PARADIGM pathway analysis of mRNASeq expression data
Lung Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C15M63SN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C15M63SN
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 34 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Signaling events mediated by the Hedgehog family 120
FOXM1 transcription factor network 110
Angiopoietin receptor Tie2-mediated signaling 102
Aurora B signaling 93
Endothelins 57
amb2 Integrin signaling 43
TCGA08_retinoblastoma 42
Glucocorticoid receptor regulatory network 40
Glypican 2 network 37
Signaling events regulated by Ret tyrosine kinase 36
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 347 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 347 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Signaling events mediated by the Hedgehog family 0.3458 120 6278 52 -0.68 0.37 1000 -1000 -0.098 -1000
FOXM1 transcription factor network 0.3170 110 5649 51 -0.8 0.002 1000 -1000 -0.2 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2939 102 8985 88 -0.68 0.048 1000 -1000 -0.12 -1000
Aurora B signaling 0.2680 93 6281 67 -0.64 0.005 1000 -1000 -0.081 -1000
Endothelins 0.1643 57 5519 96 -0.44 0.055 1000 -1000 -0.098 -1000
amb2 Integrin signaling 0.1239 43 3529 82 -0.71 0 1000 -1000 -0.093 -1000
TCGA08_retinoblastoma 0.1210 42 337 8 -0.29 0.089 1000 -1000 -0.034 -1000
Glucocorticoid receptor regulatory network 0.1153 40 4595 114 -0.63 0.42 1000 -1000 -0.094 -1000
Glypican 2 network 0.1066 37 149 4 -0.072 -0.064 1000 -1000 -0.044 -1000
Signaling events regulated by Ret tyrosine kinase 0.1037 36 2961 82 -0.22 0 1000 -1000 -0.1 -1000
Aurora C signaling 0.1009 35 251 7 -0.43 0 1000 -1000 -0.054 -1000
Visual signal transduction: Cones 0.0980 34 1296 38 -0.26 0.009 1000 -1000 -0.086 -1000
Fc-epsilon receptor I signaling in mast cells 0.0980 34 3349 97 -0.24 0.033 1000 -1000 -0.11 -1000
IL4-mediated signaling events 0.0951 33 3034 91 -0.77 0.42 1000 -1000 -0.19 -1000
Thromboxane A2 receptor signaling 0.0922 32 3361 105 -0.18 0.034 1000 -1000 -0.095 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0922 32 1702 52 -0.43 0.063 1000 -1000 -0.084 -1000
BMP receptor signaling 0.0865 30 2483 81 -0.42 0.04 1000 -1000 -0.11 -1000
PLK1 signaling events 0.0807 28 2436 85 -0.38 0.072 1000 -1000 -0.071 -1000
Canonical Wnt signaling pathway 0.0778 27 1401 51 -0.5 0.17 1000 -1000 -0.073 -1000
Presenilin action in Notch and Wnt signaling 0.0720 25 1533 61 -0.5 0.016 1000 -1000 -0.085 -1000
Glypican 1 network 0.0720 25 1207 48 -0.24 0.028 1000 -1000 -0.058 -1000
Arf6 signaling events 0.0692 24 1547 62 -0.29 0.017 1000 -1000 -0.081 -1000
Signaling mediated by p38-alpha and p38-beta 0.0692 24 1075 44 -0.12 0 1000 -1000 -0.064 -1000
TCGA08_p53 0.0663 23 164 7 -0.2 0.1 1000 -1000 -0.029 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0663 23 1846 78 -0.1 0.03 1000 -1000 -0.088 -1000
Integrins in angiogenesis 0.0634 22 1849 84 -0.48 0.036 1000 -1000 -0.12 -1000
Nongenotropic Androgen signaling 0.0634 22 1181 52 -0.15 0.061 1000 -1000 -0.076 -1000
IL23-mediated signaling events 0.0634 22 1349 60 -0.3 0.017 1000 -1000 -0.18 -1000
LPA4-mediated signaling events 0.0605 21 263 12 -0.16 0.015 1000 -1000 -0.026 -1000
FOXA2 and FOXA3 transcription factor networks 0.0605 21 991 46 -0.79 0.068 1000 -1000 -0.13 -1000
Syndecan-3-mediated signaling events 0.0605 21 747 35 -0.37 0 1000 -1000 -0.076 -1000
Nectin adhesion pathway 0.0576 20 1267 63 -0.29 0 1000 -1000 -0.096 -1000
Coregulation of Androgen receptor activity 0.0519 18 1437 76 -0.42 0.028 1000 -1000 -0.069 -1000
HIF-1-alpha transcription factor network 0.0519 18 1408 76 -0.47 0.017 1000 -1000 -0.24 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0490 17 2203 125 -0.22 0.006 1000 -1000 -0.11 -1000
IL6-mediated signaling events 0.0490 17 1343 75 -0.48 0.052 1000 -1000 -0.11 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0490 17 1186 68 -0.24 0.015 1000 -1000 -0.16 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0461 16 1973 120 -0.28 0.15 1000 -1000 -0.096 -1000
Regulation of Androgen receptor activity 0.0461 16 1140 70 -0.44 0.018 1000 -1000 -0.096 -1000
ErbB4 signaling events 0.0432 15 1054 69 -0.4 0.21 1000 -1000 -0.12 -1000
Syndecan-1-mediated signaling events 0.0432 15 538 34 -0.38 0 1000 -1000 -0.084 -1000
Osteopontin-mediated events 0.0432 15 593 38 -0.36 0.011 1000 -1000 -0.14 -1000
Calcium signaling in the CD4+ TCR pathway 0.0432 15 482 31 -0.22 0.013 1000 -1000 -0.15 -1000
Aurora A signaling 0.0403 14 866 60 -0.49 0.034 1000 -1000 -0.072 -1000
Reelin signaling pathway 0.0403 14 812 56 -0.12 0 1000 -1000 -0.12 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0403 14 483 33 -0.28 0 1000 -1000 -0.074 -1000
IL12-mediated signaling events 0.0375 13 1195 87 -0.2 0.018 1000 -1000 -0.15 -1000
Wnt signaling 0.0375 13 91 7 -0.096 0 1000 -1000 -0.065 -1000
Visual signal transduction: Rods 0.0375 13 684 52 -0.17 0 1000 -1000 -0.12 -1000
Ephrin A reverse signaling 0.0346 12 85 7 -0.026 0.002 1000 -1000 -0.039 -1000
p75(NTR)-mediated signaling 0.0346 12 1535 125 -0.37 0 1000 -1000 -0.13 -1000
HIF-2-alpha transcription factor network 0.0346 12 524 43 -0.4 0.24 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 0.0317 11 498 44 -0.22 0.022 1000 -1000 -0.082 -1000
Plasma membrane estrogen receptor signaling 0.0317 11 1009 86 -0.18 0.036 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.0288 10 1003 93 -0.054 0.04 1000 -1000 -0.094 -1000
EGFR-dependent Endothelin signaling events 0.0288 10 218 21 -0.074 0 1000 -1000 -0.087 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0259 9 787 85 -0.13 0.017 1000 -1000 -0.088 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0231 8 483 54 -0.14 0.02 1000 -1000 -0.13 -1000
Effects of Botulinum toxin 0.0231 8 214 26 -0.078 0.005 1000 -1000 -0.081 -1000
Caspase cascade in apoptosis 0.0202 7 530 74 -0.087 0.035 1000 -1000 -0.077 -1000
Regulation of nuclear SMAD2/3 signaling 0.0202 7 1024 136 -0.35 0.094 1000 -1000 -0.11 -1000
Syndecan-2-mediated signaling events 0.0202 7 510 69 -0.19 0.035 1000 -1000 -0.08 -1000
FAS signaling pathway (CD95) 0.0202 7 362 47 -0.25 0.009 1000 -1000 -0.061 -1000
JNK signaling in the CD4+ TCR pathway 0.0173 6 107 17 -0.035 0.027 1000 -1000 -0.078 -1000
Noncanonical Wnt signaling pathway 0.0173 6 167 26 -0.096 0 1000 -1000 -0.11 -1000
Hedgehog signaling events mediated by Gli proteins 0.0173 6 403 65 -0.62 0.045 1000 -1000 -0.099 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0173 6 515 74 -0.17 0.07 1000 -1000 -0.12 -1000
Syndecan-4-mediated signaling events 0.0173 6 437 67 -0.19 0.011 1000 -1000 -0.12 -1000
S1P4 pathway 0.0173 6 155 25 -0.068 0.001 1000 -1000 -0.068 -1000
Ras signaling in the CD4+ TCR pathway 0.0173 6 118 17 -0.067 0.007 1000 -1000 -0.082 -1000
Signaling events mediated by PTP1B 0.0144 5 390 76 -0.12 0.032 1000 -1000 -0.1 -1000
LPA receptor mediated events 0.0144 5 510 102 -0.12 0.036 1000 -1000 -0.12 -1000
IL2 signaling events mediated by STAT5 0.0144 5 123 22 -0.17 0.065 1000 -1000 -0.072 -1000
BCR signaling pathway 0.0144 5 574 99 -0.081 0.043 1000 -1000 -0.11 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0115 4 169 34 -0.029 0 1000 -1000 -0.083 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0115 4 133 28 -0.18 0.02 1000 -1000 -0.08 -1000
Signaling events mediated by HDAC Class III 0.0115 4 197 40 -0.14 0.047 1000 -1000 -0.067 -1000
TRAIL signaling pathway 0.0115 4 195 48 -0.07 0.048 1000 -1000 -0.083 -1000
IL1-mediated signaling events 0.0115 4 254 62 -0.071 0.043 1000 -1000 -0.12 -1000
Ephrin B reverse signaling 0.0115 4 208 48 -0.066 0.035 1000 -1000 -0.09 -1000
S1P1 pathway 0.0115 4 178 36 -0.036 0.02 1000 -1000 -0.089 -1000
Retinoic acid receptors-mediated signaling 0.0115 4 275 58 -0.24 0.036 1000 -1000 -0.089 -1000
IL27-mediated signaling events 0.0115 4 227 51 -0.16 0.011 1000 -1000 -0.11 -1000
Insulin Pathway 0.0115 4 343 74 -0.12 0.032 1000 -1000 -0.12 -1000
S1P3 pathway 0.0115 4 181 42 -0.18 0.042 1000 -1000 -0.081 -1000
Signaling events mediated by PRL 0.0115 4 142 34 -0.13 0.025 1000 -1000 -0.074 -1000
ErbB2/ErbB3 signaling events 0.0086 3 200 65 -0.09 0.052 1000 -1000 -0.086 -1000
Signaling events mediated by HDAC Class II 0.0086 3 234 75 -0.088 0 1000 -1000 -0.077 -1000
BARD1 signaling events 0.0086 3 211 57 -0.13 0.023 1000 -1000 -0.085 -1000
Cellular roles of Anthrax toxin 0.0086 3 148 39 -0.086 0.018 1000 -1000 -0.037 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0086 3 250 83 -0.087 0.05 1000 -1000 -0.093 -1000
Signaling events mediated by HDAC Class I 0.0086 3 348 104 -0.088 0.042 1000 -1000 -0.083 -1000
IL2 signaling events mediated by PI3K 0.0086 3 183 58 -0.21 0.078 1000 -1000 -0.1 -1000
EPHB forward signaling 0.0086 3 255 85 -0.066 0.036 1000 -1000 -0.11 -1000
Regulation of p38-alpha and p38-beta 0.0086 3 208 54 -0.12 0.039 1000 -1000 -0.091 -1000
Arf6 trafficking events 0.0086 3 224 71 -0.093 0.033 1000 -1000 -0.087 -1000
Circadian rhythm pathway 0.0058 2 45 22 -0.037 0.039 1000 -1000 -0.08 -1000
IFN-gamma pathway 0.0058 2 180 68 -0.077 0.067 1000 -1000 -0.12 -1000
Class I PI3K signaling events 0.0058 2 186 73 -0.055 0.032 1000 -1000 -0.092 -1000
Regulation of Telomerase 0.0058 2 288 102 -0.12 0.028 1000 -1000 -0.12 -1000
IGF1 pathway 0.0058 2 116 57 -0.01 0.046 1000 -1000 -0.12 -1000
VEGFR1 specific signals 0.0058 2 135 56 -0.22 0.05 1000 -1000 -0.099 -1000
Class IB PI3K non-lipid kinase events 0.0058 2 6 3 -0.004 -1000 1000 -1000 -0.025 -1000
p38 MAPK signaling pathway 0.0058 2 116 44 -0.077 0.035 1000 -1000 -0.08 -1000
Insulin-mediated glucose transport 0.0029 1 33 32 -0.051 0.037 1000 -1000 -0.083 -1000
Ceramide signaling pathway 0.0029 1 96 76 -0.024 0.041 1000 -1000 -0.083 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0029 1 82 45 -0.024 0.064 1000 -1000 -0.12 -1000
TCGA08_rtk_signaling 0.0029 1 43 26 -0.042 0.041 1000 -1000 -0.039 -1000
PDGFR-beta signaling pathway 0.0029 1 165 97 -0.044 0.055 1000 -1000 -0.11 -1000
E-cadherin signaling in keratinocytes 0.0029 1 67 43 -0.025 0.044 1000 -1000 -0.094 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 0 23 0 0.037 1000 -1000 -0.085 -1000
Canonical NF-kappaB pathway 0.0000 0 28 39 -0.024 0.074 1000 -1000 -0.12 -1000
PLK2 and PLK4 events 0.0000 0 2 3 -0.002 0.019 1000 -1000 -0.032 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 4 5 -0.004 0 1000 -1000 -0.044 -1000
Arf6 downstream pathway 0.0000 0 11 43 -0.025 0.026 1000 -1000 -0.05 -1000
EPO signaling pathway 0.0000 0 50 55 -0.011 0.067 1000 -1000 -0.11 -1000
mTOR signaling pathway 0.0000 0 7 53 -0.004 0.03 1000 -1000 -0.076 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 34 68 -0.051 0.045 1000 -1000 -0.086 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0000 0 35 37 -0.014 0.033 1000 -1000 -0.1 -1000
S1P5 pathway 0.0000 0 15 17 -0.011 0.007 1000 -1000 -0.076 -1000
ceramide signaling pathway 0.0000 0 28 49 -0.015 0.043 1000 -1000 -0.063 -1000
FoxO family signaling 0.0000 0 54 64 -0.099 0.083 1000 -1000 -0.098 -1000
Signaling mediated by p38-gamma and p38-delta 0.0000 0 13 15 -0.001 0.027 1000 -1000 -0.071 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 10 36 -0.008 0.02 1000 -1000 -0.089 -1000
Atypical NF-kappaB pathway 0.0000 0 5 31 -0.002 0.031 1000 -1000 -0.091 -1000
E-cadherin signaling in the nascent adherens junction 0.0000 0 63 76 -0.02 0.053 1000 -1000 -0.1 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.026 1000 -1000 -0.068 -1000
Rapid glucocorticoid signaling 0.0000 0 18 20 -0.005 0.008 1000 -1000 -0.053 -1000
E-cadherin signaling events 0.0000 0 3 5 -0.002 0 1000 -1000 -0.054 -1000
Arf1 pathway 0.0000 0 15 54 -0.009 0.023 1000 -1000 -0.047 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 -0.002 0 1000 -1000 -0.079 -1000
Total NA 1811 115104 7203 -26 -990 131000 -131000 -12 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.45 0.3 -10000 0 -0.71 159 159
IHH -0.49 0.39 -10000 0 -0.83 198 198
SHH Np/Cholesterol/GAS1 -0.078 0.18 -10000 0 -0.46 59 59
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.078 0.17 0.46 59 -10000 0 59
SMO/beta Arrestin2 -0.38 0.25 -10000 0 -0.61 168 168
SMO -0.4 0.28 -10000 0 -0.62 201 201
AKT1 -0.16 0.11 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.39 0.27 -10000 0 -0.61 201 201
STIL -0.35 0.25 -10000 0 -0.55 183 183
DHH N/PTCH2 -0.052 0.17 -10000 0 -0.59 31 31
DHH N/PTCH1 -0.38 0.25 -10000 0 -0.59 176 176
PIK3CA 0 0 -10000 0 -10000 0 0
DHH -0.059 0.2 -10000 0 -0.76 27 27
PTHLH -0.61 0.36 -10000 0 -0.96 159 159
determination of left/right symmetry -0.39 0.27 -10000 0 -0.61 201 201
PIK3R1 0 0 -10000 0 -10000 0 0
skeletal system development -0.6 0.35 -10000 0 -0.94 159 159
IHH N/Hhip -0.68 0.38 -10000 0 -0.84 279 279
DHH N/Hhip -0.42 0.31 -10000 0 -0.62 237 237
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.39 0.27 -10000 0 -0.61 201 201
pancreas development -0.5 0.36 -10000 0 -0.76 230 230
HHAT 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.013 0.099 -10000 0 -0.76 6 6
somite specification -0.39 0.27 -10000 0 -0.61 201 201
SHH Np/Cholesterol/PTCH1 -0.37 0.26 -10000 0 -0.58 181 181
SHH Np/Cholesterol/PTCH2 -0.077 0.17 -10000 0 -0.46 54 54
SHH Np/Cholesterol/Megalin -0.31 0.28 -10000 0 -0.52 208 208
SHH -0.073 0.21 -10000 0 -0.56 55 55
catabolic process -0.39 0.26 -10000 0 -0.59 201 201
SMO/Vitamin D3 -0.39 0.27 -10000 0 -0.62 181 181
SHH Np/Cholesterol/Hhip -0.37 0.27 -10000 0 -0.52 246 246
LRP2 -0.41 0.38 -10000 0 -0.76 187 187
receptor-mediated endocytosis -0.53 0.32 -10000 0 -0.75 206 206
SHH Np/Cholesterol/BOC -0.07 0.16 -10000 0 -0.44 55 55
SHH Np/Cholesterol/CDO -0.077 0.17 -10000 0 -0.45 60 60
mesenchymal cell differentiation 0.37 0.27 0.52 246 -10000 0 246
mol:Vitamin D3 -0.37 0.27 -10000 0 -0.59 181 181
IHH N/PTCH2 -0.32 0.28 -10000 0 -0.56 198 198
CDON -0.011 0.091 -10000 0 -0.76 5 5
IHH N/PTCH1 -0.4 0.26 -10000 0 -0.6 201 201
Megalin/LRPAP1 -0.31 0.29 -10000 0 -0.58 187 187
PTCH2 -0.011 0.087 -10000 0 -0.73 5 5
SHH Np/Cholesterol -0.072 0.17 -10000 0 -0.45 55 55
PTCH1 -0.39 0.26 -10000 0 -0.59 201 201
HHIP -0.5 0.36 -10000 0 -0.76 230 230
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.64 0.44 -9999 0 -1 135 135
PLK1 -0.2 0.22 -9999 0 -10000 0 0
BIRC5 -0.34 0.18 -9999 0 -0.44 250 250
HSPA1B -0.64 0.44 -9999 0 -1 136 136
MAP2K1 -0.013 0.023 -9999 0 -10000 0 0
BRCA2 -0.64 0.44 -9999 0 -1.1 132 132
FOXM1 -0.8 0.58 -9999 0 -1.3 165 165
XRCC1 -0.64 0.44 -9999 0 -1 137 137
FOXM1B/p19 -0.67 0.44 -9999 0 -1 160 160
Cyclin D1/CDK4 -0.6 0.42 -9999 0 -1 124 124
CDC2 -0.68 0.47 -9999 0 -1.1 166 166
TGFA -0.57 0.4 -9999 0 -0.95 121 121
SKP2 -0.64 0.44 -9999 0 -1 137 137
CCNE1 -0.14 0.26 -9999 0 -0.62 77 77
CKS1B -0.64 0.44 -9999 0 -1.1 134 134
RB1 -0.28 0.16 -9999 0 -0.51 29 29
FOXM1C/SP1 -0.72 0.5 -9999 0 -1.1 165 165
AURKB -0.3 0.2 -9999 0 -0.44 58 58
CENPF -0.7 0.48 -9999 0 -1.1 165 165
CDK4 0.001 0.035 -9999 0 -0.63 1 1
MYC -0.56 0.39 -9999 0 -0.91 136 136
CHEK2 -0.013 0.023 -9999 0 -10000 0 0
ONECUT1 -0.64 0.45 -9999 0 -1 145 145
CDKN2A -0.27 0.31 -9999 0 -0.6 162 162
LAMA4 -0.64 0.45 -9999 0 -1.1 136 136
FOXM1B/HNF6 -0.74 0.54 -9999 0 -1.2 145 145
FOS -0.72 0.52 -9999 0 -1.2 148 148
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.64 0.44 -9999 0 -1.1 134 134
response to radiation -0.025 0.022 -9999 0 -10000 0 0
CENPB -0.64 0.44 -9999 0 -1 135 135
CENPA -0.78 0.48 -9999 0 -1.1 181 181
NEK2 -0.76 0.49 -9999 0 -1.1 190 190
HIST1H2BA -0.65 0.44 -9999 0 -1.1 137 137
CCNA2 -0.18 0.28 -9999 0 -0.62 99 99
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.74 0.53 -9999 0 -1.2 155 155
CCNB2 -0.73 0.5 -9999 0 -1.1 167 167
CCNB1 -0.69 0.48 -9999 0 -1.1 155 155
ETV5 -0.64 0.44 -9999 0 -1.1 120 120
ESR1 -0.66 0.46 -9999 0 -1.1 138 138
CCND1 -0.61 0.43 -9999 0 -1 125 125
GSK3A -0.004 0.019 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.19 0.26 -9999 0 -0.48 143 143
CDK2 0.002 0.006 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.032 0.026 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.71 0.44 -9999 0 -1.1 178 178
GAS1 -0.65 0.45 -9999 0 -1 147 147
MMP2 -0.64 0.44 -9999 0 -1.1 138 138
RB1/FOXM1C -0.65 0.46 -9999 0 -1.1 143 143
CREBBP 0 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.47 0.53 -10000 0 -1 172 172
NCK1/PAK1/Dok-R -0.23 0.23 -10000 0 -0.45 172 172
NCK1/Dok-R -0.62 0.64 -10000 0 -1.2 172 172
PIK3CA 0.008 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.048 0.094 0.25 59 -10000 0 59
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.002 0.005 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.034 0.13 -10000 0 -0.6 7 7
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.55 0.57 -10000 0 -1.1 172 172
FN1 -0.013 0.099 -10000 0 -0.76 6 6
PLD2 -0.6 0.7 -10000 0 -1.3 172 172
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.061 0.21 -10000 0 -0.75 28 28
ELK1 -0.51 0.6 -10000 0 -1.1 172 172
GRB7 -0.003 0.046 -10000 0 -0.61 2 2
PAK1 -0.002 0.032 -10000 0 -0.61 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.59 0.61 -10000 0 -1.2 172 172
CDKN1A -0.33 0.35 -10000 0 -0.68 168 168
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.62 0.64 -10000 0 -1.2 172 172
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.33 0.38 -10000 0 -0.71 172 172
PLG -0.6 0.7 -10000 0 -1.3 172 172
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.46 0.48 -10000 0 -0.94 172 172
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 0.002 0.005 -10000 0 -10000 0 0
ANGPT2 -0.31 0.32 -10000 0 -0.71 117 117
BMX -0.68 0.74 -10000 0 -1.4 172 172
ANGPT1 -0.3 0.57 -10000 0 -1.4 67 67
tube development -0.38 0.4 -10000 0 -0.78 172 172
ANGPT4 -0.36 0.38 -10000 0 -0.76 166 166
response to hypoxia -0.031 0.036 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.68 0.7 -10000 0 -1.3 172 172
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.021 0.14 -10000 0 -0.76 12 12
STAT5A (dimer) -0.44 0.47 -10000 0 -0.9 171 171
mol:L-citrulline -0.33 0.38 -10000 0 -0.71 172 172
AGTR1 -0.29 0.38 -10000 0 -0.76 134 134
MAPK14 -0.63 0.69 -10000 0 -1.3 172 172
Tie2/SHP2 -0.55 0.61 -10000 0 -1.2 151 151
TEK -0.62 0.68 -10000 0 -1.4 151 151
RPS6KB1 -0.45 0.5 -10000 0 -0.95 172 172
Angiotensin II/AT1 -0.22 0.29 -10000 0 -0.58 134 134
Tie2/Ang1/GRB2 -0.65 0.7 -10000 0 -1.3 172 172
MAPK3 -0.53 0.62 -10000 0 -1.1 172 172
MAPK1 -0.53 0.62 -10000 0 -1.1 172 172
Tie2/Ang1/GRB7 -0.66 0.7 -10000 0 -1.3 172 172
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.6 0.7 -10000 0 -1.3 172 172
PI3K -0.57 0.63 -10000 0 -1.2 172 172
FES -0.62 0.69 -10000 0 -1.3 172 172
Crk/Dok-R -0.62 0.64 -10000 0 -1.2 172 172
Tie2/Ang1/ABIN2 -0.65 0.7 -10000 0 -1.3 172 172
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.41 0.46 -10000 0 -0.87 172 172
STAT5A 0.003 0.041 -10000 0 -0.76 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.45 0.5 -10000 0 -0.95 172 172
Tie2/Ang2 -0.56 0.59 -10000 0 -1.1 171 171
Tie2/Ang1 -0.68 0.8 -10000 0 -1.4 172 172
FOXO1 -0.41 0.47 -10000 0 -0.88 172 172
ELF1 -0.028 0.052 -10000 0 -10000 0 0
ELF2 -0.61 0.71 -10000 0 -1.3 172 172
mol:Choline -0.56 0.64 -10000 0 -1.2 172 172
cell migration -0.12 0.12 -10000 0 -10000 0 0
FYN -0.44 0.47 -10000 0 -0.91 171 171
DOK2 -0.064 0.21 -10000 0 -0.76 29 29
negative regulation of cell cycle -0.29 0.32 -10000 0 -0.61 169 169
ETS1 -0.047 0.14 -10000 0 -0.84 7 7
PXN -0.35 0.41 -10000 0 -0.76 172 172
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.38 0.44 -10000 0 -0.82 172 172
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.055 0.16 -10000 0 -0.81 11 11
MAPKKK cascade -0.56 0.64 -10000 0 -1.2 172 172
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.64 0.71 -10000 0 -1.3 172 172
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.29 0.34 -10000 0 -0.62 172 172
mol:Phosphatidic acid -0.56 0.64 -10000 0 -1.2 172 172
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.33 0.38 -10000 0 -0.71 172 172
Rac1/GTP -0.44 0.44 -10000 0 -0.88 172 172
MMP2 -0.6 0.7 -10000 0 -1.3 172 172
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.2 0.16 -9999 0 -0.44 50 50
STMN1 -0.3 0.21 -9999 0 -0.43 247 247
Aurora B/RasGAP/Survivin -0.52 0.25 -9999 0 -0.62 289 289
Chromosomal passenger complex/Cul3 protein complex -0.21 0.12 -9999 0 -0.36 78 78
BIRC5 -0.49 0.24 -9999 0 -0.61 281 281
DES -0.56 0.39 -9999 0 -0.85 221 221
Aurora C/Aurora B/INCENP -0.23 0.16 -9999 0 -0.36 36 36
Aurora B/TACC1 -0.26 0.18 -9999 0 -0.37 247 247
Aurora B/PP2A -0.3 0.2 -9999 0 -0.43 247 247
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.064 0.048 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.003 -9999 0 -10000 0 0
NDC80 -0.42 0.3 -9999 0 -0.57 257 257
Cul3 protein complex -0.019 0.085 -9999 0 -0.39 17 17
KIF2C -0.17 0.095 -9999 0 -0.24 196 196
PEBP1 -0.001 0.042 -9999 0 -0.78 1 1
KIF20A -0.2 0.29 -9999 0 -0.61 115 115
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.3 0.2 -9999 0 -0.43 247 247
SEPT1 0 0 -9999 0 -10000 0 0
SMC2 0 0 -9999 0 -10000 0 0
SMC4 0 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.12 0.077 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.001 0.005 -9999 0 -10000 0 0
H3F3B -0.16 0.11 -9999 0 -0.23 207 207
AURKB -0.43 0.28 -9999 0 -0.61 247 247
AURKC -0.004 0.052 -9999 0 -0.68 2 2
CDCA8 -0.12 0.25 -9999 0 -0.62 71 71
cytokinesis -0.33 0.18 -9999 0 -0.44 209 209
Aurora B/Septin1 -0.31 0.17 -9999 0 -0.5 96 96
AURKA -0.008 0.11 -9999 0 -0.61 11 11
INCENP 0.001 0.003 -9999 0 -10000 0 0
KLHL13 -0.024 0.12 -9999 0 -0.61 14 14
BUB1 -0.039 0.16 -9999 0 -0.61 25 25
hSgo1/Aurora B/Survivin -0.64 0.34 -9999 0 -0.77 278 278
EVI5 0.005 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.26 0.18 -9999 0 -0.53 80 80
SGOL1 -0.29 0.3 -9999 0 -0.61 166 166
CENPA -0.25 0.13 -9999 0 -0.33 238 238
NCAPG -0.099 0.22 -9999 0 -0.61 57 57
Aurora B/HC8 Proteasome -0.3 0.2 -9999 0 -0.43 247 247
NCAPD2 -0.002 0.032 -9999 0 -0.61 1 1
Aurora B/PP1-gamma -0.3 0.2 -9999 0 -0.43 247 247
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.31 0.3 -9999 0 -0.61 178 178
NPM1 -0.15 0.095 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.007 0.07 -9999 0 -0.76 3 3
mitotic prometaphase -0.011 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.2 -9999 0 -0.43 247 247
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.29 0.2 -9999 0 -0.53 106 106
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.15 0.095 -9999 0 -10000 0 0
MYLK -0.16 0.11 -9999 0 -0.23 247 247
KIF23 -0.093 0.22 -9999 0 -0.61 53 53
VIM -0.3 0.21 -9999 0 -0.44 247 247
RACGAP1 0.001 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.15 0.095 -9999 0 -10000 0 0
Chromosomal passenger complex -0.27 0.16 -9999 0 -0.36 236 236
Chromosomal passenger complex/EVI5 -0.5 0.27 -9999 0 -0.66 237 237
TACC1 -0.004 0.058 -9999 0 -0.76 2 2
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.018 0.24 -9999 0 -0.59 37 37
PTK2B 0.004 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.067 0.28 -9999 0 -0.82 28 28
EDN1 -0.041 0.27 -9999 0 -0.8 34 34
EDN3 -0.098 0.25 -9999 0 -0.73 47 47
EDN2 -0.09 0.22 -9999 0 -0.63 50 50
HRAS/GDP -0.18 0.3 -9999 0 -0.64 84 84
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.048 0.22 -9999 0 -0.55 35 35
ADCY4 -0.077 0.24 -9999 0 -0.6 41 41
ADCY5 -0.079 0.22 -9999 0 -0.55 46 46
ADCY6 -0.045 0.19 -9999 0 -0.54 31 31
ADCY7 -0.045 0.19 -9999 0 -0.56 27 27
ADCY1 -0.046 0.19 -9999 0 -0.56 26 26
ADCY2 -0.082 0.22 -9999 0 -0.61 30 30
ADCY3 -0.044 0.19 -9999 0 -0.56 25 25
ADCY8 -0.19 0.26 -9999 0 -0.65 42 42
ADCY9 -0.045 0.19 -9999 0 -0.56 26 26
arachidonic acid secretion -0.15 0.28 -9999 0 -0.51 106 106
ETB receptor/Endothelin-1/Gq/GTP -0.31 0.36 -9999 0 -0.61 157 157
GNAO1 -0.006 0.061 -9999 0 -0.66 3 3
HRAS 0.007 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.055 0.27 -9999 0 -0.55 37 37
ETA receptor/Endothelin-1/Gs/GTP 0.047 0.26 -9999 0 -0.52 39 39
mol:GTP 0 0.004 -9999 0 -10000 0 0
COL3A1 -0.04 0.27 -9999 0 -0.55 60 60
EDNRB -0.44 0.38 -9999 0 -0.76 203 203
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.027 0.26 -9999 0 -0.63 39 39
CYSLTR1 -0.064 0.34 -9999 0 -0.86 42 42
SLC9A1 0.001 0.13 -9999 0 -0.38 11 11
mol:GDP -0.2 0.34 -9999 0 -0.69 89 89
SLC9A3 -0.36 0.38 -9999 0 -0.61 217 217
RAF1 -0.21 0.33 -9999 0 -0.65 104 104
JUN -0.047 0.22 -9999 0 -0.71 16 16
JAK2 -0.018 0.24 -9999 0 -0.59 37 37
mol:IP3 -0.21 0.32 -9999 0 -0.68 89 89
ETA receptor/Endothelin-1 0.036 0.33 -9999 0 -0.68 37 37
PLCB1 0.006 0.005 -9999 0 -10000 0 0
PLCB2 -0.006 0.1 -9999 0 -0.76 6 6
ETA receptor/Endothelin-3 -0.052 0.22 -9999 0 -0.55 49 49
FOS -0.23 0.39 -9999 0 -0.91 72 72
Gai/GDP -0.006 0.075 -9999 0 -0.96 1 1
CRK 0.004 0.005 -9999 0 -10000 0 0
mol:Ca ++ -0.24 0.37 -9999 0 -0.73 102 102
BCAR1 0.007 0.005 -9999 0 -10000 0 0
PRKCB1 -0.2 0.3 -9999 0 -0.64 90 90
GNAQ 0.008 0.042 -9999 0 -0.76 1 1
GNAZ -0.011 0.091 -9999 0 -0.76 5 5
GNAL -0.004 0.058 -9999 0 -0.76 2 2
Gs family/GDP -0.21 0.26 -9999 0 -0.62 85 85
ETA receptor/Endothelin-1/Gq/GTP -0.057 0.24 -9999 0 -0.49 55 55
MAPK14 -0.24 0.3 -9999 0 -0.66 90 90
TRPC6 -0.074 0.3 -9999 0 -0.9 28 28
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.002 0.041 -9999 0 -0.76 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.26 0.31 -9999 0 -0.62 116 116
ETB receptor/Endothelin-2 -0.39 0.31 -9999 0 -0.6 226 226
ETB receptor/Endothelin-3 -0.4 0.32 -9999 0 -0.63 223 223
ETB receptor/Endothelin-1 -0.37 0.35 -9999 0 -0.62 217 217
MAPK3 -0.24 0.39 -9999 0 -0.79 96 96
MAPK1 -0.24 0.39 -9999 0 -0.81 91 91
Rac1/GDP -0.18 0.3 -9999 0 -0.64 84 84
cAMP biosynthetic process -0.076 0.21 -9999 0 -0.58 35 35
MAPK8 -0.069 0.27 -9999 0 -0.65 41 41
SRC 0 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.18 -9999 0 -0.5 32 32
p130Cas/CRK/Src/PYK2 -0.18 0.32 -9999 0 -0.66 86 86
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.18 0.3 -9999 0 -0.64 84 84
COL1A2 -0.24 0.31 -9999 0 -0.71 68 68
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.042 0.19 -9999 0 -0.47 52 52
mol:DAG -0.21 0.32 -9999 0 -0.68 89 89
MAP2K2 -0.22 0.34 -9999 0 -0.66 110 110
MAP2K1 -0.22 0.34 -9999 0 -0.66 110 110
EDNRA 0.031 0.13 -9999 0 -0.64 4 4
positive regulation of muscle contraction -0.02 0.21 -9999 0 -0.61 21 21
Gq family/GDP -0.2 0.31 -9999 0 -0.71 80 80
HRAS/GTP -0.22 0.33 -9999 0 -0.68 92 92
PRKCH -0.19 0.3 -9999 0 -0.67 81 81
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.2 0.3 -9999 0 -0.68 81 81
PRKCB -0.21 0.32 -9999 0 -0.7 84 84
PRKCE -0.2 0.3 -9999 0 -0.67 84 84
PRKCD -0.2 0.3 -9999 0 -0.67 81 81
PRKCG -0.22 0.32 -9999 0 -0.68 89 89
regulation of vascular smooth muscle contraction -0.28 0.46 -9999 0 -1.1 74 74
PRKCQ -0.23 0.35 -9999 0 -0.73 93 93
PLA2G4A -0.17 0.31 -9999 0 -0.56 106 106
GNA14 -0.17 0.32 -9999 0 -0.76 80 80
GNA15 0.006 0.042 -9999 0 -0.76 1 1
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.008 0.006 -9999 0 -10000 0 0
Rac1/GTP 0.055 0.27 -9999 0 -0.55 37 37
MMP1 -0.26 0.26 -9999 0 -0.47 189 189
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.06 0.2 -9999 0 -0.66 31 31
alphaM/beta2 Integrin/GPIbA -0.061 0.21 -9999 0 -0.68 31 31
alphaM/beta2 Integrin/proMMP-9 -0.091 0.21 -9999 0 -0.51 62 62
PLAUR 0 0 -9999 0 -10000 0 0
HMGB1 0 0.003 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.056 0.19 -9999 0 -0.64 30 30
AGER -0.71 0.2 -9999 0 -0.77 322 322
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG -0.05 0.19 -9999 0 -0.76 23 23
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.5 0.25 -9999 0 -0.54 322 322
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.058 0.18 -9999 0 -0.61 33 33
CYR61 -0.039 0.17 -9999 0 -0.76 18 18
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.2 0.28 -9999 0 -0.59 83 83
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.19 0.33 -9999 0 -0.76 85 85
MYH2 -0.33 0.36 -9999 0 -0.78 106 106
MST1R -0.05 0.19 -9999 0 -0.76 23 23
leukocyte activation during inflammatory response -0.086 0.21 -9999 0 -0.54 49 49
APOB -0.051 0.19 -9999 0 -0.73 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.007 0.07 -9999 0 -0.76 3 3
JAM3 0 0 -9999 0 -10000 0 0
GP1BA -0.009 0.081 -9999 0 -0.76 4 4
alphaM/beta2 Integrin/CTGF -0.067 0.22 -9999 0 -0.68 34 34
alphaM/beta2 Integrin -0.25 0.35 -9999 0 -0.7 88 88
JAM3 homodimer 0 0 -9999 0 -10000 0 0
ICAM2 -0.037 0.16 -9999 0 -0.76 17 17
ICAM1 -0.057 0.2 -9999 0 -0.76 26 26
phagocytosis triggered by activation of immune response cell surface activating receptor -0.23 0.35 -9999 0 -0.68 88 88
cell adhesion -0.061 0.21 -9999 0 -0.68 31 31
NFKB1 -0.5 0.3 -9999 0 -0.91 94 94
THY1 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.045 0.15 -9999 0 -0.49 32 32
alphaM/beta2 Integrin/LRP/tPA -0.057 0.19 -9999 0 -0.6 31 31
IL6 -0.54 0.41 -9999 0 -1.1 96 96
ITGB2 -0.027 0.14 -9999 0 -0.76 12 12
elevation of cytosolic calcium ion concentration -0.071 0.19 -9999 0 -0.58 32 32
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.27 -9999 0 -0.63 61 61
JAM2 -0.1 0.26 -9999 0 -0.76 47 47
alphaM/beta2 Integrin/ICAM1 -0.11 0.27 -9999 0 -0.64 58 58
alphaM/beta2 Integrin/uPA/Plg -0.074 0.19 -9999 0 -0.61 30 30
RhoA/GTP -0.3 0.36 -9999 0 -0.82 87 87
positive regulation of phagocytosis -0.18 0.25 -9999 0 -0.72 49 49
Ron/MSP -0.038 0.14 -9999 0 -0.58 23 23
alphaM/beta2 Integrin/uPAR/uPA -0.071 0.19 -9999 0 -0.58 32 32
alphaM/beta2 Integrin/uPAR -0.056 0.19 -9999 0 -0.64 30 30
PLAU -0.037 0.14 -9999 0 -0.61 21 21
PLAT -0.007 0.065 -9999 0 -0.61 4 4
actin filament polymerization -0.31 0.32 -9999 0 -0.72 106 106
MST1 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) -0.087 0.21 -9999 0 -0.55 49 49
TNF -0.46 0.28 -9999 0 -0.84 94 94
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.078 0.21 -9999 0 -0.54 50 50
fibrinolysis -0.073 0.19 -9999 0 -0.6 30 30
HCK -0.004 0.058 -9999 0 -0.76 2 2
dendritic cell antigen processing and presentation -0.23 0.35 -9999 0 -0.68 88 88
VTN -0.31 0.37 -9999 0 -0.76 143 143
alphaM/beta2 Integrin/CYR61 -0.081 0.23 -9999 0 -0.64 44 44
LPA -0.019 0.11 -9999 0 -0.61 11 11
LRP1 -0.004 0.058 -9999 0 -0.76 2 2
cell migration -0.086 0.21 -9999 0 -0.62 31 31
FN1 -0.013 0.099 -9999 0 -0.76 6 6
alphaM/beta2 Integrin/Thy1 -0.056 0.19 -9999 0 -0.64 30 30
MPO -0.031 0.15 -9999 0 -0.76 14 14
KNG1 -0.017 0.1 -9999 0 -0.61 10 10
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.25 0.33 -9999 0 -0.77 79 79
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.003 0.046 -9999 0 -0.61 2 2
CTGF -0.018 0.11 -9999 0 -0.76 8 8
alphaM/beta2 Integrin/Hck -0.058 0.2 -9999 0 -0.65 31 31
ITGAM -0.06 0.2 -9999 0 -0.77 27 27
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.19 0.36 -9999 0 -0.69 94 94
HP -0.23 0.35 -9999 0 -0.76 107 107
leukocyte adhesion -0.46 0.3 -9999 0 -0.78 114 114
SELP -0.19 0.33 -9999 0 -0.76 85 85
TCGA08_retinoblastoma

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
CDKN2B -0.061 0.2 -10000 0 -0.73 29 29
CDKN2C 0.031 0.033 -10000 0 -10000 0 0
CDKN2A -0.29 0.31 -10000 0 -0.63 162 162
CCND2 0.077 0.085 0.27 29 -0.16 1 30
RB1 -0.084 0.088 -10000 0 -0.27 29 29
CDK4 0.089 0.091 0.27 29 -10000 0 29
CDK6 0.086 0.093 0.29 29 -10000 0 29
G1/S progression 0.077 0.094 0.27 29 -10000 0 29
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.074 0.1 -10000 0 -10000 0 0
SMARCC2 0.012 0 -10000 0 -10000 0 0
SMARCC1 0.012 0 -10000 0 -10000 0 0
TBX21 -0.23 0.35 -10000 0 -0.85 64 64
SUMO2 0.002 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.018 0 -10000 0 -10000 0 0
FKBP4 -0.002 0.032 -10000 0 -0.61 1 1
FKBP5 0 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.15 0.11 0.35 35 -10000 0 35
PRL -0.1 0.13 -10000 0 -0.72 1 1
cortisol/GR alpha (dimer)/TIF2 0.35 0.25 0.6 137 -10000 0 137
RELA -0.045 0.1 -10000 0 -10000 0 0
FGG -0.11 0.49 0.52 63 -0.62 160 223
GR beta/TIF2 0.15 0.12 0.37 45 -0.39 1 46
IFNG -0.39 0.26 -10000 0 -0.71 87 87
apoptosis 0.024 0.14 0.43 1 -0.62 2 3
CREB1 0.001 0.031 -10000 0 -10000 0 0
histone acetylation -0.029 0.16 0.35 2 -0.37 21 23
BGLAP -0.12 0.15 -10000 0 -0.55 5 5
GR/PKAc 0.14 0.1 0.34 27 -10000 0 27
NF kappa B1 p50/RelA -0.082 0.18 -10000 0 -0.53 16 16
SMARCD1 0.012 0 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.32 38 -10000 0 38
GATA3 -0.023 0.16 -10000 0 -0.74 16 16
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.22 0.47 -10000 0 -1.4 45 45
GSK3B 0.002 0.006 -10000 0 -10000 0 0
NR1I3 0.043 0.13 -10000 0 -0.57 1 1
CSN2 0.19 0.16 0.45 35 -10000 0 35
BRG1/BAF155/BAF170/BAF60A 0 0 -10000 0 -10000 0 0
NFATC1 0 0.041 -10000 0 -0.76 1 1
POU2F1 0.005 0.016 -10000 0 -10000 0 0
CDKN1A 0.027 0.016 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.005 -10000 0 -10000 0 0
SFN -0.051 0.17 -10000 0 -0.61 29 29
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.15 0.34 29 -10000 0 29
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.018 0.21 0.39 1 -0.91 14 15
JUN -0.32 0.17 -10000 0 -0.58 62 62
IL4 -0.14 0.15 -10000 0 -0.55 9 9
CDK5R1 -0.014 0.096 -10000 0 -0.6 9 9
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.5 0.26 -10000 0 -0.68 182 182
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.14 0.1 0.34 29 -10000 0 29
cortisol/GR alpha (monomer) 0.42 0.32 0.72 143 -10000 0 143
NCOA2 -0.002 0.041 -10000 0 -0.76 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.21 0.28 -10000 0 -0.85 55 55
AP-1/NFAT1-c-4 -0.6 0.26 -10000 0 -0.77 192 192
AFP -0.22 0.17 -10000 0 -0.72 10 10
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.51 29 -10000 0 29
TP53 0.03 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.62 0.26 -10000 0 -0.76 214 214
KRT14 -0.4 0.25 -10000 0 -0.64 126 126
TBP 0.018 0 -10000 0 -10000 0 0
CREBBP 0.11 0.073 0.34 1 -10000 0 1
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0.013 0.034 -10000 0 -10000 0 0
AP-1 -0.61 0.26 -10000 0 -0.77 201 201
MAPK14 0.002 0.006 -10000 0 -10000 0 0
MAPK10 -0.009 0.091 -10000 0 -0.76 5 5
MAPK11 0.002 0.006 -10000 0 -10000 0 0
KRT5 -0.63 0.26 -10000 0 -0.72 276 276
interleukin-1 receptor activity 0.01 0.032 -10000 0 -10000 0 0
NCOA1 0.013 0.001 -10000 0 -10000 0 0
STAT1 0.018 0 -10000 0 -10000 0 0
CGA -0.14 0.18 -10000 0 -0.64 15 15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.23 0.21 0.51 89 -10000 0 89
MAPK3 0.002 0.006 -10000 0 -10000 0 0
MAPK1 0.002 0.006 -10000 0 -10000 0 0
ICAM1 -0.28 0.43 -10000 0 -1 60 60
NFKB1 -0.045 0.1 -10000 0 -10000 0 0
MAPK8 -0.27 0.17 -10000 0 -0.52 73 73
MAPK9 0.002 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.021 0.14 0.44 1 -0.66 2 3
BAX 0.027 0.016 -10000 0 -10000 0 0
POMC -0.26 0.26 -10000 0 -0.65 72 72
EP300 0.12 0.074 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0.37 0.25 0.61 141 -10000 0 141
proteasomal ubiquitin-dependent protein catabolic process 0.088 0.075 0.27 9 -10000 0 9
SGK1 0.18 0.084 -10000 0 -10000 0 0
IL13 -0.32 0.22 -10000 0 -0.77 41 41
IL6 -0.41 0.56 -10000 0 -1.3 86 86
PRKACG -0.002 0.032 -10000 0 -0.61 1 1
IL5 -0.28 0.18 -10000 0 -0.8 19 19
IL2 -0.39 0.21 -10000 0 -0.67 84 84
CDK5 0.001 0.004 -10000 0 -10000 0 0
PRKACB 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.23 0.28 -10000 0 -0.72 56 56
CDK5R1/CDK5 -0.009 0.071 -10000 0 -0.44 9 9
NF kappa B1 p50/RelA/PKAc -0.056 0.13 -10000 0 -0.54 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.34 0.23 0.57 129 -10000 0 129
SMARCA4 0.012 0 -10000 0 -10000 0 0
chromatin remodeling 0.22 0.15 0.4 91 -10000 0 91
NF kappa B1 p50/RelA/Cbp 0.037 0.18 0.39 13 -0.57 2 15
JUN (dimer) -0.32 0.17 -10000 0 -0.58 62 62
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.49 0.52 -10000 0 -1.1 153 153
NR3C1 0.23 0.21 0.52 85 -10000 0 85
NR4A1 -0.14 0.3 -10000 0 -0.75 66 66
TIF2/SUV420H1 -0.002 0.031 -10000 0 -0.58 1 1
MAPKKK cascade 0.024 0.14 0.43 1 -0.62 2 3
cortisol/GR alpha (dimer)/Src-1 0.36 0.25 0.61 137 -10000 0 137
PBX1 0 0.06 -10000 0 -0.76 2 2
POU1F1 -0.004 0.058 -10000 0 -0.6 3 3
SELE -0.49 0.62 -10000 0 -1.4 109 109
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.22 0.15 0.4 91 -10000 0 91
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.34 0.23 0.57 129 -10000 0 129
mol:cortisol 0.23 0.21 0.44 132 -10000 0 132
MMP1 -0.36 0.2 -10000 0 -0.52 205 205
Glypican 2 network

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
MDK -0.017 0.1 -9999 0 -0.61 10 10
GPC2 -0.072 0.2 -9999 0 -0.61 41 41
GPC2/Midkine -0.064 0.16 -9999 0 -0.46 49 49
