PARADIGM pathway analysis of mRNASeq expression and copy number data
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 63 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
Signaling events regulated by Ret tyrosine kinase 92
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 90
Signaling mediated by p38-alpha and p38-beta 82
Endothelins 79
Nongenotropic Androgen signaling 73
IGF1 pathway 73
Reelin signaling pathway 65
IL4-mediated signaling events 64
Signaling events mediated by the Hedgehog family 63
Thromboxane A2 receptor signaling 61
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 408 . 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 ( 408 ).

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
Signaling events regulated by Ret tyrosine kinase 0.2255 92 7565 82 -0.24 0.031 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2206 90 6140 68 -0.68 0.35 1000 -1000 -0.028 -1000
Signaling mediated by p38-alpha and p38-beta 0.2010 82 3645 44 -0.23 0.027 1000 -1000 -0.012 -1000
Endothelins 0.1936 79 7649 96 -0.38 0.089 1000 -1000 -0.039 -1000
Nongenotropic Androgen signaling 0.1789 73 3828 52 -0.26 0.15 1000 -1000 -0.022 -1000
IGF1 pathway 0.1789 73 4177 57 -0.2 0.049 1000 -1000 -0.027 -1000
Reelin signaling pathway 0.1593 65 3658 56 -0.15 0.062 1000 -1000 -0.03 -1000
IL4-mediated signaling events 0.1569 64 5859 91 -0.71 0.51 1000 -1000 -0.038 -1000
Signaling events mediated by the Hedgehog family 0.1544 63 3287 52 -0.14 0.14 1000 -1000 -0.019 -1000
Thromboxane A2 receptor signaling 0.1495 61 6451 105 -0.22 0.049 1000 -1000 -0.027 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1471 60 4682 78 -0.28 0.1 1000 -1000 -0.043 -1000
Aurora B signaling 0.1446 59 3993 67 -0.32 0.24 1000 -1000 -0.027 -1000
p75(NTR)-mediated signaling 0.1348 55 6894 125 -0.11 0.078 1000 -1000 -0.044 -1000
TCGA08_retinoblastoma 0.1250 51 410 8 -0.025 0.11 1000 -1000 -0.005 -1000
Fc-epsilon receptor I signaling in mast cells 0.1225 50 4941 97 -0.13 0.029 1000 -1000 -0.039 -1000
Glypican 2 network 0.1225 50 200 4 0.037 0.093 1000 -1000 0.013 -1000
Plasma membrane estrogen receptor signaling 0.1225 50 4320 86 -0.27 0.15 1000 -1000 -0.04 -1000
LPA receptor mediated events 0.1176 48 4959 102 -0.24 0.068 1000 -1000 -0.057 -1000
Ephrin A reverse signaling 0.1152 47 333 7 -0.057 0.011 1000 -1000 -0.001 -1000
TCR signaling in naïve CD8+ T cells 0.1152 47 4390 93 -0.12 0.05 1000 -1000 -0.035 -1000
Integrins in angiogenesis 0.1103 45 3816 84 -0.23 0.1 1000 -1000 -0.03 -1000
S1P4 pathway 0.1103 45 1132 25 -0.12 0.046 1000 -1000 -0.016 -1000
Calcium signaling in the CD4+ TCR pathway 0.1054 43 1334 31 -0.2 0.026 1000 -1000 -0.03 -1000
Ras signaling in the CD4+ TCR pathway 0.1054 43 743 17 -0.12 0.037 1000 -1000 -0.012 -1000
IL23-mediated signaling events 0.1005 41 2505 60 -0.47 0.037 1000 -1000 -0.067 -1000
Rapid glucocorticoid signaling 0.0980 40 801 20 -0.17 0.059 1000 -1000 -0.002 -1000
BMP receptor signaling 0.0956 39 3228 81 -0.26 0.072 1000 -1000 -0.031 -1000
PDGFR-alpha signaling pathway 0.0931 38 1675 44 -0.3 0.039 1000 -1000 -0.021 -1000
amb2 Integrin signaling 0.0931 38 3128 82 -0.29 0.068 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0931 38 1997 52 -0.25 0.038 1000 -1000 -0.021 -1000
S1P1 pathway 0.0931 38 1380 36 -0.3 0.026 1000 -1000 -0.026 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0931 38 4560 120 -0.24 0.17 1000 -1000 -0.036 -1000
IL12-mediated signaling events 0.0882 36 3191 87 -0.4 0.057 1000 -1000 -0.044 -1000
HIF-1-alpha transcription factor network 0.0882 36 2803 76 -0.12 0.069 1000 -1000 -0.03 -1000
Glypican 1 network 0.0882 36 1732 48 -0.19 0.048 1000 -1000 -0.012 -1000
Glucocorticoid receptor regulatory network 0.0882 36 4200 114 -0.52 0.16 1000 -1000 -0.042 -1000
IL6-mediated signaling events 0.0882 36 2732 75 -0.2 0.062 1000 -1000 -0.04 -1000
PLK1 signaling events 0.0858 35 2977 85 -0.028 0.16 1000 -1000 -0.014 -1000
S1P5 pathway 0.0858 35 595 17 -0.12 0.079 1000 -1000 -0.009 -1000
LPA4-mediated signaling events 0.0833 34 409 12 -0.13 0.008 1000 -1000 -0.018 -1000
JNK signaling in the CD4+ TCR pathway 0.0833 34 590 17 -0.17 0.031 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0809 33 1810 54 -0.15 0.062 1000 -1000 -0.029 -1000
S1P3 pathway 0.0784 32 1376 42 -0.12 0.041 1000 -1000 -0.031 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0784 32 2857 88 -0.17 0.051 1000 -1000 -0.055 -1000
Coregulation of Androgen receptor activity 0.0760 31 2392 76 -0.18 0.11 1000 -1000 -0.006 -1000
BCR signaling pathway 0.0735 30 2977 99 -0.1 0.037 1000 -1000 -0.043 -1000
FOXM1 transcription factor network 0.0735 30 1556 51 -0.18 0.11 1000 -1000 -0.026 -1000
Syndecan-1-mediated signaling events 0.0711 29 1009 34 -0.076 0.13 1000 -1000 -0.022 -1000
Osteopontin-mediated events 0.0686 28 1075 38 -0.12 0.1 1000 -1000 -0.017 -1000
Syndecan-2-mediated signaling events 0.0686 28 1950 69 -0.041 0.056 1000 -1000 -0.027 -1000
Arf6 signaling events 0.0686 28 1786 62 -0.17 0.059 1000 -1000 -0.042 -1000
Aurora C signaling 0.0686 28 201 7 0 0.11 1000 -1000 -0.01 -1000
Wnt signaling 0.0662 27 195 7 -0.011 0.03 1000 -1000 -0.009 -1000
FAS signaling pathway (CD95) 0.0637 26 1228 47 -0.53 0.044 1000 -1000 -0.038 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0613 25 874 34 -0.022 0.039 1000 -1000 -0.02 -1000
Visual signal transduction: Cones 0.0588 24 935 38 -0.077 0.078 1000 -1000 -0.003 -1000
ErbB2/ErbB3 signaling events 0.0564 23 1511 65 -0.18 0.038 1000 -1000 -0.057 -1000
Noncanonical Wnt signaling pathway 0.0564 23 601 26 -0.072 0.03 1000 -1000 -0.031 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0564 23 2023 85 -0.23 0.039 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 0.0564 23 1438 61 -0.12 0.11 1000 -1000 -0.032 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0539 22 1636 74 -0.19 0.064 1000 -1000 -0.046 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0515 21 694 33 -0.22 0.11 1000 -1000 -0.021 -1000
Class IB PI3K non-lipid kinase events 0.0515 21 63 3 0 -1000 1000 -1000 -0.015 -1000
Aurora A signaling 0.0490 20 1213 60 -0.21 0.16 1000 -1000 -0.009 -1000
Regulation of Androgen receptor activity 0.0490 20 1414 70 -0.18 0.036 1000 -1000 -0.031 -1000
Canonical Wnt signaling pathway 0.0466 19 1007 51 -0.082 0.11 1000 -1000 -0.039 -1000
Syndecan-4-mediated signaling events 0.0466 19 1322 67 -0.13 0.067 1000 -1000 -0.032 -1000
Visual signal transduction: Rods 0.0466 19 1014 52 -0.077 0.1 1000 -1000 -0.024 -1000
ceramide signaling pathway 0.0441 18 884 49 0 0.05 1000 -1000 -0.028 -1000
Effects of Botulinum toxin 0.0441 18 486 26 -0.01 0.056 1000 -1000 -0.002 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0417 17 503 28 -0.12 0.059 1000 -1000 -0.014 -1000
Cellular roles of Anthrax toxin 0.0417 17 667 39 -0.077 0.036 1000 -1000 -0.023 -1000
Ceramide signaling pathway 0.0417 17 1322 76 -0.19 0.071 1000 -1000 -0.025 -1000
TCGA08_p53 0.0417 17 125 7 -0.004 0.027 1000 -1000 -0.002 -1000
Hedgehog signaling events mediated by Gli proteins 0.0392 16 1094 65 -0.12 0.065 1000 -1000 -0.025 -1000
Nectin adhesion pathway 0.0392 16 1032 63 -0.034 0.055 1000 -1000 -0.033 -1000
Ephrin B reverse signaling 0.0392 16 777 48 -0.038 0.041 1000 -1000 -0.022 -1000
Insulin Pathway 0.0392 16 1210 74 -0.19 0.065 1000 -1000 -0.03 -1000
Signaling events mediated by PTP1B 0.0368 15 1179 76 -0.11 0.042 1000 -1000 -0.019 -1000
PDGFR-beta signaling pathway 0.0368 15 1468 97 -0.079 0.058 1000 -1000 -0.036 -1000
ErbB4 signaling events 0.0343 14 976 69 -0.18 0.046 1000 -1000 -0.027 -1000
IL27-mediated signaling events 0.0343 14 724 51 -0.18 0.048 1000 -1000 -0.033 -1000
Caspase cascade in apoptosis 0.0319 13 1029 74 -0.049 0.05 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 0.0319 13 784 58 -0.062 0.12 1000 -1000 -0.026 -1000
Regulation of p38-alpha and p38-beta 0.0319 13 716 54 -0.1 0.06 1000 -1000 -0.035 -1000
IL2 signaling events mediated by STAT5 0.0319 13 292 22 -0.037 0.076 1000 -1000 -0.023 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0294 12 1065 83 -0.25 0.044 1000 -1000 -0.022 -1000
EPHB forward signaling 0.0294 12 1082 85 -0.013 0.069 1000 -1000 -0.049 -1000
EGFR-dependent Endothelin signaling events 0.0294 12 272 21 -0.037 0.074 1000 -1000 -0.034 -1000
Regulation of nuclear SMAD2/3 signaling 0.0270 11 1628 136 -0.15 0.092 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0270 11 760 68 -0.14 0.064 1000 -1000 -0.025 -1000
IL1-mediated signaling events 0.0270 11 695 62 -0.011 0.059 1000 -1000 -0.022 -1000
FOXA2 and FOXA3 transcription factor networks 0.0245 10 494 46 -0.14 0.18 1000 -1000 -0.042 -1000
IFN-gamma pathway 0.0245 10 690 68 -0.12 0.081 1000 -1000 -0.059 -1000
Signaling events mediated by HDAC Class III 0.0245 10 409 40 -0.18 0.051 1000 -1000 -0.031 -1000
E-cadherin signaling in the nascent adherens junction 0.0245 10 795 76 -0.039 0.051 1000 -1000 -0.041 -1000
a4b1 and a4b7 Integrin signaling 0.0221 9 47 5 0.013 0.027 1000 -1000 0.009 -1000
Syndecan-3-mediated signaling events 0.0221 9 348 35 -0.062 0.062 1000 -1000 -0.012 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0221 9 445 45 -0.007 0.065 1000 -1000 -0.028 -1000
Arf6 trafficking events 0.0221 9 643 71 -0.29 0.049 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0221 9 306 34 -0.061 0.043 1000 -1000 -0.026 -1000
BARD1 signaling events 0.0196 8 492 57 -0.049 0.093 1000 -1000 -0.033 -1000
EPO signaling pathway 0.0196 8 455 55 -0.022 0.072 1000 -1000 -0.026 -1000
mTOR signaling pathway 0.0196 8 428 53 -0.029 0.037 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0196 8 326 37 -0.014 0.052 1000 -1000 -0.025 -1000
Signaling mediated by p38-gamma and p38-delta 0.0196 8 125 15 -0.011 0.026 1000 -1000 -0.023 -1000
Regulation of Telomerase 0.0196 8 883 102 -0.12 0.083 1000 -1000 -0.024 -1000
E-cadherin signaling events 0.0196 8 42 5 0.01 0.037 1000 -1000 0.013 -1000
Retinoic acid receptors-mediated signaling 0.0172 7 408 58 -0.052 0.059 1000 -1000 -0.02 -1000
TCGA08_rtk_signaling 0.0172 7 206 26 -0.04 0.06 1000 -1000 -0.012 -1000
E-cadherin signaling in keratinocytes 0.0172 7 318 43 -0.029 0.04 1000 -1000 -0.014 -1000
Class I PI3K signaling events 0.0147 6 500 73 -0.024 0.049 1000 -1000 -0.03 -1000
Insulin-mediated glucose transport 0.0123 5 160 32 -0.14 0.048 1000 -1000 -0.017 -1000
HIF-2-alpha transcription factor network 0.0123 5 221 43 -0.12 0.12 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0123 5 211 36 -0.043 0.045 1000 -1000 -0.02 -1000
FoxO family signaling 0.0098 4 263 64 -0.018 0.11 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class II 0.0074 3 294 75 -0.054 0.061 1000 -1000 -0.019 -1000
PLK2 and PLK4 events 0.0074 3 11 3 0.015 0.032 1000 -1000 -0.009 -1000
TRAIL signaling pathway 0.0074 3 148 48 -0.017 0.06 1000 -1000 -0.023 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0074 3 82 27 0 0.066 1000 -1000 -0.021 -1000
Canonical NF-kappaB pathway 0.0049 2 94 39 0 0.067 1000 -1000 -0.016 -1000
Arf6 downstream pathway 0.0049 2 105 43 -0.051 0.052 1000 -1000 -0.024 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0049 2 371 125 -0.039 0.071 1000 -1000 -0.032 -1000
VEGFR1 specific signals 0.0049 2 137 56 -0.053 0.069 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 0.0049 2 121 44 -0.004 0.06 1000 -1000 -0.016 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0025 1 29 23 0.005 0.05 1000 -1000 -0.011 -1000
Circadian rhythm pathway 0.0025 1 30 22 -0.01 0.058 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class I 0.0025 1 133 104 -0.051 0.066 1000 -1000 -0.029 -1000
Atypical NF-kappaB pathway 0.0025 1 51 31 0 0.035 1000 -1000 -0.009 -1000
Arf1 pathway 0.0000 0 47 54 0 0.048 1000 -1000 -0.011 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.072 1000 -1000 0 -1000
Total NA 3307 200704 7203 -17 -990 131000 -131000 -3.3 -131000
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.028 0.082 -10000 0 -0.42 12 12
Crk/p130 Cas/Paxillin -0.13 0.13 -10000 0 -0.27 158 158
JUN -0.1 0.13 0.19 1 -0.24 110 111
HRAS 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.16 -10000 0 -0.28 178 178
RAP1A 0.028 0.003 -10000 0 -10000 0 0
FRS2 0.031 0.04 0.33 7 -10000 0 7
RAP1A/GDP 0.02 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.1 0.16 -10000 0 -0.27 179 179
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.11 0.14 -10000 0 -0.26 184 184
RHOA 0.026 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.092 0.15 -10000 0 -0.24 182 182
GRB7 0.028 0.084 0.31 14 -0.47 7 21
RET51/GFRalpha1/GDNF -0.1 0.16 -10000 0 -0.27 185 185
MAPKKK cascade -0.1 0.14 -10000 0 -0.26 164 164
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.15 -10000 0 -0.26 189 189
lamellipodium assembly -0.12 0.13 -10000 0 -0.25 159 159
RET51/GFRalpha1/GDNF/SHC -0.098 0.16 -10000 0 -0.27 175 175
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.1 0.14 -10000 0 -0.26 170 170
RET9/GFRalpha1/GDNF/Shank3 -0.11 0.14 -10000 0 -0.26 184 184
MAPK3 -0.098 0.13 0.34 1 -0.23 173 174
DOK1 0.027 0.011 0.21 1 -10000 0 1
DOK6 -0.14 0.23 -10000 0 -0.47 132 132
PXN 0.027 0.004 -10000 0 -10000 0 0
neurite development -0.12 0.14 0.3 1 -0.31 81 82
DOK5 -0.014 0.14 0.25 3 -0.47 33 36
GFRA1 -0.24 0.24 -10000 0 -0.47 216 216
MAPK8 -0.099 0.12 -10000 0 -0.23 173 173
HRAS/GTP -0.11 0.16 -10000 0 -0.28 168 168
tube development -0.096 0.14 0.21 7 -0.25 180 187
MAPK1 -0.097 0.13 0.34 1 -0.23 174 175
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.098 0.12 0.17 3 -0.23 169 172
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
PDLIM7 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.17 0.21 -10000 0 -0.34 221 221
SHC1 0.026 0.017 0.33 1 -10000 0 1
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.16 -10000 0 -0.27 184 184
RET51/GFRalpha1/GDNF/Dok5 -0.12 0.18 -10000 0 -0.29 187 187
PRKCA 0.022 0.049 -10000 0 -0.47 4 4
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
CREB1 -0.12 0.14 -10000 0 -0.27 166 166
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.095 0.12 -10000 0 -0.23 161 161
RET51/GFRalpha1/GDNF/Grb7 -0.1 0.16 0.24 2 -0.28 179 181
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.016 0.085 0.21 7 -0.47 11 18
DOK4 0.027 0.005 -10000 0 -10000 0 0
JNK cascade -0.099 0.12 0.19 1 -0.33 33 34
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.14 0.22 4 -0.26 175 179
SHANK3 0.026 0.006 -10000 0 -10000 0 0
RASA1 0.027 0.006 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.095 0.12 -10000 0 -0.23 161 161
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.099 0.13 0.21 1 -0.23 172 173
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.1 0.13 -10000 0 -0.24 175 175
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.14 -10000 0 -0.24 164 164
PI3K -0.16 0.19 -10000 0 -0.36 170 170
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.094 0.14 -10000 0 -0.25 180 180
GRB10 0.02 0.055 -10000 0 -0.47 5 5
activation of MAPKK activity -0.087 0.12 -10000 0 -0.22 169 169
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.16 0.27 4 -0.27 176 180
GAB1 0.026 0.006 -10000 0 -10000 0 0
IRS1 0.017 0.065 -10000 0 -0.47 7 7
IRS2 0.009 0.091 -10000 0 -0.47 14 14
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.14 -10000 0 -0.24 164 164
RET51/GFRalpha1/GDNF/PKC alpha -0.1 0.16 -10000 0 -0.28 179 179
GRB2 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GDNF 0.006 0.033 0.29 3 -10000 0 3
RAC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.11 0.16 -10000 0 -0.27 188 188
Rac1/GTP -0.13 0.16 -10000 0 -0.3 154 154
RET9/GFRalpha1/GDNF -0.12 0.15 -10000 0 -0.29 184 184
GFRalpha1/GDNF -0.14 0.18 -10000 0 -0.34 184 184
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.035 0.042 0.24 12 -10000 0 12
NFATC2 -0.11 0.26 -10000 0 -0.56 76 76
NFATC3 -0.093 0.14 -10000 0 -0.27 132 132
CD40LG -0.48 0.52 -10000 0 -0.94 202 202
ITCH 0.006 0.079 0.25 1 -0.22 41 42
CBLB 0.007 0.078 -10000 0 -0.22 41 41
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.3 0.45 -10000 0 -0.95 95 95
JUNB 0.021 0.055 -10000 0 -0.47 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.096 -10000 0 -0.27 42 42
T cell anergy -0.022 0.13 0.25 1 -0.38 41 42
TLE4 -0.079 0.21 -10000 0 -0.52 55 55
Jun/NFAT1-c-4/p21SNFT -0.4 0.54 -10000 0 -0.93 186 186
AP-1/NFAT1-c-4 -0.53 0.64 -10000 0 -1.1 202 202
IKZF1 -0.082 0.21 -10000 0 -0.51 56 56
T-helper 2 cell differentiation -0.22 0.34 -10000 0 -0.86 69 69
AP-1/NFAT1 -0.15 0.24 -10000 0 -0.44 129 129
CALM1 0.017 0.062 -10000 0 -10000 0 0
EGR2 -0.48 0.66 -10000 0 -1.1 180 180
EGR3 -0.68 0.75 -10000 0 -1.4 200 200
NFAT1/FOXP3 -0.059 0.21 0.35 4 -0.44 66 70
EGR1 -0.085 0.21 -10000 0 -0.47 92 92
JUN 0.003 0.094 -10000 0 -0.47 14 14
EGR4 0.017 0.081 0.21 7 -0.47 10 17
mol:Ca2+ -0.007 0.052 -10000 0 -0.16 42 42
GBP3 -0.079 0.19 -10000 0 -0.46 56 56
FOSL1 -0.006 0.12 -10000 0 -0.47 27 27
NFAT1-c-4/MAF/IRF4 -0.39 0.54 -10000 0 -0.92 186 186
DGKA -0.074 0.18 -10000 0 -0.44 57 57
CREM 0.026 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.41 0.52 -10000 0 -0.92 185 185
CTLA4 -0.063 0.18 0.26 1 -0.41 63 64
NFAT1-c-4 (dimer)/EGR1 -0.45 0.58 -10000 0 -1 191 191
NFAT1-c-4 (dimer)/EGR4 -0.4 0.54 -10000 0 -0.93 188 188
FOS -0.13 0.23 -10000 0 -0.47 124 124
IFNG -0.15 0.3 -10000 0 -0.73 61 61
T cell activation -0.23 0.3 -10000 0 -0.65 90 90
MAF 0.014 0.077 -10000 0 -0.47 10 10
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.35 0.46 0.77 190 -10000 0 190
TNF -0.4 0.49 -10000 0 -0.88 190 190
FASLG -0.65 0.78 -10000 0 -1.3 206 206
TBX21 0.009 0.11 0.23 1 -0.47 21 22
BATF3 0.023 0.058 0.21 4 -0.47 5 9
PRKCQ -0.012 0.14 0.24 4 -0.47 31 35
PTPN1 -0.075 0.18 -10000 0 -0.44 58 58
NFAT1-c-4/ICER1 -0.4 0.53 -10000 0 -0.91 190 190
GATA3 -0.003 0.12 0.33 2 -0.47 24 26
T-helper 1 cell differentiation -0.15 0.29 -10000 0 -0.71 61 61
IL2RA -0.3 0.43 -10000 0 -0.87 106 106
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.073 0.18 -10000 0 -0.45 54 54
E2F1 0.082 0.096 0.25 97 -10000 0 97
PPARG -0.005 0.12 0.33 2 -0.47 25 27
SLC3A2 -0.075 0.18 -10000 0 -0.44 56 56
IRF4 -0.001 0.12 0.21 3 -0.47 23 26
PTGS2 -0.5 0.54 -10000 0 -0.97 206 206
CSF2 -0.45 0.51 -10000 0 -0.92 202 202
JunB/Fra1/NFAT1-c-4 -0.4 0.53 -10000 0 -0.91 188 188
IL4 -0.23 0.36 -10000 0 -0.92 69 69
IL5 -0.46 0.5 -10000 0 -0.91 203 203
IL2 -0.23 0.3 -10000 0 -0.67 85 85
IL3 -0.071 0.15 -10000 0 -0.86 9 9
RNF128 -0.027 0.18 0.25 1 -0.55 43 44
NFATC1 -0.35 0.47 -10000 0 -0.78 189 189
CDK4 0.22 0.28 0.6 94 -10000 0 94
PTPRK -0.074 0.18 -10000 0 -0.45 53 53
IL8 -0.48 0.52 -10000 0 -0.94 205 205
POU2F1 0.025 0.009 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.23 0.46 -10000 0 -1 99 99
MKNK1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.045 0.16 -10000 0 -0.31 103 103
ATF2/c-Jun -0.059 0.18 -10000 0 -0.55 29 29
MAPK11 -0.043 0.15 -10000 0 -0.31 97 97
MITF -0.085 0.21 -10000 0 -0.39 117 117
MAPKAPK5 -0.058 0.17 0.28 1 -0.36 100 101
KRT8 -0.068 0.19 -10000 0 -0.38 103 103
MAPKAPK3 0.026 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.07 0.23 -10000 0 -0.45 103 103
CEBPB -0.056 0.17 -10000 0 -0.36 94 94
SLC9A1 -0.062 0.18 -10000 0 -0.36 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.061 0.18 -10000 0 -0.36 100 100
p38alpha-beta/MNK1 -0.041 0.19 -10000 0 -0.37 96 96
JUN -0.06 0.18 -10000 0 -0.6 24 24
PPARGC1A -0.2 0.25 -10000 0 -0.39 225 225
USF1 -0.048 0.16 0.28 1 -0.35 85 86
RAB5/GDP/GDI1 -0.035 0.13 -10000 0 -0.26 91 91
NOS2 -0.065 0.21 -10000 0 -0.66 20 20
DDIT3 -0.06 0.18 -10000 0 -0.36 100 100
RAB5A 0.026 0.007 -10000 0 -10000 0 0
HSPB1 -0.05 0.14 0.27 4 -0.3 97 101
p38alpha-beta/HBP1 -0.038 0.19 -10000 0 -0.37 92 92
CREB1 -0.071 0.19 -10000 0 -0.39 101 101
RAB5/GDP 0.019 0.005 -10000 0 -10000 0 0
EIF4E -0.056 0.16 0.24 2 -0.33 95 97
RPS6KA4 -0.063 0.18 -10000 0 -0.36 103 103
PLA2G4A -0.072 0.18 0.24 2 -0.35 107 109
GDI1 -0.06 0.17 -10000 0 -0.36 101 101
TP53 -0.091 0.21 -10000 0 -0.44 102 102
RPS6KA5 -0.069 0.19 -10000 0 -0.38 104 104
ESR1 -0.12 0.23 -10000 0 -0.4 147 147
HBP1 0.027 0.004 -10000 0 -10000 0 0
MEF2C -0.07 0.18 -10000 0 -0.37 108 108
MEF2A -0.063 0.18 -10000 0 -0.36 103 103
EIF4EBP1 -0.069 0.19 -10000 0 -0.39 97 97
KRT19 -0.074 0.2 -10000 0 -0.38 107 107
ELK4 -0.061 0.17 -10000 0 -0.35 103 103
ATF6 -0.05 0.16 -10000 0 -0.35 87 87
ATF1 -0.068 0.19 -10000 0 -0.38 101 101
p38alpha-beta/MAPKAPK2 -0.04 0.19 -10000 0 -0.37 96 96
p38alpha-beta/MAPKAPK3 -0.04 0.19 -10000 0 -0.37 96 96
Endothelins

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
AKT1 -0.077 0.17 -10000 0 -0.41 64 64
PTK2B 0.023 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.099 0.25 -10000 0 -0.7 44 44
EDN1 -0.021 0.085 0.34 3 -0.38 8 11
EDN3 0.001 0.037 0.23 7 -10000 0 7
EDN2 0.012 0.13 0.22 29 -0.47 22 51
HRAS/GDP -0.14 0.25 0.26 3 -0.49 103 106
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.19 -10000 0 -0.44 65 65
ADCY4 -0.14 0.21 0.32 5 -0.36 144 149
ADCY5 -0.24 0.26 -10000 0 -0.43 231 231
ADCY6 -0.14 0.21 0.32 5 -0.36 140 145
ADCY7 -0.14 0.21 0.32 5 -0.36 143 148
ADCY1 -0.14 0.21 0.32 5 -0.35 154 159
ADCY2 -0.2 0.24 0.29 1 -0.4 197 198
ADCY3 -0.14 0.21 0.32 5 -0.36 137 142
ADCY8 -0.13 0.2 0.32 3 -0.36 129 132
ADCY9 -0.14 0.22 0.32 5 -0.34 172 177
arachidonic acid secretion -0.18 0.28 0.33 5 -0.48 162 167
ETB receptor/Endothelin-1/Gq/GTP -0.053 0.16 -10000 0 -0.36 75 75
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
HRAS 0.024 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.028 0.17 -10000 0 -0.38 61 61
ETA receptor/Endothelin-1/Gs/GTP -0.13 0.22 -10000 0 -0.35 176 176
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.083 0.2 -10000 0 -0.46 62 62
EDNRB -0.031 0.16 -10000 0 -0.47 44 44
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.072 0.17 -10000 0 -0.45 51 51
CYSLTR1 -0.089 0.2 -10000 0 -0.55 51 51
SLC9A1 -0.035 0.093 -10000 0 -0.26 43 43
mol:GDP -0.16 0.26 0.26 3 -0.51 114 117
SLC9A3 -0.076 0.24 -10000 0 -0.66 40 40
RAF1 -0.18 0.29 0.3 11 -0.47 160 171
JUN -0.12 0.31 -10000 0 -0.85 49 49
JAK2 -0.073 0.16 -10000 0 -0.42 59 59
mol:IP3 -0.1 0.21 -10000 0 -0.45 89 89
ETA receptor/Endothelin-1 -0.054 0.21 -10000 0 -0.47 66 66
PLCB1 0.01 0.081 -10000 0 -0.47 11 11
PLCB2 0.019 0.037 -10000 0 -0.47 2 2
ETA receptor/Endothelin-3 -0.038 0.15 0.25 1 -0.4 49 50
FOS -0.32 0.45 0.35 4 -0.86 152 156
Gai/GDP -0.3 0.43 -10000 0 -0.85 141 141
CRK 0.025 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.13 0.24 -10000 0 -0.51 91 91
BCAR1 0.027 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.21 0.22 1 -0.42 100 101
GNAQ 0.02 0.015 -10000 0 -10000 0 0
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
GNAL -0.17 0.24 -10000 0 -0.47 163 163
Gs family/GDP -0.22 0.28 0.25 2 -0.51 155 157
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.18 -10000 0 -0.38 79 79
MAPK14 -0.057 0.16 0.22 2 -0.4 55 57
TRPC6 -0.1 0.27 -10000 0 -0.74 44 44
GNAI2 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.028 0.003 -10000 0 -10000 0 0
GNAI1 0.024 0.043 -10000 0 -0.47 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.054 0.16 -10000 0 -0.41 54 54
ETB receptor/Endothelin-2 -0.013 0.14 0.24 2 -0.36 56 58
ETB receptor/Endothelin-3 -0.009 0.12 0.24 1 -0.34 43 44
ETB receptor/Endothelin-1 -0.019 0.14 0.25 3 -0.36 50 53
MAPK3 -0.29 0.41 0.35 5 -0.74 164 169
MAPK1 -0.29 0.41 0.35 5 -0.74 164 169
Rac1/GDP -0.14 0.24 0.26 1 -0.49 100 101
cAMP biosynthetic process -0.21 0.24 0.26 6 -0.45 166 172
MAPK8 -0.13 0.32 -10000 0 -0.79 60 60
SRC 0.026 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.12 0.19 -10000 0 -0.4 104 104
p130Cas/CRK/Src/PYK2 -0.14 0.26 0.33 6 -0.55 90 96
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.24 0.26 1 -0.49 99 100
COL1A2 -0.1 0.28 -10000 0 -0.79 45 45
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.04 0.18 0.24 2 -0.38 75 77
mol:DAG -0.11 0.21 -10000 0 -0.46 89 89
MAP2K2 -0.23 0.33 0.32 9 -0.58 166 175
MAP2K1 -0.23 0.33 0.32 7 -0.58 166 173
EDNRA -0.085 0.19 -10000 0 -0.5 62 62
positive regulation of muscle contraction -0.061 0.15 0.25 5 -0.38 54 59
Gq family/GDP -0.13 0.25 0.29 1 -0.48 106 107
HRAS/GTP -0.17 0.26 0.24 3 -0.49 123 126
PRKCH -0.11 0.21 0.22 1 -0.46 81 82
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.11 0.21 0.23 5 -0.46 83 88
PRKCB -0.17 0.25 0.25 3 -0.48 130 133
PRKCE -0.11 0.21 0.22 1 -0.46 81 82
PRKCD -0.11 0.21 0.22 2 -0.46 83 85
PRKCG -0.11 0.21 0.31 2 -0.44 93 95
regulation of vascular smooth muscle contraction -0.38 0.53 0.38 3 -1 151 154
PRKCQ -0.12 0.23 0.25 8 -0.48 94 102
PLA2G4A -0.2 0.31 0.33 5 -0.52 163 168
GNA14 -0.034 0.16 -10000 0 -0.47 45 45
GNA15 0.02 0.044 -10000 0 -0.47 3 3
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.027 -10000 0 -0.47 1 1
Rac1/GTP -0.028 0.17 -10000 0 -0.38 62 62
MMP1 0.089 0.13 0.37 39 -0.78 1 40
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.007 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.066 0.15 -10000 0 -0.26 148 148
regulation of S phase of mitotic cell cycle -0.061 0.12 -10000 0 -0.24 125 125
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
HRAS 0.024 0.008 -10000 0 -10000 0 0
SHBG/T-DHT 0.017 0.006 -10000 0 -10000 0 0
PELP1 0.024 0.008 -10000 0 -10000 0 0
AKT1 0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.087 0.12 0.19 2 -0.26 103 105
T-DHT/AR -0.11 0.17 -10000 0 -0.34 145 145
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 128 128
GNAI2 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.003 -10000 0 -10000 0 0
GNAI1 0.023 0.043 -10000 0 -0.47 3 3
mol:GDP -0.14 0.19 -10000 0 -0.38 143 143
cell proliferation -0.16 0.21 0.26 2 -0.44 125 127
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
FOS -0.26 0.37 -10000 0 -0.78 132 132
mol:Ca2+ -0.04 0.043 -10000 0 -0.081 181 181
MAPK3 -0.13 0.17 0.26 3 -0.35 109 112
MAPK1 -0.073 0.12 -10000 0 -0.28 50 50
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
mol:IP3 -0.001 0.002 -10000 0 -0.004 128 128
cAMP biosynthetic process 0.028 0.037 0.18 5 -10000 0 5
GNG2 0.02 0.06 -10000 0 -0.47 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 128 128
HRAS/GTP -0.072 0.13 -10000 0 -0.25 131 131
actin cytoskeleton reorganization 0.035 0.021 -10000 0 -0.23 1 1
SRC 0.025 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 128 128
PI3K 0.032 0.02 -10000 0 -0.28 1 1
apoptosis 0.15 0.22 0.43 132 -0.25 1 133
T-DHT/AR/PELP1 -0.085 0.15 -10000 0 -0.29 142 142
HRAS/GDP -0.12 0.18 -10000 0 -0.37 143 143
CREB1 -0.16 0.23 0.26 1 -0.47 132 133
RAC1-CDC42/GTP 0.044 0.025 -10000 0 -0.24 1 1
AR -0.16 0.24 -10000 0 -0.47 145 145
GNB1 0.027 0.003 -10000 0 -10000 0 0
RAF1 -0.078 0.12 0.21 1 -0.25 114 115
RAC1-CDC42/GDP -0.098 0.19 -10000 0 -0.35 137 137
T-DHT/AR/PELP1/Src -0.065 0.14 -10000 0 -0.26 131 131
MAP2K2 -0.088 0.12 0.18 8 -0.26 105 113
T-DHT/AR/PELP1/Src/PI3K -0.061 0.12 -10000 0 -0.24 125 125
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
SHBG 0.023 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.16 0.22 -10000 0 -0.45 127 127
mol:T-DHT 0 0.001 0.001 9 -0.003 78 87
RAC1 0.026 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.15 0.18 -10000 0 -0.34 157 157
CDC42 0.028 0.003 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.027 0.004 -10000 0 -10000 0 0
PTK2 0.025 0.009 -10000 0 -10000 0 0
CRKL -0.095 0.13 -10000 0 -0.25 170 170
GRB2/SOS1/SHC 0.049 0.021 0.24 1 -10000 0 1
HRAS 0.025 0.008 -10000 0 -10000 0 0
IRS1/Crk -0.092 0.14 -10000 0 -0.24 177 177
IGF-1R heterotetramer/IGF1/PTP1B -0.083 0.16 -10000 0 -0.28 162 162
AKT1 -0.084 0.12 0.25 3 -0.35 8 11
BAD -0.081 0.11 0.18 11 -0.34 8 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.094 0.13 -10000 0 -0.24 170 170
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.14 0.21 4 -0.25 176 180
RAF1 -0.061 0.12 0.3 1 -0.43 8 9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.069 0.15 -10000 0 -0.24 170 170
YWHAZ 0.021 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.099 0.15 -10000 0 -0.27 178 178
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.083 0.12 0.25 3 -0.35 8 11
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.049 0.11 0.28 1 -0.35 8 9
PXN 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.069 0.12 -10000 0 -0.22 149 149
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.045 0.14 -10000 0 -0.22 152 152
IGF-1R heterotetramer -0.018 0.062 -10000 0 -0.51 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.081 0.15 -10000 0 -0.25 176 176
Crk/p130 Cas/Paxillin -0.064 0.14 -10000 0 -0.23 170 170
IGF1R -0.018 0.063 -10000 0 -0.51 2 2
IGF1 -0.2 0.25 -10000 0 -0.48 176 176
IRS2/Crk -0.091 0.14 -10000 0 -0.25 169 169
PI3K -0.066 0.14 -10000 0 -0.24 164 164
apoptosis 0.047 0.099 0.32 5 -0.22 2 7
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
PRKCD -0.13 0.18 0.2 2 -0.34 169 171
RAF1/14-3-3 E -0.044 0.12 0.3 1 -0.37 8 9
BAD/14-3-3 -0.05 0.1 0.23 2 -0.34 5 7
PRKCZ -0.086 0.12 0.23 4 -0.35 11 15
Crk/p130 Cas/Paxillin/FAK1 -0.051 0.11 -10000 0 -0.32 5 5
PTPN1 0.025 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.14 0.19 -10000 0 -0.36 175 175
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.059 0.15 -10000 0 -0.24 153 153
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.089 0.14 -10000 0 -0.24 176 176
GRB10 0.02 0.055 -10000 0 -0.47 5 5
PTPN11 -0.098 0.13 -10000 0 -0.25 176 176
IRS1 -0.11 0.14 -10000 0 -0.27 178 178
IRS2 -0.1 0.14 -10000 0 -0.26 172 172
IGF-1R heterotetramer/IGF1 -0.14 0.2 -10000 0 -0.36 177 177
GRB2 0.027 0.005 -10000 0 -10000 0 0
PDPK1 -0.081 0.13 0.28 1 -0.23 148 149
YWHAE 0.025 0.008 -10000 0 -10000 0 0
PRKD1 -0.15 0.2 0.2 1 -0.36 172 173
SHC1 0.026 0.017 0.33 1 -10000 0 1
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.046 0.034 0.24 4 -10000 0 4
VLDLR 0.012 0.077 -10000 0 -0.47 10 10
CRKL 0.028 0.014 0.21 2 -10000 0 2
LRPAP1 0.028 0.016 0.33 1 -10000 0 1
FYN 0.022 0.043 -10000 0 -0.47 3 3
ITGA3 0.03 0.027 0.23 7 -10000 0 7
RELN/VLDLR/Fyn -0.071 0.16 -10000 0 -0.28 142 142
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.047 -10000 0 -0.24 4 4
AKT1 -0.084 0.14 0.15 1 -0.26 142 143
MAP2K7 0.027 0.005 -10000 0 -10000 0 0
RAPGEF1 0.025 0.009 -10000 0 -10000 0 0
DAB1 -0.017 0.14 0.22 24 -0.47 33 57
RELN/LRP8/DAB1 -0.069 0.18 0.27 4 -0.28 156 160
LRPAP1/LRP8 0.062 0.052 0.24 3 -10000 0 3
RELN/LRP8/DAB1/Fyn -0.061 0.18 0.27 4 -0.27 158 162
DAB1/alpha3/beta1 Integrin -0.061 0.16 0.24 1 -0.25 148 149
long-term memory -0.1 0.22 0.28 4 -0.32 180 184
DAB1/LIS1 -0.055 0.17 0.26 3 -0.26 153 156
DAB1/CRLK/C3G -0.059 0.16 -10000 0 -0.26 135 135
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DAB1/NCK2 -0.052 0.18 0.26 3 -0.26 153 156
ARHGEF2 0.026 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.08 0.2 0.21 3 -0.47 81 84
CDK5R1 0.038 0.05 0.24 22 -10000 0 22
RELN -0.15 0.23 0.21 4 -0.47 139 143
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
RELN/LRP8/Fyn -0.055 0.18 0.29 3 -0.29 139 142
GRIN2A/RELN/LRP8/DAB1/Fyn -0.11 0.22 0.4 1 -0.33 183 184
MAPK8 0.023 0.043 -10000 0 -0.47 3 3
RELN/VLDLR/DAB1 -0.081 0.17 0.22 1 -0.28 157 158
ITGB1 0.026 0.006 -10000 0 -10000 0 0
MAP1B -0.12 0.17 0.33 2 -0.3 173 175
RELN/LRP8 -0.051 0.18 0.27 5 -0.29 135 140
GRIN2B/RELN/LRP8/DAB1/Fyn -0.053 0.19 0.28 4 -0.27 156 160
PI3K 0.035 0.023 -10000 0 -0.34 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.04 0.021 0.24 1 -10000 0 1
RAP1A -0.087 0.14 0.37 5 -0.42 15 20
PAFAH1B1 0.025 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.025 0.027 0.21 1 -0.47 1 2
CRLK/C3G 0.036 0.017 -10000 0 -10000 0 0
GRIN2B 0.004 0.042 0.21 12 -10000 0 12
NCK2 0.027 0.004 -10000 0 -10000 0 0
neuron differentiation -0.054 0.12 0.19 1 -0.32 37 38
neuron adhesion -0.075 0.14 0.34 7 -0.42 12 19
LRP8 0.062 0.073 0.22 74 -10000 0 74
GSK3B -0.08 0.13 -10000 0 -0.24 135 135
RELN/VLDLR/DAB1/Fyn -0.071 0.16 0.22 1 -0.26 159 160
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.086 0.15 0.17 1 -0.27 146 147
CDK5 0.027 0.004 -10000 0 -10000 0 0
MAPT -0.011 0.16 0.76 9 -0.42 33 42
neuron migration -0.1 0.16 0.3 7 -0.31 132 139
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.054 0.12 0.19 1 -0.32 37 38
RELN/VLDLR -0.043 0.17 0.28 4 -0.27 136 140
IL4-mediated signaling events

