Glioblastoma Multiforme: PARADIGM pathway analysis of mRNA expression data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 70 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
HIF-1-alpha transcription factor network 142
Syndecan-4-mediated signaling events 100
FOXM1 transcription factor network 92
Angiopoietin receptor Tie2-mediated signaling 81
Noncanonical Wnt signaling pathway 76
LPA receptor mediated events 71
Endothelins 70
HIF-2-alpha transcription factor network 68
Syndecan-1-mediated signaling events 67
Wnt signaling 67
Results

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • 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.

Pathway.Name 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
HIF-1-alpha transcription factor network 142 10848 76 -0.37 0.022 1000 -1000 -0.036 -1000
Syndecan-4-mediated signaling events 100 6736 67 -0.18 0.022 1000 -1000 -0.006 -1000
FOXM1 transcription factor network 92 4720 51 -0.42 0.019 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 81 7161 88 -0.31 0.066 1000 -1000 -0.044 -1000
Noncanonical Wnt signaling pathway 76 1976 26 -0.033 0.019 1000 -1000 -0.026 -1000
LPA receptor mediated events 71 7287 102 -0.2 0.019 1000 -1000 -0.022 -1000
Endothelins 70 6787 96 -0.17 0.042 1000 -1000 -0.013 -1000
HIF-2-alpha transcription factor network 68 2951 43 -0.17 0.13 1000 -1000 -0.073 -1000
Syndecan-1-mediated signaling events 67 2301 34 -0.097 0.019 1000 -1000 -0.003 -1000
Wnt signaling 67 475 7 -0.033 0.019 1000 -1000 0.009 -1000
Glypican 2 network 66 267 4 -0.025 0 1000 -1000 0 -1000
EGFR-dependent Endothelin signaling events 65 1382 21 -0.08 0.014 1000 -1000 0 -1000
PDGFR-alpha signaling pathway 64 2843 44 -0.12 0.019 1000 -1000 -0.003 -1000
S1P4 pathway 61 1548 25 -0.046 0.017 1000 -1000 0 -1000
Effects of Botulinum toxin 60 1570 26 -0.087 0.023 1000 -1000 0 -1000
ErbB2/ErbB3 signaling events 59 3856 65 -0.082 0.025 1000 -1000 -0.027 -1000
Fc-epsilon receptor I signaling in mast cells 59 5807 97 -0.078 0.021 1000 -1000 -0.027 -1000
Syndecan-2-mediated signaling events 58 4020 69 -0.091 0.019 1000 -1000 -0.001 -1000
S1P5 pathway 58 994 17 -0.046 0.034 1000 -1000 -0.006 -1000
Thromboxane A2 receptor signaling 54 5751 105 -0.11 0.039 1000 -1000 -0.032 -1000
amb2 Integrin signaling 54 4484 82 -0.097 0.025 1000 -1000 -0.022 -1000
Syndecan-3-mediated signaling events 53 1856 35 -0.091 0.041 1000 -1000 -0.007 -1000
Osteopontin-mediated events 51 1951 38 -0.066 0.018 1000 -1000 -0.015 -1000
Nongenotropic Androgen signaling 51 2699 52 -0.1 0.052 1000 -1000 -0.014 -1000
EPHB forward signaling 50 4285 85 -0.04 0.027 1000 -1000 -0.024 -1000
S1P1 pathway 49 1798 36 -0.07 0.015 1000 -1000 -0.02 -1000
Signaling events mediated by VEGFR1 and VEGFR2 48 6123 125 -0.081 0.023 1000 -1000 -0.024 -1000
BCR signaling pathway 46 4571 99 -0.078 0.029 1000 -1000 -0.031 -1000
S1P3 pathway 46 1938 42 -0.065 0.016 1000 -1000 -0.013 -1000
TCGA08_retinoblastoma 45 360 8 -0.016 0.006 1000 -1000 -0.004 -1000
Glypican 1 network 44 2135 48 -0.078 0.019 1000 -1000 -0.008 -1000
PLK2 and PLK4 events 43 131 3 -0.013 0.017 1000 -1000 0.007 -1000
E-cadherin signaling in keratinocytes 43 1882 43 -0.08 0.027 1000 -1000 -0.006 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 42 2892 68 -0.12 0.036 1000 -1000 -0.029 -1000
IL6-mediated signaling events 41 3081 75 -0.084 0.035 1000 -1000 -0.009 -1000
Reelin signaling pathway 40 2246 56 -0.031 0.051 1000 -1000 -0.002 -1000
Class I PI3K signaling events 40 2946 73 -0.058 0.038 1000 -1000 -0.008 -1000
IL1-mediated signaling events 39 2447 62 -0.034 0.035 1000 -1000 -0.019 -1000
IL2 signaling events mediated by STAT5 39 863 22 -0.12 0.019 1000 -1000 -0.005 -1000
Signaling events mediated by HDAC Class III 38 1536 40 -0.052 0.038 1000 -1000 -0.017 -1000
TCGA08_p53 38 272 7 -0.021 0.013 1000 -1000 -0.001 -1000
TCGA08_rtk_signaling 37 969 26 -0.08 0.028 1000 -1000 -0.008 -1000
IGF1 pathway 37 2146 57 -0.022 0.021 1000 -1000 -0.017 -1000
Signaling events mediated by PTP1B 36 2802 76 -0.081 0.045 1000 -1000 -0.02 -1000
Ceramide signaling pathway 36 2763 76 -0.045 0.037 1000 -1000 -0.012 -1000
Aurora B signaling 36 2426 67 -0.052 0.028 1000 -1000 -0.01 -1000
PLK1 signaling events 35 2978 85 -0.064 0.024 1000 -1000 -0.016 -1000
IL2 signaling events mediated by PI3K 35 2061 58 -0.07 0.034 1000 -1000 -0.016 -1000
Integrins in angiogenesis 35 2965 84 -0.068 0.03 1000 -1000 -0.019 -1000
mTOR signaling pathway 34 1811 53 -0.042 0.026 1000 -1000 -0.02 -1000
IFN-gamma pathway 34 2322 68 -0.048 0.039 1000 -1000 -0.028 -1000
FoxO family signaling 34 2182 64 -0.16 0.022 1000 -1000 -0.015 -1000
Stabilization and expansion of the E-cadherin adherens junction 34 2566 74 -0.08 0.033 1000 -1000 -0.024 -1000
Neurotrophic factor-mediated Trk receptor signaling 34 4108 120 -0.066 0.048 1000 -1000 -0.023 -1000
Ephrin B reverse signaling 33 1629 48 -0.077 0.032 1000 -1000 -0.018 -1000
Regulation of nuclear SMAD2/3 signaling 32 4449 136 -0.28 0.27 1000 -1000 -0.026 -1000
Ras signaling in the CD4+ TCR pathway 32 545 17 -0.015 0.016 1000 -1000 -0.004 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 31 1717 54 -0.022 0.022 1000 -1000 -0.001 -1000
Aurora A signaling 30 1853 60 -0.03 0.027 1000 -1000 -0.002 -1000
IL4-mediated signaling events 30 2819 91 -0.39 0.09 1000 -1000 -0.12 -1000
Paxillin-independent events mediated by a4b1 and a4b7 30 1144 37 -0.079 0.047 1000 -1000 -0.005 -1000
Signaling events mediated by PRL 30 1053 34 -0.037 0.022 1000 -1000 -0.003 -1000
Sphingosine 1-phosphate (S1P) pathway 29 838 28 -0.046 0.024 1000 -1000 0 -1000
Plasma membrane estrogen receptor signaling 29 2544 86 -0.082 0.036 1000 -1000 -0.03 -1000
p38 MAPK signaling pathway 29 1309 44 -0.048 0.022 1000 -1000 -0.023 -1000
p75(NTR)-mediated signaling 28 3502 125 -0.1 0.041 1000 -1000 -0.021 -1000
Arf6 downstream pathway 28 1204 43 -0.031 0.021 1000 -1000 -0.009 -1000
Presenilin action in Notch and Wnt signaling 27 1693 61 -0.12 0.04 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 27 1462 54 -0.04 0.034 1000 -1000 -0.002 -1000
PDGFR-beta signaling pathway 27 2711 97 -0.073 0.035 1000 -1000 -0.021 -1000
EPO signaling pathway 26 1476 55 -0.017 0.044 1000 -1000 -0.001 -1000
Paxillin-dependent events mediated by a4b1 26 949 36 -0.079 0.048 1000 -1000 -0.018 -1000
E-cadherin signaling in the nascent adherens junction 26 1980 76 -0.031 0.04 1000 -1000 -0.03 -1000
BMP receptor signaling 25 2080 81 -0.05 0.048 1000 -1000 -0.031 -1000
FAS signaling pathway (CD95) 25 1204 47 -0.027 0.024 1000 -1000 -0.016 -1000
IL23-mediated signaling events 25 1531 60 -0.21 0.03 1000 -1000 -0.012 -1000
Canonical Wnt signaling pathway 24 1252 51 -0.14 0.08 1000 -1000 -0.015 -1000
Regulation of Telomerase 24 2480 102 -0.08 0.036 1000 -1000 -0.041 -1000
Class I PI3K signaling events mediated by Akt 23 1566 68 -0.014 0.038 1000 -1000 -0.007 -1000
Signaling mediated by p38-gamma and p38-delta 23 347 15 -0.019 0.022 1000 -1000 0 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 23 1043 45 -0.028 0.027 1000 -1000 -0.021 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 23 1824 78 -0.022 0.034 1000 -1000 -0.022 -1000
BARD1 signaling events 22 1299 57 -0.02 0.036 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 22 1479 65 -0.045 0.04 1000 -1000 -0.018 -1000
Insulin Pathway 22 1687 74 -0.031 0.04 1000 -1000 -0.02 -1000
E-cadherin signaling events 22 110 5 0.008 0.027 1000 -1000 0.008 -1000
Arf6 signaling events 21 1326 62 -0.08 0.048 1000 -1000 0 -1000
Glucocorticoid receptor regulatory network 21 2478 114 -0.21 0.062 1000 -1000 -0.032 -1000
Calcium signaling in the CD4+ TCR pathway 21 661 31 -0.042 0.083 1000 -1000 -0.029 -1000
VEGFR1 specific signals 21 1222 56 -0.071 0.031 1000 -1000 -0.007 -1000
Coregulation of Androgen receptor activity 20 1593 76 -0.045 0.038 1000 -1000 -0.014 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 20 464 23 -0.01 0.024 1000 -1000 -0.007 -1000
ErbB4 signaling events 20 1392 69 -0.084 0.034 1000 -1000 -0.011 -1000
Circadian rhythm pathway 20 450 22 -0.014 0.019 1000 -1000 -0.029 -1000
TRAIL signaling pathway 20 980 48 -0.014 0.033 1000 -1000 -0.008 -1000
Visual signal transduction: Cones 19 729 38 -0.065 0.042 1000 -1000 0 -1000
Retinoic acid receptors-mediated signaling 19 1123 58 -0.051 0.045 1000 -1000 -0.013 -1000
IL12-mediated signaling events 18 1594 87 -0.17 0.04 1000 -1000 -0.067 -1000
JNK signaling in the CD4+ TCR pathway 18 312 17 -0.012 0.028 1000 -1000 -0.003 -1000
Insulin-mediated glucose transport 18 595 32 -0.006 0.019 1000 -1000 0 -1000
Signaling events mediated by HDAC Class I 18 1907 104 -0.025 0.031 1000 -1000 -0.014 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 17 1482 85 -0.12 0.031 1000 -1000 -0.025 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 17 583 33 -0.019 0.037 1000 -1000 -0.005 -1000
Signaling events regulated by Ret tyrosine kinase 16 1374 82 -0.032 0.047 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class II 15 1197 75 -0.017 0.044 1000 -1000 -0.016 -1000
Nectin adhesion pathway 15 960 63 -0.015 0.046 1000 -1000 -0.033 -1000
Atypical NF-kappaB pathway 15 485 31 -0.016 0.028 1000 -1000 -0.002 -1000
FOXA2 and FOXA3 transcription factor networks 14 682 46 -0.022 0.15 1000 -1000 -0.013 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 14 1214 83 -0.035 0.05 1000 -1000 -0.01 -1000
TCR signaling in naïve CD8+ T cells 14 1380 93 -0.031 0.039 1000 -1000 -0.027 -1000
Caspase cascade in apoptosis 13 989 74 -0.055 0.032 1000 -1000 -0.016 -1000
Cellular roles of Anthrax toxin 13 526 39 -0.087 0.018 1000 -1000 -0.005 -1000
ceramide signaling pathway 13 676 49 -0.01 0.025 1000 -1000 -0.006 -1000
Regulation of Androgen receptor activity 13 919 70 -0.032 0.064 1000 -1000 -0.015 -1000
Signaling mediated by p38-alpha and p38-beta 12 546 44 -0.001 0.03 1000 -1000 -0.001 -1000
Arf6 trafficking events 12 888 71 -0.028 0.03 1000 -1000 -0.011 -1000
Canonical NF-kappaB pathway 11 460 39 -0.01 0.061 1000 -1000 0 -1000
IL27-mediated signaling events 11 562 51 -0.009 0.026 1000 -1000 -0.022 -1000
Sumoylation by RanBP2 regulates transcriptional repression 11 307 27 -0.01 0.036 1000 -1000 -0.018 -1000
Aurora C signaling 9 65 7 0 0.03 1000 -1000 -0.004 -1000
RXR and RAR heterodimerization with other nuclear receptor 9 480 52 -0.029 0.057 1000 -1000 -0.013 -1000
Nephrin/Neph1 signaling in the kidney podocyte 8 300 34 -0.028 0.047 1000 -1000 -0.013 -1000
Signaling events mediated by the Hedgehog family 8 428 52 -0.016 0.053 1000 -1000 -0.006 -1000
Arf1 pathway 8 457 54 -0.003 0.028 1000 -1000 -0.005 -1000
LPA4-mediated signaling events 7 89 12 0 0.015 1000 -1000 0 -1000
Alternative NF-kappaB pathway 6 87 13 0 0.048 1000 -1000 0 -1000
Rapid glucocorticoid signaling 4 85 20 0 0.018 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 3 17 5 0.016 0.026 1000 -1000 0.008 -1000
Visual signal transduction: Rods 2 136 52 0 0.043 1000 -1000 0 -1000
Ephrin A reverse signaling 0 1 7 0 0.026 1000 -1000 0 -1000
Class IB PI3K non-lipid kinase events 0 0 3 -0.019 0.019 1000 -1000 -0.009 -1000
Total 4292 248855 7203 -8.9 4.8 131000 -131000 -2 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.32 0.52 -9999 0 -0.9 194 194
HDAC7 -0.003 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.22 0.45 -9999 0 -0.78 167 167
SMAD4 -0.003 0.079 -9999 0 -0.26 44 44
ID2 -0.32 0.53 -9999 0 -0.91 194 194
AP1 -0.029 0.11 -9999 0 -0.24 93 93
ABCG2 -0.34 0.54 -9999 0 -0.9 207 207
HIF1A -0.04 0.095 -9999 0 -0.14 166 166
TFF3 -0.32 0.52 -9999 0 -0.9 193 193
GATA2 0.019 0.012 -9999 0 -0.11 4 4
AKT1 -0.043 0.11 -9999 0 -0.2 90 90
response to hypoxia -0.043 0.072 -9999 0 -0.12 178 178
MCL1 -0.32 0.52 -9999 0 -0.89 196 196
NDRG1 -0.34 0.54 -9999 0 -0.9 207 207
SERPINE1 -0.35 0.54 -9999 0 -0.92 207 207
FECH -0.32 0.52 -9999 0 -0.9 193 193
FURIN -0.32 0.52 -9999 0 -0.89 193 193
NCOA2 0.02 0.01 -9999 0 -0.11 3 3
EP300 -0.038 0.12 -9999 0 -0.38 31 31
HMOX1 -0.35 0.54 -9999 0 -0.91 206 206
BHLHE40 -0.33 0.51 -9999 0 -0.88 199 199
BHLHE41 -0.33 0.51 -9999 0 -0.88 199 199
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.015 0.13 -9999 0 -0.21 73 73
ENG -0.028 0.1 -9999 0 -0.22 50 50
JUN -0.001 0.077 -9999 0 -0.28 37 37
RORA -0.33 0.52 -9999 0 -0.91 195 195
ABCB1 -0.16 0.34 -9999 0 -1.2 42 42
TFRC -0.33 0.53 -9999 0 -0.91 196 196
CXCR4 -0.34 0.53 -9999 0 -0.91 202 202
TF -0.37 0.53 -9999 0 -0.89 221 221
CITED2 -0.33 0.52 -9999 0 -0.9 195 195
HIF1A/ARNT -0.35 0.7 -9999 0 -1.1 176 176
LDHA -0.11 0.32 -9999 0 -1.2 38 38
ETS1 -0.32 0.52 -9999 0 -0.88 196 196
PGK1 -0.32 0.53 -9999 0 -0.9 198 198
NOS2 -0.33 0.51 -9999 0 -0.88 199 199
ITGB2 -0.34 0.54 -9999 0 -0.92 200 200
ALDOA -0.32 0.52 -9999 0 -0.9 193 193
Cbp/p300/CITED2 -0.32 0.55 -9999 0 -0.96 184 184
FOS -0.046 0.12 -9999 0 -0.22 146 146
HK2 -0.32 0.52 -9999 0 -0.89 195 195
SP1 0.019 0.021 -9999 0 -10000 0 0
GCK -0.047 0.16 -9999 0 -0.52 18 18
HK1 -0.32 0.52 -9999 0 -0.88 199 199
NPM1 -0.32 0.52 -9999 0 -0.88 199 199
EGLN1 -0.32 0.52 -9999 0 -0.9 194 194
CREB1 0.019 0.038 -9999 0 -0.27 7 7
PGM1 -0.32 0.52 -9999 0 -0.89 195 195
SMAD3 0.019 0.006 -9999 0 -0.11 1 1
EDN1 -0.048 0.17 -9999 0 -0.64 21 21
IGFBP1 -0.32 0.52 -9999 0 -0.89 197 197
VEGFA -0.26 0.4 -9999 0 -0.7 200 200
HIF1A/JAB1 -0.013 0.074 -9999 0 -0.28 17 17
CP -0.35 0.54 -9999 0 -0.91 206 206
CXCL12 -0.32 0.52 -9999 0 -0.89 196 196
COPS5 0.017 0.03 -9999 0 -0.29 5 5
SMAD3/SMAD4 0.013 0.056 -9999 0 -0.19 36 36
BNIP3 -0.32 0.53 -9999 0 -0.9 196 196
EGLN3 -0.33 0.52 -9999 0 -0.88 205 205
CA9 -0.32 0.52 -9999 0 -0.88 202 202
TERT -0.32 0.52 -9999 0 -0.89 193 193
ENO1 -0.32 0.52 -9999 0 -0.9 194 194
PFKL -0.32 0.52 -9999 0 -0.88 199 199
NCOA1 -0.005 0.084 -9999 0 -0.28 43 43
ADM -0.35 0.54 -9999 0 -0.9 213 213
ARNT -0.033 0.075 -9999 0 -0.13 118 118
HNF4A 0.022 0.004 -9999 0 -10000 0 0
ADFP -0.35 0.54 -9999 0 -0.92 203 203
SLC2A1 -0.23 0.39 -9999 0 -0.67 189 189
LEP -0.32 0.52 -9999 0 -0.88 196 196
HIF1A/ARNT/Cbp/p300 -0.23 0.46 -9999 0 -0.78 174 174
EPO -0.14 0.3 -9999 0 -0.55 122 122
CREBBP -0.032 0.11 -9999 0 -0.32 27 27
HIF1A/ARNT/Cbp/p300/HDAC7 -0.25 0.48 -9999 0 -0.82 173 173
PFKFB3 -0.33 0.53 -9999 0 -0.9 202 202
NT5E -0.34 0.53 -9999 0 -0.9 208 208
Syndecan-4-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
PTK2 -0.038 0.15 -10000 0 -0.48 45 45
Syndecan-4/Syndesmos -0.17 0.28 -10000 0 -0.47 205 205
positive regulation of JNK cascade -0.16 0.26 -10000 0 -0.45 206 206
Syndecan-4/ADAM12 -0.16 0.28 -10000 0 -0.46 205 205
CCL5 0.006 0.039 -10000 0 -10000 0 0
Rac1/GDP 0.011 0.024 -10000 0 -0.2 7 7
DNM2 0.019 0 -10000 0 -10000 0 0
ITGA5 -0.002 0.07 -10000 0 -0.19 53 53
SDCBP 0.011 0.05 -10000 0 -0.29 14 14
PLG 0.022 0.006 -10000 0 -10000 0 0
ADAM12 0.016 0.019 -10000 0 -0.11 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.002 0.01 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.17 0.28 -10000 0 -0.47 205 205
Syndecan-4/CXCL12/CXCR4 -0.18 0.29 -10000 0 -0.48 206 206
Syndecan-4/Laminin alpha3 -0.17 0.28 -10000 0 -0.46 206 206
MDK -0.025 0.1 -10000 0 -0.24 89 89
Syndecan-4/FZD7 -0.18 0.3 -10000 0 -0.5 206 206
Syndecan-4/Midkine -0.18 0.3 -10000 0 -0.49 205 205
FZD7 -0.047 0.12 -10000 0 -0.22 148 148
Syndecan-4/FGFR1/FGF -0.14 0.27 -10000 0 -0.42 206 206
THBS1 0 0.046 -10000 0 -0.11 79 79
integrin-mediated signaling pathway -0.17 0.28 -10000 0 -0.47 208 208
positive regulation of MAPKKK cascade -0.16 0.26 -10000 0 -0.45 206 206
Syndecan-4/TACI -0.16 0.28 -10000 0 -0.46 205 205
CXCR4 -0.032 0.11 -10000 0 -0.22 111 111
cell adhesion 0.002 0.074 -10000 0 -0.26 33 33
Syndecan-4/Dynamin -0.16 0.28 -10000 0 -0.46 205 205
Syndecan-4/TSP1 -0.17 0.28 -10000 0 -0.46 206 206
Syndecan-4/GIPC -0.16 0.28 -10000 0 -0.46 205 205
Syndecan-4/RANTES -0.17 0.28 -10000 0 -0.46 205 205
ITGB1 0.019 0 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.01 0.034 -10000 0 -0.11 38 38
RAC1 0.015 0.036 -10000 0 -0.29 7 7
PRKCA 0.022 0.028 0.12 2 -10000 0 2
Syndecan-4/alpha-Actinin -0.18 0.3 -10000 0 -0.5 206 206
TFPI -0.02 0.086 -10000 0 -0.17 106 106
F2 0.007 0.016 -10000 0 -0.13 2 2
alpha5/beta1 Integrin 0.013 0.049 -10000 0 -0.19 24 24
positive regulation of cell adhesion -0.16 0.27 -10000 0 -0.45 206 206
ACTN1 -0.034 0.11 -10000 0 -0.24 109 109
TNC -0.041 0.12 -10000 0 -0.25 118 118
Syndecan-4/CXCL12 -0.17 0.28 -10000 0 -0.47 205 205
FGF6 0.019 0 -10000 0 -10000 0 0
RHOA 0.015 0.036 -10000 0 -0.29 7 7
CXCL12 -0.001 0.048 -10000 0 -0.29 1 1
TNFRSF13B 0.019 0.006 -10000 0 -0.11 1 1
FGF2 0.013 0.036 -10000 0 -0.16 19 19
FGFR1 0.019 0.008 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.17 0.28 -10000 0 -0.47 205 205
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.004 0.066 -10000 0 -0.24 34 34
cell migration -0.003 0.003 -10000 0 -10000 0 0
PRKCD 0.015 0.029 -10000 0 -0.11 27 27
vasculogenesis -0.16 0.27 -10000 0 -0.44 206 206
SDC4 -0.18 0.3 -10000 0 -0.5 205 205
Syndecan-4/Tenascin C -0.18 0.3 -10000 0 -0.5 207 207
Syndecan-4/PI-4-5-P2/PKC alpha -0.003 0.007 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.16 0.29 -10000 0 -0.46 206 206
MMP9 -0.1 0.13 -10000 0 -0.21 271 271
Rac1/GTP 0.002 0.076 -10000 0 -0.27 33 33
cytoskeleton organization -0.16 0.26 -10000 0 -0.44 206 206
GIPC1 0.019 0 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.18 0.29 -10000 0 -0.48 205 205
FOXM1 transcription factor network

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
NFATC3 -0.22 0.6 -9999 0 -1.2 113 113
PLK1 0.013 0.063 -9999 0 -10000 0 0
BIRC5 -0.15 0.45 -9999 0 -1.3 64 64
HSPA1B -0.23 0.6 -9999 0 -1.2 122 122
MAP2K1 0.012 0.058 -9999 0 -0.3 8 8
BRCA2 -0.22 0.6 -9999 0 -1.2 113 113
FOXM1 -0.42 1 -9999 0 -2.1 119 119
XRCC1 -0.22 0.6 -9999 0 -1.2 117 117
FOXM1B/p19 -0.4 0.6 -9999 0 -1.4 125 125
Cyclin D1/CDK4 -0.22 0.56 -9999 0 -1.1 125 125
CDC2 -0.26 0.67 -9999 0 -1.4 123 123
TGFA -0.18 0.52 -9999 0 -1 120 120
SKP2 -0.22 0.6 -9999 0 -1.2 110 110
CCNE1 0.01 0.035 -9999 0 -0.12 37 37
CKS1B -0.24 0.62 -9999 0 -1.3 118 118
RB1 -0.17 0.34 -9999 0 -0.75 97 97
FOXM1C/SP1 -0.31 0.74 -9999 0 -1.5 122 122
AURKB 0.012 0.087 -9999 0 -1.4 1 1
CENPF -0.26 0.64 -9999 0 -1.3 129 129
CDK4 -0.008 0.07 -9999 0 -0.15 80 80
MYC -0.2 0.54 -9999 0 -1 125 125
CHEK2 0.009 0.057 -9999 0 -0.15 29 29
ONECUT1 -0.22 0.58 -9999 0 -1.2 122 122
CDKN2A -0.021 0.059 -9999 0 -0.11 155 155
LAMA4 -0.22 0.6 -9999 0 -1.2 114 114
FOXM1B/HNF6 -0.3 0.74 -9999 0 -1.5 122 122
FOS -0.3 0.66 -9999 0 -1.2 153 153
SP1 0.018 0.01 -9999 0 -10000 0 0
CDC25B -0.23 0.61 -9999 0 -1.3 117 117
response to radiation 0.001 0.034 -9999 0 -10000 0 0
CENPB -0.23 0.6 -9999 0 -1.2 113 113
CENPA -0.23 0.61 -9999 0 -1.3 115 115
NEK2 -0.22 0.6 -9999 0 -1.2 113 113
HIST1H2BA -0.23 0.6 -9999 0 -1.2 122 122
CCNA2 -0.027 0.1 -9999 0 -0.2 117 117
EP300 0.012 0.046 -9999 0 -0.24 15 15
CCNB1/CDK1 -0.34 0.8 -9999 0 -1.6 129 129
CCNB2 -0.26 0.64 -9999 0 -1.3 122 122
CCNB1 -0.28 0.68 -9999 0 -1.4 127 127
ETV5 -0.26 0.64 -9999 0 -1.2 136 136
ESR1 -0.22 0.6 -9999 0 -1.2 113 113
CCND1 -0.22 0.57 -9999 0 -1.1 125 125
GSK3A 0.018 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.003 0.087 -9999 0 -0.18 71 71
CDK2 0.011 0.037 -9999 0 -0.13 29 29
G2/M transition of mitotic cell cycle 0.001 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.67 -9999 0 -1.4 121 121
GAS1 -0.24 0.61 -9999 0 -1.3 116 116
MMP2 -0.26 0.64 -9999 0 -1.3 129 129
RB1/FOXM1C -0.23 0.6 -9999 0 -1.2 127 127
CREBBP 0.019 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.24 0.42 -10000 0 -0.84 156 156
NCK1/PAK1/Dok-R -0.13 0.18 -10000 0 -0.4 149 149
NCK1/Dok-R -0.14 0.37 -10000 0 -0.91 99 99
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
mol:beta2-estradiol 0.043 0.091 0.23 99 -10000 0 99
RELA 0.018 0.02 -10000 0 -0.23 3 3
SHC1 0.003 0.052 -10000 0 -0.15 48 48
Rac/GDP 0.011 0.024 -10000 0 -0.2 7 7
F2 0.066 0.094 0.26 99 -10000 0 99
TNIP2 0.016 0.031 -10000 0 -0.24 7 7
NF kappa B/RelA -0.12 0.36 -10000 0 -0.86 99 99
FN1 0.001 0.071 -10000 0 -0.26 34 34
PLD2 -0.15 0.38 -10000 0 -0.94 99 99
PTPN11 0.015 0.033 -10000 0 -0.27 7 7
GRB14 0.001 0.047 -10000 0 -0.12 70 70
ELK1 -0.13 0.35 -10000 0 -0.86 99 99
GRB7 0.016 0.019 -10000 0 -0.11 11 11
PAK1 0.017 0.017 -10000 0 -0.11 9 9
Tie2/Ang1/alpha5/beta1 Integrin -0.14 0.38 -10000 0 -0.91 99 99
CDKN1A -0.2 0.36 -10000 0 -0.72 153 153
ITGA5 -0.002 0.07 -10000 0 -0.19 53 53
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.15 0.37 -10000 0 -0.91 99 99
CRK 0.009 0.054 -10000 0 -0.28 17 17
mol:NO -0.17 0.31 -10000 0 -0.61 160 160
PLG -0.15 0.38 -10000 0 -0.94 99 99
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.2 0.38 -10000 0 -0.8 136 136
GRB2 0.014 0.039 -10000 0 -0.26 10 10
PIK3R1 -0.016 0.096 -10000 0 -0.27 62 62
ANGPT2 -0.27 0.47 -10000 0 -1.1 110 110
BMX -0.15 0.38 -10000 0 -0.94 99 99
ANGPT1 -0.21 0.45 -10000 0 -1.1 99 99
tube development -0.22 0.37 -10000 0 -0.71 178 178
ANGPT4 0.016 0.007 -10000 0 -10000 0 0
response to hypoxia -0.012 0.026 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.39 -10000 0 -0.97 99 99
alpha5/beta1 Integrin 0.013 0.049 -10000 0 -0.19 24 24
FGF2 0.015 0.036 -10000 0 -0.15 19 19
STAT5A (dimer) -0.25 0.44 -10000 0 -0.82 186 186
mol:L-citrulline -0.17 0.31 -10000 0 -0.61 160 160
AGTR1 0.01 0.025 -10000 0 -0.12 13 13
MAPK14 -0.17 0.39 -10000 0 -0.95 99 99
Tie2/SHP2 -0.019 0.13 -10000 0 -0.79 6 6
TEK -0.028 0.14 -10000 0 -0.92 5 5
RPS6KB1 -0.21 0.38 -10000 0 -0.79 146 146
Angiotensin II/AT1 0.004 0.026 -10000 0 -0.11 6 6
Tie2/Ang1/GRB2 -0.15 0.39 -10000 0 -0.96 99 99
MAPK3 -0.14 0.36 -10000 0 -0.88 99 99
MAPK1 -0.14 0.36 -10000 0 -0.88 99 99
Tie2/Ang1/GRB7 -0.15 0.39 -10000 0 -0.96 99 99
NFKB1 0.014 0.037 -10000 0 -0.23 11 11
MAPK8 -0.15 0.38 -10000 0 -0.94 99 99
PI3K -0.26 0.46 -10000 0 -0.94 146 146
FES -0.17 0.38 -10000 0 -0.94 99 99
Crk/Dok-R -0.15 0.37 -10000 0 -0.91 99 99
Tie2/Ang1/ABIN2 -0.15 0.39 -10000 0 -0.96 99 99
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.21 0.37 -10000 0 -0.75 158 158
STAT5A 0.018 0.008 -10000 0 -0.11 2 2
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.22 0.38 -10000 0 -0.79 147 147
Tie2/Ang2 -0.31 0.52 -10000 0 -0.99 177 177
Tie2/Ang1 -0.16 0.4 -10000 0 -1 99 99
FOXO1 -0.24 0.41 -10000 0 -0.79 178 178
ELF1 0.017 0.046 -10000 0 -0.25 14 14
ELF2 -0.15 0.37 -10000 0 -0.92 99 99
mol:Choline -0.14 0.37 -10000 0 -0.91 99 99
cell migration -0.073 0.098 -10000 0 -0.22 153 153
FYN -0.25 0.42 -10000 0 -0.82 178 178
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.18 0.32 -10000 0 -0.59 192 192
ETS1 -0.024 0.093 -10000 0 -0.21 99 99
PXN -0.17 0.32 -10000 0 -0.65 148 148
ITGB1 0.019 0 -10000 0 -10000 0 0
NOS3 -0.2 0.35 -10000 0 -0.7 158 158
RAC1 0.015 0.036 -10000 0 -0.29 7 7
TNF -0.027 0.096 -10000 0 -0.22 99 99
MAPKKK cascade -0.14 0.37 -10000 0 -0.91 99 99
RASA1 0.003 0.069 -10000 0 -0.28 29 29
Tie2/Ang1/Shc -0.16 0.39 -10000 0 -0.97 99 99
NCK1 0.014 0.036 -10000 0 -0.19 14 14
vasculogenesis -0.15 0.28 -10000 0 -0.55 161 161
mol:Phosphatidic acid -0.14 0.37 -10000 0 -0.91 99 99
mol:Angiotensin II -0.005 0.012 -10000 0 -10000 0 0
mol:NADP -0.17 0.31 -10000 0 -0.61 160 160
Rac1/GTP -0.2 0.36 -10000 0 -0.74 147 147
MMP2 -0.16 0.39 -10000 0 -0.97 99 99
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.025 0.11 -9999 0 -0.19 136 136
mol:DAG -0.022 0.1 -9999 0 -0.18 136 136
PLCG1 -0.023 0.11 -9999 0 -0.18 136 136
YES1 -0.031 0.11 -9999 0 -0.19 135 135
FZD3 -0.028 0.1 -9999 0 -0.22 103 103
FZD6 -0.02 0.076 -9999 0 -0.14 129 129
G protein -0.023 0.11 -9999 0 -0.19 136 136
MAP3K7 -0.017 0.096 -9999 0 -0.22 62 62
mol:Ca2+ -0.022 0.1 -9999 0 -0.17 136 136
mol:IP3 -0.022 0.1 -9999 0 -0.18 136 136
NLK -0.006 0.16 -9999 0 -0.9 16 16
GNB1 0.007 0.061 -9999 0 -0.29 21 21
CAMK2A -0.018 0.096 -9999 0 -0.23 56 56
MAP3K7IP1 0.019 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.033 0.11 -9999 0 -0.2 134 134
CSNK1A1 0.014 0.038 -9999 0 -0.29 8 8
GNAS -0.029 0.1 -9999 0 -0.19 134 134
GO:0007205 -0.025 0.1 -9999 0 -0.26 56 56
WNT6 0.019 0 -9999 0 -10000 0 0
WNT4 0.018 0.013 -9999 0 -0.11 5 5
NFAT1/CK1 alpha -0.019 0.11 -9999 0 -0.25 61 61
GNG2 0 0 -9999 0 -10000 0 0
WNT5A -0.027 0.1 -9999 0 -0.24 96 96
WNT11 0.017 0.016 -9999 0 -0.11 8 8
CDC42 -0.027 0.1 -9999 0 -0.18 136 136
LPA receptor mediated 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
GNB1/GNG2 -0.011 0.072 -10000 0 -0.18 68 68
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.077 -10000 0 -0.21 41 41
AP1 -0.045 0.095 -10000 0 -0.19 125 125
mol:PIP3 -0.061 0.081 -10000 0 -0.16 169 169
AKT1 -0.011 0.095 -10000 0 -0.26 50 50
PTK2B -0.006 0.056 -10000 0 -0.16 60 60
RHOA -0.005 0.059 -10000 0 -0.42 7 7
PIK3CB 0.018 0.013 -10000 0 -0.11 5 5
mol:Ca2+ 0.007 0.035 -10000 0 -0.14 20 20
MAGI3 0 0 0.001 9 -10000 0 9
RELA 0.018 0.02 -10000 0 -0.23 3 3
apoptosis -0.014 0.073 -10000 0 -0.2 61 61
HRAS/GDP 0.007 0.037 -10000 0 -0.19 18 18
positive regulation of microtubule depolymerization -0.024 0.087 -10000 0 -0.16 122 122
NF kappa B1 p50/RelA -0.022 0.053 -10000 0 -0.15 63 63
endothelial cell migration -0.038 0.13 -10000 0 -0.4 60 60
ADCY4 -0.054 0.12 -10000 0 -0.26 109 109
ADCY5 -0.054 0.12 -10000 0 -0.26 109 109
ADCY6 -0.05 0.12 -10000 0 -0.26 101 101
ADCY7 -0.054 0.13 -10000 0 -0.27 106 106
ADCY1 -0.05 0.12 -10000 0 -0.26 101 101
ADCY2 -0.05 0.12 -10000 0 -0.26 101 101
ADCY3 -0.054 0.12 -10000 0 -0.26 109 109
ADCY8 -0.053 0.12 -10000 0 -0.26 102 102
ADCY9 -0.05 0.12 -10000 0 -0.26 101 101
GSK3B -0.008 0.066 -10000 0 -0.16 72 72
arachidonic acid secretion -0.054 0.14 -10000 0 -0.27 113 113
GNG2 0 0.001 0.001 70 -10000 0 70
TRIP6 -0.031 0.11 -10000 0 -0.29 81 81
GNAO1 -0.021 0.079 -10000 0 -0.2 76 76
HRAS 0.009 0.055 -10000 0 -0.28 18 18
NFKBIA -0.006 0.075 -10000 0 -0.22 41 41
GAB1 0.003 0.056 -10000 0 -0.15 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.008 0.2 -10000 0 -0.93 23 23
JUN -0.002 0.077 -10000 0 -0.28 37 37
LPA/LPA2/NHERF2 0.004 0.026 -10000 0 -0.064 60 60
TIAM1 -0.021 0.23 -10000 0 -1.1 23 23
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
mol:IP3 0.007 0.036 -10000 0 -0.14 20 20
PLCB3 0.009 0.023 -10000 0 -10000 0 0
FOS -0.046 0.12 -10000 0 -0.22 146 146
positive regulation of mitosis -0.054 0.14 -10000 0 -0.27 113 113
LPA/LPA1-2-3 -0.017 0.056 -10000 0 -0.12 102 102
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -0.001 78 78
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation -0.004 0.067 -10000 0 -0.17 68 68
GNAZ -0.019 0.081 -10000 0 -0.2 75 75
EGFR/PI3K-beta/Gab1 -0.063 0.083 -10000 0 -0.16 169 169
positive regulation of dendritic cell cytokine production -0.017 0.056 -10000 0 -0.12 102 102
LPA/LPA2/MAGI-3 -0.007 0.023 -10000 0 -0.049 102 102
ARHGEF1 -0.008 0.074 -10000 0 -0.17 81 81
GNAI2 -0.015 0.079 -10000 0 -0.22 60 60
GNAI3 -0.011 0.069 -10000 0 -0.18 64 64
GNAI1 -0.027 0.08 -10000 0 -0.21 73 73
LPA/LPA3 -0.01 0.029 -10000 0 -0.063 102 102
LPA/LPA2 -0.01 0.029 -10000 0 -0.062 102 102
LPA/LPA1 -0.023 0.075 -10000 0 -0.16 102 102
HB-EGF/EGFR -0.093 0.093 -10000 0 -0.18 261 261
HBEGF -0.06 0.089 -10000 0 -0.19 153 153
mol:DAG 0.007 0.036 -10000 0 -0.14 20 20
cAMP biosynthetic process -0.053 0.13 -10000 0 -0.26 113 113
NFKB1 0.014 0.037 -10000 0 -0.23 11 11
SRC 0.019 0 -10000 0 -10000 0 0
GNB1 0.007 0.06 -10000 0 -0.29 21 21
LYN -0.022 0.097 -10000 0 -0.23 75 75
GNAQ -0.001 0.026 -10000 0 -0.06 77 77
LPAR2 0 0.001 0.001 8 -0.002 81 89
LPAR3 0 0.001 -10000 0 -0.001 92 92
LPAR1 -0.015 0.045 -10000 0 -0.098 102 102
IL8 -0.2 0.2 -10000 0 -0.42 226 226
PTK2 -0.009 0.062 -10000 0 -0.15 72 72
Rac1/GDP 0.011 0.024 -10000 0 -0.2 7 7
CASP3 -0.014 0.073 -10000 0 -0.2 61 61
EGFR -0.08 0.12 -10000 0 -0.25 128 128
PLCG1 0.001 0.04 -10000 0 -0.093 62 62
PLD2 -0.007 0.054 -10000 0 -0.11 97 97
G12/G13 -0.007 0.083 -10000 0 -0.19 82 82
PI3K-beta -0.035 0.081 -10000 0 -0.25 48 48
cell migration -0.002 0.073 -10000 0 -0.26 29 29
SLC9A3R2 0.019 0 -10000 0 -10000 0 0
PXN -0.004 0.068 -10000 0 -0.17 68 68
HRAS/GTP -0.056 0.14 -10000 0 -0.28 113 113
RAC1 0.015 0.036 -10000 0 -0.29 7 7
MMP9 -0.097 0.13 -10000 0 -0.21 271 271
PRKCE 0.019 0 -10000 0 -10000 0 0
PRKCD 0.008 0.036 -10000 0 -0.13 20 20
Gi(beta/gamma) -0.055 0.14 -10000 0 -0.29 105 105
mol:LPA -0.015 0.045 -10000 0 -0.098 102 102
TRIP6/p130 Cas/FAK1/Paxillin -0.021 0.1 -10000 0 -0.24 70 70
MAPKKK cascade -0.054 0.14 -10000 0 -0.27 113 113
contractile ring contraction involved in cytokinesis -0.005 0.058 -10000 0 -0.41 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.001 0.025 -10000 0 -0.06 75 75
GNA15 -0.002 0.029 -10000 0 -0.063 84 84
GNA12 -0.005 0.082 -10000 0 -0.29 39 39
GNA13 0.016 0.021 -10000 0 -0.11 14 14
MAPT -0.024 0.089 -10000 0 -0.17 122 122
GNA11 -0.007 0.051 -10000 0 -0.12 63 63
Rac1/GTP -0.01 0.21 -10000 0 -1 23 23
MMP2 -0.038 0.13 -10000 0 -0.4 60 60
Endothelins

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
AKT1 -0.079 0.14 -9999 0 -0.29 134 134
PTK2B 0.018 0.013 -9999 0 -0.11 5 5
mol:Ca2+ -0.023 0.16 -9999 0 -0.56 31 31
EDN1 -0.039 0.086 -9999 0 -0.18 108 108
EDN3 0.015 0.022 -9999 0 -0.11 15 15
EDN2 0.018 0.01 -9999 0 -0.11 3 3
HRAS/GDP -0.047 0.15 -9999 0 -0.36 70 70
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.034 0.11 -9999 0 -0.28 65 65
ADCY4 -0.063 0.11 -9999 0 -0.25 108 108
ADCY5 -0.063 0.11 -9999 0 -0.25 108 108
ADCY6 -0.055 0.11 -9999 0 -0.24 107 107
ADCY7 -0.058 0.12 -9999 0 -0.25 112 112
ADCY1 -0.055 0.11 -9999 0 -0.24 107 107
ADCY2 -0.055 0.11 -9999 0 -0.25 107 107
ADCY3 -0.063 0.11 -9999 0 -0.25 108 108
ADCY8 -0.061 0.11 -9999 0 -0.25 112 112
ADCY9 -0.055 0.11 -9999 0 -0.26 98 98
arachidonic acid secretion -0.095 0.24 -9999 0 -0.5 109 109
ETB receptor/Endothelin-1/Gq/GTP -0.043 0.11 -9999 0 -0.26 83 83
GNAO1 -0.014 0.085 -9999 0 -0.2 81 81
HRAS 0.008 0.055 -9999 0 -0.28 18 18
ETA receptor/Endothelin-1/G12/GTP -0.067 0.15 -9999 0 -0.3 116 116
ETA receptor/Endothelin-1/Gs/GTP -0.053 0.13 -9999 0 -0.27 98 98
mol:GTP 0 0.005 -9999 0 -10000 0 0
COL3A1 -0.12 0.2 -9999 0 -0.44 129 129
EDNRB -0.062 0.12 -9999 0 -0.28 113 113
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.071 0.14 -9999 0 -0.33 89 89
CYSLTR1 -0.08 0.13 -9999 0 -0.28 132 132
SLC9A1 -0.043 0.09 -9999 0 -0.21 86 86
mol:GDP -0.055 0.15 -9999 0 -0.37 68 68
SLC9A3 -0.11 0.24 -9999 0 -0.51 104 104
RAF1 -0.071 0.19 -9999 0 -0.42 95 95
JUN -0.056 0.28 -9999 0 -1.1 34 34
JAK2 -0.075 0.14 -9999 0 -0.28 130 130
mol:IP3 -0.039 0.11 -9999 0 -0.3 55 55
ETA receptor/Endothelin-1 -0.088 0.17 -9999 0 -0.34 130 130
PLCB1 0.014 0.024 -9999 0 -0.12 17 17
PLCB2 0.018 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-3 -0.039 0.1 -9999 0 -0.19 122 122
FOS -0.14 0.34 -9999 0 -0.9 86 86
Gai/GDP -0.095 0.29 -9999 0 -0.82 67 67
CRK 0.009 0.054 -9999 0 -0.28 17 17
mol:Ca ++ -0.092 0.18 -9999 0 -0.38 115 115
BCAR1 0 0 -9999 0 -10000 0 0
PRKCB1 -0.044 0.12 -9999 0 -0.3 63 63
GNAQ 0.014 0.024 -9999 0 -0.11 17 17
GNAZ -0.008 0.083 -9999 0 -0.23 56 56
GNAL 0.018 0.01 -9999 0 -0.11 3 3
Gs family/GDP -0.044 0.14 -9999 0 -0.34 66 66
ETA receptor/Endothelin-1/Gq/GTP -0.044 0.13 -9999 0 -0.29 80 80
MAPK14 -0.028 0.099 -9999 0 -0.26 53 53
TRPC6 -0.025 0.17 -9999 0 -0.59 31 31
GNAI2 0 0.074 -9999 0 -0.28 34 34
GNAI3 0.014 0.038 -9999 0 -0.29 8 8
GNAI1 -0.046 0.11 -9999 0 -0.2 157 157
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.033 0.1 -9999 0 -0.27 58 58
ETB receptor/Endothelin-2 -0.028 0.089 -9999 0 -0.2 105 105
ETB receptor/Endothelin-3 -0.03 0.089 -9999 0 -0.2 107 107
ETB receptor/Endothelin-1 -0.069 0.12 -9999 0 -0.22 170 170
MAPK3 -0.12 0.31 -9999 0 -0.8 87 87
MAPK1 -0.13 0.33 -9999 0 -0.82 88 88
Rac1/GDP -0.045 0.15 -9999 0 -0.36 67 67
cAMP biosynthetic process -0.036 0.1 -9999 0 -0.24 82 82
MAPK8 -0.038 0.19 -9999 0 -0.65 36 36
SRC 0.019 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.097 0.18 -9999 0 -0.35 121 121
p130Cas/CRK/Src/PYK2 -0.035 0.16 -9999 0 -0.48 47 47
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.053 0.16 -9999 0 -0.37 77 77
COL1A2 -0.16 0.26 -9999 0 -0.56 133 133
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.037 0.099 -9999 0 -0.2 100 100
mol:DAG -0.04 0.11 -9999 0 -0.3 55 55
MAP2K2 -0.093 0.24 -9999 0 -0.59 90 90
MAP2K1 -0.095 0.25 -9999 0 -0.6 90 90
EDNRA -0.072 0.14 -9999 0 -0.24 163 163
positive regulation of muscle contraction -0.064 0.13 -9999 0 -0.29 102 102
Gq family/GDP -0.025 0.15 -9999 0 -0.35 64 64
HRAS/GTP -0.05 0.14 -9999 0 -0.35 69 69
PRKCH -0.037 0.11 -9999 0 -0.29 58 58
RAC1 0.015 0.036 -9999 0 -0.29 7 7
PRKCA -0.036 0.11 -9999 0 -0.29 56 56
PRKCB -0.041 0.11 -9999 0 -0.29 60 60
PRKCE -0.036 0.11 -9999 0 -0.29 57 57
PRKCD -0.039 0.12 -9999 0 -0.29 61 61
PRKCG -0.037 0.11 -9999 0 -0.3 57 57
regulation of vascular smooth muscle contraction -0.17 0.41 -9999 0 -1.1 86 86
PRKCQ -0.038 0.11 -9999 0 -0.29 59 59
PLA2G4A -0.11 0.26 -9999 0 -0.55 109 109
GNA14 0.015 0.023 -9999 0 -0.11 15 15
GNA15 0.011 0.034 -9999 0 -0.13 26 26
GNA12 -0.005 0.082 -9999 0 -0.29 39 39
GNA11 0.003 0.07 -9999 0 -0.3 27 27
Rac1/GTP -0.058 0.14 -9999 0 -0.3 99 99
MMP1 0.042 0.084 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.005 0.039 -10000 0 -10000 0 0
oxygen homeostasis -0.008 0.014 -10000 0 -10000 0 0
TCEB2 0.019 0 -10000 0 -10000 0 0
TCEB1 0.013 0.041 -10000 0 -0.27 10 10
VHL/Elongin B/Elongin C/HIF2A -0.029 0.11 -10000 0 -0.25 60 60
EPO -0.11 0.25 -10000 0 -0.48 124 124
FIH (dimer) 0.009 0.016 -10000 0 -10000 0 0
APEX1 0.003 0.039 -10000 0 -0.33 5 5
SERPINE1 -0.17 0.3 -10000 0 -0.57 153 153
FLT1 -0.003 0.043 -10000 0 -10000 0 0
ADORA2A -0.13 0.26 -10000 0 -0.5 132 132
germ cell development -0.13 0.26 -10000 0 -0.46 159 159
SLC11A2 -0.13 0.27 -10000 0 -0.52 132 132
BHLHE40 -0.14 0.27 -10000 0 -0.48 159 159
HIF1AN 0.009 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.057 0.17 -10000 0 -0.3 115 115
ETS1 0.029 0.014 -10000 0 -10000 0 0
CITED2 -0.062 0.24 -10000 0 -1.1 27 27
KDR -0.03 0.17 -10000 0 -1.1 11 11
PGK1 -0.14 0.28 -10000 0 -0.54 136 136
SIRT1 0.008 0.048 -10000 0 -0.16 32 32
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.14 0.33 -10000 0 -0.55 157 157
EPAS1 -0.044 0.12 -10000 0 -0.24 87 87
SP1 0.026 0.004 -10000 0 -10000 0 0
ABCG2 -0.16 0.3 -10000 0 -0.55 157 157
EFNA1 -0.14 0.28 -10000 0 -0.54 135 135
FXN -0.13 0.26 -10000 0 -0.5 132 132
POU5F1 -0.14 0.27 -10000 0 -0.48 159 159
neuron apoptosis 0.13 0.32 0.54 157 -10000 0 157
EP300 0.012 0.046 -10000 0 -0.24 15 15
EGLN3 -0.014 0.069 -10000 0 -0.17 72 72
EGLN2 0.009 0.016 -10000 0 -10000 0 0
EGLN1 0 0.055 -10000 0 -0.25 20 20
VHL/Elongin B/Elongin C 0.023 0.024 -10000 0 -0.16 9 9
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.006 0.022 -10000 0 -0.093 1 1
SLC2A1 -0.14 0.27 -10000 0 -0.52 137 137
TWIST1 -0.17 0.29 -10000 0 -0.51 181 181
ELK1 0.022 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.054 0.16 -10000 0 -0.3 114 114
VEGFA -0.17 0.3 -10000 0 -0.56 163 163
CREBBP 0.019 0 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.007 0.049 -9999 0 -0.16 37 37
CCL5 0.006 0.039 -9999 0 -10000 0 0
SDCBP 0.011 0.05 -9999 0 -0.29 14 14
FGFR/FGF2/Syndecan-1 -0.053 0.089 -9999 0 -0.17 148 148
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.046 0.091 -9999 0 -0.22 57 57
Syndecan-1/Syntenin -0.044 0.091 -9999 0 -0.22 56 56
MAPK3 -0.043 0.093 -9999 0 -0.23 58 58
HGF/MET 0.018 0.03 -9999 0 -0.14 4 4
TGFB1/TGF beta receptor Type II 0.007 0.049 -9999 0 -0.16 37 37
BSG 0.001 0.068 -9999 0 -0.22 39 39
keratinocyte migration -0.045 0.09 -9999 0 -0.22 57 57
Syndecan-1/RANTES -0.047 0.09 -9999 0 -0.21 65 65
Syndecan-1/CD147 -0.046 0.1 -9999 0 -0.24 60 60
Syndecan-1/Syntenin/PIP2 -0.044 0.088 -9999 0 -0.21 56 56
LAMA5 0.006 0.053 -9999 0 -0.18 33 33
positive regulation of cell-cell adhesion -0.043 0.086 -9999 0 -0.21 56 56
MMP7 -0.014 0.057 -9999 0 -0.11 135 135
HGF 0.016 0.02 -9999 0 -0.11 13 13
Syndecan-1/CASK -0.051 0.084 -9999 0 -0.16 146 146
Syndecan-1/HGF/MET -0.038 0.091 -9999 0 -0.22 46 46
regulation of cell adhesion -0.042 0.095 -9999 0 -0.23 63 63
HPSE 0.003 0.055 -9999 0 -0.15 52 52
positive regulation of cell migration -0.053 0.089 -9999 0 -0.17 148 148
SDC1 -0.053 0.09 -9999 0 -0.18 148 148
Syndecan-1/Collagen -0.053 0.089 -9999 0 -0.17 148 148
PPIB 0.004 0.066 -9999 0 -0.29 25 25
MET 0.008 0.037 -9999 0 -0.11 47 47
PRKACA 0.019 0 -9999 0 -10000 0 0
MMP9 -0.097 0.13 -9999 0 -0.21 271 271
MAPK1 -0.046 0.098 -9999 0 -0.24 64 64
homophilic cell adhesion -0.053 0.089 -9999 0 -0.17 148 148
MMP1 0.002 0.044 -9999 0 -0.11 70 70
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.033 0.11 -9999 0 -0.2 134 134
FZD6 -0.02 0.076 -9999 0 -0.14 129 129
WNT6 0.019 0 -9999 0 -10000 0 0
WNT4 0.018 0.013 -9999 0 -0.11 5 5
FZD3 -0.028 0.1 -9999 0 -0.22 103 103
WNT5A -0.027 0.1 -9999 0 -0.24 96 96
WNT11 0.017 0.016 -9999 0 -0.11 8 8
Glypican 2 network

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
MDK -0.025 0.1 -9999 0 -0.24 89 89
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.016 0.071 -9999 0 -0.16 89 89
neuron projection morphogenesis -0.016 0.07 -9999 0 -0.16 89 89
EGFR-dependent Endothelin 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
HRAS 0.009 0.055 -9999 0 -0.28 18 18
EGFR -0.08 0.12 -9999 0 -0.29 97 97
EGF/EGFR -0.042 0.073 -9999 0 -0.14 145 145
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.022 0.069 -9999 0 -0.13 110 110
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.029 0.099 -9999 0 -0.2 119 119
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.014 0.025 -9999 0 -0.11 21 21
EGF/EGFR dimer/SHC -0.034 0.075 -9999 0 -0.15 120 120
mol:GDP -0.024 0.067 -9999 0 -0.13 110 110
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.007 0.041 -9999 0 -0.12 48 48
GRB2/SOS1 0.011 0.026 -9999 0 -0.17 10 10
HRAS/GTP -0.027 0.064 -9999 0 -0.12 120 120
SHC1 0.004 0.052 -9999 0 -0.14 48 48
HRAS/GDP -0.023 0.069 -9999 0 -0.13 120 120
FRAP1 -0.024 0.059 -9999 0 -0.12 110 110
EGF/EGFR dimer -0.044 0.082 -9999 0 -0.19 107 107
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.014 0.039 -9999 0 -0.26 10 10
ETA receptor/Endothelin-1 -0.014 0.075 -9999 0 -0.18 69 69
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.022 0.079 -10000 0 -0.16 100 100
PDGF/PDGFRA/CRKL -0.017 0.076 -10000 0 -0.19 72 72
positive regulation of JUN kinase activity -0.01 0.067 -10000 0 -0.14 86 86
CRKL 0.018 0.01 -10000 0 -0.11 3 3
PDGF/PDGFRA/Caveolin-3 -0.016 0.076 -10000 0 -0.19 72 72
AP1 -0.12 0.27 -10000 0 -0.72 85 85
mol:IP3 -0.013 0.061 -10000 0 -0.21 31 31
PLCG1 -0.012 0.061 -10000 0 -0.11 100 100
PDGF/PDGFRA/alphaV Integrin -0.027 0.092 -10000 0 -0.21 89 89
RAPGEF1 0.019 0 -10000 0 -10000 0 0
CRK 0.009 0.054 -10000 0 -0.28 17 17
mol:Ca2+ -0.029 0.079 -10000 0 -0.2 77 77
CAV3 0.019 0.008 -10000 0 -0.11 2 2
CAV1 -0.071 0.13 -10000 0 -0.22 197 197
SHC/Grb2/SOS1 -0.009 0.068 -10000 0 -0.15 86 86
PDGF/PDGFRA/Shf -0.03 0.072 -10000 0 -0.18 88 88
FOS -0.12 0.27 -10000 0 -0.71 85 85
JUN -0.018 0.069 0.25 10 -0.25 28 38
oligodendrocyte development -0.027 0.091 -10000 0 -0.21 89 89
GRB2 0.014 0.039 -10000 0 -0.26 10 10
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
mol:DAG -0.013 0.061 -10000 0 -0.21 31 31
PDGF/PDGFRA -0.022 0.079 -10000 0 -0.16 100 100
actin cytoskeleton reorganization -0.018 0.077 -10000 0 -0.19 73 73
SRF 0.019 0.033 -10000 0 -0.17 14 14
SHC1 0.004 0.052 -10000 0 -0.14 48 48
PI3K -0.037 0.1 -10000 0 -0.19 145 145
PDGF/PDGFRA/Crk/C3G -0.006 0.073 -10000 0 -0.16 84 84
JAK1 -0.015 0.071 -10000 0 -0.2 49 49
ELK1/SRF -0.009 0.072 -10000 0 -0.16 79 79
SHB 0.016 0.02 -10000 0 -0.11 13 13
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.018 0.049 -10000 0 -0.26 14 14
GO:0007205 -0.037 0.093 -10000 0 -0.25 71 71
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction -0.01 0.067 -10000 0 -0.14 86 86
PDGF/PDGFRA/SHB -0.018 0.077 -10000 0 -0.19 73 73
PDGF/PDGFRA/Caveolin-1 -0.078 0.12 -10000 0 -0.23 176 176
ITGAV 0.003 0.067 -10000 0 -0.25 32 32
ELK1 -0.033 0.083 -10000 0 -0.21 79 79
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
PDGF/PDGFRA/Crk -0.023 0.085 -10000 0 -0.2 84 84
JAK-STAT cascade -0.015 0.071 -10000 0 -0.2 49 49
cell proliferation -0.03 0.072 -10000 0 -0.17 88 88
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.014 0.085 -9999 0 -0.2 81 81
CDC42/GTP -0.034 0.11 -9999 0 -0.19 141 141
PLCG1 -0.04 0.12 -9999 0 -0.2 141 141
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0.074 -9999 0 -0.28 34 34
GNAI3 0.014 0.038 -9999 0 -0.29 8 8
G12/G13 0.009 0.059 -9999 0 -0.19 39 39
cell migration -0.033 0.11 -9999 0 -0.19 141 141
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 -0.039 0.11 -9999 0 -0.2 141 141
MAPK1 -0.043 0.12 -9999 0 -0.21 141 141
S1P/S1P5/Gi -0.046 0.12 -9999 0 -0.22 141 141
GNAI1 -0.046 0.11 -9999 0 -0.2 157 157
CDC42/GDP 0.013 0.01 -9999 0 -0.07 8 8
S1P/S1P5/G12 -0.001 0.046 -9999 0 -0.16 39 39
RHOA 0.008 0.044 -9999 0 -0.14 39 39
S1P/S1P4/Gi -0.046 0.12 -9999 0 -0.22 141 141
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.008 0.083 -9999 0 -0.23 56 56
S1P/S1P4/G12/G13 0.01 0.045 -9999 0 -0.14 39 39
GNA12 -0.005 0.082 -9999 0 -0.29 39 39
GNA13 0.016 0.021 -9999 0 -0.11 14 14
CDC42 0.017 0.016 -9999 0 -0.11 8 8
Effects of Botulinum toxin

