PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1ZS2TF6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Kidney Renal Clear Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1ZS2TF6
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 46 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
HIF-1-alpha transcription factor network 185
Nephrin/Neph1 signaling in the kidney podocyte 165
TCR signaling in naïve CD8+ T cells 134
TCGA08_p53 132
TCGA08_retinoblastoma 118
FOXA2 and FOXA3 transcription factor networks 114
Aurora B signaling 111
Syndecan-4-mediated signaling events 110
IL12-mediated signaling events 105
FOXM1 transcription factor network 99
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
HIF-1-alpha transcription factor network 185 14061 76 -1.3 0.026 1000 -1000 -0.18 -1000
Nephrin/Neph1 signaling in the kidney podocyte 165 5639 34 -0.62 0.016 1000 -1000 -0.1 -1000
TCR signaling in naïve CD8+ T cells 134 12464 93 -0.67 0.33 1000 -1000 -0.11 -1000
TCGA08_p53 132 927 7 -0.66 0.31 1000 -1000 -0.028 -1000
TCGA08_retinoblastoma 118 951 8 -0.85 0.22 1000 -1000 -0.044 -1000
FOXA2 and FOXA3 transcription factor networks 114 5246 46 -1.3 0.025 1000 -1000 -0.1 -1000
Aurora B signaling 111 7463 67 -0.42 0.016 1000 -1000 -0.11 -1000
Syndecan-4-mediated signaling events 110 7420 67 -0.65 0.11 1000 -1000 -0.14 -1000
IL12-mediated signaling events 105 9159 87 -0.72 0.17 1000 -1000 -0.15 -1000
FOXM1 transcription factor network 99 5051 51 -0.83 0.04 1000 -1000 -0.2 -1000
Glypican 1 network 96 4645 48 -0.57 0.045 1000 -1000 -0.073 -1000
PDGFR-alpha signaling pathway 90 3963 44 -0.28 0.034 1000 -1000 -0.098 -1000
amb2 Integrin signaling 80 6587 82 -0.57 0.016 1000 -1000 -0.12 -1000
JNK signaling in the CD4+ TCR pathway 73 1247 17 -0.43 0.016 1000 -1000 -0.094 -1000
IL4-mediated signaling events 70 6441 91 -0.84 0.54 1000 -1000 -0.18 -1000
EGFR-dependent Endothelin signaling events 67 1420 21 -0.68 0.016 1000 -1000 -0.11 -1000
Aurora C signaling 65 460 7 -0.4 0.014 1000 -1000 -0.07 -1000
Glypican 2 network 62 251 4 -0.12 -1000 1000 -1000 -0.052 -1000
Caspase cascade in apoptosis 61 4523 74 -0.33 0.16 1000 -1000 -0.084 -1000
Syndecan-1-mediated signaling events 59 2034 34 -0.41 0.016 1000 -1000 -0.1 -1000
HIF-2-alpha transcription factor network 59 2559 43 -0.76 0.33 1000 -1000 -0.1 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 54 1808 33 -0.83 0.016 1000 -1000 -0.1 -1000
BMP receptor signaling 53 4364 81 -0.7 0.016 1000 -1000 -0.14 -1000
IL23-mediated signaling events 49 2984 60 -0.41 0.021 1000 -1000 -0.2 -1000
Signaling events mediated by the Hedgehog family 46 2403 52 -0.45 0.12 1000 -1000 -0.12 -1000
Fc-epsilon receptor I signaling in mast cells 43 4248 97 -0.35 0.042 1000 -1000 -0.13 -1000
IL27-mediated signaling events 39 2033 51 -0.61 0.074 1000 -1000 -0.11 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 39 2706 68 -0.55 0.067 1000 -1000 -0.16 -1000
Effects of Botulinum toxin 38 999 26 -0.37 0.016 1000 -1000 -0.091 -1000
Ephrin A reverse signaling 36 257 7 -0.058 0 1000 -1000 -0.044 -1000
Calcium signaling in the CD4+ TCR pathway 36 1137 31 -0.48 0.016 1000 -1000 -0.15 -1000
Arf6 signaling events 35 2174 62 -0.68 0.016 1000 -1000 -0.096 -1000
p75(NTR)-mediated signaling 35 4478 125 -0.43 0.016 1000 -1000 -0.14 -1000
VEGFR1 specific signals 33 1867 56 -0.48 0.049 1000 -1000 -0.12 -1000
EPO signaling pathway 32 1780 55 -0.29 0.018 1000 -1000 -0.13 -1000
S1P1 pathway 32 1187 36 -0.38 0.018 1000 -1000 -0.099 -1000
IL2 signaling events mediated by PI3K 32 1893 58 -0.46 0.033 1000 -1000 -0.11 -1000
IL2 signaling events mediated by STAT5 32 722 22 -0.47 0.038 1000 -1000 -0.058 -1000
LPA4-mediated signaling events 30 360 12 -0.17 0.028 1000 -1000 -0.033 -1000
BCR signaling pathway 30 3024 99 -0.35 0.034 1000 -1000 -0.13 -1000
PLK1 signaling events 29 2506 85 -0.4 0.016 1000 -1000 -0.087 -1000
Coregulation of Androgen receptor activity 27 2102 76 -0.94 0.033 1000 -1000 -0.074 -1000
Regulation of Telomerase 27 2776 102 -0.68 0.045 1000 -1000 -0.14 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 25 1389 54 -0.66 0.031 1000 -1000 -0.14 -1000
Glucocorticoid receptor regulatory network 25 2928 114 -0.41 0.15 1000 -1000 -0.11 -1000
IL6-mediated signaling events 25 1909 75 -0.28 0.078 1000 -1000 -0.12 -1000
Integrins in angiogenesis 24 2070 84 -0.38 0.04 1000 -1000 -0.13 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 23 1829 78 -0.32 0.046 1000 -1000 -0.11 -1000
Reelin signaling pathway 21 1184 56 -0.24 0.016 1000 -1000 -0.14 -1000
Signaling events mediated by PTP1B 20 1583 76 -0.68 0.048 1000 -1000 -0.11 -1000
Aurora A signaling 20 1204 60 -0.24 0.054 1000 -1000 -0.1 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 20 940 45 -0.59 0.061 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 20 1780 88 -0.32 0.079 1000 -1000 -0.17 -1000
Visual signal transduction: Rods 20 1081 52 -0.28 0.016 1000 -1000 -0.13 -1000
Neurotrophic factor-mediated Trk receptor signaling 19 2321 120 -0.17 0.15 1000 -1000 -0.12 -1000
Syndecan-2-mediated signaling events 18 1298 69 -0.57 0.056 1000 -1000 -0.097 -1000
Regulation of nuclear SMAD2/3 signaling 16 2254 136 -0.46 0.091 1000 -1000 -0.13 -1000
Endothelins 16 1548 96 -0.35 0.089 1000 -1000 -0.12 -1000
Wnt signaling 15 111 7 -0.073 0.016 1000 -1000 -0.063 -1000
S1P3 pathway 15 649 42 -0.38 0.062 1000 -1000 -0.092 -1000
FoxO family signaling 14 902 64 -0.57 0.12 1000 -1000 -0.1 -1000
Sphingosine 1-phosphate (S1P) pathway 13 372 28 -0.14 0.024 1000 -1000 -0.09 -1000
Thromboxane A2 receptor signaling 13 1443 105 -0.68 0.069 1000 -1000 -0.1 -1000
Ceramide signaling pathway 13 1045 76 -0.68 0.23 1000 -1000 -0.093 -1000
Paxillin-independent events mediated by a4b1 and a4b7 13 517 37 -0.3 0.022 1000 -1000 -0.13 -1000
LPA receptor mediated events 13 1427 102 -0.39 0.062 1000 -1000 -0.13 -1000
Class I PI3K signaling events 13 989 73 -0.48 0.036 1000 -1000 -0.12 -1000
PLK2 and PLK4 events 12 38 3 -0.014 0.01 1000 -1000 -0.031 -1000
IFN-gamma pathway 12 817 68 -0.38 0.017 1000 -1000 -0.14 -1000
FAS signaling pathway (CD95) 12 603 47 -0.45 0.031 1000 -1000 -0.071 -1000
Canonical Wnt signaling pathway 12 661 51 -0.19 0.096 1000 -1000 -0.089 -1000
E-cadherin signaling events 12 62 5 -0.023 0.016 1000 -1000 -0.07 -1000
ErbB4 signaling events 11 760 69 -0.18 0.11 1000 -1000 -0.12 -1000
Regulation of Androgen receptor activity 11 797 70 -0.97 0.04 1000 -1000 -0.1 -1000
Noncanonical Wnt signaling pathway 10 270 26 -0.12 0.016 1000 -1000 -0.12 -1000
Presenilin action in Notch and Wnt signaling 10 646 61 -0.19 0.092 1000 -1000 -0.1 -1000
S1P5 pathway 10 174 17 -0.14 0.045 1000 -1000 -0.081 -1000
Nongenotropic Androgen signaling 10 534 52 -0.17 0.074 1000 -1000 -0.096 -1000
Signaling events mediated by VEGFR1 and VEGFR2 10 1340 125 -0.4 0.044 1000 -1000 -0.15 -1000
Stabilization and expansion of the E-cadherin adherens junction 10 788 74 -0.68 0.1 1000 -1000 -0.13 -1000
a4b1 and a4b7 Integrin signaling 9 48 5 -0.022 0.016 1000 -1000 -0.067 -1000
S1P4 pathway 9 249 25 -0.14 0.035 1000 -1000 -0.086 -1000
TCGA08_rtk_signaling 8 213 26 -0.28 0.041 1000 -1000 -0.033 -1000
Visual signal transduction: Cones 7 294 38 -0.036 0.016 1000 -1000 -0.097 -1000
Signaling events regulated by Ret tyrosine kinase 7 647 82 -0.059 0.032 1000 -1000 -0.12 -1000
Canonical NF-kappaB pathway 6 256 39 -0.2 0.074 1000 -1000 -0.12 -1000
Signaling events mediated by PRL 6 219 34 -0.056 0.049 1000 -1000 -0.08 -1000
Insulin-mediated glucose transport 5 168 32 -0.079 0.067 1000 -1000 -0.089 -1000
Signaling events mediated by HDAC Class III 5 208 40 -0.065 0.032 1000 -1000 -0.069 -1000
IL1-mediated signaling events 5 355 62 -0.096 0.062 1000 -1000 -0.16 -1000
Signaling mediated by p38-gamma and p38-delta 5 76 15 0 0.037 1000 -1000 -0.051 -1000
Syndecan-3-mediated signaling events 5 187 35 -0.04 0.016 1000 -1000 -0.1 -1000
E-cadherin signaling in the nascent adherens junction 5 394 76 -0.026 0.068 1000 -1000 -0.12 -1000
Class IB PI3K non-lipid kinase events 5 15 3 -0.007 0.007 1000 -1000 -0.024 -1000
p38 MAPK signaling pathway 5 252 44 -0.11 0.051 1000 -1000 -0.095 -1000
Arf6 downstream pathway 4 198 43 -0.034 0.034 1000 -1000 -0.068 -1000
Ephrin B reverse signaling 4 220 48 -0.022 0.034 1000 -1000 -0.11 -1000
Ras signaling in the CD4+ TCR pathway 4 71 17 -0.037 0.055 1000 -1000 -0.069 -1000
BARD1 signaling events 3 176 57 -0.18 0.044 1000 -1000 -0.11 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 3 304 85 -0.037 0.081 1000 -1000 -0.11 -1000
EPHB forward signaling 3 310 85 -0.073 0.075 1000 -1000 -0.13 -1000
E-cadherin signaling in keratinocytes 3 131 43 -0.3 0.056 1000 -1000 -0.11 -1000
ErbB2/ErbB3 signaling events 2 153 65 -0.13 0.061 1000 -1000 -0.1 -1000
Osteopontin-mediated events 2 84 38 -0.029 0.1 1000 -1000 -0.15 -1000
Cellular roles of Anthrax toxin 2 103 39 -0.023 0.028 1000 -1000 -0.044 -1000
ceramide signaling pathway 2 117 49 -0.12 0.054 1000 -1000 -0.069 -1000
RXR and RAR heterodimerization with other nuclear receptor 2 128 52 -0.029 0.092 1000 -1000 -0.11 -1000
Paxillin-dependent events mediated by a4b1 2 82 36 -0.031 0.031 1000 -1000 -0.12 -1000
Signaling mediated by p38-alpha and p38-beta 2 90 44 -0.043 0.052 1000 -1000 -0.073 -1000
Regulation of p38-alpha and p38-beta 2 132 54 -0.04 0.074 1000 -1000 -0.086 -1000
Arf6 trafficking events 2 166 71 -0.13 0.05 1000 -1000 -0.11 -1000
IGF1 pathway 2 125 57 -0.068 0.073 1000 -1000 -0.14 -1000
Insulin Pathway 2 169 74 -0.034 0.057 1000 -1000 -0.14 -1000
Plasma membrane estrogen receptor signaling 2 247 86 -0.16 0.076 1000 -1000 -0.12 -1000
PDGFR-beta signaling pathway 2 209 97 -0.057 0.09 1000 -1000 -0.13 -1000
Signaling events mediated by HDAC Class II 1 103 75 -0.026 0.051 1000 -1000 -0.097 -1000
Circadian rhythm pathway 1 25 22 -0.019 0.066 1000 -1000 -0.095 -1000
Hedgehog signaling events mediated by Gli proteins 1 124 65 -0.062 0.093 1000 -1000 -0.089 -1000
Class I PI3K signaling events mediated by Akt 1 81 68 -0.079 0.061 1000 -1000 -0.11 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 1 154 83 -0.079 0.081 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class I 1 153 104 -0.029 0.064 1000 -1000 -0.11 -1000
Retinoic acid receptors-mediated signaling 1 92 58 -0.022 0.065 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 1 37 31 -0.024 0.036 1000 -1000 -0.1 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 0 23 0 0.063 1000 -1000 -0.1 -1000
mTOR signaling pathway 0 36 53 -0.005 0.046 1000 -1000 -0.086 -1000
Nectin adhesion pathway 0 29 63 -0.015 0.082 1000 -1000 -0.1 -1000
TRAIL signaling pathway 0 19 48 -0.002 0.072 1000 -1000 -0.091 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 0 0.039 1000 -1000 -0.083 -1000
Rapid glucocorticoid signaling 0 10 20 -0.005 0.016 1000 -1000 -0.06 -1000
Arf1 pathway 0 25 54 -0.011 0.035 1000 -1000 -0.062 -1000
Alternative NF-kappaB pathway 0 8 13 -0.006 0.016 1000 -1000 -0.097 -1000
Total 3588 198274 7203 -41 -990 131000 -131000 -14 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.98 0.53 -9999 0 -1.4 278 278
HDAC7 0.014 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.68 0.33 -9999 0 -0.9 286 286
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.98 0.53 -9999 0 -1.4 276 276
AP1 -0.012 0.081 -9999 0 -0.57 10 10
ABCG2 -0.98 0.53 -9999 0 -1.4 279 279
HIF1A -0.1 0.048 -9999 0 -10000 0 0
TFF3 -0.99 0.53 -9999 0 -1.4 276 276
GATA2 0.003 0.1 -9999 0 -0.76 9 9
AKT1 -0.094 0.052 -9999 0 -10000 0 0
response to hypoxia -0.13 0.058 -9999 0 -10000 0 0
MCL1 -0.98 0.53 -9999 0 -1.4 278 278
NDRG1 -0.98 0.53 -9999 0 -1.4 276 276
SERPINE1 -1 0.56 -9999 0 -1.4 278 278
FECH -0.98 0.53 -9999 0 -1.3 292 292
FURIN -0.98 0.53 -9999 0 -1.4 276 276
NCOA2 0.005 0.07 -9999 0 -0.76 4 4
EP300 -0.1 0.074 -9999 0 -0.34 6 6
HMOX1 -0.99 0.55 -9999 0 -1.4 278 278
BHLHE40 -0.98 0.53 -9999 0 -1.4 276 276
BHLHE41 -1.1 0.58 -9999 0 -1.5 292 292
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.077 0.046 -9999 0 -10000 0 0
ENG -0.056 0.055 -9999 0 -10000 0 0
JUN 0.016 0.003 -9999 0 -10000 0 0
RORA -0.98 0.53 -9999 0 -1.4 278 278
ABCB1 -0.3 0.42 -9999 0 -1.3 63 63
TFRC -0.98 0.53 -9999 0 -1.4 279 279
CXCR4 -1.1 0.6 -9999 0 -1.5 294 294
TF -1 0.58 -9999 0 -1.4 288 288
CITED2 -0.98 0.53 -9999 0 -1.4 279 279
HIF1A/ARNT -1.3 0.85 -9999 0 -1.8 312 312
LDHA -0.085 0.064 -9999 0 -0.86 2 2
ETS1 -0.98 0.53 -9999 0 -1.4 275 275
PGK1 -0.98 0.53 -9999 0 -1.4 279 279
NOS2 -0.98 0.53 -9999 0 -1.4 280 280
ITGB2 -1 0.57 -9999 0 -1.4 300 300
ALDOA -0.98 0.53 -9999 0 -1.4 273 273
Cbp/p300/CITED2 -0.98 0.53 -9999 0 -1.4 275 275
FOS 0 0.11 -9999 0 -0.76 10 10
HK2 -1.2 0.58 -9999 0 -1.5 358 358
SP1 0.021 0.029 -9999 0 -10000 0 0
GCK -0.18 0.18 -9999 0 -1.1 10 10
HK1 -0.98 0.53 -9999 0 -1.4 278 278
NPM1 -0.98 0.53 -9999 0 -1.4 276 276
EGLN1 -0.98 0.53 -9999 0 -1.4 278 278
CREB1 0.026 0.002 -9999 0 -10000 0 0
PGM1 -0.98 0.53 -9999 0 -1.4 276 276
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.092 0.17 -9999 0 -0.8 19 19
IGFBP1 -1 0.57 -9999 0 -1.4 285 285
VEGFA -0.77 0.41 -9999 0 -1.1 218 218
HIF1A/JAB1 -0.052 0.026 -9999 0 -10000 0 0
CP -1.2 0.59 -9999 0 -1.5 349 349
CXCL12 -0.98 0.53 -9999 0 -1.4 280 280
COPS5 0.011 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.98 0.53 -9999 0 -1.4 273 273
EGLN3 -1.3 0.51 -9999 0 -1.5 375 375
CA9 -1.3 0.47 -9999 0 -1.5 382 382
TERT -1 0.55 -9999 0 -1.4 302 302
ENO1 -0.98 0.53 -9999 0 -1.4 276 276
PFKL -0.98 0.53 -9999 0 -1.4 276 276
NCOA1 0.014 0.004 -9999 0 -10000 0 0
ADM -1 0.57 -9999 0 -1.4 292 292
ARNT -0.1 0.046 -9999 0 -10000 0 0
HNF4A -0.046 0.22 -9999 0 -0.76 41 41
ADFP -0.99 0.53 -9999 0 -1.3 306 306
SLC2A1 -0.63 0.33 -9999 0 -0.97 152 152
LEP -1 0.55 -9999 0 -1.4 292 292
HIF1A/ARNT/Cbp/p300 -0.7 0.33 -9999 0 -0.93 288 288
EPO -0.61 0.39 -9999 0 -1.1 170 170
CREBBP -0.1 0.074 -9999 0 -0.34 6 6
HIF1A/ARNT/Cbp/p300/HDAC7 -0.75 0.38 -9999 0 -0.99 289 289
PFKFB3 -0.98 0.53 -9999 0 -1.4 279 279
NT5E -0.98 0.53 -9999 0 -1.4 278 278
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.49 0.26 0.63 374 -10000 0 374
KIRREL -0.049 0.078 -10000 0 -0.84 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.5 0.26 -10000 0 -0.63 374 374
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.04 -10000 0 -0.86 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.54 0.31 -10000 0 -0.86 209 209
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.42 0.25 -10000 0 -0.67 209 209
FYN -0.51 0.3 -10000 0 -0.81 209 209
mol:Ca2+ -0.53 0.31 -10000 0 -0.84 209 209
mol:DAG -0.54 0.31 -10000 0 -0.85 209 209
NPHS2 -0.42 0.39 -10000 0 -0.82 231 231
mol:IP3 -0.54 0.31 -10000 0 -0.85 209 209
regulation of endocytosis -0.48 0.28 -10000 0 -0.76 209 209
Nephrin/NEPH1/podocin/Cholesterol -0.55 0.32 -10000 0 -0.66 398 398
establishment of cell polarity -0.49 0.26 -10000 0 -0.63 374 374
Nephrin/NEPH1/podocin/NCK1-2 -0.5 0.3 -10000 0 -0.8 209 209
Nephrin/NEPH1/beta Arrestin2 -0.49 0.29 -10000 0 -0.78 209 209
NPHS1 -0.62 0.33 -10000 0 -0.8 374 374
Nephrin/NEPH1/podocin -0.52 0.3 -10000 0 -0.82 209 209
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.54 0.31 -10000 0 -0.86 209 209
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.54 0.31 -10000 0 -0.86 209 209
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.5 0.3 -10000 0 -0.8 209 209
cytoskeleton organization -0.54 0.32 -10000 0 -0.86 209 209
Nephrin/NEPH1 -0.37 0.2 -10000 0 -0.47 374 374
Nephrin/NEPH1/ZO-1 -0.4 0.22 -10000 0 -0.55 209 209
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.34 0.33 -10000 0 -0.7 214 214
FYN -0.42 0.5 -10000 0 -0.93 223 223
LAT/GRAP2/SLP76 -0.37 0.39 -10000 0 -0.77 218 218
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.26 0.29 -10000 0 -0.54 222 222
B2M 0.009 0.009 -10000 0 -10000 0 0
IKBKG -0.081 0.071 -10000 0 -0.19 67 67
MAP3K8 0.012 0.057 -10000 0 -0.86 2 2
mol:Ca2+ -0.12 0.045 -10000 0 -0.14 315 315
integrin-mediated signaling pathway -0.018 0.1 -10000 0 -0.58 15 15
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.42 0.45 -10000 0 -0.87 228 228
TRPV6 -0.67 0.26 -10000 0 -0.77 417 417
CD28 -0.06 0.24 -10000 0 -0.87 37 37
SHC1 -0.45 0.49 -10000 0 -0.94 227 227
receptor internalization -0.53 0.57 -10000 0 -1.1 231 231
PRF1 -0.5 0.6 -10000 0 -1.1 212 212
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.19 0.22 -10000 0 -0.42 205 205
LAT -0.52 0.54 -10000 0 -1 243 243
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 216 216
CD3E -0.37 0.44 -10000 0 -0.88 205 205
CD3G -0.33 0.43 -10000 0 -0.87 186 186
RASGRP2 -0.023 0.029 -10000 0 -0.14 2 2
RASGRP1 -0.24 0.28 -10000 0 -0.51 218 218
HLA-A 0.006 0.041 -10000 0 -0.88 1 1
RASSF5 -0.012 0.15 -10000 0 -0.86 15 15
RAP1A/GTP/RAPL -0.018 0.1 -10000 0 -0.59 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.038 0.082 -10000 0 -0.14 3 3
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.15 0.13 -10000 0 -0.34 92 92
PRKCA -0.14 0.17 -10000 0 -0.31 180 180
GRAP2 -0.046 0.22 -10000 0 -0.86 34 34
mol:IP3 -0.16 0.34 0.26 144 -0.5 210 354
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.54 0.64 -10000 0 -1.1 230 230
ORAI1 0.33 0.13 0.38 416 -10000 0 416
CSK -0.47 0.51 -10000 0 -0.98 226 226
B7 family/CD28 -0.53 0.52 -10000 0 -1 227 227
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.58 0.63 -10000 0 -1.2 231 231
PTPN6 -0.45 0.53 -10000 0 -1 217 217
VAV1 -0.5 0.54 -10000 0 -1 235 235
Monovalent TCR/CD3 -0.46 0.54 -10000 0 -1 221 221
CBL 0.016 0 -10000 0 -10000 0 0
LCK -0.45 0.53 -10000 0 -1 220 220
PAG1 -0.47 0.51 -10000 0 -0.98 227 227
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.55 0.64 -10000 0 -1.2 225 225
CD80 -0.19 0.37 -10000 0 -0.87 108 108
CD86 -0.13 0.32 -10000 0 -0.87 76 76
PDK1/CARD11/BCL10/MALT1 -0.18 0.16 -10000 0 -0.38 130 130
HRAS 0.016 0 -10000 0 -10000 0 0
GO:0035030 -0.36 0.42 -10000 0 -0.78 227 227
CD8A -0.4 0.44 -10000 0 -0.87 225 225
CD8B -0.31 0.43 -10000 0 -0.88 174 174
PTPRC -0.091 0.28 -10000 0 -0.87 54 54
PDK1/PKC theta -0.33 0.36 -10000 0 -0.7 222 222
CSK/PAG1 -0.45 0.5 -10000 0 -0.96 223 223
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I -0.001 0.031 -10000 0 -0.68 1 1
GRAP2/SLP76 -0.44 0.44 -10000 0 -0.9 223 223
STIM1 0.18 0.064 -10000 0 -10000 0 0
RAS family/GTP -0.065 0.11 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.6 0.66 -10000 0 -1.2 231 231
mol:DAG -0.21 0.26 -10000 0 -0.46 218 218
RAP1A/GDP -0.014 0.035 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.42 -10000 0 -0.87 159 159
cytotoxic T cell degranulation -0.46 0.56 -10000 0 -1 219 219
RAP1A/GTP -0.008 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.32 0.35 -10000 0 -0.67 228 228
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.27 0.44 0.3 98 -0.71 216 314
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.48 0.44 -10000 0 -0.87 272 272
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.39 0.35 -10000 0 -0.74 224 224
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.52 0.56 -10000 0 -1.1 230 230
CARD11 -0.17 0.36 -10000 0 -0.86 101 101
PRKCB -0.14 0.17 -10000 0 -0.31 200 200
PRKCE -0.14 0.17 -10000 0 -0.31 205 205
PRKCQ -0.4 0.43 -10000 0 -0.82 230 230
LCP2 -0.043 0.22 -10000 0 -0.86 32 32
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.21 0.24 -10000 0 -0.45 221 221
IKK complex -0.029 0.084 -10000 0 -10000 0 0
RAS family/GDP -0.012 0.011 -10000 0 -10000 0 0
MAP3K14 -0.13 0.18 -10000 0 -0.51 6 6
PDPK1 -0.24 0.27 -10000 0 -0.51 217 217
TCR/CD3/MHC I/CD8/Fyn -0.57 0.66 -10000 0 -1.2 222 222
TCGA08_p53

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
CDKN2A -0.66 0.13 -10000 0 -0.68 463 463
TP53 -0.17 0.037 -10000 0 -10000 0 0
Senescence -0.17 0.036 -10000 0 -10000 0 0
Apoptosis -0.17 0.036 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.31 0.06 0.33 463 -10000 0 463
MDM4 0.014 0.04 -10000 0 -0.86 1 1
TCGA08_retinoblastoma

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
CDKN2B -0.009 0.089 -10000 0 -0.88 5 5
CDKN2C 0.079 0.017 -10000 0 -10000 0 0
CDKN2A -0.85 0.16 -10000 0 -0.88 463 463
CCND2 0.18 0.046 0.46 5 -10000 0 5
RB1 -0.2 0.048 -10000 0 -0.48 5 5
CDK4 0.22 0.05 0.22 462 -10000 0 462
CDK6 0.2 0.052 0.51 5 -0.18 1 6
G1/S progression 0.2 0.052 0.47 5 -10000 0 5
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.45 0.48 -9999 0 -1.1 117 117
PCK1 -0.94 0.72 -9999 0 -1.4 286 286
HNF4A -0.59 0.58 -9999 0 -1.4 125 125
KCNJ11 -0.45 0.51 -9999 0 -1.2 100 100
AKT1 -0.17 0.18 -9999 0 -10000 0 0
response to starvation -0.02 0.039 -9999 0 -10000 0 0
DLK1 -0.56 0.58 -9999 0 -1.3 157 157
NKX2-1 -0.048 0.21 -9999 0 -0.82 3 3
ACADM -0.45 0.48 -9999 0 -1.1 119 119
TAT -0.52 0.35 -9999 0 -0.92 151 151
CEBPB -0.026 0.14 -9999 0 -0.92 12 12
CEBPA -0.019 0.12 -9999 0 -0.9 9 9
TTR -0.91 0.48 -9999 0 -1.2 321 321
PKLR -0.51 0.56 -9999 0 -1.3 122 122
APOA1 -0.56 0.57 -9999 0 -1.3 128 128
CPT1C -0.45 0.48 -9999 0 -1.1 120 120
ALAS1 -0.17 0.2 -9999 0 -10000 0 0
TFRC -0.63 0.42 -9999 0 -0.99 224 224
FOXF1 -0.004 0.12 -9999 0 -0.84 10 10
NF1 0.025 0.001 -9999 0 -10000 0 0
HNF1A (dimer) -0.001 0.083 -9999 0 -0.81 4 4
CPT1A -0.45 0.48 -9999 0 -1.1 116 116
HMGCS1 -0.45 0.48 -9999 0 -1.1 119 119
NR3C1 0.003 0.067 -9999 0 -0.97 1 1
CPT1B -0.47 0.5 -9999 0 -1.2 125 125
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.017 0.005 -9999 0 -10000 0 0
GCK -0.46 0.49 -9999 0 -1.1 122 122
CREB1 -0.027 0.065 -9999 0 -10000 0 0
IGFBP1 -0.32 0.42 -9999 0 -1 112 112
PDX1 -0.19 0.22 -9999 0 -1.1 5 5
UCP2 -0.45 0.48 -9999 0 -1.1 122 122
ALDOB -0.95 0.63 -9999 0 -1.2 368 368
AFP -0.74 0.51 -9999 0 -0.99 310 310
BDH1 -0.6 0.57 -9999 0 -1.2 195 195
HADH -0.44 0.49 -9999 0 -1.2 95 95
F2 -0.66 0.62 -9999 0 -1.3 178 178
HNF1A -0.001 0.083 -9999 0 -0.81 4 4
G6PC -0.81 0.66 -9999 0 -1.5 227 227
SLC2A2 -0.32 0.47 -9999 0 -1.7 41 41
INS 0.01 0.055 -9999 0 -10000 0 0
FOXA1 -0.4 0.41 -9999 0 -0.99 137 137
FOXA3 -0.62 0.38 -9999 0 -0.84 313 313
FOXA2 -0.52 0.57 -9999 0 -1.3 131 131
ABCC8 -0.45 0.49 -9999 0 -1.2 96 96
ALB -1.3 0.49 -9999 0 -1.4 421 421
Aurora B signaling

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
Condensin I complex -0.25 0.32 -9999 0 -0.68 154 154
STMN1 -0.3 0.35 -9999 0 -0.66 229 229
Aurora B/RasGAP/Survivin -0.41 0.48 -9999 0 -0.87 233 233
Chromosomal passenger complex/Cul3 protein complex -0.17 0.23 -9999 0 -0.49 138 138
BIRC5 -0.25 0.41 -9999 0 -0.89 140 140
DES -0.38 0.34 -9999 0 -0.58 306 306
Aurora C/Aurora B/INCENP -0.24 0.28 -9999 0 -0.53 230 230
Aurora B/TACC1 -0.27 0.3 -9999 0 -0.58 229 229
Aurora B/PP2A -0.3 0.34 -9999 0 -0.66 229 229
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.074 0.091 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.008 -9999 0 -10000 0 0
NDC80 -0.42 0.5 -9999 0 -0.9 233 233
Cul3 protein complex -0.015 0.084 -9999 0 -0.48 15 15
KIF2C -0.16 0.18 -9999 0 -0.34 187 187
PEBP1 0.007 0.008 -9999 0 -10000 0 0
KIF20A -0.4 0.44 -9999 0 -0.87 228 228
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.3 0.34 -9999 0 -0.66 229 229
SEPT1 -0.1 0.3 -9999 0 -0.86 63 63
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.19 0.24 -9999 0 -0.45 189 189
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.004 -9999 0 -10000 0 0
H3F3B -0.17 0.21 -9999 0 -0.39 229 229
AURKB -0.41 0.44 -9999 0 -0.87 229 229
AURKC 0.014 0.04 -9999 0 -0.86 1 1
CDCA8 -0.026 0.17 -9999 0 -0.9 18 18
cytokinesis -0.35 0.37 -9999 0 -0.76 196 196
Aurora B/Septin1 -0.37 0.42 -9999 0 -0.83 193 193
AURKA 0.001 0.099 -9999 0 -0.87 6 6
INCENP 0.007 0.009 -9999 0 -10000 0 0
KLHL13 -0.008 0.14 -9999 0 -0.76 15 15
BUB1 -0.4 0.44 -9999 0 -0.87 223 223
hSgo1/Aurora B/Survivin -0.4 0.49 -9999 0 -0.85 234 234
EVI5 0.009 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.32 0.34 -9999 0 -0.72 180 180
SGOL1 -0.015 0.16 -9999 0 -0.86 17 17
CENPA -0.3 0.35 -9999 0 -0.63 236 236
NCAPG -0.29 0.42 -9999 0 -0.86 167 167
Aurora B/HC8 Proteasome -0.3 0.34 -9999 0 -0.66 229 229
NCAPD2 0.016 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.3 0.34 -9999 0 -0.66 229 229
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.14 0.34 -9999 0 -0.86 84 84
NPM1 -0.22 0.24 -9999 0 -0.47 229 229
RASA1 0.016 0 -9999 0 -10000 0 0
KLHL9 0.016 0 -9999 0 -10000 0 0
mitotic prometaphase -0.01 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.34 -9999 0 -0.66 229 229
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.35 0.38 -9999 0 -0.79 188 188
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.22 0.24 -9999 0 -0.47 229 229
MYLK -0.17 0.21 -9999 0 -0.39 229 229
KIF23 -0.008 0.11 -9999 0 -0.88 8 8
VIM -0.35 0.41 -9999 0 -0.74 241 241
RACGAP1 0.003 0.058 -9999 0 -0.88 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.22 0.24 -9999 0 -0.47 229 229
Chromosomal passenger complex -0.36 0.41 -9999 0 -0.76 225 225
Chromosomal passenger complex/EVI5 -0.37 0.48 -9999 0 -1 136 136
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.056 0.14 -9999 0 -0.54 37 37
Syndecan-4/Syndesmos -0.47 0.4 -9999 0 -0.85 218 218
positive regulation of JNK cascade -0.54 0.38 -9999 0 -0.85 263 263
Syndecan-4/ADAM12 -0.58 0.5 -9999 0 -1 241 241
CCL5 -0.36 0.44 -9999 0 -0.86 206 206
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.052 0.24 -9999 0 -0.86 37 37
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.38 0.37 -9999 0 -0.73 256 256
ADAM12 -0.23 0.4 -9999 0 -0.86 135 135
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.1 0.071 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.48 0.4 -9999 0 -0.86 221 221
Syndecan-4/CXCL12/CXCR4 -0.6 0.43 -9999 0 -0.94 263 263
Syndecan-4/Laminin alpha3 -0.47 0.4 -9999 0 -0.85 221 221
MDK -0.052 0.24 -9999 0 -0.86 37 37
Syndecan-4/FZD7 -0.47 0.4 -9999 0 -0.85 219 219
Syndecan-4/Midkine -0.5 0.42 -9999 0 -0.89 229 229
FZD7 0.014 0.035 -9999 0 -0.76 1 1
Syndecan-4/FGFR1/FGF -0.44 0.34 -9999 0 -0.77 220 220
THBS1 0.014 0.035 -9999 0 -0.76 1 1
integrin-mediated signaling pathway -0.45 0.36 -9999 0 -0.8 222 222
positive regulation of MAPKKK cascade -0.54 0.38 -9999 0 -0.85 263 263
Syndecan-4/TACI -0.51 0.43 -9999 0 -0.9 229 229
CXCR4 -0.3 0.42 -9999 0 -0.86 170 170
cell adhesion -0.009 0.12 -9999 0 -0.51 14 14
Syndecan-4/Dynamin -0.47 0.4 -9999 0 -0.85 218 218
Syndecan-4/TSP1 -0.47 0.4 -9999 0 -0.85 219 219
Syndecan-4/GIPC -0.47 0.4 -9999 0 -0.85 219 219
Syndecan-4/RANTES -0.65 0.46 -9999 0 -1 272 272
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.007 0.13 -9999 0 -0.77 14 14
LAMA3 0.007 0.089 -9999 0 -0.86 5 5
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.11 0.067 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.47 0.4 -9999 0 -0.85 218 218
TFPI 0 0.11 -9999 0 -0.82 9 9
F2 -0.32 0.43 -9999 0 -0.87 182 182
alpha5/beta1 Integrin -0.051 0.18 -9999 0 -0.67 37 37
positive regulation of cell adhesion -0.46 0.39 -9999 0 -0.82 224 224
ACTN1 0.014 0.04 -9999 0 -0.86 1 1
TNC 0 0.11 -9999 0 -0.76 10 10
Syndecan-4/CXCL12 -0.47 0.4 -9999 0 -0.85 222 222
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 0.003 0.099 -9999 0 -0.76 8 8
TNFRSF13B -0.065 0.25 -9999 0 -0.86 43 43
FGF2 0.009 0.073 -9999 0 -0.78 4 4
FGFR1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.48 0.39 -9999 0 -0.86 218 218
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.043 0.23 -9999 0 -0.83 37 37
cell migration -0.03 0.022 -9999 0 -10000 0 0
PRKCD 0.024 0.047 -9999 0 -0.85 1 1
vasculogenesis -0.44 0.37 -9999 0 -0.8 219 219
SDC4 -0.52 0.44 -9999 0 -0.94 218 218
Syndecan-4/Tenascin C -0.48 0.39 -9999 0 -0.85 222 222
Syndecan-4/PI-4-5-P2/PKC alpha -0.08 0.055 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.47 0.4 -9999 0 -0.85 218 218
MMP9 -0.39 0.44 -9999 0 -0.86 223 223
Rac1/GTP -0.018 0.12 -9999 0 -0.53 14 14
cytoskeleton organization -0.44 0.37 -9999 0 -0.8 218 218
GIPC1 0.014 0.035 -9999 0 -0.76 1 1
Syndecan-4/TFPI -0.48 0.4 -9999 0 -0.85 223 223
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.17 0.26 -10000 0 -0.65 66 66
TBX21 -0.56 0.68 -10000 0 -1.3 197 197
B2M 0.01 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.021 -10000 0 -10000 0 0
IL12RB1 -0.28 0.43 -10000 0 -0.91 152 152
GADD45B -0.31 0.43 -10000 0 -0.81 155 155
IL12RB2 -0.11 0.31 -10000 0 -0.88 67 67
GADD45G -0.32 0.44 -10000 0 -0.8 173 173
natural killer cell activation -0.01 0.03 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.002 0.099 -10000 0 -0.87 6 6
IL2RA -0.16 0.35 -10000 0 -0.86 96 96
IFNG -0.39 0.44 -10000 0 -0.86 220 220
STAT3 (dimer) -0.39 0.47 -10000 0 -0.87 201 201
HLA-DRB5 -0.04 0.22 -10000 0 -0.86 31 31
FASLG -0.62 0.7 -10000 0 -1.3 226 226
NF kappa B2 p52/RelB -0.53 0.54 -10000 0 -1.1 206 206
CD4 0 0.12 -10000 0 -0.86 9 9
SOCS1 0.007 0.089 -10000 0 -0.86 5 5
EntrezGene:6955 -0.002 0.01 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 216 216
CD3E -0.36 0.44 -10000 0 -0.87 205 205
CD3G -0.33 0.43 -10000 0 -0.87 186 186
IL12Rbeta2/JAK2 -0.083 0.25 -10000 0 -0.69 67 67
CCL3 -0.5 0.63 -10000 0 -1.2 186 186
CCL4 -0.52 0.67 -10000 0 -1.2 199 199
HLA-A 0.008 0.041 -10000 0 -0.87 1 1
IL18/IL18R -0.15 0.31 -10000 0 -0.6 153 153
NOS2 -0.38 0.5 -10000 0 -0.93 176 176
IL12/IL12R/TYK2/JAK2/SPHK2 -0.17 0.26 -10000 0 -0.66 63 63
IL1R1 -0.46 0.6 -10000 0 -1.2 169 169
IL4 0.014 0.031 -10000 0 -10000 0 0
JAK2 0.012 0.021 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.72 0.83 -10000 0 -1.5 242 242
RAB7A -0.25 0.37 -10000 0 -0.7 117 117
lysosomal transport -0.24 0.36 -10000 0 -0.67 117 117
FOS -0.38 0.5 -10000 0 -0.95 189 189
STAT4 (dimer) -0.42 0.53 -10000 0 -0.98 198 198
STAT5A (dimer) -0.66 0.62 -10000 0 -1.2 230 230
GZMA -0.58 0.71 -10000 0 -1.3 206 206
GZMB -0.54 0.68 -10000 0 -1.3 187 187
HLX -0.083 0.28 -10000 0 -0.86 54 54
LCK -0.53 0.7 -10000 0 -1.2 203 203
TCR/CD3/MHC II/CD4 -0.38 0.47 -10000 0 -0.88 212 212
IL2/IL2R -0.44 0.42 -10000 0 -0.71 293 293
MAPK14 -0.32 0.44 -10000 0 -0.8 178 178
CCR5 -0.49 0.6 -10000 0 -1.1 193 193
IL1B 0.005 0.082 -10000 0 -0.86 4 4
STAT6 -0.086 0.15 -10000 0 -10000 0 0
STAT4 -0.039 0.21 -10000 0 -0.86 30 30
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.014 0.04 -10000 0 -0.86 1 1
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.095 0.3 -10000 0 -0.9 57 57
CD8A -0.4 0.44 -10000 0 -0.87 225 225
CD8B -0.31 0.43 -10000 0 -0.87 174 174
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.17 0.26 0.65 66 -10000 0 66
IL2RB -0.47 0.44 -10000 0 -0.86 263 263
proteasomal ubiquitin-dependent protein catabolic process -0.38 0.48 -10000 0 -0.87 197 197
IL2RG -0.045 0.22 -10000 0 -0.86 33 33
IL12 -0.072 0.24 -10000 0 -0.72 58 58
STAT5A 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.42 -10000 0 -0.87 159 159
IL2 -0.008 0.12 -10000 0 -0.86 10 10
SPHK2 0.012 0.05 -10000 0 -0.76 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.01 0.047 -10000 0 -0.92 1 1
IL12/IL12R/TYK2/JAK2 -0.6 0.79 -10000 0 -1.4 207 207
MAP2K3 -0.32 0.44 -10000 0 -0.8 181 181
RIPK2 0.014 0.04 -10000 0 -0.86 1 1
MAP2K6 -0.32 0.44 -10000 0 -0.8 181 181
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.011 0.069 -10000 0 -0.86 3 3
IL18RAP -0.25 0.41 -10000 0 -0.87 143 143
IL12Rbeta1/TYK2 -0.21 0.35 -10000 0 -0.72 152 152
EOMES -0.31 0.38 -10000 0 -0.74 205 205
STAT1 (dimer) -0.46 0.51 -10000 0 -0.96 221 221
T cell proliferation -0.28 0.37 -10000 0 -0.66 187 187
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.1 -10000 0 -0.82 7 7
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.38 0.33 -10000 0 -0.75 184 184
ATF2 -0.28 0.41 -10000 0 -0.76 157 157
FOXM1 transcription factor network