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
BCL2L1 -0.43 0.58 -10000 0 -1.2 115 115
STAT6 (cleaved dimer) -0.48 0.6 -10000 0 -1.2 132 132
IGHG1 -0.12 0.2 -10000 0 -0.64 4 4
IGHG3 -0.43 0.55 -10000 0 -1.1 131 131
AKT1 -0.2 0.33 -10000 0 -0.79 54 54
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.3 -10000 0 -0.82 38 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.21 0.35 -10000 0 -0.81 56 56
THY1 -0.45 0.58 -10000 0 -1.2 117 117
MYB 0.053 0.076 0.23 56 -0.47 1 57
HMGA1 0.031 0.026 0.21 8 -10000 0 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.27 0.41 -10000 0 -0.78 109 109
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.22 0.36 -10000 0 -0.82 56 56
SP1 0.025 0.031 -10000 0 -10000 0 0
INPP5D 0.018 0.06 -10000 0 -0.47 6 6
SOCS5 0.03 0.033 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.6 -10000 0 -1.2 130 130
SOCS1 -0.28 0.36 -10000 0 -0.74 113 113
SOCS3 -0.29 0.46 -10000 0 -1.2 61 61
FCER2 -0.68 0.74 -10000 0 -1.4 197 197
PARP14 0.016 0.026 -10000 0 -10000 0 0
CCL17 -0.44 0.58 -10000 0 -1.2 117 117
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.28 -10000 0 -0.66 47 47
T cell proliferation -0.45 0.6 -10000 0 -1.2 122 122
IL4R/JAK1 -0.45 0.58 -10000 0 -1.2 123 123
EGR2 -0.62 0.73 -10000 0 -1.4 154 154
JAK2 -0.012 0.051 -10000 0 -10000 0 0
JAK3 0.026 0.023 0.22 2 -10000 0 2
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
JAK1 0.009 0.029 -10000 0 -10000 0 0
COL1A2 -0.18 0.39 -10000 0 -1.5 28 28
CCL26 -0.46 0.59 -10000 0 -1.2 128 128
IL4R -0.47 0.62 -10000 0 -1.3 122 122
PTPN6 0.031 0.025 0.2 1 -10000 0 1
IL13RA2 -0.46 0.59 -10000 0 -1.2 125 125
IL13RA1 -0.014 0.054 -10000 0 -10000 0 0
IRF4 -0.23 0.48 -10000 0 -1.2 67 67
ARG1 -0.098 0.21 -10000 0 -0.7 15 15
CBL -0.26 0.38 -10000 0 -0.76 98 98
GTF3A 0.03 0.021 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.012 0.073 -10000 0 -10000 0 0
IRF4/BCL6 -0.19 0.43 -10000 0 -1.1 64 64
CD40LG -0.035 0.16 0.25 1 -0.47 43 44
MAPK14 -0.28 0.43 -10000 0 -0.88 90 90
mitosis -0.19 0.31 -10000 0 -0.74 54 54
STAT6 -0.53 0.73 -10000 0 -1.4 131 131
SPI1 0.026 0.059 0.21 5 -0.46 5 10
RPS6KB1 -0.18 0.3 -10000 0 -0.71 50 50
STAT6 (dimer) -0.53 0.73 -10000 0 -1.4 131 131
STAT6 (dimer)/PARP14 -0.52 0.66 -10000 0 -1.3 131 131
mast cell activation 0.009 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.22 0.36 -10000 0 -0.82 61 61
FRAP1 -0.2 0.33 -10000 0 -0.79 54 54
LTA -0.46 0.6 -10000 0 -1.2 126 126
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.51 0.68 1.3 131 -10000 0 131
CCL11 -0.47 0.61 -10000 0 -1.2 126 126
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.34 -10000 0 -0.83 49 49
IL2RG 0.018 0.08 0.21 9 -0.46 9 18
IL10 -0.47 0.61 -10000 0 -1.3 121 121
IRS1 0.017 0.065 -10000 0 -0.47 7 7
IRS2 0.009 0.091 -10000 0 -0.47 14 14
IL4 -0.1 0.22 -10000 0 -1.1 11 11
IL5 -0.45 0.58 -10000 0 -1.2 119 119
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.48 -10000 0 -0.92 130 130
COL1A1 -0.14 0.32 -10000 0 -1.6 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.6 -10000 0 -1.3 114 114
IL2R gamma/JAK3 0.029 0.067 0.33 2 -0.34 9 11
TFF3 -0.58 0.71 -10000 0 -1.4 152 152
ALOX15 -0.44 0.58 -10000 0 -1.2 118 118
MYBL1 0.027 0.02 0.21 4 -10000 0 4
T-helper 2 cell differentiation -0.38 0.5 -10000 0 -0.98 133 133
SHC1 0.026 0.017 0.33 1 -10000 0 1
CEBPB 0.028 0.027 -10000 0 -0.47 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.33 -10000 0 -0.77 52 52
mol:PI-3-4-5-P3 -0.2 0.33 -10000 0 -0.79 54 54
PI3K -0.22 0.36 -10000 0 -0.87 54 54
DOK2 0.014 0.071 0.21 2 -0.47 8 10
ETS1 0.026 0.031 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.25 -10000 0 -0.61 41 41
ITGB3 -0.5 0.65 -10000 0 -1.3 130 130
PIGR -0.71 0.72 -10000 0 -1.4 203 203
IGHE 0.033 0.065 0.17 27 -0.31 1 28
MAPKKK cascade -0.14 0.25 -10000 0 -0.59 41 41
BCL6 0.031 0.012 -10000 0 -10000 0 0
OPRM1 -0.45 0.57 -10000 0 -1.2 120 120
RETNLB -0.45 0.58 -10000 0 -1.2 116 116
SELP -0.55 0.7 -10000 0 -1.4 141 141
AICDA -0.43 0.55 -10000 0 -1.2 116 116
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 -0.029 0.2 -10000 0 -0.56 47 47
IHH 0.034 0.1 0.26 30 -0.26 17 47
SHH Np/Cholesterol/GAS1 -0.12 0.16 -10000 0 -0.28 186 186
LRPAP1 0.028 0.016 0.33 1 -10000 0 1
dorsoventral neural tube patterning 0.12 0.16 0.28 186 -10000 0 186
SMO/beta Arrestin2 -0.037 0.16 -10000 0 -0.44 33 33
SMO -0.053 0.16 -10000 0 -0.46 34 34
AKT1 -0.019 0.14 -10000 0 -0.53 17 17
ARRB2 0.025 0.008 -10000 0 -10000 0 0
BOC -0.016 0.14 0.21 1 -0.47 35 36
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.052 0.16 -10000 0 -0.45 34 34
STIL -0.084 0.15 -10000 0 -0.32 61 61
DHH N/PTCH2 0.005 0.11 -10000 0 -0.34 36 36
DHH N/PTCH1 -0.007 0.13 -10000 0 -0.3 58 58
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DHH 0 0.1 -10000 0 -0.47 19 19
PTHLH -0.069 0.31 -10000 0 -0.89 48 48
determination of left/right symmetry -0.052 0.16 -10000 0 -0.45 34 34
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
skeletal system development -0.068 0.31 -10000 0 -0.88 48 48
IHH N/Hhip -0.061 0.19 -10000 0 -0.38 100 100
DHH N/Hhip -0.068 0.17 -10000 0 -0.35 109 109
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.052 0.16 -10000 0 -0.45 34 34
pancreas development -0.098 0.21 0.21 1 -0.47 97 98
HHAT 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.035 0.023 -10000 0 -0.34 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.055 0.18 0.21 2 -0.47 66 68
somite specification -0.052 0.16 -10000 0 -0.45 34 34
SHH Np/Cholesterol/PTCH1 -0.089 0.15 -10000 0 -0.33 55 55
SHH Np/Cholesterol/PTCH2 -0.086 0.14 -10000 0 -0.27 151 151
SHH Np/Cholesterol/Megalin -0.065 0.15 0.23 2 -0.26 139 141
SHH -0.11 0.16 -10000 0 -0.34 140 140
catabolic process -0.006 0.12 -10000 0 -0.32 50 50
SMO/Vitamin D3 -0.092 0.17 -10000 0 -0.41 45 45
SHH Np/Cholesterol/Hhip -0.14 0.17 -10000 0 -0.3 197 197
LRP2 0.06 0.08 0.22 81 -10000 0 81
receptor-mediated endocytosis -0.098 0.17 -10000 0 -0.44 36 36
SHH Np/Cholesterol/BOC -0.092 0.15 -10000 0 -0.27 155 155
SHH Np/Cholesterol/CDO -0.11 0.15 -10000 0 -0.27 176 176
mesenchymal cell differentiation 0.14 0.17 0.3 197 -10000 0 197
mol:Vitamin D3 -0.084 0.16 -10000 0 -0.33 55 55
IHH N/PTCH2 0.019 0.11 0.21 1 -0.34 26 27
CDON -0.033 0.16 -10000 0 -0.47 48 48
IHH N/PTCH1 0.01 0.14 -10000 0 -0.32 51 51
Megalin/LRPAP1 0.063 0.058 0.24 4 -10000 0 4
PTCH2 0.004 0.1 -10000 0 -0.47 19 19
SHH Np/Cholesterol -0.081 0.13 -10000 0 -0.26 141 141
PTCH1 -0.006 0.12 -10000 0 -0.32 50 50
HHIP -0.098 0.21 0.21 1 -0.47 97 98
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.015 0.086 0.23 7 -0.47 11 18
GNB1/GNG2 -0.081 0.09 -10000 0 -0.18 165 165
AKT1 -0.059 0.13 0.28 5 -0.22 77 82
EGF 0.034 0.047 0.21 24 -10000 0 24
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.008 0.063 0.28 1 -0.27 2 3
mol:Ca2+ -0.098 0.18 0.32 4 -0.3 173 177
LYN 0.008 0.058 0.28 1 -0.33 1 2
RhoA/GTP -0.04 0.077 0.17 3 -0.13 141 144
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.2 0.33 4 -0.34 166 170
GNG2 0.02 0.06 -10000 0 -0.47 6 6
ARRB2 0.025 0.008 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.03 0.14 -10000 0 -0.47 24 24
G beta5/gamma2 -0.1 0.12 -10000 0 -0.24 162 162
PRKCH -0.12 0.2 0.34 3 -0.34 168 171
DNM1 0.017 0.06 -10000 0 -0.47 6 6
TXA2/TP beta/beta Arrestin3 0.001 0.075 -10000 0 -0.55 6 6
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.001 0.1 -10000 0 -0.47 18 18
G12 family/GTP -0.11 0.16 -10000 0 -0.3 158 158
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.026 0.029 0.33 1 -0.47 1 2
RhoA/GTP/ROCK1 0.034 0.011 -10000 0 -10000 0 0
mol:GDP 0.049 0.12 0.3 26 -0.24 3 29
mol:NADP 0.028 0.01 0.21 1 -10000 0 1
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.082 0.2 -10000 0 -0.47 87 87
mol:IP3 -0.13 0.22 0.34 4 -0.37 173 177
cell morphogenesis 0.033 0.011 -10000 0 -10000 0 0
PLCB2 -0.18 0.29 0.42 2 -0.5 173 175
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.005 0.081 0.28 1 -0.22 17 18
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.004 0.067 0.26 2 -0.27 9 11
RHOA 0.026 0.006 -10000 0 -10000 0 0
PTGIR 0.026 0.025 -10000 0 -0.47 1 1
PRKCB1 -0.13 0.21 0.38 2 -0.36 173 175
GNAQ 0.025 0.009 -10000 0 -10000 0 0
mol:L-citrulline 0.028 0.01 0.21 1 -10000 0 1
TXA2/TXA2-R family -0.19 0.29 0.43 2 -0.52 167 169
LCK 0.007 0.067 0.28 1 -0.32 3 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.02 0.055 -10000 0 -0.21 9 9
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.059 -10000 0 -0.37 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.055 -10000 0 -0.2 7 7
MAPK14 -0.072 0.14 0.27 4 -0.23 163 167
TGM2/GTP -0.15 0.24 0.42 3 -0.42 168 171
MAPK11 -0.073 0.14 0.27 4 -0.23 163 167
ARHGEF1 -0.057 0.1 0.22 3 -0.18 150 153
GNAI2 0.026 0.006 -10000 0 -10000 0 0
JNK cascade -0.13 0.22 0.35 4 -0.38 168 172
RAB11/GDP 0.027 0.004 -10000 0 -10000 0 0
ICAM1 -0.09 0.17 0.31 4 -0.28 166 170
cAMP biosynthetic process -0.12 0.2 0.33 4 -0.34 173 177
Gq family/GTP/EBP50 -0.02 0.088 0.21 2 -0.19 76 78
actin cytoskeleton reorganization 0.033 0.011 -10000 0 -10000 0 0
SRC 0.006 0.06 0.28 1 -0.33 1 2
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.027 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.015 0.084 0.24 14 -0.26 7 21
VCAM1 -0.1 0.18 0.31 4 -0.3 165 169
TP beta/Gq family/GDP/G beta5/gamma2 -0.03 0.14 -10000 0 -0.47 24 24
platelet activation -0.096 0.18 0.34 4 -0.3 166 170
PGI2/IP 0.019 0.018 -10000 0 -0.34 1 1
PRKACA 0.007 0.054 -10000 0 -0.24 19 19
Gq family/GDP/G beta5/gamma2 -0.029 0.13 -10000 0 -0.43 25 25
TXA2/TP beta/beta Arrestin2 -0.016 0.11 -10000 0 -0.39 28 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.001 0.051 0.2 1 -0.22 19 20
mol:DAG -0.14 0.24 0.4 2 -0.41 173 175
EGFR 0.021 0.085 0.33 8 -0.47 9 17
TXA2/TP alpha -0.17 0.27 0.44 2 -0.47 172 174
Gq family/GTP -0.02 0.089 0.23 2 -0.23 57 59
YES1 0.009 0.06 0.28 1 -0.33 1 2
GNAI2/GTP 0.011 0.052 -10000 0 -0.21 13 13
PGD2/DP 0.002 0.073 -10000 0 -0.34 18 18
SLC9A3R1 0.037 0.043 0.22 21 -10000 0 21
FYN 0.007 0.065 0.28 1 -0.28 4 5
mol:NO 0.028 0.01 0.21 1 -10000 0 1
GNA15 0.023 0.043 -10000 0 -0.47 3 3
PGK/cGMP -0.034 0.13 -10000 0 -0.28 86 86
RhoA/GDP 0.027 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.031 0.091 -10000 0 -0.4 8 8
NOS3 0.028 0.01 0.21 1 -10000 0 1
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.2 0.33 4 -0.34 158 162
PRKCB -0.16 0.23 0.38 2 -0.4 167 169
PRKCE -0.11 0.2 0.33 5 -0.34 160 165
PRKCD -0.13 0.22 0.32 5 -0.38 169 174
PRKCG -0.13 0.22 0.38 3 -0.38 166 169
muscle contraction -0.17 0.27 0.42 3 -0.48 168 171
PRKCZ -0.12 0.2 0.33 4 -0.34 167 171
ARR3 -0.009 0.018 -10000 0 -10000 0 0
TXA2/TP beta 0.024 0.061 -10000 0 -0.22 18 18
PRKCQ -0.12 0.22 0.33 8 -0.36 160 168
MAPKKK cascade -0.16 0.26 0.4 2 -0.45 173 175
SELE -0.14 0.22 0.31 4 -0.39 165 169
TP beta/GNAI2/GDP/G beta/gamma 0.037 0.068 -10000 0 -0.33 2 2
ROCK1 0.027 0.006 -10000 0 -10000 0 0
GNA14 -0.031 0.16 -10000 0 -0.47 45 45
chemotaxis -0.22 0.33 0.46 2 -0.61 165 167
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.006 -10000 0 -10000 0 0
GNA11 0.026 0.025 -10000 0 -0.47 1 1
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.072 0.18 0.26 1 -0.4 83 84
CRKL -0.08 0.18 -10000 0 -0.41 87 87
HRAS -0.075 0.19 -10000 0 -0.39 85 85
mol:PIP3 -0.078 0.18 -10000 0 -0.38 93 93
SPRED1 0.027 0.005 -10000 0 -10000 0 0
SPRED2 0.027 0.005 -10000 0 -10000 0 0
GAB1 -0.09 0.19 -10000 0 -0.43 90 90
FOXO3 -0.074 0.18 -10000 0 -0.38 90 90
AKT1 -0.079 0.19 -10000 0 -0.41 90 90
BAD -0.073 0.18 -10000 0 -0.38 85 85
megakaryocyte differentiation -0.091 0.19 -10000 0 -0.42 94 94
GSK3B -0.069 0.18 0.32 1 -0.38 85 86
RAF1 -0.054 0.15 0.26 3 -0.37 36 39
SHC1 0.026 0.017 0.33 1 -10000 0 1
STAT3 -0.091 0.19 -10000 0 -0.42 92 92
STAT1 -0.22 0.45 -10000 0 -1 95 95
HRAS/SPRED1 -0.052 0.16 -10000 0 -0.33 71 71
cell proliferation -0.09 0.19 -10000 0 -0.42 91 91
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.08 0.2 -10000 0 -0.42 93 93
HRAS/SPRED2 -0.051 0.16 -10000 0 -0.32 78 78
LYN/TEC/p62DOK -0.051 0.19 -10000 0 -0.4 80 80
MAPK3 -0.026 0.13 0.25 10 -0.28 25 35
STAP1 -0.1 0.2 -10000 0 -0.44 96 96
GRAP2 -0.026 0.15 -10000 0 -0.47 43 43
JAK2 -0.18 0.39 -10000 0 -0.87 93 93
STAT1 (dimer) -0.22 0.44 -10000 0 -0.98 95 95
mol:Gleevec 0.002 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.062 0.21 -10000 0 -0.42 88 88
actin filament polymerization -0.088 0.19 -10000 0 -0.42 91 91
LYN 0.025 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.14 0.27 -10000 0 -0.6 95 95
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
CBL/CRKL/GRB2 -0.053 0.18 -10000 0 -0.38 83 83
PI3K -0.058 0.2 -10000 0 -0.4 84 84
PTEN 0.026 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.24 0.54 -10000 0 -1.2 90 90
MAPK8 -0.092 0.19 -10000 0 -0.43 91 91
STAT3 (dimer) -0.089 0.19 -10000 0 -0.42 91 91
positive regulation of transcription -0.017 0.11 0.23 11 -0.23 25 36
mol:GDP -0.076 0.19 -10000 0 -0.4 85 85
PIK3C2B -0.091 0.19 -10000 0 -0.43 93 93
CBL/CRKL -0.064 0.18 -10000 0 -0.39 87 87
FER -0.092 0.19 -10000 0 -0.43 93 93
SH2B3 -0.087 0.19 -10000 0 -0.42 92 92
PDPK1 -0.071 0.17 -10000 0 -0.36 87 87
SNAI2 -0.091 0.19 -10000 0 -0.43 86 86
positive regulation of cell proliferation -0.16 0.32 -10000 0 -0.72 96 96
KITLG 0.009 0.063 -10000 0 -0.49 5 5
cell motility -0.16 0.32 -10000 0 -0.72 96 96
PTPN6 0.031 0.015 0.21 1 -10000 0 1
EPOR -0.071 0.24 -10000 0 -0.98 14 14
STAT5A (dimer) -0.13 0.27 -10000 0 -0.6 95 95
SOCS1 0.027 0.011 0.21 1 -10000 0 1
cell migration 0.1 0.2 0.44 97 -10000 0 97
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO 0.03 0.058 0.22 31 -10000 0 31
VAV1 0.008 0.098 0.21 2 -0.47 16 18
GRB10 -0.093 0.19 -10000 0 -0.43 90 90
PTPN11 0.029 0.01 -10000 0 -10000 0 0
SCF/KIT -0.094 0.2 -10000 0 -0.45 94 94
GO:0007205 0.004 0.01 -10000 0 -10000 0 0
MAP2K1 -0.031 0.14 0.26 9 -0.3 30 39
CBL 0.026 0.007 -10000 0 -10000 0 0
KIT -0.28 0.56 -10000 0 -1.3 95 95
MAP2K2 -0.029 0.14 0.26 10 -0.3 30 40
SHC/Grb2/SOS1 -0.051 0.19 -10000 0 -0.41 76 76
STAT5A -0.13 0.28 -10000 0 -0.61 95 95
GRB2 0.027 0.005 -10000 0 -10000 0 0
response to radiation -0.088 0.19 0.28 1 -0.42 86 87
SHC/GRAP2 0.004 0.11 0.24 1 -0.34 36 37
PTPRO -0.092 0.19 -10000 0 -0.43 94 94
SH2B2 -0.09 0.19 -10000 0 -0.42 91 91
DOK1 0.027 0.011 0.21 1 -10000 0 1
MATK -0.1 0.2 -10000 0 -0.44 97 97
CREBBP 0.01 0.064 -10000 0 -10000 0 0
BCL2 -0.13 0.37 -10000 0 -1.2 33 33
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.053 0.075 0.22 8 -0.25 3 11
STMN1 0.026 0.051 0.38 3 -10000 0 3
Aurora B/RasGAP/Survivin 0.18 0.12 0.3 167 -0.19 4 171
Chromosomal passenger complex/Cul3 protein complex -0.011 0.12 0.2 12 -0.26 39 51
BIRC5 0.16 0.095 0.22 288 -0.48 1 289
DES -0.32 0.31 -10000 0 -0.53 247 247
Aurora C/Aurora B/INCENP 0.1 0.07 0.23 10 -0.12 1 11
Aurora B/TACC1 0.071 0.072 0.17 7 -0.19 5 12
Aurora B/PP2A 0.095 0.073 0.18 52 -0.15 3 55
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.02 0.14 5 -0.1 3 8
mitotic metaphase/anaphase transition -0.002 0.004 -10000 0 -10000 0 0
NDC80 0.021 0.1 0.36 26 -0.19 2 28
Cul3 protein complex -0.028 0.13 -10000 0 -0.28 84 84
KIF2C 0.078 0.057 0.18 30 -10000 0 30
PEBP1 0.027 0.005 -10000 0 -10000 0 0
KIF20A 0.16 0.086 0.22 289 -10000 0 289
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.094 0.074 0.18 135 -0.15 3 138
SEPT1 0.027 0.03 0.21 3 -0.47 1 4
SMC2 0.025 0.013 0.21 1 -10000 0 1
SMC4 0.026 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.039 0.19 0.26 4 -0.55 33 37
PSMA3 0.027 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.004 -10000 0 -10000 0 0
H3F3B 0.038 0.036 0.2 3 -0.2 3 6
AURKB 0.12 0.099 0.23 178 -10000 0 178
AURKC 0.033 0.033 0.21 13 -10000 0 13
CDCA8 0.083 0.088 0.23 108 -10000 0 108
cytokinesis 0.061 0.085 0.24 8 -0.32 9 17
Aurora B/Septin1 0.11 0.13 0.29 28 -0.28 19 47
AURKA 0.085 0.093 0.22 122 -10000 0 122
INCENP 0.031 0.011 0.22 1 -10000 0 1
KLHL13 -0.077 0.2 -10000 0 -0.47 85 85
BUB1 0.064 0.077 0.22 79 -10000 0 79
hSgo1/Aurora B/Survivin 0.22 0.15 0.34 221 -0.2 3 224
EVI5 0.03 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.13 0.11 0.26 105 -0.3 1 106
SGOL1 0.11 0.1 0.22 170 -10000 0 170
CENPA 0.082 0.089 0.22 34 -0.25 5 39
NCAPG 0.11 0.093 0.21 177 -10000 0 177
Aurora B/HC8 Proteasome 0.097 0.073 0.19 29 -0.15 3 32
NCAPD2 0.028 0.016 0.33 1 -10000 0 1
Aurora B/PP1-gamma 0.097 0.073 0.22 3 -0.15 2 5
RHOA 0.026 0.006 -10000 0 -10000 0 0
NCAPH 0.14 0.094 0.22 249 -10000 0 249
NPM1 0.014 0.14 0.24 2 -0.39 32 34
RASA1 0.027 0.006 -10000 0 -10000 0 0
KLHL9 0.022 0.011 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.097 0.073 0.19 27 -0.15 3 30
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin 0.14 0.11 0.27 131 -0.28 2 133
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
NSUN2 0.039 0.11 0.21 19 -0.3 29 48
MYLK -0.078 0.17 0.19 3 -0.32 133 136
KIF23 0.12 0.095 0.22 197 -10000 0 197
VIM 0.037 0.067 0.3 13 -0.36 4 17
RACGAP1 0.033 0.02 0.22 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.007 0.17 0.24 1 -0.46 33 34
Chromosomal passenger complex 0.074 0.074 0.19 35 -0.24 4 39
Chromosomal passenger complex/EVI5 0.24 0.15 0.37 190 -0.25 1 191
TACC1 0.021 0.036 -10000 0 -0.47 2 2
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
CUL3 0.025 0.008 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.038 0.012 -10000 0 -10000 0 0
Necdin/E2F1 0.027 0.14 0.24 20 -0.34 39 59
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.028 0.17 -10000 0 -0.29 114 114
NGF (dimer)/p75(NTR)/BEX1 -0.078 0.2 0.35 1 -0.35 132 133
NT-4/5 (dimer)/p75(NTR) -0.061 0.18 0.24 1 -0.36 103 104
IKBKB 0.025 0.009 -10000 0 -10000 0 0
AKT1 -0.057 0.15 0.36 2 -0.28 105 107
IKBKG 0.027 0.005 -10000 0 -10000 0 0
BDNF -0.057 0.18 -10000 0 -0.47 67 67
MGDIs/NGR/p75(NTR)/LINGO1 0.001 0.16 0.29 10 -0.29 84 94
FURIN 0.028 0.01 0.21 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.071 0.18 0.24 1 -0.32 131 132
LINGO1 0.035 0.038 0.21 18 -10000 0 18
Sortilin/TRAF6/NRIF 0.026 0.018 -10000 0 -10000 0 0
proBDNF (dimer) -0.056 0.18 -10000 0 -0.47 67 67
NTRK1 0.025 0.032 0.23 7 -10000 0 7
RTN4R 0.055 0.07 0.22 60 -10000 0 60
neuron apoptosis -0.079 0.19 0.33 4 -0.47 49 53
IRAK1 0.027 0.004 -10000 0 -10000 0 0
SHC1 -0.071 0.16 0.23 1 -0.33 101 102
ARHGDIA 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.062 0.036 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.038 0.18 0.24 1 -0.3 116 117
MAGEH1 0.025 0.035 -10000 0 -0.47 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.068 0.2 0.24 1 -0.33 136 137
Mammalian IAPs/DIABLO 0.05 0.072 -10000 0 -0.26 18 18
proNGF (dimer) -0.039 0.17 -10000 0 -0.47 53 53
MAGED1 0.027 0.003 -10000 0 -10000 0 0
APP 0.026 0.025 -10000 0 -0.47 1 1
NT-4/5 (dimer) -0.007 0.12 -10000 0 -0.47 27 27
ZNF274 0.027 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.053 0.15 -10000 0 -0.28 113 113
NGF -0.039 0.17 -10000 0 -0.47 53 53
cell cycle arrest -0.07 0.14 0.24 12 -0.26 115 127
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.05 0.14 -10000 0 -0.28 93 93
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.038 0.16 0.24 1 -0.3 99 100
NCSTN 0.024 0.01 -10000 0 -10000 0 0
mol:GTP -0.057 0.18 0.23 1 -0.33 117 118
PSENEN 0.026 0.006 -10000 0 -10000 0 0
mol:ceramide -0.07 0.15 0.19 9 -0.3 115 124
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.043 0.12 0.24 1 -0.38 30 31
p75(NTR)/beta APP -0.037 0.15 0.24 1 -0.34 84 85
BEX1 -0.016 0.14 0.21 6 -0.47 32 38
mol:GDP -0.09 0.16 0.22 1 -0.33 116 117
NGF (dimer) 0.023 0.14 -10000 0 -0.28 67 67
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.015 0.15 0.29 8 -0.26 82 90
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
RAC1/GTP -0.045 0.15 0.21 1 -0.28 113 114
MYD88 0.026 0.006 -10000 0 -10000 0 0
CHUK 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.057 0.18 0.24 1 -0.33 117 118
RHOB 0.027 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.071 0.066 0.24 24 -10000 0 24
NT3 (dimer) -0.063 0.19 0.21 1 -0.47 72 73
TP53 -0.066 0.14 0.35 3 -0.26 122 125
PRDM4 -0.07 0.16 0.19 10 -0.3 115 125
BDNF (dimer) -0.026 0.19 0.29 6 -0.31 112 118
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
SORT1 0.028 0.002 -10000 0 -10000 0 0
activation of caspase activity -0.032 0.17 -10000 0 -0.28 114 114
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.038 0.17 -10000 0 -0.3 114 114
RHOC 0.028 0.002 -10000 0 -10000 0 0
XIAP 0.028 0.015 0.33 1 -10000 0 1
MAPK10 -0.11 0.18 0.39 1 -0.38 97 98
DIABLO 0.027 0.004 -10000 0 -10000 0 0
SMPD2 -0.07 0.16 0.19 9 -0.3 115 124
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.055 0.18 0.24 1 -0.33 115 116
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.098 0.2 0.24 1 -0.38 133 134
MAPK8 -0.09 0.18 0.36 5 -0.36 93 98
MAPK9 -0.09 0.18 0.43 3 -0.36 94 97
APAF1 0.027 0.004 -10000 0 -10000 0 0
NTF3 -0.063 0.19 0.21 1 -0.47 72 73
NTF4 -0.007 0.12 -10000 0 -0.47 27 27
NDN -0.026 0.15 -10000 0 -0.47 43 43
RAC1/GDP 0.02 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.028 0.16 -10000 0 -0.27 111 111
p75 CTF/Sortilin/TRAF6/NRIF 0.061 0.027 0.24 1 -10000 0 1
RhoA-B-C/GTP -0.057 0.18 0.23 1 -0.33 117 118
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.039 0.17 -10000 0 -0.28 126 126
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.052 0.17 0.24 1 -0.29 130 131
PRKACB 0.025 0.035 -10000 0 -0.47 2 2
proBDNF (dimer)/p75 ECD -0.024 0.14 -10000 0 -0.34 64 64
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.005 0.11 0.33 3 -0.47 19 22
BIRC2 0.028 0.022 0.33 2 -10000 0 2
neuron projection morphogenesis -0.094 0.16 0.2 1 -0.34 107 108
BAD -0.098 0.18 0.38 3 -0.37 94 97
RIPK2 0.024 0.01 -10000 0 -10000 0 0
NGFR -0.076 0.2 0.24 5 -0.47 86 91
CYCS -0.063 0.15 0.28 2 -0.28 112 114
ADAM17 0.027 0.016 0.33 1 -10000 0 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.034 0.16 -10000 0 -0.3 96 96
BCL2L11 -0.098 0.18 0.38 3 -0.37 93 96
BDNF (dimer)/p75(NTR) -0.097 0.2 0.24 1 -0.37 133 134
PI3K -0.037 0.17 -10000 0 -0.3 107 107
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.038 0.18 0.24 1 -0.3 115 116
NDNL2 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
PRKCI 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.082 0.2 0.24 1 -0.39 116 117
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.038 0.18 0.24 1 -0.3 115 116
TRAF6 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.024 0.043 -10000 0 -0.47 3 3
PLG -0.005 0.03 0.21 5 -10000 0 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.19 0.21 1 -0.34 153 154
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
NGFRAP1 0.025 0.035 -10000 0 -0.47 2 2
CASP3 -0.091 0.17 0.35 3 -0.35 94 97
E2F1 0.078 0.095 0.24 97 -10000 0 97
CASP9 0.027 0.003 -10000 0 -10000 0 0
IKK complex -0.014 0.15 -10000 0 -0.38 37 37
NGF (dimer)/TRKA -0.002 0.12 0.24 1 -0.34 45 46
MMP7 0.039 0.14 0.22 78 -0.47 20 98
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.027 0.17 -10000 0 -0.28 110 110
MMP3 -0.018 0.18 0.23 33 -0.47 48 81
APAF-1/Caspase 9 -0.061 0.13 -10000 0 -0.37 28 28
TCGA08_retinoblastoma

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
CDKN2B 0.027 0.057 0.22 22 -0.44 1 23
CDKN2C 0.027 0.026 0.23 2 -10000 0 2
CDKN2A 0.11 0.1 0.22 187 -10000 0 187
CCND2 -0.023 0.065 0.2 1 -0.2 26 27
RB1 0.016 0.073 0.32 10 -0.22 12 22
CDK4 -0.021 0.061 0.2 1 -0.34 10 11
CDK6 -0.025 0.069 0.21 1 -0.31 14 15
G1/S progression 0.027 0.11 0.18 112 -0.33 11 123
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.024 0.035 -10000 0 -0.47 2 2
LAT2 -0.075 0.15 -10000 0 -0.33 82 82
AP1 -0.13 0.23 -10000 0 -0.46 98 98
mol:PIP3 -0.078 0.2 0.32 6 -0.38 86 92
IKBKB -0.051 0.14 0.25 13 -0.27 68 81
AKT1 -0.029 0.17 0.32 25 -0.36 28 53
IKBKG -0.059 0.13 0.24 8 -0.27 71 79
MS4A2 -0.1 0.21 -10000 0 -0.46 108 108
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
MAP3K1 -0.061 0.17 0.25 10 -0.39 57 67
mol:Ca2+ -0.055 0.16 0.24 13 -0.29 86 99
LYN 0.026 0.012 -10000 0 -10000 0 0
CBLB -0.075 0.15 -10000 0 -0.32 83 83
SHC1 0.026 0.017 0.33 1 -10000 0 1
RasGAP/p62DOK -0.029 0.13 -10000 0 -0.26 98 98
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.018 0.06 -10000 0 -0.47 6 6
PLD2 -0.048 0.17 0.31 20 -0.28 114 134
PTPN13 -0.069 0.18 -10000 0 -0.53 19 19
PTPN11 0.018 0.023 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.032 0.14 0.33 10 -0.32 27 37
SYK 0.02 0.052 -10000 0 -0.48 4 4
GRB2 0.027 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.095 0.18 -10000 0 -0.39 90 90
LAT -0.072 0.15 -10000 0 -0.33 80 80
PAK2 -0.072 0.19 0.26 10 -0.42 61 71
NFATC2 -0.11 0.21 -10000 0 -0.55 67 67
HRAS -0.084 0.2 0.29 2 -0.44 72 74
GAB2 0.025 0.025 -10000 0 -0.47 1 1
PLA2G1B 0.017 0.08 -10000 0 -0.82 3 3
Fc epsilon R1 -0.075 0.19 0.22 1 -0.34 123 124
Antigen/IgE/Fc epsilon R1 -0.066 0.17 0.21 1 -0.31 122 123
mol:GDP -0.092 0.21 0.24 1 -0.48 67 68
JUN 0.01 0.091 -10000 0 -0.47 14 14
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.024 0.026 -10000 0 -0.47 1 1
FOS -0.12 0.23 -10000 0 -0.47 124 124
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.075 0.16 -10000 0 -0.34 84 84
CHUK -0.061 0.13 0.26 6 -0.27 71 77
KLRG1 -0.067 0.14 -10000 0 -0.3 80 80
VAV1 -0.083 0.16 -10000 0 -0.34 90 90
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.073 0.15 -10000 0 -0.33 80 80
negative regulation of mast cell degranulation -0.053 0.15 -10000 0 -0.35 51 51
BTK -0.1 0.22 -10000 0 -0.53 62 62
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.095 0.2 -10000 0 -0.35 120 120
GAB2/PI3K/SHP2 -0.068 0.13 -10000 0 -0.29 70 70
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.078 0.17 -10000 0 -0.34 87 87
RAF1 0.017 0.09 -10000 0 -0.91 3 3
Fc epsilon R1/FcgammaRIIB/SHIP -0.064 0.19 -10000 0 -0.31 130 130
FCER1G 0.029 0.059 0.23 14 -0.46 3 17
FCER1A -0.075 0.2 0.22 1 -0.48 79 80
Antigen/IgE/Fc epsilon R1/Fyn -0.056 0.17 -10000 0 -0.29 123 123
MAPK3 0.016 0.081 -10000 0 -0.83 3 3
MAPK1 0.016 0.081 -10000 0 -0.83 3 3
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.059 0.22 -10000 0 -0.64 42 42
DUSP1 -0.1 0.22 -10000 0 -0.47 105 105
NF-kappa-B/RelA -0.031 0.082 -10000 0 -0.17 55 55
actin cytoskeleton reorganization -0.071 0.18 -10000 0 -0.5 26 26
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.069 0.18 -10000 0 -0.43 55 55
FER -0.074 0.15 -10000 0 -0.33 83 83
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.061 0.14 -10000 0 -0.42 52 52
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 -0.083 0.21 0.33 3 -0.42 86 89
cytokine secretion -0.027 0.055 -10000 0 -0.15 12 12
SPHK1 -0.076 0.15 -10000 0 -0.33 80 80
PTK2 -0.075 0.18 -10000 0 -0.55 21 21
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.098 0.2 -10000 0 -0.4 90 90
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.077 0.2 0.34 4 -0.38 87 91
MAP2K2 0.012 0.082 -10000 0 -0.85 3 3
MAP2K1 0.012 0.082 -10000 0 -0.85 3 3
MAP2K7 0.027 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.057 0.13 -10000 0 -0.32 50 50
MAP2K4 -0.07 0.3 -10000 0 -0.9 46 46
Fc epsilon R1/FcgammaRIIB -0.072 0.19 -10000 0 -0.33 130 130
mol:Choline -0.047 0.17 0.3 20 -0.28 114 134
SHC/Grb2/SOS1 -0.038 0.16 -10000 0 -0.37 46 46
FYN 0.022 0.043 -10000 0 -0.47 3 3
DOK1 0.027 0.011 0.21 1 -10000 0 1
PXN -0.067 0.18 -10000 0 -0.53 18 18
HCLS1 -0.074 0.15 -10000 0 -0.33 81 81
PRKCB -0.088 0.18 0.3 5 -0.35 86 91
FCGR2B -0.005 0.12 0.25 3 -0.47 24 27
IGHE 0 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.054 0.15 -10000 0 -0.36 51 51
LCP2 0.022 0.043 -10000 0 -0.47 3 3
PLA2G4A -0.085 0.16 -10000 0 -0.34 93 93
RASA1 0.027 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.047 0.17 0.3 20 -0.28 114 134
IKK complex -0.033 0.11 0.26 13 -0.21 58 71
WIPF1 0.012 0.084 -10000 0 -0.47 12 12
Glypican 2 network

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
MDK 0.037 0.047 0.22 23 -9999 0 23
GPC2 0.093 0.092 0.22 139 -9999 0 139
GPC2/Midkine 0.088 0.076 0.29 19 -9999 0 19
neuron projection morphogenesis 0.088 0.076 0.29 19 -9999 0 19
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.009 0.12 -10000 0 -0.25 67 67
ER alpha/Gai/GDP/Gbeta gamma -0.19 0.31 -10000 0 -0.61 117 117
AKT1 -0.16 0.36 -10000 0 -0.86 82 82
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.16 0.37 -10000 0 -0.88 82 82
mol:Ca2+ -0.054 0.16 -10000 0 -0.39 64 64
IGF1R 0.025 0.035 -10000 0 -0.47 2 2
E2/ER alpha (dimer)/Striatin -0.017 0.12 -10000 0 -0.28 64 64
SHC1 0.026 0.017 0.33 1 -10000 0 1
apoptosis 0.15 0.34 0.81 82 -10000 0 82
RhoA/GTP -0.013 0.084 -10000 0 -0.22 56 56
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.14 0.26 -10000 0 -0.51 112 112
regulation of stress fiber formation 0.025 0.08 0.3 3 -0.31 1 4
E2/ERA-ERB (dimer) -0.017 0.12 -10000 0 -0.28 66 66
KRAS 0.027 0.016 0.33 1 -10000 0 1
G13/GTP -0.014 0.11 -10000 0 -0.26 64 64
pseudopodium formation -0.025 0.08 0.31 1 -0.3 3 4
E2/ER alpha (dimer)/PELP1 -0.019 0.12 -10000 0 -0.28 65 65
GRB2 0.027 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.06 -10000 0 -0.47 6 6
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
HRAS 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.28 -10000 0 -0.63 86 86
E2/ER beta (dimer) 0.021 0.01 0.15 2 -10000 0 2
mol:GDP -0.043 0.14 -10000 0 -0.34 70 70
mol:NADP -0.14 0.28 -10000 0 -0.63 86 86
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
mol:IP3 -0.065 0.16 -10000 0 -0.4 64 64
IGF-1R heterotetramer 0.025 0.035 -10000 0 -0.47 2 2
PLCB1 -0.06 0.16 -10000 0 -0.42 60 60
PLCB2 -0.057 0.16 -10000 0 -0.41 62 62
IGF1 -0.19 0.24 -10000 0 -0.47 176 176
mol:L-citrulline -0.14 0.28 -10000 0 -0.63 86 86
RHOA 0.026 0.006 -10000 0 -10000 0 0
Gai/GDP -0.27 0.4 -10000 0 -0.78 144 144
JNK cascade 0.021 0.01 0.15 2 -10000 0 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.028 0.014 0.21 2 -10000 0 2
GNAQ 0.025 0.009 -10000 0 -10000 0 0
ESR1 -0.054 0.18 -10000 0 -0.47 66 66
Gq family/GDP/Gbeta gamma -0.023 0.16 -10000 0 -0.71 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.018 0.11 -10000 0 -0.39 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.13 0.26 -10000 0 -0.5 110 110
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
E2/ER alpha (dimer) -0.038 0.13 -10000 0 -0.33 66 66
STRN 0.027 0.005 -10000 0 -10000 0 0
GNAL -0.17 0.24 -10000 0 -0.47 163 163
PELP1 0.025 0.008 -10000 0 -10000 0 0
MAPK11 0.014 0.006 -10000 0 -10000 0 0
GNAI2 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.028 0.003 -10000 0 -10000 0 0
GNAI1 0.024 0.043 -10000 0 -0.47 3 3
HBEGF -0.17 0.29 0.35 10 -0.57 109 119
cAMP biosynthetic process -0.11 0.16 -10000 0 -0.27 189 189
SRC -0.18 0.29 0.35 1 -0.57 115 116
PI3K 0.035 0.023 -10000 0 -0.34 1 1
GNB1 0.027 0.003 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.015 0.14 -10000 0 -0.33 55 55
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.18 0.23 -10000 0 -0.46 144 144
Gs family/GTP -0.11 0.17 -10000 0 -0.28 189 189
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.021 0.22 1 -10000 0 1
vasodilation -0.14 0.26 -10000 0 -0.6 86 86
mol:DAG -0.065 0.16 -10000 0 -0.4 64 64
Gs family/GDP/Gbeta gamma -0.11 0.17 -10000 0 -0.4 75 75
MSN -0.027 0.085 0.31 1 -0.33 3 4
Gq family/GTP -0.052 0.17 -10000 0 -0.44 59 59
mol:PI-3-4-5-P3 -0.15 0.35 -10000 0 -0.84 82 82
NRAS 0.028 0.002 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.14 0.26 0.6 86 -10000 0 86
GRB2/SOS1 0.039 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.14 -10000 0 -0.33 67 67
NOS3 -0.15 0.3 -10000 0 -0.68 86 86
GNA11 0.026 0.025 -10000 0 -0.47 1 1
MAPKKK cascade -0.12 0.28 -10000 0 -0.66 80 80
E2/ER alpha (dimer)/PELP1/Src -0.15 0.27 0.27 1 -0.53 113 114
ruffle organization -0.025 0.08 0.31 1 -0.3 3 4
ROCK2 -0.013 0.094 0.34 2 -0.32 2 4
GNA14 -0.031 0.16 -10000 0 -0.47 45 45
GNA15 0.023 0.043 -10000 0 -0.47 3 3
GNA13 0.027 0.006 -10000 0 -10000 0 0
MMP9 -0.16 0.28 0.4 10 -0.57 101 111
MMP2 -0.18 0.29 0.3 3 -0.58 111 114
LPA receptor mediated events

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
GNB1/GNG2 0.005 0.12 -10000 0 -0.26 58 58
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.11 0.3 1 -0.3 19 20
AP1 -0.1 0.19 -10000 0 -0.31 158 158
mol:PIP3 -0.037 0.11 -10000 0 -0.29 48 48
AKT1 -0.001 0.098 0.25 4 -0.31 10 14
PTK2B -0.056 0.12 0.2 2 -0.29 62 64
RHOA -0.005 0.067 0.28 1 -0.27 13 14
PIK3CB 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.083 0.23 4 -0.24 32 36
MAGI3 0.028 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.04 0.13 0.19 1 -0.28 80 81
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.059 0.13 0.23 9 -0.32 50 59
NF kappa B1 p50/RelA -0.037 0.12 -10000 0 -0.3 53 53
endothelial cell migration -0.046 0.17 -10000 0 -0.45 56 56
ADCY4 -0.13 0.21 -10000 0 -0.41 116 116
ADCY5 -0.24 0.28 -10000 0 -0.52 167 167
ADCY6 -0.13 0.2 -10000 0 -0.41 114 114
ADCY7 -0.13 0.2 -10000 0 -0.41 113 113
ADCY1 -0.12 0.2 -10000 0 -0.4 113 113
ADCY2 -0.2 0.26 -10000 0 -0.46 158 158
ADCY3 -0.12 0.2 -10000 0 -0.41 113 113
ADCY8 -0.12 0.2 -10000 0 -0.4 109 109
ADCY9 -0.13 0.22 -10000 0 -0.43 116 116
GSK3B -0.05 0.12 0.2 9 -0.32 43 52
arachidonic acid secretion -0.14 0.21 -10000 0 -0.42 125 125
GNG2 0.02 0.06 -10000 0 -0.47 6 6
TRIP6 0.019 0.017 -10000 0 -10000 0 0
GNAO1 -0.11 0.18 -10000 0 -0.33 150 150
HRAS 0.025 0.008 -10000 0 -10000 0 0
NFKBIA -0.039 0.11 0.3 1 -0.3 35 36
GAB1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.02 0.16 -10000 0 -0.83 13 13
JUN 0.01 0.091 -10000 0 -0.47 14 14
LPA/LPA2/NHERF2 0.028 0.034 -10000 0 -10000 0 0
TIAM1 0.001 0.18 -10000 0 -0.97 13 13
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
mol:IP3 -0.021 0.083 0.23 4 -0.24 33 37
PLCB3 0.013 0.03 0.2 3 -10000 0 3
FOS -0.12 0.23 -10000 0 -0.47 124 124
positive regulation of mitosis -0.14 0.21 -10000 0 -0.42 125 125
LPA/LPA1-2-3 -0.015 0.14 0.23 1 -0.28 81 82
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation -0.036 0.12 0.29 1 -0.34 30 31
GNAZ -0.083 0.16 -10000 0 -0.31 125 125
EGFR/PI3K-beta/Gab1 -0.03 0.12 -10000 0 -0.3 48 48
positive regulation of dendritic cell cytokine production -0.016 0.14 0.22 1 -0.27 81 82
LPA/LPA2/MAGI-3 0.029 0.034 -10000 0 -10000 0 0
ARHGEF1 -0.001 0.11 0.2 29 -0.25 46 75
GNAI2 -0.023 0.11 -10000 0 -0.28 56 56
GNAI3 -0.024 0.11 -10000 0 -0.28 58 58
GNAI1 -0.024 0.11 -10000 0 -0.28 57 57
LPA/LPA3 -0.016 0.1 0.15 3 -0.25 55 58
LPA/LPA2 0.013 0.034 0.15 1 -0.11 21 22
LPA/LPA1 -0.026 0.13 -10000 0 -0.33 58 58
HB-EGF/EGFR 0.021 0.094 0.26 12 -0.33 21 33
HBEGF 0.01 0.085 0.3 6 -0.38 14 20
mol:DAG -0.021 0.083 0.23 4 -0.24 33 37
cAMP biosynthetic process -0.16 0.23 0.29 1 -0.43 141 142
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
GNB1 0.027 0.003 -10000 0 -10000 0 0
LYN -0.029 0.11 0.27 3 -0.3 32 35
GNAQ -0.011 0.079 0.19 1 -0.26 33 34
LPAR2 0.029 0.023 0.29 3 -10000 0 3
LPAR3 -0.012 0.14 0.24 5 -0.47 33 38
LPAR1 -0.022 0.14 -10000 0 -0.35 53 53
IL8 -0.097 0.22 0.34 1 -0.5 76 77
PTK2 -0.028 0.12 0.21 8 -0.27 65 73
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
CASP3 -0.04 0.13 0.19 1 -0.28 80 81
EGFR 0.021 0.085 0.33 8 -0.47 9 17
PLCG1 -0.021 0.093 0.21 6 -0.26 41 47
PLD2 -0.034 0.12 0.21 8 -0.27 74 82
G12/G13 0.007 0.11 -10000 0 -0.26 52 52
PI3K-beta -0.021 0.093 -10000 0 -0.31 17 17
cell migration 0.002 0.074 0.2 2 -0.26 12 14
SLC9A3R2 0.027 0.006 -10000 0 -10000 0 0
PXN -0.036 0.12 0.29 1 -0.34 30 31
HRAS/GTP -0.14 0.22 -10000 0 -0.43 124 124
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 0.068 0.1 0.22 102 -0.47 5 107
PRKCE 0.027 0.006 -10000 0 -10000 0 0
PRKCD -0.023 0.084 0.23 3 -0.24 31 34
Gi(beta/gamma) -0.12 0.2 -10000 0 -0.39 116 116
mol:LPA -0.01 0.044 -10000 0 -0.17 28 28
TRIP6/p130 Cas/FAK1/Paxillin -0.021 0.13 0.3 1 -0.4 20 21
MAPKKK cascade -0.14 0.21 -10000 0 -0.42 125 125
contractile ring contraction involved in cytokinesis -0.004 0.069 0.28 1 -0.26 14 15
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.041 0.12 0.19 1 -0.27 75 76
GNA15 -0.011 0.081 0.19 1 -0.26 35 36
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.006 -10000 0 -10000 0 0
MAPT -0.062 0.13 0.24 8 -0.33 50 58
GNA11 -0.009 0.081 0.19 1 -0.27 32 33
Rac1/GTP 0.02 0.16 -10000 0 -0.88 13 13
MMP2 -0.046 0.17 -10000 0 -0.45 56 56
Ephrin A reverse 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
MAPKKK cascade -0.019 0.12 -10000 0 -0.29 64 64
EFNA5 0.011 0.088 0.21 1 -0.47 13 14
FYN -0.031 0.11 0.19 5 -0.26 67 72
neuron projection morphogenesis -0.019 0.12 -10000 0 -0.29 64 64
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.019 0.12 -10000 0 -0.29 64 64
EPHA5 -0.057 0.16 0.21 2 -0.47 53 55
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 -0.029 0.23 0.28 16 -0.5 61 77
FYN -0.079 0.3 0.29 12 -0.66 71 83
LAT/GRAP2/SLP76 -0.052 0.25 0.26 8 -0.53 71 79
IKBKB 0.025 0.009 -10000 0 -10000 0 0
AKT1 -0.046 0.2 0.25 9 -0.41 76 85
B2M 0.026 0.01 -10000 0 -10000 0 0
IKBKG -0.006 0.059 0.11 8 -0.13 43 51
MAP3K8 0.024 0.035 -10000 0 -0.47 2 2
mol:Ca2+ -0.019 0.023 0.083 3 -0.063 40 43
integrin-mediated signaling pathway 0.033 0.032 -10000 0 -0.28 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.079 0.28 0.29 8 -0.61 75 83
TRPV6 -0.046 0.18 0.93 5 -0.46 40 45
CD28 0.008 0.099 0.21 2 -0.47 16 18
SHC1 -0.065 0.28 0.28 21 -0.57 77 98
receptor internalization -0.087 0.29 0.2 3 -0.57 86 89
PRF1 -0.089 0.34 -10000 0 -0.85 52 52
KRAS 0.027 0.016 0.33 1 -10000 0 1
GRB2 0.027 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.024 0.16 0.24 7 -0.34 65 72
LAT -0.071 0.28 0.26 10 -0.57 79 89
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.012 0.14 0.22 3 -0.48 32 35
CD3E -0.021 0.15 -10000 0 -0.48 39 39
CD3G -0.026 0.15 -10000 0 -0.47 42 42
RASGRP2 -0.038 0.079 0.081 1 -0.17 103 104
RASGRP1 -0.035 0.2 0.26 9 -0.43 66 75
HLA-A 0 0.005 -10000 0 -10000 0 0
RASSF5 0.022 0.049 -10000 0 -0.47 4 4
RAP1A/GTP/RAPL 0.033 0.032 -10000 0 -0.28 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.073 0.15 19 -0.14 42 61
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.034 0.081 -10000 0 -0.21 59 59
PRKCA -0.019 0.12 0.17 15 -0.27 60 75
GRAP2 -0.026 0.15 -10000 0 -0.47 43 43
mol:IP3 -0.042 0.18 0.22 35 -0.4 70 105
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.081 0.27 -10000 0 -0.63 62 62
ORAI1 0.024 0.12 0.4 2 -0.76 5 7
CSK -0.076 0.28 0.27 9 -0.59 78 87
B7 family/CD28 -0.033 0.29 0.29 8 -0.62 64 72
CHUK 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.1 0.32 -10000 0 -0.67 80 80
PTPN6 -0.079 0.28 0.24 10 -0.59 78 88
VAV1 -0.082 0.29 0.26 8 -0.6 78 86
Monovalent TCR/CD3 -0.057 0.21 -10000 0 -0.46 67 67
CBL 0.026 0.007 -10000 0 -10000 0 0
LCK -0.079 0.3 0.28 12 -0.66 70 82
PAG1 -0.071 0.28 0.26 11 -0.58 78 89
RAP1A 0.028 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.099 0.32 -10000 0 -0.65 81 81
CD80 0.05 0.065 0.21 54 -10000 0 54
CD86 0.022 0.051 0.21 1 -0.47 4 5
PDK1/CARD11/BCL10/MALT1 -0.03 0.1 -10000 0 -0.25 61 61
HRAS 0.025 0.008 -10000 0 -10000 0 0
GO:0035030 -0.056 0.22 0.23 6 -0.51 64 70
CD8A -0.02 0.15 0.22 1 -0.48 39 40
CD8B -0.013 0.14 0.22 7 -0.48 35 42
PTPRC -0.027 0.16 0.21 2 -0.47 44 46
PDK1/PKC theta -0.054 0.24 0.27 11 -0.51 74 85
CSK/PAG1 -0.063 0.28 0.29 18 -0.56 77 95
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 -0.07 0.29 0.27 6 -0.6 79 85
STIM1 0.008 0.044 -10000 0 -10000 0 0
RAS family/GTP 0.015 0.094 0.18 18 -0.18 42 60
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.096 0.31 0.2 2 -0.62 86 88
mol:DAG -0.057 0.15 0.11 7 -0.35 72 79
RAP1A/GDP 0.006 0.035 0.079 11 -0.065 23 34
PLCG1 0.026 0.007 -10000 0 -10000 0 0
CD247 0.018 0.062 0.21 1 -0.47 6 7
cytotoxic T cell degranulation -0.083 0.31 -10000 0 -0.8 52 52
RAP1A/GTP -0.015 0.029 -10000 0 -0.064 103 103
mol:PI-3-4-5-P3 -0.058 0.23 0.26 10 -0.49 75 85
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.052 0.24 0.24 35 -0.52 70 105
NRAS 0.028 0.002 -10000 0 -10000 0 0
ZAP70 0.01 0.091 0.21 1 -0.47 14 15
GRB2/SOS1 0.039 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.064 0.23 -10000 0 -0.52 71 71
MALT1 0.026 0.007 -10000 0 -10000 0 0
TRAF6 0.026 0.008 -10000 0 -10000 0 0
CD8 heterodimer -0.02 0.18 0.32 1 -0.45 53 54
CARD11 0.022 0.066 0.3 4 -0.47 6 10
PRKCB -0.056 0.15 0.16 8 -0.31 83 91
PRKCE -0.017 0.12 0.17 14 -0.27 58 72
PRKCQ -0.067 0.28 0.28 10 -0.58 77 87
LCP2 0.022 0.043 -10000 0 -0.47 3 3
BCL10 0.027 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.035 0.17 0.23 11 -0.35 73 84
IKK complex 0.001 0.069 0.16 19 -0.12 43 62
RAS family/GDP -0.005 0.013 -10000 0 -10000 0 0
MAP3K14 -0.017 0.12 0.19 9 -0.26 61 70
PDPK1 -0.041 0.18 0.25 8 -0.4 71 79
TCR/CD3/MHC I/CD8/Fyn -0.12 0.35 -10000 0 -0.75 78 78
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.038 0.021 -10000 0 -0.34 1 1
alphaV beta3 Integrin -0.082 0.2 -10000 0 -0.35 131 131
PTK2 -0.08 0.21 0.33 7 -0.5 50 57
IGF1R 0.025 0.035 -10000 0 -0.47 2 2
PI4KB 0.024 0.009 -10000 0 -10000 0 0
MFGE8 0.025 0.035 -10000 0 -0.47 2 2
SRC 0.026 0.007 -10000 0 -10000 0 0
CDKN1B -0.11 0.23 -10000 0 -0.61 62 62
VEGFA 0.027 0.005 -10000 0 -10000 0 0
ILK -0.12 0.24 -10000 0 -0.6 73 73
ROCK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.11 0.23 -10000 0 -0.56 73 73
PTK2B -0.006 0.091 0.36 1 -0.25 41 42
alphaV/beta3 Integrin/JAM-A -0.09 0.2 0.28 1 -0.35 135 136
CBL 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.014 0.11 -10000 0 -0.29 44 44
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.08 0.17 -10000 0 -0.27 176 176
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.028 0.11 -10000 0 -0.37 23 23
alphaV/beta3 Integrin/Syndecan-1 0.011 0.11 -10000 0 -0.28 46 46
PI4KA 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.26 -10000 0 -0.4 196 196
PI4 Kinase 0.035 0.015 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.056 0.14 -10000 0 -0.29 43 43
RPS6KB1 -0.18 0.22 -10000 0 -0.46 125 125
TLN1 0.025 0.009 -10000 0 -10000 0 0
MAPK3 -0.23 0.34 -10000 0 -0.65 142 142
GPR124 -0.016 0.13 -10000 0 -0.47 32 32
MAPK1 -0.23 0.34 -10000 0 -0.65 143 143
PXN 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
alphaV/beta3 Integrin/Tumstatin -0.069 0.18 -10000 0 -0.32 129 129
cell adhesion 0.008 0.1 -10000 0 -0.29 42 42
ANGPTL3 0.017 0.03 0.21 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.049 0.025 -10000 0 -0.28 1 1
IGF-1R heterotetramer 0.025 0.035 -10000 0 -0.47 2 2
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.024 0.035 -10000 0 -0.47 2 2
ITGB3 -0.027 0.15 -10000 0 -0.47 44 44
IGF1 -0.19 0.24 -10000 0 -0.47 176 176
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.014 0.14 -10000 0 -0.35 55 55
apoptosis 0.027 0.006 -10000 0 -10000 0 0
CD47 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.015 0.1 -10000 0 -0.29 41 41
VCL 0.027 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.027 0.17 -10000 0 -0.36 76 76
CSF1 0.009 0.094 -10000 0 -0.47 15 15
PIK3C2A -0.12 0.24 -10000 0 -0.59 73 73
PI4 Kinase/Pyk2 -0.084 0.17 -10000 0 -0.32 117 117
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.028 0.1 -10000 0 -0.27 41 41
FAK1/Vinculin -0.052 0.18 0.34 8 -0.4 48 56
alphaV beta3/Integrin/ppsTEM5 -0.014 0.14 -10000 0 -0.36 55 55
RHOA 0.026 0.006 -10000 0 -10000 0 0
VTN -0.045 0.18 0.21 7 -0.47 60 67
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 -0.13 0.23 -10000 0 -0.47 127 127
F11R -0.077 0.15 -10000 0 -0.34 102 102
alphaV/beta3 Integrin/Lactadherin 0.014 0.11 -10000 0 -0.28 45 45
alphaV/beta3 Integrin/TGFBR2 0.014 0.11 -10000 0 -0.29 41 41
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.065 -10000 0 -0.26 15 15
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.014 0.093 -10000 0 -0.26 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.025 0.094 0.21 26 -0.47 11 37
alphaV/beta3 Integrin/Pyk2 0.013 0.094 -10000 0 -0.25 41 41
SDC1 0.019 0.06 -10000 0 -0.47 6 6
VAV3 0.012 0.07 0.21 17 -0.24 18 35
PTPN11 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.017 0.065 -10000 0 -0.47 7 7
FAK1/Paxillin -0.052 0.18 0.34 8 -0.4 49 57
cell migration -0.048 0.16 0.29 14 -0.36 48 62
ITGAV 0.027 0.006 -10000 0 -10000 0 0
PI3K -0.073 0.19 0.25 1 -0.32 128 129
SPP1 0.1 0.091 0.21 161 -10000 0 161
KDR 0.025 0.035 -10000 0 -0.47 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.006 -10000 0 -10000 0 0
COL4A3 -0.1 0.21 0.21 4 -0.47 102 106
angiogenesis -0.21 0.35 0.29 2 -0.65 140 142
Rac1/GTP 0.023 0.062 0.28 1 -0.22 16 17
EDIL3 -0.041 0.17 -10000 0 -0.47 55 55
cell proliferation 0.014 0.1 -10000 0 -0.29 41 41
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
CDC42/GTP -0.085 0.17 -10000 0 -0.31 120 120
PLCG1 -0.092 0.16 -10000 0 -0.32 114 114
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.028 0.003 -10000 0 -10000 0 0
G12/G13 0.037 0.012 -10000 0 -10000 0 0
cell migration -0.084 0.16 -10000 0 -0.3 120 120
S1PR5 0.031 0.051 0.23 13 -0.47 2 15
S1PR4 0.025 0.046 0.21 3 -0.47 3 6
MAPK3 -0.093 0.16 -10000 0 -0.31 118 118
MAPK1 -0.096 0.17 -10000 0 -0.32 119 119
S1P/S1P5/Gi -0.094 0.18 -10000 0 -0.33 119 119
GNAI1 0.024 0.043 -10000 0 -0.47 3 3
CDC42/GDP 0.02 0.002 -10000 0 -10000 0 0
S1P/S1P5/G12 0.036 0.031 -10000 0 -0.28 2 2
RHOA 0.026 0.053 0.2 29 -0.24 2 31
S1P/S1P4/Gi -0.097 0.18 -10000 0 -0.3 152 152
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
S1P/S1P4/G12/G13 0.046 0.03 -10000 0 -0.26 2 2
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.028 0.003 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.012 0.07 -10000 0 -0.31 18 18
NFATC2 -0.047 0.11 -10000 0 -0.3 65 65
NFATC3 -0.001 0.028 -10000 0 -10000 0 0
CD40LG -0.18 0.26 -10000 0 -0.54 110 110
PTGS2 -0.2 0.28 -10000 0 -0.56 133 133
JUNB 0.021 0.055 -10000 0 -0.47 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.023 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.023 -10000 0 -10000 0 0
CALM1 0.02 0.018 -10000 0 -10000 0 0
JUN 0.003 0.092 -10000 0 -0.48 14 14
mol:Ca2+ -0.004 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
FOSL1 -0.006 0.12 -10000 0 -0.47 27 27
CREM 0.026 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.05 0.18 -10000 0 -0.38 58 58
FOS -0.13 0.23 -10000 0 -0.47 124 124
IFNG -0.14 0.24 -10000 0 -0.48 100 100
AP-1/NFAT1-c-4 -0.15 0.3 -10000 0 -0.56 103 103
FASLG -0.16 0.24 -10000 0 -0.5 102 102
NFAT1-c-4/ICER1 -0.047 0.13 -10000 0 -0.29 68 68
IL2RA -0.16 0.25 -10000 0 -0.51 103 103
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.15 0.24 -10000 0 -0.49 101 101
JunB/Fra1/NFAT1-c-4 -0.051 0.16 -10000 0 -0.32 71 71
IL4 -0.16 0.23 -10000 0 -0.49 102 102
IL2 -0.01 0.14 -10000 0 -0.95 8 8
IL3 -0.018 0.13 -10000 0 -0.72 13 13
FKBP1A 0.026 0.006 -10000 0 -10000 0 0
BATF3 0.023 0.058 0.21 4 -0.47 5 9
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.009 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.12 0.22 -10000 0 -0.51 60 60
MAP3K8 0.021 0.036 -10000 0 -0.47 2 2
FOS -0.086 0.17 -10000 0 -0.4 61 61
PRKCA 0.011 0.052 -10000 0 -0.47 4 4
PTPN7 0.007 0.067 0.19 4 -0.47 6 10
HRAS 0.025 0.008 -10000 0 -10000 0 0
PRKCB -0.12 0.22 -10000 0 -0.47 112 112
NRAS 0.027 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.037 0.026 -10000 0 -10000 0 0
MAPK3 -0.044 0.13 -10000 0 -0.55 14 14
MAP2K1 -0.1 0.2 -10000 0 -0.4 116 116
ELK1 0.01 0.027 -10000 0 -10000 0 0
BRAF -0.1 0.19 -10000 0 -0.39 114 114
mol:GTP -0.001 0.002 -10000 0 -0.005 128 128
MAPK1 -0.046 0.13 -10000 0 -0.54 16 16
RAF1 -0.094 0.18 0.22 1 -0.39 104 105
KRAS 0.026 0.016 0.33 1 -10000 0 1
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.21 0.58 -10000 0 -1.3 73 73
IL23A -0.16 0.5 -10000 0 -1.2 57 57
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.5 -10000 0 -1.1 68 68
positive regulation of T cell mediated cytotoxicity -0.2 0.57 -10000 0 -1.2 69 69
ITGA3 -0.16 0.49 -10000 0 -1.1 62 62
IL17F -0.1 0.34 -10000 0 -0.7 65 65
IL12B 0.021 0.072 0.27 12 -10000 0 12
STAT1 (dimer) -0.19 0.54 -10000 0 -1.2 69 69
CD4 -0.16 0.49 -10000 0 -1.1 62 62
IL23 -0.15 0.48 -10000 0 -1.1 58 58
IL23R 0.014 0.11 -10000 0 -0.88 1 1
IL1B -0.18 0.54 -10000 0 -1.2 60 60
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.16 0.49 -10000 0 -1.1 63 63
TYK2 0.013 0.044 -10000 0 -10000 0 0
STAT4 0.002 0.11 -10000 0 -0.47 20 20
STAT3 0.027 0.005 -10000 0 -10000 0 0
IL18RAP 0.004 0.11 -10000 0 -0.46 20 20
IL12RB1 0.011 0.1 0.25 20 -0.5 10 30
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.021 0.089 0.21 16 -0.37 9 25
IL23R/JAK2 0.026 0.14 -10000 0 -0.79 1 1
positive regulation of chronic inflammatory response -0.2 0.57 -10000 0 -1.2 69 69
natural killer cell activation 0 0.009 -10000 0 -10000 0 0
JAK2 0.018 0.055 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
NFKB1 0.028 0.006 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.14 0.46 -10000 0 -1 58 58
ALOX12B -0.16 0.49 -10000 0 -1.1 65 65
CXCL1 -0.21 0.56 -10000 0 -1.2 72 72
T cell proliferation -0.2 0.57 -10000 0 -1.2 69 69
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
IL17A -0.054 0.29 -10000 0 -0.56 49 49
PI3K -0.18 0.52 -10000 0 -1.1 68 68
IFNG 0.008 0.038 0.11 3 -0.11 7 10
STAT3 (dimer) -0.16 0.49 -10000 0 -1.1 66 66
IL18R1 0.026 0.035 -10000 0 -0.46 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.097 0.36 -10000 0 -0.78 53 53
IL18/IL18R 0.037 0.09 -10000 0 -0.29 26 26
macrophage activation -0.008 0.023 0.043 2 -0.045 26 28
TNF -0.17 0.51 -10000 0 -1.1 59 59
STAT3/STAT4 -0.19 0.53 -10000 0 -1.2 69 69
STAT4 (dimer) -0.2 0.55 -10000 0 -1.2 71 71
IL18 0.02 0.06 -10000 0 -0.46 6 6
IL19 -0.16 0.49 -10000 0 -1.1 63 63
STAT5A (dimer) -0.19 0.54 -10000 0 -1.2 67 67
STAT1 0.029 0.019 0.21 4 -10000 0 4
SOCS3 -0.022 0.15 -10000 0 -0.47 40 40
CXCL9 -0.17 0.52 -10000 0 -1.1 68 68
MPO -0.16 0.49 -10000 0 -1.1 67 67
positive regulation of humoral immune response -0.2 0.57 -10000 0 -1.2 69 69
IL23/IL23R/JAK2/TYK2 -0.22 0.61 -10000 0 -1.3 69 69
IL6 -0.47 0.73 -10000 0 -1.2 188 188
STAT5A 0.026 0.025 -10000 0 -0.47 1 1
IL2 0.015 0.021 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.009 -10000 0 -10000 0 0
CD3E -0.21 0.57 -10000 0 -1.2 78 78
keratinocyte proliferation -0.2 0.57 -10000 0 -1.2 69 69
NOS2 -0.17 0.5 -10000 0 -1.1 66 66
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.074 0.14 -10000 0 -0.24 162 162
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.018 0.073 0.29 17 -0.33 6 23
GNB1/GNG2 0.031 0.039 -10000 0 -0.28 6 6
GNB1 0.027 0.003 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.094 0.13 -10000 0 -0.26 163 163
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 0.028 0.034 0.069 163 -10000 0 163
GNAL -0.17 0.24 -10000 0 -0.47 163 163
GNG2 0.02 0.06 -10000 0 -0.47 6 6
CRH 0.059 0.12 0.23 106 -0.47 6 112
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.027 -10000 0 -0.31 3 3
MAPK11 0.008 0.002 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.057 0.17 0.28 1 -0.26 156 157
SMAD6-7/SMURF1 0.051 0.027 -10000 0 -0.28 1 1
NOG 0.035 0.056 0.22 31 -10000 0 31
SMAD9 -0.15 0.26 -10000 0 -0.52 124 124
SMAD4 0.026 0.007 -10000 0 -10000 0 0
SMAD5 -0.03 0.12 -10000 0 -0.43 18 18
BMP7/USAG1 -0.19 0.23 -10000 0 -0.39 207 207
SMAD5/SKI -0.025 0.13 -10000 0 -0.43 17 17
SMAD1 0.028 0.034 -10000 0 -10000 0 0
BMP2 -0.023 0.15 -10000 0 -0.47 40 40
SMAD1/SMAD1/SMAD4 0.028 0.056 -10000 0 -0.4 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B 0.041 0.09 0.21 54 -0.47 6 60
BMPR1A-1B/BAMBI 0.032 0.11 -10000 0 -0.3 35 35
AHSG 0.023 0.075 0.22 46 -10000 0 46
CER1 -0.006 0.017 -10000 0 -10000 0 0
BMP2-4/CER1 -0.003 0.12 -10000 0 -0.29 53 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.056 0.14 -10000 0 -0.38 34 34
BMP2-4 (homodimer) -0.012 0.13 -10000 0 -0.34 54 54
RGMB 0.026 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.072 0.062 -10000 0 -0.26 6 6
RGMA -0.11 0.22 -10000 0 -0.47 114 114
SMURF1 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.054 0.13 -10000 0 -0.36 36 36
BMP2-4/USAG1 -0.09 0.18 -10000 0 -0.31 151 151
SMAD6/SMURF1/SMAD5 -0.025 0.13 -10000 0 -0.41 19 19
SOSTDC1 -0.14 0.22 0.21 6 -0.47 125 131
BMP7/BMPR2/BMPR1A-1B -0.051 0.16 -10000 0 -0.26 144 144
SKI 0.027 0.003 -10000 0 -10000 0 0
BMP6 (homodimer) 0.026 0.028 0.21 2 -0.47 1 3
HFE2 0.004 0.029 0.21 4 -10000 0 4
ZFYVE16 0.026 0.006 -10000 0 -10000 0 0
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.019 0.15 -10000 0 -0.32 74 74
SMAD5/SMAD5/SMAD4 -0.023 0.13 -10000 0 -0.41 19 19
MAPK1 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.034 0.12 -10000 0 -0.34 29 29
BMP7 (homodimer) -0.15 0.23 -10000 0 -0.47 141 141
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.048 0.047 0.24 4 -10000 0 4
SMAD1/SKI 0.036 0.068 -10000 0 -0.49 1 1
SMAD6 0.027 0.03 0.21 3 -0.47 1 4
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.012 0.13 0.24 3 -0.3 51 54
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.013 0.19 0.21 61 -0.47 55 116
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.051 0.017 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.049 0.065 -10000 0 -0.34 6 6
CHRDL1 -0.26 0.24 -10000 0 -0.47 229 229
ENDOFIN/SMAD1 0.036 0.067 -10000 0 -0.48 1 1
SMAD6-7/SMURF1/SMAD1 0.056 0.072 -10000 0 -0.46 1 1
SMAD6/SMURF1 0.027 0.004 -10000 0 -10000 0 0
BAMBI -0.006 0.13 0.21 7 -0.47 29 36
SMURF2 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.18 0.19 -10000 0 -0.32 241 241
BMP2-4/GREM1 -0.024 0.17 -10000 0 -0.29 104 104
SMAD7 0.026 0.007 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.14 0.26 -10000 0 -0.49 124 124
SMAD1/SMAD6 0.036 0.068 -10000 0 -0.49 1 1
TAK1/SMAD6 0.038 0.011 -10000 0 -10000 0 0
BMP7 -0.15 0.23 -10000 0 -0.47 141 141
BMP6 0.026 0.028 0.21 2 -0.47 1 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.049 0.14 -10000 0 -0.36 39 39
PPM1A 0.027 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.036 0.067 -10000 0 -0.49 1 1
SMAD7/SMURF1 0.038 0.011 -10000 0 -10000 0 0
CTDSPL 0.026 0.006 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.028 0.015 0.33 1 -10000 0 1
CTDSP1 0.026 0.007 -10000 0 -10000 0 0
PPP1R15A 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.072 0.16 0.2 1 -0.42 46 47
CHRD -0.016 0.14 0.21 1 -0.47 35 36
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.067 0.14 -10000 0 -0.39 38 38
BMP4 0.008 0.1 0.21 5 -0.47 17 22
FST 0.005 0.12 0.21 10 -0.47 21 31
BMP2-4/NOG 0.009 0.13 0.29 3 -0.3 54 57
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.04 0.16 -10000 0 -0.25 141 141
PDGFR-alpha signaling pathway