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
STX1A 0.007 0.016 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.016 0.048 -9999 0 -0.19 25 25
STXBP1 -0.021 0.094 -9999 0 -0.21 93 93
ACh/CHRNA1 -0.009 0.038 -9999 0 -0.066 150 150
RAB3GAP2/RIMS1/UNC13B 0.023 0.052 -9999 0 -0.17 33 33
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.018 0.011 -9999 0 -0.11 4 4
mol:ACh -0.026 0.045 -9999 0 -0.095 141 141
RAB3GAP2 0.012 0.045 -9999 0 -0.25 14 14
STX1A/SNAP25/VAMP2 -0.028 0.092 -9999 0 -0.21 69 69
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.009 0.038 -9999 0 -0.066 150 150
UNC13B 0.002 0.068 -9999 0 -0.24 35 35
CHRNA1 0.015 0.022 -9999 0 -0.11 16 16
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.054 0.083 -9999 0 -0.11 287 287
SNAP25 -0.061 0.092 -9999 0 -0.22 135 135
VAMP2 0.001 0.026 -9999 0 -0.2 8 8
SYT1 -0.087 0.12 -9999 0 -0.19 274 274
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.003 0.057 -9999 0 -0.14 67 67
STX1A/SNAP25 fragment 1/VAMP2 -0.028 0.092 -9999 0 -0.21 69 69
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.011 0.014 -10000 0 -0.081 8 8
RAS family/GTP -0.022 0.098 -10000 0 -0.16 140 140
NFATC4 -0.01 0.064 0.15 13 -0.12 63 76
ERBB2IP 0 0.074 -10000 0 -0.28 34 34
HSP90 (dimer) 0.018 0.019 -10000 0 -0.29 2 2
mammary gland morphogenesis -0.021 0.073 0.17 4 -0.14 114 118
JUN 0.001 0.081 -10000 0 -0.37 8 8
HRAS 0.009 0.055 -10000 0 -0.28 18 18
DOCK7 -0.023 0.069 0.16 9 -0.14 114 123
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.022 0.072 0.17 7 -0.14 112 119
AKT1 0.001 0.04 -10000 0 -0.18 23 23
BAD 0.011 0.018 -10000 0 -0.096 11 11
MAPK10 -0.011 0.056 0.12 5 -0.15 40 45
mol:GTP 0 0.001 -10000 0 -0.004 41 41
ErbB2/ErbB3/neuregulin 1 beta -0.021 0.079 0.18 6 -0.15 114 120
RAF1 -0.027 0.1 -10000 0 -0.2 93 93
ErbB2/ErbB3/neuregulin 2 -0.028 0.065 -10000 0 -0.14 105 105
STAT3 -0.043 0.25 -10000 0 -0.95 37 37
cell migration -0.011 0.061 0.13 5 -0.16 37 42
mol:PI-3-4-5-P3 -0.001 0.001 0.003 6 -0.003 116 122
cell proliferation -0.062 0.23 -10000 0 -0.58 66 66
FOS -0.058 0.2 -10000 0 -0.45 96 96
NRAS -0.01 0.086 -10000 0 -0.24 59 59
mol:Ca2+ -0.021 0.073 0.17 4 -0.14 114 118
MAPK3 -0.043 0.18 -10000 0 -0.5 49 49
MAPK1 -0.053 0.21 -10000 0 -0.56 55 55
JAK2 -0.019 0.073 0.16 10 -0.14 113 123
NF2 0.013 0.007 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.031 0.084 0.12 1 -0.18 114 115
NRG1 0.018 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.011 0.026 -10000 0 -0.17 10 10
MAPK8 -0.022 0.093 0.18 4 -0.19 107 111
MAPK9 -0.003 0.047 0.11 11 -0.1 29 40
ERBB2 0.013 0.072 0.29 33 -10000 0 33
ERBB3 -0.082 0.12 -10000 0 -0.18 262 262
SHC1 0.004 0.052 -10000 0 -0.14 48 48
RAC1 0.015 0.036 -10000 0 -0.29 7 7
apoptosis 0.001 0.047 0.24 16 -10000 0 16
STAT3 (dimer) -0.041 0.24 -10000 0 -0.93 37 37
RNF41 0.012 0.014 -10000 0 -0.059 13 13
FRAP1 0.011 0.015 -10000 0 -0.084 10 10
RAC1-CDC42/GTP -0.026 0.045 -10000 0 -0.1 114 114
ErbB2/ErbB2/HSP90 (dimer) 0.025 0.048 0.21 32 -0.17 1 33
CHRNA1 -0.025 0.14 -10000 0 -0.38 48 48
myelination -0.008 0.063 0.15 13 -0.18 11 24
PPP3CB -0.016 0.069 0.16 10 -0.13 112 122
KRAS 0.011 0.049 -10000 0 -0.28 14 14
RAC1-CDC42/GDP -0.01 0.081 -10000 0 -0.15 116 116
NRG2 0.019 0.006 -10000 0 -0.11 1 1
mol:GDP -0.031 0.084 0.12 2 -0.18 114 116
SOS1 0 0.001 -10000 0 -0.003 17 17
MAP2K2 -0.025 0.1 -10000 0 -0.22 79 79
SRC 0.019 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -0.003 7 7
PTPN11 -0.017 0.073 0.16 12 -0.14 113 125
MAP2K1 -0.058 0.19 -10000 0 -0.46 64 64
heart morphogenesis -0.021 0.073 0.17 4 -0.14 114 118
RAS family/GDP -0.02 0.099 -10000 0 -0.17 136 136
GRB2 0.014 0.039 -10000 0 -0.26 10 10
PRKACA 0.009 0.008 -10000 0 -10000 0 0
CHRNE 0.008 0.026 -10000 0 -0.15 8 8
HSP90AA1 0.018 0.019 -10000 0 -0.29 2 2
activation of caspase activity -0.001 0.04 0.18 23 -10000 0 23
nervous system development -0.021 0.073 0.17 4 -0.14 114 118
CDC42 0.017 0.016 -10000 0 -0.11 8 8
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.014 0.093 -9999 0 -0.27 60 60
LAT2 -0.027 0.13 -9999 0 -0.3 82 82
AP1 -0.036 0.16 -9999 0 -0.38 74 74
mol:PIP3 -0.019 0.14 -9999 0 -0.3 84 84
IKBKB -0.006 0.084 -9999 0 -0.2 66 66
AKT1 -0.034 0.13 -9999 0 -0.29 83 83
IKBKG -0.006 0.084 -9999 0 -0.2 67 67
MS4A2 0.021 0.006 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA -0.012 0.086 -9999 0 -0.22 66 66
MAP3K1 -0.022 0.13 -9999 0 -0.32 66 66
mol:Ca2+ -0.011 0.11 -9999 0 -0.23 84 84
LYN -0.019 0.1 -9999 0 -0.26 72 72
CBLB -0.027 0.13 -9999 0 -0.3 82 82
SHC1 0.004 0.052 -9999 0 -0.14 48 48
RasGAP/p62DOK 0.015 0.054 -9999 0 -0.15 39 39
positive regulation of cell migration -0.001 0.045 -9999 0 -0.15 39 39
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.012 0.07 -9999 0 -0.13 125 125
PTPN13 -0.052 0.2 -9999 0 -0.52 63 63
PTPN11 0.013 0.036 -9999 0 -0.28 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.026 0.13 -9999 0 -0.28 81 81
SYK -0.005 0.075 -9999 0 -0.31 25 25
GRB2 0.014 0.039 -9999 0 -0.26 10 10
LAT/PLCgamma1/GRB2/SLP76/GADs -0.051 0.12 -9999 0 -0.3 84 84
LAT -0.028 0.13 -9999 0 -0.3 82 82
PAK2 -0.029 0.14 -9999 0 -0.35 67 67
NFATC2 -0.01 0.019 -9999 0 -0.062 20 20
HRAS -0.034 0.15 -9999 0 -0.37 69 69
GAB2 -0.005 0.082 -9999 0 -0.27 44 44
PLA2G1B -0.003 0.18 -9999 0 -0.95 18 18
Fc epsilon R1 0.001 0.067 -9999 0 -0.14 84 84
Antigen/IgE/Fc epsilon R1 0.003 0.059 -9999 0 -0.12 84 84
mol:GDP -0.034 0.15 -9999 0 -0.38 68 68
JUN -0.002 0.077 -9999 0 -0.28 37 37
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
FOS -0.046 0.12 -9999 0 -0.22 146 146
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.032 0.14 -9999 0 -0.31 83 83
CHUK -0.007 0.084 -9999 0 -0.2 68 68
KLRG1 -0.019 0.12 -9999 0 -0.29 70 70
VAV1 -0.03 0.13 -9999 0 -0.3 82 82
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.027 0.13 -9999 0 -0.3 82 82
negative regulation of mast cell degranulation -0.024 0.11 -9999 0 -0.29 61 61
BTK -0.034 0.15 -9999 0 -0.4 58 58
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.052 0.11 -9999 0 -0.2 153 153
GAB2/PI3K/SHP2 -0.059 0.11 -9999 0 -0.27 90 90
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.032 0.14 -9999 0 -0.34 69 69
RAF1 -0.011 0.19 -9999 0 -1 18 18
Fc epsilon R1/FcgammaRIIB/SHIP -0.037 0.095 -9999 0 -0.15 173 173
FCER1G -0.025 0.1 -9999 0 -0.23 90 90
FCER1A 0.013 0.027 -9999 0 -0.11 23 23
Antigen/IgE/Fc epsilon R1/Fyn -0.006 0.082 -9999 0 -0.14 126 126
MAPK3 -0.003 0.18 -9999 0 -0.94 18 18
MAPK1 -0.007 0.19 -9999 0 -0.99 18 18
NFKB1 0.014 0.037 -9999 0 -0.23 11 11
MAPK8 0.015 0.076 -9999 0 -0.61 5 5
DUSP1 -0.005 0.065 -9999 0 -0.15 74 74
NF-kappa-B/RelA 0.002 0.056 -9999 0 -0.12 66 66
actin cytoskeleton reorganization -0.047 0.19 -9999 0 -0.52 60 60
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.04 0.16 -9999 0 -0.38 72 72
FER -0.028 0.13 -9999 0 -0.29 83 83
RELA 0.018 0.02 -9999 0 -0.23 3 3
ITK 0.002 0.033 -9999 0 -0.11 20 20
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.029 0.15 -9999 0 -0.38 62 62
cytokine secretion -0.013 0.033 -9999 0 -0.092 65 65
SPHK1 -0.031 0.13 -9999 0 -0.3 83 83
PTK2 -0.05 0.2 -9999 0 -0.55 60 60
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.052 0.13 -9999 0 -0.31 84 84
EDG1 -0.001 0.045 -9999 0 -0.15 39 39
mol:DAG -0.032 0.15 -9999 0 -0.37 72 72
MAP2K2 -0.007 0.18 -9999 0 -0.95 18 18
MAP2K1 -0.008 0.18 -9999 0 -0.96 18 18
MAP2K7 0.019 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.016 0.11 -9999 0 -0.3 56 56
MAP2K4 0.016 0.098 -9999 0 -0.98 5 5
Fc epsilon R1/FcgammaRIIB -0.04 0.1 -9999 0 -0.17 173 173
mol:Choline -0.012 0.07 -9999 0 -0.13 125 125
SHC/Grb2/SOS1 -0.02 0.13 -9999 0 -0.29 84 84
FYN -0.019 0.1 -9999 0 -0.28 68 68
DOK1 0.019 0 -9999 0 -10000 0 0
PXN -0.041 0.19 -9999 0 -0.5 60 60
HCLS1 -0.047 0.16 -9999 0 -0.35 93 93
PRKCB -0.017 0.11 -9999 0 -0.24 84 84
FCGR2B -0.078 0.12 -9999 0 -0.2 234 234
IGHE -0.001 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.024 0.11 -9999 0 -0.3 61 61
LCP2 -0.012 0.086 -9999 0 -0.22 70 70
PLA2G4A -0.044 0.15 -9999 0 -0.33 93 93
RASA1 0.003 0.069 -9999 0 -0.28 29 29
mol:Phosphatidic acid -0.012 0.07 -9999 0 -0.13 125 125
IKK complex 0.004 0.067 -9999 0 -0.15 65 65
WIPF1 0.013 0.038 -9999 0 -0.18 17 17
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.013 0.08 -9999 0 -0.17 94 94
EPHB2 0.013 0.027 -9999 0 -0.11 24 24
Syndecan-2/TACI -0.003 0.065 -9999 0 -0.16 75 75
LAMA1 0 0 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.007 0.081 -9999 0 -0.14 114 114
HRAS 0.009 0.055 -9999 0 -0.28 18 18
Syndecan-2/CASK -0.015 0.061 -9999 0 -0.16 78 78
ITGA5 -0.002 0.07 -9999 0 -0.19 53 53
BAX 0.013 0.097 -9999 0 -0.94 5 5
EPB41 0.019 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.006 0.067 -9999 0 -0.15 81 81
LAMA3 0.01 0.034 -9999 0 -0.11 38 38
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.036 0.11 -9999 0 -0.21 128 128
Syndecan-2/MMP2 -0.028 0.091 -9999 0 -0.18 123 123
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.003 0.067 -9999 0 -0.19 49 49
dendrite morphogenesis -0.006 0.067 -9999 0 -0.16 77 77
Syndecan-2/GM-CSF -0.003 0.065 -9999 0 -0.15 75 75
determination of left/right symmetry 0.007 0.036 -9999 0 -0.21 9 9
Syndecan-2/PKC delta -0.007 0.066 -9999 0 -0.16 77 77
GNB2L1 0.018 0.019 -9999 0 -0.29 2 2
MAPK3 0.001 0.057 -9999 0 -0.13 75 75
MAPK1 -0.003 0.065 -9999 0 -0.15 76 76
Syndecan-2/RACK1 0.003 0.067 -9999 0 -0.14 86 86
NF1 0.019 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.036 -9999 0 -0.21 9 9
ITGA2 -0.026 0.095 -9999 0 -0.19 114 114
MAPK8 0.014 0.048 -9999 0 -0.38 6 6
Syndecan-2/alpha2/beta1 Integrin -0.013 0.075 -9999 0 -0.14 110 110
Syndecan-2/Kininogen -0.003 0.065 -9999 0 -0.15 75 75
ITGB1 0.019 0 -9999 0 -10000 0 0
SRC 0.002 0.061 -9999 0 -0.12 86 86
Syndecan-2/CASK/Protein 4.1 -0.002 0.058 -9999 0 -0.14 75 75
extracellular matrix organization -0.01 0.07 -9999 0 -0.16 89 89
actin cytoskeleton reorganization -0.013 0.08 -9999 0 -0.17 94 94
Syndecan-2/Caveolin-2/Ras -0.024 0.094 -9999 0 -0.17 129 129
Syndecan-2/Laminin alpha3 -0.008 0.068 -9999 0 -0.15 82 82
Syndecan-2/RasGAP 0.005 0.078 -9999 0 -0.14 101 101
alpha5/beta1 Integrin 0.013 0.049 -9999 0 -0.19 24 24
PRKCD 0.012 0.029 -9999 0 -0.11 27 27
Syndecan-2 dimer -0.006 0.067 -9999 0 -0.16 77 77
GO:0007205 0.002 0.013 -9999 0 -0.13 5 5
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.006 0.074 -9999 0 -0.22 24 24
RHOA 0.015 0.036 -9999 0 -0.29 7 7
SDCBP 0.011 0.05 -9999 0 -0.29 14 14
TNFRSF13B 0.019 0.006 -9999 0 -0.11 1 1
RASA1 0.003 0.069 -9999 0 -0.28 29 29
alpha2/beta1 Integrin -0.003 0.067 -9999 0 -0.19 49 49
Syndecan-2/Synbindin -0.006 0.072 -9999 0 -0.17 77 77
TGFB1 0.007 0.049 -9999 0 -0.16 37 37
CASP3 -0.005 0.065 -9999 0 -0.15 78 78
FN1 0.001 0.071 -9999 0 -0.26 34 34
Syndecan-2/IL8 -0.063 0.11 -9999 0 -0.19 181 181
SDC2 0.007 0.036 -9999 0 -0.21 9 9
KNG1 0.019 0.006 -9999 0 -0.11 1 1
Syndecan-2/Neurofibromin -0.003 0.065 -9999 0 -0.15 75 75
TRAPPC4 0.014 0.038 -9999 0 -0.27 9 9
CSF2 0.019 0 -9999 0 -10000 0 0
Syndecan-2/TGFB1 -0.01 0.071 -9999 0 -0.16 89 89
Syndecan-2/Syntenin/PI-4-5-P2 -0.006 0.067 -9999 0 -0.15 81 81
Syndecan-2/Ezrin -0.004 0.064 -9999 0 -0.15 77 77
PRKACA 0.001 0.057 -9999 0 -0.13 75 75
angiogenesis -0.063 0.11 -9999 0 -0.19 181 181
MMP2 -0.027 0.1 -9999 0 -0.22 102 102
IL8 -0.091 0.13 -9999 0 -0.21 255 255
calcineurin-NFAT signaling pathway -0.003 0.065 -9999 0 -0.15 75 75
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.034 0.11 0.19 142 -10000 0 142
GNAI2 0 0.074 -10000 0 -0.28 34 34
S1P/S1P5/G12 -0.001 0.046 -10000 0 -0.16 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.014 0.085 -10000 0 -0.2 81 81
RhoA/GTP -0.035 0.12 -10000 0 -0.2 142 142
negative regulation of cAMP metabolic process -0.046 0.12 -10000 0 -0.22 141 141
GNAZ -0.008 0.083 -10000 0 -0.23 56 56
GNAI3 0.014 0.038 -10000 0 -0.29 8 8
GNA12 -0.005 0.082 -10000 0 -0.29 39 39
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.046 0.12 -10000 0 -0.22 141 141
RhoA/GDP 0.011 0.024 -10000 0 -0.2 7 7
RHOA 0.015 0.036 -10000 0 -0.29 7 7
GNAI1 -0.046 0.11 -10000 0 -0.2 157 157
Thromboxane A2 receptor 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
TGM2 0.016 0.019 -10000 0 -0.11 11 11
GNB1/GNG2 -0.047 0.074 -10000 0 -0.17 140 140
AKT1 -0.027 0.12 -10000 0 -0.2 157 157
EGF 0.014 0.025 -10000 0 -0.11 21 21
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.024 0.035 -10000 0 -0.19 4 4
mol:Ca2+ -0.036 0.15 -10000 0 -0.28 140 140
LYN 0.022 0.04 -10000 0 -0.19 9 9
RhoA/GTP -0.031 0.057 -10000 0 -0.12 140 140
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.051 0.17 -10000 0 -0.32 140 140
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.013 0.039 -10000 0 -0.29 7 7
TP alpha/Gq family/GDP/G beta5/gamma2 0.015 0.067 -10000 0 -0.25 30 30
G beta5/gamma2 -0.06 0.095 -10000 0 -0.22 140 140
PRKCH -0.048 0.17 -10000 0 -0.32 140 140
DNM1 0.017 0.017 -10000 0 -0.11 9 9
TXA2/TP beta/beta Arrestin3 0.017 0.015 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.002 140 140
PTGDR 0.019 0 -10000 0 -10000 0 0
G12 family/GTP -0.08 0.13 -10000 0 -0.29 140 140
ADRBK1 0.018 0.014 -10000 0 -0.11 6 6
ADRBK2 0.019 0.006 -10000 0 -0.11 1 1
RhoA/GTP/ROCK1 0.021 0.029 -10000 0 -0.17 11 11
mol:GDP 0.003 0.086 0.18 1 -10000 0 1
mol:NADP 0.019 0.006 -10000 0 -0.11 1 1
RAB11A 0.016 0.033 -10000 0 -0.29 6 6
PRKG1 0.019 0 -10000 0 -10000 0 0
mol:IP3 -0.051 0.18 -10000 0 -0.34 140 140
cell morphogenesis 0.021 0.029 -10000 0 -0.17 11 11
PLCB2 -0.077 0.23 -10000 0 -0.45 140 140
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.028 0.03 -10000 0 -0.12 1 1
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.017 0.044 -10000 0 -0.19 14 14
RHOA 0.015 0.036 -10000 0 -0.29 7 7
PTGIR 0.019 0 -10000 0 -10000 0 0
PRKCB1 -0.056 0.18 -10000 0 -0.35 140 140
GNAQ 0.015 0.023 -10000 0 -0.11 17 17
mol:L-citrulline 0.019 0.006 -10000 0 -0.11 1 1
TXA2/TXA2-R family -0.085 0.24 -10000 0 -0.48 140 140
LCK 0.028 0.03 -10000 0 -0.12 2 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.037 0.015 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.16 -10000 0 -0.51 47 47
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.034 0.022 -10000 0 -10000 0 0
MAPK14 -0.026 0.12 -10000 0 -0.22 140 140
TGM2/GTP -0.056 0.2 -10000 0 -0.37 140 140
MAPK11 -0.026 0.12 -10000 0 -0.22 140 140
ARHGEF1 -0.018 0.094 -10000 0 -0.17 140 140
GNAI2 0 0.074 -10000 0 -0.28 34 34
JNK cascade -0.056 0.19 -10000 0 -0.36 140 140
RAB11/GDP 0.015 0.032 -10000 0 -0.29 6 6
ICAM1 -0.039 0.14 -10000 0 -0.27 140 140
cAMP biosynthetic process -0.046 0.17 -10000 0 -0.31 140 140
Gq family/GTP/EBP50 0.009 0.051 -10000 0 -0.17 34 34
actin cytoskeleton reorganization 0.021 0.029 -10000 0 -0.17 11 11
SRC 0.028 0.029 -10000 0 -10000 0 0
GNB5 0.017 0.019 -10000 0 -0.14 7 7
GNB1 0.007 0.061 -10000 0 -0.29 21 21
EGF/EGFR -0.019 0.095 -10000 0 -0.2 83 83
VCAM1 -0.065 0.18 -10000 0 -0.36 140 140
TP beta/Gq family/GDP/G beta5/gamma2 0.015 0.067 -10000 0 -0.25 30 30
platelet activation -0.034 0.16 -10000 0 -0.28 140 140
PGI2/IP 0.014 0.001 -10000 0 -10000 0 0
PRKACA 0.022 0.002 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.016 0.061 -10000 0 -0.23 30 30
TXA2/TP beta/beta Arrestin2 0.015 0.029 -10000 0 -0.2 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.024 0.003 -10000 0 -10000 0 0
mol:DAG -0.062 0.2 -10000 0 -0.38 140 140
EGFR -0.08 0.12 -10000 0 -0.29 97 97
TXA2/TP alpha -0.067 0.22 -10000 0 -0.42 140 140
Gq family/GTP 0.009 0.037 -10000 0 -0.14 29 29
YES1 0.025 0.038 -10000 0 -0.18 9 9
GNAI2/GTP 0 0.026 -10000 0 -10000 0 0
PGD2/DP 0.014 0.001 -10000 0 -10000 0 0
SLC9A3R1 0.01 0.042 -10000 0 -0.15 30 30
FYN 0.02 0.052 -10000 0 -0.19 26 26
mol:NO 0.019 0.006 -10000 0 -0.11 1 1
GNA15 0.012 0.033 -10000 0 -0.12 26 26
PGK/cGMP 0.025 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.035 -10000 0 -0.29 7 7
TP alpha/TGM2/GDP/G beta/gamma 0.034 0.028 -10000 0 -10000 0 0
NOS3 0.019 0.006 -10000 0 -0.11 1 1
RAC1 0.015 0.036 -10000 0 -0.29 7 7
PRKCA -0.048 0.17 -10000 0 -0.32 140 140
PRKCB -0.052 0.17 -10000 0 -0.33 140 140
PRKCE -0.049 0.17 -10000 0 -0.33 140 140
PRKCD -0.057 0.18 -10000 0 -0.36 140 140
PRKCG -0.056 0.18 -10000 0 -0.35 140 140
muscle contraction -0.075 0.23 -10000 0 -0.44 140 140
PRKCZ -0.048 0.17 -10000 0 -0.32 140 140
ARR3 0.019 0 -10000 0 -10000 0 0
TXA2/TP beta 0.039 0.009 -10000 0 -10000 0 0
PRKCQ -0.05 0.17 -10000 0 -0.33 140 140
MAPKKK cascade -0.066 0.21 -10000 0 -0.4 140 140
SELE -0.04 0.15 -10000 0 -0.28 140 140
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.051 -10000 0 -0.22 15 15
ROCK1 0.016 0.031 -10000 0 -0.26 6 6
GNA14 0.015 0.022 -10000 0 -0.11 15 15
chemotaxis -0.11 0.29 -10000 0 -0.58 140 140
GNA12 -0.005 0.082 -10000 0 -0.29 39 39
GNA13 0.016 0.021 -10000 0 -0.11 14 14
GNA11 0.003 0.069 -10000 0 -0.29 27 27
Rac1/GTP 0.011 0.024 -10000 0 -0.2 7 7
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.018 0.094 -9999 0 -0.18 117 117
alphaM/beta2 Integrin/GPIbA 0.008 0.067 -9999 0 -0.15 74 74
alphaM/beta2 Integrin/proMMP-9 -0.06 0.1 -9999 0 -0.17 202 202
PLAUR -0.009 0.078 -9999 0 -0.18 73 73
HMGB1 0.019 0.014 -9999 0 -0.29 1 1
alphaM/beta2 Integrin/Talin -0.004 0.08 -9999 0 -0.17 87 87
AGER 0.019 0.012 -9999 0 -0.12 4 4
RAP1A 0.018 0.019 -9999 0 -0.29 2 2
SELPLG 0.018 0.014 -9999 0 -0.11 6 6
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.024 0.068 -9999 0 -0.19 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.097 0.13 -9999 0 -0.21 271 271
CYR61 -0.058 0.12 -9999 0 -0.22 168 168
TLN1 -0.003 0.065 -9999 0 -0.16 64 64
Rap1/GTP -0.014 0.055 -9999 0 -0.23 17 17
RHOA 0.015 0.036 -9999 0 -0.29 7 7
P-selectin oligomer 0.018 0.011 -9999 0 -0.11 4 4
MYH2 0.015 0.061 -9999 0 -0.22 16 16
MST1R 0.017 0.015 -9999 0 -0.11 7 7
leukocyte activation during inflammatory response 0.015 0.057 -9999 0 -0.12 74 74
APOB 0.018 0.011 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.027 0.1 -9999 0 -0.22 102 102
JAM3 -0.007 0.085 -9999 0 -0.28 46 46
GP1BA 0.019 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.024 0.097 -9999 0 -0.17 137 137
alphaM/beta2 Integrin 0.001 0.072 -9999 0 -0.27 16 16
JAM3 homodimer -0.007 0.085 -9999 0 -0.28 46 46
ICAM2 0.011 0.041 -9999 0 -0.15 26 26
ICAM1 0.005 0.041 -9999 0 -0.11 58 58
phagocytosis triggered by activation of immune response cell surface activating receptor 0.001 0.072 -9999 0 -0.27 16 16
cell adhesion 0.008 0.067 -9999 0 -0.15 74 74
NFKB1 0.013 0.067 -9999 0 -0.2 12 12
THY1 -0.019 0.097 -9999 0 -0.29 56 56
RhoA/GDP 0.011 0.024 -9999 0 -0.2 7 7
Lipoprotein(a) 0.025 0.007 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.027 0.11 -9999 0 -0.18 142 142
IL6 0.006 0.072 -9999 0 -0.28 1 1
ITGB2 -0.032 0.11 -9999 0 -0.23 109 109
elevation of cytosolic calcium ion concentration -0.017 0.1 -9999 0 -0.19 104 104
alphaM/beta2 Integrin/JAM2/JAM3 -0.008 0.11 -9999 0 -0.19 115 115
JAM2 -0.008 0.087 -9999 0 -0.28 49 49
alphaM/beta2 Integrin/ICAM1 0.017 0.067 -9999 0 -0.12 74 74
alphaM/beta2 Integrin/uPA/Plg -0.003 0.084 -9999 0 -0.16 89 89
RhoA/GTP 0.011 0.065 -9999 0 -0.23 18 18
positive regulation of phagocytosis -0.014 0.11 -9999 0 -0.26 78 78
Ron/MSP 0.025 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPAR/uPA -0.016 0.1 -9999 0 -0.19 104 104
alphaM/beta2 Integrin/uPAR -0.008 0.087 -9999 0 -0.17 97 97
PLAU -0.022 0.086 -9999 0 -0.29 35 35
PLAT -0.042 0.11 -9999 0 -0.22 134 134
actin filament polymerization 0.015 0.06 -9999 0 -0.22 16 16
MST1 0.016 0.02 -9999 0 -0.11 13 13
alphaM/beta2 Integrin/lipoprotein(a) 0.018 0.059 -9999 0 -0.12 74 74
TNF 0.015 0.061 -9999 0 -0.28 1 1
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.016 0.089 -9999 0 -0.18 96 96
fibrinolysis -0.004 0.083 -9999 0 -0.16 89 89
HCK -0.033 0.11 -9999 0 -0.21 120 120
dendritic cell antigen processing and presentation 0.001 0.072 -9999 0 -0.27 16 16
VTN 0.018 0.01 -9999 0 -0.11 3 3
alphaM/beta2 Integrin/CYR61 -0.037 0.1 -9999 0 -0.17 165 165
LPA 0.019 0 -9999 0 -10000 0 0
LRP1 -0.007 0.079 -9999 0 -0.21 61 61
cell migration -0.07 0.11 -9999 0 -0.18 215 215
FN1 0.001 0.071 -9999 0 -0.26 34 34
alphaM/beta2 Integrin/Thy1 -0.014 0.092 -9999 0 -0.18 113 113
MPO 0.019 0 -9999 0 -10000 0 0
KNG1 0.019 0.006 -9999 0 -0.11 1 1
RAP1/GDP 0.012 0.011 -9999 0 -0.16 2 2
ROCK1 0.014 0.064 -9999 0 -0.24 17 17
ELA2 0.019 0 -9999 0 -10000 0 0
PLG 0.019 0 -9999 0 -10000 0 0
CTGF -0.037 0.11 -9999 0 -0.23 118 118
alphaM/beta2 Integrin/Hck -0.02 0.11 -9999 0 -0.21 115 115
ITGAM 0.02 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.019 0.064 -9999 0 -0.13 74 74
HP -0.013 0.056 -9999 0 -0.11 132 132
leukocyte adhesion -0.016 0.13 -9999 0 -0.31 58 58
SELP 0.018 0.011 -9999 0 -0.11 4 4
Syndecan-3-mediated signaling events

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
CTTN 0.018 0.017 -9999 0 -0.16 4 4
Syndecan-3/Src/Cortactin -0.045 0.21 -9999 0 -0.54 76 76
Syndecan-3/Neurocan -0.076 0.22 -9999 0 -0.6 76 76
POMC 0.018 0.013 -9999 0 -0.11 5 5
EGFR -0.08 0.12 -9999 0 -0.29 97 97
Syndecan-3/EGFR -0.084 0.2 -9999 0 -0.56 77 77
AGRP 0.019 0 -9999 0 -10000 0 0
NCSTN 0.008 0.056 -9999 0 -0.26 20 20
PSENEN 0.013 0.041 -9999 0 -0.27 10 10
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.018 0.02 -9999 0 -0.23 3 3
APH1A 0.015 0.036 -9999 0 -0.27 8 8
NCAN -0.074 0.14 -9999 0 -0.29 138 138
long-term memory -0.055 0.21 -9999 0 -0.55 77 77
Syndecan-3/IL8 -0.08 0.2 -9999 0 -0.55 77 77
PSEN1 0.011 0.047 -9999 0 -0.26 15 15
Src/Cortactin 0.027 0.012 -9999 0 -0.19 1 1
FYN -0.019 0.1 -9999 0 -0.28 68 68
limb bud formation -0.065 0.19 -9999 0 -0.52 76 76
MC4R 0.019 0.006 -9999 0 -0.11 1 1
SRC 0.019 0 -9999 0 -10000 0 0
PTN -0.015 0.097 -9999 0 -0.29 58 58
FGFR/FGF/Syndecan-3 -0.065 0.19 -9999 0 -0.53 76 76
neuron projection morphogenesis -0.072 0.23 -9999 0 -0.57 84 84
Syndecan-3/AgRP -0.053 0.19 -9999 0 -0.5 76 76
Syndecan-3/AgRP/MC4R -0.04 0.18 -9999 0 -0.48 76 76
Fyn/Cortactin 0.001 0.073 -9999 0 -0.2 63 63
SDC3 -0.066 0.2 -9999 0 -0.54 76 76
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.078 0.2 -9999 0 -0.54 77 77
IL8 -0.091 0.13 -9999 0 -0.21 255 255
Syndecan-3/Fyn/Cortactin -0.056 0.21 -9999 0 -0.56 77 77
Syndecan-3/CASK -0.064 0.18 -9999 0 -0.51 76 76
alpha-MSH/MC4R 0.027 0.01 -9999 0 -10000 0 0
Gamma Secretase 0.041 0.063 -9999 0 -0.17 33 33
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.006 0.087 -9999 0 -0.21 50 50
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.12 -9999 0 -0.29 56 56
alphaV/beta3 Integrin/Osteopontin/Src -0.006 0.096 -9999 0 -0.23 73 73
AP1 -0.033 0.17 -9999 0 -0.35 93 93
ILK -0.004 0.098 -9999 0 -0.26 50 50
bone resorption -0.016 0.11 -9999 0 -0.25 73 73
PTK2B 0.018 0.013 -9999 0 -0.11 5 5
PYK2/p130Cas 0.009 0.096 -9999 0 -0.22 58 58
ITGAV 0 0.072 -9999 0 -0.26 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.015 0.083 -9999 0 -0.19 89 89
alphaV/beta3 Integrin/Osteopontin 0.009 0.096 -9999 0 -0.21 73 73
MAP3K1 -0.002 0.084 -9999 0 -0.18 77 77
JUN -0.002 0.078 -9999 0 -0.28 37 37
MAPK3 -0.005 0.095 -9999 0 -0.22 64 64
MAPK1 -0.008 0.1 -9999 0 -0.23 69 69
Rac1/GDP 0.011 0.024 -9999 0 -0.2 7 7
NFKB1 0.014 0.037 -9999 0 -0.23 11 11
MAPK8 -0.001 0.08 -9999 0 -0.17 80 80
ITGB3 0.016 0.018 -9999 0 -0.12 2 2
NFKBIA -0.011 0.12 -9999 0 -0.3 59 59
FOS -0.047 0.12 -9999 0 -0.22 146 146
CD44 -0.039 0.12 -9999 0 -0.25 115 115
CHUK 0.016 0.025 -9999 0 -0.15 10 10
PLAU -0.066 0.28 -9999 0 -1 37 37
NF kappa B1 p50/RelA 0.005 0.12 -9999 0 -0.3 52 52
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0.018 0.02 -9999 0 -0.23 3 3
alphaV beta3 Integrin 0.013 0.058 -9999 0 -0.18 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.008 0.098 -9999 0 -0.22 76 76
VAV3 -0.019 0.1 -9999 0 -0.23 82 82
MAP3K14 -0.003 0.089 -9999 0 -0.19 82 82
ROCK2 0.015 0.022 -9999 0 -0.11 16 16
SPP1 -0.013 0.095 -9999 0 -0.3 52 52
RAC1 0.015 0.036 -9999 0 -0.29 7 7
Rac1/GTP -0.016 0.1 -9999 0 -0.25 68 68
MMP2 -0.05 0.17 -9999 0 -0.33 112 112
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.004 0.036 -10000 0 -0.2 16 16
GNB1/GNG2 0.015 0.035 -10000 0 -0.14 21 21
regulation of S phase of mitotic cell cycle -0.011 0.091 -10000 0 -0.2 84 84
GNAO1 -0.014 0.085 -10000 0 -0.2 81 81
HRAS 0.008 0.055 -10000 0 -0.28 18 18
SHBG/T-DHT 0.013 0 -10000 0 -10000 0 0
PELP1 0.014 0.036 -10000 0 -0.29 7 7
AKT1 0.001 0.042 -10000 0 -0.2 22 22
MAP2K1 0 0.07 -10000 0 -0.13 85 85
T-DHT/AR 0.01 0.017 -10000 0 -0.07 22 22
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 82 82
GNAI2 0 0.074 -10000 0 -0.28 34 34
GNAI3 0.014 0.038 -10000 0 -0.29 8 8
GNAI1 -0.046 0.11 -10000 0 -0.2 157 157
mol:GDP -0.019 0.044 -10000 0 -0.16 26 26
cell proliferation -0.05 0.18 -10000 0 -0.41 92 92
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
FOS -0.1 0.29 -10000 0 -0.74 89 89
mol:Ca2+ -0.012 0.03 -10000 0 -0.058 130 130
MAPK3 -0.027 0.12 -10000 0 -0.27 94 94
MAPK1 -0.031 0.14 -10000 0 -0.27 92 92
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
mol:IP3 -0.001 0.002 -10000 0 -0.004 82 82
cAMP biosynthetic process 0.012 0.02 0.065 35 -10000 0 35
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 82 82
HRAS/GTP 0.017 0.046 -10000 0 -0.15 22 22
actin cytoskeleton reorganization -0.002 0.068 -10000 0 -0.14 85 85
SRC 0.019 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 82 82
PI3K -0.011 0.078 -10000 0 -0.18 88 88
apoptosis 0.052 0.18 0.43 91 -10000 0 91
T-DHT/AR/PELP1 0.019 0.026 -10000 0 -0.14 9 9
HRAS/GDP -0.002 0.061 -10000 0 -0.16 43 43
CREB1 -0.057 0.2 -10000 0 -0.46 91 91
RAC1-CDC42/GTP 0.003 0.072 -10000 0 -0.14 85 85
AR 0.013 0.026 -10000 0 -0.11 22 22
GNB1 0.007 0.061 -10000 0 -0.29 21 21
RAF1 0.005 0.06 -10000 0 -0.19 26 26
RAC1-CDC42/GDP 0.012 0.058 -10000 0 -0.19 20 20
T-DHT/AR/PELP1/Src 0.029 0.026 -10000 0 -0.14 7 7
MAP2K2 0.001 0.067 -10000 0 -0.13 74 74
T-DHT/AR/PELP1/Src/PI3K -0.011 0.091 -10000 0 -0.2 84 84
GNAZ -0.008 0.083 -10000 0 -0.23 56 56
SHBG 0.019 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.063 0.2 -10000 0 -0.48 73 73
mol:T-DHT 0 0.001 0.002 2 -0.002 75 77
RAC1 0.015 0.036 -10000 0 -0.29 7 7
GNRH1 0.01 0 -10000 0 -10000 0 0
Gi family/GTP -0.04 0.1 -10000 0 -0.19 141 141
CDC42 0.017 0.016 -10000 0 -0.11 8 8
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.022 0.016 -10000 0 -10000 0 0
cell-cell adhesion 0.027 0.054 0.17 50 -10000 0 50
Ephrin B/EPHB2/RasGAP 0.013 0.08 -10000 0 -0.14 94 94
ITSN1 0.016 0.031 -10000 0 -0.29 5 5
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
SHC1 0.004 0.052 -10000 0 -0.14 48 48
Ephrin B1/EPHB3 0.021 0.019 -10000 0 -10000 0 0
Ephrin B1/EPHB1 0.012 0.033 -10000 0 -0.16 6 6
HRAS/GDP -0.037 0.087 -10000 0 -0.21 84 84
Ephrin B/EPHB1/GRB7 0.01 0.074 -10000 0 -0.14 88 88
Endophilin/SYNJ1 0.001 0.054 -10000 0 -0.12 83 83
KRAS 0.011 0.048 -10000 0 -0.28 14 14
Ephrin B/EPHB1/Src 0.011 0.073 -10000 0 -0.13 88 88
endothelial cell migration -0.018 0.098 -10000 0 -0.17 134 134
GRB2 0.014 0.039 -10000 0 -0.26 10 10
GRB7 0.016 0.019 -10000 0 -0.11 11 11
PAK1 0.005 0.054 -10000 0 -0.11 83 83
HRAS 0.009 0.055 -10000 0 -0.28 18 18
RRAS -0.006 0.067 -10000 0 -0.14 89 89
DNM1 0.017 0.017 -10000 0 -0.11 9 9
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.008 0.067 -10000 0 -0.14 88 88
lamellipodium assembly -0.027 0.054 -10000 0 -0.17 50 50
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.011 0.092 -10000 0 -0.2 90 90
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
EPHB2 0.013 0.027 -10000 0 -0.11 24 24
EPHB3 0.01 0.032 -10000 0 -0.11 35 35
EPHB1 -0.005 0.057 -10000 0 -0.12 91 91
EPHB4 0.019 0.006 -10000 0 -0.11 1 1
mol:GDP -0.017 0.1 -10000 0 -0.24 83 83
Ephrin B/EPHB2 0.011 0.063 -10000 0 -0.12 83 83
Ephrin B/EPHB3 0.01 0.063 -10000 0 -0.12 83 83
JNK cascade 0.011 0.043 -10000 0 -0.17 18 18
Ephrin B/EPHB1 0.002 0.07 -10000 0 -0.14 88 88
RAP1/GDP -0.008 0.095 -10000 0 -0.22 83 83
EFNB2 -0.035 0.11 -10000 0 -0.25 105 105
EFNB3 0.016 0.022 -10000 0 -0.13 11 11
EFNB1 0.019 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.009 0.072 -10000 0 -0.15 97 97
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.018 0.019 -10000 0 -0.29 2 2
CDC42/GTP 0.002 0.087 -10000 0 -0.18 84 84
Rap1/GTP -0.03 0.061 -10000 0 -0.19 51 51
axon guidance 0.022 0.016 -10000 0 -10000 0 0
MAPK3 -0.004 0.085 -10000 0 -0.22 47 47
MAPK1 -0.007 0.092 -10000 0 -0.23 53 53
Rac1/GDP -0.008 0.1 -10000 0 -0.23 83 83
actin cytoskeleton reorganization -0.037 0.077 -10000 0 -0.2 69 69
CDC42/GDP -0.007 0.098 -10000 0 -0.22 83 83
PI3K -0.015 0.1 -10000 0 -0.17 134 134
EFNA5 0.019 0.006 -10000 0 -0.11 1 1
Ephrin B2/EPHB4 -0.006 0.067 -10000 0 -0.16 83 83
Ephrin B/EPHB2/Intersectin/N-WASP -0.001 0.081 -10000 0 -0.17 85 85
CDC42 0.017 0.016 -10000 0 -0.11 8 8
RAS family/GTP -0.036 0.077 -10000 0 -0.2 70 70
PTK2 0.002 0.052 -10000 0 -0.29 16 16
MAP4K4 0.011 0.043 -10000 0 -0.17 18 18
SRC 0.019 0 -10000 0 -10000 0 0
KALRN 0.017 0.018 -10000 0 -0.11 10 10
Intersectin/N-WASP 0.024 0.03 -10000 0 -0.19 10 10
neuron projection morphogenesis 0.009 0.079 -10000 0 -0.18 54 54
MAP2K1 -0.008 0.089 -10000 0 -0.18 92 92
WASL 0.016 0.03 -10000 0 -0.29 5 5
Ephrin B1/EPHB1-2/NCK1 0.027 0.044 -10000 0 -0.14 12 12
cell migration -0.009 0.097 -10000 0 -0.21 86 86
NRAS -0.01 0.086 -10000 0 -0.24 59 59
SYNJ1 0.001 0.055 -10000 0 -0.12 83 83
PXN 0.018 0.011 -10000 0 -0.11 4 4
TF -0.026 0.073 -10000 0 -0.16 104 104
HRAS/GTP 0.001 0.079 -10000 0 -0.18 53 53
Ephrin B1/EPHB1-2 0.02 0.036 -10000 0 -0.11 14 14
cell adhesion mediated by integrin 0.01 0.052 0.12 81 -10000 0 81
RAC1 0.015 0.036 -10000 0 -0.29 7 7
mol:GTP 0.002 0.078 -10000 0 -0.18 46 46
RAC1-CDC42/GTP -0.026 0.055 -10000 0 -0.16 54 54
RASA1 0.003 0.069 -10000 0 -0.28 29 29
RAC1-CDC42/GDP 0 0.1 -10000 0 -0.22 83 83
ruffle organization -0.001 0.078 -10000 0 -0.19 54 54
NCK1 0.014 0.036 -10000 0 -0.19 14 14
receptor internalization 0.003 0.052 -10000 0 -0.11 83 83
Ephrin B/EPHB2/KALRN 0.019 0.066 -10000 0 -0.12 83 83
ROCK1 0.019 0.016 -10000 0 -10000 0 0
RAS family/GDP -0.04 0.083 -10000 0 -0.22 68 68
Rac1/GTP -0.028 0.057 -10000 0 -0.18 50 50
Ephrin B/EPHB1/Src/Paxillin -0.005 0.077 -10000 0 -0.17 88 88
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.047 0.11 -9999 0 -0.2 149 149
PDGFRB 0.01 0.044 -9999 0 -0.18 21 21
SPHK1 -0.005 0.025 -9999 0 -10000 0 0
mol:S1P 0.001 0.037 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.064 0.19 -9999 0 -0.43 84 84
GNAO1 -0.014 0.086 -9999 0 -0.2 81 81
PDGFB-D/PDGFRB/PLCgamma1 -0.055 0.17 -9999 0 -0.42 66 66
PLCG1 -0.058 0.18 -9999 0 -0.41 78 78
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.044 -9999 0 -0.18 21 21
GNAI2 0 0.074 -9999 0 -0.28 34 34
GNAI3 0.014 0.038 -9999 0 -0.3 8 8
GNAI1 -0.046 0.11 -9999 0 -0.2 157 157
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.044 0.12 -9999 0 -0.2 141 141
S1P1/S1P -0.034 0.11 -9999 0 -0.3 49 49
negative regulation of cAMP metabolic process -0.063 0.19 -9999 0 -0.41 86 86
MAPK3 -0.058 0.18 -9999 0 -0.48 62 62
calcium-dependent phospholipase C activity -0.001 0.002 -9999 0 -10000 0 0
Rac1/GDP 0.011 0.024 -9999 0 -0.2 7 7
RhoA/GDP 0.011 0.024 -9999 0 -0.2 7 7
KDR -0.002 0.067 -9999 0 -0.15 72 72
PLCB2 -0.027 0.098 -9999 0 -0.27 48 48
RAC1 0.015 0.036 -9999 0 -0.29 7 7
RhoA/GTP -0.042 0.085 -9999 0 -0.27 46 46
receptor internalization -0.032 0.1 -9999 0 -0.28 49 49
PTGS2 -0.063 0.17 -9999 0 -0.55 41 41
Rac1/GTP -0.042 0.087 -9999 0 -0.28 43 43
RHOA 0.015 0.036 -9999 0 -0.29 7 7
VEGFA -0.07 0.13 -9999 0 -0.25 156 156
negative regulation of T cell proliferation -0.063 0.19 -9999 0 -0.41 86 86
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.008 0.084 -9999 0 -0.24 56 56
MAPK1 -0.061 0.19 -9999 0 -0.49 64 64
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 -9999 0 -0.32 55 55
ABCC1 0.014 0.024 -9999 0 -0.12 17 17
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.016 0.048 -9999 0 -0.19 25 25
AKT1 -0.081 0.21 -9999 0 -0.44 94 94
PTK2B -0.033 0.11 -9999 0 -0.29 56 56
VEGFR2 homodimer/Frs2 0.006 0.089 -9999 0 -0.34 22 22
CAV1 -0.071 0.13 -9999 0 -0.22 197 197
CALM1 0.007 0.056 -9999 0 -0.21 28 28
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.034 0.12 -9999 0 -0.29 56 56
endothelial cell proliferation -0.049 0.17 -9999 0 -0.36 80 80
mol:Ca2+ -0.041 0.13 -9999 0 -0.27 87 87
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.035 0.13 -9999 0 -0.31 63 63
RP11-342D11.1 -0.048 0.13 -9999 0 -0.28 86 86
CDH5 -0.016 0.088 -9999 0 -0.2 84 84
VEGFA homodimer -0.017 0.079 -9999 0 -0.15 122 122
SHC1 0.004 0.052 -9999 0 -0.14 48 48
SHC2 0.001 0.071 -9999 0 -0.26 35 35
HRAS/GDP -0.06 0.11 -9999 0 -0.31 64 64
SH2D2A 0.019 0.006 -9999 0 -0.11 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.027 0.14 -9999 0 -0.41 41 41
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.033 0.12 -9999 0 -0.3 54 54
VEGFR1 homodimer 0.019 0.008 -9999 0 -0.11 2 2
SHC/GRB2/SOS1 -0.033 0.14 -9999 0 -0.32 65 65
GRB10 -0.057 0.16 -9999 0 -0.41 67 67
PTPN11 0.015 0.033 -9999 0 -0.27 7 7
GRB2 0.014 0.039 -9999 0 -0.26 10 10
PAK1 0.017 0.017 -9999 0 -0.11 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.04 0.14 -9999 0 -0.32 71 71
HRAS 0.009 0.055 -9999 0 -0.28 18 18
VEGF/Rho/ROCK1/Integrin Complex -0.032 0.14 -9999 0 -0.35 50 50
HIF1A 0.011 0.047 -9999 0 -0.27 14 14
FRS2 0.018 0.013 -9999 0 -0.11 5 5
oxygen and reactive oxygen species metabolic process -0.035 0.13 -9999 0 -0.31 63 63
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.019 0.006 -9999 0 -0.11 1 1
Nck/Pak 0.023 0.029 -9999 0 -0.18 8 8
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.051 0.14 -9999 0 -0.32 75 75
mol:GDP -0.038 0.13 -9999 0 -0.31 65 65
mol:NADP -0.027 0.12 -9999 0 -0.39 33 33
eNOS/Hsp90 -0.018 0.12 -9999 0 -0.37 33 33
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
mol:IP3 -0.042 0.13 -9999 0 -0.28 87 87
HIF1A/ARNT 0.023 0.033 -9999 0 -0.19 12 12
SHB 0.016 0.02 -9999 0 -0.11 13 13
VEGFA -0.072 0.13 -9999 0 -0.23 188 188
VEGFC 0.01 0.033 -9999 0 -10000 0 0
FAK1/Vinculin -0.045 0.17 -9999 0 -0.4 63 63
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.015 0.036 -9999 0 -0.29 7 7
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.027 0.13 -9999 0 -0.3 57 57
PTPN6 0.005 0.057 -9999 0 -0.2 33 33
EPAS1 0.003 0.076 -9999 0 -0.28 28 28
mol:L-citrulline -0.027 0.12 -9999 0 -0.39 33 33
ITGAV 0.003 0.067 -9999 0 -0.25 32 32
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.023 0.12 -9999 0 -0.3 49 49
VEGFR2 homodimer/VEGFA homodimer -0.04 0.15 -9999 0 -0.3 86 86
VEGFR2/3 heterodimer 0.006 0.089 -9999 0 -0.34 22 22
VEGFB 0.017 0.023 -9999 0 -0.29 3 3
MAPK11 -0.046 0.14 -9999 0 -0.34 62 62
VEGFR2 homodimer -0.003 0.1 -9999 0 -0.38 25 25
FLT1 0.019 0.008 -9999 0 -0.11 2 2
NEDD4 0.009 0.033 -9999 0 -0.12 25 25
MAPK3 -0.037 0.12 -9999 0 -0.3 56 56
MAPK1 -0.039 0.12 -9999 0 -0.31 58 58
VEGFA145/NRP2 -0.037 0.093 -9999 0 -0.19 125 125
VEGFR1/2 heterodimer 0.006 0.089 -9999 0 -0.34 22 22
KDR -0.003 0.1 -9999 0 -0.38 25 25
VEGFA165/NRP1/VEGFR2 homodimer -0.031 0.13 -9999 0 -0.3 68 68
SRC 0.019 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.038 0.12 -9999 0 -0.32 56 56
PI3K -0.06 0.18 -9999 0 -0.4 85 85
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.036 0.12 -9999 0 -0.28 63 63
FES -0.042 0.13 -9999 0 -0.28 86 86
GAB1 -0.063 0.17 -9999 0 -0.39 76 76
VEGFR2 homodimer/VEGFA homodimer/Src -0.033 0.12 -9999 0 -0.29 54 54
CTNNB1 0.017 0.023 -9999 0 -0.29 3 3
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0.019 0.006 -9999 0 -0.11 1 1
eNOS/Caveolin-1 -0.043 0.14 -9999 0 -0.35 57 57
VEGFR2 homodimer/VEGFA homodimer/Yes -0.04 0.13 -9999 0 -0.29 69 69
PI3K/GAB1 -0.076 0.2 -9999 0 -0.37 141 141
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.015 0.12 -9999 0 -0.28 50 50
PRKACA 0.019 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.014 0.088 -9999 0 -0.32 23 23
HSP90AA1 0.018 0.019 -9999 0 -0.29 2 2
CDC42 -0.042 0.13 -9999 0 -0.28 86 86
actin cytoskeleton reorganization -0.033 0.12 -9999 0 -0.29 54 54
PTK2 -0.056 0.18 -9999 0 -0.43 61 61
EDG1 -0.048 0.15 -9999 0 -0.35 72 72
mol:DAG -0.042 0.13 -9999 0 -0.28 87 87
CaM/Ca2+ -0.036 0.13 -9999 0 -0.33 58 58
MAP2K3 -0.037 0.12 -9999 0 -0.3 64 64
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.047 0.17 -9999 0 -0.41 69 69
PLCG1 -0.042 0.13 -9999 0 -0.28 87 87
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.021 0.12 -9999 0 -0.3 46 46
IQGAP1 -0.009 0.087 -9999 0 -0.27 50 50
YES1 0.005 0.061 -9999 0 -0.24 28 28
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.035 0.12 -9999 0 -0.3 58 58
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.04 0.12 -9999 0 -0.27 70 70
cell migration -0.047 0.18 -9999 0 -0.41 68 68
mol:PI-3-4-5-P3 -0.056 0.17 -9999 0 -0.37 85 85
FYN -0.019 0.1 -9999 0 -0.28 68 68
VEGFB/NRP1 -0.038 0.12 -9999 0 -0.3 64 64
mol:NO -0.027 0.12 -9999 0 -0.39 33 33
PXN 0.018 0.011 -9999 0 -0.11 4 4
HRAS/GTP -0.062 0.11 -9999 0 -0.31 64 64
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.05 0.16 -9999 0 -0.41 67 67
VHL 0 0 -9999 0 -10000 0 0
ITGB3 0.019 0.008 -9999 0 -0.11 2 2
NOS3 -0.032 0.14 -9999 0 -0.43 33 33
VEGFR2 homodimer/VEGFA homodimer/Sck -0.041 0.14 -9999 0 -0.32 63 63
RAC1 0.015 0.036 -9999 0 -0.29 7 7
PRKCA -0.036 0.12 -9999 0 -0.29 66 66
PRKCB -0.042 0.12 -9999 0 -0.26 87 87
VCL 0.017 0.023 -9999 0 -0.29 3 3
VEGFA165/NRP1 -0.044 0.13 -9999 0 -0.28 86 86
VEGFR1/2 heterodimer/VEGFA homodimer -0.033 0.12 -9999 0 -0.29 57 57
VEGFA165/NRP2 -0.037 0.093 -9999 0 -0.19 125 125
MAPKKK cascade -0.041 0.15 -9999 0 -0.35 77 77
NRP2 0.017 0.016 -9999 0 -0.11 8 8
VEGFC homodimer 0.01 0.033 -9999 0 -10000 0 0
NCK1 0.014 0.036 -9999 0 -0.19 14 14
ROCK1 0.016 0.031 -9999 0 -0.26 6 6
FAK1/Paxillin -0.045 0.17 -9999 0 -0.4 61 61
MAP3K13 -0.041 0.13 -9999 0 -0.28 86 86
PDPK1 -0.052 0.15 -9999 0 -0.33 85 85
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.017 0.12 0.19 1 -0.29 70 71
IKBKB 0.008 0.072 0.2 8 -0.21 23 31
AKT1 -0.018 0.072 0.16 3 -0.18 61 64
IKBKG 0.005 0.073 0.18 2 -0.21 35 37
CALM1 -0.03 0.14 0.18 18 -0.36 64 82
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
MAP3K1 -0.017 0.13 -10000 0 -0.39 44 44
MAP3K7 0.007 0.059 -10000 0 -0.25 24 24
mol:Ca2+ -0.031 0.15 0.18 20 -0.38 61 81
DOK1 0.019 0 -10000 0 -10000 0 0
AP-1 -0.016 0.091 0.14 10 -0.21 71 81
LYN -0.018 0.098 -10000 0 -0.25 72 72
BLNK -0.036 0.11 -10000 0 -0.29 66 66
SHC1 0.004 0.052 -10000 0 -0.14 48 48
BCR complex 0.027 0.013 -10000 0 -0.14 2 2
CD22 -0.029 0.11 -10000 0 -0.36 42 42
CAMK2G -0.028 0.14 0.18 18 -0.33 65 83
CSNK2A1 0.01 0.053 -10000 0 -0.29 16 16
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.041 0.081 -10000 0 -0.27 46 46
GO:0007205 -0.032 0.15 0.18 20 -0.38 61 81
SYK -0.005 0.072 -10000 0 -0.29 25 25
ELK1 -0.026 0.14 0.18 20 -0.36 60 80
NFATC1 -0.019 0.1 -10000 0 -0.32 44 44
B-cell antigen/BCR complex 0.027 0.013 -10000 0 -0.14 2 2
PAG1/CSK 0.01 0.03 -10000 0 -0.2 11 11
NFKBIB 0.011 0.033 0.09 1 -0.13 11 12
HRAS -0.026 0.13 0.17 8 -0.34 55 63
NFKBIA 0.013 0.029 0.09 1 -0.13 6 7
NF-kappa-B/RelA/I kappa B beta 0.016 0.03 0.092 1 -0.13 9 10
RasGAP/Csk -0.012 0.082 -10000 0 -0.13 145 145
mol:GDP -0.028 0.15 0.18 20 -0.37 60 80
PTEN 0.013 0.038 -10000 0 -0.18 17 17
CD79B 0.018 0.011 -10000 0 -0.11 4 4
NF-kappa-B/RelA/I kappa B alpha 0.017 0.028 0.092 2 -0.11 9 11
GRB2 0.014 0.039 -10000 0 -0.26 10 10
PI3K/BCAP/CD19 -0.053 0.17 -10000 0 -0.43 70 70
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
mol:IP3 -0.032 0.15 0.18 20 -0.39 61 81
CSK 0.013 0.044 -10000 0 -0.29 11 11
FOS -0.044 0.14 0.17 13 -0.35 68 81
CHUK 0.003 0.075 0.18 2 -0.22 32 34
IBTK 0.014 0.039 -10000 0 -0.26 10 10
CARD11/BCL10/MALT1/TAK1 -0.019 0.13 0.22 2 -0.33 63 65
PTPN6 -0.029 0.12 -10000 0 -0.36 46 46
RELA 0.018 0.02 -10000 0 -0.23 3 3
BCL2A1 0.007 0.03 -10000 0 -0.077 42 42
VAV2 -0.028 0.12 -10000 0 -0.4 40 40
ubiquitin-dependent protein catabolic process 0.015 0.032 0.092 1 -0.12 11 12
BTK 0.012 0.009 -10000 0 -10000 0 0
CD19 -0.03 0.11 -10000 0 -0.36 42 42
MAP4K1 0.019 0.006 -10000 0 -0.11 1 1
CD72 0.016 0.019 -10000 0 -0.11 12 12
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 -0.01 0.11 -10000 0 -0.33 45 45
SH3BP5 -0.003 0.075 -10000 0 -0.22 48 48
PIK3AP1 -0.034 0.16 0.19 20 -0.41 61 81
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.035 0.19 -10000 0 -0.48 66 66
RAF1 -0.024 0.13 0.17 8 -0.35 50 58
RasGAP/p62DOK/SHIP -0.013 0.069 -10000 0 -0.12 142 142
CD79A 0.018 0.013 -10000 0 -10000 0 0
re-entry into mitotic cell cycle -0.016 0.09 0.14 10 -0.21 71 81
RASA1 0.003 0.069 -10000 0 -0.28 29 29
MAPK3 -0.013 0.11 0.15 7 -0.3 48 55
MAPK1 -0.016 0.11 0.15 7 -0.3 54 61
CD72/SHP1 -0.02 0.11 -10000 0 -0.35 45 45
NFKB1 0.014 0.037 -10000 0 -0.23 11 11
MAPK8 -0.009 0.11 -10000 0 -0.33 44 44
actin cytoskeleton organization -0.021 0.11 -10000 0 -0.35 42 42
NF-kappa-B/RelA 0.029 0.072 0.18 1 -0.25 18 19
Calcineurin -0.016 0.13 -10000 0 -0.35 51 51
PI3K -0.053 0.11 -10000 0 -0.31 60 60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.036 0.17 0.2 20 -0.44 61 81
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.019 0.14 -10000 0 -0.46 40 40
DAPP1 -0.032 0.15 -10000 0 -0.5 40 40
cytokine secretion -0.017 0.097 -10000 0 -0.3 44 44
mol:DAG -0.032 0.15 0.18 20 -0.39 61 81
PLCG2 -0.002 0.069 -10000 0 -0.19 52 52
MAP2K1 -0.02 0.12 0.16 7 -0.34 48 55
B-cell antigen/BCR complex/FcgammaRIIB -0.023 0.077 -10000 0 -0.15 118 118
mol:PI-3-4-5-P3 -0.04 0.078 0.16 4 -0.23 57 61
ETS1 -0.02 0.12 0.18 18 -0.3 64 82
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.005 0.11 -10000 0 -0.27 50 50
B-cell antigen/BCR complex/LYN -0.034 0.12 -10000 0 -0.31 69 69
MALT1 0.013 0.036 -10000 0 -0.16 18 18
TRAF6 0.018 0.019 -10000 0 -0.29 2 2
RAC1 -0.023 0.12 -10000 0 -0.37 42 42
B-cell antigen/BCR complex/LYN/SYK -0.01 0.12 -10000 0 -0.32 57 57
CARD11 -0.03 0.14 0.18 20 -0.36 61 81
FCGR2B -0.078 0.12 -10000 0 -0.2 234 234
PPP3CA 0.002 0.069 -10000 0 -0.27 31 31
BCL10 0.016 0.028 -10000 0 -0.23 6 6
IKK complex 0.011 0.034 0.1 9 -0.085 18 27
PTPRC -0.031 0.11 -10000 0 -0.23 107 107
PDPK1 -0.015 0.062 0.15 3 -0.16 56 59
PPP3CB 0.016 0.024 -10000 0 -0.15 9 9
PPP3CC 0.019 0 -10000 0 -10000 0 0
POU2F2 0.014 0.025 -10000 0 -0.082 17 17
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.011 0.043 -9999 0 -0.18 21 21
mol:S1P 0.001 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.048 0.14 -9999 0 -0.24 147 147
GNAO1 -0.012 0.085 -9999 0 -0.2 81 81
S1P/S1P3/G12/G13 0.012 0.045 -9999 0 -0.14 39 39
AKT1 -0.026 0.16 -9999 0 -0.62 30 30
AKT3 -0.055 0.14 -9999 0 -0.55 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.043 -9999 0 -0.18 21 21
GNAI2 0.002 0.074 -9999 0 -0.28 34 34
GNAI3 0.016 0.038 -9999 0 -0.29 8 8
GNAI1 -0.044 0.11 -9999 0 -0.2 157 157
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.001 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.001 0.068 -9999 0 -0.22 39 39
mol:Ca2+ -0.036 0.12 -9999 0 -0.28 73 73
MAPK3 -0.031 0.12 -9999 0 -0.31 53 53
MAPK1 -0.034 0.12 -9999 0 -0.32 58 58
JAK2 -0.04 0.13 -9999 0 -0.3 75 75
CXCR4 -0.048 0.13 -9999 0 -0.28 97 97
FLT1 0.021 0.008 -9999 0 -0.11 2 2
RhoA/GDP 0.011 0.024 -9999 0 -0.2 7 7
Rac1/GDP 0.011 0.024 -9999 0 -0.2 7 7
SRC -0.031 0.12 -9999 0 -0.28 65 65
S1P/S1P3/Gi -0.037 0.12 -9999 0 -0.28 73 73
RAC1 0.015 0.036 -9999 0 -0.29 7 7
RhoA/GTP -0.026 0.12 -9999 0 -0.3 55 55
VEGFA -0.065 0.13 -9999 0 -0.22 188 188
S1P/S1P2/Gi -0.04 0.12 -9999 0 -0.21 141 141
VEGFR1 homodimer/VEGFA homodimer -0.028 0.093 -9999 0 -0.19 119 119
RHOA 0.015 0.036 -9999 0 -0.29 7 7
S1P/S1P3/Gq 0.012 0.045 -9999 0 -0.16 29 29
GNAQ 0.015 0.023 -9999 0 -0.11 17 17
GNAZ -0.006 0.083 -9999 0 -0.23 56 56
G12/G13 0.009 0.059 -9999 0 -0.19 39 39
GNA14 0.015 0.022 -9999 0 -0.11 15 15
GNA15 0.012 0.033 -9999 0 -0.12 26 26
GNA12 -0.005 0.082 -9999 0 -0.29 39 39
GNA13 0.016 0.021 -9999 0 -0.11 14 14
GNA11 0.003 0.069 -9999 0 -0.29 27 27
Rac1/GTP -0.026 0.12 -9999 0 -0.31 54 54
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.019 -10000 0 -10000 0 0
CDKN2C -0.011 0.091 -10000 0 -0.24 69 69
CDKN2A -0.016 0.058 -10000 0 -0.11 138 138
CCND2 0.002 0.034 0.13 28 -0.099 2 30
RB1 -0.003 0.037 -10000 0 -0.14 28 28
CDK4 0.003 0.039 0.15 28 -0.13 3 31
CDK6 0.006 0.037 0.15 28 -10000 0 28
G1/S progression 0.001 0.042 0.14 36 -10000 0 36
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.018 0.057 -10000 0 -0.16 41 41
fibroblast growth factor receptor signaling pathway 0.017 0.057 -10000 0 -0.16 41 41
LAMA1 0 0 -10000 0 -10000 0 0
PRNP -0.002 0.076 -10000 0 -0.26 41 41
GPC1/SLIT2 -0.007 0.068 -10000 0 -0.2 40 40
SMAD2 0.01 0.05 -10000 0 -0.14 43 43
GPC1/PrPc/Cu2+ -0.002 0.072 -10000 0 -0.19 57 57
GPC1/Laminin alpha1 -0.005 0.056 -10000 0 -0.15 62 62
TDGF1 0.018 0.014 -10000 0 -0.11 6 6
CRIPTO/GPC1 0.008 0.061 -10000 0 -0.2 37 37
APP/GPC1 0.005 0.069 -10000 0 -0.22 41 41
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.006 0.059 -10000 0 -0.18 40 40
FLT1 0.019 0.008 -10000 0 -0.11 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0.018 0.056 -10000 0 -0.16 42 42
SERPINC1 0.019 0.006 -10000 0 -0.11 1 1
FYN -0.001 0.079 -10000 0 -0.27 38 38
FGR 0.003 0.058 -10000 0 -0.18 39 39
positive regulation of MAPKKK cascade -0.036 0.15 -10000 0 -0.34 78 78
SLIT2 -0.005 0.05 -10000 0 -0.11 97 97
GPC1/NRG 0.009 0.058 -10000 0 -0.19 37 37
NRG1 0.019 0 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.031 0.094 -10000 0 -0.17 144 144
LYN 0.002 0.06 -10000 0 -0.19 39 39
mol:Spermine -0.008 0.055 -10000 0 -0.2 37 37
cell growth 0.017 0.057 -10000 0 -0.16 41 41
BMP signaling pathway 0.009 0.082 0.22 62 -10000 0 62
SRC 0.009 0.049 -10000 0 -0.16 37 37
TGFBR1 0.019 0.006 -10000 0 -0.11 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.078 0.11 -10000 0 -0.17 272 272
GPC1 -0.009 0.082 -10000 0 -0.22 62 62
TGFBR1 (dimer) 0.019 0.006 -10000 0 -0.11 1 1
VEGFA -0.068 0.13 -10000 0 -0.22 188 188
BLK 0.009 0.049 -10000 0 -0.16 37 37
HCK -0.004 0.067 -10000 0 -0.21 41 41
FGF2 0.013 0.036 -10000 0 -0.16 19 19
FGFR1 0.019 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer 0.019 0.008 -10000 0 -0.11 2 2
TGFBR2 0.013 0.035 -10000 0 -0.14 21 21
cell death 0.005 0.069 -10000 0 -0.22 41 41
ATIII/GPC1 0.009 0.059 -10000 0 -0.19 37 37
PLA2G2A/GPC1 -0.058 0.094 -10000 0 -0.21 124 124
LCK 0.008 0.051 -10000 0 -0.17 37 37
neuron differentiation 0.009 0.058 -10000 0 -0.19 37 37
PrPc/Cu2+ 0 0.052 -10000 0 -0.17 41 41
APP 0.013 0.042 -10000 0 -0.29 10 10
TGFBR2 (dimer) 0.012 0.035 -10000 0 -0.14 21 21
PLK2 and PLK4 events

