PARADIGM pathway analysis of mRNASeq expression and copy number data
Skin Cutaneous Melanoma (Metastatic)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1G73CST
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1G73CST
Overview
Introduction

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

Summary

There were 52 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
BCR signaling pathway 125
IL4-mediated signaling events 121
TCR signaling in naïve CD8+ T cells 106
IL23-mediated signaling events 102
Nephrin/Neph1 signaling in the kidney podocyte 81
IL12-mediated signaling events 78
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 61
Caspase cascade in apoptosis 59
JNK signaling in the CD4+ TCR pathway 55
Calcium signaling in the CD4+ TCR pathway 55
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 367 . 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 ( 367 ).

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
BCR signaling pathway 0.3406 125 12465 99 -0.71 0.043 1000 -1000 -0.045 -1000
IL4-mediated signaling events 0.3297 121 11067 91 -1.3 1 1000 -1000 -0.051 -1000
TCR signaling in naïve CD8+ T cells 0.2888 106 9887 93 -0.56 0.12 1000 -1000 -0.031 -1000
IL23-mediated signaling events 0.2779 102 6149 60 -0.76 0.035 1000 -1000 -0.042 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.2207 81 2767 34 -0.15 0.035 1000 -1000 -0.031 -1000
IL12-mediated signaling events 0.2125 78 6837 87 -0.68 0.11 1000 -1000 -0.027 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1662 61 4154 68 -0.57 0.12 1000 -1000 -0.045 -1000
Caspase cascade in apoptosis 0.1608 59 4407 74 -0.16 0.12 1000 -1000 -0.026 -1000
JNK signaling in the CD4+ TCR pathway 0.1499 55 939 17 -0.22 0.033 1000 -1000 -0.018 -1000
Calcium signaling in the CD4+ TCR pathway 0.1499 55 1711 31 -0.35 0.035 1000 -1000 -0.034 -1000
E-cadherin signaling events 0.1499 55 276 5 -0.08 0.035 1000 -1000 0.019 -1000
IL27-mediated signaling events 0.1417 52 2679 51 -0.26 0.17 1000 -1000 -0.026 -1000
FAS signaling pathway (CD95) 0.1390 51 2438 47 -0.095 0.076 1000 -1000 -0.027 -1000
Ras signaling in the CD4+ TCR pathway 0.1390 51 880 17 -0.14 0.063 1000 -1000 -0.007 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.1253 46 3440 74 -0.08 0.08 1000 -1000 -0.04 -1000
E-cadherin signaling in the nascent adherens junction 0.1199 44 3393 76 -0.092 0.052 1000 -1000 -0.034 -1000
a4b1 and a4b7 Integrin signaling 0.1117 41 207 5 -0.03 0.011 1000 -1000 0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.1117 41 1874 45 -0.17 0.073 1000 -1000 -0.02 -1000
Thromboxane A2 receptor signaling 0.1063 39 4147 105 -0.12 0.057 1000 -1000 -0.024 -1000
amb2 Integrin signaling 0.1035 38 3149 82 -0.18 0.044 1000 -1000 -0.018 -1000
Glucocorticoid receptor regulatory network 0.1035 38 4390 114 -0.42 0.23 1000 -1000 -0.035 -1000
Signaling events regulated by Ret tyrosine kinase 0.1035 38 3158 82 -0.069 0.035 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 0.1008 37 2192 58 -0.15 0.06 1000 -1000 -0.023 -1000
IL2 signaling events mediated by STAT5 0.1008 37 817 22 -0.16 0.036 1000 -1000 -0.011 -1000
Class I PI3K signaling events 0.1008 37 2730 73 -0.38 0.069 1000 -1000 -0.016 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1008 37 3328 88 -0.21 0.046 1000 -1000 -0.052 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0981 36 1366 37 -0.22 0.049 1000 -1000 -0.015 -1000
Endothelins 0.0981 36 3550 96 -0.15 0.036 1000 -1000 -0.03 -1000
FOXA2 and FOXA3 transcription factor networks 0.0926 34 1571 46 -0.42 0.04 1000 -1000 -0.033 -1000
Syndecan-1-mediated signaling events 0.0872 32 1099 34 -0.095 0.035 1000 -1000 -0.008 -1000
Fc-epsilon receptor I signaling in mast cells 0.0872 32 3152 97 -0.1 0.06 1000 -1000 -0.03 -1000
E-cadherin signaling in keratinocytes 0.0872 32 1407 43 -0.08 0.037 1000 -1000 -0.013 -1000
S1P4 pathway 0.0872 32 812 25 -0.11 0.045 1000 -1000 -0.014 -1000
ceramide signaling pathway 0.0817 30 1505 49 -0.1 0.05 1000 -1000 -0.022 -1000
IFN-gamma pathway 0.0790 29 1984 68 -0.12 0.045 1000 -1000 -0.031 -1000
LPA receptor mediated events 0.0763 28 2889 102 -0.072 0.045 1000 -1000 -0.048 -1000
Syndecan-4-mediated signaling events 0.0763 28 1922 67 -0.17 0.046 1000 -1000 -0.026 -1000
HIF-1-alpha transcription factor network 0.0708 26 2025 76 -0.083 0.11 1000 -1000 -0.007 -1000
Atypical NF-kappaB pathway 0.0708 26 807 31 -0.14 0.049 1000 -1000 -0.005 -1000
Visual signal transduction: Cones 0.0681 25 982 38 -0.14 0.043 1000 -1000 -0.005 -1000
Glypican 1 network 0.0654 24 1179 48 -0.22 0.038 1000 -1000 -0.023 -1000
Osteopontin-mediated events 0.0627 23 897 38 -0.036 0.049 1000 -1000 -0.017 -1000
TRAIL signaling pathway 0.0627 23 1109 48 -0.03 0.053 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 0.0627 23 1266 54 -0.24 0.072 1000 -1000 -0.034 -1000
Visual signal transduction: Rods 0.0627 23 1220 52 -0.14 0.047 1000 -1000 -0.013 -1000
Aurora C signaling 0.0572 21 150 7 -0.056 0.032 1000 -1000 -0.009 -1000
Ceramide signaling pathway 0.0572 21 1602 76 -0.1 0.079 1000 -1000 -0.017 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0572 21 1121 52 -0.18 0.079 1000 -1000 -0.016 -1000
Ephrin A reverse signaling 0.0545 20 141 7 0 0.025 1000 -1000 0 -1000
Paxillin-dependent events mediated by a4b1 0.0545 20 721 36 -0.04 0.059 1000 -1000 -0.03 -1000
Arf6 signaling events 0.0518 19 1211 62 -0.1 0.073 1000 -1000 -0.027 -1000
IL6-mediated signaling events 0.0518 19 1483 75 -0.18 0.056 1000 -1000 -0.025 -1000
Plasma membrane estrogen receptor signaling 0.0490 18 1585 86 -0.054 0.062 1000 -1000 -0.031 -1000
Signaling events mediated by PTP1B 0.0463 17 1333 76 -0.24 0.063 1000 -1000 -0.032 -1000
EPO signaling pathway 0.0463 17 982 55 -0.038 0.053 1000 -1000 -0.018 -1000
Signaling events mediated by the Hedgehog family 0.0436 16 852 52 -0.2 0.058 1000 -1000 -0.012 -1000
Integrins in angiogenesis 0.0436 16 1407 84 -0.14 0.077 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0409 15 1354 85 -0.037 0.074 1000 -1000 -0.031 -1000
Nectin adhesion pathway 0.0409 15 1002 63 -0.18 0.072 1000 -1000 -0.032 -1000
EPHB forward signaling 0.0409 15 1329 85 -0.054 0.067 1000 -1000 -0.044 -1000
PDGFR-beta signaling pathway 0.0381 14 1440 97 -0.3 0.087 1000 -1000 -0.029 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0381 14 1110 78 -0.074 0.09 1000 -1000 -0.029 -1000
Cellular roles of Anthrax toxin 0.0354 13 533 39 -0.12 0.042 1000 -1000 -0.013 -1000
p75(NTR)-mediated signaling 0.0354 13 1673 125 -0.1 0.088 1000 -1000 -0.032 -1000
BMP receptor signaling 0.0354 13 1126 81 -0.14 0.074 1000 -1000 -0.018 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0354 13 1136 83 -0.097 0.066 1000 -1000 -0.013 -1000
LPA4-mediated signaling events 0.0327 12 146 12 -0.047 0.01 1000 -1000 -0.009 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0327 12 342 28 -0.11 0.066 1000 -1000 -0.012 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0327 12 1478 120 -0.075 0.084 1000 -1000 -0.036 -1000
Noncanonical Wnt signaling pathway 0.0300 11 310 26 -0.001 0.052 1000 -1000 -0.017 -1000
Syndecan-2-mediated signaling events 0.0300 11 826 69 -0.17 0.058 1000 -1000 -0.02 -1000
IL1-mediated signaling events 0.0300 11 689 62 -0.032 0.09 1000 -1000 -0.019 -1000
Ephrin B reverse signaling 0.0300 11 552 48 -0.1 0.048 1000 -1000 -0.029 -1000
ErbB2/ErbB3 signaling events 0.0272 10 658 65 -0.023 0.06 1000 -1000 -0.048 -1000
Canonical Wnt signaling pathway 0.0272 10 521 51 -0.027 0.075 1000 -1000 -0.03 -1000
EGFR-dependent Endothelin signaling events 0.0272 10 225 21 -0.02 0.055 1000 -1000 -0.027 -1000
Presenilin action in Notch and Wnt signaling 0.0245 9 601 61 -0.067 0.088 1000 -1000 -0.039 -1000
Canonical NF-kappaB pathway 0.0218 8 312 39 -0.054 0.073 1000 -1000 -0.005 -1000
TCGA08_rtk_signaling 0.0218 8 209 26 -0.04 0.082 1000 -1000 -0.021 -1000
TCGA08_retinoblastoma 0.0218 8 70 8 -0.002 0.027 1000 -1000 -0.004 -1000
Aurora B signaling 0.0218 8 536 67 -0.097 0.089 1000 -1000 -0.027 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0191 7 389 54 -0.078 0.064 1000 -1000 -0.013 -1000
mTOR signaling pathway 0.0191 7 372 53 -0.02 0.058 1000 -1000 -0.02 -1000
Signaling mediated by p38-gamma and p38-delta 0.0191 7 114 15 -0.004 0.034 1000 -1000 -0.014 -1000
Effects of Botulinum toxin 0.0191 7 194 26 -0.026 0.045 1000 -1000 0 -1000
HIF-2-alpha transcription factor network 0.0163 6 273 43 -0.16 0.17 1000 -1000 -0.045 -1000
Signaling events mediated by HDAC Class I 0.0163 6 663 104 -0.064 0.081 1000 -1000 -0.031 -1000
Glypican 2 network 0.0163 6 27 4 0.025 0.036 1000 -1000 0.021 -1000
Insulin Pathway 0.0163 6 455 74 -0.059 0.083 1000 -1000 -0.024 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0163 6 204 33 -0.009 0.077 1000 -1000 -0.023 -1000
Class IB PI3K non-lipid kinase events 0.0163 6 18 3 -0.027 0.027 1000 -1000 -0.023 -1000
Regulation of Androgen receptor activity 0.0163 6 463 70 -0.057 0.055 1000 -1000 -0.02 -1000
ErbB4 signaling events 0.0136 5 362 69 -0.031 0.054 1000 -1000 -0.01 -1000
PLK1 signaling events 0.0136 5 425 85 -0.008 0.069 1000 -1000 -0.027 -1000
FoxO family signaling 0.0136 5 350 64 -0.41 0.095 1000 -1000 -0.022 -1000
Signaling mediated by p38-alpha and p38-beta 0.0136 5 228 44 -0.005 0.061 1000 -1000 -0.016 -1000
Wnt signaling 0.0136 5 41 7 0.007 0.033 1000 -1000 0.001 -1000
Regulation of Telomerase 0.0136 5 578 102 -0.11 0.077 1000 -1000 -0.023 -1000
VEGFR1 specific signals 0.0136 5 282 56 -0.047 0.084 1000 -1000 -0.017 -1000
S1P3 pathway 0.0136 5 213 42 -0.037 0.054 1000 -1000 -0.012 -1000
Regulation of nuclear SMAD2/3 signaling 0.0109 4 551 136 -0.11 0.13 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 0.0109 4 322 68 -0.054 0.066 1000 -1000 -0.018 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0109 4 522 125 -0.075 0.087 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 0.0109 4 146 34 -0.054 0.078 1000 -1000 -0.031 -1000
p38 MAPK signaling pathway 0.0109 4 193 44 -0.011 0.057 1000 -1000 -0.011 -1000
Hedgehog signaling events mediated by Gli proteins 0.0082 3 211 65 0 0.081 1000 -1000 -0.021 -1000
Arf6 downstream pathway 0.0082 3 162 43 -0.051 0.064 1000 -1000 -0.03 -1000
S1P1 pathway 0.0082 3 134 36 0 0.052 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 0.0082 3 213 58 -0.033 0.067 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 0.0082 3 135 35 -0.018 0.088 1000 -1000 -0.012 -1000
Nongenotropic Androgen signaling 0.0082 3 160 52 -0.041 0.057 1000 -1000 -0.015 -1000
IGF1 pathway 0.0082 3 189 57 -0.025 0.085 1000 -1000 -0.022 -1000
Arf1 pathway 0.0082 3 206 54 -0.008 0.05 1000 -1000 -0.008 -1000
Coregulation of Androgen receptor activity 0.0054 2 178 76 -0.015 0.06 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class II 0.0054 2 150 75 -0.039 0.089 1000 -1000 -0.016 -1000
Aurora A signaling 0.0054 2 124 60 0 0.075 1000 -1000 -0.005 -1000
PDGFR-alpha signaling pathway 0.0054 2 119 44 -0.019 0.071 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class III 0.0054 2 102 40 -0.056 0.057 1000 -1000 -0.034 -1000
Reelin signaling pathway 0.0054 2 155 56 -0.002 0.079 1000 -1000 -0.016 -1000
Arf6 trafficking events 0.0054 2 206 71 -0.052 0.064 1000 -1000 -0.033 -1000
FOXM1 transcription factor network 0.0054 2 121 51 0.008 0.26 1000 -1000 -0.046 -1000
Insulin-mediated glucose transport 0.0027 1 48 32 0 0.064 1000 -1000 -0.014 -1000
Rapid glucocorticoid signaling 0.0027 1 36 20 -0.009 0.041 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 7 23 0.007 0.069 1000 -1000 -0.008 -1000
BARD1 signaling events 0.0000 0 38 57 -0.078 0.091 1000 -1000 -0.037 -1000
PLK2 and PLK4 events 0.0000 0 2 3 0.018 -1000 1000 -1000 -0.003 -1000
Circadian rhythm pathway 0.0000 0 6 22 -0.012 0.08 1000 -1000 -0.021 -1000
S1P5 pathway 0.0000 0 9 17 -0.039 0.041 1000 -1000 -0.003 -1000
TCGA08_p53 0.0000 0 1 7 0 0.031 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 11 27 0 0.082 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.089 1000 -1000 0 -1000
Total NA 2740 171097 7203 -16 -990 131000 -131000 -2.8 -131000
BCR signaling pathway

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
JUN -0.29 0.26 -10000 0 -0.49 216 216
IKBKB -0.12 0.14 0.22 1 -0.29 94 95
AKT1 -0.17 0.13 0.26 1 -0.27 225 226
IKBKG -0.12 0.14 -10000 0 -0.28 115 115
CALM1 -0.32 0.33 -10000 0 -0.58 194 194
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
MAP3K1 -0.44 0.38 -10000 0 -0.73 222 222
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.34 0.36 -10000 0 -0.62 196 196
DOK1 0.035 0.002 -10000 0 -10000 0 0
AP-1 -0.15 0.14 -10000 0 -0.27 192 192
LYN 0.016 0.084 -10000 0 -0.42 13 13
BLNK -0.11 0.21 -10000 0 -0.42 116 116
SHC1 0.032 0.011 -10000 0 -10000 0 0
BCR complex -0.27 0.26 -10000 0 -0.47 225 225
CD22 -0.47 0.42 -10000 0 -0.78 220 220
CAMK2G -0.29 0.3 -10000 0 -0.53 193 193
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
INPP5D -0.038 0.16 -10000 0 -0.42 58 58
SHC/GRB2/SOS1 -0.24 0.26 -10000 0 -0.42 215 215
GO:0007205 -0.35 0.37 -10000 0 -0.63 197 197
SYK -0.012 0.13 -10000 0 -0.42 36 36
ELK1 -0.33 0.34 -10000 0 -0.59 194 194
NFATC1 -0.37 0.32 0.32 1 -0.6 225 226
B-cell antigen/BCR complex -0.27 0.26 -10000 0 -0.47 225 225
PAG1/CSK 0.043 0.031 -10000 0 -0.3 2 2
NFKBIB -0.025 0.053 0.13 1 -0.13 18 19
HRAS -0.3 0.31 -10000 0 -0.54 196 196
NFKBIA -0.024 0.053 0.13 1 -0.13 18 19
NF-kappa-B/RelA/I kappa B beta -0.014 0.045 0.14 1 -0.094 6 7
RasGAP/Csk -0.17 0.22 -10000 0 -0.34 218 218
mol:GDP -0.33 0.35 -10000 0 -0.6 195 195
PTEN 0.03 0.012 -10000 0 -10000 0 0
CD79B -0.2 0.22 -10000 0 -0.42 186 186
NF-kappa-B/RelA/I kappa B alpha -0.013 0.045 0.14 1 -0.093 4 5
GRB2 0.034 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.42 0.34 -10000 0 -0.66 234 234
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.35 0.38 -10000 0 -0.62 210 210
CSK 0.034 0.006 -10000 0 -10000 0 0
FOS -0.3 0.3 -10000 0 -0.55 193 193
CHUK -0.14 0.15 -10000 0 -0.31 130 130
IBTK 0.032 0.011 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.27 0.32 0.25 1 -0.53 191 192
PTPN6 -0.48 0.43 -10000 0 -0.79 219 219
RELA 0.034 0.007 -10000 0 -10000 0 0
BCL2A1 -0.01 0.037 -10000 0 -0.11 3 3
VAV2 -0.54 0.45 -10000 0 -0.86 228 228
ubiquitin-dependent protein catabolic process -0.02 0.052 0.14 1 -0.12 18 19
BTK -0.15 0.41 -10000 0 -1 65 65
CD19 -0.5 0.43 -10000 0 -0.8 226 226
MAP4K1 -0.044 0.17 -10000 0 -0.42 64 64
CD72 -0.066 0.18 -10000 0 -0.42 79 79
PAG1 0.029 0.035 -10000 0 -0.42 2 2
MAPK14 -0.35 0.31 0.24 1 -0.58 218 219
SH3BP5 0.035 0.005 -10000 0 -10000 0 0
PIK3AP1 -0.38 0.42 -10000 0 -0.67 209 209
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.51 0.58 -10000 0 -0.89 214 214
RAF1 -0.28 0.29 -10000 0 -0.51 195 195
RasGAP/p62DOK/SHIP -0.2 0.25 -10000 0 -0.38 222 222
CD79A -0.22 0.22 -10000 0 -0.42 210 210
re-entry into mitotic cell cycle -0.15 0.14 -10000 0 -0.27 191 191
RASA1 0.032 0.025 -10000 0 -0.42 1 1
MAPK3 -0.22 0.23 0.24 1 -0.42 186 187
MAPK1 -0.22 0.23 0.24 1 -0.42 183 184
CD72/SHP1 -0.47 0.42 0.26 1 -0.78 222 223
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.36 0.31 -10000 0 -0.59 221 221
actin cytoskeleton organization -0.42 0.35 -10000 0 -0.67 227 227
NF-kappa-B/RelA -0.019 0.087 0.25 1 -0.19 17 18
Calcineurin -0.25 0.28 -10000 0 -0.48 193 193
PI3K -0.39 0.31 -10000 0 -0.6 240 240
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.4 0.44 -10000 0 -0.7 211 211
SOS1 0.035 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.59 0.52 -10000 0 -0.97 226 226
DAPP1 -0.71 0.63 -10000 0 -1.2 226 226
cytokine secretion -0.34 0.29 0.32 1 -0.55 225 226
mol:DAG -0.35 0.38 -10000 0 -0.62 210 210
PLCG2 -0.002 0.12 -10000 0 -0.42 29 29
MAP2K1 -0.25 0.26 0.25 1 -0.47 187 188
B-cell antigen/BCR complex/FcgammaRIIB -0.22 0.24 -10000 0 -0.4 221 221
mol:PI-3-4-5-P3 -0.26 0.19 -10000 0 -0.39 234 234
ETS1 -0.26 0.26 -10000 0 -0.48 191 191
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.26 0.31 -10000 0 -0.48 224 224
B-cell antigen/BCR complex/LYN -0.42 0.4 -10000 0 -0.74 209 209
MALT1 0.033 0.024 -10000 0 -0.42 1 1
TRAF6 0.035 0.006 -10000 0 -10000 0 0
RAC1 -0.46 0.39 -10000 0 -0.74 226 226
B-cell antigen/BCR complex/LYN/SYK -0.45 0.43 -10000 0 -0.76 219 219
CARD11 -0.35 0.38 0.26 1 -0.65 191 192
FCGR2B 0.013 0.09 -10000 0 -0.42 15 15
PPP3CA 0.034 0.006 -10000 0 -10000 0 0
BCL10 0.035 0.006 -10000 0 -10000 0 0
IKK complex -0.043 0.055 0.16 1 -0.12 30 31
PTPRC -0.097 0.2 -10000 0 -0.42 104 104
PDPK1 -0.17 0.12 -10000 0 -0.26 225 225
PPP3CB 0.032 0.01 -10000 0 -10000 0 0
PPP3CC 0.033 0.008 -10000 0 -10000 0 0
POU2F2 -0.015 0.045 -10000 0 -0.1 18 18
IL4-mediated signaling events

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
BCL2L1 -0.85 0.61 -10000 0 -1.3 200 200
STAT6 (cleaved dimer) -0.92 0.66 -10000 0 -1.4 225 225
IGHG1 -0.24 0.17 -10000 0 -0.37 107 107
IGHG3 -0.83 0.58 -10000 0 -1.2 217 217
AKT1 -0.52 0.47 -10000 0 -1.1 135 135
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.56 0.62 -10000 0 -1.3 125 125
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.58 0.57 -10000 0 -1.3 129 129
THY1 -0.86 0.61 -10000 0 -1.3 201 201
MYB 0.015 0.084 -10000 0 -0.42 13 13
HMGA1 0.029 0.035 -10000 0 -0.42 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.62 0.54 -10000 0 -0.96 213 213
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.62 0.61 -10000 0 -1.3 135 135
SP1 0.036 0.013 -10000 0 -10000 0 0
INPP5D -0.037 0.16 -10000 0 -0.42 58 58
SOCS5 0.048 0.023 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.91 0.66 -10000 0 -1.4 219 219
SOCS1 -0.53 0.36 -10000 0 -0.79 207 207
SOCS3 -0.48 0.4 -10000 0 -0.93 128 128
FCER2 -1.3 0.68 -10000 0 -1.6 293 293
PARP14 0.013 0.049 -10000 0 -0.42 3 3
CCL17 -0.89 0.64 -10000 0 -1.4 202 202
GRB2 0.034 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.45 0.45 -10000 0 -0.97 126 126
T cell proliferation -0.9 0.66 -10000 0 -1.4 213 213
IL4R/JAK1 -0.86 0.62 -10000 0 -1.3 205 205
EGR2 -0.97 0.63 -10000 0 -1.4 227 227
JAK2 -0.042 0.066 -10000 0 -0.44 5 5
JAK3 0.007 0.11 -10000 0 -0.39 25 25
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
JAK1 0.001 0.027 -10000 0 -10000 0 0
COL1A2 -0.22 0.21 -10000 0 -1.2 8 8
CCL26 -0.86 0.61 -10000 0 -1.3 204 204
IL4R -0.93 0.67 -10000 0 -1.4 204 204
PTPN6 -0.061 0.19 -10000 0 -0.4 88 88
IL13RA2 -0.88 0.62 -10000 0 -1.4 207 207
IL13RA1 -0.04 0.045 -10000 0 -10000 0 0
IRF4 -0.66 0.6 -10000 0 -1.1 201 201
ARG1 -0.24 0.27 -10000 0 -0.97 28 28
CBL -0.58 0.49 -10000 0 -0.9 211 211
GTF3A 0.033 0.015 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.048 0.071 -10000 0 -0.32 5 5
IRF4/BCL6 -0.57 0.56 -10000 0 -1 201 201
CD40LG -0.21 0.22 -10000 0 -0.42 195 195
MAPK14 -0.56 0.49 -10000 0 -0.96 178 178
mitosis -0.48 0.42 -10000 0 -0.96 135 135
STAT6 -1.1 0.89 -10000 0 -1.7 215 215
SPI1 0.008 0.11 -10000 0 -0.42 23 23
RPS6KB1 -0.45 0.4 -10000 0 -0.91 134 134
STAT6 (dimer) -1.1 0.88 -10000 0 -1.7 215 215
STAT6 (dimer)/PARP14 -1 0.74 -10000 0 -1.4 255 255
mast cell activation 0.017 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.6 0.6 -10000 0 -1.3 136 136
FRAP1 -0.52 0.47 -10000 0 -1.1 135 135
LTA -1 0.73 -10000 0 -1.6 215 215
FES 0.024 0.066 -10000 0 -0.42 8 8
T-helper 1 cell differentiation 1 0.76 1.5 216 -10000 0 216
CCL11 -0.83 0.58 -10000 0 -1.3 204 204
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.58 0.59 -10000 0 -1.3 131 131
IL2RG -0.099 0.2 -10000 0 -0.4 112 112
IL10 -0.87 0.63 -10000 0 -1.4 203 203
IRS1 0.032 0.011 -10000 0 -10000 0 0
IRS2 0.034 0.008 -10000 0 -10000 0 0
IL4 -0.2 0.26 -10000 0 -1.3 17 17
IL5 -0.86 0.61 -10000 0 -1.3 201 201
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.68 0.52 -10000 0 -1 209 209
COL1A1 -0.25 0.25 -10000 0 -1.2 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.9 0.66 -10000 0 -1.4 199 199
IL2R gamma/JAK3 -0.071 0.18 -10000 0 -0.34 111 111
TFF3 -0.93 0.66 -10000 0 -1.4 207 207
ALOX15 -0.86 0.62 -10000 0 -1.3 202 202
MYBL1 0.029 0.035 -10000 0 -0.42 2 2
T-helper 2 cell differentiation -0.8 0.62 -10000 0 -1.2 215 215
SHC1 0.032 0.011 -10000 0 -10000 0 0
CEBPB 0.034 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.57 0.56 -10000 0 -1.2 133 133
mol:PI-3-4-5-P3 -0.52 0.47 -10000 0 -1.1 135 135
PI3K -0.57 0.55 -10000 0 -1.2 134 134
DOK2 -0.01 0.13 -10000 0 -0.42 35 35
ETS1 0.045 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.41 0.41 -10000 0 -0.89 127 127
ITGB3 -0.88 0.62 -10000 0 -1.4 205 205
PIGR -0.93 0.68 -10000 0 -1.5 205 205
IGHE 0.055 0.059 0.19 33 -10000 0 33
MAPKKK cascade -0.4 0.39 -10000 0 -0.86 127 127
BCL6 0.04 0.011 -10000 0 -10000 0 0
OPRM1 -0.86 0.61 -10000 0 -1.3 199 199
RETNLB -0.86 0.61 -10000 0 -1.3 204 204
SELP -0.97 0.71 -10000 0 -1.5 214 214
AICDA -1.1 0.67 -10000 0 -1.5 258 258
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.26 0.39 0.3 9 -0.68 162 171
FYN -0.43 0.56 0.27 2 -1 164 166
LAT/GRAP2/SLP76 -0.29 0.4 -10000 0 -0.71 164 164
IKBKB 0.034 0.007 -10000 0 -10000 0 0
AKT1 -0.22 0.3 0.18 1 -0.53 164 165
B2M 0.026 0.043 -10000 0 -0.43 3 3
IKBKG -0.051 0.089 0.11 10 -0.15 147 157
MAP3K8 0.021 0.07 -10000 0 -0.42 9 9
mol:Ca2+ -0.018 0.035 0.089 24 -0.054 112 136
integrin-mediated signaling pathway 0.013 0.085 -10000 0 -0.25 34 34
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.36 0.47 -10000 0 -0.85 166 166
TRPV6 0.12 0.37 1.2 39 -10000 0 39
CD28 -0.039 0.17 -10000 0 -0.42 58 58
SHC1 -0.4 0.52 0.29 11 -0.94 164 175
receptor internalization -0.48 0.61 -10000 0 -1.1 170 170
PRF1 -0.52 0.67 -10000 0 -1.3 155 155
KRAS 0.034 0.006 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.16 0.24 0.18 1 -0.42 158 159
LAT -0.42 0.53 -10000 0 -0.98 163 163
EntrezGene:6955 -0.003 0.004 -10000 0 -10000 0 0
CD3D -0.12 0.22 -10000 0 -0.43 123 123
CD3E -0.1 0.21 -10000 0 -0.43 106 106
CD3G -0.098 0.2 -10000 0 -0.42 102 102
RASGRP2 -0.088 0.097 0.072 1 -0.18 184 185
RASGRP1 -0.23 0.32 0.22 3 -0.57 162 165
HLA-A -0.004 0.007 -10000 0 -10000 0 0
RASSF5 -0.013 0.13 -10000 0 -0.42 36 36
RAP1A/GTP/RAPL 0.014 0.085 -10000 0 -0.25 34 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.047 0.091 0.15 8 -0.14 156 164
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.11 0.14 -10000 0 -0.26 157 157
PRKCA -0.12 0.17 -10000 0 -0.31 156 156
GRAP2 -0.015 0.14 -10000 0 -0.42 39 39
mol:IP3 -0.21 0.28 -10000 0 -0.51 163 163
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.49 0.64 -10000 0 -1.2 158 158
ORAI1 -0.11 0.31 0.36 1 -1 39 40
CSK -0.42 0.54 0.22 4 -0.99 163 167
B7 family/CD28 -0.42 0.59 -10000 0 -1 161 161
CHUK 0.032 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.53 0.68 0.2 2 -1.2 166 168
PTPN6 -0.45 0.58 0.2 1 -1.1 163 164
VAV1 -0.42 0.54 0.2 1 -0.98 164 165
Monovalent TCR/CD3 -0.31 0.43 -10000 0 -0.74 161 161
CBL 0.032 0.011 -10000 0 -10000 0 0
LCK -0.49 0.63 0.24 3 -1.2 163 166
PAG1 -0.41 0.54 0.22 14 -0.98 164 178
RAP1A 0.034 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.53 0.68 0.2 2 -1.2 167 169
CD80 -0.061 0.18 -10000 0 -0.42 75 75
CD86 -0.022 0.15 -10000 0 -0.42 44 44
PDK1/CARD11/BCL10/MALT1 -0.12 0.18 -10000 0 -0.32 158 158
HRAS 0.034 0.006 -10000 0 -10000 0 0
GO:0035030 -0.32 0.42 0.18 1 -0.77 162 163
CD8A -0.13 0.22 -10000 0 -0.43 133 133
CD8B -0.14 0.22 -10000 0 -0.43 135 135
PTPRC -0.1 0.2 -10000 0 -0.42 104 104
PDK1/PKC theta -0.28 0.37 0.23 1 -0.69 161 162
CSK/PAG1 -0.4 0.52 0.26 5 -0.95 163 168
SOS1 0.035 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.008 0.036 -10000 0 -0.31 3 3
GRAP2/SLP76 -0.36 0.49 -10000 0 -0.88 165 165
STIM1 -0.021 0.06 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.12 0.18 10 -0.19 147 157
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.56 0.72 -10000 0 -1.3 170 170
mol:DAG -0.2 0.24 -10000 0 -0.45 163 163
RAP1A/GDP -0.018 0.043 0.077 7 -0.065 143 150
PLCG1 0.033 0.01 -10000 0 -10000 0 0
CD247 -0.1 0.21 -10000 0 -0.42 107 107
cytotoxic T cell degranulation -0.47 0.61 -10000 0 -1.1 158 158
RAP1A/GTP -0.032 0.036 -10000 0 -0.068 180 180
mol:PI-3-4-5-P3 -0.27 0.36 0.2 1 -0.66 164 165
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.29 0.38 -10000 0 -0.7 163 163
NRAS 0.034 0.008 -10000 0 -10000 0 0
ZAP70 -0.12 0.22 -10000 0 -0.42 126 126
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.29 0.38 -10000 0 -0.7 163 163
MALT1 0.033 0.024 -10000 0 -0.42 1 1
TRAF6 0.034 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.17 0.28 -10000 0 -0.51 147 147
CARD11 -0.074 0.19 -10000 0 -0.42 85 85
PRKCB -0.15 0.2 0.2 1 -0.36 164 165
PRKCE -0.12 0.17 0.2 1 -0.31 159 160
PRKCQ -0.34 0.44 0.24 1 -0.81 165 166
LCP2 0.015 0.09 -10000 0 -0.42 15 15
BCL10 0.035 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.18 0.25 0.18 1 -0.44 163 164
IKK complex -0.034 0.08 0.17 7 -0.12 145 152
RAS family/GDP -0.014 0.021 -10000 0 -0.04 117 117
MAP3K14 -0.12 0.18 0.14 3 -0.31 157 160
PDPK1 -0.2 0.28 0.18 1 -0.5 161 162
TCR/CD3/MHC I/CD8/Fyn -0.55 0.71 -10000 0 -1.3 164 164
IL23-mediated signaling events

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
CCL2 -0.5 0.67 -9999 0 -1.2 152 152
IL23A -0.53 0.7 -9999 0 -1.3 154 154
NF kappa B1 p50/RelA/I kappa B alpha -0.53 0.73 -9999 0 -1.3 155 155
positive regulation of T cell mediated cytotoxicity -0.64 0.85 -9999 0 -1.5 157 157
ITGA3 -0.51 0.67 -9999 0 -1.2 152 152
IL17F -0.31 0.41 -9999 0 -0.75 155 155
IL12B -0.01 0.087 -9999 0 -0.45 8 8
STAT1 (dimer) -0.6 0.8 -9999 0 -1.4 156 156
CD4 -0.51 0.68 -9999 0 -1.3 151 151
IL23 -0.5 0.67 -9999 0 -1.2 155 155
IL23R -0.038 0.13 -9999 0 -1.3 2 2
IL1B -0.56 0.73 -9999 0 -1.4 152 152
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.59 0.72 -9999 0 -1.3 179 179
TYK2 -0.001 0.046 -9999 0 -10000 0 0
STAT4 -0.079 0.2 -9999 0 -0.42 92 92
STAT3 0.035 0.005 -9999 0 -10000 0 0
IL18RAP -0.12 0.21 -9999 0 -0.42 117 117
IL12RB1 -0.11 0.21 -9999 0 -0.45 96 96
PIK3CA 0.034 0.006 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 -0.072 0.17 -9999 0 -0.34 96 96
IL23R/JAK2 -0.031 0.16 -9999 0 -1.3 2 2
positive regulation of chronic inflammatory response -0.64 0.85 -9999 0 -1.5 157 157
natural killer cell activation 0.006 0.009 -9999 0 -10000 0 0
JAK2 -0.002 0.075 -9999 0 -0.45 5 5
PIK3R1 0.034 0.007 -9999 0 -10000 0 0
NFKB1 0.033 0.007 -9999 0 -10000 0 0
RELA 0.032 0.008 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.47 0.62 -9999 0 -1.1 155 155
ALOX12B -0.5 0.66 -9999 0 -1.2 153 153
CXCL1 -0.51 0.66 -9999 0 -1.2 157 157
T cell proliferation -0.64 0.85 -9999 0 -1.5 157 157
NFKBIA 0.033 0.006 -9999 0 -10000 0 0
IL17A -0.22 0.33 -9999 0 -0.57 151 151
PI3K -0.55 0.75 -9999 0 -1.4 156 156
IFNG -0.048 0.068 -9999 0 -0.12 152 152
STAT3 (dimer) -0.51 0.7 -9999 0 -1.3 155 155
IL18R1 -0.045 0.16 -9999 0 -0.42 57 57
IL23/IL23R/JAK2/TYK2/SOCS3 -0.31 0.47 -9999 0 -0.81 144 144
IL18/IL18R -0.14 0.25 -9999 0 -0.43 143 143
macrophage activation -0.02 0.024 -9999 0 -0.045 152 152
TNF -0.57 0.75 -9999 0 -1.4 153 153
STAT3/STAT4 -0.58 0.77 -9999 0 -1.4 159 159
STAT4 (dimer) -0.62 0.82 -9999 0 -1.5 160 160
IL18 -0.067 0.18 -9999 0 -0.42 72 72
IL19 -0.5 0.66 -9999 0 -1.2 153 153
STAT5A (dimer) -0.6 0.8 -9999 0 -1.4 156 156
STAT1 0.033 0.033 -9999 0 -0.42 2 2
SOCS3 0.03 0.041 -9999 0 -0.42 3 3
CXCL9 -0.66 0.78 -9999 0 -1.4 176 176
MPO -0.53 0.68 -9999 0 -1.3 157 157
positive regulation of humoral immune response -0.64 0.85 -9999 0 -1.5 157 157
IL23/IL23R/JAK2/TYK2 -0.76 1 -9999 0 -1.8 156 156
IL6 -0.51 0.68 -9999 0 -1.3 152 152
STAT5A 0.033 0.024 -9999 0 -0.42 1 1
IL2 0.004 0.031 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.009 -9999 0 -10000 0 0
CD3E -0.61 0.76 -9999 0 -1.4 158 158
keratinocyte proliferation -0.64 0.85 -9999 0 -1.5 157 157
NOS2 -0.5 0.66 -9999 0 -1.2 152 152
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.087 0.17 0.3 134 -10000 0 134
KIRREL 0.001 0.051 -10000 0 -0.42 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.087 0.17 -10000 0 -0.3 134 134
PLCG1 0.033 0.01 -10000 0 -10000 0 0
ARRB2 0.033 0.009 -10000 0 -10000 0 0
WASL 0.031 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.039 0.14 -10000 0 -0.23 122 122
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.06 0.12 -10000 0 -0.23 119 119
FYN -0.055 0.13 0.24 20 -0.22 133 153
mol:Ca2+ -0.041 0.13 -10000 0 -0.22 123 123
mol:DAG -0.04 0.14 -10000 0 -0.22 123 123
NPHS2 -0.01 0.038 -10000 0 -10000 0 0
mol:IP3 -0.04 0.14 -10000 0 -0.22 123 123
regulation of endocytosis -0.044 0.12 -10000 0 -0.2 132 132
Nephrin/NEPH1/podocin/Cholesterol -0.054 0.13 -10000 0 -0.22 133 133
establishment of cell polarity -0.087 0.17 -10000 0 -0.3 134 134
Nephrin/NEPH1/podocin/NCK1-2 -0.028 0.14 -10000 0 -0.21 131 131
Nephrin/NEPH1/beta Arrestin2 -0.044 0.12 -10000 0 -0.2 132 132
NPHS1 -0.15 0.22 -10000 0 -0.42 145 145
Nephrin/NEPH1/podocin -0.052 0.12 -10000 0 -0.22 133 133
TJP1 0.034 0.007 -10000 0 -10000 0 0
NCK1 0.034 0.006 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.04 0.14 -10000 0 -0.23 123 123
CD2AP 0.031 0.026 -10000 0 -0.42 1 1
Nephrin/NEPH1/podocin/GRB2 -0.042 0.14 -10000 0 -0.23 130 130
GRB2 0.034 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.055 0.13 0.25 24 -0.2 127 151
cytoskeleton organization -0.081 0.14 0.2 5 -0.28 117 122
Nephrin/NEPH1 -0.055 0.12 -10000 0 -0.21 134 134
Nephrin/NEPH1/ZO-1 -0.054 0.14 -10000 0 -0.24 133 133
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.11 0.25 -10000 0 -0.44 117 117
TBX21 -0.48 0.77 -10000 0 -1.4 135 135
B2M 0.03 0.042 -10000 0 -0.42 3 3
TYK2 0.01 0.048 -10000 0 -10000 0 0
IL12RB1 -0.098 0.22 -10000 0 -0.46 96 96
GADD45B -0.38 0.66 -10000 0 -1.2 136 136
IL12RB2 -0.005 0.076 -10000 0 -0.43 8 8
GADD45G -0.42 0.69 -10000 0 -1.3 137 137
natural killer cell activation -0.005 0.026 0.049 2 -0.04 92 94
RELB 0.035 0.004 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
IL18 -0.057 0.18 -10000 0 -0.43 72 72
IL2RA -0.062 0.18 -10000 0 -0.42 76 76
IFNG -0.12 0.21 -10000 0 -0.42 120 120
STAT3 (dimer) -0.31 0.55 -10000 0 -1 137 137
HLA-DRB5 0.001 0.001 -10000 0 -10000 0 0
FASLG -0.49 0.79 -10000 0 -1.5 138 138
NF kappa B2 p52/RelB -0.43 0.74 -10000 0 -1.3 137 137
CD4 -0.007 0.13 -10000 0 -0.42 34 34
SOCS1 0.011 0.1 -10000 0 -0.42 19 19
EntrezGene:6955 0.001 0.003 -10000 0 -0.019 2 2
CD3D -0.12 0.21 -10000 0 -0.42 123 123
CD3E -0.099 0.2 -10000 0 -0.42 106 106
CD3G -0.094 0.2 -10000 0 -0.42 102 102
IL12Rbeta2/JAK2 0.003 0.086 -10000 0 -0.32 13 13
CCL3 -0.42 0.72 -10000 0 -1.3 131 131
CCL4 -0.46 0.76 -10000 0 -1.4 132 132
HLA-A 0 0.003 -10000 0 -0.02 2 2
IL18/IL18R -0.11 0.28 -10000 0 -0.42 143 143
NOS2 -0.44 0.73 -10000 0 -1.3 135 135
IL12/IL12R/TYK2/JAK2/SPHK2 -0.1 0.23 -10000 0 -0.41 115 115
IL1R1 -0.42 0.7 -10000 0 -1.3 131 131
IL4 0.004 0.041 -10000 0 -10000 0 0
JAK2 0.007 0.07 -10000 0 -0.46 5 5
EntrezGene:6957 0.001 0.003 -10000 0 -0.021 2 2
TCR/CD3/MHC I/CD8 -0.51 0.7 -10000 0 -1.2 155 155
RAB7A -0.27 0.5 -10000 0 -0.91 129 129
lysosomal transport -0.25 0.47 -10000 0 -0.85 129 129
FOS -0.31 0.51 -10000 0 -0.95 132 132
STAT4 (dimer) -0.39 0.68 -10000 0 -1.2 140 140
STAT5A (dimer) -0.47 0.74 -10000 0 -1.3 151 151
GZMA -0.49 0.78 -10000 0 -1.5 133 133
GZMB -0.51 0.79 -10000 0 -1.5 143 143
HLX 0.031 0.011 -10000 0 -10000 0 0
LCK -0.56 0.88 -10000 0 -1.5 146 146
TCR/CD3/MHC II/CD4 -0.28 0.4 -10000 0 -0.67 163 163
IL2/IL2R -0.097 0.25 -10000 0 -0.41 129 129
MAPK14 -0.4 0.69 -10000 0 -1.2 141 141
CCR5 -0.42 0.71 -10000 0 -1.3 132 132
IL1B -0.031 0.14 -10000 0 -0.45 34 34
STAT6 -0.054 0.19 -10000 0 -0.27 117 117
STAT4 -0.079 0.2 -10000 0 -0.42 92 92
STAT3 0.035 0.005 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
NFKB1 0.034 0.006 -10000 0 -10000 0 0
NFKB2 0.032 0.01 -10000 0 -10000 0 0
IL12B 0.003 0.08 -10000 0 -0.44 8 8
CD8A -0.13 0.22 -10000 0 -0.42 133 133
CD8B -0.13 0.22 -10000 0 -0.42 135 135
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.11 0.25 0.44 117 -10000 0 117
IL2RB -0.042 0.17 -10000 0 -0.42 61 61
proteasomal ubiquitin-dependent protein catabolic process -0.32 0.58 -10000 0 -1 140 140
IL2RG -0.1 0.21 -10000 0 -0.42 112 112
IL12 -0.001 0.11 -10000 0 -0.33 27 27
STAT5A 0.033 0.024 -10000 0 -0.42 1 1
CD247 -0.1 0.2 -10000 0 -0.42 107 107
IL2 0.022 0.009 -10000 0 -10000 0 0
SPHK2 0.035 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.013 0.11 -10000 0 -0.45 19 19
IL12/IL12R/TYK2/JAK2 -0.68 1.1 -10000 0 -2 138 138
MAP2K3 -0.42 0.72 -10000 0 -1.3 143 143
RIPK2 0.032 0.011 -10000 0 -10000 0 0
MAP2K6 -0.42 0.72 -10000 0 -1.3 140 140
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.001 -10000 0 -10000 0 0
IL18RAP -0.11 0.22 -10000 0 -0.42 117 117
IL12Rbeta1/TYK2 -0.059 0.18 -10000 0 -0.35 96 96
EOMES -0.14 0.4 -10000 0 -1.3 35 35
STAT1 (dimer) -0.38 0.57 -10000 0 -0.98 160 160
T cell proliferation -0.24 0.44 -10000 0 -0.77 141 141
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.035 0.17 -10000 0 -0.43 57 57
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.27 0.48 -10000 0 -0.84 141 141
ATF2 -0.34 0.6 -10000 0 -1.1 140 140
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.061 0.19 -10000 0 -0.4 80 80
NFATC2 -0.14 0.34 -10000 0 -0.63 99 99
NFATC3 -0.009 0.079 -10000 0 -0.21 10 10
CD40LG -0.42 0.49 -10000 0 -0.92 154 154
ITCH 0.031 0.019 -10000 0 -0.21 1 1
CBLB 0.033 0.018 -10000 0 -0.21 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.44 0.62 -10000 0 -1.1 146 146
JUNB 0.035 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.039 0.026 -10000 0 -0.25 1 1
T cell anergy 0.002 0.063 -10000 0 -0.32 1 1
TLE4 -0.11 0.28 -10000 0 -0.56 80 80
Jun/NFAT1-c-4/p21SNFT -0.21 0.41 -10000 0 -0.79 93 93
AP-1/NFAT1-c-4 -0.34 0.53 -10000 0 -0.98 127 127
IKZF1 -0.16 0.35 -10000 0 -0.75 86 86
T-helper 2 cell differentiation -0.24 0.4 -10000 0 -0.83 99 99
AP-1/NFAT1 -0.1 0.26 -10000 0 -0.46 95 95
CALM1 0.041 0.015 -10000 0 -0.16 1 1
EGR2 -0.16 0.34 -10000 0 -0.85 44 44
EGR3 -0.17 0.37 -10000 0 -0.89 48 48
NFAT1/FOXP3 -0.14 0.34 -10000 0 -0.62 106 106
EGR1 0.026 0.022 -10000 0 -10000 0 0
JUN -0.008 0.042 -10000 0 -10000 0 0
EGR4 0.024 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.01 -10000 0 -0.15 1 1
GBP3 -0.12 0.29 -10000 0 -0.6 78 78
FOSL1 0.015 0.09 -10000 0 -0.42 15 15
NFAT1-c-4/MAF/IRF4 -0.17 0.38 -10000 0 -0.76 76 76
DGKA -0.11 0.28 -10000 0 -0.55 80 80
CREM 0.032 0.01 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.39 -10000 0 -0.79 78 78
CTLA4 -0.16 0.34 -10000 0 -0.66 102 102
NFAT1-c-4 (dimer)/EGR1 -0.18 0.4 -10000 0 -0.82 77 77
NFAT1-c-4 (dimer)/EGR4 -0.18 0.4 -10000 0 -0.81 80 80
FOS -0.007 0.042 -10000 0 -10000 0 0
IFNG -0.57 0.7 -10000 0 -1.3 177 177
T cell activation -0.13 0.24 -10000 0 -0.65 34 34
MAF 0.034 0.007 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.12 0.29 1 19 -10000 0 19
TNF -0.22 0.41 -10000 0 -0.85 91 91
FASLG -0.55 0.8 -10000 0 -1.6 126 126
TBX21 -0.12 0.2 -10000 0 -0.34 141 141
BATF3 0.026 0.053 -10000 0 -0.42 5 5
PRKCQ -0.1 0.21 -10000 0 -0.42 106 106
PTPN1 -0.099 0.25 -10000 0 -0.51 78 78
NFAT1-c-4/ICER1 -0.17 0.39 -10000 0 -0.78 78 78
GATA3 -0.047 0.17 -10000 0 -0.42 64 64
T-helper 1 cell differentiation -0.55 0.66 -10000 0 -1.2 177 177
IL2RA -0.4 0.58 -10000 0 -1 147 147
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.099 0.25 -10000 0 -0.5 83 83
E2F1 0.038 0.011 -10000 0 -10000 0 0
PPARG 0.03 0.047 -10000 0 -0.42 4 4
SLC3A2 -0.097 0.25 -10000 0 -0.49 83 83
IRF4 -0.005 0.12 -10000 0 -0.42 29 29
PTGS2 -0.32 0.42 -10000 0 -0.83 127 127
CSF2 -0.32 0.43 -10000 0 -0.84 131 131
JunB/Fra1/NFAT1-c-4 -0.16 0.38 -10000 0 -0.76 77 77
IL4 -0.25 0.42 -10000 0 -0.88 98 98
IL5 -0.33 0.43 -10000 0 -0.84 131 131
IL2 -0.13 0.24 -10000 0 -0.67 32 32
IL3 -0.068 0.2 -10000 0 -0.92 16 16
RNF128 0.024 0.035 -10000 0 -0.52 1 1
NFATC1 -0.12 0.29 -10000 0 -1 19 19
CDK4 0.1 0.2 0.61 19 -10000 0 19
PTPRK -0.095 0.25 -10000 0 -0.53 71 71
IL8 -0.34 0.42 -10000 0 -0.84 131 131
POU2F1 0.032 0.011 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.11 0.23 0.29 1 -0.44 102 103
ACTA1 -0.14 0.25 0.23 5 -0.48 116 121
NUMA1 -0.11 0.24 0.26 1 -0.47 99 100
SPTAN1 -0.15 0.25 0.3 1 -0.49 116 117
LIMK1 -0.13 0.25 0.24 11 -0.47 114 125
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BIRC2 0.028 0.042 -10000 0 -0.42 3 3
BAX 0.035 0.004 -10000 0 -10000 0 0
CASP10 -0.12 0.2 -10000 0 -0.4 112 112
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.035 0.002 -10000 0 -10000 0 0
PTK2 -0.11 0.23 0.29 1 -0.45 101 102
DIABLO 0.034 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.14 0.25 0.3 1 -0.48 116 117
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.034 0.006 -10000 0 -10000 0 0
GSN -0.15 0.26 0.3 1 -0.49 116 117
MADD 0.035 0.005 -10000 0 -10000 0 0
TFAP2A -0.14 0.33 -10000 0 -0.74 80 80
BID -0.075 0.13 -10000 0 -0.25 119 119
MAP3K1 -0.042 0.13 -10000 0 -0.51 12 12
TRADD 0.034 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.051 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.16 0.28 0.3 3 -0.53 117 120
CASP9 0.035 0.005 -10000 0 -10000 0 0
DNA repair -0.008 0.08 0.21 12 -0.17 29 41
neuron apoptosis -0.007 0.13 -10000 0 -0.69 11 11
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.13 0.26 0.31 2 -0.52 100 102
APAF1 0.035 0.006 -10000 0 -10000 0 0
CASP6 -0.081 0.24 -10000 0 -0.73 22 22
TRAF2 0.033 0.009 -10000 0 -10000 0 0
ICAD/CAD -0.14 0.25 0.39 3 -0.47 116 119
CASP7 0.073 0.15 0.28 103 -0.67 1 104
KRT18 -0.09 0.25 -10000 0 -0.66 53 53
apoptosis -0.1 0.22 0.31 1 -0.43 92 93
DFFA -0.14 0.26 0.26 4 -0.49 116 120
DFFB -0.14 0.25 0.28 3 -0.49 116 119
PARP1 0.008 0.081 0.17 29 -0.21 12 41
actin filament polymerization 0.12 0.23 0.44 114 -0.31 4 118
TNF -0.054 0.18 -10000 0 -0.42 69 69
CYCS -0.05 0.088 -10000 0 -0.19 82 82
SATB1 -0.089 0.23 -10000 0 -0.66 32 32
SLK -0.14 0.25 0.3 1 -0.48 116 117
p15 BID/BAX -0.061 0.13 -10000 0 -0.22 134 134
CASP2 -0.049 0.15 0.22 13 -0.33 58 71
JNK cascade 0.042 0.13 0.5 12 -10000 0 12
CASP3 -0.15 0.27 0.33 1 -0.51 116 117
LMNB2 -0.036 0.18 0.26 4 -0.4 45 49
RIPK1 0.031 0.012 -10000 0 -10000 0 0
CASP4 0.031 0.026 -10000 0 -0.42 1 1
Mammalian IAPs/DIABLO -0.014 0.14 -10000 0 -0.23 108 108
negative regulation of DNA binding -0.13 0.33 -10000 0 -0.72 80 80
stress fiber formation -0.14 0.25 0.3 1 -0.48 116 117
GZMB -0.13 0.23 -10000 0 -0.45 113 113
CASP1 0.006 0.066 -10000 0 -0.31 14 14
LMNB1 -0.047 0.2 0.25 5 -0.44 51 56
APP -0.007 0.13 -10000 0 -0.7 11 11
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.001 -10000 0 -10000 0 0
VIM -0.099 0.21 0.32 1 -0.42 94 95
LMNA -0.037 0.17 0.25 4 -0.37 54 58
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.063 0.15 -10000 0 -0.35 65 65
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.14 0.25 0.32 2 -0.48 116 118
APAF-1/Caspase 9 0.038 0.093 0.37 3 -0.55 4 7
nuclear fragmentation during apoptosis -0.11 0.24 0.26 1 -0.46 99 100
CFL2 -0.13 0.24 0.31 4 -0.45 114 118
GAS2 -0.15 0.25 0.29 1 -0.49 115 116
positive regulation of apoptosis -0.035 0.18 0.26 5 -0.4 52 57
PRF1 -0.08 0.19 -10000 0 -0.42 91 91
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.033 0.21 -10000 0 -0.36 92 92
MAP4K1 -0.044 0.17 -10000 0 -0.42 64 64
MAP3K8 0.021 0.07 -10000 0 -0.42 9 9
PRKCB -0.097 0.21 -10000 0 -0.42 107 107
DBNL 0.031 0.011 -10000 0 -10000 0 0
CRKL 0.033 0.01 -10000 0 -10000 0 0
MAP3K1 -0.061 0.19 -10000 0 -0.49 50 50
JUN -0.21 0.37 -10000 0 -0.71 121 121
MAP3K7 -0.057 0.19 -10000 0 -0.49 49 49
GRAP2 -0.015 0.14 -10000 0 -0.42 39 39
CRK 0.033 0.009 -10000 0 -10000 0 0
MAP2K4 -0.064 0.22 0.22 8 -0.49 58 66
LAT -0.021 0.15 -10000 0 -0.42 45 45
LCP2 0.015 0.09 -10000 0 -0.42 15 15
MAPK8 -0.22 0.39 -10000 0 -0.74 123 123
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.06 0.21 -10000 0 -0.43 70 70
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.02 0.2 -10000 0 -0.33 89 89
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.035 0.064 -10000 0 -0.22 17 17
NFATC2 -0.04 0.08 -10000 0 -0.29 24 24
NFATC3 -0.028 0.047 -10000 0 -0.12 11 11
CD40LG -0.35 0.35 0.39 1 -0.63 204 205
PTGS2 -0.24 0.28 0.39 1 -0.54 152 153
JUNB 0.035 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.015 0.036 -10000 0 -0.088 1 1
CaM/Ca2+ -0.015 0.035 -10000 0 -0.087 1 1
CALM1 0.005 0.034 -10000 0 -10000 0 0
JUN 0.001 0.035 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.015 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.017 -10000 0 -10000 0 0
FOSL1 0.015 0.09 -10000 0 -0.42 15 15
CREM 0.032 0.01 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.19 -10000 0 -0.33 125 125
FOS 0.004 0.034 -10000 0 -10000 0 0
IFNG -0.31 0.34 0.39 1 -0.62 179 180
AP-1/NFAT1-c-4 -0.28 0.37 -10000 0 -0.64 160 160
FASLG -0.29 0.34 0.39 1 -0.64 157 158
NFAT1-c-4/ICER1 -0.075 0.13 -10000 0 -0.25 87 87
IL2RA -0.29 0.33 0.39 1 -0.61 165 166
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSF2 -0.25 0.29 0.39 1 -0.54 160 161
JunB/Fra1/NFAT1-c-4 -0.07 0.14 -10000 0 -0.29 58 58
IL4 -0.26 0.29 0.39 1 -0.54 159 160
IL2 -0.008 0.14 -10000 0 -1 7 7
IL3 -0.038 0.18 -10000 0 -0.84 17 17
FKBP1A 0.033 0.008 -10000 0 -10000 0 0
BATF3 0.025 0.053 -10000 0 -0.42 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.032 0.011 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.017 0.14 -9999 0 -0.25 92 92
E-cadherin/beta catenin -0.039 0.15 -9999 0 -0.3 92 92
CTNNB1 0.035 0.005 -9999 0 -10000 0 0
JUP 0.033 0.008 -9999 0 -10000 0 0
CDH1 -0.08 0.2 -9999 0 -0.42 92 92
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.033 0.034 -10000 0 -0.42 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.17 0.3 0.6 92 -10000 0 92
IL27/IL27R/JAK1 -0.12 0.32 -10000 0 -0.85 40 40
TBX21 -0.18 0.27 -10000 0 -0.55 107 107
IL12B 0.008 0.068 -10000 0 -0.42 8 8
IL12A -0.013 0.068 -10000 0 -0.3 19 19
IL6ST 0.005 0.071 -10000 0 -0.43 8 8
IL27RA/JAK1 -0.064 0.28 -10000 0 -1.2 20 20
IL27 -0.037 0.14 -10000 0 -0.43 40 40
TYK2 0.012 0.033 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.033 0.1 -10000 0 -0.57 1 1
T-helper 2 cell differentiation 0.17 0.3 0.6 92 -10000 0 92
T cell proliferation during immune response 0.17 0.3 0.6 92 -10000 0 92
MAPKKK cascade -0.17 0.3 -10000 0 -0.6 92 92
STAT3 0.035 0.005 -10000 0 -10000 0 0
STAT2 0.035 0.005 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
IL12RB1 -0.086 0.2 -10000 0 -0.42 96 96
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.15 0.23 0.36 1 -0.52 82 83
IL27/IL27R/JAK2/TYK2 -0.18 0.31 -10000 0 -0.61 92 92
positive regulation of T cell mediated cytotoxicity -0.17 0.3 -10000 0 -0.6 92 92
STAT1 (dimer) -0.16 0.35 0.51 1 -0.71 76 77
JAK2 0.012 0.058 -10000 0 -0.42 5 5
JAK1 0.035 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.16 0.3 -10000 0 -0.58 92 92
T cell proliferation -0.16 0.3 -10000 0 -0.6 84 84
IL12/IL12R/TYK2/JAK2 -0.18 0.34 -10000 0 -0.81 57 57
IL17A 0.033 0.1 -10000 0 -0.57 1 1
mast cell activation 0.17 0.3 0.6 92 -10000 0 92
IFNG -0.046 0.068 -10000 0 -0.13 142 142
T cell differentiation -0.009 0.011 -10000 0 -0.023 138 138
STAT3 (dimer) -0.16 0.3 -10000 0 -0.58 92 92
STAT5A (dimer) -0.16 0.3 -10000 0 -0.57 93 93
STAT4 (dimer) -0.2 0.34 -10000 0 -0.62 114 114
STAT4 -0.079 0.2 -10000 0 -0.42 92 92
T cell activation -0.003 0.029 0.12 18 -10000 0 18
IL27R/JAK2/TYK2 -0.068 0.29 -10000 0 -1.1 23 23
GATA3 -0.26 0.54 -10000 0 -1.3 80 80
IL18 -0.054 0.12 -10000 0 -0.3 72 72
positive regulation of mast cell cytokine production -0.15 0.29 -10000 0 -0.56 92 92
IL27/EBI3 -0.075 0.18 -10000 0 -0.36 98 98
IL27RA -0.081 0.3 -10000 0 -1.3 20 20
IL6 0.014 0.084 -10000 0 -0.42 13 13
STAT5A 0.033 0.024 -10000 0 -0.42 1 1
monocyte differentiation -0.002 0.004 -10000 0 -0.013 1 1
IL2 0.023 0.11 0.48 20 -10000 0 20
IL1B -0.023 0.088 -10000 0 -0.3 34 34
EBI3 -0.077 0.18 -10000 0 -0.42 81 81
TNF -0.052 0.12 -10000 0 -0.3 69 69
FAS signaling pathway (CD95)