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
PDGFRA -0.061 0.17 -10000 0 -0.49 55 55
PDGF/PDGFRA/CRKL -0.028 0.12 -10000 0 -0.34 53 53
positive regulation of JUN kinase activity 0.019 0.1 -10000 0 -0.26 44 44
CRKL 0.028 0.014 0.21 2 -10000 0 2
PDGF/PDGFRA/Caveolin-3 -0.033 0.12 -10000 0 -0.35 51 51
AP1 -0.29 0.43 -10000 0 -0.9 128 128
mol:IP3 -0.052 0.12 -10000 0 -0.36 51 51
PLCG1 -0.052 0.12 -10000 0 -0.36 51 51
PDGF/PDGFRA/alphaV Integrin -0.029 0.13 -10000 0 -0.34 55 55
RAPGEF1 0.025 0.009 -10000 0 -10000 0 0
CRK 0.025 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.052 0.12 -10000 0 -0.36 51 51
CAV3 -0.003 0.029 0.25 3 -10000 0 3
CAV1 0.005 0.1 -10000 0 -0.47 18 18
SHC/Grb2/SOS1 0.021 0.1 -10000 0 -0.26 44 44
PDGF/PDGFRA/Shf -0.034 0.14 -10000 0 -0.36 58 58
FOS -0.3 0.41 -10000 0 -0.89 128 128
JUN -0.048 0.075 -10000 0 -0.4 14 14
oligodendrocyte development -0.029 0.13 -10000 0 -0.34 55 55
GRB2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
mol:DAG -0.052 0.12 -10000 0 -0.36 51 51
PDGF/PDGFRA -0.061 0.17 -10000 0 -0.49 55 55
actin cytoskeleton reorganization -0.028 0.12 -10000 0 -0.34 52 52
SRF 0.021 0.014 -10000 0 -10000 0 0
SHC1 0.026 0.017 0.33 1 -10000 0 1
PI3K 0.003 0.11 -10000 0 -0.28 49 49
PDGF/PDGFRA/Crk/C3G 0 0.11 -10000 0 -0.28 53 53
JAK1 -0.044 0.12 -10000 0 -0.34 55 55
ELK1/SRF -0.032 0.11 0.16 13 -0.29 51 64
SHB 0.024 0.009 -10000 0 -10000 0 0
SHF 0.02 0.06 -10000 0 -0.47 6 6
CSNK2A1 0.039 0.024 -10000 0 -10000 0 0
GO:0007205 -0.059 0.13 -10000 0 -0.39 51 51
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction 0.019 0.1 -10000 0 -0.26 44 44
PDGF/PDGFRA/SHB -0.028 0.12 -10000 0 -0.34 52 52
PDGF/PDGFRA/Caveolin-1 -0.042 0.16 -10000 0 -0.39 60 60
ITGAV 0.027 0.006 -10000 0 -10000 0 0
ELK1 -0.064 0.12 0.23 2 -0.35 52 54
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.029 0.12 -10000 0 -0.34 53 53
JAK-STAT cascade -0.044 0.12 -10000 0 -0.34 55 55
cell proliferation -0.034 0.14 -10000 0 -0.35 58 58
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.035 0.14 0.29 1 -0.38 45 46
alphaM/beta2 Integrin/GPIbA -0.01 0.11 0.29 2 -0.36 21 23
alphaM/beta2 Integrin/proMMP-9 0.02 0.14 0.28 11 -0.44 18 29
PLAUR 0.027 0.005 -10000 0 -10000 0 0
HMGB1 -0.006 0.04 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.012 0.1 0.29 1 -0.37 19 20
AGER -0.004 0.048 0.19 6 -10000 0 6
RAP1A 0.028 0.003 -10000 0 -10000 0 0
SELPLG 0.02 0.066 0.21 2 -0.47 7 9
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.053 0.16 0.3 1 -0.23 163 164
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.068 0.1 0.22 102 -0.47 5 107
CYR61 -0.11 0.22 -10000 0 -0.47 114 114
TLN1 0.025 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.005 0.14 -10000 0 -0.42 25 25
RHOA 0.026 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.065 0.19 -10000 0 -0.47 73 73
MYH2 -0.024 0.13 -10000 0 -0.39 26 26
MST1R 0.013 0.096 0.23 8 -0.47 14 22
leukocyte activation during inflammatory response -0.06 0.14 0.25 1 -0.29 96 97
APOB -0.047 0.17 0.23 7 -0.47 56 63
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.011 0.13 -10000 0 -0.47 31 31
JAM3 -0.004 0.12 -10000 0 -0.47 25 25
GP1BA 0.024 0.039 0.21 8 -0.47 1 9
alphaM/beta2 Integrin/CTGF -0.064 0.18 0.29 1 -0.38 81 82
alphaM/beta2 Integrin -0.028 0.15 -10000 0 -0.42 32 32
JAM3 homodimer -0.004 0.12 -10000 0 -0.47 25 25
ICAM2 0.025 0.025 -10000 0 -0.47 1 1
ICAM1 0.03 0.037 0.21 9 -0.47 1 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.026 0.15 -10000 0 -0.44 30 30
cell adhesion -0.011 0.11 0.29 2 -0.36 21 23
NFKB1 -0.13 0.21 0.34 5 -0.36 166 171
THY1 0.028 0.017 0.21 3 -10000 0 3
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
Lipoprotein(a) -0.034 0.14 -10000 0 -0.3 80 80
alphaM/beta2 Integrin/LRP/tPA -0.015 0.13 0.3 3 -0.36 34 37
IL6 -0.29 0.37 0.37 3 -0.69 180 183
ITGB2 -0.012 0.082 0.21 8 -0.49 7 15
elevation of cytosolic calcium ion concentration 0.014 0.12 0.26 4 -0.34 19 23
alphaM/beta2 Integrin/JAM2/JAM3 -0.083 0.2 0.3 1 -0.36 113 114
JAM2 -0.099 0.22 -10000 0 -0.47 103 103
alphaM/beta2 Integrin/ICAM1 0.007 0.12 0.33 2 -0.3 32 34
alphaM/beta2 Integrin/uPA/Plg 0.012 0.12 0.26 4 -0.34 21 25
RhoA/GTP -0.024 0.13 -10000 0 -0.36 35 35
positive regulation of phagocytosis -0.022 0.15 0.21 2 -0.47 27 29
Ron/MSP 0.034 0.081 0.3 1 -0.34 15 16
alphaM/beta2 Integrin/uPAR/uPA 0.015 0.12 0.27 4 -0.34 19 23
alphaM/beta2 Integrin/uPAR -0.013 0.11 0.29 1 -0.38 19 20
PLAU 0.052 0.065 0.22 53 -10000 0 53
PLAT 0.005 0.1 0.33 2 -0.47 17 19
actin filament polymerization -0.022 0.12 0.23 2 -0.38 26 28
MST1 0.036 0.052 0.22 22 -0.47 1 23
alphaM/beta2 Integrin/lipoprotein(a) -0.058 0.15 0.25 2 -0.29 96 98
TNF -0.12 0.19 0.4 2 -0.46 30 32
RAP1B 0.026 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.005 0.12 0.27 4 -0.36 22 26
fibrinolysis 0.011 0.12 0.28 2 -0.34 21 23
HCK 0.014 0.08 0.21 5 -0.47 10 15
dendritic cell antigen processing and presentation -0.026 0.15 -10000 0 -0.44 30 30
VTN -0.045 0.18 0.21 7 -0.47 60 67
alphaM/beta2 Integrin/CYR61 -0.09 0.2 0.29 1 -0.38 112 113
LPA -0.022 0.13 0.21 6 -0.47 31 37
LRP1 0.022 0.049 -10000 0 -0.47 4 4
cell migration -0.028 0.15 0.24 5 -0.39 41 46
FN1 0.025 0.094 0.21 26 -0.47 11 37
alphaM/beta2 Integrin/Thy1 -0.011 0.11 0.29 1 -0.36 21 22
MPO 0.021 0.021 0.21 2 -10000 0 2
KNG1 -0.016 0.004 -10000 0 -10000 0 0
RAP1/GDP 0.034 0.011 -10000 0 -10000 0 0
ROCK1 -0.015 0.13 -10000 0 -0.38 27 27
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.005 0.03 0.21 5 -10000 0 5
CTGF -0.067 0.19 -10000 0 -0.47 76 76
alphaM/beta2 Integrin/Hck -0.014 0.13 0.29 4 -0.43 22 26
ITGAM -0.027 0.11 0.2 3 -0.49 18 21
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.052 0.16 0.3 2 -0.33 80 82
HP 0.037 0.073 0.22 44 -0.47 2 46
leukocyte adhesion -0.12 0.21 0.29 1 -0.43 93 94
SELP -0.065 0.19 -10000 0 -0.47 73 73
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.026 0.078 0.58 2 -10000 0 2
VDR 0.026 0.038 0.33 1 -0.47 2 3
FAM120B 0.026 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.023 0.12 -10000 0 -0.37 17 17
RXRs/LXRs/DNA/Oxysterols -0.003 0.11 -10000 0 -0.34 16 16
MED1 0.026 0.006 -10000 0 -10000 0 0
mol:9cRA 0.005 0.002 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.003 0.095 -10000 0 -0.26 46 46
RXRs/NUR77 -0.16 0.19 0.25 1 -0.31 226 227
RXRs/PPAR -0.048 0.12 0.18 1 -0.24 105 106
NCOR2 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.025 -10000 0 -0.33 2 2
RARs/VDR/DNA/Vit D3 0.033 0.089 0.22 1 -0.25 34 35
RARA 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.038 0.33 1 -0.47 2 3
RARs/RARs/DNA/9cRA 0.023 0.08 -10000 0 -0.24 33 33
RARG 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.037 0.11 0.63 12 -10000 0 12
RARs/THRs/DNA/SMRT -0.003 0.096 -10000 0 -0.25 48 48
THRA 0.027 0.005 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.025 -10000 0 -0.33 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.017 0.13 0.24 1 -0.24 93 94
NR1H4 -0.069 0.19 0.21 16 -0.47 72 88
RXRs/LXRs/DNA 0.006 0.13 -10000 0 -0.23 83 83
NR1H2 0.032 0.006 -10000 0 -10000 0 0
NR1H3 0.031 0.009 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.011 0.13 0.25 2 -0.24 90 92
NR4A1 -0.25 0.24 -10000 0 -0.47 224 224
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.063 0.15 -10000 0 -0.25 135 135
RXRG -0.092 0.21 0.33 1 -0.46 95 96
RXR alpha/CCPG 0.038 0.016 -10000 0 -10000 0 0
RXRA 0.029 0.01 -10000 0 -10000 0 0
RXRB 0.033 0.004 -10000 0 -10000 0 0
THRB -0.003 0.12 -10000 0 -0.47 24 24
PPARG -0.005 0.12 0.33 2 -0.47 25 27
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF 0 0.11 -10000 0 -10000 0 0
mol:Oxysterols 0.005 0.002 -10000 0 -10000 0 0
cholesterol transport -0.003 0.11 -10000 0 -0.33 16 16
PPARA 0.024 0.035 -10000 0 -0.47 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.015 0.14 -10000 0 -0.47 34 34
RXRs/NUR77/BCL2 -0.18 0.18 0.18 1 -0.3 236 237
SREBF1 -0.003 0.1 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.017 0.13 0.24 1 -0.24 93 94
ABCA1 -0.001 0.1 -10000 0 -10000 0 0
RARs/THRs 0.032 0.12 -10000 0 -0.28 48 48
RXRs/FXR -0.059 0.18 0.25 1 -0.29 135 136
BCL2 0.008 0.094 -10000 0 -0.47 15 15
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.03 0.029 -10000 0 -0.34 1 1
PDGFRB 0.014 0.074 -10000 0 -0.48 9 9
SPHK1 0.001 0.084 -10000 0 -0.85 2 2
mol:S1P -0.006 0.086 0.31 2 -0.76 2 4
S1P1/S1P/Gi -0.19 0.26 -10000 0 -0.48 142 142
GNAO1 -0.13 0.23 -10000 0 -0.47 124 124
PDGFB-D/PDGFRB/PLCgamma1 -0.15 0.24 0.28 3 -0.44 130 133
PLCG1 -0.17 0.24 0.3 1 -0.46 136 137
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.014 0.074 -10000 0 -0.47 9 9
GNAI2 0.016 0.02 -10000 0 -10000 0 0
GNAI3 0.018 0.019 -10000 0 -10000 0 0
GNAI1 0.015 0.046 -10000 0 -0.48 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.001 0.022 -10000 0 -0.28 1 1
S1P1/S1P -0.017 0.089 0.24 3 -0.44 3 6
negative regulation of cAMP metabolic process -0.18 0.25 -10000 0 -0.46 142 142
MAPK3 -0.22 0.3 0.3 3 -0.58 145 148
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
KDR 0.023 0.036 -10000 0 -0.47 2 2
PLCB2 -0.008 0.092 0.26 4 -0.36 4 8
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.023 0.067 -10000 0 -0.37 3 3
receptor internalization -0.019 0.08 -10000 0 -0.41 3 3
PTGS2 -0.3 0.44 -10000 0 -0.98 109 109
Rac1/GTP -0.023 0.067 -10000 0 -0.37 3 3
RHOA 0.026 0.006 -10000 0 -10000 0 0
VEGFA 0.025 0.009 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.18 0.25 -10000 0 -0.46 142 142
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.088 0.2 -10000 0 -0.47 87 87
MAPK1 -0.22 0.31 -10000 0 -0.58 146 146
S1P1/S1P/PDGFB-D/PDGFRB -0.02 0.12 0.26 4 -0.38 10 14
ABCC1 0.026 0.019 0.27 2 -10000 0 2
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.028 0.014 0.21 2 -10000 0 2
RAS family/GTP/Tiam1 -0.081 0.11 -10000 0 -0.24 70 70
NT3 (dimer)/TRKC -0.19 0.23 -10000 0 -0.39 215 215
NT3 (dimer)/TRKB -0.17 0.25 0.26 1 -0.4 192 193
SHC/Grb2/SOS1/GAB1/PI3K 0.026 0.015 -10000 0 -10000 0 0
RAPGEF1 0.025 0.009 -10000 0 -10000 0 0
BDNF -0.057 0.18 -10000 0 -0.47 67 67
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.005 -10000 0 -10000 0 0
NTRK1 0.025 0.032 0.23 7 -10000 0 7
NTRK2 -0.13 0.23 0.21 7 -0.47 131 138
NTRK3 -0.21 0.24 -10000 0 -0.47 189 189
NT-4/5 (dimer)/TRKB -0.14 0.22 0.29 1 -0.37 179 180
neuron apoptosis 0.17 0.23 0.46 123 -10000 0 123
SHC 2-3/Grb2 -0.18 0.26 -10000 0 -0.51 123 123
SHC1 0.026 0.017 0.33 1 -10000 0 1
SHC2 -0.18 0.27 -10000 0 -0.56 107 107
SHC3 -0.19 0.26 -10000 0 -0.52 126 126
STAT3 (dimer) 0.032 0.054 -10000 0 -0.34 7 7
NT3 (dimer)/TRKA -0.065 0.18 0.25 3 -0.32 123 126
RIN/GDP -0.049 0.11 0.24 3 -0.25 21 24
GIPC1 0.027 0.004 -10000 0 -10000 0 0
KRAS 0.027 0.016 0.33 1 -10000 0 1
DNAJA3 -0.074 0.15 -10000 0 -0.31 100 100
RIN/GTP 0.012 0.008 0.15 1 -10000 0 1
CCND1 0.017 0.12 0.36 13 -0.73 7 20
MAGED1 0.027 0.003 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.007 0.12 -10000 0 -0.47 27 27
SHC/GRB2/SOS1 0.049 0.021 0.24 1 -10000 0 1
GRB2 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.001 0.14 0.24 1 -0.32 57 58
TRKA/NEDD4-2 0.037 0.022 0.24 1 -10000 0 1
ELMO1 0.023 0.043 -10000 0 -0.47 3 3
RhoG/GTP/ELMO1/DOCK1 0.031 0.041 -10000 0 -0.34 4 4
NGF -0.039 0.17 -10000 0 -0.47 53 53
HRAS 0.025 0.008 -10000 0 -10000 0 0
DOCK1 0.024 0.035 -10000 0 -0.47 2 2
GAB2 0.025 0.025 -10000 0 -0.47 1 1
RIT2 -0.012 0.016 0.21 1 -10000 0 1
RIT1 0.026 0.007 -10000 0 -10000 0 0
FRS2 0.031 0.04 0.33 7 -10000 0 7
DNM1 0.017 0.06 -10000 0 -0.47 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.055 0.16 -10000 0 -0.3 100 100
mol:GDP -0.077 0.15 0.33 2 -0.35 31 33
NGF (dimer) -0.039 0.17 -10000 0 -0.47 53 53
RhoG/GDP 0.017 0.031 -10000 0 -0.33 3 3
RIT1/GDP -0.047 0.11 0.28 2 -0.25 21 23
TIAM1 0.023 0.043 -10000 0 -0.47 3 3
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
BDNF (dimer)/TRKB -0.11 0.2 -10000 0 -0.32 171 171
KIDINS220/CRKL/C3G 0.036 0.017 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.017 0.24 1 -10000 0 1
FRS2 family/SHP2 0.053 0.029 0.24 6 -10000 0 6
SHC/GRB2/SOS1/GAB1 0.06 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.063 0.19 0.21 1 -0.47 72 73
RAP1/GDP -0.048 0.086 -10000 0 -0.21 20 20
KIDINS220/CRKL 0.027 0.014 0.21 2 -10000 0 2
BDNF (dimer) -0.056 0.18 -10000 0 -0.47 67 67
ubiquitin-dependent protein catabolic process 0.012 0.11 0.23 1 -0.28 43 44
Schwann cell development -0.046 0.035 -10000 0 -10000 0 0
EHD4 0.027 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.064 0.035 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.021 0.057 -10000 0 -0.26 3 3
RAP1B 0.026 0.008 -10000 0 -10000 0 0
RAP1A 0.028 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.24 0.24 0.34 1 -0.38 264 265
ABL1 0.025 0.009 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.039 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.044 0.11 -10000 0 -0.37 14 14
STAT3 0.032 0.054 -10000 0 -0.33 7 7
axon guidance -0.23 0.22 -10000 0 -0.36 264 264
MAPK3 -0.022 0.11 0.19 15 -0.28 55 70
MAPK1 -0.023 0.12 0.19 16 -0.29 55 71
CDC42/GDP -0.047 0.11 0.25 3 -0.25 21 24
NTF3 -0.063 0.19 0.21 1 -0.47 72 73
NTF4 -0.007 0.12 -10000 0 -0.47 27 27
NGF (dimer)/TRKA/FAIM 0.012 0.11 0.24 1 -0.29 45 46
PI3K 0.035 0.023 -10000 0 -0.34 1 1
FRS3 0.027 0.004 -10000 0 -10000 0 0
FAIM 0.026 0.006 -10000 0 -10000 0 0
GAB1 0.026 0.006 -10000 0 -10000 0 0
RASGRF1 -0.078 0.15 0.17 1 -0.31 104 105
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.18 0.2 -10000 0 -0.35 213 213
RGS19 0.026 0.012 0.21 1 -10000 0 1
CDC42 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.091 0.3 4 -0.41 4 8
Rac1/GDP -0.045 0.11 0.25 3 -0.24 22 25
NGF (dimer)/TRKA/GRIT -0.002 0.1 -10000 0 -0.28 45 45
neuron projection morphogenesis -0.057 0.16 -10000 0 -0.53 11 11
NGF (dimer)/TRKA/NEDD4-2 0.012 0.11 0.24 1 -0.28 43 44
MAP2K1 0.041 0.069 0.37 6 -10000 0 6
NGFR -0.076 0.2 0.24 5 -0.47 86 91
NGF (dimer)/TRKA/GIPC/GAIP -0.009 0.1 -10000 0 -0.28 42 42
RAS family/GTP/PI3K 0.022 0.022 0.17 1 -0.3 1 2
FRS2 family/SHP2/GRB2/SOS1 0.071 0.038 -10000 0 -10000 0 0
NRAS 0.028 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.01 -10000 0 -10000 0 0
PRKCI 0.026 0.007 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.024 0.043 -10000 0 -0.47 3 3
MAPKKK cascade -0.092 0.24 -10000 0 -0.67 55 55
RASA1 0.027 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.036 0.024 0.24 1 -10000 0 1
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.092 0.19 -10000 0 -0.3 165 165
NGF (dimer)/TRKA/p62/Atypical PKCs 0.032 0.11 -10000 0 -0.25 44 44
MATK 0.001 0.12 0.21 5 -0.47 23 28
NEDD4L 0.026 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.061 0.064 -10000 0 -0.18 38 38
NGF (dimer)/TRKA -0.074 0.16 0.18 1 -0.32 104 105
Rac1/GTP -0.086 0.11 -10000 0 -0.26 79 79
FRS2 family/SHP2/CRK family 0.066 0.042 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.008 0.11 0.27 1 -0.34 17 18
TBX21 -0.13 0.48 -10000 0 -1.2 57 57
B2M 0.025 0.015 -10000 0 -10000 0 0
TYK2 0.018 0.035 -10000 0 -10000 0 0
IL12RB1 0.016 0.1 0.23 20 -0.51 10 30
GADD45B -0.083 0.39 -10000 0 -0.96 53 53
IL12RB2 0.039 0.1 0.22 57 -0.48 6 63
GADD45G -0.091 0.38 -10000 0 -0.96 49 49
natural killer cell activation -0.002 0.022 0.051 4 -0.043 58 62
RELB 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 0.019 0.062 -10000 0 -0.47 6 6
IL2RA 0.012 0.11 0.21 19 -0.47 17 36
IFNG 0.057 0.085 0.22 81 -10000 0 81
STAT3 (dimer) -0.08 0.34 -10000 0 -0.81 61 61
HLA-DRB5 -0.006 0.01 -10000 0 -0.023 98 98
FASLG -0.12 0.48 -10000 0 -1.1 67 67
NF kappa B2 p52/RelB -0.11 0.44 -10000 0 -1 64 64
CD4 0.01 0.042 -10000 0 -0.47 2 2
SOCS1 0.027 0.011 0.21 1 -10000 0 1
EntrezGene:6955 -0.007 0.015 -10000 0 -0.028 119 119
CD3D -0.028 0.14 0.2 3 -0.47 32 35
CD3E -0.036 0.14 -10000 0 -0.47 39 39
CD3G -0.041 0.15 -10000 0 -0.47 42 42
IL12Rbeta2/JAK2 0.037 0.088 0.24 3 -0.36 6 9
CCL3 -0.13 0.48 -10000 0 -1.2 56 56
CCL4 -0.15 0.52 -10000 0 -1.3 61 61
HLA-A 0 0.008 -10000 0 -0.04 14 14
IL18/IL18R 0.046 0.1 -10000 0 -0.31 26 26
NOS2 -0.094 0.41 -10000 0 -1 55 55
IL12/IL12R/TYK2/JAK2/SPHK2 0.009 0.12 0.27 1 -0.34 18 19
IL1R1 -0.11 0.44 -10000 0 -1.1 55 55
IL4 0.001 0.036 -10000 0 -10000 0 0
JAK2 0.017 0.033 -10000 0 -10000 0 0
EntrezGene:6957 -0.006 0.013 -10000 0 -0.025 110 110
TCR/CD3/MHC I/CD8 -0.13 0.34 -10000 0 -0.8 65 65
RAB7A -0.05 0.32 -10000 0 -0.76 50 50
lysosomal transport -0.044 0.3 -10000 0 -0.71 51 51
FOS -0.4 0.62 -10000 0 -1.1 156 156
STAT4 (dimer) -0.076 0.39 0.46 1 -0.88 64 65
STAT5A (dimer) -0.095 0.45 0.49 1 -1 64 65
GZMA -0.15 0.51 -10000 0 -1.2 62 62
GZMB -0.14 0.49 -10000 0 -1.2 61 61
HLX 0.028 0.01 0.21 1 -10000 0 1
LCK -0.14 0.49 -10000 0 -1.2 64 64
TCR/CD3/MHC II/CD4 -0.1 0.2 -10000 0 -0.32 146 146
IL2/IL2R 0.039 0.11 0.29 4 -0.32 24 28
MAPK14 -0.082 0.39 -10000 0 -0.93 57 57
CCR5 -0.09 0.4 -10000 0 -1 51 51
IL1B 0.005 0.12 0.23 15 -0.49 18 33
STAT6 -0.008 0.15 -10000 0 -0.59 8 8
STAT4 0.002 0.11 -10000 0 -0.47 20 20
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.029 0.019 0.21 4 -10000 0 4
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.005 -10000 0 -10000 0 0
IL12B 0.017 0.055 0.23 14 -10000 0 14
CD8A -0.021 0.15 0.22 1 -0.47 39 40
CD8B -0.014 0.14 0.22 7 -0.47 35 42
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.008 0.11 0.34 17 -0.27 1 18
IL2RB 0.022 0.058 0.27 2 -0.47 5 7
proteasomal ubiquitin-dependent protein catabolic process -0.06 0.35 0.45 1 -0.78 64 65
IL2RG 0.021 0.079 0.21 9 -0.47 9 18
IL12 0.029 0.064 0.24 4 -10000 0 4
STAT5A 0.026 0.025 -10000 0 -0.47 1 1
CD247 0.004 0.064 0.21 1 -0.47 6 7
IL2 -0.005 0.02 -10000 0 -10000 0 0
SPHK2 0.028 0.01 0.21 1 -10000 0 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.021 0.046 0.23 8 -10000 0 8
IL12/IL12R/TYK2/JAK2 -0.16 0.58 0.47 1 -1.3 64 65
MAP2K3 -0.095 0.41 -10000 0 -0.98 57 57
RIPK2 0.024 0.01 -10000 0 -10000 0 0
MAP2K6 -0.083 0.39 -10000 0 -0.9 59 59
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.012 -10000 0 -0.026 109 109
IL18RAP 0.002 0.11 -10000 0 -0.47 20 20
IL12Rbeta1/TYK2 0.028 0.085 0.23 3 -0.39 9 12
EOMES -0.065 0.29 -10000 0 -1.2 23 23
STAT1 (dimer) -0.052 0.35 0.46 1 -0.8 59 60
T cell proliferation -0.048 0.28 0.41 1 -0.62 64 65
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.025 0.039 -10000 0 -0.48 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.069 0.28 -10000 0 -0.67 62 62
ATF2 -0.072 0.35 -10000 0 -0.84 57 57
HIF-1-alpha transcription factor network

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
PKM2 -0.038 0.31 0.45 1 -0.65 46 47
HDAC7 0.029 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.031 0.35 -10000 0 -0.7 39 39
SMAD4 0.027 0.007 -10000 0 -10000 0 0
ID2 -0.024 0.32 -10000 0 -0.68 42 42
AP1 -0.081 0.19 -10000 0 -0.37 120 120
ABCG2 -0.031 0.33 -10000 0 -0.67 48 48
HIF1A 0.01 0.086 -10000 0 -0.18 18 18
TFF3 -0.068 0.37 -10000 0 -0.69 65 65
GATA2 0.026 0.07 0.22 12 -0.47 6 18
AKT1 0.005 0.099 -10000 0 -0.21 24 24
response to hypoxia -0.011 0.087 -10000 0 -0.19 36 36
MCL1 -0.029 0.3 -10000 0 -0.67 40 40
NDRG1 -0.021 0.31 -10000 0 -0.67 38 38
SERPINE1 -0.025 0.32 -10000 0 -0.67 45 45
FECH -0.025 0.32 -10000 0 -0.68 41 41
FURIN -0.024 0.32 -10000 0 -0.68 42 42
NCOA2 0.002 0.11 -10000 0 -0.47 20 20
EP300 0.003 0.13 -10000 0 -0.31 39 39
HMOX1 -0.021 0.32 0.53 1 -0.68 42 43
BHLHE40 -0.025 0.32 -10000 0 -0.67 44 44
BHLHE41 -0.028 0.33 -10000 0 -0.7 42 42
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.059 0.12 -10000 0 -0.34 1 1
ENG 0.035 0.096 0.35 1 -0.3 1 2
JUN 0.011 0.091 -10000 0 -0.47 14 14
RORA -0.03 0.33 -10000 0 -0.69 44 44
ABCB1 -0.12 0.36 -10000 0 -0.99 55 55
TFRC -0.018 0.32 -10000 0 -0.66 42 42
CXCR4 -0.027 0.33 -10000 0 -0.7 43 43
TF -0.019 0.33 0.52 3 -0.68 44 47
CITED2 -0.022 0.32 -10000 0 -0.68 41 41
HIF1A/ARNT 0.069 0.44 0.72 6 -0.77 37 43
LDHA -0.025 0.19 -10000 0 -0.67 23 23
ETS1 -0.025 0.32 -10000 0 -0.68 41 41
PGK1 -0.024 0.32 -10000 0 -0.68 42 42
NOS2 -0.022 0.33 0.52 1 -0.69 43 44
ITGB2 -0.025 0.33 -10000 0 -0.69 44 44
ALDOA -0.021 0.32 -10000 0 -0.68 40 40
Cbp/p300/CITED2 -0.022 0.36 -10000 0 -0.79 45 45
FOS -0.12 0.23 -10000 0 -0.47 124 124
HK2 -0.019 0.32 -10000 0 -0.67 42 42
SP1 0.014 0.052 -10000 0 -0.15 8 8
GCK -0.045 0.37 -10000 0 -1.3 27 27
HK1 -0.023 0.32 -10000 0 -0.68 41 41
NPM1 -0.024 0.32 -10000 0 -0.68 42 42
EGLN1 -0.023 0.32 -10000 0 -0.68 41 41
CREB1 0.032 0.007 -10000 0 -10000 0 0
PGM1 -0.024 0.32 -10000 0 -0.67 43 43
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.043 0.21 -10000 0 -0.71 15 15
IGFBP1 -0.017 0.32 -10000 0 -0.67 43 43
VEGFA 0.002 0.28 -10000 0 -0.61 38 38
HIF1A/JAB1 0.028 0.064 -10000 0 -0.16 3 3
CP -0.064 0.37 0.52 1 -0.67 71 72
CXCL12 -0.089 0.39 -10000 0 -0.72 78 78
COPS5 0.026 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.012 -10000 0 -10000 0 0
BNIP3 -0.027 0.32 -10000 0 -0.67 43 43
EGLN3 -0.028 0.32 -10000 0 -0.69 42 42
CA9 0.011 0.36 0.52 5 -0.67 49 54
TERT 0.012 0.34 0.54 7 -0.68 39 46
ENO1 -0.023 0.32 -10000 0 -0.68 42 42
PFKL -0.023 0.32 -10000 0 -0.68 42 42
NCOA1 0.027 0.006 -10000 0 -10000 0 0
ADM -0.026 0.32 -10000 0 -0.68 41 41
ARNT 0.015 0.073 -10000 0 -0.22 1 1
HNF4A 0.035 0.07 0.22 38 -0.18 2 40
ADFP -0.038 0.31 0.45 1 -0.65 46 47
SLC2A1 0.002 0.28 -10000 0 -0.61 36 36
LEP -0.043 0.35 0.52 1 -0.68 57 58
HIF1A/ARNT/Cbp/p300 0.018 0.36 -10000 0 -0.72 39 39
EPO 0.019 0.24 0.56 2 -0.58 16 18
CREBBP 0.004 0.13 -10000 0 -0.3 39 39
HIF1A/ARNT/Cbp/p300/HDAC7 0.032 0.35 -10000 0 -0.7 38 38
PFKFB3 -0.031 0.31 -10000 0 -0.67 41 41
NT5E -0.042 0.35 -10000 0 -0.68 57 57
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.21 -10000 0 -0.38 133 133
fibroblast growth factor receptor signaling pathway -0.099 0.21 -10000 0 -0.38 133 133
LAMA1 0.04 0.12 0.22 66 -0.47 14 80
PRNP 0.015 0.073 -10000 0 -0.47 9 9
GPC1/SLIT2 -0.12 0.18 -10000 0 -0.33 168 168
SMAD2 0.016 0.033 0.19 9 -0.26 2 11
GPC1/PrPc/Cu2+ 0.025 0.048 -10000 0 -0.28 9 9
GPC1/Laminin alpha1 0.044 0.089 0.26 5 -0.33 14 19
TDGF1 0.009 0.028 0.21 3 -10000 0 3
CRIPTO/GPC1 0.034 0.017 -10000 0 -10000 0 0
APP/GPC1 0.036 0.023 -10000 0 -0.32 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.013 0.008 -10000 0 -10000 0 0
FLT1 0.027 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.043 0.033 -10000 0 -0.28 2 2
SERPINC1 0.033 0.057 0.22 30 -10000 0 30
FYN 0.011 0.027 -10000 0 -0.28 3 3
FGR 0.012 0.023 -10000 0 -0.29 2 2
positive regulation of MAPKKK cascade 0.003 0.1 0.3 6 -0.33 11 17
SLIT2 -0.18 0.24 -10000 0 -0.47 168 168
GPC1/NRG -0.013 0.13 0.24 2 -0.33 56 58
NRG1 -0.038 0.18 0.22 18 -0.47 56 74
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.048 0.021 -10000 0 -10000 0 0
LYN 0.013 0.008 -10000 0 -10000 0 0
mol:Spermine 0.007 0.003 -10000 0 -10000 0 0
cell growth -0.099 0.21 -10000 0 -0.38 133 133
BMP signaling pathway -0.026 0.012 -10000 0 -0.21 1 1
SRC 0.013 0.008 -10000 0 -10000 0 0
TGFBR1 0.025 0.009 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.19 0.25 0.21 3 -0.47 178 181
GPC1 0.026 0.012 0.21 1 -10000 0 1
TGFBR1 (dimer) 0.025 0.009 -10000 0 -10000 0 0
VEGFA 0.027 0.005 -10000 0 -10000 0 0
BLK -0.01 0.08 -10000 0 -0.28 30 30
HCK 0.006 0.046 -10000 0 -0.29 9 9
FGF2 -0.13 0.23 -10000 0 -0.47 127 127
FGFR1 -0.066 0.19 -10000 0 -0.47 73 73
VEGFR1 homodimer 0.027 0.005 -10000 0 -10000 0 0
TGFBR2 0.024 0.035 -10000 0 -0.47 2 2
cell death 0.036 0.023 -10000 0 -0.32 1 1
ATIII/GPC1 0.041 0.036 0.24 2 -10000 0 2
PLA2G2A/GPC1 -0.12 0.19 -10000 0 -0.33 178 178
LCK 0.011 0.031 -10000 0 -0.28 4 4
neuron differentiation -0.013 0.13 0.24 2 -0.33 56 58
PrPc/Cu2+ 0.012 0.052 -10000 0 -0.33 9 9
APP 0.026 0.025 -10000 0 -0.47 1 1
TGFBR2 (dimer) 0.024 0.035 -10000 0 -0.47 2 2
Glucocorticoid receptor regulatory network

