PARADIGM pathway analysis of mRNA expression data
Glioblastoma Multiforme (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1222RQN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Glioblastoma Multiforme (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1222RQN
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 48 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
TCGA08_retinoblastoma 228
Glypican 2 network 225
HIF-1-alpha transcription factor network 215
FOXM1 transcription factor network 206
Endothelins 138
Osteopontin-mediated events 127
Syndecan-1-mediated signaling events 122
EGFR-dependent Endothelin signaling events 118
amb2 Integrin signaling 112
LPA receptor mediated events 108
Results
Summary Table

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
TCGA08_retinoblastoma 228 1827 8 -0.23 0.072 1000 -1000 -0.004 -1000
Glypican 2 network 225 900 4 -0.23 0 1000 -1000 0 -1000
HIF-1-alpha transcription factor network 215 16342 76 -0.55 0.023 1000 -1000 -0.01 -1000
FOXM1 transcription factor network 206 10542 51 -0.75 0.017 1000 -1000 -0.044 -1000
Endothelins 138 13264 96 -0.47 0.083 1000 -1000 -0.011 -1000
Osteopontin-mediated events 127 4850 38 -0.32 0.017 1000 -1000 -0.003 -1000
Syndecan-1-mediated signaling events 122 4165 34 -0.29 0.018 1000 -1000 -0.002 -1000
EGFR-dependent Endothelin signaling events 118 2490 21 -0.14 0.017 1000 -1000 0 -1000
amb2 Integrin signaling 112 9199 82 -0.24 0.022 1000 -1000 0 -1000
LPA receptor mediated events 108 11098 102 -0.18 0.017 1000 -1000 -0.027 -1000
PLK1 signaling events 89 7617 85 -0.25 0.022 1000 -1000 -0.005 -1000
Syndecan-4-mediated signaling events 89 5974 67 -0.39 0.021 1000 -1000 -0.01 -1000
BARD1 signaling events 85 4868 57 -0.26 0.049 1000 -1000 -0.016 -1000
Signaling events mediated by VEGFR1 and VEGFR2 84 10510 125 -0.25 0.026 1000 -1000 -0.03 -1000
HIF-2-alpha transcription factor network 75 3246 43 -0.21 0.11 1000 -1000 -0.042 -1000
Wnt signaling 71 497 7 -0.12 0.017 1000 -1000 0.005 -1000
Fc-epsilon receptor I signaling in mast cells 70 6862 97 -0.19 0.032 1000 -1000 -0.031 -1000
Aurora B signaling 67 4508 67 -0.31 0.023 1000 -1000 -0.019 -1000
VEGFR1 specific signals 61 3458 56 -0.25 0.039 1000 -1000 -0.011 -1000
Regulation of nuclear SMAD2/3 signaling 60 8220 136 -0.28 0.16 1000 -1000 -0.01 -1000
PDGFR-alpha signaling pathway 56 2466 44 -0.25 0.023 1000 -1000 -0.002 -1000
S1P1 pathway 54 1963 36 -0.21 0.022 1000 -1000 -0.027 -1000
Stabilization and expansion of the E-cadherin adherens junction 53 3966 74 -0.35 0.033 1000 -1000 -0.031 -1000
Noncanonical Wnt signaling pathway 51 1336 26 -0.12 0.017 1000 -1000 -0.019 -1000
Paxillin-independent events mediated by a4b1 and a4b7 51 1889 37 -0.27 0.042 1000 -1000 -0.004 -1000
TCGA08_p53 51 360 7 -0.024 0.009 1000 -1000 -0.004 -1000
FAS signaling pathway (CD95) 49 2331 47 -0.045 0.031 1000 -1000 -0.009 -1000
Circadian rhythm pathway 48 1075 22 -0.046 0.026 1000 -1000 -0.009 -1000
Class I PI3K signaling events 48 3533 73 -0.094 0.035 1000 -1000 -0.003 -1000
Ras signaling in the CD4+ TCR pathway 46 787 17 -0.095 0.016 1000 -1000 -0.006 -1000
IL1-mediated signaling events 45 2791 62 -0.12 0.049 1000 -1000 -0.01 -1000
Aurora A signaling 44 2681 60 -0.16 0.042 1000 -1000 -0.002 -1000
Integrins in angiogenesis 40 3434 84 -0.22 0.04 1000 -1000 -0.011 -1000
BCR signaling pathway 40 4057 99 -0.088 0.048 1000 -1000 -0.03 -1000
E-cadherin signaling in keratinocytes 39 1702 43 -0.14 0.028 1000 -1000 -0.005 -1000
Signaling events mediated by HDAC Class I 38 4030 104 -0.13 0.034 1000 -1000 -0.014 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 37 2907 78 -0.047 0.032 1000 -1000 -0.014 -1000
Syndecan-2-mediated signaling events 35 2437 69 -0.19 0.034 1000 -1000 -0.001 -1000
Angiopoietin receptor Tie2-mediated signaling 35 3121 88 -0.2 0.037 1000 -1000 -0.046 -1000
Syndecan-3-mediated signaling events 34 1214 35 -0.14 0.032 1000 -1000 -0.007 -1000
Glypican 1 network 32 1557 48 -0.22 0.028 1000 -1000 -0.005 -1000
S1P3 pathway 32 1363 42 -0.21 0.022 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 31 735 23 -0.086 0.018 1000 -1000 0 -1000
Plasma membrane estrogen receptor signaling 31 2716 86 -0.42 0.13 1000 -1000 -0.026 -1000
Visual signal transduction: Cones 29 1104 38 -0.13 0.04 1000 -1000 0 -1000
Signaling mediated by p38-alpha and p38-beta 29 1301 44 -0.044 0.033 1000 -1000 0 -1000
Nongenotropic Androgen signaling 28 1486 52 -0.059 0.027 1000 -1000 -0.014 -1000
Paxillin-dependent events mediated by a4b1 27 994 36 -0.27 0.042 1000 -1000 -0.011 -1000
EPO signaling pathway 26 1464 55 -0.033 0.053 1000 -1000 -0.006 -1000
Signaling events mediated by PRL 26 893 34 -0.038 0.025 1000 -1000 -0.003 -1000
Arf6 downstream pathway 25 1092 43 -0.016 0.025 1000 -1000 -0.012 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 25 1728 68 -0.19 0.083 1000 -1000 -0.03 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 24 1080 45 -0.13 0.026 1000 -1000 -0.017 -1000
Canonical Wnt signaling pathway 24 1270 51 -0.11 0.099 1000 -1000 -0.015 -1000
IL6-mediated signaling events 24 1814 75 -0.2 0.034 1000 -1000 -0.02 -1000
Caspase cascade in apoptosis 23 1702 74 -0.13 0.024 1000 -1000 -0.013 -1000
Signaling events mediated by PTP1B 23 1798 76 -0.2 0.033 1000 -1000 -0.009 -1000
TRAIL signaling pathway 23 1135 48 -0.02 0.022 1000 -1000 -0.012 -1000
RXR and RAR heterodimerization with other nuclear receptor 23 1210 52 -0.24 0.051 1000 -1000 0 -1000
FoxO family signaling 23 1498 64 -0.2 0.022 1000 -1000 -0.006 -1000
Regulation of Telomerase 23 2395 102 -0.14 0.044 1000 -1000 -0.028 -1000
IL23-mediated signaling events 23 1430 60 -0.025 0.047 1000 -1000 -0.018 -1000
ErbB2/ErbB3 signaling events 22 1454 65 -0.094 0.022 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 22 1376 61 -0.092 0.035 1000 -1000 -0.01 -1000
TCGA08_rtk_signaling 22 585 26 -0.14 0.021 1000 -1000 -0.003 -1000
Glucocorticoid receptor regulatory network 21 2469 114 -0.099 0.075 1000 -1000 -0.021 -1000
Ceramide signaling pathway 21 1600 76 -0.13 0.039 1000 -1000 -0.007 -1000
IL2 signaling events mediated by PI3K 21 1258 58 -0.043 0.037 1000 -1000 -0.014 -1000
Cellular roles of Anthrax toxin 20 818 39 -0.084 0.016 1000 -1000 -0.007 -1000
BMP receptor signaling 20 1635 81 -0.086 0.047 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 20 1583 76 -0.086 0.039 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 19 1479 76 -0.34 0.047 1000 -1000 -0.006 -1000
IFN-gamma pathway 19 1358 68 -0.064 0.043 1000 -1000 -0.031 -1000
ceramide signaling pathway 19 941 49 -0.13 0.025 1000 -1000 -0.014 -1000
Neurotrophic factor-mediated Trk receptor signaling 19 2293 120 -0.12 0.05 1000 -1000 -0.024 -1000
Regulation of p38-alpha and p38-beta 18 976 54 -0.053 0.033 1000 -1000 0 -1000
Retinoic acid receptors-mediated signaling 17 1039 58 -0.18 0.068 1000 -1000 -0.009 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 16 889 54 -0.086 0.026 1000 -1000 -0.011 -1000
TCR signaling in naïve CD8+ T cells 16 1565 93 -0.094 0.033 1000 -1000 -0.025 -1000
IL2 signaling events mediated by STAT5 16 367 22 -0.096 0.042 1000 -1000 -0.001 -1000
IL4-mediated signaling events 15 1417 91 -0.15 0.05 1000 -1000 -0.11 -1000
Canonical NF-kappaB pathway 14 548 39 -0.13 0.06 1000 -1000 0 -1000
IL12-mediated signaling events 14 1258 87 -0.22 0.048 1000 -1000 -0.058 -1000
ErbB4 signaling events 14 973 69 -0.14 0.05 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 14 1854 125 -0.12 0.082 1000 -1000 -0.033 -1000
PDGFR-beta signaling pathway 14 1450 97 -0.066 0.04 1000 -1000 -0.03 -1000
Signaling mediated by p38-gamma and p38-delta 13 208 15 -0.013 0.025 1000 -1000 -0.004 -1000
Insulin Pathway 13 1014 74 -0.11 0.048 1000 -1000 -0.026 -1000
Arf6 signaling events 12 757 62 -0.14 0.044 1000 -1000 0 -1000
IGF1 pathway 12 714 57 -0.032 0.034 1000 -1000 -0.009 -1000
Class I PI3K signaling events mediated by Akt 11 808 68 -0.026 0.036 1000 -1000 -0.007 -1000
Nectin adhesion pathway 11 693 63 -0.086 0.054 1000 -1000 -0.033 -1000
Signaling events mediated by the Hedgehog family 10 537 52 -0.03 0.045 1000 -1000 -0.008 -1000
JNK signaling in the CD4+ TCR pathway 10 185 17 -0.017 0.027 1000 -1000 -0.01 -1000
Thromboxane A2 receptor signaling 10 1123 105 -0.14 0.035 1000 -1000 -0.035 -1000
Calcium signaling in the CD4+ TCR pathway 10 314 31 -0.081 0.055 1000 -1000 -0.02 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 10 354 33 -0.039 0.041 1000 -1000 0 -1000
E-cadherin signaling events 10 51 5 0.004 0.023 1000 -1000 0.003 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 9 772 85 -0.084 0.049 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 9 259 27 -0.036 0.036 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 8 241 28 -0.036 0.024 1000 -1000 0 -1000
Hedgehog signaling events mediated by Gli proteins 8 552 65 -0.065 0.042 1000 -1000 -0.004 -1000
Aurora C signaling 8 58 7 -0.005 0.02 1000 -1000 0 -1000
Atypical NF-kappaB pathway 8 265 31 -0.012 0.033 1000 -1000 0 -1000
EPHB forward signaling 8 699 85 -0.094 0.048 1000 -1000 -0.034 -1000
mTOR signaling pathway 7 371 53 -0.1 0.034 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class III 7 294 40 -0.034 0.038 1000 -1000 -0.012 -1000
Signaling events regulated by Ret tyrosine kinase 7 615 82 -0.021 0.043 1000 -1000 -0.025 -1000
Ephrin B reverse signaling 7 358 48 -0.016 0.026 1000 -1000 -0.013 -1000
S1P5 pathway 6 104 17 -0.036 0.017 1000 -1000 -0.007 -1000
Nephrin/Neph1 signaling in the kidney podocyte 5 177 34 -0.027 0.047 1000 -1000 -0.008 -1000
FOXA2 and FOXA3 transcription factor networks 5 268 46 -0.017 0.19 1000 -1000 -0.002 -1000
Arf6 trafficking events 5 406 71 -0.026 0.028 1000 -1000 -0.007 -1000
p38 MAPK signaling pathway 5 250 44 -0.02 0.048 1000 -1000 -0.009 -1000
Regulation of Androgen receptor activity 5 389 70 -0.028 0.067 1000 -1000 -0.011 -1000
Insulin-mediated glucose transport 4 132 32 -0.01 0.021 1000 -1000 0 -1000
Reelin signaling pathway 4 267 56 -0.003 0.08 1000 -1000 -0.002 -1000
IL27-mediated signaling events 4 206 51 -0.025 0.044 1000 -1000 -0.018 -1000
S1P4 pathway 4 124 25 -0.036 0.022 1000 -1000 0 -1000
Signaling events mediated by HDAC Class II 3 237 75 -0.029 0.043 1000 -1000 -0.015 -1000
a4b1 and a4b7 Integrin signaling 3 17 5 0.013 0.023 1000 -1000 0.004 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 3 269 83 -0.061 0.047 1000 -1000 -0.008 -1000
LPA4-mediated signaling events 1 12 12 0 0.014 1000 -1000 -0.003 -1000
Effects of Botulinum toxin 1 42 26 0 0.035 1000 -1000 -0.001 -1000
Arf1 pathway 1 71 54 0 0.027 1000 -1000 -0.002 -1000
Alternative NF-kappaB pathway 1 22 13 0 0.049 1000 -1000 0 -1000
PLK2 and PLK4 events 0 0 3 0.012 0.017 1000 -1000 0.004 -1000
Ephrin A reverse signaling 0 2 7 0 0.023 1000 -1000 0 -1000
Rapid glucocorticoid signaling 0 4 20 0 0.017 1000 -1000 0 -1000
Visual signal transduction: Rods 0 5 52 0 0.042 1000 -1000 -0.004 -1000
Class IB PI3K non-lipid kinase events 0 0 3 -0.017 0.017 1000 -1000 -0.006 -1000
Total 4529 255713 7203 -16 5.1 131000 -131000 -1.7 -131000
TCGA08_retinoblastoma

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
CDKN2B 0 0.018 -10000 0 -10000 0 0
CDKN2C -0.23 0.21 -10000 0 -0.41 310 310
CDKN2A -0.013 0.13 -10000 0 -0.38 58 58
CCND2 0.043 0.061 0.089 311 -10000 0 311
RB1 -0.048 0.068 -10000 0 -0.097 314 314
CDK4 0.031 0.071 0.14 115 -0.081 87 202
CDK6 0.072 0.073 0.13 321 -10000 0 321
G1/S progression 0.048 0.068 0.097 311 -10000 0 311
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.23 0.21 -9999 0 -0.41 300 300
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.16 0.15 -9999 0 -0.29 300 300
neuron projection morphogenesis -0.16 0.15 -9999 0 -0.29 300 300
HIF-1-alpha 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
PKM2 -0.45 0.47 -10000 0 -0.79 301 301
HDAC7 -0.006 0.012 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.37 0.36 28 -0.65 269 297
SMAD4 -0.085 0.18 -10000 0 -0.41 127 127
ID2 -0.45 0.47 -10000 0 -0.79 300 300
AP1 -0.047 0.13 -10000 0 -0.29 125 125
ABCG2 -0.45 0.47 -10000 0 -0.79 302 302
HIF1A -0.062 0.08 -10000 0 -0.15 93 93
TFF3 -0.45 0.47 -10000 0 -0.79 303 303
GATA2 0.017 0.019 -10000 0 -0.41 1 1
AKT1 -0.055 0.082 0.32 1 -0.25 8 9
response to hypoxia -0.068 0.068 0.3 1 -0.13 222 223
MCL1 -0.45 0.47 -10000 0 -0.8 301 301
NDRG1 -0.45 0.47 -10000 0 -0.79 301 301
SERPINE1 -0.52 0.53 -10000 0 -0.88 313 313
FECH -0.45 0.47 -10000 0 -0.79 301 301
FURIN -0.45 0.47 -10000 0 -0.79 301 301
NCOA2 0.019 0.001 -10000 0 -10000 0 0
EP300 -0.026 0.12 0.45 5 -0.2 5 10
HMOX1 -0.55 0.53 -10000 0 -0.9 329 329
BHLHE40 -0.45 0.47 -10000 0 -0.8 301 301
BHLHE41 -0.45 0.47 -10000 0 -0.8 301 301
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.1 0.13 -10000 0 -0.24 172 172
ENG -0.07 0.15 0.34 5 -0.29 91 96
JUN 0.017 0.019 -10000 0 -0.41 1 1
RORA -0.45 0.47 -10000 0 -0.79 300 300
ABCB1 -0.093 0.087 -10000 0 -0.18 233 233
TFRC -0.45 0.47 -10000 0 -0.79 303 303
CXCR4 -0.54 0.53 -10000 0 -0.88 324 324
TF -0.42 0.47 -10000 0 -0.81 270 270
CITED2 -0.45 0.48 -10000 0 -0.8 301 301
HIF1A/ARNT -0.49 0.57 0.48 28 -0.93 284 312
LDHA -0.052 0.054 -10000 0 -10000 0 0
ETS1 -0.45 0.47 -10000 0 -0.79 301 301
PGK1 -0.45 0.47 -10000 0 -0.79 301 301
NOS2 -0.45 0.47 -10000 0 -0.8 301 301
ITGB2 -0.52 0.53 -10000 0 -0.89 310 310
ALDOA -0.45 0.47 -10000 0 -0.79 301 301
Cbp/p300/CITED2 -0.45 0.48 -10000 0 -0.83 284 284
FOS -0.084 0.18 -10000 0 -0.41 125 125
HK2 -0.45 0.47 -10000 0 -0.79 301 301
SP1 0.023 0.008 -10000 0 -10000 0 0
GCK -0.037 0.17 0.58 5 -0.26 6 11
HK1 -0.45 0.47 -10000 0 -0.8 299 299
NPM1 -0.45 0.47 -10000 0 -0.79 301 301
EGLN1 -0.45 0.47 -10000 0 -0.79 301 301
CREB1 0.023 0.002 -10000 0 -10000 0 0
PGM1 -0.45 0.47 -10000 0 -0.79 301 301
SMAD3 0.017 0.003 -10000 0 -10000 0 0
EDN1 -0.036 0.15 0.51 1 -0.28 44 45
IGFBP1 -0.45 0.47 -10000 0 -0.8 302 302
VEGFA -0.41 0.42 -10000 0 -0.71 317 317
HIF1A/JAB1 -0.033 0.054 -10000 0 -0.4 2 2
CP -0.49 0.51 -10000 0 -0.85 308 308
CXCL12 -0.45 0.48 -10000 0 -0.8 301 301
COPS5 0.018 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.048 0.13 -10000 0 -0.28 127 127
BNIP3 -0.45 0.47 -10000 0 -0.79 301 301
EGLN3 -0.45 0.47 -10000 0 -0.79 301 301
CA9 -0.46 0.48 -10000 0 -0.81 302 302
TERT -0.45 0.47 -10000 0 -0.79 301 301
ENO1 -0.45 0.47 -10000 0 -0.79 301 301
PFKL -0.45 0.47 -10000 0 -0.79 301 301
NCOA1 0.017 0.003 -10000 0 -10000 0 0
ADM -0.55 0.52 -10000 0 -0.88 328 328
ARNT -0.063 0.07 -10000 0 -0.14 160 160
HNF4A 0.021 0 -10000 0 -10000 0 0
ADFP -0.52 0.52 -10000 0 -0.88 316 316
SLC2A1 -0.32 0.36 -10000 0 -0.64 268 268
LEP -0.45 0.47 -10000 0 -0.79 301 301
HIF1A/ARNT/Cbp/p300 -0.35 0.38 0.36 28 -0.68 269 297
EPO -0.18 0.28 0.54 3 -0.44 230 233
CREBBP -0.026 0.12 0.43 6 -0.2 5 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.39 0.4 0.35 28 -0.7 297 325
PFKFB3 -0.45 0.47 -10000 0 -0.79 301 301
NT5E -0.47 0.48 -10000 0 -0.82 305 305
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.55 0.55 -9999 0 -1 275 275
PLK1 -0.03 0.098 -9999 0 -0.46 22 22
BIRC5 -0.18 0.23 -9999 0 -0.46 212 212
HSPA1B -0.56 0.55 -9999 0 -1 284 284
MAP2K1 -0.013 0.036 -9999 0 -10000 0 0
BRCA2 -0.55 0.55 -9999 0 -1 275 275
FOXM1 -0.75 0.8 -9999 0 -1.3 304 304
XRCC1 -0.55 0.55 -9999 0 -1 275 275
FOXM1B/p19 -0.63 0.61 -9999 0 -1.1 284 284
Cyclin D1/CDK4 -0.6 0.55 -9999 0 -1 290 290
CDC2 -0.63 0.63 -9999 0 -1.1 284 284
TGFA -0.49 0.48 -9999 0 -0.91 273 273
SKP2 -0.55 0.55 -9999 0 -1 275 275
CCNE1 0.005 0.05 -9999 0 -0.42 7 7
CKS1B -0.59 0.58 -9999 0 -1.1 279 279
RB1 -0.26 0.23 -9999 0 -0.47 228 228
FOXM1C/SP1 -0.68 0.68 -9999 0 -1.2 278 278
AURKB -0.034 0.11 -9999 0 -0.46 27 27
CENPF -0.6 0.59 -9999 0 -1.1 282 282
CDK4 -0.27 0.21 -9999 0 -0.43 343 343
MYC -0.53 0.5 -9999 0 -0.93 293 293
CHEK2 -0.025 0.085 -9999 0 -0.46 16 16
ONECUT1 -0.55 0.54 -9999 0 -1 276 276
CDKN2A -0.031 0.13 -9999 0 -0.41 58 58
LAMA4 -0.55 0.55 -9999 0 -1 276 276
FOXM1B/HNF6 -0.68 0.68 -9999 0 -1.3 276 276
FOS -0.59 0.56 -9999 0 -1 292 292
SP1 0.016 0.006 -9999 0 -10000 0 0
CDC25B -0.56 0.56 -9999 0 -1 277 277
response to radiation -0.02 0.026 -9999 0 -10000 0 0
CENPB -0.56 0.56 -9999 0 -1 277 277
CENPA -0.57 0.58 -9999 0 -1.1 275 275
NEK2 -0.56 0.56 -9999 0 -1 275 275
HIST1H2BA -0.56 0.55 -9999 0 -1 284 284
CCNA2 -0.1 0.19 -9999 0 -0.43 139 139
EP300 0.017 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.71 0.71 -9999 0 -1.3 290 290
CCNB2 -0.65 0.6 -9999 0 -1.1 305 305
CCNB1 -0.64 0.63 -9999 0 -1.1 290 290
ETV5 -0.55 0.55 -9999 0 -1 275 275
ESR1 -0.55 0.55 -9999 0 -1 275 275
CCND1 -0.56 0.53 -9999 0 -1 280 280
GSK3A -0.009 0.029 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.075 0.16 -9999 0 -0.31 146 146
CDK2 -0.011 0.097 -9999 0 -0.43 27 27
G2/M transition of mitotic cell cycle -0.024 0.033 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.61 0.62 -9999 0 -1.1 275 275
GAS1 -0.57 0.56 -9999 0 -1 280 280
MMP2 -0.63 0.57 -9999 0 -1.1 304 304
RB1/FOXM1C -0.59 0.55 -9999 0 -1 284 284
CREBBP 0.017 0 -9999 0 -10000 0 0
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.26 0.22 -10000 0 -0.35 397 397
PTK2B 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.039 0.099 -10000 0 -0.54 4 4
EDN1 -0.11 0.11 -10000 0 -0.24 143 143
EDN3 0.014 0.037 -10000 0 -0.41 4 4
EDN2 0.016 0.019 -10000 0 -0.41 1 1
HRAS/GDP -0.023 0.1 -10000 0 -0.22 53 53
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.087 0.1 -10000 0 -0.2 182 182
ADCY4 -0.21 0.18 -10000 0 -0.29 396 396
ADCY5 -0.21 0.18 -10000 0 -0.29 396 396
ADCY6 -0.21 0.18 -10000 0 -0.34 291 291
ADCY7 -0.21 0.18 -10000 0 -0.35 291 291
ADCY1 -0.21 0.18 -10000 0 -0.34 291 291
ADCY2 -0.21 0.18 -10000 0 -0.34 291 291
ADCY3 -0.21 0.18 -10000 0 -0.29 396 396
ADCY8 -0.21 0.18 -10000 0 -0.34 293 293
ADCY9 -0.21 0.18 -10000 0 -0.34 291 291
arachidonic acid secretion -0.067 0.14 -10000 0 -0.3 102 102
ETB receptor/Endothelin-1/Gq/GTP -0.032 0.062 -10000 0 -0.18 38 38
GNAO1 0.002 0.005 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
ETA receptor/Endothelin-1/G12/GTP -0.23 0.21 0.25 1 -0.37 314 315
ETA receptor/Endothelin-1/Gs/GTP -0.22 0.2 0.24 1 -0.3 396 397
mol:GTP 0 0.003 -10000 0 -10000 0 0
COL3A1 -0.41 0.28 -10000 0 -0.55 400 400
EDNRB -0.046 0.11 -10000 0 -0.42 40 40
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.26 0.21 -10000 0 -0.41 291 291
CYSLTR1 -0.26 0.21 -10000 0 -0.35 397 397
SLC9A1 -0.13 0.11 -10000 0 -0.21 291 291
mol:GDP -0.03 0.11 0.18 1 -0.23 55 56
SLC9A3 -0.084 0.12 -10000 0 -0.38 30 30
RAF1 -0.05 0.12 -10000 0 -0.26 96 96
JUN -0.041 0.098 -10000 0 -0.44 5 5
JAK2 -0.26 0.22 -10000 0 -0.35 396 396
mol:IP3 -0.077 0.09 -10000 0 -0.18 166 166
ETA receptor/Endothelin-1 -0.3 0.25 0.28 1 -0.41 397 398
PLCB1 0.016 0.002 -10000 0 -10000 0 0
PLCB2 0.016 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.16 0.18 -10000 0 -0.42 157 157
FOS -0.075 0.18 -10000 0 -0.38 125 125
Gai/GDP -0.47 0.17 -10000 0 -0.52 482 482
CRK 0.017 0 -10000 0 -10000 0 0
mol:Ca ++ -0.23 0.21 -10000 0 -0.37 317 317
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.015 0.046 -10000 0 -0.19 19 19
GNAQ 0.018 0.004 -10000 0 -10000 0 0
GNAZ 0.015 0.006 -10000 0 -10000 0 0
GNAL 0.017 0 -10000 0 -10000 0 0
Gs family/GDP -0.023 0.1 -10000 0 -0.22 53 53
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.12 -10000 0 -0.21 264 264
MAPK14 -0.018 0.052 -10000 0 -0.16 27 27
TRPC6 -0.04 0.1 -10000 0 -0.5 5 5
GNAI2 0.017 0.001 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNAI1 0.014 0.02 -10000 0 -0.41 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.021 0.055 -10000 0 -0.16 32 32
ETB receptor/Endothelin-2 -0.022 0.082 -10000 0 -0.29 41 41
ETB receptor/Endothelin-3 -0.023 0.085 -10000 0 -0.29 44 44
ETB receptor/Endothelin-1 -0.11 0.12 -10000 0 -0.25 168 168
MAPK3 -0.068 0.17 -10000 0 -0.36 116 116
MAPK1 -0.072 0.17 -10000 0 -0.36 116 116
Rac1/GDP -0.022 0.1 -10000 0 -0.22 53 53
cAMP biosynthetic process -0.17 0.16 -10000 0 -0.3 279 279
MAPK8 -0.053 0.11 -10000 0 -0.36 12 12
SRC 0.017 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.033 0.078 -10000 0 -0.2 87 87
p130Cas/CRK/Src/PYK2 0.005 0.098 -10000 0 -0.28 12 12
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.024 0.1 -10000 0 -0.22 54 54
COL1A2 -0.35 0.29 -10000 0 -0.57 307 307
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.16 0.18 -10000 0 -0.3 266 266
mol:DAG -0.077 0.09 -10000 0 -0.18 166 166
MAP2K2 -0.06 0.14 -10000 0 -0.3 115 115
MAP2K1 -0.059 0.15 -10000 0 -0.3 115 115
EDNRA -0.24 0.23 -10000 0 -0.4 288 288
positive regulation of muscle contraction -0.22 0.19 -10000 0 -0.36 293 293
Gq family/GDP 0.033 0.097 -10000 0 -0.24 18 18
HRAS/GTP -0.04 0.1 -10000 0 -0.2 89 89
PRKCH -0.071 0.09 -10000 0 -0.18 154 154
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.07 0.088 -10000 0 -0.18 157 157
PRKCB -0.075 0.088 -10000 0 -0.18 166 166
PRKCE -0.071 0.087 -10000 0 -0.18 157 157
PRKCD -0.071 0.089 -10000 0 -0.18 157 157
PRKCG -0.071 0.089 -10000 0 -0.18 164 164
regulation of vascular smooth muscle contraction -0.08 0.19 -10000 0 -0.4 127 127
PRKCQ -0.072 0.088 -10000 0 -0.18 164 164
PLA2G4A -0.071 0.15 -10000 0 -0.32 102 102
GNA14 0.016 0.027 -10000 0 -0.41 2 2
GNA15 0.012 0.049 -10000 0 -0.41 7 7
GNA12 0.014 0.037 -10000 0 -0.41 4 4
GNA11 0.017 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.23 0.21 0.25 1 -0.38 291 292
MMP1 0.083 0.15 0.19 243 -0.34 43 286
Osteopontin-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
IKK alpha homodimer -0.066 0.13 -9999 0 -0.23 186 186
NF kappa B1 p50/RelA/I kappa B alpha -0.056 0.14 -9999 0 -0.3 83 83
alphaV/beta3 Integrin/Osteopontin/Src -0.097 0.16 -9999 0 -0.31 185 185
AP1 -0.2 0.22 -9999 0 -0.43 203 203
ILK -0.08 0.13 -9999 0 -0.24 185 185
bone resorption -0.21 0.16 -9999 0 -0.31 306 306
PTK2B 0.017 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.065 0.14 -9999 0 -0.23 200 200
ITGAV 0 0.074 -9999 0 -0.42 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.22 0.13 -9999 0 -0.28 416 416
alphaV/beta3 Integrin/Osteopontin -0.076 0.15 -9999 0 -0.27 185 185
MAP3K1 -0.082 0.13 -9999 0 -0.25 186 186
JUN 0.014 0.019 -9999 0 -0.41 1 1
MAPK3 -0.079 0.14 -9999 0 -0.25 185 185
MAPK1 -0.08 0.14 -9999 0 -0.25 185 185
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
MAPK8 -0.084 0.12 -9999 0 -0.24 186 186
ITGB3 0.013 0.011 -9999 0 -10000 0 0
NFKBIA -0.075 0.14 -9999 0 -0.29 112 112
FOS -0.087 0.18 -9999 0 -0.42 125 125
CD44 -0.32 0.18 -9999 0 -0.41 416 416
CHUK 0.016 0.019 -9999 0 -0.41 1 1
PLAU -0.13 0.22 -9999 0 -0.48 131 131
NF kappa B1 p50/RelA -0.06 0.15 -9999 0 -0.33 83 83
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.009 0.057 -9999 0 -0.29 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.087 0.15 -9999 0 -0.26 200 200
VAV3 -0.093 0.14 -9999 0 -0.25 222 222
MAP3K14 -0.079 0.14 -9999 0 -0.25 185 185
ROCK2 0.017 0 -9999 0 -10000 0 0
SPP1 -0.14 0.21 -9999 0 -0.42 181 181
RAC1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.079 0.14 -9999 0 -0.24 168 168
MMP2 -0.24 0.24 -9999 0 -0.44 298 298
Syndecan-1-mediated signaling events

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
TGFB1 -0.005 0.094 -9999 0 -0.41 27 27
CCL5 -0.006 0.096 -9999 0 -0.41 28 28
SDCBP 0.017 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.077 0.14 -9999 0 -0.21 219 219
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 -0.072 0.14 -9999 0 -0.3 109 109
Syndecan-1/Syntenin -0.067 0.14 -9999 0 -0.3 100 100
MAPK3 -0.19 0.16 -9999 0 -0.25 395 395
HGF/MET 0.018 0.046 -9999 0 -0.28 12 12
TGFB1/TGF beta receptor Type II -0.005 0.094 -9999 0 -0.41 27 27
BSG 0.017 0 -9999 0 -10000 0 0
keratinocyte migration -0.071 0.14 -9999 0 -0.3 109 109
Syndecan-1/RANTES -0.077 0.16 -9999 0 -0.33 107 107
Syndecan-1/CD147 -0.2 0.17 -9999 0 -0.27 395 395
Syndecan-1/Syntenin/PIP2 -0.065 0.13 -9999 0 -0.29 100 100
LAMA5 0.006 0.069 -9999 0 -0.41 14 14
positive regulation of cell-cell adhesion -0.064 0.13 -9999 0 -0.28 100 100
MMP7 -0.046 0.15 -9999 0 -0.41 78 78
HGF 0.015 0.026 -9999 0 -0.41 2 2
Syndecan-1/CASK -0.074 0.13 -9999 0 -0.3 100 100
Syndecan-1/HGF/MET -0.062 0.14 -9999 0 -0.29 108 108
regulation of cell adhesion -0.18 0.15 -9999 0 -0.32 216 216
HPSE -0.019 0.12 -9999 0 -0.41 44 44
positive regulation of cell migration -0.077 0.14 -9999 0 -0.21 219 219
SDC1 -0.078 0.14 -9999 0 -0.21 219 219
Syndecan-1/Collagen -0.077 0.14 -9999 0 -0.21 219 219
PPIB -0.29 0.2 -9999 0 -0.41 374 374
MET 0.009 0.058 -9999 0 -0.41 10 10
PRKACA 0.017 0 -9999 0 -10000 0 0
MMP9 -0.13 0.2 -9999 0 -0.41 179 179
MAPK1 -0.19 0.16 -9999 0 -0.25 393 393
homophilic cell adhesion -0.077 0.14 -9999 0 -0.21 219 219
MMP1 -0.018 0.12 -9999 0 -0.41 43 43
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.016 0.019 -9999 0 -0.41 1 1
EGFR -0.14 0.21 -9999 0 -0.41 194 194
EGF/EGFR -0.11 0.14 -9999 0 -0.22 304 304
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.067 0.12 -9999 0 -0.2 237 237
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.11 0.2 -9999 0 -0.41 154 154
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.015 0.026 -9999 0 -0.41 2 2
EGF/EGFR dimer/SHC -0.088 0.14 -9999 0 -0.24 238 238
mol:GDP -0.068 0.12 -9999 0 -0.2 237 237
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.01 0.055 -9999 0 -0.41 9 9
GRB2/SOS1 0.013 0.001 -9999 0 -10000 0 0
HRAS/GTP -0.066 0.1 -9999 0 -0.18 238 238
SHC1 -0.021 0.12 -9999 0 -0.41 47 47
HRAS/GDP -0.062 0.11 -9999 0 -0.18 238 238
FRAP1 -0.07 0.11 -9999 0 -0.19 237 237
EGF/EGFR dimer -0.09 0.15 -9999 0 -0.28 196 196
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.017 0.002 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.07 0.15 -9999 0 -0.29 158 158
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.2 0.18 -9999 0 -0.31 357 357
alphaM/beta2 Integrin/GPIbA -0.079 0.14 -9999 0 -0.24 221 221
alphaM/beta2 Integrin/proMMP-9 -0.16 0.19 -9999 0 -0.31 299 299
PLAUR -0.021 0.12 -9999 0 -0.41 47 47
HMGB1 0.015 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.1 0.16 -9999 0 -0.26 242 242
AGER 0.012 0.04 -9999 0 -0.43 4 4
RAP1A 0.017 0 -9999 0 -10000 0 0
SELPLG 0.017 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.065 0.14 -9999 0 -0.22 223 223
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.2 -9999 0 -0.41 179 179
CYR61 -0.12 0.2 -9999 0 -0.41 163 163
TLN1 -0.02 0.12 -9999 0 -0.41 46 46
Rap1/GTP -0.037 0.09 -9999 0 -0.18 110 110
RHOA 0.017 0.001 -9999 0 -10000 0 0
P-selectin oligomer 0.016 0.019 -9999 0 -0.41 1 1
MYH2 -0.024 0.096 -9999 0 -0.2 83 83
MST1R 0.015 0.026 -9999 0 -0.41 2 2
leukocyte activation during inflammatory response -0.062 0.12 -9999 0 -0.2 224 224
APOB 0.015 0.032 -9999 0 -0.41 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.19 0.21 -9999 0 -0.41 251 251
JAM3 0.016 0.019 -9999 0 -0.41 1 1
GP1BA 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.096 0.15 -9999 0 -0.26 237 237
alphaM/beta2 Integrin -0.046 0.1 -9999 0 -0.22 111 111
JAM3 homodimer 0.016 0.019 -9999 0 -0.41 1 1
ICAM2 0.015 0.032 -9999 0 -0.41 3 3
ICAM1 0.002 0.078 -9999 0 -0.41 18 18
phagocytosis triggered by activation of immune response cell surface activating receptor -0.046 0.1 -9999 0 -0.22 111 111
cell adhesion -0.079 0.14 -9999 0 -0.24 221 221
NFKB1 -0.07 0.15 -9999 0 -0.22 237 237
THY1 0.012 0.008 -9999 0 -10000 0 0
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
Lipoprotein(a) 0.022 0.02 -9999 0 -0.24 3 3
alphaM/beta2 Integrin/LRP/tPA -0.18 0.18 -9999 0 -0.28 353 353
IL6 -0.08 0.18 -9999 0 -0.5 56 56
ITGB2 -0.16 0.21 -9999 0 -0.42 221 221
elevation of cytosolic calcium ion concentration -0.13 0.21 -9999 0 -0.32 256 256
alphaM/beta2 Integrin/JAM2/JAM3 -0.097 0.14 -9999 0 -0.23 267 267
JAM2 -0.044 0.15 -9999 0 -0.41 75 75
alphaM/beta2 Integrin/ICAM1 -0.061 0.13 -9999 0 -0.21 231 231
alphaM/beta2 Integrin/uPA/Plg -0.11 0.18 -9999 0 -0.28 255 255
RhoA/GTP -0.029 0.1 -9999 0 -0.2 110 110
positive regulation of phagocytosis -0.089 0.16 -9999 0 -0.25 224 224
Ron/MSP 0.021 0.038 -9999 0 -0.28 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.13 0.21 -9999 0 -0.32 256 256
alphaM/beta2 Integrin/uPAR -0.099 0.17 -9999 0 -0.28 227 227
PLAU -0.083 0.18 -9999 0 -0.41 123 123
PLAT -0.18 0.21 -9999 0 -0.41 244 244
actin filament polymerization -0.023 0.093 -9999 0 -0.2 83 83
MST1 0.012 0.045 -9999 0 -0.41 6 6
alphaM/beta2 Integrin/lipoprotein(a) -0.06 0.12 -9999 0 -0.2 224 224
TNF -0.062 0.14 -9999 0 -0.39 42 42
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.13 0.19 -9999 0 -0.32 255 255
fibrinolysis -0.11 0.18 -9999 0 -0.28 255 255
HCK -0.053 0.16 -9999 0 -0.41 86 86
dendritic cell antigen processing and presentation -0.046 0.1 -9999 0 -0.22 111 111
VTN 0.015 0.026 -9999 0 -0.41 2 2
alphaM/beta2 Integrin/CYR61 -0.15 0.19 -9999 0 -0.31 286 286
LPA 0.017 0 -9999 0 -10000 0 0
LRP1 0.002 0.078 -9999 0 -0.41 18 18
cell migration -0.24 0.22 -9999 0 -0.35 389 389
FN1 -0.065 0.17 -9999 0 -0.41 101 101
alphaM/beta2 Integrin/Thy1 -0.077 0.12 -9999 0 -0.24 189 189
MPO 0.017 0 -9999 0 -10000 0 0
KNG1 0.016 0.019 -9999 0 -0.41 1 1
RAP1/GDP 0.012 0 -9999 0 -10000 0 0
ROCK1 -0.024 0.096 -9999 0 -0.2 83 83
ELA2 0.017 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
CTGF -0.014 0.11 -9999 0 -0.41 38 38
alphaM/beta2 Integrin/Hck -0.12 0.19 -9999 0 -0.32 224 224
ITGAM 0.015 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.13 -9999 0 -0.21 221 221
HP -0.051 0.16 -9999 0 -0.41 84 84
leukocyte adhesion -0.074 0.12 -9999 0 -0.2 196 196
SELP 0.016 0.019 -9999 0 -0.41 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.069 0.091 -10000 0 -0.16 251 251
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.053 -10000 0 -0.21 5 5
AP1 -0.1 0.12 -10000 0 -0.19 303 303
mol:PIP3 -0.12 0.11 -10000 0 -0.24 194 194
AKT1 -0.032 0.073 0.17 3 -0.21 9 12
PTK2B -0.041 0.059 -10000 0 -0.1 251 251
RHOA -0.035 0.049 -10000 0 -0.15 6 6
PIK3CB 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.029 -10000 0 -10000 0 0
MAGI3 0 0.001 -10000 0 -0.003 13 13
RELA 0.017 0 -10000 0 -10000 0 0
apoptosis -0.098 0.12 -10000 0 -0.19 285 285
HRAS/GDP 0.012 0.013 -10000 0 -0.29 1 1
positive regulation of microtubule depolymerization -0.006 0.069 0.22 4 -10000 0 4
NF kappa B1 p50/RelA -0.055 0.06 -10000 0 -0.17 19 19
endothelial cell migration -0.18 0.21 -10000 0 -0.4 251 251
ADCY4 -0.015 0.054 -10000 0 -0.18 47 47
ADCY5 -0.015 0.054 -10000 0 -0.18 47 47
ADCY6 -0.015 0.053 -10000 0 -0.18 45 45
ADCY7 -0.016 0.056 -10000 0 -0.19 48 48
ADCY1 -0.015 0.053 -10000 0 -0.18 45 45
ADCY2 -0.015 0.053 -10000 0 -0.18 45 45
ADCY3 -0.015 0.054 -10000 0 -0.18 47 47
ADCY8 -0.015 0.054 -10000 0 -0.18 46 46
ADCY9 -0.015 0.053 -10000 0 -0.18 45 45
GSK3B -0.035 0.056 -10000 0 -0.11 9 9
arachidonic acid secretion -0.048 0.069 -10000 0 -0.13 198 198
GNG2 0 0.001 -10000 0 -0.004 23 23
TRIP6 -0.11 0.11 -10000 0 -0.21 285 285
GNAO1 -0.005 0.032 -10000 0 -0.18 16 16
HRAS 0.016 0.019 -10000 0 -0.41 1 1
NFKBIA -0.02 0.047 -10000 0 -0.14 5 5
GAB1 0.014 0.037 -10000 0 -0.41 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.14 -10000 0 -0.7 21 21
JUN 0.016 0.019 -10000 0 -0.41 1 1
LPA/LPA2/NHERF2 -0.024 0.04 -10000 0 -0.07 2 2
TIAM1 -0.008 0.16 -10000 0 -0.8 21 21
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.009 0.03 -10000 0 -10000 0 0
PLCB3 -0.017 0.035 -10000 0 -10000 0 0
FOS -0.084 0.18 -10000 0 -0.41 125 125
positive regulation of mitosis -0.048 0.069 -10000 0 -0.13 198 198
LPA/LPA1-2-3 -0.077 0.088 -10000 0 -0.17 251 251
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation -0.041 0.065 -10000 0 -0.11 251 251
GNAZ -0.068 0.097 -10000 0 -0.18 216 216
EGFR/PI3K-beta/Gab1 -0.12 0.12 -10000 0 -0.25 194 194
positive regulation of dendritic cell cytokine production -0.077 0.087 -10000 0 -0.17 251 251
LPA/LPA2/MAGI-3 -0.032 0.036 -10000 0 -0.07 251 251
ARHGEF1 -0.06 0.089 -10000 0 -0.15 252 252
GNAI2 -0.079 0.1 -10000 0 -0.18 251 251
GNAI3 -0.11 0.13 -10000 0 -0.22 282 282
GNAI1 -0.072 0.098 -10000 0 -0.18 223 223
LPA/LPA3 -0.04 0.045 -10000 0 -0.087 251 251
LPA/LPA2 -0.04 0.045 -10000 0 -0.087 251 251
LPA/LPA1 -0.1 0.12 -10000 0 -0.23 251 251
HB-EGF/EGFR -0.16 0.16 -10000 0 -0.27 320 320
HBEGF -0.086 0.14 -10000 0 -0.29 179 179
mol:DAG -0.009 0.03 -10000 0 -10000 0 0
cAMP biosynthetic process 0.001 0.089 0.15 9 -0.16 51 60
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
SRC 0.017 0 -10000 0 -10000 0 0
GNB1 0.017 0.002 -10000 0 -10000 0 0
LYN -0.039 0.073 -10000 0 -0.19 65 65
GNAQ -0.023 0.035 -10000 0 -0.06 251 251
LPAR2 0 0.001 -10000 0 -0.003 15 15
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.063 0.07 -10000 0 -0.14 251 251
IL8 -0.16 0.15 -10000 0 -0.28 295 295
PTK2 -0.065 0.084 -10000 0 -0.15 251 251
Rac1/GDP 0.013 0 -10000 0 -10000 0 0
CASP3 -0.098 0.12 -10000 0 -0.19 285 285
EGFR -0.14 0.21 -10000 0 -0.41 194 194
PLCG1 -0.016 0.033 -10000 0 -0.05 253 253
PLD2 -0.065 0.084 -10000 0 -0.15 251 251
G12/G13 -0.064 0.1 -10000 0 -0.17 252 252
PI3K-beta -0.054 0.06 -10000 0 -0.2 5 5
cell migration -0.046 0.059 -10000 0 -0.21 21 21
SLC9A3R2 0.017 0 -10000 0 -10000 0 0
PXN -0.041 0.066 -10000 0 -0.11 251 251
HRAS/GTP -0.049 0.07 -10000 0 -0.14 196 196
RAC1 0.017 0 -10000 0 -10000 0 0
MMP9 -0.13 0.2 -10000 0 -0.41 179 179
PRKCE 0.017 0.001 -10000 0 -10000 0 0
PRKCD -0.005 0.028 -10000 0 -10000 0 0
Gi(beta/gamma) -0.017 0.056 -10000 0 -0.19 50 50
mol:LPA -0.063 0.07 -10000 0 -0.14 251 251
TRIP6/p130 Cas/FAK1/Paxillin -0.11 0.1 -10000 0 -0.16 381 381
MAPKKK cascade -0.048 0.069 -10000 0 -0.13 198 198
contractile ring contraction involved in cytokinesis -0.035 0.049 -10000 0 -0.16 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.024 0.036 -10000 0 -0.061 253 253
GNA15 -0.026 0.043 -10000 0 -0.22 8 8
GNA12 0.014 0.037 -10000 0 -0.41 4 4
GNA13 0.016 0.026 -10000 0 -0.41 2 2
MAPT -0.022 0.048 -10000 0 -10000 0 0
GNA11 -0.023 0.035 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.15 -10000 0 -0.73 21 21
MMP2 -0.18 0.21 -10000 0 -0.41 251 251
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.006 0.012 0.041 37 -10000 0 37
BUB1B -0.098 0.12 -10000 0 -0.23 213 213
PLK1 -0.012 0.035 -10000 0 -0.12 37 37
PLK1S1 -0.008 0.02 -10000 0 -0.066 37 37
KIF2A -0.006 0.033 0.14 2 -0.14 19 21
regulation of mitotic centrosome separation -0.012 0.035 -10000 0 -0.12 37 37
GOLGA2 0.017 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.074 0.12 -10000 0 -0.23 185 185
WEE1 -0.099 0.11 -10000 0 -0.22 218 218
cytokinesis -0.1 0.14 -10000 0 -0.28 188 188
PP2A-alpha B56 0.004 0.038 -10000 0 -0.22 2 2
AURKA -0.008 0.036 -10000 0 -0.15 25 25
PICH/PLK1 -0.2 0.2 -10000 0 -0.34 307 307
CENPE -0.034 0.094 -10000 0 -0.26 70 70
RhoA/GTP 0.013 0.001 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.006 0.033 0.14 2 -0.14 19 21
PPP2CA 0.017 0.001 -10000 0 -10000 0 0
FZR1 0.017 0 -10000 0 -10000 0 0
TPX2 -0.065 0.067 -10000 0 -0.12 296 296
PAK1 0.015 0.001 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
CLSPN -0.001 0.019 -10000 0 -0.1 7 7
GORASP1 0.017 0 -10000 0 -10000 0 0
metaphase -0.001 0.002 -10000 0 -0.01 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.008 0.02 -10000 0 -0.066 37 37
G2 phase of mitotic cell cycle -0.002 0.002 -10000 0 -0.011 19 19
STAG2 -0.005 0.094 -10000 0 -0.41 27 27
GRASP65/GM130/RAB1/GTP -0.011 0.028 -10000 0 -10000 0 0
spindle elongation -0.012 0.035 -10000 0 -0.12 37 37
ODF2 0.015 0.002 -10000 0 -10000 0 0
BUB1 -0.013 0.036 -10000 0 -0.24 4 4
TPT1 -0.003 0.02 -10000 0 -0.088 16 16
CDC25C 0.001 0.019 -10000 0 -0.099 7 7
CDC25B -0.007 0.074 -10000 0 -0.42 16 16
SGOL1 -0.006 0.012 -10000 0 -0.041 37 37
RHOA 0.017 0.001 -10000 0 -10000 0 0
CCNB1/CDK1 -0.2 0.2 -10000 0 -0.31 366 366
CDC14B 0.008 0.002 -10000 0 -10000 0 0
CDC20 -0.23 0.21 -10000 0 -0.41 304 304
PLK1/PBIP1 -0.18 0.083 -10000 0 -0.21 450 450
mitosis -0.003 0.005 0.016 9 -0.021 21 30
FBXO5 -0.084 0.11 -10000 0 -0.21 196 196
CDC2 -0.15 0.21 -10000 0 -0.42 194 194
NDC80 -0.13 0.2 -10000 0 -0.41 184 184
metaphase plate congression -0.002 0.021 -10000 0 -0.092 16 16
ERCC6L -0.2 0.2 -10000 0 -0.33 307 307
NLP/gamma Tubulin -0.008 0.024 -10000 0 -0.086 31 31
microtubule cytoskeleton organization -0.003 0.02 -10000 0 -0.088 16 16
G2/M transition DNA damage checkpoint -0.002 0.002 -10000 0 -0.009 15 15
PPP1R12A 0.016 0.019 -10000 0 -0.41 1 1
interphase -0.002 0.002 -10000 0 -0.009 15 15
PLK1/PRC1-2 -0.15 0.2 -10000 0 -0.35 249 249
GRASP65/GM130/RAB1/GTP/PLK1 0.019 0.032 -10000 0 -0.15 7 7
RAB1A 0.017 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.014 0.055 -10000 0 -0.22 30 30
mitotic prometaphase -0.001 0.001 -10000 0 -0.008 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.048 -10000 0 -0.11 16 16
microtubule-based process -0.078 0.12 -10000 0 -0.24 186 186
Golgi organization -0.012 0.035 -10000 0 -0.12 37 37
Cohesin/SA2 -0.014 0.059 -10000 0 -0.2 43 43
PPP1CB/MYPT1 0.022 0.023 -10000 0 -0.29 3 3
KIF20A -0.13 0.2 -10000 0 -0.41 186 186
APC/C/CDC20 -0.13 0.13 -10000 0 -0.24 304 304
PPP2R1A 0.017 0.003 -10000 0 -10000 0 0
chromosome segregation -0.17 0.082 -10000 0 -0.2 450 450
PRC1 -0.16 0.21 -10000 0 -0.41 224 224
ECT2 -0.081 0.12 -10000 0 -0.24 183 183
C13orf34 -0.014 0.055 -10000 0 -0.25 24 24
NUDC -0.002 0.021 -10000 0 -0.092 16 16
regulation of attachment of spindle microtubules to kinetochore -0.097 0.12 -10000 0 -0.23 213 213
spindle assembly -0.01 0.031 -10000 0 -0.1 37 37
spindle stabilization -0.008 0.02 -10000 0 -0.066 37 37
APC/C/HCDH1 0.018 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 -0.079 0.12 -10000 0 -0.24 186 186
CCNB1 -0.23 0.22 -10000 0 -0.42 296 296
PPP1CB 0.015 0.026 -10000 0 -0.41 2 2
BTRC 0.017 0 -10000 0 -10000 0 0
ROCK2 0.003 0.024 -10000 0 -0.12 7 7
TUBG1 -0.003 0.023 -10000 0 -0.11 15 15
G2/M transition of mitotic cell cycle -0.2 0.19 -10000 0 -0.31 366 366
MLF1IP -0.25 0.11 -10000 0 -0.3 450 450
INCENP 0.016 0.001 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.031 0.099 -9999 0 -0.22 104 104
Syndecan-4/Syndesmos -0.066 0.12 -9999 0 -0.22 181 181
positive regulation of JNK cascade -0.15 0.17 -9999 0 -0.35 176 176
Syndecan-4/ADAM12 -0.058 0.13 -9999 0 -0.29 80 80
CCL5 -0.006 0.096 -9999 0 -0.41 28 28
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DNM2 0.017 0 -9999 0 -10000 0 0
ITGA5 -0.043 0.15 -9999 0 -0.41 74 74
SDCBP 0.017 0 -9999 0 -10000 0 0
PLG 0.019 0.005 -9999 0 -10000 0 0
ADAM12 0.016 0.019 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.025 0.04 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.066 0.12 -9999 0 -0.22 181 181
Syndecan-4/CXCL12/CXCR4 -0.15 0.18 -9999 0 -0.37 176 176
Syndecan-4/Laminin alpha3 -0.063 0.13 -9999 0 -0.3 89 89
MDK -0.23 0.21 -9999 0 -0.41 300 300
Syndecan-4/FZD7 -0.15 0.16 -9999 0 -0.36 148 148
Syndecan-4/Midkine -0.17 0.16 -9999 0 -0.25 366 366
FZD7 -0.18 0.21 -9999 0 -0.41 245 245
Syndecan-4/FGFR1/FGF -0.045 0.13 -9999 0 -0.27 83 83
THBS1 -0.018 0.12 -9999 0 -0.41 43 43
integrin-mediated signaling pathway -0.24 0.12 -9999 0 -0.36 230 230
positive regulation of MAPKKK cascade -0.15 0.17 -9999 0 -0.35 176 176
Syndecan-4/TACI -0.058 0.13 -9999 0 -0.29 80 80
CXCR4 -0.21 0.21 -9999 0 -0.41 276 276
cell adhesion -0.026 0.091 -9999 0 -0.2 102 102
Syndecan-4/Dynamin -0.058 0.13 -9999 0 -0.29 80 80
Syndecan-4/TSP1 -0.073 0.15 -9999 0 -0.33 97 97
Syndecan-4/GIPC -0.058 0.13 -9999 0 -0.29 80 80
Syndecan-4/RANTES -0.068 0.14 -9999 0 -0.32 90 90
ITGB1 0.017 0 -9999 0 -10000 0 0
LAMA1 0 0 -9999 0 -10000 0 0
LAMA3 0.005 0.071 -9999 0 -0.41 15 15
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCA 0.021 0.03 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.073 0.14 -9999 0 -0.31 95 95
TFPI -0.077 0.18 -9999 0 -0.41 116 116
F2 0.01 0.028 -9999 0 -0.42 2 2
alpha5/beta1 Integrin -0.018 0.11 -9999 0 -0.28 74 74
positive regulation of cell adhesion -0.064 0.13 -9999 0 -0.29 89 89
ACTN1 -0.017 0.12 -9999 0 -0.41 42 42
TNC -0.39 0.089 -9999 0 -0.41 505 505
Syndecan-4/CXCL12 -0.063 0.14 -9999 0 -0.31 83 83
FGF6 0.017 0 -9999 0 -10000 0 0
RHOA 0.017 0.001 -9999 0 -10000 0 0
CXCL12 0.005 0.071 -9999 0 -0.41 15 15
TNFRSF13B 0.017 0 -9999 0 -10000 0 0
FGF2 0.015 0.026 -9999 0 -0.41 2 2
FGFR1 0.015 0.026 -9999 0 -0.41 2 2
Syndecan-4/PI-4-5-P2 -0.066 0.12 -9999 0 -0.22 181 181
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.064 0.17 -9999 0 -0.41 101 101
cell migration -0.012 0.012 -9999 0 -10000 0 0
PRKCD 0.019 0.005 -9999 0 -10000 0 0
vasculogenesis -0.071 0.14 -9999 0 -0.32 97 97
SDC4 -0.063 0.13 -9999 0 -0.23 181 181
Syndecan-4/Tenascin C -0.24 0.13 -9999 0 -0.37 230 230
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.029 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.058 0.13 -9999 0 -0.29 80 80
MMP9 -0.13 0.2 -9999 0 -0.41 179 179
Rac1/GTP -0.026 0.092 -9999 0 -0.2 101 101
cytoskeleton organization -0.064 0.12 -9999 0 -0.21 181 181
GIPC1 0.017 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.1 0.15 -9999 0 -0.33 117 117
BARD1 signaling events