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
SPTAN1 0.033 0.073 0.17 82 -0.18 2 84
RFC1 0.037 0.077 0.17 88 -0.18 2 90
PRKDC 0.05 0.1 0.2 97 -0.18 2 99
RIPK1 0.031 0.012 -10000 0 -10000 0 0
CASP7 0.005 0.19 0.24 41 -0.57 29 70
FASLG/FAS/FADD/FAF1 -0.001 0.12 0.2 43 -0.25 47 90
MAP2K4 -0.035 0.18 0.24 3 -0.42 43 46
mol:ceramide -0.044 0.16 -10000 0 -0.3 89 89
GSN 0.033 0.072 0.17 80 -0.18 2 82
FASLG/FAS/FADD/FAF1/Caspase 8 -0.026 0.14 0.23 1 -0.28 58 59
FAS 0.026 0.054 -10000 0 -0.42 5 5
BID 0.065 0.14 0.29 98 -10000 0 98
MAP3K1 -0.004 0.16 0.23 13 -0.45 27 40
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
RB1 0.038 0.077 0.17 92 -0.18 2 94
CFLAR 0.035 0.004 -10000 0 -10000 0 0
HGF/MET 0.033 0.09 -10000 0 -0.26 27 27
ARHGDIB 0.027 0.1 0.18 85 -0.23 19 104
FADD 0.033 0.012 -10000 0 -10000 0 0
actin filament polymerization -0.032 0.072 0.18 2 -0.17 80 82
NFKB1 -0.019 0.15 -10000 0 -0.7 13 13
MAPK8 -0.036 0.19 -10000 0 -0.46 38 38
DFFA 0.037 0.076 0.17 90 -0.18 2 92
DNA fragmentation during apoptosis 0.037 0.077 0.17 89 -0.18 2 91
FAS/FADD/MET 0.033 0.082 -10000 0 -0.25 24 24
CFLAR/RIP1 0.046 0.018 -10000 0 -10000 0 0
FAIM3 -0.095 0.2 -10000 0 -0.42 102 102
FAF1 0.034 0.011 -10000 0 -10000 0 0
PARP1 0.038 0.076 0.17 91 -0.18 2 93
DFFB 0.037 0.078 0.17 89 -0.18 2 91
CHUK -0.02 0.13 -10000 0 -0.64 12 12
FASLG -0.091 0.2 -10000 0 -0.42 99 99
FAS/FADD 0.041 0.041 -10000 0 -0.3 4 4
HGF 0.024 0.058 -10000 0 -0.42 6 6
LMNA 0.033 0.068 0.2 5 -10000 0 5
CASP6 0.036 0.074 0.17 87 -0.17 1 88
CASP10 0.027 0.058 -10000 0 -0.42 6 6
CASP3 0.047 0.089 0.2 88 -10000 0 88
PTPN13 0.029 0.047 -10000 0 -0.42 4 4
CASP8 0.076 0.16 0.34 99 -10000 0 99
IL6 -0.051 0.28 -10000 0 -1.2 20 20
MET 0.006 0.1 -10000 0 -0.42 20 20
ICAD/CAD 0.033 0.07 0.23 4 -0.17 1 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.045 0.16 -10000 0 -0.3 89 89
activation of caspase activity by cytochrome c 0.065 0.14 0.29 98 -10000 0 98
PAK2 0.038 0.078 0.17 90 -0.18 2 92
BCL2 0.035 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.11 0.3 -9999 0 -0.59 97 97
MAP3K8 0.021 0.07 -9999 0 -0.42 9 9
FOS -0.13 0.3 -9999 0 -0.6 99 99
PRKCA 0.033 0.025 -9999 0 -0.42 1 1
PTPN7 -0.062 0.18 -9999 0 -0.42 76 76
HRAS 0.035 0.006 -9999 0 -10000 0 0
PRKCB -0.097 0.21 -9999 0 -0.42 107 107
NRAS 0.034 0.008 -9999 0 -10000 0 0
RAS family/GTP 0.063 0.02 -9999 0 -10000 0 0
MAPK3 -0.14 0.31 -9999 0 -0.63 96 96
MAP2K1 -0.075 0.2 -9999 0 -0.37 105 105
ELK1 0.036 0.003 -9999 0 -10000 0 0
BRAF -0.064 0.17 -9999 0 -0.36 89 89
mol:GTP 0 0 -9999 0 -10000 0 0
MAPK1 -0.14 0.31 -9999 0 -0.63 97 97
RAF1 -0.075 0.18 -9999 0 -0.35 104 104
KRAS 0.034 0.006 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.029 0.1 -10000 0 -0.21 92 92
epithelial cell differentiation -0.003 0.12 -10000 0 -0.21 91 91
CYFIP2 0.015 0.09 -10000 0 -0.42 15 15
ENAH -0.032 0.076 0.27 3 -0.26 1 4
EGFR 0.027 0.035 -10000 0 -0.42 2 2
EPHA2 0.03 0.047 -10000 0 -0.42 4 4
MYO6 -0.033 0.1 0.21 7 -0.2 91 98
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.065 -10000 0 -0.24 15 15
AQP5 -0.029 0.089 -10000 0 -0.31 4 4
CTNND1 0.035 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.03 0.1 0.22 6 -0.2 89 95
regulation of calcium-dependent cell-cell adhesion -0.037 0.11 0.22 6 -0.2 97 103
EGF 0.001 0.11 -10000 0 -0.42 25 25
NCKAP1 0.035 0.003 -10000 0 -10000 0 0
AQP3 -0.078 0.16 0.4 1 -0.4 51 52
cortical microtubule organization -0.003 0.12 -10000 0 -0.21 91 91
GO:0000145 -0.046 0.089 0.18 10 -0.19 89 99
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.001 0.13 -10000 0 -0.21 91 91
MLLT4 0.029 0.014 -10000 0 -10000 0 0
ARF6/GDP -0.05 0.074 -10000 0 -0.19 77 77
ARF6 0.035 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.073 0.044 -10000 0 -0.23 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.031 0.088 0.23 4 -0.24 3 7
PVRL2 0.035 0.004 -10000 0 -10000 0 0
ZYX -0.028 0.098 0.22 5 -0.2 81 86
ARF6/GTP 0.08 0.047 -10000 0 -0.21 3 3
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
EGFR/EGFR/EGF/EGF -0.026 0.12 -10000 0 -0.21 103 103
RhoA/GDP 0 0.12 -10000 0 -0.2 91 91
actin cytoskeleton organization -0.039 0.098 0.2 7 -0.2 91 98
IGF-1R heterotetramer 0.034 0.006 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
IGF1R 0.034 0.006 -10000 0 -10000 0 0
IGF1 0.03 0.041 -10000 0 -0.42 3 3
DIAPH1 -0.017 0.22 -10000 0 -0.57 36 36
Wnt receptor signaling pathway 0.003 0.12 0.21 91 -10000 0 91
RHOA 0.035 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.051 0.074 -10000 0 -0.19 77 77
CTNNA1 0.033 0.008 -10000 0 -10000 0 0
VCL -0.04 0.099 0.2 7 -0.2 91 98
EFNA1 0.032 0.011 -10000 0 -10000 0 0
LPP -0.049 0.09 0.19 9 -0.2 91 100
Ephrin A1/EPHA2 -0.005 0.11 -10000 0 -0.2 81 81
SEC6/SEC8 -0.032 0.083 -10000 0 -0.19 69 69
MGAT3 -0.037 0.11 0.22 6 -0.21 97 103
HGF/MET -0.019 0.13 -10000 0 -0.22 94 94
HGF 0.024 0.058 -10000 0 -0.42 6 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.029 0.1 -10000 0 -0.21 92 92
actin cable formation 0.004 0.11 0.28 18 -0.26 7 25
KIAA1543 -0.055 0.096 0.18 10 -0.2 102 112
KIFC3 -0.033 0.1 0.22 6 -0.2 91 97
NCK1 0.034 0.006 -10000 0 -10000 0 0
EXOC3 0.032 0.01 -10000 0 -10000 0 0
ACTN1 -0.032 0.1 0.21 8 -0.2 92 100
NCK1/GIT1 0.049 0.012 -10000 0 -10000 0 0
mol:GDP -0.003 0.12 -10000 0 -0.21 91 91
EXOC4 0.031 0.012 -10000 0 -10000 0 0
STX4 -0.031 0.1 0.21 8 -0.2 91 99
PIP5K1C -0.031 0.1 0.22 6 -0.2 89 95
LIMA1 0.035 0.005 -10000 0 -10000 0 0
ABI1 0.032 0.01 -10000 0 -10000 0 0
ROCK1 -0.025 0.1 0.44 4 -0.3 1 5
adherens junction assembly -0.04 0.1 0.3 3 -0.37 6 9
IGF-1R heterotetramer/IGF1 -0.007 0.11 -10000 0 -0.2 92 92
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.023 -10000 0 -10000 0 0
MET 0.006 0.1 -10000 0 -0.42 20 20
PLEKHA7 -0.04 0.11 0.22 6 -0.21 102 108
mol:GTP 0.071 0.043 -10000 0 -0.23 3 3
establishment of epithelial cell apical/basal polarity -0.012 0.12 0.32 11 -10000 0 11
cortical actin cytoskeleton stabilization -0.029 0.1 -10000 0 -0.21 92 92
regulation of cell-cell adhesion -0.039 0.098 0.2 7 -0.2 91 98
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.029 0.1 -10000 0 -0.21 92 92
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.089 0.2 -10000 0 -0.39 107 107
KLHL20 -0.012 0.096 0.21 7 -0.22 23 30
CYFIP2 0.015 0.09 -10000 0 -0.42 15 15
Rac1/GDP -0.032 0.13 0.26 1 -0.25 75 76
ENAH -0.085 0.19 -10000 0 -0.39 99 99
AP1M1 0.035 0.004 -10000 0 -10000 0 0
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.092 -10000 0 -0.18 66 66
ABI1/Sra1/Nap1 -0.036 0.051 -10000 0 -0.15 31 31
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.032 0.16 -10000 0 -0.25 123 123
RAPGEF1 -0.066 0.17 0.24 3 -0.35 88 91
CTNND1 0.035 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.085 0.2 -10000 0 -0.4 106 106
CRK -0.076 0.18 -10000 0 -0.37 94 94
E-cadherin/gamma catenin/alpha catenin -0.017 0.14 -10000 0 -0.25 91 91
alphaE/beta7 Integrin 0.004 0.12 -10000 0 -0.29 48 48
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
NCKAP1 0.035 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.03 -10000 0 -10000 0 0
DLG1 -0.088 0.2 -10000 0 -0.4 100 100
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.058 -10000 0 -0.13 67 67
MLLT4 0.029 0.014 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.047 0.069 -10000 0 -0.22 21 21
PI3K -0.026 0.076 -10000 0 -0.17 67 67
ARF6 0.035 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.039 0.15 -10000 0 -0.3 92 92
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
E-cadherin(dimer)/Ca2+ 0.001 0.13 -10000 0 -0.21 91 91
AKT1 -0.007 0.056 0.16 4 -10000 0 4
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
RhoA/GDP -0.026 0.14 0.28 4 -0.25 78 82
actin cytoskeleton organization -0.006 0.075 0.17 9 -0.16 23 32
CDC42/GDP -0.028 0.14 0.28 4 -0.25 79 83
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.036 0.1 -10000 0 -0.21 93 93
ITGB7 -0.026 0.15 -10000 0 -0.42 49 49
RAC1 0.031 0.012 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.002 0.14 -10000 0 -0.23 91 91
E-cadherin/Ca2+/beta catenin/alpha catenin -0.012 0.12 -10000 0 -0.21 91 91
mol:GDP -0.048 0.14 0.28 4 -0.28 79 83
CDC42/GTP/IQGAP1 0.045 0.011 -10000 0 -10000 0 0
JUP 0.033 0.008 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.02 0.14 0.27 3 -0.25 76 79
RAC1/GTP/IQGAP1 0.041 0.017 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.052 0.007 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
CTNNA1 0.033 0.008 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.002 0.056 0.14 12 -0.11 20 32
NME1 0.034 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.089 0.2 -10000 0 -0.4 99 99
regulation of cell-cell adhesion -0.018 0.075 -10000 0 -0.16 68 68
WASF2 -0.004 0.043 0.11 4 -0.097 6 10
Rap1/GTP -0.012 0.1 -10000 0 -0.19 67 67
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.021 0.16 -10000 0 -0.23 124 124
CCND1 0.001 0.066 0.16 12 -0.13 20 32
VAV2 -0.092 0.24 0.36 1 -0.66 27 28
RAP1/GDP -0.011 0.12 0.3 3 -0.21 76 79
adherens junction assembly -0.086 0.19 -10000 0 -0.39 99 99
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.032 0.01 -10000 0 -10000 0 0
PIP5K1C 0.035 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.029 0.15 -10000 0 -0.23 121 121
E-cadherin/beta catenin -0.069 0.14 -10000 0 -0.31 95 95
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.085 0.19 -10000 0 -0.39 100 100
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.057 0.12 -10000 0 -0.35 27 27
E-cadherin/beta catenin/alpha catenin -0.016 0.14 -10000 0 -0.25 91 91
ITGAE 0.033 0.009 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.088 0.21 -10000 0 -0.41 106 106
a4b1 and a4b7 Integrin 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
ITGB1 0.032 0.011 -9999 0 -10000 0 0
ITGB7 -0.026 0.15 -9999 0 -0.42 49 49
ITGA4 -0.013 0.14 -9999 0 -0.42 39 39
alpha4/beta7 Integrin -0.03 0.16 -9999 0 -0.32 80 80
alpha4/beta1 Integrin 0.011 0.11 -9999 0 -0.29 39 39
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.034 0.008 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.018 0.13 -10000 0 -0.29 29 29
NEF -0.036 0.067 -10000 0 -0.2 35 35
NFKBIA -0.007 0.062 -10000 0 -0.14 2 2
BIRC3 -0.12 0.22 -10000 0 -0.46 108 108
CYCS -0.032 0.12 0.2 17 -0.25 72 89
RIPK1 0.031 0.012 -10000 0 -10000 0 0
CD247 -0.14 0.25 -10000 0 -0.48 123 123
MAP2K7 -0.034 0.17 0.3 1 -0.48 22 23
protein ubiquitination -0.02 0.14 0.25 6 -0.38 25 31
CRADD 0.034 0.006 -10000 0 -10000 0 0
DAXX 0.032 0.011 -10000 0 -10000 0 0
FAS 0.026 0.053 -10000 0 -0.42 5 5
BID -0.045 0.13 0.19 8 -0.26 83 91
NF-kappa-B/RelA/I kappa B alpha -0.027 0.15 -10000 0 -0.25 109 109
TRADD 0.034 0.007 -10000 0 -10000 0 0
MAP3K5 0.03 0.026 -10000 0 -0.42 1 1
CFLAR 0.035 0.003 -10000 0 -10000 0 0
FADD 0.033 0.008 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.028 0.15 -10000 0 -0.25 109 109
MAPK8 -0.03 0.16 0.28 1 -0.44 21 22
APAF1 0.034 0.006 -10000 0 -10000 0 0
TRAF1 0.025 0.058 -10000 0 -0.42 6 6
TRAF2 0.033 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.049 0.14 0.2 9 -0.27 89 98
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.045 0.17 -10000 0 -0.46 33 33
CHUK -0.024 0.15 0.25 6 -0.4 27 33
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.073 0.058 -10000 0 -0.21 5 5
TCRz/NEF -0.13 0.23 -10000 0 -0.44 123 123
TNF -0.054 0.18 -10000 0 -0.42 69 69
FASLG -0.17 0.29 -10000 0 -0.56 122 122
NFKB1 -0.006 0.061 -10000 0 -0.14 2 2
TNFR1A/BAG4/TNF-alpha 0.002 0.12 -10000 0 -0.25 66 66
CASP6 -0.003 0.15 -10000 0 -0.56 13 13
CASP7 -0.15 0.26 0.31 6 -0.48 132 138
RELA -0.006 0.061 -10000 0 -0.097 102 102
CASP2 0.031 0.011 -10000 0 -10000 0 0
CASP3 -0.14 0.26 0.31 6 -0.47 129 135
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.048 0.015 -10000 0 -10000 0 0
CASP8 0.035 0.004 -10000 0 -10000 0 0
CASP9 0.035 0.005 -10000 0 -10000 0 0
MAP3K14 -0.037 0.16 0.27 2 -0.44 30 32
APAF-1/Caspase 9 -0.093 0.19 -10000 0 -0.37 100 100
BCL2 -0.027 0.14 0.27 1 -0.42 19 20
Thromboxane A2 receptor 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
TGM2 0.031 0.026 -10000 0 -0.42 1 1
GNB1/GNG2 -0.055 0.083 -10000 0 -0.19 91 91
AKT1 -0.017 0.12 0.34 1 -0.22 61 62
EGF 0.001 0.11 -10000 0 -0.42 25 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.004 0.089 0.39 2 -0.21 38 40
mol:Ca2+ -0.042 0.16 -10000 0 -0.3 97 97
LYN 0.011 0.07 0.29 2 -0.22 15 17
RhoA/GTP -0.014 0.072 -10000 0 -0.13 80 80
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.19 -10000 0 -0.37 96 96
GNG2 0.027 0.058 -10000 0 -0.42 6 6
ARRB2 0.033 0.009 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.016 0.11 -10000 0 -0.41 18 18
G beta5/gamma2 -0.067 0.11 -10000 0 -0.25 90 90
PRKCH -0.053 0.18 -10000 0 -0.34 94 94
DNM1 0.029 0.013 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.013 0.019 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.022 0.074 -10000 0 -0.42 10 10
G12 family/GTP -0.051 0.15 -10000 0 -0.31 89 89
ADRBK1 0.034 0.007 -10000 0 -10000 0 0
ADRBK2 0.029 0.042 -10000 0 -0.42 3 3
RhoA/GTP/ROCK1 0.046 0.009 -10000 0 -10000 0 0
mol:GDP 0.017 0.13 0.35 23 -10000 0 23
mol:NADP 0.03 0.026 -10000 0 -0.42 1 1
RAB11A 0.035 0.005 -10000 0 -10000 0 0
PRKG1 0.019 0.018 -10000 0 -10000 0 0
mol:IP3 -0.06 0.2 -10000 0 -0.38 96 96
cell morphogenesis 0.045 0.009 -10000 0 -10000 0 0
PLCB2 -0.095 0.27 -10000 0 -0.52 95 95
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.091 0.1 -10000 0 -0.18 191 191
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.005 0.083 0.39 2 -0.21 31 33
RHOA 0.035 0.005 -10000 0 -10000 0 0
PTGIR 0.031 0.041 -10000 0 -0.42 3 3
PRKCB1 -0.059 0.2 -10000 0 -0.37 94 94
GNAQ 0.033 0.009 -10000 0 -10000 0 0
mol:L-citrulline 0.03 0.026 -10000 0 -0.42 1 1
TXA2/TXA2-R family -0.1 0.27 -10000 0 -0.54 95 95
LCK -0.046 0.11 0.17 1 -0.2 119 120
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.032 0.049 -10000 0 -0.19 14 14
TXA2-R family/G12 family/GDP/G beta/gamma 0.02 0.087 -10000 0 -0.41 12 12
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.037 0.049 -10000 0 -0.19 13 13
MAPK14 -0.027 0.14 0.22 6 -0.25 85 91
TGM2/GTP -0.071 0.22 -10000 0 -0.43 92 92
MAPK11 -0.034 0.13 0.24 2 -0.24 90 92
ARHGEF1 -0.018 0.1 0.17 7 -0.18 84 91
GNAI2 0.035 0.005 -10000 0 -10000 0 0
JNK cascade -0.065 0.2 -10000 0 -0.4 95 95
RAB11/GDP 0.034 0.006 -10000 0 -10000 0 0
ICAM1 -0.042 0.15 -10000 0 -0.29 93 93
cAMP biosynthetic process -0.06 0.19 -10000 0 -0.36 94 94
Gq family/GTP/EBP50 -0.02 0.092 -10000 0 -0.21 40 40
actin cytoskeleton reorganization 0.045 0.009 -10000 0 -10000 0 0
SRC 0.018 0.063 0.36 3 -0.18 6 9
GNB5 0.033 0.024 -10000 0 -0.42 1 1
GNB1 0.034 0.007 -10000 0 -10000 0 0
EGF/EGFR -0.094 0.14 0.25 5 -0.27 108 113
VCAM1 -0.062 0.18 -10000 0 -0.36 94 94
TP beta/Gq family/GDP/G beta5/gamma2 -0.016 0.11 -10000 0 -0.41 18 18
platelet activation -0.036 0.17 0.28 2 -0.31 93 95
PGI2/IP 0.023 0.029 -10000 0 -0.29 3 3
PRKACA 0.017 0.047 -10000 0 -0.22 13 13
Gq family/GDP/G beta5/gamma2 -0.014 0.11 -10000 0 -0.39 19 19
TXA2/TP beta/beta Arrestin2 0.004 0.062 -10000 0 -0.33 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.045 -10000 0 -0.21 14 14
mol:DAG -0.068 0.22 -10000 0 -0.42 94 94
EGFR 0.027 0.035 -10000 0 -0.42 2 2
TXA2/TP alpha -0.088 0.25 -10000 0 -0.5 94 94
Gq family/GTP -0.022 0.091 0.23 2 -0.21 62 64
YES1 0.019 0.058 0.32 1 -0.18 10 11
GNAI2/GTP 0.025 0.049 -10000 0 -0.18 16 16
PGD2/DP 0.017 0.052 -10000 0 -0.29 10 10
SLC9A3R1 0.034 0.007 -10000 0 -10000 0 0
FYN 0.02 0.061 0.32 3 -0.18 8 11
mol:NO 0.03 0.026 -10000 0 -0.42 1 1
GNA15 0.021 0.077 -10000 0 -0.42 11 11
PGK/cGMP 0.018 0.031 -10000 0 -0.26 1 1
RhoA/GDP 0.034 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.051 0.062 -10000 0 -0.19 15 15
NOS3 0.03 0.026 -10000 0 -0.42 1 1
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA -0.049 0.18 0.28 1 -0.35 90 91
PRKCB -0.082 0.21 -10000 0 -0.41 97 97
PRKCE -0.047 0.18 -10000 0 -0.34 93 93
PRKCD -0.061 0.2 -10000 0 -0.38 95 95
PRKCG -0.062 0.2 -10000 0 -0.39 94 94
muscle contraction -0.097 0.26 -10000 0 -0.51 95 95
PRKCZ -0.056 0.18 0.35 1 -0.35 94 95
ARR3 0.021 0.007 -10000 0 -10000 0 0
TXA2/TP beta 0.038 0.056 0.2 1 -0.19 16 17
PRKCQ -0.083 0.2 -10000 0 -0.4 97 97
MAPKKK cascade -0.09 0.25 -10000 0 -0.48 96 96
SELE -0.058 0.18 -10000 0 -0.35 94 94
TP beta/GNAI2/GDP/G beta/gamma 0.057 0.062 -10000 0 -0.19 16 16
ROCK1 0.035 0.004 -10000 0 -10000 0 0
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
chemotaxis -0.12 0.31 -10000 0 -0.63 94 94
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
GNA11 0.035 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.009 -10000 0 -10000 0 0
amb2 Integrin signaling

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.004 0.14 -10000 0 -0.35 44 44
alphaM/beta2 Integrin/GPIbA -0.13 0.2 -10000 0 -0.31 188 188
alphaM/beta2 Integrin/proMMP-9 -0.034 0.19 -10000 0 -0.37 74 74
PLAUR 0.033 0.024 -10000 0 -0.42 1 1
HMGB1 0.019 0.036 -10000 0 -0.15 1 1
alphaM/beta2 Integrin/Talin 0.004 0.14 -10000 0 -0.33 43 43
AGER 0.017 0.034 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
SELPLG -0.004 0.13 -10000 0 -0.42 31 31
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.006 0.18 -10000 0 -0.29 90 90
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.036 0.16 -10000 0 -0.42 55 55
CYR61 0.031 0.034 -10000 0 -0.42 2 2
TLN1 0.032 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.072 0.19 -10000 0 -0.41 63 63
RHOA 0.035 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.096 0.2 -10000 0 -0.42 103 103
MYH2 -0.1 0.2 -10000 0 -0.46 61 61
MST1R 0.013 0.095 -10000 0 -0.42 17 17
leukocyte activation during inflammatory response -0.002 0.12 -10000 0 -0.3 42 42
APOB 0.023 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.027 0.036 -10000 0 -0.42 2 2
JAM3 0.029 0.014 -10000 0 -10000 0 0
GP1BA -0.18 0.22 -10000 0 -0.42 175 175
alphaM/beta2 Integrin/CTGF 0 0.14 -10000 0 -0.33 44 44
alphaM/beta2 Integrin -0.1 0.21 -10000 0 -0.47 65 65
JAM3 homodimer 0.029 0.014 -10000 0 -10000 0 0
ICAM2 0.006 0.11 -10000 0 -0.42 23 23
ICAM1 0.027 0.062 -10000 0 -0.42 7 7
phagocytosis triggered by activation of immune response cell surface activating receptor -0.1 0.21 -10000 0 -0.47 66 66
cell adhesion -0.13 0.2 -10000 0 -0.31 188 188
NFKB1 -0.052 0.23 0.4 3 -0.43 83 86
THY1 0.029 0.035 -10000 0 -0.42 2 2
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.022 0.016 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.019 0.14 -10000 0 -0.32 40 40
IL6 -0.063 0.22 0.38 3 -0.44 76 79
ITGB2 -0.031 0.15 -10000 0 -0.44 42 42
elevation of cytosolic calcium ion concentration 0.014 0.14 -10000 0 -0.32 42 42
alphaM/beta2 Integrin/JAM2/JAM3 0.016 0.14 -10000 0 -0.33 42 42
JAM2 0.032 0.034 -10000 0 -0.42 2 2
alphaM/beta2 Integrin/ICAM1 0.026 0.16 -10000 0 -0.3 60 60
alphaM/beta2 Integrin/uPA/Plg 0.008 0.13 -10000 0 -0.32 42 42
RhoA/GTP -0.11 0.21 -10000 0 -0.46 67 67
positive regulation of phagocytosis -0.075 0.22 -10000 0 -0.44 71 71
Ron/MSP 0.033 0.076 -10000 0 -0.3 18 18
alphaM/beta2 Integrin/uPAR/uPA 0.016 0.14 -10000 0 -0.33 42 42
alphaM/beta2 Integrin/uPAR 0.002 0.14 -10000 0 -0.34 44 44
PLAU 0.03 0.026 -10000 0 -0.42 1 1
PLAT 0.032 0.025 -10000 0 -0.42 1 1
actin filament polymerization -0.099 0.19 -10000 0 -0.44 60 60
MST1 0.033 0.024 -10000 0 -0.42 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.001 0.12 -10000 0 -0.3 42 42
TNF -0.13 0.31 -10000 0 -0.69 80 80
RAP1B 0.034 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.001 0.14 -10000 0 -0.34 44 44
fibrinolysis 0.006 0.13 -10000 0 -0.32 42 42
HCK -0.002 0.12 -10000 0 -0.42 28 28
dendritic cell antigen processing and presentation -0.1 0.21 -10000 0 -0.47 66 66
VTN -0.02 0.14 -10000 0 -0.42 43 43
alphaM/beta2 Integrin/CYR61 0.001 0.14 -10000 0 -0.34 45 45
LPA 0.016 0.006 -10000 0 -10000 0 0
LRP1 0.034 0.007 -10000 0 -10000 0 0
cell migration -0.038 0.17 -10000 0 -0.34 75 75
FN1 0.021 0.077 -10000 0 -0.42 11 11
alphaM/beta2 Integrin/Thy1 0.001 0.14 -10000 0 -0.33 46 46
MPO -0.003 0.12 -10000 0 -0.42 29 29
KNG1 0.021 0.01 -10000 0 -10000 0 0
RAP1/GDP 0.044 0.013 -10000 0 -10000 0 0
ROCK1 -0.1 0.2 0.28 1 -0.45 62 63
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.016 0.006 -10000 0 -10000 0 0
CTGF 0.03 0.013 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Hck -0.011 0.18 -10000 0 -0.46 44 44
ITGAM 0.005 0.086 -10000 0 -0.37 14 14
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.068 0.22 -10000 0 -0.34 120 120
HP -0.069 0.18 -10000 0 -0.42 80 80
leukocyte adhesion -0.014 0.16 -10000 0 -0.38 47 47
SELP -0.096 0.2 -10000 0 -0.42 103 103
Glucocorticoid receptor regulatory network

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
PCK2 0.082 0.097 0.28 31 -10000 0 31
SMARCC2 0.036 0.005 -10000 0 -10000 0 0
SMARCC1 0.036 0.005 -10000 0 -10000 0 0
TBX21 -0.21 0.32 -10000 0 -0.7 104 104
SUMO2 0.036 0.012 -10000 0 -10000 0 0
STAT1 (dimer) 0.003 0.11 -10000 0 -0.28 44 44
FKBP4 0.034 0.007 -10000 0 -10000 0 0
FKBP5 0.003 0.11 -10000 0 -0.42 23 23
GR alpha/HSP90/FKBP51/HSP90 0.096 0.12 0.29 68 -0.21 7 75
PRL -0.045 0.11 -10000 0 -0.45 2 2
cortisol/GR alpha (dimer)/TIF2 0.19 0.26 0.54 106 -10000 0 106
RELA 0.015 0.072 -10000 0 -0.18 29 29
FGG 0.15 0.21 0.44 103 -10000 0 103
GR beta/TIF2 0.11 0.13 0.3 91 -10000 0 91
IFNG -0.42 0.53 -10000 0 -1.1 136 136
apoptosis 0.085 0.15 0.5 36 -10000 0 36
CREB1 0.036 0.01 -10000 0 -10000 0 0
histone acetylation -0.071 0.14 -10000 0 -0.35 58 58
BGLAP -0.061 0.14 -10000 0 -0.41 24 24
GR/PKAc 0.13 0.11 0.3 74 -10000 0 74
NF kappa B1 p50/RelA 0.022 0.13 -10000 0 -0.3 35 35
SMARCD1 0.036 0.006 -10000 0 -10000 0 0
MDM2 0.087 0.11 0.22 118 -10000 0 118
GATA3 -0.045 0.17 -10000 0 -0.42 64 64
AKT1 0.029 0.005 -10000 0 -10000 0 0
CSF2 -0.088 0.16 -10000 0 -0.6 11 11
GSK3B 0.037 0.011 -10000 0 -10000 0 0
NR1I3 0.11 0.16 0.51 34 -10000 0 34
CSN2 0.12 0.18 0.36 107 -10000 0 107
BRG1/BAF155/BAF170/BAF60A 0.093 0.023 -10000 0 -10000 0 0
NFATC1 0.025 0.07 -10000 0 -0.42 9 9
POU2F1 0.029 0.02 -10000 0 -10000 0 0
CDKN1A 0.023 0.056 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.003 0.009 -10000 0 -10000 0 0
SFN 0.027 0.015 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.096 0.12 0.3 55 -0.2 6 61
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.095 0.14 0.48 29 -10000 0 29
JUN -0.14 0.19 -10000 0 -0.41 88 88
IL4 -0.098 0.16 -10000 0 -0.5 26 26
CDK5R1 0.034 0.025 -10000 0 -0.42 1 1
PRKACA 0.035 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.052 0.11 0.22 17 -0.3 28 45
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.12 0.3 66 -0.19 7 73
cortisol/GR alpha (monomer) 0.23 0.32 0.64 117 -10000 0 117
NCOA2 0.032 0.011 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.02 0.074 -10000 0 -0.16 6 6
AP-1/NFAT1-c-4 -0.2 0.27 -10000 0 -0.51 137 137
AFP -0.11 0.14 -10000 0 -0.54 2 2
SUV420H1 0.034 0.008 -10000 0 -10000 0 0
IRF1 0.06 0.27 0.41 54 -0.66 33 87
TP53 0.05 0.015 -10000 0 -10000 0 0
PPP5C 0.035 0.004 -10000 0 -10000 0 0
KRT17 -0.19 0.27 -10000 0 -0.58 92 92
KRT14 -0.1 0.14 -10000 0 -0.48 14 14
TBP 0.039 0.015 -10000 0 -10000 0 0
CREBBP 0.042 0.012 -10000 0 -10000 0 0
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
HDAC2 0.03 0.012 -10000 0 -10000 0 0
AP-1 -0.2 0.28 -10000 0 -0.52 137 137
MAPK14 0.033 0.014 -10000 0 -10000 0 0
MAPK10 0.029 0.018 -10000 0 -10000 0 0
MAPK11 0.035 0.013 -10000 0 -10000 0 0
KRT5 -0.25 0.38 -10000 0 -0.84 85 85
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.037 0.006 -10000 0 -10000 0 0
STAT1 0.004 0.11 -10000 0 -0.28 44 44
CGA -0.085 0.15 -10000 0 -0.47 21 21
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.1 0.13 0.35 47 -10000 0 47
MAPK3 0.038 0.01 -10000 0 -10000 0 0
MAPK1 0.035 0.012 -10000 0 -10000 0 0
ICAM1 -0.12 0.23 -10000 0 -0.62 43 43
NFKB1 0.014 0.075 -10000 0 -0.2 22 22
MAPK8 -0.12 0.18 -10000 0 -0.38 91 91
MAPK9 0.035 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.082 0.15 0.5 34 -10000 0 34
BAX 0.014 0.043 -10000 0 -10000 0 0
POMC -0.25 0.5 -10000 0 -1.5 45 45
EP300 0.038 0.016 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.2 0.26 0.54 113 -10000 0 113
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.091 0.2 75 -10000 0 75
SGK1 0.057 0.073 -10000 0 -10000 0 0
IL13 -0.23 0.32 -10000 0 -0.73 88 88
IL6 -0.12 0.26 -10000 0 -0.67 47 47
PRKACG 0.019 0.009 -10000 0 -10000 0 0
IL5 -0.21 0.28 -10000 0 -0.73 64 64
IL2 -0.2 0.27 -10000 0 -0.63 76 76
CDK5 0.032 0.012 -10000 0 -10000 0 0
PRKACB 0.035 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
IL8 -0.12 0.22 -10000 0 -0.55 54 54
CDK5R1/CDK5 0.047 0.028 -10000 0 -0.3 1 1
NF kappa B1 p50/RelA/PKAc 0.057 0.11 -10000 0 -0.25 20 20
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.2 0.25 0.51 122 -10000 0 122
SMARCA4 0.037 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.16 0.36 100 -10000 0 100
NF kappa B1 p50/RelA/Cbp 0.062 0.11 0.34 1 -0.3 6 7
JUN (dimer) -0.14 0.19 -10000 0 -0.41 87 87
YWHAH 0.034 0.008 -10000 0 -10000 0 0
VIPR1 -0.2 0.32 -10000 0 -0.69 102 102
NR3C1 0.15 0.21 0.42 109 -10000 0 109
NR4A1 -0.016 0.16 -10000 0 -0.45 42 42
TIF2/SUV420H1 0.045 0.019 -10000 0 -10000 0 0
MAPKKK cascade 0.085 0.15 0.5 36 -10000 0 36
cortisol/GR alpha (dimer)/Src-1 0.21 0.27 0.53 126 -10000 0 126
PBX1 0.028 0.021 -10000 0 -10000 0 0
POU1F1 0.017 0.02 -10000 0 -10000 0 0
SELE -0.16 0.33 -10000 0 -0.74 75 75
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.16 0.36 100 -10000 0 100
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.2 0.25 0.51 122 -10000 0 122
mol:cortisol 0.14 0.19 0.37 119 -10000 0 119
MMP1 -0.14 0.33 -10000 0 -1 42 42
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.058 -10000 0 -0.36 6 6
Crk/p130 Cas/Paxillin -0.05 0.1 -10000 0 -0.24 66 66
JUN -0.029 0.092 0.2 1 -0.28 9 10
HRAS 0.034 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.004 0.12 -10000 0 -0.23 78 78
RAP1A 0.034 0.007 -10000 0 -10000 0 0
FRS2 0.034 0.008 -10000 0 -10000 0 0
RAP1A/GDP 0.025 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.002 0.13 -10000 0 -0.23 82 82
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.017 0.12 -10000 0 -0.23 81 81
RHOA 0.035 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.002 0.11 -10000 0 -0.2 79 79
GRB7 0.029 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.002 0.13 -10000 0 -0.23 82 82
MAPKKK cascade -0.023 0.11 -10000 0 -0.22 73 73
BCAR1 0.034 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.019 0.12 -10000 0 -0.23 80 80
lamellipodium assembly -0.034 0.11 -10000 0 -0.23 70 70
RET51/GFRalpha1/GDNF/SHC -0.002 0.12 -10000 0 -0.23 72 72
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.014 0.11 -10000 0 -0.23 71 71
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.12 -10000 0 -0.23 78 78
MAPK3 -0.026 0.1 0.19 18 -0.2 73 91
DOK1 0.035 0.002 -10000 0 -10000 0 0
DOK6 0.023 0.062 -10000 0 -0.42 7 7
PXN 0.034 0.006 -10000 0 -10000 0 0
neurite development -0.017 0.095 0.26 3 -0.28 5 8
DOK5 0.021 0.043 -10000 0 -0.42 3 3
GFRA1 -0.069 0.19 -10000 0 -0.42 81 81
MAPK8 -0.027 0.096 -10000 0 -0.2 80 80
HRAS/GTP -0.013 0.13 -10000 0 -0.24 80 80
tube development -0.012 0.11 0.22 5 -0.22 74 79
MAPK1 -0.024 0.099 0.19 17 -0.2 68 85
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.031 0.1 -10000 0 -0.21 77 77
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
PDLIM7 0.033 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.005 0.13 -10000 0 -0.23 73 73
SHC1 0.032 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.002 0.13 -10000 0 -0.23 82 82
RET51/GFRalpha1/GDNF/Dok5 -0.01 0.12 -10000 0 -0.23 74 74
PRKCA 0.032 0.025 -10000 0 -0.42 1 1
HRAS/GDP 0.025 0.004 -10000 0 -10000 0 0
CREB1 -0.032 0.11 -10000 0 -0.23 72 72
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.028 0.097 -10000 0 -0.21 71 71
RET51/GFRalpha1/GDNF/Grb7 -0.007 0.13 -10000 0 -0.23 81 81
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.03 0.026 -10000 0 -0.42 1 1
DOK4 0.034 0.007 -10000 0 -10000 0 0
JNK cascade -0.029 0.091 0.2 1 -0.27 9 10
RET9/GFRalpha1/GDNF/FRS2 -0.017 0.12 -10000 0 -0.23 80 80
SHANK3 0.032 0.01 -10000 0 -10000 0 0
RASA1 0.032 0.025 -10000 0 -0.42 1 1
NCK1 0.034 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.028 0.098 -10000 0 -0.21 73 73
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.03 0.11 -10000 0 -0.21 88 88
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.03 0.11 -10000 0 -0.21 88 88
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.097 -10000 0 -0.21 70 70
PI3K -0.043 0.16 0.24 2 -0.32 71 73
SOS1 0.035 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.002 0.11 -10000 0 -0.22 74 74
GRB10 0.032 0.011 -10000 0 -10000 0 0
activation of MAPKK activity -0.022 0.1 -10000 0 -0.21 80 80
RET51/GFRalpha1/GDNF/FRS2 -0.003 0.13 -10000 0 -0.23 81 81
GAB1 0.035 0.004 -10000 0 -10000 0 0
IRS1 0.032 0.011 -10000 0 -10000 0 0
IRS2 0.034 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.022 0.097 -10000 0 -0.21 69 69
RET51/GFRalpha1/GDNF/PKC alpha -0.003 0.13 -10000 0 -0.23 78 78
GRB2 0.034 0.007 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GDNF 0.019 0.058 -10000 0 -0.42 6 6
RAC1 0.031 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.004 0.13 -10000 0 -0.23 81 81
Rac1/GTP -0.035 0.13 -10000 0 -0.27 70 70
RET9/GFRalpha1/GDNF -0.031 0.12 -10000 0 -0.25 81 81
GFRalpha1/GDNF -0.04 0.14 -10000 0 -0.3 81 81
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.13 0.28 -10000 0 -0.64 66 66
UGCG -0.054 0.23 -10000 0 -0.85 26 26
AKT1/mTOR/p70S6K/Hsp90/TERT -0.066 0.24 0.27 2 -0.46 68 70
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.053 0.23 -10000 0 -0.84 26 26
mol:DAG -0.084 0.28 -10000 0 -0.89 38 38
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.086 0.25 0.3 2 -0.46 100 102
FRAP1 -0.11 0.29 0.31 2 -0.52 106 108
FOXO3 -0.12 0.28 0.31 2 -0.51 108 110
AKT1 -0.13 0.31 0.32 2 -0.55 108 110
GAB2 0.034 0.009 -10000 0 -10000 0 0
SMPD1 -0.017 0.15 -10000 0 -0.99 8 8
SGMS1 -0.078 0.26 -10000 0 -0.82 38 38
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 0.011 0.004 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
cell proliferation -0.084 0.26 0.25 1 -0.7 47 48
EIF3A 0.032 0.01 -10000 0 -10000 0 0
PI3K 0.053 0.015 -10000 0 -10000 0 0
RPS6KB1 -0.004 0.15 -10000 0 -1 6 6
mol:sphingomyelin -0.084 0.28 -10000 0 -0.89 38 38
natural killer cell activation 0.001 0 -10000 0 -10000 0 0
JAK3 0.006 0.12 -10000 0 -0.42 25 25
PIK3R1 0.036 0.008 -10000 0 -10000 0 0
JAK1 0.037 0.005 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MYC -0.079 0.25 0.39 1 -0.54 50 51
MYB -0.031 0.28 -10000 0 -1.2 19 19
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.15 0.32 -10000 0 -0.57 119 119
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.14 -10000 0 -0.92 6 6
mol:PI-3-4-5-P3 -0.14 0.31 -10000 0 -0.55 120 120
Rac1/GDP 0.029 0.014 -10000 0 -10000 0 0
T cell proliferation -0.13 0.29 -10000 0 -0.52 115 115
SHC1 0.032 0.011 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.016 -10000 0 -0.065 19 19
PRKCZ -0.14 0.3 -10000 0 -0.55 115 115
NF kappa B1 p50/RelA -0.076 0.26 0.32 2 -0.46 98 100
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.15 0.31 -10000 0 -0.56 111 111
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
RELA 0.034 0.007 -10000 0 -10000 0 0
IL2RA -0.062 0.18 -10000 0 -0.42 76 76
IL2RB -0.04 0.17 -10000 0 -0.42 61 61
TERT 0.029 0.013 -10000 0 -10000 0 0
E2F1 0.008 0.11 -10000 0 -0.45 19 19
SOS1 0.036 0.003 -10000 0 -10000 0 0
RPS6 0.031 0.012 -10000 0 -10000 0 0
mol:cAMP -0.001 0.007 0.032 17 -10000 0 17
PTPN11 0.035 0.006 -10000 0 -10000 0 0
IL2RG -0.1 0.21 -10000 0 -0.42 112 112
actin cytoskeleton organization -0.13 0.29 -10000 0 -0.52 115 115
GRB2 0.035 0.007 -10000 0 -10000 0 0
IL2 0.025 0.01 -10000 0 -10000 0 0
PIK3CA 0.037 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.06 0.029 -10000 0 -10000 0 0
LCK -0.13 0.22 -10000 0 -0.42 138 138
BCL2 -0.077 0.22 -10000 0 -0.46 59 59
IL2 signaling events mediated by STAT5