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
NFATC3 -0.2 0.68 -10000 0 -1.2 113 113
PLK1 -0.11 0.41 -10000 0 -0.8 124 124
BIRC5 -0.14 0.43 -10000 0 -0.79 140 140
HSPA1B -0.2 0.68 -10000 0 -1.2 109 109
MAP2K1 0.04 0.047 -10000 0 -10000 0 0
BRCA2 -0.21 0.69 -10000 0 -1.2 114 114
FOXM1 -0.39 1 -10000 0 -1.9 119 119
XRCC1 -0.2 0.68 -10000 0 -1.2 112 112
FOXM1B/p19 -0.5 0.5 0.51 1 -1.2 127 128
Cyclin D1/CDK4 -0.2 0.61 -10000 0 -1.1 102 102
CDC2 -0.23 0.73 -10000 0 -1.3 119 119
TGFA -0.17 0.61 -10000 0 -1.1 100 100
SKP2 -0.2 0.68 -10000 0 -1.2 113 113
CCNE1 0.004 0.1 -10000 0 -0.88 6 6
CKS1B -0.2 0.68 -10000 0 -1.2 114 114
RB1 -0.2 0.26 -10000 0 -0.69 90 90
FOXM1C/SP1 -0.3 0.78 -10000 0 -1.5 119 119
AURKB -0.26 0.47 -10000 0 -0.74 229 229
CENPF -0.22 0.72 -10000 0 -1.3 114 114
CDK4 0.02 0.022 -10000 0 -10000 0 0
MYC -0.16 0.61 -10000 0 -1.1 112 112
CHEK2 0.038 0.064 -10000 0 -0.91 1 1
ONECUT1 -0.2 0.66 -10000 0 -1.2 113 113
CDKN2A -0.83 0.16 -10000 0 -0.86 463 463
LAMA4 -0.29 0.7 -10000 0 -1.3 118 118
FOXM1B/HNF6 -0.29 0.8 -10000 0 -1.5 115 115
FOS -0.21 0.69 -10000 0 -1.2 114 114
SP1 0.017 0.005 -10000 0 -10000 0 0
CDC25B -0.2 0.69 -10000 0 -1.2 113 113
response to radiation 0.013 0.05 -10000 0 -10000 0 0
CENPB -0.2 0.68 -10000 0 -1.2 112 112
CENPA -0.3 0.78 -10000 0 -1.4 137 137
NEK2 -0.26 0.76 -10000 0 -1.4 125 125
HIST1H2BA -0.21 0.68 -10000 0 -1.2 111 111
CCNA2 -0.16 0.36 -10000 0 -0.88 96 96
EP300 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.29 0.82 -10000 0 -1.6 116 116
CCNB2 -0.26 0.76 -10000 0 -1.4 122 122
CCNB1 -0.23 0.73 -10000 0 -1.3 114 114
ETV5 -0.2 0.68 -10000 0 -1.2 112 112
ESR1 -0.2 0.68 -10000 0 -1.2 113 113
CCND1 -0.19 0.64 -10000 0 -1.1 103 103
GSK3A 0.036 0.042 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.084 0.29 -10000 0 -0.64 96 96
CDK2 0.015 0.016 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.014 0.059 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.44 0.59 -10000 0 -1.4 128 128
GAS1 -0.24 0.71 -10000 0 -1.2 128 128
MMP2 -0.2 0.68 -10000 0 -1.2 113 113
RB1/FOXM1C -0.22 0.68 -10000 0 -1.2 111 111
CREBBP 0.016 0 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.005 0.051 -10000 0 -0.5 5 5
fibroblast growth factor receptor signaling pathway -0.005 0.051 -10000 0 -0.5 5 5
LAMA1 -0.007 0.13 -10000 0 -0.77 14 14
PRNP 0.016 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.23 -10000 0 -0.57 99 99
SMAD2 0.045 0.022 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.001 0.023 -10000 0 -0.5 1 1
GPC1/Laminin alpha1 -0.018 0.1 -10000 0 -0.58 15 15
TDGF1 -0.57 0.33 -10000 0 -0.76 364 364
CRIPTO/GPC1 -0.43 0.25 -10000 0 -0.57 364 364
APP/GPC1 -0.002 0.037 -10000 0 -0.57 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.36 0.22 -10000 0 -0.48 364 364
FLT1 0.008 0.08 -10000 0 -0.86 4 4
GPC1/TGFB/TGFBR1/TGFBR2 -0.001 0.022 -10000 0 -0.48 1 1
SERPINC1 -0.066 0.24 -10000 0 -0.77 49 49
FYN -0.36 0.22 -10000 0 -0.48 364 364
FGR -0.36 0.23 -10000 0 -0.49 364 364
positive regulation of MAPKKK cascade -0.37 0.25 -10000 0 -0.69 60 60
SLIT2 -0.14 0.31 -10000 0 -0.76 98 98
GPC1/NRG -0.014 0.089 -10000 0 -0.57 12 12
NRG1 -0.002 0.12 -10000 0 -0.76 11 11
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.26 0.3 -10000 0 -0.59 216 216
LYN -0.36 0.22 -10000 0 -0.48 364 364
mol:Spermine 0.014 0.027 -10000 0 -0.58 1 1
cell growth -0.005 0.051 -10000 0 -0.5 5 5
BMP signaling pathway -0.014 0.035 0.76 1 -10000 0 1
SRC -0.36 0.22 -10000 0 -0.48 364 364
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.075 0.26 -10000 0 -0.86 47 47
GPC1 0.014 0.035 -10000 0 -0.76 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA -0.38 0.44 -10000 0 -0.86 215 215
BLK -0.4 0.26 -10000 0 -0.52 369 369
HCK -0.39 0.25 -10000 0 -0.51 373 373
FGF2 0.009 0.073 -10000 0 -0.78 4 4
FGFR1 0.016 0 -10000 0 -10000 0 0
VEGFR1 homodimer 0.008 0.08 -10000 0 -0.86 4 4
TGFBR2 0.016 0 -10000 0 -10000 0 0
cell death -0.002 0.037 -10000 0 -0.57 2 2
ATIII/GPC1 -0.061 0.18 -10000 0 -0.58 50 50
PLA2G2A/GPC1 -0.067 0.2 -10000 0 -0.66 48 48
LCK -0.39 0.24 -10000 0 -0.51 372 372
neuron differentiation -0.014 0.089 -10000 0 -0.57 12 12
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0.035 -10000 0 -0.76 1 1
TGFBR2 (dimer) 0.016 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.28 0.38 -9999 0 -0.76 184 184
PDGF/PDGFRA/CRKL -0.21 0.27 -9999 0 -0.55 184 184
positive regulation of JUN kinase activity -0.16 0.2 -9999 0 -0.52 1 1
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.22 0.27 -9999 0 -0.56 185 185
AP1 -0.16 0.24 -9999 0 -1.3 10 10
mol:IP3 -0.2 0.29 -9999 0 -0.57 184 184
PLCG1 -0.2 0.29 -9999 0 -0.57 184 184
PDGF/PDGFRA/alphaV Integrin -0.21 0.27 -9999 0 -0.55 184 184
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.29 -9999 0 -0.56 184 184
CAV3 0.003 0.04 -9999 0 -0.86 1 1
CAV1 -0.05 0.23 -9999 0 -0.86 36 36
SHC/Grb2/SOS1 -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/Shf -0.21 0.27 -9999 0 -0.55 185 185
FOS -0.12 0.26 -9999 0 -1.2 10 10
JUN -0.013 0.017 -9999 0 -10000 0 0
oligodendrocyte development -0.21 0.27 -9999 0 -0.55 184 184
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:DAG -0.2 0.29 -9999 0 -0.57 184 184
PDGF/PDGFRA -0.28 0.38 -9999 0 -0.76 184 184
actin cytoskeleton reorganization -0.21 0.27 -9999 0 -0.55 184 184
SRF 0.034 0.009 -9999 0 -10000 0 0
SHC1 0.014 0.04 -9999 0 -0.86 1 1
PI3K -0.18 0.23 -9999 0 -0.46 184 184
PDGF/PDGFRA/Crk/C3G -0.18 0.23 -9999 0 -0.5 6 6
JAK1 -0.19 0.28 -9999 0 -0.55 184 184
ELK1/SRF -0.15 0.2 -9999 0 -10000 0 0
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.014 0.035 -9999 0 -0.76 1 1
CSNK2A1 0.017 0.022 -9999 0 -10000 0 0
GO:0007205 -0.2 0.3 -9999 0 -0.58 184 184
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/SHB -0.21 0.27 -9999 0 -0.55 184 184
PDGF/PDGFRA/Caveolin-1 -0.26 0.3 -9999 0 -0.59 212 212
ITGAV 0.016 0 -9999 0 -10000 0 0
ELK1 -0.16 0.27 -9999 0 -0.5 184 184
PIK3CA 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.21 0.27 -9999 0 -0.55 184 184
JAK-STAT cascade -0.19 0.28 -9999 0 -0.55 184 184
cell proliferation -0.21 0.27 -9999 0 -0.55 185 185
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.15 0.29 -9999 0 -0.67 105 105
alphaM/beta2 Integrin/GPIbA -0.14 0.28 -9999 0 -0.66 102 102
alphaM/beta2 Integrin/proMMP-9 -0.4 0.43 -9999 0 -0.76 254 254
PLAUR -0.028 0.19 -9999 0 -0.86 24 24
HMGB1 0.015 0.013 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.14 0.28 -9999 0 -0.67 101 101
AGER -0.13 0.33 -9999 0 -0.86 79 79
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.048 0.23 -9999 0 -0.86 35 35
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.23 0.34 -9999 0 -0.66 158 158
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.39 0.44 -9999 0 -0.86 223 223
CYR61 0.008 0.079 -9999 0 -0.76 5 5
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.26 0.21 -9999 0 -0.56 114 114
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.02 0.16 -9999 0 -0.76 22 22
MYH2 -0.35 0.26 -9999 0 -0.65 177 177
MST1R 0.006 0.088 -9999 0 -0.78 6 6
leukocyte activation during inflammatory response -0.28 0.35 -9999 0 -0.64 210 210
APOB -0.27 0.41 -9999 0 -0.86 158 158
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.007 0.089 -9999 0 -0.86 5 5
JAM3 0.016 0 -9999 0 -10000 0 0
GP1BA 0.014 0.035 -9999 0 -0.76 1 1
alphaM/beta2 Integrin/CTGF -0.15 0.29 -9999 0 -0.67 105 105
alphaM/beta2 Integrin -0.31 0.25 -9999 0 -0.54 216 216
JAM3 homodimer 0.016 0 -9999 0 -10000 0 0
ICAM2 0.016 0 -9999 0 -10000 0 0
ICAM1 -0.003 0.13 -9999 0 -0.86 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.31 0.25 -9999 0 -0.53 216 216
cell adhesion -0.14 0.28 -9999 0 -0.66 102 102
NFKB1 -0.18 0.37 -9999 0 -0.95 58 58
THY1 0.014 0.035 -9999 0 -0.76 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.2 0.28 -9999 0 -0.6 159 159
alphaM/beta2 Integrin/LRP/tPA -0.14 0.27 -9999 0 -0.62 103 103
IL6 -0.2 0.41 -9999 0 -0.91 91 91
ITGB2 -0.17 0.36 -9999 0 -0.86 99 99
elevation of cytosolic calcium ion concentration -0.16 0.3 -9999 0 -0.63 119 119
alphaM/beta2 Integrin/JAM2/JAM3 -0.13 0.26 -9999 0 -0.61 101 101
JAM2 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.14 0.28 -9999 0 -0.84 39 39
alphaM/beta2 Integrin/uPA/Plg -0.37 0.34 -9999 0 -0.87 104 104
RhoA/GTP -0.38 0.27 -9999 0 -0.68 179 179
positive regulation of phagocytosis -0.26 0.27 -9999 0 -0.69 111 111
Ron/MSP -0.016 0.098 -9999 0 -0.63 12 12
alphaM/beta2 Integrin/uPAR/uPA -0.16 0.3 -9999 0 -0.64 119 119
alphaM/beta2 Integrin/uPAR -0.17 0.32 -9999 0 -0.7 116 116
PLAU 0.004 0.093 -9999 0 -0.76 7 7
PLAT -0.004 0.12 -9999 0 -0.76 12 12
actin filament polymerization -0.34 0.24 -9999 0 -0.61 177 177
MST1 0.005 0.098 -9999 0 -0.86 6 6
alphaM/beta2 Integrin/lipoprotein(a) -0.29 0.36 -9999 0 -0.65 210 210
TNF -0.15 0.34 -9999 0 -0.85 62 62
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.15 0.29 -9999 0 -0.66 108 108
fibrinolysis -0.36 0.34 -9999 0 -0.85 104 104
HCK -0.034 0.2 -9999 0 -0.86 27 27
dendritic cell antigen processing and presentation -0.31 0.25 -9999 0 -0.53 216 216
VTN -0.11 0.29 -9999 0 -0.77 76 76
alphaM/beta2 Integrin/CYR61 -0.15 0.29 -9999 0 -0.66 106 106
LPA 0.002 0.069 -9999 0 -0.86 3 3
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.37 0.41 -9999 0 -0.7 255 255
FN1 -0.052 0.24 -9999 0 -0.86 37 37
alphaM/beta2 Integrin/Thy1 -0.14 0.29 -9999 0 -0.67 101 101
MPO -0.013 0.15 -9999 0 -0.86 15 15
KNG1 -0.57 0.33 -9999 0 -0.76 363 363
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.34 0.26 -9999 0 -0.64 166 166
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.4 0.38 -9999 0 -0.76 256 256
CTGF 0.006 0.086 -9999 0 -0.76 6 6
alphaM/beta2 Integrin/Hck -0.17 0.35 -9999 0 -0.77 105 105
ITGAM -0.02 0.17 -9999 0 -0.87 19 19
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.19 0.35 -9999 0 -0.74 111 111
HP -0.21 0.38 -9999 0 -0.86 121 121
leukocyte adhesion -0.18 0.27 -9999 0 -0.78 57 57
SELP -0.02 0.16 -9999 0 -0.76 22 22
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.43 0.55 -9999 0 -0.93 221 221
MAP4K1 -0.35 0.43 -9999 0 -0.86 197 197
MAP3K8 0.012 0.057 -9999 0 -0.86 2 2
PRKCB 0.007 0.085 -9999 0 -0.82 5 5
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.16 0.3 -9999 0 -0.62 121 121
JUN 0.001 0.076 -9999 0 -0.53 4 4
MAP3K7 -0.16 0.3 -9999 0 -0.62 121 121
GRAP2 -0.046 0.22 -9999 0 -0.86 34 34
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.14 0.29 -9999 0 -0.59 121 121
LAT -0.25 0.4 -9999 0 -0.86 143 143
LCP2 -0.043 0.22 -9999 0 -0.86 32 32
MAPK8 -0.011 0.081 -9999 0 -0.57 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.21 0.3 -9999 0 -0.67 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.41 0.52 -9999 0 -1.2 121 121
IL4-mediated signaling events

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
BCL2L1 -0.48 0.48 -10000 0 -1.2 93 93
STAT6 (cleaved dimer) -0.59 0.5 -10000 0 -1.2 157 157
IGHG1 -0.17 0.19 -10000 0 -0.68 11 11
IGHG3 -0.48 0.46 -10000 0 -1.1 118 118
AKT1 -0.28 0.34 -10000 0 -0.83 80 80
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.25 0.32 -10000 0 -0.81 84 84
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.3 -10000 0 -0.79 63 63
THY1 -0.48 0.49 -10000 0 -1.2 97 97
MYB -0.22 0.39 -10000 0 -0.86 130 130
HMGA1 0.014 0.04 -10000 0 -0.86 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.4 0.43 -10000 0 -0.99 115 115
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.3 -10000 0 -0.8 63 63
SP1 0.022 0.015 -10000 0 -10000 0 0
INPP5D 0.008 0.08 -10000 0 -0.86 4 4
SOCS5 0.026 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.48 -10000 0 -1.2 142 142
SOCS1 -0.33 0.34 -10000 0 -0.82 63 63
SOCS3 -0.3 0.35 -10000 0 -0.93 61 61
FCER2 -0.42 0.44 -10000 0 -1.2 72 72
PARP14 0.016 0.004 -10000 0 -10000 0 0
CCL17 -0.51 0.51 -10000 0 -1.2 109 109
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.23 0.28 -10000 0 -0.77 54 54
T cell proliferation -0.51 0.52 -10000 0 -1.2 118 118
IL4R/JAK1 -0.48 0.48 -10000 0 -1.2 107 107
EGR2 -0.49 0.5 -10000 0 -1.2 94 94
JAK2 0.008 0.023 -10000 0 -10000 0 0
JAK3 -0.17 0.36 -10000 0 -0.87 102 102
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.007 0.016 -10000 0 -10000 0 0
COL1A2 -0.22 0.31 -10000 0 -0.92 58 58
CCL26 -0.49 0.49 -10000 0 -1.2 98 98
IL4R -0.51 0.52 -10000 0 -1.2 107 107
PTPN6 0.027 0.012 -10000 0 -10000 0 0
IL13RA2 -0.55 0.56 -10000 0 -1.3 123 123
IL13RA1 0.008 0.023 -10000 0 -10000 0 0
IRF4 -0.28 0.44 -10000 0 -1 116 116
ARG1 -0.17 0.27 -10000 0 -0.8 41 41
CBL -0.36 0.4 -10000 0 -0.95 106 106
GTF3A 0.011 0.03 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.006 0.044 -10000 0 -10000 0 0
IRF4/BCL6 -0.28 0.39 -10000 0 -0.95 110 110
CD40LG -0.09 0.31 -10000 0 -0.92 57 57
MAPK14 -0.36 0.4 -10000 0 -0.95 105 105
mitosis -0.27 0.32 -10000 0 -0.78 80 80
STAT6 -0.55 0.56 -10000 0 -1.3 115 115
SPI1 -0.097 0.3 -10000 0 -0.86 64 64
RPS6KB1 -0.25 0.31 -10000 0 -0.77 68 68
STAT6 (dimer) -0.56 0.56 -10000 0 -1.3 115 115
STAT6 (dimer)/PARP14 -0.51 0.52 -10000 0 -1.2 112 112
mast cell activation 0.012 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.31 0.37 -10000 0 -0.89 96 96
FRAP1 -0.28 0.34 -10000 0 -0.83 80 80
LTA -0.61 0.56 -10000 0 -1.3 140 140
FES 0.012 0.05 -10000 0 -0.76 2 2
T-helper 1 cell differentiation 0.54 0.54 1.3 115 -10000 0 115
CCL11 -0.7 0.61 -10000 0 -1.3 205 205
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.3 0.35 -10000 0 -0.85 91 91
IL2RG -0.04 0.22 -10000 0 -0.86 33 33
IL10 -0.5 0.51 -10000 0 -1.2 108 108
IRS1 0.012 0.05 -10000 0 -0.76 2 2
IRS2 0.001 0.11 -10000 0 -0.86 8 8
IL4 -0.11 0.13 -10000 0 -10000 0 0
IL5 -0.49 0.48 -10000 0 -1.2 102 102
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.38 -10000 0 -0.88 101 101
COL1A1 -0.41 0.44 -10000 0 -0.92 185 185
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.48 0.49 -10000 0 -1.2 88 88
IL2R gamma/JAK3 -0.17 0.37 -10000 0 -0.84 105 105
TFF3 -0.5 0.51 -10000 0 -1.3 94 94
ALOX15 -0.49 0.49 -10000 0 -1.2 97 97
MYBL1 -0.052 0.24 -10000 0 -0.86 37 37
T-helper 2 cell differentiation -0.43 0.42 -10000 0 -0.98 117 117
SHC1 0.014 0.04 -10000 0 -0.86 1 1
CEBPB -0.002 0.14 -10000 0 -0.87 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.3 -10000 0 -0.77 67 67
mol:PI-3-4-5-P3 -0.28 0.34 -10000 0 -0.83 80 80
PI3K -0.3 0.36 -10000 0 -0.9 81 81
DOK2 -0.035 0.21 -10000 0 -0.86 28 28
ETS1 0.028 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.28 -10000 0 -0.76 54 54
ITGB3 -0.48 0.49 -10000 0 -1.2 96 96
PIGR -0.84 0.71 -10000 0 -1.5 248 248
IGHE 0.028 0.093 0.29 10 -0.37 4 14
MAPKKK cascade -0.21 0.27 -10000 0 -0.74 54 54
BCL6 0.012 0.006 -10000 0 -10000 0 0
OPRM1 -0.49 0.48 -10000 0 -1.2 103 103
RETNLB -0.49 0.48 -10000 0 -1.2 104 104
SELP -0.51 0.53 -10000 0 -1.3 109 109
AICDA -0.62 0.55 -10000 0 -1.2 171 171
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.016 0 -9999 0 -10000 0 0
EGFR -0.001 0.12 -9999 0 -0.85 9 9
EGF/EGFR -0.39 0.17 -9999 0 -0.87 27 27
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.37 0.14 -9999 0 -0.91 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.012 0.057 -9999 0 -0.86 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.68 0.23 -9999 0 -0.76 432 432
EGF/EGFR dimer/SHC -0.45 0.16 -9999 0 -0.5 433 433
mol:GDP -0.37 0.14 -9999 0 -0.89 9 9
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.017 0.17 -9999 0 -0.86 18 18
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.34 0.13 -9999 0 -0.82 9 9
SHC1 0.014 0.04 -9999 0 -0.86 1 1
HRAS/GDP -0.34 0.13 -9999 0 -0.83 9 9
FRAP1 -0.35 0.13 -9999 0 -0.86 9 9
EGF/EGFR dimer -0.52 0.19 -9999 0 -0.58 433 433
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.028 0.13 -9999 0 -0.66 20 20
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.016 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.26 0.27 -9999 0 -0.53 230 230
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.065 0.068 -9999 0 -10000 0 0
AURKB -0.4 0.44 -9999 0 -0.86 229 229
AURKC 0.014 0.04 -9999 0 -0.86 1 1
Glypican 2 network

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
MDK -0.052 0.24 -9999 0 -0.86 37 37
GPC2 -0.083 0.28 -9999 0 -0.86 54 54
GPC2/Midkine -0.12 0.29 -9999 0 -0.74 80 80
neuron projection morphogenesis -0.12 0.29 -9999 0 -0.74 80 80
Caspase cascade in apoptosis

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
TOP1 -0.13 0.27 -10000 0 -0.58 102 102
ACTA1 -0.19 0.36 -10000 0 -0.68 155 155
NUMA1 -0.13 0.27 -10000 0 -0.58 103 103
SPTAN1 -0.19 0.36 -10000 0 -0.68 154 154
LIMK1 -0.19 0.36 -10000 0 -0.68 153 153
BIRC3 -0.12 0.32 -10000 0 -0.86 74 74
BIRC2 0.011 0.007 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.28 0.47 -10000 0 -0.88 168 168
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0.007 -10000 0 -10000 0 0
PTK2 -0.13 0.27 -10000 0 -0.58 103 103
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.18 0.35 -10000 0 -0.66 154 154
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.19 0.36 -10000 0 -0.68 152 152
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.3 0.28 -10000 0 -0.54 263 263
BID -0.09 0.17 -10000 0 -0.37 100 100
MAP3K1 -0.043 0.11 -10000 0 -0.22 73 73
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.19 0.36 -10000 0 -0.68 154 154
CASP9 0.016 0.001 -10000 0 -10000 0 0
DNA repair 0.012 0.095 -10000 0 -0.21 33 33
neuron apoptosis 0.011 0.046 -10000 0 -0.62 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.17 0.35 -10000 0 -0.77 100 100
APAF1 0.016 0.001 -10000 0 -10000 0 0
CASP6 -0.05 0.16 -10000 0 -0.52 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.17 0.35 -10000 0 -0.77 100 100
CASP7 0.051 0.13 0.34 74 -10000 0 74
KRT18 -0.002 0.047 -10000 0 -0.3 2 2
apoptosis -0.17 0.33 -10000 0 -0.7 104 104
DFFA -0.19 0.36 -10000 0 -0.8 100 100
DFFB -0.19 0.36 -10000 0 -0.8 100 100
PARP1 -0.013 0.095 0.21 33 -10000 0 33
actin filament polymerization 0.16 0.33 0.72 100 -10000 0 100
TNF 0.002 0.11 -10000 0 -0.81 8 8
CYCS -0.068 0.13 -10000 0 -0.27 114 114
SATB1 -0.037 0.15 -10000 0 -0.48 3 3
SLK -0.19 0.36 -10000 0 -0.8 100 100
p15 BID/BAX -0.073 0.16 -10000 0 -10000 0 0
CASP2 0.031 0.09 -10000 0 -0.43 1 1
JNK cascade 0.043 0.11 0.22 73 -10000 0 73
CASP3 -0.21 0.38 -10000 0 -0.72 154 154
LMNB2 0.011 0.086 -10000 0 -0.41 3 3
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.016 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.081 0.19 -10000 0 -0.52 74 74
negative regulation of DNA binding -0.29 0.28 -10000 0 -0.54 263 263
stress fiber formation -0.18 0.35 -10000 0 -0.78 100 100
GZMB -0.33 0.51 -10000 0 -0.99 168 168
CASP1 0.023 0 -10000 0 -10000 0 0
LMNB1 0.008 0.091 -10000 0 -0.37 7 7
APP 0.011 0.046 -10000 0 -0.62 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.17 0.31 -10000 0 -0.67 106 106
LMNA 0.011 0.086 -10000 0 -0.39 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.03 0.074 -10000 0 -0.41 7 7
LRDD 0.003 0.1 -10000 0 -0.85 7 7
SREBF1 -0.19 0.36 -10000 0 -0.68 155 155
APAF-1/Caspase 9 -0.009 0.063 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.13 0.26 -10000 0 -0.52 130 130
CFL2 -0.17 0.34 -10000 0 -0.75 100 100
GAS2 -0.2 0.36 -10000 0 -0.68 158 158
positive regulation of apoptosis 0.015 0.087 -10000 0 -0.4 3 3
PRF1 -0.22 0.39 -10000 0 -0.86 126 126
Syndecan-1-mediated signaling events

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
TGFB1 0.007 0.089 -9999 0 -0.86 5 5
CCL5 -0.36 0.44 -9999 0 -0.86 206 206
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.21 0.23 -9999 0 -0.59 79 79
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 -0.2 0.22 -9999 0 -0.56 79 79
Syndecan-1/Syntenin -0.19 0.22 -9999 0 -0.56 79 79
MAPK3 -0.16 0.2 -9999 0 -0.54 46 46
HGF/MET -0.034 0.15 -9999 0 -0.67 24 24
TGFB1/TGF beta receptor Type II 0.007 0.089 -9999 0 -0.86 5 5
BSG 0.016 0 -9999 0 -10000 0 0
keratinocyte migration -0.19 0.21 -9999 0 -0.55 79 79
Syndecan-1/RANTES -0.41 0.34 -9999 0 -0.69 250 250
Syndecan-1/CD147 -0.2 0.18 -9999 0 -0.53 79 79
Syndecan-1/Syntenin/PIP2 -0.21 0.19 -9999 0 -0.54 79 79
LAMA5 0.014 0.035 -9999 0 -0.76 1 1
positive regulation of cell-cell adhesion -0.2 0.18 -9999 0 -0.53 79 79
MMP7 -0.12 0.3 -9999 0 -0.77 83 83
HGF -0.021 0.17 -9999 0 -0.81 21 21
Syndecan-1/CASK -0.2 0.22 -9999 0 -0.57 79 79
Syndecan-1/HGF/MET -0.22 0.22 -9999 0 -0.58 94 94
regulation of cell adhesion -0.14 0.19 -9999 0 -0.67 13 13
HPSE 0.012 0.05 -9999 0 -0.76 2 2
positive regulation of cell migration -0.21 0.23 -9999 0 -0.59 79 79
SDC1 -0.22 0.23 -9999 0 -0.6 79 79
Syndecan-1/Collagen -0.21 0.23 -9999 0 -0.59 79 79
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.089 -9999 0 -0.86 5 5
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.39 0.44 -9999 0 -0.86 223 223
MAPK1 -0.16 0.2 -9999 0 -0.7 13 13
homophilic cell adhesion -0.21 0.22 -9999 0 -0.59 79 79
MMP1 -0.15 0.34 -9999 0 -0.83 95 95
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.027 0.083 -10000 0 -0.73 6 6
oxygen homeostasis -0.001 0.015 -10000 0 -10000 0 0
TCEB2 0.014 0.035 -10000 0 -0.76 1 1
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.23 0.14 -10000 0 -0.59 2 2
EPO -0.4 0.41 -10000 0 -0.83 183 183
FIH (dimer) 0.014 0.02 -10000 0 -10000 0 0
APEX1 0.013 0.014 -10000 0 -10000 0 0
SERPINE1 -0.34 0.4 -10000 0 -0.92 102 102
FLT1 -0.017 0.073 -10000 0 -0.76 4 4
ADORA2A -0.3 0.34 -10000 0 -0.82 68 68
germ cell development -0.4 0.44 -10000 0 -0.89 183 183
SLC11A2 -0.28 0.34 -10000 0 -0.81 68 68
BHLHE40 -0.28 0.34 -10000 0 -0.81 68 68
HIF1AN 0.014 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.3 0.22 -10000 0 -0.52 200 200
ETS1 0.037 0.004 -10000 0 -10000 0 0
CITED2 -0.02 0.024 -10000 0 -10000 0 0
KDR -0.014 0.068 -10000 0 -1.4 1 1
PGK1 -0.28 0.34 -10000 0 -0.81 68 68
SIRT1 0.012 0.007 -10000 0 -10000 0 0
response to hypoxia -0.002 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.34 0.41 -10000 0 -0.99 74 74
EPAS1 -0.27 0.19 -10000 0 -0.44 202 202
SP1 0.026 0.005 -10000 0 -10000 0 0
ABCG2 -0.29 0.34 -10000 0 -0.81 69 69
EFNA1 -0.29 0.34 -10000 0 -0.81 69 69
FXN -0.3 0.34 -10000 0 -0.82 68 68
POU5F1 -0.42 0.47 -10000 0 -0.95 183 183
neuron apoptosis 0.33 0.39 0.94 74 -10000 0 74
EP300 0.016 0 -10000 0 -10000 0 0
EGLN3 -0.76 0.29 -10000 0 -0.87 424 424
EGLN2 0.011 0.016 -10000 0 -10000 0 0
EGLN1 0.014 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.001 0.022 -10000 0 -0.48 1 1
VHL 0.016 0 -10000 0 -10000 0 0
ARNT 0.013 0.014 -10000 0 -10000 0 0
SLC2A1 -0.31 0.36 -10000 0 -0.89 74 74
TWIST1 -0.3 0.34 -10000 0 -0.83 71 71
ELK1 0.026 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.26 0.2 -10000 0 -0.54 75 75
VEGFA -0.46 0.48 -10000 0 -0.93 221 221
CREBBP 0.016 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.008 0.14 -9999 0 -0.79 14 14
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.014 0.035 -9999 0 -0.76 1 1
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 -0.08 0.045 -9999 0 -10000 0 0
HIF1A -0.098 0.036 -9999 0 -10000 0 0
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.018 -9999 0 -10000 0 0
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.83 0.16 -9999 0 -0.86 463 463
ARNT/IPAS -0.017 0.1 -9999 0 -0.6 14 14
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.014 0.04 -9999 0 -0.86 1 1
HIF1A/ARNT -0.08 0.045 -9999 0 -10000 0 0
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.002 0.034 -9999 0 -0.53 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.08 0.045 -9999 0 -10000 0 0
PHD1-3/OS9 -0.46 0.17 -9999 0 -0.52 424 424
HIF1A/RACK1/Elongin B/Elongin C -0.065 0.036 -9999 0 -0.5 2 2
VHL 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.08 0.045 -9999 0 -10000 0 0
EGLN3 -0.76 0.28 -9999 0 -0.86 424 424
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.001 0.013 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.56 0.11 -9999 0 -0.57 463 463
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.6 0.32 -9999 0 -0.87 253 253
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.12 0.32 -9999 0 -0.85 78 78
SMAD9 -0.064 0.084 -9999 0 -0.58 9 9
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.18 0.17 -9999 0 -0.52 17 17
BMP7/USAG1 -0.7 0.35 -9999 0 -0.81 416 416
SMAD5/SKI -0.17 0.16 -9999 0 -0.5 13 13
SMAD1 0.002 0.042 -9999 0 -10000 0 0
BMP2 0.009 0.073 -9999 0 -0.78 4 4
SMAD1/SMAD1/SMAD4 0 0 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.51 0.36 -9999 0 -0.76 328 328
BMPR1A-1B/BAMBI -0.34 0.23 -9999 0 -0.49 330 330
AHSG -0.009 0.12 -9999 0 -0.86 9 9
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.005 0.052 -9999 0 -0.52 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.11 -9999 0 -0.5 17 17
BMP2-4 (homodimer) -0.006 0.06 -9999 0 -0.59 5 5
RGMB 0.012 0.057 -9999 0 -0.86 2 2
BMP6/BMPR2/BMPR1A-1B -0.3 0.2 -9999 0 -0.52 1 1
RGMA 0.008 0.079 -9999 0 -0.76 5 5
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.17 0.14 -9999 0 -0.57 17 17
BMP2-4/USAG1 -0.31 0.24 -9999 0 -0.88 5 5
SMAD6/SMURF1/SMAD5 -0.17 0.16 -9999 0 -0.5 13 13
SOSTDC1 -0.48 0.37 -9999 0 -0.76 305 305
BMP7/BMPR2/BMPR1A-1B -0.59 0.31 -9999 0 -0.87 235 235
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.009 0.07 -9999 0 -0.76 4 4
HFE2 -0.017 0.16 -9999 0 -0.86 16 16
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.016 0.094 -9999 0 -0.54 14 14
SMAD5/SMAD5/SMAD4 -0.17 0.16 -9999 0 -0.5 13 13
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.1 -9999 0 -0.51 13 13
BMP7 (homodimer) -0.51 0.36 -9999 0 -0.76 323 323
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.017 0.1 -9999 0 -0.64 13 13
SMAD1/SKI 0.012 0.039 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.016 0.093 -9999 0 -0.55 14 14
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.18 0.34 -9999 0 -0.77 118 118
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.39 0.26 -9999 0 -0.57 328 328
CHRDL1 -0.39 0.38 -9999 0 -0.76 253 253
ENDOFIN/SMAD1 0.012 0.039 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.005 0.003 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI 0.008 0.079 -9999 0 -0.76 5 5
SMURF2 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.26 0.25 -9999 0 -0.49 255 255
BMP2-4/GREM1 -0.13 0.22 -9999 0 -0.5 121 121
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.037 0.089 -9999 0 -0.54 9 9
SMAD1/SMAD6 0.012 0.039 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.51 0.36 -9999 0 -0.76 323 323
BMP6 0.009 0.07 -9999 0 -0.76 4 4
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.13 -9999 0 -0.46 17 17
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.012 0.039 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.21 0.18 -9999 0 -0.6 56 56
CHRD -0.001 0.12 -9999 0 -0.79 10 10
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.17 0.13 -9999 0 -0.58 17 17
BMP4 0.014 0.035 -9999 0 -0.76 1 1
FST -0.072 0.25 -9999 0 -0.78 53 53
BMP2-4/NOG -0.096 0.21 -9999 0 -0.56 82 82
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.56 0.29 -9999 0 -0.83 235 235
IL23-mediated signaling events