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
BARD1/CSTF1 -0.048 0.13 -10000 0 -0.28 126 126
ATM -0.003 0.091 -10000 0 -0.41 25 25
UBE2D3 0.017 0.001 -10000 0 -10000 0 0
PRKDC -0.002 0.088 -10000 0 -0.41 23 23
ATR 0.017 0 -10000 0 -10000 0 0
UBE2L3 0.017 0 -10000 0 -10000 0 0
FANCD2 0.005 0.042 -10000 0 -0.18 25 25
protein ubiquitination -0.035 0.14 -10000 0 -0.24 149 149
XRCC5 0.017 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
M/R/N Complex 0.035 0 -10000 0 -10000 0 0
MRE11A 0.017 0 -10000 0 -10000 0 0
DNA-PK 0.023 0.055 -10000 0 -0.23 23 23
FA complex/FANCD2/Ubiquitin 0 0.071 -10000 0 -0.17 68 68
FANCF 0.015 0.026 -10000 0 -0.41 2 2
BRCA1 0.013 0.042 -10000 0 -0.41 5 5
CCNE1 0.011 0.049 -10000 0 -0.41 7 7
CDK2/Cyclin E1 0.006 0.082 -10000 0 -0.32 30 30
FANCG -0.036 0.14 -10000 0 -0.41 66 66
BRCA1/BACH1/BARD1 -0.051 0.14 -10000 0 -0.29 127 127
FANCE 0.016 0.019 -10000 0 -0.41 1 1
FANCC 0.017 0 -10000 0 -10000 0 0
NBN 0.017 0 -10000 0 -10000 0 0
FANCA 0.017 0 -10000 0 -10000 0 0
DNA repair -0.14 0.16 -10000 0 -0.34 154 154
BRCA1/BARD1/ubiquitin -0.051 0.14 -10000 0 -0.29 127 127
BARD1/DNA-PK -0.026 0.12 -10000 0 -0.22 139 139
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.048 0.13 0.28 126 -10000 0 126
BRCA1/BARD1/CTIP/M/R/N Complex -0.1 0.1 -10000 0 -0.24 141 141
BRCA1/BACH1/BARD1/TopBP1 -0.032 0.12 -10000 0 -0.24 127 127
BRCA1/BARD1/P53 -0.048 0.15 -10000 0 -0.25 167 167
BARD1/CSTF1/BRCA1 -0.031 0.12 -10000 0 -0.24 127 127
BRCA1/BACH1 0.013 0.041 -10000 0 -0.41 5 5
BARD1 -0.085 0.18 -10000 0 -0.41 126 126
PCNA -0.26 0.2 -10000 0 -0.41 343 343
BRCA1/BARD1/UbcH5C -0.031 0.12 -10000 0 -0.24 127 127
BRCA1/BARD1/UbcH7 -0.031 0.12 -10000 0 -0.24 127 127
BRCA1/BARD1/RAD51/PCNA -0.17 0.17 -10000 0 -0.27 360 360
BARD1/DNA-PK/P53 -0.045 0.15 -10000 0 -0.24 172 172
BRCA1/BARD1/Ubiquitin -0.051 0.14 -10000 0 -0.29 127 127
BRCA1/BARD1/CTIP -0.22 0.16 -10000 0 -0.28 424 424
FA complex 0.01 0.051 -10000 0 -0.12 68 68
BARD1/EWS -0.048 0.13 -10000 0 -0.28 126 126
RBBP8 -0.23 0.14 -10000 0 -0.3 412 412
TP53 -0.039 0.14 -10000 0 -0.41 69 69
TOPBP1 0.016 0.019 -10000 0 -0.41 1 1
G1/S transition of mitotic cell cycle 0.049 0.14 0.25 167 -10000 0 167
BRCA1/BARD1 -0.032 0.15 -10000 0 -0.24 149 149
CSTF1 0.017 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.059 0.13 -10000 0 -0.29 126 126
CDK2 -0.005 0.094 -10000 0 -0.41 27 27
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.017 0 -10000 0 -10000 0 0
RAD50 0.017 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.051 0.14 -10000 0 -0.29 127 127
EWSR1 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.016 0.053 -10000 0 -0.28 16 16
AKT1 -0.048 0.11 -10000 0 -0.28 48 48
PTK2B -0.088 0.13 -10000 0 -0.19 295 295
VEGFR2 homodimer/Frs2 0.021 0.072 -10000 0 -0.33 20 20
CAV1 -0.25 0.21 -10000 0 -0.41 325 325
CALM1 0.016 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.097 0.14 -10000 0 -0.22 289 289
endothelial cell proliferation -0.039 0.1 -10000 0 -0.25 49 49
mol:Ca2+ -0.09 0.14 -10000 0 -0.4 39 39
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.13 0.18 -10000 0 -0.25 326 326
RP11-342D11.1 -0.096 0.13 -10000 0 -0.2 292 292
CDH5 -0.006 0.098 -10000 0 -0.41 29 29
VEGFA homodimer -0.098 0.12 -10000 0 -0.21 288 288
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
SHC2 0.017 0 -10000 0 -10000 0 0
HRAS/GDP -0.093 0.13 -10000 0 -0.37 55 55
SH2D2A 0.017 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.047 0.11 -10000 0 -0.31 36 36
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.095 0.14 -10000 0 -0.22 289 289
VEGFR1 homodimer 0.017 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.093 0.15 -10000 0 -0.41 55 55
GRB10 -0.095 0.15 -10000 0 -0.48 39 39
PTPN11 0.017 0 -10000 0 -10000 0 0
GRB2 0.017 0.002 -10000 0 -10000 0 0
PAK1 0.017 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.13 0.19 -10000 0 -0.25 327 327
HRAS 0.016 0.019 -10000 0 -0.41 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.034 0.077 -10000 0 -0.2 40 40
HIF1A 0.015 0.026 -10000 0 -0.41 2 2
FRS2 0.015 0.032 -10000 0 -0.41 3 3
oxygen and reactive oxygen species metabolic process -0.13 0.17 -10000 0 -0.25 326 326
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.017 0 -10000 0 -10000 0 0
Nck/Pak 0.019 0.044 -10000 0 -0.28 11 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.097 0.14 -10000 0 -0.22 288 288
mol:GDP -0.095 0.14 -10000 0 -0.4 55 55
mol:NADP -0.041 0.098 -10000 0 -0.27 35 35
eNOS/Hsp90 -0.034 0.096 -10000 0 -0.26 35 35
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.091 0.14 -10000 0 -0.4 39 39
HIF1A/ARNT 0.024 0.019 -10000 0 -0.28 2 2
SHB 0.017 0 -10000 0 -10000 0 0
VEGFA -0.21 0.22 -10000 0 -0.41 286 286
VEGFC 0.007 0.066 -10000 0 -0.41 13 13
FAK1/Vinculin -0.058 0.12 -10000 0 -0.3 40 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.089 0.14 -10000 0 -0.2 295 295
PTPN6 0.008 0.061 -10000 0 -0.41 11 11
EPAS1 0.018 0.051 -10000 0 -0.24 17 17
mol:L-citrulline -0.041 0.098 -10000 0 -0.27 35 35
ITGAV 0.004 0.073 -10000 0 -0.41 16 16
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.084 0.14 -10000 0 -0.2 289 289
VEGFR2 homodimer/VEGFA homodimer -0.095 0.16 -10000 0 -0.22 292 292
VEGFR2/3 heterodimer 0.022 0.069 -10000 0 -0.35 17 17
VEGFB 0.017 0 -10000 0 -10000 0 0
MAPK11 -0.089 0.13 -10000 0 -0.39 39 39
VEGFR2 homodimer 0.016 0.08 -10000 0 -0.41 17 17
FLT1 0.017 0 -10000 0 -10000 0 0
NEDD4 0.008 0.066 -10000 0 -0.39 14 14
MAPK3 -0.086 0.12 -10000 0 -0.37 39 39
MAPK1 -0.086 0.12 -10000 0 -0.37 39 39
VEGFA145/NRP2 -0.14 0.16 -10000 0 -0.28 287 287
VEGFR1/2 heterodimer 0.022 0.069 -10000 0 -0.35 17 17
KDR 0.016 0.08 -10000 0 -0.41 17 17
VEGFA165/NRP1/VEGFR2 homodimer -0.081 0.14 -10000 0 -0.4 39 39
SRC 0.017 0 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.084 0.13 -10000 0 -0.37 39 39
PI3K -0.066 0.13 -10000 0 -0.33 51 51
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.1 0.14 -10000 0 -0.22 298 298
FES -0.092 0.14 -10000 0 -0.41 39 39
GAB1 -0.077 0.13 -10000 0 -0.32 58 58
VEGFR2 homodimer/VEGFA homodimer/Src -0.095 0.14 -10000 0 -0.22 289 289
CTNNB1 0.017 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.017 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.14 0.14 -10000 0 -0.27 222 222
VEGFR2 homodimer/VEGFA homodimer/Yes -0.13 0.16 -10000 0 -0.24 325 325
PI3K/GAB1 -0.052 0.12 -10000 0 -0.3 51 51
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.079 0.14 -10000 0 -0.3 53 53
PRKACA 0.017 0 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.026 0.078 -10000 0 -0.28 28 28
HSP90AA1 0.017 0 -10000 0 -10000 0 0
CDC42 -0.092 0.14 -10000 0 -0.41 39 39
actin cytoskeleton reorganization -0.095 0.14 -10000 0 -0.22 289 289
PTK2 -0.068 0.12 -10000 0 -0.32 40 40
EDG1 -0.089 0.14 -10000 0 -0.4 39 39
mol:DAG -0.091 0.14 -10000 0 -0.4 39 39
CaM/Ca2+ -0.079 0.13 -10000 0 -0.37 39 39
MAP2K3 -0.085 0.13 -10000 0 -0.39 39 39
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.089 0.16 -10000 0 -0.49 39 39
PLCG1 -0.092 0.14 -10000 0 -0.41 39 39
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.082 0.14 -10000 0 -0.2 289 289
IQGAP1 -0.086 0.18 -10000 0 -0.41 127 127
YES1 -0.048 0.15 -10000 0 -0.41 80 80
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.095 0.14 -10000 0 -0.22 289 289
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.1 0.15 -10000 0 -0.22 297 297
cell migration -0.076 0.14 -10000 0 -0.27 126 126
mol:PI-3-4-5-P3 -0.062 0.12 -10000 0 -0.31 51 51
FYN 0.015 0.026 -10000 0 -0.41 2 2
VEGFB/NRP1 -0.085 0.13 -10000 0 -0.38 39 39
mol:NO -0.041 0.098 -10000 0 -0.27 35 35
PXN 0.017 0 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.12 -10000 0 -0.37 55 55
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.091 0.16 -10000 0 -0.49 39 39
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.017 0 -10000 0 -10000 0 0
NOS3 -0.045 0.11 -10000 0 -0.3 35 35
VEGFR2 homodimer/VEGFA homodimer/Sck -0.095 0.14 -10000 0 -0.22 289 289
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.084 0.13 -10000 0 -0.38 39 39
PRKCB -0.088 0.13 -10000 0 -0.38 39 39
VCL 0.017 0 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.094 0.14 -10000 0 -0.21 292 292
VEGFR1/2 heterodimer/VEGFA homodimer -0.095 0.14 -10000 0 -0.22 289 289
VEGFA165/NRP2 -0.14 0.16 -10000 0 -0.28 287 287
MAPKKK cascade -0.083 0.15 0.25 1 -0.41 55 56
NRP2 0.016 0.019 -10000 0 -0.41 1 1
VEGFC homodimer 0.007 0.066 -10000 0 -0.41 13 13
NCK1 0.008 0.061 -10000 0 -0.41 11 11
ROCK1 0.017 0 -10000 0 -10000 0 0
FAK1/Paxillin -0.058 0.12 -10000 0 -0.3 40 40
MAP3K13 -0.092 0.14 -10000 0 -0.41 39 39
PDPK1 -0.056 0.11 -10000 0 -0.28 51 51
HIF-2-alpha transcription factor network

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
MMP14 -0.008 0.032 -10000 0 -0.41 2 2
oxygen homeostasis -0.008 0.013 -10000 0 -10000 0 0
TCEB2 0.017 0 -10000 0 -10000 0 0
TCEB1 0.017 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.017 0.075 -10000 0 -0.19 13 13
EPO -0.076 0.18 -10000 0 -0.28 182 182
FIH (dimer) 0.006 0.016 -10000 0 -10000 0 0
APEX1 0.005 0.021 -10000 0 -10000 0 0
SERPINE1 -0.18 0.28 -10000 0 -0.47 228 228
FLT1 -0.006 0.027 -10000 0 -10000 0 0
ADORA2A -0.11 0.2 -10000 0 -0.34 182 182
germ cell development -0.11 0.2 -10000 0 -0.34 182 182
SLC11A2 -0.11 0.21 -10000 0 -0.35 182 182
BHLHE40 -0.12 0.2 -10000 0 -0.35 182 182
HIF1AN 0.006 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.045 0.13 -10000 0 -0.26 43 43
ETS1 0.027 0.012 -10000 0 -10000 0 0
CITED2 -0.016 0.066 -10000 0 -0.4 14 14
KDR -0.016 0.077 -10000 0 -0.42 17 17
PGK1 -0.11 0.21 -10000 0 -0.35 182 182
SIRT1 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.11 0.25 -10000 0 -0.39 182 182
EPAS1 -0.029 0.083 0.29 1 -0.22 13 14
SP1 0.023 0.004 -10000 0 -10000 0 0
ABCG2 -0.11 0.21 -10000 0 -0.35 183 183
EFNA1 -0.12 0.22 -10000 0 -0.36 191 191
FXN -0.11 0.2 -10000 0 -0.34 182 182
POU5F1 -0.12 0.2 -10000 0 -0.35 182 182
neuron apoptosis 0.11 0.24 0.38 182 -10000 0 182
EP300 0.017 0 -10000 0 -10000 0 0
EGLN3 0.003 0.042 -10000 0 -0.44 4 4
EGLN2 0.006 0.016 -10000 0 -10000 0 0
EGLN1 0.006 0.025 -10000 0 -0.42 1 1
VHL/Elongin B/Elongin C 0.023 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.005 0.021 -10000 0 -10000 0 0
SLC2A1 -0.11 0.2 -10000 0 -0.34 183 183
TWIST1 -0.12 0.22 -10000 0 -0.36 192 192
ELK1 0.021 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.044 0.13 -10000 0 -0.26 43 43
VEGFA -0.21 0.28 -10000 0 -0.42 298 298
CREBBP 0.017 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.047 0.1 -9999 0 -0.16 221 221
FZD6 -0.065 0.17 -9999 0 -0.41 101 101
WNT6 0.017 0 -9999 0 -10000 0 0
WNT4 0.015 0.026 -9999 0 -0.41 2 2
FZD3 0.014 0.032 -9999 0 -0.41 3 3
WNT5A -0.12 0.2 -9999 0 -0.41 168 168
WNT11 0.015 0.026 -9999 0 -0.41 2 2
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 0.016 0.019 -10000 0 -0.41 1 1
LAT2 -0.058 0.1 -10000 0 -0.24 78 78
AP1 -0.063 0.12 -10000 0 -0.27 99 99
mol:PIP3 -0.054 0.11 -10000 0 -0.27 66 66
IKBKB -0.026 0.07 -10000 0 -0.18 41 41
AKT1 -0.056 0.11 0.22 16 -0.31 17 33
IKBKG -0.026 0.07 -10000 0 -0.18 41 41
MS4A2 0.021 0.005 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA -0.004 0.091 -10000 0 -0.41 25 25
MAP3K1 -0.041 0.095 -10000 0 -0.21 81 81
mol:Ca2+ -0.041 0.092 -10000 0 -0.21 66 66
LYN -0.038 0.14 -10000 0 -0.42 64 64
CBLB -0.057 0.1 -10000 0 -0.23 80 80
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
RasGAP/p62DOK 0.024 0.044 -10000 0 -0.21 18 18
positive regulation of cell migration 0.009 0.001 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.078 0.1 -10000 0 -0.18 260 260
PTPN13 -0.049 0.1 -10000 0 -0.31 38 38
PTPN11 0.013 0.01 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.027 0.089 0.21 9 -0.2 40 49
SYK -0.015 0.11 -10000 0 -0.42 36 36
GRB2 0.017 0.002 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.078 0.1 -10000 0 -0.26 76 76
LAT -0.058 0.1 -10000 0 -0.26 67 67
PAK2 -0.048 0.1 -10000 0 -0.23 88 88
NFATC2 -0.039 0.04 -10000 0 -0.079 260 260
HRAS -0.046 0.099 -10000 0 -0.21 91 91
GAB2 0.016 0.019 -10000 0 -0.41 1 1
PLA2G1B 0.031 0.021 -10000 0 -10000 0 0
Fc epsilon R1 -0.1 0.14 -10000 0 -0.24 260 260
Antigen/IgE/Fc epsilon R1 -0.09 0.13 -10000 0 -0.22 260 260
mol:GDP -0.045 0.096 -10000 0 -0.22 77 77
JUN 0.016 0.019 -10000 0 -0.41 1 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.015 0.004 -10000 0 -10000 0 0
FOS -0.084 0.18 -10000 0 -0.41 125 125
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.063 0.11 -10000 0 -0.16 260 260
CHUK -0.026 0.07 -10000 0 -0.18 42 42
KLRG1 -0.06 0.1 -10000 0 -0.24 76 76
VAV1 -0.059 0.1 -10000 0 -0.24 80 80
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.057 0.1 -10000 0 -0.23 80 80
negative regulation of mast cell degranulation -0.057 0.095 -10000 0 -0.23 76 76
BTK -0.047 0.094 -10000 0 -0.22 77 77
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.07 0.11 -10000 0 -0.2 156 156
GAB2/PI3K/SHP2 -0.086 0.09 -10000 0 -0.24 52 52
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.077 0.13 -10000 0 -0.18 273 273
RAF1 0.025 0.019 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.17 -10000 0 -0.27 283 283
FCER1G -0.19 0.22 -10000 0 -0.41 256 256
FCER1A 0.005 0.059 -10000 0 -0.42 10 10
Antigen/IgE/Fc epsilon R1/Fyn -0.078 0.12 -10000 0 -0.2 260 260
MAPK3 0.032 0.02 -10000 0 -10000 0 0
MAPK1 0.028 0.027 -10000 0 -10000 0 0
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK8 -0.004 0.076 -10000 0 -0.34 21 21
DUSP1 0.002 0.078 -10000 0 -0.41 18 18
NF-kappa-B/RelA -0.014 0.047 -10000 0 -0.12 40 40
actin cytoskeleton reorganization -0.043 0.099 -10000 0 -0.32 28 28
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.044 0.1 -10000 0 -0.22 88 88
FER -0.057 0.1 -10000 0 -0.26 66 66
RELA 0.017 0 -10000 0 -10000 0 0
ITK -0.011 0.032 -10000 0 -0.093 31 31
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.044 0.099 -10000 0 -0.24 67 67
cytokine secretion -0.02 0.026 -10000 0 -0.096 32 32
SPHK1 -0.065 0.11 -10000 0 -0.25 90 90
PTK2 -0.045 0.1 -10000 0 -0.33 28 28
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.081 0.1 -10000 0 -0.27 76 76
EDG1 0.009 0.001 -10000 0 -10000 0 0
mol:DAG -0.05 0.11 -10000 0 -0.26 67 67
MAP2K2 0.026 0.016 -10000 0 -10000 0 0
MAP2K1 0.029 0.025 -10000 0 -10000 0 0
MAP2K7 0.017 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.055 0.1 -10000 0 -0.25 66 66
MAP2K4 -0.008 0.14 -10000 0 -0.72 21 21
Fc epsilon R1/FcgammaRIIB -0.14 0.18 -10000 0 -0.29 283 283
mol:Choline -0.077 0.1 -10000 0 -0.18 260 260
SHC/Grb2/SOS1 -0.063 0.12 -10000 0 -0.27 95 95
FYN 0.015 0.026 -10000 0 -0.41 2 2
DOK1 0.017 0 -10000 0 -10000 0 0
PXN -0.039 0.096 -10000 0 -0.31 28 28
HCLS1 -0.094 0.16 -10000 0 -0.22 257 257
PRKCB -0.04 0.09 -10000 0 -0.21 67 67
FCGR2B -0.088 0.18 -10000 0 -0.41 129 129
IGHE -0.004 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.057 0.096 -10000 0 -0.23 76 76
LCP2 -0.008 0.1 -10000 0 -0.41 30 30
PLA2G4A -0.11 0.14 -10000 0 -0.28 172 172
RASA1 0.017 0.002 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.077 0.1 -10000 0 -0.18 260 260
IKK complex -0.014 0.056 -10000 0 -0.14 39 39
WIPF1 0.008 0.061 -10000 0 -0.41 11 11
Aurora B signaling

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
Condensin I complex -0.16 0.18 -9999 0 -0.22 406 406
STMN1 0.001 0.067 -9999 0 -0.29 27 27
Aurora B/RasGAP/Survivin -0.083 0.15 -9999 0 -0.26 208 208
Chromosomal passenger complex/Cul3 protein complex -0.038 0.085 -9999 0 -0.13 212 212
BIRC5 -0.16 0.21 -9999 0 -0.42 212 212
DES -0.004 0.058 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.017 0.057 -9999 0 -0.22 29 29
Aurora B/TACC1 0.009 0.057 -9999 0 -0.24 26 26
Aurora B/PP2A 0.009 0.069 -9999 0 -0.29 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.007 0.021 -9999 0 -0.082 27 27
mitotic metaphase/anaphase transition 0 0.003 -9999 0 -10000 0 0
NDC80 -0.1 0.17 -9999 0 -0.33 185 185
Cul3 protein complex 0.023 0.003 -9999 0 -10000 0 0
KIF2C -0.046 0.1 -9999 0 -0.18 157 157
PEBP1 0.014 0.005 -9999 0 -10000 0 0
KIF20A -0.14 0.21 -9999 0 -0.42 186 186
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.008 0.069 -9999 0 -0.29 27 27
SEPT1 0 0 -9999 0 -10000 0 0
SMC2 -0.032 0.14 -9999 0 -0.41 61 61
SMC4 -0.31 0.18 -9999 0 -0.41 402 402
NSUN2/NPM1/Nucleolin -0.023 0.078 -9999 0 -0.29 29 29
PSMA3 0.017 0.001 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B 0.004 0.044 -9999 0 -0.19 27 27
AURKB -0.006 0.097 -9999 0 -0.42 27 27
AURKC 0.015 0.026 -9999 0 -0.41 2 2
CDCA8 0 0.079 -9999 0 -0.43 17 17
cytokinesis -0.11 0.2 -9999 0 -0.34 187 187
Aurora B/Septin1 -0.1 0.19 -9999 0 -0.33 187 187
AURKA 0.001 0.08 -9999 0 -0.42 19 19
INCENP 0.013 0.007 -9999 0 -10000 0 0
KLHL13 0 0 -9999 0 -10000 0 0
BUB1 0.014 0.038 -9999 0 -0.42 4 4
hSgo1/Aurora B/Survivin -0.084 0.14 -9999 0 -0.24 212 212
EVI5 0.016 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.22 -9999 0 -0.38 180 180
SGOL1 0 0 -9999 0 -10000 0 0
CENPA -0.039 0.11 -9999 0 -0.25 87 87
NCAPG -0.077 0.18 -9999 0 -0.41 116 116
Aurora B/HC8 Proteasome 0.009 0.069 -9999 0 -0.29 27 27
NCAPD2 -0.068 0.17 -9999 0 -0.41 105 105
Aurora B/PP1-gamma 0.009 0.069 -9999 0 -0.29 27 27
RHOA 0.017 0.001 -9999 0 -10000 0 0
NCAPH 0.004 0.073 -9999 0 -0.41 16 16
NPM1 -0.009 0.064 -9999 0 -0.24 32 32
RASA1 0.017 0.002 -9999 0 -10000 0 0
KLHL9 0.017 0.003 -9999 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.068 -9999 0 -0.29 27 27
PPP1CC 0.017 0.001 -9999 0 -10000 0 0
Centraspindlin -0.13 0.23 -9999 0 -0.38 204 204
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
NSUN2 -0.013 0.055 -9999 0 -0.24 27 27
MYLK -0.003 0.059 -9999 0 -0.2 42 42
KIF23 -0.049 0.16 -9999 0 -0.42 79 79
VIM -0.01 0.085 -9999 0 -0.29 45 45
RACGAP1 -0.12 0.2 -9999 0 -0.42 166 166
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.006 0.055 -9999 0 -0.23 27 27
Chromosomal passenger complex -0.066 0.13 -9999 0 -0.21 186 186
Chromosomal passenger complex/EVI5 -0.069 0.16 -9999 0 -0.24 212 212
TACC1 0.017 0.001 -9999 0 -10000 0 0
PPP2R5D 0.017 0 -9999 0 -10000 0 0
CUL3 0.017 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.016 -9999 0 -0.22 2 2
VEGFR1 homodimer/NRP1 0.019 0.015 -9999 0 -0.23 2 2
mol:DAG 0.019 0.047 -9999 0 -0.2 23 23
VEGFR1 homodimer/NRP1/VEGFR 121 -0.099 0.12 -9999 0 -0.21 288 288
CaM/Ca2+ 0.026 0.045 -9999 0 -0.18 22 22
HIF1A 0.024 0.026 -9999 0 -0.4 2 2
GAB1 0.014 0.037 -9999 0 -0.41 4 4
AKT1 0.016 0.059 -9999 0 -0.31 3 3
PLCG1 0.019 0.047 -9999 0 -0.2 23 23
NOS3 0.03 0.042 -9999 0 -0.21 2 2
CBL 0.017 0 -9999 0 -10000 0 0
mol:NO 0.03 0.042 -9999 0 -0.21 2 2
FLT1 0.025 0.018 -9999 0 -0.27 2 2
PGF 0 0.084 -9999 0 -0.41 21 21
VEGFR1 homodimer/NRP2/VEGFR121 -0.092 0.12 -9999 0 -0.2 289 289
CALM1 0.016 0.004 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
eNOS/Hsp90 0.039 0.042 -9999 0 -0.2 2 2
endothelial cell proliferation 0.021 0.04 -9999 0 -0.17 21 21
mol:Ca2+ 0.018 0.046 -9999 0 -0.2 23 23
MAPK3 0.019 0.04 -9999 0 -10000 0 0
MAPK1 0.018 0.04 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
PLGF homodimer 0 0.084 -9999 0 -0.41 21 21
PRKACA 0.017 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.25 0.21 -9999 0 -0.41 325 325
VEGFA homodimer -0.22 0.21 -9999 0 -0.41 286 286
VEGFR1 homodimer/VEGFA homodimer -0.11 0.13 -9999 0 -0.23 288 288
platelet activating factor biosynthetic process 0.02 0.039 -9999 0 -10000 0 0
PI3K 0.026 0.069 -9999 0 -0.2 43 43
PRKCA 0.018 0.043 -9999 0 -0.18 23 23
PRKCB 0.013 0.042 -9999 0 -0.18 23 23
VEGFR1 homodimer/PLGF homodimer 0.021 0.053 -9999 0 -0.23 23 23
VEGFA -0.22 0.21 -9999 0 -0.41 286 286
VEGFB 0.017 0 -9999 0 -10000 0 0
mol:IP3 0.019 0.047 -9999 0 -0.2 23 23
RASA1 0.027 0.014 -9999 0 -0.2 2 2
NRP2 0.016 0.019 -9999 0 -0.41 1 1
VEGFR1 homodimer 0.025 0.018 -9999 0 -0.27 2 2
VEGFB homodimer 0.017 0 -9999 0 -10000 0 0
NCK1 0.008 0.061 -9999 0 -0.41 11 11
eNOS/Caveolin-1 -0.079 0.1 -9999 0 -0.27 28 28
PTPN11 0.017 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.068 -9999 0 -0.19 43 43
mol:L-citrulline 0.03 0.042 -9999 0 -0.21 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.099 0.13 -9999 0 -0.2 314 314
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.096 0.12 -9999 0 -0.2 297 297
CD2AP -0.023 0.12 -9999 0 -0.41 49 49
PI3K/GAB1 0.031 0.07 -9999 0 -0.37 3 3
PDPK1 0.014 0.06 -9999 0 -0.36 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.092 0.12 -9999 0 -0.2 288 288
mol:NADP 0.03 0.042 -9999 0 -0.21 2 2
HSP90AA1 0.017 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.098 0.13 -9999 0 -0.2 314 314
VEGFR1 homodimer/NRP2 0.031 0.019 -9999 0 -0.23 3 3
Regulation of nuclear SMAD2/3 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
EP300 0.008 0.012 -10000 0 -10000 0 0
HSPA8 0.019 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.018 0.16 0.18 19 -0.26 121 140
AKT1 0.016 0.037 -10000 0 -0.41 4 4
GSC 0.017 0.037 0.11 13 -10000 0 13
NKX2-5 0.016 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.025 0.098 0.24 61 -10000 0 61
SMAD2-3/SMAD4/SP1 -0.083 0.15 -10000 0 -0.3 110 110
SMAD4 -0.11 0.2 -10000 0 -0.42 137 137
CBFB 0.014 0.037 -10000 0 -0.41 4 4
SAP18 0.018 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.007 0.059 -10000 0 -0.24 25 25
SMAD3/SMAD4/VDR -0.034 0.11 -10000 0 -0.26 64 64
MYC -0.097 0.19 -10000 0 -0.42 137 137
CDKN2B 0.043 0.053 -10000 0 -10000 0 0
AP1 -0.074 0.14 -10000 0 -0.29 122 122
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.013 0.095 -10000 0 -0.19 91 91
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.065 -10000 0 -0.24 8 8
SP3 -0.045 0.15 -10000 0 -0.41 77 77
CREB1 0.017 0 -10000 0 -10000 0 0
FOXH1 0.016 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.037 0.14 -10000 0 -0.26 124 124
GATA3 0.018 0.041 -10000 0 -0.41 5 5
SKI/SIN3/HDAC complex/NCoR1 0.005 0.058 -10000 0 -0.17 21 21
MEF2C/TIF2 -0.016 0.083 -10000 0 -0.21 34 34
endothelial cell migration 0.16 0.2 0.4 215 -10000 0 215
MAX 0.025 0.012 -10000 0 -10000 0 0
RBBP7 0.018 0.001 -10000 0 -10000 0 0
RBBP4 -0.064 0.17 -10000 0 -0.41 101 101
RUNX2 0.017 0 -10000 0 -10000 0 0
RUNX3 0.015 0.032 -10000 0 -0.41 3 3
RUNX1 0.017 0 -10000 0 -10000 0 0
CTBP1 0.017 0.002 -10000 0 -10000 0 0
NR3C1 0.025 0.012 -10000 0 -10000 0 0
VDR 0.017 0 -10000 0 -10000 0 0
CDKN1A -0.098 0.17 -10000 0 -0.37 112 112
KAT2B -0.003 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.034 0.11 -10000 0 -0.23 113 113
DCP1A 0.017 0 -10000 0 -10000 0 0
SKI 0.018 0.001 -10000 0 -10000 0 0
SERPINE1 -0.16 0.2 -10000 0 -0.4 215 215
SMAD3/SMAD4/ATF2 -0.058 0.14 -10000 0 -0.27 127 127
SMAD3/SMAD4/ATF3 -0.11 0.18 -10000 0 -0.31 208 208
SAP30 0.018 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.016 0.029 -10000 0 -0.24 2 2
JUN -0.077 0.14 -10000 0 -0.28 120 120
SMAD3/SMAD4/IRF7 -0.058 0.15 -10000 0 -0.27 137 137
TFE3 -0.032 0.06 -10000 0 -0.15 16 16
COL1A2 -0.2 0.21 -10000 0 -0.41 261 261
mesenchymal cell differentiation 0.058 0.14 0.27 125 -10000 0 125
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.017 0 -10000 0 -10000 0 0
FOS -0.094 0.18 -10000 0 -0.42 125 125
SMAD3/SMAD4/Max -0.037 0.14 -10000 0 -0.27 117 117
Cbp/p300/SNIP1 0.029 0.008 -10000 0 -10000 0 0
ZBTB17 0.015 0 -10000 0 -10000 0 0
LAMC1 -0.18 0.24 -10000 0 -0.45 217 217
TGIF2/HDAC complex/SMAD3/SMAD4 -0.061 0.15 -10000 0 -0.27 135 135
IRF7 0.01 0.064 -10000 0 -0.41 12 12
ESR1 0.03 0.017 -10000 0 -10000 0 0
HNF4A 0.017 0 -10000 0 -10000 0 0
MEF2C -0.024 0.085 -10000 0 -0.22 54 54
SMAD2-3/SMAD4 -0.058 0.14 -10000 0 -0.26 128 128
Cbp/p300/Src-1 0.022 0.017 -10000 0 -10000 0 0
IGHV3OR16-13 -0.012 0.026 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.011 0.052 -10000 0 -0.41 8 8
CREBBP 0.011 0.008 -10000 0 -10000 0 0
SKIL 0.017 0 -10000 0 -10000 0 0
HDAC1 -0.036 0.14 -10000 0 -0.41 66 66
HDAC2 0.014 0.042 -10000 0 -0.41 5 5
SNIP1 0.018 0.002 -10000 0 -10000 0 0
GCN5L2 0.01 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.11 0.18 -10000 0 -0.29 247 247
MSG1/HSC70 0.013 0.066 -10000 0 -0.28 25 25
SMAD2 0.018 0.008 -10000 0 -10000 0 0
SMAD3 -0.023 0.062 -10000 0 -0.17 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.026 0.085 -10000 0 -0.18 89 89
SMAD2/SMAD2/SMAD4 -0.028 0.076 0.15 1 -0.15 119 120
NCOR1 0.018 0.001 -10000 0 -10000 0 0
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA1 0.017 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.025 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.069 0.14 -10000 0 -0.29 99 99
IFNB1 -0.054 0.12 -10000 0 -0.27 92 92
SMAD3/SMAD4/MEF2C -0.024 0.11 -10000 0 -0.26 54 54
CITED1 -0.003 0.091 -10000 0 -0.41 25 25
SMAD2-3/SMAD4/ARC105 -0.041 0.12 -10000 0 -0.23 117 117
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.005 0.07 -10000 0 -0.26 6 6
RUNX1-3/PEBPB2 0.031 0.031 -10000 0 -0.23 7 7
SMAD7 -0.083 0.15 -10000 0 -0.3 136 136
MYC/MIZ-1 -0.06 0.14 -10000 0 -0.29 137 137
SMAD3/SMAD4 -0.17 0.14 -10000 0 -0.27 294 294
IL10 -0.048 0.12 -10000 0 -0.3 62 62
PIASy/HDAC complex 0.022 0.006 -10000 0 -10000 0 0
PIAS3 0.013 0.027 -10000 0 -0.42 2 2
CDK2 -0.01 0.094 -10000 0 -0.41 27 27
IL5 -0.048 0.12 -10000 0 -0.3 62 62
CDK4 -0.27 0.2 -10000 0 -0.42 343 343
PIAS4 0.022 0.006 -10000 0 -10000 0 0
ATF3 -0.071 0.17 -10000 0 -0.41 108 108
SMAD3/SMAD4/SP1 -0.11 0.16 -10000 0 -0.28 193 193
FOXG1 0.016 0.006 -10000 0 -10000 0 0
FOXO3 0.018 0.026 -10000 0 -0.28 4 4
FOXO1 0.012 0.053 -10000 0 -0.3 14 14
FOXO4 0.018 0.026 -10000 0 -0.28 4 4
heart looping -0.024 0.085 -10000 0 -0.22 54 54
CEBPB 0.009 0.061 -10000 0 -0.41 11 11
SMAD3/SMAD4/DLX1 -0.066 0.14 -10000 0 -0.26 141 141
MYOD1 0.017 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.058 0.14 -10000 0 -0.26 137 137
SMAD3/SMAD4/GATA3 -0.05 0.15 -10000 0 -0.31 86 86
SnoN/SIN3/HDAC complex/NCoR1 0.017 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.03 0.13 -10000 0 -0.26 82 82
SMAD3/SMAD4/SP1-3 -0.12 0.2 -10000 0 -0.38 144 144
MED15 0.017 0 -10000 0 -10000 0 0
SP1 -0.029 0.053 -10000 0 -0.14 12 12
SIN3B 0.018 0.001 -10000 0 -10000 0 0
SIN3A 0.001 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.1 -10000 0 -0.22 79 79
ITGB5 -0.12 0.18 -10000 0 -0.38 128 128
TGIF/SIN3/HDAC complex/CtBP -0.073 0.086 -10000 0 -0.19 139 139
SMAD3/SMAD4/AR -0.062 0.14 -10000 0 -0.27 137 137
AR 0.011 0.052 -10000 0 -0.41 8 8
negative regulation of cell growth -0.043 0.1 -10000 0 -0.2 121 121
SMAD3/SMAD4/MYOD -0.058 0.14 -10000 0 -0.26 133 133
E2F5 0.017 0 -10000 0 -10000 0 0
E2F4 0.017 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.017 0.097 -10000 0 -0.21 79 79
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.074 -10000 0 -0.22 19 19
TFDP1 0.005 0.071 -10000 0 -0.41 15 15
SMAD3/SMAD4/AP1 -0.066 0.15 -10000 0 -0.29 121 121
SMAD3/SMAD4/RUNX2 -0.058 0.14 -10000 0 -0.27 125 125
TGIF2 0.011 0.052 -10000 0 -0.41 8 8
TGIF1 -0.28 0.2 -10000 0 -0.41 372 372
ATF2 0.017 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.032 0.13 -9999 0 -0.42 51 51
PDGF/PDGFRA/CRKL -0.007 0.089 -9999 0 -0.28 51 51
positive regulation of JUN kinase activity -0.014 0.092 -9999 0 -0.21 94 94
CRKL 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.007 0.089 -9999 0 -0.28 51 51
AP1 -0.089 0.19 -9999 0 -0.41 125 125
mol:IP3 -0.021 0.091 -9999 0 -0.29 51 51
PLCG1 -0.021 0.091 -9999 0 -0.29 51 51
PDGF/PDGFRA/alphaV Integrin -0.016 0.1 -9999 0 -0.28 67 67
RAPGEF1 0.017 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ -0.021 0.091 -9999 0 -0.29 51 51
CAV3 0.017 0 -9999 0 -10000 0 0
CAV1 -0.25 0.21 -9999 0 -0.41 325 325
SHC/Grb2/SOS1 -0.013 0.093 -9999 0 -0.21 94 94
PDGF/PDGFRA/Shf -0.021 0.086 -9999 0 -0.28 51 51
FOS -0.091 0.18 -9999 0 -0.41 125 125
JUN -0.011 0.027 -9999 0 -0.34 1 1
oligodendrocyte development -0.016 0.1 -9999 0 -0.28 67 67
GRB2 0.017 0.002 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
mol:DAG -0.021 0.091 -9999 0 -0.29 51 51
PDGF/PDGFRA -0.032 0.13 -9999 0 -0.42 51 51
actin cytoskeleton reorganization -0.007 0.089 -9999 0 -0.28 51 51
SRF 0.02 0.007 -9999 0 -10000 0 0
SHC1 -0.021 0.12 -9999 0 -0.41 47 47
PI3K -0.006 0.093 -9999 0 -0.24 69 69
PDGF/PDGFRA/Crk/C3G 0.007 0.077 -9999 0 -0.23 51 51
JAK1 -0.016 0.086 -9999 0 -0.28 51 51
ELK1/SRF -0.004 0.062 -9999 0 -0.18 51 51
SHB 0.017 0 -9999 0 -10000 0 0
SHF 0 0 -9999 0 -10000 0 0
CSNK2A1 0.023 0.014 -9999 0 -10000 0 0
GO:0007205 -0.022 0.086 -9999 0 -0.28 51 51
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.014 0.092 -9999 0 -0.21 94 94
PDGF/PDGFRA/SHB -0.007 0.089 -9999 0 -0.28 51 51
PDGF/PDGFRA/Caveolin-1 -0.2 0.17 -9999 0 -0.31 348 348
ITGAV 0.004 0.073 -9999 0 -0.41 16 16
ELK1 -0.02 0.077 -9999 0 -0.24 51 51
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PDGF/PDGFRA/Crk -0.007 0.089 -9999 0 -0.28 51 51
JAK-STAT cascade -0.016 0.086 -9999 0 -0.28 51 51
cell proliferation -0.021 0.086 -9999 0 -0.28 51 51
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.14 0.16 -9999 0 -0.29 289 289
PDGFRB 0.014 0.032 -9999 0 -0.41 3 3
SPHK1 -0.006 0.041 -9999 0 -0.2 19 19
mol:S1P -0.005 0.051 -9999 0 -0.2 26 26
S1P1/S1P/Gi -0.08 0.1 -9999 0 -0.27 83 83
GNAO1 0.002 0.005 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.064 0.088 -9999 0 -0.23 78 78
PLCG1 -0.068 0.093 -9999 0 -0.24 84 84
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.014 0.032 -9999 0 -0.41 3 3
GNAI2 0.022 0.004 -9999 0 -10000 0 0
GNAI3 -0.036 0.14 -9999 0 -0.41 65 65
GNAI1 0.013 0.019 -9999 0 -0.41 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.11 0.14 -9999 0 -0.23 289 289
S1P1/S1P -0.074 0.11 -9999 0 -0.24 72 72
negative regulation of cAMP metabolic process -0.079 0.099 -9999 0 -0.26 83 83
MAPK3 -0.076 0.11 -9999 0 -0.3 70 70
calcium-dependent phospholipase C activity 0 0.002 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
KDR 0.007 0.076 -9999 0 -0.41 17 17
PLCB2 -0.067 0.1 -9999 0 -0.26 41 41
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.068 0.092 -9999 0 -0.25 41 41
receptor internalization -0.071 0.1 -9999 0 -0.22 73 73
PTGS2 -0.084 0.12 -9999 0 -0.32 70 70
Rac1/GTP -0.068 0.092 -9999 0 -0.25 38 38
RHOA 0.017 0.001 -9999 0 -10000 0 0
VEGFA -0.21 0.21 -9999 0 -0.4 286 286
negative regulation of T cell proliferation -0.079 0.099 -9999 0 -0.26 83 83
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.015 0.006 -9999 0 -10000 0 0
MAPK1 -0.074 0.11 -9999 0 -0.3 67 67
S1P1/S1P/PDGFB-D/PDGFRB -0.07 0.12 -9999 0 -0.25 73 73
ABCC1 0.01 0.056 -9999 0 -0.41 9 9
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.11 0.059 -10000 0 -0.13 456 456
epithelial cell differentiation 0.029 0.042 -10000 0 -0.19 18 18
CYFIP2 0.01 0.008 -10000 0 -10000 0 0
ENAH 0.008 0.072 -10000 0 -0.26 21 21
EGFR -0.14 0.21 -10000 0 -0.41 194 194
EPHA2 0.006 0.069 -10000 0 -0.41 14 14
MYO6 0.018 0.037 -10000 0 -0.18 18 18
CTNNB1 0.017 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.02 0.017 -10000 0 -10000 0 0
AQP5 0.027 0.033 -10000 0 -0.15 18 18
CTNND1 0.009 0.058 -10000 0 -0.41 10 10
mol:PI-4-5-P2 0.017 0.036 -10000 0 -0.18 17 17
regulation of calcium-dependent cell-cell adhesion 0.018 0.037 -10000 0 -0.18 18 18
EGF 0.015 0.026 -10000 0 -0.41 2 2
NCKAP1 0.017 0 -10000 0 -10000 0 0
AQP3 0.024 0.045 -10000 0 -0.32 3 3
cortical microtubule organization 0.029 0.042 -10000 0 -0.19 18 18
GO:0000145 0.012 0.033 -10000 0 -0.17 17 17
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.043 -10000 0 -0.19 18 18
MLLT4 0.017 0 -10000 0 -10000 0 0
ARF6/GDP -0.019 0.068 -10000 0 -0.35 15 15
ARF6 0.017 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.022 0.084 -10000 0 -0.26 38 38
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.015 0.078 -10000 0 -0.22 39 39
PVRL2 0.017 0 -10000 0 -10000 0 0
ZYX -0.032 0.098 -10000 0 -0.19 140 140
ARF6/GTP 0.028 0.08 -10000 0 -0.24 38 38
CDH1 0.011 0.052 -10000 0 -0.41 8 8
EGFR/EGFR/EGF/EGF -0.05 0.11 -10000 0 -0.18 207 207
RhoA/GDP 0.03 0.039 -10000 0 -0.18 18 18
actin cytoskeleton organization 0.019 0.035 -10000 0 -0.17 18 18
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
GIT1 0.017 0 -10000 0 -10000 0 0
IGF1R 0.017 0 -10000 0 -10000 0 0
IGF1 0.014 0.037 -10000 0 -0.41 4 4
DIAPH1 -0.13 0.2 -10000 0 -0.36 225 225
Wnt receptor signaling pathway -0.029 0.042 0.19 18 -10000 0 18
RHOA 0.017 0.001 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.068 -10000 0 -0.35 15 15
CTNNA1 0.017 0 -10000 0 -10000 0 0
VCL 0.019 0.036 -10000 0 -0.17 18 18
EFNA1 -0.002 0.088 -10000 0 -0.41 23 23
LPP 0.003 0.068 -10000 0 -0.19 55 55
Ephrin A1/EPHA2 0.012 0.071 -10000 0 -0.2 47 47
SEC6/SEC8 -0.005 0.029 -10000 0 -10000 0 0
MGAT3 0.018 0.037 -10000 0 -0.18 18 18
HGF/MET 0.022 0.052 -10000 0 -0.19 27 27
HGF 0.015 0.026 -10000 0 -0.41 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.11 0.059 -10000 0 -0.13 456 456
actin cable formation -0.006 0.07 -10000 0 -0.23 27 27
KIAA1543 0.007 0.034 -10000 0 -0.18 18 18
KIFC3 0.018 0.037 -10000 0 -0.18 18 18
NCK1 0.008 0.061 -10000 0 -0.41 11 11
EXOC3 0.017 0 -10000 0 -10000 0 0
ACTN1 0.002 0.072 -10000 0 -0.2 54 54
NCK1/GIT1 0.019 0.044 -10000 0 -0.28 11 11
mol:GDP 0.029 0.042 -10000 0 -0.19 18 18
EXOC4 0 0 -10000 0 -10000 0 0
STX4 0.018 0.037 -10000 0 -0.18 18 18
PIP5K1C 0.018 0.036 -10000 0 -0.18 17 17
LIMA1 -0.35 0.15 -10000 0 -0.41 454 454
ABI1 0.017 0 -10000 0 -10000 0 0
ROCK1 0.015 0.069 -10000 0 -0.31 15 15
adherens junction assembly 0.015 0.037 -10000 0 -0.16 18 18
IGF-1R heterotetramer/IGF1 0.025 0.044 -10000 0 -0.19 20 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.025 0 -10000 0 -10000 0 0
MET 0.009 0.058 -10000 0 -0.41 10 10
PLEKHA7 0.007 0.036 -10000 0 -0.18 18 18
mol:GTP 0.021 0.084 -10000 0 -0.26 38 38
establishment of epithelial cell apical/basal polarity 0.026 0.033 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.11 0.059 -10000 0 -0.13 456 456
regulation of cell-cell adhesion 0.019 0.035 -10000 0 -0.17 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.11 0.059 -10000 0 -0.13 456 456
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.035 0.096 -9999 0 -0.25 51 51
mol:DAG -0.032 0.088 -9999 0 -0.23 51 51
PLCG1 -0.032 0.09 -9999 0 -0.23 51 51
YES1 -0.072 0.13 -9999 0 -0.28 111 111
FZD3 0.014 0.032 -9999 0 -0.41 3 3
FZD6 -0.065 0.17 -9999 0 -0.41 101 101
G protein -0.031 0.091 -9999 0 -0.24 51 51
MAP3K7 -0.02 0.074 -9999 0 -0.19 48 48
mol:Ca2+ -0.031 0.086 -9999 0 -0.22 51 51
mol:IP3 -0.032 0.088 -9999 0 -0.23 51 51
NLK 0.016 0.056 -9999 0 -0.71 3 3
GNB1 0.017 0.002 -9999 0 -10000 0 0
CAMK2A -0.024 0.078 -9999 0 -0.21 47 47
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.047 0.1 -9999 0 -0.16 221 221
CSNK1A1 0.017 0 -9999 0 -10000 0 0
GNAS -0.041 0.096 -9999 0 -0.26 51 51
GO:0007205 -0.032 0.084 -9999 0 -0.22 51 51
WNT6 0.017 0 -9999 0 -10000 0 0
WNT4 0.015 0.026 -9999 0 -0.41 2 2
NFAT1/CK1 alpha -0.055 0.12 -9999 0 -0.25 111 111
GNG2 0 0 -9999 0 -10000 0 0
WNT5A -0.12 0.2 -9999 0 -0.41 168 168
WNT11 0.015 0.026 -9999 0 -0.41 2 2
CDC42 -0.066 0.13 -9999 0 -0.27 111 111
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.031 -9999 0 -0.28 5 5
CRKL 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DOCK1 0.017 0 -9999 0 -10000 0 0
ITGA4 0.013 0.042 -9999 0 -0.41 5 5
alpha4/beta7 Integrin/MAdCAM1 0.041 0.034 -9999 0 -0.29 5 5
EPO 0.017 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.022 0.041 -9999 0 -0.38 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.023 0.03 -9999 0 -0.28 5 5
EPO/EPOR (dimer) 0.025 0 -9999 0 -10000 0 0
lamellipodium assembly 0.01 0.037 -9999 0 -0.16 17 17
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PI3K 0.009 0.065 -9999 0 -0.28 25 25
ARF6 0.017 0 -9999 0 -10000 0 0
JAK2 0.028 0.016 -9999 0 -0.14 5 5
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
MADCAM1 0.017 0 -9999 0 -10000 0 0
cell adhesion 0.039 0.034 -9999 0 -0.29 5 5
CRKL/CBL 0.025 0 -9999 0 -10000 0 0
ITGB1 0.017 0 -9999 0 -10000 0 0
SRC -0.13 0.11 -9999 0 -0.21 353 353
ITGB7 0.015 0.026 -9999 0 -0.41 2 2
RAC1 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.15 0.13 -9999 0 -0.24 353 353
p130Cas/Crk/Dock1 -0.1 0.099 -9999 0 -0.17 353 353
VCAM1 -0.27 0.2 -9999 0 -0.41 351 351
RHOA 0.017 0.001 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.024 -9999 0 -0.21 5 5
BCAR1 -0.12 0.1 -9999 0 -0.19 353 353
EPOR 0.017 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP 0.01 0.038 -9999 0 -0.16 17 17
TCGA08_p53

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
CDKN2A -0.024 0.093 -10000 0 -0.29 58 58
TP53 -0.02 0.066 0.16 16 -0.17 57 73
Senescence -0.02 0.066 0.16 16 -0.17 57 73
Apoptosis -0.02 0.066 0.16 16 -0.17 57 73
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.009 0.07 0.16 52 -0.26 18 70
MDM4 0.007 0.066 -10000 0 -0.41 13 13
FAS signaling pathway (CD95)

