031
84_STAT5A 0.03 0.14 0.15 0.031
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/BLCA-TP/9827962/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BLCA-TP/10005780/Gistic2_Analysis_10005811/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