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
GAB2 0.033 0.009 -10000 0 -10000 0 0
ELF1 -0.039 0.15 -10000 0 -0.31 84 84
CCNA2 0.034 0.024 -10000 0 -0.42 1 1
PIK3CA 0.035 0.006 -10000 0 -10000 0 0
JAK3 0.005 0.11 -10000 0 -0.42 25 25
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
JAK1 0.035 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.16 0.33 -10000 0 -0.59 120 120
SHC1 0.032 0.011 -10000 0 -10000 0 0
SP1 0.019 0.094 -10000 0 -0.33 24 24
IL2RA -0.13 0.29 -10000 0 -0.63 88 88
IL2RB -0.042 0.17 -10000 0 -0.42 61 61
SOS1 0.036 0.003 -10000 0 -10000 0 0
IL2RG -0.1 0.21 -10000 0 -0.42 112 112
G1/S transition of mitotic cell cycle -0.033 0.22 0.28 1 -0.7 33 34
PTPN11 0.035 0.006 -10000 0 -10000 0 0
CCND2 -0.02 0.18 -10000 0 -0.67 25 25
LCK -0.14 0.22 -10000 0 -0.42 138 138
GRB2 0.034 0.007 -10000 0 -10000 0 0
IL2 0.023 0.009 -10000 0 -10000 0 0
CDK6 0.029 0.042 -10000 0 -0.42 3 3
CCND3 -0.12 0.28 0.29 1 -0.53 101 102
Class I PI3K 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
ARF5/GTP 0.027 0.046 0.3 5 -10000 0 5
DAPP1 -0.29 0.39 0.34 1 -0.64 158 159
Src family/SYK family/BLNK-LAT/BTK-ITK -0.38 0.44 0.4 1 -0.8 165 166
mol:DAG -0.12 0.16 0.23 6 -0.29 143 149
HRAS 0.037 0.009 -10000 0 -10000 0 0
RAP1A 0.036 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.007 0.12 0.2 2 -0.34 28 30
PLCG2 -0.002 0.12 -10000 0 -0.42 29 29
PLCG1 0.033 0.01 -10000 0 -10000 0 0
ARF5 0.031 0.011 -10000 0 -10000 0 0
mol:GTP -0.002 0.058 0.3 10 -10000 0 10
ARF1/GTP 0.012 0.054 0.3 8 -10000 0 8
RHOA 0.035 0.005 -10000 0 -10000 0 0
YES1 0.034 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.03 0.18 11 -10000 0 11
ADAP1 -0.011 0.053 0.28 5 -0.21 7 12
ARAP3 -0.002 0.057 0.3 10 -10000 0 10
INPPL1 0.033 0.009 -10000 0 -10000 0 0
PREX1 0.03 0.035 -10000 0 -0.42 2 2
ARHGEF6 0.016 0.093 -10000 0 -0.42 16 16
ARHGEF7 0.034 0.008 -10000 0 -10000 0 0
ARF1 0.032 0.011 -10000 0 -10000 0 0
NRAS 0.036 0.01 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
ARF6 0.035 0.004 -10000 0 -10000 0 0
FGR -0.01 0.14 -10000 0 -0.42 36 36
mol:Ca2+ -0.054 0.076 0.16 9 -0.14 126 135
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
ZAP70 -0.12 0.22 -10000 0 -0.42 126 126
mol:IP3 -0.08 0.1 0.18 7 -0.2 135 142
LYN 0.016 0.084 -10000 0 -0.42 13 13
ARF1/GDP 0.01 0.12 0.2 1 -0.32 29 30
RhoA/GDP 0.042 0.082 0.26 9 -0.26 5 14
PDK1/Src/Hsp90 0.064 0.023 -10000 0 -10000 0 0
BLNK -0.11 0.21 -10000 0 -0.42 116 116
actin cytoskeleton reorganization 0.02 0.12 0.26 20 -0.31 18 38
SRC 0.033 0.01 -10000 0 -10000 0 0
PLEKHA2 -0.029 0.091 -10000 0 -0.26 49 49
RAC1 0.031 0.012 -10000 0 -10000 0 0
PTEN 0.027 0.018 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
ARF6/GTP 0.031 0.052 0.3 10 -10000 0 10
RhoA/GTP -0.002 0.059 0.24 18 -10000 0 18
Src family/SYK family/BLNK-LAT -0.38 0.46 -10000 0 -0.78 171 171
BLK -0.24 0.22 -10000 0 -0.42 216 216
PDPK1 0.035 0.003 -10000 0 -10000 0 0
CYTH1 -0.003 0.055 0.28 10 -10000 0 10
HCK -0.002 0.12 -10000 0 -0.42 28 28
CYTH3 -0.006 0.043 0.28 5 -10000 0 5
CYTH2 -0.002 0.057 0.28 11 -10000 0 11
KRAS 0.037 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.026 0.048 0.22 7 -0.29 3 10
SGK1 0.015 0.085 -10000 0 -0.31 19 19
INPP5D -0.037 0.16 -10000 0 -0.42 58 58
mol:GDP -0.007 0.13 0.22 4 -0.32 35 39
SOS1 0.035 0.003 -10000 0 -10000 0 0
SYK -0.012 0.13 -10000 0 -0.42 36 36
ARF6/GDP 0.023 0.082 0.28 15 -0.26 5 20
mol:PI-3-4-5-P3 -0.003 0.055 0.28 10 -10000 0 10
ARAP3/RAP1A/GTP 0.021 0.03 0.18 11 -10000 0 11
VAV1 -0.052 0.18 -10000 0 -0.42 70 70
mol:PI-3-4-P2 -0.029 0.11 -10000 0 -0.3 54 54
RAS family/GTP/PI3K Class I 0.069 0.057 0.21 45 -10000 0 45
PLEKHA1 -0.024 0.082 -10000 0 -0.25 43 43
Rac1/GDP 0.005 0.12 0.2 2 -0.32 30 32
LAT -0.021 0.15 -10000 0 -0.42 45 45
Rac1/GTP -0.018 0.15 -10000 0 -0.41 33 33
ITK -0.043 0.088 0.28 5 -0.21 64 69
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.18 0.22 0.23 3 -0.43 148 151
LCK -0.14 0.22 -10000 0 -0.42 138 138
BTK -0.029 0.083 0.28 8 -0.21 42 50
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.092 0.34 -10000 0 -0.82 62 62
NCK1/PAK1/Dok-R -0.082 0.15 -10000 0 -0.41 61 61
NCK1/Dok-R -0.14 0.42 -10000 0 -1 62 62
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.03 0.087 0.22 61 -10000 0 61
RELA 0.034 0.007 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
Rac/GDP 0.023 0.009 -10000 0 -10000 0 0
F2 0.025 0.099 0.25 57 -10000 0 57
TNIP2 0.034 0.007 -10000 0 -10000 0 0
NF kappa B/RelA -0.11 0.39 -10000 0 -0.94 62 62
FN1 0.021 0.077 -10000 0 -0.42 11 11
PLD2 -0.15 0.4 -10000 0 -1 62 62
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GRB14 0.027 0.013 -10000 0 -10000 0 0
ELK1 -0.13 0.37 -10000 0 -0.93 62 62
GRB7 0.029 0.012 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.41 -10000 0 -0.99 62 62
CDKN1A -0.036 0.22 -10000 0 -0.51 56 56
ITGA5 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.42 -10000 0 -1 62 62
CRK 0.033 0.009 -10000 0 -10000 0 0
mol:NO -0.045 0.27 0.38 1 -0.62 62 63
PLG -0.15 0.4 -10000 0 -1 62 62
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.087 0.33 -10000 0 -0.8 62 62
GRB2 0.034 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
ANGPT2 -0.039 0.18 -10000 0 -0.58 7 7
BMX -0.18 0.42 -10000 0 -1.1 62 62
ANGPT1 -0.21 0.47 -10000 0 -1.2 60 60
tube development -0.056 0.24 -10000 0 -0.57 61 61
ANGPT4 0.01 0.015 -10000 0 -10000 0 0
response to hypoxia -0.011 0.026 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.42 -10000 0 -1.1 62 62
alpha5/beta1 Integrin 0.046 0.018 -10000 0 -10000 0 0
FGF2 0.029 0.035 -10000 0 -0.42 2 2
STAT5A (dimer) -0.051 0.28 -10000 0 -0.64 61 61
mol:L-citrulline -0.045 0.27 0.38 1 -0.62 62 63
AGTR1 0.017 0.008 -10000 0 -10000 0 0
MAPK14 -0.14 0.39 -10000 0 -0.98 62 62
Tie2/SHP2 -0.045 0.22 -10000 0 -0.81 17 17
TEK -0.05 0.23 -10000 0 -0.87 18 18
RPS6KB1 -0.086 0.33 -10000 0 -0.78 62 62
Angiotensin II/AT1 0.015 0.007 -10000 0 -10000 0 0
Tie2/Ang1/GRB2 -0.14 0.42 -10000 0 -1 62 62
MAPK3 -0.14 0.38 -10000 0 -0.95 62 62
MAPK1 -0.14 0.38 -10000 0 -0.95 62 62
Tie2/Ang1/GRB7 -0.15 0.42 -10000 0 -1.1 62 62
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.15 0.4 -10000 0 -1 62 62
PI3K -0.11 0.38 -10000 0 -0.93 62 62
FES -0.14 0.4 -10000 0 -0.98 62 62
Crk/Dok-R -0.14 0.42 -10000 0 -1 62 62
Tie2/Ang1/ABIN2 -0.15 0.42 -10000 0 -1.1 62 62
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.078 0.31 -10000 0 -0.74 62 62
STAT5A 0.034 0.024 -10000 0 -0.42 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.074 0.33 -10000 0 -0.78 61 61
Tie2/Ang2 -0.08 0.31 -10000 0 -0.73 61 61
Tie2/Ang1 -0.16 0.43 -10000 0 -1.1 62 62
FOXO1 -0.08 0.31 -10000 0 -0.74 62 62
ELF1 0.041 0.019 -10000 0 -0.12 1 1
ELF2 -0.14 0.4 -10000 0 -1 62 62
mol:Choline -0.14 0.39 -10000 0 -0.98 62 62
cell migration -0.046 0.086 -10000 0 -0.23 62 62
FYN -0.067 0.27 -10000 0 -0.64 61 61
DOK2 -0.01 0.13 -10000 0 -0.42 35 35
negative regulation of cell cycle -0.029 0.21 -10000 0 -0.47 57 57
ETS1 0.001 0.095 -10000 0 -0.24 49 49
PXN -0.052 0.29 0.38 1 -0.66 61 62
ITGB1 0.032 0.011 -10000 0 -10000 0 0
NOS3 -0.061 0.3 -10000 0 -0.7 62 62
RAC1 0.031 0.012 -10000 0 -10000 0 0
TNF -0.086 0.2 -10000 0 -0.39 105 105
MAPKKK cascade -0.14 0.39 -10000 0 -0.98 62 62
RASA1 0.032 0.025 -10000 0 -0.42 1 1
Tie2/Ang1/Shc -0.15 0.42 -10000 0 -1 62 62
NCK1 0.034 0.006 -10000 0 -10000 0 0
vasculogenesis -0.036 0.25 0.35 3 -0.55 62 65
mol:Phosphatidic acid -0.14 0.39 -10000 0 -0.98 62 62
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.045 0.27 0.38 1 -0.62 62 63
Rac1/GTP -0.079 0.31 -10000 0 -0.74 62 62
MMP2 -0.15 0.4 -10000 0 -1 62 62
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.029 0.13 -10000 0 -0.29 64 64
CRKL 0.033 0.01 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DOCK1 0.032 0.01 -10000 0 -10000 0 0
ITGA4 -0.013 0.14 -10000 0 -0.42 39 39
alpha4/beta7 Integrin/MAdCAM1 -0.15 0.19 -10000 0 -0.28 234 234
EPO 0.027 0.012 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.16 -10000 0 -0.32 80 80
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.011 0.11 -10000 0 -0.29 39 39
EPO/EPOR (dimer) 0.043 0.016 -10000 0 -10000 0 0
lamellipodium assembly 0.018 0.076 -10000 0 -0.55 5 5
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
ARF6 0.035 0.004 -10000 0 -10000 0 0
JAK2 -0.003 0.1 -10000 0 -0.28 37 37
PXN 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
MADCAM1 -0.22 0.22 -10000 0 -0.42 203 203
cell adhesion -0.15 0.19 -10000 0 -0.27 234 234
CRKL/CBL 0.044 0.02 -10000 0 -10000 0 0
ITGB1 0.032 0.011 -10000 0 -10000 0 0
SRC -0.038 0.13 0.19 3 -0.3 67 70
ITGB7 -0.026 0.15 -10000 0 -0.42 49 49
RAC1 0.031 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.014 0.16 -10000 0 -0.32 73 73
p130Cas/Crk/Dock1 -0.005 0.13 0.21 3 -0.27 61 64
VCAM1 -0.04 0.17 -10000 0 -0.42 60 60
RHOA 0.035 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.097 -10000 0 -0.22 39 39
BCAR1 -0.043 0.12 0.18 4 -0.28 67 71
EPOR 0.035 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.011 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.079 -10000 0 -0.57 5 5
Endothelins

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
AKT1 0.005 0.13 0.29 22 -0.26 48 70
PTK2B 0.028 0.048 -10000 0 -0.42 4 4
mol:Ca2+ -0.032 0.22 0.65 1 -0.59 26 27
EDN1 0.016 0.1 0.23 22 -0.21 34 56
EDN3 0 0.093 -10000 0 -0.42 17 17
EDN2 0.017 0.002 -10000 0 -10000 0 0
HRAS/GDP -0.049 0.2 0.31 3 -0.43 56 59
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.014 0.16 0.2 11 -0.4 37 48
ADCY4 0.024 0.13 0.21 39 -0.26 31 70
ADCY5 -0.018 0.15 0.21 24 -0.26 65 89
ADCY6 0.026 0.12 0.22 32 -0.33 13 45
ADCY7 0.023 0.12 0.21 36 -0.27 22 58
ADCY1 -0.007 0.13 0.22 24 -0.25 44 68
ADCY2 0.004 0.11 0.21 24 -0.26 25 49
ADCY3 0.025 0.12 0.22 34 -0.32 14 48
ADCY8 0.017 0.11 0.21 23 -0.22 33 56
ADCY9 0.028 0.12 0.21 47 -0.25 27 74
arachidonic acid secretion -0.031 0.18 0.36 3 -0.4 44 47
ETB receptor/Endothelin-1/Gq/GTP -0.003 0.11 -10000 0 -0.26 44 44
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
HRAS 0.035 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.036 0.14 0.37 18 -0.24 41 59
ETA receptor/Endothelin-1/Gs/GTP 0.031 0.13 0.34 21 -0.23 46 67
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
COL3A1 0.006 0.13 0.29 23 -0.35 16 39
EDNRB 0.03 0.028 -10000 0 -0.42 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.014 0.18 0.29 18 -0.46 35 53
CYSLTR1 -0.021 0.2 0.29 23 -0.5 44 67
SLC9A1 0.011 0.078 0.2 21 -0.24 9 30
mol:GDP -0.065 0.21 0.3 3 -0.44 60 63
SLC9A3 -0.15 0.3 0.43 1 -0.57 103 104
RAF1 -0.056 0.19 0.36 1 -0.41 57 58
JUN -0.042 0.23 0.48 1 -0.64 27 28
JAK2 0.003 0.13 0.29 20 -0.27 46 66
mol:IP3 -0.025 0.17 0.23 2 -0.4 44 46
ETA receptor/Endothelin-1 0.024 0.17 0.42 22 -0.31 50 72
PLCB1 0.018 0.084 -10000 0 -0.42 13 13
PLCB2 0.022 0.074 -10000 0 -0.42 10 10
ETA receptor/Endothelin-3 0.004 0.098 0.19 14 -0.23 32 46
FOS -0.028 0.16 0.46 1 -0.43 22 23
Gai/GDP -0.016 0.18 -10000 0 -0.75 19 19
CRK 0.033 0.009 -10000 0 -10000 0 0
mol:Ca ++ -0.017 0.19 0.26 12 -0.46 38 50
BCAR1 0.034 0.008 -10000 0 -10000 0 0
PRKCB1 -0.026 0.17 0.22 2 -0.38 47 49
GNAQ 0.035 0.01 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
GNAL 0.024 0.053 -10000 0 -0.42 5 5
Gs family/GDP -0.055 0.19 0.32 2 -0.42 54 56
ETA receptor/Endothelin-1/Gq/GTP -0.003 0.14 0.21 14 -0.36 34 48
MAPK14 -0.015 0.13 0.3 1 -0.35 33 34
TRPC6 -0.035 0.22 0.66 1 -0.62 25 26
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.011 0.14 -10000 0 -0.36 33 33
ETB receptor/Endothelin-2 0.03 0.027 -10000 0 -0.3 1 1
ETB receptor/Endothelin-3 0.01 0.075 -10000 0 -0.3 18 18
ETB receptor/Endothelin-1 0.026 0.083 0.2 10 -0.27 9 19
MAPK3 -0.038 0.17 0.38 2 -0.48 27 29
MAPK1 -0.04 0.18 0.38 2 -0.48 28 30
Rac1/GDP -0.046 0.19 0.32 2 -0.42 54 56
cAMP biosynthetic process -0.018 0.15 0.25 19 -0.35 34 53
MAPK8 -0.055 0.26 0.51 1 -0.64 48 49
SRC 0.033 0.01 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.013 0.05 -10000 0 -0.32 3 3
p130Cas/CRK/Src/PYK2 -0.053 0.21 0.44 2 -0.45 54 56
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.045 0.19 0.32 2 -0.42 54 56
COL1A2 0.013 0.12 0.3 15 -0.42 9 24
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.021 0.079 0.18 18 -0.17 23 41
mol:DAG -0.025 0.17 0.23 2 -0.4 44 46
MAP2K2 -0.048 0.18 0.41 2 -0.41 47 49
MAP2K1 -0.048 0.18 0.33 3 -0.41 47 50
EDNRA 0.016 0.11 0.24 23 -0.19 60 83
positive regulation of muscle contraction 0.019 0.12 0.25 40 -0.25 31 71
Gq family/GDP -0.046 0.22 -10000 0 -0.45 58 58
HRAS/GTP -0.063 0.2 0.37 1 -0.42 64 65
PRKCH -0.026 0.17 0.21 2 -0.41 40 42
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA -0.025 0.17 0.24 8 -0.39 44 52
PRKCB -0.081 0.22 0.2 1 -0.43 78 79
PRKCE -0.025 0.17 0.23 4 -0.4 41 45
PRKCD -0.026 0.17 0.22 4 -0.4 41 45
PRKCG -0.029 0.17 0.21 2 -0.4 43 45
regulation of vascular smooth muscle contraction -0.038 0.18 0.49 1 -0.51 22 23
PRKCQ -0.071 0.2 0.2 1 -0.43 65 66
PLA2G4A -0.035 0.19 0.37 3 -0.42 44 47
GNA14 -0.035 0.16 -10000 0 -0.42 56 56
GNA15 0.022 0.078 -10000 0 -0.42 11 11
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA11 0.036 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.036 0.14 0.37 18 -0.24 41 59
MMP1 -0.04 0.2 0.56 4 -0.78 22 26
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.16 0.27 -10000 0 -0.6 69 69
PCK1 -0.072 0.14 -10000 0 -0.57 3 3
HNF4A -0.15 0.27 -10000 0 -0.84 22 22
KCNJ11 -0.2 0.34 -10000 0 -0.71 83 83
AKT1 -0.097 0.17 -10000 0 -0.35 66 66
response to starvation 0.001 0.005 -10000 0 -10000 0 0
DLK1 -0.19 0.32 -10000 0 -0.69 80 80
NKX2-1 -0.078 0.16 0.31 4 -0.32 68 72
ACADM -0.16 0.27 -10000 0 -0.6 66 66
TAT -0.081 0.15 -10000 0 -0.59 6 6
CEBPB 0.031 0.016 -10000 0 -10000 0 0
CEBPA -0.005 0.13 -10000 0 -0.42 31 31
TTR -0.082 0.27 -10000 0 -0.93 25 25
PKLR -0.42 0.47 -10000 0 -0.84 193 193
APOA1 -0.18 0.32 -10000 0 -0.91 31 31
CPT1C -0.17 0.3 -10000 0 -0.71 54 54
ALAS1 -0.067 0.16 -10000 0 -0.6 3 3
TFRC -0.098 0.2 -10000 0 -0.54 19 19
FOXF1 0.007 0.1 -10000 0 -0.42 21 21
NF1 0.04 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.006 -10000 0 -10000 0 0
CPT1A -0.15 0.28 -10000 0 -0.61 64 64
HMGCS1 -0.15 0.27 -10000 0 -0.66 47 47
NR3C1 0.033 0.009 -10000 0 -10000 0 0
CPT1B -0.15 0.28 -10000 0 -0.67 48 48
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.005 -10000 0 -10000 0 0
GCK -0.2 0.36 -10000 0 -0.88 59 59
CREB1 0.031 0.018 -10000 0 -10000 0 0
IGFBP1 -0.062 0.14 -10000 0 -0.51 2 2
PDX1 -0.074 0.16 -10000 0 -0.75 2 2
UCP2 -0.2 0.36 -10000 0 -0.73 88 88
ALDOB -0.17 0.29 -10000 0 -0.63 78 78
AFP 0.002 0.053 -10000 0 -10000 0 0
BDH1 -0.16 0.28 -10000 0 -0.65 57 57
HADH -0.17 0.3 -10000 0 -0.64 76 76
F2 -0.18 0.32 -10000 0 -0.93 28 28
HNF1A 0.034 0.006 -10000 0 -10000 0 0
G6PC 0.001 0.085 -10000 0 -10000 0 0
SLC2A2 -0.096 0.19 -10000 0 -0.7 5 5
INS -0.022 0.005 -10000 0 -10000 0 0
FOXA1 0.031 0.021 -10000 0 -10000 0 0
FOXA3 0.016 0.094 -10000 0 -0.41 16 16
FOXA2 -0.2 0.35 -10000 0 -0.72 79 79
ABCC8 -0.18 0.29 -10000 0 -0.63 78 78
ALB 0.004 0.053 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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 0.033 0.034 -10000 0 -0.42 2 2
CCL5 -0.095 0.2 -10000 0 -0.42 105 105
SDCBP 0.032 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.028 0.14 0.21 8 -0.28 68 76
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 -0.022 0.15 0.22 8 -0.36 38 46
Syndecan-1/Syntenin -0.017 0.14 0.21 5 -0.38 28 33
MAPK3 -0.018 0.14 0.22 8 -0.4 25 33
HGF/MET 0.019 0.091 -10000 0 -0.3 25 25
TGFB1/TGF beta receptor Type II 0.033 0.033 -10000 0 -0.42 2 2
BSG 0.035 0.004 -10000 0 -10000 0 0
keratinocyte migration -0.021 0.14 0.22 8 -0.35 38 46
Syndecan-1/RANTES -0.074 0.19 0.24 8 -0.41 62 70
Syndecan-1/CD147 0 0.15 0.32 2 -0.41 26 28
Syndecan-1/Syntenin/PIP2 -0.018 0.13 -10000 0 -0.37 28 28
LAMA5 0.031 0.025 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion -0.018 0.13 -10000 0 -0.36 28 28
MMP7 0.017 0.07 -10000 0 -0.42 9 9
HGF 0.024 0.058 -10000 0 -0.42 6 6
Syndecan-1/CASK -0.041 0.13 -10000 0 -0.27 72 72
Syndecan-1/HGF/MET -0.02 0.16 0.34 1 -0.44 32 33
regulation of cell adhesion -0.024 0.13 0.25 3 -0.38 24 27
HPSE 0.035 0.004 -10000 0 -10000 0 0
positive regulation of cell migration -0.028 0.14 0.21 8 -0.28 68 76
SDC1 -0.032 0.14 -10000 0 -0.28 71 71
Syndecan-1/Collagen -0.028 0.14 0.21 8 -0.28 68 76
PPIB 0.035 0.004 -10000 0 -10000 0 0
MET 0.006 0.1 -10000 0 -0.42 20 20
PRKACA 0.035 0.003 -10000 0 -10000 0 0
MMP9 -0.036 0.16 -10000 0 -0.42 55 55
MAPK1 -0.017 0.13 0.22 8 -0.39 24 32
homophilic cell adhesion -0.027 0.14 0.23 10 -0.28 68 78
MMP1 0.002 0.1 -10000 0 -0.42 21 21
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.034 0.007 -10000 0 -10000 0 0
LAT2 -0.034 0.17 0.2 4 -0.43 44 48
AP1 -0.069 0.28 -10000 0 -0.57 75 75
mol:PIP3 -0.052 0.24 0.3 21 -0.51 63 84
IKBKB -0.027 0.14 0.25 20 -0.28 59 79
AKT1 0.024 0.12 0.32 40 -0.23 2 42
IKBKG -0.029 0.14 0.23 22 -0.28 60 82
MS4A2 0.027 0.021 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
MAP3K1 -0.049 0.2 0.26 10 -0.44 64 74
mol:Ca2+ -0.031 0.18 0.27 23 -0.37 63 86
LYN 0.017 0.087 -10000 0 -0.43 13 13
CBLB -0.019 0.13 0.2 3 -0.36 36 39
SHC1 0.032 0.011 -10000 0 -10000 0 0
RasGAP/p62DOK 0.06 0.026 -10000 0 -0.22 1 1
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.037 0.16 -10000 0 -0.42 58 58
PLD2 0.024 0.11 0.31 36 -0.2 20 56
PTPN13 -0.007 0.16 0.32 1 -0.48 22 23
PTPN11 0.031 0.02 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.015 0.11 0.28 17 -0.28 14 31
SYK -0.011 0.14 -10000 0 -0.43 36 36
GRB2 0.034 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.064 0.22 -10000 0 -0.52 62 62
LAT -0.039 0.16 0.18 1 -0.4 49 50
PAK2 -0.058 0.23 0.26 9 -0.5 64 73
NFATC2 -0.019 0.12 -10000 0 -0.5 20 20
HRAS -0.065 0.25 0.28 8 -0.55 64 72
GAB2 0.033 0.009 -10000 0 -10000 0 0
PLA2G1B 0.011 0.13 -10000 0 -0.9 7 7
Fc epsilon R1 0.034 0.081 -10000 0 -0.25 24 24
Antigen/IgE/Fc epsilon R1 0.033 0.074 -10000 0 -0.22 24 24
mol:GDP -0.091 0.27 0.35 1 -0.6 70 71
JUN 0.031 0.011 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
FOS 0.033 0.008 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.016 0.14 0.22 1 -0.37 39 40
CHUK -0.029 0.14 0.24 18 -0.28 59 77
KLRG1 -0.021 0.12 -10000 0 -0.31 45 45
VAV1 -0.047 0.18 0.2 2 -0.44 52 54
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.015 0.12 0.21 1 -0.37 31 32
negative regulation of mast cell degranulation -0.023 0.18 0.22 9 -0.37 62 71
BTK -0.1 0.31 0.24 1 -0.67 73 74
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.025 0.15 -10000 0 -0.33 55 55
GAB2/PI3K/SHP2 -0.003 0.052 -10000 0 -0.2 15 15
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.018 0.14 -10000 0 -0.36 41 41
RAF1 0.005 0.14 -10000 0 -0.99 7 7
Fc epsilon R1/FcgammaRIIB/SHIP 0.02 0.15 -10000 0 -0.3 59 59
FCER1G 0.002 0.11 -10000 0 -0.42 23 23
FCER1A 0.026 0.029 -10000 0 -0.43 1 1
Antigen/IgE/Fc epsilon R1/Fyn 0.044 0.074 -10000 0 -0.2 24 24
MAPK3 0.011 0.13 -10000 0 -0.91 7 7
MAPK1 0.009 0.13 -10000 0 -0.91 7 7
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.056 0.28 -10000 0 -0.72 45 45
DUSP1 0.033 0.01 -10000 0 -10000 0 0
NF-kappa-B/RelA -0.008 0.088 0.16 9 -0.18 55 64
actin cytoskeleton reorganization -0.005 0.16 -10000 0 -0.5 22 22
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.031 0.22 0.36 1 -0.48 60 61
FER -0.016 0.13 0.2 3 -0.36 34 37
RELA 0.034 0.007 -10000 0 -10000 0 0
ITK -0.096 0.18 -10000 0 -0.37 106 106
SOS1 0.035 0.003 -10000 0 -10000 0 0
PLCG1 -0.07 0.27 0.3 11 -0.6 65 76
cytokine secretion -0.012 0.057 -10000 0 -0.14 39 39
SPHK1 -0.02 0.13 0.2 2 -0.38 35 37
PTK2 -0.006 0.16 -10000 0 -0.52 22 22
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.055 0.22 0.26 1 -0.51 62 63
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.039 0.22 0.31 21 -0.48 59 80
MAP2K2 0.004 0.14 -10000 0 -0.93 7 7
MAP2K1 0.005 0.14 -10000 0 -0.93 7 7
MAP2K7 0.035 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.006 0.12 0.23 6 -0.3 40 46
MAP2K4 -0.012 0.23 -10000 0 -0.87 24 24
Fc epsilon R1/FcgammaRIIB 0.042 0.1 -10000 0 -0.27 32 32
mol:Choline 0.024 0.11 0.31 36 -0.2 20 56
SHC/Grb2/SOS1 0.029 0.14 -10000 0 -0.36 32 32
FYN 0.031 0.012 -10000 0 -10000 0 0
DOK1 0.035 0.002 -10000 0 -10000 0 0
PXN -0.005 0.15 -10000 0 -0.48 22 22
HCLS1 -0.044 0.18 0.2 3 -0.43 54 57
PRKCB -0.049 0.18 0.27 18 -0.38 66 84
FCGR2B 0.013 0.09 -10000 0 -0.42 15 15
IGHE 0 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.023 0.18 0.22 9 -0.38 62 71
LCP2 0.015 0.09 -10000 0 -0.42 15 15
PLA2G4A -0.017 0.13 0.2 2 -0.36 35 37
RASA1 0.032 0.025 -10000 0 -0.42 1 1
mol:Phosphatidic acid 0.024 0.11 0.31 36 -0.2 20 56
IKK complex -0.014 0.11 0.24 18 -0.21 53 71
WIPF1 0.029 0.053 -10000 0 -0.42 5 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.069 0.23 2 -0.27 3 5
adherens junction organization -0.041 0.12 -10000 0 -0.23 91 91
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.073 0.25 1 -0.21 2 3
FMN1 -0.04 0.12 -10000 0 -0.23 88 88
mol:IP3 -0.011 0.066 0.22 1 -0.2 4 5
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.035 0.12 -10000 0 -0.23 88 88
CTNNB1 0.037 0.007 -10000 0 -10000 0 0
AKT1 -0.007 0.084 0.2 2 -0.24 5 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.059 0.18 -10000 0 -0.34 95 95
CTNND1 0.035 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.03 0.1 -10000 0 -0.22 75 75
VASP -0.036 0.11 -10000 0 -0.22 88 88
ZYX -0.032 0.1 -10000 0 -0.22 76 76
JUB -0.036 0.11 -10000 0 -0.22 88 88
EGFR(dimer) -0.025 0.12 -10000 0 -0.22 83 83
E-cadherin/beta catenin-gamma catenin -0.013 0.13 -10000 0 -0.23 92 92
mol:PI-3-4-5-P3 0.009 0.099 0.23 1 -0.25 5 6
PIK3CA 0.035 0.007 -10000 0 -10000 0 0
PI3K 0.009 0.1 0.23 1 -0.25 5 6
FYN -0.016 0.076 0.22 2 -0.24 19 21
mol:Ca2+ -0.01 0.065 0.22 1 -0.2 4 5
JUP 0.036 0.01 -10000 0 -10000 0 0
PIK3R1 0.035 0.008 -10000 0 -10000 0 0
mol:DAG -0.011 0.066 0.22 1 -0.2 4 5
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
RhoA/GDP 0.009 0.085 0.26 4 -0.2 3 7
establishment of polarity of embryonic epithelium -0.035 0.11 -10000 0 -0.22 88 88
SRC 0.033 0.01 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
EGFR 0.027 0.035 -10000 0 -0.42 2 2
CASR -0.016 0.062 0.19 4 -0.19 3 7
RhoA/GTP 0.004 0.072 0.22 2 -0.18 4 6
AKT2 -0.009 0.085 0.2 2 -0.23 5 7
actin cable formation -0.038 0.12 0.19 6 -0.22 85 91
apoptosis 0.007 0.084 0.25 6 -0.22 4 10
CTNNA1 0.034 0.009 -10000 0 -10000 0 0
mol:GDP -0.013 0.067 0.2 4 -0.21 4 8
PIP5K1A -0.031 0.1 -10000 0 -0.22 75 75
PLCG1 -0.011 0.067 0.22 1 -0.21 4 5
Rac1/GTP -0.015 0.12 -10000 0 -0.21 82 82
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
CDC42/GTP -0.033 0.12 -10000 0 -0.24 57 57
PLCG1 -0.04 0.11 -10000 0 -0.22 83 83
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
G12/G13 0.045 0.018 -10000 0 -10000 0 0
cell migration -0.033 0.12 -10000 0 -0.23 57 57
S1PR5 0.034 0.008 -10000 0 -10000 0 0
S1PR4 -0.11 0.21 -10000 0 -0.42 118 118
MAPK3 -0.045 0.11 -10000 0 -0.22 89 89
MAPK1 -0.042 0.11 -10000 0 -0.22 89 89
S1P/S1P5/Gi 0.022 0.037 -10000 0 -0.19 3 3
GNAI1 0.031 0.012 -10000 0 -10000 0 0
CDC42/GDP 0.026 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.04 0.019 -10000 0 -10000 0 0
RHOA -0.028 0.12 0.22 27 -0.21 97 124
S1P/S1P4/Gi -0.047 0.12 -10000 0 -0.23 91 91
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
S1P/S1P4/G12/G13 -0.022 0.13 -10000 0 -0.22 98 98
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.083 0.19 0.23 1 -0.42 66 67
BAG4 0.034 0.008 -10000 0 -10000 0 0
BAD -0.018 0.069 0.15 7 -0.15 44 51
NFKBIA 0.035 0.004 -10000 0 -10000 0 0
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BAX -0.019 0.068 0.15 6 -0.14 50 56
EnzymeConsortium:3.1.4.12 -0.016 0.048 0.078 5 -0.097 65 70
IKBKB -0.077 0.18 0.34 1 -0.4 63 64
MAP2K2 -0.014 0.073 0.21 7 -0.2 10 17
MAP2K1 -0.014 0.073 0.21 7 -0.2 11 18
SMPD1 -0.014 0.052 0.093 2 -0.14 21 23
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.07 0.2 0.33 6 -0.42 62 68
MAP2K4 -0.014 0.064 0.16 3 -0.17 15 18
protein ubiquitination -0.079 0.19 0.24 1 -0.41 64 65
EnzymeConsortium:2.7.1.37 -0.014 0.078 0.22 6 -0.21 13 19
response to UV 0 0.001 0.003 8 -0.002 13 21
RAF1 -0.016 0.07 0.18 4 -0.18 16 20
CRADD 0.035 0.006 -10000 0 -10000 0 0
mol:ceramide -0.02 0.07 0.13 5 -0.14 63 68
I-kappa-B-alpha/RELA/p50/ubiquitin 0.045 0.011 -10000 0 -10000 0 0
MADD 0.035 0.006 -10000 0 -10000 0 0
MAP3K1 -0.018 0.069 0.15 5 -0.15 48 53
TRADD 0.034 0.007 -10000 0 -10000 0 0
RELA/p50 0.034 0.007 -10000 0 -10000 0 0
MAPK3 -0.01 0.074 0.21 7 -0.2 9 16
MAPK1 -0.011 0.075 0.21 7 -0.21 11 18
p50/RELA/I-kappa-B-alpha 0.05 0.012 -10000 0 -10000 0 0
FADD -0.08 0.19 0.26 5 -0.43 61 66
KSR1 -0.017 0.07 0.16 6 -0.15 48 54
MAPK8 -0.013 0.059 0.17 2 -0.17 9 11
TRAF2 0.033 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.003 4 -0.002 3 7
CHUK -0.078 0.18 -10000 0 -0.4 65 65
TNF R/SODD 0.048 0.015 -10000 0 -10000 0 0
TNF -0.054 0.18 -10000 0 -0.42 69 69
CYCS -0.013 0.069 0.14 9 -0.17 21 30
IKBKG -0.079 0.18 -10000 0 -0.4 65 65
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.093 0.2 -10000 0 -0.44 66 66
RELA 0.034 0.007 -10000 0 -10000 0 0
RIPK1 0.031 0.012 -10000 0 -10000 0 0
AIFM1 -0.02 0.067 0.14 7 -0.14 50 57
TNF/TNF R/SODD 0.002 0.12 -10000 0 -0.25 66 66
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
response to heat 0 0.001 0.003 4 -0.002 3 7
CASP8 0.002 0.13 -10000 0 -0.66 11 11
NSMAF -0.071 0.19 0.23 9 -0.42 61 70
response to hydrogen peroxide 0 0.001 0.003 8 -0.002 13 21
BCL2 0.035 0.005 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.024 0.13 0.23 1 -0.2 118 119
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.033 0.01 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.029 0.14 0.29 2 -0.33 30 32
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.021 0.066 -10000 0 -0.27 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.086 -10000 0 -0.22 25 25
CaM/Ca2+ -0.019 0.13 -10000 0 -0.2 103 103
RAP1A 0.034 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.043 0.12 0.28 1 -0.21 105 106
AKT1 -0.041 0.11 0.29 4 -0.26 12 16
MAP2K1 -0.049 0.1 0.24 2 -0.26 13 15
MAP3K11 -0.046 0.11 0.3 2 -0.2 88 90
IFNGR1 0.014 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.12 -10000 0 -0.37 26 26
Rap1/GTP -0.034 0.086 -10000 0 -0.22 11 11
CRKL/C3G 0.045 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.013 0.14 -10000 0 -0.21 117 117
CEBPB -0.001 0.11 0.41 2 -0.35 2 4
STAT3 0.035 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.059 0.29 -10000 0 -1.2 20 20
STAT1 -0.051 0.12 0.31 2 -0.21 88 90
CALM1 0.034 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.12 0.21 -10000 0 -0.42 120 120
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.036 0.12 0.34 1 -0.21 78 79
CEBPB/PTGES2/Cbp/p300 0.01 0.084 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.13 -10000 0 -0.2 118 118
MAPK3 -0.018 0.11 0.4 1 -0.69 2 3
STAT1 (dimer) -0.023 0.12 -10000 0 -0.31 23 23
MAPK1 -0.026 0.13 0.4 1 -0.72 5 6
JAK2 0.007 0.06 -10000 0 -0.43 5 5
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
JAK1 0.014 0.033 -10000 0 -10000 0 0
CAMK2D 0.035 0.005 -10000 0 -10000 0 0
DAPK1 0.009 0.081 0.36 2 -10000 0 2
SMAD7 -0.004 0.054 0.17 5 -0.15 8 13
CBL/CRKL/C3G -0.019 0.11 0.31 2 -0.24 13 15
PI3K -0.018 0.13 -10000 0 -0.2 86 86
IFNG -0.12 0.21 -10000 0 -0.42 120 120
apoptosis 0.006 0.075 0.3 2 -0.32 1 3
CAMK2G 0.032 0.01 -10000 0 -10000 0 0
STAT3 (dimer) 0.035 0.005 -10000 0 -10000 0 0
CAMK2A 0.024 0.048 -10000 0 -0.42 4 4
CAMK2B 0.021 0.063 -10000 0 -0.42 7 7
FRAP1 -0.051 0.093 0.27 4 -0.24 12 16
PRKCD -0.039 0.11 0.29 4 -0.25 13 17
RAP1B 0.034 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.023 0.086 -10000 0 -0.22 25 25
PTPN2 0.034 0.007 -10000 0 -10000 0 0
EP300 0.032 0.011 -10000 0 -10000 0 0
IRF1 -0.07 0.17 0.26 2 -0.44 46 48
STAT1 (dimer)/PIASy -0.035 0.12 0.35 2 -0.28 20 22
SOCS1 -0.038 0.31 -10000 0 -1.3 20 20
mol:GDP -0.021 0.11 0.29 2 -0.22 17 19
CASP1 -0.009 0.071 0.17 5 -0.24 18 23
PTGES2 0.033 0.009 -10000 0 -10000 0 0
IRF9 0.019 0.052 0.17 6 -10000 0 6
mol:PI-3-4-5-P3 -0.028 0.12 -10000 0 -0.2 86 86
RAP1/GDP -0.019 0.099 -10000 0 -0.22 11 11
CBL -0.042 0.11 0.3 2 -0.2 87 89
MAP3K1 -0.046 0.11 0.3 2 -0.2 86 88
PIAS1 0.035 0.005 -10000 0 -10000 0 0
PIAS4 0.035 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.023 0.086 -10000 0 -0.22 25 25
PTPN11 -0.051 0.11 0.3 1 -0.21 105 106
CREBBP 0.034 0.007 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.017 0.11 -10000 0 -0.23 56 56
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.092 0.24 1 -0.28 11 12
AP1 0.006 0.089 -10000 0 -0.2 53 53
mol:PIP3 -0.016 0.074 -10000 0 -0.19 50 50
AKT1 0.013 0.089 0.25 6 -0.28 8 14
PTK2B -0.028 0.11 0.18 1 -0.24 51 52
RHOA 0.014 0.065 0.19 7 -0.29 7 14
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.064 0.22 6 -0.25 11 17
MAGI3 0.034 0.007 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
apoptosis -0.019 0.09 -10000 0 -0.23 54 54
HRAS/GDP 0.025 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.026 0.097 0.19 5 -0.26 30 35
NF kappa B1 p50/RelA -0.008 0.097 -10000 0 -0.27 26 26
endothelial cell migration -0.019 0.097 -10000 0 -0.25 51 51
ADCY4 -0.036 0.13 -10000 0 -0.32 57 57
ADCY5 -0.072 0.16 -10000 0 -0.39 65 65
ADCY6 -0.035 0.13 -10000 0 -0.31 59 59
ADCY7 -0.035 0.13 -10000 0 -0.32 57 57
ADCY1 -0.062 0.15 -10000 0 -0.36 58 58
ADCY2 -0.044 0.13 -10000 0 -0.32 59 59
ADCY3 -0.036 0.13 -10000 0 -0.31 58 58
ADCY8 -0.035 0.12 -10000 0 -0.31 53 53
ADCY9 -0.036 0.13 -10000 0 -0.31 59 59
GSK3B -0.026 0.1 0.19 4 -0.27 33 37
arachidonic acid secretion -0.037 0.13 -10000 0 -0.3 62 62
GNG2 0.027 0.057 -10000 0 -0.42 6 6
TRIP6 0.024 0.02 -10000 0 -10000 0 0
GNAO1 -0.025 0.091 -10000 0 -0.24 52 52
HRAS 0.034 0.006 -10000 0 -10000 0 0
NFKBIA -0.015 0.086 0.23 1 -0.3 13 14
GAB1 0.035 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.018 0.26 -10000 0 -0.88 29 29
JUN 0.031 0.011 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.045 0.029 -10000 0 -0.24 3 3
TIAM1 -0.043 0.3 -10000 0 -1.1 29 29
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.002 0.059 0.2 4 -0.27 9 13
PLCB3 0.023 0.032 0.19 6 -0.22 3 9
FOS 0.033 0.008 -10000 0 -10000 0 0
positive regulation of mitosis -0.037 0.13 -10000 0 -0.3 62 62
LPA/LPA1-2-3 0.009 0.1 -10000 0 -0.22 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.034 0.007 -10000 0 -10000 0 0
stress fiber formation -0.016 0.11 0.2 1 -0.28 34 35
GNAZ -0.02 0.091 -10000 0 -0.24 51 51
EGFR/PI3K-beta/Gab1 -0.006 0.082 -10000 0 -0.2 50 50
positive regulation of dendritic cell cytokine production 0.008 0.1 -10000 0 -0.22 54 54
LPA/LPA2/MAGI-3 0.044 0.03 -10000 0 -0.18 5 5
ARHGEF1 0.013 0.1 0.21 39 -0.2 47 86
GNAI2 -0.018 0.093 -10000 0 -0.24 53 53
GNAI3 -0.016 0.091 -10000 0 -0.24 50 50
GNAI1 -0.019 0.091 -10000 0 -0.24 51 51
LPA/LPA3 0.018 0.018 -10000 0 -0.11 2 2
LPA/LPA2 0.024 0.03 -10000 0 -0.22 5 5
LPA/LPA1 -0.02 0.11 -10000 0 -0.29 55 55
HB-EGF/EGFR -0.01 0.098 -10000 0 -0.25 50 50
HBEGF -0.024 0.1 -10000 0 -0.3 47 47
mol:DAG -0.002 0.059 0.2 4 -0.27 9 13
cAMP biosynthetic process -0.041 0.13 0.22 4 -0.31 62 66
NFKB1 0.034 0.006 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
GNB1 0.034 0.007 -10000 0 -10000 0 0
LYN -0.018 0.12 0.24 2 -0.38 22 24
GNAQ 0.016 0.027 -10000 0 -0.25 3 3
LPAR2 0.031 0.041 -10000 0 -0.42 3 3
LPAR3 0.025 0.015 -10000 0 -10000 0 0
LPAR1 -0.031 0.16 -10000 0 -0.4 55 55
IL8 -0.032 0.13 0.33 1 -0.35 32 33
PTK2 -0.006 0.076 0.19 6 -0.21 40 46
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
CASP3 -0.019 0.09 -10000 0 -0.23 54 54
EGFR 0.027 0.035 -10000 0 -0.42 2 2
PLCG1 0 0.058 0.16 4 -0.29 7 11
PLD2 -0.012 0.086 0.19 6 -0.21 53 59
G12/G13 0.019 0.097 -10000 0 -0.22 48 48
PI3K-beta -0.005 0.079 -10000 0 -0.3 10 10
cell migration 0.004 0.09 0.2 1 -0.26 28 29
SLC9A3R2 0.035 0.004 -10000 0 -10000 0 0
PXN -0.016 0.11 0.2 1 -0.29 34 35
HRAS/GTP -0.039 0.13 -10000 0 -0.31 60 60
RAC1 0.031 0.012 -10000 0 -10000 0 0
MMP9 -0.036 0.16 -10000 0 -0.42 55 55
PRKCE 0.035 0.004 -10000 0 -10000 0 0
PRKCD -0.004 0.065 0.2 8 -0.29 6 14
Gi(beta/gamma) -0.028 0.13 -10000 0 -0.3 59 59
mol:LPA 0.002 0.012 -10000 0 -0.16 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.016 0.11 -10000 0 -0.26 22 22
MAPKKK cascade -0.037 0.13 -10000 0 -0.3 62 62
contractile ring contraction involved in cytokinesis 0.014 0.065 0.19 7 -0.28 7 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.022 0.095 -10000 0 -0.24 56 56
GNA15 0.01 0.055 -10000 0 -0.26 13 13
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
MAPT -0.027 0.1 0.19 5 -0.27 30 35
GNA11 0.017 0.025 -10000 0 -0.23 3 3
Rac1/GTP -0.02 0.27 -10000 0 -0.94 29 29
MMP2 -0.019 0.098 -10000 0 -0.25 51 51
Syndecan-4-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
PTK2 0.011 0.11 -10000 0 -0.51 13 13
Syndecan-4/Syndesmos -0.037 0.22 -10000 0 -0.5 56 56
positive regulation of JNK cascade -0.039 0.22 -10000 0 -0.49 58 58
Syndecan-4/ADAM12 -0.042 0.21 -10000 0 -0.49 56 56
CCL5 -0.095 0.2 -10000 0 -0.42 105 105
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DNM2 0.035 0.003 -10000 0 -10000 0 0
ITGA5 0.034 0.006 -10000 0 -10000 0 0
SDCBP 0.032 0.01 -10000 0 -10000 0 0
PLG 0.009 0.02 -10000 0 -10000 0 0
ADAM12 0.029 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.035 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.027 0.016 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.078 0.2 -10000 0 -0.5 55 55
Syndecan-4/CXCL12/CXCR4 -0.041 0.24 -10000 0 -0.52 58 58
Syndecan-4/Laminin alpha3 -0.043 0.22 -10000 0 -0.5 55 55
MDK 0.029 0.042 -10000 0 -0.42 3 3
Syndecan-4/FZD7 -0.037 0.22 -10000 0 -0.5 56 56
Syndecan-4/Midkine -0.04 0.21 -10000 0 -0.5 56 56
FZD7 0.034 0.024 -10000 0 -0.42 1 1
Syndecan-4/FGFR1/FGF -0.028 0.2 -10000 0 -0.47 54 54
THBS1 0.03 0.012 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.038 0.21 -10000 0 -0.48 58 58
positive regulation of MAPKKK cascade -0.039 0.22 -10000 0 -0.49 58 58
Syndecan-4/TACI -0.13 0.23 -10000 0 -0.58 58 58
CXCR4 0.001 0.12 -10000 0 -0.42 28 28
cell adhesion 0.014 0.054 0.2 7 -0.24 11 18
Syndecan-4/Dynamin -0.037 0.21 -10000 0 -0.49 56 56
Syndecan-4/TSP1 -0.043 0.21 -10000 0 -0.49 56 56
Syndecan-4/GIPC -0.036 0.21 -10000 0 -0.49 56 56
Syndecan-4/RANTES -0.092 0.25 -10000 0 -0.6 55 55
ITGB1 0.032 0.011 -10000 0 -10000 0 0
LAMA1 0.006 0.013 -10000 0 -10000 0 0
LAMA3 0.02 0.081 -10000 0 -0.42 12 12
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA 0.023 0.15 0.84 11 -0.39 1 12
Syndecan-4/alpha-Actinin -0.038 0.22 -10000 0 -0.49 56 56
TFPI 0.034 0.024 -10000 0 -0.42 1 1
F2 0.013 0.027 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.046 0.018 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.069 0.2 -10000 0 -0.49 55 55
ACTN1 0.033 0.024 -10000 0 -0.42 1 1
TNC 0.02 0.074 -10000 0 -0.42 10 10
Syndecan-4/CXCL12 -0.043 0.22 -10000 0 -0.5 56 56
FGF6 0.017 0.003 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
CXCL12 0.018 0.077 -10000 0 -0.42 11 11
TNFRSF13B -0.17 0.22 -10000 0 -0.42 164 164
FGF2 0.03 0.035 -10000 0 -0.42 2 2
FGFR1 0.031 0.012 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.063 0.2 -10000 0 -0.49 56 56
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.016 0.076 -10000 0 -0.4 11 11
cell migration -0.013 0.012 -10000 0 -10000 0 0
PRKCD 0.029 0.022 -10000 0 -10000 0 0
vasculogenesis -0.04 0.2 -10000 0 -0.47 56 56
SDC4 -0.057 0.21 -10000 0 -0.52 55 55
Syndecan-4/Tenascin C -0.041 0.22 -10000 0 -0.5 58 58
Syndecan-4/PI-4-5-P2/PKC alpha -0.022 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.037 0.21 -10000 0 -0.5 52 52
MMP9 -0.035 0.16 -10000 0 -0.42 55 55
Rac1/GTP 0.014 0.055 0.2 7 -0.25 11 18
cytoskeleton organization -0.035 0.21 -10000 0 -0.48 56 56
GIPC1 0.035 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.038 0.22 -10000 0 -0.5 56 56
HIF-1-alpha transcription factor network