neuron projection morphogenesis -0.064 0.16 -9999 0 -0.45 49 49
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.047 0.057 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.14 -9999 0 -0.44 14 14
JUN -0.069 0.14 -9999 0 -0.44 10 10
HRAS 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.18 0.23 -9999 0 -0.5 90 90
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.18 0.23 -9999 0 -0.5 90 90
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.17 0.22 -9999 0 -0.49 86 86
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.16 0.2 -9999 0 -0.7 13 13
GRB7 -0.003 0.046 -9999 0 -0.61 2 2
RET51/GFRalpha1/GDNF -0.18 0.23 -9999 0 -0.5 90 90
MAPKKK cascade -0.14 0.18 -9999 0 -0.59 15 15
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.17 0.22 -9999 0 -0.43 140 140
lamellipodium assembly -0.1 0.14 -9999 0 -0.4 14 14
RET51/GFRalpha1/GDNF/SHC -0.18 0.23 -9999 0 -0.5 90 90
PIK3CA 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.17 0.22 -9999 0 -0.49 86 86
RET9/GFRalpha1/GDNF/Shank3 -0.18 0.23 -9999 0 -0.44 139 139
MAPK3 -0.15 0.19 -9999 0 -0.66 13 13
DOK1 0 0 -9999 0 -10000 0 0
DOK6 -0.064 0.21 -9999 0 -0.76 29 29
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.15 0.18 -9999 0 -0.56 26 26
DOK5 -0.006 0.061 -9999 0 -0.66 3 3
GFRA1 -0.19 0.33 -9999 0 -0.76 86 86
MAPK8 -0.08 0.15 -9999 0 -0.47 10 10
HRAS/GTP -0.16 0.2 -9999 0 -0.52 33 33
tube development -0.16 0.21 -9999 0 -0.47 86 86
MAPK1 -0.15 0.19 -9999 0 -0.66 13 13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.14 -9999 0 -0.34 86 86
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.2 0.25 -9999 0 -0.51 106 106
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.18 0.23 -9999 0 -0.5 90 90
RET51/GFRalpha1/GDNF/Dok5 -0.18 0.23 -9999 0 -0.5 91 91
PRKCA -0.002 0.041 -9999 0 -0.76 1 1
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.11 0.16 -9999 0 -0.36 86 86
PIK3R1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.14 -9999 0 -0.34 86 86
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.23 -9999 0 -0.5 91 91
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.023 0.12 -9999 0 -0.62 13 13
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.067 0.14 -9999 0 -0.43 10 10
RET9/GFRalpha1/GDNF/FRS2 -0.17 0.22 -9999 0 -0.43 139 139
SHANK3 -0.004 0.058 -9999 0 -0.76 2 2
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.14 -9999 0 -0.34 86 86
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.15 -9999 0 -0.5 10 10
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.11 0.15 -9999 0 -0.38 30 30
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.15 -9999 0 -0.47 13 13
PI3K -0.15 0.21 -9999 0 -0.48 88 88
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.16 0.21 -9999 0 -0.47 86 86
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.11 0.14 -9999 0 -0.49 10 10
RET51/GFRalpha1/GDNF/FRS2 -0.18 0.23 -9999 0 -0.5 90 90
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.002 0.041 -9999 0 -0.76 1 1
IRS2 -0.002 0.041 -9999 0 -0.76 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.15 -9999 0 -0.38 33 33
RET51/GFRalpha1/GDNF/PKC alpha -0.18 0.23 -9999 0 -0.5 90 90
GRB2 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.11 0.23 -9999 0 -0.61 61 61
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.18 0.23 -9999 0 -0.5 91 91
Rac1/GTP -0.12 0.16 -9999 0 -0.49 14 14
RET9/GFRalpha1/GDNF -0.19 0.24 -9999 0 -0.48 139 139
GFRalpha1/GDNF -0.22 0.28 -9999 0 -0.55 139 139
Aurora C signaling

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
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.24 0.16 -9999 0 -0.72 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.068 0.044 -9999 0 -10000 0 0
AURKB -0.43 0.27 -9999 0 -0.61 247 247
AURKC -0.004 0.052 -9999 0 -0.68 2 2
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.083 -9999 0 -0.42 12 12
RGS9BP -0.026 0.14 -9999 0 -0.76 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.046 -9999 0 -0.61 2 2
mol:Na + -0.17 0.19 -9999 0 -0.38 155 155
mol:ADP -0.014 0.11 -9999 0 -0.44 20 20
GNAT2 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.058 0.17 -9999 0 -0.52 39 39
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.031 0.13 -9999 0 -0.61 18 18
CNGB3 -0.26 0.3 -9999 0 -0.61 151 151
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.22 0.22 -9999 0 -0.39 200 200
Cone PDE6 -0.05 0.14 -9999 0 -0.84 2 2
Cone Metarhodopsin II -0.02 0.081 -9999 0 -0.35 20 20
Na + (4 Units) -0.22 0.21 -9999 0 -0.39 200 200
GNAT2/GDP -0.05 0.14 -9999 0 -0.44 39 39
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.005 -9999 0 -10000 0 0
Cone Transducin -0.018 0.087 -9999 0 -0.42 15 15
SLC24A2 -0.13 0.25 -9999 0 -0.61 76 76
GNB3/GNGT2 -0.023 0.11 -9999 0 -0.54 15 15
GNB3 -0.007 0.065 -9999 0 -0.61 4 4
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 -0.009 0.072 -9999 0 -0.61 5 5
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.17 0.19 -9999 0 -0.38 155 155
mol:Pi -0.058 0.17 -9999 0 -0.52 39 39
Cone CNG Channel -0.14 0.15 -9999 0 -0.62 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.13 0.25 -9999 0 -0.6 76 76
RGS9 -0.064 0.21 -9999 0 -0.76 29 29
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 -0.024 0.13 -9999 0 -0.76 11 11
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0 0 -9999 0 -10000 0 0
LAT2 -0.16 0.25 -9999 0 -0.66 51 51
AP1 -0.19 0.26 -9999 0 -0.64 70 70
mol:PIP3 -0.14 0.28 -9999 0 -0.68 52 52
IKBKB -0.06 0.15 -9999 0 -0.34 48 48
AKT1 -0.17 0.24 -9999 0 -0.66 46 46
IKBKG -0.059 0.15 -9999 0 -0.34 48 48
MS4A2 -0.17 0.32 -9999 0 -0.77 78 78
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.007 0.005 -9999 0 -10000 0 0
MAP3K1 -0.086 0.22 -9999 0 -0.54 48 48
mol:Ca2+ -0.096 0.21 -9999 0 -0.47 52 52
LYN 0.008 0.006 -9999 0 -10000 0 0
CBLB -0.15 0.23 -9999 0 -0.65 47 47
SHC1 0.001 0.004 -9999 0 -10000 0 0
RasGAP/p62DOK -0.07 0.16 -9999 0 -0.46 53 53
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.007 0.07 -9999 0 -0.76 3 3
PLD2 -0.2 0.28 -9999 0 -0.58 96 96
PTPN13 -0.12 0.24 -9999 0 -0.61 48 48
PTPN11 0.006 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.071 0.19 -9999 0 -0.42 48 48
SYK 0.008 0.006 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.19 0.26 -9999 0 -0.71 52 52
LAT -0.15 0.23 -9999 0 -0.65 47 47
PAK2 -0.11 0.25 -9999 0 -0.61 51 51
NFATC2 -0.15 0.3 -9999 0 -0.97 37 37
HRAS -0.13 0.28 -9999 0 -0.69 52 52
GAB2 -0.018 0.11 -9999 0 -0.76 8 8
PLA2G1B -0.005 0.035 -9999 0 -10000 0 0
Fc epsilon R1 -0.24 0.34 -9999 0 -0.65 131 131
Antigen/IgE/Fc epsilon R1 -0.23 0.32 -9999 0 -0.6 131 131
mol:GDP -0.14 0.3 -9999 0 -0.74 52 52
JUN 0 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.005 -9999 0 -10000 0 0
FOS -0.12 0.28 -9999 0 -0.76 55 55
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.16 0.25 -9999 0 -0.54 82 82
CHUK -0.059 0.15 -9999 0 -0.34 48 48
KLRG1 -0.15 0.23 -9999 0 -0.64 48 48
VAV1 -0.15 0.24 -9999 0 -0.66 47 47
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.15 0.23 -9999 0 -0.65 47 47
negative regulation of mast cell degranulation -0.14 0.22 -9999 0 -0.61 47 47
BTK -0.18 0.31 -9999 0 -0.8 54 54
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.19 0.3 -9999 0 -0.84 48 48
GAB2/PI3K/SHP2 -0.18 0.26 -9999 0 -0.75 46 46
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.16 0.24 -9999 0 -0.68 48 48
RAF1 0.024 0.028 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.22 0.32 -9999 0 -0.85 48 48
FCER1G -0.012 0.12 -9999 0 -0.78 8 8
FCER1A -0.2 0.34 -9999 0 -0.77 91 91
Antigen/IgE/Fc epsilon R1/Fyn -0.21 0.3 -9999 0 -0.56 131 131
MAPK3 0.033 0.023 -9999 0 -10000 0 0
MAPK1 0.033 0.023 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.016 0.068 -9999 0 -10000 0 0
DUSP1 -0.12 0.27 -9999 0 -0.76 53 53
NF-kappa-B/RelA -0.055 0.073 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.12 0.24 -9999 0 -0.62 47 47
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.14 0.23 -9999 0 -0.63 48 48
FER -0.15 0.23 -9999 0 -0.65 47 47
RELA 0 0 -9999 0 -10000 0 0
ITK -0.078 0.18 -9999 0 -0.68 27 27
SOS1 0.001 0.004 -9999 0 -10000 0 0
PLCG1 -0.14 0.3 -9999 0 -0.74 52 52
cytokine secretion -0.04 0.053 -9999 0 -10000 0 0
SPHK1 -0.15 0.23 -9999 0 -0.65 47 47
PTK2 -0.13 0.26 -9999 0 -0.66 47 47
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.2 0.28 -9999 0 -0.75 52 52
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.13 0.28 -9999 0 -0.65 52 52
MAP2K2 0.03 0.024 -9999 0 -10000 0 0
MAP2K1 0.03 0.024 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.14 0.22 -9999 0 -0.59 48 48
MAP2K4 0.011 0.013 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.23 0.32 -9999 0 -0.6 132 132
mol:Choline -0.19 0.28 -9999 0 -0.57 96 96
SHC/Grb2/SOS1 -0.14 0.22 -9999 0 -0.61 46 46
FYN 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PXN -0.11 0.23 -9999 0 -0.6 46 46
HCLS1 -0.15 0.23 -9999 0 -0.64 48 48
PRKCB -0.098 0.21 -9999 0 -0.48 52 52
FCGR2B -0.007 0.07 -9999 0 -0.76 3 3
IGHE -0.004 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.14 0.23 -9999 0 -0.62 47 47
LCP2 -0.007 0.071 -9999 0 -0.76 3 3
PLA2G4A -0.15 0.24 -9999 0 -0.65 49 49
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.19 0.28 -9999 0 -0.57 96 96
IKK complex -0.03 0.12 -9999 0 -0.27 14 14
WIPF1 0 0 -9999 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.37 0.55 -10000 0 -1.2 70 70
STAT6 (cleaved dimer) -0.43 0.49 -10000 0 -1.2 91 91
IGHG1 -0.11 0.19 -10000 0 -0.41 2 2
IGHG3 -0.36 0.52 -10000 0 -1.1 89 89
AKT1 -0.13 0.26 -10000 0 -1.1 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.09 0.22 -10000 0 -1.2 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.28 -10000 0 -1.3 4 4
THY1 -0.37 0.55 -10000 0 -1.2 70 70
MYB -0.025 0.12 -10000 0 -0.63 14 14
HMGA1 -0.005 0.056 -10000 0 -0.61 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.18 0.31 -10000 0 -0.7 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.28 -10000 0 -1 7 7
SP1 0.017 0.001 -10000 0 -10000 0 0
INPP5D -0.007 0.07 -10000 0 -0.76 3 3
SOCS5 0.018 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.42 0.49 -10000 0 -1.2 75 75
SOCS1 -0.21 0.36 -10000 0 -0.78 54 54
SOCS3 -0.14 0.28 -10000 0 -1.1 5 5
FCER2 -0.32 0.52 -10000 0 -1.3 52 52
PARP14 0.009 0.005 -10000 0 -10000 0 0
CCL17 -0.44 0.64 -10000 0 -1.4 87 87
GRB2 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.23 -10000 0 -0.82 7 7
T cell proliferation -0.36 0.55 -10000 0 -1.3 70 70
IL4R/JAK1 -0.37 0.55 -10000 0 -1.2 70 70
EGR2 -0.38 0.57 -10000 0 -1.3 75 75
JAK2 -0.001 0.034 -10000 0 -10000 0 0
JAK3 0.013 0.007 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
JAK1 0.01 0.015 -10000 0 -10000 0 0
COL1A2 -0.089 0.18 -10000 0 -0.6 2 2
CCL26 -0.4 0.56 -10000 0 -1.3 78 78
IL4R -0.39 0.59 -10000 0 -1.3 71 71
PTPN6 0.018 0.014 -10000 0 -10000 0 0
IL13RA2 -0.4 0.58 -10000 0 -1.3 75 75
IL13RA1 -0.001 0.034 -10000 0 -10000 0 0
IRF4 -0.15 0.34 -10000 0 -0.85 54 54
ARG1 -0.1 0.24 -10000 0 -0.8 21 21
CBL -0.17 0.3 -10000 0 -0.78 13 13
GTF3A 0.013 0.015 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
IL13RA1/JAK2 0 0.051 -10000 0 -10000 0 0
IRF4/BCL6 -0.16 0.29 -10000 0 -0.82 48 48
CD40LG -0.11 0.29 -10000 0 -0.76 58 58
MAPK14 -0.16 0.3 -10000 0 -1.1 6 6
mitosis -0.12 0.25 -10000 0 -0.98 4 4
STAT6 -0.44 0.64 -10000 0 -1.4 81 81
SPI1 -0.036 0.18 -10000 0 -0.76 21 21
RPS6KB1 -0.11 0.25 -10000 0 -0.92 4 4
STAT6 (dimer) -0.44 0.65 -10000 0 -1.4 81 81
STAT6 (dimer)/PARP14 -0.41 0.59 -10000 0 -1.4 74 74
mast cell activation 0.007 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.15 0.3 -10000 0 -0.82 23 23
FRAP1 -0.13 0.26 -10000 0 -1.1 4 4
LTA -0.37 0.55 -10000 0 -1.2 71 71
FES -0.004 0.058 -10000 0 -0.76 2 2
T-helper 1 cell differentiation 0.42 0.62 1.3 82 -10000 0 82
CCL11 -0.36 0.53 -10000 0 -1.2 70 70
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.13 0.27 -10000 0 -1.1 6 6
IL2RG 0.004 0.082 -10000 0 -0.75 4 4
IL10 -0.37 0.55 -10000 0 -1.3 68 68
IRS1 -0.002 0.041 -10000 0 -0.76 1 1
IRS2 -0.002 0.041 -10000 0 -0.76 1 1
IL4 -0.071 0.14 -10000 0 -10000 0 0
IL5 -0.37 0.55 -10000 0 -1.3 68 68
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.29 0.43 -10000 0 -0.92 71 71
COL1A1 -0.14 0.24 -10000 0 -0.69 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.38 0.56 -10000 0 -1.3 67 67
IL2R gamma/JAK3 0.001 0.063 -10000 0 -0.57 4 4
TFF3 -0.41 0.62 -10000 0 -1.4 74 74
ALOX15 -0.59 0.77 -10000 0 -1.5 123 123
MYBL1 0 0 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.29 0.44 -10000 0 -0.95 72 72
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.01 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.27 -10000 0 -1.1 6 6
mol:PI-3-4-5-P3 -0.13 0.26 -10000 0 -1.1 4 4
PI3K -0.13 0.28 -10000 0 -1.2 4 4
DOK2 -0.064 0.21 -10000 0 -0.76 29 29
ETS1 0.003 0.1 -10000 0 -0.73 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.1 0.22 -10000 0 -0.79 7 7
ITGB3 -0.38 0.56 -10000 0 -1.3 72 72
PIGR -0.77 0.84 -10000 0 -1.6 177 177
IGHE 0.026 0.044 -10000 0 -10000 0 0
MAPKKK cascade -0.098 0.22 -10000 0 -0.77 7 7
BCL6 0.001 0.005 -10000 0 -10000 0 0
OPRM1 -0.38 0.55 -10000 0 -1.3 68 68
RETNLB -0.38 0.55 -10000 0 -1.3 70 70
SELP -0.54 0.75 -10000 0 -1.6 100 100
AICDA -0.36 0.52 -10000 0 -1.2 72 72
Thromboxane A2 receptor signaling

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
TGM2 -0.044 0.19 -10000 0 -0.76 23 23
GNB1/GNG2 -0.067 0.089 -10000 0 -0.22 31 31
AKT1 -0.028 0.13 -10000 0 -0.23 17 17
EGF -0.019 0.12 -10000 0 -0.74 9 9
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.042 0.14 -10000 0 -0.62 12 12
mol:Ca2+ -0.063 0.18 -10000 0 -0.31 119 119
LYN -0.018 0.076 -10000 0 -0.53 4 4
RhoA/GTP -0.044 0.059 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.071 0.2 -10000 0 -0.35 116 116
GNG2 -0.004 0.058 -10000 0 -0.76 2 2
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.017 0.1 -10000 0 -0.62 3 3
G beta5/gamma2 -0.088 0.12 -10000 0 -0.3 38 38
PRKCH -0.077 0.21 -10000 0 -0.36 109 109
DNM1 0 0 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 -0.002 0.012 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.026 0.14 -10000 0 -0.76 12 12
G12 family/GTP -0.11 0.14 -10000 0 -0.32 58 58
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 0 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.13 0.39 18 -10000 0 18
mol:NADP -0.004 0.058 -10000 0 -0.76 2 2
RAB11A 0 0 -10000 0 -10000 0 0
PRKG1 -0.042 0.17 -10000 0 -0.76 19 19
mol:IP3 -0.087 0.22 -10000 0 -0.39 119 119
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.13 0.3 -10000 0 -0.53 119 119
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.033 0.11 -10000 0 -0.59 7 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.019 0.086 -10000 0 -0.6 5 5
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.024 0.13 -10000 0 -0.76 11 11
PRKCB1 -0.088 0.22 -10000 0 -0.39 118 118
GNAQ -0.002 0.041 -10000 0 -0.76 1 1
mol:L-citrulline -0.004 0.058 -10000 0 -0.76 2 2
TXA2/TXA2-R family -0.13 0.3 -10000 0 -0.54 117 117
LCK -0.019 0.08 -10000 0 -0.54 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.023 0.099 -10000 0 -0.72 4 4
TXA2-R family/G12 family/GDP/G beta/gamma 0.02 0.036 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.022 0.098 -10000 0 -0.72 4 4
MAPK14 -0.035 0.14 -10000 0 -0.25 25 25
TGM2/GTP -0.11 0.26 -10000 0 -0.52 60 60
MAPK11 -0.035 0.14 -10000 0 -0.25 24 24
ARHGEF1 -0.028 0.11 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade -0.088 0.23 -10000 0 -0.4 117 117
RAB11/GDP 0 0 -10000 0 -10000 0 0
ICAM1 -0.065 0.19 -10000 0 -0.31 116 116
cAMP biosynthetic process -0.082 0.21 -10000 0 -0.4 62 62
Gq family/GTP/EBP50 -0.035 0.12 -10000 0 -0.54 4 4
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.018 0.076 -10000 0 -0.53 4 4
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR 0.023 0.098 -10000 0 -0.41 8 8
VCAM1 -0.06 0.17 -10000 0 -0.3 116 116
TP beta/Gq family/GDP/G beta5/gamma2 -0.017 0.1 -10000 0 -0.62 3 3
platelet activation -0.049 0.19 -10000 0 -0.33 50 50
PGI2/IP -0.019 0.1 -10000 0 -0.58 11 11
PRKACA -0.025 0.11 -10000 0 -0.44 20 20
Gq family/GDP/G beta5/gamma2 -0.02 0.11 -10000 0 -0.56 4 4
TXA2/TP beta/beta Arrestin2 -0.001 0.008 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.01 0.12 -10000 0 -0.76 5 5
mol:DAG -0.1 0.25 -10000 0 -0.44 116 116
EGFR -0.025 0.13 -10000 0 -0.68 13 13
TXA2/TP alpha -0.12 0.28 -10000 0 -0.56 62 62
Gq family/GTP -0.066 0.13 -10000 0 -0.29 80 80
YES1 -0.018 0.076 -10000 0 -0.53 4 4
GNAI2/GTP -0.021 0.089 -10000 0 -0.64 4 4
PGD2/DP -0.02 0.11 -10000 0 -0.58 12 12
SLC9A3R1 -0.005 0.056 -10000 0 -0.61 3 3
FYN -0.018 0.076 -10000 0 -0.53 4 4
mol:NO -0.004 0.058 -10000 0 -0.76 2 2
GNA15 -0.002 0.041 -10000 0 -0.76 1 1
PGK/cGMP -0.03 0.12 -10000 0 -0.53 20 20
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.049 0.16 -10000 0 -0.76 12 12
NOS3 -0.004 0.058 -10000 0 -0.76 2 2
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.078 0.21 -10000 0 -0.4 52 52
PRKCB -0.083 0.22 -10000 0 -0.38 110 110
PRKCE -0.078 0.21 -10000 0 -0.37 109 109
PRKCD -0.086 0.22 -10000 0 -0.39 115 115
PRKCG -0.098 0.23 -10000 0 -0.41 116 116
muscle contraction -0.12 0.28 -10000 0 -0.5 117 117
PRKCZ -0.071 0.2 -10000 0 -0.35 116 116
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.023 0.1 -10000 0 -0.74 4 4
PRKCQ -0.097 0.23 -10000 0 -0.4 117 117
MAPKKK cascade -0.11 0.27 -10000 0 -0.47 119 119
SELE -0.1 0.23 -10000 0 -0.42 116 116
TP beta/GNAI2/GDP/G beta/gamma -0.024 0.11 -10000 0 -0.7 6 6
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.76 80 80
chemotaxis -0.16 0.34 -10000 0 -0.62 116 116
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 0 0 -10000 0 -10000 0 0
Rac1/GTP 0 0 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.035 0.03 -9999 0 -10000 0 0
VDR -0.002 0.041 -9999 0 -0.76 1 1
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.15 0.18 -9999 0 -0.54 9 9
RXRs/LXRs/DNA/Oxysterols -0.11 0.17 -9999 0 -0.65 9 9
MED1 0 0 -9999 0 -10000 0 0
mol:9cRA 0.004 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.014 0.066 -9999 0 -0.31 16 16
RXRs/NUR77 -0.33 0.29 -9999 0 -0.53 217 217
RXRs/PPAR -0.2 0.2 -9999 0 -0.63 23 23
NCOR2 -0.002 0.041 -9999 0 -0.76 1 1
VDR/VDR/Vit D3 -0.002 0.031 -9999 0 -0.58 1 1
RARs/VDR/DNA/Vit D3 -0.002 0.032 -9999 0 -0.42 2 2
RARA 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.002 0.041 -9999 0 -0.76 1 1
RARs/RARs/DNA/9cRA -0.001 0.023 -9999 0 -0.43 1 1
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.063 0.054 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.015 0.067 -9999 0 -0.31 17 17
THRA 0 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.031 -9999 0 -0.58 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.26 0.22 -9999 0 -0.45 198 198
NR1H4 -0.005 0.056 -9999 0 -0.61 3 3
RXRs/LXRs/DNA -0.23 0.2 -9999 0 -0.57 9 9
NR1H2 0.015 0.004 -9999 0 -10000 0 0
NR1H3 0.014 0.005 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.24 0.21 -9999 0 -0.42 199 199
NR4A1 -0.14 0.3 -9999 0 -0.76 64 64
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.14 0.15 -9999 0 -0.34 10 10
RXRG -0.43 0.38 -9999 0 -0.76 198 198
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.015 0.004 -9999 0 -10000 0 0
RXRB 0.014 0.004 -9999 0 -10000 0 0
THRB -0.033 0.16 -9999 0 -0.76 15 15
PPARG -0.088 0.24 -9999 0 -0.76 40 40
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.12 0.24 -9999 0 -1.2 11 11
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.11 0.16 -9999 0 -0.64 9 9
PPARA 0 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.002 0.041 -9999 0 -0.76 1 1
RXRs/NUR77/BCL2 -0.24 0.21 -9999 0 -0.38 217 217
SREBF1 -0.096 0.15 -9999 0 -0.61 8 8
RXRs/RXRs/DNA/9cRA -0.26 0.22 -9999 0 -0.45 198 198
ABCA1 -0.096 0.15 -9999 0 -0.61 8 8
RARs/THRs -0.019 0.088 -9999 0 -0.42 16 16
RXRs/FXR -0.26 0.22 -9999 0 -0.45 198 198
BCL2 -0.002 0.032 -9999 0 -0.61 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.19 0.23 -9999 0 -0.59 51 51
SMAD6-7/SMURF1 -0.064 0.17 -9999 0 -0.5 45 45
NOG -0.028 0.14 -9999 0 -0.76 13 13
SMAD9 -0.097 0.21 -9999 0 -0.61 45 45
SMAD4 0 0 -9999 0 -10000 0 0
SMAD5 -0.021 0.13 -9999 0 -0.5 12 12
BMP7/USAG1 -0.25 0.29 -9999 0 -0.54 165 165
SMAD5/SKI -0.048 0.11 -9999 0 -0.51 8 8
SMAD1 0.036 0.025 -9999 0 -10000 0 0
BMP2 -0.1 0.26 -9999 0 -0.76 47 47
SMAD1/SMAD1/SMAD4 -0.042 0.11 -9999 0 -10000 0 0
BMPR1A 0 0 -9999 0 -10000 0 0
BMPR1B -0.055 0.2 -9999 0 -0.76 25 25
BMPR1A-1B/BAMBI -0.038 0.13 -9999 0 -0.48 27 27
AHSG -0.01 0.079 -9999 0 -0.61 6 6
CER1 -0.003 0.046 -9999 0 -0.61 2 2
BMP2-4/CER1 -0.082 0.19 -9999 0 -0.52 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.07 0.14 -9999 0 -0.5 20 20
BMP2-4 (homodimer) -0.092 0.22 -9999 0 -0.6 53 53
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.037 0.13 -9999 0 -0.46 28 28
RGMA -0.066 0.19 -9999 0 -0.61 38 38
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.065 0.13 -9999 0 -0.46 20 20
BMP2-4/USAG1 -0.17 0.3 -9999 0 -0.6 100 100
SMAD6/SMURF1/SMAD5 -0.048 0.11 -9999 0 -0.51 8 8
SOSTDC1 -0.15 0.3 -9999 0 -0.76 69 69
BMP7/BMPR2/BMPR1A-1B -0.14 0.19 -9999 0 -0.53 30 30
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.009 0.081 -9999 0 -0.76 4 4
HFE2 -0.005 0.056 -9999 0 -0.61 3 3
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.083 0.2 -9999 0 -0.52 55 55
SMAD5/SMAD5/SMAD4 -0.048 0.11 -9999 0 -0.51 8 8
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.053 0.11 -9999 0 -0.47 11 11
BMP7 (homodimer) -0.2 0.29 -9999 0 -0.61 112 112
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.014 0.084 -9999 0 -0.5 10 10
SMAD1/SKI 0.04 0.023 -9999 0 -10000 0 0
SMAD6 -0.096 0.25 -9999 0 -0.76 44 44
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.085 0.2 -9999 0 -0.51 58 58
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.42 0.28 -9999 0 -0.61 242 242
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.041 0.15 -9999 0 -0.58 25 25
CHRDL1 -0.38 0.38 -9999 0 -0.76 175 175
ENDOFIN/SMAD1 0.04 0.023 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.048 0.12 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.003 0.046 -9999 0 -0.61 2 2
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.32 0.32 -9999 0 -0.57 197 197
BMP2-4/GREM1 -0.33 0.22 -9999 0 -0.43 270 270
SMAD7 -0.002 0.041 -9999 0 -0.76 1 1
SMAD8A/SMAD8A/SMAD4 -0.089 0.2 -9999 0 -0.57 45 45
SMAD1/SMAD6 0.04 0.023 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.2 0.29 -9999 0 -0.61 112 112
BMP6 -0.009 0.081 -9999 0 -0.76 4 4
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.061 0.12 -9999 0 -0.44 20 20
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.04 0.023 -9999 0 -10000 0 0
SMAD7/SMURF1 -0.002 0.031 -9999 0 -0.58 1 1
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.093 0.15 -9999 0 -0.51 29 29
CHRD -0.006 0.066 -9999 0 -0.71 3 3
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.075 0.14 -9999 0 -0.52 20 20
BMP4 -0.019 0.12 -9999 0 -0.74 9 9
FST -0.11 0.24 -9999 0 -0.61 64 64
BMP2-4/NOG -0.097 0.22 -9999 0 -0.54 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.13 0.18 -9999 0 -0.5 30 30
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.072 0.081 0.16 166 -10000 0 166
BUB1B -0.14 0.11 -10000 0 -0.24 136 136
PLK1 -0.015 0.038 -10000 0 -0.14 5 5
PLK1S1 -0.003 0.021 -10000 0 -10000 0 0
KIF2A -0.005 0.034 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.014 0.038 -10000 0 -0.14 5 5
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.2 0.24 -10000 0 -0.44 152 152
WEE1 -0.007 0.041 -10000 0 -10000 0 0
cytokinesis -0.08 0.13 -10000 0 -0.28 73 73
PP2A-alpha B56 -0.008 0.025 -10000 0 -10000 0 0
AURKA -0.006 0.03 -10000 0 -0.14 5 5
PICH/PLK1 -0.13 0.18 -10000 0 -0.5 40 40
CENPE -0.032 0.11 -10000 0 -0.38 27 27
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.005 0.034 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 -0.067 0.056 -10000 0 -0.13 33 33
PAK1 0.002 0.033 -10000 0 -0.6 1 1
SPC24 -0.16 0.26 -10000 0 -0.61 89 89
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN -0.011 0.039 -10000 0 -0.14 11 11
GORASP1 0 0 -10000 0 -10000 0 0
metaphase -0.001 0.004 -10000 0 -0.012 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.008 0.021 -10000 0 -0.069 5 5
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -10000 0 0
STAG2 0 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.012 -10000 0 -10000 0 0
spindle elongation -0.014 0.038 -10000 0 -0.14 5 5
ODF2 0.004 0.005 -10000 0 -10000 0 0
BUB1 -0.005 0.035 -10000 0 -10000 0 0
TPT1 -0.003 0.021 -10000 0 -10000 0 0
CDC25C -0.089 0.065 -10000 0 -0.14 149 149
CDC25B 0.009 0.003 -10000 0 -10000 0 0
SGOL1 -0.072 0.081 -10000 0 -0.16 166 166
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.034 0.089 -10000 0 -0.32 3 3
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 -0.38 0.29 -10000 0 -0.61 218 218
PLK1/PBIP1 -0.036 0.077 -10000 0 -0.36 17 17
mitosis -0.001 0.004 0.024 6 -10000 0 6
FBXO5 -0.005 0.034 -10000 0 -10000 0 0
CDC2 -0.001 0.004 -10000 0 -0.013 11 11
NDC80 -0.19 0.28 -10000 0 -0.61 108 108
metaphase plate congression -0.008 0.026 -10000 0 -10000 0 0
ERCC6L -0.13 0.18 -10000 0 -0.48 38 38
NLP/gamma Tubulin -0.006 0.023 -10000 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.021 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.004 0.005 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.15 0.2 -10000 0 -0.4 125 125
GRASP65/GM130/RAB1/GTP/PLK1 -0.009 0.016 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.028 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.047 0.039 -10000 0 -10000 0 0
microtubule-based process -0.13 0.17 -10000 0 -0.37 115 115
Golgi organization -0.014 0.038 -10000 0 -0.14 5 5
Cohesin/SA2 -0.02 0.026 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.2 0.28 -10000 0 -0.61 115 115
APC/C/CDC20 -0.23 0.18 -10000 0 -0.37 218 218
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation -0.035 0.076 -10000 0 -0.35 17 17
PRC1 -0.051 0.17 -10000 0 -0.61 29 29
ECT2 -0.018 0.079 -10000 0 -0.38 13 13
C13orf34 -0.003 0.029 -10000 0 -10000 0 0
NUDC -0.008 0.026 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.14 0.11 -10000 0 -0.24 136 136
spindle assembly -0.009 0.031 -10000 0 -0.11 3 3
spindle stabilization -0.003 0.021 -10000 0 -10000 0 0
APC/C/HCDH1 0 0 -10000 0 -10000 0 0
MKLP2/PLK1 -0.13 0.17 -10000 0 -0.37 115 115
CCNB1 -0.069 0.2 -10000 0 -0.6 45 45
PPP1CB 0.004 0.005 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 0 0.026 -10000 0 -10000 0 0
TUBG1 -0.003 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.035 0.086 -10000 0 -0.31 3 3
MLF1IP -0.017 0.1 -10000 0 -0.46 17 17
INCENP 0.005 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.004 0.015 -10000 0 -10000 0 0
FBXW11 0 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 0 -10000 0 -10000 0 0
DKK2 -0.12 0.28 -10000 0 -0.76 54 54
TLE1 0.004 0.015 -10000 0 -10000 0 0
MACF1 0.004 0.058 -10000 0 -0.76 2 2
CTNNB1 0.073 0.1 0.29 9 -10000 0 9
WIF1 -0.5 0.36 -10000 0 -0.76 229 229
beta catenin/RanBP3 0.004 0.091 0.39 15 -10000 0 15
KREMEN2 -0.38 0.29 -10000 0 -0.6 220 220
DKK1 -0.051 0.18 -10000 0 -0.65 27 27
beta catenin/beta TrCP1 0.074 0.096 0.28 9 -10000 0 9
FZD1 0.003 0.005 -10000 0 -10000 0 0
AXIN2 -0.034 0.27 -10000 0 -1.5 11 11
AXIN1 0.009 0.005 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.022 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.098 0.055 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.023 0.069 0.24 26 -10000 0 26
Axin1/APC/GSK3/beta catenin/Macf1 0.068 0.045 -10000 0 -10000 0 0
HNF1A -0.007 0.082 -10000 0 -0.61 6 6
CTBP1 0.004 0.016 -10000 0 -10000 0 0
MYC 0.008 0.049 -10000 0 -10000 0 0
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.31 0.25 -10000 0 -0.45 235 235
NKD1 -0.079 0.23 -10000 0 -0.74 37 37
TCF4 0.002 0.044 -10000 0 -0.76 1 1
TCF3 0.004 0.016 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.002 0.025 -10000 0 -10000 0 0
Ran/GTP 0 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.098 0.44 17 -10000 0 17
LEF1 0.002 0.037 -10000 0 -0.61 1 1
DVL1 0.084 0.062 -10000 0 -10000 0 0
CSNK2A1 0.004 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.1 0.065 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.26 0.21 -10000 0 -0.4 228 228
LRP6 0.007 0.005 -10000 0 -10000 0 0
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.011 0.002 -10000 0 -10000 0 0
CCND1 -0.016 0.2 -10000 0 -1.5 6 6
WNT1 0.003 0.047 -10000 0 -0.6 2 2
GSK3A 0.009 0.005 -10000 0 -10000 0 0
GSK3B 0.003 0.005 -10000 0 -10000 0 0
FRAT1 -0.002 0.041 -10000 0 -0.76 1 1
PPP2R5D 0.081 0.11 0.38 37 -10000 0 37
APC 0.012 0.03 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.17 0.12 0.26 228 -10000 0 228
CREBBP 0.004 0.016 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0 0 -10000 0 -10000 0 0
HDAC1 0.001 0.006 -10000 0 -10000 0 0
AES 0 0.003 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.002 0.032 -10000 0 -0.61 1 1
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0 0.002 -10000 0 -10000 0 0
AP1 -0.098 0.21 -10000 0 -0.44 76 76
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 0 0.002 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.001 0.04 -10000 0 -10000 0 0
NICD/RBPSUH 0 0 -10000 0 -10000 0 0
WIF1 -0.5 0.36 -10000 0 -0.76 229 229
NOTCH1 0 0 -10000 0 -10000 0 0
PSENEN 0 0 -10000 0 -10000 0 0
KREMEN2 -0.38 0.29 -10000 0 -0.61 220 220
DKK1 -0.051 0.18 -10000 0 -0.65 27 27
beta catenin/beta TrCP1 0.016 0.063 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 -0.004 0.029 0.31 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0 0.031 -10000 0 -10000 0 0
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.12 0.28 -10000 0 -0.76 55 55
JUN 0 0 -10000 0 -10000 0 0
MAP3K7 0.001 0.004 -10000 0 -10000 0 0
CTNNB1 0.01 0.068 0.23 7 -10000 0 7
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.31 0.25 -10000 0 -0.45 235 235
HNF1A -0.01 0.079 -10000 0 -0.61 6 6
CTBP1 0 0.003 -10000 0 -10000 0 0
MYC 0.002 0.014 -10000 0 -10000 0 0
NKD1 -0.079 0.23 -10000 0 -0.74 37 37
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.001 0.016 -10000 0 -10000 0 0
apoptosis -0.098 0.21 -10000 0 -0.44 76 76
Delta 1/NOTCHprecursor 0 0 -10000 0 -10000 0 0
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.002 0.014 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.004 0.029 0.31 1 -10000 0 1
DVL1 -0.048 0.048 -10000 0 -0.68 1 1
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.26 0.21 -10000 0 -0.4 228 228
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.001 0.007 -10000 0 -10000 0 0
CCND1 -0.023 0.19 -10000 0 -1.5 6 6
WNT1 -0.003 0.046 -10000 0 -0.61 2 2
Axin1/APC/beta catenin 0.01 0.047 0.28 1 -0.37 1 2
DKK2 -0.12 0.28 -10000 0 -0.76 54 54
NOTCH1 precursor/DVL1 -0.024 0.033 -10000 0 -0.56 1 1
GSK3B 0 0.002 -10000 0 -10000 0 0
FRAT1 -0.002 0.041 -10000 0 -0.76 1 1
NOTCH/Deltex homolog 1 -0.001 0.016 -10000 0 -10000 0 0
PPP2R5D 0.012 0.11 0.31 37 -0.25 1 38
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.3 0.21 -10000 0 -0.45 229 229
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
Glypican 1 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
GPC1/FGF2 dimer/FGFR1 dimer -0.037 0.13 -10000 0 -0.53 13 13
fibroblast growth factor receptor signaling pathway -0.037 0.13 -10000 0 -0.53 13 13
LAMA1 -0.19 0.28 -10000 0 -0.61 108 108
PRNP 0 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.13 0.24 -10000 0 -0.57 82 82
SMAD2 -0.023 0.14 -10000 0 -0.45 27 27
GPC1/PrPc/Cu2+ -0.017 0.079 -10000 0 -0.38 16 16
GPC1/Laminin alpha1 -0.16 0.23 -10000 0 -0.48 112 112
TDGF1 -0.005 0.056 -10000 0 -0.61 3 3
CRIPTO/GPC1 -0.024 0.1 -10000 0 -0.44 19 19
APP/GPC1 -0.02 0.092 -10000 0 -0.44 16 16
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.002 0.09 -10000 0 -0.37 19 19
FLT1 0 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.056 0.15 -10000 0 -0.45 43 43
SERPINC1 -0.007 0.065 -10000 0 -0.61 4 4
FYN 0.002 0.09 -10000 0 -0.37 19 19
FGR -0.036 0.16 -10000 0 -0.45 43 43
positive regulation of MAPKKK cascade 0.004 0.1 -10000 0 -0.41 9 9
SLIT2 -0.15 0.3 -10000 0 -0.76 69 69
GPC1/NRG -0.039 0.13 -10000 0 -0.5 27 27
NRG1 -0.024 0.13 -10000 0 -0.76 11 11
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.017 0.077 -10000 0 -0.37 16 16
LYN 0.002 0.09 -10000 0 -0.37 19 19
mol:Spermine -0.011 0.096 -10000 0 -0.45 16 16
cell growth -0.037 0.13 -10000 0 -0.53 13 13
BMP signaling pathway 0.028 0.13 0.6 16 -10000 0 16
SRC 0.002 0.09 -10000 0 -0.37 19 19
TGFBR1 0 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.24 0.35 -10000 0 -0.76 110 110
GPC1 -0.028 0.13 -10000 0 -0.61 16 16
TGFBR1 (dimer) 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.023 0.14 -10000 0 -0.41 37 37
HCK -0.001 0.097 -10000 0 -0.38 21 21
FGF2 -0.026 0.14 -10000 0 -0.76 12 12
FGFR1 -0.004 0.058 -10000 0 -0.76 2 2
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
TGFBR2 -0.059 0.2 -10000 0 -0.76 27 27
cell death -0.02 0.092 -10000 0 -0.44 16 16
ATIII/GPC1 -0.025 0.1 -10000 0 -0.44 20 20
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.58 120 120
LCK 0 0.094 -10000 0 -0.38 20 20
neuron differentiation -0.038 0.13 -10000 0 -0.49 27 27
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.059 0.2 -10000 0 -0.76 27 27
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.014 0.091 -9999 0 -0.55 9 9
ARNO/beta Arrestin1-2 -0.16 0.24 -9999 0 -0.49 96 96
EGFR -0.025 0.13 -9999 0 -0.68 13 13
EPHA2 -0.007 0.07 -9999 0 -0.76 3 3
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.033 0.13 -9999 0 -0.55 21 21
ARRB2 0.008 0.013 -9999 0 -0.23 1 1
mol:GTP 0.017 0.02 -9999 0 -10000 0 0
ARRB1 -0.12 0.27 -9999 0 -0.76 53 53
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.017 0.1 -9999 0 -0.6 10 10
EGF -0.019 0.12 -9999 0 -0.74 9 9
somatostatin receptor activity 0 0 -9999 0 -0.001 75 75
ARAP2 -0.002 0.041 -9999 0 -0.76 1 1
mol:GDP -0.11 0.16 -9999 0 -0.34 88 88
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 60 60
ITGA2B -0.028 0.14 -9999 0 -0.76 13 13
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.042 -9999 0 -0.45 3 3
ADAP1 -0.007 0.07 -9999 0 -0.76 3 3
KIF13B -0.015 0.11 -9999 0 -0.76 7 7
HGF/MET -0.11 0.22 -9999 0 -0.57 64 64
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.11 0.15 -9999 0 -0.32 89 89
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.028 0.12 -9999 0 -0.53 13 13
ADRB2 -0.22 0.35 -9999 0 -0.76 102 102
receptor agonist activity 0 0 -9999 0 0 94 94
actin filament binding 0 0 -9999 0 -0.001 88 88
SRC 0 0 -9999 0 -10000 0 0
ITGB3 -0.013 0.099 -9999 0 -0.76 6 6
GNAQ 0.002 0.041 -9999 0 -0.76 1 1
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 60 60
ARF6/GDP -0.01 0.073 -9999 0 -0.37 3 3
ARF6/GDP/GULP/ACAP1 -0.11 0.14 -9999 0 -0.47 20 20
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.025 0.1 -9999 0 -0.45 19 19
ACAP1 -0.002 0.041 -9999 0 -0.76 1 1
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.018 -9999 0 -0.34 1 1
EFNA1 0 0 -9999 0 -10000 0 0
HGF -0.13 0.29 -9999 0 -0.76 61 61
CYTH3 0.01 0 -9999 0 -10000 0 0
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 66 66
endosomal lumen acidification 0 0 -9999 0 -0.001 60 60
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.009 0.081 -9999 0 -0.76 4 4
GNAQ/ARNO 0.004 0.024 -9999 0 -0.43 1 1
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 10 10
MET -0.006 0.066 -9999 0 -0.71 3 3
GNA14 -0.18 0.32 -9999 0 -0.76 80 80
GNA15 -0.002 0.041 -9999 0 -0.76 1 1
GIT1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 67 67
GNA11 0 0 -9999 0 -10000 0 0
LHCGR -0.002 0.032 -9999 0 -0.6 1 1
AGTR1 -0.29 0.37 -9999 0 -0.76 134 134
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.018 -9999 0 -0.34 1 1
IPCEF1/ARNO -0.022 0.092 -9999 0 -0.42 13 13
alphaIIb/beta3 Integrin -0.032 0.13 -9999 0 -0.58 19 19
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.098 0.37 -9999 0 -1.3 29 29
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.031 0.12 -9999 0 -0.45 5 5
ATF2/c-Jun -0.006 0.096 -9999 0 -10000 0 0
MAPK11 -0.031 0.12 -9999 0 -0.45 5 5
MITF -0.028 0.15 -9999 0 -0.37 48 48
MAPKAPK5 -0.026 0.14 -9999 0 -0.37 46 46
KRT8 -0.026 0.14 -9999 0 -0.37 46 46
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.047 0.18 -9999 0 -0.47 46 46
CEBPB -0.026 0.14 -9999 0 -0.37 46 46
SLC9A1 -0.026 0.14 -9999 0 -0.37 46 46
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.02 0.14 -9999 0 -0.55 5 5
p38alpha-beta/MNK1 -0.06 0.13 -9999 0 -0.62 5 5
JUN -0.005 0.095 -9999 0 -10000 0 0
PPARGC1A -0.12 0.28 -9999 0 -0.58 66 66
USF1 -0.026 0.14 -9999 0 -0.37 46 46