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
CCL2 -0.26 0.48 -10000 0 -1.1 44 44
IL23A -0.24 0.48 -10000 0 -1.1 38 38
NF kappa B1 p50/RelA/I kappa B alpha -0.33 0.39 -10000 0 -1.1 63 63
positive regulation of T cell mediated cytotoxicity -0.29 0.53 -10000 0 -1.2 66 66
ITGA3 -0.25 0.47 -10000 0 -1.1 40 40
IL17F -0.15 0.35 -10000 0 -0.77 23 23
IL12B -0.088 0.3 -10000 0 -0.89 57 57
STAT1 (dimer) -0.29 0.5 -10000 0 -1.2 64 64
CD4 -0.26 0.48 -10000 0 -1.1 56 56
IL23 -0.28 0.49 -10000 0 -1.2 55 55
IL23R -0.012 0.15 -10000 0 -0.8 9 9
IL1B -0.26 0.49 -10000 0 -1.2 43 43
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.25 0.48 -10000 0 -1.1 43 43
TYK2 0.016 0.025 -10000 0 -10000 0 0
STAT4 -0.039 0.21 -10000 0 -0.86 30 30
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.26 0.41 -10000 0 -0.88 143 143
IL12RB1 -0.27 0.43 -10000 0 -0.89 152 152
PIK3CA 0.016 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.21 0.34 -10000 0 -0.7 152 152
IL23R/JAK2 -0.011 0.16 -10000 0 -0.79 8 8
positive regulation of chronic inflammatory response -0.29 0.53 -10000 0 -1.2 66 66
natural killer cell activation 0.002 0.012 0.063 9 -10000 0 9
JAK2 0.021 0.035 -10000 0 -10000 0 0
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
NFKB1 0.01 0.009 -10000 0 -10000 0 0
RELA 0.01 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.27 0.47 -10000 0 -1.1 55 55
ALOX12B -0.31 0.51 -10000 0 -1.1 69 69
CXCL1 -0.3 0.53 -10000 0 -1.3 58 58
T cell proliferation -0.29 0.53 -10000 0 -1.2 66 66
NFKBIA 0.01 0.009 -10000 0 -10000 0 0
IL17A -0.1 0.29 -10000 0 -10000 0 0
PI3K -0.34 0.4 -10000 0 -1.1 68 68
IFNG -0.054 0.069 0.14 3 -0.12 205 208
STAT3 (dimer) -0.32 0.38 -10000 0 -1.1 63 63
IL18R1 -0.003 0.1 -10000 0 -0.82 7 7
IL23/IL23R/JAK2/TYK2/SOCS3 -0.19 0.38 -10000 0 -0.87 56 56
IL18/IL18R -0.2 0.29 -10000 0 -0.62 153 153
macrophage activation -0.017 0.018 -10000 0 -0.045 6 6
TNF -0.26 0.49 -10000 0 -1.2 44 44
STAT3/STAT4 -0.37 0.44 -10000 0 -1.2 77 77
STAT4 (dimer) -0.32 0.54 -10000 0 -1.2 74 74
IL18 -0.002 0.097 -10000 0 -0.86 6 6
IL19 -0.26 0.47 -10000 0 -1.1 43 43
STAT5A (dimer) -0.29 0.5 -10000 0 -1.2 65 65
STAT1 0.014 0.04 -10000 0 -0.86 1 1
SOCS3 0.012 0.057 -10000 0 -0.86 2 2
CXCL9 -0.41 0.6 -10000 0 -1.1 149 149
MPO -0.26 0.48 -10000 0 -1.1 61 61
positive regulation of humoral immune response -0.29 0.53 -10000 0 -1.2 66 66
IL23/IL23R/JAK2/TYK2 -0.31 0.55 -10000 0 -1.3 65 65
IL6 -0.3 0.53 -10000 0 -1.2 69 69
STAT5A 0.016 0 -10000 0 -10000 0 0
IL2 -0.017 0.12 -10000 0 -0.86 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.063 9 -10000 0 9
CD3E -0.4 0.6 -10000 0 -1.2 146 146
keratinocyte proliferation -0.29 0.53 -10000 0 -1.2 66 66
NOS2 -0.26 0.48 -10000 0 -1.1 61 61
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.25 0.26 -10000 0 -0.75 31 31
IHH -0.1 0.24 -10000 0 -0.83 45 45
SHH Np/Cholesterol/GAS1 -0.038 0.13 -10000 0 -0.46 39 39
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.037 0.13 0.46 39 -10000 0 39
SMO/beta Arrestin2 -0.15 0.16 -10000 0 -0.61 32 32
SMO -0.14 0.19 -10000 0 -0.64 32 32
AKT1 -0.042 0.091 -10000 0 -10000 0 0
ARRB2 0.014 0.04 -10000 0 -0.86 1 1
BOC 0.016 0 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.14 0.19 -10000 0 -0.63 32 32
STIL -0.098 0.17 -10000 0 -0.68 10 10
DHH N/PTCH2 -0.045 0.16 -10000 0 -0.64 34 34
DHH N/PTCH1 -0.16 0.16 -10000 0 -0.63 35 35
PIK3CA 0.016 0 -10000 0 -10000 0 0
DHH -0.001 0.11 -10000 0 -0.76 10 10
PTHLH -0.45 0.41 -10000 0 -0.74 301 301
determination of left/right symmetry -0.14 0.19 -10000 0 -0.63 32 32
PIK3R1 0.016 0 -10000 0 -10000 0 0
skeletal system development -0.44 0.4 -10000 0 -0.74 301 301
IHH N/Hhip -0.21 0.32 -10000 0 -0.66 149 149
DHH N/Hhip -0.16 0.26 -10000 0 -0.59 127 127
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.14 0.19 -10000 0 -0.63 32 32
pancreas development -0.18 0.34 -10000 0 -0.77 119 119
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.033 0.19 -10000 0 -0.76 30 30
somite specification -0.14 0.19 -10000 0 -0.63 32 32
SHH Np/Cholesterol/PTCH1 -0.14 0.15 -10000 0 -0.68 10 10
SHH Np/Cholesterol/PTCH2 -0.036 0.13 -10000 0 -0.51 34 34
SHH Np/Cholesterol/Megalin -0.048 0.15 -10000 0 -0.5 46 46
SHH 0.018 0.087 -10000 0 -0.58 10 10
catabolic process -0.16 0.2 -10000 0 -0.66 31 31
SMO/Vitamin D3 -0.14 0.15 -10000 0 -0.59 35 35
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.47 125 125
LRP2 -0.05 0.22 -10000 0 -0.76 41 41
receptor-mediated endocytosis -0.16 0.18 -10000 0 -0.78 19 19
SHH Np/Cholesterol/BOC -0.009 0.065 -10000 0 -0.46 10 10
SHH Np/Cholesterol/CDO -0.072 0.18 -10000 0 -0.53 65 65
mesenchymal cell differentiation 0.12 0.21 0.46 125 -10000 0 125
mol:Vitamin D3 -0.11 0.18 -10000 0 -0.68 10 10
IHH N/PTCH2 -0.087 0.22 -10000 0 -0.62 67 67
CDON -0.087 0.28 -10000 0 -0.86 56 56
IHH N/PTCH1 -0.16 0.2 -10000 0 -0.67 31 31
Megalin/LRPAP1 -0.049 0.16 -10000 0 -0.57 41 41
PTCH2 -0.028 0.19 -10000 0 -0.86 24 24
SHH Np/Cholesterol -0.01 0.067 -10000 0 -0.47 10 10
PTCH1 -0.16 0.2 -10000 0 -0.66 31 31
HHIP -0.18 0.34 -10000 0 -0.77 119 119
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.016 0 -9999 0 -10000 0 0
LAT2 -0.17 0.24 -9999 0 -0.71 62 62
AP1 -0.16 0.21 -9999 0 -0.57 78 78
mol:PIP3 -0.24 0.34 -9999 0 -0.72 134 134
IKBKB -0.093 0.17 -9999 0 -0.34 75 75
AKT1 -0.18 0.22 -9999 0 -0.73 23 23
IKBKG -0.093 0.17 -9999 0 -0.35 72 72
MS4A2 -0.18 0.36 -9999 0 -0.86 102 102
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.008 -9999 0 -10000 0 0
MAP3K1 -0.13 0.27 -9999 0 -0.58 95 95
mol:Ca2+ -0.17 0.24 -9999 0 -0.5 127 127
LYN 0.011 0.009 -9999 0 -10000 0 0
CBLB -0.12 0.16 -9999 0 -0.54 24 24
SHC1 0.014 0.04 -9999 0 -0.86 1 1
RasGAP/p62DOK -0.001 0.024 -9999 0 -0.53 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.008 0.08 -9999 0 -0.86 4 4
PLD2 -0.19 0.29 -9999 0 -0.92 23 23
PTPN13 -0.076 0.16 -9999 0 -0.5 14 14
PTPN11 0.014 0.007 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.051 0.17 -9999 0 -0.4 12 12
SYK 0.007 0.051 -9999 0 -0.77 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.31 0.32 -9999 0 -0.77 137 137
LAT -0.27 0.3 -9999 0 -0.66 155 155
PAK2 -0.16 0.3 -9999 0 -0.64 110 110
NFATC2 -0.07 0.085 -9999 0 -0.64 1 1
HRAS -0.19 0.33 -9999 0 -0.71 118 118
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B 0.042 0.027 -9999 0 -10000 0 0
Fc epsilon R1 -0.27 0.33 -9999 0 -0.63 207 207
Antigen/IgE/Fc epsilon R1 -0.26 0.31 -9999 0 -0.59 207 207
mol:GDP -0.22 0.36 -9999 0 -0.78 125 125
JUN 0.016 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.008 -9999 0 -10000 0 0
FOS 0 0.11 -9999 0 -0.76 10 10
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.14 0.17 -9999 0 -0.58 24 24
CHUK -0.093 0.17 -9999 0 -0.34 76 76
KLRG1 -0.13 0.16 -9999 0 -0.55 24 24
VAV1 -0.24 0.31 -9999 0 -0.71 131 131
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.12 0.16 -9999 0 -0.54 24 24
negative regulation of mast cell degranulation -0.12 0.16 -9999 0 -0.55 26 26
BTK -0.19 0.24 -9999 0 -0.63 92 92
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.18 0.22 -9999 0 -0.58 86 86
GAB2/PI3K/SHP2 -0.2 0.24 -9999 0 -0.83 23 23
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.13 0.16 -9999 0 -0.56 24 24
RAF1 0.028 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.33 0.4 -9999 0 -1.1 86 86
FCER1G -0.19 0.37 -9999 0 -0.87 107 107
FCER1A -0.025 0.16 -9999 0 -0.78 21 21
Antigen/IgE/Fc epsilon R1/Fyn -0.24 0.29 -9999 0 -0.56 195 195
MAPK3 0.041 0.026 -9999 0 -10000 0 0
MAPK1 0.041 0.026 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.012 0.072 -9999 0 -10000 0 0
DUSP1 0.014 0.04 -9999 0 -0.86 1 1
NF-kappa-B/RelA -0.072 0.075 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.082 0.16 -9999 0 -0.48 23 23
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.23 0.3 -9999 0 -0.74 110 110
FER -0.12 0.16 -9999 0 -0.55 25 25
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.16 0.2 -9999 0 -0.43 159 159
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.21 0.37 -9999 0 -0.77 126 126
cytokine secretion -0.053 0.054 -9999 0 -10000 0 0
SPHK1 -0.16 0.22 -9999 0 -0.66 57 57
PTK2 -0.086 0.17 -9999 0 -0.5 23 23
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.26 0.32 -9999 0 -0.77 112 112
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.2 0.32 -9999 0 -0.68 110 110
MAP2K2 0.036 0.032 -9999 0 -0.43 1 1
MAP2K1 0.037 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.12 0.15 -9999 0 -0.53 24 24
MAP2K4 0.017 0.016 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.35 0.42 -9999 0 -0.74 221 221
mol:Choline -0.19 0.29 -9999 0 -0.89 23 23
SHC/Grb2/SOS1 -0.11 0.14 -9999 0 -0.51 19 19
FYN 0.016 0 -9999 0 -10000 0 0
DOK1 0.016 0 -9999 0 -10000 0 0
PXN -0.07 0.16 -9999 0 -0.48 11 11
HCLS1 -0.14 0.19 -9999 0 -0.66 32 32
PRKCB -0.15 0.23 -9999 0 -0.49 108 108
FCGR2B -0.16 0.35 -9999 0 -0.86 97 97
IGHE -0.006 0.011 -9999 0 -10000 0 0
KLRG1/SHIP -0.12 0.16 -9999 0 -0.57 26 26
LCP2 -0.044 0.22 -9999 0 -0.87 32 32
PLA2G4A -0.13 0.16 -9999 0 -0.55 26 26
RASA1 0.016 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.19 0.29 -9999 0 -0.89 23 23
IKK complex -0.051 0.13 -9999 0 -0.29 1 1
WIPF1 0.016 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.008 0.09 -10000 0 -0.86 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.074 0.2 0.61 29 -0.44 3 32
IL27/IL27R/JAK1 -0.079 0.35 0.58 1 -0.86 51 52
TBX21 -0.21 0.41 0.5 1 -0.76 143 144
IL12B -0.096 0.28 -10000 0 -0.87 57 57
IL12A 0.008 0.033 -10000 0 -0.69 1 1
IL6ST -0.005 0.11 -10000 0 -0.77 10 10
IL27RA/JAK1 0.009 0.063 -10000 0 -0.7 1 1
IL27 -0.044 0.21 -10000 0 -0.88 29 29
TYK2 0.011 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.024 0.13 -10000 0 -0.74 2 2
T-helper 2 cell differentiation 0.074 0.2 0.61 29 -0.44 3 32
T cell proliferation during immune response 0.074 0.2 0.61 29 -0.44 3 32
MAPKKK cascade -0.074 0.2 0.44 3 -0.61 29 32
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.015 0.041 -10000 0 -0.87 1 1
IL12RB1 -0.27 0.41 -10000 0 -0.87 152 152
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.16 0.35 0.5 1 -0.71 90 91
IL27/IL27R/JAK2/TYK2 -0.076 0.2 0.44 3 -0.62 29 32
positive regulation of T cell mediated cytotoxicity -0.074 0.2 0.44 3 -0.61 29 32
STAT1 (dimer) -0.062 0.5 0.54 108 -0.98 64 172
JAK2 0.011 0.012 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.079 0.18 0.39 3 -0.63 21 24
T cell proliferation -0.12 0.25 0.4 1 -0.7 47 48
IL12/IL12R/TYK2/JAK2 -0.18 0.27 -10000 0 -0.76 43 43
IL17A -0.024 0.13 -10000 0 -0.74 2 2
mast cell activation 0.074 0.2 0.61 29 -0.44 3 32
IFNG -0.041 0.066 0.13 3 -0.11 220 223
T cell differentiation -0.011 0.011 0.03 3 -0.026 131 134
STAT3 (dimer) -0.079 0.18 0.39 3 -0.63 21 24
STAT5A (dimer) -0.079 0.18 0.39 3 -0.62 22 25
STAT4 (dimer) -0.11 0.24 0.39 2 -0.76 42 44
STAT4 -0.039 0.21 -10000 0 -0.86 30 30
T cell activation -0.012 0.007 0.1 1 -10000 0 1
IL27R/JAK2/TYK2 -0.037 0.094 -10000 0 -0.71 1 1
GATA3 -0.61 0.69 -10000 0 -1.3 230 230
IL18 0.005 0.077 -10000 0 -0.68 6 6
positive regulation of mast cell cytokine production -0.078 0.17 0.38 3 -0.62 21 24
IL27/EBI3 -0.13 0.33 -10000 0 -0.83 80 80
IL27RA -0.003 0.065 -10000 0 -0.76 1 1
IL6 -0.087 0.28 -10000 0 -0.83 59 59
STAT5A 0.016 0 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0 0.091 -10000 0 -0.6 10 10
IL1B 0.009 0.061 -10000 0 -0.66 4 4
EBI3 -0.12 0.32 -10000 0 -0.88 71 71
TNF 0.003 0.083 -10000 0 -0.63 8 8
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.19 0.36 -10000 0 -1.1 67 67
NFATC2 -0.081 0.23 -10000 0 -0.76 11 11
NFATC3 -0.023 0.064 -10000 0 -10000 0 0
CD40LG -0.25 0.46 -10000 0 -1.1 62 62
ITCH 0.054 0.059 -10000 0 -10000 0 0
CBLB 0.054 0.059 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.55 0.57 -10000 0 -1.1 206 206
JUNB 0.013 0.05 -10000 0 -0.76 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.012 0.059 -10000 0 -10000 0 0
T cell anergy 0.024 0.094 -10000 0 -10000 0 0
TLE4 -0.031 0.17 -10000 0 -0.83 3 3
Jun/NFAT1-c-4/p21SNFT -0.24 0.28 -10000 0 -0.94 32 32
AP-1/NFAT1-c-4 -0.31 0.37 -10000 0 -1.1 49 49
IKZF1 -0.14 0.37 -10000 0 -0.89 89 89
T-helper 2 cell differentiation -0.35 0.28 -10000 0 -0.73 103 103
AP-1/NFAT1 -0.094 0.16 -10000 0 -0.88 4 4
CALM1 0.028 0.037 -10000 0 -10000 0 0
EGR2 -0.11 0.28 -10000 0 -1.4 7 7
EGR3 -0.11 0.28 -10000 0 -1.5 6 6
NFAT1/FOXP3 -0.29 0.41 -10000 0 -0.94 111 111
EGR1 0.006 0.093 -10000 0 -0.76 7 7
JUN 0.005 0.022 -10000 0 -10000 0 0
EGR4 0.007 0.069 -10000 0 -0.86 3 3
mol:Ca2+ 0.007 0.041 -10000 0 -10000 0 0
GBP3 -0.034 0.18 -10000 0 -0.84 5 5
FOSL1 -0.026 0.19 -10000 0 -0.86 23 23
NFAT1-c-4/MAF/IRF4 -0.28 0.36 -10000 0 -0.9 101 101
DGKA -0.034 0.18 -10000 0 -1.1 4 4
CREM 0.014 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.21 -10000 0 -1 6 6
CTLA4 -0.43 0.59 -10000 0 -1 216 216
NFAT1-c-4 (dimer)/EGR1 -0.17 0.23 -10000 0 -0.97 13 13
NFAT1-c-4 (dimer)/EGR4 -0.17 0.22 -10000 0 -0.98 10 10
FOS -0.011 0.11 -10000 0 -0.77 10 10
IFNG -0.5 0.52 -10000 0 -1 215 215
T cell activation -0.052 0.22 -10000 0 -0.86 12 12
MAF 0.016 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.067 0.2 0.91 3 -10000 0 3
TNF -0.097 0.27 -10000 0 -1.1 11 11
FASLG -0.35 0.47 -10000 0 -0.95 67 67
TBX21 -0.3 0.44 -10000 0 -0.93 156 156
BATF3 -0.058 0.24 -10000 0 -0.86 40 40
PRKCQ -0.032 0.12 -10000 0 -0.76 12 12
PTPN1 -0.031 0.17 -10000 0 -0.76 4 4
NFAT1-c-4/ICER1 -0.17 0.21 -10000 0 -0.93 9 9
GATA3 -0.35 0.39 -10000 0 -0.76 230 230
T-helper 1 cell differentiation -0.49 0.5 -10000 0 -1 215 215
IL2RA -0.39 0.46 -10000 0 -1.1 120 120
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.031 0.17 -10000 0 -0.83 3 3
E2F1 -0.074 0.28 -10000 0 -0.86 54 54
PPARG 0.016 0.001 -10000 0 -10000 0 0
SLC3A2 -0.031 0.17 -10000 0 -0.83 3 3
IRF4 -0.19 0.37 -10000 0 -0.86 114 114
PTGS2 -0.22 0.4 -10000 0 -1.1 38 38
CSF2 -0.22 0.4 -10000 0 -1.1 35 35
JunB/Fra1/NFAT1-c-4 -0.18 0.22 -10000 0 -0.91 12 12
IL4 -0.36 0.29 -10000 0 -0.77 99 99
IL5 -0.21 0.38 -10000 0 -1 28 28
IL2 -0.053 0.22 -10000 0 -0.88 12 12
IL3 -0.051 0.049 -10000 0 -10000 0 0
RNF128 0.032 0.16 -10000 0 -0.8 18 18
NFATC1 -0.067 0.2 -10000 0 -0.91 3 3
CDK4 0.038 0.18 -10000 0 -10000 0 0
PTPRK -0.031 0.17 -10000 0 -0.83 3 3
IL8 -0.23 0.42 -10000 0 -1.1 40 40
POU2F1 0.016 0.003 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.008 0.069 -9999 0 -0.66 5 5
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.019 0.11 -9999 0 -0.67 14 14
STXBP1 0.014 0.035 -9999 0 -0.76 1 1
ACh/CHRNA1 -0.28 0.32 -9999 0 -0.63 212 212
RAB3GAP2/RIMS1/UNC13B -0.017 0.097 -9999 0 -0.58 14 14
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.014 0.15 -9999 0 -0.86 14 14
mol:ACh -0.008 0.053 -9999 0 -0.13 71 71
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.037 0.099 -9999 0 -0.62 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.28 0.31 -9999 0 -0.63 212 212
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.37 0.44 -9999 0 -0.86 212 212
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.088 0.21 -9999 0 -0.54 81 81
SNAP25 -0.038 0.12 -9999 0 -0.33 68 68
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.12 0.29 -9999 0 -0.76 81 81
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.007 0.062 -9999 0 -0.56 6 6
STX1A/SNAP25 fragment 1/VAMP2 -0.037 0.099 -9999 0 -0.62 4 4
Ephrin A reverse signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.057 0.17 -9999 0 -0.54 51 51
EFNA5 -0.057 0.23 -9999 0 -0.76 45 45
FYN -0.027 0.16 -9999 0 -0.49 51 51
neuron projection morphogenesis -0.057 0.17 -9999 0 -0.54 51 51
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.058 0.17 -9999 0 -0.54 51 51
EPHA5 -0.009 0.11 -9999 0 -0.86 8 8
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.015 0.047 -9999 0 -10000 0 0
NFATC2 -0.016 0.055 -9999 0 -0.63 1 1
NFATC3 -0.015 0.047 -9999 0 -10000 0 0
CD40LG -0.32 0.43 -9999 0 -0.95 100 100
PTGS2 -0.3 0.39 -9999 0 -0.86 95 95
JUNB 0.012 0.05 -9999 0 -0.76 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.021 0.018 -9999 0 -10000 0 0
CaM/Ca2+ -0.021 0.018 -9999 0 -10000 0 0
CALM1 0.005 0.013 -9999 0 -10000 0 0
JUN 0.006 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.021 0.019 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.002 0.003 -9999 0 -10000 0 0
FOSL1 -0.026 0.19 -9999 0 -0.86 23 23
CREM 0.015 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.19 0.2 -9999 0 -0.75 32 32
FOS -0.011 0.11 -9999 0 -0.77 10 10
IFNG -0.45 0.52 -9999 0 -0.99 211 211
AP-1/NFAT1-c-4 -0.42 0.41 -9999 0 -1.1 94 94
FASLG -0.48 0.52 -9999 0 -0.99 216 216
NFAT1-c-4/ICER1 -0.081 0.075 -9999 0 -0.56 1 1
IL2RA -0.35 0.45 -9999 0 -0.99 105 105
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.3 0.39 -9999 0 -0.86 91 91
JunB/Fra1/NFAT1-c-4 -0.095 0.12 -9999 0 -0.58 17 17
IL4 -0.29 0.37 -9999 0 -0.83 89 89
IL2 -0.013 0.11 -9999 0 -0.77 10 10
IL3 -0.029 0.026 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.058 0.24 -9999 0 -0.86 40 40
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.003 -9999 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.004 0.045 -9999 0 -0.5 4 4
ARNO/beta Arrestin1-2 -0.017 0.061 -9999 0 -10000 0 0
EGFR -0.001 0.12 -9999 0 -0.85 9 9
EPHA2 0.014 0.035 -9999 0 -0.76 1 1
USP6 0.014 0.04 -9999 0 -0.86 1 1
IQSEC1 0.015 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.52 0.19 -9999 0 -0.58 433 433
ARRB2 -0.012 0.1 -9999 0 -0.39 33 33
mol:GTP -0.011 0.048 -9999 0 -0.24 2 2
ARRB1 0.016 0 -9999 0 -10000 0 0
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.089 0.28 -9999 0 -0.86 57 57
EGF -0.68 0.23 -9999 0 -0.76 432 432
somatostatin receptor activity 0 0 -9999 0 -0.001 11 11
ARAP2 0.014 0.035 -9999 0 -0.76 1 1
mol:GDP -0.056 0.094 -9999 0 -0.36 17 17
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 5 5
ITGA2B -0.012 0.15 -9999 0 -0.86 15 15
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.002 0.031 -9999 0 -0.52 1 1
ADAP1 0.009 0.07 -9999 0 -0.76 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.034 0.15 -9999 0 -0.67 24 24
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.086 0.09 -9999 0 -0.35 17 17
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.45 0.16 -9999 0 -0.5 433 433
ADRB2 0.012 0.05 -9999 0 -0.76 2 2
receptor agonist activity 0 0 -9999 0 0 12 12
actin filament binding 0 0 -9999 0 -0.001 13 13
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 0.014 0.035 -9999 0 -0.76 1 1
GNAQ 0.015 0.003 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 10 10
ARF6/GDP -0.068 0.14 -9999 0 -0.39 5 5
ARF6/GDP/GULP/ACAP1 -0.23 0.26 -9999 0 -0.54 183 183
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.017 0.092 -9999 0 -0.52 14 14
ACAP1 -0.32 0.43 -9999 0 -0.86 184 184
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.041 0.15 -9999 0 -0.59 33 33
EFNA1 0.014 0.04 -9999 0 -0.86 1 1
HGF -0.021 0.17 -9999 0 -0.81 21 21
CYTH3 0.015 0 -9999 0 -10000 0 0
CYTH2 0.01 0.001 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 10 10
endosomal lumen acidification 0 0 -9999 0 -0.001 16 16
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.012 0.14 -9999 0 -0.76 17 17
GNAQ/ARNO 0.004 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 -10000 0 0
MET 0.006 0.089 -9999 0 -0.86 5 5
GNA14 0.004 0.093 -9999 0 -0.76 7 7
GNA15 -0.006 0.14 -9999 0 -0.86 12 12
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 11 11
GNA11 0.012 0.05 -9999 0 -0.76 2 2
LHCGR -0.052 0.22 -9999 0 -0.86 32 32
AGTR1 -0.026 0.18 -9999 0 -0.76 26 26
desensitization of G-protein coupled receptor protein signaling pathway -0.04 0.15 -9999 0 -0.59 33 33
IPCEF1/ARNO -0.35 0.13 -9999 0 -0.82 8 8
alphaIIb/beta3 Integrin -0.022 0.12 -9999 0 -0.66 16 16
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.001 0.026 -9999 0 -0.57 1 1
Necdin/E2F1 -0.078 0.22 -9999 0 -0.68 55 55
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.088 0.22 -9999 0 -0.98 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.28 0.32 -9999 0 -0.58 233 233
NT-4/5 (dimer)/p75(NTR) -0.06 0.19 -9999 0 -0.67 43 43
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.04 0.23 -9999 0 -0.55 74 74
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.11 0.31 -9999 0 -0.86 68 68
MGDIs/NGR/p75(NTR)/LINGO1 -0.077 0.21 -9999 0 -0.62 60 60
FURIN 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.13 0.26 -9999 0 -0.63 96 96
LINGO1 -0.021 0.18 -9999 0 -0.86 20 20
Sortilin/TRAF6/NRIF -0.001 0.015 -9999 0 -10000 0 0
proBDNF (dimer) -0.11 0.3 -9999 0 -0.86 68 68
NTRK1 -0.047 0.21 -9999 0 -0.76 38 38
RTN4R 0.003 0.1 -9999 0 -0.85 7 7
neuron apoptosis -0.073 0.24 -9999 0 -0.7 33 33
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.071 0.26 -9999 0 -0.65 76 76
ARHGDIA 0.014 0.035 -9999 0 -0.76 1 1
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.094 0.23 -9999 0 -0.6 74 74
MAGEH1 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.097 0.23 -9999 0 -0.6 75 75
Mammalian IAPs/DIABLO -0.081 0.19 -9999 0 -0.52 74 74
proNGF (dimer) -0.072 0.26 -9999 0 -0.86 48 48
MAGED1 0.014 0.04 -9999 0 -0.86 1 1
APP 0.014 0.035 -9999 0 -0.76 1 1
NT-4/5 (dimer) -0.004 0.089 -9999 0 -0.86 5 5
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.089 0.22 -9999 0 -0.56 74 74
NGF -0.072 0.26 -9999 0 -0.86 48 48
cell cycle arrest -0.022 0.27 -9999 0 -0.58 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.05 0.12 -9999 0 -0.57 11 11
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.052 0.17 -9999 0 -0.58 43 43
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.1 0.25 -9999 0 -0.65 75 75
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.054 0.24 -9999 0 -0.59 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.039 0.094 -9999 0 -0.44 11 11
p75(NTR)/beta APP -0.054 0.18 -9999 0 -0.66 39 39
BEX1 -0.27 0.37 -9999 0 -0.76 177 177
mol:GDP -0.082 0.26 -9999 0 -0.66 75 75
NGF (dimer) -0.36 0.31 -9999 0 -0.85 84 84
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.071 0.2 -9999 0 -0.57 60 60
PIK3R1 0.016 0 -9999 0 -10000 0 0
RAC1/GTP -0.09 0.22 -9999 0 -0.58 75 75
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.1 0.25 -9999 0 -0.65 75 75
RHOB 0.016 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.075 0.21 -9999 0 -0.67 54 54
NT3 (dimer) 0.006 0.09 -9999 0 -0.79 6 6
TP53 -0.051 0.24 -9999 0 -0.91 11 11
PRDM4 -0.055 0.24 -9999 0 -0.6 74 74
BDNF (dimer) -0.43 0.37 -9999 0 -0.89 134 134
PIK3CA 0.016 0 -9999 0 -10000 0 0
SORT1 0.014 0.035 -9999 0 -0.76 1 1
activation of caspase activity -0.087 0.21 -9999 0 -0.96 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.094 0.23 -9999 0 -0.6 74 74
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.032 0.22 -9999 0 -0.64 28 28
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.055 0.24 -9999 0 -0.6 74 74
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.1 0.25 -9999 0 -0.65 76 76
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.06 0.19 -9999 0 -0.66 44 44
MAPK8 -0.029 0.22 -9999 0 -0.64 27 27
MAPK9 -0.029 0.22 -9999 0 -0.64 27 27
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 0.006 0.09 -9999 0 -0.79 6 6
NTF4 -0.004 0.089 -9999 0 -0.86 5 5
NDN 0.011 0.061 -9999 0 -0.76 3 3
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.08 0.2 -9999 0 -0.91 11 11
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.02 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.1 0.24 -9999 0 -0.64 75 75
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.11 0.23 -9999 0 -0.98 11 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.12 0.24 -9999 0 -0.58 94 94
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.094 0.23 -9999 0 -0.66 68 68
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.32 -9999 0 -0.86 74 74
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.001 0.26 -9999 0 -0.56 58 58
BAD -0.018 0.21 -9999 0 -0.6 27 27
RIPK2 0.014 0.04 -9999 0 -0.86 1 1
NGFR -0.054 0.24 -9999 0 -0.86 38 38
CYCS -0.043 0.23 -9999 0 -0.97 11 11
ADAM17 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.094 0.23 -9999 0 -0.6 76 76
BCL2L11 -0.017 0.21 -9999 0 -0.6 27 27
BDNF (dimer)/p75(NTR) -0.14 0.3 -9999 0 -0.72 96 96
PI3K -0.093 0.23 -9999 0 -0.59 75 75
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.094 0.23 -9999 0 -0.6 74 74
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.12 0.28 -9999 0 -0.75 75 75
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.095 0.23 -9999 0 -0.6 75 75
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.061 -9999 0 -0.76 3 3
PLG -0.4 0.38 -9999 0 -0.76 256 256
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.14 0.25 -9999 0 -0.72 46 46
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.011 0.19 -9999 0 -0.54 27 27
E2F1 -0.083 0.28 -9999 0 -0.86 54 54
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.076 0.15 -9999 0 -0.6 14 14
NGF (dimer)/TRKA -0.11 0.24 -9999 0 -0.64 84 84
MMP7 -0.12 0.3 -9999 0 -0.77 83 83
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.088 0.22 -9999 0 -0.56 74 74
MMP3 -0.075 0.26 -9999 0 -0.86 46 46
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.69 13 13
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.006 0.062 -9999 0 -0.68 4 4
VEGFR1 homodimer/NRP1 -0.006 0.063 -9999 0 -0.69 4 4
mol:DAG -0.26 0.29 -9999 0 -0.97 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 -0.24 0.27 -9999 0 -0.54 216 216
CaM/Ca2+ -0.27 0.24 -9999 0 -0.92 4 4
HIF1A 0.023 0.032 -9999 0 -10000 0 0
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.22 0.2 -9999 0 -0.89 3 3
PLCG1 -0.27 0.29 -9999 0 -0.99 4 4
NOS3 -0.18 0.24 -9999 0 -0.87 3 3
CBL 0.016 0 -9999 0 -10000 0 0
mol:NO -0.17 0.23 -9999 0 -0.81 3 3
FLT1 0.034 0.074 -9999 0 -0.78 4 4
PGF -0.48 0.44 -9999 0 -0.86 268 268
VEGFR1 homodimer/NRP2/VEGFR121 -0.24 0.27 -9999 0 -1 6 6
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
eNOS/Hsp90 -0.16 0.23 -9999 0 -0.78 3 3
endothelial cell proliferation -0.2 0.25 -9999 0 -0.86 5 5
mol:Ca2+ -0.26 0.28 -9999 0 -0.95 4 4
MAPK3 -0.21 0.26 -9999 0 -0.94 3 3
MAPK1 -0.21 0.26 -9999 0 -0.94 3 3
PIK3R1 0.016 0 -9999 0 -10000 0 0
PLGF homodimer -0.48 0.44 -9999 0 -0.86 268 268
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.05 0.23 -9999 0 -0.86 36 36
VEGFA homodimer -0.38 0.44 -9999 0 -0.86 215 215
VEGFR1 homodimer/VEGFA homodimer -0.26 0.29 -9999 0 -0.58 216 216
platelet activating factor biosynthetic process -0.2 0.25 -9999 0 -0.9 3 3
PI3K -0.27 0.24 -9999 0 -0.94 4 4
PRKCA -0.24 0.27 -9999 0 -0.89 4 4
PRKCB -0.24 0.27 -9999 0 -0.92 6 6
VEGFR1 homodimer/PLGF homodimer -0.32 0.29 -9999 0 -0.58 269 269
VEGFA -0.38 0.44 -9999 0 -0.86 215 215
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.26 0.29 -9999 0 -0.97 4 4
RASA1 0.049 0.061 -9999 0 -0.62 4 4
NRP2 0.003 0.11 -9999 0 -0.86 7 7
VEGFR1 homodimer 0.034 0.074 -9999 0 -0.77 4 4
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.19 0.26 -9999 0 -0.81 28 28
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.27 0.24 -9999 0 -0.92 4 4
mol:L-citrulline -0.17 0.23 -9999 0 -0.81 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.22 0.25 -9999 0 -0.95 4 4
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.24 0.27 -9999 0 -1 4 4
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.25 0.23 -9999 0 -0.99 3 3
PDPK1 -0.22 0.26 -9999 0 -0.96 3 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.24 0.27 -9999 0 -1 4 4
mol:NADP -0.17 0.23 -9999 0 -0.81 3 3
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.22 0.24 -9999 0 -0.92 4 4
VEGFR1 homodimer/NRP2 -0.014 0.091 -9999 0 -0.61 11 11
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.022 0.18 -9999 0 -10000 0 0
CRKL -0.097 0.22 -9999 0 -10000 0 0
mol:DAG -0.13 0.17 -9999 0 -10000 0 0
HRAS -0.11 0.15 -9999 0 -10000 0 0
MAPK8 -0.14 0.26 -9999 0 -0.48 172 172
RAP1A -0.097 0.22 -9999 0 -10000 0 0
GAB1 -0.097 0.22 -9999 0 -10000 0 0
MAPK14 -0.14 0.26 -9999 0 -0.48 172 172
EPO -0.29 0.42 -9999 0 -0.85 172 172
PLCG1 -0.13 0.17 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.007 0.019 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.2 0.27 -9999 0 -0.55 172 172
GAB1/SHC/GRB2/SOS1 -0.12 0.16 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.23 0.32 -9999 0 -0.65 172 172
IRS2 -0.11 0.23 -9999 0 -0.74 3 3
STAT1 -0.068 0.21 -9999 0 -10000 0 0
STAT5B -0.073 0.21 -9999 0 -10000 0 0
cell proliferation -0.12 0.24 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.12 0.15 -9999 0 -0.71 1 1
TEC -0.097 0.22 -9999 0 -10000 0 0
SOCS3 0.012 0.057 -9999 0 -0.86 2 2
STAT1 (dimer) -0.066 0.21 -9999 0 -10000 0 0
JAK2 0.006 0.018 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.1 0.24 -9999 0 -0.43 172 172
EPO/EPOR -0.23 0.32 -9999 0 -0.65 172 172
LYN 0.018 0.001 -9999 0 -10000 0 0
TEC/VAV2 -0.084 0.22 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.019 -9999 0 -10000 0 0
SHC1 0.014 0.04 -9999 0 -0.86 1 1
EPO/EPOR (dimer)/LYN -0.16 0.28 -9999 0 -0.54 172 172
mol:IP3 -0.13 0.17 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.14 0.18 -9999 0 -0.79 3 3
SH2B3 0.006 0.018 -9999 0 -10000 0 0
NFKB1 -0.14 0.26 -9999 0 -0.48 172 172
EPO/EPOR (dimer)/JAK2/SOCS3 -0.11 0.15 -9999 0 -0.53 2 2
PTPN6 -0.11 0.23 -9999 0 -0.42 172 172
TEC/VAV2/GRB2 -0.13 0.17 -9999 0 -10000 0 0
EPOR 0.007 0.019 -9999 0 -10000 0 0
INPP5D 0.008 0.08 -9999 0 -0.86 4 4
mol:GDP -0.12 0.16 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.002 0.11 -9999 0 -0.82 8 8
CRKL/CBL/C3G -0.13 0.17 -9999 0 -10000 0 0
VAV2 -0.097 0.22 -9999 0 -10000 0 0
CBL -0.097 0.22 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.13 0.17 -9999 0 -10000 0 0
STAT5A -0.073 0.21 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.048 0.21 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.01 0.081 -9999 0 -0.63 8 8
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK -0.2 0.29 -9999 0 -0.87 28 28
BCL2 -0.022 0.18 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 215 215
PDGFRB 0.016 0.004 -9999 0 -10000 0 0
SPHK1 -0.031 0.1 -9999 0 -0.36 40 40
mol:S1P -0.024 0.095 -9999 0 -0.4 6 6
S1P1/S1P/Gi -0.047 0.14 -9999 0 -0.49 14 14
GNAO1 0.011 0.078 -9999 0 -0.84 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.055 0.088 -9999 0 -0.67 1 1
PLCG1 -0.028 0.13 -9999 0 -0.49 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.004 -9999 0 -10000 0 0
GNAI2 0.018 0.005 -9999 0 -10000 0 0
GNAI3 0.015 0.006 -9999 0 -10000 0 0
GNAI1 0.01 0.062 -9999 0 -0.76 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.25 0.3 -9999 0 -0.58 215 215
S1P1/S1P -0.21 0.21 -9999 0 -0.61 23 23
negative regulation of cAMP metabolic process -0.045 0.14 -9999 0 -0.48 14 14
MAPK3 -0.038 0.17 -9999 0 -0.57 24 24
calcium-dependent phospholipase C activity 0 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.013 0.035 -9999 0 -0.76 1 1
PLCB2 -0.2 0.26 -9999 0 -0.67 56 56
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.17 0.17 -9999 0 -0.5 22 22
receptor internalization -0.2 0.2 -9999 0 -0.4 217 217
PTGS2 -0.049 0.24 -9999 0 -0.99 25 25
Rac1/GTP -0.17 0.17 -9999 0 -0.51 21 21
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 215 215
negative regulation of T cell proliferation -0.045 0.14 -9999 0 -0.48 14 14
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.062 -9999 0 -0.76 3 3
MAPK1 -0.038 0.17 -9999 0 -0.57 24 24
S1P1/S1P/PDGFB-D/PDGFRB -0.17 0.24 -9999 0 -0.62 22 22
ABCC1 0.015 0.005 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.13 0.24 -10000 0 -0.78 34 34
UGCG -0.022 0.031 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT -0.086 0.2 -10000 0 -0.48 55 55
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.008 0.045 -10000 0 -10000 0 0
mol:DAG -0.004 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.11 0.17 -10000 0 -0.55 38 38
FRAP1 -0.09 0.23 -10000 0 -0.61 48 48
FOXO3 -0.081 0.22 -10000 0 -0.66 32 32
AKT1 -0.098 0.24 -10000 0 -0.64 50 50
GAB2 0.015 0.005 -10000 0 -10000 0 0
SMPD1 -0.022 0.031 -10000 0 -10000 0 0
SGMS1 -0.022 0.031 -10000 0 -10000 0 0
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 0.029 0.006 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation -0.023 0.096 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
RPS6KB1 -0.029 0.088 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.006 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.17 0.36 -10000 0 -0.86 102 102
PIK3R1 0.019 0.004 -10000 0 -10000 0 0
JAK1 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
MYC -0.08 0.23 -10000 0 -0.63 41 41
MYB -0.19 0.34 -10000 0 -0.73 130 130
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.13 0.26 -10000 0 -0.68 61 61
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.037 0.064 -10000 0 -0.45 1 1
mol:PI-3-4-5-P3 -0.12 0.25 -10000 0 -0.65 61 61
Rac1/GDP 0 0 -10000 0 -10000 0 0
T cell proliferation -0.1 0.24 -10000 0 -0.6 59 59
SHC1 0.013 0.04 -10000 0 -0.86 1 1
RAC1 0.015 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.008 0.026 -10000 0 -0.051 130 130
PRKCZ -0.11 0.25 -10000 0 -0.64 59 59
NF kappa B1 p50/RelA -0.1 0.16 -10000 0 -0.59 26 26
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.16 0.27 -10000 0 -0.58 102 102
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.16 0.35 -10000 0 -0.86 96 96
IL2RB -0.46 0.44 -10000 0 -0.86 263 263
TERT -0.12 0.31 -10000 0 -0.86 70 70
E2F1 -0.1 0.2 -10000 0 -0.37 161 161
SOS1 0.014 0.006 -10000 0 -10000 0 0
RPS6 0.014 0.04 -10000 0 -0.86 1 1
mol:cAMP 0.004 0.013 0.025 130 -10000 0 130
PTPN11 0.015 0.005 -10000 0 -10000 0 0
IL2RG -0.042 0.22 -10000 0 -0.86 33 33
actin cytoskeleton organization -0.1 0.24 -10000 0 -0.6 59 59
GRB2 0.014 0.006 -10000 0 -10000 0 0
IL2 -0.006 0.12 -10000 0 -0.86 10 10
PIK3CA 0.018 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.033 0.021 -10000 0 -10000 0 0
LCK -0.021 0.18 -10000 0 -0.85 22 22
BCL2 -0.056 0.18 -10000 0 -0.55 18 18
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0 -9999 0 -10000 0 0
ELF1 -0.044 0.14 -9999 0 -10000 0 0
CCNA2 -0.16 0.35 -9999 0 -0.86 96 96
PIK3CA 0.017 0 -9999 0 -10000 0 0
JAK3 -0.17 0.36 -9999 0 -0.86 102 102
PIK3R1 0.017 0 -9999 0 -10000 0 0
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.11 0.25 -9999 0 -0.66 56 56
SHC1 0.015 0.04 -9999 0 -0.86 1 1
SP1 0.024 0.023 -9999 0 -10000 0 0
IL2RA -0.12 0.33 -9999 0 -0.78 96 96
IL2RB -0.47 0.44 -9999 0 -0.86 263 263
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG -0.044 0.22 -9999 0 -0.86 33 33
G1/S transition of mitotic cell cycle -0.049 0.2 -9999 0 -0.55 13 13
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.038 0.053 -9999 0 -0.78 2 2
LCK -0.023 0.18 -9999 0 -0.85 22 22
GRB2 0.017 0 -9999 0 -10000 0 0
IL2 -0.008 0.12 -9999 0 -0.86 10 10
CDK6 0.014 0.035 -9999 0 -0.76 1 1
CCND3 -0.084 0.21 -9999 0 -0.67 27 27
LPA4-mediated signaling events

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
ADCY4 0.028 0 -9999 0 -10000 0 0
ADCY5 0.007 0.1 -9999 0 -0.5 19 19
ADCY6 0.028 0 -9999 0 -10000 0 0
ADCY7 0.008 0.11 -9999 0 -0.59 15 15
ADCY1 0.017 0.074 -9999 0 -0.52 9 9
ADCY2 -0.13 0.26 -9999 0 -0.58 122 122
ADCY3 0.028 0 -9999 0 -10000 0 0
ADCY8 -0.17 0.28 -9999 0 -0.59 149 149
PRKCE 0.015 0 -9999 0 -10000 0 0
ADCY9 0.028 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.089 0.17 -9999 0 -0.51 46 46
BCR signaling pathway