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.013 0.083 -9999 0 -0.19 82 82
PLK4 0.017 0.017 -9999 0 -0.11 9 9
regulation of centriole replication -0.002 0.058 -9999 0 -0.19 40 40
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.017 0.14 -10000 0 -0.28 85 85
adherens junction organization 0 0.098 -10000 0 -0.3 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.033 0.13 -10000 0 -0.29 70 70
FMN1 0.001 0.086 -10000 0 -0.26 37 37
mol:IP3 -0.009 0.11 -10000 0 -0.26 57 57
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.091 -10000 0 -0.28 37 37
CTNNB1 0.017 0.024 -10000 0 -0.3 3 3
AKT1 -0.008 0.12 -10000 0 -0.3 57 57
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.016 0.085 -10000 0 -0.37 18 18
CTNND1 0 0.075 -10000 0 -0.3 31 31
mol:PI-4-5-P2 0.005 0.085 -10000 0 -0.24 40 40
VASP 0.005 0.088 -10000 0 -0.3 30 30
ZYX -0.006 0.11 -10000 0 -0.33 41 41
JUB 0.001 0.086 -10000 0 -0.26 37 37
EGFR(dimer) -0.02 0.11 -10000 0 -0.29 51 51
E-cadherin/beta catenin-gamma catenin 0.027 0.037 -10000 0 -0.11 28 28
mol:PI-3-4-5-P3 -0.004 0.12 -10000 0 -0.28 57 57
PIK3CA -0.012 0.088 -10000 0 -0.23 66 66
PI3K -0.004 0.12 -10000 0 -0.28 57 57
FYN -0.028 0.16 -10000 0 -0.4 70 70
mol:Ca2+ -0.009 0.11 -10000 0 -0.26 57 57
JUP 0.007 0.037 -10000 0 -0.11 47 47
PIK3R1 -0.015 0.097 -10000 0 -0.27 62 62
mol:DAG -0.009 0.11 -10000 0 -0.26 57 57
CDH1 0.011 0.03 -10000 0 -0.11 29 29
RhoA/GDP -0.033 0.12 -10000 0 -0.29 71 71
establishment of polarity of embryonic epithelium 0.005 0.087 -10000 0 -0.29 31 31
SRC 0.019 0 -10000 0 -10000 0 0
RAC1 0.015 0.036 -10000 0 -0.29 7 7
RHOA 0.015 0.036 -10000 0 -0.29 7 7
EGFR -0.08 0.12 -10000 0 -0.29 97 97
CASR -0.005 0.1 -10000 0 -0.24 57 57
RhoA/GTP -0.001 0.1 -10000 0 -0.28 45 45
AKT2 -0.003 0.11 -10000 0 -0.28 48 48
actin cable formation 0.004 0.086 -10000 0 -0.29 31 31
apoptosis 0.013 0.13 0.25 85 -10000 0 85
CTNNA1 0.011 0.05 -10000 0 -0.3 13 13
mol:GDP -0.036 0.13 -10000 0 -0.28 81 81
PIP5K1A 0.005 0.087 -10000 0 -0.25 40 40
PLCG1 -0.01 0.11 -10000 0 -0.27 57 57
Rac1/GTP -0.025 0.11 -10000 0 -0.28 50 50
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.025 0.006 -10000 0 -10000 0 0
NFATC2 0.015 0.16 -10000 0 -0.44 34 34
NFATC3 -0.005 0.1 0.29 12 -0.22 72 84
CD40LG -0.08 0.3 -10000 0 -0.71 79 79
ITCH 0.019 0.047 -10000 0 -0.19 9 9
CBLB 0.019 0.046 -10000 0 -0.2 7 7
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.014 0.2 -10000 0 -0.51 43 43
JUNB -0.003 0.067 -10000 0 -0.17 63 63
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.057 -10000 0 -0.21 16 16
T cell anergy 0.006 0.06 -10000 0 -0.27 10 10
TLE4 0.022 0.11 -10000 0 -0.3 30 30
Jun/NFAT1-c-4/p21SNFT -0.051 0.31 -10000 0 -0.73 78 78
AP-1/NFAT1-c-4 -0.063 0.36 -10000 0 -0.8 79 79
IKZF1 0.023 0.1 -10000 0 -0.29 32 32
T-helper 2 cell differentiation 0.006 0.14 -10000 0 -0.46 24 24
AP-1/NFAT1 -0.006 0.16 -10000 0 -0.33 74 74
CALM1 0.014 0.051 -10000 0 -0.2 19 19
EGR2 -0.087 0.42 0.5 3 -0.99 78 81
EGR3 -0.095 0.42 0.49 3 -1 75 78
NFAT1/FOXP3 0.036 0.11 -10000 0 -0.29 32 32
EGR1 -0.032 0.11 -10000 0 -0.24 107 107
JUN -0.002 0.074 -10000 0 -0.28 33 33
EGR4 0.019 0.013 -10000 0 -0.11 5 5
mol:Ca2+ 0.004 0.02 -10000 0 -10000 0 0
GBP3 0.011 0.1 -10000 0 -0.3 32 32
FOSL1 0.007 0.038 -10000 0 -0.11 51 51
NFAT1-c-4/MAF/IRF4 -0.029 0.31 -10000 0 -0.71 79 79
DGKA 0.023 0.1 -10000 0 -0.29 30 30
CREM 0.017 0.014 -10000 0 -0.11 6 6
NFAT1-c-4/PPARG -0.042 0.31 -10000 0 -0.73 79 79
CTLA4 0.027 0.084 -10000 0 -0.23 32 32
NFAT1-c-4 (dimer)/EGR1 -0.058 0.33 -10000 0 -0.79 79 79
NFAT1-c-4 (dimer)/EGR4 -0.034 0.31 -10000 0 -0.73 79 79
FOS -0.041 0.11 -10000 0 -0.21 133 133
IFNG 0.01 0.13 -10000 0 -0.43 12 12
T cell activation -0.034 0.2 -10000 0 -0.6 37 37
MAF 0.008 0.059 -10000 0 -0.27 22 22
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.033 0.25 0.59 77 -0.48 6 83
TNF -0.055 0.3 -10000 0 -0.71 79 79
FASLG -0.1 0.43 -10000 0 -1.1 79 79
TBX21 0.025 0.007 -10000 0 -0.1 1 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.018 0.024 -10000 0 -0.11 19 19
PTPN1 0.018 0.13 -10000 0 -0.38 33 33
NFAT1-c-4/ICER1 -0.043 0.31 -10000 0 -0.73 79 79
GATA3 0.02 0.018 -10000 0 -0.11 10 10
T-helper 1 cell differentiation 0.01 0.13 -10000 0 -0.42 13 13
IL2RA -0.017 0.2 -10000 0 -0.49 52 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.013 0.13 -10000 0 -0.38 40 40
E2F1 0.012 0.045 -10000 0 -0.22 15 15
PPARG 0.015 0.023 -10000 0 -0.11 18 18
SLC3A2 0.01 0.14 -10000 0 -0.46 32 32
IRF4 0.019 0.006 -10000 0 -0.11 1 1
PTGS2 -0.088 0.3 -10000 0 -0.71 79 79
CSF2 -0.08 0.3 -10000 0 -0.71 79 79
JunB/Fra1/NFAT1-c-4 -0.042 0.31 -10000 0 -0.72 79 79
IL4 0.005 0.15 -10000 0 -0.48 23 23
IL5 -0.08 0.3 -10000 0 -0.71 79 79
IL2 -0.035 0.2 -10000 0 -0.61 37 37
IL3 -0.006 0.061 -10000 0 -0.64 2 2
RNF128 0.006 0.065 -10000 0 -0.26 7 7
NFATC1 -0.033 0.25 0.48 6 -0.59 77 83
CDK4 -0.012 0.26 0.49 28 -1.1 15 43
PTPRK -0.003 0.17 -10000 0 -0.48 51 51
IL8 -0.12 0.32 -10000 0 -0.74 86 86
POU2F1 0.022 0.028 -10000 0 -0.29 2 2
IL6-mediated signaling events

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
BCL2L1 -0.01 0.26 -10000 0 -0.68 44 44
CRP -0.008 0.26 -10000 0 -0.68 44 44
cell cycle arrest -0.025 0.3 -10000 0 -0.74 55 55
TIMP1 -0.084 0.36 -10000 0 -0.8 93 93
IL6ST 0.003 0.075 -10000 0 -0.28 32 32
Rac1/GDP 0.031 0.11 0.23 8 -0.33 25 33
AP1 -0.032 0.22 -10000 0 -0.57 58 58
GAB2 -0.004 0.082 -10000 0 -0.27 44 44
TNFSF11 -0.008 0.26 -10000 0 -0.7 40 40
HSP90B1 -0.035 0.29 -10000 0 -1 38 38
GAB1 0.004 0.056 -10000 0 -0.15 49 49
MAPK14 0.033 0.075 -10000 0 -0.31 11 11
AKT1 -0.019 0.2 -10000 0 -0.57 43 43
FOXO1 -0.026 0.2 -10000 0 -0.57 46 46
MAP2K6 0.029 0.085 0.22 8 -0.27 23 31
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 0.029 0.14 -10000 0 -0.36 34 34
MITF 0.023 0.098 0.23 8 -0.29 27 35
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.007 0.06 -10000 0 -0.28 21 21
A2M -0.072 0.32 -10000 0 -1.3 36 36
CEBPB 0.002 0.078 -10000 0 -0.22 51 51
GRB2/SOS1/GAB family/SHP2 -0.016 0.16 -10000 0 -0.47 47 47
STAT3 -0.031 0.32 -10000 0 -0.8 55 55
STAT1 0.011 0.066 -10000 0 -0.79 3 3
CEBPD -0.042 0.34 -10000 0 -0.93 55 55
PIK3CA -0.01 0.086 -10000 0 -0.22 66 66
PI3K -0.014 0.094 -10000 0 -0.21 88 88
JUN -0.002 0.077 -10000 0 -0.28 37 37
PIAS3/MITF 0.028 0.1 0.22 7 -0.27 31 38
MAPK11 0.034 0.075 -10000 0 -0.31 10 10
STAT3 (dimer)/FOXO1 -0.036 0.31 -10000 0 -0.67 80 80
GRB2/SOS1/GAB family -0.006 0.13 -10000 0 -0.31 60 60
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.015 0.13 -10000 0 -0.28 70 70
GRB2 0.015 0.039 -10000 0 -0.26 10 10
JAK2 0.013 0.026 -10000 0 -10000 0 0
LBP -0.007 0.25 -10000 0 -0.63 48 48
PIK3R1 -0.014 0.095 -10000 0 -0.27 62 62
JAK1 0.003 0.073 -10000 0 -0.26 34 34
MYC -0.069 0.37 -10000 0 -0.87 80 80
FGG -0.009 0.26 -10000 0 -0.72 38 38
macrophage differentiation -0.025 0.3 -10000 0 -0.74 55 55
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.034 0.07 -10000 0 -0.19 31 31
JUNB -0.027 0.29 -10000 0 -0.77 49 49
FOS -0.046 0.12 -10000 0 -0.22 146 146
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.024 0.1 0.24 8 -0.3 27 35
STAT1/PIAS1 0.024 0.12 0.26 8 -0.31 31 39
GRB2/SOS1/GAB family/SHP2/PI3K -0.02 0.19 -10000 0 -0.48 53 53
STAT3 (dimer) -0.029 0.31 -10000 0 -0.79 55 55
PRKCD 0.025 0.18 -10000 0 -0.42 45 45
IL6R 0.021 0.007 -10000 0 -10000 0 0
SOCS3 0.035 0.069 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.019 0.088 -10000 0 -0.21 54 54
Rac1/GTP 0.029 0.12 0.24 1 -0.33 29 30
HCK -0.033 0.11 -10000 0 -0.21 120 120
MAPKKK cascade -0.026 0.21 -10000 0 -0.64 46 46
bone resorption -0.005 0.24 -10000 0 -0.65 42 42
IRF1 -0.024 0.29 -10000 0 -0.78 48 48
mol:GDP 0.025 0.1 0.24 8 -0.3 25 33
SOS1 0.001 0.004 -10000 0 -10000 0 0
VAV1 0.025 0.1 0.24 8 -0.3 25 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.026 0.089 -10000 0 -0.35 21 21
PTPN11 0.011 0.094 -10000 0 -0.84 6 6
IL6/IL6RA 0.014 0.038 -10000 0 -10000 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.021 0.081 -10000 0 -0.22 46 46
gp130 (dimer)/JAK2/JAK2/LMO4 0.024 0.065 -10000 0 -0.19 38 38
IL6 -0.004 0.052 -10000 0 -0.11 101 101
PIAS3 0.014 0.033 -10000 0 -0.19 12 12
PTPRE -0.016 0.085 -10000 0 -0.24 61 61
PIAS1 0.008 0.056 -10000 0 -0.29 18 18
RAC1 0.015 0.036 -10000 0 -0.3 7 7
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.021 0.081 0.2 13 -0.24 30 43
LMO4 0.014 0.053 -10000 0 -0.3 14 14
STAT3 (dimer)/PIAS3 -0.021 0.29 -10000 0 -0.73 55 55
MCL1 -0.012 0.18 -10000 0 -0.66 26 26
Reelin signaling pathway

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
CDK5R1/CDK5 0.014 0.049 -9999 0 -0.19 25 25
VLDLR -0.021 0.093 -9999 0 -0.2 97 97
CRKL 0.018 0.01 -9999 0 -0.11 3 3
LRPAP1 0.013 0.043 -9999 0 -0.28 11 11
FYN -0.019 0.1 -9999 0 -0.28 68 68
ITGA3 0.005 0.042 -9999 0 -0.11 57 57
RELN/VLDLR/Fyn -0.016 0.085 -9999 0 -0.17 108 108
MAPK8IP1/MKK7/MAP3K11/JNK1 0.051 0.028 -9999 0 -0.14 7 7
AKT1 -0.03 0.11 -9999 0 -0.2 123 123
MAP2K7 0.019 0 -9999 0 -10000 0 0
RAPGEF1 0.019 0 -9999 0 -10000 0 0
DAB1 0.019 0.006 -9999 0 -0.11 1 1
RELN/LRP8/DAB1 0.024 0.033 -9999 0 -0.13 10 10
LRPAP1/LRP8 0.018 0.043 -9999 0 -0.2 16 16
RELN/LRP8/DAB1/Fyn 0.013 0.066 -9999 0 -0.15 63 63
DAB1/alpha3/beta1 Integrin 0.015 0.054 -9999 0 -0.11 64 64
long-term memory 0.024 0.066 -9999 0 -0.19 18 18
DAB1/LIS1 0.015 0.071 -9999 0 -0.14 69 69
DAB1/CRLK/C3G 0.019 0.052 -9999 0 -0.11 61 61
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
DAB1/NCK2 0.016 0.071 -9999 0 -0.14 70 70
ARHGEF2 0.014 0.034 -9999 0 -0.18 13 13
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.017 0.016 -9999 0 -0.11 8 8
CDK5R1 0.014 0.025 -9999 0 -0.11 21 21
RELN 0.007 0.038 -9999 0 -0.11 50 50
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
RELN/LRP8/Fyn 0.003 0.075 -9999 0 -0.18 66 66
GRIN2A/RELN/LRP8/DAB1/Fyn 0.022 0.069 -9999 0 -0.14 63 63
MAPK8 0.019 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 0.008 0.056 -9999 0 -0.14 54 54
ITGB1 0.019 0 -9999 0 -10000 0 0
MAP1B -0.006 0.067 -9999 0 -0.16 68 68
RELN/LRP8 0.022 0.045 -9999 0 -0.15 20 20
GRIN2B/RELN/LRP8/DAB1/Fyn 0.023 0.069 -9999 0 -0.14 63 63
PI3K -0.016 0.093 -9999 0 -0.21 88 88
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.018 0.029 -9999 0 -0.19 1 1
RAP1A 0.013 0.05 -9999 0 -0.16 12 12
PAFAH1B1 0.009 0.055 -9999 0 -0.29 17 17
MAPK8IP1 0.016 0.019 -9999 0 -0.11 11 11
CRLK/C3G 0.028 0.007 -9999 0 -10000 0 0
GRIN2B 0.019 0 -9999 0 -10000 0 0
NCK2 0.009 0.054 -9999 0 -0.28 17 17
neuron differentiation 0.015 0.068 -9999 0 -0.28 13 13
neuron adhesion 0.017 0.049 -9999 0 -0.15 14 14
LRP8 0.01 0.043 -9999 0 -0.16 28 28
GSK3B -0.031 0.12 -9999 0 -0.21 123 123
RELN/VLDLR/DAB1/Fyn -0.003 0.075 -9999 0 -0.14 109 109
MAP3K11 0.017 0.021 -9999 0 -0.18 5 5
RELN/VLDLR/DAB1/P13K -0.03 0.1 -9999 0 -0.2 123 123
CDK5 0.004 0.064 -9999 0 -0.24 31 31
MAPT -0.029 0.089 -9999 0 -0.24 71 71
neuron migration -0.022 0.12 -9999 0 -0.28 72 72
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.015 0.068 -9999 0 -0.29 13 13
RELN/VLDLR 0.01 0.067 -9999 0 -0.14 73 73
Class I PI3K 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
ARF5/GTP 0.002 0.065 0.18 6 -0.15 62 68
DAPP1 -0.031 0.13 -10000 0 -0.33 69 69
Src family/SYK family/BLNK-LAT/BTK-ITK -0.058 0.21 -10000 0 -0.49 80 80
mol:DAG -0.014 0.096 0.17 3 -0.21 79 82
HRAS 0.013 0.04 -10000 0 -0.28 9 9
RAP1A 0.017 0.015 -10000 0 -0.31 1 1
ARF5/GDP -0.008 0.11 -10000 0 -0.26 65 65
PLCG2 -0.002 0.069 -10000 0 -0.19 52 52
PLCG1 0.017 0.025 -10000 0 -0.29 3 3
ARF5 0.014 0.04 -10000 0 -0.29 9 9
mol:GTP -0.015 0.056 0.18 6 -0.15 60 66
ARF1/GTP -0.006 0.061 0.17 6 -0.16 59 65
RHOA 0.015 0.036 -10000 0 -0.29 7 7
YES1 0.005 0.061 -10000 0 -0.24 28 28
RAP1A/GTP 0 0.06 0.18 6 -0.15 60 66
ADAP1 -0.006 0.056 0.17 6 -0.14 60 66
ARAP3 -0.015 0.055 0.18 6 -0.15 60 66
INPPL1 0.016 0.033 -10000 0 -0.29 6 6
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 -0.009 0.088 -10000 0 -0.28 48 48
ARHGEF7 0 0.071 -10000 0 -0.25 37 37
ARF1 0.014 0.036 -10000 0 -0.29 7 7
NRAS 0.008 0.049 -10000 0 -0.18 27 27
FYN -0.019 0.1 -10000 0 -0.28 68 68
ARF6 0.018 0.015 -10000 0 -0.2 2 2
FGR 0.005 0.048 -10000 0 -0.14 46 46
mol:Ca2+ -0.002 0.05 -10000 0 -0.1 79 79
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.003 0.066 -10000 0 -0.23 35 35
ZAP70 0.019 0.006 -10000 0 -0.11 1 1
mol:IP3 -0.006 0.069 -10000 0 -0.14 80 80
LYN -0.018 0.098 -10000 0 -0.25 72 72
ARF1/GDP -0.008 0.11 -10000 0 -0.26 63 63
RhoA/GDP 0 0.084 0.18 4 -0.18 73 77
PDK1/Src/Hsp90 0.038 0.012 -10000 0 -0.15 2 2
BLNK -0.036 0.11 -10000 0 -0.29 66 66
actin cytoskeleton reorganization -0.005 0.1 0.18 4 -0.3 38 42
SRC 0.019 0 -10000 0 -10000 0 0
PLEKHA2 0.011 0.015 -10000 0 -0.05 30 30
RAC1 0.015 0.036 -10000 0 -0.29 7 7
PTEN 0.013 0.036 -10000 0 -0.17 17 17
HSP90AA1 0.018 0.019 -10000 0 -0.29 2 2
ARF6/GTP 0.004 0.059 0.18 6 -0.14 59 65
RhoA/GTP 0.003 0.063 0.18 6 -0.15 62 68
Src family/SYK family/BLNK-LAT -0.057 0.2 -10000 0 -0.46 80 80
BLK 0.018 0.011 -10000 0 -0.11 4 4
PDPK1 0.019 0 -10000 0 -10000 0 0
CYTH1 -0.006 0.056 0.17 6 -0.14 60 66
HCK -0.033 0.11 -10000 0 -0.21 120 120
CYTH3 -0.006 0.056 0.17 6 -0.14 60 66
CYTH2 -0.006 0.056 0.17 6 -0.14 60 66
KRAS 0.013 0.04 -10000 0 -0.28 9 9
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.052 0.14 5 -0.22 13 18
SGK1 0.01 0.04 -10000 0 -0.16 14 14
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.018 0.11 -10000 0 -0.27 62 62
SOS1 0 0 -10000 0 -10000 0 0
SYK -0.005 0.072 -10000 0 -0.29 25 25
ARF6/GDP -0.003 0.079 0.16 6 -0.17 74 80
mol:PI-3-4-5-P3 -0.006 0.059 0.18 6 -0.15 60 66
ARAP3/RAP1A/GTP 0 0.06 0.18 6 -0.15 60 66
VAV1 0.016 0.019 -10000 0 -0.11 12 12
mol:PI-3-4-P2 0.008 0.022 -10000 0 -0.2 6 6
RAS family/GTP/PI3K Class I 0.012 0.065 0.18 6 -0.15 60 66
PLEKHA1 0.01 0.022 -10000 0 -0.068 28 28
Rac1/GDP -0.008 0.12 -10000 0 -0.27 62 62
LAT 0.018 0.014 -10000 0 -10000 0 0
Rac1/GTP -0.02 0.16 -10000 0 -0.42 54 54
ITK -0.001 0.057 0.18 6 -0.14 60 66
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.025 0.13 0.19 3 -0.28 84 87
LCK 0.017 0.016 -10000 0 -0.11 8 8
BTK -0.001 0.057 0.18 6 -0.14 60 66
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.011 0.024 -9999 0 -0.2 7 7
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.008 0.057 -9999 0 -0.27 20 20
ERC1 -0.002 0.075 -9999 0 -0.24 43 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.032 0.12 -9999 0 -0.31 69 69
IRAK/TOLLIP 0.019 0.038 -9999 0 -0.15 23 23
IKBKB 0.019 0 -9999 0 -10000 0 0
IKBKG 0.019 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 0.009 0.039 -9999 0 -0.14 6 6
IL1A 0.013 0.026 -9999 0 -0.11 23 23
IL1B -0.027 0.075 -9999 0 -0.18 83 83
IRAK/TRAF6/p62/Atypical PKCs 0.027 0.053 -9999 0 -0.15 38 38
IL1R2 -0.003 0.049 -9999 0 -0.11 91 91
IL1R1 0.016 0.02 -9999 0 -0.11 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.023 0.1 -9999 0 -0.31 46 46
TOLLIP 0.016 0.021 -9999 0 -0.11 14 14
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.019 0.006 -9999 0 -0.11 1 1
TAK1/TAB1/TAB2 0.025 0.055 -9999 0 -0.18 31 31
IKK complex/ELKS 0.026 0.09 -9999 0 -0.29 33 33
JUN 0.021 0.05 -9999 0 -0.23 15 15
MAP3K7 0.007 0.059 -9999 0 -0.25 24 24
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.034 0.1 -9999 0 -0.16 171 171
IL1 alpha/IL1R1/IL1RAP/MYD88 0.015 0.07 -9999 0 -0.15 61 61
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.023 0.067 -9999 0 -0.14 61 61
IL1 beta fragment/IL1R1/IL1RAP -0.023 0.085 -9999 0 -0.17 107 107
NFKB1 0.014 0.037 -9999 0 -0.23 11 11
MAPK8 0.023 0.046 -9999 0 -0.14 34 34
IRAK1 0.015 0.027 -9999 0 -0.2 7 7
IL1RN/IL1R1 0.025 0.016 -9999 0 -10000 0 0
IRAK4 0.019 0.008 -9999 0 -0.11 2 2
PRKCI 0.015 0.028 -9999 0 -0.14 15 15
TRAF6 0.018 0.019 -9999 0 -0.29 2 2
PI3K -0.016 0.093 -9999 0 -0.21 88 88
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.027 0.12 -9999 0 -0.3 69 69
CHUK 0.016 0.025 -9999 0 -0.15 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.023 0.085 -9999 0 -0.17 107 107
IL1 beta/IL1R2 -0.029 0.078 -9999 0 -0.15 118 118
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.063 -9999 0 -0.14 48 48
NF kappa B1 p50/RelA -0.028 0.095 -9999 0 -0.2 87 87
IRAK3 0.018 0.014 -9999 0 -0.11 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.013 0.079 -9999 0 -0.15 107 107
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.076 -9999 0 -0.19 61 61
IL1 alpha/IL1R1/IL1RAP 0.014 0.055 -9999 0 -0.14 44 44
RELA 0.018 0.02 -9999 0 -0.23 3 3
MAP3K7IP1 0.019 0 -9999 0 -10000 0 0
SQSTM1 0.004 0.062 -9999 0 -0.22 32 32
MYD88 0 0.075 -9999 0 -0.29 33 33
IRAK/TRAF6/MEKK3 0.032 0.038 -9999 0 -0.13 25 25
IL1RAP -0.013 0.084 -9999 0 -0.2 77 77
UBE2N 0.015 0.036 -9999 0 -0.29 7 7
IRAK/TRAF6 -0.03 0.06 -9999 0 -0.19 43 43
CASP1 -0.033 0.11 -9999 0 -0.29 75 75
IL1RN/IL1R2 0.012 0.036 -9999 0 -0.14 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.022 0.098 -9999 0 -0.17 118 118
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.099 -9999 0 -0.32 35 35
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
IL1RN 0.018 0.011 -9999 0 -0.11 4 4
TRAF6/TAK1/TAB1/TAB2 0.033 0.054 -9999 0 -0.16 34 34
MAP2K6 0.021 0.048 -9999 0 -0.15 34 34
IL2 signaling events mediated by STAT5

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
GAB2 -0.005 0.082 -9999 0 -0.27 44 44
ELF1 0.016 0.051 -9999 0 -0.28 12 12
CCNA2 -0.026 0.095 -9999 0 -0.19 117 117
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
JAK3 0.019 0.002 -9999 0 -10000 0 0
PIK3R1 -0.014 0.095 -9999 0 -0.27 62 62
JAK1 0.001 0.071 -9999 0 -0.26 34 34
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.006 0.2 -9999 0 -0.53 47 47
SHC1 0.005 0.052 -9999 0 -0.14 48 48
SP1 -0.034 0.12 -9999 0 -0.28 99 99
IL2RA 0.019 0.043 -9999 0 -10000 0 0
IL2RB 0.015 0.024 -9999 0 -0.11 19 19
SOS1 0 0.002 -9999 0 -10000 0 0
IL2RG 0.014 0.027 -9999 0 -0.11 24 24
G1/S transition of mitotic cell cycle -0.12 0.28 -9999 0 -0.56 135 135
PTPN11 0.016 0.034 -9999 0 -0.27 7 7
CCND2 -0.088 0.22 -9999 0 -0.55 99 99
LCK 0.017 0.016 -9999 0 -0.11 8 8
GRB2 0.014 0.039 -9999 0 -0.26 10 10
IL2 0.019 0.006 -9999 0 -0.11 1 1
CDK6 0.019 0 -9999 0 -10000 0 0
CCND3 -0.006 0.21 -9999 0 -0.74 31 31
Signaling events mediated by HDAC Class III

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
EP300 0.012 0.046 -10000 0 -0.24 15 15
HDAC4 0.007 0.056 -10000 0 -0.29 16 16
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.015 0.045 0.2 6 -0.12 51 57
CDKN1A -0.052 0.17 -10000 0 -0.52 62 62
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.014 0.035 -10000 0 -0.17 15 15
FOXO3 -0.007 0.042 0.29 5 -0.16 18 23
FOXO1 -0.012 0.088 -10000 0 -0.23 67 67
FOXO4 0.017 0.032 -10000 0 -0.2 11 11
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.018 0.019 -10000 0 -0.29 2 2
TAT 0.019 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0 -10000 0 -10000 0 0
PPARGC1A -0.006 0.067 -10000 0 -0.15 76 76
FHL2 -0.027 0.088 -10000 0 -0.16 134 134
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.031 0.048 0.14 41 -0.22 7 48
HIST2H4A 0.015 0.045 0.12 51 -0.2 6 57
SIRT1/FOXO3a 0.013 0.051 0.14 45 -0.12 18 63
SIRT1 0.024 0.063 0.18 41 -0.17 20 61
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.035 0.054 0.14 35 -0.17 21 56
SIRT1/Histone H1b 0.03 0.049 0.15 38 -0.19 10 48
apoptosis -0.037 0.047 0.17 11 -0.14 41 52
SIRT1/PGC1A 0.015 0.053 0.13 32 -0.15 22 54
p53/SIRT1 0.031 0.11 0.34 48 -0.19 28 76
SIRT1/FOXO4 0.032 0.048 0.15 40 -0.18 10 50
FOXO1/FHL2/SIRT1 -0.003 0.073 0.14 18 -0.15 70 88
HIST1H1E 0.015 0.033 -10000 0 -0.2 11 11
SIRT1/p300 0.027 0.056 0.14 40 -0.2 17 57
muscle cell differentiation -0.022 0.039 0.16 6 -0.13 41 47
TP53 0.012 0.083 0.18 45 -0.2 42 87
KU70/SIRT1/BAX 0.038 0.048 0.14 41 -0.17 11 52
CREBBP 0.019 0 -10000 0 -10000 0 0
MEF2D 0.019 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.032 0.044 0.14 41 -0.19 6 47
ACSS2 0.015 0.045 0.12 51 -0.2 6 57
SIRT1/PCAF/MYOD 0.022 0.039 0.13 41 -0.16 6 47
TCGA08_p53

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
CDKN2A -0.013 0.037 -9999 0 -0.07 156 156
TP53 -0.021 0.065 -9999 0 -0.27 31 31
Senescence -0.021 0.065 -9999 0 -0.27 31 31
Apoptosis -0.021 0.065 -9999 0 -0.27 31 31
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.011 0.025 -9999 0 -10000 0 0
MDM4 0.013 0.026 -9999 0 -0.11 23 23
TCGA08_rtk_signaling

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
PDGFRA -0.042 0.11 -10000 0 -0.2 148 148
HRAS 0.009 0.055 -10000 0 -0.28 18 18
EGFR -0.08 0.12 -10000 0 -0.29 97 97
AKT 0.019 0.026 0.13 3 -0.12 4 7
FOXO3 0.002 0.07 -10000 0 -0.27 32 32
AKT1 0.005 0.063 -10000 0 -0.25 28 28
FOXO1 -0.012 0.088 -10000 0 -0.23 67 67
AKT3 0.018 0.011 -10000 0 -0.11 4 4
FOXO4 0.019 0 -10000 0 -10000 0 0
MET 0.008 0.037 -10000 0 -0.11 47 47
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
PIK3CB 0.018 0.013 -10000 0 -0.11 5 5
NRAS -0.01 0.086 -10000 0 -0.24 59 59
PIK3CG 0.019 0 -10000 0 -10000 0 0
PIK3R3 0.017 0.016 -10000 0 -0.11 8 8
PIK3R2 0.018 0.01 -10000 0 -0.11 3 3
NF1 0.019 0 -10000 0 -10000 0 0
RAS -0.049 0.086 -10000 0 -0.17 130 130
ERBB2 0.019 0.008 -10000 0 -0.11 2 2
proliferation/survival/translation -0.015 0.085 0.33 23 -0.18 2 25
PI3K -0.021 0.069 0.13 3 -0.13 120 123
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
KRAS 0.011 0.048 -10000 0 -0.28 14 14
FOXO 0.028 0.028 0.14 3 -0.049 4 7
AKT2 0.019 0 -10000 0 -10000 0 0
PTEN 0.013 0.038 -10000 0 -0.18 17 17
IGF1 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
NCK2 0.009 0.054 -10000 0 -0.28 17 17
PTK2 0.009 0.054 -10000 0 -0.27 18 18
CRKL 0.006 0.047 -10000 0 -0.16 27 27
GRB2/SOS1/SHC 0.014 0.039 -10000 0 -0.17 16 16
HRAS 0.009 0.055 -10000 0 -0.28 18 18
IRS1/Crk 0.007 0.055 -10000 0 -0.16 41 41
IGF-1R heterotetramer/IGF1/PTP1B 0.018 0.055 -10000 0 -0.17 33 33
AKT1 -0.014 0.089 -10000 0 -0.17 98 98
BAD -0.012 0.087 -10000 0 -0.21 59 59
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.005 0.05 -10000 0 -0.18 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.01 0.052 -10000 0 -0.16 32 32
RAF1 -0.022 0.16 -10000 0 -0.57 32 32
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.014 0.052 -10000 0 -0.16 34 34
YWHAZ 0.014 0.037 -10000 0 -0.23 11 11
IGF-1R heterotetramer/IGF1/IRS1 0.007 0.053 -10000 0 -0.15 38 38
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
RPS6KB1 -0.009 0.074 -10000 0 -0.15 98 98
GNB2L1 0.018 0.019 -10000 0 -0.29 2 2
positive regulation of MAPKKK cascade -0.018 0.12 0.2 2 -0.42 34 36
PXN 0.018 0.011 -10000 0 -0.11 4 4
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.011 0.026 -10000 0 -0.17 10 10
HRAS/GTP -0.019 0.049 -10000 0 -0.15 51 51
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.021 0.054 -10000 0 -0.13 42 42
IGF-1R heterotetramer 0.009 0.048 -10000 0 -0.17 28 28
IGF-1R heterotetramer/IGF1/IRS/Nck 0.013 0.06 -10000 0 -0.17 41 41
Crk/p130 Cas/Paxillin 0.015 0.053 -10000 0 -0.14 40 40
IGF1R 0.009 0.048 -10000 0 -0.17 28 28
IGF1 0.011 0.029 -10000 0 -0.1 28 28
IRS2/Crk -0.007 0.079 -10000 0 -0.17 82 82
PI3K -0.004 0.089 -10000 0 -0.17 100 100
apoptosis 0.003 0.084 0.22 51 -10000 0 51
HRAS/GDP 0.007 0.037 -10000 0 -0.19 18 18
PRKCD 0.006 0.063 -10000 0 -0.22 31 31
RAF1/14-3-3 E -0.009 0.14 -10000 0 -0.46 34 34
BAD/14-3-3 -0.003 0.089 -10000 0 -0.23 51 51
PRKCZ -0.014 0.073 -10000 0 -0.15 99 99
Crk/p130 Cas/Paxillin/FAK1 -0.003 0.08 -10000 0 -0.22 44 44
PTPN1 0.013 0.042 -10000 0 -0.29 10 10
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.005 0.065 -10000 0 -0.23 30 30
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.003 0.078 -10000 0 -0.16 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.007 0.058 -10000 0 -0.17 41 41
GRB10 -0.018 0.091 -10000 0 -0.2 89 89
PTPN11 0.006 0.048 -10000 0 -0.17 27 27
IRS1 0.003 0.049 -10000 0 -0.16 37 37
IRS2 -0.004 0.067 -10000 0 -0.2 43 43
IGF-1R heterotetramer/IGF1 0.008 0.058 -10000 0 -0.22 27 27
GRB2 0.014 0.039 -10000 0 -0.26 10 10
PDPK1 -0.012 0.078 -10000 0 -0.16 99 99
YWHAE 0.011 0.045 -10000 0 -0.21 19 19
PRKD1 -0.001 0.078 -10000 0 -0.24 41 41
SHC1 0.004 0.052 -10000 0 -0.14 48 48
Signaling events mediated by PTP1B

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
PDGFRB 0.011 0.043 -10000 0 -0.18 21 21
Jak2/Leptin Receptor -0.002 0.063 -10000 0 -0.27 3 3
PTP1B/AKT1 -0.036 0.11 -10000 0 -0.27 64 64
FYN -0.019 0.1 -10000 0 -0.28 68 68
p210 bcr-abl/PTP1B -0.045 0.1 -10000 0 -0.28 57 57
EGFR -0.081 0.12 -10000 0 -0.28 109 109
EGF/EGFR -0.066 0.11 -10000 0 -0.29 70 70
CSF1 0.019 0 -10000 0 -10000 0 0
AKT1 0.005 0.064 -10000 0 -0.26 28 28
INSR 0.019 0.002 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.043 0.12 -10000 0 -0.28 75 75
Insulin Receptor/Insulin -0.011 0.096 -10000 0 -0.28 36 36
HCK -0.033 0.11 -10000 0 -0.21 120 120
CRK 0.009 0.054 -10000 0 -0.28 17 17
TYK2 -0.043 0.11 -10000 0 -0.3 60 60
EGF 0.01 0.026 -10000 0 -0.11 21 21
YES1 0.005 0.061 -10000 0 -0.24 28 28
CAV1 -0.076 0.13 -10000 0 -0.3 89 89
TXN 0.006 0.051 -10000 0 -0.23 19 19
PTP1B/IRS1/GRB2 -0.035 0.11 -10000 0 -0.27 68 68
cell migration 0.045 0.1 0.28 57 -10000 0 57
STAT3 -0.003 0.08 -10000 0 -0.29 37 37
PRLR 0.023 0 -10000 0 -10000 0 0
ITGA2B 0.018 0.001 -10000 0 -10000 0 0
CSF1R -0.042 0.11 -10000 0 -0.29 83 83
Prolactin Receptor/Prolactin 0.035 0.014 -10000 0 -10000 0 0
FGR 0.005 0.048 -10000 0 -0.14 46 46
PTP1B/p130 Cas -0.043 0.098 -10000 0 -0.26 58 58
Crk/p130 Cas -0.037 0.1 -10000 0 -0.26 65 65
DOK1 -0.029 0.099 -10000 0 -0.3 41 41
JAK2 -0.007 0.061 -10000 0 -0.3 2 2
Jak2/Leptin Receptor/Leptin -0.01 0.11 -10000 0 -0.28 47 47
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
PTPN1 -0.045 0.1 -10000 0 -0.28 57 57
LYN -0.018 0.098 -10000 0 -0.25 72 72
CDH2 -0.006 0.082 -10000 0 -0.26 46 46
SRC -0.008 0.09 -10000 0 -0.56 11 11
ITGB3 0.018 0.008 -10000 0 -0.11 2 2
CAT1/PTP1B -0.069 0.17 -10000 0 -0.38 92 92
CAPN1 0.017 0.006 -10000 0 -0.11 1 1
CSK 0.013 0.044 -10000 0 -0.29 11 11
PI3K -0.026 0.12 -10000 0 -0.31 59 59
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.007 0.099 -10000 0 -0.26 46 46
negative regulation of transcription -0.007 0.06 -10000 0 -0.29 2 2
FCGR2A -0.032 0.1 -10000 0 -0.22 114 114
FER 0.014 0.018 -10000 0 -0.11 10 10
alphaIIb/beta3 Integrin 0.025 0.006 -10000 0 -10000 0 0
BLK 0.018 0.011 -10000 0 -0.11 4 4
Insulin Receptor/Insulin/Shc 0.029 0.033 -10000 0 -0.16 9 9
RHOA 0.013 0.036 -10000 0 -0.3 7 7
LEPR 0.016 0.019 -10000 0 -0.11 11 11
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.014 0.039 -10000 0 -0.26 10 10
mol:NADPH -0.002 0.002 -10000 0 -10000 0 0
TRPV6 -0.046 0.16 -10000 0 -0.39 77 77
PRL 0.02 0.019 -10000 0 -10000 0 0
SOCS3 0.012 0.012 -10000 0 -10000 0 0
SPRY2 -0.051 0.13 -10000 0 -0.27 127 127
Insulin Receptor/Insulin/IRS1 0.025 0.044 -10000 0 -0.16 24 24
CSF1/CSF1R -0.05 0.12 -10000 0 -0.3 68 68
Ras protein signal transduction 0.018 0.039 0.11 9 -0.19 8 17
IRS1 -0.002 0.07 -10000 0 -0.19 53 53
INS 0.019 0.002 -10000 0 -10000 0 0
LEP 0.019 0.001 -10000 0 -10000 0 0
STAT5B -0.025 0.085 -10000 0 -0.26 35 35
STAT5A -0.025 0.085 -10000 0 -0.26 33 33
GRB2 0.014 0.039 -10000 0 -0.26 10 10
PDGFB-D/PDGFRB -0.037 0.1 -10000 0 -0.27 61 61
CSN2 0.034 0.02 -10000 0 -10000 0 0
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
LAT -0.063 0.18 -10000 0 -0.52 66 66
YBX1 0.016 0.062 -10000 0 -0.31 18 18
LCK 0.017 0.016 -10000 0 -0.11 8 8
SHC1 0.004 0.052 -10000 0 -0.14 48 48
NOX4 -0.015 0.086 -10000 0 -0.21 76 76
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.022 0.079 -10000 0 -0.19 87 87
MAP4K4 0.015 0.061 -10000 0 -0.27 10 10
BAG4 0.018 0.011 -10000 0 -0.11 4 4
PKC zeta/ceramide 0.011 0.03 0.075 87 -10000 0 87
NFKBIA 0.002 0.067 -10000 0 -0.24 34 34
BIRC3 0 0.046 -10000 0 -0.11 78 78
BAX 0.011 0.042 -10000 0 -0.38 5 5
RIPK1 0.016 0.019 -10000 0 -0.11 11 11
AKT1 -0.004 0.058 -10000 0 -0.26 24 24
BAD 0.014 0.036 0.085 85 -0.14 5 90
SMPD1 0.008 0.043 -10000 0 -0.12 50 50
RB1 0.015 0.034 0.085 85 -0.14 2 87
FADD/Caspase 8 0.028 0.05 -10000 0 -0.19 2 2
MAP2K4 0.017 0.035 0.086 81 -0.12 4 85
NSMAF 0.006 0.063 -10000 0 -0.28 24 24
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.016 0.037 0.086 78 -0.13 11 89
EGF 0.014 0.025 -10000 0 -0.11 21 21
mol:ceramide 0.013 0.035 0.087 87 -10000 0 87
MADD 0.018 0.015 -10000 0 -0.2 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.021 0.078 -10000 0 -0.19 84 84
ASAH1 0.017 0.023 -10000 0 -0.29 3 3
negative regulation of cell cycle 0.015 0.034 0.085 85 -0.14 2 87
cell proliferation 0.034 0.038 -10000 0 -0.096 14 14
BID -0.006 0.15 -10000 0 -0.61 27 27
MAP3K1 0.015 0.034 0.085 86 -0.069 1 87
EIF2A 0.014 0.037 0.082 80 -0.12 14 94
TRADD 0.019 0 -10000 0 -10000 0 0
CRADD 0.017 0.015 -10000 0 -0.11 7 7
MAPK3 0.022 0.037 0.093 2 -0.11 14 16
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.019 0.048 0.091 12 -0.17 18 30
Cathepsin D/ceramide 0.019 0.034 0.088 78 -0.051 29 107
FADD 0.021 0.049 -10000 0 -0.18 3 3
KSR1 0.016 0.032 0.085 87 -10000 0 87
MAPK8 0.02 0.032 0.09 3 -10000 0 3
PRKRA 0.012 0.041 0.085 82 -0.14 14 96
PDGFA -0.045 0.12 -10000 0 -0.22 141 141
TRAF2 0.019 0 -10000 0 -10000 0 0
IGF1 0.014 0.025 -10000 0 -0.11 21 21
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.013 0.035 0.087 87 -10000 0 87
CTSD 0.005 0.053 -10000 0 -0.16 43 43
regulation of nitric oxide biosynthetic process 0.024 0.03 -10000 0 -0.19 9 9
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.037 0.04 -10000 0 -0.1 14 14
PRKCD 0.012 0.029 -10000 0 -0.11 27 27
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.021 0.078 -10000 0 -0.19 84 84
RelA/NF kappa B1 0.024 0.03 -10000 0 -0.19 9 9
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.019 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.019 0.051 -10000 0 -0.17 4 4
TNFR1A/BAG4/TNF-alpha 0.02 0.057 -10000 0 -0.16 50 50
mol:Sphingosine-1-phosphate -0.022 0.079 -10000 0 -0.19 87 87
MAP2K1 0.017 0.039 0.087 77 -0.13 16 93
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.018 0.02 -10000 0 -0.23 3 3
CYCS 0.011 0.033 -10000 0 -0.16 9 9
TNFRSF1A -0.01 0.091 -10000 0 -0.29 50 50
NFKB1 0.014 0.037 -10000 0 -0.23 11 11
TNFR1A/BAG4 0.007 0.065 -10000 0 -0.19 50 50
EIF2AK2 0.015 0.039 0.086 80 -0.13 14 94
TNF-alpha/TNFR1A/FAN 0.013 0.071 -10000 0 -0.17 65 65
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.045 -10000 0 -0.33 2 2
MAP2K2 0.019 0.037 0.087 73 -0.12 12 85
SMPD3 0.011 0.047 -10000 0 -0.16 11 11
TNF 0.018 0.01 -10000 0 -0.11 3 3
PKC zeta/PAR4 0.014 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.01 0.033 0.088 52 -10000 0 52
NF kappa B1/RelA/I kappa B alpha 0.033 0.044 -10000 0 -0.14 30 30
AIFM1 0.01 0.034 -10000 0 -0.18 7 7
BCL2 0.019 0 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex -0.025 0.13 -9999 0 -0.26 89 89
STMN1 0.007 0.043 -9999 0 -0.14 33 33
Aurora B/RasGAP/Survivin -0.007 0.082 -9999 0 -0.16 107 107
Chromosomal passenger complex/Cul3 protein complex -0.036 0.092 -9999 0 -0.21 79 79
BIRC5 -0.032 0.11 -9999 0 -0.22 111 111
DES 0.015 0.054 -9999 0 -1.1 1 1
Aurora C/Aurora B/INCENP 0.028 0.024 -9999 0 -0.11 5 5
Aurora B/TACC1 0.016 0.036 -9999 0 -0.17 15 15
Aurora B/PP2A 0.021 0.025 -9999 0 -0.17 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.002 0.06 -9999 0 -0.21 35 35
mitotic metaphase/anaphase transition 0 0.002 -9999 0 -10000 0 0
NDC80 -0.01 0.068 -9999 0 -0.14 99 99
Cul3 protein complex -0.016 0.077 -9999 0 -0.16 116 116
KIF2C -0.027 0.14 -9999 0 -0.37 56 56
PEBP1 0.011 0.048 -9999 0 -0.28 14 14
KIF20A -0.029 0.1 -9999 0 -0.21 109 109
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.01 0.054 -9999 0 -0.2 29 29
SEPT1 0 0 -9999 0 -10000 0 0
SMC2 0 0.064 -9999 0 -0.17 53 53
SMC4 -0.009 0.083 -9999 0 -0.22 62 62
NSUN2/NPM1/Nucleolin 0.001 0.063 -9999 0 -0.39 4 4
PSMA3 0.012 0.043 -9999 0 -0.25 13 13
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B 0.008 0.039 -9999 0 -0.23 12 12
AURKB 0.01 0.034 -9999 0 -0.12 32 32
AURKC 0.015 0.022 -9999 0 -0.11 16 16
CDCA8 0.003 0.059 -9999 0 -0.17 44 44
cytokinesis -0.036 0.18 -9999 0 -0.48 59 59
Aurora B/Septin1 -0.031 0.16 -9999 0 -0.44 59 59
AURKA 0.006 0.056 -9999 0 -0.2 32 32
INCENP 0.018 0.007 -9999 0 -0.12 1 1
KLHL13 0 0 -9999 0 -10000 0 0
BUB1 0.017 0.018 -9999 0 -0.11 10 10
hSgo1/Aurora B/Survivin -0.007 0.061 -9999 0 -0.14 84 84
EVI5 0.018 0.008 -9999 0 -0.11 2 2
RhoA/GTP -0.02 0.15 -9999 0 -0.34 75 75
SGOL1 0 0 -9999 0 -10000 0 0
CENPA -0.015 0.12 -9999 0 -0.39 38 38
NCAPG -0.018 0.089 -9999 0 -0.2 89 89
Aurora B/HC8 Proteasome 0.017 0.039 -9999 0 -0.18 14 14
NCAPD2 -0.008 0.079 -9999 0 -0.2 64 64
Aurora B/PP1-gamma 0.019 0.033 -9999 0 -0.2 7 7
RHOA 0.015 0.036 -9999 0 -0.29 7 7
NCAPH 0.011 0.034 -9999 0 -0.12 28 28
NPM1 0.005 0.053 -9999 0 -0.37 8 8
RASA1 0.003 0.069 -9999 0 -0.28 29 29
KLHL9 -0.052 0.13 -9999 0 -0.28 126 126
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.039 -9999 0 -0.18 14 14
PPP1CC 0.016 0.033 -9999 0 -0.29 6 6
Centraspindlin -0.027 0.16 -9999 0 -0.36 78 78
RhoA/GDP 0.011 0.024 -9999 0 -0.2 7 7
NSUN2 0.003 0.03 -9999 0 -0.47 1 1
MYLK -0.033 0.091 -9999 0 -0.24 83 83
KIF23 -0.01 0.078 -9999 0 -0.18 78 78
VIM -0.002 0.065 -9999 0 -0.21 44 44
RACGAP1 -0.013 0.091 -9999 0 -0.24 68 68
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.002 0.065 -9999 0 -0.35 15 15
Chromosomal passenger complex -0.021 0.12 -9999 0 -0.3 67 67
Chromosomal passenger complex/EVI5 0.011 0.081 -9999 0 -0.16 77 77
TACC1 0.01 0.049 -9999 0 -0.29 13 13
PPP2R5D 0.018 0.013 -9999 0 -0.11 5 5
CUL3 0.018 0.019 -9999 0 -0.29 2 2
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.005 0.02 3 -10000 0 3
BUB1B -0.027 0.099 -10000 0 -0.28 60 60
PLK1 0.005 0.021 -10000 0 -0.07 21 21
PLK1S1 0.003 0.01 -10000 0 -0.035 8 8
KIF2A -0.004 0.05 -10000 0 -0.15 48 48
regulation of mitotic centrosome separation 0.005 0.021 -10000 0 -0.07 21 21
GOLGA2 0.013 0.041 -10000 0 -0.27 10 10
Hec1/SPC24 -0.002 0.054 -10000 0 -0.14 58 58
WEE1 -0.03 0.15 -10000 0 -0.66 27 27
cytokinesis -0.039 0.14 -10000 0 -0.36 69 69
PP2A-alpha B56 0.024 0.056 -10000 0 -0.29 4 4
AURKA 0.002 0.042 -10000 0 -0.23 15 15
PICH/PLK1 -0.028 0.12 -10000 0 -0.21 123 123
CENPE -0.002 0.044 -10000 0 -0.14 36 36
RhoA/GTP 0.011 0.024 -10000 0 -0.2 7 7
positive regulation of microtubule depolymerization -0.004 0.05 -10000 0 -0.15 48 48
PPP2CA 0.011 0.05 -10000 0 -0.28 15 15
FZR1 0.019 0 -10000 0 -10000 0 0
TPX2 -0.033 0.093 -10000 0 -0.24 90 90
PAK1 0.016 0.017 -10000 0 -0.11 9 9
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.011 0.047 -10000 0 -0.27 14 14
CLSPN 0.01 0.012 -10000 0 -10000 0 0
GORASP1 0.006 0.061 -10000 0 -0.28 22 22
metaphase -0.001 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.003 0.01 -10000 0 -0.035 8 8
G2 phase of mitotic cell cycle -0.001 0.002 -10000 0 -0.01 15 15
STAG2 0.005 0.065 -10000 0 -0.29 24 24
GRASP65/GM130/RAB1/GTP -0.018 0.15 -10000 0 -0.66 23 23
spindle elongation 0.005 0.021 -10000 0 -0.07 21 21
ODF2 0.016 0.018 -10000 0 -10000 0 0
BUB1 0.014 0.027 -10000 0 -10000 0 0
TPT1 0.009 0.01 -10000 0 -10000 0 0
CDC25C 0.011 0.012 -10000 0 -10000 0 0
CDC25B 0.001 0.066 -10000 0 -0.27 28 28
SGOL1 0.001 0.005 -10000 0 -0.02 3 3
RHOA 0.015 0.036 -10000 0 -0.29 7 7
CCNB1/CDK1 -0.038 0.14 -10000 0 -0.29 109 109
CDC14B 0.003 0.036 -10000 0 -0.19 17 17
CDC20 -0.042 0.12 -10000 0 -0.24 127 127
PLK1/PBIP1 -0.018 0.058 -10000 0 -0.13 94 94
mitosis 0 0.006 0.032 15 -10000 0 15
FBXO5 -0.014 0.07 -10000 0 -0.23 43 43
CDC2 -0.032 0.1 -10000 0 -0.2 123 123
NDC80 -0.019 0.093 -10000 0 -0.21 89 89
metaphase plate congression 0.001 0.054 -10000 0 -0.3 16 16
ERCC6L -0.038 0.14 -10000 0 -0.27 110 110
NLP/gamma Tubulin 0.001 0.027 -10000 0 -0.11 23 23
microtubule cytoskeleton organization 0.009 0.01 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.011 0.046 -10000 0 -0.25 15 15
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.022 0.1 -10000 0 -0.19 120 120
GRASP65/GM130/RAB1/GTP/PLK1 0.023 0.052 -10000 0 -0.15 36 36
RAB1A 0.012 0.046 -10000 0 -0.29 12 12
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.004 0.025 -10000 0 -0.081 27 27
mitotic prometaphase 0 0.004 0.023 16 -10000 0 16
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.073 -10000 0 -0.37 14 14
microtubule-based process 0.004 0.047 -10000 0 -0.12 51 51
Golgi organization 0.005 0.021 -10000 0 -0.07 21 21
Cohesin/SA2 0.008 0.037 -10000 0 -0.13 27 27
PPP1CB/MYPT1 0.02 0.041 -10000 0 -0.2 16 16
KIF20A -0.028 0.1 -10000 0 -0.21 109 109
APC/C/CDC20 0.004 0.047 -10000 0 -0.13 41 41
PPP2R1A 0.003 0.069 -10000 0 -0.29 27 27
chromosome segregation -0.018 0.057 -10000 0 -0.13 94 94
PRC1 -0.041 0.12 -10000 0 -0.24 121 121
ECT2 -0.011 0.058 -10000 0 -0.14 72 72
C13orf34 0.005 0.023 -10000 0 -0.069 27 27
NUDC 0.001 0.054 -10000 0 -0.3 16 16
regulation of attachment of spindle microtubules to kinetochore -0.027 0.098 -10000 0 -0.28 60 60
spindle assembly 0.003 0.024 -10000 0 -0.077 28 28
spindle stabilization 0.003 0.01 -10000 0 -0.035 8 8
APC/C/HCDH1 0.016 0.031 -10000 0 -0.16 16 16
MKLP2/PLK1 0.004 0.047 -10000 0 -0.12 51 51
CCNB1 -0.041 0.12 -10000 0 -0.24 122 122
PPP1CB 0.015 0.034 -10000 0 -0.27 7 7
BTRC 0.019 0 -10000 0 -10000 0 0
ROCK2 0.013 0.027 -10000 0 -0.17 6 6
TUBG1 -0.001 0.052 -10000 0 -0.25 22 22
G2/M transition of mitotic cell cycle -0.064 0.13 -10000 0 -0.29 108 108
MLF1IP -0.033 0.078 -10000 0 -0.2 84 84
INCENP 0.019 0.006 -10000 0 -0.11 1 1
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.097 -9999 0 -0.42 8 8
UGCG -0.029 0.19 -9999 0 -0.81 28 28
AKT1/mTOR/p70S6K/Hsp90/TERT 0.009 0.14 -9999 0 -0.3 73 73
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucosylceramide -0.029 0.19 -9999 0 -0.79 28 28
mol:DAG -0.014 0.13 -9999 0 -0.91 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.19 -9999 0 -0.4 83 83
FRAP1 -0.017 0.21 -9999 0 -0.44 84 84
FOXO3 -0.029 0.22 -9999 0 -0.47 89 89
AKT1 -0.032 0.23 -9999 0 -0.48 88 88
GAB2 -0.005 0.082 -9999 0 -0.27 44 44
SMPD1 0.012 0.034 -9999 0 -10000 0 0
SGMS1 -0.003 0.1 -9999 0 -0.66 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
mol:GDP -0.019 0.075 -9999 0 -0.18 88 88
CALM1 0.007 0.056 -9999 0 -0.21 28 28
cell proliferation -0.036 0.2 -9999 0 -0.37 93 93
EIF3A 0.011 0.048 -9999 0 -0.29 12 12
PI3K -0.013 0.094 -9999 0 -0.21 88 88
RPS6KB1 0.02 0.024 -9999 0 -10000 0 0
mol:sphingomyelin -0.014 0.13 -9999 0 -0.91 10 10
natural killer cell activation 0 0.003 -9999 0 -0.01 50 50
JAK3 0.02 0.004 -9999 0 -10000 0 0
PIK3R1 -0.013 0.095 -9999 0 -0.27 62 62
JAK1 0.002 0.071 -9999 0 -0.26 34 34
NFKB1 0.014 0.037 -9999 0 -0.23 11 11
MYC -0.07 0.32 -9999 0 -0.8 74 74
MYB 0.028 0.029 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.012 0.17 -9999 0 -0.33 92 92
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.04 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.17 -9999 0 -0.37 67 67
Rac1/GDP -0.008 0.076 -9999 0 -0.16 89 89
T cell proliferation -0.01 0.16 -9999 0 -0.35 67 67
SHC1 0.004 0.052 -9999 0 -0.14 48 48
RAC1 0.015 0.036 -9999 0 -0.29 7 7
positive regulation of cyclin-dependent protein kinase activity 0.004 0.004 -9999 0 -10000 0 0
PRKCZ -0.012 0.16 -9999 0 -0.36 67 67
NF kappa B1 p50/RelA 0.001 0.19 -9999 0 -0.39 81 81
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.005 0.1 -9999 0 -0.34 27 27
HSP90AA1 0.018 0.019 -9999 0 -0.29 2 2
RELA 0.018 0.02 -9999 0 -0.23 3 3
IL2RA 0.012 0.029 -9999 0 -0.11 28 28
IL2RB 0.016 0.024 -9999 0 -0.11 19 19
TERT 0.019 0.008 -9999 0 -0.11 2 2
E2F1 0.026 0.021 -9999 0 -10000 0 0
SOS1 0 0.003 -9999 0 -0.009 49 49
RPS6 0.015 0.036 -9999 0 -0.29 7 7
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 0.015 0.034 -9999 0 -0.27 7 7
IL2RG 0.014 0.027 -9999 0 -0.11 24 24
actin cytoskeleton organization -0.01 0.16 -9999 0 -0.35 67 67
GRB2 0.014 0.039 -9999 0 -0.26 10 10
IL2 0.02 0.007 -9999 0 -0.12 1 1
PIK3CA -0.01 0.087 -9999 0 -0.22 66 66
Rac1/GTP 0.005 0.078 -9999 0 -0.15 89 89
LCK 0.018 0.016 -9999 0 -0.11 8 8
BCL2 0.002 0.16 -9999 0 -0.44 39 39
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.045 0.096 -9999 0 -0.2 132 132
alphaV beta3 Integrin 0.025 0.049 -9999 0 -0.16 31 31
PTK2 -0.031 0.14 -9999 0 -0.32 60 60
IGF1R -0.001 0.07 -9999 0 -0.21 46 46
PI4KB 0.018 0.017 -9999 0 -0.16 4 4
MFGE8 0.016 0.025 -9999 0 -0.29 2 2
SRC 0.019 0 -9999 0 -10000 0 0
CDKN1B 0.003 0.092 -9999 0 -0.36 29 29
VEGFA -0.068 0.13 -9999 0 -0.22 188 188
ILK 0.013 0.07 -9999 0 -0.37 15 15
ROCK1 0.016 0.031 -9999 0 -0.26 6 6
AKT1 0.012 0.076 -9999 0 -0.38 17 17
PTK2B -0.025 0.075 -9999 0 -0.14 136 136
alphaV/beta3 Integrin/JAM-A 0.03 0.054 -9999 0 -0.15 35 35
CBL 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.028 0.042 -9999 0 -0.15 25 25
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.021 0.065 -9999 0 -0.14 59 59
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.021 0.1 -9999 0 -0.32 29 29
alphaV/beta3 Integrin/Syndecan-1 0.017 0.052 -9999 0 -0.16 28 28
PI4KA -0.007 0.083 -9999 0 -0.26 49 49
IGF-1R heterotetramer/IGF1/IRS1 0.009 0.076 -9999 0 -0.24 29 29
PI4 Kinase 0.009 0.061 -9999 0 -0.2 40 40
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
alphaV/beta3 Integrin/Osteopontin 0.011 0.076 -9999 0 -0.18 63 63
RPS6KB1 0.005 0.071 -9999 0 -0.23 28 28
TLN1 -0.003 0.065 -9999 0 -0.16 64 64
MAPK3 0.008 0.1 -9999 0 -0.39 28 28
GPR124 0.014 0.024 -9999 0 -0.11 19 19
MAPK1 0.004 0.11 -9999 0 -0.4 29 29
PXN 0.018 0.011 -9999 0 -0.11 4 4
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
alphaV/beta3 Integrin/Tumstatin 0.028 0.042 -9999 0 -0.15 25 25
cell adhesion 0.027 0.053 -9999 0 -0.17 33 33
ANGPTL3 0.019 0.006 -9999 0 -0.11 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.025 0.083 -9999 0 -0.16 132 132
IGF-1R heterotetramer -0.001 0.07 -9999 0 -0.21 46 46
Rac1/GDP 0.011 0.024 -9999 0 -0.2 7 7
TGFBR2 0.013 0.035 -9999 0 -0.14 21 21
ITGB3 0.019 0.008 -9999 0 -0.11 2 2
IGF1 0.014 0.025 -9999 0 -0.11 21 21
RAC1 0.015 0.036 -9999 0 -0.29 7 7
regulation of cell-matrix adhesion 0.025 0.043 -9999 0 -0.15 25 25
apoptosis 0.003 0.067 -9999 0 -0.25 32 32
CD47 0.012 0.043 -9999 0 -0.21 16 16
alphaV/beta3 Integrin/CD47 0.024 0.051 -9999 0 -0.16 32 32
VCL 0.017 0.023 -9999 0 -0.29 3 3
alphaV/beta3 Integrin/Del1 0.028 0.042 -9999 0 -0.15 25 25
CSF1 0.019 0 -9999 0 -10000 0 0
PIK3C2A 0.013 0.023 -9999 0 -10000 0 0
PI4 Kinase/Pyk2 -0.035 0.069 -9999 0 -0.2 49 49
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.021 0.089 -9999 0 -0.15 136 136
FAK1/Vinculin -0.016 0.12 -9999 0 -0.27 52 52
alphaV beta3/Integrin/ppsTEM5 0.025 0.044 -9999 0 -0.15 25 25
RHOA 0.015 0.036 -9999 0 -0.29 7 7
VTN 0.018 0.01 -9999 0 -0.11 3 3
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 0.013 0.036 -9999 0 -0.16 19 19
F11R 0.007 0.044 -9999 0 -0.21 14 14
alphaV/beta3 Integrin/Lactadherin 0.027 0.045 -9999 0 -0.16 27 27
alphaV/beta3 Integrin/TGFBR2 0.024 0.047 -9999 0 -0.15 32 32
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.028 0.037 -9999 0 -0.14 25 25
HSP90AA1 0.018 0.019 -9999 0 -0.29 2 2
alphaV/beta3 Integrin/Talin 0.015 0.053 -9999 0 -0.14 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.001 0.071 -9999 0 -0.26 34 34
alphaV/beta3 Integrin/Pyk2 -0.018 0.081 -9999 0 -0.14 136 136
SDC1 0 0.046 -9999 0 -0.11 77 77
VAV3 0.009 0.044 -9999 0 -0.16 25 25
PTPN11 0.015 0.033 -9999 0 -0.27 7 7
IRS1 -0.002 0.07 -9999 0 -0.19 53 53
FAK1/Paxillin -0.016 0.12 -9999 0 -0.27 51 51
cell migration -0.011 0.11 -9999 0 -0.25 51 51
ITGAV 0.003 0.067 -9999 0 -0.25 32 32
PI3K 0.011 0.091 -9999 0 -0.22 46 46
SPP1 -0.011 0.092 -9999 0 -0.29 51 51
KDR 0.001 0.057 -9999 0 -0.14 59 59
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.003 0.067 -9999 0 -0.25 32 32
COL4A3 0.019 0 -9999 0 -10000 0 0
angiogenesis 0.008 0.11 -9999 0 -0.42 28 28
Rac1/GTP 0.008 0.058 -9999 0 -0.13 65 65
EDIL3 0.019 0 -9999 0 -10000 0 0
cell proliferation 0.024 0.047 -9999 0 -0.15 32 32
mTOR signaling pathway