RAB5/GDP/GDI1 -0.042 0.092 -9999 0 -0.43 5 5
NOS2 -0.096 0.33 -9999 0 -1.2 22 22
DDIT3 -0.026 0.14 -9999 0 -0.37 46 46
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.012 0.12 -9999 0 -0.47 5 5
p38alpha-beta/HBP1 -0.06 0.13 -9999 0 -0.62 5 5
CREB1 -0.023 0.15 -9999 0 -0.38 46 46
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.015 0.13 -9999 0 -0.56 5 5
RPS6KA4 -0.026 0.14 -9999 0 -0.56 5 5
PLA2G4A -0.02 0.14 -9999 0 -0.58 9 9
GDI1 -0.026 0.14 -9999 0 -0.37 46 46
TP53 -0.036 0.18 -9999 0 -0.46 46 46
RPS6KA5 -0.026 0.14 -9999 0 -0.37 46 46
ESR1 -0.045 0.18 -9999 0 -0.42 56 56
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.03 0.16 -9999 0 -0.38 48 48
MEF2A -0.026 0.14 -9999 0 -0.56 5 5
EIF4EBP1 -0.026 0.15 -9999 0 -0.38 46 46
KRT19 -0.032 0.17 -9999 0 -0.41 47 47
ELK4 -0.026 0.14 -9999 0 -0.37 46 46
ATF6 -0.026 0.14 -9999 0 -0.37 46 46
ATF1 -0.023 0.15 -9999 0 -0.38 46 46
p38alpha-beta/MAPKAPK2 -0.06 0.13 -9999 0 -0.62 5 5
p38alpha-beta/MAPKAPK3 -0.06 0.13 -9999 0 -0.62 5 5
TCGA08_p53

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
CDKN2A -0.2 0.23 -10000 0 -0.45 162 162
TP53 -0.054 0.058 -10000 0 -10000 0 0
Senescence -0.054 0.058 -10000 0 -10000 0 0
Apoptosis -0.054 0.058 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.1 0.11 0.32 2 -10000 0 2
MDM4 0 0 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.002 0.14 -10000 0 -0.38 40 40
CRKL -0.007 0.14 -10000 0 -0.41 37 37
HRAS -0.01 0.15 -10000 0 -0.61 8 8
mol:PIP3 -0.02 0.13 -10000 0 -0.39 39 39
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.015 0.15 -10000 0 -0.43 39 39
FOXO3 -0.001 0.13 -10000 0 -0.37 37 37
AKT1 -0.009 0.14 -10000 0 -0.4 37 37
BAD -0.001 0.13 -10000 0 -0.37 37 37
megakaryocyte differentiation -0.039 0.19 -10000 0 -0.47 52 52
GSK3B -0.001 0.13 -10000 0 -0.37 37 37
RAF1 0.015 0.13 -10000 0 -0.47 8 8
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.015 0.15 -10000 0 -0.43 39 39
STAT1 -0.057 0.34 -10000 0 -1 37 37
HRAS/SPRED1 -0.041 0.1 -10000 0 -0.47 8 8
cell proliferation -0.014 0.14 -10000 0 -0.42 39 39
PIK3CA 0 0 -10000 0 -10000 0 0
TEC -0.002 0.041 -10000 0 -0.76 1 1
RPS6KB1 -0.015 0.15 -10000 0 -0.43 39 39
HRAS/SPRED2 -0.041 0.1 -10000 0 -0.47 8 8
LYN/TEC/p62DOK -0.045 0.12 -10000 0 -0.4 38 38
MAPK3 0.026 0.094 -10000 0 -0.32 8 8
STAP1 -0.037 0.2 -10000 0 -0.5 48 48
GRAP2 -0.035 0.16 -10000 0 -0.76 16 16
JAK2 -0.094 0.26 -10000 0 -0.86 37 37
STAT1 (dimer) -0.054 0.33 -10000 0 -1 37 37
mol:Gleevec -0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.046 0.13 -10000 0 -0.4 39 39
actin filament polymerization -0.014 0.14 -10000 0 -0.42 39 39
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.038 0.24 -10000 0 -0.67 39 39
PIK3R1 0 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.04 0.11 -10000 0 -0.36 37 37
PI3K -0.045 0.13 -10000 0 -0.4 37 37
PTEN 0 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.083 0.41 -10000 0 -1.3 37 37
MAPK8 -0.015 0.15 -10000 0 -0.43 39 39
STAT3 (dimer) -0.014 0.14 -10000 0 -0.42 39 39
positive regulation of transcription 0.027 0.08 -10000 0 -0.26 7 7
mol:GDP -0.054 0.14 -10000 0 -0.65 8 8
PIK3C2B -0.016 0.15 -10000 0 -0.44 39 39
CBL/CRKL 0 0.13 -10000 0 -0.38 37 37
FER -0.015 0.15 -10000 0 -0.43 39 39
SH2B3 -0.016 0.15 -10000 0 -0.43 40 40
PDPK1 -0.011 0.12 -10000 0 -0.36 37 37
SNAI2 -0.015 0.15 -10000 0 -0.43 39 39
positive regulation of cell proliferation -0.032 0.25 -10000 0 -0.74 37 37
KITLG 0.009 0.059 -10000 0 -0.77 2 2
cell motility -0.032 0.25 -10000 0 -0.74 37 37
PTPN6 0.004 0.01 -10000 0 -10000 0 0
EPOR 0.016 0.097 -10000 0 -10000 0 0
STAT5A (dimer) -0.022 0.21 -10000 0 -0.61 37 37
SOCS1 -0.002 0.041 -10000 0 -0.76 1 1
cell migration 0.027 0.17 0.44 47 -10000 0 47
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.005 0.092 -10000 0 -0.6 8 8
VAV1 -0.002 0.041 -10000 0 -0.76 1 1
GRB10 -0.015 0.15 -10000 0 -0.43 39 39
PTPN11 0.003 0.008 -10000 0 -10000 0 0
SCF/KIT -0.052 0.14 -10000 0 -0.46 39 39
GO:0007205 0 0.008 -10000 0 -10000 0 0
MAP2K1 0.023 0.1 -10000 0 -0.35 8 8
CBL 0 0 -10000 0 -10000 0 0
KIT -0.1 0.44 -10000 0 -1.4 37 37
MAP2K2 0.023 0.1 -10000 0 -0.35 8 8
SHC/Grb2/SOS1 -0.044 0.12 -10000 0 -0.4 37 37
STAT5A -0.024 0.21 -10000 0 -0.63 37 37
GRB2 0 0 -10000 0 -10000 0 0
response to radiation -0.014 0.14 -10000 0 -0.42 39 39
SHC/GRAP2 -0.027 0.12 -10000 0 -0.58 16 16
PTPRO -0.04 0.19 -10000 0 -0.48 52 52
SH2B2 -0.015 0.15 -10000 0 -0.43 39 39
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.028 0.17 -10000 0 -0.45 47 47
CREBBP 0.03 0.01 -10000 0 -10000 0 0
BCL2 0.016 0.096 -10000 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.015 0.092 -9999 0 -0.58 9 9
alphaV beta3 Integrin -0.026 0.12 -9999 0 -0.52 17 17
PTK2 -0.18 0.22 -9999 0 -0.7 20 20
IGF1R 0 0 -9999 0 -10000 0 0
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
CDKN1B -0.25 0.3 -9999 0 -0.6 141 141
VEGFA 0 0 -9999 0 -10000 0 0
ILK -0.25 0.3 -9999 0 -0.6 141 141
ROCK1 0 0 -9999 0 -10000 0 0
AKT1 -0.23 0.28 -9999 0 -0.56 141 141
PTK2B 0.017 0.11 -9999 0 -0.52 12 12
alphaV/beta3 Integrin/JAM-A -0.19 0.24 -9999 0 -0.87 11 11
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.013 0.076 -9999 0 -0.5 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.061 -9999 0 -0.45 6 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.12 0.16 -9999 0 -0.69 10 10
alphaV/beta3 Integrin/Syndecan-1 -0.01 0.07 -9999 0 -0.5 7 7
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.034 0.13 -9999 0 -0.77 6 6
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.24 0.18 -9999 0 -0.61 6 6
RPS6KB1 -0.031 0.12 -9999 0 -0.71 6 6
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.11 0.18 -9999 0 -0.82 17 17
GPR124 0 0 -9999 0 -10000 0 0
MAPK1 -0.11 0.18 -9999 0 -0.82 17 17
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.32 0.25 -9999 0 -0.51 221 221
cell adhesion -0.013 0.071 -9999 0 -0.46 6 6
ANGPTL3 -0.007 0.065 -9999 0 -0.61 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.013 0.079 -9999 0 -0.5 9 9
IGF-1R heterotetramer 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.059 0.2 -9999 0 -0.76 27 27
ITGB3 -0.013 0.099 -9999 0 -0.76 6 6
IGF1 -0.013 0.096 -9999 0 -0.73 6 6
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.009 0.064 -9999 0 -0.49 6 6
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.004 0.058 -9999 0 -0.76 2 2
alphaV/beta3 Integrin/CD47 -0.011 0.074 -9999 0 -0.5 8 8
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.023 0.11 -9999 0 -0.52 15 15
CSF1 0 0 -9999 0 -10000 0 0
PIK3C2A -0.25 0.3 -9999 0 -0.6 141 141
PI4 Kinase/Pyk2 -0.17 0.22 -9999 0 -0.79 16 16
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.019 0.11 -9999 0 -0.56 12 12
FAK1/Vinculin -0.14 0.17 -9999 0 -0.51 20 20
alphaV beta3/Integrin/ppsTEM5 -0.009 0.064 -9999 0 -0.5 6 6
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.31 0.37 -9999 0 -0.76 143 143
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.026 0.14 -9999 0 -0.76 12 12
F11R 0 0.11 -9999 0 -0.58 12 12
alphaV/beta3 Integrin/Lactadherin -0.009 0.064 -9999 0 -0.5 6 6
alphaV/beta3 Integrin/TGFBR2 -0.046 0.16 -9999 0 -0.56 29 29
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.008 0.059 -9999 0 -0.46 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.013 0.099 -9999 0 -0.76 6 6
alphaV/beta3 Integrin/Pyk2 -0.018 0.1 -9999 0 -0.52 12 12
SDC1 -0.002 0.041 -9999 0 -0.76 1 1
VAV3 0.036 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.002 0.041 -9999 0 -0.76 1 1
FAK1/Paxillin -0.14 0.17 -9999 0 -0.51 20 20
cell migration -0.12 0.16 -9999 0 -0.51 12 12
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.17 0.21 -9999 0 -0.79 11 11
SPP1 -0.37 0.29 -9999 0 -0.61 214 214
KDR -0.02 0.12 -9999 0 -0.76 9 9
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.48 0.36 -9999 0 -0.76 221 221
angiogenesis -0.12 0.23 -9999 0 -0.82 17 17
Rac1/GTP 0 0 -9999 0 -10000 0 0
EDIL3 -0.022 0.13 -9999 0 -0.76 10 10
cell proliferation -0.046 0.16 -9999 0 -0.55 29 29
Nongenotropic Androgen signaling

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.091 0.18 -10000 0 -0.46 68 68
regulation of S phase of mitotic cell cycle -0.06 0.13 -10000 0 -0.32 16 16
GNAO1 -0.006 0.061 -10000 0 -0.66 3 3
HRAS 0 0 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
MAP2K1 -0.051 0.17 -10000 0 -0.48 16 16
T-DHT/AR -0.11 0.23 -10000 0 -0.59 67 67
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 55 55
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.041 -10000 0 -0.76 1 1
mol:GDP -0.11 0.22 -10000 0 -0.57 67 67
cell proliferation -0.069 0.22 -10000 0 -0.66 16 16
PIK3CA 0 0 -10000 0 -10000 0 0
FOS -0.12 0.33 -10000 0 -0.86 55 55
mol:Ca2+ -0.013 0.023 -10000 0 -0.1 5 5
MAPK3 -0.059 0.19 -10000 0 -0.59 16 16
MAPK1 -0.027 0.1 -10000 0 -0.3 16 16
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 55 55
cAMP biosynthetic process 0.011 0.022 -10000 0 -10000 0 0
GNG2 -0.004 0.058 -10000 0 -0.76 2 2
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 55 55
HRAS/GTP -0.084 0.16 -10000 0 -0.42 67 67
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 55 55
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.061 0.19 0.45 55 -10000 0 55
T-DHT/AR/PELP1 -0.098 0.2 -10000 0 -0.5 67 67
HRAS/GDP -0.1 0.21 -10000 0 -0.54 67 67
CREB1 -0.067 0.21 -10000 0 -0.48 55 55
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.15 0.3 -10000 0 -0.76 67 67
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.057 0.17 -10000 0 -0.47 16 16
RAC1-CDC42/GDP -0.099 0.2 -10000 0 -0.51 67 67
T-DHT/AR/PELP1/Src -0.089 0.18 -10000 0 -0.46 67 67
MAP2K2 -0.051 0.17 -10000 0 -0.48 16 16
T-DHT/AR/PELP1/Src/PI3K -0.06 0.13 -10000 0 -0.33 16 16
GNAZ -0.011 0.091 -10000 0 -0.76 5 5
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.023 0.067 -10000 0 -0.64 2 2
mol:T-DHT 0 0.001 -10000 0 -0.003 39 39
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.007 0.045 -10000 0 -0.58 2 2
Gi family/GTP -0.042 0.089 -10000 0 -0.45 5 5
CDC42 0 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.15 0.44 -10000 0 -1.2 30 30
IL23A -0.16 0.44 -10000 0 -1.2 32 32
NF kappa B1 p50/RelA/I kappa B alpha -0.22 0.36 -10000 0 -1.1 39 39
positive regulation of T cell mediated cytotoxicity -0.17 0.46 -10000 0 -1.2 39 39
ITGA3 -0.16 0.44 -10000 0 -1.2 34 34
IL17F -0.078 0.29 -10000 0 -0.74 23 23
IL12B 0.016 0.025 -10000 0 -10000 0 0
STAT1 (dimer) -0.18 0.43 -10000 0 -1.1 39 39
CD4 -0.14 0.42 -10000 0 -1.1 38 38
IL23 -0.16 0.41 -10000 0 -1.1 32 32
IL23R 0 0.087 -10000 0 -10000 0 0
IL1B -0.16 0.44 -10000 0 -1.2 28 28
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.15 0.41 -10000 0 -1 37 37
TYK2 0.01 0.019 -10000 0 -10000 0 0
STAT4 -0.011 0.091 -10000 0 -0.76 5 5
STAT3 0 0.002 -10000 0 -10000 0 0
IL18RAP -0.027 0.16 -10000 0 -0.76 16 16
IL12RB1 -0.035 0.19 -10000 0 -0.79 20 20
PIK3CA 0 0.002 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.024 0.15 -10000 0 -0.61 20 20
IL23R/JAK2 -0.001 0.11 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.17 0.46 -10000 0 -1.2 39 39
natural killer cell activation 0 0.008 0.035 1 -10000 0 1
JAK2 0.017 0.024 -10000 0 -10000 0 0
PIK3R1 0 0.002 -10000 0 -10000 0 0
NFKB1 0.006 0.007 -10000 0 -10000 0 0
RELA 0.006 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.4 -10000 0 -1 32 32
ALOX12B -0.2 0.43 -10000 0 -1 45 45
CXCL1 -0.16 0.46 -10000 0 -1.2 41 41
T cell proliferation -0.17 0.46 -10000 0 -1.2 39 39
NFKBIA 0.006 0.007 -10000 0 -10000 0 0
IL17A -0.058 0.25 -10000 0 -0.6 17 17
PI3K -0.22 0.37 -10000 0 -1.1 39 39
IFNG -0.002 0.03 0.1 1 -0.11 13 14
STAT3 (dimer) -0.21 0.35 -10000 0 -1 38 38
IL18R1 0.002 0.071 -10000 0 -0.76 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.072 0.28 -10000 0 -0.79 19 19
IL18/IL18R -0.029 0.13 -10000 0 -0.54 19 19
macrophage activation -0.013 0.017 -10000 0 -0.044 29 29
TNF -0.17 0.46 -10000 0 -1.2 38 38
STAT3/STAT4 -0.23 0.37 -10000 0 -1.1 40 40
STAT4 (dimer) -0.19 0.44 -10000 0 -1.2 40 40
IL18 0.005 0.058 -10000 0 -0.76 2 2
IL19 -0.15 0.41 -10000 0 -1.2 24 24
STAT5A (dimer) -0.18 0.43 -10000 0 -1.2 38 38
STAT1 0 0 -10000 0 -10000 0 0
SOCS3 -0.004 0.058 -10000 0 -0.76 2 2
CXCL9 -0.15 0.44 -10000 0 -1.1 39 39
MPO -0.16 0.46 -10000 0 -1.2 38 38
positive regulation of humoral immune response -0.17 0.46 -10000 0 -1.2 39 39
IL23/IL23R/JAK2/TYK2 -0.18 0.5 -10000 0 -1.3 39 39
IL6 -0.3 0.62 -10000 0 -1.3 81 81
STAT5A -0.002 0.041 -10000 0 -0.76 1 1
IL2 0.006 0.009 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.008 0.035 1 -10000 0 1
CD3E -0.14 0.42 -10000 0 -1.1 33 33
keratinocyte proliferation -0.17 0.46 -10000 0 -1.2 39 39
NOS2 -0.19 0.49 -10000 0 -1.2 48 48
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.027 0.15 -9999 0 -0.52 29 29
ADCY5 -0.027 0.15 -9999 0 -0.52 29 29
ADCY6 0.014 0.048 -9999 0 -0.5 3 3
ADCY7 0.014 0.048 -9999 0 -0.5 3 3
ADCY1 0.012 0.056 -9999 0 -0.5 4 4
ADCY2 -0.033 0.14 -9999 0 -0.42 40 40
ADCY3 0.015 0.039 -9999 0 -0.5 2 2
ADCY8 -0.16 0.24 -9999 0 -0.5 117 117
PRKCE 0.007 0.045 -9999 0 -0.58 2 2
ADCY9 0.014 0.048 -9999 0 -0.5 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.081 0.14 -9999 0 -0.4 31 31
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.29 0.36 -10000 0 -0.89 31 31
PCK1 -0.15 0.23 -10000 0 -0.83 13 13
HNF4A -0.35 0.43 -10000 0 -1.1 43 43
KCNJ11 -0.3 0.41 -10000 0 -1.1 27 27
AKT1 0 0.09 -10000 0 -10000 0 0
response to starvation -0.011 0.036 -10000 0 -10000 0 0
DLK1 -0.32 0.4 -10000 0 -1 33 33
NKX2-1 -0.79 0.81 0.49 1 -1.6 183 184
ACADM -0.29 0.36 -10000 0 -0.87 37 37
TAT -0.13 0.21 -10000 0 -0.84 8 8
CEBPB 0.004 0.006 -10000 0 -10000 0 0
CEBPA 0 0.059 -10000 0 -0.76 2 2
TTR -0.062 0.2 -10000 0 -0.9 11 11
PKLR -0.3 0.36 -10000 0 -0.94 24 24
APOA1 -0.48 0.6 -10000 0 -1.4 72 72
CPT1C -0.29 0.36 -10000 0 -0.86 41 41
ALAS1 -0.12 0.19 -10000 0 -10000 0 0
TFRC -0.17 0.27 -10000 0 -1 8 8
FOXF1 -0.001 0.25 0.3 6 -0.67 39 45
NF1 0.016 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.015 0.089 -10000 0 -0.63 6 6
CPT1A -0.29 0.36 -10000 0 -0.9 27 27
HMGCS1 -0.29 0.36 -10000 0 -0.87 37 37
NR3C1 0.017 0.014 -10000 0 -10000 0 0
CPT1B -0.29 0.36 -10000 0 -0.88 34 34
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.007 0.032 -10000 0 -10000 0 0
GCK -0.3 0.37 -10000 0 -0.93 28 28
CREB1 0.008 0.017 -10000 0 -10000 0 0
IGFBP1 -0.13 0.18 -10000 0 -0.69 4 4
PDX1 -0.19 0.26 -10000 0 -0.68 33 33
UCP2 -0.29 0.36 -10000 0 -0.86 43 43
ALDOB -0.29 0.38 -10000 0 -0.96 22 22
AFP 0.012 0.15 -10000 0 -0.81 3 3
BDH1 -0.29 0.36 -10000 0 -0.97 16 16
HADH -0.29 0.38 -10000 0 -0.96 19 19
F2 -0.37 0.45 -10000 0 -1.1 41 41
HNF1A -0.015 0.089 -10000 0 -0.63 6 6
G6PC 0.009 0.099 -10000 0 -0.74 2 2
SLC2A2 -0.18 0.24 -10000 0 -0.91 2 2
INS -0.009 0.014 -10000 0 -10000 0 0
FOXA1 0.068 0.14 0.37 2 -0.59 8 10
FOXA3 -0.01 0.16 -10000 0 -0.77 12 12
FOXA2 -0.34 0.44 -10000 0 -0.98 37 37
ABCC8 -0.32 0.42 -10000 0 -1.1 28 28
ALB 0.026 0.13 -10000 0 -0.83 2 2
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.011 0.062 -9999 0 -0.38 9 9
Syndecan-3/Neurocan -0.021 0.078 -9999 0 -0.31 24 24
POMC -0.06 0.18 -9999 0 -0.62 34 34
EGFR -0.025 0.13 -9999 0 -0.68 13 13
Syndecan-3/EGFR -0.013 0.069 -9999 0 -0.36 13 13
AGRP -0.37 0.38 -9999 0 -0.76 169 169
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.042 0.15 -9999 0 -0.61 24 24
long-term memory 0 0 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.014 0.066 -9999 0 -0.32 15 15
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0 0 -9999 0 -10000 0 0
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R -0.03 0.13 -9999 0 -0.61 17 17
SRC 0 0 -9999 0 -10000 0 0
PTN -0.021 0.12 -9999 0 -0.74 10 10
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.028 0.087 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.2 0.21 -9999 0 -0.42 169 169
Syndecan-3/AgRP/MC4R -0.21 0.21 -9999 0 -0.41 169 169
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.014 0.065 -9999 0 -0.32 15 15
IL8 -0.027 0.13 -9999 0 -0.63 15 15
Syndecan-3/Fyn/Cortactin 0 0 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.066 0.16 -9999 0 -0.45 51 51
Gamma Secretase 0 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.002 0.041 -9999 0 -0.76 1 1
alphaV beta3 Integrin -0.01 0.075 -9999 0 -0.58 6 6
PTK2 -0.1 0.15 -9999 0 -0.61 18 18
positive regulation of JNK cascade -0.028 0.076 -9999 0 -0.34 18 18
CDC42/GDP -0.012 0.12 -9999 0 -0.47 18 18
Rac1/GDP -0.011 0.11 -9999 0 -0.46 18 18
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.034 0.094 -9999 0 -0.43 18 18
nectin-3/I-afadin -0.03 0.13 -9999 0 -0.58 18 18
RAPGEF1 -0.022 0.13 -9999 0 -0.54 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.034 0.15 -9999 0 -0.63 18 18
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.76 1 1
TLN1 -0.017 0.15 -9999 0 -0.51 25 25
Rap1/GTP -0.028 0.081 -9999 0 -0.37 18 18
IQGAP1 0 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 -0.03 0.13 -9999 0 -0.58 18 18
PVR 0 0 -9999 0 -10000 0 0
Necl-5(dimer) 0 0 -9999 0 -10000 0 0
mol:GDP -0.022 0.14 -9999 0 -0.59 18 18
MLLT4 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K -0.023 0.095 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.21 0.22 -9999 0 -0.44 165 165
positive regulation of lamellipodium assembly -0.031 0.082 -9999 0 -0.36 19 19
PVRL1 -0.29 0.3 -9999 0 -0.61 165 165
PVRL3 -0.039 0.17 -9999 0 -0.76 18 18
PVRL2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 -0.002 0.041 -9999 0 -0.76 1 1
CLDN1 -0.1 0.23 -9999 0 -0.62 58 58
JAM-A/CLDN1 -0.079 0.17 -9999 0 -0.54 20 20
SRC -0.065 0.16 -9999 0 -0.72 18 18
ITGB3 -0.013 0.099 -9999 0 -0.76 6 6
nectin-1(dimer)/I-afadin/I-afadin -0.21 0.22 -9999 0 -0.44 165 165
FARP2 -0.026 0.14 -9999 0 -0.58 18 18
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.026 0.11 -9999 0 -0.5 18 18
nectin-1/I-afadin -0.21 0.22 -9999 0 -0.44 165 165
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 -0.2 0.21 -9999 0 -0.62 18 18
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.028 0.076 -9999 0 -0.34 18 18
alphaV/beta3 Integrin/Talin -0.046 0.14 -9999 0 -0.78 8 8
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 -0.048 0.15 -9999 0 -0.54 25 25
VAV2 -0.029 0.14 -9999 0 -0.58 20 20
RAP1/GDP -0.031 0.096 -9999 0 -0.43 18 18
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.026 0.11 -9999 0 -0.5 18 18
nectin-3(dimer)/I-afadin/I-afadin -0.03 0.13 -9999 0 -0.58 18 18
Rac1/GTP -0.037 0.1 -9999 0 -0.44 19 19
PTPRM -0.053 0.17 -9999 0 -0.48 38 38
E-cadherin/beta catenin/alpha catenin -0.14 0.14 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.002 0.004 -9999 0 -10000 0 0
SVIL 0.002 0.004 -9999 0 -10000 0 0
ZNF318 0 0.006 -9999 0 -10000 0 0
JMJD2C -0.006 0.03 -9999 0 -0.086 41 41
T-DHT/AR/Ubc9 -0.13 0.21 -9999 0 -0.55 67 67
CARM1 0 0 -9999 0 -10000 0 0
PRDX1 0 0.001 -9999 0 -10000 0 0
PELP1 0 0.001 -9999 0 -10000 0 0
CTNNB1 0.002 0.004 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
PTK2B 0.002 0.004 -9999 0 -10000 0 0
MED1 0 0.002 -9999 0 -10000 0 0
MAK -0.046 0.18 -9999 0 -0.76 21 21
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 -0.001 0.041 -9999 0 -0.76 1 1
GSN 0.002 0.004 -9999 0 -10000 0 0
NCOA2 -0.002 0.041 -9999 0 -0.76 1 1
NCOA6 0.002 0.004 -9999 0 -10000 0 0
DNA-PK 0 0.006 -9999 0 -10000 0 0
NCOA4 0 0 -9999 0 -10000 0 0
PIAS3 0.002 0.004 -9999 0 -10000 0 0
cell proliferation -0.084 0.23 -9999 0 -0.95 21 21
XRCC5 0 0.002 -9999 0 -10000 0 0
UBE3A 0.002 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.14 0.23 -9999 0 -0.57 73 73
FHL2 -0.053 0.079 -9999 0 -0.59 1 1
RANBP9 0.002 0.004 -9999 0 -10000 0 0
JMJD1A -0.036 0.071 -9999 0 -0.13 118 118
CDK6 -0.003 0.046 -9999 0 -0.61 2 2
TGFB1I1 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.14 0.22 -9999 0 -0.56 71 71
XRCC6 0 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.24 -9999 0 -0.58 67 67
CTDSP1 0.001 0.004 -9999 0 -10000 0 0
CTDSP2 0 0.004 -9999 0 -10000 0 0
BRCA1 0.002 0.004 -9999 0 -10000 0 0
TCF4 -0.002 0.041 -9999 0 -0.76 1 1
CDKN2A -0.28 0.3 -9999 0 -0.61 162 162
SRF 0.017 0.006 -9999 0 -10000 0 0
NKX3-1 -0.11 0.13 -9999 0 -0.59 1 1
KLK3 0.028 0.051 -9999 0 -10000 0 0
TMF1 0.001 0.004 -9999 0 -10000 0 0
HNRNPA1 0 0.002 -9999 0 -10000 0 0
AOF2 0 0.002 -9999 0 -10000 0 0
APPL1 0.02 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.13 0.21 -9999 0 -0.55 67 67
AR -0.16 0.31 -9999 0 -0.79 67 67
UBA3 0.001 0.004 -9999 0 -10000 0 0
PATZ1 0 0.002 -9999 0 -10000 0 0
PAWR 0.001 0.004 -9999 0 -10000 0 0
PRKDC 0 0.002 -9999 0 -10000 0 0
PA2G4 0 0.003 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.12 0.2 -9999 0 -0.51 67 67
RPS6KA3 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.13 0.21 -9999 0 -0.55 67 67
LATS2 0 0.002 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.12 0.2 -9999 0 -0.51 67 67
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 0.002 0.004 -9999 0 -10000 0 0
KLK2 -0.1 0.16 -9999 0 -0.47 41 41
CASP8 0 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.5 68 68
TMPRSS2 -0.42 0.56 -9999 0 -1.2 118 118
CCND1 -0.015 0.1 -9999 0 -0.74 7 7
PIAS1 0.002 0.005 -9999 0 -10000 0 0
mol:T-DHT -0.021 0.038 -9999 0 -0.08 86 86
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.002 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.21 -9999 0 -0.55 69 69
CMTM2 -0.12 0.28 -9999 0 -0.76 54 54
SNURF -0.022 0.13 -9999 0 -0.76 10 10
ZMIZ1 -0.006 0.033 -9999 0 -10000 0 0
CCND3 0 0.001 -9999 0 -10000 0 0
TGIF1 0 0.002 -9999 0 -10000 0 0
FKBP4 0 0.033 -9999 0 -0.61 1 1
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.2 0.42 -9999 0 -1.2 20 20
HDAC7 -0.008 0.014 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.33 -9999 0 -0.92 20 20
SMAD4 0 0.002 -9999 0 -10000 0 0
ID2 -0.2 0.42 -9999 0 -1.2 20 20
AP1 -0.093 0.21 -9999 0 -0.58 55 55
ABCG2 -0.24 0.47 -9999 0 -1.3 29 29
HIF1A -0.023 0.07 -9999 0 -10000 0 0
TFF3 -0.24 0.46 -9999 0 -1.3 27 27
GATA2 -0.079 0.25 -9999 0 -0.76 40 40
AKT1 -0.035 0.056 -9999 0 -10000 0 0
response to hypoxia -0.049 0.063 -9999 0 -10000 0 0
MCL1 -0.2 0.42 -9999 0 -1.2 20 20
NDRG1 -0.21 0.42 -9999 0 -1.2 21 21
SERPINE1 -0.2 0.42 -9999 0 -1.2 20 20
FECH -0.2 0.42 -9999 0 -1.2 20 20
FURIN -0.2 0.42 -9999 0 -1.2 20 20
NCOA2 0.007 0.042 -9999 0 -0.76 1 1
EP300 -0.026 0.088 -9999 0 -10000 0 0
HMOX1 -0.21 0.42 -9999 0 -1.2 21 21
BHLHE40 -0.2 0.42 -9999 0 -1.2 20 20
BHLHE41 -0.21 0.44 -9999 0 -1.3 24 24
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.033 0.085 -9999 0 -0.52 5 5
ENG 0 0.14 -9999 0 -0.86 6 6
JUN 0.008 0.006 -9999 0 -10000 0 0
RORA -0.2 0.42 -9999 0 -1.2 20 20
ABCB1 -0.22 0.46 -9999 0 -1.3 49 49
TFRC -0.2 0.42 -9999 0 -1.2 20 20
CXCR4 -0.2 0.42 -9999 0 -1.2 20 20
TF -0.23 0.45 -9999 0 -1.2 25 25
CITED2 -0.21 0.43 -9999 0 -1.2 20 20
HIF1A/ARNT -0.25 0.47 -9999 0 -1.4 23 23
LDHA -0.034 0.047 -9999 0 -10000 0 0
ETS1 -0.21 0.44 -9999 0 -1.3 22 22
PGK1 -0.2 0.42 -9999 0 -1.2 20 20
NOS2 -0.25 0.47 -9999 0 -1.3 33 33
ITGB2 -0.22 0.45 -9999 0 -1.3 25 25
ALDOA -0.2 0.42 -9999 0 -1.2 20 20
Cbp/p300/CITED2 -0.25 0.42 -9999 0 -1.3 20 20
FOS -0.11 0.28 -9999 0 -0.76 55 55
HK2 -0.2 0.42 -9999 0 -1.2 20 20
SP1 0.009 0.032 -9999 0 -10000 0 0
GCK -0.037 0.16 -9999 0 -1.1 2 2
HK1 -0.2 0.42 -9999 0 -1.2 20 20
NPM1 -0.2 0.42 -9999 0 -1.2 20 20
EGLN1 -0.2 0.42 -9999 0 -1.2 20 20
CREB1 0.017 0 -9999 0 -10000 0 0
PGM1 -0.2 0.42 -9999 0 -1.2 20 20
SMAD3 0 0.002 -9999 0 -10000 0 0
EDN1 -0.2 0.42 -9999 0 -1.2 42 42
IGFBP1 -0.21 0.43 -9999 0 -1.2 23 23
VEGFA -0.25 0.3 -9999 0 -0.86 16 16
HIF1A/JAB1 -0.017 0.029 -9999 0 -10000 0 0
CP -0.22 0.45 -9999 0 -1.3 24 24
CXCL12 -0.23 0.46 -9999 0 -1.3 27 27
COPS5 0.009 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.004 -9999 0 -10000 0 0
BNIP3 -0.2 0.42 -9999 0 -1.2 20 20
EGLN3 -0.25 0.47 -9999 0 -1.3 30 30
CA9 -0.45 0.45 -9999 0 -1.3 41 41
TERT -0.31 0.48 -9999 0 -1.3 32 32
ENO1 -0.2 0.42 -9999 0 -1.2 20 20
PFKL -0.2 0.42 -9999 0 -1.2 20 20
NCOA1 0.005 0.005 -9999 0 -10000 0 0
ADM -0.21 0.43 -9999 0 -1.2 21 21
ARNT -0.024 0.069 -9999 0 -10000 0 0
HNF4A -0.001 0.088 -9999 0 -0.61 7 7
ADFP -0.21 0.42 -9999 0 -1.2 22 22
SLC2A1 -0.47 0.34 -9999 0 -0.96 66 66
LEP -0.26 0.47 -9999 0 -1.2 31 31
HIF1A/ARNT/Cbp/p300 -0.22 0.34 -9999 0 -0.93 24 24
EPO -0.09 0.26 -9999 0 -0.87 5 5
CREBBP -0.026 0.088 -9999 0 -0.33 1 1
HIF1A/ARNT/Cbp/p300/HDAC7 -0.27 0.37 -9999 0 -0.97 33 33
PFKFB3 -0.2 0.42 -9999 0 -1.2 20 20
NT5E -0.21 0.43 -9999 0 -1.2 20 20
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.01 0.075 -9999 0 -0.58 6 6
AKT1 -0.001 0.18 -9999 0 -0.63 10 10
PTK2B -0.044 0.22 -9999 0 -0.91 10 10
VEGFR2 homodimer/Frs2 -0.1 0.23 -9999 0 -0.54 65 65
CAV1 -0.22 0.34 -9999 0 -0.76 99 99
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.092 0.21 -9999 0 -0.49 65 65
endothelial cell proliferation 0.006 0.18 -9999 0 -0.58 12 12
mol:Ca2+ -0.04 0.2 -9999 0 -0.82 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.086 0.2 -9999 0 -0.88 9 9
RP11-342D11.1 -0.047 0.2 -9999 0 -0.45 65 65
CDH5 -0.13 0.28 -9999 0 -0.76 58 58
VEGFA homodimer 0 0 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.004 0.058 -9999 0 -0.76 2 2
HRAS/GDP -0.069 0.16 -9999 0 -0.7 9 9
SH2D2A -0.002 0.041 -9999 0 -0.76 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.066 0.15 -9999 0 -0.64 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.093 0.21 -9999 0 -0.49 66 66
VEGFR1 homodimer 0 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.077 0.18 -9999 0 -0.79 9 9
GRB10 -0.04 0.2 -9999 0 -0.82 9 9
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
PAK1 -0.002 0.032 -9999 0 -0.61 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.15 0.29 -9999 0 -0.9 34 34
HRAS 0 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.051 0.11 -9999 0 -0.48 10 10
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 0 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.085 0.19 -9999 0 -0.86 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.033 0.16 -9999 0 -0.76 15 15
Nck/Pak -0.001 0.024 -9999 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.092 0.21 -9999 0 -0.49 65 65
mol:GDP -0.074 0.17 -9999 0 -0.76 9 9
mol:NADP 0 0.16 -9999 0 -0.52 11 11
eNOS/Hsp90 0.005 0.15 -9999 0 -0.5 10 10
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 -0.041 0.21 -9999 0 -0.84 9 9
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0 0 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin -0.029 0.21 -9999 0 -0.85 10 10
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.093 0.22 -9999 0 -0.98 10 10
PTPN6 0 0 -9999 0 -10000 0 0
EPAS1 -0.14 0.29 -9999 0 -0.72 65 65
mol:L-citrulline 0 0.16 -9999 0 -0.52 11 11
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.086 0.2 -9999 0 -0.88 9 9
VEGFR2 homodimer/VEGFA homodimer -0.091 0.21 -9999 0 -0.49 65 65
VEGFR2/3 heterodimer -0.12 0.26 -9999 0 -0.59 72 72
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 -0.038 0.21 -9999 0 -0.85 9 9
VEGFR2 homodimer -0.091 0.27 -9999 0 -0.63 65 65
FLT1 0 0 -9999 0 -10000 0 0
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 -0.032 0.2 -9999 0 -0.71 12 12
MAPK1 -0.032 0.2 -9999 0 -0.71 12 12
VEGFA145/NRP2 -0.005 0.053 -9999 0 -0.57 3 3
VEGFR1/2 heterodimer -0.1 0.23 -9999 0 -0.54 65 65
KDR -0.092 0.27 -9999 0 -0.63 65 65
VEGFA165/NRP1/VEGFR2 homodimer -0.086 0.2 -9999 0 -0.92 9 9
SRC 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.032 0.2 -9999 0 -0.73 12 12
PI3K -0.078 0.18 -9999 0 -0.78 10 10
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.092 0.21 -9999 0 -0.49 65 65
FES -0.044 0.22 -9999 0 -0.85 10 10
GAB1 -0.08 0.18 -9999 0 -0.82 9 9
VEGFR2 homodimer/VEGFA homodimer/Src -0.092 0.21 -9999 0 -0.49 65 65
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.095 0.23 -9999 0 -0.57 37 37
VEGFR2 homodimer/VEGFA homodimer/Yes -0.092 0.21 -9999 0 -0.49 65 65
PI3K/GAB1 -0.002 0.18 -9999 0 -0.64 10 10
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.083 0.19 -9999 0 -0.87 9 9
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.11 0.25 -9999 0 -0.54 72 72
HSP90AA1 0 0 -9999 0 -10000 0 0
CDC42 -0.042 0.21 -9999 0 -0.86 9 9
actin cytoskeleton reorganization -0.093 0.21 -9999 0 -0.49 66 66
PTK2 -0.039 0.23 -9999 0 -0.96 10 10
EDG1 -0.047 0.2 -9999 0 -0.45 65 65
mol:DAG -0.041 0.21 -9999 0 -0.84 9 9
CaM/Ca2+ -0.076 0.17 -9999 0 -0.76 9 9
MAP2K3 -0.031 0.2 -9999 0 -0.81 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.085 0.19 -9999 0 -0.87 9 9
PLCG1 -0.042 0.21 -9999 0 -0.86 9 9
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.086 0.2 -9999 0 -0.88 9 9
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.092 0.21 -9999 0 -0.49 65 65
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.092 0.21 -9999 0 -0.49 65 65
cell migration -0.025 0.21 -9999 0 -0.76 10 10
mol:PI-3-4-5-P3 -0.073 0.16 -9999 0 -0.7 10 10
FYN 0 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.078 0.18 -9999 0 -0.78 9 9
mol:NO 0 0.16 -9999 0 -0.52 11 11
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.069 0.16 -9999 0 -0.7 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.085 0.19 -9999 0 -0.87 9 9
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.013 0.099 -9999 0 -0.76 6 6
NOS3 -0.005 0.17 -9999 0 -0.6 11 11
VEGFR2 homodimer/VEGFA homodimer/Sck -0.095 0.22 -9999 0 -0.5 65 65
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.031 0.2 -9999 0 -0.77 10 10
PRKCB -0.043 0.22 -9999 0 -0.87 11 11
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.084 0.19 -9999 0 -0.45 65 65
VEGFR1/2 heterodimer/VEGFA homodimer -0.092 0.21 -9999 0 -0.49 65 65
VEGFA165/NRP2 -0.005 0.053 -9999 0 -0.57 3 3
MAPKKK cascade -0.068 0.15 -9999 0 -0.7 9 9
NRP2 -0.007 0.07 -9999 0 -0.76 3 3
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 0 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.029 0.21 -9999 0 -0.85 10 10
MAP3K13 -0.042 0.21 -9999 0 -0.86 9 9
PDPK1 -0.004 0.17 -9999 0 -0.61 10 10
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.25 -9999 0 -0.74 10 10
CRP -0.15 0.26 -9999 0 -0.76 11 11
cell cycle arrest -0.18 0.28 -9999 0 -0.65 45 45
TIMP1 -0.11 0.22 -9999 0 -0.66 5 5
IL6ST -0.011 0.12 -9999 0 -0.76 9 9
Rac1/GDP -0.072 0.18 -9999 0 -0.69 11 11
AP1 -0.023 0.17 -9999 0 -0.49 13 13
GAB2 -0.001 0.12 -9999 0 -0.76 8 8
TNFSF11 -0.16 0.27 -9999 0 -0.7 23 23
HSP90B1 0 0.05 -9999 0 -10000 0 0
GAB1 0.014 0.008 -9999 0 -10000 0 0
MAPK14 -0.041 0.18 -9999 0 -0.74 10 10
AKT1 0.044 0.053 -9999 0 -10000 0 0
FOXO1 0.051 0.049 -9999 0 -10000 0 0
MAP2K6 -0.064 0.18 -9999 0 -0.76 10 10
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
MAP2K4 -0.08 0.2 -9999 0 -0.7 10 10
MITF -0.074 0.19 -9999 0 -0.64 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M -0.44 0.69 -9999 0 -1.5 108 108
CEBPB 0.016 0.004 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.026 0.12 -9999 0 -0.58 4 4
STAT3 -0.18 0.29 -9999 0 -0.69 45 45
STAT1 -0.009 0.017 -9999 0 -10000 0 0
CEBPD -0.15 0.26 -9999 0 -0.82 10 10
PIK3CA 0.011 0.003 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
JUN 0.007 0.005 -9999 0 -10000 0 0
PIAS3/MITF -0.09 0.16 -9999 0 -0.66 12 12
MAPK11 -0.041 0.18 -9999 0 -0.74 10 10
STAT3 (dimer)/FOXO1 -0.18 0.3 -9999 0 -0.78 33 33
GRB2/SOS1/GAB family -0.04 0.17 -9999 0 -0.67 10 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.062 0.19 -9999 0 -0.49 33 33
GRB2 0.014 0.008 -9999 0 -10000 0 0
JAK2 0 0 -9999 0 -10000 0 0
LBP -0.12 0.22 -9999 0 -0.71 4 4
PIK3R1 0.009 0.004 -9999 0 -10000 0 0
JAK1 0.011 0.005 -9999 0 -10000 0 0
MYC -0.14 0.25 -9999 0 -0.74 10 10
FGG -0.48 0.57 -9999 0 -1.1 160 160
macrophage differentiation -0.18 0.28 -9999 0 -0.65 45 45
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.21 -9999 0 -0.52 51 51
JUNB -0.14 0.25 -9999 0 -0.74 11 11
FOS -0.11 0.28 -9999 0 -0.76 55 55
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.083 0.2 -9999 0 -0.47 50 50
STAT1/PIAS1 -0.093 0.18 -9999 0 -0.46 42 42
GRB2/SOS1/GAB family/SHP2/PI3K 0.025 0.058 -9999 0 -0.31 1 1
STAT3 (dimer) -0.18 0.29 -9999 0 -0.68 45 45
PRKCD -0.093 0.22 -9999 0 -0.74 9 9
IL6R -0.009 0.12 -9999 0 -0.76 9 9
SOCS3 -0.028 0.18 -9999 0 -0.99 5 5
gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.084 -9999 0 -0.48 10 10
Rac1/GTP -0.11 0.17 -9999 0 -0.66 13 13
HCK 0 0.058 -9999 0 -0.76 2 2
MAPKKK cascade 0.043 0.12 -9999 0 -0.57 8 8
bone resorption -0.16 0.26 -9999 0 -0.66 23 23
IRF1 -0.14 0.25 -9999 0 -0.74 10 10
mol:GDP -0.075 0.19 -9999 0 -0.5 31 31
SOS1 0.015 0.013 -9999 0 -10000 0 0
VAV1 -0.076 0.2 -9999 0 -0.55 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.059 0.19 -9999 0 -0.74 13 13
PTPN11 -0.007 0.014 -9999 0 -10000 0 0
IL6/IL6RA -0.13 0.26 -9999 0 -0.61 77 77
gp130 (dimer)/TYK2/TYK2/LMO4 -0.008 0.083 -9999 0 -0.48 10 10
gp130 (dimer)/JAK2/JAK2/LMO4 -0.008 0.083 -9999 0 -0.48 10 10
IL6 -0.15 0.31 -9999 0 -0.76 73 73
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.011 0.043 -9999 0 -0.75 1 1
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0.003 0.005 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.09 0.18 -9999 0 -0.44 50 50
LMO4 0.007 0.035 -9999 0 -0.62 1 1
STAT3 (dimer)/PIAS3 -0.22 0.23 -9999 0 -0.65 45 45
MCL1 0.052 0.047 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.002 0.1 -10000 0 -0.6 10 10
NFATC2 -0.03 0.27 -10000 0 -0.74 39 39
NFATC3 0.011 0.055 -10000 0 -10000 0 0
CD40LG -0.18 0.47 -10000 0 -1.1 53 53
ITCH 0.001 0.11 -10000 0 -10000 0 0
CBLB 0.001 0.11 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.13 0.26 -10000 0 -1 17 17
JUNB -0.002 0.041 -10000 0 -0.76 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.045 0.11 -10000 0 -10000 0 0
T cell anergy -0.045 0.17 -10000 0 -0.45 43 43
TLE4 -0.001 0.21 -10000 0 -0.75 12 12
Jun/NFAT1-c-4/p21SNFT -0.11 0.25 -10000 0 -1 15 15
AP-1/NFAT1-c-4 -0.24 0.39 -10000 0 -1.3 30 30
IKZF1 -0.008 0.24 -10000 0 -0.86 15 15
T-helper 2 cell differentiation -0.037 0.27 -10000 0 -0.84 26 26
AP-1/NFAT1 -0.15 0.24 -10000 0 -0.65 41 41
CALM1 -0.024 0.06 -10000 0 -10000 0 0
EGR2 -0.002 0.29 -10000 0 -1.3 10 10
EGR3 -0.014 0.33 -10000 0 -1.3 15 15
NFAT1/FOXP3 -0.077 0.18 -10000 0 -0.68 14 14
EGR1 -0.022 0.15 -10000 0 -0.76 14 14
JUN 0.004 0.023 -10000 0 -10000 0 0
EGR4 -0.002 0.081 -10000 0 -0.61 6 6
mol:Ca2+ -0.027 0.069 -10000 0 -10000 0 0
GBP3 -0.027 0.27 -10000 0 -0.88 23 23
FOSL1 -0.002 0.032 -10000 0 -0.61 1 1
NFAT1-c-4/MAF/IRF4 -0.087 0.24 -10000 0 -0.95 16 16
DGKA 0.001 0.2 -10000 0 -0.68 14 14
CREM 0 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.29 -10000 0 -1 21 21
CTLA4 -0.002 0.18 -10000 0 -0.66 8 8
NFAT1-c-4 (dimer)/EGR1 -0.11 0.27 -10000 0 -1 20 20
NFAT1-c-4 (dimer)/EGR4 -0.096 0.25 -10000 0 -0.93 19 19
FOS -0.12 0.28 -10000 0 -0.77 55 55
IFNG -0.15 0.33 -10000 0 -0.89 46 46
T cell activation -0.035 0.23 -10000 0 -0.75 15 15
MAF 0 0.001 -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 -0.01 0.2 0.85 9 -10000 0 9
TNF -0.032 0.3 -10000 0 -0.93 24 24
FASLG -0.073 0.44 -10000 0 -1.5 25 25
TBX21 -0.066 0.24 -10000 0 -0.76 36 36
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.055 0.22 -10000 0 -0.77 30 30
PTPN1 0.001 0.2 -10000 0 -0.68 14 14
NFAT1-c-4/ICER1 -0.091 0.24 -10000 0 -0.95 18 18
GATA3 -0.033 0.16 -10000 0 -0.74 16 16
T-helper 1 cell differentiation -0.14 0.32 -10000 0 -0.82 52 52
IL2RA -0.14 0.25 -10000 0 -0.94 20 20
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.001 0.2 -10000 0 -0.68 14 14
E2F1 0.015 0.005 -10000 0 -10000 0 0
PPARG -0.088 0.24 -10000 0 -0.76 40 40
SLC3A2 0.001 0.2 -10000 0 -0.69 13 13
IRF4 -0.004 0.058 -10000 0 -0.76 2 2
PTGS2 -0.15 0.43 -10000 0 -1.1 42 42
CSF2 -0.17 0.44 -10000 0 -1.1 43 43
JunB/Fra1/NFAT1-c-4 -0.086 0.23 -10000 0 -0.93 16 16
IL4 -0.041 0.29 -10000 0 -0.89 25 25
IL5 -0.12 0.38 -10000 0 -1 27 27
IL2 -0.036 0.23 -10000 0 -0.76 15 15
IL3 -0.039 0.05 -10000 0 -10000 0 0
RNF128 -0.076 0.3 -10000 0 -0.82 47 47
NFATC1 0.01 0.2 -10000 0 -0.89 8 8
CDK4 -0.003 0.16 0.64 5 -10000 0 5
PTPRK 0.001 0.2 -10000 0 -0.68 14 14
IL8 -0.13 0.39 -10000 0 -1 32 32
POU2F1 0 0.003 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.072 0.1 -10000 0 -0.33 3 3
NT3 (dimer)/TRKC -0.2 0.28 -10000 0 -0.59 115 115
NT3 (dimer)/TRKB -0.12 0.2 -10000 0 -0.42 99 99
SHC/Grb2/SOS1/GAB1/PI3K 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.11 0.27 -10000 0 -0.76 52 52
PIK3CA 0 0 -10000 0 -10000 0 0
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 -0.015 0.11 -10000 0 -0.76 7 7
NTRK2 -0.14 0.27 -10000 0 -0.67 70 70
NTRK3 -0.25 0.36 -10000 0 -0.76 115 115
NT-4/5 (dimer)/TRKB -0.13 0.2 -10000 0 -0.43 102 102