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
PCK2 0.053 0.079 -10000 0 -10000 0 0
SMARCC2 0.024 0.021 -10000 0 -10000 0 0
SMARCC1 0.024 0.02 -10000 0 -10000 0 0
TBX21 -0.06 0.18 -10000 0 -0.7 24 24
SUMO2 0.019 0.017 -10000 0 -10000 0 0
STAT1 (dimer) 0.035 0.02 0.22 4 -10000 0 4
FKBP4 0.026 0.006 -10000 0 -10000 0 0
FKBP5 0.007 0.099 -10000 0 -0.47 17 17
GR alpha/HSP90/FKBP51/HSP90 0.068 0.11 0.26 20 -0.24 9 29
PRL -0.031 0.09 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.12 0.21 0.44 61 -0.36 5 66
RELA -0.12 0.14 -10000 0 -0.26 145 145
FGG 0.12 0.18 0.39 72 -10000 0 72
GR beta/TIF2 0.05 0.12 0.25 33 -0.3 13 46
IFNG -0.14 0.23 -10000 0 -0.56 51 51
apoptosis -0.049 0.18 -10000 0 -0.52 12 12
CREB1 0.032 0.012 -10000 0 -10000 0 0
histone acetylation -0.079 0.12 -10000 0 -0.34 42 42
BGLAP -0.04 0.1 -10000 0 -0.41 2 2
GR/PKAc 0.075 0.099 0.29 9 -0.24 1 10
NF kappa B1 p50/RelA -0.21 0.25 -10000 0 -0.41 223 223
SMARCD1 0.024 0.022 -10000 0 -10000 0 0
MDM2 0.066 0.083 0.19 77 -10000 0 77
GATA3 0 0.12 0.33 2 -0.46 24 26
AKT1 0.022 0.005 -10000 0 -10000 0 0
CSF2 -0.057 0.098 -10000 0 -0.49 2 2
GSK3B 0.019 0.018 -10000 0 -10000 0 0
NR1I3 -0.012 0.18 0.48 1 -0.49 5 6
CSN2 0.09 0.15 0.33 63 -10000 0 63
BRG1/BAF155/BAF170/BAF60A 0.06 0.062 -10000 0 -0.25 13 13
NFATC1 0.004 0.1 -10000 0 -0.47 18 18
POU2F1 0.027 0.011 -10000 0 -10000 0 0
CDKN1A 0.009 0.12 0.75 1 -1.3 2 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN 0.038 0.067 0.21 32 -0.47 3 35
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.086 0.11 0.28 19 -0.25 5 24
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.16 0.36 0.47 1 -0.77 99 100
JUN -0.07 0.16 0.33 4 -0.37 55 59
IL4 -0.068 0.13 -10000 0 -0.5 17 17
CDK5R1 0.037 0.05 0.24 22 -10000 0 22
PRKACA 0.027 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.14 0.16 0.22 1 -0.38 94 95
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.08 0.11 0.29 12 -0.27 4 16
cortisol/GR alpha (monomer) 0.16 0.23 0.5 74 -10000 0 74
NCOA2 0 0.11 -10000 0 -0.47 20 20
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.14 0.24 -10000 0 -0.48 129 129
AP-1/NFAT1-c-4 -0.18 0.31 -10000 0 -0.57 117 117
AFP -0.058 0.14 0.47 2 -0.46 5 7
SUV420H1 0.027 0.006 -10000 0 -10000 0 0
IRF1 0.095 0.12 0.4 9 -10000 0 9
TP53 0.037 0.041 -10000 0 -0.51 2 2
PPP5C 0.027 0.004 -10000 0 -10000 0 0
KRT17 -0.19 0.35 -10000 0 -0.96 46 46
KRT14 -0.02 0.18 0.48 4 -1.3 4 8
TBP 0.034 0.008 -10000 0 -10000 0 0
CREBBP -0.011 0.07 0.31 4 -0.28 16 20
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.024 0.006 -10000 0 -10000 0 0
AP-1 -0.18 0.31 -10000 0 -0.57 116 116
MAPK14 0.019 0.018 -10000 0 -10000 0 0
MAPK10 -0.024 0.14 -10000 0 -0.47 35 35
MAPK11 0.018 0.018 -10000 0 -10000 0 0
KRT5 -0.37 0.54 -10000 0 -1.1 126 126
interleukin-1 receptor activity -0.002 0.003 -10000 0 -10000 0 0
NCOA1 0.028 0.006 -10000 0 -10000 0 0
STAT1 0.035 0.02 0.22 4 -10000 0 4
CGA -0.048 0.1 -10000 0 -0.33 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.027 0.11 -10000 0 -0.41 11 11
MAPK3 0.018 0.018 -10000 0 -10000 0 0
MAPK1 0.018 0.018 -10000 0 -10000 0 0
ICAM1 -0.2 0.25 -10000 0 -0.53 102 102
NFKB1 -0.12 0.14 -10000 0 -0.26 145 145
MAPK8 -0.057 0.14 0.41 2 -0.3 51 53
MAPK9 0.019 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.053 0.18 -10000 0 -0.55 12 12
BAX 0.014 0.063 -10000 0 -10000 0 0
POMC -0.22 0.27 0.5 1 -0.76 30 31
EP300 -0.012 0.065 0.26 3 -0.28 15 18
cortisol/GR alpha (dimer)/p53 0.14 0.2 0.46 59 -10000 0 59
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.065 0.18 32 -10000 0 32
SGK1 -0.033 0.28 -10000 0 -1.3 17 17
IL13 -0.13 0.21 -10000 0 -0.57 39 39
IL6 -0.52 0.56 -10000 0 -1.1 188 188
PRKACG -0.01 0.015 -10000 0 -10000 0 0
IL5 -0.12 0.18 -10000 0 -0.61 14 14
IL2 -0.16 0.23 -10000 0 -0.56 57 57
CDK5 0.026 0.006 -10000 0 -10000 0 0
PRKACB 0.025 0.035 -10000 0 -0.47 2 2
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.3 0.42 -10000 0 -0.88 105 105
CDK5R1/CDK5 0.042 0.034 0.25 3 -10000 0 3
NF kappa B1 p50/RelA/PKAc -0.14 0.21 -10000 0 -0.38 137 137
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.2 0.43 70 -10000 0 70
SMARCA4 0.025 0.02 -10000 0 -10000 0 0
chromatin remodeling 0.084 0.14 0.32 44 -0.42 6 50
NF kappa B1 p50/RelA/Cbp -0.18 0.22 -10000 0 -0.42 144 144
JUN (dimer) -0.07 0.16 0.33 4 -0.37 55 59
YWHAH 0.027 0.006 -10000 0 -10000 0 0
VIPR1 -0.05 0.17 0.36 1 -0.72 17 18
NR3C1 0.093 0.14 0.32 58 -10000 0 58
NR4A1 -0.25 0.25 -10000 0 -0.47 224 224
TIF2/SUV420H1 0.016 0.082 -10000 0 -0.34 20 20
MAPKKK cascade -0.049 0.18 -10000 0 -0.52 12 12
cortisol/GR alpha (dimer)/Src-1 0.14 0.2 0.45 67 -10000 0 67
PBX1 0.006 0.099 -10000 0 -0.46 17 17
POU1F1 0.008 0.028 0.22 3 -10000 0 3
SELE -0.48 0.54 -10000 0 -1 185 185
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.084 0.14 0.32 44 -0.42 6 50
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.2 0.43 70 -10000 0 70
mol:cortisol 0.079 0.13 0.27 79 -10000 0 79
MMP1 -0.013 0.16 -10000 0 -0.82 9 9
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 -0.013 0.21 -10000 0 -0.73 9 9
CRP -0.014 0.22 0.55 3 -0.74 8 11
cell cycle arrest -0.04 0.23 -10000 0 -0.65 25 25
TIMP1 -0.014 0.19 -10000 0 -0.66 8 8
IL6ST -0.04 0.17 -10000 0 -0.47 55 55
Rac1/GDP -0.1 0.23 -10000 0 -0.48 80 80
AP1 -0.012 0.16 -10000 0 -0.48 13 13
GAB2 0.028 0.026 -10000 0 -0.46 1 1
TNFSF11 -0.034 0.22 -10000 0 -0.86 11 11
HSP90B1 0.032 0.07 -10000 0 -10000 0 0
GAB1 0.028 0.007 -10000 0 -10000 0 0
MAPK14 -0.15 0.27 -10000 0 -0.62 80 80
AKT1 0.04 0.045 0.27 1 -0.32 2 3
FOXO1 0.041 0.05 -10000 0 -10000 0 0
MAP2K6 -0.14 0.24 -10000 0 -0.51 89 89
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 -0.077 0.22 0.43 1 -0.48 68 69
MITF -0.13 0.23 -10000 0 -0.48 91 91
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.004 -10000 0 -10000 0 0
A2M -0.11 0.41 -10000 0 -1.3 41 41
CEBPB 0.03 0.027 -10000 0 -0.47 1 1
GRB2/SOS1/GAB family/SHP2 0.002 0.11 0.3 3 -0.52 5 8
STAT3 -0.047 0.24 -10000 0 -0.69 25 25
STAT1 -0.005 0.14 -10000 0 -0.83 10 10
CEBPD -0.02 0.22 0.51 1 -0.81 9 10
PIK3CA 0.027 0.007 -10000 0 -10000 0 0
PI3K 0.037 0.024 -10000 0 -0.34 1 1
JUN 0.01 0.091 -10000 0 -0.47 14 14
PIAS3/MITF -0.11 0.22 -10000 0 -0.46 83 83
MAPK11 -0.15 0.27 -10000 0 -0.62 79 79
STAT3 (dimer)/FOXO1 -0.029 0.22 0.4 1 -0.59 25 26
GRB2/SOS1/GAB family -0.072 0.21 0.29 1 -0.48 56 57
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.22 -10000 0 -0.48 81 81
GRB2 0.029 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.01 -10000 0 -10000 0 0
LBP 0.007 0.18 -10000 0 -0.61 6 6
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
JAK1 0.026 0.016 -10000 0 -10000 0 0
MYC -0.034 0.29 0.51 1 -1 21 22
FGG -0.031 0.2 -10000 0 -0.73 9 9
macrophage differentiation -0.04 0.23 -10000 0 -0.65 25 25
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.1 0.21 -10000 0 -0.31 175 175
JUNB -0.037 0.22 -10000 0 -0.82 12 12
FOS -0.12 0.23 -10000 0 -0.47 124 124
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.23 -10000 0 -0.49 84 84
STAT1/PIAS1 -0.08 0.21 -10000 0 -0.47 58 58
GRB2/SOS1/GAB family/SHP2/PI3K 0.041 0.039 -10000 0 -0.34 1 1
STAT3 (dimer) -0.041 0.23 -10000 0 -0.68 24 24
PRKCD -0.054 0.22 0.4 3 -0.53 43 46
IL6R -0.012 0.13 -10000 0 -0.47 30 30
SOCS3 -0.2 0.38 0.39 1 -1 62 63
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.13 -10000 0 -0.28 56 56
Rac1/GTP -0.094 0.23 0.27 1 -0.49 73 74
HCK 0.015 0.08 0.21 5 -0.47 10 15
MAPKKK cascade 0.031 0.1 -10000 0 -0.56 5 5
bone resorption -0.03 0.21 -10000 0 -0.8 11 11
IRF1 -0.032 0.2 -10000 0 -0.73 9 9
mol:GDP -0.12 0.23 -10000 0 -0.48 87 87
SOS1 0.029 0.008 -10000 0 -10000 0 0
VAV1 -0.12 0.23 -10000 0 -0.49 87 87
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.17 0.31 0.46 1 -0.68 81 82
PTPN11 0.014 0.044 -10000 0 -0.72 1 1
IL6/IL6RA -0.12 0.21 -10000 0 -0.37 160 160
gp130 (dimer)/TYK2/TYK2/LMO4 0.007 0.12 -10000 0 -0.28 55 55
gp130 (dimer)/JAK2/JAK2/LMO4 0.001 0.12 -10000 0 -0.28 55 55
IL6 -0.18 0.24 -10000 0 -0.47 170 170
PIAS3 0.024 0.009 -10000 0 -10000 0 0
PTPRE 0.015 0.034 0.23 2 -0.46 1 3
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.13 0.21 -10000 0 -0.32 173 173
LMO4 0.027 0.032 -10000 0 -0.48 1 1
STAT3 (dimer)/PIAS3 -0.045 0.23 -10000 0 -0.67 25 25
MCL1 0.062 0.079 0.41 2 -10000 0 2
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.028 0.044 0.13 3 -0.18 22 25
BUB1B 0.026 0.042 0.14 10 -0.16 6 16
PLK1 0.02 0.03 0.1 21 -0.088 2 23
PLK1S1 0.017 0.028 0.11 14 -0.15 4 18
KIF2A 0.016 0.028 0.16 3 -10000 0 3
regulation of mitotic centrosome separation 0.02 0.03 0.1 21 -0.087 2 23
GOLGA2 0.025 0.009 -10000 0 -10000 0 0
Hec1/SPC24 0.13 0.11 0.24 186 -10000 0 186
WEE1 0.007 0.093 -10000 0 -0.31 30 30
cytokinesis 0.044 0.07 0.22 5 -0.28 9 14
PP2A-alpha B56 0.07 0.089 -10000 0 -0.51 7 7
AURKA 0.034 0.037 0.15 16 -0.17 1 17
PICH/PLK1 0.041 0.048 0.2 13 -10000 0 13
CENPE 0.011 0.03 0.16 3 -0.19 1 4
RhoA/GTP 0.02 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.017 0.029 0.16 3 -10000 0 3
PPP2CA 0.027 0.005 -10000 0 -10000 0 0
FZR1 0.027 0.005 -10000 0 -10000 0 0
TPX2 0.053 0.049 0.17 44 -10000 0 44
PAK1 0.025 0.026 -10000 0 -0.47 1 1
SPC24 0.099 0.093 0.22 153 -10000 0 153
FBXW11 0.026 0.007 -10000 0 -10000 0 0
CLSPN 0.04 0.037 0.14 7 -0.2 1 8
GORASP1 0.026 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.003 0.013 9 -0.011 3 12
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.009 0.015 0.049 24 -0.046 2 26
G2 phase of mitotic cell cycle 0.001 0.004 0.012 42 -10000 0 42
STAG2 0.027 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.013 0.076 -10000 0 -0.55 7 7
spindle elongation 0.02 0.03 0.1 21 -0.087 2 23
ODF2 0.026 0.009 -10000 0 -10000 0 0
BUB1 0.047 0.094 -10000 0 -0.55 7 7
TPT1 0.003 0.052 0.1 1 -0.17 29 30
CDC25C 0.054 0.068 0.23 2 -0.27 12 14
CDC25B 0.03 0.025 0.22 6 -10000 0 6
SGOL1 0.028 0.044 0.18 22 -0.13 3 25
RHOA 0.026 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.072 0.072 0.27 6 -10000 0 6
CDC14B 0.006 0.017 -10000 0 -0.34 1 1
CDC20 0.13 0.095 0.22 228 -10000 0 228
PLK1/PBIP1 0.012 0.022 0.095 7 -10000 0 7
mitosis -0.004 0.008 0.024 2 -0.016 87 89
FBXO5 0.012 0.027 0.11 2 -0.11 2 4
CDC2 0.003 0.003 0.012 11 -0.009 3 14
NDC80 0.095 0.1 0.23 134 -10000 0 134
metaphase plate congression 0.019 0.032 -10000 0 -0.25 4 4
ERCC6L 0.041 0.055 0.21 8 -10000 0 8
NLP/gamma Tubulin 0.013 0.018 0.07 14 -0.067 1 15
microtubule cytoskeleton organization 0.003 0.052 0.1 1 -0.17 29 30
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 2 -10000 0 2
PPP1R12A 0.028 0.005 -10000 0 -10000 0 0
interphase -0.001 0.002 0.014 2 -10000 0 2
PLK1/PRC1-2 0.15 0.097 0.23 158 -0.16 1 159
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.031 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.017 0.027 0.094 27 -0.069 1 28
mitotic prometaphase 0 0.002 0.018 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.063 -10000 0 -0.34 6 6
microtubule-based process 0.12 0.07 0.17 273 -0.12 1 274
Golgi organization 0.02 0.03 0.1 21 -0.087 2 23
Cohesin/SA2 0.031 0.026 0.12 2 -10000 0 2
PPP1CB/MYPT1 0.04 0.011 -10000 0 -10000 0 0
KIF20A 0.16 0.085 0.21 289 -10000 0 289
APC/C/CDC20 0.11 0.074 0.17 223 -0.12 1 224
PPP2R1A 0.027 0.006 -10000 0 -10000 0 0
chromosome segregation 0.012 0.022 0.093 7 -10000 0 7
PRC1 0.063 0.074 0.21 77 -10000 0 77
ECT2 0.027 0.06 0.22 28 -0.12 1 29
C13orf34 0.017 0.026 0.082 30 -0.079 1 31
NUDC 0.019 0.032 -10000 0 -0.25 4 4
regulation of attachment of spindle microtubules to kinetochore 0.026 0.041 0.14 10 -0.16 6 16
spindle assembly 0.016 0.026 0.089 22 -0.081 1 23
spindle stabilization 0.017 0.028 0.11 14 -0.15 4 18
APC/C/HCDH1 0.022 0.018 -10000 0 -0.28 1 1
MKLP2/PLK1 0.12 0.07 0.17 273 -0.12 1 274
CCNB1 0.094 0.092 0.22 143 -10000 0 143
PPP1CB 0.028 0.006 -10000 0 -10000 0 0
BTRC 0.027 0.005 -10000 0 -10000 0 0
ROCK2 0.017 0.07 0.19 1 -0.38 9 10
TUBG1 0.017 0.02 0.11 1 -0.18 1 2
G2/M transition of mitotic cell cycle 0.015 0.037 0.17 8 -10000 0 8
MLF1IP 0.006 0.01 -10000 0 -10000 0 0
INCENP 0.028 0.01 0.21 1 -10000 0 1
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.079 0.16 0.38 63 -10000 0 63
GNAI2 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.036 0.031 -10000 0 -0.28 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
RhoA/GTP -0.08 0.17 -10000 0 -0.39 63 63
negative regulation of cAMP metabolic process -0.093 0.17 -10000 0 -0.32 119 119
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
GNAI3 0.028 0.003 -10000 0 -10000 0 0
GNA12 0.026 0.007 -10000 0 -10000 0 0
S1PR5 0.031 0.051 0.23 13 -0.47 2 15
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.094 0.18 -10000 0 -0.33 119 119
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
GNAI1 0.024 0.043 -10000 0 -0.47 3 3
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.004 0.014 -10000 0 -0.28 1 1
ADCY5 -0.13 0.14 -10000 0 -0.28 184 184
ADCY6 -0.004 0.001 -10000 0 -10000 0 0
ADCY7 -0.004 0.001 -10000 0 -10000 0 0
ADCY1 -0.004 0.019 0.24 1 -0.28 1 2
ADCY2 -0.087 0.13 -10000 0 -0.28 120 120
ADCY3 -0.004 0.001 -10000 0 -10000 0 0
ADCY8 -0.007 0.013 0.24 1 -10000 0 1
PRKCE 0.008 0.002 -10000 0 -10000 0 0
ADCY9 -0.008 0.037 -10000 0 -0.28 7 7
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.029 0.12 0.24 26 -0.19 68 94
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.021 0.12 -10000 0 -0.29 44 44
MAP4K1 0.015 0.079 0.21 3 -0.47 10 13
MAP3K8 0.024 0.035 -10000 0 -0.47 2 2
PRKCB -0.11 0.22 -10000 0 -0.47 112 112
DBNL 0.027 0.005 -10000 0 -10000 0 0
CRKL 0.028 0.014 0.21 2 -10000 0 2
MAP3K1 -0.005 0.11 -10000 0 -0.4 16 16
JUN -0.17 0.3 -10000 0 -0.6 125 125
MAP3K7 -0.006 0.11 -10000 0 -0.38 18 18
GRAP2 -0.026 0.15 -10000 0 -0.47 43 43
CRK 0.025 0.008 -10000 0 -10000 0 0
MAP2K4 -0.008 0.12 -10000 0 -0.4 22 22
LAT 0.027 0.011 0.21 1 -10000 0 1
LCP2 0.022 0.043 -10000 0 -0.47 3 3
MAPK8 -0.17 0.31 -10000 0 -0.61 127 127
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.002 0.12 -10000 0 -0.4 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.031 0.11 -10000 0 -0.27 43 43
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR 0.012 0.077 -10000 0 -0.47 10 10
LRPAP1 0.028 0.016 0.33 1 -10000 0 1
NUDC 0.027 0.003 -10000 0 -10000 0 0
RELN/LRP8 -0.051 0.18 0.27 5 -0.29 135 140
CaM/Ca2+ 0.02 0.003 -10000 0 -10000 0 0
KATNA1 0.027 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.079 0.13 0.19 7 -0.26 134 141
IQGAP1/CaM 0.039 0.009 -10000 0 -10000 0 0
DAB1 -0.017 0.14 0.22 24 -0.47 33 57
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 0.051 0.063 0.22 52 -10000 0 52
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.062 0.052 0.24 3 -10000 0 3
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.004 -10000 0 -10000 0 0
CDK5R1 0.038 0.05 0.24 22 -10000 0 22
LIS1/Poliovirus Protein 3A 0.01 0.004 -10000 0 -10000 0 0
CDK5R2 0.026 0.051 0.21 25 -10000 0 25
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.091 0.18 0.23 1 -0.31 157 158
YWHAE 0.025 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.055 0.12 0.28 1 -0.26 21 22
MAP1B -0.023 0.085 -10000 0 -0.28 41 41
RAC1 0.013 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.058 0.12 0.19 1 -0.24 121 122
RELN -0.15 0.23 0.21 4 -0.47 139 143
PAFAH/LIS1 0.044 0.047 0.23 1 -10000 0 1
LIS1/CLIP170 0.027 0.012 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.04 0.1 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.092 0.17 0.24 2 -0.29 141 143
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.065 0.12 0.21 1 -0.26 40 41
LIS1/IQGAP1 0.027 0.011 -10000 0 -10000 0 0
RHOA 0.014 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.038 0.048 0.23 22 -10000 0 22
PAFAH1B2 0.026 0.006 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0 0.065 -10000 0 -0.29 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.048 0.12 0.28 1 -0.27 8 9
LRP8 0.062 0.073 0.22 74 -10000 0 74
NDEL1/Katanin 60 -0.058 0.12 0.28 1 -0.27 16 17
P39/CDK5 -0.065 0.13 0.22 6 -0.24 130 136
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.027 0.011 -10000 0 -10000 0 0
CDK5 -0.087 0.12 0.18 7 -0.25 134 141
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.01 -10000 0 -10000 0 0
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.07 0.16 0.28 1 -0.27 147 148
RELN/VLDLR -0.043 0.17 0.28 4 -0.27 136 140
CDC42 0.014 0.006 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0.073 -10000 0 -0.47 9 9
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.1 0.17 -10000 0 -0.29 152 152
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
S1P/S1P3/G12/G13 0.039 0.041 0.22 1 -0.26 4 5
AKT1 -0.047 0.17 -10000 0 -0.61 27 27
AKT3 -0.065 0.24 -10000 0 -1.1 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.073 -10000 0 -0.47 9 9
GNAI2 0.025 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.01 -10000 0 -10000 0 0
GNAI1 0.023 0.044 -10000 0 -0.47 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.02 0.053 0.33 1 -0.47 4 5
S1PR2 0.027 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.2 -10000 0 -0.44 80 80
MAPK3 -0.098 0.18 -10000 0 -0.42 78 78
MAPK1 -0.1 0.18 -10000 0 -0.42 80 80
JAK2 -0.1 0.21 0.23 1 -0.45 85 86
CXCR4 -0.1 0.19 -10000 0 -0.43 80 80
FLT1 0.027 0.014 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
SRC -0.095 0.18 -10000 0 -0.43 75 75
S1P/S1P3/Gi -0.1 0.2 -10000 0 -0.44 80 80
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.092 0.19 -10000 0 -0.41 81 81
VEGFA 0.027 0.014 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.092 0.18 -10000 0 -0.33 121 121
VEGFR1 homodimer/VEGFA homodimer 0.041 0.022 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.009 0.094 0.17 1 -0.25 51 52
GNAQ 0.025 0.009 -10000 0 -10000 0 0
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
G12/G13 0.037 0.012 -10000 0 -10000 0 0
GNA14 -0.031 0.16 -10000 0 -0.47 45 45
GNA15 0.023 0.043 -10000 0 -0.47 3 3
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.006 -10000 0 -10000 0 0
GNA11 0.026 0.025 -10000 0 -0.47 1 1
Rac1/GTP -0.09 0.18 -10000 0 -0.41 77 77
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.038 0.27 -10000 0 -0.81 42 42
NCK1/PAK1/Dok-R -0.049 0.12 -10000 0 -0.4 42 42
NCK1/Dok-R -0.049 0.32 -10000 0 -0.95 42 42
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol 0.013 0.068 0.24 34 -10000 0 34
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.027 0.017 0.33 1 -10000 0 1
Rac/GDP 0.02 0.005 -10000 0 -10000 0 0
F2 0.027 0.096 0.25 57 -10000 0 57
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.022 0.3 -10000 0 -0.89 42 42
FN1 0.025 0.094 0.21 26 -0.47 11 37
PLD2 -0.066 0.31 -10000 0 -0.97 42 42
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB14 0.051 0.065 0.21 54 -10000 0 54
ELK1 -0.044 0.29 -10000 0 -0.88 42 42
GRB7 0.028 0.084 0.31 14 -0.47 7 21
PAK1 0.025 0.025 -10000 0 -0.47 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.035 0.33 -10000 0 -0.98 42 42
CDKN1A -0.037 0.2 -10000 0 -0.59 36 36
ITGA5 0.009 0.094 -10000 0 -0.47 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.049 0.32 -10000 0 -0.96 42 42
CRK 0.025 0.008 -10000 0 -10000 0 0
mol:NO -0.018 0.21 -10000 0 -0.61 42 42
PLG -0.068 0.31 -10000 0 -0.98 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.04 0.26 -10000 0 -0.79 42 42
GRB2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
ANGPT2 -0.099 0.21 -10000 0 -0.64 34 34
BMX -0.11 0.33 -10000 0 -1 42 42
ANGPT1 -0.078 0.34 -10000 0 -1.2 34 34
tube development -0.051 0.22 -10000 0 -0.62 44 44
ANGPT4 0.022 0.034 0.23 8 -10000 0 8
response to hypoxia -0.005 0.021 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.038 0.34 -10000 0 -1 42 42
alpha5/beta1 Integrin 0.024 0.072 -10000 0 -0.34 15 15
FGF2 -0.13 0.23 -10000 0 -0.47 127 127
STAT5A (dimer) -0.048 0.25 -10000 0 -0.71 40 40
mol:L-citrulline -0.018 0.21 -10000 0 -0.61 42 42
AGTR1 -0.17 0.24 -10000 0 -0.47 161 161
MAPK14 -0.06 0.32 -10000 0 -0.99 42 42
Tie2/SHP2 -0.032 0.22 -10000 0 -0.92 18 18
TEK -0.022 0.23 -10000 0 -1 18 18
RPS6KB1 -0.035 0.27 -10000 0 -0.79 41 41
Angiotensin II/AT1 -0.12 0.17 -10000 0 -0.33 161 161
Tie2/Ang1/GRB2 -0.051 0.33 -10000 0 -0.99 42 42
MAPK3 -0.057 0.29 -10000 0 -0.89 42 42
MAPK1 -0.058 0.29 -10000 0 -0.9 42 42
Tie2/Ang1/GRB7 -0.051 0.33 -10000 0 -1 42 42
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.065 0.31 -10000 0 -0.97 42 42
PI3K -0.056 0.3 -10000 0 -0.92 42 42
FES -0.067 0.32 -10000 0 -0.99 42 42
Crk/Dok-R -0.049 0.32 -10000 0 -0.95 42 42
Tie2/Ang1/ABIN2 -0.051 0.33 -10000 0 -1 42 42
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.029 0.25 -10000 0 -0.73 42 42
STAT5A 0.026 0.025 -10000 0 -0.47 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.025 0.27 -10000 0 -0.78 42 42
Tie2/Ang2 -0.074 0.27 -10000 0 -0.83 39 39
Tie2/Ang1 -0.066 0.34 -10000 0 -1 42 42
FOXO1 -0.025 0.25 -10000 0 -0.73 42 42
ELF1 0.027 0.027 -10000 0 -10000 0 0
ELF2 -0.059 0.31 -10000 0 -0.95 42 42
mol:Choline -0.061 0.3 -10000 0 -0.93 42 42
cell migration -0.025 0.074 -10000 0 -0.23 43 43
FYN -0.061 0.24 -10000 0 -0.7 43 43
DOK2 0.014 0.071 0.21 2 -0.47 8 10
negative regulation of cell cycle -0.032 0.19 -10000 0 -0.54 36 36
ETS1 0.011 0.076 -10000 0 -0.24 32 32
PXN -0.014 0.24 0.41 3 -0.65 42 45
ITGB1 0.026 0.006 -10000 0 -10000 0 0
NOS3 -0.026 0.24 -10000 0 -0.69 42 42
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF 0.02 0.092 0.23 20 -0.25 34 54
MAPKKK cascade -0.061 0.3 -10000 0 -0.93 42 42
RASA1 0.027 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.051 0.32 -10000 0 -0.98 42 42
NCK1 0.026 0.006 -10000 0 -10000 0 0
vasculogenesis -0.013 0.19 -10000 0 -0.55 42 42
mol:Phosphatidic acid -0.061 0.3 -10000 0 -0.93 42 42
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.018 0.21 -10000 0 -0.61 42 42
Rac1/GTP -0.032 0.25 -10000 0 -0.74 42 42
MMP2 -0.077 0.33 -10000 0 -1 42 42
Coregulation of Androgen receptor activity

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
NRIP1 0.024 0.025 0.33 1 -10000 0 1
SVIL 0.02 0.04 -10000 0 -0.47 2 2
ZNF318 0.031 0.035 0.2 14 -10000 0 14
JMJD2C 0.008 0.012 0.047 5 -10000 0 5
T-DHT/AR/Ubc9 -0.089 0.16 -10000 0 -0.3 145 145
CARM1 0.026 0.009 -10000 0 -10000 0 0
PRDX1 0.028 0.004 -10000 0 -10000 0 0
PELP1 0.026 0.009 -10000 0 -10000 0 0
CTNNB1 0.024 0.018 -10000 0 -10000 0 0
AKT1 0.028 0.01 -10000 0 -10000 0 0
PTK2B 0.021 0.017 -10000 0 -10000 0 0
MED1 0.028 0.012 -10000 0 -10000 0 0
MAK 0.034 0.043 0.21 22 -10000 0 22
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.021 0.04 -10000 0 -0.47 2 2
GSN 0.018 0.047 -10000 0 -0.47 3 3
NCOA2 -0.001 0.11 -10000 0 -0.47 20 20
NCOA6 0.023 0.026 0.33 1 -10000 0 1
DNA-PK 0.051 0.035 0.22 4 -10000 0 4
NCOA4 0.027 0.006 -10000 0 -10000 0 0
PIAS3 0.022 0.018 -10000 0 -10000 0 0
cell proliferation -0.004 0.073 0.32 1 -0.43 6 7
XRCC5 0.027 0.009 -10000 0 -10000 0 0
UBE3A 0.022 0.027 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.18 -10000 0 -0.33 155 155
FHL2 -0.027 0.12 -10000 0 -0.73 6 6
RANBP9 0.023 0.02 -10000 0 -10000 0 0
JMJD1A -0.016 0.05 0.055 1 -0.12 68 69
CDK6 0.015 0.077 -10000 0 -0.47 10 10
TGFB1I1 0.008 0.09 -10000 0 -0.47 13 13
T-DHT/AR/CyclinD1 -0.084 0.16 0.22 3 -0.3 134 137
XRCC6 0.028 0.009 -10000 0 -10000 0 0
T-DHT/AR -0.09 0.18 -10000 0 -0.29 170 170
CTDSP1 0.024 0.012 -10000 0 -10000 0 0
CTDSP2 0.03 0.02 -10000 0 -10000 0 0
BRCA1 0.024 0.023 0.22 1 -10000 0 1
TCF4 0.021 0.062 -10000 0 -0.47 6 6
CDKN2A 0.11 0.11 0.22 190 -10000 0 190
SRF 0.033 0.018 -10000 0 -0.15 1 1
NKX3-1 -0.072 0.11 -10000 0 -0.18 170 170
KLK3 -0.045 0.28 -10000 0 -1.4 16 16
TMF1 0.024 0.011 -10000 0 -10000 0 0
HNRNPA1 0.029 0.011 -10000 0 -10000 0 0
AOF2 -0.002 0.015 -10000 0 -0.076 16 16
APPL1 0.016 0.019 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.087 0.16 -10000 0 -0.3 144 144
AR -0.16 0.24 -10000 0 -0.48 145 145
UBA3 0.024 0.013 -10000 0 -10000 0 0
PATZ1 0.028 0.012 -10000 0 -10000 0 0
PAWR 0.025 0.026 -10000 0 -0.47 1 1
PRKDC 0.026 0.011 -10000 0 -10000 0 0
PA2G4 0.029 0.015 -10000 0 -10000 0 0
UBE2I 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.076 0.15 -10000 0 -0.27 144 144
RPS6KA3 0.024 0.021 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.088 0.16 -10000 0 -0.3 144 144
LATS2 0.027 0.028 -10000 0 -0.47 1 1
T-DHT/AR/PRX1 -0.076 0.15 -10000 0 -0.27 144 144
Cyclin D3/CDK11 p58 0.02 0.004 -10000 0 -10000 0 0
VAV3 0.023 0.05 0.21 4 -0.47 3 7
KLK2 -0.031 0.079 -10000 0 -0.42 2 2
CASP8 0.027 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.082 0.16 -10000 0 -0.29 140 140
TMPRSS2 -0.18 0.37 -10000 0 -0.94 73 73
CCND1 0.025 0.087 0.32 14 -0.47 7 21
PIAS1 0.023 0.027 -10000 0 -10000 0 0
mol:T-DHT -0.005 0.019 -10000 0 -0.051 45 45
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.021 0.037 -10000 0 -0.17 14 14
T-DHT/AR/CDK6 -0.094 0.17 -10000 0 -0.31 149 149
CMTM2 0.029 0.022 0.21 5 -10000 0 5
SNURF -0.012 0.12 -10000 0 -0.47 27 27
ZMIZ1 0.017 0.031 -10000 0 -10000 0 0
CCND3 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.013 -10000 0 -10000 0 0
FKBP4 0.023 0.021 -10000 0 -10000 0 0
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 -0.051 0.16 0.26 1 -0.4 44 45
IKBKB -0.018 0.1 -10000 0 -0.3 23 23
AKT1 -0.04 0.11 0.23 10 -0.24 41 51
IKBKG -0.013 0.1 -10000 0 -0.31 22 22
CALM1 -0.036 0.14 -10000 0 -0.4 34 34
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
MAP3K1 -0.076 0.22 -10000 0 -0.54 52 52
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.037 0.15 -10000 0 -0.41 37 37
DOK1 0.027 0.011 0.21 1 -10000 0 1
AP-1 -0.046 0.11 0.22 2 -0.25 38 40
LYN 0.025 0.008 -10000 0 -10000 0 0
BLNK 0.011 0.087 -10000 0 -0.47 13 13
SHC1 0.026 0.017 0.33 1 -10000 0 1
BCR complex -0.027 0.17 0.3 7 -0.38 69 76
CD22 -0.1 0.25 -10000 0 -0.57 70 70
CAMK2G -0.029 0.13 -10000 0 -0.41 28 28
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
INPP5D 0.018 0.06 -10000 0 -0.47 6 6
SHC/GRB2/SOS1 -0.018 0.11 -10000 0 -0.39 14 14
GO:0007205 -0.039 0.15 -10000 0 -0.42 38 38
SYK 0.02 0.049 -10000 0 -0.47 4 4
ELK1 -0.036 0.15 0.35 1 -0.41 34 35
NFATC1 -0.092 0.22 0.23 1 -0.49 70 71
B-cell antigen/BCR complex -0.027 0.17 0.3 7 -0.38 69 76
PAG1/CSK 0.035 0.015 -10000 0 -10000 0 0
NFKBIB 0.011 0.043 -10000 0 -0.13 7 7
HRAS -0.036 0.14 0.26 1 -0.39 37 38
NFKBIA 0.012 0.042 -10000 0 -0.12 6 6
NF-kappa-B/RelA/I kappa B beta 0.017 0.037 -10000 0 -10000 0 0
RasGAP/Csk -0.001 0.16 0.29 6 -0.33 65 71
mol:GDP -0.038 0.15 -10000 0 -0.41 37 37
PTEN 0.026 0.007 -10000 0 -10000 0 0
CD79B 0.011 0.097 0.21 7 -0.47 15 22
NF-kappa-B/RelA/I kappa B alpha 0.017 0.037 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.098 0.22 -10000 0 -0.51 64 64
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
mol:IP3 -0.04 0.15 -10000 0 -0.42 38 38
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.098 0.17 -10000 0 -0.4 61 61
CHUK -0.02 0.11 -10000 0 -0.32 30 30
IBTK 0.026 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.011 0.14 0.27 1 -0.4 26 27
PTPN6 -0.1 0.23 -10000 0 -0.56 66 66
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.011 0.034 -10000 0 -0.11 3 3
VAV2 -0.1 0.24 -10000 0 -0.58 62 62
ubiquitin-dependent protein catabolic process 0.015 0.042 -10000 0 -0.12 7 7
BTK -0.042 0.26 -10000 0 -1.1 24 24
CD19 -0.095 0.23 -10000 0 -0.59 55 55
MAP4K1 0.015 0.079 0.21 3 -0.47 10 13
CD72 0.031 0.034 0.21 13 -10000 0 13
PAG1 0.024 0.01 -10000 0 -10000 0 0
MAPK14 -0.062 0.19 -10000 0 -0.47 48 48
SH3BP5 0.025 0.026 -10000 0 -0.47 1 1
PIK3AP1 -0.044 0.17 -10000 0 -0.48 35 35
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.071 0.24 -10000 0 -0.52 67 67
RAF1 -0.015 0.14 0.26 9 -0.39 28 37
RasGAP/p62DOK/SHIP -0.004 0.16 0.26 7 -0.34 64 71
CD79A -0.051 0.19 0.21 14 -0.47 69 83
re-entry into mitotic cell cycle -0.046 0.11 0.22 2 -0.25 36 38
RASA1 0.027 0.006 -10000 0 -10000 0 0
MAPK3 -0.006 0.12 0.27 8 -0.4 16 24
MAPK1 -0.008 0.12 0.27 13 -0.39 17 30
CD72/SHP1 -0.069 0.24 0.31 7 -0.54 60 67
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.062 0.19 0.32 2 -0.46 51 53
actin cytoskeleton organization -0.086 0.21 0.33 1 -0.5 58 59
NF-kappa-B/RelA 0.037 0.071 -10000 0 -10000 0 0
Calcineurin -0.014 0.13 -10000 0 -0.39 25 25
PI3K -0.099 0.18 -10000 0 -0.44 71 71
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.041 0.16 -10000 0 -0.42 42 42
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.076 0.27 -10000 0 -0.75 45 45
DAPP1 -0.096 0.29 -10000 0 -0.82 47 47
cytokine secretion -0.084 0.2 0.23 1 -0.45 69 70
mol:DAG -0.04 0.15 -10000 0 -0.42 38 38
PLCG2 0.026 0.039 0.21 3 -0.47 2 5
MAP2K1 -0.013 0.13 0.25 9 -0.4 22 31
B-cell antigen/BCR complex/FcgammaRIIB -0.023 0.18 0.29 7 -0.39 65 72
mol:PI-3-4-5-P3 -0.073 0.13 0.26 1 -0.31 65 66
ETS1 -0.025 0.12 0.25 2 -0.38 27 29
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.002 0.15 0.29 7 -0.29 72 79
B-cell antigen/BCR complex/LYN -0.068 0.22 -10000 0 -0.62 42 42
MALT1 0.026 0.007 -10000 0 -10000 0 0
TRAF6 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.092 0.22 0.34 1 -0.55 57 58
B-cell antigen/BCR complex/LYN/SYK -0.067 0.24 -10000 0 -0.55 60 60
CARD11 -0.033 0.15 0.3 1 -0.41 37 38
FCGR2B -0.005 0.12 0.25 3 -0.47 24 27
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.001 0.052 0.15 5 -0.13 16 21
PTPRC -0.026 0.16 0.21 2 -0.47 44 46
PDPK1 -0.043 0.1 0.22 11 -0.22 55 66
PPP3CB 0.027 0.006 -10000 0 -10000 0 0
PPP3CC 0.023 0.01 -10000 0 -10000 0 0
POU2F2 0.013 0.032 0.13 3 -0.11 1 4
FOXM1 transcription factor network

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
NFATC3 0.077 0.41 0.77 2 -0.92 20 22
PLK1 0.079 0.13 -10000 0 -0.97 4 4
BIRC5 0.1 0.12 -10000 0 -1.1 2 2
HSPA1B 0.075 0.41 0.71 1 -0.92 20 21
MAP2K1 0.042 0.063 -10000 0 -10000 0 0
BRCA2 0.078 0.41 0.85 2 -0.92 20 22
FOXM1 0.069 0.46 0.71 1 -1.1 24 25
XRCC1 0.076 0.41 0.78 3 -0.91 21 24
FOXM1B/p19 -0.014 0.41 -10000 0 -0.97 28 28
Cyclin D1/CDK4 0.068 0.4 0.66 5 -0.87 24 29
CDC2 0.07 0.42 0.68 1 -0.92 25 26
TGFA 0.064 0.38 0.62 2 -0.82 24 26
SKP2 0.096 0.42 0.76 10 -0.91 20 30
CCNE1 0.065 0.087 0.26 64 -10000 0 64
CKS1B 0.071 0.4 0.64 1 -0.87 25 26
RB1 0.068 0.25 0.45 22 -0.71 14 36
FOXM1C/SP1 0.059 0.44 -10000 0 -0.99 28 28
AURKB 0.026 0.27 -10000 0 -0.84 30 30
CENPF 0.088 0.41 0.77 1 -0.92 20 21
CDK4 0.033 0.034 0.34 1 -10000 0 1
MYC 0.038 0.39 0.6 1 -0.88 27 28
CHEK2 0.043 0.064 0.32 1 -10000 0 1
ONECUT1 0.069 0.4 0.66 2 -0.86 25 27
CDKN2A 0.096 0.1 0.2 189 -0.26 1 190
LAMA4 0.063 0.43 -10000 0 -1.1 20 20
FOXM1B/HNF6 0.06 0.43 0.69 1 -1 24 25
FOS -0.18 0.65 0.74 1 -1 136 137
SP1 0.027 0.01 -10000 0 -10000 0 0
CDC25B 0.081 0.41 0.78 4 -0.96 17 21
response to radiation 0.02 0.042 -10000 0 -10000 0 0
CENPB 0.081 0.41 0.78 4 -0.96 17 21
CENPA 0.091 0.41 0.71 1 -0.95 18 19
NEK2 0.088 0.41 -10000 0 -0.91 21 21
HIST1H2BA 0.075 0.41 0.76 4 -0.94 19 23
CCNA2 0.081 0.089 0.23 105 -10000 0 105
EP300 0.027 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.059 0.44 -10000 0 -1.1 21 21
CCNB2 0.086 0.41 -10000 0 -0.94 18 18
CCNB1 0.073 0.42 -10000 0 -0.96 21 21
ETV5 0.08 0.41 0.77 4 -0.98 17 21
ESR1 -0.062 0.58 -10000 0 -1.1 83 83
CCND1 0.047 0.39 0.68 2 -0.89 24 26
GSK3A 0.037 0.054 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.11 0.11 0.28 71 -10000 0 71
CDK2 0.03 0.017 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.025 0.051 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.056 0.41 -10000 0 -0.94 24 24
GAS1 -0.095 0.64 -10000 0 -1.1 96 96
MMP2 0.016 0.51 -10000 0 -1.2 40 40
RB1/FOXM1C 0.056 0.4 0.65 7 -0.9 25 32
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.005 -10000 0 -10000 0 0
CCL5 0.011 0.11 0.21 13 -0.47 18 31
SDCBP 0.025 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.037 0.1 0.3 15 -0.4 4 19
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 0.04 0.094 0.26 12 -0.39 4 16
Syndecan-1/Syntenin 0.043 0.096 0.28 12 -0.39 4 16
MAPK3 0.04 0.091 0.27 14 -0.35 4 18
HGF/MET -0.037 0.16 0.24 2 -0.34 86 88
TGFB1/TGF beta receptor Type II 0.027 0.005 -10000 0 -10000 0 0
BSG 0.027 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.04 0.093 0.26 12 -0.38 4 16
Syndecan-1/RANTES 0.038 0.12 0.28 15 -0.41 11 26
Syndecan-1/CD147 0.059 0.1 0.28 14 -0.36 4 18
Syndecan-1/Syntenin/PIP2 0.038 0.09 0.25 11 -0.38 4 15
LAMA5 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.037 0.088 0.24 11 -0.37 4 15
MMP7 0.039 0.14 0.22 78 -0.47 20 98
HGF -0.076 0.2 0.21 7 -0.47 86 93
Syndecan-1/CASK 0.028 0.093 0.26 13 -0.39 4 17
Syndecan-1/HGF/MET 0.007 0.16 0.28 14 -0.4 21 35
regulation of cell adhesion 0.032 0.087 0.26 14 -0.37 3 17
HPSE 0.04 0.07 0.22 36 -0.47 3 39
positive regulation of cell migration 0.037 0.1 0.3 15 -0.4 4 19
SDC1 0.037 0.1 0.31 13 -0.28 12 25
Syndecan-1/Collagen 0.037 0.1 0.3 15 -0.4 4 19
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET 0.029 0.022 0.33 2 -10000 0 2
PRKACA 0.027 0.003 -10000 0 -10000 0 0
MMP9 0.068 0.1 0.22 102 -0.47 5 107
MAPK1 0.041 0.092 0.27 14 -0.38 3 17
homophilic cell adhesion 0.038 0.1 0.3 16 -0.4 4 20
MMP1 0.13 0.1 0.22 222 -0.47 1 223
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.014 0.094 -10000 0 -0.24 43 43
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.098 0.32 7 -10000 0 7
alphaV/beta3 Integrin/Osteopontin/Src 0.094 0.07 -10000 0 -10000 0 0
AP1 -0.067 0.2 -10000 0 -0.49 44 44
ILK -0.014 0.095 -10000 0 -0.26 43 43
bone resorption 0.003 0.1 0.32 1 -0.33 10 11
PTK2B 0.023 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.065 0.13 0.29 4 -0.23 32 36
ITGAV 0.03 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.021 0.076 0.24 1 -0.33 17 18
alphaV/beta3 Integrin/Osteopontin 0.068 0.14 -10000 0 -0.28 43 43
MAP3K1 -0.014 0.095 -10000 0 -0.26 43 43
JUN 0.01 0.091 -10000 0 -0.47 14 14
MAPK3 -0.012 0.084 0.2 8 -0.24 40 48
MAPK1 -0.012 0.087 0.2 2 -0.24 42 44
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.021 0.089 0.2 9 -0.25 43 52
ITGB3 -0.024 0.15 -10000 0 -0.46 44 44
NFKBIA -0.006 0.082 0.32 1 -0.26 6 7
FOS -0.12 0.23 -10000 0 -0.47 124 124
CD44 0.013 0.082 0.33 1 -0.47 11 12
CHUK 0.027 0.005 -10000 0 -10000 0 0
PLAU 0.008 0.099 0.36 1 -10000 0 1
NF kappa B1 p50/RelA 0.046 0.094 0.32 1 -10000 0 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.003 0.12 -10000 0 -0.33 44 44
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.017 0.095 -10000 0 -0.25 46 46
VAV3 -0.024 0.089 0.2 10 -0.24 40 50
MAP3K14 -0.011 0.094 0.2 1 -0.26 43 44
ROCK2 0.018 0.065 -10000 0 -0.47 7 7
SPP1 0.1 0.092 0.22 161 -10000 0 161
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.013 0.085 -10000 0 -0.23 36 36
MMP2 -0.096 0.18 0.33 1 -0.5 51 52
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.009 0.095 0.17 25 -0.29 30 55
EPHB2 0.04 0.047 0.21 28 -10000 0 28
Syndecan-2/TACI -0.01 0.1 0.16 7 -0.29 44 51
LAMA1 0.04 0.12 0.22 66 -0.47 14 80
Syndecan-2/alpha2 ITGB1 0.022 0.11 0.27 6 -0.26 41 47
HRAS 0.025 0.008 -10000 0 -10000 0 0
Syndecan-2/CASK -0.008 0.067 -10000 0 -0.28 24 24
ITGA5 0.009 0.094 -10000 0 -0.47 15 15
BAX -0.007 0.058 -10000 0 -10000 0 0
EPB41 0.028 0.002 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.007 0.064 -10000 0 -0.25 23 23
LAMA3 0.003 0.15 0.22 35 -0.47 32 67
EZR 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.022 0.049 -10000 0 -0.47 4 4
Syndecan-2/MMP2 -0.011 0.11 -10000 0 -0.34 39 39
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.038 0.027 0.24 1 -0.34 1 2
dendrite morphogenesis 0.017 0.085 0.18 26 -0.28 24 50
Syndecan-2/GM-CSF 0.031 0.1 0.29 8 -0.28 24 32
determination of left/right symmetry -0.009 0.08 -10000 0 -0.33 24 24
Syndecan-2/PKC delta 0.007 0.07 -10000 0 -0.27 23 23
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 0.031 0.093 0.2 60 -0.26 21 81
MAPK1 0.031 0.097 0.2 62 -0.26 24 86
Syndecan-2/RACK1 0.017 0.065 -10000 0 -0.23 24 24
NF1 0.026 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.08 -10000 0 -0.33 24 24
ITGA2 0.028 0.035 0.24 5 -0.47 1 6
MAPK8 -0.006 0.067 -10000 0 -0.27 24 24
Syndecan-2/alpha2/beta1 Integrin 0.038 0.1 0.26 9 -0.25 31 40
Syndecan-2/Kininogen 0.002 0.067 -10000 0 -0.28 21 21
ITGB1 0.026 0.006 -10000 0 -10000 0 0
SRC 0.023 0.084 0.18 49 -0.22 24 73
Syndecan-2/CASK/Protein 4.1 0.007 0.066 -10000 0 -0.25 24 24
extracellular matrix organization 0.007 0.072 -10000 0 -0.28 24 24
actin cytoskeleton reorganization 0.009 0.095 0.17 25 -0.29 30 55
Syndecan-2/Caveolin-2/Ras 0.016 0.075 -10000 0 -0.26 26 26
Syndecan-2/Laminin alpha3 0.002 0.11 0.25 5 -0.29 43 48
Syndecan-2/RasGAP 0.026 0.067 -10000 0 -0.22 24 24
alpha5/beta1 Integrin 0.024 0.072 -10000 0 -0.34 15 15
PRKCD 0.026 0.007 -10000 0 -10000 0 0
Syndecan-2 dimer 0.017 0.086 0.18 26 -0.28 24 50
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.014 0.061 -10000 0 -0.22 24 24
RHOA 0.026 0.006 -10000 0 -10000 0 0
SDCBP 0.025 0.008 -10000 0 -10000 0 0
TNFRSF13B -0.013 0.13 0.21 7 -0.47 28 35
RASA1 0.027 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.038 0.027 0.24 1 -0.34 1 2
Syndecan-2/Synbindin 0.006 0.072 -10000 0 -0.28 24 24
TGFB1 0.027 0.005 -10000 0 -10000 0 0
CASP3 0.028 0.091 0.2 58 -0.25 21 79
FN1 0.025 0.094 0.21 26 -0.47 11 37
Syndecan-2/IL8 -0.025 0.12 0.16 1 -0.3 61 62
SDC2 -0.009 0.08 -10000 0 -0.33 24 24
KNG1 -0.016 0.004 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.006 0.072 -10000 0 -0.28 24 24
TRAPPC4 0.026 0.007 -10000 0 -10000 0 0
CSF2 0.056 0.075 0.21 74 -10000 0 74
Syndecan-2/TGFB1 0.007 0.072 -10000 0 -0.28 24 24
Syndecan-2/Syntenin/PI-4-5-P2 0.007 0.064 -10000 0 -0.25 23 23
Syndecan-2/Ezrin 0.02 0.069 -10000 0 -0.25 23 23
PRKACA 0.028 0.095 0.2 61 -0.25 24 85
angiogenesis -0.024 0.12 0.16 1 -0.3 61 62
MMP2 -0.011 0.13 -10000 0 -0.47 31 31
IL8 -0.041 0.17 0.21 1 -0.47 56 57
calcineurin-NFAT signaling pathway -0.01 0.1 0.16 7 -0.29 44 51
Arf6 signaling events

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
CENTA1/KIF3B 0.028 0.03 -10000 0 -0.28 3 3
ARNO/beta Arrestin1-2 0.004 0.097 -10000 0 -0.78 2 2
EGFR 0.021 0.085 0.33 8 -0.47 9 17
EPHA2 0.021 0.055 -10000 0 -0.47 5 5
USP6 0.025 0.008 -10000 0 -10000 0 0
IQSEC1 0.025 0.018 0.33 1 -10000 0 1
EGFR/EGFR/EGF/EGF 0.04 0.071 0.24 7 -0.34 9 16
ARRB2 0.01 0.006 -10000 0 -10000 0 0
mol:GTP 0.018 0.049 0.14 32 -0.16 6 38
ARRB1 0.021 0.049 -10000 0 -0.47 4 4
FBXO8 0.026 0.006 -10000 0 -10000 0 0
TSHR 0.019 0.032 0.21 7 -10000 0 7
EGF 0.034 0.047 0.21 24 -10000 0 24
somatostatin receptor activity 0 0 0.001 6 -0.001 80 86
ARAP2 0.024 0.035 -10000 0 -0.47 2 2
mol:GDP -0.068 0.14 0.21 2 -0.28 88 90
mol:PI-3-4-5-P3 0 0 0.001 3 -0.001 42 45
ITGA2B 0.04 0.052 0.22 31 -10000 0 31
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.047 0.24 5 -0.26 4 9
ADAP1 0.023 0.043 -10000 0 -0.47 3 3
KIF13B 0.023 0.01 -10000 0 -10000 0 0
HGF/MET -0.037 0.16 0.24 2 -0.34 86 88
PXN 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.063 0.13 0.21 6 -0.27 81 87
EGFR/EGFR/EGF/EGF/ARFGEP100 0.05 0.063 0.24 8 -0.29 7 15
ADRB2 -0.034 0.16 -10000 0 -0.47 49 49
receptor agonist activity 0 0 0 6 0 81 87
actin filament binding 0 0 0 4 -0.001 83 87
SRC 0.026 0.007 -10000 0 -10000 0 0
ITGB3 -0.027 0.15 -10000 0 -0.47 44 44
GNAQ 0.025 0.009 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 11 -0.001 52 63
ARF6/GDP -0.018 0.15 0.27 7 -0.42 32 39
ARF6/GDP/GULP/ACAP1 -0.078 0.18 -10000 0 -0.35 96 96
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.11 -10000 0 -0.26 42 42
ACAP1 0.015 0.079 0.21 4 -0.47 10 14
ACAP2 0.026 0.007 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.023 0.18 2 -10000 0 2
EFNA1 0.031 0.039 0.3 8 -10000 0 8
HGF -0.076 0.2 0.21 7 -0.47 86 93
CYTH3 0.007 0.002 -10000 0 -10000 0 0
CYTH2 0.014 0.071 -10000 0 -0.99 2 2
NCK1 0.026 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0 10 0 60 70
endosomal lumen acidification 0 0 0 19 0 74 93
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.045 0.18 -10000 0 -0.47 59 59
GNAQ/ARNO 0.027 0.067 -10000 0 -0.91 2 2
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 3 0 14 17
MET 0.029 0.022 0.33 2 -10000 0 2
GNA14 -0.031 0.16 -10000 0 -0.47 45 45
GNA15 0.023 0.043 -10000 0 -0.47 3 3
GIT1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 11 -0.001 72 83
GNA11 0.026 0.025 -10000 0 -0.47 1 1
LHCGR -0.005 0.025 0.21 2 -10000 0 2
AGTR1 -0.17 0.24 -10000 0 -0.47 161 161
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.023 0.18 2 -10000 0 2
IPCEF1/ARNO 0.041 0.08 -10000 0 -0.83 2 2
alphaIIb/beta3 Integrin 0.006 0.12 -10000 0 -0.34 44 44
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.028 0.01 0.21 1 -10000 0 1
Aurora C/Aurora B/INCENP 0.094 0.068 0.26 6 -0.12 3 9
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.011 0.006 -10000 0 -10000 0 0
AURKB 0.11 0.095 0.21 178 -10000 0 178
AURKC 0.033 0.033 0.21 13 -10000 0 13
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.011 0.12 0.35 1 -0.3 48 49
FZD6 0.023 0.011 -10000 0 -10000 0 0
WNT6 0.03 0.096 0.21 36 -0.47 10 46
WNT4 -0.002 0.12 0.21 3 -0.47 25 28
FZD3 0.021 0.036 -10000 0 -0.47 2 2
WNT5A 0.022 0.071 0.21 10 -0.47 7 17
WNT11 0.017 0.12 0.22 33 -0.47 20 53
FAS signaling pathway (CD95)