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
GBL 0.016 0.029 -10000 0 -0.2 8 8
MKNK1 0.003 0.068 -10000 0 -0.27 30 30
mol:PIP3 -0.025 0.083 0.19 4 -0.18 97 101
FRAP1 -0.002 0.09 -10000 0 -0.55 12 12
AKT1 -0.021 0.093 0.19 4 -0.19 95 99
INSR 0.019 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0 -10000 0 -10000 0 0
mol:GTP -0.007 0.098 0.17 4 -0.24 55 59
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.022 0.055 -10000 0 -0.18 41 41
TSC2 0.009 0.052 -10000 0 -0.23 22 22
RHEB/GDP -0.011 0.085 -10000 0 -0.22 54 54
TSC1 0.008 0.055 -10000 0 -0.25 21 21
Insulin Receptor/IRS1 0.004 0.062 -10000 0 -0.28 24 24
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.002 0.068 -10000 0 -0.2 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.011 0.048 -10000 0 -0.29 12 12
RPS6KB1 -0.001 0.066 0.16 3 -0.22 24 27
MAP3K5 -0.02 0.087 -10000 0 -0.29 49 49
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
apoptosis -0.019 0.087 -10000 0 -0.29 49 49
mol:LY294002 0 0 0.001 28 -0.001 19 47
EIF4B 0.002 0.066 0.16 3 -0.23 22 25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.011 0.069 -10000 0 -0.23 21 21
eIF4E/eIF4G1/eIF4A1 -0.022 0.065 -10000 0 -0.27 26 26
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.013 0.091 -10000 0 -0.18 99 99
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.058 0.15 4 -0.18 25 29
FKBP1A 0.007 0.052 -10000 0 -0.18 31 31
RHEB/GTP -0.001 0.088 -10000 0 -0.21 54 54
mol:Amino Acids 0 0 0.001 28 -0.001 19 47
FKBP12/Rapamycin 0.006 0.035 -10000 0 -0.12 31 31
PDPK1 -0.019 0.079 0.19 4 -0.16 93 97
EIF4E 0.002 0.07 -10000 0 -0.28 31 31
ASK1/PP5C -0.038 0.19 -10000 0 -0.57 58 58
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.002 0.097 -10000 0 -0.37 31 31
TSC1/TSC2 -0.007 0.11 0.19 4 -0.26 55 59
tumor necrosis factor receptor activity 0 0 0.001 19 -0.001 28 47
RPS6 0.015 0.036 -10000 0 -0.29 7 7
PPP5C 0.017 0.015 -10000 0 -0.11 7 7
EIF4G1 0 0.073 -10000 0 -0.27 34 34
IRS1 -0.008 0.064 -10000 0 -0.3 24 24
INS 0.019 0 -10000 0 -10000 0 0
PTEN 0.013 0.037 -10000 0 -0.17 17 17
PDK2 -0.019 0.079 0.19 4 -0.16 94 98
EIF4EBP1 -0.042 0.26 -10000 0 -1.1 27 27
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
PPP2R5D 0.002 0.081 -10000 0 -0.48 12 12
peptide biosynthetic process 0.023 0.003 -10000 0 -10000 0 0
RHEB 0.019 0 -10000 0 -10000 0 0
EIF4A1 0.015 0.033 -10000 0 -0.27 7 7
mol:Rapamycin 0 0.001 0.003 6 -0.002 37 43
EEF2 0.023 0.003 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.032 0.25 -10000 0 -1.1 27 27
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.024 0.062 -10000 0 -0.14 53 53
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.018 0.01 -10000 0 -0.11 3 3
STAT1 (dimer)/Cbp/p300 0.026 0.083 -10000 0 -0.21 37 37
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.014 0.066 -10000 0 -0.17 52 52
antigen processing and presentation of peptide antigen via MHC class I -0.047 0.092 -10000 0 -0.2 114 114
CaM/Ca2+ 0.022 0.071 -10000 0 -0.15 58 58
RAP1A 0.018 0.019 -10000 0 -0.29 2 2
STAT1 (dimer)/SHP2 0.012 0.062 -10000 0 -0.18 24 24
AKT1 -0.012 0.1 -10000 0 -0.26 53 53
MAP2K1 0.013 0.058 -10000 0 -0.21 18 18
MAP3K11 0.012 0.055 -10000 0 -0.13 53 53
IFNGR1 0.013 0.038 -10000 0 -0.21 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.028 0.14 -10000 0 -0.29 81 81
Rap1/GTP -0.01 0.032 -10000 0 -0.15 16 16
CRKL/C3G 0.028 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.033 0.061 -10000 0 -0.13 52 52
CEBPB 0.02 0.12 -10000 0 -0.43 23 23
STAT3 -0.003 0.079 -10000 0 -0.29 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.039 0.052 -10000 0 -10000 0 0
STAT1 0.006 0.059 -10000 0 -0.13 60 60
CALM1 0.007 0.056 -10000 0 -0.22 28 28
IFN-gamma (dimer) 0.017 0.012 -10000 0 -0.12 3 3
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
STAT1 (dimer)/PIAS1 0.012 0.072 -10000 0 -0.24 26 26
CEBPB/PTGES2/Cbp/p300 -0.022 0.088 -10000 0 -0.33 30 30
mol:Ca2+ 0.022 0.06 -10000 0 -0.14 53 53
MAPK3 0.024 0.066 -10000 0 -0.41 4 4
STAT1 (dimer) -0.035 0.14 -10000 0 -0.3 86 86
MAPK1 0.005 0.15 -10000 0 -0.76 17 17
JAK2 0.013 0.028 -10000 0 -0.11 23 23
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
JAK1 0.012 0.042 -10000 0 -0.22 14 14
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.026 0.091 -10000 0 -0.4 13 13
SMAD7 -0.007 0.064 -10000 0 -0.14 62 62
CBL/CRKL/C3G 0.031 0.053 -10000 0 -0.17 14 14
PI3K -0.001 0.095 -10000 0 -0.24 48 48
IFNG 0.017 0.012 -10000 0 -0.12 3 3
apoptosis 0.021 0.075 0.21 2 -0.34 11 13
CAMK2G 0.007 0.047 -10000 0 -0.14 40 40
STAT3 (dimer) -0.003 0.079 -10000 0 -0.29 37 37
CAMK2A 0.018 0.01 -10000 0 -0.11 3 3
CAMK2B -0.048 0.11 -10000 0 -0.19 166 166
FRAP1 -0.008 0.094 -10000 0 -0.25 50 50
PRKCD -0.009 0.087 -10000 0 -0.23 50 50
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.047 0.092 -10000 0 -0.2 114 114
PTPN2 0.018 0.013 -10000 0 -0.11 5 5
EP300 0.012 0.046 -10000 0 -0.24 15 15
IRF1 0.014 0.083 -10000 0 -0.27 27 27
STAT1 (dimer)/PIASy 0.013 0.059 -10000 0 -0.2 17 17
SOCS1 0.021 0.002 -10000 0 -10000 0 0
mol:GDP 0.028 0.05 -10000 0 -0.17 14 14
CASP1 -0.023 0.091 -10000 0 -0.19 99 99
PTGES2 0.019 0 -10000 0 -10000 0 0
IRF9 0.02 0.064 -10000 0 -0.2 31 31
mol:PI-3-4-5-P3 -0.01 0.089 -10000 0 -0.24 48 48
RAP1/GDP 0.018 0.043 -10000 0 -0.15 16 16
CBL 0.012 0.052 -10000 0 -0.13 53 53
MAP3K1 0.012 0.054 -10000 0 -0.14 40 40
PIAS1 0.008 0.056 -10000 0 -0.29 18 18
PIAS4 0.018 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.047 0.092 -10000 0 -0.2 114 114
PTPN11 0.008 0.054 -10000 0 -0.14 52 52
CREBBP 0.019 0.001 -10000 0 -10000 0 0
RAPGEF1 0.019 0 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.013 0.082 -9999 0 -0.42 8 8
PLK1 -0.041 0.22 -9999 0 -0.67 24 24
CDKN1B -0.037 0.19 -9999 0 -0.38 84 84
FOXO3 -0.05 0.24 -9999 0 -0.46 105 105
KAT2B -0.003 0.02 -9999 0 -0.043 91 91
FOXO1/SIRT1 0.005 0.09 -9999 0 -0.28 37 37
CAT -0.054 0.27 -9999 0 -1 22 22
CTNNB1 0.017 0.023 -9999 0 -0.29 3 3
AKT1 0.002 0.069 -9999 0 -0.3 22 22
FOXO1 0.006 0.09 -9999 0 -0.29 33 33
MAPK10 -0.002 0.069 -9999 0 -0.18 60 60
mol:GTP -0.001 0.004 -9999 0 -10000 0 0
FOXO4 -0.029 0.21 -9999 0 -0.49 62 62
response to oxidative stress -0.001 0.022 -9999 0 -0.041 92 92
FOXO3A/SIRT1 -0.065 0.23 -9999 0 -0.46 109 109
XPO1 0.017 0.024 -9999 0 -0.29 3 3
EP300 0.013 0.046 -9999 0 -0.24 15 15
BCL2L11 0.018 0.031 -9999 0 -10000 0 0
FOXO1/SKP2 0.014 0.086 -9999 0 -0.29 29 29
mol:GDP -0.001 0.022 -9999 0 -0.041 92 92
RAN 0.015 0.031 -9999 0 -0.24 7 7
GADD45A -0.1 0.34 -9999 0 -0.9 74 74
YWHAQ 0.018 0.019 -9999 0 -0.29 2 2
FOXO1/14-3-3 family 0.018 0.16 -9999 0 -0.55 24 24
MST1 0.011 0.03 -9999 0 -0.13 7 7
CSNK1D 0.01 0.052 -9999 0 -0.27 17 17
CSNK1E 0.003 0.064 -9999 0 -0.23 34 34
FOXO4/14-3-3 family 0 0.16 -9999 0 -0.41 44 44
YWHAB 0.015 0.036 -9999 0 -0.29 7 7
MAPK8 0.01 0.047 -9999 0 -0.15 28 28
MAPK9 0.009 0.05 -9999 0 -0.16 31 31
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0.011 0.045 -9999 0 -0.21 19 19
YWHAZ 0.014 0.037 -9999 0 -0.23 11 11
SIRT1 0.004 0.048 -9999 0 -0.17 32 32
SOD2 -0.13 0.36 -9999 0 -0.81 104 104
RBL2 -0.061 0.3 -9999 0 -1 34 34
RAL/GDP 0.012 0.051 -9999 0 -0.18 28 28
CHUK 0.011 0.034 -9999 0 -0.19 6 6
Ran/GTP 0.011 0.023 -9999 0 -0.17 7 7
CSNK1G2 0.018 0.014 -9999 0 -0.29 1 1
RAL/GTP 0.013 0.051 -9999 0 -0.16 28 28
CSNK1G1 0.019 0 -9999 0 -10000 0 0
FASLG 0.018 0.031 -9999 0 -10000 0 0
SKP2 0.017 0.018 -9999 0 -10000 0 0
USP7 0.014 0.039 -9999 0 -0.28 9 9
IKBKB 0.014 0.023 -9999 0 -10000 0 0
CCNB1 -0.16 0.45 -9999 0 -1.1 97 97
FOXO1-3a-4/beta catenin -0.033 0.21 -9999 0 -0.39 97 97
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.085 -9999 0 -0.28 29 29
CSNK1A1 0.014 0.038 -9999 0 -0.29 8 8
SGK1 -0.003 0.02 -9999 0 -0.043 91 91
CSNK1G3 0.017 0.025 -9999 0 -0.22 5 5
Ran/GTP/Exportin 1 0.022 0.029 -9999 0 -0.21 6 6
ZFAND5 -0.013 0.18 -9999 0 -0.55 31 31
SFN 0.002 0.044 -9999 0 -0.11 70 70
CDK2 0.014 0.034 -9999 0 -0.12 29 29
FOXO3A/14-3-3 -0.004 0.17 -9999 0 -0.48 36 36
CREBBP 0.022 0.002 -9999 0 -10000 0 0
FBXO32 -0.045 0.22 -9999 0 -0.42 105 105
BCL6 -0.084 0.34 -9999 0 -1.1 43 43
RALB 0.013 0.037 -9999 0 -0.19 15 15
RALA 0.005 0.063 -9999 0 -0.27 26 26
YWHAH -0.006 0.083 -9999 0 -0.26 49 49
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.006 0.11 -10000 0 -0.25 65 65
epithelial cell differentiation 0.024 0.059 -10000 0 -0.18 34 34
CYFIP2 -0.02 0.099 -10000 0 -0.25 75 75
ENAH 0.014 0.069 -10000 0 -0.2 35 35
EGFR -0.08 0.12 -10000 0 -0.29 97 97
EPHA2 0.008 0.036 -10000 0 -0.11 45 45
MYO6 0.011 0.065 -10000 0 -0.2 36 36
CTNNB1 0.017 0.023 -10000 0 -0.29 3 3
ABI1/Sra1/Nap1 0.009 0.072 -10000 0 -0.17 70 70
AQP5 0.017 0.089 -10000 0 -0.38 20 20
CTNND1 0.001 0.073 -10000 0 -0.29 31 31
mol:PI-4-5-P2 0.01 0.068 -10000 0 -0.21 39 39
regulation of calcium-dependent cell-cell adhesion 0.015 0.052 -10000 0 -0.17 34 34
EGF 0.014 0.025 -10000 0 -0.11 21 21
NCKAP1 0.019 0 -10000 0 -10000 0 0
AQP3 0.016 0.09 -10000 0 -0.38 20 20
cortical microtubule organization 0.024 0.059 -10000 0 -0.18 34 34
GO:0000145 0.005 0.064 -10000 0 -0.2 39 39
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.06 -10000 0 -0.18 34 34
MLLT4 0.019 0 -10000 0 -10000 0 0
ARF6/GDP -0.018 0.054 -10000 0 -0.21 27 27
ARF6 0.018 0.015 -10000 0 -0.2 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.028 0.053 -10000 0 -0.14 36 36
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.13 -10000 0 -0.32 63 63
PVRL2 0.016 0.026 -10000 0 -0.19 7 7
ZYX 0.002 0.078 -10000 0 -0.23 45 45
ARF6/GTP 0.033 0.052 -10000 0 -0.14 31 31
CDH1 0.012 0.03 -10000 0 -0.11 29 29
EGFR/EGFR/EGF/EGF -0.024 0.078 -10000 0 -0.14 113 113
RhoA/GDP 0.024 0.06 -10000 0 -0.17 38 38
actin cytoskeleton organization 0.012 0.065 -10000 0 -0.2 36 36
IGF-1R heterotetramer -0.001 0.07 -10000 0 -0.21 46 46
GIT1 0.019 0.006 -10000 0 -0.11 1 1
IGF1R -0.001 0.07 -10000 0 -0.21 46 46
IGF1 0.014 0.025 -10000 0 -0.11 21 21
DIAPH1 -0.035 0.21 -10000 0 -0.57 69 69
Wnt receptor signaling pathway -0.024 0.059 0.18 34 -10000 0 34
RHOA 0.015 0.036 -10000 0 -0.29 7 7
RhoA/GTP -0.019 0.057 -10000 0 -0.22 28 28
CTNNA1 0.011 0.048 -10000 0 -0.29 13 13
VCL 0.012 0.066 -10000 0 -0.2 36 36
EFNA1 -0.001 0.07 -10000 0 -0.21 46 46
LPP 0.004 0.076 -10000 0 -0.24 36 36
Ephrin A1/EPHA2 0.009 0.066 -10000 0 -0.15 59 59
SEC6/SEC8 -0.011 0.043 -10000 0 -0.2 19 19
MGAT3 0.015 0.053 -10000 0 -0.17 34 34
HGF/MET 0.016 0.055 -10000 0 -0.16 34 34
HGF 0.016 0.02 -10000 0 -0.11 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.006 0.11 -10000 0 -0.25 65 65
actin cable formation -0.006 0.11 -10000 0 -0.26 65 65
KIAA1543 0.003 0.048 -10000 0 -0.16 34 34
KIFC3 0.015 0.053 -10000 0 -0.17 34 34
NCK1 0.014 0.036 -10000 0 -0.19 14 14
EXOC3 0.017 0.021 -10000 0 -0.2 4 4
ACTN1 0.003 0.073 -10000 0 -0.24 36 36
NCK1/GIT1 0.024 0.026 -10000 0 -0.19 6 6
mol:GDP 0.024 0.059 -10000 0 -0.18 34 34
EXOC4 0 0 -10000 0 -10000 0 0
STX4 0.013 0.064 -10000 0 -0.2 36 36
PIP5K1C 0.01 0.069 -10000 0 -0.21 39 39
LIMA1 -0.013 0.09 -10000 0 -0.24 66 66
ABI1 0.008 0.055 -10000 0 -0.24 22 22
ROCK1 0.017 0.066 -10000 0 -0.2 29 29
adherens junction assembly 0.007 0.089 -10000 0 -0.34 27 27
IGF-1R heterotetramer/IGF1 0.011 0.066 -10000 0 -0.16 50 50
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.026 0.018 -10000 0 -0.19 3 3
MET 0.008 0.037 -10000 0 -0.11 47 47
PLEKHA7 0.004 0.051 -10000 0 -0.17 34 34
mol:GTP 0.026 0.052 -10000 0 -0.14 36 36
establishment of epithelial cell apical/basal polarity 0.022 0.06 -10000 0 -0.25 18 18
cortical actin cytoskeleton stabilization -0.006 0.11 -10000 0 -0.25 65 65
regulation of cell-cell adhesion 0.012 0.065 -10000 0 -0.2 36 36
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.006 0.11 -10000 0 -0.25 65 65
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.018 0.01 -10000 0 -0.11 3 3
RAS family/GTP/Tiam1 -0.006 0.096 -10000 0 -0.22 76 76
NT3 (dimer)/TRKC 0.021 0.032 -10000 0 -0.2 7 7
NT3 (dimer)/TRKB -0.01 0.074 -10000 0 -0.15 95 95
SHC/Grb2/SOS1/GAB1/PI3K -0.022 0.11 -10000 0 -0.23 93 93
RAPGEF1 0.019 0 -10000 0 -10000 0 0
BDNF 0.004 0.042 -10000 0 -0.11 62 62
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
DYNLT1 0.012 0.045 -10000 0 -0.28 12 12
NTRK1 0.018 0.011 -10000 0 -0.11 4 4
NTRK2 -0.043 0.12 -10000 0 -0.23 132 132
NTRK3 0.01 0.043 -10000 0 -0.29 7 7
NT-4/5 (dimer)/TRKB -0.02 0.07 -10000 0 -0.16 95 95
neuron apoptosis 0.033 0.13 0.33 61 -10000 0 61
SHC 2-3/Grb2 -0.036 0.14 -10000 0 -0.36 61 61
SHC1 0.004 0.052 -10000 0 -0.14 48 48
SHC2 -0.039 0.13 -10000 0 -0.4 48 48
SHC3 -0.041 0.13 -10000 0 -0.4 46 46
STAT3 (dimer) -0.025 0.12 -10000 0 -0.32 64 64
NT3 (dimer)/TRKA 0.027 0.03 -10000 0 -0.1 2 2
RIN/GDP 0.001 0.075 -10000 0 -0.21 38 38
GIPC1 0.019 0 -10000 0 -10000 0 0
KRAS 0.011 0.048 -10000 0 -0.28 14 14
DNAJA3 -0.004 0.044 0.18 3 -0.17 8 11
RIN/GTP -0.019 0.056 -10000 0 -0.092 164 164
CCND1 -0.04 0.16 -10000 0 -0.41 64 64
MAGED1 0.004 0.066 -10000 0 -0.28 26 26
PTPN11 0.015 0.033 -10000 0 -0.27 7 7
RICS 0.001 0.066 -10000 0 -0.21 41 41
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.014 0.039 -10000 0 -0.17 16 16
GRB2 0.014 0.039 -10000 0 -0.26 10 10
NGF (dimer)/TRKA/MATK 0.025 0.009 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.022 0.024 -10000 0 -0.19 1 1
ELMO1 -0.047 0.11 -10000 0 -0.21 154 154
RhoG/GTP/ELMO1/DOCK1 -0.017 0.073 -10000 0 -0.16 90 90
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.009 0.055 -10000 0 -0.28 18 18
DOCK1 0.011 0.047 -10000 0 -0.22 19 19
GAB2 -0.005 0.082 -10000 0 -0.27 44 44
RIT2 -0.031 0.084 -10000 0 -0.14 164 164
RIT1 -0.008 0.083 -10000 0 -0.23 57 57
FRS2 0.018 0.013 -10000 0 -0.11 5 5
DNM1 0.017 0.017 -10000 0 -0.11 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.009 0.054 -10000 0 -0.28 17 17
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.022 0.069 0.17 3 -0.2 37 40
mol:GDP 0.005 0.1 -10000 0 -0.31 34 34
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP -0.03 0.077 -10000 0 -0.14 154 154
RIT1/GDP 0.007 0.081 -10000 0 -0.2 46 46
TIAM1 0.003 0.066 -10000 0 -0.23 35 35
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
BDNF (dimer)/TRKB -0.015 0.083 -10000 0 -0.17 106 106
KIDINS220/CRKL/C3G 0.028 0.007 -10000 0 -10000 0 0
SHC/RasGAP 0.007 0.062 -10000 0 -0.2 35 35
FRS2 family/SHP2 0.036 0.022 -10000 0 -0.15 6 6
SHC/GRB2/SOS1/GAB1 0.016 0.047 -10000 0 -0.14 29 29
RIT1/GTP -0.004 0.056 -10000 0 -0.2 38 38
NT3 (dimer) 0.018 0.01 -10000 0 -0.11 3 3
RAP1/GDP -0.017 0.049 -10000 0 -0.17 36 36
KIDINS220/CRKL 0.018 0.01 -10000 0 -0.11 3 3
BDNF (dimer) 0.004 0.042 -10000 0 -0.11 62 62
ubiquitin-dependent protein catabolic process 0.02 0.02 -10000 0 -0.16 1 1
Schwann cell development -0.014 0.021 -10000 0 -0.088 10 10
EHD4 0.007 0.057 -10000 0 -0.23 25 25
FRS2 family/GRB2/SOS1 0.033 0.023 -10000 0 -0.14 8 8
FRS2 family/SHP2/CRK family/C3G/GAB2 0.018 0.071 -10000 0 -0.35 12 12
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.018 0.019 -10000 0 -0.29 2 2
CDC42/GTP -0.016 0.089 -10000 0 -0.21 68 68
ABL1 -0.012 0.093 -10000 0 -0.28 55 55
SH2B family/GRB2/SOS1 0.011 0.026 -10000 0 -0.17 10 10
Rap1/GTP 0.01 0.055 -10000 0 -0.2 11 11
STAT3 -0.025 0.12 -10000 0 -0.32 64 64
axon guidance -0.022 0.082 -10000 0 -0.2 68 68
MAPK3 0.022 0.008 -10000 0 -10000 0 0
MAPK1 0.021 0.014 -10000 0 -0.19 1 1
CDC42/GDP 0.013 0.072 -10000 0 -0.2 35 35
NTF3 0.018 0.01 -10000 0 -0.11 3 3
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.021 0.027 -10000 0 -0.16 10 10
PI3K -0.016 0.093 -10000 0 -0.21 88 88
FRS3 0.019 0.006 -10000 0 -10000 0 0
FAIM 0.011 0.045 -10000 0 -0.21 18 18
GAB1 0.003 0.056 -10000 0 -0.15 50 50
RASGRF1 -0.003 0.043 0.16 4 -0.15 9 13
SOS1 0 0 -10000 0 -10000 0 0
MCF2L 0.013 0.04 -10000 0 -0.18 14 14
RGS19 0.013 0.041 -10000 0 -0.29 9 9
CDC42 0.017 0.016 -10000 0 -0.11 8 8
RAS family/GTP 0.008 0.099 -10000 0 -0.37 26 26
Rac1/GDP 0.013 0.075 -10000 0 -0.21 35 35
NGF (dimer)/TRKA/GRIT 0.015 0.039 -10000 0 -0.16 22 22
neuron projection morphogenesis -0.066 0.26 -10000 0 -0.94 38 38
NGF (dimer)/TRKA/NEDD4-2 0.02 0.02 -10000 0 -0.16 1 1
MAP2K1 0.009 0.046 -10000 0 -0.15 29 29
NGFR 0.002 0.044 -10000 0 -0.11 70 70
NGF (dimer)/TRKA/GIPC/GAIP 0.023 0.047 -10000 0 -0.22 16 16
RAS family/GTP/PI3K -0.033 0.12 -10000 0 -0.22 127 127
FRS2 family/SHP2/GRB2/SOS1 0.04 0.033 -10000 0 -0.18 10 10
NRAS -0.01 0.086 -10000 0 -0.24 59 59
GRB2/SOS1 0.011 0.026 -10000 0 -0.17 10 10
PRKCI 0.015 0.028 -10000 0 -0.14 15 15
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.015 0.036 -10000 0 -0.29 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.008 0.079 -10000 0 -0.52 10 10
RASA1 0.003 0.069 -10000 0 -0.28 29 29
TRKA/c-Abl 0.006 0.066 -10000 0 -0.19 52 52
SQSTM1 0.004 0.062 -10000 0 -0.22 32 32
BDNF (dimer)/TRKB/GIPC 0 0.077 -10000 0 -0.15 94 94
NGF (dimer)/TRKA/p62/Atypical PKCs 0.024 0.035 -10000 0 -0.13 22 22
MATK 0.018 0.01 -10000 0 -0.11 3 3
NEDD4L 0.011 0.033 -10000 0 -0.12 32 32
RAS family/GDP -0.025 0.055 -10000 0 -0.17 54 54
NGF (dimer)/TRKA -0.007 0.046 0.19 4 -0.16 9 13
Rac1/GTP -0.035 0.068 -10000 0 -0.2 59 59
FRS2 family/SHP2/CRK family 0.048 0.038 -10000 0 -0.13 20 20
Ephrin B reverse signaling

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
EFNB2 -0.035 0.11 -10000 0 -0.25 105 105
EPHB2 0.014 0.027 -10000 0 -0.11 24 24
EFNB1 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.052 -10000 0 -0.21 7 7
Ephrin B2/EPHB1-2 -0.008 0.072 -10000 0 -0.14 96 96
neuron projection morphogenesis 0.016 0.044 -10000 0 -0.2 7 7
Ephrin B1/EPHB1-2/Tiam1 0.024 0.048 -10000 0 -0.12 13 13
DNM1 0.017 0.017 -10000 0 -0.11 8 8
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.041 0.17 -10000 0 -0.56 49 49
YES1 -0.06 0.24 -10000 0 -0.81 48 48
Ephrin B1/EPHB1-2/NCK2 0.028 0.044 -10000 0 -0.12 8 8
PI3K -0.049 0.2 -10000 0 -0.63 52 52
mol:GDP 0.023 0.047 -10000 0 -0.12 13 13
ITGA2B 0.019 0 -10000 0 -10000 0 0
endothelial cell proliferation -0.006 0.066 -10000 0 -0.16 83 83
FYN -0.071 0.25 -10000 0 -0.84 48 48
MAP3K7 -0.046 0.18 -10000 0 -0.59 48 48
FGR -0.059 0.23 -10000 0 -0.78 48 48
TIAM1 0.003 0.066 -10000 0 -0.23 35 35
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
RGS3 0.017 0.016 -10000 0 -0.11 8 8
cell adhesion -0.038 0.19 -10000 0 -0.58 51 51
LYN -0.073 0.23 -10000 0 -0.79 48 48
Ephrin B1/EPHB1-2/Src Family Kinases -0.058 0.22 -10000 0 -0.74 48 48
Ephrin B1/EPHB1-2 -0.049 0.18 -10000 0 -0.63 48 48
SRC -0.055 0.23 -10000 0 -0.78 48 48
ITGB3 0.019 0.008 -10000 0 -0.11 2 2
EPHB1 -0.005 0.057 -10000 0 -0.12 91 91
EPHB4 0.019 0.006 -10000 0 -0.11 1 1
RAC1 0.015 0.036 -10000 0 -0.29 7 7
Ephrin B2/EPHB4 -0.006 0.067 -10000 0 -0.16 83 83
alphaIIb/beta3 Integrin 0.028 0.006 -10000 0 -10000 0 0
BLK -0.056 0.23 -10000 0 -0.78 48 48
HCK -0.077 0.24 -10000 0 -0.8 48 48
regulation of stress fiber formation -0.026 0.043 0.12 8 -10000 0 8
MAPK8 -0.035 0.16 -10000 0 -0.53 49 49
Ephrin B1/EPHB1-2/RGS3 0.032 0.038 -10000 0 -0.12 6 6
endothelial cell migration -0.051 0.17 -10000 0 -0.55 48 48
NCK2 0.009 0.054 -10000 0 -0.28 17 17
PTPN13 -0.006 0.098 -10000 0 -0.36 33 33
regulation of focal adhesion formation -0.026 0.043 0.12 8 -10000 0 8
chemotaxis -0.031 0.037 0.12 6 -10000 0 6
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
Rac1/GTP 0.023 0.048 -10000 0 -0.21 7 7
angiogenesis -0.048 0.18 -10000 0 -0.62 48 48
LCK -0.056 0.23 -10000 0 -0.78 48 48
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.002 0.048 -10000 0 -0.25 15 15
HSPA8 0.01 0.057 -10000 0 -0.29 18 18
SMAD3/SMAD4/ER alpha 0.045 0.078 0.2 33 -0.17 20 53
AKT1 0.006 0.064 -10000 0 -0.28 23 23
GSC 0.013 0.024 -10000 0 -10000 0 0
NKX2-5 0.014 0.025 -10000 0 -0.11 18 18
muscle cell differentiation -0.01 0.11 0.31 44 -10000 0 44
SMAD2-3/SMAD4/SP1 0.018 0.12 -10000 0 -0.25 57 57
SMAD4 0.007 0.068 -10000 0 -0.19 37 37
CBFB 0.017 0.018 -10000 0 -0.15 5 5
SAP18 0.011 0.052 -10000 0 -0.29 15 15
Cbp/p300/MSG1 -0.023 0.081 -10000 0 -0.17 107 107
SMAD3/SMAD4/VDR 0.021 0.09 -10000 0 -0.21 43 43
MYC -0.026 0.098 -10000 0 -0.22 96 96
CDKN2B 0.029 0.048 -10000 0 -10000 0 0
AP1 -0.007 0.13 -10000 0 -0.32 63 63
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.15 -10000 0 -0.46 33 33
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.025 0.18 -10000 0 -0.45 56 56
SP3 0.012 0.047 -10000 0 -0.29 12 12
CREB1 0.015 0.033 -10000 0 -0.27 7 7
FOXH1 0.019 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.035 0.083 0.17 19 -0.2 31 50
GATA3 0.023 0.017 -10000 0 -0.1 1 1
SKI/SIN3/HDAC complex/NCoR1 0.012 0.1 -10000 0 -0.36 23 23
MEF2C/TIF2 0.028 0.077 -10000 0 -0.27 24 24
endothelial cell migration 0.27 0.51 1.3 111 -10000 0 111
MAX 0.028 0.018 -10000 0 -10000 0 0
RBBP7 0.016 0.034 -10000 0 -0.25 8 8
RBBP4 -0.005 0.079 -10000 0 -0.24 50 50
RUNX2 0.019 0 -10000 0 -10000 0 0
RUNX3 0.014 0.024 -10000 0 -0.11 19 19
RUNX1 0.019 0 -10000 0 -10000 0 0
CTBP1 0.007 0.059 -10000 0 -0.29 20 20
NR3C1 0.024 0.041 -10000 0 -0.3 7 7
VDR 0.019 0.008 -10000 0 -0.11 2 2
CDKN1A -0.12 0.39 -10000 0 -1.2 62 62
KAT2B -0.004 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.025 0.072 -10000 0 -0.18 46 46
DCP1A 0.012 0.046 -10000 0 -0.29 12 12
SKI 0.02 0.001 -10000 0 -10000 0 0
SERPINE1 -0.28 0.52 -10000 0 -1.3 111 111
SMAD3/SMAD4/ATF2 0.022 0.071 -10000 0 -0.16 38 38
SMAD3/SMAD4/ATF3 -0.008 0.11 -10000 0 -0.2 99 99
SAP30 0.017 0.027 -10000 0 -0.29 4 4
Cbp/p300/PIAS3 0.014 0.046 -10000 0 -0.17 18 18
JUN -0.014 0.13 -10000 0 -0.32 62 62
SMAD3/SMAD4/IRF7 0.024 0.077 -10000 0 -0.18 34 34
TFE3 -0.006 0.065 -10000 0 -0.2 37 37
COL1A2 -0.13 0.26 -10000 0 -0.72 81 81
mesenchymal cell differentiation -0.023 0.07 0.16 38 -10000 0 38
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.019 0 -10000 0 -10000 0 0
FOS -0.02 0.096 -10000 0 -0.19 97 97
SMAD3/SMAD4/Max 0.04 0.072 0.17 19 -0.17 24 43
Cbp/p300/SNIP1 0.025 0.033 -10000 0 -0.16 11 11
ZBTB17 0.017 0.006 -10000 0 -0.11 1 1
LAMC1 -0.009 0.12 -10000 0 -0.34 51 51
TGIF2/HDAC complex/SMAD3/SMAD4 0.021 0.072 -10000 0 -0.18 30 30
IRF7 0.014 0.043 -10000 0 -0.17 24 24
ESR1 0.029 0.025 -10000 0 -10000 0 0
HNF4A 0.019 0 -10000 0 -10000 0 0
MEF2C 0.018 0.079 -10000 0 -0.27 27 27
SMAD2-3/SMAD4 0.022 0.087 -10000 0 -0.22 34 34
Cbp/p300/Src-1 0.008 0.064 -10000 0 -0.18 48 48
IGHV3OR16-13 -0.005 0.064 -10000 0 -0.59 6 6
TGIF2/HDAC complex 0.014 0.024 -10000 0 -0.11 19 19
CREBBP 0.012 0.012 -10000 0 -10000 0 0
SKIL 0.019 0.006 -10000 0 -0.11 1 1
HDAC1 0.014 0.04 -10000 0 -0.22 13 13
HDAC2 0.005 0.061 -10000 0 -0.22 33 33
SNIP1 0.02 0.01 -10000 0 -0.11 3 3
GCN5L2 0.009 0.03 -10000 0 -0.18 9 9
SMAD3/SMAD4/TFE3 0.009 0.11 -10000 0 -0.23 63 63
MSG1/HSC70 -0.027 0.093 -10000 0 -0.2 111 111
SMAD2 0.013 0.05 -10000 0 -0.28 14 14
SMAD3 0.015 0.041 -10000 0 -0.11 25 25
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.073 -10000 0 -0.2 38 38
SMAD2/SMAD2/SMAD4 -0.011 0.065 0.11 2 -0.22 37 39
NCOR1 0.01 0.054 -10000 0 -0.27 18 18
NCOA2 0.018 0.01 -10000 0 -0.11 3 3
NCOA1 -0.006 0.083 -10000 0 -0.28 43 43
MYOD/E2A 0.028 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.03 0.12 -10000 0 -0.24 48 48
IFNB1 0.023 0.062 -10000 0 -0.19 16 16
SMAD3/SMAD4/MEF2C 0.035 0.094 -10000 0 -0.28 28 28
CITED1 -0.054 0.12 -10000 0 -0.22 162 162
SMAD2-3/SMAD4/ARC105 0.035 0.082 -10000 0 -0.22 26 26
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.01 0.16 -10000 0 -0.45 47 47
RUNX1-3/PEBPB2 0.035 0.019 -10000 0 -0.15 1 1
SMAD7 -0.041 0.2 -10000 0 -0.5 66 66
MYC/MIZ-1 -0.007 0.069 -10000 0 -0.2 54 54
SMAD3/SMAD4 -0.099 0.21 -10000 0 -0.46 120 120
IL10 0.03 0.059 -10000 0 -0.22 9 9
PIASy/HDAC complex 0.025 0.012 -10000 0 -10000 0 0
PIAS3 0.012 0.034 -10000 0 -0.19 12 12
CDK2 0.005 0.037 -10000 0 -0.13 29 29
IL5 0.03 0.059 -10000 0 -0.22 9 9
CDK4 -0.013 0.067 -10000 0 -0.15 80 80
PIAS4 0.025 0.012 -10000 0 -10000 0 0
ATF3 -0.036 0.11 -10000 0 -0.22 121 121
SMAD3/SMAD4/SP1 0.001 0.12 -10000 0 -0.23 72 72
FOXG1 -0.03 0.11 -10000 0 -0.27 91 91
FOXO3 0.013 0.046 -10000 0 -0.21 18 18
FOXO1 0.003 0.06 -10000 0 -0.2 35 35
FOXO4 0.013 0.044 -10000 0 -0.19 22 22
heart looping 0.018 0.078 -10000 0 -0.27 27 27
CEBPB -0.003 0.076 -10000 0 -0.22 51 51
SMAD3/SMAD4/DLX1 0.013 0.067 -10000 0 -0.15 48 48
MYOD1 0.019 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.023 0.07 -10000 0 -0.18 26 26
SMAD3/SMAD4/GATA3 0.036 0.075 -10000 0 -0.23 13 13
SnoN/SIN3/HDAC complex/NCoR1 0.019 0.006 -10000 0 -0.11 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.042 0.066 -10000 0 -0.18 14 14
SMAD3/SMAD4/SP1-3 0.014 0.12 -10000 0 -0.24 57 57
MED15 0.018 0.013 -10000 0 -0.11 5 5
SP1 -0.011 0.057 -10000 0 -0.12 92 92
SIN3B 0.017 0.025 -10000 0 -0.2 6 6
SIN3A 0.001 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.038 0.076 -10000 0 -0.21 31 31
ITGB5 -0.004 0.11 -10000 0 -0.27 47 47
TGIF/SIN3/HDAC complex/CtBP -0.004 0.13 -10000 0 -0.44 29 29
SMAD3/SMAD4/AR 0.02 0.071 -10000 0 -0.15 44 44
AR 0.014 0.026 -10000 0 -0.11 22 22
negative regulation of cell growth -0.018 0.14 -10000 0 -0.32 73 73
SMAD3/SMAD4/MYOD 0.023 0.07 -10000 0 -0.16 38 38
E2F5 0.019 0 -10000 0 -10000 0 0
E2F4 0.019 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.031 0.08 -10000 0 -0.2 40 40
SMAD2-3/SMAD4/FOXO1-3a-4 -0.01 0.16 -10000 0 -0.47 40 40
TFDP1 0.005 0.059 -10000 0 -0.2 33 33
SMAD3/SMAD4/AP1 0.002 0.14 -10000 0 -0.32 62 62
SMAD3/SMAD4/RUNX2 0.023 0.07 -10000 0 -0.16 38 38
TGIF2 0.014 0.024 -10000 0 -0.11 19 19
TGIF1 -0.005 0.077 -10000 0 -0.22 55 55
ATF2 0.017 0.017 -10000 0 -0.11 9 9
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.015 0.14 -9999 0 -0.29 89 89
MAP3K8 0.003 0.042 -9999 0 -0.11 62 62
FOS -0.006 0.095 -9999 0 -0.34 21 21
PRKCA 0.016 0.008 -9999 0 -10000 0 0
PTPN7 0.014 0.017 -9999 0 -0.12 5 5
HRAS 0.008 0.055 -9999 0 -0.28 18 18
PRKCB -0.002 0.006 -9999 0 -0.015 85 85
NRAS -0.01 0.086 -9999 0 -0.24 59 59
RAS family/GTP 0.008 0.069 -9999 0 -0.17 59 59
MAPK3 0.012 0.041 -9999 0 -10000 0 0
MAP2K1 0.001 0.057 -9999 0 -0.25 17 17
ELK1 0.014 0.013 -9999 0 -10000 0 0
BRAF 0.008 0.025 -9999 0 -10000 0 0
mol:GTP -0.001 0.002 -9999 0 -0.004 85 85
MAPK1 -0.002 0.1 -9999 0 -0.57 13 13
RAF1 -0.003 0.077 -9999 0 -0.39 18 18
KRAS 0.011 0.049 -9999 0 -0.28 14 14
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.008 0.056 -9999 0 -0.29 18 18
VLDLR -0.021 0.093 -9999 0 -0.2 97 97
LRPAP1 0.013 0.043 -9999 0 -0.28 11 11
NUDC 0.01 0.053 -9999 0 -0.29 16 16
RELN/LRP8 0.022 0.045 -9999 0 -0.15 20 20
CaM/Ca2+ 0.006 0.038 -9999 0 -0.2 16 16
KATNA1 0.012 0.045 -9999 0 -0.28 12 12
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 0.009 0.054 -9999 0 -0.2 24 24
IQGAP1/CaM 0.001 0.074 -9999 0 -0.2 58 58
DAB1 0.019 0.006 -9999 0 -0.11 1 1
IQGAP1 -0.009 0.087 -9999 0 -0.27 50 50
PLA2G7 0.007 0.038 -9999 0 -0.11 49 49
CALM1 0.007 0.056 -9999 0 -0.21 28 28
DYNLT1 0.012 0.045 -9999 0 -0.28 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.018 0.043 -9999 0 -0.2 16 16
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0.036 -9999 0 -0.14 23 23
CDK5R1 0.014 0.025 -9999 0 -0.11 21 21
LIS1/Poliovirus Protein 3A 0.005 0.049 -9999 0 -0.2 26 26
CDK5R2 0.015 0.023 -9999 0 -0.11 17 17
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 0.007 0.061 -9999 0 -0.15 54 54
YWHAE 0.011 0.045 -9999 0 -0.21 19 19
NDEL1/14-3-3 E 0.01 0.09 -9999 0 -0.29 29 29
MAP1B -0.022 0.082 -9999 0 -0.24 62 62
RAC1 -0.001 0.071 -9999 0 -0.29 18 18
p35/CDK5 0.004 0.072 -9999 0 -0.15 74 74
RELN 0.007 0.038 -9999 0 -0.11 50 50
PAFAH/LIS1 0.012 0.055 -9999 0 -0.2 26 26
LIS1/CLIP170 0.015 0.056 -9999 0 -0.2 28 28
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.006 0.1 -9999 0 -0.28 45 45
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.013 0.1 -9999 0 -0.23 83 83
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.002 0.086 -9999 0 -0.28 28 28
LIS1/IQGAP1 0.003 0.077 -9999 0 -0.19 62 62
RHOA -0.001 0.076 -9999 0 -0.32 16 16
PAFAH1B1 0.013 0.039 -9999 0 -0.19 19 19
PAFAH1B3 -0.007 0.08 -9999 0 -0.22 57 57
PAFAH1B2 0.019 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.004 0.094 -9999 0 -0.21 71 71
NDEL1/Katanin 60/Dynein heavy chain 0.014 0.098 -9999 0 -0.28 36 36
LRP8 0.01 0.043 -9999 0 -0.16 28 28
NDEL1/Katanin 60 0.01 0.091 -9999 0 -0.28 31 31
P39/CDK5 0.004 0.072 -9999 0 -0.15 72 72
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.014 0.07 -9999 0 -0.27 28 28
CDK5 0.008 0.059 -9999 0 -0.21 27 27
PPP2R5D 0.018 0.013 -9999 0 -0.11 5 5
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.013 0.048 -9999 0 -0.17 28 28
CSNK2A1 0.01 0.053 -9999 0 -0.29 16 16
RELN/VLDLR/DAB1/LIS1 0.012 0.071 -9999 0 -0.14 69 69
RELN/VLDLR 0.01 0.067 -9999 0 -0.14 73 73
CDC42 0.004 0.046 -9999 0 -0.13 48 48
Aurora A signaling