neuron apoptosis 0.15 0.2 0.48 70 -10000 0 70
SHC 2-3/Grb2 -0.16 0.22 -10000 0 -0.53 70 70
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.064 0.11 -10000 0 -0.58 6 6
SHC3 -0.18 0.28 -10000 0 -0.68 73 73
STAT3 (dimer) -0.007 0.051 -10000 0 -0.38 6 6
NT3 (dimer)/TRKA -0.045 0.13 -10000 0 -0.4 39 39
RIN/GDP -0.052 0.098 -10000 0 -0.29 3 3
GIPC1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
DNAJA3 -0.028 0.078 -10000 0 -0.48 1 1
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.008 0.13 -10000 0 -0.9 7 7
MAGED1 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.017 0.11 -10000 0 -0.76 8 8
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.04 0.14 -10000 0 -0.5 28 28
TRKA/NEDD4-2 -0.012 0.081 -10000 0 -0.58 7 7
ELMO1 -0.018 0.11 -10000 0 -0.76 8 8
RhoG/GTP/ELMO1/DOCK1 -0.012 0.075 -10000 0 -0.5 8 8
NGF -0.023 0.13 -10000 0 -0.73 11 11
HRAS 0 0 -10000 0 -10000 0 0
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.018 0.11 -10000 0 -0.76 8 8
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
DNM1 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.037 0.096 -10000 0 -0.42 9 9
mol:GDP -0.077 0.14 -10000 0 -0.41 6 6
NGF (dimer) -0.023 0.13 -10000 0 -0.73 11 11
RhoG/GDP -0.013 0.088 -10000 0 -0.58 8 8
RIT1/GDP -0.048 0.098 -10000 0 -0.28 3 3
TIAM1 0 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.16 0.26 -10000 0 -0.51 107 107
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.008 0.077 -10000 0 -0.72 4 4
RAP1/GDP -0.053 0.071 -10000 0 -10000 0 0
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.11 0.27 -10000 0 -0.76 52 52
ubiquitin-dependent protein catabolic process -0.025 0.11 -10000 0 -0.48 18 18
Schwann cell development -0.056 0.037 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.006 0.038 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.24 0.3 -10000 0 -0.79 56 56
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.053 0.085 -10000 0 -0.39 1 1
STAT3 -0.007 0.05 -10000 0 -0.38 6 6
axon guidance -0.23 0.27 -10000 0 -0.73 56 56
MAPK3 -0.009 0.13 -10000 0 -0.46 26 26
MAPK1 -0.009 0.13 -10000 0 -0.46 26 26
CDC42/GDP -0.048 0.098 -10000 0 -0.28 3 3
NTF3 -0.008 0.077 -10000 0 -0.72 4 4
NTF4 -0.018 0.11 -10000 0 -0.76 8 8
NGF (dimer)/TRKA/FAIM -0.025 0.11 -10000 0 -0.48 18 18
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.28 0.22 -10000 0 -0.44 216 216
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.15 0.26 -10000 0 -0.51 115 115
RGS19 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.058 0.083 -10000 0 -10000 0 0
Rac1/GDP -0.048 0.098 -10000 0 -0.28 3 3
NGF (dimer)/TRKA/GRIT -0.025 0.11 -10000 0 -0.49 18 18
neuron projection morphogenesis -0.002 0.085 -10000 0 -0.48 2 2
NGF (dimer)/TRKA/NEDD4-2 -0.025 0.11 -10000 0 -0.48 18 18
MAP2K1 0.036 0 -10000 0 -10000 0 0
NGFR -0.049 0.16 -10000 0 -0.61 28 28
NGF (dimer)/TRKA/GIPC/GAIP -0.015 0.066 -10000 0 -10000 0 0
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 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.06 0.14 -10000 0 -0.64 16 16
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.012 0.081 -10000 0 -0.58 7 7
SQSTM1 0 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.14 0.24 -10000 0 -0.54 67 67
NGF (dimer)/TRKA/p62/Atypical PKCs -0.021 0.09 -10000 0 -0.42 16 16
MATK -0.024 0.13 -10000 0 -0.76 11 11
NEDD4L 0 0 -10000 0 -10000 0 0
RAS family/GDP -0.048 0.068 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.031 0.084 -10000 0 -0.32 16 16
Rac1/GTP -0.18 0.13 -10000 0 -0.34 102 102
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.02 0 -9999 0 -10000 0 0
SMARCC1 0.007 0.008 -9999 0 -10000 0 0
REL 0 0.001 -9999 0 -10000 0 0
HDAC7 -0.032 0.12 -9999 0 -10000 0 0
JUN 0.001 0.004 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.002 0.041 -9999 0 -0.76 1 1
KAT5 0 0.001 -9999 0 -10000 0 0
MAPK14 0.011 0.031 -9999 0 -0.47 1 1
FOXO1 0 0 -9999 0 -10000 0 0
T-DHT/AR -0.039 0.13 -9999 0 -10000 0 0
MAP2K6 0.005 0.035 -9999 0 -0.63 1 1
BRM/BAF57 -0.002 0.031 -9999 0 -0.58 1 1
MAP2K4 0.007 0.007 -9999 0 -10000 0 0
SMARCA2 -0.001 0.041 -9999 0 -0.76 1 1
PDE9A -0.11 0.24 -9999 0 -0.79 24 24
NCOA2 0.004 0.041 -9999 0 -0.76 1 1
CEBPA -0.004 0.058 -9999 0 -0.76 2 2
EHMT2 0.001 0.004 -9999 0 -10000 0 0
cell proliferation -0.054 0.18 -9999 0 -0.54 14 14
NR0B1 -0.2 0.28 -9999 0 -0.61 115 115
EGR1 -0.029 0.15 -9999 0 -0.76 14 14
RXRs/9cRA -0.26 0.22 -9999 0 -0.46 198 198
AR/RACK1/Src -0.017 0.078 -9999 0 -10000 0 0
AR/GR -0.061 0.12 -9999 0 -0.34 32 32
GNB2L1 0.006 0.005 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -9999 0 -10000 0 0
MAPK8 0.012 0.016 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.015 0.078 -9999 0 -10000 0 0
SRC 0.018 0.043 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
KLK3 -0.15 0.17 -9999 0 -0.6 22 22
APPBP2 0.008 0.006 -9999 0 -10000 0 0
TRIM24 0.002 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.038 0.056 -9999 0 -10000 0 0
TMPRSS2 -0.44 0.59 -9999 0 -1.2 118 118
RXRG -0.43 0.38 -9999 0 -0.76 198 198
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.006 0.005 -9999 0 -10000 0 0
NR2C2 0 0 -9999 0 -10000 0 0
KLK2 -0.029 0.15 -9999 0 -0.51 2 2
AR -0.05 0.15 -9999 0 -0.38 37 37
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
MDM2 0 0.002 -9999 0 -10000 0 0
SRY -0.003 0.046 -9999 0 -0.61 2 2
GATA2 -0.088 0.24 -9999 0 -0.76 40 40
MYST2 0 0.001 -9999 0 -10000 0 0
HOXB13 -0.36 0.3 -9999 0 -0.6 207 207
T-DHT/AR/RACK1/Src -0.015 0.073 -9999 0 -10000 0 0
positive regulation of transcription -0.087 0.24 -9999 0 -0.76 40 40
DNAJA1 0.008 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.002 -9999 0 -10000 0 0
NCOA1 0.015 0.004 -9999 0 -10000 0 0
SPDEF -0.11 0.27 -9999 0 -0.75 51 51
T-DHT/AR/TIF2 0.013 0.06 -9999 0 -0.38 1 1
T-DHT/AR/Hsp90 -0.038 0.056 -9999 0 -10000 0 0
GSK3B 0.007 0.006 -9999 0 -10000 0 0
NR2C1 0 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.01 0.046 -9999 0 -10000 0 0
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0 0.002 -9999 0 -10000 0 0
POU2F1 0.013 0.022 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.14 0.16 -9999 0 -0.5 17 17
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0.002 0.004 -9999 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.087 0.13 -10000 0 -0.53 19 19
epithelial cell differentiation -0.041 0.11 -10000 0 -0.57 5 5
ITCH 0.022 0.027 -10000 0 -10000 0 0
WWP1 -0.035 0.088 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
EGFR -0.025 0.13 -10000 0 -0.68 13 13
PRL -0.012 0.085 -10000 0 -0.61 7 7
neuron projection morphogenesis 0.004 0.091 -10000 0 -10000 0 0
PTPRZ1 -0.4 0.29 -10000 0 -0.61 230 230
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.042 0.078 -10000 0 -0.5 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.057 0.098 -10000 0 -0.49 11 11
ADAM17 0.022 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.054 0.11 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.2 0.24 -10000 0 -0.55 98 98
NCOR1 0 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.052 0.089 -10000 0 -0.54 4 4
GRIN2B -0.028 0.1 -10000 0 -0.52 4 4
ErbB4/ErbB2/betacellulin -0.071 0.13 -10000 0 -0.55 14 14
STAT1 0 0 -10000 0 -10000 0 0
HBEGF -0.042 0.17 -10000 0 -0.76 19 19
PRLR -0.035 0.15 -10000 0 -0.65 19 19
E4ICDs/ETO2 -0.068 0.099 -10000 0 -0.57 5 5
axon guidance 0.06 0.078 -10000 0 -10000 0 0
NEDD4 0.022 0.027 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.035 0.12 -10000 0 -0.47 26 26
CBFA2T3 -0.011 0.091 -10000 0 -0.76 5 5
ErbB4/ErbB2/HBEGF -0.062 0.11 -10000 0 -0.55 7 7
MAPK3 -0.038 0.072 -10000 0 -10000 0 0
STAT1 (dimer) -0.061 0.078 -10000 0 -10000 0 0
MAPK1 -0.038 0.072 -10000 0 -10000 0 0
JAK2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.052 0.089 -10000 0 -0.54 4 4
NRG1 0.012 0.11 -10000 0 -0.58 11 11
NRG3 -0.22 0.34 -10000 0 -0.76 98 98
NRG2 -0.09 0.24 -10000 0 -0.76 41 41
NRG4 -0.086 0.21 -10000 0 -0.61 49 49
heart development 0.06 0.078 -10000 0 -10000 0 0
neural crest cell migration -0.051 0.088 -10000 0 -0.54 4 4
ERBB2 0.031 0.013 -10000 0 -10000 0 0
WWOX/E4ICDs -0.061 0.078 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.11 0.16 -10000 0 -0.51 28 28
apoptosis 0.21 0.27 0.56 98 -10000 0 98
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.18 -10000 0 -0.54 41 41
ErbB4/ErbB2/epiregulin -0.12 0.18 -10000 0 -0.55 32 32
ErbB4/ErbB4/betacellulin/betacellulin -0.097 0.15 -10000 0 -0.56 26 26
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.09 0.14 -10000 0 -0.63 11 11
MDM2 -0.038 0.096 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.041 0.084 -10000 0 -0.53 4 4
STAT5A 0.061 0.075 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.065 0.12 -10000 0 -0.67 8 8
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.056 0.071 -10000 0 -10000 0 0
STAT5A (dimer) -0.044 0.12 -10000 0 -0.62 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.05 0.073 -10000 0 -10000 0 0
LRIG1 -0.002 0.041 -10000 0 -0.76 1 1
EREG -0.15 0.3 -10000 0 -0.74 72 72
BTC -0.057 0.2 -10000 0 -0.76 26 26
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.06 0.078 -10000 0 -10000 0 0
ERBB4 -0.074 0.097 -10000 0 -10000 0 0
STAT5B 0 0 -10000 0 -10000 0 0
YAP1 -0.021 0.039 -10000 0 -0.6 1 1
GRB2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.083 0.12 -10000 0 -10000 0 0
glial cell differentiation 0.056 0.071 -10000 0 -10000 0 0
WWOX 0 0 -10000 0 -10000 0 0
cell proliferation -0.022 0.16 -10000 0 -0.8 4 4
Syndecan-1-mediated 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
TGFB1 0 0 -9999 0 -10000 0 0
CCL5 -0.011 0.091 -9999 0 -0.76 5 5
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.11 -9999 0 -0.44 5 5
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 -0.11 0.092 -9999 0 -0.41 7 7
Syndecan-1/Syntenin -0.1 0.089 -9999 0 -0.41 5 5
MAPK3 -0.069 0.098 -9999 0 -0.48 1 1
HGF/MET -0.11 0.22 -9999 0 -0.57 64 64
TGFB1/TGF beta receptor Type II 0 0 -9999 0 -10000 0 0
BSG 0 0 -9999 0 -10000 0 0
keratinocyte migration -0.11 0.091 -9999 0 -0.4 7 7
Syndecan-1/RANTES -0.11 0.11 -9999 0 -0.5 9 9
Syndecan-1/CD147 -0.096 0.083 -9999 0 -0.52 1 1
Syndecan-1/Syntenin/PIP2 -0.1 0.086 -9999 0 -0.4 5 5
LAMA5 -0.004 0.058 -9999 0 -0.76 2 2
positive regulation of cell-cell adhesion -0.099 0.085 -9999 0 -0.39 5 5
MMP7 -0.033 0.14 -9999 0 -0.64 18 18
HGF -0.13 0.29 -9999 0 -0.76 61 61
Syndecan-1/CASK -0.098 0.11 -9999 0 -0.42 5 5
Syndecan-1/HGF/MET -0.17 0.17 -9999 0 -0.48 64 64
regulation of cell adhesion -0.06 0.096 -9999 0 -0.46 1 1
HPSE 0 0 -9999 0 -10000 0 0
positive regulation of cell migration -0.1 0.11 -9999 0 -0.44 5 5
SDC1 -0.1 0.11 -9999 0 -0.44 5 5
Syndecan-1/Collagen -0.1 0.11 -9999 0 -0.44 5 5
PPIB 0 0 -9999 0 -10000 0 0
MET -0.006 0.066 -9999 0 -0.71 3 3
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.058 0.18 -9999 0 -0.61 33 33
MAPK1 -0.069 0.098 -9999 0 -0.48 1 1
homophilic cell adhesion -0.1 0.11 -9999 0 -0.44 5 5
MMP1 -0.38 0.29 -9999 0 -0.61 216 216
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.18 0.14 -9999 0 -0.7 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.15 0.12 -9999 0 -0.61 2 2
alphaV/beta3 Integrin/Osteopontin/Src -0.26 0.21 -9999 0 -0.43 214 214
AP1 -0.21 0.18 -9999 0 -0.66 30 30
ILK -0.18 0.18 -9999 0 -0.73 2 2
bone resorption -0.16 0.13 -9999 0 -0.63 4 4
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.17 0.14 -9999 0 -0.68 2 2
ITGAV 0.011 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.003 0.044 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Osteopontin -0.23 0.18 -9999 0 -0.59 6 6
MAP3K1 -0.18 0.18 -9999 0 -0.66 3 3
JUN 0 0 -9999 0 -10000 0 0
MAPK3 -0.16 0.17 -9999 0 -0.7 2 2
MAPK1 -0.16 0.17 -9999 0 -0.7 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 -0.16 0.17 -9999 0 -0.62 3 3
ITGB3 -0.002 0.1 -9999 0 -0.76 6 6
NFKBIA -0.14 0.16 -9999 0 -0.67 2 2
FOS -0.12 0.28 -9999 0 -0.76 55 55
CD44 -0.004 0.058 -9999 0 -0.76 2 2
CHUK 0 0 -9999 0 -10000 0 0
PLAU -0.14 0.17 -9999 0 -0.6 13 13
NF kappa B1 p50/RelA -0.15 0.12 -9999 0 -0.59 2 2
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.01 0.074 -9999 0 -0.57 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.18 0.18 -9999 0 -0.65 3 3
VAV3 -0.16 0.17 -9999 0 -0.7 2 2
MAP3K14 -0.18 0.18 -9999 0 -0.65 3 3
ROCK2 0 0 -9999 0 -10000 0 0
SPP1 -0.36 0.3 -9999 0 -0.6 214 214
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.16 0.13 -9999 0 -0.64 2 2
MMP2 -0.15 0.18 -9999 0 -0.66 9 9
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.012 0.04 -9999 0 -0.52 1 1
NFATC2 -0.044 0.17 -9999 0 -0.54 37 37
NFATC3 0.013 0.028 -9999 0 -10000 0 0
CD40LG -0.17 0.39 -9999 0 -0.87 63 63
PTGS2 -0.14 0.35 -9999 0 -0.86 42 42
JUNB -0.002 0.041 -9999 0 -0.76 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.011 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.011 -9999 0 -10000 0 0
CALM1 -0.001 0.003 -9999 0 -10000 0 0
JUN -0.001 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.006 0.01 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.002 0.032 -9999 0 -0.61 1 1
CREM 0 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.09 0.17 -9999 0 -0.6 23 23
FOS -0.12 0.28 -9999 0 -0.76 55 55
IFNG -0.12 0.31 -9999 0 -0.82 23 23
AP-1/NFAT1-c-4 -0.22 0.32 -9999 0 -0.78 68 68
FASLG -0.12 0.33 -9999 0 -0.91 24 24
NFAT1-c-4/ICER1 -0.071 0.15 -9999 0 -0.53 26 26
IL2RA -0.12 0.3 -9999 0 -0.84 20 20
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.16 0.37 -9999 0 -0.83 53 53
JunB/Fra1/NFAT1-c-4 -0.068 0.15 -9999 0 -0.51 26 26
IL4 -0.12 0.3 -9999 0 -0.84 19 19
IL2 -0.006 0.015 -9999 0 -10000 0 0
IL3 -0.019 0.024 -9999 0 -10000 0 0
FKBP1A 0 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0 0.003 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.021 0.037 -9999 0 -10000 0 0
BIRC5 -0.49 0.24 -9999 0 -0.61 281 281
NFKBIA 0.024 0.038 -9999 0 -10000 0 0
CPEB1 -0.048 0.18 -9999 0 -0.76 22 22
AKT1 0.024 0.038 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.019 0.033 -9999 0 -10000 0 0
NDEL1/TACC3 0.021 0.04 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.015 0.007 -9999 0 -10000 0 0
PAK1/Aurora A 0.02 0.043 -9999 0 -0.37 1 1
MDM2 0 0 -9999 0 -10000 0 0
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.29 0.22 -9999 0 -0.44 233 233
TP53 0.023 0.026 -9999 0 -10000 0 0
DLG7 0.015 0.037 -9999 0 -10000 0 0
AURKAIP1 0 0 -9999 0 -10000 0 0
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.022 0.043 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.033 -9999 0 -10000 0 0
AURKA 0.023 0.046 -9999 0 -10000 0 0
AURKB -0.1 0.057 -9999 0 -0.18 10 10
CDC25B 0.025 0.033 -9999 0 -10000 0 0
G2/M transition checkpoint 0.018 0.033 -9999 0 -10000 0 0
mRNA polyadenylation -0.012 0.12 -9999 0 -0.45 22 22
Aurora A/CPEB -0.012 0.12 -9999 0 -0.45 22 22
Aurora A/TACC1/TRAP/chTOG 0.026 0.047 -9999 0 -0.42 2 2
BRCA1 0 0 -9999 0 -10000 0 0
centrosome duplication 0.02 0.043 -9999 0 -0.37 1 1
regulation of centrosome cycle 0.02 0.04 -9999 0 -10000 0 0
spindle assembly 0.018 0.046 -9999 0 -0.41 2 2
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.24 0.12 -9999 0 -0.44 11 11
CENPA -0.088 0.047 -9999 0 -0.2 10 10
Aurora A/PP2A 0.021 0.037 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.034 0.028 -9999 0 -10000 0 0
negative regulation of DNA binding 0.023 0.026 -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 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.019 0.033 -9999 0 -10000 0 0
mitotic prometaphase 0.028 0.019 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.046 -9999 0 -10000 0 0
TACC1 -0.004 0.058 -9999 0 -0.76 2 2
TACC3 -0.003 0.046 -9999 0 -0.61 2 2
Aurora A/Antizyme1 0.024 0.034 -9999 0 -10000 0 0
Aurora A/RasGAP 0.021 0.037 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.015 0.007 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.02 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.29 0.22 -9999 0 -0.44 233 233
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.22 0.17 -9999 0 -0.49 11 11
PAK1 -0.002 0.032 -9999 0 -0.61 1 1
CKAP5 0 0 -9999 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.011 0.07 -9999 0 -0.44 9 9
VLDLR -0.004 0.058 -9999 0 -0.76 2 2
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN 0 0 -9999 0 -10000 0 0
ITGA3 -0.015 0.11 -9999 0 -0.76 7 7
RELN/VLDLR/Fyn -0.07 0.18 -9999 0 -0.5 49 49
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.002 0.028 -9999 0 -0.42 1 1
AKT1 -0.025 0.12 -9999 0 -0.53 2 2
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.042 0.15 -9999 0 -0.61 24 24
RELN/LRP8/DAB1 -0.088 0.18 -9999 0 -0.47 47 47
LRPAP1/LRP8 -0.004 0.041 -9999 0 -0.44 3 3
RELN/LRP8/DAB1/Fyn -0.082 0.16 -9999 0 -0.44 47 47
DAB1/alpha3/beta1 Integrin -0.083 0.16 -9999 0 -0.73 5 5
long-term memory -0.12 0.19 -9999 0 -0.73 10 10
DAB1/LIS1 -0.078 0.16 -9999 0 -0.67 4 4
DAB1/CRLK/C3G -0.075 0.15 -9999 0 -0.65 4 4
PIK3CA 0 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.079 0.16 -9999 0 -0.68 4 4
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.072 0.21 -9999 0 -0.69 36 36
CDK5R1 -0.016 0.096 -9999 0 -0.61 9 9
RELN -0.1 0.26 -9999 0 -0.75 48 48
PIK3R1 0 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.071 0.17 -9999 0 -0.48 51 51
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.2 -9999 0 -0.47 62 62
MAPK8 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.088 0.18 -9999 0 -0.44 70 70
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.085 0.17 -9999 0 -0.44 48 48
RELN/LRP8 -0.071 0.17 -9999 0 -0.48 51 51
GRIN2B/RELN/LRP8/DAB1/Fyn -0.086 0.17 -9999 0 -0.45 39 39
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.012 0.081 -9999 0 -0.58 7 7
RAP1A -0.07 0.14 -9999 0 -0.6 4 4
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.052 -9999 0 -0.68 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.009 0.072 -9999 0 -0.61 5 5
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.006 0.089 -9999 0 -0.34 1 1
neuron adhesion -0.071 0.14 -9999 0 -0.67 4 4
LRP8 -0.005 0.056 -9999 0 -0.61 3 3
GSK3B -0.017 0.12 -9999 0 -0.5 2 2
RELN/VLDLR/DAB1/Fyn -0.082 0.17 -9999 0 -0.45 48 48
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.056 0.12 -9999 0 -0.33 48 48
CDK5 0 0 -9999 0 -10000 0 0
MAPT -0.001 0.094 -9999 0 -0.69 6 6
neuron migration -0.018 0.16 -9999 0 -0.56 3 3
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.037 0.075 -9999 0 -0.34 1 1
RELN/VLDLR -0.066 0.16 -9999 0 -0.46 46 46
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.26 0.36 -9999 0 -0.76 117 117
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0 0 -9999 0 -10000 0 0
TCEB1 0 0 -9999 0 -10000 0 0
HIF1A/p53 -0.011 0.025 -9999 0 -10000 0 0
HIF1A -0.013 0.029 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.28 0.3 -9999 0 -0.61 162 162
ARNT/IPAS -0.19 0.27 -9999 0 -0.58 117 117
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.011 0.025 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 0 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.011 0.025 -9999 0 -10000 0 0
PHD1-3/OS9 -0.056 0.12 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.009 0.019 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.011 0.025 -9999 0 -10000 0 0
EGLN3 -0.1 0.23 -9999 0 -0.61 59 59
EGLN2 0 0 -9999 0 -10000 0 0
EGLN1 0 0 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.15 0.15 -9999 0 -0.38 28 28
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0 0.13 -10000 0 -0.42 14 14
TBX21 -0.1 0.5 -10000 0 -1.3 43 43
B2M 0.011 0.004 -10000 0 -10000 0 0
TYK2 0.016 0.017 -10000 0 -10000 0 0
IL12RB1 -0.029 0.19 -10000 0 -0.79 20 20
GADD45B -0.034 0.37 -10000 0 -1.1 26 26
IL12RB2 -0.045 0.19 -10000 0 -0.6 35 35
GADD45G -0.017 0.32 -10000 0 -1 21 21
natural killer cell activation 0.005 0.02 -10000 0 -10000 0 0
RELB -0.002 0.032 -10000 0 -0.61 1 1
RELA 0 0 -10000 0 -10000 0 0
IL18 0.009 0.059 -10000 0 -0.76 2 2
IL2RA -0.005 0.056 -10000 0 -0.61 3 3
IFNG -0.011 0.087 -10000 0 -0.73 5 5
STAT3 (dimer) -0.007 0.29 -10000 0 -0.82 24 24
HLA-DRB5 -0.055 0.21 -10000 0 -0.76 29 29
FASLG -0.048 0.4 -10000 0 -1.2 27 27
NF kappa B2 p52/RelB -0.13 0.29 -10000 0 -0.9 32 32
CD4 0 0.082 -10000 0 -0.76 4 4
SOCS1 -0.002 0.041 -10000 0 -0.76 1 1
EntrezGene:6955 -0.002 0.011 -10000 0 -10000 0 0
CD3D -0.005 0.11 -10000 0 -0.77 7 7
CD3E -0.003 0.1 -10000 0 -0.76 6 6
CD3G -0.021 0.15 -10000 0 -0.77 14 14
IL12Rbeta2/JAK2 -0.02 0.14 -10000 0 -0.44 35 35
CCL3 -0.028 0.34 -10000 0 -1 25 25
CCL4 -0.03 0.35 -10000 0 -1 27 27
HLA-A 0.011 0.004 -10000 0 -10000 0 0
IL18/IL18R 0.018 0.15 -10000 0 -0.56 19 19
NOS2 -0.084 0.45 -10000 0 -1.2 41 41
IL12/IL12R/TYK2/JAK2/SPHK2 0.001 0.13 -10000 0 -0.39 17 17
IL1R1 -0.03 0.35 -10000 0 -0.99 28 28
IL4 -0.003 0.02 -10000 0 -10000 0 0
JAK2 0.016 0.017 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.02 0.29 -10000 0 -1.3 14 14
RAB7A 0.007 0.28 -10000 0 -0.81 20 20
lysosomal transport 0.011 0.26 -10000 0 -0.76 20 20
FOS -0.2 0.54 -10000 0 -1.3 69 69
STAT4 (dimer) -0.01 0.33 -10000 0 -0.94 27 27
STAT5A (dimer) -0.13 0.3 -10000 0 -0.94 30 30
GZMA -0.036 0.37 -10000 0 -1.1 27 27
GZMB -0.035 0.37 -10000 0 -1.1 25 25
HLX -0.002 0.041 -10000 0 -0.76 1 1
LCK -0.038 0.38 -10000 0 -1 30 30
TCR/CD3/MHC II/CD4 -0.069 0.28 -10000 0 -0.83 29 29
IL2/IL2R -0.009 0.07 -10000 0 -0.56 4 4
MAPK14 -0.016 0.34 -10000 0 -0.97 26 26
CCR5 -0.021 0.33 -10000 0 -1.1 20 20
IL1B 0.007 0.087 -10000 0 -0.79 4 4
STAT6 0.017 0.1 -10000 0 -10000 0 0
STAT4 -0.011 0.091 -10000 0 -0.76 5 5
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B 0.017 0.017 -10000 0 -10000 0 0
CD8A 0.002 0.083 -10000 0 -0.76 4 4
CD8B -0.016 0.14 -10000 0 -0.71 13 13
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0 0.13 0.41 14 -10000 0 14
IL2RB -0.002 0.041 -10000 0 -0.76 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.3 -10000 0 -0.84 27 27
IL2RG -0.009 0.081 -10000 0 -0.76 4 4
IL12 0.016 0.085 -10000 0 -0.59 6 6
STAT5A -0.002 0.041 -10000 0 -0.76 1 1
CD247 -0.003 0.1 -10000 0 -0.77 6 6
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.1 -10000 0 -0.77 6 6
IL12/IL12R/TYK2/JAK2 -0.051 0.43 -10000 0 -1.1 33 33
MAP2K3 -0.019 0.34 -10000 0 -0.97 26 26
RIPK2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.019 0.34 -10000 0 -0.97 26 26
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.039 0.19 -10000 0 -0.76 22 22
IL18RAP -0.022 0.16 -10000 0 -0.77 16 16
IL12Rbeta1/TYK2 -0.013 0.15 -10000 0 -0.61 20 20
EOMES -0.022 0.22 -10000 0 -1.4 8 8
STAT1 (dimer) -0.005 0.29 -10000 0 -0.79 25 25
T cell proliferation 0.004 0.26 -10000 0 -0.69 25 25
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.007 0.073 -10000 0 -0.77 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.23 -10000 0 -0.77 26 26
ATF2 -0.003 0.31 -10000 0 -0.87 26 26
Wnt signaling

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
Noncanonical Wnts/FZD -0.047 0.091 -9999 0 -0.42 2 2
FZD6 0 0 -9999 0 -10000 0 0
WNT6 -0.096 0.22 -9999 0 -0.61 55 55
WNT4 -0.014 0.095 -9999 0 -0.67 7 7
FZD3 0 0 -9999 0 -10000 0 0
WNT5A -0.013 0.089 -9999 0 -0.63 7 7
WNT11 -0.041 0.16 -9999 0 -0.71 20 20
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.008 0.059 -9999 0 -0.45 6 6
Metarhodopsin II/Arrestin -0.002 0.029 -9999 0 -0.38 2 2
PDE6G/GNAT1/GTP -0.012 0.073 -9999 0 -0.43 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.01 0.079 -9999 0 -0.61 6 6
GRK1 -0.003 0.046 -9999 0 -0.61 2 2
CNG Channel -0.063 0.14 -9999 0 -0.62 6 6
mol:Na + -0.11 0.16 -9999 0 -0.56 20 20
mol:ADP -0.003 0.046 -9999 0 -0.6 2 2
RGS9-1/Gbeta5/R9AP -0.058 0.17 -9999 0 -0.52 39 39
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.11 0.17 -9999 0 -0.58 20 20
CNGB1 -0.063 0.18 -9999 0 -0.61 36 36
RDH5 -0.002 0.041 -9999 0 -0.76 1 1
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.1 0.16 -9999 0 -0.54 20 20
Na + (4 Units) -0.099 0.15 -9999 0 -0.52 20 20
RGS9 -0.064 0.21 -9999 0 -0.76 29 29
GNB1/GNGT1 -0.13 0.2 -9999 0 -0.44 99 99
GNAT1/GDP -0.056 0.15 -9999 0 -0.45 39 39
GUCY2D 0 0 -9999 0 -10000 0 0
GNGT1 -0.17 0.27 -9999 0 -0.61 99 99
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.033 0.11 -9999 0 -0.44 21 21
mol:11-cis-retinal -0.002 0.041 -9999 0 -0.76 1 1
mol:cGMP -0.085 0.14 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.004 0.046 -9999 0 -0.49 3 3
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.009 0.072 -9999 0 -0.61 5 5
Metarhodopsin II -0.004 0.037 -9999 0 -0.35 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.09 0.15 -9999 0 -10000 0 0
RGS9BP -0.026 0.14 -9999 0 -0.76 12 12
Metarhodopsin II/Transducin -0.052 0.082 -9999 0 -0.46 1 1
GCAP Family/Ca ++ -0.092 0.15 -9999 0 -10000 0 0
PDE6A/B -0.03 0.13 -9999 0 -0.56 19 19
mol:Pi -0.058 0.17 -9999 0 -0.52 39 39
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.1 0.16 -9999 0 -0.67 2 2
PDE6B -0.017 0.11 -9999 0 -0.74 8 8
PDE6A -0.023 0.13 -9999 0 -0.73 11 11
PDE6G -0.009 0.081 -9999 0 -0.76 4 4
RHO -0.003 0.046 -9999 0 -0.61 2 2
PDE6 -0.072 0.17 -9999 0 -0.93 3 3
GUCA1A -0.16 0.27 -9999 0 -0.61 93 93
GC2/GCAP Family -0.092 0.15 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0 0 -9999 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade -0.019 0.085 -9999 0 -0.39 17 17
EFNA5 -0.004 0.058 -9999 0 -0.76 2 2
FYN 0.002 0.08 -9999 0 -0.35 17 17
neuron projection morphogenesis -0.019 0.085 -9999 0 -0.39 17 17
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.019 0.085 -9999 0 -0.39 17 17
EPHA5 -0.026 0.12 -9999 0 -0.61 15 15
p75(NTR)-mediated 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
Sortilin/TRAF6 -0.003 0.044 -9999 0 -0.58 2 2
Necdin/E2F1 -0.003 0.044 -9999 0 -0.58 2 2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.04 0.11 -9999 0 -0.45 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.2 -9999 0 -0.47 79 79
NT-4/5 (dimer)/p75(NTR) -0.049 0.14 -9999 0 -0.47 36 36
IKBKB -0.002 0.032 -9999 0 -0.61 1 1
AKT1 -0.005 0.12 -9999 0 -0.72 1 1
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.11 0.27 -9999 0 -0.76 52 52
MGDIs/NGR/p75(NTR)/LINGO1 -0.062 0.15 -9999 0 -0.4 54 54
FURIN 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.2 -9999 0 -0.48 77 77
LINGO1 -0.051 0.17 -9999 0 -0.61 29 29
Sortilin/TRAF6/NRIF -0.002 0.027 -9999 0 -10000 0 0
proBDNF (dimer) -0.11 0.27 -9999 0 -0.76 52 52
NTRK1 -0.015 0.11 -9999 0 -0.76 7 7
RTN4R -0.002 0.041 -9999 0 -0.76 1 1
neuron apoptosis -0.04 0.17 -9999 0 -0.6 9 9
IRAK1 0 0 -9999 0 -10000 0 0
SHC1 -0.023 0.14 -9999 0 -0.53 9 9
ARHGDIA 0 0 -9999 0 -10000 0 0
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 -0.043 0.12 -9999 0 -0.48 11 11
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.045 0.12 -9999 0 -0.47 13 13
Mammalian IAPs/DIABLO -0.006 0.053 -9999 0 -0.45 5 5
proNGF (dimer) -0.023 0.13 -9999 0 -0.73 11 11
MAGED1 0 0 -9999 0 -10000 0 0
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.017 0.11 -9999 0 -0.76 8 8
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.038 0.11 -9999 0 -0.46 9 9
NGF -0.023 0.13 -9999 0 -0.73 11 11
cell cycle arrest -0.02 0.14 -9999 0 -0.44 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.022 0.067 -9999 0 -0.49 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.041 0.12 -9999 0 -0.4 36 36
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.044 0.13 -9999 0 -0.53 9 9
PSENEN 0 0 -9999 0 -10000 0 0
mol:ceramide -0.016 0.13 -9999 0 -0.47 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.016 0.051 -9999 0 -0.39 1 1
p75(NTR)/beta APP -0.036 0.12 -9999 0 -0.44 28 28
BEX1 -0.097 0.25 -9999 0 -0.72 47 47
mol:GDP -0.031 0.14 -9999 0 -0.41 38 38
NGF (dimer) -0.034 0.12 -9999 0 -0.5 13 13
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.055 0.13 -9999 0 -0.62 5 5
PIK3R1 0 0 -9999 0 -10000 0 0
RAC1/GTP -0.039 0.11 -9999 0 -0.46 9 9
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.045 0.13 -9999 0 -0.53 9 9
RHOB -0.002 0.041 -9999 0 -0.76 1 1
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0 0 -9999 0 -10000 0 0
NT3 (dimer) -0.008 0.077 -9999 0 -0.72 4 4
TP53 -0.084 0.16 -9999 0 -0.69 5 5
PRDM4 -0.016 0.13 -9999 0 -0.48 11 11
BDNF (dimer) -0.29 0.26 -9999 0 -0.69 65 65
PIK3CA 0 0 -9999 0 -10000 0 0
SORT1 -0.004 0.058 -9999 0 -0.76 2 2
activation of caspase activity -0.039 0.11 -9999 0 -0.44 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.043 0.12 -9999 0 -0.48 11 11
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.021 0.15 -9999 0 -0.56 6 6
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.016 0.13 -9999 0 -0.48 11 11
APH1B 0 0 -9999 0 -10000 0 0
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.048 0.14 -9999 0 -0.41 40 40
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.042 0.13 -9999 0 -0.45 32 32
MAPK8 -0.017 0.15 -9999 0 -0.59 4 4
MAPK9 -0.017 0.15 -9999 0 -0.59 4 4
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.008 0.077 -9999 0 -0.72 4 4
NTF4 -0.018 0.11 -9999 0 -0.76 8 8
NDN -0.004 0.058 -9999 0 -0.76 2 2
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.035 0.1 -9999 0 -0.68 1 1
p75 CTF/Sortilin/TRAF6/NRIF -0.003 0.034 -9999 0 -0.45 2 2
RhoA-B-C/GTP -0.044 0.13 -9999 0 -0.53 9 9
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.09 0.17 -9999 0 -0.73 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.096 0.19 -9999 0 -0.48 54 54
PRKACB 0 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.086 0.21 -9999 0 -0.58 52 52
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.011 0.091 -9999 0 -0.76 5 5
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.011 0.13 -9999 0 -0.46 10 10
BAD -0.01 0.14 -9999 0 -0.56 4 4
RIPK2 0 0 -9999 0 -10000 0 0
NGFR -0.049 0.16 -9999 0 -0.61 28 28
CYCS -0.008 0.12 -9999 0 -0.44 11 11
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.04 0.12 -9999 0 -0.48 9 9
BCL2L11 -0.01 0.14 -9999 0 -0.56 4 4
BDNF (dimer)/p75(NTR) -0.12 0.24 -9999 0 -0.56 75 75
PI3K -0.04 0.12 -9999 0 -0.48 9 9
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.043 0.12 -9999 0 -0.48 11 11
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.053 0.15 -9999 0 -0.48 38 38
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.043 0.12 -9999 0 -0.48 11 11
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG -0.003 0.046 -9999 0 -0.61 2 2
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.095 0.18 -9999 0 -0.67 11 11
SQSTM1 0 0 -9999 0 -10000 0 0
NGFRAP1 0 0 -9999 0 -10000 0 0
CASP3 -0.007 0.14 -9999 0 -0.51 4 4
E2F1 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.025 0.087 -9999 0 -0.54 1 1
NGF (dimer)/TRKA -0.029 0.12 -9999 0 -0.56 18 18
MMP7 -0.033 0.14 -9999 0 -0.64 18 18
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.04 0.11 -9999 0 -0.73 1 1
MMP3 -0.37 0.3 -9999 0 -0.61 212 212
APAF-1/Caspase 9 -0.032 0.086 -9999 0 -0.54 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.013 0.029 -10000 0 -10000 0 0
oxygen homeostasis -0.01 0.012 -10000 0 -10000 0 0
TCEB2 0 0 -10000 0 -10000 0 0
TCEB1 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.11 0.13 -10000 0 -0.47 8 8
EPO -0.17 0.21 -10000 0 -0.68 11 11
FIH (dimer) 0.003 0.009 -10000 0 -10000 0 0
APEX1 0.004 0.012 -10000 0 -10000 0 0
SERPINE1 -0.21 0.24 -10000 0 -0.78 10 10
FLT1 -0.031 0.15 -10000 0 -1 7 7
ADORA2A -0.2 0.23 -10000 0 -0.76 10 10
germ cell development -0.2 0.23 -10000 0 -0.77 11 11
SLC11A2 -0.21 0.24 -10000 0 -0.78 10 10
BHLHE40 -0.21 0.24 -10000 0 -0.78 10 10
HIF1AN 0.003 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.15 0.16 -10000 0 -0.49 34 34
ETS1 0.008 0.11 -10000 0 -0.77 7 7
CITED2 -0.035 0.17 -10000 0 -1.3 6 6
KDR -0.056 0.25 -10000 0 -1.3 13 13
PGK1 -0.21 0.24 -10000 0 -0.78 10 10
SIRT1 0.001 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.24 0.27 -10000 0 -0.83 23 23
EPAS1 -0.13 0.17 -10000 0 -0.42 58 58
SP1 0.017 0 -10000 0 -10000 0 0
ABCG2 -0.24 0.31 -10000 0 -1 29 29
EFNA1 -0.21 0.24 -10000 0 -0.78 10 10
FXN -0.2 0.23 -10000 0 -0.73 13 13
POU5F1 -0.21 0.24 -10000 0 -0.81 11 11
neuron apoptosis 0.24 0.26 0.8 23 -10000 0 23
EP300 0 0 -10000 0 -10000 0 0
EGLN3 -0.1 0.23 -10000 0 -0.62 59 59
EGLN2 0.003 0.009 -10000 0 -10000 0 0
EGLN1 0.003 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.004 0.012 -10000 0 -10000 0 0
SLC2A1 -0.4 0.28 -10000 0 -0.77 64 64
TWIST1 -0.3 0.31 -10000 0 -0.78 48 48
ELK1 0.017 0.002 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.15 0.16 -10000 0 -0.5 26 26
VEGFA -0.21 0.24 -10000 0 -0.75 13 13
CREBBP 0 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA 0 0.068 -9999 0 -0.7 3 3
PDGF/PDGFRA/CRKL -0.005 0.048 -9999 0 -0.51 3 3
positive regulation of JUN kinase activity -0.003 0.036 -9999 0 -0.42 2 2
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.11 0.23 -9999 0 -0.58 64 64
AP1 -0.18 0.4 -9999 0 -1.1 55 55
mol:IP3 0.009 0.056 -9999 0 -0.52 3 3
PLCG1 0.009 0.056 -9999 0 -0.53 3 3
PDGF/PDGFRA/alphaV Integrin -0.005 0.048 -9999 0 -0.51 3 3
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.009 0.056 -9999 0 -0.52 3 3
CAV3 -0.13 0.29 -9999 0 -0.76 61 61
CAV1 -0.22 0.34 -9999 0 -0.76 99 99
SHC/Grb2/SOS1 -0.003 0.036 -9999 0 -0.43 2 2
PDGF/PDGFRA/Shf -0.005 0.048 -9999 0 -0.51 3 3
FOS -0.14 0.41 -9999 0 -1.1 55 55
JUN -0.01 0.023 -9999 0 -10000 0 0
oligodendrocyte development -0.005 0.048 -9999 0 -0.51 3 3
GRB2 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
mol:DAG 0.009 0.056 -9999 0 -0.52 3 3
PDGF/PDGFRA 0 0.067 -9999 0 -0.7 3 3
actin cytoskeleton reorganization -0.005 0.048 -9999 0 -0.51 3 3
SRF 0.022 0.01 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.004 0.04 -9999 0 -0.47 2 2
PDGF/PDGFRA/Crk/C3G -0.004 0.04 -9999 0 -0.48 2 2
JAK1 0.014 0.05 -9999 0 -0.51 3 3
ELK1/SRF -0.005 0.035 -9999 0 -10000 0 0
SHB 0 0 -9999 0 -10000 0 0
SHF 0 0 -9999 0 -10000 0 0
CSNK2A1 0.009 0.021 -9999 0 -10000 0 0
GO:0007205 0.009 0.057 -9999 0 -0.52 3 3
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.003 0.036 -9999 0 -0.42 2 2
PDGF/PDGFRA/SHB -0.005 0.048 -9999 0 -0.51 3 3
PDGF/PDGFRA/Caveolin-1 -0.17 0.27 -9999 0 -0.59 101 101
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 0.011 0.059 -9999 0 -0.51 2 2
PIK3CA 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.005 0.048 -9999 0 -0.51 3 3
JAK-STAT cascade 0.014 0.05 -9999 0 -0.51 3 3
cell proliferation -0.005 0.048 -9999 0 -0.51 3 3
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.02 0.096 -10000 0 -0.45 15 15
ER alpha/Gai/GDP/Gbeta gamma -0.024 0.1 -10000 0 -0.47 14 14
AKT1 0 0.17 -10000 0 -0.82 14 14
PIK3CA 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.004 0.17 -10000 0 -0.83 14 14
mol:Ca2+ -0.087 0.24 -10000 0 -0.5 80 80
IGF1R 0 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.02 0.099 -10000 0 -0.5 14 14
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.002 0.16 0.78 14 -10000 0 14
RhoA/GTP -0.015 0.073 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.025 0.11 -10000 0 -0.53 14 14
regulation of stress fiber formation -0.035 0.066 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.021 0.1 -10000 0 -0.49 15 15
KRAS 0 0 -10000 0 -10000 0 0
G13/GTP -0.019 0.091 -10000 0 -0.46 14 14
pseudopodium formation 0.035 0.066 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.02 0.099 -10000 0 -0.5 14 14
GRB2 0 0 -10000 0 -10000 0 0
GNG2 -0.004 0.058 -10000 0 -0.76 2 2
GNAO1 -0.006 0.061 -10000 0 -0.66 3 3
HRAS 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.02 0.12 -10000 0 -0.54 15 15
E2/ER beta (dimer) -0.001 0.024 -10000 0 -0.45 1 1
mol:GDP -0.021 0.1 -10000 0 -0.52 14 14
mol:NADP 0.02 0.12 -10000 0 -0.54 15 15
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.092 0.25 -10000 0 -0.52 80 80
IGF-1R heterotetramer 0 0 -10000 0 -10000 0 0
PLCB1 -0.12 0.23 -10000 0 -0.53 80 80
PLCB2 -0.13 0.24 -10000 0 -0.54 82 82
IGF1 -0.013 0.096 -10000 0 -0.73 6 6
mol:L-citrulline 0.02 0.12 -10000 0 -0.54 15 15
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.009 0.053 -10000 0 -0.68 1 1
JNK cascade -0.001 0.024 -10000 0 -0.45 1 1
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.002 0.032 -10000 0 -0.61 1 1
GNAQ -0.002 0.041 -10000 0 -0.76 1 1
ESR1 -0.031 0.15 -10000 0 -0.76 14 14
Gq family/GDP/Gbeta gamma -0.071 0.14 -10000 0 -0.86 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.021 0.069 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.025 0.11 -10000 0 -0.53 14 14
GNAZ -0.011 0.091 -10000 0 -0.76 5 5
E2/ER alpha (dimer) -0.024 0.12 -10000 0 -0.58 14 14
STRN 0 0 -10000 0 -10000 0 0
GNAL -0.004 0.058 -10000 0 -0.76 2 2
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.015 0.021 -10000 0 -0.38 1 1