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
SPTAN1 -0.004 0.043 0.21 10 -0.19 8 18
RFC1 -0.003 0.05 0.2 15 -0.19 9 24
PRKDC 0.012 0.077 0.22 41 -0.19 9 50
RIPK1 0.03 0.009 -10000 0 -10000 0 0
CASP7 -0.03 0.14 -10000 0 -0.68 14 14
FASLG/FAS/FADD/FAF1 -0.019 0.075 0.22 5 -0.28 16 21
MAP2K4 -0.11 0.19 -10000 0 -0.42 63 63
mol:ceramide -0.046 0.12 -10000 0 -0.36 23 23
GSN -0.005 0.047 0.21 11 -0.2 9 20
FASLG/FAS/FADD/FAF1/Caspase 8 -0.029 0.095 0.21 1 -0.31 22 23
FAS 0 0.06 -10000 0 -0.48 5 5
BID -0.015 0.035 0.25 6 -10000 0 6
MAP3K1 -0.057 0.14 0.26 1 -0.42 28 29
MAP3K7 0.022 0.009 -10000 0 -10000 0 0
RB1 -0.003 0.058 0.22 14 -0.22 8 22
CFLAR 0.031 0.008 -10000 0 -10000 0 0
HGF/MET -0.022 0.14 0.24 2 -0.29 90 92
ARHGDIB 0 0.057 0.22 19 -0.19 9 28
FADD 0.01 0.046 0.32 6 -10000 0 6
actin filament polymerization 0.006 0.049 0.2 7 -0.21 11 18
NFKB1 -0.064 0.13 -10000 0 -0.56 8 8
MAPK8 -0.19 0.27 -10000 0 -0.48 175 175
DFFA -0.004 0.052 0.22 14 -0.19 10 24
DNA fragmentation during apoptosis -0.004 0.057 0.22 16 -0.19 1 17
FAS/FADD/MET 0.019 0.06 0.24 6 -0.3 5 11
CFLAR/RIP1 0.044 0.017 -10000 0 -10000 0 0
FAIM3 0.026 0.053 0.21 4 -0.47 4 8
FAF1 0.002 0.03 -10000 0 -10000 0 0
PARP1 -0.004 0.049 0.2 14 -0.19 10 24
DFFB -0.003 0.054 0.22 15 -0.19 10 25
CHUK -0.057 0.11 -10000 0 -0.58 5 5
FASLG -0.013 0.099 0.21 6 -0.48 15 21
FAS/FADD 0.007 0.058 0.24 4 -0.35 5 9
HGF -0.076 0.2 0.21 7 -0.47 86 93
LMNA 0.005 0.066 0.22 23 -10000 0 23
CASP6 -0.003 0.049 0.2 15 -0.19 9 24
CASP10 0.005 0.027 -10000 0 -10000 0 0
CASP3 0.003 0.048 0.25 14 -10000 0 14
PTPN13 0.018 0.065 -10000 0 -0.47 7 7
CASP8 -0.019 0.039 0.35 4 -10000 0 4
IL6 -0.53 0.64 -10000 0 -1.2 182 182
MET 0.029 0.022 0.33 2 -10000 0 2
ICAD/CAD -0.002 0.052 0.22 13 -10000 0 13
FASLG/FAS/FADD/FAF1/Caspase 10 -0.047 0.12 -10000 0 -0.36 23 23
activation of caspase activity by cytochrome c -0.015 0.035 0.25 6 -10000 0 6
PAK2 0.005 0.063 0.21 28 -0.19 5 33
BCL2 0.009 0.094 -10000 0 -0.47 15 15
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.002 0.12 0.35 40 -10000 0 40
KIRREL -0.022 0.15 -10000 0 -0.48 40 40
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.002 0.12 -10000 0 -0.35 40 40
PLCG1 0.026 0.007 -10000 0 -10000 0 0
ARRB2 0.025 0.008 -10000 0 -10000 0 0
WASL 0.027 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.028 0.1 -10000 0 -0.26 40 40
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0 0.078 -10000 0 -0.24 36 36
FYN -0.005 0.11 0.29 14 -0.26 41 55
mol:Ca2+ 0.026 0.099 -10000 0 -0.26 36 36
mol:DAG 0.027 0.1 -10000 0 -0.26 36 36
NPHS2 0.014 0.057 0.23 19 -10000 0 19
mol:IP3 0.027 0.1 -10000 0 -0.26 36 36
regulation of endocytosis 0.016 0.092 -10000 0 -0.24 40 40
Nephrin/NEPH1/podocin/Cholesterol 0.015 0.099 0.22 2 -0.26 40 42
establishment of cell polarity -0.002 0.12 -10000 0 -0.35 40 40
Nephrin/NEPH1/podocin/NCK1-2 0.039 0.1 -10000 0 -0.24 37 37
Nephrin/NEPH1/beta Arrestin2 0.017 0.093 -10000 0 -0.24 40 40
NPHS1 0.007 0.043 0.23 6 -10000 0 6
Nephrin/NEPH1/podocin 0.015 0.099 -10000 0 -0.26 41 41
TJP1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
NCK2 0.027 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.1 -10000 0 -0.26 36 36
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.028 0.1 -10000 0 -0.26 38 38
GRB2 0.027 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.003 0.11 0.3 14 -0.25 40 54
cytoskeleton organization -0.008 0.088 0.21 7 -0.27 35 42
Nephrin/NEPH1 0.003 0.085 -10000 0 -0.24 40 40
Nephrin/NEPH1/ZO-1 0.014 0.1 -10000 0 -0.28 40 40
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.042 0.04 0.21 1 -0.24 6 7
RGS9BP 0.01 0.091 0.29 3 -0.47 13 16
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.012 0.017 0.21 1 -10000 0 1
mol:Na + 0.022 0.1 -10000 0 -0.29 32 32
mol:ADP -0.011 0.017 0.29 1 -10000 0 1
GNAT2 0.021 0.029 0.24 4 -10000 0 4
RGS9-1/Gbeta5/R9AP -0.028 0.15 0.24 2 -0.29 90 92
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.03 0.015 -10000 0 -10000 0 0
GRK7 0.019 0.024 0.33 1 -10000 0 1
CNGB3 0.078 0.098 0.24 108 -10000 0 108
Cone Metarhodopsin II/X-Arrestin 0.013 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.1 0.2 43 -0.27 31 74
Cone PDE6 -0.013 0.14 -10000 0 -0.26 89 89
Cone Metarhodopsin II 0.026 0.014 0.2 1 -10000 0 1
Na + (4 Units) 0.035 0.11 0.24 26 -0.27 31 57
GNAT2/GDP -0.012 0.13 0.22 3 -0.25 90 93
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.031 0.18 10 -10000 0 10
Cone Transducin 0.045 0.043 0.22 1 -0.26 6 7
SLC24A2 0.023 0.051 0.22 22 -10000 0 22
GNB3/GNGT2 0.033 0.047 -10000 0 -0.34 6 6
GNB3 0.023 0.044 0.21 1 -0.47 3 4
GNAT2/GTP 0.02 0.012 0.15 3 -10000 0 3
CNGA3 -0.035 0.14 -10000 0 -0.47 39 39
ARR3 -0.009 0.018 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.023 0.11 -10000 0 -0.29 32 32
mol:Pi -0.028 0.14 0.23 2 -0.29 90 92
Cone CNG Channel 0.043 0.1 -10000 0 -0.25 32 32
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.023 0.051 0.22 22 -10000 0 22
RGS9 -0.077 0.2 -10000 0 -0.47 84 84
PDE6C -0.008 0.017 -10000 0 -10000 0 0
GNGT2 0.022 0.049 -10000 0 -0.47 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.008 0.023 0.21 2 -10000 0 2
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 -0.004 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.11 -10000 0 -0.29 10 10
NFATC4 -0.031 0.096 0.25 10 -0.32 7 17
ERBB2IP 0.026 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.026 0.11 0.29 3 -0.26 58 61
JUN -0.007 0.084 0.22 7 -0.32 1 8
HRAS 0.025 0.008 -10000 0 -10000 0 0
DOCK7 -0.032 0.11 0.29 5 -0.28 16 21
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.12 0.25 3 -0.26 54 57
AKT1 0.005 0.007 -10000 0 -10000 0 0
BAD -0.003 0.005 -10000 0 -10000 0 0
MAPK10 -0.026 0.086 0.19 14 -0.21 22 36
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.026 0.12 0.31 3 -0.27 58 61
RAF1 -0.012 0.096 0.27 3 -0.31 8 11
ErbB2/ErbB3/neuregulin 2 -0.091 0.14 0.22 2 -0.28 147 149
STAT3 0.024 0.063 -10000 0 -0.84 2 2
cell migration -0.021 0.082 0.22 12 -0.23 10 22
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.066 0.22 -10000 0 -0.61 25 25
FOS -0.12 0.26 0.3 1 -0.48 132 133
NRAS 0.027 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.11 0.29 3 -0.26 58 61
MAPK3 -0.031 0.17 0.33 2 -0.52 17 19
MAPK1 -0.034 0.18 0.33 2 -0.55 18 20
JAK2 -0.032 0.1 0.29 3 -0.27 16 19
NF2 0.002 0.064 -10000 0 -0.61 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.013 0.1 0.19 6 -0.25 54 60
NRG1 -0.038 0.18 0.22 18 -0.47 56 74
GRB2/SOS1 0.038 0.01 -10000 0 -10000 0 0
MAPK8 -0.037 0.12 0.26 4 -0.27 56 60
MAPK9 -0.015 0.07 0.2 12 -0.21 2 14
ERBB2 -0.009 0.052 0.27 13 -10000 0 13
ERBB3 0.015 0.08 0.32 2 -0.47 10 12
SHC1 0.026 0.017 0.33 1 -10000 0 1
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.01 0.017 -10000 0 -0.15 1 1
STAT3 (dimer) 0.024 0.062 -10000 0 -0.82 2 2
RNF41 -0.007 0.009 -10000 0 -10000 0 0
FRAP1 -0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.03 0.069 -10000 0 -0.21 15 15
ErbB2/ErbB2/HSP90 (dimer) 0.008 0.038 0.21 11 -10000 0 11
CHRNA1 -0.016 0.14 0.3 2 -0.4 17 19
myelination -0.025 0.1 0.26 13 -0.34 5 18
PPP3CB -0.029 0.099 0.28 5 -0.26 16 21
KRAS 0.027 0.016 0.33 1 -10000 0 1
RAC1-CDC42/GDP 0.008 0.11 0.24 2 -0.33 5 7
NRG2 -0.18 0.24 -10000 0 -0.47 164 164
mol:GDP -0.013 0.1 0.19 7 -0.25 54 61
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K2 -0.018 0.096 0.26 4 -0.32 8 12
SRC 0.026 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.032 0.1 0.28 4 -0.25 57 61
MAP2K1 -0.057 0.18 -10000 0 -0.62 12 12
heart morphogenesis -0.026 0.11 0.29 3 -0.26 58 61
RAS family/GDP 0.01 0.11 0.26 1 -0.37 4 5
GRB2 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.002 0.073 -10000 0 -0.64 5 5
CHRNE 0.005 0.024 0.11 3 -0.19 1 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.005 0.007 -10000 0 -10000 0 0
nervous system development -0.026 0.11 0.29 3 -0.26 58 61
CDC42 0.028 0.003 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.055 0.18 -10000 0 -0.47 65 65
GNB1/GNG2 0.006 0.13 0.32 1 -0.39 18 19
mol:DAG -0.011 0.12 0.2 3 -0.38 16 19
PLCG1 -0.011 0.12 0.2 3 -0.39 16 19
YES1 -0.014 0.11 0.27 2 -0.42 15 17
FZD3 0.021 0.036 -10000 0 -0.47 2 2
FZD6 0.023 0.011 -10000 0 -10000 0 0
G protein 0.014 0.14 0.31 8 -0.4 16 24
MAP3K7 -0.069 0.14 0.2 2 -0.33 50 52
mol:Ca2+ -0.01 0.11 0.2 3 -0.37 16 19
mol:IP3 -0.011 0.12 0.2 3 -0.38 16 19
NLK 0.007 0.046 -10000 0 -0.88 1 1
GNB1 0.027 0.003 -10000 0 -10000 0 0
CAMK2A -0.072 0.15 0.21 2 -0.35 54 56
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.011 0.12 0.35 1 -0.3 48 49
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
GNAS -0.018 0.11 0.22 2 -0.42 16 18
GO:0007205 -0.015 0.11 -10000 0 -0.37 16 16
WNT6 0.03 0.096 0.21 36 -0.47 10 46
WNT4 -0.002 0.12 0.21 3 -0.47 25 28
NFAT1/CK1 alpha -0.029 0.15 0.28 2 -0.38 27 29
GNG2 0.02 0.06 -10000 0 -0.47 6 6
WNT5A 0.022 0.071 0.21 10 -0.47 7 17
WNT11 0.017 0.12 0.22 33 -0.47 20 53
CDC42 -0.008 0.12 0.2 12 -0.4 15 27
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 0.038 0.019 0.24 2 -10000 0 2
CRKL -0.022 0.14 0.3 4 -0.5 14 18
mol:PIP3 -0.002 0.062 -10000 0 -0.87 2 2
AKT1 -0.004 0.057 -10000 0 -0.76 2 2
PTK2B 0.023 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.02 0.13 0.33 2 -0.5 12 14
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.013 0.14 0.24 2 -0.28 79 81
MAP3K5 -0.017 0.14 0.36 2 -0.48 15 17
HGF/MET/CIN85/CBL/ENDOPHILINS -0.001 0.14 0.24 1 -0.26 85 86
AP1 -0.077 0.17 0.18 1 -0.32 119 120
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.017 0.33 1 -10000 0 1
apoptosis -0.23 0.37 -10000 0 -0.75 133 133
STAT3 (dimer) -0.03 0.11 -10000 0 -0.31 22 22
GAB1/CRKL/SHP2/PI3K 0.007 0.13 0.39 1 -0.5 11 12
INPP5D 0.018 0.06 -10000 0 -0.47 6 6
CBL/CRK -0.012 0.13 0.27 2 -0.5 12 14
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.007 -10000 0 -10000 0 0
ELK1 0.003 0.087 0.34 17 -0.2 1 18
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.019 0.081 -10000 0 -0.24 21 21
PAK1 0.002 0.067 0.27 1 -0.73 2 3
HGF/MET/RANBP10 -0.016 0.14 0.24 2 -0.28 84 86
HRAS -0.037 0.14 -10000 0 -0.54 16 16
DOCK1 -0.022 0.13 0.33 4 -0.5 13 17
GAB1 -0.03 0.14 0.26 1 -0.52 15 16
CRK -0.025 0.14 0.28 2 -0.49 15 17
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.066 0.2 -10000 0 -0.45 75 75
JUN 0.01 0.091 -10000 0 -0.47 14 14
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.032 0.087 0.17 2 -0.19 86 88
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
cell morphogenesis -0.012 0.14 0.33 14 -0.37 14 28
GRB2/SHC -0.004 0.091 0.22 1 -0.24 13 14
FOS -0.12 0.23 -10000 0 -0.47 124 124
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.003 0.087 0.34 17 -0.2 1 18
HGF/MET/MUC20 -0.03 0.13 -10000 0 -0.28 86 86
cell migration -0.005 0.088 0.22 1 -0.24 13 14
GRB2 0.027 0.005 -10000 0 -10000 0 0
CBL 0.026 0.007 -10000 0 -10000 0 0
MET/RANBP10 0.039 0.018 0.24 2 -10000 0 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.024 0.11 -10000 0 -0.24 74 74
MET/MUC20 0.02 0.003 -10000 0 -10000 0 0
RAP1B -0.006 0.13 0.3 6 -0.51 10 16
RAP1A -0.019 0.12 0.39 1 -0.51 10 11
HGF/MET/RANBP9 -0.012 0.13 0.24 2 -0.28 75 77
RAF1 -0.016 0.15 0.31 1 -0.5 15 16
STAT3 -0.03 0.11 -10000 0 -0.31 22 22
cell proliferation -0.033 0.16 0.27 8 -0.34 67 75
RPS6KB1 -0.001 0.034 -10000 0 -10000 0 0
MAPK3 -0.004 0.092 0.66 5 -10000 0 5
MAPK1 -0.001 0.11 0.65 8 -10000 0 8
RANBP9 0.026 0.008 -10000 0 -10000 0 0
MAPK8 -0.006 0.13 0.32 4 -0.47 13 17
SRC -0.028 0.098 -10000 0 -0.23 71 71
PI3K -0.004 0.092 -10000 0 -0.24 15 15
MET/Glomulin 0.019 0.029 0.24 2 -10000 0 2
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.009 0.15 0.3 2 -0.48 14 16
MET 0.029 0.022 0.33 2 -10000 0 2
MAP4K1 -0.021 0.15 0.38 1 -0.5 16 17
PTK2 0.025 0.009 -10000 0 -10000 0 0
MAP2K2 -0.009 0.15 0.3 3 -0.48 14 17
BAD -0.003 0.06 0.38 1 -0.73 2 3
MAP2K4 -0.012 0.12 0.31 4 -0.45 13 17
SHP2/GRB2/SOS1/GAB1 -0.005 0.12 -10000 0 -0.5 10 10
INPPL1 0.026 0.006 -10000 0 -10000 0 0
PXN 0.027 0.004 -10000 0 -10000 0 0
SH3KBP1 0.027 0.005 -10000 0 -10000 0 0
HGS -0.031 0.079 0.15 2 -0.18 82 84
PLCgamma1/PKC 0.019 0.005 -10000 0 -10000 0 0
HGF -0.076 0.2 0.21 7 -0.47 86 93
RASA1 0.027 0.006 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
PTPRJ 0.026 0.007 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.004 0.096 -10000 0 -0.19 75 75
PDPK1 -0.004 0.058 -10000 0 -0.81 2 2
HGF/MET/SHIP -0.022 0.15 0.24 2 -0.29 88 90
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.002 0.14 -10000 0 -0.38 44 44
HDAC1 0.027 0.011 -10000 0 -10000 0 0
AES 0.027 0.007 -10000 0 -10000 0 0
FBXW11 0.026 0.007 -10000 0 -10000 0 0
DTX1 0.014 0.091 0.21 6 -0.47 13 19
LRP6/FZD1 0.039 0.022 -10000 0 -0.34 1 1
TLE1 0.024 0.026 -10000 0 -0.47 1 1
AP1 -0.075 0.16 -10000 0 -0.28 132 132
NCSTN 0.024 0.01 -10000 0 -10000 0 0
ADAM10 0.027 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.018 0.18 -10000 0 -0.65 26 26
NICD/RBPSUH 0.008 0.14 -10000 0 -0.37 44 44
WIF1 -0.085 0.19 0.21 9 -0.47 77 86
NOTCH1 -0.018 0.13 -10000 0 -0.39 41 41
PSENEN 0.026 0.006 -10000 0 -10000 0 0
KREMEN2 0.095 0.091 0.21 151 -10000 0 151
DKK1 -0.033 0.18 0.22 15 -0.47 55 70
beta catenin/beta TrCP1 0.041 0.065 0.27 3 -10000 0 3
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.009 -10000 0 -10000 0 0
AXIN1 -0.011 0.088 -10000 0 -0.35 13 13
CtBP/CBP/TCF1/TLE1/AES 0.018 0.052 0.29 2 -0.33 2 4
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.12 0.23 -10000 0 -0.47 124 124
JUN 0.01 0.091 -10000 0 -0.47 14 14
MAP3K7 0.026 0.007 -10000 0 -10000 0 0
CTNNB1 0.031 0.071 0.27 9 -0.25 1 10
MAPK3 0.027 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.11 0.092 0.29 38 -0.2 3 41
HNF1A 0.029 0.021 0.21 5 -10000 0 5
CTBP1 0.027 0.017 0.33 1 -10000 0 1
MYC -0.041 0.29 -10000 0 -1.3 19 19
NKD1 0.002 0.12 0.21 5 -0.47 22 27
FZD1 0.027 0.027 0.21 1 -0.47 1 2
NOTCH1 precursor/Deltex homolog 1 0.003 0.15 -10000 0 -0.4 42 42
apoptosis -0.074 0.16 -10000 0 -0.28 132 132
Delta 1/NOTCHprecursor 0.005 0.14 -10000 0 -0.38 44 44
DLL1 0.024 0.045 0.21 2 -0.47 3 5
PPARD 0.021 0.047 -10000 0 -0.75 1 1
Gamma Secretase 0.062 0.036 -10000 0 -10000 0 0
APC -0.014 0.1 -10000 0 -0.5 11 11
DVL1 0.009 0.034 -10000 0 -0.26 3 3
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.04 0.15 0.28 7 -0.3 55 62
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.013 0.01 -10000 0 -10000 0 0
CCND1 -0.008 0.2 -10000 0 -1.3 10 10
WNT1 0.018 0.026 0.21 3 -10000 0 3
Axin1/APC/beta catenin 0.024 0.11 0.29 5 -0.43 6 11
DKK2 0.064 0.082 0.21 88 -0.47 1 89
NOTCH1 precursor/DVL1 -0.011 0.13 -10000 0 -0.5 9 9
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.004 0.15 -10000 0 -0.4 42 42
PPP2R5D 0.028 0.065 0.26 20 -0.31 3 23
MAPK1 0.027 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.003 0.13 -10000 0 -0.26 73 73
RBPJ 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.01 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.016 0.045 -10000 0 -0.22 13 13
epithelial cell differentiation 0.042 0.056 -10000 0 -0.24 13 13
CYFIP2 0.014 0.077 -10000 0 -0.47 10 10
ENAH 0.018 0.09 0.3 19 -0.29 1 20
EGFR 0.021 0.085 0.33 8 -0.47 9 17
EPHA2 0.021 0.055 -10000 0 -0.47 5 5
MYO6 0.017 0.063 0.19 25 -0.23 13 38
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.042 0.055 -10000 0 -0.28 10 10
AQP5 0.02 0.058 0.37 2 -10000 0 2
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.063 0.19 26 -0.23 12 38
regulation of calcium-dependent cell-cell adhesion 0.019 0.073 0.2 24 -0.23 17 41
EGF 0.034 0.047 0.21 24 -10000 0 24
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.077 0.19 -10000 0 -0.47 68 68
cortical microtubule organization 0.042 0.056 -10000 0 -0.24 13 13
GO:0000145 0 0.061 0.18 26 -0.22 12 38
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.047 0.058 -10000 0 -0.24 13 13
MLLT4 0.026 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.017 0.042 -10000 0 -0.23 13 13
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.047 0.24 5 -0.26 4 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.009 0.055 0.19 16 -0.21 12 28
PVRL2 0.027 0.005 -10000 0 -10000 0 0
ZYX 0.018 0.065 0.19 26 -0.23 13 39
ARF6/GTP 0.064 0.048 -10000 0 -0.24 4 4
CDH1 0.01 0.087 -10000 0 -0.47 13 13
EGFR/EGFR/EGF/EGF 0.031 0.071 -10000 0 -0.24 21 21
RhoA/GDP 0.042 0.055 -10000 0 -0.23 13 13
actin cytoskeleton organization 0.009 0.058 0.18 22 -0.23 12 34
IGF-1R heterotetramer 0.025 0.035 -10000 0 -0.47 2 2
GIT1 0.026 0.006 -10000 0 -10000 0 0
IGF1R 0.025 0.035 -10000 0 -0.47 2 2
IGF1 -0.19 0.24 -10000 0 -0.47 176 176
DIAPH1 0.004 0.15 -10000 0 -0.56 19 19
Wnt receptor signaling pathway -0.042 0.056 0.24 13 -10000 0 13
RHOA 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.042 -10000 0 -0.22 14 14
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
VCL 0.009 0.059 0.18 22 -0.23 12 34
EFNA1 0.031 0.039 0.3 8 -10000 0 8
LPP -0.005 0.058 0.18 18 -0.22 14 32
Ephrin A1/EPHA2 0.032 0.06 -10000 0 -0.24 15 15
SEC6/SEC8 0.005 0.037 -10000 0 -0.22 9 9
MGAT3 0.019 0.074 0.21 24 -0.24 17 41
HGF/MET -0.018 0.12 -10000 0 -0.23 93 93
HGF -0.076 0.2 0.21 7 -0.47 86 93
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.016 0.046 -10000 0 -0.22 13 13
actin cable formation 0.041 0.097 0.28 32 -0.25 1 33
KIAA1543 -0.002 0.063 0.18 25 -0.24 13 38
KIFC3 0.016 0.063 0.2 23 -0.23 13 36
NCK1 0.026 0.006 -10000 0 -10000 0 0
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ACTN1 0.016 0.062 0.19 24 -0.23 13 37
NCK1/GIT1 0.037 0.012 -10000 0 -10000 0 0
mol:GDP 0.042 0.056 -10000 0 -0.24 13 13
EXOC4 0.027 0.005 -10000 0 -10000 0 0
STX4 0.017 0.062 0.2 23 -0.23 12 35
PIP5K1C 0.018 0.064 0.3 3 -0.23 12 15
LIMA1 0.027 0.004 -10000 0 -10000 0 0
ABI1 0.026 0.007 -10000 0 -10000 0 0
ROCK1 0.022 0.099 0.34 18 -0.34 1 19
adherens junction assembly 0.005 0.077 0.29 4 -0.44 1 5
IGF-1R heterotetramer/IGF1 -0.079 0.14 -10000 0 -0.23 177 177
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET 0.029 0.022 0.33 2 -10000 0 2
PLEKHA7 0.016 0.066 0.19 25 -0.25 13 38
mol:GTP 0.057 0.046 0.24 5 -0.26 4 9
establishment of epithelial cell apical/basal polarity 0.03 0.1 0.35 18 -10000 0 18
cortical actin cytoskeleton stabilization 0.016 0.045 -10000 0 -0.22 13 13
regulation of cell-cell adhesion 0.009 0.058 0.18 22 -0.23 12 34
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.016 0.046 -10000 0 -0.22 13 13
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.22 0.25 -10000 0 -0.47 198 198
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.011 0.21 1 -10000 0 1
TCEB1 0.024 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.02 0.057 -10000 0 -0.26 13 13
HIF1A 0.009 0.048 -10000 0 -0.26 10 10
COPS5 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.059 0.038 -10000 0 -10000 0 0
FIH (dimer) 0.027 0.005 -10000 0 -10000 0 0
CDKN2A 0.11 0.1 0.22 190 -10000 0 190
ARNT/IPAS -0.13 0.18 -10000 0 -0.34 177 177
HIF1AN 0.027 0.005 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.018 0.05 -10000 0 -0.27 8 8
CUL2 0.026 0.006 -10000 0 -10000 0 0
OS9 0.027 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.045 0.024 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.021 0.057 -10000 0 -0.26 13 13
PHD1-3/OS9 0.056 0.051 -10000 0 -0.26 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.036 0.061 -10000 0 -0.25 12 12
VHL 0.025 0.009 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.019 0.057 -10000 0 -0.27 12 12
EGLN3 0.017 0.069 -10000 0 -0.47 8 8
EGLN2 0.027 0.005 -10000 0 -10000 0 0
EGLN1 0.027 0.004 -10000 0 -10000 0 0
TP53 0.025 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.034 0.065 -10000 0 -0.48 6 6
ARNT 0.024 0.01 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p19ARF 0.062 0.096 0.21 26 -0.27 12 38
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0 0.11 0.47 21 -10000 0 21
PI3K Class IB/PDE3B 0 0.11 -10000 0 -0.47 21 21
PDE3B 0 0.11 -10000 0 -0.47 21 21
Aurora A signaling

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
Aurora A/GADD45A 0.014 0.045 -10000 0 -10000 0 0
BIRC5 0.16 0.093 0.22 288 -0.47 1 289
NFKBIA -0.002 0.039 0.23 3 -10000 0 3
CPEB1 -0.21 0.24 -10000 0 -0.47 189 189
AKT1 -0.002 0.039 0.22 3 -10000 0 3
NDEL1 0.025 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.012 0.04 -10000 0 -10000 0 0
NDEL1/TACC3 0.045 0.047 0.23 6 -10000 0 6
GADD45A 0.028 0.002 -10000 0 -10000 0 0
GSK3B -0.008 0.024 -10000 0 -10000 0 0
PAK1/Aurora A 0.012 0.045 -10000 0 -0.29 1 1
MDM2 0.036 0.054 0.33 13 -10000 0 13
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.06 0.087 0.3 43 -10000 0 43
TP53 0.015 0.056 0.21 12 -0.2 12 24
DLG7 -0.001 0.034 0.15 13 -10000 0 13
AURKAIP1 0.028 0.01 0.21 1 -10000 0 1
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.048 0.051 0.25 7 -10000 0 7
G2/M transition of mitotic cell cycle 0.012 0.039 -10000 0 -10000 0 0
AURKA 0.009 0.046 0.19 13 -0.16 2 15
AURKB 0.062 0.057 0.15 19 -0.26 3 22
CDC25B 0.011 0.029 -10000 0 -10000 0 0
G2/M transition checkpoint -0.001 0.025 -10000 0 -0.14 1 1
mRNA polyadenylation -0.12 0.13 -10000 0 -0.26 180 180
Aurora A/CPEB -0.12 0.13 -10000 0 -0.26 180 180
Aurora A/TACC1/TRAP/chTOG 0.042 0.046 -10000 0 -0.25 2 2
BRCA1 0.028 0.01 0.21 1 -10000 0 1
centrosome duplication 0.012 0.045 -10000 0 -0.29 1 1
regulation of centrosome cycle 0.044 0.046 0.22 6 -10000 0 6
spindle assembly 0.041 0.045 -10000 0 -0.25 2 2
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.076 0.26 14 -0.23 1 15
CENPA 0.081 0.061 0.18 27 -0.28 3 30
Aurora A/PP2A 0.014 0.044 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.016 0.042 0.21 5 -10000 0 5
negative regulation of DNA binding 0.014 0.058 0.21 12 -0.2 14 26
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.027 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A -0.001 0.026 -10000 0 -0.14 1 1
mitotic prometaphase -0.009 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.046 0.19 13 -0.16 2 15
TACC1 0.021 0.036 -10000 0 -0.47 2 2
TACC3 0.043 0.059 0.24 30 -10000 0 30
Aurora A/Antizyme1 0.044 0.037 -10000 0 -10000 0 0
Aurora A/RasGAP 0.014 0.042 -10000 0 -10000 0 0
OAZ1 0.027 0.005 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.008 0.024 -10000 0 -10000 0 0
GIT1 0.026 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.026 -10000 0 -0.28 1 1
Importin alpha/Importin beta/TPX2 0.06 0.087 0.3 43 -10000 0 43
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.032 0.093 0.26 42 -10000 0 42
PAK1 0.025 0.025 -10000 0 -0.47 1 1
CKAP5 0.026 0.007 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0.006 -10000 0 -10000 0 0
SMARCC1 0.01 0.039 -10000 0 -0.73 1 1
REL 0.024 0.047 0.28 2 -0.47 3 5
HDAC7 -0.054 0.13 -10000 0 -0.31 57 57
JUN 0.01 0.091 -10000 0 -0.47 14 14
EP300 0.027 0.006 -10000 0 -10000 0 0
KAT2B 0.025 0.025 -10000 0 -0.47 1 1
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 0.002 0.041 -10000 0 -0.34 4 4
FOXO1 0.024 0.026 -10000 0 -0.47 1 1
T-DHT/AR -0.044 0.14 -10000 0 -0.32 59 59
MAP2K6 0.011 0.059 0.21 1 -0.47 5 6
BRM/BAF57 0.032 0.021 -10000 0 -10000 0 0
MAP2K4 0.015 0.022 -10000 0 -10000 0 0
SMARCA2 0.022 0.013 -10000 0 -10000 0 0
PDE9A -0.13 0.37 -10000 0 -1 55 55
NCOA2 0 0.11 -10000 0 -0.47 20 20
CEBPA 0.03 0.049 0.24 10 -0.47 2 12
EHMT2 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.015 0.17 0.35 23 -0.39 25 48
NR0B1 0.016 0.061 0.21 32 -10000 0 32
EGR1 -0.087 0.21 -10000 0 -0.47 92 92
RXRs/9cRA -0.032 0.13 0.22 1 -0.26 93 94
AR/RACK1/Src -0.014 0.1 0.3 4 -0.29 8 12
AR/GR -0.079 0.14 0.22 1 -0.26 140 141
GNB2L1 0.027 0.006 -10000 0 -10000 0 0
PKN1 0.026 0.025 -10000 0 -0.47 1 1
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0.002 0.037 -10000 0 -0.34 3 3
T-DHT/AR/TIF2/CARM1 -0.025 0.12 0.27 2 -0.31 26 28
SRC -0.006 0.069 0.2 28 -0.24 7 35
NR3C1 0.013 0.081 -10000 0 -0.47 11 11
KLK3 -0.093 0.25 0.33 1 -0.92 24 25
APPBP2 0.016 0.023 -10000 0 -10000 0 0
TRIM24 0.027 0.019 0.2 3 -10000 0 3
T-DHT/AR/TIP60 -0.03 0.092 0.26 2 -0.3 10 12
TMPRSS2 -0.18 0.43 -10000 0 -1 76 76
RXRG -0.11 0.2 0.33 1 -0.47 95 96
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.025 0.009 -10000 0 -10000 0 0
RXRB 0.027 0.003 -10000 0 -10000 0 0
CARM1 0.027 0.004 -10000 0 -10000 0 0
NR2C2 0.025 0.03 0.33 1 -0.47 1 2
KLK2 -0.012 0.1 0.35 3 -0.34 10 13
AR -0.086 0.14 -10000 0 -0.28 134 134
SENP1 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.036 0.054 0.33 13 -10000 0 13
SRY 0.001 0.006 0.028 16 -10000 0 16
GATA2 0.025 0.07 0.22 13 -0.47 6 19
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.038 0.17 0.23 9 -0.47 54 63
T-DHT/AR/RACK1/Src -0.016 0.1 0.35 4 -0.3 8 12
positive regulation of transcription 0.025 0.07 0.22 13 -0.47 6 19
DNAJA1 0.016 0.022 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.037 0.22 13 -10000 0 13
NCOA1 0.031 0.017 -10000 0 -10000 0 0
SPDEF -0.015 0.17 0.21 33 -0.47 46 79
T-DHT/AR/TIF2 -0.024 0.1 0.25 2 -0.32 19 21
T-DHT/AR/Hsp90 -0.029 0.093 0.26 2 -0.29 10 12
GSK3B 0.025 0.009 -10000 0 -10000 0 0
NR2C1 0.027 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.014 0.057 0.22 7 -0.25 8 15
SIRT1 0.027 0.005 -10000 0 -10000 0 0
ZMIZ2 0.028 0.008 -10000 0 -10000 0 0
POU2F1 0.005 0.064 -10000 0 -0.17 22 22
T-DHT/AR/DAX-1 -0.029 0.1 0.32 5 -0.28 12 17
CREBBP 0.026 0.007 -10000 0 -10000 0 0
SMARCE1 0.025 0.011 -10000 0 -10000 0 0
Canonical Wnt signaling 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
HDAC1 0.031 0.028 0.19 3 -10000 0 3
AES 0.03 0.023 0.2 1 -10000 0 1
FBXW11 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.022 -10000 0 -0.33 1 1
SMAD4 0.026 0.007 -10000 0 -10000 0 0
DKK2 0.065 0.082 0.21 88 -0.47 1 89
TLE1 0.027 0.033 0.17 1 -0.47 1 2
MACF1 0.027 0.006 -10000 0 -10000 0 0
CTNNB1 0.053 0.092 0.28 10 -0.4 3 13
WIF1 -0.082 0.19 0.21 9 -0.47 77 86
beta catenin/RanBP3 0.041 0.14 0.4 43 -0.35 3 46
KREMEN2 0.095 0.091 0.21 151 -10000 0 151
DKK1 -0.033 0.18 0.22 15 -0.47 55 70
beta catenin/beta TrCP1 0.065 0.086 0.28 9 -0.36 3 12
FZD1 0.027 0.027 0.21 1 -0.47 1 2
AXIN2 -0.061 0.36 0.58 17 -1.3 26 43
AXIN1 0.027 0.006 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.024 0.11 -10000 0 -0.5 13 13
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.018 0.16 -10000 0 -0.56 19 19
Axin1/APC/GSK3 0.041 0.058 0.25 6 -0.26 1 7
Axin1/APC/GSK3/beta catenin/Macf1 0.032 0.067 0.37 1 -0.4 2 3
HNF1A 0.033 0.032 0.2 8 -10000 0 8
CTBP1 0.031 0.029 0.27 2 -10000 0 2
MYC 0.017 0.37 0.57 56 -1.4 18 74
RANBP3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.11 0.092 0.29 38 -0.2 3 41
NKD1 0.002 0.12 0.21 5 -0.47 22 27
TCF4 0.022 0.062 0.18 1 -0.45 6 7
TCF3 0.03 0.025 0.2 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.064 0.028 -10000 0 -0.26 1 1
Ran/GTP 0.02 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.16 0.44 36 -0.44 7 43
LEF1 0.034 0.033 0.2 8 -10000 0 8
DVL1 0.037 0.052 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.017 0.15 -10000 0 -0.51 16 16
DKK1/LRP6/Kremen 2 0.041 0.15 0.28 7 -0.3 55 62
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.031 0.027 0.2 2 -10000 0 2
NLK 0.023 0.013 -10000 0 -10000 0 0
CCND1 0.033 0.28 0.6 44 -1.5 7 51
WNT1 0.021 0.024 0.21 3 -10000 0 3
GSK3A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
PPP2R5D 0.045 0.07 0.28 21 -0.24 2 23
APC 0.018 0.046 0.46 2 -0.24 1 3
WNT1/LRP6/FZD1 0.057 0.081 0.22 73 -10000 0 73
CREBBP 0.029 0.023 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.004 0.13 -10000 0 -0.54 16 16
Syndecan-4/Syndesmos 0.036 0.14 0.36 3 -0.7 7 10
positive regulation of JNK cascade -0.019 0.18 0.35 3 -0.52 20 23
Syndecan-4/ADAM12 0.044 0.15 0.38 4 -0.7 7 11
CCL5 0.011 0.11 0.21 13 -0.47 18 31
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
DNM2 0.027 0.004 -10000 0 -10000 0 0
ITGA5 0.009 0.094 -10000 0 -0.47 15 15
SDCBP 0.025 0.008 -10000 0 -10000 0 0
PLG 0.001 0.034 0.2 5 -10000 0 5
ADAM12 0.045 0.056 0.21 40 -10000 0 40
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.035 0.027 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.042 0.17 0.36 2 -0.66 10 12
Syndecan-4/CXCL12/CXCR4 -0.02 0.19 0.36 3 -0.57 20 23
Syndecan-4/Laminin alpha3 0.025 0.16 0.4 2 -0.69 8 10
MDK 0.037 0.047 0.22 23 -10000 0 23
Syndecan-4/FZD7 0.028 0.15 0.36 3 -0.68 8 11
Syndecan-4/Midkine 0.043 0.15 0.37 4 -0.7 7 11
FZD7 0.006 0.099 -10000 0 -0.47 17 17
Syndecan-4/FGFR1/FGF -0.066 0.21 -10000 0 -0.51 42 42
THBS1 0.012 0.084 -10000 0 -0.47 12 12
integrin-mediated signaling pathway 0.024 0.16 0.36 3 -0.66 10 13
positive regulation of MAPKKK cascade -0.019 0.18 0.35 3 -0.52 20 23
Syndecan-4/TACI 0.017 0.15 0.36 2 -0.62 11 13
CXCR4 0.017 0.069 -10000 0 -0.47 8 8
cell adhesion 0.011 0.082 0.2 14 -0.33 14 28
Syndecan-4/Dynamin 0.035 0.14 0.36 3 -0.75 6 9
Syndecan-4/TSP1 0.031 0.15 0.36 3 -0.72 8 11
Syndecan-4/GIPC 0.036 0.14 0.36 3 -0.7 7 10
Syndecan-4/RANTES 0.028 0.16 0.38 3 -0.66 11 14
ITGB1 0.026 0.006 -10000 0 -10000 0 0
LAMA1 0.04 0.12 0.22 66 -0.47 14 80
LAMA3 0.003 0.15 0.22 35 -0.47 32 67
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.019 0.16 0.76 17 -0.43 4 21
Syndecan-4/alpha-Actinin 0.036 0.14 0.36 3 -0.7 7 10
TFPI 0.017 0.069 -10000 0 -0.47 8 8
F2 0.039 0.052 0.22 28 -10000 0 28
alpha5/beta1 Integrin 0.024 0.072 -10000 0 -0.34 15 15
positive regulation of cell adhesion 0.01 0.16 0.34 2 -0.63 11 13
ACTN1 0.027 0.005 -10000 0 -10000 0 0
TNC -0.001 0.12 0.21 9 -0.47 25 34
Syndecan-4/CXCL12 -0.025 0.19 0.36 3 -0.59 19 22
FGF6 -0.016 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
CXCL12 -0.11 0.22 -10000 0 -0.47 108 108
TNFRSF13B -0.013 0.13 0.21 7 -0.47 28 35
FGF2 -0.13 0.23 -10000 0 -0.47 127 127
FGFR1 -0.066 0.19 -10000 0 -0.47 73 73
Syndecan-4/PI-4-5-P2 0.009 0.13 0.36 1 -0.7 7 8
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.092 0.2 26 -0.45 11 37
cell migration -0.02 0.016 -10000 0 -10000 0 0
PRKCD 0.021 0.02 -10000 0 -10000 0 0
vasculogenesis 0.031 0.14 0.36 3 -0.68 8 11
SDC4 0.019 0.14 0.39 1 -0.76 7 8
Syndecan-4/Tenascin C 0.024 0.16 0.36 3 -0.7 10 13
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.022 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.031 0.14 0.36 3 -0.75 6 9
MMP9 0.067 0.1 0.22 100 -0.46 5 105
Rac1/GTP 0.011 0.084 0.2 14 -0.34 14 28
cytoskeleton organization 0.036 0.14 0.36 3 -0.66 7 10
GIPC1 0.027 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.032 0.15 0.36 3 -0.69 8 11
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.014 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.021 0.008 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.036 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.013 0.029 0.21 4 -10000 0 4
GRK1 -0.012 0.017 0.21 1 -10000 0 1
CNG Channel 0.045 0.11 0.25 2 -0.24 40 42
mol:Na + 0.058 0.099 0.28 3 -0.25 24 27
mol:ADP -0.012 0.017 0.21 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.028 0.15 0.24 2 -0.29 90 92
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.077 0.11 0.3 5 -0.25 24 29
CNGB1 0.1 0.094 0.21 173 -10000 0 173
RDH5 0.026 0.025 -10000 0 -0.47 1 1
SAG -0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.033 0.082 0.3 8 -0.26 10 18
Na + (4 Units) 0.041 0.085 0.29 1 -0.24 24 25
RGS9 -0.077 0.2 -10000 0 -0.47 84 84
GNB1/GNGT1 0.046 0.031 0.24 3 -10000 0 3
GNAT1/GDP -0.014 0.13 0.22 2 -0.25 88 90
GUCY2D 0.035 0.06 0.21 39 -10000 0 39
GNGT1 0.032 0.049 0.23 20 -10000 0 20
GUCY2F -0.012 0.015 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.017 0.055 0.19 3 -0.25 15 18
mol:11-cis-retinal 0.026 0.025 -10000 0 -0.47 1 1
mol:cGMP 0.047 0.044 0.4 1 -0.24 1 2
GNB1 0.027 0.003 -10000 0 -10000 0 0
Rhodopsin 0.032 0.021 -10000 0 -0.34 1 1
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.008 0.13 0.21 25 -0.47 25 50
Metarhodopsin II 0.022 0.009 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.066 0.055 0.28 2 -0.25 1 3
RGS9BP 0.01 0.091 0.29 3 -0.47 13 16
Metarhodopsin II/Transducin 0.017 0.02 0.16 3 -0.17 1 4
GCAP Family/Ca ++ 0.047 0.032 -10000 0 -0.27 1 1
PDE6A/B 0.025 0.074 -10000 0 -0.34 15 15
mol:Pi -0.028 0.14 0.23 2 -0.29 90 92
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.052 0.031 0.22 3 -10000 0 3
PDE6B 0.008 0.094 0.21 1 -0.47 15 16
PDE6A 0.026 0.025 0.21 5 -10000 0 5
PDE6G 0.034 0.04 0.23 15 -10000 0 15
RHO -0.007 0.018 -10000 0 -10000 0 0
PDE6 -0.01 0.15 0.27 1 -0.26 96 97
GUCA1A 0.027 0.049 0.22 21 -10000 0 21
GC2/GCAP Family 0.057 0.034 -10000 0 -0.27 1 1
GUCA1C -0.013 0.016 0.21 1 -10000 0 1
GUCA1B 0.027 0.033 0.33 2 -0.47 1 3
ceramide signaling pathway

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.004 0.11 0.23 4 -0.43 12 16
BAG4 0.023 0.01 -10000 0 -10000 0 0
BAD 0.013 0.05 0.18 5 -0.16 4 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 0.005 0.11 0.33 3 -0.47 19 22
BAX 0.013 0.051 0.17 7 -0.16 5 12
EnzymeConsortium:3.1.4.12 0.008 0.032 0.08 11 -0.089 12 23
IKBKB 0.02 0.12 0.3 11 -0.41 11 22
MAP2K2 0.034 0.084 0.22 51 -10000 0 51
MAP2K1 0.033 0.084 0.22 50 -10000 0 50
SMPD1 0.006 0.043 0.11 2 -0.14 17 19
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.29 10 -0.41 11 21
MAP2K4 0.016 0.049 0.19 9 -0.16 2 11
protein ubiquitination 0.015 0.12 0.31 4 -0.41 12 16
EnzymeConsortium:2.7.1.37 0.036 0.086 0.22 52 -10000 0 52
response to UV 0 0.001 0.002 55 -10000 0 55
RAF1 0.034 0.087 0.22 52 -0.18 2 54
CRADD 0.028 0.004 -10000 0 -10000 0 0
mol:ceramide 0.013 0.05 0.13 10 -0.13 20 30
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.009 -10000 0 -10000 0 0
MADD 0.026 0.007 -10000 0 -10000 0 0
MAP3K1 0.014 0.049 0.15 9 -0.16 4 13
TRADD 0.027 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.037 0.083 0.22 52 -10000 0 52
MAPK1 0.036 0.083 0.22 51 -10000 0 51
p50/RELA/I-kappa-B-alpha 0.039 0.01 -10000 0 -10000 0 0
FADD 0.015 0.12 0.27 8 -0.42 11 19
KSR1 0.019 0.063 0.21 19 -0.16 4 23
MAPK8 0.016 0.058 0.22 12 -0.2 3 15
TRAF2 0.025 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.002 16 -10000 0 16
CHUK 0.009 0.11 0.31 3 -0.41 12 15
TNF R/SODD 0.034 0.016 -10000 0 -10000 0 0
TNF 0.037 0.042 0.21 21 -10000 0 21
CYCS 0.02 0.056 0.17 18 -0.16 2 20
IKBKG 0.013 0.12 0.3 4 -0.41 12 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.003 0.12 -10000 0 -0.42 15 15
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.026 0.007 -10000 0 -10000 0 0
AIFM1 0.018 0.054 0.17 15 -0.15 4 19
TNF/TNF R/SODD 0.05 0.036 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.002 16 -10000 0 16
CASP8 0.002 0.14 -10000 0 -0.56 20 20
NSMAF 0.013 0.12 0.27 8 -0.42 12 20
response to hydrogen peroxide 0 0.001 0.002 55 -10000 0 55
BCL2 0.008 0.094 -10000 0 -0.47 15 15
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.009 0.014 0.29 1 -10000 0 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.021 0.066 -10000 0 -0.33 13 13
STXBP1 0.013 0.077 -10000 0 -0.47 10 10
ACh/CHRNA1 0.038 0.068 0.17 68 -0.14 5 73
RAB3GAP2/RIMS1/UNC13B 0.035 0.061 -10000 0 -0.28 13 13
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 -0.005 0.088 0.21 1 -0.47 13 14
mol:ACh -0.004 0.041 0.077 24 -0.13 27 51
RAB3GAP2 0.027 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.013 0.085 -10000 0 -0.25 23 23
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.038 0.068 0.17 68 -0.14 5 73
UNC13B 0.025 0.009 -10000 0 -10000 0 0
CHRNA1 0.056 0.072 0.21 69 -10000 0 69
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.008 0.1 0.18 8 -0.3 37 45
SNAP25 -0.01 0.069 0.2 2 -0.27 25 27
VAMP2 0.005 0.002 -10000 0 -10000 0 0
SYT1 -0.01 0.14 0.21 8 -0.47 33 41
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.017 0.047 0.22 1 -0.28 9 10
STX1A/SNAP25 fragment 1/VAMP2 0.013 0.085 -10000 0 -0.25 23 23
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.028 0.01 0.21 1 -10000 0 1
SPHK1 0.051 0.069 0.21 56 -0.47 1 57
GNAI2 0.026 0.006 -10000 0 -10000 0 0
mol:S1P 0.021 0.023 0.18 3 -0.26 1 4
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
mol:Sphinganine-1-P 0.019 0.022 -10000 0 -0.34 1 1
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.059 0.038 -10000 0 -10000 0 0
GNAI3 0.028 0.003 -10000 0 -10000 0 0
G12/G13 0.037 0.012 -10000 0 -10000 0 0
S1PR3 0.021 0.052 0.33 1 -0.47 4 5
S1PR2 0.027 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.012 0.024 0.14 1 -0.21 2 3
S1PR5 0.031 0.051 0.23 13 -0.47 2 15
S1PR4 0.025 0.046 0.21 3 -0.47 3 6
GNAI1 0.024 0.043 -10000 0 -0.47 3 3
S1P/S1P5/G12 0.052 0.047 0.26 2 -0.23 3 5
S1P/S1P3/Gq -0.029 0.14 -10000 0 -0.3 73 73
S1P/S1P4/Gi -0.087 0.18 -10000 0 -0.41 68 68
GNAQ 0.025 0.009 -10000 0 -10000 0 0
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
GNA14 -0.031 0.16 -10000 0 -0.47 45 45
GNA15 0.023 0.043 -10000 0 -0.47 3 3
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.006 -10000 0 -10000 0 0
GNA11 0.026 0.025 -10000 0 -0.47 1 1
ABCC1 0.027 0.019 0.27 2 -10000 0 2
Cellular roles of Anthrax toxin

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
ANTXR1 0.022 0.049 -10000 0 -0.47 4 4
ANTXR2 -0.003 0.12 -10000 0 -0.47 25 25
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.016 -10000 0 -0.065 26 26
monocyte activation 0.006 0.086 -10000 0 -0.38 18 18
MAP2K2 -0.001 0.096 -10000 0 -0.57 11 11
MAP2K1 -0.005 0.015 -10000 0 -0.094 1 1
MAP2K7 -0.005 0.016 0.13 1 -0.094 1 2
MAP2K6 -0.008 0.032 0.13 1 -0.22 6 7
CYAA -0.019 0.061 -10000 0 -0.25 26 26
MAP2K4 -0.004 0.013 -10000 0 -0.094 1 1
IL1B -0.015 0.062 0.17 5 -0.21 29 34
Channel 0.014 0.075 -10000 0 -0.26 26 26
NLRP1 -0.008 0.035 0.13 1 -0.23 8 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.001 0.055 -10000 0 -0.38 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.016 0.065 26 -10000 0 26
MAPK3 -0.005 0.016 0.13 1 -0.094 1 2
MAPK1 -0.004 0.019 0.13 4 -0.094 1 5
PGR -0.077 0.11 -10000 0 -0.24 124 124
PA/Cellular Receptors 0.014 0.082 -10000 0 -0.29 26 26
apoptosis -0.004 0.016 -10000 0 -0.065 26 26
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.014 0.071 -10000 0 -0.25 26 26
macrophage activation 0.004 0.043 0.17 23 -10000 0 23
TNF 0.036 0.042 0.21 21 -10000 0 21
VCAM1 0.006 0.087 -10000 0 -0.38 18 18
platelet activation 0.001 0.055 -10000 0 -0.38 7 7
MAPKKK cascade -0.001 0.028 0.11 2 -0.1 7 9
IL18 -0.008 0.047 0.11 2 -0.22 14 16
negative regulation of macrophage activation -0.004 0.016 -10000 0 -0.065 26 26
LEF -0.004 0.016 -10000 0 -0.065 26 26
CASP1 -0.005 0.033 0.062 1 -0.1 29 30
mol:cAMP 0.001 0.055 -10000 0 -0.39 7 7
necrosis -0.004 0.016 -10000 0 -0.065 26 26
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.014 0.071 -10000 0 -0.25 26 26
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.015 0.015 0.3 1 -10000 0 1
MAP4K4 0.013 0.075 0.21 5 -0.3 6 11
BAG4 0.023 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide 0.005 0.053 -10000 0 -0.19 26 26
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 0.005 0.11 0.33 3 -0.47 19 22
BAX 0.005 0.041 -10000 0 -0.4 3 3
RIPK1 0.026 0.007 -10000 0 -10000 0 0
AKT1 0.001 0.058 0.66 3 -10000 0 3
BAD -0.009 0.046 0.18 3 -0.18 22 25
SMPD1 0.012 0.067 0.16 13 -0.2 21 34
RB1 -0.01 0.043 0.2 1 -0.18 22 23
FADD/Caspase 8 0.024 0.093 0.24 19 -0.31 7 26
MAP2K4 -0.008 0.046 0.18 5 -0.18 20 25
NSMAF 0.025 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.018 0.078 0.21 47 -0.18 10 57
EGF 0.034 0.047 0.21 24 -10000 0 24
mol:ceramide -0.01 0.046 -10000 0 -0.2 23 23
MADD 0.026 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0.015 0.3 1 -10000 0 1
ASAH1 0.023 0.01 -10000 0 -10000 0 0
negative regulation of cell cycle -0.01 0.043 0.2 1 -0.18 22 23
cell proliferation -0.053 0.12 0.33 3 -0.2 141 144
BID 0.007 0.12 -10000 0 -0.55 12 12
MAP3K1 -0.01 0.046 0.19 2 -0.18 23 25
EIF2A 0.001 0.065 0.2 23 -0.19 2 25
TRADD 0.027 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.02 0.074 0.2 46 -0.19 1 47
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.073 0.2 42 -0.19 1 43
Cathepsin D/ceramide 0.008 0.047 -10000 0 -0.18 23 23
FADD 0.021 0.079 0.23 17 -0.29 5 22
KSR1 -0.003 0.055 0.19 14 -0.18 20 34
MAPK8 -0.003 0.056 -10000 0 -0.21 8 8
PRKRA -0.01 0.043 0.18 1 -0.18 22 23
PDGFA 0.027 0.016 0.33 1 -10000 0 1
TRAF2 0.025 0.009 -10000 0 -10000 0 0
IGF1 -0.19 0.24 -10000 0 -0.47 176 176
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.01 0.046 -10000 0 -0.19 23 23
CTSD 0.026 0.008 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.056 0.13 0.35 3 -0.21 141 144
PRKCD 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.024 0.043 -10000 0 -0.47 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0.015 0.3 1 -10000 0 1
RelA/NF kappa B1 0.039 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.025 -10000 0 -0.47 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.061 0.18 1 -0.29 8 9
TNFR1A/BAG4/TNF-alpha 0.05 0.035 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.015 0.015 0.3 1 -10000 0 1
MAP2K1 0.016 0.074 0.2 44 -0.19 1 45
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS 0.01 0.044 0.15 12 -0.17 2 14
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.016 -10000 0 -10000 0 0
EIF2AK2 -0.007 0.05 0.21 8 -0.18 18 26
TNF-alpha/TNFR1A/FAN 0.054 0.033 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.021 0.086 -10000 0 -0.36 15 15
MAP2K2 0.016 0.073 0.2 44 -0.19 1 45
SMPD3 0.022 0.054 0.21 4 -0.24 6 10
TNF 0.036 0.042 0.21 21 -10000 0 21
PKC zeta/PAR4 0.036 0.038 -10000 0 -0.34 4 4
mol:PHOSPHOCHOLINE -0.005 0.038 -10000 0 -0.14 16 16
NF kappa B1/RelA/I kappa B alpha 0.071 0.041 -10000 0 -0.24 4 4
AIFM1 0.007 0.046 0.16 12 -0.17 3 15
BCL2 0.008 0.094 -10000 0 -0.47 15 15
TCGA08_p53