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
SPTAN1 -0.024 0.057 -10000 0 -0.14 101 101
RFC1 -0.024 0.057 -10000 0 -0.14 103 103
PRKDC -0.034 0.077 -10000 0 -0.17 117 117
RIPK1 0.01 0.055 -10000 0 -0.41 9 9
CASP7 -0.009 0.071 -10000 0 -0.23 31 31
FASLG/FAS/FADD/FAF1 -0.002 0.062 0.14 25 -0.15 65 90
MAP2K4 0.002 0.078 -10000 0 -0.23 29 29
mol:ceramide 0.01 0.069 -10000 0 -0.22 23 23
GSN -0.031 0.068 -10000 0 -0.15 116 116
FASLG/FAS/FADD/FAF1/Caspase 8 0.007 0.063 0.13 24 -0.19 25 49
FAS -0.039 0.14 -10000 0 -0.42 68 68
BID -0.004 0.043 0.14 1 -0.25 16 17
MAP3K1 -0.013 0.077 -10000 0 -0.23 34 34
MAP3K7 0.016 0.019 -10000 0 -0.41 1 1
RB1 -0.024 0.057 -10000 0 -0.14 103 103
CFLAR 0.013 0.041 -10000 0 -0.41 5 5
HGF/MET 0.014 0.074 -10000 0 -0.24 41 41
ARHGDIB -0.045 0.088 -10000 0 -0.18 139 139
FADD 0.015 0.027 -10000 0 -0.41 2 2
actin filament polymerization 0.031 0.068 0.15 116 -10000 0 116
NFKB1 0.007 0.045 -10000 0 -0.24 2 2
MAPK8 0.001 0.093 -10000 0 -0.28 34 34
DFFA -0.024 0.057 -10000 0 -0.14 103 103
DNA fragmentation during apoptosis -0.024 0.057 -10000 0 -0.14 103 103
FAS/FADD/MET -0.006 0.099 -10000 0 -0.24 79 79
CFLAR/RIP1 0.018 0.049 -10000 0 -0.28 14 14
FAIM3 0.016 0.019 -10000 0 -0.41 1 1
FAF1 0.016 0.007 -10000 0 -10000 0 0
PARP1 -0.024 0.057 -10000 0 -0.14 103 103
DFFB -0.024 0.057 -10000 0 -0.14 103 103
CHUK 0.009 0.042 -10000 0 -0.21 3 3
FASLG 0.016 0.007 -10000 0 -10000 0 0
FAS/FADD -0.017 0.11 -10000 0 -0.29 70 70
HGF 0.015 0.026 -10000 0 -0.41 2 2
LMNA -0.032 0.081 -10000 0 -0.27 33 33
CASP6 -0.035 0.079 -10000 0 -0.17 118 118
CASP10 0.017 0.004 -10000 0 -10000 0 0
CASP3 -0.032 0.066 -10000 0 -0.16 103 103
PTPN13 -0.007 0.099 -10000 0 -0.41 30 30
CASP8 -0.009 0.039 0.22 1 -0.3 9 10
IL6 -0.011 0.13 -10000 0 -0.39 52 52
MET 0.009 0.058 -10000 0 -0.41 10 10
ICAD/CAD -0.019 0.053 -10000 0 -0.14 9 9
FASLG/FAS/FADD/FAF1/Caspase 10 0.01 0.069 -10000 0 -0.22 23 23
activation of caspase activity by cytochrome c -0.004 0.043 0.14 1 -0.24 16 17
PAK2 -0.034 0.079 -10000 0 -0.17 115 115
BCL2 0.017 0 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification -0.046 0.19 -10000 0 -0.42 100 100
CLOCK 0.009 0.038 -10000 0 -0.44 3 3
TIMELESS/CRY2 -0.035 0.15 -10000 0 -0.35 100 100
DEC1/BMAL1 0.024 0.007 -10000 0 -10000 0 0
ATR 0.017 0 -10000 0 -10000 0 0
NR1D1 -0.007 0.08 -10000 0 -0.17 100 100
ARNTL 0.012 0.016 -10000 0 -10000 0 0
TIMELESS -0.046 0.16 -10000 0 -0.38 100 100
NPAS2 0.011 0.024 -10000 0 -0.41 1 1
CRY2 0.017 0 -10000 0 -10000 0 0
mol:CO 0.006 0.034 0.077 100 -10000 0 100
CHEK1 -0.032 0.14 -10000 0 -0.41 60 60
mol:HEME -0.006 0.034 -10000 0 -0.077 100 100
PER1 0.015 0.032 -10000 0 -0.41 3 3
BMAL/CLOCK/NPAS2 0.026 0.05 -10000 0 -0.29 4 4
BMAL1/CLOCK -0.003 0.1 -10000 0 -0.34 4 4
S phase of mitotic cell cycle -0.046 0.19 -10000 0 -0.42 100 100
TIMELESS/CHEK1/ATR -0.046 0.19 -10000 0 -0.43 100 100
mol:NADPH -0.006 0.034 -10000 0 -0.077 100 100
PER1/TIMELESS -0.036 0.15 -10000 0 -0.35 100 100
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.017 0 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.028 0.078 -9999 0 -0.16 132 132
DAPP1 -0.015 0.088 -9999 0 -0.2 75 75
Src family/SYK family/BLNK-LAT/BTK-ITK -0.036 0.14 -9999 0 -0.3 87 87
mol:DAG -0.019 0.078 -9999 0 -0.16 80 80
HRAS 0.01 0.021 -9999 0 -0.41 1 1
RAP1A 0.015 0.004 -9999 0 -10000 0 0
ARF5/GDP 0.003 0.053 -9999 0 -0.19 25 25
PLCG2 0.009 0.058 -9999 0 -0.41 10 10
PLCG1 0.017 0 -9999 0 -10000 0 0
ARF5 0.017 0 -9999 0 -10000 0 0
mol:GTP -0.039 0.078 -9999 0 -0.17 132 132
ARF1/GTP -0.033 0.073 -9999 0 -0.16 132 132
RHOA 0.017 0.001 -9999 0 -10000 0 0
YES1 -0.048 0.15 -9999 0 -0.41 80 80
RAP1A/GTP -0.032 0.082 -9999 0 -0.17 132 132
ADAP1 -0.037 0.075 -9999 0 -0.17 132 132
ARAP3 -0.038 0.077 -9999 0 -0.17 132 132
INPPL1 0.017 0 -9999 0 -10000 0 0
PREX1 0 0 -9999 0 -10000 0 0
ARHGEF6 0.01 0.052 -9999 0 -0.41 8 8
ARHGEF7 0.016 0.019 -9999 0 -0.41 1 1
ARF1 0.017 0.001 -9999 0 -10000 0 0
NRAS -0.094 0.19 -9999 0 -0.41 137 137
FYN 0.015 0.026 -9999 0 -0.41 2 2
ARF6 0.017 0 -9999 0 -10000 0 0
FGR 0.003 0.076 -9999 0 -0.41 17 17
mol:Ca2+ -0.006 0.042 -9999 0 -0.12 17 17
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.016 0.003 -9999 0 -10000 0 0
ZAP70 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.01 0.057 -9999 0 -0.13 55 55
LYN -0.035 0.14 -9999 0 -0.41 64 64
ARF1/GDP 0.003 0.053 -9999 0 -0.19 25 25
RhoA/GDP -0.018 0.08 -9999 0 -0.15 132 132
PDK1/Src/Hsp90 0.035 0 -9999 0 -10000 0 0
BLNK -0.038 0.14 -9999 0 -0.41 68 68
actin cytoskeleton reorganization -0.012 0.069 -9999 0 -0.18 11 11
SRC 0.017 0 -9999 0 -10000 0 0
PLEKHA2 0.011 0.011 -9999 0 -0.24 1 1
RAC1 0.017 0 -9999 0 -10000 0 0
PTEN 0.019 0.027 -9999 0 -0.4 2 2
HSP90AA1 0.017 0 -9999 0 -10000 0 0
ARF6/GTP -0.028 0.078 -9999 0 -0.16 132 132
RhoA/GTP -0.028 0.079 -9999 0 -0.16 132 132
Src family/SYK family/BLNK-LAT -0.032 0.13 -9999 0 -0.28 91 91
BLK 0.017 0 -9999 0 -10000 0 0
PDPK1 0.017 0 -9999 0 -10000 0 0
CYTH1 -0.037 0.075 -9999 0 -0.17 132 132
HCK -0.053 0.16 -9999 0 -0.41 86 86
CYTH3 -0.037 0.075 -9999 0 -0.17 132 132
CYTH2 -0.037 0.075 -9999 0 -0.17 132 132
KRAS 0.011 0.011 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.005 0.044 -9999 0 -10000 0 0
SGK1 -0.008 0.047 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.006 0.053 -9999 0 -0.21 25 25
SOS1 0 0 -9999 0 -10000 0 0
SYK -0.012 0.11 -9999 0 -0.41 36 36
ARF6/GDP -0.021 0.076 -9999 0 -0.15 132 132
mol:PI-3-4-5-P3 -0.038 0.079 -9999 0 -0.17 132 132
ARAP3/RAP1A/GTP -0.032 0.083 -9999 0 -0.17 132 132
VAV1 0.016 0.019 -9999 0 -0.41 1 1
mol:PI-3-4-P2 0.009 0 -9999 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.024 0.089 -9999 0 -0.18 134 134
PLEKHA1 0.01 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.003 0.053 -9999 0 -0.19 25 25
LAT 0.016 0.019 -9999 0 -0.41 1 1
Rac1/GTP 0.011 0.041 -9999 0 -0.15 24 24
ITK -0.034 0.08 -9999 0 -0.17 134 134
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.03 0.1 -9999 0 -0.21 93 93
LCK 0.014 0.037 -9999 0 -0.41 4 4
BTK -0.032 0.077 -9999 0 -0.16 133 133
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.021 0.11 -10000 0 -0.2 127 127
MAP3K8 -0.018 0.12 -10000 0 -0.42 42 42
FOS -0.012 0.069 -10000 0 -0.18 20 20
PRKCA 0.013 0.009 -10000 0 -10000 0 0
PTPN7 0.011 0.022 -10000 0 -0.41 1 1
HRAS 0.016 0.019 -10000 0 -0.41 1 1
PRKCB -0.002 0.006 0.01 2 -0.012 125 127
NRAS -0.095 0.19 -10000 0 -0.41 137 137
RAS family/GTP -0.034 0.1 -10000 0 -0.21 134 134
MAPK3 0.004 0.038 -10000 0 -0.19 1 1
MAP2K1 -0.009 0.048 -10000 0 -0.12 52 52
ELK1 0.011 0.013 -10000 0 -10000 0 0
BRAF -0.003 0.028 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 0.002 1 -0.004 125 126
MAPK1 -0.005 0.062 -10000 0 -0.27 18 18
RAF1 -0.003 0.029 -10000 0 -0.17 1 1
KRAS 0.016 0.002 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.013 0.001 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
ERC1 0.016 0.019 -9999 0 -0.41 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.047 0.1 -9999 0 -0.23 95 95
IRAK/TOLLIP 0.025 0.002 -9999 0 -10000 0 0
IKBKB 0.017 0 -9999 0 -10000 0 0
IKBKG 0.017 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 0 0.085 -9999 0 -0.28 43 43
IL1A 0.015 0.032 -9999 0 -0.41 3 3
IL1B -0.088 0.15 -9999 0 -0.3 178 178
IRAK/TRAF6/p62/Atypical PKCs 0.038 0.013 -9999 0 -0.18 2 2
IL1R2 -0.015 0.11 -9999 0 -0.41 40 40
IL1R1 0.015 0.032 -9999 0 -0.41 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.035 0.09 -9999 0 -0.22 71 71
TOLLIP 0.017 0 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.034 0.012 -9999 0 -0.23 1 1
IKK complex/ELKS 0.049 0.015 -9999 0 -0.25 1 1
JUN 0.027 0.012 -9999 0 -0.16 1 1
MAP3K7 0.016 0.019 -9999 0 -0.41 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.056 0.14 -9999 0 -0.22 196 196
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.013 0.12 -9999 0 -0.23 112 112
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.11 -9999 0 -0.21 113 113
IL1 beta fragment/IL1R1/IL1RAP -0.069 0.15 -9999 0 -0.24 198 198
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
MAPK8 0.027 0.009 -9999 0 -0.16 1 1
IRAK1 0.016 0.001 -9999 0 -10000 0 0
IL1RN/IL1R1 0.024 0.023 -9999 0 -0.28 3 3
IRAK4 0.016 0.019 -9999 0 -0.41 1 1
PRKCI 0.016 0.019 -9999 0 -0.41 1 1
TRAF6 0.017 0 -9999 0 -10000 0 0
PI3K 0.009 0.065 -9999 0 -0.28 25 25
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.043 0.1 -9999 0 -0.26 72 72
CHUK 0.016 0.019 -9999 0 -0.41 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.069 0.15 -9999 0 -0.24 198 198
IL1 beta/IL1R2 -0.082 0.15 -9999 0 -0.26 201 201
IRAK/TRAF6/TAK1/TAB1/TAB2 0.048 0.01 -9999 0 -0.17 1 1
NF kappa B1 p50/RelA -0.056 0.13 -9999 0 -0.28 75 75
IRAK3 0.015 0.026 -9999 0 -0.41 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.056 0.14 -9999 0 -0.22 198 198
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.071 -9999 0 -0.13 113 113
IL1 alpha/IL1R1/IL1RAP 0.009 0.081 -9999 0 -0.24 50 50
RELA 0.017 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
SQSTM1 0.016 0.019 -9999 0 -0.41 1 1
MYD88 -0.041 0.15 -9999 0 -0.41 72 72
IRAK/TRAF6/MEKK3 0.035 0.002 -9999 0 -10000 0 0
IL1RAP -0.019 0.12 -9999 0 -0.41 45 45
UBE2N 0.017 0.001 -9999 0 -10000 0 0
IRAK/TRAF6 -0.053 0.11 -9999 0 -0.18 197 197
CASP1 -0.12 0.2 -9999 0 -0.41 172 172
IL1RN/IL1R2 0.002 0.082 -9999 0 -0.28 40 40
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.085 0.17 -9999 0 -0.27 221 221
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.063 -9999 0 -0.22 11 11
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
IL1RN 0.017 0 -9999 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.042 0.01 -9999 0 -0.18 1 1
MAP2K6 0.027 0.01 -9999 0 -0.17 1 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.002 0.077 -9999 0 -0.23 47 47
BIRC5 -0.16 0.21 -9999 0 -0.41 212 212
NFKBIA 0.017 0.031 -9999 0 -0.19 2 2
CPEB1 0.013 0.007 -9999 0 -10000 0 0
AKT1 0.016 0.036 -9999 0 -0.21 5 5
NDEL1 0.016 0.004 -9999 0 -10000 0 0
Aurora A/BRCA1 0.02 0.036 -9999 0 -0.14 19 19
NDEL1/TACC3 -0.009 0.093 -9999 0 -0.2 92 92
GADD45A -0.02 0.12 -9999 0 -0.41 46 46
GSK3B 0.019 0.007 -9999 0 -10000 0 0
PAK1/Aurora A 0.024 0.03 -9999 0 -0.12 16 16
MDM2 0.002 0.078 -9999 0 -0.41 18 18
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.15 0.15 -9999 0 -0.28 296 296
TP53 -0.001 0.065 -9999 0 -0.14 80 80
DLG7 -0.091 0.13 -9999 0 -0.24 230 230
AURKAIP1 0.017 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0.019 -9999 0 -0.41 1 1
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.01 0.099 -9999 0 -0.22 92 92
G2/M transition of mitotic cell cycle 0.02 0.036 -9999 0 -0.14 19 19
AURKA 0.018 0.036 -9999 0 -0.15 19 19
AURKB -0.002 0.047 -9999 0 -0.18 30 30
CDC25B 0.015 0.04 -9999 0 -0.16 17 17
G2/M transition checkpoint 0.01 0.025 -9999 0 -0.11 19 19
mRNA polyadenylation 0.017 0.022 -9999 0 -0.11 8 8
Aurora A/CPEB 0.017 0.022 -9999 0 -0.11 8 8
Aurora A/TACC1/TRAP/chTOG 0.042 0.027 -9999 0 -10000 0 0
BRCA1 0.013 0.042 -9999 0 -0.41 5 5
centrosome duplication 0.024 0.03 -9999 0 -0.12 16 16
regulation of centrosome cycle -0.009 0.091 -9999 0 -0.2 92 92
spindle assembly 0.041 0.027 -9999 0 -10000 0 0
TDRD7 0.017 0.001 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.05 0.12 -9999 0 -0.19 208 208
CENPA -0.004 0.054 -9999 0 -0.12 83 83
Aurora A/PP2A 0.024 0.03 -9999 0 -0.14 1 1
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process -0.051 0.091 -9999 0 -0.16 190 190
negative regulation of DNA binding -0.001 0.064 -9999 0 -0.14 80 80
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.025 0.013 -9999 0 -0.28 1 1
RASA1 0.017 0.002 -9999 0 -10000 0 0
Ajuba/Aurora A 0.011 0.025 -9999 0 -0.11 19 19
mitotic prometaphase 0 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.036 -9999 0 -0.15 19 19
TACC1 0.017 0.001 -9999 0 -10000 0 0
TACC3 -0.061 0.16 -9999 0 -0.41 96 96
Aurora A/Antizyme1 0.033 0.028 -9999 0 -0.12 1 1
Aurora A/RasGAP 0.024 0.03 -9999 0 -0.14 1 1
OAZ1 0.017 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.019 0.007 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.034 0.012 -9999 0 -0.23 1 1
Importin alpha/Importin beta/TPX2 -0.15 0.15 -9999 0 -0.28 296 296
PPP2R5D 0.017 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.1 0.12 -9999 0 -0.21 296 296
PAK1 0.017 0 -9999 0 -10000 0 0
CKAP5 0.017 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.15 0.16 -9999 0 -0.3 291 291
alphaV beta3 Integrin 0.026 0.049 -9999 0 -0.23 18 18
PTK2 -0.058 0.095 -9999 0 -0.28 28 28
IGF1R 0.017 0 -9999 0 -10000 0 0
PI4KB 0.016 0.019 -9999 0 -0.41 1 1
MFGE8 0.015 0.032 -9999 0 -0.41 3 3
SRC 0.017 0 -9999 0 -10000 0 0
CDKN1B 0.022 0.023 -9999 0 -0.19 2 2
VEGFA -0.22 0.21 -9999 0 -0.41 286 286
ILK 0.022 0.023 -9999 0 -0.19 2 2
ROCK1 0.017 0 -9999 0 -10000 0 0
AKT1 0.021 0.028 -9999 0 -0.18 6 6
PTK2B -0.1 0.12 -9999 0 -0.2 297 297
alphaV/beta3 Integrin/JAM-A 0.021 0.071 -9999 0 -0.19 53 53
CBL 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.027 0.046 -9999 0 -0.23 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.04 0.033 -9999 0 -0.21 9 9
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.04 0.07 -9999 0 -0.21 21 21
alphaV/beta3 Integrin/Syndecan-1 0.003 0.092 -9999 0 -0.25 60 60
PI4KA 0.006 0.008 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.011 0.1 -9999 0 -0.19 114 114
PI4 Kinase 0.009 0.014 -9999 0 -0.14 1 1
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
alphaV/beta3 Integrin/Osteopontin -0.065 0.14 -9999 0 -0.25 185 185
RPS6KB1 -0.013 0.095 -9999 0 -0.36 13 13
TLN1 -0.02 0.12 -9999 0 -0.41 46 46
MAPK3 0.003 0.069 -9999 0 -0.18 49 49
GPR124 0.014 0.037 -9999 0 -0.41 4 4
MAPK1 0.003 0.068 -9999 0 -0.19 45 45
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.027 0.046 -9999 0 -0.23 16 16
cell adhesion 0.029 0.045 -9999 0 -0.2 20 20
ANGPTL3 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.12 0.14 -9999 0 -0.24 291 291
IGF-1R heterotetramer 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.049 -9999 0 -0.41 7 7
ITGB3 0.017 0 -9999 0 -10000 0 0
IGF1 0.014 0.037 -9999 0 -0.41 4 4
RAC1 0.017 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.051 -9999 0 -0.23 20 20
apoptosis 0.004 0.073 -9999 0 -0.41 16 16
CD47 0.015 0.026 -9999 0 -0.41 2 2
alphaV/beta3 Integrin/CD47 0.026 0.049 -9999 0 -0.23 18 18
VCL 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.027 0.046 -9999 0 -0.23 16 16
CSF1 0.017 0 -9999 0 -10000 0 0
PIK3C2A 0.012 0.023 -9999 0 -0.19 2 2
PI4 Kinase/Pyk2 -0.054 0.079 -9999 0 -0.28 23 23
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.14 -9999 0 -0.22 297 297
FAK1/Vinculin -0.044 0.084 -9999 0 -0.23 28 28
alphaV beta3/Integrin/ppsTEM5 0.025 0.051 -9999 0 -0.23 20 20
RHOA 0.017 0.001 -9999 0 -10000 0 0
VTN 0.015 0.026 -9999 0 -0.41 2 2
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 0.015 0.026 -9999 0 -0.41 2 2
F11R -0.002 0.075 -9999 0 -0.28 35 35
alphaV/beta3 Integrin/Lactadherin 0.025 0.05 -9999 0 -0.23 19 19
alphaV/beta3 Integrin/TGFBR2 0.023 0.055 -9999 0 -0.23 23 23
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.026 0.042 -9999 0 -0.21 16 16
HSP90AA1 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.005 0.084 -9999 0 -0.23 57 57
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.065 0.17 -9999 0 -0.41 101 101
alphaV/beta3 Integrin/Pyk2 -0.097 0.13 -9999 0 -0.2 297 297
SDC1 -0.022 0.12 -9999 0 -0.41 48 48
VAV3 0.001 0.069 -9999 0 -0.21 48 48
PTPN11 0.017 0 -9999 0 -10000 0 0
IRS1 0.013 0.042 -9999 0 -0.41 5 5
FAK1/Paxillin -0.044 0.084 -9999 0 -0.23 28 28
cell migration -0.038 0.079 -9999 0 -0.21 28 28
ITGAV 0.004 0.073 -9999 0 -0.41 16 16
PI3K 0.022 0.072 -9999 0 -0.18 51 51
SPP1 -0.13 0.2 -9999 0 -0.41 181 181
KDR 0.003 0.076 -9999 0 -0.41 17 17
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.004 0.073 -9999 0 -0.41 16 16
COL4A3 0.017 0 -9999 0 -10000 0 0
angiogenesis 0.008 0.064 -9999 0 -0.22 18 18
Rac1/GTP 0.011 0.065 -9999 0 -0.19 48 48
EDIL3 0.017 0 -9999 0 -10000 0 0
cell proliferation 0.023 0.055 -9999 0 -0.23 23 23
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0 0.077 -10000 0 -0.2 49 49
IKBKB 0.007 0.051 -10000 0 -0.16 23 23
AKT1 -0.013 0.069 0.18 1 -0.17 59 60
IKBKG 0.007 0.053 -10000 0 -0.16 25 25
CALM1 -0.011 0.079 -10000 0 -0.25 38 38
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
MAP3K1 -0.01 0.095 -10000 0 -0.24 57 57
MAP3K7 0.016 0.019 -10000 0 -0.41 1 1
mol:Ca2+ -0.015 0.086 -10000 0 -0.27 40 40
DOK1 0.017 0 -10000 0 -10000 0 0
AP-1 -0.011 0.071 -10000 0 -0.17 49 49
LYN -0.035 0.14 -10000 0 -0.41 64 64
BLNK -0.038 0.14 -10000 0 -0.41 68 68
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
BCR complex 0.024 0.028 -10000 0 -0.41 2 2
CD22 -0.038 0.11 -10000 0 -0.24 94 94
CAMK2G -0.006 0.058 0.14 1 -0.23 26 27
CSNK2A1 0.017 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.07 0.14 -10000 0 -0.27 135 135
GO:0007205 -0.016 0.087 -10000 0 -0.28 40 40
SYK -0.012 0.11 -10000 0 -0.41 36 36
ELK1 -0.012 0.083 -10000 0 -0.26 40 40
NFATC1 -0.019 0.093 0.14 1 -0.23 66 67
B-cell antigen/BCR complex 0.024 0.028 -10000 0 -0.41 2 2
PAG1/CSK 0.013 0 -10000 0 -10000 0 0
NFKBIB 0.013 0.021 -10000 0 -0.085 2 2
HRAS -0.016 0.093 -10000 0 -0.25 56 56
NFKBIA 0.013 0.021 -10000 0 -0.086 2 2
NF-kappa-B/RelA/I kappa B beta 0.017 0.02 -10000 0 -0.091 4 4
RasGAP/Csk -0.009 0.11 -10000 0 -0.19 126 126
mol:GDP -0.013 0.084 -10000 0 -0.26 40 40
PTEN 0.015 0.026 -10000 0 -0.41 2 2
CD79B 0.016 0.019 -10000 0 -0.41 1 1
NF-kappa-B/RelA/I kappa B alpha 0.017 0.02 -10000 0 -0.092 4 4
GRB2 0.017 0.002 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.024 0.11 -10000 0 -0.29 60 60
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.016 0.088 -10000 0 -0.24 53 53
CSK 0.017 0 -10000 0 -10000 0 0
FOS -0.051 0.12 -10000 0 -0.22 148 148
CHUK 0.007 0.053 -10000 0 -0.16 26 26
IBTK 0.017 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.006 0.093 -10000 0 -0.23 61 61
PTPN6 -0.037 0.11 -10000 0 -0.25 94 94
RELA 0.017 0 -10000 0 -10000 0 0
BCL2A1 -0.001 0.037 -10000 0 -0.064 129 129
VAV2 -0.034 0.12 -10000 0 -0.29 67 67
ubiquitin-dependent protein catabolic process 0.016 0.02 -10000 0 -0.08 2 2
BTK 0.011 0.009 -10000 0 -10000 0 0
CD19 -0.038 0.11 -10000 0 -0.24 94 94
MAP4K1 0.016 0.019 -10000 0 -0.41 1 1
CD72 0.017 0 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.086 -10000 0 -0.21 51 51
SH3BP5 0.016 0.005 -10000 0 -10000 0 0
PIK3AP1 -0.018 0.09 -10000 0 -0.23 62 62
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.009 0.11 -10000 0 -0.34 40 40
RAF1 -0.012 0.089 -10000 0 -0.26 46 46
RasGAP/p62DOK/SHIP -0.013 0.099 -10000 0 -0.19 126 126
CD79A 0.015 0.026 -10000 0 -0.41 2 2
re-entry into mitotic cell cycle -0.011 0.071 -10000 0 -0.17 49 49
RASA1 0.017 0.002 -10000 0 -10000 0 0
MAPK3 -0.001 0.079 0.16 2 -0.23 40 42
MAPK1 -0.002 0.079 0.26 1 -0.23 40 41
CD72/SHP1 -0.027 0.11 -10000 0 -0.24 94 94
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK8 -0.004 0.085 -10000 0 -0.21 49 49
actin cytoskeleton organization -0.027 0.1 -10000 0 -0.26 65 65
NF-kappa-B/RelA 0.037 0.035 -10000 0 -0.15 2 2
Calcineurin 0.006 0.069 -10000 0 -0.22 32 32
PI3K -0.061 0.11 -10000 0 -0.3 80 80
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.019 0.095 -10000 0 -0.24 62 62
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.011 0.094 -10000 0 -0.68 1 1
DAPP1 -0.022 0.095 -10000 0 -0.57 1 1
cytokine secretion -0.017 0.088 0.14 1 -0.22 66 67
mol:DAG -0.016 0.088 -10000 0 -0.24 53 53
PLCG2 0.009 0.058 -10000 0 -0.41 10 10
MAP2K1 -0.007 0.083 0.17 1 -0.25 41 42
B-cell antigen/BCR complex/FcgammaRIIB -0.032 0.12 -10000 0 -0.24 129 129
mol:PI-3-4-5-P3 -0.046 0.084 0.27 1 -0.23 75 76
ETS1 0.048 0.091 0.22 18 -0.2 30 48
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.022 0.16 -10000 0 -0.3 111 111
B-cell antigen/BCR complex/LYN -0.043 0.11 -10000 0 -0.22 135 135
MALT1 -0.003 0.091 -10000 0 -0.41 25 25
TRAF6 0.017 0 -10000 0 -10000 0 0
RAC1 -0.029 0.11 -10000 0 -0.27 65 65
B-cell antigen/BCR complex/LYN/SYK -0.042 0.16 -10000 0 -0.31 106 106
CARD11 -0.015 0.083 -10000 0 -0.26 40 40
FCGR2B -0.088 0.18 -10000 0 -0.41 129 129
PPP3CA 0.014 0.007 -10000 0 -10000 0 0
BCL10 0.015 0.032 -10000 0 -0.41 3 3
IKK complex 0.011 0.025 -10000 0 -0.068 12 12
PTPRC -0.086 0.18 -10000 0 -0.41 127 127
PDPK1 -0.016 0.069 0.17 1 -0.16 66 67
PPP3CB 0.017 0.002 -10000 0 -10000 0 0
PPP3CC 0.017 0 -10000 0 -10000 0 0
POU2F2 0.016 0.013 -10000 0 -0.052 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.02 0.048 -10000 0 -0.16 31 31
adherens junction organization 0.02 0.038 -10000 0 -0.18 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.041 0.1 -10000 0 -0.28 21 21
FMN1 0.019 0.038 -10000 0 -0.14 20 20
mol:IP3 0.017 0.047 -10000 0 -0.17 26 26
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.02 0.04 -10000 0 -0.15 20 20
CTNNB1 0.017 0.002 -10000 0 -10000 0 0
AKT1 0.02 0.051 -10000 0 -0.16 30 30
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.041 -10000 0 -0.23 7 7
CTNND1 0.009 0.059 -10000 0 -0.41 10 10
mol:PI-4-5-P2 0.022 0.04 -10000 0 -0.19 11 11
VASP 0.022 0.04 -10000 0 -0.19 11 11
ZYX -0.026 0.094 -10000 0 -0.18 137 137
JUB 0.019 0.038 -10000 0 -0.14 20 20
EGFR(dimer) -0.046 0.11 -10000 0 -0.18 202 202
E-cadherin/beta catenin-gamma catenin 0.022 0.063 -10000 0 -0.29 19 19
mol:PI-3-4-5-P3 0.024 0.052 -10000 0 -0.17 27 27
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
PI3K 0.024 0.053 -10000 0 -0.18 27 27
FYN 0.023 0.044 -10000 0 -0.21 6 6
mol:Ca2+ 0.017 0.047 -10000 0 -0.16 26 26
JUP 0.004 0.073 -10000 0 -0.41 16 16
PIK3R1 0.016 0.005 -10000 0 -10000 0 0
mol:DAG 0.017 0.047 -10000 0 -0.17 26 26
CDH1 0.011 0.052 -10000 0 -0.41 8 8
RhoA/GDP -0.041 0.1 -10000 0 -0.16 196 196
establishment of polarity of embryonic epithelium 0.022 0.039 -10000 0 -0.19 11 11
SRC 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
EGFR -0.14 0.21 -10000 0 -0.41 194 194
CASR 0.018 0.044 -10000 0 -0.15 26 26
RhoA/GTP 0.023 0.045 -10000 0 -0.15 26 26
AKT2 0.022 0.048 -10000 0 -0.16 26 26
actin cable formation 0.021 0.039 -10000 0 -0.18 11 11
apoptosis -0.019 0.048 0.15 31 -10000 0 31
CTNNA1 0.018 0.002 -10000 0 -10000 0 0
mol:GDP -0.051 0.1 -10000 0 -0.17 207 207
PIP5K1A 0.022 0.04 -10000 0 -0.19 11 11
PLCG1 0.017 0.048 -10000 0 -0.17 26 26
Rac1/GTP -0.037 0.1 -10000 0 -0.16 200 200
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.032 0.11 -9999 0 -0.18 187 187
Ran/GTP/Exportin 1/HDAC1 -0.022 0.058 -9999 0 -0.17 66 66
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.086 -9999 0 -0.13 187 187
SUMO1 0.017 0 -9999 0 -10000 0 0
ZFPM1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.005 -9999 0 -0.11 1 1
FKBP3 0.017 0.001 -9999 0 -10000 0 0
Histones -0.032 0.092 -9999 0 -0.21 69 69
YY1/LSF 0.026 0 -9999 0 -10000 0 0
SMG5 0.017 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.03 0.081 -9999 0 -0.14 186 186
I kappa B alpha/HDAC1 -0.043 0.096 -9999 0 -0.24 67 67
SAP18 0.017 0 -9999 0 -10000 0 0
RELA -0.02 0.07 -9999 0 -0.12 185 185
HDAC1/Smad7 0.001 0.091 -9999 0 -0.24 66 66
RANGAP1 0.017 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.014 0.063 -9999 0 -10000 0 0
NuRD/MBD3 Complex -0.009 0.068 -9999 0 -0.19 40 40
NF kappa B1 p50/RelA -0.013 0.069 -9999 0 -0.25 4 4
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.016 0.019 -9999 0 -0.41 1 1
GATA1 0.017 0 -9999 0 -10000 0 0
Mad/Max 0.025 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.007 0.073 -9999 0 -0.19 40 40
RBBP7 0.017 0 -9999 0 -10000 0 0
NPC 0.01 0.009 -9999 0 -0.2 1 1
RBBP4 -0.065 0.17 -9999 0 -0.41 101 101
MAX 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.017 0 -9999 0 -10000 0 0
NFKBIA -0.025 0.068 -9999 0 -0.12 186 186
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.01 0.07 -9999 0 -0.11 150 150
SIN3 complex 0.033 0 -9999 0 -10000 0 0
SMURF1 0.017 0 -9999 0 -10000 0 0
CHD3 0.017 0 -9999 0 -10000 0 0
SAP30 0.017 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.017 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.008 0.056 -9999 0 -10000 0 0
YY1/HDAC2 0.024 0.024 -9999 0 -0.22 5 5
YY1/HDAC1 -0.005 0.082 -9999 0 -0.22 66 66
NuRD/MBD2 Complex (MeCP1) -0.009 0.068 -9999 0 -0.19 40 40
PPARG -0.033 0.088 -9999 0 -0.15 189 189
HDAC8/hEST1B 0.023 0 -9999 0 -10000 0 0
UBE2I 0.017 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A -0.13 0.2 -9999 0 -0.41 183 183
HDAC3/SMRT (N-CoR2) -0.014 0.063 -9999 0 -0.1 185 185
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.001 0.09 -9999 0 -0.24 66 66
CREBBP 0.017 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.011 0.076 -9999 0 -0.2 40 40
HDAC1 -0.036 0.14 -9999 0 -0.41 66 66
HDAC3 -0.025 0.068 -9999 0 -0.12 185 185
HDAC2 0.013 0.042 -9999 0 -0.41 5 5
YY1 0.018 0 -9999 0 -10000 0 0
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0.016 0.019 -9999 0 -0.41 1 1
NCOR2 0.017 0 -9999 0 -10000 0 0
MXD1 0.017 0 -9999 0 -10000 0 0
STAT3 0.019 0.027 -9999 0 -0.18 10 10
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0.019 -9999 0 -0.41 1 1
YY1/LSF/HDAC1 0.006 0.077 -9999 0 -0.2 66 66
YY1/SAP30/HDAC1 0.006 0.077 -9999 0 -0.2 66 66
EP300 0.017 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.027 -9999 0 -0.18 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.068 -9999 0 -0.12 186 186
histone deacetylation -0.009 0.068 -9999 0 -0.19 40 40
STAT3 (dimer non-phopshorylated)/HDAC3 -0.009 0.063 -9999 0 -0.22 10 10
nuclear export -0.023 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A -0.023 0.12 -9999 0 -0.41 49 49
GATA2/HDAC3 -0.014 0.064 -9999 0 -0.2 1 1
GATA1/HDAC1 -0.013 0.1 -9999 0 -0.28 66 66
GATA1/HDAC3 -0.014 0.063 -9999 0 -10000 0 0
CHD4 0.017 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.083 0.15 -9999 0 -0.28 185 185
SIN3/HDAC complex/Mad/Max 0.001 0.059 -9999 0 -0.18 21 21
NuRD Complex -0.007 0.076 -9999 0 -0.2 40 40
positive regulation of chromatin silencing -0.033 0.09 -9999 0 -0.21 69 69
SIN3B 0.017 0 -9999 0 -10000 0 0
MTA2 0.017 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0.017 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.006 0.071 -9999 0 -0.18 66 66
HDAC complex -0.036 0.13 -9999 0 -0.24 150 150
GATA1/Fog1 0.013 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 -0.001 0.094 -9999 0 -0.24 69 69
TNF 0.015 0.026 -9999 0 -0.41 2 2
negative regulation of cell growth 0.001 0.058 -9999 0 -0.18 21 21
NuRD/MBD2/PRMT5 Complex -0.009 0.068 -9999 0 -0.19 40 40
Ran/GTP/Exportin 1 0.034 0.006 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.027 0.084 -9999 0 -0.14 186 186
SIN3/HDAC complex/NCoR1 -0.005 0.064 -9999 0 -0.11 104 104
TFCP2 0.017 0 -9999 0 -10000 0 0
NR2C1 0.017 0 -9999 0 -10000 0 0
MBD3 0.017 0 -9999 0 -10000 0 0
MBD2 0.017 0 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.004 0.085 -10000 0 -0.23 53 53
CRKL 0.001 0.089 -10000 0 -0.24 53 53
HRAS 0.007 0.097 -10000 0 -0.23 53 53
mol:PIP3 -0.008 0.086 0.18 3 -0.24 52 55
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.017 0 -10000 0 -10000 0 0
GAB1 -0.002 0.093 -10000 0 -0.26 53 53
FOXO3 0.004 0.089 -10000 0 -0.24 52 52
AKT1 0 0.095 -10000 0 -0.26 52 52
BAD 0.004 0.089 -10000 0 -0.24 47 47
megakaryocyte differentiation 0.001 0.088 -10000 0 -0.25 49 49
GSK3B 0.005 0.09 -10000 0 -0.24 47 47
RAF1 0.01 0.083 -10000 0 -0.19 52 52
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
STAT3 -0.004 0.095 -10000 0 -0.25 64 64
STAT1 -0.004 0.16 -10000 0 -0.44 53 53
HRAS/SPRED1 0.006 0.082 -10000 0 -0.2 53 53
cell proliferation 0 0.091 -10000 0 -0.24 60 60
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
TEC 0.017 0 -10000 0 -10000 0 0
RPS6KB1 0.002 0.095 -10000 0 -0.26 53 53
HRAS/SPRED2 0.015 0.085 -10000 0 -0.19 52 52
LYN/TEC/p62DOK -0.004 0.11 -10000 0 -0.24 57 57
MAPK3 0.017 0.064 -10000 0 -0.2 12 12
STAP1 -0.001 0.093 -10000 0 -0.25 62 62
GRAP2 0.017 0 -10000 0 -10000 0 0
JAK2 -0.001 0.14 -10000 0 -0.4 53 53
STAT1 (dimer) -0.003 0.15 -10000 0 -0.41 62 62
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.02 0.093 -10000 0 -0.24 53 53
actin filament polymerization -0.004 0.09 -10000 0 -0.25 62 62
LYN -0.035 0.14 -10000 0 -0.41 64 64
STAP1/STAT5A (dimer) 0.004 0.12 -10000 0 -0.33 53 53
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.018 0.087 -10000 0 -0.22 53 53
PI3K 0.007 0.097 -10000 0 -0.25 46 46
PTEN 0.015 0.026 -10000 0 -0.41 2 2
SCF/KIT/EPO/EPOR 0.008 0.17 -10000 0 -0.47 53 53
MAPK8 -0.001 0.092 -10000 0 -0.25 60 60
STAT3 (dimer) -0.004 0.093 -10000 0 -0.24 64 64
positive regulation of transcription 0.017 0.055 -10000 0 -0.17 12 12
mol:GDP 0.006 0.1 -10000 0 -0.24 54 54
PIK3C2B -0.004 0.095 -10000 0 -0.25 63 63
CBL/CRKL 0.01 0.087 -10000 0 -0.23 53 53
FER -0.001 0.092 -10000 0 -0.26 53 53
SH2B3 -0.004 0.097 -10000 0 -0.26 62 62
PDPK1 -0.004 0.081 -10000 0 -0.22 52 52
SNAI2 -0.047 0.12 -10000 0 -0.29 65 65
positive regulation of cell proliferation -0.002 0.14 -10000 0 -0.38 53 53
KITLG 0.018 0.011 -10000 0 -10000 0 0
cell motility -0.002 0.14 -10000 0 -0.38 53 53
PTPN6 0.008 0.062 -10000 0 -0.41 11 11
EPOR 0.024 0.065 -10000 0 -10000 0 0
STAT5A (dimer) 0.003 0.12 -10000 0 -0.33 53 53
SOCS1 0.017 0 -10000 0 -10000 0 0
cell migration 0 0.091 0.25 53 -10000 0 53
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.018 0.005 -10000 0 -10000 0 0
VAV1 0.016 0.019 -10000 0 -0.41 1 1
GRB10 -0.007 0.1 -10000 0 -0.28 53 53
PTPN11 0.017 0.004 -10000 0 -10000 0 0
SCF/KIT -0.004 0.097 -10000 0 -0.26 62 62
GO:0007205 0 0.006 -10000 0 -10000 0 0
MAP2K1 0.013 0.068 -10000 0 -0.22 14 14
CBL 0.017 0 -10000 0 -10000 0 0
KIT 0.032 0.071 -10000 0 -0.41 12 12
MAP2K2 0.013 0.069 -10000 0 -0.22 14 14
SHC/Grb2/SOS1 -0.006 0.11 -10000 0 -0.28 54 54
STAT5A 0.003 0.12 -10000 0 -0.34 53 53
GRB2 0.017 0.002 -10000 0 -10000 0 0
response to radiation -0.046 0.12 -10000 0 -0.28 67 67
SHC/GRAP2 -0.002 0.088 -10000 0 -0.28 47 47
PTPRO 0 0.089 -10000 0 -0.26 49 49
SH2B2 -0.004 0.092 -10000 0 -0.25 62 62
DOK1 0.017 0 -10000 0 -10000 0 0
MATK -0.001 0.092 -10000 0 -0.26 53 53
CREBBP 0.026 0.03 -10000 0 -10000 0 0
BCL2 0.024 0.064 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin -0.03 0.11 -9999 0 -0.24 105 105
EPHB2 0.015 0.026 -9999 0 -0.41 2 2
Syndecan-2/TACI 0.019 0.036 -9999 0 -0.25 8 8
LAMA1 0 0 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.009 0.1 -9999 0 -0.21 106 106
HRAS 0.016 0.019 -9999 0 -0.41 1 1
Syndecan-2/CASK 0.007 0.034 -9999 0 -0.25 8 8
ITGA5 -0.043 0.15 -9999 0 -0.41 74 74
BAX 0.018 0.056 -9999 0 -0.3 14 14
EPB41 0.017 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.032 -9999 0 -0.22 8 8
LAMA3 0.005 0.071 -9999 0 -0.41 15 15
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.041 0.15 -9999 0 -0.41 72 72
Syndecan-2/MMP2 -0.1 0.13 -9999 0 -0.24 254 254
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.029 0.12 -9999 0 -0.28 93 93
dendrite morphogenesis 0.018 0.039 -9999 0 -0.24 10 10
Syndecan-2/GM-CSF 0.019 0.036 -9999 0 -0.25 8 8
determination of left/right symmetry 0.01 0.041 -9999 0 -0.23 13 13
Syndecan-2/PKC delta 0.019 0.036 -9999 0 -0.25 8 8
GNB2L1 0.017 0 -9999 0 -10000 0 0
MAPK3 0.019 0.032 -9999 0 -0.22 8 8
MAPK1 0.018 0.032 -9999 0 -0.22 8 8
Syndecan-2/RACK1 0.027 0.033 -9999 0 -0.2 9 9
NF1 0.017 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.041 -9999 0 -0.23 13 13
ITGA2 -0.058 0.16 -9999 0 -0.41 93 93
MAPK8 0.017 0.042 -9999 0 -0.24 13 13
Syndecan-2/alpha2/beta1 Integrin -0.012 0.091 -9999 0 -0.2 99 99
Syndecan-2/Kininogen 0.018 0.037 -9999 0 -0.25 9 9
ITGB1 0.017 0 -9999 0 -10000 0 0
SRC 0.021 0.03 -9999 0 -0.19 9 9
Syndecan-2/CASK/Protein 4.1 0.017 0.032 -9999 0 -0.22 8 8
extracellular matrix organization 0.006 0.067 -9999 0 -0.24 34 34
actin cytoskeleton reorganization -0.03 0.11 -9999 0 -0.24 105 105
Syndecan-2/Caveolin-2/Ras -0.004 0.091 -9999 0 -0.22 76 76
Syndecan-2/Laminin alpha3 0.012 0.056 -9999 0 -0.24 23 23
Syndecan-2/RasGAP 0.034 0.033 -9999 0 -0.19 9 9
alpha5/beta1 Integrin -0.018 0.11 -9999 0 -0.28 74 74
PRKCD 0.017 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.018 0.039 -9999 0 -0.24 10 10
GO:0007205 0.002 0.01 -9999 0 -0.11 1 1
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.033 0.031 -9999 0 -0.18 9 9
RHOA 0.017 0.001 -9999 0 -10000 0 0
SDCBP 0.017 0 -9999 0 -10000 0 0
TNFRSF13B 0.017 0 -9999 0 -10000 0 0
RASA1 0.017 0.002 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.029 0.12 -9999 0 -0.28 93 93
Syndecan-2/Synbindin 0.019 0.036 -9999 0 -0.25 8 8
TGFB1 -0.005 0.094 -9999 0 -0.41 27 27
CASP3 -0.023 0.093 -9999 0 -0.21 103 103
FN1 -0.065 0.17 -9999 0 -0.41 101 101
Syndecan-2/IL8 -0.037 0.11 -9999 0 -0.24 121 121
SDC2 0.01 0.041 -9999 0 -0.24 13 13
KNG1 0.016 0.019 -9999 0 -0.41 1 1
Syndecan-2/Neurofibromin 0.019 0.036 -9999 0 -0.25 8 8
TRAPPC4 0.017 0.001 -9999 0 -10000 0 0
CSF2 0.017 0 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.006 0.067 -9999 0 -0.24 34 34
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.032 -9999 0 -0.22 8 8
Syndecan-2/Ezrin 0.017 0.032 -9999 0 -0.22 8 8
PRKACA 0.019 0.032 -9999 0 -0.22 8 8
angiogenesis -0.037 0.11 -9999 0 -0.24 121 121
MMP2 -0.19 0.21 -9999 0 -0.41 251 251
IL8 -0.076 0.18 -9999 0 -0.41 115 115
calcineurin-NFAT signaling pathway 0.019 0.036 -9999 0 -0.25 8 8
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.13 0.17 -10000 0 -0.44 52 52
NCK1/PAK1/Dok-R -0.083 0.075 -10000 0 -0.24 47 47
NCK1/Dok-R -0.011 0.11 -10000 0 -0.31 8 8
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
mol:beta2-estradiol 0.012 0.044 0.12 78 -10000 0 78
RELA 0.017 0 -10000 0 -10000 0 0
SHC1 -0.022 0.12 -10000 0 -0.41 47 47
Rac/GDP 0.013 0 -10000 0 -10000 0 0
F2 0.037 0.054 -10000 0 -0.42 2 2
TNIP2 0.008 0.061 -10000 0 -0.41 11 11
NF kappa B/RelA 0.005 0.11 -10000 0 -0.31 10 10
FN1 -0.065 0.17 -10000 0 -0.41 101 101
PLD2 -0.013 0.1 -10000 0 -0.27 46 46
PTPN11 0.017 0 -10000 0 -10000 0 0
GRB14 0.002 0.078 -10000 0 -0.41 18 18
ELK1 -0.003 0.098 -10000 0 -0.26 6 6
GRB7 0.016 0.019 -10000 0 -0.41 1 1
PAK1 0.017 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.055 0.17 -10000 0 -0.4 60 60
CDKN1A -0.16 0.2 -10000 0 -0.47 93 93
ITGA5 -0.043 0.15 -10000 0 -0.41 74 74
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.007 0.1 -10000 0 -0.27 15 15
CRK 0.017 0 -10000 0 -10000 0 0
mol:NO -0.1 0.14 -10000 0 -0.36 52 52
PLG -0.013 0.1 -10000 0 -0.27 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.1 0.15 -10000 0 -0.4 50 50
GRB2 0.017 0.002 -10000 0 -10000 0 0
PIK3R1 0.015 0.004 -10000 0 -10000 0 0
ANGPT2 -0.2 0.21 -10000 0 -0.39 279 279
BMX -0.013 0.1 -10000 0 -0.27 46 46
ANGPT1 -0.038 0.13 -10000 0 -0.34 78 78
tube development -0.16 0.19 0.28 1 -0.44 86 87
ANGPT4 0.012 0.005 -10000 0 -10000 0 0
response to hypoxia -0.006 0.012 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.014 0.11 -10000 0 -0.28 41 41
alpha5/beta1 Integrin -0.018 0.11 -10000 0 -0.28 74 74
FGF2 0.02 0.027 -10000 0 -0.41 2 2
STAT5A (dimer) -0.17 0.22 -10000 0 -0.51 87 87
mol:L-citrulline -0.1 0.14 -10000 0 -0.36 52 52
AGTR1 0.002 0.029 -10000 0 -0.41 2 2
MAPK14 -0.047 0.12 -10000 0 -0.33 39 39
Tie2/SHP2 0.016 0.045 -10000 0 -0.21 1 1
TEK 0.009 0.05 -10000 0 -0.24 1 1
RPS6KB1 -0.1 0.15 -10000 0 -0.4 43 43
Angiotensin II/AT1 -0.006 0.026 -10000 0 -0.29 2 2
Tie2/Ang1/GRB2 -0.006 0.11 -10000 0 -0.28 15 15
MAPK3 -0.009 0.098 -10000 0 -0.26 40 40
MAPK1 -0.01 0.096 -10000 0 -0.26 40 40
Tie2/Ang1/GRB7 -0.007 0.11 -10000 0 -0.28 15 15
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK8 -0.013 0.1 -10000 0 -0.27 46 46
PI3K -0.12 0.16 -10000 0 -0.41 57 57
FES -0.049 0.12 -10000 0 -0.33 39 39
Crk/Dok-R -0.007 0.1 -10000 0 -0.27 15 15
Tie2/Ang1/ABIN2 -0.011 0.11 -10000 0 -0.28 41 41
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.12 0.16 -10000 0 -0.41 52 52
STAT5A 0.016 0.019 -10000 0 -0.41 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.1 0.15 -10000 0 -0.4 43 43
Tie2/Ang2 -0.19 0.23 -10000 0 -0.53 87 87
Tie2/Ang1 -0.016 0.11 -10000 0 -0.29 46 46
FOXO1 -0.14 0.18 -10000 0 -0.43 80 80
ELF1 0.016 0.049 -10000 0 -0.41 7 7
ELF2 -0.015 0.11 -10000 0 -0.28 46 46
mol:Choline -0.012 0.1 -10000 0 -0.27 46 46
cell migration -0.064 0.057 -10000 0 -0.16 101 101
FYN -0.17 0.2 -10000 0 -0.48 86 86
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.14 0.19 -10000 0 -0.44 88 88
ETS1 0.008 0.047 -10000 0 -10000 0 0
PXN -0.089 0.14 -10000 0 -0.36 42 42
ITGB1 0.017 0 -10000 0 -10000 0 0
NOS3 -0.11 0.16 -10000 0 -0.4 52 52
RAC1 0.017 0 -10000 0 -10000 0 0
TNF 0.002 0.053 -10000 0 -0.41 2 2
MAPKKK cascade -0.012 0.1 -10000 0 -0.27 46 46
RASA1 0.017 0.002 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.031 0.12 -10000 0 -0.32 43 43
NCK1 0.008 0.061 -10000 0 -0.41 11 11
vasculogenesis -0.097 0.14 -10000 0 -0.33 52 52
mol:Phosphatidic acid -0.012 0.1 -10000 0 -0.27 46 46
mol:Angiotensin II -0.009 0.01 -10000 0 -10000 0 0
mol:NADP -0.1 0.14 -10000 0 -0.36 52 52
Rac1/GTP -0.099 0.14 -10000 0 -0.38 43 43
MMP2 -0.11 0.14 -10000 0 -0.37 61 61
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.017 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.023 0.063 -9999 0 -0.21 25 25
Syndecan-3/Neurocan 0.003 0.062 -9999 0 -0.2 37 37
POMC 0.017 0 -9999 0 -10000 0 0
EGFR -0.14 0.21 -9999 0 -0.41 194 194
Syndecan-3/EGFR -0.073 0.12 -9999 0 -0.21 219 219
AGRP 0.017 0 -9999 0 -10000 0 0
NCSTN -0.007 0.099 -9999 0 -0.41 30 30
PSENEN 0.017 0.001 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.017 0 -9999 0 -10000 0 0
APH1A 0.008 0.061 -9999 0 -0.41 11 11
NCAN 0.013 0.027 -9999 0 -0.41 2 2
long-term memory 0.014 0.065 -9999 0 -0.22 30 30
Syndecan-3/IL8 -0.042 0.11 -9999 0 -0.21 145 145
PSEN1 0.016 0.019 -9999 0 -0.41 1 1
Src/Cortactin 0.025 0 -9999 0 -10000 0 0
FYN 0.015 0.026 -9999 0 -0.41 2 2
limb bud formation 0.001 0.058 -9999 0 -0.26 21 21
MC4R 0.016 0.019 -9999 0 -0.41 1 1
SRC 0.017 0 -9999 0 -10000 0 0
PTN 0.016 0.004 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-3 0.001 0.059 -9999 0 -0.26 21 21
neuron projection morphogenesis 0.016 0.05 -9999 0 -0.23 12 12
Syndecan-3/AgRP 0.003 0.073 -9999 0 -0.25 36 36
Syndecan-3/AgRP/MC4R 0.013 0.073 -9999 0 -0.24 37 37
Fyn/Cortactin 0.023 0.02 -9999 0 -0.28 2 2
SDC3 0.001 0.059 -9999 0 -0.26 21 21
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.041 0.11 -9999 0 -0.21 145 145
IL8 -0.076 0.18 -9999 0 -0.41 115 115
Syndecan-3/Fyn/Cortactin 0.014 0.066 -9999 0 -0.23 30 30
Syndecan-3/CASK -0.007 0.071 -9999 0 -0.25 36 36
alpha-MSH/MC4R 0.025 0.013 -9999 0 -0.28 1 1
Gamma Secretase 0.032 0.068 -9999 0 -0.2 40 40
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.04 -10000 0 -0.23 12 12
fibroblast growth factor receptor signaling pathway 0.028 0.04 -10000 0 -0.23 12 12
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.016 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 0.012 0.037 -10000 0 -0.22 11 11
SMAD2 0.018 0.038 -10000 0 -0.21 15 15
GPC1/PrPc/Cu2+ 0.018 0.032 -10000 0 -0.24 8 8
GPC1/Laminin alpha1 0.008 0.037 -10000 0 -0.29 8 8
TDGF1 0.015 0.026 -10000 0 -0.41 2 2
CRIPTO/GPC1 0.02 0.042 -10000 0 -0.28 10 10
APP/GPC1 0.021 0.038 -10000 0 -0.28 8 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.022 0.1 -10000 0 -0.24 86 86
FLT1 0.017 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.027 0.045 -10000 0 -0.23 15 15
SERPINC1 0.016 0.019 -10000 0 -0.41 1 1
FYN 0.015 0.038 -10000 0 -0.23 12 12
FGR 0.009 0.056 -10000 0 -0.23 27 27
positive regulation of MAPKKK cascade -0.022 0.095 -10000 0 -0.22 77 77
SLIT2 0.009 0.033 -10000 0 -0.41 3 3
GPC1/NRG 0.021 0.038 -10000 0 -0.28 8 8
NRG1 0.017 0 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.11 0.14 -10000 0 -0.24 289 289
LYN -0.014 0.09 -10000 0 -0.24 73 73
mol:Spermine 0.004 0.036 -10000 0 -0.29 8 8
cell growth 0.028 0.04 -10000 0 -0.23 12 12
BMP signaling pathway -0.011 0.052 0.41 8 -10000 0 8
SRC 0.017 0.035 -10000 0 -0.23 10 10
TGFBR1 0.017 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.21 -10000 0 -0.41 191 191
GPC1 0.011 0.052 -10000 0 -0.41 8 8
TGFBR1 (dimer) 0.017 0 -10000 0 -10000 0 0
VEGFA -0.22 0.21 -10000 0 -0.41 286 286
BLK 0.017 0.035 -10000 0 -0.23 10 10
HCK -0.025 0.1 -10000 0 -0.24 95 95
FGF2 0.015 0.026 -10000 0 -0.41 2 2
FGFR1 0.015 0.026 -10000 0 -0.41 2 2
VEGFR1 homodimer 0.017 0 -10000 0 -10000 0 0
TGFBR2 0.011 0.049 -10000 0 -0.41 7 7
cell death 0.021 0.038 -10000 0 -0.28 8 8
ATIII/GPC1 0.02 0.04 -10000 0 -0.28 9 9
PLA2G2A/GPC1 -0.091 0.15 -10000 0 -0.29 196 196
LCK 0.015 0.043 -10000 0 -0.25 13 13
neuron differentiation 0.021 0.038 -10000 0 -0.28 8 8
PrPc/Cu2+ 0.012 0.003 -10000 0 -10000 0 0
APP 0.017 0.001 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.011 0.049 -10000 0 -0.41 7 7
S1P3 pathway