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.041 -10000 0 -0.76 1 1
HBEGF 0.008 0.12 -10000 0 -0.94 2 2
cAMP biosynthetic process -0.02 0.087 -10000 0 -0.4 17 17
SRC 0.022 0.11 -10000 0 -0.74 2 2
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.021 0.097 -10000 0 -0.47 14 14
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.024 0.096 -10000 0 -0.6 4 4
Gs family/GTP -0.02 0.088 -10000 0 -0.41 17 17
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.02 0.12 -10000 0 -0.51 15 15
mol:DAG -0.092 0.25 -10000 0 -0.52 80 80
Gs family/GDP/Gbeta gamma -0.021 0.092 -10000 0 -0.44 14 14
MSN 0.036 0.07 -10000 0 -10000 0 0
Gq family/GTP -0.13 0.25 -10000 0 -0.56 80 80
mol:PI-3-4-5-P3 -0.002 0.16 -10000 0 -0.8 14 14
NRAS 0 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.02 0.12 0.51 15 -10000 0 15
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.02 0.095 -10000 0 -0.48 14 14
NOS3 0.019 0.13 -10000 0 -0.56 15 15
GNA11 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.024 0.14 -10000 0 -0.64 14 14
E2/ER alpha (dimer)/PELP1/Src -0.027 0.12 -10000 0 -0.56 14 14
ruffle organization 0.035 0.066 -10000 0 -10000 0 0
ROCK2 -0.014 0.067 -10000 0 -10000 0 0
GNA14 -0.18 0.32 -10000 0 -0.76 80 80
GNA15 -0.002 0.041 -10000 0 -0.76 1 1
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.001 0.13 -10000 0 -0.68 2 2
MMP2 0.026 0.12 -10000 0 -1 2 2
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.034 0.13 -10000 0 -0.56 16 16
FYN 0.012 0.2 -10000 0 -0.73 20 20
LAT/GRAP2/SLP76 -0.046 0.16 -10000 0 -0.64 20 20
IKBKB -0.002 0.032 -10000 0 -0.61 1 1
AKT1 0.031 0.13 -10000 0 -0.47 18 18
B2M 0.011 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.028 -10000 0 -0.18 1 1
MAP3K8 -0.007 0.07 -10000 0 -0.76 3 3
mol:Ca2+ -0.007 0.026 -10000 0 -0.12 14 14
integrin-mediated signaling pathway -0.001 0.027 -10000 0 -0.5 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.021 0.19 -10000 0 -0.72 18 18
TRPV6 -0.025 0.14 -10000 0 -0.71 13 13
CD28 0.005 0.059 -10000 0 -0.77 2 2
SHC1 0.016 0.19 -10000 0 -0.72 17 17
receptor internalization 0.004 0.2 -10000 0 -0.78 18 18
PRF1 -0.021 0.3 -10000 0 -1.2 19 19
KRAS 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
COT/AKT1 0.032 0.11 -10000 0 -0.42 14 14
LAT 0.016 0.18 -10000 0 -0.72 17 17
EntrezGene:6955 0.001 0.004 -10000 0 -10000 0 0
CD3D -0.005 0.11 -10000 0 -0.77 7 7
CD3E -0.002 0.1 -10000 0 -0.77 6 6
CD3G -0.02 0.15 -10000 0 -0.77 14 14
RASGRP2 -0.019 0.072 -10000 0 -0.18 59 59
RASGRP1 0.033 0.13 -10000 0 -0.45 19 19
HLA-A 0.011 0.004 -10000 0 -10000 0 0
RASSF5 -0.002 0.041 -10000 0 -0.76 1 1
RAP1A/GTP/RAPL -0.001 0.027 -10000 0 -0.5 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.049 -10000 0 -0.13 18 18
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.05 -10000 0 -0.26 7 7
PRKCA -0.02 0.069 -10000 0 -0.3 14 14
GRAP2 -0.034 0.16 -10000 0 -0.76 16 16
mol:IP3 -0.026 0.12 0.26 9 -0.48 16 25
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.004 0.21 -10000 0 -0.82 16 16
ORAI1 0.013 0.074 0.35 13 -0.59 1 14
CSK 0.014 0.19 -10000 0 -0.73 17 17
B7 family/CD28 -0.054 0.21 -10000 0 -0.85 18 18
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.003 0.22 -10000 0 -0.88 17 17
PTPN6 0.012 0.19 -10000 0 -0.75 17 17
VAV1 0.016 0.19 -10000 0 -0.73 17 17
Monovalent TCR/CD3 -0.014 0.2 -10000 0 -0.71 19 19
CBL 0 0 -10000 0 -10000 0 0
LCK 0.009 0.21 -10000 0 -0.78 18 18
PAG1 0.013 0.19 -10000 0 -0.71 18 18
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.002 0.22 -10000 0 -0.83 19 19
CD80 -0.012 0.13 -10000 0 -0.76 10 10
CD86 0.001 0.083 -10000 0 -0.77 4 4
PDK1/CARD11/BCL10/MALT1 -0.018 0.061 -10000 0 -0.31 8 8
HRAS 0 0 -10000 0 -10000 0 0
GO:0035030 0.015 0.17 -10000 0 -0.66 18 18
CD8A 0.002 0.083 -10000 0 -0.77 4 4
CD8B -0.016 0.14 -10000 0 -0.72 13 13
PTPRC -0.037 0.18 -10000 0 -0.76 21 21
PDK1/PKC theta 0.027 0.17 -10000 0 -0.59 19 19
CSK/PAG1 0.018 0.18 -10000 0 -0.73 15 15
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0 0.001 -10000 0 -10000 0 0
GRAP2/SLP76 -0.054 0.19 -10000 0 -0.76 20 20
STIM1 0.008 0.036 -10000 0 -10000 0 0
RAS family/GTP 0.04 0.055 -10000 0 -0.18 9 9
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0 0.23 -10000 0 -0.87 18 18
mol:DAG -0.027 0.1 -10000 0 -0.43 16 16
RAP1A/GDP 0.011 0.021 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.003 0.1 -10000 0 -0.77 6 6
cytotoxic T cell degranulation -0.016 0.27 -10000 0 -1.1 19 19
RAP1A/GTP -0.011 0.024 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.15 -10000 0 -0.57 18 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.036 0.15 0.27 9 -0.64 16 25
NRAS 0 0 -10000 0 -10000 0 0
ZAP70 -0.004 0.1 -10000 0 -0.76 6 6
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.042 0.15 -10000 0 -0.61 19 19
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.026 0.13 -10000 0 -0.64 14 14
CARD11 -0.004 0.052 -10000 0 -0.68 2 2
PRKCB -0.026 0.092 -10000 0 -0.36 21 21
PRKCE -0.02 0.07 -10000 0 -0.28 18 18
PRKCQ 0.016 0.19 -10000 0 -0.68 20 20
LCP2 -0.006 0.07 -10000 0 -0.76 3 3
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.033 0.11 -10000 0 -0.39 18 18
IKK complex 0.039 0.044 -10000 0 -0.12 5 5
RAS family/GDP -0.002 0.007 -10000 0 -10000 0 0
MAP3K14 0.036 0.085 -10000 0 -0.33 10 10
PDPK1 0.034 0.12 -10000 0 -0.46 15 15
TCR/CD3/MHC I/CD8/Fyn 0 0.22 -10000 0 -0.79 20 20
EGFR-dependent Endothelin 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
HRAS 0 0 -9999 0 -10000 0 0
EGFR -0.025 0.13 -9999 0 -0.68 13 13
EGF/EGFR -0.066 0.18 -9999 0 -0.49 42 42
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.024 0.098 -9999 0 -0.45 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.004 0.058 -9999 0 -0.76 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.019 0.12 -9999 0 -0.74 9 9
EGF/EGFR dimer/SHC -0.028 0.12 -9999 0 -0.47 21 21
mol:GDP -0.024 0.097 -9999 0 -0.44 13 13
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.074 0.23 -9999 0 -0.76 34 34
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.022 0.089 -9999 0 -0.77 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.022 0.091 -9999 0 -0.78 1 1
FRAP1 -0.023 0.093 -9999 0 -0.43 13 13
EGF/EGFR dimer -0.033 0.13 -9999 0 -0.55 21 21
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.059 0.18 -9999 0 -0.59 35 35
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.005 0.049 -9999 0 -0.53 3 3
CRKL -0.016 0.11 -9999 0 -0.31 2 2
mol:PIP3 -0.017 0.006 -9999 0 -10000 0 0
AKT1 0.002 0.005 -9999 0 -10000 0 0
PTK2B 0 0 -9999 0 -10000 0 0
RAPGEF1 -0.008 0.1 -9999 0 -10000 0 0
RANBP10 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.091 0.19 -9999 0 -0.49 64 64
MAP3K5 -0.001 0.11 -9999 0 -0.51 2 2
HGF/MET/CIN85/CBL/ENDOPHILINS -0.082 0.17 -9999 0 -0.45 63 63
AP1 -0.082 0.19 -9999 0 -0.51 55 55
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
apoptosis -0.1 0.27 -9999 0 -0.72 55 55
STAT3 (dimer) -0.023 0.13 -9999 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K -0.038 0.08 -9999 0 -10000 0 0
INPP5D -0.007 0.07 -9999 0 -0.76 3 3
CBL/CRK -0.009 0.1 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0 0 -9999 0 -10000 0 0
PTEN 0 0 -9999 0 -10000 0 0
ELK1 -0.004 0.025 -9999 0 -0.25 3 3
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.032 0.068 -9999 0 -10000 0 0
PAK1 0.008 0.018 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.091 0.19 -9999 0 -0.49 64 64
HRAS -0.07 0.15 -9999 0 -0.71 2 2
DOCK1 -0.008 0.1 -9999 0 -10000 0 0
GAB1 -0.024 0.11 -9999 0 -0.33 2 2
CRK -0.016 0.11 -9999 0 -10000 0 0
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.1 0.21 -9999 0 -0.55 63 63
JUN 0 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.046 0.096 -9999 0 -0.25 63 63
PIK3R1 0 0 -9999 0 -10000 0 0
cell morphogenesis 0.002 0.13 -9999 0 -10000 0 0
GRB2/SHC -0.038 0.08 -9999 0 -10000 0 0
FOS -0.12 0.28 -9999 0 -0.76 55 55
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.004 0.025 -9999 0 -0.25 3 3
HGF/MET/MUC20 -0.092 0.19 -9999 0 -0.5 64 64
cell migration -0.038 0.079 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
MET/RANBP10 -0.005 0.049 -9999 0 -0.53 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.057 0.12 -9999 0 -10000 0 0
MET/MUC20 -0.005 0.05 -9999 0 -0.54 3 3
RAP1B 0 0.099 -9999 0 -10000 0 0
RAP1A 0 0.099 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.091 0.19 -9999 0 -0.49 64 64
RAF1 -0.032 0.16 -9999 0 -0.66 2 2
STAT3 -0.055 0.12 -9999 0 -10000 0 0
cell proliferation -0.032 0.18 -9999 0 -0.44 2 2
RPS6KB1 -0.016 0.033 -9999 0 -10000 0 0
MAPK3 -0.007 0.022 -9999 0 -0.24 2 2
MAPK1 -0.007 0.022 -9999 0 -10000 0 0
RANBP9 0 0 -9999 0 -10000 0 0
MAPK8 0.017 0.091 -9999 0 -0.39 1 1
SRC -0.021 0.13 -9999 0 -10000 0 0
PI3K -0.038 0.08 -9999 0 -10000 0 0
MET/Glomulin -0.004 0.045 -9999 0 -0.48 3 3
SOS1 0 0 -9999 0 -10000 0 0
MAP2K1 -0.022 0.15 -9999 0 -0.6 2 2
MET -0.006 0.066 -9999 0 -0.71 3 3
MAP4K1 -0.008 0.11 -9999 0 -0.55 2 2
PTK2 0 0 -9999 0 -10000 0 0
MAP2K2 -0.022 0.15 -9999 0 -0.6 2 2
BAD 0.009 0.005 -9999 0 -10000 0 0
MAP2K4 0.007 0.099 -9999 0 -0.46 2 2
SHP2/GRB2/SOS1/GAB1 -0.04 0.087 -9999 0 -0.46 2 2
INPPL1 0 0 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
SH3KBP1 0 0 -9999 0 -10000 0 0
HGS -0.041 0.087 -9999 0 -0.32 2 2
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.13 0.29 -9999 0 -0.76 61 61
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
PTPRJ 0 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.043 0.091 -9999 0 -10000 0 0
PDPK1 -0.006 0.005 -9999 0 -10000 0 0
HGF/MET/SHIP -0.095 0.2 -9999 0 -0.51 65 65
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.004 0.058 -9999 0 -0.76 2 2
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.071 0.17 -9999 0 -0.48 51 51
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.038 0.16 -9999 0 -0.45 45 45
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.042 0.15 -9999 0 -0.61 24 24
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.002 0.041 -9999 0 -0.76 1 1
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.004 0.041 -9999 0 -0.44 3 3
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.016 0.096 -9999 0 -0.61 9 9
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.14 0.26 -9999 0 -0.61 82 82
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.096 0.2 -9999 0 -0.47 70 70
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.082 0.13 -9999 0 -0.5 11 11
MAP1B -0.003 0.023 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.062 0.14 -9999 0 -0.64 2 2
RELN -0.1 0.26 -9999 0 -0.75 48 48
PAFAH/LIS1 -0.001 0.027 -9999 0 -0.5 1 1
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.061 0.1 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.054 0.12 -9999 0 -0.58 3 3
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.089 0.14 -9999 0 -0.54 11 11
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.02 0 -9999 0 -10000 0 0
PAFAH1B3 -0.004 0.052 -9999 0 -0.68 2 2
PAFAH1B2 0 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.002 0.014 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.077 0.12 -9999 0 -10000 0 0
LRP8 -0.005 0.056 -9999 0 -0.61 3 3
NDEL1/Katanin 60 -0.082 0.13 -9999 0 -0.5 11 11
P39/CDK5 -0.12 0.18 -9999 0 -0.68 10 10
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.027 0.16 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.081 0.17 -9999 0 -0.44 48 48
RELN/VLDLR -0.066 0.16 -9999 0 -0.46 46 46
CDC42 0 0 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.006 0.043 -9999 0 -0.45 3 3
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.064 0.18 -9999 0 -0.58 38 38
STXBP1 -0.007 0.07 -9999 0 -0.76 3 3
ACh/CHRNA1 -0.019 0.086 -9999 0 -0.44 13 13
RAB3GAP2/RIMS1/UNC13B -0.055 0.16 -9999 0 -0.51 36 36
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 -0.078 0.23 -9999 0 -0.75 36 36
mol:ACh 0.005 0.025 -9999 0 -0.15 8 8
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.048 0.12 -9999 0 -0.61 2 2
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.019 0.085 -9999 0 -0.44 13 13
UNC13B -0.007 0.07 -9999 0 -0.76 3 3
CHRNA1 -0.024 0.12 -9999 0 -0.65 13 13
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.02 0.086 -9999 0 -0.42 15 15
SNAP25 -0.001 0.05 -9999 0 -0.32 8 8
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.026 0.12 -9999 0 -0.61 15 15
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.008 0.058 -9999 0 -0.44 6 6
STX1A/SNAP25 fragment 1/VAMP2 -0.048 0.12 -9999 0 -0.61 2 2
Caspase cascade in apoptosis

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
TOP1 0.003 0.12 -10000 0 -0.54 14 14
ACTA1 -0.009 0.16 -10000 0 -0.72 14 14
NUMA1 0.003 0.12 -10000 0 -0.54 14 14
SPTAN1 -0.007 0.16 -10000 0 -0.72 14 14
LIMK1 -0.007 0.16 -10000 0 -0.72 14 14
BIRC3 -0.011 0.091 -10000 0 -0.76 5 5
BIRC2 0.01 0.002 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 -0.008 0.16 -10000 0 -0.7 17 17
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0.001 -10000 0 -10000 0 0
PTK2 0.003 0.12 -10000 0 -0.54 14 14
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.006 0.15 -10000 0 -0.7 14 14
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.007 0.16 -10000 0 -0.72 14 14
MADD 0 0 -10000 0 -10000 0 0
TFAP2A -0.087 0.13 -10000 0 -0.77 10 10
BID 0.007 0.073 -10000 0 -0.32 16 16
MAP3K1 0.005 0.045 -10000 0 -0.23 8 8
TRADD 0 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 -0.007 0.16 -10000 0 -0.72 14 14
CASP9 0.001 0.002 -10000 0 -10000 0 0
DNA repair -0.004 0.032 0.17 6 -0.21 1 7
neuron apoptosis 0.02 0.016 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.15 -10000 0 -0.69 14 14
APAF1 0.001 0.002 -10000 0 -10000 0 0
CASP6 0.019 0.074 -10000 0 -0.46 3 3
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD 0 0.15 -10000 0 -0.69 14 14
CASP7 -0.005 0.047 0.37 5 -10000 0 5
KRT18 0.014 0.02 -10000 0 -10000 0 0
apoptosis 0.006 0.14 -10000 0 -0.63 14 14
DFFA -0.007 0.16 -10000 0 -0.72 14 14
DFFB -0.007 0.16 -10000 0 -0.72 14 14
PARP1 0.004 0.032 0.21 1 -0.17 6 7
actin filament polymerization 0 0.14 0.65 14 -10000 0 14
TNF -0.024 0.13 -10000 0 -0.75 11 11
CYCS 0.009 0.055 -10000 0 -0.26 10 10
SATB1 0.024 0.073 -10000 0 -0.43 3 3
SLK -0.007 0.16 -10000 0 -0.72 14 14
p15 BID/BAX -0.013 0.061 -10000 0 -0.34 8 8
CASP2 0.034 0.054 -10000 0 -10000 0 0
JNK cascade -0.005 0.045 0.23 8 -10000 0 8
CASP3 -0.015 0.16 -10000 0 -0.77 14 14
LMNB2 0.033 0.052 -10000 0 -0.32 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.002 0.041 -10000 0 -0.76 1 1
Mammalian IAPs/DIABLO -0.006 0.053 -10000 0 -0.45 5 5
negative regulation of DNA binding -0.086 0.12 -10000 0 -0.76 10 10
stress fiber formation -0.006 0.15 -10000 0 -0.7 14 14
GZMB -0.018 0.18 -10000 0 -0.81 16 16
CASP1 0.011 0.062 -10000 0 -0.74 2 2
LMNB1 0.033 0.052 -10000 0 -0.32 1 1
APP 0.02 0.016 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
VIM 0.001 0.13 -10000 0 -0.61 14 14
LMNA 0.033 0.052 -10000 0 -0.32 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.011 0.049 -10000 0 -10000 0 0
LRDD -0.002 0.041 -10000 0 -0.76 1 1
SREBF1 -0.007 0.16 -10000 0 -0.72 14 14
APAF-1/Caspase 9 -0.002 0.021 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.003 0.12 -10000 0 -0.53 14 14
CFL2 0 0.15 -10000 0 -0.67 14 14
GAS2 -0.064 0.22 -10000 0 -0.53 50 50
positive regulation of apoptosis 0.035 0.051 -10000 0 -0.31 1 1
PRF1 -0.033 0.15 -10000 0 -0.76 15 15
Regulation of nuclear SMAD2/3 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
EP300 0.007 0.013 -10000 0 -10000 0 0
HSPA8 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.024 0.11 -10000 0 -0.53 14 14
AKT1 0.007 0.021 -10000 0 -10000 0 0
GSC -0.033 0.14 -10000 0 -0.47 5 5
NKX2-5 -0.3 0.3 -10000 0 -0.6 174 174
muscle cell differentiation 0.094 0.098 0.51 2 -10000 0 2
SMAD2-3/SMAD4/SP1 -0.008 0.036 -10000 0 -10000 0 0
SMAD4 0.016 0.028 -10000 0 -10000 0 0
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.008 0.04 -10000 0 -0.48 1 1
SMAD3/SMAD4/VDR 0.008 0.035 -10000 0 -10000 0 0
MYC 0.007 0.024 -10000 0 -10000 0 0
CDKN2B -0.09 0.41 -10000 0 -1.5 29 29
AP1 -0.054 0.14 -10000 0 -0.51 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.03 0.09 -10000 0 -0.44 4 4
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.045 0.17 -10000 0 -0.61 29 29
SMAD3/SMAD4/GR -0.004 0.018 -10000 0 -10000 0 0
GATA3 -0.035 0.16 -10000 0 -0.74 16 16
SKI/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
MEF2C/TIF2 -0.17 0.18 -10000 0 -0.66 18 18
endothelial cell migration -0.013 0.023 -10000 0 -10000 0 0
MAX 0 0 -10000 0 -10000 0 0
RBBP7 0 0 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
RUNX2 0 0 -10000 0 -10000 0 0
RUNX3 0 0 -10000 0 -10000 0 0
RUNX1 0 0 -10000 0 -10000 0 0
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 0 0 -10000 0 -10000 0 0
VDR -0.002 0.041 -10000 0 -0.76 1 1
CDKN1A 0.058 0.044 -10000 0 -10000 0 0
KAT2B 0.001 0.041 -10000 0 -0.76 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.044 0.11 -10000 0 -0.48 6 6
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 0.013 0.023 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.002 0.019 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.005 0.042 -10000 0 -0.5 2 2
SAP30 0 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.015 0.032 -10000 0 -10000 0 0
JUN -0.011 0.16 -10000 0 -0.49 1 1
SMAD3/SMAD4/IRF7 -0.004 0.036 -10000 0 -0.55 1 1
TFE3 0.017 0.001 -10000 0 -10000 0 0
COL1A2 0.006 0.049 -10000 0 -0.43 2 2
mesenchymal cell differentiation 0.002 0.018 -10000 0 -10000 0 0
DLX1 -0.35 0.3 -10000 0 -0.61 199 199
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.11 0.28 -10000 0 -0.75 55 55
SMAD3/SMAD4/Max -0.004 0.018 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0 0.02 -10000 0 -0.36 1 1
ZBTB17 0.006 0.019 -10000 0 -10000 0 0
LAMC1 0.047 0.031 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.002 0.019 -10000 0 -10000 0 0
IRF7 -0.003 0.041 -10000 0 -0.76 1 1
ESR1 -0.031 0.15 -10000 0 -0.76 14 14
HNF4A -0.012 0.085 -10000 0 -0.61 7 7
MEF2C -0.16 0.21 -10000 0 -0.68 18 18
SMAD2-3/SMAD4 -0.009 0.03 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.01 0.022 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.002 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.006 0.01 -10000 0 -10000 0 0
SKIL 0 0 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 -0.002 0.033 -10000 0 -0.61 1 1
GCN5L2 0.003 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.002 0.022 -10000 0 -10000 0 0
MSG1/HSC70 -0.003 0.039 -10000 0 -0.51 2 2
SMAD2 0.005 0.027 -10000 0 -10000 0 0
SMAD3 0.018 0.025 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.038 0.029 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.014 0.027 -10000 0 -0.42 1 1
NCOR1 0 0 -10000 0 -10000 0 0
NCOA2 -0.002 0.041 -10000 0 -0.76 1 1
NCOA1 0 0 -10000 0 -10000 0 0
MYOD/E2A -0.055 0.14 -10000 0 -0.44 43 43
SMAD2-3/SMAD4/SP1/MIZ-1 0.03 0.058 -10000 0 -10000 0 0
IFNB1 0.034 0.05 -10000 0 -0.5 2 2
SMAD3/SMAD4/MEF2C -0.17 0.18 -10000 0 -0.68 15 15
CITED1 -0.004 0.052 -10000 0 -0.68 2 2
SMAD2-3/SMAD4/ARC105 -0.007 0.024 -10000 0 -10000 0 0
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.012 0.15 -10000 0 -0.48 29 29
RUNX1-3/PEBPB2 0 0 -10000 0 -10000 0 0
SMAD7 -0.037 0.12 -10000 0 -1.1 1 1
MYC/MIZ-1 0.013 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4 0.032 0.073 0.29 6 -10000 0 6
IL10 0.02 0.13 -10000 0 -0.98 2 2
PIASy/HDAC complex 0.007 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.007 -10000 0 -10000 0 0
CDK2 0.005 0.01 -10000 0 -10000 0 0
IL5 0.017 0.11 -10000 0 -0.67 1 1
CDK4 0.004 0.035 -10000 0 -0.61 1 1
PIAS4 0.007 0.005 -10000 0 -10000 0 0
ATF3 -0.004 0.058 -10000 0 -0.76 2 2
SMAD3/SMAD4/SP1 0.001 0.028 -10000 0 -10000 0 0
FOXG1 -0.063 0.18 -10000 0 -0.61 36 36
FOXO3 0.016 0.028 -10000 0 -10000 0 0
FOXO1 0.016 0.028 -10000 0 -10000 0 0
FOXO4 0.016 0.028 -10000 0 -10000 0 0
heart looping -0.16 0.21 -10000 0 -0.67 18 18
CEBPB 0.009 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.22 0.19 -10000 0 -0.44 34 34
MYOD1 -0.075 0.2 -10000 0 -0.61 43 43
SMAD3/SMAD4/HNF4 -0.01 0.056 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.026 0.11 -10000 0 -0.52 15 15
SnoN/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.001 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.003 0.025 -10000 0 -10000 0 0
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.01 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.2 0.2 -10000 0 -0.65 21 21
ITGB5 0.056 0.037 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.1 0.21 -10000 0 -0.52 67 67
AR -0.15 0.3 -10000 0 -0.76 67 67
negative regulation of cell growth 0.002 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.05 0.13 -10000 0 -0.43 9 9
E2F5 0 0 -10000 0 -10000 0 0
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.03 0.086 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.018 0.094 -10000 0 -10000 0 0
TFDP1 -0.003 0.046 -10000 0 -0.61 2 2
SMAD3/SMAD4/AP1 -0.054 0.14 -10000 0 -0.51 1 1
SMAD3/SMAD4/RUNX2 -0.002 0.019 -10000 0 -10000 0 0
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.01 0.07 -9999 0 -0.5 7 7
EPHB2 -0.005 0.056 -9999 0 -0.61 3 3
Syndecan-2/TACI -0.012 0.073 -9999 0 -0.45 9 9
LAMA1 -0.19 0.28 -9999 0 -0.61 108 108
Syndecan-2/alpha2 ITGB1 -0.018 0.085 -9999 0 -0.42 15 15
HRAS 0 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.001 0.027 -9999 0 -0.5 1 1
ITGA5 0 0 -9999 0 -10000 0 0
BAX 0.035 0.025 -9999 0 -10000 0 0
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.001 0.024 -9999 0 -0.45 1 1
LAMA3 -0.031 0.15 -9999 0 -0.76 14 14
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.024 0.13 -9999 0 -0.76 11 11
Syndecan-2/MMP2 -0.006 0.053 -9999 0 -0.5 4 4
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0 0 -9999 0 -10000 0 0
dendrite morphogenesis -0.005 0.043 -9999 0 -0.4 4 4
Syndecan-2/GM-CSF -0.066 0.17 -9999 0 -0.5 46 46
determination of left/right symmetry 0.016 0.032 -9999 0 -0.57 1 1
Syndecan-2/PKC delta -0.001 0.026 -9999 0 -0.49 1 1
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 -0.034 0.16 -9999 0 -0.45 46 46
MAPK1 -0.034 0.16 -9999 0 -0.45 46 46
Syndecan-2/RACK1 -0.001 0.023 -9999 0 -0.42 1 1
NF1 0 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.016 0.032 -9999 0 -0.57 1 1
ITGA2 0 0 -9999 0 -10000 0 0
MAPK8 0.03 0.028 -9999 0 -0.49 1 1
Syndecan-2/alpha2/beta1 Integrin -0.096 0.14 -9999 0 -0.73 1 1
Syndecan-2/Kininogen -0.012 0.067 -9999 0 -0.38 11 11
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.032 0.023 -9999 0 -0.4 1 1
Syndecan-2/CASK/Protein 4.1 -0.001 0.024 -9999 0 -0.45 1 1
extracellular matrix organization -0.001 0.026 -9999 0 -0.49 1 1
actin cytoskeleton reorganization -0.01 0.069 -9999 0 -0.49 7 7
Syndecan-2/Caveolin-2/Ras -0.016 0.082 -9999 0 -0.45 12 12
Syndecan-2/Laminin alpha3 -0.021 0.1 -9999 0 -0.5 15 15
Syndecan-2/RasGAP -0.001 0.021 -9999 0 -0.4 1 1
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.005 0.043 -9999 0 -0.4 4 4
GO:0007205 0 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.001 0.021 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.016 0.11 -9999 0 -0.7 8 8
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin -0.001 0.026 -9999 0 -0.49 1 1
TGFB1 0 0 -9999 0 -10000 0 0
CASP3 0.028 0.025 -9999 0 -0.44 1 1
FN1 -0.013 0.099 -9999 0 -0.76 6 6
Syndecan-2/IL8 -0.018 0.083 -9999 0 -0.4 16 16
SDC2 0.016 0.032 -9999 0 -0.58 1 1
KNG1 -0.017 0.1 -9999 0 -0.61 10 10
Syndecan-2/Neurofibromin -0.001 0.026 -9999 0 -0.49 1 1
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.099 0.26 -9999 0 -0.76 45 45
Syndecan-2/TGFB1 -0.001 0.026 -9999 0 -0.49 1 1
Syndecan-2/Syntenin/PI-4-5-P2 -0.001 0.024 -9999 0 -0.45 1 1
Syndecan-2/Ezrin -0.001 0.024 -9999 0 -0.45 1 1
PRKACA 0.028 0.025 -9999 0 -0.44 1 1
angiogenesis -0.018 0.083 -9999 0 -0.39 16 16
MMP2 -0.007 0.07 -9999 0 -0.76 3 3
IL8 -0.027 0.13 -9999 0 -0.63 15 15
calcineurin-NFAT signaling pathway -0.012 0.073 -9999 0 -0.45 9 9
FAS signaling pathway (CD95)

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
SPTAN1 0.001 0.015 -10000 0 -10000 0 0
RFC1 0.001 0.015 -10000 0 -10000 0 0
PRKDC 0.001 0.015 -10000 0 -10000 0 0
RIPK1 0 0.002 -10000 0 -10000 0 0
CASP7 -0.016 0.033 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.019 0.072 0.25 3 -0.34 13 16
MAP2K4 -0.022 0.14 -10000 0 -0.52 3 3
mol:ceramide -0.012 0.11 -10000 0 -0.43 13 13
GSN 0.001 0.015 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.029 0.087 -10000 0 -0.42 13 13
FAS 0.009 0.005 -10000 0 -10000 0 0
BID 0.001 0.017 0.31 1 -10000 0 1
MAP3K1 -0.004 0.082 -10000 0 -0.28 3 3
MAP3K7 0.008 0.004 -10000 0 -10000 0 0
RB1 0.001 0.015 -10000 0 -10000 0 0
CFLAR 0 0.002 -10000 0 -10000 0 0
HGF/MET -0.096 0.2 -10000 0 -0.51 66 66
ARHGDIB 0.001 0.015 -10000 0 -10000 0 0
FADD 0.009 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.001 0.015 -10000 0 -10000 0 0
NFKB1 -0.046 0.084 -10000 0 -10000 0 0
MAPK8 -0.05 0.2 -10000 0 -0.43 72 72
DFFA 0.001 0.015 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.001 0.015 -10000 0 -10000 0 0
FAS/FADD/MET -0.004 0.043 -10000 0 -0.46 3 3
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.001 0.041 -10000 0 -0.76 1 1
FAF1 0.009 0.005 -10000 0 -10000 0 0
PARP1 0.001 0.015 -10000 0 -10000 0 0
DFFB 0.001 0.015 -10000 0 -10000 0 0
CHUK -0.04 0.074 -10000 0 -10000 0 0
FASLG -0.02 0.15 -10000 0 -0.76 13 13
FAS/FADD -0.001 0.003 -10000 0 -10000 0 0
HGF -0.13 0.29 -10000 0 -0.76 61 61
LMNA 0.001 0.013 -10000 0 -10000 0 0
CASP6 0.001 0.015 -10000 0 -10000 0 0
CASP10 0.007 0.041 -10000 0 -0.76 1 1
CASP3 0.001 0.017 -10000 0 -10000 0 0
PTPN13 -0.009 0.081 -10000 0 -0.76 4 4
CASP8 0.001 0.023 0.43 1 -10000 0 1
IL6 -0.25 0.55 -10000 0 -1.3 73 73
MET -0.006 0.066 -10000 0 -0.71 3 3
ICAD/CAD 0.001 0.014 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.012 0.11 -10000 0 -0.43 13 13
activation of caspase activity by cytochrome c 0.001 0.017 0.31 1 -10000 0 1
PAK2 0.001 0.014 -10000 0 -10000 0 0
BCL2 0.001 0.033 -10000 0 -0.61 1 1
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.028 0.12 -9999 0 -0.49 20 20
MAP4K1 -0.007 0.07 -9999 0 -0.76 3 3
MAP3K8 -0.007 0.07 -9999 0 -0.76 3 3
PRKCB -0.024 0.13 -9999 0 -0.76 11 11
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.021 0.09 -9999 0 -0.69 2 2
JUN 0.008 0.13 -9999 0 -0.7 11 11
MAP3K7 0.021 0.09 -9999 0 -0.69 2 2
GRAP2 -0.035 0.16 -9999 0 -0.76 16 16
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.027 0.095 -9999 0 -0.64 3 3
LAT 0 0 -9999 0 -10000 0 0
LCP2 -0.007 0.07 -9999 0 -0.76 3 3
MAPK8 0.001 0.14 -9999 0 -0.75 11 11
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.02 0.087 -9999 0 -0.73 2 2
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.027 0.11 -9999 0 -0.46 20 20
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.081 0.24 -9999 0 -0.76 37 37
GNB1/GNG2 -0.042 0.086 -9999 0 -0.57 2 2
mol:DAG -0.001 0.095 -9999 0 -0.51 2 2
PLCG1 -0.001 0.098 -9999 0 -0.53 2 2
YES1 -0.013 0.098 -9999 0 -0.48 1 1
FZD3 0 0 -9999 0 -10000 0 0
FZD6 0 0 -9999 0 -10000 0 0
G protein -0.039 0.08 -9999 0 -0.54 2 2
MAP3K7 -0.018 0.14 -9999 0 -0.53 8 8
mol:Ca2+ -0.001 0.093 -9999 0 -0.5 2 2
mol:IP3 -0.001 0.095 -9999 0 -0.51 2 2
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.027 0.15 -9999 0 -0.58 8 8
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.047 0.091 -9999 0 -0.42 2 2
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.013 0.098 -9999 0 -0.48 1 1
GO:0007205 0 0.094 -9999 0 -0.61 1 1
WNT6 -0.096 0.22 -9999 0 -0.61 55 55
WNT4 -0.014 0.095 -9999 0 -0.67 7 7
NFAT1/CK1 alpha -0.073 0.13 -9999 0 -0.58 5 5
GNG2 -0.004 0.058 -9999 0 -0.76 2 2
WNT5A -0.013 0.089 -9999 0 -0.63 7 7
WNT11 -0.041 0.16 -9999 0 -0.71 20 20
CDC42 -0.005 0.094 -9999 0 -0.45 1 1
Hedgehog signaling events mediated by Gli proteins

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.007 0.006 -9999 0 -10000 0 0
GNB1/GNG2 -0.004 0.043 -9999 0 -0.46 3 3
forebrain development -0.089 0.14 -9999 0 -0.46 6 6
GNAO1 -0.001 0.062 -9999 0 -0.66 3 3
SMO/beta Arrestin2 -0.001 0.025 -9999 0 -0.46 1 1
SMO 0.004 0.034 -9999 0 -0.62 1 1
ARRB2 0.005 0.006 -9999 0 -10000 0 0
GLI3/SPOP 0.045 0.018 -9999 0 -10000 0 0
mol:GTP -0.003 0.004 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.005 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.004 -9999 0 -10000 0 0
GNAI1 0.003 0.042 -9999 0 -0.76 1 1
XPO1 0.006 0.007 -9999 0 -10000 0 0
GLI1/Su(fu) -0.11 0.11 -9999 0 -0.72 1 1
SAP30 0.007 0.006 -9999 0 -10000 0 0
mol:GDP 0.004 0.034 -9999 0 -0.62 1 1
MIM/GLI2A -0.033 0.051 -9999 0 -10000 0 0
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.005 0.005 -9999 0 -10000 0 0
GLI2 0.039 0.02 -9999 0 -10000 0 0
GLI3 0.041 0.019 -9999 0 -10000 0 0
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.006 0.006 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.004 0.058 -9999 0 -0.76 2 2
Gi family/GTP 0.001 0.054 -9999 0 -0.42 1 1
SIN3B 0.007 0.006 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
GLI3/Su(fu) -0.001 0.01 -9999 0 -10000 0 0
GLI2/Su(fu) 0.025 0.033 -9999 0 -10000 0 0
FOXA2 -0.62 0.6 -9999 0 -1.2 178 178
neural tube patterning -0.089 0.14 -9999 0 -0.46 6 6
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0 0.009 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 -0.033 0.05 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.089 0.14 -9999 0 -0.46 6 6
SUFU 0.012 0.018 -9999 0 -10000 0 0
LGALS3 0 0 -9999 0 -10000 0 0
catabolic process -0.001 0.013 -9999 0 -10000 0 0
GLI3A/CBP 0.006 0.028 -9999 0 -10000 0 0
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.091 0.15 -9999 0 -0.48 6 6
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.007 0.006 -9999 0 -10000 0 0
Su(fu)/Galectin3 0 0.009 -9999 0 -10000 0 0
GNAZ -0.006 0.092 -9999 0 -0.76 5 5
RBBP4 0.006 0.006 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP 0.041 0.019 -9999 0 -10000 0 0
STK36 0.006 0.007 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.008 0.054 -9999 0 -0.72 1 1
PTCH1 -0.082 0.17 -9999 0 -1.2 3 3
MIM/GLI1 -0.24 0.29 -9999 0 -0.52 178 178
CREBBP 0.006 0.028 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.031 0.03 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.001 0.017 -10000 0 -0.32 1 1
epithelial cell differentiation -0.001 0.023 -10000 0 -0.42 1 1
CYFIP2 -0.02 0.12 -10000 0 -0.76 9 9
ENAH 0.058 0.032 -10000 0 -10000 0 0
EGFR -0.025 0.13 -10000 0 -0.68 13 13
EPHA2 -0.007 0.07 -10000 0 -0.76 3 3
MYO6 -0.001 0.021 -10000 0 -0.4 1 1
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.079 -10000 0 -0.5 9 9
AQP5 -0.17 0.26 -10000 0 -0.56 105 105
CTNND1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.021 -10000 0 -0.39 1 1
regulation of calcium-dependent cell-cell adhesion -0.12 0.18 -10000 0 -0.4 103 103
EGF -0.019 0.12 -10000 0 -0.74 9 9
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.084 0.2 -10000 0 -0.56 52 52
cortical microtubule organization -0.001 0.023 -10000 0 -0.42 1 1
GO:0000145 0.033 0.022 -10000 0 -0.37 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.001 0.023 -10000 0 -0.42 1 1
MLLT4 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.004 0.035 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.004 0.041 -10000 0 -0.45 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.044 0.022 -10000 0 -10000 0 0
PVRL2 0 0 -10000 0 -10000 0 0
ZYX -0.001 0.021 -10000 0 -0.4 1 1
ARF6/GTP -0.004 0.038 -10000 0 -0.41 3 3
CDH1 -0.002 0.041 -10000 0 -0.76 1 1
EGFR/EGFR/EGF/EGF -0.023 0.092 -10000 0 -0.78 1 1
RhoA/GDP -0.001 0.021 -10000 0 -10000 0 0
actin cytoskeleton organization 0.039 0.022 -10000 0 -10000 0 0
IGF-1R heterotetramer 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
IGF1R 0 0 -10000 0 -10000 0 0
IGF1 -0.013 0.096 -10000 0 -0.73 6 6
DIAPH1 -0.017 0.1 -10000 0 -0.65 9 9
Wnt receptor signaling pathway 0.001 0.023 0.42 1 -10000 0 1
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.004 0.035 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL 0.04 0.023 -10000 0 -10000 0 0
EFNA1 0 0 -10000 0 -10000 0 0
LPP 0.04 0.022 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.004 0.041 -10000 0 -10000 0 0
SEC6/SEC8 -0.001 0.019 -10000 0 -10000 0 0
MGAT3 -0.12 0.19 -10000 0 -0.41 103 103
HGF/MET -0.072 0.15 -10000 0 -0.78 1 1
HGF -0.13 0.29 -10000 0 -0.76 61 61
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.001 0.017 -10000 0 -0.32 1 1
actin cable formation 0.07 0.033 -10000 0 -10000 0 0
KIAA1543 0.04 0.022 -10000 0 -10000 0 0
KIFC3 -0.001 0.021 -10000 0 -0.4 1 1
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.001 0.021 -10000 0 -0.4 1 1
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.001 0.023 -10000 0 -0.42 1 1
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.001 0.021 -10000 0 -0.4 1 1
PIP5K1C -0.001 0.021 -10000 0 -0.4 1 1
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.003 0.031 -10000 0 -10000 0 0
adherens junction assembly 0.054 0.022 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.007 0.052 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.006 0.066 -10000 0 -0.71 3 3
PLEKHA7 -0.001 0.021 -10000 0 -0.4 1 1
mol:GTP -0.004 0.041 -10000 0 -0.44 3 3
establishment of epithelial cell apical/basal polarity -0.001 0.018 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.001 0.017 -10000 0 -0.32 1 1
regulation of cell-cell adhesion 0.039 0.022 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.001 0.017 -10000 0 -0.32 1 1
Syndecan-4-mediated signaling 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
PTK2 0.011 0.085 -9999 0 -0.62 6 6
Syndecan-4/Syndesmos 0.006 0.079 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.047 0.11 -9999 0 -0.55 3 3
Syndecan-4/ADAM12 -0.075 0.16 -9999 0 -0.46 14 14
CCL5 -0.011 0.091 -9999 0 -0.76 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.004 0.046 -9999 0 -0.61 2 2
ADAM12 -0.16 0.26 -9999 0 -0.61 90 90
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.016 0.039 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.091 0.17 -9999 0 -0.5 9 9
Syndecan-4/CXCL12/CXCR4 -0.05 0.11 -9999 0 -0.58 3 3
Syndecan-4/Laminin alpha3 -0.011 0.12 -9999 0 -0.61 6 6
MDK -0.017 0.1 -9999 0 -0.61 10 10
Syndecan-4/FZD7 0.005 0.08 -9999 0 -10000 0 0
Syndecan-4/Midkine -0.003 0.098 -9999 0 -0.62 1 1
FZD7 -0.002 0.032 -9999 0 -0.61 1 1
Syndecan-4/FGFR1/FGF -0.038 0.1 -9999 0 -0.6 5 5
THBS1 0 0 -9999 0 -10000 0 0
integrin-mediated signaling pathway -0.002 0.094 -9999 0 -0.67 1 1
positive regulation of MAPKKK cascade -0.047 0.11 -9999 0 -0.55 3 3
Syndecan-4/TACI -0.003 0.096 -9999 0 -10000 0 0
CXCR4 0 0 -9999 0 -10000 0 0
cell adhesion -0.004 0.054 -9999 0 -0.37 7 7
Syndecan-4/Dynamin 0.006 0.079 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.006 0.079 -9999 0 -10000 0 0
Syndecan-4/GIPC 0.006 0.079 -9999 0 -10000 0 0
Syndecan-4/RANTES 0 0.091 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.19 0.28 -9999 0 -0.61 108 108
LAMA3 -0.031 0.15 -9999 0 -0.76 14 14
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.007 0.044 -9999 0 -0.69 1 1
Syndecan-4/alpha-Actinin 0.006 0.079 -9999 0 -10000 0 0
TFPI -0.05 0.19 -9999 0 -0.76 23 23
F2 -0.014 0.1 -9999 0 -0.6 10 10
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.097 0.18 -9999 0 -0.7 7 7
ACTN1 0 0 -9999 0 -10000 0 0
TNC -0.017 0.1 -9999 0 -0.64 9 9
Syndecan-4/CXCL12 -0.023 0.13 -9999 0 -0.61 3 3
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.053 0.19 -9999 0 -0.76 24 24
TNFRSF13B -0.016 0.11 -9999 0 -0.7 8 8
FGF2 -0.026 0.14 -9999 0 -0.76 12 12
FGFR1 -0.004 0.058 -9999 0 -0.76 2 2
Syndecan-4/PI-4-5-P2 -0.001 0.079 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.01 0.098 -9999 0 -0.75 6 6
cell migration -0.006 0.016 -9999 0 -10000 0 0
PRKCD 0.002 0.007 -9999 0 -10000 0 0
vasculogenesis 0.006 0.077 -9999 0 -10000 0 0
SDC4 0 0.083 -9999 0 -10000 0 0
Syndecan-4/Tenascin C -0.003 0.096 -9999 0 -0.7 1 1
Syndecan-4/PI-4-5-P2/PKC alpha -0.012 0.031 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.006 0.079 -9999 0 -10000 0 0
MMP9 -0.048 0.18 -9999 0 -0.61 33 33
Rac1/GTP -0.004 0.055 -9999 0 -0.38 7 7
cytoskeleton organization 0.006 0.077 -9999 0 -10000 0 0
GIPC1 0 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.022 0.13 -9999 0 -0.63 3 3
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.006 0.061 -9999 0 -0.66 3 3
CDC42/GTP -0.031 0.091 -9999 0 -0.48 3 3
PLCG1 0.001 0.11 -9999 0 -0.5 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.03 0.09 -9999 0 -0.47 3 3
S1PR5 -0.006 0.061 -9999 0 -0.66 3 3
S1PR4 -0.068 0.22 -9999 0 -0.76 31 31