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
PKM2 0.005 0.28 0.42 2 -0.61 39 41
HDAC7 0.036 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.037 0.34 -10000 0 -0.67 38 38
SMAD4 0.036 0.005 -10000 0 -10000 0 0
ID2 0.029 0.3 -10000 0 -0.62 37 37
AP1 0.045 0.025 -10000 0 -10000 0 0
ABCG2 0.015 0.32 -10000 0 -0.68 38 38
HIF1A 0.029 0.077 -10000 0 -0.18 4 4
TFF3 -0.016 0.33 -10000 0 -0.64 51 51
GATA2 0.035 0.011 -10000 0 -10000 0 0
AKT1 0.016 0.099 -10000 0 -0.22 18 18
response to hypoxia -0.004 0.082 -10000 0 -0.16 51 51
MCL1 0.02 0.28 -10000 0 -0.62 34 34
NDRG1 0.03 0.29 -10000 0 -0.64 32 32
SERPINE1 0.018 0.28 -10000 0 -0.62 36 36
FECH 0.029 0.29 -10000 0 -0.64 35 35
FURIN 0.027 0.29 -10000 0 -0.62 36 36
NCOA2 0.033 0.011 -10000 0 -10000 0 0
EP300 0.014 0.14 -10000 0 -0.31 39 39
HMOX1 0.028 0.29 -10000 0 -0.66 32 32
BHLHE40 0.03 0.3 -10000 0 -0.66 32 32
BHLHE41 0.024 0.3 -10000 0 -0.64 37 37
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.11 0.11 -10000 0 -10000 0 0
ENG 0.055 0.088 0.33 3 -10000 0 3
JUN 0.032 0.013 -10000 0 -10000 0 0
RORA 0.028 0.29 -10000 0 -0.64 34 34
ABCB1 -0.039 0.32 -10000 0 -1 30 30
TFRC 0.03 0.29 -10000 0 -0.62 37 37
CXCR4 0.015 0.32 -10000 0 -0.74 35 35
TF -0.03 0.32 -10000 0 -0.67 44 44
CITED2 0.027 0.29 -10000 0 -0.62 37 37
HIF1A/ARNT 0.059 0.37 -10000 0 -0.77 28 28
LDHA 0.042 0.12 -10000 0 -0.83 4 4
ETS1 0.026 0.29 -10000 0 -0.66 32 32
PGK1 0.03 0.3 -10000 0 -0.65 33 33
NOS2 0.019 0.29 -10000 0 -0.62 37 37
ITGB2 0.003 0.33 -10000 0 -0.7 42 42
ALDOA 0.028 0.3 -10000 0 -0.63 36 36
Cbp/p300/CITED2 0.004 0.36 -10000 0 -0.75 42 42
FOS 0.034 0.011 -10000 0 -10000 0 0
HK2 0.03 0.3 -10000 0 -0.63 36 36
SP1 0.031 0.042 -10000 0 -0.12 20 20
GCK -0.083 0.46 -10000 0 -1.3 43 43
HK1 0.025 0.29 -10000 0 -0.64 35 35
NPM1 0.028 0.29 -10000 0 -0.64 34 34
EGLN1 0.022 0.28 -10000 0 -0.6 37 37
CREB1 0.042 0.009 -10000 0 -10000 0 0
PGM1 0.026 0.29 -10000 0 -0.65 34 34
SMAD3 0.036 0.005 -10000 0 -10000 0 0
EDN1 0.021 0.21 -10000 0 -0.6 19 19
IGFBP1 0.014 0.28 -10000 0 -0.63 34 34
VEGFA 0.022 0.27 -10000 0 -0.59 33 33
HIF1A/JAB1 0.048 0.058 -10000 0 -0.14 1 1
CP -0.047 0.35 -10000 0 -0.68 53 53
CXCL12 0.019 0.3 -10000 0 -0.67 36 36
COPS5 0.033 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4 0.052 0.01 -10000 0 -10000 0 0
BNIP3 0.024 0.29 -10000 0 -0.64 35 35
EGLN3 0.027 0.3 -10000 0 -0.63 36 36
CA9 -0.005 0.28 -10000 0 -0.65 33 33
TERT 0.021 0.29 -10000 0 -0.65 32 32
ENO1 0.025 0.29 -10000 0 -0.63 36 36
PFKL 0.027 0.29 -10000 0 -0.64 35 35
NCOA1 0.035 0.006 -10000 0 -10000 0 0
ADM -0.005 0.28 -10000 0 -0.66 32 32
ARNT 0.032 0.068 -10000 0 -0.14 3 3
HNF4A 0.009 0.045 -10000 0 -10000 0 0
ADFP 0.005 0.28 0.42 2 -0.61 39 41
SLC2A1 0.029 0.28 -10000 0 -0.58 38 38
LEP -0.004 0.27 -10000 0 -0.66 30 30
HIF1A/ARNT/Cbp/p300 0.029 0.34 -10000 0 -0.69 38 38
EPO 0.051 0.2 -10000 0 -0.52 7 7
CREBBP 0.012 0.14 -10000 0 -0.3 43 43
HIF1A/ARNT/Cbp/p300/HDAC7 0.046 0.34 -10000 0 -0.69 34 34
PFKFB3 0.022 0.29 -10000 0 -0.63 36 36
NT5E 0.005 0.28 -10000 0 -0.63 36 36
Atypical NF-kappaB 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
BCL3/RelA 0.049 0.021 -10000 0 -0.3 1 1
FBXW11 0.033 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.038 0.011 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.05 0.16 0.21 1 -0.35 58 59
NFKBIA -0.068 0.16 -10000 0 -0.29 112 112
MAPK14 0.032 0.011 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.036 0.014 -10000 0 -10000 0 0
ARRB2 0.017 0.008 -10000 0 -10000 0 0
REL 0.035 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.036 0.024 -10000 0 -0.25 2 2
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.036 0.013 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.027 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
NFKB1 0.018 0.005 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.067 0.14 -10000 0 -0.26 114 114
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.047 0.16 0.2 1 -0.35 58 59
SRC 0.033 0.01 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.14 -10000 0 -0.26 112 112
IKBKB 0.034 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.008 -10000 0 -10000 0 0
SYK -0.012 0.13 -10000 0 -0.42 36 36
I kappa B alpha/PIK3R1 -0.056 0.16 0.21 1 -0.28 112 113
cell death -0.045 0.15 0.2 1 -0.33 58 59
NF kappa B1 p105/c-Rel 0.038 0.011 -10000 0 -10000 0 0
LCK -0.14 0.22 -10000 0 -0.42 138 138
BCL3 0.033 0.034 -10000 0 -0.42 2 2
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.008 0.1 -10000 0 -0.21 64 64
RGS9BP 0.035 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.017 0.004 -10000 0 -10000 0 0
mol:Na + 0.023 0.012 -10000 0 -10000 0 0
mol:ADP -0.015 0.006 -10000 0 -10000 0 0
GNAT2 0.032 0.008 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.056 0.15 -10000 0 -0.25 138 138
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.036 0.013 -10000 0 -10000 0 0
GRK7 0.027 0.01 -10000 0 -10000 0 0
CNGB3 0.021 0.011 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.034 0.17 12 -10000 0 12
Cone PDE6 -0.038 0.14 -10000 0 -0.22 136 136
Cone Metarhodopsin II 0.027 0.01 -10000 0 -10000 0 0
Na + (4 Units) 0.027 0.018 -10000 0 -10000 0 0
GNAT2/GDP -0.035 0.14 -10000 0 -0.21 133 133
GNB5 0.033 0.024 -10000 0 -0.42 1 1
mol:GMP (4 units) 0 0.037 0.17 14 -10000 0 14
Cone Transducin 0.009 0.11 -10000 0 -0.22 64 64
SLC24A2 0.015 0.006 -10000 0 -10000 0 0
GNB3/GNGT2 -0.016 0.13 -10000 0 -0.3 68 68
GNB3 0.03 0.041 -10000 0 -0.42 3 3
GNAT2/GTP 0.024 0.006 -10000 0 -10000 0 0
CNGA3 0.018 0.001 -10000 0 -10000 0 0
ARR3 0.021 0.007 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.024 0.012 -10000 0 -10000 0 0
mol:Pi -0.056 0.15 -10000 0 -0.25 138 138
Cone CNG Channel 0.043 0.026 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.015 0.006 -10000 0 -10000 0 0
RGS9 -0.14 0.22 -10000 0 -0.42 144 144
PDE6C 0.016 0.005 -10000 0 -10000 0 0
GNGT2 -0.049 0.18 -10000 0 -0.42 67 67
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.023 0.01 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.031 0.047 -10000 0 -0.26 2 2
fibroblast growth factor receptor signaling pathway 0.031 0.047 -10000 0 -0.26 2 2
LAMA1 0.006 0.013 -10000 0 -10000 0 0
PRNP 0.032 0.025 -10000 0 -0.42 1 1
GPC1/SLIT2 0.021 0.046 -10000 0 -0.29 4 4
SMAD2 0.01 0.019 0.19 1 -10000 0 1
GPC1/PrPc/Cu2+ 0.025 0.031 -10000 0 -0.25 1 1
GPC1/Laminin alpha1 -0.008 0.022 -10000 0 -10000 0 0
TDGF1 -0.052 0.17 -10000 0 -0.42 63 63
CRIPTO/GPC1 -0.033 0.12 -10000 0 -0.3 63 63
APP/GPC1 0.025 0.043 -10000 0 -0.3 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.036 0.096 -10000 0 -0.25 60 60
FLT1 0.034 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.038 0.04 -10000 0 -10000 0 0
SERPINC1 0.027 0.013 -10000 0 -10000 0 0
FYN -0.035 0.094 -10000 0 -0.25 58 58
FGR -0.059 0.12 -10000 0 -0.26 89 89
positive regulation of MAPKKK cascade -0.22 0.24 0.19 1 -0.43 163 164
SLIT2 0.026 0.048 -10000 0 -0.42 4 4
GPC1/NRG 0.023 0.042 -10000 0 -0.3 3 3
NRG1 0.026 0.042 -10000 0 -0.42 3 3
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.034 0.041 -10000 0 -10000 0 0
LYN -0.044 0.11 -10000 0 -0.26 70 70
mol:Spermine 0.007 0.005 -10000 0 -10000 0 0
cell growth 0.031 0.047 -10000 0 -0.26 2 2
BMP signaling pathway -0.022 0.017 -10000 0 -10000 0 0
SRC -0.035 0.096 -10000 0 -0.25 60 60
TGFBR1 0.033 0.009 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.005 0.097 -10000 0 -0.42 18 18
GPC1 0.022 0.017 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.033 0.009 -10000 0 -10000 0 0
VEGFA 0.03 0.013 -10000 0 -10000 0 0
BLK -0.18 0.16 -10000 0 -0.29 228 228
HCK -0.053 0.12 -10000 0 -0.26 81 81
FGF2 0.03 0.035 -10000 0 -0.42 2 2
FGFR1 0.031 0.012 -10000 0 -10000 0 0
VEGFR1 homodimer 0.034 0.007 -10000 0 -10000 0 0
TGFBR2 0.035 0.005 -10000 0 -10000 0 0
cell death 0.025 0.043 -10000 0 -0.3 3 3
ATIII/GPC1 0.023 0.031 -10000 0 -10000 0 0
PLA2G2A/GPC1 0.004 0.075 -10000 0 -0.3 18 18
LCK -0.13 0.16 -10000 0 -0.28 169 169
neuron differentiation 0.023 0.042 -10000 0 -0.3 3 3
PrPc/Cu2+ 0.024 0.018 -10000 0 -0.29 1 1
APP 0.031 0.041 -10000 0 -0.42 3 3
TGFBR2 (dimer) 0.035 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.014 0.099 0.2 2 -0.22 49 51
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.1 0.34 3 -0.33 8 11
alphaV/beta3 Integrin/Osteopontin/Src 0.021 0.1 -10000 0 -0.29 37 37
AP1 0.034 0.1 -10000 0 -0.34 8 8
ILK -0.001 0.098 -10000 0 -0.24 48 48
bone resorption -0.008 0.12 -10000 0 -0.34 15 15
PTK2B 0.028 0.048 -10000 0 -0.42 4 4
PYK2/p130Cas 0.017 0.14 -10000 0 -0.23 79 79
ITGAV 0.038 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.049 0.021 -10000 0 -0.3 1 1
alphaV/beta3 Integrin/Osteopontin 0.029 0.12 -10000 0 -0.27 49 49
MAP3K1 -0.004 0.099 0.2 4 -0.24 49 53
JUN 0.032 0.011 -10000 0 -10000 0 0
MAPK3 -0.01 0.091 0.2 2 -0.23 48 50
MAPK1 -0.01 0.088 0.2 2 -0.22 48 50
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 -0.012 0.088 0.2 4 -0.22 48 52
ITGB3 0.012 0.098 -10000 0 -0.42 18 18
NFKBIA -0.011 0.087 0.2 2 -0.29 16 18
FOS 0.034 0.008 -10000 0 -10000 0 0
CD44 0.033 0.024 -10000 0 -0.42 1 1
CHUK 0.032 0.01 -10000 0 -10000 0 0
PLAU 0.002 0.11 -10000 0 -1.1 1 1
NF kappa B1 p50/RelA 0.044 0.1 -10000 0 -0.31 7 7
BCAR1 0.034 0.007 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.034 0.077 -10000 0 -0.29 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.028 0.12 0.2 4 -0.25 77 81
VAV3 -0.036 0.11 0.19 3 -0.24 76 79
MAP3K14 -0.002 0.099 0.2 2 -0.24 48 50
ROCK2 0.035 0.004 -10000 0 -10000 0 0
SPP1 -0.008 0.14 -10000 0 -0.41 37 37
RAC1 0.031 0.012 -10000 0 -10000 0 0
Rac1/GTP -0.018 0.1 0.19 1 -0.22 67 68
MMP2 0.001 0.085 0.32 2 -0.32 9 11
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.009 0.13 -10000 0 -0.42 35 35
positive regulation of NF-kappaB transcription factor activity 0.011 0.1 -10000 0 -0.3 35 35
MAP2K4 0.004 0.1 -10000 0 -0.35 19 19
IKBKB 0.034 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.058 -10000 0 -0.42 6 6
TNFRSF10A -0.016 0.14 -10000 0 -0.42 40 40
SMPD1 -0.002 0.066 -10000 0 -0.19 38 38
IKBKG 0.035 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.029 0.026 -10000 0 -0.42 1 1
TRAIL/TRAILR2 0.011 0.11 -10000 0 -0.31 38 38
TRAIL/TRAILR3 -0.001 0.13 -10000 0 -0.31 50 50
TRAIL/TRAILR1 -0.016 0.15 -10000 0 -0.35 59 59
TRAIL/TRAILR4 0.011 0.1 -10000 0 -0.3 35 35
TRAIL/TRAILR1/DAP3/GTP 0.01 0.12 -10000 0 -0.27 50 50
IKK complex 0.014 0.088 -10000 0 -0.34 9 9
RIPK1 0.031 0.012 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.008 -10000 0 -10000 0 0
MAPK3 -0.011 0.092 -10000 0 -0.3 35 35
MAP3K1 -0.007 0.12 -10000 0 -0.38 24 24
TRAILR4 (trimer) 0.029 0.026 -10000 0 -0.42 1 1
TRADD 0.034 0.007 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.016 0.14 -10000 0 -0.42 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.015 0.12 -10000 0 -0.29 52 52
CFLAR 0.035 0.003 -10000 0 -10000 0 0
MAPK1 -0.01 0.089 -10000 0 -0.3 32 32
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.13 -10000 0 -0.25 52 52
mol:ceramide -0.002 0.066 -10000 0 -0.19 38 38
FADD 0.033 0.008 -10000 0 -10000 0 0
MAPK8 0.002 0.1 -10000 0 -0.33 20 20
TRAF2 0.033 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.009 0.1 -10000 0 -0.42 20 20
CHUK 0.032 0.01 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.007 0.14 -10000 0 -0.3 56 56
DAP3 0.032 0.011 -10000 0 -10000 0 0
CASP10 -0.03 0.14 0.21 1 -0.36 40 41
JNK cascade 0.011 0.1 -10000 0 -0.3 35 35
TRAIL (trimer) -0.009 0.13 -10000 0 -0.42 35 35
TNFRSF10C 0.009 0.1 -10000 0 -0.42 20 20
TRAIL/TRAILR1/DAP3/GTP/FADD 0.024 0.12 -10000 0 -0.26 47 47
TRAIL/TRAILR2/FADD 0.032 0.099 -10000 0 -0.26 35 35
cell death -0.002 0.066 -10000 0 -0.19 38 38
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.007 0.083 -10000 0 -0.24 32 32
TRAILR2 (trimer) 0.026 0.058 -10000 0 -0.42 6 6
CASP8 0.013 0.085 -10000 0 -0.73 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.053 0.096 -10000 0 -0.22 32 32
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.04 0.018 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.031 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.058 -10000 0 -0.42 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.033 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.019 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.034 0.007 -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 0.034 0.007 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
MAP3K12 0.035 0.005 -10000 0 -10000 0 0
FGR -0.01 0.14 -10000 0 -0.42 36 36
p38 alpha/TAB1 -0.12 0.17 -10000 0 -0.33 101 101
PRKG1 0.018 0.018 -10000 0 -10000 0 0
DUSP8 0.028 0.014 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.095 0.18 0.2 2 -0.37 74 76
apoptosis -0.11 0.16 -10000 0 -0.32 101 101
RAL/GTP 0.042 0.016 -10000 0 -10000 0 0
LYN 0.016 0.084 -10000 0 -0.42 13 13
DUSP1 0.033 0.01 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.072 0.037 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.012 -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 0.031 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.041 0.016 -10000 0 -10000 0 0
MAPK11 -0.13 0.21 0.29 3 -0.42 86 89
BLK -0.24 0.22 -10000 0 -0.42 216 216
HCK -0.002 0.12 -10000 0 -0.42 28 28
MAP2K3 0.033 0.009 -10000 0 -10000 0 0
DUSP16 0.034 0.006 -10000 0 -10000 0 0
DUSP10 0.027 0.048 -10000 0 -0.42 4 4
TRAF6/MEKK3 0.043 0.011 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.1 0.2 0.23 4 -0.38 92 96
positive regulation of innate immune response -0.14 0.23 0.32 3 -0.46 90 93
LCK -0.14 0.22 -10000 0 -0.42 138 138
p38alpha-beta/MKP7 -0.12 0.22 0.31 1 -0.44 89 90
p38alpha-beta/MKP5 -0.12 0.22 0.33 2 -0.44 85 87
PGK/cGMP 0.01 0.018 -10000 0 -10000 0 0
PAK2 0.035 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.12 0.23 0.32 3 -0.44 89 92
CDC42 0.035 0.005 -10000 0 -10000 0 0
RALB 0.035 0.003 -10000 0 -10000 0 0
RALA 0.031 0.011 -10000 0 -10000 0 0
PAK3 0.027 0.012 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.035 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.002 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.023 0.006 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP -0.009 0.1 -10000 0 -0.25 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.017 0.003 -10000 0 -10000 0 0
GRK1 0.017 0.004 -10000 0 -10000 0 0
CNG Channel -0.022 0.14 -10000 0 -0.26 84 84
mol:Na + 0.03 0.051 -10000 0 -0.21 10 10
mol:ADP 0.017 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.056 0.15 -10000 0 -0.25 138 138
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.042 0.056 -10000 0 -0.22 10 10
CNGB1 0.026 0.01 -10000 0 -10000 0 0
RDH5 0.029 0.047 -10000 0 -0.42 4 4
SAG 0.017 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.11 0.33 34 -10000 0 34
Na + (4 Units) 0.029 0.047 -10000 0 -0.2 10 10
RGS9 -0.14 0.22 -10000 0 -0.42 144 144
GNB1/GNGT1 0.029 0.025 -10000 0 -10000 0 0
GNAT1/GDP -0.043 0.14 -10000 0 -0.22 138 138
GUCY2D 0.029 0.012 -10000 0 -10000 0 0
GNGT1 0.018 0.013 -10000 0 -10000 0 0
GUCY2F 0.018 0 -10000 0 -10000 0 0
GNB5 0.033 0.024 -10000 0 -0.42 1 1
mol:GMP (4 units) -0.04 0.13 -10000 0 -0.28 81 81
mol:11-cis-retinal 0.029 0.047 -10000 0 -0.42 4 4
mol:cGMP 0.032 0.045 -10000 0 -0.22 5 5
GNB1 0.034 0.007 -10000 0 -10000 0 0
Rhodopsin 0.033 0.037 -10000 0 -0.3 4 4
SLC24A1 0.035 0.005 -10000 0 -10000 0 0
CNGA1 0.026 0.053 -10000 0 -0.42 5 5
Metarhodopsin II 0.021 0.007 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.047 0.047 -10000 0 -0.23 5 5
RGS9BP 0.035 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.008 0.01 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.033 0.042 -10000 0 -0.23 5 5
PDE6A/B -0.008 0.12 -10000 0 -0.29 57 57
mol:Pi -0.056 0.15 -10000 0 -0.25 138 138
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.032 0.028 -10000 0 -10000 0 0
PDE6B -0.037 0.16 -10000 0 -0.42 57 57
PDE6A 0.031 0.011 -10000 0 -10000 0 0
PDE6G -0.033 0.16 -10000 0 -0.42 54 54
RHO 0.017 0.003 -10000 0 -10000 0 0
PDE6 -0.091 0.2 -10000 0 -0.29 168 168
GUCA1A 0.023 0.015 -10000 0 -10000 0 0
GC2/GCAP Family 0.04 0.048 -10000 0 -0.24 5 5
GUCA1C 0.017 0.003 -10000 0 -10000 0 0
GUCA1B 0.026 0.053 -10000 0 -0.42 5 5
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.034 0.006 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.003 0.12 -9999 0 -0.22 74 74
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.001 0.039 -9999 0 -0.29 2 2
AURKB 0.032 0.025 -9999 0 -0.42 1 1
AURKC -0.056 0.18 -9999 0 -0.42 73 73
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.04 -10000 0 -0.3 6 6
MAP4K4 -0.076 0.17 -10000 0 -0.41 63 63
BAG4 0.034 0.008 -10000 0 -10000 0 0
PKC zeta/ceramide -0.002 0.072 0.15 2 -0.19 40 42
NFKBIA 0.035 0.004 -10000 0 -10000 0 0
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BAX 0.004 0.043 -10000 0 -0.34 3 3
RIPK1 0.031 0.012 -10000 0 -10000 0 0
AKT1 -0.003 0.012 -10000 0 -10000 0 0
BAD -0.02 0.068 0.19 7 -0.18 41 48
SMPD1 -0.016 0.11 0.17 25 -0.21 66 91
RB1 -0.02 0.066 0.19 4 -0.19 40 44
FADD/Caspase 8 -0.065 0.18 0.25 4 -0.42 60 64
MAP2K4 -0.02 0.06 0.17 3 -0.18 36 39
NSMAF 0.032 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.02 0.062 0.18 4 -0.18 37 41
EGF 0.001 0.11 -10000 0 -0.42 25 25
mol:ceramide -0.022 0.066 0.13 6 -0.19 42 48
MADD 0.035 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0.033 -10000 0 -0.3 4 4
ASAH1 0.033 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.02 0.066 0.19 4 -0.18 40 44
cell proliferation 0.015 0.068 -10000 0 -0.21 3 3
BID -0.049 0.18 -10000 0 -0.52 28 28
MAP3K1 -0.02 0.063 0.16 4 -0.18 39 43
EIF2A -0.02 0.059 0.17 5 -0.18 32 37
TRADD 0.034 0.007 -10000 0 -10000 0 0
CRADD 0.034 0.006 -10000 0 -10000 0 0
MAPK3 -0.012 0.06 0.17 4 -0.22 2 6
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.06 0.17 4 -0.21 3 7
Cathepsin D/ceramide -0.001 0.071 0.15 2 -0.18 42 44
FADD -0.072 0.17 0.22 2 -0.41 61 63
KSR1 -0.02 0.065 0.19 3 -0.19 39 42
MAPK8 -0.023 0.08 -10000 0 -0.26 15 15
PRKRA -0.022 0.062 0.14 2 -0.18 40 42
PDGFA 0.024 0.058 -10000 0 -0.42 6 6
TRAF2 0.033 0.009 -10000 0 -10000 0 0
IGF1 0.03 0.041 -10000 0 -0.42 3 3
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.066 0.13 6 -0.19 42 48
CTSD 0.034 0.007 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.049 0.013 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.017 0.073 -10000 0 -0.22 3 3
PRKCD 0.034 0.006 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0.033 -10000 0 -0.3 4 4
RelA/NF kappa B1 0.049 0.013 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.016 0.09 -10000 0 -0.42 15 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.074 0.18 -10000 0 -0.43 63 63
TNFR1A/BAG4/TNF-alpha 0.002 0.12 -10000 0 -0.25 66 66
mol:Sphingosine-1-phosphate 0.012 0.04 -10000 0 -0.3 6 6
MAP2K1 -0.018 0.061 0.17 7 -0.23 2 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.007 -10000 0 -10000 0 0
CYCS 0.001 0.035 0.19 1 -0.16 4 5
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.048 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.022 0.058 0.14 1 -0.18 38 39
TNF-alpha/TNFR1A/FAN 0.003 0.12 -10000 0 -0.25 63 63
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.027 0.13 -10000 0 -0.4 24 24
MAP2K2 -0.019 0.061 0.17 6 -0.2 6 12
SMPD3 -0.034 0.14 0.16 13 -0.29 58 71
TNF -0.054 0.18 -10000 0 -0.42 69 69
PKC zeta/PAR4 0.033 0.074 -10000 0 -0.3 17 17
mol:PHOSPHOCHOLINE -0.005 0.071 0.18 25 -0.15 27 52
NF kappa B1/RelA/I kappa B alpha 0.079 0.072 -10000 0 -0.21 17 17
AIFM1 -0.007 0.048 0.18 2 -0.16 6 8
BCL2 0.035 0.005 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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 0.012 0.1 0.36 1 -1.2 2 3
VDR 0.032 0.034 -10000 0 -0.42 2 2
FAM120B 0.031 0.012 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.15 -10000 0 -0.3 62 62
RXRs/LXRs/DNA/Oxysterols -0.068 0.2 -10000 0 -0.42 76 76
MED1 0.034 0.006 -10000 0 -10000 0 0
mol:9cRA -0.005 0.024 -10000 0 -0.11 5 5
RARs/THRs/DNA/Src-1 0.028 0.051 -10000 0 -0.21 14 14
RXRs/NUR77 0.003 0.13 -10000 0 -0.24 62 62
RXRs/PPAR -0.02 0.1 -10000 0 -0.22 67 67
NCOR2 0.034 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.024 -10000 0 -0.29 2 2
RARs/VDR/DNA/Vit D3 0.067 0.061 -10000 0 -0.21 15 15
RARA 0.034 0.006 -10000 0 -10000 0 0
NCOA1 0.035 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.032 0.034 -10000 0 -0.42 2 2
RARs/RARs/DNA/9cRA 0.046 0.056 -10000 0 -0.22 13 13
RARG 0.035 0.005 -10000 0 -10000 0 0
RPS6KB1 0.03 0.086 0.54 8 -0.42 2 10
RARs/THRs/DNA/SMRT 0.029 0.051 -10000 0 -0.21 14 14
THRA 0.034 0.006 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.024 0.024 -10000 0 -0.29 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.011 0.13 0.31 1 -0.23 65 66
NR1H4 0.017 0.003 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.005 0.15 -10000 0 -0.24 60 60
NR1H2 0.022 0.037 -10000 0 -0.1 3 3
NR1H3 0.02 0.051 -10000 0 -0.43 2 2
RXRs/VDR/DNA/Vit D3 0.001 0.12 -10000 0 -0.22 63 63
NR4A1 0.033 0.024 -10000 0 -0.42 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.028 0.097 -10000 0 -0.2 72 72
RXRG -0.064 0.18 -10000 0 -0.42 72 72
RXR alpha/CCPG 0.036 0.034 -10000 0 -10000 0 0
RXRA 0.022 0.036 -10000 0 -0.1 4 4
RXRB 0.019 0.036 -10000 0 -10000 0 0
THRB 0.027 0.036 -10000 0 -0.42 2 2
PPARG 0.03 0.047 -10000 0 -0.42 4 4
PPARD 0.031 0.011 -10000 0 -10000 0 0
TNF -0.18 0.41 -10000 0 -1 70 70
mol:Oxysterols -0.004 0.021 -10000 0 -0.094 3 3
cholesterol transport -0.068 0.2 -10000 0 -0.41 76 76
PPARA 0.032 0.01 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.084 -10000 0 -0.42 13 13
RXRs/NUR77/BCL2 -0.023 0.098 -10000 0 -0.22 64 64
SREBF1 -0.061 0.18 -10000 0 -0.49 28 28
RXRs/RXRs/DNA/9cRA -0.011 0.13 0.31 1 -0.23 65 66
ABCA1 -0.062 0.18 -10000 0 -0.49 27 27
RARs/THRs 0.079 0.069 -10000 0 -0.23 14 14
RXRs/FXR -0.003 0.12 -10000 0 -0.24 62 62
BCL2 0.035 0.005 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.01 0.075 -10000 0 -0.25 26 26
EFNA5 0.025 0.062 -10000 0 -0.42 7 7
FYN 0 0.07 0.19 11 -0.22 26 37
neuron projection morphogenesis 0.01 0.075 -10000 0 -0.25 26 26
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.011 0.076 -10000 0 -0.25 26 26
EPHA5 0.002 0.099 -10000 0 -0.42 19 19
Paxillin-dependent events mediated by a4b1

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
CRKL 0.033 0.01 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.016 -10000 0 -10000 0 0
DOCK1 0.032 0.01 -10000 0 -10000 0 0
ITGA4 -0.013 0.14 -10000 0 -0.42 39 39
RAC1 0.031 0.012 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.16 -10000 0 -0.32 80 80
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.031 0.098 -10000 0 -0.25 39 39
alpha4/beta7 Integrin/Paxillin -0.007 0.13 -10000 0 -0.25 79 79
lamellipodium assembly 0.018 0.097 -10000 0 -0.4 15 15
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
ARF6 0.035 0.004 -10000 0 -10000 0 0
TLN1 0.032 0.011 -10000 0 -10000 0 0
PXN 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
ARF6/GTP 0.041 0.084 -10000 0 -0.19 39 39
cell adhesion 0.039 0.088 -10000 0 -0.2 39 39
CRKL/CBL 0.044 0.02 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.025 0.087 -10000 0 -0.22 39 39
ITGB1 0.032 0.011 -10000 0 -10000 0 0
ITGB7 -0.026 0.15 -10000 0 -0.42 49 49
ARF6/GDP 0.036 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.002 0.15 -10000 0 -0.28 72 72
p130Cas/Crk/Dock1 0.059 0.027 -10000 0 -10000 0 0
VCAM1 -0.04 0.17 -10000 0 -0.42 60 60
alpha4/beta1 Integrin/Paxillin/Talin 0.041 0.09 -10000 0 -0.2 39 39
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.091 -10000 0 -0.21 39 39
BCAR1 0.034 0.007 -10000 0 -10000 0 0
mol:GDP -0.04 0.089 0.21 39 -10000 0 39
CBL 0.032 0.011 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.041 0.09 -10000 0 -0.2 39 39
Rac1/GTP 0.017 0.11 -10000 0 -0.45 15 15
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 0.031 0.052 -10000 0 -0.25 11 11
ARNO/beta Arrestin1-2 0.043 0.084 -10000 0 -0.81 3 3
EGFR 0.027 0.035 -10000 0 -0.42 2 2
EPHA2 0.03 0.047 -10000 0 -0.42 4 4
USP6 0.033 0.009 -10000 0 -10000 0 0
IQSEC1 0.035 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.015 0.089 -10000 0 -0.3 26 26
ARRB2 0.012 0.003 -10000 0 -10000 0 0
mol:GTP -0.019 0.066 0.17 2 -0.17 35 37
ARRB1 0.033 0.009 -10000 0 -10000 0 0
FBXO8 0.035 0.005 -10000 0 -10000 0 0
TSHR -0.003 0.12 -10000 0 -0.42 29 29
EGF 0.001 0.11 -10000 0 -0.42 25 25
somatostatin receptor activity 0 0 0.001 20 -0.001 44 64
ARAP2 0.026 0.062 -10000 0 -0.42 7 7
mol:GDP 0.006 0.1 0.19 20 -0.26 29 49
mol:PI-3-4-5-P3 0 0 0.001 18 -0.001 24 42
ITGA2B 0.031 0.012 -10000 0 -10000 0 0
ARF6 0.035 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.073 0.044 -10000 0 -0.23 3 3
ADAP1 0.018 0.077 -10000 0 -0.42 11 11
KIF13B 0.033 0.008 -10000 0 -10000 0 0
HGF/MET 0.019 0.091 -10000 0 -0.3 25 25
PXN 0.034 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.007 0.12 0.25 18 -0.26 42 60
EGFR/EGFR/EGF/EGF/ARFGEP100 0.031 0.084 -10000 0 -0.25 26 26
ADRB2 0.031 0.034 -10000 0 -0.42 2 2
receptor agonist activity 0 0 0 9 0 40 49
actin filament binding 0 0 0.001 18 0 44 62
SRC 0.033 0.01 -10000 0 -10000 0 0
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
GNAQ 0.033 0.009 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 25 -0.001 31 56
ARF6/GDP -0.065 0.19 0.24 2 -0.38 69 71
ARF6/GDP/GULP/ACAP1 -0.028 0.17 0.23 7 -0.31 65 72
alphaIIb/beta3 Integrin/paxillin/GIT1 0.061 0.071 -10000 0 -0.22 18 18
ACAP1 -0.1 0.21 -10000 0 -0.42 110 110
ACAP2 0.035 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.015 0.017 -10000 0 -10000 0 0
EFNA1 0.032 0.011 -10000 0 -10000 0 0
HGF 0.024 0.058 -10000 0 -0.42 6 6
CYTH3 0.009 0.003 -10000 0 -10000 0 0
CYTH2 0.017 0.094 -10000 0 -1 3 3
NCK1 0.034 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 19 0 44 63
endosomal lumen acidification 0 0 0.001 19 0 32 51
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.014 0.095 -10000 0 -0.42 17 17
GNAQ/ARNO 0.036 0.089 -10000 0 -0.93 3 3
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 15 0 4 19
MET 0.006 0.1 -10000 0 -0.42 20 20
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GIT1 0.034 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 21 -0.001 36 57
GNA11 0.035 0.004 -10000 0 -10000 0 0
LHCGR 0.015 0.009 -10000 0 -10000 0 0
AGTR1 0.016 0.006 -10000 0 -10000 0 0
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.017 -10000 0 -10000 0 0
IPCEF1/ARNO 0.025 0.1 -10000 0 -0.86 3 3
alphaIIb/beta3 Integrin 0.023 0.077 -10000 0 -0.3 18 18
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.053 0.26 0.6 2 -0.65 29 31
CRP -0.051 0.26 0.69 2 -0.64 34 36
cell cycle arrest -0.078 0.29 0.54 2 -0.7 43 45
TIMP1 -0.027 0.22 0.52 2 -0.56 25 27
IL6ST 0.018 0.07 -10000 0 -0.42 8 8
Rac1/GDP -0.012 0.15 -10000 0 -0.35 39 39
AP1 0.042 0.14 -10000 0 -0.53 12 12
GAB2 0.033 0.009 -10000 0 -10000 0 0
TNFSF11 -0.18 0.46 0.57 1 -0.99 84 85
HSP90B1 0.013 0.16 -10000 0 -0.86 10 10
GAB1 0.035 0.005 -10000 0 -10000 0 0
MAPK14 0.025 0.11 0.26 3 -0.54 6 9
AKT1 0.035 0.091 -10000 0 -0.43 10 10
FOXO1 0.037 0.089 -10000 0 -0.45 8 8
MAP2K6 0.015 0.099 0.23 3 -0.33 17 20
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.03 0.17 0.38 1 -0.41 41 42
MITF 0.006 0.1 0.2 1 -0.28 24 25
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.035 0.003 -10000 0 -10000 0 0
A2M 0.006 0.16 -10000 0 -1.1 7 7
CEBPB 0.034 0.016 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.028 0.11 -10000 0 -0.47 10 10
STAT3 -0.084 0.3 0.54 2 -0.74 43 45
STAT1 0.015 0.097 -10000 0 -0.89 4 4
CEBPD -0.055 0.26 0.57 1 -0.66 31 32
PIK3CA 0.036 0.007 -10000 0 -10000 0 0
PI3K 0.051 0.014 -10000 0 -10000 0 0
JUN 0.031 0.011 -10000 0 -10000 0 0
PIAS3/MITF 0.028 0.11 0.24 13 -0.3 16 29
MAPK11 0.024 0.1 0.26 2 -0.53 6 8
STAT3 (dimer)/FOXO1 -0.033 0.23 -10000 0 -0.54 32 32
GRB2/SOS1/GAB family 0.054 0.13 -10000 0 -0.36 16 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.003 0.12 -10000 0 -0.31 37 37
GRB2 0.034 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.053 -10000 0 -0.42 5 5
LBP -0.18 0.43 0.58 2 -0.85 94 96
PIK3R1 0.035 0.007 -10000 0 -10000 0 0
JAK1 0.032 0.018 -10000 0 -10000 0 0
MYC -0.045 0.26 0.57 1 -0.68 22 23
FGG -0.068 0.26 0.56 1 -0.66 32 33
macrophage differentiation -0.078 0.29 0.54 2 -0.7 43 45
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.05 0.1 -10000 0 -0.29 20 20
JUNB -0.061 0.25 0.55 1 -0.62 33 34
FOS 0.033 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.008 0.097 -10000 0 -0.32 20 20
STAT1/PIAS1 0.02 0.12 -10000 0 -0.31 20 20
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.093 -10000 0 -0.5 8 8
STAT3 (dimer) -0.083 0.3 0.54 2 -0.73 43 45
PRKCD -0.032 0.22 0.37 13 -0.48 45 58
IL6R 0.026 0.052 -10000 0 -0.44 4 4
SOCS3 0.05 0.15 0.41 2 -1.1 3 5
gp130 (dimer)/JAK1/JAK1/LMO4 0.049 0.069 -10000 0 -0.25 9 9
Rac1/GTP -0.02 0.16 -10000 0 -0.38 39 39
HCK -0.002 0.12 -10000 0 -0.42 28 28
MAPKKK cascade 0.036 0.13 0.35 1 -0.57 11 12
bone resorption -0.17 0.43 0.57 1 -0.91 84 85
IRF1 -0.12 0.39 0.57 1 -0.97 52 53
mol:GDP -0.017 0.14 -10000 0 -0.34 43 43
SOS1 0.035 0.004 -10000 0 -10000 0 0
VAV1 -0.017 0.14 -10000 0 -0.35 43 43
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.037 0.11 0.28 1 -0.62 5 6
PTPN11 0.009 0.12 -10000 0 -0.81 7 7
IL6/IL6RA 0.025 0.077 -10000 0 -0.34 13 13
gp130 (dimer)/TYK2/TYK2/LMO4 0.056 0.058 -10000 0 -0.25 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 0.048 0.073 -10000 0 -0.31 11 11
IL6 0.009 0.087 -10000 0 -0.43 13 13
PIAS3 0.032 0.011 -10000 0 -10000 0 0
PTPRE 0.025 0.054 -10000 0 -0.4 5 5
PIAS1 0.035 0.005 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.008 0.074 0.17 1 -0.25 20 21
LMO4 0.026 0.034 -10000 0 -0.42 1 1
STAT3 (dimer)/PIAS3 -0.069 0.28 -10000 0 -0.7 39 39
MCL1 0.056 0.1 -10000 0 -0.6 3 3
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.053 0.075 -10000 0 -0.22 21 21
ER alpha/Gai/GDP/Gbeta gamma -0.018 0.15 -10000 0 -0.44 29 29
AKT1 -0.054 0.27 -10000 0 -0.69 52 52
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.052 0.27 -10000 0 -0.7 52 52
mol:Ca2+ -0.049 0.16 -10000 0 -0.37 60 60
IGF1R 0.034 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.037 0.04 -10000 0 -0.25 6 6
SHC1 0.032 0.011 -10000 0 -10000 0 0
apoptosis 0.049 0.25 0.66 52 -10000 0 52
RhoA/GTP 0.025 0.032 -10000 0 -0.19 6 6
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.026 0.14 0.25 4 -0.38 22 26
regulation of stress fiber formation -0.007 0.057 -10000 0 -0.22 7 7
E2/ERA-ERB (dimer) 0.027 0.063 -10000 0 -0.25 17 17
KRAS 0.034 0.006 -10000 0 -10000 0 0
G13/GTP 0.034 0.037 -10000 0 -0.22 6 6
pseudopodium formation 0.007 0.057 0.22 7 -10000 0 7
E2/ER alpha (dimer)/PELP1 0.036 0.038 -10000 0 -0.25 5 5
GRB2 0.034 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.058 -10000 0 -0.42 6 6
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
HRAS 0.034 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.012 0.18 0.27 1 -0.42 48 49
E2/ER beta (dimer) 0.016 0.055 -10000 0 -0.29 11 11
mol:GDP 0 0.081 -10000 0 -0.29 17 17
mol:NADP -0.012 0.18 0.27 1 -0.42 48 49
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.054 0.16 -10000 0 -0.39 60 60
IGF-1R heterotetramer 0.034 0.006 -10000 0 -10000 0 0
PLCB1 -0.044 0.16 -10000 0 -0.38 58 58
PLCB2 -0.046 0.16 -10000 0 -0.38 61 61
IGF1 0.03 0.041 -10000 0 -0.42 3 3
mol:L-citrulline -0.012 0.18 0.27 1 -0.42 48 49
RHOA 0.035 0.005 -10000 0 -10000 0 0
Gai/GDP -0.005 0.15 -10000 0 -0.61 19 19
JNK cascade 0.016 0.055 -10000 0 -0.29 11 11
BCAR1 0.034 0.007 -10000 0 -10000 0 0
ESR2 0.021 0.077 -10000 0 -0.42 11 11
GNAQ 0.033 0.009 -10000 0 -10000 0 0
ESR1 0.023 0.058 -10000 0 -0.42 6 6
Gq family/GDP/Gbeta gamma -0.009 0.14 -10000 0 -0.51 18 18
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.04 0.082 -10000 0 -0.51 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.025 0.13 0.25 3 -0.4 17 20
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
E2/ER alpha (dimer) 0.018 0.041 -10000 0 -0.29 6 6
STRN 0.035 0.004 -10000 0 -10000 0 0
GNAL 0.024 0.053 -10000 0 -0.42 5 5
PELP1 0.033 0.009 -10000 0 -10000 0 0
MAPK11 0.012 0.042 -10000 0 -0.25 9 9
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
HBEGF -0.007 0.18 0.34 22 -0.44 34 56
cAMP biosynthetic process 0.017 0.058 -10000 0 -0.21 20 20
SRC -0.011 0.14 0.24 5 -0.42 27 32
PI3K 0.049 0.014 -10000 0 -10000 0 0
GNB1 0.034 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.029 0.094 -10000 0 -0.26 20 20
SOS1 0.035 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.006 0.091 -10000 0 -0.33 16 16
Gs family/GTP 0.024 0.062 -10000 0 -0.21 20 20
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.062 0.02 -10000 0 -10000 0 0
vasodilation -0.01 0.17 0.26 1 -0.4 48 49
mol:DAG -0.054 0.16 -10000 0 -0.39 60 60
Gs family/GDP/Gbeta gamma 0.002 0.085 -10000 0 -0.27 17 17
MSN 0.007 0.059 0.22 7 -10000 0 7
Gq family/GTP -0.036 0.16 -10000 0 -0.38 60 60
mol:PI-3-4-5-P3 -0.048 0.26 -10000 0 -0.68 52 52
NRAS 0.034 0.008 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.01 0.17 0.4 48 -0.26 1 49
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.09 -10000 0 -0.27 17 17
NOS3 -0.015 0.19 0.27 1 -0.44 48 49
GNA11 0.035 0.004 -10000 0 -10000 0 0
MAPKKK cascade 0.002 0.19 0.3 5 -0.46 45 50
E2/ER alpha (dimer)/PELP1/Src 0.023 0.14 0.27 9 -0.4 23 32
ruffle organization 0.007 0.057 0.22 7 -10000 0 7
ROCK2 0.028 0.057 0.23 7 -10000 0 7
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GNA13 0.034 0.007 -10000 0 -10000 0 0
MMP9 -0.027 0.17 0.37 10 -0.44 34 44
MMP2 0.001 0.14 0.31 8 -0.41 24 32
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.003 0.15 -10000 0 -0.38 41 41
PTP1B/AKT1 0.03 0.077 0.24 2 -0.26 12 14
FYN 0.031 0.012 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.014 0.077 0.25 2 -0.28 12 14
EGFR 0.026 0.037 -10000 0 -0.42 2 2
EGF/EGFR 0.013 0.094 -10000 0 -0.24 30 30
CSF1 0.029 0.047 -10000 0 -0.42 4 4
AKT1 0.035 0.006 -10000 0 -10000 0 0
INSR 0.036 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.003 0.1 0.29 1 -0.26 31 32
Insulin Receptor/Insulin 0.047 0.078 0.28 1 -0.3 7 8
HCK -0.002 0.12 -10000 0 -0.42 28 28
CRK 0.033 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.075 0.23 4 -0.27 12 16
EGF 0.002 0.12 -10000 0 -0.42 25 25
YES1 0.034 0.007 -10000 0 -10000 0 0
CAV1 0.028 0.092 0.22 19 -0.28 11 30
TXN 0.033 0.009 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.038 0.082 0.21 1 -0.26 11 12
cell migration -0.014 0.077 0.28 12 -0.25 2 14
STAT3 0.035 0.006 -10000 0 -10000 0 0
PRLR 0.024 0.016 -10000 0 -10000 0 0
ITGA2B 0.03 0.013 -10000 0 -10000 0 0
CSF1R 0.015 0.09 -10000 0 -0.42 15 15
Prolactin Receptor/Prolactin 0.02 0.028 -10000 0 -10000 0 0
FGR -0.01 0.14 -10000 0 -0.42 36 36
PTP1B/p130 Cas 0.03 0.077 0.24 2 -0.27 11 13
Crk/p130 Cas 0.043 0.081 0.3 1 -0.26 10 11
DOK1 0.017 0.083 0.28 1 -0.3 12 13
JAK2 -0.018 0.15 0.3 1 -0.39 44 45
Jak2/Leptin Receptor/Leptin 0.022 0.12 -10000 0 -0.34 16 16
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
PTPN1 0.014 0.077 0.26 2 -0.28 12 14
LYN 0.016 0.084 -10000 0 -0.42 13 13
CDH2 -0.017 0.14 -10000 0 -0.42 40 40
SRC 0.039 0.048 -10000 0 -0.67 1 1
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
CAT1/PTP1B -0.12 0.24 0.26 5 -0.43 102 107
CAPN1 0.034 0.007 -10000 0 -10000 0 0
CSK 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.063 0.075 0.26 1 -0.31 5 6
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.11 -10000 0 -0.33 15 15
negative regulation of transcription -0.018 0.15 0.3 1 -0.39 44 45
FCGR2A 0.027 0.048 -10000 0 -0.42 4 4
FER 0.034 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.022 0.077 -10000 0 -0.3 18 18
BLK -0.24 0.22 -10000 0 -0.42 216 216
Insulin Receptor/Insulin/Shc 0.052 0.022 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
LEPR 0.034 0.005 -10000 0 -10000 0 0
BCAR1 0.034 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.034 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.24 0.3 0.36 1 -0.56 138 139
PRL 0.013 0.02 -10000 0 -10000 0 0
SOCS3 0.005 0.18 -10000 0 -1.2 8 8
SPRY2 0.034 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.052 0.024 -10000 0 -10000 0 0
CSF1/CSF1R 0.033 0.099 -10000 0 -0.28 19 19
Ras protein signal transduction 0.006 0.09 0.49 11 -10000 0 11
IRS1 0.032 0.011 -10000 0 -10000 0 0
INS 0.015 0.011 -10000 0 -10000 0 0
LEP 0.021 0.017 -10000 0 -10000 0 0
STAT5B 0.007 0.11 0.25 2 -0.36 17 19
STAT5A 0.007 0.11 0.23 3 -0.35 18 21
GRB2 0.034 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.031 0.075 0.24 2 -0.26 11 13
CSN2 0.009 0.047 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
LAT -0.026 0.18 -10000 0 -0.48 47 47
YBX1 0.045 0.007 -10000 0 -10000 0 0
LCK -0.14 0.22 -10000 0 -0.42 138 138
SHC1 0.032 0.011 -10000 0 -10000 0 0
NOX4 0.024 0.037 -10000 0 -0.42 2 2
EPO signaling pathway

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
BCL2L1 0.032 0.11 0.38 1 -0.42 5 6
CRKL -0.004 0.093 0.29 2 -0.26 5 7
mol:DAG 0.002 0.092 -10000 0 -0.35 15 15
HRAS 0.016 0.1 0.32 9 -0.32 1 10
MAPK8 0.029 0.085 0.19 48 -0.25 13 61
RAP1A -0.003 0.097 0.3 3 -0.25 6 9
GAB1 -0.004 0.098 0.3 3 -0.24 7 10
MAPK14 0.021 0.076 0.19 32 -0.25 13 45
EPO 0.016 0.029 -10000 0 -10000 0 0
PLCG1 0.002 0.094 -10000 0 -0.36 15 15
EPOR/TRPC2/IP3 Receptors 0.025 0.029 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.053 0.043 -10000 0 -0.28 3 3
GAB1/SHC/GRB2/SOS1 0.029 0.097 0.29 2 -0.26 2 4
EPO/EPOR (dimer) 0.035 0.035 -10000 0 -10000 0 0
IRS2 -0.001 0.096 0.24 6 -0.22 9 15
STAT1 0.014 0.11 -10000 0 -0.37 17 17
STAT5B 0.009 0.1 -10000 0 -0.35 17 17
cell proliferation 0.008 0.073 0.18 34 -0.23 13 47
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.13 -10000 0 -0.31 40 40
TEC -0.008 0.1 0.29 2 -0.29 11 13
SOCS3 0.03 0.041 -10000 0 -0.42 3 3
STAT1 (dimer) 0.014 0.11 -10000 0 -0.36 17 17
JAK2 0.018 0.058 -10000 0 -0.42 5 5
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.028 0.12 0.24 1 -0.18 80 81
EPO/EPOR 0.035 0.035 -10000 0 -10000 0 0
LYN 0.018 0.084 -10000 0 -0.42 13 13
TEC/VAV2 0.004 0.11 0.22 5 -0.27 14 19
elevation of cytosolic calcium ion concentration 0.025 0.029 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.048 0.071 -10000 0 -0.28 13 13
mol:IP3 0.002 0.092 -10000 0 -0.35 15 15
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.004 0.15 0.31 2 -0.32 55 57
SH2B3 0.024 0.029 -10000 0 -10000 0 0
NFKB1 0.032 0.089 0.2 46 -0.25 13 59
EPO/EPOR (dimer)/JAK2/SOCS3 0.016 0.038 -10000 0 -0.22 7 7
PTPN6 -0.01 0.096 -10000 0 -0.18 75 75
TEC/VAV2/GRB2 0.015 0.11 0.3 1 -0.25 13 14
EPOR 0.025 0.029 -10000 0 -10000 0 0
INPP5D -0.037 0.16 -10000 0 -0.42 58 58
mol:GDP 0.028 0.098 0.29 2 -0.26 2 4
SOS1 0.035 0.003 -10000 0 -10000 0 0
PLCG2 -0.002 0.12 -10000 0 -0.42 29 29
CRKL/CBL/C3G 0.02 0.098 0.3 1 -0.26 4 5
VAV2 -0.001 0.098 0.22 8 -0.23 12 20
CBL 0.002 0.09 0.3 3 -0.23 7 10
SHC/Grb2/SOS1 0.009 0.087 -10000 0 -0.23 4 4
STAT5A 0.009 0.1 -10000 0 -0.34 18 18
GRB2 0.034 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.026 0.11 -10000 0 -0.35 14 14
LYN/PLCgamma2 0.013 0.11 -10000 0 -0.32 33 33
PTPN11 0.034 0.006 -10000 0 -10000 0 0
BTK -0.038 0.15 0.27 4 -0.32 64 68
BCL2 0.035 0.11 0.35 1 -0.41 6 7
Signaling events mediated by the Hedgehog family

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
TGFB2 0.034 0.062 -10000 0 -0.37 6 6
IHH 0.043 0.033 -10000 0 -0.16 4 4
SHH Np/Cholesterol/GAS1 0.023 0.014 -10000 0 -10000 0 0
LRPAP1 0.034 0.008 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.022 0.014 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.057 0.083 -10000 0 -0.34 6 6
SMO 0.027 0.07 -10000 0 -0.31 9 9
AKT1 0.032 0.08 -10000 0 -0.33 11 11
ARRB2 0.033 0.009 -10000 0 -10000 0 0
BOC 0.034 0.007 -10000 0 -10000 0 0
ADRBK1 0.034 0.007 -10000 0 -10000 0 0
heart looping 0.027 0.069 -10000 0 -0.31 9 9
STIL 0.045 0.077 0.21 48 -0.25 4 52
DHH N/PTCH2 0.035 0.064 -10000 0 -0.3 12 12
DHH N/PTCH1 0.039 0.074 -10000 0 -0.26 17 17
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
DHH 0.019 0.077 -10000 0 -0.42 11 11
PTHLH 0.026 0.099 -10000 0 -0.63 7 7
determination of left/right symmetry 0.027 0.069 -10000 0 -0.31 9 9
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
skeletal system development 0.026 0.099 -10000 0 -0.63 7 7
IHH N/Hhip 0.04 0.024 -10000 0 -10000 0 0
DHH N/Hhip 0.025 0.059 -10000 0 -0.3 11 11
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.027 0.069 -10000 0 -0.31 9 9
pancreas development 0.017 0.002 -10000 0 -10000 0 0
HHAT 0.03 0.026 -10000 0 -0.42 1 1
PI3K 0.049 0.014 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.031 0.025 -10000 0 -0.42 1 1
somite specification 0.027 0.069 -10000 0 -0.31 9 9
SHH Np/Cholesterol/PTCH1 0.026 0.04 -10000 0 -0.26 4 4
SHH Np/Cholesterol/PTCH2 0.023 0.019 -10000 0 -0.23 1 1
SHH Np/Cholesterol/Megalin -0.087 0.12 -10000 0 -0.23 157 157
SHH -0.01 0.005 -10000 0 -10000 0 0
catabolic process 0.034 0.062 -10000 0 -0.42 6 6
SMO/Vitamin D3 0.036 0.064 0.21 16 -0.27 5 21
SHH Np/Cholesterol/Hhip 0.015 0.008 -10000 0 -10000 0 0
LRP2 -0.2 0.22 -10000 0 -0.42 193 193
receptor-mediated endocytosis -0.059 0.12 -10000 0 -0.31 20 20
SHH Np/Cholesterol/BOC 0.024 0.014 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.023 0.014 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.015 0.008 -10000 0 -10000 0 0
mol:Vitamin D3 0.058 0.084 0.23 50 -0.26 4 54
IHH N/PTCH2 0.051 0.033 -10000 0 -0.32 1 1
CDON 0.032 0.011 -10000 0 -10000 0 0
IHH N/PTCH1 0.043 0.067 -10000 0 -0.38 7 7
Megalin/LRPAP1 -0.13 0.17 -10000 0 -0.3 190 190
PTCH2 0.033 0.024 -10000 0 -0.42 1 1
SHH Np/Cholesterol 0.015 0.007 -10000 0 -10000 0 0
PTCH1 0.034 0.063 -10000 0 -0.42 6 6
HHIP 0.017 0.002 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.042 0.023 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.039 0.077 -10000 0 -0.25 20 20
PTK2 -0.01 0.14 0.34 12 -0.35 21 33
IGF1R 0.034 0.006 -10000 0 -10000 0 0
PI4KB 0.032 0.011 -10000 0 -10000 0 0
MFGE8 0.033 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
CDKN1B -0.03 0.15 -10000 0 -0.41 47 47
VEGFA 0.03 0.013 -10000 0 -10000 0 0
ILK -0.031 0.15 -10000 0 -0.41 48 48
ROCK1 0.035 0.004 -10000 0 -10000 0 0
AKT1 -0.034 0.14 -10000 0 -0.39 47 47
PTK2B 0.021 0.079 0.2 36 -0.21 17 53
alphaV/beta3 Integrin/JAM-A 0.026 0.12 -10000 0 -0.23 57 57
CBL 0.032 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.034 0.07 -10000 0 -0.25 18 18
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.077 0.039 -10000 0 -0.23 3 3
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.084 -10000 0 -0.22 17 17
alphaV/beta3 Integrin/Syndecan-1 0.039 0.086 -10000 0 -0.27 23 23
PI4KA 0.033 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.045 0.087 -10000 0 -0.24 26 26
PI4 Kinase 0.043 0.02 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.014 0.12 -10000 0 -0.28 49 49
RPS6KB1 -0.004 0.074 0.34 1 -0.37 5 6
TLN1 0.032 0.011 -10000 0 -10000 0 0
MAPK3 -0.017 0.12 -10000 0 -0.41 24 24
GPR124 0.033 0.008 -10000 0 -10000 0 0
MAPK1 -0.018 0.12 -10000 0 -0.4 24 24
PXN 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.069 0.16 -10000 0 -0.26 143 143
cell adhesion 0.033 0.072 -10000 0 -0.26 18 18
ANGPTL3 0.017 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.053 0.033 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.034 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
TGFBR2 0.035 0.005 -10000 0 -10000 0 0
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
IGF1 0.03 0.041 -10000 0 -0.42 3 3
RAC1 0.031 0.012 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.043 0.071 -10000 0 -0.25 17 17
apoptosis 0.035 0.004 -10000 0 -10000 0 0
CD47 0.034 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.044 0.072 -10000 0 -0.25 18 18
VCL 0.032 0.01 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.024 0.074 -10000 0 -0.25 18 18
CSF1 0.029 0.047 -10000 0 -0.42 4 4
PIK3C2A -0.031 0.15 -10000 0 -0.41 48 48
PI4 Kinase/Pyk2 0.004 0.085 -10000 0 -0.2 41 41
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.056 0.068 -10000 0 -0.23 14 14
FAK1/Vinculin 0.007 0.12 0.32 13 -0.29 19 32
alphaV beta3/Integrin/ppsTEM5 0.043 0.071 -10000 0 -0.25 17 17
RHOA 0.035 0.005 -10000 0 -10000 0 0
VTN -0.02 0.14 -10000 0 -0.42 43 43
BCAR1 0.034 0.007 -10000 0 -10000 0 0
FGF2 0.03 0.035 -10000 0 -0.42 2 2
F11R 0.008 0.047 -10000 0 -0.3 8 8
alphaV/beta3 Integrin/Lactadherin 0.041 0.073 -10000 0 -0.25 18 18
alphaV/beta3 Integrin/TGFBR2 0.045 0.073 -10000 0 -0.25 18 18
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.073 0.046 -10000 0 -0.22 4 4
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Talin 0.039 0.066 -10000 0 -0.22 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.077 -10000 0 -0.42 11 11
alphaV/beta3 Integrin/Pyk2 0.047 0.075 0.2 22 -0.21 17 39
SDC1 0.026 0.062 -10000 0 -0.42 7 7
VAV3 0.017 0.041 0.19 6 -0.24 6 12
PTPN11 0.034 0.006 -10000 0 -10000 0 0
IRS1 0.032 0.011 -10000 0 -10000 0 0
FAK1/Paxillin 0.007 0.13 0.32 13 -0.29 18 31
cell migration 0.004 0.12 0.29 15 -0.27 16 31
ITGAV 0.035 0.004 -10000 0 -10000 0 0
PI3K 0.041 0.12 -10000 0 -0.21 52 52
SPP1 -0.011 0.14 -10000 0 -0.42 37 37
KDR 0.034 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.035 0.004 -10000 0 -10000 0 0
COL4A3 -0.14 0.22 -10000 0 -0.42 137 137
angiogenesis -0.017 0.15 0.27 1 -0.44 24 25
Rac1/GTP 0.03 0.039 0.19 3 -0.22 6 9
EDIL3 0.023 0.017 -10000 0 -10000 0 0
cell proliferation 0.044 0.072 -10000 0 -0.25 18 18
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.028 0.068 -10000 0 -0.3 14 14
CRKL 0.036 0.12 0.3 16 -0.37 11 27
mol:PIP3 -0.002 0.012 -10000 0 -10000 0 0
AKT1 -0.006 0.019 -10000 0 -10000 0 0
PTK2B 0.028 0.048 -10000 0 -0.42 4 4
RAPGEF1 0.034 0.11 0.31 13 -0.38 9 22
RANBP10 0.034 0.007 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.034 0.084 -10000 0 -0.26 24 24
MAP3K5 -0.01 0.16 0.28 8 -0.42 29 37
HGF/MET/CIN85/CBL/ENDOPHILINS 0.048 0.085 -10000 0 -0.23 25 25
AP1 0.038 0.05 0.17 8 -10000 0 8
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
apoptosis 0.018 0.14 -10000 0 -0.78 9 9
STAT3 (dimer) 0.01 0.085 -10000 0 -0.25 25 25
GAB1/CRKL/SHP2/PI3K 0.074 0.12 0.33 9 -0.36 9 18
INPP5D -0.037 0.16 -10000 0 -0.42 58 58
CBL/CRK 0.041 0.11 0.27 8 -0.37 10 18
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.033 0.01 -10000 0 -10000 0 0
PTEN 0.03 0.012 -10000 0 -10000 0 0
ELK1 0.021 0.13 0.35 40 -10000 0 40
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.01 0.057 -10000 0 -0.23 9 9
PAK1 0.003 0.045 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.036 0.085 -10000 0 -0.26 25 25
HRAS -0.003 0.14 -10000 0 -0.52 24 24
DOCK1 0.033 0.11 0.29 17 -0.37 9 26
GAB1 0.022 0.11 0.25 2 -0.39 12 14
CRK 0.025 0.11 0.28 6 -0.38 11 17
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.14 -10000 0 -0.46 27 27
JUN 0.031 0.011 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.004 0.065 -10000 0 -0.23 25 25
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
cell morphogenesis 0.042 0.13 0.35 21 -0.41 6 27
GRB2/SHC 0.036 0.075 0.18 13 -0.2 21 34
FOS 0.033 0.008 -10000 0 -10000 0 0
GLMN 0.002 0.026 -10000 0 -0.24 4 4
cell motility 0.021 0.13 0.35 40 -10000 0 40
HGF/MET/MUC20 0.019 0.077 -10000 0 -0.26 25 25
cell migration 0.035 0.073 0.18 13 -0.2 21 34
GRB2 0.034 0.007 -10000 0 -10000 0 0
CBL 0.032 0.011 -10000 0 -10000 0 0
MET/RANBP10 0.025 0.079 -10000 0 -0.29 20 20
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.011 0.074 -10000 0 -0.24 25 25
MET/MUC20 0.005 0.072 -10000 0 -0.29 20 20
RAP1B 0.037 0.11 0.31 15 -0.35 9 24
RAP1A 0.036 0.11 0.31 14 -0.35 9 23
HGF/MET/RANBP9 0.036 0.076 -10000 0 -0.25 20 20
RAF1 0.015 0.14 -10000 0 -0.49 24 24
STAT3 0.01 0.086 -10000 0 -0.25 25 25
cell proliferation 0.032 0.12 0.29 15 -0.35 20 35
RPS6KB1 0.006 0.051 -10000 0 -0.3 7 7
MAPK3 0.007 0.13 0.5 12 -10000 0 12
MAPK1 0.015 0.14 0.54 16 -10000 0 16
RANBP9 0.031 0.012 -10000 0 -10000 0 0
MAPK8 -0.01 0.17 0.3 6 -0.38 41 47
SRC 0.008 0.077 -10000 0 -0.23 25 25
PI3K 0.037 0.081 0.18 16 -0.21 24 40
MET/Glomulin 0.003 0.073 -10000 0 -0.25 23 23
SOS1 0.035 0.003 -10000 0 -10000 0 0
MAP2K1 0.019 0.14 0.33 1 -0.47 23 24
MET 0.006 0.1 -10000 0 -0.42 20 20
MAP4K1 -0.011 0.17 0.28 9 -0.44 29 38
PTK2 0.031 0.012 -10000 0 -10000 0 0
MAP2K2 0.018 0.14 0.36 2 -0.47 23 25
BAD -0.005 0.027 -10000 0 -10000 0 0
MAP2K4 -0.007 0.14 0.28 6 -0.39 27 33
SHP2/GRB2/SOS1/GAB1 0.034 0.11 -10000 0 -0.32 26 26
INPPL1 0.033 0.009 -10000 0 -10000 0 0
PXN 0.034 0.006 -10000 0 -10000 0 0
SH3KBP1 0.035 0.004 -10000 0 -10000 0 0
HGS -0.007 0.06 -10000 0 -0.22 25 25
PLCgamma1/PKC 0.024 0.007 -10000 0 -10000 0 0
HGF 0.024 0.058 -10000 0 -0.42 6 6
RASA1 0.032 0.025 -10000 0 -0.42 1 1
NCK1 0.034 0.006 -10000 0 -10000 0 0
PTPRJ 0.034 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.043 0.079 0.18 17 -0.21 24 41
PDPK1 -0.005 0.021 -10000 0 -10000 0 0
HGF/MET/SHIP -0.008 0.14 -10000 0 -0.28 69 69
Nectin adhesion pathway