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
PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
mol:S1P 0.001 0.001 -9999 0 -0.015 1 1
S1P1/S1P/Gi -0.015 0.052 -9999 0 -0.15 62 62
GNAO1 0.002 0.005 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.021 0.025 -9999 0 -0.21 6 6
AKT1 0 0.02 -9999 0 -0.16 7 7
AKT3 -0.058 0.065 -9999 0 -0.18 36 36
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
GNAI2 0.018 0.002 -9999 0 -10000 0 0
GNAI3 -0.035 0.14 -9999 0 -0.41 65 65
GNAI1 0.015 0.02 -9999 0 -0.41 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.001 -9999 0 -0.022 1 1
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.017 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.016 -9999 0 -0.13 4 4
MAPK3 0.002 0.015 -9999 0 -0.23 1 1
MAPK1 0.002 0.015 -9999 0 -0.23 1 1
JAK2 -0.074 0.081 -9999 0 -0.15 262 262
CXCR4 -0.11 0.11 -9999 0 -0.21 273 273
FLT1 0.019 0.002 -9999 0 -10000 0 0
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.002 0.015 -9999 0 -0.23 1 1
S1P/S1P3/Gi 0.002 0.016 -9999 0 -0.13 4 4
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.011 0.039 -9999 0 -0.16 13 13
VEGFA -0.21 0.21 -9999 0 -0.41 286 286
S1P/S1P2/Gi 0.001 0.014 -9999 0 -0.12 4 4
VEGFR1 homodimer/VEGFA homodimer -0.14 0.16 -9999 0 -0.28 286 286
RHOA 0.017 0.001 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.019 -9999 0 -0.13 9 9
GNAQ 0.017 0 -9999 0 -10000 0 0
GNAZ 0.016 0.006 -9999 0 -10000 0 0
G12/G13 0.022 0.033 -9999 0 -0.28 6 6
GNA14 0.015 0.026 -9999 0 -0.41 2 2
GNA15 0.011 0.049 -9999 0 -0.41 7 7
GNA12 0.014 0.037 -9999 0 -0.41 4 4
GNA13 0.015 0.026 -9999 0 -0.41 2 2
GNA11 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.011 0.039 -9999 0 -0.16 13 13
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.086 0.18 -9999 0 -0.41 127 127
SMAD2 0.013 0.02 -9999 0 -0.12 2 2
SMAD3 0.018 0.04 -9999 0 -0.12 37 37
SMAD3/SMAD4 0.001 0.068 -9999 0 -0.23 10 10
SMAD4/Ubc9/PIASy -0.03 0.12 -9999 0 -0.23 127 127
SMAD2/SMAD2/SMAD4 -0.01 0.1 -9999 0 -0.19 123 123
PPM1A 0.017 0 -9999 0 -10000 0 0
CALM1 0.016 0.004 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.032 0.097 -9999 0 -0.2 127 127
MAP3K1 0.016 0.019 -9999 0 -0.41 1 1
TRAP-1/SMAD4 -0.049 0.13 -9999 0 -0.28 127 127
MAPK3 0.017 0 -9999 0 -10000 0 0
MAPK1 0.017 0.003 -9999 0 -10000 0 0
NUP214 0.017 0 -9999 0 -10000 0 0
CTDSP1 0.015 0.032 -9999 0 -0.41 3 3
CTDSP2 -0.013 0.11 -9999 0 -0.41 37 37
CTDSPL 0.017 0 -9999 0 -10000 0 0
KPNB1 0.017 0 -9999 0 -10000 0 0
TGFBRAP1 0.017 0 -9999 0 -10000 0 0
UBE2I 0.017 0 -9999 0 -10000 0 0
NUP153 0.015 0.026 -9999 0 -0.41 2 2
KPNA2 0.007 0.064 -9999 0 -0.41 12 12
PIAS4 0.017 0 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.03 0.003 -10000 0 -10000 0 0
ER alpha/Gai/GDP/Gbeta gamma -0.063 0.064 -10000 0 -0.2 63 63
AKT1 0.007 0.03 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.005 0.03 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.018 -10000 0 -0.14 2 2
IGF1R 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.023 0 -10000 0 -10000 0 0
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
apoptosis -0.007 0.03 -10000 0 -10000 0 0
RhoA/GTP -0.044 0.074 -10000 0 -0.17 135 135
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.047 0.046 -10000 0 -0.15 49 49
regulation of stress fiber formation 0.13 0.11 0.29 96 -0.21 1 97
E2/ERA-ERB (dimer) 0.023 0 -10000 0 -10000 0 0
KRAS 0.017 0.002 -10000 0 -10000 0 0
G13/GTP 0.021 0.015 -10000 0 -0.22 2 2
pseudopodium formation -0.13 0.11 0.21 1 -0.29 96 97
E2/ER alpha (dimer)/PELP1 0.023 0 -10000 0 -10000 0 0
GRB2 0.017 0.002 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.002 0.005 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.03 0.037 -10000 0 -0.16 8 8
E2/ER beta (dimer) 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.006 0.052 -10000 0 -0.2 2 2
mol:NADP -0.03 0.037 -10000 0 -0.16 8 8
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 0.03 0.018 -10000 0 -0.14 2 2
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
PLCB1 0.028 0.019 -10000 0 -0.15 2 2
PLCB2 0.028 0.019 -10000 0 -0.15 2 2
IGF1 0.014 0.037 -10000 0 -0.41 4 4
mol:L-citrulline -0.03 0.037 -10000 0 -0.16 8 8
RHOA 0.017 0.001 -10000 0 -10000 0 0
Gai/GDP -0.42 0.15 -10000 0 -0.46 481 481
JNK cascade 0.013 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.017 0 -10000 0 -10000 0 0
GNAQ 0.017 0 -10000 0 -10000 0 0
ESR1 0.017 0 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.026 0.026 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.008 0.067 -10000 0 -0.48 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.059 0.074 -10000 0 -0.24 56 56
GNAZ 0.015 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.013 0 -10000 0 -10000 0 0
STRN 0.017 0 -10000 0 -10000 0 0
GNAL 0.017 0 -10000 0 -10000 0 0
PELP1 0.017 0 -10000 0 -10000 0 0
MAPK11 0.016 0 -10000 0 -10000 0 0
GNAI2 0.017 0.001 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNAI1 0.014 0.02 -10000 0 -0.41 1 1
HBEGF -0.16 0.1 -10000 0 -0.22 327 327
cAMP biosynthetic process 0.02 0 -10000 0 -10000 0 0
SRC -0.059 0.062 -10000 0 -0.19 66 66
PI3K 0.009 0.065 -10000 0 -0.28 25 25
GNB1 0.017 0.002 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.002 0.05 -10000 0 -0.21 2 2
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.05 0.061 -10000 0 -0.2 58 58
Gs family/GTP 0.025 0 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.03 0.11 -10000 0 -0.21 134 134
vasodilation -0.03 0.036 -10000 0 -0.15 8 8
mol:DAG 0.03 0.018 -10000 0 -0.14 2 2
Gs family/GDP/Gbeta gamma -0.02 0.034 -10000 0 -0.22 1 1
MSN -0.14 0.11 0.21 1 -0.32 96 97
Gq family/GTP 0.028 0.02 -10000 0 -0.16 2 2
mol:PI-3-4-5-P3 0.005 0.03 -10000 0 -10000 0 0
NRAS -0.094 0.19 -10000 0 -0.41 137 137
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.03 0.036 0.15 8 -10000 0 8
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
RhoA/GDP 0.002 0.053 -10000 0 -0.24 1 1
NOS3 -0.031 0.038 -10000 0 -0.18 3 3
GNA11 0.017 0 -10000 0 -10000 0 0
MAPKKK cascade -0.015 0.047 -10000 0 -0.2 9 9
E2/ER alpha (dimer)/PELP1/Src -0.048 0.048 -10000 0 -0.16 49 49
ruffle organization -0.13 0.11 0.21 1 -0.29 96 97
ROCK2 -0.018 0.083 0.22 1 -0.33 1 2
GNA14 0.015 0.026 -10000 0 -0.41 2 2
GNA15 0.011 0.049 -10000 0 -0.41 7 7
GNA13 0.015 0.026 -10000 0 -0.41 2 2
MMP9 -0.13 0.11 -10000 0 -0.24 229 229
MMP2 -0.15 0.12 -10000 0 -0.25 286 286
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.02 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 + -0.068 0.12 -9999 0 -0.24 184 184
mol:ADP 0 0 -9999 0 -10000 0 0
GNAT2 0.017 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.003 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0 -9999 0 -10000 0 0
GRK7 0 0 -9999 0 -10000 0 0
CNGB3 0.017 0 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.06 0.11 -9999 0 -0.21 184 184
Cone PDE6 0.04 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II 0 0 -9999 0 -10000 0 0
Na + (4 Units) -0.052 0.12 -9999 0 -0.21 184 184
GNAT2/GDP 0.03 0.003 -9999 0 -10000 0 0
GNB5 0.017 0.002 -9999 0 -10000 0 0
mol:GMP (4 units) 0.02 0 -9999 0 -10000 0 0
Cone Transducin 0.022 0 -9999 0 -10000 0 0
SLC24A2 0.017 0 -9999 0 -10000 0 0
GNB3/GNGT2 0.013 0 -9999 0 -10000 0 0
GNB3 0.017 0 -9999 0 -10000 0 0
GNAT2/GTP 0.013 0 -9999 0 -10000 0 0
CNGA3 -0.13 0.2 -9999 0 -0.41 184 184
ARR3 0.017 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.068 0.12 -9999 0 -0.24 184 184
mol:Pi 0.023 0.003 -9999 0 -10000 0 0
Cone CNG Channel -0.036 0.11 -9999 0 -0.18 184 184
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.017 0 -9999 0 -10000 0 0
RGS9 0.017 0 -9999 0 -10000 0 0
PDE6C 0.017 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 0.017 0 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.011 0.096 -9999 0 -0.37 31 31
MKNK1 0.017 0 -9999 0 -10000 0 0
MAPK14 0.015 0.049 -9999 0 -0.17 31 31
ATF2/c-Jun 0.027 0.034 -9999 0 -0.39 1 1
MAPK11 0.017 0.042 -9999 0 -0.16 29 29
MITF 0.021 0.046 -9999 0 -0.16 33 33
MAPKAPK5 0.022 0.044 -9999 0 -0.15 31 31
KRT8 0.011 0.069 -9999 0 -0.19 53 53
MAPKAPK3 0.015 0.026 -9999 0 -0.41 2 2
MAPKAPK2 0.017 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.022 0.059 -9999 0 -0.21 31 31
CEBPB 0.018 0.06 -9999 0 -0.19 36 36
SLC9A1 0.022 0.044 -9999 0 -0.15 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.025 0.045 -9999 0 -0.15 32 32
p38alpha-beta/MNK1 0.033 0.048 -9999 0 -0.16 31 31
JUN 0.025 0.034 -9999 0 -0.39 1 1
PPARGC1A 0.021 0.048 -9999 0 -0.16 33 33
USF1 0.015 0.044 -9999 0 -0.16 31 31
RAB5/GDP/GDI1 0.021 0.033 -9999 0 -0.13 9 9
NOS2 0.014 0.044 -9999 0 -0.16 31 31
DDIT3 0.006 0.074 -9999 0 -0.18 67 67
RAB5A 0.017 0 -9999 0 -10000 0 0
HSPB1 0.016 0.05 -9999 0 -0.24 10 10
p38alpha-beta/HBP1 0.033 0.048 -9999 0 -0.16 31 31
CREB1 0.026 0.043 -9999 0 -0.14 31 31
RAB5/GDP 0.013 0 -9999 0 -10000 0 0
EIF4E 0.02 0.043 -9999 0 -0.14 35 35
RPS6KA4 0.022 0.044 -9999 0 -0.15 31 31
PLA2G4A -0.044 0.12 -9999 0 -0.23 144 144
GDI1 0.023 0.039 -9999 0 -0.16 23 23
TP53 -0.005 0.078 -9999 0 -0.17 95 95
RPS6KA5 0.022 0.044 -9999 0 -0.15 31 31
ESR1 0.022 0.044 -9999 0 -0.15 31 31
HBP1 0.017 0 -9999 0 -10000 0 0
MEF2C 0.02 0.039 -9999 0 -0.16 22 22
MEF2A 0.022 0.044 -9999 0 -0.15 31 31
EIF4EBP1 -0.009 0.057 -9999 0 -0.19 31 31
KRT19 0.011 0.068 -9999 0 -0.18 54 54
ELK4 0.022 0.044 -9999 0 -0.15 31 31
ATF6 0.022 0.044 -9999 0 -0.15 31 31
ATF1 0.022 0.047 -9999 0 -0.16 31 31
p38alpha-beta/MAPKAPK2 0.033 0.048 -9999 0 -0.16 31 31
p38alpha-beta/MAPKAPK3 0.032 0.051 -9999 0 -0.16 33 33
Nongenotropic Androgen signaling

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
PTK2 0.009 0.001 -10000 0 -10000 0 0
GNB1/GNG2 0.018 0.029 -10000 0 -0.22 8 8
regulation of S phase of mitotic cell cycle 0.014 0.038 -10000 0 -0.13 32 32
GNAO1 0.002 0.005 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
SHBG/T-DHT 0.012 0 -10000 0 -10000 0 0
PELP1 0.017 0.001 -10000 0 -10000 0 0
AKT1 0.007 0.026 -10000 0 -0.29 4 4
MAP2K1 0.005 0.044 -10000 0 -0.18 10 10
T-DHT/AR 0.008 0.037 -10000 0 -0.29 8 8
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.005 127 127
GNAI2 0.017 0.001 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNAI1 0.014 0.019 -10000 0 -0.41 1 1
mol:GDP -0.007 0.036 -10000 0 -0.14 31 31
cell proliferation -0.011 0.096 -10000 0 -0.21 22 22
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
FOS -0.046 0.15 -10000 0 -0.32 125 125
mol:Ca2+ 0 0.006 -10000 0 -0.047 8 8
MAPK3 -0.003 0.073 -10000 0 -0.24 5 5
MAPK1 -0.011 0.07 -10000 0 -0.23 21 21
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.001 0.001 -10000 0 -0.003 127 127
cAMP biosynthetic process 0.001 0.005 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.001 -10000 0 -0.003 127 127
HRAS/GTP 0.018 0.037 -10000 0 -0.2 9 9
actin cytoskeleton reorganization 0.015 0.044 -10000 0 -0.18 24 24
SRC 0.017 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.001 -10000 0 -0.003 127 127
PI3K 0.01 0.055 -10000 0 -0.23 25 25
apoptosis 0.018 0.098 0.19 127 -10000 0 127
T-DHT/AR/PELP1 0.018 0.032 -10000 0 -0.24 8 8
HRAS/GDP 0.012 0.039 -10000 0 -0.17 14 14
CREB1 -0.019 0.1 -10000 0 -0.2 125 125
RAC1-CDC42/GTP 0.021 0.046 -10000 0 -0.18 24 24
AR 0.01 0.053 -10000 0 -0.41 8 8
GNB1 0.017 0.002 -10000 0 -10000 0 0
RAF1 0.009 0.04 -10000 0 -0.19 10 10
RAC1-CDC42/GDP 0.023 0.039 -10000 0 -0.19 8 8
T-DHT/AR/PELP1/Src 0.027 0.031 -10000 0 -0.22 8 8
MAP2K2 0.006 0.045 -10000 0 -0.18 10 10
T-DHT/AR/PELP1/Src/PI3K 0.014 0.038 -10000 0 -0.13 32 32
GNAZ 0.015 0.006 -10000 0 -10000 0 0
SHBG 0.017 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.059 0.063 -10000 0 -0.19 65 65
mol:T-DHT 0 0.001 -10000 0 -0.002 107 107
RAC1 0.017 0 -10000 0 -10000 0 0
GNRH1 0.009 0 -10000 0 -10000 0 0
Gi family/GTP -0.001 0.021 -10000 0 -0.15 8 8
CDC42 0.017 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.017 0 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.003 -10000 0 -10000 0 0
DOCK1 0.017 0 -10000 0 -10000 0 0
ITGA4 0.013 0.042 -10000 0 -0.41 5 5
RAC1 0.017 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.022 0.041 -10000 0 -0.38 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.017 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.032 0.026 -10000 0 -0.23 5 5
alpha4/beta7 Integrin/Paxillin 0.032 0.033 -10000 0 -0.29 5 5
lamellipodium assembly 0.018 0.05 -10000 0 -0.26 1 1
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
PI3K 0.009 0.065 -10000 0 -0.28 25 25
ARF6 0.017 0 -10000 0 -10000 0 0
TLN1 -0.02 0.12 -10000 0 -0.41 46 46
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.021 -10000 0 -0.17 5 5
cell adhesion 0.021 0.07 -10000 0 -0.19 50 50
CRKL/CBL 0.025 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.033 0.023 -10000 0 -0.21 5 5
ITGB1 0.017 0 -10000 0 -10000 0 0
ITGB7 0.015 0.026 -10000 0 -0.41 2 2
ARF6/GDP 0.013 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.11 0.11 -10000 0 -0.19 353 353
p130Cas/Crk/Dock1 0.023 0 -10000 0 -10000 0 0
VCAM1 -0.27 0.2 -10000 0 -0.41 351 351
alpha4/beta1 Integrin/Paxillin/Talin 0.022 0.071 -10000 0 -0.2 50 50
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.023 -10000 0 -0.19 5 5
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.041 0.022 0.19 5 -10000 0 5
CBL 0.017 0 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
GIT1 0.017 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.022 0.071 -10000 0 -0.2 50 50
Rac1/GTP 0.018 0.053 -10000 0 -0.28 1 1
EPO signaling pathway

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
BCL2L1 0.033 0.072 -10000 0 -0.24 18 18
CRKL 0.027 0.04 -10000 0 -0.17 19 19
mol:DAG 0.017 0.076 -10000 0 -0.17 64 64
HRAS 0.015 0.068 -10000 0 -0.3 8 8
MAPK8 -0.001 0.079 -10000 0 -0.22 64 64
RAP1A 0.027 0.04 -10000 0 -0.17 19 19
GAB1 0.026 0.043 -10000 0 -0.17 23 23
MAPK14 -0.002 0.08 -10000 0 -0.22 66 66
EPO 0.019 0.007 -10000 0 -10000 0 0
PLCG1 0.017 0.077 -10000 0 -0.18 64 64
EPOR/TRPC2/IP3 Receptors 0.019 0.007 -10000 0 -10000 0 0
RAPGEF1 0.017 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.038 0.006 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.017 0.073 -10000 0 -0.18 52 52
EPO/EPOR (dimer) 0.028 0.011 -10000 0 -10000 0 0
IRS2 0.027 0.039 -10000 0 -0.17 18 18
STAT1 0.019 0.088 -10000 0 -0.18 76 76
STAT5B 0.021 0.077 -10000 0 -0.17 64 64
cell proliferation -0.001 0.074 -10000 0 -0.2 66 66
GAB1/SHIP/PIK3R1/SHP2/SHC 0.012 0.065 -10000 0 -0.3 8 8
TEC 0.027 0.04 -10000 0 -0.17 19 19
SOCS3 0.017 0 -10000 0 -10000 0 0
STAT1 (dimer) 0.019 0.087 -10000 0 -0.18 76 76
JAK2 0.018 0.007 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.053 0.047 -10000 0 -0.18 19 19
EPO/EPOR 0.028 0.011 -10000 0 -10000 0 0
LYN -0.033 0.14 -10000 0 -0.41 64 64
TEC/VAV2 0.038 0.04 -10000 0 -0.16 19 19
elevation of cytosolic calcium ion concentration 0.018 0.007 -10000 0 -10000 0 0
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
EPO/EPOR (dimer)/LYN 0.009 0.096 -10000 0 -0.25 64 64
mol:IP3 0.017 0.076 -10000 0 -0.17 64 64
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.036 -10000 0 -0.16 15 15
SH2B3 0.01 0.059 -10000 0 -0.41 10 10
NFKB1 -0.003 0.084 -10000 0 -0.22 66 66
EPO/EPOR (dimer)/JAK2/SOCS3 0.017 0.02 0.16 10 -10000 0 10
PTPN6 0.024 0.041 -10000 0 -0.18 19 19
TEC/VAV2/GRB2 0.045 0.04 -10000 0 -0.3 2 2
EPOR 0.019 0.007 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.073 -10000 0 -0.18 52 52
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.009 0.058 -10000 0 -0.41 10 10
CRKL/CBL/C3G 0.046 0.04 -10000 0 -0.3 2 2
VAV2 0.027 0.04 -10000 0 -0.17 19 19
CBL 0.027 0.04 -10000 0 -0.17 19 19
SHC/Grb2/SOS1 0.008 0.071 -10000 0 -0.18 59 59
STAT5A 0.021 0.078 -10000 0 -0.17 65 65
GRB2 0.017 0.002 -10000 0 -10000 0 0
STAT5 (dimer) 0.038 0.083 -10000 0 -0.3 13 13
LYN/PLCgamma2 -0.016 0.12 -10000 0 -0.32 65 65
PTPN11 0.017 0 -10000 0 -10000 0 0
BTK 0.027 0.042 -10000 0 -0.18 19 19
BCL2 0.033 0.072 -10000 0 -0.24 18 18
Signaling events mediated by PRL

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
CCNE1 0.011 0.049 -10000 0 -0.41 7 7
mol:Halofuginone 0.004 0.015 -10000 0 -0.17 4 4
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.009 0.052 -10000 0 -0.14 54 54
PRL-3/alpha Tubulin 0.007 0.073 -10000 0 -0.28 31 31
mol:Ca2+ 0.009 0.052 0.22 31 -10000 0 31
AGT 0.016 0.005 -10000 0 -10000 0 0
CCNA2 -0.038 0.1 -10000 0 -0.2 148 148
TUBA1B 0.017 0 -10000 0 -10000 0 0
EGR1 0.011 0.051 -10000 0 -0.28 16 16
CDK2/Cyclin E1 0.012 0.076 -10000 0 -0.21 35 35
MAPK3 0 0.071 -10000 0 -0.28 31 31
PRL-2 /Rab GGTase beta 0.025 0.001 -10000 0 -10000 0 0
MAPK1 -0.001 0.071 -10000 0 -0.28 31 31
PTP4A1 0.015 0.044 -10000 0 -0.21 19 19
PTP4A3 -0.008 0.1 -10000 0 -0.41 31 31
PTP4A2 0.017 0.001 -10000 0 -10000 0 0
ITGB1 0 0.071 -10000 0 -0.28 31 31
SRC 0.017 0 -10000 0 -10000 0 0
RAC1 0.015 0.042 -10000 0 -0.14 32 32
Rab GGTase beta/Rab GGTase alpha 0.025 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.024 0.043 -10000 0 -0.19 20 20
RABGGTA 0.017 0 -10000 0 -10000 0 0
BCAR1 0.002 0.051 0.21 31 -10000 0 31
RHOC -0.032 0.081 -10000 0 -0.14 185 185
RHOA 0.015 0.042 -10000 0 -0.14 32 32
cell motility -0.004 0.055 -10000 0 -0.21 13 13
PRL-1/alpha Tubulin 0.024 0.042 -10000 0 -0.19 19 19
PRL-3/alpha1 Integrin -0.005 0.071 -10000 0 -0.29 31 31
ROCK1 -0.004 0.055 -10000 0 -0.2 14 14
RABGGTB 0.017 0 -10000 0 -10000 0 0
CDK2 -0.005 0.094 -10000 0 -0.41 27 27
mitosis 0.015 0.044 -10000 0 -0.21 19 19
ATF5 0.016 0.019 -10000 0 -0.41 1 1
Arf6 downstream 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
PLAUR -0.006 0.12 -10000 0 -0.38 47 47
regulation of axonogenesis -0.013 0.029 0.13 3 -10000 0 3
myoblast fusion -0.002 0.062 0.2 47 -10000 0 47
mol:GTP 0.001 0.041 -10000 0 -0.13 47 47
regulation of calcium-dependent cell-cell adhesion -0.016 0.041 0.12 45 -10000 0 45
ARF1/GTP 0.014 0.033 -10000 0 -10000 0 0
mol:GM1 0 0.03 -10000 0 -0.095 47 47
mol:Choline 0.011 0.03 -10000 0 -0.22 2 2
lamellipodium assembly 0.001 0.063 -10000 0 -0.2 47 47
MAPK3 0.007 0.059 -10000 0 -0.18 47 47
ARF6/GTP/NME1/Tiam1 0.016 0.041 -10000 0 -0.12 45 45
ARF1 0.017 0.001 -10000 0 -10000 0 0
ARF6/GDP 0.002 0.062 -10000 0 -0.2 47 47
ARF1/GDP 0.01 0.058 -10000 0 -0.18 47 47
ARF6 0.011 0.027 -10000 0 -10000 0 0
RAB11A 0.017 0.001 -10000 0 -10000 0 0
TIAM1 0.015 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.059 -10000 0 -0.18 47 47
actin filament bundle formation -0.012 0.059 0.18 47 -10000 0 47
KALRN 0.003 0.049 -10000 0 -0.15 47 47
RAB11FIP3/RAB11A 0.025 0.001 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.059 -10000 0 -0.18 47 47
NME1 -0.001 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.059 -10000 0 -0.18 47 47
substrate adhesion-dependent cell spreading 0.001 0.041 -10000 0 -0.13 47 47
cortical actin cytoskeleton organization 0.001 0.063 -10000 0 -0.2 47 47
RAC1 0.017 0 -10000 0 -10000 0 0
liver development 0.001 0.041 -10000 0 -0.13 47 47
ARF6/GTP 0.001 0.041 -10000 0 -0.13 47 47
RhoA/GTP 0.014 0.033 -10000 0 -10000 0 0
mol:GDP -0.001 0.062 -10000 0 -0.2 47 47
ARF6/GTP/RAB11FIP3/RAB11A 0.025 0.03 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
PLD1 0.009 0.035 -10000 0 -0.26 2 2
RAB11FIP3 0.017 0 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.063 -10000 0 -0.2 47 47
ruffle organization 0.013 0.029 -10000 0 -0.13 3 3
regulation of epithelial cell migration 0.001 0.041 -10000 0 -0.13 47 47
PLD2 0.01 0.031 -10000 0 -10000 0 0
PIP5K1A 0.013 0.029 -10000 0 -0.13 3 3
mol:Phosphatidic acid 0.011 0.03 -10000 0 -0.22 2 2
Rac1/GTP 0.001 0.063 -10000 0 -0.2 47 47
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.022 0.005 -10000 0 -10000 0 0
NFATC2 0.041 0.11 -10000 0 -0.28 16 16
NFATC3 0.03 0.086 0.19 4 -0.18 3 7
CD40LG -0.038 0.18 -10000 0 -0.39 57 57
ITCH 0.026 0.037 -10000 0 -0.17 17 17
CBLB 0.026 0.034 -10000 0 -0.16 16 16
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.004 0.12 -10000 0 -0.35 15 15
JUNB 0.011 0.052 -10000 0 -0.41 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.043 -10000 0 -0.21 16 16
T cell anergy 0.012 0.053 -10000 0 -0.22 18 18
TLE4 0.031 0.072 -10000 0 -0.22 5 5
Jun/NFAT1-c-4/p21SNFT 0.028 0.16 -10000 0 -0.31 25 25
AP-1/NFAT1-c-4 -0.022 0.22 -10000 0 -0.46 46 46
IKZF1 0.031 0.072 -10000 0 -0.24 3 3
T-helper 2 cell differentiation 0.019 0.092 -10000 0 -0.32 1 1
AP-1/NFAT1 -0.029 0.14 -10000 0 -0.25 103 103
CALM1 0.022 0.026 -10000 0 -10000 0 0
EGR2 0.075 0.14 0.3 74 -0.37 14 88
EGR3 0.083 0.12 0.3 74 -0.34 4 78
NFAT1/FOXP3 0.042 0.082 -10000 0 -0.19 12 12
EGR1 0.006 0.071 -10000 0 -0.41 15 15
JUN 0.013 0.028 -10000 0 -0.4 1 1
EGR4 0.018 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.029 -10000 0 -0.14 20 20
GBP3 0.024 0.069 -10000 0 -0.19 14 14
FOSL1 0.007 0.066 -10000 0 -0.41 13 13
NFAT1-c-4/MAF/IRF4 0.033 0.15 -10000 0 -0.28 21 21
DGKA 0.031 0.072 -10000 0 -0.19 12 12
CREM 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.022 0.16 -10000 0 -0.3 26 26
CTLA4 0.037 0.055 -10000 0 -0.19 3 3
NFAT1-c-4 (dimer)/EGR1 0.022 0.16 -10000 0 -0.31 27 27
NFAT1-c-4 (dimer)/EGR4 0.028 0.16 -10000 0 -0.29 24 24
FOS -0.087 0.18 -10000 0 -0.42 125 125
IFNG 0.019 0.08 -10000 0 -0.21 9 9
T cell activation -0.003 0.11 -10000 0 -0.35 3 3
MAF 0.017 0.019 -10000 0 -0.41 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.083 0.13 0.32 6 -0.3 74 80
TNF 0.016 0.14 -10000 0 -0.32 11 11
FASLG -0.013 0.21 -10000 0 -0.38 81 81
TBX21 0.022 0.004 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.02 0.001 -10000 0 -10000 0 0
PTPN1 0.031 0.072 -10000 0 -0.19 12 12
NFAT1-c-4/ICER1 0.022 0.16 -10000 0 -0.3 24 24
GATA3 0.016 0.042 -10000 0 -0.41 5 5
T-helper 1 cell differentiation 0.019 0.08 -10000 0 -0.21 8 8
IL2RA 0.003 0.13 -10000 0 -0.37 15 15
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.024 0.16 -10000 0 -0.34 98 98
E2F1 -0.059 0.062 -10000 0 -10000 0 0
PPARG 0.013 0.041 -10000 0 -0.41 5 5
SLC3A2 0.025 0.093 -10000 0 -0.32 18 18
IRF4 0.017 0.019 -10000 0 -0.41 1 1
PTGS2 -0.049 0.2 -10000 0 -0.49 51 51
CSF2 -0.038 0.18 -10000 0 -0.42 46 46
JunB/Fra1/NFAT1-c-4 0.023 0.16 -10000 0 -0.3 23 23
IL4 0.019 0.093 -10000 0 -0.33 1 1
IL5 -0.038 0.18 -10000 0 -0.44 38 38
IL2 -0.003 0.11 -10000 0 -0.36 3 3
IL3 -0.001 0.03 -10000 0 -10000 0 0
RNF128 0.016 0.076 -10000 0 -0.37 19 19
NFATC1 0.083 0.13 0.3 74 -0.32 6 80
CDK4 -0.19 0.18 0.26 6 -0.44 155 161
PTPRK 0.031 0.072 -10000 0 -0.22 5 5
IL8 -0.08 0.23 -10000 0 -0.48 98 98
POU2F1 0.023 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.017 0 -9999 0 -10000 0 0
Caspase 8 (4 units) 0.019 0.066 -9999 0 -0.26 12 12
NEF 0.004 0 -9999 0 -10000 0 0
NFKBIA 0.012 0.032 -9999 0 -0.5 1 1
BIRC3 0.002 0.11 -9999 0 -0.39 36 36
CYCS 0.013 0.054 -9999 0 -0.2 12 12
RIPK1 0.01 0.055 -9999 0 -0.41 9 9
CD247 0.019 0.026 -9999 0 -0.41 2 2
MAP2K7 0.02 0.044 -9999 0 -0.22 1 1
protein ubiquitination 0.009 0.056 -9999 0 -0.18 8 8
CRADD 0.017 0 -9999 0 -10000 0 0
DAXX 0.016 0.019 -9999 0 -0.41 1 1
FAS -0.038 0.14 -9999 0 -0.41 68 68
BID 0.01 0.056 -9999 0 -0.21 12 12
NF-kappa-B/RelA/I kappa B alpha 0.026 0.07 -9999 0 -0.23 36 36
TRADD 0.017 0 -9999 0 -10000 0 0
MAP3K5 0.017 0.001 -9999 0 -10000 0 0
CFLAR 0.013 0.042 -9999 0 -0.41 5 5
FADD 0.015 0.026 -9999 0 -0.41 2 2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.026 0.071 -9999 0 -0.23 36 36
MAPK8 0.023 0.042 -9999 0 -10000 0 0
APAF1 0.017 0 -9999 0 -10000 0 0
TRAF1 0.016 0.019 -9999 0 -0.41 1 1
TRAF2 0.017 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.054 -9999 0 -0.24 5 5
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.004 0.064 -9999 0 -0.17 24 24
CHUK 0.009 0.058 -9999 0 -0.19 8 8
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.014 0.091 -9999 0 -0.2 75 75
TCRz/NEF 0.021 0.019 -9999 0 -0.28 2 2
TNF 0.015 0.026 -9999 0 -0.41 2 2
FASLG 0.022 0.015 -9999 0 -0.23 2 2
NFKB1 0.01 0.045 -9999 0 -0.43 4 4
TNFR1A/BAG4/TNF-alpha -0.059 0.13 -9999 0 -0.23 185 185
CASP6 0.023 0.068 -9999 0 -0.32 7 7
CASP7 0.007 0.11 -9999 0 -0.28 51 51
RELA 0.013 0.023 -9999 0 -10000 0 0
CASP2 0.016 0.019 -9999 0 -0.41 1 1
CASP3 -0.002 0.11 -9999 0 -0.28 48 48
TNFRSF1A -0.13 0.2 -9999 0 -0.41 183 183
TNFR1A/BAG4 -0.082 0.15 -9999 0 -0.28 183 183
CASP8 0.01 0.055 -9999 0 -0.41 9 9
CASP9 0.014 0.037 -9999 0 -0.41 4 4
MAP3K14 0.006 0.062 -9999 0 -0.21 8 8
APAF-1/Caspase 9 0.012 0.089 -9999 0 -0.28 37 37
BCL2 0.025 0.04 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 -0.023 0.14 -10000 0 -0.39 66 66
AES 0.028 0.02 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.019 0.044 -10000 0 -0.28 11 11
SMAD4 -0.086 0.18 -10000 0 -0.41 127 127
DKK2 0.009 0.058 -10000 0 -0.41 10 10
TLE1 0.028 0.02 -10000 0 -10000 0 0
MACF1 0.018 0.001 -10000 0 -10000 0 0
CTNNB1 0.065 0.034 0.22 1 -10000 0 1
WIF1 0.002 0.006 -10000 0 -10000 0 0
beta catenin/RanBP3 0.092 0.13 0.26 188 -10000 0 188
KREMEN2 0.017 0 -10000 0 -10000 0 0
DKK1 -0.078 0.18 -10000 0 -0.41 117 117
beta catenin/beta TrCP1 0.072 0.033 0.22 1 -10000 0 1
FZD1 0.009 0.058 -10000 0 -0.41 10 10
AXIN2 -0.043 0.066 -10000 0 -0.13 169 169
AXIN1 0.018 0 -10000 0 -10000 0 0
RAN 0.017 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.046 0.035 -10000 0 -0.31 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.065 -10000 0 -0.2 1 1
Axin1/APC/GSK3 0.059 0.02 0.19 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.056 0.036 -10000 0 -10000 0 0
HNF1A 0.028 0.021 -10000 0 -10000 0 0
CTBP1 0.028 0.022 -10000 0 -10000 0 0
MYC -0.11 0.19 -10000 0 -0.43 137 137
RANBP3 0.018 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.038 -10000 0 -0.23 11 11
NKD1 0 0 -10000 0 -10000 0 0
TCF4 0.028 0.022 -10000 0 -10000 0 0
TCF3 0.028 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.038 0.036 -10000 0 -0.21 11 11
Ran/GTP 0.014 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.099 0.14 0.28 169 -0.18 1 170
LEF1 0.027 0.038 -10000 0 -0.39 3 3
DVL1 0.004 0.012 -10000 0 -10000 0 0
CSNK2A1 0.017 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.04 0.052 -10000 0 -0.2 1 1
DKK1/LRP6/Kremen 2 -0.025 0.11 -10000 0 -0.23 118 118
LRP6 0.016 0.019 -10000 0 -0.41 1 1
CSNK1A1 0.031 0.024 -10000 0 -10000 0 0
NLK 0.015 0.005 -10000 0 -10000 0 0
CCND1 -0.087 0.17 -10000 0 -0.44 98 98
WNT1 0.017 0.001 -10000 0 -10000 0 0
GSK3A 0.017 0.001 -10000 0 -10000 0 0
GSK3B 0.017 0.002 -10000 0 -10000 0 0
FRAT1 0.016 0.019 -10000 0 -0.41 1 1
PPP2R5D 0.007 0.016 -10000 0 -10000 0 0
APC 0.021 0.031 -10000 0 -0.19 11 11
WNT1/LRP6/FZD1 0.003 0.011 -10000 0 -0.12 2 2
CREBBP 0.028 0.021 -10000 0 -10000 0 0
IL6-mediated signaling events

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.038 0.16 -10000 0 -0.43 36 36
CRP -0.038 0.16 -10000 0 -0.43 36 36
cell cycle arrest -0.059 0.17 -10000 0 -0.44 56 56
TIMP1 -0.2 0.22 -10000 0 -0.46 145 145
IL6ST 0.016 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.007 0.075 -10000 0 -0.23 16 16
AP1 -0.035 0.1 -10000 0 -0.25 45 45
GAB2 0.017 0.019 -10000 0 -0.41 1 1
TNFSF11 -0.038 0.16 -10000 0 -0.43 36 36
HSP90B1 0.014 0.055 -10000 0 -0.39 2 2
GAB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK14 0.019 0.048 -10000 0 -10000 0 0
AKT1 0.028 0.039 -10000 0 -0.22 5 5
FOXO1 0.025 0.05 -10000 0 -0.29 4 4
MAP2K6 0.012 0.056 -10000 0 -0.17 13 13
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.001 0.096 -10000 0 -0.3 14 14
MITF 0.004 0.067 -10000 0 -0.2 28 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.016 0.019 -10000 0 -0.41 1 1
A2M -0.009 0.11 -10000 0 -0.44 30 30
CEBPB 0.015 0.062 -10000 0 -0.41 11 11
GRB2/SOS1/GAB family/SHP2 0.009 0.052 0.14 1 -0.28 4 5
STAT3 -0.061 0.18 -10000 0 -0.45 56 56
STAT1 0.003 0.046 -10000 0 -0.24 14 14
CEBPD -0.038 0.16 -10000 0 -0.43 36 36
PIK3CA -0.002 0.091 -10000 0 -0.41 25 25
PI3K 0.011 0.065 -10000 0 -0.28 25 25
JUN 0.016 0.019 -10000 0 -0.41 1 1
PIAS3/MITF 0.011 0.068 -10000 0 -0.21 18 18
MAPK11 0.02 0.047 -10000 0 -10000 0 0
STAT3 (dimer)/FOXO1 -0.036 0.16 -10000 0 -0.44 30 30
GRB2/SOS1/GAB family 0.007 0.077 -10000 0 -0.22 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.008 0.085 -10000 0 -0.18 68 68
GRB2 0.017 0.003 -10000 0 -10000 0 0
JAK2 0.017 0 -10000 0 -10000 0 0
LBP -0.026 0.15 -10000 0 -0.44 22 22
PIK3R1 0.016 0.005 -10000 0 -10000 0 0
JAK1 0.017 0.003 -10000 0 -10000 0 0
MYC -0.084 0.22 -10000 0 -0.46 97 97
FGG -0.041 0.17 -10000 0 -0.46 40 40
macrophage differentiation -0.059 0.17 -10000 0 -0.44 56 56
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.025 0.078 -10000 0 -0.21 52 52
JUNB -0.04 0.16 -10000 0 -0.45 37 37
FOS -0.085 0.18 -10000 0 -0.41 125 125
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.002 0.069 -10000 0 -0.2 32 32
STAT1/PIAS1 -0.004 0.086 -10000 0 -0.23 30 30
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.033 -10000 0 -0.23 2 2
STAT3 (dimer) -0.061 0.18 -10000 0 -0.45 56 56
PRKCD -0.008 0.12 -10000 0 -0.36 14 14
IL6R 0.018 0.003 -10000 0 -10000 0 0
SOCS3 0.027 0.04 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.033 0.018 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.084 -10000 0 -0.26 16 16
HCK -0.053 0.16 -10000 0 -0.41 86 86
MAPKKK cascade 0.014 0.051 -10000 0 -0.35 4 4
bone resorption -0.036 0.16 -10000 0 -0.42 36 36
IRF1 -0.061 0.2 -10000 0 -0.48 72 72
mol:GDP 0.003 0.07 -10000 0 -0.2 27 27
SOS1 0.001 0.003 -10000 0 -10000 0 0
VAV1 0.003 0.07 -10000 0 -0.21 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.025 0.047 -10000 0 -0.25 2 2
PTPN11 0.011 0.017 -10000 0 -10000 0 0
IL6/IL6RA -0.006 0.095 -10000 0 -0.29 52 52
gp130 (dimer)/TYK2/TYK2/LMO4 0.033 0.016 -10000 0 -0.23 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.034 0.012 -10000 0 -10000 0 0
IL6 -0.026 0.13 -10000 0 -0.42 52 52
PIAS3 0.015 0.026 -10000 0 -0.41 2 2
PTPRE 0.017 0.01 -10000 0 -10000 0 0
PIAS1 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.004 0.055 -10000 0 -0.15 51 51
LMO4 0.016 0.008 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.044 0.17 -10000 0 -0.48 37 37
MCL1 0.03 0.049 -10000 0 -0.38 4 4
Caspase cascade in apoptosis

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
TOP1 0.01 0.055 -10000 0 -0.2 10 10
ACTA1 0.004 0.062 0.14 20 -0.19 19 39
NUMA1 0.01 0.055 -10000 0 -0.21 9 9
SPTAN1 0.012 0.063 0.16 30 -0.19 12 42
LIMK1 0.006 0.06 0.15 15 -0.18 18 33
BIRC3 -0.01 0.1 -10000 0 -0.41 33 33
BIRC2 0.017 0 -10000 0 -10000 0 0
BAX 0.011 0.049 -10000 0 -0.41 7 7
CASP10 0.006 0.056 -10000 0 -0.25 22 22
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.009 0.056 -10000 0 -0.2 11 11
DIABLO 0.017 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.014 0.065 0.16 30 -0.19 12 42
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.017 0 -10000 0 -10000 0 0
GSN 0 0.068 0.15 15 -0.19 29 44
MADD 0.017 0.001 -10000 0 -10000 0 0
TFAP2A 0.019 0.026 -10000 0 -0.28 1 1
BID 0.006 0.041 -10000 0 -0.14 35 35
MAP3K1 0.011 0.029 -10000 0 -0.19 1 1
TRADD 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0.027 -10000 0 -0.28 4 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.011 0.087 0.16 13 -0.22 52 65
CASP9 0.014 0.037 -10000 0 -0.41 4 4
DNA repair -0.006 0.039 0.11 11 -0.13 23 34
neuron apoptosis 0.015 0.036 -10000 0 -0.56 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.012 0.059 0.16 2 -0.22 9 11
APAF1 0.017 0 -10000 0 -10000 0 0
CASP6 0.004 0.055 -10000 0 -10000 0 0
TRAF2 0.017 0 -10000 0 -10000 0 0
ICAD/CAD 0.01 0.058 0.15 8 -0.21 9 17
CASP7 -0.008 0.07 0.19 26 -0.18 55 81
KRT18 0.001 0.049 -10000 0 -0.2 19 19
apoptosis 0.005 0.071 0.18 2 -0.22 17 19
DFFA 0.006 0.06 0.15 15 -0.18 17 32
DFFB 0.006 0.06 0.15 15 -0.18 18 33
PARP1 0.006 0.039 0.13 23 -0.11 11 34
actin filament polymerization -0.006 0.056 0.17 17 -0.14 15 32
TNF 0.015 0.026 -10000 0 -0.41 2 2
CYCS 0.011 0.029 -10000 0 -0.11 19 19
SATB1 0.024 0.059 -10000 0 -10000 0 0
SLK 0.006 0.06 0.15 15 -0.18 17 32
p15 BID/BAX 0.013 0.047 -10000 0 -0.14 41 41
CASP2 -0.005 0.058 -10000 0 -0.16 25 25
JNK cascade -0.011 0.029 0.19 1 -10000 0 1
CASP3 0.003 0.064 0.15 22 -0.19 19 41
LMNB2 0.002 0.051 -10000 0 -0.23 5 5
RIPK1 0.01 0.055 -10000 0 -0.41 9 9
CASP4 -0.07 0.17 -10000 0 -0.41 107 107
Mammalian IAPs/DIABLO 0.018 0.059 -10000 0 -0.21 33 33
negative regulation of DNA binding 0.019 0.026 -10000 0 -0.28 1 1
stress fiber formation 0.007 0.059 0.15 14 -0.18 17 31
GZMB 0.004 0.066 -10000 0 -0.31 22 22
CASP1 -0.087 0.14 -10000 0 -0.26 194 194
LMNB1 -0.014 0.059 -10000 0 -0.21 12 12
APP 0.015 0.037 -10000 0 -0.56 1 1
TNFRSF1A -0.13 0.2 -10000 0 -0.41 183 183
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.039 -10000 0 -0.29 9 9
VIM 0.002 0.072 0.18 7 -0.22 21 28
LMNA 0.005 0.048 -10000 0 -0.2 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.008 0.061 -10000 0 -0.18 24 24
LRDD 0.017 0 -10000 0 -10000 0 0
SREBF1 0.006 0.06 0.15 15 -0.18 17 32
APAF-1/Caspase 9 0.01 0.026 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.01 0.054 -10000 0 -0.2 9 9
CFL2 0.006 0.057 0.14 15 -0.18 17 32
GAS2 -0.009 0.083 0.15 14 -0.2 56 70
positive regulation of apoptosis -0.003 0.054 -10000 0 -0.22 8 8
PRF1 0.007 0.064 -10000 0 -0.41 12 12
Signaling events mediated by PTP1B