MAPK3 0.001 0.11 -9999 0 -0.5 3 3
MAPK1 0.001 0.11 -9999 0 -0.5 3 3
S1P/S1P5/Gi -0.008 0.044 -9999 0 -10000 0 0
GNAI1 -0.002 0.041 -9999 0 -0.76 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.039 -9999 0 -0.42 3 3
RHOA -0.012 0.13 -9999 0 -0.42 31 31
S1P/S1P4/Gi -0.035 0.1 -9999 0 -0.33 32 32
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.011 0.091 -9999 0 -0.76 5 5
S1P/S1P4/G12/G13 -0.041 0.13 -9999 0 -0.46 31 31
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.067 0.14 -9999 0 -0.63 4 4
MAP3K8 0.002 0.071 -9999 0 -0.76 3 3
FOS -0.003 0.11 -9999 0 -0.52 4 4
PRKCA 0.007 0.042 -9999 0 -0.77 1 1
PTPN7 0.006 0.053 -9999 0 -0.68 2 2
HRAS 0 0 -9999 0 -10000 0 0
PRKCB -0.015 0.14 -9999 0 -0.76 11 11
NRAS 0 0 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.007 0.066 -9999 0 -0.62 1 1
MAP2K1 0.005 0.11 -9999 0 -0.51 12 12
ELK1 -0.002 0.004 -9999 0 -10000 0 0
BRAF -0.022 0.093 -9999 0 -0.51 12 12
mol:GTP -0.001 0.002 -9999 0 -0.006 55 55
MAPK1 0.007 0.066 -9999 0 -0.62 1 1
RAF1 -0.022 0.093 -9999 0 -0.51 12 12
KRAS 0 0 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.002 0.041 -10000 0 -0.76 1 1
Jak2/Leptin Receptor -0.023 0.093 -10000 0 -0.39 17 17
PTP1B/AKT1 -0.008 0.03 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.022 0.044 -10000 0 -0.32 2 2
EGFR -0.015 0.13 -10000 0 -0.68 13 13
EGF/EGFR -0.027 0.1 -10000 0 -0.5 13 13
CSF1 0 0 -10000 0 -10000 0 0
AKT1 0.01 0.003 -10000 0 -10000 0 0
INSR 0.01 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.002 0.1 -10000 0 -0.4 10 10
Insulin Receptor/Insulin -0.006 0.023 -10000 0 -10000 0 0
HCK -0.004 0.058 -10000 0 -0.76 2 2
CRK 0 0 -10000 0 -10000 0 0
TYK2 0.028 0.042 -10000 0 -10000 0 0
EGF -0.009 0.12 -10000 0 -0.75 9 9
YES1 0 0 -10000 0 -10000 0 0
CAV1 -0.032 0.12 -10000 0 -0.49 11 11
TXN 0.008 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.008 0.038 -10000 0 -0.48 1 1
cell migration -0.022 0.044 0.32 2 -10000 0 2
STAT3 0.006 0.005 -10000 0 -10000 0 0
PRLR -0.035 0.15 -10000 0 -0.65 19 19
ITGA2B -0.028 0.14 -10000 0 -0.76 13 13
CSF1R -0.011 0.091 -10000 0 -0.76 5 5
Prolactin Receptor/Prolactin -0.035 0.12 -10000 0 -0.47 26 26
FGR -0.055 0.2 -10000 0 -0.76 25 25
PTP1B/p130 Cas 0.026 0.041 -10000 0 -10000 0 0
Crk/p130 Cas -0.007 0.029 -10000 0 -10000 0 0
DOK1 0.032 0.043 -10000 0 -0.33 1 1
JAK2 0.014 0.049 -10000 0 -0.32 1 1
Jak2/Leptin Receptor/Leptin -0.052 0.09 -10000 0 -0.52 2 2
PIK3R1 0 0 -10000 0 -10000 0 0
PTPN1 0.022 0.045 -10000 0 -0.32 2 2
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.044 0.16 -10000 0 -0.61 25 25
SRC 0.023 0.018 -10000 0 -10000 0 0
ITGB3 -0.013 0.099 -10000 0 -0.76 6 6
CAT1/PTP1B 0.016 0.12 -10000 0 -0.47 10 10
CAPN1 0.007 0.005 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.019 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.047 0.084 -10000 0 -0.55 2 2
negative regulation of transcription 0.014 0.048 -10000 0 -0.32 1 1
FCGR2A -0.013 0.099 -10000 0 -0.76 6 6
FER 0.008 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.032 0.13 -10000 0 -0.58 19 19
BLK -0.036 0.16 -10000 0 -0.7 18 18
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.007 0.005 -10000 0 -10000 0 0
LEPR -0.034 0.16 -10000 0 -0.76 17 17
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 0 0.13 -10000 0 -0.56 12 12
PRL -0.012 0.085 -10000 0 -0.61 7 7
SOCS3 0.001 0.11 -10000 0 -1.4 2 2
SPRY2 0 0.072 -10000 0 -0.77 3 3
Insulin Receptor/Insulin/IRS1 -0.001 0.027 -10000 0 -0.51 1 1
CSF1/CSF1R -0.013 0.057 -10000 0 -0.42 5 5
Ras protein signal transduction 0.006 0.014 -10000 0 -10000 0 0
IRS1 -0.002 0.041 -10000 0 -0.76 1 1
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.12 0.25 -10000 0 -0.6 71 71
STAT5B 0.021 0.043 -10000 0 -10000 0 0
STAT5A 0.02 0.042 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.024 0.05 -10000 0 -0.49 1 1
CSN2 -0.011 0.039 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
LAT 0.014 0.069 -10000 0 -0.48 6 6
YBX1 0.012 0.008 -10000 0 -10000 0 0
LCK -0.002 0.041 -10000 0 -0.76 1 1
SHC1 0 0 -10000 0 -10000 0 0
NOX4 0.005 0.033 -10000 0 -0.6 1 1
LPA receptor mediated 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
GNB1/GNG2 -0.006 0.071 -9999 0 -0.82 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.018 0.053 -9999 0 -10000 0 0
AP1 -0.072 0.16 -9999 0 -0.87 3 3
mol:PIP3 -0.021 0.084 -9999 0 -0.65 2 2
AKT1 -0.004 0.043 -9999 0 -0.71 1 1
PTK2B 0.018 0.039 -9999 0 -0.34 2 2
RHOA 0.029 0.017 -9999 0 -10000 0 0
PIK3CB 0 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0 0.088 -9999 0 -0.46 3 3
MAGI3 0 0.001 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.011 0.062 -9999 0 -0.43 5 5
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.068 -9999 0 -0.43 6 6
NF kappa B1 p50/RelA -0.025 0.074 -9999 0 -0.66 1 1
endothelial cell migration 0.016 0.094 -9999 0 -0.97 3 3
ADCY4 0.014 0.11 -9999 0 -0.65 5 5
ADCY5 0.014 0.096 -9999 0 -0.63 3 3
ADCY6 0.032 0.077 -9999 0 -0.63 3 3
ADCY7 0.031 0.081 -9999 0 -0.9 2 2
ADCY1 0.031 0.076 -9999 0 -0.76 2 2
ADCY2 0.016 0.088 -9999 0 -0.8 2 2
ADCY3 0.032 0.075 -9999 0 -0.76 2 2
ADCY8 -0.041 0.13 -9999 0 -0.82 3 3
ADCY9 0.031 0.082 -9999 0 -0.72 3 3
GSK3B 0.025 0.037 -9999 0 -0.38 1 1
arachidonic acid secretion 0.036 0.072 -9999 0 -0.73 2 2
GNG2 -0.004 0.057 -9999 0 -0.76 2 2
TRIP6 0 0.004 -9999 0 -10000 0 0
GNAO1 0.017 0.07 -9999 0 -0.59 4 4
HRAS 0 0 -9999 0 -10000 0 0
NFKBIA 0.017 0.081 -9999 0 -10000 0 0
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.005 0.07 -9999 0 -0.92 2 2
JUN 0 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.005 0.047 -9999 0 -0.5 3 3
TIAM1 -0.006 0.083 -9999 0 -1.1 2 2
PIK3R1 0 0.001 -9999 0 -10000 0 0
mol:IP3 -0.001 0.09 -9999 0 -0.47 3 3
PLCB3 0.021 0.045 -9999 0 -0.45 3 3
FOS -0.12 0.28 -9999 0 -0.76 55 55
positive regulation of mitosis 0.036 0.072 -9999 0 -0.73 2 2
LPA/LPA1-2-3 -0.014 0.076 -9999 0 -0.51 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.026 0.05 -9999 0 -0.52 1 1
GNAZ 0.013 0.08 -9999 0 -0.55 6 6
EGFR/PI3K-beta/Gab1 -0.022 0.088 -9999 0 -0.69 2 2
positive regulation of dendritic cell cytokine production -0.014 0.076 -9999 0 -0.51 5 5
LPA/LPA2/MAGI-3 -0.001 0.007 -9999 0 -10000 0 0
ARHGEF1 -0.003 0.043 -9999 0 -0.72 1 1
GNAI2 0.021 0.052 -9999 0 -0.83 1 1
GNAI3 0.021 0.052 -9999 0 -0.83 1 1
GNAI1 0.02 0.073 -9999 0 -1.3 1 1
LPA/LPA3 -0.014 0.081 -9999 0 -0.5 9 9
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.005 0.057 -9999 0 -0.55 3 3
HB-EGF/EGFR -0.078 0.17 -9999 0 -0.44 62 62
HBEGF -0.056 0.18 -9999 0 -0.49 52 52
mol:DAG -0.001 0.09 -9999 0 -0.47 3 3
cAMP biosynthetic process 0.018 0.084 -9999 0 -0.73 3 3
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
GNB1 0 0.001 -9999 0 -10000 0 0
LYN 0.017 0.081 -9999 0 -10000 0 0
GNAQ -0.01 0.055 -9999 0 -0.39 5 5
LPAR2 0 0.001 -9999 0 -10000 0 0
LPAR3 -0.017 0.11 -9999 0 -0.67 9 9
LPAR1 -0.004 0.053 -9999 0 -0.96 1 1
IL8 -0.02 0.14 -9999 0 -0.44 17 17
PTK2 0.021 0.077 -9999 0 -0.48 5 5
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.011 0.062 -9999 0 -0.43 5 5
EGFR -0.019 0.13 -9999 0 -0.68 13 13
PLCG1 -0.015 0.089 -9999 0 -0.38 8 8
PLD2 0.021 0.077 -9999 0 -0.48 5 5
G12/G13 -0.004 0.046 -9999 0 -0.77 1 1
PI3K-beta -0.005 0.053 -9999 0 -0.89 1 1
cell migration 0.002 0.034 -9999 0 -0.26 1 1
SLC9A3R2 -0.007 0.07 -9999 0 -0.76 3 3
PXN 0.026 0.051 -9999 0 -0.53 1 1
HRAS/GTP -0.009 0.07 -9999 0 -0.77 2 2
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.058 0.18 -9999 0 -0.6 33 33
PRKCE 0.005 0.058 -9999 0 -0.76 2 2
PRKCD 0.007 0.086 -9999 0 -0.48 2 2
Gi(beta/gamma) -0.01 0.082 -9999 0 -0.89 2 2
mol:LPA -0.001 0.016 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.002 0.064 -9999 0 -0.66 1 1
MAPKKK cascade 0.036 0.072 -9999 0 -0.73 2 2
contractile ring contraction involved in cytokinesis 0.029 0.017 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.1 0.17 -9999 0 -0.4 84 84
GNA15 -0.01 0.057 -9999 0 -0.41 5 5
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT 0.024 0.07 -9999 0 -0.44 6 6
GNA11 -0.009 0.051 -9999 0 -0.39 4 4
Rac1/GTP -0.005 0.074 -9999 0 -0.98 2 2
MMP2 0.016 0.094 -9999 0 -0.98 3 3
IL2 signaling events mediated by STAT5

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
GAB2 -0.007 0.12 -9999 0 -0.76 8 8
ELF1 0.015 0.023 -9999 0 -10000 0 0
CCNA2 -0.17 0.27 -9999 0 -0.61 99 99
PIK3CA 0.011 0.001 -9999 0 -10000 0 0
JAK3 0.011 0.001 -9999 0 -10000 0 0
PIK3R1 0.011 0.001 -9999 0 -10000 0 0
JAK1 0.011 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.06 0.063 -9999 0 -0.81 1 1
SHC1 0.011 0.001 -9999 0 -10000 0 0
SP1 -0.001 0.02 -9999 0 -0.38 1 1
IL2RA 0.024 0.046 -9999 0 -0.46 3 3
IL2RB 0.009 0.041 -9999 0 -0.76 1 1
SOS1 0.011 0.001 -9999 0 -10000 0 0
IL2RG 0.002 0.082 -9999 0 -0.76 4 4
G1/S transition of mitotic cell cycle -0.022 0.1 -9999 0 -0.72 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
CCND2 0.024 0.054 -9999 0 -0.97 1 1
LCK 0.009 0.041 -9999 0 -0.76 1 1
GRB2 0.011 0.001 -9999 0 -10000 0 0
IL2 0.006 0.005 -9999 0 -10000 0 0
CDK6 -0.003 0.046 -9999 0 -0.61 2 2
CCND3 0.065 0.055 -9999 0 -0.65 1 1
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.021 0.086 -10000 0 -0.48 5 5
IKBKB 0.019 0.046 -10000 0 -0.27 1 1
AKT1 0.007 0.083 -10000 0 -0.28 7 7
IKBKG 0.022 0.047 -10000 0 -0.28 2 2
CALM1 -0.001 0.08 -10000 0 -0.5 5 5
PIK3CA 0 0 -10000 0 -10000 0 0
MAP3K1 0.009 0.13 -10000 0 -0.68 7 7
MAP3K7 0 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.085 0.23 3 -0.54 5 8
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.004 0.086 0.18 1 -0.28 4 5
LYN 0 0.002 -10000 0 -10000 0 0
BLNK -0.002 0.041 -10000 0 -0.76 1 1
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.026 0.12 -10000 0 -0.53 17 17
CD22 -0.072 0.21 -10000 0 -0.61 34 34
CAMK2G 0.006 0.075 -10000 0 -0.45 5 5
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D -0.006 0.07 -10000 0 -0.76 3 3
SHC/GRB2/SOS1 -0.017 0.076 -10000 0 -0.73 1 1
GO:0007205 -0.009 0.087 0.23 3 -0.55 5 8
SYK 0 0.001 -10000 0 -10000 0 0
ELK1 -0.001 0.082 -10000 0 -0.51 5 5
NFATC1 0.001 0.11 -10000 0 -0.53 8 8
B-cell antigen/BCR complex -0.026 0.12 -10000 0 -0.53 17 17
PAG1/CSK -0.003 0.044 -10000 0 -0.58 2 2
NFKBIB 0.016 0.018 0.08 1 -10000 0 1
HRAS 0.006 0.078 -10000 0 -0.49 5 5
NFKBIA 0.016 0.017 0.08 1 -10000 0 1
NF-kappa-B/RelA/I kappa B beta 0.019 0.015 -10000 0 -10000 0 0
RasGAP/Csk -0.022 0.1 -10000 0 -0.83 3 3
mol:GDP -0.011 0.084 -10000 0 -0.53 5 5
PTEN 0 0 -10000 0 -10000 0 0
CD79B -0.004 0.058 -10000 0 -0.76 2 2
NF-kappa-B/RelA/I kappa B alpha 0.019 0.015 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.004 0.13 -10000 0 -0.57 9 9
PIK3R1 0 0 -10000 0 -10000 0 0
mol:IP3 -0.018 0.086 0.23 3 -0.56 5 8
CSK 0 0 -10000 0 -10000 0 0
FOS -0.058 0.17 -10000 0 -0.41 57 57
CHUK 0.022 0.047 -10000 0 -0.29 1 1
IBTK 0 0.001 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.016 0.066 -10000 0 -0.57 3 3
PTPN6 -0.067 0.19 -10000 0 -0.78 16 16
RELA 0 0.001 -10000 0 -10000 0 0
BCL2A1 0.017 0.022 -10000 0 -0.13 6 6
VAV2 -0.052 0.16 -10000 0 -0.65 15 15
ubiquitin-dependent protein catabolic process 0.02 0.017 0.083 1 -10000 0 1
BTK -0.081 0.29 -10000 0 -1.1 25 25
CD19 -0.058 0.16 -10000 0 -0.66 15 15
MAP4K1 -0.007 0.07 -10000 0 -0.76 3 3
CD72 0 0 -10000 0 -10000 0 0
PAG1 -0.004 0.058 -10000 0 -0.76 2 2
MAPK14 0.017 0.11 -10000 0 -0.58 6 6
SH3BP5 -0.009 0.081 -10000 0 -0.76 4 4
PIK3AP1 0 0.098 0.26 3 -0.54 7 10
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.018 0.093 -10000 0 -0.52 9 9
RAF1 0.013 0.073 -10000 0 -0.54 3 3
RasGAP/p62DOK/SHIP -0.024 0.1 -10000 0 -0.8 3 3
CD79A -0.031 0.14 -10000 0 -0.67 16 16
re-entry into mitotic cell cycle -0.004 0.085 0.18 1 -0.28 4 5
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.025 0.062 -10000 0 -0.5 2 2
MAPK1 0.025 0.062 -10000 0 -0.5 2 2
CD72/SHP1 -0.061 0.17 -10000 0 -0.7 16 16
NFKB1 0 0.001 -10000 0 -10000 0 0
MAPK8 0.017 0.11 -10000 0 -0.58 6 6
actin cytoskeleton organization -0.005 0.14 -10000 0 -0.71 7 7
NF-kappa-B/RelA 0.043 0.029 0.16 1 -10000 0 1
Calcineurin -0.014 0.059 -10000 0 -0.59 2 2
PI3K -0.06 0.14 -10000 0 -0.54 15 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.016 0.083 0.26 3 -0.54 5 8
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.032 0.14 -10000 0 -0.96 6 6
DAPP1 -0.035 0.16 -10000 0 -1.2 5 5
cytokine secretion 0.002 0.11 -10000 0 -0.49 8 8
mol:DAG -0.018 0.086 0.23 3 -0.56 5 8
PLCG2 0 0.001 -10000 0 -10000 0 0
MAP2K1 0.019 0.068 -10000 0 -0.57 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.026 0.12 -10000 0 -0.51 18 18
mol:PI-3-4-5-P3 -0.044 0.097 -10000 0 -0.42 8 8
ETS1 0.005 0.093 -10000 0 -0.47 9 9
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.02 0.09 -10000 0 -0.46 9 9
B-cell antigen/BCR complex/LYN -0.036 0.15 -10000 0 -0.8 8 8
MALT1 0 0.001 -10000 0 -10000 0 0
TRAF6 0.001 0.003 -10000 0 -10000 0 0
RAC1 -0.007 0.15 -10000 0 -0.78 7 7
B-cell antigen/BCR complex/LYN/SYK -0.064 0.18 -10000 0 -0.72 16 16
CARD11 -0.004 0.089 -10000 0 -0.52 6 6
FCGR2B -0.007 0.07 -10000 0 -0.76 3 3
PPP3CA 0 0 -10000 0 -10000 0 0
BCL10 0 0.001 -10000 0 -10000 0 0
IKK complex 0.018 0.024 -10000 0 -10000 0 0
PTPRC -0.046 0.18 -10000 0 -0.76 21 21
PDPK1 -0.029 0.066 -10000 0 -0.28 6 6
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.011 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.029 0.11 0.45 22 -10000 0 22
KIRREL 0.001 0.072 -10000 0 -0.76 3 3
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.029 0.11 -10000 0 -0.45 22 22
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.022 0.083 -10000 0 -0.44 3 3
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.012 0.047 -10000 0 -0.34 3 3
FYN -0.003 0.078 -10000 0 -0.42 3 3
mol:Ca2+ -0.022 0.082 -10000 0 -0.44 3 3
mol:DAG -0.022 0.082 -10000 0 -0.44 3 3
NPHS2 -0.002 0.047 -10000 0 -0.6 2 2
mol:IP3 -0.022 0.082 -10000 0 -0.44 3 3
regulation of endocytosis -0.018 0.068 -10000 0 -0.39 3 3
Nephrin/NEPH1/podocin/Cholesterol -0.023 0.085 -10000 0 -0.45 3 3
establishment of cell polarity -0.029 0.11 -10000 0 -0.45 22 22
Nephrin/NEPH1/podocin/NCK1-2 -0.02 0.074 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 -0.018 0.068 -10000 0 -0.39 3 3
NPHS1 -0.026 0.14 -10000 0 -0.6 19 19
Nephrin/NEPH1/podocin -0.02 0.074 -10000 0 -0.42 3 3
TJP1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.022 0.083 -10000 0 -0.44 3 3
CD2AP 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.022 0.083 -10000 0 -0.44 3 3
GRB2 0 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.02 0.13 -10000 0 -0.52 15 15
cytoskeleton organization -0.015 0.059 -10000 0 -0.42 3 3
Nephrin/NEPH1 -0.021 0.08 -10000 0 -0.32 22 22
Nephrin/NEPH1/ZO-1 -0.023 0.088 -10000 0 -0.47 3 3
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0.02 0.011 -9999 0 -10000 0 0
GNAO1 -0.006 0.061 -9999 0 -0.66 3 3
mol:Sphinganine-1-P 0.02 0 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0 0.006 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.008 -9999 0 -10000 0 0
S1PR5 -0.006 0.061 -9999 0 -0.66 3 3
S1PR4 -0.068 0.22 -9999 0 -0.76 31 31
GNAI1 -0.002 0.041 -9999 0 -0.76 1 1
S1P/S1P5/G12 -0.003 0.035 -9999 0 -0.44 1 1
S1P/S1P3/Gq -0.067 0.13 -9999 0 -0.64 3 3
S1P/S1P4/Gi -0.033 0.098 -9999 0 -0.52 3 3
GNAQ -0.002 0.041 -9999 0 -0.76 1 1
GNAZ -0.011 0.091 -9999 0 -0.76 5 5
GNA14 -0.18 0.32 -9999 0 -0.76 80 80
GNA15 -0.002 0.041 -9999 0 -0.76 1 1
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
ABCC1 -0.002 0.032 -9999 0 -0.61 1 1
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 0 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.009 0.065 0.44 7 -10000 0 7
CDKN1A 0 0 -10000 0 -10000 0 0
KAT2B -0.002 0.041 -10000 0 -0.76 1 1
BAX 0 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.003 0.046 -10000 0 -0.61 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.043 0.15 -10000 0 -0.44 44 44
PPARGC1A -0.14 0.3 -10000 0 -0.76 65 65
FHL2 -0.003 0.046 -10000 0 -0.61 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0 -10000 0 -10000 0 0
HIST2H4A 0.009 0.065 -10000 0 -0.44 7 7
SIRT1/FOXO3a 0 0 -10000 0 -10000 0 0
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.007 0.03 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
SIRT1/PGC1A -0.094 0.2 -10000 0 -0.5 65 65
p53/SIRT1 0 0 -10000 0 -10000 0 0
SIRT1/FOXO4 0 0 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.002 0.026 -10000 0 -10000 0 0
HIST1H1E 0.011 0.042 -10000 0 -10000 0 0
SIRT1/p300 0 0 -10000 0 -10000 0 0
muscle cell differentiation 0.047 0.12 0.49 1 -10000 0 1
TP53 0 0 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.003 0.033 -10000 0 -0.44 2 2
ACSS2 0.018 0 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.047 0.12 -10000 0 -0.5 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0 0 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity -0.025 0.12 -10000 0 -0.57 15 15
MAP2K4 0.042 0.009 -10000 0 -10000 0 0
IKBKB -0.002 0.032 -10000 0 -0.61 1 1
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.002 0.041 -10000 0 -0.76 1 1
SMPD1 0 0 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.033 0.16 -10000 0 -0.76 15 15
TRAIL/TRAILR2 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.053 0.17 -10000 0 -0.58 32 32
TRAIL/TRAILR1 -0.002 0.031 -10000 0 -0.58 1 1
TRAIL/TRAILR4 -0.025 0.12 -10000 0 -0.58 15 15
TRAIL/TRAILR1/DAP3/GTP -0.001 0.024 -10000 0 -0.46 1 1
IKK complex -0.001 0.011 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.02 0 -10000 0 -10000 0 0
MAP3K1 0 0.008 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.033 0.15 -10000 0 -0.76 15 15
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.002 0.041 -10000 0 -0.76 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.017 -10000 0 -10000 0 0
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP -0.001 0.022 -10000 0 -0.42 1 1
mol:ceramide 0 0 -10000 0 -10000 0 0
FADD 0 0 -10000 0 -10000 0 0
MAPK8 0.048 0.009 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.07 0.22 -10000 0 -0.76 32 32
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.001 0.027 -10000 0 -0.5 1 1
DAP3 0 0 -10000 0 -10000 0 0
CASP10 0.011 0.066 0.3 15 -0.4 1 16
JNK cascade -0.025 0.12 -10000 0 -0.57 15 15
TRAIL (trimer) 0 0 -10000 0 -10000 0 0
TNFRSF10C -0.07 0.22 -10000 0 -0.76 32 32
TRAIL/TRAILR1/DAP3/GTP/FADD -0.001 0.023 -10000 0 -0.42 1 1
TRAIL/TRAILR2/FADD 0 0 -10000 0 -10000 0 0
cell death 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0 -10000 0 -10000 0 0
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0 0.002 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.03 -10000 0 -10000 0 0
IRAK/TOLLIP 0 0 -10000 0 -10000 0 0
IKBKB -0.002 0.032 -10000 0 -0.61 1 1
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.071 0.18 -10000 0 -0.5 49 49
IL1A -0.055 0.19 -10000 0 -0.68 28 28
IL1B 0.01 0.078 -10000 0 -0.58 6 6
IRAK/TRAF6/p62/Atypical PKCs 0 0 -10000 0 -10000 0 0
IL1R2 -0.042 0.15 -10000 0 -0.61 24 24
IL1R1 -0.004 0.058 -10000 0 -0.76 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.04 0.23 5 -10000 0 5
TOLLIP 0 0 -10000 0 -10000 0 0
TICAM2 -0.002 0.041 -10000 0 -0.76 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.005 -10000 0 -10000 0 0
JUN 0.043 0.016 -10000 0 -10000 0 0
MAP3K7 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.009 0.059 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.034 0.12 -10000 0 -0.5 15 15
PIK3R1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.032 0.11 -10000 0 -0.79 2 2
IL1 beta fragment/IL1R1/IL1RAP -0.01 0.067 -10000 0 -0.45 8 8
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.038 0.016 -10000 0 -10000 0 0
IRAK1 0.023 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.008 0.075 -10000 0 -0.66 4 4
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.006 0.039 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.01 0.067 -10000 0 -0.45 8 8
IL1 beta/IL1R2 -0.034 0.12 -10000 0 -0.41 29 29
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.008 0.053 -10000 0 -10000 0 0
IRAK3 -0.018 0.11 -10000 0 -0.76 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.01 0.063 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.021 0.077 -10000 0 -0.56 2 2
IL1 alpha/IL1R1/IL1RAP -0.037 0.13 -10000 0 -0.46 28 28
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0 -10000 0 -10000 0 0
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -10000 0 -10000 0 0
IL1RAP 0 0 -10000 0 -10000 0 0
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.008 0.051 -10000 0 -10000 0 0
CASP1 -0.004 0.058 -10000 0 -0.76 2 2
IL1RN/IL1R2 -0.035 0.12 -10000 0 -0.45 27 27
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.01 0.063 -10000 0 -10000 0 0
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.016 0.063 -10000 0 -0.56 2 2
PIK3CA 0 0 -10000 0 -10000 0 0
IL1RN -0.006 0.066 -10000 0 -0.71 3 3
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.001 0.015 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 -0.002 0.041 -10000 0 -0.76 1 1
EPHB2 0.004 0.057 -10000 0 -0.6 3 3
EFNB1 0.02 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.033 0.092 -10000 0 -0.57 1 1
Ephrin B2/EPHB1-2 -0.041 0.11 -10000 0 -0.34 41 41
neuron projection morphogenesis -0.031 0.088 -10000 0 -0.55 1 1
Ephrin B1/EPHB1-2/Tiam1 -0.036 0.1 -10000 0 -0.62 1 1
DNM1 0 0 -10000 0 -10000 0 0
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.013 0.082 -10000 0 -0.74 4 4
YES1 -0.011 0.1 -10000 0 -0.97 4 4
Ephrin B1/EPHB1-2/NCK2 -0.036 0.1 -10000 0 -0.62 1 1
PI3K -0.009 0.081 -10000 0 -0.75 4 4
mol:GDP -0.035 0.099 -10000 0 -0.61 1 1
ITGA2B -0.028 0.14 -10000 0 -0.76 13 13
endothelial cell proliferation -0.001 0.027 -10000 0 -0.5 1 1
FYN -0.011 0.1 -10000 0 -0.97 4 4
MAP3K7 -0.009 0.085 -10000 0 -0.79 4 4
FGR -0.024 0.12 -10000 0 -1 4 4
TIAM1 0 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.029 0.11 -10000 0 -0.59 6 6
LYN -0.011 0.1 -10000 0 -0.97 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.01 0.098 -10000 0 -0.92 4 4
Ephrin B1/EPHB1-2 -0.012 0.091 -10000 0 -0.85 4 4
SRC -0.011 0.1 -10000 0 -0.96 4 4
ITGB3 -0.013 0.099 -10000 0 -0.76 6 6
EPHB1 -0.066 0.19 -10000 0 -0.6 38 38
EPHB4 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.027 -10000 0 -0.5 1 1
alphaIIb/beta3 Integrin -0.032 0.13 -10000 0 -0.58 19 19
BLK -0.018 0.11 -10000 0 -1 4 4
HCK -0.012 0.1 -10000 0 -0.96 4 4
regulation of stress fiber formation 0.035 0.099 0.61 1 -10000 0 1
MAPK8 0.02 0.078 -10000 0 -0.7 4 4
Ephrin B1/EPHB1-2/RGS3 -0.036 0.1 -10000 0 -0.62 1 1
endothelial cell migration -0.009 0.078 -10000 0 -0.64 5 5
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.006 0.094 -10000 0 -0.87 4 4
regulation of focal adhesion formation 0.035 0.099 0.61 1 -10000 0 1
chemotaxis 0.035 0.099 0.61 1 -10000 0 1
PIK3CA 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.032 0.09 -10000 0 -0.56 1 1
angiogenesis -0.012 0.091 -10000 0 -0.84 4 4
LCK -0.011 0.11 -10000 0 -1 4 4
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.015 0.092 -9999 0 -0.58 9 9
PDGFRB 0.008 0.042 -9999 0 -0.76 1 1
SPHK1 -0.006 0.019 -9999 0 -10000 0 0
mol:S1P -0.009 0.029 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.011 0.13 -9999 0 -0.7 3 3
GNAO1 0.005 0.063 -9999 0 -0.66 3 3
PDGFB-D/PDGFRB/PLCgamma1 -0.034 0.1 -9999 0 -0.58 4 4
PLCG1 0.017 0.12 -9999 0 -0.65 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.042 -9999 0 -0.76 1 1
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.01 0.003 -9999 0 -10000 0 0
GNAI1 0.008 0.042 -9999 0 -0.77 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.002 0.082 -9999 0 -0.5 9 9
S1P1/S1P -0.021 0.072 -9999 0 -0.4 9 9
negative regulation of cAMP metabolic process 0.012 0.12 -9999 0 -0.68 3 3
MAPK3 0.004 0.18 -9999 0 -0.55 29 29
calcium-dependent phospholipase C activity -0.001 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 -0.02 0.12 -9999 0 -0.76 9 9
PLCB2 0.015 0.09 -9999 0 -0.38 9 9
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.018 0.061 -9999 0 -0.42 3 3
receptor internalization -0.02 0.068 -9999 0 -0.38 9 9
PTGS2 -0.036 0.32 -9999 0 -1.1 29 29
Rac1/GTP -0.018 0.061 -9999 0 -0.42 3 3
RHOA 0 0 -9999 0 -10000 0 0
VEGFA 0 0.001 -9999 0 -10000 0 0
negative regulation of T cell proliferation 0.012 0.12 -9999 0 -0.68 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.001 0.092 -9999 0 -0.76 5 5
MAPK1 0.004 0.18 -9999 0 -0.55 29 29
S1P1/S1P/PDGFB-D/PDGFRB 0.02 0.095 -9999 0 -0.62 3 3
ABCC1 0.008 0.033 -9999 0 -0.6 1 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 0 0 -9999 0 -10000 0 0
VDR -0.002 0.041 -9999 0 -0.76 1 1
Cbp/p300/PCAF -0.001 0.027 -9999 0 -0.5 1 1
EP300 0 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.036 0.027 -9999 0 -0.31 1 1
KAT2B -0.002 0.041 -9999 0 -0.76 1 1
MAPK14 0 0 -9999 0 -10000 0 0
AKT1 0.023 0.033 -9999 0 -0.32 1 1
RAR alpha/9cRA/Cyclin H -0.006 0.028 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.033 0.032 -9999 0 -0.42 1 1
CDC2 0.001 0 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.008 0.03 -9999 0 -10000 0 0
NCOR2 -0.002 0.041 -9999 0 -0.76 1 1
VDR/VDR/Vit D3 -0.002 0.031 -9999 0 -0.58 1 1
RXRs/RARs/NRIP1/9cRA -0.028 0.084 -9999 0 -0.74 1 1
NCOA2 -0.002 0.041 -9999 0 -0.76 1 1
NCOA3 0 0 -9999 0 -10000 0 0
NCOA1 0 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.002 0.041 -9999 0 -0.76 1 1
RARG 0.011 0 -9999 0 -10000 0 0
RAR gamma1/9cRA 0 0 -9999 0 -10000 0 0
MAPK3 0.011 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
MAPK8 0.011 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.071 0.075 -9999 0 -0.83 1 1
RARA 0.015 0.043 -9999 0 -0.29 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.033 0.036 -9999 0 -0.42 1 1
PRKCA 0.011 0.041 -9999 0 -0.76 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.046 0.093 -9999 0 -0.79 1 1
RXRG -0.24 0.23 -9999 0 -0.43 198 198
RXRA 0.022 0.041 -9999 0 -0.32 1 1
RXRB 0.008 0.065 -9999 0 -0.42 1 1
VDR/Vit D3/DNA -0.002 0.031 -9999 0 -0.58 1 1
RBP1 -0.024 0.12 -9999 0 -0.61 14 14
CRBP1/9-cic-RA -0.018 0.088 -9999 0 -0.45 14 14
RARB 0.01 0.041 -9999 0 -0.76 1 1
PRKCG -0.028 0.15 -9999 0 -0.6 22 22
MNAT1 0 0 -9999 0 -10000 0 0
RAR alpha/RXRs -0.035 0.083 -9999 0 -0.8 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.016 0.072 -9999 0 -0.59 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.038 -9999 0 -0.41 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.046 0.093 -9999 0 -0.79 1 1
positive regulation of DNA binding -0.006 0.026 -9999 0 -10000 0 0
NRIP1 -0.042 0.087 -9999 0 -0.7 1 1
RXRs/RARs -0.054 0.094 -9999 0 -0.79 1 1
RXRs/RXRs/DNA/9cRA -0.076 0.078 -9999 0 -0.87 1 1
PRKACA 0 0 -9999 0 -10000 0 0
CDK7 0 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.004 0.018 -9999 0 -10000 0 0
CCNH 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.002 0.032 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.006 0.063 -10000 0 -10000 0 0
IL27/IL27R/JAK1 -0.021 0.089 -10000 0 -10000 0 0
TBX21 -0.023 0.22 -10000 0 -0.6 37 37
IL12B 0.01 0.004 -10000 0 -10000 0 0
IL12A 0 0.078 -10000 0 -0.58 6 6
IL6ST -0.01 0.12 -10000 0 -0.77 9 9
IL27RA/JAK1 -0.002 0.014 -10000 0 -10000 0 0
IL27 0.009 0.007 -10000 0 -10000 0 0
TYK2 0.011 0.003 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.082 0.16 -10000 0 -0.73 3 3
T-helper 2 cell differentiation -0.006 0.063 -10000 0 -10000 0 0
T cell proliferation during immune response -0.006 0.063 -10000 0 -10000 0 0
MAPKKK cascade 0.006 0.063 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 0.001 0.003 -10000 0 -10000 0 0
IL12RB1 -0.034 0.18 -10000 0 -0.76 20 20
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.012 0.19 -10000 0 -0.64 9 9
IL27/IL27R/JAK2/TYK2 0.006 0.063 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.006 0.063 -10000 0 -10000 0 0
STAT1 (dimer) -0.049 0.16 0.51 4 -0.72 3 7
JAK2 0.006 0.006 -10000 0 -10000 0 0
JAK1 0.001 0.003 -10000 0 -10000 0 0
STAT2 (dimer) 0.006 0.059 -10000 0 -10000 0 0
T cell proliferation -0.068 0.19 -10000 0 -0.55 10 10
IL12/IL12R/TYK2/JAK2 0.01 0.094 -10000 0 -0.59 2 2
IL17A -0.082 0.16 -10000 0 -0.73 3 3
mast cell activation -0.006 0.063 -10000 0 -10000 0 0
IFNG 0.007 0.02 -10000 0 -0.13 4 4
T cell differentiation -0.002 0.005 -10000 0 -0.023 3 3
STAT3 (dimer) 0.006 0.059 -10000 0 -10000 0 0
STAT5A (dimer) 0.005 0.063 -10000 0 -10000 0 0
STAT4 (dimer) 0 0.079 -10000 0 -0.45 2 2
STAT4 -0.011 0.091 -10000 0 -0.76 5 5
T cell activation -0.007 0.002 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.015 0.071 -10000 0 -10000 0 0
GATA3 -0.052 0.28 -10000 0 -1.4 14 14
IL18 0.007 0.045 -10000 0 -0.58 2 2
positive regulation of mast cell cytokine production 0.006 0.058 -10000 0 -10000 0 0
IL27/EBI3 0 0.024 -10000 0 -0.44 1 1
IL27RA 0.007 0.017 -10000 0 -10000 0 0
IL6 -0.16 0.31 -10000 0 -0.76 73 73
STAT5A -0.002 0.041 -10000 0 -0.76 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.001 0.005 -10000 0 -10000 0 0
IL1B 0.003 0.064 -10000 0 -0.58 4 4
EBI3 0.004 0.033 -10000 0 -0.6 1 1
TNF -0.008 0.1 -10000 0 -0.57 11 11
Insulin Pathway

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
CBL/APS/CAP -0.05 0.13 -9999 0 -10000 0 0
TC10/GTP -0.047 0.12 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.025 -9999 0 -0.46 1 1
HRAS 0 0 -9999 0 -10000 0 0
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.061 0.21 -9999 0 -0.75 28 28
FOXO3 -0.005 0.016 -9999 0 -10000 0 0
AKT1 -0.029 0.095 -9999 0 -10000 0 0
INSR 0.011 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 0 -9999 0 -10000 0 0
SORBS1 -0.094 0.25 -9999 0 -0.76 43 43
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.032 0 -9999 0 -10000 0 0
CAV1 -0.11 0.21 -9999 0 -0.44 99 99
CBL/APS/CAP/Crk-II/C3G -0.052 0.14 -9999 0 -0.42 43 43
Insulin Receptor/Insulin/IRS1/NCK2 -0.001 0.025 -9999 0 -0.46 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.022 -9999 0 -0.4 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.001 0.014 -9999 0 -10000 0 0
RPS6KB1 0.022 0.1 -9999 0 -10000 0 0
PARD6A 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.025 0.084 -9999 0 -10000 0 0
HRAS/GTP -0.004 0.037 -9999 0 -10000 0 0
Insulin Receptor 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.001 0.023 -9999 0 -0.43 1 1
PRKCI -0.008 0.025 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.031 0.1 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.001 0.022 -9999 0 -0.41 1 1
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 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 -0.029 0.095 -9999 0 -10000 0 0
PRKCZ -0.008 0.025 -9999 0 -10000 0 0
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.005 0.044 -9999 0 -0.41 4 4
F2RL2 -0.12 0.24 -9999 0 -0.61 66 66
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.056 0.15 -9999 0 -0.45 43 43
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D 0.019 0.049 -9999 0 -0.44 4 4
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.002 0.008 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.002 0.041 -9999 0 -0.76 1 1
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.019 0.049 -9999 0 -0.43 4 4
GRB2 0 0 -9999 0 -10000 0 0
EIF4EBP1 0.009 0.12 -9999 0 -10000 0 0
PTPRA 0.011 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.001 0.017 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.001 0.025 -9999 0 -0.47 1 1
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.06 0.12 -9999 0 -0.42 2 2
S1P3 pathway

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.002 0.041 -9999 0 -0.76 1 1
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.007 0.044 -9999 0 -0.31 6 6
GNAO1 0.006 0.062 -9999 0 -0.66 3 3
S1P/S1P3/G12/G13 0 0.001 -9999 0 -10000 0 0
AKT1 -0.004 0.028 -9999 0 -0.46 1 1
AKT3 0.04 0.075 -9999 0 -1.3 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.002 0.041 -9999 0 -0.76 1 1
GNAI2 0.012 0.002 -9999 0 -10000 0 0
GNAI3 0.011 0.001 -9999 0 -10000 0 0
GNAI1 0.009 0.041 -9999 0 -0.76 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.012 0.002 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.033 0.046 -9999 0 -10000 0 0
MAPK3 0.039 0.044 -9999 0 -10000 0 0
MAPK1 0.039 0.044 -9999 0 -10000 0 0
JAK2 0.042 0.043 -9999 0 -10000 0 0
CXCR4 0.039 0.044 -9999 0 -10000 0 0
FLT1 0.013 0.001 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.039 0.044 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.033 0.046 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.006 0.035 -9999 0 -10000 0 0
VEGFA 0.013 0.001 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.03 0.045 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.022 0.004 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.076 0.14 -9999 0 -0.33 80 80
GNAQ -0.002 0.041 -9999 0 -0.76 1 1
GNAZ 0 0.092 -9999 0 -0.76 5 5
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.32 -9999 0 -0.76 80 80
GNA15 -0.002 0.041 -9999 0 -0.76 1 1
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.006 0.035 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.13 0.25 -9999 0 -0.61 77 77
mol:Halofuginone 0 0 -9999 0 -10000 0 0
ITGA1 -0.007 0.07 -9999 0 -0.76 3 3
CDKN1A -0.007 0.033 -9999 0 -10000 0 0
PRL-3/alpha Tubulin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.086 -9999 0 -0.57 8 8
AGT -0.017 0.11 -9999 0 -0.74 8 8
CCNA2 -0.076 0.18 -9999 0 -0.72 7 7
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.002 0.12 -9999 0 -0.57 14 14
CDK2/Cyclin E1 -0.07 0.12 -9999 0 -0.46 3 3
MAPK3 0.02 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.02 0 -9999 0 -10000 0 0
PTP4A1 0.015 0.093 -9999 0 -10000 0 0
PTP4A3 0 0 -9999 0 -10000 0 0
PTP4A2 0 0 -9999 0 -10000 0 0
ITGB1 0.02 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 -0.007 0.033 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.021 0.087 -9999 0 -10000 0 0
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC -0.007 0.033 -9999 0 -10000 0 0
RHOA -0.007 0.033 -9999 0 -10000 0 0
cell motility 0.025 0.042 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.016 0.08 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.005 0.053 -9999 0 -0.58 3 3
ROCK1 0.025 0.042 -9999 0 -10000 0 0
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis 0.015 0.092 -9999 0 -0.44 14 14
ATF5 -0.009 0.072 -9999 0 -0.61 5 5
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.019 0.003 -9999 0 -10000 0 0
RAS family/GTP -0.009 0.048 -9999 0 -10000 0 0
NFATC4 0.03 0.058 -9999 0 -10000 0 0
ERBB2IP 0.002 0.005 -9999 0 -10000 0 0
HSP90 (dimer) 0 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.011 0.064 -9999 0 -10000 0 0
JUN 0.038 0.066 -9999 0 -0.5 1 1
HRAS 0 0 -9999 0 -10000 0 0
DOCK7 0.027 0.069 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.014 0.075 -9999 0 -0.43 11 11
AKT1 0.011 0.002 -9999 0 -10000 0 0
BAD 0.019 0.001 -9999 0 -10000 0 0
MAPK10 -0.009 0.042 -9999 0 -10000 0 0
mol:GTP 0 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.012 0.068 -9999 0 -10000 0 0
RAF1 0.045 0.062 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.054 0.15 -9999 0 -0.46 41 41
STAT3 0 0 -9999 0 -10000 0 0
cell migration 0.04 0.044 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation 0.021 0.17 -9999 0 -0.62 4 4
FOS -0.017 0.23 -9999 0 -0.52 56 56
NRAS 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.064 -9999 0 -10000 0 0
MAPK3 0.034 0.12 -9999 0 -0.64 1 1
MAPK1 0.034 0.12 -9999 0 -0.64 1 1
JAK2 0.026 0.069 -9999 0 -10000 0 0
NF2 -0.001 0.003 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.013 0.065 -9999 0 -0.34 11 11
NRG1 -0.015 0.14 -9999 0 -0.76 11 11
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 0.03 0.064 -9999 0 -10000 0 0
MAPK9 -0.005 0.03 -9999 0 -10000 0 0
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 0.009 0.005 -9999 0 -10000 0 0
SHC1 0.008 0.004 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.003 0.009 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
RNF41 0.025 0.005 -9999 0 -10000 0 0
FRAP1 0.01 0.002 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.008 0.043 -9999 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 0.031 0.13 -9999 0 -0.6 6 6
myelination 0.036 0.056 -9999 0 -10000 0 0
PPP3CB 0.025 0.065 -9999 0 -10000 0 0
KRAS 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.009 0.05 -9999 0 -10000 0 0
NRG2 -0.09 0.24 -9999 0 -0.76 41 41
mol:GDP 0.013 0.064 -9999 0 -0.34 11 11
SOS1 0.008 0.004 -9999 0 -10000 0 0
MAP2K2 0.052 0.064 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.025 0.069 -9999 0 -10000 0 0
MAP2K1 0.024 0.12 -9999 0 -0.49 4 4
heart morphogenesis -0.011 0.064 -9999 0 -10000 0 0