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
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.028 0.076 -10000 0 -0.3 18 18
PTK2 0.001 0.1 -10000 0 -0.35 13 13
positive regulation of JNK cascade 0.002 0.11 -10000 0 -0.3 18 18
CDC42/GDP 0.011 0.16 -10000 0 -0.39 29 29
Rac1/GDP 0.009 0.15 -10000 0 -0.39 28 28
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.007 0.14 -10000 0 -0.37 18 18
nectin-3/I-afadin 0.03 0.055 -10000 0 -0.29 8 8
RAPGEF1 0 0.13 -10000 0 -0.4 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.007 0.14 -10000 0 -0.44 16 16
PDGFB-D/PDGFRB 0.032 0.01 -10000 0 -10000 0 0
TLN1 0.003 0.021 -10000 0 -10000 0 0
Rap1/GTP 0.004 0.1 -10000 0 -0.3 13 13
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.051 0.03 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.03 0.055 -10000 0 -0.29 8 8
PVR 0.034 0.024 -10000 0 -0.42 1 1
Necl-5(dimer) 0.034 0.024 -10000 0 -0.42 1 1
mol:GDP -0.009 0.18 -10000 0 -0.48 29 29
MLLT4 0.029 0.014 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.072 0.059 -10000 0 -0.2 8 8
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.039 0.024 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.001 0.12 -10000 0 -0.33 31 31
PVRL1 0.031 0.012 -10000 0 -10000 0 0
PVRL3 0.022 0.066 -10000 0 -0.42 8 8
PVRL2 0.035 0.004 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
CDH1 -0.08 0.2 -10000 0 -0.42 92 92
CLDN1 -0.18 0.22 -10000 0 -0.42 169 169
JAM-A/CLDN1 -0.065 0.15 -10000 0 -0.24 151 151
SRC -0.011 0.15 -10000 0 -0.46 20 20
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
nectin-1(dimer)/I-afadin/I-afadin 0.039 0.024 -10000 0 -10000 0 0
FARP2 -0.007 0.18 -10000 0 -0.51 21 21
RAC1 0.031 0.012 -10000 0 -10000 0 0
CTNNA1 0.033 0.008 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.044 0.058 -10000 0 -0.25 9 9
nectin-1/I-afadin 0.039 0.024 -10000 0 -10000 0 0
nectin-2/I-afadin 0.042 0.023 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.041 0.017 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.042 0.056 -10000 0 -0.24 8 8
CDC42/GTP/IQGAP1/filamentous actin 0.045 0.011 -10000 0 -10000 0 0
F11R 0.024 0.058 -10000 0 -0.42 6 6
positive regulation of filopodium formation 0.002 0.11 -10000 0 -0.3 18 18
alphaV/beta3 Integrin/Talin 0.027 0.067 0.24 3 -0.2 13 16
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.042 0.023 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.042 0.023 -10000 0 -10000 0 0
PIP5K1C 0.007 0.024 -10000 0 -0.15 8 8
VAV2 -0.018 0.21 -10000 0 -0.57 31 31
RAP1/GDP 0.017 0.14 -10000 0 -0.35 28 28
ITGAV 0.035 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.045 0.056 -10000 0 -0.25 8 8
nectin-3(dimer)/I-afadin/I-afadin 0.03 0.055 -10000 0 -0.29 8 8
Rac1/GTP 0 0.15 -10000 0 -0.4 31 31
PTPRM 0.012 0.028 -10000 0 -0.16 8 8
E-cadherin/beta catenin/alpha catenin 0.005 0.13 -10000 0 -0.2 91 91
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 0.027 0.069 -10000 0 -0.24 22 22
cell-cell adhesion 0.01 0.061 0.2 29 -10000 0 29
Ephrin B/EPHB2/RasGAP 0.056 0.096 -10000 0 -0.21 35 35
ITSN1 0.035 0.005 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.04 0.02 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.036 0.043 -10000 0 -0.25 7 7
HRAS/GDP 0.019 0.083 -10000 0 -0.23 22 22
Ephrin B/EPHB1/GRB7 0.058 0.087 -10000 0 -0.21 27 27
Endophilin/SYNJ1 0.001 0.07 0.18 10 -0.2 34 44
KRAS 0.034 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.059 0.086 -10000 0 -0.21 25 25
endothelial cell migration 0.061 0.03 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
GRB7 0.029 0.012 -10000 0 -10000 0 0
PAK1 0.001 0.073 0.19 1 -0.21 26 27
HRAS 0.034 0.006 -10000 0 -10000 0 0
RRAS 0.002 0.072 0.19 12 -0.2 34 46
DNM1 0.029 0.013 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.003 0.065 0.18 9 -0.2 25 34
lamellipodium assembly -0.01 0.061 -10000 0 -0.2 29 29
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.018 0.062 -10000 0 -0.25 4 4
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
EPHB2 0.016 0.09 -10000 0 -0.42 15 15
EPHB3 0.032 0.011 -10000 0 -10000 0 0
EPHB1 0.024 0.062 -10000 0 -0.42 7 7
EPHB4 0.032 0.01 -10000 0 -10000 0 0
mol:GDP -0.005 0.072 0.22 3 -0.24 22 25
Ephrin B/EPHB2 0.043 0.087 -10000 0 -0.21 34 34
Ephrin B/EPHB3 0.049 0.073 -10000 0 -0.21 21 21
JNK cascade 0.01 0.071 0.24 10 -0.23 19 29
Ephrin B/EPHB1 0.046 0.081 -10000 0 -0.21 28 28
RAP1/GDP 0.032 0.098 0.24 22 -0.26 5 27
EFNB2 0.033 0.009 -10000 0 -10000 0 0
EFNB3 0.007 0.1 -10000 0 -0.42 21 21
EFNB1 0.034 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.04 0.075 -10000 0 -0.24 20 20
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.033 0.1 -10000 0 -0.24 30 30
Rap1/GTP 0.009 0.072 -10000 0 -0.26 4 4
axon guidance 0.027 0.069 -10000 0 -0.24 22 22
MAPK3 0.016 0.063 0.2 4 -0.24 3 7
MAPK1 0.021 0.067 0.2 13 -0.24 3 16
Rac1/GDP 0.01 0.085 0.23 9 -0.27 5 14
actin cytoskeleton reorganization -0.011 0.064 -10000 0 -0.25 6 6
CDC42/GDP 0.021 0.098 0.23 24 -0.27 5 29
PI3K 0.067 0.033 -10000 0 -10000 0 0
EFNA5 0.025 0.062 -10000 0 -0.42 7 7
Ephrin B2/EPHB4 0.04 0.018 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.008 0.076 -10000 0 -0.22 33 33
CDC42 0.035 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.069 -10000 0 -0.29 3 3
PTK2 0.061 0.18 0.54 43 -10000 0 43
MAP4K4 0.01 0.072 0.24 10 -0.23 19 29
SRC 0.033 0.01 -10000 0 -10000 0 0
KALRN 0.032 0.034 -10000 0 -0.42 2 2
Intersectin/N-WASP 0.045 0.018 -10000 0 -10000 0 0
neuron projection morphogenesis 0.028 0.12 0.31 33 -0.33 3 36
MAP2K1 0.011 0.059 -10000 0 -0.25 3 3
WASL 0.031 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.063 0.08 -10000 0 -0.24 20 20
cell migration 0.023 0.092 0.26 6 -0.27 5 11
NRAS 0.034 0.008 -10000 0 -10000 0 0
SYNJ1 0.001 0.071 0.18 10 -0.2 34 44
PXN 0.034 0.006 -10000 0 -10000 0 0
TF -0.054 0.098 0.18 8 -0.22 76 84
HRAS/GTP 0.032 0.086 -10000 0 -0.2 32 32
Ephrin B1/EPHB1-2 0.042 0.075 -10000 0 -0.24 20 20
cell adhesion mediated by integrin 0.013 0.056 0.21 21 -0.19 7 28
RAC1 0.031 0.012 -10000 0 -10000 0 0
mol:GTP 0.034 0.091 -10000 0 -0.21 37 37
RAC1-CDC42/GTP -0.006 0.064 -10000 0 -0.25 5 5
RASA1 0.032 0.025 -10000 0 -0.42 1 1
RAC1-CDC42/GDP 0.022 0.088 0.23 9 -0.26 5 14
ruffle organization 0.011 0.12 0.34 22 -0.33 2 24
NCK1 0.034 0.006 -10000 0 -10000 0 0
receptor internalization -0.021 0.061 0.18 7 -0.2 27 34
Ephrin B/EPHB2/KALRN 0.056 0.098 -10000 0 -0.22 35 35
ROCK1 0.02 0.021 0.19 4 -10000 0 4
RAS family/GDP -0.016 0.062 -10000 0 -0.21 20 20
Rac1/GTP -0.001 0.068 -10000 0 -0.2 29 29
Ephrin B/EPHB1/Src/Paxillin 0.015 0.066 -10000 0 -0.21 25 25
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.006 0.13 0.24 2 -0.44 20 22
PDGFB-D/PDGFRB/SLAP -0.007 0.12 -10000 0 -0.3 54 54
PDGFB-D/PDGFRB/APS/CBL 0.049 0.051 -10000 0 -0.24 7 7
AKT1 0.028 0.077 0.36 8 -10000 0 8
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.008 0.14 0.29 3 -0.47 22 25
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
FGR -0.034 0.2 0.33 1 -0.55 39 40
mol:Ca2+ -0.021 0.14 0.25 5 -0.52 21 26
MYC 0.016 0.14 0.4 10 -0.44 8 18
SHC1 0.032 0.011 -10000 0 -10000 0 0
HRAS/GDP 0.052 0.048 0.18 10 -0.21 1 11
LRP1/PDGFRB/PDGFB 0.059 0.028 -10000 0 -10000 0 0
GRB10 0.032 0.011 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GO:0007205 -0.021 0.15 0.25 5 -0.53 21 26
PTEN 0.03 0.012 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
GRB7 0.029 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.048 0.017 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.043 0.021 -10000 0 -10000 0 0
cell cycle arrest -0.007 0.12 -10000 0 -0.3 54 54
HRAS 0.034 0.006 -10000 0 -10000 0 0
HIF1A 0.018 0.074 0.31 10 -10000 0 10
GAB1 -0.037 0.15 0.29 4 -0.51 22 26
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.028 0.14 0.3 6 -0.45 21 27
PDGFB-D/PDGFRB 0.061 0.031 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.017 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.12 0.26 1 -0.39 19 20
positive regulation of MAPKKK cascade 0.048 0.017 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 -0.021 0.15 0.25 5 -0.54 21 26
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.034 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.041 0.022 -10000 0 -10000 0 0
SHB 0.028 0.035 -10000 0 -0.42 2 2
BLK -0.3 0.27 -10000 0 -0.5 226 226
PTPN2 0.035 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.018 -10000 0 -10000 0 0
BCAR1 0.034 0.007 -10000 0 -10000 0 0
VAV2 -0.037 0.16 0.31 5 -0.53 23 28
CBL 0.032 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.048 0.017 -10000 0 -10000 0 0
LCK -0.18 0.28 -10000 0 -0.52 139 139
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
ACP1 0.035 0.005 -10000 0 -10000 0 0
HCK -0.02 0.19 0.34 1 -0.58 30 31
ABL1 -0.059 0.16 0.25 5 -0.41 41 46
PDGFB-D/PDGFRB/CBL -0.053 0.17 -10000 0 -0.57 25 25
PTPN1 0.032 0.011 -10000 0 -10000 0 0
SNX15 0.034 0.007 -10000 0 -10000 0 0
STAT3 0.035 0.005 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
cell proliferation 0.017 0.14 0.38 11 -0.39 10 21
SLA -0.036 0.16 -10000 0 -0.42 54 54
actin cytoskeleton reorganization 0.047 0.059 0.32 5 -0.21 2 7
SRC 0.02 0.059 0.3 2 -0.26 1 3
PI3K 0.013 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.052 0.032 -10000 0 -10000 0 0
SH2B2 0.023 0.062 -10000 0 -0.42 7 7
PLCgamma1/SPHK1 -0.009 0.15 0.29 3 -0.49 22 25
LYN 0.001 0.14 0.3 2 -0.6 13 15
LRP1 0.034 0.007 -10000 0 -10000 0 0
SOS1 0.035 0.003 -10000 0 -10000 0 0
STAT5B 0.035 0.005 -10000 0 -10000 0 0
STAT5A 0.033 0.024 -10000 0 -0.42 1 1
NCK1-2/p130 Cas 0.087 0.048 -10000 0 -10000 0 0
SPHK1 0.03 0.042 -10000 0 -0.42 3 3
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.021 0.15 0.25 5 -0.54 21 26
PLCG1 -0.023 0.15 0.26 4 -0.55 21 25
NHERF/PDGFRB 0.063 0.024 -10000 0 -10000 0 0
YES1 0.016 0.094 0.32 2 -0.53 6 8
cell migration 0.062 0.024 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.079 0.052 -10000 0 -10000 0 0
SLC9A3R2 0.035 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.071 0.038 -10000 0 -10000 0 0
FYN -0.03 0.18 0.31 2 -0.48 43 45
DOK1 0.037 0.053 0.18 42 -10000 0 42
HRAS/GTP 0.025 0.004 -10000 0 -10000 0 0
PDGFB 0.033 0.009 -10000 0 -10000 0 0
RAC1 -0.013 0.16 0.33 8 -0.5 21 29
PRKCD 0.037 0.054 0.18 41 -10000 0 41
FER 0.036 0.053 0.18 40 -10000 0 40
MAPKKK cascade 0.029 0.089 0.32 15 -10000 0 15
RASA1 0.036 0.056 0.18 41 -0.24 1 42
NCK1 0.034 0.006 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.059 0.049 0.19 40 -10000 0 40
PDGFB-D/PDGFRB/SHB 0.041 0.033 -10000 0 -0.3 2 2
chemotaxis -0.057 0.15 0.24 6 -0.4 41 47
STAT1-3-5/STAT1-3-5 0.071 0.046 -10000 0 -0.21 3 3
Bovine Papilomavirus E5/PDGFRB 0.023 0.009 -10000 0 -10000 0 0
PTPRJ 0.034 0.006 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.018 0.09 0.29 4 -0.38 7 11
CRKL 0.046 0.09 0.26 16 -0.36 6 22
HRAS 0.014 0.11 0.24 2 -0.34 14 16
mol:PIP3 0.071 0.1 0.27 34 -0.33 7 41
SPRED1 0.033 0.008 -10000 0 -10000 0 0
SPRED2 0.035 0.003 -10000 0 -10000 0 0
GAB1 0.046 0.085 0.21 9 -0.37 6 15
FOXO3 0.065 0.11 0.32 12 -0.33 9 21
AKT1 0.069 0.11 0.34 10 -0.34 11 21
BAD 0.067 0.11 0.32 13 -0.32 10 23
megakaryocyte differentiation 0.031 0.084 0.21 8 -0.35 8 16
GSK3B 0.067 0.11 0.33 13 -0.32 11 24
RAF1 0.023 0.099 0.26 8 -0.29 14 22
SHC1 0.032 0.011 -10000 0 -10000 0 0
STAT3 0.043 0.084 0.21 8 -0.37 6 14
STAT1 0.032 0.16 -10000 0 -0.84 9 9
HRAS/SPRED1 0.032 0.1 0.25 4 -0.3 12 16
cell proliferation 0.038 0.083 0.21 8 -0.36 7 15
PIK3CA 0.035 0.006 -10000 0 -10000 0 0
TEC 0.023 0.07 -10000 0 -0.42 9 9
RPS6KB1 0.063 0.097 0.27 11 -0.36 7 18
HRAS/SPRED2 0.034 0.1 0.25 4 -0.29 13 17
LYN/TEC/p62DOK 0.075 0.098 0.28 1 -0.33 9 10
MAPK3 0.025 0.083 0.24 11 -0.25 5 16
STAP1 -0.066 0.12 0.2 1 -0.39 10 11
GRAP2 -0.015 0.14 -10000 0 -0.42 39 39
JAK2 0.039 0.14 -10000 0 -0.74 9 9
STAT1 (dimer) 0.033 0.16 -10000 0 -0.82 9 9
mol:Gleevec -0.003 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.04 0.11 -10000 0 -0.31 17 17
actin filament polymerization 0.042 0.095 0.33 10 -0.38 6 16
LYN 0.016 0.084 -10000 0 -0.42 13 13
STAP1/STAT5A (dimer) -0.072 0.14 0.33 1 -0.52 13 14
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.069 0.091 0.29 9 -0.32 7 16
PI3K 0.09 0.099 0.29 11 -0.35 7 18
PTEN 0.03 0.012 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.045 0.18 -10000 0 -1.1 7 7
MAPK8 0.038 0.084 0.21 8 -0.37 7 15
STAT3 (dimer) 0.043 0.083 0.21 8 -0.37 6 14
positive regulation of transcription 0.024 0.074 0.22 11 -0.21 4 15
mol:GDP 0.012 0.11 -10000 0 -0.34 18 18
PIK3C2B 0.047 0.1 0.32 17 -0.37 7 24
CBL/CRKL 0.058 0.09 0.28 10 -0.33 7 17
FER 0.042 0.089 0.25 9 -0.37 7 16
SH2B3 0.045 0.085 0.21 9 -0.37 6 15
PDPK1 0.068 0.1 0.27 32 -0.31 7 39
SNAI2 0.041 0.09 0.23 9 -0.37 7 16
positive regulation of cell proliferation 0.038 0.14 -10000 0 -0.65 9 9
KITLG 0.035 0.027 -10000 0 -0.42 1 1
cell motility 0.038 0.14 -10000 0 -0.65 9 9
PTPN6 -0.074 0.19 -10000 0 -0.41 88 88
EPOR 0.054 0.064 -10000 0 -0.52 1 1
STAT5A (dimer) 0.041 0.12 0.32 3 -0.61 7 10
SOCS1 0.011 0.1 -10000 0 -0.42 19 19
cell migration -0.027 0.09 0.39 7 -0.24 5 12
SOS1 0.035 0.003 -10000 0 -10000 0 0
EPO 0.028 0.015 -10000 0 -10000 0 0
VAV1 -0.052 0.18 -10000 0 -0.42 70 70
GRB10 0.038 0.087 0.26 5 -0.37 7 12
PTPN11 0.032 0.008 -10000 0 -10000 0 0
SCF/KIT 0.05 0.092 0.23 9 -0.38 7 16
GO:0007205 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 0.022 0.088 0.25 10 -0.26 8 18
CBL 0.032 0.011 -10000 0 -10000 0 0
KIT 0.021 0.19 -10000 0 -1.2 8 8
MAP2K2 0.02 0.087 0.24 11 -0.25 9 20
SHC/Grb2/SOS1 0.081 0.092 0.28 1 -0.35 7 8
STAT5A 0.04 0.13 0.32 3 -0.63 7 10
GRB2 0.034 0.007 -10000 0 -10000 0 0
response to radiation 0.042 0.09 0.24 10 -0.36 7 17
SHC/GRAP2 0.015 0.095 -10000 0 -0.3 30 30
PTPRO 0.031 0.085 0.21 8 -0.36 8 16
SH2B2 0.035 0.083 0.21 3 -0.38 6 9
DOK1 0.035 0.002 -10000 0 -10000 0 0
MATK 0.025 0.09 0.2 4 -0.4 7 11
CREBBP 0.05 0.024 -10000 0 -10000 0 0
BCL2 0.049 0.097 -10000 0 -0.81 2 2
Cellular roles of Anthrax toxin

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
ANTXR1 0.033 0.008 -10000 0 -10000 0 0
ANTXR2 0.032 0.034 -10000 0 -0.42 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.004 -10000 0 -0.057 2 2
monocyte activation -0.12 0.26 -10000 0 -0.5 104 104
MAP2K2 0.019 0.046 -10000 0 -0.6 2 2
MAP2K1 -0.002 0.004 -10000 0 -10000 0 0
MAP2K7 -0.002 0.003 -10000 0 -10000 0 0
MAP2K6 -0.006 0.027 -10000 0 -0.21 6 6
CYAA -0.005 0.015 -10000 0 -0.21 2 2
MAP2K4 -0.002 0.008 0.14 1 -10000 0 1
IL1B -0.035 0.095 0.11 2 -0.26 47 49
Channel 0.04 0.024 -10000 0 -0.22 2 2
NLRP1 -0.022 0.061 -10000 0 -0.21 35 35
CALM1 0.034 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.005 0.069 -10000 0 -0.38 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.004 0.057 2 -10000 0 2
MAPK3 -0.002 0.004 -10000 0 -10000 0 0
MAPK1 -0.002 0.008 0.14 1 -10000 0 1
PGR -0.002 0.008 0.14 1 -10000 0 1
PA/Cellular Receptors 0.042 0.027 -10000 0 -0.25 2 2
apoptosis -0.001 0.004 -10000 0 -0.057 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.039 0.023 -10000 0 -0.21 2 2
macrophage activation -0.003 0.007 0.13 1 -10000 0 1
TNF -0.054 0.18 -10000 0 -0.42 69 69
VCAM1 -0.12 0.26 -10000 0 -0.5 102 102
platelet activation 0.005 0.069 -10000 0 -0.38 11 11
MAPKKK cascade -0.002 0.017 -10000 0 -0.075 3 3
IL18 -0.049 0.11 0.11 2 -0.25 72 74
negative regulation of macrophage activation -0.001 0.004 -10000 0 -0.057 2 2
LEF -0.001 0.004 -10000 0 -0.057 2 2
CASP1 -0.011 0.054 -10000 0 -0.18 28 28
mol:cAMP 0.005 0.069 -10000 0 -0.39 11 11
necrosis -0.001 0.004 -10000 0 -0.057 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.039 0.023 -10000 0 -0.21 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
p75(NTR)-mediated 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
Sortilin/TRAF6 0.045 0.038 -10000 0 -0.3 4 4
Necdin/E2F1 0.04 0.053 -10000 0 -0.3 8 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.068 0.06 -10000 0 -0.22 8 8
NGF (dimer)/p75(NTR)/BEX1 0.038 0.049 -10000 0 -0.25 4 4
NT-4/5 (dimer)/p75(NTR) 0.025 0.041 -10000 0 -0.3 4 4
IKBKB 0.034 0.007 -10000 0 -10000 0 0
AKT1 0.023 0.055 0.2 19 -0.21 4 23
IKBKG 0.035 0.004 -10000 0 -10000 0 0
BDNF -0.075 0.19 -10000 0 -0.42 88 88
MGDIs/NGR/p75(NTR)/LINGO1 0.033 0.062 -10000 0 -0.28 8 8
FURIN 0.034 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.026 0.14 -10000 0 -0.26 92 92
LINGO1 0.028 0.027 -10000 0 -0.42 1 1
Sortilin/TRAF6/NRIF 0.037 0.036 -10000 0 -0.2 5 5
proBDNF (dimer) -0.075 0.19 -10000 0 -0.42 88 88
NTRK1 0.018 0.077 -10000 0 -0.42 11 11
RTN4R 0.026 0.048 -10000 0 -0.42 4 4
neuron apoptosis -0.025 0.14 0.33 6 -0.41 14 20
IRAK1 0.035 0.004 -10000 0 -10000 0 0
SHC1 0.011 0.031 -10000 0 -0.25 4 4
ARHGDIA 0.034 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.026 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.088 0.044 -10000 0 -0.2 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.065 0.055 -10000 0 -0.23 8 8
MAGEH1 0.035 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.056 0.07 -10000 0 -0.23 16 16
Mammalian IAPs/DIABLO -0.013 0.14 -10000 0 -0.23 108 108
proNGF (dimer) 0.031 0.011 -10000 0 -10000 0 0
MAGED1 0.035 0.003 -10000 0 -10000 0 0
APP 0.031 0.041 -10000 0 -0.42 3 3
NT-4/5 (dimer) 0.017 0.002 -10000 0 -10000 0 0
ZNF274 0.035 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.046 0.038 0.18 10 -0.21 4 14
NGF 0.031 0.011 -10000 0 -10000 0 0
cell cycle arrest -0.001 0.082 0.31 18 -0.2 8 26
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.029 0.032 -10000 0 -0.24 3 3
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.043 -10000 0 -0.26 4 4
NCSTN 0.032 0.011 -10000 0 -10000 0 0
mol:GTP 0.047 0.047 -10000 0 -0.25 4 4
PSENEN 0.035 0.004 -10000 0 -10000 0 0
mol:ceramide 0.012 0.048 0.19 9 -0.22 9 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.037 0.043 -10000 0 -0.29 2 2
p75(NTR)/beta APP 0.034 0.053 -10000 0 -0.3 7 7
BEX1 0.027 0.014 -10000 0 -10000 0 0
mol:GDP 0.001 0.027 -10000 0 -0.25 4 4
NGF (dimer) 0.048 0.055 -10000 0 -0.22 9 9
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.053 0.061 -10000 0 -0.25 8 8
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RAC1/GTP 0.038 0.041 -10000 0 -0.21 4 4
MYD88 0.034 0.024 -10000 0 -0.42 1 1
CHUK 0.032 0.01 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.048 0.047 -10000 0 -0.25 4 4
RHOB 0.035 0.005 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.047 0.016 -10000 0 -10000 0 0
NT3 (dimer) 0.028 0.012 -10000 0 -10000 0 0
TP53 -0.036 0.11 0.2 12 -0.21 83 95
PRDM4 0.014 0.048 0.19 10 -0.23 8 18
BDNF (dimer) -0.032 0.12 -10000 0 -0.23 92 92
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
SORT1 0.029 0.047 -10000 0 -0.42 4 4
activation of caspase activity 0.061 0.056 -10000 0 -0.22 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.064 0.055 -10000 0 -0.23 8 8
RHOC 0.034 0.007 -10000 0 -10000 0 0
XIAP 0.035 0.002 -10000 0 -10000 0 0
MAPK10 -0.014 0.11 0.32 10 -0.32 7 17
DIABLO 0.034 0.006 -10000 0 -10000 0 0
SMPD2 0.012 0.049 0.19 9 -0.22 9 18
APH1B 0.031 0.041 -10000 0 -0.42 3 3
APH1A 0.032 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.056 -10000 0 -0.25 8 8
PSEN1 0.035 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.05 0.011 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.031 0.044 -10000 0 -0.3 4 4
MAPK8 -0.011 0.11 0.33 10 -0.31 8 18
MAPK9 -0.01 0.11 0.33 10 -0.31 8 18
APAF1 0.034 0.006 -10000 0 -10000 0 0
NTF3 0.028 0.012 -10000 0 -10000 0 0
NTF4 0.017 0.002 -10000 0 -10000 0 0
NDN 0.022 0.074 -10000 0 -0.42 10 10
RAC1/GDP 0.023 0.009 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.072 0.044 -10000 0 -0.2 4 4
p75 CTF/Sortilin/TRAF6/NRIF 0.079 0.042 -10000 0 -0.23 4 4
RhoA-B-C/GTP 0.046 0.046 -10000 0 -0.25 4 4
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.008 0.14 -10000 0 -0.22 90 90
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.004 0.14 -10000 0 -0.23 91 91
PRKACB 0.035 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.033 0.15 -10000 0 -0.3 88 88
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.1 0.2 -10000 0 -0.42 108 108
BIRC2 0.029 0.042 -10000 0 -0.42 3 3
neuron projection morphogenesis -0.005 0.041 0.18 2 -0.22 8 10
BAD -0.015 0.11 0.32 11 -0.3 10 21
RIPK2 0.032 0.011 -10000 0 -10000 0 0
NGFR 0.024 0.048 -10000 0 -0.42 4 4
CYCS 0.015 0.057 0.25 11 -0.21 8 19
ADAM17 0.035 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.061 0.049 -10000 0 -0.23 4 4
BCL2L11 -0.016 0.11 0.32 11 -0.3 10 21
BDNF (dimer)/p75(NTR) -0.045 0.15 -10000 0 -0.3 90 90
PI3K 0.065 0.047 -10000 0 -0.22 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.063 0.056 -10000 0 -0.23 8 8
NDNL2 0.034 0.007 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
PRKCI 0.034 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.033 0.044 -10000 0 -0.3 4 4
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.065 0.055 -10000 0 -0.23 8 8
TRAF6 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
PLG 0.016 0.006 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.035 0.11 -10000 0 -0.22 89 89
SQSTM1 0.033 0.008 -10000 0 -10000 0 0
NGFRAP1 0.031 0.012 -10000 0 -10000 0 0
CASP3 -0.013 0.11 0.32 11 -0.29 10 21
E2F1 0.033 0.009 -10000 0 -10000 0 0
CASP9 0.035 0.005 -10000 0 -10000 0 0
IKK complex 0.055 0.075 -10000 0 -0.26 5 5
NGF (dimer)/TRKA 0.031 0.062 -10000 0 -0.3 11 11
MMP7 0.017 0.07 -10000 0 -0.42 9 9
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.076 0.058 -10000 0 -0.22 8 8
MMP3 0.014 0.016 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.034 0.093 -10000 0 -0.31 5 5
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.01 0.09 -10000 0 -0.22 39 39
SMAD6-7/SMURF1 0.061 0.026 -10000 0 -10000 0 0
NOG -0.1 0.2 -10000 0 -0.42 105 105
SMAD9 0.007 0.12 -10000 0 -0.45 22 22
SMAD4 0.035 0.005 -10000 0 -10000 0 0
SMAD5 0.023 0.07 -10000 0 -0.34 7 7
BMP7/USAG1 -0.11 0.16 -10000 0 -0.32 134 134
SMAD5/SKI 0.035 0.096 -10000 0 -0.37 10 10
SMAD1 0.043 0.043 -10000 0 -10000 0 0
BMP2 0.024 0.058 -10000 0 -0.42 6 6
SMAD1/SMAD1/SMAD4 0.048 0.052 -10000 0 -0.35 1 1
BMPR1A 0.032 0.01 -10000 0 -10000 0 0
BMPR1B 0.014 0.017 -10000 0 -10000 0 0
BMPR1A-1B/BAMBI 0.012 0.054 -10000 0 -0.25 7 7
AHSG 0.022 0.011 -10000 0 -10000 0 0
CER1 0.019 0.011 -10000 0 -10000 0 0
BMP2-4/CER1 0.038 0.059 -10000 0 -0.24 12 12
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.017 0.073 -10000 0 -0.32 8 8
BMP2-4 (homodimer) 0.033 0.066 -10000 0 -0.29 13 13
RGMB 0.031 0.011 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.042 0.034 -10000 0 -10000 0 0
RGMA 0.029 0.035 -10000 0 -0.42 2 2
SMURF1 0.032 0.01 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.01 0.055 -10000 0 -0.26 8 8
BMP2-4/USAG1 -0.075 0.15 -10000 0 -0.26 139 139
SMAD6/SMURF1/SMAD5 0.031 0.095 0.26 1 -0.37 10 11
SOSTDC1 -0.14 0.21 -10000 0 -0.42 133 133
BMP7/BMPR2/BMPR1A-1B 0.019 0.067 -10000 0 -0.23 19 19
SKI 0.034 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.03 0.012 -10000 0 -10000 0 0
HFE2 0.016 0.006 -10000 0 -10000 0 0
ZFYVE16 0.034 0.008 -10000 0 -10000 0 0
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
BMP2-4/CHRD 0.045 0.065 -10000 0 -0.25 13 13
SMAD5/SMAD5/SMAD4 0.037 0.097 0.26 1 -0.36 11 12
MAPK1 0.033 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.031 0.067 -10000 0 -0.24 8 8
BMP7 (homodimer) 0 0.099 -10000 0 -0.42 19 19
NUP214 0.033 0.009 -10000 0 -10000 0 0
BMP6/FETUA 0.033 0.021 -10000 0 -10000 0 0
SMAD1/SKI 0.056 0.059 -10000 0 -0.35 2 2
SMAD6 0.034 0.007 -10000 0 -10000 0 0
CTDSP2 0.034 0.007 -10000 0 -10000 0 0
BMP2-4/FETUA 0.039 0.063 -10000 0 -0.25 13 13
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.012 0.092 -10000 0 -0.42 16 16
BMPR2 (homodimer) 0.035 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.065 0.022 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.01 0.031 -10000 0 -10000 0 0
CHRDL1 -0.013 0.13 -10000 0 -0.42 36 36
ENDOFIN/SMAD1 0.056 0.059 -10000 0 -0.35 2 2
SMAD6-7/SMURF1/SMAD1 0.074 0.066 -10000 0 -0.41 1 1
SMAD6/SMURF1 0.032 0.01 -10000 0 -10000 0 0
BAMBI 0.023 0.062 -10000 0 -0.42 7 7
SMURF2 0.034 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 0.015 0.12 -10000 0 -0.28 43 43
BMP2-4/GREM1 0.032 0.09 -10000 0 -0.26 27 27
SMAD7 0.035 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.024 0.12 -10000 0 -0.41 24 24
SMAD1/SMAD6 0.051 0.06 -10000 0 -0.35 2 2
TAK1/SMAD6 0.043 0.02 -10000 0 -10000 0 0
BMP7 0 0.099 -10000 0 -0.42 19 19
BMP6 0.03 0.012 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.014 0.061 -10000 0 -0.3 6 6
PPM1A 0.035 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.057 0.061 -10000 0 -0.35 2 2
SMAD7/SMURF1 0.047 0.017 -10000 0 -10000 0 0
CTDSPL 0.035 0.005 -10000 0 -10000 0 0
PPP1CA 0.034 0.007 -10000 0 -10000 0 0
XIAP 0.035 0.002 -10000 0 -10000 0 0
CTDSP1 0.035 0.004 -10000 0 -10000 0 0
PPP1R15A 0.035 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.003 0.087 -10000 0 -0.26 26 26
CHRD 0.032 0.01 -10000 0 -10000 0 0
BMPR2 0.035 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.006 0.055 -10000 0 -0.25 11 11
BMP4 0.026 0.062 -10000 0 -0.42 7 7
FST 0.001 0.11 -10000 0 -0.42 24 24
BMP2-4/NOG -0.043 0.15 -10000 0 -0.26 113 113
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.029 0.068 -10000 0 -0.22 17 17
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.033 0.009 -10000 0 -10000 0 0
NFATC1 0.041 0.085 0.28 3 -0.35 5 8
NFATC2 0.009 0.083 0.17 3 -0.26 19 22
NFATC3 0.026 0.028 -10000 0 -0.33 2 2
YWHAE 0.033 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.09 0.17 0.19 1 -0.35 99 100
Exportin 1/Ran/NUP214 0.066 0.02 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.067 0.19 -10000 0 -0.36 92 92
BCL2/BAX 0.051 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
BAX 0.035 0.004 -10000 0 -10000 0 0
MAPK14 0.032 0.011 -10000 0 -10000 0 0
BAD 0.034 0.006 -10000 0 -10000 0 0
CABIN1/MEF2D -0.066 0.17 -10000 0 -0.32 94 94
Calcineurin A alpha-beta B1/BCL2 0.035 0.005 -10000 0 -10000 0 0
FKBP8 0.035 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.065 0.16 0.32 94 -10000 0 94
KPNB1 0.034 0.006 -10000 0 -10000 0 0
KPNA2 0.034 0.007 -10000 0 -10000 0 0
XPO1 0.035 0.002 -10000 0 -10000 0 0
SFN 0.027 0.015 -10000 0 -10000 0 0
MAP3K8 0.021 0.07 -10000 0 -0.42 9 9
NFAT4/CK1 alpha 0.041 0.03 0.18 3 -0.18 2 5
MEF2D/NFAT1/Cbp/p300 0.054 0.09 -10000 0 -0.28 10 10
CABIN1 -0.09 0.17 0.19 1 -0.35 99 100
CALM1 0.035 0.006 -10000 0 -10000 0 0
RAN 0.035 0.006 -10000 0 -10000 0 0
MAP3K1 0.034 0.007 -10000 0 -10000 0 0
CAMK4 -0.026 0.15 -10000 0 -0.42 48 48
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.035 0.004 -10000 0 -10000 0 0
YWHAH 0.034 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.005 0.13 -10000 0 -0.3 59 59
YWHAB 0.033 0.01 -10000 0 -10000 0 0
MAPK8 0.032 0.011 -10000 0 -10000 0 0
MAPK9 0.033 0.009 -10000 0 -10000 0 0
YWHAG 0.033 0.01 -10000 0 -10000 0 0
FKBP1A 0.033 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.059 0.099 0.25 4 -0.32 8 12
PRKCH 0.033 0.024 -10000 0 -0.42 1 1
CABIN1/Cbp/p300 0.048 0.017 -10000 0 -10000 0 0
CASP3 0.035 0.006 -10000 0 -10000 0 0
PIM1 0.031 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.023 0.006 -10000 0 -10000 0 0
apoptosis 0.024 0.021 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.039 0.037 -10000 0 -10000 0 0
PRKCB -0.097 0.21 -10000 0 -0.42 107 107
PRKCE 0.035 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.036 0.046 -10000 0 -0.3 2 2
BAD/BCL-XL 0.047 0.016 -10000 0 -10000 0 0
PRKCD 0.034 0.006 -10000 0 -10000 0 0
NUP214 0.033 0.009 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
PRKCA 0.032 0.025 -10000 0 -0.42 1 1
PRKCG 0.028 0.01 -10000 0 -10000 0 0
PRKCQ -0.088 0.2 -10000 0 -0.42 97 97
FKBP38/BCL2 0.051 0.008 -10000 0 -10000 0 0
EP300 0.032 0.011 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.058 0.084 0.28 3 -0.36 4 7
CaM/Ca2+/FKBP38 0.047 0.009 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSNK1A1 0.019 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.007 0.099 -10000 0 -0.25 48 48
NFATc/ERK1 0.059 0.086 0.28 3 -0.35 4 7
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.074 0.2 -10000 0 -0.36 106 106
NR4A1 0.047 0.09 0.23 15 -0.28 9 24
GSK3B 0.035 0.006 -10000 0 -10000 0 0
positive T cell selection 0.026 0.028 -10000 0 -0.33 2 2
NFAT1/CK1 alpha 0.014 0.059 -10000 0 -0.23 11 11
RCH1/ KPNB1 0.05 0.012 -10000 0 -10000 0 0
YWHAQ 0.035 0.004 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
AKAP5 -0.04 0.17 -10000 0 -0.42 60 60
MEF2D 0.032 0.011 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
NFATc/p38 alpha 0.046 0.082 0.28 2 -0.35 4 6
CREBBP 0.035 0.004 -10000 0 -10000 0 0
BCL2 0.035 0.005 -10000 0 -10000 0 0
LPA4-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
ADCY4 0.002 0.026 -10000 0 -0.25 4 4
ADCY5 -0.047 0.1 -10000 0 -0.25 74 74
ADCY6 0.005 0.002 -10000 0 -10000 0 0
ADCY7 0.004 0.013 -10000 0 -0.25 1 1
ADCY1 -0.031 0.088 -10000 0 -0.25 51 51
ADCY2 -0.003 0.008 -10000 0 -10000 0 0
ADCY3 0.005 0.001 -10000 0 -10000 0 0
ADCY8 -0.003 0.007 -10000 0 -10000 0 0
PRKCE 0.01 0.001 -10000 0 -10000 0 0
ADCY9 0.005 0.001 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.006 0.065 0.2 15 -0.17 1 16
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.035 0.004 -10000 0 -10000 0 0
SPHK1 0.03 0.041 -10000 0 -0.42 3 3
GNAI2 0.035 0.005 -10000 0 -10000 0 0
mol:S1P 0.018 0.028 -10000 0 -0.24 4 4
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
mol:Sphinganine-1-P 0.016 0.029 -10000 0 -0.3 3 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.066 0.046 -10000 0 -0.18 4 4
GNAI3 0.034 0.007 -10000 0 -10000 0 0
G12/G13 0.045 0.018 -10000 0 -10000 0 0
S1PR3 0.029 0.042 -10000 0 -0.42 3 3
S1PR2 0.035 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.01 0.028 -10000 0 -0.2 4 4
S1PR5 0.034 0.008 -10000 0 -10000 0 0
S1PR4 -0.11 0.21 -10000 0 -0.42 118 118
GNAI1 0.031 0.012 -10000 0 -10000 0 0
S1P/S1P5/G12 0.048 0.042 -10000 0 -0.19 4 4
S1P/S1P3/Gq -0.028 0.15 -10000 0 -0.29 80 80
S1P/S1P4/Gi -0.029 0.12 0.2 1 -0.25 47 48
GNAQ 0.033 0.009 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
GNA11 0.035 0.004 -10000 0 -10000 0 0
ABCC1 0.034 0.024 -10000 0 -0.42 1 1
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.033 0.01 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.006 0.068 -10000 0 -0.21 22 22
NT3 (dimer)/TRKC 0.018 0.088 -10000 0 -0.3 25 25
NT3 (dimer)/TRKB 0.034 0.057 -10000 0 -0.24 8 8
SHC/Grb2/SOS1/GAB1/PI3K 0.035 0.018 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
BDNF -0.075 0.19 -10000 0 -0.42 88 88
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
DYNLT1 0.031 0.011 -10000 0 -10000 0 0
NTRK1 0.018 0.077 -10000 0 -0.42 11 11
NTRK2 0.024 0.048 -10000 0 -0.42 4 4
NTRK3 0.002 0.11 -10000 0 -0.42 25 25
NT-4/5 (dimer)/TRKB 0.03 0.054 -10000 0 -0.25 8 8
neuron apoptosis 0.029 0.12 0.35 18 -10000 0 18
SHC 2-3/Grb2 -0.032 0.13 -10000 0 -0.38 18 18
SHC1 0.032 0.011 -10000 0 -10000 0 0
SHC2 -0.037 0.11 -10000 0 -0.4 16 16
SHC3 -0.044 0.13 -10000 0 -0.42 26 26
STAT3 (dimer) 0.042 0.013 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.033 0.07 -10000 0 -0.26 14 14
RIN/GDP 0.043 0.091 0.27 15 -0.23 9 24
GIPC1 0.035 0.003 -10000 0 -10000 0 0
KRAS 0.034 0.006 -10000 0 -10000 0 0
DNAJA3 -0.002 0.056 -10000 0 -0.24 14 14
RIN/GTP 0.013 0.002 -10000 0 -10000 0 0
CCND1 0.025 0.011 -10000 0 -10000 0 0
MAGED1 0.035 0.003 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.017 0.002 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.061 0.026 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.018 0.11 -10000 0 -0.27 42 42
TRKA/NEDD4-2 0.033 0.067 -10000 0 -0.29 14 14
ELMO1 0.014 0.087 -10000 0 -0.42 14 14
RhoG/GTP/ELMO1/DOCK1 0.028 0.057 -10000 0 -0.24 14 14
NGF 0.031 0.011 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
DOCK1 0.032 0.01 -10000 0 -10000 0 0
GAB2 0.033 0.009 -10000 0 -10000 0 0
RIT2 0.017 0.003 -10000 0 -10000 0 0
RIT1 0.032 0.011 -10000 0 -10000 0 0
FRS2 0.034 0.008 -10000 0 -10000 0 0
DNM1 0.029 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.017 0.074 -10000 0 -0.23 18 18
mol:GDP 0.048 0.12 0.33 16 -0.33 11 27
NGF (dimer) 0.031 0.011 -10000 0 -10000 0 0
RhoG/GDP 0.011 0.061 -10000 0 -0.29 14 14
RIT1/GDP 0.035 0.079 0.24 7 -0.23 9 16
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.024 0.13 -10000 0 -0.25 91 91
KIDINS220/CRKL/C3G 0.045 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.044 0.026 -10000 0 -0.3 1 1
FRS2 family/SHP2 0.06 0.027 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.076 0.034 -10000 0 -10000 0 0
RIT1/GTP 0.024 0.008 -10000 0 -10000 0 0
NT3 (dimer) 0.028 0.012 -10000 0 -10000 0 0
RAP1/GDP 0.032 0.066 0.16 5 -0.2 7 12
KIDINS220/CRKL 0.033 0.01 -10000 0 -10000 0 0
BDNF (dimer) -0.075 0.19 -10000 0 -0.42 88 88
ubiquitin-dependent protein catabolic process 0.044 0.065 -10000 0 -0.25 14 14
Schwann cell development -0.014 0.022 -10000 0 -10000 0 0
EHD4 0.034 0.008 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.074 0.036 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.031 0.044 -10000 0 -0.25 1 1
RAP1B 0.034 0.007 -10000 0 -10000 0 0
RAP1A 0.034 0.007 -10000 0 -10000 0 0
CDC42/GTP -0.025 0.12 -10000 0 -0.22 96 96
ABL1 0.033 0.009 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
Rap1/GTP 0.011 0.085 -10000 0 -0.36 7 7
STAT3 0.042 0.013 -10000 0 -10000 0 0
axon guidance -0.034 0.11 -10000 0 -0.21 96 96
MAPK3 0.002 0.1 0.19 29 -0.25 42 71
MAPK1 0.001 0.098 0.19 27 -0.24 42 69
CDC42/GDP 0.051 0.092 0.26 18 -0.23 9 27
NTF3 0.028 0.012 -10000 0 -10000 0 0
NTF4 0.017 0.002 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.044 0.066 -10000 0 -0.25 14 14
PI3K 0.049 0.014 -10000 0 -10000 0 0
FRS3 0.032 0.011 -10000 0 -10000 0 0
FAIM 0.031 0.041 -10000 0 -0.42 3 3
GAB1 0.035 0.004 -10000 0 -10000 0 0
RASGRF1 -0.013 0.075 -10000 0 -0.26 13 13
SOS1 0.035 0.003 -10000 0 -10000 0 0
MCF2L -0.009 0.065 -10000 0 -0.25 23 23
RGS19 0.032 0.01 -10000 0 -10000 0 0
CDC42 0.035 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.068 0.088 0.31 8 -0.4 5 13
Rac1/GDP 0.041 0.086 0.25 13 -0.24 8 21
NGF (dimer)/TRKA/GRIT 0.029 0.053 -10000 0 -0.25 11 11
neuron projection morphogenesis 0.02 0.14 -10000 0 -0.8 9 9
NGF (dimer)/TRKA/NEDD4-2 0.045 0.065 -10000 0 -0.25 14 14
MAP2K1 0.043 0.061 0.2 46 -10000 0 46
NGFR 0.024 0.048 -10000 0 -0.42 4 4
NGF (dimer)/TRKA/GIPC/GAIP 0.02 0.054 -10000 0 -0.27 9 9
RAS family/GTP/PI3K 0.032 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.084 0.043 -10000 0 -10000 0 0
NRAS 0.034 0.008 -10000 0 -10000 0 0
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
PRKCI 0.034 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
MAPKKK cascade -0.012 0.14 -10000 0 -0.54 23 23
RASA1 0.032 0.025 -10000 0 -0.42 1 1
TRKA/c-Abl 0.034 0.06 -10000 0 -0.29 11 11
SQSTM1 0.033 0.008 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.003 0.13 -10000 0 -0.23 89 89
NGF (dimer)/TRKA/p62/Atypical PKCs 0.07 0.067 -10000 0 -0.21 12 12
MATK -0.018 0.15 -10000 0 -0.42 43 43
NEDD4L 0.031 0.041 -10000 0 -0.42 3 3
RAS family/GDP -0.011 0.036 -10000 0 -0.17 9 9
NGF (dimer)/TRKA 0.004 0.058 -10000 0 -0.25 15 15
Rac1/GTP -0.009 0.067 -10000 0 -0.24 16 16
FRS2 family/SHP2/CRK family 0.079 0.046 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.003 0.11 -10000 0 -0.42 23 23
GNB1/GNG2 0.044 0.085 -10000 0 -0.25 17 17
mol:DAG 0.02 0.072 0.19 5 -0.24 15 20
PLCG1 0.02 0.073 0.19 5 -0.25 15 20
YES1 0.003 0.063 -10000 0 -0.23 19 19
FZD3 0.033 0.009 -10000 0 -10000 0 0
FZD6 0.014 0.087 -10000 0 -0.42 14 14
G protein 0.052 0.089 0.24 10 -0.26 12 22
MAP3K7 0.003 0.059 0.18 4 -0.26 7 11
mol:Ca2+ 0.02 0.07 0.18 5 -0.24 15 20
mol:IP3 0.02 0.072 0.19 5 -0.24 15 20
NLK -0.001 0.13 -10000 0 -0.75 10 10
GNB1 0.034 0.007 -10000 0 -10000 0 0
CAMK2A 0.008 0.066 0.19 5 -0.25 10 15
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.007 0.064 -10000 0 -0.25 19 19
CSNK1A1 0.033 0.009 -10000 0 -10000 0 0
GNAS 0.004 0.06 -10000 0 -0.24 16 16
GO:0007205 0.012 0.071 0.21 6 -0.27 9 15
WNT6 0.033 0.008 -10000 0 -10000 0 0
WNT4 0.021 0.017 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.031 0.093 0.27 8 -0.3 9 17
GNG2 0.027 0.058 -10000 0 -0.42 6 6
WNT5A 0.024 0.066 -10000 0 -0.42 8 8
WNT11 0.023 0.017 -10000 0 -10000 0 0
CDC42 0.004 0.064 0.2 3 -0.24 15 18
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.025 0.051 -10000 0 -0.24 12 12
EPHB2 0.016 0.09 -10000 0 -0.42 15 15
Syndecan-2/TACI -0.08 0.13 -10000 0 -0.24 143 143
LAMA1 0.006 0.013 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.053 0.061 -10000 0 -0.24 10 10
HRAS 0.034 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.01 0.019 -10000 0 -0.24 2 2
ITGA5 0.034 0.006 -10000 0 -10000 0 0
BAX 0.01 0.017 -10000 0 -10000 0 0
EPB41 0.034 0.024 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion 0.03 0.022 -10000 0 -0.22 2 2
LAMA3 0.02 0.081 -10000 0 -0.42 12 12
EZR 0.028 0.042 -10000 0 -0.42 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.032 0.011 -10000 0 -10000 0 0
Syndecan-2/MMP2 0.026 0.033 -10000 0 -0.24 4 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.044 0.026 -10000 0 -0.3 1 1
dendrite morphogenesis 0.021 0.058 -10000 0 -0.24 16 16
Syndecan-2/GM-CSF 0.027 0.028 -10000 0 -0.24 3 3
determination of left/right symmetry 0.014 0.023 -10000 0 -0.29 2 2
Syndecan-2/PKC delta 0.032 0.024 -10000 0 -0.24 2 2
GNB2L1 0.033 0.008 -10000 0 -10000 0 0
MAPK3 0.032 0.056 0.19 33 -0.22 3 36
MAPK1 0.03 0.054 0.19 30 -0.22 3 33
Syndecan-2/RACK1 0.046 0.028 -10000 0 -0.2 2 2
NF1 0.034 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.014 0.023 -10000 0 -0.29 2 2
ITGA2 0.032 0.025 -10000 0 -0.42 1 1
MAPK8 0.013 0.02 -10000 0 -0.24 2 2
Syndecan-2/alpha2/beta1 Integrin 0.021 0.029 -10000 0 -0.21 2 2
Syndecan-2/Kininogen 0.023 0.024 -10000 0 -0.24 2 2
ITGB1 0.032 0.011 -10000 0 -10000 0 0
SRC 0.034 0.051 0.19 32 -0.2 2 34
Syndecan-2/CASK/Protein 4.1 0.029 0.025 -10000 0 -0.22 3 3
extracellular matrix organization 0.032 0.028 -10000 0 -0.24 3 3
actin cytoskeleton reorganization 0.025 0.051 -10000 0 -0.24 12 12
Syndecan-2/Caveolin-2/Ras 0.045 0.031 -10000 0 -0.22 2 2
Syndecan-2/Laminin alpha3 0.025 0.056 -10000 0 -0.29 10 10
Syndecan-2/RasGAP 0.058 0.037 -10000 0 -0.2 3 3
alpha5/beta1 Integrin 0.046 0.018 -10000 0 -10000 0 0
PRKCD 0.034 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.058 -10000 0 -0.24 16 16
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 0.041 0.034 0.2 4 -0.19 3 7
RHOA 0.035 0.005 -10000 0 -10000 0 0
SDCBP 0.032 0.01 -10000 0 -10000 0 0
TNFRSF13B -0.17 0.22 -10000 0 -0.42 164 164
RASA1 0.032 0.025 -10000 0 -0.42 1 1
alpha2/beta1 Integrin 0.044 0.026 -10000 0 -0.3 1 1
Syndecan-2/Synbindin 0.03 0.025 -10000 0 -0.24 2 2
TGFB1 0.033 0.034 -10000 0 -0.42 2 2
CASP3 0.037 0.056 0.2 36 -0.22 2 38
FN1 0.021 0.077 -10000 0 -0.42 11 11
Syndecan-2/IL8 0.022 0.036 -10000 0 -0.24 5 5
SDC2 0.014 0.023 -10000 0 -0.29 2 2
KNG1 0.021 0.01 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.032 0.024 -10000 0 -0.24 2 2
TRAPPC4 0.032 0.011 -10000 0 -10000 0 0
CSF2 0.026 0.026 -10000 0 -0.42 1 1
Syndecan-2/TGFB1 0.032 0.028 -10000 0 -0.24 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.03 0.022 -10000 0 -0.22 2 2
Syndecan-2/Ezrin 0.043 0.039 -10000 0 -0.22 5 5
PRKACA 0.037 0.055 0.2 34 -0.22 2 36
angiogenesis 0.022 0.036 -10000 0 -0.24 5 5
MMP2 0.027 0.036 -10000 0 -0.42 2 2
IL8 0.022 0.043 -10000 0 -0.42 3 3
calcineurin-NFAT signaling pathway -0.079 0.13 -10000 0 -0.24 143 143
IL1-mediated signaling events