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
PDGFRB 0.015 0.032 -10000 0 -0.41 3 3
Jak2/Leptin Receptor 0.017 0.034 -10000 0 -0.16 3 3
PTP1B/AKT1 -0.002 0.048 -10000 0 -0.2 7 7
FYN 0.015 0.026 -10000 0 -0.41 2 2
p210 bcr-abl/PTP1B -0.01 0.045 -10000 0 -0.15 11 11
EGFR -0.14 0.21 -10000 0 -0.41 194 194
EGF/EGFR -0.055 0.1 -10000 0 -0.18 197 197
CSF1 0.017 0 -10000 0 -10000 0 0
AKT1 0.014 0.037 -10000 0 -0.41 4 4
INSR 0.017 0 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.049 -10000 0 -0.2 6 6
Insulin Receptor/Insulin 0.018 0.041 -10000 0 -0.21 4 4
HCK -0.053 0.16 -10000 0 -0.41 86 86
CRK 0.017 0 -10000 0 -10000 0 0
TYK2 -0.006 0.044 -10000 0 -0.18 5 5
EGF 0.013 0.027 -10000 0 -0.41 2 2
YES1 -0.048 0.15 -10000 0 -0.41 80 80
CAV1 -0.069 0.068 -10000 0 -0.16 150 150
TXN 0.015 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.003 0.05 -10000 0 -0.17 8 8
cell migration 0.01 0.045 0.15 11 -10000 0 11
STAT3 0.009 0.059 -10000 0 -0.41 10 10
PRLR 0.02 0 -10000 0 -10000 0 0
ITGA2B 0.016 0 -10000 0 -10000 0 0
CSF1R -0.016 0.12 -10000 0 -0.41 41 41
Prolactin Receptor/Prolactin 0.029 0.033 -10000 0 -0.28 6 6
FGR 0.003 0.076 -10000 0 -0.41 17 17
PTP1B/p130 Cas -0.01 0.042 -10000 0 -0.12 41 41
Crk/p130 Cas -0.003 0.044 -10000 0 -0.14 7 7
DOK1 0.003 0.04 -10000 0 -0.16 4 4
JAK2 0.011 0.03 -10000 0 -10000 0 0
Jak2/Leptin Receptor/Leptin 0.022 0.051 -10000 0 -0.23 6 6
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
PTPN1 -0.01 0.046 -10000 0 -0.13 42 42
LYN -0.035 0.14 -10000 0 -0.41 64 64
CDH2 0.014 0.032 -10000 0 -0.41 3 3
SRC 0.014 0.019 -10000 0 -10000 0 0
ITGB3 0.016 0 -10000 0 -10000 0 0
CAT1/PTP1B -0.027 0.093 -10000 0 -0.22 76 76
CAPN1 0.016 0.001 -10000 0 -10000 0 0
CSK 0.017 0 -10000 0 -10000 0 0
PI3K 0.015 0.057 -10000 0 -0.19 18 18
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.048 -10000 0 -0.23 6 6
negative regulation of transcription 0.011 0.03 -10000 0 -10000 0 0
FCGR2A -0.2 0.22 -10000 0 -0.41 266 266
FER 0.015 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.023 0.001 -10000 0 -10000 0 0
BLK 0.017 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.011 0.077 -10000 0 -0.24 47 47
RHOA 0.016 0.001 -10000 0 -10000 0 0
LEPR 0.014 0.032 -10000 0 -0.41 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.017 0.002 -10000 0 -10000 0 0
mol:NADPH -0.002 0.002 -10000 0 -10000 0 0
TRPV6 -0.021 0.1 -10000 0 -0.23 75 75
PRL 0.015 0.045 -10000 0 -0.41 6 6
SOCS3 0.009 0.009 -10000 0 -10000 0 0
SPRY2 0.009 0.053 -10000 0 -0.42 8 8
Insulin Receptor/Insulin/IRS1 0.033 0.026 -10000 0 -0.24 5 5
CSF1/CSF1R -0.011 0.068 -10000 0 -0.18 43 43
Ras protein signal transduction 0.013 0.031 0.29 5 -10000 0 5
IRS1 0.013 0.042 -10000 0 -0.41 5 5
INS 0.017 0 -10000 0 -10000 0 0
LEP 0.017 0 -10000 0 -10000 0 0
STAT5B 0.003 0.039 -10000 0 -0.16 2 2
STAT5A 0.003 0.039 -10000 0 -0.16 2 2
GRB2 0.017 0.002 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.048 -10000 0 -0.18 7 7
CSN2 0.023 0.015 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
LAT -0.065 0.081 -10000 0 -0.18 52 52
YBX1 0.015 0.064 -10000 0 -0.4 12 12
LCK 0.014 0.037 -10000 0 -0.41 4 4
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
NOX4 -0.042 0.15 -10000 0 -0.42 70 70
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.02 0.12 -9999 0 -0.41 46 46
positive regulation of NF-kappaB transcription factor activity -0.002 0.087 -9999 0 -0.28 46 46
MAP2K4 0.018 0.042 -9999 0 -0.19 4 4
IKBKB 0.017 0 -9999 0 -10000 0 0
TNFRSF10B 0.011 0.049 -9999 0 -0.41 7 7
TNFRSF10A 0 0 -9999 0 -10000 0 0
SMPD1 0.002 0.043 -9999 0 -0.13 52 52
IKBKG 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.017 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.006 0.094 -9999 0 -0.29 52 52
TRAIL/TRAILR3 -0.002 0.087 -9999 0 -0.28 46 46
TRAIL/TRAILR1 -0.014 0.085 -9999 0 -0.29 46 46
TRAIL/TRAILR4 -0.002 0.087 -9999 0 -0.28 46 46
TRAIL/TRAILR1/DAP3/GTP 0.001 0.067 -9999 0 -0.22 46 46
IKK complex 0.021 0.037 -9999 0 -0.15 5 5
RIPK1 0.01 0.055 -9999 0 -0.41 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.009 0.085 -9999 0 -0.28 46 46
MAP3K1 0.016 0.047 -9999 0 -0.21 5 5
TRAILR4 (trimer) 0.017 0 -9999 0 -10000 0 0
TRADD 0.017 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.011 0.049 -9999 0 -0.13 54 54
CFLAR 0.013 0.042 -9999 0 -0.41 5 5
MAPK1 -0.006 0.081 -9999 0 -0.28 41 41
TRAIL/TRAILR1/FADD/TRADD/RIP 0.016 0.076 -9999 0 -0.2 54 54
mol:ceramide 0.002 0.043 -9999 0 -0.13 52 52
FADD 0.015 0.026 -9999 0 -0.41 2 2
MAPK8 0.02 0.04 -9999 0 -0.2 3 3
TRAF2 0.017 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.017 0 -9999 0 -10000 0 0
CHUK 0.016 0.019 -9999 0 -0.41 1 1
TRAIL/TRAILR1/FADD 0 0.076 -9999 0 -0.24 47 47
DAP3 0.017 0 -9999 0 -10000 0 0
CASP10 -0.006 0.063 -9999 0 -0.2 47 47
JNK cascade -0.002 0.087 -9999 0 -0.28 46 46
TRAIL (trimer) -0.02 0.12 -9999 0 -0.41 46 46
TNFRSF10C 0.017 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.01 0.067 -9999 0 -0.2 47 47
TRAIL/TRAILR2/FADD 0.007 0.084 -9999 0 -0.24 53 53
cell death 0.002 0.043 -9999 0 -0.13 52 52
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.053 -9999 0 -0.13 60 60
TRAILR2 (trimer) 0.011 0.049 -9999 0 -0.41 7 7
CASP8 0.01 0.035 -9999 0 -0.28 2 2
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.022 0.083 -9999 0 -0.2 60 60
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.005 0.093 -9999 0 -0.39 28 28
VDR 0.017 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.074 0.079 -9999 0 -0.26 5 5
RXRs/LXRs/DNA/Oxysterols -0.12 0.11 -9999 0 -0.18 356 356
MED1 0.017 0 -9999 0 -10000 0 0
mol:9cRA -0.021 0.016 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.031 0.005 -9999 0 -10000 0 0
RXRs/NUR77 -0.008 0.044 -9999 0 -0.26 3 3
RXRs/PPAR 0.001 0.028 -9999 0 -0.16 5 5
NCOR2 0.017 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.041 0 -9999 0 -10000 0 0
RARA 0.017 0 -9999 0 -10000 0 0
NCOA1 0.017 0.003 -9999 0 -10000 0 0
VDR/VDR/DNA 0.017 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.02 0.009 -9999 0 -10000 0 0
RARG 0.017 0 -9999 0 -10000 0 0
RPS6KB1 0.017 0.057 -9999 0 -0.22 28 28
RARs/THRs/DNA/SMRT 0.032 0 -9999 0 -10000 0 0
THRA 0.017 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.035 0.056 -9999 0 -0.29 3 3
NR1H4 0.017 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA -0.041 0.075 -9999 0 -0.26 7 7
NR1H2 -0.006 0.017 -9999 0 -10000 0 0
NR1H3 -0.012 0.041 -9999 0 -0.42 4 4
RXRs/VDR/DNA/Vit D3 -0.008 0.041 -9999 0 -0.24 3 3
NR4A1 0.017 0 -9999 0 -10000 0 0
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.015 0.032 -9999 0 -0.15 3 3
RXRG -0.009 0.037 -9999 0 -0.44 3 3
RXR alpha/CCPG -0.003 0.012 -9999 0 -10000 0 0
RXRA -0.006 0.017 -9999 0 -10000 0 0
RXRB -0.009 0.02 -9999 0 -10000 0 0
THRB 0.017 0 -9999 0 -10000 0 0
PPARG 0.013 0.042 -9999 0 -0.41 5 5
PPARD 0.017 0 -9999 0 -10000 0 0
TNF -0.1 0.1 -9999 0 -0.3 7 7
mol:Oxysterols -0.017 0.014 -9999 0 -10000 0 0
cholesterol transport -0.11 0.11 -9999 0 -0.18 356 356
PPARA 0.017 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.017 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 0.013 0.016 -9999 0 -0.15 3 3
SREBF1 -0.1 0.099 -9999 0 -0.28 5 5
RXRs/RXRs/DNA/9cRA -0.035 0.056 -9999 0 -0.29 3 3
ABCA1 -0.24 0.18 -9999 0 -0.35 380 380
RARs/THRs 0.051 0 -9999 0 -10000 0 0
RXRs/FXR -0.008 0.044 -9999 0 -0.26 3 3
BCL2 0.017 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.016 0.041 -9999 0 -0.27 1 1
PLK1 -0.078 0.15 -9999 0 -0.51 25 25
CDKN1B -0.071 0.1 -9999 0 -0.23 39 39
FOXO3 -0.083 0.14 -9999 0 -0.3 56 56
KAT2B -0.012 0.016 -9999 0 -0.041 26 26
FOXO1/SIRT1 0.014 0.045 -9999 0 -0.25 2 2
CAT -0.071 0.13 -9999 0 -0.35 28 28
CTNNB1 0.017 0 -9999 0 -10000 0 0
AKT1 -0.001 0.042 -9999 0 -0.43 4 4
FOXO1 0.011 0.046 -9999 0 -0.15 36 36
MAPK10 -0.002 0.044 -9999 0 -0.21 21 21
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
FOXO4 -0.013 0.08 -9999 0 -0.24 24 24
response to oxidative stress -0.01 0.016 -9999 0 -0.038 29 29
FOXO3A/SIRT1 -0.094 0.12 -9999 0 -0.31 54 54
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 0.018 0.001 -9999 0 -10000 0 0
BCL2L11 0.006 0.022 -9999 0 -10000 0 0
FOXO1/SKP2 0.018 0.048 -9999 0 -0.29 4 4
mol:GDP -0.01 0.016 -9999 0 -0.038 29 29
RAN 0.017 0.002 -9999 0 -10000 0 0
GADD45A -0.063 0.14 -9999 0 -0.42 47 47
YWHAQ 0.017 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.012 0.044 -9999 0 -0.16 5 5
MST1 -0.004 0.05 -9999 0 -0.43 6 6
CSNK1D 0.015 0.026 -9999 0 -0.41 2 2
CSNK1E 0.017 0.001 -9999 0 -10000 0 0
FOXO4/14-3-3 family -0.035 0.079 -9999 0 -0.25 28 28
YWHAB 0.017 0.001 -9999 0 -10000 0 0
MAPK8 -0.008 0.063 -9999 0 -0.21 45 45
MAPK9 -0.007 0.063 -9999 0 -0.21 45 45
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
YWHAZ 0.017 0.002 -9999 0 -10000 0 0
SIRT1 0.013 0.006 -9999 0 -10000 0 0
SOD2 -0.2 0.2 -9999 0 -0.36 292 292
RBL2 -0.051 0.1 -9999 0 -0.32 2 2
RAL/GDP -0.009 0.074 -9999 0 -0.25 45 45
CHUK 0 0.026 -9999 0 -0.4 1 1
Ran/GTP 0.012 0.005 -9999 0 -10000 0 0
CSNK1G2 0.017 0 -9999 0 -10000 0 0
RAL/GTP -0.008 0.069 -9999 0 -0.22 45 45
CSNK1G1 0.017 0 -9999 0 -10000 0 0
FASLG 0.006 0.022 -9999 0 -10000 0 0
SKP2 0.015 0.026 -9999 0 -0.41 2 2
USP7 0.017 0.002 -9999 0 -10000 0 0
IKBKB 0.001 0.02 -9999 0 -10000 0 0
CCNB1 -0.18 0.21 -9999 0 -0.36 296 296
FOXO1-3a-4/beta catenin -0.08 0.13 -9999 0 -0.32 17 17
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.047 -9999 0 -0.29 4 4
CSNK1A1 0.017 0 -9999 0 -10000 0 0
SGK1 -0.012 0.016 -9999 0 -0.041 26 26
CSNK1G3 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.007 -9999 0 -10000 0 0
ZFAND5 -0.005 0.071 -9999 0 -0.23 10 10
SFN -0.01 0.1 -9999 0 -0.41 33 33
CDK2 -0.003 0.094 -9999 0 -0.41 27 27
FOXO3A/14-3-3 -0.041 0.072 -9999 0 -0.2 41 41
CREBBP 0.019 0.002 -9999 0 -10000 0 0
FBXO32 -0.076 0.12 -9999 0 -0.32 37 37
BCL6 -0.059 0.12 -9999 0 -0.43 19 19
RALB 0.016 0.019 -9999 0 -0.41 1 1
RALA -0.019 0.12 -9999 0 -0.41 44 44
YWHAH 0.008 0.009 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.028 0.11 -9999 0 -0.28 36 36
RAD9A 0.016 0.019 -9999 0 -0.41 1 1
AP1 -0.049 0.13 -9999 0 -0.29 125 125
IFNAR2 0.017 0.005 -9999 0 -10000 0 0
AKT1 0.018 0.021 -9999 0 -0.2 4 4
ER alpha/Oestrogen 0.012 0.003 -9999 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.006 0.061 -9999 0 -0.13 54 54
EGF 0.015 0.026 -9999 0 -0.41 2 2
SMG5 0.017 0 -9999 0 -10000 0 0
SMG6 0.017 0 -9999 0 -10000 0 0
SP3/HDAC2 -0.023 0.12 -9999 0 -0.3 78 78
TERT/c-Abl -0.024 0.1 -9999 0 -0.29 25 25
SAP18 0.017 0.001 -9999 0 -10000 0 0
MRN complex 0.035 0 -9999 0 -10000 0 0
WT1 0.013 0.042 -9999 0 -0.42 5 5
WRN 0.013 0.042 -9999 0 -0.41 5 5
SP1 0.016 0.008 -9999 0 -10000 0 0
SP3 -0.046 0.15 -9999 0 -0.41 77 77
TERF2IP 0.016 0.005 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.009 0.1 -9999 0 -0.3 15 15
Mad/Max 0.025 0.006 -9999 0 -10000 0 0
TERT -0.029 0.11 -9999 0 -0.29 37 37
CCND1 -0.053 0.17 -9999 0 -0.39 98 98
MAX 0.017 0.002 -9999 0 -10000 0 0
RBBP7 0.017 0.001 -9999 0 -10000 0 0
RBBP4 -0.065 0.17 -9999 0 -0.41 101 101
TERF2 0.016 0.01 -9999 0 -10000 0 0
PTGES3 0.017 0.001 -9999 0 -10000 0 0
SIN3A 0 0.001 -9999 0 -10000 0 0
Telomerase/911 0.026 0.034 -9999 0 -0.2 7 7
CDKN1B -0.005 0.086 -9999 0 -0.22 71 71
RAD1 0.015 0.026 -9999 0 -0.41 2 2
XRCC5 0.017 0 -9999 0 -10000 0 0
XRCC6 0.017 0 -9999 0 -10000 0 0
SAP30 0.017 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.024 0.01 -9999 0 -10000 0 0
UBE3A 0.017 0.002 -9999 0 -10000 0 0
JUN 0.016 0.019 -9999 0 -0.41 1 1
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.006 -9999 0 -10000 0 0
FOS -0.085 0.18 -9999 0 -0.41 125 125
IFN-gamma/IRF1 -0.007 0.11 -9999 0 -0.28 71 71
PARP2 0.017 0.001 -9999 0 -10000 0 0
BLM -0.083 0.18 -9999 0 -0.41 124 124
Telomerase 0.013 0.034 -9999 0 -0.17 7 7
IRF1 -0.036 0.14 -9999 0 -0.41 70 70
ESR1 0.017 0.001 -9999 0 -10000 0 0
KU/TER 0.025 0 -9999 0 -10000 0 0
ATM/TRF2 0.011 0.055 -9999 0 -0.24 25 25
ubiquitin-dependent protein catabolic process -0.003 0.064 -9999 0 -0.15 41 41
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.003 0.065 -9999 0 -0.15 40 40
HDAC1 -0.037 0.14 -9999 0 -0.41 66 66
HDAC2 0.012 0.043 -9999 0 -0.42 5 5
ATM -0.007 0.056 -9999 0 -0.26 25 25
SMAD3 0.002 0.066 -9999 0 -0.28 27 27
ABL1 0.016 0.019 -9999 0 -0.41 1 1
MXD1 0.017 0.002 -9999 0 -10000 0 0
MRE11A 0.017 0 -9999 0 -10000 0 0
HUS1 0.017 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0.019 -9999 0 -0.41 1 1
TERT/NF kappa B1/14-3-3 -0.003 0.1 -9999 0 -0.3 10 10
NR2F2 0.014 0.037 -9999 0 -0.41 4 4
MAPK3 0.017 0.004 -9999 0 -10000 0 0
MAPK1 0.017 0.005 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II -0.005 0.094 -9999 0 -0.41 27 27
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
HNRNPC 0.017 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.007 0.056 -9999 0 -0.26 25 25
NBN 0.017 0 -9999 0 -10000 0 0
EGFR -0.14 0.21 -9999 0 -0.41 194 194
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.09 0.15 -9999 0 -0.28 196 196
MYC -0.094 0.19 -9999 0 -0.41 137 137
IL2 0.016 0.009 -9999 0 -10000 0 0
KU 0.025 0 -9999 0 -10000 0 0
RAD50 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
TGFB1 -0.005 0.094 -9999 0 -0.41 27 27
TRF2/BLM -0.044 0.12 -9999 0 -0.26 124 124
FRAP1 0.016 0.019 -9999 0 -0.41 1 1
KU/TERT -0.013 0.11 -9999 0 -0.31 12 12
SP1/HDAC2 0.021 0.034 -9999 0 -0.3 5 5
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.009 0.1 -9999 0 -0.3 15 15
Smad3/Myc -0.054 0.13 -9999 0 -0.25 153 153
911 complex 0.033 0.02 -9999 0 -0.23 3 3
IFNG 0.02 0.019 -9999 0 -0.41 1 1
Telomerase/PinX1 -0.033 0.09 -9999 0 -0.3 15 15
Telomerase/AKT1/mTOR/p70S6K 0.024 0.04 -9999 0 -0.21 3 3
SIN3B 0.017 0.001 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
Telomerase/EST1B -0.009 0.1 -9999 0 -0.3 15 15
response to DNA damage stimulus 0 0.014 -9999 0 -0.062 25 25
MRN complex/TRF2/Rap1 0.044 0.017 -9999 0 -10000 0 0
TRF2/WRN 0.021 0.03 -9999 0 -0.26 5 5
Telomerase/hnRNP C1/C2 -0.009 0.1 -9999 0 -0.3 15 15
E2F1 0.017 0.005 -9999 0 -10000 0 0
ZNFX1 0 0.001 -9999 0 -10000 0 0
PIF1 0 0 -9999 0 -10000 0 0
NCL 0.017 0 -9999 0 -10000 0 0
DKC1 0.011 0.049 -9999 0 -0.41 7 7
telomeric DNA binding 0 0 -9999 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.025 0.29 -9999 0 -0.55 86 86
IL23A 0.027 0.23 -9999 0 -0.69 20 20
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.23 -9999 0 -0.56 40 40
positive regulation of T cell mediated cytotoxicity 0.028 0.24 -9999 0 -0.6 40 40
ITGA3 0.025 0.24 -9999 0 -0.58 40 40
IL17F 0.025 0.18 -9999 0 -0.44 33 33
IL12B 0.025 0.029 -9999 0 -10000 0 0
STAT1 (dimer) 0.017 0.23 -9999 0 -0.58 40 40
CD4 0.026 0.24 -9999 0 -0.6 39 39
IL23 0.026 0.22 -9999 0 -0.7 18 18
IL23R 0.018 0.064 -9999 0 -0.13 18 18
IL1B 0.027 0.24 -9999 0 -0.58 43 43
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 0.032 0.22 -9999 0 -0.55 39 39
TYK2 0.02 0.027 -9999 0 -0.39 1 1
STAT4 0.01 0.008 -9999 0 -10000 0 0
STAT3 0.009 0.058 -9999 0 -0.41 10 10
IL18RAP 0.018 0.002 -9999 0 -10000 0 0
IL12RB1 0.021 0.021 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
IL12Rbeta1/TYK2 0.028 0.029 -9999 0 -0.26 1 1
IL23R/JAK2 0.034 0.085 -9999 0 -0.18 5 5
positive regulation of chronic inflammatory response 0.028 0.24 -9999 0 -0.6 40 40
natural killer cell activation -0.001 0.006 -9999 0 -10000 0 0
JAK2 0.025 0.029 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.038 -9999 0 -0.42 4 4
RELA 0.018 0.003 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.027 0.22 -9999 0 -0.67 18 18
ALOX12B 0.032 0.22 -9999 0 -0.55 39 39
CXCL1 0.022 0.25 -9999 0 -0.64 39 39
T cell proliferation 0.028 0.24 -9999 0 -0.6 40 40
NFKBIA 0.017 0.019 -9999 0 -0.42 1 1
IL17A 0.047 0.16 -9999 0 -0.38 22 22
PI3K 0.024 0.22 -9999 0 -0.57 32 32
IFNG 0.012 0.017 -9999 0 -0.045 16 16
STAT3 (dimer) 0.028 0.22 -9999 0 -0.57 33 33
IL18R1 0.018 0.002 -9999 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.039 0.16 -9999 0 -0.4 18 18
IL18/IL18R 0.016 0.075 -9999 0 -0.23 45 45
macrophage activation 0.001 0.014 -9999 0 -0.037 19 19
TNF 0.029 0.23 -9999 0 -0.57 40 40
STAT3/STAT4 -0.017 0.2 -9999 0 -0.57 36 36
STAT4 (dimer) -0.018 0.2 -9999 0 -0.58 36 36
IL18 -0.019 0.12 -9999 0 -0.41 45 45
IL19 0.033 0.22 -9999 0 -0.55 39 39
STAT5A (dimer) 0.024 0.23 -9999 0 -0.58 39 39
STAT1 0.002 0.078 -9999 0 -0.41 18 18
SOCS3 0.017 0 -9999 0 -10000 0 0
CXCL9 0.01 0.25 -9999 0 -0.62 39 39
MPO 0.033 0.22 -9999 0 -0.55 39 39
positive regulation of humoral immune response 0.028 0.24 -9999 0 -0.6 40 40
IL23/IL23R/JAK2/TYK2 0.027 0.24 -9999 0 -0.61 40 40
IL6 0.014 0.26 -9999 0 -0.7 36 36
STAT5A 0.016 0.019 -9999 0 -0.41 1 1
IL2 0.018 0.004 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.006 -9999 0 -10000 0 0
CD3E 0.032 0.22 -9999 0 -0.55 39 39
keratinocyte proliferation 0.028 0.24 -9999 0 -0.6 40 40
NOS2 0.026 0.22 -9999 0 -0.55 39 39
ErbB2/ErbB3 signaling events

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.01 0.022 -10000 0 -0.24 4 4
RAS family/GTP -0.034 0.11 -10000 0 -0.19 134 134
NFATC4 0.015 0.04 -10000 0 -10000 0 0
ERBB2IP -0.008 0.1 -10000 0 -0.41 31 31
HSP90 (dimer) 0.017 0 -10000 0 -10000 0 0
mammary gland morphogenesis 0.019 0.054 0.15 17 -0.15 31 48
JUN 0.015 0.047 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
DOCK7 0.009 0.046 -10000 0 -0.16 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.005 0.085 0.16 16 -0.2 65 81
AKT1 0.007 0.026 -10000 0 -0.29 4 4
BAD 0.01 0.022 -10000 0 -0.24 4 4
MAPK10 0.01 0.025 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.021 0.057 0.16 17 -0.17 5 22
RAF1 -0.032 0.1 -10000 0 -0.21 66 66
ErbB2/ErbB3/neuregulin 2 0.015 0.066 0.16 30 -0.21 32 62
STAT3 0.019 0.027 -10000 0 -10000 0 0
cell migration 0.011 0.029 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -10000 0 -0.003 4 4
cell proliferation -0.026 0.12 -10000 0 -0.35 16 16
FOS -0.039 0.13 -10000 0 -0.24 131 131
NRAS -0.094 0.19 -10000 0 -0.41 137 137
mol:Ca2+ 0.019 0.054 0.15 17 -0.15 31 48
MAPK3 -0.017 0.098 -10000 0 -0.33 8 8
MAPK1 -0.028 0.11 -10000 0 -0.38 15 15
JAK2 0.016 0.047 -10000 0 -0.16 3 3
NF2 0.012 0.007 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.061 -10000 0 -0.15 74 74
NRG1 0.017 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
MAPK8 0.022 0.042 -10000 0 -0.17 1 1
MAPK9 0.019 0.029 -10000 0 -10000 0 0
ERBB2 0.009 0.052 0.22 31 -10000 0 31
ERBB3 -0.01 0.1 -10000 0 -0.41 32 32
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
RAC1 0.017 0 -10000 0 -10000 0 0
apoptosis -0.007 0.022 0.23 4 -10000 0 4
STAT3 (dimer) 0.019 0.027 -10000 0 -10000 0 0
RNF41 0.012 0.02 -10000 0 -0.21 4 4
FRAP1 0.01 0.024 -10000 0 -0.24 5 5
RAC1-CDC42/GTP -0.006 0.027 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.022 0.035 0.16 31 -10000 0 31
CHRNA1 -0.011 0.085 -10000 0 -0.24 15 15
myelination 0.021 0.042 -10000 0 -10000 0 0
PPP3CB 0.015 0.045 -10000 0 -10000 0 0
KRAS 0.017 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.014 0.058 -10000 0 -0.18 9 9
NRG2 0.017 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.061 -10000 0 -0.15 74 74
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.027 0.096 -10000 0 -0.23 47 47
SRC 0.017 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.016 0.047 -10000 0 -10000 0 0
MAP2K1 -0.028 0.12 -10000 0 -0.4 22 22
heart morphogenesis 0.019 0.054 0.15 17 -0.15 31 48
RAS family/GDP -0.033 0.11 -10000 0 -0.2 134 134
GRB2 0.017 0.002 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
CHRNE 0.01 0.013 -10000 0 -10000 0 0
HSP90AA1 0.017 0 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.026 0.29 4 -10000 0 4
nervous system development 0.019 0.054 0.15 17 -0.15 31 48
CDC42 0.017 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.006 0.057 -10000 0 -0.2 34 34
HDAC1 -0.03 0.14 -10000 0 -0.4 66 66
AES 0.019 0.004 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.019 0.044 -10000 0 -0.29 11 11
TLE1 0.019 0.004 -10000 0 -10000 0 0
AP1 -0.02 0.068 -10000 0 -0.14 125 125
NCSTN -0.007 0.099 -10000 0 -0.41 30 30
ADAM10 0.003 0.078 -10000 0 -0.41 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.016 0.08 -10000 0 -10000 0 0
NICD/RBPSUH 0.018 0.059 -10000 0 -0.19 34 34
WIF1 0.002 0.006 -10000 0 -10000 0 0
NOTCH1 0.009 0.06 -10000 0 -0.21 34 34
PSENEN 0.017 0.001 -10000 0 -10000 0 0
KREMEN2 0.017 0 -10000 0 -10000 0 0
DKK1 -0.078 0.18 -10000 0 -0.41 117 117
beta catenin/beta TrCP1 0.023 0.03 -10000 0 -10000 0 0
APH1B 0.017 0 -10000 0 -10000 0 0
APH1A 0.008 0.061 -10000 0 -0.41 11 11
AXIN1 0.003 0.028 0.18 5 -10000 0 5
CtBP/CBP/TCF1/TLE1/AES 0.035 0.065 0.17 31 -0.13 32 63
PSEN1 0.016 0.019 -10000 0 -0.41 1 1
FOS -0.084 0.18 -10000 0 -0.41 125 125
JUN 0.016 0.019 -10000 0 -0.41 1 1
MAP3K7 0.019 0.02 -10000 0 -0.41 1 1
CTNNB1 0.016 0.028 -10000 0 -10000 0 0
MAPK3 0.017 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.029 0.038 -10000 0 -0.24 11 11
HNF1A 0.019 0.004 -10000 0 -10000 0 0
CTBP1 0.019 0.005 -10000 0 -10000 0 0
MYC -0.092 0.18 -10000 0 -0.4 137 137
NKD1 0.001 0.002 -10000 0 -10000 0 0
FZD1 0.009 0.059 -10000 0 -0.41 10 10
NOTCH1 precursor/Deltex homolog 1 0.007 0.057 -10000 0 -0.2 34 34
apoptosis -0.02 0.068 -10000 0 -0.14 125 125
Delta 1/NOTCHprecursor 0.007 0.057 -10000 0 -0.2 34 34
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.003 0.031 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.068 -10000 0 -0.2 40 40
APC -0.01 0.063 0.18 2 -0.29 21 23
DVL1 0.003 0.009 -10000 0 -10000 0 0
CSNK2A1 0.016 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0.02 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.025 0.11 -10000 0 -0.23 118 118
LRP6 0.016 0.019 -10000 0 -0.41 1 1
CSNK1A1 0.016 0.002 -10000 0 -10000 0 0
NLK 0.028 0.017 -10000 0 -0.18 1 1
CCND1 -0.065 0.17 -10000 0 -0.41 98 98
WNT1 0.017 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.024 0.052 0.19 2 -0.2 6 8
DKK2 0.009 0.058 -10000 0 -0.41 10 10
NOTCH1 precursor/DVL1 0.01 0.051 -10000 0 -0.2 13 13
GSK3B 0.017 0.002 -10000 0 -10000 0 0
FRAT1 0.017 0.019 -10000 0 -0.4 1 1
NOTCH/Deltex homolog 1 0.006 0.057 -10000 0 -0.2 34 34
PPP2R5D 0.002 0.007 -10000 0 -10000 0 0
MAPK1 0.017 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.003 0.023 -10000 0 -0.21 2 2
RBPJ 0.017 0 -10000 0 -10000 0 0
CREBBP 0.013 0.01 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.025 0.13 -9999 0 -0.41 51 51
HRAS 0.016 0.019 -9999 0 -0.41 1 1
EGFR -0.14 0.21 -9999 0 -0.41 194 194
AKT 0.015 0.035 -9999 0 -0.27 5 5
FOXO3 0.017 0 -9999 0 -10000 0 0
AKT1 0.014 0.037 -9999 0 -0.41 4 4
FOXO1 0.008 0.061 -9999 0 -0.41 11 11
AKT3 0.016 0.019 -9999 0 -0.41 1 1
FOXO4 0.017 0 -9999 0 -10000 0 0
MET 0.009 0.058 -9999 0 -0.41 10 10
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PIK3CB 0.017 0 -9999 0 -10000 0 0
NRAS -0.094 0.19 -9999 0 -0.41 137 137
PIK3CG 0.017 0 -9999 0 -10000 0 0
PIK3R3 0.016 0.019 -9999 0 -0.41 1 1
PIK3R2 0.017 0 -9999 0 -10000 0 0
NF1 0.017 0 -9999 0 -10000 0 0
RAS -0.047 0.063 -9999 0 -0.17 61 61
ERBB2 0.017 0 -9999 0 -10000 0 0
proliferation/survival/translation -0.041 0.026 -9999 0 -10000 0 0
PI3K -0.028 0.056 -9999 0 -0.12 71 71
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
KRAS 0.017 0.002 -9999 0 -10000 0 0
FOXO 0.021 0.034 -9999 0 -0.13 11 11
AKT2 0.017 0 -9999 0 -10000 0 0
PTEN 0.015 0.026 -9999 0 -0.41 2 2
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.052 0.2 5 -0.32 10 15
SMARCC2 0.016 0.019 -10000 0 -0.41 1 1
SMARCC1 0.002 0.078 -10000 0 -0.41 18 18
TBX21 0.016 0.033 0.17 1 -0.19 1 2
SUMO2 0.018 0.004 -10000 0 -10000 0 0
STAT1 (dimer) -0.012 0.11 -10000 0 -0.26 62 62
FKBP4 0.017 0 -10000 0 -10000 0 0
FKBP5 -0.004 0.093 -10000 0 -0.41 26 26
GR alpha/HSP90/FKBP51/HSP90 -0.009 0.048 0.2 1 -0.26 11 12
PRL 0.014 0.056 -10000 0 -0.42 6 6
cortisol/GR alpha (dimer)/TIF2 -0.015 0.059 0.32 6 -0.32 2 8
RELA -0.01 0.073 -10000 0 -0.2 40 40
FGG -0.021 0.061 0.29 2 -0.41 5 7
GR beta/TIF2 -0.005 0.026 0.17 2 -0.14 1 3
IFNG -0.038 0.13 -10000 0 -0.28 92 92
apoptosis 0.022 0.078 0.36 18 -0.27 2 20
CREB1 0.023 0.024 -10000 0 -0.18 7 7
histone acetylation 0.013 0.025 0.15 1 -10000 0 1
BGLAP 0.017 0.034 -10000 0 -0.18 1 1
GR/PKAc 0.006 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.014 0.14 -10000 0 -0.24 111 111
SMARCD1 0.017 0 -10000 0 -10000 0 0
MDM2 -0.009 0.029 0.16 1 -0.13 14 15
GATA3 0.026 0.042 -10000 0 -0.4 5 5
AKT1 0.01 0.041 0.14 3 -0.42 4 7
CSF2 0.004 0.04 -10000 0 -0.15 2 2
GSK3B 0.018 0.004 -10000 0 -10000 0 0
NR1I3 0.075 0.1 0.35 20 -0.25 2 22
CSN2 0 0.086 0.32 28 -0.29 2 30
BRG1/BAF155/BAF170/BAF60A 0.035 0.047 -10000 0 -0.21 19 19
NFATC1 0.026 0 -10000 0 -10000 0 0
POU2F1 0.022 0.015 -10000 0 -10000 0 0
CDKN1A -0.058 0.15 -10000 0 -0.32 108 108
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.005 -10000 0 -10000 0 0
SFN -0.01 0.1 -10000 0 -0.41 33 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.012 0.063 -10000 0 -0.23 30 30
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.069 0.11 0.34 16 -0.33 6 22
JUN 0.018 0.058 -10000 0 -0.3 9 9
IL4 0.018 0.033 -10000 0 -0.18 1 1
CDK5R1 0.014 0.007 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.021 0.081 0.12 7 -0.25 46 53
GR alpha/HSP90/FKBP51/HSP90/PP5C 0 0.045 0.2 1 -0.24 11 12
cortisol/GR alpha (monomer) -0.022 0.07 0.35 6 -0.39 2 8
NCOA2 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.071 0.18 -10000 0 -0.4 125 125
AP-1/NFAT1-c-4 -0.027 0.13 -10000 0 -0.42 22 22
AFP 0.016 0.062 -10000 0 -0.51 2 2
SUV420H1 0.016 0.019 -10000 0 -0.41 1 1
IRF1 -0.043 0.11 0.22 2 -0.31 64 66
TP53 -0.046 0.17 -10000 0 -0.43 71 71
PPP5C 0.017 0 -10000 0 -10000 0 0
KRT17 -0.043 0.14 -10000 0 -0.31 90 90
KRT14 0.003 0.063 -10000 0 -0.48 8 8
TBP 0.025 0.019 -10000 0 -0.4 1 1
CREBBP 0.01 0.018 0.16 7 -10000 0 7
HDAC1 -0.042 0.14 -10000 0 -0.42 66 66
HDAC2 0.011 0.042 -10000 0 -0.41 5 5
AP-1 -0.027 0.13 -10000 0 -0.42 22 22
MAPK14 0.017 0.027 -10000 0 -0.41 2 2
MAPK10 0.01 0.01 -10000 0 -10000 0 0
MAPK11 0.018 0.004 -10000 0 -10000 0 0
KRT5 -0.043 0.14 -10000 0 -0.31 92 92
interleukin-1 receptor activity -0.002 0 -10000 0 -10000 0 0
NCOA1 0.017 0.01 -10000 0 -10000 0 0
STAT1 -0.012 0.11 -10000 0 -0.26 62 62
CGA 0.012 0.059 -10000 0 -0.38 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.007 0.034 0.18 5 -0.21 3 8
MAPK3 0.018 0.005 -10000 0 -10000 0 0
MAPK1 0.018 0.005 -10000 0 -10000 0 0
ICAM1 -0.053 0.16 -10000 0 -0.33 106 106
NFKB1 -0.013 0.084 -10000 0 -0.23 43 43
MAPK8 0.019 0.048 0.19 1 -0.23 7 8
MAPK9 0.018 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.022 0.077 0.32 25 -0.28 2 27
BAX -0.035 0.099 -10000 0 -0.24 70 70
POMC -0.045 0.083 0.21 1 -10000 0 1
EP300 0.01 0.018 0.16 7 -10000 0 7
cortisol/GR alpha (dimer)/p53 -0.029 0.088 0.34 5 -0.33 22 27
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.018 0.12 1 -0.19 1 2
SGK1 0.025 0.029 0.18 8 -10000 0 8
IL13 -0.015 0.092 -10000 0 -0.26 21 21
IL6 -0.069 0.2 -10000 0 -0.39 115 115
PRKACG 0.017 0 -10000 0 -10000 0 0
IL5 -0.004 0.087 0.24 6 -0.24 6 12
IL2 -0.037 0.13 -10000 0 -0.28 92 92
CDK5 0.017 0.005 -10000 0 -10000 0 0
PRKACB 0.016 0.005 -10000 0 -10000 0 0
HSP90AA1 0.017 0 -10000 0 -10000 0 0
IL8 -0.099 0.23 -10000 0 -0.47 135 135
CDK5R1/CDK5 0.021 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.021 0.1 -10000 0 -0.26 36 36
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.011 0.055 0.3 7 -0.29 2 9
SMARCA4 0.017 0.001 -10000 0 -10000 0 0
chromatin remodeling -0.007 0.034 0.2 4 -0.17 7 11
NF kappa B1 p50/RelA/Cbp 0.004 0.11 0.21 3 -0.28 41 44
JUN (dimer) 0.018 0.058 -10000 0 -0.3 9 9
YWHAH 0.008 0.009 -10000 0 -10000 0 0
VIPR1 0.016 0.033 -10000 0 -0.19 1 1
NR3C1 -0.013 0.039 0.2 4 -0.21 2 6
NR4A1 0.023 0.001 -10000 0 -10000 0 0
TIF2/SUV420H1 0.025 0.014 -10000 0 -0.28 1 1
MAPKKK cascade 0.022 0.078 0.36 18 -0.27 2 20
cortisol/GR alpha (dimer)/Src-1 -0.014 0.054 0.36 3 -0.28 2 5
PBX1 0.022 0.015 -10000 0 -10000 0 0
POU1F1 0.022 0.015 -10000 0 -10000 0 0
SELE -0.045 0.14 -10000 0 -0.29 110 110
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.007 0.034 0.2 4 -0.17 7 11
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.011 0.055 0.3 7 -0.29 2 9
mol:cortisol -0.017 0.041 0.17 5 -0.16 9 14
MMP1 -0.025 0.13 -10000 0 -0.44 43 43
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.041 -10000 0 -0.28 10 10
MAP4K4 -0.014 0.067 -10000 0 -0.2 24 24
BAG4 0.017 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.005 0.019 0.1 10 -0.1 8 18
NFKBIA 0.016 0.019 -10000 0 -0.41 1 1
BIRC3 -0.01 0.1 -10000 0 -0.41 33 33
BAX 0.004 0.021 -10000 0 -0.15 7 7
RIPK1 0.01 0.055 -10000 0 -0.41 9 9
AKT1 0.007 0.034 -10000 0 -0.38 4 4
BAD -0.001 0.02 0.11 10 -10000 0 10
SMPD1 -0.021 0.056 -10000 0 -0.097 185 185
RB1 -0.001 0.02 0.11 10 -10000 0 10
FADD/Caspase 8 -0.007 0.068 -10000 0 -0.18 32 32
MAP2K4 0.002 0.02 -10000 0 -0.19 1 1
NSMAF 0.015 0.026 -10000 0 -0.41 2 2
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.002 0.021 0.11 10 -0.19 1 11
EGF 0.015 0.026 -10000 0 -0.41 2 2
mol:ceramide -0.005 0.021 0.12 10 -0.11 8 18
MADD 0.017 0.001 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.012 0.041 -10000 0 -0.28 10 10
ASAH1 0.017 0.001 -10000 0 -10000 0 0
negative regulation of cell cycle -0.001 0.02 0.11 10 -10000 0 10
cell proliferation 0.026 0.026 -10000 0 -0.16 5 5
BID -0.002 0.053 -10000 0 -0.2 5 5
MAP3K1 -0.001 0.022 0.11 10 -0.2 1 11
EIF2A 0.003 0.019 -10000 0 -10000 0 0
TRADD 0.017 0 -10000 0 -10000 0 0
CRADD 0.017 0 -10000 0 -10000 0 0
MAPK3 0.011 0.022 -10000 0 -0.18 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.027 -10000 0 -0.18 2 2
Cathepsin D/ceramide 0.001 0.042 0.11 10 -0.19 19 29
FADD -0.015 0.068 -10000 0 -0.19 26 26
KSR1 -0.001 0.02 0.11 10 -0.1 3 13
MAPK8 0.008 0.023 0.11 10 -0.12 1 11
PRKRA -0.001 0.02 0.11 10 -10000 0 10
PDGFA 0.009 0.058 -10000 0 -0.41 10 10
TRAF2 0.017 0 -10000 0 -10000 0 0
IGF1 0.014 0.037 -10000 0 -0.41 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.005 0.021 0.12 10 -0.11 8 18
CTSD 0.004 0.073 -10000 0 -0.41 16 16
regulation of nitric oxide biosynthetic process 0.023 0.027 -10000 0 -0.28 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.028 0.027 -10000 0 -0.16 5 5
PRKCD 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.012 0.041 -10000 0 -0.28 10 10
RelA/NF kappa B1 0.023 0.027 -10000 0 -0.28 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.017 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.018 0.072 -10000 0 -0.21 24 24
TNFR1A/BAG4/TNF-alpha -0.059 0.13 -10000 0 -0.23 185 185
mol:Sphingosine-1-phosphate 0.012 0.041 -10000 0 -0.28 10 10
MAP2K1 0.005 0.02 -10000 0 -0.18 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
CYCS 0.002 0.018 -10000 0 -0.16 1 1
TNFRSF1A -0.13 0.2 -10000 0 -0.41 183 183
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
TNFR1A/BAG4 -0.082 0.15 -10000 0 -0.28 183 183
EIF2AK2 0.003 0.02 0.11 12 -10000 0 12
TNF-alpha/TNFR1A/FAN -0.06 0.13 -10000 0 -0.23 187 187
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.051 -10000 0 -0.18 15 15
MAP2K2 0.005 0.02 -10000 0 -0.18 1 1
SMPD3 -0.018 0.058 -10000 0 -0.096 185 185
TNF 0.015 0.026 -10000 0 -0.41 2 2
PKC zeta/PAR4 0.013 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.013 0.022 0.1 8 -0.087 1 9
NF kappa B1/RelA/I kappa B alpha 0.039 0.023 -10000 0 -0.19 5 5
AIFM1 -0.001 0.028 -10000 0 -0.14 12 12
BCL2 0.017 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.034 0.044 -10000 0 -0.26 5 5
UGCG 0.012 0.026 -10000 0 -0.22 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.017 0.092 -10000 0 -0.22 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.012 0.026 -10000 0 -0.22 1 1
mol:DAG 0.006 0.01 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.1 -10000 0 -0.24 36 36
FRAP1 0.002 0.12 -10000 0 -0.26 51 51
FOXO3 -0.003 0.12 -10000 0 -0.26 50 50
AKT1 -0.008 0.13 -10000 0 -0.2 137 137
GAB2 0.015 0.019 -10000 0 -0.41 1 1
SMPD1 0.013 0.024 -10000 0 -10000 0 0
SGMS1 0.012 0.027 -10000 0 -0.26 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.001 0.053 -10000 0 -0.23 25 25
CALM1 0.016 0.004 -10000 0 -10000 0 0
cell proliferation -0.001 0.077 -10000 0 -0.18 21 21
EIF3A 0.017 0 -10000 0 -10000 0 0
PI3K 0.011 0.066 -10000 0 -0.28 25 25
RPS6KB1 0.017 0.027 -10000 0 -0.34 1 1
mol:sphingomyelin 0.006 0.01 -10000 0 -10000 0 0
natural killer cell activation -0.001 0.003 -10000 0 -0.006 136 136
JAK3 0.018 0.003 -10000 0 -10000 0 0
PIK3R1 0.017 0.006 -10000 0 -10000 0 0
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MYC -0.043 0.18 -10000 0 -0.35 137 137
MYB 0.023 0.05 -10000 0 -0.38 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.092 -10000 0 -0.22 39 39
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.026 -10000 0 -0.3 1 1
mol:PI-3-4-5-P3 0.008 0.09 -10000 0 -0.22 39 39
Rac1/GDP 0.01 0.049 -10000 0 -0.21 24 24
T cell proliferation 0.008 0.086 -10000 0 -0.2 40 40
SHC1 -0.022 0.12 -10000 0 -0.41 47 47
RAC1 0.017 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.005 -10000 0 -0.039 8 8
PRKCZ 0.007 0.088 -10000 0 -0.21 40 40
NF kappa B1 p50/RelA 0.014 0.12 -10000 0 -0.25 43 43
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.03 0.047 -10000 0 -0.28 5 5
HSP90AA1 0.017 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
IL2RA 0.011 0.046 -10000 0 -0.41 6 6
IL2RB 0.015 0.038 -10000 0 -0.42 4 4
TERT 0.017 0 -10000 0 -10000 0 0
E2F1 0.023 0.032 -10000 0 -0.23 8 8
SOS1 -0.001 0.003 -10000 0 -0.006 135 135
RPS6 0.017 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.002 0.018 8 -10000 0 8
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG 0.01 0.056 -10000 0 -0.42 9 9
actin cytoskeleton organization 0.008 0.086 -10000 0 -0.2 40 40
GRB2 0.016 0.003 -10000 0 -10000 0 0
IL2 0.018 0.004 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
Rac1/GTP 0.019 0.051 -10000 0 -0.2 24 24
LCK 0.014 0.038 -10000 0 -0.42 4 4
BCL2 0.012 0.1 -10000 0 -0.22 46 46
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.037 -10000 0 -0.41 4 4
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.004 -10000 0 -0.051 4 4
monocyte activation -0.084 0.071 -10000 0 -0.13 353 353
MAP2K2 0.012 0.002 -10000 0 -10000 0 0
MAP2K1 0.004 0.004 -10000 0 -10000 0 0
MAP2K7 0.005 0.004 -10000 0 -10000 0 0
MAP2K6 0.005 0.004 -10000 0 -10000 0 0
CYAA 0.002 0.018 -10000 0 -0.2 4 4
MAP2K4 0.004 0.004 -10000 0 -10000 0 0
IL1B -0.006 0.036 -10000 0 -0.21 14 14
Channel 0.009 0.02 -10000 0 -0.22 4 4
NLRP1 0.005 0.004 -10000 0 -10000 0 0
CALM1 0.016 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.01 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.004 0.051 4 -10000 0 4
MAPK3 0.005 0.004 -10000 0 -10000 0 0
MAPK1 0.004 0.004 -10000 0 -10000 0 0
PGR 0.005 0.004 -10000 0 -10000 0 0
PA/Cellular Receptors 0.01 0.022 -10000 0 -0.24 4 4
apoptosis 0 0.004 -10000 0 -0.051 4 4
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.009 0.018 -10000 0 -0.19 4 4
macrophage activation 0.007 0.004 -10000 0 -10000 0 0
TNF 0.015 0.026 -10000 0 -0.41 2 2
VCAM1 -0.084 0.071 -10000 0 -0.13 353 353
platelet activation 0.01 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.009 -10000 0 -10000 0 0
IL18 -0.018 0.061 -10000 0 -0.22 45 45
negative regulation of macrophage activation 0 0.004 -10000 0 -0.051 4 4
LEF 0 0.004 -10000 0 -0.051 4 4
CASP1 -0.005 0.015 -10000 0 -0.07 3 3
mol:cAMP 0.01 0.006 -10000 0 -10000 0 0
necrosis 0 0.004 -10000 0 -0.051 4 4
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.009 0.019 -10000 0 -0.2 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.04 0.051 -9999 0 -0.19 25 25
SMAD6-7/SMURF1 0.034 0.012 -9999 0 -0.23 1 1
NOG 0 0 -9999 0 -10000 0 0
SMAD9 0.02 0.019 -9999 0 -10000 0 0
SMAD4 -0.086 0.18 -9999 0 -0.41 127 127
SMAD5 0.02 0.034 -9999 0 -0.16 10 10
BMP7/USAG1 0.02 0.04 -9999 0 -0.28 9 9
SMAD5/SKI 0.029 0.035 -9999 0 -0.19 5 5
SMAD1 -0.004 0.074 -9999 0 -0.14 114 114
BMP2 -0.027 0.13 -9999 0 -0.41 54 54
SMAD1/SMAD1/SMAD4 -0.058 0.084 -9999 0 -0.26 49 49
BMPR1A 0.012 0.045 -9999 0 -0.41 6 6
BMPR1B 0.016 0.019 -9999 0 -0.41 1 1
BMPR1A-1B/BAMBI 0.014 0.074 -9999 0 -0.25 39 39
AHSG 0.015 0.026 -9999 0 -0.41 2 2
CER1 0.017 0 -9999 0 -10000 0 0
BMP2-4/CER1 0.003 0.087 -9999 0 -0.23 62 62
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.016 0.046 -9999 0 -0.2 9 9
BMP2-4 (homodimer) -0.011 0.1 -9999 0 -0.28 62 62
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.04 0.033 -9999 0 -0.21 9 9
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.007 0.039 -9999 0 -0.095 64 64
BMP2-4/USAG1 0 0.094 -9999 0 -0.24 66 66
SMAD6/SMURF1/SMAD5 0.029 0.035 -9999 0 -0.19 5 5
SOSTDC1 0.011 0.049 -9999 0 -0.41 7 7
BMP7/BMPR2/BMPR1A-1B 0.04 0.033 -9999 0 -0.21 9 9
SKI 0.017 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.015 0.026 -9999 0 -0.41 2 2
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.013 0.042 -9999 0 -0.41 5 5
MAP3K7 0.016 0.019 -9999 0 -0.41 1 1
BMP2-4/CHRD 0.003 0.087 -9999 0 -0.23 62 62
SMAD5/SMAD5/SMAD4 -0.019 0.098 -9999 0 -0.18 129 129
MAPK1 0.017 0.003 -9999 0 -10000 0 0
TAK1/TAB family 0.035 0.041 -9999 0 -0.16 6 6
BMP7 (homodimer) 0.015 0.026 -9999 0 -0.41 2 2
NUP214 0.017 0 -9999 0 -10000 0 0
BMP6/FETUA 0.023 0.027 -9999 0 -0.28 4 4
SMAD1/SKI 0.003 0.075 -9999 0 -0.25 8 8
SMAD6 0.017 0 -9999 0 -10000 0 0
CTDSP2 -0.013 0.11 -9999 0 -0.41 37 37
BMP2-4/FETUA 0.002 0.089 -9999 0 -0.24 63 63
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
GREM1 -0.002 0.088 -9999 0 -0.41 23 23
BMPR2 (homodimer) 0.017 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.032 0.029 -9999 0 -0.23 6 6
BMPR1A-1B (homodimer) 0.021 0.035 -9999 0 -0.28 7 7
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 0.001 0.077 -9999 0 -0.23 13 13
SMAD6-7/SMURF1/SMAD1 0.016 0.075 -9999 0 -0.26 6 6
SMAD6/SMURF1 0.017 0 -9999 0 -10000 0 0
BAMBI -0.011 0.1 -9999 0 -0.41 34 34
SMURF2 0.015 0.026 -9999 0 -0.41 2 2
BMP2-4/CHRDL1 -0.007 0.084 -9999 0 -0.24 62 62
BMP2-4/GREM1 -0.008 0.1 -9999 0 -0.24 82 82
SMAD7 0.016 0.019 -9999 0 -0.41 1 1
SMAD8A/SMAD8A/SMAD4 -0.023 0.096 -9999 0 -0.19 127 127
SMAD1/SMAD6 0.003 0.075 -9999 0 -0.25 8 8
TAK1/SMAD6 0.025 0.013 -9999 0 -0.28 1 1
BMP7 0.015 0.026 -9999 0 -0.41 2 2
BMP6 0.015 0.026 -9999 0 -0.41 2 2
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.013 0.038 -9999 0 -0.19 5 5
PPM1A 0.017 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.002 0.075 -9999 0 -0.23 10 10
SMAD7/SMURF1 0.025 0.013 -9999 0 -0.28 1 1
CTDSPL 0.017 0 -9999 0 -10000 0 0
PPP1CA 0.017 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.015 0.032 -9999 0 -0.41 3 3
PPP1R15A 0.016 0.019 -9999 0 -0.41 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.007 0.046 -9999 0 -0.14 26 26
CHRD 0.017 0 -9999 0 -10000 0 0
BMPR2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.006 0.045 -9999 0 -0.11 64 64
BMP4 0.011 0.052 -9999 0 -0.41 8 8
FST 0.004 0.073 -9999 0 -0.41 16 16
BMP2-4/NOG -0.007 0.084 -9999 0 -0.24 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.047 0.031 -9999 0 -0.19 9 9
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.025 0.029 -9999 0 -0.15 8 8
KLHL20 0.004 0.065 -9999 0 -0.13 94 94
CYFIP2 0.01 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.033 0.027 -9999 0 -0.14 2 2
ENAH 0.016 0.054 -9999 0 -0.18 34 34
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 0 4 4
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0.017 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.02 -9999 0 -0.13 2 2
ABI1/Sra1/Nap1 -0.015 0.032 -9999 0 -0.099 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.037 -9999 0 -0.23 9 9
RAPGEF1 0.027 0.026 -9999 0 -10000 0 0
CTNND1 0.009 0.058 -9999 0 -0.41 10 10
regulation of calcium-dependent cell-cell adhesion 0.024 0.03 -9999 0 -0.14 13 13
CRK 0.026 0.028 -9999 0 -0.14 8 8
E-cadherin/gamma catenin/alpha catenin 0.023 0.064 -9999 0 -0.29 19 19
alphaE/beta7 Integrin 0.024 0.019 -9999 0 -0.28 2 2
IQGAP1 -0.086 0.18 -9999 0 -0.41 127 127
NCKAP1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.022 0.001 -9999 0 -10000 0 0
DLG1 0.025 0.03 -9999 0 -0.16 9 9
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.025 -9999 0 -0.12 12 12
MLLT4 0.017 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.021 0.004 -9999 0 -10000 0 0
PI3K -0.008 0.031 -9999 0 -0.16 11 11
ARF6 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -0.001 96 96
E-cadherin/gamma catenin 0.012 0.073 -9999 0 -0.35 19 19
TIAM1 0.016 0.003 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.032 0.043 -9999 0 -0.2 18 18
AKT1 0.016 0.028 -9999 0 -0.12 8 8
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
CDH1 0.01 0.052 -9999 0 -0.41 8 8
RhoA/GDP 0.034 0.025 -9999 0 -10000 0 0
actin cytoskeleton organization 0.004 0.049 -9999 0 -0.098 94 94
CDC42/GDP 0.035 0.025 -9999 0 -0.14 1 1
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.043 -9999 0 -0.16 28 28
ITGB7 0.015 0.026 -9999 0 -0.41 2 2
RAC1 0.017 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.035 0.046 -9999 0 -0.21 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin 0.027 0.028 -9999 0 -0.2 8 8
mol:GDP 0.027 0.027 -9999 0 -0.15 3 3
CDC42/GTP/IQGAP1 -0.04 0.11 -9999 0 -0.24 127 127
JUP 0.004 0.073 -9999 0 -0.41 16 16
p120 catenin/RhoA/GDP 0.036 0.032 -9999 0 -0.15 5 5
RAC1/GTP/IQGAP1 -0.04 0.11 -9999 0 -0.24 127 127
PIP5K1C/AP1M1 0.012 0.002 -9999 0 -10000 0 0
RHOA 0.017 0.001 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.013 0.074 -9999 0 -0.17 98 98
NME1 0 0 -9999 0 -0.001 98 98
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.025 0.029 -9999 0 -0.15 8 8
regulation of cell-cell adhesion -0.003 0.016 -9999 0 -0.11 2 2
WASF2 -0.008 0.018 -9999 0 -0.055 13 13
Rap1/GTP 0.025 0.026 -9999 0 -0.14 4 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.061 -9999 0 -0.25 20 20
CCND1 -0.017 0.09 -9999 0 -0.2 98 98
VAV2 0.031 0.03 -9999 0 -10000 0 0
RAP1/GDP 0.028 0.026 -9999 0 -0.14 5 5
adherens junction assembly 0.025 0.028 -9999 0 -0.15 8 8
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.017 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0.003 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.037 0.058 -9999 0 -0.24 20 20
E-cadherin/beta catenin 0.019 0.032 -9999 0 -0.16 8 8
mol:GTP 0 0 -9999 0 -0.001 98 98
SRC 0.025 0.029 -9999 0 -0.16 8 8
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
Rac1/GTP -0.037 0.077 -9999 0 -0.2 94 94
E-cadherin/beta catenin/alpha catenin 0.03 0.033 -9999 0 -0.24 8 8
ITGAE 0.017 0.001 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.03 -9999 0 -0.14 13 13
Coregulation of Androgen receptor activity