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
JUN -0.057 0.17 -10000 0 -0.41 40 40
IKBKB -0.025 0.1 -10000 0 -0.28 1 1
AKT1 -0.026 0.12 -10000 0 -0.3 8 8
IKBKG -0.025 0.11 -10000 0 -0.3 1 1
CALM1 -0.044 0.1 -10000 0 -0.5 3 3
PIK3CA 0.016 0 -10000 0 -10000 0 0
MAP3K1 -0.12 0.25 -10000 0 -0.63 67 67
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.057 0.11 0.27 1 -0.5 4 5
DOK1 0.016 0 -10000 0 -10000 0 0
AP-1 -0.012 0.09 -10000 0 -10000 0 0
LYN 0.016 0 -10000 0 -10000 0 0
BLNK 0.014 0.035 -10000 0 -0.76 1 1
SHC1 0.014 0.04 -10000 0 -0.86 1 1
BCR complex -0.17 0.3 -10000 0 -0.68 123 123
CD22 -0.16 0.24 -10000 0 -0.68 51 51
CAMK2G -0.031 0.1 -10000 0 -0.5 2 2
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.008 0.08 -10000 0 -0.86 4 4
SHC/GRB2/SOS1 -0.11 0.19 -10000 0 -0.85 4 4
GO:0007205 -0.057 0.11 -10000 0 -0.51 4 4
SYK 0.013 0.05 -10000 0 -0.76 2 2
ELK1 -0.044 0.11 -10000 0 -0.51 3 3
NFATC1 -0.075 0.2 -10000 0 -0.5 62 62
B-cell antigen/BCR complex -0.17 0.3 -10000 0 -0.68 123 123
PAG1/CSK -0.003 0.043 -10000 0 -0.67 2 2
NFKBIB 0.004 0.038 -10000 0 -10000 0 0
HRAS -0.039 0.12 -10000 0 -0.49 4 4
NFKBIA 0.005 0.038 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.013 0.031 -10000 0 -10000 0 0
RasGAP/Csk -0.22 0.33 -10000 0 -1 47 47
mol:GDP -0.052 0.1 0.29 1 -0.48 4 5
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B 0.01 0.069 -10000 0 -0.86 3 3
NF-kappa-B/RelA/I kappa B alpha 0.013 0.031 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.083 0.22 -10000 0 -0.57 59 59
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.068 0.11 0.27 1 -0.52 4 5
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.04 0.11 -10000 0 -0.5 5 5
CHUK -0.025 0.11 -10000 0 -0.3 2 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.13 0.2 -10000 0 -0.54 75 75
PTPN6 -0.14 0.22 -10000 0 -0.68 39 39
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 -0.012 0.069 -10000 0 -0.14 103 103
VAV2 -0.17 0.29 -10000 0 -0.8 69 69
ubiquitin-dependent protein catabolic process 0.01 0.037 -10000 0 -10000 0 0
BTK -0.086 0.17 0.46 1 -0.42 96 97
CD19 -0.2 0.33 -10000 0 -0.9 73 73
MAP4K1 -0.35 0.43 -10000 0 -0.86 197 197
CD72 -0.2 0.38 -10000 0 -0.86 116 116
PAG1 0.012 0.057 -10000 0 -0.86 2 2
MAPK14 -0.089 0.22 -10000 0 -0.53 63 63
SH3BP5 0.014 0.035 -10000 0 -0.76 1 1
PIK3AP1 -0.04 0.11 -10000 0 -0.55 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.12 0.24 -10000 0 -0.57 79 79
RAF1 -0.026 0.12 -10000 0 -0.54 2 2
RasGAP/p62DOK/SHIP -0.22 0.32 -10000 0 -0.97 48 48
CD79A -0.21 0.38 -10000 0 -0.86 123 123
re-entry into mitotic cell cycle -0.012 0.09 -10000 0 -10000 0 0
RASA1 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.1 -10000 0 -10000 0 0
MAPK1 -0.002 0.1 -10000 0 -10000 0 0
CD72/SHP1 -0.24 0.33 -10000 0 -0.83 96 96
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.089 0.22 -10000 0 -0.52 64 64
actin cytoskeleton organization -0.1 0.26 -10000 0 -0.67 63 63
NF-kappa-B/RelA 0.034 0.058 -10000 0 -10000 0 0
Calcineurin -0.044 0.071 -10000 0 -0.44 2 2
PI3K -0.14 0.22 -10000 0 -0.6 64 64
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.064 0.1 -10000 0 -0.55 4 4
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.28 0.32 -10000 0 -0.74 129 129
DAPP1 -0.11 0.19 -10000 0 -0.61 36 36
cytokine secretion -0.069 0.19 -10000 0 -0.47 62 62
mol:DAG -0.068 0.11 0.27 1 -0.52 4 5
PLCG2 0.002 0.11 -10000 0 -0.82 8 8
MAP2K1 -0.014 0.11 -10000 0 -0.48 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.26 0.38 -10000 0 -0.73 173 173
mol:PI-3-4-5-P3 -0.1 0.15 -10000 0 -0.41 60 60
ETS1 -0.019 0.093 -10000 0 -0.44 2 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.13 0.22 -10000 0 -0.98 3 3
B-cell antigen/BCR complex/LYN -0.14 0.22 -10000 0 -0.58 69 69
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.11 0.28 -10000 0 -0.73 63 63
B-cell antigen/BCR complex/LYN/SYK -0.17 0.25 -10000 0 -0.67 65 65
CARD11 -0.15 0.26 -10000 0 -0.61 102 102
FCGR2B -0.16 0.35 -10000 0 -0.86 97 97
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.004 0.047 -10000 0 -10000 0 0
PTPRC -0.083 0.28 -10000 0 -0.86 54 54
PDPK1 -0.062 0.1 -10000 0 -0.3 7 7
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 -0.001 0.059 -10000 0 -0.14 64 64
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0 0.058 0.29 17 -10000 0 17
BUB1B -0.025 0.13 -10000 0 -0.51 24 24
PLK1 -0.014 0.06 -10000 0 -0.2 10 10
PLK1S1 0 0.031 -10000 0 -10000 0 0
KIF2A -0.004 0.072 -10000 0 -0.6 3 3
regulation of mitotic centrosome separation -0.014 0.059 -10000 0 -0.2 10 10
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.19 0.34 -10000 0 -0.72 121 121
WEE1 -0.003 0.057 -10000 0 -0.3 5 5
cytokinesis -0.22 0.27 -10000 0 -0.5 228 228
PP2A-alpha B56 -0.15 0.16 -10000 0 -10000 0 0
AURKA -0.003 0.046 -10000 0 -0.3 6 6
PICH/PLK1 -0.047 0.17 -10000 0 -0.84 18 18
CENPE -0.068 0.21 -10000 0 -0.63 59 59
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.004 0.071 -10000 0 -0.6 3 3
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.014 0.035 -10000 0 -0.76 1 1
TPX2 -0.053 0.12 -10000 0 -0.26 120 120
PAK1 0.016 0.002 -10000 0 -10000 0 0
SPC24 -0.082 0.28 -10000 0 -0.86 53 53
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.027 0.097 -10000 0 -0.28 56 56
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.004 0.01 -10000 0 -0.02 124 124
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.031 -10000 0 -0.098 10 10
G2 phase of mitotic cell cycle 0.001 0.002 -10000 0 -0.014 6 6
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.013 -10000 0 -10000 0 0
spindle elongation -0.014 0.059 -10000 0 -0.2 10 10
ODF2 0.016 0.002 -10000 0 -10000 0 0
BUB1 -0.18 0.19 -10000 0 -0.48 2 2
TPT1 0 0.031 -10000 0 -10000 0 0
CDC25C -0.13 0.17 -10000 0 -0.31 224 224
CDC25B 0.006 0.091 -10000 0 -0.88 5 5
SGOL1 0 0.058 -10000 0 -0.29 17 17
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.025 0.11 -10000 0 -0.74 9 9
CDC14B 0.016 0.002 -10000 0 -10000 0 0
CDC20 -0.058 0.24 -10000 0 -0.86 40 40
PLK1/PBIP1 -0.04 0.11 -10000 0 -0.58 16 16
mitosis -0.001 0.004 0.03 6 -10000 0 6
FBXO5 0.001 0.045 -10000 0 -0.21 2 2
CDC2 -0.001 0.004 -10000 0 -0.023 9 9
NDC80 -0.18 0.36 -10000 0 -0.86 104 104
metaphase plate congression -0.006 0.042 -10000 0 -10000 0 0
ERCC6L -0.039 0.17 -10000 0 -0.82 18 18
NLP/gamma Tubulin -0.004 0.035 -10000 0 -0.12 5 5
microtubule cytoskeleton organization 0 0.031 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.016 0.002 -10000 0 -10000 0 0
interphase 0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.27 0.29 -10000 0 -0.57 228 228
GRASP65/GM130/RAB1/GTP/PLK1 -0.014 0.027 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.039 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -10000 0 -0.012 117 117
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.043 -10000 0 -10000 0 0
microtubule-based process -0.26 0.31 -10000 0 -0.58 228 228
Golgi organization -0.014 0.059 -10000 0 -0.2 10 10
Cohesin/SA2 -0.025 0.046 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.4 0.44 -10000 0 -0.86 228 228
APC/C/CDC20 -0.048 0.18 -10000 0 -0.64 40 40
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.04 0.11 -10000 0 -0.57 16 16
PRC1 0.005 0.098 -10000 0 -0.86 6 6
ECT2 -0.001 0.054 -10000 0 -10000 0 0
C13orf34 0.002 0.043 -10000 0 -10000 0 0
NUDC -0.006 0.042 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.025 0.12 -10000 0 -0.51 24 24
spindle assembly -0.008 0.048 -10000 0 -0.18 6 6
spindle stabilization 0 0.031 -10000 0 -10000 0 0
APC/C/HCDH1 -0.001 0.023 -10000 0 -0.5 1 1
MKLP2/PLK1 -0.26 0.31 -10000 0 -0.59 228 228
CCNB1 0.001 0.11 -10000 0 -0.88 8 8
PPP1CB 0.016 0.002 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.005 0.046 -10000 0 -0.47 1 1
TUBG1 0 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.027 0.1 -10000 0 -0.71 9 9
MLF1IP -0.009 0.12 -10000 0 -0.69 15 15
INCENP 0.008 0.008 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.038 -9999 0 -0.8 1 1
SVIL 0.015 0.007 -9999 0 -10000 0 0
ZNF318 0.016 0.022 -9999 0 -10000 0 0
JMJD2C 0 0.02 -9999 0 -0.11 15 15
T-DHT/AR/Ubc9 -0.077 0.11 -9999 0 -0.56 22 22
CARM1 0.015 0.003 -9999 0 -10000 0 0
PRDX1 0.016 0.001 -9999 0 -10000 0 0
PELP1 0.016 0.003 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
AKT1 0.017 0.006 -9999 0 -10000 0 0
PTK2B 0.015 0.003 -9999 0 -10000 0 0
MED1 0.013 0.009 -9999 0 -10000 0 0
MAK 0.016 0.022 -9999 0 -10000 0 0
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.013 0.038 -9999 0 -0.8 1 1
GSN 0.015 0.007 -9999 0 -10000 0 0
NCOA2 0.009 0.07 -9999 0 -0.76 4 4
NCOA6 0.016 0.003 -9999 0 -10000 0 0
DNA-PK 0.005 0.026 -9999 0 -10000 0 0
NCOA4 0.015 0.002 -9999 0 -10000 0 0
PIAS3 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.027 0.026 -9999 0 -10000 0 0
XRCC5 0.016 0.005 -9999 0 -10000 0 0
UBE3A 0.014 0.012 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.094 0.15 -9999 0 -0.6 35 35
FHL2 -0.037 0.098 -9999 0 -1.2 3 3
RANBP9 0.016 0.003 -9999 0 -10000 0 0
JMJD1A -0.12 0.054 -9999 0 -0.14 419 419
CDK6 0.014 0.035 -9999 0 -0.76 1 1
TGFB1I1 0.013 0.041 -9999 0 -0.86 1 1
T-DHT/AR/CyclinD1 -0.1 0.16 -9999 0 -0.6 42 42
XRCC6 0.016 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.12 -9999 0 -0.6 22 22
CTDSP1 0.015 0.003 -9999 0 -10000 0 0
CTDSP2 0.015 0.017 -9999 0 -10000 0 0
BRCA1 0.015 0.007 -9999 0 -10000 0 0
TCF4 0.014 0.013 -9999 0 -10000 0 0
CDKN2A -0.83 0.16 -9999 0 -0.86 463 463
SRF 0.027 0.01 -9999 0 -10000 0 0
NKX3-1 -0.19 0.068 -9999 0 -10000 0 0
KLK3 0.025 0.14 -9999 0 -0.7 18 18
TMF1 0.015 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.012 -9999 0 -10000 0 0
AOF2 -0.001 0.01 -9999 0 -10000 0 0
APPL1 0.033 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.076 0.11 -9999 0 -0.55 22 22
AR -0.068 0.16 -9999 0 -0.8 22 22
UBA3 0.015 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.012 -9999 0 -10000 0 0
PAWR 0.014 0.035 -9999 0 -0.76 1 1
PRKDC 0.016 0.005 -9999 0 -10000 0 0
PA2G4 0.014 0.012 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.069 0.1 -9999 0 -0.51 22 22
RPS6KA3 0.015 0.007 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.078 0.11 -9999 0 -0.56 22 22
LATS2 0.014 0.011 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.068 0.1 -9999 0 -0.51 22 22
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.007 0.13 -9999 0 -0.76 14 14
KLK2 -0.082 0.14 -9999 0 -0.81 15 15
CASP8 0.016 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.063 0.12 -9999 0 -0.59 17 17
TMPRSS2 -0.94 0.35 -9999 0 -1.1 419 419
CCND1 -0.021 0.18 -9999 0 -0.86 20 20
PIAS1 0.014 0.012 -9999 0 -10000 0 0
mol:T-DHT -0.062 0.026 -9999 0 -0.072 412 412
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.013 0.018 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.11 -9999 0 -0.57 22 22
CMTM2 -0.001 0.12 -9999 0 -0.86 9 9
SNURF -0.011 0.14 -9999 0 -0.76 16 16
ZMIZ1 -0.032 0.021 -9999 0 -10000 0 0
CCND3 0.016 0.001 -9999 0 -10000 0 0
TGIF1 0.014 0.012 -9999 0 -10000 0 0
FKBP4 0.016 0.003 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.24 0.28 -9999 0 -0.85 71 71
RAD9A 0.016 0 -9999 0 -10000 0 0
AP1 -0.012 0.082 -9999 0 -0.57 10 10
IFNAR2 0.014 0.007 -9999 0 -10000 0 0
AKT1 0.014 0.069 -9999 0 -0.43 10 10
ER alpha/Oestrogen -0.002 0.038 -9999 0 -0.59 2 2
NFX1/SIN3/HDAC complex 0.045 0.052 -9999 0 -10000 0 0
EGF -0.68 0.23 -9999 0 -0.76 432 432
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.22 0.26 -9999 0 -0.79 69 69
SAP18 0.013 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.36 0.39 -9999 0 -0.76 229 229
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.015 0.007 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.19 0.23 -9999 0 -0.72 59 59
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.25 0.29 -9999 0 -0.88 71 71
CCND1 -0.22 0.27 -9999 0 -0.79 74 74
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.006 -9999 0 -10000 0 0
RBBP4 0.013 0.006 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.013 0.006 -9999 0 -10000 0 0
Telomerase/911 0 0.025 -9999 0 -10000 0 0
CDKN1B -0.23 0.3 -9999 0 -0.55 220 220
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 -0.016 0.16 -9999 0 -0.86 16 16
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.014 0.006 -9999 0 -10000 0 0
JUN 0.014 0.006 -9999 0 -10000 0 0
E6 -0.001 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.002 0.11 -9999 0 -0.76 10 10
IFN-gamma/IRF1 -0.3 0.32 -9999 0 -0.65 220 220
PARP2 0.016 0 -9999 0 -10000 0 0
BLM -0.004 0.13 -9999 0 -0.86 11 11
Telomerase -0.016 0.16 -9999 0 -0.43 17 17
IRF1 0.016 0.041 -9999 0 -0.86 1 1
ESR1 0.01 0.05 -9999 0 -0.76 2 2
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.051 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.006 0.031 -9999 0 -10000 0 0
HDAC1 0.013 0.006 -9999 0 -10000 0 0
HDAC2 0.015 0.007 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.024 0.07 -9999 0 -0.66 5 5
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.18 0.25 -9999 0 -0.75 59 59
NR2F2 0.006 0.013 -9999 0 -10000 0 0
MAPK3 0.008 0.099 -9999 0 -0.67 10 10
MAPK1 0.008 0.099 -9999 0 -0.67 10 10
TGFB1/TGF beta receptor Type II 0.007 0.089 -9999 0 -0.86 5 5
NFKB1 0.016 0 -9999 0 -10000 0 0
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.016 0 -9999 0 -10000 0 0
EGFR -0.001 0.12 -9999 0 -0.85 9 9
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.52 0.19 -9999 0 -0.58 433 433
MYC -0.015 0.16 -9999 0 -0.87 16 16
IL2 -0.009 0.13 -9999 0 -0.87 10 10
KU 0 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.007 0.089 -9999 0 -0.86 5 5
TRF2/BLM -0.014 0.094 -9999 0 -0.63 11 11
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.22 0.26 -9999 0 -0.78 68 68
SP1/HDAC2 0.006 0.013 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.19 0.23 -9999 0 -0.72 59 59
Smad3/Myc -0.018 0.12 -9999 0 -0.6 20 20
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.38 0.43 -9999 0 -0.85 220 220
Telomerase/PinX1 -0.19 0.23 -9999 0 -0.72 59 59
Telomerase/AKT1/mTOR/p70S6K -0.014 0.08 -9999 0 -0.53 2 2
SIN3B 0.013 0.006 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.19 0.23 -9999 0 -0.72 59 59
response to DNA damage stimulus 0.004 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.19 0.23 -9999 0 -0.72 59 59
E2F1 -0.085 0.28 -9999 0 -0.87 54 54
ZNFX1 0.013 0.006 -9999 0 -10000 0 0
PIF1 -0.13 0.33 -9999 0 -0.86 79 79
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.23 -9999 0 -0.49 160 160
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.12 0.23 -9999 0 -0.52 5 5
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.009 0.13 -9999 0 -0.86 11 11
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.66 0.38 -9999 0 -0.86 366 366
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.03 -9999 0 -0.67 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 0.016 0 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.29 -9999 0 -0.86 61 61
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.18 0.24 -9999 0 -0.5 169 169
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.14 0.17 -9999 0 -0.6 15 15
MAP1B -0.001 0.021 -9999 0 -0.33 2 2
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.18 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.76 159 159
PAFAH/LIS1 -0.44 0.24 -9999 0 -0.58 366 366
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.1 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.14 -9999 0 -0.7 1 1
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.14 0.19 -9999 0 -0.65 15 15
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0.035 -9999 0 -0.76 1 1
PAFAH1B2 0.016 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.001 0.013 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.16 -9999 0 -0.56 15 15
LRP8 0.014 0.04 -9999 0 -0.86 1 1
NDEL1/Katanin 60 -0.14 0.17 -9999 0 -0.6 15 15
P39/CDK5 -0.18 0.23 -9999 0 -0.87 15 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.096 0.22 -9999 0 -0.48 5 5
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.15 0.2 -9999 0 -0.91 1 1
RELN/VLDLR -0.15 0.21 -9999 0 -0.52 5 5
CDC42 0 0 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.018 0.11 -10000 0 -1.4 1 1
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.018 0 -10000 0 -10000 0 0
TBX21 -0.25 0.41 -10000 0 -0.82 159 159
SUMO2 0.01 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.024 0.056 -10000 0 -1.2 1 1
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 0.003 0.1 -10000 0 -0.85 7 7
GR alpha/HSP90/FKBP51/HSP90 0.05 0.13 0.39 5 -0.59 7 12
PRL -0.01 0.11 -10000 0 -0.55 1 1
cortisol/GR alpha (dimer)/TIF2 0.13 0.29 0.56 81 -0.71 1 82
RELA 0.006 0.075 -10000 0 -10000 0 0
FGG -0.16 0.43 0.59 11 -0.73 139 150
GR beta/TIF2 0.054 0.14 0.39 9 -0.56 5 14
IFNG -0.41 0.44 -10000 0 -0.86 199 199
apoptosis -0.098 0.22 -10000 0 -0.62 10 10
CREB1 -0.017 0.11 -10000 0 -0.4 3 3
histone acetylation 0.018 0.13 0.39 7 -0.39 7 14
BGLAP -0.004 0.12 -10000 0 -0.53 3 3
GR/PKAc 0.061 0.1 0.39 3 -0.6 1 4
NF kappa B1 p50/RelA 0.015 0.14 -10000 0 -0.58 3 3
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.044 0.093 0.35 6 -10000 0 6
GATA3 -0.35 0.39 -10000 0 -0.75 230 230
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.026 0.16 -10000 0 -0.71 15 15
GSK3B 0.01 0.008 -10000 0 -10000 0 0
NR1I3 -0.06 0.22 -10000 0 -0.83 10 10
CSN2 0.038 0.19 0.5 4 -0.66 1 5
BRG1/BAF155/BAF170/BAF60A 0 0.004 -10000 0 -10000 0 0
NFATC1 0.018 0.005 -10000 0 -10000 0 0
POU2F1 0.02 0.005 -10000 0 -10000 0 0
CDKN1A 0.05 0.055 -10000 0 -0.72 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.079 0.27 -10000 0 -0.84 53 53
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.005 0.21 0.37 3 -0.59 24 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.057 0.22 -10000 0 -0.85 8 8
JUN -0.22 0.25 -10000 0 -0.64 67 67
IL4 -0.02 0.12 -10000 0 -0.58 2 2
CDK5R1 0.012 0.007 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.26 0.31 2 -0.7 68 70
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.056 0.12 0.38 4 -0.6 4 8
cortisol/GR alpha (monomer) 0.14 0.34 0.66 88 -0.81 1 89
NCOA2 0.009 0.07 -10000 0 -0.76 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.05 0.13 -10000 0 -0.82 10 10
AP-1/NFAT1-c-4 -0.32 0.34 -10000 0 -0.86 78 78
AFP -0.37 0.57 -10000 0 -1.4 107 107
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.079 0.15 0.53 6 -0.62 1 7
TP53 0.044 0.022 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.24 0.41 -10000 0 -1.2 60 60
KRT14 -0.13 0.29 -10000 0 -0.84 61 61
TBP 0.029 0.001 -10000 0 -10000 0 0
CREBBP 0.042 0.076 -10000 0 -10000 0 0
HDAC1 0.01 0.008 -10000 0 -10000 0 0
HDAC2 0.011 0.014 -10000 0 -10000 0 0
AP-1 -0.32 0.34 -10000 0 -0.86 81 81
MAPK14 0.009 0.008 -10000 0 -10000 0 0
MAPK10 0 0.079 -10000 0 -0.77 5 5
MAPK11 0.01 0.008 -10000 0 -10000 0 0
KRT5 -0.25 0.38 -10000 0 -0.88 100 100
interleukin-1 receptor activity 0 0.011 -10000 0 -10000 0 0
NCOA1 0.019 0.002 -10000 0 -10000 0 0
STAT1 0.025 0.056 -10000 0 -1.2 1 1
CGA -0.13 0.38 -10000 0 -1.2 50 50
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.086 0.15 0.46 31 -10000 0 31
MAPK3 0.008 0.008 -10000 0 -10000 0 0
MAPK1 0.009 0.008 -10000 0 -10000 0 0
ICAM1 -0.042 0.22 -10000 0 -0.8 20 20
NFKB1 0.006 0.075 -10000 0 -10000 0 0
MAPK8 -0.14 0.19 -10000 0 -0.5 46 46
MAPK9 0.009 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.1 0.23 -10000 0 -0.65 12 12
BAX 0.052 0.029 -10000 0 -10000 0 0
POMC -0.033 0.17 -10000 0 -0.92 4 4
EP300 0.042 0.077 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.15 0.29 0.57 87 -0.7 1 88
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.071 0.29 1 -10000 0 1
SGK1 0.099 0.094 -10000 0 -10000 0 0
IL13 -0.35 0.28 -10000 0 -0.78 98 98
IL6 -0.11 0.37 -10000 0 -0.98 63 63
PRKACG 0.003 0.006 -10000 0 -10000 0 0
IL5 -0.28 0.21 -10000 0 -0.68 49 49
IL2 -0.17 0.25 -10000 0 -0.9 21 21
CDK5 0.012 0.007 -10000 0 -10000 0 0
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.071 0.29 -10000 0 -0.89 41 41
CDK5R1/CDK5 0 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.027 0.099 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.26 0.55 70 -0.65 1 71
SMARCA4 0.018 0 -10000 0 -10000 0 0
chromatin remodeling 0.097 0.15 0.42 29 -10000 0 29
NF kappa B1 p50/RelA/Cbp 0.062 0.13 -10000 0 -10000 0 0
JUN (dimer) -0.21 0.25 -10000 0 -0.64 68 68
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.055 0.22 -10000 0 -0.8 23 23
NR3C1 0.075 0.19 0.51 30 -0.95 1 31
NR4A1 -0.002 0.14 -10000 0 -0.74 17 17
TIF2/SUV420H1 -0.005 0.052 -10000 0 -0.57 4 4
MAPKKK cascade -0.098 0.22 -10000 0 -0.62 10 10
cortisol/GR alpha (dimer)/Src-1 0.14 0.29 0.56 87 -0.8 1 88
PBX1 0 0.12 -10000 0 -0.76 12 12
POU1F1 0.009 0.009 -10000 0 -10000 0 0
SELE -0.086 0.35 -10000 0 -1.2 34 34
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.097 0.15 0.42 29 -10000 0 29
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.26 0.55 70 -0.65 1 71
mol:cortisol 0.057 0.2 0.43 53 -10000 0 53
MMP1 -0.23 0.4 -10000 0 -0.99 95 95
IL6-mediated signaling events

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
BCL2L1 -0.14 0.31 -9999 0 -0.78 34 34
CRP -0.2 0.4 -9999 0 -0.91 88 88
cell cycle arrest -0.18 0.36 -9999 0 -0.81 75 75
TIMP1 -0.15 0.34 -9999 0 -0.81 57 57
IL6ST -0.004 0.11 -9999 0 -0.75 10 10
Rac1/GDP -0.14 0.26 -9999 0 -0.6 84 84
AP1 0.026 0.1 -9999 0 -10000 0 0
GAB2 0.012 0.008 -9999 0 -10000 0 0
TNFSF11 -0.19 0.38 -9999 0 -0.9 62 62
HSP90B1 0.005 0.092 -9999 0 -10000 0 0
GAB1 0.013 0.007 -9999 0 -10000 0 0
MAPK14 0.023 0.13 -9999 0 -0.71 3 3
AKT1 0.061 0.032 -9999 0 -10000 0 0
FOXO1 0.078 0.016 -9999 0 -10000 0 0
MAP2K6 -0.011 0.13 -9999 0 -0.66 4 4
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.14 0.28 -9999 0 -0.67 63 63
MITF -0.02 0.14 -9999 0 -0.72 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.016 0 -9999 0 -10000 0 0
A2M 0.028 0.005 -9999 0 -10000 0 0
CEBPB 0.001 0.14 -9999 0 -0.86 12 12
GRB2/SOS1/GAB family/SHP2 0.003 0.07 -9999 0 -10000 0 0
STAT3 -0.19 0.38 -9999 0 -0.85 75 75
STAT1 -0.006 0.025 -9999 0 -0.49 1 1
CEBPD -0.14 0.32 -9999 0 -0.78 35 35
PIK3CA 0.018 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
JUN 0.01 0.008 -9999 0 -10000 0 0
PIAS3/MITF -0.013 0.13 -9999 0 -0.68 2 2
MAPK11 0.023 0.13 -9999 0 -0.71 3 3
STAT3 (dimer)/FOXO1 -0.068 0.28 -9999 0 -0.66 15 15
GRB2/SOS1/GAB family -0.044 0.1 -9999 0 -0.64 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.033 0.15 -9999 0 -0.63 10 10
GRB2 0.013 0.007 -9999 0 -10000 0 0
JAK2 0.016 0 -9999 0 -10000 0 0
LBP -0.27 0.45 -9999 0 -0.89 140 140
PIK3R1 0.017 0 -9999 0 -10000 0 0
JAK1 0.015 0.006 -9999 0 -10000 0 0
MYC -0.15 0.33 -9999 0 -0.77 55 55
FGG -0.28 0.44 -9999 0 -0.89 116 116
macrophage differentiation -0.18 0.36 -9999 0 -0.81 75 75
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.066 0.17 -9999 0 -0.55 27 27
JUNB -0.14 0.31 -9999 0 -0.75 42 42
FOS -0.006 0.11 -9999 0 -0.76 10 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.15 -9999 0 -0.43 24 24
STAT1/PIAS1 -0.043 0.16 -9999 0 -0.48 20 20
GRB2/SOS1/GAB family/SHP2/PI3K 0.023 0.035 -9999 0 -10000 0 0
STAT3 (dimer) -0.19 0.38 -9999 0 -0.85 75 75
PRKCD -0.15 0.31 -9999 0 -0.73 54 54
IL6R 0.015 0.006 -9999 0 -10000 0 0
SOCS3 0.038 0.12 -9999 0 -0.78 2 2
gp130 (dimer)/JAK1/JAK1/LMO4 -0.008 0.07 -9999 0 -0.48 10 10
Rac1/GTP -0.18 0.24 -9999 0 -0.61 91 91
HCK -0.036 0.2 -9999 0 -0.87 27 27
MAPKKK cascade 0.028 0.061 -9999 0 -10000 0 0
bone resorption -0.18 0.36 -9999 0 -0.84 62 62
IRF1 -0.14 0.32 -9999 0 -0.78 36 36
mol:GDP -0.15 0.27 -9999 0 -0.6 96 96
SOS1 0.01 0.008 -9999 0 -10000 0 0
VAV1 -0.15 0.28 -9999 0 -0.62 96 96
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.003 0.12 -9999 0 -0.66 2 2
PTPN11 -0.004 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.079 0.21 -9999 0 -0.64 59 59
gp130 (dimer)/TYK2/TYK2/LMO4 -0.008 0.069 -9999 0 -0.48 10 10
gp130 (dimer)/JAK2/JAK2/LMO4 -0.008 0.069 -9999 0 -0.48 10 10
IL6 -0.092 0.28 -9999 0 -0.84 59 59
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.017 0.017 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
RAC1 0.015 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.03 0.13 -9999 0 -0.4 12 12
LMO4 0.012 0.014 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.22 0.3 -9999 0 -0.81 62 62
MCL1 0.077 0.015 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 215 215
alphaV beta3 Integrin -0.005 0.051 -9999 0 -0.5 5 5
PTK2 -0.14 0.23 -9999 0 -0.55 45 45
IGF1R 0.016 0 -9999 0 -10000 0 0
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.014 0.04 -9999 0 -0.86 1 1
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.086 0.2 -9999 0 -0.53 76 76
VEGFA -0.38 0.44 -9999 0 -0.86 215 215
ILK -0.086 0.2 -9999 0 -0.53 76 76
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.079 0.18 -9999 0 -0.5 68 68
PTK2B -0.19 0.27 -9999 0 -0.89 1 1
alphaV/beta3 Integrin/JAM-A -0.069 0.16 -9999 0 -0.49 9 9
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.22 0.24 -9999 0 -0.48 220 220
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.068 -9999 0 -0.52 7 7
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.15 -9999 0 -0.48 45 45
alphaV/beta3 Integrin/Syndecan-1 -0.006 0.054 -9999 0 -0.48 6 6
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.046 0.14 -9999 0 -0.88 3 3
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.004 0.044 -9999 0 -0.48 4 4
RPS6KB1 -0.042 0.13 -9999 0 -0.8 3 3
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.04 0.085 -9999 0 -0.62 3 3
GPR124 0.012 0.057 -9999 0 -0.86 2 2
MAPK1 -0.04 0.085 -9999 0 -0.62 3 3
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.055 0.15 -9999 0 -0.48 54 54
cell adhesion -0.17 0.18 -9999 0 -0.84 1 1
ANGPTL3 -0.34 0.38 -9999 0 -0.76 219 219
VEGFR2 homodimer/VEGFA homodimer/Src -0.26 0.29 -9999 0 -0.58 215 215
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.016 0 -9999 0 -10000 0 0
ITGB3 0.014 0.035 -9999 0 -0.76 1 1
IGF1 0.003 0.11 -9999 0 -0.86 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.003 0.043 -9999 0 -0.54 3 3
apoptosis 0.016 0 -9999 0 -10000 0 0
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.001 0.022 -9999 0 -0.48 1 1
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.014 0.085 -9999 0 -0.52 13 13
CSF1 0.016 0 -9999 0 -10000 0 0
PIK3C2A -0.086 0.2 -9999 0 -0.53 76 76
PI4 Kinase/Pyk2 -0.24 0.25 -9999 0 -0.76 45 45
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.24 0.26 -9999 0 -0.52 215 215
FAK1/Vinculin -0.11 0.19 -9999 0 -0.55 2 2
alphaV beta3/Integrin/ppsTEM5 -0.003 0.043 -9999 0 -0.55 3 3
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.11 0.29 -9999 0 -0.77 76 76
BCAR1 0.014 0.035 -9999 0 -0.76 1 1
FGF2 0.009 0.073 -9999 0 -0.78 4 4
F11R 0.026 0.057 -9999 0 -0.59 4 4
alphaV/beta3 Integrin/Lactadherin -0.002 0.034 -9999 0 -0.53 2 2
alphaV/beta3 Integrin/TGFBR2 -0.001 0.022 -9999 0 -0.48 1 1
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.001 0.02 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.001 0.02 -9999 0 -0.45 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.052 0.24 -9999 0 -0.86 37 37
alphaV/beta3 Integrin/Pyk2 -0.22 0.24 -9999 0 -0.89 1 1
SDC1 0.008 0.079 -9999 0 -0.76 5 5
VAV3 0.04 0.08 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.012 0.05 -9999 0 -0.76 2 2
FAK1/Paxillin -0.11 0.19 -9999 0 -0.55 2 2
cell migration -0.088 0.18 -9999 0 -0.53 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
PI3K -0.061 0.14 -9999 0 -10000 0 0
SPP1 0.011 0.061 -9999 0 -0.76 3 3
KDR 0.014 0.035 -9999 0 -0.76 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.016 0 -9999 0 -10000 0 0
COL4A3 -0.07 0.24 -9999 0 -0.76 53 53
angiogenesis 0.005 0.14 -9999 0 -0.8 1 1
Rac1/GTP -0.011 0.063 -9999 0 -10000 0 0
EDIL3 -0.005 0.13 -9999 0 -0.8 12 12
cell proliferation -0.001 0.022 -9999 0 -0.48 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.17 0.27 -10000 0 -0.53 89 89
CRKL 0.019 0.11 -10000 0 -0.68 4 4
HRAS -0.045 0.18 -10000 0 -0.51 41 41
mol:PIP3 -0.002 0.1 -10000 0 -0.45 18 18
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.016 0 -10000 0 -10000 0 0
GAB1 0.007 0.12 -10000 0 -0.5 18 18
FOXO3 0.025 0.1 -10000 0 -0.6 4 4
AKT1 0.015 0.11 -10000 0 -0.45 18 18
BAD 0.024 0.1 -10000 0 -0.6 4 4
megakaryocyte differentiation -0.066 0.21 -10000 0 -0.52 53 53
GSK3B 0.025 0.1 -10000 0 -0.6 4 4
RAF1 -0.012 0.16 -10000 0 -0.54 3 3
SHC1 0.014 0.04 -10000 0 -0.86 1 1
STAT3 0.008 0.12 -10000 0 -0.5 18 18
STAT1 -0.014 0.23 -10000 0 -1 18 18
HRAS/SPRED1 -0.068 0.12 -10000 0 -0.42 20 20
cell proliferation 0.008 0.12 -10000 0 -0.48 18 18
PIK3CA 0.016 0 -10000 0 -10000 0 0
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.12 -10000 0 -0.48 20 20
HRAS/SPRED2 -0.068 0.12 -10000 0 -0.42 20 20
LYN/TEC/p62DOK -0.017 0.099 -10000 0 -0.67 4 4
MAPK3 0.011 0.12 -10000 0 -0.37 2 2
STAP1 -0.32 0.22 -10000 0 -0.43 365 365
GRAP2 -0.046 0.22 -10000 0 -0.86 34 34
JAK2 -0.066 0.18 -10000 0 -0.91 18 18
STAT1 (dimer) -0.012 0.23 -10000 0 -1 18 18
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.13 0.22 -10000 0 -0.56 46 46
actin filament polymerization 0.003 0.13 -10000 0 -0.48 23 23
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.3 0.23 -10000 0 -0.86 27 27
PIK3R1 0.016 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.012 0.09 -10000 0 -0.59 4 4
PI3K -0.017 0.1 -10000 0 -0.46 18 18
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.33 -10000 0 -1.3 20 20
MAPK8 0.008 0.12 -10000 0 -0.5 18 18
STAT3 (dimer) 0.008 0.12 -10000 0 -0.48 18 18
positive regulation of transcription 0.014 0.1 -10000 0 -10000 0 0
mol:GDP -0.12 0.2 -10000 0 -0.62 44 44
PIK3C2B 0.008 0.12 -10000 0 -0.5 18 18
CBL/CRKL 0.027 0.11 -10000 0 -0.62 4 4
FER 0.007 0.12 -10000 0 -0.51 19 19
SH2B3 0.008 0.12 -10000 0 -0.5 18 18
PDPK1 0.009 0.098 -10000 0 -0.57 4 4
SNAI2 0.007 0.12 -10000 0 -0.52 18 18
positive regulation of cell proliferation 0.001 0.18 -10000 0 -0.79 18 18
KITLG 0 0.11 -10000 0 -0.78 9 9
cell motility 0.001 0.18 -10000 0 -0.79 18 18
PTPN6 0.008 0.011 -10000 0 -10000 0 0
EPOR 0.041 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.005 0.16 -10000 0 -0.65 19 19
SOCS1 0.007 0.089 -10000 0 -0.86 5 5
cell migration 0.046 0.19 0.5 66 -10000 0 66
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.3 0.42 -10000 0 -0.86 172 172
VAV1 -0.2 0.38 -10000 0 -0.86 119 119
GRB10 0.007 0.12 -10000 0 -0.5 18 18
PTPN11 0.008 0.01 -10000 0 -10000 0 0
SCF/KIT -0.034 0.11 -10000 0 -0.47 27 27
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.005 0.13 -10000 0 -0.42 2 2
CBL 0.016 0 -10000 0 -10000 0 0
KIT -0.007 0.27 -10000 0 -1.1 25 25
MAP2K2 0.004 0.13 -10000 0 -0.42 2 2
SHC/Grb2/SOS1 -0.018 0.1 -10000 0 -0.67 4 4
STAT5A 0.004 0.16 -10000 0 -0.67 19 19
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation 0.007 0.12 -10000 0 -0.5 18 18
SHC/GRAP2 -0.048 0.17 -10000 0 -0.66 35 35
PTPRO -0.068 0.21 -10000 0 -0.53 53 53
SH2B2 0.002 0.13 -10000 0 -0.49 23 23
DOK1 0.016 0 -10000 0 -10000 0 0
MATK -0.047 0.2 -10000 0 -0.51 66 66
CREBBP 0.045 0.012 -10000 0 -10000 0 0
BCL2 0.043 0.067 -10000 0 -10000 0 0
Reelin 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
CDK5R1/CDK5 0 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ITGA3 0.014 0.04 -9999 0 -0.86 1 1
RELN/VLDLR/Fyn -0.16 0.23 -9999 0 -0.49 159 159
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.042 -9999 0 -0.83 1 1
AKT1 -0.066 0.16 -9999 0 -0.56 1 1
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.009 0.13 -9999 0 -0.86 11 11
RELN/LRP8/DAB1 -0.16 0.22 -9999 0 -0.46 170 170
LRPAP1/LRP8 -0.001 0.03 -9999 0 -0.67 1 1
RELN/LRP8/DAB1/Fyn -0.15 0.21 -9999 0 -0.52 16 16
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.83 1 1
long-term memory -0.21 0.25 -9999 0 -0.89 22 22
DAB1/LIS1 -0.14 0.19 -9999 0 -0.86 1 1
DAB1/CRLK/C3G -0.13 0.18 -9999 0 -0.83 1 1
PIK3CA 0.016 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.14 0.19 -9999 0 -0.87 1 1
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.11 0.3 -9999 0 -0.84 68 68
CDK5R1 0.016 0 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.76 159 159
PIK3R1 0.016 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.16 0.23 -9999 0 -0.49 160 160
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.26 -9999 0 -0.78 32 32
MAPK8 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.46 169 169
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.15 0.2 -9999 0 -0.88 2 2
RELN/LRP8 -0.16 0.23 -9999 0 -0.49 160 160
GRIN2B/RELN/LRP8/DAB1/Fyn -0.15 0.21 -9999 0 -0.64 6 6
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.001 0.03 -9999 0 -0.67 1 1
RAP1A -0.12 0.16 -9999 0 -0.76 1 1
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0.05 -9999 0 -0.76 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.008 0.057 -9999 0 -0.86 2 2
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.028 0.12 -9999 0 -0.54 2 2
neuron adhesion -0.05 0.2 -9999 0 -0.71 1 1
LRP8 0.014 0.04 -9999 0 -0.86 1 1
GSK3B -0.052 0.15 -9999 0 -0.53 1 1
RELN/VLDLR/DAB1/Fyn -0.15 0.21 -9999 0 -0.53 15 15
MAP3K11 0.014 0.035 -9999 0 -0.76 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.15 -9999 0 -0.6 1 1
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT 0.015 0.087 -9999 0 -0.71 6 6
neuron migration -0.059 0.21 -9999 0 -0.61 1 1
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.058 0.1 -9999 0 -0.55 2 2
RELN/VLDLR -0.15 0.21 -9999 0 -0.52 5 5
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.045 0.099 -10000 0 -0.56 4 4
PTP1B/AKT1 -0.031 0.045 -10000 0 -0.42 2 2
FYN 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.048 0.051 -10000 0 -0.37 5 5
EGFR -0.015 0.12 -10000 0 -0.87 9 9
EGF/EGFR -0.38 0.14 -10000 0 -0.42 431 431
CSF1 0.016 0 -10000 0 -10000 0 0
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.048 0.086 -10000 0 -0.46 15 15
Insulin Receptor/Insulin -0.011 0.031 -10000 0 -10000 0 0
HCK -0.034 0.2 -10000 0 -0.86 27 27
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 -0.034 0.049 -10000 0 -0.45 2 2
EGF -0.68 0.23 -10000 0 -0.76 432 432
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.15 0.1 -10000 0 -0.42 38 38
TXN 0.002 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.031 0.046 -10000 0 -0.44 4 4
cell migration 0.048 0.051 0.37 5 -10000 0 5
STAT3 0.015 0.003 -10000 0 -10000 0 0
PRLR -0.09 0.24 -10000 0 -0.76 57 57
ITGA2B -0.025 0.15 -10000 0 -0.86 15 15
CSF1R 0.003 0.11 -10000 0 -0.86 7 7
Prolactin Receptor/Prolactin -0.068 0.19 -10000 0 -0.58 57 57
FGR 0.01 0.069 -10000 0 -0.86 3 3
PTP1B/p130 Cas -0.036 0.05 -10000 0 -0.43 3 3
Crk/p130 Cas -0.03 0.04 -10000 0 -0.42 2 2
DOK1 -0.018 0.044 -10000 0 -0.38 2 2
JAK2 -0.05 0.11 -10000 0 -0.42 14 14
Jak2/Leptin Receptor/Leptin -0.051 0.13 -10000 0 -0.7 3 3
PIK3R1 0.016 0 -10000 0 -10000 0 0
PTPN1 -0.048 0.051 -10000 0 -0.37 5 5
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.007 0.13 -10000 0 -0.76 14 14
SRC 0 0.02 -10000 0 -10000 0 0
ITGB3 0 0.035 -10000 0 -0.76 1 1
CAT1/PTP1B -0.24 0.14 -10000 0 -0.56 39 39
CAPN1 0.002 0.005 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K 0.011 0.029 -10000 0 -10000 0 0
mol:H2O2 -0.007 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.033 0.12 -10000 0 -0.66 3 3
negative regulation of transcription -0.049 0.11 -10000 0 -0.41 14 14
FCGR2A -0.025 0.18 -10000 0 -0.86 22 22
FER 0 0.035 -10000 0 -0.77 1 1
alphaIIb/beta3 Integrin -0.022 0.12 -10000 0 -0.66 16 16
BLK -0.04 0.21 -10000 0 -0.86 30 30
Insulin Receptor/Insulin/Shc -0.001 0.027 -10000 0 -0.59 1 1
RHOA 0.002 0.005 -10000 0 -10000 0 0
LEPR 0.014 0.004 -10000 0 -10000 0 0
BCAR1 0.014 0.035 -10000 0 -0.76 1 1
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.23 0.16 -10000 0 -0.56 55 55
PRL 0 0.002 -10000 0 -10000 0 0
SOCS3 0.028 0.051 -10000 0 -0.74 2 2
SPRY2 0.001 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.002 0.032 -10000 0 -0.5 2 2
CSF1/CSF1R -0.037 0.071 -10000 0 -0.51 9 9
Ras protein signal transduction 0.039 0.016 -10000 0 -10000 0 0
IRS1 0.012 0.05 -10000 0 -0.76 2 2
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.073 0.26 -10000 0 -0.86 46 46
STAT5B -0.043 0.065 -10000 0 -0.46 4 4
STAT5A -0.043 0.065 -10000 0 -0.46 4 4
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.035 0.048 -10000 0 -0.45 2 2
CSN2 -0.006 0.067 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
LAT -0.11 0.17 -10000 0 -0.35 145 145
YBX1 0.003 0.008 -10000 0 -10000 0 0
LCK -0.024 0.18 -10000 0 -0.85 22 22
SHC1 0.014 0.04 -10000 0 -0.86 1 1
NOX4 -0.007 0.078 -10000 0 -0.77 5 5
Aurora A signaling