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
UBC13/UEV1A 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0.032 0.034 -10000 0 -0.42 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.034 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.01 0.076 -10000 0 -0.34 8 8
IRAK/TOLLIP 0.04 0.01 -10000 0 -10000 0 0
IKBKB 0.034 0.007 -10000 0 -10000 0 0
IKBKG 0.035 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.003 0.12 -10000 0 -0.3 53 53
IL1A 0.03 0.01 -10000 0 -10000 0 0
IL1B -0.018 0.1 -10000 0 -0.32 37 37
IRAK/TRAF6/p62/Atypical PKCs 0.077 0.039 -10000 0 -0.2 2 2
IL1R2 -0.03 0.16 -10000 0 -0.42 53 53
IL1R1 0.033 0.033 -10000 0 -0.42 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.084 -10000 0 -0.36 11 11
TOLLIP 0.034 0.006 -10000 0 -10000 0 0
TICAM2 0.028 0.048 -10000 0 -0.42 4 4
MAP3K3 0.034 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.037 0.064 -10000 0 -0.3 1 1
JUN -0.008 0.025 0.15 2 -0.18 5 7
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.046 0.11 -10000 0 -0.23 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88 0.077 0.037 -10000 0 -0.23 3 3
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.09 0.04 -10000 0 -0.2 3 3
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.1 -10000 0 -0.25 43 43
NFKB1 0.034 0.006 -10000 0 -10000 0 0
MAPK8 0.007 0.026 0.17 2 -0.19 5 7
IRAK1 0.02 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.041 0.06 -10000 0 -0.3 11 11
IRAK4 0.034 0.006 -10000 0 -10000 0 0
PRKCI 0.034 0.006 -10000 0 -10000 0 0
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.082 -10000 0 -0.31 12 12
CHUK 0.032 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.1 -10000 0 -0.25 43 43
IL1 beta/IL1R2 -0.032 0.15 -10000 0 -0.3 82 82
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.032 0.095 -10000 0 -0.22 33 33
IRAK3 0.028 0.053 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.042 0.11 -10000 0 -0.24 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.035 0.032 -10000 0 -0.28 3 3
IL1 alpha/IL1R1/IL1RAP 0.057 0.036 -10000 0 -0.25 2 2
RELA 0.034 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.033 0.008 -10000 0 -10000 0 0
MYD88 0.034 0.024 -10000 0 -0.42 1 1
IRAK/TRAF6/MEKK3 0.057 0.018 -10000 0 -10000 0 0
IL1RAP 0.032 0.01 -10000 0 -10000 0 0
UBE2N 0.035 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 0.014 0.088 -10000 0 -0.22 35 35
CASP1 0.015 0.087 -10000 0 -0.42 14 14
IL1RN/IL1R2 -0.007 0.13 -10000 0 -0.3 60 60
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.033 0.11 -10000 0 -0.24 43 43
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.033 0.061 -10000 0 -0.36 7 7
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
IL1RN 0.024 0.07 -10000 0 -0.42 9 9
TRAF6/TAK1/TAB1/TAB2 0.045 0.018 -10000 0 -10000 0 0
MAP2K6 0.018 0.032 0.18 3 -0.2 6 9
Ephrin B reverse signaling

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
EFNB2 0.033 0.009 -10000 0 -10000 0 0
EPHB2 0.015 0.091 -10000 0 -0.42 15 15
EFNB1 0.013 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.039 0.097 -10000 0 -0.24 30 30
Ephrin B2/EPHB1-2 0.038 0.075 -10000 0 -0.25 20 20
neuron projection morphogenesis 0.021 0.085 -10000 0 -0.23 30 30
Ephrin B1/EPHB1-2/Tiam1 0.033 0.1 -10000 0 -0.25 35 35
DNM1 0.029 0.013 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.014 0.087 -10000 0 -0.5 11 11
YES1 -0.003 0.13 -10000 0 -0.75 11 11
Ephrin B1/EPHB1-2/NCK2 0.048 0.075 -10000 0 -0.24 19 19
PI3K 0.03 0.1 -10000 0 -0.52 11 11
mol:GDP 0.031 0.1 -10000 0 -0.25 36 36
ITGA2B 0.031 0.012 -10000 0 -10000 0 0
endothelial cell proliferation 0.039 0.018 -10000 0 -10000 0 0
FYN -0.015 0.14 -10000 0 -0.75 11 11
MAP3K7 -0.014 0.096 0.2 1 -0.54 11 12
FGR -0.017 0.14 -10000 0 -0.76 11 11
TIAM1 0.008 0.1 -10000 0 -0.42 21 21
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RGS3 0.033 0.009 -10000 0 -10000 0 0
cell adhesion 0.004 0.11 -10000 0 -0.49 12 12
LYN -0.008 0.13 -10000 0 -0.73 11 11
Ephrin B1/EPHB1-2/Src Family Kinases -0.012 0.12 -10000 0 -0.69 11 11
Ephrin B1/EPHB1-2 -0.016 0.1 -10000 0 -0.59 11 11
SRC -0.002 0.13 -10000 0 -0.73 11 11
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
EPHB1 0.023 0.063 -10000 0 -0.42 7 7
EPHB4 0.032 0.01 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.04 0.018 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.023 0.077 -10000 0 -0.3 18 18
BLK -0.1 0.15 -10000 0 -0.79 11 11
HCK -0.015 0.14 -10000 0 -0.74 11 11
regulation of stress fiber formation -0.046 0.074 0.24 19 -10000 0 19
MAPK8 -0.013 0.083 -10000 0 -0.47 11 11
Ephrin B1/EPHB1-2/RGS3 0.048 0.075 -10000 0 -0.24 19 19
endothelial cell migration 0 0.09 0.19 7 -0.46 9 16
NCK2 0.035 0.004 -10000 0 -10000 0 0
PTPN13 0.036 0.053 -10000 0 -0.54 3 3
regulation of focal adhesion formation -0.046 0.074 0.24 19 -10000 0 19
chemotaxis -0.046 0.073 0.24 19 -10000 0 19
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.031 0.091 -10000 0 -0.24 30 30
angiogenesis -0.015 0.1 -10000 0 -0.58 11 11
LCK -0.064 0.15 -10000 0 -0.78 11 11
ErbB2/ErbB3 signaling events

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
USP8 -0.004 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.052 0.084 -10000 0 -0.24 9 9
NFATC4 -0.013 0.051 0.24 2 -0.19 10 12
ERBB2IP 0.034 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.033 0.024 -10000 0 -0.42 1 1
mammary gland morphogenesis 0.023 0.066 -10000 0 -0.23 17 17
JUN 0.037 0.066 0.24 4 -10000 0 4
HRAS 0.034 0.006 -10000 0 -10000 0 0
DOCK7 -0.003 0.059 0.17 1 -0.22 17 18
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.039 0.067 -10000 0 -0.23 16 16
AKT1 0.009 0.005 -10000 0 -10000 0 0
BAD 0.001 0.006 -10000 0 -10000 0 0
MAPK10 -0.001 0.051 0.2 7 -10000 0 7
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.026 0.071 -10000 0 -0.24 17 17
RAF1 0.031 0.094 0.29 8 -0.26 9 17
ErbB2/ErbB3/neuregulin 2 0.029 0.063 -10000 0 -0.25 16 16
STAT3 0.02 0.13 -10000 0 -0.83 8 8
cell migration 0.013 0.062 0.22 14 -0.16 1 15
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.001 0.24 0.38 2 -0.58 48 50
FOS 0.023 0.15 0.32 2 -0.33 47 49
NRAS 0.034 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.066 -10000 0 -0.23 17 17
MAPK3 0.009 0.19 0.38 2 -0.46 44 46
MAPK1 0.004 0.2 0.38 2 -0.47 45 47
JAK2 -0.008 0.059 -10000 0 -0.22 17 17
NF2 0.016 0.008 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.011 0.057 -10000 0 -0.23 16 16
NRG1 0.025 0.043 -10000 0 -0.42 3 3
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
MAPK8 0.018 0.069 0.22 3 -0.25 13 16
MAPK9 0.003 0.055 0.2 10 -10000 0 10
ERBB2 -0.023 0.007 -10000 0 -10000 0 0
ERBB3 0.017 0.087 -10000 0 -0.42 14 14
SHC1 0.032 0.011 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
apoptosis -0.002 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.13 -10000 0 -0.81 8 8
RNF41 -0.006 0.005 -10000 0 -10000 0 0
FRAP1 -0.002 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.005 0.04 -10000 0 -0.17 13 13
ErbB2/ErbB2/HSP90 (dimer) 0.017 0.018 -10000 0 -10000 0 0
CHRNA1 -0.015 0.25 0.36 2 -0.63 48 50
myelination -0.012 0.054 0.24 3 -0.19 1 4
PPP3CB -0.003 0.055 -10000 0 -0.21 17 17
KRAS 0.034 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.049 0.067 -10000 0 -0.21 13 13
NRG2 0.029 0.042 -10000 0 -0.42 3 3
mol:GDP 0.011 0.057 -10000 0 -0.23 16 16
SOS1 0.035 0.003 -10000 0 -10000 0 0
MAP2K2 0.016 0.1 0.29 7 -0.3 8 15
SRC 0.033 0.01 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.003 0.059 0.17 1 -0.22 17 18
MAP2K1 0.017 0.17 -10000 0 -0.56 9 9
heart morphogenesis 0.023 0.066 -10000 0 -0.23 17 17
RAS family/GDP 0.06 0.081 -10000 0 -0.21 14 14
GRB2 0.034 0.007 -10000 0 -10000 0 0
PRKACA 0.021 0.007 -10000 0 -10000 0 0
CHRNE 0.016 0.019 0.12 1 -10000 0 1
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
activation of caspase activity -0.009 0.005 -10000 0 -10000 0 0
nervous system development 0.023 0.066 -10000 0 -0.23 17 17
CDC42 0.035 0.005 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.029 0.024 -10000 0 -0.42 1 1
AES 0.031 0.005 -10000 0 -10000 0 0
FBXW11 0.033 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.046 0.018 -10000 0 -10000 0 0
SMAD4 0.035 0.005 -10000 0 -10000 0 0
DKK2 0.029 0.042 -10000 0 -0.42 3 3
TLE1 0.028 0.025 -10000 0 -0.42 1 1
MACF1 0.035 0.005 -10000 0 -10000 0 0
CTNNB1 0.013 0.092 0.33 2 -0.36 7 9
WIF1 0.019 0.016 -10000 0 -10000 0 0
beta catenin/RanBP3 -0.003 0.077 0.36 1 -0.34 5 6
KREMEN2 -0.027 0.16 -10000 0 -0.42 50 50
DKK1 -0.023 0.14 -10000 0 -0.42 42 42
beta catenin/beta TrCP1 0.03 0.09 0.42 1 -0.32 7 8
FZD1 0.032 0.011 -10000 0 -10000 0 0
AXIN2 0.018 0.12 0.56 10 -1.4 1 11
AXIN1 0.035 0.003 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.029 0.091 -10000 0 -0.52 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.03 0.11 0.25 1 -0.47 8 9
Axin1/APC/GSK3 0.029 0.063 0.27 4 -0.28 4 8
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.1 0.37 3 -0.37 7 10
HNF1A 0.031 0.006 -10000 0 -10000 0 0
CTBP1 0.03 0.008 -10000 0 -10000 0 0
MYC 0.075 0.19 0.59 35 -10000 0 35
RANBP3 0.035 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.018 0.11 -10000 0 -0.25 52 52
NKD1 0.025 0.058 -10000 0 -0.42 6 6
TCF4 0.027 0.041 -10000 0 -0.42 3 3
TCF3 0.031 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.057 0.08 -10000 0 -0.23 23 23
Ran/GTP 0.025 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.01 0.084 0.43 1 -0.6 2 3
LEF1 0.016 0.081 -10000 0 -0.42 12 12
DVL1 0.02 0.055 -10000 0 -0.41 3 3
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.04 0.12 0.27 1 -0.52 8 9
DKK1/LRP6/Kremen 2 -0.017 0.14 -10000 0 -0.27 79 79
LRP6 0.035 0.006 -10000 0 -10000 0 0
CSNK1A1 0.029 0.009 -10000 0 -10000 0 0
NLK 0.035 0.007 -10000 0 -10000 0 0
CCND1 0.039 0.14 0.57 20 -10000 0 20
WNT1 -0.002 0.12 -10000 0 -0.42 28 28
GSK3A 0.035 0.004 -10000 0 -10000 0 0
GSK3B 0.034 0.006 -10000 0 -10000 0 0
FRAT1 0.031 0.026 -10000 0 -0.42 1 1
PPP2R5D 0.025 0.042 0.25 5 -0.25 1 6
APC 0.02 0.082 0.21 31 -0.21 22 53
WNT1/LRP6/FZD1 0.013 0.063 -10000 0 -0.2 21 21
CREBBP 0.031 0.005 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.006 -9999 0 -10000 0 0
EGFR 0.027 0.035 -9999 0 -0.42 2 2
EGF/EGFR 0.028 0.073 -9999 0 -0.2 27 27
EGF/EGFR dimer/SHC/GRB2/SOS1 0.055 0.083 -9999 0 -0.21 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.033 0.009 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.001 0.11 -9999 0 -0.42 25 25
EGF/EGFR dimer/SHC 0.028 0.081 -9999 0 -0.25 24 24
mol:GDP 0.049 0.079 -9999 0 -0.21 23 23
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.027 0.042 -9999 0 -0.42 3 3
GRB2/SOS1 0.05 0.011 -9999 0 -10000 0 0
HRAS/GTP 0.032 0.067 -9999 0 -0.2 23 23
SHC1 0.032 0.011 -9999 0 -10000 0 0
HRAS/GDP 0.049 0.077 -9999 0 -0.2 23 23
FRAP1 -0.02 0.048 -9999 0 -0.2 23 23
EGF/EGFR dimer 0.015 0.089 -9999 0 -0.3 26 26
SOS1 0.035 0.003 -9999 0 -10000 0 0
GRB2 0.034 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.039 0.038 -9999 0 -0.3 3 3
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.026 0.11 -10000 0 -0.37 24 24
HDAC1 0.03 0.024 -10000 0 -0.42 1 1
AES 0.034 0.004 -10000 0 -10000 0 0
FBXW11 0.033 0.008 -10000 0 -10000 0 0
DTX1 -0.067 0.19 -10000 0 -0.42 82 82
LRP6/FZD1 0.046 0.017 -10000 0 -10000 0 0
TLE1 0.031 0.025 -10000 0 -0.42 1 1
AP1 0.019 0.037 -10000 0 -0.22 6 6
NCSTN 0.032 0.011 -10000 0 -10000 0 0
ADAM10 0.034 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.053 -10000 0 -0.55 2 2
NICD/RBPSUH 0.033 0.11 -10000 0 -0.38 23 23
WIF1 0.022 0.012 -10000 0 -10000 0 0
NOTCH1 0.008 0.11 -10000 0 -0.4 23 23
PSENEN 0.035 0.004 -10000 0 -10000 0 0
KREMEN2 -0.027 0.16 -10000 0 -0.42 50 50
DKK1 -0.023 0.14 -10000 0 -0.42 42 42
beta catenin/beta TrCP1 0.058 0.058 0.29 5 -10000 0 5
APH1B 0.031 0.041 -10000 0 -0.42 3 3
APH1A 0.032 0.011 -10000 0 -10000 0 0
AXIN1 0.012 0.054 0.3 2 -0.32 1 3
CtBP/CBP/TCF1/TLE1/AES 0.017 0.04 -10000 0 -0.21 2 2
PSEN1 0.035 0.005 -10000 0 -10000 0 0
FOS 0.033 0.008 -10000 0 -10000 0 0
JUN 0.031 0.011 -10000 0 -10000 0 0
MAP3K7 0.03 0.01 -10000 0 -10000 0 0
CTNNB1 0.04 0.062 0.29 5 -10000 0 5
MAPK3 0.035 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.019 0.11 -10000 0 -0.25 52 52
HNF1A 0.034 0.006 -10000 0 -10000 0 0
CTBP1 0.033 0.007 -10000 0 -10000 0 0
MYC 0.031 0.019 -10000 0 -10000 0 0
NKD1 0.024 0.058 -10000 0 -0.42 6 6
FZD1 0.032 0.01 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.013 0.15 -10000 0 -0.44 26 26
apoptosis 0.019 0.037 -10000 0 -0.22 6 6
Delta 1/NOTCHprecursor 0.029 0.11 -10000 0 -0.37 24 24
DLL1 0.029 0.035 -10000 0 -0.42 2 2
PPARD 0.029 0.041 -10000 0 -0.67 1 1
Gamma Secretase 0.088 0.044 -10000 0 -0.2 2 2
APC -0.001 0.099 0.3 2 -0.45 11 13
DVL1 0.026 0.046 -10000 0 -0.38 3 3
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.017 0.14 -10000 0 -0.27 79 79
LRP6 0.034 0.006 -10000 0 -10000 0 0
CSNK1A1 0.034 0.009 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.027 0.075 -10000 0 -0.77 3 3
WNT1 -0.003 0.12 -10000 0 -0.42 28 28
Axin1/APC/beta catenin 0.045 0.11 0.35 7 -0.42 6 13
DKK2 0.029 0.042 -10000 0 -0.42 3 3
NOTCH1 precursor/DVL1 0.018 0.13 -10000 0 -0.48 13 13
GSK3B 0.034 0.006 -10000 0 -10000 0 0
FRAT1 0.03 0.025 -10000 0 -0.42 1 1
NOTCH/Deltex homolog 1 -0.017 0.15 -10000 0 -0.44 26 26
PPP2R5D 0.027 0.033 0.25 5 -10000 0 5
MAPK1 0.033 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.047 0.079 -10000 0 -0.23 23 23
RBPJ 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.038 0.005 -10000 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.036 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.051 0.094 0.28 5 -0.28 9 14
ERC1 0.034 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.031 0.07 -10000 0 -0.3 15 15
NFKBIA 0.023 0.028 0.22 7 -10000 0 7
BIRC2 0.029 0.042 -10000 0 -0.42 3 3
IKBKB 0.034 0.007 -10000 0 -10000 0 0
RIPK2 0.032 0.011 -10000 0 -10000 0 0
IKBKG 0.033 0.067 -10000 0 -0.39 4 4
IKK complex/A20 0.015 0.15 -10000 0 -0.38 27 27
NEMO/A20/RIP2 0.032 0.011 -10000 0 -10000 0 0
XPO1 0.035 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.039 0.1 -10000 0 -0.34 18 18
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.046 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.1 -10000 0 -0.32 18 18
BCL10/MALT1/TRAF6 0.066 0.025 -10000 0 -0.25 1 1
NOD2 0.01 0.1 -10000 0 -0.42 19 19
NFKB1 0.037 0.006 -10000 0 -10000 0 0
RELA 0.036 0.008 -10000 0 -10000 0 0
MALT1 0.033 0.024 -10000 0 -0.42 1 1
cIAP1/UbcH5C 0.044 0.035 -10000 0 -0.3 3 3
ATM 0.032 0.011 -10000 0 -10000 0 0
TNF/TNFR1A -0.019 0.13 -10000 0 -0.3 68 68
TRAF6 0.034 0.006 -10000 0 -10000 0 0
PRKCA 0.032 0.025 -10000 0 -0.42 1 1
CHUK 0.032 0.01 -10000 0 -10000 0 0
UBE2D3 0.034 0.006 -10000 0 -10000 0 0
TNF -0.054 0.18 -10000 0 -0.42 69 69
NF kappa B1 p50/RelA 0.073 0.027 -10000 0 -10000 0 0
BCL10 0.035 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.028 0.22 7 -10000 0 7
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.009 -10000 0 -10000 0 0
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
IKK complex 0.048 0.11 0.26 1 -0.34 18 19
CYLD 0.034 0.007 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.055 0.11 0.27 1 -0.33 17 18
TCGA08_rtk_signaling

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
PDGFRA 0.028 0.048 -10000 0 -0.42 4 4
HRAS 0.034 0.006 -10000 0 -10000 0 0
EGFR 0.027 0.035 -10000 0 -0.42 2 2
AKT 0.062 0.079 0.26 20 -0.18 3 23
FOXO3 0.031 0.012 -10000 0 -10000 0 0
AKT1 0.035 0.005 -10000 0 -10000 0 0
FOXO1 0.034 0.007 -10000 0 -10000 0 0
AKT3 0.031 0.011 -10000 0 -10000 0 0
FOXO4 0.035 0 -10000 0 -10000 0 0
MET 0.006 0.1 -10000 0 -0.42 20 20
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PIK3CB 0.034 0.006 -10000 0 -10000 0 0
NRAS 0.034 0.008 -10000 0 -10000 0 0
PIK3CG -0.023 0.15 -10000 0 -0.42 44 44
PIK3R3 0.035 0.005 -10000 0 -10000 0 0
PIK3R2 0.035 0.003 -10000 0 -10000 0 0
NF1 0.034 0.007 -10000 0 -10000 0 0
RAS 0.021 0.044 -10000 0 -0.12 22 22
ERBB2 0.034 0.006 -10000 0 -10000 0 0
proliferation/survival/translation -0.04 0.078 0.23 13 -0.21 1 14
PI3K 0.04 0.082 0.22 33 -0.14 18 51
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
KRAS 0.034 0.006 -10000 0 -10000 0 0
FOXO 0.082 0.068 0.23 29 -10000 0 29
AKT2 0.035 0.004 -10000 0 -10000 0 0
PTEN 0.03 0.012 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.021 0.022 -10000 0 -10000 0 0
CDKN2C 0.025 0.018 -10000 0 -10000 0 0
CDKN2A 0.01 0.017 -10000 0 -10000 0 0
CCND2 -0.002 0.017 0.1 1 -0.11 2 3
RB1 -0.001 0.019 -10000 0 -0.18 2 2
CDK4 0 0.012 0.12 1 -10000 0 1
CDK6 -0.001 0.018 0.12 1 -0.13 3 4
G1/S progression 0.027 0.066 0.17 59 -0.14 1 60
Aurora B signaling

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
Condensin I complex 0.023 0.049 -10000 0 -0.19 11 11
STMN1 0.017 0.024 -10000 0 -0.29 2 2
Aurora B/RasGAP/Survivin 0.061 0.035 -10000 0 -0.25 2 2
Chromosomal passenger complex/Cul3 protein complex 0.002 0.068 -10000 0 -0.29 10 10
BIRC5 0.035 0.008 -10000 0 -10000 0 0
DES -0.058 0.24 -10000 0 -0.61 55 55
Aurora C/Aurora B/INCENP 0.003 0.12 -10000 0 -0.22 74 74
Aurora B/TACC1 0.042 0.021 -10000 0 -0.24 1 1
Aurora B/PP2A 0.043 0.027 -10000 0 -0.29 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.013 0.009 -10000 0 -0.13 1 1
mitotic metaphase/anaphase transition 0 0.003 -10000 0 -10000 0 0
NDC80 0.015 0.033 -10000 0 -0.3 4 4
Cul3 protein complex 0.038 0.059 -10000 0 -0.24 10 10
KIF2C 0.022 0.023 -10000 0 -10000 0 0
PEBP1 0.035 0.006 -10000 0 -10000 0 0
KIF20A 0.033 0.025 -10000 0 -0.42 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.045 0.03 -10000 0 -0.3 2 2
SEPT1 -0.097 0.21 -10000 0 -0.42 107 107
SMC2 0.032 0.025 -10000 0 -0.42 1 1
SMC4 0.034 0.006 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.002 0.15 -10000 0 -0.52 27 27
PSMA3 0.035 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -10000 0 -10000 0 0
H3F3B 0.018 0.017 -10000 0 -0.28 1 1
AURKB 0.033 0.026 -10000 0 -0.42 1 1
AURKC -0.056 0.18 -10000 0 -0.42 73 73
CDCA8 0.036 0.005 -10000 0 -10000 0 0
cytokinesis 0.03 0.056 0.2 2 -0.3 5 7
Aurora B/Septin1 -0.007 0.14 0.27 2 -0.35 21 23
AURKA 0.033 0.01 -10000 0 -10000 0 0
INCENP 0.036 0.006 -10000 0 -10000 0 0
KLHL13 0.017 0.074 -10000 0 -0.42 10 10
BUB1 0.036 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.06 0.027 -10000 0 -0.23 1 1
EVI5 0.035 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.064 0.062 -10000 0 -0.22 6 6
SGOL1 0.035 0.004 -10000 0 -10000 0 0
CENPA 0.021 0.062 -10000 0 -0.24 11 11
NCAPG 0.032 0.034 -10000 0 -0.42 2 2
Aurora B/HC8 Proteasome 0.048 0.023 -10000 0 -0.29 1 1
NCAPD2 0.034 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.048 0.023 -10000 0 -0.29 1 1
RHOA 0.035 0.005 -10000 0 -10000 0 0
NCAPH 0.034 0.024 -10000 0 -0.42 1 1
NPM1 -0.011 0.13 -10000 0 -0.49 15 15
RASA1 0.032 0.025 -10000 0 -0.42 1 1
KLHL9 0.029 0.014 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.023 -10000 0 -0.29 1 1
PPP1CC 0.034 0.006 -10000 0 -10000 0 0
Centraspindlin 0.054 0.062 -10000 0 -0.23 7 7
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
NSUN2 -0.008 0.14 -10000 0 -0.42 24 24
MYLK 0.016 0.032 -10000 0 -0.28 4 4
KIF23 0.035 0.024 -10000 0 -0.42 1 1
VIM 0.017 0.018 -10000 0 -0.29 1 1
RACGAP1 0.036 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.001 0.092 -10000 0 -0.3 26 26
Chromosomal passenger complex 0.021 0.049 -10000 0 -0.22 8 8
Chromosomal passenger complex/EVI5 0.089 0.045 -10000 0 -0.23 1 1
TACC1 0.034 0.008 -10000 0 -10000 0 0
PPP2R5D 0.032 0.011 -10000 0 -10000 0 0
CUL3 0.035 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.034 0.006 -10000 0 -10000 0 0
VLDLR 0.021 0.067 -10000 0 -0.42 8 8
LRPAP1 0.034 0.008 -10000 0 -10000 0 0
NUDC 0.035 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.043 0.038 -10000 0 -10000 0 0
CaM/Ca2+ 0.025 0.004 -10000 0 -10000 0 0
KATNA1 0.031 0.012 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.032 0.057 0.19 40 -10000 0 40
IQGAP1/CaM 0.049 0.013 -10000 0 -10000 0 0
DAB1 0.021 0.012 -10000 0 -10000 0 0
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
PLA2G7 -0.078 0.19 -10000 0 -0.42 89 89
CALM1 0.034 0.006 -10000 0 -10000 0 0
DYNLT1 0.031 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.049 0.013 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.034 0.006 -10000 0 -10000 0 0
CDK5R1 0.033 0.024 -10000 0 -0.42 1 1
LIS1/Poliovirus Protein 3A 0.013 0.005 -10000 0 -10000 0 0
CDK5R2 0.026 0.015 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.024 0.054 -10000 0 -0.25 7 7
YWHAE 0.033 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.057 0.085 0.32 27 -10000 0 27
MAP1B 0.007 0.005 -10000 0 -10000 0 0
RAC1 0.016 0.009 -10000 0 -10000 0 0
p35/CDK5 0.028 0.032 0.19 10 -0.21 1 11
RELN 0.024 0.016 -10000 0 -10000 0 0
PAFAH/LIS1 -0.032 0.12 -10000 0 -0.25 84 84
LIS1/CLIP170 0.036 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.038 0.037 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.003 0.072 -10000 0 -0.23 22 22
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.027 0.067 0.28 18 -0.2 1 19
LIS1/IQGAP1 0.035 0.014 -10000 0 -10000 0 0
RHOA 0.018 0.008 -10000 0 -10000 0 0
PAFAH1B1 0.017 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.035 0.004 -10000 0 -10000 0 0
PAFAH1B2 0.032 0.011 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.025 0.034 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.064 0.08 0.32 23 -10000 0 23
LRP8 0.035 0.004 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.051 0.081 0.32 23 -10000 0 23
P39/CDK5 0.02 0.035 0.19 10 -10000 0 10
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.036 0.014 -10000 0 -10000 0 0
CDK5 0.008 0.033 0.19 11 -10000 0 11
PPP2R5D 0.032 0.011 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.031 0.012 -10000 0 -10000 0 0
CSNK2A1 0.033 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.033 0.051 -10000 0 -0.22 7 7
RELN/VLDLR 0.051 0.055 -10000 0 -0.23 7 7
CDC42 0.018 0.008 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.035 0.004 -10000 0 -10000 0 0
mol:PIP3 0.007 0.021 -10000 0 -0.18 2 2
FRAP1 0.02 0.064 -10000 0 -0.38 7 7
AKT1 0.021 0.052 0.16 41 -0.19 1 42
INSR 0.035 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.035 0.007 -10000 0 -10000 0 0
mol:GTP 0.053 0.05 0.21 2 -10000 0 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.015 0.027 -10000 0 -0.16 4 4
TSC2 0.035 0.003 -10000 0 -10000 0 0
RHEB/GDP 0.025 0.024 -10000 0 -10000 0 0
TSC1 0.033 0.009 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.028 0.032 -10000 0 -0.19 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.043 0.042 -10000 0 -0.18 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.032 0.01 -10000 0 -10000 0 0
RPS6KB1 0.04 0.068 0.22 5 -0.29 5 10
MAP3K5 -0.015 0.064 -10000 0 -0.18 45 45
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
apoptosis -0.014 0.064 -10000 0 -0.18 45 45
mol:LY294002 0 0 -10000 0 -0.001 5 5
EIF4B 0.037 0.063 0.21 5 -0.26 5 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.053 0.059 0.22 3 -0.24 5 8
eIF4E/eIF4G1/eIF4A1 0.022 0.038 -10000 0 -0.22 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.049 0.032 -10000 0 -0.17 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.041 0.17 8 -10000 0 8
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
RHEB/GTP 0.048 0.044 0.22 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 5 5
FKBP12/Rapamycin 0.025 0.006 -10000 0 -10000 0 0
PDPK1 -0.004 0.027 0.16 5 -0.19 1 6
EIF4E 0.034 0.006 -10000 0 -10000 0 0
ASK1/PP5C -0.02 0.21 -10000 0 -0.55 46 46
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.048 -10000 0 -0.22 12 12
TSC1/TSC2 0.058 0.054 0.22 3 -10000 0 3
tumor necrosis factor receptor activity 0 0 0.001 5 -10000 0 5
RPS6 0.031 0.012 -10000 0 -10000 0 0
PPP5C 0.035 0.004 -10000 0 -10000 0 0
EIF4G1 0.034 0.006 -10000 0 -10000 0 0
IRS1 0.007 0.029 -10000 0 -0.2 6 6
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.03 0.012 -10000 0 -10000 0 0
PDK2 -0.004 0.027 0.16 5 -0.19 1 6
EIF4EBP1 0.001 0.18 -10000 0 -1 11 11
PIK3CA 0.035 0.006 -10000 0 -10000 0 0
PPP2R5D 0.034 0.079 0.24 7 -0.34 7 14
peptide biosynthetic process 0.017 0.013 0.18 2 -10000 0 2
RHEB 0.031 0.011 -10000 0 -10000 0 0
EIF4A1 0.033 0.009 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 33 -10000 0 33
EEF2 0.017 0.013 0.18 2 -10000 0 2
eIF4E/4E-BP1 0.018 0.17 -10000 0 -0.96 11 11
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0 0.037 -10000 0 -0.25 8 8
SNTA1 0.032 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0 0.04 -10000 0 -0.25 9 9
MAPK12 -0.004 0.04 -10000 0 -0.24 10 10
CCND1 0.015 0.04 -10000 0 -0.33 2 2
p38 gamma/SNTA1 0.028 0.063 0.2 23 -0.22 11 34
MAP2K3 0.033 0.009 -10000 0 -10000 0 0
PKN1 0.034 0.024 -10000 0 -0.42 1 1
G2/M transition checkpoint 0 0.049 0.21 7 -0.24 10 17
MAP2K6 0.001 0.033 -10000 0 -0.24 7 7
MAPT 0.007 0.076 0.19 7 -0.3 10 17
MAPK13 0.01 0.046 -10000 0 -0.3 8 8
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.009 0.016 -10000 0 -0.29 1 1
Effects of Botulinum toxin

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
STX1A 0.009 0.003 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.027 -10000 0 -0.3 1 1
STXBP1 0.033 0.009 -10000 0 -10000 0 0
ACh/CHRNA1 -0.011 0.096 0.11 2 -0.25 48 50
RAB3GAP2/RIMS1/UNC13B 0.045 0.034 -10000 0 -0.26 1 1
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 0.022 0.012 -10000 0 -10000 0 0
mol:ACh 0.006 0.031 0.088 32 -0.067 6 38
RAB3GAP2 0.032 0.011 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.039 0.041 -10000 0 -0.19 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.011 0.096 0.11 2 -0.25 48 50
UNC13B 0.03 0.026 -10000 0 -0.42 1 1
CHRNA1 -0.026 0.15 -10000 0 -0.42 48 48
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.022 0.029 -10000 0 -0.17 2 2
SNAP25 0.005 0.004 -10000 0 -10000 0 0
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 0.027 0.027 -10000 0 -0.42 1 1
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.027 0.014 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.039 0.041 -10000 0 -0.19 1 1
HIF-2-alpha transcription factor network

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
MMP14 0.058 0.08 -10000 0 -0.48 6 6
oxygen homeostasis 0.009 0.008 -10000 0 -10000 0 0
TCEB2 0.034 0.024 -10000 0 -0.42 1 1
TCEB1 0.032 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.07 -10000 0 -10000 0 0
EPO 0.11 0.1 -10000 0 -10000 0 0
FIH (dimer) 0.038 0.028 -10000 0 -0.41 1 1
APEX1 0.043 0.017 -10000 0 -10000 0 0
SERPINE1 0.12 0.11 0.37 11 -0.37 1 12
FLT1 0.026 0.16 -10000 0 -0.52 22 22
ADORA2A 0.11 0.13 0.36 17 -0.41 9 26
germ cell development 0.11 0.11 0.37 7 -0.36 1 8
SLC11A2 0.13 0.11 0.37 12 -0.37 1 13
BHLHE40 0.13 0.11 0.38 11 -0.37 1 12
HIF1AN 0.038 0.029 -10000 0 -0.41 1 1
HIF2A/ARNT/SIRT1 0.11 0.087 0.33 1 -10000 0 1
ETS1 0.044 0.016 -10000 0 -10000 0 0
CITED2 0.011 0.16 -10000 0 -0.5 25 25
KDR 0.024 0.16 -10000 0 -0.52 19 19
PGK1 0.13 0.11 0.37 12 -0.37 1 13
SIRT1 0.032 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.17 0.13 -10000 0 -0.41 1 1
EPAS1 0.068 0.058 0.2 19 -10000 0 19
SP1 0.041 0.006 -10000 0 -10000 0 0
ABCG2 0.12 0.15 0.37 12 -0.41 18 30
EFNA1 0.12 0.1 -10000 0 -0.37 1 1
FXN 0.12 0.11 0.37 17 -0.36 1 18
POU5F1 0.12 0.11 0.37 7 -0.37 1 8
neuron apoptosis -0.16 0.13 0.4 1 -10000 0 1
EP300 0.032 0.011 -10000 0 -10000 0 0
EGLN3 0.04 0.036 -10000 0 -0.41 2 2
EGLN2 0.042 0.013 -10000 0 -10000 0 0
EGLN1 0.04 0.015 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.062 0.029 -10000 0 -0.25 1 1
VHL 0.035 0.005 -10000 0 -10000 0 0
ARNT 0.04 0.017 -10000 0 -10000 0 0
SLC2A1 0.12 0.11 0.37 16 -0.36 1 17
TWIST1 0.086 0.1 0.37 6 -0.36 1 7
ELK1 0.042 0.004 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.11 0.093 -10000 0 -10000 0 0
VEGFA 0.12 0.11 0.38 7 -0.37 1 8
CREBBP 0.035 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.009 0.14 -10000 0 -0.27 68 68
Ran/GTP/Exportin 1/HDAC1 0.009 0.011 -10000 0 -0.19 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.15 0.24 1 -0.3 57 58
SUMO1 0.035 0.003 -10000 0 -10000 0 0
ZFPM1 0.032 0.025 -10000 0 -0.42 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.02 0.007 -10000 0 -10000 0 0
FKBP3 0.035 0.004 -10000 0 -10000 0 0
Histones 0.038 0.11 -10000 0 -0.31 13 13
YY1/LSF 0.04 0.056 0.19 2 -0.22 9 11
SMG5 0.032 0.01 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.089 -10000 0 -0.21 57 57
I kappa B alpha/HDAC1 0.01 0.1 -10000 0 -0.34 12 12
SAP18 0.034 0.008 -10000 0 -10000 0 0
RELA 0.006 0.087 0.29 1 -0.37 2 3
HDAC1/Smad7 0.063 0.024 -10000 0 -10000 0 0
RANGAP1 0.032 0.01 -10000 0 -10000 0 0
HDAC3/TR2 0.011 0.1 -10000 0 -0.35 12 12
NuRD/MBD3 Complex 0.036 0.048 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA 0.015 0.12 0.27 3 -0.34 15 18
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.033 0.008 -10000 0 -10000 0 0
GATA1 0.017 0.002 -10000 0 -10000 0 0
Mad/Max 0.051 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.034 0.068 -10000 0 -0.31 6 6
RBBP7 0.035 0.003 -10000 0 -10000 0 0
NPC 0.021 0.002 -10000 0 -10000 0 0
RBBP4 0.035 0.005 -10000 0 -10000 0 0
MAX 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.033 0.008 -10000 0 -10000 0 0
NFKBIA -0.011 0.089 -10000 0 -0.38 9 9
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.037 0.031 -10000 0 -0.34 1 1
SIN3 complex 0.081 0.028 -10000 0 -10000 0 0
SMURF1 0.032 0.01 -10000 0 -10000 0 0
CHD3 0.033 0.009 -10000 0 -10000 0 0
SAP30 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.033 0.009 -10000 0 -10000 0 0
YY1/HDAC3 0.007 0.078 -10000 0 -0.36 7 7
YY1/HDAC2 0.042 0.039 -10000 0 -0.2 2 2
YY1/HDAC1 0.043 0.045 0.19 2 -0.21 3 5
NuRD/MBD2 Complex (MeCP1) 0.037 0.051 -10000 0 -0.33 2 2
PPARG -0.023 0.15 -10000 0 -0.3 70 70
HDAC8/hEST1B 0.065 0.022 -10000 0 -10000 0 0
UBE2I 0.035 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.034 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.01 0.1 -10000 0 -0.35 12 12
MBD3L2 0.017 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.062 0.024 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.042 0.057 -10000 0 -0.32 1 1
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
HDAC3 -0.003 0.07 -10000 0 -0.38 1 1
HDAC2 0.031 0.012 -10000 0 -10000 0 0
YY1 0.024 0.022 -10000 0 -0.23 2 2
HDAC8 0.035 0 -10000 0 -10000 0 0
SMAD7 0.035 0.005 -10000 0 -10000 0 0
NCOR2 0.034 0.006 -10000 0 -10000 0 0
MXD1 0.035 0.002 -10000 0 -10000 0 0
STAT3 0.027 0.01 -10000 0 -10000 0 0
NFKB1 0.034 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.055 0.06 -10000 0 -0.21 10 10
YY1/SAP30/HDAC1 0.06 0.046 -10000 0 -0.19 3 3
EP300 0.032 0.011 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.089 -10000 0 -0.38 9 9
histone deacetylation 0.034 0.057 -10000 0 -0.26 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.02 0.071 -10000 0 -0.34 3 3
nuclear export -0.064 0.021 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GATAD2B 0.032 0.011 -10000 0 -10000 0 0
GATAD2A 0.035 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.008 0.1 -10000 0 -0.36 12 12
GATA1/HDAC1 0.037 0.019 -10000 0 -0.3 1 1
GATA1/HDAC3 -0.002 0.1 -10000 0 -0.36 12 12
CHD4 0.034 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.019 0.13 -10000 0 -0.3 68 68
SIN3/HDAC complex/Mad/Max 0.033 0.044 -10000 0 -0.33 1 1
NuRD Complex 0.044 0.059 -10000 0 -0.3 2 2
positive regulation of chromatin silencing 0.035 0.11 -10000 0 -0.31 13 13
SIN3B 0.035 0.003 -10000 0 -10000 0 0
MTA2 0.035 0.005 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
XPO1 0.035 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.059 0.032 0.18 1 -0.17 2 3
HDAC complex 0.078 0.035 -10000 0 -0.23 1 1
GATA1/Fog1 0.036 0.02 -10000 0 -0.3 1 1
FKBP25/HDAC1/HDAC2 0.061 0.03 -10000 0 -0.25 1 1
TNF -0.054 0.18 -10000 0 -0.42 69 69
negative regulation of cell growth 0.031 0.051 -10000 0 -0.25 5 5
NuRD/MBD2/PRMT5 Complex 0.037 0.051 -10000 0 -0.33 2 2
Ran/GTP/Exportin 1 0.06 0.029 -10000 0 -0.16 1 1
NF kappa B/RelA/I kappa B alpha -0.023 0.13 -10000 0 -0.3 54 54
SIN3/HDAC complex/NCoR1 0.03 0.04 -10000 0 -0.23 1 1
TFCP2 0.026 0.062 -10000 0 -0.42 7 7
NR2C1 0.034 0.006 -10000 0 -10000 0 0
MBD3 0.032 0.034 -10000 0 -0.42 2 2
MBD2 0.035 0.005 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.029 0.042 -9999 0 -0.42 3 3
GPC2 0.025 0.058 -9999 0 -0.42 6 6
GPC2/Midkine 0.036 0.056 -9999 0 -0.3 9 9
neuron projection morphogenesis 0.036 0.056 -9999 0 -0.3 9 9
Insulin Pathway