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
NRIP1 0.015 0.037 -9999 0 -0.41 4 4
SVIL 0.003 0.08 -9999 0 -0.41 19 19
ZNF318 0.014 0 -9999 0 -10000 0 0
JMJD2C 0.023 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.03 0.034 -9999 0 -0.23 8 8
CARM1 0.017 0 -9999 0 -10000 0 0
PRDX1 0.017 0.001 -9999 0 -10000 0 0
PELP1 0.017 0 -9999 0 -10000 0 0
CTNNB1 0.018 0 -9999 0 -10000 0 0
AKT1 0.013 0.037 -9999 0 -0.41 4 4
PTK2B 0.018 0 -9999 0 -10000 0 0
MED1 0.016 0 -9999 0 -10000 0 0
MAK 0.008 0.052 -9999 0 -0.41 8 8
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 -0.026 0.13 -9999 0 -0.41 54 54
GSN 0.006 0.071 -9999 0 -0.41 15 15
NCOA2 0.017 0 -9999 0 -10000 0 0
NCOA6 0.018 0.001 -9999 0 -10000 0 0
DNA-PK 0.02 0.055 -9999 0 -0.24 23 23
NCOA4 0.017 0.001 -9999 0 -10000 0 0
PIAS3 0.016 0.026 -9999 0 -0.41 2 2
cell proliferation 0.012 0.033 -9999 0 -0.24 8 8
XRCC5 0.017 0 -9999 0 -10000 0 0
UBE3A 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.019 0.032 -9999 0 -0.23 8 8
FHL2 0.028 0.038 -9999 0 -0.37 4 4
RANBP9 0.018 0.001 -9999 0 -10000 0 0
JMJD1A 0.021 0.065 -9999 0 -0.4 12 12
CDK6 0.017 0 -9999 0 -10000 0 0
TGFB1I1 -0.34 0.16 -9999 0 -0.41 441 441
T-DHT/AR/CyclinD1 -0.017 0.11 -9999 0 -0.24 103 103
XRCC6 0.017 0 -9999 0 -10000 0 0
T-DHT/AR 0.047 0.04 -9999 0 -0.22 8 8
CTDSP1 0.015 0.032 -9999 0 -0.41 3 3
CTDSP2 -0.015 0.11 -9999 0 -0.41 37 37
BRCA1 0.014 0.042 -9999 0 -0.41 5 5
TCF4 0.016 0.002 -9999 0 -10000 0 0
CDKN2A -0.031 0.13 -9999 0 -0.41 58 58
SRF 0.021 0.011 -9999 0 -10000 0 0
NKX3-1 0.032 0.038 -9999 0 -0.18 11 11
KLK3 0.017 0.029 -9999 0 -10000 0 0
TMF1 0.014 0.037 -9999 0 -0.41 4 4
HNRNPA1 0.016 0 -9999 0 -10000 0 0
AOF2 0.013 0.049 -9999 0 -0.41 7 7
APPL1 0.014 0.026 -9999 0 -0.29 4 4
T-DHT/AR/Caspase 8 0.024 0.049 -9999 0 -0.24 17 17
AR 0.015 0.052 -9999 0 -0.4 8 8
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.016 0 -9999 0 -10000 0 0
PAWR 0.017 0 -9999 0 -10000 0 0
PRKDC -0.002 0.088 -9999 0 -0.41 23 23
PA2G4 0.015 0.019 -9999 0 -0.41 1 1
UBE2I 0.017 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.028 0.032 -9999 0 -0.2 9 9
RPS6KA3 0.018 0.019 -9999 0 -0.41 1 1
T-DHT/AR/ARA70 0.03 0.034 -9999 0 -0.23 8 8
LATS2 -0.001 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.027 0.031 -9999 0 -0.2 8 8
Cyclin D3/CDK11 p58 0.012 0.013 -9999 0 -0.29 1 1
VAV3 -0.011 0.11 -9999 0 -0.41 36 36
KLK2 0.033 0.017 -9999 0 -10000 0 0
CASP8 0.009 0.056 -9999 0 -0.41 9 9
T-DHT/AR/TIF2/CARM1 0.04 0.033 -9999 0 -0.2 8 8
TMPRSS2 0.031 0.047 -9999 0 -0.22 14 14
CCND1 -0.062 0.17 -9999 0 -0.41 98 98
PIAS1 0.019 0 -9999 0 -10000 0 0
mol:T-DHT 0.005 0.006 -9999 0 -0.045 7 7
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.02 0 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.029 0.034 -9999 0 -0.23 8 8
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.021 0.009 -9999 0 -10000 0 0
CCND3 0.016 0.019 -9999 0 -0.41 1 1
TGIF1 -0.29 0.2 -9999 0 -0.41 372 372
FKBP4 0.018 0 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.028 0.046 -10000 0 -0.18 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.017 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.01 0.11 -10000 0 -0.25 70 70
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.027 0.042 -10000 0 -0.24 13 13
antigen processing and presentation of peptide antigen via MHC class I -0.051 0.077 -10000 0 -0.18 113 113
CaM/Ca2+ 0.028 0.042 -10000 0 -0.17 12 12
RAP1A 0.017 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.009 0.068 -10000 0 -0.22 32 32
AKT1 0.008 0.053 -10000 0 -0.17 33 33
MAP2K1 0.017 0.036 -10000 0 -0.19 4 4
MAP3K11 0.016 0.038 -10000 0 -0.17 14 14
IFNGR1 0.007 0.067 -10000 0 -0.41 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.003 0.033 -10000 0 -0.19 10 10
Rap1/GTP -0.006 0.022 -10000 0 -0.16 4 4
CRKL/C3G 0.025 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.042 0.041 -10000 0 -0.19 15 15
CEBPB 0.037 0.056 -10000 0 -0.27 4 4
STAT3 0.009 0.058 -10000 0 -0.41 10 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.043 0.036 -10000 0 -10000 0 0
STAT1 0.003 0.066 -10000 0 -0.22 32 32
CALM1 0.016 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.016 0.019 -10000 0 -0.41 1 1
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
STAT1 (dimer)/PIAS1 0.012 0.065 -10000 0 -0.2 32 32
CEBPB/PTGES2/Cbp/p300 -0.002 0.041 -10000 0 -0.23 4 4
mol:Ca2+ 0.026 0.045 -10000 0 -0.18 14 14
MAPK3 0.03 0.035 -10000 0 -10000 0 0
STAT1 (dimer) -0.064 0.11 -10000 0 -0.24 113 113
MAPK1 0.013 0.11 -10000 0 -0.58 15 15
JAK2 0.017 0.006 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.038 0.042 -10000 0 -0.19 3 3
SMAD7 -0.001 0.06 -10000 0 -0.12 50 50
CBL/CRKL/C3G 0.031 0.039 -10000 0 -0.15 14 14
PI3K 0.016 0.059 -10000 0 -0.18 35 35
IFNG 0.016 0.019 -10000 0 -0.41 1 1
apoptosis 0.026 0.043 0.22 4 -0.21 1 5
CAMK2G 0.008 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.009 0.058 -10000 0 -0.41 10 10
CAMK2A 0.016 0.004 -10000 0 -10000 0 0
CAMK2B 0.002 0.006 -10000 0 -10000 0 0
FRAP1 0.016 0.058 0.19 3 -0.2 11 14
PRKCD 0.015 0.059 0.2 2 -0.17 29 31
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.051 0.077 -10000 0 -0.18 113 113
PTPN2 0.016 0.019 -10000 0 -0.41 1 1
EP300 0.017 0.002 -10000 0 -10000 0 0
IRF1 -0.015 0.14 -10000 0 -0.36 70 70
STAT1 (dimer)/PIASy 0.009 0.065 -10000 0 -0.21 32 32
SOCS1 0.017 0.003 -10000 0 -10000 0 0
mol:GDP 0.028 0.037 -10000 0 -0.15 14 14
CASP1 -0.044 0.12 -10000 0 -0.21 172 172
PTGES2 0.017 0 -10000 0 -10000 0 0
IRF9 0.029 0.028 -10000 0 -0.12 1 1
mol:PI-3-4-5-P3 0.008 0.054 -10000 0 -0.17 35 35
RAP1/GDP 0.02 0.031 -10000 0 -0.16 4 4
CBL 0.015 0.038 -10000 0 -0.17 14 14
MAP3K1 0.016 0.039 -10000 0 -0.17 15 15
PIAS1 0.017 0 -10000 0 -10000 0 0
PIAS4 0.017 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.051 0.077 -10000 0 -0.18 113 113
PTPN11 0.011 0.039 -10000 0 -0.18 14 14
CREBBP 0.017 0.002 -10000 0 -10000 0 0
RAPGEF1 0.017 0 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.013 0.074 -10000 0 -0.21 24 24
BAG4 0.017 0 -10000 0 -10000 0 0
BAD 0.003 0.027 -10000 0 -10000 0 0
NFKBIA 0.016 0.019 -10000 0 -0.41 1 1
BIRC3 -0.009 0.1 -10000 0 -0.41 33 33
BAX 0.001 0.036 -10000 0 -0.21 7 7
EnzymeConsortium:3.1.4.12 -0.002 0.021 -10000 0 -0.055 24 24
IKBKB -0.009 0.071 -10000 0 -0.2 24 24
MAP2K2 0.01 0.026 -10000 0 -0.15 1 1
MAP2K1 0.009 0.025 -10000 0 -0.15 1 1
SMPD1 0.002 0.021 -10000 0 -0.051 21 21
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.008 0.073 -10000 0 -0.2 29 29
MAP2K4 0.006 0.026 -10000 0 -0.16 1 1
protein ubiquitination -0.009 0.071 0.15 1 -0.2 24 25
EnzymeConsortium:2.7.1.37 0.015 0.03 -10000 0 -0.15 1 1
response to UV 0 0 -10000 0 -0.001 1 1
RAF1 0.008 0.027 -10000 0 -0.16 1 1
CRADD 0.017 0 -10000 0 -10000 0 0
mol:ceramide 0 0.028 -10000 0 -0.073 24 24
I-kappa-B-alpha/RELA/p50/ubiquitin 0.023 0.011 -10000 0 -0.24 1 1
MADD 0.017 0.002 -10000 0 -10000 0 0
MAP3K1 0.003 0.028 -10000 0 -0.17 1 1
TRADD 0.017 0 -10000 0 -10000 0 0
RELA/p50 0.017 0 -10000 0 -10000 0 0
MAPK3 0.014 0.028 -10000 0 -0.14 1 1
MAPK1 0.012 0.028 -10000 0 -0.14 1 1
p50/RELA/I-kappa-B-alpha 0.025 0.013 -10000 0 -0.28 1 1
FADD -0.014 0.074 -10000 0 -0.21 26 26
KSR1 0.004 0.027 -10000 0 -10000 0 0
MAPK8 0.013 0.032 0.13 15 -0.14 1 16
TRAF2 0.017 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.01 0.071 -10000 0 -0.2 25 25
TNF R/SODD -0.082 0.15 -10000 0 -0.28 183 183
TNF 0.016 0.026 -10000 0 -0.41 2 2
CYCS 0.002 0.03 -10000 0 -0.12 7 7
IKBKG -0.009 0.071 -10000 0 -0.2 24 24
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.017 0.077 -10000 0 -0.22 24 24
RELA 0.017 0 -10000 0 -10000 0 0
RIPK1 0.01 0.055 -10000 0 -0.41 9 9
AIFM1 0 0.033 -10000 0 -0.15 7 7
TNF/TNF R/SODD -0.059 0.13 -10000 0 -0.23 185 185
TNFRSF1A -0.13 0.2 -10000 0 -0.41 183 183
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.032 -10000 0 -10000 0 0
NSMAF -0.013 0.073 -10000 0 -0.2 26 26
response to hydrogen peroxide 0 0 -10000 0 -0.001 1 1
BCL2 0.017 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.017 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.01 0.065 -10000 0 -0.12 132 132
NT3 (dimer)/TRKC 0.025 0.004 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.021 0.052 -10000 0 -0.23 20 20
SHC/Grb2/SOS1/GAB1/PI3K 0.004 0.057 -10000 0 -0.14 71 71
RAPGEF1 0.017 0 -10000 0 -10000 0 0
BDNF 0.005 0.008 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
DYNLT1 -0.044 0.15 -10000 0 -0.41 75 75
NTRK1 0.015 0.026 -10000 0 -0.41 2 2
NTRK2 0.015 0.005 -10000 0 -10000 0 0
NTRK3 0.017 0.003 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.011 0.05 -10000 0 -0.23 22 22
neuron apoptosis 0.01 0.048 0.19 17 -10000 0 17
SHC 2-3/Grb2 -0.011 0.051 -10000 0 -0.2 17 17
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
SHC2 -0.012 0.05 -10000 0 -0.17 37 37
SHC3 -0.014 0.06 -10000 0 -0.19 40 40
STAT3 (dimer) -0.027 0.11 -10000 0 -0.24 104 104
NT3 (dimer)/TRKA 0.023 0.058 -10000 0 -0.24 23 23
RIN/GDP 0.014 0.029 -10000 0 -0.12 6 6
GIPC1 0.017 0 -10000 0 -10000 0 0
KRAS 0.017 0.002 -10000 0 -10000 0 0
DNAJA3 0.002 0.043 -10000 0 -0.17 23 23
RIN/GTP 0.005 0.023 -10000 0 -0.29 3 3
CCND1 -0.058 0.17 -10000 0 -0.4 104 104
MAGED1 0.017 0.001 -10000 0 -10000 0 0
PTPN11 0.017 0 -10000 0 -10000 0 0
RICS 0.012 0.008 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0 0.074 -10000 0 -0.24 47 47
GRB2 0.017 0.002 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.022 0.016 -10000 0 -0.24 2 2
TRKA/NEDD4-2 0.024 0.019 -10000 0 -0.28 2 2
ELMO1 0.011 0.008 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.015 0.011 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
DOCK1 0.017 0 -10000 0 -10000 0 0
GAB2 0.016 0.019 -10000 0 -0.41 1 1
RIT2 0.007 0.033 -10000 0 -0.41 3 3
RIT1 -0.12 0.2 -10000 0 -0.41 163 163
FRS2 0.015 0.032 -10000 0 -0.41 3 3
DNM1 0.003 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.017 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.004 0.04 -10000 0 -0.17 19 19
mol:GDP 0.016 0.048 -10000 0 -0.14 14 14
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.008 0.006 -10000 0 -10000 0 0
RIT1/GDP -0.023 0.08 -10000 0 -0.13 159 159
TIAM1 0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.001 0.044 -10000 0 -0.23 12 12
KIDINS220/CRKL/C3G 0.025 0 -10000 0 -10000 0 0
SHC/RasGAP -0.003 0.088 -10000 0 -0.28 47 47
FRS2 family/SHP2 0.033 0.02 -10000 0 -0.23 3 3
SHC/GRB2/SOS1/GAB1 0.009 0.072 -10000 0 -0.21 51 51
RIT1/GTP -0.08 0.14 -10000 0 -0.29 163 163
NT3 (dimer) 0.017 0 -10000 0 -10000 0 0
RAP1/GDP -0.005 0.021 -10000 0 -10000 0 0
KIDINS220/CRKL 0.017 0 -10000 0 -10000 0 0
BDNF (dimer) 0.005 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.022 0.016 -10000 0 -0.24 2 2
Schwann cell development -0.002 0.007 -10000 0 -10000 0 0
EHD4 -0.01 0.1 -10000 0 -0.41 34 34
FRS2 family/GRB2/SOS1 0.031 0.019 -10000 0 -0.21 3 3
FRS2 family/SHP2/CRK family/C3G/GAB2 0.033 0.011 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP 0.002 0.03 -10000 0 -10000 0 0
ABL1 0.016 0.019 -10000 0 -0.41 1 1
SH2B family/GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
Rap1/GTP 0.005 0.021 -10000 0 -10000 0 0
STAT3 -0.027 0.11 -10000 0 -0.24 104 104
axon guidance 0 0.027 -10000 0 -10000 0 0
MAPK3 0.019 0.014 -10000 0 -0.21 2 2
MAPK1 0.018 0.014 -10000 0 -0.21 2 2
CDC42/GDP 0.02 0.037 -10000 0 -0.1 4 4
NTF3 0.017 0 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.013 0.05 -10000 0 -0.24 20 20
PI3K 0.009 0.065 -10000 0 -0.28 25 25
FRS3 0.017 0 -10000 0 -10000 0 0
FAIM 0.002 0.078 -10000 0 -0.41 18 18
GAB1 0.014 0.037 -10000 0 -0.41 4 4
RASGRF1 0.001 0.045 -10000 0 -0.17 25 25
SOS1 0 0 -10000 0 -10000 0 0
MCF2L 0.018 0.008 -10000 0 -10000 0 0
RGS19 0.017 0 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.061 -10000 0 -0.18 28 28
Rac1/GDP 0.02 0.037 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT 0.016 0.019 -10000 0 -0.24 2 2
neuron projection morphogenesis 0 0.064 -10000 0 -0.37 1 1
NGF (dimer)/TRKA/NEDD4-2 0.022 0.016 -10000 0 -0.24 2 2
MAP2K1 0.001 0.064 -10000 0 -0.19 51 51
NGFR -0.001 0.086 -10000 0 -0.41 22 22
NGF (dimer)/TRKA/GIPC/GAIP -0.015 0.052 -10000 0 -0.14 76 76
RAS family/GTP/PI3K -0.023 0.076 -10000 0 -0.14 157 157
FRS2 family/SHP2/GRB2/SOS1 0.039 0.018 -10000 0 -0.19 3 3
NRAS -0.094 0.19 -10000 0 -0.41 137 137
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
PRKCI 0.016 0.019 -10000 0 -0.41 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.003 0.031 -10000 0 -0.17 1 1
RASA1 0.017 0.002 -10000 0 -10000 0 0
TRKA/c-Abl 0.024 0.023 -10000 0 -0.28 3 3
SQSTM1 0.016 0.019 -10000 0 -0.41 1 1
BDNF (dimer)/TRKB/GIPC -0.005 0.049 -10000 0 -0.21 15 15
NGF (dimer)/TRKA/p62/Atypical PKCs 0.029 0.02 -10000 0 -0.2 4 4
MATK 0.017 0 -10000 0 -10000 0 0
NEDD4L 0.017 0 -10000 0 -10000 0 0
RAS family/GDP -0.025 0.041 -10000 0 -0.15 25 25
NGF (dimer)/TRKA -0.001 0.046 -10000 0 -0.14 44 44
Rac1/GTP -0.015 0.033 -10000 0 -0.14 15 15
FRS2 family/SHP2/CRK family 0.05 0.018 -10000 0 -0.19 3 3
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.019 0.034 -9999 0 -0.24 9 9
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.01 0.055 -9999 0 -0.41 9 9
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.002 0.027 -9999 0 -0.12 23 23
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.048 0.15 -9999 0 -0.41 80 80
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0 -9999 0 -10000 0 0
FYN 0.015 0.026 -9999 0 -0.41 2 2
MAP3K12 0.017 0 -9999 0 -10000 0 0
FGR 0.003 0.076 -9999 0 -0.41 17 17
p38 alpha/TAB1 -0.003 0.067 -9999 0 -0.16 48 48
PRKG1 0.017 0 -9999 0 -10000 0 0
DUSP8 0.013 0.007 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.005 0.064 -9999 0 -0.16 47 47
apoptosis -0.003 0.065 -9999 0 -0.15 49 49
RAL/GTP 0.001 0.073 -9999 0 -0.24 45 45
LYN -0.035 0.14 -9999 0 -0.41 64 64
DUSP1 0.002 0.078 -9999 0 -0.41 18 18
PAK1 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.033 0 -9999 0 -10000 0 0
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
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 0.023 0 -9999 0 -10000 0 0
MAPK11 -0.014 0.076 -9999 0 -0.18 54 54
BLK 0.017 0 -9999 0 -10000 0 0
HCK -0.053 0.16 -9999 0 -0.41 86 86
MAP2K3 0.017 0 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 0.011 0.049 -9999 0 -0.41 7 7
TRAF6/MEKK3 0.022 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
MAPK14 -0.01 0.07 -9999 0 -0.15 77 77
positive regulation of innate immune response -0.015 0.086 -9999 0 -0.18 77 77
LCK 0.014 0.037 -9999 0 -0.41 4 4
p38alpha-beta/MKP7 -0.016 0.083 -9999 0 -0.18 77 77
p38alpha-beta/MKP5 -0.01 0.09 -9999 0 -0.21 57 57
PGK/cGMP 0.013 0 -9999 0 -10000 0 0
PAK2 -0.002 0.088 -9999 0 -0.41 23 23
p38alpha-beta/MKP1 -0.013 0.096 -9999 0 -0.22 58 58
CDC42 0.017 0 -9999 0 -10000 0 0
RALB 0.016 0.019 -9999 0 -0.41 1 1
RALA -0.019 0.12 -9999 0 -0.41 44 44
PAK3 0.003 0.006 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.036 0.14 -10000 0 -0.41 66 66
HDAC3 0.017 0 -10000 0 -10000 0 0
VDR 0.017 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.023 0 -10000 0 -10000 0 0
EP300 0.017 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.011 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.015 0.026 -10000 0 -0.41 2 2
AKT1 0.068 0.053 0.12 233 -0.12 3 236
RAR alpha/9cRA/Cyclin H 0.012 0.053 -10000 0 -0.2 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.031 0.006 -10000 0 -10000 0 0
CDC2 -0.14 0.21 -10000 0 -0.41 194 194
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.025 0.005 -10000 0 -10000 0 0
NCOR2 0.017 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.043 0.036 -10000 0 -0.23 4 4
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA3 0.015 0.032 -10000 0 -0.41 3 3
NCOA1 0.017 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.017 0 -10000 0 -10000 0 0
RARG 0.018 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.024 0.001 -10000 0 -10000 0 0
MAPK3 0.018 0.001 -10000 0 -10000 0 0
MAPK1 0.017 0.003 -10000 0 -10000 0 0
MAPK8 0.018 0.002 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.011 0.052 -10000 0 -0.23 4 4
RARA 0.025 0.005 -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 0.032 0.004 -10000 0 -10000 0 0
PRKCA 0.019 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.022 0.045 -10000 0 -0.32 4 4
RXRG 0.025 0.016 -10000 0 -0.17 3 3
RXRA -0.014 0.061 -10000 0 -0.2 4 4
RXRB 0.026 0.005 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0 -10000 0 -10000 0 0
RBP1 -0.18 0.21 -10000 0 -0.41 237 237
CRBP1/9-cic-RA -0.12 0.15 -10000 0 -0.29 237 237
RARB 0.019 0.002 -10000 0 -10000 0 0
PRKCG 0.019 0.004 -10000 0 -10000 0 0
MNAT1 0.016 0.019 -10000 0 -0.41 1 1
RAR alpha/RXRs 0.056 0.059 -10000 0 -0.23 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.049 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.028 0.038 -10000 0 -0.3 4 4
positive regulation of DNA binding 0.007 0.048 -10000 0 -0.19 7 7
NRIP1 0.032 0.043 -10000 0 -0.4 4 4
RXRs/RARs 0.028 0.032 -10000 0 -0.23 4 4
RXRs/RXRs/DNA/9cRA 0.004 0.051 -10000 0 -0.24 4 4
PRKACA 0.017 0 -10000 0 -10000 0 0
CDK7 0.015 0.026 -10000 0 -0.41 2 2
TFIIH 0.033 0.02 -10000 0 -0.23 3 3
RAR alpha/9cRA 0.045 0.016 -10000 0 -0.16 3 3
CCNH 0.017 0.001 -10000 0 -10000 0 0
CREBBP 0.017 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.032 0.02 -10000 0 -0.17 5 5
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.017 0.002 -9999 0 -10000 0 0
VLDLR 0.015 0.032 -9999 0 -0.41 3 3
LRPAP1 0.017 0 -9999 0 -10000 0 0
NUDC 0.017 0 -9999 0 -10000 0 0
RELN/LRP8 0.015 0.026 -9999 0 -0.23 3 3
CaM/Ca2+ 0.012 0.003 -9999 0 -10000 0 0
KATNA1 0.012 0.045 -9999 0 -0.41 6 6
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 0.01 0.019 -9999 0 -0.21 2 2
IQGAP1/CaM -0.047 0.13 -9999 0 -0.27 127 127
DAB1 0.017 0 -9999 0 -10000 0 0
IQGAP1 -0.086 0.18 -9999 0 -0.41 127 127
PLA2G7 0.011 0.052 -9999 0 -0.41 8 8
CALM1 0.016 0.004 -9999 0 -10000 0 0
DYNLT1 -0.044 0.15 -9999 0 -0.41 75 75
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.025 0 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.014 0.007 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.013 0.001 -9999 0 -10000 0 0
CDK5R2 0.007 0.008 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 0.014 0.029 -9999 0 -0.23 4 4
YWHAE 0.017 0.001 -9999 0 -10000 0 0
NDEL1/14-3-3 E 0.025 0.045 -9999 0 -10000 0 0
MAP1B 0.006 0.002 -9999 0 -10000 0 0
RAC1 -0.01 0.048 -9999 0 -0.096 127 127
p35/CDK5 0.013 0.019 -9999 0 -0.18 1 1
RELN 0.006 0.033 -9999 0 -0.41 3 3
PAFAH/LIS1 0.022 0.032 -9999 0 -0.23 8 8
LIS1/CLIP170 0.026 0.003 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.004 0.039 -9999 0 -0.27 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.015 0.02 -9999 0 -10000 0 0
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.023 0.043 -9999 0 -0.16 1 1
LIS1/IQGAP1 -0.037 0.11 -9999 0 -0.23 127 127
RHOA -0.01 0.048 -9999 0 -0.096 127 127
PAFAH1B1 0.017 0.002 -9999 0 -10000 0 0
PAFAH1B3 0.016 0.019 -9999 0 -0.41 1 1
PAFAH1B2 0.017 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.023 0.008 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.047 -9999 0 -10000 0 0
LRP8 0.017 0 -9999 0 -10000 0 0
NDEL1/Katanin 60 0.024 0.047 -9999 0 -10000 0 0
P39/CDK5 0.006 0.016 -9999 0 -0.18 1 1
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.003 -9999 0 -10000 0 0
CDK5 0.009 0.017 -9999 0 -0.19 2 2
PPP2R5D 0.017 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.002 -9999 0 -10000 0 0
CSNK2A1 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.029 -9999 0 -0.19 4 4
RELN/VLDLR 0.019 0.03 -9999 0 -0.21 4 4
CDC42 -0.01 0.048 -9999 0 -0.096 127 127
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.016 0.071 -9999 0 -0.2 34 34
FYN 0.011 0.079 -9999 0 -0.25 26 26
LAT/GRAP2/SLP76 0.026 0.074 -9999 0 -0.22 34 34
IKBKB 0.017 0 -9999 0 -10000 0 0
AKT1 0.029 0.054 -9999 0 -0.21 14 14
B2M 0.018 0.004 -9999 0 -10000 0 0
IKBKG 0.016 0.026 -9999 0 -0.086 12 12
MAP3K8 -0.017 0.12 -9999 0 -0.41 42 42
mol:Ca2+ -0.001 0.006 -9999 0 -10000 0 0
integrin-mediated signaling pathway 0.011 0 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.029 0.068 -9999 0 -0.26 15 15
TRPV6 0.002 0.003 -9999 0 -10000 0 0
CD28 0.017 0.001 -9999 0 -10000 0 0
SHC1 0.011 0.081 -9999 0 -0.19 59 59
receptor internalization 0.029 0.046 -9999 0 -0.24 8 8
PRF1 0.027 0.073 -9999 0 -0.41 13 13
KRAS 0.017 0.002 -9999 0 -10000 0 0
GRB2 0.017 0.002 -9999 0 -10000 0 0
COT/AKT1 0.022 0.076 -9999 0 -0.2 43 43
LAT 0.027 0.055 -9999 0 -0.28 8 8
EntrezGene:6955 0.001 0.002 -9999 0 -10000 0 0
CD3D 0.002 0.083 -9999 0 -0.42 20 20
CD3E 0.017 0.019 -9999 0 -0.42 1 1
CD3G 0.017 0.019 -9999 0 -0.42 1 1
RASGRP2 0.01 0.008 -9999 0 -10000 0 0
RASGRP1 -0.006 0.076 -9999 0 -0.23 30 30
HLA-A 0.017 0.019 -9999 0 -0.41 1 1
RASSF5 0 0 -9999 0 -10000 0 0
RAP1A/GTP/RAPL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:GDP 0.004 0.032 -9999 0 -0.082 25 25
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.01 0.03 -9999 0 -0.12 22 22
PRKCA 0.021 0.042 -9999 0 -0.14 24 24
GRAP2 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.014 0.047 -9999 0 -0.2 24 24
EntrezGene:6957 0.001 0.003 -9999 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.025 0.039 -9999 0 -0.26 6 6
ORAI1 0 0 -9999 0 -10000 0 0
CSK 0.026 0.055 -9999 0 -0.24 12 12
B7 family/CD28 0.033 0.082 -9999 0 -0.24 34 34
CHUK 0.016 0.019 -9999 0 -0.41 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.025 0.059 -9999 0 -0.24 14 14
PTPN6 0.02 0.07 -9999 0 -0.3 17 17
VAV1 0.027 0.056 -9999 0 -0.25 12 12
Monovalent TCR/CD3 0.017 0.041 -9999 0 -0.17 20 20
CBL 0.017 0 -9999 0 -10000 0 0
LCK 0.01 0.079 -9999 0 -0.25 26 26
PAG1 0.024 0.055 -9999 0 -0.23 14 14
RAP1A 0.017 0 -9999 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.023 0.062 -9999 0 -0.23 19 19
CD80 0.017 0.019 -9999 0 -0.41 1 1
CD86 -0.003 0.091 -9999 0 -0.41 25 25
PDK1/CARD11/BCL10/MALT1 -0.011 0.036 -9999 0 -0.14 23 23
HRAS 0.016 0.019 -9999 0 -0.41 1 1
GO:0035030 0.019 0.07 -9999 0 -0.21 34 34
CD8A 0.001 0.003 -9999 0 -10000 0 0
CD8B 0.016 0.027 -9999 0 -0.42 2 2
PTPRC -0.086 0.18 -9999 0 -0.41 127 127
PDK1/PKC theta 0.033 0.063 -9999 0 -0.24 14 14
CSK/PAG1 0.026 0.053 -9999 0 -0.24 12 12
SOS1 0 0 -9999 0 -10000 0 0
peptide-MHC class I 0.026 0.015 -9999 0 -0.28 1 1
GRAP2/SLP76 0.027 0.08 -9999 0 -0.24 35 35
STIM1 0.002 0.003 -9999 0 -10000 0 0
RAS family/GTP -0.006 0.053 -9999 0 -0.11 53 53
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.029 0.047 -9999 0 -0.25 8 8
mol:DAG -0.013 0.044 -9999 0 -0.18 24 24
RAP1A/GDP 0.004 0.015 -9999 0 -0.04 15 15
PLCG1 0.017 0 -9999 0 -10000 0 0
CD247 0.016 0.027 -9999 0 -0.42 2 2
cytotoxic T cell degranulation 0.027 0.071 -9999 0 -0.4 13 13
RAP1A/GTP 0 0.002 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.061 -9999 0 -0.23 15 15
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.015 0.058 -9999 0 -0.24 24 24
NRAS -0.094 0.19 -9999 0 -0.41 137 137
ZAP70 0.017 0 -9999 0 -10000 0 0
GRB2/SOS1 0.013 0.001 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.023 0.071 -9999 0 -0.24 24 24
MALT1 -0.003 0.091 -9999 0 -0.41 25 25
TRAF6 0.017 0 -9999 0 -10000 0 0
CD8 heterodimer 0.013 0.019 -9999 0 -0.29 2 2
CARD11 0 0 -9999 0 -10000 0 0
PRKCB -0.01 0.032 -9999 0 -0.14 25 25
PRKCE 0.021 0.042 -9999 0 -0.14 24 24
PRKCQ 0.031 0.067 -9999 0 -0.26 15 15
LCP2 -0.007 0.099 -9999 0 -0.41 30 30
BCL10 0.015 0.032 -9999 0 -0.41 3 3
regulation of survival gene product expression 0.028 0.049 -9999 0 -0.19 13 13
IKK complex 0.025 0.022 -9999 0 -0.068 7 7
RAS family/GDP -0.013 0.02 -9999 0 -0.046 136 136
MAP3K14 0.021 0.061 -9999 0 -0.16 44 44
PDPK1 0.03 0.053 -9999 0 -0.2 13 13
TCR/CD3/MHC I/CD8/Fyn 0.028 0.051 -9999 0 -0.3 7 7
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0.019 -9999 0 -0.41 1 1
ELF1 0.018 0.055 -9999 0 -0.32 13 13
CCNA2 -0.096 0.19 -9999 0 -0.41 139 139
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
JAK3 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
JAK1 0.018 0.002 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.054 -9999 0 -0.18 18 18
SHC1 -0.02 0.12 -9999 0 -0.41 47 47
SP1 0.019 0.039 -9999 0 -0.22 14 14
IL2RA 0.018 0.056 -9999 0 -0.33 13 13
IL2RB 0.014 0.037 -9999 0 -0.41 4 4
SOS1 0.001 0 -9999 0 -10000 0 0
IL2RG 0.01 0.056 -9999 0 -0.41 9 9
G1/S transition of mitotic cell cycle -0.027 0.1 -9999 0 -0.24 55 55
PTPN11 0.018 0 -9999 0 -10000 0 0
CCND2 0.014 0.068 -9999 0 -0.4 14 14
LCK 0.014 0.037 -9999 0 -0.41 4 4
GRB2 0.017 0.002 -9999 0 -10000 0 0
IL2 0.018 0 -9999 0 -10000 0 0
CDK6 0.017 0 -9999 0 -10000 0 0
CCND3 0.042 0.052 -9999 0 -0.19 11 11
IL4-mediated signaling events

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.053 0.22 -10000 0 -0.71 11 11
STAT6 (cleaved dimer) -0.11 0.16 -10000 0 -0.71 12 12
IGHG1 -0.015 0.12 -10000 0 -0.39 13 13
IGHG3 -0.058 0.21 -10000 0 -0.69 11 11
AKT1 -0.004 0.15 -10000 0 -0.5 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.015 0.11 -10000 0 -0.38 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.008 0.14 -10000 0 -0.53 5 5
THY1 -0.076 0.28 -10000 0 -0.64 72 72
MYB 0.011 0.052 -10000 0 -0.41 8 8
HMGA1 0.016 0.019 -10000 0 -0.41 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.013 0.16 -10000 0 -0.5 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.011 0.14 -10000 0 -0.46 8 8
SP1 -0.021 0.045 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.015 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.041 0.21 -10000 0 -0.76 9 9
SOCS1 -0.012 0.18 -10000 0 -0.54 9 9
SOCS3 -0.006 0.14 -10000 0 -0.55 4 4
FCER2 -0.034 0.19 -10000 0 -0.69 6 6
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.053 0.22 -10000 0 -0.71 11 11
GRB2 0.017 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.015 0.14 -10000 0 -0.41 17 17
T cell proliferation -0.042 0.22 -10000 0 -0.78 9 9
IL4R/JAK1 -0.056 0.22 -10000 0 -0.72 12 12
EGR2 -0.057 0.24 -10000 0 -0.71 17 17
JAK2 0.012 0.03 -10000 0 -10000 0 0
JAK3 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.017 0.013 -10000 0 -10000 0 0
COL1A2 -0.15 0.23 -10000 0 -0.42 169 169
CCL26 -0.059 0.22 -10000 0 -0.72 11 11
IL4R -0.06 0.24 -10000 0 -0.73 14 14
PTPN6 0.01 0.06 -10000 0 -0.4 11 11
IL13RA2 -0.13 0.28 -10000 0 -0.67 42 42
IL13RA1 -0.054 0.16 -10000 0 -0.43 80 80
IRF4 0.017 0.075 -10000 0 -0.62 1 1
ARG1 0.002 0.11 -10000 0 -0.44 7 7
CBL -0.016 0.15 -10000 0 -0.53 7 7
GTF3A 0.014 0.027 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
IL13RA1/JAK2 -0.029 0.12 -10000 0 -0.3 80 80
IRF4/BCL6 0.013 0.078 -10000 0 -0.56 1 1
CD40LG 0.024 0.003 -10000 0 -10000 0 0
MAPK14 -0.012 0.15 -10000 0 -0.56 6 6
mitosis -0.002 0.15 -10000 0 -0.48 8 8
STAT6 -0.052 0.24 -10000 0 -0.57 40 40
SPI1 0.016 0.053 -10000 0 -0.41 8 8
RPS6KB1 0 0.14 -10000 0 -0.46 9 9
STAT6 (dimer) -0.038 0.24 -10000 0 -0.57 41 41
STAT6 (dimer)/PARP14 -0.067 0.22 -10000 0 -0.74 11 11
mast cell activation 0 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.001 0.13 -10000 0 -0.44 9 9
FRAP1 -0.004 0.15 -10000 0 -0.5 8 8
LTA -0.054 0.22 -10000 0 -0.72 11 11
FES 0.017 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.05 0.24 0.66 20 -10000 0 20
CCL11 -0.054 0.22 -10000 0 -0.67 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.002 0.13 -10000 0 -0.44 8 8
IL2RG 0.013 0.056 -10000 0 -0.41 9 9
IL10 -0.053 0.22 -10000 0 -0.71 11 11
IRS1 0.013 0.042 -10000 0 -0.41 5 5
IRS2 0.017 0.002 -10000 0 -10000 0 0
IL4 0.004 0.087 -10000 0 -10000 0 0
IL5 -0.053 0.22 -10000 0 -0.71 11 11
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.053 0.22 -10000 0 -0.59 18 18
COL1A1 -0.043 0.19 -10000 0 -0.47 66 66
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.055 0.22 -10000 0 -0.76 10 10
IL2R gamma/JAK3 0.026 0.041 -10000 0 -0.29 9 9
TFF3 -0.058 0.23 -10000 0 -0.69 19 19
ALOX15 -0.053 0.22 -10000 0 -0.71 11 11
MYBL1 -0.048 0.15 -10000 0 -0.41 80 80
T-helper 2 cell differentiation -0.041 0.2 -10000 0 -0.67 9 9
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
CEBPB 0.013 0.061 -10000 0 -0.41 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.006 0.14 -10000 0 -0.48 6 6
mol:PI-3-4-5-P3 -0.003 0.15 -10000 0 -0.5 8 8
PI3K -0.005 0.15 -10000 0 -0.52 8 8
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.016 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.012 0.14 -10000 0 -0.4 15 15
ITGB3 -0.053 0.22 -10000 0 -0.71 11 11
PIGR -0.054 0.23 -10000 0 -0.71 12 12
IGHE 0.021 0.05 0.13 59 -0.11 3 62
MAPKKK cascade -0.012 0.13 -10000 0 -0.41 14 14
BCL6 0.003 0.074 -10000 0 -0.41 16 16
OPRM1 -0.053 0.22 -10000 0 -0.71 11 11
RETNLB -0.059 0.22 -10000 0 -0.72 11 11
SELP -0.054 0.22 -10000 0 -0.72 11 11
AICDA -0.053 0.21 -10000 0 -0.74 9 9
Canonical NF-kappaB pathway

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
FBXW11 0.019 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.024 -9999 0 -0.16 2 2
ERC1 0.016 0.019 -9999 0 -0.41 1 1
RIP2/NOD2 0.02 0.04 -9999 0 -0.28 9 9
NFKBIA 0.025 0.027 -9999 0 -0.24 5 5
BIRC2 0.017 0 -9999 0 -10000 0 0
IKBKB 0.017 0 -9999 0 -10000 0 0
RIPK2 0.016 0.019 -9999 0 -0.41 1 1
IKBKG 0.031 0.024 -9999 0 -0.17 1 1
IKK complex/A20 -0.017 0.1 -9999 0 -0.23 25 25
NEMO/A20/RIP2 0.016 0.019 -9999 0 -0.41 1 1
XPO1 0.017 0 -9999 0 -10000 0 0
NEMO/ATM 0.03 0.051 -9999 0 -0.17 26 26
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.023 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.043 0.028 -9999 0 -0.32 1 1
BCL10/MALT1/TRAF6 0.021 0.06 -9999 0 -0.23 28 28
NOD2 0.011 0.052 -9999 0 -0.41 8 8
NFKB1 0.016 0.037 -9999 0 -0.41 4 4
RELA 0.019 0.004 -9999 0 -10000 0 0
MALT1 -0.003 0.091 -9999 0 -0.41 25 25
cIAP1/UbcH5C 0.025 0.001 -9999 0 -10000 0 0
ATM -0.003 0.091 -9999 0 -0.41 25 25
TNF/TNFR1A -0.083 0.15 -9999 0 -0.28 185 185
TRAF6 0.017 0 -9999 0 -10000 0 0
PRKCA 0.017 0 -9999 0 -10000 0 0
CHUK 0.016 0.019 -9999 0 -0.41 1 1
UBE2D3 0.017 0.001 -9999 0 -10000 0 0
TNF 0.015 0.026 -9999 0 -0.41 2 2
NF kappa B1 p50/RelA 0.042 0.026 -9999 0 -0.22 5 5
BCL10 0.015 0.032 -9999 0 -0.41 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.027 -9999 0 -0.24 5 5
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.004 -9999 0 -10000 0 0
TNFRSF1A -0.13 0.2 -9999 0 -0.41 183 183
IKK complex 0.048 0.027 -9999 0 -0.15 2 2
CYLD 0.017 0 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.053 0.028 -9999 0 -10000 0 0
IL12-mediated 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
IL12/IL12R/TYK2/JAK2/SOCS1 0.037 0.043 -10000 0 -0.17 1 1
TBX21 0.045 0.12 -10000 0 -0.37 23 23
B2M 0.017 0 -10000 0 -10000 0 0
TYK2 0.017 0.026 -10000 0 -0.44 1 1
IL12RB1 0.017 0.016 -10000 0 -10000 0 0
GADD45B 0.046 0.12 -10000 0 -0.41 18 18
IL12RB2 0.018 0.017 -10000 0 -10000 0 0
GADD45G 0.044 0.12 -10000 0 -0.34 26 26
natural killer cell activation 0.002 0.014 -10000 0 -10000 0 0
RELB 0.016 0.019 -10000 0 -0.41 1 1
RELA 0.017 0 -10000 0 -10000 0 0
IL18 -0.017 0.12 -10000 0 -0.41 45 45
IL2RA 0.012 0.045 -10000 0 -0.41 6 6
IFNG 0.016 0.019 -10000 0 -0.41 1 1
STAT3 (dimer) 0.042 0.14 -10000 0 -0.4 14 14
HLA-DRB5 -0.002 0.005 -10000 0 -10000 0 0
FASLG 0.045 0.12 -10000 0 -0.37 23 23
NF kappa B2 p52/RelB 0.028 0.14 -10000 0 -0.39 18 18
CD4 -0.001 0.081 -10000 0 -0.42 19 19
SOCS1 0.017 0 -10000 0 -10000 0 0
EntrezGene:6955 -0.003 0.006 -10000 0 -10000 0 0
CD3D -0.003 0.082 -10000 0 -0.42 20 20
CD3E 0.014 0.02 -10000 0 -0.41 1 1
CD3G 0.012 0.021 -10000 0 -0.41 1 1
IL12Rbeta2/JAK2 0.028 0.027 -10000 0 -10000 0 0
CCL3 0.038 0.12 -10000 0 -0.35 30 30
CCL4 0.045 0.14 -10000 0 -0.44 26 26
HLA-A 0.016 0.019 -10000 0 -0.41 1 1
IL18/IL18R 0.033 0.083 -10000 0 -0.23 45 45
NOS2 0.039 0.12 -10000 0 -0.34 25 25
IL12/IL12R/TYK2/JAK2/SPHK2 0.037 0.043 -10000 0 -0.17 1 1
IL1R1 0.044 0.13 -10000 0 -0.38 25 25
IL4 0.015 0.014 -10000 0 -10000 0 0
JAK2 0.017 0.016 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.016 0.032 -10000 0 -0.18 7 7
RAB7A 0.048 0.12 -10000 0 -0.41 5 5
lysosomal transport 0.048 0.12 -10000 0 -0.4 5 5
FOS -0.08 0.2 -10000 0 -0.4 131 131
STAT4 (dimer) 0.038 0.13 -10000 0 -0.41 11 11
STAT5A (dimer) 0.027 0.14 -10000 0 -0.38 19 19
GZMA 0.034 0.15 -10000 0 -0.45 28 28
GZMB 0.038 0.14 -10000 0 -0.46 23 23
HLX 0.013 0.042 -10000 0 -0.41 5 5
LCK 0.041 0.13 -10000 0 -0.38 29 29
TCR/CD3/MHC II/CD4 -0.075 0.1 -10000 0 -0.23 110 110
IL2/IL2R 0.035 0.053 -10000 0 -0.26 15 15
MAPK14 0.043 0.13 -10000 0 -0.42 11 11
CCR5 0.043 0.13 -10000 0 -0.44 17 17
IL1B 0.006 0.07 -10000 0 -0.41 14 14
STAT6 0.033 0.048 -10000 0 -0.18 3 3
STAT4 0.01 0.008 -10000 0 -10000 0 0
STAT3 0.009 0.058 -10000 0 -0.41 10 10
STAT1 0.002 0.078 -10000 0 -0.41 18 18
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
NFKB2 0.017 0 -10000 0 -10000 0 0
IL12B 0.018 0.017 -10000 0 -10000 0 0
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.015 0.026 -10000 0 -0.41 2 2
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.037 0.043 0.17 1 -10000 0 1
IL2RB 0.014 0.037 -10000 0 -0.41 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.13 -10000 0 -0.38 11 11
IL2RG 0.01 0.055 -10000 0 -0.41 9 9
IL12 0.028 0.027 -10000 0 -10000 0 0
STAT5A 0.016 0.019 -10000 0 -0.41 1 1
CD247 0.013 0.027 -10000 0 -0.42 2 2
IL2 0.017 0 -10000 0 -10000 0 0
SPHK2 0.017 0 -10000 0 -10000 0 0
FRAP1 0.016 0.019 -10000 0 -0.41 1 1
IL12A 0.017 0.016 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.046 0.13 -10000 0 -0.39 25 25
MAP2K3 0.039 0.13 -10000 0 -0.42 11 11
RIPK2 0.016 0.019 -10000 0 -0.41 1 1
MAP2K6 0.039 0.13 -10000 0 -0.42 11 11
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.22 0.21 -10000 0 -0.42 291 291
IL18RAP 0.02 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.025 0.028 -10000 0 -0.32 1 1
EOMES -0.002 0.019 0.05 2 -10000 0 2
STAT1 (dimer) 0.039 0.13 -10000 0 -0.41 12 12
T cell proliferation 0.024 0.11 -10000 0 -0.34 12 12
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.006 -10000 0 -10000 0 0
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.028 0.088 -10000 0 -0.36 16 16
ATF2 0.045 0.13 -10000 0 -0.41 9 9
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.029 0.028 -10000 0 -0.22 3 3
epithelial cell differentiation 0.032 0.031 -10000 0 -10000 0 0
ITCH 0.018 0.02 -10000 0 -0.41 1 1
WWP1 0.025 0.025 -10000 0 -0.26 2 2
FYN 0.015 0.026 -10000 0 -0.41 2 2
EGFR -0.14 0.21 -10000 0 -0.41 194 194
PRL 0.012 0.045 -10000 0 -0.41 6 6
neuron projection morphogenesis 0.021 0.059 -10000 0 -0.19 7 7
PTPRZ1 -0.003 0.087 -10000 0 -0.41 23 23
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.032 0.068 -10000 0 -0.21 8 8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.026 0.028 -10000 0 -0.21 6 6
ADAM17 0.014 0.041 -10000 0 -0.4 5 5
ErbB4/ErbB4 0.026 0.025 -10000 0 -0.24 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.017 0.023 -10000 0 -0.26 1 1
NCOR1 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.034 0.026 -10000 0 -0.22 2 2
GRIN2B 0.033 0.024 -10000 0 -0.21 2 2
ErbB4/ErbB2/betacellulin 0.035 0.027 -10000 0 -0.22 2 2
STAT1 0.002 0.078 -10000 0 -0.41 18 18
HBEGF 0.015 0.026 -10000 0 -0.41 2 2
PRLR 0.017 0 -10000 0 -10000 0 0
E4ICDs/ETO2 0.029 0.025 -10000 0 -0.26 1 1
axon guidance 0.023 0.031 -10000 0 -0.27 1 1
NEDD4 0.007 0.069 -10000 0 -0.41 14 14
Prolactin receptor/Prolactin receptor/Prolactin 0.022 0.033 -10000 0 -0.28 6 6
CBFA2T3 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.034 0.03 -10000 0 -0.22 2 2
MAPK3 0.022 0.061 -10000 0 -0.2 8 8
STAT1 (dimer) 0.021 0.051 -10000 0 -0.22 19 19
MAPK1 0.021 0.061 -10000 0 -0.2 8 8
JAK2 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.03 0.026 -10000 0 -0.22 2 2
NRG1 0.016 0.028 -10000 0 -0.27 5 5
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.017 0 -10000 0 -10000 0 0
NRG4 0 0 -10000 0 -10000 0 0
heart development 0.023 0.031 -10000 0 -0.27 1 1
neural crest cell migration 0.029 0.026 -10000 0 -0.22 2 2
ERBB2 0.016 0.028 -10000 0 -0.27 5 5
WWOX/E4ICDs 0.029 0.025 -10000 0 -0.26 1 1
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
ErbB4/EGFR/neuregulin 4 -0.054 0.11 -10000 0 -0.19 194 194
apoptosis -0.022 0.026 0.24 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.029 0.025 -10000 0 -0.26 1 1
ErbB4/ErbB2/epiregulin 0.031 0.043 -10000 0 -0.23 8 8
ErbB4/ErbB4/betacellulin/betacellulin 0.029 0.025 -10000 0 -0.26 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.05 0.035 -10000 0 -10000 0 0
MDM2 0.018 0.047 -10000 0 -0.21 20 20
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.03 0.027 -10000 0 -0.19 7 7
STAT5A 0.027 0.031 -10000 0 -0.25 1 1
ErbB4/EGFR/neuregulin 1 beta -0.046 0.11 -10000 0 -0.19 195 195
DLG4 0.017 0 -10000 0 -10000 0 0
GRB2/SHC -0.002 0.088 -10000 0 -0.28 47 47
E4ICDs/TAB2/NCoR1 0.038 0.023 -10000 0 -0.24 1 1
STAT5A (dimer) 0.047 0.036 -10000 0 -10000 0 0
MAP3K7IP2 0.017 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.034 0.031 -10000 0 -0.25 1 1
LRIG1 -0.002 0.087 -10000 0 -0.41 23 23
EREG 0.009 0.058 -10000 0 -0.41 10 10
BTC 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.023 0.031 -10000 0 -0.27 1 1
ERBB4 0.026 0.025 -10000 0 -0.24 2 2
STAT5B 0.017 0 -10000 0 -10000 0 0
YAP1 -0.001 0.061 -10000 0 -0.2 46 46
GRB2 0.017 0.002 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.023 0.026 -10000 0 -0.2 4 4
glial cell differentiation -0.038 0.023 0.24 1 -10000 0 1
WWOX 0.017 0 -10000 0 -10000 0 0
cell proliferation 0.033 0.025 -10000 0 -0.2 1 1
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.025 0 -9999 0 -10000 0 0
Necdin/E2F1 0.016 0.012 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.03 0.047 -9999 0 -0.19 22 22
NGF (dimer)/p75(NTR)/BEX1 0.007 0.048 -9999 0 -0.24 17 17
NT-4/5 (dimer)/p75(NTR) 0 0.06 -9999 0 -0.29 22 22
IKBKB 0.017 0 -9999 0 -10000 0 0
AKT1 0.001 0.066 -9999 0 -0.2 47 47
IKBKG 0.017 0 -9999 0 -10000 0 0
BDNF 0.005 0.008 -9999 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.001 0.051 -9999 0 -0.24 22 22
FURIN 0.017 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.002 0.04 -9999 0 -0.23 10 10
LINGO1 0 0 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.014 0.048 -9999 0 -0.34 2 2
proBDNF (dimer) 0.005 0.008 -9999 0 -10000 0 0
NTRK1 0.015 0.026 -9999 0 -0.41 2 2
RTN4R 0 0 -9999 0 -10000 0 0
neuron apoptosis 0.052 0.071 -9999 0 -0.21 12 12
IRAK1 0.017 0.001 -9999 0 -10000 0 0
SHC1 -0.017 0.088 -9999 0 -0.24 67 67
ARHGDIA 0.017 0 -9999 0 -10000 0 0
RhoA/GTP 0.013 0.001 -9999 0 -10000 0 0
Gamma Secretase 0.032 0.068 -9999 0 -0.2 40 40
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.021 0.047 -9999 0 -0.21 20 20
MAGEH1 0.016 0.005 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.012 0.043 -9999 0 -0.21 15 15
Mammalian IAPs/DIABLO 0.018 0.059 -9999 0 -0.21 33 33
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.017 0.001 -9999 0 -10000 0 0
APP 0.017 0.001 -9999 0 -10000 0 0
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.013 0.042 -9999 0 -0.41 5 5
RhoA/GDP/RHOGDI 0.018 0.045 -9999 0 -0.2 22 22
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest 0 0.042 -9999 0 -0.2 22 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0 0.059 -9999 0 -0.13 93 93
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.012 0.052 -9999 0 -0.24 22 22
NCSTN -0.007 0.099 -9999 0 -0.41 30 30
mol:GTP 0.01 0.051 -9999 0 -0.23 22 22
PSENEN 0.017 0.001 -9999 0 -10000 0 0
mol:ceramide 0.01 0.046 -9999 0 -0.21 22 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.026 -9999 0 -10000 0 0
p75(NTR)/beta APP 0.012 0.062 -9999 0 -0.28 22 22
BEX1 0.012 0.008 -9999 0 -10000 0 0
mol:GDP -0.004 0.049 -9999 0 -0.24 22 22
NGF (dimer) -0.003 0.087 -9999 0 -0.21 78 78
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.012 0.047 -9999 0 -0.22 22 22
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
RAC1/GTP 0.011 0.044 -9999 0 -0.2 22 22
MYD88 -0.041 0.15 -9999 0 -0.41 72 72
CHUK 0.016 0.019 -9999 0 -0.41 1 1
NGF (dimer)/p75(NTR)/PKA 0.011 0.051 -9999 0 -0.23 22 22
RHOB 0.013 0.037 -9999 0 -0.41 4 4
RHOA 0.017 0.001 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.013 0 -9999 0 -10000 0 0
NT3 (dimer) 0.017 0 -9999 0 -10000 0 0
TP53 -0.015 0.061 -9999 0 -0.21 38 38
PRDM4 0.01 0.046 -9999 0 -0.21 22 22
BDNF (dimer) -0.012 0.068 -9999 0 -0.23 32 32
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
SORT1 0.017 0 -9999 0 -10000 0 0
activation of caspase activity 0.027 0.046 -9999 0 -0.19 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.023 0.049 -9999 0 -0.21 22 22
RHOC -0.12 0.2 -9999 0 -0.41 164 164
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 0.044 0.06 -9999 0 -10000 0 0
DIABLO 0.017 0 -9999 0 -10000 0 0
SMPD2 0.01 0.046 -9999 0 -0.21 22 22
APH1B 0.017 0 -9999 0 -10000 0 0
APH1A 0.008 0.061 -9999 0 -0.41 11 11
proNGF (dimer)/p75(NTR)/Sortilin 0.012 0.052 -9999 0 -0.24 22 22
PSEN1 0.016 0.019 -9999 0 -0.41 1 1
APAF-1/Pro-Caspase 9 0.023 0.027 -9999 0 -0.28 4 4
NT3 (dimer)/p75(NTR) 0.013 0.062 -9999 0 -0.28 22 22
MAPK8 0.081 0.053 -9999 0 -10000 0 0
MAPK9 0.08 0.053 -9999 0 -10000 0 0
APAF1 0.017 0 -9999 0 -10000 0 0
NTF3 0.017 0 -9999 0 -10000 0 0
NTF4 0 0 -9999 0 -10000 0 0
NDN 0.011 0.008 -9999 0 -10000 0 0
RAC1/GDP 0.013 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.04 0.11 -9999 0 -0.19 171 171
p75 CTF/Sortilin/TRAF6/NRIF 0.039 0.034 -9999 0 -0.21 10 10
RhoA-B-C/GTP 0.01 0.051 -9999 0 -0.23 22 22
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.007 0.041 -9999 0 -0.19 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.006 0.039 -9999 0 -0.21 10 10
PRKACB 0.016 0.005 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.005 0.026 -9999 0 -0.23 5 5
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.1 -9999 0 -0.41 33 33
BIRC2 0.017 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.007 0.035 -9999 0 -0.2 15 15
BAD 0.082 0.052 -9999 0 -10000 0 0
RIPK2 0.016 0.019 -9999 0 -0.41 1 1
NGFR -0.001 0.086 -9999 0 -0.41 22 22
CYCS 0.014 0.043 -9999 0 -0.19 22 22
ADAM17 0.013 0.042 -9999 0 -0.41 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.022 0.05 -9999 0 -0.21 23 23
BCL2L11 0.082 0.052 -9999 0 -10000 0 0
BDNF (dimer)/p75(NTR) -0.002 0.046 -9999 0 -0.28 10 10
PI3K 0.01 0.072 -9999 0 -0.22 43 43
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.012 0.047 -9999 0 -0.22 22 22
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
PRKCI 0.016 0.019 -9999 0 -0.41 1 1
NGF (dimer)/p75(NTR) 0 0.06 -9999 0 -0.29 22 22
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.023 0.049 -9999 0 -0.21 22 22
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.007 0.049 -9999 0 -0.2 19 19
SQSTM1 0.016 0.019 -9999 0 -0.41 1 1
NGFRAP1 0.017 0.002 -9999 0 -10000 0 0
CASP3 0.078 0.051 -9999 0 -10000 0 0
E2F1 0.017 0 -9999 0 -10000 0 0
CASP9 0.014 0.037 -9999 0 -0.41 4 4
IKK complex 0.037 0.029 -9999 0 -0.19 3 3
NGF (dimer)/TRKA 0.012 0.019 -9999 0 -0.29 2 2
MMP7 -0.046 0.15 -9999 0 -0.41 78 78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.029 0.052 -9999 0 -0.19 27 27
MMP3 0.011 0.049 -9999 0 -0.41 7 7
APAF-1/Caspase 9 -0.016 0.046 -9999 0 -0.31 1 1
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.011 0.061 -9999 0 -0.23 15 15
PDGFB-D/PDGFRB/SLAP 0.002 0.082 -9999 0 -0.3 37 37
PDGFB-D/PDGFRB/APS/CBL 0.021 0.02 -9999 0 -0.24 3 3
AKT1 0.025 0.051 -9999 0 -0.24 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.058 -9999 0 -0.21 22 22
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
FGR 0.004 0.044 -9999 0 -0.2 17 17
mol:Ca2+ 0.008 0.038 -9999 0 -0.22 4 4
MYC -0.066 0.17 -9999 0 -0.34 138 138
SHC1 -0.021 0.12 -9999 0 -0.41 47 47
HRAS/GDP 0.027 0.022 -9999 0 -0.18 5 5
LRP1/PDGFRB/PDGFB 0.023 0.053 -9999 0 -0.24 21 21
GRB10 0.004 0.073 -9999 0 -0.41 16 16
PTPN11 0.017 0 -9999 0 -10000 0 0
GO:0007205 0.008 0.039 -9999 0 -0.22 4 4
PTEN 0.015 0.026 -9999 0 -0.41 2 2
GRB2 0.017 0.002 -9999 0 -10000 0 0
GRB7 0.016 0.019 -9999 0 -0.41 1 1
PDGFB-D/PDGFRB/SHP2 0.023 0.023 -9999 0 -0.28 3 3
PDGFB-D/PDGFRB/GRB10 0.013 0.058 -9999 0 -0.29 19 19
cell cycle arrest 0.002 0.082 -9999 0 -0.3 37 37
HRAS 0.016 0.019 -9999 0 -0.41 1 1
HIF1A 0.025 0.049 -9999 0 -0.21 1 1
GAB1 -0.008 0.065 -9999 0 -0.21 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.008 0.065 -9999 0 -0.21 18 18
PDGFB-D/PDGFRB 0.027 0.029 -9999 0 -0.24 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.023 0.023 -9999 0 -0.28 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.003 0.079 -9999 0 -0.23 25 25
positive regulation of MAPKKK cascade 0.023 0.023 -9999 0 -0.28 3 3
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
mol:IP3 0.008 0.039 -9999 0 -0.22 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.017 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.022 0.027 -9999 0 -0.28 4 4
SHB 0.017 0 -9999 0 -10000 0 0
BLK -0.002 0.022 -9999 0 -0.21 4 4
PTPN2 0.015 0.019 -9999 0 -0.42 1 1
PDGFB-D/PDGFRB/SNX15 0.023 0.023 -9999 0 -0.28 3 3
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 -0.024 0.093 -9999 0 -0.23 50 50
CBL 0.017 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.023 0.023 -9999 0 -0.28 3 3
LCK -0.005 0.028 -9999 0 -0.2 8 8
PDGFRB 0.014 0.033 -9999 0 -0.42 3 3
ACP1 0.017 0.001 -9999 0 -10000 0 0
HCK -0.031 0.064 -9999 0 -0.2 40 40
ABL1 -0.003 0.055 -9999 0 -0.18 17 17
PDGFB-D/PDGFRB/CBL -0.006 0.065 -9999 0 -0.21 17 17
PTPN1 0.016 0.003 -9999 0 -10000 0 0
SNX15 0.017 0 -9999 0 -10000 0 0
STAT3 0.009 0.058 -9999 0 -0.41 10 10
STAT1 0.002 0.078 -9999 0 -0.41 18 18
cell proliferation -0.06 0.16 -9999 0 -0.32 138 138
SLA -0.011 0.11 -9999 0 -0.41 35 35
actin cytoskeleton reorganization 0.026 0.036 -9999 0 -0.18 15 15
SRC -0.003 0.022 -9999 0 -0.21 4 4
PI3K -0.01 0.038 -9999 0 -0.18 12 12
PDGFB-D/PDGFRB/GRB7/SHC 0.008 0.081 -9999 0 -0.24 50 50
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.007 0.06 -9999 0 -0.21 22 22
LYN -0.025 0.06 -9999 0 -0.2 35 35
LRP1 0.002 0.078 -9999 0 -0.41 18 18
SOS1 0 0 -9999 0 -10000 0 0
STAT5B 0.017 0 -9999 0 -10000 0 0
STAT5A 0.016 0.019 -9999 0 -0.41 1 1
NCK1-2/p130 Cas 0.032 0.04 -9999 0 -0.19 15 15
SPHK1 0.001 0.082 -9999 0 -0.41 20 20
EDG1 0.017 0.002 -9999 0 -10000 0 0
mol:DAG 0.008 0.039 -9999 0 -0.22 4 4
PLCG1 0.008 0.039 -9999 0 -0.23 4 4
NHERF/PDGFRB 0.032 0.026 -9999 0 -0.24 5 5
YES1 -0.029 0.063 -9999 0 -0.19 41 41
cell migration 0.031 0.026 -9999 0 -0.24 5 5
SHC/Grb2/SOS1 0.016 0.07 -9999 0 -0.2 49 49
SLC9A3R2 0.017 0 -9999 0 -10000 0 0
SLC9A3R1 0.015 0.026 -9999 0 -0.41 2 2
NHERF1-2/PDGFRB/PTEN 0.04 0.029 -9999 0 -0.21 7 7
FYN -0.014 0.064 -9999 0 -0.31 21 21
DOK1 0.021 0.021 -9999 0 -0.21 4 4
HRAS/GTP 0.012 0.013 -9999 0 -0.29 1 1
PDGFB 0.017 0 -9999 0 -10000 0 0
RAC1 -0.041 0.12 -9999 0 -0.23 139 139
PRKCD 0.02 0.021 -9999 0 -0.21 4 4
FER 0.02 0.021 -9999 0 -0.21 4 4
MAPKKK cascade -0.018 0.057 -9999 0 -0.19 49 49
RASA1 0.02 0.022 -9999 0 -0.21 4 4
NCK1 0.008 0.061 -9999 0 -0.41 11 11
NCK2 0.017 0.001 -9999 0 -10000 0 0
p62DOK/Csk 0.033 0.019 -9999 0 -0.19 4 4
PDGFB-D/PDGFRB/SHB 0.023 0.023 -9999 0 -0.28 3 3
chemotaxis -0.003 0.054 -9999 0 -0.18 17 17
STAT1-3-5/STAT1-3-5 0.025 0.055 -9999 0 -0.19 31 31
Bovine Papilomavirus E5/PDGFRB 0.009 0.023 -9999 0 -0.29 3 3
PTPRJ 0.017 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.005 0.041 -9999 0 -0.24 15 15
SNTA1 0.017 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.01 0.042 -9999 0 -0.23 15 15
MAPK12 0.015 0.02 -9999 0 -0.13 10 10
CCND1 -0.013 0.062 -9999 0 -0.14 98 98
p38 gamma/SNTA1 0.025 0.02 -9999 0 -10000 0 0
MAP2K3 0.017 0 -9999 0 -10000 0 0
PKN1 0.009 0.058 -9999 0 -0.41 10 10
G2/M transition checkpoint 0.015 0.02 -9999 0 -0.13 10 10
MAP2K6 0.013 0.023 -9999 0 -0.15 10 10
MAPT 0.009 0.035 -9999 0 -0.18 15 15
MAPK13 0.009 0.05 -9999 0 -0.28 15 15
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.011 0.027 -9999 0 -0.18 10 10
Insulin Pathway