RAS family/GDP -0.009 0.048 -9999 0 -10000 0 0
GRB2 0.008 0.004 -9999 0 -10000 0 0
PRKACA -0.001 0.005 -9999 0 -10000 0 0
CHRNE 0.018 0.02 -9999 0 -0.24 1 1
HSP90AA1 0 0 -9999 0 -10000 0 0
activation of caspase activity -0.011 0.002 -9999 0 -10000 0 0
nervous system development -0.011 0.064 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.003 0.034 -9999 0 -0.45 2 2
HDAC3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.056 0.17 -9999 0 -0.58 34 34
GATA1/HDAC5 -0.056 0.17 -9999 0 -0.58 34 34
GATA2/HDAC5 -0.066 0.18 -9999 0 -0.58 40 40
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.003 0.046 -9999 0 -0.61 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
GATA2 -0.088 0.24 -9999 0 -0.76 40 40
HDAC4/RFXANK 0 0 -9999 0 -10000 0 0
BCOR 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0 0 -9999 0 -10000 0 0
HDAC5 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.003 0.044 -9999 0 -0.58 2 2
Histones -0.001 0.009 -9999 0 -10000 0 0
ADRBK1 0 0 -9999 0 -10000 0 0
HDAC4 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0 0 -9999 0 -10000 0 0
HDAC6 0 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0 0 -9999 0 -10000 0 0
CAMK4 -0.009 0.081 -9999 0 -0.76 4 4
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
GATA1 -0.074 0.23 -9999 0 -0.76 34 34
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
NR3C1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
RANGAP1 0 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.027 -9999 0 -0.5 1 1
HDAC4/SRF -0.006 0.053 -9999 0 -0.5 4 4
HDAC4/ER alpha -0.023 0.11 -9999 0 -0.58 14 14
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.001 0.008 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.031 0.15 -9999 0 -0.76 14 14
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.007 0.07 -9999 0 -0.76 3 3
RAN 0 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.005 0.045 -9999 0 -0.42 3 3
GNG2 -0.004 0.058 -9999 0 -0.76 2 2
NCOR2 -0.002 0.041 -9999 0 -0.76 1 1
TUBB2A 0 0 -9999 0 -10000 0 0
HDAC11 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
ANKRA2 0 0 -9999 0 -10000 0 0
RFXANK 0 0 -9999 0 -10000 0 0
nuclear import 0 0 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
PRKDC 0 0 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
UBE2L3 0 0 -9999 0 -10000 0 0
FANCD2 0.023 0 -9999 0 -10000 0 0
protein ubiquitination -0.066 0.12 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
M/R/N Complex 0 0 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
DNA-PK 0 0 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.003 0.016 -9999 0 -10000 0 0
FANCF 0 0 -9999 0 -10000 0 0
BRCA1 0 0 -9999 0 -10000 0 0
CCNE1 -0.13 0.25 -9999 0 -0.61 77 77
CDK2/Cyclin E1 -0.098 0.18 -9999 0 -0.44 77 77
FANCG -0.003 0.046 -9999 0 -0.61 2 2
BRCA1/BACH1/BARD1 0 0 -9999 0 -10000 0 0
FANCE 0 0 -9999 0 -10000 0 0
FANCC 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
FANCA -0.003 0.046 -9999 0 -0.61 2 2
DNA repair 0.003 0.11 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0 0 -9999 0 -10000 0 0
BARD1/DNA-PK 0 0 -9999 0 -10000 0 0
FANCL -0.002 0.032 -9999 0 -0.61 1 1
mRNA polyadenylation 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0 0 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0 0 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0 0 -9999 0 -10000 0 0
BRCA1/BACH1 0 0 -9999 0 -10000 0 0
BARD1 0 0 -9999 0 -10000 0 0
PCNA 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.049 0.12 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0 0 -9999 0 -10000 0 0
FA complex -0.002 0.021 -9999 0 -10000 0 0
BARD1/EWS 0 0 -9999 0 -10000 0 0
RBBP8 0.02 0 -9999 0 -10000 0 0
TP53 0 0 -9999 0 -10000 0 0
TOPBP1 0 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle 0 0 -9999 0 -10000 0 0
BRCA1/BARD1 -0.067 0.13 -9999 0 -10000 0 0
CSTF1 0 0 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 -0.091 0.22 -9999 0 -0.61 52 52
RAD50 0 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0 0 -9999 0 -10000 0 0
EWSR1 0 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.002 0.041 -10000 0 -0.76 1 1
ANTXR2 -0.004 0.058 -10000 0 -0.76 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.009 -10000 0 -0.12 2 2
monocyte activation -0.003 0.085 -10000 0 -0.45 12 12
MAP2K2 0 0.004 -10000 0 -10000 0 0
MAP2K1 -0.001 0.008 -10000 0 -10000 0 0
MAP2K7 -0.001 0.008 -10000 0 -10000 0 0
MAP2K6 -0.002 0.019 -10000 0 -0.33 1 1
CYAA 0.011 0.052 -10000 0 -0.64 2 2
MAP2K4 -0.001 0.008 -10000 0 -10000 0 0
IL1B 0.008 0.06 -10000 0 -0.46 5 5
Channel -0.004 0.054 -10000 0 -0.68 2 2
NLRP1 -0.006 0.051 -10000 0 -0.47 4 4
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.009 0.12 2 -10000 0 2
MAPK3 -0.001 0.008 -10000 0 -10000 0 0
MAPK1 -0.001 0.008 -10000 0 -10000 0 0
PGR -0.086 0.18 -10000 0 -0.45 67 67
PA/Cellular Receptors -0.004 0.057 -10000 0 -0.73 2 2
apoptosis -0.001 0.009 -10000 0 -0.12 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.004 0.051 -10000 0 -0.64 2 2
macrophage activation 0.018 0.008 -10000 0 -10000 0 0
TNF -0.024 0.13 -10000 0 -0.75 11 11
VCAM1 -0.017 0.083 -10000 0 -0.45 12 12
platelet activation -0.001 0.011 -10000 0 -10000 0 0
MAPKKK cascade -0.015 0.01 0.12 1 -10000 0 1
IL18 0.01 0.05 -10000 0 -0.33 6 6
negative regulation of macrophage activation -0.001 0.009 -10000 0 -0.12 2 2
LEF -0.001 0.009 -10000 0 -0.12 2 2
CASP1 -0.004 0.038 -10000 0 -0.31 4 4
mol:cAMP -0.001 0.011 -10000 0 -10000 0 0
necrosis -0.001 0.009 -10000 0 -0.12 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.004 0.052 -10000 0 -0.65 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.046 0.023 -10000 0 -0.34 1 1
NFATC2 0.003 0.07 -10000 0 -0.4 1 1
NFATC3 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.005 0.11 -10000 0 -0.52 9 9
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.032 0.099 -10000 0 -0.51 11 11
BCL2/BAX -0.001 0.024 -10000 0 -0.44 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.004 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.004 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.004 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.006 0.1 -10000 0 -0.5 9 9
Calcineurin A alpha-beta B1/BCL2 -0.002 0.032 -10000 0 -0.6 1 1
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.006 0.1 0.49 9 -10000 0 9
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 0 0 -10000 0 -10000 0 0
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.051 0.17 -10000 0 -0.61 29 29
MAP3K8 0.002 0.071 -10000 0 -0.76 3 3
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.069 0.13 -10000 0 -0.47 12 12
CABIN1 -0.006 0.11 -10000 0 -0.53 9 9
CALM1 0.009 0.004 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.009 0.081 -10000 0 -0.76 4 4
mol:Ca2+ -0.002 0.008 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.003 0.044 -10000 0 -0.58 2 2
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0.004 -10000 0 -10000 0 0
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.004 0.021 -10000 0 -10000 0 0
PRKCH 0 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.009 0.004 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0.009 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.026 -10000 0 -10000 0 0
PRKCB -0.024 0.13 -10000 0 -0.76 11 11
PRKCE -0.004 0.058 -10000 0 -0.76 2 2
JNK2/NFAT4 0 0 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.004 -10000 0 -10000 0 0
PRKCA -0.002 0.041 -10000 0 -0.76 1 1
PRKCG -0.038 0.15 -10000 0 -0.61 22 22
PRKCQ -0.066 0.21 -10000 0 -0.76 30 30
FKBP38/BCL2 -0.001 0.024 -10000 0 -0.44 1 1
EP300 -0.001 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.044 0.029 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.006 0.054 -10000 0 -0.51 4 4
NFATc/ERK1 0.05 0.022 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.032 0.099 -10000 0 -0.52 10 10
NR4A1 -0.087 0.29 -10000 0 -0.7 64 64
GSK3B 0.009 0.004 -10000 0 -10000 0 0
positive T cell selection 0.017 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.021 0.046 -10000 0 -0.37 1 1
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0.009 0.004 -10000 0 -10000 0 0
AKAP5 -0.004 0.058 -10000 0 -0.76 2 2
MEF2D -0.001 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.044 0.029 -10000 0 -10000 0 0
CREBBP -0.001 0.001 -10000 0 -10000 0 0
BCL2 -0.002 0.032 -10000 0 -0.61 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.014 0.078 -9999 0 -0.46 10 10
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.066 -9999 0 -0.39 10 10
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.041 -9999 0 -0.76 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.006 0.033 -9999 0 -10000 0 0
YY1/LSF -0.001 0.015 -9999 0 -10000 0 0
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.01 0.058 -9999 0 -0.34 10 10
I kappa B alpha/HDAC1 -0.007 0.04 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.009 0.051 -9999 0 -0.3 10 10
HDAC1/Smad7 -0.001 0.027 -9999 0 -0.5 1 1
RANGAP1 0 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.007 0.04 -9999 0 -10000 0 0
NuRD/MBD3 Complex -0.001 0.011 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.008 0.046 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.088 0.24 -9999 0 -0.76 40 40
GATA1 -0.074 0.23 -9999 0 -0.76 34 34
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.022 0.067 -9999 0 -0.46 1 1
RBBP7 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0 0 -9999 0 -10000 0 0
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.008 0.045 -9999 0 -10000 0 0
KAT2B -0.002 0.041 -9999 0 -0.76 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.007 0.037 -9999 0 -10000 0 0
YY1/HDAC2 -0.001 0.015 -9999 0 -10000 0 0
YY1/HDAC1 -0.001 0.015 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0 0 -9999 0 -10000 0 0
PPARG -0.054 0.14 -9999 0 -0.38 49 49
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.008 0.046 -9999 0 -0.45 1 1
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.001 0.026 -9999 0 -0.49 1 1
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.012 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.008 0.045 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0.026 0.02 -9999 0 -0.34 1 1
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 -0.002 0.041 -9999 0 -0.76 1 1
NCOR2 -0.002 0.041 -9999 0 -0.76 1 1
MXD1 0 0 -9999 0 -10000 0 0
STAT3 0.023 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.014 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.001 0.014 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.023 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.045 -9999 0 -10000 0 0
histone deacetylation 0.042 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.006 0.035 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.059 0.15 -9999 0 -0.46 40 40
GATA1/HDAC1 -0.056 0.17 -9999 0 -0.58 34 34
GATA1/HDAC3 -0.051 0.14 -9999 0 -0.47 34 34
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.018 0.099 -9999 0 -0.56 11 11
SIN3/HDAC complex/Mad/Max 0 0 -9999 0 -10000 0 0
NuRD Complex -0.001 0.011 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.006 0.033 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 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 -0.058 0.17 -9999 0 -0.58 35 35
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.024 0.13 -9999 0 -0.75 11 11
negative regulation of cell growth 0.042 0 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 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 -0.012 0.07 -9999 0 -0.41 10 10
SIN3/HDAC complex/NCoR1 0 0 -9999 0 -10000 0 0
TFCP2 0 0 -9999 0 -10000 0 0
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 -0.002 0.041 -9999 0 -0.76 1 1
MBD2 0 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.053 0.054 -10000 0 -0.84 1 1
UGCG -0.001 0.008 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.038 0.065 -10000 0 -0.54 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.026 0.013 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.039 -10000 0 -0.62 1 1
FRAP1 0.076 0.062 -10000 0 -0.74 1 1
FOXO3 0.078 0.057 -10000 0 -0.7 1 1
AKT1 0.073 0.061 -10000 0 -0.77 1 1
GAB2 -0.007 0.12 -10000 0 -0.76 8 8
SMPD1 -0.001 0.008 -10000 0 -10000 0 0
SGMS1 -0.001 0.008 -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 0.021 0.002 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.047 0.026 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.03 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0.001 0 -10000 0 -10000 0 0
JAK3 0.013 0.001 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
JAK1 0.013 0.001 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.077 0.052 -10000 0 -0.6 1 1
MYB 0.011 0.12 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.064 0.066 -10000 0 -0.86 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.02 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.064 0.065 -10000 0 -0.82 1 1
Rac1/GDP 0 0 -10000 0 -10000 0 0
T cell proliferation 0.069 0.06 -10000 0 -0.74 1 1
SHC1 0.011 0.002 -10000 0 -10000 0 0
RAC1 0 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.009 -10000 0 -0.042 14 14
PRKCZ 0.07 0.062 -10000 0 -0.79 1 1
NF kappa B1 p50/RelA -0.006 0.038 -10000 0 -0.61 1 1
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.046 0.06 -10000 0 -0.94 1 1
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA 0.005 0.057 -10000 0 -0.61 3 3
IL2RB 0.011 0.041 -10000 0 -0.76 1 1
TERT -0.21 0.29 -10000 0 -0.61 119 119
E2F1 0.017 0.055 -10000 0 -0.45 2 2
SOS1 0.011 0.002 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.02 14 -10000 0 14
PTPN11 0.011 0.002 -10000 0 -10000 0 0
IL2RG 0.004 0.082 -10000 0 -0.76 4 4
actin cytoskeleton organization 0.069 0.06 -10000 0 -0.74 1 1
GRB2 0.011 0.002 -10000 0 -10000 0 0
IL2 0.008 0.005 -10000 0 -10000 0 0
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
Rac1/GTP 0.029 0.006 -10000 0 -10000 0 0
LCK 0.011 0.041 -10000 0 -0.76 1 1
BCL2 0.077 0.054 -10000 0 -0.54 1 1
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.006 0.051 -10000 0 -0.43 5 5
cell-cell adhesion 0.03 0.082 0.5 1 -10000 0 1
Ephrin B/EPHB2/RasGAP -0.006 0.042 -10000 0 -0.42 1 1
ITSN1 0 0 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.016 0.077 -10000 0 -0.38 15 15
Ephrin B1/EPHB1 -0.041 0.12 -10000 0 -0.38 38 38
HRAS/GDP -0.03 0.083 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.038 0.1 -10000 0 -0.42 1 1
Endophilin/SYNJ1 -0.005 0.04 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.036 0.099 -10000 0 -0.42 1 1
endothelial cell migration -0.001 0.022 -10000 0 -0.42 1 1
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.003 0.046 -10000 0 -0.61 2 2
PAK1 -0.008 0.051 -10000 0 -10000 0 0
HRAS 0 0 -10000 0 -10000 0 0
RRAS -0.005 0.04 -10000 0 -10000 0 0
DNM1 0 0 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.034 0.094 -10000 0 -0.4 1 1
lamellipodium assembly -0.03 0.082 -10000 0 -0.5 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.018 0.05 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPHB2 -0.005 0.056 -10000 0 -0.61 3 3
EPHB3 -0.026 0.12 -10000 0 -0.61 15 15
EPHB1 -0.066 0.19 -10000 0 -0.61 38 38
EPHB4 0 0 -10000 0 -10000 0 0
mol:GDP -0.02 0.085 -10000 0 -0.44 1 1
Ephrin B/EPHB2 -0.006 0.043 -10000 0 -0.42 1 1
Ephrin B/EPHB3 -0.016 0.071 -10000 0 -0.42 1 1
JNK cascade -0.004 0.11 -10000 0 -0.61 1 1
Ephrin B/EPHB1 -0.037 0.1 -10000 0 -0.42 1 1
RAP1/GDP -0.017 0.074 -10000 0 -10000 0 0
EFNB2 -0.002 0.041 -10000 0 -0.76 1 1
EFNB3 -0.003 0.046 -10000 0 -0.61 2 2
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.041 0.11 -10000 0 -0.35 41 41
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.031 0.083 -10000 0 -0.49 1 1
Rap1/GTP -0.03 0.081 -10000 0 -0.5 1 1
axon guidance -0.006 0.051 -10000 0 -0.42 5 5
MAPK3 0.027 0.056 -10000 0 -10000 0 0
MAPK1 0.027 0.056 -10000 0 -10000 0 0
Rac1/GDP -0.018 0.078 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.025 0.068 -10000 0 -0.41 1 1
CDC42/GDP -0.018 0.078 -10000 0 -0.4 1 1
PI3K -0.001 0.023 -10000 0 -0.42 1 1
EFNA5 -0.004 0.058 -10000 0 -0.76 2 2
Ephrin B2/EPHB4 -0.001 0.027 -10000 0 -0.5 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.003 0.025 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.029 0.079 -10000 0 -0.49 1 1
PTK2 0.009 0.025 -10000 0 -10000 0 0
MAP4K4 -0.004 0.11 -10000 0 -0.62 1 1
SRC 0 0 -10000 0 -10000 0 0
KALRN -0.004 0.058 -10000 0 -0.76 2 2
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.024 0.062 -10000 0 -10000 0 0
MAP2K1 0.021 0.058 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.039 0.11 -10000 0 -0.66 1 1
cell migration 0.029 0.06 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
SYNJ1 -0.005 0.04 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
TF 0.007 0.1 -10000 0 -10000 0 0
HRAS/GTP -0.033 0.088 -10000 0 -0.54 1 1
Ephrin B1/EPHB1-2 -0.04 0.11 -10000 0 -0.34 40 40
cell adhesion mediated by integrin 0.001 0.047 0.42 1 -10000 0 1
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.035 0.095 -10000 0 -0.58 1 1
RAC1-CDC42/GTP -0.04 0.093 -10000 0 -0.5 2 2
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.017 0.074 -10000 0 -10000 0 0
ruffle organization 0.021 0.1 -10000 0 -0.5 1 1
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.036 0.043 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.008 0.053 -10000 0 -0.42 3 3
ROCK1 0.007 0.073 -10000 0 -0.34 15 15
RAS family/GDP -0.022 0.06 -10000 0 -10000 0 0
Rac1/GTP -0.032 0.086 -10000 0 -0.53 1 1
Ephrin B/EPHB1/Src/Paxillin -0.019 0.052 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.002 0.032 -9999 0 -0.61 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.002 0.022 -9999 0 -0.26 2 2
response to UV 0 0 -9999 0 -10000 0 0
YES1 0 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 0 -9999 0 -10000 0 0
FYN 0 0 -9999 0 -10000 0 0
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.055 0.2 -9999 0 -0.76 25 25
p38 alpha/TAB1 -0.012 0.044 -9999 0 -0.38 1 1
PRKG1 -0.042 0.17 -9999 0 -0.76 19 19
DUSP8 -0.02 0.12 -9999 0 -0.76 9 9
PGK/cGMP/p38 alpha -0.031 0.1 -9999 0 -0.41 20 20
apoptosis -0.012 0.042 -9999 0 -0.36 1 1
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.27 -9999 0 -0.76 53 53
PAK1 -0.002 0.032 -9999 0 -0.61 1 1
SRC 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.032 0.082 -9999 0 -0.36 8 8
BLK -0.036 0.16 -9999 0 -0.7 18 18
HCK -0.004 0.058 -9999 0 -0.76 2 2
MAP2K3 0 0 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 0 0 -9999 0 -10000 0 0
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.034 0.062 -9999 0 -0.35 2 2
positive regulation of innate immune response 0.039 0.089 -9999 0 -0.38 8 8
LCK -0.002 0.041 -9999 0 -0.76 1 1
p38alpha-beta/MKP7 -0.019 0.066 -9999 0 -0.53 1 1
p38alpha-beta/MKP5 -0.019 0.066 -9999 0 -0.53 1 1
PGK/cGMP -0.032 0.13 -9999 0 -0.58 19 19
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.068 0.14 -9999 0 -0.54 13 13
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.006 0.066 -9999 0 -0.71 3 3
Arf6 trafficking events

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
SLC2A4 -0.004 0.058 -10000 0 -0.76 2 2
CLTC 0.028 0.011 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.023 0.008 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.018 -10000 0 -0.34 1 1
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.008 -10000 0 -10000 0 0
CPE 0.012 0.045 -10000 0 -0.46 3 3
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.001 0.008 -10000 0 -10000 0 0
CTNND1 0.028 0.018 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.007 -10000 0 -10000 0 0
TSHR 0.005 0.066 -10000 0 -0.38 10 10
INS 0.011 0.003 -10000 0 -10000 0 0
BIN1 -0.002 0.041 -10000 0 -0.76 1 1
mol:Choline -0.001 0.008 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.021 -10000 0 -0.38 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.018 -10000 0 -0.34 1 1
JUP 0.025 0.008 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.024 -10000 0 -0.46 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.024 0.017 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.001 0.016 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.001 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.044 0.12 -10000 0 -0.37 3 3
clathrin heavy chain/ACAP1 0.033 0.012 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.028 0.018 -10000 0 -10000 0 0
NME1 0.015 0.021 -10000 0 -0.38 1 1
clathrin coat assembly 0.028 0.011 -10000 0 -10000 0 0
IL2RA 0.024 0.017 -10000 0 -10000 0 0
VAMP3 0.016 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.003 0.029 -10000 0 -0.37 2 2
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.001 0.01 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.029 0.007 -10000 0 -10000 0 0
SDC1 0.024 0.017 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.02 -10000 0 -0.38 1 1
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.001 0.016 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.008 -10000 0 -10000 0 0
endocytosis 0.001 0.024 0.45 1 -10000 0 1
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.093 0.2 -10000 0 -0.4 102 102
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP -0.001 0.018 -10000 0 -0.34 1 1
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.082 0.19 -10000 0 -0.4 93 93
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.001 0.015 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification -0.001 0.015 -9999 0 -10000 0 0
CLOCK 0.013 0 -9999 0 -10000 0 0
TIMELESS/CRY2 0 0 -9999 0 -10000 0 0
DEC1/BMAL1 -0.027 0.1 -9999 0 -0.44 21 21
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.039 0 -9999 0 -10000 0 0
ARNTL 0.013 0 -9999 0 -10000 0 0
TIMELESS 0.039 0 -9999 0 -10000 0 0
NPAS2 0.013 0 -9999 0 -10000 0 0
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.012 0 -9999 0 -10000 0 0
CHEK1 -0.002 0.032 -9999 0 -0.61 1 1
mol:HEME 0.012 0 -9999 0 -10000 0 0
PER1 -0.004 0.058 -9999 0 -0.76 2 2
BMAL/CLOCK/NPAS2 0.036 0 -9999 0 -10000 0 0
BMAL1/CLOCK 0.037 0.042 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.001 0.015 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.016 -9999 0 -10000 0 0
mol:NADPH 0.012 0 -9999 0 -10000 0 0
PER1/TIMELESS -0.002 0.033 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.037 0.14 -9999 0 -0.61 21 21
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.005 0.045 -9999 0 -0.42 2 2
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.004 0.036 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.001 0.007 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.015 0.048 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.042 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.005 0.042 -9999 0 -10000 0 0
AKT1 -0.004 0.037 -9999 0 -10000 0 0
MAP2K1 0.043 0.048 -9999 0 -10000 0 0
MAP3K11 0.034 0.049 -9999 0 -10000 0 0
IFNGR1 0.01 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.057 0.14 -9999 0 -0.49 29 29
Rap1/GTP -0.004 0.031 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.006 0.046 -9999 0 -10000 0 0
CEBPB 0.042 0.13 -9999 0 -0.73 2 2
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.008 0.077 -9999 0 -1.2 1 1
STAT1 -0.005 0.042 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) 0 0.088 -9999 0 -0.72 5 5
PIK3CA 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.004 0.04 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 -0.019 0.068 -9999 0 -0.41 2 2
mol:Ca2+ -0.005 0.044 -9999 0 -0.41 2 2
MAPK3 0.044 0.066 -9999 0 -0.45 1 1
STAT1 (dimer) -0.018 0.064 -9999 0 -10000 0 0
MAPK1 0.044 0.066 -9999 0 -10000 0 0
JAK2 0.01 0.005 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
JAK1 0.01 0.005 -9999 0 -10000 0 0
CAMK2D 0 0 -9999 0 -10000 0 0
DAPK1 0.02 0.19 -9999 0 -0.65 25 25
SMAD7 0.036 0.049 -9999 0 -0.34 1 1
CBL/CRKL/C3G -0.004 0.038 -9999 0 -10000 0 0
PI3K -0.005 0.04 -9999 0 -10000 0 0
IFNG 0 0.088 -9999 0 -0.73 5 5
apoptosis 0.018 0.13 -9999 0 -0.44 25 25
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.063 0.21 -9999 0 -0.76 29 29
CAMK2B -0.077 0.2 -9999 0 -0.6 44 44
FRAP1 0.045 0.041 -9999 0 -10000 0 0
PRKCD -0.004 0.037 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.015 0.048 -9999 0 -10000 0 0
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.067 0.041 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.004 0.041 -9999 0 -10000 0 0
SOCS1 -0.004 0.079 -9999 0 -1.5 1 1
mol:GDP -0.004 0.036 -9999 0 -10000 0 0
CASP1 0.036 0.052 -9999 0 -0.34 2 2
PTGES2 0 0 -9999 0 -10000 0 0
IRF9 0.045 0.042 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.039 -9999 0 -10000 0 0
RAP1/GDP -0.004 0.031 -9999 0 -10000 0 0
CBL 0.033 0.048 -9999 0 -10000 0 0
MAP3K1 0.035 0.049 -9999 0 -0.4 2 2
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.015 0.048 -9999 0 -10000 0 0
PTPN11 0.028 0.049 -9999 0 -0.41 2 2
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
Class I PI3K 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
ARF5/GTP -0.002 0.026 -9999 0 -10000 0 0
DAPP1 0.011 0.11 -9999 0 -0.5 12 12
Src family/SYK family/BLNK-LAT/BTK-ITK 0.008 0.17 -9999 0 -0.61 19 19
mol:DAG 0.03 0.088 -9999 0 -0.28 14 14
HRAS 0.011 0.002 -9999 0 -10000 0 0
RAP1A 0 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.032 0.039 -9999 0 -0.3 1 1
PLCG2 0 0 -9999 0 -10000 0 0
PLCG1 0 0 -9999 0 -10000 0 0
ARF5 0 0 -9999 0 -10000 0 0
mol:GTP -0.002 0.028 -9999 0 -10000 0 0
ARF1/GTP -0.002 0.027 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
YES1 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.002 0.028 -9999 0 -10000 0 0
ADAP1 -0.005 0.044 -9999 0 -10000 0 0
ARAP3 -0.002 0.028 -9999 0 -0.37 2 2
INPPL1 0 0 -9999 0 -10000 0 0
PREX1 -0.004 0.058 -9999 0 -0.76 2 2
ARHGEF6 -0.018 0.11 -9999 0 -0.76 8 8
ARHGEF7 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
NRAS 0.011 0.002 -9999 0 -10000 0 0
FYN 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
FGR -0.055 0.2 -9999 0 -0.76 25 25
mol:Ca2+ 0.027 0.047 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0 0 -9999 0 -10000 0 0
ZAP70 -0.013 0.099 -9999 0 -0.76 6 6
mol:IP3 0.031 0.064 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
ARF1/GDP 0.032 0.039 -9999 0 -0.3 1 1
RhoA/GDP -0.004 0.027 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK -0.002 0.041 -9999 0 -0.76 1 1
actin cytoskeleton reorganization 0.053 0.043 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PLEKHA2 0.023 0.048 -9999 0 -0.49 3 3
RAC1 0 0 -9999 0 -10000 0 0
PTEN 0 0.003 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.026 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.026 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.032 0.1 -9999 0 -0.49 12 12
BLK -0.036 0.16 -9999 0 -0.7 18 18
PDPK1 0 0 -9999 0 -10000 0 0
CYTH1 -0.002 0.026 -9999 0 -10000 0 0
HCK -0.004 0.058 -9999 0 -0.76 2 2
CYTH3 -0.002 0.026 -9999 0 -10000 0 0
CYTH2 -0.002 0.026 -9999 0 -10000 0 0
KRAS 0.011 0.002 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.001 0.013 -9999 0 -10000 0 0
SGK1 -0.001 0.014 -9999 0 -10000 0 0
INPP5D -0.007 0.07 -9999 0 -0.76 3 3
mol:GDP 0.028 0.041 -9999 0 -0.32 1 1
SOS1 0 0 -9999 0 -10000 0 0
SYK 0 0 -9999 0 -10000 0 0
ARF6/GDP -0.004 0.027 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.028 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.002 0.028 -9999 0 -10000 0 0
VAV1 -0.002 0.041 -9999 0 -0.76 1 1
mol:PI-3-4-P2 0.015 0.055 -9999 0 -0.58 3 3
RAS family/GTP/PI3K Class I -0.002 0.028 -9999 0 -0.37 2 2
PLEKHA1 0.023 0.048 -9999 0 -0.49 3 3
Rac1/GDP 0.032 0.039 -9999 0 -0.3 1 1
LAT 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.01 0.058 -9999 0 -0.58 1 1
ITK -0.032 0.11 -9999 0 -0.39 27 27
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.029 0.12 -9999 0 -0.4 17 17
LCK -0.002 0.041 -9999 0 -0.76 1 1
BTK -0.03 0.1 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.089 0.21 -9999 0 -0.75 4 4
RAD9A 0 0 -9999 0 -10000 0 0
AP1 -0.092 0.21 -9999 0 -0.58 55 55
IFNAR2 0.008 0.006 -9999 0 -10000 0 0
AKT1 -0.001 0.061 -9999 0 -0.31 6 6
ER alpha/Oestrogen -0.024 0.12 -9999 0 -0.59 14 14
NFX1/SIN3/HDAC complex 0.028 0.022 -9999 0 -10000 0 0
EGF -0.013 0.12 -9999 0 -0.75 9 9
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0.001 -9999 0 -10000 0 0
TERT/c-Abl -0.12 0.16 -9999 0 -0.76 3 3
SAP18 0.007 0.005 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.028 0.14 -9999 0 -0.61 20 20
WRN -0.002 0.041 -9999 0 -0.76 1 1
SP1 0.009 0.006 -9999 0 -10000 0 0
SP3 0.007 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.1 0.15 -9999 0 -0.68 3 3
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.091 0.21 -9999 0 -0.85 3 3
CCND1 -0.087 0.24 -9999 0 -1.2 7 7
MAX 0.007 0.005 -9999 0 -10000 0 0
RBBP7 0.007 0.005 -9999 0 -10000 0 0
RBBP4 0.007 0.005 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0.007 0.005 -9999 0 -10000 0 0
Telomerase/911 0.017 0.034 -9999 0 -10000 0 0
CDKN1B 0.016 0.06 -9999 0 -0.48 4 4
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 0.007 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.007 0.005 -9999 0 -10000 0 0
JUN 0.006 0.006 -9999 0 -10000 0 0
E6 -0.002 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0.001 -9999 0 -10000 0 0
FOS -0.12 0.28 -9999 0 -0.76 55 55
IFN-gamma/IRF1 -0.008 0.065 -9999 0 -0.55 5 5
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.01 0.079 -9999 0 -0.61 6 6
Telomerase -0.019 0.043 -9999 0 -10000 0 0
IRF1 0.01 0.008 -9999 0 -10000 0 0
ESR1 -0.024 0.15 -9999 0 -0.76 14 14
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.011 0.02 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0 -9999 0 -10000 0 0
HDAC1 0.007 0.005 -9999 0 -10000 0 0
HDAC2 0.008 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.023 0.005 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.007 0.005 -9999 0 -10000 0 0
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 0 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.16 -9999 0 -0.75 3 3
NR2F2 0.009 0.013 -9999 0 -10000 0 0
MAPK3 0.011 0.009 -9999 0 -10000 0 0
MAPK1 0.011 0.009 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.005 0.007 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 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 0 -9999 0 -10000 0 0
EGFR -0.019 0.13 -9999 0 -0.68 13 13
mol:Oestrogen -0.002 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.033 0.14 -9999 0 -0.55 21 21
MYC 0.007 0.005 -9999 0 -10000 0 0
IL2 0.002 0.012 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
TGFB1 0.005 0.007 -9999 0 -10000 0 0
TRF2/BLM -0.007 0.053 -9999 0 -0.41 6 6
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.12 0.16 -9999 0 -0.76 3 3
SP1/HDAC2 0 0.002 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.15 -9999 0 -0.68 3 3
Smad3/Myc 0.01 0.015 -9999 0 -10000 0 0
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.001 0.088 -9999 0 -0.73 5 5
Telomerase/PinX1 -0.1 0.15 -9999 0 -0.68 3 3
Telomerase/AKT1/mTOR/p70S6K 0 0.064 -9999 0 -10000 0 0
SIN3B 0.007 0.005 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.1 0.15 -9999 0 -0.68 3 3
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN -0.002 0.029 -9999 0 -0.54 1 1
Telomerase/hnRNP C1/C2 -0.1 0.15 -9999 0 -0.68 3 3
E2F1 0.008 0.006 -9999 0 -10000 0 0
ZNFX1 0.007 0.005 -9999 0 -10000 0 0
PIF1 -0.026 0.12 -9999 0 -0.61 15 15
NCL 0 0 -9999 0 -10000 0 0
DKC1 0 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0 0 -9999 0 -10000 0 0
PTK2 0 0 -9999 0 -10000 0 0
CRKL 0.016 0.055 -9999 0 -0.39 6 6
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0 0 -9999 0 -10000 0 0
IRS1/Crk -0.007 0.052 -9999 0 -0.4 5 5
IGF-1R heterotetramer/IGF1/PTP1B -0.008 0.058 -9999 0 -0.46 5 5
AKT1 0.036 0.048 -9999 0 -10000 0 0
BAD 0.042 0.046 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0.055 -9999 0 -0.4 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.052 -9999 0 -0.4 5 5
RAF1 0.044 0.044 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.007 0.049 -9999 0 -0.38 5 5
YWHAZ 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.008 0.057 -9999 0 -0.42 6 6
PIK3CA 0 0 -9999 0 -10000 0 0
RPS6KB1 0.036 0.048 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.039 0.039 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 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 -0.006 0.043 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.046 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.009 0.012 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.052 -9999 0 -0.4 5 5
Crk/p130 Cas/Paxillin -0.006 0.046 -9999 0 -10000 0 0
IGF1R 0.009 0.012 -9999 0 -10000 0 0
IGF1 -0.003 0.098 -9999 0 -0.74 6 6
IRS2/Crk -0.008 0.053 -9999 0 -0.38 6 6
PI3K -0.007 0.049 -9999 0 -0.37 5 5
apoptosis 0.005 0.034 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.03 0.062 -9999 0 -0.47 5 5
RAF1/14-3-3 E 0.046 0.039 -9999 0 -10000 0 0
BAD/14-3-3 0.045 0.043 -9999 0 -10000 0 0
PRKCZ 0.036 0.048 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.005 0.035 -9999 0 -10000 0 0
PTPN1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.008 0.06 -9999 0 -0.5 5 5
BCAR1 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.007 0.05 -9999 0 -0.4 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.007 0.052 -9999 0 -0.4 5 5
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0.055 -9999 0 -0.4 5 5
IRS1 0.009 0.059 -9999 0 -0.42 6 6
IRS2 0.015 0.061 -9999 0 -0.4 7 7
IGF-1R heterotetramer/IGF1 -0.01 0.074 -9999 0 -0.56 6 6
GRB2 0 0 -9999 0 -10000 0 0
PDPK1 -0.006 0.045 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKD1 0.018 0.098 -9999 0 -0.46 13 13
SHC1 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0 0 -9999 0 -10000 0 0
mol:DAG 0.024 0.065 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -9999 0 -10000 0 0
CaM/Ca2+ -0.01 0.054 -9999 0 -10000 0 0
HIF1A 0 0 -9999 0 -10000 0 0
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.008 0.041 -9999 0 -10000 0 0
PLCG1 0.024 0.066 -9999 0 -10000 0 0
NOS3 0.047 0.059 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.046 0.057 -9999 0 -10000 0 0
FLT1 0.027 0 -9999 0 -10000 0 0
PGF -0.021 0.11 -9999 0 -0.61 12 12
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.041 -9999 0 -0.44 3 3
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.05 0.056 -9999 0 -10000 0 0
endothelial cell proliferation 0.029 0.078 -9999 0 -10000 0 0
mol:Ca2+ 0.024 0.065 -9999 0 -10000 0 0
MAPK3 0.036 0.062 -9999 0 -10000 0 0
MAPK1 0.036 0.062 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
PLGF homodimer -0.021 0.11 -9999 0 -0.6 12 12
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.22 0.34 -9999 0 -0.76 99 99
VEGFA homodimer 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.042 0.061 -9999 0 -10000 0 0
PI3K -0.01 0.054 -9999 0 -10000 0 0
PRKCA 0.029 0.066 -9999 0 -10000 0 0
PRKCB 0.016 0.099 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer -0.013 0.067 -9999 0 -10000 0 0
VEGFA 0 0 -9999 0 -10000 0 0
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.024 0.065 -9999 0 -10000 0 0
RASA1 0.036 0 -9999 0 -10000 0 0
NRP2 -0.007 0.07 -9999 0 -0.76 3 3
VEGFR1 homodimer 0.027 0 -9999 0 -10000 0 0
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.066 0.19 -9999 0 -0.63 3 3
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.01 0.054 -9999 0 -10000 0 0
mol:L-citrulline 0.046 0.057 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -9999 0 -10000 0 0
CD2AP 0 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.01 0.05 -9999 0 -10000 0 0
PDPK1 -0.009 0.05 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -9999 0 -10000 0 0
mol:NADP 0.046 0.057 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.004 0.045 -9999 0 -0.49 3 3
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.004 0.057 0.76 2 -10000 0 2
PI3K Class IB/PDE3B -0.004 0.057 -10000 0 -0.76 2 2
PDE3B -0.004 0.058 -10000 0 -0.76 2 2
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
MAP2K3 0.027 0.025 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.035 0.023 -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 -0.007 0.07 -9999 0 -0.76 3 3
TXN 0.008 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GADD45B -0.024 0.13 -9999 0 -0.76 11 11
MAP3K1 0 0 -9999 0 -10000 0 0
MAP3K6 0 0 -9999 0 -10000 0 0
MAP3K7 0 0 -9999 0 -10000 0 0
MAP3K4 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.002 0.005 -9999 0 -10000 0 0
TRAF6 0.008 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.077 0.2 -9999 0 -0.61 44 44
CCM2 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.048 0.13 -9999 0 -0.38 44 44