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
Aurora A/GADD45A 0.02 0.046 -9999 0 -10000 0 0
BIRC5 -0.24 0.4 -9999 0 -0.86 140 140
NFKBIA 0.048 0.041 -9999 0 -10000 0 0
CPEB1 -0.14 0.31 -9999 0 -0.77 94 94
AKT1 0.048 0.041 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.018 0.042 -9999 0 -10000 0 0
NDEL1/TACC3 0.016 0.078 -9999 0 -0.74 4 4
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.014 0.019 -9999 0 -10000 0 0
PAK1/Aurora A 0.02 0.046 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB 0.012 0.05 -9999 0 -0.76 2 2
TPX2 -0.14 0.3 -9999 0 -0.67 120 120
TP53 0.025 0.037 -9999 0 -10000 0 0
DLG7 0.02 0.045 -9999 0 -10000 0 0
AURKAIP1 0.012 0.05 -9999 0 -0.76 2 2
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.017 0.082 -9999 0 -0.77 4 4
G2/M transition of mitotic cell cycle 0.018 0.041 -9999 0 -10000 0 0
AURKA 0.027 0.056 -9999 0 -10000 0 0
AURKB -0.14 0.15 -9999 0 -0.29 229 229
CDC25B 0.018 0.064 -9999 0 -0.58 2 2
G2/M transition checkpoint 0.016 0.051 -9999 0 -0.45 2 2
mRNA polyadenylation -0.073 0.19 -9999 0 -0.45 94 94
Aurora A/CPEB -0.074 0.19 -9999 0 -0.46 94 94
Aurora A/TACC1/TRAP/chTOG -0.003 0.024 -9999 0 -10000 0 0
BRCA1 0.016 0 -9999 0 -10000 0 0
centrosome duplication 0.02 0.046 -9999 0 -10000 0 0
regulation of centrosome cycle -0.007 0.068 -9999 0 -0.73 4 4
spindle assembly -0.003 0.024 -9999 0 -10000 0 0
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.14 0.21 -9999 0 -0.71 6 6
CENPA -0.12 0.14 -9999 0 -0.3 160 160
Aurora A/PP2A 0.02 0.046 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.054 0.036 -9999 0 -10000 0 0
negative regulation of DNA binding 0.025 0.037 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.016 0.051 -9999 0 -0.45 2 2
mitotic prometaphase 0.038 0.04 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.056 -9999 0 -10000 0 0
TACC1 0.016 0 -9999 0 -10000 0 0
TACC3 0.008 0.08 -9999 0 -0.86 4 4
Aurora A/Antizyme1 0.02 0.053 -9999 0 -0.44 1 1
Aurora A/RasGAP 0.02 0.046 -9999 0 -10000 0 0
OAZ1 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0.019 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.14 0.3 -9999 0 -0.67 120 120
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.092 0.25 -9999 0 -0.52 120 120
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.016 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.016 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.1 0.092 -9999 0 -10000 0 0
NEF -0.06 0.085 -9999 0 -10000 0 0
NFKBIA 0.001 0.045 -9999 0 -10000 0 0
BIRC3 -0.07 0.31 -9999 0 -0.79 74 74
CYCS -0.082 0.14 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.38 0.48 -9999 0 -1.1 159 159
MAP2K7 -0.044 0.11 -9999 0 -10000 0 0
protein ubiquitination 0.06 0.072 -9999 0 -0.42 3 3
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.016 0 -9999 0 -10000 0 0
BID -0.097 0.15 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.05 0.12 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.05 0.12 -9999 0 -10000 0 0
MAPK8 -0.031 0.1 -9999 0 -10000 0 0
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.014 0.04 -9999 0 -0.86 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.14 0.13 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.059 -9999 0 -10000 0 0
CHUK 0.061 0.076 -9999 0 -0.47 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.41 0.45 -9999 0 -0.75 264 264
TNF 0.002 0.11 -9999 0 -0.81 8 8
FASLG -0.59 0.61 -9999 0 -1.1 264 264
NFKB1 0.001 0.045 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.009 0.068 -9999 0 -0.53 8 8
CASP6 -0.05 0.052 -9999 0 -10000 0 0
CASP7 -0.063 0.21 -9999 0 -0.55 51 51
RELA 0.001 0.045 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 -0.063 0.21 -9999 0 -0.55 51 51
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0 0 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.053 0.082 -9999 0 -0.53 3 3
APAF-1/Caspase 9 -0.13 0.18 -9999 0 -0.56 51 51
BCL2 -0.019 0.097 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.081 0.31 -10000 0 -0.91 26 26
NCK1/PAK1/Dok-R -0.081 0.1 -10000 0 -0.45 11 11
NCK1/Dok-R -0.079 0.26 -10000 0 -1.1 26 26
PIK3CA 0.002 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol -0.007 0.034 0.32 3 -10000 0 3
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.006 0.041 -10000 0 -0.87 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.32 0.42 -10000 0 -0.86 182 182
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.053 0.22 -10000 0 -0.97 26 26
FN1 -0.052 0.24 -10000 0 -0.86 37 37
PLD2 0.038 0.29 -10000 0 -1.1 26 26
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.029 0.18 -10000 0 -0.76 28 28
ELK1 0.066 0.26 -10000 0 -0.98 26 26
GRB7 0.004 0.093 -10000 0 -0.76 7 7
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.29 -10000 0 -1 38 38
CDKN1A -0.11 0.31 -10000 0 -0.69 17 17
ITGA5 -0.052 0.24 -10000 0 -0.86 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.079 0.26 -10000 0 -1.1 26 26
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO -0.046 0.26 -10000 0 -0.68 21 21
PLG -0.19 0.35 -10000 0 -1.3 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.2 -10000 0 -0.85 26 26
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.009 -10000 0 -10000 0 0
ANGPT2 -0.21 0.38 -10000 0 -0.65 151 151
BMX -0.04 0.34 -10000 0 -1.1 26 26
ANGPT1 0.079 0.19 -10000 0 -1.3 6 6
tube development -0.13 0.34 -10000 0 -0.74 22 22
ANGPT4 -0.021 0.16 -10000 0 -0.87 16 16
response to hypoxia -0.002 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.049 0.31 -10000 0 -1.2 26 26
alpha5/beta1 Integrin -0.051 0.18 -10000 0 -0.67 37 37
FGF2 0.011 0.075 -10000 0 -0.78 4 4
STAT5A (dimer) -0.15 0.36 -10000 0 -0.85 23 23
mol:L-citrulline -0.046 0.26 -10000 0 -0.68 21 21
AGTR1 -0.037 0.17 -10000 0 -0.76 26 26
MAPK14 0.002 0.3 -10000 0 -1.2 26 26
Tie2/SHP2 -0.058 0.25 -10000 0 -1.1 25 25
TEK -0.049 0.28 -10000 0 -1.2 25 25
RPS6KB1 -0.043 0.28 -10000 0 -0.87 26 26
Angiotensin II/AT1 -0.044 0.13 -10000 0 -0.59 26 26
Tie2/Ang1/GRB2 -0.027 0.29 -10000 0 -1.1 26 26
MAPK3 0.05 0.27 -10000 0 -1 26 26
MAPK1 0.05 0.27 -10000 0 -1 26 26
Tie2/Ang1/GRB7 -0.032 0.3 -10000 0 -1.2 26 26
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.038 0.29 -10000 0 -1.1 26 26
PI3K -0.066 0.32 -10000 0 -1.1 26 26
FES -0.004 0.31 -10000 0 -1.1 27 27
Crk/Dok-R -0.079 0.26 -10000 0 -1.1 26 26
Tie2/Ang1/ABIN2 -0.027 0.29 -10000 0 -1.1 26 26
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.07 0.29 -10000 0 -0.8 26 26
STAT5A 0.016 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.043 0.28 -10000 0 -0.87 26 26
Tie2/Ang2 -0.19 0.4 -10000 0 -1.1 22 22
Tie2/Ang1 0.03 0.32 -10000 0 -1.2 26 26
FOXO1 -0.1 0.31 -10000 0 -0.82 24 24
ELF1 0.025 0.013 -10000 0 -10000 0 0
ELF2 0.034 0.3 -10000 0 -1.1 26 26
mol:Choline 0.041 0.28 -10000 0 -1 26 26
cell migration -0.055 0.071 -10000 0 -10000 0 0
FYN -0.15 0.36 -10000 0 -0.86 22 22
DOK2 -0.035 0.21 -10000 0 -0.86 28 28
negative regulation of cell cycle -0.094 0.3 -10000 0 -0.62 16 16
ETS1 0.029 0.033 -10000 0 -10000 0 0
PXN -0.022 0.25 -10000 0 -0.73 21 21
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 -0.057 0.28 -10000 0 -0.75 26 26
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.009 0.11 -10000 0 -0.8 8 8
MAPKKK cascade 0.041 0.28 -10000 0 -1 26 26
RASA1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.001 0.3 -10000 0 -1.1 26 26
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis -0.038 0.24 -10000 0 -0.6 21 21
mol:Phosphatidic acid 0.041 0.28 -10000 0 -1 26 26
mol:Angiotensin II -0.017 0.022 -10000 0 -10000 0 0
mol:NADP -0.046 0.26 -10000 0 -0.68 21 21
Rac1/GTP -0.13 0.19 -10000 0 -0.8 26 26
MMP2 0.033 0.3 -10000 0 -1.1 26 26
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.069 -9999 0 -0.68 5 5
Metarhodopsin II/Arrestin -0.019 0.1 -9999 0 -0.6 15 15
PDE6G/GNAT1/GTP -0.012 0.079 -9999 0 -0.56 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.002 0.089 -9999 0 -0.86 5 5
GRK1 0.003 0.006 -9999 0 -10000 0 0
CNG Channel -0.11 0.21 -9999 0 -0.92 11 11
mol:Na + -0.11 0.21 -9999 0 -0.82 18 18
mol:ADP 0.003 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.035 0.13 -9999 0 -0.5 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.22 -9999 0 -0.86 18 18
CNGB1 -0.005 0.11 -9999 0 -0.86 8 8
RDH5 0 0.12 -9999 0 -0.83 9 9
SAG 0.002 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.074 0.22 -9999 0 -0.78 18 18
Na + (4 Units) -0.1 0.19 -9999 0 -0.75 18 18
RGS9 -0.005 0.13 -9999 0 -0.82 12 12
GNB1/GNGT1 -0.22 0.32 -9999 0 -0.67 161 161
GNAT1/GDP -0.035 0.12 -9999 0 -0.54 11 11
GUCY2D -0.028 0.18 -9999 0 -0.86 22 22
GNGT1 -0.28 0.41 -9999 0 -0.86 161 161
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.036 0.14 -9999 0 -0.58 27 27
mol:11-cis-retinal 0 0.12 -9999 0 -0.83 9 9
mol:cGMP -0.039 0.14 -9999 0 -1 1 1
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.033 0.14 -9999 0 -0.66 24 24
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.13 0.3 -9999 0 -0.76 91 91
Metarhodopsin II -0.017 0.096 -9999 0 -0.55 15 15
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.041 0.14 -9999 0 -0.55 34 34
RGS9BP -0.019 0.16 -9999 0 -0.76 21 21
Metarhodopsin II/Transducin -0.11 0.16 -9999 0 -0.62 9 9
GCAP Family/Ca ++ -0.016 0.098 -9999 0 -0.56 14 14
PDE6A/B -0.035 0.15 -9999 0 -0.67 25 25
mol:Pi -0.035 0.13 -9999 0 -0.5 33 33
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.19 0.26 -9999 0 -0.55 162 162
PDE6B 0.008 0.079 -9999 0 -0.76 5 5
PDE6A -0.025 0.18 -9999 0 -0.86 21 21
PDE6G 0.007 0.081 -9999 0 -0.78 5 5
RHO -0.017 0.15 -9999 0 -0.86 15 15
PDE6 -0.056 0.16 -9999 0 -0.84 8 8
GUCA1A -0.01 0.12 -9999 0 -0.86 9 9
GC2/GCAP Family -0.016 0.098 -9999 0 -0.58 12 12
GUCA1C 0.001 0.05 -9999 0 -0.76 2 2
GUCA1B 0.008 0.08 -9999 0 -0.86 4 4
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.014 0.057 -10000 0 -0.62 1 1
NT3 (dimer)/TRKC -0.039 0.15 -10000 0 -0.61 31 31
NT3 (dimer)/TRKB -0.14 0.25 -10000 0 -0.55 125 125
SHC/Grb2/SOS1/GAB1/PI3K -0.001 0.012 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.11 0.31 -10000 0 -0.86 68 68
PIK3CA 0.016 0 -10000 0 -10000 0 0
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 -0.047 0.21 -10000 0 -0.76 38 38
NTRK2 -0.13 0.3 -10000 0 -0.76 91 91
NTRK3 -0.028 0.18 -10000 0 -0.76 27 27
NT-4/5 (dimer)/TRKB -0.14 0.26 -10000 0 -0.56 123 123
neuron apoptosis 0.15 0.19 0.58 46 -10000 0 46
SHC 2-3/Grb2 -0.16 0.21 -10000 0 -0.65 46 46
SHC1 0.014 0.04 -10000 0 -0.86 1 1
SHC2 -0.1 0.15 -10000 0 -0.5 35 35
SHC3 -0.17 0.25 -10000 0 -0.61 93 93
STAT3 (dimer) 0.011 0.07 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.09 0.21 -10000 0 -0.56 78 78
RIN/GDP 0.048 0.063 -10000 0 -0.32 1 1
GIPC1 0.014 0.035 -10000 0 -0.76 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.075 0.15 -10000 0 -0.63 15 15
RIN/GTP -0.001 0.031 -10000 0 -0.68 1 1
CCND1 0.007 0.16 -10000 0 -0.78 20 20
MAGED1 0.014 0.04 -10000 0 -0.86 1 1
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.004 0.089 -10000 0 -0.86 5 5
SHC/GRB2/SOS1 -0.001 0.026 -10000 0 -0.58 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.16 0.28 -10000 0 -0.6 124 124
TRKA/NEDD4-2 -0.046 0.16 -10000 0 -0.58 38 38
ELMO1 0.012 0.057 -10000 0 -0.86 2 2
RhoG/GTP/ELMO1/DOCK1 -0.002 0.038 -10000 0 -0.59 2 2
NGF -0.072 0.26 -10000 0 -0.86 48 48
HRAS 0.016 0 -10000 0 -10000 0 0
DOCK1 0.016 0 -10000 0 -10000 0 0
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0.002 0.04 -10000 0 -0.86 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.001 0.12 -10000 0 -0.86 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.075 0.15 -10000 0 -0.6 17 17
mol:GDP 0.062 0.085 -10000 0 -0.52 1 1
NGF (dimer) -0.072 0.26 -10000 0 -0.86 48 48
RhoG/GDP -0.003 0.044 -10000 0 -0.68 2 2
RIT1/GDP 0.055 0.062 -10000 0 -0.32 1 1
TIAM1 0.014 0.035 -10000 0 -0.76 1 1
PIK3R1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.17 0.27 -10000 0 -0.56 147 147
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.001 0.03 -10000 0 -0.67 1 1
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 -0.001 0.024 -10000 0 -0.52 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.006 0.09 -10000 0 -0.79 6 6
RAP1/GDP -0.008 0.03 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.11 0.3 -10000 0 -0.86 68 68
ubiquitin-dependent protein catabolic process -0.096 0.21 -10000 0 -0.55 84 84
Schwann cell development -0.027 0.033 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.15 0.24 -10000 0 -0.83 28 28
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.052 0.08 -10000 0 -10000 0 0
STAT3 0.011 0.07 -10000 0 -10000 0 0
axon guidance -0.14 0.22 -10000 0 -0.77 28 28
MAPK3 -0.11 0.27 -10000 0 -0.59 90 90
MAPK1 -0.11 0.27 -10000 0 -0.59 90 90
CDC42/GDP 0.055 0.062 -10000 0 -10000 0 0
NTF3 0.006 0.09 -10000 0 -0.79 6 6
NTF4 -0.004 0.089 -10000 0 -0.86 5 5
NGF (dimer)/TRKA/FAIM -0.096 0.21 -10000 0 -0.55 84 84
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.086 0.17 -10000 0 -0.61 25 25
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L 0.001 0.14 -10000 0 -0.52 31 31
RGS19 0.016 0 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.068 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.062 -10000 0 -0.32 1 1
NGF (dimer)/TRKA/GRIT -0.098 0.22 -10000 0 -0.56 84 84
neuron projection morphogenesis -0.027 0.15 -10000 0 -0.54 15 15
NGF (dimer)/TRKA/NEDD4-2 -0.097 0.21 -10000 0 -0.55 84 84
MAP2K1 0.053 0.024 -10000 0 -10000 0 0
NGFR -0.054 0.24 -10000 0 -0.86 38 38
NGF (dimer)/TRKA/GIPC/GAIP -0.056 0.12 -10000 0 -0.6 2 2
RAS family/GTP/PI3K 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.061 -10000 0 -0.76 3 3
MAPKKK cascade -0.1 0.19 -10000 0 -0.57 53 53
RASA1 0.016 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.045 0.16 -10000 0 -0.57 38 38
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.16 0.25 -10000 0 -0.6 67 67
NGF (dimer)/TRKA/p62/Atypical PKCs -0.083 0.18 -10000 0 -0.88 3 3
MATK -0.078 0.27 -10000 0 -0.86 51 51
NEDD4L 0.014 0.035 -10000 0 -0.76 1 1
RAS family/GDP -0.007 0.029 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.081 0.16 -10000 0 -0.48 40 40
Rac1/GTP -0.047 0.086 -10000 0 -0.42 5 5
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.045 0.15 -9999 0 -0.58 37 37
EPHB2 0.001 0.11 -9999 0 -0.78 9 9
Syndecan-2/TACI -0.052 0.16 -9999 0 -0.58 43 43
LAMA1 -0.007 0.13 -9999 0 -0.77 14 14
Syndecan-2/alpha2 ITGB1 -0.007 0.056 -9999 0 -0.49 5 5
HRAS 0.016 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0 0 -9999 0 -10000 0 0
ITGA5 -0.052 0.24 -9999 0 -0.86 37 37
BAX 0.056 0 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 0.007 0.089 -9999 0 -0.86 5 5
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.003 0.11 -9999 0 -0.86 7 7
Syndecan-2/MMP2 -0.006 0.059 -9999 0 -0.58 5 5
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.002 0.037 -9999 0 -0.57 2 2
dendrite morphogenesis -0.009 0.069 -9999 0 -0.51 9 9
Syndecan-2/GM-CSF -0.017 0.097 -9999 0 -0.58 14 14
determination of left/right symmetry 0.027 0 -9999 0 -10000 0 0
Syndecan-2/PKC delta -0.001 0.026 -9999 0 -0.58 1 1
GNB2L1 0.014 0.04 -9999 0 -0.86 1 1
MAPK3 0.022 0.095 -9999 0 -0.52 14 14
MAPK1 0.022 0.095 -9999 0 -0.52 14 14
Syndecan-2/RACK1 -0.001 0.023 -9999 0 -0.5 1 1
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.027 0 -9999 0 -10000 0 0
ITGA2 0.012 0.05 -9999 0 -0.76 2 2
MAPK8 0.048 0 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.014 0.079 -9999 0 -0.83 1 1
Syndecan-2/Kininogen -0.37 0.21 -9999 0 -0.49 363 363
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.049 0.024 -9999 0 -0.47 1 1
Syndecan-2/CASK/Protein 4.1 0 0 -9999 0 -10000 0 0
extracellular matrix organization -0.006 0.058 -9999 0 -0.58 5 5
actin cytoskeleton reorganization -0.044 0.15 -9999 0 -0.58 37 37
Syndecan-2/Caveolin-2/Ras -0.008 0.063 -9999 0 -0.53 7 7
Syndecan-2/Laminin alpha3 -0.006 0.059 -9999 0 -0.58 5 5
Syndecan-2/RasGAP -0.001 0.021 -9999 0 -0.47 1 1
alpha5/beta1 Integrin -0.051 0.18 -9999 0 -0.67 37 37
PRKCD 0.014 0.04 -9999 0 -0.86 1 1
Syndecan-2 dimer -0.01 0.069 -9999 0 -0.51 9 9
GO:0007205 0.005 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.001 0.02 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.065 0.25 -9999 0 -0.86 43 43
RASA1 0.016 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.002 0.037 -9999 0 -0.57 2 2
Syndecan-2/Synbindin 0 0 -9999 0 -10000 0 0
TGFB1 0.007 0.089 -9999 0 -0.86 5 5
CASP3 0.043 0.026 -9999 0 -0.52 1 1
FN1 -0.052 0.24 -9999 0 -0.86 37 37
Syndecan-2/IL8 -0.036 0.14 -9999 0 -0.56 31 31
SDC2 0.027 0 -9999 0 -10000 0 0
KNG1 -0.57 0.33 -9999 0 -0.76 363 363
Syndecan-2/Neurofibromin 0 0 -9999 0 -10000 0 0
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.018 0.15 -9999 0 -0.86 14 14
Syndecan-2/TGFB1 -0.006 0.059 -9999 0 -0.58 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -9999 0 -10000 0 0
PRKACA 0.045 0 -9999 0 -10000 0 0
angiogenesis -0.036 0.14 -9999 0 -0.56 31 31
MMP2 0.007 0.089 -9999 0 -0.86 5 5
IL8 -0.04 0.21 -9999 0 -0.85 31 31
calcineurin-NFAT signaling pathway -0.052 0.16 -9999 0 -0.58 43 43
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.015 0.01 -10000 0 -10000 0 0
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.025 0.083 -10000 0 -0.51 2 2
AKT1 0.02 0.006 -10000 0 -10000 0 0
GSC -0.024 0.22 -10000 0 -0.76 39 39
NKX2-5 -0.048 0.22 -10000 0 -0.86 32 32
muscle cell differentiation 0.033 0.11 0.57 10 -10000 0 10
SMAD2-3/SMAD4/SP1 0.035 0.079 -10000 0 -10000 0 0
SMAD4 0.032 0.03 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.005 0.034 -10000 0 -0.56 1 1
SMAD3/SMAD4/VDR 0.012 0.05 -10000 0 -10000 0 0
MYC -0.028 0.16 -10000 0 -0.86 16 16
CDKN2B 0.056 0.086 -10000 0 -0.74 3 3
AP1 0.061 0.071 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.011 0.046 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.039 0.069 -10000 0 -0.53 1 1
SP3 0.02 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.051 0.24 -10000 0 -0.88 36 36
SMAD3/SMAD4/GR 0.009 0.045 -10000 0 -0.6 1 1
GATA3 -0.35 0.38 -10000 0 -0.75 230 230
SKI/SIN3/HDAC complex/NCoR1 0.056 0.042 -10000 0 -10000 0 0
MEF2C/TIF2 -0.068 0.18 -10000 0 -0.93 10 10
endothelial cell migration 0.091 0.26 0.74 65 -10000 0 65
MAX 0.008 0.02 -10000 0 -10000 0 0
RBBP7 0.015 0.005 -10000 0 -10000 0 0
RBBP4 0.015 0.005 -10000 0 -10000 0 0
RUNX2 -0.008 0.14 -10000 0 -0.86 13 13
RUNX3 -0.37 0.44 -10000 0 -0.86 210 210
RUNX1 -0.048 0.23 -10000 0 -0.86 35 35
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.006 0.045 -10000 0 -0.87 1 1
VDR 0.011 0.061 -10000 0 -0.76 3 3
CDKN1A 0.083 0.077 -10000 0 -0.64 2 2
KAT2B 0.014 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.048 0.17 -10000 0 -0.61 36 36
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.005 -10000 0 -10000 0 0
SERPINE1 -0.093 0.26 -10000 0 -0.74 65 65
SMAD3/SMAD4/ATF2 0.009 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.003 0.06 -10000 0 -0.5 5 5
SAP30 -0.014 0.16 -10000 0 -0.86 16 16
Cbp/p300/PIAS3 0.008 0.029 -10000 0 -10000 0 0
JUN 0.077 0.067 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.01 0.11 -10000 0 -0.56 16 16
TFE3 0.022 0.011 -10000 0 -10000 0 0
COL1A2 -0.098 0.26 -10000 0 -0.75 64 64
mesenchymal cell differentiation 0.007 0.1 0.59 13 -10000 0 13
DLX1 -0.46 0.44 -10000 0 -0.86 260 260
TCF3 0.016 0 -10000 0 -10000 0 0
FOS 0.009 0.11 -10000 0 -0.74 10 10
SMAD3/SMAD4/Max 0.01 0.035 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0 -10000 0 -10000 0 0
ZBTB17 -0.002 0.047 -10000 0 -0.73 2 2
LAMC1 0.072 0.042 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.009 0.031 -10000 0 -10000 0 0
IRF7 -0.011 0.16 -10000 0 -0.85 16 16
ESR1 0.005 0.054 -10000 0 -0.76 2 2
HNF4A -0.05 0.22 -10000 0 -0.76 41 41
MEF2C -0.002 0.22 -10000 0 -0.82 17 17
SMAD2-3/SMAD4 0.006 0.032 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.006 0.021 -10000 0 -10000 0 0
IGHV3OR16-13 -0.051 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.008 -10000 0 -10000 0 0
SKIL 0.016 0 -10000 0 -10000 0 0
HDAC1 0.015 0.005 -10000 0 -10000 0 0
HDAC2 0.015 0.005 -10000 0 -10000 0 0
SNIP1 0.015 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.011 0.037 -10000 0 -10000 0 0
MSG1/HSC70 0.003 0.033 -10000 0 -0.67 1 1
SMAD2 0.022 0.019 -10000 0 -10000 0 0
SMAD3 0.033 0.027 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.064 0.03 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.025 0.02 -10000 0 -10000 0 0
NCOR1 0.015 0.005 -10000 0 -10000 0 0
NCOA2 0.009 0.07 -10000 0 -0.76 4 4
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A -0.038 0.15 -10000 0 -0.67 27 27
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.086 -10000 0 -10000 0 0
IFNB1 0.047 0.1 -10000 0 -0.53 4 4
SMAD3/SMAD4/MEF2C -0.02 0.2 -10000 0 -0.85 12 12
CITED1 0.012 0.04 -10000 0 -0.86 1 1
SMAD2-3/SMAD4/ARC105 0.008 0.031 -10000 0 -10000 0 0
RBL1 0.016 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.078 0.064 -10000 0 -0.58 1 1
RUNX1-3/PEBPB2 -0.29 0.32 -10000 0 -0.61 231 231
SMAD7 0.052 0.08 -10000 0 -10000 0 0
MYC/MIZ-1 -0.024 0.12 -10000 0 -0.65 18 18
SMAD3/SMAD4 -0.018 0.12 -10000 0 -10000 0 0
IL10 -0.2 0.32 -10000 0 -1 31 31
PIASy/HDAC complex 0.018 0.01 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.17 0.26 -10000 0 -0.76 15 15
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.018 0.01 -10000 0 -10000 0 0
ATF3 0.008 0.079 -10000 0 -0.76 5 5
SMAD3/SMAD4/SP1 -0.012 0.054 -10000 0 -10000 0 0
FOXG1 -0.026 0.17 -10000 0 -0.87 19 19
FOXO3 0.037 0.008 -10000 0 -10000 0 0
FOXO1 0.037 0.008 -10000 0 -10000 0 0
FOXO4 0.037 0.008 -10000 0 -10000 0 0
heart looping -0.001 0.22 -10000 0 -0.8 17 17
CEBPB -0.004 0.14 -10000 0 -0.87 12 12
SMAD3/SMAD4/DLX1 -0.32 0.29 -10000 0 -0.58 260 260
MYOD1 -0.043 0.2 -10000 0 -0.86 27 27
SMAD3/SMAD4/HNF4 -0.034 0.14 -10000 0 -0.54 16 16
SMAD3/SMAD4/GATA3 -0.24 0.26 -10000 0 -0.52 120 120
SnoN/SIN3/HDAC complex/NCoR1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.24 0.28 -10000 0 -0.67 49 49
SMAD3/SMAD4/SP1-3 -0.006 0.044 -10000 0 -10000 0 0
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.012 0.051 -10000 0 -10000 0 0
SIN3B 0.015 0.005 -10000 0 -10000 0 0
SIN3A 0.015 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.073 0.22 -10000 0 -0.88 19 19
ITGB5 0.085 0.066 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.054 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.014 0.11 -10000 0 -0.5 19 19
AR -0.02 0.16 -10000 0 -0.76 22 22
negative regulation of cell growth 0.063 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.025 0.14 -10000 0 -0.6 27 27
E2F5 0.016 0 -10000 0 -10000 0 0
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.036 0.14 -10000 0 -0.64 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 0.074 0.044 -10000 0 -10000 0 0
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.01 0.066 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.007 0.1 -10000 0 -0.59 13 13
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.016 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 0.002 0.22 -10000 0 -0.88 3 3
PTK2B 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.086 0.12 -10000 0 -0.76 2 2
EDN1 -0.04 0.2 -10000 0 -0.76 19 19
EDN3 -0.02 0.16 -10000 0 -0.86 16 16
EDN2 -0.088 0.28 -10000 0 -0.82 59 59
HRAS/GDP 0.055 0.16 -10000 0 -0.73 6 6
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.022 0.15 -10000 0 -0.52 11 11
ADCY4 0.005 0.17 -10000 0 -0.74 3 3
ADCY5 -0.012 0.2 -10000 0 -0.7 12 12
ADCY6 0.005 0.17 -10000 0 -0.74 3 3
ADCY7 -0.011 0.2 -10000 0 -0.73 7 7
ADCY1 -0.003 0.18 -10000 0 -0.74 4 4
ADCY2 -0.13 0.27 -10000 0 -0.71 28 28
ADCY3 0.005 0.17 -10000 0 -0.74 3 3
ADCY8 -0.16 0.28 -10000 0 -0.74 34 34
ADCY9 0.005 0.17 -10000 0 -0.74 3 3
arachidonic acid secretion 0.081 0.15 -10000 0 -0.58 6 6
ETB receptor/Endothelin-1/Gq/GTP 0.034 0.11 -10000 0 -0.54 7 7
GNAO1 0.009 0.078 -10000 0 -0.84 4 4
HRAS 0.016 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.019 0.22 0.38 65 -0.83 3 68
ETA receptor/Endothelin-1/Gs/GTP -0.018 0.21 0.36 65 -0.79 3 68
mol:GTP 0.004 0.002 -10000 0 -10000 0 0
COL3A1 -0.051 0.35 -10000 0 -0.95 51 51
EDNRB 0.006 0.071 -10000 0 -0.79 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.049 0.31 -10000 0 -0.76 46 46
CYSLTR1 0.002 0.22 -10000 0 -0.84 4 4
SLC9A1 -0.016 0.12 -10000 0 -0.42 1 1
mol:GDP 0.048 0.18 -10000 0 -0.7 9 9
SLC9A3 -0.35 0.3 -10000 0 -0.66 144 144
RAF1 0.051 0.16 -10000 0 -0.73 7 7
JUN 0.089 0.12 -10000 0 -10000 0 0
JAK2 0.002 0.22 -10000 0 -0.56 18 18
mol:IP3 0.019 0.17 -10000 0 -0.59 13 13
ETA receptor/Endothelin-1 -0.034 0.28 0.45 65 -0.57 53 118
PLCB1 0.005 0.093 -10000 0 -0.76 7 7
PLCB2 -0.078 0.27 -10000 0 -0.86 52 52
ETA receptor/Endothelin-3 -0.024 0.16 -10000 0 -0.68 18 18
FOS 0.065 0.2 -10000 0 -0.91 11 11
Gai/GDP 0.039 0.071 -10000 0 -0.63 1 1
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.001 0.24 -10000 0 -0.78 14 14
BCAR1 0.014 0.035 -10000 0 -0.76 1 1
PRKCB1 0.021 0.16 -10000 0 -0.56 13 13
GNAQ 0.02 0.003 -10000 0 -10000 0 0
GNAZ 0.011 0.061 -10000 0 -0.76 3 3
GNAL 0.016 0 -10000 0 -10000 0 0
Gs family/GDP -0.042 0.1 -10000 0 -0.66 7 7
ETA receptor/Endothelin-1/Gq/GTP 0.044 0.14 -10000 0 -0.5 9 9
MAPK14 0.026 0.13 -10000 0 -0.6 7 7
TRPC6 0.086 0.13 -10000 0 -0.81 2 2
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.061 -10000 0 -0.76 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.016 0.14 -10000 0 -0.55 11 11
ETB receptor/Endothelin-2 -0.085 0.21 -10000 0 -0.63 62 62
ETB receptor/Endothelin-3 -0.03 0.13 -10000 0 -0.66 19 19
ETB receptor/Endothelin-1 -0.037 0.17 -10000 0 -0.62 20 20
MAPK3 0.065 0.19 -10000 0 -0.73 13 13
MAPK1 0.065 0.19 -10000 0 -0.72 14 14
Rac1/GDP 0.055 0.16 -10000 0 -0.73 6 6
cAMP biosynthetic process -0.063 0.19 -10000 0 -0.62 13 13
MAPK8 0.081 0.13 -10000 0 -0.69 1 1
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.005 0.085 -10000 0 -0.58 3 3
p130Cas/CRK/Src/PYK2 0.076 0.17 -10000 0 -0.72 6 6
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.055 0.16 -10000 0 -0.73 6 6
COL1A2 -0.11 0.34 -10000 0 -0.9 62 62
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.08 0.23 -10000 0 -0.63 61 61
mol:DAG 0.019 0.17 -10000 0 -0.59 13 13
MAP2K2 0.061 0.17 -10000 0 -0.71 8 8
MAP2K1 0.062 0.17 -10000 0 -0.72 7 7
EDNRA -0.011 0.14 -10000 0 -0.98 2 2
positive regulation of muscle contraction 0.014 0.19 -10000 0 -0.78 3 3
Gq family/GDP -0.031 0.14 -10000 0 -0.71 12 12
HRAS/GTP 0.039 0.17 -10000 0 -0.7 9 9
PRKCH 0.031 0.16 -10000 0 -0.68 7 7
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.031 0.16 -10000 0 -0.68 7 7
PRKCB 0.025 0.18 -10000 0 -0.74 11 11
PRKCE 0.03 0.16 -10000 0 -0.64 8 8
PRKCD 0.03 0.16 -10000 0 -0.65 8 8
PRKCG 0.006 0.19 -10000 0 -0.71 16 16
regulation of vascular smooth muscle contraction 0.065 0.22 -10000 0 -1 12 12
PRKCQ 0.019 0.18 -10000 0 -0.7 10 10
PLA2G4A 0.081 0.16 -10000 0 -0.64 6 6
GNA14 0.009 0.093 -10000 0 -0.76 7 7
GNA15 -0.003 0.14 -10000 0 -0.86 12 12
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.016 0.05 -10000 0 -0.76 2 2
Rac1/GTP -0.019 0.22 0.38 65 -0.83 3 68
MMP1 -0.14 0.37 -10000 0 -0.86 95 95
Wnt signaling

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.063 0.13 -9999 0 -0.61 7 7
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.01 0.15 -9999 0 -0.86 14 14
WNT4 -0.073 0.25 -9999 0 -0.76 55 55
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.061 -9999 0 -0.76 3 3
WNT11 -0.037 0.2 -9999 0 -0.77 32 32
S1P3 pathway

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
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.04 0.045 -9999 0 -10000 0 0
GNAO1 0.011 0.078 -9999 0 -0.84 4 4
S1P/S1P3/G12/G13 -0.001 0.02 -9999 0 -0.44 1 1
AKT1 -0.002 0.013 -9999 0 -10000 0 0
AKT3 -0.024 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 0.013 0.061 -9999 0 -0.76 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.017 0.035 -9999 0 -0.76 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.054 0.049 -9999 0 -0.54 1 1
MAPK3 0.062 0.047 -9999 0 -0.51 1 1
MAPK1 0.062 0.047 -9999 0 -0.51 1 1
JAK2 -0.025 0.13 -9999 0 -0.48 2 2
CXCR4 -0.13 0.26 -9999 0 -0.47 171 171
FLT1 0.012 0.08 -9999 0 -0.86 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.062 0.047 -9999 0 -0.51 1 1
S1P/S1P3/Gi 0.054 0.05 -9999 0 -0.55 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.036 -9999 0 -0.49 1 1
VEGFA -0.38 0.44 -9999 0 -0.86 215 215
S1P/S1P2/Gi 0.049 0.043 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.28 0.35 -9999 0 -0.67 216 216
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.009 0.072 -9999 0 -0.6 1 1
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.013 0.061 -9999 0 -0.76 3 3
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 0.004 0.093 -9999 0 -0.76 7 7
GNA15 -0.006 0.14 -9999 0 -0.86 12 12
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.012 0.05 -9999 0 -0.76 2 2
Rac1/GTP -0.005 0.036 -9999 0 -0.49 1 1
FoxO family signaling

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
G6PC -0.57 0.68 -9999 0 -1.3 224 224
PLK1 -0.13 0.37 -9999 0 -0.79 89 89
CDKN1B 0.062 0.16 -9999 0 -10000 0 0
FOXO3 -0.042 0.23 -9999 0 -0.66 12 12
KAT2B 0.013 0.02 -9999 0 -10000 0 0
FOXO1/SIRT1 -0.14 0.21 -9999 0 -10000 0 0
CAT -0.028 0.21 -9999 0 -0.69 5 5
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.008 0.038 -9999 0 -10000 0 0
FOXO1 -0.16 0.23 -9999 0 -0.41 224 224
MAPK10 0.032 0.052 -9999 0 -0.44 5 5
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.045 -9999 0 -10000 0 0
response to oxidative stress -0.029 0.045 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.028 0.2 -9999 0 -0.6 5 5
XPO1 0.017 0 -9999 0 -10000 0 0
EP300 -0.004 0.027 -9999 0 -10000 0 0
BCL2L11 0.011 0.043 -9999 0 -10000 0 0
FOXO1/SKP2 -0.14 0.21 -9999 0 -0.4 3 3
mol:GDP -0.029 0.045 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.097 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.084 -9999 0 -10000 0 0
MST1 0.002 0.1 -9999 0 -0.88 6 6
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.046 0.093 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.038 0.019 -9999 0 -10000 0 0
MAPK9 0.037 0.019 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.037 0.028 -9999 0 -10000 0 0
SOD2 0.013 0.21 -9999 0 -0.68 7 7
RBL2 0.022 0.16 -9999 0 -10000 0 0
RAL/GDP 0.008 0.023 -9999 0 -10000 0 0
CHUK 0.013 0.02 -9999 0 -10000 0 0
Ran/GTP 0.015 0.006 -9999 0 -10000 0 0
CSNK1G2 0.014 0.035 -9999 0 -0.76 1 1
RAL/GTP 0.024 0.026 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.36 0.39 -9999 0 -0.73 252 252
SKP2 0.016 0 -9999 0 -10000 0 0
USP7 0.018 0.001 -9999 0 -10000 0 0
IKBKB 0.013 0.02 -9999 0 -10000 0 0
CCNB1 -0.034 0.23 -9999 0 -0.98 8 8
FOXO1-3a-4/beta catenin -0.071 0.1 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -9999 0 -0.4 3 3
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.013 0.02 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.019 0.016 -9999 0 -10000 0 0
ZFAND5 0.11 0.042 -9999 0 -10000 0 0
SFN -0.079 0.27 -9999 0 -0.84 53 53
CDK2 -0.018 0.041 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.013 0.097 -9999 0 -10000 0 0
CREBBP -0.018 0.041 -9999 0 -10000 0 0
FBXO32 -0.03 0.22 -9999 0 -0.85 5 5
BCL6 0.022 0.16 -9999 0 -10000 0 0
RALB 0.018 0 -9999 0 -10000 0 0
RALA 0.018 0 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.012 0.05 -9999 0 -0.76 2 2
SPHK1 -0.058 0.24 -9999 0 -0.86 40 40
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.001 0.095 -9999 0 -0.31 42 42
GNAO1 0.009 0.078 -9999 0 -0.84 4 4
mol:Sphinganine-1-P -0.03 0.2 -9999 0 -0.66 42 42
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.017 0.056 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.014 0.035 -9999 0 -0.76 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.023 0.075 -9999 0 -10000 0 0
S1PR5 -0.14 0.33 -9999 0 -0.86 82 82
S1PR4 -0.03 0.2 -9999 0 -0.86 25 25
GNAI1 0.011 0.061 -9999 0 -0.76 3 3
S1P/S1P5/G12 -0.11 0.21 -9999 0 -0.54 82 82
S1P/S1P3/Gq -0.023 0.085 -9999 0 -0.45 14 14
S1P/S1P4/Gi 0.024 0.097 -9999 0 -0.39 11 11
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.011 0.061 -9999 0 -0.76 3 3
GNA14 0.004 0.093 -9999 0 -0.76 7 7
GNA15 -0.006 0.14 -9999 0 -0.86 12 12
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.012 0.05 -9999 0 -0.76 2 2
ABCC1 0.016 0 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 -0.003 0.12 -10000 0 -0.86 9 9
GNB1/GNG2 -0.034 0.062 -10000 0 -0.22 11 11
AKT1 0.056 0.1 -10000 0 -0.25 1 1
EGF -0.68 0.23 -10000 0 -0.76 432 432
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.034 0.082 -10000 0 -0.61 2 2
mol:Ca2+ 0.043 0.14 -10000 0 -0.34 19 19
LYN -0.032 0.073 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.037 -10000 0 -0.19 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.052 0.15 -10000 0 -0.38 16 16
GNG2 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.04 -10000 0 -0.86 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.03 0.077 -10000 0 -0.44 6 6
G beta5/gamma2 -0.045 0.081 -10000 0 -0.29 13 13
PRKCH 0.044 0.15 -10000 0 -0.4 13 13
DNM1 -0.001 0.12 -10000 0 -0.86 9 9
TXA2/TP beta/beta Arrestin3 -0.013 0.042 -10000 0 -0.28 9 9
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.12 0.32 -10000 0 -0.86 76 76
G12 family/GTP -0.042 0.089 -10000 0 -0.32 17 17
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.016 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.1 0.3 10 -10000 0 10
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 0 0.11 -10000 0 -0.76 10 10
mol:IP3 0.04 0.17 -10000 0 -0.42 21 21
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.031 0.21 -10000 0 -0.59 21 21
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.056 0.13 -10000 0 -0.61 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.054 0.12 -10000 0 -0.6 9 9
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.014 0.04 -10000 0 -0.86 1 1
PRKCB1 0.039 0.16 -10000 0 -0.38 35 35
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.038 0.21 -10000 0 -0.53 37 37
LCK -0.049 0.12 -10000 0 -0.6 12 12
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.043 0.099 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.027 0.037 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.043 0.098 -10000 0 -10000 0 0
MAPK14 0.055 0.11 -10000 0 -0.31 1 1
TGM2/GTP 0.039 0.19 -10000 0 -0.49 19 19
MAPK11 0.055 0.11 -10000 0 -0.31 1 1
ARHGEF1 0.043 0.087 -10000 0 -0.33 1 1
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.046 0.16 -10000 0 -0.4 24 24
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 0.046 0.13 -10000 0 -0.38 11 11
cAMP biosynthetic process 0.037 0.16 -10000 0 -0.39 21 21
Gq family/GTP/EBP50 0.027 0.059 -10000 0 -0.47 1 1
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.032 0.073 -10000 0 -10000 0 0
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.089 0.11 -10000 0 -0.39 20 20
VCAM1 0.044 0.14 -10000 0 -0.35 19 19
TP beta/Gq family/GDP/G beta5/gamma2 0.03 0.077 -10000 0 -0.44 6 6
platelet activation 0.069 0.15 -10000 0 -0.34 11 11
PGI2/IP -0.001 0.031 -10000 0 -0.68 1 1
PRKACA -0.055 0.13 -10000 0 -0.34 77 77
Gq family/GDP/G beta5/gamma2 0.025 0.078 -10000 0 -0.44 6 6
TXA2/TP beta/beta Arrestin2 -0.013 0.059 -10000 0 -0.42 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.02 0.13 -10000 0 -10000 0 0
mol:DAG 0.039 0.18 -10000 0 -0.43 35 35
EGFR -0.001 0.12 -10000 0 -0.85 9 9
TXA2/TP alpha 0.036 0.2 -10000 0 -0.54 24 24
Gq family/GTP -0.004 0.054 -10000 0 -0.48 1 1
YES1 -0.032 0.073 -10000 0 -10000 0 0
GNAI2/GTP -0.037 0.085 -10000 0 -10000 0 0
PGD2/DP -0.11 0.25 -10000 0 -0.68 76 76
SLC9A3R1 0.016 0 -10000 0 -10000 0 0
FYN -0.032 0.073 -10000 0 -10000 0 0
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 -0.006 0.14 -10000 0 -0.86 12 12
PGK/cGMP -0.01 0.071 -10000 0 -0.5 10 10
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.049 0.11 -10000 0 -0.71 1 1
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.044 0.15 -10000 0 -0.4 13 13
PRKCB 0.042 0.16 -10000 0 -0.44 17 17
PRKCE 0.046 0.15 -10000 0 -0.4 15 15
PRKCD 0.043 0.16 -10000 0 -0.41 17 17
PRKCG 0.032 0.18 -10000 0 -0.51 23 23
muscle contraction 0.045 0.2 -10000 0 -0.53 22 22
PRKCZ 0.051 0.15 -10000 0 -0.38 17 17
ARR3 0.004 0.007 -10000 0 -10000 0 0
TXA2/TP beta -0.042 0.096 -10000 0 -10000 0 0
PRKCQ 0.038 0.16 -10000 0 -0.43 18 18
MAPKKK cascade 0.038 0.19 -10000 0 -0.49 23 23
SELE 0.039 0.15 -10000 0 -0.42 32 32
TP beta/GNAI2/GDP/G beta/gamma -0.04 0.093 -10000 0 -10000 0 0
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 0.004 0.093 -10000 0 -0.76 7 7
chemotaxis 0.039 0.23 -10000 0 -0.61 35 35
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.012 0.05 -10000 0 -0.76 2 2
Rac1/GTP 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.028 0.039 -10000 0 -0.57 2 2
MAP4K4 0.025 0.094 -10000 0 -0.48 1 1
BAG4 0.016 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.1 0.047 -10000 0 -0.49 3 3
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.12 0.32 -10000 0 -0.86 74 74
BAX -0.043 0.018 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.047 0.008 -10000 0 -10000 0 0
BAD -0.099 0.035 -10000 0 -0.27 1 1
SMPD1 0.026 0.043 -10000 0 -0.28 1 1
RB1 -0.098 0.036 -10000 0 -10000 0 0
FADD/Caspase 8 0.04 0.088 -10000 0 -0.43 1 1
MAP2K4 -0.082 0.034 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.086 0.058 -10000 0 -0.59 4 4
EGF -0.68 0.23 -10000 0 -0.76 432 432
mol:ceramide -0.12 0.038 0.2 1 -10000 0 1
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.031 0 -10000 0 -10000 0 0
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.097 0.036 -10000 0 -10000 0 0
cell proliferation -0.055 0.064 -10000 0 -0.45 11 11
BID -0.012 0.066 -10000 0 -10000 0 0
MAP3K1 -0.098 0.036 -10000 0 -10000 0 0
EIF2A -0.068 0.033 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.066 0.053 -10000 0 -0.54 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.066 0.053 -10000 0 -0.54 4 4
Cathepsin D/ceramide -0.099 0.034 -10000 0 -0.27 1 1
FADD 0.025 0.094 -10000 0 -0.48 1 1
KSR1 -0.1 0.061 -10000 0 -0.63 4 4
MAPK8 -0.077 0.037 -10000 0 -0.35 2 2
PRKRA -0.098 0.036 -10000 0 -10000 0 0
PDGFA 0.016 0 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 0.003 0.11 -10000 0 -0.86 7 7
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.12 0.038 0.2 1 -10000 0 1
CTSD 0.014 0.035 -10000 0 -0.76 1 1
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.058 0.07 -10000 0 -0.49 11 11
PRKCD 0.014 0.04 -10000 0 -0.86 1 1
PRKCZ 0.011 0.061 -10000 0 -0.76 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.031 0 -10000 0 -10000 0 0
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.035 -10000 0 -0.76 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.035 0.078 -10000 0 -0.51 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.068 -10000 0 -0.53 8 8
mol:Sphingosine-1-phosphate 0.028 0.039 -10000 0 -0.57 2 2
MAP2K1 -0.072 0.055 -10000 0 -0.55 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.064 0.023 -10000 0 -10000 0 0
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 -0.082 0.034 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.009 0.068 -10000 0 -0.53 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.016 0.036 -10000 0 -10000 0 0
MAP2K2 -0.073 0.054 -10000 0 -0.55 4 4
SMPD3 0.026 0.053 -10000 0 -0.33 2 2
TNF 0.002 0.11 -10000 0 -0.81 8 8
PKC zeta/PAR4 -0.005 0.052 -10000 0 -0.57 4 4
mol:PHOSPHOCHOLINE 0.23 0.085 0.26 432 -10000 0 432
NF kappa B1/RelA/I kappa B alpha -0.003 0.036 -10000 0 -10000 0 0
AIFM1 -0.064 0.023 -10000 0 -10000 0 0
BCL2 0.016 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.017 0.093 -9999 0 -0.52 16 16
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.014 0.16 -9999 0 -0.86 16 16
alpha4/beta7 Integrin/MAdCAM1 -0.026 0.11 -9999 0 -0.52 24 24
EPO -0.3 0.42 -9999 0 -0.86 172 172
alpha4/beta7 Integrin -0.022 0.12 -9999 0 -0.67 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.022 0.12 -9999 0 -0.67 16 16
EPO/EPOR (dimer) -0.24 0.32 -9999 0 -0.67 172 172
lamellipodium assembly 0.003 0.013 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.13 0.17 -9999 0 -0.66 7 7
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
MADCAM1 -0.002 0.11 -9999 0 -0.86 8 8
cell adhesion -0.026 0.11 -9999 0 -0.52 24 24
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.01 0.14 -9999 0 -1 1 1
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.036 0.14 -9999 0 -0.6 26 26
p130Cas/Crk/Dock1 -0.028 0.11 -9999 0 -0.84 2 2
VCAM1 -0.011 0.15 -9999 0 -0.84 15 15
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.017 0.094 -9999 0 -10000 0 0
BCAR1 0.022 0.14 -9999 0 -0.93 2 2
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0.003 0.013 -9999 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 -0.02 0.089 -9999 0 -0.43 20 20
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.035 -9999 0 -10000 0 0
AP1 -0.029 0.098 -9999 0 -10000 0 0
mol:PIP3 -0.026 0.091 -9999 0 -10000 0 0
AKT1 -0.013 0.055 -9999 0 -10000 0 0
PTK2B 0.034 0.058 -9999 0 -10000 0 0
RHOA 0.036 0.037 -9999 0 -10000 0 0
PIK3CB 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0.051 0.054 -9999 0 -0.46 2 2
MAGI3 0.011 0.061 -9999 0 -0.76 3 3
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.021 0.085 -9999 0 -0.38 24 24
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.046 0.071 -9999 0 -0.42 1 1
NF kappa B1 p50/RelA -0.018 0.072 -9999 0 -10000 0 0
endothelial cell migration 0.008 0.13 -9999 0 -0.54 25 25
ADCY4 0.033 0.12 -9999 0 -0.48 22 22
ADCY5 0.024 0.13 -9999 0 -0.5 24 24
ADCY6 0.033 0.12 -9999 0 -0.48 22 22
ADCY7 0.027 0.12 -9999 0 -0.48 22 22
ADCY1 0.029 0.12 -9999 0 -0.48 22 22
ADCY2 -0.015 0.14 -9999 0 -0.52 22 22
ADCY3 0.033 0.12 -9999 0 -0.48 22 22
ADCY8 -0.026 0.14 -9999 0 -0.49 22 22
ADCY9 0.033 0.12 -9999 0 -0.48 22 22
GSK3B 0.043 0.055 -9999 0 -10000 0 0
arachidonic acid secretion 0.04 0.11 -9999 0 -0.44 20 20
GNG2 0.015 0 -9999 0 -10000 0 0
TRIP6 0 0.003 -9999 0 -10000 0 0
GNAO1 0.009 0.12 -9999 0 -0.49 24 24
HRAS 0.016 0 -9999 0 -10000 0 0
NFKBIA 0.062 0.063 -9999 0 -10000 0 0
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0 0.04 -9999 0 -0.86 1 1
JUN 0.016 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.002 0.024 -9999 0 -0.49 1 1
TIAM1 -0.001 0.047 -9999 0 -1 1 1
PIK3R1 0.015 0 -9999 0 -10000 0 0
mol:IP3 0.052 0.055 -9999 0 -0.47 2 2
PLCB3 0.037 0.024 -9999 0 -0.44 1 1
FOS 0 0.11 -9999 0 -0.76 10 10
positive regulation of mitosis 0.04 0.11 -9999 0 -0.44 20 20
LPA/LPA1-2-3 -0.025 0.1 -9999 0 -0.46 16 16
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.035 -9999 0 -0.76 1 1
stress fiber formation 0.04 0.076 -9999 0 -10000 0 0
GNAZ 0.01 0.12 -9999 0 -0.49 23 23
EGFR/PI3K-beta/Gab1 -0.027 0.094 -9999 0 -10000 0 0
positive regulation of dendritic cell cytokine production -0.025 0.1 -9999 0 -0.46 16 16
LPA/LPA2/MAGI-3 -0.004 0.04 -9999 0 -0.49 3 3
ARHGEF1 0.031 0.096 -9999 0 -0.49 1 1
GNAI2 0.014 0.11 -9999 0 -0.48 20 20
GNAI3 0.014 0.11 -9999 0 -0.48 20 20
GNAI1 0.01 0.12 -9999 0 -0.49 23 23
LPA/LPA3 -0.007 0.062 -9999 0 -0.67 4 4
LPA/LPA2 -0.001 0.012 -9999 0 -10000 0 0
LPA/LPA1 -0.027 0.12 -9999 0 -0.52 25 25
HB-EGF/EGFR -0.28 0.29 -9999 0 -0.58 229 229
HBEGF -0.29 0.35 -9999 0 -0.67 223 223
mol:DAG 0.052 0.055 -9999 0 -0.47 2 2
cAMP biosynthetic process 0.021 0.12 -9999 0 -0.46 21 21
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
LYN 0.062 0.063 -9999 0 -10000 0 0
GNAQ -0.004 0.037 -9999 0 -0.4 4 4
LPAR2 0.016 0 -9999 0 -10000 0 0
LPAR3 0.002 0.08 -9999 0 -0.86 4 4
LPAR1 -0.012 0.15 -9999 0 -0.74 20 20
IL8 -0.074 0.2 -9999 0 -0.5 32 32
PTK2 0.025 0.1 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.021 0.086 -9999 0 -0.38 24 24
EGFR -0.001 0.12 -9999 0 -0.85 9 9
PLCG1 0.019 0.056 -9999 0 -0.41 4 4
PLD2 0.025 0.1 -9999 0 -0.48 4 4
G12/G13 -0.02 0.089 -9999 0 -10000 0 0
PI3K-beta -0.015 0.064 -9999 0 -10000 0 0
cell migration -0.008 0.033 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.035 -9999 0 -0.76 1 1
PXN 0.04 0.077 -9999 0 -10000 0 0
HRAS/GTP -0.025 0.098 -9999 0 -0.46 20 20
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.39 0.44 -9999 0 -0.86 223 223
PRKCE 0.015 0.004 -9999 0 -10000 0 0
PRKCD 0.059 0.057 -9999 0 -0.46 1 1
Gi(beta/gamma) -0.025 0.097 -9999 0 -0.45 20 20
mol:LPA 0.004 0.022 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.018 0.081 -9999 0 -10000 0 0
MAPKKK cascade 0.04 0.11 -9999 0 -0.44 20 20
contractile ring contraction involved in cytokinesis 0.036 0.037 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.01 0.062 -9999 0 -0.41 11 11
GNA15 -0.014 0.076 -9999 0 -0.43 15 15
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT 0.047 0.072 -9999 0 -0.43 1 1
GNA11 -0.006 0.044 -9999 0 -0.39 6 6
Rac1/GTP 0 0.042 -9999 0 -0.92 1 1
MMP2 0.008 0.13 -9999 0 -0.54 25 25
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0 0 -9999 0 -10000 0 0
DAPP1 0.029 0.12 -9999 0 -0.45 17 17
Src family/SYK family/BLNK-LAT/BTK-ITK -0.15 0.26 -9999 0 -0.72 55 55
mol:DAG -0.076 0.15 -9999 0 -0.31 71 71
HRAS 0.017 0 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
ARF5/GDP 0.017 0.075 -9999 0 -10000 0 0
PLCG2 0.002 0.11 -9999 0 -0.82 8 8
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP 0 0 -9999 0 -10000 0 0
ADAP1 -0.003 0.034 -9999 0 -10000 0 0
ARAP3 0 0 -9999 0 -10000 0 0
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.016 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.01 0.069 -9999 0 -0.86 3 3
mol:Ca2+ -0.025 0.078 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.014 0.035 -9999 0 -0.76 1 1
ZAP70 -0.48 0.44 -9999 0 -0.86 272 272
mol:IP3 -0.041 0.11 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.017 0.075 -9999 0 -10000 0 0
RhoA/GDP -0.003 0.006 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK 0.014 0.035 -9999 0 -0.76 1 1
actin cytoskeleton reorganization 0.044 0.082 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.036 0.056 -9999 0 -0.57 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.21 0.24 -9999 0 -0.56 130 130
BLK -0.04 0.21 -9999 0 -0.86 30 30
PDPK1 0.016 0 -9999 0 -10000 0 0
CYTH1 0 0 -9999 0 -10000 0 0
HCK -0.034 0.2 -9999 0 -0.86 27 27
CYTH3 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
KRAS 0.017 0 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0 0 -9999 0 -10000 0 0
SGK1 0 0 -9999 0 -10000 0 0
INPP5D 0.008 0.08 -9999 0 -0.86 4 4
mol:GDP 0.009 0.079 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.012 0.05 -9999 0 -0.76 2 2
ARF6/GDP -0.003 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP 0 0 -9999 0 -10000 0 0
VAV1 -0.2 0.38 -9999 0 -0.86 119 119
mol:PI-3-4-P2 0.025 0.063 -9999 0 -0.67 4 4
RAS family/GTP/PI3K Class I 0 0 -9999 0 -10000 0 0
PLEKHA1 0.036 0.056 -9999 0 -0.57 4 4
Rac1/GDP 0.017 0.075 -9999 0 -10000 0 0
LAT -0.25 0.4 -9999 0 -0.86 143 143
Rac1/GTP -0.003 0.1 -9999 0 -10000 0 0
ITK -0.15 0.22 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.12 0.21 -9999 0 -0.46 72 72
LCK -0.024 0.18 -9999 0 -0.85 22 22
BTK -0.094 0.18 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.014 0.16 -9999 0 -0.86 16 16
PLK4 0.01 0.069 -9999 0 -0.86 3 3
regulation of centriole replication 0.003 0.14 -9999 0 -0.67 19 19
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.2 0.22 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.16 0.17 -9999 0 -1.2 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.026 0.028 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.11 0.091 -9999 0 -0.37 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.18 0.2 -9999 0 -1 1 1
AKT1 -0.16 0.17 -9999 0 -10000 0 0
MAP2K1 -0.13 0.22 -9999 0 -10000 0 0
MAP3K11 -0.15 0.23 -9999 0 -0.81 1 1
IFNGR1 0.001 0.019 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.28 0.29 -9999 0 -0.75 109 109
Rap1/GTP -0.13 0.14 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.21 0.23 -9999 0 -10000 0 0
CEBPB -0.07 0.2 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.2 0.22 -9999 0 -1 2 2
STAT1 -0.15 0.24 -9999 0 -1 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.38 0.43 -9999 0 -0.85 220 220
PIK3CA 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.17 0.19 -9999 0 -0.95 1 1
CEBPB/PTGES2/Cbp/p300 -0.076 0.085 -9999 0 -0.47 1 1
mol:Ca2+ -0.2 0.21 -9999 0 -10000 0 0
MAPK3 -0.091 0.2 -9999 0 -10000 0 0
STAT1 (dimer) -0.14 0.12 -9999 0 -0.54 1 1
MAPK1 -0.091 0.2 -9999 0 -10000 0 0
JAK2 0.001 0.019 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
JAK1 0.001 0.019 -9999 0 -10000 0 0
CAMK2D 0.016 0 -9999 0 -10000 0 0
DAPK1 -0.025 0.15 -9999 0 -0.63 2 2
SMAD7 -0.023 0.082 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.16 0.18 -9999 0 -10000 0 0
PI3K -0.17 0.19 -9999 0 -10000 0 0
IFNG -0.38 0.44 -9999 0 -0.86 220 220
apoptosis -0.038 0.12 -9999 0 -0.44 2 2
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.26 0.37 -9999 0 -0.76 168 168
CAMK2B -0.11 0.28 -9999 0 -0.76 75 75
FRAP1 -0.11 0.2 -9999 0 -10000 0 0
PRKCD -0.14 0.2 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.11 0.091 -9999 0 -0.37 1 1
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
IRF1 -0.059 0.19 -9999 0 -0.93 1 1
STAT1 (dimer)/PIASy -0.17 0.19 -9999 0 -0.95 1 1
SOCS1 0.012 0.079 -9999 0 -0.73 5 5
mol:GDP -0.16 0.17 -9999 0 -10000 0 0
CASP1 -0.023 0.082 -9999 0 -10000 0 0
PTGES2 0.013 0.05 -9999 0 -0.76 2 2
IRF9 0.017 0.076 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.17 0.18 -9999 0 -10000 0 0
RAP1/GDP -0.13 0.14 -9999 0 -10000 0 0
CBL -0.15 0.23 -9999 0 -10000 0 0
MAP3K1 -0.15 0.23 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.11 0.091 -9999 0 -0.37 1 1
PTPN11 -0.17 0.24 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.013 0.045 -10000 0 -10000 0 0
RFC1 0.013 0.045 -10000 0 -10000 0 0
PRKDC 0.013 0.045 -10000 0 -10000 0 0
RIPK1 0.013 0.005 -10000 0 -10000 0 0
CASP7 -0.023 0.068 0.25 5 -10000 0 5
FASLG/FAS/FADD/FAF1 -0.14 0.16 -10000 0 -0.35 21 21
MAP2K4 -0.089 0.16 -10000 0 -0.42 21 21
mol:ceramide -0.16 0.2 -10000 0 -0.48 30 30
GSN 0.013 0.045 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.18 0.18 -10000 0 -0.44 21 21
FAS 0.015 0.006 -10000 0 -10000 0 0
BID 0.02 0.07 -10000 0 -10000 0 0
MAP3K1 -0.037 0.1 -10000 0 -10000 0 0
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
RB1 0.013 0.045 -10000 0 -10000 0 0
CFLAR 0.013 0.005 -10000 0 -10000 0 0
HGF/MET -0.036 0.15 -10000 0 -0.58 30 30
ARHGDIB 0.013 0.045 -10000 0 -10000 0 0
FADD 0.015 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.045 -10000 0 -10000 0 0
NFKB1 -0.065 0.071 -10000 0 -10000 0 0
MAPK8 -0.086 0.18 -10000 0 -0.51 21 21
DFFA 0.013 0.045 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.013 0.045 -10000 0 -10000 0 0
FAS/FADD/MET -0.006 0.058 -10000 0 -0.57 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.052 0.24 -10000 0 -0.86 37 37
FAF1 0.015 0.006 -10000 0 -10000 0 0
PARP1 0.013 0.045 -10000 0 -10000 0 0
DFFB 0.013 0.045 -10000 0 -10000 0 0
CHUK -0.052 0.06 -10000 0 -10000 0 0
FASLG -0.45 0.44 -10000 0 -0.87 252 252
FAS/FADD 0 0 -10000 0 -10000 0 0
HGF -0.021 0.17 -10000 0 -0.81 21 21
LMNA 0.011 0.049 -10000 0 -0.52 1 1
CASP6 0.013 0.045 -10000 0 -10000 0 0
CASP10 0.015 0.006 -10000 0 -10000 0 0
CASP3 0.015 0.052 -10000 0 -10000 0 0
PTPN13 0.004 0.093 -10000 0 -0.76 7 7
CASP8 0.031 0.11 0.4 37 -10000 0 37
IL6 -0.12 0.32 -10000 0 -0.92 59 59
MET 0.007 0.089 -10000 0 -0.86 5 5
ICAD/CAD 0.013 0.045 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.16 0.2 -10000 0 -0.49 30 30
activation of caspase activity by cytochrome c 0.02 0.07 -10000 0 -10000 0 0
PAK2 0.013 0.045 -10000 0 -10000 0 0
BCL2 0.016 0.001 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.005 0.018 -10000 0 -10000 0 0
AES 0.004 0.016 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.029 0.19 -10000 0 -0.83 25 25
TLE1 0.004 0.016 -10000 0 -10000 0 0
MACF1 0.016 0.003 -10000 0 -10000 0 0
CTNNB1 0.051 0.1 -10000 0 -0.45 1 1
WIF1 -0.009 0.093 -10000 0 -0.77 7 7
beta catenin/RanBP3 0.004 0.11 0.36 19 -10000 0 19
KREMEN2 -0.081 0.27 -10000 0 -0.86 52 52
DKK1 -0.016 0.16 -10000 0 -0.84 18 18
beta catenin/beta TrCP1 0.057 0.094 -10000 0 -10000 0 0
FZD1 0.015 0.005 -10000 0 -10000 0 0
AXIN2 0.012 0.081 -10000 0 -1.4 1 1
AXIN1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.018 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.074 0.065 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.04 0.084 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.1 -10000 0 -10000 0 0
HNF1A -0.002 0.071 -10000 0 -0.75 4 4
CTBP1 0.005 0.017 -10000 0 -10000 0 0
MYC -0.005 0.14 -10000 0 -0.75 16 16
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.091 0.21 -10000 0 -0.57 76 76
NKD1 -0.19 0.34 -10000 0 -0.76 127 127
TCF4 0.005 0.017 -10000 0 -10000 0 0
TCF3 0.005 0.016 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.026 0.11 -10000 0 -0.52 24 24
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.018 0.1 0.36 34 -10000 0 34
LEF1 -0.023 0.15 -10000 0 -0.87 15 15
DVL1 0.004 0.036 -10000 0 -0.33 1 1
CSNK2A1 0.015 0.003 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.083 0.071 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.083 0.22 -10000 0 -0.62 64 64
LRP6 0.016 0.003 -10000 0 -10000 0 0
CSNK1A1 0.005 0.018 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.01 0.16 -10000 0 -0.75 20 20
WNT1 -0.03 0.19 -10000 0 -0.86 24 24
GSK3A 0.016 0.004 -10000 0 -10000 0 0
GSK3B 0.015 0.005 -10000 0 -10000 0 0
FRAT1 0.014 0.005 -10000 0 -10000 0 0
PPP2R5D 0.096 0.16 0.36 126 -10000 0 126
APC -0.019 0.11 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.013 0.067 0.28 7 -10000 0 7
CREBBP 0.005 0.016 -10000 0 -10000 0 0
E-cadherin signaling events