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
Aurora A/GADD45A 0.005 0.08 -10000 0 -0.25 38 38
BIRC5 -0.03 0.1 -10000 0 -0.22 111 111
NFKBIA 0.007 0.06 -10000 0 -0.18 43 43
CPEB1 -0.004 0.076 -10000 0 -0.22 51 51
AKT1 0.009 0.066 -10000 0 -0.24 29 29
NDEL1 0.013 0.043 -10000 0 -0.28 11 11
Aurora A/BRCA1 0.015 0.05 -10000 0 -0.18 25 25
NDEL1/TACC3 0.013 0.071 -10000 0 -0.19 47 47
GADD45A -0.022 0.1 -10000 0 -0.26 78 78
GSK3B 0.007 0.064 -10000 0 -0.26 26 26
PAK1/Aurora A 0.016 0.056 -10000 0 -0.2 25 25
MDM2 0.011 0.032 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.019 0.079 -10000 0 -0.19 89 89
TP53 0.004 0.081 -10000 0 -0.28 33 33
DLG7 -0.011 0.069 -10000 0 -0.18 66 66
AURKAIP1 0.018 0.015 -10000 0 -0.2 2 2
ARHGEF7 0 0.071 -10000 0 -0.25 37 37
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.014 0.075 -10000 0 -0.2 47 47
G2/M transition of mitotic cell cycle 0.015 0.049 -10000 0 -0.18 25 25
AURKA 0.012 0.063 0.14 16 -0.24 25 41
AURKB 0.006 0.037 -10000 0 -0.16 17 17
CDC25B 0.001 0.095 -10000 0 -0.32 36 36
G2/M transition checkpoint 0.003 0.047 -10000 0 -0.18 25 25
mRNA polyadenylation 0.004 0.064 -10000 0 -0.16 57 57
Aurora A/CPEB 0.004 0.064 -10000 0 -0.16 57 57
Aurora A/TACC1/TRAP/chTOG 0.021 0.087 -10000 0 -0.25 35 35
BRCA1 0.017 0.015 -10000 0 -0.11 7 7
centrosome duplication 0.016 0.056 -10000 0 -0.2 25 25
regulation of centrosome cycle 0.012 0.07 -10000 0 -0.18 47 47
spindle assembly 0.019 0.086 -10000 0 -0.24 35 35
TDRD7 0.004 0.065 -10000 0 -0.27 27 27
Aurora A/RasGAP/Survivin 0.004 0.086 -10000 0 -0.24 42 42
CENPA -0.006 0.092 -10000 0 -0.35 31 31
Aurora A/PP2A 0.017 0.055 -10000 0 -0.2 25 25
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0 0.078 -10000 0 -0.25 35 35
negative regulation of DNA binding 0 0.084 -10000 0 -0.28 33 33
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.015 0.05 -10000 0 -0.19 28 28
RASA1 0.003 0.069 -10000 0 -0.28 29 29
Ajuba/Aurora A 0.004 0.047 -10000 0 -0.18 25 25
mitotic prometaphase -0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.063 0.14 16 -0.24 25 41
TACC1 0.01 0.049 -10000 0 -0.29 13 13
TACC3 -0.004 0.075 -10000 0 -0.21 54 54
Aurora A/Antizyme1 0.027 0.053 -10000 0 -0.18 27 27
Aurora A/RasGAP 0.012 0.073 -10000 0 -0.29 25 25
OAZ1 0.017 0.023 -10000 0 -0.29 3 3
RAN 0.016 0.031 -10000 0 -0.24 7 7
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.021 0.011 -10000 0 -10000 0 0
GIT1 0.019 0.006 -10000 0 -0.11 1 1
GIT1/beta-PIX/PAK1 0.026 0.045 -10000 0 -0.15 29 29
Importin alpha/Importin beta/TPX2 -0.019 0.079 -10000 0 -0.19 89 89
PPP2R5D 0.018 0.013 -10000 0 -0.11 5 5
Aurora A/TPX2 -0.009 0.087 -10000 0 -0.18 85 85
PAK1 0.017 0.017 -10000 0 -0.11 9 9
CKAP5 0.004 0.066 -10000 0 -0.29 25 25
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.08 0.36 -10000 0 -1 28 28
STAT6 (cleaved dimer) -0.17 0.27 -10000 0 -0.85 50 50
IGHG1 -0.037 0.23 -10000 0 -0.62 38 38
IGHG3 -0.087 0.34 -10000 0 -0.9 38 38
AKT1 -0.035 0.26 -10000 0 -0.72 34 34
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.004 0.18 -10000 0 -0.48 18 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.03 0.25 -10000 0 -0.69 30 30
THY1 -0.16 0.5 -10000 0 -1.3 65 65
MYB 0.013 0.028 -10000 0 -0.11 26 26
HMGA1 0.016 0.019 -10000 0 -0.11 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.021 0.23 -10000 0 -0.54 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.026 0.24 -10000 0 -0.69 26 26
SP1 -0.001 0.05 -10000 0 -0.14 36 36
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.011 0.032 -10000 0 -0.2 7 7
STAT6 (dimer)/ETS1 -0.07 0.34 -10000 0 -0.91 38 38
SOCS1 -0.031 0.27 -10000 0 -0.66 35 35
SOCS3 -0.003 0.2 -10000 0 -0.65 3 3
FCER2 -0.05 0.29 -10000 0 -0.74 26 26
PARP14 0.002 0.001 -10000 0 -10000 0 0
CCL17 -0.079 0.35 -10000 0 -1 26 26
GRB2 0.014 0.039 -10000 0 -0.26 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.015 0.2 -10000 0 -0.58 25 25
T cell proliferation -0.085 0.36 -10000 0 -0.98 39 39
IL4R/JAK1 -0.092 0.36 -10000 0 -0.99 36 36
EGR2 -0.14 0.48 -10000 0 -1.3 59 59
JAK2 0.014 0.048 -10000 0 -0.15 12 12
JAK3 0.023 0.004 -10000 0 -10000 0 0
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
JAK1 0.005 0.073 -10000 0 -0.26 34 34
COL1A2 -0.18 0.47 -10000 0 -1.2 81 81
CCL26 -0.087 0.35 -10000 0 -0.94 38 38
IL4R -0.086 0.38 -10000 0 -1.1 28 28
PTPN6 0.005 0.057 -10000 0 -0.19 33 33
IL13RA2 -0.39 0.65 -10000 0 -1.2 201 201
IL13RA1 -0.007 0.091 -10000 0 -0.29 40 40
IRF4 0.029 0.098 -10000 0 -10000 0 0
ARG1 -0.002 0.16 -10000 0 -0.58 12 12
CBL -0.017 0.22 -10000 0 -0.51 31 31
GTF3A 0.02 0.024 -10000 0 -0.2 3 3
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
IL13RA1/JAK2 0.009 0.084 -10000 0 -0.19 39 39
IRF4/BCL6 0.019 0.1 -10000 0 -10000 0 0
CD40LG 0.028 0.001 -10000 0 -10000 0 0
MAPK14 -0.012 0.22 -10000 0 -0.53 23 23
mitosis -0.031 0.25 -10000 0 -0.67 34 34
STAT6 -0.092 0.4 -10000 0 -1 38 38
SPI1 0.019 0.028 -10000 0 -10000 0 0
RPS6KB1 -0.026 0.24 -10000 0 -0.64 34 34
STAT6 (dimer) -0.092 0.4 -10000 0 -1 38 38
STAT6 (dimer)/PARP14 -0.098 0.36 -10000 0 -0.98 38 38
mast cell activation -0.001 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.008 0.2 -10000 0 -0.5 23 23
FRAP1 -0.035 0.26 -10000 0 -0.72 34 34
LTA -0.079 0.36 -10000 0 -1.1 26 26
FES 0.017 0.016 -10000 0 -0.11 8 8
T-helper 1 cell differentiation 0.09 0.39 1 38 -10000 0 38
CCL11 -0.08 0.34 -10000 0 -1 26 26
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.003 0.2 -10000 0 -0.51 18 18
IL2RG 0.017 0.027 -10000 0 -0.1 24 24
IL10 -0.079 0.35 -10000 0 -1 26 26
IRS1 -0.002 0.07 -10000 0 -0.19 53 53
IRS2 -0.021 0.1 -10000 0 -0.25 79 79
IL4 0.013 0.12 -10000 0 -10000 0 0
IL5 -0.079 0.35 -10000 0 -1 26 26
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.075 0.34 -10000 0 -0.84 40 40
COL1A1 -0.018 0.21 -10000 0 -1.2 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.091 0.36 -10000 0 -1.1 30 30
IL2R gamma/JAK3 0.031 0.02 -10000 0 -10000 0 0
TFF3 -0.082 0.36 -10000 0 -1.1 27 27
ALOX15 -0.079 0.35 -10000 0 -1 26 26
MYBL1 -0.016 0.085 -10000 0 -0.18 93 93
T-helper 2 cell differentiation -0.064 0.31 -10000 0 -0.77 42 42
SHC1 0.004 0.052 -10000 0 -0.14 48 48
CEBPB 0.002 0.077 -10000 0 -0.22 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.034 0.25 -10000 0 -0.66 36 36
mol:PI-3-4-5-P3 -0.034 0.26 -10000 0 -0.72 34 34
PI3K -0.039 0.27 -10000 0 -0.77 34 34
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.016 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.014 0.2 -10000 0 -0.57 29 29
ITGB3 -0.079 0.36 -10000 0 -1.1 26 26
PIGR -0.079 0.36 -10000 0 -1.1 26 26
IGHE 0.005 0.077 0.2 35 -0.18 28 63
MAPKKK cascade -0.013 0.2 -10000 0 -0.56 29 29
BCL6 -0.009 0.082 -10000 0 -0.23 56 56
OPRM1 -0.079 0.35 -10000 0 -1 30 30
RETNLB -0.087 0.35 -10000 0 -0.94 38 38
SELP -0.079 0.36 -10000 0 -1.1 26 26
AICDA -0.079 0.34 -10000 0 -1 27 27
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.027 0.017 -9999 0 -0.26 1 1
CRKL 0.018 0.01 -9999 0 -0.11 3 3
Rac1/GDP 0.011 0.024 -9999 0 -0.2 7 7
DOCK1 0.011 0.047 -9999 0 -0.22 19 19
ITGA4 0.016 0.019 -9999 0 -0.11 12 12
alpha4/beta7 Integrin/MAdCAM1 0.044 0.025 -9999 0 -0.13 7 7
EPO 0.019 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.026 0.016 -9999 0 -0.14 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.009 0.054 -9999 0 -0.28 17 17
alpha4/beta1 Integrin 0.026 0.014 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.028 0 -9999 0 -10000 0 0
lamellipodium assembly -0.011 0.1 -9999 0 -0.33 22 22
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
PI3K -0.016 0.093 -9999 0 -0.21 88 88
ARF6 0.018 0.015 -9999 0 -0.2 2 2
JAK2 0.031 0.015 -9999 0 -10000 0 0
PXN 0.018 0.011 -9999 0 -0.11 4 4
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
MADCAM1 0.019 0.006 -9999 0 -0.11 1 1
cell adhesion 0.043 0.025 -9999 0 -0.13 7 7
CRKL/CBL 0.028 0.007 -9999 0 -10000 0 0
ITGB1 0.019 0 -9999 0 -10000 0 0
SRC -0.022 0.069 -9999 0 -0.13 144 144
ITGB7 0.018 0.01 -9999 0 -0.11 3 3
RAC1 0.015 0.036 -9999 0 -0.29 7 7
alpha4/beta1 Integrin/VCAM1 -0.023 0.083 -9999 0 -0.15 144 144
p130Cas/Crk/Dock1 -0.011 0.075 -9999 0 -0.12 152 152
VCAM1 -0.079 0.14 -9999 0 -0.24 202 202
RHOA 0.015 0.036 -9999 0 -0.29 7 7
alpha4/beta1 Integrin/Paxillin/GIT1 0.047 0.015 -9999 0 -10000 0 0
BCAR1 -0.023 0.062 -9999 0 -0.12 144 144
EPOR 0.019 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.019 0 -9999 0 -10000 0 0
GIT1 0.019 0.006 -9999 0 -0.11 1 1
Rac1/GTP -0.012 0.1 -9999 0 -0.36 20 20
Signaling events mediated by PRL

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
CCNE1 0.01 0.033 -10000 0 -0.11 37 37
mol:Halofuginone -0.001 0.033 -10000 0 -0.19 15 15
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.037 0.16 -10000 0 -0.4 76 76
PRL-3/alpha Tubulin 0.012 0.05 -10000 0 -0.19 24 24
mol:Ca2+ -0.023 0.088 0.29 12 -0.2 73 85
AGT -0.035 0.11 -10000 0 -0.26 104 104
CCNA2 -0.011 0.12 -10000 0 -0.64 17 17
TUBA1B 0.018 0.014 -10000 0 -0.29 1 1
EGR1 0.002 0.072 -10000 0 -0.36 18 18
CDK2/Cyclin E1 -0.025 0.15 -10000 0 -0.36 76 76
MAPK3 0.005 0.047 -10000 0 -0.19 23 23
PRL-2 /Rab GGTase beta 0.022 0.039 -10000 0 -0.22 12 12
MAPK1 0 0.056 -10000 0 -0.19 36 36
PTP4A1 -0.002 0.12 -10000 0 -0.64 18 18
PTP4A3 -0.004 0.07 -10000 0 -0.18 63 63
PTP4A2 0.017 0.025 -10000 0 -0.2 6 6
ITGB1 0.005 0.047 -10000 0 -0.19 23 23
SRC 0.019 0 -10000 0 -10000 0 0
RAC1 -0.01 0.12 -10000 0 -0.37 44 44
Rab GGTase beta/Rab GGTase alpha 0.022 0.034 -10000 0 -0.19 11 11
PRL-1/ATF-5 -0.007 0.13 -10000 0 -0.67 15 15
RABGGTA 0.017 0.016 -10000 0 -0.11 8 8
BCAR1 0.006 0.062 0.28 23 -10000 0 23
RHOC -0.013 0.12 -10000 0 -0.38 47 47
RHOA -0.012 0.14 -10000 0 -0.43 41 41
cell motility -0.014 0.13 -10000 0 -0.39 44 44
PRL-1/alpha Tubulin -0.007 0.13 -10000 0 -0.67 15 15
PRL-3/alpha1 Integrin -0.001 0.047 -10000 0 -0.12 63 63
ROCK1 -0.014 0.13 -10000 0 -0.39 44 44
RABGGTB 0.012 0.045 -10000 0 -0.25 14 14
CDK2 0.011 0.034 -10000 0 -0.12 29 29
mitosis -0.002 0.12 -10000 0 -0.63 18 18
ATF5 0.018 0.01 -10000 0 -0.11 3 3
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.019 0 -9999 0 -10000 0 0
SPHK1 0.008 0.037 -9999 0 -0.11 46 46
GNAI2 0 0.074 -9999 0 -0.28 34 34
mol:S1P 0.016 0.016 -9999 0 -10000 0 0
GNAO1 -0.014 0.085 -9999 0 -0.2 81 81
mol:Sphinganine-1-P 0.014 0.024 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.021 0.045 -9999 0 -0.13 39 39
GNAI3 0.014 0.038 -9999 0 -0.29 8 8
G12/G13 0.009 0.059 -9999 0 -0.19 39 39
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.001 0.068 -9999 0 -0.22 39 39
S1P1/S1P 0.019 0.033 -9999 0 -0.18 10 10
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.046 0.11 -9999 0 -0.2 157 157
S1P/S1P5/G12 0.01 0.044 -9999 0 -0.14 39 39
S1P/S1P3/Gq 0.024 0.03 -9999 0 -0.18 8 8
S1P/S1P4/Gi -0.037 0.12 -9999 0 -0.23 127 127
GNAQ 0.015 0.023 -9999 0 -0.11 17 17
GNAZ -0.008 0.083 -9999 0 -0.23 56 56
GNA14 0.015 0.022 -9999 0 -0.11 15 15
GNA15 0.012 0.033 -9999 0 -0.12 26 26
GNA12 -0.005 0.082 -9999 0 -0.29 39 39
GNA13 0.016 0.021 -9999 0 -0.11 14 14
GNA11 0.003 0.069 -9999 0 -0.29 27 27
ABCC1 0.015 0.023 -9999 0 -0.11 17 17
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.028 0.031 -10000 0 -0.13 21 21
ER alpha/Gai/GDP/Gbeta gamma -0.037 0.18 -10000 0 -0.41 72 72
AKT1 -0.038 0.19 -10000 0 -0.59 44 44
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.036 0.19 -10000 0 -0.59 44 44
mol:Ca2+ 0.024 0.039 -10000 0 -0.16 2 2
IGF1R -0.001 0.07 -10000 0 -0.21 46 46
E2/ER alpha (dimer)/Striatin 0.026 0 -10000 0 -10000 0 0
SHC1 0.004 0.052 -10000 0 -0.14 48 48
apoptosis 0.036 0.18 0.56 44 -10000 0 44
RhoA/GTP -0.017 0.049 -10000 0 -0.13 62 62
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.05 0.13 -10000 0 -0.38 51 51
regulation of stress fiber formation -0.008 0.06 0.2 29 -10000 0 29
E2/ERA-ERB (dimer) 0.026 0 -10000 0 -10000 0 0
KRAS 0.011 0.048 -10000 0 -0.28 14 14
G13/GTP 0.023 0.011 -10000 0 -10000 0 0
pseudopodium formation 0.008 0.06 -10000 0 -0.2 29 29
E2/ER alpha (dimer)/PELP1 0.023 0.021 -10000 0 -0.16 7 7
GRB2 0.014 0.039 -10000 0 -0.26 10 10
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 -0.014 0.085 -10000 0 -0.2 81 81
HRAS 0.009 0.055 -10000 0 -0.28 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.024 0.13 -10000 0 -0.36 52 52
E2/ER beta (dimer) 0.014 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.033 -10000 0 -0.18 1 1
mol:NADP -0.024 0.13 -10000 0 -0.36 52 52
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
mol:IP3 0.024 0.039 -10000 0 -0.16 2 2
IGF-1R heterotetramer -0.001 0.07 -10000 0 -0.21 46 46
PLCB1 0.021 0.041 -10000 0 -0.17 2 2
PLCB2 0.023 0.04 -10000 0 -0.17 2 2
IGF1 0.014 0.025 -10000 0 -0.11 21 21
mol:L-citrulline -0.024 0.13 -10000 0 -0.36 52 52
RHOA 0.015 0.036 -10000 0 -0.29 7 7
Gai/GDP -0.082 0.24 -10000 0 -0.7 64 64
JNK cascade 0.014 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.019 0 -10000 0 -10000 0 0
GNAQ 0.015 0.023 -10000 0 -0.11 17 17
ESR1 0.019 0 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma -0.004 0.15 -10000 0 -0.52 36 36
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.003 0.14 -10000 0 -0.73 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.026 0.14 -10000 0 -0.37 56 56
GNAZ -0.008 0.083 -10000 0 -0.23 56 56
E2/ER alpha (dimer) 0.014 0 -10000 0 -10000 0 0
STRN 0.019 0 -10000 0 -10000 0 0
GNAL 0.018 0.01 -10000 0 -0.11 3 3
PELP1 0.015 0.036 -10000 0 -0.29 7 7
MAPK11 0.018 0 -10000 0 -10000 0 0
GNAI2 0 0.074 -10000 0 -0.28 34 34
GNAI3 0.014 0.038 -10000 0 -0.29 8 8
GNAI1 -0.046 0.11 -10000 0 -0.2 157 157
HBEGF -0.068 0.16 -10000 0 -0.4 74 74
cAMP biosynthetic process 0.022 0.004 -10000 0 -10000 0 0
SRC -0.042 0.17 -10000 0 -0.39 72 72
PI3K -0.016 0.093 -10000 0 -0.21 88 88
GNB1 0.007 0.061 -10000 0 -0.29 21 21
G13/GDP/Gbeta gamma 0.019 0.045 -10000 0 -0.2 10 10
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.05 0.11 -10000 0 -0.3 60 60
Gs family/GTP 0.028 0.005 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.068 -10000 0 -0.17 59 59
vasodilation -0.022 0.13 -10000 0 -0.35 52 52
mol:DAG 0.024 0.039 -10000 0 -0.16 2 2
Gs family/GDP/Gbeta gamma -0.01 0.033 -10000 0 -0.19 10 10
MSN 0.008 0.064 -10000 0 -0.22 28 28
Gq family/GTP 0.021 0.042 -10000 0 -0.19 2 2
mol:PI-3-4-5-P3 -0.034 0.18 -10000 0 -0.57 44 44
NRAS -0.01 0.086 -10000 0 -0.24 59 59
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.022 0.13 0.35 52 -10000 0 52
GRB2/SOS1 0.011 0.026 -10000 0 -0.17 10 10
RhoA/GDP 0.024 0.04 -10000 0 -0.22 4 4
NOS3 -0.026 0.14 -10000 0 -0.38 52 52
GNA11 0.003 0.069 -10000 0 -0.29 27 27
MAPKKK cascade 0 0.11 -10000 0 -0.41 20 20
E2/ER alpha (dimer)/PELP1/Src -0.026 0.14 -10000 0 -0.4 51 51
ruffle organization 0.008 0.06 -10000 0 -0.2 29 29
ROCK2 0.012 0.056 -10000 0 -0.12 63 63
GNA14 0.015 0.022 -10000 0 -0.11 15 15
GNA15 0.012 0.033 -10000 0 -0.12 26 26
GNA13 0.016 0.021 -10000 0 -0.11 14 14
MMP9 -0.069 0.16 -10000 0 -0.38 87 87
MMP2 -0.05 0.17 -10000 0 -0.41 72 72
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.001 0.061 -9999 0 -0.16 60 60
TRAF2/ASK1 0.007 0.054 -9999 0 -0.16 49 49
ATM 0.01 0.042 -9999 0 -0.15 30 30
MAP2K3 0.001 0.085 -9999 0 -0.3 28 28
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.002 0.088 -9999 0 -0.24 54 54
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.005 0.041 -9999 0 -0.11 58 58
TXN 0.002 0.037 -9999 0 -0.24 12 12
CALM1 0.007 0.056 -9999 0 -0.21 28 28
GADD45A -0.022 0.1 -9999 0 -0.26 78 78
GADD45B -0.005 0.072 -9999 0 -0.18 66 66
MAP3K1 0.015 0.022 -9999 0 -0.11 16 16
MAP3K6 0.016 0.019 -9999 0 -0.11 11 11
MAP3K7 0.007 0.059 -9999 0 -0.25 24 24
MAP3K4 -0.002 0.076 -9999 0 -0.26 39 39
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.003 0.066 -9999 0 -0.19 51 51
TAK1/TAB family -0.004 0.075 -9999 0 -0.28 30 30
RAC1/OSM/MEKK3 0.022 0.019 -9999 0 -0.14 7 7
TRAF2 0.019 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.015 0.064 -9999 0 -0.25 28 28
TRAF6 0.008 0.047 -9999 0 -0.23 20 20
RAC1 0.015 0.036 -9999 0 -0.29 7 7
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.048 0.11 -9999 0 -0.19 166 166
CCM2 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.019 0.08 -9999 0 -0.18 88 88
MAPK11 0.019 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.023 0.092 -9999 0 -0.16 128 128
OSM/MEKK3 0.014 0.004 -9999 0 -0.07 1 1
TAOK1 0.003 0.028 -9999 0 -0.24 6 6
TAOK2 0.012 0.028 -9999 0 -0.23 6 6
TAOK3 0.005 0.052 -9999 0 -0.24 20 20
MAP3K7IP1 0.019 0 -9999 0 -10000 0 0
MAPK14 0.018 0.013 -9999 0 -0.11 5 5
MAP3K7IP2 0.008 0.057 -9999 0 -0.27 20 20
MAP3K5 -0.014 0.092 -9999 0 -0.25 65 65
MAP3K10 0.019 0 -9999 0 -10000 0 0
MAP3K3 0.019 0.006 -9999 0 -0.11 1 1
TRX/ASK1 0.009 0.043 -9999 0 -0.24 12 12
GADD45/MTK1/MTK1 -0.007 0.086 -9999 0 -0.16 95 95
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.025 0.026 -10000 0 -0.19 7 7
Necdin/E2F1 -0.059 0.096 -10000 0 -0.19 168 168
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.025 0.048 -10000 0 -0.15 24 24
NGF (dimer)/p75(NTR)/BEX1 -0.023 0.073 -10000 0 -0.16 111 111
NT-4/5 (dimer)/p75(NTR) 0.003 0.028 -10000 0 -0.07 70 70
IKBKB 0.019 0 -10000 0 -10000 0 0
AKT1 -0.016 0.08 -10000 0 -0.17 84 84
IKBKG 0.019 0 -10000 0 -10000 0 0
BDNF 0.004 0.042 -10000 0 -0.11 62 62
MGDIs/NGR/p75(NTR)/LINGO1 0.004 0.023 -10000 0 -10000 0 0
FURIN 0.018 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.017 0.044 -10000 0 -0.12 20 20
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.016 0.059 -10000 0 -0.3 15 15
proBDNF (dimer) 0.004 0.042 -10000 0 -0.11 62 62
NTRK1 0.018 0.011 -10000 0 -0.11 4 4
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis -0.006 0.12 -10000 0 -0.4 32 32
IRAK1 0.008 0.057 -10000 0 -0.27 20 20
SHC1 0.004 0.029 -10000 0 -0.11 6 6
ARHGDIA 0.015 0.022 -10000 0 -0.11 15 15
RhoA/GTP 0.011 0.024 -10000 0 -0.2 7 7
Gamma Secretase 0.041 0.063 -10000 0 -0.17 33 33
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.005 0.06 -10000 0 -0.14 69 69
MAGEH1 -0.018 0.098 -10000 0 -0.25 72 72
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.043 0.078 -10000 0 -0.14 188 188
Mammalian IAPs/DIABLO 0.023 0.037 -10000 0 -0.21 6 6
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.004 0.066 -10000 0 -0.28 26 26
APP 0.013 0.042 -10000 0 -0.29 10 10
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0 0.072 -10000 0 -0.26 36 36
RhoA/GDP/RHOGDI 0.018 0.031 -10000 0 -0.11 14 14
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.023 0.047 0.11 95 -0.1 12 107
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.006 0.067 -10000 0 -0.19 46 46
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.015 0.028 -10000 0 -0.16 2 2
NCSTN 0.008 0.056 -10000 0 -0.26 20 20
mol:GTP 0.003 0.05 -10000 0 -0.16 35 35
PSENEN 0.013 0.041 -10000 0 -0.27 10 10
mol:ceramide 0.013 0.027 -10000 0 -0.13 7 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.061 -10000 0 -0.19 35 35
p75(NTR)/beta APP 0.012 0.042 -10000 0 -0.19 10 10
BEX1 -0.047 0.12 -10000 0 -0.26 125 125
mol:GDP -0.001 0.021 -10000 0 -10000 0 0
NGF (dimer) 0.017 0.034 -10000 0 -0.093 1 1
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.014 0.027 -10000 0 -0.098 7 7
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
RAC1/GTP 0.012 0.027 -10000 0 -0.13 7 7
MYD88 0 0.075 -10000 0 -0.29 33 33
CHUK 0.016 0.025 -10000 0 -0.15 10 10
NGF (dimer)/p75(NTR)/PKA 0.004 0.05 -10000 0 -0.16 35 35
RHOB -0.012 0.087 -10000 0 -0.29 43 43
RHOA 0.015 0.036 -10000 0 -0.29 7 7
MAGE-G1/E2F1 0.014 0.004 -10000 0 -0.07 1 1
NT3 (dimer) 0.018 0.01 -10000 0 -0.11 3 3
TP53 0.004 0.054 -10000 0 -0.14 41 41
PRDM4 0.013 0.027 -10000 0 -0.13 7 7
BDNF (dimer) 0.017 0.045 -10000 0 -0.14 4 4
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
SORT1 0.016 0.031 -10000 0 -0.24 7 7
activation of caspase activity 0.022 0.046 -10000 0 -0.14 24 24
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.024 0.033 -10000 0 -0.13 9 9
RHOC 0.012 0.045 -10000 0 -0.28 12 12
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.004 0.099 -10000 0 -0.28 44 44
DIABLO 0.016 0.028 -10000 0 -0.26 5 5
SMPD2 0.013 0.027 -10000 0 -0.13 7 7
APH1B 0.018 0.02 -10000 0 -0.23 3 3
APH1A 0.015 0.036 -10000 0 -0.27 8 8
proNGF (dimer)/p75(NTR)/Sortilin 0.014 0.032 -10000 0 -0.15 7 7
PSEN1 0.011 0.047 -10000 0 -0.26 15 15
APAF-1/Pro-Caspase 9 0.025 0.02 -10000 0 -0.19 2 2
NT3 (dimer)/p75(NTR) 0.016 0.032 -10000 0 -0.14 1 1
MAPK8 0.016 0.06 -10000 0 -0.23 17 17
MAPK9 0.015 0.065 -10000 0 -0.25 20 20
APAF1 0.019 0 -10000 0 -10000 0 0
NTF3 0.018 0.01 -10000 0 -0.11 3 3
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.1 0.14 -10000 0 -0.22 269 269
RAC1/GDP 0.011 0.024 -10000 0 -0.2 7 7
RhoA-B-C/GDP 0.005 0.075 -10000 0 -0.17 65 65
p75 CTF/Sortilin/TRAF6/NRIF 0.035 0.048 -10000 0 -0.14 35 35
RhoA-B-C/GTP 0.003 0.049 -10000 0 -0.16 35 35
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.024 0.057 -10000 0 -0.13 35 35
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.027 0.044 -10000 0 -0.16 7 7
PRKACB -0.002 0.076 -10000 0 -0.26 39 39
proBDNF (dimer)/p75 ECD 0.017 0.032 -10000 0 -0.14 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0 0.046 -10000 0 -0.11 78 78
BIRC2 0.016 0.03 -10000 0 -0.29 5 5
neuron projection morphogenesis -0.033 0.075 0.11 46 -0.17 65 111
BAD 0.01 0.08 -10000 0 -0.26 28 28
RIPK2 0.017 0.021 -10000 0 -0.18 5 5
NGFR 0.002 0.044 -10000 0 -0.11 70 70
CYCS 0.01 0.042 -10000 0 -0.14 28 28
ADAM17 0.017 0.015 -10000 0 -0.11 7 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.025 0.03 -10000 0 -0.14 4 4
BCL2L11 0.011 0.078 -10000 0 -0.26 27 27
BDNF (dimer)/p75(NTR) 0.006 0.043 -10000 0 -0.14 13 13
PI3K -0.008 0.074 -10000 0 -0.15 94 94
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.014 0.029 -10000 0 -0.14 7 7
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.011 0.045 -10000 0 -0.21 19 19
PRKCI 0.015 0.028 -10000 0 -0.14 15 15
NGF (dimer)/p75(NTR) 0.003 0.028 -10000 0 -0.07 70 70
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.017 0.048 -10000 0 -0.14 30 30
TRAF6 0.018 0.019 -10000 0 -0.29 2 2
RAC1 0.015 0.036 -10000 0 -0.29 7 7
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.019 0 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.012 0.035 -10000 0 -0.19 6 6
SQSTM1 0.004 0.062 -10000 0 -0.22 32 32
NGFRAP1 0.011 0.048 -10000 0 -0.29 13 13
CASP3 0.01 0.078 -10000 0 -0.25 29 29
E2F1 0.019 0.006 -10000 0 -0.11 1 1
CASP9 0.014 0.029 -10000 0 -0.13 18 18
IKK complex 0.031 0.054 -10000 0 -0.27 10 10
NGF (dimer)/TRKA 0.014 0.007 -10000 0 -0.07 4 4
MMP7 -0.014 0.057 -10000 0 -0.11 135 135
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.023 0.049 -10000 0 -0.13 35 35
MMP3 0.015 0.022 -10000 0 -0.11 15 15
APAF-1/Caspase 9 -0.009 0.036 -10000 0 -0.16 20 20
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.031 0.22 -10000 0 -0.88 31 31
regulation of axonogenesis -0.012 0.041 0.15 30 -10000 0 30
myoblast fusion 0.005 0.098 0.38 31 -10000 0 31
mol:GTP -0.001 0.056 -10000 0 -0.22 31 31
regulation of calcium-dependent cell-cell adhesion -0.004 0.068 0.19 53 -10000 0 53
ARF1/GTP 0.01 0.05 -10000 0 -0.16 36 36
mol:GM1 -0.001 0.041 -10000 0 -0.16 30 30
mol:Choline 0.012 0.037 -10000 0 -0.13 30 30
lamellipodium assembly -0.006 0.11 -10000 0 -0.42 31 31
MAPK3 0.003 0.08 -10000 0 -0.3 31 31
ARF6/GTP/NME1/Tiam1 0.004 0.068 -10000 0 -0.19 53 53
ARF1 0.014 0.036 -10000 0 -0.29 7 7
ARF6/GDP -0.005 0.098 -10000 0 -0.39 31 31
ARF1/GDP 0.003 0.094 -10000 0 -0.35 33 33
ARF6 0.01 0.033 -10000 0 -0.12 30 30
RAB11A 0.016 0.033 -10000 0 -0.29 6 6
TIAM1 0.001 0.067 -10000 0 -0.23 35 35
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.001 0.082 -10000 0 -0.31 31 31
actin filament bundle formation -0.001 0.095 0.35 33 -10000 0 33
KALRN -0.001 0.075 -10000 0 -0.29 31 31
RAB11FIP3/RAB11A 0.021 0.04 -10000 0 -0.22 12 12
RhoA/GDP 0.001 0.096 -10000 0 -0.36 33 33
NME1 -0.001 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.094 -10000 0 -0.35 32 32
substrate adhesion-dependent cell spreading -0.001 0.056 -10000 0 -0.22 31 31
cortical actin cytoskeleton organization -0.006 0.11 -10000 0 -0.42 31 31
RAC1 0.015 0.036 -10000 0 -0.29 7 7
liver development -0.001 0.056 -10000 0 -0.22 31 31
ARF6/GTP -0.001 0.056 -10000 0 -0.22 31 31
RhoA/GTP 0.011 0.051 -10000 0 -0.17 35 35
mol:GDP -0.006 0.098 -10000 0 -0.39 31 31
ARF6/GTP/RAB11FIP3/RAB11A 0.019 0.052 -10000 0 -0.14 41 41
RHOA 0.015 0.036 -10000 0 -0.29 7 7
PLD1 0.009 0.043 -10000 0 -0.16 30 30
RAB11FIP3 0.013 0.041 -10000 0 -0.21 15 15
tube morphogenesis -0.006 0.11 -10000 0 -0.42 31 31
ruffle organization 0.012 0.041 -10000 0 -0.15 30 30
regulation of epithelial cell migration -0.001 0.056 -10000 0 -0.22 31 31
PLD2 0.009 0.043 -10000 0 -0.16 30 30
PIP5K1A 0.012 0.041 -10000 0 -0.15 30 30
mol:Phosphatidic acid 0.012 0.037 -10000 0 -0.13 30 30
Rac1/GTP -0.006 0.11 -10000 0 -0.42 31 31
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.034 0.16 -10000 0 -0.51 53 53
HDAC1 0.019 0.033 -10000 0 -0.2 8 8
AES 0.013 0.045 -10000 0 -0.22 16 16
FBXW11 0.011 0.047 -10000 0 -0.27 14 14
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.021 0.026 -10000 0 -0.16 2 2
TLE1 0.017 0.026 -10000 0 -0.2 6 6
AP1 -0.025 0.099 -10000 0 -0.23 84 84
NCSTN 0.008 0.056 -10000 0 -0.26 20 20
ADAM10 0.008 0.036 -10000 0 -0.11 45 45
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.01 0.12 -10000 0 -0.41 23 23
NICD/RBPSUH -0.025 0.17 -10000 0 -0.51 53 53
WIF1 -0.006 0.051 -10000 0 -0.11 100 100
NOTCH1 -0.034 0.17 -10000 0 -0.53 53 53
PSENEN 0.013 0.041 -10000 0 -0.28 10 10
KREMEN2 0.019 0.006 -10000 0 -0.11 1 1
DKK1 -0.018 0.058 -10000 0 -0.11 150 150
beta catenin/beta TrCP1 0.016 0.068 -10000 0 -0.29 16 16
APH1B 0.018 0.02 -10000 0 -0.23 3 3
APH1A 0.015 0.036 -10000 0 -0.27 8 8
AXIN1 -0.005 0.056 0.19 7 -0.19 3 10
CtBP/CBP/TCF1/TLE1/AES 0.035 0.071 0.26 9 -0.32 5 14
PSEN1 0.011 0.047 -10000 0 -0.26 15 15
FOS -0.046 0.12 -10000 0 -0.22 146 146
JUN -0.002 0.077 -10000 0 -0.28 37 37
MAP3K7 0.012 0.048 -10000 0 -0.24 17 17
CTNNB1 0.008 0.06 -10000 0 -0.26 14 14
MAPK3 0.019 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.031 0.025 -10000 0 -0.13 2 2
HNF1A 0.02 0.005 -10000 0 -10000 0 0
CTBP1 0.01 0.055 -10000 0 -0.29 17 17
MYC -0.12 0.39 -10000 0 -1.3 54 54
NKD1 0 0.002 -10000 0 -10000 0 0
FZD1 0.015 0.023 -10000 0 -0.11 17 17
NOTCH1 precursor/Deltex homolog 1 -0.034 0.16 -10000 0 -0.5 53 53
apoptosis -0.025 0.099 -10000 0 -0.23 84 84
Delta 1/NOTCHprecursor -0.034 0.16 -10000 0 -0.5 53 53
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.008 0.033 -10000 0 -10000 0 0
Gamma Secretase 0.04 0.063 -10000 0 -0.18 33 33
APC -0.04 0.17 0.19 7 -0.65 33 40
DVL1 0.007 0.1 -10000 0 -0.45 22 22
CSNK2A1 0.009 0.053 -10000 0 -0.29 16 16
MAP3K7IP1 0.021 0.007 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.012 0.041 -10000 0 -0.12 6 6
LRP6 0.013 0.029 -10000 0 -0.12 22 22
CSNK1A1 0.014 0.038 -10000 0 -0.29 8 8
NLK 0.013 0.064 -10000 0 -0.25 25 25
CCND1 -0.097 0.34 -10000 0 -1.3 39 39
WNT1 0.019 0.006 -10000 0 -10000 0 0
Axin1/APC/beta catenin -0.01 0.13 0.2 3 -0.4 42 45
DKK2 0.013 0.028 -10000 0 -0.11 25 25
NOTCH1 precursor/DVL1 -0.024 0.19 -10000 0 -0.51 61 61
GSK3B 0.004 0.066 -10000 0 -0.26 29 29
FRAT1 0.016 0.023 -10000 0 -0.12 12 12
NOTCH/Deltex homolog 1 -0.034 0.16 -10000 0 -0.51 53 53
PPP2R5D 0.014 0.041 -10000 0 -0.18 18 18
MAPK1 0.009 0.051 -10000 0 -0.22 22 22
WNT1/LRP6/FZD1 0.027 0.039 -10000 0 -0.14 2 2
RBPJ 0.012 0.041 -10000 0 -0.2 17 17
CREBBP 0.018 0.008 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.024 0.011 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0.019 -9999 0 -0.11 11 11
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.019 0.006 -9999 0 -0.11 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.014 0.034 -9999 0 -0.18 13 13
RAC1-CDC42/GTP/PAK family -0.006 0.063 -9999 0 -0.16 71 71
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.005 0.061 -9999 0 -0.24 28 28
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.019 0.006 -9999 0 -0.11 1 1
FYN -0.019 0.1 -9999 0 -0.28 68 68
MAP3K12 0.019 0 -9999 0 -10000 0 0
FGR 0.005 0.048 -9999 0 -0.14 46 46
p38 alpha/TAB1 0 0.1 -9999 0 -0.23 64 64
PRKG1 0.019 0 -9999 0 -10000 0 0
DUSP8 0.013 0.027 -9999 0 -0.11 24 24
PGK/cGMP/p38 alpha -0.003 0.1 -9999 0 -0.23 63 63
apoptosis 0 0.1 -9999 0 -0.22 64 64
RAL/GTP 0.014 0.043 -9999 0 -0.16 27 27
LYN -0.018 0.098 -9999 0 -0.25 72 72
DUSP1 -0.005 0.065 -9999 0 -0.15 74 74
PAK1 0.017 0.017 -9999 0 -0.11 9 9
SRC 0.019 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.034 0.021 -9999 0 -0.14 7 7
TRAF6 0.018 0.019 -9999 0 -0.29 2 2
RAC1 0.015 0.036 -9999 0 -0.29 7 7
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.022 0.023 -9999 0 -0.16 7 7
MAPK11 -0.019 0.13 -9999 0 -0.29 76 76
BLK 0.018 0.011 -9999 0 -0.11 4 4
HCK -0.033 0.11 -9999 0 -0.21 120 120
MAP2K3 0.018 0.01 -9999 0 -0.11 3 3
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 0.01 0.035 -9999 0 -0.12 36 36
TRAF6/MEKK3 0.024 0.011 -9999 0 -0.14 2 2
MAP3K7IP1 0.019 0 -9999 0 -10000 0 0
MAPK14 -0.009 0.11 -9999 0 -0.25 65 65
positive regulation of innate immune response -0.018 0.15 -9999 0 -0.33 73 73
LCK 0.017 0.016 -9999 0 -0.11 8 8
p38alpha-beta/MKP7 -0.02 0.14 -9999 0 -0.32 73 73
p38alpha-beta/MKP5 -0.012 0.14 -9999 0 -0.32 72 72
PGK/cGMP 0.014 0 -9999 0 -10000 0 0
PAK2 0.014 0.028 -9999 0 -0.29 1 1
p38alpha-beta/MKP1 -0.017 0.15 -9999 0 -0.32 75 75
CDC42 0.017 0.016 -9999 0 -0.11 8 8
RALB 0.013 0.037 -9999 0 -0.18 15 15
RALA 0.005 0.063 -9999 0 -0.26 26 26
PAK3 -0.04 0.11 -9999 0 -0.19 146 146
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.003 0.1 -10000 0 -0.32 31 31
PDGFB-D/PDGFRB/SLAP -0.019 0.09 -10000 0 -0.21 82 82
PDGFB-D/PDGFRB/APS/CBL 0.021 0.025 -10000 0 -0.16 8 8
AKT1 0 0.082 -10000 0 -0.22 46 46
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.001 0.098 -10000 0 -0.36 24 24
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
FGR -0.014 0.097 -10000 0 -0.5 13 13
mol:Ca2+ -0.003 0.099 -10000 0 -0.4 22 22
MYC -0.066 0.25 -10000 0 -0.71 64 64
SHC1 0.004 0.052 -10000 0 -0.14 48 48
HRAS/GDP 0.016 0.059 -10000 0 -0.15 50 50
LRP1/PDGFRB/PDGFB 0.017 0.059 -10000 0 -0.17 37 37
GRB10 -0.018 0.091 -10000 0 -0.2 89 89
PTPN11 0.015 0.033 -10000 0 -0.27 7 7
GO:0007205 -0.004 0.1 -10000 0 -0.4 22 22
PTEN 0.013 0.038 -10000 0 -0.18 17 17
GRB2 0.014 0.039 -10000 0 -0.26 10 10
GRB7 0.016 0.019 -10000 0 -0.11 11 11
PDGFB-D/PDGFRB/SHP2 0.02 0.038 -10000 0 -0.2 14 14
PDGFB-D/PDGFRB/GRB10 -0.004 0.071 -10000 0 -0.2 52 52
cell cycle arrest -0.019 0.09 -10000 0 -0.21 82 82
HRAS 0.009 0.055 -10000 0 -0.28 18 18
HIF1A 0.001 0.082 -10000 0 -0.22 47 47
GAB1 -0.016 0.12 -10000 0 -0.37 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.012 0.11 -10000 0 -0.32 40 40
PDGFB-D/PDGFRB 0.027 0.041 -10000 0 -0.17 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.016 0.047 -10000 0 -0.2 22 22
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.001 0.11 -10000 0 -0.27 55 55
positive regulation of MAPKKK cascade 0.019 0.038 -10000 0 -0.2 14 14
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
mol:IP3 -0.004 0.1 -10000 0 -0.41 22 22
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.013 0.044 -10000 0 -0.29 11 11
PDGFB-D/PDGFRB/GRB7 0.021 0.035 -10000 0 -0.21 9 9
SHB 0.016 0.02 -10000 0 -0.11 13 13
BLK -0.001 0.044 -10000 0 -0.23 8 8
PTPN2 0.017 0.013 -10000 0 -0.11 5 5
PDGFB-D/PDGFRB/SNX15 0.022 0.031 -10000 0 -0.2 8 8
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.03 0.15 -10000 0 -0.34 70 70
CBL 0.019 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.022 0.031 -10000 0 -0.2 8 8
LCK -0.003 0.045 -10000 0 -0.26 7 7
PDGFRB 0.01 0.044 -10000 0 -0.18 21 21
ACP1 0.01 0.051 -10000 0 -0.25 18 18
HCK -0.073 0.19 -10000 0 -0.51 73 73
ABL1 -0.017 0.11 -10000 0 -0.32 42 42
PDGFB-D/PDGFRB/CBL -0.018 0.13 -10000 0 -0.42 35 35
PTPN1 0.013 0.043 -10000 0 -0.3 10 10
SNX15 0.019 0 -10000 0 -10000 0 0
STAT3 -0.003 0.079 -10000 0 -0.29 37 37
STAT1 0.008 0.04 -10000 0 -0.12 41 41
cell proliferation -0.056 0.22 -10000 0 -0.61 66 66
SLA -0.04 0.11 -10000 0 -0.22 127 127
actin cytoskeleton reorganization 0.024 0.049 -10000 0 -0.15 32 32
SRC -0.002 0.043 -10000 0 -0.23 9 9
PI3K -0.028 0.061 -10000 0 -0.2 41 41
PDGFB-D/PDGFRB/GRB7/SHC 0.023 0.045 -10000 0 -0.16 21 21
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.001 0.1 -10000 0 -0.37 24 24
LYN -0.058 0.16 -10000 0 -0.47 65 65
LRP1 -0.007 0.079 -10000 0 -0.21 61 61
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.018 0.015 -10000 0 -0.2 2 2
STAT5A 0.019 0.008 -10000 0 -0.11 2 2
NCK1-2/p130 Cas 0.03 0.053 -10000 0 -0.15 32 32
SPHK1 0.008 0.037 -10000 0 -0.11 46 46
EDG1 0.001 0.068 -10000 0 -0.22 39 39
mol:DAG -0.004 0.1 -10000 0 -0.41 22 22
PLCG1 -0.004 0.1 -10000 0 -0.42 22 22
NHERF/PDGFRB 0.028 0.038 -10000 0 -0.16 15 15
YES1 -0.024 0.12 -10000 0 -0.48 29 29
cell migration 0.027 0.038 -10000 0 -0.16 15 15
SHC/Grb2/SOS1 0.027 0.052 -10000 0 -0.15 30 30
SLC9A3R2 0.019 0 -10000 0 -10000 0 0
SLC9A3R1 0.01 0.042 -10000 0 -0.15 30 30
NHERF1-2/PDGFRB/PTEN 0.035 0.043 -10000 0 -0.14 22 22
FYN -0.067 0.2 -10000 0 -0.56 66 66
DOK1 0.02 0.032 -10000 0 -0.14 18 18
HRAS/GTP 0.007 0.037 -10000 0 -0.2 17 17
PDGFB 0.019 0 -10000 0 -10000 0 0
RAC1 -0.043 0.19 -10000 0 -0.47 73 73
PRKCD 0.017 0.037 -10000 0 -0.14 22 22
FER 0.019 0.034 -10000 0 -0.14 18 18
MAPKKK cascade -0.008 0.038 0.091 3 -0.14 28 31
RASA1 0.017 0.041 -10000 0 -0.18 18 18
NCK1 0.014 0.036 -10000 0 -0.19 14 14
NCK2 0.009 0.054 -10000 0 -0.28 17 17
p62DOK/Csk 0.029 0.04 -10000 0 -0.13 26 26
PDGFB-D/PDGFRB/SHB 0.02 0.035 -10000 0 -0.2 9 9
chemotaxis -0.016 0.11 -10000 0 -0.32 42 42
STAT1-3-5/STAT1-3-5 0.024 0.054 -10000 0 -0.14 32 32
Bovine Papilomavirus E5/PDGFRB 0.008 0.03 -10000 0 -0.19 9 9
PTPRJ 0.019 0 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.025 0.093 -10000 0 -0.31 14 14
CRKL 0.021 0.049 -10000 0 -0.17 8 8
mol:DAG 0.011 0.09 -10000 0 -0.21 59 59
HRAS 0.015 0.067 -10000 0 -0.21 27 27
MAPK8 0.012 0.054 -10000 0 -0.14 57 57
RAP1A 0.021 0.05 -10000 0 -0.17 11 11
GAB1 0.016 0.053 -10000 0 -0.19 12 12
MAPK14 0.011 0.054 -10000 0 -0.14 57 57
EPO 0.02 0.006 -10000 0 -10000 0 0
PLCG1 0.011 0.091 -10000 0 -0.22 59 59
EPOR/TRPC2/IP3 Receptors 0.02 0.006 -10000 0 -10000 0 0
RAPGEF1 0.019 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.04 0.009 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.019 0.064 -10000 0 -0.2 24 24
EPO/EPOR (dimer) 0.029 0.013 -10000 0 -10000 0 0
IRS2 0.01 0.068 -10000 0 -0.22 32 32
STAT1 0.015 0.094 -10000 0 -0.3 25 25
STAT5B 0.016 0.09 -10000 0 -0.21 57 57
cell proliferation 0.013 0.049 -10000 0 -0.12 57 57
GAB1/SHIP/PIK3R1/SHP2/SHC 0.002 0.075 -10000 0 -0.2 44 44
TEC 0.021 0.048 -10000 0 -0.17 8 8
SOCS3 0.019 0 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.092 -10000 0 -0.29 25 25
JAK2 0.014 0.028 -10000 0 -0.11 23 23
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
EPO/EPOR (dimer)/JAK2 0.044 0.061 -10000 0 -0.12 45 45
EPO/EPOR 0.029 0.013 -10000 0 -10000 0 0
LYN -0.017 0.098 -10000 0 -0.25 72 72
TEC/VAV2 0.033 0.05 -10000 0 -0.18 6 6
elevation of cytosolic calcium ion concentration 0.02 0.006 -10000 0 -10000 0 0
SHC1 0.004 0.052 -10000 0 -0.14 48 48
EPO/EPOR (dimer)/LYN 0.022 0.068 -10000 0 -0.16 57 57
mol:IP3 0.011 0.09 -10000 0 -0.21 59 59
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.002 0.09 -10000 0 -0.23 51 51
SH2B3 0.013 0.037 -10000 0 -0.15 20 20
NFKB1 0.01 0.057 -10000 0 -0.14 59 59
EPO/EPOR (dimer)/JAK2/SOCS3 0.031 0.052 0.2 43 -10000 0 43
PTPN6 0.018 0.048 -10000 0 -0.12 44 44
TEC/VAV2/GRB2 0.039 0.057 -10000 0 -0.22 10 10
EPOR 0.02 0.006 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.064 -10000 0 -0.2 24 24
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 -0.002 0.069 -10000 0 -0.19 52 52
CRKL/CBL/C3G 0.041 0.05 -10000 0 -0.2 4 4
VAV2 0.021 0.048 -10000 0 -0.17 8 8
CBL 0.021 0.048 -10000 0 -0.17 8 8
SHC/Grb2/SOS1 0.013 0.058 -10000 0 -0.2 22 22
STAT5A 0.016 0.09 -10000 0 -0.21 57 57
GRB2 0.014 0.039 -10000 0 -0.26 10 10
STAT5 (dimer) 0.036 0.089 -10000 0 -0.25 23 23
LYN/PLCgamma2 -0.009 0.095 -10000 0 -0.23 72 72
PTPN11 0.015 0.033 -10000 0 -0.27 7 7
BTK 0.02 0.05 -10000 0 -0.17 9 9
BCL2 0.027 0.092 -10000 0 -0.37 5 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.018 0.01 -9999 0 -0.11 3 3
Rac1/GDP 0.01 0.034 -9999 0 -0.29 7 7
DOCK1 0.011 0.047 -9999 0 -0.22 19 19
ITGA4 0.016 0.019 -9999 0 -0.11 12 12
RAC1 0.015 0.036 -9999 0 -0.29 7 7
alpha4/beta7 Integrin 0.026 0.016 -9999 0 -0.14 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.009 0.054 -9999 0 -0.28 17 17
alpha4/beta1 Integrin 0.037 0.012 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.038 0.015 -9999 0 -10000 0 0
lamellipodium assembly -0.028 0.15 -9999 0 -0.34 87 87
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
PI3K -0.016 0.093 -9999 0 -0.21 88 88
ARF6 0.018 0.015 -9999 0 -0.2 2 2
TLN1 -0.003 0.065 -9999 0 -0.16 64 64
PXN 0.02 0.007 -9999 0 -10000 0 0
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
ARF6/GTP 0.044 0.014 -9999 0 -10000 0 0
cell adhesion 0.034 0.038 -9999 0 -0.12 18 18
CRKL/CBL 0.028 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.038 0.013 -9999 0 -10000 0 0
ITGB1 0.019 0 -9999 0 -10000 0 0
ITGB7 0.018 0.01 -9999 0 -0.11 3 3
ARF6/GDP 0.013 0.014 -9999 0 -0.2 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.005 0.074 -9999 0 -0.12 140 140
p130Cas/Crk/Dock1 0.015 0.044 -9999 0 -0.18 24 24
VCAM1 -0.079 0.14 -9999 0 -0.24 202 202
alpha4/beta1 Integrin/Paxillin/Talin 0.036 0.039 -9999 0 -0.12 18 18
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.014 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP -0.046 0.013 -9999 0 -10000 0 0
CBL 0.019 0 -9999 0 -10000 0 0
PRKACA 0.019 0 -9999 0 -10000 0 0
GIT1 0.019 0.006 -9999 0 -0.11 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.036 0.039 -9999 0 -0.12 18 18
Rac1/GTP -0.033 0.16 -9999 0 -0.37 87 87
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.017 0.074 -9999 0 -0.34 16 16
KLHL20 0.011 0.065 -9999 0 -0.2 29 29
CYFIP2 -0.02 0.099 -9999 0 -0.25 75 75
Rac1/GDP 0.028 0.072 -9999 0 -0.28 23 23
ENAH 0.012 0.087 -9999 0 -0.38 20 20
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 0 22 22
RAP1A 0.018 0.019 -9999 0 -0.29 2 2
CTNNB1 0.017 0.023 -9999 0 -0.29 3 3
CDC42/GTP -0.012 0.052 -9999 0 -0.23 23 23
ABI1/Sra1/Nap1 -0.019 0.043 -9999 0 -0.14 44 44
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.04 0.033 -9999 0 -0.14 11 11
RAPGEF1 0.02 0.074 -9999 0 -0.31 21 21
CTNND1 0.001 0.073 -9999 0 -0.29 31 31
regulation of calcium-dependent cell-cell adhesion 0.015 0.076 -9999 0 -0.36 16 16
CRK 0.017 0.08 -9999 0 -0.34 21 21
E-cadherin/gamma catenin/alpha catenin 0.023 0.046 -9999 0 -0.13 36 36
alphaE/beta7 Integrin 0.024 0.027 -9999 0 -0.19 7 7
IQGAP1 -0.009 0.087 -9999 0 -0.27 50 50
NCKAP1 0.019 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.024 0.01 -9999 0 -0.14 2 2
DLG1 0.015 0.078 -9999 0 -0.35 17 17
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.054 -9999 0 -0.2 36 36
MLLT4 0.019 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.015 0.036 -9999 0 -0.14 24 24
PI3K -0.026 0.071 -9999 0 -0.26 36 36
ARF6 0.018 0.015 -9999 0 -0.2 2 2
mol:Ca2+ 0 0 -9999 0 0 37 37
E-cadherin/gamma catenin 0.016 0.039 -9999 0 -0.14 25 25
TIAM1 0.003 0.066 -9999 0 -0.23 35 35
E-cadherin(dimer)/Ca2+ 0.027 0.06 -9999 0 -0.18 34 34
AKT1 0.006 0.061 -9999 0 -0.19 38 38
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
CDH1 0.012 0.03 -9999 0 -0.11 29 29
RhoA/GDP 0.029 0.069 -9999 0 -0.26 23 23
actin cytoskeleton organization 0.01 0.049 -9999 0 -0.15 29 29
CDC42/GDP 0.029 0.068 -9999 0 -0.26 22 22
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.004 0.068 -9999 0 -0.24 33 33
ITGB7 0.018 0.01 -9999 0 -0.11 3 3
RAC1 0.015 0.036 -9999 0 -0.29 7 7
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.03 0.065 -9999 0 -0.19 34 34
E-cadherin/Ca2+/beta catenin/alpha catenin 0.025 0.033 -9999 0 -0.14 15 15
mol:GDP 0.021 0.075 -9999 0 -0.31 21 21
CDC42/GTP/IQGAP1 0.009 0.053 -9999 0 -0.16 45 45
JUP 0.008 0.037 -9999 0 -0.11 47 47
p120 catenin/RhoA/GDP 0.029 0.077 -9999 0 -0.25 33 33
RAC1/GTP/IQGAP1 0.007 0.056 -9999 0 -0.16 51 51
PIP5K1C/AP1M1 0.005 0.041 -9999 0 -0.16 27 27
RHOA 0.015 0.036 -9999 0 -0.29 7 7
CDC42 0.017 0.016 -9999 0 -0.11 8 8
CTNNA1 0.011 0.048 -9999 0 -0.29 13 13
positive regulation of S phase of mitotic cell cycle 0 0.054 -9999 0 -0.14 50 50
NME1 0 0 -9999 0 0 105 105
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.014 0.081 -9999 0 -0.37 17 17
regulation of cell-cell adhesion -0.011 0.045 -9999 0 -0.2 23 23
WASF2 -0.011 0.023 -9999 0 -0.078 44 44
Rap1/GTP 0.019 0.067 -9999 0 -0.23 29 29
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.049 -9999 0 -0.14 20 20
CCND1 -0.001 0.066 -9999 0 -0.18 50 50
VAV2 0.024 0.079 -9999 0 -0.4 13 13
RAP1/GDP 0.022 0.068 -9999 0 -0.27 22 22
adherens junction assembly 0.015 0.078 -9999 0 -0.36 17 17
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.008 0.055 -9999 0 -0.24 22 22
PIP5K1C 0.006 0.061 -9999 0 -0.24 27 27
regulation of heterotypic cell-cell adhesion 0.037 0.048 -9999 0 -0.14 22 22
E-cadherin/beta catenin 0.008 0.034 -9999 0 -0.15 16 16
mol:GTP 0 0 -9999 0 0 106 106
SRC 0.017 0.074 -9999 0 -0.34 16 16
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
Rac1/GTP -0.031 0.082 -9999 0 -0.32 29 29
E-cadherin/beta catenin/alpha catenin 0.029 0.04 -9999 0 -0.17 15 15
ITGAE 0.014 0.037 -9999 0 -0.24 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.015 0.078 -9999 0 -0.36 16 16
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.041 0.041 -9999 0 -0.12 18 18
SMAD6-7/SMURF1 0.034 0.022 -9999 0 -0.15 3 3
NOG 0 0 -9999 0 -10000 0 0
SMAD9 0.017 0.046 -9999 0 -0.49 3 3
SMAD4 -0.004 0.079 -9999 0 -0.26 44 44
SMAD5 0.007 0.082 -9999 0 -0.31 25 25
BMP7/USAG1 0.022 0.024 -9999 0 -10000 0 0
SMAD5/SKI 0.017 0.08 -9999 0 -0.29 25 25
SMAD1 -0.013 0.16 -9999 0 -0.41 56 56
BMP2 -0.02 0.089 -9999 0 -0.18 101 101
SMAD1/SMAD1/SMAD4 -0.038 0.12 -9999 0 -0.34 56 56
BMPR1A 0.011 0.045 -9999 0 -0.29 10 10
BMPR1B 0.018 0.011 -9999 0 -0.11 4 4
BMPR1A-1B/BAMBI -0.009 0.075 -9999 0 -0.16 94 94
AHSG 0.019 0.008 -9999 0 -0.11 2 2
CER1 0.019 0 -9999 0 -10000 0 0
BMP2-4/CER1 0.011 0.057 -9999 0 -0.15 45 45
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.002 0.077 -9999 0 -0.26 22 22
BMP2-4 (homodimer) -0.003 0.066 -9999 0 -0.19 45 45
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.038 0.039 -9999 0 -0.14 18 18
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.019 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.001 0.054 -9999 0 -0.15 55 55
BMP2-4/USAG1 0.007 0.062 -9999 0 -0.15 54 54
SMAD6/SMURF1/SMAD5 0.017 0.08 -9999 0 -0.29 25 25
SOSTDC1 0.011 0.031 -9999 0 -0.11 32 32
BMP7/BMPR2/BMPR1A-1B 0.04 0.036 -9999 0 -0.13 18 18
SKI 0.019 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.014 0.025 -9999 0 -0.11 20 20
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.004 0.064 -9999 0 -0.25 29 29
MAP3K7 0.007 0.059 -9999 0 -0.25 24 24
BMP2-4/CHRD 0.011 0.057 -9999 0 -0.15 45 45
SMAD5/SMAD5/SMAD4 0.012 0.091 -9999 0 -0.31 29 29
MAPK1 0.009 0.051 -9999 0 -0.22 22 22
TAK1/TAB family 0.026 0.072 -9999 0 -0.25 18 18
BMP7 (homodimer) 0.017 0.015 -9999 0 -0.11 7 7
NUP214 0.019 0 -9999 0 -10000 0 0
BMP6/FETUA 0.025 0.019 -9999 0 -0.14 1 1
SMAD1/SKI -0.001 0.15 -9999 0 -0.38 56 56
SMAD6 0.019 0 -9999 0 -10000 0 0
CTDSP2 0.004 0.052 -9999 0 -0.14 50 50
BMP2-4/FETUA 0.011 0.058 -9999 0 -0.15 47 47
MAP3K7IP1 0.019 0 -9999 0 -10000 0 0
GREM1 0.006 0.039 -9999 0 -0.11 52 52
BMPR2 (homodimer) 0.014 0.039 -9999 0 -0.26 10 10
GADD34/PP1CA 0.02 0.055 -9999 0 -0.17 36 36
BMPR1A-1B (homodimer) 0.022 0.032 -9999 0 -0.19 10 10
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 -0.006 0.16 -9999 0 -0.41 56 56
SMAD6-7/SMURF1/SMAD1 0.013 0.15 -9999 0 -0.36 56 56
SMAD6/SMURF1 0.019 0 -9999 0 -10000 0 0
BAMBI -0.05 0.11 -9999 0 -0.2 167 167
SMURF2 0.011 0.047 -9999 0 -0.26 15 15
BMP2-4/CHRDL1 0 0.055 -9999 0 -0.16 45 45
BMP2-4/GREM1 0.003 0.062 -9999 0 -0.15 52 52
SMAD7 0.011 0.035 -9999 0 -0.13 27 27
SMAD8A/SMAD8A/SMAD4 0.021 0.057 -9999 0 -0.39 6 6
SMAD1/SMAD6 -0.001 0.15 -9999 0 -0.38 56 56
TAK1/SMAD6 0.02 0.042 -9999 0 -0.19 19 19
BMP7 0.017 0.015 -9999 0 -0.11 7 7
BMP6 0.014 0.025 -9999 0 -0.11 20 20
MAP3K7IP2 0.008 0.057 -9999 0 -0.27 20 20
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.007 0.057 -9999 0 -0.21 14 14
PPM1A 0.017 0.023 -9999 0 -0.29 3 3
SMAD1/SMURF2 -0.004 0.16 -9999 0 -0.41 56 56
SMAD7/SMURF1 0.023 0.025 -9999 0 -0.19 3 3
CTDSPL 0.019 0.006 -9999 0 -0.11 1 1
PPP1CA 0.009 0.055 -9999 0 -0.29 17 17
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.011 0.049 -9999 0 -0.27 15 15
PPP1R15A 0.013 0.028 -9999 0 -0.11 25 25
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.003 0.055 -9999 0 -0.2 14 14
CHRD 0.019 0 -9999 0 -10000 0 0
BMPR2 0.014 0.039 -9999 0 -0.26 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM 0 0.06 -9999 0 -0.16 55 55
BMP4 0.013 0.028 -9999 0 -10000 0 0
FST 0.008 0.037 -9999 0 -0.11 47 47
BMP2-4/NOG 0 0.055 -9999 0 -0.16 45 45
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.048 0.035 -9999 0 -0.12 18 18
FAS signaling pathway (CD95)