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
CBL/APS/CAP 0.029 0.02 -9999 0 -0.18 5 5
TC10/GTP 0.027 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.044 0.025 -9999 0 -0.21 5 5
HRAS 0.016 0.019 -9999 0 -0.41 1 1
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 0.002 0.078 -9999 0 -0.41 18 18
FOXO3 0.012 0.013 -9999 0 -10000 0 0
AKT1 0.021 0.061 -9999 0 -0.33 1 1
INSR 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.048 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.004 0.073 -9999 0 -0.41 16 16
SORBS1 0.017 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
PTPN1 0.024 0.009 -9999 0 -10000 0 0
CAV1 -0.11 0.11 -9999 0 -0.2 325 325
CBL/APS/CAP/Crk-II/C3G 0.041 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.044 0.025 -9999 0 -0.21 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.049 -9999 0 -0.18 27 27
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.023 0.044 -9999 0 -0.23 3 3
RPS6KB1 0.022 0.058 -9999 0 -0.3 1 1
PARD6A 0.017 0 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.016 0.011 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.022 0.053 -9999 0 -0.29 1 1
HRAS/GTP -0.016 0.051 -9999 0 -0.17 50 50
Insulin Receptor 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.029 0.077 -9999 0 -0.21 49 49
PRKCI 0.025 0.027 -9999 0 -0.17 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.014 0.047 -9999 0 -0.17 43 43
SHC1 -0.021 0.12 -9999 0 -0.41 47 47
negative regulation of MAPKKK cascade 0.029 0.033 -9999 0 -0.19 11 11
PI3K 0.03 0.052 -9999 0 -0.18 27 27
NCK2 0.017 0.001 -9999 0 -10000 0 0
RHOQ 0.017 0 -9999 0 -10000 0 0
mol:H2O2 0 0.001 -9999 0 -10000 0 0
HRAS/GDP 0.012 0.013 -9999 0 -0.29 1 1
AKT2 0.023 0.059 -9999 0 -0.33 1 1
PRKCZ 0.015 0.026 -9999 0 -0.16 6 6
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP 0.003 0.066 -9999 0 -0.2 49 49
F2RL2 0.017 0 -9999 0 -10000 0 0
TRIP10 0.012 0.045 -9999 0 -0.41 6 6
Insulin Receptor/Insulin/Shc 0.013 0.071 -9999 0 -0.22 47 47
TC10/GTP/CIP4/Exocyst 0.02 0.028 -9999 0 -0.24 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.021 0.068 -9999 0 -0.2 47 47
RAPGEF1 0.017 0 -9999 0 -10000 0 0
RASA1 0.017 0.002 -9999 0 -10000 0 0
NCK1 0.008 0.061 -9999 0 -0.41 11 11
CBL/APS/CAP/Crk-II 0.033 0 -9999 0 -10000 0 0
TC10/GDP 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.016 0.087 -9999 0 -0.22 60 60
INPP5D 0.011 0.021 -9999 0 -0.2 5 5
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.002 0.005 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0 -9999 0 -10000 0 0
IRS1 0.013 0.042 -9999 0 -0.41 5 5
p62DOK/RasGAP 0.03 0.034 -9999 0 -0.19 11 11
INS 0.019 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.011 0.02 -9999 0 -0.2 5 5
GRB2 0.017 0.002 -9999 0 -10000 0 0
EIF4EBP1 -0.071 0.11 -9999 0 -0.31 27 27
PTPRA 0.019 0.002 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
TC10/GTP/CIP4 0.02 0.028 -9999 0 -0.24 6 6
PDPK1 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.013 0.048 -9999 0 -0.13 49 49
Insulin Receptor/Insulin/IRS1 0.033 0.024 -9999 0 -0.22 5 5
Insulin Receptor/Insulin/IRS3 0.028 0 -9999 0 -10000 0 0
Par3/Par6 0.038 0.025 -9999 0 -0.19 6 6
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.011 0.016 -10000 0 -0.24 2 2
ARNO/beta Arrestin1-2 0.025 0.009 -10000 0 -0.17 1 1
EGFR -0.14 0.21 -10000 0 -0.41 194 194
EPHA2 0.006 0.069 -10000 0 -0.41 14 14
USP6 0.017 0 -10000 0 -10000 0 0
IQSEC1 0.017 0.002 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.089 0.15 -10000 0 -0.28 196 196
ARRB2 0.015 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.005 0.042 2 -10000 0 2
ARRB1 0.017 0 -10000 0 -10000 0 0
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.014 0.037 -10000 0 -0.41 4 4
EGF 0.015 0.026 -10000 0 -0.41 2 2
somatostatin receptor activity 0 0 -10000 0 0 1 1
ARAP2 0 0 -10000 0 0 1 1
mol:GDP 0.019 0.019 -10000 0 -0.089 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 0 1 1
ITGA2B 0.017 0 -10000 0 -10000 0 0
ARF6 0.017 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.022 0.084 -10000 0 -0.26 38 38
ADAP1 0 0 -10000 0 -10000 0 0
KIF13B 0.015 0.026 -10000 0 -0.41 2 2
HGF/MET 0.018 0.046 -10000 0 -0.28 12 12
PXN 0.017 0 -10000 0 -10000 0 0
ARF6/GTP 0.028 0.033 -10000 0 -0.094 1 1
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.065 0.13 -10000 0 -0.23 194 194
ADRB2 0.016 0.019 -10000 0 -0.41 1 1
receptor agonist activity 0 0 0 4 0 1 5
actin filament binding 0 0 -10000 0 0 1 1
SRC 0.017 0 -10000 0 -10000 0 0
ITGB3 0.017 0 -10000 0 -10000 0 0
GNAQ 0.017 0 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -10000 0 0 1 1
ARF6/GDP 0.021 0.024 -10000 0 -0.11 6 6
ARF6/GDP/GULP/ACAP1 0.033 0.023 -10000 0 -0.16 3 3
alphaIIb/beta3 Integrin/paxillin/GIT1 0.044 0 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 -10000 0 0
ACAP2 0 0 -10000 0 0 1 1
LHCGR/beta Arrestin2 0.018 0 -10000 0 -10000 0 0
EFNA1 -0.002 0.088 -10000 0 -0.41 23 23
HGF 0.015 0.026 -10000 0 -0.41 2 2
CYTH3 0 0 -10000 0 0 1 1
CYTH2 0 0 -10000 0 -0.002 2 2
NCK1 0.008 0.061 -10000 0 -0.41 11 11
fibronectin binding 0 0 -10000 0 0 1 1
endosomal lumen acidification 0 0 -10000 0 0 1 1
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.015 0.032 -10000 0 -0.41 3 3
GNAQ/ARNO 0.013 0.001 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 0 1 1
PIP3-E 0.001 0.004 -10000 0 -10000 0 0
MET 0.009 0.058 -10000 0 -0.41 10 10
GNA14 0.016 0.026 -10000 0 -0.41 2 2
GNA15 0.011 0.049 -10000 0 -0.41 7 7
GIT1 0.017 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 0 1 1
GNA11 0.017 0 -10000 0 -10000 0 0
LHCGR 0.017 0 -10000 0 -10000 0 0
AGTR1 0.016 0.026 -10000 0 -0.41 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0 -10000 0 -10000 0 0
IPCEF1/ARNO -0.029 0.042 -10000 0 -0.18 6 6
alphaIIb/beta3 Integrin 0.025 0 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.017 0.001 -10000 0 -10000 0 0
PTK2 0.017 0.001 -10000 0 -10000 0 0
CRKL 0.018 0.023 -10000 0 -0.16 9 9
GRB2/SOS1/SHC 0 0.074 -10000 0 -0.24 47 47
HRAS 0.016 0.019 -10000 0 -0.41 1 1
IRS1/Crk 0.022 0.024 -10000 0 -0.16 9 9
IGF-1R heterotetramer/IGF1/PTP1B 0.031 0.022 -10000 0 -0.21 4 4
AKT1 0.012 0.046 -10000 0 -0.17 28 28
BAD 0.021 0.05 -10000 0 -0.16 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.018 0.023 -10000 0 -0.16 9 9
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.024 0.024 -10000 0 -0.16 9 9
RAF1 0.027 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.029 0.024 -10000 0 -0.15 9 9
YWHAZ 0.017 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.026 -10000 0 -0.18 9 9
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
RPS6KB1 0.013 0.044 -10000 0 -0.17 25 25
GNB2L1 0.017 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.02 0.047 0.28 2 -10000 0 2
PXN 0.017 0 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
HRAS/GTP -0.001 0.06 -10000 0 -0.18 53 53
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.016 0.072 -10000 0 -0.21 50 50
IGF-1R heterotetramer 0.017 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.025 -10000 0 -0.16 9 9
Crk/p130 Cas/Paxillin 0.031 0.022 -10000 0 -0.14 9 9
IGF1R 0.017 0.008 -10000 0 -10000 0 0
IGF1 0.014 0.037 -10000 0 -0.41 4 4
IRS2/Crk 0.025 0.023 -10000 0 -0.14 9 9
PI3K 0.027 0.052 -10000 0 -0.18 30 30
apoptosis -0.028 0.047 -10000 0 -10000 0 0
HRAS/GDP 0.012 0.013 -10000 0 -0.29 1 1
PRKCD 0.015 0.035 -10000 0 -0.16 7 7
RAF1/14-3-3 E 0.034 0.045 -10000 0 -10000 0 0
BAD/14-3-3 0.029 0.049 -10000 0 -10000 0 0
PRKCZ 0.009 0.042 -10000 0 -0.17 24 24
Crk/p130 Cas/Paxillin/FAK1 0.021 0.04 -10000 0 -10000 0 0
PTPN1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.013 0.038 -10000 0 -0.17 7 7
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.009 0.092 -10000 0 -0.24 63 63
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.024 0.024 -10000 0 -0.16 9 9
GRB10 0.004 0.073 -10000 0 -0.41 16 16
PTPN11 0.018 0.023 -10000 0 -0.16 9 9
IRS1 0.014 0.025 -10000 0 -0.18 9 9
IRS2 0.017 0.023 -10000 0 -0.16 9 9
IGF-1R heterotetramer/IGF1 0.021 0.028 -10000 0 -0.28 4 4
GRB2 0.017 0.002 -10000 0 -10000 0 0
PDPK1 0.014 0.046 -10000 0 -0.18 24 24
YWHAE 0.017 0.001 -10000 0 -10000 0 0
PRKD1 -0.032 0.09 -10000 0 -0.18 131 131
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
Class I PI3K signaling events mediated by Akt

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.035 0.004 -10000 0 -10000 0 0
CDKN1B 0.02 0.037 -10000 0 -0.14 27 27
CDKN1A 0 0.069 -10000 0 -0.16 80 80
FRAP1 0.016 0.019 -10000 0 -0.41 1 1
PRKDC -0.002 0.088 -10000 0 -0.41 23 23
FOXO3 0.02 0.037 -10000 0 -0.14 27 27
AKT1 0.017 0.038 -10000 0 -0.15 27 27
BAD 0.017 0 -10000 0 -10000 0 0
AKT3 0.015 0.009 -10000 0 -0.18 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0.037 -10000 0 -0.14 27 27
AKT1/ASK1 0.025 0.037 -10000 0 -0.13 27 27
BAD/YWHAZ 0.034 0.004 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.016 0.019 -10000 0 -0.41 1 1
JNK cascade -0.024 0.036 0.13 27 -10000 0 27
TSC1 0.019 0.037 -10000 0 -0.14 27 27
YWHAZ 0.017 0.002 -10000 0 -10000 0 0
AKT1/RAF1 0.026 0.039 -10000 0 -0.14 28 28
EP300 0.017 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.038 -10000 0 -0.15 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.02 0.037 -10000 0 -0.14 27 27
YWHAQ 0.017 0 -10000 0 -10000 0 0
TBC1D4 0.016 0 -10000 0 -10000 0 0
MAP3K5 0.017 0.001 -10000 0 -10000 0 0
MAPKAP1 0.017 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.002 0.036 0.15 10 -10000 0 10
YWHAH 0.008 0.009 -10000 0 -10000 0 0
AKT1S1 0.016 0.037 -10000 0 -0.14 27 27
CASP9 0.018 0.045 -10000 0 -0.16 28 28
YWHAB 0.017 0.001 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.037 -10000 0 -0.18 1 1
GBL 0.017 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.035 0 -10000 0 -10000 0 0
YWHAE 0.017 0.001 -10000 0 -10000 0 0
SRC 0.017 0 -10000 0 -10000 0 0
AKT2/p21CIP1 0.004 0.066 -10000 0 -0.16 55 55
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.015 -10000 0 -0.17 1 1
CHUK 0.019 0.038 -10000 0 -0.14 28 28
BAD/BCL-XL 0.036 0.037 -10000 0 -0.17 1 1
mTORC2 0.033 0.011 -10000 0 -0.21 1 1
AKT2 0.015 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.005 0.048 -10000 0 -0.2 10 10
PDPK1 0.017 0 -10000 0 -10000 0 0
MDM2 0.013 0.051 -10000 0 -0.16 44 44
MAPKKK cascade -0.026 0.039 0.14 28 -10000 0 28
MDM2/Cbp/p300 0.031 0.052 -10000 0 -0.16 19 19
TSC1/TSC2 0.022 0.036 -10000 0 -0.13 27 27
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.05 -10000 0 -0.16 19 19
glucose import 0.018 0 -10000 0 -10000 0 0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.027 0.027 -10000 0 -0.22 1 1
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.018 0 -10000 0 -10000 0 0
GSK3A 0.02 0.037 -10000 0 -0.14 27 27
FOXO1 0.016 0.047 -10000 0 -0.15 37 37
GSK3B 0.02 0.036 -10000 0 -0.14 26 26
SFN -0.01 0.1 -10000 0 -0.41 33 33
G1/S transition of mitotic cell cycle 0.022 0.035 -10000 0 -0.18 1 1
p27Kip1/14-3-3 family 0.012 0.026 -10000 0 -0.13 7 7
PRKACA 0.017 0 -10000 0 -10000 0 0
KPNA1 0.017 0 -10000 0 -10000 0 0
HSP90AA1 0.017 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.017 0 -10000 0 -10000 0 0
CREBBP 0.017 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
alphaV beta3 Integrin 0.016 0.053 -9999 0 -0.28 16 16
PTK2 0.026 0.04 -9999 0 -0.18 7 7
positive regulation of JNK cascade 0 0.007 -9999 0 -10000 0 0
CDC42/GDP 0.053 0.02 -9999 0 -10000 0 0
Rac1/GDP 0.054 0.02 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0.017 0 -9999 0 -10000 0 0
CDC42/GTP 0.04 0.018 -9999 0 -10000 0 0
nectin-3/I-afadin 0.024 0.019 -9999 0 -0.28 2 2
RAPGEF1 0.04 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.04 0.023 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
TLN1 0 0.059 -9999 0 -0.19 46 46
Rap1/GTP 0 0.008 -9999 0 -10000 0 0
IQGAP1 -0.086 0.18 -9999 0 -0.41 127 127
Rap1/GTP/I-afadin 0.022 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.024 0.019 -9999 0 -0.28 2 2
PVR 0.017 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.017 0 -9999 0 -10000 0 0
mol:GDP 0.049 0.022 -9999 0 -10000 0 0
MLLT4 0.017 0 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PI3K 0.034 0.056 -9999 0 -0.19 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly 0 0.008 -9999 0 -10000 0 0
PVRL1 0.017 0 -9999 0 -10000 0 0
PVRL3 0.015 0.026 -9999 0 -0.41 2 2
PVRL2 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
CDH1 0.011 0.052 -9999 0 -0.41 8 8
CLDN1 0.01 0.055 -9999 0 -0.41 9 9
JAM-A/CLDN1 0.024 0.079 -9999 0 -0.26 35 35
SRC 0.035 0.025 -9999 0 -0.18 2 2
ITGB3 0.017 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
FARP2 0.046 0.021 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.034 0.017 -9999 0 -0.23 2 2
nectin-1/I-afadin 0.025 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0.025 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin -0.04 0.11 -9999 0 -0.24 127 127
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.034 0.017 -9999 0 -0.23 2 2
CDC42/GTP/IQGAP1/filamentous actin -0.04 0.11 -9999 0 -0.24 127 127
F11R -0.01 0.1 -9999 0 -0.41 33 33
positive regulation of filopodium formation 0 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.013 0.072 -9999 0 -0.19 56 56
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
PIP5K1C 0.017 0.009 -9999 0 -10000 0 0
VAV2 0.047 0.022 -9999 0 -10000 0 0
RAP1/GDP 0.041 0.019 -9999 0 -10000 0 0
ITGAV 0.004 0.073 -9999 0 -0.41 16 16
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.034 0.017 -9999 0 -0.23 2 2
nectin-3(dimer)/I-afadin/I-afadin 0.024 0.019 -9999 0 -0.28 2 2
Rac1/GTP 0.045 0.018 -9999 0 -10000 0 0
PTPRM 0.016 0.009 -9999 0 -0.12 2 2
E-cadherin/beta catenin/alpha catenin 0.047 0.028 -9999 0 -0.18 8 8
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.033 0.074 -10000 0 -0.32 22 22
IHH 0.024 0.023 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 -0.002 0.073 -10000 0 -0.21 58 58
LRPAP1 0.017 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.002 0.073 0.21 58 -10000 0 58
SMO/beta Arrestin2 0.045 0.047 -10000 0 -0.27 7 7
SMO 0.038 0.048 -10000 0 -0.28 7 7
AKT1 0.029 0.055 -10000 0 -0.27 11 11
ARRB2 0.017 0 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.017 0 -10000 0 -10000 0 0
heart looping 0.038 0.048 -10000 0 -0.28 7 7
STIL 0.005 0.084 -10000 0 -0.18 75 75
DHH N/PTCH2 0.013 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.025 0.053 -10000 0 -0.22 22 22
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.033 0.076 -10000 0 -0.33 22 22
determination of left/right symmetry 0.038 0.048 -10000 0 -0.28 7 7
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
skeletal system development 0.033 0.075 -10000 0 -0.33 22 22
IHH N/Hhip 0.016 0.012 -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 0.038 0.048 -10000 0 -0.28 7 7
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.017 0 -10000 0 -10000 0 0
PI3K 0.009 0.065 -10000 0 -0.28 25 25
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.03 0.13 -10000 0 -0.41 58 58
somite specification 0.038 0.048 -10000 0 -0.28 7 7
SHH Np/Cholesterol/PTCH1 0.035 0.048 -10000 0 -0.3 7 7
SHH Np/Cholesterol/PTCH2 0.024 0 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.023 0.01 -10000 0 -0.21 1 1
SHH 0.018 0 -10000 0 -10000 0 0
catabolic process 0.03 0.061 -10000 0 -0.25 22 22
SMO/Vitamin D3 0.042 0.047 -10000 0 -0.27 7 7
SHH Np/Cholesterol/Hhip 0.012 0 -10000 0 -10000 0 0
LRP2 0.016 0.019 -10000 0 -0.41 1 1
receptor-mediated endocytosis 0.042 0.044 -10000 0 -0.25 7 7
SHH Np/Cholesterol/BOC 0.012 0 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.024 0 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.012 0 -10000 0 -10000 0 0
mol:Vitamin D3 0.037 0.049 -10000 0 -0.3 7 7
IHH N/PTCH2 0.029 0.014 -10000 0 -10000 0 0
CDON 0.017 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.037 0.063 -10000 0 -0.25 22 22
Megalin/LRPAP1 0.025 0.013 -10000 0 -0.28 1 1
PTCH2 0.017 0 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.015 0 -10000 0 -10000 0 0
PTCH1 0.03 0.061 -10000 0 -0.25 22 22
HHIP 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.029 0.06 -9999 0 -0.21 32 32
MAP4K1 0.016 0.019 -9999 0 -0.41 1 1
MAP3K8 -0.017 0.12 -9999 0 -0.41 42 42
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
MAP3K1 0.021 0.034 -9999 0 -0.18 1 1
JUN 0.019 0.015 -9999 0 -10000 0 0
MAP3K7 0.021 0.034 -9999 0 -0.18 1 1
GRAP2 0.017 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.045 -9999 0 -0.18 15 15
LAT 0.016 0.019 -9999 0 -0.41 1 1
LCP2 -0.007 0.099 -9999 0 -0.41 30 30
MAPK8 0.016 0.014 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.035 -9999 0 -0.12 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 0.027 0.056 -9999 0 -0.19 32 32
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.013 0.037 -10000 0 -0.41 4 4
GNB1/GNG2 -0.045 0.035 -10000 0 -0.14 15 15
AKT1 -0.016 0.081 -10000 0 -0.17 6 6
EGF 0.015 0.026 -10000 0 -0.41 2 2
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.023 0.033 -10000 0 -0.16 17 17
mol:Ca2+ -0.029 0.11 -10000 0 -0.23 15 15
LYN 0.007 0.059 -10000 0 -0.15 64 64
RhoA/GTP -0.031 0.026 -10000 0 -0.12 3 3
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.047 0.12 -10000 0 -0.26 37 37
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.027 0.019 -10000 0 -0.13 7 7
G beta5/gamma2 -0.058 0.045 -10000 0 -0.19 15 15
PRKCH -0.041 0.12 -10000 0 -0.28 16 16
DNM1 0.003 0.007 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.002 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.002 3 3
PTGDR 0.017 0 -10000 0 -10000 0 0
G12 family/GTP -0.071 0.055 -10000 0 -0.22 19 19
ADRBK1 0.017 0 -10000 0 -10000 0 0
ADRBK2 0.017 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.023 0.002 -10000 0 -10000 0 0
mol:GDP 0.003 0.065 0.16 1 -10000 0 1
mol:NADP 0.017 0 -10000 0 -10000 0 0
RAB11A 0.017 0.001 -10000 0 -10000 0 0
PRKG1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.039 0.12 -10000 0 -0.28 15 15
cell morphogenesis 0.023 0.002 -10000 0 -10000 0 0
PLCB2 -0.054 0.14 -10000 0 -0.36 15 15
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.029 0.006 -10000 0 -10000 0 0
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.067 -10000 0 -0.15 86 86
RHOA 0.017 0.001 -10000 0 -10000 0 0
PTGIR 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.009 0.049 -10000 0 -0.31 3 3
GNAQ 0.017 0 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.062 0.15 -10000 0 -0.38 15 15
LCK 0.027 0.016 -10000 0 -0.15 4 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.033 0.002 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.039 -10000 0 -0.31 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.033 0.002 -10000 0 -10000 0 0
MAPK14 -0.028 0.093 -10000 0 -0.18 39 39
TGM2/GTP -0.035 0.13 -10000 0 -0.3 15 15
MAPK11 -0.028 0.093 -10000 0 -0.18 37 37
ARHGEF1 -0.018 0.07 -10000 0 -0.14 15 15
GNAI2 0.017 0.001 -10000 0 -10000 0 0
JNK cascade -0.045 0.13 -10000 0 -0.29 15 15
RAB11/GDP 0.017 0.001 -10000 0 -10000 0 0
ICAM1 -0.035 0.11 -10000 0 -0.3 15 15
cAMP biosynthetic process -0.032 0.11 -10000 0 -0.25 15 15
Gq family/GTP/EBP50 0.02 0.021 -10000 0 -0.13 8 8
actin cytoskeleton reorganization 0.023 0.002 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
GNB5 0.017 0.002 -10000 0 -10000 0 0
GNB1 0.017 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.013 0.061 -10000 0 -0.16 34 34
VCAM1 -0.078 0.13 -10000 0 -0.25 30 30
TP beta/Gq family/GDP/G beta5/gamma2 0.027 0.019 -10000 0 -0.13 7 7
platelet activation -0.03 0.12 -10000 0 -0.24 17 17
PGI2/IP 0.013 0.001 -10000 0 -10000 0 0
PRKACA 0.019 0.001 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.026 0.019 -10000 0 -0.12 7 7
TXA2/TP beta/beta Arrestin2 0.002 0.006 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.019 0.002 -10000 0 -10000 0 0
mol:DAG -0.049 0.13 -10000 0 -0.32 15 15
EGFR -0.14 0.21 -10000 0 -0.41 194 194
TXA2/TP alpha -0.041 0.14 -10000 0 -0.33 15 15
Gq family/GTP 0.016 0.017 -10000 0 -0.11 9 9
YES1 0.002 0.065 -10000 0 -0.15 80 80
GNAI2/GTP 0.023 0.005 -10000 0 -10000 0 0
PGD2/DP 0.013 0.001 -10000 0 -10000 0 0
SLC9A3R1 0.015 0.026 -10000 0 -0.41 2 2
FYN 0.027 0.013 -10000 0 -0.15 2 2
mol:NO 0.017 0 -10000 0 -10000 0 0
GNA15 0.011 0.049 -10000 0 -0.41 7 7
PGK/cGMP 0.023 0.001 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.034 0.018 -10000 0 -0.16 4 4
NOS3 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.041 0.12 -10000 0 -0.27 15 15
PRKCB -0.046 0.12 -10000 0 -0.27 15 15
PRKCE -0.044 0.12 -10000 0 -0.28 15 15
PRKCD -0.051 0.12 -10000 0 -0.29 15 15
PRKCG -0.047 0.12 -10000 0 -0.29 15 15
muscle contraction -0.056 0.14 -10000 0 -0.36 15 15
PRKCZ -0.041 0.12 -10000 0 -0.26 15 15
ARR3 0.017 0 -10000 0 -10000 0 0
TXA2/TP beta 0.034 0.005 -10000 0 -10000 0 0
PRKCQ -0.044 0.12 -10000 0 -0.27 15 15
MAPKKK cascade -0.051 0.13 -10000 0 -0.33 15 15
SELE -0.038 0.11 -10000 0 -0.24 15 15
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.004 -10000 0 -10000 0 0
ROCK1 0.017 0 -10000 0 -10000 0 0
GNA14 0.015 0.026 -10000 0 -0.41 2 2
chemotaxis -0.077 0.16 -10000 0 -0.44 15 15
GNA12 0.014 0.037 -10000 0 -0.41 4 4
GNA13 0.015 0.026 -10000 0 -0.41 2 2
GNA11 0.017 0 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.001 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.021 0.012 -9999 0 -10000 0 0
NFATC2 0.012 0.01 -9999 0 -10000 0 0
NFATC3 0.021 0.012 -9999 0 -10000 0 0
CD40LG 0.019 0.1 -9999 0 -0.33 15 15
PTGS2 0.009 0.13 -9999 0 -0.39 31 31
JUNB 0.011 0.052 -9999 0 -0.41 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.008 -9999 0 -10000 0 0
CaM/Ca2+ 0.015 0.008 -9999 0 -10000 0 0
CALM1 0.018 0.005 -9999 0 -10000 0 0
JUN 0.019 0.019 -9999 0 -0.41 1 1
mol:Ca2+ 0.002 0.004 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.011 -9999 0 -0.24 1 1
FOSL1 0.007 0.066 -9999 0 -0.41 13 13
CREM 0.017 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.055 0.041 -9999 0 -0.19 3 3
FOS -0.081 0.18 -9999 0 -0.41 125 125
IFNG 0.019 0.1 -9999 0 -0.33 16 16
AP-1/NFAT1-c-4 0.05 0.13 -9999 0 -0.37 15 15
FASLG 0.019 0.1 -9999 0 -0.33 15 15
NFAT1-c-4/ICER1 0.039 0.026 -9999 0 -0.12 2 2
IL2RA 0.017 0.11 -9999 0 -0.37 17 17
FKBP12/FK506 0.012 0.013 -9999 0 -0.29 1 1
CSF2 0.019 0.1 -9999 0 -0.33 15 15
JunB/Fra1/NFAT1-c-4 0.042 0.051 -9999 0 -0.18 20 20
IL4 0.019 0.1 -9999 0 -0.33 15 15
IL2 0.001 0.004 -9999 0 -10000 0 0
IL3 0.003 0.008 -9999 0 -10000 0 0
FKBP1A 0.016 0.019 -9999 0 -0.41 1 1
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.023 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.017 0 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.017 0 -9999 0 -10000 0 0
TCEB1 0.017 0 -9999 0 -10000 0 0
HIF1A/p53 -0.001 0.072 -9999 0 -0.18 69 69
HIF1A 0.015 0.021 -9999 0 -0.11 3 3
COPS5 0.017 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.041 0 -9999 0 -10000 0 0
FIH (dimer) 0.017 0 -9999 0 -10000 0 0
CDKN2A -0.03 0.13 -9999 0 -0.41 58 58
ARNT/IPAS 0.025 0 -9999 0 -10000 0 0
HIF1AN 0.017 0 -9999 0 -10000 0 0
GNB2L1 0.017 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.024 0.023 -9999 0 -10000 0 0
CUL2 0.017 0 -9999 0 -10000 0 0
OS9 -0.018 0.12 -9999 0 -0.41 43 43
RACK1/Elongin B/Elongin C 0.035 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.024 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 0.021 0.072 -9999 0 -0.21 48 48
HIF1A/RACK1/Elongin B/Elongin C 0.038 0.024 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.024 0.023 -9999 0 -10000 0 0
EGLN3 0.014 0.037 -9999 0 -0.41 4 4
EGLN2 0.017 0 -9999 0 -10000 0 0
EGLN1 0.016 0.019 -9999 0 -0.41 1 1
TP53 -0.039 0.14 -9999 0 -0.41 69 69
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.028 0.005 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
ARD1A 0.016 0.019 -9999 0 -0.41 1 1
RBX1 0.017 0 -9999 0 -10000 0 0
HIF1A/p19ARF 0.003 0.071 -9999 0 -0.19 58 58
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.023 0.064 -9999 0 -0.29 19 19
E-cadherin/beta catenin 0.021 0.038 -9999 0 -0.28 8 8
CTNNB1 0.017 0 -9999 0 -10000 0 0
JUP 0.004 0.073 -9999 0 -0.41 16 16
CDH1 0.011 0.052 -9999 0 -0.41 8 8
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.02 0.042 -10000 0 -0.28 10 10
CRKL 0.027 0.022 -10000 0 -10000 0 0
mol:PIP3 -0.011 0.023 0.35 2 -10000 0 2
AKT1 -0.003 0.025 0.26 2 -0.21 4 6
PTK2B 0.017 0 -10000 0 -10000 0 0
RAPGEF1 0.03 0.021 -10000 0 -10000 0 0
RANBP10 0.017 0 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
HGF/MET/SHIP2 0.029 0.04 -10000 0 -0.23 12 12
MAP3K5 0.038 0.022 -10000 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS 0.028 0.036 -10000 0 -0.21 12 12
AP1 -0.042 0.12 -10000 0 -0.25 125 125
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
apoptosis -0.015 0.082 -10000 0 -0.66 2 2
STAT3 (dimer) 0.029 0.021 -10000 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K 0.038 0.047 -10000 0 -0.26 1 1
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.037 0.022 -10000 0 -10000 0 0
PTPN11 0.017 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.017 0 -10000 0 -10000 0 0
PTEN 0.015 0.026 -10000 0 -0.41 2 2
ELK1 -0.001 0.044 0.21 17 -0.16 10 27
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.021 0.015 -10000 0 -10000 0 0
PAK1 0 0.023 0.24 2 -0.2 4 6
HGF/MET/RANBP10 0.029 0.04 -10000 0 -0.23 12 12
HRAS 0.028 0.029 -10000 0 -0.16 10 10
DOCK1 0.03 0.021 -10000 0 -10000 0 0
GAB1 0.025 0.023 -10000 0 -10000 0 0
CRK 0.027 0.022 -10000 0 -10000 0 0
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.028 -10000 0 -0.16 10 10
JUN 0.016 0.019 -10000 0 -0.41 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.01 0.022 -10000 0 -0.14 12 12
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
cell morphogenesis 0.041 0.047 -10000 0 -0.19 1 1
GRB2/SHC 0.011 0.067 -10000 0 -0.18 55 55
FOS -0.084 0.18 -10000 0 -0.41 125 125
GLMN 0.003 0 -10000 0 -10000 0 0
cell motility -0.001 0.044 0.21 17 -0.16 10 27
HGF/MET/MUC20 0.017 0.039 -10000 0 -0.24 12 12
cell migration 0.011 0.066 -10000 0 -0.18 55 55
GRB2 0.017 0.002 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
MET/RANBP10 0.02 0.042 -10000 0 -0.28 10 10
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.028 0.023 -10000 0 -10000 0 0
MET/MUC20 0.007 0.041 -10000 0 -0.29 10 10
RAP1B 0.029 0.02 -10000 0 -10000 0 0
RAP1A 0.032 0.02 -10000 0 -10000 0 0
HGF/MET/RANBP9 0.029 0.04 -10000 0 -0.23 12 12
RAF1 0.03 0.029 -10000 0 -10000 0 0
STAT3 0.029 0.021 -10000 0 -10000 0 0
cell proliferation 0.018 0.06 -10000 0 -0.23 9 9
RPS6KB1 0.012 0.01 -10000 0 -0.087 1 1
MAPK3 -0.013 0.02 -10000 0 -10000 0 0
MAPK1 0.006 0.11 0.59 17 -10000 0 17
RANBP9 0.017 0.001 -10000 0 -10000 0 0
MAPK8 0.049 0.027 -10000 0 -10000 0 0
SRC 0.028 0.021 -10000 0 -10000 0 0
PI3K 0.019 0.049 -10000 0 -0.17 31 31
MET/Glomulin 0.01 0.036 -10000 0 -0.25 10 10
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.032 0.028 -10000 0 -10000 0 0
MET 0.009 0.058 -10000 0 -0.41 10 10
MAP4K1 0.035 0.022 -10000 0 -10000 0 0
PTK2 0.017 0.001 -10000 0 -10000 0 0
MAP2K2 0.032 0.028 -10000 0 -0.16 1 1
BAD 0 0.023 0.24 2 -0.2 4 6
MAP2K4 0.038 0.022 -10000 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 0.028 0.027 -10000 0 -10000 0 0
INPPL1 0.017 0 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.013 0.021 -10000 0 -0.13 10 10
PLCgamma1/PKC 0.013 0 -10000 0 -10000 0 0
HGF 0.015 0.026 -10000 0 -0.41 2 2
RASA1 0.017 0.002 -10000 0 -10000 0 0
NCK1 0.008 0.061 -10000 0 -0.41 11 11
PTPRJ 0.017 0 -10000 0 -10000 0 0
NCK/PLCgamma1 0.027 0.037 -10000 0 -0.15 21 21
PDPK1 -0.006 0.018 0.29 2 -10000 0 2
HGF/MET/SHIP 0.017 0.039 -10000 0 -0.24 12 12
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 -0.036 0.14 -9999 0 -0.41 66 66
Ran/GTP/Exportin 1/HDAC4 0 0.007 -9999 0 -0.16 1 1
MDM2/SUMO1 0.025 0.039 -9999 0 -0.18 18 18
HDAC4 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.02 0.053 -9999 0 -0.16 66 66
SUMO1 0.017 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.014 0.005 -9999 0 -0.11 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.02 0.005 -9999 0 -0.096 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0.019 -9999 0 -0.41 1 1
SUMO1/HDAC4 0.033 0.005 -9999 0 -10000 0 0
SUMO1/HDAC1 0.006 0.071 -9999 0 -0.18 66 66
RANGAP1 0.017 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.036 0.046 -9999 0 -0.21 18 18
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0.005 -9999 0 -0.11 1 1
Ran/GTP 0.026 0.006 -9999 0 -0.093 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.002 0.078 -9999 0 -0.41 18 18
UBE2I 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.005 -9999 0 -10000 0 0
NPC 0.01 0.009 -9999 0 -0.2 1 1
PIAS2 0.017 0 -9999 0 -10000 0 0
PIAS1 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.017 0 -9999 0 -10000 0 0
SPHK1 0.001 0.082 -9999 0 -0.41 20 20
GNAI2 0.017 0.001 -9999 0 -10000 0 0
mol:S1P 0.009 0.04 -9999 0 -0.16 27 27
GNAO1 0.002 0.005 -9999 0 -10000 0 0
mol:Sphinganine-1-P 0.006 0.058 -9999 0 -0.28 20 20
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.024 0.04 -9999 0 -0.21 8 8
GNAI3 -0.036 0.14 -9999 0 -0.41 65 65
G12/G13 0.022 0.033 -9999 0 -0.28 6 6
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.017 0.001 -9999 0 -10000 0 0
S1P1/S1P 0.018 0.035 -9999 0 -0.13 26 26
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 0.014 0.02 -9999 0 -0.41 1 1
S1P/S1P5/G12 0.014 0.037 -9999 0 -0.13 31 31
S1P/S1P3/Gq 0.023 0.029 -9999 0 -0.17 7 7
S1P/S1P4/Gi 0 0.027 -9999 0 -0.2 6 6
GNAQ 0.017 0 -9999 0 -10000 0 0
GNAZ 0.015 0.006 -9999 0 -10000 0 0
GNA14 0.015 0.026 -9999 0 -0.41 2 2
GNA15 0.011 0.049 -9999 0 -0.41 7 7
GNA12 0.014 0.037 -9999 0 -0.41 4 4
GNA13 0.015 0.026 -9999 0 -0.41 2 2
GNA11 0.017 0 -9999 0 -10000 0 0
ABCC1 0.01 0.055 -9999 0 -0.41 9 9
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 -0.037 0.14 -9999 0 -0.41 66 66
HDAC2 0.013 0.042 -9999 0 -0.41 5 5
GNB1/GNG2 0.023 0.012 -9999 0 -0.24 1 1
forebrain development 0.02 0.049 -9999 0 -0.31 8 8
GNAO1 0.002 0.005 -9999 0 -10000 0 0
SMO/beta Arrestin2 0.027 0.014 -9999 0 -0.28 1 1
SMO 0.017 0.019 -9999 0 -0.41 1 1
ARRB2 0.018 0.001 -9999 0 -10000 0 0
GLI3/SPOP 0.02 0.04 -9999 0 -0.21 3 3
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.017 0.001 -9999 0 -10000 0 0
GNAI2 0.018 0.001 -9999 0 -10000 0 0
SIN3/HDAC complex 0.032 0.001 -9999 0 -10000 0 0
GNAI1 0.014 0.02 -9999 0 -0.41 1 1
XPO1 0.019 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) -0.001 0.038 -9999 0 -0.28 7 7
SAP30 0.017 0 -9999 0 -10000 0 0
mol:GDP 0.017 0.019 -9999 0 -0.41 1 1
MIM/GLI2A 0.023 0.007 -9999 0 -10000 0 0
IFT88 0.017 0 -9999 0 -10000 0 0
GNAI3 -0.035 0.14 -9999 0 -0.41 65 65
GLI2 0.035 0.008 -9999 0 -10000 0 0
GLI3 0.011 0.04 -9999 0 -0.14 13 13
CSNK1D 0.015 0.026 -9999 0 -0.41 2 2
CSNK1E 0.017 0.001 -9999 0 -10000 0 0
SAP18 0.017 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.017 0 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
Gi family/GTP 0.001 0.017 -9999 0 -0.13 5 5
SIN3B 0.017 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.017 0.031 -9999 0 -0.17 3 3
GLI2/Su(fu) 0.037 0.01 -9999 0 -10000 0 0
FOXA2 0.03 0.037 -9999 0 -0.38 4 4
neural tube patterning 0.02 0.049 -9999 0 -0.31 8 8
SPOP 0.017 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.006 -9999 0 -0.11 1 1
GNB1 0.017 0.002 -9999 0 -10000 0 0
CSNK1G2 0.017 0 -9999 0 -10000 0 0
CSNK1G3 0.017 0 -9999 0 -10000 0 0
MTSS1 0.023 0.007 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.02 0.049 -9999 0 -0.31 8 8
SUFU 0.009 0.007 -9999 0 -0.13 1 1
LGALS3 -0.033 0.14 -9999 0 -0.41 61 61
catabolic process 0.041 0.039 -9999 0 -0.18 3 3
GLI3A/CBP 0.023 0.03 -9999 0 -0.22 8 8
KIF3A 0.016 0.005 -9999 0 -10000 0 0
GLI1 0.02 0.05 -9999 0 -0.31 8 8
RAB23 0.013 0.042 -9999 0 -0.41 5 5
CSNK1A1 0.017 0 -9999 0 -10000 0 0
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.017 0 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.007 0.074 -9999 0 -0.21 61 61
GNAZ 0.015 0.006 -9999 0 -10000 0 0
RBBP4 -0.065 0.17 -9999 0 -0.41 101 101
CSNK1G1 0.017 0 -9999 0 -10000 0 0
PIAS1 0.017 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GLI2/SPOP 0.042 0.008 -9999 0 -10000 0 0
STK36 0.002 0.002 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.01 0.039 -9999 0 -0.12 53 53
PTCH1 0.023 0.063 -9999 0 -0.47 7 7
MIM/GLI1 0.038 0.054 -9999 0 -0.3 10 10
CREBBP 0.023 0.03 -9999 0 -0.22 8 8
Su(fu)/SIN3/HDAC complex -0.005 0.062 -9999 0 -0.19 23 23
Aurora C signaling

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
INCENP 0.017 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.02 0.056 -9999 0 -0.21 29 29
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.01 0.017 -9999 0 -10000 0 0
AURKB -0.005 0.094 -9999 0 -0.41 27 27
AURKC 0.015 0.026 -9999 0 -0.41 2 2
Atypical NF-kappaB pathway

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.025 0 -9999 0 -10000 0 0
FBXW11 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.023 -9999 0 -0.23 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.043 -9999 0 -0.25 6 6
NFKBIA 0.012 0.037 -9999 0 -0.11 40 40
MAPK14 0.015 0.026 -9999 0 -0.41 2 2
NF kappa B1 p105/p50 0.024 0.023 -9999 0 -0.23 4 4
ARRB2 0.014 0.012 -9999 0 -0.18 2 2
REL 0.017 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.024 0.023 -9999 0 -0.23 4 4
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.024 0.023 -9999 0 -0.23 4 4
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
NF kappa B1 p50 dimer 0.016 0.026 -9999 0 -0.28 4 4
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.026 -9999 0 -0.28 4 4
RELA 0.017 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.017 0.038 -9999 0 -0.11 40 40
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.033 0.043 -9999 0 -0.23 7 7
SRC 0.017 0 -9999 0 -10000 0 0
PI3K 0.009 0.065 -9999 0 -0.28 25 25
NF kappa B1 p50/RelA 0.017 0.038 -9999 0 -0.11 40 40
IKBKB 0.017 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
SYK -0.012 0.11 -9999 0 -0.41 36 36
I kappa B alpha/PIK3R1 0.021 0.033 -9999 0 -0.18 3 3
cell death 0.032 0.041 -9999 0 -0.22 7 7
NF kappa B1 p105/c-Rel 0.024 0.023 -9999 0 -0.23 4 4
LCK 0.014 0.037 -9999 0 -0.41 4 4
BCL3 0.017 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.022 0.016 -10000 0 -0.24 2 2
cell-cell adhesion 0.004 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.047 0.019 -10000 0 -0.19 2 2
ITSN1 0.017 0 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
SHC1 -0.021 0.12 -10000 0 -0.41 47 47
Ephrin B1/EPHB3 0.017 0.04 -10000 0 -0.24 13 13
Ephrin B1/EPHB1 0.017 0.039 -10000 0 -0.24 12 12
HRAS/GDP 0.024 0.029 -10000 0 -0.15 12 12
Ephrin B/EPHB1/GRB7 0.043 0.038 -10000 0 -0.19 12 12
Endophilin/SYNJ1 0.022 0.014 -10000 0 -0.18 2 2
KRAS 0.017 0.002 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.043 0.036 -10000 0 -0.19 11 11
endothelial cell migration 0.023 0.048 -10000 0 -0.19 23 23
GRB2 0.017 0.002 -10000 0 -10000 0 0
GRB7 0.016 0.019 -10000 0 -0.41 1 1
PAK1 0.027 0.014 -10000 0 -0.18 2 2
HRAS 0.016 0.019 -10000 0 -0.41 1 1
RRAS 0.016 0.039 -10000 0 -0.18 19 19
DNM1 0.003 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.02 0.03 -10000 0 -0.18 11 11
lamellipodium assembly -0.004 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.05 -10000 0 -0.12 58 58
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
EPHB2 0.015 0.026 -10000 0 -0.41 2 2
EPHB3 0.007 0.066 -10000 0 -0.41 13 13
EPHB1 0.007 0.064 -10000 0 -0.41 12 12
EPHB4 0.017 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.029 -10000 0 -0.16 1 1
Ephrin B/EPHB2 0.038 0.017 -10000 0 -0.19 2 2
Ephrin B/EPHB3 0.033 0.037 -10000 0 -0.19 13 13
JNK cascade 0.016 0.046 -10000 0 -0.19 26 26
Ephrin B/EPHB1 0.034 0.035 -10000 0 -0.19 11 11
RAP1/GDP 0.03 0.028 -10000 0 -0.14 1 1
EFNB2 0.016 0.003 -10000 0 -10000 0 0
EFNB3 0.017 0.001 -10000 0 -10000 0 0
EFNB1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.026 0.038 -10000 0 -0.21 13 13
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP 0.037 0.032 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.024 -10000 0 -0.15 13 13
axon guidance 0.022 0.016 -10000 0 -0.24 2 2
MAPK3 0.018 0.044 -10000 0 -0.18 5 5
MAPK1 0.017 0.044 -10000 0 -0.18 5 5
Rac1/GDP 0.033 0.029 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.031 0.053 -10000 0 -0.26 4 4
CDC42/GDP 0.033 0.029 -10000 0 -10000 0 0
PI3K 0.026 0.049 -10000 0 -0.19 23 23
EFNA5 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.03 0.012 -10000 0 -0.12 2 2
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP -0.041 0.069 -10000 0 -0.32 4 4
PTK2 0.008 0.007 -10000 0 -10000 0 0
MAP4K4 0.016 0.047 -10000 0 -0.19 26 26
SRC 0.017 0 -10000 0 -10000 0 0
KALRN 0.017 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0.025 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.04 0.028 -10000 0 -10000 0 0
MAP2K1 0.016 0.047 -10000 0 -0.17 7 7
WASL 0.017 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.032 0.053 -10000 0 -0.21 25 25
cell migration 0.024 0.048 0.17 3 -0.18 7 10
NRAS -0.094 0.19 -10000 0 -0.41 137 137
SYNJ1 0.022 0.015 -10000 0 -0.18 2 2
PXN 0.017 0 -10000 0 -10000 0 0
TF 0.016 0.02 -10000 0 -10000 0 0
HRAS/GTP 0.034 0.034 -10000 0 -0.16 14 14
Ephrin B1/EPHB1-2 0.027 0.039 -10000 0 -0.21 14 14
cell adhesion mediated by integrin -0.015 0.031 -10000 0 -0.16 4 4
RAC1 0.017 0 -10000 0 -10000 0 0
mol:GTP 0.038 0.036 -10000 0 -0.17 13 13
RAC1-CDC42/GTP -0.007 0.032 -10000 0 -10000 0 0
RASA1 0.017 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.041 0.028 -10000 0 -10000 0 0
ruffle organization 0.03 0.032 -10000 0 -10000 0 0
NCK1 0.008 0.061 -10000 0 -0.41 11 11
receptor internalization 0.005 0.012 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.048 0.018 -10000 0 -0.19 2 2
ROCK1 0.014 0.036 -10000 0 -0.21 13 13
RAS family/GDP -0.032 0.055 -10000 0 -0.25 4 4
Rac1/GTP -0.004 0.025 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.027 0.024 -10000 0 -0.12 12 12
mTOR signaling 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
GBL 0.017 0 -10000 0 -10000 0 0
MKNK1 0.017 0 -10000 0 -10000 0 0
mol:PIP3 0.002 0.044 0.22 2 -0.18 24 26
FRAP1 0.018 0.026 -10000 0 -0.37 1 1
AKT1 0.007 0.04 0.16 2 -0.16 24 26
INSR 0.017 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0 -10000 0 -10000 0 0
mol:GTP 0.027 0.042 0.19 1 -0.14 25 26
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.025 -10000 0 -0.15 9 9
TSC2 0.017 0 -10000 0 -10000 0 0
RHEB/GDP 0.016 0.034 -10000 0 -0.13 25 25
TSC1 0.016 0.019 -10000 0 -0.41 1 1
Insulin Receptor/IRS1 0.017 0.015 -10000 0 -0.14 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.018 0.036 -10000 0 -0.15 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.017 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.034 0.17 1 -0.26 1 2
MAP3K5 0.007 0.008 -10000 0 -0.086 4 4
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
apoptosis 0.007 0.008 -10000 0 -0.086 4 4
mol:LY294002 0 0 0.001 1 -0.001 5 6
EIF4B 0.024 0.031 0.16 1 -0.22 1 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.031 0.16 1 -0.21 1 2
eIF4E/eIF4G1/eIF4A1 -0.005 0.025 -10000 0 -0.18 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.046 -10000 0 -0.18 27 27
mTOR/RHEB/GTP/Raptor/GBL 0.027 0.028 0.16 1 -0.2 1 2
FKBP1A 0.016 0.019 -10000 0 -0.41 1 1
RHEB/GTP 0.024 0.037 -10000 0 -0.16 2 2
mol:Amino Acids 0 0 0.001 1 -0.001 5 6
FKBP12/Rapamycin 0.012 0.013 -10000 0 -0.29 1 1
PDPK1 0.005 0.041 0.17 2 -0.17 24 26
EIF4E 0.014 0.037 -10000 0 -0.41 4 4
ASK1/PP5C 0.028 0.05 -10000 0 -0.45 5 5
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.021 0.016 -10000 0 -0.16 4 4
TSC1/TSC2 0.03 0.045 0.2 1 -0.15 25 26
tumor necrosis factor receptor activity 0 0 0.001 5 -0.001 1 6
RPS6 0.017 0 -10000 0 -10000 0 0
PPP5C 0.017 0 -10000 0 -10000 0 0
EIF4G1 0.014 0.037 -10000 0 -0.41 4 4
IRS1 0.007 0.015 -10000 0 -0.15 5 5
INS 0.017 0 -10000 0 -10000 0 0
PTEN 0.015 0.026 -10000 0 -0.41 2 2
PDK2 0.005 0.041 0.17 2 -0.17 24 26
EIF4EBP1 -0.1 0.12 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
PPP2R5D 0.02 0.024 -10000 0 -0.33 1 1
peptide biosynthetic process 0.02 0 -10000 0 -10000 0 0
RHEB 0.017 0 -10000 0 -10000 0 0
EIF4A1 0.009 0.058 -10000 0 -0.41 10 10
mol:Rapamycin 0 0.001 0.003 1 -0.002 24 25
EEF2 0.02 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.087 0.11 -10000 0 -0.41 2 2
Signaling events mediated by HDAC Class III