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
CDKN2A 0.028 0.039 0.29 6 -10000 0 6
TP53 -0.004 0.052 -10000 0 -0.18 29 29
Senescence -0.004 0.052 -10000 0 -0.18 29 29
Apoptosis -0.004 0.052 -10000 0 -0.18 29 29
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.004 0.088 0.32 27 -0.2 5 32
MDM4 0.027 0.004 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.002 -10000 0 -10000 0 0
HDAC2 0.026 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.032 0.087 -10000 0 -0.29 26 26
forebrain development -0.098 0.25 -10000 0 -0.61 63 63
GNAO1 -0.12 0.23 -10000 0 -0.47 124 124
SMO/beta Arrestin2 0.019 0.083 -10000 0 -0.33 21 21
SMO 0.002 0.11 -10000 0 -0.47 21 21
ARRB2 0.026 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.037 0.087 0.28 2 -0.48 3 5
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.027 0.006 -10000 0 -10000 0 0
GNAI2 0.027 0.007 -10000 0 -10000 0 0
SIN3/HDAC complex 0.065 0.021 -10000 0 -10000 0 0
GNAI1 0.024 0.043 -10000 0 -0.47 3 3
XPO1 0.028 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) -0.08 0.24 -10000 0 -0.72 36 36
SAP30 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.002 0.11 -10000 0 -0.47 21 21
MIM/GLI2A 0.03 0.017 -10000 0 -10000 0 0
IFT88 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.028 0.003 -10000 0 -10000 0 0
GLI2 -0.006 0.097 0.22 2 -0.3 18 20
GLI3 0.025 0.087 0.29 2 -0.5 3 5
CSNK1D 0.027 0.006 -10000 0 -10000 0 0
CSNK1E 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.027 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.006 -10000 0 -10000 0 0
GNG2 0.02 0.06 -10000 0 -0.47 6 6
Gi family/GTP -0.1 0.2 -10000 0 -0.35 126 126
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.027 0.093 -10000 0 -0.47 7 7
GLI2/Su(fu) -0.005 0.12 -10000 0 -0.36 28 28
FOXA2 0.022 0.078 -10000 0 -0.66 3 3
neural tube patterning -0.098 0.25 -10000 0 -0.61 63 63
SPOP 0.027 0.005 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.015 0.074 -10000 0 -0.38 5 5
GNB1 0.027 0.003 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
MTSS1 0.03 0.017 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.098 0.25 -10000 0 -0.61 63 63
SUFU 0.011 0.058 -10000 0 -0.41 4 4
LGALS3 0.026 0.025 -10000 0 -0.47 1 1
catabolic process 0.023 0.12 -10000 0 -0.45 9 9
GLI3A/CBP -0.018 0.13 -10000 0 -0.34 54 54
KIF3A 0.027 0.005 -10000 0 -10000 0 0
GLI1 -0.1 0.26 -10000 0 -0.65 58 58
RAB23 0.026 0.025 -10000 0 -0.47 1 1
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.015 0.074 -10000 0 -0.36 6 6
GNAZ -0.08 0.2 -10000 0 -0.47 87 87
RBBP4 0.028 0.002 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.003 0.099 -10000 0 -0.32 15 15
STK36 0.028 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.098 0.18 -10000 0 -0.43 73 73
PTCH1 -0.087 0.23 -10000 0 -0.75 27 27
MIM/GLI1 -0.072 0.24 -10000 0 -0.61 54 54
CREBBP -0.018 0.13 -10000 0 -0.34 54 54
Su(fu)/SIN3/HDAC complex 0.023 0.057 -10000 0 -0.35 5 5
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0.073 -10000 0 -0.47 9 9
alphaV beta3 Integrin -0.003 0.12 -10000 0 -0.34 44 44
PTK2 -0.015 0.13 -10000 0 -0.45 25 25
positive regulation of JNK cascade -0.013 0.12 -10000 0 -0.33 31 31
CDC42/GDP -0.003 0.16 -10000 0 -0.42 38 38
Rac1/GDP -0.004 0.16 -10000 0 -0.41 37 37
RAP1B 0.026 0.008 -10000 0 -10000 0 0
RAP1A 0.028 0.003 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.009 0.15 -10000 0 -0.41 31 31
nectin-3/I-afadin 0.013 0.094 -10000 0 -0.33 27 27
RAPGEF1 -0.001 0.15 0.33 2 -0.44 30 32
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.16 -10000 0 -0.49 32 32
PDGFB-D/PDGFRB 0.016 0.073 -10000 0 -0.47 9 9
TLN1 -0.006 0.048 -10000 0 -0.33 4 4
Rap1/GTP -0.004 0.1 -10000 0 -0.34 21 21
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.046 0.019 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.013 0.094 -10000 0 -0.33 27 27
PVR 0.027 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.005 -10000 0 -10000 0 0
mol:GDP -0.022 0.19 -10000 0 -0.51 38 38
MLLT4 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.041 0.093 -10000 0 -0.25 33 33
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.023 -10000 0 -0.34 1 1
positive regulation of lamellipodium assembly -0.018 0.13 -10000 0 -0.33 36 36
PVRL1 0.025 0.025 -10000 0 -0.47 1 1
PVRL3 -0.006 0.12 0.21 2 -0.47 27 29
PVRL2 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
CDH1 0.01 0.087 -10000 0 -0.47 13 13
CLDN1 0.009 0.1 0.23 7 -0.47 17 24
JAM-A/CLDN1 0.022 0.098 -10000 0 -0.26 36 36
SRC -0.023 0.17 -10000 0 -0.55 32 32
ITGB3 -0.027 0.15 -10000 0 -0.47 44 44
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.023 -10000 0 -0.34 1 1
FARP2 -0.026 0.21 -10000 0 -0.56 35 35
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.028 0.086 -10000 0 -0.28 27 27
nectin-1/I-afadin 0.036 0.023 -10000 0 -0.34 1 1
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.026 0.087 -10000 0 -0.28 28 28
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.007 -10000 0 -10000 0 0
F11R 0.021 0.027 -10000 0 -0.47 1 1
positive regulation of filopodium formation -0.013 0.12 -10000 0 -0.33 31 31
alphaV/beta3 Integrin/Talin 0.003 0.11 0.27 3 -0.28 36 39
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
PIP5K1C -0.005 0.055 -10000 0 -0.2 25 25
VAV2 -0.034 0.21 -10000 0 -0.54 35 35
RAP1/GDP 0.004 0.14 -10000 0 -0.41 23 23
ITGAV 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.028 0.085 -10000 0 -0.28 26 26
nectin-3(dimer)/I-afadin/I-afadin 0.013 0.094 -10000 0 -0.33 27 27
Rac1/GTP -0.014 0.16 -10000 0 -0.4 35 35
PTPRM -0.005 0.07 -10000 0 -0.23 31 31
E-cadherin/beta catenin/alpha catenin 0.055 0.065 -10000 0 -0.25 12 12
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.003 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.028 0.018 0.27 2 -10000 0 2
EPHB2 0.041 0.047 0.21 28 -10000 0 28
EFNB1 0.009 0.043 -10000 0 -0.34 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.04 0.092 -10000 0 -0.25 28 28
Ephrin B2/EPHB1-2 0.04 0.081 0.27 1 -0.26 23 24
neuron projection morphogenesis 0.023 0.081 -10000 0 -0.24 28 28
Ephrin B1/EPHB1-2/Tiam1 0.035 0.096 0.28 1 -0.27 29 30
DNM1 0.018 0.06 -10000 0 -0.47 6 6
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.009 0.093 0.24 2 -0.48 14 16
YES1 -0.011 0.14 -10000 0 -0.7 15 15
Ephrin B1/EPHB1-2/NCK2 0.039 0.093 0.28 1 -0.26 28 29
PI3K 0.023 0.1 -10000 0 -0.47 15 15
mol:GDP 0.034 0.095 0.28 1 -0.26 29 30
ITGA2B 0.04 0.052 0.22 31 -10000 0 31
endothelial cell proliferation 0.035 0.011 -10000 0 -10000 0 0
FYN -0.014 0.14 -10000 0 -0.73 15 15
MAP3K7 -0.013 0.097 -10000 0 -0.52 14 14
FGR -0.01 0.14 -10000 0 -0.7 16 16
TIAM1 0.023 0.043 -10000 0 -0.47 3 3
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.005 0.11 -10000 0 -0.45 13 13
LYN -0.011 0.14 -10000 0 -0.71 15 15
Ephrin B1/EPHB1-2/Src Family Kinases -0.016 0.13 -10000 0 -0.64 16 16
Ephrin B1/EPHB1-2 -0.013 0.1 -10000 0 -0.56 14 14
SRC -0.009 0.14 -10000 0 -0.69 16 16
ITGB3 -0.027 0.15 -10000 0 -0.47 44 44
EPHB1 -0.002 0.12 0.21 4 -0.47 25 29
EPHB4 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.036 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.006 0.12 -10000 0 -0.34 44 44
BLK -0.026 0.15 -10000 0 -0.72 16 16
HCK -0.015 0.14 -10000 0 -0.7 16 16
regulation of stress fiber formation -0.037 0.092 0.26 28 -0.28 1 29
MAPK8 -0.008 0.1 0.32 2 -0.49 14 16
Ephrin B1/EPHB1-2/RGS3 0.04 0.092 0.28 1 -0.25 29 30
endothelial cell migration -0.005 0.091 0.31 2 -0.41 15 17
NCK2 0.027 0.004 -10000 0 -10000 0 0
PTPN13 0.015 0.08 -10000 0 -0.58 7 7
regulation of focal adhesion formation -0.037 0.092 0.26 28 -0.28 1 29
chemotaxis -0.038 0.091 0.25 29 -0.28 1 30
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.087 -10000 0 -0.25 28 28
angiogenesis -0.014 0.11 -10000 0 -0.55 15 15
LCK -0.01 0.14 -10000 0 -0.69 16 16
Insulin Pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.075 0.14 -10000 0 -0.23 170 170
TC10/GTP -0.07 0.13 -10000 0 -0.22 165 165
Insulin Receptor/Insulin/IRS1/Shp2 0.052 0.052 -10000 0 -0.26 7 7
HRAS 0.025 0.008 -10000 0 -10000 0 0
APS homodimer 0.029 0.021 0.21 5 -10000 0 5
GRB14 0.051 0.065 0.21 54 -10000 0 54
FOXO3 -0.028 0.18 -10000 0 -0.56 39 39
AKT1 0.004 0.064 0.33 4 -10000 0 4
INSR 0.031 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.054 0.035 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.02 0.055 -10000 0 -0.47 5 5
SORBS1 -0.19 0.24 -10000 0 -0.47 180 180
CRK 0.025 0.008 -10000 0 -10000 0 0
PTPN1 0.01 0.022 -10000 0 -10000 0 0
CAV1 0 0.068 0.21 1 -0.26 23 24
CBL/APS/CAP/Crk-II/C3G -0.065 0.16 -10000 0 -0.24 173 173
Insulin Receptor/Insulin/IRS1/NCK2 0.053 0.051 -10000 0 -0.26 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.044 -10000 0 -0.23 7 7
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.028 0.067 -10000 0 -0.34 8 8
RPS6KB1 0.001 0.059 0.32 4 -10000 0 4
PARD6A 0.025 0.025 -10000 0 -0.47 1 1
CBL 0.026 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.018 0.038 -10000 0 -0.48 2 2
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.027 0.048 -10000 0 -10000 0 0
HRAS/GTP 0.01 0.035 -10000 0 -0.22 4 4
Insulin Receptor 0.031 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.058 0.053 -10000 0 -0.24 6 6
PRKCI 0.028 0.049 -10000 0 -0.49 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.027 0.041 -10000 0 -0.23 5 5
SHC1 0.026 0.017 0.33 1 -10000 0 1
negative regulation of MAPKKK cascade 0.044 0.039 -10000 0 -0.4 2 2
PI3K 0.049 0.049 -10000 0 -0.23 7 7
NCK2 0.027 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.006 -10000 0 -10000 0 0
AKT2 0.005 0.064 0.33 4 -10000 0 4
PRKCZ 0.024 0.066 -10000 0 -0.46 4 4
SH2B2 0.029 0.021 0.21 5 -10000 0 5
SHC/SHIP 0.024 0.045 0.21 2 -0.23 9 11
F2RL2 0.013 0.1 0.21 12 -0.47 15 27
TRIP10 0.026 0.025 -10000 0 -0.47 1 1
Insulin Receptor/Insulin/Shc 0.044 0.024 0.22 1 -10000 0 1
TC10/GTP/CIP4/Exocyst 0.035 0.017 -10000 0 -0.26 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.065 0.036 -10000 0 -10000 0 0
RAPGEF1 0.025 0.009 -10000 0 -10000 0 0
RASA1 0.027 0.006 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.076 0.16 -10000 0 -0.26 174 174
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.054 0.043 -10000 0 -0.27 3 3
INPP5D 0.008 0.048 0.21 1 -0.24 12 13
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.04 0.2 -10000 0 -0.73 30 30
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.017 0.065 -10000 0 -0.47 7 7
p62DOK/RasGAP 0.045 0.04 -10000 0 -0.41 2 2
INS 0.019 0.011 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.008 0.048 0.21 1 -0.24 12 13
GRB2 0.027 0.005 -10000 0 -10000 0 0
EIF4EBP1 0.007 0.067 0.33 5 -10000 0 5
PTPRA 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.035 0.017 -10000 0 -0.26 1 1
PDPK1 0.026 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.019 0.042 -10000 0 -0.25 4 4
Insulin Receptor/Insulin/IRS1 0.038 0.046 -10000 0 -0.26 7 7
Insulin Receptor/Insulin/IRS3 0.036 0.018 -10000 0 -10000 0 0
Par3/Par6 0.047 0.065 -10000 0 -0.24 15 15
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0.073 -10000 0 -0.47 9 9
Jak2/Leptin Receptor 0.01 0.16 0.28 10 -0.38 35 45
PTP1B/AKT1 0.025 0.079 0.19 1 -0.31 7 8
FYN 0.022 0.043 -10000 0 -0.47 3 3
p210 bcr-abl/PTP1B 0.016 0.081 0.19 4 -0.29 10 14
EGFR 0.022 0.085 0.32 8 -0.47 9 17
EGF/EGFR 0.034 0.093 0.24 8 -0.28 12 20
CSF1 0.009 0.094 -10000 0 -0.47 15 15
AKT1 0.027 0.005 -10000 0 -10000 0 0
INSR 0.027 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.036 0.095 0.23 13 -0.28 10 23
Insulin Receptor/Insulin 0.035 0.076 -10000 0 -0.32 4 4
HCK 0.014 0.08 0.21 5 -0.47 10 15
CRK 0.025 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.081 0.25 5 -0.31 7 12
EGF 0.037 0.047 0.22 24 -10000 0 24
YES1 0.025 0.008 -10000 0 -10000 0 0
CAV1 0.02 0.091 0.21 6 -0.28 12 18
TXN 0.027 0.016 0.21 2 -10000 0 2
PTP1B/IRS1/GRB2 0.032 0.087 -10000 0 -0.28 10 10
cell migration -0.016 0.081 0.29 10 -0.19 4 14
STAT3 0.027 0.004 -10000 0 -10000 0 0
PRLR 0.02 0.12 0.26 28 -0.47 17 45
ITGA2B 0.04 0.052 0.22 31 -10000 0 31
CSF1R 0.004 0.11 0.21 2 -0.47 19 21
Prolactin Receptor/Prolactin 0.027 0.087 0.24 10 -0.34 15 25
FGR 0.025 0.035 -10000 0 -0.47 2 2
PTP1B/p130 Cas 0.026 0.08 0.2 1 -0.31 7 8
Crk/p130 Cas 0.033 0.082 -10000 0 -0.3 7 7
DOK1 0.014 0.093 0.22 1 -0.29 19 20
JAK2 0.002 0.16 0.26 7 -0.38 39 46
Jak2/Leptin Receptor/Leptin -0.02 0.17 0.3 2 -0.37 54 56
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
PTPN1 0.016 0.082 0.19 4 -0.29 10 14
LYN 0.025 0.008 -10000 0 -10000 0 0
CDH2 0.041 0.073 0.22 40 -0.47 3 43
SRC 0.027 0.078 -10000 0 -0.47 7 7
ITGB3 -0.027 0.15 -10000 0 -0.47 44 44
CAT1/PTP1B 0.007 0.13 0.29 12 -0.34 18 30
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.075 -10000 0 -0.33 3 3
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.024 0.17 -10000 0 -0.38 55 55
negative regulation of transcription 0.004 0.15 0.26 7 -0.38 39 46
FCGR2A 0.028 0.045 0.23 12 -0.47 1 13
FER 0.025 0.036 -10000 0 -0.47 2 2
alphaIIb/beta3 Integrin 0.006 0.13 -10000 0 -0.34 44 44
BLK -0.011 0.14 0.21 15 -0.47 30 45
Insulin Receptor/Insulin/Shc 0.042 0.021 0.23 1 -10000 0 1
RHOA 0.027 0.007 -10000 0 -10000 0 0
LEPR 0.008 0.098 -10000 0 -0.46 17 17
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.027 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.018 0.14 0.26 6 -0.37 27 33
PRL 0.008 0.038 0.25 7 -10000 0 7
SOCS3 -0.11 0.4 -10000 0 -1.3 43 43
SPRY2 0.018 0.065 -10000 0 -0.47 7 7
Insulin Receptor/Insulin/IRS1 0.036 0.048 -10000 0 -0.29 7 7
CSF1/CSF1R 0.019 0.12 -10000 0 -0.33 23 23
Ras protein signal transduction 0.009 0.1 0.53 14 -10000 0 14
IRS1 0.017 0.065 -10000 0 -0.47 7 7
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.018 0.14 0.21 15 -0.47 35 50
STAT5B 0.02 0.1 0.21 10 -0.32 15 25
STAT5A 0.02 0.11 0.21 10 -0.32 16 26
GRB2 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.024 0.091 0.2 1 -0.29 16 17
CSN2 0.025 0.073 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
LAT 0.038 0.058 -10000 0 -0.42 3 3
YBX1 0.035 0.016 0.33 1 -10000 0 1
LCK 0.024 0.051 0.21 2 -0.47 4 6
SHC1 0.026 0.017 0.33 1 -10000 0 1
NOX4 0.041 0.05 0.22 30 -10000 0 30
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.033 0.12 0.29 7 -0.4 17 24
PDGFB-D/PDGFRB/SLAP 0.016 0.095 -10000 0 -0.4 18 18
PDGFB-D/PDGFRB/APS/CBL 0.045 0.055 -10000 0 -0.28 9 9
AKT1 0.028 0.092 0.35 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.043 0.14 0.27 19 -0.42 19 38
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
FGR 0.012 0.087 0.33 1 -0.37 10 11
mol:Ca2+ 0.019 0.13 0.27 17 -0.44 21 38
MYC 0.028 0.22 0.37 16 -0.67 25 41
SHC1 0.026 0.017 0.33 1 -10000 0 1
HRAS/GDP 0.038 0.063 0.18 1 -0.23 9 10
LRP1/PDGFRB/PDGFB 0.042 0.061 -10000 0 -0.28 12 12
GRB10 0.02 0.055 -10000 0 -0.47 5 5
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GO:0007205 0.019 0.14 0.27 16 -0.45 21 37
PTEN 0.026 0.007 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
GRB7 0.028 0.084 0.31 14 -0.47 7 21
PDGFB-D/PDGFRB/SHP2 0.032 0.054 -10000 0 -0.34 8 8
PDGFB-D/PDGFRB/GRB10 0.026 0.07 -10000 0 -0.34 14 14
cell cycle arrest 0.016 0.095 -10000 0 -0.4 18 18
HRAS 0.025 0.008 -10000 0 -10000 0 0
HIF1A 0.023 0.087 0.32 12 -10000 0 12
GAB1 0.019 0.13 0.34 5 -0.43 18 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.022 0.12 0.28 16 -0.44 13 29
PDGFB-D/PDGFRB 0.037 0.057 -10000 0 -0.3 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.032 0.051 -10000 0 -0.34 7 7
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.026 0.11 0.27 5 -0.43 11 16
positive regulation of MAPKKK cascade 0.031 0.054 -10000 0 -0.34 8 8
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
mol:IP3 0.019 0.14 0.27 16 -0.45 21 37
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.031 0.084 0.24 12 -0.34 16 28
SHB 0.024 0.009 -10000 0 -10000 0 0
BLK -0.079 0.21 -10000 0 -0.44 88 88
PTPN2 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.031 0.057 -10000 0 -0.34 9 9
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.019 0.14 0.33 9 -0.44 20 29
CBL 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.057 -10000 0 -0.32 10 10
LCK 0.009 0.1 0.33 1 -0.42 14 15
PDGFRB 0.017 0.075 -10000 0 -0.48 9 9
ACP1 0.026 0.006 -10000 0 -10000 0 0
HCK 0.001 0.14 0.35 1 -0.56 17 18
ABL1 0.017 0.12 0.27 16 -0.43 14 30
PDGFB-D/PDGFRB/CBL 0.012 0.15 0.34 4 -0.5 21 25
PTPN1 0.026 0.008 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.029 0.019 0.21 4 -10000 0 4
cell proliferation 0.032 0.2 0.35 20 -0.6 25 45
SLA 0.009 0.088 0.21 1 -0.47 13 14
actin cytoskeleton reorganization 0.051 0.082 0.34 9 -0.23 7 16
SRC 0.013 0.073 0.34 1 -0.34 6 7
PI3K 0.005 0.038 -10000 0 -0.23 8 8
PDGFB-D/PDGFRB/GRB7/SHC 0.043 0.073 0.24 11 -0.28 14 25
SH2B2 0.029 0.021 0.21 5 -10000 0 5
PLCgamma1/SPHK1 0.043 0.14 0.29 13 -0.44 19 32
LYN 0.013 0.081 0.33 1 -0.38 7 8
LRP1 0.022 0.049 -10000 0 -0.47 4 4
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.027 0.004 -10000 0 -10000 0 0
STAT5A 0.026 0.025 -10000 0 -0.47 1 1
NCK1-2/p130 Cas 0.055 0.058 -10000 0 -0.24 8 8
SPHK1 0.052 0.07 0.22 56 -0.48 1 57
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.019 0.14 0.27 16 -0.45 21 37
PLCG1 0.019 0.14 0.28 16 -0.46 21 37
NHERF/PDGFRB 0.049 0.06 0.24 1 -0.28 9 10
YES1 0.001 0.1 -10000 0 -0.42 16 16
cell migration 0.048 0.06 0.24 1 -0.28 9 10
SHC/Grb2/SOS1 0.056 0.057 -10000 0 -0.24 7 7
SLC9A3R2 0.027 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.037 0.043 0.22 21 -10000 0 21
NHERF1-2/PDGFRB/PTEN 0.058 0.06 0.24 1 -0.26 9 10
FYN -0.013 0.13 -10000 0 -0.43 28 28
DOK1 0.031 0.07 0.18 49 -0.26 8 57
HRAS/GTP 0.019 0.006 -10000 0 -10000 0 0
PDGFB 0.027 0.011 0.21 1 -10000 0 1
RAC1 0.022 0.16 0.34 12 -0.44 28 40
PRKCD 0.028 0.071 0.18 46 -0.27 9 55
FER 0.028 0.071 0.18 43 -0.26 10 53
MAPKKK cascade 0.028 0.093 0.4 8 -0.24 4 12
RASA1 0.029 0.07 0.18 45 -0.26 9 54
NCK1 0.026 0.006 -10000 0 -10000 0 0
NCK2 0.027 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.043 0.064 0.27 1 -0.24 8 9
PDGFB-D/PDGFRB/SHB 0.029 0.054 -10000 0 -0.34 8 8
chemotaxis 0.017 0.12 0.27 16 -0.42 14 30
STAT1-3-5/STAT1-3-5 0.047 0.055 -10000 0 -0.23 10 10
Bovine Papilomavirus E5/PDGFRB 0.012 0.054 -10000 0 -0.32 10 10
PTPRJ 0.026 0.007 -10000 0 -10000 0 0
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 0.069 -10000 0 -0.37 3 3
epithelial cell differentiation 0.012 0.087 -10000 0 -0.41 3 3
ITCH 0.029 0.02 0.31 1 -10000 0 1
WWP1 0.033 0.057 -10000 0 -10000 0 0
FYN 0.022 0.043 -10000 0 -0.47 3 3
EGFR 0.021 0.085 0.33 8 -0.47 9 17
PRL 0.001 0.038 0.25 7 -10000 0 7
neuron projection morphogenesis 0.019 0.11 0.31 10 -0.35 1 11
PTPRZ1 -0.072 0.22 0.21 41 -0.47 89 130
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.019 0.1 -10000 0 -0.38 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.009 0.098 0.3 1 -0.32 6 7
ADAM17 0.029 0.019 0.31 1 -10000 0 1
ErbB4/ErbB4 0.03 0.041 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.043 0.055 -10000 0 -10000 0 0
NCOR1 0.025 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.002 0.1 0.27 1 -0.33 5 6
GRIN2B -0.009 0.099 0.27 3 -0.35 4 7
ErbB4/ErbB2/betacellulin 0.019 0.094 0.28 3 -0.31 2 5
STAT1 0.029 0.019 0.21 4 -10000 0 4
HBEGF 0.012 0.084 -10000 0 -0.47 12 12
PRLR 0.019 0.12 0.26 28 -0.47 17 45
E4ICDs/ETO2 0.035 0.066 -10000 0 -10000 0 0
axon guidance 0.024 0.097 0.29 10 -10000 0 10
NEDD4 0.026 0.026 -10000 0 -0.45 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.025 0.085 0.24 10 -0.34 15 25
CBFA2T3 0.012 0.084 -10000 0 -0.47 12 12
ErbB4/ErbB2/HBEGF 0.041 0.064 0.28 3 -0.42 1 4
MAPK3 0.014 0.1 0.3 4 -0.36 1 5
STAT1 (dimer) 0.046 0.049 -10000 0 -10000 0 0
MAPK1 0.017 0.1 0.3 5 -0.36 1 6
JAK2 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.004 0.096 0.28 4 -0.36 2 6
NRG1 -0.032 0.12 0.31 3 -0.34 54 57
NRG3 0.011 0.043 0.21 13 -10000 0 13
NRG2 -0.18 0.24 -10000 0 -0.47 164 164
NRG4 -0.019 0.14 -10000 0 -0.47 37 37
heart development 0.024 0.097 0.29 10 -10000 0 10
neural crest cell migration -0.004 0.095 0.27 4 -0.35 2 6
ERBB2 0.025 0.054 0.3 14 -10000 0 14
WWOX/E4ICDs 0.039 0.048 -10000 0 -10000 0 0
SHC1 0.026 0.017 0.33 1 -10000 0 1
ErbB4/EGFR/neuregulin 4 0.028 0.11 0.3 2 -0.37 7 9
apoptosis -0.026 0.076 0.41 3 -0.26 1 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.07 0.15 -10000 0 -0.34 16 16
ErbB4/ErbB2/epiregulin 0.033 0.11 0.3 7 -0.3 4 11
ErbB4/ErbB4/betacellulin/betacellulin 0.01 0.1 -10000 0 -0.33 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.043 0.094 0.32 2 -0.36 2 4
MDM2 0.042 0.077 0.28 32 -10000 0 32
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.004 0.093 -10000 0 -0.28 6 6
STAT5A 0.027 0.1 0.32 7 -0.42 1 8
ErbB4/EGFR/neuregulin 1 beta -0.001 0.11 0.28 3 -0.32 7 10
DLG4 0.025 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.037 0.016 0.24 1 -10000 0 1
E4ICDs/TAB2/NCoR1 0.034 0.043 -10000 0 -10000 0 0
STAT5A (dimer) 0.027 0.11 0.31 1 -0.44 3 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.042 0.1 0.34 2 -10000 0 2
LRIG1 -0.014 0.14 -10000 0 -0.47 33 33
EREG -0.017 0.19 0.22 53 -0.47 55 108
BTC -0.035 0.16 -10000 0 -0.47 49 49
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.02 0.094 0.3 8 -10000 0 8
ERBB4 0.021 0.026 -10000 0 -10000 0 0
STAT5B 0.027 0.004 -10000 0 -10000 0 0
YAP1 0.013 0.081 0.34 1 -0.47 9 10
GRB2 0.027 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.027 0.08 0.27 1 -0.34 2 3
glial cell differentiation -0.033 0.042 -10000 0 -10000 0 0
WWOX 0.023 0.026 -10000 0 -0.47 1 1
cell proliferation -0.032 0.15 0.33 7 -0.52 12 19
IL27-mediated signaling events

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
TGFB1 0.029 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 0.013 0.12 0.41 7 -0.48 1 8
IL27/IL27R/JAK1 0.039 0.15 0.56 4 -10000 0 4
TBX21 -0.013 0.16 0.5 3 -0.46 21 24
IL12B 0.027 0.039 0.22 14 -10000 0 14
IL12A 0.009 0.015 0.29 1 -10000 0 1
IL6ST -0.04 0.17 -10000 0 -0.47 55 55
IL27RA/JAK1 0.024 0.036 -10000 0 -10000 0 0
IL27 0.034 0.05 0.22 23 -10000 0 23
TYK2 0.03 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.098 0.15 -10000 0 -0.42 4 4
T-helper 2 cell differentiation 0.013 0.12 0.41 7 -0.48 1 8
T cell proliferation during immune response 0.013 0.12 0.41 7 -0.48 1 8
MAPKKK cascade -0.013 0.12 0.48 1 -0.41 7 8
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT2 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.029 0.02 0.22 4 -10000 0 4
IL12RB1 0.025 0.088 0.21 20 -0.47 10 30
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.002 0.15 0.48 4 -0.48 11 15
IL27/IL27R/JAK2/TYK2 -0.014 0.12 0.48 1 -0.42 7 8
positive regulation of T cell mediated cytotoxicity -0.013 0.12 0.48 1 -0.41 7 8
STAT1 (dimer) 0.042 0.21 0.6 22 -0.54 10 32
JAK2 0.026 0.011 -10000 0 -10000 0 0
JAK1 0.028 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.001 0.12 0.43 1 -0.4 7 8
T cell proliferation -0.11 0.18 0.44 1 -0.42 59 60
IL12/IL12R/TYK2/JAK2 0.005 0.2 -10000 0 -0.76 22 22
IL17A -0.098 0.15 -10000 0 -0.42 4 4
mast cell activation 0.013 0.12 0.41 7 -0.48 1 8
IFNG 0.007 0.031 0.17 1 -0.098 4 5
T cell differentiation -0.001 0.005 0.011 2 -0.016 12 14
STAT3 (dimer) -0.002 0.12 0.43 1 -0.4 7 8
STAT5A (dimer) -0.002 0.12 0.43 1 -0.4 7 8
STAT4 (dimer) -0.012 0.13 0.43 1 -0.4 15 16
STAT4 0.002 0.11 -10000 0 -0.47 20 20
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.012 0.11 -10000 0 -10000 0 0
GATA3 -0.015 0.39 0.6 45 -1.3 26 71
IL18 0.003 0.041 -10000 0 -0.33 6 6
positive regulation of mast cell cytokine production -0.001 0.12 0.43 1 -0.39 7 8
IL27/EBI3 0.048 0.056 0.24 8 -0.34 3 11
IL27RA 0.008 0.028 -10000 0 -10000 0 0
IL6 -0.18 0.24 -10000 0 -0.47 170 170
STAT5A 0.026 0.025 -10000 0 -0.47 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.013 0.03 -10000 0 -10000 0 0
IL1B -0.004 0.074 0.29 2 -0.33 18 20
EBI3 0.029 0.05 0.22 7 -0.47 3 10
TNF 0.01 0.009 -10000 0 -10000 0 0
Caspase cascade in apoptosis

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.008 0.12 -10000 0 -0.45 18 18
ACTA1 -0.028 0.14 -10000 0 -0.45 27 27
NUMA1 -0.01 0.12 -10000 0 -0.39 29 29
SPTAN1 -0.029 0.14 -10000 0 -0.48 24 24
LIMK1 -0.028 0.14 -10000 0 -0.49 23 23
BIRC3 0.005 0.11 0.33 3 -0.47 19 22
BIRC2 0.028 0.022 0.33 2 -10000 0 2
BAX 0.027 0.004 -10000 0 -10000 0 0
CASP10 -0.033 0.096 -10000 0 -0.37 27 27
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.015 0.33 1 -10000 0 1
PTK2 -0.01 0.12 -10000 0 -0.4 27 27
DIABLO 0.027 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.029 0.13 -10000 0 -0.47 24 24
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.004 -10000 0 -10000 0 0
GSN -0.032 0.14 -10000 0 -0.49 25 25
MADD 0.026 0.007 -10000 0 -10000 0 0
TFAP2A 0.033 0.1 -10000 0 -0.63 7 7
BID -0.008 0.062 0.18 1 -0.23 27 28
MAP3K1 -0.018 0.1 -10000 0 -0.39 21 21
TRADD 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.04 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.027 0.14 0.34 1 -0.48 24 25
CASP9 0.028 0.003 -10000 0 -10000 0 0
DNA repair -0.002 0.052 0.19 4 -0.16 9 13
neuron apoptosis 0.009 0.096 -10000 0 -0.68 6 6
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.02 0.14 -10000 0 -0.43 31 31
APAF1 0.027 0.004 -10000 0 -10000 0 0
CASP6 -0.002 0.14 -10000 0 -0.75 10 10
TRAF2 0.025 0.009 -10000 0 -10000 0 0
ICAD/CAD -0.03 0.13 -10000 0 -0.48 23 23
CASP7 -0.001 0.093 0.28 19 -0.25 20 39
KRT18 0.018 0.057 -10000 0 -0.49 3 3
apoptosis -0.016 0.14 0.27 2 -0.5 22 24
DFFA -0.03 0.14 -10000 0 -0.48 24 24
DFFB -0.03 0.14 -10000 0 -0.49 23 23
PARP1 0.002 0.052 0.16 9 -0.19 4 13
actin filament polymerization 0.027 0.12 0.46 22 -10000 0 22
TNF 0.036 0.042 0.21 21 -10000 0 21
CYCS -0.002 0.053 0.18 1 -0.2 16 17
SATB1 -0.001 0.14 -10000 0 -0.7 10 10
SLK -0.029 0.14 -10000 0 -0.48 24 24
p15 BID/BAX 0.004 0.07 -10000 0 -0.26 15 15
CASP2 0.007 0.07 0.21 4 -0.28 8 12
JNK cascade 0.018 0.1 0.39 21 -10000 0 21
CASP3 -0.03 0.14 -10000 0 -0.48 26 26
LMNB2 0.013 0.11 -10000 0 -0.37 16 16
RIPK1 0.026 0.007 -10000 0 -10000 0 0
CASP4 0.027 0.016 0.33 1 -10000 0 1
Mammalian IAPs/DIABLO 0.05 0.072 -10000 0 -0.26 18 18
negative regulation of DNA binding 0.033 0.1 -10000 0 -0.62 7 7
stress fiber formation -0.029 0.13 -10000 0 -0.47 24 24
GZMB -0.017 0.12 -10000 0 -0.42 29 29
CASP1 0.008 0.047 -10000 0 -0.3 9 9
LMNB1 0.011 0.12 -10000 0 -0.41 18 18
APP 0.008 0.098 -10000 0 -0.69 6 6
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.002 -10000 0 -10000 0 0
VIM -0.014 0.14 0.28 2 -0.48 23 25
LMNA 0.019 0.079 -10000 0 -0.31 9 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.008 0.072 -10000 0 -0.27 11 11
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.027 0.14 0.29 1 -0.48 23 24
APAF-1/Caspase 9 0.016 0.063 -10000 0 -0.54 3 3
nuclear fragmentation during apoptosis -0.01 0.12 -10000 0 -0.39 29 29
CFL2 -0.028 0.13 -10000 0 -0.47 22 22
GAS2 -0.049 0.15 -10000 0 -0.45 30 30
positive regulation of apoptosis 0.018 0.1 -10000 0 -0.38 14 14
PRF1 0.012 0.1 0.21 11 -0.47 16 27
IL2 signaling events mediated by PI3K