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
SPTAN1 -0.014 0.059 -10000 0 -0.18 49 49
RFC1 -0.009 0.053 -10000 0 -0.21 31 31
PRKDC -0.011 0.056 -10000 0 -0.21 32 32
RIPK1 0.016 0.019 -10000 0 -0.11 10 10
CASP7 -0.01 0.11 -10000 0 -0.61 16 16
FASLG/FAS/FADD/FAF1 -0.005 0.082 0.17 34 -0.18 69 103
MAP2K4 -0.001 0.098 -10000 0 -0.31 22 22
mol:ceramide 0.006 0.079 -10000 0 -0.24 24 24
GSN -0.013 0.055 -10000 0 -0.21 30 30
FASLG/FAS/FADD/FAF1/Caspase 8 0.005 0.085 0.16 21 -0.24 22 43
FAS -0.027 0.099 -10000 0 -0.2 111 111
BID -0.007 0.04 -10000 0 -0.17 26 26
MAP3K1 -0.004 0.083 -10000 0 -0.36 19 19
MAP3K7 0.007 0.059 -10000 0 -0.25 24 24
RB1 -0.004 0.046 -10000 0 -0.24 18 18
CFLAR 0.016 0.024 -10000 0 -0.15 9 9
HGF/MET 0.012 0.062 -10000 0 -0.16 53 53
ARHGDIB -0.015 0.061 -10000 0 -0.19 48 48
FADD 0.017 0.021 -10000 0 -0.2 4 4
actin filament polymerization 0.013 0.055 0.21 30 -10000 0 30
NFKB1 -0.001 0.095 -10000 0 -0.78 7 7
MAPK8 0.002 0.094 -10000 0 -0.41 8 8
DFFA -0.005 0.046 -10000 0 -0.23 20 20
DNA fragmentation during apoptosis -0.004 0.042 -10000 0 -0.24 15 15
FAS/FADD/MET 0.002 0.066 -10000 0 -0.15 68 68
CFLAR/RIP1 0.024 0.021 -10000 0 -0.19 2 2
FAIM3 0.019 0.008 -10000 0 -0.11 2 2
FAF1 0.006 0.061 -10000 0 -0.28 22 22
PARP1 -0.005 0.048 -10000 0 -0.24 20 20
DFFB -0.004 0.042 -10000 0 -0.25 15 15
CHUK 0.002 0.089 -10000 0 -0.73 7 7
FASLG 0.019 0.003 -10000 0 -10000 0 0
FAS/FADD -0.005 0.072 -10000 0 -0.19 56 56
HGF 0.016 0.02 -10000 0 -0.11 13 13
LMNA -0.002 0.046 -10000 0 -0.22 20 20
CASP6 -0.006 0.048 -10000 0 -0.24 19 19
CASP10 0.019 0.002 -10000 0 -10000 0 0
CASP3 -0.01 0.048 -10000 0 -0.28 15 15
PTPN13 -0.011 0.09 -10000 0 -0.27 54 54
CASP8 -0.006 0.013 -10000 0 -10000 0 0
IL6 -0.004 0.093 -10000 0 -0.64 6 6
MET 0.008 0.037 -10000 0 -0.11 47 47
ICAD/CAD 0 0.043 -10000 0 -0.21 20 20
FASLG/FAS/FADD/FAF1/Caspase 10 0.005 0.08 -10000 0 -0.24 24 24
activation of caspase activity by cytochrome c -0.007 0.04 -10000 0 -0.17 26 26
PAK2 -0.006 0.044 -10000 0 -0.24 16 16
BCL2 0.019 0 -10000 0 -10000 0 0
IL23-mediated 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
CCL2 -0.21 0.53 -9999 0 -1.1 135 135
IL23A -0.025 0.28 -9999 0 -1 18 18
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.27 -9999 0 -0.74 33 33
positive regulation of T cell mediated cytotoxicity -0.024 0.28 -9999 0 -0.82 32 32
ITGA3 -0.022 0.27 -9999 0 -0.88 20 20
IL17F -0.027 0.22 -9999 0 -0.55 41 41
IL12B 0.022 0.03 -9999 0 -10000 0 0
STAT1 (dimer) -0.025 0.27 -9999 0 -0.79 32 32
CD4 -0.045 0.34 -9999 0 -1.1 35 35
IL23 -0.024 0.28 -9999 0 -0.97 19 19
IL23R 0.005 0.069 -9999 0 -0.14 29 29
IL1B -0.039 0.32 -9999 0 -1.2 23 23
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.014 0.26 -9999 0 -0.79 24 24
TYK2 0.01 0.055 -9999 0 -0.29 14 14
STAT4 0.012 0.03 -9999 0 -0.11 30 30
STAT3 -0.003 0.079 -9999 0 -0.29 37 37
IL18RAP 0.018 0.015 -9999 0 -0.11 7 7
IL12RB1 0.019 0.024 -9999 0 -0.15 1 1
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
IL12Rbeta1/TYK2 0.018 0.049 -9999 0 -0.18 21 21
IL23R/JAK2 0.018 0.093 -9999 0 -0.18 21 21
positive regulation of chronic inflammatory response -0.024 0.28 -9999 0 -0.82 32 32
natural killer cell activation 0 0.006 -9999 0 -10000 0 0
JAK2 0.016 0.042 -9999 0 -0.12 18 18
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
NFKB1 0.015 0.038 -9999 0 -0.23 11 11
RELA 0.018 0.02 -9999 0 -0.23 3 3
positive regulation of dendritic cell antigen processing and presentation -0.021 0.27 -9999 0 -0.92 19 19
ALOX12B -0.014 0.26 -9999 0 -0.79 23 23
CXCL1 -0.02 0.26 -9999 0 -0.83 20 20
T cell proliferation -0.024 0.28 -9999 0 -0.82 32 32
NFKBIA 0.003 0.068 -9999 0 -0.24 34 34
IL17A -0.001 0.19 -9999 0 -0.44 39 39
PI3K -0.039 0.28 -9999 0 -0.78 38 38
IFNG 0.012 0.016 -9999 0 -10000 0 0
STAT3 (dimer) -0.037 0.28 -9999 0 -0.75 41 41
IL18R1 0.019 0.011 -9999 0 -0.11 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.005 0.18 -9999 0 -0.47 24 24
IL18/IL18R 0.03 0.039 -9999 0 -0.14 13 13
macrophage activation -0.002 0.016 -9999 0 -0.042 18 18
TNF -0.021 0.27 -9999 0 -0.91 19 19
STAT3/STAT4 -0.024 0.27 -9999 0 -0.77 34 34
STAT4 (dimer) -0.024 0.27 -9999 0 -0.79 32 32
IL18 0 0.056 -9999 0 -0.13 70 70
IL19 -0.014 0.26 -9999 0 -0.79 23 23
STAT5A (dimer) -0.021 0.27 -9999 0 -0.79 32 32
STAT1 0.008 0.04 -9999 0 -0.12 41 41
SOCS3 0.019 0 -9999 0 -10000 0 0
CXCL9 -0.023 0.26 -9999 0 -0.82 20 20
MPO -0.014 0.26 -9999 0 -0.83 19 19
positive regulation of humoral immune response -0.024 0.28 -9999 0 -0.82 32 32
IL23/IL23R/JAK2/TYK2 -0.026 0.29 -9999 0 -0.84 32 32
IL6 -0.025 0.26 -9999 0 -0.86 20 20
STAT5A 0.019 0.008 -9999 0 -0.11 2 2
IL2 0.021 0.007 -9999 0 -0.1 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0.006 -9999 0 -10000 0 0
CD3E -0.014 0.26 -9999 0 -0.81 21 21
keratinocyte proliferation -0.024 0.28 -9999 0 -0.82 32 32
NOS2 -0.021 0.26 -9999 0 -0.74 32 32
Canonical Wnt signaling pathway

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
HDAC1 0.027 0.045 0.19 10 -0.23 6 16
AES 0.025 0.046 0.17 12 -0.19 11 23
FBXW11 0.011 0.047 -10000 0 -0.27 14 14
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.021 0.026 -10000 0 -0.16 2 2
SMAD4 -0.004 0.079 -10000 0 -0.26 44 44
DKK2 0.013 0.028 -10000 0 -0.11 25 25
TLE1 0.026 0.036 0.16 10 -0.18 5 15
MACF1 -0.005 0.082 -10000 0 -0.28 42 42
CTNNB1 0.029 0.085 0.2 2 -0.35 17 19
WIF1 -0.005 0.051 -10000 0 -0.11 100 100
beta catenin/RanBP3 0.063 0.15 0.38 75 -0.32 6 81
KREMEN2 0.019 0.006 -10000 0 -0.11 1 1
DKK1 -0.018 0.058 -10000 0 -0.11 150 150
beta catenin/beta TrCP1 0.037 0.089 0.21 1 -0.36 18 19
FZD1 0.015 0.023 -10000 0 -0.11 17 17
AXIN2 -0.04 0.093 0.12 2 -0.25 74 76
AXIN1 0.019 0.001 -10000 0 -10000 0 0
RAN 0.016 0.031 -10000 0 -0.24 7 7
Axin1/APC/GSK3/beta catenin 0.009 0.16 -10000 0 -0.64 26 26
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.13 0.25 5 -0.45 24 29
Axin1/APC/GSK3 0.02 0.096 0.19 1 -0.37 23 24
Axin1/APC/GSK3/beta catenin/Macf1 0.013 0.12 -10000 0 -0.4 34 34
HNF1A 0.03 0.03 0.16 12 -10000 0 12
CTBP1 0.023 0.048 0.16 9 -0.29 8 17
MYC -0.14 0.41 -10000 0 -1.3 54 54
RANBP3 0.019 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.031 0.025 -10000 0 -0.13 2 2
NKD1 0 0 -10000 0 -10000 0 0
TCF4 0.009 0.078 0.18 7 -0.27 32 39
TCF3 0.03 0.03 0.16 12 -10000 0 12
WNT1/LRP6/FZD1/Axin1 0.043 0.023 -10000 0 -0.13 1 1
Ran/GTP 0.013 0.021 -10000 0 -0.2 5 5
CtBP/CBP/TCF/TLE1/AES 0.08 0.18 0.48 71 -0.39 6 77
LEF1 0.029 0.036 0.18 12 -0.11 5 17
DVL1 0.018 0.11 -10000 0 -0.48 17 17
CSNK2A1 0.01 0.053 -10000 0 -0.29 16 16
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.005 0.18 -10000 0 -0.55 34 34
DKK1/LRP6/Kremen 2 0.012 0.041 -10000 0 -0.12 6 6
LRP6 0.013 0.029 -10000 0 -0.12 22 22
CSNK1A1 0.029 0.044 0.19 11 -0.29 4 15
NLK 0.001 0.06 -10000 0 -0.25 21 21
CCND1 -0.12 0.35 -10000 0 -1.3 39 39
WNT1 0.019 0.006 -10000 0 -10000 0 0
GSK3A 0.019 0.001 -10000 0 -10000 0 0
GSK3B 0.004 0.066 -10000 0 -0.26 29 29
FRAT1 0.016 0.023 -10000 0 -0.13 12 12
PPP2R5D 0.021 0.044 -10000 0 -0.21 15 15
APC 0.024 0.027 -10000 0 -0.18 5 5
WNT1/LRP6/FZD1 0.024 0.05 -10000 0 -0.25 9 9
CREBBP 0.03 0.03 0.16 12 -10000 0 12
Regulation of Telomerase

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
Telomerase catalytic core complex 0 0.15 -10000 0 -0.57 15 15
RAD9A 0.018 0.013 -10000 0 -0.11 5 5
AP1 -0.03 0.11 -10000 0 -0.24 93 93
IFNAR2 0.018 0.02 -10000 0 -0.29 2 2
AKT1 0.012 0.061 -10000 0 -0.27 22 22
ER alpha/Oestrogen 0.014 0.004 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex 0.004 0.092 -10000 0 -0.27 37 37
EGF 0.014 0.025 -10000 0 -0.11 21 21
SMG5 0.019 0.008 -10000 0 -0.11 2 2
SMG6 0.016 0.019 -10000 0 -0.11 11 11
SP3/HDAC2 0.014 0.059 -10000 0 -0.21 29 29
TERT/c-Abl -0.005 0.16 -10000 0 -0.56 22 22
SAP18 0.01 0.052 -10000 0 -0.29 15 15
MRN complex 0.036 0.019 -10000 0 -0.15 4 4
WT1 0.017 0.017 -10000 0 -10000 0 0
WRN 0.014 0.024 -10000 0 -10000 0 0
SP1 0.019 0.009 -10000 0 -10000 0 0
SP3 0.012 0.047 -10000 0 -0.29 12 12
TERF2IP 0.006 0.061 -10000 0 -0.28 23 23
Telomerase/Nucleolin -0.003 0.14 -10000 0 -0.53 20 20
Mad/Max 0.028 0.009 -10000 0 -10000 0 0
TERT -0.001 0.16 -10000 0 -0.6 13 13
CCND1 -0.046 0.3 -10000 0 -1 40 40
MAX 0.019 0.006 -10000 0 -0.11 1 1
RBBP7 0.015 0.034 -10000 0 -0.25 8 8
RBBP4 -0.005 0.079 -10000 0 -0.24 50 50
TERF2 -0.002 0.068 -10000 0 -0.23 43 43
PTGES3 0.016 0.03 -10000 0 -0.29 5 5
SIN3A 0 0.001 -10000 0 -10000 0 0
Telomerase/911 0.029 0.1 -10000 0 -0.52 11 11
CDKN1B 0 0.1 -10000 0 -0.38 32 32
RAD1 0.014 0.034 -10000 0 -0.18 13 13
XRCC5 0.014 0.038 -10000 0 -0.27 9 9
XRCC6 0.018 0.019 -10000 0 -0.29 2 2
SAP30 0.017 0.027 -10000 0 -0.29 4 4
TRF2/PARP2 0.005 0.072 -10000 0 -0.21 50 50
UBE3A 0.017 0.027 -10000 0 -0.29 4 4
JUN -0.002 0.077 -10000 0 -0.28 37 37
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.013 0.019 -10000 0 -0.2 4 4
FOS -0.046 0.12 -10000 0 -0.22 146 146
IFN-gamma/IRF1 0.011 0.072 -10000 0 -0.21 45 45
PARP2 0.006 0.059 -10000 0 -0.25 25 25
BLM -0.036 0.11 -10000 0 -0.25 110 110
Telomerase 0.013 0.075 -10000 0 -0.44 9 9
IRF1 -0.004 0.07 -10000 0 -0.15 84 84
ESR1 0.019 0.001 -10000 0 -10000 0 0
KU/TER 0.024 0.03 -10000 0 -0.19 10 10
ATM/TRF2 0.015 0.041 -10000 0 -0.098 45 45
ubiquitin-dependent protein catabolic process 0.01 0.092 -10000 0 -0.31 26 26
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.009 0.095 -10000 0 -0.32 26 26
HDAC1 0.013 0.04 -10000 0 -0.22 13 13
HDAC2 0.004 0.062 -10000 0 -0.22 33 33
ATM 0.011 0.05 0.16 39 -0.23 6 45
SMAD3 0.013 0.033 -10000 0 -0.19 9 9
ABL1 -0.012 0.093 -10000 0 -0.28 55 55
MXD1 0.019 0.006 -10000 0 -0.11 1 1
MRE11A 0.019 0.006 -10000 0 -0.11 1 1
HUS1 0.019 0.006 -10000 0 -0.11 1 1
RPS6KB1 0.019 0.008 -10000 0 -0.11 2 2
TERT/NF kappa B1/14-3-3 0.016 0.16 -10000 0 -0.55 17 17
NR2F2 -0.03 0.1 -10000 0 -0.22 106 106
MAPK3 0.021 0.007 -10000 0 -10000 0 0
MAPK1 0.014 0.035 -10000 0 -0.19 13 13
TGFB1/TGF beta receptor Type II 0.007 0.049 -10000 0 -0.16 37 37
NFKB1 0.014 0.037 -10000 0 -0.23 11 11
HNRNPC 0.018 0.019 -10000 0 -0.29 2 2
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.05 0.16 39 -0.23 6 45
NBN 0.017 0.027 -10000 0 -0.29 4 4
EGFR -0.08 0.12 -10000 0 -0.25 126 126
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.044 0.082 -10000 0 -0.19 107 107
MYC -0.023 0.098 -10000 0 -0.21 96 96
IL2 0.019 0.01 -10000 0 -0.11 1 1
KU 0.024 0.03 -10000 0 -0.19 10 10
RAD50 0.018 0.013 -10000 0 -0.11 5 5
HSP90AA1 0.018 0.019 -10000 0 -0.29 2 2
TGFB1 0.007 0.049 -10000 0 -0.16 37 37
TRF2/BLM -0.022 0.097 -10000 0 -0.2 104 104
FRAP1 0.019 0.006 -10000 0 -0.11 1 1
KU/TERT 0.014 0.15 -10000 0 -0.56 15 15
SP1/HDAC2 0.019 0.046 -10000 0 -0.18 21 21
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0 0.14 -10000 0 -0.5 18 18
Smad3/Myc -0.002 0.063 -10000 0 -0.15 67 67
911 complex 0.035 0.023 -10000 0 -0.15 5 5
IFNG 0.015 0.035 -10000 0 -0.12 30 30
Telomerase/PinX1 -0.032 0.12 -10000 0 -0.51 18 18
Telomerase/AKT1/mTOR/p70S6K 0.028 0.1 -10000 0 -0.6 8 8
SIN3B 0.017 0.025 -10000 0 -0.2 6 6
YWHAE 0.011 0.045 -10000 0 -0.21 19 19
Telomerase/EST1B 0 0.14 -10000 0 -0.5 18 18
response to DNA damage stimulus 0.006 0.017 0.055 39 -0.077 6 45
MRN complex/TRF2/Rap1 0.034 0.068 -10000 0 -0.17 45 45
TRF2/WRN 0.01 0.054 -10000 0 -0.16 43 43
Telomerase/hnRNP C1/C2 0 0.14 -10000 0 -0.51 18 18
E2F1 0.019 0.009 -10000 0 -0.12 1 1
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.01 0.051 -10000 0 -0.27 16 16
DKC1 0.012 0.042 -10000 0 -0.19 18 18
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0.015 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0.032 -10000 0 -0.14 13 13
CDKN1B -0.003 0.12 -10000 0 -0.39 40 40
CDKN1A -0.008 0.12 -10000 0 -0.39 40 40
FRAP1 0.019 0.006 -10000 0 -0.11 1 1
PRKDC 0.002 0.065 -10000 0 -0.2 41 41
FOXO3 -0.005 0.13 -10000 0 -0.42 40 40
AKT1 -0.004 0.12 -10000 0 -0.39 40 40
BAD 0.014 0.036 -10000 0 -0.25 9 9
AKT3 0.017 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.001 0.11 -10000 0 -0.37 40 40
AKT1/ASK1 -0.008 0.13 -10000 0 -0.41 40 40
BAD/YWHAZ 0.033 0.033 -10000 0 -0.16 13 13
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.008 0.057 -10000 0 -0.28 19 19
JNK cascade 0.008 0.12 0.39 40 -10000 0 40
TSC1 -0.003 0.12 -10000 0 -0.4 40 40
YWHAZ 0.014 0.037 -10000 0 -0.23 11 11
AKT1/RAF1 0.003 0.13 -10000 0 -0.41 40 40
EP300 0.012 0.046 -10000 0 -0.24 15 15
mol:GDP -0.004 0.12 -10000 0 -0.38 40 40
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.003 0.12 -10000 0 -0.4 40 40
YWHAQ 0.018 0.019 -10000 0 -0.29 2 2
TBC1D4 0.018 0.01 -10000 0 -10000 0 0
MAP3K5 -0.014 0.092 -10000 0 -0.25 65 65
MAPKAP1 0.013 0.038 -10000 0 -0.21 13 13
negative regulation of cell cycle 0.001 0.12 0.38 28 -10000 0 28
YWHAH -0.006 0.083 -10000 0 -0.26 49 49
AKT1S1 -0.004 0.11 -10000 0 -0.37 40 40
CASP9 -0.001 0.11 -10000 0 -0.37 40 40
YWHAB 0.015 0.036 -10000 0 -0.29 7 7
p27Kip1/KPNA1 0.002 0.12 -10000 0 -0.38 42 42
GBL 0.016 0.029 -10000 0 -0.2 8 8
PDK1/Src/Hsp90 0.038 0.012 -10000 0 -0.15 2 2
YWHAE 0.011 0.045 -10000 0 -0.21 19 19
SRC 0.019 0 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.009 0.11 -10000 0 -0.34 40 40
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.055 -10000 0 -0.48 4 4
CHUK 0 0.11 -10000 0 -0.37 40 40
BAD/BCL-XL 0.017 0.11 -10000 0 -0.34 40 40
mTORC2 0.032 0.028 -10000 0 -0.15 10 10
AKT2 0.017 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.002 0.15 -10000 0 -0.4 46 46
PDPK1 0.019 0 -10000 0 -10000 0 0
MDM2 -0.003 0.11 -10000 0 -0.37 40 40
MAPKKK cascade -0.003 0.12 0.4 40 -10000 0 40
MDM2/Cbp/p300 0.016 0.11 -10000 0 -0.36 40 40
TSC1/TSC2 -0.003 0.13 -10000 0 -0.42 40 40
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.11 -10000 0 -0.34 40 40
glucose import 0.02 0.011 -10000 0 -0.13 1 1
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.015 0.073 -10000 0 -0.22 43 43
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.021 0.008 -10000 0 -10000 0 0
GSK3A 0.001 0.11 -10000 0 -0.37 40 40
FOXO1 -0.008 0.13 -10000 0 -0.42 40 40
GSK3B -0.005 0.13 -10000 0 -0.43 40 40
SFN 0.002 0.044 -10000 0 -0.11 70 70
G1/S transition of mitotic cell cycle -0.001 0.12 -10000 0 -0.41 40 40
p27Kip1/14-3-3 family 0.007 0.13 -10000 0 -0.44 23 23
PRKACA 0.019 0 -10000 0 -10000 0 0
KPNA1 0.013 0.042 -10000 0 -0.29 10 10
HSP90AA1 0.018 0.019 -10000 0 -0.29 2 2
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.019 0 -10000 0 -10000 0 0
CREBBP 0.019 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.01 0.016 -9999 0 -0.05 37 37
SNTA1 0.007 0.043 -9999 0 -0.13 45 45
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.014 0.021 -9999 0 -0.045 59 59
MAPK12 0.016 0.028 -9999 0 -0.16 11 11
CCND1 -0.017 0.1 -9999 0 -0.37 41 41
p38 gamma/SNTA1 0.022 0.031 -9999 0 -0.15 11 11
MAP2K3 0.018 0.01 -9999 0 -0.11 3 3
PKN1 0.008 0.049 -9999 0 -0.18 28 28
G2/M transition checkpoint 0.016 0.028 -9999 0 -0.16 11 11
MAP2K6 0.014 0.031 -9999 0 -0.19 11 11
MAPT -0.019 0.097 -9999 0 -0.24 79 79
MAPK13 0.015 0.021 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.01 0.036 -9999 0 -0.23 11 11
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.011 -9999 0 -0.11 4 4
Caspase 8 (4 units) 0.006 0.09 -9999 0 -0.29 22 22
NEF 0.005 0 -9999 0 -10000 0 0
NFKBIA -0.001 0.068 -9999 0 -0.24 34 34
BIRC3 0.006 0.062 -9999 0 -0.2 13 13
CYCS -0.004 0.089 -9999 0 -0.28 32 32
RIPK1 0.016 0.019 -9999 0 -0.11 11 11
CD247 0.022 0.015 -9999 0 -10000 0 0
MAP2K7 0.006 0.098 -9999 0 -0.4 15 15
protein ubiquitination 0.026 0.063 -9999 0 -0.21 17 17
CRADD 0.017 0.015 -9999 0 -0.11 7 7
DAXX 0.017 0.018 -9999 0 -0.15 5 5
FAS -0.027 0.099 -9999 0 -0.2 111 111
BID -0.007 0.091 -9999 0 -0.28 31 31
NF-kappa-B/RelA/I kappa B alpha 0.021 0.062 -9999 0 -0.16 37 37
TRADD 0.019 0 -9999 0 -10000 0 0
MAP3K5 -0.014 0.092 -9999 0 -0.25 65 65
CFLAR 0.016 0.024 -9999 0 -0.15 9 9
FADD 0.017 0.021 -9999 0 -0.2 4 4
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.021 0.062 -9999 0 -0.16 37 37
MAPK8 0.011 0.093 -9999 0 -0.38 15 15
APAF1 0.019 0 -9999 0 -10000 0 0
TRAF1 0.017 0.015 -9999 0 -0.11 7 7
TRAF2 0.019 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.005 0.088 -9999 0 -0.18 91 91
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.022 0.075 -9999 0 -0.26 17 17
CHUK 0.026 0.067 -9999 0 -0.22 17 17
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.009 0.08 -9999 0 -0.14 92 92
TCRz/NEF 0.024 0.01 -9999 0 -10000 0 0
TNF 0.018 0.01 -9999 0 -0.11 3 3
FASLG 0.027 0.008 -9999 0 -10000 0 0
NFKB1 0.011 0.039 -9999 0 -0.23 11 11
TNFR1A/BAG4/TNF-alpha 0.02 0.057 -9999 0 -0.16 50 50
CASP6 0.008 0.11 -9999 0 -0.45 19 19
CASP7 0.002 0.1 -9999 0 -0.32 28 28
RELA 0.014 0.025 -9999 0 -0.24 3 3
CASP2 0.017 0.017 -9999 0 -0.11 9 9
CASP3 0.005 0.1 -9999 0 -0.31 25 25
TNFRSF1A -0.01 0.091 -9999 0 -0.29 50 50
TNFR1A/BAG4 0.007 0.065 -9999 0 -0.19 50 50
CASP8 0.016 0.021 -9999 0 -0.11 14 14
CASP9 0.014 0.029 -9999 0 -0.13 18 18
MAP3K14 0.024 0.071 -9999 0 -0.24 17 17
APAF-1/Caspase 9 -0.028 0.066 -9999 0 -0.22 38 38
BCL2 0.015 0.087 -9999 0 -0.35 15 15
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.011 0.095 -10000 0 -0.37 25 25
CRKL 0.009 0.099 -10000 0 -0.4 25 25
HRAS 0.023 0.096 -10000 0 -0.32 29 29
mol:PIP3 -0.006 0.098 0.28 3 -0.38 25 28
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.019 0.006 -10000 0 -0.11 1 1
GAB1 0.005 0.1 -10000 0 -0.42 25 25
FOXO3 -0.016 0.14 -10000 0 -0.41 48 48
AKT1 -0.015 0.13 -10000 0 -0.41 47 47
BAD -0.011 0.13 -10000 0 -0.38 47 47
megakaryocyte differentiation -0.001 0.1 -10000 0 -0.43 25 25
GSK3B -0.015 0.14 -10000 0 -0.41 48 48
RAF1 0.023 0.085 -10000 0 -0.27 32 32
SHC1 0.004 0.052 -10000 0 -0.14 48 48
STAT3 0.005 0.1 -10000 0 -0.42 25 25
STAT1 0.003 0.21 -10000 0 -0.92 25 25
HRAS/SPRED1 0.018 0.083 -10000 0 -0.27 29 29
cell proliferation 0.01 0.099 -10000 0 -0.4 25 25
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
TEC 0.019 0 -10000 0 -10000 0 0
RPS6KB1 0.005 0.1 -10000 0 -0.41 25 25
HRAS/SPRED2 0.028 0.085 -10000 0 -0.27 29 29
LYN/TEC/p62DOK 0.015 0.11 -10000 0 -0.4 25 25
MAPK3 0.023 0.071 -10000 0 -0.21 33 33
STAP1 0.009 0.1 -10000 0 -0.41 25 25
GRAP2 0.019 0 -10000 0 -10000 0 0
JAK2 0.007 0.18 -10000 0 -0.78 25 25
STAT1 (dimer) 0.004 0.21 -10000 0 -0.9 25 25
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.029 0.099 -10000 0 -0.38 25 25
actin filament polymerization 0.005 0.099 -10000 0 -0.41 25 25
LYN -0.018 0.098 -10000 0 -0.25 72 72
STAP1/STAT5A (dimer) 0.016 0.13 -10000 0 -0.56 25 25
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
CBL/CRKL/GRB2 0.023 0.095 -10000 0 -0.36 25 25
PI3K -0.004 0.12 -10000 0 -0.37 35 35
PTEN 0.013 0.038 -10000 0 -0.18 17 17
SCF/KIT/EPO/EPOR 0.005 0.25 -10000 0 -1.1 25 25
MAPK8 0.01 0.1 -10000 0 -0.41 25 25
STAT3 (dimer) 0.005 0.1 -10000 0 -0.41 25 25
positive regulation of transcription 0.023 0.061 0.13 2 -0.17 33 35
mol:GDP 0.026 0.093 -10000 0 -0.34 25 25
PIK3C2B 0.004 0.1 -10000 0 -0.42 25 25
CBL/CRKL 0.017 0.097 -10000 0 -0.37 25 25
FER 0.009 0.1 -10000 0 -0.41 25 25
SH2B3 0.003 0.1 -10000 0 -0.42 25 25
PDPK1 -0.002 0.092 0.27 3 -0.35 25 28
SNAI2 -0.005 0.11 -10000 0 -0.45 25 25
positive regulation of cell proliferation 0.008 0.16 -10000 0 -0.69 25 25
KITLG 0.021 0.01 -10000 0 -10000 0 0
cell motility 0.008 0.16 -10000 0 -0.69 25 25
PTPN6 0.005 0.056 -10000 0 -0.2 33 33
EPOR 0.034 0.067 -10000 0 -10000 0 0
STAT5A (dimer) 0.014 0.14 -10000 0 -0.57 25 25
SOCS1 0.019 0 -10000 0 -10000 0 0
cell migration -0.01 0.1 0.4 25 -10000 0 25
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.02 0.006 -10000 0 -10000 0 0
VAV1 0.016 0.019 -10000 0 -0.11 12 12
GRB10 0 0.11 -10000 0 -0.43 25 25
PTPN11 0.014 0.033 -10000 0 -0.26 7 7
SCF/KIT 0.006 0.11 -10000 0 -0.43 25 25
GO:0007205 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 0.022 0.074 -10000 0 -0.22 35 35
CBL 0.019 0 -10000 0 -10000 0 0
KIT -0.022 0.26 -10000 0 -1.2 25 25
MAP2K2 0.023 0.073 -10000 0 -0.22 34 34
SHC/Grb2/SOS1 0.01 0.098 -10000 0 -0.39 25 25
STAT5A 0.014 0.14 -10000 0 -0.58 25 25
GRB2 0.014 0.039 -10000 0 -0.26 10 10
response to radiation -0.005 0.11 -10000 0 -0.44 25 25
SHC/GRAP2 0.018 0.036 -10000 0 -0.19 9 9
PTPRO -0.001 0.11 -10000 0 -0.44 25 25
SH2B2 0.005 0.1 -10000 0 -0.41 25 25
DOK1 0.019 0 -10000 0 -10000 0 0
MATK 0.01 0.1 -10000 0 -0.41 25 25
CREBBP 0.031 0.029 -10000 0 -10000 0 0
BCL2 0.034 0.065 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.019 0.044 -10000 0 -0.19 22 22
ATM 0.01 0.042 -10000 0 -0.15 30 30
UBE2D3 0.017 0.023 -10000 0 -0.29 3 3
PRKDC 0.002 0.065 -10000 0 -0.2 41 41
ATR 0.011 0.049 -10000 0 -0.26 16 16
UBE2L3 0.014 0.038 -10000 0 -0.29 8 8
FANCD2 0.006 0.053 -10000 0 -0.26 17 17
protein ubiquitination 0.029 0.052 -10000 0 -0.13 34 34
XRCC5 0.014 0.038 -10000 0 -0.27 9 9
XRCC6 0.018 0.019 -10000 0 -0.29 2 2
M/R/N Complex 0.036 0.019 -10000 0 -0.15 4 4
MRE11A 0.019 0.006 -10000 0 -0.11 1 1
DNA-PK 0.025 0.052 -10000 0 -0.19 26 26
FA complex/FANCD2/Ubiquitin 0.017 0.072 -10000 0 -0.3 20 20
FANCF 0.011 0.048 -10000 0 -0.25 16 16
BRCA1 0.017 0.015 -10000 0 -0.11 7 7
CCNE1 0.01 0.033 -10000 0 -0.11 37 37
CDK2/Cyclin E1 0.017 0.036 -10000 0 -0.14 14 14
FANCG 0 0.064 -10000 0 -0.18 50 50
BRCA1/BACH1/BARD1 0.018 0.045 -10000 0 -0.19 23 23
FANCE 0.018 0.011 -10000 0 -0.11 4 4
FANCC 0.019 0.008 -10000 0 -10000 0 0
NBN 0.017 0.027 -10000 0 -0.29 4 4
FANCA 0.019 0.006 -10000 0 -0.11 1 1
DNA repair 0.021 0.077 -10000 0 -0.3 15 15
BRCA1/BARD1/ubiquitin 0.018 0.045 -10000 0 -0.19 23 23
BARD1/DNA-PK 0.029 0.065 -10000 0 -0.17 41 41
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.019 0.044 0.19 22 -10000 0 22
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.067 -10000 0 -0.23 28 28
BRCA1/BACH1/BARD1/TopBP1 0.017 0.064 -10000 0 -0.16 54 54
BRCA1/BARD1/P53 0.021 0.067 -10000 0 -0.15 58 58
BARD1/CSTF1/BRCA1 0.029 0.04 -10000 0 -0.15 23 23
BRCA1/BACH1 0.017 0.015 -10000 0 -0.11 7 7
BARD1 0.006 0.063 -10000 0 -0.28 24 24
PCNA 0.004 0.065 -10000 0 -0.25 30 30
BRCA1/BARD1/UbcH5C 0.029 0.044 -10000 0 -0.16 24 24
BRCA1/BARD1/UbcH7 0.027 0.047 -10000 0 -0.16 29 29
BRCA1/BARD1/RAD51/PCNA 0.032 0.057 -10000 0 -0.16 38 38
BARD1/DNA-PK/P53 0.023 0.076 -10000 0 -0.15 68 68
BRCA1/BARD1/Ubiquitin 0.018 0.045 -10000 0 -0.19 23 23
BRCA1/BARD1/CTIP 0.015 0.064 -10000 0 -0.16 49 49
FA complex 0.016 0.059 -10000 0 -0.21 21 21
BARD1/EWS 0.019 0.044 -10000 0 -0.19 22 22
RBBP8 0.001 0.055 -10000 0 -0.19 34 34
TP53 -0.007 0.077 -10000 0 -0.2 62 62
TOPBP1 -0.003 0.078 -10000 0 -0.27 40 40
G1/S transition of mitotic cell cycle -0.02 0.067 0.15 58 -10000 0 58
BRCA1/BARD1 0.034 0.054 -10000 0 -0.13 34 34
CSTF1 0.019 0.006 -10000 0 -0.11 1 1
BARD1/EWS-Fli1 0.005 0.042 -10000 0 -0.2 22 22
CDK2 0.011 0.034 -10000 0 -0.12 29 29
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.018 0.01 -10000 0 -0.11 3 3
RAD50 0.018 0.013 -10000 0 -0.11 5 5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.018 0.045 -10000 0 -0.19 23 23
EWSR1 0.019 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.013 0.04 -9999 0 -0.22 13 13
HDAC2 0.004 0.061 -9999 0 -0.22 33 33
GNB1/GNG2 0.019 0.036 -9999 0 -0.16 21 21
forebrain development 0.021 0.067 -9999 0 -0.4 5 5
GNAO1 -0.013 0.085 -9999 0 -0.2 81 81
SMO/beta Arrestin2 0.026 0.029 -9999 0 -0.19 7 7
SMO 0.019 0.011 -9999 0 -0.11 4 4
ARRB2 0.014 0.039 -9999 0 -0.29 7 7
GLI3/SPOP -0.003 0.11 -9999 0 -0.29 57 57
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.004 0.066 -9999 0 -0.26 29 29
GNAI2 0.001 0.074 -9999 0 -0.28 34 34
SIN3/HDAC complex 0.029 0.038 -9999 0 -0.16 19 19
GNAI1 -0.045 0.11 -9999 0 -0.2 157 157
XPO1 0.02 0.024 -9999 0 -0.29 3 3
GLI1/Su(fu) 0.022 0.063 -9999 0 -0.4 5 5
SAP30 0.016 0.027 -9999 0 -0.29 4 4
mol:GDP 0.019 0.011 -9999 0 -0.11 4 4
MIM/GLI2A 0.026 0.005 -9999 0 -10000 0 0
IFT88 0.017 0.022 -9999 0 -0.17 6 6
GNAI3 0.015 0.038 -9999 0 -0.29 8 8
GLI2 0.018 0.093 -9999 0 -0.39 20 20
GLI3 -0.01 0.11 -9999 0 -0.28 56 56
CSNK1D 0.01 0.052 -9999 0 -0.27 17 17
CSNK1E 0.003 0.064 -9999 0 -0.23 34 34
SAP18 0.01 0.052 -9999 0 -0.29 15 15
embryonic digit morphogenesis 0.017 0.022 -9999 0 -0.17 6 6
GNG2 0 0 -9999 0 -10000 0 0
Gi family/GTP -0.035 0.12 -9999 0 -0.28 72 72
SIN3B 0.016 0.025 -9999 0 -0.2 6 6
SIN3A 0 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0 0.091 -9999 0 -0.27 41 41
GLI2/Su(fu) 0.021 0.084 -9999 0 -0.33 22 22
FOXA2 0.033 0.027 -9999 0 -10000 0 0
neural tube patterning 0.021 0.067 -9999 0 -0.4 5 5
SPOP 0.008 0.058 -9999 0 -0.29 19 19
Su(fu)/PIAS1 0.015 0.034 -9999 0 -0.13 24 24
GNB1 0.007 0.061 -9999 0 -0.29 21 21
CSNK1G2 0.018 0.014 -9999 0 -0.29 1 1
CSNK1G3 0.017 0.025 -9999 0 -0.22 5 5
MTSS1 0.026 0.005 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.021 0.067 -9999 0 -0.4 5 5
SUFU 0.009 0.017 -9999 0 -0.13 7 7
LGALS3 -0.039 0.12 -9999 0 -0.27 106 106
catabolic process 0.011 0.14 -9999 0 -0.46 36 36
GLI3A/CBP 0.027 0.016 -9999 0 -10000 0 0
KIF3A -0.007 0.083 -9999 0 -0.26 49 49
GLI1 0.021 0.068 -9999 0 -0.41 5 5
RAB23 0.01 0.041 -9999 0 -0.14 31 31
CSNK1A1 0.014 0.038 -9999 0 -0.29 8 8
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.015 0.034 -9999 0 -0.25 8 8
Su(fu)/Galectin3 -0.009 0.062 -9999 0 -0.14 100 100
GNAZ -0.007 0.083 -9999 0 -0.23 56 56
RBBP4 -0.005 0.079 -9999 0 -0.24 50 50
CSNK1G1 0.019 0 -9999 0 -10000 0 0
PIAS1 0.008 0.056 -9999 0 -0.29 18 18
PRKACA 0.019 0 -9999 0 -10000 0 0
GLI2/SPOP 0.023 0.098 -9999 0 -0.37 25 25
STK36 0.003 0.002 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.041 0.14 -9999 0 -0.37 58 58
PTCH1 0.026 0.065 -9999 0 -0.53 2 2
MIM/GLI1 0.04 0.07 -9999 0 -0.48 3 3
CREBBP 0.027 0.016 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.006 0.098 -9999 0 -0.25 51 51
Insulin Pathway