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
EP300 0.017 0 -10000 0 -10000 0 0
HDAC4 0.017 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.014 -10000 0 -10000 0 0
CDKN1A -0.019 0.098 -10000 0 -0.3 54 54
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.011 0.049 -10000 0 -0.41 7 7
FOXO3 -0.006 0.003 -10000 0 -10000 0 0
FOXO1 0.008 0.061 -10000 0 -0.41 11 11
FOXO4 0.018 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
TAT 0.017 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0 -10000 0 -10000 0 0
PPARGC1A 0.015 0.032 -10000 0 -0.41 3 3
FHL2 0.013 0.037 -10000 0 -0.41 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.019 -10000 0 -10000 0 0
HIST2H4A 0.011 0.014 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.012 0.02 -10000 0 -10000 0 0
SIRT1 0.022 0.027 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.038 0.018 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.029 0.021 -10000 0 -0.12 1 1
apoptosis -0.034 0.035 0.23 7 -10000 0 7
SIRT1/PGC1A 0.025 0.027 -10000 0 -0.24 3 3
p53/SIRT1 -0.004 0.12 0.25 43 -0.28 69 112
SIRT1/FOXO4 0.03 0.02 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.028 0.044 -10000 0 -0.21 15 15
HIST1H1E 0.018 0.007 -10000 0 -0.15 1 1
SIRT1/p300 0.029 0.019 -10000 0 -10000 0 0
muscle cell differentiation -0.019 0.018 -10000 0 -10000 0 0
TP53 -0.034 0.15 -10000 0 -0.41 69 69
KU70/SIRT1/BAX 0.034 0.035 -10000 0 -0.23 7 7
CREBBP 0.017 0 -10000 0 -10000 0 0
MEF2D 0.017 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.019 -10000 0 -10000 0 0
ACSS2 0.011 0.014 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.019 0.018 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.026 0.006 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.007 0.024 -9999 0 -0.18 5 5
JUN 0.028 0.023 -9999 0 -0.17 1 1
HRAS 0.016 0.019 -9999 0 -0.41 1 1
RET51/GFRalpha1/GDNF/GRB10 0.035 0.047 -9999 0 -0.21 19 19
RAP1A 0.017 0 -9999 0 -10000 0 0
FRS2 0.015 0.032 -9999 0 -0.41 3 3
RAP1A/GDP 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.043 0.019 -9999 0 -0.21 3 3
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.032 0.015 -9999 0 -0.21 2 2
RHOA 0.017 0.001 -9999 0 -10000 0 0
RAP1A/GTP 0.04 0.017 -9999 0 -0.18 3 3
GRB7 0.016 0.019 -9999 0 -0.41 1 1
RET51/GFRalpha1/GDNF 0.043 0.019 -9999 0 -0.21 3 3
MAPKKK cascade 0.029 0.022 -9999 0 -0.15 4 4
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.03 0.028 -9999 0 -0.21 7 7
lamellipodium assembly 0.02 0.036 -9999 0 -0.18 5 5
RET51/GFRalpha1/GDNF/SHC 0.021 0.076 -9999 0 -0.22 48 48
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
RET9/GFRalpha1/GDNF/SHC 0.011 0.073 -9999 0 -0.22 47 47
RET9/GFRalpha1/GDNF/Shank3 0.021 0.015 -9999 0 -0.22 2 2
MAPK3 0.026 0.015 -9999 0 -0.17 3 3
DOK1 0.017 0 -9999 0 -10000 0 0
DOK6 0 0 -9999 0 -10000 0 0
PXN 0.017 0 -9999 0 -10000 0 0
neurite development 0.03 0.015 -9999 0 -0.15 3 3
DOK5 0.015 0.019 -9999 0 -0.41 1 1
GFRA1 0.015 0.026 -9999 0 -0.41 2 2
MAPK8 0.028 0.023 -9999 0 -10000 0 0
HRAS/GTP 0.037 0.027 -9999 0 -0.17 4 4
tube development 0.023 0.014 -9999 0 -0.2 2 2
MAPK1 0.026 0.016 -9999 0 -0.17 3 3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.025 0.015 -9999 0 -0.12 5 5
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
PDLIM7 0.017 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.039 0.018 -9999 0 -0.19 3 3
SHC1 -0.021 0.12 -9999 0 -0.41 47 47
RET51/GFRalpha1/GDNF/Dok4 0.043 0.019 -9999 0 -0.21 3 3
RET51/GFRalpha1/GDNF/Dok5 0.039 0.024 -9999 0 -0.21 4 4
PRKCA 0.017 0 -9999 0 -10000 0 0
HRAS/GDP 0.012 0.013 -9999 0 -0.29 1 1
CREB1 0.014 0.045 -9999 0 -0.13 47 47
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.012 0.047 -9999 0 -0.13 51 51
RET51/GFRalpha1/GDNF/Grb7 0.042 0.022 -9999 0 -0.21 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
RET 0.016 0.019 -9999 0 -0.41 1 1
DOK4 0.017 0 -9999 0 -10000 0 0
JNK cascade 0.028 0.023 -9999 0 -0.16 1 1
RET9/GFRalpha1/GDNF/FRS2 0.031 0.024 -9999 0 -0.21 5 5
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0.017 0.002 -9999 0 -10000 0 0
NCK1 0.008 0.061 -9999 0 -0.41 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.045 -9999 0 -0.14 47 47
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.03 0.016 -9999 0 -0.12 6 6
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.028 0.025 -9999 0 -0.12 14 14
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.012 0.046 -9999 0 -0.13 48 48
PI3K 0.027 0.047 -9999 0 -0.2 10 10
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.029 0.014 -9999 0 -0.2 2 2
GRB10 0.004 0.073 -9999 0 -0.41 16 16
activation of MAPKK activity 0.029 0.015 -9999 0 -0.11 5 5
RET51/GFRalpha1/GDNF/FRS2 0.041 0.027 -9999 0 -0.21 6 6
GAB1 0.014 0.037 -9999 0 -0.41 4 4
IRS1 0.013 0.042 -9999 0 -0.41 5 5
IRS2 0.017 0.002 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.017 0.048 -9999 0 -0.12 52 52
RET51/GFRalpha1/GDNF/PKC alpha 0.043 0.019 -9999 0 -0.21 3 3
GRB2 0.017 0.002 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GDNF 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.04 0.031 -9999 0 -0.21 8 8
Rac1/GTP 0.025 0.042 -9999 0 -0.2 5 5
RET9/GFRalpha1/GDNF 0.022 0.016 -9999 0 -0.24 2 2
GFRalpha1/GDNF 0.024 0.019 -9999 0 -0.28 2 2
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.016 0.003 -10000 0 -10000 0 0
EPHB2 0.016 0.026 -10000 0 -0.41 2 2
EFNB1 0.003 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.024 -10000 0 -0.18 1 1
Ephrin B2/EPHB1-2 0.026 0.039 -10000 0 -0.21 13 13
neuron projection morphogenesis 0.004 0.019 -10000 0 -0.17 1 1
Ephrin B1/EPHB1-2/Tiam1 0.005 0.024 -10000 0 -0.2 1 1
DNM1 0.003 0.006 -10000 0 -10000 0 0
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.007 0.038 -10000 0 -0.16 8 8
YES1 -0.015 0.053 -10000 0 -0.25 13 13
Ephrin B1/EPHB1-2/NCK2 0.005 0.024 -10000 0 -0.2 1 1
PI3K 0.01 0.062 -10000 0 -0.2 32 32
mol:GDP 0.005 0.023 -10000 0 -0.19 1 1
ITGA2B 0.017 0 -10000 0 -10000 0 0
endothelial cell proliferation 0.022 0.005 -10000 0 -10000 0 0
FYN -0.006 0.047 -10000 0 -0.22 8 8
MAP3K7 -0.007 0.038 -10000 0 -0.16 31 31
FGR -0.01 0.046 -10000 0 -0.2 8 8
TIAM1 0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
RGS3 0.016 0.019 -10000 0 -0.41 1 1
cell adhesion 0.015 0.057 -10000 0 -0.2 14 14
LYN -0.013 0.049 -10000 0 -0.25 5 5
Ephrin B1/EPHB1-2/Src Family Kinases -0.008 0.041 -10000 0 -0.19 11 11
Ephrin B1/EPHB1-2 -0.009 0.042 -10000 0 -0.18 30 30
SRC -0.008 0.044 -10000 0 -0.2 8 8
ITGB3 0.017 0 -10000 0 -10000 0 0
EPHB1 0.008 0.064 -10000 0 -0.41 12 12
EPHB4 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.025 0 -10000 0 -10000 0 0
BLK -0.006 0.045 -10000 0 -0.2 7 7
HCK -0.016 0.051 -10000 0 -0.25 7 7
regulation of stress fiber formation -0.005 0.023 0.19 1 -10000 0 1
MAPK8 0.015 0.043 -10000 0 -0.17 1 1
Ephrin B1/EPHB1-2/RGS3 0.005 0.024 -10000 0 -0.2 1 1
endothelial cell migration -0.001 0.04 0.13 14 -0.14 30 44
NCK2 0.017 0.001 -10000 0 -10000 0 0
PTPN13 -0.009 0.098 -10000 0 -0.41 30 30
regulation of focal adhesion formation -0.005 0.023 0.19 1 -10000 0 1
chemotaxis -0.005 0.023 0.19 1 -10000 0 1
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
Rac1/GTP 0.005 0.022 -10000 0 -0.18 1 1
angiogenesis -0.009 0.041 -10000 0 -0.18 30 30
LCK -0.008 0.045 -10000 0 -0.2 8 8
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.015 0.038 0.16 12 -10000 0 12
GNAI2 0.017 0.001 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.022 -10000 0 -0.24 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.002 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.039 -10000 0 -0.16 12 12
negative regulation of cAMP metabolic process 0.001 0.01 -10000 0 -0.1 3 3
GNAZ 0.015 0.006 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNA12 0.014 0.037 -10000 0 -0.41 4 4
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.01 -10000 0 -0.1 3 3
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
GNAI1 0.014 0.02 -10000 0 -0.41 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.027 0.022 0.28 2 -10000 0 2
KIRREL 0.018 0.02 -10000 0 -0.41 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.027 0.022 -10000 0 -0.28 2 2
PLCG1 0.017 0 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
WASL 0.017 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.019 0.078 -10000 0 -0.22 51 51
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.029 0.021 -10000 0 -0.12 4 4
FYN 0.019 0.017 -10000 0 -0.17 4 4
mol:Ca2+ 0.043 0.023 -10000 0 -0.19 2 2
mol:DAG 0.044 0.024 -10000 0 -0.19 2 2
NPHS2 0.019 0.006 -10000 0 -10000 0 0
mol:IP3 0.044 0.024 -10000 0 -0.19 2 2
regulation of endocytosis 0.037 0.019 -10000 0 -0.16 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.034 0.023 -10000 0 -0.2 2 2
establishment of cell polarity 0.027 0.022 -10000 0 -0.28 2 2
Nephrin/NEPH1/podocin/NCK1-2 0.047 0.037 -10000 0 -0.17 13 13
Nephrin/NEPH1/beta Arrestin2 0.039 0.019 -10000 0 -0.16 4 4
NPHS1 0.018 0.02 -10000 0 -0.41 1 1
Nephrin/NEPH1/podocin 0.032 0.019 -10000 0 -0.17 4 4
TJP1 0.017 0 -10000 0 -10000 0 0
NCK1 0.008 0.061 -10000 0 -0.41 11 11
NCK2 0.017 0.001 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.045 0.024 -10000 0 -0.19 2 2
CD2AP -0.023 0.12 -10000 0 -0.41 49 49
Nephrin/NEPH1/podocin/GRB2 0.044 0.023 -10000 0 -0.19 2 2
GRB2 0.017 0.002 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.022 0.023 -10000 0 -0.19 5 5
cytoskeleton organization 0.031 0.023 0.19 2 -0.15 2 4
Nephrin/NEPH1 0.023 0.016 -10000 0 -0.19 2 2
Nephrin/NEPH1/ZO-1 0.036 0.018 -10000 0 -0.22 2 2
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.12 0.1 -10000 0 -0.44 6 6
PCK1 0.11 0.073 -10000 0 -0.38 5 5
HNF4A 0.14 0.11 -10000 0 -0.58 5 5
KCNJ11 0.14 0.11 -10000 0 -0.46 5 5
AKT1 0.096 0.069 -10000 0 -0.26 7 7
response to starvation 0.005 0.004 -10000 0 -10000 0 0
DLK1 0.12 0.16 -10000 0 -0.46 13 13
NKX2-1 0.1 0.076 0.27 17 -0.31 4 21
ACADM 0.12 0.1 -10000 0 -0.43 7 7
TAT 0.11 0.065 -10000 0 -0.4 2 2
CEBPB 0.013 0.061 -10000 0 -0.41 11 11
CEBPA 0.01 0.074 -10000 0 -0.41 16 16
TTR 0.095 0.083 -10000 0 -0.56 4 4
PKLR 0.12 0.1 -10000 0 -0.46 5 5
APOA1 0.15 0.12 -10000 0 -0.77 3 3
CPT1C 0.12 0.099 -10000 0 -0.47 5 5
ALAS1 0.11 0.068 -10000 0 -0.33 2 2
TFRC 0.13 0.093 -10000 0 -0.3 11 11
FOXF1 -0.017 0.11 -10000 0 -0.41 36 36
NF1 0.023 0.006 -10000 0 -0.13 1 1
HNF1A (dimer) 0.033 0.004 -10000 0 -10000 0 0
CPT1A 0.12 0.1 -10000 0 -0.46 5 5
HMGCS1 0.12 0.1 -10000 0 -0.51 4 4
NR3C1 0.026 0.019 -10000 0 -10000 0 0
CPT1B 0.12 0.1 -10000 0 -0.51 4 4
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.023 0 -10000 0 -10000 0 0
GCK 0.12 0.1 -10000 0 -0.51 4 4
CREB1 0.025 0.011 -10000 0 -10000 0 0
IGFBP1 0.09 0.085 -10000 0 -0.31 13 13
PDX1 0.12 0.066 -10000 0 -0.29 2 2
UCP2 0.095 0.16 -10000 0 -0.42 20 20
ALDOB 0.14 0.11 -10000 0 -0.45 5 5
AFP 0.026 0.031 -10000 0 -0.33 3 3
BDH1 0.12 0.1 -10000 0 -0.46 5 5
HADH 0.14 0.11 -10000 0 -0.44 6 6
F2 0.15 0.12 -10000 0 -0.97 2 2
HNF1A 0.033 0.004 -10000 0 -10000 0 0
G6PC 0.048 0.037 -10000 0 -0.23 1 1
SLC2A2 0.13 0.082 -10000 0 -0.5 2 2
INS 0.008 0.019 -10000 0 -10000 0 0
FOXA1 0.012 0.019 0.13 3 -0.19 3 6
FOXA3 0.036 0.025 -10000 0 -0.12 8 8
FOXA2 0.19 0.13 -10000 0 -0.53 5 5
ABCC8 0.14 0.11 -10000 0 -0.45 5 5
ALB 0.026 0.031 -10000 0 -0.33 3 3
Arf6 trafficking events

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
SLC2A4 0.017 0 -9999 0 -10000 0 0
CLTC 0.018 0.013 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.01 0.033 -9999 0 -0.097 44 44
Dynamin 2/GTP 0.018 0 -9999 0 -10000 0 0
EXOC4 0 0 -9999 0 -10000 0 0
CD59 0.014 0.017 -9999 0 -10000 0 0
CPE 0.014 0.004 -9999 0 -10000 0 0
CTNNB1 0.017 0 -9999 0 -10000 0 0
membrane fusion 0.009 0.035 -9999 0 -0.11 44 44
CTNND1 0.014 0.029 -9999 0 -0.2 10 10
DNM2 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.022 -9999 0 -0.11 1 1
TSHR 0.014 0.022 -9999 0 -0.24 4 4
INS 0.015 0.008 -9999 0 -10000 0 0
BIN1 0.016 0.005 -9999 0 -10000 0 0
mol:Choline 0.009 0.035 -9999 0 -0.11 44 44
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.006 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0.017 0 -9999 0 -10000 0 0
JUP 0.011 0.029 -9999 0 -0.12 16 16
ASAP2/amphiphysin II 0.02 0.006 -9999 0 -10000 0 0
ARF6/GTP 0.013 0 -9999 0 -10000 0 0
CDH1 0.012 0.022 -9999 0 -0.11 8 8
clathrin-independent pinocytosis 0.013 0 -9999 0 -10000 0 0
MAPK8IP3 0.017 0 -9999 0 -10000 0 0
positive regulation of endocytosis 0.013 0 -9999 0 -10000 0 0
EXOC2 0.017 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0.024 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.016 0.019 -9999 0 -0.41 1 1
regulation of calcium-dependent cell-cell adhesion -0.026 0.02 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.015 0.011 -9999 0 -0.24 1 1
ARF6/GTP/JIP3 0.023 0 -9999 0 -10000 0 0
ACAP1 0.009 0.031 -9999 0 -0.092 44 44
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 0.014 0.017 -9999 0 -10000 0 0
clathrin heavy chain/ACAP1 0.016 0.027 -9999 0 -0.14 1 1
JIP4/KLC1 0.024 0.018 -9999 0 -0.21 1 1
EXOC1 0.011 0.049 -9999 0 -0.41 7 7
exocyst 0.019 0.025 -9999 0 -10000 0 0
RALA/GTP -0.012 0.083 -9999 0 -0.29 44 44
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.023 0.011 -9999 0 -0.24 1 1
receptor recycling 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.018 0 -9999 0 -10000 0 0
NME1 0.006 0 -9999 0 -10000 0 0
clathrin coat assembly 0.018 0.013 -9999 0 -10000 0 0
IL2RA 0.013 0.021 -9999 0 -0.11 6 6
VAMP3 0.015 0.011 -9999 0 -0.24 1 1
GLUT4/clathrin heavy chain/ACAP1 0.023 0.027 -9999 0 -0.13 1 1
EXOC6 0 0 -9999 0 -10000 0 0
PLD1 0.009 0.032 -9999 0 -0.18 2 2
PLD2 0.009 0.03 -9999 0 -10000 0 0
EXOC5 0.003 0.076 -9999 0 -0.41 17 17
PIP5K1C 0.015 0.021 -9999 0 -0.11 1 1
SDC1 0.003 0.042 -9999 0 -0.17 8 8
ARF6/GDP 0.013 0 -9999 0 -10000 0 0
EXOC7 0.017 0 -9999 0 -10000 0 0
E-cadherin/beta catenin 0.028 0.021 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.009 0.035 -9999 0 -0.11 44 44
endocytosis -0.02 0.006 -9999 0 -10000 0 0
SCAMP2 0.017 0 -9999 0 -10000 0 0
ADRB2 0.02 0.015 -9999 0 -0.17 1 1
EXOC3 0.017 0 -9999 0 -10000 0 0
ASAP2 0 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0.017 0 -9999 0 -10000 0 0
KLC1 0.013 0.008 -9999 0 -10000 0 0
AVPR2 0.02 0.013 -9999 0 -10000 0 0
RALA -0.019 0.12 -9999 0 -0.41 44 44
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.028 0.032 -9999 0 -0.15 10 10
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.02 0.002 -10000 0 -10000 0 0
TRAF2/ASK1 0.023 0.002 -10000 0 -10000 0 0
ATM -0.003 0.091 -10000 0 -0.41 25 25
MAP2K3 0.048 0.035 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.046 0.035 -10000 0 -0.12 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.007 0.066 -10000 0 -0.41 13 13
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.016 0.004 -10000 0 -10000 0 0
GADD45A -0.02 0.12 -10000 0 -0.41 46 46
GADD45B 0.01 0.055 -10000 0 -0.41 9 9
MAP3K1 0.016 0.019 -10000 0 -0.41 1 1
MAP3K6 0.015 0.032 -10000 0 -0.41 3 3
MAP3K7 0.016 0.019 -10000 0 -0.41 1 1
MAP3K4 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.023 0.023 -10000 0 -0.28 3 3
TAK1/TAB family 0.012 0.009 0.12 2 -0.12 1 3
RAC1/OSM/MEKK3 0.022 0 -10000 0 -10000 0 0
TRAF2 0.017 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.022 -10000 0 -10000 0 0
TRAF6 0.015 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.002 0.006 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.008 -10000 0 -10000 0 0
MAPK11 0.017 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.005 0.012 -10000 0 -10000 0 0
OSM/MEKK3 0.013 0 -10000 0 -10000 0 0
TAOK1 -0.002 0.042 -10000 0 -0.19 25 25
TAOK2 0.005 0.042 -10000 0 -0.18 25 25
TAOK3 0.005 0.042 -10000 0 -0.18 25 25
MAP3K7IP1 0.017 0 -10000 0 -10000 0 0
MAPK14 0.015 0.026 -10000 0 -0.41 2 2
MAP3K7IP2 0.017 0 -10000 0 -10000 0 0
MAP3K5 0.017 0.001 -10000 0 -10000 0 0
MAP3K10 0.017 0 -10000 0 -10000 0 0
MAP3K3 0.017 0 -10000 0 -10000 0 0
TRX/ASK1 0.018 0.002 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.011 0.081 -10000 0 -0.2 66 66
Regulation of Androgen receptor activity

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
HDAC1 -0.028 0.099 -9999 0 -0.29 66 66
SMARCC1 0.012 0.075 -9999 0 -0.39 18 18
REL 0.016 0 -9999 0 -10000 0 0
HDAC7 0.038 0.03 -9999 0 -10000 0 0
JUN 0.017 0.019 -9999 0 -0.41 1 1
EP300 0.017 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.02 0.019 -9999 0 -0.28 2 2
FOXO1 0.008 0.061 -9999 0 -0.41 11 11
T-DHT/AR 0.058 0.035 -9999 0 -10000 0 0
MAP2K6 0.019 0.002 -9999 0 -10000 0 0
BRM/BAF57 0.027 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.004 -9999 0 -10000 0 0
SMARCA2 0.018 0 -9999 0 -10000 0 0
PDE9A 0.034 0.044 -9999 0 -0.39 5 5
NCOA2 0.018 0 -9999 0 -10000 0 0
CEBPA 0.004 0.074 -9999 0 -0.41 16 16
EHMT2 0.018 0 -9999 0 -10000 0 0
cell proliferation 0.067 0.031 -9999 0 -0.18 1 1
NR0B1 -0.023 0.12 -9999 0 -0.41 49 49
EGR1 0.005 0.071 -9999 0 -0.41 15 15
RXRs/9cRA 0.033 0.018 -9999 0 -0.21 3 3
AR/RACK1/Src 0.043 0.02 -9999 0 -0.15 2 2
AR/GR 0.034 0.02 -9999 0 -0.12 1 1
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.009 0.058 -9999 0 -0.41 10 10
RCHY1 0.017 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
MAPK8 0.02 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.052 0.023 -9999 0 -0.16 2 2
SRC 0.024 0.016 -9999 0 -0.18 2 2
NR3C1 0.017 0 -9999 0 -10000 0 0
KLK3 0.025 0.024 -9999 0 -10000 0 0
APPBP2 0.018 0.002 -9999 0 -10000 0 0
TRIM24 0.011 0.055 -9999 0 -0.41 9 9
T-DHT/AR/TIP60 0.023 0.018 -9999 0 -0.17 2 2
TMPRSS2 0.035 0.035 -9999 0 -0.33 4 4
RXRG 0.015 0.032 -9999 0 -0.41 3 3
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.017 0 -9999 0 -10000 0 0
RXRB 0.017 0 -9999 0 -10000 0 0
CARM1 0.018 0 -9999 0 -10000 0 0
NR2C2 0.017 0 -9999 0 -10000 0 0
KLK2 0.055 0.02 -9999 0 -10000 0 0
AR 0.026 0.022 -9999 0 -0.12 8 8
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
MDM2 0.001 0.078 -9999 0 -0.41 18 18
SRY 0.015 0.019 -9999 0 -0.41 1 1
GATA2 0.016 0.019 -9999 0 -0.41 1 1
MYST2 0.017 0 -9999 0 -10000 0 0
HOXB13 0.018 0 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.039 0.02 -9999 0 -0.16 2 2
positive regulation of transcription 0.016 0.019 -9999 0 -0.41 1 1
DNAJA1 0.018 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.062 -9999 0 -0.15 81 81
NCOA1 0.017 0.02 -9999 0 -10000 0 0
SPDEF 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2 0.035 0.021 -9999 0 -0.12 1 1
T-DHT/AR/Hsp90 0.034 0.021 -9999 0 -0.17 2 2
GSK3B 0.018 0.002 -9999 0 -10000 0 0
NR2C1 0.017 0 -9999 0 -10000 0 0
mol:T-DHT 0.023 0.017 -9999 0 -0.2 2 2
SIRT1 0.017 0 -9999 0 -10000 0 0
ZMIZ2 0.016 0 -9999 0 -10000 0 0
POU2F1 0.028 0.009 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 0.015 0.064 -9999 0 -0.18 50 50
CREBBP 0.017 0 -9999 0 -10000 0 0
SMARCE1 0.018 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.01 0.028 -9999 0 -0.2 1 1
CaM/Ca2+ 0.012 0.003 -9999 0 -10000 0 0
AKT1 0.014 0.037 -9999 0 -0.41 4 4
AKT2 0.017 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 -0.002 0.03 -9999 0 -0.13 4 4
YWHAZ 0.017 0.002 -9999 0 -10000 0 0
CALM1 0.016 0.004 -9999 0 -10000 0 0
YWHAQ 0.017 0 -9999 0 -10000 0 0
TBC1D4 0.015 0.026 -9999 0 -0.28 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.008 0.009 -9999 0 -10000 0 0
YWHAB 0.017 0.001 -9999 0 -10000 0 0
SNARE/Synip 0.021 0.007 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP 0.017 0 -9999 0 -10000 0 0
PRKCI 0.016 0.019 -9999 0 -0.41 1 1
AS160/CaM/Ca2+ 0.012 0.003 -9999 0 -10000 0 0
RHOQ 0.017 0 -9999 0 -10000 0 0
GYS1 0.004 0.063 -9999 0 -0.22 40 40
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.012 0.045 -9999 0 -0.41 6 6
TC10/GTP/CIP4/Exocyst 0.02 0.028 -9999 0 -0.24 6 6
AS160/14-3-3 0.006 0.037 -9999 0 -0.13 24 24
VAMP2 0.015 0.005 -9999 0 -10000 0 0
SLC2A4 -0.003 0.031 -9999 0 -0.14 4 4
STX4 0.017 0 -9999 0 -10000 0 0
GSK3B 0.021 0.017 -9999 0 -0.18 4 4
SFN -0.01 0.1 -9999 0 -0.41 33 33
LNPEP 0.016 0.019 -9999 0 -0.41 1 1
YWHAE 0.017 0.001 -9999 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.02 0.011 -10000 0 -10000 0 0
VLDLR 0.015 0.032 -10000 0 -0.41 3 3
CRKL 0.017 0 -10000 0 -10000 0 0
LRPAP1 0.017 0 -10000 0 -10000 0 0
FYN 0.015 0.026 -10000 0 -0.41 2 2
ITGA3 0.002 0.08 -10000 0 -0.41 19 19
RELN/VLDLR/Fyn 0.013 0.03 -10000 0 -0.23 4 4
MAPK8IP1/MKK7/MAP3K11/JNK1 0.051 0 -10000 0 -10000 0 0
AKT1 0.002 0.043 -10000 0 -0.18 21 21
MAP2K7 0.017 0 -10000 0 -10000 0 0
RAPGEF1 0.017 0 -10000 0 -10000 0 0
DAB1 0.017 0 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.014 0.024 -10000 0 -0.21 3 3
LRPAP1/LRP8 0.025 0 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.017 0.026 -10000 0 -0.19 3 3
DAB1/alpha3/beta1 Integrin 0.014 0.035 -10000 0 -0.2 6 6
long-term memory 0.016 0.027 -10000 0 -0.18 2 2
DAB1/LIS1 0.021 0.031 -10000 0 -0.18 4 4
DAB1/CRLK/C3G 0.017 0.026 -10000 0 -0.17 4 4
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
DAB1/NCK2 0.022 0.031 -10000 0 -0.18 4 4
ARHGEF2 0.017 0 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.011 0.008 -10000 0 -10000 0 0
CDK5R1 0.014 0.007 -10000 0 -10000 0 0
RELN 0.006 0.033 -10000 0 -0.41 3 3
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.014 0.027 -10000 0 -0.23 3 3
GRIN2A/RELN/LRP8/DAB1/Fyn 0.016 0.028 -10000 0 -0.19 2 2
MAPK8 0.017 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.013 0.026 -10000 0 -0.21 4 4
ITGB1 0.017 0 -10000 0 -10000 0 0
MAP1B 0.011 0.018 -10000 0 -0.18 2 2
RELN/LRP8 0.015 0.026 -10000 0 -0.23 3 3
GRIN2B/RELN/LRP8/DAB1/Fyn 0.021 0.031 -10000 0 -0.19 3 3
PI3K 0.009 0.065 -10000 0 -0.28 25 25
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.058 -10000 0 -0.28 19 19
RAP1A 0.08 0.052 -10000 0 -10000 0 0
PAFAH1B1 0.017 0.002 -10000 0 -10000 0 0
MAPK8IP1 0.017 0 -10000 0 -10000 0 0
CRLK/C3G 0.025 0 -10000 0 -10000 0 0
GRIN2B 0.017 0 -10000 0 -10000 0 0
NCK2 0.017 0.001 -10000 0 -10000 0 0
neuron differentiation 0.016 0.021 -10000 0 -0.12 2 2
neuron adhesion 0.077 0.058 -10000 0 -0.32 1 1
LRP8 0.017 0 -10000 0 -10000 0 0
GSK3B 0.003 0.041 -10000 0 -0.18 17 17
RELN/VLDLR/DAB1/Fyn 0.016 0.029 -10000 0 -0.19 4 4
MAP3K11 0.017 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.002 0.043 -10000 0 -0.16 30 30
CDK5 0.016 0.004 -10000 0 -10000 0 0
MAPT 0.024 0.08 0.33 33 -10000 0 33
neuron migration 0.01 0.035 -10000 0 -0.16 10 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.016 0.021 -10000 0 -0.12 2 2
RELN/VLDLR 0.019 0.03 -10000 0 -0.21 4 4
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 0.002 0.094 -10000 0 -0.4 27 27
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.025 0.011 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.037 0.019 -10000 0 -10000 0 0
TBX21 0.024 0.033 -10000 0 -0.27 1 1
IL12B 0.018 0.001 -10000 0 -10000 0 0
IL12A 0.009 0 -10000 0 -10000 0 0
IL6ST 0.018 0.001 -10000 0 -10000 0 0
IL27RA/JAK1 0.022 0.003 -10000 0 -10000 0 0
IL27 0.001 0.001 -10000 0 -10000 0 0
TYK2 0.017 0.019 -10000 0 -0.41 1 1
T-helper cell lineage commitment 0.002 0.07 -10000 0 -0.34 5 5
T-helper 2 cell differentiation -0.025 0.011 -10000 0 -10000 0 0
T cell proliferation during immune response -0.025 0.011 -10000 0 -10000 0 0
MAPKKK cascade 0.025 0.011 -10000 0 -10000 0 0
STAT3 0.009 0.058 -10000 0 -0.41 10 10
STAT2 0.017 0 -10000 0 -10000 0 0
STAT1 0.003 0.078 -10000 0 -0.41 18 18
IL12RB1 0.017 0 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.025 0.033 -10000 0 -0.27 1 1
IL27/IL27R/JAK2/TYK2 0.025 0.011 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.025 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.037 0.046 0.28 4 -0.34 1 5
JAK2 0.017 0.001 -10000 0 -10000 0 0
JAK1 0.017 0.002 -10000 0 -10000 0 0
STAT2 (dimer) 0.034 0.012 -10000 0 -10000 0 0
T cell proliferation 0.009 0.062 -10000 0 -0.27 2 2
IL12/IL12R/TYK2/JAK2 0.044 0.011 -10000 0 -10000 0 0
IL17A 0.002 0.071 -10000 0 -0.34 5 5
mast cell activation -0.025 0.011 -10000 0 -10000 0 0
IFNG 0.011 0.004 -10000 0 -0.072 1 1
T cell differentiation 0.001 0.001 -10000 0 -0.013 1 1
STAT3 (dimer) 0.03 0.031 -10000 0 -0.18 2 2
STAT5A (dimer) 0.033 0.015 -10000 0 -10000 0 0
STAT4 (dimer) 0.019 0.02 -10000 0 -10000 0 0
STAT4 0.01 0.008 -10000 0 -10000 0 0
T cell activation -0.006 0 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.04 0.011 -10000 0 -10000 0 0
GATA3 0.003 0.034 -10000 0 -0.35 5 5
IL18 -0.016 0.083 -10000 0 -0.29 45 45
positive regulation of mast cell cytokine production 0.03 0.03 -10000 0 -0.17 2 2
IL27/EBI3 0.011 0.023 -10000 0 -0.29 3 3
IL27RA 0.012 0.002 -10000 0 -10000 0 0
IL6 -0.018 0.13 -10000 0 -0.4 52 52
STAT5A 0.016 0.019 -10000 0 -0.41 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.005 0.002 -10000 0 -10000 0 0
IL1B 0.001 0.048 -10000 0 -0.29 14 14
EBI3 0.014 0.032 -10000 0 -0.41 3 3
TNF 0.008 0.018 -10000 0 -0.29 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.002 0.005 -9999 0 -10000 0 0
CDC42/GTP -0.015 0.039 -9999 0 -0.16 12 12
PLCG1 0.002 0.01 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.017 0.001 -9999 0 -10000 0 0
GNAI3 -0.036 0.14 -9999 0 -0.41 65 65
G12/G13 0.022 0.033 -9999 0 -0.28 6 6
cell migration -0.015 0.038 -9999 0 -0.16 12 12
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0.002 0.01 -9999 0 -10000 0 0
MAPK1 0.002 0.01 -9999 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.01 -9999 0 -0.1 3 3
GNAI1 0.014 0.02 -9999 0 -0.41 1 1
CDC42/GDP 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.01 0.022 -9999 0 -0.24 4 4
RHOA 0.016 0.023 -9999 0 -0.2 6 6
S1P/S1P4/Gi 0.001 0.01 -9999 0 -0.1 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.015 0.006 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 0.019 0.025 -9999 0 -0.22 6 6
GNA12 0.014 0.037 -9999 0 -0.41 4 4
GNA13 0.015 0.026 -9999 0 -0.41 2 2
CDC42 0.017 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.033 0.004 -9999 0 -10000 0 0
HDAC3 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.007 -9999 0 -0.17 1 1
GATA1/HDAC4 0.025 0 -9999 0 -10000 0 0
GATA1/HDAC5 0.025 0 -9999 0 -10000 0 0
GATA2/HDAC5 0.025 0.013 -9999 0 -0.28 1 1
HDAC5/BCL6/BCoR 0.024 0.053 -9999 0 -0.23 21 21
HDAC9 0.015 0.026 -9999 0 -0.41 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.035 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.025 0.013 -9999 0 -0.28 1 1
HDAC5/YWHAB 0.025 0.002 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.005 -9999 0 -0.11 1 1
GATA2 0.016 0.019 -9999 0 -0.41 1 1
HDAC4/RFXANK -0.006 0.093 -9999 0 -0.28 53 53
BCOR 0.013 0.042 -9999 0 -0.41 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0 0 -9999 0 -10000 0 0
HDAC5 0.017 0 -9999 0 -10000 0 0
GNB1/GNG2 0.013 0.001 -9999 0 -10000 0 0
Histones 0.024 0.008 -9999 0 -0.1 2 2
ADRBK1 0.017 0 -9999 0 -10000 0 0
HDAC4 0.017 0 -9999 0 -10000 0 0
XPO1 0.017 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.025 0.013 -9999 0 -0.28 1 1
HDAC4/Ubc9 0.025 0 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.025 0.002 -9999 0 -10000 0 0
TUBA1B 0.017 0 -9999 0 -10000 0 0
HDAC6 0.017 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.006 0.093 -9999 0 -0.28 53 53
CAMK4 0.017 0 -9999 0 -10000 0 0
Tubulin/HDAC6 0.033 0.009 -9999 0 -10000 0 0
SUMO1 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.017 0.001 -9999 0 -10000 0 0
GATA1 0.017 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
NR3C1 0.017 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.033 0.005 -9999 0 -10000 0 0
SRF 0.017 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.025 0.002 -9999 0 -10000 0 0
Tubulin 0.024 0.006 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.025 0.002 -9999 0 -10000 0 0
GNB1 0.017 0.002 -9999 0 -10000 0 0
RANGAP1 0.017 0 -9999 0 -10000 0 0
BCL6/BCoR 0.013 0.061 -9999 0 -0.28 21 21
HDAC4/HDAC3/SMRT (N-CoR2) 0.035 0 -9999 0 -10000 0 0
HDAC4/SRF 0.035 0 -9999 0 -10000 0 0
HDAC4/ER alpha 0.025 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.023 0.008 -9999 0 -0.1 2 2
cell motility 0.032 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.017 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.013 0 -9999 0 -10000 0 0
BCL6 0.004 0.073 -9999 0 -0.41 16 16
HDAC4/CaMK II delta B 0.017 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.025 0 -9999 0 -10000 0 0
ESR1 0.017 0 -9999 0 -10000 0 0
HDAC6/HDAC11 0.025 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.006 -9999 0 -10000 0 0
NPC 0.01 0.009 -9999 0 -0.2 1 1
MEF2C 0.014 0.006 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
HDAC4/MEF2C 0.043 0.019 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
NCOR2 0.017 0 -9999 0 -10000 0 0
TUBB2A 0.016 0.004 -9999 0 -10000 0 0
HDAC11 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
RANBP2 0.016 0.019 -9999 0 -0.41 1 1
ANKRA2 0.016 0.019 -9999 0 -0.41 1 1
RFXANK -0.026 0.13 -9999 0 -0.41 53 53
nuclear import -0.029 0.002 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.017 0 -9999 0 -10000 0 0
ITGB7 0.015 0.026 -9999 0 -0.41 2 2
ITGA4 0.013 0.042 -9999 0 -0.41 5 5
alpha4/beta7 Integrin 0.022 0.041 -9999 0 -0.38 5 5
alpha4/beta1 Integrin 0.023 0.03 -9999 0 -0.28 5 5
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0 -10000 0 -10000 0 0
NFATC1 0.038 0.016 -10000 0 -10000 0 0
NFATC2 0.01 0.031 -10000 0 -0.11 7 7
NFATC3 0.012 0.003 -10000 0 -10000 0 0
YWHAE 0.017 0.001 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.001 0.011 -10000 0 -0.14 2 2
Exportin 1/Ran/NUP214 0.035 0.003 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.029 0.012 -10000 0 -10000 0 0
BCL2/BAX 0.021 0.035 -10000 0 -0.28 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.003 -10000 0 -10000 0 0
BAX 0.011 0.049 -10000 0 -0.41 7 7
MAPK14 0.016 0.026 -10000 0 -0.41 2 2
BAD 0.017 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.015 0.011 -10000 0 -0.13 2 2
Calcineurin A alpha-beta B1/BCL2 0.017 0 -10000 0 -10000 0 0
FKBP8 0.017 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.015 0.011 0.13 2 -10000 0 2
KPNB1 0.017 0 -10000 0 -10000 0 0
KPNA2 0.007 0.064 -10000 0 -0.41 12 12
XPO1 0.017 0 -10000 0 -10000 0 0
SFN -0.01 0.1 -10000 0 -0.41 33 33
MAP3K8 -0.017 0.12 -10000 0 -0.41 42 42
NFAT4/CK1 alpha 0.027 0.011 -10000 0 -0.19 1 1
MEF2D/NFAT1/Cbp/p300 0.047 0.031 -10000 0 -10000 0 0
CABIN1 0.001 0.011 -10000 0 -0.14 2 2
CALM1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.017 0.001 -10000 0 -10000 0 0
MAP3K1 0.016 0.019 -10000 0 -0.41 1 1
CAMK4 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0 -10000 0 -10000 0 0
MAPK3 0.017 0 -10000 0 -10000 0 0
YWHAH 0.008 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.026 0 -10000 0 -10000 0 0
YWHAB 0.017 0.001 -10000 0 -10000 0 0
MAPK8 0.017 0 -10000 0 -10000 0 0
MAPK9 0.017 0.001 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.016 0.019 -10000 0 -0.41 1 1
NFAT1-c-4/YWHAQ 0.043 0.024 -10000 0 -10000 0 0
PRKCH 0.015 0.026 -10000 0 -0.41 2 2
CABIN1/Cbp/p300 0.026 0 -10000 0 -10000 0 0
CASP3 -0.061 0.16 -10000 0 -0.41 96 96
PIM1 0.015 0.026 -10000 0 -0.41 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.011 -10000 0 -0.24 1 1
apoptosis 0.015 0.019 -10000 0 -0.15 7 7
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.038 -10000 0 -0.14 25 25
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.017 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.005 -10000 0 -10000 0 0
BAD/BCL-XL 0.025 0 -10000 0 -10000 0 0
PRKCD 0.017 0 -10000 0 -10000 0 0
NUP214 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.017 0 -10000 0 -10000 0 0
PRKCG 0.017 0 -10000 0 -10000 0 0
PRKCQ 0.017 0 -10000 0 -10000 0 0
FKBP38/BCL2 0.025 0 -10000 0 -10000 0 0
EP300 0.018 0 -10000 0 -10000 0 0
PRKCB1 0.001 0.004 -10000 0 -10000 0 0
CSNK2A1 0.017 0 -10000 0 -10000 0 0
NFATc/JNK1 0.047 0.017 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.023 0.005 -10000 0 -10000 0 0
FKBP12/FK506 0.012 0.013 -10000 0 -0.29 1 1
CSNK1A1 0.016 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.023 0.005 -10000 0 -10000 0 0
NFATc/ERK1 0.046 0.017 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.029 0.012 -10000 0 -10000 0 0
NR4A1 0.032 0.028 -10000 0 -10000 0 0
GSK3B 0.017 0.002 -10000 0 -10000 0 0
positive T cell selection 0.012 0.003 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.013 0.023 -10000 0 -10000 0 0
RCH1/ KPNB1 0.018 0.046 -10000 0 -0.28 12 12
YWHAQ 0.017 0 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
AKAP5 0.017 0 -10000 0 -10000 0 0
MEF2D 0.018 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.017 0.002 -10000 0 -10000 0 0
NFATc/p38 alpha 0.046 0.022 -10000 0 -0.21 2 2
CREBBP 0.018 0 -10000 0 -10000 0 0
BCL2 0.017 0 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.006 0 -9999 0 -10000 0 0
ADCY5 0.006 0 -9999 0 -10000 0 0
ADCY6 0.012 0 -9999 0 -10000 0 0
ADCY7 0.009 0.024 -9999 0 -0.24 5 5
ADCY1 0.012 0 -9999 0 -10000 0 0
ADCY2 0.012 0 -9999 0 -10000 0 0
ADCY3 0.006 0 -9999 0 -10000 0 0
ADCY8 0.008 0.029 -9999 0 -0.24 7 7
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 0.012 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.014 0.013 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.025 0.001 -10000 0 -10000 0 0
STXBP1 0.002 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.029 0.021 -10000 0 -0.24 3 3
RAB3GAP2/RIMS1/UNC13B 0.035 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.017 0 -10000 0 -10000 0 0
mol:ACh 0.029 0.012 0.05 32 -0.037 1 33
RAB3GAP2 0.017 0 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.001 0.006 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.029 0.021 -10000 0 -0.24 3 3
UNC13B 0.017 0.001 -10000 0 -10000 0 0
CHRNA1 0.015 0.032 -10000 0 -0.41 3 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.008 -10000 0 -10000 0 0
SNAP25 0.001 0.002 -10000 0 -10000 0 0
VAMP2 0.005 0.002 -10000 0 -10000 0 0
SYT1 0.001 0.004 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.003 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.001 0.006 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.015 0.006 0.11 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.007 -10000 0 -0.077 2 2
AP2 0.012 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.024 0.001 -10000 0 -10000 0 0
CLTB 0.017 0.001 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.002 -10000 0 -10000 0 0
CD4 0.002 0.08 -10000 0 -0.41 19 19
CLTA 0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
ARFGAP1 0.009 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.007 -10000 0 -0.15 1 1
ARF1/GTP 0.01 0.006 -10000 0 -0.12 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.019 0.002 -10000 0 -10000 0 0
mol:Choline 0.007 0.007 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.017 0.001 -10000 0 -10000 0 0
DDEF1 0.007 0.007 -10000 0 -0.14 1 1
ARF1/GDP 0.007 0.002 -10000 0 -10000 0 0
AP2M1 0.017 0.002 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.001 -10000 0 -10000 0 0
Rac/GTP 0.013 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.002 -10000 0 -10000 0 0
ARFIP2 0.016 0.001 -10000 0 -10000 0 0
COPA 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.019 0.003 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.011 0.001 -10000 0 -10000 0 0
GGA3 0.017 0 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.004 -10000 0 -10000 0 0
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.021 0.002 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.018 0.003 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.023 0.001 -10000 0 -10000 0 0
CYTH2 0 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.022 0.001 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.013 0 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.02 0.023 -10000 0 -0.1 19 19
PLD2 0.007 0.007 -10000 0 -0.15 1 1
ARF-GAP1/v-SNARE 0.009 0 -10000 0 -10000 0 0
PIP5K1A 0.008 0.007 -10000 0 -0.15 1 1
ARF1/GTP/Membrin/GBF1/p115 0.016 0.005 -10000 0 -0.099 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.007 -10000 0 -0.14 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0 -10000 0 -10000 0 0
GOSR2 0.012 0.003 -10000 0 -0.059 1 1
USO1 0.012 0.003 -10000 0 -0.059 1 1
GBF1 0.012 0.003 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.023 0.002 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.013 0.049 -10000 0 -0.24 19 19
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 0.024 0.023 -9999 0 -0.28 3 3
FBXW11 0.017 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
CHUK 0.016 0.019 -9999 0 -0.41 1 1
NF kappa B2 p100/RelB 0.049 0.021 -9999 0 -0.19 4 4
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
MAP3K14 0.015 0.026 -9999 0 -0.41 2 2
NF kappa B1 p50/RelB 0.023 0.03 -9999 0 -0.28 5 5
RELB 0.016 0.019 -9999 0 -0.41 1 1
NFKB2 0.017 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.023 0.011 -9999 0 -0.24 1 1
regulation of B cell activation 0.022 0.011 -9999 0 -0.24 1 1
PLK2 and PLK4 events

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
PLK2 0.012 0.008 -9999 0 -9999 0 0
PLK4 0.017 0 -9999 0 -9999 0 0
regulation of centriole replication 0.012 0.008 -9999 0 -9999 0 0
Ephrin A reverse 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
MAPKKK cascade 0.023 0 -9999 0 -10000 0 0
EFNA5 0.017 0 -9999 0 -10000 0 0
FYN 0.018 0.015 -9999 0 -0.21 2 2
neuron projection morphogenesis 0.023 0 -9999 0 -10000 0 0
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.023 0 -9999 0 -10000 0 0
EPHA5 0.017 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.02 0.002 -9999 0 -10000 0 0
MAPK9 0.007 0.001 -9999 0 -10000 0 0
adrenocorticotropin secretion 0.008 0.013 -9999 0 -0.29 1 1
GNB1/GNG2 0.011 0.001 -9999 0 -10000 0 0
GNB1 0.017 0.002 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.007 0.012 -9999 0 -0.19 2 2
Gs family/GTP 0.011 0 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.017 0 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.016 0.019 -9999 0 -0.41 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.007 0 -9999 0 -10000 0 0
MAPK11 0.007 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.017 0 -9999 0 -10000 0 0
GNAT1/GTP 0.013 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.023 0.011 -9999 0 -0.24 1 1
PDE6G/GNAT1/GTP 0.023 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 0.017 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel 0.034 0 -9999 0 -10000 0 0
mol:Na + 0.027 0 -9999 0 -10000 0 0
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.003 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.034 0 -9999 0 -10000 0 0
CNGB1 0.017 0 -9999 0 -10000 0 0
RDH5 0.016 0.019 -9999 0 -0.41 1 1
SAG 0.016 0.019 -9999 0 -0.41 1 1
mol:Ca2+ 0.027 0 -9999 0 -10000 0 0
Na + (4 Units) 0.024 0 -9999 0 -10000 0 0
RGS9 0.017 0 -9999 0 -10000 0 0
GNB1/GNGT1 0.025 0.003 -9999 0 -10000 0 0
GNAT1/GDP 0.03 0.003 -9999 0 -10000 0 0
GUCY2D 0.017 0 -9999 0 -10000 0 0
GNGT1 0.017 0 -9999 0 -10000 0 0
GUCY2F 0.017 0 -9999 0 -10000 0 0
GNB5 0.017 0.002 -9999 0 -10000 0 0
mol:GMP (4 units) 0.028 0 -9999 0 -10000 0 0
mol:11-cis-retinal 0.016 0.019 -9999 0 -0.41 1 1
mol:cGMP 0.022 0 -9999 0 -10000 0 0
GNB1 0.017 0.002 -9999 0 -10000 0 0
Rhodopsin 0.025 0.013 -9999 0 -0.28 1 1
SLC24A1 0.017 0 -9999 0 -10000 0 0
CNGA1 0.017 0 -9999 0 -10000 0 0
Metarhodopsin II 0.011 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.022 0 -9999 0 -10000 0 0
RGS9BP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Transducin 0.021 0.002 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.011 0 -9999 0 -10000 0 0
PDE6A/B 0.025 0 -9999 0 -10000 0 0
mol:Pi 0.023 0.003 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.033 0.004 -9999 0 -10000 0 0
PDE6B 0.017 0 -9999 0 -10000 0 0
PDE6A 0.017 0 -9999 0 -10000 0 0
PDE6G 0.017 0 -9999 0 -10000 0 0
RHO 0.017 0 -9999 0 -10000 0 0
PDE6 0.042 0.005 -9999 0 -10000 0 0
GUCA1A 0 0 -9999 0 -10000 0 0
GC2/GCAP Family 0.022 0 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.017 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 -0.017 0 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.017 0 -9999 0 -9999 0 0
PDE3B 0.017 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 529 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 -0.073 0.041 0.041 0.041
47_PPARGC1A 0.017 0.017 0.017 0.017
105_BMP4 0.017 0.017 0.017 0.017
105_BMP6 0.017 0.017 0.017 0.017
105_BMP7 0.017 0.017 0.017 0.017
105_BMP2 0.017 0.017 -0.41 0.017
131_RELN/VLDLR 0.044 -0.092 0.044 0
30_TGFB1/TGF beta receptor Type II -0.41 0.017 0.019 -0.41
84_STAT5B -0.16 -0.098 0.033 -0.098
84_STAT5A -0.16 -0.098 0.033 -0.098
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/3023688/2.GDAC_MergeDataFiles.Finished/GBM-TP.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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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