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
CBL/APS/CAP 0.045 0.053 -10000 0 -0.2 11 11
TC10/GTP 0.043 0.051 -10000 0 -0.19 11 11
Insulin Receptor/Insulin/IRS1/Shp2 0.075 0.028 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
APS homodimer 0.023 0.062 -10000 0 -0.42 7 7
GRB14 0.027 0.013 -10000 0 -10000 0 0
FOXO3 -0.042 0.21 -10000 0 -0.61 45 45
AKT1 0 0.042 0.21 2 -10000 0 2
INSR 0.039 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.074 0.039 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.032 0.011 -10000 0 -10000 0 0
SORBS1 0.027 0.048 -10000 0 -0.42 4 4
CRK 0.033 0.009 -10000 0 -10000 0 0
PTPN1 0.01 0.016 -10000 0 -10000 0 0
CAV1 0.02 0.025 0.17 7 -10000 0 7
CBL/APS/CAP/Crk-II/C3G 0.068 0.066 -10000 0 -0.2 11 11
Insulin Receptor/Insulin/IRS1/NCK2 0.076 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.06 0.025 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.039 0.044 -10000 0 -0.32 3 3
RPS6KB1 -0.003 0.037 0.2 2 -10000 0 2
PARD6A 0.034 0.007 -10000 0 -10000 0 0
CBL 0.032 0.011 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.033 -10000 0 -0.56 1 1
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.046 0.032 0.19 2 -10000 0 2
HRAS/GTP -0.002 0.066 -10000 0 -0.19 35 35
Insulin Receptor 0.039 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.079 0.041 -10000 0 -10000 0 0
PRKCI 0.045 0.037 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.037 0.019 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.055 0.04 -10000 0 -0.48 1 1
PI3K 0.073 0.03 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
RHOQ 0.035 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.004 -10000 0 -10000 0 0
AKT2 0 0.041 0.21 2 -10000 0 2
PRKCZ 0.035 0.07 -10000 0 -0.48 1 1
SH2B2 0.023 0.062 -10000 0 -0.42 7 7
SHC/SHIP 0.01 0.082 0.19 3 -0.2 43 46
F2RL2 -0.014 0.14 -10000 0 -0.42 37 37
TRIP10 0.035 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.053 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.047 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.083 0.039 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
RASA1 0.032 0.025 -10000 0 -0.42 1 1
NCK1 0.034 0.006 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.058 0.063 -10000 0 -0.22 11 11
TC10/GDP 0.026 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.066 0.036 -10000 0 -10000 0 0
INPP5D -0.015 0.088 0.17 6 -0.21 57 63
SOS1 0.035 0.003 -10000 0 -10000 0 0
SGK1 -0.059 0.22 -10000 0 -0.65 44 44
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
IRS1 0.032 0.011 -10000 0 -10000 0 0
p62DOK/RasGAP 0.055 0.041 -10000 0 -0.48 1 1
INS 0.022 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.015 0.087 0.17 6 -0.21 57 63
GRB2 0.034 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.003 0.037 0.2 1 -10000 0 1
PTPRA 0.037 0.01 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.047 0.007 -10000 0 -10000 0 0
PDPK1 0.035 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.054 0.025 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.045 0.016 -10000 0 -10000 0 0
Par3/Par6 0.043 0.089 -10000 0 -0.21 36 36
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.018 0.07 -9999 0 -0.42 9 9
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.034 0.024 -9999 0 -0.42 1 1
TCEB1 0.032 0.011 -9999 0 -10000 0 0
HIF1A/p53 0.018 0.085 -9999 0 -0.26 28 28
HIF1A 0.003 0.078 -9999 0 -0.27 26 26
COPS5 0.032 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.077 0.049 -9999 0 -0.22 1 1
FIH (dimer) 0.031 0.026 -9999 0 -0.42 1 1
CDKN2A 0.009 0.016 -9999 0 -10000 0 0
ARNT/IPAS 0.031 0.055 -9999 0 -0.3 8 8
HIF1AN 0.031 0.026 -9999 0 -0.42 1 1
GNB2L1 0.033 0.008 -9999 0 -10000 0 0
HIF1A/ARNT 0.013 0.082 -9999 0 -0.26 27 27
CUL2 0.032 0.01 -9999 0 -10000 0 0
OS9 0.034 0.008 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.06 0.031 -9999 0 -0.25 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.02 0.087 -9999 0 -0.26 28 28
PHD1-3/OS9 0.074 0.041 -9999 0 -0.23 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.045 0.085 -9999 0 -0.26 16 16
VHL 0.035 0.005 -9999 0 -10000 0 0
HSP90AA1 0.033 0.024 -9999 0 -0.42 1 1
HIF1A/JAB1 0.019 0.079 -9999 0 -0.26 21 21
EGLN3 0.032 0.034 -9999 0 -0.42 2 2
EGLN2 0.035 0.004 -9999 0 -10000 0 0
EGLN1 0.032 0.011 -9999 0 -10000 0 0
TP53 0.033 0.009 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.04 0.076 -9999 0 -0.6 4 4
ARNT 0.032 0.011 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.032 0.01 -9999 0 -10000 0 0
HIF1A/p19ARF -0.009 0.073 -9999 0 -0.25 27 27
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.027 0.057 0.42 6 -10000 0 6
PI3K Class IB/PDE3B 0.027 0.058 -10000 0 -0.42 6 6
PDE3B 0.027 0.058 -10000 0 -0.42 6 6
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.017 -10000 0 -0.3 1 1
SMARCC1 0.02 0.012 -10000 0 -10000 0 0
REL 0.035 0.003 -10000 0 -10000 0 0
HDAC7 0.026 0.07 0.22 1 -0.21 5 6
JUN 0.031 0.011 -10000 0 -10000 0 0
EP300 0.032 0.011 -10000 0 -10000 0 0
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
KAT5 0.034 0.007 -10000 0 -10000 0 0
MAPK14 0.012 0.042 -10000 0 -0.3 6 6
FOXO1 0.034 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.055 0.08 -10000 0 -0.2 15 15
MAP2K6 0.027 0.058 -10000 0 -0.42 6 6
BRM/BAF57 0.045 0.019 -10000 0 -10000 0 0
MAP2K4 0.033 0.011 -10000 0 -10000 0 0
SMARCA2 0.031 0.012 -10000 0 -10000 0 0
PDE9A 0.013 0.12 -10000 0 -0.66 9 9
NCOA2 0.032 0.011 -10000 0 -10000 0 0
CEBPA -0.004 0.13 -10000 0 -0.42 31 31
EHMT2 0.032 0.011 -10000 0 -10000 0 0
cell proliferation 0.054 0.13 0.34 28 -0.29 9 37
NR0B1 0.018 0.001 -10000 0 -10000 0 0
EGR1 0.03 0.012 -10000 0 -10000 0 0
RXRs/9cRA 0.003 0.11 -10000 0 -0.22 62 62
AR/RACK1/Src 0.043 0.076 0.24 8 -0.21 6 14
AR/GR 0.033 0.051 -10000 0 -0.18 4 4
GNB2L1 0.034 0.008 -10000 0 -10000 0 0
PKN1 0.034 0.024 -10000 0 -0.42 1 1
RCHY1 0.035 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.017 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.047 0.061 0.23 3 -0.22 4 7
SRC 0.019 0.073 0.19 52 -0.21 4 56
NR3C1 0.033 0.009 -10000 0 -10000 0 0
KLK3 -0.003 0.044 -10000 0 -10000 0 0
APPBP2 0.033 0.014 -10000 0 -10000 0 0
TRIM24 0.031 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.035 0.066 0.21 5 -0.23 6 11
TMPRSS2 -0.014 0.22 -10000 0 -0.86 21 21
RXRG -0.057 0.18 -10000 0 -0.42 72 72
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.033 0.009 -10000 0 -10000 0 0
RXRB 0.032 0.011 -10000 0 -10000 0 0
CARM1 0.035 0.003 -10000 0 -10000 0 0
NR2C2 0.035 0.005 -10000 0 -10000 0 0
KLK2 0.033 0.059 0.28 1 -10000 0 1
AR 0.015 0.04 0.15 15 -0.16 4 19
SENP1 0.034 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
MDM2 0.033 0.008 -10000 0 -10000 0 0
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.033 0.008 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.012 0.016 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.046 0.078 0.23 18 -0.22 6 24
positive regulation of transcription 0.033 0.008 -10000 0 -10000 0 0
DNAJA1 0.03 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.013 -10000 0 -0.17 1 1
NCOA1 0.039 0.012 -10000 0 -10000 0 0
SPDEF 0.024 0.015 -10000 0 -10000 0 0
T-DHT/AR/TIF2 0.04 0.075 0.24 16 -0.26 4 20
T-DHT/AR/Hsp90 0.036 0.068 0.21 6 -0.22 7 13
GSK3B 0.035 0.007 -10000 0 -10000 0 0
NR2C1 0.034 0.006 -10000 0 -10000 0 0
mol:T-DHT 0 0.04 0.22 6 -0.22 4 10
SIRT1 0.032 0.01 -10000 0 -10000 0 0
ZMIZ2 0.031 0.011 -10000 0 -10000 0 0
POU2F1 0.034 0.034 -10000 0 -0.11 2 2
T-DHT/AR/DAX-1 0.022 0.064 0.2 5 -0.23 6 11
CREBBP 0.035 0.004 -10000 0 -10000 0 0
SMARCE1 0.034 0.006 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.031 0.065 -10000 0 -0.22 2 2
epithelial cell differentiation 0.026 0.056 -10000 0 -10000 0 0
ITCH 0.039 0.018 -10000 0 -10000 0 0
WWP1 0.023 0.069 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
EGFR 0.027 0.035 -10000 0 -0.42 2 2
PRL 0.02 0.013 -10000 0 -10000 0 0
neuron projection morphogenesis 0.036 0.08 0.26 17 -0.25 1 18
PTPRZ1 -0.012 0.13 -10000 0 -0.42 34 34
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.054 0.071 -10000 0 -0.27 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.02 0.053 -10000 0 -0.3 1 1
ADAM17 0.041 0.015 -10000 0 -10000 0 0
ErbB4/ErbB4 0.018 0.063 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.01 0.1 -10000 0 -0.25 28 28
NCOR1 0.033 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.032 0.055 -10000 0 -0.27 1 1
GRIN2B 0.013 0.05 0.26 2 -0.26 1 3
ErbB4/ErbB2/betacellulin 0.03 0.053 -10000 0 -10000 0 0
STAT1 0.033 0.033 -10000 0 -0.42 2 2
HBEGF 0.033 0.009 -10000 0 -10000 0 0
PRLR 0.024 0.016 -10000 0 -10000 0 0
E4ICDs/ETO2 0.017 0.087 -10000 0 -0.22 23 23
axon guidance 0.033 0.068 0.28 3 -10000 0 3
NEDD4 0.04 0.016 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.02 0.029 -10000 0 -10000 0 0
CBFA2T3 0.001 0.12 -10000 0 -0.42 26 26
ErbB4/ErbB2/HBEGF 0.037 0.053 -10000 0 -10000 0 0
MAPK3 0.043 0.08 0.27 15 -0.26 1 16
STAT1 (dimer) 0.034 0.069 -10000 0 -0.22 2 2
MAPK1 0.039 0.076 0.28 9 -0.26 1 10
JAK2 0.024 0.053 -10000 0 -0.42 5 5
ErbB4/ErbB2/neuregulin 1 beta 0.02 0.051 -10000 0 -0.29 1 1
NRG1 0.015 0.032 -10000 0 -0.3 3 3
NRG3 -0.031 0.14 -10000 0 -0.42 44 44
NRG2 0.029 0.042 -10000 0 -0.42 3 3
NRG4 0.018 0.074 -10000 0 -0.42 10 10
heart development 0.033 0.068 0.28 3 -10000 0 3
neural crest cell migration 0.02 0.05 -10000 0 -0.28 1 1
ERBB2 0.023 0.01 -10000 0 -10000 0 0
WWOX/E4ICDs 0.033 0.066 -10000 0 -0.22 2 2
SHC1 0.032 0.011 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.031 0.081 -10000 0 -0.3 5 5
apoptosis 0.027 0.13 0.32 53 -10000 0 53
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.029 0.07 -10000 0 -0.26 3 3
ErbB4/ErbB2/epiregulin 0.033 0.052 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.024 0.066 -10000 0 -0.22 2 2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.035 0.074 -10000 0 -10000 0 0
MDM2 0.019 0.07 0.26 12 -0.22 2 14
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.03 0.044 -10000 0 -0.22 3 3
STAT5A 0.031 0.065 0.25 4 -0.29 1 5
ErbB4/EGFR/neuregulin 1 beta 0.028 0.058 -10000 0 -0.29 1 1
DLG4 0.033 0.009 -10000 0 -10000 0 0
GRB2/SHC 0.045 0.018 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.028 0.06 -10000 0 -0.2 1 1
STAT5A (dimer) 0.038 0.068 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.051 0.069 0.27 2 -10000 0 2
LRIG1 0.033 0.024 -10000 0 -0.42 1 1
EREG 0.026 0.012 -10000 0 -10000 0 0
BTC 0.023 0.012 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.029 0.062 0.28 1 -10000 0 1
ERBB4 0.018 0.063 -10000 0 -10000 0 0
STAT5B 0.035 0.005 -10000 0 -10000 0 0
YAP1 0.005 0.086 -10000 0 -0.37 16 16
GRB2 0.034 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.032 0.066 -10000 0 -0.29 4 4
glial cell differentiation -0.028 0.059 0.2 1 -10000 0 1
WWOX 0.034 0.008 -10000 0 -10000 0 0
cell proliferation 0.026 0.061 0.26 5 -0.28 1 6
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.008 0.019 0.13 5 -0.1 1 6
BUB1B 0.013 0.032 0.12 2 -0.18 2 4
PLK1 0.014 0.024 0.079 16 -0.11 2 18
PLK1S1 0.016 0.028 0.094 10 -0.19 4 14
KIF2A 0.013 0.031 0.21 5 -10000 0 5
regulation of mitotic centrosome separation 0.014 0.024 0.079 16 -0.11 2 18
GOLGA2 0.033 0.009 -10000 0 -10000 0 0
Hec1/SPC24 0.05 0.039 0.15 1 -0.18 5 6
WEE1 0.021 0.058 -10000 0 -0.31 9 9
cytokinesis 0.021 0.052 0.17 3 -0.19 11 14
PP2A-alpha B56 0.069 0.086 -10000 0 -0.52 7 7
AURKA 0.016 0.019 0.11 1 -0.17 1 2
PICH/PLK1 0.025 0.026 0.14 1 -0.18 2 3
CENPE 0.007 0.034 -10000 0 -0.19 7 7
RhoA/GTP 0.026 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.013 0.031 0.21 5 -10000 0 5
PPP2CA 0.033 0.008 -10000 0 -10000 0 0
FZR1 0.035 0.004 -10000 0 -10000 0 0
TPX2 0.019 0.023 0.12 3 -0.14 1 4
PAK1 0.033 0.009 -10000 0 -10000 0 0
SPC24 0.034 0.024 -10000 0 -0.42 1 1
FBXW11 0.033 0.008 -10000 0 -10000 0 0
CLSPN 0.016 0.031 -10000 0 -0.24 4 4
GORASP1 0.035 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.013 0.044 16 -0.05 3 19
G2 phase of mitotic cell cycle 0 0.003 0.011 24 -10000 0 24
STAG2 0.035 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.024 0.067 -10000 0 -0.53 5 5
spindle elongation 0.014 0.024 0.079 16 -0.11 2 18
ODF2 0.034 0.009 -10000 0 -10000 0 0
BUB1 0.032 0.084 -10000 0 -0.56 7 7
TPT1 0.011 0.035 -10000 0 -0.16 12 12
CDC25C 0.006 0.07 -10000 0 -0.28 20 20
CDC25B 0.035 0.008 -10000 0 -10000 0 0
SGOL1 0.008 0.019 0.1 1 -0.13 5 6
RHOA 0.035 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.049 0.032 -10000 0 -0.16 1 1
CDC14B 0.009 0.003 -10000 0 -10000 0 0
CDC20 0.035 0.004 -10000 0 -10000 0 0
PLK1/PBIP1 0.012 0.028 0.12 1 -0.17 5 6
mitosis -0.002 0.003 0.021 2 -10000 0 2
FBXO5 0.005 0.034 0.1 1 -0.14 3 4
CDC2 0.002 0.002 -10000 0 -0.009 6 6
NDC80 0.03 0.041 -10000 0 -0.42 3 3
metaphase plate congression 0.019 0.023 -10000 0 -0.23 2 2
ERCC6L 0.028 0.033 -10000 0 -0.17 3 3
NLP/gamma Tubulin 0.009 0.016 0.082 1 -0.074 4 5
microtubule cytoskeleton organization 0.011 0.035 -10000 0 -0.16 12 12
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 8 -10000 0 8
PPP1R12A 0.035 0.006 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 8 -10000 0 8
PLK1/PRC1-2 0.05 0.032 0.15 1 -0.22 1 2
GRASP65/GM130/RAB1/GTP/PLK1 0.066 0.027 -10000 0 -10000 0 0
RAB1A 0.035 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.012 0.023 0.081 16 -0.09 1 17
mitotic prometaphase -0.001 0.002 0.018 2 -10000 0 2
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.052 -10000 0 -0.51 3 3
microtubule-based process 0.033 0.027 0.14 1 -0.23 1 2
Golgi organization 0.014 0.024 0.079 16 -0.11 2 18
Cohesin/SA2 0.03 0.022 -10000 0 -0.12 1 1
PPP1CB/MYPT1 0.05 0.011 -10000 0 -10000 0 0
KIF20A 0.032 0.025 -10000 0 -0.42 1 1
APC/C/CDC20 0.034 0.026 0.14 1 -0.12 1 2
PPP2R1A 0.035 0.004 -10000 0 -10000 0 0
chromosome segregation 0.012 0.027 0.11 1 -0.17 5 6
PRC1 0.034 0.006 -10000 0 -10000 0 0
ECT2 0.013 0.028 0.2 4 -0.12 1 5
C13orf34 0.012 0.022 0.073 16 -0.11 1 17
NUDC 0.019 0.023 -10000 0 -0.23 2 2
regulation of attachment of spindle microtubules to kinetochore 0.013 0.032 0.12 2 -0.18 2 4
spindle assembly 0.011 0.02 0.082 5 -0.09 2 7
spindle stabilization 0.016 0.028 0.094 10 -0.19 4 14
APC/C/HCDH1 0.031 0.009 -10000 0 -10000 0 0
MKLP2/PLK1 0.033 0.027 0.14 1 -0.23 1 2
CCNB1 0.035 0.007 -10000 0 -10000 0 0
PPP1CB 0.035 0.005 -10000 0 -10000 0 0
BTRC 0.032 0.01 -10000 0 -10000 0 0
ROCK2 0.023 0.038 -10000 0 -0.25 4 4
TUBG1 0.012 0.029 -10000 0 -0.16 8 8
G2/M transition of mitotic cell cycle 0.015 0.023 -10000 0 -0.15 1 1
MLF1IP 0.006 0.032 -10000 0 -0.3 4 4
INCENP 0.035 0.006 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.015 0.039 -10000 0 -10000 0 0
PLK1 -0.025 0.19 -10000 0 -0.75 4 4
CDKN1B 0.095 0.14 0.36 2 -0.34 16 18
FOXO3 -0.023 0.21 -10000 0 -0.53 25 25
KAT2B 0.018 0.049 -10000 0 -0.41 2 2
FOXO1/SIRT1 0.055 0.045 0.25 1 -10000 0 1
CAT -0.024 0.19 -10000 0 -0.75 4 4
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
AKT1 0.023 0.038 -10000 0 -10000 0 0
FOXO1 0.024 0.042 0.23 3 -10000 0 3
MAPK10 0.035 0.045 0.19 25 -10000 0 25
mol:GTP 0.002 0 -10000 0 -10000 0 0
FOXO4 0.067 0.064 0.28 2 -10000 0 2
response to oxidative stress 0.002 0.019 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.072 0.15 -10000 0 -0.59 5 5
XPO1 0.036 0.002 -10000 0 -10000 0 0
EP300 0.033 0.011 -10000 0 -10000 0 0
BCL2L11 0.015 0.1 -10000 0 -1.2 2 2
FOXO1/SKP2 0.039 0.036 -10000 0 -10000 0 0
mol:GDP 0.002 0.019 -10000 0 -10000 0 0
RAN 0.036 0.006 -10000 0 -10000 0 0
GADD45A 0.079 0.13 -10000 0 -0.58 3 3
YWHAQ 0.035 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.06 0.081 0.25 1 -0.29 9 10
MST1 0.02 0.044 -10000 0 -0.43 1 1
CSNK1D 0.034 0.008 -10000 0 -10000 0 0
CSNK1E 0.033 0.01 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.042 0.065 -10000 0 -0.34 4 4
YWHAB 0.033 0.01 -10000 0 -10000 0 0
MAPK8 0.044 0.049 0.2 33 -10000 0 33
MAPK9 0.045 0.049 0.2 34 -10000 0 34
YWHAG 0.033 0.01 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
SIRT1 0.047 0.033 -10000 0 -10000 0 0
SOD2 0.051 0.16 -10000 0 -0.54 14 14
RBL2 -0.006 0.21 -10000 0 -0.74 17 17
RAL/GDP 0.048 0.021 -10000 0 -10000 0 0
CHUK 0.022 0.035 -10000 0 -10000 0 0
Ran/GTP 0.029 0.005 -10000 0 -10000 0 0
CSNK1G2 0.035 0.004 -10000 0 -10000 0 0
RAL/GTP 0.052 0.022 -10000 0 -10000 0 0
CSNK1G1 0.035 0.004 -10000 0 -10000 0 0
FASLG -0.41 0.66 -10000 0 -1.4 119 119
SKP2 0.033 0.009 -10000 0 -10000 0 0
USP7 0.036 0.004 -10000 0 -10000 0 0
IKBKB 0.021 0.037 -10000 0 -10000 0 0
CCNB1 -0.024 0.19 -10000 0 -0.74 4 4
FOXO1-3a-4/beta catenin 0.06 0.14 -10000 0 -0.35 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.036 -10000 0 -10000 0 0
CSNK1A1 0.033 0.009 -10000 0 -10000 0 0
SGK1 0.021 0.036 -10000 0 -10000 0 0
CSNK1G3 0.033 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.052 0.009 -10000 0 -10000 0 0
ZFAND5 0.065 0.058 -10000 0 -10000 0 0
SFN 0.027 0.015 -10000 0 -10000 0 0
CDK2 0.035 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.035 0.076 -10000 0 -0.35 5 5
CREBBP 0.035 0.004 -10000 0 -10000 0 0
FBXO32 -0.008 0.2 -10000 0 -0.83 5 5
BCL6 0.008 0.18 -10000 0 -0.7 8 8
RALB 0.036 0.003 -10000 0 -10000 0 0
RALA 0.032 0.012 -10000 0 -10000 0 0
YWHAH 0.034 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.02 0.093 -10000 0 -0.91 3 3
MKNK1 0.035 0.004 -10000 0 -10000 0 0
MAPK14 0.036 0.047 -10000 0 -0.33 4 4
ATF2/c-Jun 0.032 0.042 -10000 0 -0.32 1 1
MAPK11 0.037 0.046 -10000 0 -0.33 4 4
MITF 0.018 0.074 -10000 0 -0.3 17 17
MAPKAPK5 0.03 0.048 -10000 0 -0.37 4 4
KRT8 -0.005 0.11 -10000 0 -0.29 42 42
MAPKAPK3 0.035 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.031 0.011 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.047 0.07 -10000 0 -0.51 4 4
CEBPB 0.028 0.048 -10000 0 -0.37 4 4
SLC9A1 0.03 0.048 -10000 0 -0.37 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.034 0.05 -10000 0 -0.36 4 4
p38alpha-beta/MNK1 0.061 0.064 -10000 0 -0.42 4 4
JUN 0.033 0.045 -10000 0 -0.32 1 1
PPARGC1A 0.013 0.068 -10000 0 -0.3 14 14
USF1 0.028 0.046 -10000 0 -0.35 4 4
RAB5/GDP/GDI1 0.042 0.042 -10000 0 -0.28 3 3
NOS2 0.027 0.071 -10000 0 -0.74 2 2
DDIT3 0.03 0.048 -10000 0 -0.37 4 4
RAB5A 0.035 0.004 -10000 0 -10000 0 0
HSPB1 0.029 0.067 0.29 16 -0.3 4 20
p38alpha-beta/HBP1 0.057 0.065 -10000 0 -0.41 4 4
CREB1 0.032 0.051 -10000 0 -0.36 4 4
RAB5/GDP 0.026 0.003 -10000 0 -10000 0 0
EIF4E 0.038 0.069 0.25 3 -0.37 4 7
RPS6KA4 0.031 0.044 -10000 0 -0.38 3 3
PLA2G4A 0.03 0.063 0.25 1 -0.29 6 7
GDI1 0.031 0.044 -10000 0 -0.38 3 3
TP53 0.016 0.06 -10000 0 -0.5 4 4
RPS6KA5 0.028 0.053 -10000 0 -0.33 6 6
ESR1 0.021 0.072 -10000 0 -0.37 10 10
HBP1 0.032 0.011 -10000 0 -10000 0 0
MEF2C 0.028 0.05 -10000 0 -0.34 5 5
MEF2A 0.03 0.048 -10000 0 -0.37 4 4
EIF4EBP1 0.03 0.056 -10000 0 -0.41 4 4
KRT19 0.024 0.05 -10000 0 -0.38 4 4
ELK4 0.028 0.046 -10000 0 -0.35 4 4
ATF6 0.029 0.046 -10000 0 -0.35 4 4
ATF1 0.032 0.051 -10000 0 -0.36 4 4
p38alpha-beta/MAPKAPK2 0.057 0.061 -10000 0 -0.37 4 4
p38alpha-beta/MAPKAPK3 0.061 0.064 -10000 0 -0.41 4 4
Wnt 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
Noncanonical Wnts/FZD 0.007 0.064 -9999 0 -0.25 19 19
FZD6 0.014 0.087 -9999 0 -0.42 14 14
WNT6 0.033 0.008 -9999 0 -10000 0 0
WNT4 0.021 0.017 -9999 0 -10000 0 0
FZD3 0.033 0.009 -9999 0 -10000 0 0
WNT5A 0.024 0.066 -9999 0 -0.42 8 8
WNT11 0.023 0.017 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.015 0.13 -9999 0 -0.9 3 3
RAD9A 0.034 0.007 -9999 0 -10000 0 0
AP1 0.045 0.024 -9999 0 -10000 0 0
IFNAR2 0.036 0.007 -9999 0 -10000 0 0
AKT1 0.02 0.027 -9999 0 -0.16 6 6
ER alpha/Oestrogen 0.018 0.041 -9999 0 -0.29 6 6
NFX1/SIN3/HDAC complex 0.042 0.036 -9999 0 -0.23 1 1
EGF 0.002 0.11 -9999 0 -0.42 25 25
SMG5 0.032 0.01 -9999 0 -10000 0 0
SMG6 0.033 0.009 -9999 0 -10000 0 0
SP3/HDAC2 0.049 0.019 -9999 0 -10000 0 0
TERT/c-Abl 0.027 0.13 -9999 0 -0.83 3 3
SAP18 0.034 0.008 -9999 0 -10000 0 0
MRN complex 0.056 0.037 -9999 0 -0.25 2 2
WT1 0.016 0.012 -9999 0 -10000 0 0
WRN 0.033 0.008 -9999 0 -10000 0 0
SP1 0.037 0.008 -9999 0 -10000 0 0
SP3 0.036 0.004 -9999 0 -10000 0 0
TERF2IP 0.034 0.007 -9999 0 -10000 0 0
Telomerase/Nucleolin 0.052 0.12 -9999 0 -0.82 2 2
Mad/Max 0.053 0.011 -9999 0 -10000 0 0
TERT 0.014 0.13 -9999 0 -0.94 3 3
CCND1 0.026 0.12 -9999 0 -0.85 2 2
MAX 0.035 0.006 -9999 0 -10000 0 0
RBBP7 0.036 0.003 -9999 0 -10000 0 0
RBBP4 0.035 0.005 -9999 0 -10000 0 0
TERF2 0.033 0.015 -9999 0 -10000 0 0
PTGES3 0.034 0.006 -9999 0 -10000 0 0
SIN3A 0.034 0.007 -9999 0 -10000 0 0
Telomerase/911 0.052 0.058 -9999 0 -0.28 1 1
CDKN1B -0.075 0.15 -9999 0 -0.26 130 130
RAD1 0.033 0.009 -9999 0 -10000 0 0
XRCC5 0.035 0.004 -9999 0 -10000 0 0
XRCC6 0.032 0.01 -9999 0 -10000 0 0
SAP30 0.035 0.006 -9999 0 -10000 0 0
TRF2/PARP2 0.05 0.016 -9999 0 -10000 0 0
UBE3A 0.035 0.007 -9999 0 -10000 0 0
JUN 0.032 0.012 -9999 0 -10000 0 0
E6 0.001 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.027 0.006 -9999 0 -10000 0 0
FOS 0.034 0.009 -9999 0 -10000 0 0
IFN-gamma/IRF1 -0.081 0.18 -9999 0 -0.31 136 136
PARP2 0.035 0.005 -9999 0 -10000 0 0
BLM 0.034 0.007 -9999 0 -10000 0 0
Telomerase 0.056 0.07 -9999 0 -0.33 4 4
IRF1 -0.002 0.13 -9999 0 -0.41 32 32
ESR1 0.024 0.058 -9999 0 -0.42 6 6
KU/TER 0.047 0.016 -9999 0 -10000 0 0
ATM/TRF2 0.047 0.017 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.047 0.042 -9999 0 -0.28 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.048 0.041 -9999 0 -0.29 1 1
HDAC1 0.034 0.024 -9999 0 -0.42 1 1
HDAC2 0.033 0.013 -9999 0 -10000 0 0
ATM 0.013 0.009 -9999 0 -10000 0 0
SMAD3 0.017 0.023 -9999 0 -0.3 2 2
ABL1 0.033 0.009 -9999 0 -10000 0 0
MXD1 0.036 0.004 -9999 0 -10000 0 0
MRE11A 0.032 0.01 -9999 0 -10000 0 0
HUS1 0.031 0.011 -9999 0 -10000 0 0
RPS6KB1 0.034 0.007 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.053 0.13 -9999 0 -1 2 2
NR2F2 0.033 0.007 -9999 0 -10000 0 0
MAPK3 0.01 0.012 -9999 0 -10000 0 0
MAPK1 0.01 0.012 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.032 0.034 -9999 0 -0.42 2 2
NFKB1 0.034 0.006 -9999 0 -10000 0 0
HNRNPC 0.035 0.005 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.009 -9999 0 -10000 0 0
NBN 0.032 0.011 -9999 0 -10000 0 0
EGFR 0.027 0.036 -9999 0 -0.42 2 2
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR 0.016 0.089 -9999 0 -0.3 26 26
MYC 0.032 0.012 -9999 0 -10000 0 0
IL2 0.022 0.016 -9999 0 -10000 0 0
KU 0.047 0.016 -9999 0 -10000 0 0
RAD50 0.031 0.034 -9999 0 -0.42 2 2
HSP90AA1 0.033 0.024 -9999 0 -0.42 1 1
TGFB1 0.032 0.034 -9999 0 -0.42 2 2
TRF2/BLM 0.05 0.018 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT 0.043 0.13 -9999 0 -0.84 3 3
SP1/HDAC2 0.05 0.02 -9999 0 -10000 0 0
PINX1 0.033 0.009 -9999 0 -10000 0 0
Telomerase/EST1A 0.052 0.12 -9999 0 -0.82 2 2
Smad3/Myc 0.034 0.014 -9999 0 -10000 0 0
911 complex 0.058 0.029 -9999 0 -10000 0 0
IFNG -0.11 0.21 -9999 0 -0.41 120 120
Telomerase/PinX1 0.051 0.12 -9999 0 -0.81 2 2
Telomerase/AKT1/mTOR/p70S6K 0.028 0.089 -9999 0 -0.42 8 8
SIN3B 0.035 0.003 -9999 0 -10000 0 0
YWHAE 0.033 0.009 -9999 0 -10000 0 0
Telomerase/EST1B 0.048 0.12 -9999 0 -0.82 2 2
response to DNA damage stimulus -0.003 0.031 -9999 0 -0.1 30 30
MRN complex/TRF2/Rap1 0.077 0.048 -9999 0 -0.22 2 2
TRF2/WRN 0.049 0.018 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.053 0.12 -9999 0 -0.82 2 2
E2F1 0.034 0.011 -9999 0 -10000 0 0
ZNFX1 0.032 0.01 -9999 0 -10000 0 0
PIF1 0.031 0.041 -9999 0 -0.42 3 3
NCL 0.035 0.005 -9999 0 -10000 0 0
DKC1 0.035 0.004 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.043 0.014 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.02 0.006 -10000 0 -10000 0 0
mol:DAG 0.017 0.044 0.2 5 -0.22 9 14
VEGFR1 homodimer/NRP1/VEGFR 121 0.034 0.018 -10000 0 -10000 0 0
CaM/Ca2+ 0.036 0.045 -10000 0 -0.21 9 9
HIF1A 0.044 0.007 -10000 0 -10000 0 0
GAB1 0.035 0.004 -10000 0 -10000 0 0
AKT1 0.019 0.047 -10000 0 -10000 0 0
PLCG1 0.017 0.044 0.2 5 -0.22 9 14
NOS3 0.04 0.065 0.28 1 -0.52 1 2
CBL 0.032 0.011 -10000 0 -10000 0 0
mol:NO 0.041 0.064 0.28 1 -0.5 1 2
FLT1 0.027 0.008 -10000 0 -10000 0 0
PGF 0.022 0.074 -10000 0 -0.42 10 10
VEGFR1 homodimer/NRP2/VEGFR121 0.053 0.028 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
eNOS/Hsp90 0.06 0.065 0.29 1 -0.49 1 2
endothelial cell proliferation -0.027 0.11 -10000 0 -0.38 13 13
mol:Ca2+ 0.017 0.044 0.2 5 -0.22 9 14
MAPK3 -0.007 0.038 0.18 5 -0.2 9 14
MAPK1 -0.006 0.036 0.18 5 -0.2 1 6
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
PLGF homodimer 0.022 0.074 -10000 0 -0.42 10 10
PRKACA 0.035 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.032 0.011 -10000 0 -10000 0 0
VEGFA homodimer 0.03 0.013 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.038 0.02 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.016 0.069 -10000 0 -10000 0 0
PI3K 0.072 0.053 -10000 0 -0.21 9 9
PRKCA 0.006 0.041 0.19 5 -0.21 9 14
PRKCB -0.047 0.11 0.19 3 -0.23 87 90
VEGFR1 homodimer/PLGF homodimer 0.037 0.046 -10000 0 -0.24 9 9
VEGFA 0.03 0.013 -10000 0 -10000 0 0
VEGFB 0.034 0.006 -10000 0 -10000 0 0
mol:IP3 0.017 0.044 0.2 5 -0.22 9 14
RASA1 0.024 0.029 0.2 7 -0.22 1 8
NRP2 0.035 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer 0.027 0.008 -10000 0 -10000 0 0
VEGFB homodimer 0.034 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.047 0.067 0.29 1 -0.49 1 2
PTPN11 0.034 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.069 0.052 -10000 0 -0.2 9 9
mol:L-citrulline 0.041 0.064 0.28 1 -0.5 1 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.067 0.041 -10000 0 -0.21 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.052 0.029 -10000 0 -10000 0 0
CD2AP 0.031 0.026 -10000 0 -0.42 1 1
PI3K/GAB1 0.084 0.057 -10000 0 -0.2 9 9
PDPK1 0.022 0.045 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.053 0.028 -10000 0 -10000 0 0
mol:NADP 0.041 0.064 0.28 1 -0.5 1 2
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.064 0.04 -10000 0 -0.21 1 1
VEGFR1 homodimer/NRP2 0.044 0.013 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.01 -10000 0 -10000 0 0
mol:S1P 0.001 0 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.017 0.033 -10000 0 -0.18 6 6
GNAO1 0.02 0.029 -10000 0 -0.42 1 1
S1P/S1P3/G12/G13 0.054 0.038 -10000 0 -0.22 3 3
AKT1 0.026 0.089 -10000 0 -0.4 14 14
AKT3 0.041 0.044 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.01 -10000 0 -10000 0 0
GNAI2 0.036 0.005 -10000 0 -10000 0 0
GNAI3 0.035 0.007 -10000 0 -10000 0 0
GNAI1 0.032 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.031 0.042 -10000 0 -0.42 3 3
S1PR2 0.035 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.047 -10000 0 -0.23 6 6
MAPK3 0.027 0.045 -10000 0 -0.24 4 4
MAPK1 0.023 0.043 -10000 0 -0.24 4 4
JAK2 0.021 0.084 0.23 1 -0.34 11 12
CXCR4 0.017 0.069 -10000 0 -0.3 9 9
FLT1 0.036 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
SRC 0.025 0.042 -10000 0 -0.26 3 3
S1P/S1P3/Gi 0.029 0.047 -10000 0 -0.23 6 6
RAC1 0.031 0.012 -10000 0 -10000 0 0
RhoA/GTP 0.042 0.059 -10000 0 -0.25 3 3
VEGFA 0.032 0.014 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.029 0.037 -10000 0 -0.18 3 3
VEGFR1 homodimer/VEGFA homodimer 0.049 0.024 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.013 0.11 -10000 0 -0.24 63 63
GNAQ 0.033 0.009 -10000 0 -10000 0 0
GNAZ 0.028 0.036 -10000 0 -0.42 2 2
G12/G13 0.045 0.018 -10000 0 -10000 0 0
GNA14 -0.037 0.16 -10000 0 -0.42 56 56
GNA15 0.021 0.077 -10000 0 -0.42 11 11
GNA12 0.031 0.011 -10000 0 -10000 0 0
GNA13 0.034 0.007 -10000 0 -10000 0 0
GNA11 0.035 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.056 -10000 0 -0.23 4 4
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.032 0.012 -10000 0 -10000 0 0
HSPA8 0.032 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.065 0.064 -10000 0 -0.27 5 5
AKT1 0.035 0.016 -10000 0 -10000 0 0
GSC 0.008 0.065 -10000 0 -10000 0 0
NKX2-5 0.001 0.005 -10000 0 -10000 0 0
muscle cell differentiation -0.063 0.06 0.51 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.12 0.054 -10000 0 -10000 0 0
SMAD4 0.043 0.034 -10000 0 -10000 0 0
CBFB 0.034 0.007 -10000 0 -10000 0 0
SAP18 0.034 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.048 0.068 -10000 0 -0.25 15 15
SMAD3/SMAD4/VDR 0.1 0.059 -10000 0 -0.22 2 2
MYC 0.03 0.013 -10000 0 -10000 0 0
CDKN2B -0.11 0.25 -10000 0 -0.67 26 26
AP1 0.061 0.039 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.041 0.066 -10000 0 -0.36 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.031 0.047 -10000 0 -0.32 5 5
SP3 0.037 0.002 -10000 0 -10000 0 0
CREB1 0.035 0.003 -10000 0 -10000 0 0
FOXH1 0.031 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.075 0.047 -10000 0 -10000 0 0
GATA3 -0.052 0.18 -10000 0 -0.41 71 71
SKI/SIN3/HDAC complex/NCoR1 0.028 0.056 -10000 0 -0.37 3 3
MEF2C/TIF2 0.05 0.052 0.36 2 -0.38 2 4
endothelial cell migration -0.02 0.085 0.66 4 -10000 0 4
MAX 0.033 0.006 -10000 0 -10000 0 0
RBBP7 0.035 0.003 -10000 0 -10000 0 0
RBBP4 0.035 0.005 -10000 0 -10000 0 0
RUNX2 0.029 0.035 -10000 0 -0.42 2 2
RUNX3 0.005 0.11 -10000 0 -0.42 24 24
RUNX1 0.031 0.041 -10000 0 -0.42 3 3
CTBP1 0.034 0.008 -10000 0 -10000 0 0
NR3C1 0.032 0.009 -10000 0 -10000 0 0
VDR 0.032 0.034 -10000 0 -0.42 2 2
CDKN1A 0.037 0.046 -10000 0 -0.54 1 1
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
SMAD2/SMAD2/SMAD4/FOXH1 0.073 0.043 -10000 0 -10000 0 0
DCP1A 0.034 0.006 -10000 0 -10000 0 0
SKI 0.034 0.007 -10000 0 -10000 0 0
SERPINE1 0.02 0.086 -10000 0 -0.67 4 4
SMAD3/SMAD4/ATF2 0.079 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.07 0.049 -10000 0 -10000 0 0
SAP30 0.035 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.058 0.03 -10000 0 -10000 0 0
JUN 0.04 0.034 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.076 0.06 -10000 0 -0.27 4 4
TFE3 0.041 0.007 -10000 0 -10000 0 0
COL1A2 0.024 0.027 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.07 0.055 0.29 2 -10000 0 2
DLX1 0.008 0.1 -10000 0 -0.42 19 19
TCF3 0.035 0.005 -10000 0 -10000 0 0
FOS 0.039 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/Max 0.076 0.048 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.064 0.024 -10000 0 -10000 0 0
ZBTB17 0.034 0.006 -10000 0 -10000 0 0
LAMC1 0.039 0.034 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.074 0.049 -10000 0 -10000 0 0
IRF7 0.03 0.047 -10000 0 -0.42 4 4
ESR1 0.023 0.058 -10000 0 -0.42 6 6
HNF4A 0.022 0.013 -10000 0 -10000 0 0
MEF2C 0.052 0.076 0.45 4 -0.4 2 6
SMAD2-3/SMAD4 0.086 0.048 -10000 0 -0.17 1 1
Cbp/p300/Src-1 0.063 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.013 0.045 -10000 0 -0.43 3 3
TGIF2/HDAC complex 0.033 0.009 -10000 0 -10000 0 0
CREBBP 0.035 0.006 -10000 0 -10000 0 0
SKIL 0.034 0.006 -10000 0 -10000 0 0
HDAC1 0.033 0.024 -10000 0 -0.42 1 1
HDAC2 0.031 0.012 -10000 0 -10000 0 0
SNIP1 0.035 0.004 -10000 0 -10000 0 0
GCN5L2 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.094 0.045 -10000 0 -10000 0 0
MSG1/HSC70 0.029 0.072 -10000 0 -0.29 16 16
SMAD2 0.037 0.016 -10000 0 -10000 0 0
SMAD3 0.041 0.032 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.036 0.044 -10000 0 -0.22 6 6
SMAD2/SMAD2/SMAD4 0.023 0.046 0.2 3 -0.26 2 5
NCOR1 0.033 0.009 -10000 0 -10000 0 0
NCOA2 0.032 0.011 -10000 0 -10000 0 0
NCOA1 0.035 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.044 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.13 0.061 -10000 0 -0.2 1 1
IFNB1 0.024 0.041 -10000 0 -0.24 3 3
SMAD3/SMAD4/MEF2C 0.093 0.07 -10000 0 -0.38 2 2
CITED1 0.014 0.092 -10000 0 -0.42 16 16
SMAD2-3/SMAD4/ARC105 0.097 0.053 -10000 0 -10000 0 0
RBL1 0.033 0.01 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.04 0.069 -10000 0 -0.48 5 5
RUNX1-3/PEBPB2 0.043 0.087 -10000 0 -0.26 25 25
SMAD7 0.077 0.033 -10000 0 -10000 0 0
MYC/MIZ-1 0.043 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4 0.032 0.044 -10000 0 -0.36 2 2
IL10 -0.024 0.15 -10000 0 -0.39 35 35
PIASy/HDAC complex 0.035 0.005 -10000 0 -10000 0 0
PIAS3 0.032 0.011 -10000 0 -10000 0 0
CDK2 0.035 0.006 -10000 0 -10000 0 0
IL5 -0.022 0.12 -10000 0 -0.25 68 68
CDK4 0.034 0.009 -10000 0 -10000 0 0
PIAS4 0.035 0.005 -10000 0 -10000 0 0
ATF3 0.031 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.093 0.047 -10000 0 -10000 0 0
FOXG1 0.013 0.024 -10000 0 -10000 0 0
FOXO3 0.017 0.018 -10000 0 -10000 0 0
FOXO1 0.018 0.018 -10000 0 -10000 0 0
FOXO4 0.019 0.018 -10000 0 -10000 0 0
heart looping 0.052 0.075 0.45 4 -0.4 2 6
CEBPB 0.032 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.056 0.088 -10000 0 -0.26 19 19
MYOD1 0.026 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.064 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.012 0.16 -10000 0 -0.28 74 74
SnoN/SIN3/HDAC complex/NCoR1 0.034 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.082 0.099 -10000 0 -0.23 25 25
SMAD3/SMAD4/SP1-3 0.12 0.049 -10000 0 -10000 0 0
MED15 0.033 0.009 -10000 0 -10000 0 0
SP1 0.041 0.007 -10000 0 -10000 0 0
SIN3B 0.035 0.003 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.074 0.045 -10000 0 -0.21 2 2
ITGB5 0.043 0.034 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.034 0.052 -10000 0 -0.39 2 2
SMAD3/SMAD4/AR 0.056 0.05 -10000 0 -10000 0 0
AR 0.02 0.017 -10000 0 -10000 0 0
negative regulation of cell growth 0.052 0.052 -10000 0 -0.33 1 1
SMAD3/SMAD4/MYOD 0.073 0.046 -10000 0 -10000 0 0
E2F5 0.023 0.062 -10000 0 -0.42 7 7
E2F4 0.034 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.091 0.055 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.037 0.053 -10000 0 -0.36 5 5
TFDP1 0.033 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.089 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.07 0.055 -10000 0 -0.29 2 2
TGIF2 0.033 0.009 -10000 0 -10000 0 0
TGIF1 0.034 0.007 -10000 0 -10000 0 0
ATF2 0.035 0.002 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.05 0.024 -10000 0 -10000 0 0
CDKN1B 0.026 0.051 0.23 3 -0.28 7 10
CDKN1A 0.036 0.07 0.21 25 -0.28 8 33
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.033 0.009 -10000 0 -10000 0 0
FOXO3 0.024 0.039 -10000 0 -0.28 3 3
AKT1 0.028 0.042 -10000 0 -0.28 5 5
BAD 0.034 0.006 -10000 0 -10000 0 0
AKT3 0.018 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.024 0.05 -10000 0 -0.28 8 8
AKT1/ASK1 0.043 0.058 -10000 0 -0.26 9 9
BAD/YWHAZ 0.062 0.025 -10000 0 -10000 0 0
RICTOR 0.031 0.025 -10000 0 -0.42 1 1
RAF1 0.035 0.005 -10000 0 -10000 0 0
JNK cascade -0.041 0.057 0.25 9 -10000 0 9
TSC1 0.024 0.045 -10000 0 -0.27 6 6
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
AKT1/RAF1 0.052 0.06 -10000 0 -0.27 9 9
EP300 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.026 0.051 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.023 0.05 -10000 0 -0.28 8 8
YWHAQ 0.035 0.004 -10000 0 -10000 0 0
TBC1D4 0.015 0.032 0.24 6 -0.23 1 7
MAP3K5 0.03 0.026 -10000 0 -0.42 1 1
MAPKAP1 0.033 0.009 -10000 0 -10000 0 0
negative regulation of cell cycle -0.054 0.057 0.28 1 -0.23 8 9
YWHAH 0.034 0.008 -10000 0 -10000 0 0
AKT1S1 0.024 0.051 -10000 0 -0.28 7 7
CASP9 0.025 0.051 0.23 3 -0.28 7 10
YWHAB 0.033 0.01 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.052 0.064 0.29 5 -0.27 7 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.064 0.023 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
AKT2/p21CIP1 0.046 0.072 0.22 33 -0.24 7 40
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.032 -10000 0 -0.25 3 3
CHUK 0.025 0.039 -10000 0 -0.27 4 4
BAD/BCL-XL 0.052 0.057 -10000 0 -0.27 7 7
mTORC2 0.038 0.021 -10000 0 -0.22 1 1
AKT2 0.02 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.059 0.065 0.25 7 -0.28 2 9
PDPK1 0.035 0.003 -10000 0 -10000 0 0
MDM2 0.029 0.054 0.21 10 -0.28 6 16
MAPKKK cascade -0.051 0.059 0.27 9 -10000 0 9
MDM2/Cbp/p300 0.066 0.067 0.29 4 -0.26 6 10
TSC1/TSC2 0.021 0.042 -10000 0 -0.28 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.064 0.28 4 -0.25 6 10
glucose import 0.009 0.024 0.21 5 -10000 0 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.028 0.038 0.18 1 -0.17 3 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.009 0.024 0.21 5 -10000 0 5
GSK3A 0.024 0.051 0.2 1 -0.28 8 9
FOXO1 0.025 0.05 0.21 2 -0.28 7 9
GSK3B 0.024 0.052 0.21 2 -0.28 8 10
SFN 0.027 0.015 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.028 0.057 0.25 2 -0.28 7 9
p27Kip1/14-3-3 family 0.044 0.044 -10000 0 -0.29 1 1
PRKACA 0.035 0.003 -10000 0 -10000 0 0
KPNA1 0.034 0.006 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
YWHAG 0.033 0.01 -10000 0 -10000 0 0
RHEB 0.031 0.011 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.028 0.076 -10000 0 -0.3 18 18
AKT1 0.061 0.079 0.37 4 -0.34 1 5
PTK2B 0.03 0.075 0.36 3 -10000 0 3
VEGFR2 homodimer/Frs2 0.045 0.017 -10000 0 -10000 0 0
CAV1 0.032 0.011 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.056 0.031 -10000 0 -10000 0 0
endothelial cell proliferation 0.021 0.13 0.29 21 -0.29 8 29
mol:Ca2+ 0.041 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.072 0.042 -10000 0 -10000 0 0
RP11-342D11.1 0.018 0.026 0.18 8 -10000 0 8
CDH5 0.034 0.007 -10000 0 -10000 0 0
VEGFA homodimer 0.071 0.038 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
SHC2 0.022 0.036 -10000 0 -0.42 2 2
HRAS/GDP 0.053 0.032 -10000 0 -10000 0 0
SH2D2A -0.003 0.12 -10000 0 -0.42 28 28
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.035 0.1 -10000 0 -0.43 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.036 0.074 -10000 0 -0.22 24 24
VEGFR1 homodimer 0.034 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.085 0.049 -10000 0 -10000 0 0
GRB10 0.039 0.042 -10000 0 -10000 0 0
PTPN11 0.034 0.006 -10000 0 -10000 0 0
GRB2 0.034 0.007 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.087 0.045 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.037 0.057 -10000 0 -0.27 4 4
HIF1A 0.035 0.005 -10000 0 -10000 0 0
FRS2 0.034 0.008 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.069 0.041 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.033 0.01 -10000 0 -10000 0 0
Nck/Pak 0.047 0.016 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.052 0.034 -10000 0 -10000 0 0
mol:GDP 0.066 0.039 -10000 0 -10000 0 0
mol:NADP 0.071 0.075 0.32 9 -0.31 2 11
eNOS/Hsp90 0.087 0.072 0.33 9 -0.3 2 11
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 0.041 0.046 -10000 0 -10000 0 0
HIF1A/ARNT 0.046 0.017 -10000 0 -10000 0 0
SHB 0.028 0.035 -10000 0 -0.42 2 2
VEGFA 0.032 0.013 -10000 0 -10000 0 0
VEGFC 0.034 0.006 -10000 0 -10000 0 0
FAK1/Vinculin 0.065 0.073 0.32 5 -10000 0 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.035 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.06 0.066 -10000 0 -0.2 14 14
PTPN6 -0.075 0.19 -10000 0 -0.42 88 88
EPAS1 0.045 0.01 -10000 0 -10000 0 0
mol:L-citrulline 0.071 0.075 0.32 9 -0.31 2 11
ITGAV 0.035 0.004 -10000 0 -10000 0 0
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.072 0.04 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.063 0.031 -10000 0 -10000 0 0
VEGFR2/3 heterodimer 0.044 0.019 -10000 0 -10000 0 0
VEGFB 0.034 0.006 -10000 0 -10000 0 0
MAPK11 0.038 0.066 0.32 7 -10000 0 7
VEGFR2 homodimer 0.03 0.011 -10000 0 -10000 0 0
FLT1 0.034 0.007 -10000 0 -10000 0 0
NEDD4 0.036 0.007 -10000 0 -10000 0 0
MAPK3 0.013 0.087 0.33 8 -10000 0 8
MAPK1 0.017 0.091 0.32 12 -10000 0 12
VEGFA145/NRP2 0.045 0.021 -10000 0 -10000 0 0
VEGFR1/2 heterodimer 0.045 0.017 -10000 0 -10000 0 0
KDR 0.03 0.011 -10000 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.067 0.034 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.023 0.09 0.31 12 -10000 0 12
PI3K 0.054 0.054 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.057 0.031 -10000 0 -10000 0 0
FES 0.038 0.056 -10000 0 -10000 0 0
GAB1 0.051 0.043 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.054 0.032 -10000 0 -10000 0 0
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
SOS1 0.035 0.003 -10000 0 -10000 0 0
ARNT 0.032 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.074 0.072 0.34 6 -0.32 1 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.056 0.031 -10000 0 -10000 0 0
PI3K/GAB1 0.062 0.073 0.27 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.08 0.047 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.06 0.026 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
CDC42 0.045 0.047 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.035 0.074 -10000 0 -0.22 24 24
PTK2 0.04 0.062 0.28 4 -10000 0 4
EDG1 0.018 0.026 0.18 8 -10000 0 8
mol:DAG 0.041 0.046 -10000 0 -10000 0 0
CaM/Ca2+ 0.055 0.044 -10000 0 -10000 0 0
MAP2K3 0.036 0.063 0.36 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.072 0.052 -10000 0 -10000 0 0
PLCG1 0.041 0.046 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.063 0.049 -10000 0 -0.2 2 2
IQGAP1 0.034 0.006 -10000 0 -10000 0 0
YES1 0.034 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.057 0.03 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.003 0.12 -10000 0 -0.22 78 78
cell migration 0.077 0.089 0.32 15 -10000 0 15
mol:PI-3-4-5-P3 0.052 0.052 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
VEGFB/NRP1 0.036 0.027 0.2 1 -10000 0 1
mol:NO 0.071 0.075 0.32 9 -0.31 2 11
PXN 0.034 0.006 -10000 0 -10000 0 0
HRAS/GTP 0.032 0.02 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.049 0.031 -10000 0 -10000 0 0
VHL 0.035 0.005 -10000 0 -10000 0 0
ITGB3 0.009 0.098 -10000 0 -0.42 18 18
NOS3 0.073 0.078 0.34 8 -0.35 2 10
VEGFR2 homodimer/VEGFA homodimer/Sck 0.043 0.039 -10000 0 -0.22 2 2
RAC1 0.031 0.012 -10000 0 -10000 0 0
PRKCA 0.033 0.061 0.26 10 -10000 0 10
PRKCB -0.018 0.11 0.26 10 -0.22 2 12
VCL 0.032 0.01 -10000 0 -10000 0 0
VEGFA165/NRP1 0.04 0.03 -10000 0 -10000 0 0
VEGFR1/2 heterodimer/VEGFA homodimer 0.057 0.031 -10000 0 -10000 0 0
VEGFA165/NRP2 0.045 0.021 -10000 0 -10000 0 0
MAPKKK cascade 0.05 0.051 0.36 1 -10000 0 1
NRP2 0.035 0.004 -10000 0 -10000 0 0
VEGFC homodimer 0.034 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.006 -10000 0 -10000 0 0
ROCK1 0.035 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.067 0.076 0.32 5 -10000 0 5
MAP3K13 0.043 0.048 -10000 0 -10000 0 0
PDPK1 0.046 0.053 0.25 3 -10000 0 3
Signaling events mediated by PRL

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
CCNE1 0.035 0.004 -10000 0 -10000 0 0
mol:Halofuginone 0.005 0.003 -10000 0 -10000 0 0
ITGA1 0.033 0.009 -10000 0 -10000 0 0
CDKN1A 0.022 0.039 -10000 0 -0.3 4 4
PRL-3/alpha Tubulin 0.044 0.026 -10000 0 -0.3 1 1
mol:Ca2+ -0.054 0.095 -10000 0 -0.31 44 44
AGT -0.032 0.15 -10000 0 -0.42 49 49
CCNA2 0.018 0.052 -10000 0 -10000 0 0
TUBA1B 0.035 0.005 -10000 0 -10000 0 0
EGR1 0.018 0.01 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.078 0.053 0.28 1 -0.27 5 6
MAPK3 0.016 0.018 -10000 0 -0.3 1 1
PRL-2 /Rab GGTase beta 0.051 0.009 -10000 0 -10000 0 0
MAPK1 0.015 0.018 -10000 0 -0.3 1 1
PTP4A1 0.007 0.006 -10000 0 -10000 0 0
PTP4A3 0.03 0.026 -10000 0 -0.42 1 1
PTP4A2 0.035 0.005 -10000 0 -10000 0 0
ITGB1 0.015 0.018 -10000 0 -0.3 1 1
SRC 0.033 0.01 -10000 0 -10000 0 0
RAC1 0.019 0.046 -10000 0 -0.32 5 5
Rab GGTase beta/Rab GGTase alpha 0.051 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 0.05 0.059 0.36 4 -10000 0 4
RABGGTA 0.035 0.005 -10000 0 -10000 0 0
BCAR1 -0.019 0.021 0.34 1 -10000 0 1
RHOC 0.022 0.044 -10000 0 -0.33 4 4
RHOA 0.022 0.047 -10000 0 -0.32 5 5
cell motility 0.049 0.065 0.32 5 -0.33 3 8
PRL-1/alpha Tubulin 0.049 0.058 0.36 4 -10000 0 4
PRL-3/alpha1 Integrin 0.041 0.028 -10000 0 -0.3 1 1
ROCK1 0.049 0.059 0.32 4 -0.35 2 6
RABGGTB 0.035 0.005 -10000 0 -10000 0 0
CDK2 0.035 0.004 -10000 0 -10000 0 0
mitosis 0.007 0.006 -10000 0 -10000 0 0
ATF5 0.035 0.004 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.023 0.021 -10000 0 -0.2 1 1
TRAF2/ASK1 0.04 0.023 -10000 0 -0.25 1 1
ATM 0.032 0.011 -10000 0 -10000 0 0
MAP2K3 -0.011 0.12 -10000 0 -0.35 24 24
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.002 0.1 0.25 1 -0.31 25 26
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.011 0.13 -10000 0 -0.42 35 35
TXN 0.01 0.003 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
GADD45A 0.035 0.005 -10000 0 -10000 0 0
GADD45B 0.035 0.004 -10000 0 -10000 0 0
MAP3K1 0.034 0.007 -10000 0 -10000 0 0
MAP3K6 0.035 0.005 -10000 0 -10000 0 0
MAP3K7 0.032 0.011 -10000 0 -10000 0 0
MAP3K4 0.031 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.044 0.025 -10000 0 -0.3 1 1
TAK1/TAB family -0.009 0.031 -10000 0 -0.14 16 16
RAC1/OSM/MEKK3 0.057 0.025 -10000 0 -10000 0 0
TRAF2 0.033 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.015 0.099 -10000 0 -0.28 23 23
TRAF6 0.01 0.002 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.021 0.063 -10000 0 -0.42 7 7
CCM2 0.031 0.011 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.033 0.044 -10000 0 -0.25 7 7
MAPK11 0.033 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.044 0.05 -10000 0 -0.22 8 8
OSM/MEKK3 0.045 0.019 -10000 0 -10000 0 0
TAOK1 0.018 0.007 -10000 0 -10000 0 0
TAOK2 0.018 0.007 -10000 0 -10000 0 0
TAOK3 0.018 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.011 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.03 0.026 -10000 0 -0.42 1 1
MAP3K10 0.035 0.004 -10000 0 -10000 0 0
MAP3K3 0.034 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.027 0.024 -10000 0 -0.11 8 8
GADD45/MTK1/MTK1 0.043 0.087 -10000 0 -0.21 35 35
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.033 0.024 -10000 0 -0.42 1 1
HDAC2 0.031 0.011 -10000 0 -10000 0 0
GNB1/GNG2 0.049 0.063 -10000 0 -0.25 13 13
forebrain development 0.049 0.07 -10000 0 -0.33 5 5
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
SMO/beta Arrestin2 0.038 0.053 -10000 0 -0.29 8 8
SMO 0.022 0.067 -10000 0 -0.42 8 8
ARRB2 0.034 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.049 0.074 0.24 1 -0.27 3 4
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.034 0.006 -10000 0 -10000 0 0
GNAI2 0.035 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.081 0.028 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
XPO1 0.037 0.006 -10000 0 -10000 0 0
GLI1/Su(fu) 0.04 0.073 -10000 0 -0.35 2 2
SAP30 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0.022 0.067 -10000 0 -0.42 8 8
MIM/GLI2A 0.027 0.042 -10000 0 -0.42 3 3
IFT88 0.032 0.025 -10000 0 -0.42 1 1
GNAI3 0.034 0.008 -10000 0 -10000 0 0
GLI2 0.036 0.058 0.22 6 -0.24 3 9
GLI3 0.032 0.073 0.23 1 -0.26 5 6
CSNK1D 0.034 0.008 -10000 0 -10000 0 0
CSNK1E 0.033 0.01 -10000 0 -10000 0 0
SAP18 0.034 0.008 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.032 0.025 -10000 0 -0.42 1 1
GNG2 0.027 0.058 -10000 0 -0.42 6 6
Gi family/GTP 0.018 0.052 -10000 0 -0.24 10 10
SIN3B 0.035 0.003 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.087 0.22 1 -0.31 14 15
GLI2/Su(fu) 0.042 0.065 0.24 3 -0.25 8 11
FOXA2 0.028 0.074 -10000 0 -0.6 4 4
neural tube patterning 0.049 0.07 -10000 0 -0.33 5 5
SPOP 0.034 0.006 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.038 0.062 -10000 0 -0.19 1 1
GNB1 0.034 0.007 -10000 0 -10000 0 0
CSNK1G2 0.035 0.004 -10000 0 -10000 0 0
CSNK1G3 0.033 0.008 -10000 0 -10000 0 0
MTSS1 0.027 0.042 -10000 0 -0.42 3 3
embryonic limb morphogenesis 0.049 0.07 -10000 0 -0.33 5 5
SUFU 0.024 0.03 -10000 0 -0.15 8 8
LGALS3 0.016 0.09 -10000 0 -0.42 15 15
catabolic process 0.072 0.09 0.33 3 -0.33 3 6
GLI3A/CBP 0.042 0.029 -10000 0 -0.32 2 2
KIF3A 0.033 0.008 -10000 0 -10000 0 0
GLI1 0.05 0.071 -10000 0 -0.34 5 5
RAB23 0.032 0.01 -10000 0 -10000 0 0
CSNK1A1 0.033 0.009 -10000 0 -10000 0 0
IFT172 0.03 0.047 -10000 0 -0.42 4 4
RBBP7 0.035 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.03 0.076 -10000 0 -0.24 12 12
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
RBBP4 0.035 0.005 -10000 0 -10000 0 0
CSNK1G1 0.035 0.004 -10000 0 -10000 0 0
PIAS1 0.035 0.005 -10000 0 -10000 0 0
PRKACA 0.035 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.052 0.057 0.25 3 -0.21 3 6
STK36 0.036 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.021 0.058 -10000 0 -0.27 8 8
PTCH1 0.046 0.1 -10000 0 -1 2 2
MIM/GLI1 0.06 0.069 -10000 0 -0.33 3 3
CREBBP 0.042 0.029 -10000 0 -0.32 2 2
Su(fu)/SIN3/HDAC complex 0.037 0.063 0.22 2 -0.37 4 6
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.026 0.06 -10000 0 -1 1 1
regulation of axonogenesis -0.014 0.032 0.23 5 -10000 0 5
myoblast fusion -0.035 0.033 0.39 1 -10000 0 1
mol:GTP 0.024 0.026 -10000 0 -0.16 6 6
regulation of calcium-dependent cell-cell adhesion -0.051 0.075 0.23 22 -10000 0 22
ARF1/GTP 0.041 0.027 -10000 0 -0.17 1 1
mol:GM1 0.011 0.018 -10000 0 -0.17 1 1
mol:Choline 0.014 0.017 -10000 0 -0.15 1 1
lamellipodium assembly 0.022 0.049 -10000 0 -0.34 5 5
MAPK3 0.03 0.026 -10000 0 -0.34 1 1
ARF6/GTP/NME1/Tiam1 0.052 0.076 -10000 0 -0.23 22 22
ARF1 0.032 0.011 -10000 0 -10000 0 0
ARF6/GDP 0.035 0.033 -10000 0 -0.4 1 1
ARF1/GDP 0.037 0.043 -10000 0 -0.37 1 1
ARF6 0.042 0.012 -10000 0 -0.14 1 1
RAB11A 0.035 0.005 -10000 0 -10000 0 0
TIAM1 0.01 0.11 -10000 0 -0.42 21 21
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.029 0.026 -10000 0 -0.34 1 1
actin filament bundle formation -0.045 0.041 0.24 3 -10000 0 3
KALRN 0.021 0.029 -10000 0 -0.24 3 3
RAB11FIP3/RAB11A 0.051 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.045 0.041 -10000 0 -0.25 3 3
NME1 0.036 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.041 0.042 -10000 0 -0.28 2 2
substrate adhesion-dependent cell spreading 0.024 0.026 -10000 0 -0.16 6 6
cortical actin cytoskeleton organization 0.022 0.049 -10000 0 -0.34 5 5
RAC1 0.031 0.012 -10000 0 -10000 0 0
liver development 0.024 0.026 -10000 0 -0.16 6 6
ARF6/GTP 0.024 0.026 -10000 0 -0.16 6 6
RhoA/GTP 0.044 0.025 -10000 0 -0.17 1 1
mol:GDP 0.02 0.039 -10000 0 -0.23 6 6
ARF6/GTP/RAB11FIP3/RAB11A 0.064 0.027 -10000 0 -0.15 1 1
RHOA 0.035 0.005 -10000 0 -10000 0 0
PLD1 0.025 0.021 -10000 0 -0.17 1 1
RAB11FIP3 0.035 0.003 -10000 0 -10000 0 0
tube morphogenesis 0.022 0.049 -10000 0 -0.34 5 5
ruffle organization 0.014 0.032 -10000 0 -0.23 5 5
regulation of epithelial cell migration 0.024 0.026 -10000 0 -0.16 6 6
PLD2 0.024 0.021 -10000 0 -0.17 1 1
PIP5K1A 0.014 0.032 -10000 0 -0.23 5 5
mol:Phosphatidic acid 0.014 0.017 -10000 0 -0.15 1 1
Rac1/GTP 0.022 0.049 -10000 0 -0.34 5 5
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.042 0.023 -10000 0 -10000 0 0
PDGFRB 0.034 0.01 -10000 0 -10000 0 0
SPHK1 0.006 0.099 -10000 0 -0.68 7 7
mol:S1P 0.01 0.089 -10000 0 -0.58 7 7
S1P1/S1P/Gi 0.023 0.074 0.24 2 -0.34 7 9
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/PLCgamma1 0.052 0.086 0.28 10 -0.32 5 15
PLCG1 0.015 0.068 0.25 4 -0.34 5 9
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.01 -10000 0 -10000 0 0
GNAI2 0.035 0.008 -10000 0 -10000 0 0
GNAI3 0.035 0.008 -10000 0 -10000 0 0
GNAI1 0.032 0.013 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.006 0.009 -10000 0 -10000 0 0
S1P1/S1P 0.017 0.071 -10000 0 -0.44 6 6
negative regulation of cAMP metabolic process 0.023 0.073 0.24 2 -0.33 7 9
MAPK3 0.018 0.085 0.34 2 -0.48 5 7
calcium-dependent phospholipase C activity 0 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
KDR 0.034 0.008 -10000 0 -10000 0 0
PLCB2 0.034 0.093 0.3 7 -0.41 7 14
RAC1 0.031 0.012 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.058 -10000 0 -0.37 6 6
receptor internalization 0.015 0.065 -10000 0 -0.41 6 6
PTGS2 0.035 0.13 0.4 2 -1 3 5
Rac1/GTP 0.014 0.058 -10000 0 -0.37 6 6
RHOA 0.035 0.005 -10000 0 -10000 0 0
VEGFA 0.03 0.013 -10000 0 -10000 0 0
negative regulation of T cell proliferation 0.023 0.073 0.24 2 -0.33 7 9
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
MAPK1 0.018 0.082 -10000 0 -0.48 5 5
S1P1/S1P/PDGFB-D/PDGFRB 0.039 0.075 0.27 3 -0.35 7 10
ABCC1 0.035 0.024 -10000 0 -0.42 1 1
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 0.034 0.024 -10000 0 -0.42 1 1
HDAC3 0.033 0.008 -10000 0 -10000 0 0
VDR 0.032 0.034 -10000 0 -0.42 2 2
Cbp/p300/PCAF 0.061 0.033 -10000 0 -0.25 2 2
EP300 0.032 0.011 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.036 0.059 0.18 6 -0.25 3 9
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
MAPK14 0.032 0.011 -10000 0 -10000 0 0
AKT1 0.009 0.069 0.23 4 -0.24 18 22
RAR alpha/9cRA/Cyclin H 0.054 0.063 -10000 0 -0.22 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.056 -10000 0 -0.22 6 6
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.035 0.03 -10000 0 -0.16 5 5
NCOR2 0.034 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.024 0.024 -10000 0 -0.29 2 2
RXRs/RARs/NRIP1/9cRA 0.028 0.081 -10000 0 -0.41 2 2
NCOA2 0.032 0.011 -10000 0 -10000 0 0
NCOA3 0.033 0.01 -10000 0 -10000 0 0
NCOA1 0.035 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.032 0.034 -10000 0 -0.42 2 2
RARG 0.036 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.047 0.008 -10000 0 -10000 0 0
MAPK3 0.036 0.004 -10000 0 -10000 0 0
MAPK1 0.033 0.009 -10000 0 -10000 0 0
MAPK8 0.033 0.011 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.03 0.07 -10000 0 -0.36 3 3
RARA 0.024 0.016 -10000 0 -0.2 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.019 0.053 -10000 0 -0.21 7 7
PRKCA 0.035 0.025 -10000 0 -0.42 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 0.023 0.087 -10000 0 -0.38 4 4
RXRG -0.033 0.12 -10000 0 -0.28 70 70
RXRA 0.026 0.024 -10000 0 -0.2 1 1
RXRB 0.026 0.02 -10000 0 -0.28 1 1
VDR/Vit D3/DNA 0.024 0.024 -10000 0 -0.29 2 2
RBP1 0.026 0.058 -10000 0 -0.42 6 6
CRBP1/9-cic-RA 0.019 0.041 -10000 0 -0.29 6 6
RARB 0.021 0.084 -10000 0 -0.42 13 13
PRKCG 0.031 0.01 -10000 0 -10000 0 0
MNAT1 0.035 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs 0.01 0.072 0.25 1 -0.38 4 5
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.029 0.088 0.26 1 -0.4 7 8
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.077 0.26 2 -0.28 6 8
RXRs/RARs/NRIP1/9cRA/HDAC3 0.022 0.087 -10000 0 -0.38 4 4
positive regulation of DNA binding 0.042 0.056 -10000 0 -0.21 3 3
NRIP1 0.025 0.086 -10000 0 -0.49 1 1
RXRs/RARs 0.024 0.09 -10000 0 -0.35 8 8
RXRs/RXRs/DNA/9cRA 0.007 0.056 -10000 0 -0.36 3 3
PRKACA 0.035 0.003 -10000 0 -10000 0 0
CDK7 0.034 0.007 -10000 0 -10000 0 0
TFIIH 0.067 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.066 0.056 -10000 0 -10000 0 0
CCNH 0.034 0.008 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.06 0.027 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.033 0.008 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.051 0.056 -9999 0 -0.36 3 3
Syndecan-3/Neurocan 0.035 0.045 -9999 0 -0.37 3 3
POMC -0.018 0.14 -9999 0 -0.42 42 42
EGFR 0.027 0.035 -9999 0 -0.42 2 2
Syndecan-3/EGFR 0.037 0.045 -9999 0 -0.31 3 3
AGRP 0.026 0.011 -9999 0 -10000 0 0
NCSTN 0.032 0.011 -9999 0 -10000 0 0
PSENEN 0.035 0.004 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.031 0.041 -9999 0 -0.42 3 3
APH1A 0.032 0.011 -9999 0 -10000 0 0
NCAN 0.028 0.011 -9999 0 -10000 0 0
long-term memory 0.053 0.049 -9999 0 -0.34 3 3
Syndecan-3/IL8 0.032 0.051 -9999 0 -0.37 3 3
PSEN1 0.035 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.046 0.017 -9999 0 -10000 0 0
FYN 0.031 0.012 -9999 0 -10000 0 0
limb bud formation 0.014 0.037 -9999 0 -0.39 3 3
MC4R 0.023 0.014 -9999 0 -10000 0 0
SRC 0.033 0.01 -9999 0 -10000 0 0
PTN 0.023 0.017 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-3 0.014 0.038 -9999 0 -0.39 3 3
neuron projection morphogenesis 0.052 0.067 -9999 0 -0.35 3 3
Syndecan-3/AgRP 0.033 0.043 -9999 0 -0.37 3 3
Syndecan-3/AgRP/MC4R 0.043 0.051 -9999 0 -0.36 3 3
Fyn/Cortactin 0.044 0.02 -9999 0 -10000 0 0
SDC3 0.014 0.038 -9999 0 -0.39 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.032 0.051 -9999 0 -0.36 3 3
IL8 0.022 0.043 -9999 0 -0.42 3 3
Syndecan-3/Fyn/Cortactin 0.054 0.05 -9999 0 -0.35 3 3
Syndecan-3/CASK 0.012 0.036 -9999 0 -0.37 3 3
alpha-MSH/MC4R -0.003 0.11 -9999 0 -0.3 41 41
Gamma Secretase 0.088 0.044 -9999 0 -0.2 2 2
Nongenotropic Androgen signaling