MAPK11 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.043 0.11 -9999 0 -10000 0 0
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 0.015 0 -9999 0 -10000 0 0
TAOK2 0.015 0 -9999 0 -10000 0 0
TAOK3 0.015 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAP3K10 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
TRX/ASK1 0 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.017 0.084 -9999 0 -0.42 14 14
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.001 0.019 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.036 0.031 0.24 1 -10000 0 1
YWHAZ 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.02 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP -0.003 0.046 -10000 0 -0.61 2 2
PRKCI 0 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0 0 -10000 0 -10000 0 0
GYS1 0.029 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.009 0.031 -10000 0 -10000 0 0
VAMP2 0 0 -10000 0 -10000 0 0
SLC2A4 0.037 0.033 0.24 1 -10000 0 1
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.023 0 -10000 0 -10000 0 0
SFN -0.051 0.17 -10000 0 -0.61 29 29
LNPEP 0 0 -10000 0 -10000 0 0
YWHAE 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
SPHK2 0.02 0 -10000 0 -10000 0 0
MAP4K4 0.032 0.056 -10000 0 -10000 0 0
BAG4 0 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.004 0.017 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.011 0.091 -10000 0 -0.76 5 5
BAX 0.001 0.008 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.018 0.004 -10000 0 -10000 0 0
BAD -0.003 0.017 -10000 0 -10000 0 0
SMPD1 0.019 0.045 -10000 0 -0.23 10 10
RB1 -0.003 0.017 -10000 0 -10000 0 0
FADD/Caspase 8 0.041 0.053 -10000 0 -10000 0 0
MAP2K4 0.004 0.016 -10000 0 -10000 0 0
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.016 -10000 0 -10000 0 0
EGF -0.019 0.12 -10000 0 -0.74 9 9
mol:ceramide -0.012 0.018 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.02 0 -10000 0 -10000 0 0
ASAH1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.003 0.017 -10000 0 -10000 0 0
cell proliferation -0.007 0.045 -10000 0 -0.35 5 5
BID 0.024 0.039 -10000 0 -10000 0 0
MAP3K1 -0.003 0.017 -10000 0 -10000 0 0
EIF2A 0.011 0.015 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.015 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.015 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.004 0.017 -10000 0 -10000 0 0
FADD 0.032 0.056 -10000 0 -10000 0 0
KSR1 -0.003 0.017 -10000 0 -10000 0 0
MAPK8 0.008 0.016 -10000 0 -10000 0 0
PRKRA -0.003 0.017 -10000 0 -10000 0 0
PDGFA 0 0 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.013 0.096 -10000 0 -0.73 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.012 0.018 -10000 0 -10000 0 0
CTSD 0 0 -10000 0 -10000 0 0
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 -0.008 0.048 -10000 0 -0.38 5 5
PRKCD 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.02 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 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.011 0.051 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.015 0.085 -10000 0 -0.48 11 11
mol:Sphingosine-1-phosphate 0.02 0 -10000 0 -10000 0 0
MAP2K1 0.011 0.015 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS 0 0.013 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 0.004 0.016 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.015 0.085 -10000 0 -0.48 11 11
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.027 -10000 0 -10000 0 0
MAP2K2 0.011 0.015 -10000 0 -10000 0 0
SMPD3 0.015 0.075 -10000 0 -0.32 14 14
TNF -0.024 0.13 -10000 0 -0.75 11 11
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.005 0.045 0.27 8 -10000 0 8
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0 0.013 -10000 0 -10000 0 0
BCL2 -0.002 0.032 -10000 0 -0.61 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.01 0.044 -9999 0 -10000 0 0
NEF -0.007 0.038 -9999 0 -10000 0 0
NFKBIA -0.002 0.013 -9999 0 -10000 0 0
BIRC3 0.029 0.096 -9999 0 -0.77 5 5
CYCS 0.036 0.061 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.02 0.11 -9999 0 -0.82 6 6
MAP2K7 0.037 0.05 -9999 0 -10000 0 0
protein ubiquitination 0.057 0.041 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS 0 0 -9999 0 -10000 0 0
BID 0.03 0.064 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.005 0.039 -9999 0 -10000 0 0
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
CFLAR 0 0 -9999 0 -10000 0 0
FADD 0 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.005 0.039 -9999 0 -10000 0 0
MAPK8 0.043 0.047 -9999 0 -10000 0 0
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 0 0 -9999 0 -10000 0 0
TRAF2 0 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.013 0.059 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.007 0.035 -9999 0 -10000 0 0
CHUK 0.058 0.043 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.023 0.11 -9999 0 -0.48 17 17
TNF -0.024 0.13 -9999 0 -0.75 11 11
FASLG -0.015 0.19 -9999 0 -0.81 17 17
NFKB1 -0.002 0.013 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.015 0.085 -9999 0 -0.48 11 11
CASP6 -0.006 0.027 -9999 0 -10000 0 0
CASP7 0.064 0.09 -9999 0 -0.61 5 5
RELA -0.002 0.013 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.064 0.09 -9999 0 -0.61 5 5
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0 0 -9999 0 -10000 0 0
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.054 0.045 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.013 0.066 -9999 0 -0.5 5 5
BCL2 0.047 0.048 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.006 0.066 -10000 0 -0.71 3 3
HRAS 0 0 -10000 0 -10000 0 0
EGFR -0.025 0.13 -10000 0 -0.68 13 13
AKT 0.034 0.025 -10000 0 -0.38 1 1
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 -0.002 0.041 -10000 0 -0.76 1 1
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.006 0.066 -10000 0 -0.71 3 3
PIK3CA 0 0 -10000 0 -10000 0 0
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
PIK3CG -0.042 0.17 -10000 0 -0.76 19 19
PIK3R3 0 0 -10000 0 -10000 0 0
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 0 0 -10000 0 -10000 0 0
RAS 0.016 0.037 -10000 0 -10000 0 0
ERBB2 0 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.023 0.031 0.23 1 -10000 0 1
PI3K 0.019 0.049 -10000 0 -0.27 2 2
PIK3R1 0 0 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
FOXO 0.041 0.014 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.005 0.037 -9999 0 -0.64 1 1
PDGFB-D/PDGFRB/SLAP -0.028 0.13 -9999 0 -0.61 16 16
PDGFB-D/PDGFRB/APS/CBL -0.001 0.026 -9999 0 -0.49 1 1
AKT1 -0.006 0.045 -9999 0 -0.56 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.032 0.045 -9999 0 -0.67 1 1
PIK3CA 0 0 -9999 0 -10000 0 0
FGR -0.044 0.16 -9999 0 -0.62 25 25
mol:Ca2+ 0.028 0.046 -9999 0 -0.71 1 1
MYC 0.045 0.052 -9999 0 -0.47 1 1
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.022 -9999 0 -0.4 1 1
LRP1/PDGFRB/PDGFB -0.004 0.046 -9999 0 -0.5 3 3
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.028 0.047 -9999 0 -0.72 1 1
PTEN 0 0 -9999 0 -10000 0 0
GRB2 0 0 -9999 0 -10000 0 0
GRB7 -0.003 0.046 -9999 0 -0.61 2 2
PDGFB-D/PDGFRB/SHP2 -0.002 0.031 -9999 0 -0.58 1 1
PDGFB-D/PDGFRB/GRB10 -0.002 0.031 -9999 0 -0.58 1 1
cell cycle arrest -0.028 0.13 -9999 0 -0.61 16 16
HRAS 0 0 -9999 0 -10000 0 0
HIF1A 0.055 0.047 -9999 0 -0.48 1 1
GAB1 0.029 0.059 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.034 0.054 -9999 0 -0.67 1 1
PDGFB-D/PDGFRB 0.002 0.029 -9999 0 -0.51 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.031 -9999 0 -0.58 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.006 0.04 -9999 0 -0.64 1 1
positive regulation of MAPKKK cascade -0.002 0.031 -9999 0 -0.57 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
mol:IP3 0.028 0.048 -9999 0 -0.73 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.001 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.004 0.046 -9999 0 -0.49 3 3
SHB 0 0 -9999 0 -10000 0 0
BLK -0.023 0.11 -9999 0 -0.6 12 12
PTPN2 0.011 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.031 -9999 0 -0.58 1 1
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.03 0.07 -9999 0 -0.77 1 1
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.031 -9999 0 -0.58 1 1
LCK -0.003 0.042 -9999 0 -0.56 2 2
PDGFRB 0.009 0.042 -9999 0 -0.77 1 1
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.004 0.053 -9999 0 -0.57 3 3
ABL1 0.025 0.056 -9999 0 -0.67 1 1
PDGFB-D/PDGFRB/CBL 0.026 0.063 -9999 0 -0.78 1 1
PTPN1 0.011 0.001 -9999 0 -10000 0 0
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 0 0 -9999 0 -10000 0 0
cell proliferation 0.045 0.049 -9999 0 -0.43 1 1
SLA -0.035 0.16 -9999 0 -0.76 16 16
actin cytoskeleton reorganization 0.002 0.024 -9999 0 -10000 0 0
SRC -0.001 0.027 -9999 0 -0.5 1 1
PI3K -0.006 0.05 -9999 0 -0.63 1 1
PDGFB-D/PDGFRB/GRB7/SHC -0.004 0.039 -9999 0 -0.41 3 3
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.032 0.047 -9999 0 -0.7 1 1
LYN 0 0.027 -9999 0 -0.5 1 1
LRP1 -0.004 0.058 -9999 0 -0.76 2 2
SOS1 0 0 -9999 0 -10000 0 0
STAT5B 0 0 -9999 0 -10000 0 0
STAT5A -0.002 0.041 -9999 0 -0.76 1 1
NCK1-2/p130 Cas 0 0.022 -9999 0 -10000 0 0
SPHK1 0.01 0.002 -9999 0 -10000 0 0
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.028 0.048 -9999 0 -0.73 1 1
PLCG1 0.028 0.049 -9999 0 -0.76 1 1
NHERF/PDGFRB -0.009 0.07 -9999 0 -0.54 5 5
YES1 0 0.027 -9999 0 -0.49 1 1
cell migration -0.009 0.069 -9999 0 -0.54 5 5
SHC/Grb2/SOS1 0 0.022 -9999 0 -10000 0 0
SLC9A3R2 -0.007 0.07 -9999 0 -0.76 3 3
SLC9A3R1 -0.005 0.056 -9999 0 -0.61 3 3
NHERF1-2/PDGFRB/PTEN -0.008 0.063 -9999 0 -0.53 4 4
FYN 0 0.027 -9999 0 -0.5 1 1
DOK1 0.029 0.026 -9999 0 -0.45 1 1
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.041 0.064 -9999 0 -0.68 1 1
PRKCD 0.03 0.026 -9999 0 -0.46 1 1
FER 0.03 0.026 -9999 0 -0.46 1 1
MAPKKK cascade -0.001 0.021 -9999 0 -10000 0 0
RASA1 0.03 0.026 -9999 0 -0.46 1 1
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk 0.001 0.024 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.002 0.031 -9999 0 -0.58 1 1
chemotaxis 0.025 0.055 -9999 0 -0.64 1 1
STAT1-3-5/STAT1-3-5 -0.002 0.029 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.002 0.032 -9999 0 -0.59 1 1
PTPRJ 0 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0 0.008 -9999 0 -10000 0 0
adherens junction organization 0.034 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP -0.011 0.056 -9999 0 -10000 0 0
FMN1 0.015 0.1 -9999 0 -0.39 19 19
mol:IP3 0 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.001 0.017 -9999 0 -0.31 1 1
CTNNB1 0 0.001 -9999 0 -10000 0 0
AKT1 -0.001 0.01 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.001 0.026 -9999 0 -0.48 1 1
CTNND1 0.011 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.039 0.017 -9999 0 -10000 0 0
VASP 0.039 0.018 -9999 0 -10000 0 0
ZYX 0.039 0.018 -9999 0 -10000 0 0
JUB 0.039 0.018 -9999 0 -10000 0 0
EGFR(dimer) -0.013 0.066 -9999 0 -0.39 6 6
E-cadherin/beta catenin-gamma catenin -0.001 0.026 -9999 0 -0.48 1 1
mol:PI-3-4-5-P3 -0.001 0.011 -9999 0 -10000 0 0
PIK3CA 0.011 0 -9999 0 -10000 0 0
PI3K -0.001 0.011 -9999 0 -10000 0 0
FYN 0.044 0.036 -9999 0 -10000 0 0
mol:Ca2+ 0 0.008 -9999 0 -10000 0 0
JUP 0 0.001 -9999 0 -10000 0 0
PIK3R1 0.011 0 -9999 0 -10000 0 0
mol:DAG 0 0.009 -9999 0 -10000 0 0
CDH1 -0.002 0.041 -9999 0 -0.76 1 1
RhoA/GDP -0.011 0.056 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.039 0.017 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
EGFR -0.025 0.13 -9999 0 -0.68 13 13
CASR 0.036 0.045 -9999 0 -10000 0 0
RhoA/GTP 0 0.007 -9999 0 -10000 0 0
AKT2 -0.001 0.01 -9999 0 -10000 0 0
actin cable formation 0.022 0.097 -9999 0 -0.37 19 19
apoptosis 0.001 0.01 -9999 0 -10000 0 0
CTNNA1 0.011 0.001 -9999 0 -10000 0 0
mol:GDP -0.012 0.061 -9999 0 -10000 0 0
PIP5K1A 0.039 0.018 -9999 0 -10000 0 0
PLCG1 0 0.009 -9999 0 -10000 0 0
Rac1/GTP -0.012 0.06 -9999 0 -0.36 6 6
homophilic cell adhesion 0.001 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0 0 -9999 0 -9999 0 0
SMAD2 0.013 0 -9999 0 -9999 0 0
SMAD3 0.037 0 -9999 0 -9999 0 0
SMAD3/SMAD4 0 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 0 -9999 0 -9999 0 0
CALM1 0 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0 0 -9999 0 -9999 0 0
MAP3K1 0 0 -9999 0 -9999 0 0
TRAP-1/SMAD4 0 0 -9999 0 -9999 0 0
MAPK3 0 0 -9999 0 -9999 0 0
MAPK1 0 0 -9999 0 -9999 0 0
NUP214 0 0 -9999 0 -9999 0 0
CTDSP1 0 0 -9999 0 -9999 0 0
CTDSP2 0 0 -9999 0 -9999 0 0
CTDSPL 0 0 -9999 0 -9999 0 0
KPNB1 0 0 -9999 0 -9999 0 0
TGFBRAP1 0 0 -9999 0 -9999 0 0
UBE2I 0 0 -9999 0 -9999 0 0
NUP153 0 0 -9999 0 -9999 0 0
KPNA2 0 0 -9999 0 -9999 0 0
PIAS4 0 0 -9999 0 -9999 0 0
Canonical NF-kappaB 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
FBXW11 0 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 0.02 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.003 0.044 -9999 0 -0.58 2 2
NFKBIA 0.043 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.002 0.032 -9999 0 -0.61 1 1
RIPK2 0 0 -9999 0 -10000 0 0
IKBKG -0.001 0.019 -9999 0 -10000 0 0
IKK complex/A20 -0.013 0.063 -9999 0 -10000 0 0
NEMO/A20/RIP2 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM -0.001 0.017 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.002 0.02 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.004 0.058 -9999 0 -0.76 2 2
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.018 0.099 -9999 0 -0.56 11 11
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.002 0.041 -9999 0 -0.76 1 1
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.024 0.13 -9999 0 -0.75 11 11
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex -0.002 0.022 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.003 0.028 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0 0 -9999 0 -10000 0 0
PLK4 -0.002 0.032 -9999 0 -0.61 1 1
regulation of centriole replication 0.019 0.025 -9999 0 -0.44 1 1
a4b1 and a4b7 Integrin 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
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.004 0.058 -9999 0 -0.76 2 2
ITGA4 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.003 0.044 -9999 0 -0.58 2 2
alpha4/beta1 Integrin 0 0 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.039 0.002 -10000 0 -10000 0 0
regulation of axonogenesis -0.025 0.019 -10000 0 -10000 0 0
myoblast fusion 0.001 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.001 0.018 0.34 1 -10000 0 1
ARF1/GTP 0 0.002 -10000 0 -10000 0 0
mol:GM1 0.009 0.004 -10000 0 -10000 0 0
mol:Choline 0.024 0.029 -10000 0 -0.35 2 2
lamellipodium assembly -0.001 0.013 -10000 0 -10000 0 0
MAPK3 0.026 0.003 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.019 -10000 0 -0.35 1 1
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.011 -10000 0 -10000 0 0
ARF1/GDP 0 0.01 -10000 0 -10000 0 0
ARF6 0.009 0.002 -10000 0 -10000 0 0
RAB11A 0 0 -10000 0 -10000 0 0
TIAM1 0.012 0.001 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.026 0.003 -10000 0 -10000 0 0
actin filament bundle formation 0.001 0.009 -10000 0 -10000 0 0
KALRN -0.002 0.034 -10000 0 -0.45 2 2
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.001 0.009 -10000 0 -10000 0 0
NME1 0.01 0.033 -10000 0 -0.6 1 1
Rac1/GDP -0.001 0.009 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0.004 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.001 0.013 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development 0 0.004 -10000 0 -10000 0 0
ARF6/GTP 0 0.004 -10000 0 -10000 0 0
RhoA/GTP 0 0.002 -10000 0 -10000 0 0
mol:GDP -0.001 0.012 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0 0.001 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.016 0.033 -10000 0 -0.41 2 2
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.013 -10000 0 -10000 0 0
ruffle organization 0.025 0.019 -10000 0 -10000 0 0
regulation of epithelial cell migration 0 0.004 -10000 0 -10000 0 0
PLD2 0.018 0.003 -10000 0 -10000 0 0
PIP5K1A -0.001 0.017 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.024 0.029 -10000 0 -0.35 2 2
Rac1/GTP -0.001 0.013 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.067 0.036 -10000 0 -10000 0 0
CRKL 0.037 0.047 -10000 0 -10000 0 0
mol:DAG -0.005 0.029 -10000 0 -10000 0 0
HRAS -0.005 0.031 -10000 0 -10000 0 0
MAPK8 0.026 0.05 -10000 0 -10000 0 0
RAP1A 0.037 0.047 -10000 0 -10000 0 0
GAB1 0.037 0.047 -10000 0 -10000 0 0
MAPK14 0.026 0.05 -10000 0 -10000 0 0
EPO -0.003 0.091 -10000 0 -0.6 8 8
PLCG1 -0.005 0.03 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.012 0.005 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.011 0.071 -10000 0 -0.67 2 2
GAB1/SHC/GRB2/SOS1 -0.005 0.033 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.007 0.065 -10000 0 -0.43 8 8
IRS2 0.036 0.053 -10000 0 -10000 0 0
STAT1 0.052 0.039 -10000 0 -10000 0 0
STAT5B -0.005 0.03 -10000 0 -10000 0 0
cell proliferation 0.033 0.047 -10000 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.008 0.043 -10000 0 -10000 0 0
TEC 0.036 0.053 -10000 0 -10000 0 0
SOCS3 -0.004 0.058 -10000 0 -0.76 2 2
STAT1 (dimer) 0.052 0.038 -10000 0 -10000 0 0
JAK2 0.012 0.005 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.039 0.051 -10000 0 -0.38 1 1
EPO/EPOR -0.007 0.065 -10000 0 -0.43 8 8
LYN 0.012 0.001 -10000 0 -10000 0 0
TEC/VAV2 0.04 0.067 -10000 0 -0.77 1 1
elevation of cytosolic calcium ion concentration 0.012 0.005 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.022 0.056 -10000 0 -0.34 8 8
mol:IP3 -0.005 0.029 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.01 0.051 -10000 0 -10000 0 0
SH2B3 0.009 0.041 -10000 0 -0.76 1 1
NFKB1 0.026 0.05 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.005 0.04 0.31 1 -0.43 1 2
PTPN6 0.031 0.049 -10000 0 -0.38 1 1
TEC/VAV2/GRB2 -0.009 0.056 -10000 0 -0.74 1 1
EPOR 0.012 0.005 -10000 0 -10000 0 0
INPP5D -0.007 0.07 -10000 0 -0.76 3 3
mol:GDP -0.005 0.034 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0 0 -10000 0 -10000 0 0
CRKL/CBL/C3G -0.006 0.036 -10000 0 -10000 0 0
VAV2 0.035 0.057 -10000 0 -10000 0 0
CBL 0.037 0.047 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.006 0.036 -10000 0 -10000 0 0
STAT5A -0.006 0.044 -10000 0 -0.64 1 1
GRB2 0 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.062 0.052 -10000 0 -0.56 1 1
LYN/PLCgamma2 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
BTK 0.006 0.13 -10000 0 -0.71 2 2
BCL2 0.067 0.041 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.001 0.018 -10000 0 -0.33 1 1
FRAP1 0.013 0.003 -10000 0 -10000 0 0
AKT1 -0.001 0.014 -10000 0 -10000 0 0
INSR 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.003 -10000 0 -10000 0 0
TSC2 0 0.001 -10000 0 -10000 0 0
RHEB/GDP 0 0.009 -10000 0 -10000 0 0
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.001 0.022 -10000 0 -0.4 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.025 0.008 -10000 0 -10000 0 0
MAP3K5 0.009 0 -10000 0 -10000 0 0
PIK3R1 0 0 -10000 0 -10000 0 0
apoptosis 0.009 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.002 1 1
EIF4B 0.03 0.008 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0 0.005 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.019 -10000 0 -0.36 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.029 0.005 -10000 0 -10000 0 0
FKBP1A 0.01 0.001 -10000 0 -10000 0 0
RHEB/GTP 0 0.009 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.002 1 1
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.001 0.016 -10000 0 -10000 0 0
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C 0 0.001 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.015 0 -10000 0 -10000 0 0
TSC1/TSC2 -0.001 0.012 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.002 1 -10000 0 1
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 0.006 0.024 -10000 0 -0.44 1 1
INS 0 0 -10000 0 -10000 0 0
PTEN 0 0.001 -10000 0 -10000 0 0
PDK2 -0.001 0.016 -10000 0 -10000 0 0
EIF4EBP1 0.004 0.026 -10000 0 -10000 0 0
PIK3CA 0 0 -10000 0 -10000 0 0
PPP2R5D 0.02 0.003 -10000 0 -10000 0 0
peptide biosynthetic process 0.015 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.015 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.004 0.019 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.02 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.034 0 -9999 0 -10000 0 0
CDKN1A 0.034 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0 0 -9999 0 -10000 0 0
FOXO3 0.034 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0 0 -9999 0 -10000 0 0
AKT3 0.014 0.024 -9999 0 -0.42 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.034 0 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0 0 -9999 0 -10000 0 0
RAF1 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.034 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
AKT1/RAF1 0 0 -9999 0 -10000 0 0
EP300 0 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 0.034 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.022 0 -9999 0 -10000 0 0
MAP3K5 0 0 -9999 0 -10000 0 0
MAPKAP1 0 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.032 0.026 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
AKT1S1 0.034 0 -9999 0 -10000 0 0
CASP9 0.034 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0 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 0 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0 -9999 0 -10000 0 0
CHUK 0.034 0 -9999 0 -10000 0 0
BAD/BCL-XL 0 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.015 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.045 0.028 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
MDM2 0.034 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 0.04 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
glucose import 0.025 0.036 -9999 0 -0.44 2 2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.028 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.025 0.036 -9999 0 -0.45 2 2
GSK3A 0.034 0 -9999 0 -10000 0 0
FOXO1 0.034 0 -9999 0 -10000 0 0
GSK3B 0.034 0 -9999 0 -10000 0 0
SFN -0.051 0.17 -9999 0 -0.61 29 29
G1/S transition of mitotic cell cycle 0.04 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.031 0.039 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
KPNA1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
RHEB 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.002 0.029 -9999 0 -0.39 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 -0.004 0.038 -9999 0 -0.45 2 2
EPO -0.014 0.091 -9999 0 -0.61 8 8
alpha4/beta7 Integrin -0.003 0.044 -9999 0 -0.58 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.01 0.066 -9999 0 -0.44 8 8
lamellipodium assembly 0 0.001 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.004 0.029 -9999 0 -10000 0 0
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
MADCAM1 -0.002 0.032 -9999 0 -0.61 1 1
cell adhesion -0.004 0.038 -9999 0 -0.44 2 2
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.025 0.045 -9999 0 -0.45 2 2
ITGB7 -0.004 0.058 -9999 0 -0.76 2 2
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.005 0.047 -9999 0 -0.5 2 2
p130Cas/Crk/Dock1 -0.004 0.034 -9999 0 -10000 0 0
VCAM1 -0.008 0.073 -9999 0 -0.68 4 4
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0 0 -9999 0 -10000 0 0
BCAR1 0.033 0.042 -9999 0 -10000 0 0
EPOR 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.001 -9999 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.007 0.038 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.039 -9999 0 -0.42 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 -0.006 0.061 -9999 0 -0.66 3 3
RhoA/GTP -0.007 0.039 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.008 0.044 -9999 0 -10000 0 0
GNAZ -0.011 0.091 -9999 0 -0.76 5 5
GNAI3 0 0 -9999 0 -10000 0 0
GNA12 0 0 -9999 0 -10000 0 0
S1PR5 -0.006 0.061 -9999 0 -0.66 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.008 0.044 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
GNAI1 -0.002 0.041 -9999 0 -0.76 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.036 0.059 -9999 0 -10000 0 0
BAG4 0 0 -9999 0 -10000 0 0
BAD 0.027 0.022 -9999 0 -10000 0 0
NFKBIA 0 0 -9999 0 -10000 0 0
BIRC3 -0.011 0.091 -9999 0 -0.76 5 5
BAX 0.027 0.022 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.017 -9999 0 -10000 0 0
IKBKB 0.041 0.059 -9999 0 -10000 0 0
MAP2K2 0.038 0.024 -9999 0 -10000 0 0
MAP2K1 0.038 0.024 -9999 0 -10000 0 0
SMPD1 0.017 0.017 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.042 0.058 -9999 0 -10000 0 0
MAP2K4 0.033 0.023 -9999 0 -10000 0 0
protein ubiquitination 0.043 0.058 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.043 0.027 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
RAF1 0.033 0.024 -9999 0 -10000 0 0
CRADD 0.01 0.001 -9999 0 -10000 0 0
mol:ceramide 0.021 0.023 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.01 0.001 -9999 0 -10000 0 0
MAP3K1 0.027 0.023 -9999 0 -10000 0 0
TRADD 0.01 0.001 -9999 0 -10000 0 0
RELA/p50 0 0 -9999 0 -10000 0 0
MAPK3 0.04 0.024 -9999 0 -10000 0 0
MAPK1 0.04 0.024 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.036 0.059 -9999 0 -10000 0 0
KSR1 0.028 0.024 -9999 0 -10000 0 0
MAPK8 0.038 0.021 -9999 0 -10000 0 0
TRAF2 0 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.041 0.057 -9999 0 -10000 0 0
TNF R/SODD 0 0 -9999 0 -10000 0 0
TNF -0.014 0.13 -9999 0 -0.75 11 11
CYCS 0.028 0.022 -9999 0 -10000 0 0
IKBKG 0.041 0.057 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.03 0.062 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
RIPK1 0 0.001 -9999 0 -10000 0 0
AIFM1 0.028 0.022 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.015 0.085 -9999 0 -0.48 11 11
TNFRSF1A 0 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.023 0.017 -9999 0 -10000 0 0
NSMAF 0.036 0.059 -9999 0 -10000 0 0
response to hydrogen peroxide 0 0 -9999 0 -10000 0 0
BCL2 -0.002 0.032 -9999 0 -0.61 1 1
FoxO family 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
G6PC 0.025 0.037 -9999 0 -10000 0 0
PLK1 -0.099 0.23 -9999 0 -0.75 1 1
CDKN1B 0.047 0.092 -9999 0 -10000 0 0
FOXO3 -0.026 0.16 -9999 0 -0.64 1 1
KAT2B 0.006 0.045 -9999 0 -0.77 1 1
FOXO1/SIRT1 0.018 0.027 -9999 0 -10000 0 0
CAT -0.016 0.15 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.01 0.016 -9999 0 -10000 0 0
FOXO1 0.028 0.023 -9999 0 -10000 0 0
MAPK10 0.024 0.055 -9999 0 -0.43 5 5
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.082 0.031 -9999 0 -10000 0 0
response to oxidative stress -0.004 0.021 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.068 0.1 -9999 0 -10000 0 0
XPO1 0.011 0 -9999 0 -10000 0 0
EP300 0.007 0.006 -9999 0 -10000 0 0
BCL2L11 0.016 0.029 -9999 0 -10000 0 0
FOXO1/SKP2 -0.003 0.029 -9999 0 -10000 0 0
mol:GDP -0.004 0.021 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
GADD45A 0.047 0.076 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.056 0.031 -9999 0 -10000 0 0
MST1 0.009 0.015 -9999 0 -10000 0 0
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.04 0.041 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.031 0.008 -9999 0 -10000 0 0
MAPK9 0.03 0.008 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ 0 0 -9999 0 -10000 0 0
SIRT1 0.008 0.013 -9999 0 -10000 0 0
SOD2 0.056 0.1 -9999 0 -10000 0 0
RBL2 0.017 0.12 -9999 0 -10000 0 0
RAL/GDP 0.014 0.015 -9999 0 -10000 0 0
CHUK 0.009 0.015 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.017 0.018 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG -0.038 0.28 -9999 0 -1.5 13 13
SKP2 -0.003 0.046 -9999 0 -0.61 2 2
USP7 0.011 0 -9999 0 -10000 0 0
IKBKB 0.007 0.035 -9999 0 -0.59 1 1
CCNB1 -0.04 0.19 -9999 0 -0.75 1 1
FOXO1-3a-4/beta catenin -0.016 0.039 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.029 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.009 0.015 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.083 0.028 -9999 0 -10000 0 0
SFN -0.051 0.17 -9999 0 -0.61 29 29
CDK2 0.007 0.007 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.022 0.054 -9999 0 -10000 0 0
CREBBP 0.007 0.007 -9999 0 -10000 0 0
FBXO32 -0.021 0.16 -9999 0 -10000 0 0
BCL6 0.017 0.12 -9999 0 -10000 0 0
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.027 0 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.026 0.021 -9999 0 -0.37 1 1
MAPK12 0.027 0.019 -9999 0 -10000 0 0
CCND1 0.011 0.062 -9999 0 -0.45 6 6
p38 gamma/SNTA1 -0.001 0.016 -9999 0 -10000 0 0
MAP2K3 0 0 -9999 0 -10000 0 0
PKN1 0 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.027 0.019 -9999 0 -10000 0 0
MAP2K6 0.021 0.021 -9999 0 -0.37 1 1
MAPT 0.023 0.05 -9999 0 -0.38 5 5
MAPK13 0.02 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.003 0.044 -9999 0 -0.58 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.003 0.034 -9999 0 -0.45 2 2
lamellipodium assembly 0 0 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.02 0 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.004 0.058 -9999 0 -0.76 2 2
ARF6/GDP 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.004 0.039 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.008 0.073 -9999 0 -0.68 4 4
alpha4/beta1 Integrin/Paxillin/Talin 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0 0 -9999 0 -10000 0 0
Rac1/GTP 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.001 0.02 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.018 -9999 0 -10000 0 0
NFKBIA 0.026 0.016 -9999 0 -0.26 1 1
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.02 -9999 0 -10000 0 0
ARRB2 0.015 0 -9999 0 -10000 0 0
REL 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.02 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.02 -9999 0 -10000 0 0
PIK3CA 0 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer -0.001 0.024 -9999 0 -0.44 1 1
PIK3R1 0 0 -9999 0 -10000 0 0
NFKB1 0.019 0.025 -9999 0 -0.44 1 1
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.017 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.001 0.018 -9999 0 -10000 0 0
SRC 0 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.001 0.015 -9999 0 -10000 0 0
IKBKB -0.002 0.032 -9999 0 -0.61 1 1
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 -0.001 0.013 -9999 0 -10000 0 0
cell death -0.001 0.017 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.001 0.02 -9999 0 -10000 0 0
LCK -0.002 0.041 -9999 0 -0.76 1 1
BCL3 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.002 0.029 -9999 0 -0.55 1 1
KLHL20 -0.006 0.035 -9999 0 -0.38 1 1
CYFIP2 -0.02 0.12 -9999 0 -0.76 9 9
Rac1/GDP 0.053 0.023 -9999 0 -10000 0 0
ENAH -0.002 0.029 -9999 0 -0.55 1 1
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.014 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.034 -9999 0 -0.26 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.004 0.041 -9999 0 -0.45 3 3
RAPGEF1 0.048 0.027 -9999 0 -0.46 1 1
CTNND1 0 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.002 0.031 -9999 0 -0.57 1 1
CRK 0.042 0.03 -9999 0 -0.51 1 1
E-cadherin/gamma catenin/alpha catenin -0.001 0.027 -9999 0 -0.49 1 1
alphaE/beta7 Integrin -0.003 0.044 -9999 0 -0.58 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.002 0.029 -9999 0 -0.55 1 1
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.01 -9999 0 -10000 0 0
MLLT4 0 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.018 -9999 0 -10000 0 0
PI3K -0.001 0.013 -9999 0 -10000 0 0
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.002 0.031 -9999 0 -0.58 1 1
TIAM1 0 0 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.001 0.023 -9999 0 -0.42 1 1
AKT1 0 0.007 -9999 0 -10000 0 0
PIK3R1 0 0 -9999 0 -10000 0 0
CDH1 -0.002 0.041 -9999 0 -0.76 1 1
RhoA/GDP 0.053 0.023 -9999 0 -10000 0 0
actin cytoskeleton organization -0.004 0.025 -9999 0 -0.27 1 1
CDC42/GDP 0.053 0.023 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.001 0.017 -9999 0 -0.32 1 1
ITGB7 -0.004 0.058 -9999 0 -0.76 2 2
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.001 0.024 -9999 0 -0.45 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin -0.001 0.023 -9999 0 -0.43 1 1
mol:GDP 0.052 0.026 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP -0.001 0.019 -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 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.006 0.037 -9999 0 -0.26 7 7
NME1 -0.002 0.032 -9999 0 -0.6 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.002 0.029 -9999 0 -0.55 1 1
regulation of cell-cell adhesion -0.001 0.012 -9999 0 -10000 0 0
WASF2 -0.004 0.017 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.016 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.004 0.039 -9999 0 -0.42 3 3
CCND1 -0.007 0.046 -9999 0 -0.32 7 7
VAV2 0.041 0.067 -9999 0 -0.67 3 3
RAP1/GDP -0.001 0.017 -9999 0 -10000 0 0
adherens junction assembly -0.002 0.028 -9999 0 -0.53 1 1
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.003 0.037 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.001 0.025 -9999 0 -0.47 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.002 0.029 -9999 0 -0.55 1 1
PIK3CA 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.009 0.061 -9999 0 -0.56 2 2
E-cadherin/beta catenin/alpha catenin -0.001 0.027 -9999 0 -0.49 1 1
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.031 -9999 0 -0.59 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0 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 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0 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 0.026 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0 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 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 0 -9999 0 -9999 0 0
UBE2I 0 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 0 -9999 0 -9999 0 0
PIAS1 0 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.005 0.046 -10000 0 -0.43 4 4
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.034 -10000 0 -0.45 2 2
GNB1/GNG2 -0.003 0.038 -10000 0 -0.5 2 2
GNB1 0 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.003 0.036 -10000 0 -0.47 2 2
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0.008 0.11 2 -10000 0 2
GNAL -0.004 0.058 -10000 0 -0.76 2 2
GNG2 -0.004 0.058 -10000 0 -0.76 2 2
CRH -0.003 0.046 -10000 0 -0.61 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0 -10000 0 -10000 0 0
MAPK11 0.008 0 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.001 0.027 -9999 0 -0.5 1 1
E-cadherin/beta catenin -0.002 0.031 -9999 0 -0.58 1 1
CTNNB1 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
CDH1 -0.002 0.041 -9999 0 -0.76 1 1
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0 -9999 0 -10000 0 0
AP2 -0.001 0.024 -9999 0 -0.44 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0 -9999 0 -10000 0 0
CD4 -0.009 0.081 -9999 0 -0.76 4 4
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0 -9999 0 -10000 0 0
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 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.01 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 -0.002 0.032 -9999 0 -0.61 1 1
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 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.023 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0 -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 0.01 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 -0.003 0.028 -9999 0 -0.26 4 4
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0 -9999 0 -10000 0 0
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 0.01 0 -9999 0 -10000 0 0
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 -0.007 0.056 -9999 0 -0.47 5 5
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 0 -9999 0 -10000 0 0
FBXW11 0 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 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.016 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.024 -9999 0 -0.44 1 1
RELB -0.002 0.032 -9999 0 -0.61 1 1
NFKB2 0 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.001 0.02 -9999 0 -0.38 1 1
regulation of B cell activation -0.001 0.02 -9999 0 -0.38 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 347 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.98.8023 TCGA.98.8022 TCGA.98.8021 TCGA.98.8020
109_MAP3K5 0.049 0.049 0.049 0.049
47_PPARGC1A 0 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 -0.61 0
105_BMP2 0 0 0 0
131_RELN/VLDLR 0 0 0 0
30_TGFB1/TGF beta receptor Type II 0.014 0.015 0 0
84_STAT5B 0.04 0.042 0.04 0.025
84_STAT5A 0.04 0.042 0.04 0.025
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/LUSC-TP/3353194/LUSC-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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