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.022 0.11 -9999 0 -0.51 21 21
E-cadherin/beta catenin -0.023 0.11 -9999 0 -0.57 19 19
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.011 0.061 -9999 0 -0.76 3 3
CDH1 -0.015 0.15 -9999 0 -0.76 19 19
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.07 -10000 0 -10000 0 0
epithelial cell differentiation -0.047 0.11 -10000 0 -10000 0 0
ITCH 0.056 0.018 -10000 0 -10000 0 0
WWP1 -0.098 0.066 -10000 0 -10000 0 0
FYN 0.016 0 -10000 0 -10000 0 0
EGFR -0.001 0.12 -10000 0 -0.85 9 9
PRL 0.006 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.016 0.074 -10000 0 -10000 0 0
PTPRZ1 -0.088 0.26 -10000 0 -0.77 61 61
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.051 0.065 -10000 0 -0.55 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.081 0.086 -10000 0 -0.56 7 7
ADAM17 0.056 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.14 0.084 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.1 -10000 0 -0.64 10 10
NCOR1 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.073 0.068 -10000 0 -0.52 7 7
GRIN2B -0.054 0.085 -10000 0 -0.58 2 2
ErbB4/ErbB2/betacellulin -0.14 0.17 -10000 0 -0.52 69 69
STAT1 0.014 0.04 -10000 0 -0.86 1 1
HBEGF 0.016 0 -10000 0 -10000 0 0
PRLR -0.076 0.25 -10000 0 -0.76 57 57
E4ICDs/ETO2 -0.11 0.079 -10000 0 -0.7 2 2
axon guidance -0.015 0.071 -10000 0 -10000 0 0
NEDD4 0.056 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.069 0.19 -10000 0 -0.58 57 57
CBFA2T3 0.012 0.057 -10000 0 -0.86 2 2
ErbB4/ErbB2/HBEGF -0.065 0.038 -10000 0 -0.52 1 1
MAPK3 -0.027 0.076 -10000 0 -10000 0 0
STAT1 (dimer) -0.11 0.072 -10000 0 -0.54 1 1
MAPK1 -0.027 0.076 -10000 0 -10000 0 0
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.075 0.073 -10000 0 -0.52 8 8
NRG1 0.041 0.094 -10000 0 -0.57 11 11
NRG3 -0.003 0.13 -10000 0 -0.86 10 10
NRG2 -0.002 0.12 -10000 0 -0.85 10 10
NRG4 -0.059 0.23 -10000 0 -0.78 44 44
heart development -0.015 0.071 -10000 0 -10000 0 0
neural crest cell migration -0.074 0.072 -10000 0 -0.52 8 8
ERBB2 0.052 0.042 -10000 0 -0.57 2 2
WWOX/E4ICDs -0.11 0.075 -10000 0 -0.7 1 1
SHC1 0.014 0.04 -10000 0 -0.86 1 1
ErbB4/EGFR/neuregulin 4 -0.15 0.15 -10000 0 -0.57 49 49
apoptosis 0.11 0.062 0.44 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.089 -10000 0 -0.53 10 10
ErbB4/ErbB2/epiregulin -0.098 0.13 -10000 0 -0.6 24 24
ErbB4/ErbB4/betacellulin/betacellulin -0.18 0.19 -10000 0 -0.6 76 76
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.12 0.14 -10000 0 -0.52 44 44
MDM2 -0.11 0.073 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.051 0.068 -10000 0 -0.51 7 7
STAT5A -0.003 0.066 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.083 0.096 -10000 0 -0.57 14 14
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.03 -10000 0 -0.67 1 1
E4ICDs/TAB2/NCoR1 -0.11 0.047 -10000 0 -10000 0 0
STAT5A (dimer) -0.05 0.12 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.005 0.063 -10000 0 -10000 0 0
LRIG1 0.016 0 -10000 0 -10000 0 0
EREG -0.04 0.21 -10000 0 -0.86 30 30
BTC -0.11 0.28 -10000 0 -0.76 76 76
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.015 0.071 -10000 0 -10000 0 0
ERBB4 -0.14 0.085 -10000 0 -10000 0 0
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.034 0.016 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.11 0.14 -10000 0 -0.53 36 36
glial cell differentiation 0.1 0.047 -10000 0 -10000 0 0
WWOX 0.014 0.04 -10000 0 -0.86 1 1
cell proliferation -0.076 0.16 -10000 0 -0.62 9 9
Regulation of Androgen receptor activity

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
HDAC1 0.031 0.002 -9999 0 -10000 0 0
SMARCC1 0.027 0.009 -9999 0 -10000 0 0
REL 0.01 0.05 -9999 0 -0.76 2 2
HDAC7 -0.097 0.08 -9999 0 -0.67 2 2
JUN 0.015 0.003 -9999 0 -10000 0 0
EP300 0.015 0.003 -9999 0 -10000 0 0
KAT2B 0.015 0.003 -9999 0 -10000 0 0
KAT5 0.016 0 -9999 0 -10000 0 0
MAPK14 0.001 0.041 -9999 0 -0.61 2 2
FOXO1 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.082 -9999 0 -0.72 2 2
MAP2K6 -0.001 0.051 -9999 0 -0.78 2 2
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.002 0.006 -9999 0 -10000 0 0
SMARCA2 0.015 0.003 -9999 0 -10000 0 0
PDE9A -0.12 0.13 -9999 0 -1.2 5 5
NCOA2 0.009 0.07 -9999 0 -0.76 4 4
CEBPA -0.001 0.12 -9999 0 -0.86 9 9
EHMT2 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.089 0.089 -9999 0 -0.53 1 1
NR0B1 -0.05 0.21 -9999 0 -0.86 30 30
EGR1 0.004 0.093 -9999 0 -0.76 7 7
RXRs/9cRA -0.005 0.049 -9999 0 -0.54 4 4
AR/RACK1/Src -0.013 0.054 -9999 0 -0.59 1 1
AR/GR 0.003 0.081 -9999 0 -0.77 2 2
GNB2L1 0.014 0.04 -9999 0 -0.86 1 1
PKN1 0.015 0.003 -9999 0 -10000 0 0
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.004 0.011 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.014 0.065 -9999 0 -0.6 1 1
SRC 0.005 0.038 -9999 0 -10000 0 0
NR3C1 0.014 0.04 -9999 0 -0.86 1 1
KLK3 -0.05 0.18 -9999 0 -0.74 19 19
APPBP2 0.002 0.006 -9999 0 -10000 0 0
TRIM24 0.015 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.024 0.044 -9999 0 -0.59 2 2
TMPRSS2 -0.97 0.37 -9999 0 -1.1 419 419
RXRG 0.006 0.08 -9999 0 -0.87 4 4
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.016 0.001 -9999 0 -10000 0 0
RXRB 0.016 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.003 -9999 0 -10000 0 0
NR2C2 0.016 0.001 -9999 0 -10000 0 0
KLK2 -0.018 0.12 -9999 0 -0.62 15 15
AR -0.008 0.08 -9999 0 -0.4 11 11
SENP1 0.016 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0.013 0.009 -9999 0 -10000 0 0
SRY 0.002 0.007 -9999 0 -10000 0 0
GATA2 0.001 0.1 -9999 0 -0.76 9 9
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.17 0.35 -9999 0 -0.86 96 96
T-DHT/AR/RACK1/Src -0.013 0.052 -9999 0 -0.6 1 1
positive regulation of transcription 0.001 0.1 -9999 0 -0.76 9 9
DNAJA1 0.002 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.002 -9999 0 -10000 0 0
NCOA1 0.024 0.005 -9999 0 -10000 0 0
SPDEF -0.18 0.37 -9999 0 -0.87 108 108
T-DHT/AR/TIF2 0.024 0.044 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 -0.025 0.043 -9999 0 -0.58 2 2
GSK3B 0.002 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.009 0.042 -9999 0 -0.51 2 2
SIRT1 0.015 0.003 -9999 0 -10000 0 0
ZMIZ2 0.013 0.009 -9999 0 -10000 0 0
POU2F1 0.004 0.014 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.063 0.14 -9999 0 -0.59 24 24
CREBBP 0.015 0.003 -9999 0 -10000 0 0
SMARCE1 0.015 0.003 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.014 0.04 -9999 0 -0.86 1 1
GNB1/GNG2 -0.054 0.11 -9999 0 -0.54 7 7
mol:DAG 0.011 0.13 -9999 0 -0.49 7 7
PLCG1 0.011 0.13 -9999 0 -0.51 7 7
YES1 -0.01 0.14 -9999 0 -0.57 7 7
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.049 0.1 -9999 0 -0.51 7 7
MAP3K7 -0.1 0.22 -9999 0 -0.56 44 44
mol:Ca2+ 0.011 0.13 -9999 0 -0.47 7 7
mol:IP3 0.011 0.13 -9999 0 -0.49 7 7
NLK -0.008 0.01 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.24 -9999 0 -0.62 44 44
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.063 0.13 -9999 0 -0.61 7 7
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.01 0.14 -9999 0 -0.57 7 7
GO:0007205 0.012 0.13 -9999 0 -0.48 7 7
WNT6 -0.01 0.15 -9999 0 -0.86 14 14
WNT4 -0.073 0.25 -9999 0 -0.76 55 55
NFAT1/CK1 alpha -0.048 0.1 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.061 -9999 0 -0.76 3 3
WNT11 -0.037 0.2 -9999 0 -0.77 32 32
CDC42 0.002 0.14 -9999 0 -0.54 7 7
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0 0 -10000 0 -10000 0 0
HDAC1 0.003 0.011 -10000 0 -10000 0 0
AES 0.003 0.007 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.054 0.22 -10000 0 -0.76 43 43
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.097 0.16 -10000 0 -0.91 3 3
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.016 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.012 0.067 -10000 0 -0.45 1 1
NICD/RBPSUH 0 0 -10000 0 -10000 0 0
WIF1 -0.003 0.094 -10000 0 -0.77 7 7
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.081 0.27 -10000 0 -0.86 52 52
DKK1 -0.016 0.16 -10000 0 -0.84 18 18
beta catenin/beta TrCP1 0.084 0.085 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 -0.011 0.035 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.008 0.047 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS 0 0.11 -10000 0 -0.76 10 10
JUN 0.016 0 -10000 0 -10000 0 0
MAP3K7 0.002 0.008 -10000 0 -10000 0 0
CTNNB1 0.08 0.092 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.091 0.21 -10000 0 -0.57 76 76
HNF1A -0.003 0.069 -10000 0 -0.76 4 4
CTBP1 0.003 0.007 -10000 0 -10000 0 0
MYC -0.016 0.14 -10000 0 -0.73 16 16
NKD1 -0.19 0.34 -10000 0 -0.76 127 127
FZD1 0.016 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.036 0.11 -10000 0 -10000 0 0
apoptosis -0.096 0.16 -10000 0 -0.9 3 3
Delta 1/NOTCHprecursor 0 0 -10000 0 -10000 0 0
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.007 0.024 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.011 0.035 -10000 0 -10000 0 0
DVL1 -0.006 0.034 -10000 0 -0.48 2 2
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.083 0.22 -10000 0 -0.62 64 64
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.004 0.014 -10000 0 -10000 0 0
CCND1 -0.021 0.15 -10000 0 -0.73 20 20
WNT1 -0.029 0.19 -10000 0 -0.86 24 24
Axin1/APC/beta catenin 0.081 0.051 -10000 0 -10000 0 0
DKK2 -0.029 0.19 -10000 0 -0.83 25 25
NOTCH1 precursor/DVL1 -0.003 0.024 -10000 0 -10000 0 0
GSK3B 0.012 0.007 -10000 0 -10000 0 0
FRAT1 0.002 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.036 0.11 -10000 0 -10000 0 0
PPP2R5D 0.092 0.16 0.36 126 -10000 0 126
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.033 0.12 -10000 0 -0.52 25 25
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.02 0.005 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.045 0.092 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 82 82
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.009 0.078 -9999 0 -0.84 4 4
RhoA/GTP -0.046 0.094 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.052 0.11 -9999 0 -10000 0 0
GNAZ 0.011 0.061 -9999 0 -0.76 3 3
GNAI3 0.016 0 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
S1PR5 -0.14 0.33 -9999 0 -0.86 82 82
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
GNAI1 0.011 0.061 -9999 0 -0.76 3 3
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.02 0.093 -10000 0 -0.45 22 22
regulation of S phase of mitotic cell cycle -0.013 0.063 -10000 0 -10000 0 0
GNAO1 0.009 0.078 -10000 0 -0.84 4 4
HRAS 0.016 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.05 0.15 -10000 0 -0.51 47 47
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.049 0.088 -10000 0 -10000 0 0
T-DHT/AR -0.027 0.12 -10000 0 -0.58 22 22
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.008 9 9
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.061 -10000 0 -0.76 3 3
mol:GDP -0.025 0.11 -10000 0 -0.55 22 22
cell proliferation 0.074 0.1 -10000 0 -0.66 2 2
PIK3CA 0.016 0 -10000 0 -10000 0 0
FOS 0.06 0.14 -10000 0 -0.83 10 10
mol:Ca2+ -0.003 0.014 -10000 0 -0.11 4 4
MAPK3 0.066 0.096 -10000 0 -0.58 2 2
MAPK1 0.046 0.051 -10000 0 -0.3 2 2
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 10 10
cAMP biosynthetic process -0.045 0.15 -10000 0 -0.49 47 47
GNG2 0.016 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 10 10
HRAS/GTP -0.018 0.083 -10000 0 -0.45 1 1
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.016 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 10 10
PI3K 0 0 -10000 0 -10000 0 0
apoptosis -0.064 0.087 0.6 2 -10000 0 2
T-DHT/AR/PELP1 -0.023 0.1 -10000 0 -0.5 22 22
HRAS/GDP -0.023 0.11 -10000 0 -0.51 22 22
CREB1 0.064 0.092 -10000 0 -0.65 2 2
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.02 0.16 -10000 0 -0.76 22 22
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 0.037 0.09 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.022 0.1 -10000 0 -0.48 22 22
T-DHT/AR/PELP1/Src -0.02 0.094 -10000 0 -0.45 22 22
MAP2K2 0.048 0.09 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K -0.013 0.063 -10000 0 -10000 0 0
GNAZ 0.011 0.061 -10000 0 -0.76 3 3
SHBG -0.061 0.23 -10000 0 -0.76 47 47
Gi family/GNB1/GNG2/GDP -0.008 0.045 -10000 0 -0.45 2 2
mol:T-DHT 0 0 -10000 0 -0.004 8 8
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.17 0.31 -10000 0 -0.68 129 129
Gi family/GTP -0.013 0.06 -10000 0 -0.48 4 4
CDC42 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.001 0.026 -9999 0 -0.57 1 1
AKT1 -0.051 0.19 -9999 0 -0.69 2 2
PTK2B -0.15 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/Frs2 -0.003 0.044 -9999 0 -0.84 1 1
CAV1 -0.05 0.23 -9999 0 -0.86 36 36
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.23 0.25 -9999 0 -1.3 1 1
endothelial cell proliferation -0.037 0.19 -9999 0 -0.69 1 1
mol:Ca2+ -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.21 0.24 -9999 0 -1.2 1 1
RP11-342D11.1 -0.17 0.26 -9999 0 -1.1 1 1
CDH5 0.014 0.04 -9999 0 -0.86 1 1
VEGFA homodimer -0.23 0.26 -9999 0 -0.52 215 215
SHC1 0.014 0.04 -9999 0 -0.86 1 1
SHC2 0.009 0.075 -9999 0 -0.81 4 4
HRAS/GDP -0.17 0.18 -9999 0 -0.91 1 1
SH2D2A -0.28 0.42 -9999 0 -0.86 164 164
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.15 -9999 0 -0.79 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.4 0.34 -9999 0 -1 65 65
VEGFR1 homodimer 0.008 0.08 -9999 0 -0.86 4 4
SHC/GRB2/SOS1 -0.18 0.21 -9999 0 -1.1 1 1
GRB10 -0.16 0.26 -9999 0 -1.1 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.2 0.22 -9999 0 -1 2 2
HRAS 0.016 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.084 0.094 -9999 0 -0.58 1 1
HIF1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.21 0.23 -9999 0 -1.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.23 0.25 -9999 0 -1.3 1 1
mol:GDP -0.18 0.2 -9999 0 -1 1 1
mol:NADP -0.061 0.19 -9999 0 -0.62 1 1
eNOS/Hsp90 -0.05 0.18 -9999 0 -0.57 1 1
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.16 0.27 -9999 0 -1.1 1 1
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA -0.37 0.44 -9999 0 -0.86 215 215
VEGFC 0.014 0.04 -9999 0 -0.86 1 1
FAK1/Vinculin -0.1 0.22 -9999 0 -1 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.21 0.24 -9999 0 -1.2 1 1
PTPN6 0.016 0 -9999 0 -10000 0 0
EPAS1 0.026 0.039 -9999 0 -0.73 1 1
mol:L-citrulline -0.061 0.19 -9999 0 -0.62 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer -0.22 0.25 -9999 0 -1.3 1 1
VEGFR2/3 heterodimer -0.003 0.044 -9999 0 -0.84 1 1
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.15 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer 0.043 0.052 -9999 0 -0.74 2 2
FLT1 0.008 0.08 -9999 0 -0.86 4 4
NEDD4 0.018 0.001 -9999 0 -10000 0 0
MAPK3 -0.14 0.25 -9999 0 -0.76 2 2
MAPK1 -0.14 0.25 -9999 0 -0.76 2 2
VEGFA145/NRP2 -0.3 0.33 -9999 0 -0.67 220 220
VEGFR1/2 heterodimer -0.007 0.067 -9999 0 -0.62 5 5
KDR 0.044 0.053 -9999 0 -0.74 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.21 0.23 -9999 0 -1.2 2 2
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.14 0.25 -9999 0 -0.78 2 2
PI3K -0.16 0.18 -9999 0 -0.82 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.23 0.25 -9999 0 -1.3 1 1
FES -0.16 0.27 -9999 0 -1 2 2
GAB1 -0.16 0.19 -9999 0 -0.82 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.23 0.25 -9999 0 -1.3 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.081 0.2 -9999 0 -0.61 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes -0.23 0.25 -9999 0 -1.3 1 1
PI3K/GAB1 -0.051 0.19 -9999 0 -0.69 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.2 0.22 -9999 0 -1.2 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.004 0.046 -9999 0 -0.78 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 -0.16 0.27 -9999 0 -1.2 1 1
actin cytoskeleton reorganization -0.4 0.33 -9999 0 -1 65 65
PTK2 -0.12 0.24 -9999 0 -1.1 1 1
EDG1 -0.17 0.26 -9999 0 -1.1 1 1
mol:DAG -0.16 0.27 -9999 0 -1.1 1 1
CaM/Ca2+ -0.18 0.21 -9999 0 -1 1 1
MAP2K3 -0.14 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.21 0.23 -9999 0 -1.2 1 1
PLCG1 -0.16 0.27 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.21 0.24 -9999 0 -1.2 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.23 0.25 -9999 0 -1.3 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.23 0.25 -9999 0 -1.3 1 1
cell migration -0.05 0.2 -9999 0 -0.77 1 1
mol:PI-3-4-5-P3 -0.15 0.17 -9999 0 -0.74 4 4
FYN 0.016 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.19 0.21 -9999 0 -1 1 1
mol:NO -0.061 0.19 -9999 0 -0.62 1 1
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.17 0.18 -9999 0 -0.92 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.21 0.23 -9999 0 -1.2 1 1
VHL 0.016 0 -9999 0 -10000 0 0
ITGB3 0.014 0.035 -9999 0 -0.76 1 1
NOS3 -0.071 0.2 -9999 0 -0.73 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck -0.23 0.26 -9999 0 -1.1 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.14 0.25 -9999 0 -1 1 1
PRKCB -0.14 0.26 -9999 0 -0.96 2 2
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.23 0.26 -9999 0 -1.1 4 4
VEGFA165/NRP2 -0.3 0.33 -9999 0 -0.67 220 220
MAPKKK cascade -0.16 0.18 -9999 0 -0.92 1 1
NRP2 0.003 0.11 -9999 0 -0.86 7 7
VEGFC homodimer 0.014 0.04 -9999 0 -0.86 1 1
NCK1 0.016 0 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.1 0.22 -9999 0 -1 1 1
MAP3K13 -0.16 0.27 -9999 0 -1.2 1 1
PDPK1 -0.068 0.2 -9999 0 -0.63 4 4
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.012 0.058 -9999 0 -10000 0 0
epithelial cell differentiation -0.016 0.08 -9999 0 -10000 0 0
CYFIP2 0.003 0.099 -9999 0 -0.76 8 8
ENAH 0.08 0.064 -9999 0 -10000 0 0
EGFR -0.001 0.12 -9999 0 -0.85 9 9
EPHA2 0.014 0.035 -9999 0 -0.76 1 1
MYO6 0.033 0.099 -9999 0 -0.8 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.062 -9999 0 -0.48 8 8
AQP5 -0.17 0.24 -9999 0 -0.53 147 147
CTNND1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.035 0.084 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.019 0.12 -9999 0 -0.49 14 14
EGF -0.68 0.23 -9999 0 -0.76 432 432
NCKAP1 0.016 0 -9999 0 -10000 0 0
AQP3 -0.051 0.16 -9999 0 -0.58 35 35
cortical microtubule organization -0.016 0.08 -9999 0 -10000 0 0
GO:0000145 0.035 0.08 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.081 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GDP -0.013 0.062 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.002 0.031 -9999 0 -0.52 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.052 0.084 -9999 0 -0.59 1 1
PVRL2 0.016 0 -9999 0 -10000 0 0
ZYX 0.035 0.085 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.028 -9999 0 -10000 0 0
CDH1 -0.015 0.15 -9999 0 -0.76 19 19
EGFR/EGFR/EGF/EGF -0.35 0.15 -9999 0 -0.79 26 26
RhoA/GDP -0.015 0.074 -9999 0 -10000 0 0
actin cytoskeleton organization 0.042 0.094 -9999 0 -0.73 2 2
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
IGF1R 0.016 0 -9999 0 -10000 0 0
IGF1 0.003 0.11 -9999 0 -0.86 7 7
DIAPH1 -0.011 0.09 -9999 0 -0.7 8 8
Wnt receptor signaling pathway 0.016 0.08 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.063 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
VCL 0.042 0.096 -9999 0 -0.76 2 2
EFNA1 0.014 0.04 -9999 0 -0.86 1 1
LPP 0.045 0.089 -9999 0 -0.81 1 1
Ephrin A1/EPHA2 -0.016 0.075 -9999 0 -10000 0 0
SEC6/SEC8 -0.013 0.063 -9999 0 -10000 0 0
MGAT3 0.019 0.12 -9999 0 -0.5 14 14
HGF/MET -0.037 0.13 -9999 0 -0.96 4 4
HGF -0.021 0.17 -9999 0 -0.81 21 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.012 0.059 -9999 0 -10000 0 0
actin cable formation 0.1 0.07 -9999 0 -10000 0 0
KIAA1543 0.037 0.13 -9999 0 -0.87 6 6
KIFC3 0.034 0.087 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
EXOC3 0.016 0 -9999 0 -10000 0 0
ACTN1 0.034 0.093 -9999 0 -0.88 1 1
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP -0.016 0.08 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
STX4 0.035 0.085 -9999 0 -10000 0 0
PIP5K1C 0.035 0.085 -9999 0 -10000 0 0
LIMA1 0.016 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
ROCK1 -0.012 0.054 -9999 0 -10000 0 0
adherens junction assembly 0.059 0.13 -9999 0 -0.8 7 7
IGF-1R heterotetramer/IGF1 -0.021 0.087 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.007 0.089 -9999 0 -0.86 5 5
PLEKHA7 0.032 0.1 -9999 0 -0.8 3 3
mol:GTP -0.002 0.031 -9999 0 -0.52 1 1
establishment of epithelial cell apical/basal polarity 0.072 0.076 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.012 0.058 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.042 0.094 -9999 0 -0.73 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.012 0.059 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.014 0.16 -9999 0 -0.86 16 16
alpha4/beta7 Integrin -0.022 0.12 -9999 0 -0.67 16 16
alpha4/beta1 Integrin -0.022 0.12 -9999 0 -0.67 16 16
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.009 0.078 -9999 0 -0.84 4 4
CDC42/GTP -0.017 0.061 -9999 0 -10000 0 0
PLCG1 0.035 0.078 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.017 0.06 -9999 0 -10000 0 0
S1PR5 -0.14 0.33 -9999 0 -0.86 82 82
S1PR4 -0.03 0.2 -9999 0 -0.86 25 25
MAPK3 0.035 0.078 -9999 0 -10000 0 0
MAPK1 0.035 0.078 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.052 0.11 -9999 0 -10000 0 0
GNAI1 0.011 0.061 -9999 0 -0.76 3 3
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 82 82
RHOA 0.016 0.12 -9999 0 -0.49 25 25
S1P/S1P4/Gi -0.02 0.07 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.061 -9999 0 -0.76 3 3
S1P/S1P4/G12/G13 -0.028 0.12 -9999 0 -0.53 25 25
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.28 0.38 -9999 0 -0.76 184 184
HRAS 0.016 0 -9999 0 -10000 0 0
EGFR -0.001 0.12 -9999 0 -0.85 9 9
AKT 0.036 0.03 -9999 0 -10000 0 0
FOXO3 0.016 0 -9999 0 -10000 0 0
AKT1 0.016 0 -9999 0 -10000 0 0
FOXO1 0.016 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
FOXO4 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.089 -9999 0 -0.86 5 5
PIK3CA 0.016 0 -9999 0 -10000 0 0
PIK3CB 0.016 0 -9999 0 -10000 0 0
NRAS 0.016 0 -9999 0 -10000 0 0
PIK3CG 0.01 0.069 -9999 0 -0.86 3 3
PIK3R3 0.016 0 -9999 0 -10000 0 0
PIK3R2 0.016 0 -9999 0 -10000 0 0
NF1 0.016 0 -9999 0 -10000 0 0
RAS -0.041 0.099 -9999 0 -0.38 5 5
ERBB2 0.012 0.05 -9999 0 -0.76 2 2
proliferation/survival/translation -0.041 0.013 -9999 0 -10000 0 0
PI3K -0.022 0.092 -9999 0 -0.3 5 5
PIK3R1 0.016 0 -9999 0 -10000 0 0
KRAS 0.016 0 -9999 0 -10000 0 0
FOXO 0.041 0.034 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.028 0.12 -9999 0 -0.51 26 26
RGS9BP -0.019 0.16 -9999 0 -0.76 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
mol:Na + -0.012 0.085 -9999 0 -0.59 10 10
mol:ADP 0.013 0.033 -9999 0 -0.68 1 1
GNAT2 0.014 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.035 0.13 -9999 0 -0.5 33 33
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.027 -9999 0 -0.59 1 1
GRK7 0.01 0.041 -9999 0 -0.86 1 1
CNGB3 -0.008 0.11 -9999 0 -0.86 8 8
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.12 -9999 0 -0.65 14 14
Cone PDE6 -0.033 0.12 -9999 0 -0.91 1 1
Cone Metarhodopsin II -0.001 0.025 -9999 0 -0.56 1 1
Na + (4 Units) -0.019 0.12 -9999 0 -0.65 14 14
GNAT2/GDP -0.03 0.11 -9999 0 -0.5 7 7
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.015 0.045 -9999 0 -0.54 3 3
Cone Transducin -0.029 0.12 -9999 0 -0.54 26 26
SLC24A2 -0.01 0.1 -9999 0 -0.86 7 7
GNB3/GNGT2 -0.036 0.15 -9999 0 -0.67 26 26
GNB3 -0.033 0.2 -9999 0 -0.86 26 26
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0.001 0.057 -9999 0 -0.86 2 2
ARR3 0.004 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.012 0.085 -9999 0 -0.6 10 10
mol:Pi -0.035 0.13 -9999 0 -0.5 33 33
Cone CNG Channel -0.013 0.085 -9999 0 -0.96 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.01 0.1 -9999 0 -0.86 7 7
RGS9 -0.005 0.13 -9999 0 -0.82 12 12
PDE6C 0.003 0.057 -9999 0 -0.86 2 2
GNGT2 0.016 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.04 -9999 0 -0.86 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.011 0.035 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.032 0.091 -9999 0 -0.49 4 4
JUN 0.032 0.1 -9999 0 -0.53 4 4
HRAS 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.048 0.15 -9999 0 -0.69 10 10
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.048 0.15 -9999 0 -0.69 10 10
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.038 0.13 -9999 0 -0.48 38 38
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.042 0.14 -9999 0 -0.69 7 7
GRB7 0.004 0.093 -9999 0 -0.76 7 7
RET51/GFRalpha1/GDNF -0.048 0.15 -9999 0 -0.71 9 9
MAPKKK cascade -0.037 0.12 -9999 0 -0.72 4 4
BCAR1 0.014 0.035 -9999 0 -0.76 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.035 0.12 -9999 0 -0.47 36 36
lamellipodium assembly -0.03 0.085 -9999 0 -0.44 4 4
RET51/GFRalpha1/GDNF/SHC -0.049 0.15 -9999 0 -0.67 11 11
PIK3CA 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.034 0.12 -9999 0 -0.47 35 35
RET9/GFRalpha1/GDNF/Shank3 -0.033 0.12 -9999 0 -0.47 34 34
MAPK3 0.011 0.14 -9999 0 -0.79 4 4
DOK1 0.016 0 -9999 0 -10000 0 0
DOK6 0 0.11 -9999 0 -0.76 10 10
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.039 0.12 -9999 0 -0.75 4 4
DOK5 -0.005 0.13 -9999 0 -0.77 13 13
GFRA1 -0.035 0.19 -9999 0 -0.77 31 31
MAPK8 0.021 0.11 -9999 0 -0.56 4 4
HRAS/GTP -0.042 0.14 -9999 0 -0.85 4 4
tube development -0.031 0.11 -9999 0 -0.5 6 6
MAPK1 0.011 0.14 -9999 0 -0.79 4 4
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.022 0.078 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.008 0.08 -9999 0 -0.86 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.053 0.17 -9999 0 -0.76 15 15
SHC1 0.014 0.04 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.048 0.15 -9999 0 -0.69 10 10
RET51/GFRalpha1/GDNF/Dok5 -0.059 0.19 -9999 0 -0.84 15 15
PRKCA 0.016 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.028 0.093 -9999 0 -0.53 4 4
PIK3R1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.022 0.079 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.054 0.17 -9999 0 -0.56 41 41
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.011 0.14 -9999 0 -0.77 16 16
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade 0.032 0.1 -9999 0 -0.52 4 4
RET9/GFRalpha1/GDNF/FRS2 -0.033 0.12 -9999 0 -0.47 34 34
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.079 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.031 0.099 -9999 0 -0.61 4 4
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.031 0.099 -9999 0 -0.61 4 4
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.033 0.11 -9999 0 -0.76 4 4
PI3K -0.045 0.13 -9999 0 -0.74 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.031 0.11 -9999 0 -0.5 6 6
GRB10 0.016 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.028 0.089 -9999 0 -0.53 4 4
RET51/GFRalpha1/GDNF/FRS2 -0.048 0.15 -9999 0 -0.5 46 46
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.012 0.05 -9999 0 -0.76 2 2
IRS2 0.001 0.11 -9999 0 -0.86 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.033 0.11 -9999 0 -0.76 4 4
RET51/GFRalpha1/GDNF/PKC alpha -0.048 0.15 -9999 0 -0.71 9 9
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.001 0.069 -9999 0 -0.86 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.049 0.16 -9999 0 -0.51 39 39
Rac1/GTP -0.036 0.1 -9999 0 -0.54 4 4
RET9/GFRalpha1/GDNF -0.037 0.13 -9999 0 -0.52 34 34
GFRalpha1/GDNF -0.042 0.15 -9999 0 -0.6 34 34
Canonical NF-kappaB 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
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.074 0.074 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.16 0.29 -9999 0 -0.67 118 118
NFKBIA 0.065 0 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.014 0.04 -9999 0 -0.86 1 1
IKBKG -0.049 0.086 -9999 0 -10000 0 0
IKK complex/A20 -0.043 0.082 -9999 0 -0.59 2 2
NEMO/A20/RIP2 0.014 0.04 -9999 0 -0.86 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM -0.044 0.077 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.036 0.063 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.2 0.38 -9999 0 -0.86 118 118
NFKB1 0.02 0 -9999 0 -10000 0 0
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.016 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.01 0.079 -9999 0 -0.62 8 8
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.002 0.11 -9999 0 -0.81 8 8
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.065 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.04 0.071 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.037 0.065 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.005 0.098 -10000 0 -0.86 6 6
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0 -10000 0 -10000 0 0
CDKN1A 0.041 0.031 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.024 0.12 -10000 0 -0.67 17 17
mol:Ca2+ -0.021 0.17 0.41 17 -0.66 26 43
AGT -0.03 0.19 -10000 0 -0.83 26 26
CCNA2 -0.056 0.23 -10000 0 -0.89 4 4
TUBA1B 0.016 0 -10000 0 -10000 0 0
EGR1 0.024 0.071 -10000 0 -0.56 7 7
CDK2/Cyclin E1 -0.008 0.055 -10000 0 -0.47 6 6
MAPK3 0.006 0.13 -10000 0 -0.67 17 17
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.13 -10000 0 -0.67 17 17
PTP4A1 0.045 0.057 -10000 0 -10000 0 0
PTP4A3 -0.015 0.16 -10000 0 -0.86 17 17
PTP4A2 0.016 0 -10000 0 -10000 0 0
ITGB1 0.006 0.13 -10000 0 -0.67 17 17
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.032 0.06 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha -0.002 0.037 -10000 0 -0.57 2 2
PRL-1/ATF-5 0.045 0.068 -10000 0 -10000 0 0
RABGGTA 0.012 0.05 -10000 0 -0.76 2 2
BCAR1 0.013 0.08 0.41 17 -0.59 1 18
RHOC 0.032 0.06 -10000 0 -10000 0 0
RHOA 0.032 0.06 -10000 0 -10000 0 0
cell motility 0.038 0.062 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.049 0.053 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.024 0.12 -10000 0 -0.67 17 17
ROCK1 0.038 0.062 -10000 0 -10000 0 0
RABGGTB 0.016 0 -10000 0 -10000 0 0
CDK2 0.016 0 -10000 0 -10000 0 0
mitosis 0.045 0.057 -10000 0 -10000 0 0
ATF5 0.01 0.069 -10000 0 -0.86 3 3
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.006 0.036 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.065 0.091 0.32 32 -0.36 2 34
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.031 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP -0.066 0.25 -10000 0 -0.86 43 43
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.044 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.061 -10000 0 -0.76 3 3
TRIP10 0.016 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.022 0.062 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 0.067 0.094 0.33 32 -0.4 2 34
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.035 0 -10000 0 -10000 0 0
SFN -0.079 0.27 -10000 0 -0.84 53 53
LNPEP 0.014 0.035 -10000 0 -0.76 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.026 0.032 0.67 1 -10000 0 1
CDKN1A -0.003 0.042 -10000 0 -0.65 2 2
KAT2B 0.016 0 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.016 0 -10000 0 -10000 0 0
FOXO4 0.031 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT 0 0.1 -10000 0 -0.86 7 7
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.018 0.16 -10000 0 -0.67 27 27
PPARGC1A -0.065 0.24 -10000 0 -0.76 50 50
FHL2 0.011 0.061 -10000 0 -0.76 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.008 -10000 0 -10000 0 0
HIST2H4A 0.026 0.032 -10000 0 -0.67 1 1
SIRT1/FOXO3a 0 0.007 -10000 0 -10000 0 0
SIRT1 0.001 0.011 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.008 -10000 0 -10000 0 0
SIRT1/Histone H1b 0 0.015 -10000 0 -10000 0 0
apoptosis -0.001 0.008 -10000 0 -10000 0 0
SIRT1/PGC1A -0.052 0.15 -10000 0 -0.5 50 50
p53/SIRT1 0.002 0.024 0.38 2 -10000 0 2
SIRT1/FOXO4 0.001 0.009 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.002 0.036 -10000 0 -0.45 3 3
HIST1H1E 0.029 0.015 -10000 0 -0.3 1 1
SIRT1/p300 0.001 0.008 -10000 0 -10000 0 0
muscle cell differentiation 0.032 0.13 0.57 27 -10000 0 27
TP53 0.001 0.011 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.001 0.008 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.009 0.081 -10000 0 -0.67 7 7
ACSS2 0.028 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.032 0.13 -10000 0 -0.58 27 27
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.061 -9999 0 -0.76 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.023 -9999 0 -10000 0 0
IRAK/TOLLIP 0 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.09 0.22 -9999 0 -0.62 69 69
IL1A -0.008 0.14 -9999 0 -0.86 12 12
IL1B 0.025 0.062 -9999 0 -0.64 4 4
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.029 -9999 0 -10000 0 0
IL1R2 -0.082 0.26 -9999 0 -0.8 58 58
IL1R1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.019 -9999 0 -10000 0 0
TOLLIP 0.016 0 -9999 0 -10000 0 0
TICAM2 0.016 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.042 0.047 -9999 0 -10000 0 0
JUN 0.062 0.025 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.006 0.05 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.015 0.088 -9999 0 -0.52 14 14
PIK3R1 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.014 0.082 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP -0.006 0.057 -9999 0 -0.52 5 5
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.053 0.027 -9999 0 -10000 0 0
IRAK1 0.031 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.024 0.12 -9999 0 -0.67 17 17
IRAK4 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.025 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.006 0.057 -9999 0 -0.52 5 5
IL1 beta/IL1R2 -0.067 0.18 -9999 0 -0.52 62 62
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.005 0.044 -9999 0 -10000 0 0
IRAK3 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.006 0.05 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.046 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.017 0.097 -9999 0 -0.58 14 14
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.016 0 -9999 0 -10000 0 0
MYD88 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
IL1RAP 0.012 0.057 -9999 0 -0.86 2 2
UBE2N 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.004 0.04 -9999 0 -10000 0 0
CASP1 0.016 0 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.096 0.23 -9999 0 -0.63 73 73
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.006 0.053 -9999 0 -10000 0 0
TMEM189-UBE2V1 0.007 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.031 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
IL1RN -0.015 0.16 -9999 0 -0.86 17 17
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.044 0.028 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.036 0.055 -9999 0 -0.5 5 5
SNTA1 0.012 0.053 -9999 0 -0.81 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.037 0.048 -9999 0 -0.48 4 4
MAPK12 0.03 0.083 -9999 0 -0.5 11 11
CCND1 0.013 0.07 -9999 0 -0.28 20 20
p38 gamma/SNTA1 0.034 0.088 -9999 0 -0.52 10 10
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.016 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.03 0.082 -9999 0 -0.5 11 11
MAP2K6 0.031 0.037 -9999 0 -0.48 2 2
MAPT 0.033 0.068 -9999 0 -0.46 6 6
MAPK13 0.026 0.055 -9999 0 -0.57 4 4
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.022 0.019 -9999 0 -0.39 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.014 0.07 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.011 0.072 -9999 0 -0.48 11 11
POMC 0.014 0.035 -9999 0 -0.76 1 1
EGFR -0.001 0.12 -9999 0 -0.85 9 9
Syndecan-3/EGFR -0.01 0.068 -9999 0 -0.47 10 10
AGRP 0.006 0.05 -9999 0 -0.76 2 2
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.007 0.12 -9999 0 -0.86 10 10
long-term memory -0.001 0.017 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.032 0.12 -9999 0 -0.48 32 32
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.019 -9999 0 -0.43 1 1
MC4R -0.01 0.11 -9999 0 -0.86 8 8
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.012 0.14 -9999 0 -0.76 17 17
FGFR/FGF/Syndecan-3 -0.001 0.02 -9999 0 -0.43 1 1
neuron projection morphogenesis -0.022 0.089 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.003 0.032 -9999 0 -0.41 3 3
Syndecan-3/AgRP/MC4R -0.01 0.067 -9999 0 -0.47 8 8
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.02 -9999 0 -0.43 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.031 0.12 -9999 0 -0.47 32 32
IL8 -0.04 0.21 -9999 0 -0.85 31 31
Syndecan-3/Fyn/Cortactin -0.001 0.017 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.019 -9999 0 -0.41 1 1
alpha-MSH/MC4R -0.012 0.089 -9999 0 -0.66 9 9
Gamma Secretase 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.02 0.1 -9999 0 -0.52 19 19
KLHL20 -0.013 0.045 -9999 0 -0.33 1 1
CYFIP2 0.003 0.099 -9999 0 -0.76 8 8
Rac1/GDP 0.068 0.076 -9999 0 -10000 0 0
ENAH -0.02 0.1 -9999 0 -0.52 19 19
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.047 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.011 0.037 -9999 0 -0.22 7 7
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.085 -9999 0 -10000 0 0
RAPGEF1 0.055 0.099 -9999 0 -10000 0 0
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.11 -9999 0 -0.54 19 19
CRK 0.043 0.11 -9999 0 -0.48 19 19
E-cadherin/gamma catenin/alpha catenin -0.022 0.11 -9999 0 -0.51 21 21
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.02 0.1 -9999 0 -0.52 19 19
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.033 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.02 -9999 0 -0.45 1 1
PI3K -0.009 0.043 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.026 0.12 -9999 0 -0.59 21 21
TIAM1 0.014 0.035 -9999 0 -0.76 1 1
E-cadherin(dimer)/Ca2+ -0.016 0.08 -9999 0 -10000 0 0
AKT1 -0.005 0.024 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
CDH1 -0.015 0.15 -9999 0 -0.76 19 19
RhoA/GDP 0.068 0.075 -9999 0 -10000 0 0
actin cytoskeleton organization -0.01 0.033 -9999 0 -0.23 1 1
CDC42/GDP 0.068 0.075 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.068 -9999 0 -0.33 21 21
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.017 0.085 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.017 0.083 -9999 0 -0.42 19 19
mol:GDP 0.064 0.087 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.061 -9999 0 -0.76 3 3
p120 catenin/RhoA/GDP -0.012 0.06 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.035 0.066 -9999 0 -0.26 20 20
NME1 0.016 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.02 0.1 -9999 0 -0.52 19 19
regulation of cell-cell adhesion -0.008 0.041 -9999 0 -10000 0 0
WASF2 -0.005 0.019 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.054 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.088 -9999 0 -0.83 1 1
CCND1 -0.017 0.068 -9999 0 -0.33 20 20
VAV2 0.05 0.1 -9999 0 -0.46 19 19
RAP1/GDP -0.011 0.056 -9999 0 -10000 0 0
adherens junction assembly 0.033 0.11 -9999 0 -0.5 19 19
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.017 0.083 -9999 0 -0.79 1 1
E-cadherin/beta catenin -0.018 0.09 -9999 0 -0.46 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.02 0.1 -9999 0 -0.52 19 19
PIK3CA 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.021 0.073 -9999 0 -0.6 1 1
E-cadherin/beta catenin/alpha catenin -0.019 0.095 -9999 0 -0.48 19 19
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.11 -9999 0 -0.56 19 19
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.007 0.081 0.78 5 -10000 0 5
PI3K Class IB/PDE3B 0.007 0.081 -10000 0 -0.78 5 5
PDE3B 0.007 0.081 -10000 0 -0.78 5 5
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0.016 0 -9999 0 -10000 0 0
MAP2K3 0.038 0.042 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.051 0.041 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.004 0.13 -9999 0 -0.86 11 11
TXN 0.011 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
GADD45A 0.016 0 -9999 0 -10000 0 0
GADD45B 0.016 0 -9999 0 -10000 0 0
MAP3K1 0.016 0 -9999 0 -10000 0 0
MAP3K6 0.014 0.035 -9999 0 -0.76 1 1
MAP3K7 0.016 0 -9999 0 -10000 0 0
MAP3K4 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.026 -9999 0 -0.57 1 1
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.003 0.011 -9999 0 -10000 0 0
TRAF6 0.011 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.11 0.28 -9999 0 -0.76 75 75
CCM2 0.016 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.079 0.18 -9999 0 -0.5 75 75
MAPK11 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.071 0.16 -9999 0 -0.45 75 75
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.02 0.035 -9999 0 -0.42 3 3
TAOK2 0.023 0 -9999 0 -10000 0 0
TAOK3 0.023 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAP3K10 0.014 0.035 -9999 0 -0.76 1 1
MAP3K3 0.016 0 -9999 0 -10000 0 0
TRX/ASK1 0 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.011 0.073 -9999 0 -0.5 10 10
Arf6 downstream 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
PLAUR 0.021 0.17 -10000 0 -0.72 24 24
regulation of axonogenesis -0.034 0.032 -10000 0 -10000 0 0
myoblast fusion 0.016 0.069 0.32 24 -10000 0 24
mol:GTP -0.01 0.043 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.041 0.46 1 -10000 0 1
ARF1/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GM1 0.007 0.035 -10000 0 -10000 0 0
mol:Choline 0.033 0.03 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.072 -10000 0 -0.33 24 24
MAPK3 0.024 0.068 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.041 -10000 0 -0.46 1 1
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.07 -10000 0 -0.32 24 24
ARF1/GDP -0.014 0.062 -10000 0 -10000 0 0
ARF6 0.009 0.024 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.016 0.035 -10000 0 -0.76 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.068 -10000 0 -10000 0 0
actin filament bundle formation 0.014 0.062 -10000 0 -10000 0 0
KALRN -0.012 0.055 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.001 0.026 -10000 0 -0.57 1 1
RhoA/GDP -0.014 0.062 -10000 0 -10000 0 0
NME1 0.017 0.004 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.062 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.01 0.043 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.016 0.073 -10000 0 -0.33 24 24
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.01 0.043 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.043 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GDP -0.016 0.07 -10000 0 -0.32 24 24
ARF6/GTP/RAB11FIP3/RAB11A -0.006 0.03 -10000 0 -0.47 1 1
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.021 0.035 -10000 0 -10000 0 0
RAB11FIP3 0.014 0.035 -10000 0 -0.76 1 1
tube morphogenesis -0.016 0.072 -10000 0 -0.33 24 24
ruffle organization 0.034 0.032 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.043 -10000 0 -10000 0 0
PLD2 0.021 0.035 -10000 0 -10000 0 0
PIP5K1A 0.034 0.032 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.033 0.03 -10000 0 -10000 0 0
Rac1/GTP -0.016 0.073 -10000 0 -0.33 24 24
Ephrin B reverse signaling