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
PTK2 0.009 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.03 0.048 -10000 0 -0.22 5 5
regulation of S phase of mitotic cell cycle 0.023 0.015 -10000 0 -10000 0 0
GNAO1 0.019 0.029 -10000 0 -0.42 1 1
HRAS 0.035 0.006 -10000 0 -10000 0 0
SHBG/T-DHT 0.02 0.01 -10000 0 -10000 0 0
PELP1 0.033 0.009 -10000 0 -10000 0 0
AKT1 0.01 0.002 -10000 0 -10000 0 0
MAP2K1 0.02 0.054 0.19 31 -10000 0 31
T-DHT/AR 0.011 0.018 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.035 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNAI1 0.031 0.012 -10000 0 -10000 0 0
mol:GDP -0.001 0.014 -10000 0 -10000 0 0
cell proliferation 0.038 0.061 0.27 9 -10000 0 9
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
FOS 0.039 0.049 0.26 1 -10000 0 1
mol:Ca2+ 0.002 0.007 -10000 0 -0.048 3 3
MAPK3 0.028 0.055 0.3 4 -10000 0 4
MAPK1 0.028 0.051 0.21 2 -0.3 5 7
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:IP3 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.003 0.008 -10000 0 -10000 0 0
GNG2 0.027 0.058 -10000 0 -0.42 6 6
potassium channel inhibitor activity 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.044 0.028 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.045 0.022 -10000 0 -10000 0 0
SRC 0.033 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
PI3K 0.045 0.012 -10000 0 -10000 0 0
apoptosis -0.041 0.054 0.28 2 -0.26 4 6
T-DHT/AR/PELP1 0.022 0.028 -10000 0 -10000 0 0
HRAS/GDP 0.012 0.025 -10000 0 -10000 0 0
CREB1 0.042 0.055 0.26 4 -0.3 2 6
RAC1-CDC42/GTP 0.057 0.028 -10000 0 -10000 0 0
AR 0.02 0.017 -10000 0 -10000 0 0
GNB1 0.034 0.007 -10000 0 -10000 0 0
RAF1 0.034 0.052 0.2 31 -10000 0 31
RAC1-CDC42/GDP 0.041 0.028 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.037 0.032 -10000 0 -10000 0 0
MAP2K2 0.019 0.053 0.19 29 -10000 0 29
T-DHT/AR/PELP1/Src/PI3K 0.023 0.015 -10000 0 -10000 0 0
GNAZ 0.027 0.036 -10000 0 -0.42 2 2
SHBG 0.03 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.009 0.081 -10000 0 -0.4 8 8
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
GNRH1 0.003 0.042 -10000 0 -0.29 7 7
Gi family/GTP 0.01 0.03 -10000 0 -0.17 4 4
CDC42 0.035 0.005 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.035 0.004 -10000 0 -10000 0 0
PTK2 0.031 0.012 -10000 0 -10000 0 0
CRKL 0.019 0.027 0.17 3 -0.22 3 6
GRB2/SOS1/SHC 0.061 0.026 -10000 0 -10000 0 0
HRAS 0.034 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.029 0.027 -10000 0 -0.22 3 3
IGF-1R heterotetramer/IGF1/PTP1B 0.056 0.039 -10000 0 -0.24 3 3
AKT1 0.014 0.038 0.18 9 -0.19 3 12
BAD -0.002 0.038 0.18 7 -0.18 3 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.026 0.17 2 -0.22 3 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.041 0.032 0.22 2 -0.22 3 5
RAF1 0.024 0.067 0.28 1 -0.38 7 8
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.075 0.038 -10000 0 -0.21 2 2
YWHAZ 0.032 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.041 0.03 0.16 1 -0.24 3 4
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
RPS6KB1 0.014 0.035 0.19 6 -0.19 2 8
GNB2L1 0.033 0.008 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.023 0.071 0.28 4 -0.33 6 10
PXN 0.034 0.006 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.05 0.011 -10000 0 -10000 0 0
HRAS/GTP 0.036 0.025 -10000 0 -0.19 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.085 0.045 -10000 0 -0.19 1 1
IGF-1R heterotetramer 0.035 0.015 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.06 0.036 -10000 0 -0.22 3 3
Crk/p130 Cas/Paxillin 0.072 0.038 0.24 1 -0.2 3 4
IGF1R 0.035 0.015 -10000 0 -10000 0 0
IGF1 0.034 0.044 -10000 0 -0.43 3 3
IRS2/Crk 0.031 0.028 0.17 2 -0.21 3 5
PI3K 0.074 0.039 -10000 0 -0.21 3 3
apoptosis -0.025 0.038 -10000 0 -0.19 6 6
HRAS/GDP 0.025 0.004 -10000 0 -10000 0 0
PRKCD 0.026 0.057 0.21 2 -0.29 7 9
RAF1/14-3-3 E 0.038 0.065 0.28 1 -0.33 7 8
BAD/14-3-3 0.026 0.039 0.19 6 -10000 0 6
PRKCZ 0.013 0.04 0.18 8 -0.19 5 13
Crk/p130 Cas/Paxillin/FAK1 0.043 0.033 -10000 0 -10000 0 0
PTPN1 0.032 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.022 0.053 -10000 0 -0.29 8 8
BCAR1 0.034 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.068 0.041 -10000 0 -0.19 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.035 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.038 0.032 -10000 0 -0.22 3 3
GRB10 0.032 0.011 -10000 0 -10000 0 0
PTPN11 0.021 0.027 0.17 3 -0.22 3 6
IRS1 0.019 0.03 0.13 5 -0.23 3 8
IRS2 0.02 0.028 0.17 3 -0.22 3 6
IGF-1R heterotetramer/IGF1 0.046 0.038 -10000 0 -0.32 3 3
GRB2 0.034 0.007 -10000 0 -10000 0 0
PDPK1 0.025 0.038 0.2 7 -0.2 3 10
YWHAE 0.033 0.009 -10000 0 -10000 0 0
PRKD1 0.027 0.052 -10000 0 -0.29 6 6
SHC1 0.032 0.011 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.018 0.033 0.15 19 -10000 0 19
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0.044 0.14 21 -0.2 2 23
AP2 0.05 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.042 0.018 -10000 0 -10000 0 0
CLTB 0.033 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.022 0.013 -10000 0 -10000 0 0
CD4 -0.008 0.13 -10000 0 -0.42 34 34
CLTA 0.032 0.011 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.01 0.011 -10000 0 -10000 0 0
ARF1/GTP 0.039 0.018 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.013 0.009 -10000 0 -10000 0 0
mol:Choline 0.009 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.033 0.011 -10000 0 -10000 0 0
DDEF1 0.008 0.011 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.014 -10000 0 -0.11 1 1
AP2M1 0.034 0.006 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.015 0.009 -10000 0 -10000 0 0
Rac/GTP 0.025 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.043 0.021 -10000 0 -10000 0 0
ARFIP2 0.026 0.019 -10000 0 -10000 0 0
COPA 0.032 0.011 -10000 0 -10000 0 0
RAC1 0.031 0.012 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.048 0.14 5 -0.2 9 14
ARF1/GTP/ARHGAP10 0.022 0.009 -10000 0 -10000 0 0
GGA3 0.034 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.025 0.044 -10000 0 -0.23 8 8
AP2A1 0.035 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.044 -10000 0 -0.21 11 11
ARF1/GDP/Membrin 0.025 0.05 -10000 0 -0.24 11 11
Arfaptin 2/Rac/GDP 0.04 0.017 -10000 0 -10000 0 0
CYTH2 0.038 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.042 0.018 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.023 0.009 -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 0.008 0.074 -10000 0 -0.22 27 27
PLD2 0.009 0.011 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.009 0.003 -10000 0 -10000 0 0
PIP5K1A 0.01 0.011 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.022 0.027 -10000 0 -0.12 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.009 0.011 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.003 -10000 0 -10000 0 0
GOSR2 0.013 0.036 -10000 0 -0.31 4 4
USO1 0.015 0.026 -10000 0 -0.32 2 2
GBF1 0.002 0.067 -10000 0 -0.31 16 16
ARF1/GTP/Arfaptin 2 0.044 0.018 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.093 -10000 0 -0.25 34 34
Coregulation of Androgen receptor activity

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
NRIP1 0.034 0.007 -9999 0 -10000 0 0
SVIL 0.032 0.01 -9999 0 -10000 0 0
ZNF318 0.032 0.011 -9999 0 -10000 0 0
JMJD2C 0.002 0.007 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.025 0.041 -9999 0 -0.16 3 3
CARM1 0.035 0.003 -9999 0 -10000 0 0
PRDX1 0.029 0.053 -9999 0 -0.42 5 5
PELP1 0.033 0.009 -9999 0 -10000 0 0
CTNNB1 0.035 0.005 -9999 0 -10000 0 0
AKT1 0.035 0.005 -9999 0 -10000 0 0
PTK2B 0.028 0.048 -9999 0 -0.42 4 4
MED1 0.034 0.006 -9999 0 -10000 0 0
MAK 0.03 0.012 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.032 0.01 -9999 0 -10000 0 0
GSN 0.033 0.009 -9999 0 -10000 0 0
NCOA2 0.032 0.011 -9999 0 -10000 0 0
NCOA6 0.033 0.009 -9999 0 -10000 0 0
DNA-PK 0.06 0.027 -9999 0 -10000 0 0
NCOA4 0.032 0.011 -9999 0 -10000 0 0
PIAS3 0.032 0.011 -9999 0 -10000 0 0
cell proliferation 0.019 0.016 -9999 0 -10000 0 0
XRCC5 0.035 0.004 -9999 0 -10000 0 0
UBE3A 0.034 0.006 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.015 0.061 -9999 0 -0.24 13 13
FHL2 0.021 0.11 -9999 0 -0.79 6 6
RANBP9 0.031 0.012 -9999 0 -10000 0 0
JMJD1A 0.001 0.028 -9999 0 -0.13 15 15
CDK6 0.029 0.042 -9999 0 -0.42 3 3
TGFB1I1 0.034 0.024 -9999 0 -0.42 1 1
T-DHT/AR/CyclinD1 0.022 0.04 -9999 0 -0.19 2 2
XRCC6 0.032 0.01 -9999 0 -10000 0 0
T-DHT/AR 0.027 0.061 -9999 0 -0.19 18 18
CTDSP1 0.035 0.004 -9999 0 -10000 0 0
CTDSP2 0.034 0.007 -9999 0 -10000 0 0
BRCA1 0.035 0.005 -9999 0 -10000 0 0
TCF4 0.03 0.041 -9999 0 -0.42 3 3
CDKN2A 0.009 0.016 -9999 0 -10000 0 0
SRF 0.037 0.022 -9999 0 -0.15 3 3
NKX3-1 -0.003 0.05 -9999 0 -0.24 15 15
KLK3 0.001 0.037 -9999 0 -10000 0 0
TMF1 0.034 0.007 -9999 0 -10000 0 0
HNRNPA1 0.035 0.004 -9999 0 -10000 0 0
AOF2 0 0 -9999 0 -10000 0 0
APPL1 0.019 0.004 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.025 0.041 -9999 0 -0.17 3 3
AR 0.017 0.03 -9999 0 -0.15 2 2
UBA3 0.034 0.007 -9999 0 -10000 0 0
PATZ1 0.034 0.007 -9999 0 -10000 0 0
PAWR 0.016 0.09 -9999 0 -0.42 15 15
PRKDC 0.033 0.009 -9999 0 -10000 0 0
PA2G4 0.035 0.005 -9999 0 -10000 0 0
UBE2I 0.035 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.022 0.034 -9999 0 -0.082 1 1
RPS6KA3 0.035 0.003 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.022 0.04 -9999 0 -0.19 2 2
LATS2 0.034 0.008 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.02 0.047 -9999 0 -0.2 7 7
Cyclin D3/CDK11 p58 0.024 0.008 -9999 0 -10000 0 0
VAV3 0.029 0.042 -9999 0 -0.42 3 3
KLK2 0.008 0.03 -9999 0 -10000 0 0
CASP8 0.035 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.038 0.045 -9999 0 -0.17 2 2
TMPRSS2 -0.015 0.18 -9999 0 -0.88 15 15
CCND1 0.033 0.01 -9999 0 -10000 0 0
PIAS1 0.035 0.005 -9999 0 -10000 0 0
mol:T-DHT 0 0.017 -9999 0 -0.067 19 19
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.035 0.004 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.021 0.047 -9999 0 -0.22 5 5
CMTM2 0.031 0.01 -9999 0 -10000 0 0
SNURF 0.02 0.077 -9999 0 -0.42 11 11
ZMIZ1 0.03 0.027 -9999 0 -0.14 2 2
CCND3 0.032 0.011 -9999 0 -10000 0 0
TGIF1 0.034 0.007 -9999 0 -10000 0 0
FKBP4 0.034 0.007 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.077 0.041 -10000 0 -0.22 3 3
HDAC3 0.033 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.009 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.037 0.009 -10000 0 -10000 0 0
GATA1/HDAC5 0.038 0.008 -10000 0 -10000 0 0
GATA2/HDAC5 0.048 0.016 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.067 0.018 -10000 0 -10000 0 0
HDAC9 0.012 0.09 -10000 0 -0.42 15 15
Glucocorticoid receptor/Hsp90/HDAC6 0.065 0.025 -10000 0 -0.23 1 1
HDAC4/ANKRA2 0.047 0.024 -10000 0 -0.3 1 1
HDAC5/YWHAB 0.047 0.016 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.02 0.007 -10000 0 -10000 0 0
GATA2 0.033 0.008 -10000 0 -10000 0 0
HDAC4/RFXANK 0.049 0.014 -10000 0 -10000 0 0
BCOR 0.035 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.033 0.01 -10000 0 -10000 0 0
HDAC5 0.034 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.045 0.041 -10000 0 -0.29 5 5
Histones 0.032 0.061 -10000 0 -0.29 4 4
ADRBK1 0.034 0.007 -10000 0 -10000 0 0
HDAC4 0.033 0.008 -10000 0 -10000 0 0
XPO1 0.035 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.048 0.022 -10000 0 -0.3 1 1
HDAC4/Ubc9 0.049 0.013 -10000 0 -10000 0 0
HDAC7 0.034 0.006 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.048 0.015 -10000 0 -10000 0 0
TUBA1B 0.035 0.005 -10000 0 -10000 0 0
HDAC6 0.035 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.05 0.011 -10000 0 -10000 0 0
CAMK4 -0.026 0.15 -10000 0 -0.42 48 48
Tubulin/HDAC6 0.061 0.026 -10000 0 -10000 0 0
SUMO1 0.035 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.033 0.01 -10000 0 -10000 0 0
GATA1 0.017 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.033 0.009 -10000 0 -10000 0 0
NR3C1 0.033 0.009 -10000 0 -10000 0 0
SUMO1/HDAC4 0.059 0.029 0.18 1 -10000 0 1
SRF 0.032 0.011 -10000 0 -10000 0 0
HDAC4/YWHAB 0.046 0.017 -10000 0 -10000 0 0
Tubulin 0.045 0.019 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.046 0.017 -10000 0 -10000 0 0
GNB1 0.034 0.007 -10000 0 -10000 0 0
RANGAP1 0.032 0.01 -10000 0 -10000 0 0
BCL6/BCoR 0.051 0.01 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.063 0.024 -10000 0 -10000 0 0
HDAC4/SRF 0.022 0.1 -10000 0 -0.25 41 41
HDAC4/ER alpha 0.039 0.047 -10000 0 -0.29 6 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.061 -10000 0 -0.29 4 4
cell motility 0.061 0.025 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.035 0.003 -10000 0 -10000 0 0
HDAC7/HDAC3 0.048 0.015 -10000 0 -10000 0 0
BCL6 0.034 0.006 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.033 0.008 -10000 0 -10000 0 0
Hsp90/HDAC6 0.05 0.02 -10000 0 -0.3 1 1
ESR1 0.023 0.058 -10000 0 -0.42 6 6
HDAC6/HDAC11 0.051 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.06 0.029 -10000 0 -0.16 1 1
NPC 0.021 0.002 -10000 0 -10000 0 0
MEF2C 0.031 0.034 -10000 0 -0.42 2 2
RAN 0.034 0.006 -10000 0 -10000 0 0
HDAC4/MEF2C 0.089 0.042 -10000 0 -0.19 2 2
GNG2 0.027 0.058 -10000 0 -0.42 6 6
NCOR2 0.034 0.006 -10000 0 -10000 0 0
TUBB2A 0.031 0.012 -10000 0 -10000 0 0
HDAC11 0.035 0.005 -10000 0 -10000 0 0
HSP90AA1 0.033 0.024 -10000 0 -0.42 1 1
RANBP2 0.035 0.003 -10000 0 -10000 0 0
ANKRA2 0.033 0.025 -10000 0 -0.42 1 1
RFXANK 0.035 0.004 -10000 0 -10000 0 0
nuclear import -0.039 0.02 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A 0.047 0.028 -10000 0 -10000 0 0
BIRC5 0.034 0.007 -10000 0 -10000 0 0
NFKBIA 0.013 0.013 -10000 0 -10000 0 0
CPEB1 0.001 0.12 -10000 0 -0.42 27 27
AKT1 0.013 0.013 -10000 0 -10000 0 0
NDEL1 0.033 0.009 -10000 0 -10000 0 0
Aurora A/BRCA1 0.034 0.021 -10000 0 -10000 0 0
NDEL1/TACC3 0.056 0.03 -10000 0 -10000 0 0
GADD45A 0.035 0.005 -10000 0 -10000 0 0
GSK3B 0.033 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.045 0.027 -10000 0 -10000 0 0
MDM2 0.033 0.008 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.018 0.006 -10000 0 -10000 0 0
TP53 0.026 0.025 0.17 1 -0.18 3 4
DLG7 0.014 0.013 -10000 0 -10000 0 0
AURKAIP1 0.034 0.007 -10000 0 -10000 0 0
ARHGEF7 0.034 0.008 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.06 0.032 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.034 0.021 -10000 0 -10000 0 0
AURKA 0.024 0.017 0.15 1 -10000 0 1
AURKB 0.017 0.025 -10000 0 -0.27 2 2
CDC25B 0.024 0.013 -10000 0 -10000 0 0
G2/M transition checkpoint 0.013 0.016 -10000 0 -10000 0 0
mRNA polyadenylation 0.016 0.066 -10000 0 -0.21 24 24
Aurora A/CPEB 0.016 0.066 -10000 0 -0.21 24 24
Aurora A/TACC1/TRAP/chTOG 0.075 0.041 -10000 0 -0.2 1 1
BRCA1 0.035 0.005 -10000 0 -10000 0 0
centrosome duplication 0.044 0.027 -10000 0 -10000 0 0
regulation of centrosome cycle 0.055 0.03 -10000 0 -10000 0 0
spindle assembly 0.072 0.04 -10000 0 -0.2 1 1
TDRD7 0.032 0.025 -10000 0 -0.42 1 1
Aurora A/RasGAP/Survivin 0.07 0.038 -10000 0 -0.2 1 1
CENPA 0.019 0.037 -10000 0 -0.27 5 5
Aurora A/PP2A 0.042 0.029 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.034 0.04 0.19 8 -10000 0 8
negative regulation of DNA binding 0.018 0.05 0.17 2 -0.18 20 22
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.049 0.014 -10000 0 -10000 0 0
RASA1 0.032 0.025 -10000 0 -0.42 1 1
Ajuba/Aurora A 0.013 0.016 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.017 0.15 1 -10000 0 1
TACC1 0.034 0.008 -10000 0 -10000 0 0
TACC3 0.034 0.008 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.063 0.03 -10000 0 -10000 0 0
Aurora A/RasGAP 0.045 0.032 -10000 0 -0.24 1 1
OAZ1 0.035 0.004 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.034 0.008 -10000 0 -10000 0 0
GIT1 0.034 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.062 0.025 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.018 0.006 -10000 0 -10000 0 0
PPP2R5D 0.032 0.011 -10000 0 -10000 0 0
Aurora A/TPX2 0.031 0.021 -10000 0 -10000 0 0
PAK1 0.033 0.009 -10000 0 -10000 0 0
CKAP5 0.034 0.006 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.03 0.048 -10000 0 -0.42 4 4
PDGF/PDGFRA/CRKL 0.042 0.04 -10000 0 -0.28 4 4
positive regulation of JUN kinase activity 0.069 0.043 -10000 0 -0.21 3 3
CRKL 0.033 0.01 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.033 0.035 -10000 0 -0.28 4 4
AP1 0.016 0.044 -10000 0 -10000 0 0
mol:IP3 0.014 0.031 -10000 0 -0.3 3 3
PLCG1 0.014 0.031 -10000 0 -0.3 3 3
PDGF/PDGFRA/alphaV Integrin 0.046 0.038 -10000 0 -0.28 4 4
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
CRK 0.033 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.031 -10000 0 -0.3 3 3
CAV3 0.017 0.002 -10000 0 -10000 0 0
CAV1 0.032 0.011 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.071 0.044 -10000 0 -0.21 3 3
PDGF/PDGFRA/Shf 0.043 0.039 -10000 0 -0.28 4 4
FOS -0.001 0.036 0.32 1 -10000 0 1
JUN -0.019 0.014 -10000 0 -10000 0 0
oligodendrocyte development 0.045 0.038 -10000 0 -0.28 4 4
GRB2 0.034 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
mol:DAG 0.014 0.031 -10000 0 -0.3 3 3
PDGF/PDGFRA 0.03 0.048 -10000 0 -0.42 4 4
actin cytoskeleton reorganization 0.037 0.045 -10000 0 -0.29 5 5
SRF 0.014 0.01 -10000 0 -10000 0 0
SHC1 0.032 0.011 -10000 0 -10000 0 0
PI3K 0.06 0.039 -10000 0 -0.22 4 4
PDGF/PDGFRA/Crk/C3G 0.056 0.042 -10000 0 -0.23 4 4
JAK1 0.015 0.033 -10000 0 -0.28 4 4
ELK1/SRF 0.019 0.04 0.16 21 -0.23 2 23
SHB 0.028 0.035 -10000 0 -0.42 2 2
SHF 0.034 0.007 -10000 0 -10000 0 0
CSNK2A1 0.029 0.015 -10000 0 -10000 0 0
GO:0007205 0.006 0.031 -10000 0 -0.32 3 3
SOS1 0.035 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.069 0.043 -10000 0 -0.21 3 3
PDGF/PDGFRA/SHB 0.037 0.045 -10000 0 -0.29 5 5
PDGF/PDGFRA/Caveolin-1 0.04 0.04 -10000 0 -0.28 4 4
ITGAV 0.035 0.004 -10000 0 -10000 0 0
ELK1 0.003 0.026 0.25 1 -0.28 2 3
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.042 0.04 -10000 0 -0.28 4 4
JAK-STAT cascade 0.015 0.033 -10000 0 -0.28 4 4
cell proliferation 0.043 0.039 -10000 0 -0.28 4 4
Signaling events mediated by HDAC Class III

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
EP300 0.032 0.011 -10000 0 -10000 0 0
HDAC4 0.033 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 -0.005 0.051 0.3 10 -10000 0 10
CDKN1A -0.006 0.005 -10000 0 -10000 0 0
KAT2B 0.032 0.034 -10000 0 -0.42 2 2
BAX 0.035 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.005 -10000 0 -10000 0 0
FOXO1 0.034 0.007 -10000 0 -10000 0 0
FOXO4 0.02 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.01 -10000 0 -10000 0 0
TAT 0.017 0.003 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.003 0.028 -10000 0 -0.3 2 2
PPARGC1A 0.009 0.074 -10000 0 -0.42 10 10
FHL2 0.029 0.053 -10000 0 -0.42 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.041 0.019 -10000 0 -10000 0 0
HIST2H4A 0.005 0.051 -10000 0 -0.3 10 10
SIRT1/FOXO3a -0.002 0.059 -10000 0 -0.19 30 30
SIRT1 0.028 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.054 0.029 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.047 0.038 0.18 10 -10000 0 10
apoptosis -0.056 0.026 -10000 0 -10000 0 0
SIRT1/PGC1A 0.014 0.051 -10000 0 -0.25 10 10
p53/SIRT1 0.036 0.015 -10000 0 -10000 0 0
SIRT1/FOXO4 0.04 0.03 0.18 2 -10000 0 2
FOXO1/FHL2/SIRT1 0.054 0.039 -10000 0 -0.22 5 5
HIST1H1E 0.018 0.009 -10000 0 -10000 0 0
SIRT1/p300 0.04 0.019 -10000 0 -10000 0 0
muscle cell differentiation -0.038 0.027 0.25 2 -0.23 1 3
TP53 0.029 0.008 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.057 0.026 -10000 0 -10000 0 0
CREBBP 0.035 0.004 -10000 0 -10000 0 0
MEF2D 0.032 0.011 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.032 0.011 -10000 0 -10000 0 0
ACSS2 0.014 0.007 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.038 0.027 0.23 1 -0.26 2 3
Reelin 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
CDK5R1/CDK5 0.044 0.025 -10000 0 -0.3 1 1
VLDLR 0.021 0.067 -10000 0 -0.42 8 8
CRKL 0.033 0.01 -10000 0 -10000 0 0
LRPAP1 0.034 0.008 -10000 0 -10000 0 0
FYN 0.031 0.012 -10000 0 -10000 0 0
ITGA3 0.032 0.01 -10000 0 -10000 0 0
RELN/VLDLR/Fyn 0.03 0.055 -10000 0 -0.25 7 7
MAPK8IP1/MKK7/MAP3K11/JNK1 0.079 0.047 -10000 0 -0.2 1 1
AKT1 0.002 0.043 -10000 0 -0.2 7 7
MAP2K7 0.035 0.004 -10000 0 -10000 0 0
RAPGEF1 0.033 0.009 -10000 0 -10000 0 0
DAB1 0.021 0.012 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.034 0.035 -10000 0 -10000 0 0
LRPAP1/LRP8 0.049 0.013 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.046 0.036 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin 0.039 0.051 -10000 0 -0.2 7 7
long-term memory 0.048 0.042 -10000 0 -10000 0 0
DAB1/LIS1 0.052 0.058 -10000 0 -0.21 7 7
DAB1/CRLK/C3G 0.041 0.051 -10000 0 -0.2 7 7
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
DAB1/NCK2 0.055 0.059 -10000 0 -0.21 7 7
ARHGEF2 0.031 0.026 -10000 0 -0.42 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.031 0.01 -10000 0 -10000 0 0
CDK5R1 0.033 0.024 -10000 0 -0.42 1 1
RELN 0.024 0.016 -10000 0 -10000 0 0
PIK3R1 0.034 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.039 0.039 -10000 0 -10000 0 0
GRIN2A/RELN/LRP8/DAB1/Fyn 0.058 0.044 -10000 0 -10000 0 0
MAPK8 0.032 0.01 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.023 0.049 -10000 0 -0.23 7 7
ITGB1 0.032 0.011 -10000 0 -10000 0 0
MAP1B 0.016 0.049 0.17 4 -0.21 7 11
RELN/LRP8 0.043 0.038 -10000 0 -10000 0 0
GRIN2B/RELN/LRP8/DAB1/Fyn 0.052 0.044 -10000 0 -10000 0 0
PI3K 0.049 0.014 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.042 0.022 -10000 0 -10000 0 0
RAP1A 0.019 0.079 0.32 8 -10000 0 8
PAFAH1B1 0.033 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.033 0.008 -10000 0 -10000 0 0
CRLK/C3G 0.045 0.018 -10000 0 -10000 0 0
GRIN2B 0.022 0.013 -10000 0 -10000 0 0
NCK2 0.035 0.004 -10000 0 -10000 0 0
neuron differentiation 0.02 0.062 -10000 0 -0.28 6 6
neuron adhesion 0.015 0.08 0.32 7 -10000 0 7
LRP8 0.035 0.004 -10000 0 -10000 0 0
GSK3B 0.004 0.045 -10000 0 -0.19 7 7
RELN/VLDLR/DAB1/Fyn 0.037 0.05 -10000 0 -0.22 7 7
MAP3K11 0.034 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.014 0.036 -10000 0 -0.21 7 7
CDK5 0.031 0.011 -10000 0 -10000 0 0
MAPT -0.002 0.063 0.68 3 -10000 0 3
neuron migration 0.02 0.078 0.24 25 -0.24 1 26
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.021 0.06 -10000 0 -0.28 5 5
RELN/VLDLR 0.051 0.055 -10000 0 -0.23 7 7
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.03 0.013 -10000 0 -10000 0 0
CLTC 0.031 0.058 -10000 0 -0.37 6 6
calcium ion-dependent exocytosis 0.026 0.029 -10000 0 -10000 0 0
Dynamin 2/GTP 0.035 0.008 -10000 0 -10000 0 0
EXOC4 0.031 0.012 -10000 0 -10000 0 0
CD59 0.022 0.042 -10000 0 -0.29 5 5
CPE 0.017 0.025 -10000 0 -0.25 3 3
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
membrane fusion 0.025 0.029 -10000 0 -10000 0 0
CTNND1 0.02 0.02 0.19 5 -10000 0 5
DNM2 0.035 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.038 0.17 1 -0.23 2 3
TSHR -0.003 0.072 -10000 0 -0.25 29 29
INS 0.006 0.081 -10000 0 -0.46 10 10
BIN1 0.017 0.09 -10000 0 -0.42 15 15
mol:Choline 0.025 0.029 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.004 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.035 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.035 0.008 -10000 0 -10000 0 0
JUP 0.021 0.041 -10000 0 -0.29 5 5
ASAP2/amphiphysin II 0.055 0.058 -10000 0 -0.22 15 15
ARF6/GTP 0.026 0.003 -10000 0 -10000 0 0
CDH1 -0.024 0.093 -10000 0 -0.39 6 6
clathrin-independent pinocytosis 0.026 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.035 0.003 -10000 0 -10000 0 0
positive regulation of endocytosis 0.026 0.003 -10000 0 -10000 0 0
EXOC2 0.031 0.012 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.028 0.046 -10000 0 -0.2 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.034 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.015 0.089 0.32 6 -10000 0 6
positive regulation of phagocytosis 0.019 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.047 0.007 -10000 0 -10000 0 0
ACAP1 -0.005 0.063 -10000 0 -0.19 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.019 0.049 -10000 0 -0.3 6 6
clathrin heavy chain/ACAP1 0.023 0.053 0.27 1 -0.29 6 7
JIP4/KLC1 0.064 0.016 -10000 0 -10000 0 0
EXOC1 0.035 0.005 -10000 0 -10000 0 0
exocyst 0.028 0.046 -10000 0 -0.21 2 2
RALA/GTP 0.023 0.008 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.046 0.01 -10000 0 -10000 0 0
receptor recycling 0.026 0.003 -10000 0 -10000 0 0
CTNNA1 0.019 0.021 0.19 5 -10000 0 5
NME1 0.019 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0.031 0.06 -10000 0 -0.36 6 6
IL2RA -0.015 0.088 -10000 0 -0.42 6 6
VAMP3 0.019 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.034 0.052 -10000 0 -0.27 7 7
EXOC6 0.031 0.026 -10000 0 -0.42 1 1
PLD1 0.018 0.011 -10000 0 -10000 0 0
PLD2 0.017 0.011 -10000 0 -10000 0 0
EXOC5 0.035 0.005 -10000 0 -10000 0 0
PIP5K1C 0.023 0.034 -10000 0 -0.23 2 2
SDC1 0.017 0.052 -10000 0 -0.31 6 6
ARF6/GDP 0.032 0.007 -10000 0 -10000 0 0
EXOC7 0.034 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.017 0.092 -10000 0 -0.33 6 6
mol:Phosphatidic acid 0.025 0.029 -10000 0 -10000 0 0
endocytosis -0.052 0.057 0.22 15 -10000 0 15
SCAMP2 0.034 0.006 -10000 0 -10000 0 0
ADRB2 0.028 0.06 0.23 1 -0.34 6 7
EXOC3 0.032 0.01 -10000 0 -10000 0 0
ASAP2 0.035 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.04 0.009 -10000 0 -10000 0 0
KLC1 0.034 0.006 -10000 0 -10000 0 0
AVPR2 0.03 0.061 -10000 0 -0.35 6 6
RALA 0.031 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.015 0.089 0.36 1 -0.31 6 7
FOXM1 transcription factor network

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
NFATC3 0.24 0.15 -10000 0 -1 2 2
PLK1 0.084 0.062 -10000 0 -0.55 2 2
BIRC5 0.08 0.076 -10000 0 -0.67 2 2
HSPA1B 0.26 0.17 0.7 2 -1 2 4
MAP2K1 0.07 0.027 -10000 0 -10000 0 0
BRCA2 0.24 0.2 0.7 1 -1.1 6 7
FOXM1 0.26 0.17 -10000 0 -1.2 2 2
XRCC1 0.24 0.15 -10000 0 -1 2 2
FOXM1B/p19 0.048 0.15 -10000 0 -1.1 2 2
Cyclin D1/CDK4 0.21 0.16 -10000 0 -0.86 2 2
CDC2 0.25 0.16 -10000 0 -1.1 2 2
TGFA 0.19 0.18 -10000 0 -0.85 3 3
SKP2 0.25 0.16 -10000 0 -0.96 2 2
CCNE1 0.043 0.007 -10000 0 -10000 0 0
CKS1B 0.24 0.15 -10000 0 -1 2 2
RB1 0.16 0.13 -10000 0 -0.87 2 2
FOXM1C/SP1 0.25 0.16 -10000 0 -1.1 2 2
AURKB 0.042 0.18 -10000 0 -0.69 13 13
CENPF 0.26 0.17 0.69 1 -1.2 2 3
CDK4 0.048 0.014 -10000 0 -10000 0 0
MYC 0.21 0.16 -10000 0 -0.88 2 2
CHEK2 0.067 0.03 -10000 0 -10000 0 0
ONECUT1 0.14 0.18 -10000 0 -0.96 2 2
CDKN2A 0.008 0.013 -10000 0 -10000 0 0
LAMA4 0.24 0.15 -10000 0 -1 2 2
FOXM1B/HNF6 0.14 0.19 -10000 0 -1.1 2 2
FOS 0.24 0.15 -10000 0 -1 2 2
SP1 0.036 0.005 -10000 0 -10000 0 0
CDC25B 0.25 0.16 -10000 0 -1 2 2
response to radiation 0.033 0.016 -10000 0 -10000 0 0
CENPB 0.25 0.16 -10000 0 -1 2 2
CENPA 0.24 0.17 -10000 0 -1.4 2 2
NEK2 0.26 0.19 0.69 1 -1.3 3 4
HIST1H2BA 0.26 0.17 0.69 2 -1 2 4
CCNA2 0.042 0.026 -10000 0 -0.43 1 1
EP300 0.032 0.011 -10000 0 -10000 0 0
CCNB1/CDK1 0.25 0.16 -10000 0 -1.2 2 2
CCNB2 0.24 0.2 0.73 2 -0.99 6 8
CCNB1 0.25 0.16 -10000 0 -1.1 2 2
ETV5 0.24 0.16 0.7 1 -1 3 4
ESR1 0.23 0.22 -10000 0 -0.99 9 9
CCND1 0.2 0.16 -10000 0 -0.93 2 2
GSK3A 0.067 0.023 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.1 0.031 -10000 0 -10000 0 0
CDK2 0.043 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.038 0.018 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.23 0.17 -10000 0 -1.1 2 2
GAS1 0.24 0.18 -10000 0 -1 5 5
MMP2 0.24 0.18 -10000 0 -1 4 4
RB1/FOXM1C 0.22 0.17 0.6 1 -0.88 3 4
CREBBP 0.035 0.004 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.036 0.11 -9999 0 -0.33 13 13
CaM/Ca2+ 0.025 0.004 -9999 0 -10000 0 0
AKT1 0.035 0.005 -9999 0 -10000 0 0
AKT2 0.035 0.004 -9999 0 -10000 0 0
STXBP4 0.034 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.012 0.11 -9999 0 -0.36 14 14
YWHAZ 0.032 0.011 -9999 0 -10000 0 0
CALM1 0.034 0.006 -9999 0 -10000 0 0
YWHAQ 0.035 0.004 -9999 0 -10000 0 0
TBC1D4 0.017 0.017 -9999 0 -0.3 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.034 0.008 -9999 0 -10000 0 0
YWHAB 0.033 0.01 -9999 0 -10000 0 0
SNARE/Synip 0.064 0.023 -9999 0 -10000 0 0
YWHAG 0.033 0.01 -9999 0 -10000 0 0
ASIP 0.027 0.013 -9999 0 -10000 0 0
PRKCI 0.034 0.006 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0.025 0.004 -9999 0 -10000 0 0
RHOQ 0.035 0.003 -9999 0 -10000 0 0
GYS1 0.018 0.005 -9999 0 -10000 0 0
PRKCZ 0.032 0.034 -9999 0 -0.42 2 2
TRIP10 0.035 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.047 0.007 -9999 0 -10000 0 0
AS160/14-3-3 0.029 0.044 -9999 0 -0.22 4 4
VAMP2 0.033 0.009 -9999 0 -10000 0 0
SLC2A4 0.01 0.12 -9999 0 -0.4 14 14
STX4 0.035 0.004 -9999 0 -10000 0 0
GSK3B 0.029 0.008 -9999 0 -10000 0 0
SFN 0.027 0.015 -9999 0 -10000 0 0
LNPEP 0.034 0.008 -9999 0 -10000 0 0
YWHAE 0.033 0.009 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.042 0.05 -10000 0 -0.21 10 10
MAPK9 0.01 0.003 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.009 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.041 0.035 -10000 0 -0.24 5 5
GNB1 0.034 0.007 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.003 -10000 0 -10000 0 0
Gs family/GTP 0.015 0.03 -10000 0 -0.22 5 5
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 0.002 0.007 0.062 5 -10000 0 5
GNAL 0.024 0.053 -10000 0 -0.42 5 5
GNG2 0.027 0.058 -10000 0 -0.42 6 6
CRH 0.016 0.005 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.003 -10000 0 -10000 0 0
MAPK11 0.01 0.003 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.035 0.005 -10000 0 -10000 0 0
SMAD2 0.007 0.035 0.17 1 -0.2 1 2
SMAD3 0.039 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4 0.053 0.05 -10000 0 -0.36 4 4
SMAD4/Ubc9/PIASy 0.069 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.064 0.047 -10000 0 -10000 0 0
PPM1A 0.035 0.005 -10000 0 -10000 0 0
CALM1 0.034 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.027 0.037 -10000 0 -0.19 1 1
MAP3K1 0.034 0.007 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.051 0.008 -10000 0 -10000 0 0
MAPK3 0.035 0.004 -10000 0 -10000 0 0
MAPK1 0.033 0.009 -10000 0 -10000 0 0
NUP214 0.033 0.009 -10000 0 -10000 0 0
CTDSP1 0.035 0.004 -10000 0 -10000 0 0
CTDSP2 0.034 0.007 -10000 0 -10000 0 0
CTDSPL 0.035 0.005 -10000 0 -10000 0 0
KPNB1 0.034 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.035 0.003 -10000 0 -10000 0 0
UBE2I 0.035 0.003 -10000 0 -10000 0 0
NUP153 0.031 0.012 -10000 0 -10000 0 0
KPNA2 0.034 0.007 -10000 0 -10000 0 0
PIAS4 0.035 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.048 0.015 -9999 0 -10000 0 0
ATM 0.032 0.011 -9999 0 -10000 0 0
UBE2D3 0.034 0.006 -9999 0 -10000 0 0
PRKDC 0.033 0.009 -9999 0 -10000 0 0
ATR 0.034 0.006 -9999 0 -10000 0 0
UBE2L3 0.033 0.009 -9999 0 -10000 0 0
FANCD2 0.027 0.01 -9999 0 -10000 0 0
protein ubiquitination 0.083 0.034 -9999 0 -10000 0 0
XRCC5 0.035 0.004 -9999 0 -10000 0 0
XRCC6 0.032 0.01 -9999 0 -10000 0 0
M/R/N Complex 0.056 0.037 -9999 0 -0.25 2 2
MRE11A 0.032 0.01 -9999 0 -10000 0 0
DNA-PK 0.06 0.027 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.006 0.13 -9999 0 -0.47 21 21
FANCF 0.035 0.005 -9999 0 -10000 0 0
BRCA1 0.035 0.005 -9999 0 -10000 0 0
CCNE1 0.035 0.004 -9999 0 -10000 0 0
CDK2/Cyclin E1 0.051 0.009 -9999 0 -10000 0 0
FANCG 0.032 0.011 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 0.051 0.01 -9999 0 -10000 0 0
FANCE 0.032 0.011 -9999 0 -10000 0 0
FANCC 0.033 0.009 -9999 0 -10000 0 0
NBN 0.032 0.011 -9999 0 -10000 0 0
FANCA 0.033 0.008 -9999 0 -10000 0 0
DNA repair 0.018 0.072 -9999 0 -0.4 5 5
BRCA1/BARD1/ubiquitin 0.051 0.01 -9999 0 -10000 0 0
BARD1/DNA-PK 0.076 0.034 -9999 0 -10000 0 0
FANCL 0.035 0.003 -9999 0 -10000 0 0
mRNA polyadenylation -0.047 0.015 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.023 0.056 -9999 0 -0.23 4 4
BRCA1/BACH1/BARD1/TopBP1 0.068 0.016 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0.081 0.029 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.064 0.023 -9999 0 -10000 0 0
BRCA1/BACH1 0.035 0.005 -9999 0 -10000 0 0
BARD1 0.035 0.004 -9999 0 -10000 0 0
PCNA 0.034 0.008 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.068 0.017 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.064 0.022 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.08 0.03 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0.083 0.043 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.051 0.01 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0.053 0.021 -9999 0 -10000 0 0
FA complex 0.029 0.038 -9999 0 -0.25 4 4
BARD1/EWS 0.049 0.013 -9999 0 -10000 0 0
RBBP8 0.017 0.006 -9999 0 -10000 0 0
TP53 0.033 0.009 -9999 0 -10000 0 0
TOPBP1 0.034 0.006 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.078 0.028 -9999 0 -10000 0 0
BRCA1/BARD1 0.091 0.037 -9999 0 -10000 0 0
CSTF1 0.032 0.01 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0.026 0.003 -9999 0 -10000 0 0
CDK2 0.035 0.004 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 0.034 0.008 -9999 0 -10000 0 0
RAD50 0.031 0.034 -9999 0 -0.42 2 2
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.051 0.01 -9999 0 -10000 0 0
EWSR1 0.033 0.008 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.034 0.007 -9999 0 -10000 0 0
PLK4 0.034 0.024 -9999 0 -0.42 1 1
regulation of centriole replication 0.018 0.017 -9999 0 -0.3 1 1
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 0.062 0.031 -9999 0 -10000 0 0
CLOCK 0.037 0.006 -9999 0 -10000 0 0
TIMELESS/CRY2 0.05 0.021 -9999 0 -10000 0 0
DEC1/BMAL1 0.038 0.011 -9999 0 -10000 0 0
ATR 0.034 0.006 -9999 0 -10000 0 0
NR1D1 0.032 0.01 -9999 0 -10000 0 0
ARNTL 0.038 0.006 -9999 0 -10000 0 0
TIMELESS 0.031 0.01 -9999 0 -10000 0 0
NPAS2 0.034 0.041 -9999 0 -0.41 3 3
CRY2 0.034 0.006 -9999 0 -10000 0 0
mol:CO -0.012 0 -9999 0 -10000 0 0
CHEK1 0.032 0.011 -9999 0 -10000 0 0
mol:HEME 0.012 0 -9999 0 -10000 0 0
PER1 0.033 0.009 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.08 0.034 -9999 0 -0.24 3 3
BMAL1/CLOCK 0.042 0.039 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.062 0.031 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.063 0.032 -9999 0 -10000 0 0
mol:NADPH 0.012 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.049 0.02 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.016 0.005 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.039 0.044 -9999 0 -10000 0 0
GNAI2 0.035 0.005 -9999 0 -10000 0 0
S1P/S1P5/G12 0.04 0.019 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.019 0.029 -9999 0 -0.42 1 1
RhoA/GTP 0.041 0.045 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process 0.022 0.037 -9999 0 -0.19 3 3
GNAZ 0.027 0.036 -9999 0 -0.42 2 2
GNAI3 0.034 0.007 -9999 0 -10000 0 0
GNA12 0.031 0.011 -9999 0 -10000 0 0
S1PR5 0.034 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.037 -9999 0 -0.19 3 3
RhoA/GDP 0.026 0.004 -9999 0 -10000 0 0
RHOA 0.035 0.005 -9999 0 -10000 0 0
GNAI1 0.031 0.012 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.003 0.005 -10000 0 -9999 0 0
TP53 0.001 0.004 -10000 0 -9999 0 0
Senescence 0.001 0.004 -10000 0 -9999 0 0
Apoptosis 0.001 0.004 -10000 0 -9999 0 0
Activated_Oncogenes 0 0 -10000 0 -9999 0 0
MDM2 0.003 0.017 0.29 1 -9999 0 1
MDM4 0.031 0.012 -10000 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.034 0.024 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC4 0.009 0.006 -10000 0 -10000 0 0
MDM2/SUMO1 0.058 0.031 0.18 1 -0.15 1 2
HDAC4 0.033 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.008 0.012 -10000 0 -0.17 1 1
SUMO1 0.035 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.016 0.013 -10000 0 -0.18 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.016 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.034 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.035 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.059 0.029 0.18 1 -10000 0 1
SUMO1/HDAC1 0.059 0.032 0.18 1 -0.17 2 3
RANGAP1 0.032 0.01 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.082 0.027 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.02 0.007 -10000 0 -10000 0 0
Ran/GTP 0.043 0.026 -10000 0 -0.16 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.008 -10000 0 -10000 0 0
UBE2I 0.035 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.025 -10000 0 -0.16 1 1
NPC 0.021 0.002 -10000 0 -10000 0 0
PIAS2 0.035 0.005 -10000 0 -10000 0 0
PIAS1 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.046 0.017 -9999 0 -9999 0 0
FBXW11 0.033 0.008 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.008 -9999 0 -9999 0 0
CHUK 0.032 0.01 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.089 0.038 -9999 0 -9999 0 0
NFKB1 0.034 0.006 -9999 0 -9999 0 0
MAP3K14 0.034 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.051 0.01 -9999 0 -9999 0 0
RELB 0.035 0.004 -9999 0 -9999 0 0
NFKB2 0.032 0.01 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.043 0.014 -9999 0 -9999 0 0
regulation of B cell activation 0.043 0.014 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 366 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z2.AA3V TCGA.Z2.AA3S TCGA.Z2.A8RT TCGA.YG.AA3P
109_MAP3K5 0.045 -0.34 0.045 -0.46
47_PPARGC1A 0.035 0.035 0.035 0.035
105_BMP4 0.035 0.035 0.035 0
105_BMP6 0.035 0.035 0.035 0.035
105_BMP7 0 0.035 0.035 0
105_BMP2 0.035 0.035 0.035 0.035
131_RELN/VLDLR 0.091 0 0 0.091
30_TGFB1/TGF beta receptor Type II 0.035 0.035 0.035 0.035
84_STAT5B 0.045 -0.22 0.027 -0.24
84_STAT5A 0.045 -0.22 0.027 -0.24
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/SKCM-TM/14527799/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/SKCM-TM/15087669/Gistic2_Analysis_15087685/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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