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
CBL/APS/CAP 0.024 0.033 -9999 0 -0.11 24 24
TC10/GTP 0.023 0.035 -9999 0 -0.13 25 25
Insulin Receptor/Insulin/IRS1/Shp2 0.034 0.049 -9999 0 -0.14 30 30
HRAS 0.009 0.055 -9999 0 -0.28 18 18
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 0.001 0.047 -9999 0 -0.12 70 70
FOXO3 -0.031 0.18 -9999 0 -0.79 28 28
AKT1 -0.006 0.083 -9999 0 -0.23 43 43
INSR 0.019 0.007 -9999 0 -0.036 2 2
Insulin Receptor/Insulin 0.039 0.065 -9999 0 -0.34 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 -0.018 0.091 -9999 0 -0.2 89 89
SORBS1 0.019 0 -9999 0 -10000 0 0
CRK 0.009 0.054 -9999 0 -0.28 17 17
PTPN1 0.014 0.058 -9999 0 -0.34 10 10
CAV1 -0.002 0.058 -9999 0 -0.17 43 43
CBL/APS/CAP/Crk-II/C3G 0.04 0.029 -9999 0 -0.12 16 16
Insulin Receptor/Insulin/IRS1/NCK2 0.031 0.058 -9999 0 -0.16 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.078 -9999 0 -0.15 99 99
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.021 0.07 -9999 0 -0.35 14 14
RPS6KB1 -0.003 0.077 -9999 0 -0.21 43 43
PARD6A 0.015 0.026 -9999 0 -0.14 12 12
CBL 0.019 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.02 0.013 -9999 0 -10000 0 0
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.005 0.084 -9999 0 -0.25 36 36
HRAS/GTP -0.014 0.04 -9999 0 -0.12 50 50
Insulin Receptor 0.019 0.007 -9999 0 -0.036 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.033 0.058 -9999 0 -0.14 39 39
PRKCI 0.01 0.095 -9999 0 -0.48 17 17
Insulin Receptor/Insulin/GRB14/PDK1 -0.03 0.06 -9999 0 -0.18 49 49
SHC1 0.004 0.052 -9999 0 -0.14 48 48
negative regulation of MAPKKK cascade 0.028 0.045 -9999 0 -0.26 5 5
PI3K 0.006 0.083 -9999 0 -0.15 99 99
NCK2 0.009 0.054 -9999 0 -0.28 17 17
RHOQ 0.011 0.048 -9999 0 -0.28 14 14
mol:H2O2 -0.002 0.007 -9999 0 -10000 0 0
HRAS/GDP 0.007 0.037 -9999 0 -0.19 18 18
AKT2 -0.001 0.07 -9999 0 -0.19 36 36
PRKCZ -0.017 0.082 -9999 0 -0.47 16 16
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP 0.01 0.042 -9999 0 -0.13 34 34
F2RL2 0.019 0.008 -9999 0 -0.11 2 2
TRIP10 0.015 0.029 -9999 0 -0.15 13 13
Insulin Receptor/Insulin/Shc 0.028 0.033 -9999 0 -0.15 9 9
TC10/GTP/CIP4/Exocyst 0.019 0.033 -9999 0 -0.16 16 16
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.034 0.04 -9999 0 -0.15 16 16
RAPGEF1 0.019 0 -9999 0 -10000 0 0
RASA1 0.003 0.069 -9999 0 -0.28 29 29
NCK1 0.014 0.036 -9999 0 -0.19 14 14
CBL/APS/CAP/Crk-II 0.032 0.03 -9999 0 -0.14 16 16
TC10/GDP 0.009 0.033 -9999 0 -0.19 14 14
Insulin Receptor/Insulin/SHC/GRB10 0.018 0.065 -9999 0 -0.15 51 51
INPP5D 0.005 0.033 -9999 0 -0.13 24 24
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.003 0.007 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0.033 -9999 0 -0.27 7 7
IRS1 -0.002 0.07 -9999 0 -0.19 53 53
p62DOK/RasGAP 0.028 0.046 -9999 0 -0.26 5 5
INS 0.019 0.007 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.005 0.033 -9999 0 -0.13 24 24
GRB2 0.014 0.039 -9999 0 -0.26 10 10
EIF4EBP1 -0.006 0.082 -9999 0 -0.22 46 46
PTPRA 0.017 0.024 -9999 0 -0.22 4 4
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
TC10/GTP/CIP4 0.019 0.033 -9999 0 -0.16 16 16
PDPK1 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.011 0.056 -9999 0 -0.17 39 39
Insulin Receptor/Insulin/IRS1 0.025 0.042 -9999 0 -0.15 24 24
Insulin Receptor/Insulin/IRS3 0.028 0.014 -9999 0 -10000 0 0
Par3/Par6 0.036 0.033 -9999 0 -0.12 18 18
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.027 0.037 -9999 0 -0.11 28 28
E-cadherin/beta catenin 0.022 0.026 -9999 0 -0.19 3 3
CTNNB1 0.017 0.023 -9999 0 -0.29 3 3
JUP 0.008 0.037 -9999 0 -0.11 47 47
CDH1 0.012 0.03 -9999 0 -0.11 29 29
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.003 0.048 -9999 0 -0.13 57 57
ARNO/beta Arrestin1-2 0.022 0.022 -9999 0 -0.099 8 8
EGFR -0.08 0.12 -9999 0 -0.29 97 97
EPHA2 0.008 0.036 -9999 0 -0.11 45 45
USP6 0.017 0.017 -9999 0 -0.11 9 9
IQSEC1 0.016 0.022 -9999 0 -0.13 10 10
EGFR/EGFR/EGF/EGF -0.044 0.082 -9999 0 -0.19 107 107
ARRB2 0.013 0.029 -9999 0 -0.23 7 7
mol:GTP 0.006 0.01 -9999 0 -10000 0 0
ARRB1 0.018 0.011 -9999 0 -0.11 4 4
FBXO8 0 0 -9999 0 -10000 0 0
TSHR 0.015 0.022 -9999 0 -0.11 16 16
EGF 0.014 0.025 -9999 0 -0.11 21 21
somatostatin receptor activity 0 0 -9999 0 0 7 7
ARAP2 0 0 -9999 0 0 1 1
mol:GDP 0.016 0.034 -9999 0 -0.13 16 16
mol:PI-3-4-5-P3 0 0 -9999 0 0 3 3
ITGA2B 0.019 0 -9999 0 -10000 0 0
ARF6 0.018 0.015 -9999 0 -0.2 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.028 0.053 -9999 0 -0.14 36 36
ADAP1 0 0 -9999 0 -10000 0 0
KIF13B -0.009 0.085 -9999 0 -0.24 57 57
HGF/MET 0.018 0.03 -9999 0 -0.14 4 4
PXN 0.018 0.011 -9999 0 -0.11 4 4
ARF6/GTP 0.022 0.039 -9999 0 -0.17 3 3
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.027 0.072 -9999 0 -0.15 108 108
ADRB2 0.01 0.032 -9999 0 -0.11 35 35
receptor agonist activity 0 0 -9999 0 0 2 2
actin filament binding 0 0 -9999 0 0 7 7
SRC 0.019 0 -9999 0 -10000 0 0
ITGB3 0.019 0.008 -9999 0 -0.11 2 2
GNAQ 0.015 0.023 -9999 0 -0.11 17 17
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 4 4
ARF6/GDP 0.026 0.03 -9999 0 -0.37 1 1
ARF6/GDP/GULP/ACAP1 0.005 0.055 -9999 0 -0.16 11 11
alphaIIb/beta3 Integrin/paxillin/GIT1 0.048 0.01 -9999 0 -10000 0 0
ACAP1 0 0 -9999 0 -10000 0 0
ACAP2 0 0 -9999 0 0 1 1
LHCGR/beta Arrestin2 0.017 0.022 -9999 0 -0.17 7 7
EFNA1 -0.001 0.07 -9999 0 -0.21 46 46
HGF 0.016 0.02 -9999 0 -0.11 13 13
CYTH3 0 0 -9999 0 0 2 2
CYTH2 0 0.001 -9999 0 -0.003 6 6
NCK1 0.014 0.036 -9999 0 -0.19 14 14
fibronectin binding 0 0 -9999 0 0 3 3
endosomal lumen acidification 0 0 -9999 0 0 16 16
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.046 0.11 -9999 0 -0.18 173 173
GNAQ/ARNO 0.012 0.01 -9999 0 -0.042 17 17
mol:Phosphatidic acid 0 0 -9999 0 0 1 1
PIP3-E 0.002 0.048 -9999 0 -0.12 64 64
MET 0.008 0.037 -9999 0 -0.11 47 47
GNA14 0.015 0.022 -9999 0 -0.11 15 15
GNA15 0.012 0.033 -9999 0 -0.12 26 26
GIT1 0.019 0.006 -9999 0 -0.11 1 1
mol:PI-4-5-P2 0 0 -9999 0 0 3 3
GNA11 0.003 0.069 -9999 0 -0.29 27 27
LHCGR 0.019 0 -9999 0 -10000 0 0
AGTR1 0.016 0.02 -9999 0 -0.11 13 13
desensitization of G-protein coupled receptor protein signaling pathway 0.017 0.022 -9999 0 -0.17 7 7
IPCEF1/ARNO -0.022 0.059 -9999 0 -0.11 123 123
alphaIIb/beta3 Integrin 0.028 0.006 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory 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
PCK2 -0.029 0.12 0.29 3 -0.72 13 16
SMARCC2 -0.001 0.075 -10000 0 -0.28 35 35
SMARCC1 0.012 0.038 -10000 0 -0.15 23 23
TBX21 0.039 0.036 -10000 0 -10000 0 0
SUMO2 0.02 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.007 0.055 -10000 0 -0.17 35 35
FKBP4 0.014 0.029 -10000 0 -0.13 17 17
FKBP5 -0.023 0.087 -10000 0 -0.16 121 121
GR alpha/HSP90/FKBP51/HSP90 -0.01 0.067 -10000 0 -0.2 26 26
PRL 0.042 0.041 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.029 0.073 -10000 0 -0.32 1 1
RELA -0.031 0.077 -10000 0 -0.15 139 139
FGG -0.019 0.083 -10000 0 -0.32 1 1
GR beta/TIF2 -0.001 0.052 -10000 0 -0.24 9 9
IFNG 0.042 0.068 -10000 0 -10000 0 0
apoptosis -0.002 0.21 0.46 30 -0.58 30 60
CREB1 0.024 0.036 -10000 0 -0.29 6 6
histone acetylation 0.024 0.043 -10000 0 -0.22 8 8
BGLAP 0.037 0.049 -10000 0 -10000 0 0
GR/PKAc 0.02 0.062 -10000 0 -0.2 21 21
NF kappa B1 p50/RelA -0.055 0.13 -10000 0 -0.25 144 144
SMARCD1 0.018 0.013 -10000 0 -0.11 5 5
MDM2 -0.005 0.033 -10000 0 -10000 0 0
GATA3 0.032 0.018 -10000 0 -10000 0 0
AKT1 0.005 0.066 0.16 13 -0.26 26 39
CSF2 0.028 0.032 -10000 0 -10000 0 0
GSK3B 0.005 0.067 -10000 0 -0.27 28 28
NR1I3 0.01 0.19 0.46 21 -0.52 23 44
CSN2 -0.015 0.073 -10000 0 -0.29 1 1
BRG1/BAF155/BAF170/BAF60A 0.021 0.08 -10000 0 -0.21 48 48
NFATC1 0.029 0 -10000 0 -10000 0 0
POU2F1 0.021 0.028 -10000 0 -0.24 3 3
CDKN1A -0.15 0.44 -10000 0 -1.3 62 62
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 -10000 0 -10000 0 0
SFN 0.002 0.044 -10000 0 -0.11 70 70
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.002 0.07 -10000 0 -0.19 32 32
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.057 0.3 0.44 21 -0.72 78 99
JUN 0.05 0.064 -10000 0 -0.25 5 5
IL4 0.045 0.035 -10000 0 -10000 0 0
CDK5R1 0.014 0.025 -10000 0 -0.11 21 21
PRKACA 0.019 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.028 0.073 -10000 0 -0.26 32 32
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.007 0.064 -10000 0 -0.19 21 21
cortisol/GR alpha (monomer) -0.046 0.082 -10000 0 -0.38 1 1
NCOA2 0.018 0.01 -10000 0 -0.11 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.007 0.076 -10000 0 -0.27 26 26
AP-1/NFAT1-c-4 0.062 0.1 -10000 0 -0.37 7 7
AFP 0.05 0.067 -10000 0 -10000 0 0
SUV420H1 -0.009 0.088 -10000 0 -0.28 49 49
IRF1 -0.027 0.14 -10000 0 -0.73 17 17
TP53 -0.04 0.18 -10000 0 -0.5 66 66
PPP5C 0.017 0.015 -10000 0 -0.11 7 7
KRT17 0.038 0.077 -10000 0 -10000 0 0
KRT14 0.026 0.048 0.39 1 -10000 0 1
TBP 0.023 0.032 -10000 0 -0.28 4 4
CREBBP 0.01 0.007 -10000 0 -10000 0 0
HDAC1 0.007 0.037 -10000 0 -0.22 12 12
HDAC2 0.003 0.061 -10000 0 -0.22 33 33
AP-1 0.062 0.1 -10000 0 -0.37 7 7
MAPK14 0.019 0.015 -10000 0 -0.11 5 5
MAPK10 -0.016 0.098 -10000 0 -0.29 58 58
MAPK11 0.02 0.007 -10000 0 -10000 0 0
KRT5 0.04 0.074 -10000 0 -10000 0 0
interleukin-1 receptor activity -0.002 0 -10000 0 -10000 0 0
NCOA1 -0.006 0.084 -10000 0 -0.29 42 42
STAT1 0.007 0.055 -10000 0 -0.17 35 35
CGA 0.039 0.047 -10000 0 -0.35 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.047 0.07 -10000 0 -0.45 7 7
MAPK3 0.02 0.01 -10000 0 -10000 0 0
MAPK1 0.011 0.05 -10000 0 -0.22 21 21
ICAM1 -0.02 0.11 -10000 0 -10000 0 0
NFKB1 -0.033 0.081 -10000 0 -0.15 143 143
MAPK8 0.053 0.045 -10000 0 -10000 0 0
MAPK9 0.017 0.029 -10000 0 -0.23 6 6
cortisol/GR alpha (dimer) -0.004 0.22 0.47 27 -0.61 30 57
BAX -0.038 0.18 -10000 0 -1.4 5 5
POMC 0.035 0.06 -10000 0 -10000 0 0
EP300 0.002 0.046 -10000 0 -0.3 11 11
cortisol/GR alpha (dimer)/p53 -0.056 0.12 -10000 0 -0.42 19 19
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.073 0.24 39 -10000 0 39
SGK1 -0.006 0.051 -10000 0 -0.31 11 11
IL13 0.048 0.058 -10000 0 -10000 0 0
IL6 -0.028 0.11 -10000 0 -10000 0 0
PRKACG 0.019 0 -10000 0 -10000 0 0
IL5 0.043 0.051 -10000 0 -10000 0 0
IL2 0.042 0.067 -10000 0 -10000 0 0
CDK5 0.005 0.061 -10000 0 -0.24 29 29
PRKACB -0.002 0.076 -10000 0 -0.26 39 39
HSP90AA1 0.018 0.019 -10000 0 -0.29 2 2
IL8 -0.21 0.39 -10000 0 -0.85 139 139
CDK5R1/CDK5 0.015 0.049 -10000 0 -0.18 25 25
NF kappa B1 p50/RelA/PKAc -0.018 0.11 -10000 0 -0.2 47 47
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.011 0.082 -10000 0 -0.56 1 1
SMARCA4 -0.004 0.08 -10000 0 -0.27 42 42
chromatin remodeling -0.024 0.12 -10000 0 -0.4 32 32
NF kappa B1 p50/RelA/Cbp -0.032 0.11 -10000 0 -0.23 35 35
JUN (dimer) 0.05 0.064 -10000 0 -0.25 5 5
YWHAH -0.006 0.083 -10000 0 -0.26 49 49
VIPR1 0.037 0.042 -10000 0 -10000 0 0
NR3C1 -0.018 0.069 -10000 0 -0.35 9 9
NR4A1 0.024 0.01 -10000 0 -10000 0 0
TIF2/SUV420H1 0.008 0.062 -10000 0 -0.19 46 46
MAPKKK cascade -0.002 0.21 0.46 30 -0.58 30 60
cortisol/GR alpha (dimer)/Src-1 -0.033 0.098 -10000 0 -0.37 12 12
PBX1 0.021 0.033 -10000 0 -0.23 7 7
POU1F1 0.025 0.008 -10000 0 -10000 0 0
SELE -0.012 0.11 -10000 0 -10000 0 0
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.024 0.12 -10000 0 -0.41 32 32
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.011 0.082 -10000 0 -0.56 1 1
mol:cortisol -0.028 0.051 -10000 0 -0.2 1 1
MMP1 0.013 0.064 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 0.02 0.033 -9999 0 -0.15 16 16
NFATC2 0.009 0.032 -9999 0 -0.16 16 16
NFATC3 0.02 0.033 -9999 0 -0.15 16 16
CD40LG 0.046 0.084 -9999 0 -0.27 12 12
PTGS2 0.037 0.093 -9999 0 -0.28 14 14
JUNB -0.003 0.067 -9999 0 -0.17 63 63
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.039 -9999 0 -0.18 19 19
CaM/Ca2+ 0.011 0.039 -9999 0 -0.18 19 19
CALM1 0.009 0.056 -9999 0 -0.21 28 28
JUN 0.002 0.077 -9999 0 -0.27 37 37
mol:Ca2+ 0.002 0.003 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.029 -9999 0 -0.096 31 31
FOSL1 0.007 0.038 -9999 0 -0.11 51 51
CREM 0.017 0.014 -9999 0 -0.11 6 6
Jun/NFAT1-c-4/p21SNFT 0.055 0.061 -9999 0 -0.22 14 14
FOS -0.042 0.12 -9999 0 -0.21 146 146
IFNG 0.045 0.085 -9999 0 -0.27 13 13
AP-1/NFAT1-c-4 0.083 0.11 -9999 0 -0.29 14 14
FASLG 0.046 0.084 -9999 0 -0.27 12 12
NFAT1-c-4/ICER1 0.043 0.034 -9999 0 -0.13 7 7
IL2RA 0.043 0.087 -9999 0 -0.27 13 13
FKBP12/FK506 0.006 0.035 -9999 0 -0.12 31 31
CSF2 0.046 0.084 -9999 0 -0.27 12 12
JunB/Fra1/NFAT1-c-4 0.041 0.053 -9999 0 -0.14 12 12
IL4 0.046 0.084 -9999 0 -0.27 12 12
IL2 0.005 0.009 -9999 0 -10000 0 0
IL3 0.009 0.05 -9999 0 -0.75 2 2
FKBP1A 0.007 0.052 -9999 0 -0.18 31 31
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.022 0.028 -9999 0 -0.13 14 14
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.031 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.018 0.027 -9999 0 -10000 0 0
mol:DAG 0.025 0.029 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 -0.016 0.073 -9999 0 -0.27 8 8
CaM/Ca2+ 0.027 0.044 -9999 0 -0.25 4 4
HIF1A 0.021 0.047 -9999 0 -0.28 12 12
GAB1 0.003 0.056 -9999 0 -0.15 50 50
AKT1 -0.005 0.1 -9999 0 -0.35 30 30
PLCG1 0.025 0.03 -9999 0 -10000 0 0
NOS3 0.02 0.072 -9999 0 -0.33 12 12
CBL 0.019 0 -9999 0 -10000 0 0
mol:NO 0.02 0.07 -9999 0 -0.32 12 12
FLT1 0.025 0.033 -9999 0 -10000 0 0
PGF 0.009 0.036 -9999 0 -0.12 39 39
VEGFR1 homodimer/NRP2/VEGFR121 -0.007 0.077 -9999 0 -0.26 9 9
CALM1 0.007 0.056 -9999 0 -0.21 28 28
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
eNOS/Hsp90 0.029 0.073 -9999 0 -0.32 13 13
endothelial cell proliferation 0.021 0.04 -9999 0 -0.28 3 3
mol:Ca2+ 0.025 0.029 -9999 0 -10000 0 0
MAPK3 0.027 0.025 -9999 0 -10000 0 0
MAPK1 0.025 0.029 -9999 0 -0.23 2 2
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
PLGF homodimer 0.009 0.036 -9999 0 -0.12 39 39
PRKACA 0.019 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.071 0.13 -9999 0 -0.22 197 197
VEGFA homodimer -0.067 0.13 -9999 0 -0.22 188 188
VEGFR1 homodimer/VEGFA homodimer -0.018 0.082 -9999 0 -0.3 8 8
platelet activating factor biosynthetic process 0.027 0.028 -9999 0 -0.22 2 2
PI3K 0.013 0.081 -9999 0 -0.27 17 17
PRKCA 0.025 0.027 -9999 0 -10000 0 0
PRKCB 0.019 0.026 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.026 0.034 -9999 0 -10000 0 0
VEGFA -0.068 0.13 -9999 0 -0.22 188 188
VEGFB 0.017 0.023 -9999 0 -0.29 3 3
mol:IP3 0.025 0.029 -9999 0 -10000 0 0
RASA1 0.026 0.04 -9999 0 -0.27 7 7
NRP2 0.017 0.016 -9999 0 -0.11 8 8
VEGFR1 homodimer 0.025 0.033 -9999 0 -10000 0 0
VEGFB homodimer 0.017 0.023 -9999 0 -0.29 3 3
NCK1 0.014 0.036 -9999 0 -0.19 14 14
eNOS/Caveolin-1 0.009 0.087 -9999 0 -0.34 21 21
PTPN11 0.015 0.033 -9999 0 -0.27 7 7
mol:PI-3-4-5-P3 0.012 0.079 -9999 0 -0.27 17 17
mol:L-citrulline 0.02 0.07 -9999 0 -0.32 12 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.003 0.081 -9999 0 -0.27 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.008 0.081 -9999 0 -0.26 14 14
CD2AP 0.003 0.062 -9999 0 -0.2 40 40
PI3K/GAB1 0.017 0.083 -9999 0 -0.25 25 25
PDPK1 0.004 0.069 -9999 0 -0.25 17 17
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.007 0.081 -9999 0 -0.29 11 11
mol:NADP 0.02 0.07 -9999 0 -0.32 12 12
HSP90AA1 0.018 0.019 -9999 0 -0.29 2 2
ubiquitin-dependent protein catabolic process -0.004 0.08 -9999 0 -0.27 10 10
VEGFR1 homodimer/NRP2 0.031 0.029 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 -0.001 0.078 -9999 0 -0.27 40 40
SVIL 0.008 0.038 -9999 0 -0.11 50 50
ZNF318 0.015 0.013 -9999 0 -0.11 5 5
JMJD2C 0.026 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.027 0.029 -9999 0 -10000 0 0
CARM1 0.018 0.015 -9999 0 -0.2 2 2
PRDX1 0.012 0.044 -9999 0 -0.24 14 14
PELP1 0.014 0.036 -9999 0 -0.29 7 7
CTNNB1 0.018 0.023 -9999 0 -0.29 3 3
AKT1 0.004 0.063 -9999 0 -0.26 28 28
PTK2B 0.019 0.013 -9999 0 -0.11 5 5
MED1 -0.003 0.078 -9999 0 -0.29 36 36
MAK 0.01 0.026 -9999 0 -0.11 22 22
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 -0.01 0.08 -9999 0 -0.29 31 31
GSN 0 0.065 -9999 0 -0.29 18 18
NCOA2 0.018 0.01 -9999 0 -0.11 3 3
NCOA6 0.004 0.07 -9999 0 -0.28 29 29
DNA-PK 0.022 0.052 -9999 0 -0.19 26 26
NCOA4 0.014 0.038 -9999 0 -0.29 8 8
PIAS3 0.015 0.033 -9999 0 -0.19 12 12
cell proliferation 0.006 0.028 -9999 0 -10000 0 0
XRCC5 0.013 0.038 -9999 0 -0.27 9 9
UBE3A 0.019 0.027 -9999 0 -0.29 4 4
T-DHT/AR/SNURF 0.013 0.027 -9999 0 -0.067 2 2
FHL2 -0.045 0.2 -9999 0 -0.74 37 37
RANBP9 0.012 0.05 -9999 0 -0.29 14 14
JMJD1A 0.022 0.062 -9999 0 -0.29 20 20
CDK6 0.019 0 -9999 0 -10000 0 0
TGFB1I1 -0.01 0.089 -9999 0 -0.25 58 58
T-DHT/AR/CyclinD1 0.004 0.059 -9999 0 -0.14 53 53
XRCC6 0.017 0.019 -9999 0 -0.29 2 2
T-DHT/AR 0.019 0.074 -9999 0 -0.15 46 46
CTDSP1 0.011 0.049 -9999 0 -0.29 13 13
CTDSP2 0.002 0.052 -9999 0 -0.14 50 50
BRCA1 0.019 0.015 -9999 0 -0.11 7 7
TCF4 -0.009 0.085 -9999 0 -0.28 47 47
CDKN2A -0.02 0.059 -9999 0 -0.11 156 156
SRF 0.007 0.039 -9999 0 -0.12 37 37
NKX3-1 0.017 0.096 -9999 0 -0.46 18 18
KLK3 0.02 0.035 -9999 0 -10000 0 0
TMF1 0.015 0.034 -9999 0 -0.23 9 9
HNRNPA1 0.016 0.027 -9999 0 -0.29 4 4
AOF2 0.004 0.066 -9999 0 -0.22 37 37
APPL1 0.006 0.046 -9999 0 -0.19 25 25
T-DHT/AR/Caspase 8 0.023 0.032 -9999 0 -0.11 2 2
AR 0.014 0.03 -9999 0 -0.1 22 22
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.018 0 -9999 0 -10000 0 0
PAWR 0.019 0 -9999 0 -10000 0 0
PRKDC 0.001 0.065 -9999 0 -0.2 41 41
PA2G4 0.014 0.031 -9999 0 -0.29 5 5
UBE2I 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.019 0.039 -9999 0 -0.13 18 18
RPS6KA3 0.015 0.032 -9999 0 -0.14 18 18
T-DHT/AR/ARA70 0.024 0.036 -9999 0 -0.15 8 8
LATS2 -0.001 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.02 0.035 -9999 0 -0.15 10 10
Cyclin D3/CDK11 p58 0.006 0.037 -9999 0 -0.16 24 24
VAV3 -0.022 0.091 -9999 0 -0.18 110 110
KLK2 0.027 0.031 -9999 0 -10000 0 0
CASP8 0.015 0.021 -9999 0 -0.11 14 14
T-DHT/AR/TIF2/CARM1 0.038 0.03 -9999 0 -0.13 1 1
TMPRSS2 0.016 0.096 -9999 0 -0.46 18 18
CCND1 -0.021 0.088 -9999 0 -0.17 112 112
PIAS1 0.011 0.057 -9999 0 -0.29 18 18
mol:T-DHT 0 0.016 -9999 0 -0.054 37 37
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.022 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.026 0.029 -9999 0 -10000 0 0
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.008 0.087 -9999 0 -0.26 52 52
CCND3 0.008 0.055 -9999 0 -0.23 24 24
TGIF1 -0.007 0.077 -9999 0 -0.22 55 55
FKBP4 0.016 0.029 -9999 0 -0.13 17 17
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 -0.004 0.079 -10000 0 -0.26 44 44
SMAD2 0.003 0.051 0.2 2 -0.22 16 18
SMAD3 0.019 0.065 -10000 0 -0.39 8 8
SMAD3/SMAD4 -0.01 0.18 -10000 0 -0.51 49 49
SMAD4/Ubc9/PIASy 0.024 0.049 -10000 0 -0.15 36 36
SMAD2/SMAD2/SMAD4 0.016 0.091 -10000 0 -0.31 22 22
PPM1A 0.017 0.023 -10000 0 -0.29 3 3
CALM1 0.007 0.056 -10000 0 -0.21 28 28
SMAD2/SMAD4 0.009 0.056 -10000 0 -0.23 18 18
MAP3K1 0.015 0.022 -10000 0 -0.11 16 16
TRAP-1/SMAD4 0.009 0.061 -10000 0 -0.19 43 43
MAPK3 0.019 0.006 -10000 0 -10000 0 0
MAPK1 0.009 0.051 -10000 0 -0.22 22 22
NUP214 0.019 0 -10000 0 -10000 0 0
CTDSP1 0.011 0.049 -10000 0 -0.27 15 15
CTDSP2 0.004 0.052 -10000 0 -0.14 50 50
CTDSPL 0.019 0.006 -10000 0 -0.11 1 1
KPNB1 0.007 0.06 -10000 0 -0.28 21 21
TGFBRAP1 0.015 0.033 -10000 0 -0.29 6 6
UBE2I 0.019 0 -10000 0 -10000 0 0
NUP153 0.004 0.066 -10000 0 -0.27 28 28
KPNA2 0 0.074 -10000 0 -0.27 36 36
PIAS4 0.019 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 0.008 0.13 -10000 0 -0.63 19 19
epithelial cell differentiation 0.013 0.12 -10000 0 -0.64 18 18
ITCH 0.015 0.024 -10000 0 -0.093 23 23
WWP1 -0.014 0.23 -10000 0 -1.2 18 18
FYN -0.019 0.1 -10000 0 -0.28 68 68
EGFR -0.08 0.12 -10000 0 -0.29 97 97
PRL 0.016 0.019 -10000 0 -0.11 12 12
neuron projection morphogenesis 0.02 0.11 -10000 0 -0.45 22 22
PTPRZ1 -0.01 0.09 -10000 0 -0.29 49 49
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.031 0.11 -10000 0 -0.5 20 20
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.01 0.11 -10000 0 -0.56 19 19
ADAM17 0.014 0.025 -10000 0 -0.11 7 7
ErbB4/ErbB4 0.004 0.14 -10000 0 -0.69 19 19
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.003 0.12 -10000 0 -0.63 19 19
NCOR1 0.009 0.054 -10000 0 -0.27 18 18
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.01 0.12 -10000 0 -0.54 22 22
GRIN2B 0.01 0.12 -10000 0 -0.55 20 20
ErbB4/ErbB2/betacellulin 0.02 0.11 -10000 0 -0.53 19 19
STAT1 0.008 0.04 -10000 0 -0.12 41 41
HBEGF 0.015 0.022 -10000 0 -0.11 15 15
PRLR 0.019 0 -10000 0 -10000 0 0
E4ICDs/ETO2 0.009 0.13 -10000 0 -0.63 19 19
axon guidance -0.001 0.16 -10000 0 -0.8 18 18
NEDD4 0.01 0.034 -10000 0 -0.11 25 25
Prolactin receptor/Prolactin receptor/Prolactin 0.026 0.014 -10000 0 -10000 0 0
CBFA2T3 0.016 0.019 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.018 0.11 -10000 0 -0.53 19 19
MAPK3 0.021 0.1 -10000 0 -0.47 20 20
STAT1 (dimer) 0.006 0.13 -10000 0 -0.62 19 19
MAPK1 0.019 0.11 -10000 0 -0.47 22 22
JAK2 0.013 0.026 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.015 0.11 -10000 0 -0.53 19 19
NRG1 0.018 0.016 -10000 0 -10000 0 0
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.019 0.006 -10000 0 -0.11 1 1
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.001 0.16 -10000 0 -0.8 18 18
neural crest cell migration 0.015 0.11 -10000 0 -0.52 19 19
ERBB2 0.018 0.016 -10000 0 -10000 0 0
WWOX/E4ICDs 0.01 0.13 -10000 0 -0.63 19 19
SHC1 0.004 0.052 -10000 0 -0.14 48 48
ErbB4/EGFR/neuregulin 4 -0.037 0.13 -10000 0 -0.59 21 21
apoptosis -0.004 0.12 0.58 19 -10000 0 19
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.01 0.13 -10000 0 -0.63 19 19
ErbB4/ErbB2/epiregulin 0.018 0.11 -10000 0 -0.53 19 19
ErbB4/ErbB4/betacellulin/betacellulin 0.01 0.13 -10000 0 -0.63 19 19
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.034 0.12 -10000 0 -0.54 19 19
MDM2 0.003 0.12 -10000 0 -0.63 19 19
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.016 0.1 -10000 0 -0.51 18 18
STAT5A 0.003 0.15 -10000 0 -0.76 18 18
ErbB4/EGFR/neuregulin 1 beta -0.009 0.12 -10000 0 -0.59 18 18
DLG4 0.019 0 -10000 0 -10000 0 0
GRB2/SHC 0.014 0.046 -10000 0 -0.21 16 16
E4ICDs/TAB2/NCoR1 0.011 0.13 -10000 0 -0.63 19 19
STAT5A (dimer) 0.023 0.14 -10000 0 -0.7 18 18
MAP3K7IP2 0.008 0.057 -10000 0 -0.27 20 20
STAT5B (dimer) 0.008 0.15 -10000 0 -0.76 18 18
LRIG1 -0.02 0.098 -10000 0 -0.24 80 80
EREG 0.015 0.023 -10000 0 -0.11 17 17
BTC 0.019 0.006 -10000 0 -0.11 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.16 -10000 0 -0.81 18 18
ERBB4 0.004 0.14 -10000 0 -0.7 19 19
STAT5B 0.018 0.015 -10000 0 -0.2 2 2
YAP1 -0.084 0.21 -10000 0 -0.51 96 96
GRB2 0.014 0.039 -10000 0 -0.26 10 10
ErbB4/ErbB2/neuregulin 4 0.007 0.11 -10000 0 -0.54 19 19
glial cell differentiation -0.011 0.13 0.62 19 -10000 0 19
WWOX 0.019 0.008 -10000 0 -0.11 2 2
cell proliferation 0.019 0.11 -10000 0 -0.57 18 18
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.004 0.17 -10000 0 -1.1 12 12
CLOCK 0.009 0.055 -10000 0 -0.25 19 19
TIMELESS/CRY2 0.001 0.18 -10000 0 -1.1 12 12
DEC1/BMAL1 0.005 0.065 -10000 0 -0.19 49 49
ATR 0.011 0.049 -10000 0 -0.26 16 16
NR1D1 0.013 0.07 -10000 0 -10000 0 0
ARNTL -0.014 0.093 -10000 0 -0.24 70 70
TIMELESS -0.007 0.18 -10000 0 -1.2 12 12
NPAS2 0.018 0.019 -10000 0 -0.11 9 9
CRY2 0.017 0.016 -10000 0 -0.11 8 8
mol:CO -0.006 0.024 0.14 12 -10000 0 12
CHEK1 0.006 0.046 -10000 0 -0.13 48 48
mol:HEME 0.006 0.024 -10000 0 -0.14 12 12
PER1 -0.003 0.077 -10000 0 -0.25 44 44
BMAL/CLOCK/NPAS2 0.017 0.076 -10000 0 -0.17 59 59
BMAL1/CLOCK -0.009 0.14 -10000 0 -0.56 20 20
S phase of mitotic cell cycle 0.004 0.17 -10000 0 -1.1 12 12
TIMELESS/CHEK1/ATR 0.003 0.18 -10000 0 -1.1 12 12
mol:NADPH 0.006 0.024 -10000 0 -0.14 12 12
PER1/TIMELESS -0.005 0.18 -10000 0 -1.1 12 12
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.014 0.079 -9999 0 -0.16 96 96
positive regulation of NF-kappaB transcription factor activity 0.005 0.056 -9999 0 -0.19 28 28
MAP2K4 0.021 0.049 -9999 0 -0.21 8 8
IKBKB 0.019 0 -9999 0 -10000 0 0
TNFRSF10B 0.015 0.022 -9999 0 -0.11 15 15
TNFRSF10A 0 0 -9999 0 -10000 0 0
SMPD1 0.005 0.035 -9999 0 -0.12 29 29
IKBKG 0.019 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.006 -9999 0 -0.11 1 1
TRAIL/TRAILR2 0.003 0.058 -9999 0 -0.19 33 33
TRAIL/TRAILR3 0.005 0.056 -9999 0 -0.19 30 30
TRAIL/TRAILR1 -0.008 0.053 -9999 0 -0.11 96 96
TRAIL/TRAILR4 0.005 0.056 -9999 0 -0.19 28 28
TRAIL/TRAILR1/DAP3/GTP 0.003 0.049 -9999 0 -0.15 40 40
IKK complex 0.029 0.029 -9999 0 -0.27 2 2
RIPK1 0.016 0.019 -9999 0 -0.11 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.009 0.033 -9999 0 -0.2 13 13
MAPK3 -0.001 0.053 -9999 0 -0.19 28 28
MAP3K1 0.019 0.049 -9999 0 -0.19 8 8
TRAILR4 (trimer) 0.019 0.006 -9999 0 -0.11 1 1
TRADD 0.019 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.014 0.045 -9999 0 -0.16 30 30
CFLAR 0.016 0.024 -9999 0 -0.15 9 9
MAPK1 -0.007 0.063 -9999 0 -0.2 42 42
TRAIL/TRAILR1/FADD/TRADD/RIP 0.024 0.046 -9999 0 -0.12 30 30
mol:ceramide 0.005 0.035 -9999 0 -0.12 29 29
FADD 0.017 0.021 -9999 0 -0.2 4 4
MAPK8 0.023 0.048 -9999 0 -0.3 2 2
TRAF2 0.019 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.008 -9999 0 -0.11 2 2
CHUK 0.016 0.025 -9999 0 -0.15 10 10
TRAIL/TRAILR1/FADD 0.005 0.048 -9999 0 -0.16 31 31
DAP3 0.011 0.048 -9999 0 -0.28 14 14
CASP10 -0.002 0.05 -9999 0 -0.19 30 30
JNK cascade 0.005 0.056 -9999 0 -0.19 28 28
TRAIL (trimer) -0.014 0.079 -9999 0 -0.16 96 96
TNFRSF10C 0.019 0.008 -9999 0 -0.11 2 2
TRAIL/TRAILR1/DAP3/GTP/FADD 0.012 0.051 -9999 0 -0.14 41 41
TRAIL/TRAILR2/FADD 0.015 0.053 -9999 0 -0.15 36 36
cell death 0.005 0.035 -9999 0 -0.12 29 29
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.019 0.046 -9999 0 -0.19 3 3
TRAILR2 (trimer) 0.015 0.022 -9999 0 -0.11 15 15
CASP8 0.014 0.022 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.033 0.05 -9999 0 -0.12 30 30
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.023 0 -9999 0 -10000 0 0
RGS9BP 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.024 0.07 -9999 0 -0.16 99 99
mol:ADP 0 0 -9999 0 -10000 0 0
GNAT2 0.019 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.016 -9999 0 -0.16 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.026 0 -9999 0 -10000 0 0
GRK7 0 0 -9999 0 -10000 0 0
CNGB3 0.019 0 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ -0.019 0.061 -9999 0 -0.14 99 99
Cone PDE6 0.042 0.016 -9999 0 -0.12 1 1
Cone Metarhodopsin II 0 0 -9999 0 -10000 0 0
Na + (4 Units) -0.011 0.066 -9999 0 -0.13 99 99
GNAT2/GDP 0.031 0.015 -9999 0 -0.13 1 1
GNB5 0.017 0.019 -9999 0 -0.14 7 7
mol:GMP (4 units) 0.023 0 -9999 0 -10000 0 0
Cone Transducin 0.025 0 -9999 0 -10000 0 0
SLC24A2 0.019 0.008 -9999 0 -0.11 2 2
GNB3/GNGT2 0.014 0 -9999 0 -10000 0 0
GNB3 0.019 0 -9999 0 -10000 0 0
GNAT2/GTP 0.014 0 -9999 0 -10000 0 0
CNGA3 -0.065 0.12 -9999 0 -0.2 206 206
ARR3 0.019 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.024 0.07 -9999 0 -0.16 99 99
mol:Pi 0.022 0.016 -9999 0 -0.16 1 1
Cone CNG Channel 0.003 0.062 -9999 0 -0.11 99 99
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.019 0.008 -9999 0 -0.11 2 2
RGS9 0.016 0.02 -9999 0 -0.11 13 13
PDE6C 0.019 0 -9999 0 -10000 0 0
GNGT2 0 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.019 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.013 0.04 -10000 0 -0.22 13 13
HDAC3 0.018 0.014 -10000 0 -0.29 1 1
VDR 0.019 0.008 -10000 0 -0.11 2 2
Cbp/p300/PCAF 0.021 0.027 -10000 0 -0.16 11 11
EP300 0.012 0.046 -10000 0 -0.24 15 15
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.032 0.034 -10000 0 -0.21 5 5
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.018 0.013 -10000 0 -0.11 5 5
AKT1 0.045 0.073 0.18 87 -0.18 16 103
RAR alpha/9cRA/Cyclin H 0.021 0.085 -10000 0 -0.27 25 25
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.024 0.055 -10000 0 -0.26 16 16
CDC2 -0.03 0.1 -10000 0 -0.19 123 123
response to UV -0.001 0.007 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.023 0.022 -10000 0 -10000 0 0
NCOR2 0.019 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.005 -10000 0 -0.07 2 2
RXRs/RARs/NRIP1/9cRA 0.019 0.15 -10000 0 -0.52 35 35
NCOA2 0.018 0.01 -10000 0 -0.11 3 3
NCOA3 0.018 0.013 -10000 0 -0.11 5 5
NCOA1 -0.006 0.083 -10000 0 -0.28 43 43
VDR/VDR/DNA 0.019 0.008 -10000 0 -0.11 2 2
RARG 0.019 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.025 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.008 -10000 0 -10000 0 0
MAPK1 0.009 0.051 -10000 0 -0.22 22 22
MAPK8 0.018 0.009 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.018 0.097 -10000 0 -0.32 35 35
RARA 0.023 0.024 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.031 0.028 -10000 0 -0.2 5 5
PRKCA 0.018 0.016 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.006 0.16 -10000 0 -0.59 35 35
RXRG 0.023 0.026 -10000 0 -10000 0 0
RXRA 0.003 0.074 -10000 0 -0.26 14 14
RXRB 0.024 0.024 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.005 -10000 0 -0.07 2 2
RBP1 -0.051 0.12 -10000 0 -0.24 145 145
CRBP1/9-cic-RA -0.033 0.083 -10000 0 -0.16 145 145
RARB 0.019 0.01 -10000 0 -0.12 1 1
PRKCG 0.018 0.016 -10000 0 -10000 0 0
MNAT1 0.015 0.033 -10000 0 -0.19 11 11
RAR alpha/RXRs 0.039 0.12 -10000 0 -0.37 26 26
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.038 0.081 -10000 0 -0.26 26 26
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.033 -10000 0 -0.16 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 0.007 0.16 -10000 0 -0.59 35 35
positive regulation of DNA binding 0.014 0.078 -10000 0 -0.25 25 25
NRIP1 -0.027 0.29 -10000 0 -1.1 35 35
RXRs/RARs 0.017 0.12 -10000 0 -0.41 35 35
RXRs/RXRs/DNA/9cRA 0.008 0.097 -10000 0 -0.33 35 35
PRKACA 0.019 0 -10000 0 -10000 0 0
CDK7 0.011 0.048 -10000 0 -0.24 17 17
TFIIH 0.027 0.056 -10000 0 -0.2 24 24
RAR alpha/9cRA 0.039 0.05 -10000 0 -0.24 10 10
CCNH 0.011 0.048 -10000 0 -0.28 14 14
CREBBP 0.019 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.028 0.044 -10000 0 -0.2 12 12
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.036 0.064 -10000 0 -0.22 12 12
TBX21 0.016 0.17 -10000 0 -0.54 14 14
B2M 0.017 0.027 -10000 0 -0.29 4 4
TYK2 0.008 0.066 -10000 0 -0.3 21 21
IL12RB1 0.02 0.018 -10000 0 -0.13 1 1
GADD45B -0.016 0.28 -10000 0 -1.1 28 28
IL12RB2 0.021 0.017 -10000 0 -10000 0 0
GADD45G 0.02 0.16 -10000 0 -0.54 8 8
natural killer cell activation 0.002 0.015 -10000 0 -10000 0 0
RELB 0.018 0.011 -10000 0 -0.11 4 4
RELA 0.018 0.02 -10000 0 -0.23 3 3
IL18 0 0.058 -10000 0 -0.14 56 56
IL2RA 0.012 0.029 -10000 0 -0.11 28 28
IFNG 0.018 0.01 -10000 0 -0.11 3 3
STAT3 (dimer) 0.011 0.21 -10000 0 -0.56 37 37
HLA-DRB5 -0.003 0.008 -10000 0 -10000 0 0
FASLG 0.016 0.17 -10000 0 -0.6 8 8
NF kappa B2 p52/RelB 0.017 0.16 -10000 0 -0.48 22 22
CD4 -0.007 0.071 -10000 0 -0.19 56 56
SOCS1 0.019 0 -10000 0 -10000 0 0
EntrezGene:6955 -0.003 0.009 -10000 0 -10000 0 0
CD3D 0.005 0.036 -10000 0 -0.12 39 39
CD3E 0.015 0.013 -10000 0 -0.12 2 2
CD3G 0.012 0.022 -10000 0 -0.13 3 3
IL12Rbeta2/JAK2 0.028 0.034 -10000 0 -10000 0 0
CCL3 0.008 0.17 -10000 0 -0.49 22 22
CCL4 -0.042 0.31 -10000 0 -1 38 38
HLA-A 0.012 0.046 -10000 0 -0.29 12 12
IL18/IL18R 0.04 0.053 -10000 0 -0.15 14 14
NOS2 0.012 0.16 -10000 0 -0.41 32 32
IL12/IL12R/TYK2/JAK2/SPHK2 0.036 0.064 -10000 0 -0.22 12 12
IL1R1 0.015 0.17 -10000 0 -0.6 8 8
IL4 0.017 0.015 -10000 0 -10000 0 0
JAK2 0.015 0.032 -10000 0 -0.12 14 14
EntrezGene:6957 -0.003 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.016 0.039 -10000 0 -0.17 11 11
RAB7A 0.009 0.24 -10000 0 -0.83 28 28
lysosomal transport 0.012 0.23 -10000 0 -0.76 29 29
FOS -0.17 0.46 -10000 0 -1.2 85 85
STAT4 (dimer) 0.029 0.19 -10000 0 -0.55 26 26
STAT5A (dimer) 0.018 0.16 -10000 0 -0.48 21 21
GZMA 0.01 0.17 -10000 0 -0.64 6 6
GZMB 0.012 0.17 -10000 0 -0.6 9 9
HLX 0.015 0.023 -10000 0 -0.11 17 17
LCK 0.011 0.17 -10000 0 -0.5 23 23
TCR/CD3/MHC II/CD4 -0.045 0.12 -10000 0 -0.24 104 104
IL2/IL2R 0.039 0.032 -10000 0 -0.14 2 2
MAPK14 0.01 0.23 -10000 0 -0.73 30 30
CCR5 0.02 0.17 -10000 0 -0.61 10 10
IL1B -0.008 0.068 -10000 0 -0.13 96 96
STAT6 0.019 0.071 -10000 0 -0.21 5 5
STAT4 0.012 0.03 -10000 0 -0.11 30 30
STAT3 -0.003 0.079 -10000 0 -0.29 37 37
STAT1 0.008 0.04 -10000 0 -0.12 41 41
NFKB1 0.014 0.037 -10000 0 -0.23 11 11
NFKB2 0.019 0.008 -10000 0 -0.11 2 2
IL12B 0.021 0.017 -10000 0 -10000 0 0
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.018 0.011 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.036 0.064 0.22 12 -10000 0 12
IL2RB 0.014 0.024 -10000 0 -0.11 19 19
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.18 -10000 0 -0.51 26 26
IL2RG 0.013 0.027 -10000 0 -0.11 24 24
IL12 0.032 0.027 -10000 0 -10000 0 0
STAT5A 0.019 0.008 -10000 0 -0.11 2 2
CD247 0.014 0.018 -10000 0 -0.11 7 7
IL2 0.019 0.006 -10000 0 -0.11 1 1
SPHK2 0.019 0 -10000 0 -10000 0 0
FRAP1 0.019 0.006 -10000 0 -0.11 1 1
IL12A 0.02 0.017 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.01 0.18 -10000 0 -0.53 22 22
MAP2K3 0.011 0.21 -10000 0 -0.66 30 30
RIPK2 0.017 0.021 -10000 0 -0.18 5 5
MAP2K6 0.011 0.21 -10000 0 -0.66 30 30
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.05 0.12 -10000 0 -0.24 138 138
IL18RAP 0.019 0.017 -10000 0 -0.11 7 7
IL12Rbeta1/TYK2 0.021 0.053 -10000 0 -0.22 20 20
EOMES -0.001 0.021 0.059 5 -10000 0 5
STAT1 (dimer) 0.028 0.16 -10000 0 -0.46 21 21
T cell proliferation 0.019 0.16 -10000 0 -0.45 32 32
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.014 -10000 0 -0.11 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.051 0.14 -10000 0 -0.5 34 34
ATF2 0.015 0.21 -10000 0 -0.67 30 30
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.03 0.051 -9999 0 -0.13 40 40
MAP4K1 0.019 0.006 -9999 0 -0.11 1 1
MAP3K8 0.004 0.042 -9999 0 -0.11 62 62
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0.018 0.01 -9999 0 -0.11 3 3
MAP3K1 0.013 0.055 -9999 0 -0.22 6 6
JUN 0.01 0.041 -9999 0 -0.22 1 1
MAP3K7 0.012 0.063 -9999 0 -0.24 15 15
GRAP2 0.019 0 -9999 0 -10000 0 0
CRK 0.009 0.054 -9999 0 -0.28 17 17
MAP2K4 0.013 0.063 -9999 0 -0.21 17 17
LAT 0.018 0.014 -9999 0 -10000 0 0
LCP2 -0.012 0.086 -9999 0 -0.21 70 70
MAPK8 0.016 0.018 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.012 0.058 -9999 0 -0.16 40 40
LAT/GRAP2/SLP76/HPK1/HIP-55 0.028 0.048 -9999 0 -0.12 40 40
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.017 0.069 -9999 0 -0.25 23 23
CaM/Ca2+ 0.006 0.038 -9999 0 -0.14 28 28
AKT1 0.005 0.063 -9999 0 -0.25 28 28
AKT2 0.019 0 -9999 0 -10000 0 0
STXBP4 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.007 0.069 -9999 0 -0.28 21 21
YWHAZ 0.014 0.037 -9999 0 -0.23 11 11
CALM1 0.007 0.056 -9999 0 -0.21 28 28
YWHAQ 0.018 0.019 -9999 0 -0.29 2 2
TBC1D4 0.009 0.045 -9999 0 -0.19 23 23
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH -0.006 0.083 -9999 0 -0.26 49 49
YWHAB 0.015 0.036 -9999 0 -0.29 7 7
SNARE/Synip 0.014 0.042 -9999 0 -0.17 19 19
YWHAG 0 0 -9999 0 -10000 0 0
ASIP 0.019 0 -9999 0 -10000 0 0
PRKCI 0.015 0.028 -9999 0 -0.14 15 15
AS160/CaM/Ca2+ 0.006 0.038 -9999 0 -0.14 28 28
RHOQ 0.011 0.048 -9999 0 -0.28 14 14
GYS1 -0.003 0.11 -9999 0 -0.41 31 31
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.015 0.029 -9999 0 -0.15 13 13
TC10/GTP/CIP4/Exocyst 0.019 0.033 -9999 0 -0.16 16 16
AS160/14-3-3 0.002 0.12 -9999 0 -0.3 44 44
VAMP2 0.006 0.048 -9999 0 -0.15 40 40
SLC2A4 0.006 0.076 -9999 0 -0.3 21 21
STX4 0.011 0.048 -9999 0 -0.28 14 14
GSK3B 0.003 0.095 -9999 0 -0.35 31 31
SFN 0.002 0.044 -9999 0 -0.11 70 70
LNPEP 0.018 0.011 -9999 0 -10000 0 0
YWHAE 0.011 0.045 -9999 0 -0.21 19 19
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.02 0.086 -9999 0 -0.2 58 58
Ran/GTP/Exportin 1/HDAC1 -0.008 0.034 -9999 0 -0.13 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.008 0.11 -9999 0 -0.27 60 60
SUMO1 0.017 0.027 -9999 0 -0.29 4 4
ZFPM1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.036 -9999 0 -0.16 21 21
FKBP3 0.016 0.033 -9999 0 -0.29 6 6
Histones 0.017 0.074 -9999 0 -0.24 26 26
YY1/LSF 0.023 0.043 -9999 0 -0.23 12 12
SMG5 0.019 0.008 -9999 0 -0.11 2 2
RAN 0.016 0.031 -9999 0 -0.24 7 7
I kappa B alpha/HDAC3 0 0.094 -9999 0 -0.22 68 68
I kappa B alpha/HDAC1 0.002 0.1 -9999 0 -0.32 39 39
SAP18 0.01 0.052 -9999 0 -0.29 15 15
RELA 0.011 0.079 -9999 0 -0.18 60 60
HDAC1/Smad7 0.03 0.033 -9999 0 -0.16 11 11
RANGAP1 0.017 0.015 -9999 0 -0.11 7 7
HDAC3/TR2 0.017 0.064 -9999 0 -0.29 14 14
NuRD/MBD3 Complex -0.003 0.13 -9999 0 -0.4 36 36
NF kappa B1 p50/RelA 0.017 0.078 -9999 0 -0.17 60 60
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.018 0.011 -9999 0 -0.11 4 4
GATA1 0.019 0 -9999 0 -10000 0 0
Mad/Max 0.028 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.002 0.13 -9999 0 -0.39 36 36
RBBP7 0.015 0.034 -9999 0 -0.25 8 8
NPC 0.006 0.027 -9999 0 -0.14 18 18
RBBP4 -0.005 0.079 -9999 0 -0.24 50 50
MAX 0.019 0.006 -9999 0 -0.11 1 1
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.011 0.047 -9999 0 -0.27 14 14
NFKBIA -0.007 0.1 -9999 0 -0.36 34 34
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.004 0.097 -9999 0 -0.38 22 22
SIN3 complex 0.029 0.038 -9999 0 -0.16 19 19
SMURF1 0.019 0 -9999 0 -10000 0 0
CHD3 0.019 0.006 -9999 0 -0.11 1 1
SAP30 0.017 0.027 -9999 0 -0.29 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.009 0.054 -9999 0 -0.27 18 18
YY1/HDAC3 0.016 0.073 -9999 0 -0.35 13 13
YY1/HDAC2 0.021 0.041 -9999 0 -0.22 11 11
YY1/HDAC1 0.023 0.041 -9999 0 -0.22 11 11
NuRD/MBD2 Complex (MeCP1) 0.003 0.11 -9999 0 -0.34 31 31
PPARG 0.003 0.088 -9999 0 -0.22 64 64
HDAC8/hEST1B 0.026 0.005 -9999 0 -10000 0 0
UBE2I 0.019 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0.047 -9999 0 -0.27 14 14
TNFRSF1A -0.01 0.091 -9999 0 -0.29 50 50
HDAC3/SMRT (N-CoR2) 0.017 0.064 -9999 0 -0.29 14 14
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.03 0.033 -9999 0 -0.16 11 11
CREBBP 0.019 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.001 0.12 -9999 0 -0.37 37 37
HDAC1 0.013 0.04 -9999 0 -0.22 13 13
HDAC3 0.007 0.069 -9999 0 -0.31 15 15
HDAC2 0.004 0.061 -9999 0 -0.22 33 33
YY1 0.016 0.041 -9999 0 -0.25 11 11
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0.011 0.035 -9999 0 -0.13 27 27
NCOR2 0.019 0 -9999 0 -10000 0 0
MXD1 0.019 0.006 -9999 0 -0.11 1 1
STAT3 0.003 0.08 -9999 0 -0.25 43 43
NFKB1 0.014 0.037 -9999 0 -0.23 11 11
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.007 0.057 -9999 0 -0.26 22 22
YY1/LSF/HDAC1 0.029 0.05 -9999 0 -0.17 26 26
YY1/SAP30/HDAC1 0.031 0.044 -9999 0 -0.16 22 22
EP300 0.012 0.046 -9999 0 -0.24 15 15
STAT3 (dimer non-phopshorylated) 0.003 0.08 -9999 0 -0.25 43 43
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.1 -9999 0 -0.36 34 34
histone deacetylation 0.004 0.1 -9999 0 -0.34 31 31
STAT3 (dimer non-phopshorylated)/HDAC3 0.007 0.1 -9999 0 -0.37 25 25
nuclear export -0.025 0.005 -9999 0 -10000 0 0
PRKACA 0.019 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0.075 -9999 0 -0.29 33 33
GATA2/HDAC3 0.017 0.065 -9999 0 -0.29 14 14
GATA1/HDAC1 0.024 0.028 -9999 0 -0.19 8 8
GATA1/HDAC3 0.017 0.064 -9999 0 -0.29 14 14
CHD4 0.007 0.059 -9999 0 -0.29 20 20
TNF-alpha/TNFR1A 0.007 0.065 -9999 0 -0.19 50 50
SIN3/HDAC complex/Mad/Max 0.012 0.088 -9999 0 -0.33 22 22
NuRD Complex 0.004 0.12 -9999 0 -0.38 37 37
positive regulation of chromatin silencing 0.015 0.072 -9999 0 -0.24 26 26
SIN3B 0.017 0.025 -9999 0 -0.2 6 6
MTA2 0.019 0.006 -9999 0 -0.11 1 1
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0.017 0.023 -9999 0 -0.29 3 3
SUMO1/HDAC1 0.027 0.043 -9999 0 -0.18 11 11
HDAC complex 0.022 0.075 -9999 0 -0.18 49 49
GATA1/Fog1 0.014 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.024 0.052 -9999 0 -0.17 29 29
TNF 0.018 0.01 -9999 0 -0.11 3 3
negative regulation of cell growth 0.012 0.087 -9999 0 -0.33 22 22
NuRD/MBD2/PRMT5 Complex 0.003 0.11 -9999 0 -0.34 31 31
Ran/GTP/Exportin 1 0.03 0.046 -9999 0 -0.16 21 21
NF kappa B/RelA/I kappa B alpha 0.002 0.11 -9999 0 -0.28 59 59
SIN3/HDAC complex/NCoR1 0.002 0.11 -9999 0 -0.37 26 26
TFCP2 0.012 0.043 -9999 0 -0.25 13 13
NR2C1 0.019 0 -9999 0 -10000 0 0
MBD3 0.008 0.056 -9999 0 -0.29 18 18
MBD2 0.019 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.014 0.043 -10000 0 -0.2 14 14
CRKL 0.015 0.078 -10000 0 -0.47 12 12
mol:PIP3 -0.01 0.037 0.23 9 -10000 0 9
AKT1 -0.005 0.039 0.22 5 -0.15 20 25
PTK2B 0.018 0.013 -10000 0 -0.11 5 5
RAPGEF1 0.018 0.074 -10000 0 -0.44 12 12
RANBP10 0.019 0 -10000 0 -10000 0 0
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
HGF/MET/SHIP2 0.027 0.034 -10000 0 -0.14 10 10
MAP3K5 0.014 0.084 -10000 0 -0.38 15 15
HGF/MET/CIN85/CBL/ENDOPHILINS 0.028 0.025 -10000 0 -0.093 4 4
AP1 -0.027 0.092 -10000 0 -0.2 93 93
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.004 0.052 -10000 0 -0.14 48 48
apoptosis -0.12 0.31 -10000 0 -0.78 93 93
STAT3 (dimer) 0.015 0.073 -10000 0 -0.28 22 22
GAB1/CRKL/SHP2/PI3K 0.013 0.11 -10000 0 -0.4 24 24
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.021 0.082 -10000 0 -0.41 14 14
PTPN11 0.015 0.033 -10000 0 -0.27 7 7
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.017 0.025 -10000 0 -0.29 3 3
PTEN 0.013 0.038 -10000 0 -0.18 17 17
ELK1 -0.001 0.04 0.23 13 -10000 0 13
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.016 0.043 -10000 0 -0.18 19 19
PAK1 -0.001 0.037 0.21 5 -0.14 18 23
HGF/MET/RANBP10 0.03 0.027 -10000 0 -0.1 4 4
HRAS 0.011 0.098 -10000 0 -0.52 14 14
DOCK1 0.015 0.078 -10000 0 -0.45 12 12
GAB1 0.011 0.082 -10000 0 -0.49 12 12
CRK 0.011 0.084 -10000 0 -0.44 14 14
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.08 -10000 0 -0.44 14 14
JUN -0.002 0.077 -10000 0 -0.28 37 37
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.012 0.014 -10000 0 -10000 0 0
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
cell morphogenesis 0.007 0.099 -10000 0 -0.3 38 38
GRB2/SHC 0.024 0.037 -10000 0 -0.13 15 15
FOS -0.046 0.12 -10000 0 -0.22 146 146
GLMN 0.002 0.016 0.086 2 -0.19 3 5
cell motility -0.001 0.04 0.23 13 -10000 0 13
HGF/MET/MUC20 0.017 0.025 -10000 0 -0.11 4 4
cell migration 0.023 0.036 -10000 0 -0.13 15 15
GRB2 0.014 0.039 -10000 0 -0.26 10 10
CBL 0.019 0 -10000 0 -10000 0 0
MET/RANBP10 0.02 0.026 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.016 0.062 -10000 0 -0.27 13 13
MET/MUC20 0.007 0.024 -10000 0 -10000 0 0
RAP1B 0.018 0.07 -10000 0 -0.41 12 12
RAP1A 0.022 0.071 -10000 0 -0.41 12 12
HGF/MET/RANBP9 0.025 0.04 -10000 0 -0.14 18 18
RAF1 0.01 0.1 -10000 0 -0.47 19 19
STAT3 0.015 0.073 -10000 0 -0.29 22 22
cell proliferation 0.019 0.068 -10000 0 -0.3 15 15
RPS6KB1 0.013 0.011 -10000 0 -10000 0 0
MAPK3 -0.013 0.016 -10000 0 -10000 0 0
MAPK1 0.005 0.11 0.71 13 -10000 0 13
RANBP9 0.011 0.05 -10000 0 -0.29 14 14
MAPK8 0.019 0.082 -10000 0 -0.33 17 17
SRC 0.019 0.058 -10000 0 -0.25 13 13
PI3K 0.003 0.067 -10000 0 -0.14 82 82
MET/Glomulin 0.01 0.025 -10000 0 -0.15 4 4
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.013 0.1 -10000 0 -0.46 19 19
MET 0.008 0.037 -10000 0 -0.11 47 47
MAP4K1 0.023 0.076 -10000 0 -0.44 12 12
PTK2 0.009 0.054 -10000 0 -0.27 18 18
MAP2K2 0.014 0.099 -10000 0 -0.44 19 19
BAD -0.002 0.041 0.21 5 -0.16 21 26
MAP2K4 0.016 0.08 -10000 0 -0.35 16 16
SHP2/GRB2/SOS1/GAB1 -0.013 0.067 -10000 0 -0.35 18 18
INPPL1 0.016 0.033 -10000 0 -0.29 6 6
PXN 0.018 0.011 -10000 0 -0.11 4 4
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.013 0.017 -10000 0 -0.16 2 2
PLCgamma1/PKC 0.013 0.017 -10000 0 -0.2 3 3
HGF 0.016 0.02 -10000 0 -0.11 13 13
RASA1 0.003 0.069 -10000 0 -0.28 29 29
NCK1 0.014 0.036 -10000 0 -0.19 14 14
PTPRJ 0.019 0 -10000 0 -10000 0 0
NCK/PLCgamma1 0.031 0.027 -10000 0 -0.13 7 7
PDPK1 -0.004 0.031 0.2 8 -10000 0 8
HGF/MET/SHIP 0.017 0.025 -10000 0 -0.11 4 4
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.017 0.018 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.019 0 -9999 0 -10000 0 0
TCEB1 0.013 0.041 -9999 0 -0.27 10 10
HIF1A/p53 0.018 0.044 -9999 0 -0.21 9 9
HIF1A 0.013 0.035 -9999 0 -0.21 6 6
COPS5 0.016 0.03 -9999 0 -0.29 5 5
VHL/Elongin B/Elongin C/RBX1/CUL2 0.032 0.053 -9999 0 -0.15 33 33
FIH (dimer) 0.019 0 -9999 0 -10000 0 0
CDKN2A -0.019 0.059 -9999 0 -0.11 156 156
ARNT/IPAS 0.026 0.013 -9999 0 -10000 0 0
HIF1AN 0.019 0 -9999 0 -10000 0 0
GNB2L1 0.018 0.019 -9999 0 -0.29 2 2
HIF1A/ARNT 0.024 0.035 -9999 0 -0.2 6 6
CUL2 0.005 0.064 -9999 0 -0.26 27 27
OS9 -0.005 0.069 -9999 0 -0.17 67 67
RACK1/Elongin B/Elongin C 0.035 0.029 -9999 0 -0.17 10 10
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.023 0.038 -9999 0 -0.22 6 6
PHD1-3/OS9 0.016 0.067 -9999 0 -0.17 43 43
HIF1A/RACK1/Elongin B/Elongin C 0.037 0.043 -9999 0 -0.2 7 7
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0.018 0.019 -9999 0 -0.29 2 2
HIF1A/JAB1 0.023 0.039 -9999 0 -0.21 8 8
EGLN3 -0.005 0.067 -9999 0 -0.16 72 72
EGLN2 0.019 0 -9999 0 -10000 0 0
EGLN1 0.009 0.052 -9999 0 -0.24 20 20
TP53 -0.007 0.077 -9999 0 -0.2 62 62
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.015 0.095 -9999 0 -0.66 9 9
ARNT 0.019 0.006 -9999 0 -0.11 1 1
ARD1A 0.018 0.017 -9999 0 -0.16 4 4
RBX1 0.013 0.041 -9999 0 -0.27 10 10
HIF1A/p19ARF 0.008 0.045 -9999 0 -0.21 8 8
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.012 0.089 -9999 0 -0.43 20 20
Crk/p130 Cas/Paxillin -0.032 0.071 -9999 0 -0.24 43 43
JUN 0.022 0.059 -9999 0 -0.27 14 14
HRAS 0.009 0.055 -9999 0 -0.28 18 18
RET51/GFRalpha1/GDNF/GRB10 0.024 0.055 -9999 0 -0.13 45 45
RAP1A 0.018 0.019 -9999 0 -0.29 2 2
FRS2 0.018 0.013 -9999 0 -0.11 5 5
RAP1A/GDP 0.013 0.013 -9999 0 -0.2 2 2
RET51/GFRalpha1/GDNF/DOK1 0.047 0.015 -9999 0 -10000 0 0
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.015 0.033 -9999 0 -0.27 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.009 0.054 -9999 0 -0.28 17 17
RET9/GFRalpha1/GDNF/Enigma 0.037 0.005 -9999 0 -10000 0 0
RHOA 0.015 0.036 -9999 0 -0.29 7 7
RAP1A/GTP 0.043 0.016 -9999 0 -0.11 2 2
GRB7 0.016 0.019 -9999 0 -0.11 11 11
RET51/GFRalpha1/GDNF 0.047 0.015 -9999 0 -10000 0 0
MAPKKK cascade 0.026 0.044 -9999 0 -0.21 12 12
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.025 0.039 -9999 0 -0.13 25 25
lamellipodium assembly -0.03 0.072 -9999 0 -0.22 47 47
RET51/GFRalpha1/GDNF/SHC 0.037 0.034 -9999 0 -0.13 9 9
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
RET9/GFRalpha1/GDNF/SHC 0.028 0.03 -9999 0 -0.13 11 11
RET9/GFRalpha1/GDNF/Shank3 0.024 0.004 -9999 0 -10000 0 0
MAPK3 0.031 0.013 -9999 0 -0.1 2 2
DOK1 0.019 0 -9999 0 -10000 0 0
DOK6 0 0 -9999 0 -10000 0 0
PXN 0.018 0.011 -9999 0 -0.11 4 4
neurite development 0.031 0.037 -9999 0 -0.18 13 13
DOK5 -0.026 0.11 -9999 0 -0.27 82 82
GFRA1 0.019 0.008 -9999 0 -0.11 2 2
MAPK8 0.025 0.048 -9999 0 -0.16 29 29
HRAS/GTP 0.035 0.042 -9999 0 -0.17 12 12
tube development 0.025 0.019 -9999 0 -0.13 8 8
MAPK1 0.03 0.015 -9999 0 -0.1 2 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.026 0.037 -9999 0 -0.23 10 10
Rac1/GDP 0.011 0.024 -9999 0 -0.2 7 7
SRC 0.019 0 -9999 0 -10000 0 0
PDLIM7 0.019 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.043 0.014 -9999 0 -10000 0 0
SHC1 0.004 0.052 -9999 0 -0.14 48 48
RET51/GFRalpha1/GDNF/Dok4 0.047 0.015 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok5 0.02 0.063 -9999 0 -0.13 73 73
PRKCA 0.019 0 -9999 0 -10000 0 0
HRAS/GDP 0.007 0.037 -9999 0 -0.2 17 17
CREB1 0.02 0.049 -9999 0 -0.21 20 20
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.014 0.046 -9999 0 -0.17 28 28
RET51/GFRalpha1/GDNF/Grb7 0.045 0.019 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
RET 0.015 0.022 -9999 0 -0.11 15 15
DOK4 0.019 0 -9999 0 -10000 0 0
JNK cascade 0.022 0.058 -9999 0 -0.27 14 14
RET9/GFRalpha1/GDNF/FRS2 0.036 0.009 -9999 0 -10000 0 0
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0.003 0.069 -9999 0 -0.28 29 29
NCK1 0.014 0.036 -9999 0 -0.19 14 14
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.016 0.037 -9999 0 -0.18 16 16
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.031 0.038 -9999 0 -0.22 10 10
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.024 0.052 -9999 0 -0.18 29 29
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.021 0.038 -9999 0 -0.17 16 16
PI3K -0.002 0.11 -9999 0 -0.31 44 44
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.031 0.02 -9999 0 -0.13 8 8
GRB10 -0.018 0.091 -9999 0 -0.2 89 89
activation of MAPKK activity 0.029 0.043 -9999 0 -0.26 10 10
RET51/GFRalpha1/GDNF/FRS2 0.046 0.017 -9999 0 -10000 0 0
GAB1 0.003 0.056 -9999 0 -0.15 50 50
IRS1 -0.002 0.07 -9999 0 -0.19 53 53
IRS2 -0.021 0.1 -9999 0 -0.25 79 79
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.019 0.048 -9999 0 -0.16 28 28
RET51/GFRalpha1/GDNF/PKC alpha 0.047 0.015 -9999 0 -10000 0 0
GRB2 0.014 0.039 -9999 0 -0.26 10 10
PRKACA 0.019 0 -9999 0 -10000 0 0
GDNF 0.019 0 -9999 0 -10000 0 0
RAC1 0.015 0.036 -9999 0 -0.29 7 7
RET51/GFRalpha1/GDNF/IRS1 0.034 0.043 -9999 0 -0.13 24 24
Rac1/GTP -0.007 0.098 -9999 0 -0.26 47 47
RET9/GFRalpha1/GDNF 0.026 0.005 -9999 0 -10000 0 0
GFRalpha1/GDNF 0.028 0.006 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.027 0.037 -10000 0 -0.14 21 21
HDAC3 0.018 0.014 -10000 0 -0.29 1 1
Ran/GTP/Exportin 1/HDAC4 -0.009 0.034 -10000 0 -0.12 37 37
GATA1/HDAC4 0.02 0.039 -10000 0 -0.19 16 16
GATA1/HDAC5 0.026 0.016 -10000 0 -0.19 1 1
GATA2/HDAC5 0.026 0.017 -10000 0 -0.19 1 1
HDAC5/BCL6/BCoR 0.016 0.058 -10000 0 -0.16 43 43
HDAC9 -0.017 0.094 -10000 0 -0.24 74 74
Glucocorticoid receptor/Hsp90/HDAC6 0.033 0.035 -10000 0 -0.16 16 16
HDAC4/ANKRA2 0.017 0.047 -10000 0 -0.2 21 21
HDAC5/YWHAB 0.023 0.031 -10000 0 -0.22 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.036 -10000 0 -0.16 21 21
GATA2 0.018 0.011 -10000 0 -0.11 4 4
HDAC4/RFXANK 0.011 0.058 -10000 0 -0.2 34 34
BCOR 0.01 0.032 -10000 0 -0.11 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.016 0.022 -10000 0 -0.13 11 11
GNB1/GNG2 0.006 0.041 -10000 0 -0.2 21 21
Histones 0.003 0.069 -10000 0 -0.17 60 60
ADRBK1 0.018 0.014 -10000 0 -0.11 6 6
HDAC4 0.007 0.056 -10000 0 -0.29 16 16
XPO1 0.017 0.023 -10000 0 -0.29 3 3
HDAC5/ANKRA2 0.023 0.029 -10000 0 -0.19 7 7
HDAC4/Ubc9 0.02 0.039 -10000 0 -0.19 16 16
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.021 0.035 -10000 0 -0.19 11 11
TUBA1B 0.018 0.014 -10000 0 -0.29 1 1
HDAC6 0.019 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.018 0.045 -10000 0 -0.19 21 21
CAMK4 0.018 0.011 -10000 0 -0.11 4 4
Tubulin/HDAC6 0.024 0.051 -10000 0 -0.16 39 39
SUMO1 0.017 0.027 -10000 0 -0.29 4 4
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.036 -10000 0 -0.29 7 7
GATA1 0.019 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.011 0.045 -10000 0 -0.21 19 19
NR3C1 0.01 0.052 -10000 0 -0.28 16 16
SUMO1/HDAC4 0.024 0.045 -10000 0 -0.27 5 5
SRF 0.019 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.017 0.049 -10000 0 -0.21 21 21
Tubulin 0.012 0.059 -10000 0 -0.2 39 39
HDAC4/14-3-3 E 0.014 0.051 -10000 0 -0.2 26 26
GNB1 0.007 0.061 -10000 0 -0.29 21 21
RANGAP1 0.017 0.015 -10000 0 -0.11 7 7
BCL6/BCoR 0.004 0.063 -10000 0 -0.2 40 40
HDAC4/HDAC3/SMRT (N-CoR2) 0.031 0.035 -10000 0 -0.15 17 17
HDAC4/SRF 0.031 0.036 -10000 0 -0.16 16 16
HDAC4/ER alpha 0.02 0.039 -10000 0 -0.19 16 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.003 0.069 -10000 0 -0.17 60 60
cell motility 0.024 0.051 -10000 0 -0.16 39 39
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.019 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.014 0.009 -10000 0 -0.2 1 1
BCL6 -0.007 0.082 -10000 0 -0.23 56 56
HDAC4/CaMK II delta B 0.007 0.056 -10000 0 -0.29 16 16
Hsp90/HDAC6 0.028 0.013 -10000 0 -0.19 2 2
ESR1 0.019 0 -10000 0 -10000 0 0
HDAC6/HDAC11 0.028 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.046 -10000 0 -0.16 21 21
NPC 0.006 0.027 -10000 0 -0.14 18 18
MEF2C 0.009 0.051 -10000 0 -0.21 24 24
RAN 0.016 0.031 -10000 0 -0.24 7 7
HDAC4/MEF2C 0.044 0.044 -10000 0 -0.12 29 29
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.019 0 -10000 0 -10000 0 0
TUBB2A -0.004 0.081 -10000 0 -0.29 40 40
HDAC11 0.019 0 -10000 0 -10000 0 0
HSP90AA1 0.018 0.019 -10000 0 -0.29 2 2
RANBP2 0.007 0.057 -10000 0 -0.26 22 22
ANKRA2 0.015 0.034 -10000 0 -0.23 9 9
RFXANK 0.007 0.06 -10000 0 -0.28 22 22
nuclear import -0.017 0.064 0.23 27 -10000 0 27
Nectin adhesion pathway