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
BCL2L1 0.041 0.086 -10000 0 -0.77 1 1
UGCG -0.062 0.23 -10000 0 -0.59 59 59
AKT1/mTOR/p70S6K/Hsp90/TERT 0.073 0.12 0.28 9 -0.3 11 20
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.059 0.22 -10000 0 -0.58 59 59
mol:DAG 0.009 0.11 -10000 0 -0.77 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.044 0.15 0.32 1 -0.44 25 26
FRAP1 0.036 0.16 0.34 1 -0.49 27 28
FOXO3 0.039 0.14 0.31 2 -0.43 23 25
AKT1 0.039 0.15 0.34 1 -0.45 26 27
GAB2 0.025 0.026 -10000 0 -0.47 1 1
SMPD1 -0.014 0.16 -10000 0 -0.57 28 28
SGMS1 0.016 0.082 -10000 0 -0.56 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 0.006 0.017 -10000 0 -0.28 1 1
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.001 0.18 0.28 3 -0.48 29 32
EIF3A 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.038 0.025 -10000 0 -0.33 1 1
RPS6KB1 0.033 0.023 -10000 0 -10000 0 0
mol:sphingomyelin 0.009 0.11 -10000 0 -0.77 7 7
natural killer cell activation 0 0.003 -10000 0 -0.013 8 8
JAK3 0.03 0.014 0.22 2 -10000 0 2
PIK3R1 0.026 0.026 -10000 0 -0.46 1 1
JAK1 0.029 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC 0.039 0.24 0.38 7 -0.92 20 27
MYB 0.063 0.086 0.43 1 -1.1 1 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.12 0.25 1 -0.45 11 12
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.054 0.032 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.04 0.12 0.24 1 -0.44 11 12
Rac1/GDP 0.02 0.021 -10000 0 -0.25 1 1
T cell proliferation 0.039 0.11 0.3 2 -0.43 10 12
SHC1 0.026 0.017 0.33 1 -10000 0 1
RAC1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.007 0.008 0.027 36 -0.076 1 37
PRKCZ 0.038 0.11 0.36 1 -0.44 10 11
NF kappa B1 p50/RelA 0.056 0.15 0.33 1 -0.44 23 24
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.024 0.073 -10000 0 -0.43 7 7
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA 0.012 0.11 0.21 19 -0.47 17 36
IL2RB 0.023 0.058 0.27 2 -0.47 5 7
TERT 0.12 0.11 0.24 174 -10000 0 174
E2F1 0.066 0.059 0.26 5 -0.31 1 6
SOS1 0.027 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.01 -10000 0 -10000 0 0
mol:cAMP -0.003 0.004 0.032 1 -0.015 15 16
PTPN11 0.026 0.01 -10000 0 -10000 0 0
IL2RG 0.022 0.079 0.22 9 -0.47 9 18
actin cytoskeleton organization 0.039 0.11 0.3 2 -0.43 10 12
GRB2 0.027 0.007 -10000 0 -10000 0 0
IL2 0.019 0.013 -10000 0 -10000 0 0
PIK3CA 0.027 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.044 0.032 -10000 0 -0.24 1 1
LCK 0.025 0.051 0.22 2 -0.47 4 6
BCL2 0.021 0.21 -10000 0 -0.75 22 22
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.034 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.021 0.056 0.21 1 -0.47 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.017 0.015 -10000 0 -0.19 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 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 0.006 -10000 0 -10000 0 0
FYN 0.022 0.043 -10000 0 -0.47 3 3
MAP3K12 0.026 0.025 -10000 0 -0.47 1 1
FGR 0.025 0.035 -10000 0 -0.47 2 2
p38 alpha/TAB1 -0.037 0.081 -10000 0 -0.28 30 30
PRKG1 -0.082 0.2 -10000 0 -0.47 87 87
DUSP8 0.001 0.11 -10000 0 -0.47 20 20
PGK/cGMP/p38 alpha -0.038 0.14 -10000 0 -0.32 54 54
apoptosis -0.036 0.078 -10000 0 -0.27 30 30
RAL/GTP 0.036 0.009 -10000 0 -10000 0 0
LYN 0.025 0.008 -10000 0 -10000 0 0
DUSP1 -0.1 0.22 -10000 0 -0.47 105 105
PAK1 0.025 0.025 -10000 0 -0.47 1 1
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.06 0.027 -10000 0 -10000 0 0
TRAF6 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.027 0.01 0.21 1 -10000 0 1
RAC1-CDC42/GTP 0.035 0.009 -10000 0 -10000 0 0
MAPK11 0.011 0.12 0.28 7 -0.32 19 26
BLK -0.011 0.14 0.21 15 -0.47 30 45
HCK 0.014 0.08 0.21 5 -0.47 10 15
MAP2K3 0.025 0.008 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.03 0.021 0.21 5 -10000 0 5
TRAF6/MEKK3 0.031 0.012 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.12 0.23 10 -0.32 28 38
positive regulation of innate immune response 0.01 0.14 0.3 7 -0.35 25 32
LCK 0.024 0.051 0.21 2 -0.47 4 6
p38alpha-beta/MKP7 0.02 0.14 0.33 5 -0.34 23 28
p38alpha-beta/MKP5 0.02 0.14 0.34 4 -0.36 21 25
PGK/cGMP -0.057 0.14 -10000 0 -0.33 87 87
PAK2 0.026 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.029 0.17 0.28 2 -0.36 53 55
CDC42 0.028 0.003 -10000 0 -10000 0 0
RALB 0.027 0.004 -10000 0 -10000 0 0
RALA 0.028 0.016 0.33 1 -10000 0 1
PAK3 0.014 0.041 0.21 12 -10000 0 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 0.026 0.025 -10000 0 -0.47 1 1
ELF1 0.02 0.078 -10000 0 -0.35 16 16
CCNA2 0.076 0.083 0.22 105 -10000 0 105
PIK3CA 0.027 0.007 -10000 0 -10000 0 0
JAK3 0.029 0.013 0.21 2 -10000 0 2
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
JAK1 0.028 0.003 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.047 0.098 0.27 1 -0.51 5 6
SHC1 0.027 0.017 0.33 1 -10000 0 1
SP1 0.005 0.098 -10000 0 -0.34 31 31
IL2RA -0.007 0.15 -10000 0 -0.7 17 17
IL2RB 0.022 0.058 0.27 2 -0.47 5 7
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG 0.021 0.079 0.21 9 -0.47 9 18
G1/S transition of mitotic cell cycle -0.02 0.22 0.36 3 -0.7 34 37
PTPN11 0.027 0.005 -10000 0 -10000 0 0
CCND2 -0.037 0.2 -10000 0 -0.73 31 31
LCK 0.024 0.051 0.21 2 -0.47 4 6
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL2 0.017 0.011 -10000 0 -10000 0 0
CDK6 0.015 0.077 -10000 0 -0.47 10 10
CCND3 0.054 0.095 0.35 1 -0.61 2 3
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.025 0.018 0.33 1 -10000 0 1
NFATC1 0.009 0.099 0.31 2 -0.33 12 14
NFATC2 -0.035 0.079 -10000 0 -0.22 25 25
NFATC3 0.011 0.034 -10000 0 -0.36 3 3
YWHAE 0.025 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.036 0.14 0.27 7 -0.35 40 47
Exportin 1/Ran/NUP214 0.044 0.02 -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 0.23 2 -0.36 33 35
BCL2/BAX 0.024 0.071 -10000 0 -0.33 15 15
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.021 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.021 -10000 0 -10000 0 0
BAX 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
BAD 0.027 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.026 0.13 0.24 5 -0.35 33 38
Calcineurin A alpha-beta B1/BCL2 0.008 0.093 -10000 0 -0.47 15 15
FKBP8 0.027 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.025 0.13 0.35 33 -0.24 5 38
KPNB1 0.027 0.005 -10000 0 -10000 0 0
KPNA2 0.029 0.022 0.24 4 -10000 0 4
XPO1 0.026 0.005 -10000 0 -10000 0 0
SFN 0.038 0.067 0.21 32 -0.47 3 35
MAP3K8 0.02 0.035 -10000 0 -0.47 2 2
NFAT4/CK1 alpha 0 0.036 -10000 0 -0.22 3 3
MEF2D/NFAT1/Cbp/p300 -0.12 0.17 -10000 0 -0.28 186 186
CABIN1 -0.036 0.14 0.27 7 -0.35 40 47
CALM1 0.022 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.007 -10000 0 -10000 0 0
CAMK4 0.016 0.07 0.21 1 -0.47 8 9
mol:Ca2+ -0.008 0.008 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.027 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.039 0.015 -10000 0 -10000 0 0
YWHAB 0.025 0.008 -10000 0 -10000 0 0
MAPK8 0.019 0.043 -10000 0 -0.47 3 3
MAPK9 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.003 -10000 0 -10000 0 0
FKBP1A 0.026 0.006 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.004 0.11 0.33 1 -0.35 13 14
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0 0.035 -10000 0 -10000 0 0
CASP3 0.023 0.006 -10000 0 -10000 0 0
PIM1 0.027 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.006 0.013 -10000 0 -10000 0 0
apoptosis 0.016 0.023 0.19 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.049 0.18 2 -0.25 2 4
PRKCB -0.11 0.22 -10000 0 -0.47 112 112
PRKCE 0.027 0.006 -10000 0 -10000 0 0
JNK2/NFAT4 0.023 0.041 -10000 0 -0.33 3 3
BAD/BCL-XL 0.036 0.018 0.24 1 -10000 0 1
PRKCD 0.026 0.007 -10000 0 -10000 0 0
NUP214 0.024 0.008 -10000 0 -10000 0 0
PRKCZ 0.019 0.043 -10000 0 -0.47 3 3
PRKCA 0.022 0.049 -10000 0 -0.47 4 4
PRKCG 0.012 0.046 0.23 13 -10000 0 13
PRKCQ -0.011 0.13 0.24 4 -0.47 31 35
FKBP38/BCL2 0.024 0.071 -10000 0 -0.33 15 15
EP300 0.003 0.025 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
NFATc/JNK1 0.015 0.1 0.33 1 -0.33 10 11
CaM/Ca2+/FKBP38 0.009 0.027 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 -0.006 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.003 0.05 -10000 0 -0.29 8 8
NFATc/ERK1 0.022 0.095 0.31 2 -0.33 8 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.14 0.23 2 -0.35 36 38
NR4A1 -0.25 0.25 0.23 1 -0.46 226 227
GSK3B 0.022 0.007 -10000 0 -10000 0 0
positive T cell selection 0.011 0.034 -10000 0 -0.36 3 3
NFAT1/CK1 alpha -0.029 0.066 -10000 0 -0.22 13 13
RCH1/ KPNB1 0.041 0.017 0.24 1 -10000 0 1
YWHAQ 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -10000 0 -10000 0 0
AKAP5 0.029 0.019 0.21 4 -10000 0 4
MEF2D 0.004 0.024 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.021 0.012 -10000 0 -10000 0 0
NFATc/p38 alpha 0.019 0.098 0.34 1 -0.33 9 10
CREBBP 0.003 0.024 -10000 0 -10000 0 0
BCL2 0.008 0.094 -10000 0 -0.47 15 15
EPHB forward 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
Ephrin A5/EPHB2 0.033 0.066 -10000 0 -0.28 13 13
cell-cell adhesion 0.011 0.06 0.22 25 -10000 0 25
Ephrin B/EPHB2/RasGAP 0.069 0.068 0.29 1 -0.25 9 10
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
SHC1 0.026 0.017 0.33 1 -10000 0 1
Ephrin B1/EPHB3 0.037 0.032 -10000 0 -0.28 2 2
Ephrin B1/EPHB1 0.016 0.078 -10000 0 -0.28 25 25
HRAS/GDP 0.005 0.086 -10000 0 -0.28 14 14
Ephrin B/EPHB1/GRB7 0.042 0.1 0.26 1 -0.25 37 38
Endophilin/SYNJ1 0.012 0.055 0.35 1 -0.23 9 10
KRAS 0.027 0.016 0.33 1 -10000 0 1
Ephrin B/EPHB1/Src 0.04 0.095 0.26 1 -0.25 33 34
endothelial cell migration 0.049 0.028 -10000 0 -0.24 1 1
GRB2 0.027 0.005 -10000 0 -10000 0 0
GRB7 0.028 0.084 0.31 14 -0.47 7 21
PAK1 0.012 0.065 0.35 1 -0.24 11 12
HRAS 0.025 0.008 -10000 0 -10000 0 0
RRAS 0.01 0.057 0.36 1 -0.24 11 12
DNM1 0.017 0.06 -10000 0 -0.47 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.003 0.084 0.35 1 -0.23 32 33
lamellipodium assembly -0.011 0.06 -10000 0 -0.22 25 25
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.008 0.079 -10000 0 -0.24 22 22
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
EPHB2 0.04 0.047 0.21 28 -10000 0 28
EPHB3 0.032 0.055 0.23 16 -0.47 2 18
EPHB1 -0.002 0.12 0.21 4 -0.47 25 29
EPHB4 0.027 0.004 -10000 0 -10000 0 0
mol:GDP -0.004 0.07 -10000 0 -0.29 13 13
Ephrin B/EPHB2 0.057 0.062 0.27 1 -0.25 9 10
Ephrin B/EPHB3 0.05 0.062 0.22 2 -0.25 11 13
JNK cascade 0.009 0.095 0.36 13 -0.25 25 38
Ephrin B/EPHB1 0.031 0.089 0.25 1 -0.25 33 34
RAP1/GDP 0.014 0.089 0.37 2 -0.3 5 7
EFNB2 0.028 0.018 0.27 2 -10000 0 2
EFNB3 0.017 0.082 0.21 8 -0.47 10 18
EFNB1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.039 0.082 0.27 1 -0.26 23 24
RAP1B 0.026 0.008 -10000 0 -10000 0 0
RAP1A 0.028 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.029 0.087 -10000 0 -0.26 15 15
Rap1/GTP 0.007 0.066 -10000 0 -0.24 5 5
axon guidance 0.033 0.065 -10000 0 -0.28 13 13
MAPK3 0.003 0.075 0.31 2 -0.3 5 7
MAPK1 0.003 0.075 0.2 7 -0.3 5 12
Rac1/GDP 0.003 0.088 0.36 1 -0.29 8 9
actin cytoskeleton reorganization -0.008 0.058 -10000 0 -0.24 6 6
CDC42/GDP 0.004 0.09 0.38 2 -0.27 13 15
PI3K 0.054 0.03 -10000 0 -0.24 1 1
EFNA5 0.011 0.088 0.21 1 -0.47 13 14
Ephrin B2/EPHB4 0.036 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.025 0.044 -10000 0 -0.22 8 8
CDC42 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.063 -10000 0 -0.24 4 4
PTK2 0.053 0.17 0.57 39 -10000 0 39
MAP4K4 0.009 0.095 0.36 13 -0.25 25 38
SRC 0.026 0.007 -10000 0 -10000 0 0
KALRN 0.026 0.04 0.21 4 -0.47 2 6
Intersectin/N-WASP 0.039 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis 0.016 0.092 0.29 15 -0.29 3 18
MAP2K1 0.003 0.074 -10000 0 -0.3 6 6
WASL 0.027 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.054 0.088 -10000 0 -0.26 25 25
cell migration 0.016 0.1 0.26 6 -0.35 6 12
NRAS 0.028 0.002 -10000 0 -10000 0 0
SYNJ1 0.012 0.055 0.36 1 -0.24 9 10
PXN 0.027 0.004 -10000 0 -10000 0 0
TF -0.01 0.067 0.25 5 -0.24 16 21
HRAS/GTP 0.027 0.08 -10000 0 -0.22 29 29
Ephrin B1/EPHB1-2 0.039 0.083 -10000 0 -0.26 25 25
cell adhesion mediated by integrin 0.002 0.052 0.24 9 -0.19 12 21
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0.032 0.086 -10000 0 -0.23 33 33
RAC1-CDC42/GTP -0.007 0.064 -10000 0 -0.22 25 25
RASA1 0.027 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.014 0.089 0.35 1 -0.29 7 8
ruffle organization -0.005 0.088 0.37 3 -0.26 1 4
NCK1 0.026 0.006 -10000 0 -10000 0 0
receptor internalization -0.008 0.061 0.27 2 -0.24 12 14
Ephrin B/EPHB2/KALRN 0.068 0.072 0.29 1 -0.25 11 12
ROCK1 0.023 0.046 0.19 23 -0.26 2 25
RAS family/GDP -0.013 0.054 -10000 0 -0.25 5 5
Rac1/GTP 0.001 0.066 -10000 0 -0.23 25 25
Ephrin B/EPHB1/Src/Paxillin 0.005 0.076 -10000 0 -0.24 32 32
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.008 -10000 0 -10000 0 0
EGFR 0.021 0.085 0.33 8 -0.47 9 17
EGF/EGFR 0.013 0.11 -10000 0 -0.24 55 55
EGF/EGFR dimer/SHC/GRB2/SOS1 0.074 0.057 0.35 1 -0.24 3 4
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.037 0.16 -10000 0 -0.47 52 52
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.034 0.047 0.21 24 -10000 0 24
EGF/EGFR dimer/SHC 0.052 0.063 0.25 8 -0.29 7 15
mol:GDP 0.066 0.054 0.32 1 -0.24 3 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.026 0.052 0.28 5 -0.47 3 8
GRB2/SOS1 0.039 0.01 -10000 0 -10000 0 0
HRAS/GTP 0.04 0.039 0.22 1 -0.23 3 4
SHC1 0.026 0.017 0.33 1 -10000 0 1
HRAS/GDP 0.058 0.052 0.28 1 -0.23 3 4
FRAP1 -0.006 0.035 0.16 11 -0.23 3 14
EGF/EGFR dimer 0.04 0.071 0.24 7 -0.34 9 16
SOS1 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.009 0.13 0.24 3 -0.34 51 54
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.026 0.01 -10000 0 -10000 0 0
HSPA8 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.02 0.14 -10000 0 -0.32 66 66
AKT1 0.027 0.017 -10000 0 -10000 0 0
GSC 0.02 0.062 -10000 0 -10000 0 0
NKX2-5 -0.001 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.004 0.11 0.54 7 -10000 0 7
SMAD2-3/SMAD4/SP1 0.058 0.1 -10000 0 -0.31 13 13
SMAD4 0.009 0.054 -10000 0 -0.22 4 4
CBFB 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.027 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.051 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.056 0.07 -10000 0 -0.37 2 2
MYC -0.002 0.1 -10000 0 -0.47 18 18
CDKN2B -0.14 0.3 -10000 0 -1.1 18 18
AP1 -0.05 0.17 -10000 0 -0.5 27 27
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.024 0.071 -10000 0 -0.35 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.008 0.079 -10000 0 -0.36 11 11
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.006 -10000 0 -10000 0 0
FOXH1 0.074 0.091 0.24 89 -10000 0 89
SMAD3/SMAD4/GR 0.017 0.092 -10000 0 -0.33 14 14
GATA3 -0.008 0.12 0.33 2 -0.45 26 28
SKI/SIN3/HDAC complex/NCoR1 0.019 0.058 -10000 0 -0.42 3 3
MEF2C/TIF2 0.013 0.11 0.32 2 -0.4 16 18
endothelial cell migration -0.015 0.15 1.2 6 -10000 0 6
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.028 0.002 -10000 0 -10000 0 0
RUNX2 0.028 0.031 0.21 4 -0.47 1 5
RUNX3 0.01 0.091 -10000 0 -0.47 14 14
RUNX1 0.027 0.006 -10000 0 -10000 0 0
CTBP1 0.027 0.016 0.33 1 -10000 0 1
NR3C1 0.012 0.081 -10000 0 -0.47 11 11
VDR 0.026 0.038 0.33 1 -0.47 2 3
CDKN1A 0.005 0.12 -10000 0 -1 3 3
KAT2B 0.024 0.026 -10000 0 -0.47 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.08 0.08 0.26 10 -0.25 5 15
DCP1A 0.026 0.007 -10000 0 -10000 0 0
SKI 0.028 0.003 -10000 0 -10000 0 0
SERPINE1 0.014 0.15 -10000 0 -1.2 6 6
SMAD3/SMAD4/ATF2 0.029 0.07 -10000 0 -0.24 2 2
SMAD3/SMAD4/ATF3 -0.025 0.15 -10000 0 -0.33 72 72
SAP30 0.027 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.044 0.025 -10000 0 -10000 0 0
JUN -0.06 0.16 -10000 0 -0.5 27 27
SMAD3/SMAD4/IRF7 0.035 0.077 -10000 0 -0.29 3 3
TFE3 0.031 0.015 -10000 0 -0.19 1 1
COL1A2 -0.02 0.24 -10000 0 -0.9 27 27
mesenchymal cell differentiation -0.029 0.072 0.24 4 -10000 0 4
DLX1 0.041 0.059 0.21 41 -10000 0 41
TCF3 0.027 0.005 -10000 0 -10000 0 0
FOS -0.13 0.23 -10000 0 -0.48 124 124
SMAD3/SMAD4/Max 0.025 0.07 -10000 0 -0.25 2 2
Cbp/p300/SNIP1 0.049 0.02 -10000 0 -10000 0 0
ZBTB17 0.026 0.007 -10000 0 -10000 0 0
LAMC1 0.01 0.056 -10000 0 -0.53 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.028 0.067 -10000 0 -0.23 3 3
IRF7 0.031 0.043 0.22 13 -0.47 1 14
ESR1 -0.052 0.18 -10000 0 -0.46 66 66
HNF4A 0.035 0.065 0.22 40 -10000 0 40
MEF2C 0.022 0.1 0.33 2 -0.45 12 14
SMAD2-3/SMAD4 0.041 0.074 -10000 0 -0.26 6 6
Cbp/p300/Src-1 0.048 0.022 -10000 0 -10000 0 0
IGHV3OR16-13 -0.001 0.064 -10000 0 -0.34 13 13
TGIF2/HDAC complex 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.025 0.009 -10000 0 -10000 0 0
SKIL 0.027 0.016 0.33 1 -10000 0 1
HDAC1 0.028 0.002 -10000 0 -10000 0 0
HDAC2 0.026 0.007 -10000 0 -10000 0 0
SNIP1 0.027 0.003 -10000 0 -10000 0 0
GCN5L2 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.046 0.069 -10000 0 -0.28 2 2
MSG1/HSC70 0.041 0.021 -10000 0 -10000 0 0
SMAD2 0.027 0.025 -10000 0 -10000 0 0
SMAD3 0.007 0.053 -10000 0 -0.2 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.04 -10000 0 -0.23 1 1
SMAD2/SMAD2/SMAD4 0.006 0.061 0.23 4 -0.24 4 8
NCOR1 0.025 0.009 -10000 0 -10000 0 0
NCOA2 0 0.11 -10000 0 -0.47 20 20
NCOA1 0.027 0.006 -10000 0 -10000 0 0
MYOD/E2A 0.03 0.01 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.07 0.1 -10000 0 -0.33 10 10
IFNB1 0.004 0.048 -10000 0 -0.34 1 1
SMAD3/SMAD4/MEF2C 0.043 0.12 -10000 0 -0.47 12 12
CITED1 0.03 0.027 0.21 8 -10000 0 8
SMAD2-3/SMAD4/ARC105 0.055 0.072 -10000 0 -0.28 2 2
RBL1 0.027 0.019 0.27 2 -10000 0 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.013 0.11 -10000 0 -0.53 11 11
RUNX1-3/PEBPB2 0.04 0.061 -10000 0 -0.28 13 13
SMAD7 -0.032 0.16 -10000 0 -0.51 21 21
MYC/MIZ-1 0.013 0.08 -10000 0 -0.34 18 18
SMAD3/SMAD4 0.004 0.074 -10000 0 -0.44 6 6
IL10 -0.006 0.15 -10000 0 -0.44 28 28
PIASy/HDAC complex 0.027 0.006 -10000 0 -10000 0 0
PIAS3 0.024 0.01 -10000 0 -10000 0 0
CDK2 0.026 0.008 -10000 0 -10000 0 0
IL5 -0.001 0.12 -10000 0 -0.3 24 24
CDK4 0.027 0.017 0.33 1 -10000 0 1
PIAS4 0.027 0.006 -10000 0 -10000 0 0
ATF3 -0.059 0.19 -10000 0 -0.47 70 70
SMAD3/SMAD4/SP1 0.039 0.095 -10000 0 -0.31 14 14
FOXG1 0.021 0.076 0.21 51 -10000 0 51
FOXO3 0.015 0.017 -10000 0 -10000 0 0
FOXO1 0.014 0.025 -10000 0 -0.35 1 1
FOXO4 0.016 0.018 -10000 0 -10000 0 0
heart looping 0.022 0.1 0.33 2 -0.44 12 14
CEBPB 0.024 0.028 -10000 0 -0.47 1 1
SMAD3/SMAD4/DLX1 0.04 0.081 -10000 0 -0.23 3 3
MYOD1 -0.016 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.037 0.08 0.26 1 -0.23 4 5
SMAD3/SMAD4/GATA3 0.006 0.12 -10000 0 -0.31 41 41
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.016 0.33 1 -10000 0 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.049 0.089 -10000 0 -0.3 13 13
SMAD3/SMAD4/SP1-3 0.056 0.092 -10000 0 -0.3 8 8
MED15 0.027 0.006 -10000 0 -10000 0 0
SP1 0.023 0.042 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.077 0.087 0.25 6 -0.3 9 15
ITGB5 0.009 0.068 -10000 0 -0.32 3 3
TGIF/SIN3/HDAC complex/CtBP 0.031 0.049 -10000 0 -0.4 2 2
SMAD3/SMAD4/AR -0.092 0.17 -10000 0 -0.31 145 145
AR -0.15 0.24 -10000 0 -0.47 145 145
negative regulation of cell growth -0.011 0.09 -10000 0 -0.34 9 9
SMAD3/SMAD4/MYOD 0.018 0.069 -10000 0 -0.24 3 3
E2F5 0.023 0.03 0.21 2 -0.47 1 3
E2F4 0.027 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.092 0.082 -10000 0 -0.26 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.018 0.077 -10000 0 -0.38 11 11
TFDP1 0.026 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.036 0.18 -10000 0 -0.5 27 27
SMAD3/SMAD4/RUNX2 0.029 0.072 -10000 0 -0.24 4 4
TGIF2 0.026 0.007 -10000 0 -10000 0 0
TGIF1 0.025 0.008 -10000 0 -10000 0 0
ATF2 0.027 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.014 0.015 0.3 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.032 0.025 0.22 1 -10000 0 1
CDKN1B 0.019 0.052 -10000 0 -0.29 6 6
CDKN1A 0.015 0.057 -10000 0 -0.29 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.008 -10000 0 -10000 0 0
FOXO3 0.02 0.037 -10000 0 -0.28 3 3
AKT1 0.011 0.038 -10000 0 -0.28 6 6
BAD 0.027 0.003 -10000 0 -10000 0 0
AKT3 0.004 0.059 -10000 0 -0.3 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.017 0.053 -10000 0 -0.29 7 7
AKT1/ASK1 0.039 0.064 -10000 0 -0.28 8 8
BAD/YWHAZ 0.042 0.025 -10000 0 -10000 0 0
RICTOR 0.024 0.009 -10000 0 -10000 0 0
RAF1 0.025 0.018 0.33 1 -10000 0 1
JNK cascade -0.036 0.061 0.27 8 -10000 0 8
TSC1 0.017 0.049 -10000 0 -0.28 6 6
YWHAZ 0.021 0.012 -10000 0 -10000 0 0
AKT1/RAF1 0.039 0.062 -10000 0 -0.29 6 6
EP300 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.018 0.056 -10000 0 -0.28 11 11
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.018 0.049 -10000 0 -0.29 6 6
YWHAQ 0.026 0.006 -10000 0 -10000 0 0
TBC1D4 0.013 0.033 0.24 8 -10000 0 8
MAP3K5 0.025 0.025 -10000 0 -0.47 1 1
MAPKAP1 0.025 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.053 0.066 0.32 2 -0.22 11 13
YWHAH 0.027 0.006 -10000 0 -10000 0 0
AKT1S1 0.017 0.052 -10000 0 -0.29 7 7
CASP9 0.017 0.055 -10000 0 -0.29 8 8
YWHAB 0.025 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.041 0.068 0.25 1 -0.27 8 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.049 0.02 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.058 0.25 3 -0.31 2 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.029 -10000 0 -0.26 2 2
CHUK 0.019 0.044 -10000 0 -0.28 5 5
BAD/BCL-XL 0.038 0.061 0.27 1 -0.28 5 6
mTORC2 0.027 0.015 -10000 0 -10000 0 0
AKT2 0.015 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.059 0.082 0.26 13 -0.35 3 16
PDPK1 0.026 0.006 -10000 0 -10000 0 0
MDM2 0.029 0.071 0.26 3 -0.28 8 11
MAPKKK cascade -0.039 0.061 0.28 6 -10000 0 6
MDM2/Cbp/p300 0.064 0.08 0.29 3 -0.27 5 8
TSC1/TSC2 0.018 0.044 0.24 1 -0.28 4 5
proteasomal ubiquitin-dependent protein catabolic process 0.061 0.077 0.28 3 -0.26 5 8
glucose import -0.14 0.13 0.21 1 -0.25 236 237
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.021 0.041 0.2 3 -0.18 2 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.14 0.13 0.21 1 -0.25 236 237
GSK3A 0.02 0.057 -10000 0 -0.29 7 7
FOXO1 0.015 0.053 -10000 0 -0.28 8 8
GSK3B 0.02 0.061 -10000 0 -0.29 8 8
SFN 0.038 0.067 0.21 32 -0.47 3 35
G1/S transition of mitotic cell cycle 0.031 0.071 0.25 4 -0.28 7 11
p27Kip1/14-3-3 family 0.033 0.045 0.24 1 -0.33 1 2
PRKACA 0.027 0.003 -10000 0 -10000 0 0
KPNA1 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.027 0.003 -10000 0 -10000 0 0
RHEB 0.027 0.003 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
IL1-mediated 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
UBC13/UEV1A 0.02 0.003 -10000 0 -10000 0 0
PRKCZ 0.024 0.043 -10000 0 -0.47 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.017 0.049 -10000 0 -0.25 2 2
IRAK/TOLLIP 0.029 0.011 -10000 0 -10000 0 0
IKBKB 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.027 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.027 0.13 0.28 9 -0.34 40 49
IL1A 0.004 0.15 0.22 40 -0.47 34 74
IL1B -0.005 0.094 0.43 2 -0.35 25 27
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.04 -10000 0 -0.23 3 3
IL1R2 0.035 0.087 0.22 37 -0.47 7 44
IL1R1 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.067 0.24 1 -0.29 4 5
TOLLIP 0.025 0.008 -10000 0 -10000 0 0
TICAM2 0.025 0.026 -10000 0 -0.47 1 1
MAP3K3 0.026 0.006 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.027 0.063 -10000 0 -0.3 1 1
JUN -0.011 0.051 0.16 10 -0.21 18 28
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.047 0.081 -10000 0 -0.24 23 23
IL1 alpha/IL1R1/IL1RAP/MYD88 0.05 0.1 0.27 5 -0.26 32 37
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.059 0.1 0.32 2 -0.24 32 34
IL1 beta fragment/IL1R1/IL1RAP 0.028 0.08 0.22 4 -0.27 23 27
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.003 0.042 0.17 12 -0.22 7 19
IRAK1 0.015 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.04 0.041 -10000 0 -0.3 4 4
IRAK4 0.027 0.004 -10000 0 -10000 0 0
PRKCI 0.026 0.007 -10000 0 -10000 0 0
TRAF6 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.035 0.023 -10000 0 -0.34 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.059 0.29 1 -0.27 4 5
CHUK 0.027 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.028 0.08 0.22 4 -0.27 23 27
IL1 beta/IL1R2 0.017 0.1 0.22 3 -0.31 31 34
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.033 0.071 -10000 0 -0.23 23 23
IRAK3 0.013 0.081 -10000 0 -0.47 11 11
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.05 0.08 0.26 1 -0.24 22 23
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.075 0.2 1 -0.22 33 34
IL1 alpha/IL1R1/IL1RAP 0.038 0.11 0.27 5 -0.28 33 38
RELA 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
MYD88 0.026 0.006 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.024 -10000 0 -10000 0 0
IL1RAP 0.032 0.035 0.23 11 -10000 0 11
UBE2N 0.027 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.019 0.06 -10000 0 -0.21 22 22
CASP1 0.015 0.073 -10000 0 -0.47 9 9
IL1RN/IL1R2 0.046 0.078 0.28 3 -0.37 9 12
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.04 0.08 0.24 3 -0.25 22 25
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.077 -10000 0 -0.32 6 6
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
IL1RN 0.029 0.053 0.21 11 -0.47 3 14
TRAF6/TAK1/TAB1/TAB2 0.036 0.014 -10000 0 -10000 0 0
MAP2K6 0.017 0.041 0.18 13 -0.23 5 18
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.11 0.13 0.59 1 -10000 0 1
PCK1 0.11 0.1 -10000 0 -10000 0 0
HNF4A 0.14 0.16 0.61 11 -10000 0 11
KCNJ11 0.097 0.24 -10000 0 -0.83 19 19
AKT1 0.094 0.11 0.33 1 -0.54 1 2
response to starvation 0.006 0.007 -10000 0 -10000 0 0
DLK1 0.096 0.26 0.62 2 -0.85 20 22
NKX2-1 0.18 0.17 0.38 120 -10000 0 120
ACADM 0.11 0.14 -10000 0 -0.8 1 1
TAT 0.1 0.1 -10000 0 -10000 0 0
CEBPB 0.028 0.026 -10000 0 -0.46 1 1
CEBPA 0.035 0.05 0.25 10 -0.47 2 12
TTR 0.092 0.17 0.54 10 -10000 0 10
PKLR 0.13 0.15 0.57 3 -10000 0 3
APOA1 0.16 0.17 0.66 3 -10000 0 3
CPT1C 0.11 0.14 0.52 2 -0.66 2 4
ALAS1 0.11 0.11 -10000 0 -10000 0 0
TFRC 0.15 0.13 0.53 1 -10000 0 1
FOXF1 -0.14 0.24 -10000 0 -0.47 140 140
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.048 0.028 0.23 5 -10000 0 5
CPT1A 0.12 0.15 0.58 4 -1 1 5
HMGCS1 0.14 0.16 0.56 9 -0.51 1 10
NR3C1 0.025 0.082 -10000 0 -0.46 11 11
CPT1B 0.11 0.14 -10000 0 -1 1 1
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.014 -10000 0 -10000 0 0
GCK 0.072 0.26 -10000 0 -0.8 27 27
CREB1 0.033 0.011 -10000 0 -10000 0 0
IGFBP1 0.097 0.098 -10000 0 -10000 0 0
PDX1 0.14 0.12 -10000 0 -10000 0 0
UCP2 0.12 0.14 0.58 2 -10000 0 2
ALDOB 0.13 0.16 0.54 1 -0.56 1 2
AFP 0.012 0.092 -10000 0 -10000 0 0
BDH1 0.12 0.14 0.52 2 -10000 0 2
HADH 0.13 0.16 0.69 1 -10000 0 1
F2 0.15 0.17 0.65 3 -10000 0 3
HNF1A 0.048 0.028 0.23 5 -10000 0 5
G6PC 0.061 0.062 -10000 0 -10000 0 0
SLC2A2 0.13 0.12 -10000 0 -10000 0 0
INS -0.028 0.011 -10000 0 -10000 0 0
FOXA1 -0.009 0.16 -10000 0 -0.46 42 42
FOXA3 0.098 0.085 0.31 25 -10000 0 25
FOXA2 0.18 0.2 0.67 2 -0.63 1 3
ABCC8 0.12 0.15 -10000 0 -10000 0 0
ALB 0.018 0.095 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.078 0.063 0.32 2 -10000 0 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.028 0.014 0.21 2 -10000 0 2
STAT1 (dimer)/Cbp/p300 0.064 0.051 0.3 5 -10000 0 5
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 0.063 -10000 0 -0.22 8 8
CaM/Ca2+ 0.075 0.058 0.29 2 -10000 0 2
RAP1A 0.028 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.041 0.041 0.29 1 -10000 0 1
AKT1 0.035 0.075 0.31 14 -10000 0 14
MAP2K1 0.021 0.057 0.29 7 -10000 0 7
MAP3K11 0.025 0.057 0.29 7 -10000 0 7
IFNGR1 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.077 0.19 -10000 0 -0.36 114 114
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.036 0.017 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.081 0.066 0.29 2 -10000 0 2
CEBPB 0.048 0.1 0.34 2 -0.57 5 7
STAT3 0.027 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.073 0.12 -10000 0 -0.68 7 7
STAT1 0.026 0.056 0.29 6 -10000 0 6
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.066 0.085 0.23 81 -10000 0 81
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.048 0.055 0.29 8 -10000 0 8
CEBPB/PTGES2/Cbp/p300 0.03 0.058 -10000 0 -0.34 5 5
mol:Ca2+ 0.072 0.06 0.31 2 -10000 0 2
MAPK3 0.031 0.097 -10000 0 -0.71 4 4
STAT1 (dimer) -0.003 0.088 -10000 0 -0.32 6 6
MAPK1 0.028 0.11 -10000 0 -0.74 5 5
JAK2 0.026 0.012 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
JAK1 0.03 0.008 -10000 0 -10000 0 0
CAMK2D 0.025 0.035 -10000 0 -0.47 2 2
DAPK1 0.041 0.091 0.33 1 -0.52 6 7
SMAD7 0.012 0.053 0.19 10 -0.17 3 13
CBL/CRKL/C3G 0.053 0.051 0.28 5 -10000 0 5
PI3K 0.064 0.056 0.26 2 -0.24 1 3
IFNG 0.066 0.085 0.23 81 -10000 0 81
apoptosis 0.03 0.092 0.27 1 -0.39 13 14
CAMK2G 0.027 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.004 -10000 0 -10000 0 0
CAMK2A -0.12 0.22 -10000 0 -0.47 119 119
CAMK2B 0.046 0.062 0.22 43 -10000 0 43
FRAP1 0.023 0.074 0.3 14 -10000 0 14
PRKCD 0.035 0.075 0.31 14 -10000 0 14
RAP1B 0.026 0.008 -10000 0 -10000 0 0
negative regulation of cell growth -0.009 0.063 -10000 0 -0.22 8 8
PTPN2 0.026 0.007 -10000 0 -10000 0 0
EP300 0.027 0.006 -10000 0 -10000 0 0
IRF1 0.025 0.049 0.26 5 -10000 0 5
STAT1 (dimer)/PIASy 0.045 0.055 0.28 8 -10000 0 8
SOCS1 0.008 0.14 -10000 0 -1 7 7
mol:GDP 0.048 0.046 0.27 4 -10000 0 4
CASP1 0.008 0.061 0.18 9 -0.25 8 17
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 0.031 0.036 0.16 3 -0.16 2 5
mol:PI-3-4-5-P3 0.045 0.043 -10000 0 -0.24 1 1
RAP1/GDP 0.038 0.028 -10000 0 -10000 0 0
CBL 0.023 0.056 0.29 6 -10000 0 6
MAP3K1 0.024 0.055 0.29 6 -10000 0 6
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.027 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.009 0.063 -10000 0 -0.22 8 8
PTPN11 0.023 0.053 0.3 4 -10000 0 4
CREBBP 0.026 0.007 -10000 0 -10000 0 0
RAPGEF1 0.025 0.009 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.027 0.006 -10000 0 -10000 0 0
HDAC4 0.025 0.008 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.018 0.051 -10000 0 -0.31 11 11
CDKN1A -0.01 0.048 -10000 0 -0.69 2 2
KAT2B 0.025 0.025 -10000 0 -0.47 1 1
BAX 0.027 0.004 -10000 0 -10000 0 0
FOXO3 -0.006 0.003 -10000 0 -10000 0 0
FOXO1 0.024 0.026 -10000 0 -0.47 1 1
FOXO4 0.016 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.027 0.005 -10000 0 -10000 0 0
TAT 0.019 0.046 0.21 17 -10000 0 17
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.012 0.017 -10000 0 -0.34 1 1
PPARGC1A -0.18 0.24 0.21 1 -0.47 164 165
FHL2 0.023 0.043 -10000 0 -0.47 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.012 -10000 0 -10000 0 0
HIST2H4A 0.018 0.051 0.31 11 -10000 0 11
SIRT1/FOXO3a 0.017 0.022 -10000 0 -10000 0 0
SIRT1 0.025 0.013 0.2 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.046 0.021 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.023 0.047 -10000 0 -0.2 6 6
apoptosis -0.05 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A -0.097 0.16 -10000 0 -0.28 164 164
p53/SIRT1 0.029 0.028 0.39 2 -10000 0 2
SIRT1/FOXO4 0.017 0.046 -10000 0 -0.2 7 7
FOXO1/FHL2/SIRT1 0.043 0.034 -10000 0 -0.24 4 4
HIST1H1E 0.018 0.022 0.21 3 -10000 0 3
SIRT1/p300 0.037 0.013 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.023 0.29 1 -0.22 1 2
TP53 0.023 0.015 0.2 2 -10000 0 2
KU70/SIRT1/BAX 0.051 0.016 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
MEF2D 0.026 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.039 0.029 -10000 0 -10000 0 0
ACSS2 0.013 0.017 0.19 3 -10000 0 3
SIRT1/PCAF/MYOD 0.029 0.023 0.22 1 -0.29 1 2
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.002 0.1 -10000 0 -0.41 17 17
KLHL20 0.009 0.086 0.2 3 -0.2 34 37
CYFIP2 0.014 0.077 -10000 0 -0.47 10 10
Rac1/GDP 0.026 0.092 0.27 10 -0.26 11 21
ENAH 0.003 0.1 -10000 0 -0.35 29 29
AP1M1 0.027 0.004 -10000 0 -10000 0 0
RAP1B 0.026 0.008 -10000 0 -10000 0 0
RAP1A 0.028 0.003 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.017 0.046 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.021 0.045 -10000 0 -0.14 36 36
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.073 -10000 0 -0.27 17 17
RAPGEF1 0.013 0.1 0.26 7 -0.36 17 24
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.11 -10000 0 -0.35 30 30
CRK 0.009 0.097 -10000 0 -0.39 16 16
E-cadherin/gamma catenin/alpha catenin 0.037 0.068 -10000 0 -0.3 14 14
alphaE/beta7 Integrin 0.032 0.043 -10000 0 -0.33 5 5
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.046 0.019 -10000 0 -10000 0 0
DLG1 0.003 0.098 -10000 0 -0.34 27 27
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.029 -10000 0 -10000 0 0
MLLT4 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.046 0.032 -10000 0 -0.26 3 3
PI3K 0.003 0.038 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.024 0.074 -10000 0 -0.36 14 14
TIAM1 0.023 0.043 -10000 0 -0.47 3 3
E-cadherin(dimer)/Ca2+ 0.047 0.058 -10000 0 -0.24 13 13
AKT1 0.016 0.039 0.15 1 -10000 0 1
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
CDH1 0.01 0.087 -10000 0 -0.47 13 13
RhoA/GDP 0.027 0.093 0.28 10 -0.26 13 23
actin cytoskeleton organization 0.01 0.067 0.16 7 -0.15 34 41
CDC42/GDP 0.028 0.095 0.27 11 -0.26 13 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.01 0.051 -10000 0 -0.24 14 14
ITGB7 0.021 0.055 -10000 0 -0.47 5 5
RAC1 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.051 0.062 -10000 0 -0.26 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.053 -10000 0 -0.24 13 13
mol:GDP 0.014 0.1 0.28 11 -0.3 13 24
CDC42/GTP/IQGAP1 0.036 0.007 -10000 0 -10000 0 0
JUP 0.024 0.035 -10000 0 -0.47 2 2
p120 catenin/RhoA/GDP 0.031 0.092 0.28 7 -0.26 13 20
RAC1/GTP/IQGAP1 0.035 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.04 0.008 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
CDC42 0.028 0.003 -10000 0 -10000 0 0
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.055 0.15 13 -0.17 8 21
NME1 0.027 0.011 0.21 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.005 0.098 -10000 0 -0.36 25 25
regulation of cell-cell adhesion 0.01 0.039 -10000 0 -10000 0 0
WASF2 0.006 0.037 -10000 0 -10000 0 0
Rap1/GTP 0.027 0.062 0.28 2 -10000 0 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.078 -10000 0 -0.27 18 18
CCND1 0.013 0.064 0.16 12 -0.21 8 20
VAV2 -0.028 0.2 -10000 0 -0.56 38 38
RAP1/GDP 0.031 0.077 0.28 6 -10000 0 6
adherens junction assembly 0.006 0.095 -10000 0 -0.35 25 25
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.007 -10000 0 -10000 0 0
PIP5K1C 0.027 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.04 0.074 -10000 0 -0.26 18 18
E-cadherin/beta catenin 0.002 0.062 -10000 0 -0.32 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.002 0.1 -10000 0 -0.4 19 19
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.039 0.1 -10000 0 -0.32 35 35
E-cadherin/beta catenin/alpha catenin 0.039 0.062 -10000 0 -0.28 13 13
ITGAE 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.002 0.11 -10000 0 -0.36 30 30
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.026 0.006 -10000 0 -10000 0 0
ITGB7 0.021 0.055 -10000 0 -0.47 5 5
ITGA4 0.013 0.085 0.21 1 -0.47 12 13
alpha4/beta7 Integrin 0.024 0.076 -10000 0 -0.34 17 17
alpha4/beta1 Integrin 0.027 0.065 -10000 0 -0.34 12 12
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.026 0.017 0.33 1 -10000 0 1
Syndecan-3/Src/Cortactin 0.018 0.12 -10000 0 -0.48 2 2
Syndecan-3/Neurocan 0.033 0.049 0.28 2 -0.4 3 5
POMC 0.025 0.063 0.21 10 -0.47 5 15
EGFR 0.021 0.085 0.33 8 -0.47 9 17
Syndecan-3/EGFR 0.03 0.058 0.26 3 -0.26 9 12
AGRP 0.008 0.031 0.25 3 -10000 0 3
NCSTN 0.024 0.01 -10000 0 -10000 0 0
PSENEN 0.026 0.006 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.009 -10000 0 -10000 0 0
NCAN 0.013 0.042 0.22 11 -10000 0 11
long-term memory 0.045 0.057 0.25 1 -0.55 2 3
Syndecan-3/IL8 0 0.096 -10000 0 -0.25 41 41
PSEN1 0.027 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.035 0.018 0.24 1 -10000 0 1
FYN 0.022 0.043 -10000 0 -0.47 3 3
limb bud formation 0.01 0.036 -10000 0 -0.49 2 2
MC4R 0.002 0.031 0.21 5 -10000 0 5
SRC 0.026 0.007 -10000 0 -10000 0 0
PTN -0.062 0.21 0.21 20 -0.47 80 100
FGFR/FGF/Syndecan-3 0.01 0.037 -10000 0 -0.49 2 2
neuron projection morphogenesis 0 0.11 0.34 3 -0.47 2 5
Syndecan-3/AgRP 0.028 0.044 -10000 0 -0.39 3 3
Syndecan-3/AgRP/MC4R 0.045 0.052 0.31 1 -0.47 2 3
Fyn/Cortactin 0.033 0.032 0.24 1 -0.34 2 3
SDC3 0.01 0.037 -10000 0 -0.5 2 2
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0 0.095 -10000 0 -0.24 41 41
IL8 -0.041 0.17 0.21 1 -0.47 56 57
Syndecan-3/Fyn/Cortactin 0.046 0.059 0.26 1 -0.56 2 3
Syndecan-3/CASK 0.008 0.037 -10000 0 -0.39 3 3
alpha-MSH/MC4R 0.032 0.049 -10000 0 -0.34 5 5
Gamma Secretase 0.062 0.036 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.023 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.032 0.079 -10000 0 -0.36 4 4
NEF -0.007 0.051 -10000 0 -0.21 20 20
NFKBIA 0.022 0.03 -10000 0 -10000 0 0
BIRC3 0.004 0.12 -10000 0 -0.46 21 21
CYCS 0.021 0.086 0.21 12 -0.27 15 27
RIPK1 0.026 0.007 -10000 0 -10000 0 0
CD247 0.013 0.071 0.21 1 -0.26 21 22
MAP2K7 0.027 0.13 -10000 0 -0.57 12 12
protein ubiquitination 0.026 0.076 0.23 2 -0.36 2 4
CRADD 0.027 0.004 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.02 0.055 -10000 0 -0.47 5 5
BID 0.019 0.085 0.19 24 -0.28 17 41
NF-kappa-B/RelA/I kappa B alpha 0.046 0.07 -10000 0 -0.26 17 17
TRADD 0.027 0.006 -10000 0 -10000 0 0
MAP3K5 0.025 0.025 -10000 0 -0.47 1 1
CFLAR 0.027 0.006 -10000 0 -10000 0 0
FADD 0.03 0.037 0.33 6 -10000 0 6
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.046 0.07 -10000 0 -0.27 17 17
MAPK8 0.027 0.13 0.31 2 -0.57 10 12
APAF1 0.027 0.004 -10000 0 -10000 0 0
TRAF1 0.023 0.037 0.21 1 -0.47 2 3
TRAF2 0.025 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.089 0.2 23 -0.28 19 42
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.084 0.26 1 -0.37 6 7
CHUK 0.026 0.078 0.24 2 -0.39 2 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.065 0.055 -10000 0 -0.3 4 4
TCRz/NEF 0.009 0.074 0.15 1 -0.3 21 22
TNF 0.036 0.042 0.21 21 -10000 0 21
FASLG -0.006 0.12 0.31 1 -0.49 21 22
NFKB1 0.022 0.03 -10000 0 -0.15 2 2
TNFR1A/BAG4/TNF-alpha 0.05 0.035 -10000 0 -10000 0 0
CASP6 0.028 0.13 -10000 0 -0.5 17 17
CASP7 0.015 0.15 0.32 3 -0.46 24 27
RELA 0.023 0.028 -10000 0 -10000 0 0
CASP2 0.027 0.004 -10000 0 -10000 0 0
CASP3 0.015 0.15 0.32 3 -0.45 27 30
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.033 0.016 -10000 0 -10000 0 0
CASP8 0.026 0.006 -10000 0 -10000 0 0
CASP9 0.027 0.003 -10000 0 -10000 0 0
MAP3K14 0.026 0.086 0.25 1 -0.41 3 4
APAF-1/Caspase 9 0.015 0.1 -10000 0 -0.36 17 17
BCL2 0.018 0.12 0.3 2 -0.51 12 14
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.29 0.23 -10000 0 -0.47 259 259
CLTC 0.019 0.07 -10000 0 -0.39 9 9
calcium ion-dependent exocytosis 0.014 0.03 0.21 2 -10000 0 2
Dynamin 2/GTP 0.027 0.008 -10000 0 -10000 0 0
EXOC4 0.027 0.005 -10000 0 -10000 0 0
CD59 0.014 0.047 -10000 0 -0.31 7 7
CPE 0.004 0.055 -10000 0 -0.28 14 14
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
membrane fusion 0.015 0.017 -10000 0 -10000 0 0
CTNND1 0.019 0.033 0.19 15 -10000 0 15
DNM2 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.017 0.051 0.2 2 -0.28 5 7
TSHR 0.01 0.016 -10000 0 -10000 0 0
INS -0.021 0.13 -10000 0 -0.47 30 30
BIN1 -0.033 0.16 -10000 0 -0.47 49 49
mol:Choline 0.015 0.017 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.006 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.008 -10000 0 -10000 0 0
JUP 0.012 0.05 -10000 0 -0.3 8 8
ASAP2/amphiphysin II 0.012 0.099 -10000 0 -0.26 46 46
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.007 0.061 -10000 0 -0.31 8 8
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.027 0.031 0.21 4 -0.47 1 5
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.026 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.038 0.039 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.027 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.037 0.069 0.3 9 -0.26 1 10
positive regulation of phagocytosis 0.015 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.022 -10000 0 -0.28 1 1
ACAP1 0.017 0.027 -10000 0 -0.19 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.05 0.1 -10000 0 -0.39 9 9
clathrin heavy chain/ACAP1 0.022 0.063 0.25 2 -0.33 8 10
JIP4/KLC1 0.049 0.016 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.023 0.027 -10000 0 -10000 0 0
RALA/GTP 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.019 0.033 0.19 15 -10000 0 15
NME1 0.015 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0.023 0.073 0.27 1 -0.38 9 10
IL2RA 0.013 0.066 -10000 0 -0.3 7 7
VAMP3 0.015 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.11 -10000 0 -0.33 18 18
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.014 0.01 -10000 0 -10000 0 0
PLD2 0.015 0.011 0.13 1 -10000 0 1
EXOC5 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.015 0.034 0.2 1 -0.21 4 5
SDC1 0.012 0.052 -10000 0 -0.3 7 7
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.027 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.039 0.071 0.27 1 -0.31 9 10
mol:Phosphatidic acid 0.015 0.017 -10000 0 -10000 0 0
endocytosis -0.011 0.098 0.26 46 -10000 0 46
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 -0.006 0.095 -10000 0 -0.36 11 11
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ASAP2 0.027 0.006 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.01 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.001 0.1 0.25 1 -0.4 10 11
RALA 0.028 0.016 0.33 1 -10000 0 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.037 0.072 0.29 3 -0.3 7 10
Signaling events mediated by PRL

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
CCNE1 0.062 0.085 0.25 64 -10000 0 64
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.026 0.006 -10000 0 -10000 0 0
CDKN1A -0.005 0.073 -10000 0 -0.47 6 6
PRL-3/alpha Tubulin 0.036 0.013 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.1 -10000 0 -0.35 44 44
AGT -0.03 0.16 0.21 3 -0.47 48 51
CCNA2 -0.043 0.1 0.38 1 -10000 0 1
TUBA1B 0.027 0.003 -10000 0 -10000 0 0
EGR1 -0.061 0.14 -10000 0 -0.32 92 92
CDK2/Cyclin E1 0.043 0.1 0.35 3 -0.45 6 9
MAPK3 0.013 0.005 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.006 -10000 0 -10000 0 0
MAPK1 0.013 0.005 -10000 0 -10000 0 0
PTP4A1 -0.041 0.099 -10000 0 -10000 0 0
PTP4A3 0.025 0.009 -10000 0 -10000 0 0
PTP4A2 0.028 0.001 -10000 0 -10000 0 0
ITGB1 0.013 0.006 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1 0 0.048 -10000 0 -0.51 1 1
Rab GGTase beta/Rab GGTase alpha 0.039 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.021 0.11 -10000 0 -10000 0 0
RABGGTA 0.027 0.006 -10000 0 -10000 0 0
BCAR1 -0.016 0.007 -10000 0 -10000 0 0
RHOC 0.001 0.042 -10000 0 -10000 0 0
RHOA -0.008 0.078 -10000 0 -0.4 11 11
cell motility 0.007 0.08 0.29 2 -0.29 10 12
PRL-1/alpha Tubulin -0.021 0.11 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.035 0.015 -10000 0 -10000 0 0
ROCK1 0.01 0.077 0.29 2 -0.29 9 11
RABGGTB 0.027 0.004 -10000 0 -10000 0 0
CDK2 0.027 0.005 -10000 0 -10000 0 0
mitosis -0.041 0.099 -10000 0 -10000 0 0
ATF5 0.029 0.019 0.21 4 -10000 0 4
BARD1 signaling events

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
BARD1/CSTF1 0.028 0.057 -10000 0 -0.34 9 9
ATM 0.026 0.007 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.025 0.008 -10000 0 -10000 0 0
ATR 0.026 0.006 -10000 0 -10000 0 0
UBE2L3 0.027 0.006 -10000 0 -10000 0 0
FANCD2 0.022 0.024 0.24 4 -10000 0 4
protein ubiquitination 0.07 0.07 -10000 0 -0.25 8 8
XRCC5 0.026 0.007 -10000 0 -10000 0 0
XRCC6 0.027 0.005 -10000 0 -10000 0 0
M/R/N Complex 0.044 0.023 -10000 0 -10000 0 0
MRE11A 0.027 0.006 -10000 0 -10000 0 0
DNA-PK 0.047 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.005 0.14 -10000 0 -0.5 23 23
FANCF 0.025 0.027 0.21 1 -0.47 1 2
BRCA1 0.028 0.01 0.21 1 -10000 0 1
CCNE1 0.062 0.085 0.25 64 -10000 0 64
CDK2/Cyclin E1 0.061 0.057 0.24 19 -10000 0 19
FANCG 0.025 0.008 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.031 0.054 -10000 0 -0.34 8 8
FANCE 0.028 0.01 0.21 1 -10000 0 1
FANCC 0.025 0.013 0.21 1 -10000 0 1
NBN 0.023 0.01 -10000 0 -10000 0 0
FANCA 0.04 0.049 0.22 27 -10000 0 27
DNA repair 0.019 0.093 0.27 9 -0.36 9 18
BRCA1/BARD1/ubiquitin 0.031 0.054 -10000 0 -0.34 8 8
BARD1/DNA-PK 0.054 0.05 -10000 0 -0.26 7 7
FANCL 0.027 0.011 0.21 1 -10000 0 1
mRNA polyadenylation -0.028 0.056 0.34 9 -10000 0 9
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.055 -10000 0 -0.26 1 1
BRCA1/BACH1/BARD1/TopBP1 0.043 0.051 -10000 0 -0.28 8 8
BRCA1/BARD1/P53 0.051 0.053 -10000 0 -0.26 8 8
BARD1/CSTF1/BRCA1 0.042 0.051 -10000 0 -0.28 8 8
BRCA1/BACH1 0.028 0.01 0.21 1 -10000 0 1
BARD1 0.015 0.073 -10000 0 -0.47 9 9
PCNA 0.027 0.011 0.21 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.045 0.05 -10000 0 -0.28 8 8
BRCA1/BARD1/UbcH7 0.043 0.051 -10000 0 -0.28 8 8
BRCA1/BARD1/RAD51/PCNA 0.088 0.082 0.24 1 -0.27 8 9
BARD1/DNA-PK/P53 0.057 0.054 -10000 0 -0.24 7 7
BRCA1/BARD1/Ubiquitin 0.031 0.054 -10000 0 -0.34 8 8
BRCA1/BARD1/CTIP 0.034 0.046 -10000 0 -0.26 8 8
FA complex 0.021 0.065 0.22 2 -0.26 10 12
BARD1/EWS 0.029 0.056 -10000 0 -0.34 9 9
RBBP8 0.014 0.005 -10000 0 -10000 0 0
TP53 0.025 0.008 -10000 0 -10000 0 0
TOPBP1 0.027 0.006 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.049 0.052 0.26 8 -10000 0 8
BRCA1/BARD1 0.077 0.075 -10000 0 -0.25 8 8
CSTF1 0.026 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.052 -10000 0 -0.33 9 9
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.093 0.09 0.21 144 -10000 0 144
RAD50 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.031 0.054 -10000 0 -0.34 8 8
EWSR1 0.026 0.006 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.046 0.08 0.36 1 -10000 0 1
CRKL 0.025 0.052 0.29 4 -10000 0 4
mol:DAG 0.038 0.047 0.28 1 -10000 0 1
HRAS 0.042 0.077 0.31 15 -10000 0 15
MAPK8 0.029 0.064 0.22 23 -0.28 3 26
RAP1A 0.026 0.053 0.29 4 -10000 0 4
GAB1 0.026 0.052 0.29 4 -10000 0 4
MAPK14 0.032 0.059 0.22 25 -10000 0 25
EPO 0.042 0.057 0.23 31 -10000 0 31
PLCG1 0.039 0.047 0.28 1 -10000 0 1
EPOR/TRPC2/IP3 Receptors 0.033 0.031 0.24 8 -10000 0 8
RAPGEF1 0.025 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.031 0.11 0.23 1 -0.3 36 37
GAB1/SHC/GRB2/SOS1 0.052 0.047 0.27 2 -10000 0 2
EPO/EPOR (dimer) 0.053 0.044 0.21 5 -10000 0 5
IRS2 0.016 0.071 0.29 4 -0.24 14 18
STAT1 0.045 0.063 0.27 2 -10000 0 2
STAT5B 0.042 0.054 0.28 1 -10000 0 1
cell proliferation 0.02 0.071 0.22 31 -0.26 3 34
GAB1/SHIP/PIK3R1/SHP2/SHC 0.035 0.044 -10000 0 -0.28 1 1
TEC 0.026 0.052 0.29 4 -10000 0 4
SOCS3 -0.022 0.15 -10000 0 -0.47 40 40
STAT1 (dimer) 0.044 0.062 0.27 2 -10000 0 2
JAK2 0.025 0.013 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
EPO/EPOR (dimer)/JAK2 0.072 0.059 -10000 0 -10000 0 0
EPO/EPOR 0.053 0.044 0.21 5 -10000 0 5
LYN 0.025 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.038 0.048 0.28 2 -0.22 1 3
elevation of cytosolic calcium ion concentration 0.033 0.031 0.24 8 -10000 0 8
SHC1 0.026 0.017 0.33 1 -10000 0 1
EPO/EPOR (dimer)/LYN 0.063 0.045 0.24 1 -10000 0 1
mol:IP3 0.038 0.047 0.28 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.035 0.082 0.29 6 -0.31 5 11
SH2B3 0.028 0.011 -10000 0 -10000 0 0
NFKB1 0.032 0.059 0.22 25 -10000 0 25
EPO/EPOR (dimer)/JAK2/SOCS3 -0.006 0.075 0.19 1 -0.22 38 39
PTPN6 0.026 0.052 0.31 4 -10000 0 4
TEC/VAV2/GRB2 0.047 0.051 0.29 2 -10000 0 2
EPOR 0.033 0.032 0.24 8 -10000 0 8
INPP5D 0.018 0.06 -10000 0 -0.47 6 6
mol:GDP 0.051 0.048 0.27 2 -10000 0 2
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.039 0.21 3 -0.47 2 5
CRKL/CBL/C3G 0.047 0.049 0.29 2 -10000 0 2
VAV2 0.024 0.052 0.29 4 -0.22 1 5
CBL 0.026 0.051 0.29 4 -10000 0 4
SHC/Grb2/SOS1 0.037 0.038 -10000 0 -10000 0 0
STAT5A 0.041 0.057 0.28 1 -0.28 1 2
GRB2 0.027 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.056 0.079 0.29 1 -0.3 11 12
LYN/PLCgamma2 0.037 0.026 -10000 0 -0.34 1 1
PTPN11 0.027 0.005 -10000 0 -10000 0 0
BTK 0.014 0.077 0.29 4 -0.24 20 24
BCL2 0.031 0.18 0.37 2 -0.82 15 17
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.05 -10000 0 -0.24 8 8
FRAP1 0.016 0.047 -10000 0 -0.43 2 2
AKT1 0.004 0.057 0.2 2 -0.23 6 8
INSR 0.027 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.027 0.059 0.24 4 -0.21 1 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.012 0.02 -10000 0 -10000 0 0
TSC2 0.027 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.011 0.038 -10000 0 -0.19 2 2
TSC1 0.025 0.009 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.073 -10000 0 -0.22 37 37
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.026 0.028 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 0.025 0.051 0.24 2 -10000 0 2
MAP3K5 0.003 0.046 0.2 7 -0.19 14 21
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
apoptosis 0.004 0.046 0.2 7 -0.19 14 21
mol:LY294002 0 0 -10000 0 -0.001 36 36
EIF4B 0.024 0.05 0.26 4 -10000 0 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.045 0.24 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1 0.017 0.027 -10000 0 -0.26 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.02 0.067 -10000 0 -0.2 29 29
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.045 0.18 9 -10000 0 9
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
RHEB/GTP 0.03 0.052 0.22 2 -10000 0 2
mol:Amino Acids 0 0 -10000 0 -0.001 36 36
FKBP12/Rapamycin 0.02 0.005 -10000 0 -10000 0 0
PDPK1 -0.007 0.056 0.18 4 -0.25 6 10
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.023 0.11 -10000 0 -0.54 15 15
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.013 0.033 -10000 0 -0.22 7 7
TSC1/TSC2 0.03 0.064 0.26 4 -0.22 1 5
tumor necrosis factor receptor activity 0 0 0.001 36 -10000 0 36
RPS6 0.024 0.01 -10000 0 -10000 0 0
PPP5C 0.027 0.004 -10000 0 -10000 0 0
EIF4G1 0.026 0.006 -10000 0 -10000 0 0
IRS1 -0.013 0.072 -10000 0 -0.23 37 37
INS -0.016 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.007 -10000 0 -10000 0 0
PDK2 -0.008 0.055 0.16 16 -0.25 6 22
EIF4EBP1 -0.029 0.26 -10000 0 -1 25 25
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PPP2R5D 0.019 0.049 -10000 0 -0.39 2 2
peptide biosynthetic process 0.011 0.013 0.18 2 -10000 0 2
RHEB 0.027 0.003 -10000 0 -10000 0 0
EIF4A1 0.025 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 14 -10000 0 14
EEF2 0.011 0.013 0.18 2 -10000 0 2
eIF4E/4E-BP1 -0.017 0.24 -10000 0 -0.96 25 25
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.01 0.064 -10000 0 -0.32 14 14
CRKL 0.028 0.014 0.21 2 -10000 0 2
Rac1/GDP 0.02 0.005 -10000 0 -10000 0 0
DOCK1 0.024 0.035 -10000 0 -0.47 2 2
ITGA4 0.013 0.085 0.21 1 -0.47 12 13
alpha4/beta7 Integrin/MAdCAM1 0.052 0.072 -10000 0 -0.26 17 17
EPO 0.033 0.057 0.22 31 -10000 0 31
alpha4/beta7 Integrin 0.024 0.076 -10000 0 -0.34 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.027 0.065 -10000 0 -0.34 12 12
EPO/EPOR (dimer) 0.05 0.04 0.24 2 -10000 0 2
lamellipodium assembly 0.016 0.079 -10000 0 -0.47 6 6
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.023 -10000 0 -0.34 1 1
ARF6 0.027 0.005 -10000 0 -10000 0 0
JAK2 0.017 0.054 -10000 0 -0.28 11 11
PXN 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
MADCAM1 0.028 0.038 0.21 14 -10000 0 14
cell adhesion 0.05 0.071 -10000 0 -0.26 17 17
CRKL/CBL 0.038 0.015 -10000 0 -10000 0 0
ITGB1 0.026 0.006 -10000 0 -10000 0 0
SRC 0.005 0.084 0.19 15 -0.31 22 37
ITGB7 0.021 0.055 -10000 0 -0.47 5 5
RAC1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.029 0.099 -10000 0 -0.35 23 23
p130Cas/Crk/Dock1 0.031 0.088 0.36 1 -0.27 19 20
VCAM1 0.008 0.1 0.21 2 -0.47 17 19
RHOA 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.06 -10000 0 -0.26 12 12
BCAR1 -0.014 0.079 0.2 15 -0.29 21 36
EPOR 0.031 0.029 0.23 8 -10000 0 8
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.007 -10000 0 -10000 0 0
GIT1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.082 -10000 0 -0.49 6 6
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.004 0.025 0.51 1 -10000 0 1
SNTA1 0.025 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.007 0.03 0.36 2 -10000 0 2
MAPK12 -0.002 0.029 0.18 1 -0.25 5 6
CCND1 0.011 0.072 0.19 13 -0.4 8 21
p38 gamma/SNTA1 0.021 0.049 0.19 16 -0.23 6 22
MAP2K3 0.025 0.008 -10000 0 -10000 0 0
PKN1 0.026 0.025 -10000 0 -0.47 1 1
G2/M transition checkpoint 0.007 0.051 0.2 18 -0.25 5 23
MAP2K6 0 0.033 -10000 0 -0.27 6 6
MAPT -0.011 0.097 0.24 8 -0.3 33 41
MAPK13 0.015 0.028 0.56 1 -10000 0 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.016 -10000 0 -0.31 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex 0.067 0.11 -10000 0 -0.5 3 3
RAD9A 0.03 0.026 0.23 6 -10000 0 6
AP1 -0.079 0.19 -10000 0 -0.36 120 120
IFNAR2 0.03 0.008 -10000 0 -10000 0 0
AKT1 -0.011 0.082 -10000 0 -0.19 65 65
ER alpha/Oestrogen -0.036 0.13 -10000 0 -0.33 66 66
NFX1/SIN3/HDAC complex 0.039 0.035 -10000 0 -0.24 2 2
EGF 0.038 0.045 0.21 24 -10000 0 24
SMG5 0.026 0.007 -10000 0 -10000 0 0
SMG6 0.025 0.008 -10000 0 -10000 0 0
SP3/HDAC2 0.044 0.016 -10000 0 -10000 0 0
TERT/c-Abl 0.064 0.11 -10000 0 -0.5 2 2
SAP18 0.027 0.005 -10000 0 -10000 0 0
MRN complex 0.044 0.023 -10000 0 -10000 0 0
WT1 0.049 0.066 0.22 50 -10000 0 50
WRN 0.024 0.01 -10000 0 -10000 0 0
SP1 0.032 0.01 -10000 0 -10000 0 0
SP3 0.029 0.006 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.075 0.1 -10000 0 -0.47 2 2
Mad/Max 0.043 0.015 -10000 0 -10000 0 0
TERT 0.067 0.11 -10000 0 -0.51 3 3
CCND1 0.071 0.19 -10000 0 -1.1 7 7
MAX 0.029 0.006 -10000 0 -10000 0 0
RBBP7 0.028 0.004 -10000 0 -10000 0 0
RBBP4 0.028 0.002 -10000 0 -10000 0 0
TERF2 0.024 0.012 -10000 0 -10000 0 0
PTGES3 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
Telomerase/911 0.06 0.054 0.3 1 -10000 0 1
CDKN1B 0.028 0.028 0.24 6 -10000 0 6
RAD1 0.024 0.009 -10000 0 -10000 0 0
XRCC5 0.026 0.007 -10000 0 -10000 0 0
XRCC6 0.027 0.005 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.013 -10000 0 -10000 0 0
UBE3A 0.028 0.006 -10000 0 -10000 0 0
JUN 0.012 0.091 -10000 0 -0.47 14 14
E6 0.002 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.007 -10000 0 -10000 0 0
FOS -0.12 0.23 -10000 0 -0.47 124 124
IFN-gamma/IRF1 0.073 0.06 0.26 6 -10000 0 6
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.033 0.034 0.22 12 -10000 0 12
Telomerase 0.023 0.068 -10000 0 -0.5 2 2
IRF1 0.032 0.007 -10000 0 -10000 0 0
ESR1 -0.053 0.18 -10000 0 -0.47 66 66
KU/TER 0.038 0.011 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.013 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.042 0.044 -10000 0 -0.32 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.042 0.045 -10000 0 -0.33 1 1
HDAC1 0.028 0.002 -10000 0 -10000 0 0
HDAC2 0.03 0.011 -10000 0 -10000 0 0
ATM 0.011 0.01 -10000 0 -10000 0 0
SMAD3 0.012 0.005 -10000 0 -10000 0 0
ABL1 0.025 0.009 -10000 0 -10000 0 0
MXD1 0.029 0.011 0.22 1 -10000 0 1
MRE11A 0.027 0.006 -10000 0 -10000 0 0
HUS1 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 0.026 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.066 0.12 -10000 0 -0.46 3 3
NR2F2 0.022 0.025 -10000 0 -0.47 1 1
MAPK3 0.004 0.013 -10000 0 -10000 0 0
MAPK1 0.004 0.014 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.01 -10000 0 -10000 0 0
NBN 0.023 0.01 -10000 0 -10000 0 0
EGFR 0.023 0.085 0.33 8 -0.46 9 17
mol:Oestrogen 0.001 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.043 0.071 0.24 7 -0.33 9 16
MYC 0.003 0.1 -10000 0 -0.47 18 18
IL2 0.024 0.011 -10000 0 -10000 0 0
KU 0.038 0.011 -10000 0 -10000 0 0
RAD50 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.026 0.005 -10000 0 -10000 0 0
TRF2/BLM 0.042 0.026 0.22 2 -10000 0 2
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.083 0.11 -10000 0 -0.49 2 2
SP1/HDAC2 0.048 0.018 -10000 0 -10000 0 0
PINX1 0.023 0.01 -10000 0 -10000 0 0
Telomerase/EST1A 0.074 0.1 -10000 0 -0.47 2 2
Smad3/Myc 0.01 0.065 -10000 0 -0.28 18 18
911 complex 0.048 0.026 -10000 0 -10000 0 0
IFNG 0.068 0.082 0.23 81 -10000 0 81
Telomerase/PinX1 0.066 0.1 -10000 0 -0.47 2 2
Telomerase/AKT1/mTOR/p70S6K 0.031 0.074 -10000 0 -0.33 2 2
SIN3B 0.028 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
Telomerase/EST1B 0.072 0.097 -10000 0 -0.48 2 2
response to DNA damage stimulus 0.001 0.024 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.059 0.035 -10000 0 -10000 0 0
TRF2/WRN 0.033 0.018 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.078 0.099 -10000 0 -0.47 2 2
E2F1 0.081 0.095 0.24 97 -10000 0 97
ZNFX1 0.026 0.008 -10000 0 -10000 0 0
PIF1 0.041 0.057 0.21 33 -0.47 1 34
NCL 0.026 0.008 -10000 0 -10000 0 0
DKC1 0.027 0.005 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
E-cadherin signaling 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
E-cadherin/beta catenin-gamma catenin 0.037 0.068 -9999 0 -0.3 14 14
E-cadherin/beta catenin 0.025 0.067 -9999 0 -0.34 13 13
CTNNB1 0.027 0.006 -9999 0 -10000 0 0
JUP 0.024 0.035 -9999 0 -0.47 2 2
CDH1 0.01 0.087 -9999 0 -0.47 13 13
Retinoic acid receptors-mediated signaling