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.016 0 -10000 0 -10000 0 0
EPHB2 0.001 0.11 -10000 0 -0.78 9 9
EFNB1 0.018 0.095 -10000 0 -0.67 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.018 0.092 -10000 0 -0.76 2 2
Ephrin B2/EPHB1-2 -0.011 0.076 -10000 0 -0.52 10 10
neuron projection morphogenesis -0.017 0.088 -10000 0 -0.72 2 2
Ephrin B1/EPHB1-2/Tiam1 -0.02 0.1 -10000 0 -0.83 2 2
DNM1 -0.001 0.12 -10000 0 -0.86 9 9
cell-cell signaling 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.025 0.086 -10000 0 -0.68 7 7
YES1 -0.013 0.11 -10000 0 -0.9 7 7
Ephrin B1/EPHB1-2/NCK2 -0.019 0.094 -10000 0 -0.66 2 2
PI3K -0.009 0.083 -10000 0 -0.68 7 7
mol:GDP -0.019 0.099 -10000 0 -0.81 2 2
ITGA2B -0.012 0.15 -10000 0 -0.86 15 15
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.013 0.11 -10000 0 -0.9 7 7
MAP3K7 -0.01 0.087 -10000 0 -0.72 7 7
FGR -0.013 0.11 -10000 0 -0.9 7 7
TIAM1 0.014 0.035 -10000 0 -0.76 1 1
PIK3R1 0.016 0 -10000 0 -10000 0 0
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion -0.019 0.12 -10000 0 -0.6 11 11
LYN -0.013 0.11 -10000 0 -0.9 7 7
Ephrin B1/EPHB1-2/Src Family Kinases -0.013 0.1 -10000 0 -0.85 7 7
Ephrin B1/EPHB1-2 -0.014 0.095 -10000 0 -0.79 7 7
SRC -0.013 0.11 -10000 0 -0.9 7 7
ITGB3 0.014 0.035 -10000 0 -0.76 1 1
EPHB1 0.012 0.054 -10000 0 -0.81 2 2
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.022 0.12 -10000 0 -0.66 16 16
BLK -0.02 0.11 -10000 0 -0.89 7 7
HCK -0.019 0.12 -10000 0 -0.94 7 7
regulation of stress fiber formation 0.019 0.093 0.65 2 -10000 0 2
MAPK8 0.034 0.082 -10000 0 -0.64 7 7
Ephrin B1/EPHB1-2/RGS3 -0.019 0.094 -10000 0 -0.83 1 1
endothelial cell migration -0.007 0.075 -10000 0 -0.62 7 7
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.008 0.1 -10000 0 -0.86 7 7
regulation of focal adhesion formation 0.019 0.093 0.65 2 -10000 0 2
chemotaxis 0.019 0.093 0.81 1 -10000 0 1
PIK3CA 0.016 0 -10000 0 -10000 0 0
Rac1/GTP -0.018 0.09 -10000 0 -0.75 2 2
angiogenesis -0.014 0.094 -10000 0 -0.78 7 7
LCK -0.018 0.11 -10000 0 -0.92 7 7
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.051 0.11 -9999 0 -0.65 4 4
MAP3K8 0.012 0.057 -9999 0 -0.86 2 2
FOS 0.043 0.1 -9999 0 -0.55 4 4
PRKCA 0.017 0.003 -9999 0 -10000 0 0
PTPN7 -0.037 0.21 -9999 0 -0.86 30 30
HRAS 0.016 0.002 -9999 0 -10000 0 0
PRKCB 0.008 0.086 -9999 0 -0.83 5 5
NRAS 0.016 0.002 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.031 0.082 -9999 0 -0.52 2 2
MAP2K1 0.055 0.057 -9999 0 -0.48 5 5
ELK1 0.017 0.003 -9999 0 -10000 0 0
BRAF -0.005 0.045 -9999 0 -0.46 4 4
mol:GTP 0 0.001 -9999 0 -0.006 9 9
MAPK1 0.031 0.082 -9999 0 -0.52 2 2
RAF1 -0.005 0.045 -9999 0 -0.46 4 4
KRAS 0.016 0.002 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.004 0.045 -10000 0 -0.57 3 3
ATM 0.016 0 -10000 0 -10000 0 0
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.035 0 -10000 0 -10000 0 0
protein ubiquitination -0.008 0.062 -10000 0 -10000 0 0
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.035 0.069 -10000 0 -0.52 1 1
FANCF 0.016 0 -10000 0 -10000 0 0
BRCA1 0.016 0 -10000 0 -10000 0 0
CCNE1 0.005 0.098 -10000 0 -0.86 6 6
CDK2/Cyclin E1 -0.008 0.074 -10000 0 -0.67 6 6
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.045 -10000 0 -0.57 3 3
FANCE 0.014 0.04 -10000 0 -0.86 1 1
FANCC 0.016 0 -10000 0 -10000 0 0
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.18 0.36 -10000 0 -0.86 105 105
DNA repair 0.044 0.13 -10000 0 -0.67 5 5
BRCA1/BARD1/ubiquitin -0.004 0.045 -10000 0 -0.57 3 3
BARD1/DNA-PK -0.003 0.034 -10000 0 -10000 0 0
FANCL 0.016 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.004 0.045 0.57 3 -10000 0 3
BRCA1/BARD1/CTIP/M/R/N Complex -0.002 0.022 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.003 0.038 -10000 0 -10000 0 0
BRCA1/BARD1/P53 -0.003 0.034 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.003 0.038 -10000 0 -10000 0 0
BRCA1/BACH1 0.016 0 -10000 0 -10000 0 0
BARD1 0.011 0.061 -10000 0 -0.76 3 3
PCNA 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.003 0.038 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 -0.003 0.038 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.016 0.088 -10000 0 -0.52 12 12
BARD1/DNA-PK/P53 -0.003 0.032 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.045 -10000 0 -0.57 3 3
BRCA1/BARD1/CTIP -0.003 0.034 -10000 0 -10000 0 0
FA complex -0.059 0.11 -10000 0 -0.57 1 1
BARD1/EWS -0.004 0.045 -10000 0 -0.57 3 3
RBBP8 0.031 0 -10000 0 -10000 0 0
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.003 0.034 -10000 0 -10000 0 0
BRCA1/BARD1 -0.009 0.062 -10000 0 -10000 0 0
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.004 0.046 -10000 0 -0.58 3 3
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.006 0.14 -10000 0 -0.86 12 12
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.045 -10000 0 -0.57 3 3
EWSR1 0.016 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.007 0.068 -9999 0 -0.67 5 5
CRKL 0.041 0.065 -9999 0 -0.46 2 2
mol:PIP3 -0.03 0.003 -9999 0 -10000 0 0
AKT1 0.001 0.002 -9999 0 -10000 0 0
PTK2B 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.05 0.062 -9999 0 -10000 0 0
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.029 0.13 -9999 0 -0.58 24 24
MAP3K5 -0.024 0.12 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.026 0.12 -9999 0 -0.6 14 14
AP1 -0.012 0.076 -9999 0 -0.52 10 10
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.04 -9999 0 -0.86 1 1
apoptosis 0.006 0.1 -9999 0 -0.7 10 10
STAT3 (dimer) 0.042 0.075 -9999 0 -0.51 2 2
GAB1/CRKL/SHP2/PI3K -0.009 0.043 -9999 0 -10000 0 0
INPP5D 0.008 0.08 -9999 0 -0.86 4 4
CBL/CRK 0.048 0.062 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 0 0.031 -9999 0 -0.29 5 5
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.008 0.039 -9999 0 -0.34 2 2
PAK1 0.011 0.002 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.029 0.13 -9999 0 -0.58 24 24
HRAS 0.032 0.095 -9999 0 -0.72 2 2
DOCK1 0.05 0.062 -9999 0 -0.43 2 2
GAB1 0.031 0.068 -9999 0 -0.49 2 2
CRK 0.041 0.065 -9999 0 -0.46 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.022 0.1 -9999 0 -0.55 12 12
JUN 0.016 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.013 0.061 -9999 0 -0.4 5 5
PIK3R1 0.016 0 -9999 0 -10000 0 0
cell morphogenesis 0.081 0.074 -9999 0 -10000 0 0
GRB2/SHC -0.012 0.058 -9999 0 -0.54 3 3
FOS 0 0.11 -9999 0 -0.76 10 10
GLMN 0 0 -9999 0 -10000 0 0
cell motility 0 0.031 -9999 0 -0.29 5 5
HGF/MET/MUC20 -0.03 0.13 -9999 0 -0.59 24 24
cell migration -0.012 0.057 -9999 0 -0.52 3 3
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
MET/RANBP10 -0.007 0.068 -9999 0 -0.67 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.069 -9999 0 -0.57 2 2
MET/MUC20 -0.007 0.069 -9999 0 -0.68 5 5
RAP1B 0.058 0.059 -9999 0 -10000 0 0
RAP1A 0.058 0.059 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.029 0.13 -9999 0 -0.58 24 24
RAF1 0.042 0.09 -9999 0 -0.66 2 2
STAT3 -0.014 0.063 -9999 0 -0.52 2 2
cell proliferation 0.055 0.099 -9999 0 -0.64 3 3
RPS6KB1 -0.004 0.02 -9999 0 -10000 0 0
MAPK3 -0.006 0.028 -9999 0 -0.27 5 5
MAPK1 -0.006 0.028 -9999 0 -0.27 5 5
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.014 0.093 -9999 0 -10000 0 0
SRC 0.043 0.076 -9999 0 -0.54 2 2
PI3K -0.011 0.05 -9999 0 -0.46 2 2
MET/Glomulin 0.009 0.064 -9999 0 -0.61 5 5
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 0.051 0.085 -9999 0 -0.6 2 2
MET 0.007 0.089 -9999 0 -0.86 5 5
MAP4K1 -0.037 0.12 -9999 0 -0.42 5 5
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 0.05 0.087 -9999 0 -0.6 2 2
BAD 0.01 0.02 -9999 0 -0.43 1 1
MAP2K4 -0.012 0.11 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.011 0.057 -9999 0 -0.57 2 2
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.012 0.055 -9999 0 -0.49 2 2
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.021 0.17 -9999 0 -0.81 21 21
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
PTPRJ 0.016 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.012 0.054 -9999 0 -0.48 2 2
PDPK1 -0.013 0.003 -9999 0 -10000 0 0
HGF/MET/SHIP -0.034 0.14 -9999 0 -0.6 27 27
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.057 0.16 -10000 0 -0.5 54 54
cell-cell adhesion 0.01 0.064 0.64 2 -10000 0 2
Ephrin B/EPHB2/RasGAP -0.011 0.073 -10000 0 -0.6 3 3
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.016 0 -10000 0 -10000 0 0
SHC1 0.014 0.04 -10000 0 -0.86 1 1
Ephrin B1/EPHB3 -0.014 0.082 -10000 0 -0.5 13 13
Ephrin B1/EPHB1 -0.002 0.035 -10000 0 -0.54 2 2
HRAS/GDP -0.005 0.04 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.011 0.066 -10000 0 -0.49 1 1
Endophilin/SYNJ1 0.04 0.076 -10000 0 -0.56 3 3
KRAS 0.016 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.005 0.046 -10000 0 -0.49 1 1
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 0.004 0.093 -10000 0 -0.76 7 7
PAK1 0.051 0.077 -10000 0 -0.78 1 1
HRAS 0.016 0 -10000 0 -10000 0 0
RRAS 0.04 0.077 -10000 0 -0.78 1 1
DNM1 -0.001 0.12 -10000 0 -0.86 9 9
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.047 0.05 -10000 0 -10000 0 0
lamellipodium assembly -0.01 0.064 -10000 0 -0.64 2 2
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.004 0.03 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
EPHB2 0.001 0.11 -10000 0 -0.78 9 9
EPHB3 -0.005 0.13 -10000 0 -0.77 13 13
EPHB1 0.012 0.053 -10000 0 -0.81 2 2
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP 0 0.051 -10000 0 -10000 0 0
Ephrin B/EPHB2 -0.012 0.075 -10000 0 -0.61 3 3
Ephrin B/EPHB3 -0.015 0.082 -10000 0 -0.67 2 2
JNK cascade 0.043 0.075 -10000 0 -0.56 4 4
Ephrin B/EPHB1 -0.005 0.048 -10000 0 -0.5 1 1
RAP1/GDP 0 0.045 -10000 0 -10000 0 0
EFNB2 0.016 0 -10000 0 -10000 0 0
EFNB3 0.009 0.07 -10000 0 -0.76 4 4
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.011 0.076 -10000 0 -0.52 10 10
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.071 -10000 0 -0.72 2 2
Rap1/GTP -0.01 0.064 -10000 0 -0.66 2 2
axon guidance -0.057 0.16 -10000 0 -0.5 54 54
MAPK3 0.068 0.033 -10000 0 -10000 0 0
MAPK1 0.068 0.033 -10000 0 -10000 0 0
Rac1/GDP 0 0.048 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.008 0.048 -10000 0 -0.45 1 1
CDC42/GDP 0 0.048 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EFNA5 -0.057 0.23 -10000 0 -0.76 45 45
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.008 0.051 -10000 0 -0.61 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.01 0.063 -10000 0 -0.63 2 2
PTK2 0.002 0.016 -10000 0 -10000 0 0
MAP4K4 0.043 0.076 -10000 0 -0.82 1 1
SRC 0.016 0 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.051 -10000 0 -0.5 2 2
MAP2K1 0.059 0.035 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.011 0.075 -10000 0 -0.61 4 4
cell migration 0.07 0.038 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.04 0.077 -10000 0 -0.57 3 3
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.073 0.23 -10000 0 -0.78 2 2
HRAS/GTP -0.011 0.07 -10000 0 -0.7 2 2
Ephrin B1/EPHB1-2 -0.011 0.076 -10000 0 -0.52 10 10
cell adhesion mediated by integrin 0.008 0.055 0.47 5 -10000 0 5
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.012 0.076 -10000 0 -0.77 2 2
RAC1-CDC42/GTP -0.018 0.092 -10000 0 -0.87 3 3
RASA1 0.016 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0 0.045 -10000 0 -10000 0 0
ruffle organization 0.075 0.078 -10000 0 -0.66 2 2
NCK1 0.016 0 -10000 0 -10000 0 0
receptor internalization 0.041 0.1 -10000 0 -0.73 1 1
Ephrin B/EPHB2/KALRN -0.011 0.073 -10000 0 -0.6 3 3
ROCK1 0.021 0.079 -10000 0 -0.45 13 13
RAS family/GDP -0.008 0.047 -10000 0 -10000 0 0
Rac1/GTP -0.011 0.069 -10000 0 -0.7 2 2
Ephrin B/EPHB1/Src/Paxillin -0.004 0.032 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.06 0.046 -10000 0 -0.46 1 1
adherens junction organization 0.041 0.078 -10000 0 -0.68 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.06 -10000 0 -10000 0 0
FMN1 0.025 0.12 -10000 0 -0.67 1 1
mol:IP3 -0.007 0.035 -10000 0 -0.48 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.065 -10000 0 -0.72 1 1
CTNNB1 0.001 0.006 -10000 0 -10000 0 0
AKT1 0.056 0.052 -10000 0 -0.51 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.016 0.11 -10000 0 -0.54 19 19
CTNND1 0.017 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.046 0.071 -10000 0 -0.65 1 1
VASP 0.046 0.072 -10000 0 -0.67 1 1
ZYX 0.046 0.072 -10000 0 -0.67 1 1
JUB 0.044 0.077 -10000 0 -0.67 1 1
EGFR(dimer) -0.021 0.084 -10000 0 -0.48 9 9
E-cadherin/beta catenin-gamma catenin -0.021 0.1 -10000 0 -0.49 21 21
mol:PI-3-4-5-P3 -0.009 0.043 -10000 0 -0.55 1 1
PIK3CA 0.017 0.001 -10000 0 -10000 0 0
PI3K -0.009 0.044 -10000 0 -0.56 1 1
FYN -0.24 0.13 -10000 0 -0.44 14 14
mol:Ca2+ -0.007 0.034 -10000 0 -0.47 1 1
JUP -0.004 0.06 -10000 0 -0.76 3 3
PIK3R1 0.017 0.001 -10000 0 -10000 0 0
mol:DAG -0.007 0.035 -10000 0 -0.48 1 1
CDH1 -0.03 0.15 -10000 0 -0.76 19 19
RhoA/GDP -0.013 0.06 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.046 0.071 -10000 0 -0.65 1 1
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.001 0.12 -10000 0 -0.85 9 9
CASR -0.3 0.15 -10000 0 -0.53 14 14
RhoA/GTP -0.006 0.03 -10000 0 -0.43 1 1
AKT2 0.056 0.052 -10000 0 -0.51 1 1
actin cable formation 0.035 0.11 -10000 0 -0.64 1 1
apoptosis 0.008 0.038 0.5 1 -10000 0 1
CTNNA1 0.017 0.004 -10000 0 -10000 0 0
mol:GDP -0.014 0.066 -10000 0 -0.49 1 1
PIP5K1A 0.046 0.072 -10000 0 -0.67 1 1
PLCG1 -0.007 0.036 -10000 0 -0.5 1 1
Rac1/GTP -0.019 0.076 -10000 0 -0.61 1 1
homophilic cell adhesion 0.002 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.029 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.012 0.065 -10000 0 -0.71 2 2
NFATC4 0.027 0.072 -10000 0 -0.46 1 1
ERBB2IP 0.008 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.016 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.016 0.074 -10000 0 -0.65 1 1
JUN 0.038 0.077 -10000 0 -0.41 1 1
HRAS 0.015 0.001 -10000 0 -10000 0 0
DOCK7 0.022 0.085 -10000 0 -0.61 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.02 0.099 -10000 0 -0.89 2 2
AKT1 0.016 0.002 -10000 0 -10000 0 0
BAD 0.027 0.024 -10000 0 -0.5 1 1
MAPK10 -0.01 0.043 -10000 0 -0.4 1 1
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.017 0.08 -10000 0 -0.73 1 1
RAF1 0.042 0.087 -10000 0 -0.66 2 2
ErbB2/ErbB3/neuregulin 2 -0.022 0.1 -10000 0 -0.49 21 21
STAT3 0 0.002 -10000 0 -10000 0 0
cell migration 0.061 0.052 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.088 0.26 -10000 0 -0.6 6 6
FOS -0.036 0.19 -10000 0 -0.51 10 10
NRAS 0.015 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.074 -10000 0 -0.65 1 1
MAPK3 -0.057 0.21 -10000 0 -0.75 1 1
MAPK1 -0.057 0.21 -10000 0 -0.75 1 1
JAK2 0.022 0.085 -10000 0 -0.61 1 1
NF2 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.008 0.088 -10000 0 -0.38 19 19
NRG1 -0.009 0.12 -10000 0 -0.76 11 11
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 0.027 0.078 -10000 0 -0.45 1 1
MAPK9 -0.007 0.034 -10000 0 -10000 0 0
ERBB2 -0.002 0.038 -10000 0 -0.59 2 2
ERBB3 -0.005 0.1 -10000 0 -0.76 9 9
SHC1 0.007 0.041 -10000 0 -0.86 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.002 0.016 0.34 1 -10000 0 1
STAT3 (dimer) 0 0.002 -10000 0 -10000 0 0
RNF41 0.038 0.005 -10000 0 -10000 0 0
FRAP1 0.015 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.01 0.048 -10000 0 -0.4 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.032 -10000 0 -0.5 2 2
CHRNA1 -0.13 0.28 -10000 0 -0.57 7 7
myelination 0.054 0.068 -10000 0 -0.45 1 1
PPP3CB 0.022 0.08 -10000 0 -0.56 1 1
KRAS 0.015 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.013 0.068 -10000 0 -0.73 2 2
NRG2 -0.002 0.12 -10000 0 -0.85 10 10
mol:GDP 0.008 0.087 -10000 0 -0.37 19 19
SOS1 0.009 0.008 -10000 0 -10000 0 0
MAP2K2 0.048 0.09 -10000 0 -0.72 1 1
SRC 0.016 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.021 0.084 -10000 0 -0.61 1 1
MAP2K1 -0.039 0.18 -10000 0 -0.56 5 5
heart morphogenesis -0.016 0.074 -10000 0 -0.65 1 1
RAS family/GDP -0.012 0.065 -10000 0 -0.71 2 2
GRB2 0.009 0.008 -10000 0 -10000 0 0
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.021 0.024 -10000 0 -0.24 1 1
HSP90AA1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.016 0.002 -10000 0 -10000 0 0
nervous system development -0.016 0.074 -10000 0 -0.65 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.007 0.055 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.046 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src -0.004 0.044 -9999 0 -0.56 3 3
AP1 -0.013 0.074 -9999 0 -0.68 3 3
ILK 0.066 0.047 -9999 0 -10000 0 0
bone resorption -0.022 0.096 -9999 0 -0.77 2 2
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.005 0.044 -9999 0 -10000 0 0
ITGAV 0.022 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.029 0.14 -9999 0 -0.66 21 21
alphaV/beta3 Integrin/Osteopontin -0.004 0.043 -9999 0 -0.5 2 2
MAP3K1 0.066 0.047 -9999 0 -0.46 2 2
JUN 0.016 0.002 -9999 0 -10000 0 0
MAPK3 0.078 0.07 -9999 0 -10000 0 0
MAPK1 0.078 0.07 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.079 0.047 -9999 0 -10000 0 0
ITGB3 0.021 0.036 -9999 0 -0.76 1 1
NFKBIA 0.091 0.07 -9999 0 -10000 0 0
FOS 0 0.11 -9999 0 -0.76 10 10
CD44 -0.021 0.18 -9999 0 -0.86 20 20
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU 0.092 0.16 -9999 0 -1.1 7 7
NF kappa B1 p50/RelA -0.008 0.048 -9999 0 -10000 0 0
BCAR1 0.014 0.035 -9999 0 -0.76 1 1
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.001 0.026 -9999 0 -0.58 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.062 0.055 -9999 0 -10000 0 0
VAV3 0.059 0.097 -9999 0 -0.8 1 1
MAP3K14 0.064 0.071 -9999 0 -10000 0 0
ROCK2 0.014 0.035 -9999 0 -0.76 1 1
SPP1 0.018 0.061 -9999 0 -0.75 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.014 0.073 -9999 0 -0.73 1 1
MMP2 0.1 0.11 -9999 0 -0.73 5 5
Cellular roles of Anthrax toxin

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
ANTXR1 0.016 0 -10000 0 -10000 0 0
ANTXR2 0.014 0.035 -10000 0 -0.76 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.004 -10000 0 -0.095 1 1
monocyte activation 0.005 0.087 -10000 0 -0.36 22 22
MAP2K2 -0.002 0.037 -10000 0 -0.8 1 1
MAP2K1 0 0.003 -10000 0 -10000 0 0
MAP2K7 0 0.003 -10000 0 -10000 0 0
MAP2K6 -0.002 0.029 -10000 0 -0.44 2 2
CYAA 0.021 0.021 -10000 0 -0.43 1 1
MAP2K4 0 0.003 -10000 0 -10000 0 0
IL1B 0.018 0.052 -10000 0 -0.48 4 4
Channel -0.001 0.021 -10000 0 -0.46 1 1
NLRP1 -0.006 0.053 -10000 0 -0.53 5 5
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.004 0.095 1 -10000 0 1
MAPK3 0 0.003 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
PGR -0.015 0.081 -10000 0 -0.45 16 16
PA/Cellular Receptors -0.001 0.023 -10000 0 -0.5 1 1
apoptosis 0 0.004 -10000 0 -0.095 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.001 0.019 -10000 0 -0.43 1 1
macrophage activation 0.028 0.004 -10000 0 -10000 0 0
TNF 0.002 0.11 -10000 0 -0.81 8 8
VCAM1 -0.016 0.084 -10000 0 -0.36 22 22
platelet activation 0 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.023 0.009 -10000 0 -10000 0 0
IL18 0.016 0.063 -10000 0 -0.51 6 6
negative regulation of macrophage activation 0 0.004 -10000 0 -0.095 1 1
LEF 0 0.004 -10000 0 -0.095 1 1
CASP1 -0.003 0.024 -10000 0 -0.23 5 5
mol:cAMP 0 0.005 -10000 0 -10000 0 0
necrosis 0 0.004 -10000 0 -0.095 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.001 0.02 -10000 0 -0.43 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
ceramide 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
MAP4K4 0.027 0.1 -9999 0 -10000 0 0
BAG4 0.016 0 -9999 0 -10000 0 0
BAD 0.031 0.041 -9999 0 -0.4 1 1
NFKBIA 0.016 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.32 -9999 0 -0.86 74 74
BAX 0.032 0.037 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.011 0.028 -9999 0 -0.099 1 1
IKBKB 0.037 0.097 -9999 0 -10000 0 0
MAP2K2 0.046 0.055 -9999 0 -10000 0 0
MAP2K1 0.047 0.052 -9999 0 -0.38 4 4
SMPD1 0.019 0.028 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.038 0.098 -9999 0 -10000 0 0
MAP2K4 0.041 0.035 -9999 0 -10000 0 0
protein ubiquitination 0.04 0.098 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.054 0.053 -9999 0 -0.38 4 4
response to UV 0.001 0 -9999 0 -10000 0 0
RAF1 0.039 0.054 -9999 0 -0.42 4 4
CRADD 0.016 0.002 -9999 0 -10000 0 0
mol:ceramide 0.022 0.038 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.016 0.002 -9999 0 -10000 0 0
MAP3K1 0.032 0.037 -9999 0 -10000 0 0
TRADD 0.016 0.002 -9999 0 -10000 0 0
RELA/p50 0.016 0 -9999 0 -10000 0 0
MAPK3 0.05 0.052 -9999 0 -0.37 4 4
MAPK1 0.05 0.052 -9999 0 -0.37 4 4
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.027 0.1 -9999 0 -10000 0 0
KSR1 0.029 0.057 -9999 0 -0.45 4 4
MAPK8 0.05 0.034 -9999 0 -10000 0 0
TRAF2 0.016 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.037 0.097 -9999 0 -10000 0 0
TNF R/SODD 0 0 -9999 0 -10000 0 0
TNF 0.002 0.11 -9999 0 -0.81 8 8
CYCS 0.033 0.037 -9999 0 -10000 0 0
IKBKG 0.037 0.097 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.1 -9999 0 -0.44 1 1
RELA 0.016 0 -9999 0 -10000 0 0
RIPK1 0.016 0.001 -9999 0 -10000 0 0
AIFM1 0.033 0.037 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.009 0.068 -9999 0 -0.53 8 8
TNFRSF1A 0.016 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.028 0.03 -9999 0 -10000 0 0
NSMAF 0.028 0.099 -9999 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -9999 0 -10000 0 0
BCL2 0.016 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.006 0.075 -9999 0 -0.73 5 5
VDR 0.011 0.061 -9999 0 -0.76 3 3
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.076 0.052 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.086 0.065 -9999 0 -10000 0 0
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA 0.009 0.009 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.019 0.072 -9999 0 -10000 0 0
RXRs/NUR77 -0.018 0.091 -9999 0 -0.5 6 6
RXRs/PPAR 0.058 0.031 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.004 0.046 -9999 0 -0.58 3 3
RARs/VDR/DNA/Vit D3 -0.004 0.042 -9999 0 -10000 0 0
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.061 -9999 0 -0.76 3 3
RARs/RARs/DNA/9cRA -0.001 0.027 -9999 0 -0.42 2 2
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.036 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.019 0.072 -9999 0 -10000 0 0
THRA 0.014 0.035 -9999 0 -0.76 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.004 0.046 -9999 0 -0.58 3 3
RXRs/PPAR/9cRA/PGJ2/DNA -0.003 0.055 -9999 0 -0.5 4 4
NR1H4 -0.01 0.14 -9999 0 -0.76 16 16
RXRs/LXRs/DNA 0.008 0.059 -9999 0 -10000 0 0
NR1H2 0.023 0.036 -9999 0 -0.75 1 1
NR1H3 0.025 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.005 0.055 -9999 0 -0.48 4 4
NR4A1 -0.01 0.14 -9999 0 -0.76 16 16
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.041 0.069 -9999 0 -0.34 5 5
RXRG 0.014 0.08 -9999 0 -0.85 4 4
RXR alpha/CCPG 0 0.004 -9999 0 -10000 0 0
RXRA 0.024 0.004 -9999 0 -10000 0 0
RXRB 0.025 0.006 -9999 0 -10000 0 0
THRB -0.029 0.18 -9999 0 -0.76 28 28
PPARG 0.016 0 -9999 0 -10000 0 0
PPARD 0.016 0 -9999 0 -10000 0 0
TNF 0.083 0.13 -9999 0 -0.88 8 8
mol:Oxysterols 0.009 0.008 -9999 0 -10000 0 0
cholesterol transport 0.086 0.064 -9999 0 -10000 0 0
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.012 0.05 -9999 0 -0.76 2 2
RXRs/NUR77/BCL2 -0.012 0.06 -9999 0 -10000 0 0
SREBF1 0.092 0.068 -9999 0 -0.66 1 1
RXRs/RXRs/DNA/9cRA 0.005 0.059 -9999 0 -0.5 4 4
ABCA1 0.091 0.074 -9999 0 -0.66 2 2
RARs/THRs -0.026 0.099 -9999 0 -10000 0 0
RXRs/FXR -0.018 0.092 -9999 0 -0.51 7 7
BCL2 0.016 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0.002 0.013 -9999 0 -10000 0 0
DOCK1 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.014 0.16 -9999 0 -0.86 16 16
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.022 0.12 -9999 0 -0.67 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.019 0.1 -9999 0 -0.58 16 16
alpha4/beta7 Integrin/Paxillin -0.017 0.094 -9999 0 -0.52 16 16
lamellipodium assembly 0.002 0.022 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
TLN1 0.016 0 -9999 0 -10000 0 0
PXN 0.031 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.015 0.079 -9999 0 -10000 0 0
cell adhesion -0.016 0.086 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.017 0.094 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ARF6/GDP 0.002 0.013 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.031 0.12 -9999 0 -0.98 1 1
p130Cas/Crk/Dock1 -0.001 0.022 -9999 0 -0.48 1 1
VCAM1 -0.011 0.15 -9999 0 -0.84 15 15
alpha4/beta1 Integrin/Paxillin/Talin -0.016 0.087 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.016 0.087 -9999 0 -10000 0 0
BCAR1 0.014 0.035 -9999 0 -0.76 1 1
mol:GDP 0.016 0.086 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.016 0.087 -9999 0 -10000 0 0
Rac1/GTP 0.002 0.023 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.007 0.26 -9999 0 -1.1 25 25
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.023 0.073 -9999 0 -10000 0 0
ATF2/c-Jun 0.046 0.056 -9999 0 -10000 0 0
MAPK11 0.023 0.073 -9999 0 -10000 0 0
MITF 0.045 0.088 -9999 0 -10000 0 0
MAPKAPK5 0.045 0.088 -9999 0 -10000 0 0
KRT8 0.044 0.09 -9999 0 -10000 0 0
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.033 0.11 -9999 0 -10000 0 0
CEBPB 0.034 0.11 -9999 0 -10000 0 0
SLC9A1 0.045 0.088 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.052 0.087 -9999 0 -10000 0 0
p38alpha-beta/MNK1 -0.018 0.07 -9999 0 -10000 0 0
JUN 0.047 0.056 -9999 0 -10000 0 0
PPARGC1A -0.001 0.16 -9999 0 -0.38 50 50
USF1 0.045 0.088 -9999 0 -10000 0 0
RAB5/GDP/GDI1 -0.013 0.049 -9999 0 -10000 0 0
NOS2 0.041 0.12 -9999 0 -0.79 6 6
DDIT3 0.042 0.094 -9999 0 -10000 0 0
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 0.049 0.076 -9999 0 -0.48 1 1
p38alpha-beta/HBP1 -0.018 0.07 -9999 0 -10000 0 0
CREB1 0.05 0.092 -9999 0 -10000 0 0
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.049 0.075 -9999 0 -10000 0 0
RPS6KA4 0.045 0.088 -9999 0 -10000 0 0
PLA2G4A 0.045 0.087 -9999 0 -10000 0 0
GDI1 0.045 0.088 -9999 0 -10000 0 0
TP53 0.047 0.11 -9999 0 -10000 0 0
RPS6KA5 0.045 0.088 -9999 0 -10000 0 0
ESR1 0.043 0.092 -9999 0 -10000 0 0
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C 0.045 0.088 -9999 0 -10000 0 0
MEF2A 0.045 0.088 -9999 0 -10000 0 0
EIF4EBP1 0.045 0.094 -9999 0 -10000 0 0
KRT19 -0.043 0.21 -9999 0 -0.91 8 8
ELK4 0.045 0.088 -9999 0 -10000 0 0
ATF6 0.045 0.088 -9999 0 -10000 0 0
ATF1 0.05 0.092 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK2 -0.018 0.07 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK3 -0.018 0.07 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.012 0.05 -9999 0 -0.76 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.007 0.039 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
MAP3K12 0.016 0 -9999 0 -10000 0 0
FGR 0.01 0.069 -9999 0 -0.86 3 3
p38 alpha/TAB1 -0.012 0.039 -9999 0 -0.31 2 2
PRKG1 0 0.11 -9999 0 -0.76 10 10
DUSP8 0.014 0.035 -9999 0 -0.76 1 1
PGK/cGMP/p38 alpha -0.018 0.059 -9999 0 -0.44 2 2
apoptosis -0.012 0.037 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 0.014 0.04 -9999 0 -0.86 1 1
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 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 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.057 0.084 -9999 0 -0.42 2 2
BLK -0.04 0.21 -9999 0 -0.86 30 30
HCK -0.034 0.2 -9999 0 -0.86 27 27
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.012 0.057 -9999 0 -0.86 2 2
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.057 0.067 -9999 0 -0.34 2 2
positive regulation of innate immune response 0.068 0.091 -9999 0 -0.44 2 2
LCK -0.024 0.18 -9999 0 -0.85 22 22
p38alpha-beta/MKP7 0.074 0.088 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.072 0.092 -9999 0 -10000 0 0
PGK/cGMP -0.012 0.083 -9999 0 -0.58 10 10
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.073 0.09 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.01 0.14 -9999 0 -0.83 14 14
Arf6 trafficking events