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
PDGFRB 0.011 0.043 -9999 0 -0.18 21 21
alphaV beta3 Integrin 0.016 0.048 -9999 0 -0.19 25 25
PTK2 0.014 0.087 -9999 0 -0.36 20 20
positive regulation of JNK cascade -0.003 0.034 -9999 0 -0.28 5 5
CDC42/GDP 0.044 0.057 -9999 0 -0.38 5 5
Rac1/GDP 0.045 0.062 -9999 0 -0.34 8 8
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0.018 0.019 -9999 0 -0.29 2 2
CTNNB1 0.017 0.023 -9999 0 -0.29 3 3
CDC42/GTP 0.035 0.05 -9999 0 -0.35 5 5
nectin-3/I-afadin 0.018 0.033 -9999 0 -0.19 5 5
RAPGEF1 0.03 0.063 -9999 0 -0.37 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.028 0.068 -9999 0 -0.39 9 9
PDGFB-D/PDGFRB 0.011 0.043 -9999 0 -0.18 21 21
TLN1 0 0.065 -9999 0 -0.24 30 30
Rap1/GTP -0.007 0.038 -9999 0 -0.27 7 7
IQGAP1 -0.009 0.087 -9999 0 -0.27 50 50
Rap1/GTP/I-afadin 0.024 0.01 -9999 0 -0.14 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.018 0.033 -9999 0 -0.19 5 5
PVR 0.019 0.008 -9999 0 -0.11 2 2
Necl-5(dimer) 0.019 0.008 -9999 0 -0.11 2 2
mol:GDP 0.039 0.066 -9999 0 -0.47 5 5
MLLT4 0.019 0 -9999 0 -10000 0 0
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
PI3K 0.01 0.085 -9999 0 -0.16 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.028 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.004 0.039 -9999 0 -0.28 7 7
PVRL1 0.019 0 -9999 0 -10000 0 0
PVRL3 0.005 0.047 -9999 0 -0.13 51 51
PVRL2 0.016 0.026 -9999 0 -0.19 7 7
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
CDH1 0.012 0.03 -9999 0 -0.11 29 29
CLDN1 0.016 0.019 -9999 0 -0.11 11 11
JAM-A/CLDN1 0.03 0.045 -9999 0 -0.12 26 26
SRC 0.029 0.067 -9999 0 -0.53 5 5
ITGB3 0.019 0.008 -9999 0 -0.11 2 2
nectin-1(dimer)/I-afadin/I-afadin 0.028 0 -9999 0 -10000 0 0
FARP2 0.037 0.062 -9999 0 -0.46 5 5
RAC1 0.015 0.036 -9999 0 -0.29 7 7
CTNNA1 0.011 0.048 -9999 0 -0.29 13 13
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.03 0.03 -9999 0 -0.14 7 7
nectin-1/I-afadin 0.028 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0.026 0.018 -9999 0 -0.19 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.007 0.056 -9999 0 -0.16 51 51
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.03 0.029 -9999 0 -0.15 5 5
CDC42/GTP/IQGAP1/filamentous actin 0.009 0.053 -9999 0 -0.16 45 45
F11R 0.004 0.051 -9999 0 -0.14 49 49
positive regulation of filopodium formation -0.003 0.034 -9999 0 -0.28 5 5
alphaV/beta3 Integrin/Talin 0.008 0.078 -9999 0 -0.24 32 32
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.026 0.018 -9999 0 -0.19 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.026 0.018 -9999 0 -0.19 3 3
PIP5K1C 0.003 0.061 -9999 0 -0.25 25 25
VAV2 0.038 0.063 -9999 0 -0.47 5 5
RAP1/GDP 0.036 0.053 -9999 0 -0.35 5 5
ITGAV 0.003 0.067 -9999 0 -0.25 32 32
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.028 0.035 -9999 0 -0.16 8 8
nectin-3(dimer)/I-afadin/I-afadin 0.018 0.033 -9999 0 -0.19 5 5
Rac1/GTP 0.037 0.056 -9999 0 -0.34 7 7
PTPRM 0.001 0.061 -9999 0 -0.26 25 25
E-cadherin/beta catenin/alpha catenin 0.046 0.037 -9999 0 -0.12 18 18
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.017 0.016 -9999 0 -0.11 8 8
Atypical NF-kappaB 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
BCL3/RelA 0.027 0.015 -9999 0 -0.19 2 2
FBXW11 0.011 0.047 -9999 0 -0.27 14 14
NF kappa B1 p50/c-Rel 0.027 0.022 -9999 0 -0.15 7 7
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.063 -9999 0 -0.27 13 13
NFKBIA 0.005 0.062 -9999 0 -0.19 41 41
MAPK14 0.018 0.013 -9999 0 -0.11 5 5
NF kappa B1 p105/p50 0.022 0.036 -9999 0 -0.16 18 18
ARRB2 0.013 0.029 -9999 0 -0.23 7 7
REL 0.019 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.022 -9999 0 -0.15 7 7
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.026 0.024 -9999 0 -0.15 9 9
PIK3CA -0.011 0.086 -9999 0 -0.22 66 66
NF kappa B1 p50 dimer 0.018 0.025 -9999 0 -0.19 7 7
PIK3R1 -0.015 0.095 -9999 0 -0.27 62 62
NFKB1 0.017 0.025 -9999 0 -0.19 7 7
RELA 0.018 0.02 -9999 0 -0.23 3 3
positive regulation of anti-apoptosis 0.019 0.039 -9999 0 -0.2 2 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.028 0.064 -9999 0 -0.27 13 13
SRC 0.019 0 -9999 0 -10000 0 0
PI3K -0.016 0.093 -9999 0 -0.21 88 88
NF kappa B1 p50/RelA 0.019 0.04 -9999 0 -0.2 2 2
IKBKB 0.019 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0.047 -9999 0 -0.27 14 14
SYK -0.005 0.072 -9999 0 -0.29 25 25
I kappa B alpha/PIK3R1 0.009 0.076 -9999 0 -0.22 43 43
cell death 0.027 0.062 -9999 0 -0.26 13 13
NF kappa B1 p105/c-Rel 0.027 0.022 -9999 0 -0.15 7 7
LCK 0.017 0.016 -9999 0 -0.11 8 8
BCL3 0.019 0.008 -9999 0 -0.11 2 2
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.084 0.22 -10000 0 -0.73 24 24
PCK1 0.084 0.14 -10000 0 -0.66 4 4
HNF4A 0.11 0.18 -10000 0 -0.76 8 8
KCNJ11 0.1 0.2 -10000 0 -0.66 16 16
AKT1 0.069 0.13 -10000 0 -0.4 20 20
response to starvation 0.006 0.003 -10000 0 -10000 0 0
DLK1 0.1 0.21 -10000 0 -0.75 12 12
NKX2-1 0.077 0.12 -10000 0 -10000 0 0
ACADM 0.095 0.2 -10000 0 -0.8 13 13
TAT 0.083 0.14 -10000 0 -0.65 6 6
CEBPB 0.001 0.076 -10000 0 -0.22 51 51
CEBPA -0.022 0.1 -10000 0 -0.22 104 104
TTR 0.039 0.18 -10000 0 -0.6 18 18
PKLR 0.099 0.18 -10000 0 -0.69 12 12
APOA1 0.12 0.22 -10000 0 -0.85 11 11
CPT1C 0.091 0.18 -10000 0 -0.69 12 12
ALAS1 0.056 0.27 -10000 0 -1.3 16 16
TFRC 0.042 0.33 -10000 0 -1 39 39
FOXF1 -0.002 0.04 -10000 0 -0.12 55 55
NF1 0.021 0.028 -10000 0 -0.15 10 10
HNF1A (dimer) 0.038 0.003 -10000 0 -10000 0 0
CPT1A 0.099 0.18 -10000 0 -0.71 11 11
HMGCS1 0.095 0.18 -10000 0 -0.71 12 12
NR3C1 0.021 0.054 -10000 0 -0.28 15 15
CPT1B 0.099 0.18 -10000 0 -0.71 11 11
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.026 0 -10000 0 -10000 0 0
GCK 0.098 0.18 -10000 0 -0.71 11 11
CREB1 0.024 0.035 -10000 0 -0.29 6 6
IGFBP1 0.069 0.14 -10000 0 -0.68 6 6
PDX1 0.11 0.12 -10000 0 -10000 0 0
UCP2 0.049 0.28 -10000 0 -0.69 57 57
ALDOB 0.11 0.2 -10000 0 -0.74 12 12
AFP 0.023 0.033 -10000 0 -10000 0 0
BDH1 0.085 0.21 -10000 0 -0.71 23 23
HADH 0.11 0.22 -10000 0 -0.82 16 16
F2 0.12 0.22 -10000 0 -0.85 11 11
HNF1A 0.038 0.003 -10000 0 -10000 0 0
G6PC 0.02 0.092 -10000 0 -0.38 1 1
SLC2A2 0.11 0.14 -10000 0 -0.47 3 3
INS 0.013 0.029 0.2 6 -10000 0 6
FOXA1 0.013 0.011 -10000 0 -10000 0 0
FOXA3 0.026 0.058 -10000 0 -0.2 26 26
FOXA2 0.15 0.24 -10000 0 -0.85 12 12
ABCC8 0.11 0.2 -10000 0 -0.74 12 12
ALB 0.024 0.03 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.015 0.023 -10000 0 -0.11 17 17
NFATC1 0.012 0.12 -10000 0 -0.44 25 25
NFATC2 0.013 0.054 -10000 0 -0.16 29 29
NFATC3 0.01 0.025 -10000 0 -0.12 16 16
YWHAE 0.011 0.045 -10000 0 -0.21 19 19
Calcineurin A alpha-beta B1/CABIN1 0.026 0.029 -10000 0 -0.17 1 1
Exportin 1/Ran/NUP214 0.036 0.027 -10000 0 -0.2 6 6
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.043 0.038 -10000 0 -0.17 1 1
BCL2/BAX 0.025 0.024 -10000 0 -0.19 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.038 -10000 0 -0.14 28 28
CaM/Ca2+ 0.007 0.038 -10000 0 -0.14 28 28
BAX 0.014 0.035 -10000 0 -0.17 15 15
MAPK14 0.018 0.013 -10000 0 -0.11 5 5
BAD 0.014 0.036 -10000 0 -0.25 9 9
CABIN1/MEF2D 0.035 0.029 -10000 0 -0.15 1 1
Calcineurin A alpha-beta B1/BCL2 0.019 0 -10000 0 -10000 0 0
FKBP8 0.018 0.014 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.035 0.029 0.15 1 -10000 0 1
KPNB1 0.007 0.06 -10000 0 -0.28 21 21
KPNA2 0 0.074 -10000 0 -0.27 36 36
XPO1 0.017 0.023 -10000 0 -0.29 3 3
SFN 0.002 0.044 -10000 0 -0.11 70 70
MAP3K8 0.004 0.042 -10000 0 -0.11 62 62
NFAT4/CK1 alpha 0.022 0.046 -10000 0 -0.19 19 19
MEF2D/NFAT1/Cbp/p300 0.05 0.063 -10000 0 -0.25 14 14
CABIN1 0.026 0.03 -10000 0 -0.17 1 1
CALM1 0.007 0.056 -10000 0 -0.21 28 28
RAN 0.016 0.031 -10000 0 -0.24 7 7
MAP3K1 0.015 0.022 -10000 0 -0.11 16 16
CAMK4 0.018 0.011 -10000 0 -0.11 4 4
mol:Ca2+ 0.001 0 -10000 0 -10000 0 0
MAPK3 0.019 0.006 -10000 0 -10000 0 0
YWHAH -0.006 0.083 -10000 0 -0.26 49 49
Calcineurin A alpha-beta B1/AKAP79/PKA 0.028 0.004 -10000 0 -10000 0 0
YWHAB 0.015 0.036 -10000 0 -0.29 7 7
MAPK8 0.019 0 -10000 0 -10000 0 0
MAPK9 0.016 0.028 -10000 0 -0.23 6 6
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.007 0.052 -10000 0 -0.18 31 31
NFAT1-c-4/YWHAQ 0.03 0.1 -10000 0 -0.36 25 25
PRKCH 0.016 0.019 -10000 0 -0.11 12 12
CABIN1/Cbp/p300 0.024 0.032 -10000 0 -0.19 11 11
CASP3 0.009 0.053 -10000 0 -0.25 20 20
PIM1 0.017 0.017 -10000 0 -0.11 9 9
Calcineurin A alpha-beta B1/FKBP12/FK506 0.007 0.029 -10000 0 -0.097 31 31
apoptosis 0.013 0.033 -10000 0 -0.19 12 12
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.11 -10000 0 -0.38 26 26
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.019 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.02 0.026 -10000 0 -0.12 16 16
BAD/BCL-XL 0.022 0.03 -10000 0 -0.19 7 7
PRKCD 0.012 0.029 -10000 0 -0.11 27 27
NUP214 0.019 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.019 0 -10000 0 -10000 0 0
PRKCG 0.019 0 -10000 0 -10000 0 0
PRKCQ 0.014 0.024 -10000 0 -0.11 19 19
FKBP38/BCL2 0.027 0.01 -10000 0 -10000 0 0
EP300 0.012 0.046 -10000 0 -0.24 15 15
PRKCB1 -0.003 0.057 -10000 0 -0.13 77 77
CSNK2A1 0.01 0.053 -10000 0 -0.29 16 16
NFATc/JNK1 0.023 0.11 -10000 0 -0.41 25 25
CaM/Ca2+/FKBP38 0.019 0.035 -10000 0 -0.15 20 20
FKBP12/FK506 0.006 0.035 -10000 0 -0.12 31 31
CSNK1A1 0.011 0.041 -10000 0 -0.14 28 28
CaM/Ca2+/CAMK IV 0.019 0.034 -10000 0 -0.16 17 17
NFATc/ERK1 0.023 0.11 -10000 0 -0.41 25 25
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.041 0.04 -10000 0 -0.19 3 3
NR4A1 0.038 0.054 -10000 0 -0.25 11 11
GSK3B 0.004 0.066 -10000 0 -0.26 29 29
positive T cell selection 0.01 0.025 -10000 0 -0.12 16 16
NFAT1/CK1 alpha 0.013 0.064 -10000 0 -0.27 18 18
RCH1/ KPNB1 0.006 0.068 -10000 0 -0.2 49 49
YWHAQ 0.018 0.019 -10000 0 -0.29 2 2
PRKACA 0.019 0 -10000 0 -10000 0 0
AKAP5 0.019 0.006 -10000 0 -0.11 1 1
MEF2D 0.02 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0.037 -10000 0 -0.23 11 11
NFATc/p38 alpha 0.023 0.11 -10000 0 -0.41 25 25
CREBBP 0.02 0 -10000 0 -10000 0 0
BCL2 0.019 0 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.029 0.06 -9999 0 -0.25 13 13
FYN 0.003 0.1 -9999 0 -0.3 36 36
LAT/GRAP2/SLP76 0.031 0.073 -9999 0 -0.27 14 14
IKBKB 0.019 0 -9999 0 -10000 0 0
AKT1 0.028 0.07 -9999 0 -0.22 21 21
B2M 0.018 0.027 -9999 0 -0.3 4 4
IKBKG 0.021 0.027 -9999 0 -0.081 15 15
MAP3K8 0.004 0.042 -9999 0 -0.11 62 62
mol:Ca2+ -0.001 0.004 -9999 0 -0.026 7 7
integrin-mediated signaling pathway 0.012 0.011 -9999 0 -0.16 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.029 0.085 -9999 0 -0.29 20 20
TRPV6 0.003 0.004 -9999 0 -10000 0 0
CD28 0.019 0.001 -9999 0 -10000 0 0
SHC1 0.028 0.062 -9999 0 -0.29 10 10
receptor internalization 0.034 0.042 -9999 0 -0.19 2 2
PRF1 0.031 0.047 -9999 0 -10000 0 0
KRAS 0.011 0.048 -9999 0 -0.28 14 14
GRB2 0.014 0.039 -9999 0 -0.26 10 10
COT/AKT1 0.029 0.063 -9999 0 -0.18 20 20
LAT 0.032 0.058 -9999 0 -0.27 9 9
EntrezGene:6955 0.001 0.002 -9999 0 -10000 0 0
CD3D 0.01 0.034 -9999 0 -0.11 39 39
CD3E 0.019 0.009 -9999 0 -0.12 2 2
CD3G 0.017 0.019 -9999 0 -10000 0 0
RASGRP2 0.011 0.01 -9999 0 -10000 0 0
RASGRP1 -0.012 0.12 -9999 0 -0.23 99 99
HLA-A 0.013 0.047 -9999 0 -0.3 12 12
RASSF5 0 0 -9999 0 -10000 0 0
RAP1A/GTP/RAPL 0.012 0.011 -9999 0 -0.16 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
mol:GDP 0.008 0.042 -9999 0 -0.095 35 35
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.028 -9999 0 -0.13 18 18
PRKCA 0.026 0.041 -9999 0 -0.15 11 11
GRAP2 0.019 0 -9999 0 -10000 0 0
mol:IP3 -0.014 0.041 -9999 0 -0.22 12 12
EntrezGene:6957 0.001 0.002 -9999 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.028 0.034 -9999 0 -10000 0 0
ORAI1 0 0 -9999 0 -10000 0 0
CSK 0.031 0.059 -9999 0 -0.28 8 8
B7 family/CD28 0.039 0.072 -9999 0 -0.24 15 15
CHUK 0.016 0.025 -9999 0 -0.15 10 10
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.03 0.061 -9999 0 -0.29 9 9
PTPN6 0.025 0.068 -9999 0 -0.25 15 15
VAV1 0.032 0.059 -9999 0 -0.27 8 8
Monovalent TCR/CD3 0.023 0.021 -9999 0 -0.14 1 1
CBL 0.019 0 -9999 0 -10000 0 0
LCK 0.016 0.082 -9999 0 -0.29 19 19
PAG1 0.028 0.057 -9999 0 -0.27 9 9
RAP1A 0.018 0.019 -9999 0 -0.29 2 2
TCR/CD3/MHC I/CD8/LCK 0.027 0.062 -9999 0 -0.29 9 9
CD80 0.019 0.006 -9999 0 -0.11 1 1
CD86 -0.003 0.074 -9999 0 -0.21 53 53
PDK1/CARD11/BCL10/MALT1 -0.011 0.034 -9999 0 -0.15 22 22
HRAS 0.009 0.055 -9999 0 -0.28 18 18
GO:0035030 0.025 0.062 -9999 0 -0.21 15 15
CD8A 0.001 0.002 -9999 0 -10000 0 0
CD8B 0.019 0.012 -9999 0 -0.12 1 1
PTPRC -0.031 0.11 -9999 0 -0.23 107 107
PDK1/PKC theta 0.036 0.075 -9999 0 -0.27 15 15
CSK/PAG1 0.029 0.058 -9999 0 -0.27 8 8
SOS1 0 0 -9999 0 -10000 0 0
peptide-MHC class I 0.023 0.039 -9999 0 -0.2 16 16
GRAP2/SLP76 0.031 0.079 -9999 0 -0.28 17 17
STIM1 0.003 0.004 -9999 0 -10000 0 0
RAS family/GTP 0.007 0.066 -9999 0 -0.15 49 49
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.035 0.043 -9999 0 -0.2 2 2
mol:DAG -0.013 0.038 -9999 0 -0.19 15 15
RAP1A/GDP 0.006 0.02 -9999 0 -0.045 33 33
PLCG1 0.017 0.025 -9999 0 -0.29 3 3
CD247 0.018 0.015 -9999 0 -0.11 7 7
cytotoxic T cell degranulation 0.031 0.047 -9999 0 -10000 0 0
RAP1A/GTP 0 0.004 -9999 0 -0.052 2 2
mol:PI-3-4-5-P3 0.029 0.076 -9999 0 -0.26 20 20
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.015 0.049 -9999 0 -0.26 12 12
NRAS -0.01 0.086 -9999 0 -0.24 59 59
ZAP70 0.019 0.006 -9999 0 -0.11 1 1
GRB2/SOS1 0.011 0.026 -9999 0 -0.17 10 10
LAT/GRAP2/SLP76/VAV1 0.028 0.068 -9999 0 -0.25 15 15
MALT1 0.013 0.036 -9999 0 -0.16 18 18
TRAF6 0.018 0.019 -9999 0 -0.29 2 2
CD8 heterodimer 0.015 0.009 -9999 0 -0.078 1 1
CARD11 0 0 -9999 0 -10000 0 0
PRKCB -0.01 0.028 -9999 0 -0.14 16 16
PRKCE 0.026 0.041 -9999 0 -0.14 12 12
PRKCQ 0.032 0.08 -9999 0 -0.3 15 15
LCP2 -0.012 0.086 -9999 0 -0.21 70 70
BCL10 0.016 0.028 -9999 0 -0.23 6 6
regulation of survival gene product expression 0.027 0.063 -9999 0 -0.19 21 21
IKK complex 0.03 0.025 -9999 0 -0.064 6 6
RAS family/GDP -0.007 0.014 -9999 0 -0.036 80 80
MAP3K14 0.027 0.051 -9999 0 -0.15 16 16
PDPK1 0.031 0.066 -9999 0 -0.21 19 19
TCR/CD3/MHC I/CD8/Fyn 0.03 0.05 -9999 0 -0.28 3 3
Caspase cascade in apoptosis

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
TOP1 0.019 0.064 -10000 0 -0.26 20 20
ACTA1 0.015 0.04 -10000 0 -0.17 11 11
NUMA1 0.025 0.043 -10000 0 -0.23 7 7
SPTAN1 0.01 0.053 -10000 0 -0.16 23 23
LIMK1 0.02 0.037 -10000 0 -0.15 10 10
BIRC3 0 0.046 -10000 0 -0.11 78 78
BIRC2 0.016 0.03 -10000 0 -0.29 5 5
BAX 0.014 0.035 -10000 0 -0.17 15 15
CASP10 0.013 0.025 -10000 0 -0.053 62 62
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.019 0.064 -10000 0 -0.24 22 22
DIABLO 0.016 0.028 -10000 0 -0.26 5 5
apoptotic nuclear changes 0.01 0.052 -10000 0 -0.16 23 23
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.017 0.015 -10000 0 -0.11 7 7
GSN 0.011 0.047 -10000 0 -0.18 13 13
MADD 0.018 0.015 -10000 0 -0.2 2 2
TFAP2A 0.029 0.021 -10000 0 -10000 0 0
BID 0.002 0.049 -10000 0 -0.2 26 26
MAP3K1 0.016 0.018 -10000 0 -10000 0 0
TRADD 0.019 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.025 0.02 -10000 0 -0.19 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.049 -10000 0 -0.2 11 11
CASP9 0.014 0.029 -10000 0 -0.13 18 18
DNA repair -0.009 0.043 0.28 8 -10000 0 8
neuron apoptosis 0.013 0.096 -10000 0 -0.67 10 10
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.026 0.042 -10000 0 -0.26 3 3
APAF1 0.019 0 -10000 0 -10000 0 0
CASP6 0.022 0.1 -10000 0 -0.88 6 6
TRAF2 0.019 0 -10000 0 -10000 0 0
ICAD/CAD 0.021 0.039 -10000 0 -0.18 5 5
CASP7 -0.006 0.067 -10000 0 -0.36 16 16
KRT18 0.015 0.025 -10000 0 -10000 0 0
apoptosis 0.014 0.068 -10000 0 -0.27 16 16
DFFA 0.018 0.041 -10000 0 -0.17 8 8
DFFB 0.019 0.037 -10000 0 -0.16 6 6
PARP1 0.008 0.043 -10000 0 -0.28 8 8
actin filament polymerization -0.019 0.035 0.14 10 -10000 0 10
TNF 0.018 0.01 -10000 0 -0.11 3 3
CYCS 0.01 0.03 -10000 0 -0.26 4 4
SATB1 0.004 0.11 -10000 0 -0.84 6 6
SLK 0.015 0.043 -10000 0 -0.18 8 8
p15 BID/BAX 0.011 0.047 -10000 0 -0.18 26 26
CASP2 0.025 0.044 -10000 0 -10000 0 0
JNK cascade -0.016 0.018 -10000 0 -10000 0 0
CASP3 0.016 0.039 -10000 0 -0.16 11 11
LMNB2 0.029 0.069 -10000 0 -0.38 9 9
RIPK1 0.016 0.019 -10000 0 -0.11 11 11
CASP4 -0.025 0.1 -10000 0 -0.23 96 96
Mammalian IAPs/DIABLO 0.023 0.037 -10000 0 -0.21 6 6
negative regulation of DNA binding 0.029 0.021 -10000 0 -10000 0 0
stress fiber formation 0.015 0.042 -10000 0 -0.17 8 8
GZMB 0.01 0.032 -10000 0 -0.14 9 9
CASP1 -0.055 0.15 -10000 0 -0.34 97 97
LMNB1 0.009 0.1 -10000 0 -0.28 45 45
APP 0.013 0.098 -10000 0 -0.68 10 10
TNFRSF1A -0.01 0.091 -10000 0 -0.29 50 50
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.013 -10000 0 -0.07 14 14
VIM 0.014 0.068 -10000 0 -0.29 14 14
LMNA 0.032 0.053 -10000 0 -0.33 7 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.023 0.047 -10000 0 -0.17 1 1
LRDD 0.018 0.01 -10000 0 -0.11 3 3
SREBF1 0.015 0.04 -10000 0 -0.16 9 9
APAF-1/Caspase 9 0.002 0.049 0.21 1 -0.69 2 3
nuclear fragmentation during apoptosis 0.025 0.043 -10000 0 -0.23 7 7
CFL2 0.019 0.035 -10000 0 -0.14 10 10
GAS2 0.013 0.039 -10000 0 -0.15 11 11
positive regulation of apoptosis 0.023 0.078 -10000 0 -0.37 11 11
PRF1 0.008 0.036 -10000 0 -0.11 44 44
Cellular roles of Anthrax toxin

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
ANTXR1 0.015 0.022 -10000 0 -0.11 16 16
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.002 -10000 0 -10000 0 0
monocyte activation -0.086 0.16 -10000 0 -0.36 140 140
MAP2K2 0.012 0.03 -10000 0 -0.68 1 1
MAP2K1 0.005 0.005 -10000 0 -0.044 4 4
MAP2K7 0.006 0.002 -10000 0 -10000 0 0
MAP2K6 0.006 0.003 -10000 0 -0.044 1 1
CYAA 0.003 0.009 -10000 0 -0.045 16 16
MAP2K4 0.005 0.007 -10000 0 -0.046 8 8
IL1B -0.013 0.039 -10000 0 -0.16 18 18
Channel 0.01 0.011 -10000 0 -0.049 16 16
NLRP1 0.006 0.002 -10000 0 -10000 0 0
CALM1 0.007 0.056 -10000 0 -0.21 28 28
negative regulation of phagocytosis -0.004 0.082 -10000 0 -0.47 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.002 -10000 0 -10000 0 0
MAPK3 0.006 0.003 -10000 0 -0.044 1 1
MAPK1 0.005 0.007 -10000 0 -0.046 9 9
PGR 0.006 0.002 -10000 0 -10000 0 0
PA/Cellular Receptors 0.011 0.012 -10000 0 -0.056 16 16
apoptosis 0 0.002 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.01 0.009 -10000 0 -0.043 16 16
macrophage activation 0.006 0.022 -10000 0 -0.12 13 13
TNF 0.018 0.01 -10000 0 -0.11 3 3
VCAM1 -0.087 0.16 -10000 0 -0.36 140 140
platelet activation -0.004 0.082 -10000 0 -0.47 16 16
MAPKKK cascade -0.008 0.009 0.07 3 -10000 0 3
IL18 -0.008 0.034 -10000 0 -0.15 12 12
negative regulation of macrophage activation 0 0.002 -10000 0 -10000 0 0
LEF 0 0.002 -10000 0 -10000 0 0
CASP1 0.004 0.005 -10000 0 -0.08 1 1
mol:cAMP -0.004 0.083 -10000 0 -0.47 16 16
necrosis 0 0.002 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.01 0.01 -10000 0 -0.046 16 16
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.013 0.082 -9999 0 -0.32 12 12
BAG4 0.018 0.011 -9999 0 -0.11 4 4
BAD 0.014 0.032 -9999 0 -0.14 10 10
NFKBIA 0.002 0.067 -9999 0 -0.24 34 34
BIRC3 0 0.046 -9999 0 -0.11 78 78
BAX 0.014 0.03 -9999 0 -0.12 9 9
EnzymeConsortium:3.1.4.12 0.007 0.019 -9999 0 -0.062 9 9
IKBKB 0.013 0.081 -9999 0 -0.3 12 12
MAP2K2 0.02 0.035 -9999 0 -0.15 12 12
MAP2K1 0.019 0.038 -9999 0 -0.14 16 16
SMPD1 0.012 0.019 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.024 0.072 -9999 0 -0.24 8 8
MAP2K4 0.017 0.03 -9999 0 -0.12 8 8
protein ubiquitination 0.013 0.082 -9999 0 -0.31 12 12
EnzymeConsortium:2.7.1.37 0.022 0.037 -9999 0 -0.16 12 12
response to UV 0 0 -9999 0 -0.001 7 7
RAF1 0.017 0.036 -9999 0 -0.13 18 18
CRADD 0.017 0.015 -9999 0 -0.11 7 7
mol:ceramide 0.012 0.027 -9999 0 -0.098 6 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.015 0.041 -9999 0 -0.16 26 26
MADD 0.018 0.015 -9999 0 -0.2 2 2
MAP3K1 0.015 0.027 -9999 0 -0.098 7 7
TRADD 0.019 0 -9999 0 -10000 0 0
RELA/p50 0.018 0.02 -9999 0 -0.23 3 3
MAPK3 0.023 0.036 -9999 0 -0.15 12 12
MAPK1 0.02 0.046 -9999 0 -0.21 14 14
p50/RELA/I-kappa-B-alpha 0.016 0.049 -9999 0 -0.19 26 26
FADD 0.019 0.072 -9999 0 -0.23 10 10
KSR1 0.016 0.026 -9999 0 -0.1 4 4
MAPK8 0.021 0.029 -9999 0 -0.12 5 5
TRAF2 0.019 0 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -0.001 3 3
CHUK 0.012 0.081 -9999 0 -0.31 12 12
TNF R/SODD 0.007 0.065 -9999 0 -0.19 50 50
TNF 0.018 0.01 -9999 0 -0.11 3 3
CYCS 0.013 0.031 -9999 0 -0.12 11 11
IKBKG 0.013 0.081 -9999 0 -0.3 12 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.016 0.075 -9999 0 -0.21 50 50
RELA 0.018 0.02 -9999 0 -0.23 3 3
RIPK1 0.016 0.019 -9999 0 -0.11 11 11
AIFM1 0.012 0.033 -9999 0 -0.13 13 13
TNF/TNF R/SODD 0.02 0.057 -9999 0 -0.16 50 50
TNFRSF1A -0.01 0.091 -9999 0 -0.29 50 50
response to heat 0 0 -9999 0 -0.001 3 3
CASP8 0.025 0.046 -9999 0 -0.63 2 2
NSMAF 0.016 0.077 -9999 0 -0.28 13 13
response to hydrogen peroxide 0 0 -9999 0 -0.001 7 7
BCL2 0.019 0 -9999 0 -10000 0 0
Regulation 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
HDAC1 0.007 0.026 -10000 0 -0.15 13 13
SMARCC1 0.001 0.14 -10000 0 -1.2 5 5
REL 0.018 0 -10000 0 -10000 0 0
HDAC7 0.03 0.064 -10000 0 -0.22 18 18
JUN -0.001 0.077 -10000 0 -0.28 37 37
EP300 0.012 0.046 -10000 0 -0.24 15 15
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.012 -10000 0 -0.15 1 1
FOXO1 -0.012 0.088 -10000 0 -0.23 67 67
T-DHT/AR 0.051 0.074 -10000 0 -0.23 18 18
MAP2K6 0.02 0.007 -10000 0 -0.12 1 1
BRM/BAF57 0.028 0.019 -10000 0 -0.19 3 3
MAP2K4 0.016 0.032 -10000 0 -0.17 12 12
SMARCA2 0.018 0.015 -10000 0 -0.11 7 7
PDE9A -0.003 0.2 -10000 0 -0.92 24 24
NCOA2 0.019 0.01 -10000 0 -0.11 3 3
CEBPA -0.028 0.1 -10000 0 -0.22 104 104
EHMT2 0.019 0.006 -10000 0 -0.11 1 1
cell proliferation 0.064 0.076 0.23 4 -0.3 8 12
NR0B1 -0.004 0.049 -10000 0 -0.11 92 92
EGR1 -0.032 0.11 -10000 0 -0.24 107 107
RXRs/9cRA 0.037 0.011 -10000 0 -0.13 1 1
AR/RACK1/Src 0.048 0.033 -10000 0 -0.26 2 2
AR/GR 0.026 0.057 -10000 0 -0.2 26 26
GNB2L1 0.018 0.019 -10000 0 -0.29 2 2
PKN1 0.009 0.049 -10000 0 -0.18 28 28
RCHY1 0.013 0.042 -10000 0 -0.29 10 10
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.021 0.022 -10000 0 -0.19 4 4
T-DHT/AR/TIF2/CARM1 0.054 0.035 -10000 0 -0.22 3 3
SRC 0.03 0.017 -10000 0 -0.1 3 3
NR3C1 0.01 0.052 -10000 0 -0.28 16 16
KLK3 0.01 0.07 -10000 0 -0.41 1 1
APPBP2 0.008 0.061 -10000 0 -0.28 22 22
TRIM24 0.007 0.061 -10000 0 -0.25 26 26
T-DHT/AR/TIP60 0.025 0.03 -10000 0 -0.16 6 6
TMPRSS2 0.033 0.063 -10000 0 -0.74 2 2
RXRG 0.018 0.013 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.019 0.014 -10000 0 -0.29 1 1
RXRB 0.019 0 -10000 0 -10000 0 0
CARM1 0.019 0.015 -10000 0 -0.2 2 2
NR2C2 0.019 0 -10000 0 -10000 0 0
KLK2 0.057 0.031 -10000 0 -0.24 2 2
AR 0.022 0.05 -10000 0 -0.19 24 24
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0.018 0.019 -10000 0 -0.29 2 2
MDM2 0.009 0.032 -10000 0 -10000 0 0
SRY 0.017 0.01 -10000 0 -0.11 3 3
GATA2 0.018 0.011 -10000 0 -0.11 4 4
MYST2 0.001 0.072 -10000 0 -0.27 34 34
HOXB13 0.02 0.006 -10000 0 -0.11 1 1
T-DHT/AR/RACK1/Src 0.044 0.033 -10000 0 -0.2 4 4
positive regulation of transcription 0.018 0.011 -10000 0 -0.11 4 4
DNAJA1 0.006 0.064 -10000 0 -0.28 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.042 -10000 0 -0.28 10 10
NCOA1 0.017 0.037 -10000 0 -0.24 8 8
SPDEF 0.021 0.006 -10000 0 -0.11 1 1
T-DHT/AR/TIF2 0.03 0.06 -10000 0 -0.22 20 20
T-DHT/AR/Hsp90 0.037 0.034 -10000 0 -0.19 5 5
GSK3B 0.004 0.066 -10000 0 -0.26 29 29
NR2C1 0.019 0 -10000 0 -10000 0 0
mol:T-DHT 0.028 0.019 -10000 0 -0.12 3 3
SIRT1 0.008 0.048 -10000 0 -0.16 32 32
ZMIZ2 0.017 0 -10000 0 -10000 0 0
POU2F1 0.023 0.036 -10000 0 -0.21 4 4
T-DHT/AR/DAX-1 0.028 0.039 -10000 0 -0.16 7 7
CREBBP 0.019 0 -10000 0 -10000 0 0
SMARCE1 0.018 0.023 -10000 0 -0.29 3 3
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.012 0.056 -9999 0 -10000 0 0
MKNK1 0.003 0.068 -9999 0 -0.27 30 30
MAPK14 0.013 0.037 -9999 0 -0.13 12 12
ATF2/c-Jun 0.003 0.11 -9999 0 -0.43 34 34
MAPK11 0.014 0.033 -9999 0 -0.12 8 8
MITF 0.017 0.046 -9999 0 -0.22 7 7
MAPKAPK5 0.022 0.033 -9999 0 -10000 0 0
KRT8 0.018 0.041 -9999 0 -0.22 1 1
MAPKAPK3 0.016 0.023 -9999 0 -0.16 8 8
MAPKAPK2 0.019 0.008 -9999 0 -0.11 2 2
p38alpha-beta/CK2 0.019 0.046 -9999 0 -0.23 1 1
CEBPB 0.006 0.07 -9999 0 -0.23 33 33
SLC9A1 0.021 0.038 -9999 0 -0.29 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.019 0.051 -9999 0 -0.2 8 8
p38alpha-beta/MNK1 0.02 0.06 -9999 0 -0.18 27 27
JUN 0.002 0.11 -9999 0 -0.43 34 34
PPARGC1A 0.007 0.059 -9999 0 -0.23 20 20
USF1 0.013 0.033 -9999 0 -0.17 1 1
RAB5/GDP/GDI1 0.002 0.082 -9999 0 -0.25 43 43
NOS2 0.013 0.033 -9999 0 -0.17 1 1
DDIT3 0.003 0.065 -9999 0 -0.22 30 30
RAB5A 0.004 0.067 -9999 0 -0.29 26 26
HSPB1 0.009 0.052 -9999 0 -0.16 34 34
p38alpha-beta/HBP1 0.03 0.039 -9999 0 -0.17 1 1
CREB1 0.024 0.036 -9999 0 -0.19 2 2
RAB5/GDP 0.004 0.046 -9999 0 -0.2 26 26
EIF4E 0.01 0.055 -9999 0 -0.17 31 31
RPS6KA4 0.022 0.033 -9999 0 -10000 0 0
PLA2G4A -0.001 0.061 -9999 0 -0.18 36 36
GDI1 0.003 0.086 -9999 0 -0.28 40 40
TP53 0.011 0.044 -9999 0 -0.2 6 6
RPS6KA5 0.018 0.037 -9999 0 -0.2 1 1
ESR1 0.022 0.033 -9999 0 -10000 0 0
HBP1 0.019 0 -9999 0 -10000 0 0
MEF2C 0.015 0.057 -9999 0 -0.27 13 13
MEF2A 0.018 0.048 -9999 0 -0.25 9 9
EIF4EBP1 0.02 0.041 -9999 0 -0.19 5 5
KRT19 0.018 0.041 -9999 0 -0.17 7 7
ELK4 0.022 0.033 -9999 0 -0.16 1 1
ATF6 0.021 0.036 -9999 0 -0.27 1 1
ATF1 0.022 0.037 -9999 0 -0.19 1 1
p38alpha-beta/MAPKAPK2 0.03 0.04 -9999 0 -0.17 1 1
p38alpha-beta/MAPKAPK3 0.029 0.042 -9999 0 -0.18 3 3
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.019 0 -10000 0 -10000 0 0
CLTC 0.014 0.052 -10000 0 -0.45 3 3
calcium ion-dependent exocytosis 0.006 0.064 -10000 0 -0.25 23 23
Dynamin 2/GTP 0.02 0.007 -10000 0 -0.14 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.009 0.056 -10000 0 -0.38 5 5
CPE 0.014 0.016 -10000 0 -0.18 2 2
CTNNB1 0.017 0.023 -10000 0 -0.29 3 3
membrane fusion 0.006 0.062 -10000 0 -0.18 43 43
CTNND1 0.02 0.013 -10000 0 -0.26 1 1
DNM2 0.019 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.06 -10000 0 -0.24 21 21
TSHR 0.016 0.014 -10000 0 -0.16 1 1
INS 0.015 0.018 -10000 0 -10000 0 0
BIN1 -0.016 0.092 -10000 0 -0.23 74 74
mol:Choline 0.006 0.062 -10000 0 -0.18 43 43
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.008 -10000 0 -0.16 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.018 0.015 -10000 0 -0.2 2 2
mol:Ca2+ 0.019 0.007 -10000 0 -0.14 1 1
JUP 0.011 0.043 -10000 0 -0.76 1 1
ASAP2/amphiphysin II 0.006 0.05 -10000 0 -0.14 49 49
ARF6/GTP 0.014 0.01 -10000 0 -0.13 2 2
CDH1 0.013 0.043 -10000 0 -0.76 1 1
clathrin-independent pinocytosis 0.014 0.01 -10000 0 -0.13 2 2
MAPK8IP3 0.019 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0.014 0.01 -10000 0 -0.13 2 2
EXOC2 0.015 0.022 -10000 0 -0.11 15 15
substrate adhesion-dependent cell spreading 0.011 0.052 -10000 0 -0.36 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.001 0.071 -10000 0 -0.26 33 33
regulation of calcium-dependent cell-cell adhesion -0.028 0.042 0.47 2 -10000 0 2
positive regulation of phagocytosis 0.016 0.018 -10000 0 -0.26 2 2
ARF6/GTP/JIP3 0.025 0.009 -10000 0 -0.16 1 1
ACAP1 0.005 0.059 -10000 0 -0.17 43 43
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.041 -10000 0 -0.76 1 1
clathrin heavy chain/ACAP1 0.012 0.064 -10000 0 -0.26 14 14
JIP4/KLC1 0.016 0.069 -10000 0 -0.2 43 43
EXOC1 0.008 0.051 -10000 0 -0.2 25 25
exocyst 0.011 0.052 -10000 0 -0.37 4 4
RALA/GTP 0.005 0.043 -10000 0 -0.2 22 22
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.015 0.044 -10000 0 -0.16 28 28
receptor recycling 0.014 0.01 -10000 0 -0.13 2 2
CTNNA1 0.02 0.013 -10000 0 -0.26 1 1
NME1 0.007 0.008 -10000 0 -0.16 1 1
clathrin coat assembly 0.014 0.051 -10000 0 -0.44 3 3
IL2RA 0.013 0.042 -10000 0 -0.76 1 1
VAMP3 0.016 0.018 -10000 0 -0.26 2 2
GLUT4/clathrin heavy chain/ACAP1 0.018 0.061 -10000 0 -0.24 14 14
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.006 0.056 -10000 0 -0.22 22 22
PLD2 0.006 0.055 -10000 0 -0.22 22 22
EXOC5 -0.006 0.073 -10000 0 -0.18 65 65
PIP5K1C 0.009 0.061 -10000 0 -0.25 21 21
SDC1 0.01 0.043 -10000 0 -0.76 1 1
ARF6/GDP 0.014 0.008 -10000 0 -0.11 2 2
EXOC7 0.018 0.014 -10000 0 -0.29 1 1
E-cadherin/beta catenin 0.03 0.044 -10000 0 -0.49 2 2
mol:Phosphatidic acid 0.006 0.062 -10000 0 -0.18 43 43
endocytosis -0.005 0.05 0.14 49 -10000 0 49
SCAMP2 0.006 0.062 -10000 0 -0.29 22 22
ADRB2 0.015 0.05 -10000 0 -0.43 3 3
EXOC3 0.017 0.021 -10000 0 -0.2 4 4
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.019 0.007 -10000 0 -0.14 1 1
KLC1 -0.002 0.077 -10000 0 -0.28 37 37
AVPR2 0.018 0.048 -10000 0 -0.42 3 3
RALA 0.005 0.063 -10000 0 -0.26 26 26
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.07 -10000 0 -0.25 22 22
Canonical NF-kappaB 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
FBXW11 0.01 0.053 -9999 0 -0.28 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.069 -9999 0 -0.26 12 12
ERC1 -0.002 0.075 -9999 0 -0.24 43 43
RIP2/NOD2 0.025 0.02 -9999 0 -0.19 2 2
NFKBIA 0.01 0.086 -9999 0 -0.31 31 31
BIRC2 0.016 0.03 -9999 0 -0.29 5 5
IKBKB 0.019 0 -9999 0 -10000 0 0
RIPK2 0.017 0.021 -9999 0 -0.18 5 5
IKBKG 0.037 0.034 -9999 0 -0.28 4 4
IKK complex/A20 0.049 0.055 -9999 0 -0.24 5 5
NEMO/A20/RIP2 0.017 0.021 -9999 0 -0.18 5 5
XPO1 0.017 0.023 -9999 0 -0.29 3 3
NEMO/ATM 0.043 0.037 -9999 0 -0.26 5 5
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0.031 -9999 0 -0.24 7 7
Exportin 1/RanGTP 0.023 0.026 -9999 0 -0.21 6 6
IKK complex/ELKS 0.041 0.048 -9999 0 -0.27 5 5
BCL10/MALT1/TRAF6 0.033 0.03 -9999 0 -0.15 11 11
NOD2 0.016 0.02 -9999 0 -0.11 13 13
NFKB1 0.012 0.043 -9999 0 -0.24 11 11
RELA 0.016 0.026 -9999 0 -0.23 3 3
MALT1 0.013 0.036 -9999 0 -0.16 18 18
cIAP1/UbcH5C 0.025 0.031 -9999 0 -0.25 6 6
ATM 0.01 0.042 -9999 0 -0.15 30 30
TNF/TNFR1A 0.007 0.065 -9999 0 -0.19 50 50
TRAF6 0.018 0.019 -9999 0 -0.29 2 2
PRKCA 0.019 0 -9999 0 -10000 0 0
CHUK 0.016 0.025 -9999 0 -0.15 10 10
UBE2D3 0.017 0.023 -9999 0 -0.29 3 3
TNF 0.018 0.01 -9999 0 -0.11 3 3
NF kappa B1 p50/RelA 0.03 0.068 -9999 0 -0.2 38 38
BCL10 0.016 0.028 -9999 0 -0.23 6 6
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.086 -9999 0 -0.31 31 31
beta TrCP1/SCF ubiquitin ligase complex 0.01 0.053 -9999 0 -0.28 14 14
TNFRSF1A -0.01 0.091 -9999 0 -0.29 50 50
IKK complex 0.055 0.035 -9999 0 -0.27 3 3
CYLD 0.018 0.016 -9999 0 -0.17 3 3
IKK complex/PKC alpha 0.061 0.035 -9999 0 -0.26 3 3
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.015 0.049 -10000 0 -0.28 9 9
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.009 0.076 0.4 12 -10000 0 12
IL27/IL27R/JAK1 0.022 0.065 -10000 0 -10000 0 0
TBX21 0.015 0.066 -10000 0 -0.33 9 9
IL12B 0.02 0 -10000 0 -10000 0 0
IL12A 0.011 0 -10000 0 -10000 0 0
IL6ST 0 0.075 -10000 0 -0.3 30 30
IL27RA/JAK1 0.018 0.029 -10000 0 -10000 0 0
IL27 0 0.002 -10000 0 -10000 0 0
TYK2 0.008 0.061 -10000 0 -0.29 21 21
T-helper cell lineage commitment 0.018 0.038 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.009 0.076 0.4 12 -10000 0 12
T cell proliferation during immune response -0.009 0.076 0.4 12 -10000 0 12
MAPKKK cascade 0.009 0.076 -10000 0 -0.4 12 12
STAT3 -0.003 0.079 -10000 0 -0.29 37 37
STAT2 0.019 0 -10000 0 -10000 0 0
STAT1 0.008 0.04 -10000 0 -0.12 41 41
IL12RB1 0.019 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.017 0.066 -10000 0 -0.33 9 9
IL27/IL27R/JAK2/TYK2 0.009 0.076 -10000 0 -0.41 12 12
positive regulation of T cell mediated cytotoxicity 0.009 0.076 -10000 0 -0.4 12 12
STAT1 (dimer) 0.022 0.083 -10000 0 -0.42 9 9
JAK2 0.013 0.027 -10000 0 -10000 0 0
JAK1 0.001 0.071 -10000 0 -0.26 34 34
STAT2 (dimer) 0.019 0.074 -10000 0 -0.38 12 12
T cell proliferation 0.006 0.076 -10000 0 -0.4 12 12
IL12/IL12R/TYK2/JAK2 0.016 0.17 -10000 0 -0.83 20 20
IL17A 0.018 0.038 -10000 0 -10000 0 0
mast cell activation -0.009 0.076 0.4 12 -10000 0 12
IFNG 0.007 0.019 -10000 0 -0.096 12 12
T cell differentiation 0 0.003 -10000 0 -0.017 13 13
STAT3 (dimer) 0.014 0.091 -10000 0 -0.47 12 12
STAT5A (dimer) 0.019 0.074 -10000 0 -0.38 12 12
STAT4 (dimer) 0.016 0.077 -10000 0 -0.4 12 12
STAT4 0.012 0.03 -10000 0 -0.11 30 30
T cell activation -0.008 0.004 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.026 0.065 -10000 0 -10000 0 0
GATA3 0.007 0.017 -10000 0 -10000 0 0
IL18 -0.002 0.036 -10000 0 -0.2 9 9
positive regulation of mast cell cytokine production 0.014 0.089 -10000 0 -0.46 12 12
IL27/EBI3 0.012 0.014 -10000 0 -0.076 1 1
IL27RA 0.011 0.012 -10000 0 -10000 0 0
IL6 0.002 0.051 -10000 0 -10000 0 0
STAT5A 0.019 0.008 -10000 0 -0.11 2 2
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.005 0.006 -10000 0 -10000 0 0
IL1B -0.009 0.046 -10000 0 -0.092 102 102
EBI3 0.015 0.022 -10000 0 -0.11 15 15
TNF 0.01 0.006 -10000 0 -0.07 3 3
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.013 0.04 -9999 0 -0.22 13 13
Ran/GTP/Exportin 1/HDAC4 -0.01 0.038 -9999 0 -0.16 21 21
MDM2/SUMO1 0.026 0.038 -9999 0 -0.25 4 4
HDAC4 0.007 0.056 -9999 0 -0.29 16 16
Ran/GTP/Exportin 1/HDAC1 -0.008 0.038 -9999 0 -0.15 28 28
SUMO1 0.017 0.027 -9999 0 -0.29 4 4
NPC/RanGAP1/SUMO1 0.009 0.037 -9999 0 -0.16 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.016 0.04 -9999 0 -0.16 21 21
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.016 0.031 -9999 0 -0.24 7 7
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.007 0.057 -9999 0 -0.26 22 22
SUMO1/HDAC4 0.024 0.045 -9999 0 -0.27 5 5
SUMO1/HDAC1 0.027 0.043 -9999 0 -0.18 11 11
RANGAP1 0.017 0.015 -9999 0 -0.11 7 7
MDM2/SUMO1/SUMO1 0.036 0.042 -9999 0 -0.14 21 21
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.036 -9999 0 -0.16 21 21
Ran/GTP 0.021 0.04 -9999 0 -0.15 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.011 0.032 -9999 0 -10000 0 0
UBE2I 0.019 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.045 -9999 0 -0.16 21 21
NPC 0.006 0.027 -9999 0 -0.14 18 18
PIAS2 0.018 0.011 -9999 0 -0.11 4 4
PIAS1 0.008 0.056 -9999 0 -0.29 18 18
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0.019 0.006 -9999 0 -0.11 1 1
Aurora C/Aurora B/INCENP 0.03 0.024 -9999 0 -0.1 5 5
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.006 0.062 -9999 0 -0.42 11 11
AURKB 0.011 0.033 -9999 0 -0.12 32 32
AURKC 0.015 0.022 -9999 0 -0.11 16 16
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.001 0.14 -10000 0 -1.1 9 9
VDR 0.019 0.008 -10000 0 -0.11 2 2
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.025 0.097 -10000 0 -0.26 48 48
RXRs/LXRs/DNA/Oxysterols 0.016 0.15 -10000 0 -0.41 52 52
MED1 -0.002 0.078 -10000 0 -0.29 36 36
mol:9cRA 0 0.017 -10000 0 -0.073 5 5
RARs/THRs/DNA/Src-1 0.022 0.053 -10000 0 -0.16 41 41
RXRs/NUR77 0.05 0.04 -10000 0 -0.15 1 1
RXRs/PPAR 0.036 0.027 -10000 0 -0.18 1 1
NCOR2 0.019 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.005 -10000 0 -0.07 2 2
RARs/VDR/DNA/Vit D3 0.045 0.007 -10000 0 -10000 0 0
RARA 0.019 0 -10000 0 -10000 0 0
NCOA1 -0.006 0.083 -10000 0 -0.28 43 43
VDR/VDR/DNA 0.019 0.008 -10000 0 -0.11 2 2
RARs/RARs/DNA/9cRA 0.033 0.014 -10000 0 -10000 0 0
RARG 0.019 0 -10000 0 -10000 0 0
RPS6KB1 -0.005 0.055 -10000 0 -0.39 9 9
RARs/THRs/DNA/SMRT 0.037 0.01 -10000 0 -0.15 1 1
THRA 0.017 0.02 -10000 0 -0.13 8 8
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.005 -10000 0 -0.07 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.04 0.058 0.29 2 -0.18 6 8
NR1H4 0.019 0.008 -10000 0 -0.11 2 2
RXRs/LXRs/DNA 0.057 0.076 -10000 0 -0.22 14 14
NR1H2 0.018 0.02 -10000 0 -10000 0 0
NR1H3 0.014 0.038 -10000 0 -0.15 16 16
RXRs/VDR/DNA/Vit D3 0.047 0.037 -10000 0 -0.14 1 1
NR4A1 0.019 0.008 -10000 0 -0.11 2 2
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.061 -10000 0 -0.24 15 15
RXRG 0.018 0.021 -10000 0 -10000 0 0
RXR alpha/CCPG 0.014 0.015 -10000 0 -0.2 1 1
RXRA 0.018 0.022 -10000 0 -0.3 1 1
RXRB 0.019 0.019 -10000 0 -10000 0 0
THRB 0.019 0 -10000 0 -10000 0 0
PPARG 0.015 0.024 -10000 0 -0.11 18 18
PPARD 0.019 0 -10000 0 -10000 0 0
TNF 0.021 0.14 -10000 0 -0.56 12 12
mol:Oxysterols 0.001 0.015 -10000 0 -10000 0 0
cholesterol transport 0.016 0.15 -10000 0 -0.4 52 52
PPARA 0.019 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.008 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 0.03 0.016 -10000 0 -0.17 1 1
SREBF1 0.008 0.19 -10000 0 -0.81 18 18
RXRs/RXRs/DNA/9cRA 0.04 0.058 0.29 2 -0.18 6 8
ABCA1 -0.029 0.28 -10000 0 -0.92 47 47
RARs/THRs 0.055 0.013 -10000 0 -0.12 1 1
RXRs/FXR 0.05 0.04 -10000 0 -0.15 1 1
BCL2 0.019 0 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.028 0.011 -9999 0 -10000 0 0
KIRREL 0.019 0.013 -9999 0 -0.12 5 5
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.028 0.011 -9999 0 -10000 0 0
PLCG1 0.017 0.025 -9999 0 -0.29 3 3
ARRB2 0.013 0.039 -9999 0 -0.29 7 7
WASL 0.016 0.03 -9999 0 -0.29 5 5
Nephrin/NEPH1/podocin/CD2AP 0.036 0.044 -9999 0 -0.15 19 19
ChemicalAbstracts:57-88-5 0 0 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.026 0.047 -9999 0 -0.23 12 12
FYN 0.021 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0.045 0.02 -9999 0 -0.17 3 3
mol:DAG 0.046 0.02 -9999 0 -0.17 3 3
NPHS2 0.02 0.003 -9999 0 -10000 0 0
mol:IP3 0.046 0.02 -9999 0 -0.17 3 3
regulation of endocytosis 0.027 0.045 -9999 0 -0.17 9 9
Nephrin/NEPH1/podocin/Cholesterol 0.036 0.01 -9999 0 -10000 0 0
establishment of cell polarity 0.028 0.011 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.047 0.046 -9999 0 -0.16 21 21
Nephrin/NEPH1/beta Arrestin2 0.028 0.046 -9999 0 -0.17 9 9
NPHS1 0.02 0.006 -9999 0 -0.11 1 1
Nephrin/NEPH1/podocin 0.023 0.04 -9999 0 -0.084 63 63
TJP1 0.01 0.046 -9999 0 -0.19 22 22
NCK1 0.014 0.036 -9999 0 -0.19 14 14
NCK2 0.009 0.054 -9999 0 -0.28 17 17
heterophilic cell adhesion 0 0 -9999 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.047 0.02 -9999 0 -0.17 3 3
CD2AP 0.003 0.062 -9999 0 -0.2 40 40
Nephrin/NEPH1/podocin/GRB2 0.045 0.029 -9999 0 -0.18 8 8
GRB2 0.014 0.039 -9999 0 -0.26 10 10
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
TRPC6 0.021 0.016 -9999 0 -0.079 1 1
cytoskeleton organization 0.028 0.044 -9999 0 -0.22 12 12
Nephrin/NEPH1 0.024 0.007 -9999 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.032 0.033 -9999 0 -0.18 10 10
Signaling events mediated by the Hedgehog family

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
TGFB2 0.043 0.041 -10000 0 -10000 0 0
IHH 0.028 0.014 -10000 0 -0.094 1 1
SHH Np/Cholesterol/GAS1 0.012 0.039 -10000 0 -0.14 24 24
LRPAP1 0.013 0.043 -10000 0 -0.28 11 11
dorsoventral neural tube patterning -0.012 0.039 0.14 24 -10000 0 24
SMO/beta Arrestin2 0.053 0.031 -10000 0 -10000 0 0
SMO 0.047 0.027 -10000 0 -10000 0 0
AKT1 -0.012 0.15 -10000 0 -0.49 33 33
ARRB2 0.013 0.039 -10000 0 -0.29 7 7
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.018 0.014 -10000 0 -0.11 6 6
heart looping 0.047 0.027 -10000 0 -10000 0 0
STIL 0.035 0.032 -10000 0 -0.18 2 2
DHH N/PTCH2 0.014 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.031 0.029 -10000 0 -10000 0 0
PIK3CA -0.011 0.086 -10000 0 -0.22 66 66
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.044 0.041 -10000 0 -10000 0 0
determination of left/right symmetry 0.047 0.027 -10000 0 -10000 0 0
PIK3R1 -0.015 0.095 -10000 0 -0.27 62 62
skeletal system development 0.044 0.04 -10000 0 -10000 0 0
IHH N/Hhip 0.019 0.008 -10000 0 -10000 0 0
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.047 0.027 -10000 0 -10000 0 0
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.018 0.014 -10000 0 -0.11 6 6
PI3K -0.016 0.093 -10000 0 -0.21 88 88
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.073 -10000 0 -0.17 78 78
somite specification 0.047 0.027 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH1 0.043 0.029 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH2 0.026 0.007 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.025 0.011 -10000 0 -10000 0 0
SHH 0.02 0.009 -10000 0 -10000 0 0
catabolic process 0.038 0.034 -10000 0 -10000 0 0
SMO/Vitamin D3 0.051 0.029 -10000 0 -10000 0 0
SHH Np/Cholesterol/Hhip 0.014 0.006 -10000 0 -10000 0 0
LRP2 0.017 0.018 -10000 0 -0.11 10 10
receptor-mediated endocytosis 0.05 0.031 -10000 0 -10000 0 0
SHH Np/Cholesterol/BOC 0.014 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.026 0.007 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.013 0.006 -10000 0 -10000 0 0
mol:Vitamin D3 0.045 0.03 -10000 0 -10000 0 0
IHH N/PTCH2 0.034 0.008 -10000 0 -10000 0 0
CDON 0.019 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.045 0.037 -10000 0 -10000 0 0
Megalin/LRPAP1 0.022 0.032 -10000 0 -0.19 10 10
PTCH2 0.019 0 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.016 0.006 -10000 0 -10000 0 0
PTCH1 0.038 0.035 -10000 0 -10000 0 0
HHIP 0 0 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.017 0.018 -10000 0 -0.25 2 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.028 -10000 0 -0.21 7 7
AP2 0.008 0.036 -10000 0 -0.17 19 19
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.019 0.039 -10000 0 -0.18 19 19
CLTB 0.018 0.014 -10000 0 -0.29 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.032 -10000 0 -0.2 10 10
CD4 -0.003 0.07 -10000 0 -0.19 56 56
CLTA 0.017 0.023 -10000 0 -0.29 3 3
mol:GTP 0 0.003 -10000 0 -10000 0 0
ARFGAP1 0.01 0.013 -10000 0 -0.2 2 2
mol:PI-4-5-P2 0.011 0.021 0.12 13 -10000 0 13
ARF1/GTP 0.008 0.019 -10000 0 -0.13 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.018 0.032 -10000 0 -0.19 11 11
mol:Choline 0.011 0.021 0.12 13 -10000 0 13
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.018 0.008 -10000 0 -0.11 2 2
DDEF1 0.009 0.019 0.12 10 -10000 0 10
ARF1/GDP 0.007 0.013 -10000 0 -0.18 2 2
AP2M1 0.009 0.053 -10000 0 -0.25 19 19
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.027 -10000 0 -0.15 13 13
Rac/GTP 0.011 0.025 -10000 0 -0.2 7 7
ARF1/GTP/GGA3/ARF-GAP1 0.028 0.02 -10000 0 -0.12 9 9
ARFIP2 0.009 0.047 -10000 0 -0.25 17 17
COPA 0.017 0.018 -10000 0 -0.14 6 6
RAC1 0.015 0.036 -10000 0 -0.29 7 7
ARF1/GTP/coatomer protein complex 0.019 0.031 -10000 0 -0.2 9 9
ARF1/GTP/ARHGAP10 0.009 0.02 -10000 0 -0.16 7 7
GGA3 0.019 0 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.018 -10000 0 -0.14 5 5
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.02 0.032 -10000 0 -0.19 10 10
ARF1/GDP/Membrin 0.018 0.017 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.018 0.039 -10000 0 -0.17 19 19
CYTH2 0 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.022 0.021 -10000 0 -0.16 7 7
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.011 0.024 -10000 0 -0.2 7 7
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 0.01 0.063 -10000 0 -0.19 40 40
PLD2 0.011 0.021 0.12 13 -10000 0 13
ARF-GAP1/v-SNARE 0.01 0.013 -10000 0 -0.2 2 2
PIP5K1A 0.008 0.011 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.015 0.019 -10000 0 -0.14 7 7
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.021 0.12 13 -10000 0 13
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.013 -10000 0 -0.2 2 2
GOSR2 0.013 0.006 -10000 0 -10000 0 0
USO1 0.01 0.028 -10000 0 -0.3 4 4
GBF1 0.012 0.009 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.018 0.038 -10000 0 -0.16 20 20
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.007 0.053 -10000 0 -0.17 36 36
LPA4-mediated 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
ADCY4 0.007 0 -9999 0 -10000 0 0
ADCY5 0.007 0 -9999 0 -10000 0 0
ADCY6 0.014 0.003 -9999 0 -0.05 1 1
ADCY7 0.012 0.011 -9999 0 -0.05 15 15
ADCY1 0.014 0 -9999 0 -10000 0 0
ADCY2 0.014 0.005 -9999 0 -0.05 3 3
ADCY3 0.007 0 -9999 0 -10000 0 0
ADCY8 0.007 0.021 -9999 0 -0.05 64 64
PRKCE 0.01 0 -9999 0 -10000 0 0
ADCY9 0.014 0.007 -9999 0 -0.05 6 6
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.015 0.012 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.025 0.021 -9999 0 -0.19 2 2
FBXW11 0.011 0.047 -9999 0 -0.27 14 14
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0.047 -9999 0 -0.27 14 14
CHUK 0.016 0.025 -9999 0 -0.15 10 10
NF kappa B2 p100/RelB 0.048 0.033 -9999 0 -0.12 14 14
NFKB1 0.014 0.037 -9999 0 -0.23 11 11
MAP3K14 0.017 0.017 -9999 0 -0.11 9 9
NF kappa B1 p50/RelB 0.024 0.027 -9999 0 -0.19 7 7
RELB 0.018 0.011 -9999 0 -0.11 4 4
NFKB2 0.019 0.008 -9999 0 -0.11 2 2
NF kappa B2 p52/RelB 0.025 0.008 -9999 0 -10000 0 0
regulation of B cell activation 0.025 0.008 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.016 0.03 -10000 0 -0.13 21 21
MAPK9 0.007 0.022 -10000 0 -0.24 4 4
adrenocorticotropin secretion 0.009 0.01 -10000 0 -10000 0 0
GNB1/GNG2 0.006 0.034 -10000 0 -0.16 21 21
GNB1 0.007 0.061 -10000 0 -0.29 21 21
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0.005 -10000 0 -10000 0 0
Gs family/GTP 0.012 0.005 -10000 0 -0.049 3 3
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 0.001 0.015 3 -10000 0 3
GNAL 0.018 0.01 -10000 0 -0.11 3 3
GNG2 0 0 -10000 0 -10000 0 0
CRH 0.017 0.017 -10000 0 -0.11 9 9
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0 -10000 0 -10000 0 0
MAPK11 0.009 0 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.019 0 -9999 0 -10000 0 0
ITGB7 0.018 0.01 -9999 0 -0.11 3 3
ITGA4 0.016 0.019 -9999 0 -0.11 12 12
alpha4/beta7 Integrin 0.026 0.016 -9999 0 -0.14 2 2
alpha4/beta1 Integrin 0.026 0.014 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.019 0 -9999 0 -10000 0 0
GNAT1/GTP 0.014 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.005 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP 0.026 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.019 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel 0.037 0.008 -9999 0 -10000 0 0
mol:Na + 0.03 0.004 -9999 0 -10000 0 0
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.016 -9999 0 -0.16 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.038 0.005 -9999 0 -10000 0 0
CNGB1 0.019 0 -9999 0 -10000 0 0
RDH5 0.017 0.016 -9999 0 -0.11 8 8
SAG 0.019 0.008 -9999 0 -0.11 2 2
mol:Ca2+ 0.032 0.004 -9999 0 -10000 0 0
Na + (4 Units) 0.027 0.003 -9999 0 -10000 0 0
RGS9 0.016 0.02 -9999 0 -0.11 13 13
GNB1/GNGT1 0.019 0.044 -9999 0 -0.19 21 21
GNAT1/GDP 0.031 0.015 -9999 0 -0.13 1 1
GUCY2D 0.019 0 -9999 0 -10000 0 0
GNGT1 0.019 0.008 -9999 0 -0.11 2 2
GUCY2F 0.019 0 -9999 0 -10000 0 0
GNB5 0.017 0.019 -9999 0 -0.14 7 7
mol:GMP (4 units) 0.032 0.007 -9999 0 -10000 0 0
mol:11-cis-retinal 0.017 0.016 -9999 0 -0.11 8 8
mol:cGMP 0.026 0 -9999 0 -10000 0 0
GNB1 0.007 0.061 -9999 0 -0.29 21 21
Rhodopsin 0.027 0.011 -9999 0 -10000 0 0
SLC24A1 0.019 0 -9999 0 -10000 0 0
CNGA1 0.018 0.01 -9999 0 -0.11 3 3
Metarhodopsin II 0.012 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.025 0 -9999 0 -10000 0 0
RGS9BP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Transducin 0.018 0.037 -9999 0 -0.16 21 21
GCAP Family/Ca ++ 0.012 0 -9999 0 -10000 0 0
PDE6A/B 0.027 0.01 -9999 0 -10000 0 0
mol:Pi 0.022 0.016 -9999 0 -0.16 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.03 0.034 -9999 0 -0.14 21 21
PDE6B 0.018 0.013 -9999 0 -0.11 5 5
PDE6A 0.019 0.006 -9999 0 -10000 0 0
PDE6G 0.019 0 -9999 0 -10000 0 0
RHO 0.019 0 -9999 0 -10000 0 0
PDE6 0.043 0.017 -9999 0 -0.11 1 1
GUCA1A 0 0 -9999 0 -10000 0 0
GC2/GCAP Family 0.025 0 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.019 0 -9999 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.025 0.003 -9999 0 -10000 0 0
EFNA5 0.019 0.006 -9999 0 -0.11 1 1
FYN 0.02 0.01 -9999 0 -10000 0 0
neuron projection morphogenesis 0.025 0.003 -9999 0 -10000 0 0
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.026 0.003 -9999 0 -10000 0 0
EPHA5 0.019 0 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.019 0 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.019 0 -9999 0 -9999 0 0
PDE3B 0.019 0 -9999 0 -9999 0 0
Methods & Data
Input

  • Expression Data Normalization = Tumor samples were used to median center the expression data used in this analysis.

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM/1269528/2.GDAC_MergeDataFiles.Finished/GBM.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

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.

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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)
Meta

  • Maintainer = TCGA GDAC Team

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