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
HDAC1 0.028 0.002 -10000 0 -10000 0 0
HDAC3 0.027 0.005 -10000 0 -10000 0 0
VDR 0.026 0.038 0.33 1 -0.47 2 3
Cbp/p300/PCAF 0.047 0.026 -10000 0 -0.28 1 1
EP300 0.027 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.011 0.069 -10000 0 -0.29 9 9
KAT2B 0.025 0.025 -10000 0 -0.47 1 1
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.01 0.086 0.21 17 -0.24 24 41
RAR alpha/9cRA/Cyclin H 0.047 0.064 -10000 0 -0.28 4 4
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.078 -10000 0 -0.31 10 10
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.029 0.049 -10000 0 -0.36 4 4
NCOR2 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.025 -10000 0 -0.33 2 2
RXRs/RARs/NRIP1/9cRA 0.011 0.099 0.39 1 -0.44 5 6
NCOA2 0 0.11 -10000 0 -0.47 20 20
NCOA3 0.025 0.008 -10000 0 -10000 0 0
NCOA1 0.027 0.006 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.038 0.33 1 -0.47 2 3
RARG 0.028 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.037 0.006 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.024 0.043 -10000 0 -0.47 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.013 0.082 0.29 1 -0.35 7 8
RARA 0.016 0.037 0.2 2 -0.23 7 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.005 0.098 -10000 0 -0.37 14 14
PRKCA 0.024 0.049 -10000 0 -0.46 4 4
RXRs/RARs/NRIP1/9cRA/HDAC1 0.005 0.1 0.3 2 -0.42 6 8
RXRG -0.052 0.13 0.24 2 -0.3 88 90
RXRA 0.025 0.05 -10000 0 -0.22 7 7
RXRB 0.02 0.038 0.24 2 -0.27 5 7
VDR/Vit D3/DNA 0.018 0.025 -10000 0 -0.33 2 2
RBP1 0 0.12 0.21 3 -0.47 23 26
CRBP1/9-cic-RA 0 0.083 0.15 3 -0.33 23 26
RARB -0.014 0.14 -10000 0 -0.47 34 34
PRKCG 0.03 0.038 0.23 13 -10000 0 13
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.004 0.094 0.3 1 -0.47 5 6
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.015 0.094 0.26 1 -0.42 5 6
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.086 0.27 5 -0.35 6 11
RXRs/RARs/NRIP1/9cRA/HDAC3 0.004 0.1 0.3 2 -0.43 6 8
positive regulation of DNA binding 0.033 0.056 -10000 0 -0.27 4 4
NRIP1 0.006 0.1 -10000 0 -0.48 1 1
RXRs/RARs 0.001 0.11 0.27 1 -0.41 9 10
RXRs/RXRs/DNA/9cRA -0.005 0.07 -10000 0 -0.37 6 6
PRKACA 0.027 0.003 -10000 0 -10000 0 0
CDK7 0.026 0.007 -10000 0 -10000 0 0
TFIIH 0.052 0.016 -10000 0 -10000 0 0
RAR alpha/9cRA 0.059 0.045 -10000 0 -0.27 1 1
CCNH 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.05 0.018 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.04 0.17 -10000 0 -0.47 55 55
HRAS 0.025 0.008 -10000 0 -10000 0 0
EGFR 0.021 0.085 0.33 8 -0.47 9 17
AKT 0.034 0.091 0.26 8 -0.27 13 21
FOXO3 0.026 0.007 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
FOXO1 0.024 0.026 -10000 0 -0.47 1 1
AKT3 0.01 0.091 -10000 0 -0.47 14 14
FOXO4 0.028 0.01 0.21 1 -10000 0 1
MET 0.029 0.022 0.33 2 -10000 0 2
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PIK3CB 0.026 0.006 -10000 0 -10000 0 0
NRAS 0.028 0.002 -10000 0 -10000 0 0
PIK3CG 0.013 0.085 0.21 2 -0.47 12 14
PIK3R3 0.027 0.004 -10000 0 -10000 0 0
PIK3R2 0.027 0.003 -10000 0 -10000 0 0
NF1 0.026 0.006 -10000 0 -10000 0 0
RAS 0.011 0.072 0.2 6 -0.23 10 16
ERBB2 0.037 0.053 0.33 13 -10000 0 13
proliferation/survival/translation -0.037 0.068 0.25 7 -0.24 2 9
PI3K 0.026 0.075 0.22 20 -0.2 7 27
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
KRAS 0.027 0.016 0.33 1 -10000 0 1
FOXO 0.06 0.06 0.24 10 -0.11 4 14
AKT2 0.027 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.007 -10000 0 -10000 0 0
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 0.019 0.058 0.24 4 -0.29 2 6
adherens junction organization 0.019 0.07 0.23 3 -0.25 16 19
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.031 0.074 0.26 6 -0.33 2 8
FMN1 0.016 0.066 -10000 0 -0.25 14 14
mol:IP3 0.013 0.045 -10000 0 -0.28 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.019 0.071 -10000 0 -0.26 14 14
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.023 0.058 0.19 4 -0.3 2 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.021 0.095 0.27 1 -0.36 14 15
CTNND1 0.028 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.063 -10000 0 -0.25 13 13
VASP 0.016 0.066 -10000 0 -0.25 13 13
ZYX 0.016 0.068 -10000 0 -0.26 14 14
JUB 0.016 0.068 -10000 0 -0.25 14 14
EGFR(dimer) 0.029 0.086 0.23 9 -0.26 14 23
E-cadherin/beta catenin-gamma catenin 0.036 0.065 -10000 0 -0.29 14 14
mol:PI-3-4-5-P3 0.039 0.067 -10000 0 -0.31 2 2
PIK3CA 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.04 0.068 -10000 0 -0.32 2 2
FYN 0.011 0.063 0.26 4 -0.28 5 9
mol:Ca2+ 0.013 0.044 -10000 0 -0.27 2 2
JUP 0.025 0.035 -10000 0 -0.46 2 2
PIK3R1 0.026 0.026 -10000 0 -0.47 1 1
mol:DAG 0.013 0.045 -10000 0 -0.28 2 2
CDH1 0.01 0.087 -10000 0 -0.47 13 13
RhoA/GDP 0.033 0.073 0.27 5 -0.33 2 7
establishment of polarity of embryonic epithelium 0.017 0.066 -10000 0 -0.25 13 13
SRC 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
EGFR 0.021 0.085 0.33 8 -0.47 9 17
CASR 0.012 0.055 0.26 5 -0.24 3 8
RhoA/GTP 0.029 0.051 -10000 0 -0.25 2 2
AKT2 0.021 0.057 0.2 1 -0.3 2 3
actin cable formation 0.016 0.066 0.19 5 -0.25 13 18
apoptosis -0.029 0.068 0.3 2 -0.27 6 8
CTNNA1 0.028 0.006 -10000 0 -10000 0 0
mol:GDP 0.014 0.066 0.29 2 -0.3 3 5
PIP5K1A 0.013 0.064 -10000 0 -0.25 13 13
PLCG1 0.013 0.046 -10000 0 -0.28 2 2
Rac1/GTP 0.035 0.082 0.27 1 -0.25 13 14
homophilic cell adhesion 0.001 0.003 -10000 0 -10000 0 0
Class I PI3K 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
ARF5/GTP 0.026 0.045 0.3 3 -10000 0 3
DAPP1 0.007 0.11 0.28 5 -0.32 18 23
Src family/SYK family/BLNK-LAT/BTK-ITK -0.02 0.17 0.32 2 -0.47 29 31
mol:DAG 0.007 0.09 0.2 22 -0.23 16 38
HRAS 0.027 0.009 -10000 0 -10000 0 0
RAP1A 0.029 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.038 0.067 0.22 1 -0.3 5 6
PLCG2 0.026 0.039 0.21 3 -0.47 2 5
PLCG1 0.026 0.007 -10000 0 -10000 0 0
ARF5 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.004 0.042 0.31 2 -10000 0 2
ARF1/GTP 0.009 0.044 0.27 4 -10000 0 4
RHOA 0.026 0.006 -10000 0 -10000 0 0
YES1 0.025 0.008 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.031 -10000 0 -10000 0 0
ADAP1 -0.005 0.043 0.29 2 -0.24 2 4
ARAP3 -0.004 0.041 0.3 2 -10000 0 2
INPPL1 0.026 0.006 -10000 0 -10000 0 0
PREX1 0.026 0.008 -10000 0 -10000 0 0
ARHGEF6 0.024 0.043 -10000 0 -0.47 3 3
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
FYN 0.022 0.043 -10000 0 -0.47 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.035 -10000 0 -0.47 2 2
mol:Ca2+ 0.008 0.059 0.19 14 -0.15 2 16
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.023 0.043 -10000 0 -0.47 3 3
ZAP70 0.01 0.091 0.21 1 -0.47 14 15
mol:IP3 0.006 0.074 0.23 14 -0.18 12 26
LYN 0.025 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.068 0.22 1 -0.3 5 6
RhoA/GDP 0.041 0.047 0.23 1 -10000 0 1
PDK1/Src/Hsp90 0.049 0.02 -10000 0 -10000 0 0
BLNK 0.011 0.087 -10000 0 -0.47 13 13
actin cytoskeleton reorganization 0.032 0.074 0.28 4 -0.28 2 6
SRC 0.026 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.024 -10000 0 -0.28 3 3
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.024 0.012 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.04 0.29 2 -10000 0 2
RhoA/GTP -0.004 0.042 0.3 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.009 0.11 -10000 0 -0.34 24 24
BLK -0.011 0.14 0.21 15 -0.47 30 45
PDPK1 0.026 0.006 -10000 0 -10000 0 0
CYTH1 -0.005 0.039 0.29 2 -10000 0 2
HCK 0.014 0.08 0.21 5 -0.47 10 15
CYTH3 -0.004 0.039 0.29 2 -10000 0 2
CYTH2 -0.004 0.04 0.29 2 -10000 0 2
KRAS 0.028 0.016 0.31 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.001 0.094 -10000 0 -0.4 17 17
SGK1 -0.003 0.11 -10000 0 -0.4 24 24
INPP5D 0.018 0.06 -10000 0 -0.47 6 6
mol:GDP 0.025 0.067 0.22 1 -0.32 5 6
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.02 0.05 -10000 0 -0.47 4 4
ARF6/GDP 0.031 0.049 0.26 4 -10000 0 4
mol:PI-3-4-5-P3 -0.004 0.039 0.29 2 -10000 0 2
ARAP3/RAP1A/GTP 0.021 0.032 -10000 0 -10000 0 0
VAV1 0.008 0.098 0.21 2 -0.47 16 18
mol:PI-3-4-P2 0.011 0.03 -10000 0 -0.34 3 3
RAS family/GTP/PI3K Class I 0.045 0.039 -10000 0 -10000 0 0
PLEKHA1 -0.007 0.024 -10000 0 -0.28 3 3
Rac1/GDP 0.036 0.066 -10000 0 -0.3 5 5
LAT 0.027 0.011 0.21 1 -10000 0 1
Rac1/GTP 0.018 0.062 -10000 0 -0.31 5 5
ITK -0.024 0.074 0.29 2 -0.24 34 36
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.002 0.11 0.27 10 -0.32 18 28
LCK 0.024 0.051 0.21 2 -0.47 4 6
BTK -0.016 0.064 0.29 2 -0.24 20 22
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.12 0.13 -10000 0 -0.36 34 34
CaM/Ca2+ 0.02 0.003 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.027 0.006 -10000 0 -10000 0 0
STXBP4 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.13 0.13 0.24 1 -0.38 37 38
YWHAZ 0.021 0.012 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.026 0.006 -10000 0 -10000 0 0
TBC1D4 0.014 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.027 0.006 -10000 0 -10000 0 0
YWHAB 0.025 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.048 0.021 -10000 0 -10000 0 0
YWHAG 0.027 0.003 -10000 0 -10000 0 0
ASIP 0.013 0.031 0.24 4 -10000 0 4
PRKCI 0.026 0.007 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.003 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.014 0.017 0.25 2 -10000 0 2
PRKCZ 0.024 0.043 -10000 0 -0.47 3 3
TRIP10 0.026 0.025 -10000 0 -0.47 1 1
TC10/GTP/CIP4/Exocyst 0.035 0.017 -10000 0 -0.26 1 1
AS160/14-3-3 0.032 0.054 0.22 2 -0.29 2 4
VAMP2 0.025 0.008 -10000 0 -10000 0 0
SLC2A4 -0.14 0.14 0.24 1 -0.42 37 38
STX4 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.021 0.008 -10000 0 -10000 0 0
SFN 0.038 0.067 0.21 32 -0.47 3 35
LNPEP 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.029 0.11 -10000 0 -0.57 7 7
oxygen homeostasis 0.006 0.011 -10000 0 -10000 0 0
TCEB2 0.027 0.011 0.21 1 -10000 0 1
TCEB1 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.057 0.084 -10000 0 -0.26 3 3
EPO 0.097 0.15 0.43 2 -0.45 3 5
FIH (dimer) 0.031 0.018 -10000 0 -10000 0 0
APEX1 0.027 0.027 -10000 0 -10000 0 0
SERPINE1 0.085 0.16 0.42 1 -0.55 6 7
FLT1 0.027 0.12 -10000 0 -0.59 8 8
ADORA2A 0.089 0.15 0.4 5 -0.48 3 8
germ cell development 0.098 0.16 0.46 6 -0.46 5 11
SLC11A2 0.087 0.15 0.42 1 -0.45 3 4
BHLHE40 0.078 0.15 0.42 1 -0.5 5 6
HIF1AN 0.031 0.018 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.077 0.11 0.37 1 -0.29 4 5
ETS1 0.036 0.013 -10000 0 -10000 0 0
CITED2 0.031 0.098 -10000 0 -0.57 7 7
KDR 0.022 0.14 -10000 0 -0.75 8 8
PGK1 0.087 0.15 0.42 1 -0.5 3 4
SIRT1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.12 0.18 -10000 0 -0.56 3 3
EPAS1 0.04 0.079 -10000 0 -0.25 7 7
SP1 0.033 0.005 -10000 0 -10000 0 0
ABCG2 0.079 0.17 0.42 2 -0.47 12 14
EFNA1 0.088 0.15 0.46 4 -0.5 3 7
FXN 0.089 0.14 0.38 4 -0.48 3 7
POU5F1 0.097 0.16 0.48 4 -0.47 5 9
neuron apoptosis -0.12 0.18 0.55 3 -10000 0 3
EP300 0.027 0.006 -10000 0 -10000 0 0
EGLN3 0.021 0.071 -10000 0 -0.46 8 8
EGLN2 0.03 0.019 -10000 0 -10000 0 0
EGLN1 0.031 0.018 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.043 0.025 -10000 0 -10000 0 0
VHL 0.025 0.009 -10000 0 -10000 0 0
ARNT 0.025 0.025 -10000 0 -10000 0 0
SLC2A1 0.088 0.15 0.4 6 -0.48 3 9
TWIST1 0.042 0.23 0.38 6 -0.45 58 64
ELK1 0.033 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.078 0.11 -10000 0 -0.29 2 2
VEGFA 0.086 0.15 0.42 1 -0.5 3 4
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.028 0.014 0.21 2 -10000 0 2
Rac1/GDP 0.024 0.012 -10000 0 -10000 0 0
DOCK1 0.024 0.035 -10000 0 -0.47 2 2
ITGA4 0.013 0.085 0.21 1 -0.47 12 13
RAC1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.024 0.076 -10000 0 -0.34 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.041 0.06 -10000 0 -0.28 12 12
alpha4/beta7 Integrin/Paxillin 0.032 0.062 -10000 0 -0.26 17 17
lamellipodium assembly 0.009 0.077 -10000 0 -0.36 8 8
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.023 -10000 0 -0.34 1 1
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.025 0.009 -10000 0 -10000 0 0
PXN 0.015 0.003 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
ARF6/GTP 0.043 0.053 -10000 0 -0.23 12 12
cell adhesion 0.042 0.053 -10000 0 -0.24 11 11
CRKL/CBL 0.038 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.034 0.054 -10000 0 -0.26 12 12
ITGB1 0.026 0.006 -10000 0 -10000 0 0
ITGB7 0.021 0.055 -10000 0 -0.47 5 5
ARF6/GDP 0.025 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.036 0.09 -10000 0 -0.3 23 23
p130Cas/Crk/Dock1 0.045 0.032 -10000 0 -0.28 2 2
VCAM1 0.008 0.1 0.21 2 -0.47 17 19
alpha4/beta1 Integrin/Paxillin/Talin 0.043 0.054 -10000 0 -0.24 11 11
alpha4/beta1 Integrin/Paxillin/GIT1 0.045 0.056 -10000 0 -0.24 12 12
BCAR1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.043 0.055 0.24 12 -10000 0 12
CBL 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GIT1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.043 0.054 -10000 0 -0.24 11 11
Rac1/GTP 0.008 0.083 -10000 0 -0.4 8 8
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 0.015 0.056 -10000 0 -10000 0 0
PLK1 0.1 0.12 0.53 2 -10000 0 2
CDKN1B 0.11 0.099 0.37 4 -0.35 3 7
FOXO3 0.097 0.11 0.38 3 -0.39 3 6
KAT2B 0.036 0.032 -10000 0 -0.46 1 1
FOXO1/SIRT1 0.025 0.049 0.27 1 -0.23 1 2
CAT 0.095 0.11 0.48 1 -10000 0 1
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.04 0.02 -10000 0 -10000 0 0
FOXO1 0.015 0.053 0.35 1 -0.26 1 2
MAPK10 0.013 0.079 0.2 13 -0.23 33 46
mol:GTP 0.002 0 -10000 0 -10000 0 0
FOXO4 0.056 0.065 0.3 1 -10000 0 1
response to oxidative stress 0.016 0.012 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.11 0.089 0.41 1 -10000 0 1
XPO1 0.027 0.006 -10000 0 -10000 0 0
EP300 0.029 0.007 -10000 0 -10000 0 0
BCL2L11 0.037 0.091 -10000 0 -0.72 5 5
FOXO1/SKP2 0.027 0.056 0.28 4 -0.26 1 5
mol:GDP 0.016 0.012 -10000 0 -10000 0 0
RAN 0.028 0.005 -10000 0 -10000 0 0
GADD45A 0.1 0.081 -10000 0 -0.43 1 1
YWHAQ 0.026 0.006 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.05 0.099 -10000 0 -0.55 5 5
MST1 0.047 0.055 0.23 22 -0.45 1 23
CSNK1D 0.027 0.006 -10000 0 -10000 0 0
CSNK1E 0.027 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.04 0.084 -10000 0 -0.47 4 4
YWHAB 0.025 0.008 -10000 0 -10000 0 0
MAPK8 0.034 0.041 0.2 15 -0.23 3 18
MAPK9 0.034 0.033 0.2 14 -10000 0 14
YWHAG 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
YWHAZ 0.021 0.012 -10000 0 -10000 0 0
SIRT1 0.026 0.017 -10000 0 -10000 0 0
SOD2 0.1 0.097 0.49 1 -0.47 2 3
RBL2 0.085 0.14 -10000 0 -0.6 11 11
RAL/GDP 0.05 0.018 0.24 1 -10000 0 1
CHUK 0.038 0.019 -10000 0 -10000 0 0
Ran/GTP 0.023 0.004 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
RAL/GTP 0.053 0.018 0.23 1 -10000 0 1
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.018 0.3 -10000 0 -1.3 20 20
SKP2 0.029 0.038 0.26 9 -10000 0 9
USP7 0.027 0.007 -10000 0 -10000 0 0
IKBKB 0.035 0.021 -10000 0 -10000 0 0
CCNB1 0.098 0.11 0.46 1 -10000 0 1
FOXO1-3a-4/beta catenin 0.11 0.093 0.36 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.056 0.28 4 -0.26 1 5
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
SGK1 0.017 0.098 -10000 0 -0.46 16 16
CSNK1G3 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.011 -10000 0 -10000 0 0
ZFAND5 0.055 0.061 -10000 0 -10000 0 0
SFN 0.038 0.067 0.21 32 -0.47 3 35
CDK2 0.028 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.055 0.077 0.24 1 -0.5 2 3
CREBBP 0.027 0.008 -10000 0 -10000 0 0
FBXO32 0.11 0.15 0.5 8 -1.1 1 9
BCL6 0.1 0.089 -10000 0 -10000 0 0
RALB 0.028 0.004 -10000 0 -10000 0 0
RALA 0.029 0.016 0.33 1 -10000 0 1
YWHAH 0.027 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.061 0.044 -10000 0 -0.26 6 6
HDAC3 0.027 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -10000 0 -10000 0 0
GATA1/HDAC5 0.037 0.008 -10000 0 -10000 0 0
GATA2/HDAC5 0.037 0.053 0.24 1 -0.34 6 7
HDAC5/BCL6/BCoR 0.051 0.017 -10000 0 -10000 0 0
HDAC9 -0.005 0.12 -10000 0 -0.47 25 25
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.057 -10000 0 -0.28 11 11
HDAC4/ANKRA2 0.036 0.014 -10000 0 -10000 0 0
HDAC5/YWHAB 0.037 0.013 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -10000 0 -10000 0 0
GATA2 0.025 0.07 0.22 13 -0.47 6 19
HDAC4/RFXANK 0.038 0.014 -10000 0 -10000 0 0
BCOR 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.026 0.006 -10000 0 -10000 0 0
HDAC5 0.027 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.046 -10000 0 -0.34 6 6
Histones 0.006 0.069 -10000 0 -0.26 6 6
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
HDAC4 0.025 0.008 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -10000 0 -10000 0 0
HDAC4/Ubc9 0.037 0.013 -10000 0 -10000 0 0
HDAC7 0.027 0.004 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.036 0.013 -10000 0 -10000 0 0
TUBA1B 0.027 0.003 -10000 0 -10000 0 0
HDAC6 0.027 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.04 0.011 -10000 0 -10000 0 0
CAMK4 0.016 0.07 0.21 1 -0.47 8 9
Tubulin/HDAC6 0.05 0.028 -10000 0 -0.28 2 2
SUMO1 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.025 0.008 -10000 0 -10000 0 0
GATA1 0.014 0.021 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
NR3C1 0.013 0.081 -10000 0 -0.47 11 11
SUMO1/HDAC4 0.033 0.044 -10000 0 -0.28 2 2
SRF 0.027 0.005 -10000 0 -10000 0 0
HDAC4/YWHAB 0.034 0.015 -10000 0 -10000 0 0
Tubulin 0.036 0.028 -10000 0 -0.34 2 2
HDAC4/14-3-3 E 0.035 0.015 -10000 0 -10000 0 0
GNB1 0.027 0.003 -10000 0 -10000 0 0
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
BCL6/BCoR 0.038 0.011 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.049 0.019 -10000 0 -10000 0 0
HDAC4/SRF 0.041 0.051 -10000 0 -0.28 8 8
HDAC4/ER alpha -0.024 0.14 -10000 0 -0.33 66 66
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.006 0.068 -10000 0 -0.26 6 6
cell motility 0.05 0.028 -10000 0 -0.28 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -10000 0 -10000 0 0
BCL6 0.026 0.006 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.025 0.008 -10000 0 -10000 0 0
Hsp90/HDAC6 0.039 0.009 -10000 0 -10000 0 0
ESR1 -0.054 0.18 -10000 0 -0.47 66 66
HDAC6/HDAC11 0.034 0.036 0.24 1 -0.34 3 4
Ran/GTP/Exportin 1 0.033 0.046 -10000 0 -0.28 2 2
NPC 0.016 0.003 -10000 0 -10000 0 0
MEF2C 0.013 0.081 -10000 0 -0.47 11 11
RAN 0.027 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.061 0.058 -10000 0 -0.24 10 10
GNG2 0.02 0.06 -10000 0 -0.47 6 6
NCOR2 0.027 0.004 -10000 0 -10000 0 0
TUBB2A 0.024 0.035 -10000 0 -0.47 2 2
HDAC11 0.022 0.046 0.33 1 -0.47 3 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RANBP2 0.027 0.004 -10000 0 -10000 0 0
ANKRA2 0.026 0.006 -10000 0 -10000 0 0
RFXANK 0.028 0.01 0.21 1 -10000 0 1
nuclear import -0.028 0.019 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.027 0.011 0.21 1 -9999 0 1
PLK4 0.032 0.029 0.21 10 -9999 0 10
regulation of centriole replication 0.015 0.007 -10000 0 -9999 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.035 0.043 0.23 17 -10000 0 17
positive regulation of NF-kappaB transcription factor activity 0.032 0.046 0.24 1 -0.34 4 5
MAP2K4 0.027 0.042 0.24 3 -10000 0 3
IKBKB 0.025 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.023 0.011 -10000 0 -10000 0 0
TNFRSF10A 0.022 0.027 -10000 0 -0.47 1 1
SMPD1 0.013 0.01 0.15 1 -10000 0 1
IKBKG 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.055 -10000 0 -0.47 5 5
TRAIL/TRAILR2 0.036 0.028 0.24 1 -10000 0 1
TRAIL/TRAILR3 0.036 0.037 0.24 1 -0.34 1 2
TRAIL/TRAILR1 0.035 0.034 0.24 1 -0.34 1 2
TRAIL/TRAILR4 0.032 0.046 0.24 1 -0.34 4 5
TRAIL/TRAILR1/DAP3/GTP 0.042 0.032 0.22 1 -10000 0 1
IKK complex 0.017 0.047 -10000 0 -10000 0 0
RIPK1 0.026 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.005 -10000 0 -10000 0 0
MAPK3 0.017 0.026 0.3 3 -10000 0 3
MAP3K1 0.026 0.038 0.29 1 -10000 0 1
TRAILR4 (trimer) 0.017 0.055 -10000 0 -0.47 5 5
TRADD 0.027 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.022 0.027 -10000 0 -0.47 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.022 0.028 -10000 0 -0.22 1 1
CFLAR 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.017 0.025 0.3 3 -10000 0 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.05 -10000 0 -0.24 1 1
mol:ceramide 0.013 0.01 0.15 1 -10000 0 1
FADD 0.03 0.037 0.33 6 -10000 0 6
MAPK8 0.022 0.055 0.26 3 -10000 0 3
TRAF2 0.025 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.024 0.034 0.21 5 -0.47 1 6
CHUK 0.027 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.046 0.042 0.24 6 -0.28 1 7
DAP3 0.026 0.007 -10000 0 -10000 0 0
CASP10 0.027 0.059 0.25 12 -10000 0 12
JNK cascade 0.032 0.046 0.24 1 -0.34 4 5
TRAIL (trimer) 0.035 0.043 0.23 17 -10000 0 17
TNFRSF10C 0.024 0.034 0.21 5 -0.47 1 6
TRAIL/TRAILR1/DAP3/GTP/FADD 0.05 0.042 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.047 0.039 0.24 6 -10000 0 6
cell death 0.013 0.01 0.15 1 -10000 0 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.023 0.026 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.023 0.011 -10000 0 -10000 0 0
CASP8 -0.017 0.13 -10000 0 -0.56 20 20
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.06 0.048 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.028 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.005 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.036 0.058 0.22 12 -0.21 6 18
HDAC4 0.025 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.005 0.011 -10000 0 -10000 0 0
SUMO1 0.027 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.026 -10000 0 -0.2 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.01 0.022 -10000 0 -0.22 3 3
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.033 0.044 -10000 0 -0.28 2 2
SUMO1/HDAC1 0.033 0.048 -10000 0 -0.21 6 6
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.04 0.24 12 -10000 0 12
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.005 -10000 0 -10000 0 0
Ran/GTP 0.021 0.043 -10000 0 -0.19 9 9
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.036 0.054 0.33 13 -10000 0 13
UBE2I 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.025 0.051 0.2 12 -0.28 2 14
NPC 0.016 0.003 -10000 0 -10000 0 0
PIAS2 0.026 0.007 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.028 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 0.066 0.078 0.28 8 -0.32 2 10
ERC1 0.027 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.04 0.039 -10000 0 -0.34 1 1
NFKBIA 0.019 0.03 -10000 0 -10000 0 0
BIRC2 0.028 0.022 0.33 2 -10000 0 2
IKBKB 0.025 0.009 -10000 0 -10000 0 0
RIPK2 0.024 0.01 -10000 0 -10000 0 0
IKBKG 0.041 0.039 -10000 0 -10000 0 0
IKK complex/A20 0.067 0.082 0.3 1 -0.36 2 3
NEMO/A20/RIP2 0.023 0.01 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.053 0.073 0.28 2 -0.32 7 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.01 -10000 0 -10000 0 0
IKK complex/ELKS 0.05 0.067 -10000 0 -0.3 5 5
BCL10/MALT1/TRAF6 0.049 0.02 -10000 0 -10000 0 0
NOD2 0.035 0.057 0.21 24 -0.47 2 26
NFKB1 0.03 0.004 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.026 0.007 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.018 0.24 2 -10000 0 2
ATM 0.026 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.045 0.031 -10000 0 -10000 0 0
TRAF6 0.026 0.008 -10000 0 -10000 0 0
PRKCA 0.022 0.049 -10000 0 -0.47 4 4
CHUK 0.027 0.005 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF 0.036 0.042 0.21 21 -10000 0 21
NF kappa B1 p50/RelA 0.059 0.019 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.03 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.028 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.058 0.074 0.28 2 -0.3 7 9
CYLD 0.027 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.062 0.079 -10000 0 -0.35 2 2
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.027 0.02 -10000 0 -10000 0 0
regulation of axonogenesis -0.011 0.026 0.24 4 -10000 0 4
myoblast fusion -0.026 0.024 -10000 0 -10000 0 0
mol:GTP 0.018 0.027 -10000 0 -0.15 8 8
regulation of calcium-dependent cell-cell adhesion -0.051 0.04 0.26 3 -10000 0 3
ARF1/GTP 0.034 0.026 -10000 0 -10000 0 0
mol:GM1 0.008 0.02 -10000 0 -10000 0 0
mol:Choline 0.011 0.014 -10000 0 -10000 0 0
lamellipodium assembly 0.013 0.055 -10000 0 -0.34 8 8
MAPK3 0.025 0.018 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.052 0.04 -10000 0 -0.26 3 3
ARF1 0.027 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.027 0.024 -10000 0 -10000 0 0
ARF1/GDP 0.03 0.044 -10000 0 -0.25 2 2
ARF6 0.033 0.009 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 0.025 0.043 -10000 0 -0.47 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.017 -10000 0 -10000 0 0
actin filament bundle formation -0.033 0.041 0.24 2 -10000 0 2
KALRN 0.014 0.022 -10000 0 -0.25 2 2
RAB11FIP3/RAB11A 0.039 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.033 0.042 -10000 0 -0.24 2 2
NME1 0.029 0.011 0.21 1 -10000 0 1
Rac1/GDP 0.033 0.041 -10000 0 -0.25 2 2
substrate adhesion-dependent cell spreading 0.018 0.027 -10000 0 -0.15 8 8
cortical actin cytoskeleton organization 0.013 0.056 -10000 0 -0.34 8 8
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.018 0.027 -10000 0 -0.15 8 8
ARF6/GTP 0.018 0.027 -10000 0 -0.15 8 8
RhoA/GTP 0.033 0.026 -10000 0 -10000 0 0
mol:GDP 0.012 0.033 -10000 0 -0.28 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.048 0.026 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
PLD1 0.018 0.022 -10000 0 -10000 0 0
RAB11FIP3 0.027 0.005 -10000 0 -10000 0 0
tube morphogenesis 0.013 0.055 -10000 0 -0.34 8 8
ruffle organization 0.011 0.026 -10000 0 -0.24 4 4
regulation of epithelial cell migration 0.018 0.027 -10000 0 -0.15 8 8
PLD2 0.019 0.018 -10000 0 -10000 0 0
PIP5K1A 0.011 0.026 -10000 0 -0.24 4 4
mol:Phosphatidic acid 0.011 0.014 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.056 -10000 0 -0.34 8 8
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.003 0.12 -10000 0 -0.34 44 44
AKT1 0.048 0.079 0.36 3 -0.43 2 5
PTK2B 0.004 0.09 0.35 1 -0.35 3 4
VEGFR2 homodimer/Frs2 0.036 0.039 -10000 0 -0.34 1 1
CAV1 0.005 0.1 -10000 0 -0.47 18 18
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.049 0.039 -10000 0 -10000 0 0
endothelial cell proliferation 0.025 0.12 0.36 8 -0.41 3 11
mol:Ca2+ 0.027 0.049 0.37 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.06 0.033 -10000 0 -10000 0 0
RP11-342D11.1 0.017 0.043 -10000 0 -10000 0 0
CDH5 0.024 0.035 -10000 0 -0.47 2 2
VEGFA homodimer 0.054 0.032 -10000 0 -10000 0 0
SHC1 0.026 0.017 0.33 1 -10000 0 1
SHC2 -0.002 0.12 0.21 1 -0.47 24 25
HRAS/GDP 0.039 0.033 -10000 0 -10000 0 0
SH2D2A 0.028 0.023 0.24 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.062 0.072 -10000 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.049 0.03 -10000 0 -10000 0 0
VEGFR1 homodimer 0.027 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.071 0.045 -10000 0 -10000 0 0
GRB10 0.023 0.067 0.37 1 -0.47 5 6
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.027 0.005 -10000 0 -10000 0 0
PAK1 0.025 0.025 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.071 0.048 -10000 0 -0.37 2 2
HRAS 0.025 0.008 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.006 0.077 -10000 0 -0.33 6 6
HIF1A 0.027 0.01 0.21 1 -10000 0 1
FRS2 0.031 0.04 0.33 7 -10000 0 7
oxygen and reactive oxygen species metabolic process 0.058 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.025 0.025 -10000 0 -0.47 1 1
Nck/Pak 0.037 0.022 -10000 0 -0.34 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.045 0.039 -10000 0 -10000 0 0
mol:GDP 0.055 0.037 -10000 0 -10000 0 0
mol:NADP 0.05 0.078 0.34 3 -0.42 2 5
eNOS/Hsp90 0.061 0.076 0.33 3 -0.4 2 5
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
mol:IP3 0.027 0.049 0.37 1 -10000 0 1
HIF1A/ARNT 0.035 0.015 -10000 0 -10000 0 0
SHB 0.024 0.009 -10000 0 -10000 0 0
VEGFA 0.027 0.012 -10000 0 -10000 0 0
VEGFC 0.024 0.036 0.21 1 -0.47 2 3
FAK1/Vinculin 0.028 0.098 0.32 1 -0.44 2 3
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.03 0.096 -10000 0 -0.35 4 4
PTPN6 0.027 0.011 0.21 1 -10000 0 1
EPAS1 0.034 0.01 -10000 0 -10000 0 0
mol:L-citrulline 0.05 0.078 0.34 3 -0.42 2 5
ITGAV 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.06 0.043 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.051 0.042 -10000 0 -0.28 2 2
VEGFR2/3 heterodimer 0.032 0.036 -10000 0 -0.59 1 1
VEGFB 0.027 0.003 -10000 0 -10000 0 0
MAPK11 0.022 0.061 0.42 2 -10000 0 2
VEGFR2 homodimer 0.022 0.023 -10000 0 -0.4 1 1
FLT1 0.027 0.005 -10000 0 -10000 0 0
NEDD4 0.026 0.027 -10000 0 -0.46 1 1
MAPK3 0 0.086 0.28 3 -0.31 4 7
MAPK1 0.001 0.087 0.26 4 -0.31 4 8
VEGFA145/NRP2 0.022 0.079 -10000 0 -0.34 18 18
VEGFR1/2 heterodimer 0.034 0.026 -10000 0 -0.34 1 1
KDR 0.022 0.023 -10000 0 -0.4 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.038 0.071 -10000 0 -0.44 1 1
SRC 0.026 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.009 0.091 0.27 6 -0.32 3 9
PI3K 0.043 0.054 -10000 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.048 0.027 -10000 0 -10000 0 0
FES 0.029 0.048 0.37 1 -10000 0 1
GAB1 0.043 0.044 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.03 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.024 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.051 0.08 0.3 1 -0.4 2 3
VEGFR2 homodimer/VEGFA homodimer/Yes 0.045 0.03 -10000 0 -10000 0 0
PI3K/GAB1 0.046 0.069 -10000 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.071 0.05 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.044 0.041 -10000 0 -0.54 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.029 0.049 0.37 1 -10000 0 1
actin cytoskeleton reorganization 0.048 0.029 -10000 0 -10000 0 0
PTK2 0.009 0.081 -10000 0 -0.46 2 2
EDG1 0.017 0.043 -10000 0 -10000 0 0
mol:DAG 0.027 0.049 0.37 1 -10000 0 1
CaM/Ca2+ 0.041 0.049 -10000 0 -10000 0 0
MAP2K3 0.023 0.052 0.37 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.05 0.069 -10000 0 -0.48 5 5
PLCG1 0.027 0.049 0.37 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.052 0.038 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.025 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.048 0.029 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.05 0.027 -10000 0 -10000 0 0
cell migration 0.035 0.095 0.34 2 -0.43 2 4
mol:PI-3-4-5-P3 0.042 0.052 -10000 0 -0.47 1 1
FYN 0.022 0.043 -10000 0 -0.47 3 3
VEGFB/NRP1 0.032 0.043 -10000 0 -10000 0 0
mol:NO 0.05 0.078 0.34 3 -0.42 2 5
PXN 0.027 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.023 0.025 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.039 0.063 -10000 0 -0.48 5 5
VHL 0.025 0.009 -10000 0 -10000 0 0
ITGB3 -0.027 0.15 -10000 0 -0.47 44 44
NOS3 0.051 0.083 0.34 3 -0.48 2 5
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.076 -10000 0 -0.38 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.02 0.063 0.36 2 -0.44 1 3
PRKCB -0.039 0.12 -10000 0 -0.43 4 4
VCL 0.027 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 0.035 0.044 -10000 0 -10000 0 0
VEGFR1/2 heterodimer/VEGFA homodimer 0.049 0.028 -10000 0 -10000 0 0
VEGFA165/NRP2 0.022 0.079 -10000 0 -0.34 18 18
MAPKKK cascade 0.045 0.066 0.36 2 -0.4 3 5
NRP2 0.004 0.1 -10000 0 -0.47 18 18
VEGFC homodimer 0.024 0.036 0.21 1 -0.47 2 3
NCK1 0.026 0.006 -10000 0 -10000 0 0
ROCK1 0.027 0.006 -10000 0 -10000 0 0
FAK1/Paxillin 0.029 0.099 0.31 2 -0.44 2 4
MAP3K13 0.028 0.045 -10000 0 -10000 0 0
PDPK1 0.035 0.057 0.27 6 -0.43 1 7
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0.01 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.015 0.004 -10000 0 -10000 0 0
mol:DAG 0.021 0.027 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.03 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.035 0.027 -10000 0 -10000 0 0
HIF1A 0.034 0.011 0.22 1 -10000 0 1
GAB1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.027 0.045 -10000 0 -10000 0 0
PLCG1 0.021 0.028 -10000 0 -10000 0 0
NOS3 0.036 0.05 0.29 2 -0.34 1 3
CBL 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.037 0.053 0.3 3 -0.33 1 4
FLT1 0.02 0.006 -10000 0 -10000 0 0
PGF 0.033 0.033 0.21 13 -10000 0 13
VEGFR1 homodimer/NRP2/VEGFR121 0.032 0.065 -10000 0 -0.26 18 18
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
eNOS/Hsp90 0.049 0.054 0.29 2 -0.32 1 3
endothelial cell proliferation -0.023 0.11 0.32 5 -0.36 3 8
mol:Ca2+ 0.021 0.027 -10000 0 -10000 0 0
MAPK3 -0.002 0.038 -10000 0 -10000 0 0
MAPK1 -0.001 0.039 -10000 0 -10000 0 0
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
PLGF homodimer 0.033 0.033 0.21 13 -10000 0 13
PRKACA 0.027 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.005 0.1 -10000 0 -0.47 18 18
VEGFA homodimer 0.027 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.033 0.011 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.006 0.054 0.34 1 -10000 0 1
PI3K 0.058 0.037 -10000 0 -0.24 1 1
PRKCA 0.007 0.037 -10000 0 -10000 0 0
PRKCB -0.053 0.11 -10000 0 -0.27 5 5
VEGFR1 homodimer/PLGF homodimer 0.038 0.025 -10000 0 -10000 0 0
VEGFA 0.027 0.005 -10000 0 -10000 0 0
VEGFB 0.027 0.003 -10000 0 -10000 0 0
mol:IP3 0.021 0.027 -10000 0 -10000 0 0
RASA1 0.021 0.029 -10000 0 -10000 0 0
NRP2 0.004 0.1 -10000 0 -0.47 18 18
VEGFR1 homodimer 0.02 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.039 0.07 0.3 2 -0.32 1 3
PTPN11 0.027 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.056 0.036 -10000 0 -0.24 1 1
mol:L-citrulline 0.037 0.053 0.3 3 -0.33 1 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.024 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.018 -10000 0 -10000 0 0
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.069 0.044 -10000 0 -10000 0 0
PDPK1 0.028 0.048 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.046 0.018 -10000 0 -10000 0 0
mol:NADP 0.037 0.053 0.3 3 -0.33 1 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.023 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.019 0.066 -10000 0 -0.28 18 18
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.015 0.029 -10000 0 -0.31 1 1
TRAF2/ASK1 0.031 0.021 -10000 0 -0.28 1 1
ATM 0.026 0.007 -10000 0 -10000 0 0
MAP2K3 0.005 0.096 -10000 0 -0.33 18 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.015 0.075 0.23 1 -0.28 7 8
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.055 -10000 0 -0.47 5 5
TXN 0.007 0.004 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.028 0.002 -10000 0 -10000 0 0
GADD45B 0.015 0.077 -10000 0 -0.47 10 10
MAP3K1 0.026 0.007 -10000 0 -10000 0 0
MAP3K6 0.028 0.002 -10000 0 -10000 0 0
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
MAP3K4 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.021 -10000 0 -0.34 1 1
TAK1/TAB family -0.004 0.016 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.049 0.017 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.023 0.082 -10000 0 -0.28 12 12
TRAF6 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.046 0.062 0.22 43 -10000 0 43
CCM2 0.027 0.01 0.21 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.047 0.036 -10000 0 -10000 0 0
MAPK11 0.026 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.06 0.042 0.22 3 -0.26 1 4
OSM/MEKK3 0.039 0.012 -10000 0 -10000 0 0
TAOK1 0.013 0.017 -10000 0 -0.3 1 1
TAOK2 0.014 0.005 -10000 0 -10000 0 0
TAOK3 0.015 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.025 0.025 -10000 0 -0.47 1 1
MAP3K10 0.027 0.016 0.33 1 -10000 0 1
MAP3K3 0.026 0.006 -10000 0 -10000 0 0
TRX/ASK1 0.014 0.037 -10000 0 -0.27 1 1
GADD45/MTK1/MTK1 0.045 0.062 -10000 0 -0.26 13 13
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.026 0.007 -10000 0 -10000 0 0
SMAD2 0.005 0.052 0.23 4 -0.23 7 11
SMAD3 0.028 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4 0.042 0.035 -10000 0 -0.36 1 1
SMAD4/Ubc9/PIASy 0.05 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.043 0.058 -10000 0 -0.29 1 1
PPM1A 0.027 0.004 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.016 0.05 0.24 1 -0.25 3 4
MAP3K1 0.026 0.007 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.034 0.038 -10000 0 -0.33 4 4
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
CTDSP1 0.026 0.007 -10000 0 -10000 0 0
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
CTDSPL 0.026 0.006 -10000 0 -10000 0 0
KPNB1 0.027 0.005 -10000 0 -10000 0 0
TGFBRAP1 0.022 0.049 -10000 0 -0.47 4 4
UBE2I 0.027 0.006 -10000 0 -10000 0 0
NUP153 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.029 0.022 0.24 4 -10000 0 4
PIAS4 0.027 0.005 -10000 0 -10000 0 0
Circadian rhythm pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.052 0.028 -10000 0 -10000 0 0
CLOCK 0.03 0.004 -10000 0 -10000 0 0
TIMELESS/CRY2 0.041 0.021 -10000 0 -10000 0 0
DEC1/BMAL1 0.034 0.024 -10000 0 -10000 0 0
ATR 0.026 0.006 -10000 0 -10000 0 0
NR1D1 0.024 0.013 -10000 0 -10000 0 0
ARNTL 0.028 0.008 -10000 0 -10000 0 0
TIMELESS 0.024 0.013 -10000 0 -10000 0 0
NPAS2 0.027 0.035 -10000 0 -0.46 2 2
CRY2 0.026 0.007 -10000 0 -10000 0 0
mol:CO -0.01 0.002 -10000 0 -10000 0 0
CHEK1 0.029 0.025 0.24 5 -10000 0 5
mol:HEME 0.01 0.002 -10000 0 -10000 0 0
PER1 0.012 0.081 -10000 0 -0.47 11 11
BMAL/CLOCK/NPAS2 0.058 0.033 -10000 0 -0.28 2 2
BMAL1/CLOCK 0.032 0.04 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.052 0.028 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.053 0.028 -10000 0 -10000 0 0
mol:NADPH 0.01 0.002 -10000 0 -10000 0 0
PER1/TIMELESS 0.032 0.049 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.004 0.038 0.21 10 -10000 0 10
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.064 0.048 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.055 -10000 0 -10000 0 0
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.027 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.005 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.059 0.051 -10000 0 -10000 0 0
YY1/LSF 0.024 0.054 -10000 0 -0.2 10 10
SMG5 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.028 0.013 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.031 0.049 -10000 0 -10000 0 0
SAP18 0.027 0.005 -10000 0 -10000 0 0
RELA 0.029 0.026 -10000 0 -10000 0 0
HDAC1/Smad7 0.051 0.017 -10000 0 -10000 0 0
RANGAP1 0.027 0.005 -10000 0 -10000 0 0
HDAC3/TR2 0.034 0.045 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.033 0.041 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.028 0.062 -10000 0 -0.24 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.025 0.07 0.22 13 -0.47 6 19
GATA1 0.014 0.021 -10000 0 -10000 0 0
Mad/Max 0.039 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.036 0.051 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.002 -10000 0 -10000 0 0
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.007 -10000 0 -10000 0 0
NFKBIA 0.024 0.01 -10000 0 -10000 0 0
KAT2B 0.025 0.025 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.028 0.022 -10000 0 -0.35 1 1
SIN3 complex 0.065 0.021 -10000 0 -10000 0 0
SMURF1 0.027 0.004 -10000 0 -10000 0 0
CHD3 0.025 0.008 -10000 0 -10000 0 0
SAP30 0.026 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.025 0.009 -10000 0 -10000 0 0
YY1/HDAC3 0.025 0.047 -10000 0 -0.28 1 1
YY1/HDAC2 0.024 0.052 -10000 0 -0.21 5 5
YY1/HDAC1 0.024 0.054 -10000 0 -0.2 10 10
NuRD/MBD2 Complex (MeCP1) 0.028 0.049 -10000 0 -0.34 1 1
PPARG 0.009 0.073 -10000 0 -0.26 24 24
HDAC8/hEST1B 0.051 0.016 -10000 0 -10000 0 0
UBE2I 0.027 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.034 0.045 -10000 0 -10000 0 0
MBD3L2 -0.017 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.017 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.032 0.057 -10000 0 -0.31 3 3
HDAC1 0.028 0.002 -10000 0 -10000 0 0
HDAC3 0.024 0.009 -10000 0 -10000 0 0
HDAC2 0.026 0.007 -10000 0 -10000 0 0
YY1 0.019 0.016 -10000 0 -0.25 1 1
HDAC8 0.027 0.003 -10000 0 -10000 0 0
SMAD7 0.026 0.007 -10000 0 -10000 0 0
NCOR2 0.027 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.011 0.21 1 -10000 0 1
STAT3 0.021 0.008 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.037 0.054 -10000 0 -0.2 1 1
YY1/SAP30/HDAC1 0.038 0.053 -10000 0 -0.2 1 1
EP300 0.027 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.021 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.01 -10000 0 -10000 0 0
histone deacetylation 0.027 0.052 -10000 0 -0.27 3 3
STAT3 (dimer non-phopshorylated)/HDAC3 0.03 0.025 -10000 0 -10000 0 0
nuclear export -0.051 0.016 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GATAD2B 0.025 0.008 -10000 0 -10000 0 0
GATAD2A 0.027 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.031 0.063 0.23 1 -0.26 6 7
GATA1/HDAC1 0.038 0.007 -10000 0 -10000 0 0
GATA1/HDAC3 0.032 0.046 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.045 0.031 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.029 0.045 -10000 0 -0.46 1 1
NuRD Complex 0.031 0.056 -10000 0 -0.3 1 1
positive regulation of chromatin silencing 0.056 0.049 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.033 0.048 -10000 0 -0.21 6 6
HDAC complex 0.066 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.037 0.01 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.052 0.016 -10000 0 -10000 0 0
TNF 0.036 0.042 0.21 21 -10000 0 21
negative regulation of cell growth 0.027 0.05 -10000 0 -0.29 4 4
NuRD/MBD2/PRMT5 Complex 0.028 0.049 -10000 0 -0.34 1 1
Ran/GTP/Exportin 1 0.033 0.046 -10000 0 -0.28 2 2
NF kappa B/RelA/I kappa B alpha 0.023 0.039 -10000 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.016 0.054 -10000 0 -0.29 5 5
TFCP2 0.027 0.004 -10000 0 -10000 0 0
NR2C1 0.027 0.004 -10000 0 -10000 0 0
MBD3 0.027 0.005 -10000 0 -10000 0 0
MBD2 0.026 0.007 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.038 0.021 -10000 0 -0.34 1 1
FBXW11 0.026 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.026 0.032 0.23 1 -0.28 3 4
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.053 -10000 0 -10000 0 0
NFKBIA 0.019 0.043 -10000 0 -0.21 7 7
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.012 -10000 0 -10000 0 0
ARRB2 0.014 0.005 -10000 0 -10000 0 0
REL 0.024 0.046 0.27 2 -0.47 3 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.018 -10000 0 -0.27 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.011 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.021 0.018 0.25 2 -10000 0 2
PIK3R1 0.025 0.026 -10000 0 -0.47 1 1
NFKB1 0.013 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.023 0.04 -10000 0 -0.19 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.056 -10000 0 -10000 0 0
SRC 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.035 0.023 -10000 0 -0.34 1 1
NF kappa B1 p50/RelA 0.023 0.041 -10000 0 -0.19 6 6
IKBKB 0.025 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.007 -10000 0 -10000 0 0
SYK 0.02 0.05 -10000 0 -0.47 4 4
I kappa B alpha/PIK3R1 0.023 0.057 -10000 0 -0.31 2 2
cell death 0.024 0.054 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.026 0.032 0.23 1 -0.28 3 4
LCK 0.024 0.051 0.21 2 -0.47 4 6
BCL3 0.026 0.025 -10000 0 -0.47 1 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.013 0.03 0.15 16 -10000 0 16
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.023 0.026 -10000 0 -10000 0 0
AP2 0.038 0.012 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.033 0.013 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.011 -10000 0 -10000 0 0
CD4 0.024 0.035 -10000 0 -0.47 2 2
CLTA 0.025 0.009 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
ARFGAP1 0.007 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.01 -10000 0 -10000 0 0
ARF1/GTP 0.029 0.015 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.011 0.008 -10000 0 -10000 0 0
mol:Choline 0.007 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.03 0.006 -10000 0 -10000 0 0
DDEF1 0.006 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.007 0.019 -10000 0 -0.11 1 1
AP2M1 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.016 0.007 -10000 0 -10000 0 0
Rac/GTP 0.021 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.014 -10000 0 -10000 0 0
ARFIP2 0.02 0.014 -10000 0 -10000 0 0
COPA 0.024 0.01 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.05 0.16 3 -0.18 3 6
ARF1/GTP/ARHGAP10 0.018 0.008 -10000 0 -10000 0 0
GGA3 0.027 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.026 0.023 -10000 0 -0.22 2 2
AP2A1 0.027 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.008 0.037 -10000 0 -0.21 6 6
ARF1/GDP/Membrin 0.031 0.027 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.032 0.013 -10000 0 -10000 0 0
CYTH2 0.03 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.038 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.02 0.005 -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 0.027 0.036 -10000 0 -0.18 2 2
PLD2 0.007 0.01 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.002 -10000 0 -10000 0 0
PIP5K1A 0.007 0.01 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.02 0.02 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.01 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.002 -10000 0 -10000 0 0
GOSR2 0.01 0.024 -10000 0 -0.31 2 2
USO1 0.011 0.018 -10000 0 -0.31 1 1
GBF1 0.008 0.036 -10000 0 -0.31 5 5
ARF1/GTP/Arfaptin 2 0.035 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.048 0.03 -10000 0 -0.28 2 2
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 0.039 0.01 -9999 0 -9999 0 0
FBXW11 0.026 0.007 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.007 -9999 0 -9999 0 0
CHUK 0.027 0.005 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.072 0.028 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.027 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.039 0.009 -9999 0 -9999 0 0
RELB 0.027 0.005 -9999 0 -9999 0 0
NFKB2 0.027 0.005 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.035 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.035 0.009 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 404 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZF.AA5P TCGA.ZF.AA5N TCGA.ZF.AA5H TCGA.ZF.AA58
109_MAP3K5 0.035 -0.11 0.054 0.069
47_PPARGC1A 0.028 -0.017 -0.47 -0.47
105_BMP4 0.028 0.028 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 -0.47 -0.47
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR 0.072 0.064 0.072 -0.26
30_TGFB1/TGF beta receptor Type II 0.026 0.026 0.026 0.027
84_STAT5B 0.024 -0.11 0.097 0.021
84_STAT5A 0.024 -0.11 0.097 0.021
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/14522370/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BLCA-TP/15076718/GDAC_Gistic2Report_15081675/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.

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