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
SLC2A4 -0.003 0.12 -9999 0 -0.82 11 11
CLTC 0.044 0 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.037 0 -9999 0 -10000 0 0
Dynamin 2/GTP 0 0 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
CD59 0.04 0 -9999 0 -10000 0 0
CPE 0 0.12 -9999 0 -0.58 20 20
CTNNB1 0.016 0 -9999 0 -10000 0 0
membrane fusion 0 0 -9999 0 -10000 0 0
CTNND1 0.044 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.045 0 -9999 0 -10000 0 0
TSHR -0.048 0.2 -9999 0 -0.59 57 57
INS 0.017 0.001 -9999 0 -10000 0 0
BIN1 0.016 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.025 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
JUP 0.038 0.022 -9999 0 -10000 0 0
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 0.028 0.055 -9999 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 -0.05 0.23 -9999 0 -0.86 36 36
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.016 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.006 0.03 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.025 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 -0.044 0.16 -9999 0 -0.59 36 36
ACAP1 -0.019 0.024 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 0.033 0.012 -9999 0 -10000 0 0
clathrin heavy chain/ACAP1 0.043 0.011 -9999 0 -10000 0 0
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.016 0 -9999 0 -10000 0 0
exocyst 0 0 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 0.044 0 -9999 0 -10000 0 0
NME1 0.025 0 -9999 0 -10000 0 0
clathrin coat assembly 0.043 0 -9999 0 -10000 0 0
IL2RA -0.015 0.11 -9999 0 -10000 0 0
VAMP3 0.025 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.009 0.06 -9999 0 -0.43 6 6
EXOC6 0.016 0 -9999 0 -10000 0 0
PLD1 0 0 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.045 0 -9999 0 -10000 0 0
SDC1 0.037 0.029 -9999 0 -10000 0 0
ARF6/GDP 0 0 -9999 0 -10000 0 0
EXOC7 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.006 0.031 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.016 0 -9999 0 -10000 0 0
ADRB2 0.05 0.028 -9999 0 -10000 0 0
EXOC3 0.016 0 -9999 0 -10000 0 0
ASAP2 0.016 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0 0 -9999 0 -10000 0 0
KLC1 0.016 0 -9999 0 -10000 0 0
AVPR2 -0.13 0.21 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.005 0.026 -9999 0 -10000 0 0
IGF1 pathway

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.016 0 -9999 0 -10000 0 0
PTK2 0.016 0 -9999 0 -10000 0 0
CRKL 0.029 0.058 -9999 0 -0.41 7 7
GRB2/SOS1/SHC -0.001 0.026 -9999 0 -0.58 1 1
HRAS 0.016 0 -9999 0 -10000 0 0
IRS1/Crk -0.007 0.053 -9999 0 -0.41 7 7
IGF-1R heterotetramer/IGF1/PTP1B -0.008 0.062 -9999 0 -0.52 7 7
AKT1 0.057 0.051 -9999 0 -10000 0 0
BAD 0.065 0.052 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.029 0.058 -9999 0 -0.41 7 7
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.053 -9999 0 -0.41 7 7
RAF1 0.07 0.046 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.007 0.05 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.008 0.059 -9999 0 -0.43 9 9
PIK3CA 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.057 0.051 -9999 0 -10000 0 0
GNB2L1 0.014 0.04 -9999 0 -0.86 1 1
positive regulation of MAPKKK cascade 0.061 0.041 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.007 0.047 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.007 0.054 -9999 0 -0.51 1 1
IGF-1R heterotetramer 0.015 0.012 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.053 -9999 0 -0.41 7 7
Crk/p130 Cas/Paxillin -0.007 0.049 -9999 0 -10000 0 0
IGF1R 0.015 0.012 -9999 0 -10000 0 0
IGF1 0.003 0.1 -9999 0 -0.85 7 7
IRS2/Crk -0.015 0.079 -9999 0 -0.49 8 8
PI3K -0.007 0.049 -9999 0 -10000 0 0
apoptosis -0.068 0.046 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.049 0.061 -9999 0 -0.82 1 1
RAF1/14-3-3 E 0.073 0.041 -9999 0 -10000 0 0
BAD/14-3-3 0.071 0.049 -9999 0 -10000 0 0
PRKCZ 0.054 0.061 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.005 0.036 -9999 0 -10000 0 0
PTPN1 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.041 0.052 -9999 0 -10000 0 0
BCAR1 0.014 0.035 -9999 0 -0.76 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.008 0.06 -9999 0 -0.46 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.007 0.053 -9999 0 -0.41 7 7
GRB10 0.016 0 -9999 0 -10000 0 0
PTPN11 0.029 0.058 -9999 0 -0.41 7 7
IRS1 0.018 0.062 -9999 0 -0.43 9 9
IRS2 0.019 0.091 -9999 0 -0.47 15 15
IGF-1R heterotetramer/IGF1 -0.01 0.079 -9999 0 -0.66 7 7
GRB2 0.016 0 -9999 0 -10000 0 0
PDPK1 0.047 0.053 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKD1 0.05 0.049 -9999 0 -10000 0 0
SHC1 0.014 0.04 -9999 0 -0.86 1 1
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.007 0.055 -9999 0 -10000 0 0
TC10/GTP -0.005 0.048 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.002 0.029 -9999 0 -10000 0 0
HRAS 0.016 0 -9999 0 -10000 0 0
APS homodimer 0.007 0.089 -9999 0 -0.86 5 5
GRB14 -0.029 0.18 -9999 0 -0.76 28 28
FOXO3 -0.003 0.012 -9999 0 -10000 0 0
AKT1 -0.02 0.082 -9999 0 -0.67 1 1
INSR 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
SORBS1 0.014 0.035 -9999 0 -0.76 1 1
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.049 0.001 -9999 0 -10000 0 0
CAV1 -0.006 0.15 -9999 0 -0.51 36 36
CBL/APS/CAP/Crk-II/C3G -0.006 0.053 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 -0.002 0.029 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.025 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.002 0.019 -9999 0 -10000 0 0
RPS6KB1 0.057 0.093 -9999 0 -0.6 1 1
PARD6A 0.011 0.061 -9999 0 -0.76 3 3
CBL 0.016 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.018 0.071 -9999 0 -0.62 1 1
HRAS/GTP -0.006 0.051 -9999 0 -0.74 1 1
Insulin Receptor 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.003 0.035 -9999 0 -10000 0 0
PRKCI -0.005 0.019 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.022 0.09 -9999 0 -0.74 1 1
SHC1 0.014 0.04 -9999 0 -0.86 1 1
negative regulation of MAPKKK cascade 0 0.003 -9999 0 -10000 0 0
PI3K -0.002 0.026 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 -0.02 0.082 -9999 0 -0.67 1 1
PRKCZ -0.009 0.059 -9999 0 -0.7 3 3
SH2B2 0.007 0.089 -9999 0 -0.86 5 5
SHC/SHIP -0.007 0.061 -9999 0 -0.58 4 4
F2RL2 -0.034 0.2 -9999 0 -0.86 27 27
TRIP10 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.025 -9999 0 -0.55 1 1
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.023 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.006 0.057 -9999 0 -0.52 5 5
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.025 -9999 0 -0.54 1 1
INPP5D 0.031 0.065 -9999 0 -0.62 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.001 0.005 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.012 0.05 -9999 0 -0.76 2 2
p62DOK/RasGAP 0 0.003 -9999 0 -10000 0 0
INS 0.005 0.001 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.031 0.064 -9999 0 -0.61 4 4
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.037 0.14 -9999 0 -0.69 4 4
PTPRA 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.002 0.023 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.002 0.03 -9999 0 -0.46 2 2
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.031 0.12 -9999 0 -0.5 27 27
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.008 0.058 -10000 0 -0.5 4 4
ER alpha/Gai/GDP/Gbeta gamma 0.056 0.049 -10000 0 -10000 0 0
AKT1 0.05 0.053 -10000 0 -0.75 2 2
PIK3CA 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.045 0.053 -10000 0 -0.76 2 2
mol:Ca2+ -0.01 0.18 -10000 0 -0.69 9 9
IGF1R 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.003 0.039 -10000 0 -0.5 3 3
SHC1 0.014 0.04 -10000 0 -0.86 1 1
apoptosis -0.05 0.05 0.71 2 -10000 0 2
RhoA/GTP -0.001 0.023 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.006 0.039 -10000 0 -10000 0 0
regulation of stress fiber formation -0.071 0.027 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.009 0.07 -10000 0 -0.54 8 8
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.002 0.029 -10000 0 -0.46 2 2
pseudopodium formation 0.071 0.027 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.002 0.032 -10000 0 -0.5 2 2
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
GNAO1 0.009 0.078 -10000 0 -0.84 4 4
HRAS 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.066 0.051 -10000 0 -0.47 2 2
E2/ER beta (dimer) -0.008 0.072 -10000 0 -0.65 6 6
mol:GDP -0.007 0.052 -10000 0 -0.49 2 2
mol:NADP 0.066 0.051 -10000 0 -0.47 2 2
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.013 0.19 -10000 0 -0.73 9 9
IGF-1R heterotetramer 0.016 0 -10000 0 -10000 0 0
PLCB1 -0.021 0.094 -10000 0 -0.8 3 3
PLCB2 -0.065 0.16 -10000 0 -0.48 59 59
IGF1 0.003 0.11 -10000 0 -0.86 7 7
mol:L-citrulline 0.066 0.051 -10000 0 -0.47 2 2
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.047 -10000 0 -0.63 1 1
JNK cascade -0.008 0.072 -10000 0 -0.64 6 6
BCAR1 0.014 0.035 -10000 0 -0.76 1 1
ESR2 0.005 0.094 -10000 0 -0.83 6 6
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 0.012 0.05 -10000 0 -0.76 2 2
Gq family/GDP/Gbeta gamma -0.014 0.072 -10000 0 -0.6 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.053 0.027 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.006 0.04 -10000 0 -10000 0 0
GNAZ 0.011 0.061 -10000 0 -0.76 3 3
E2/ER alpha (dimer) -0.002 0.038 -10000 0 -0.58 2 2
STRN 0.014 0.035 -10000 0 -0.76 1 1
GNAL 0.016 0 -10000 0 -10000 0 0
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.018 0.065 -10000 0 -0.56 6 6
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.061 -10000 0 -0.76 3 3
HBEGF -0.037 0.14 -10000 0 -0.51 5 5
cAMP biosynthetic process -0.007 0.056 -10000 0 -0.44 8 8
SRC 0.065 0.047 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.006 0.045 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.009 0.05 -10000 0 -10000 0 0
Gs family/GTP -0.007 0.057 -10000 0 -0.45 8 8
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.065 0.049 -10000 0 -0.45 2 2
mol:DAG -0.013 0.19 -10000 0 -0.73 9 9
Gs family/GDP/Gbeta gamma -0.005 0.041 -10000 0 -10000 0 0
MSN 0.073 0.029 -10000 0 -10000 0 0
Gq family/GTP -0.017 0.08 -10000 0 -0.5 9 9
mol:PI-3-4-5-P3 0.045 0.051 -10000 0 -0.73 2 2
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.065 0.049 0.45 2 -10000 0 2
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.048 -10000 0 -0.46 2 2
NOS3 0.067 0.053 -10000 0 -0.49 2 2
GNA11 0.012 0.05 -10000 0 -0.76 2 2
MAPKKK cascade 0.076 0.052 -10000 0 -0.57 2 2
E2/ER alpha (dimer)/PELP1/Src -0.005 0.039 -10000 0 -0.48 2 2
ruffle organization 0.071 0.027 -10000 0 -10000 0 0
ROCK2 -0.002 0.026 -10000 0 -10000 0 0
GNA14 0.004 0.093 -10000 0 -0.76 7 7
GNA15 -0.006 0.14 -10000 0 -0.86 12 12
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.16 0.25 -10000 0 -0.66 7 7
MMP2 0.068 0.074 -10000 0 -0.64 2 2
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.036 0.12 -9999 0 -0.48 9 9
PDGFB-D/PDGFRB/SLAP -0.029 0.14 -9999 0 -0.67 21 21
PDGFB-D/PDGFRB/APS/CBL -0.006 0.059 -9999 0 -0.58 5 5
AKT1 -0.001 0.013 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.013 0.14 -9999 0 -0.5 9 9
PIK3CA 0.016 0 -9999 0 -10000 0 0
FGR -0.004 0.03 -9999 0 -10000 0 0
mol:Ca2+ 0.038 0.041 -9999 0 -10000 0 0
MYC 0.045 0.13 -9999 0 -0.57 16 16
SHC1 0.014 0.04 -9999 0 -0.86 1 1
HRAS/GDP 0 0.002 -9999 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.038 0.042 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 0.004 0.093 -9999 0 -0.76 7 7
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.029 0.14 -9999 0 -0.67 21 21
HRAS 0.016 0 -9999 0 -10000 0 0
HIF1A 0.09 0.017 -9999 0 -10000 0 0
GAB1 0.033 0.077 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.036 0.083 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.012 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.038 0.12 -9999 0 -0.54 6 6
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.039 0.042 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.004 0.007 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.008 0.069 -9999 0 -0.58 7 7
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.023 0.087 -9999 0 -10000 0 0
PTPN2 0.016 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.035 -9999 0 -0.76 1 1
VAV2 0.036 0.088 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0 0 -9999 0 -10000 0 0
LCK -0.02 0.088 -9999 0 -0.62 3 3
PDGFRB 0.016 0.006 -9999 0 -10000 0 0
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.021 0.083 -9999 0 -10000 0 0
ABL1 0.033 0.061 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.033 0.072 -9999 0 -10000 0 0
PTPN1 0.016 0.003 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.014 0.04 -9999 0 -0.86 1 1
cell proliferation 0.045 0.12 -9999 0 -0.51 16 16
SLA -0.023 0.18 -9999 0 -0.86 21 21
actin cytoskeleton reorganization 0.002 0.02 -9999 0 -10000 0 0
SRC -0.001 0.013 -9999 0 -10000 0 0
PI3K -0.001 0.015 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.008 0.064 -9999 0 -0.5 8 8
SH2B2 0.007 0.089 -9999 0 -0.86 5 5
PLCgamma1/SPHK1 0.012 0.14 -9999 0 -0.53 7 7
LYN -0.001 0.013 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.016 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.001 0.017 -9999 0 -10000 0 0
SPHK1 -0.057 0.24 -9999 0 -0.86 40 40
EDG1 0.001 0.003 -9999 0 -10000 0 0
mol:DAG 0.039 0.042 -9999 0 -10000 0 0
PLCG1 0.039 0.042 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.022 -9999 0 -0.49 1 1
YES1 -0.001 0.013 -9999 0 -10000 0 0
cell migration -0.001 0.022 -9999 0 -0.48 1 1
SHC/Grb2/SOS1 -0.001 0.021 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.035 -9999 0 -0.76 1 1
SLC9A3R1 0.016 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.001 0.02 -9999 0 -10000 0 0
FYN -0.001 0.013 -9999 0 -10000 0 0
DOK1 0.044 0.009 -9999 0 -10000 0 0
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.016 0 -9999 0 -10000 0 0
RAC1 0.046 0.1 -9999 0 -0.52 1 1
PRKCD 0.042 0.029 -9999 0 -0.53 1 1
FER 0.042 0.026 -9999 0 -10000 0 0
MAPKKK cascade -0.001 0.021 -9999 0 -10000 0 0
RASA1 0.043 0.014 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.007 0.018 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0 0 -9999 0 -10000 0 0
chemotaxis 0.033 0.06 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 -0.001 0.021 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0 -9999 0 -10000 0 0
PTPRJ 0.016 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.02 -10000 0 -0.44 1 1
HDAC3 0.016 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 -0.025 0.13 -10000 0 -0.67 18 18
GATA1/HDAC5 -0.026 0.13 -10000 0 -0.66 19 19
GATA2/HDAC5 -0.012 0.081 -10000 0 -0.57 10 10
HDAC5/BCL6/BCoR -0.001 0.022 -10000 0 -0.48 1 1
HDAC9 0.016 0 -10000 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.026 -10000 0 -0.58 1 1
HDAC4/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC5/YWHAB -0.001 0.026 -10000 0 -0.57 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 0.001 0.1 -10000 0 -0.76 9 9
HDAC4/RFXANK 0 0 -10000 0 -10000 0 0
BCOR 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.014 0.035 -10000 0 -0.76 1 1
HDAC5 0.014 0.035 -10000 0 -0.76 1 1
GNB1/GNG2 0 0 -10000 0 -10000 0 0
Histones -0.003 0.042 -10000 0 -0.85 1 1
ADRBK1 0.016 0 -10000 0 -10000 0 0
HDAC4 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.001 0.026 -10000 0 -0.57 1 1
HDAC4/Ubc9 0 0 -10000 0 -10000 0 0
HDAC7 0.016 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.026 -10000 0 -0.57 1 1
TUBA1B 0.016 0 -10000 0 -10000 0 0
HDAC6 0.016 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.001 0.026 -10000 0 -0.57 1 1
CAMK4 0.012 0.05 -10000 0 -0.76 2 2
Tubulin/HDAC6 -0.001 0.022 -10000 0 -0.48 1 1
SUMO1 0.016 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
GATA1 -0.02 0.17 -10000 0 -0.86 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.016 0 -10000 0 -10000 0 0
NR3C1 0.014 0.04 -10000 0 -0.86 1 1
SUMO1/HDAC4 0 0 -10000 0 -10000 0 0
SRF 0.016 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0 0 -10000 0 -10000 0 0
Tubulin -0.001 0.026 -10000 0 -0.57 1 1
HDAC4/14-3-3 E 0 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
RANGAP1 0.016 0 -10000 0 -10000 0 0
BCL6/BCoR 0 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -10000 0 -10000 0 0
HDAC4/SRF -0.002 0.031 -10000 0 -0.48 2 2
HDAC4/ER alpha -0.002 0.037 -10000 0 -0.57 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.051 0.045 -10000 0 -0.84 1 1
cell motility -0.001 0.022 -10000 0 -0.48 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.016 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 0.016 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.016 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 0.012 0.05 -10000 0 -0.76 2 2
HDAC6/HDAC11 -0.002 0.037 -10000 0 -0.57 2 2
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C 0.016 0 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
NCOR2 0.016 0 -10000 0 -10000 0 0
TUBB2A 0.014 0.035 -10000 0 -0.76 1 1
HDAC11 0.012 0.05 -10000 0 -0.76 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RANBP2 0.016 0 -10000 0 -10000 0 0
ANKRA2 0.016 0 -10000 0 -10000 0 0
RFXANK 0.016 0 -10000 0 -10000 0 0
nuclear import 0.001 0.018 0.4 1 -10000 0 1
Circadian rhythm 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
chromatin modification -0.001 0.014 -10000 0 -10000 0 0
CLOCK 0.02 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.057 0.022 -10000 0 -10000 0 0
DEC1/BMAL1 -0.001 0.03 -10000 0 -0.66 1 1
ATR 0.016 0 -10000 0 -10000 0 0
NR1D1 0.055 0.064 -10000 0 -1.3 1 1
ARNTL 0.02 0.002 -10000 0 -10000 0 0
TIMELESS 0.057 0.025 -10000 0 -10000 0 0
NPAS2 0.006 0.1 -10000 0 -0.75 9 9
CRY2 0.016 0 -10000 0 -10000 0 0
mol:CO -0.019 0.007 0.14 1 -10000 0 1
CHEK1 0.016 0 -10000 0 -10000 0 0
mol:HEME 0.019 0.007 -10000 0 -0.14 1 1
PER1 0.016 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.045 0.072 -10000 0 -0.47 9 9
BMAL1/CLOCK 0.066 0.048 -10000 0 -0.82 1 1
S phase of mitotic cell cycle -0.001 0.014 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.014 -10000 0 -10000 0 0
mol:NADPH 0.019 0.007 -10000 0 -0.14 1 1
PER1/TIMELESS 0.057 0.022 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.001 0.04 -10000 0 -0.86 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.022 -9999 0 -0.48 1 1
forebrain development 0.056 0.093 -9999 0 -0.5 2 2
GNAO1 0.009 0.078 -9999 0 -0.84 4 4
SMO/beta Arrestin2 -0.002 0.04 -9999 0 -0.62 2 2
SMO 0.015 0.036 -9999 0 -0.76 1 1
ARRB2 0.014 0.04 -9999 0 -0.86 1 1
GLI3/SPOP 0.062 0.021 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.016 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex -0.017 0.094 -9999 0 -0.52 16 16
GNAI1 0.011 0.061 -9999 0 -0.76 3 3
XPO1 0.019 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.013 0.061 -9999 0 -10000 0 0
SAP30 -0.014 0.16 -9999 0 -0.86 16 16
mol:GDP 0.015 0.036 -9999 0 -0.76 1 1
MIM/GLI2A 0.023 0.008 -9999 0 -10000 0 0
IFT88 0.014 0.035 -9999 0 -0.76 1 1
GNAI3 0.016 0.004 -9999 0 -10000 0 0
GLI2 0.058 0.032 -9999 0 -10000 0 0
GLI3 0.056 0.023 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0.035 -9999 0 -0.76 1 1
GNG2 0.016 0 -9999 0 -10000 0 0
Gi family/GTP 0.045 0.052 -9999 0 -0.56 1 1
SIN3B 0.015 0.001 -9999 0 -10000 0 0
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.058 0.043 -9999 0 -10000 0 0
GLI2/Su(fu) 0.075 0.038 -9999 0 -10000 0 0
FOXA2 -0.062 0.23 -9999 0 -0.85 35 35
neural tube patterning 0.056 0.093 -9999 0 -0.5 2 2
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.014 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0.035 -9999 0 -0.76 1 1
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.023 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.056 0.093 -9999 0 -0.5 2 2
SUFU 0.038 0.022 -9999 0 -10000 0 0
LGALS3 -0.003 0.13 -9999 0 -0.86 10 10
catabolic process 0.093 0.029 -9999 0 -10000 0 0
GLI3A/CBP 0.018 0.052 -9999 0 -0.36 3 3
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 0.056 0.094 -9999 0 -0.51 2 2
RAB23 0.016 0 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.012 0.079 -9999 0 -0.55 10 10
GNAZ 0.011 0.061 -9999 0 -0.76 3 3
RBBP4 0.016 0.001 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.061 0.03 -9999 0 -10000 0 0
STK36 0.019 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.041 0.051 -9999 0 -0.49 1 1
PTCH1 0.063 0.1 -9999 0 -1.1 1 1
MIM/GLI1 0.053 0.15 -9999 0 -0.71 1 1
CREBBP 0.018 0.052 -9999 0 -0.36 3 3
Su(fu)/SIN3/HDAC complex 0.058 0.045 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.031 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.001 0.02 -9999 0 -10000 0 0
CDKN1B 0.051 0 -9999 0 -10000 0 0
CDKN1A 0.049 0.033 -9999 0 -0.47 2 2
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.016 0 -9999 0 -10000 0 0
FOXO3 0.051 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.014 0.035 -9999 0 -0.76 1 1
AKT3 0.023 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.051 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ -0.001 0.022 -9999 0 -0.48 1 1
RICTOR 0.016 0 -9999 0 -10000 0 0
RAF1 0.016 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.051 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0 -9999 0 -10000 0 0
EP300 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.051 0 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
TBC1D4 0.034 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAPKAP1 0.016 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.042 0.051 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
AKT1S1 0.051 0 -9999 0 -10000 0 0
CASP9 0.051 0 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.058 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.002 0.029 -9999 0 -0.45 2 2
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.024 0 -9999 0 -10000 0 0
CHUK 0.051 0 -9999 0 -10000 0 0
BAD/BCL-XL -0.001 0.016 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.023 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.061 0.057 -9999 0 -10000 0 0
PDPK1 0.016 0 -9999 0 -10000 0 0
MDM2 0.051 0 -9999 0 -10000 0 0
MAPKKK cascade 0 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0 0 -9999 0 -10000 0 0
TSC1/TSC2 0.06 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
glucose import 0.031 0.079 -9999 0 -0.48 11 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.043 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.031 0.079 -9999 0 -0.48 11 11
GSK3A 0.051 0 -9999 0 -10000 0 0
FOXO1 0.051 0 -9999 0 -10000 0 0
GSK3B 0.051 0 -9999 0 -10000 0 0
SFN -0.079 0.27 -9999 0 -0.84 53 53
G1/S transition of mitotic cell cycle 0.06 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.038 0.077 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
KPNA1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
RHEB 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0 -10000 0 -10000 0 0
NFATC1 0.076 0.028 -10000 0 -10000 0 0
NFATC2 0.054 0.029 -10000 0 -10000 0 0
NFATC3 0.028 0.042 -10000 0 -0.49 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.034 0.067 -10000 0 -0.47 3 3
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.011 0.053 -10000 0 -0.53 2 2
BCL2/BAX 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+ 0 0.001 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.016 0.003 -10000 0 -10000 0 0
BAD 0.014 0.035 -10000 0 -0.76 1 1
CABIN1/MEF2D 0.039 0.064 -10000 0 -0.47 2 2
Calcineurin A alpha-beta B1/BCL2 0.016 0 -10000 0 -10000 0 0
FKBP8 0.014 0.035 -10000 0 -0.76 1 1
activation-induced cell death of T cells -0.039 0.063 0.46 2 -10000 0 2
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.016 0 -10000 0 -10000 0 0
XPO1 0.015 0.003 -10000 0 -10000 0 0
SFN -0.079 0.27 -10000 0 -0.84 53 53
MAP3K8 0.012 0.057 -10000 0 -0.86 2 2
NFAT4/CK1 alpha -0.002 0.025 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.011 0.057 -10000 0 -0.44 2 2
CABIN1 0.034 0.068 -10000 0 -0.47 3 3
CALM1 0.016 0.003 -10000 0 -10000 0 0
RAN 0.015 0.003 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
CAMK4 0.012 0.05 -10000 0 -0.76 2 2
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.005 0.052 -10000 0 -0.57 4 4
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.016 0.003 -10000 0 -10000 0 0
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.029 -10000 0 -10000 0 0
PRKCH 0.016 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0 0 -10000 0 -10000 0 0
CASP3 0.016 0.003 -10000 0 -10000 0 0
PIM1 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0.01 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.073 -10000 0 -0.54 1 1
PRKCB 0.007 0.085 -10000 0 -0.82 5 5
PRKCE 0.016 0 -10000 0 -10000 0 0
JNK2/NFAT4 -0.003 0.035 -10000 0 -0.44 3 3
BAD/BCL-XL -0.001 0.026 -10000 0 -0.57 1 1
PRKCD 0.014 0.04 -10000 0 -0.86 1 1
NUP214 0.015 0.003 -10000 0 -10000 0 0
PRKCZ 0.011 0.061 -10000 0 -0.76 3 3
PRKCA 0.016 0 -10000 0 -10000 0 0
PRKCG -0.027 0.17 -10000 0 -0.86 19 19
PRKCQ -0.004 0.12 -10000 0 -0.76 12 12
FKBP38/BCL2 -0.001 0.026 -10000 0 -0.57 1 1
EP300 0.016 0.003 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.081 0.03 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 -0.001 0.023 -10000 0 -0.51 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.002 0.032 -10000 0 -0.5 2 2
NFATc/ERK1 0.081 0.027 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.011 0.053 -10000 0 -0.53 2 2
NR4A1 0.071 0.14 -10000 0 -0.68 16 16
GSK3B 0.016 0.003 -10000 0 -10000 0 0
positive T cell selection 0.028 0.042 -10000 0 -0.49 3 3
NFAT1/CK1 alpha -0.002 0.015 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.016 0.003 -10000 0 -10000 0 0
AKAP5 0.009 0.07 -10000 0 -0.76 4 4
MEF2D 0.016 0.003 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.08 0.03 -10000 0 -10000 0 0
CREBBP 0.016 0.003 -10000 0 -10000 0 0
BCL2 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.007 0.056 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.044 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.011 0.061 -9999 0 -0.76 3 3
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones -0.003 0.023 -9999 0 -10000 0 0
YY1/LSF 0 0 -9999 0 -10000 0 0
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.042 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.004 0.028 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.046 0.042 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.028 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.064 0.011 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.049 0.038 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.001 0.1 -9999 0 -0.76 9 9
GATA1 -0.02 0.17 -9999 0 -0.86 18 18
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.037 -9999 0 -0.44 1 1
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.016 0 -9999 0 -10000 0 0
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.033 -9999 0 -10000 0 0
KAT2B 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.007 0.036 -9999 0 -10000 0 0
SIN3 complex -0.017 0.094 -9999 0 -0.52 16 16
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 -0.014 0.16 -9999 0 -0.86 16 16
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.003 0.024 -9999 0 -10000 0 0
YY1/HDAC2 0 0 -9999 0 -10000 0 0
YY1/HDAC1 0 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.064 0 -9999 0 -10000 0 0
PPARG -0.006 0.049 -9999 0 -10000 0 0
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.028 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.009 -9999 0 -10000 0 0
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.033 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.041 0 -9999 0 -10000 0 0
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0 -9999 0 -10000 0 0
STAT3 0.035 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0 0 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.017 0.091 -9999 0 -0.51 16 16
EP300 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.035 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.033 -9999 0 -10000 0 0
histone deacetylation 0.064 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.025 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.012 0.065 -9999 0 -10000 0 0
GATA1/HDAC1 -0.025 0.13 -9999 0 -0.67 18 18
GATA1/HDAC3 -0.023 0.1 -9999 0 -0.52 18 18
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.01 0.079 -9999 0 -0.62 8 8
SIN3/HDAC complex/Mad/Max 0.057 0.038 -9999 0 -10000 0 0
NuRD Complex 0 0.008 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.023 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex 0 0 -9999 0 -10000 0 0
GATA1/Fog1 -0.029 0.13 -9999 0 -0.65 21 21
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF 0.002 0.11 -9999 0 -0.81 8 8
negative regulation of cell growth 0.057 0.038 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.064 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.047 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 -0.005 0.027 -9999 0 -10000 0 0
TFCP2 0.016 0 -9999 0 -10000 0 0
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.014 0.035 -9999 0 -0.76 1 1
MBD2 0.016 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.011 0.061 -10000 0 -0.76 3 3
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.016 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.058 0.026 -10000 0 -10000 0 0
KAT2B 0.016 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.031 0.037 0.24 1 -0.31 2 3
RAR alpha/9cRA/Cyclin H -0.007 0.035 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.054 0.028 -10000 0 -10000 0 0
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.002 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.008 0.038 -10000 0 -10000 0 0
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.004 0.046 -10000 0 -0.58 3 3
RXRs/RARs/NRIP1/9cRA 0.065 0.079 -10000 0 -0.52 1 1
NCOA2 0.009 0.07 -10000 0 -0.76 4 4
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.061 -10000 0 -0.76 3 3
RARG 0.017 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.001 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.017 0.001 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.017 0.071 -10000 0 -10000 0 0
RARA 0.027 0.055 -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 0.052 0.04 -10000 0 -10000 0 0
PRKCA 0.021 0.001 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.057 0.08 -10000 0 -0.57 1 1
RXRG 0.014 0.088 -10000 0 -0.38 23 23
RXRA 0.038 0.052 -10000 0 -10000 0 0
RXRB 0.019 0.08 -10000 0 -0.37 19 19
VDR/Vit D3/DNA -0.004 0.046 -10000 0 -0.58 3 3
RBP1 0.01 0.067 -10000 0 -0.83 3 3
CRBP1/9-cic-RA -0.004 0.051 -10000 0 -0.65 3 3
RARB 0.016 0.05 -10000 0 -0.76 2 2
PRKCG -0.022 0.17 -10000 0 -0.86 19 19
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.056 0.08 -10000 0 -10000 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.063 0.071 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.041 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.057 0.08 -10000 0 -0.57 1 1
positive regulation of DNA binding -0.007 0.033 -10000 0 -10000 0 0
NRIP1 0.055 0.091 -10000 0 -1.2 1 1
RXRs/RARs 0.048 0.078 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.015 0.07 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.005 0.024 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA -0.003 0.043 -9999 0 -0.67 2 2
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.002 0.031 -9999 0 -0.49 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.037 -9999 0 -10000 0 0
NFKBIA 0.027 0.058 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0 -9999 0 -10000 0 0
ARRB2 0.022 0.019 -9999 0 -0.39 1 1
REL 0.012 0.05 -9999 0 -0.76 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.002 0.037 -9999 0 -0.58 2 2
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.027 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
NFKB1 0.031 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.036 0.057 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.008 0.036 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.011 0.046 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.012 0.05 -9999 0 -0.76 2 2
I kappa B alpha/PIK3R1 0.034 0.054 -9999 0 -10000 0 0
cell death -0.008 0.034 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.002 0.031 -9999 0 -0.49 2 2
LCK -0.024 0.18 -9999 0 -0.85 22 22
BCL3 0.012 0.057 -9999 0 -0.86 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.016 0 -9999 0 -9999 0 0
SMAD2 0.019 0 -9999 0 -9999 0 0
SMAD3 0.057 0 -9999 0 -9999 0 0
SMAD3/SMAD4 0.063 0 -9999 0 -9999 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -9999 0 0
PPM1A 0.016 0 -9999 0 -9999 0 0
CALM1 0.016 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0.027 0 -9999 0 -9999 0 0
MAP3K1 0.016 0 -9999 0 -9999 0 0
TRAP-1/SMAD4 0 0 -9999 0 -9999 0 0
MAPK3 0.016 0 -9999 0 -9999 0 0
MAPK1 0.016 0 -9999 0 -9999 0 0
NUP214 0.016 0 -9999 0 -9999 0 0
CTDSP1 0.016 0 -9999 0 -9999 0 0
CTDSP2 0.016 0 -9999 0 -9999 0 0
CTDSPL 0.016 0 -9999 0 -9999 0 0
KPNB1 0.016 0 -9999 0 -9999 0 0
TGFBRAP1 0.016 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
NUP153 0.016 0 -9999 0 -9999 0 0
KPNA2 0.016 0 -9999 0 -9999 0 0
PIAS4 0.016 0 -9999 0 -9999 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.001 0.021 -10000 0 -0.32 2 2
FRAP1 0.021 0.004 -10000 0 -10000 0 0
AKT1 -0.001 0.016 -10000 0 -10000 0 0
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.012 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.003 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.01 -10000 0 -10000 0 0
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.019 0.027 -10000 0 -0.39 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.038 0.01 -10000 0 -10000 0 0
MAP3K5 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.014 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.002 2 2
EIF4B 0.046 0.009 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.018 -10000 0 -0.37 1 1
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.022 -10000 0 -0.35 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.044 0.007 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.009 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.002 2 2
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.001 0.018 -10000 0 -10000 0 0
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.027 0.003 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.023 0 -10000 0 -10000 0 0
TSC1/TSC2 -0.001 0.013 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.002 2 -10000 0 2
RPS6 0.014 0.04 -10000 0 -0.86 1 1
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.01 0.028 -10000 0 -0.43 2 2
INS 0 0.001 -10000 0 -10000 0 0
PTEN 0 0.001 -10000 0 -10000 0 0
PDK2 -0.001 0.018 -10000 0 -10000 0 0
EIF4EBP1 -0.005 0.094 -10000 0 -0.46 20 20
PIK3CA 0.016 0 -10000 0 -10000 0 0
PPP2R5D 0.03 0.004 -10000 0 -10000 0 0
peptide biosynthetic process 0.023 0.001 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0 -10000 0 -10000 0 0
EEF2 0.023 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.005 0.084 -10000 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.001 0.026 -9999 0 -0.57 1 1
PTK2 0 0.008 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.001 0.014 -9999 0 -10000 0 0
CDC42/GDP 0.08 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.082 0.011 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.017 -9999 0 -0.36 1 1
nectin-3/I-afadin 0 0 -9999 0 -10000 0 0
RAPGEF1 0.078 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.071 0.005 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 0.047 0 -9999 0 -10000 0 0
Rap1/GTP 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.082 0.013 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly 0 0.001 -9999 0 -10000 0 0
PVRL1 0.016 0 -9999 0 -10000 0 0
PVRL3 0.016 0 -9999 0 -10000 0 0
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
CDH1 -0.015 0.15 -9999 0 -0.76 19 19
CLDN1 0.01 0.067 -9999 0 -0.83 3 3
JAM-A/CLDN1 -0.003 0.039 -9999 0 -0.49 3 3
SRC 0 0.003 -9999 0 -10000 0 0
ITGB3 0.014 0.035 -9999 0 -0.76 1 1
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.072 0.029 -9999 0 -0.54 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0 0 -9999 0 -10000 0 0
nectin-1/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.016 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.001 0.014 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.001 0.017 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
VAV2 0.072 0.006 -9999 0 -10000 0 0
RAP1/GDP 0 0.005 -9999 0 -10000 0 0
ITGAV 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.001 -9999 0 -10000 0 0
PTPRM 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.015 0.074 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.014 0.035 -9999 0 -0.76 1 1
positive regulation of NF-kappaB transcription factor activity -0.001 0.026 -9999 0 -0.57 1 1
MAP2K4 0.064 0.017 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
TNFRSF10B 0.016 0 -9999 0 -10000 0 0
TNFRSF10A 0.014 0.035 -9999 0 -0.76 1 1
SMPD1 -0.001 0.012 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.001 0.026 -9999 0 -0.57 1 1
TRAIL/TRAILR3 -0.001 0.026 -9999 0 -0.57 1 1
TRAIL/TRAILR1 -0.002 0.037 -9999 0 -0.57 2 2
TRAIL/TRAILR4 -0.001 0.026 -9999 0 -0.57 1 1
TRAIL/TRAILR1/DAP3/GTP -0.002 0.029 -9999 0 -0.45 2 2
IKK complex -0.001 0.008 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.03 0.027 -9999 0 -0.57 1 1
MAP3K1 -0.001 0.014 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.016 0 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.035 -9999 0 -0.76 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.019 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
MAPK1 0.03 0.027 -9999 0 -0.57 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP -0.002 0.026 -9999 0 -10000 0 0
mol:ceramide -0.001 0.012 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
MAPK8 0.072 0.016 -9999 0 -10000 0 0
TRAF2 0.016 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.031 -9999 0 -0.48 2 2
DAP3 0.016 0 -9999 0 -10000 0 0
CASP10 -0.001 0.024 -9999 0 -0.46 1 1
JNK cascade -0.001 0.026 -9999 0 -0.57 1 1
TRAIL (trimer) 0.014 0.035 -9999 0 -0.76 1 1
TNFRSF10C 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.027 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD -0.001 0.022 -9999 0 -0.48 1 1
cell death -0.001 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.013 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.016 0 -9999 0 -10000 0 0
CASP8 0 0.007 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.001 0.018 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.039 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.016 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 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 0 -9999 0 -10000 0 0
MAPK9 0.011 0 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.003 0.07 -9999 0 -0.68 5 5
GNB1/GNG2 0 0 -9999 0 -10000 0 0
GNB1 0.016 0 -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 0.011 0 -9999 0 -10000 0 0
Gs family/GTP 0 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 0.016 0 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
CRH -0.005 0.088 -9999 0 -0.86 5 5
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0 -9999 0 -10000 0 0
MAPK11 0.011 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.024 -9999 0 -0.53 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.028 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0 -9999 0 -10000 0 0
CD4 -0.001 0.12 -9999 0 -0.86 9 9
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.014 0.027 -9999 0 -0.58 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.022 -9999 0 -0.48 1 1
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.022 -9999 0 -0.47 1 1
AP2M1 0.016 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.02 -9999 0 -0.43 1 1
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.035 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.001 0.011 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.004 0.029 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.014 0.027 -9999 0 -0.58 1 1
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.014 0.027 -9999 0 -0.58 1 1
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.011 0.078 -9999 0 -0.58 9 9
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.006 0.061 -9999 0 -0.67 4 4
FBXW11 0.016 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 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.004 0.044 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.008 0.08 -9999 0 -0.86 4 4
NF kappa B1 p50/RelB 0 0 -9999 0 -10000 0 0
RELB 0.016 0 -9999 0 -10000 0 0
NFKB2 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 480 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.EU.5906 TCGA.EU.5905 TCGA.EU.5904 TCGA.DV.5576
109_MAP3K5 0.074 0.074 0.074 0.074
47_PPARGC1A 0.016 0.016 0.016 0.016
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 -0.76 0 -0.76 0.016
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR 0 -0.44 0 0
30_TGFB1/TGF beta receptor Type II 0.015 0.015 0.016 0.015
84_STAT5B -0.032 -0.031 0.025 0.06
84_STAT5A -0.032 -0.031 0.025 0.06
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIRC-TP/3026091/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.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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